Query psy15132
Match_columns 786
No_of_seqs 427 out of 1388
Neff 7.8
Searched_HMMs 46136
Date Fri Aug 16 21:24:24 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15132.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15132hhsearch_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 1.5E-92 3.3E-97 817.1 46.3 461 319-786 42-579 (608)
2 PRK12366 replication factor A; 100.0 3E-67 6.4E-72 610.7 56.8 539 45-782 63-621 (637)
3 TIGR00617 rpa1 replication fac 100.0 1.7E-66 3.7E-71 600.5 33.8 340 2-350 257-602 (608)
4 PRK12366 replication factor A; 100.0 4.2E-43 9.1E-48 408.6 29.7 264 9-324 360-626 (637)
5 PRK08402 replication factor A; 100.0 3.7E-38 8E-43 339.2 24.8 265 45-351 62-346 (355)
6 PRK14699 replication factor A; 100.0 4E-35 8.6E-40 328.3 40.0 401 47-645 59-465 (484)
7 PRK08402 replication factor A; 100.0 1.6E-35 3.5E-40 318.7 26.4 247 441-786 61-325 (355)
8 PRK07218 replication factor A; 100.0 9.2E-34 2E-38 310.8 32.5 312 440-785 56-395 (423)
9 PRK06386 replication factor A; 100.0 8.6E-32 1.9E-36 287.9 33.9 308 443-785 3-330 (358)
10 PRK07211 replication factor A; 100.0 3.9E-32 8.5E-37 300.0 26.8 269 441-757 52-338 (485)
11 PRK15491 replication factor A; 100.0 8.3E-30 1.8E-34 278.4 27.1 262 440-746 55-336 (374)
12 PRK07211 replication factor A; 100.0 8.2E-30 1.8E-34 281.7 22.3 191 441-650 160-354 (485)
13 PRK15491 replication factor A; 100.0 8.8E-28 1.9E-32 262.5 28.2 192 441-648 165-359 (374)
14 PF08646 Rep_fac-A_C: Replicat 100.0 1.7E-29 3.8E-34 242.9 11.0 138 204-347 1-143 (146)
15 cd04476 RPA1_DBD_C RPA1_DBD_C: 100.0 1.2E-28 2.6E-33 242.4 14.3 148 189-344 2-154 (166)
16 PF08646 Rep_fac-A_C: Replicat 100.0 3E-28 6.4E-33 234.4 12.0 118 669-786 1-123 (146)
17 cd04476 RPA1_DBD_C RPA1_DBD_C: 100.0 1.2E-27 2.6E-32 235.3 15.0 131 654-786 2-137 (166)
18 PRK14699 replication factor A; 99.9 3.9E-24 8.4E-29 240.0 33.9 266 443-751 167-451 (484)
19 cd04474 RPA1_DBD_A RPA1_DBD_A: 99.9 1.3E-25 2.8E-30 202.6 11.5 103 444-546 1-104 (104)
20 cd04475 RPA1_DBD_B RPA1_DBD_B: 99.9 7.2E-22 1.6E-26 177.8 13.4 101 59-160 1-101 (101)
21 PRK07218 replication factor A; 99.9 5.8E-20 1.3E-24 202.2 25.4 253 14-320 133-395 (423)
22 PRK06386 replication factor A; 99.8 3.5E-18 7.6E-23 183.5 25.5 251 13-321 77-331 (358)
23 cd04481 RPA1_DBD_B_like RPA1_D 99.8 1.2E-19 2.5E-24 164.8 11.2 97 61-159 1-105 (106)
24 PRK07217 replication factor A; 99.7 9.2E-17 2E-21 167.1 17.9 196 561-778 71-281 (311)
25 cd04480 RPA1_DBD_A_like RPA1_D 99.6 4.6E-16 1E-20 135.6 9.3 84 456-544 1-86 (86)
26 PF02721 DUF223: Domain of unk 99.6 6.2E-15 1.4E-19 130.9 9.1 88 481-572 1-89 (95)
27 cd04475 RPA1_DBD_B RPA1_DBD_B: 99.5 1.2E-13 2.6E-18 124.3 10.0 74 576-649 1-74 (101)
28 PRK07217 replication factor A; 99.4 1.7E-11 3.7E-16 128.0 21.1 201 46-313 73-281 (311)
29 PF04057 Rep-A_N: Replication 99.3 1.5E-12 3.2E-17 116.3 6.0 64 319-387 38-101 (101)
30 cd04477 RPA1N RPA1N: A subfami 99.3 1.1E-12 2.3E-17 116.0 2.2 61 320-386 37-97 (97)
31 cd04481 RPA1_DBD_B_like RPA1_D 99.3 1E-11 2.2E-16 112.7 7.8 69 578-648 1-76 (106)
32 cd04497 hPOT1_OB1_like hPOT1_O 99.2 1.3E-10 2.9E-15 110.4 12.3 96 43-144 1-101 (138)
33 COG1599 RFA1 Single-stranded D 99.1 1.2E-09 2.7E-14 122.6 15.0 183 439-649 159-344 (407)
34 cd04491 SoSSB_OBF SoSSB_OBF: A 99.0 4E-09 8.6E-14 91.0 10.1 81 456-546 1-81 (82)
35 PRK06461 single-stranded DNA-b 99.0 5.6E-09 1.2E-13 97.9 11.5 99 441-550 3-101 (129)
36 cd04497 hPOT1_OB1_like hPOT1_O 98.9 2.9E-09 6.4E-14 101.2 9.1 84 560-649 1-88 (138)
37 cd04491 SoSSB_OBF SoSSB_OBF: A 98.9 1.1E-08 2.3E-13 88.4 11.7 81 61-145 1-81 (82)
38 PRK06461 single-stranded DNA-b 98.9 2.5E-08 5.5E-13 93.5 12.5 94 46-147 5-99 (129)
39 KOG0851|consensus 98.8 4.2E-08 9E-13 102.9 14.8 177 441-628 3-190 (246)
40 COG1599 RFA1 Single-stranded D 98.7 2.1E-07 4.6E-12 104.6 16.5 186 440-649 47-234 (407)
41 PF01336 tRNA_anti-codon: OB-f 97.8 6.7E-05 1.4E-09 63.0 6.8 71 455-540 1-71 (75)
42 PF02765 POT1: Telomeric singl 97.8 0.00031 6.7E-09 67.6 12.1 97 45-145 1-108 (146)
43 cd04474 RPA1_DBD_A RPA1_DBD_A: 97.7 0.00015 3.3E-09 65.4 7.8 81 564-648 1-83 (104)
44 KOG3416|consensus 97.4 0.00082 1.8E-08 60.6 8.1 71 442-520 4-75 (134)
45 PF02765 POT1: Telomeric singl 97.3 0.0013 2.9E-08 63.2 9.5 84 562-649 1-93 (146)
46 PF02721 DUF223: Domain of unk 97.2 0.00035 7.6E-09 62.0 4.4 48 2-53 40-87 (95)
47 cd03524 RPA2_OBF_family RPA2_O 96.4 0.014 3E-07 47.9 7.6 59 457-522 2-61 (75)
48 PF01336 tRNA_anti-codon: OB-f 96.2 0.034 7.3E-07 46.3 8.7 68 60-139 1-71 (75)
49 KOG3416|consensus 95.9 0.044 9.5E-07 49.8 8.6 86 48-143 7-92 (134)
50 cd04483 hOBFC1_like hOBFC1_lik 95.8 0.053 1.2E-06 47.7 8.4 65 61-138 1-87 (92)
51 cd04483 hOBFC1_like hOBFC1_lik 95.7 0.042 9.1E-07 48.4 7.5 36 578-625 1-36 (92)
52 cd03524 RPA2_OBF_family RPA2_O 95.6 0.068 1.5E-06 43.7 8.3 68 61-137 1-70 (75)
53 cd04478 RPA2_DBD_D RPA2_DBD_D: 94.9 0.19 4.2E-06 44.2 9.2 66 60-138 2-72 (95)
54 cd04488 RecG_wedge_OBF RecG_we 94.7 0.19 4E-06 41.5 8.2 60 456-522 1-60 (75)
55 cd04485 DnaE_OBF DnaE_OBF: A s 94.3 0.19 4.2E-06 42.4 7.6 43 478-521 19-61 (84)
56 PF15072 DUF4539: Domain of un 94.1 0.21 4.5E-06 43.2 7.2 60 480-545 21-80 (86)
57 cd04478 RPA2_DBD_D RPA2_DBD_D: 94.1 0.22 4.7E-06 43.9 7.6 60 577-649 2-66 (95)
58 PF11325 DUF3127: Domain of un 93.3 0.36 7.8E-06 41.5 7.1 68 579-649 2-73 (84)
59 cd04489 ExoVII_LU_OBF ExoVII_L 93.1 0.33 7.1E-06 40.9 6.7 54 456-517 3-56 (78)
60 cd04490 PolII_SU_OBF PolII_SU_ 92.2 0.53 1.1E-05 40.1 6.8 53 577-640 2-58 (79)
61 cd04490 PolII_SU_OBF PolII_SU_ 92.2 0.51 1.1E-05 40.2 6.7 54 456-517 3-58 (79)
62 cd04485 DnaE_OBF DnaE_OBF: A s 91.5 1.2 2.5E-05 37.5 8.4 68 62-137 2-71 (84)
63 PRK13480 3'-5' exoribonuclease 91.4 1.2 2.6E-05 48.3 10.1 81 50-138 4-85 (314)
64 PRK13480 3'-5' exoribonuclease 91.1 0.63 1.4E-05 50.5 7.6 70 444-519 4-73 (314)
65 cd04492 YhaM_OBF_like YhaM_OBF 90.7 0.77 1.7E-05 38.8 6.4 43 478-522 19-61 (83)
66 PTZ00401 aspartyl-tRNA synthet 89.8 2.4 5.1E-05 49.7 11.3 99 440-547 63-169 (550)
67 PRK05813 single-stranded DNA-b 89.3 16 0.00035 37.5 15.6 158 452-640 8-175 (219)
68 PRK06751 single-stranded DNA-b 88.9 2.5 5.5E-05 41.7 9.2 68 452-522 2-81 (173)
69 KOG4757|consensus 88.3 1.5 3.2E-05 48.2 7.6 82 44-131 8-93 (522)
70 PF15489 CTC1: CST, telomere m 88.1 63 0.0014 40.6 21.8 288 450-755 702-1047(1144)
71 KOG0851|consensus 87.9 0.71 1.5E-05 48.1 5.0 137 2-163 78-218 (246)
72 PF11325 DUF3127: Domain of un 87.8 3.6 7.7E-05 35.4 8.2 68 62-132 2-73 (84)
73 KOG4757|consensus 87.6 1.6 3.5E-05 47.9 7.3 72 573-649 19-94 (522)
74 PF14951 DUF4503: Domain of un 87.4 1.6 3.6E-05 46.9 7.1 98 669-773 256-360 (389)
75 PF14951 DUF4503: Domain of un 87.3 1.7 3.8E-05 46.7 7.3 101 201-308 253-360 (389)
76 cd04492 YhaM_OBF_like YhaM_OBF 86.1 3.9 8.5E-05 34.4 7.8 68 62-137 2-70 (83)
77 PRK08182 single-stranded DNA-b 86.1 4.2 9.2E-05 39.1 8.7 71 452-522 2-88 (148)
78 PRK02801 primosomal replicatio 86.0 3.5 7.6E-05 36.9 7.6 66 452-520 2-79 (101)
79 PRK05733 single-stranded DNA-b 85.8 6.1 0.00013 39.0 9.8 64 451-517 4-81 (172)
80 PRK07274 single-stranded DNA-b 85.7 4.7 0.0001 37.9 8.7 63 452-517 2-75 (131)
81 cd04489 ExoVII_LU_OBF ExoVII_L 85.6 5.5 0.00012 33.3 8.4 65 62-137 4-71 (78)
82 PRK07373 DNA polymerase III su 85.5 2.1 4.5E-05 48.9 7.3 71 443-517 269-341 (449)
83 PRK07275 single-stranded DNA-b 85.2 3.2 7E-05 40.5 7.5 63 452-517 2-75 (162)
84 cd04320 AspRS_cyto_N AspRS_cyt 85.1 11 0.00025 33.5 10.6 83 455-547 2-92 (102)
85 PF02760 HIN: HIN-200/IF120x d 84.7 39 0.00086 32.6 19.0 156 456-638 4-164 (170)
86 PRK06752 single-stranded DNA-b 83.9 7 0.00015 35.6 8.8 63 452-517 2-75 (112)
87 COG1997 RPL43A Ribosomal prote 83.6 0.85 1.8E-05 39.0 2.3 29 223-253 37-66 (89)
88 cd04488 RecG_wedge_OBF RecG_we 83.6 9.9 0.00021 30.9 9.0 48 86-135 19-67 (75)
89 cd04100 Asp_Lys_Asn_RS_N Asp_L 83.5 9.3 0.0002 32.7 9.0 75 455-540 2-79 (85)
90 COG5235 RFA2 Single-stranded D 83.5 4.5 9.8E-05 40.3 7.6 54 88-143 86-143 (258)
91 PRK09010 single-stranded DNA-b 83.3 9.8 0.00021 37.7 10.0 63 452-517 6-82 (177)
92 PLN02850 aspartate-tRNA ligase 83.2 8.4 0.00018 45.1 11.1 98 440-547 67-172 (530)
93 cd04322 LysRS_N LysRS_N: N-ter 82.5 10 0.00022 34.1 9.3 77 455-547 2-83 (108)
94 cd04495 BRCA2DBD_OB3 BRCA2DBD_ 82.5 5.6 0.00012 35.1 6.9 79 61-148 1-84 (100)
95 COG5235 RFA2 Single-stranded D 82.4 3.7 8E-05 40.9 6.5 61 576-649 68-132 (258)
96 PRK06863 single-stranded DNA-b 82.0 8.5 0.00018 37.8 8.9 63 452-517 4-80 (168)
97 cd04480 RPA1_DBD_A_like RPA1_D 81.8 5.9 0.00013 34.1 7.1 49 600-648 17-67 (86)
98 PRK07459 single-stranded DNA-b 81.7 5.2 0.00011 37.1 7.1 63 452-517 3-72 (121)
99 cd04323 AsnRS_cyto_like_N AsnR 81.6 10 0.00022 32.4 8.5 75 455-540 2-78 (84)
100 PRK13732 single-stranded DNA-b 81.5 13 0.00029 36.8 10.1 64 451-517 5-82 (175)
101 PRK07772 single-stranded DNA-b 81.4 8.3 0.00018 38.6 8.8 63 452-517 4-81 (186)
102 PF09104 BRCA-2_OB3: BRCA2, ol 81.3 11 0.00024 35.7 9.0 104 47-160 5-120 (143)
103 PRK06293 single-stranded DNA-b 81.0 9.7 0.00021 37.1 8.9 63 452-517 1-71 (161)
104 PRK08763 single-stranded DNA-b 80.9 9.5 0.00021 37.3 8.8 64 451-517 4-80 (164)
105 PRK08486 single-stranded DNA-b 80.7 9.1 0.0002 38.1 8.8 62 453-517 3-77 (182)
106 PF00436 SSB: Single-strand bi 80.3 4.6 0.0001 35.8 6.1 63 453-518 2-77 (104)
107 PRK05673 dnaE DNA polymerase I 79.3 6 0.00013 50.5 8.7 83 46-136 966-1050(1135)
108 cd04496 SSB_OBF SSB_OBF: A sub 79.2 12 0.00026 32.8 8.4 60 456-518 2-73 (100)
109 cd04484 polC_OBF polC_OBF: A s 78.7 9.7 0.00021 32.6 7.3 59 455-518 2-62 (82)
110 cd04316 ND_PkAspRS_like_N ND_P 78.1 26 0.00056 31.5 10.4 81 453-547 13-97 (108)
111 cd04317 EcAspRS_like_N EcAspRS 77.7 20 0.00043 33.7 9.8 86 453-547 15-104 (135)
112 PRK05159 aspC aspartyl-tRNA sy 74.9 15 0.00033 42.0 9.7 93 442-548 4-101 (437)
113 TIGR00621 ssb single stranded 74.7 16 0.00034 35.8 8.5 64 452-518 4-80 (164)
114 PF13742 tRNA_anti_2: OB-fold 74.4 18 0.00039 32.1 8.1 57 453-517 22-79 (99)
115 PRK06642 single-stranded DNA-b 73.7 18 0.0004 34.9 8.5 63 452-517 5-82 (152)
116 PRK06958 single-stranded DNA-b 71.9 21 0.00045 35.6 8.5 63 452-517 4-80 (182)
117 PRK05673 dnaE DNA polymerase I 71.1 9.1 0.0002 48.9 7.3 71 443-517 966-1038(1135)
118 PRK07373 DNA polymerase III su 70.7 10 0.00022 43.4 6.9 74 46-127 269-344 (449)
119 KOG3056|consensus 70.3 25 0.00053 40.5 9.6 103 440-547 166-275 (578)
120 PF15489 CTC1: CST, telomere m 69.7 1.4E+02 0.0031 37.7 16.5 206 47-293 825-1050(1144)
121 PTZ00385 lysyl-tRNA synthetase 69.6 34 0.00074 40.9 11.1 77 454-546 109-191 (659)
122 PLN02502 lysyl-tRNA synthetase 69.0 24 0.00052 41.5 9.6 79 453-547 109-194 (553)
123 PF13240 zinc_ribbon_2: zinc-r 68.8 2.6 5.7E-05 26.9 1.0 21 689-714 2-22 (23)
124 COG0629 Ssb Single-stranded DN 68.8 14 0.00031 36.2 6.7 67 452-518 3-80 (167)
125 PRK00484 lysS lysyl-tRNA synth 68.6 38 0.00083 39.3 11.2 78 453-547 55-137 (491)
126 TIGR00643 recG ATP-dependent D 68.4 13 0.00027 44.8 7.5 68 442-517 23-91 (630)
127 PRK07279 dnaE DNA polymerase I 68.3 11 0.00023 47.5 6.9 71 442-517 875-946 (1034)
128 PRK07135 dnaE DNA polymerase I 67.6 14 0.00031 46.2 7.8 73 443-523 889-961 (973)
129 COG1997 RPL43A Ribosomal prote 67.4 3.9 8.5E-05 35.0 2.0 31 687-719 36-67 (89)
130 PF07754 DUF1610: Domain of un 67.0 4.5 9.7E-05 26.2 1.7 23 224-248 1-24 (24)
131 PF09104 BRCA-2_OB3: BRCA2, ol 66.3 29 0.00063 33.0 7.8 72 563-644 4-81 (143)
132 PRK07374 dnaE DNA polymerase I 66.0 14 0.0003 47.4 7.3 71 443-517 989-1061(1170)
133 PF01780 Ribosomal_L37ae: Ribo 65.8 2.7 5.8E-05 36.5 0.8 27 223-251 37-64 (90)
134 cd04498 hPOT1_OB2 hPOT1_OB2: A 65.3 18 0.00039 33.6 6.1 33 614-646 60-93 (123)
135 cd04319 PhAsnRS_like_N PhAsnRS 64.1 71 0.0015 28.4 9.8 78 455-546 2-82 (103)
136 cd04482 RPA2_OBF_like RPA2_OBF 63.8 9.3 0.0002 33.4 3.9 39 480-518 19-59 (91)
137 TIGR00499 lysS_bact lysyl-tRNA 63.3 34 0.00074 39.8 9.4 79 453-547 54-137 (496)
138 cd04318 EcAsnRS_like_N EcAsnRS 61.5 51 0.0011 27.8 8.0 71 456-540 3-76 (82)
139 TIGR00458 aspS_arch aspartyl-t 60.9 53 0.0011 37.5 10.3 89 445-547 3-97 (428)
140 PRK12445 lysyl-tRNA synthetase 60.9 32 0.00069 40.1 8.6 78 454-547 67-149 (505)
141 cd04495 BRCA2DBD_OB3 BRCA2DBD_ 60.8 27 0.00058 30.9 6.0 61 578-647 1-64 (100)
142 PRK10917 ATP-dependent DNA hel 60.3 20 0.00044 43.5 7.2 69 441-517 49-118 (681)
143 COG0017 AsnS Aspartyl/asparagi 60.2 55 0.0012 37.1 9.9 92 442-547 4-100 (435)
144 PRK05853 hypothetical protein; 60.1 30 0.00066 33.7 7.0 27 491-517 45-71 (161)
145 PF11781 RRN7: RNA polymerase 58.6 6.3 0.00014 28.2 1.5 25 688-714 10-34 (36)
146 PRK06920 dnaE DNA polymerase I 58.1 23 0.00049 45.1 7.2 73 443-520 933-1006(1107)
147 PRK06341 single-stranded DNA-b 57.6 55 0.0012 32.1 8.3 63 452-517 5-82 (166)
148 cd04487 RecJ_OBF2_like RecJ_OB 57.2 15 0.00032 30.8 3.7 39 480-518 17-55 (73)
149 TIGR00280 L37a ribosomal prote 56.3 6.4 0.00014 34.3 1.4 30 223-254 37-67 (91)
150 PF08271 TF_Zn_Ribbon: TFIIB z 55.9 9.3 0.0002 28.3 2.1 26 688-715 2-29 (43)
151 PF11781 RRN7: RNA polymerase 55.2 9.9 0.00022 27.2 2.0 25 223-249 10-34 (36)
152 PTZ00417 lysine-tRNA ligase; P 55.0 56 0.0012 38.7 9.4 78 454-547 134-219 (585)
153 PF13742 tRNA_anti_2: OB-fold 54.2 58 0.0012 28.9 7.3 68 58-136 22-93 (99)
154 TIGR00459 aspS_bact aspartyl-t 54.1 91 0.002 37.0 10.9 95 444-547 5-104 (583)
155 PRK02983 lysS lysyl-tRNA synth 54.1 53 0.0011 42.1 9.6 79 453-547 652-735 (1094)
156 PRK03976 rpl37ae 50S ribosomal 54.1 7 0.00015 34.0 1.3 28 223-252 38-66 (90)
157 PRK02801 primosomal replicatio 52.4 46 0.001 29.7 6.4 63 576-641 4-77 (101)
158 PRK10220 hypothetical protein; 52.2 11 0.00023 33.9 2.2 30 686-717 3-32 (111)
159 COG1200 RecG RecG-like helicas 51.9 77 0.0017 37.8 9.7 74 441-522 50-123 (677)
160 PTZ00255 60S ribosomal protein 51.5 8.7 0.00019 33.4 1.5 32 223-256 38-70 (90)
161 COG5189 SFP1 Putative transcri 51.3 7.9 0.00017 41.0 1.4 14 704-717 397-410 (423)
162 COG1571 Predicted DNA-binding 49.6 8.9 0.00019 42.9 1.6 31 687-719 351-381 (421)
163 PRK06826 dnaE DNA polymerase I 49.2 48 0.001 42.6 8.1 60 454-517 993-1052(1151)
164 PRK03932 asnC asparaginyl-tRNA 48.8 1.1E+02 0.0024 35.2 10.4 81 453-547 17-100 (450)
165 PRK07374 dnaE DNA polymerase I 47.9 37 0.0008 43.6 6.8 74 46-127 989-1064(1170)
166 PRK10220 hypothetical protein; 47.6 15 0.00033 32.9 2.4 28 221-250 3-30 (111)
167 PRK05813 single-stranded DNA-b 47.5 63 0.0014 33.2 7.3 61 453-517 110-175 (219)
168 PF13248 zf-ribbon_3: zinc-rib 46.6 9.9 0.00021 25.0 0.8 23 687-714 3-25 (26)
169 PF08271 TF_Zn_Ribbon: TFIIB z 46.1 21 0.00046 26.4 2.7 26 223-250 2-29 (43)
170 PF01780 Ribosomal_L37ae: Ribo 46.0 9 0.0002 33.3 0.8 26 688-715 37-63 (90)
171 KOG3056|consensus 45.9 57 0.0012 37.7 7.2 74 62-140 190-269 (578)
172 cd04498 hPOT1_OB2 hPOT1_OB2: A 45.5 39 0.00084 31.4 4.8 36 490-526 61-96 (123)
173 KOG2593|consensus 45.0 13 0.00027 41.5 1.9 29 685-715 127-163 (436)
174 cd04494 BRCA2DBD_OB2 BRCA2DBD_ 44.7 80 0.0017 33.1 7.5 58 490-550 181-238 (251)
175 TIGR00686 phnA alkylphosphonat 44.1 14 0.00031 33.1 1.7 30 686-717 2-31 (109)
176 cd04493 BRCA2DBD_OB1 BRCA2DBD_ 43.9 14 0.00031 32.8 1.7 37 321-358 23-59 (100)
177 TIGR00280 L37a ribosomal prote 41.9 13 0.00029 32.3 1.2 32 687-720 36-68 (91)
178 PRK05672 dnaE2 error-prone DNA 41.6 61 0.0013 41.3 7.4 41 479-520 974-1014(1046)
179 PRK12820 bifunctional aspartyl 41.5 1.9E+02 0.0042 35.1 11.1 95 444-547 8-110 (706)
180 COG1571 Predicted DNA-binding 41.5 14 0.00029 41.5 1.5 31 222-254 351-381 (421)
181 TIGR00686 phnA alkylphosphonat 40.8 18 0.00038 32.5 1.7 28 221-250 2-29 (109)
182 PRK03976 rpl37ae 50S ribosomal 40.7 14 0.0003 32.2 1.1 30 687-718 37-67 (90)
183 cd04484 polC_OBF polC_OBF: A s 40.1 95 0.0021 26.5 6.2 53 256-325 20-74 (82)
184 KOG0556|consensus 40.0 2.4E+02 0.0053 31.5 10.5 101 438-547 66-175 (533)
185 cd04321 ScAspRS_mt_like_N ScAs 40.0 2.4E+02 0.0051 24.1 9.7 75 455-539 2-79 (86)
186 TIGR00457 asnS asparaginyl-tRN 39.7 1.4E+02 0.003 34.4 9.4 82 453-548 17-103 (453)
187 PRK06751 single-stranded DNA-b 39.6 85 0.0018 31.0 6.6 67 59-130 4-83 (173)
188 PLN02903 aminoacyl-tRNA ligase 39.2 2E+02 0.0043 34.6 10.7 95 444-547 62-163 (652)
189 PRK14810 formamidopyrimidine-D 39.0 23 0.00049 37.8 2.7 28 219-248 238-272 (272)
190 PF07191 zinc-ribbons_6: zinc- 38.9 18 0.0004 29.9 1.5 24 223-249 3-26 (70)
191 PTZ00255 60S ribosomal protein 38.8 16 0.00034 31.9 1.2 32 687-720 37-69 (90)
192 PRK13945 formamidopyrimidine-D 38.8 25 0.00054 37.7 3.0 28 219-248 248-282 (282)
193 COG1570 XseA Exonuclease VII, 38.7 30 0.00065 39.1 3.6 55 479-540 42-97 (440)
194 PRK06826 dnaE DNA polymerase I 38.4 66 0.0014 41.4 7.0 65 55-127 989-1055(1151)
195 PRK00420 hypothetical protein; 37.8 22 0.00049 32.4 2.0 27 686-714 23-49 (112)
196 PRK07459 single-stranded DNA-b 37.6 1.2E+02 0.0026 28.1 6.9 66 576-646 5-79 (121)
197 cd04496 SSB_OBF SSB_OBF: A sub 37.6 84 0.0018 27.2 5.8 34 613-646 43-79 (100)
198 COG2888 Predicted Zn-ribbon RN 37.2 22 0.00048 28.3 1.6 28 218-247 24-57 (61)
199 PRK00476 aspS aspartyl-tRNA sy 37.1 2.4E+02 0.0051 33.7 10.9 86 453-548 18-107 (588)
200 KOG2593|consensus 37.0 17 0.00038 40.4 1.4 26 223-250 130-163 (436)
201 COG0587 DnaE DNA polymerase II 36.7 90 0.002 39.9 7.7 71 443-517 967-1038(1139)
202 PF09538 FYDLN_acid: Protein o 36.2 22 0.00047 32.3 1.7 31 686-718 9-39 (108)
203 PF14353 CpXC: CpXC protein 35.0 49 0.0011 30.8 3.9 33 240-277 38-70 (128)
204 TIGR02300 FYDLN_acid conserved 34.8 23 0.0005 32.8 1.6 31 685-717 8-38 (129)
205 PF03089 RAG2: Recombination a 34.6 46 0.001 35.3 3.9 46 228-279 66-111 (337)
206 PRK00036 primosomal replicatio 34.1 2.2E+02 0.0047 25.8 7.6 68 453-524 2-81 (107)
207 PRK10445 endonuclease VIII; Pr 33.8 29 0.00062 36.8 2.4 25 222-248 236-263 (263)
208 TIGR00621 ssb single stranded 33.5 1.4E+02 0.0029 29.3 6.9 32 615-646 52-86 (164)
209 PRK00432 30S ribosomal protein 33.5 27 0.00059 26.9 1.6 25 222-249 21-46 (50)
210 PF08792 A2L_zn_ribbon: A2L zi 33.4 30 0.00064 24.3 1.6 28 687-716 4-32 (33)
211 PF00436 SSB: Single-strand bi 33.4 1.5E+02 0.0032 25.9 6.7 67 577-646 4-83 (104)
212 PRK00286 xseA exodeoxyribonucl 33.2 1.4E+02 0.0029 34.2 8.0 90 64-163 24-121 (438)
213 TIGR02098 MJ0042_CXXC MJ0042 f 32.7 40 0.00086 24.0 2.3 27 222-250 3-35 (38)
214 PRK01103 formamidopyrimidine/5 32.6 30 0.00065 36.9 2.4 25 222-248 246-273 (274)
215 PRK05733 single-stranded DNA-b 32.5 1.3E+02 0.0027 29.8 6.5 68 576-646 7-88 (172)
216 PRK00448 polC DNA polymerase I 32.5 1.1E+02 0.0023 40.4 7.6 74 441-518 225-300 (1437)
217 PRK10917 ATP-dependent DNA hel 32.3 2.7E+02 0.0058 33.9 10.7 87 37-135 39-129 (681)
218 COG1656 Uncharacterized conser 32.2 22 0.00048 34.5 1.1 28 686-715 97-140 (165)
219 smart00531 TFIIE Transcription 32.1 31 0.00068 33.0 2.2 26 223-250 101-133 (147)
220 PRK08182 single-stranded DNA-b 31.6 1.4E+02 0.003 28.8 6.4 69 59-130 4-90 (148)
221 PRK14811 formamidopyrimidine-D 31.5 39 0.00084 36.0 3.0 26 222-249 236-264 (269)
222 KOG0402|consensus 31.5 25 0.00055 29.8 1.2 33 223-257 38-71 (92)
223 PF09538 FYDLN_acid: Protein o 31.3 29 0.00063 31.5 1.7 28 222-251 10-37 (108)
224 PF03966 Trm112p: Trm112p-like 31.3 28 0.00061 28.6 1.5 18 699-716 47-64 (68)
225 PRK06266 transcription initiat 31.2 22 0.00048 35.3 1.0 26 223-250 119-146 (178)
226 PF07191 zinc-ribbons_6: zinc- 31.0 29 0.00062 28.8 1.4 24 688-714 3-26 (70)
227 PRK05672 dnaE2 error-prone DNA 31.0 81 0.0018 40.2 6.1 73 562-644 941-1015(1046)
228 KOG3108|consensus 30.9 2E+02 0.0043 30.5 8.0 89 59-161 70-167 (265)
229 PRK00398 rpoP DNA-directed RNA 30.9 42 0.00091 25.2 2.2 25 223-249 5-30 (46)
230 PF13717 zinc_ribbon_4: zinc-r 30.7 45 0.00098 23.8 2.2 27 222-250 3-35 (36)
231 TIGR02300 FYDLN_acid conserved 30.5 31 0.00066 32.0 1.7 28 222-251 10-37 (129)
232 PF12760 Zn_Tnp_IS1595: Transp 30.4 48 0.001 24.9 2.5 25 222-248 19-45 (46)
233 PHA00626 hypothetical protein 30.2 44 0.00094 26.3 2.2 25 223-249 2-32 (59)
234 PF15072 DUF4539: Domain of un 30.1 78 0.0017 27.5 4.0 39 605-644 22-62 (86)
235 PF08274 PhnA_Zn_Ribbon: PhnA 30.0 24 0.00052 24.2 0.7 26 221-248 2-27 (30)
236 PF01599 Ribosomal_S27: Riboso 29.7 44 0.00094 25.5 2.1 26 222-248 19-46 (47)
237 PF13695 zf-3CxxC: Zinc-bindin 29.5 93 0.002 27.6 4.6 39 704-745 4-42 (98)
238 PRK06266 transcription initiat 29.2 24 0.00052 35.1 0.8 31 684-716 115-147 (178)
239 TIGR00643 recG ATP-dependent D 29.1 2.5E+02 0.0054 33.8 9.6 86 554-648 12-98 (630)
240 smart00531 TFIIE Transcription 29.0 36 0.00078 32.6 2.0 29 685-715 98-133 (147)
241 PRK06393 rpoE DNA-directed RNA 29.0 37 0.00079 27.7 1.7 38 221-267 5-42 (64)
242 smart00661 RPOL9 RNA polymeras 28.6 69 0.0015 24.4 3.2 27 688-716 2-31 (52)
243 PRK06752 single-stranded DNA-b 28.4 1.3E+02 0.0029 27.2 5.6 33 98-130 48-83 (112)
244 PRK06920 dnaE DNA polymerase I 28.3 95 0.0021 39.8 6.0 79 561-648 931-1011(1107)
245 PRK11827 hypothetical protein; 28.0 45 0.00096 26.9 2.0 28 222-251 9-37 (60)
246 PRK08486 single-stranded DNA-b 27.9 1.8E+02 0.0038 29.1 6.7 32 615-646 50-84 (182)
247 PRK07274 single-stranded DNA-b 27.0 1.8E+02 0.0039 27.3 6.3 32 98-129 48-82 (131)
248 PF13719 zinc_ribbon_5: zinc-r 27.0 56 0.0012 23.4 2.2 27 222-250 3-35 (37)
249 PRK07279 dnaE DNA polymerase I 27.0 2.6E+02 0.0056 35.6 9.3 64 57-127 884-949 (1034)
250 PRK00420 hypothetical protein; 26.9 47 0.001 30.3 2.2 26 222-249 24-49 (112)
251 PF01927 Mut7-C: Mut7-C RNAse 26.8 34 0.00075 32.7 1.4 31 685-717 90-136 (147)
252 PRK07275 single-stranded DNA-b 26.7 1.8E+02 0.004 28.4 6.4 33 98-130 48-83 (162)
253 PRK08351 DNA-directed RNA poly 26.7 62 0.0013 26.1 2.6 28 221-255 3-30 (61)
254 KOG3108|consensus 26.6 1.6E+02 0.0035 31.2 6.4 61 576-649 70-134 (265)
255 PF10571 UPF0547: Uncharacteri 26.3 40 0.00086 22.3 1.2 23 223-250 2-24 (26)
256 KOG3084|consensus 25.9 66 0.0014 34.6 3.4 49 685-737 149-203 (345)
257 KOG1885|consensus 25.5 2.4E+02 0.0052 32.2 7.7 58 453-518 105-168 (560)
258 COG1107 Archaea-specific RecJ- 25.4 72 0.0016 37.1 3.8 67 442-517 202-269 (715)
259 TIGR00373 conserved hypothetic 25.4 27 0.00059 34.0 0.4 25 223-249 111-137 (158)
260 PRK11827 hypothetical protein; 25.1 52 0.0011 26.5 1.9 29 686-716 8-37 (60)
261 PF09862 DUF2089: Protein of u 25.1 44 0.00095 30.5 1.7 28 224-259 1-28 (113)
262 PF09103 BRCA-2_OB1: BRCA2, ol 24.5 38 0.00082 31.3 1.2 39 320-359 34-72 (118)
263 TIGR00237 xseA exodeoxyribonuc 24.4 2.1E+02 0.0045 32.7 7.4 89 65-163 19-115 (432)
264 PRK08763 single-stranded DNA-b 24.3 2.6E+02 0.0056 27.4 7.0 32 615-646 53-87 (164)
265 TIGR00577 fpg formamidopyrimid 23.9 51 0.0011 35.1 2.2 23 223-247 247-272 (272)
266 PF08772 NOB1_Zn_bind: Nin one 23.8 49 0.0011 27.8 1.6 45 684-738 7-51 (73)
267 PF03966 Trm112p: Trm112p-like 23.8 51 0.0011 27.0 1.7 17 234-250 47-63 (68)
268 PRK00286 xseA exodeoxyribonucl 23.8 1.3E+02 0.0028 34.3 5.7 56 454-517 25-80 (438)
269 COG2835 Uncharacterized conser 23.6 56 0.0012 26.2 1.8 29 686-716 8-37 (60)
270 COG3877 Uncharacterized protei 23.5 57 0.0012 29.1 2.0 31 222-260 7-37 (122)
271 PRK02935 hypothetical protein; 23.5 51 0.0011 29.5 1.7 25 688-715 72-96 (110)
272 PF00096 zf-C2H2: Zinc finger, 23.2 40 0.00086 20.8 0.8 12 706-717 1-12 (23)
273 PLN02221 asparaginyl-tRNA synt 23.2 5.1E+02 0.011 30.8 10.4 84 453-548 51-138 (572)
274 PF03119 DNA_ligase_ZBD: NAD-d 22.9 61 0.0013 21.8 1.6 20 224-245 2-22 (28)
275 PF10451 Stn1: Telomere regula 22.9 2.4E+02 0.0052 29.8 6.9 58 577-641 69-131 (256)
276 PRK13945 formamidopyrimidine-D 22.7 59 0.0013 34.8 2.4 25 687-713 255-282 (282)
277 COG2824 PhnA Uncharacterized Z 22.6 85 0.0018 28.2 2.9 48 686-735 3-52 (112)
278 TIGR00373 conserved hypothetic 22.5 34 0.00073 33.3 0.5 29 684-714 107-137 (158)
279 PF07282 OrfB_Zn_ribbon: Putat 22.4 89 0.0019 25.4 2.9 29 685-715 27-56 (69)
280 COG2093 DNA-directed RNA polym 22.3 37 0.00081 27.3 0.6 34 221-259 4-37 (64)
281 COG0266 Nei Formamidopyrimidin 22.2 58 0.0013 34.6 2.2 25 222-248 246-273 (273)
282 COG2835 Uncharacterized conser 22.1 65 0.0014 25.8 1.9 28 222-251 9-37 (60)
283 TIGR00237 xseA exodeoxyribonuc 22.0 1.5E+02 0.0033 33.9 5.7 72 454-540 19-91 (432)
284 PRK13732 single-stranded DNA-b 22.0 2.8E+02 0.0061 27.5 6.8 32 615-646 55-89 (175)
285 COG1200 RecG RecG-like helicas 22.0 4.5E+02 0.0097 31.6 9.4 83 45-136 48-131 (677)
286 PRK10445 endonuclease VIII; Pr 21.8 55 0.0012 34.7 1.9 25 687-713 236-263 (263)
287 COG2824 PhnA Uncharacterized Z 21.6 1E+02 0.0022 27.6 3.2 28 221-250 3-30 (112)
288 PRK06863 single-stranded DNA-b 21.3 2.8E+02 0.0062 27.3 6.6 68 576-646 6-87 (168)
289 PF09855 DUF2082: Nucleic-acid 21.1 95 0.0021 25.4 2.7 28 706-741 1-28 (64)
290 PRK01103 formamidopyrimidine/5 20.9 57 0.0012 34.8 1.9 25 687-713 246-273 (274)
291 PRK07772 single-stranded DNA-b 20.9 2.4E+02 0.0053 28.2 6.1 33 98-130 54-89 (186)
292 smart00659 RPOLCX RNA polymera 20.8 82 0.0018 23.6 2.1 25 223-249 4-28 (44)
293 COG5189 SFP1 Putative transcri 20.7 50 0.0011 35.3 1.3 14 239-252 397-410 (423)
294 PF08696 Dna2: DNA replication 20.7 2.9E+02 0.0063 28.1 6.9 56 89-149 2-58 (209)
295 PF01927 Mut7-C: Mut7-C RNAse 20.7 60 0.0013 31.1 1.8 29 221-251 91-135 (147)
296 PRK14811 formamidopyrimidine-D 20.6 62 0.0014 34.4 2.1 27 687-715 236-265 (269)
297 PF07282 OrfB_Zn_ribbon: Putat 20.5 61 0.0013 26.4 1.6 28 221-250 28-56 (69)
298 COG4085 Predicted RNA-binding 20.5 1.1E+02 0.0024 30.5 3.5 26 723-748 71-96 (204)
299 PRK14810 formamidopyrimidine-D 20.4 58 0.0012 34.7 1.8 25 687-713 245-272 (272)
300 PF12773 DZR: Double zinc ribb 20.3 44 0.00095 25.3 0.6 32 223-257 14-45 (50)
301 PF13695 zf-3CxxC: Zinc-bindin 20.2 1.1E+02 0.0025 27.0 3.4 40 239-281 4-43 (98)
302 COG1996 RPC10 DNA-directed RNA 20.2 56 0.0012 25.1 1.1 24 223-248 8-32 (49)
303 COG1096 Predicted RNA-binding 20.0 1.5E+02 0.0032 29.6 4.3 40 671-714 124-174 (188)
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=1.5e-92 Score=817.13 Aligned_cols=461 Identities=47% Similarity=0.803 Sum_probs=404.3
Q ss_pred ccCccccCCCcceeeEEEeecccccccccCCcccceEEEEceeEeeee-ecCCCCccEEEEEEeeeeeccCcccCccccC
Q psy15132 319 YNGTKKIPDGVNINSFAMLATQLNDIITDGTLSEFTIVQIKRYIVSGV-SSGSATNRSVLIILELNIIKPGTEIGFKIGN 397 (786)
Q Consensus 319 y~~~~~~sDG~~~~~~~~la~~ln~~v~~~~L~~~~iikl~~~~~~~~-~~~~~~~~~~~ii~~~~v~~~~~~~~~~ig~ 397 (786)
-.+|++||||.|. .++||++|||+++++|.|++|+||||++|+++.+ ++| |++|||+++||+.+..+...+||+
T Consensus 42 ~ryr~~lsDg~~~-~~~ml~t~~n~~~~~~~l~~~~iv~l~~~~~~~~~~~~----~~~lii~~~ev~~~~~~~~~~ig~ 116 (608)
T TIGR00617 42 RRYRIVISDGIYY-SKAMLATQLNPLVREGELQEGTIIRLTKFEVNTIGKDG----RKVLIVYELEVVKPELKVRDKIGN 116 (608)
T ss_pred ceEEEEEECchHH-HHHHHHHHHHHHHHhCCccCCCEEEEeEEEEeEEccCC----cEEEEEEeeEEeecccccccccCC
Confidence 4678999999995 5899999999999999999999999999999999 543 799999999999987666678999
Q ss_pred CccCCCCCCCCC--CCCCCCC--CC--CC----CCC--CCCCCcC------CCCCCC-CCCCceeeecccCCCCCceEEE
Q psy15132 398 PQPLNTNTDNSS--TQQTPAA--TN--TN----GSN--GVHNNVA------IPRQAS-APVVQTHPIVSLSPYQNKWTIK 458 (786)
Q Consensus 398 p~~~~~~~~~~~--~~~~~~~--~~--~~----~~~--~~~~~~~------~~~~~~-~~~~~~~~I~~L~p~~~~w~I~ 458 (786)
|+++......+. +..++.| .. .+ .+. ....... .++.++ .+..+++||++|+||+++|+|+
T Consensus 117 p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~pI~~L~py~~~wtIk 196 (608)
T TIGR00617 117 PVTYEKYLDSWHEEQVLASKPATNPANPPNAKAPKNEVASYNNAANPERGNAPPAPNSGSTRRVMPIASLSPYQNKWTIK 196 (608)
T ss_pred CccccccccccCccccccccccccCCCCCCccCCCcccccccCCCCcccCCCCCCccccCCcceEEHHHCCCCCCceEEE
Confidence 998865200000 0000100 00 00 000 0000000 001111 1234699999999999999999
Q ss_pred EEEeecCCcceecCCCCCceEEEEEEEcCCCcEEEEEcchhHHHhhhhccCCcEEEEcceEEeccCCcccccCCceEEEE
Q psy15132 459 ARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFNDECNRFHDMIEKDKVYYISNCTLKPANKKFSSINNDYEMSF 538 (786)
Q Consensus 459 ~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~G~I~at~~~~~~~kf~~~l~~G~vy~is~~~V~~a~~~y~~~~~~yei~f 538 (786)
|||++|+++|.|++++|+|++|+|+|+|++|+|+||+|++.+++|+++|++|+||+|++|+|++++++|++++|+|||+|
T Consensus 197 aRV~~Ks~ir~~~~~~gegkvfsv~L~Degg~Irat~f~~~~dkf~~~l~eG~VY~Is~~~Vk~an~~y~~~~~~yei~f 276 (608)
T TIGR00617 197 ARVTNKSEIRTWSNARGEGKLFNVELLDESGEIRATAFNEQADKFYDIIQEGKVYYISKGSLKPANKQFTNLGNDYEMTL 276 (608)
T ss_pred EEEEeccccceecCCCCCceeeEEEEecCCCeEEEEECchHHHHHhhhcccCCEEEECceEEEEccccccCCCCCEEEEE
Confidence 99999999999999999999999999998889999999999999999999999999999999999999999999999999
Q ss_pred ccccEEEEccCCCCCCCCcceeeccCcccccccCCCceeeEEEEEEEcccceeEEeecCCceeeEEEEEEeeccccEEEE
Q psy15132 539 THSTTVIPCNEDEVGNMPSVKYCFVPLKTIAEISPDENIDVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTM 618 (786)
Q Consensus 539 ~~~T~I~~~~d~~~~~iP~~~~~f~~i~dl~~~~~~~~vDViGvV~~V~~~~~i~~k~~g~~~~kr~i~l~D~s~~~i~~ 618 (786)
+.+|.|++|+|.. ++|.+.|+|++|+||.+...+..|||||+|++|+++.++++|.+|++..+|+|+|+|+||.+|+|
T Consensus 277 ~~~T~I~~~~d~~--~iP~~~~~f~~i~dI~~~~~~~~VDVIGvV~~v~~~~~i~~k~~g~~~~kR~i~L~D~sg~sI~v 354 (608)
T TIGR00617 277 DRDTVIEECEDET--AIPKIQFNFVKIDDIGGYEGNSLVDVIGIVQSVSPTQTITSRKNNKEFPKRDITLVDDSGKSVRV 354 (608)
T ss_pred CCCeEEEECCCcc--cCCcccccceEHHHhhhhcCCCCccEEEEEeEecCceEEEEcCCCCeeeeEEEEEEeCCCCEEEE
Confidence 9999999998876 79999999999999999888889999999999999999998888999999999999999999999
Q ss_pred EEeccccccccCCCCCEEEEEeEEEeecCCc-c-----------------------------------------------
Q psy15132 619 TLWGKEAETFDASNKPVIAVKAARVSEFQGN-L----------------------------------------------- 650 (786)
Q Consensus 619 tLWg~~a~~~~~~~~~vv~i~~~~V~~f~G~-L----------------------------------------------- 650 (786)
||||++|+.|+...++||+|++++|++|+|+ |
T Consensus 355 TLWG~~A~~~~~~~~~Vva~kg~~V~~f~g~sLs~~~~S~i~iNPdipEa~~L~~w~~~~g~~~~~~s~~~~~~~~~~~~ 434 (608)
T TIGR00617 355 TLWGDDATKFDVSVQPVIAIKGVRVSDFGGKSLSTGGSSTIIVNPDIPEAEKLKGWYDNEGKGTMASSISDMMSGRVGGS 434 (608)
T ss_pred EEEhhhhhhcCCCCCCEEEEEeEEEEecCCceEeccCCceEEECCCcHHHHHHHHHHHhcCCCccceeehhccccccCCc
Confidence 9999999999999999999999999999887 5
Q ss_pred ----ccHHhHHhhcCCCCCCCceEEEEEEEEEEecCceEEeCCCCccccccccccCCceeeeCCCCCcCCceeEEEEEEE
Q psy15132 651 ----LLMREIQDQQLGMGDKADYCSVRGIIQVFRGSNTTYKACPSQDCNKKVIDQNNGMYRCEKCNKEFNTFTYRLILPV 726 (786)
Q Consensus 651 ----~ti~e~~~~~l~~~~~~~~~~v~a~I~~i~~~~~~Y~aC~~~~C~kkv~~~~~g~~~C~~C~~~~~~~~~ry~l~~ 726 (786)
+||+|++++++|.+++++||.|+|+|+.|+.++|||+|||++.|+|||++..+|.|+|++|++.+++|.|||+|++
T Consensus 435 ~~~~ktI~ei~~~~lg~~~k~~~f~v~atI~~Ik~d~~~Y~ACp~~~CnKKV~~~~~g~~~CekC~~~~~~~~~RYil~~ 514 (608)
T TIGR00617 435 NAERKTIAEIQAENLGKSDKPDYFSVKATISYLKPDNALYRACPSEDCNKKVVDQGDGTYRCEKCNKNFAEFKYRYILQI 514 (608)
T ss_pred ccccccHHHHhhhccCCCCCCcEEEEEEEEEEEecCCeEeccCChhhCCCccccCCCCCEECCCCCCCCCCccEEEEEEE
Confidence 3567777778888899999999999999999999999999777999999877799999999999999999999999
Q ss_pred EEEecCCcEEEEEehhhHHHHhCCChHHHhccccChH-----HHHHhcCCeEEEEEEEEeeccCC
Q psy15132 727 MIGDWTNSVWVTLFQNEAESILGVTAQEVGESTEDHP-----ALKKALFTQYIFRLRAKLEHYNK 786 (786)
Q Consensus 727 ~i~D~Tg~~~~~~F~~~ae~llG~sa~el~~~~~~~~-----~~~~~~~k~~~f~v~~k~~~y~~ 786 (786)
.|+|+||++|+++|++.|++|||+||+||.+++++++ +|+++.|++|+|+||+|+|+|||
T Consensus 515 ~i~D~Tg~~~~t~F~~~ae~llG~sA~eL~~l~~~~~~~~~~i~~~~~~~~~~f~~~~k~e~yn~ 579 (608)
T TIGR00617 515 SISDETGQLWVTAFNDQAEQILGKSAAELGELKEEDPDEFEAIFQEAQFVPYIFRLRVKQDTYND 579 (608)
T ss_pred EEEeCCCCEEEEEEhHHHHHHcCCCHHHHHHHHhcCHHHHHHHHHHhhCcEEEEEEEEEEcccCC
Confidence 9999999999999999999999999999999988764 88999999999999999999997
No 2
>PRK12366 replication factor A; Reviewed
Probab=100.00 E-value=3e-67 Score=610.67 Aligned_cols=539 Identities=19% Similarity=0.319 Sum_probs=414.4
Q ss_pred ecCccchhccCCC-CceEEEEEEEEeccceeEeeccCCceeeEEEEEEEeCCCCEEEEEeccccccccc-CCCCcEEEEE
Q psy15132 45 FVPLKTIAEISPD-ENIDVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWGKEAETFD-ASNKPVIAVK 122 (786)
Q Consensus 45 f~~~~~i~~~~~~-~~vDViGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~s~~~i~~tLWg~~a~~~~-~~~~~Vi~i~ 122 (786)
+.+|++|. ++ ..+++.|.|++++++++++.+. |.+...+++.|.|+|| +|++|+|++.|..++ ...|.|+-|.
T Consensus 63 ~~~I~dl~---p~~~~v~i~arV~~~~~~r~~~~~~-G~eGkv~~~~v~DetG-~Ir~t~W~~~~~~~~~le~G~v~~i~ 137 (637)
T PRK12366 63 DFKISDIE---EGQINVEITGRIIEISNIKTFTRKD-GSTGKLANITIADNTG-TIRLTLWNDNAKLLKGLKEGDVIKIE 137 (637)
T ss_pred eeEHHHCc---CCCcceEEEEEEEEccCCeEEECCC-CCccEEEEEEEEcCCC-EEEEEEEchhhhhhccCCCCCEEEEe
Confidence 44566664 34 4699999999999999998764 6677889999999999 899999999987654 3789999999
Q ss_pred eEEEeeeCCceeeeecceeEEEECCCchHHHHHHhhhhccCCCceeeeccccCCCCCCCcchhhhHHHHHhhcCCCCCCC
Q psy15132 123 AARVSEFQGGKTLSLSMSSVLSLNPDIPECHKLQGWFSTQTNTRFEPVSQRTGGMGGGAAGNLLLMREIQDQQLGMGDKA 202 (786)
Q Consensus 123 ~~kv~~f~g~~~ls~~~~s~i~~npd~pe~~~l~~w~~~~~~~~~~~~s~~~~~~~~~~~~~~~ti~ei~~~~l~~~~~~ 202 (786)
++.++.|+|..+|+++..|.|...++..+. ..+.+. ....|++|. .+
T Consensus 138 ~~~v~~~~~~~el~~~~~t~I~~~~~~d~~-------------~i~~~~------------~~~~I~el~--------~g 184 (637)
T PRK12366 138 NARSRKWNNDVELNSGSETRIDKLEKYDES-------------RYPIIK------------ENYDIPELE--------PN 184 (637)
T ss_pred ccEecccCCceEEEcCCcceEEEccccccc-------------cCCccc------------ccccccccC--------CC
Confidence 999999999999999988888765421000 000000 011233432 13
Q ss_pred cEEEEEEEEEEEecCceEEeCCCCCCCCcceeeCCCceeecccCCCcCCceeEeeeeeEEEEecCCcEEEEeehHHHHHH
Q psy15132 203 DYCSVRGIIQVFRGSNTTYKACPSQDCNKKVIDQNNGMYRCEKCNKEFNTFTYRLILPVMIGDWTNSVWVTLFQNEAESI 282 (786)
Q Consensus 203 ~~~~v~a~I~~i~~~~~~Y~aC~~~~C~kKv~~~~~~~~~C~~C~~~~~~~~~ry~l~~~v~D~Tg~~~~~~F~~~a~~i 282 (786)
.+..|.|.|..+..-.- + .+| +| ......++.|.|.||++++++||+.|+..
T Consensus 185 ~~v~v~G~V~~~~~~~~-f--------~rk-----dg--------------~~~~~r~~~l~D~TG~irvTlW~~~a~~~ 236 (637)
T PRK12366 185 LSATIEGEVTKAYPIKE-F--------TRK-----DG--------------SEGKLKSFILKDDTGSIRVTLWNDLTDIE 236 (637)
T ss_pred CeEEEEEEEEEccCcEE-E--------EEc-----CC--------------CeeEEEEEEEEcCCCcEEEEEEChhhccc
Confidence 37888999888753210 1 011 11 11234678899999999999999987320
Q ss_pred hCCChhhhhccCCChHHHHHhcCCEEEEEEeeecccccCccccCCCcceeeEEEeecccccccccCCcccceEEEEceeE
Q psy15132 283 LGVTAQEVGESTEDHPALKKALFTQYIFRLRAKLEHYNGTKKIPDGVNINSFAMLATQLNDIITDGTLSEFTIVQIKRYI 362 (786)
Q Consensus 283 lg~sa~el~~~~e~~~~~~~~~~k~~~f~v~~k~e~y~~~~~~sDG~~~~~~~~la~~ln~~v~~~~L~~~~iikl~~~~ 362 (786)
|..|++|+|+.|.
T Consensus 237 -------------------------------------------------------------------~~~g~vv~i~g~~ 249 (637)
T PRK12366 237 -------------------------------------------------------------------VNKGDIVRVKGYV 249 (637)
T ss_pred -------------------------------------------------------------------CCCCCEEEEEeEE
Confidence 2234444444332
Q ss_pred eeeeecCCCCccEEEEEEeeeeeccCcccCccccCCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCce
Q psy15132 363 VSGVSSGSATNRSVLIILELNIIKPGTEIGFKIGNPQPLNTNTDNSSTQQTPAATNTNGSNGVHNNVAIPRQASAPVVQT 442 (786)
Q Consensus 363 ~~~~~~~~~~~~~~~ii~~~~v~~~~~~~~~~ig~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 442 (786)
...-. | .+|+-... ...|..+.... ...++
T Consensus 250 ~~~~~-~-----------~~el~~~~---~~~i~~~~~~~-----------------------------------~~~~~ 279 (637)
T PRK12366 250 KQGYR-T-----------GLEISANN---IEILEKLEKEE-----------------------------------KELEI 279 (637)
T ss_pred ecCcC-C-----------ceEEEeCC---ceeeccccccc-----------------------------------cccCc
Confidence 22110 0 01110000 00111110000 01246
Q ss_pred eeecccCCC-CC-ceEEEEEEeecCCcceecCCCCCceEEEEEEEcCCCcEEEEEcchhHHHhhhhccCCcEEEEcceEE
Q psy15132 443 HPIVSLSPY-QN-KWTIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFNDECNRFHDMIEKDKVYYISNCTL 520 (786)
Q Consensus 443 ~~I~~L~p~-~~-~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~G~I~at~~~~~~~kf~~~l~~G~vy~is~~~V 520 (786)
+||++|+|| ++ +|+|+|||+.|+++|+|++.+|+|++|+++|.|++|+|++|+|++.+++|++ |++|+||+|++++|
T Consensus 280 ~pI~~L~~~~~g~~~~I~grV~~~~~~R~f~~~~g~gkv~s~~l~D~tG~IR~t~w~~~~d~~~~-l~~G~vy~is~~~v 358 (637)
T PRK12366 280 VNIEELTEFEDGEEVDVKGRIIAISDKREVERDDRTAEVQDIELADGTGRVRVSFWGEKAKILEN-LKEGDAVKIENCKV 358 (637)
T ss_pred eeHHHCCcccCCCEEEEEEEEEecCCceEEEcCCCcEEEEEEEEEcCCCeEEEEEeCchhhhhcc-cCCCCEEEEecCEE
Confidence 899999999 55 8999999999999999999999999999999999999999999999999997 59999999999999
Q ss_pred eccCCcccccCCceEEEEccccEEEEccCCCCCCCCcceeeccCcccccccC-CCceeeEEEEEEEcccceeEEeecCCc
Q psy15132 521 KPANKKFSSINNDYEMSFTHSTTVIPCNEDEVGNMPSVKYCFVPLKTIAEIS-PDENIDVLGVCIDAAELSSVTGKTNQK 599 (786)
Q Consensus 521 ~~a~~~y~~~~~~yei~f~~~T~I~~~~d~~~~~iP~~~~~f~~i~dl~~~~-~~~~vDViGvV~~V~~~~~i~~k~~g~ 599 (786)
+..+.. ...+.|||+++..|.|.+ +++. .+|.+.++|++|.+|.+.. .+..|||+|+|++++++.+|+++ +|+
T Consensus 359 k~y~~~--~~~~~~El~~~~~s~I~~-d~~~--~~p~~~~~~~~i~dI~~~~~~~~~VdVig~V~~v~~~~~i~~k-~G~ 432 (637)
T PRK12366 359 RTYYDN--EGEKRVDLNAGYSSEIIK-DESI--SFEEIEEKIYKIKDILNLEEDDNDITVIARVVEDYPVNEFERS-DGS 432 (637)
T ss_pred eecccc--CCCcCEEEEcCCceEEEe-ccCC--cccceeeccccHHHhhcccCCCcEEEEEEEEEEccCceEEEec-CCC
Confidence 843321 335789999999999998 4433 6899999999999999884 68899999999999999999876 599
Q ss_pred eeeEEEEEEeeccccEEEEEEeccccccccCCCCCEEEEEeEEEeecCCc--c-----------ccHHhHHhhc--CCCC
Q psy15132 600 TYMKRDITLVDQSQASVTMTLWGKEAETFDASNKPVIAVKAARVSEFQGN--L-----------LLMREIQDQQ--LGMG 664 (786)
Q Consensus 600 ~~~kr~i~l~D~s~~~i~~tLWg~~a~~~~~~~~~vv~i~~~~V~~f~G~--L-----------~ti~e~~~~~--l~~~ 664 (786)
+..+|+++|.|+|| +|++||||++|+ ++...|++|+|++++|++|+|+ | ....+++... +..-
T Consensus 433 ~~~~r~i~l~D~TG-~I~vtlWg~~a~-~~~~~G~vi~i~~~~V~~~~g~~~Ls~~~~s~i~~~p~~~el~~~~~~I~~i 510 (637)
T PRK12366 433 KGKVRNIELADGTG-SIRLTLWDDDAE-IEIKEGDAIKILHPYVKENGDYLDLSIGRYGRIEINPEGEIIKSNRKFIADL 510 (637)
T ss_pred EeEEEEEEEEeCCC-EEEEEEeccccc-cCCCCCCEEEEEeeEEEeCCCeeEEEecCcceEEECCCCccccccccCHHHc
Confidence 99999999999999 999999999997 6778899999999999999996 4 1111111100 0001
Q ss_pred CCCceEEEEEEEEEEecCceEEeCCCCccccccccccCCceeeeCCCCCcCCceeEEEEEEEEEEecCCcEEEEEehhhH
Q psy15132 665 DKADYCSVRGIIQVFRGSNTTYKACPSQDCNKKVIDQNNGMYRCEKCNKEFNTFTYRLILPVMIGDWTNSVWVTLFQNEA 744 (786)
Q Consensus 665 ~~~~~~~v~a~I~~i~~~~~~Y~aC~~~~C~kkv~~~~~g~~~C~~C~~~~~~~~~ry~l~~~i~D~Tg~~~~~~F~~~a 744 (786)
..++++.++|+|+.|+.++++|+||| .|+|||.+ .+|.|+|++|++. +|.|||+|++.|+|+||++|+++|++.|
T Consensus 511 ~~~~~~~v~g~i~~i~~~~~~y~aCp--~CnkKv~~-~~g~~~C~~c~~~--~p~~~~~l~~~i~D~TG~~~~t~f~e~a 585 (637)
T PRK12366 511 EEDDTVEIRGTVVDIRKQKIILYLCP--NCRKRVEE-VDGEYICEFCGEV--EPNELLMLNFTLDDGTGTINCRFYGKNV 585 (637)
T ss_pred ccCCeEEEEEEEEEEeCCCEEEeccc--ccCeEeEc-CCCcEECCCCCCC--CCcEEEEEEEEEEcCCCCEEEEEEhHHh
Confidence 22456999999999999999999999 59999985 6789999999997 8899999999999999999999999999
Q ss_pred HHHhCCChHHHhccccChHHHHHhcCCeEEEEEEEEee
Q psy15132 745 ESILGVTAQEVGESTEDHPALKKALFTQYIFRLRAKLE 782 (786)
Q Consensus 745 e~llG~sa~el~~~~~~~~~~~~~~~k~~~f~v~~k~~ 782 (786)
++||||+|+||.+|.+ +.|++++|++|.|+++++++
T Consensus 586 e~l~G~sa~el~~l~~--~~l~~~~g~~~~~~~~~k~~ 621 (637)
T PRK12366 586 EKLLGMSKEELKELNL--EALEDLLGEEVVFYGNVSFR 621 (637)
T ss_pred HHHhCCCHHHHHHHHH--HHHHHhcCcEEEEEEEEeec
Confidence 9999999999999886 58888999999999999998
No 3
>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=1.7e-66 Score=600.50 Aligned_cols=340 Identities=43% Similarity=0.757 Sum_probs=306.4
Q ss_pred ccccccCCCcCCCCCeEEEEccCcEEEEccCCCCCCCCceeEeecCccchhccCCCCceEEEEEEEEeccceeEeeccCC
Q psy15132 2 LAAPANKKFSSINNDYEMSFTHSTTVIPCNEDEVGNMPSVKYCFVPLKTIAEISPDENIDVLGVCIDAAELSSVTGKTNQ 81 (786)
Q Consensus 2 ~v~~A~~~y~~~~~~yei~f~~~T~I~~~~d~~~~~iP~~~~~f~~~~~i~~~~~~~~vDViGvV~~v~~~~~i~~k~~g 81 (786)
.|++||++|++++|+|||+|+.+|.|++|.|+ .+||++.|+|++|++|.+.+.+.+|||||+|++|+++.+|++|.+|
T Consensus 257 ~Vk~an~~y~~~~~~yei~f~~~T~I~~~~d~--~~iP~~~~~f~~i~dI~~~~~~~~VDVIGvV~~v~~~~~i~~k~~g 334 (608)
T TIGR00617 257 SLKPANKQFTNLGNDYEMTLDRDTVIEECEDE--TAIPKIQFNFVKIDDIGGYEGNSLVDVIGIVQSVSPTQTITSRKNN 334 (608)
T ss_pred EEEEccccccCCCCCEEEEECCCeEEEECCCc--ccCCcccccceEHHHhhhhcCCCCccEEEEEeEecCceEEEEcCCC
Confidence 47999999999999999999999999999764 4699999999999999998888899999999999999999988889
Q ss_pred ceeeEEEEEEEeCCCCEEEEEecccccccccCCCCcEEEEEeEEEeeeCCceeeeecceeEEEECCCchHHHHHHhhhhc
Q psy15132 82 KTYMKRDITLVDQSQASVTMTLWGKEAETFDASNKPVIAVKAARVSEFQGGKTLSLSMSSVLSLNPDIPECHKLQGWFST 161 (786)
Q Consensus 82 ~~~~kr~i~l~D~s~~~i~~tLWg~~a~~~~~~~~~Vi~i~~~kv~~f~g~~~ls~~~~s~i~~npd~pe~~~l~~w~~~ 161 (786)
++..||+|+|+|+||.+|+|||||++|.+|+...++||+|+++||++| |+++||++++|+|++|||+||+++|++||++
T Consensus 335 ~~~~kR~i~L~D~sg~sI~vTLWG~~A~~~~~~~~~Vva~kg~~V~~f-~g~sLs~~~~S~i~iNPdipEa~~L~~w~~~ 413 (608)
T TIGR00617 335 KEFPKRDITLVDDSGKSVRVTLWGDDATKFDVSVQPVIAIKGVRVSDF-GGKSLSTGGSSTIIVNPDIPEAEKLKGWYDN 413 (608)
T ss_pred CeeeeEEEEEEeCCCCEEEEEEEhhhhhhcCCCCCCEEEEEeEEEEec-CCceEeccCCceEEECCCcHHHHHHHHHHHh
Confidence 999999999999999999999999999999999999999999999999 6789999999999999999999999999998
Q ss_pred cCC-CceeeeccccCCCCCCCcchhhhHHHHHhhcCCCCCCCcEEEEEEEEEEEecCceEEeCCCCCCCCcceeeCCCce
Q psy15132 162 QTN-TRFEPVSQRTGGMGGGAAGNLLLMREIQDQQLGMGDKADYCSVRGIIQVFRGSNTTYKACPSQDCNKKVIDQNNGM 240 (786)
Q Consensus 162 ~~~-~~~~~~s~~~~~~~~~~~~~~~ti~ei~~~~l~~~~~~~~~~v~a~I~~i~~~~~~Y~aC~~~~C~kKv~~~~~~~ 240 (786)
++. ..+.+++...++..++...+++||+||++++++.+++++||+|+|+|++|+.++|||+|||++.|+|||.++++|.
T Consensus 414 ~g~~~~~~s~~~~~~~~~~~~~~~~ktI~ei~~~~lg~~~k~~~f~v~atI~~Ik~d~~~Y~ACp~~~CnKKV~~~~~g~ 493 (608)
T TIGR00617 414 EGKGTMASSISDMMSGRVGGSNAERKTIAEIQAENLGKSDKPDYFSVKATISYLKPDNALYRACPSEDCNKKVVDQGDGT 493 (608)
T ss_pred cCCCccceeehhccccccCCcccccccHHHHhhhccCCCCCCcEEEEEEEEEEEecCCeEeccCChhhCCCccccCCCCC
Confidence 874 2333443322211123356789999999999998899999999999999999999999999656999999777789
Q ss_pred eecccCCCcCCceeEeeeeeEEEEecCCcEEEEeehHHHHHHhCCChhhhhccCCChH-----HHHHhcCCEEEEEEeee
Q psy15132 241 YRCEKCNKEFNTFTYRLILPVMIGDWTNSVWVTLFQNEAESILGVTAQEVGESTEDHP-----ALKKALFTQYIFRLRAK 315 (786)
Q Consensus 241 ~~C~~C~~~~~~~~~ry~l~~~v~D~Tg~~~~~~F~~~a~~ilg~sa~el~~~~e~~~-----~~~~~~~k~~~f~v~~k 315 (786)
|+|++|+++.++|.|||+|++.|+|+||++|+++||+.|++|||++|+||.++.++++ .|.++.|++|.|+||++
T Consensus 494 ~~CekC~~~~~~~~~RYil~~~i~D~Tg~~~~t~F~~~ae~llG~sA~eL~~l~~~~~~~~~~i~~~~~~~~~~f~~~~k 573 (608)
T TIGR00617 494 YRCEKCNKNFAEFKYRYILQISISDETGQLWVTAFNDQAEQILGKSAAELGELKEEDPDEFEAIFQEAQFVPYIFRLRVK 573 (608)
T ss_pred EECCCCCCCCCCccEEEEEEEEEEeCCCCEEEEEEhHHHHHHcCCCHHHHHHHHhcCHHHHHHHHHHhhCcEEEEEEEEE
Confidence 9999999999999999999999999999999999999999999999999999876543 57889999999999999
Q ss_pred cccccCccccCCCcceeeEEEeecccccccccCCc
Q psy15132 316 LEHYNGTKKIPDGVNINSFAMLATQLNDIITDGTL 350 (786)
Q Consensus 316 ~e~y~~~~~~sDG~~~~~~~~la~~ln~~v~~~~L 350 (786)
+|+|||+.++ ++ +++-+.++|+..|+..|
T Consensus 574 ~e~yn~e~r~---~~---~v~~~~~vd~~~e~~~L 602 (608)
T TIGR00617 574 QDTYNDESRQ---KY---TVMSVDPVNYRAEAKYL 602 (608)
T ss_pred EcccCCEeeE---EE---EEEEeeeCCHHHHHHHH
Confidence 9999999887 44 68889999998877655
No 4
>PRK12366 replication factor A; Reviewed
Probab=100.00 E-value=4.2e-43 Score=408.57 Aligned_cols=264 Identities=20% Similarity=0.352 Sum_probs=235.6
Q ss_pred CCc--CCCCCeEEEEccCcEEEEccCCCCCCCCceeEeecCccchhccC-CCCceEEEEEEEEeccceeEeeccCCceee
Q psy15132 9 KFS--SINNDYEMSFTHSTTVIPCNEDEVGNMPSVKYCFVPLKTIAEIS-PDENIDVLGVCIDAAELSSVTGKTNQKTYM 85 (786)
Q Consensus 9 ~y~--~~~~~yei~f~~~T~I~~~~d~~~~~iP~~~~~f~~~~~i~~~~-~~~~vDViGvV~~v~~~~~i~~k~~g~~~~ 85 (786)
+|+ .-++.|||+|+..|.|.+ ++ ...+|.+.|+|++|++|.+++ .+..|||+|+|++++|+++|++++ |++..
T Consensus 360 ~y~~~~~~~~~El~~~~~s~I~~-d~--~~~~p~~~~~~~~i~dI~~~~~~~~~VdVig~V~~v~~~~~i~~k~-G~~~~ 435 (637)
T PRK12366 360 TYYDNEGEKRVDLNAGYSSEIIK-DE--SISFEEIEEKIYKIKDILNLEEDDNDITVIARVVEDYPVNEFERSD-GSKGK 435 (637)
T ss_pred eccccCCCcCEEEEcCCceEEEe-cc--CCcccceeeccccHHHhhcccCCCcEEEEEEEEEEccCceEEEecC-CCEeE
Confidence 566 445789999999999998 43 256899999999999999874 688999999999999999998764 88899
Q ss_pred EEEEEEEeCCCCEEEEEecccccccccCCCCcEEEEEeEEEeeeCCceeeeecceeEEEECCCchHHHHHHhhhhccCCC
Q psy15132 86 KRDITLVDQSQASVTMTLWGKEAETFDASNKPVIAVKAARVSEFQGGKTLSLSMSSVLSLNPDIPECHKLQGWFSTQTNT 165 (786)
Q Consensus 86 kr~i~l~D~s~~~i~~tLWg~~a~~~~~~~~~Vi~i~~~kv~~f~g~~~ls~~~~s~i~~npd~pe~~~l~~w~~~~~~~ 165 (786)
+|+++|.|+|| +|++||||++|. +....+++|+|++++|++|+|.++||++++|+|.+||+.|| |+.
T Consensus 436 ~r~i~l~D~TG-~I~vtlWg~~a~-~~~~~G~vi~i~~~~V~~~~g~~~Ls~~~~s~i~~~p~~~e---l~~-------- 502 (637)
T PRK12366 436 VRNIELADGTG-SIRLTLWDDDAE-IEIKEGDAIKILHPYVKENGDYLDLSIGRYGRIEINPEGEI---IKS-------- 502 (637)
T ss_pred EEEEEEEeCCC-EEEEEEeccccc-cCCCCCCEEEEEeeEEEeCCCeeEEEecCcceEEECCCCcc---ccc--------
Confidence 99999999999 999999999997 56678999999999999998878999999999999999987 210
Q ss_pred ceeeeccccCCCCCCCcchhhhHHHHHhhcCCCCCCCcEEEEEEEEEEEecCceEEeCCCCCCCCcceeeCCCceeeccc
Q psy15132 166 RFEPVSQRTGGMGGGAAGNLLLMREIQDQQLGMGDKADYCSVRGIIQVFRGSNTTYKACPSQDCNKKVIDQNNGMYRCEK 245 (786)
Q Consensus 166 ~~~~~s~~~~~~~~~~~~~~~ti~ei~~~~l~~~~~~~~~~v~a~I~~i~~~~~~Y~aC~~~~C~kKv~~~~~~~~~C~~ 245 (786)
++++|++|++ +++++++|+|.+|+.+++||+||| .|||||.+ ++|.|+|++
T Consensus 503 ------------------~~~~I~~i~~--------~~~~~v~g~i~~i~~~~~~y~aCp--~CnkKv~~-~~g~~~C~~ 553 (637)
T PRK12366 503 ------------------NRKFIADLEE--------DDTVEIRGTVVDIRKQKIILYLCP--NCRKRVEE-VDGEYICEF 553 (637)
T ss_pred ------------------cccCHHHccc--------CCeEEEEEEEEEEeCCCEEEeccc--ccCeEeEc-CCCcEECCC
Confidence 3577888765 245999999999999999999999 89999985 678999999
Q ss_pred CCCcCCceeEeeeeeEEEEecCCcEEEEeehHHHHHHhCCChhhhhccCCChHHHHHhcCCEEEEEEeeecccccCccc
Q psy15132 246 CNKEFNTFTYRLILPVMIGDWTNSVWVTLFQNEAESILGVTAQEVGESTEDHPALKKALFTQYIFRLRAKLEHYNGTKK 324 (786)
Q Consensus 246 C~~~~~~~~~ry~l~~~v~D~Tg~~~~~~F~~~a~~ilg~sa~el~~~~e~~~~~~~~~~k~~~f~v~~k~e~y~~~~~ 324 (786)
|++. +|.|||+|++.|+|+||++|+++|++.|++|||++|+||.++.+ ..|.+++|++|.|+++++++ |++++
T Consensus 554 c~~~--~p~~~~~l~~~i~D~TG~~~~t~f~e~ae~l~G~sa~el~~l~~--~~l~~~~g~~~~~~~~~k~~--~~~~r 626 (637)
T PRK12366 554 CGEV--EPNELLMLNFTLDDGTGTINCRFYGKNVEKLLGMSKEELKELNL--EALEDLLGEEVVFYGNVSFR--NEELR 626 (637)
T ss_pred CCCC--CCcEEEEEEEEEEcCCCCEEEEEEhHHhHHHhCCCHHHHHHHHH--HHHHHhcCcEEEEEEEEeec--CceeE
Confidence 9997 89999999999999999999999999999999999999998865 67888999999999999999 77664
No 5
>PRK08402 replication factor A; Reviewed
Probab=100.00 E-value=3.7e-38 Score=339.17 Aligned_cols=265 Identities=20% Similarity=0.302 Sum_probs=219.8
Q ss_pred ecCccchhccCCCCceEEEEEEEEeccceeEeeccCCceeeEEEEEEEeCCCCEEEEEeccccccc-cc-CCCCcEEEEE
Q psy15132 45 FVPLKTIAEISPDENIDVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWGKEAET-FD-ASNKPVIAVK 122 (786)
Q Consensus 45 f~~~~~i~~~~~~~~vDViGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~s~~~i~~tLWg~~a~~-~~-~~~~~Vi~i~ 122 (786)
..+|.||.. ....|.+.|.|+++++.++++++. |.....++++|.|+|| ++++||||+.|.. |+ ...|+||+|+
T Consensus 62 ~~kI~dl~~--g~~~V~v~~rVl~~~~~r~f~rrd-G~~~~V~~i~l~DeTG-~ir~TlW~~~a~~~~~~l~~Gdvi~I~ 137 (355)
T PRK08402 62 LMHISDLVP--GMRGVNIVGRVLRKYPPREYTKKD-GSTGRVASLIIYDDTG-RARVVLWDAKVAKYYNKINVGDVIKVI 137 (355)
T ss_pred ccCHHHccC--CCceeeEEEEEEEccCCceeeccC-CCcceEEEEEEEcCCC-eEEEEEechhhhhhcccCCCCCEEEEE
Confidence 345666642 236899999999999999998875 7777889999999999 7799999999986 44 5889999999
Q ss_pred eEEEeee-CCceeeeecceeEEEECCCchHHHHHHhhhhccCCCceeeeccccCCCCCCCcchhhhHHHHHhhcCCCCCC
Q psy15132 123 AARVSEF-QGGKTLSLSMSSVLSLNPDIPECHKLQGWFSTQTNTRFEPVSQRTGGMGGGAAGNLLLMREIQDQQLGMGDK 201 (786)
Q Consensus 123 ~~kv~~f-~g~~~ls~~~~s~i~~npd~pe~~~l~~w~~~~~~~~~~~~s~~~~~~~~~~~~~~~ti~ei~~~~l~~~~~ 201 (786)
+++|++| +|..+||++++|.|.+||+.|||+.+ ++++...+ ...++++|+++.+ +
T Consensus 138 ~a~V~e~~~G~~eLsvg~~s~i~~~pd~~ea~~i------------~~~~~~~~-----~~~~~k~I~ei~~-----g-- 193 (355)
T PRK08402 138 DAQVRESLSGLPELHINFRARIILNPDDPRVEEI------------PPLEEVRS-----YNYTRKKIGELEG-----G-- 193 (355)
T ss_pred CCEEeecCCCcEEEEECCCceEEeCCCccccccc------------cccccccc-----ccccccCHHHccc-----C--
Confidence 9999996 66559999999999999999998762 22221111 1356789999854 2
Q ss_pred CcEEEEEEEEEEEecCceEEeCCCCCCCCccee-eCCCceeecccCCCcCCceeEeeeeeEEEEecCCcEEEEeehHHHH
Q psy15132 202 ADYCSVRGIIQVFRGSNTTYKACPSQDCNKKVI-DQNNGMYRCEKCNKEFNTFTYRLILPVMIGDWTNSVWVTLFQNEAE 280 (786)
Q Consensus 202 ~~~~~v~a~I~~i~~~~~~Y~aC~~~~C~kKv~-~~~~~~~~C~~C~~~~~~~~~ry~l~~~v~D~Tg~~~~~~F~~~a~ 280 (786)
..|+.++|+|.+|+. +.+|+||| .|||||. +++++.|+|+.|++. .|.|||+|++.|+|+||++|+++|++.|+
T Consensus 194 d~~v~v~g~Iv~i~~-~~~y~aCp--~CnKkv~~~~~~~~~~Ce~~~~v--~p~~ryil~~~l~D~TG~~~vt~f~e~ae 268 (355)
T PRK08402 194 ERFVEVRGTIAKVYR-VLVYDACP--ECRRKVDYDPATDTWICPEHGEV--EPIKITILDFGLDDGTGYIRVTLFGDDAA 268 (355)
T ss_pred CcEEEEEEEEEEEec-CeeEecCC--CCCeEEEEecCCCCEeCCCCCCc--CcceeEEEEEEEEcCCCcEEEEEecHHHH
Confidence 278999999999997 77899999 8999998 667789999999873 78999999999999999999999999999
Q ss_pred HHhCCChhhhhcc-C---CC---h---------HHHHHhcCCEEEEEEeeecccccCccccCCCcceeeEEEeecccccc
Q psy15132 281 SILGVTAQEVGES-T---ED---H---------PALKKALFTQYIFRLRAKLEHYNGTKKIPDGVNINSFAMLATQLNDI 344 (786)
Q Consensus 281 ~ilg~sa~el~~~-~---e~---~---------~~~~~~~~k~~~f~v~~k~e~y~~~~~~sDG~~~~~~~~la~~ln~~ 344 (786)
+|||++|+||.++ + +. . ..++.++|++|.||++++++.|++.. + +++-..++|+.
T Consensus 269 ~llG~sa~el~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~rg~~~~d~y~~~~--------~-~v~~~~~vd~~ 339 (355)
T PRK08402 269 ELLGVEPEEIAEKLKELIEMGLTPKEAARKLAEEEFYNIIGREIVVRGNVIEDRFLGLI--------L-KASSWDEVDYK 339 (355)
T ss_pred HHhCCCHHHHHHHHHHhhhcccchhhhhhhHHHHHHHHhcCeEEEEEEEEEecccCCeE--------E-EEEEcccCCHH
Confidence 9999999999877 3 21 1 24678999999999999999999843 2 78889999998
Q ss_pred cccCCcc
Q psy15132 345 ITDGTLS 351 (786)
Q Consensus 345 v~~~~L~ 351 (786)
.|...|.
T Consensus 340 ~e~~~l~ 346 (355)
T PRK08402 340 REIERVR 346 (355)
T ss_pred HHHHHHH
Confidence 8877664
No 6
>PRK14699 replication factor A; Provisional
Probab=100.00 E-value=4e-35 Score=328.28 Aligned_cols=401 Identities=16% Similarity=0.276 Sum_probs=286.0
Q ss_pred CccchhccCCCCceEEEEEEEEeccceeEeeccCCceeeEEEEEEEeCCCCEEEEEeccccccccc---CCCCcEEEEEe
Q psy15132 47 PLKTIAEISPDENIDVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWGKEAETFD---ASNKPVIAVKA 123 (786)
Q Consensus 47 ~~~~i~~~~~~~~vDViGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~s~~~i~~tLWg~~a~~~~---~~~~~Vi~i~~ 123 (786)
+++||.. ....+.+.|.|.++++++++.++ +|.....++++|.|+|| +|++|||.+.|.... ...|++|-+++
T Consensus 59 kI~di~~--~~~~v~i~~rVl~i~~~r~f~r~-dG~~g~v~~~~iaDeTG-~ir~tlW~~~a~~~~~g~l~~GDvv~I~~ 134 (484)
T PRK14699 59 KIENITP--ESGPVNFIARVVSVFDTKEFTRN-DGTIGRVGNLIVGDETG-KIKLTLWDNMADLIKAGKIKAGQTLQISG 134 (484)
T ss_pred cHhHccC--CCceEEEEEEEEEecCceEEecC-CCCceEEEEEEEecCCC-eEEEEEecCccchhhhcCCCCCCEEEEcc
Confidence 3555532 34789999999999999999876 47788889999999999 999999999986544 47899999999
Q ss_pred EEEeeeCCceeeeecceeEEEECCCchHHHHHHhhhhccCCCceeeeccccCCCCCCCcchhhhHHHHHhhcCCCCCCCc
Q psy15132 124 ARVSEFQGGKTLSLSMSSVLSLNPDIPECHKLQGWFSTQTNTRFEPVSQRTGGMGGGAAGNLLLMREIQDQQLGMGDKAD 203 (786)
Q Consensus 124 ~kv~~f~g~~~ls~~~~s~i~~npd~pe~~~l~~w~~~~~~~~~~~~s~~~~~~~~~~~~~~~ti~ei~~~~l~~~~~~~ 203 (786)
+ +++.+++..|++++.|.+..-+..-+ +. .....|++|.. + ..
T Consensus 135 ~-~r~~~~g~el~~~~~~~i~~~~~~i~------------------v~-----------~~~~~I~dL~~---~----~~ 177 (484)
T PRK14699 135 Y-AKQGYSGVEVNIGNNGVLTESEEEID------------------VA-----------ANSQKIKDIKD---G----MG 177 (484)
T ss_pred e-eccCCCCceEEeCCCceeeccCcccc------------------cC-----------CCCcchhhcCC---C----CC
Confidence 6 66655678899887776653211000 00 01234555432 2 23
Q ss_pred EEEEEEEEEEEecCceEEeCCCCCCCCcceeeCCCceeecccCCCcCCceeEeeeeeEEEEecCCcEEEEeehHHHHHHh
Q psy15132 204 YCSVRGIIQVFRGSNTTYKACPSQDCNKKVIDQNNGMYRCEKCNKEFNTFTYRLILPVMIGDWTNSVWVTLFQNEAESIL 283 (786)
Q Consensus 204 ~~~v~a~I~~i~~~~~~Y~aC~~~~C~kKv~~~~~~~~~C~~C~~~~~~~~~ry~l~~~v~D~Tg~~~~~~F~~~a~~il 283 (786)
..++.|.|..+..- |-+. ..+| ...-..++.|.|.||.+++++|++.|..+-
T Consensus 178 ~V~i~gkVl~~~~~-------------R~f~-~~dG--------------~~g~v~~~~igDeTG~ir~tlW~~~a~~~~ 229 (484)
T PRK14699 178 DLNLTGKVLEISEI-------------RTFQ-RKDG--------------TSGKVGNLLLGDETGTLRVTLWDDKTDFLN 229 (484)
T ss_pred ceEEEEEEEeccCc-------------eEEe-cCCC--------------CceEEEEEEEEcCCceEEEEEECccccccc
Confidence 47888988876421 1111 1111 113456778999999999999998763211
Q ss_pred CCChhhhhccCCChHHHHHhcCCEEEE-EEeeecccccCccccCCCcceeeEEEeecccccccccCCcccceEEEEceeE
Q psy15132 284 GVTAQEVGESTEDHPALKKALFTQYIF-RLRAKLEHYNGTKKIPDGVNINSFAMLATQLNDIITDGTLSEFTIVQIKRYI 362 (786)
Q Consensus 284 g~sa~el~~~~e~~~~~~~~~~k~~~f-~v~~k~e~y~~~~~~sDG~~~~~~~~la~~ln~~v~~~~L~~~~iikl~~~~ 362 (786)
+... +..+.+ ...++...|+++ +.
T Consensus 230 ~l~~-----------------Gd~v~I~~a~vr~~~~~~~--------------------------------------~e 254 (484)
T PRK14699 230 QIEY-----------------GDTVELINAYARENAFTQK--------------------------------------VE 254 (484)
T ss_pred ccCC-----------------CCEEEEecceEeecccCCc--------------------------------------eE
Confidence 1000 111110 000111111111 01
Q ss_pred eeeeecCCCCccEEEEEEeeeeeccCcccCccccCCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCce
Q psy15132 363 VSGVSSGSATNRSVLIILELNIIKPGTEIGFKIGNPQPLNTNTDNSSTQQTPAATNTNGSNGVHNNVAIPRQASAPVVQT 442 (786)
Q Consensus 363 ~~~~~~~~~~~~~~~ii~~~~v~~~~~~~~~~ig~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 442 (786)
++.. +.+++....+ .... ..++
T Consensus 255 l~~~--------------~~s~i~~~~~-------------------~~e~-------------------------~~~~ 276 (484)
T PRK14699 255 LQVG--------------NRSIIRKSEK-------------------KVEY-------------------------EEEF 276 (484)
T ss_pred EEec--------------CceEeecccc-------------------cccc-------------------------cccc
Confidence 1110 0000000000 0000 1135
Q ss_pred eeecccCCCCCceEEEEEEeecCCcceecCCCC-CceEEEEEEEcCCCcEEEEEcchhHHHhhhhccCCcEEEEcceEEe
Q psy15132 443 HPIVSLSPYQNKWTIKARVTNKTPIREWNNARG-SGKLFSIDLLDESGEIRATMFNDECNRFHDMIEKDKVYYISNCTLK 521 (786)
Q Consensus 443 ~~I~~L~p~~~~w~I~~RV~~k~~~r~~~~~~~-~g~~~~~~L~D~~G~I~at~~~~~~~kf~~~l~~G~vy~is~~~V~ 521 (786)
+||++|+|++++|+|+|||+.++++|+|++.+| +|+++++.|.|++|+|++|+|++.+ .|++.|.+|+++.+.++.++
T Consensus 277 ~~I~~L~~~~~~v~I~grV~~~~~~r~~~~~~Gseg~v~~~~l~DeTG~Ir~T~W~~~a-~~~~~i~~Gd~v~i~~~y~~ 355 (484)
T PRK14699 277 TPIEDIKADMNNINISGRVLDISEVRTFEKKDGSPGRVGNLLLGDSTGKIRLTLWDEKT-NFLDEIDFDETVEVLNAYSR 355 (484)
T ss_pred cCHHHcCCCCceeEEEEEEEEcCCCeEEEcCCCCeeEEEEEEEECCCCeEEEEEeCccc-ccccccCCCceEEEEeEEEE
Confidence 799999999999999999999999999999777 8999999999999999999999999 78888999999988888864
Q ss_pred ccCCcccccCCceEEEEccccEEEEccCCCCCCCCcceeeccCcccccccCCCceeeEEEEEEEcccceeEEeecCCcee
Q psy15132 522 PANKKFSSINNDYEMSFTHSTTVIPCNEDEVGNMPSVKYCFVPLKTIAEISPDENIDVLGVCIDAAELSSVTGKTNQKTY 601 (786)
Q Consensus 522 ~a~~~y~~~~~~yei~f~~~T~I~~~~d~~~~~iP~~~~~f~~i~dl~~~~~~~~vDViGvV~~V~~~~~i~~k~~g~~~ 601 (786)
++..+++|||+|+..|.|.++++.. .+.++|++|++|. .+..|||+|+|++++++.+|+++ +|++.
T Consensus 356 -----~~~~~~~~eL~~~~~t~I~~~~~~~-----e~~~~~~~I~die---~~~~vdV~G~V~~v~~~~~~~~~-~g~~~ 421 (484)
T PRK14699 356 -----ENTFSQQVELNLGARGIIQKSEKKV-----EYREKFTDIADII---PGESYSVQGKVSEIGELREFERE-DGTEN 421 (484)
T ss_pred -----eccCCccEEEEecCceeEeecCCcc-----eeeeccccHHHcc---CCCeeEEEEEEEEcCCcceEEec-CCCEE
Confidence 5556789999999999999987643 4678999999995 46799999999999999999987 59999
Q ss_pred eEEEEEEeeccccEEEEEEecccccccc-CCCCCEEEEEeEEEee
Q psy15132 602 MKRDITLVDQSQASVTMTLWGKEAETFD-ASNKPVIAVKAARVSE 645 (786)
Q Consensus 602 ~kr~i~l~D~s~~~i~~tLWg~~a~~~~-~~~~~vv~i~~~~V~~ 645 (786)
.+|+++|.|+|| +|+|||||+.|+.|+ ...+.-|.+.+++++.
T Consensus 422 ~vr~i~l~D~TG-~Ir~tlWg~~A~~~~~~~~~~~v~~~~~~~~~ 465 (484)
T PRK14699 422 VVANLQLKDETG-SIRLTLWGEQAYVIEDLDIDSEIQIIDAYARY 465 (484)
T ss_pred EEEEEEEEcCCC-eEEEEEcchhhhhccccCCCCeEEEechhhhh
Confidence 999999999999 999999999999875 5667767777766654
No 7
>PRK08402 replication factor A; Reviewed
Probab=100.00 E-value=1.6e-35 Score=318.74 Aligned_cols=247 Identities=22% Similarity=0.346 Sum_probs=203.6
Q ss_pred ceeeecccCCCCCceEEEEEEeecCCcceecCCCC-CceEEEEEEEcCCCcEEEEEcchhHHHhhhhccCCcEEEEcceE
Q psy15132 441 QTHPIVSLSPYQNKWTIKARVTNKTPIREWNNARG-SGKLFSIDLLDESGEIRATMFNDECNRFHDMIEKDKVYYISNCT 519 (786)
Q Consensus 441 ~~~~I~~L~p~~~~w~I~~RV~~k~~~r~~~~~~~-~g~~~~~~L~D~~G~I~at~~~~~~~kf~~~l~~G~vy~is~~~ 519 (786)
+..+|++|.|+..+|++.|||+.+++.|.|.+.+| .|++.+++|.|++|.|++|+|++.++++++.|++|+|+.|.+++
T Consensus 61 ~~~kI~dl~~g~~~V~v~~rVl~~~~~r~f~rrdG~~~~V~~i~l~DeTG~ir~TlW~~~a~~~~~~l~~Gdvi~I~~a~ 140 (355)
T PRK08402 61 PLMHISDLVPGMRGVNIVGRVLRKYPPREYTKKDGSTGRVASLIIYDDTGRARVVLWDAKVAKYYNKINVGDVIKVIDAQ 140 (355)
T ss_pred CccCHHHccCCCceeeEEEEEEEccCCceeeccCCCcceEEEEEEEcCCCeEEEEEechhhhhhcccCCCCCEEEEECCE
Confidence 57899999999999999999999999999997655 68999999999999999999999999988899999999999999
Q ss_pred EeccCCcccccCCceEEEEccccEEEEccCCCCCCCCcceeeccCcccccccCCCceeeEEEEEEEcccceeEEeecCCc
Q psy15132 520 LKPANKKFSSINNDYEMSFTHSTTVIPCNEDEVGNMPSVKYCFVPLKTIAEISPDENIDVLGVCIDAAELSSVTGKTNQK 599 (786)
Q Consensus 520 V~~a~~~y~~~~~~yei~f~~~T~I~~~~d~~~~~iP~~~~~f~~i~dl~~~~~~~~vDViGvV~~V~~~~~i~~k~~g~ 599 (786)
|+... .+.++|++++.|.|...++.+ ..+. |.+ +.++. +
T Consensus 141 V~e~~------~G~~eLsvg~~s~i~~~pd~~--ea~~----i~~------------------------~~~~~----~- 179 (355)
T PRK08402 141 VRESL------SGLPELHINFRARIILNPDDP--RVEE----IPP------------------------LEEVR----S- 179 (355)
T ss_pred EeecC------CCcEEEEECCCceEEeCCCcc--cccc----ccc------------------------ccccc----c-
Confidence 98641 356799999999999887654 1111 000 00000 0
Q ss_pred eeeEEEEEEeeccccEEEEEEeccccccccCCCCCEEEEEeEEEeecCCccccHHhHHhhcCCCCCCCceEEEEEEEEEE
Q psy15132 600 TYMKRDITLVDQSQASVTMTLWGKEAETFDASNKPVIAVKAARVSEFQGNLLLMREIQDQQLGMGDKADYCSVRGIIQVF 679 (786)
Q Consensus 600 ~~~kr~i~l~D~s~~~i~~tLWg~~a~~~~~~~~~vv~i~~~~V~~f~G~L~ti~e~~~~~l~~~~~~~~~~v~a~I~~i 679 (786)
. . .. -++|+++++ ..+|+.+.|+|+.|
T Consensus 180 -------------~-------~----------------------~~----~k~I~ei~~-------gd~~v~v~g~Iv~i 206 (355)
T PRK08402 180 -------------Y-------N----------------------YT----RKKIGELEG-------GERFVEVRGTIAKV 206 (355)
T ss_pred -------------c-------c----------------------cc----ccCHHHccc-------CCcEEEEEEEEEEE
Confidence 0 0 00 034556533 12689999999999
Q ss_pred ecCceEEeCCCCcccccccc-ccCCceeeeCCCCCcCCceeEEEEEEEEEEecCCcEEEEEehhhHHHHhCCChHHHhcc
Q psy15132 680 RGSNTTYKACPSQDCNKKVI-DQNNGMYRCEKCNKEFNTFTYRLILPVMIGDWTNSVWVTLFQNEAESILGVTAQEVGES 758 (786)
Q Consensus 680 ~~~~~~Y~aC~~~~C~kkv~-~~~~g~~~C~~C~~~~~~~~~ry~l~~~i~D~Tg~~~~~~F~~~ae~llG~sa~el~~~ 758 (786)
+. +.+|+||| .|||||. +..+|.|+|+.|++ .+|.|||+|++.|+|+||++|+++|+|.|++|+|++|+||.++
T Consensus 207 ~~-~~~y~aCp--~CnKkv~~~~~~~~~~Ce~~~~--v~p~~ryil~~~l~D~TG~~~vt~f~e~ae~llG~sa~el~~~ 281 (355)
T PRK08402 207 YR-VLVYDACP--ECRRKVDYDPATDTWICPEHGE--VEPIKITILDFGLDDGTGYIRVTLFGDDAAELLGVEPEEIAEK 281 (355)
T ss_pred ec-CeeEecCC--CCCeEEEEecCCCCEeCCCCCC--cCcceeEEEEEEEEcCCCcEEEEEecHHHHHHhCCCHHHHHHH
Confidence 98 77999999 5999998 66778999999987 4778999999999999999999999999999999999999988
Q ss_pred -c---cC--h----------HHHHHhcCCeEEEEEEEEeeccCC
Q psy15132 759 -T---ED--H----------PALKKALFTQYIFRLRAKLEHYNK 786 (786)
Q Consensus 759 -~---~~--~----------~~~~~~~~k~~~f~v~~k~~~y~~ 786 (786)
+ +. + +.++.++|++|.|++++++|+|||
T Consensus 282 ~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~rg~~~~d~y~~ 325 (355)
T PRK08402 282 LKELIEMGLTPKEAARKLAEEEFYNIIGREIVVRGNVIEDRFLG 325 (355)
T ss_pred HHHhhhcccchhhhhhhHHHHHHHHhcCeEEEEEEEEEecccCC
Confidence 3 32 1 167799999999999999999986
No 8
>PRK07218 replication factor A; Provisional
Probab=100.00 E-value=9.2e-34 Score=310.85 Aligned_cols=312 Identities=19% Similarity=0.238 Sum_probs=251.5
Q ss_pred CceeeecccCCCCCceEEEEEEeecCCcceecCCCCCceEEEEEEEcCCCcEEEEEcchhHHHhhhhccCCcEEEEcceE
Q psy15132 440 VQTHPIVSLSPYQNKWTIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFNDECNRFHDMIEKDKVYYISNCT 519 (786)
Q Consensus 440 ~~~~~I~~L~p~~~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~G~I~at~~~~~~~kf~~~l~~G~vy~is~~~ 519 (786)
.+..+|++|.|+..+.+|+|||+.+++ |+|...+++|.+.+++|.|++|.|+.|+|++. + |++|++|.|.|+.
T Consensus 56 ~~~~kI~Di~~~~~~V~v~~kVl~i~~-rt~r~dg~~g~v~~~~igDeTG~Ir~tlW~~~-----~-l~~Gdvv~I~na~ 128 (423)
T PRK07218 56 PSSKDIKELSTDDKNVTVTGRVLTIGE-RSIRYQGDDHVIYEGILADETGTISYTAWKDF-----G-LSPGDTVTIGNAG 128 (423)
T ss_pred CCCccHhhCCCCCceeEEEEEEEEecc-eeEecCCCceEEEEEEEECCCCeEEEEEECCC-----C-CCCCCEEEEeccE
Confidence 346799999999988899999999999 99987777899999999999999999999965 2 9999999999999
Q ss_pred EeccCCcccccCCceEEEEccccEEEEccCCCCCCCCcceeeccCcccccccCCCceeeEEEEEEEcccceeEEeecCCc
Q psy15132 520 LKPANKKFSSINNDYEMSFTHSTTVIPCNEDEVGNMPSVKYCFVPLKTIAEISPDENIDVLGVCIDAAELSSVTGKTNQK 599 (786)
Q Consensus 520 V~~a~~~y~~~~~~yei~f~~~T~I~~~~d~~~~~iP~~~~~f~~i~dl~~~~~~~~vDViGvV~~V~~~~~i~~k~~g~ 599 (786)
++..+ +.+++++++.|.|.+.++.. ..|...+...+|.+|... +..|+|.|.|.++.+ .+|.++ +|.
T Consensus 129 vre~~-------g~~el~ig~~t~I~~~de~~--~~~~~~~~~~kI~DL~~g--~~~V~v~g~Vl~~~~-r~f~~~-dg~ 195 (423)
T PRK07218 129 VREWD-------GRPELNIGESTTVSLLDDSS--LPPYSIGGDKKLIDLGPG--DRGVNVEARVLELEH-REIDGR-DGE 195 (423)
T ss_pred eeccC-------CceEEeccCcceEEEcCccc--ccCccccCccchhhccCC--CCceEEEEEEEEecc-eeEEcC-CCC
Confidence 98763 55899999999999887654 333223344455555543 556999999999976 688876 464
Q ss_pred eeeEEEEEEeeccccEEEEEEeccccccccCCCCCEEEEEeEEEeecCCc--c-----ccHHhHHhh-cCC---------
Q psy15132 600 TYMKRDITLVDQSQASVTMTLWGKEAETFDASNKPVIAVKAARVSEFQGN--L-----LLMREIQDQ-QLG--------- 662 (786)
Q Consensus 600 ~~~kr~i~l~D~s~~~i~~tLWg~~a~~~~~~~~~vv~i~~~~V~~f~G~--L-----~ti~e~~~~-~l~--------- 662 (786)
...+++.|.|+|| +|++|||++.++ ...|.+|.|.++.+++|+|+ | .+|..+.++ .+.
T Consensus 196 -~~v~~giigDeTG-~Ir~tlW~~~~~---l~~Gd~v~I~na~v~e~~G~~elnv~~~t~I~~~d~~i~v~~~~~~~~I~ 270 (423)
T PRK07218 196 -TTILSGVLADETG-RLPFTDWDPLPE---IEIGASIRIEDAYVREFRGVPSVNVSEFTTVEALDREVSVSKDPPRLKIR 270 (423)
T ss_pred -eEEEEEEEECCCc-eEEEEEeccccc---CCCCCEEEEeeeEEeccCCeEEEEECCceEEEECCCCccccCCccccchh
Confidence 5689999999999 999999999773 57899999999999999998 4 222222111 000
Q ss_pred --CCCCCce-EEEEEEEEEEecCceEEeCCCCccccccccccCCceeeeCCCCCcCCceeEEEEEEEEEEecCCcEEEEE
Q psy15132 663 --MGDKADY-CSVRGIIQVFRGSNTTYKACPSQDCNKKVIDQNNGMYRCEKCNKEFNTFTYRLILPVMIGDWTNSVWVTL 739 (786)
Q Consensus 663 --~~~~~~~-~~v~a~I~~i~~~~~~Y~aC~~~~C~kkv~~~~~g~~~C~~C~~~~~~~~~ry~l~~~i~D~Tg~~~~~~ 739 (786)
....+.| ..|.|+|+.|+..+.+|.+|| .|+|+|. .|.|+.||+. ++.+-+++++.|.|+||++.+++
T Consensus 271 e~~~~~g~~~Vev~G~Iv~i~~gsgli~rCP--~C~r~v~-----~~~C~~hG~v--e~~~dlrik~vLDDGtg~~~~~~ 341 (423)
T PRK07218 271 EAVERGGIFDVELVGNIISVRDGSGLIERCP--ECGRVIQ-----KGQCRSHGAV--EGEDDLRIKAILDDGTGSVTVIL 341 (423)
T ss_pred hhhccCCcceEEEEEEEEEeccCCcceecCc--Ccccccc-----CCcCCCCCCc--CCeeeeEEEEEEECCCCeEEEEE
Confidence 0111234 799999999999999999999 6999984 2679999986 55677889999999999999999
Q ss_pred ehhhHHHHhCCChHHHhccccCh-------H-HHHHhcCCeEEEEEEEEeeccC
Q psy15132 740 FQNEAESILGVTAQEVGESTEDH-------P-ALKKALFTQYIFRLRAKLEHYN 785 (786)
Q Consensus 740 F~~~ae~llG~sa~el~~~~~~~-------~-~~~~~~~k~~~f~v~~k~~~y~ 785 (786)
|++.+++|+|++.+++.+|..+. + +...++|+.|.++-.+..+.|.
T Consensus 342 ~~e~~e~l~G~~~e~a~~~~~~~~d~~~v~~~i~~~llG~~~~v~G~~~~~~~g 395 (423)
T PRK07218 342 DRELTEIVYGGTLEDAEELAREAMDKDVVAEDIRERLVGREYRVRGNLSVDEYG 395 (423)
T ss_pred ChhhhHhHhCCCHHHHHHHHHhhhcchhhHHHHHHhhcCcEEEEEeccccccCC
Confidence 99999999999999988776431 1 4467999999999998888773
No 9
>PRK06386 replication factor A; Reviewed
Probab=100.00 E-value=8.6e-32 Score=287.89 Aligned_cols=308 Identities=16% Similarity=0.265 Sum_probs=246.9
Q ss_pred eeecccCCCCCceEEEEEEeecCCcceecCCCCCceEEEEEEEcCCCcEEEEEcchhHHHhhhhccCCcEEEEcceEEec
Q psy15132 443 HPIVSLSPYQNKWTIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFNDECNRFHDMIEKDKVYYISNCTLKP 522 (786)
Q Consensus 443 ~~I~~L~p~~~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~G~I~at~~~~~~~kf~~~l~~G~vy~is~~~V~~ 522 (786)
.+|++|.|...+.+|+|||+..+ .|.+..++|+..+.+.+|.|++|.|+.|+|+.. +.|++|++|.|.|+.++.
T Consensus 3 ~kI~DI~~~~~~V~v~akVl~~~-~r~i~~~~g~~~~~~gllgDeTG~I~fT~W~~~-----~~l~~Gd~v~i~na~v~~ 76 (358)
T PRK06386 3 SKISDINAARQNVDLKVKVLSLN-KRTIKNDRGETIYYYGIIGDETGTVPFTAWEFP-----DAVKSGDVIEIKYCYSKE 76 (358)
T ss_pred cchhhcCCCCCcEEEEEEEEEcc-ceEEecCCCCeEEEEEEEECCcceEEEEecCCc-----ccCCCCCEEEEEeEEEee
Confidence 57999999999999999999998 599988888777888899999999999999952 469999999999999987
Q ss_pred cCCcccccCCceEEEEccccEEEEccCCCCCCCCcceeeccCcccccccCCCceeeEEEEEEEcccceeEEeecCCceee
Q psy15132 523 ANKKFSSINNDYEMSFTHSTTVIPCNEDEVGNMPSVKYCFVPLKTIAEISPDENIDVLGVCIDAAELSSVTGKTNQKTYM 602 (786)
Q Consensus 523 a~~~y~~~~~~yei~f~~~T~I~~~~d~~~~~iP~~~~~f~~i~dl~~~~~~~~vDViGvV~~V~~~~~i~~k~~g~~~~ 602 (786)
.+ +.++|+++..|.|.+..|... .+ ...+..++|.||... +..|+|.|.|.++++ .++.+ +|.+..
T Consensus 77 ~~-------G~~~Lnv~~~t~v~~~~d~~i-ev-~~~~~~~KI~DL~~g--~~~v~V~akVle~~e-~e~~~--~g~~~~ 142 (358)
T PRK06386 77 YN-------GKIRIYFDSRSEVMLKPDENI-EV-KRTYKLVKIRDLSLV--TPYVSVIGKITGITK-KEYDS--DGTSKI 142 (358)
T ss_pred EC-------CEEEEEEcCceEEEecCcccc-cc-ccccCccEeEeccCC--CCceEEEEEEEEccC-ceEec--CCCccE
Confidence 53 467899999999986654421 22 122467788888664 567999999999977 57763 477788
Q ss_pred EEEEEEeeccccEEEEEEeccccccccCCCCCEEEEEeEEEeecCCc--c-----ccHHhHHhh-cCCC--------CCC
Q psy15132 603 KRDITLVDQSQASVTMTLWGKEAETFDASNKPVIAVKAARVSEFQGN--L-----LLMREIQDQ-QLGM--------GDK 666 (786)
Q Consensus 603 kr~i~l~D~s~~~i~~tLWg~~a~~~~~~~~~vv~i~~~~V~~f~G~--L-----~ti~e~~~~-~l~~--------~~~ 666 (786)
.+++.|.|+|| +|++|||++. ...|.++.|.++++++|+|+ | .++.++.+. .++. .+.
T Consensus 143 v~sg~lgDeTG-rIr~TlW~~~-----l~eGd~v~i~na~v~e~~G~~el~v~~~t~I~~~~~~iev~~~~~~I~di~~~ 216 (358)
T PRK06386 143 VYQGYIEDDTA-RVRISSFGKP-----LEDNRFVRIENARVSQYNGYIEISVGNKSVIKEVESDINLESRNIFIFEIKSP 216 (358)
T ss_pred EEEEEEEcCCC-eEEEEEcccc-----ccCCCEEEEeeeEEEccCCeEEEEeCCeEEEEECCCCcccCccccchhhhhcc
Confidence 89999999999 9999999983 46799999999999999998 4 233332111 0110 111
Q ss_pred CceEEEEEEEEEEecCceEEeCCCCccccccccccCCceeeeCCCCCcCCceeEEEEEEEEEEecCCcEEEEEehhhHHH
Q psy15132 667 ADYCSVRGIIQVFRGSNTTYKACPSQDCNKKVIDQNNGMYRCEKCNKEFNTFTYRLILPVMIGDWTNSVWVTLFQNEAES 746 (786)
Q Consensus 667 ~~~~~v~a~I~~i~~~~~~Y~aC~~~~C~kkv~~~~~g~~~C~~C~~~~~~~~~ry~l~~~i~D~Tg~~~~~~F~~~ae~ 746 (786)
.....+.|+|+.|+..+..|.+|| .|+|++. +| .|+.|++. ++.+-+++++.|.|+||.+.+++|++.+++
T Consensus 217 ~g~v~i~G~iv~i~~gsgli~rCP--~C~R~l~---~g--~C~~HG~v--~~~~dlr~k~vLDDGtg~~~~~l~~e~~e~ 287 (358)
T PRK06386 217 VGGITIMGFIVSVGQGSRIFTKCS--VCNKIIE---DG--VCKDHPDA--PVYLDIFGYFTISDGTGFVTCYANKDSFLP 287 (358)
T ss_pred CCeEEEEEEEEEEcCCcEeEecCc--CCCeEcc---CC--cCCCCCCC--CCeeEEEEEEEEECCCCeEEEEEChHHhHH
Confidence 124899999999999999999999 6999885 23 79999984 445667778899999999999999999999
Q ss_pred HhCCChHHHhccc-cChH---HHHHhcCCeEEEEEEEEeeccC
Q psy15132 747 ILGVTAQEVGEST-EDHP---ALKKALFTQYIFRLRAKLEHYN 785 (786)
Q Consensus 747 llG~sa~el~~~~-~~~~---~~~~~~~k~~~f~v~~k~~~y~ 785 (786)
|+|++.+|+.++. +-++ +=..++|+.|.|+-.+..+.|.
T Consensus 288 l~G~~lee~~~~a~~~~~~~~i~~~llGr~~~v~G~~~~~~~~ 330 (358)
T PRK06386 288 YININENEFARKASSMNPNMLIKKNLLGKCFSVTGDLRKKDDE 330 (358)
T ss_pred HhCCCHHHHHHHhhccCHHHHhhhhhcccEEEEEcceEeccCC
Confidence 9999999997543 2222 3367999999999999988874
No 10
>PRK07211 replication factor A; Reviewed
Probab=100.00 E-value=3.9e-32 Score=300.02 Aligned_cols=269 Identities=17% Similarity=0.295 Sum_probs=211.7
Q ss_pred ceeeecccCCCCCceEEEEEEeecCCcceecCC--CCCceEEEEEEEcCCCcEEEEEcchhHHHhhhhccCCcEEEEcce
Q psy15132 441 QTHPIVSLSPYQNKWTIKARVTNKTPIREWNNA--RGSGKLFSIDLLDESGEIRATMFNDECNRFHDMIEKDKVYYISNC 518 (786)
Q Consensus 441 ~~~~I~~L~p~~~~w~I~~RV~~k~~~r~~~~~--~~~g~~~~~~L~D~~G~I~at~~~~~~~kf~~~l~~G~vy~is~~ 518 (786)
.+.||++|+|++++|+|+|||+.|+++|+|++. +++|++++++|+|++|+|++|+|++.+++|++.|++|+||+|.+
T Consensus 52 e~~~I~dL~pg~~~vtI~aRV~~~~~~Rt~~~~~~~~eGkv~~v~l~DeTG~Ir~TlW~d~ad~~~~~Le~GdV~~I~~- 130 (485)
T PRK07211 52 EVNGIADIEPGMDEVKFLAKVLSIGDLRTFERDGEDEDGRVINVEVADETGSVRVAFWDEQAVAAEEELEVGQVLRIKG- 130 (485)
T ss_pred ccccHhhCCCCCCceEEEEEEeEccCceEEEeCCCCCCcEEEEEEEEcCCCeEEEEEechHhHhhhcccCCCCEEEEec-
Confidence 467999999999999999999999999999986 35899999999999999999999999999999999999999975
Q ss_pred EEeccCCcccccCCceEEEEccccEEEEccCCCCCCCCcceeeccCcccccccCCCceeeEEEEEEEcccceeEEeecCC
Q psy15132 519 TLKPANKKFSSINNDYEMSFTHSTTVIPCNEDEVGNMPSVKYCFVPLKTIAEISPDENIDVLGVCIDAAELSSVTGKTNQ 598 (786)
Q Consensus 519 ~V~~a~~~y~~~~~~yei~f~~~T~I~~~~d~~~~~iP~~~~~f~~i~dl~~~~~~~~vDViGvV~~V~~~~~i~~k~~g 598 (786)
.++ +.|+.+ ||+|+ .|+++.+.. +|....+|.+|.+|... +..+||+|+|+.++++++|.++ +|
T Consensus 131 ~~~---~~ys~~----El~i~---~ve~~~d~~---i~~~~~~~~~I~dL~~~--~~~v~I~grV~~v~~iRtf~r~-dG 194 (485)
T PRK07211 131 RPK---DGYNGL----EVSVD---KVEPDPDAE---IDVQIGDTYTVEDLSLG--LSDVTLVGVVLDTDSVRTFDRD-DG 194 (485)
T ss_pred eEe---ccccce----EEEEe---eEEEccccc---ccccccCCccHHHcCCC--CCceEEEEEEEEcCCCeEEECC-CC
Confidence 443 567653 99999 488877653 44445699999999864 6789999999999999999866 59
Q ss_pred ceeeEEEEEEeeccccEEEEEEecccccccc-CCCCCEEEEEeEEEeecCCc--c-----ccHHhHHhh--cCC------
Q psy15132 599 KTYMKRDITLVDQSQASVTMTLWGKEAETFD-ASNKPVIAVKAARVSEFQGN--L-----LLMREIQDQ--QLG------ 662 (786)
Q Consensus 599 ~~~~kr~i~l~D~s~~~i~~tLWg~~a~~~~-~~~~~vv~i~~~~V~~f~G~--L-----~ti~e~~~~--~l~------ 662 (786)
++.+.+++.|.|+|| +|++|||+++|+.|+ ...|+||.|++++|++|+|. | .++.++.++ .++
T Consensus 195 seGkv~sv~L~DeTG-~IR~TlW~d~Ad~~~~le~G~Vv~I~~a~Vre~~g~~ELsl~~~s~I~~~~dev~~vp~~~~I~ 273 (485)
T PRK07211 195 SEGRVSNLTVGDETG-RVRVTLWDDRADLAEELDAGESVEIVDGYVRERDGSLELHVGDRGAVEEVDEDVEYVPDTTPIE 273 (485)
T ss_pred CeeEEEEEEEEcCCC-eEEEEEechhhhhhccCCCCCEEEEEeeEEEecCCcEEEEECCCceEEECCcccccccccccHh
Confidence 899999999999999 799999999999986 68899999999999999665 4 222222111 011
Q ss_pred CCCCCceEEEEEEEEEEecCceEEeCCCCccccccccccCCceeeeCCCCCcCCceeEEEEEEEEEEecCCcEEEEEehh
Q psy15132 663 MGDKADYCSVRGIIQVFRGSNTTYKACPSQDCNKKVIDQNNGMYRCEKCNKEFNTFTYRLILPVMIGDWTNSVWVTLFQN 742 (786)
Q Consensus 663 ~~~~~~~~~v~a~I~~i~~~~~~Y~aC~~~~C~kkv~~~~~g~~~C~~C~~~~~~~~~ry~l~~~i~D~Tg~~~~~~F~~ 742 (786)
.-+......|.|.|..+..-. .....+|. ...+.++.|.|.||++++++|++
T Consensus 274 dl~~g~~vdV~GvV~~v~~~r--------------tf~r~dG~--------------~~~vr~l~l~D~TG~IrvTLWg~ 325 (485)
T PRK07211 274 SLEIDETVDIAGVVRSADPKR--------------TFDRDDGS--------------EGQVRNVRIQDDTGDIRVALWGE 325 (485)
T ss_pred hcCCCCceeEEEEEEEccCcE--------------EEEcCCCC--------------EeEEEEEEEEcCCCcEEEEEeCc
Confidence 113345688888888775411 11112231 12356899999999999999999
Q ss_pred hHHHHhCCChHHHhc
Q psy15132 743 EAESILGVTAQEVGE 757 (786)
Q Consensus 743 ~ae~llG~sa~el~~ 757 (786)
.|+ ++++..+.+.
T Consensus 326 ~A~--~~i~~GdvV~ 338 (485)
T PRK07211 326 KAD--LDIGPGDEVV 338 (485)
T ss_pred ccc--CCCCCCCEEE
Confidence 994 3555555443
No 11
>PRK15491 replication factor A; Provisional
Probab=99.97 E-value=8.3e-30 Score=278.40 Aligned_cols=262 Identities=19% Similarity=0.320 Sum_probs=205.3
Q ss_pred CceeeecccCCCCCceEEEEEEeecCCcceecCCCC-CceEEEEEEEcCCCcEEEEEcchhHHHhh-hhccCCcEEEEcc
Q psy15132 440 VQTHPIVSLSPYQNKWTIKARVTNKTPIREWNNARG-SGKLFSIDLLDESGEIRATMFNDECNRFH-DMIEKDKVYYISN 517 (786)
Q Consensus 440 ~~~~~I~~L~p~~~~w~I~~RV~~k~~~r~~~~~~~-~g~~~~~~L~D~~G~I~at~~~~~~~kf~-~~l~~G~vy~is~ 517 (786)
.+++||++|+|++++|+|+|||+.++++|+|++.+| +|++++++|.|++|+|++|+|++.+++|+ +.|++|+||+|++
T Consensus 55 ~~~~kI~dL~~~~~~v~i~arVl~~~~~R~f~r~dGs~g~v~~~~v~DeTG~ir~tlW~~~a~~~~~~~le~G~v~~I~~ 134 (374)
T PRK15491 55 VDTTKIADINESSSNVNFTAKVVSIFEPKEFNRNDGTTGRVGNIIVADETGSIRLTLWDDLADLIKTGDIEVGKSLNISG 134 (374)
T ss_pred cccccHHHCCCCCCceEEEEEEeeccCCeeeecCCCCceEEEEEEEEcCCCeEEEEEECchhhhhccCCcCCCCEEEEee
Confidence 467899999999999999999999999999999887 89999999999999999999999999999 6899999999987
Q ss_pred eEEeccCCcccccCCceEEEEccccEEEEccCCCCCCCCcceeeccCcccccccCCCceeeEEEEEEEcccceeEEeecC
Q psy15132 518 CTLKPANKKFSSINNDYEMSFTHSTTVIPCNEDEVGNMPSVKYCFVPLKTIAEISPDENIDVLGVCIDAAELSSVTGKTN 597 (786)
Q Consensus 518 ~~V~~a~~~y~~~~~~yei~f~~~T~I~~~~d~~~~~iP~~~~~f~~i~dl~~~~~~~~vDViGvV~~V~~~~~i~~k~~ 597 (786)
+ +++.|+. .||++++.|.|.++++.. ...|+|++|+||... +..|||.|+|+.++++.+++.+ +
T Consensus 135 ~----~~~~y~g----~Ei~i~~~~~i~~~~~~~-----~~~~~~~~I~dl~~~--~~~V~I~g~V~~~~~~r~~~~~-~ 198 (374)
T PRK15491 135 Y----AKEGYSG----IEVNIGRYGGISESDENV-----KASINSQKISDIKDG--DSDINIVGKVLDISDVRTFQKK-D 198 (374)
T ss_pred e----eccCccc----EEEEeCCCceeeeccccc-----ccccCcccHHHcCCC--CccEEEEEEEEEccCceEEEec-C
Confidence 5 4556753 699999999999986543 346789999999874 4569999999999999999987 5
Q ss_pred CceeeEEEEEEeeccccEEEEEEecccccccc-CCCCCEEEEEeEEE--eecCCc--c-----ccHHhHHhh-----cC-
Q psy15132 598 QKTYMKRDITLVDQSQASVTMTLWGKEAETFD-ASNKPVIAVKAARV--SEFQGN--L-----LLMREIQDQ-----QL- 661 (786)
Q Consensus 598 g~~~~kr~i~l~D~s~~~i~~tLWg~~a~~~~-~~~~~vv~i~~~~V--~~f~G~--L-----~ti~e~~~~-----~l- 661 (786)
|++..++++.|.|+|| +|++|||++.|+.|+ ...|.+|-+.++++ +.|+|. | .++.+..+. .+
T Consensus 199 G~~~~v~~~~l~DetG-~Ir~t~W~~~a~~~~~l~~Gd~V~i~~~~~r~~~~~g~~El~~~~~s~I~~~~~~~e~~~~f~ 277 (374)
T PRK15491 199 GSQGRVRNITIGDETG-KIRVTLWDGKTDLADKLENGDSVEIINGYARTNNYSQEVEIQIGNHGSLRKTDRNVEYEEDFT 277 (374)
T ss_pred CCeEEEEEEEEECCCC-eEEEEEecchhcccccCCCCCEEEEEeceEEEeccCCCEEEEeCCCceEEECCcccccCCCcc
Confidence 9889999999999999 699999999998875 57888998877655 467676 4 112111100 00
Q ss_pred CCC--CCCceEEEEEEEEEEecCceEEeCCCCccccccccccCCceeeeCCCCCcCCceeEEEEEEEEEEecCCcEEEEE
Q psy15132 662 GMG--DKADYCSVRGIIQVFRGSNTTYKACPSQDCNKKVIDQNNGMYRCEKCNKEFNTFTYRLILPVMIGDWTNSVWVTL 739 (786)
Q Consensus 662 ~~~--~~~~~~~v~a~I~~i~~~~~~Y~aC~~~~C~kkv~~~~~g~~~C~~C~~~~~~~~~ry~l~~~i~D~Tg~~~~~~ 739 (786)
+.. .....+.|.|.|..+..-. .+...+|. ....-++.|.|.||.+.+++
T Consensus 278 ~I~dl~~~~~~dv~G~V~~v~~~~--------------~~~~~~G~--------------~~~~r~i~l~D~Tg~Ir~tl 329 (374)
T PRK15491 278 PIADIIPGQPYSIKGAVSGLGDLK--------------EFTKSDGS--------------ENKVSNIYVSDDTGRIRIAL 329 (374)
T ss_pred CHHHcCCCCceeEEEEEEEcCCcE--------------EEEccCCC--------------EeEEEeEEEEeCCCcEEEEE
Confidence 000 1123467777777764311 11111231 11234789999999999999
Q ss_pred ehhhHHH
Q psy15132 740 FQNEAES 746 (786)
Q Consensus 740 F~~~ae~ 746 (786)
|++.|+.
T Consensus 330 Wg~~a~~ 336 (374)
T PRK15491 330 WGEKAEL 336 (374)
T ss_pred ccccccc
Confidence 9999985
No 12
>PRK07211 replication factor A; Reviewed
Probab=99.97 E-value=8.2e-30 Score=281.66 Aligned_cols=191 Identities=18% Similarity=0.343 Sum_probs=171.4
Q ss_pred ceeeecccCCCCCceEEEEEEeecCCcceecCCCC-CceEEEEEEEcCCCcEEEEEcchhHHHhhhhccCCcEEEEcceE
Q psy15132 441 QTHPIVSLSPYQNKWTIKARVTNKTPIREWNNARG-SGKLFSIDLLDESGEIRATMFNDECNRFHDMIEKDKVYYISNCT 519 (786)
Q Consensus 441 ~~~~I~~L~p~~~~w~I~~RV~~k~~~r~~~~~~~-~g~~~~~~L~D~~G~I~at~~~~~~~kf~~~l~~G~vy~is~~~ 519 (786)
+++||++|+|++.+|+|+|||+.++++|+|.+.+| +|++++++|.|++|+|++|+|++.+++| +.|++|+||+|++++
T Consensus 160 ~~~~I~dL~~~~~~v~I~grV~~v~~iRtf~r~dGseGkv~sv~L~DeTG~IR~TlW~d~Ad~~-~~le~G~Vv~I~~a~ 238 (485)
T PRK07211 160 DTYTVEDLSLGLSDVTLVGVVLDTDSVRTFDRDDGSEGRVSNLTVGDETGRVRVTLWDDRADLA-EELDAGESVEIVDGY 238 (485)
T ss_pred CCccHHHcCCCCCceEEEEEEEEcCCCeEEECCCCCeeEEEEEEEEcCCCeEEEEEechhhhhh-ccCCCCCEEEEEeeE
Confidence 46899999999999999999999999999998777 8999999999999999999999999999 789999999999999
Q ss_pred EeccCCcccccCCceEEEEccccEEEEccCCCCCCCCcceeeccCcccccccCCCceeeEEEEEEEcccceeEEeecCCc
Q psy15132 520 LKPANKKFSSINNDYEMSFTHSTTVIPCNEDEVGNMPSVKYCFVPLKTIAEISPDENIDVLGVCIDAAELSSVTGKTNQK 599 (786)
Q Consensus 520 V~~a~~~y~~~~~~yei~f~~~T~I~~~~d~~~~~iP~~~~~f~~i~dl~~~~~~~~vDViGvV~~V~~~~~i~~k~~g~ 599 (786)
|+.. .+.|||+++..|.|++++++.. .+|.. .+|.+ ...+..|||+|+|++++++.+|+++ +|+
T Consensus 239 Vre~-------~g~~ELsl~~~s~I~~~~dev~-~vp~~----~~I~d---l~~g~~vdV~GvV~~v~~~rtf~r~-dG~ 302 (485)
T PRK07211 239 VRER-------DGSLELHVGDRGAVEEVDEDVE-YVPDT----TPIES---LEIDETVDIAGVVRSADPKRTFDRD-DGS 302 (485)
T ss_pred EEec-------CCcEEEEECCCceEEECCcccc-ccccc----ccHhh---cCCCCceeEEEEEEEccCcEEEEcC-CCC
Confidence 9885 3899999999999999977432 45642 44444 4456789999999999999999866 599
Q ss_pred eeeEEEEEEeeccccEEEEEEeccccccccCCCCCEEEEEeEEEeec--CCc-c
Q psy15132 600 TYMKRDITLVDQSQASVTMTLWGKEAETFDASNKPVIAVKAARVSEF--QGN-L 650 (786)
Q Consensus 600 ~~~kr~i~l~D~s~~~i~~tLWg~~a~~~~~~~~~vv~i~~~~V~~f--~G~-L 650 (786)
+..+|+++|.|+|| +|++||||+.| .++...+++|+|++++|++| +|+ |
T Consensus 303 ~~~vr~l~l~D~TG-~IrvTLWg~~A-~~~i~~GdvV~Ikg~~V~dg~~ggleL 354 (485)
T PRK07211 303 EGQVRNVRIQDDTG-DIRVALWGEKA-DLDIGPGDEVVAADVEIQDGWQDDLEA 354 (485)
T ss_pred EeEEEEEEEEcCCC-cEEEEEeCccc-cCCCCCCCEEEEEccEEEecCCCCEEE
Confidence 99999999999999 89999999999 56889999999999999998 677 5
No 13
>PRK15491 replication factor A; Provisional
Probab=99.96 E-value=8.8e-28 Score=262.51 Aligned_cols=192 Identities=18% Similarity=0.323 Sum_probs=166.1
Q ss_pred ceeeecccCCCCCceEEEEEEeecCCcceecCCCC-CceEEEEEEEcCCCcEEEEEcchhHHHhhhhccCCcEEEEcceE
Q psy15132 441 QTHPIVSLSPYQNKWTIKARVTNKTPIREWNNARG-SGKLFSIDLLDESGEIRATMFNDECNRFHDMIEKDKVYYISNCT 519 (786)
Q Consensus 441 ~~~~I~~L~p~~~~w~I~~RV~~k~~~r~~~~~~~-~g~~~~~~L~D~~G~I~at~~~~~~~kf~~~l~~G~vy~is~~~ 519 (786)
++.+|++|.++..++.|+|||+.++++|.|.+.+| +++++++.|.|++|+|++|+|++.|++| +.|++|++|+|.++.
T Consensus 165 ~~~~I~dl~~~~~~V~I~g~V~~~~~~r~~~~~~G~~~~v~~~~l~DetG~Ir~t~W~~~a~~~-~~l~~Gd~V~i~~~~ 243 (374)
T PRK15491 165 NSQKISDIKDGDSDINIVGKVLDISDVRTFQKKDGSQGRVRNITIGDETGKIRVTLWDGKTDLA-DKLENGDSVEIINGY 243 (374)
T ss_pred CcccHHHcCCCCccEEEEEEEEEccCceEEEecCCCeEEEEEEEEECCCCeEEEEEecchhccc-ccCCCCCEEEEEece
Confidence 35789999999889999999999999999998776 4899999999999999999999999998 779999999999998
Q ss_pred EeccCCcccccCCceEEEEccccEEEEccCCCCCCCCcceeeccCcccccccCCCceeeEEEEEEEcccceeEEeecCCc
Q psy15132 520 LKPANKKFSSINNDYEMSFTHSTTVIPCNEDEVGNMPSVKYCFVPLKTIAEISPDENIDVLGVCIDAAELSSVTGKTNQK 599 (786)
Q Consensus 520 V~~a~~~y~~~~~~yei~f~~~T~I~~~~d~~~~~iP~~~~~f~~i~dl~~~~~~~~vDViGvV~~V~~~~~i~~k~~g~ 599 (786)
++. +..+|+|||+|++.|.|.++++. +.+.++|++|+||.+ +..+||+|+|++++++.+|+++ +|+
T Consensus 244 ~r~-----~~~~g~~El~~~~~s~I~~~~~~-----~e~~~~f~~I~dl~~---~~~~dv~G~V~~v~~~~~~~~~-~G~ 309 (374)
T PRK15491 244 ART-----NNYSQEVEIQIGNHGSLRKTDRN-----VEYEEDFTPIADIIP---GQPYSIKGAVSGLGDLKEFTKS-DGS 309 (374)
T ss_pred EEE-----eccCCCEEEEeCCCceEEECCcc-----cccCCCccCHHHcCC---CCceeEEEEEEEcCCcEEEEcc-CCC
Confidence 863 33568999999999999998653 255689999999986 4568999999999999999987 599
Q ss_pred eeeEEEEEEeeccccEEEEEEecccccccc-CCCCCEEEEEeEEEee-cCC
Q psy15132 600 TYMKRDITLVDQSQASVTMTLWGKEAETFD-ASNKPVIAVKAARVSE-FQG 648 (786)
Q Consensus 600 ~~~kr~i~l~D~s~~~i~~tLWg~~a~~~~-~~~~~vv~i~~~~V~~-f~G 648 (786)
+..+|+++|.|+|| +|++||||+.|+.+. ...+..|.+.++.+++ |+|
T Consensus 310 ~~~~r~i~l~D~Tg-~Ir~tlWg~~a~~~~~~~~g~~i~i~~~~~k~g~~~ 359 (374)
T PRK15491 310 ENKVSNIYVSDDTG-RIRIALWGEKAELVDKLDIDTPIKIIDAFSKSGYNE 359 (374)
T ss_pred EeEEEeEEEEeCCC-cEEEEEcccccccccccCCCCeEEEEEEEEeecCCC
Confidence 99999999999999 699999999998643 3455666677777765 544
No 14
>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=99.96 E-value=1.7e-29 Score=242.92 Aligned_cols=138 Identities=39% Similarity=0.688 Sum_probs=110.7
Q ss_pred EEEEEEEEEEEecCceEEeCCCCCCCCcceeeCCCceeecccCCCcCCceeEeeeeeEEEEecCCcEEEEeehHHHHHHh
Q psy15132 204 YCSVRGIIQVFRGSNTTYKACPSQDCNKKVIDQNNGMYRCEKCNKEFNTFTYRLILPVMIGDWTNSVWVTLFQNEAESIL 283 (786)
Q Consensus 204 ~~~v~a~I~~i~~~~~~Y~aC~~~~C~kKv~~~~~~~~~C~~C~~~~~~~~~ry~l~~~v~D~Tg~~~~~~F~~~a~~il 283 (786)
||+|+|+|..|+.++|||+|||++.|+|||...++|.|+|++|+++.++|.|||+|++.|+|+||++|+++||+.|++||
T Consensus 1 ~~~v~a~I~~I~~~~~~Y~aC~~~~C~kKv~~~~~~~y~C~~C~~~~~~~~~ry~l~~~i~D~tg~~~~~~F~~~a~~l~ 80 (146)
T PF08646_consen 1 YFTVRATIVEIKSDNWYYPACPNEKCNKKVTENGDGSYRCEKCNKTVENPKYRYRLSLKISDGTGSIWVTLFDEEAEQLL 80 (146)
T ss_dssp EEEEEEEEEEEETTTTEEEE-TSTTTS-B-EEETTTEEEETTTTEEESS-EEEEEEEEEEEETTEEEEEEEEHHHHHHHH
T ss_pred CEEEEEEEEEEECCCcEECCCCCccCCCEeecCCCcEEECCCCCCcCCCeeEEEEEEEEEEeCCCeEEEEEEhHHHHHHh
Confidence 79999999999999999999998899999997777899999999999999999999999999999999999999999999
Q ss_pred CCChhhhhccCCCh-----HHHHHhcCCEEEEEEeeecccccCccccCCCcceeeEEEeeccccccccc
Q psy15132 284 GVTAQEVGESTEDH-----PALKKALFTQYIFRLRAKLEHYNGTKKIPDGVNINSFAMLATQLNDIITD 347 (786)
Q Consensus 284 g~sa~el~~~~e~~-----~~~~~~~~k~~~f~v~~k~e~y~~~~~~sDG~~~~~~~~la~~ln~~v~~ 347 (786)
|++|+||.++.+.+ ..+.+++|++|.|+|+++.++|+++.++ ++ .++-..++|..-|+
T Consensus 81 G~~a~el~~~~~~~~~~~~~~~~~~~~~~~~f~v~~~~~~y~~e~r~---~~---~v~~i~~vd~~~e~ 143 (146)
T PF08646_consen 81 GMSADELKELKEEDPEEFPKIIKKLLGKEFVFRVRVKKESYNDESRV---KY---TVVRIEPVDYAEES 143 (146)
T ss_dssp CCHHCCCHHHCCC-HHHHHHHHHCTTT-EEEEEEEEEE--------E---EE---EEEEEEE--HHHHH
T ss_pred CCCHHHHHHHHhhchhHHHHHHHHhhCcEEEEEEEEEEhhhCCceEE---EE---EEEEeEeCCHHHHh
Confidence 99999999887653 3578899999999999999999987665 33 57777888877665
No 15
>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=99.96 E-value=1.2e-28 Score=242.44 Aligned_cols=148 Identities=38% Similarity=0.684 Sum_probs=128.1
Q ss_pred HHHHhhcCCCCCCCcEEEEEEEEEEEecCceEEeCCCCCCCCcceeeCCCceeecccCCCcCCceeEeeeeeEEEEecCC
Q psy15132 189 REIQDQQLGMGDKADYCSVRGIIQVFRGSNTTYKACPSQDCNKKVIDQNNGMYRCEKCNKEFNTFTYRLILPVMIGDWTN 268 (786)
Q Consensus 189 ~ei~~~~l~~~~~~~~~~v~a~I~~i~~~~~~Y~aC~~~~C~kKv~~~~~~~~~C~~C~~~~~~~~~ry~l~~~v~D~Tg 268 (786)
++|++.+++..+++++|.++|+|..|+.++|||+||| .|+|||.+.+++.|+|++|++..++|.+||+|++.|+|+||
T Consensus 2 ~~i~~~~~~~~~~~~~~~v~a~I~~I~~~~~~Y~aC~--~C~kkv~~~~~~~~~C~~C~~~~~~~~~ry~l~~~i~D~Tg 79 (166)
T cd04476 2 AEIKEENLGEGEKPDYFTVKATIVFIKPDNWWYPACP--GCNKKVVEEGNGTYRCEKCNKSVPNPEYRYILSLNVADHTG 79 (166)
T ss_pred chhhcccCCCCCCCCEEEEEEEEEEEcCCCeEEcccc--ccCcccEeCCCCcEECCCCCCcCCCccEEEEEEEEEEeCCC
Confidence 4566666666667899999999999999999999999 99999987554889999999999899999999999999999
Q ss_pred cEEEEeehHHHHHHhCCChhhhhccCCCh-----HHHHHhcCCEEEEEEeeecccccCccccCCCcceeeEEEeeccccc
Q psy15132 269 SVWVTLFQNEAESILGVTAQEVGESTEDH-----PALKKALFTQYIFRLRAKLEHYNGTKKIPDGVNINSFAMLATQLND 343 (786)
Q Consensus 269 ~~~~~~F~~~a~~ilg~sa~el~~~~e~~-----~~~~~~~~k~~~f~v~~k~e~y~~~~~~sDG~~~~~~~~la~~ln~ 343 (786)
++|+++||+.|++|||++|+||.++.+++ +.|.++.|++|+|+++++.++|+++.++ ++ ++.-..+++.
T Consensus 80 ~~~~~~F~~~ae~l~G~sa~el~~~~~~~~~~~~~~i~~~~gk~~~f~v~~~~~~y~~e~~~---~~---~v~~i~~~~~ 153 (166)
T cd04476 80 EAWLTLFDEVAEQIFGKSAEELLELKEEDPDAFPDAIQDLVGKTFLFRVSVKEETYNDEGRI---RY---TVVKVAPVDY 153 (166)
T ss_pred CEEEEEehHHHHHHhCCCHHHHHHHhhcCHHHHHHHHHHhhCceEEEEEEEEehhcCCcceE---EE---EEEEcccCCH
Confidence 99999999999999999999999886542 3688999999999999999999996544 33 4555666665
Q ss_pred c
Q psy15132 344 I 344 (786)
Q Consensus 344 ~ 344 (786)
.
T Consensus 154 ~ 154 (166)
T cd04476 154 K 154 (166)
T ss_pred H
Confidence 4
No 16
>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=99.95 E-value=3e-28 Score=234.37 Aligned_cols=118 Identities=47% Similarity=0.837 Sum_probs=102.0
Q ss_pred eEEEEEEEEEEecCceEEeCCCCccccccccccCCceeeeCCCCCcCCceeEEEEEEEEEEecCCcEEEEEehhhHHHHh
Q psy15132 669 YCSVRGIIQVFRGSNTTYKACPSQDCNKKVIDQNNGMYRCEKCNKEFNTFTYRLILPVMIGDWTNSVWVTLFQNEAESIL 748 (786)
Q Consensus 669 ~~~v~a~I~~i~~~~~~Y~aC~~~~C~kkv~~~~~g~~~C~~C~~~~~~~~~ry~l~~~i~D~Tg~~~~~~F~~~ae~ll 748 (786)
||+|+|+|..|+.++|||+|||++.|+|||...++|.|+|++|++..+.|.|||+|++.|+|+||++|+++||+.|++||
T Consensus 1 ~~~v~a~I~~I~~~~~~Y~aC~~~~C~kKv~~~~~~~y~C~~C~~~~~~~~~ry~l~~~i~D~tg~~~~~~F~~~a~~l~ 80 (146)
T PF08646_consen 1 YFTVRATIVEIKSDNWYYPACPNEKCNKKVTENGDGSYRCEKCNKTVENPKYRYRLSLKISDGTGSIWVTLFDEEAEQLL 80 (146)
T ss_dssp EEEEEEEEEEEETTTTEEEE-TSTTTS-B-EEETTTEEEETTTTEEESS-EEEEEEEEEEEETTEEEEEEEEHHHHHHHH
T ss_pred CEEEEEEEEEEECCCcEECCCCCccCCCEeecCCCcEEECCCCCCcCCCeeEEEEEEEEEEeCCCeEEEEEEhHHHHHHh
Confidence 79999999999999999999998889999987777899999999999999999999999999999999999999999999
Q ss_pred CCChHHHhccccChH-----HHHHhcCCeEEEEEEEEeeccCC
Q psy15132 749 GVTAQEVGESTEDHP-----ALKKALFTQYIFRLRAKLEHYNK 786 (786)
Q Consensus 749 G~sa~el~~~~~~~~-----~~~~~~~k~~~f~v~~k~~~y~~ 786 (786)
|++|+||.++.+.++ ++++++|++|.|+|+++.++|||
T Consensus 81 G~~a~el~~~~~~~~~~~~~~~~~~~~~~~~f~v~~~~~~y~~ 123 (146)
T PF08646_consen 81 GMSADELKELKEEDPEEFPKIIKKLLGKEFVFRVRVKKESYND 123 (146)
T ss_dssp CCHHCCCHHHCCC-HHHHHHHHHCTTT-EEEEEEEEEE-----
T ss_pred CCCHHHHHHHHhhchhHHHHHHHHhhCcEEEEEEEEEEhhhCC
Confidence 999999999887653 88999999999999999999985
No 17
>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=99.95 E-value=1.2e-27 Score=235.28 Aligned_cols=131 Identities=42% Similarity=0.776 Sum_probs=120.0
Q ss_pred HhHHhhcCCCCCCCceEEEEEEEEEEecCceEEeCCCCccccccccccCCceeeeCCCCCcCCceeEEEEEEEEEEecCC
Q psy15132 654 REIQDQQLGMGDKADYCSVRGIIQVFRGSNTTYKACPSQDCNKKVIDQNNGMYRCEKCNKEFNTFTYRLILPVMIGDWTN 733 (786)
Q Consensus 654 ~e~~~~~l~~~~~~~~~~v~a~I~~i~~~~~~Y~aC~~~~C~kkv~~~~~g~~~C~~C~~~~~~~~~ry~l~~~i~D~Tg 733 (786)
+++++.+++...++++|.|+|+|..|+.++|||+||| .|+|||.+..+|.|+|++|++..++|.|||+|++.|+|+||
T Consensus 2 ~~i~~~~~~~~~~~~~~~v~a~I~~I~~~~~~Y~aC~--~C~kkv~~~~~~~~~C~~C~~~~~~~~~ry~l~~~i~D~Tg 79 (166)
T cd04476 2 AEIKEENLGEGEKPDYFTVKATIVFIKPDNWWYPACP--GCNKKVVEEGNGTYRCEKCNKSVPNPEYRYILSLNVADHTG 79 (166)
T ss_pred chhhcccCCCCCCCCEEEEEEEEEEEcCCCeEEcccc--ccCcccEeCCCCcEECCCCCCcCCCccEEEEEEEEEEeCCC
Confidence 4666777766667899999999999999999999999 79999986555899999999999999999999999999999
Q ss_pred cEEEEEehhhHHHHhCCChHHHhccccCh-----HHHHHhcCCeEEEEEEEEeeccCC
Q psy15132 734 SVWVTLFQNEAESILGVTAQEVGESTEDH-----PALKKALFTQYIFRLRAKLEHYNK 786 (786)
Q Consensus 734 ~~~~~~F~~~ae~llG~sa~el~~~~~~~-----~~~~~~~~k~~~f~v~~k~~~y~~ 786 (786)
++|+++||+.|++|||+||+||.++.+++ +.|.++.|++|+|+++++.++||+
T Consensus 80 ~~~~~~F~~~ae~l~G~sa~el~~~~~~~~~~~~~~i~~~~gk~~~f~v~~~~~~y~~ 137 (166)
T cd04476 80 EAWLTLFDEVAEQIFGKSAEELLELKEEDPDAFPDAIQDLVGKTFLFRVSVKEETYND 137 (166)
T ss_pred CEEEEEehHHHHHHhCCCHHHHHHHhhcCHHHHHHHHHHhhCceEEEEEEEEehhcCC
Confidence 99999999999999999999999988764 288999999999999999999996
No 18
>PRK14699 replication factor A; Provisional
Probab=99.94 E-value=3.9e-24 Score=239.99 Aligned_cols=266 Identities=20% Similarity=0.311 Sum_probs=205.2
Q ss_pred eeecccCCCCCceEEEEEEeecCCcceecCCCC-CceEEEEEEEcCCCcEEEEEcchhHHHhhhhccCCcEEEEcceEEe
Q psy15132 443 HPIVSLSPYQNKWTIKARVTNKTPIREWNNARG-SGKLFSIDLLDESGEIRATMFNDECNRFHDMIEKDKVYYISNCTLK 521 (786)
Q Consensus 443 ~~I~~L~p~~~~w~I~~RV~~k~~~r~~~~~~~-~g~~~~~~L~D~~G~I~at~~~~~~~kf~~~l~~G~vy~is~~~V~ 521 (786)
.+|++|.|+....+|+|||+.++++|+|.+.+| +|++++++|.|++|+|++|+|++.++ +++.|++|++|+|.++.++
T Consensus 167 ~~I~dL~~~~~~V~i~gkVl~~~~~R~f~~~dG~~g~v~~~~igDeTG~ir~tlW~~~a~-~~~~l~~Gd~v~I~~a~vr 245 (484)
T PRK14699 167 QKIKDIKDGMGDLNLTGKVLEISEIRTFQRKDGTSGKVGNLLLGDETGTLRVTLWDDKTD-FLNQIEYGDTVELINAYAR 245 (484)
T ss_pred cchhhcCCCCCceEEEEEEEeccCceEEecCCCCceEEEEEEEEcCCceEEEEEECcccc-cccccCCCCEEEEecceEe
Confidence 589999999888899999999999999998776 78999999999999999999999885 7888999999999999887
Q ss_pred ccCCcccccCCceEEEEccccEEEEccCCCCCCCCcceeeccCcccccccCCCceeeEEEEEEEcccceeEEeecCCcee
Q psy15132 522 PANKKFSSINNDYEMSFTHSTTVIPCNEDEVGNMPSVKYCFVPLKTIAEISPDENIDVLGVCIDAAELSSVTGKTNQKTY 601 (786)
Q Consensus 522 ~a~~~y~~~~~~yei~f~~~T~I~~~~d~~~~~iP~~~~~f~~i~dl~~~~~~~~vDViGvV~~V~~~~~i~~k~~g~~~ 601 (786)
.. .| .+.++|+++..|.|...++.. .+ ..++.+|.+|... ...++|.|.|+++++++++.++ +|++.
T Consensus 246 ~~--~~---~~~~el~~~~~s~i~~~~~~~--e~---~~~~~~I~~L~~~--~~~v~I~grV~~~~~~r~~~~~-~Gseg 312 (484)
T PRK14699 246 EN--AF---TQKVELQVGNRSIIRKSEKKV--EY---EEEFTPIEDIKAD--MNNINISGRVLDISEVRTFEKK-DGSPG 312 (484)
T ss_pred ec--cc---CCceEEEecCceEeecccccc--cc---cccccCHHHcCCC--CceeEEEEEEEEcCCCeEEEcC-CCCee
Confidence 62 33 379999999999888775443 22 2367889999753 5789999999999999999966 58899
Q ss_pred eEEEEEEeeccccEEEEEEecccccccc-CCCCCEEEEEeEEEee--cCCc--c----cc-HHhHHh--h---c---CCC
Q psy15132 602 MKRDITLVDQSQASVTMTLWGKEAETFD-ASNKPVIAVKAARVSE--FQGN--L----LL-MREIQD--Q---Q---LGM 663 (786)
Q Consensus 602 ~kr~i~l~D~s~~~i~~tLWg~~a~~~~-~~~~~vv~i~~~~V~~--f~G~--L----~t-i~e~~~--~---~---l~~ 663 (786)
..+++.|.|+|| .|++|||+++|..++ ...++++-+.++++++ |++. | .+ +.+..+ + . ++.
T Consensus 313 ~v~~~~l~DeTG-~Ir~T~W~~~a~~~~~i~~Gd~v~i~~~y~~~~~~~~~~eL~~~~~t~I~~~~~~~e~~~~~~~I~d 391 (484)
T PRK14699 313 RVGNLLLGDSTG-KIRLTLWDEKTNFLDEIDFDETVEVLNAYSRENTFSQQVELNLGARGIIQKSEKKVEYREKFTDIAD 391 (484)
T ss_pred EEEEEEEECCCC-eEEEEEeCcccccccccCCCceEEEEeEEEEeccCCccEEEEecCceeEeecCCcceeeeccccHHH
Confidence 999999999999 799999999995544 4678889899998875 4554 3 11 111000 0 0 000
Q ss_pred CCCCceEEEEEEEEEEecCceEEeCCCCccccccccccCCceeeeCCCCCcCCceeEEEEEEEEEEecCCcEEEEEehhh
Q psy15132 664 GDKADYCSVRGIIQVFRGSNTTYKACPSQDCNKKVIDQNNGMYRCEKCNKEFNTFTYRLILPVMIGDWTNSVWVTLFQNE 743 (786)
Q Consensus 664 ~~~~~~~~v~a~I~~i~~~~~~Y~aC~~~~C~kkv~~~~~g~~~C~~C~~~~~~~~~ry~l~~~i~D~Tg~~~~~~F~~~ 743 (786)
-+....+.|.|.|..+.+-. . .. ..+| . ....-++.|.|+||++++++||+.
T Consensus 392 ie~~~~vdV~G~V~~v~~~~------------~-~~-~~~g------------~--~~~vr~i~l~D~TG~Ir~tlWg~~ 443 (484)
T PRK14699 392 IIPGESYSVQGKVSEIGELR------------E-FE-REDG------------T--ENVVANLQLKDETGSIRLTLWGEQ 443 (484)
T ss_pred ccCCCeeEEEEEEEEcCCcc------------e-EE-ecCC------------C--EEEEEEEEEEcCCCeEEEEEcchh
Confidence 12345789999998876521 1 11 1123 1 123447899999999999999999
Q ss_pred HHHHhCCC
Q psy15132 744 AESILGVT 751 (786)
Q Consensus 744 ae~llG~s 751 (786)
|+.+=.+.
T Consensus 444 A~~~~~~~ 451 (484)
T PRK14699 444 AYVIEDLD 451 (484)
T ss_pred hhhccccC
Confidence 98754444
No 19
>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=99.93 E-value=1.3e-25 Score=202.61 Aligned_cols=103 Identities=65% Similarity=1.092 Sum_probs=98.9
Q ss_pred eecccCCCCCceEEEEEEeecCCcceecCCCCCceEEEEEEEcCC-CcEEEEEcchhHHHhhhhccCCcEEEEcceEEec
Q psy15132 444 PIVSLSPYQNKWTIKARVTNKTPIREWNNARGSGKLFSIDLLDES-GEIRATMFNDECNRFHDMIEKDKVYYISNCTLKP 522 (786)
Q Consensus 444 ~I~~L~p~~~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~-G~I~at~~~~~~~kf~~~l~~G~vy~is~~~V~~ 522 (786)
||++|+|++.+|+|+|||++|+++|.|.+.+++|++|+|+|+|++ |+|+|++|++++++|++.|++|+||+|++|.|++
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 799999999999999999999999999998889999999999995 5799999999999999999999999999999999
Q ss_pred cCCcccccCCceEEEEccccEEEE
Q psy15132 523 ANKKFSSINNDYEMSFTHSTTVIP 546 (786)
Q Consensus 523 a~~~y~~~~~~yei~f~~~T~I~~ 546 (786)
|+++|++++|+|||.|+.+|.|++
T Consensus 81 a~~~y~~~~~~yeI~f~~~t~~~~ 104 (104)
T cd04474 81 ANKKFNTLKNDYEITFNRDTSIIE 104 (104)
T ss_pred ccccCCCCCCcEEEEECCCcEEeC
Confidence 999999999999999999998863
No 20
>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=7.2e-22 Score=177.80 Aligned_cols=101 Identities=50% Similarity=0.870 Sum_probs=96.4
Q ss_pred ceEEEEEEEEeccceeEeeccCCceeeEEEEEEEeCCCCEEEEEecccccccccCCCCcEEEEEeEEEeeeCCceeeeec
Q psy15132 59 NIDVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWGKEAETFDASNKPVIAVKAARVSEFQGGKTLSLS 138 (786)
Q Consensus 59 ~vDViGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~s~~~i~~tLWg~~a~~~~~~~~~Vi~i~~~kv~~f~g~~~ls~~ 138 (786)
+|||+|+|+++++++++++|++|++..||+|.|.|+|+.++.|||||++|+.+....++||+|+++|+++|+ +++|+++
T Consensus 1 ~vDvig~V~~v~~~~~i~~k~~g~~~~~r~v~i~D~t~~~i~vtLWg~~a~~~~~~~~~vv~~~~~~i~~~~-~~~l~~~ 79 (101)
T cd04475 1 IVDVIGVVKSVGPVTTITTKSTGRELDKREITLVDESGHSVELTLWGEQAELFDGSENPVIAIKGVKVSEFN-GKSLSTG 79 (101)
T ss_pred CEeEEEEEeEccCcEEEEEecCCCceeEEEEEEEeCCCCEEEEEEEHHHhhhcccCCCCEEEEEeeEEEecC-CeEEeec
Confidence 589999999999999999998788999999999999999999999999999998777999999999999998 6899999
Q ss_pred ceeEEEECCCchHHHHHHhhhh
Q psy15132 139 MSSVLSLNPDIPECHKLQGWFS 160 (786)
Q Consensus 139 ~~s~i~~npd~pe~~~l~~w~~ 160 (786)
.+|.|++||++||+.+|+.||.
T Consensus 80 ~~s~i~~np~~~e~~~l~~w~~ 101 (101)
T cd04475 80 SSSTIIINPDIPEAHKLRGWYD 101 (101)
T ss_pred CceeEEECCCcHHHHHHHHhhC
Confidence 9999999999999999999984
No 21
>PRK07218 replication factor A; Provisional
Probab=99.86 E-value=5.8e-20 Score=202.25 Aligned_cols=253 Identities=19% Similarity=0.273 Sum_probs=198.4
Q ss_pred CCCeEEEEccCcEEEEccCCCCCCCCceeEeecCccchhccCCC-CceEEEEEEEEeccceeEeeccCCceeeEEEEEEE
Q psy15132 14 NNDYEMSFTHSTTVIPCNEDEVGNMPSVKYCFVPLKTIAEISPD-ENIDVLGVCIDAAELSSVTGKTNQKTYMKRDITLV 92 (786)
Q Consensus 14 ~~~yei~f~~~T~I~~~~d~~~~~iP~~~~~f~~~~~i~~~~~~-~~vDViGvV~~v~~~~~i~~k~~g~~~~kr~i~l~ 92 (786)
....++.+.+.|.|...+++ ...| +......+|..+..+ ..|+|.|.|.++.+ ++|..+. | +...++..|.
T Consensus 133 ~g~~el~ig~~t~I~~~de~--~~~~---~~~~~~~kI~DL~~g~~~V~v~g~Vl~~~~-r~f~~~d-g-~~~v~~giig 204 (423)
T PRK07218 133 DGRPELNIGESTTVSLLDDS--SLPP---YSIGGDKKLIDLGPGDRGVNVEARVLELEH-REIDGRD-G-ETTILSGVLA 204 (423)
T ss_pred CCceEEeccCcceEEEcCcc--cccC---ccccCccchhhccCCCCceEEEEEEEEecc-eeEEcCC-C-CeEEEEEEEE
Confidence 35689999999999988653 2222 223445555555544 56999999999965 7888664 5 4568999999
Q ss_pred eCCCCEEEEEecccccccccCCCCcEEEEEeEEEeeeCCceeeeecceeEEEECCCchHHHHHHhhhhccCCCceeeecc
Q psy15132 93 DQSQASVTMTLWGKEAETFDASNKPVIAVKAARVSEFQGGKTLSLSMSSVLSLNPDIPECHKLQGWFSTQTNTRFEPVSQ 172 (786)
Q Consensus 93 D~s~~~i~~tLWg~~a~~~~~~~~~Vi~i~~~kv~~f~g~~~ls~~~~s~i~~npd~pe~~~l~~w~~~~~~~~~~~~s~ 172 (786)
|+|| +|++|||++++. ...|.+|-|.+|.+++|+|..+|+++..|.|..+|+..++..
T Consensus 205 DeTG-~Ir~tlW~~~~~---l~~Gd~v~I~na~v~e~~G~~elnv~~~t~I~~~d~~i~v~~------------------ 262 (423)
T PRK07218 205 DETG-RLPFTDWDPLPE---IEIGASIRIEDAYVREFRGVPSVNVSEFTTVEALDREVSVSK------------------ 262 (423)
T ss_pred CCCc-eEEEEEeccccc---CCCCCEEEEeeeEEeccCCeEEEEECCceEEEECCCCccccC------------------
Confidence 9999 999999999763 368999999999999999999999999999998875432211
Q ss_pred ccCCCCCCCcchhhhHHHHHhhcCCCCCCCcE-EEEEEEEEEEecCceEEeCCCCCCCCcceeeCCCceeecccCCCcCC
Q psy15132 173 RTGGMGGGAAGNLLLMREIQDQQLGMGDKADY-CSVRGIIQVFRGSNTTYKACPSQDCNKKVIDQNNGMYRCEKCNKEFN 251 (786)
Q Consensus 173 ~~~~~~~~~~~~~~ti~ei~~~~l~~~~~~~~-~~v~a~I~~i~~~~~~Y~aC~~~~C~kKv~~~~~~~~~C~~C~~~~~ 251 (786)
..+++.|.++.+. .+.| ..|.|+|..|...+-.|.+|| .|+|+|. .|.|+.|++.
T Consensus 263 ---------~~~~~~I~e~~~~------~g~~~Vev~G~Iv~i~~gsgli~rCP--~C~r~v~-----~~~C~~hG~v-- 318 (423)
T PRK07218 263 ---------DPPRLKIREAVER------GGIFDVELVGNIISVRDGSGLIERCP--ECGRVIQ-----KGQCRSHGAV-- 318 (423)
T ss_pred ---------Cccccchhhhhcc------CCcceEEEEEEEEEeccCCcceecCc--Ccccccc-----CCcCCCCCCc--
Confidence 1124567776542 2334 589999999998877888999 8999994 3799999986
Q ss_pred ceeEeeeeeEEEEecCCcEEEEeehHHHHHHhCCChhhhhccCCC----h---HHH-HHhcCCEEEEEEeeeccccc
Q psy15132 252 TFTYRLILPVMIGDWTNSVWVTLFQNEAESILGVTAQEVGESTED----H---PAL-KKALFTQYIFRLRAKLEHYN 320 (786)
Q Consensus 252 ~~~~ry~l~~~v~D~Tg~~~~~~F~~~a~~ilg~sa~el~~~~e~----~---~~~-~~~~~k~~~f~v~~k~e~y~ 320 (786)
.|.+-..+++.+.|+||++.+++|++.+++|.|++.++..++..+ . ..+ ..++|++|.++-.+..+.|.
T Consensus 319 e~~~dlrik~vLDDGtg~~~~~~~~e~~e~l~G~~~e~a~~~~~~~~d~~~v~~~i~~~llG~~~~v~G~~~~~~~g 395 (423)
T PRK07218 319 EGEDDLRIKAILDDGTGSVTVILDRELTEIVYGGTLEDAEELAREAMDKDVVAEDIRERLVGREYRVRGNLSVDEYG 395 (423)
T ss_pred CCeeeeEEEEEEECCCCeEEEEEChhhhHhHhCCCHHHHHHHHHhhhcchhhHHHHHHhhcCcEEEEEeccccccCC
Confidence 677888899999999999999999999999999999987665321 1 234 55999999999988888873
No 22
>PRK06386 replication factor A; Reviewed
Probab=99.81 E-value=3.5e-18 Score=183.50 Aligned_cols=251 Identities=14% Similarity=0.189 Sum_probs=191.8
Q ss_pred CCCCeEEEEccCcEEEEccCCCCCCCCceeEeecCccchhccCCCCceEEEEEEEEeccceeEeeccCCceeeEEEEEEE
Q psy15132 13 INNDYEMSFTHSTTVIPCNEDEVGNMPSVKYCFVPLKTIAEISPDENIDVLGVCIDAAELSSVTGKTNQKTYMKRDITLV 92 (786)
Q Consensus 13 ~~~~yei~f~~~T~I~~~~d~~~~~iP~~~~~f~~~~~i~~~~~~~~vDViGvV~~v~~~~~i~~k~~g~~~~kr~i~l~ 92 (786)
....++|.++..|.|.+..|.+ ..+ ...+..++|.||.. ....++|.|.|.++.+ .++.++ |.....+++.|.
T Consensus 77 ~~G~~~Lnv~~~t~v~~~~d~~-iev-~~~~~~~KI~DL~~--g~~~v~V~akVle~~e-~e~~~~--g~~~~v~sg~lg 149 (358)
T PRK06386 77 YNGKIRIYFDSRSEVMLKPDEN-IEV-KRTYKLVKIRDLSL--VTPYVSVIGKITGITK-KEYDSD--GTSKIVYQGYIE 149 (358)
T ss_pred ECCEEEEEEcCceEEEecCccc-ccc-ccccCccEeEeccC--CCCceEEEEEEEEccC-ceEecC--CCccEEEEEEEE
Confidence 4567899999999997765431 222 11245566777732 3467999999999977 577643 445678999999
Q ss_pred eCCCCEEEEEecccccccccCCCCcEEEEEeEEEeeeCCceeeeecceeEEEECCCchHHHHHHhhhhccCCCceeeecc
Q psy15132 93 DQSQASVTMTLWGKEAETFDASNKPVIAVKAARVSEFQGGKTLSLSMSSVLSLNPDIPECHKLQGWFSTQTNTRFEPVSQ 172 (786)
Q Consensus 93 D~s~~~i~~tLWg~~a~~~~~~~~~Vi~i~~~kv~~f~g~~~ls~~~~s~i~~npd~pe~~~l~~w~~~~~~~~~~~~s~ 172 (786)
|+|| +|++|||++. ...+.++-|.++.+.+|+|..+|+++..|.|...|+.-|+
T Consensus 150 DeTG-rIr~TlW~~~-----l~eGd~v~i~na~v~e~~G~~el~v~~~t~I~~~~~~iev-------------------- 203 (358)
T PRK06386 150 DDTA-RVRISSFGKP-----LEDNRFVRIENARVSQYNGYIEISVGNKSVIKEVESDINL-------------------- 203 (358)
T ss_pred cCCC-eEEEEEcccc-----ccCCCEEEEeeeEEEccCCeEEEEeCCeEEEEECCCCccc--------------------
Confidence 9999 9999999983 3679999999999999999999999999998876532210
Q ss_pred ccCCCCCCCcchhhhHHHHHhhcCCCCCCCcEEEEEEEEEEEecCceEEeCCCCCCCCcceeeCCCceeecccCCCcCCc
Q psy15132 173 RTGGMGGGAAGNLLLMREIQDQQLGMGDKADYCSVRGIIQVFRGSNTTYKACPSQDCNKKVIDQNNGMYRCEKCNKEFNT 252 (786)
Q Consensus 173 ~~~~~~~~~~~~~~ti~ei~~~~l~~~~~~~~~~v~a~I~~i~~~~~~Y~aC~~~~C~kKv~~~~~~~~~C~~C~~~~~~ 252 (786)
..+.+.|++|.+.. .-..+.|+|..|....-.|.+|| .|+|++.. +.|+.|++. .
T Consensus 204 ---------~~~~~~I~di~~~~-------g~v~i~G~iv~i~~gsgli~rCP--~C~R~l~~-----g~C~~HG~v--~ 258 (358)
T PRK06386 204 ---------ESRNIFIFEIKSPV-------GGITIMGFIVSVGQGSRIFTKCS--VCNKIIED-----GVCKDHPDA--P 258 (358)
T ss_pred ---------CccccchhhhhccC-------CeEEEEEEEEEEcCCcEeEecCc--CCCeEccC-----CcCCCCCCC--C
Confidence 01246688887631 12578899999998777888999 89999962 589999973 4
Q ss_pred eeEeeeeeEEEEecCCcEEEEeehHHHHHHhCCChhhhhccC-CCh-HH-H-HHhcCCEEEEEEeeecccccC
Q psy15132 253 FTYRLILPVMIGDWTNSVWVTLFQNEAESILGVTAQEVGEST-EDH-PA-L-KKALFTQYIFRLRAKLEHYNG 321 (786)
Q Consensus 253 ~~~ry~l~~~v~D~Tg~~~~~~F~~~a~~ilg~sa~el~~~~-e~~-~~-~-~~~~~k~~~f~v~~k~e~y~~ 321 (786)
+.+-..+.+.|.|+||.+.+++|++.+++|+|++-+|+.++- +-+ .. + ..++|+.|.|+-.+..+.|.-
T Consensus 259 ~~~dlr~k~vLDDGtg~~~~~l~~e~~e~l~G~~lee~~~~a~~~~~~~~i~~~llGr~~~v~G~~~~~~~~~ 331 (358)
T PRK06386 259 VYLDIFGYFTISDGTGFVTCYANKDSFLPYININENEFARKASSMNPNMLIKKNLLGKCFSVTGDLRKKDDEI 331 (358)
T ss_pred CeeEEEEEEEEECCCCeEEEEEChHHhHHHhCCCHHHHHHHhhccCHHHHhhhhhcccEEEEEcceEeccCCe
Confidence 566666778999999999999999999999999999987542 111 12 2 558999999999988887664
No 23
>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=99.81 E-value=1.2e-19 Score=164.77 Aligned_cols=97 Identities=37% Similarity=0.579 Sum_probs=89.3
Q ss_pred EEEEEEEEeccceeEeeccCCceeeEEEEEEEeCCCCEEEEEeccccccccc------CCCCcEEEEEe-EEEeeeCCce
Q psy15132 61 DVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWGKEAETFD------ASNKPVIAVKA-ARVSEFQGGK 133 (786)
Q Consensus 61 DViGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~s~~~i~~tLWg~~a~~~~------~~~~~Vi~i~~-~kv~~f~g~~ 133 (786)
||||+|++|++++++..+ |++..||+|+|+|.++.++.|||||++|.+|+ ...+||||+.. +||++|+|++
T Consensus 1 DviG~i~~v~~~~~~~~~--~~~~~kr~~~i~D~~~~~l~~tlwG~~A~~f~~~~~~~~~~~~VVav~~~~rV~~~~g~~ 78 (106)
T cd04481 1 DVIGVIVDVGPLEELPPV--NKPSRKLDFEIRDLSDERLKCTLWGEYAEEFDAKFQSAGNGEPVVAVLRFWKIKEYKGPK 78 (106)
T ss_pred CeeEEEEEecceEecccC--CccceEEEEEEEeCCCCEEEEEEEHHHHHHHHHHHHHhCCCCcEEEEEEeEEEEEEcCCc
Confidence 899999999999999887 67889999999999999999999999999986 36889998755 9999999989
Q ss_pred eeeec-ceeEEEECCCchHHHHHHhhh
Q psy15132 134 TLSLS-MSSVLSLNPDIPECHKLQGWF 159 (786)
Q Consensus 134 ~ls~~-~~s~i~~npd~pe~~~l~~w~ 159 (786)
+||.. ++|+|++||++||+.+|+..+
T Consensus 79 ~ls~~~~~s~v~inp~ipe~~~~~~~~ 105 (106)
T cd04481 79 SLSNSFGASKVYINPDIPEVPEIKMSL 105 (106)
T ss_pred EEEcCCCceEEEECCCcHHHHHHHhhC
Confidence 99999 999999999999999998653
No 24
>PRK07217 replication factor A; Reviewed
Probab=99.73 E-value=9.2e-17 Score=167.12 Aligned_cols=196 Identities=21% Similarity=0.307 Sum_probs=151.8
Q ss_pred eccCcccccccCCCceeeEEEEEEEcccceeEEeecCCceeeEEEEEEeeccccEEEEEEeccccccccCCCCCEEEEEe
Q psy15132 561 CFVPLKTIAEISPDENIDVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWGKEAETFDASNKPVIAVKA 640 (786)
Q Consensus 561 ~f~~i~dl~~~~~~~~vDViGvV~~V~~~~~i~~k~~g~~~~kr~i~l~D~s~~~i~~tLWg~~a~~~~~~~~~vv~i~~ 640 (786)
..++|.||... +..|+|.|.|+.+++.. .+ ...+.-.|.|+|| +|++|+|++.. .-....|.++.|.+
T Consensus 71 ~~~kI~Di~~~--~~~VsV~aKVl~l~e~~------~~--si~qvGllgDETG-~IkfT~W~~s~-~~~leeGd~~rI~n 138 (311)
T PRK07217 71 ELVNIADIDEP--EQWVDVTAKVVQLWEPS------SD--SIAQVGLLGDETG-TIKFTKWAKSD-LPELEEGKSYLLKN 138 (311)
T ss_pred CceeeeecCCC--CCcEEEEEEEEEecCCC------CC--ceEEEEEEEcCCc-eEEEEEccCCC-CCcccCCCEEEEEe
Confidence 34567777754 67899999999998754 12 2344568999999 99999999732 11367899999999
Q ss_pred EEEeecCCc--c-----ccHHhHHhhcCCCCCCCceEEEEEEEEEEecCceEEeCCCCccccccccccCCceeeeCCCCC
Q psy15132 641 ARVSEFQGN--L-----LLMREIQDQQLGMGDKADYCSVRGIIQVFRGSNTTYKACPSQDCNKKVIDQNNGMYRCEKCNK 713 (786)
Q Consensus 641 ~~V~~f~G~--L-----~ti~e~~~~~l~~~~~~~~~~v~a~I~~i~~~~~~Y~aC~~~~C~kkv~~~~~g~~~C~~C~~ 713 (786)
+.+++|+|+ | .++.++.+. +. -+.+...+.|+++.|++++.....||.++|+|.+. .| .|+.|++
T Consensus 139 a~v~ey~G~~~lnlg~~t~I~~~de~-Ie--V~~~~vei~G~lVdi~~GsglI~rCP~~~C~Rvl~---~g--~C~~HG~ 210 (311)
T PRK07217 139 VVTDEYQGRFSVKLNRTTSIEELDED-IE--VGDDEVEVEGALVDIQSGSGLIKRCPEEDCTRVLQ---NG--RCSEHGK 210 (311)
T ss_pred EEEeeECCEEEEEeCCceEEEeCCCC-cc--ccCccccceeEEEEEeCCCCCeecCCccccCcccc---CC--CCCCCCC
Confidence 999999998 4 334443222 11 12234789999999999999999999888999873 23 6999998
Q ss_pred cCCceeEEEEEEEEEEecCCcEEEEEehhhHHHHhCCChHHHhccccC--h------HHHHHhcCCeEEEEEE
Q psy15132 714 EFNTFTYRLILPVMIGDWTNSVWVTLFQNEAESILGVTAQEVGESTED--H------PALKKALFTQYIFRLR 778 (786)
Q Consensus 714 ~~~~~~~ry~l~~~i~D~Tg~~~~~~F~~~ae~llG~sa~el~~~~~~--~------~~~~~~~~k~~~f~v~ 778 (786)
.-+ .+-+++++.|.|+||++.+.+.++..++|.|++.+|+.+|..+ | ++-+.++|+.|.|+-.
T Consensus 211 ve~--~~DLrik~vlDDGt~~~~~~~~~e~te~l~G~~l~eak~~a~dald~~vv~~~i~~~llGr~~~v~G~ 281 (311)
T PRK07217 211 VEG--EFDLRIKGVLDDGEEVQEVIFNREATEELTGITLEEAKQMAMDALDTGVVLDELKEKLLGRYYRVTGP 281 (311)
T ss_pred cCC--ceeeEEEEEEECCCCeEEEEEChHHhHHHhCCCHHHHHHHHHHhhchhhHHHHHHHhhcCceEEEEec
Confidence 654 4667789999999999999999999999999999999887632 2 1335799999998764
No 25
>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=99.65 E-value=4.6e-16 Score=135.59 Aligned_cols=84 Identities=30% Similarity=0.529 Sum_probs=76.1
Q ss_pred EEEEEEeecCCcceecCC-CCCceEEEEEEEcCCC-cEEEEEcchhHHHhhhhccCCcEEEEcceEEeccCCcccccCCc
Q psy15132 456 TIKARVTNKTPIREWNNA-RGSGKLFSIDLLDESG-EIRATMFNDECNRFHDMIEKDKVYYISNCTLKPANKKFSSINND 533 (786)
Q Consensus 456 ~I~~RV~~k~~~r~~~~~-~~~g~~~~~~L~D~~G-~I~at~~~~~~~kf~~~l~~G~vy~is~~~V~~a~~~y~~~~~~ 533 (786)
+|+|||+ |.|... ..+|..++|+|+|++| +|+|++|++++++|++.|+||+||.|++|.|.++++.|++++|+
T Consensus 1 ~I~Vrv~-----r~W~~~~~~~~~~~~miL~De~G~~I~a~i~~~~~~~f~~~L~eg~vy~is~f~v~~~~~~y~~~~~~ 75 (86)
T cd04480 1 KICVRVL-----RLWDVYNNASGESLEMVLVDEKGNRIHATIPKRLAAKFRPLLKEGKWYTISNFEVAPNTGSYRPTDHP 75 (86)
T ss_pred CEEEEEE-----EEEcCcCCCCCcEEEEEEEcCCCCEEEEEECHHHHHhhhhhceeCCEEEEeeEEEEcCCCcccccCCc
Confidence 4899999 556532 2278999999999999 69999999999999999999999999999999999999999999
Q ss_pred eEEEEccccEE
Q psy15132 534 YEMSFTHSTTV 544 (786)
Q Consensus 534 yei~f~~~T~I 544 (786)
|+|.|..+|.|
T Consensus 76 y~I~f~~~T~V 86 (86)
T cd04480 76 YKIKFMSDTVV 86 (86)
T ss_pred EEEEeecCcCC
Confidence 99999998864
No 26
>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=99.58 E-value=6.2e-15 Score=130.88 Aligned_cols=88 Identities=27% Similarity=0.525 Sum_probs=81.5
Q ss_pred EEEEEcCCCc-EEEEEcchhHHHhhhhccCCcEEEEcceEEeccCCcccccCCceEEEEccccEEEEccCCCCCCCCcce
Q psy15132 481 SIDLLDESGE-IRATMFNDECNRFHDMIEKDKVYYISNCTLKPANKKFSSINNDYEMSFTHSTTVIPCNEDEVGNMPSVK 559 (786)
Q Consensus 481 ~~~L~D~~G~-I~at~~~~~~~kf~~~l~~G~vy~is~~~V~~a~~~y~~~~~~yei~f~~~T~I~~~~d~~~~~iP~~~ 559 (786)
.|+|+|++|. |+|+++++++++|.+.|+||+||.|++|.|.++.+.|++++|+|+|.|..+|.|.++++.+ ..| .
T Consensus 1 emvL~De~G~~I~A~I~~~~~~~f~~~l~Eg~~y~i~~F~V~~~~~~yr~t~h~y~I~f~~~T~V~~~~~~~--~~~--~ 76 (95)
T PF02721_consen 1 EMVLVDEKGDKIQATIPKELVDKFKDSLKEGSWYTISNFTVSPNSGSYRPTDHKYKINFMPNTKVTEIDPPS--DPP--F 76 (95)
T ss_pred CEEEEecCCCEEEEEECHHHHHHHHhhcccCCEEEeEeEEEEeCCCceeccCCCEEEEECCcCeEEECCCCC--CCc--e
Confidence 4799999995 9999999999999999999999999999999999999999999999999999999997654 334 8
Q ss_pred eeccCcccccccC
Q psy15132 560 YCFVPLKTIAEIS 572 (786)
Q Consensus 560 ~~f~~i~dl~~~~ 572 (786)
|+|++|++|.+..
T Consensus 77 ~~f~~F~~I~~~~ 89 (95)
T PF02721_consen 77 FNFTPFDEILEGT 89 (95)
T ss_pred EeecCHHHHhcCc
Confidence 9999999999864
No 27
>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=99.49 E-value=1.2e-13 Score=124.27 Aligned_cols=74 Identities=47% Similarity=0.787 Sum_probs=70.2
Q ss_pred eeeEEEEEEEcccceeEEeecCCceeeEEEEEEeeccccEEEEEEeccccccccCCCCCEEEEEeEEEeecCCc
Q psy15132 576 NIDVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWGKEAETFDASNKPVIAVKAARVSEFQGN 649 (786)
Q Consensus 576 ~vDViGvV~~V~~~~~i~~k~~g~~~~kr~i~l~D~s~~~i~~tLWg~~a~~~~~~~~~vv~i~~~~V~~f~G~ 649 (786)
.|||+|+|+++++++++++|++|++..+|+|.|.|+|+.+++|||||++|+.+....++||+|+++++++|+|+
T Consensus 1 ~vDvig~V~~v~~~~~i~~k~~g~~~~~r~v~i~D~t~~~i~vtLWg~~a~~~~~~~~~vv~~~~~~i~~~~~~ 74 (101)
T cd04475 1 IVDVIGVVKSVGPVTTITTKSTGRELDKREITLVDESGHSVELTLWGEQAELFDGSENPVIAIKGVKVSEFNGK 74 (101)
T ss_pred CEeEEEEEeEccCcEEEEEecCCCceeEEEEEEEeCCCCEEEEEEEHHHhhhcccCCCCEEEEEeeEEEecCCe
Confidence 48999999999999999999779999999999999999999999999999998877799999999999999986
No 28
>PRK07217 replication factor A; Reviewed
Probab=99.42 E-value=1.7e-11 Score=128.02 Aligned_cols=201 Identities=22% Similarity=0.295 Sum_probs=148.7
Q ss_pred cCccchhccCCCCceEEEEEEEEeccceeEeeccCCceeeEEEEEEEeCCCCEEEEEecccccccccCCCCcEEEEEeEE
Q psy15132 46 VPLKTIAEISPDENIDVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWGKEAETFDASNKPVIAVKAAR 125 (786)
Q Consensus 46 ~~~~~i~~~~~~~~vDViGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~s~~~i~~tLWg~~a~~~~~~~~~Vi~i~~~k 125 (786)
+++.||.. .+..|+|.|.|.++.+.+. +. .-+.=.|.|+|| +|.+|+|++.. .-....|.++-|.+|.
T Consensus 73 ~kI~Di~~--~~~~VsV~aKVl~l~e~~~------~s--i~qvGllgDETG-~IkfT~W~~s~-~~~leeGd~~rI~na~ 140 (311)
T PRK07217 73 VNIADIDE--PEQWVDVTAKVVQLWEPSS------DS--IAQVGLLGDETG-TIKFTKWAKSD-LPELEEGKSYLLKNVV 140 (311)
T ss_pred eeeeecCC--CCCcEEEEEEEEEecCCCC------Cc--eEEEEEEEcCCc-eEEEEEccCCC-CCcccCCCEEEEEeEE
Confidence 44555532 4678999999999987542 22 122336999999 99999999742 1124679999999999
Q ss_pred EeeeCCceeeeecceeEEEECCCchHHHHHHhhhhccCCCceeeeccccCCCCCCCcchhhhHHHHHhhcCCCCCCCcEE
Q psy15132 126 VSEFQGGKTLSLSMSSVLSLNPDIPECHKLQGWFSTQTNTRFEPVSQRTGGMGGGAAGNLLLMREIQDQQLGMGDKADYC 205 (786)
Q Consensus 126 v~~f~g~~~ls~~~~s~i~~npd~pe~~~l~~w~~~~~~~~~~~~s~~~~~~~~~~~~~~~ti~ei~~~~l~~~~~~~~~ 205 (786)
+++|+|..+|+++..|.|...++.-++ .+ .-.
T Consensus 141 v~ey~G~~~lnlg~~t~I~~~de~IeV---------------------------------------~~---------~~v 172 (311)
T PRK07217 141 TDEYQGRFSVKLNRTTSIEELDEDIEV---------------------------------------GD---------DEV 172 (311)
T ss_pred EeeECCEEEEEeCCceEEEeCCCCccc---------------------------------------cC---------ccc
Confidence 999999999999999988765421100 00 002
Q ss_pred EEEEEEEEEecCceEEeCCCCCCCCcceeeCCCceeecccCCCcCCceeEeeeeeEEEEecCCcEEEEeehHHHHHHhCC
Q psy15132 206 SVRGIIQVFRGSNTTYKACPSQDCNKKVIDQNNGMYRCEKCNKEFNTFTYRLILPVMIGDWTNSVWVTLFQNEAESILGV 285 (786)
Q Consensus 206 ~v~a~I~~i~~~~~~Y~aC~~~~C~kKv~~~~~~~~~C~~C~~~~~~~~~ry~l~~~v~D~Tg~~~~~~F~~~a~~ilg~ 285 (786)
.+.|.+..|...+-....||.+.|+|.+. .+.|+.|++. .+.+-..+++.+.|+||++.+.+-.+..++|.|+
T Consensus 173 ei~G~lVdi~~GsglI~rCP~~~C~Rvl~-----~g~C~~HG~v--e~~~DLrik~vlDDGt~~~~~~~~~e~te~l~G~ 245 (311)
T PRK07217 173 EVEGALVDIQSGSGLIKRCPEEDCTRVLQ-----NGRCSEHGKV--EGEFDLRIKGVLDDGEEVQEVIFNREATEELTGI 245 (311)
T ss_pred cceeEEEEEeCCCCCeecCCccccCcccc-----CCCCCCCCCc--CCceeeEEEEEEECCCCeEEEEEChHHhHHHhCC
Confidence 45678888887665666999555999994 2589999986 4566677888999999999999999999999999
Q ss_pred ChhhhhccCCC--h-----HHH-HHhcCCEEEEEEe
Q psy15132 286 TAQEVGESTED--H-----PAL-KKALFTQYIFRLR 313 (786)
Q Consensus 286 sa~el~~~~e~--~-----~~~-~~~~~k~~~f~v~ 313 (786)
+-+|+.++..+ + ..| ..++|+.|.|+-.
T Consensus 246 ~l~eak~~a~dald~~vv~~~i~~~llGr~~~v~G~ 281 (311)
T PRK07217 246 TLEEAKQMAMDALDTGVVLDELKEKLLGRYYRVTGP 281 (311)
T ss_pred CHHHHHHHHHHhhchhhHHHHHHHhhcCceEEEEec
Confidence 99998776422 1 123 3588999977764
No 29
>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=99.33 E-value=1.5e-12 Score=116.26 Aligned_cols=64 Identities=33% Similarity=0.562 Sum_probs=56.5
Q ss_pred ccCccccCCCcceeeEEEeecccccccccCCcccceEEEEceeEeeeeecCCCCccEEEEEEeeeeecc
Q psy15132 319 YNGTKKIPDGVNINSFAMLATQLNDIITDGTLSEFTIVQIKRYIVSGVSSGSATNRSVLIILELNIIKP 387 (786)
Q Consensus 319 y~~~~~~sDG~~~~~~~~la~~ln~~v~~~~L~~~~iikl~~~~~~~~~~~~~~~~~~~ii~~~~v~~~ 387 (786)
=.+|+++|||.|+ .++||++|+|+++++|.|++|+||||++|.++.+++ +|+++||+++||+.+
T Consensus 38 ~RyR~~lSDG~~~-~~amLatqln~lv~~g~l~~~siirl~~y~~n~v~~----~k~iiiil~leVv~~ 101 (101)
T PF04057_consen 38 DRYRLVLSDGVHS-IQAMLATQLNHLVESGELQKGSIIRLKQYTCNTVKN----GKKIIIILDLEVVQS 101 (101)
T ss_dssp -EEEEEEESSSEE-EEEEESGGGHHHHHTTSSSTT-EEEEEEEEEEESTT----SSEEEEEEEEEEEE-
T ss_pred ceEEEEEEChHHH-HHHHhHHHhHHHHhcCCcccCCEEEEeEEEEeeccC----CCEEEEEEeeEEEeC
Confidence 4458999999996 599999999999999999999999999999999964 389999999999863
No 30
>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=99.28 E-value=1.1e-12 Score=115.99 Aligned_cols=61 Identities=36% Similarity=0.594 Sum_probs=56.4
Q ss_pred cCccccCCCcceeeEEEeecccccccccCCcccceEEEEceeEeeeeecCCCCccEEEEEEeeeeec
Q psy15132 320 NGTKKIPDGVNINSFAMLATQLNDIITDGTLSEFTIVQIKRYIVSGVSSGSATNRSVLIILELNIIK 386 (786)
Q Consensus 320 ~~~~~~sDG~~~~~~~~la~~ln~~v~~~~L~~~~iikl~~~~~~~~~~~~~~~~~~~ii~~~~v~~ 386 (786)
.+|+.+|||.|++ ++||++|+|+++++|.|++|+||||++|+++.++ +|+++||+++||+.
T Consensus 37 RyRi~lSDG~~~~-~amLatqln~~v~~g~l~~~sIirl~~y~~~~i~-----~k~viiIldlevl~ 97 (97)
T cd04477 37 RYRILLSDGVYYV-QAMLATQLNPLVESGQLQRGSIIRLKRFICNVIK-----GKRILIILDLEVVQ 97 (97)
T ss_pred eEEEEEEChhHHH-HHHHhhhhhhHHhcCCccCCcEEEECeEEEEEec-----CcEEEEEEeeEEeC
Confidence 5689999999965 9999999999999999999999999999999995 38899999999973
No 31
>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=99.27 E-value=1e-11 Score=112.68 Aligned_cols=69 Identities=36% Similarity=0.620 Sum_probs=63.7
Q ss_pred eEEEEEEEcccceeEEeecCCceeeEEEEEEeeccccEEEEEEecccccccc------CCCCCEEEEEe-EEEeecCC
Q psy15132 578 DVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWGKEAETFD------ASNKPVIAVKA-ARVSEFQG 648 (786)
Q Consensus 578 DViGvV~~V~~~~~i~~k~~g~~~~kr~i~l~D~s~~~i~~tLWg~~a~~~~------~~~~~vv~i~~-~~V~~f~G 648 (786)
||||+|++|+++.++..+ |++..+|+++|+|.++.+++|||||++|+.|+ ...+|||++.. +||++|+|
T Consensus 1 DviG~i~~v~~~~~~~~~--~~~~~kr~~~i~D~~~~~l~~tlwG~~A~~f~~~~~~~~~~~~VVav~~~~rV~~~~g 76 (106)
T cd04481 1 DVIGVIVDVGPLEELPPV--NKPSRKLDFEIRDLSDERLKCTLWGEYAEEFDAKFQSAGNGEPVVAVLRFWKIKEYKG 76 (106)
T ss_pred CeeEEEEEecceEecccC--CccceEEEEEEEeCCCCEEEEEEEHHHHHHHHHHHHHhCCCCcEEEEEEeEEEEEEcC
Confidence 899999999999999887 88999999999999999999999999999987 36889998765 99999987
No 32
>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=99.20 E-value=1.3e-10 Score=110.38 Aligned_cols=96 Identities=18% Similarity=0.331 Sum_probs=80.0
Q ss_pred EeecCccchhccCCCCceEEEEEEEEeccceeEeeccCCceeeEEEEEEEeCCC---CEEEEEeccccccccc-CCCCcE
Q psy15132 43 YCFVPLKTIAEISPDENIDVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQ---ASVTMTLWGKEAETFD-ASNKPV 118 (786)
Q Consensus 43 ~~f~~~~~i~~~~~~~~vDViGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~s~---~~i~~tLWg~~a~~~~-~~~~~V 118 (786)
|+|++|++|.+ ..+..|||||+|++++++.. .+|+. .++.|+|.|+|+ ..+++++|++.++.+. ...|+|
T Consensus 1 ~~f~~i~~~~~-~~~~~v~vigVV~~~~~p~~----s~g~d-~~~tl~i~D~S~~~~~~l~v~~F~~~~~~LP~v~~GDV 74 (138)
T cd04497 1 YKYTPLSSALK-ESGGSVNVIGVVVDAGPPVR----SKGTD-YCCTLTITDPSLANSDGLTVKLFRPNEESLPIVKVGDI 74 (138)
T ss_pred CceEeHHHHHh-ccCCeEEEEEEEeecCCCcc----cCCCc-EEEEEEEECCCCCCCCcEEEEEECCChhhCCCCCCCCE
Confidence 57899999987 67899999999999999754 23555 899999999998 7899999999999987 488999
Q ss_pred EEEEeEEEeeeCCceeeeecc-eeEEE
Q psy15132 119 IAVKAARVSEFQGGKTLSLSM-SSVLS 144 (786)
Q Consensus 119 i~i~~~kv~~f~g~~~ls~~~-~s~i~ 144 (786)
|++++++|..|+|...+.... .|.+.
T Consensus 75 Ill~~~kv~~~~g~~~~~~~~~~ss~a 101 (138)
T cd04497 75 ILLRRVKIQSYNGKPQGISNDRGSSWA 101 (138)
T ss_pred EEEEEEEEEEECCceEEEECCCceeEE
Confidence 999999999998765443333 55553
No 33
>COG1599 RFA1 Single-stranded DNA-binding replication protein A (RPA), large (70 kD) subunit and related ssDNA-binding proteins [DNA replication, recombination, and repair]
Probab=99.08 E-value=1.2e-09 Score=122.59 Aligned_cols=183 Identities=28% Similarity=0.345 Sum_probs=143.9
Q ss_pred CCceeeecccCCCCCceEEEEEEeecCCcceecCCCCCceEEEEEEEcCC-CcEEEEEcchhHHHhhhhccCCcEEEEcc
Q psy15132 439 VVQTHPIVSLSPYQNKWTIKARVTNKTPIREWNNARGSGKLFSIDLLDES-GEIRATMFNDECNRFHDMIEKDKVYYISN 517 (786)
Q Consensus 439 ~~~~~~I~~L~p~~~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~-G~I~at~~~~~~~kf~~~l~~G~vy~is~ 517 (786)
...+.++..+.|+. ++||+.++++|+|.+.++++++++..|.|++ |.+..+.|.+. +.|++|.+.+
T Consensus 159 ~~~i~~~~~~~~~~-----~~~v~~g~~ik~~~~~~ge~~~~~~~~~d~~~~~~~~~~~~~~--------~~g~~~~ie~ 225 (407)
T COG1599 159 AREIGEESLLSPYQ-----KARVVVGSEIKTFDNQGGESKVFSNELEDEERGVIVFTDWDPS--------QDGDVYRIEG 225 (407)
T ss_pred ccccccccccCccc-----eEEEEecccceeEecCCCccceEeeeecccceeEEEeccCccc--------ccceeeeecC
Confidence 34677888888887 8999999999999999999999999999998 77888888764 9999999999
Q ss_pred eEEeccCCcccccCCceEEEEccc--cEEEEccCCCCCCCCcceeeccCcccccccCCCceeeEEEEEEEcccceeEEee
Q psy15132 518 CTLKPANKKFSSINNDYEMSFTHS--TTVIPCNEDEVGNMPSVKYCFVPLKTIAEISPDENIDVLGVCIDAAELSSVTGK 595 (786)
Q Consensus 518 ~~V~~a~~~y~~~~~~yei~f~~~--T~I~~~~d~~~~~iP~~~~~f~~i~dl~~~~~~~~vDViGvV~~V~~~~~i~~k 595 (786)
.+|+..++++... +.+++.+... +.|.++.+.. .+|..... +...++. +..+| |+.+.+...+..+
T Consensus 226 ~~v~~~~~~~~~~-~~~e~~~~~~~~~~i~~~~~~~--~~~~~~~~-~~~~~~~----~~~v~----v~~~~~c~~~~~~ 293 (407)
T COG1599 226 ARVKTKNKQPEEN-LAEELVLRVEVRVAIEKAEREE--FVDEVKES-VSLVEAD----GAVVD----VTRVPECERVVRK 293 (407)
T ss_pred cEEEEeccccccc-ccceEEEeecceeeccCCCCcc--ccceeecc-cccceec----cceEE----EEECCCceEEEeC
Confidence 9999999988877 9999999987 5555554433 34443332 2222222 23344 7788777777655
Q ss_pred cCCceeeEEEEEEeeccccEEEEEEeccccccccCCCCCEEEEEeEEEeecCCc
Q psy15132 596 TNQKTYMKRDITLVDQSQASVTMTLWGKEAETFDASNKPVIAVKAARVSEFQGN 649 (786)
Q Consensus 596 ~~g~~~~kr~i~l~D~s~~~i~~tLWg~~a~~~~~~~~~vv~i~~~~V~~f~G~ 649 (786)
++.....+++.|.|.+| +++++|||+ +..+....+++.++++.++.++.|+
T Consensus 294 -~~~~~~~~~~~l~D~~g-~~rv~~~~~-~~e~~~~~~~~~~~~~~~~~~~~~~ 344 (407)
T COG1599 294 -GGCKGHGKDIGLDDLTG-KIRVTLWGD-ATEVLINEESVEALKGINVEDASGI 344 (407)
T ss_pred -CCcccccccceEecCce-EEEEecCCC-ceEEEecccchhheeeeeeeeccch
Confidence 57778889999999988 999999998 4445567788889999999999886
No 34
>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=98.97 E-value=4e-09 Score=91.02 Aligned_cols=81 Identities=25% Similarity=0.367 Sum_probs=71.7
Q ss_pred EEEEEEeecCCcceecCCCCCceEEEEEEEcCCCcEEEEEcchhHHHhhhhccCCcEEEEcceEEeccCCcccccCCceE
Q psy15132 456 TIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFNDECNRFHDMIEKDKVYYISNCTLKPANKKFSSINNDYE 535 (786)
Q Consensus 456 ~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~G~I~at~~~~~~~kf~~~l~~G~vy~is~~~V~~a~~~y~~~~~~ye 535 (786)
+|.|||+.+++.|.|.+.+++++++++.|.|++|.|++++|++.+ .+.|++|++|.|.++.++.. .+.++
T Consensus 1 ~v~~~V~~~~~~~~~~~~g~~~~~~~~~l~D~TG~i~~~~W~~~~---~~~~~~G~vv~i~~~~v~~~-------~g~~q 70 (82)
T cd04491 1 SVEGKVLSISEPREFTRDGSEGKVQSGLVGDETGTIRFTLWDEKA---ADDLEPGDVVRIENAYVREF-------NGRLE 70 (82)
T ss_pred CEEEEEEEccCCeEeccCCCeeEEEEEEEECCCCEEEEEEECchh---cccCCCCCEEEEEeEEEEec-------CCcEE
Confidence 478999999999999854557899999999999999999999876 67799999999999999764 37789
Q ss_pred EEEccccEEEE
Q psy15132 536 MSFTHSTTVIP 546 (786)
Q Consensus 536 i~f~~~T~I~~ 546 (786)
|+++..|.|++
T Consensus 71 l~i~~~~~i~~ 81 (82)
T cd04491 71 LSVGKNSEIEK 81 (82)
T ss_pred EEeCCceEEEE
Confidence 99999998875
No 35
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=98.95 E-value=5.6e-09 Score=97.89 Aligned_cols=99 Identities=13% Similarity=0.219 Sum_probs=86.3
Q ss_pred ceeeecccCCCCCceEEEEEEeecCCcceecCCCCCceEEEEEEEcCCCcEEEEEcchhHHHhhhhccCCcEEEEcceEE
Q psy15132 441 QTHPIVSLSPYQNKWTIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFNDECNRFHDMIEKDKVYYISNCTL 520 (786)
Q Consensus 441 ~~~~I~~L~p~~~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~G~I~at~~~~~~~kf~~~l~~G~vy~is~~~V 520 (786)
++.+|++|.|...+..+.++|+.+++.|.+...++.+++.++.|.|++|.|++++|++.++ .|++|+++.|.|+.+
T Consensus 3 ~~~kI~dL~~g~~~v~~~~~V~~i~~~~~~~~k~~~~~v~~~~l~D~TG~I~~tlW~~~a~----~l~~GdvV~I~na~v 78 (129)
T PRK06461 3 MITKIKDLKPGMERVNVTVRVLEVGEPKVIQTKGGPRTISEAVVGDETGRVKLTLWGEQAG----SLKEGEVVEIENAWT 78 (129)
T ss_pred CceEHHHcCCCCCceEEEEEEEEcCCceEEEeCCCceEEEEEEEECCCCEEEEEEeCCccc----cCCCCCEEEEECcEE
Confidence 4679999999988899999999999999988776667899999999999999999998653 589999999999998
Q ss_pred eccCCcccccCCceEEEEccccEEEEccCC
Q psy15132 521 KPANKKFSSINNDYEMSFTHSTTVIPCNED 550 (786)
Q Consensus 521 ~~a~~~y~~~~~~yei~f~~~T~I~~~~d~ 550 (786)
+.. ....+|++++.+.|.+++++
T Consensus 79 ~~f-------~G~lqL~i~~~~~i~~~~~~ 101 (129)
T PRK06461 79 TLY-------RGKVQLNVGKYGSISESDDE 101 (129)
T ss_pred eee-------CCEEEEEECCCEEEEECCcc
Confidence 753 35689999999999988653
No 36
>cd04497 hPOT1_OB1_like hPOT1_OB1_like: A subfamily of OB folds similar to the first OB fold (OB1) of human protection of telomeres 1 protein (hPOT1), the single OB fold of the N-terminal domain of Schizosaccharomyces pombe POT1 (SpPOT1), and the first OB fold of the N-terminal domain of the alpha subunit (OB1Nalpha) of Oxytricha nova telomere end binding protein (OnTEBP). POT1 proteins recognize single-stranded (ss) 3-prime ends of the telomere. A 3-prime ss overhang is conserved in ciliated protozoa, yeast, and mammals. SpPOT1 is essential for telomere maintenance. It binds specifically to the ss G-rich telomeric sequence (GGTTAC) of S. pombe. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. Deletion of the S. pombe pot1+ gene results in a rapid loss of telomere sequences, chromosome mis-segregation and chromosome circularization. hPOT1 is implicated in telomere length regulation. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB
Probab=98.94 E-value=2.9e-09 Score=101.22 Aligned_cols=84 Identities=19% Similarity=0.421 Sum_probs=74.8
Q ss_pred eeccCcccccccCCCceeeEEEEEEEcccceeEEeecCCceeeEEEEEEeeccc---cEEEEEEecccccccc-CCCCCE
Q psy15132 560 YCFVPLKTIAEISPDENIDVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQ---ASVTMTLWGKEAETFD-ASNKPV 635 (786)
Q Consensus 560 ~~f~~i~dl~~~~~~~~vDViGvV~~V~~~~~i~~k~~g~~~~kr~i~l~D~s~---~~i~~tLWg~~a~~~~-~~~~~v 635 (786)
|+|++|++|.. ..+..|||||+|++++++.. ++|++ .++.|.|.|.|+ ..+++++|++.++.+. ...|+|
T Consensus 1 ~~f~~i~~~~~-~~~~~v~vigVV~~~~~p~~----s~g~d-~~~tl~i~D~S~~~~~~l~v~~F~~~~~~LP~v~~GDV 74 (138)
T cd04497 1 YKYTPLSSALK-ESGGSVNVIGVVVDAGPPVR----SKGTD-YCCTLTITDPSLANSDGLTVKLFRPNEESLPIVKVGDI 74 (138)
T ss_pred CceEeHHHHHh-ccCCeEEEEEEEeecCCCcc----cCCCc-EEEEEEEECCCCCCCCcEEEEEECCChhhCCCCCCCCE
Confidence 57899999997 57889999999999999763 34665 789999999998 7899999999999988 688999
Q ss_pred EEEEeEEEeecCCc
Q psy15132 636 IAVKAARVSEFQGN 649 (786)
Q Consensus 636 v~i~~~~V~~f~G~ 649 (786)
|++++++|+.|+|+
T Consensus 75 Ill~~~kv~~~~g~ 88 (138)
T cd04497 75 ILLRRVKIQSYNGK 88 (138)
T ss_pred EEEEEEEEEEECCc
Confidence 99999999999996
No 37
>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=98.94 E-value=1.1e-08 Score=88.36 Aligned_cols=81 Identities=23% Similarity=0.323 Sum_probs=72.1
Q ss_pred EEEEEEEEeccceeEeeccCCceeeEEEEEEEeCCCCEEEEEecccccccccCCCCcEEEEEeEEEeeeCCceeeeecce
Q psy15132 61 DVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWGKEAETFDASNKPVIAVKAARVSEFQGGKTLSLSMS 140 (786)
Q Consensus 61 DViGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~s~~~i~~tLWg~~a~~~~~~~~~Vi~i~~~kv~~f~g~~~ls~~~~ 140 (786)
+|+|.|++++++.+++ + +|+....+++.|.|+|| +|++++|++.+ ......+.++.++++++++|+|..+|++...
T Consensus 1 ~v~~~V~~~~~~~~~~-~-~g~~~~~~~~~l~D~TG-~i~~~~W~~~~-~~~~~~G~vv~i~~~~v~~~~g~~ql~i~~~ 76 (82)
T cd04491 1 SVEGKVLSISEPREFT-R-DGSEGKVQSGLVGDETG-TIRFTLWDEKA-ADDLEPGDVVRIENAYVREFNGRLELSVGKN 76 (82)
T ss_pred CEEEEEEEccCCeEec-c-CCCeeEEEEEEEECCCC-EEEEEEECchh-cccCCCCCEEEEEeEEEEecCCcEEEEeCCc
Confidence 4899999999999998 5 57788899999999999 99999999987 4445788899999999999999999999988
Q ss_pred eEEEE
Q psy15132 141 SVLSL 145 (786)
Q Consensus 141 s~i~~ 145 (786)
|.|..
T Consensus 77 ~~i~~ 81 (82)
T cd04491 77 SEIEK 81 (82)
T ss_pred eEEEE
Confidence 88764
No 38
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=98.87 E-value=2.5e-08 Score=93.52 Aligned_cols=94 Identities=19% Similarity=0.360 Sum_probs=78.6
Q ss_pred cCccchhccCCC-CceEEEEEEEEeccceeEeeccCCceeeEEEEEEEeCCCCEEEEEecccccccccCCCCcEEEEEeE
Q psy15132 46 VPLKTIAEISPD-ENIDVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWGKEAETFDASNKPVIAVKAA 124 (786)
Q Consensus 46 ~~~~~i~~~~~~-~~vDViGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~s~~~i~~tLWg~~a~~~~~~~~~Vi~i~~~ 124 (786)
++++|| .++ ..|+++|+|+++++.+.+.+|+ + ....++++|.|+|| +|.+|||++.|..+ ..+.||.|+++
T Consensus 5 ~kI~dL---~~g~~~v~~~~~V~~i~~~~~~~~k~-~-~~~v~~~~l~D~TG-~I~~tlW~~~a~~l--~~GdvV~I~na 76 (129)
T PRK06461 5 TKIKDL---KPGMERVNVTVRVLEVGEPKVIQTKG-G-PRTISEAVVGDETG-RVKLTLWGEQAGSL--KEGEVVEIENA 76 (129)
T ss_pred eEHHHc---CCCCCceEEEEEEEEcCCceEEEeCC-C-ceEEEEEEEECCCC-EEEEEEeCCccccC--CCCCEEEEECc
Confidence 344555 445 6899999999999999988873 3 45678999999999 79999999988765 56899999999
Q ss_pred EEeeeCCceeeeecceeEEEECC
Q psy15132 125 RVSEFQGGKTLSLSMSSVLSLNP 147 (786)
Q Consensus 125 kv~~f~g~~~ls~~~~s~i~~np 147 (786)
++++|+|..+|+++..|.|..-+
T Consensus 77 ~v~~f~G~lqL~i~~~~~i~~~~ 99 (129)
T PRK06461 77 WTTLYRGKVQLNVGKYGSISESD 99 (129)
T ss_pred EEeeeCCEEEEEECCCEEEEECC
Confidence 99999999999999888887543
No 39
>KOG0851|consensus
Probab=98.85 E-value=4.2e-08 Score=102.89 Aligned_cols=177 Identities=20% Similarity=0.338 Sum_probs=133.0
Q ss_pred ceeeecccCCCCCceEEEEEEeecCCcceecCC-CCCceEEEEEEEcCCCc-EEEEEcchhHHHhhhhccCCcEEEEcce
Q psy15132 441 QTHPIVSLSPYQNKWTIKARVTNKTPIREWNNA-RGSGKLFSIDLLDESGE-IRATMFNDECNRFHDMIEKDKVYYISNC 518 (786)
Q Consensus 441 ~~~~I~~L~p~~~~w~I~~RV~~k~~~r~~~~~-~~~g~~~~~~L~D~~G~-I~at~~~~~~~kf~~~l~~G~vy~is~~ 518 (786)
.++++.+|+|..++|.|.++|+ +.|... ...+..+.|+|.|+.|. |.|++......+|.+.|++|+++.|..|
T Consensus 3 ~~~~l~~l~~~~t~w~i~~~vl-----~v~~~~~~~~~~~~~~il~D~~~~~i~a~i~~~~~~~~~~~l~~~~w~~i~~f 77 (246)
T KOG0851|consen 3 GFHRLRDLSPSITGWRIQVKVL-----RVWKKYSNPNGEELRLVLADEHGVKIEATVGRRLSSKYEDNLIENEWKIITTF 77 (246)
T ss_pred cccchhhcCcCceeeEEEEEEE-----EEEEecCCCCccEEEEEEEecCCcEEEEEcchHHHhhhhhheecceeEEeeee
Confidence 5789999999999999999999 566542 23468899999999995 9999999999999999999999999999
Q ss_pred EEeccCCcccccCCceEEEEccccEEEEccCCCCCCCCcc-eeeccCccccccc--CCCceeeEEE-EEEEcccceeEEe
Q psy15132 519 TLKPANKKFSSINNDYEMSFTHSTTVIPCNEDEVGNMPSV-KYCFVPLKTIAEI--SPDENIDVLG-VCIDAAELSSVTG 594 (786)
Q Consensus 519 ~V~~a~~~y~~~~~~yei~f~~~T~I~~~~d~~~~~iP~~-~~~f~~i~dl~~~--~~~~~vDViG-vV~~V~~~~~i~~ 594 (786)
.|.++...++.+.|.|++.|...+.+...... .|-. ..+|.++..+.+. .....+|++| .+..|+.+..-.
T Consensus 78 ~v~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~v~~~~~~~~~v~~~~~~~~~v~~~~~~~- 152 (246)
T KOG0851|consen 78 GVNPNSGQVRATTHSFKINFMDFTVVTSSDTR----LPCTPWGKFTPFDSIVEDKSDKRVLVDLIGVAVYDVSQLTVTP- 152 (246)
T ss_pred eecccccceeeeeeEEEEEeccceeeccCCCC----ccceeccccchhhhhhccccCCcEEEEeeceeEEEeeeeEecc-
Confidence 99999999999999999999877777655332 2222 4567777555554 3567899988 677776654221
Q ss_pred ecCCceeeEEEEEEeeccc-----cEEEEEEeccccccc
Q psy15132 595 KTNQKTYMKRDITLVDQSQ-----ASVTMTLWGKEAETF 628 (786)
Q Consensus 595 k~~g~~~~kr~i~l~D~s~-----~~i~~tLWg~~a~~~ 628 (786)
+.++....+.+...+.++ ....|...++.|..|
T Consensus 153 -~~~~~~~~~~~~~~~~~~~~~~~~~~~c~~~~~~~~~~ 190 (246)
T KOG0851|consen 153 -AIDTDVDGFYLTFKICNKSKFSKPVLWCEACGEQATDF 190 (246)
T ss_pred -cccCCcceEEEEEeecccccccCceEEehhhcchHHhh
Confidence 135677788888888664 234444444444444
No 40
>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=98.73 E-value=2.1e-07 Score=104.62 Aligned_cols=186 Identities=17% Similarity=0.215 Sum_probs=137.9
Q ss_pred CceeeecccCCCCCceEEEEEEeecCCcceecCCCCC-ceEEEEEEEcCCCcEEE-EEcchhHHHhhhhccCCcEEEEcc
Q psy15132 440 VQTHPIVSLSPYQNKWTIKARVTNKTPIREWNNARGS-GKLFSIDLLDESGEIRA-TMFNDECNRFHDMIEKDKVYYISN 517 (786)
Q Consensus 440 ~~~~~I~~L~p~~~~w~I~~RV~~k~~~r~~~~~~~~-g~~~~~~L~D~~G~I~a-t~~~~~~~kf~~~l~~G~vy~is~ 517 (786)
..+.+|+++.+...+-.+.+||...+..+.+.+..+. +++.+..+.|+.|+++. +.|...+. ..+++|+++.|.+
T Consensus 47 ~~~~~i~~~~~~~~~~~v~~~V~~~~e~~~~~~k~g~~~~l~~~~v~Detg~v~~~~~~~~~a~---~~~e~Gdv~~i~~ 123 (407)
T COG1599 47 ESIGKISDISEASSRVNVTGRVLSIGEKKTFDRKRGAEGKLAEVLVGDETGSVKTVTLWNIAAL---EKLEPGDVIRIRN 123 (407)
T ss_pred hhcccccccchhhccccEEEEECccccceeeecccccccceEEEEEecCCCCEEEEeecccccc---ccCCccceEEecC
Confidence 3567999999999999999999999988888876664 89999999999999999 79998653 3589999999999
Q ss_pred eEEeccCCcccccCCceEEEEccccEEEEccCCCCCCCCcceeeccCcccccccCCCceeeEEEEEEEcccceeEEeecC
Q psy15132 518 CTLKPANKKFSSINNDYEMSFTHSTTVIPCNEDEVGNMPSVKYCFVPLKTIAEISPDENIDVLGVCIDAAELSSVTGKTN 597 (786)
Q Consensus 518 ~~V~~a~~~y~~~~~~yei~f~~~T~I~~~~d~~~~~iP~~~~~f~~i~dl~~~~~~~~vDViGvV~~V~~~~~i~~k~~ 597 (786)
+.+... .+..++.++..+.+...++.. ..+...+.-..+.++.... ..+ .+.|..-+++.++...
T Consensus 124 ~~~~~~-------~~~~~~~~~~~~~v~~~~~~~--~~~~~~~~~~~i~~~~~~~---~~~-~~~v~~g~~ik~~~~~-- 188 (407)
T COG1599 124 AYTSLY-------RGGKRLSVGRVGSVADVDDEE--DEARESEDAREIGEESLLS---PYQ-KARVVVGSEIKTFDNQ-- 188 (407)
T ss_pred cccccc-------cCceeeecccccccccCchhh--ccccccccccccccccccC---ccc-eEEEEecccceeEecC--
Confidence 876553 356788999988888776643 1222222223333333321 122 6677777777777654
Q ss_pred CceeeEEEEEEeeccccEEEEEEeccccccccCCCCCEEEEEeEEEeecCCc
Q psy15132 598 QKTYMKRDITLVDQSQASVTMTLWGKEAETFDASNKPVIAVKAARVSEFQGN 649 (786)
Q Consensus 598 g~~~~kr~i~l~D~s~~~i~~tLWg~~a~~~~~~~~~vv~i~~~~V~~f~G~ 649 (786)
+.+...+...|.|++-..+.+++|... ..+++..+.+++|..|++.
T Consensus 189 ~ge~~~~~~~~~d~~~~~~~~~~~~~~------~~g~~~~ie~~~v~~~~~~ 234 (407)
T COG1599 189 GGESKVFSNELEDEERGVIVFTDWDPS------QDGDVYRIEGARVKTKNKQ 234 (407)
T ss_pred CCccceEeeeecccceeEEEeccCccc------ccceeeeecCcEEEEeccc
Confidence 566778889999998448999999875 4567788888888888764
No 41
>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=97.77 E-value=6.7e-05 Score=62.99 Aligned_cols=71 Identities=27% Similarity=0.473 Sum_probs=56.5
Q ss_pred eEEEEEEeecCCcceecCCCCCceEEEEEEEcCCCcEEEEEcchhHHHhhhhccCCcEEEEcceEEeccCCcccccCCce
Q psy15132 455 WTIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFNDECNRFHDMIEKDKVYYISNCTLKPANKKFSSINNDY 534 (786)
Q Consensus 455 w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~G~I~at~~~~~~~kf~~~l~~G~vy~is~~~V~~a~~~y~~~~~~y 534 (786)
++|.|+|.++. ++.++++.++|.|++|.|++++|++...++.+.|++|+++.+. +.++..+.. ++
T Consensus 1 V~v~G~V~~~~--------~~~~~~~~~~l~D~tg~i~~~~~~~~~~~~~~~l~~g~~v~v~-G~v~~~~~~------~~ 65 (75)
T PF01336_consen 1 VTVEGRVTSIR--------RSGGKIVFFTLEDGTGSIQVVFFNEEYERFREKLKEGDIVRVR-GKVKRYNGG------EL 65 (75)
T ss_dssp EEEEEEEEEEE--------EEETTEEEEEEEETTEEEEEEEETHHHHHHHHTS-TTSEEEEE-EEEEEETTS------SE
T ss_pred CEEEEEEEEEE--------cCCCCEEEEEEEECCccEEEEEccHHhhHHhhcCCCCeEEEEE-EEEEEECCc------cE
Confidence 47899999754 2346899999999999999999998889999999999999999 788765322 35
Q ss_pred EEEEcc
Q psy15132 535 EMSFTH 540 (786)
Q Consensus 535 ei~f~~ 540 (786)
+|....
T Consensus 66 ~l~~~~ 71 (75)
T PF01336_consen 66 ELIVPK 71 (75)
T ss_dssp EEEEEE
T ss_pred EEEECE
Confidence 665543
No 42
>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=97.77 E-value=0.00031 Score=67.58 Aligned_cols=97 Identities=18% Similarity=0.286 Sum_probs=73.7
Q ss_pred ecCccchhccCCCCceEEEEEEEEeccceeEeeccCCceeeEEEEEEEeCCC-------CEEEEEecccccccccC--CC
Q psy15132 45 FVPLKTIAEISPDENIDVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQ-------ASVTMTLWGKEAETFDA--SN 115 (786)
Q Consensus 45 f~~~~~i~~~~~~~~vDViGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~s~-------~~i~~tLWg~~a~~~~~--~~ 115 (786)
|+++.+.. ...+..+||+|+|++.++.....++ |+ -....|+|.|.|. ..|.|.++-+..+.+.. ..
T Consensus 1 ~~~l~~~~-~~~~~~vnvigVV~~~~~p~~~~t~--g~-D~~~tl~i~D~S~~~~~~~~~~l~v~iF~~~~~~LP~v~~~ 76 (146)
T PF02765_consen 1 YTPLSTAK-EKFGKFVNVIGVVVDFSPPNPKKTR--GT-DYMCTLTITDPSLNDSNQKLSGLTVNIFRPHKESLPNVKSV 76 (146)
T ss_dssp BCCGGGSC-TTSSEEEEEEEEEEEEEEECTEEES--SS-CEEEEEEEEBTTCSCSSCCCCEEEEEEEESSHHHSCTTCST
T ss_pred Cccchhhh-hcCCCEEEEEEEEEEccCCcceEcC--CC-cEEEEEEEECCCCCccccccCCEEEEEECCCHHHCCCCCCC
Confidence 44555332 3467899999999999988545554 43 4688999999986 68999999888888864 34
Q ss_pred CcEEEEEeEEEeeeCCceeeeecce--eEEEE
Q psy15132 116 KPVIAVKAARVSEFQGGKTLSLSMS--SVLSL 145 (786)
Q Consensus 116 ~~Vi~i~~~kv~~f~g~~~ls~~~~--s~i~~ 145 (786)
|+||.++.++|..|+|...+-.... |.+.+
T Consensus 77 GDii~l~r~kv~~~~~~~~~~~~~~~~ss~~v 108 (146)
T PF02765_consen 77 GDIIRLRRVKVQSYNGKPQGLSNSTSNSSWAV 108 (146)
T ss_dssp THEEEEEEEEEEEETTEEEEEEECECTEEEEE
T ss_pred CCEEEEEEEEEEEECCEEEEEecCCCcEEEEE
Confidence 9999999999999998877654443 66644
No 43
>cd04474 RPA1_DBD_A RPA1_DBD_A: A subfamily of OB folds corresponding to the second OB fold, the ssDNA-binding domain (DBD)-A, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change. Although ScRPA and the hRPA have similar ssDNA-binding properties, they differ funct
Probab=97.66 E-value=0.00015 Score=65.43 Aligned_cols=81 Identities=9% Similarity=0.164 Sum_probs=65.4
Q ss_pred CcccccccCCCceeeEEEEEEEcccceeEEeecCCceeeEEEEEEeeccccEEEEEEecccccccc--CCCCCEEEEEeE
Q psy15132 564 PLKTIAEISPDENIDVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWGKEAETFD--ASNKPVIAVKAA 641 (786)
Q Consensus 564 ~i~dl~~~~~~~~vDViGvV~~V~~~~~i~~k~~g~~~~kr~i~l~D~s~~~i~~tLWg~~a~~~~--~~~~~vv~i~~~ 641 (786)
||++|... ....-+.|.|+..+++..+..+. .+....++.|.|+.|.+|++|+|++.++.|. ...|.|+.|.++
T Consensus 1 pI~~L~p~--~~~~~I~~rV~~k~~~~~f~~~~--~~g~~~~~~l~De~~~~I~~t~~~~~~~~f~~~l~eG~vy~i~~~ 76 (104)
T cd04474 1 PISSLNPY--QNKWTIKARVTNKSDIRTWSNAR--GEGKLFSFDLLDEDGGEIRATFFNDAVDKFYDLLEVGKVYYISKG 76 (104)
T ss_pred ChhHccCC--CCcEEEEEEEeeccccccccCCC--CCcEEEEEEEEECCCCEEEEEEehHHHHHhhcccccccEEEEecc
Confidence 45666654 34578999999999999887653 3455669999999777999999999999886 578999999999
Q ss_pred EEeecCC
Q psy15132 642 RVSEFQG 648 (786)
Q Consensus 642 ~V~~f~G 648 (786)
+|+.-++
T Consensus 77 ~V~~a~~ 83 (104)
T cd04474 77 SVKVANK 83 (104)
T ss_pred EEeeccc
Confidence 9986544
No 44
>KOG3416|consensus
Probab=97.36 E-value=0.00082 Score=60.63 Aligned_cols=71 Identities=15% Similarity=0.203 Sum_probs=56.8
Q ss_pred eeeecccCCCCCceEEEEEEeecCCcceecCCCCCc-eEEEEEEEcCCCcEEEEEcchhHHHhhhhccCCcEEEEcceEE
Q psy15132 442 THPIVSLSPYQNKWTIKARVTNKTPIREWNNARGSG-KLFSIDLLDESGEIRATMFNDECNRFHDMIEKDKVYYISNCTL 520 (786)
Q Consensus 442 ~~~I~~L~p~~~~w~I~~RV~~k~~~r~~~~~~~~g-~~~~~~L~D~~G~I~at~~~~~~~kf~~~l~~G~vy~is~~~V 520 (786)
..+|+||.|+.++..+..-|+.-+..+.- .+| .+.++-++|++|.|++.+|++. -..|+.||++.++++.-
T Consensus 4 ~i~ikdi~P~~kN~~v~fIvl~~g~~tkT----kdg~~v~~~kVaD~TgsI~isvW~e~----~~~~~PGDIirLt~Gy~ 75 (134)
T KOG3416|consen 4 MIFIKDIKPGLKNINVTFIVLEYGRATKT----KDGHEVRSCKVADETGSINISVWDEE----GCLIQPGDIIRLTGGYA 75 (134)
T ss_pred chhHhhcChhhhcceEEEEEEeeceeeec----cCCCEEEEEEEecccceEEEEEecCc----CcccCCccEEEecccch
Confidence 36899999999998888777754433322 134 8899999999999999999965 46799999999999754
No 45
>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=97.30 E-value=0.0013 Score=63.17 Aligned_cols=84 Identities=19% Similarity=0.385 Sum_probs=65.0
Q ss_pred ccCcccccccCCCceeeEEEEEEEcccceeEEeecCCceeeEEEEEEeeccc-------cEEEEEEecccccccc-CC-C
Q psy15132 562 FVPLKTIAEISPDENIDVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQ-------ASVTMTLWGKEAETFD-AS-N 632 (786)
Q Consensus 562 f~~i~dl~~~~~~~~vDViGvV~~V~~~~~i~~k~~g~~~~kr~i~l~D~s~-------~~i~~tLWg~~a~~~~-~~-~ 632 (786)
|+|+++... ..+..|||+|+|++..+.....+| |++ ....++|.|.|. ..|.|.++.+..+.+. .. .
T Consensus 1 ~~~l~~~~~-~~~~~vnvigVV~~~~~p~~~~t~--g~D-~~~tl~i~D~S~~~~~~~~~~l~v~iF~~~~~~LP~v~~~ 76 (146)
T PF02765_consen 1 YTPLSTAKE-KFGKFVNVIGVVVDFSPPNPKKTR--GTD-YMCTLTITDPSLNDSNQKLSGLTVNIFRPHKESLPNVKSV 76 (146)
T ss_dssp BCCGGGSCT-TSSEEEEEEEEEEEEEEECTEEES--SSC-EEEEEEEEBTTCSCSSCCCCEEEEEEEESSHHHSCTTCST
T ss_pred Cccchhhhh-cCCCEEEEEEEEEEccCCcceEcC--CCc-EEEEEEEECCCCCccccccCCEEEEEECCCHHHCCCCCCC
Confidence 455553332 357899999999999887444444 543 467999999995 5899999998888887 33 4
Q ss_pred CCEEEEEeEEEeecCCc
Q psy15132 633 KPVIAVKAARVSEFQGN 649 (786)
Q Consensus 633 ~~vv~i~~~~V~~f~G~ 649 (786)
|+||.+++++|..|+|+
T Consensus 77 GDii~l~r~kv~~~~~~ 93 (146)
T PF02765_consen 77 GDIIRLRRVKVQSYNGK 93 (146)
T ss_dssp THEEEEEEEEEEEETTE
T ss_pred CCEEEEEEEEEEEECCE
Confidence 99999999999999996
No 46
>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=97.24 E-value=0.00035 Score=61.97 Aligned_cols=48 Identities=21% Similarity=0.489 Sum_probs=41.7
Q ss_pred ccccccCCCcCCCCCeEEEEccCcEEEEccCCCCCCCCceeEeecCccchhc
Q psy15132 2 LAAPANKKFSSINNDYEMSFTHSTTVIPCNEDEVGNMPSVKYCFVPLKTIAE 53 (786)
Q Consensus 2 ~v~~A~~~y~~~~~~yei~f~~~T~I~~~~d~~~~~iP~~~~~f~~~~~i~~ 53 (786)
.|.++.++|++++|+|+|.|..+|.|.++++. ...| .|+|++|++|.+
T Consensus 40 ~V~~~~~~yr~t~h~y~I~f~~~T~V~~~~~~--~~~~--~~~f~~F~~I~~ 87 (95)
T PF02721_consen 40 TVSPNSGSYRPTDHKYKINFMPNTKVTEIDPP--SDPP--FFNFTPFDEILE 87 (95)
T ss_pred EEEeCCCceeccCCCEEEEECCcCeEEECCCC--CCCc--eEeecCHHHHhc
Confidence 47889999999999999999999999999653 3344 899999999985
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=96.42 E-value=0.014 Score=47.88 Aligned_cols=59 Identities=29% Similarity=0.518 Sum_probs=48.7
Q ss_pred EEEEEeecCCcceecCCCCCceEEEEEEEcCC-CcEEEEEcchhHHHhhhhccCCcEEEEcceEEec
Q psy15132 457 IKARVTNKTPIREWNNARGSGKLFSIDLLDES-GEIRATMFNDECNRFHDMIEKDKVYYISNCTLKP 522 (786)
Q Consensus 457 I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~-G~I~at~~~~~~~kf~~~l~~G~vy~is~~~V~~ 522 (786)
+.++|+.....++ .+..+.+.|.|.+ |.|.+++|.+..+.+...+++|+++.+. +++..
T Consensus 2 v~g~v~~~~~~~~------~~~~~~~~l~D~~~~~i~~~~~~~~~~~~~~~~~~g~~v~v~-g~v~~ 61 (75)
T cd03524 2 IVGIVVAVEEIRT------EGKVLIFTLTDGTGGTIRVTLFGELAEELENLLKEGQVVYIK-GKVKK 61 (75)
T ss_pred eEEEEEeeccccc------CCeEEEEEEEcCCCCEEEEEEEchHHHHHHhhccCCCEEEEE-EEEEe
Confidence 6678886554433 2367899999999 8899999999988998999999999999 88754
No 48
>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=96.18 E-value=0.034 Score=46.34 Aligned_cols=68 Identities=21% Similarity=0.356 Sum_probs=49.6
Q ss_pred eEEEEEEEEeccceeEeeccCCceeeEEEEEEEeCCCCEEEEEeccccccccc--CCCCcEEEEEeEEEeeeCCc-eeee
Q psy15132 60 IDVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWGKEAETFD--ASNKPVIAVKAARVSEFQGG-KTLS 136 (786)
Q Consensus 60 vDViGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~s~~~i~~tLWg~~a~~~~--~~~~~Vi~i~~~kv~~f~g~-~~ls 136 (786)
|-|.|.|+++. ++.+ ....++|.|.|| ++.+++|++.+..+. ...+.+|.+. +++..|+++ .+|.
T Consensus 1 V~v~G~V~~~~-------~~~~---~~~~~~l~D~tg-~i~~~~~~~~~~~~~~~l~~g~~v~v~-G~v~~~~~~~~~l~ 68 (75)
T PF01336_consen 1 VTVEGRVTSIR-------RSGG---KIVFFTLEDGTG-SIQVVFFNEEYERFREKLKEGDIVRVR-GKVKRYNGGELELI 68 (75)
T ss_dssp EEEEEEEEEEE-------EEET---TEEEEEEEETTE-EEEEEEETHHHHHHHHTS-TTSEEEEE-EEEEEETTSSEEEE
T ss_pred CEEEEEEEEEE-------cCCC---CEEEEEEEECCc-cEEEEEccHHhhHHhhcCCCCeEEEEE-EEEEEECCccEEEE
Confidence 46889988886 2112 355799999997 999999995544432 3688888888 789999887 7776
Q ss_pred ecc
Q psy15132 137 LSM 139 (786)
Q Consensus 137 ~~~ 139 (786)
+..
T Consensus 69 ~~~ 71 (75)
T PF01336_consen 69 VPK 71 (75)
T ss_dssp EEE
T ss_pred ECE
Confidence 543
No 49
>KOG3416|consensus
Probab=95.95 E-value=0.044 Score=49.75 Aligned_cols=86 Identities=21% Similarity=0.321 Sum_probs=63.7
Q ss_pred ccchhccCCCCceEEEEEEEEeccceeEeeccCCceeeEEEEEEEeCCCCEEEEEecccccccccCCCCcEEEEEeEEEe
Q psy15132 48 LKTIAEISPDENIDVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWGKEAETFDASNKPVIAVKAARVS 127 (786)
Q Consensus 48 ~~~i~~~~~~~~vDViGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~s~~~i~~tLWg~~a~~~~~~~~~Vi~i~~~kv~ 127 (786)
+.||.... ..+.|+=+|.+.+..+. +| +|+ ..|.....|+|| +|++.+|+|....| +.++||-+.++.-+
T Consensus 7 ikdi~P~~--kN~~v~fIvl~~g~~tk--Tk-dg~--~v~~~kVaD~Tg-sI~isvW~e~~~~~--~PGDIirLt~Gy~S 76 (134)
T KOG3416|consen 7 IKDIKPGL--KNINVTFIVLEYGRATK--TK-DGH--EVRSCKVADETG-SINISVWDEEGCLI--QPGDIIRLTGGYAS 76 (134)
T ss_pred HhhcChhh--hcceEEEEEEeeceeee--cc-CCC--EEEEEEEecccc-eEEEEEecCcCccc--CCccEEEecccchh
Confidence 45554321 34556677788776532 33 465 468889999998 99999999877665 67899999999999
Q ss_pred eeCCceeeeecceeEE
Q psy15132 128 EFQGGKTLSLSMSSVL 143 (786)
Q Consensus 128 ~f~g~~~ls~~~~s~i 143 (786)
-|+|+..|.++.+..+
T Consensus 77 i~qg~LtL~~GK~Ge~ 92 (134)
T KOG3416|consen 77 IFQGCLTLYVGKGGEV 92 (134)
T ss_pred hhcCceEEEecCCceE
Confidence 9999999988854433
No 50
>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=95.77 E-value=0.053 Score=47.70 Aligned_cols=65 Identities=15% Similarity=0.331 Sum_probs=46.9
Q ss_pred EEEEEEEEeccceeEeeccCCceeeEEEEEEEeCCCCEEEEEeccccc---------------------cccc-CCCCcE
Q psy15132 61 DVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWGKEA---------------------ETFD-ASNKPV 118 (786)
Q Consensus 61 DViGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~s~~~i~~tLWg~~a---------------------~~~~-~~~~~V 118 (786)
|++|+|.++.+ + . ....++|-|.|| .|+|.+|.... .... ...+.+
T Consensus 1 ~ivG~V~sv~~------~----~-~~~~~tLdDgTG-~Ie~~~W~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~G~v 68 (92)
T cd04483 1 DILGTVVSRRE------R----E-TFYSFGVDDGTG-VVNCVCWKNLSYAEVSSRSDAARILKSALMALKQAKVLEIGDL 68 (92)
T ss_pred CeEEEEEEEEe------c----C-CeEEEEEecCCc-eEEEEEEcCcCcccccccccccccccccccccccccccCCCCE
Confidence 58899988732 1 1 356899999999 89999998753 1111 245666
Q ss_pred EEEEeEEEeeeCCceeeeec
Q psy15132 119 IAVKAARVSEFQGGKTLSLS 138 (786)
Q Consensus 119 i~i~~~kv~~f~g~~~ls~~ 138 (786)
+-++| +++.|+|.+.|.+.
T Consensus 69 vrV~G-~i~~frg~~ql~i~ 87 (92)
T cd04483 69 LRVRG-SIRTYRGEREINAS 87 (92)
T ss_pred EEEEE-EEeccCCeeEEEEE
Confidence 66764 89999998888764
No 51
>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=95.72 E-value=0.042 Score=48.36 Aligned_cols=36 Identities=19% Similarity=0.279 Sum_probs=28.5
Q ss_pred eEEEEEEEcccceeEEeecCCceeeEEEEEEeeccccEEEEEEecccc
Q psy15132 578 DVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWGKEA 625 (786)
Q Consensus 578 DViGvV~~V~~~~~i~~k~~g~~~~kr~i~l~D~s~~~i~~tLWg~~a 625 (786)
|++|+|.++.+. .....++|.|.|| .|+|.+|....
T Consensus 1 ~ivG~V~sv~~~-----------~~~~~~tLdDgTG-~Ie~~~W~~~~ 36 (92)
T cd04483 1 DILGTVVSRRER-----------ETFYSFGVDDGTG-VVNCVCWKNLS 36 (92)
T ss_pred CeEEEEEEEEec-----------CCeEEEEEecCCc-eEEEEEEcCcC
Confidence 689999987432 1357899999999 89999998753
No 52
>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=95.64 E-value=0.068 Score=43.67 Aligned_cols=68 Identities=24% Similarity=0.460 Sum_probs=50.4
Q ss_pred EEEEEEEEeccceeEeeccCCceeeEEEEEEEeCCCCEEEEEeccccccccc--CCCCcEEEEEeEEEeeeCCceeeee
Q psy15132 61 DVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWGKEAETFD--ASNKPVIAVKAARVSEFQGGKTLSL 137 (786)
Q Consensus 61 DViGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~s~~~i~~tLWg~~a~~~~--~~~~~Vi~i~~~kv~~f~g~~~ls~ 137 (786)
++.|+|.++.+..+ |+ ....++|.|.+|.++++++|.+....+. ...+.++.+. +++..|++...|.+
T Consensus 1 ~v~g~v~~~~~~~~------~~--~~~~~~l~D~~~~~i~~~~~~~~~~~~~~~~~~g~~v~v~-g~v~~~~~~~~l~~ 70 (75)
T cd03524 1 TIVGIVVAVEEIRT------EG--KVLIFTLTDGTGGTIRVTLFGELAEELENLLKEGQVVYIK-GKVKKFRGRLQLIV 70 (75)
T ss_pred CeEEEEEeeccccc------CC--eEEEEEEEcCCCCEEEEEEEchHHHHHHhhccCCCEEEEE-EEEEecCCeEEEEe
Confidence 47899988866543 32 3568899999966999999999877652 3667788887 78888876666654
No 53
>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=94.91 E-value=0.19 Score=44.20 Aligned_cols=66 Identities=17% Similarity=0.325 Sum_probs=47.5
Q ss_pred eEEEEEEEEeccceeEeeccCCceeeEEEEEEEeCCCCEEEEEecccccc----ccc-CCCCcEEEEEeEEEeeeCCcee
Q psy15132 60 IDVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWGKEAE----TFD-ASNKPVIAVKAARVSEFQGGKT 134 (786)
Q Consensus 60 vDViGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~s~~~i~~tLWg~~a~----~~~-~~~~~Vi~i~~~kv~~f~g~~~ 134 (786)
|.++|+|+++.+- + ....++|.|.|| +|++.+|..... ... ...+.++-+.| +++.|+|.+.
T Consensus 2 v~~vG~V~~~~~~--------~---~~~~~tL~D~TG-~I~~~~W~~~~~~~~~~~~~~~~g~~v~v~G-~v~~~~g~~q 68 (95)
T cd04478 2 VTLVGVVRNVEEQ--------S---TNITYTIDDGTG-TIEVRQWLDDDNDDSSEVEPIEEGTYVRVFG-NLKSFQGKKS 68 (95)
T ss_pred EEEEEEEEeeeEc--------c---cEEEEEEECCCC-cEEEEEeCCCCCcccccccccccCCEEEEEE-EEcccCCeeE
Confidence 6788998887432 1 356899999999 899999986643 221 24566665555 7899998888
Q ss_pred eeec
Q psy15132 135 LSLS 138 (786)
Q Consensus 135 ls~~ 138 (786)
|...
T Consensus 69 l~i~ 72 (95)
T cd04478 69 IMAF 72 (95)
T ss_pred EEEE
Confidence 8754
No 54
>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=94.69 E-value=0.19 Score=41.54 Aligned_cols=60 Identities=17% Similarity=0.253 Sum_probs=41.5
Q ss_pred EEEEEEeecCCcceecCCCCCceEEEEEEEcCCCcEEEEEcchhHHHhhhhccCCcEEEEcceEEec
Q psy15132 456 TIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFNDECNRFHDMIEKDKVYYISNCTLKP 522 (786)
Q Consensus 456 ~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~G~I~at~~~~~~~kf~~~l~~G~vy~is~~~V~~ 522 (786)
+|.|+|..... + ..+ .++.+.+.+.|++|.|.+++|+.. ......|++|+.|.+.+ .+..
T Consensus 1 ~i~~~V~~~~~-~---~~~-~~~~~~~~~~D~~g~i~~~~F~~~-~~~~~~~~~G~~~~v~G-kv~~ 60 (75)
T cd04488 1 TVEGTVVSVEV-V---PRR-GRRRLKVTLSDGTGTLTLVFFNFQ-PYLKKQLPPGTRVRVSG-KVKR 60 (75)
T ss_pred CEEEEEEEEEe-c---cCC-CccEEEEEEEcCCCEEEEEEECCC-HHHHhcCCCCCEEEEEE-EEee
Confidence 36788875422 1 111 246899999999999999999831 12356799999998875 4433
No 55
>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=94.35 E-value=0.19 Score=42.40 Aligned_cols=43 Identities=16% Similarity=0.498 Sum_probs=37.5
Q ss_pred eEEEEEEEcCCCcEEEEEcchhHHHhhhhccCCcEEEEcceEEe
Q psy15132 478 KLFSIDLLDESGEIRATMFNDECNRFHDMIEKDKVYYISNCTLK 521 (786)
Q Consensus 478 ~~~~~~L~D~~G~I~at~~~~~~~kf~~~l~~G~vy~is~~~V~ 521 (786)
.++.+.|.|.+|.+.+++|++...++.+.|++|.+|.+.+ .+.
T Consensus 19 ~~~~~~l~D~tg~~~~~~f~~~~~~~~~~l~~g~~v~v~G-~v~ 61 (84)
T cd04485 19 RMAFVTLEDLTGSIEVVVFPETYEKYRDLLKEDALLLVEG-KVE 61 (84)
T ss_pred EEEEEEEEeCCCeEEEEECHHHHHHHHHHhcCCCEEEEEE-EEE
Confidence 6789999999999999999987777889999999998875 443
No 56
>PF15072 DUF4539: Domain of unknown function (DUF4539)
Probab=94.14 E-value=0.21 Score=43.25 Aligned_cols=60 Identities=23% Similarity=0.314 Sum_probs=49.2
Q ss_pred EEEEEEcCCCcEEEEEcchhHHHhhhhccCCcEEEEcceEEeccCCcccccCCceEEEEccccEEE
Q psy15132 480 FSIDLLDESGEIRATMFNDECNRFHDMIEKDKVYYISNCTLKPANKKFSSINNDYEMSFTHSTTVI 545 (786)
Q Consensus 480 ~~~~L~D~~G~I~at~~~~~~~kf~~~l~~G~vy~is~~~V~~a~~~y~~~~~~yei~f~~~T~I~ 545 (786)
..++|.|.+|+|+|++-.+..+++.+.|..|.|..+.+..| |.+....+-|+......+.
T Consensus 21 ~~v~l~DpTG~i~~tiH~~v~~~y~~~l~~GavLlLk~V~V------f~ps~~~~yLnIt~~Nlv~ 80 (86)
T PF15072_consen 21 AFVVLKDPTGEIRGTIHRKVLEEYGDELSPGAVLLLKDVTV------FSPSPRSHYLNITLNNLVR 80 (86)
T ss_pred eEEEEECCCCcEEEEEeHHHHhhcCCccccCEEEEEeeeeE------EecCCCccEEEEehhHeee
Confidence 57899999999999999999999999999999999999887 3344556666666554443
No 57
>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=94.08 E-value=0.22 Score=43.90 Aligned_cols=60 Identities=17% Similarity=0.345 Sum_probs=44.0
Q ss_pred eeEEEEEEEcccceeEEeecCCceeeEEEEEEeeccccEEEEEEeccccc----ccc-CCCCCEEEEEeEEEeecCCc
Q psy15132 577 IDVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWGKEAE----TFD-ASNKPVIAVKAARVSEFQGN 649 (786)
Q Consensus 577 vDViGvV~~V~~~~~i~~k~~g~~~~kr~i~l~D~s~~~i~~tLWg~~a~----~~~-~~~~~vv~i~~~~V~~f~G~ 649 (786)
|.++|+|+++... ..+..++|.|.|| +|++.+|....+ ..+ ...|.+|.+.| +++.|+|+
T Consensus 2 v~~vG~V~~~~~~-----------~~~~~~tL~D~TG-~I~~~~W~~~~~~~~~~~~~~~~g~~v~v~G-~v~~~~g~ 66 (95)
T cd04478 2 VTLVGVVRNVEEQ-----------STNITYTIDDGTG-TIEVRQWLDDDNDDSSEVEPIEEGTYVRVFG-NLKSFQGK 66 (95)
T ss_pred EEEEEEEEeeeEc-----------ccEEEEEEECCCC-cEEEEEeCCCCCcccccccccccCCEEEEEE-EEcccCCe
Confidence 6788999886532 1457899999999 899999987543 222 45677776655 78889886
No 58
>PF11325 DUF3127: Domain of unknown function (DUF3127); InterPro: IPR021474 This bacterial family of proteins has no known function.
Probab=93.27 E-value=0.36 Score=41.46 Aligned_cols=68 Identities=19% Similarity=0.324 Sum_probs=50.3
Q ss_pred EEEEEEEcccceeEEeecCCceeeEEEEEEeeccc--cEEEEEEecccccc-ccCCCCCEEEEE-eEEEeecCCc
Q psy15132 579 VLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQ--ASVTMTLWGKEAET-FDASNKPVIAVK-AARVSEFQGN 649 (786)
Q Consensus 579 ViGvV~~V~~~~~i~~k~~g~~~~kr~i~l~D~s~--~~i~~tLWg~~a~~-~~~~~~~vv~i~-~~~V~~f~G~ 649 (786)
+.|.|..+-+..+-.++ +| ..||++.|.-+.. ..|.+.+||+.+.. +....|..|.+. +.+-++|+|+
T Consensus 2 i~Gkii~~l~~~~g~s~-~G--w~Kre~Vlet~~qYP~~i~f~~~~dk~~~l~~~~~Gd~V~Vsf~i~~RE~~gr 73 (84)
T PF11325_consen 2 ITGKIIKVLPEQQGVSK-NG--WKKREFVLETEEQYPQKICFEFWGDKIDLLDNFQVGDEVKVSFNIEGREWNGR 73 (84)
T ss_pred cccEEEEEecCcccCcC-CC--cEEEEEEEeCCCcCCceEEEEEEcchhhhhccCCCCCEEEEEEEeeccEecce
Confidence 45776666666555555 37 9999999985554 38999999999988 557888877553 6677888876
No 59
>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=93.07 E-value=0.33 Score=40.91 Aligned_cols=54 Identities=17% Similarity=0.329 Sum_probs=43.5
Q ss_pred EEEEEEeecCCcceecCCCCCceEEEEEEEcCCCcEEEEEcchhHHHhhhhccCCcEEEEcc
Q psy15132 456 TIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFNDECNRFHDMIEKDKVYYISN 517 (786)
Q Consensus 456 ~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~G~I~at~~~~~~~kf~~~l~~G~vy~is~ 517 (786)
.|.|-|+ .+|. ..+ | ..-++|.|.+|+|.+++|.+...++.+.|++|+.+.+..
T Consensus 3 ~v~g~v~---~i~~--tk~--g-~~~~~L~D~~~~i~~~~f~~~~~~~~~~l~~g~~v~v~g 56 (78)
T cd04489 3 WVEGEIS---NLKR--PSS--G-HLYFTLKDEDASIRCVMWRSNARRLGFPLEEGMEVLVRG 56 (78)
T ss_pred EEEEEEe---cCEE--CCC--c-EEEEEEEeCCeEEEEEEEcchhhhCCCCCCCCCEEEEEE
Confidence 4666666 3454 222 4 788899999999999999999999999999999988876
No 60
>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=92.25 E-value=0.53 Score=40.15 Aligned_cols=53 Identities=21% Similarity=0.274 Sum_probs=40.0
Q ss_pred eeEEEEEEEcccceeEEeecCCceeeEEEEEEeeccccEEEEEEeccccc--ccc--CCCCCEEEEEe
Q psy15132 577 IDVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWGKEAE--TFD--ASNKPVIAVKA 640 (786)
Q Consensus 577 vDViGvV~~V~~~~~i~~k~~g~~~~kr~i~l~D~s~~~i~~tLWg~~a~--~~~--~~~~~vv~i~~ 640 (786)
+-+.|+|.++. .+|+ |+. -+.|.|.+| ++++++|.+..+ .+. ...+.+|.++|
T Consensus 2 v~i~GiI~~v~-----~TK~-g~~----~~~leD~~G-~~Ev~~F~~~~~~~~~~~~l~~d~~v~v~g 58 (79)
T cd04490 2 VSIIGMVNDVR-----STKN-GHR----IVELEDTTG-RITVLLTKDKEELFEEAEDILPDEVIGVSG 58 (79)
T ss_pred EEEEEEEeEEE-----EcCC-CCE----EEEEECCCC-EEEEEEeCchhhhhhhhhhccCCCEEEEEE
Confidence 34789999987 3453 653 899999999 899999999777 553 45666777766
No 61
>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=92.23 E-value=0.51 Score=40.25 Aligned_cols=54 Identities=24% Similarity=0.284 Sum_probs=42.9
Q ss_pred EEEEEEeecCCcceecCCCCCceEEEEEEEcCCCcEEEEEcchhHH--HhhhhccCCcEEEEcc
Q psy15132 456 TIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFNDECN--RFHDMIEKDKVYYISN 517 (786)
Q Consensus 456 ~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~G~I~at~~~~~~~--kf~~~l~~G~vy~is~ 517 (786)
.+.|.|+.. | . +.+ |+. -+.|-|.+|.+.+++|++..+ ++.+.|++|.++.+..
T Consensus 3 ~i~GiI~~v---~-~-TK~--g~~-~~~leD~~G~~Ev~~F~~~~~~~~~~~~l~~d~~v~v~g 58 (79)
T cd04490 3 SIIGMVNDV---R-S-TKN--GHR-IVELEDTTGRITVLLTKDKEELFEEAEDILPDEVIGVSG 58 (79)
T ss_pred EEEEEEeEE---E-E-cCC--CCE-EEEEECCCCEEEEEEeCchhhhhhhhhhccCCCEEEEEE
Confidence 456666643 4 2 223 333 889999999999999999999 9999999999999887
No 62
>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=91.54 E-value=1.2 Score=37.50 Aligned_cols=68 Identities=21% Similarity=0.299 Sum_probs=44.6
Q ss_pred EEEEEEEeccceeEeeccCCceeeEEEEEEEeCCCCEEEEEeccccccccc--CCCCcEEEEEeEEEeeeCCceeeee
Q psy15132 62 VLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWGKEAETFD--ASNKPVIAVKAARVSEFQGGKTLSL 137 (786)
Q Consensus 62 ViGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~s~~~i~~tLWg~~a~~~~--~~~~~Vi~i~~~kv~~f~g~~~ls~ 137 (786)
++|.|.++.. ..+|+ |+. ...++|.|.+| ++++++|++..+.+. ...+.++.+.| ++..|+|..++.+
T Consensus 2 i~g~v~~~~~---~~~k~-g~~--~~~~~l~D~tg-~~~~~~f~~~~~~~~~~l~~g~~v~v~G-~v~~~~~~~~l~~ 71 (84)
T cd04485 2 VAGLVTSVRR---RRTKK-GKR--MAFVTLEDLTG-SIEVVVFPETYEKYRDLLKEDALLLVEG-KVERRDGGLRLIA 71 (84)
T ss_pred EEEEEEEeEE---EEcCC-CCE--EEEEEEEeCCC-eEEEEECHHHHHHHHHHhcCCCEEEEEE-EEEecCCceEEEe
Confidence 5788877533 33443 542 46788999998 899999987643332 25566666665 7777866566654
No 63
>PRK13480 3'-5' exoribonuclease YhaM; Provisional
Probab=91.40 E-value=1.2 Score=48.31 Aligned_cols=81 Identities=22% Similarity=0.334 Sum_probs=57.3
Q ss_pred chhccCCCCceEEEEEEEEeccceeEeeccCCceeeEEEEEEEeCCCCEEEEEeccccccccc-CCCCcEEEEEeEEEee
Q psy15132 50 TIAEISPDENIDVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWGKEAETFD-ASNKPVIAVKAARVSE 128 (786)
Q Consensus 50 ~i~~~~~~~~vDViGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~s~~~i~~tLWg~~a~~~~-~~~~~Vi~i~~~kv~~ 128 (786)
.|.++..+..++.+..|++..-- ++| +|+. -..++|.|.|| +|+..+|+..-+... ...+.||-++| +|.+
T Consensus 4 ~i~~l~~g~~v~~~~lv~~~~~~---~~k-nG~~--yl~l~l~D~tG-~I~ak~W~~~~~~~~~~~~g~vv~v~G-~v~~ 75 (314)
T PRK13480 4 GIEELEVGEQVDHFLLIKSATKG---VAS-NGKP--FLTLILQDKSG-DIEAKLWDVSPEDEATYVPETIVHVKG-DIIN 75 (314)
T ss_pred hHhhcCCCCEeeEEEEEEEceee---ecC-CCCe--EEEEEEEcCCc-EEEEEeCCCChhhHhhcCCCCEEEEEE-EEEE
Confidence 34555668889999998886321 234 4653 56899999999 999999996533322 25667776766 6779
Q ss_pred eCCceeeeec
Q psy15132 129 FQGGKTLSLS 138 (786)
Q Consensus 129 f~g~~~ls~~ 138 (786)
|+|..++.+.
T Consensus 76 y~g~~Ql~i~ 85 (314)
T PRK13480 76 YRGRKQLKVN 85 (314)
T ss_pred ECCcceEEEE
Confidence 9998777654
No 64
>PRK13480 3'-5' exoribonuclease YhaM; Provisional
Probab=91.07 E-value=0.63 Score=50.48 Aligned_cols=70 Identities=13% Similarity=0.105 Sum_probs=49.1
Q ss_pred eecccCCCCCceEEEEEEeecCCcceecCCCCCceEEEEEEEcCCCcEEEEEcchhHHHhhhhccCCcEEEEcceE
Q psy15132 444 PIVSLSPYQNKWTIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFNDECNRFHDMIEKDKVYYISNCT 519 (786)
Q Consensus 444 ~I~~L~p~~~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~G~I~at~~~~~~~kf~~~l~~G~vy~is~~~ 519 (786)
.|++|.++. .......|..+ .+|. ++.....+.++|.|.+|+|.|.+|+.. +.....+++|+++.+.+-.
T Consensus 4 ~i~~l~~g~-~v~~~~lv~~~-~~~~---~knG~~yl~l~l~D~tG~I~ak~W~~~-~~~~~~~~~g~vv~v~G~v 73 (314)
T PRK13480 4 GIEELEVGE-QVDHFLLIKSA-TKGV---ASNGKPFLTLILQDKSGDIEAKLWDVS-PEDEATYVPETIVHVKGDI 73 (314)
T ss_pred hHhhcCCCC-EeeEEEEEEEc-eeee---cCCCCeEEEEEEEcCCcEEEEEeCCCC-hhhHhhcCCCCEEEEEEEE
Confidence 578888875 33434444443 2233 222236899999999999999999964 4567889999999888743
No 65
>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=90.66 E-value=0.77 Score=38.82 Aligned_cols=43 Identities=14% Similarity=0.318 Sum_probs=36.1
Q ss_pred eEEEEEEEcCCCcEEEEEcchhHHHhhhhccCCcEEEEcceEEec
Q psy15132 478 KLFSIDLLDESGEIRATMFNDECNRFHDMIEKDKVYYISNCTLKP 522 (786)
Q Consensus 478 ~~~~~~L~D~~G~I~at~~~~~~~kf~~~l~~G~vy~is~~~V~~ 522 (786)
.++.+.|.|.+|.|.+++|++.. .+...|++|.++.+. +.|..
T Consensus 19 ~~~~~~l~D~tg~i~~~~f~~~~-~~~~~l~~g~~v~v~-G~v~~ 61 (83)
T cd04492 19 PYLALTLQDKTGEIEAKLWDASE-EDEEKFKPGDIVHVK-GRVEE 61 (83)
T ss_pred cEEEEEEEcCCCeEEEEEcCCCh-hhHhhCCCCCEEEEE-EEEEE
Confidence 68999999999999999999654 447889999999998 55643
No 66
>PTZ00401 aspartyl-tRNA synthetase; Provisional
Probab=89.79 E-value=2.4 Score=49.68 Aligned_cols=99 Identities=23% Similarity=0.248 Sum_probs=71.0
Q ss_pred CceeeecccCCCC---CceEEEEEEeecCCcceecCCCCCceEEEEEEEcCCCcEEEEEc-c----hhHHHhhhhccCCc
Q psy15132 440 VQTHPIVSLSPYQ---NKWTIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMF-N----DECNRFHDMIEKDK 511 (786)
Q Consensus 440 ~~~~~I~~L~p~~---~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~G~I~at~~-~----~~~~kf~~~l~~G~ 511 (786)
...+.|++|++.. ...+|+|||.++ | ..|++.=++|.|.+|.|++++- + ...-+|...|..|+
T Consensus 63 ~~~~~i~~l~~~~~~g~~V~v~Grv~~~---R------~~Gk~~Fl~LRd~~~~iQ~v~~~~~~~~~~~~~~~~~l~~es 133 (550)
T PTZ00401 63 RTFIPVAVLSKPELVDKTVLIRARVSTT---R------KKGKMAFMVLRDGSDSVQAMAAVEGDVPKEMIDFIGQIPTES 133 (550)
T ss_pred CceEEHHHCCccccCCCEEEEEEEEEEE---e------cCCCeEEEEEEeCCcCEEEEEECCCccCHHHHHHHhcCCCCC
Confidence 4679999998654 457899999843 3 2367777889999999999983 2 23345667799999
Q ss_pred EEEEcceEEeccCCcccccCCceEEEEccccEEEEc
Q psy15132 512 VYYISNCTLKPANKKFSSINNDYEMSFTHSTTVIPC 547 (786)
Q Consensus 512 vy~is~~~V~~a~~~y~~~~~~yei~f~~~T~I~~~ 547 (786)
++.+.+.-+++..+.-+.....+||....-..+.++
T Consensus 134 iV~V~G~v~~~~~~~~~~~~~~~El~v~~i~vls~a 169 (550)
T PTZ00401 134 IVDVEATVCKVEQPITSTSHSDIELKVKKIHTVTES 169 (550)
T ss_pred EEEEEEEEEecCccCCCCCCccEEEEeeEEEEEeCC
Confidence 999999655543322234567899998876666555
No 67
>PRK05813 single-stranded DNA-binding protein; Provisional
Probab=89.31 E-value=16 Score=37.54 Aligned_cols=158 Identities=16% Similarity=0.196 Sum_probs=91.9
Q ss_pred CCceEEEEEEeecCCcceecCCCCCceEEEEEE-----EcCCCcEEEEEcchhHHHhhhhccCCcEEEEcceEEeccCCc
Q psy15132 452 QNKWTIKARVTNKTPIREWNNARGSGKLFSIDL-----LDESGEIRATMFNDECNRFHDMIEKDKVYYISNCTLKPANKK 526 (786)
Q Consensus 452 ~~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L-----~D~~G~I~at~~~~~~~kf~~~l~~G~vy~is~~~V~~a~~~ 526 (786)
.++..+.||+++-..+|+- ..|++ +..|.| .|+..-|.+++|..+++... |..|+-+.+.+ +++..+..
T Consensus 8 ~NkV~L~Grl~~d~e~~~~--~~G~~-~~~f~laV~R~s~~~D~i~v~v~~rlae~~~--l~kG~~v~VeG-qlrsy~~~ 81 (219)
T PRK05813 8 NNKVYLEGKVVSELEFSHE--MYGEG-FYNFKLEVPRLSDSKDILPVTVSERLLAGMD--LKVGTLVIVEG-QLRSYNKF 81 (219)
T ss_pred cCEEEEEEEEcCCceEEEE--eCCeE-EEEEEEEeeccCCCccEEEEEEEhhhhhhhc--ccCCCEEEEEE-EEEEeccC
Confidence 4678999999987777662 23443 333433 34555699999999998766 99999998886 33322111
Q ss_pred ccccCCceEEEEccccEEEEccCCCCCCCCcceeeccCcccccccCCCceeeEEEEEEEcccceeEEeecCCceeeEEEE
Q psy15132 527 FSSINNDYEMSFTHSTTVIPCNEDEVGNMPSVKYCFVPLKTIAEISPDENIDVLGVCIDAAELSSVTGKTNQKTYMKRDI 606 (786)
Q Consensus 527 y~~~~~~yei~f~~~T~I~~~~d~~~~~iP~~~~~f~~i~dl~~~~~~~~vDViGvV~~V~~~~~i~~k~~g~~~~kr~i 606 (786)
....+.|.+.+--. .|+.++... + ......|-++|.+..=-.+. .+. +|+++. .+
T Consensus 82 -~~G~~R~vl~V~a~-~i~~l~~~~---------------~---~~~~N~V~LiGrL~~DPelR--~t~-~G~~va--~f 136 (219)
T PRK05813 82 -IDGKNRLILTVFAR-NIEYCDERS---------------D---IKNPNEIFLDGYICKEPVYR--TTP-FGREIA--DL 136 (219)
T ss_pred -CCCcEEEEEEEEEE-EEEEccCCC---------------c---cCCccEEEEEEEccCCCeEE--ECC-CCCEEE--EE
Confidence 01234454444321 233332221 0 01234577889887642222 223 366544 34
Q ss_pred EEeecc----ccEEEEEEecccccccc-CCCCCEEEEEe
Q psy15132 607 TLVDQS----QASVTMTLWGKEAETFD-ASNKPVIAVKA 640 (786)
Q Consensus 607 ~l~D~s----~~~i~~tLWg~~a~~~~-~~~~~vv~i~~ 640 (786)
.|+=.. ..-|+|++||..|+... ...|.-|++.|
T Consensus 137 ~lAvnr~~~~td~i~~v~wg~~Ae~~~~l~KG~~V~V~G 175 (219)
T PRK05813 137 LLAVNRPYNKSDYIPCIAWGRNARFCKTLEVGDNIRVWG 175 (219)
T ss_pred EEEEcCCCCCceEEEEEEEhHHhHHHhhCCCCCEEEEEE
Confidence 444221 23799999999997543 46677777765
No 68
>PRK06751 single-stranded DNA-binding protein; Provisional
Probab=88.94 E-value=2.5 Score=41.69 Aligned_cols=68 Identities=15% Similarity=0.302 Sum_probs=51.6
Q ss_pred CCceEEEEEEeecCCcceecCCCCCceEEEEEEE------cCCC----c-EEEEEcchhHHHhhhhccCCcEEEEcc-eE
Q psy15132 452 QNKWTIKARVTNKTPIREWNNARGSGKLFSIDLL------DESG----E-IRATMFNDECNRFHDMIEKDKVYYISN-CT 519 (786)
Q Consensus 452 ~~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~------D~~G----~-I~at~~~~~~~kf~~~l~~G~vy~is~-~~ 519 (786)
++...|.+||++--.+|...+ | ..+.++.|+ ++.| + |.+++|+.+++.+...|+.|+-+.|.+ .+
T Consensus 2 mN~V~LiGrL~~DpelR~t~s--G-~~v~~fslAvnr~~~~~~ge~~tdwi~~v~wgk~Ae~~~~~l~KG~~V~VeGrL~ 78 (173)
T PRK06751 2 MNRVILVGRLTKDPDLRYTPN--G-VAVATFTLAVNRAFANQQGEREADFINCVIWRKQAENVANYLKKGSLAGVDGRLQ 78 (173)
T ss_pred ceEEEEEEEECCCCcEEECCC--C-CEEEEEEEEEccceecCCCCEEEEEEEEEEeCcHHHHHHHHcCCCCEEEEEEEEE
Confidence 467899999999888885432 2 356677664 3334 3 999999999999999999999999987 34
Q ss_pred Eec
Q psy15132 520 LKP 522 (786)
Q Consensus 520 V~~ 522 (786)
...
T Consensus 79 ~r~ 81 (173)
T PRK06751 79 TRN 81 (173)
T ss_pred eCc
Confidence 433
No 69
>KOG4757|consensus
Probab=88.32 E-value=1.5 Score=48.15 Aligned_cols=82 Identities=12% Similarity=0.260 Sum_probs=63.6
Q ss_pred eecCccchhccCCCCceEEEEEEEEeccceeEeeccCCceeeEEEEEEEe--CCCCEEEEEecccccccccC--CCCcEE
Q psy15132 44 CFVPLKTIAEISPDENIDVLGVCIDAAELSSVTGKTNQKTYMKRDITLVD--QSQASVTMTLWGKEAETFDA--SNKPVI 119 (786)
Q Consensus 44 ~f~~~~~i~~~~~~~~vDViGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D--~s~~~i~~tLWg~~a~~~~~--~~~~Vi 119 (786)
+|..+.+-.. ..+..|+++|+|++.+|..+-. |+. ....+.|+| .|+..+.|-|+....+++.. +.|++|
T Consensus 8 k~Iri~da~k-k~~tiVNl~GiVkef~pp~qs~----g~D-~~~tv~IvDp~~ss~gLtv~lfSkt~edLP~Ik~~GDii 81 (522)
T KOG4757|consen 8 KLIRISDALK-KKNTIVNLIGIVKEFTPPRQSL----GKD-WVCTVYIVDPDYSSIGLTVHLFSKTGEDLPVIKQVGDII 81 (522)
T ss_pred heeechHHHH-hcCcEEEEEEEEEeccChhhcc----CCc-eEEEEEEeCCCCCCCCcEEEEecCchhhCccccccCcEE
Confidence 4444444332 3578999999999999886532 443 467899999 78888999999999988864 789999
Q ss_pred EEEeEEEeeeCC
Q psy15132 120 AVKAARVSEFQG 131 (786)
Q Consensus 120 ~i~~~kv~~f~g 131 (786)
.+...|+.-|+.
T Consensus 82 llhRiKiq~y~~ 93 (522)
T KOG4757|consen 82 LLHRIKIQSYRD 93 (522)
T ss_pred EEEEEEEEEhhh
Confidence 999999998863
No 70
>PF15489 CTC1: CST, telomere maintenance, complex subunit CTC1
Probab=88.14 E-value=63 Score=40.64 Aligned_cols=288 Identities=13% Similarity=0.152 Sum_probs=145.6
Q ss_pred CCCCceEEEEEEeecCCcceecCCCCCceEEEEEEEcCCC--cEEEEEcchhHHHhhhhccCCcEEEEcce-----EEec
Q psy15132 450 PYQNKWTIKARVTNKTPIREWNNARGSGKLFSIDLLDESG--EIRATMFNDECNRFHDMIEKDKVYYISNC-----TLKP 522 (786)
Q Consensus 450 p~~~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~G--~I~at~~~~~~~kf~~~l~~G~vy~is~~-----~V~~ 522 (786)
+-...+.+.|..++.+.... ....+.|. --...|+.. ++-..|.+.. -+|++.|++|.||.+--- .|-.
T Consensus 702 ~~~~tlsF~~~g~wlGg~q~-~eg~~~~~--~e~~~~~~~~~kVlLlF~G~s-vrWF~fLhpg~vYRLva~~~~~p~l~~ 777 (1144)
T PF15489_consen 702 VPKPTLSFQVSGSWLGGTQR-KEGTGWGP--PEPLEDENKDQKVLLLFLGSS-VRWFPFLHPGQVYRLVAPNSPDPMLFG 777 (1144)
T ss_pred cCCCceEEEEEEEEecceEe-ccCcccCC--CCcCcccCCCceEEEEEecCc-eeeEeEecCCcEEEEecCCCCCceeec
Confidence 33456889999888877655 11111122 111223332 4666665665 499999999999987532 1100
Q ss_pred cCC--c--ccccCCceEEEEccccEEEEccCCCCCCCCcce-----eeccCccccccc-CCCceeeEEEEEEEcccceeE
Q psy15132 523 ANK--K--FSSINNDYEMSFTHSTTVIPCNEDEVGNMPSVK-----YCFVPLKTIAEI-SPDENIDVLGVCIDAAELSSV 592 (786)
Q Consensus 523 a~~--~--y~~~~~~yei~f~~~T~I~~~~d~~~~~iP~~~-----~~f~~i~dl~~~-~~~~~vDViGvV~~V~~~~~i 592 (786)
+.. + --...-.-.+++..+=.++.... . ++|..- ..-.++.|+... ..+..|.+-|+|.+-.-.+..
T Consensus 778 ~s~~s~r~l~~~~~~scl~vq~~W~le~~~~-~--d~~~~l~~~~~~~~ssl~~lls~s~s~sLVSFs~~I~srt~ce~~ 854 (1144)
T PF15489_consen 778 SSCVSQRPLELAGCPSCLTVQDDWTLELESS-Q--DIPPVLRISKLLPESSLSELLSSSSSDSLVSFSAEILSRTLCEPL 854 (1144)
T ss_pred CCCcccccccccCCCccEEeCCCceeccccc-c--cchhhhhhcccCccccHHHHhccCCCCceEEEEEEEEEeeeccCC
Confidence 000 0 00001122233332222222211 1 344321 223466777765 468899999999886433221
Q ss_pred E----eecCCcee------eEEEEEEeeccccEEEEEEeccccc-ccc--CCCCCEEEEEeE--EEeecCCc-c------
Q psy15132 593 T----GKTNQKTY------MKRDITLVDQSQASVTMTLWGKEAE-TFD--ASNKPVIAVKAA--RVSEFQGN-L------ 650 (786)
Q Consensus 593 ~----~k~~g~~~------~kr~i~l~D~s~~~i~~tLWg~~a~-~~~--~~~~~vv~i~~~--~V~~f~G~-L------ 650 (786)
. .+..+... ...-+++.|-.+. -.+.+.-+..- -+. .-+|.+|.|.+. ||+-+++. .
T Consensus 855 ~~~~~~~~~~~~~~~~~vkltv~L~v~D~~~p-~~ldVYi~~~h~p~plGLLPGA~V~f~~lerkVSRs~nVYC~~~psS 933 (1144)
T PF15489_consen 855 NARRWSKPGNAIASRGCVKLTVALTVADCESP-PHLDVYIEDPHLPYPLGLLPGARVLFSQLERKVSRSHNVYCCFLPSS 933 (1144)
T ss_pred ccccccCCCCCcccccccceEEEEEEecCCCC-CeEEEEecCCCCCCcccccCCceeeeehhhhhhhccCcEEEEEcCCc
Confidence 1 11111111 1123444555441 11333332211 111 356778888765 55555443 1
Q ss_pred ----ccHHhHHh-----------hcCCCCCCCceEEEEEEEEEEecCceEEeCCCCccccccccccCCceeeeCC----C
Q psy15132 651 ----LLMREIQD-----------QQLGMGDKADYCSVRGIIQVFRGSNTTYKACPSQDCNKKVIDQNNGMYRCEK----C 711 (786)
Q Consensus 651 ----~ti~e~~~-----------~~l~~~~~~~~~~v~a~I~~i~~~~~~Y~aC~~~~C~kkv~~~~~g~~~C~~----C 711 (786)
.++.+-.. +.++....+-.+.+.+.|+.|..-. .-..|. .|..-.. .| +|.. |
T Consensus 934 ~VtVlS~p~~t~~~~~~P~~~L~~~~~~~~~~~~a~~~chVV~V~~l~-L~WvCa--~C~si~~---qg--~Csr~~p~C 1005 (1144)
T PF15489_consen 934 SVTVLSFPPETNVSPPLPHIYLAELLQGSQSPFQARVSCHVVSVLSLQ-LQWVCA--HCGSICP---QG--RCSRQSPPC 1005 (1144)
T ss_pred eEEEEecCcccCCCCCCCeEEehhhhCCCCCCceEEEEEEEEEEEEEE-eeehhh--hccCccc---CC--cCCCCCCCC
Confidence 11111000 0111122333567778888875421 234666 5665222 23 3643 4
Q ss_pred CCcCCceeEEEEEEEEEEecCCcEEEEEehhhHHHHhCCChHHH
Q psy15132 712 NKEFNTFTYRLILPVMIGDWTNSVWVTLFQNEAESILGVTAQEV 755 (786)
Q Consensus 712 ~~~~~~~~~ry~l~~~i~D~Tg~~~~~~F~~~ae~llG~sa~el 755 (786)
... ....+=..++.+.|+||++.+++-++....++|.+..|-
T Consensus 1006 ~s~--~sV~qA~ar~~vEDGTaeA~v~~~~~~V~~lLgL~~~eW 1047 (1144)
T PF15489_consen 1006 PSQ--TSVFQASARLLVEDGTAEAVVWCRGHHVAALLGLSPSEW 1047 (1144)
T ss_pred CCC--cceeeEEEEEEEecCCeeEEEEECCcHHHHHhCCCHHHH
Confidence 332 223455677889999999999999999999999998864
No 71
>KOG0851|consensus
Probab=87.93 E-value=0.71 Score=48.07 Aligned_cols=137 Identities=15% Similarity=0.223 Sum_probs=83.1
Q ss_pred ccccccCCCcCCCCCeEEEEccCcEEEEccCCCCCCCCce-eEeecCccchhc--cCCCCceEEEE-EEEEeccceeEee
Q psy15132 2 LAAPANKKFSSINNDYEMSFTHSTTVIPCNEDEVGNMPSV-KYCFVPLKTIAE--ISPDENIDVLG-VCIDAAELSSVTG 77 (786)
Q Consensus 2 ~v~~A~~~y~~~~~~yei~f~~~T~I~~~~d~~~~~iP~~-~~~f~~~~~i~~--~~~~~~vDViG-vV~~v~~~~~i~~ 77 (786)
.|.++...++.+.|+|++.|.+.+.+...+. ..|-. .++|.++..+.+ .....++|++| .+..++.+..-..
T Consensus 78 ~v~~~~~~~~~~~~~~~i~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~v~~~~~~~~~v~~~~~~~~~v~~~~~~~~ 153 (246)
T KOG0851|consen 78 GVNPNSGQVRATTHSFKINFMDFTVVTSSDT----RLPCTPWGKFTPFDSIVEDKSDKRVLVDLIGVAVYDVSQLTVTPA 153 (246)
T ss_pred eecccccceeeeeeEEEEEeccceeeccCCC----CccceeccccchhhhhhccccCCcEEEEeeceeEEEeeeeEeccc
Confidence 4667788888899999999988777776543 22222 568888866653 45667899999 6777765543222
Q ss_pred ccCCceeeEEEEEEEeCCCCEEEEEecccccccccCCCCcEEEEEeEEEeeeCCceeeeecceeEEEECCCchHHHHHHh
Q psy15132 78 KTNQKTYMKRDITLVDQSQASVTMTLWGKEAETFDASNKPVIAVKAARVSEFQGGKTLSLSMSSVLSLNPDIPECHKLQG 157 (786)
Q Consensus 78 k~~g~~~~kr~i~l~D~s~~~i~~tLWg~~a~~~~~~~~~Vi~i~~~kv~~f~g~~~ls~~~~s~i~~npd~pe~~~l~~ 157 (786)
.+.....+.+...+.++ | ... +.-.+.+.++..+.+| + +. .....+.+..+|+ +...+.
T Consensus 154 --~~~~~~~~~~~~~~~~~-------~-----~~~-~~~~~c~~~~~~~~~~-~-~~-~~l~~~~~~~~~~---l~~~~~ 212 (246)
T KOG0851|consen 154 --IDTDVDGFYLTFKICNK-------S-----KFS-KPVLWCEACGEQATDF-G-RK-RSLGGGVIVIAPE---LLFWKI 212 (246)
T ss_pred --ccCCcceEEEEEeeccc-------c-----ccc-CceEEehhhcchHHhh-h-hh-eEecCCcEEccch---heeecc
Confidence 24567777777777765 0 000 1112333555566777 3 33 4455666777776 333344
Q ss_pred hhhccC
Q psy15132 158 WFSTQT 163 (786)
Q Consensus 158 w~~~~~ 163 (786)
|....|
T Consensus 213 ~~~~~G 218 (246)
T KOG0851|consen 213 WRYFDG 218 (246)
T ss_pred cccccC
Confidence 444433
No 72
>PF11325 DUF3127: Domain of unknown function (DUF3127); InterPro: IPR021474 This bacterial family of proteins has no known function.
Probab=87.83 E-value=3.6 Score=35.44 Aligned_cols=68 Identities=19% Similarity=0.301 Sum_probs=48.4
Q ss_pred EEEEEEEeccceeEeeccCCceeeEEEEEEEeCCC--CEEEEEeccccccc-ccCCCCcEEEE-EeEEEeeeCCc
Q psy15132 62 VLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQ--ASVTMTLWGKEAET-FDASNKPVIAV-KAARVSEFQGG 132 (786)
Q Consensus 62 ViGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~s~--~~i~~tLWg~~a~~-~~~~~~~Vi~i-~~~kv~~f~g~ 132 (786)
+-|.|..+-+.++-.++ +| ..||++.|.-... ..|.+.+||+.+.. +....|..|-+ -+.+-.+|+|.
T Consensus 2 i~Gkii~~l~~~~g~s~-~G--w~Kre~Vlet~~qYP~~i~f~~~~dk~~~l~~~~~Gd~V~Vsf~i~~RE~~gr 73 (84)
T PF11325_consen 2 ITGKIIKVLPEQQGVSK-NG--WKKREFVLETEEQYPQKICFEFWGDKIDLLDNFQVGDEVKVSFNIEGREWNGR 73 (84)
T ss_pred cccEEEEEecCcccCcC-CC--cEEEEEEEeCCCcCCceEEEEEEcchhhhhccCCCCCEEEEEEEeeccEecce
Confidence 45776666666655555 36 8999999985443 48999999999998 45566765544 45677888754
No 73
>KOG4757|consensus
Probab=87.59 E-value=1.6 Score=47.95 Aligned_cols=72 Identities=14% Similarity=0.298 Sum_probs=58.1
Q ss_pred CCceeeEEEEEEEcccceeEEeecCCceeeEEEEEEee--ccccEEEEEEecccccccc--CCCCCEEEEEeEEEeecCC
Q psy15132 573 PDENIDVLGVCIDAAELSSVTGKTNQKTYMKRDITLVD--QSQASVTMTLWGKEAETFD--ASNKPVIAVKAARVSEFQG 648 (786)
Q Consensus 573 ~~~~vDViGvV~~V~~~~~i~~k~~g~~~~kr~i~l~D--~s~~~i~~tLWg~~a~~~~--~~~~~vv~i~~~~V~~f~G 648 (786)
.+..|+++|+|++.+|...- + |+.. ...+.|+| .|+..+.|-|+....+++. .+.|.+|.+...++.-|+.
T Consensus 19 ~~tiVNl~GiVkef~pp~qs--~--g~D~-~~tv~IvDp~~ss~gLtv~lfSkt~edLP~Ik~~GDiillhRiKiq~y~~ 93 (522)
T KOG4757|consen 19 KNTIVNLIGIVKEFTPPRQS--L--GKDW-VCTVYIVDPDYSSIGLTVHLFSKTGEDLPVIKQVGDIILLHRIKIQSYRD 93 (522)
T ss_pred cCcEEEEEEEEEeccChhhc--c--CCce-EEEEEEeCCCCCCCCcEEEEecCchhhCccccccCcEEEEEEEEEEEhhh
Confidence 57899999999999987532 2 4433 45789999 6777899999999998887 4789999999999988765
Q ss_pred c
Q psy15132 649 N 649 (786)
Q Consensus 649 ~ 649 (786)
+
T Consensus 94 r 94 (522)
T KOG4757|consen 94 R 94 (522)
T ss_pred h
Confidence 4
No 74
>PF14951 DUF4503: Domain of unknown function (DUF4503)
Probab=87.36 E-value=1.6 Score=46.93 Aligned_cols=98 Identities=23% Similarity=0.422 Sum_probs=73.7
Q ss_pred eEEEEEEEEEEecCceE-EeCCCCccccc-ccc--ccCCceeeeCCCCCcCCceeEEEEEEEEEEec---CCcEEEEEeh
Q psy15132 669 YCSVRGIIQVFRGSNTT-YKACPSQDCNK-KVI--DQNNGMYRCEKCNKEFNTFTYRLILPVMIGDW---TNSVWVTLFQ 741 (786)
Q Consensus 669 ~~~v~a~I~~i~~~~~~-Y~aC~~~~C~k-kv~--~~~~g~~~C~~C~~~~~~~~~ry~l~~~i~D~---Tg~~~~~~F~ 741 (786)
...|.|+|+.++.+..| ++.|. .|+. |+. .++.|.|.|..|.+....|.-|.-|.+-+.=. -.++.+-+..
T Consensus 256 iCsvqG~VvgVdE~TAfSWPvCd--~CGn~rLe~~pe~rg~~~C~~Cs~~V~sP~~r~~LeVfl~Cps~p~ctvKVKL~q 333 (389)
T PF14951_consen 256 ICSVQGTVVGVDESTAFSWPVCD--RCGNGRLEQSPEDRGAFSCGDCSRVVTSPVLRMHLEVFLDCPSRPQCTVKVKLLQ 333 (389)
T ss_pred eEEEeeEEEEecCcccccCcccc--ccCCccceeCccCCCceeccchhhhccCcceeeeEEEEEeCCCCCCceEEEEEhH
Confidence 57999999999887554 79998 6864 442 24568899999999999999998888877733 2467889999
Q ss_pred hhHHHHhCCChHHHhccccChHHHHHhcCCeE
Q psy15132 742 NEAESILGVTAQEVGESTEDHPALKKALFTQY 773 (786)
Q Consensus 742 ~~ae~llG~sa~el~~~~~~~~~~~~~~~k~~ 773 (786)
+.-..||.-+|.| +....+++++||+-
T Consensus 334 ~sIsslL~~aa~e-----dg~Yev~sVLGkev 360 (389)
T PF14951_consen 334 RSISSLLMSAASE-----DGSYEVKSVLGKEV 360 (389)
T ss_pred HHHHHHHhhhhcc-----CCceehhhhhcccc
Confidence 8888888877665 22236666666653
No 75
>PF14951 DUF4503: Domain of unknown function (DUF4503)
Probab=87.27 E-value=1.7 Score=46.74 Aligned_cols=101 Identities=24% Similarity=0.407 Sum_probs=75.4
Q ss_pred CCcEEEEEEEEEEEecC-ceEEeCCCCCCCCc-cee--eCCCceeecccCCCcCCceeEeeeeeEEEEec---CCcEEEE
Q psy15132 201 KADYCSVRGIIQVFRGS-NTTYKACPSQDCNK-KVI--DQNNGMYRCEKCNKEFNTFTYRLILPVMIGDW---TNSVWVT 273 (786)
Q Consensus 201 ~~~~~~v~a~I~~i~~~-~~~Y~aC~~~~C~k-Kv~--~~~~~~~~C~~C~~~~~~~~~ry~l~~~v~D~---Tg~~~~~ 273 (786)
.+..+.|.|+|..++.+ .+.+|.|. .|+. |+. .++.|.|+|..|.+.+..|.-|..|.+-+.=. -.+.++-
T Consensus 253 vNSiCsvqG~VvgVdE~TAfSWPvCd--~CGn~rLe~~pe~rg~~~C~~Cs~~V~sP~~r~~LeVfl~Cps~p~ctvKVK 330 (389)
T PF14951_consen 253 VNSICSVQGTVVGVDESTAFSWPVCD--RCGNGRLEQSPEDRGAFSCGDCSRVVTSPVLRMHLEVFLDCPSRPQCTVKVK 330 (389)
T ss_pred CcceEEEeeEEEEecCcccccCcccc--ccCCccceeCccCCCceeccchhhhccCcceeeeEEEEEeCCCCCCceEEEE
Confidence 35679999999999976 57899999 9975 454 24678899999999999999999999877512 2366788
Q ss_pred eehHHHHHHhCCChhhhhccCCChHHHHHhcCCEE
Q psy15132 274 LFQNEAESILGVTAQEVGESTEDHPALKKALFTQY 308 (786)
Q Consensus 274 ~F~~~a~~ilg~sa~el~~~~e~~~~~~~~~~k~~ 308 (786)
+....-..||...|.|=. .-+.+..+||+.
T Consensus 331 L~q~sIsslL~~aa~edg-----~Yev~sVLGkev 360 (389)
T PF14951_consen 331 LLQRSISSLLMSAASEDG-----SYEVKSVLGKEV 360 (389)
T ss_pred EhHHHHHHHHhhhhccCC-----ceehhhhhcccc
Confidence 888888888877765511 123556666654
No 76
>cd04492 YhaM_OBF_like YhaM_OBF_like: A subfamily of OB folds similar to that found in Bacillus subtilis YhaM and Staphylococcus aureus cmp-binding factor-1 (SaCBF1). Both these proteins are 3'-to-5'exoribonucleases. YhaM requires Mn2+ or Co2+ for activity and is inactive in the presence of Mg2+. YhaM also has a Mn2+ dependent 3'-to-5'single-stranded DNA exonuclease activity. SaCBF is also a double-stranded DNA binding protein, binding specifically to cmp, the replication enhancer found in S. aureus plasmid pT181. Proteins in this group combine an N-terminal OB fold with a C-terminal HD domain. The HD domain is found in metal-dependent phosphohydrolases.
Probab=86.12 E-value=3.9 Score=34.36 Aligned_cols=68 Identities=24% Similarity=0.305 Sum_probs=42.1
Q ss_pred EEEEEEEeccceeEeeccCCceeeEEEEEEEeCCCCEEEEEecccccccc-cCCCCcEEEEEeEEEeeeCCceeeee
Q psy15132 62 VLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWGKEAETF-DASNKPVIAVKAARVSEFQGGKTLSL 137 (786)
Q Consensus 62 ViGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~s~~~i~~tLWg~~a~~~-~~~~~~Vi~i~~~kv~~f~g~~~ls~ 137 (786)
.+.+|.++. ...+|+ |+ ....++|.|.+| .+++++|++.-... ....+.++.+. +++..|+|...+..
T Consensus 2 ~~~~v~~~~---~~~tk~-g~--~~~~~~l~D~tg-~i~~~~f~~~~~~~~~l~~g~~v~v~-G~v~~~~~~~~l~~ 70 (83)
T cd04492 2 GFFLIKSKE---LRTAKN-GK--PYLALTLQDKTG-EIEAKLWDASEEDEEKFKPGDIVHVK-GRVEEYRGRLQLKI 70 (83)
T ss_pred cEEEEEEee---eecccC-CC--cEEEEEEEcCCC-eEEEEEcCCChhhHhhCCCCCEEEEE-EEEEEeCCceeEEE
Confidence 344555553 233443 44 356899999998 89999999654221 12455566565 57777866555553
No 77
>PRK08182 single-stranded DNA-binding protein; Provisional
Probab=86.06 E-value=4.2 Score=39.10 Aligned_cols=71 Identities=8% Similarity=0.258 Sum_probs=52.4
Q ss_pred CCceEEEEEEeecCCcceecCCCC-CceEEEEEEE------cCCC-------c-EEEEEcchhHHHhhhhccCCcEEEEc
Q psy15132 452 QNKWTIKARVTNKTPIREWNNARG-SGKLFSIDLL------DESG-------E-IRATMFNDECNRFHDMIEKDKVYYIS 516 (786)
Q Consensus 452 ~~~w~I~~RV~~k~~~r~~~~~~~-~g~~~~~~L~------D~~G-------~-I~at~~~~~~~kf~~~l~~G~vy~is 516 (786)
++.+.|.||+..--.+|...+... .-.+.++.|+ +++| . +.+++|+.+++.+...|+.|+-+.+.
T Consensus 2 ~N~V~LiGrLg~DPElr~t~~G~~~~~~va~fslA~~r~~~~~~Ge~~~~~t~w~~V~~wg~~Ae~v~~~l~KG~~V~V~ 81 (148)
T PRK08182 2 STHFVGEGNIGSAPEYREFPNGNDEPRRLLRLNVYFDNPVPTKDGEYEDRGGFWAPVELWHRDAEHWARLYQKGMRVLVE 81 (148)
T ss_pred ccEEEEEEECCCCCeEEECCCCCeeeeeEEEEEEEecCceECCCCCEEecCcEEEEEEEEhHHHHHHHHhcCCCCEEEEE
Confidence 467899999998888887754110 0137888885 3333 2 88999999999999999999999998
Q ss_pred c-eEEec
Q psy15132 517 N-CTLKP 522 (786)
Q Consensus 517 ~-~~V~~ 522 (786)
+ .+...
T Consensus 82 GrL~~~~ 88 (148)
T PRK08182 82 GRMERDE 88 (148)
T ss_pred EEEEecc
Confidence 7 34433
No 78
>PRK02801 primosomal replication protein N; Provisional
Probab=85.99 E-value=3.5 Score=36.90 Aligned_cols=66 Identities=9% Similarity=0.067 Sum_probs=51.7
Q ss_pred CCceEEEEEEeecCCcceecCCCCCceEEEEEEEcC-----CCc-------EEEEEcchhHHHhhhhccCCcEEEEcceE
Q psy15132 452 QNKWTIKARVTNKTPIREWNNARGSGKLFSIDLLDE-----SGE-------IRATMFNDECNRFHDMIEKDKVYYISNCT 519 (786)
Q Consensus 452 ~~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~-----~G~-------I~at~~~~~~~kf~~~l~~G~vy~is~~~ 519 (786)
+++..+.||+++..++|.-.+ | ..+.+|.|+=+ .|- |.+++|+..++.+...|..|+.+.++++-
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 467889999999999987632 2 35666665432 232 99999999999999999999999999975
Q ss_pred E
Q psy15132 520 L 520 (786)
Q Consensus 520 V 520 (786)
-
T Consensus 79 ~ 79 (101)
T PRK02801 79 S 79 (101)
T ss_pred E
Confidence 4
No 79
>PRK05733 single-stranded DNA-binding protein; Provisional
Probab=85.81 E-value=6.1 Score=38.99 Aligned_cols=64 Identities=23% Similarity=0.342 Sum_probs=49.7
Q ss_pred CCCceEEEEEEeecCCcceecCCCCCceEEEEEEE------cC-CC------c-EEEEEcchhHHHhhhhccCCcEEEEc
Q psy15132 451 YQNKWTIKARVTNKTPIREWNNARGSGKLFSIDLL------DE-SG------E-IRATMFNDECNRFHDMIEKDKVYYIS 516 (786)
Q Consensus 451 ~~~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~------D~-~G------~-I~at~~~~~~~kf~~~l~~G~vy~is 516 (786)
+++...|.|||..--.+|...+ | ..+.+|.|+ |. .| + +.+++|+..++.+...|+.|+.++|.
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 3578899999998777887644 2 256666654 22 24 2 99999999999999999999999998
Q ss_pred c
Q psy15132 517 N 517 (786)
Q Consensus 517 ~ 517 (786)
+
T Consensus 81 G 81 (172)
T PRK05733 81 G 81 (172)
T ss_pred E
Confidence 7
No 80
>PRK07274 single-stranded DNA-binding protein; Provisional
Probab=85.75 E-value=4.7 Score=37.92 Aligned_cols=63 Identities=16% Similarity=0.269 Sum_probs=48.8
Q ss_pred CCceEEEEEEeecCCcceecCCCCCceEEEEEEE------cCCC----c-EEEEEcchhHHHhhhhccCCcEEEEcc
Q psy15132 452 QNKWTIKARVTNKTPIREWNNARGSGKLFSIDLL------DESG----E-IRATMFNDECNRFHDMIEKDKVYYISN 517 (786)
Q Consensus 452 ~~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~------D~~G----~-I~at~~~~~~~kf~~~l~~G~vy~is~ 517 (786)
++...|.||+..--.+|...+ | ..+.++.|+ |+.| + +++++|+.+++.+...|+.|+-+.+.+
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 467899999998877775432 2 256666665 4445 3 899999999999999999999999887
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=85.64 E-value=5.5 Score=33.31 Aligned_cols=65 Identities=20% Similarity=0.272 Sum_probs=41.5
Q ss_pred EEEEEEEeccceeEeeccCCceeeEEEEEEEeCCCCEEEEEecccccccccC--CCCcEEEEEe-EEEeeeCCceeeee
Q psy15132 62 VLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWGKEAETFDA--SNKPVIAVKA-ARVSEFQGGKTLSL 137 (786)
Q Consensus 62 ViGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~s~~~i~~tLWg~~a~~~~~--~~~~Vi~i~~-~kv~~f~g~~~ls~ 137 (786)
|.|.|.++.. +|+ | .--++|.|.++ ++++++|.+....+.. ..+.+|.+.+ ....+|+|+..|.+
T Consensus 4 v~g~v~~i~~-----tk~-g----~~~~~L~D~~~-~i~~~~f~~~~~~~~~~l~~g~~v~v~g~v~~~~~~~~~~l~v 71 (78)
T cd04489 4 VEGEISNLKR-----PSS-G----HLYFTLKDEDA-SIRCVMWRSNARRLGFPLEEGMEVLVRGKVSFYEPRGGYQLIV 71 (78)
T ss_pred EEEEEecCEE-----CCC-c----EEEEEEEeCCe-EEEEEEEcchhhhCCCCCCCCCEEEEEEEEEEECCCCEEEEEE
Confidence 6777777642 332 4 45689999987 9999999997766543 4555555555 23334445555543
No 82
>PRK07373 DNA polymerase III subunit alpha; Reviewed
Probab=85.51 E-value=2.1 Score=48.93 Aligned_cols=71 Identities=17% Similarity=0.245 Sum_probs=52.7
Q ss_pred eeecccC--CCCCceEEEEEEeecCCcceecCCCCCceEEEEEEEcCCCcEEEEEcchhHHHhhhhccCCcEEEEcc
Q psy15132 443 HPIVSLS--PYQNKWTIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFNDECNRFHDMIEKDKVYYISN 517 (786)
Q Consensus 443 ~~I~~L~--p~~~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~G~I~at~~~~~~~kf~~~l~~G~vy~is~ 517 (786)
.++++|. +......|-|-|+.. |.....+|+ .+.-+.|-|.+|.|.+++|.+..+++.+.|++|.++.|.+
T Consensus 269 ~~~~~l~~~~~~~~v~vaG~I~~i---k~~~TKkG~-~maf~~leD~tG~ie~vvFp~~y~~~~~~l~~~~~v~v~G 341 (449)
T PRK07373 269 INLSELEEQKEKTKVSAVVMLNEV---KKIVTKKGD-PMAFLQLEDLSGQSEAVVFPKSYERISELLQVDARLIIWG 341 (449)
T ss_pred cCHHHHhcccCCCEEEEEEEEEEe---EecccCCCC-EEEEEEEEECCCCEEEEECHHHHHHHHHHhccCCEEEEEE
Confidence 3566654 223456777888754 444333332 5566789999999999999999999999999999999866
No 83
>PRK07275 single-stranded DNA-binding protein; Provisional
Probab=85.21 E-value=3.2 Score=40.50 Aligned_cols=63 Identities=13% Similarity=0.266 Sum_probs=50.3
Q ss_pred CCceEEEEEEeecCCcceecCCCCCceEEEEEEE------cCCC----c-EEEEEcchhHHHhhhhccCCcEEEEcc
Q psy15132 452 QNKWTIKARVTNKTPIREWNNARGSGKLFSIDLL------DESG----E-IRATMFNDECNRFHDMIEKDKVYYISN 517 (786)
Q Consensus 452 ~~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~------D~~G----~-I~at~~~~~~~kf~~~l~~G~vy~is~ 517 (786)
++...|.+|+++--.+|...+ | ..+.++.|+ ++.| + |++++|+..++.+...|+.|+-+.|.+
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 367789999998888887643 2 266777765 4445 3 999999999999999999999999887
No 84
>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=85.10 E-value=11 Score=33.46 Aligned_cols=83 Identities=20% Similarity=0.285 Sum_probs=54.0
Q ss_pred eEEEEEEeecCCcceecCCCCCc-eEEEEEEEcCCCcEEEEEcchh------HHHhhhhccCCcEEEEcceEEeccCCcc
Q psy15132 455 WTIKARVTNKTPIREWNNARGSG-KLFSIDLLDESGEIRATMFNDE------CNRFHDMIEKDKVYYISNCTLKPANKKF 527 (786)
Q Consensus 455 w~I~~RV~~k~~~r~~~~~~~~g-~~~~~~L~D~~G~I~at~~~~~------~~kf~~~l~~G~vy~is~~~V~~a~~~y 527 (786)
.+|+|||.++ |. .| ++.=++|.|.+|.|++++-... .-++...|..|+++.+.+--.+. .+..
T Consensus 2 V~i~Gwv~~~---R~------~g~k~~Fi~LrD~sg~iQ~v~~~~~~~~~~~~~~~~~~l~~es~V~V~G~v~~~-~~~~ 71 (102)
T cd04320 2 VLIRARVHTS---RA------QGAKLAFLVLRQQGYTIQGVLAASAEGVSKQMVKWAGSLSKESIVDVEGTVKKP-EEPI 71 (102)
T ss_pred EEEEEEEEEe---ec------CCCceEEEEEecCCceEEEEEeCCcccCCHHHHHHHhcCCCccEEEEEEEEECC-CCcc
Confidence 4788888843 33 35 6667789999999999986432 22333568999999999964432 2111
Q ss_pred cc-cCCceEEEEccccEEEEc
Q psy15132 528 SS-INNDYEMSFTHSTTVIPC 547 (786)
Q Consensus 528 ~~-~~~~yei~f~~~T~I~~~ 547 (786)
+. ....+||....-..+.++
T Consensus 72 ~~~~~~~~El~~~~i~il~~~ 92 (102)
T cd04320 72 KSCTQQDVELHIEKIYVVSEA 92 (102)
T ss_pred cCCCcCcEEEEEEEEEEEecC
Confidence 11 236799988765555443
No 85
>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=84.67 E-value=39 Score=32.56 Aligned_cols=156 Identities=14% Similarity=0.162 Sum_probs=96.0
Q ss_pred EEEEEEeecCCcceecCCC-CCceEEEEEEEcCCCcEEEEEcchhHHHhhhhccCCcEEEEcceEEeccCCcccccCCce
Q psy15132 456 TIKARVTNKTPIREWNNAR-GSGKLFSIDLLDESGEIRATMFNDECNRFHDMIEKDKVYYISNCTLKPANKKFSSINNDY 534 (786)
Q Consensus 456 ~I~~RV~~k~~~r~~~~~~-~~g~~~~~~L~D~~G~I~at~~~~~~~kf~~~l~~G~vy~is~~~V~~a~~~y~~~~~~y 534 (786)
...|-|+.-.+.=.|..+. |..++|+-+++-++.-.++.+|+-. +.+.+..++++.||++.- +.-
T Consensus 4 P~~VmVLkaTepF~Ye~~e~gkk~MFHATVATet~fF~VKVfn~~---LKeKF~~kkiI~IS~Y~~-----------~~g 69 (170)
T PF02760_consen 4 PKTVMVLKATEPFEYESPEEGKKKMFHATVATETEFFRVKVFNIN---LKEKFIPKKIIAISDYFG-----------RNG 69 (170)
T ss_dssp EEEEEEEEE---EEEECTTTCEEEEEEEEEE-SS-EEEEEES-GG---GCCTCSTTSEEEEESEEE-----------ETT
T ss_pred ceEEEEEeccCCeEEeCcccCcceEEEEEEeccccEEEEEEecch---hHhhcCCCcEEEEehhhc-----------ccc
Confidence 3567777777777787765 5668999999999999999999974 567889999999999753 233
Q ss_pred EEEEccccEEEEccCCCCCCCCcce----eeccCcccccccCCCceeeEEEEEEEcccceeEEeecCCceeeEEEEEEee
Q psy15132 535 EMSFTHSTTVIPCNEDEVGNMPSVK----YCFVPLKTIAEISPDENIDVLGVCIDAAELSSVTGKTNQKTYMKRDITLVD 610 (786)
Q Consensus 535 ei~f~~~T~I~~~~d~~~~~iP~~~----~~f~~i~dl~~~~~~~~vDViGvV~~V~~~~~i~~k~~g~~~~kr~i~l~D 610 (786)
-|.+++.|.|.++..+..-.+|.-- -.--+|++|.....+.+|+=+=.|... +.+ ....-..|.|
T Consensus 70 fLEi~~aSsVse~~~dq~~eVp~~ii~~A~~TpKI~~L~~q~~Gt~V~G~F~v~KK------~v~-----~~~~~YeI~D 138 (170)
T PF02760_consen 70 FLEINEASSVSEVNPDQKMEVPNSIIRRANETPKINDLQKQASGTFVNGLFTVHKK------TVN-----KKNTIYEIQD 138 (170)
T ss_dssp EEEE-TTSEEEE--TTC-----HHHHHHHCS---HHHHTTSSTTEEEEEEEEEEEE------EEE-----SSEEEEEEEE
T ss_pred eEEEeeccEEEecCCCceEEccHHHHHhhccCCchhHHhcCCCCcEEeEEEEEEEE------EEc-----CCeEEEEEec
Confidence 5777888999988644322566532 122468888888788887644333321 111 1234578999
Q ss_pred ccccEEEEEEeccccccccCCCCCEEEE
Q psy15132 611 QSQASVTMTLWGKEAETFDASNKPVIAV 638 (786)
Q Consensus 611 ~s~~~i~~tLWg~~a~~~~~~~~~vv~i 638 (786)
++| .+++...|.... ....+|+-+.+
T Consensus 139 nTG-~MeVvv~G~~~n-i~CEeGDKLrL 164 (170)
T PF02760_consen 139 NTG-KMEVVVYGKWHN-IKCEEGDKLRL 164 (170)
T ss_dssp TTE-EEEEEEEGGGCG-CC--TT-EEEE
T ss_pred CCC-cEEEEEeccCcc-cccCCCCeEEE
Confidence 999 899999998663 35566665533
No 86
>PRK06752 single-stranded DNA-binding protein; Validated
Probab=83.91 E-value=7 Score=35.61 Aligned_cols=63 Identities=13% Similarity=0.193 Sum_probs=49.0
Q ss_pred CCceEEEEEEeecCCcceecCCCCCceEEEEEEEc------CCC----c-EEEEEcchhHHHhhhhccCCcEEEEcc
Q psy15132 452 QNKWTIKARVTNKTPIREWNNARGSGKLFSIDLLD------ESG----E-IRATMFNDECNRFHDMIEKDKVYYISN 517 (786)
Q Consensus 452 ~~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D------~~G----~-I~at~~~~~~~kf~~~l~~G~vy~is~ 517 (786)
++...|.||+.+-..+|...+ | ..+.+|.|+- ..| + +.+++|+..++.+...|+.|+-+.+.+
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 356789999998878776432 2 3667777663 334 3 999999999999999999999999887
No 87
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=83.61 E-value=0.85 Score=38.95 Aligned_cols=29 Identities=31% Similarity=0.836 Sum_probs=23.3
Q ss_pred CCCCCCCCcc-eeeCCCceeecccCCCcCCce
Q psy15132 223 ACPSQDCNKK-VIDQNNGMYRCEKCNKEFNTF 253 (786)
Q Consensus 223 aC~~~~C~kK-v~~~~~~~~~C~~C~~~~~~~ 253 (786)
.|| .|+++ |.....|.|.|.+|+..+.-.
T Consensus 37 ~Cp--~C~~~~VkR~a~GIW~C~kCg~~fAGg 66 (89)
T COG1997 37 VCP--FCGRTTVKRIATGIWKCRKCGAKFAGG 66 (89)
T ss_pred cCC--CCCCcceeeeccCeEEcCCCCCeeccc
Confidence 799 99987 445678999999999876543
No 88
>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=83.56 E-value=9.9 Score=30.93 Aligned_cols=48 Identities=19% Similarity=0.335 Sum_probs=30.9
Q ss_pred EEEEEEEeCCCCEEEEEeccc-ccccccCCCCcEEEEEeEEEeeeCCceee
Q psy15132 86 KRDITLVDQSQASVTMTLWGK-EAETFDASNKPVIAVKAARVSEFQGGKTL 135 (786)
Q Consensus 86 kr~i~l~D~s~~~i~~tLWg~-~a~~~~~~~~~Vi~i~~~kv~~f~g~~~l 135 (786)
...+.+.|.+| .+.++.|+. .-..-....+..+.+.| |++.|+|..++
T Consensus 19 ~~~~~~~D~~g-~i~~~~F~~~~~~~~~~~~G~~~~v~G-kv~~~~~~~qi 67 (75)
T cd04488 19 RLKVTLSDGTG-TLTLVFFNFQPYLKKQLPPGTRVRVSG-KVKRFRGGLQI 67 (75)
T ss_pred EEEEEEEcCCC-EEEEEEECCCHHHHhcCCCCCEEEEEE-EEeecCCeeEE
Confidence 56889999987 899999983 21111124555665554 78888654433
No 89
>cd04100 Asp_Lys_Asn_RS_N Asp_Lys_Asn_RS_N: N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases (AspRS, AsnRS, and LysRS). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein synthesis. Included in this group are archeal and archeal-like A
Probab=83.50 E-value=9.3 Score=32.70 Aligned_cols=75 Identities=20% Similarity=0.292 Sum_probs=48.7
Q ss_pred eEEEEEEeecCCcceecCCCCCceEEEEEEEcCCCcEEEEEcchhHH---HhhhhccCCcEEEEcceEEeccCCcccccC
Q psy15132 455 WTIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFNDECN---RFHDMIEKDKVYYISNCTLKPANKKFSSIN 531 (786)
Q Consensus 455 w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~G~I~at~~~~~~~---kf~~~l~~G~vy~is~~~V~~a~~~y~~~~ 531 (786)
.+|+|||-++ | ..|++.=++|.|.+|.+++.+-....+ ++...|..|+++.+.+.-.....+. ...
T Consensus 2 V~i~Gwv~~~---R------~~g~~~Fi~Lrd~~~~iQ~v~~~~~~~~~~~~~~~l~~~s~V~v~G~~~~~~~~~--~~~ 70 (85)
T cd04100 2 VTLAGWVHSR---R------DHGGLIFIDLRDGSGIVQVVVNKEELGEFFEEAEKLRTESVVGVTGTVVKRPEGN--LAT 70 (85)
T ss_pred EEEEEEEehh---c------cCCCEEEEEEEeCCeeEEEEEECCcChHHHHHHhCCCCCCEEEEEeEEEECCCCC--CCC
Confidence 3678888732 3 235666678999999999987654322 3345699999999988644322111 234
Q ss_pred CceEEEEcc
Q psy15132 532 NDYEMSFTH 540 (786)
Q Consensus 532 ~~yei~f~~ 540 (786)
..+||....
T Consensus 71 ~~~El~~~~ 79 (85)
T cd04100 71 GEIELQAEE 79 (85)
T ss_pred CCEEEEEeE
Confidence 678887643
No 90
>COG5235 RFA2 Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [DNA replication, recombination, and repair]
Probab=83.46 E-value=4.5 Score=40.26 Aligned_cols=54 Identities=17% Similarity=0.347 Sum_probs=37.1
Q ss_pred EEEEEeCCCCEEEEEecccccccccC----CCCcEEEEEeEEEeeeCCceeeeecceeEE
Q psy15132 88 DITLVDQSQASVTMTLWGKEAETFDA----SNKPVIAVKAARVSEFQGGKTLSLSMSSVL 143 (786)
Q Consensus 88 ~i~l~D~s~~~i~~tLWg~~a~~~~~----~~~~Vi~i~~~kv~~f~g~~~ls~~~~s~i 143 (786)
-++|.|-+| .|+|+.|-..+....+ ..+..+-+- .-+++|.|+++++...-+.|
T Consensus 86 ~~~iEDGTG-~Ievr~W~~~~~~~e~~~d~~~~~yvkV~-G~lk~F~GK~~I~~~~i~~I 143 (258)
T COG5235 86 MFVIEDGTG-SIEVRFWPGNSYEEEQCKDLEEQNYVKVN-GSLKTFNGKRSISASHISAI 143 (258)
T ss_pred EEEEecCCc-eEEEEecCCCchHHHhccccccccEEEEe-cceeeeCCeeEEehhheeec
Confidence 578999998 9999999987765432 233333333 34689999998886654443
No 91
>PRK09010 single-stranded DNA-binding protein; Provisional
Probab=83.35 E-value=9.8 Score=37.74 Aligned_cols=63 Identities=25% Similarity=0.400 Sum_probs=49.9
Q ss_pred CCceEEEEEEeecCCcceecCCCCCceEEEEEEE------cC-CC------c-EEEEEcchhHHHhhhhccCCcEEEEcc
Q psy15132 452 QNKWTIKARVTNKTPIREWNNARGSGKLFSIDLL------DE-SG------E-IRATMFNDECNRFHDMIEKDKVYYISN 517 (786)
Q Consensus 452 ~~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~------D~-~G------~-I~at~~~~~~~kf~~~l~~G~vy~is~ 517 (786)
.+...|.+|+..--.+|...+ | ..+.+|.|+ |. +| + +++++|+.+++.+...|+.|+-++|++
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 578899999999888888754 2 366666654 32 23 2 799999999999999999999999987
No 92
>PLN02850 aspartate-tRNA ligase
Probab=83.16 E-value=8.4 Score=45.05 Aligned_cols=98 Identities=14% Similarity=0.194 Sum_probs=68.9
Q ss_pred CceeeecccCCC--CCceEEEEEEeecCCcceecCCCCCceEEEEEEEcCCCcEEEEEcch------hHHHhhhhccCCc
Q psy15132 440 VQTHPIVSLSPY--QNKWTIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFND------ECNRFHDMIEKDK 511 (786)
Q Consensus 440 ~~~~~I~~L~p~--~~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~G~I~at~~~~------~~~kf~~~l~~G~ 511 (786)
...+.|++|++. ....+|+|||.++ | ..|++.=++|.|..|.|++++-.. ..-+|...|..|+
T Consensus 67 ~~~~~i~~l~~~~~g~~V~v~Grv~~~---R------~~gk~~Fl~Lrd~~~~iQ~v~~~~~~~~~~~~~~~~~~l~~es 137 (530)
T PLN02850 67 REWTDVSDLGEELAGSEVLIRGRVHTI---R------GKGKSAFLVLRQSGFTVQCVVFVSEVTVSKGMVKYAKQLSRES 137 (530)
T ss_pred ceEeEhhhcchhhCCCEEEEEEEEEEE---c------cCCCeEEEEEEeCCcCEEEEEECCccccCHHHHHHHhCCCCCC
Confidence 457899999874 3467899999842 3 346776678999999999998543 3345667899999
Q ss_pred EEEEcceEEeccCCcccccCCceEEEEccccEEEEc
Q psy15132 512 VYYISNCTLKPANKKFSSINNDYEMSFTHSTTVIPC 547 (786)
Q Consensus 512 vy~is~~~V~~a~~~y~~~~~~yei~f~~~T~I~~~ 547 (786)
++.+.+--+++..+ -......+||....-..+..+
T Consensus 138 ~V~V~G~v~~~~~~-~~~~t~~~El~~~~i~vls~a 172 (530)
T PLN02850 138 VVDVEGVVSVPKKP-VKGTTQQVEIQVRKIYCVSKA 172 (530)
T ss_pred EEEEEEEEEccCcC-CCCCCccEEEEEeEEEEEeCC
Confidence 99998855543322 222234899998876666555
No 93
>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=82.51 E-value=10 Score=34.14 Aligned_cols=77 Identities=25% Similarity=0.383 Sum_probs=51.2
Q ss_pred eEEEEEEeecCCcceecCCCCCceEEEEEEEcCCCcEEEEEcch-----hHHHhhhhccCCcEEEEcceEEeccCCcccc
Q psy15132 455 WTIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFND-----ECNRFHDMIEKDKVYYISNCTLKPANKKFSS 529 (786)
Q Consensus 455 w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~G~I~at~~~~-----~~~kf~~~l~~G~vy~is~~~V~~a~~~y~~ 529 (786)
.+|+|||.+. |. .|++.=++|.|.+|.+++++-.. ...++...|..|+++.+.+.-+...
T Consensus 2 v~v~GwV~~~---R~------~g~~~Fi~lrd~~~~lQ~v~~~~~~~~~~~~~~~~~l~~g~~V~v~G~v~~~~------ 66 (108)
T cd04322 2 VSVAGRIMSK---RG------SGKLSFADLQDESGKIQVYVNKDDLGEEEFEDFKKLLDLGDIIGVTGTPFKTK------ 66 (108)
T ss_pred EEEEEEEEEE---ec------CCCeEEEEEEECCeEEEEEEECCCCCHHHHHHHHhcCCCCCEEEEEEEEEecC------
Confidence 3678888842 32 35677778999999999988533 2234445599999999987544332
Q ss_pred cCCceEEEEccccEEEEc
Q psy15132 530 INNDYEMSFTHSTTVIPC 547 (786)
Q Consensus 530 ~~~~yei~f~~~T~I~~~ 547 (786)
...+||....-..+.++
T Consensus 67 -~g~~El~~~~~~ils~~ 83 (108)
T cd04322 67 -TGELSIFVKEFTLLSKS 83 (108)
T ss_pred -CCCEEEEeCEeEEeecc
Confidence 15688877655444444
No 94
>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=82.46 E-value=5.6 Score=35.06 Aligned_cols=79 Identities=19% Similarity=0.225 Sum_probs=54.9
Q ss_pred EEEEEEEEeccceeEeeccCCceeeEEEEEEEeCCCCEEEEEecccccccccC---CCCcEEEEEeEEEeeeC--Cceee
Q psy15132 61 DVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWGKEAETFDA---SNKPVIAVKAARVSEFQ--GGKTL 135 (786)
Q Consensus 61 DViGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~s~~~i~~tLWg~~a~~~~~---~~~~Vi~i~~~kv~~f~--g~~~l 135 (786)
|++|+|++|+... +| .---+.|.|++-.-+.+-+|....+...+ +.+..||+.+...+... |-.+|
T Consensus 1 D~VGvVvsV~~~~------~g---~~~~vYLaDe~~nll~vkfw~~l~~~~~EDvvk~~~lia~SNLQwR~~s~~~iPtl 71 (100)
T cd04495 1 DTVGVVISVGKPI------EG---KFPAVYLADECLNLLCVKFWSSLEQYAYEDVVKRRVLLAASNLQWRTESTSGVPTL 71 (100)
T ss_pred CceEEEEEEcccc------cC---ccceEEEecCCcCEEEEEEecchHHhhhhhhcccceEEEEecceEeccccCCCcee
Confidence 7899999998654 12 23368899999999999999977655432 45667888776554332 44556
Q ss_pred eecceeEEEECCC
Q psy15132 136 SLSMSSVLSLNPD 148 (786)
Q Consensus 136 s~~~~s~i~~npd 148 (786)
-.+.-|.+..||-
T Consensus 72 ~Age~t~FS~nPK 84 (100)
T cd04495 72 FAGEYSTFSANPK 84 (100)
T ss_pred eeecceeecCCcc
Confidence 6666777777773
No 95
>COG5235 RFA2 Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [DNA replication, recombination, and repair]
Probab=82.39 E-value=3.7 Score=40.88 Aligned_cols=61 Identities=16% Similarity=0.353 Sum_probs=39.0
Q ss_pred eeeEEEEEEEcccceeEEeecCCceeeEEEEEEeeccccEEEEEEecccccccc----CCCCCEEEEEeEEEeecCCc
Q psy15132 576 NIDVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWGKEAETFD----ASNKPVIAVKAARVSEFQGN 649 (786)
Q Consensus 576 ~vDViGvV~~V~~~~~i~~k~~g~~~~kr~i~l~D~s~~~i~~tLWg~~a~~~~----~~~~~vv~i~~~~V~~f~G~ 649 (786)
.|-++|+|..+. ...+| .-++|.|.+| +|+|+.|...+-..+ ...+..|-+ ...+++|+|+
T Consensus 68 ~V~fVGvvrni~------~~ttn-----~~~~iEDGTG-~Ievr~W~~~~~~~e~~~d~~~~~yvkV-~G~lk~F~GK 132 (258)
T COG5235 68 NVQFVGVVRNIK------TSTTN-----SMFVIEDGTG-SIEVRFWPGNSYEEEQCKDLEEQNYVKV-NGSLKTFNGK 132 (258)
T ss_pred eEEEEEEEEeee------ecccc-----eEEEEecCCc-eEEEEecCCCchHHHhccccccccEEEE-ecceeeeCCe
Confidence 355666665543 22223 3688999999 999999998664433 233444433 4467899998
No 96
>PRK06863 single-stranded DNA-binding protein; Provisional
Probab=81.97 E-value=8.5 Score=37.84 Aligned_cols=63 Identities=24% Similarity=0.386 Sum_probs=49.4
Q ss_pred CCceEEEEEEeecCCcceecCCCCCceEEEEEEE------cC-CC------c-EEEEEcchhHHHhhhhccCCcEEEEcc
Q psy15132 452 QNKWTIKARVTNKTPIREWNNARGSGKLFSIDLL------DE-SG------E-IRATMFNDECNRFHDMIEKDKVYYISN 517 (786)
Q Consensus 452 ~~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~------D~-~G------~-I~at~~~~~~~kf~~~l~~G~vy~is~ 517 (786)
.+...|.||+...-.+|...+ | ..+.++.|+ |. .| + +++++|+..++.+...|+.|+-+.+.+
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 577899999999888888754 2 256666654 21 12 3 899999999999999999999999987
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=81.83 E-value=5.9 Score=34.08 Aligned_cols=49 Identities=16% Similarity=0.174 Sum_probs=41.3
Q ss_pred eeeEEEEEEeeccccEEEEEEecccccccc--CCCCCEEEEEeEEEeecCC
Q psy15132 600 TYMKRDITLVDQSQASVTMTLWGKEAETFD--ASNKPVIAVKAARVSEFQG 648 (786)
Q Consensus 600 ~~~kr~i~l~D~s~~~i~~tLWg~~a~~~~--~~~~~vv~i~~~~V~~f~G 648 (786)
.....++.|.|+.|..|..+.+.+.++.|. ..+|.+..|.+.+|..-.+
T Consensus 17 ~~~~~~miL~De~G~~I~a~i~~~~~~~f~~~L~eg~vy~is~f~v~~~~~ 67 (86)
T cd04480 17 SGESLEMVLVDEKGNRIHATIPKRLAAKFRPLLKEGKWYTISNFEVAPNTG 67 (86)
T ss_pred CCcEEEEEEEcCCCCEEEEEECHHHHHhhhhhceeCCEEEEeeEEEEcCCC
Confidence 455678999999999999999999998887 5788899999888876443
No 98
>PRK07459 single-stranded DNA-binding protein; Provisional
Probab=81.72 E-value=5.2 Score=37.07 Aligned_cols=63 Identities=14% Similarity=0.259 Sum_probs=49.8
Q ss_pred CCceEEEEEEeecCCcceecCCCCCceEEEEEEEcC------CCc-EEEEEcchhHHHhhhhccCCcEEEEcc
Q psy15132 452 QNKWTIKARVTNKTPIREWNNARGSGKLFSIDLLDE------SGE-IRATMFNDECNRFHDMIEKDKVYYISN 517 (786)
Q Consensus 452 ~~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~------~G~-I~at~~~~~~~kf~~~l~~G~vy~is~ 517 (786)
.+...|.||+.+--.+|...+ | ..+.++.|+=. +.+ +.+++|+.+++.+...|+.|+-+.+.+
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 356789999998877886543 2 26777777632 223 999999999999999999999999987
No 99
>cd04323 AsnRS_cyto_like_N AsnRS_cyto_like_N: N-terminal, anticodon recognition domain of the type found in human and Saccharomyces cerevisiae cytoplasmic asparaginyl-tRNA synthetase (AsnRS), in Brugia malayai AsnRs and, in various putative bacterial AsnRSs. This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic synthesis, whereas the other exclusively with
Probab=81.56 E-value=10 Score=32.40 Aligned_cols=75 Identities=13% Similarity=0.139 Sum_probs=48.4
Q ss_pred eEEEEEEeecCCcceecCCCCCceEEEEEEEcCCCcEEEEEcchhHH--HhhhhccCCcEEEEcceEEeccCCcccccCC
Q psy15132 455 WTIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFNDECN--RFHDMIEKDKVYYISNCTLKPANKKFSSINN 532 (786)
Q Consensus 455 w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~G~I~at~~~~~~~--kf~~~l~~G~vy~is~~~V~~a~~~y~~~~~ 532 (786)
-+|+|||-++ |. .|++.=++|.|.+|.+++++-.+... ++...|..|+++.+.+- +....+.. ...+
T Consensus 2 V~v~Gwv~~~---R~------~g~~~Fi~LrD~~~~iQ~v~~~~~~~~~~~~~~l~~es~V~V~G~-v~~~~~~~-~~~~ 70 (84)
T cd04323 2 VKVFGWVHRL---RS------QKKLMFLVLRDGTGFLQCVLSKKLVTEFYDAKSLTQESSVEVTGE-VKEDPRAK-QAPG 70 (84)
T ss_pred EEEEEEEEEE---ec------CCCcEEEEEEcCCeEEEEEEcCCcchhHHHHhcCCCcCEEEEEEE-EEECCccc-CCCC
Confidence 3677888742 22 25666778999999999988654322 22345899999999774 43332221 3356
Q ss_pred ceEEEEcc
Q psy15132 533 DYEMSFTH 540 (786)
Q Consensus 533 ~yei~f~~ 540 (786)
++||...+
T Consensus 71 ~~Ei~~~~ 78 (84)
T cd04323 71 GYELQVDY 78 (84)
T ss_pred CEEEEEEE
Confidence 78887754
No 100
>PRK13732 single-stranded DNA-binding protein; Provisional
Probab=81.46 E-value=13 Score=36.76 Aligned_cols=64 Identities=22% Similarity=0.345 Sum_probs=50.5
Q ss_pred CCCceEEEEEEeecCCcceecCCCCCceEEEEEEEcC-------CC------c-EEEEEcchhHHHhhhhccCCcEEEEc
Q psy15132 451 YQNKWTIKARVTNKTPIREWNNARGSGKLFSIDLLDE-------SG------E-IRATMFNDECNRFHDMIEKDKVYYIS 516 (786)
Q Consensus 451 ~~~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~-------~G------~-I~at~~~~~~~kf~~~l~~G~vy~is 516 (786)
+.+...|.+|+..--++|...+ | ..+.+|.|+-. +| + +++++|+.+++.+...|+.|+.+++.
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 3578899999998878887644 2 36777766522 24 2 79999999999999999999999998
Q ss_pred c
Q psy15132 517 N 517 (786)
Q Consensus 517 ~ 517 (786)
+
T Consensus 82 G 82 (175)
T PRK13732 82 G 82 (175)
T ss_pred E
Confidence 7
No 101
>PRK07772 single-stranded DNA-binding protein; Provisional
Probab=81.37 E-value=8.3 Score=38.55 Aligned_cols=63 Identities=10% Similarity=0.232 Sum_probs=48.0
Q ss_pred CCceEEEEEEeecCCcceecCCCCCceEEEEEEEc-------CCC-------c-EEEEEcchhHHHhhhhccCCcEEEEc
Q psy15132 452 QNKWTIKARVTNKTPIREWNNARGSGKLFSIDLLD-------ESG-------E-IRATMFNDECNRFHDMIEKDKVYYIS 516 (786)
Q Consensus 452 ~~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D-------~~G-------~-I~at~~~~~~~kf~~~l~~G~vy~is 516 (786)
.+..+|.+|++.--.+|...+ + ..+.+|.|+- ++| . |++++|+.+++.+...|+.|+-+.+.
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 456789999999888887643 2 2566666651 112 2 89999999999999999999999888
Q ss_pred c
Q psy15132 517 N 517 (786)
Q Consensus 517 ~ 517 (786)
.
T Consensus 81 G 81 (186)
T PRK07772 81 G 81 (186)
T ss_pred E
Confidence 6
No 102
>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=81.26 E-value=11 Score=35.73 Aligned_cols=104 Identities=20% Similarity=0.299 Sum_probs=56.7
Q ss_pred Cccchhc---cCCCCceEEEEEEEEeccceeEeeccCCceeeEEEEEEEeCCCCEEEEEecccccccc-c--CCCCcEEE
Q psy15132 47 PLKTIAE---ISPDENIDVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWGKEAETF-D--ASNKPVIA 120 (786)
Q Consensus 47 ~~~~i~~---~~~~~~vDViGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~s~~~i~~tLWg~~a~~~-~--~~~~~Vi~ 120 (786)
.|.+|.+ ..+=.-+|++|+|..| ..+ .| ..--+.|.|.+..-+.+.+|++...-- + ...+.+||
T Consensus 5 ~f~~l~~p~f~pp~~EvD~VG~VvsV------~~~-~~---f~~~vYLsD~~~Nll~Ikfw~~l~~~~~eDilk~~~liA 74 (143)
T PF09104_consen 5 HFSDLQDPDFQPPYGEVDTVGFVVSV------SKK-QG---FQPLVYLSDECHNLLAIKFWTGLNQYGYEDILKPGSLIA 74 (143)
T ss_dssp -CGGGGSTT--TCCCEEEEEEEEEEE------E---TT---S--EEEEE-TTS-EEEEEESS-------SS---TT-EEE
T ss_pred chhhhcCcccCCCccccceEEEEEEE------Eec-CC---CceeEEeecCCccEEEEEeccCccccchhhhcCcceEEE
Confidence 4556653 1334679999999999 111 12 122388999999899999999987321 1 26788999
Q ss_pred EEeEEE-eee-CCceeeeecceeEEEECCC---chH-HHHHHhhhh
Q psy15132 121 VKAARV-SEF-QGGKTLSLSMSSVLSLNPD---IPE-CHKLQGWFS 160 (786)
Q Consensus 121 i~~~kv-~~f-~g~~~ls~~~~s~i~~npd---~pe-~~~l~~w~~ 160 (786)
..+..- .+. .+-..+-.+.-|.+.-||- +.| ...||+-++
T Consensus 75 ~SNLqwR~~s~s~iP~~~A~d~S~FS~nPK~~hLqe~~~~Lk~~i~ 120 (143)
T PF09104_consen 75 ASNLQWRPESTSGIPTLFATDLSVFSANPKESHLQEAFNKLKNTIE 120 (143)
T ss_dssp EEEEEE-S-TTSSS-EEEEECCEEEESS-SSCCCHHHHHHHCHHHH
T ss_pred EeeeEeecccccCCCeeEeccceeeecCccHHHHHHHHHHHHHHhh
Confidence 887644 222 2444667777888888883 333 334554444
No 103
>PRK06293 single-stranded DNA-binding protein; Provisional
Probab=81.01 E-value=9.7 Score=37.11 Aligned_cols=63 Identities=13% Similarity=0.141 Sum_probs=49.0
Q ss_pred CCceEEEEEEeecCCcceecCCCCCceEEEEEEEcCC-------Cc-EEEEEcchhHHHhhhhccCCcEEEEcc
Q psy15132 452 QNKWTIKARVTNKTPIREWNNARGSGKLFSIDLLDES-------GE-IRATMFNDECNRFHDMIEKDKVYYISN 517 (786)
Q Consensus 452 ~~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~-------G~-I~at~~~~~~~kf~~~l~~G~vy~is~ 517 (786)
++...|.+|+.+--.+|...+ | ..+.+|.|+=.. -+ +++++|+..++.....|+.|+-+.+.+
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 356789999998877776533 2 367777776321 13 999999999999999999999999987
No 104
>PRK08763 single-stranded DNA-binding protein; Provisional
Probab=80.86 E-value=9.5 Score=37.34 Aligned_cols=64 Identities=23% Similarity=0.285 Sum_probs=49.8
Q ss_pred CCCceEEEEEEeecCCcceecCCCCCceEEEEEEE------cCCC------c-EEEEEcchhHHHhhhhccCCcEEEEcc
Q psy15132 451 YQNKWTIKARVTNKTPIREWNNARGSGKLFSIDLL------DESG------E-IRATMFNDECNRFHDMIEKDKVYYISN 517 (786)
Q Consensus 451 ~~~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~------D~~G------~-I~at~~~~~~~kf~~~l~~G~vy~is~ 517 (786)
+.+...|.+|+.+--.+|...+ | ..+.+|.|+ |+.| + +++++|+.+++.....|+.|+-++|.+
T Consensus 4 ~~Nkv~LiGrLg~DPelr~t~~--G-~~va~fsVA~~~~~k~~~G~~~e~t~w~~Vv~fgk~Ae~v~~~L~KGs~V~VeG 80 (164)
T PRK08763 4 GINKVILVGNLGNDPDIKYTQS--G-MTITRISLATTSVRKDREGNTQERTEWHRVKFFGKLGEIAGEYLRKGSQCYIEG 80 (164)
T ss_pred cceEEEEEEEecCCCeEEEcCC--C-CeEEEEEEEeccceecCCCCeeccceEEEEEEehHHHHHHHHhcCCCCEEEEEE
Confidence 3678899999998777776533 2 366666665 3334 2 999999999999999999999999987
No 105
>PRK08486 single-stranded DNA-binding protein; Provisional
Probab=80.67 E-value=9.1 Score=38.15 Aligned_cols=62 Identities=19% Similarity=0.300 Sum_probs=47.8
Q ss_pred CceEEEEEEeecCCcceecCCCCCceEEEEEEE------cCCC------c-EEEEEcchhHHHhhhhccCCcEEEEcc
Q psy15132 453 NKWTIKARVTNKTPIREWNNARGSGKLFSIDLL------DESG------E-IRATMFNDECNRFHDMIEKDKVYYISN 517 (786)
Q Consensus 453 ~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~------D~~G------~-I~at~~~~~~~kf~~~l~~G~vy~is~ 517 (786)
+...|.+|+++--.+|...+ | ..+.++.|+ ++.| + |.+++|+.+++.+...|+.|+-+.|.+
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 56789999998888887643 2 255566553 3333 2 999999999999999999999999987
No 106
>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=80.29 E-value=4.6 Score=35.79 Aligned_cols=63 Identities=19% Similarity=0.339 Sum_probs=43.1
Q ss_pred CceEEEEEEeecCCcceecCCCCCceEEEEEEE--c----CCC------c-EEEEEcchhHHHhhhhccCCcEEEEcce
Q psy15132 453 NKWTIKARVTNKTPIREWNNARGSGKLFSIDLL--D----ESG------E-IRATMFNDECNRFHDMIEKDKVYYISNC 518 (786)
Q Consensus 453 ~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~--D----~~G------~-I~at~~~~~~~kf~~~l~~G~vy~is~~ 518 (786)
++..|.|||...-.+|...+ | ..+.++.|+ + +.+ . +++++|+++++.+.+.++.|+.+.|.+-
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 45689999998777776642 2 245455432 2 111 3 9999999999999999999999999883
No 107
>PRK05673 dnaE DNA polymerase III subunit alpha; Validated
Probab=79.29 E-value=6 Score=50.46 Aligned_cols=83 Identities=20% Similarity=0.297 Sum_probs=56.7
Q ss_pred cCccchhccCCCCceEEEEEEEEeccceeEeeccCCceeeEEEEEEEeCCCCEEEEEeccccccccc--CCCCcEEEEEe
Q psy15132 46 VPLKTIAEISPDENIDVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWGKEAETFD--ASNKPVIAVKA 123 (786)
Q Consensus 46 ~~~~~i~~~~~~~~vDViGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~s~~~i~~tLWg~~a~~~~--~~~~~Vi~i~~ 123 (786)
.++.+|.....+..|-+.|+|+++.. +.+|+ |+. .--++|.|.+| ++++++|.+..+.+. ...+.+|.++|
T Consensus 966 ~~~~~l~~~~~g~~V~v~G~I~~vk~---~~TKk-G~~--mafltLeD~TG-~iEvviFp~~ye~~~~~L~~g~iV~V~G 1038 (1135)
T PRK05673 966 TRLADLEPTEGGSVVTVAGLVVSVRR---RVTKR-GNK--MAIVTLEDLSG-RIEVMLFSEALEKYRDLLEEDRIVVVKG 1038 (1135)
T ss_pred cCHHHHhccccCceEEEEEEEEEEEe---cccCC-CCe--EEEEEEEeCCC-cEEEEECHHHHHHHHHHhccCCEEEEEE
Confidence 45556544445778999999998754 45554 543 45689999999 899999998766553 25677777776
Q ss_pred EEEeeeCCceeee
Q psy15132 124 ARVSEFQGGKTLS 136 (786)
Q Consensus 124 ~kv~~f~g~~~ls 136 (786)
+|..+.|...+.
T Consensus 1039 -kVe~~~~~~qli 1050 (1135)
T PRK05673 1039 -QVSFDDGGLRLT 1050 (1135)
T ss_pred -EEEecCCeEEEE
Confidence 665554433333
No 108
>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=79.24 E-value=12 Score=32.76 Aligned_cols=60 Identities=17% Similarity=0.289 Sum_probs=43.2
Q ss_pred EEEEEEeecCCcceecCCCCCceEEEEEEE--c---------CCCc-EEEEEcchhHHHhhhhccCCcEEEEcce
Q psy15132 456 TIKARVTNKTPIREWNNARGSGKLFSIDLL--D---------ESGE-IRATMFNDECNRFHDMIEKDKVYYISNC 518 (786)
Q Consensus 456 ~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~--D---------~~G~-I~at~~~~~~~kf~~~l~~G~vy~is~~ 518 (786)
.|.|||...-.+|...+ | ..+.++.|+ + ..-. +++++|++.++.+...++.|+.+.+++.
T Consensus 2 ~l~G~l~~~p~~~~~~~--g-~~~~~~~v~~~~~~~~~~~~~~~~~~~~v~~~g~~a~~~~~~~~kG~~V~v~G~ 73 (100)
T cd04496 2 ILIGRLGKDPELRYTPS--G-TPVARFSLAVNRRRKDRDEEEEETDWIRVVAFGKLAENAAKYLKKGDLVYVEGR 73 (100)
T ss_pred EEEEEecCCCEEEECCC--C-CEEEEEEEEEcCceecccccccccEEEEEEEEhHHHHHHHHHhCCCCEEEEEEE
Confidence 57788887776666543 1 244444432 2 1123 9999999999999999999999999984
No 109
>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=78.65 E-value=9.7 Score=32.61 Aligned_cols=59 Identities=15% Similarity=0.219 Sum_probs=43.2
Q ss_pred eEEEEEEeecCCcceecCCCCCceEEEEEEEcCCCcEEEEEcch-hHHHhhhhcc-CCcEEEEcce
Q psy15132 455 WTIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFND-ECNRFHDMIE-KDKVYYISNC 518 (786)
Q Consensus 455 w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~G~I~at~~~~-~~~kf~~~l~-~G~vy~is~~ 518 (786)
..|+|.|... +.|...+ ...++++-+.|.++.|.+..|.. ..+.+ ..|+ +|+|+.+.+-
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---GRKILTFKVTDYTSSITVKKFLRKDEKDK-EELKSKGDWVRVRGK 62 (82)
T ss_pred EEEEEEEEEE-EEEEecC---CCEEEEEEEEcCCCCEEEEEeccCChhHH-hhcccCCCEEEEEEE
Confidence 4678888754 3455443 25788999999999999999983 33333 5689 9999988773
No 110
>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=78.10 E-value=26 Score=31.54 Aligned_cols=81 Identities=14% Similarity=0.136 Sum_probs=53.9
Q ss_pred CceEEEEEEeecCCcceecCCCCCceEEEEEEEcCCCcEEEEEcchh----HHHhhhhccCCcEEEEcceEEeccCCccc
Q psy15132 453 NKWTIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFNDE----CNRFHDMIEKDKVYYISNCTLKPANKKFS 528 (786)
Q Consensus 453 ~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~G~I~at~~~~~----~~kf~~~l~~G~vy~is~~~V~~a~~~y~ 528 (786)
...+|+|||.++ |. .|++.=++|.|.+|.|++++-++. .-++-..|..|+++.+.+--.....
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------LGGIKFVILRDREGIVQVTAPKKKVDKELFKTVRKLSRESVISVTGTVKAEPK---- 79 (108)
T ss_pred CEEEEEEEEEee---ec------cCCeEEEEEecCCeeEEEEEeCCCCCHHHHHHHhCCCCcCEEEEEEEEEeCCC----
Confidence 458999999842 33 356666789999999999886542 1123345899999999996443221
Q ss_pred ccCCceEEEEccccEEEEc
Q psy15132 529 SINNDYEMSFTHSTTVIPC 547 (786)
Q Consensus 529 ~~~~~yei~f~~~T~I~~~ 547 (786)
....|||....-..+..+
T Consensus 80 -~~~~~Ei~~~~i~il~~~ 97 (108)
T cd04316 80 -APNGVEIIPEEIEVLSEA 97 (108)
T ss_pred -CCCCEEEEEeEEEEEeCC
Confidence 135799988765444443
No 111
>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=77.69 E-value=20 Score=33.73 Aligned_cols=86 Identities=15% Similarity=0.200 Sum_probs=55.8
Q ss_pred CceEEEEEEeecCCcceecCCCCCceEEEEEEEcCCCcEEEEEcchhHH--HhhhhccCCcEEEEcceEEeccC--Cccc
Q psy15132 453 NKWTIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFNDECN--RFHDMIEKDKVYYISNCTLKPAN--KKFS 528 (786)
Q Consensus 453 ~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~G~I~at~~~~~~~--kf~~~l~~G~vy~is~~~V~~a~--~~y~ 528 (786)
...+|+|||.++ |. .|++.=++|.|.+|.+++++-....+ ++...|..|+++.+.+.-..... +.-.
T Consensus 15 ~~V~i~Gwv~~~---R~------~gk~~Fi~LrD~~g~~Q~v~~~~~~~~~~~~~~l~~gs~V~V~G~~~~~~~~~~~~~ 85 (135)
T cd04317 15 QEVTLCGWVQRR---RD------HGGLIFIDLRDRYGIVQVVFDPEEAPEFELAEKLRNESVIQVTGKVRARPEGTVNPK 85 (135)
T ss_pred CEEEEEEeEehh---cc------cCCEEEEEEecCCeeEEEEEeCCchhHHHHHhCCCCccEEEEEEEEECCCccccCCC
Confidence 457999999842 33 35666678999999999988654333 23346999999999996443211 1111
Q ss_pred ccCCceEEEEccccEEEEc
Q psy15132 529 SINNDYEMSFTHSTTVIPC 547 (786)
Q Consensus 529 ~~~~~yei~f~~~T~I~~~ 547 (786)
...+.+||....-..+.++
T Consensus 86 ~~~~~~El~~~~i~vl~~~ 104 (135)
T cd04317 86 LPTGEIEVVASELEVLNKA 104 (135)
T ss_pred CCCCcEEEEEeEEEEEECC
Confidence 2246789998765444444
No 112
>PRK05159 aspC aspartyl-tRNA synthetase; Provisional
Probab=74.88 E-value=15 Score=41.97 Aligned_cols=93 Identities=16% Similarity=0.147 Sum_probs=65.3
Q ss_pred eeeecccCCCC--CceEEEEEEeecCCcceecCCCCCceEEEEEEEcCCCcEEEEEcchh---HHHhhhhccCCcEEEEc
Q psy15132 442 THPIVSLSPYQ--NKWTIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFNDE---CNRFHDMIEKDKVYYIS 516 (786)
Q Consensus 442 ~~~I~~L~p~~--~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~G~I~at~~~~~---~~kf~~~l~~G~vy~is 516 (786)
.+.|++|++.. +..+|.|||.++ |. .|++.=++|.|.+|.|++++-.+. .-++-..|..|+++.+.
T Consensus 4 ~~~~~~l~~~~~g~~V~i~GrV~~~---R~------~gk~~Fl~LrD~~g~iQ~v~~~~~~~~~~~~~~~L~~gs~V~v~ 74 (437)
T PRK05159 4 RHLTSELTPELDGEEVTLAGWVHEI---RD------LGGIAFLILRDRSGIIQVVVKKKVDEELFETIKKLKRESVVSVT 74 (437)
T ss_pred eeEhhhCChhhCCCEEEEEEEeEee---ec------CCCeEEEEEEcCCcEEEEEEeCCccHHHHHHHhCCCCCcEEEEE
Confidence 46788888764 567999999853 32 357777889999999999885432 22334568999999999
Q ss_pred ceEEeccCCcccccCCceEEEEccccEEEEcc
Q psy15132 517 NCTLKPANKKFSSINNDYEMSFTHSTTVIPCN 548 (786)
Q Consensus 517 ~~~V~~a~~~y~~~~~~yei~f~~~T~I~~~~ 548 (786)
+.-.+.. + ....+||....-+.+..+.
T Consensus 75 G~v~~~~-~----~~~~~el~~~~i~vls~a~ 101 (437)
T PRK05159 75 GTVKANP-K----APGGVEVIPEEIEVLNKAE 101 (437)
T ss_pred EEEEcCC-C----CCCCEEEEEeEEEEEeCCC
Confidence 8544332 1 2457899987766666554
No 113
>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=74.66 E-value=16 Score=35.81 Aligned_cols=64 Identities=19% Similarity=0.275 Sum_probs=47.4
Q ss_pred CCceEEEEEEeecCCcceecCCCCCceEEEEEEE------cCCC-------cEEEEEcchhHHHhhhhccCCcEEEEcce
Q psy15132 452 QNKWTIKARVTNKTPIREWNNARGSGKLFSIDLL------DESG-------EIRATMFNDECNRFHDMIEKDKVYYISNC 518 (786)
Q Consensus 452 ~~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~------D~~G-------~I~at~~~~~~~kf~~~l~~G~vy~is~~ 518 (786)
.++..|.+||..--.+|...+ | ..+.+|.|+ |+.| -|++++|+.+++.+...|+.|+.+.|.+-
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 367789999998777776543 2 244445443 3233 39999999999999999999999999883
No 114
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain
Probab=74.40 E-value=18 Score=32.13 Aligned_cols=57 Identities=14% Similarity=0.219 Sum_probs=43.2
Q ss_pred CceEEEEEEeecCCcceecCCCCCceEEEEEEEcCCCcEEEEEcchhHHHhh-hhccCCcEEEEcc
Q psy15132 453 NKWTIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFNDECNRFH-DMIEKDKVYYISN 517 (786)
Q Consensus 453 ~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~G~I~at~~~~~~~kf~-~~l~~G~vy~is~ 517 (786)
.+.-|+|=|.. ++.. .+....|+|.|++..|+|++|.....+.. ..+++|+-+.+..
T Consensus 22 ~~vwV~GEIs~------~~~~--~~gh~YftLkD~~a~i~~~~~~~~~~~i~~~~l~~G~~V~v~g 79 (99)
T PF13742_consen 22 PNVWVEGEISN------LKRH--SSGHVYFTLKDEEASISCVIFRSRARRIRGFDLKDGDKVLVRG 79 (99)
T ss_pred CCEEEEEEEee------cEEC--CCceEEEEEEcCCcEEEEEEEHHHHhhCCCCCCCCCCEEEEEE
Confidence 44557777773 3322 23558899999888999999999988887 7899998877665
No 115
>PRK06642 single-stranded DNA-binding protein; Provisional
Probab=73.72 E-value=18 Score=34.89 Aligned_cols=63 Identities=24% Similarity=0.381 Sum_probs=49.2
Q ss_pred CCceEEEEEEeecCCcceecCCCCCceEEEEEEE------cC-CC------c-EEEEEcch-hHHHhhhhccCCcEEEEc
Q psy15132 452 QNKWTIKARVTNKTPIREWNNARGSGKLFSIDLL------DE-SG------E-IRATMFND-ECNRFHDMIEKDKVYYIS 516 (786)
Q Consensus 452 ~~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~------D~-~G------~-I~at~~~~-~~~kf~~~l~~G~vy~is 516 (786)
.+...|.||+.+-..+|...+ | ..+.++.|+ |. .| + +++++|+. +++.+...|+.|+-+++.
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 477899999998877887643 2 267777776 22 23 2 99999996 888899999999999998
Q ss_pred c
Q psy15132 517 N 517 (786)
Q Consensus 517 ~ 517 (786)
+
T Consensus 82 G 82 (152)
T PRK06642 82 G 82 (152)
T ss_pred E
Confidence 7
No 116
>PRK06958 single-stranded DNA-binding protein; Provisional
Probab=71.92 E-value=21 Score=35.55 Aligned_cols=63 Identities=24% Similarity=0.359 Sum_probs=48.2
Q ss_pred CCceEEEEEEeecCCcceecCCCCCceEEEEEEE------cC-CC------c-EEEEEcchhHHHhhhhccCCcEEEEcc
Q psy15132 452 QNKWTIKARVTNKTPIREWNNARGSGKLFSIDLL------DE-SG------E-IRATMFNDECNRFHDMIEKDKVYYISN 517 (786)
Q Consensus 452 ~~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~------D~-~G------~-I~at~~~~~~~kf~~~l~~G~vy~is~ 517 (786)
.+...|.+|+..--.+|...+ + ..+.+|.|+ |. +| + +++++|+.+++.+...|+.|+-+.|..
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 467899999998777776543 2 256566654 32 22 3 899999999999999999999999987
No 117
>PRK05673 dnaE DNA polymerase III subunit alpha; Validated
Probab=71.07 E-value=9.1 Score=48.89 Aligned_cols=71 Identities=24% Similarity=0.446 Sum_probs=52.4
Q ss_pred eeecccCC--CCCceEEEEEEeecCCcceecCCCCCceEEEEEEEcCCCcEEEEEcchhHHHhhhhccCCcEEEEcc
Q psy15132 443 HPIVSLSP--YQNKWTIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFNDECNRFHDMIEKDKVYYISN 517 (786)
Q Consensus 443 ~~I~~L~p--~~~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~G~I~at~~~~~~~kf~~~l~~G~vy~is~ 517 (786)
.++.+|.. ......+.+-|+.+ |.....+|+ .+.-++|-|.+|+|.+++|.+.-+++.+.|++|.++.|.+
T Consensus 966 ~~~~~l~~~~~g~~V~v~G~I~~v---k~~~TKkG~-~mafltLeD~TG~iEvviFp~~ye~~~~~L~~g~iV~V~G 1038 (1135)
T PRK05673 966 TRLADLEPTEGGSVVTVAGLVVSV---RRRVTKRGN-KMAIVTLEDLSGRIEVMLFSEALEKYRDLLEEDRIVVVKG 1038 (1135)
T ss_pred cCHHHHhccccCceEEEEEEEEEE---EecccCCCC-eEEEEEEEeCCCcEEEEECHHHHHHHHHHhccCCEEEEEE
Confidence 45666642 23345677777754 444333332 5667789999999999999999899999999999999866
No 118
>PRK07373 DNA polymerase III subunit alpha; Reviewed
Probab=70.67 E-value=10 Score=43.44 Aligned_cols=74 Identities=12% Similarity=0.164 Sum_probs=51.8
Q ss_pred cCccchhccCCCCceEEEEEEEEeccceeEeeccCCceeeEEEEEEEeCCCCEEEEEecccccccccC--CCCcEEEEEe
Q psy15132 46 VPLKTIAEISPDENIDVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWGKEAETFDA--SNKPVIAVKA 123 (786)
Q Consensus 46 ~~~~~i~~~~~~~~vDViGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~s~~~i~~tLWg~~a~~~~~--~~~~Vi~i~~ 123 (786)
.++.+|.....+..|-|.|+|+++.. +.+|+ |+. .--++|.|.+| ++++++|.+..+.+.. ..+.++.++|
T Consensus 269 ~~~~~l~~~~~~~~v~vaG~I~~ik~---~~TKk-G~~--maf~~leD~tG-~ie~vvFp~~y~~~~~~l~~~~~v~v~G 341 (449)
T PRK07373 269 INLSELEEQKEKTKVSAVVMLNEVKK---IVTKK-GDP--MAFLQLEDLSG-QSEAVVFPKSYERISELLQVDARLIIWG 341 (449)
T ss_pred cCHHHHhcccCCCEEEEEEEEEEeEe---cccCC-CCE--EEEEEEEECCC-CEEEEECHHHHHHHHHHhccCCEEEEEE
Confidence 35555543345667889999999754 45554 542 45688999998 8999999998777642 5666777776
Q ss_pred EEEe
Q psy15132 124 ARVS 127 (786)
Q Consensus 124 ~kv~ 127 (786)
+|.
T Consensus 342 -~v~ 344 (449)
T PRK07373 342 -KVD 344 (449)
T ss_pred -EEE
Confidence 553
No 119
>KOG3056|consensus
Probab=70.31 E-value=25 Score=40.53 Aligned_cols=103 Identities=12% Similarity=0.224 Sum_probs=68.9
Q ss_pred Cceeeec----ccCC---CCCceEEEEEEeecCCcceecCCCCCceEEEEEEEcCCCcEEEEEcchhHHHhhhhccCCcE
Q psy15132 440 VQTHPIV----SLSP---YQNKWTIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFNDECNRFHDMIEKDKV 512 (786)
Q Consensus 440 ~~~~~I~----~L~p---~~~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~G~I~at~~~~~~~kf~~~l~~G~v 512 (786)
+...+|+ .|-+ ...+|.+.|-|+.|+.++.-.+.+ .-.++.+.-++..-.+..-+|++...+++ .++.|.|
T Consensus 166 ~k~i~ls~~~~~l~r~~kf~~~Wvt~GvI~~K~~~K~t~~G~-~y~iwkL~dLk~~q~vslfLFG~a~k~~w-k~k~GtV 243 (578)
T KOG3056|consen 166 RKLIRLSGKLFNLIRGPKFEENWVTMGVIVEKSDPKFTSNGN-PYSIWKLTDLKDHQTVSLFLFGKAHKRYW-KIKLGTV 243 (578)
T ss_pred CcceeehhhhhhcccCcccccCeEEEEEEeecCCcccccCCC-ceEEEEeeecCccceeEEEEecHHHHHHh-hhccCcE
Confidence 3445565 4443 245999999999999998765421 11333333222233699999999776655 4999999
Q ss_pred EEEcceEEeccCCcccccCCceEEEEccccEEEEc
Q psy15132 513 YYISNCTLKPANKKFSSINNDYEMSFTHSTTVIPC 547 (786)
Q Consensus 513 y~is~~~V~~a~~~y~~~~~~yei~f~~~T~I~~~ 547 (786)
+-|-|+.|.+.+..- ...+.|.++..-.|.++
T Consensus 244 ialLNp~v~k~~~gs---~~~f~LsIds~~~ilei 275 (578)
T KOG3056|consen 244 IALLNPEVLKDRPGS---RKSFSLSIDSSKKILEI 275 (578)
T ss_pred EEEeCccccCCCCCC---cceEEEEecCccceEEe
Confidence 999999997654321 14677888776555555
No 120
>PF15489 CTC1: CST, telomere maintenance, complex subunit CTC1
Probab=69.72 E-value=1.4e+02 Score=37.69 Aligned_cols=206 Identities=14% Similarity=0.174 Sum_probs=112.8
Q ss_pred Cccchhc-cCCCCceEEEEEEEEeccceeEe----eccCCc----eeeE--EEEEEEeCCCCEEEEEecccc-cccccC-
Q psy15132 47 PLKTIAE-ISPDENIDVLGVCIDAAELSSVT----GKTNQK----TYMK--RDITLVDQSQASVTMTLWGKE-AETFDA- 113 (786)
Q Consensus 47 ~~~~i~~-~~~~~~vDViGvV~~v~~~~~i~----~k~~g~----~~~k--r~i~l~D~s~~~i~~tLWg~~-a~~~~~- 113 (786)
++.++.. -..+.+|.+-|+|.+-.--.... ++.++. ...+ --++..|....-. +...-+. +..+..
T Consensus 825 sl~~lls~s~s~sLVSFs~~I~srt~ce~~~~~~~~~~~~~~~~~~~vkltv~L~v~D~~~p~~-ldVYi~~~h~p~plG 903 (1144)
T PF15489_consen 825 SLSELLSSSSSDSLVSFSAEILSRTLCEPLNARRWSKPGNAIASRGCVKLTVALTVADCESPPH-LDVYIEDPHLPYPLG 903 (1144)
T ss_pred cHHHHhccCCCCceEEEEEEEEEeeeccCCccccccCCCCCcccccccceEEEEEEecCCCCCe-EEEEecCCCCCCccc
Confidence 4555553 24578999999998853222111 111111 1111 1244445544111 2222221 112221
Q ss_pred -CCCcEEEEEeE--EEeeeCCceeeeecceeEEEECCCchHHHHHHhhhhccCCCceeeeccccCCCCCCCcchhhhHHH
Q psy15132 114 -SNKPVIAVKAA--RVSEFQGGKTLSLSMSSVLSLNPDIPECHKLQGWFSTQTNTRFEPVSQRTGGMGGGAAGNLLLMRE 190 (786)
Q Consensus 114 -~~~~Vi~i~~~--kv~~f~g~~~ls~~~~s~i~~npd~pe~~~l~~w~~~~~~~~~~~~s~~~~~~~~~~~~~~~ti~e 190 (786)
-.|.+|-|.+. ||+.. |..++...+.|.|.+.-.-+|. + .....+...+.+
T Consensus 904 LLPGA~V~f~~lerkVSRs-~nVYC~~~psS~VtVlS~p~~t-----------~--------------~~~~~P~~~L~~ 957 (1144)
T PF15489_consen 904 LLPGARVLFSQLERKVSRS-HNVYCCFLPSSSVTVLSFPPET-----------N--------------VSPPLPHIYLAE 957 (1144)
T ss_pred ccCCceeeeehhhhhhhcc-CcEEEEEcCCceEEEEecCccc-----------C--------------CCCCCCeEEehh
Confidence 35667778876 78886 6788888878877664321111 0 001112334444
Q ss_pred HHhhcCCCCCCCcEEEEEEEEEEEecCceEEeCCCCCCCCcceeeCCCceeecc----cCCCcCCceeEeeeeeEEEEec
Q psy15132 191 IQDQQLGMGDKADYCSVRGIIQVFRGSNTTYKACPSQDCNKKVIDQNNGMYRCE----KCNKEFNTFTYRLILPVMIGDW 266 (786)
Q Consensus 191 i~~~~l~~~~~~~~~~v~a~I~~i~~~~~~Y~aC~~~~C~kKv~~~~~~~~~C~----~C~~~~~~~~~ry~l~~~v~D~ 266 (786)
... ....+....+.|.|+.+..=...+ .|. .|..-... | .|. .|... .-..+=...+.|.|+
T Consensus 958 ~~~----~~~~~~~a~~~chVV~V~~l~L~W-vCa--~C~si~~q---g--~Csr~~p~C~s~--~sV~qA~ar~~vEDG 1023 (1144)
T PF15489_consen 958 LLQ----GSQSPFQARVSCHVVSVLSLQLQW-VCA--HCGSICPQ---G--RCSRQSPPCPSQ--TSVFQASARLLVEDG 1023 (1144)
T ss_pred hhC----CCCCCceEEEEEEEEEEEEEEeee-hhh--hccCcccC---C--cCCCCCCCCCCC--cceeeEEEEEEEecC
Confidence 322 112233566778888775432222 676 67644321 2 363 35433 345567778889999
Q ss_pred CCcEEEEeehHHHHHHhCCChhhhhcc
Q psy15132 267 TNSVWVTLFQNEAESILGVTAQEVGES 293 (786)
Q Consensus 267 Tg~~~~~~F~~~a~~ilg~sa~el~~~ 293 (786)
||++.+++-|+....+||.+..|...+
T Consensus 1024 TaeA~v~~~~~~V~~lLgL~~~eW~~L 1050 (1144)
T PF15489_consen 1024 TAEAVVWCRGHHVAALLGLSPSEWESL 1050 (1144)
T ss_pred CeeEEEEECCcHHHHHhCCCHHHHHHH
Confidence 999999999999999999998876554
No 121
>PTZ00385 lysyl-tRNA synthetase; Provisional
Probab=69.60 E-value=34 Score=40.89 Aligned_cols=77 Identities=12% Similarity=0.194 Sum_probs=53.7
Q ss_pred ceEEEEEEeecCCcceecCCCCCceEEEEEEEcCCCcEEEEEcchh------HHHhhhhccCCcEEEEcceEEeccCCcc
Q psy15132 454 KWTIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFNDE------CNRFHDMIEKDKVYYISNCTLKPANKKF 527 (786)
Q Consensus 454 ~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~G~I~at~~~~~------~~kf~~~l~~G~vy~is~~~V~~a~~~y 527 (786)
..+|.|||.++ |. .|++.=++|.|.+|.|++++-.+. ...+...|..|+++.+.+.-.+.
T Consensus 109 ~V~vaGrV~~~---R~------~Gk~~F~~LrD~~G~IQvv~~~~~~~~~~~~~~~~~~l~~gdiV~V~G~v~~t----- 174 (659)
T PTZ00385 109 TVRVAGRVTSV---RD------IGKIIFVTIRSNGNELQVVGQVGEHFTREDLKKLKVSLRVGDIIGADGVPCRM----- 174 (659)
T ss_pred EEEEEEEEEee---ec------cCCeEEEEEEECCceEEEEEECCccCCHHHHHHHHhCCCCCCEEEEEEEEEec-----
Confidence 48999999953 33 467777789999999999996432 22233468999999998854322
Q ss_pred cccCCceEEEEccccEEEE
Q psy15132 528 SSINNDYEMSFTHSTTVIP 546 (786)
Q Consensus 528 ~~~~~~yei~f~~~T~I~~ 546 (786)
-.+.++|....-+.+.+
T Consensus 175 --~~GeleI~~~~i~lLsk 191 (659)
T PTZ00385 175 --QRGELSVAASRMLILSP 191 (659)
T ss_pred --CCceEEEEeeEEEEech
Confidence 13567777777665555
No 122
>PLN02502 lysyl-tRNA synthetase
Probab=68.97 E-value=24 Score=41.53 Aligned_cols=79 Identities=19% Similarity=0.325 Sum_probs=55.7
Q ss_pred CceEEEEEEeecCCcceecCCCCCceEEEEEEEcCCCcEEEEEcchh-------HHHhhhhccCCcEEEEcceEEeccCC
Q psy15132 453 NKWTIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFNDE-------CNRFHDMIEKDKVYYISNCTLKPANK 525 (786)
Q Consensus 453 ~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~G~I~at~~~~~-------~~kf~~~l~~G~vy~is~~~V~~a~~ 525 (786)
...+|.|||.++ |. .|++.=++|.|.+|.|++.+-.+. .+++...|..|+++.+.+.-.+..
T Consensus 109 ~~V~v~GrV~~~---R~------~Gk~~F~~LrD~~g~iQv~~~~~~~~~~~~~~~~~~~~l~~gdiV~V~G~~~~t~-- 177 (553)
T PLN02502 109 VSVSVAGRIMAK---RA------FGKLAFYDLRDDGGKIQLYADKKRLDLDEEEFEKLHSLVDRGDIVGVTGTPGKTK-- 177 (553)
T ss_pred CEEEEEEEEEEE---ec------CCCeEEEEEecCCccEEEEEECccccchhHHHHHHHhCCCCCcEEEEEEEEEecC--
Confidence 347899999953 32 368888899999999999885432 223444589999999998654432
Q ss_pred cccccCCceEEEEccccEEEEc
Q psy15132 526 KFSSINNDYEMSFTHSTTVIPC 547 (786)
Q Consensus 526 ~y~~~~~~yei~f~~~T~I~~~ 547 (786)
...++|...+-..+.++
T Consensus 178 -----~gelel~~~~i~vLs~~ 194 (553)
T PLN02502 178 -----KGELSIFPTSFEVLTKC 194 (553)
T ss_pred -----CCCEEEEEeEEEEEecc
Confidence 25788887766655555
No 123
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=68.79 E-value=2.6 Score=26.90 Aligned_cols=21 Identities=29% Similarity=1.091 Sum_probs=15.6
Q ss_pred CCCccccccccccCCceeeeCCCCCc
Q psy15132 689 CPSQDCNKKVIDQNNGMYRCEKCNKE 714 (786)
Q Consensus 689 C~~~~C~kkv~~~~~g~~~C~~C~~~ 714 (786)
|| .|++++.+ +..| |+.||..
T Consensus 2 Cp--~CG~~~~~--~~~f-C~~CG~~ 22 (23)
T PF13240_consen 2 CP--NCGAEIED--DAKF-CPNCGTP 22 (23)
T ss_pred Cc--ccCCCCCC--cCcc-hhhhCCc
Confidence 88 69999753 3444 9999974
No 124
>COG0629 Ssb Single-stranded DNA-binding protein [DNA replication, recombination, and repair]
Probab=68.78 E-value=14 Score=36.18 Aligned_cols=67 Identities=21% Similarity=0.328 Sum_probs=48.6
Q ss_pred CCceEEEEEEeecCCcceecCCCCCceEEEEE---EEcCCC-------c-EEEEEcchhHHHhhhhccCCcEEEEcce
Q psy15132 452 QNKWTIKARVTNKTPIREWNNARGSGKLFSID---LLDESG-------E-IRATMFNDECNRFHDMIEKDKVYYISNC 518 (786)
Q Consensus 452 ~~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~---L~D~~G-------~-I~at~~~~~~~kf~~~l~~G~vy~is~~ 518 (786)
.++..+.+|+++.-++|...+......++... ..|..+ + |++++|+.+++.....|+.|+-++|.+.
T Consensus 3 ~Nkv~LvG~l~~DPE~r~t~~g~~~v~~~~~a~~r~~~~~~~~~~~~t~~~~vv~wgk~Ae~~~~yl~KG~~V~VeG~ 80 (167)
T COG0629 3 MNKVILVGRLTRDPELRYTPNGGAVVALFSAAVNRRFDNQSGERDEETDWIRVVIWGKLAENAAEYLKKGSLVYVEGR 80 (167)
T ss_pred cceEEEEeecccCcceeecCCCCeeeEEEEEEeccccccCCcccccccceEEEEEehHHHHHHHHHhcCCCEEEEEEE
Confidence 56788999999999988875422111222222 333221 4 9999999999999999999999999884
No 125
>PRK00484 lysS lysyl-tRNA synthetase; Reviewed
Probab=68.64 E-value=38 Score=39.32 Aligned_cols=78 Identities=21% Similarity=0.244 Sum_probs=55.3
Q ss_pred CceEEEEEEeecCCcceecCCCCCceEEEEEEEcCCCcEEEEEcchh-----HHHhhhhccCCcEEEEcceEEeccCCcc
Q psy15132 453 NKWTIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFNDE-----CNRFHDMIEKDKVYYISNCTLKPANKKF 527 (786)
Q Consensus 453 ~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~G~I~at~~~~~-----~~kf~~~l~~G~vy~is~~~V~~a~~~y 527 (786)
...+|.|||.++ |. .|++.=++|.|.+|.|++++-.+. .+.+. .|..|+++.+.+.-++..
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------MGKASFATLQDGSGRIQLYVSKDDVGEEALEAFK-KLDLGDIIGVEGTLFKTK---- 120 (491)
T ss_pred cEEEEEEEEEEE---ec------CCceEEEEEEcCCccEEEEEECCcCCHHHHHHHh-cCCCCCEEEEEEEEEEcC----
Confidence 458999999953 43 367778899999999999885432 22333 399999999988655432
Q ss_pred cccCCceEEEEccccEEEEc
Q psy15132 528 SSINNDYEMSFTHSTTVIPC 547 (786)
Q Consensus 528 ~~~~~~yei~f~~~T~I~~~ 547 (786)
.+.+||....-..+.++
T Consensus 121 ---~ge~el~~~~~~vls~~ 137 (491)
T PRK00484 121 ---TGELSVKATELTLLTKS 137 (491)
T ss_pred ---CCcEEEEEeEEEEEecc
Confidence 25788888776655554
No 126
>TIGR00643 recG ATP-dependent DNA helicase RecG.
Probab=68.36 E-value=13 Score=44.81 Aligned_cols=68 Identities=16% Similarity=0.179 Sum_probs=51.1
Q ss_pred eeeecccCCCCCceEEEEEEeecCCcceecCCCCCceEEEEEEEc-CCCcEEEEEcchhHHHhhhhccCCcEEEEcc
Q psy15132 442 THPIVSLSPYQNKWTIKARVTNKTPIREWNNARGSGKLFSIDLLD-ESGEIRATMFNDECNRFHDMIEKDKVYYISN 517 (786)
Q Consensus 442 ~~~I~~L~p~~~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D-~~G~I~at~~~~~~~kf~~~l~~G~vy~is~ 517 (786)
..||+++.++. .-+|.|+|+... ... .+..+.+.+.+.| .+|.+.+++|+.. -....|++|+.|.+++
T Consensus 23 ~~~i~~~~~g~-~~~~~~~v~~~~---~~~--~~~~~~~~~~~~d~~~~~~~~~~F~~~--~~~~~~~~g~~~~~~G 91 (630)
T TIGR00643 23 LQTIGELLPGE-RATIVGEVLSHC---IFG--FKRRKVLKLRLKDGGYKKLELRFFNRA--FLKKKFKVGSKVVVYG 91 (630)
T ss_pred ccCHHHcCCCC-EEEEEEEEEEeE---ecc--CCCCceEEEEEEECCCCEEEEEEECCH--HHHhhCCCCCEEEEEE
Confidence 56899998874 579999998631 111 1224689999999 9999999999832 3357899999998876
No 127
>PRK07279 dnaE DNA polymerase III DnaE; Reviewed
Probab=68.30 E-value=11 Score=47.51 Aligned_cols=71 Identities=20% Similarity=0.425 Sum_probs=52.8
Q ss_pred eeeecccCCCCCceEEEEEEeecCCcceecCC-CCCceEEEEEEEcCCCcEEEEEcchhHHHhhhhccCCcEEEEcc
Q psy15132 442 THPIVSLSPYQNKWTIKARVTNKTPIREWNNA-RGSGKLFSIDLLDESGEIRATMFNDECNRFHDMIEKDKVYYISN 517 (786)
Q Consensus 442 ~~~I~~L~p~~~~w~I~~RV~~k~~~r~~~~~-~~~g~~~~~~L~D~~G~I~at~~~~~~~kf~~~l~~G~vy~is~ 517 (786)
..++++|.. .....+.|.|+.. |..... +|+ .+.-++|-|.+|+|.+++|.+...++.+.|++|.++.+.+
T Consensus 875 ~~~~~~l~~-~~~~~~~~~i~~~---~~~~tk~~g~-~maf~~leD~~g~ie~~vFp~~y~~~~~~l~~~~~~~v~G 946 (1034)
T PRK07279 875 FTPISQLVK-NSEATILVQIQSI---RVIRTKTKGQ-QMAFLSVTDTKKKLDVTLFPETYRQYKDELKEGKFYYLKG 946 (1034)
T ss_pred CccHHHHhc-CCcceEEEEEEEE---EEEEEcCCCC-eEEEEEEeeCCCcEEEEECHHHHHHHHHHhccCCEEEEEE
Confidence 346777753 2345677777743 444333 333 4667789999999999999999999999999999999866
No 128
>PRK07135 dnaE DNA polymerase III DnaE; Validated
Probab=67.62 E-value=14 Score=46.17 Aligned_cols=73 Identities=15% Similarity=0.209 Sum_probs=51.1
Q ss_pred eeecccCCCCCceEEEEEEeecCCcceecCCCCCceEEEEEEEcCCCcEEEEEcchhHHHhhhhccCCcEEEEcceEEec
Q psy15132 443 HPIVSLSPYQNKWTIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFNDECNRFHDMIEKDKVYYISNCTLKP 522 (786)
Q Consensus 443 ~~I~~L~p~~~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~G~I~at~~~~~~~kf~~~l~~G~vy~is~~~V~~ 522 (786)
.+|.+|.. ....+|.|-|+.. |... .+|+ .+.-++|-|.+|+|.+++|.+...++.+ |.+|++|+++ ++...
T Consensus 889 ~~~~~l~~-~~~~~v~g~i~~~---~~~~-K~g~-~maf~~~eD~~~~~e~~~F~~~~~~~~~-l~~~~~~~~~-~~~~~ 960 (973)
T PRK07135 889 IRLKDLRI-NTEYRLAIEVKNV---KRLR-KANK-EYKKVILSDDSVEITIFVNDNDYLLFET-LKKGDIYEFL-ISKSK 960 (973)
T ss_pred hhHHHhcC-CCeEEEEEEEEEE---EEEe-eCCC-eEEEEEEEECCCcEEEEEcHHHHHHHHH-hhcCCEEEEE-EEEcC
Confidence 46777743 3345677777754 3333 2332 5667789999999999999998888886 8888888884 34433
Q ss_pred c
Q psy15132 523 A 523 (786)
Q Consensus 523 a 523 (786)
+
T Consensus 961 ~ 961 (973)
T PRK07135 961 N 961 (973)
T ss_pred C
Confidence 3
No 129
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=67.36 E-value=3.9 Score=35.03 Aligned_cols=31 Identities=26% Similarity=0.823 Sum_probs=22.9
Q ss_pred eCCCCccccccccc-cCCceeeeCCCCCcCCcee
Q psy15132 687 KACPSQDCNKKVID-QNNGMYRCEKCNKEFNTFT 719 (786)
Q Consensus 687 ~aC~~~~C~kkv~~-~~~g~~~C~~C~~~~~~~~ 719 (786)
..|| .|.++.+. ...|.|.|.+|+..+.-..
T Consensus 36 ~~Cp--~C~~~~VkR~a~GIW~C~kCg~~fAGga 67 (89)
T COG1997 36 HVCP--FCGRTTVKRIATGIWKCRKCGAKFAGGA 67 (89)
T ss_pred CcCC--CCCCcceeeeccCeEEcCCCCCeecccc
Confidence 4699 69987543 4578999999998765443
No 130
>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=66.99 E-value=4.5 Score=26.15 Aligned_cols=23 Identities=17% Similarity=0.706 Sum_probs=17.2
Q ss_pred CCCCCCCcceeeCC-CceeecccCCC
Q psy15132 224 CPSQDCNKKVIDQN-NGMYRCEKCNK 248 (786)
Q Consensus 224 C~~~~C~kKv~~~~-~~~~~C~~C~~ 248 (786)
|. .|+.-+.+.. .-.|.|++|+.
T Consensus 1 C~--sC~~~i~~r~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 1 CT--SCGRPIAPREQAVPFPCPNCGF 24 (24)
T ss_pred Cc--cCCCcccCcccCceEeCCCCCC
Confidence 66 7988887543 45899999974
No 131
>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=66.30 E-value=29 Score=33.01 Aligned_cols=72 Identities=14% Similarity=0.316 Sum_probs=40.7
Q ss_pred cCccccccc---CCCceeeEEEEEEEcccceeEEeecCCceeeEEEEEEeeccccEEEEEEecccccc-c-c-CCCCCEE
Q psy15132 563 VPLKTIAEI---SPDENIDVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWGKEAET-F-D-ASNKPVI 636 (786)
Q Consensus 563 ~~i~dl~~~---~~~~~vDViGvV~~V~~~~~i~~k~~g~~~~kr~i~l~D~s~~~i~~tLWg~~a~~-~-~-~~~~~vv 636 (786)
++|++|.+- +.=.-||++|+|+.|. .+ .| ..--+.|.|+...-+.+-.|++...- + + ..++.+|
T Consensus 4 ~~f~~l~~p~f~pp~~EvD~VG~VvsV~------~~-~~---f~~~vYLsD~~~Nll~Ikfw~~l~~~~~eDilk~~~li 73 (143)
T PF09104_consen 4 THFSDLQDPDFQPPYGEVDTVGFVVSVS------KK-QG---FQPLVYLSDECHNLLAIKFWTGLNQYGYEDILKPGSLI 73 (143)
T ss_dssp --CGGGGSTT--TCCCEEEEEEEEEEEE---------TT---S--EEEEE-TTS-EEEEEESS-------SS---TT-EE
T ss_pred echhhhcCcccCCCccccceEEEEEEEE------ec-CC---CceeEEeecCCccEEEEEeccCccccchhhhcCcceEE
Confidence 345666653 2345799999999981 11 12 12238899999989999999986521 1 2 4788899
Q ss_pred EEEeEEEe
Q psy15132 637 AVKAARVS 644 (786)
Q Consensus 637 ~i~~~~V~ 644 (786)
++.+..-+
T Consensus 74 A~SNLqwR 81 (143)
T PF09104_consen 74 AASNLQWR 81 (143)
T ss_dssp EEEEEEE-
T ss_pred EEeeeEee
Confidence 99887654
No 132
>PRK07374 dnaE DNA polymerase III subunit alpha; Validated
Probab=66.04 E-value=14 Score=47.38 Aligned_cols=71 Identities=20% Similarity=0.316 Sum_probs=52.8
Q ss_pred eeecccC--CCCCceEEEEEEeecCCcceecCCCCCceEEEEEEEcCCCcEEEEEcchhHHHhhhhccCCcEEEEcc
Q psy15132 443 HPIVSLS--PYQNKWTIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFNDECNRFHDMIEKDKVYYISN 517 (786)
Q Consensus 443 ~~I~~L~--p~~~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~G~I~at~~~~~~~kf~~~l~~G~vy~is~ 517 (786)
.++++|. +......|.|-|+.. |.....+|+ .+.-++|-|++|.+.+++|.+.-.++...|++|.++.+.+
T Consensus 989 ~~~~~l~~~~~~~~v~v~g~i~~~---k~~~Tk~G~-~maf~~leD~tg~~e~vvFp~~y~~~~~~l~~~~~~~v~g 1061 (1170)
T PRK07374 989 ISLSSLEEQPDKAKVSAIAMIPEM---KQVTTRKGD-RMAILQLEDLTGSCEAVVFPKSYERLSDHLMTDTRLLVWA 1061 (1170)
T ss_pred cCHHHHhcccCCCEEEEEEEEEEe---EecccCCCC-EEEEEEEEECCCCEEEEECHHHHHHHHHHhccCCEEEEEE
Confidence 4566664 223456777777754 444333432 5566789999999999999999999999999999999865
No 133
>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=65.76 E-value=2.7 Score=36.51 Aligned_cols=27 Identities=41% Similarity=1.047 Sum_probs=21.3
Q ss_pred CCCCCCCCcc-eeeCCCceeecccCCCcCC
Q psy15132 223 ACPSQDCNKK-VIDQNNGMYRCEKCNKEFN 251 (786)
Q Consensus 223 aC~~~~C~kK-v~~~~~~~~~C~~C~~~~~ 251 (786)
-|| .|.|. |.....|.|.|.+|+..+.
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 588 89886 4456788999999998653
No 134
>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=65.29 E-value=18 Score=33.58 Aligned_cols=33 Identities=3% Similarity=0.185 Sum_probs=27.0
Q ss_pred cEEEEEEeccccccc-cCCCCCEEEEEeEEEeec
Q psy15132 614 ASVTMTLWGKEAETF-DASNKPVIAVKAARVSEF 646 (786)
Q Consensus 614 ~~i~~tLWg~~a~~~-~~~~~~vv~i~~~~V~~f 646 (786)
.+|.+|+|++.|+-. +.+.|..|+|++++++..
T Consensus 60 ~ti~It~yD~H~~~ar~lK~GdfV~L~NVhiK~~ 93 (123)
T cd04498 60 LTIDILVYDNHVELAKSLKPGDFVRIYNVHAKSY 93 (123)
T ss_pred EEEEEEEEcchHHHHhhCCCCCEEEEEEEEEEec
Confidence 589999999987532 268899999999999754
No 135
>cd04319 PhAsnRS_like_N PhAsnRS_like_N: N-terminal, anticodon recognition domain of the type found in Pyrococcus horikoshii AsnRS asparaginyl-tRNA synthetase (AsnRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The archeal enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose.
Probab=64.08 E-value=71 Score=28.37 Aligned_cols=78 Identities=18% Similarity=0.168 Sum_probs=49.2
Q ss_pred eEEEEEEeecCCcceecCCCCCceEEEEEEEcCCCcEEEEEcchhH-HHhh--hhccCCcEEEEcceEEeccCCcccccC
Q psy15132 455 WTIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFNDEC-NRFH--DMIEKDKVYYISNCTLKPANKKFSSIN 531 (786)
Q Consensus 455 w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~G~I~at~~~~~~-~kf~--~~l~~G~vy~is~~~V~~a~~~y~~~~ 531 (786)
.+|.|||.++ |. .|++.=++|.|.+|.+++.+-.+.. +.|. ..|..|+++.+.+.-.. ... ..
T Consensus 2 V~v~Gwv~~~---R~------~gk~~Fi~lrD~~g~iQ~v~~~~~~~~~~~~~~~l~~~s~v~V~G~v~~-~~~----~~ 67 (103)
T cd04319 2 VTLAGWVYRK---RE------VGKKAFIVLRDSTGIVQAVFSKDLNEEAYREAKKVGIESSVIVEGAVKA-DPR----AP 67 (103)
T ss_pred EEEEEEEEeE---Ec------CCCeEEEEEecCCeeEEEEEeCCCCHHHHHHHhCCCCCCEEEEEEEEEE-CCC----CC
Confidence 3678888742 32 3566666899999999998865311 1222 35889999999885333 211 13
Q ss_pred CceEEEEccccEEEE
Q psy15132 532 NDYEMSFTHSTTVIP 546 (786)
Q Consensus 532 ~~yei~f~~~T~I~~ 546 (786)
..+||....-..+.+
T Consensus 68 ~~~Ei~~~~i~vl~~ 82 (103)
T cd04319 68 GGAEVHGEKLEIIQN 82 (103)
T ss_pred CCEEEEEEEEEEEec
Confidence 469998866444443
No 136
>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=63.84 E-value=9.3 Score=33.45 Aligned_cols=39 Identities=10% Similarity=0.182 Sum_probs=33.3
Q ss_pred EEEEEEcCCCcEEEEEcchh--HHHhhhhccCCcEEEEcce
Q psy15132 480 FSIDLLDESGEIRATMFNDE--CNRFHDMIEKDKVYYISNC 518 (786)
Q Consensus 480 ~~~~L~D~~G~I~at~~~~~--~~kf~~~l~~G~vy~is~~ 518 (786)
.-|.|.|+++.|++++|... ..+....|++|+-+.+.+.
T Consensus 19 ~yFtlkD~~~~i~cv~f~~~g~~~~~~~~l~~Gd~V~v~G~ 59 (91)
T cd04482 19 VFFKISDGTGEIDCAAYEPTKEFRDVVRLLIPGDEVTVYGS 59 (91)
T ss_pred EEEEEECCCcEEEEEEECcccccccccCCCCCCCEEEEEEE
Confidence 66788999999999999987 6778888999998877764
No 137
>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=63.28 E-value=34 Score=39.77 Aligned_cols=79 Identities=19% Similarity=0.268 Sum_probs=55.2
Q ss_pred CceEEEEEEeecCCcceecCCCCCceEEEEEEEcCCCcEEEEEcchhH-----HHhhhhccCCcEEEEcceEEeccCCcc
Q psy15132 453 NKWTIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFNDEC-----NRFHDMIEKDKVYYISNCTLKPANKKF 527 (786)
Q Consensus 453 ~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~G~I~at~~~~~~-----~kf~~~l~~G~vy~is~~~V~~a~~~y 527 (786)
...+|.|||.++ | ..|++.=++|.|.+|.|++.+-.+.+ +.+...|..|+++.+.+.-.+..
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---R------SMGKATFITLQDESGQIQLYVNKDDLPEDFYEFDEYLLDLGDIIGVTGYPFKTK---- 120 (496)
T ss_pred CEEEEEEEEEEE---e------cCCCeEEEEEEcCCccEEEEEECCcCcHHHHHHHHhcCCCCCEEEEEEEEEECC----
Confidence 357899999953 4 23677778999999999998854321 22233589999999999654322
Q ss_pred cccCCceEEEEccccEEEEc
Q psy15132 528 SSINNDYEMSFTHSTTVIPC 547 (786)
Q Consensus 528 ~~~~~~yei~f~~~T~I~~~ 547 (786)
...++|..+.-+.+..+
T Consensus 121 ---~gelel~~~~i~ilsk~ 137 (496)
T TIGR00499 121 ---TGELSVHVTELQILTKA 137 (496)
T ss_pred ---CCcEEEEeeEEEEEecC
Confidence 35688888776666555
No 138
>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=61.53 E-value=51 Score=27.82 Aligned_cols=71 Identities=17% Similarity=0.211 Sum_probs=46.3
Q ss_pred EEEEEEeecCCcceecCCCCCceEEEEEEEcCCC--cEEEEEcchhHH-HhhhhccCCcEEEEcceEEeccCCcccccCC
Q psy15132 456 TIKARVTNKTPIREWNNARGSGKLFSIDLLDESG--EIRATMFNDECN-RFHDMIEKDKVYYISNCTLKPANKKFSSINN 532 (786)
Q Consensus 456 ~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~G--~I~at~~~~~~~-kf~~~l~~G~vy~is~~~V~~a~~~y~~~~~ 532 (786)
+|+|||.++ |. .|++.=++|.|.+| .+++++-.+... ++...|..|+++.+.+--.....+ ..
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 577887732 32 35666677889988 499988654321 233568999999999964433211 35
Q ss_pred ceEEEEcc
Q psy15132 533 DYEMSFTH 540 (786)
Q Consensus 533 ~yei~f~~ 540 (786)
++||...+
T Consensus 69 ~~El~~~~ 76 (82)
T cd04318 69 PFELQAEK 76 (82)
T ss_pred CEEEEEEE
Confidence 78887654
No 139
>TIGR00458 aspS_arch aspartyl-tRNA synthetase, archaeal type. In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, aspS_arch, represents aspartyl-tRNA synthetases from the eukaryotic cytosol and from the Archaea. In some species, this enzyme aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently transamidated to Asn-tRNA(asn).
Probab=60.94 E-value=53 Score=37.47 Aligned_cols=89 Identities=17% Similarity=0.178 Sum_probs=59.0
Q ss_pred ecccCCC--CCceEEEEEEeecCCcceecCCCCCceEEEEEEEcCCCcEEEEEcchh----HHHhhhhccCCcEEEEcce
Q psy15132 445 IVSLSPY--QNKWTIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFNDE----CNRFHDMIEKDKVYYISNC 518 (786)
Q Consensus 445 I~~L~p~--~~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~G~I~at~~~~~----~~kf~~~l~~G~vy~is~~ 518 (786)
+++|++. ....+|+|||.++ |. .|++.=++|.|.+|.|++++-... .-++...|..|+++.+.+.
T Consensus 3 ~~~l~~~~~g~~v~i~G~v~~~---R~------~g~~~Fi~lrd~~g~iQ~v~~~~~~~~~~~~~~~~l~~~s~v~v~G~ 73 (428)
T TIGR00458 3 SADIKPEMDGQEVTFMGWVHEI---RD------LGGLIFVLLRDREGLIQITAPAKKVSKNLFKWAKKLNLESVVAVRGI 73 (428)
T ss_pred hhhCchhhCCCEEEEEEEEEEE---ec------CCCcEEEEEEeCCeeEEEEEECCcCCHHHHHHHhCCCCCcEEEEEEE
Confidence 3455532 2457899999843 33 367777789999999999886432 1123356999999999885
Q ss_pred EEeccCCcccccCCceEEEEccccEEEEc
Q psy15132 519 TLKPANKKFSSINNDYEMSFTHSTTVIPC 547 (786)
Q Consensus 519 ~V~~a~~~y~~~~~~yei~f~~~T~I~~~ 547 (786)
-+. ..+ ....+||....-+.+..+
T Consensus 74 v~~-~~~----~~~~~el~~~~i~vl~~~ 97 (428)
T TIGR00458 74 VKI-KEK----APGGFEIIPTKIEVINEA 97 (428)
T ss_pred EEe-cCC----CCCcEEEEEeEEEEEecC
Confidence 442 211 246789988876666555
No 140
>PRK12445 lysyl-tRNA synthetase; Reviewed
Probab=60.87 E-value=32 Score=40.09 Aligned_cols=78 Identities=14% Similarity=0.197 Sum_probs=54.9
Q ss_pred ceEEEEEEeecCCcceecCCCCCceEEEEEEEcCCCcEEEEEcchhH--HHh---hhhccCCcEEEEcceEEeccCCccc
Q psy15132 454 KWTIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFNDEC--NRF---HDMIEKDKVYYISNCTLKPANKKFS 528 (786)
Q Consensus 454 ~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~G~I~at~~~~~~--~kf---~~~l~~G~vy~is~~~V~~a~~~y~ 528 (786)
..+|.|||.++ |. .|++.=++|.|.+|.|++.+-.+.. +.| ...|..|+++.+.+.-.+..
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------MGKASFVTLQDVGGRIQLYVARDSLPEGVYNDQFKKWDLGDIIGARGTLFKTQ----- 132 (505)
T ss_pred EEEEEEEEEEE---ec------CCCcEEEEEEeCCccEEEEEECCccchhhHHHHHhcCCCCCEEEEEEEEEecC-----
Confidence 47999999853 33 3677778899999999998864322 122 34689999999988655432
Q ss_pred ccCCceEEEEccccEEEEc
Q psy15132 529 SINNDYEMSFTHSTTVIPC 547 (786)
Q Consensus 529 ~~~~~yei~f~~~T~I~~~ 547 (786)
.+.++|....-..+..+
T Consensus 133 --~gelel~~~~~~llsk~ 149 (505)
T PRK12445 133 --TGELSIHCTELRLLTKA 149 (505)
T ss_pred --CCcEEEEEeEEEEEecC
Confidence 35788888776665554
No 141
>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=60.76 E-value=27 Score=30.92 Aligned_cols=61 Identities=13% Similarity=0.167 Sum_probs=44.1
Q ss_pred eEEEEEEEcccceeEEeecCCceeeEEEEEEeeccccEEEEEEecccccccc---CCCCCEEEEEeEEEeecC
Q psy15132 578 DVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWGKEAETFD---ASNKPVIAVKAARVSEFQ 647 (786)
Q Consensus 578 DViGvV~~V~~~~~i~~k~~g~~~~kr~i~l~D~s~~~i~~tLWg~~a~~~~---~~~~~vv~i~~~~V~~f~ 647 (786)
|++|+|++|+... +...-.+.|.|+.-.-+-+-+|....+... ..++..|++.+...+.+.
T Consensus 1 D~VGvVvsV~~~~---------~g~~~~vYLaDe~~nll~vkfw~~l~~~~~EDvvk~~~lia~SNLQwR~~s 64 (100)
T cd04495 1 DTVGVVISVGKPI---------EGKFPAVYLADECLNLLCVKFWSSLEQYAYEDVVKRRVLLAASNLQWRTES 64 (100)
T ss_pred CceEEEEEEcccc---------cCccceEEEecCCcCEEEEEEecchHHhhhhhhcccceEEEEecceEeccc
Confidence 7899999998654 123457999999999999999996543221 355667788877766543
No 142
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=60.33 E-value=20 Score=43.47 Aligned_cols=69 Identities=17% Similarity=0.324 Sum_probs=51.2
Q ss_pred ceeeecccCCCCCceEEEEEEeecCCcceecCCCCCceEEEEEEEcCCCcEEEEEcchhHHHh-hhhccCCcEEEEcc
Q psy15132 441 QTHPIVSLSPYQNKWTIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFNDECNRF-HDMIEKDKVYYISN 517 (786)
Q Consensus 441 ~~~~I~~L~p~~~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~G~I~at~~~~~~~kf-~~~l~~G~vy~is~ 517 (786)
...+|+++.++. ..+|.|+|......+ . ..+.+.+.+.|++|.|.+++|+-- ..| ...|++|+.|.+++
T Consensus 49 ~~~~i~~l~~g~-~vtv~g~V~~~~~~~---~---~~~~~~v~l~D~tg~i~l~~F~~n-~~~~~~~l~~G~~~~v~G 118 (681)
T PRK10917 49 RLKPIAELRPGE-KVTVEGEVLSAEVVF---G---KRRRLTVTVSDGTGNLTLRFFNFN-QPYLKKQLKVGKRVAVYG 118 (681)
T ss_pred CcCCHHHCCCCC-EEEEEEEEEEEEEcc---C---CceEEEEEEEECCeEEEEEEEccC-cHHHHhhCCCCCEEEEEE
Confidence 356899998764 679999999652211 1 246899999999999999999410 123 57799999998886
No 143
>COG0017 AsnS Aspartyl/asparaginyl-tRNA synthetases [Translation, ribosomal structure and biogenesis]
Probab=60.20 E-value=55 Score=37.06 Aligned_cols=92 Identities=20% Similarity=0.242 Sum_probs=64.2
Q ss_pred eeeecccCCCC--CceEEEEEEeecCCcceecCCCCCceEEEEEEEcCCCcEEEEEcch-h-HHHh-hhhccCCcEEEEc
Q psy15132 442 THPIVSLSPYQ--NKWTIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFND-E-CNRF-HDMIEKDKVYYIS 516 (786)
Q Consensus 442 ~~~I~~L~p~~--~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~G~I~at~~~~-~-~~kf-~~~l~~G~vy~is 516 (786)
.+.|+++.+.. +..+|.|-|-.+ +..|++.=+.|.|.+|.|+|++... . -+.| -..|..+.++.+.
T Consensus 4 ~~~i~di~~~~~~~~V~v~GWV~~~---------R~~g~i~Fi~lrDgsg~iQ~v~~~~~~~~~~~~~~~L~~es~v~V~ 74 (435)
T COG0017 4 RTYIKDIKPHVGGQEVTVRGWVHNK---------RDLGKIIFLVLRDGSGFIQAVVPKNKVYEELFKAKKLTLESSVVVT 74 (435)
T ss_pred eeeHHhhhccCCCcEEEEEEEeeee---------cccCCeEEEEEEcCCcEEEEEEECCCCcHHHhhhhcCCCccEEEEE
Confidence 45778887764 467777777642 3456777778999999999999742 2 2222 2468899999998
Q ss_pred ceEEeccCCcccccCCceEEEEccccEEEEc
Q psy15132 517 NCTLKPANKKFSSINNDYEMSFTHSTTVIPC 547 (786)
Q Consensus 517 ~~~V~~a~~~y~~~~~~yei~f~~~T~I~~~ 547 (786)
+--.. +.+ .++.|||...+=..+...
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 85443 222 478999999986666655
No 144
>PRK05853 hypothetical protein; Validated
Probab=60.12 E-value=30 Score=33.73 Aligned_cols=27 Identities=7% Similarity=0.069 Sum_probs=25.5
Q ss_pred EEEEEcchhHHHhhhhccCCcEEEEcc
Q psy15132 491 IRATMFNDECNRFHDMIEKDKVYYISN 517 (786)
Q Consensus 491 I~at~~~~~~~kf~~~l~~G~vy~is~ 517 (786)
|.+++|+.+++.+...|+.|+-+.+.+
T Consensus 45 i~V~~wg~lAe~v~~~L~KG~~V~V~G 71 (161)
T PRK05853 45 ITVNCWGRLVTGVGAALGKGAPVIVVG 71 (161)
T ss_pred EEEEEEhHHHHHHHHHcCCCCEEEEEE
Confidence 899999999999999999999998887
No 145
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=58.60 E-value=6.3 Score=28.18 Aligned_cols=25 Identities=28% Similarity=1.022 Sum_probs=20.7
Q ss_pred CCCCccccccccccCCceeeeCCCCCc
Q psy15132 688 ACPSQDCNKKVIDQNNGMYRCEKCNKE 714 (786)
Q Consensus 688 aC~~~~C~kkv~~~~~g~~~C~~C~~~ 714 (786)
+|+ .|.......++|.|.|..||..
T Consensus 10 ~C~--~C~~~~~~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 10 PCP--VCGSRWFYSDDGFYYCDRCGHQ 34 (36)
T ss_pred cCC--CCCCeEeEccCCEEEhhhCceE
Confidence 588 5988877778999999999864
No 146
>PRK06920 dnaE DNA polymerase III DnaE; Reviewed
Probab=58.15 E-value=23 Score=45.15 Aligned_cols=73 Identities=15% Similarity=0.274 Sum_probs=53.3
Q ss_pred eeecccCCC-CCceEEEEEEeecCCcceecCCCCCceEEEEEEEcCCCcEEEEEcchhHHHhhhhccCCcEEEEcceEE
Q psy15132 443 HPIVSLSPY-QNKWTIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFNDECNRFHDMIEKDKVYYISNCTL 520 (786)
Q Consensus 443 ~~I~~L~p~-~~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~G~I~at~~~~~~~kf~~~l~~G~vy~is~~~V 520 (786)
.++.+|... .....|.|-|+.. |.....+|+ .+.-++|-|++|.+.+++|.+..+++.+.|++|.++.+.+ +|
T Consensus 933 ~~~~~l~~~~~~~v~v~g~i~~~---~~~~tk~g~-~maf~~leD~tg~~e~~vFp~~y~~~~~~l~~~~~~~v~G-~v 1006 (1107)
T PRK06920 933 PSLAQAMRHKKKVQRAIVYITSV---KVIRTKKGQ-KMAFITFCDQNDEMEAVVFPETYIHFSDKLQEGAIVLVDG-TI 1006 (1107)
T ss_pred cCHHHHhhcCCCEEEEEEEEEEe---EeecCCCCC-eEEEEEEeeCCCcEEEEECHHHHHHHHHHhccCCEEEEEE-EE
Confidence 466666532 2345777777743 444444433 4566789999999999999999999999999999999865 44
No 147
>PRK06341 single-stranded DNA-binding protein; Provisional
Probab=57.61 E-value=55 Score=32.13 Aligned_cols=63 Identities=24% Similarity=0.410 Sum_probs=46.6
Q ss_pred CCceEEEEEEeecCCcceecCCCCCceEEEEEEEcC-------CC------c-EEEEEcch-hHHHhhhhccCCcEEEEc
Q psy15132 452 QNKWTIKARVTNKTPIREWNNARGSGKLFSIDLLDE-------SG------E-IRATMFND-ECNRFHDMIEKDKVYYIS 516 (786)
Q Consensus 452 ~~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~-------~G------~-I~at~~~~-~~~kf~~~l~~G~vy~is 516 (786)
++...|.+|+..-..+|...+ + ..+.++.|+=. .| + +++++|++ +++.+...|+.|+.+.+.
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 467899999998777776533 2 25666654331 23 2 78999996 888888999999999998
Q ss_pred c
Q psy15132 517 N 517 (786)
Q Consensus 517 ~ 517 (786)
.
T Consensus 82 G 82 (166)
T PRK06341 82 G 82 (166)
T ss_pred E
Confidence 7
No 148
>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=57.20 E-value=15 Score=30.80 Aligned_cols=39 Identities=21% Similarity=0.263 Sum_probs=32.1
Q ss_pred EEEEEEcCCCcEEEEEcchhHHHhhhhccCCcEEEEcce
Q psy15132 480 FSIDLLDESGEIRATMFNDECNRFHDMIEKDKVYYISNC 518 (786)
Q Consensus 480 ~~~~L~D~~G~I~at~~~~~~~kf~~~l~~G~vy~is~~ 518 (786)
.-|.|.|+.+.|+|++|.....+....+++|+-+.+.+-
T Consensus 17 vyfsLkD~~a~i~cv~f~~~~~~~~~~l~~Gd~V~v~G~ 55 (73)
T cd04487 17 TIFTLRDETGTVWAAAFEEAGVRAYPEVEVGDIVRVTGE 55 (73)
T ss_pred EEEEEEcCCEEEEEEEEchhccCCcCCCCCCCEEEEEEE
Confidence 677889988899999999876666678999997766653
No 149
>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=56.31 E-value=6.4 Score=34.28 Aligned_cols=30 Identities=37% Similarity=0.846 Sum_probs=23.1
Q ss_pred CCCCCCCCcc-eeeCCCceeecccCCCcCCcee
Q psy15132 223 ACPSQDCNKK-VIDQNNGMYRCEKCNKEFNTFT 254 (786)
Q Consensus 223 aC~~~~C~kK-v~~~~~~~~~C~~C~~~~~~~~ 254 (786)
.|| .|.|. |.....|.|.|.+|+..+.---
T Consensus 37 ~Cp--fCgk~~vkR~a~GIW~C~~C~~~~AGGA 67 (91)
T TIGR00280 37 VCP--FCGKKTVKRGSTGIWTCRKCGAKFAGGA 67 (91)
T ss_pred cCC--CCCCCceEEEeeEEEEcCCCCCEEeCCc
Confidence 799 89764 6666788999999998764433
No 150
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=55.90 E-value=9.3 Score=28.31 Aligned_cols=26 Identities=31% Similarity=0.836 Sum_probs=19.1
Q ss_pred CCCCccccccc--cccCCceeeeCCCCCcC
Q psy15132 688 ACPSQDCNKKV--IDQNNGMYRCEKCNKEF 715 (786)
Q Consensus 688 aC~~~~C~kkv--~~~~~g~~~C~~C~~~~ 715 (786)
.|| .|+.+. .+...|.+.|..||...
T Consensus 2 ~Cp--~Cg~~~~~~D~~~g~~vC~~CG~Vl 29 (43)
T PF08271_consen 2 KCP--NCGSKEIVFDPERGELVCPNCGLVL 29 (43)
T ss_dssp SBT--TTSSSEEEEETTTTEEEETTT-BBE
T ss_pred CCc--CCcCCceEEcCCCCeEECCCCCCEe
Confidence 599 698873 45567899999998754
No 151
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=55.15 E-value=9.9 Score=27.18 Aligned_cols=25 Identities=28% Similarity=1.022 Sum_probs=20.8
Q ss_pred CCCCCCCCcceeeCCCceeecccCCCc
Q psy15132 223 ACPSQDCNKKVIDQNNGMYRCEKCNKE 249 (786)
Q Consensus 223 aC~~~~C~kKv~~~~~~~~~C~~C~~~ 249 (786)
.|+ .|.......++|.|.|..|+..
T Consensus 10 ~C~--~C~~~~~~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 10 PCP--VCGSRWFYSDDGFYYCDRCGHQ 34 (36)
T ss_pred cCC--CCCCeEeEccCCEEEhhhCceE
Confidence 599 8998876778999999999853
No 152
>PTZ00417 lysine-tRNA ligase; Provisional
Probab=54.96 E-value=56 Score=38.74 Aligned_cols=78 Identities=18% Similarity=0.222 Sum_probs=50.6
Q ss_pred ceEEEEEEeecCCcceecCCCCCc-eEEEEEEEcCCCcEEEEEcchh-------HHHhhhhccCCcEEEEcceEEeccCC
Q psy15132 454 KWTIKARVTNKTPIREWNNARGSG-KLFSIDLLDESGEIRATMFNDE-------CNRFHDMIEKDKVYYISNCTLKPANK 525 (786)
Q Consensus 454 ~w~I~~RV~~k~~~r~~~~~~~~g-~~~~~~L~D~~G~I~at~~~~~-------~~kf~~~l~~G~vy~is~~~V~~a~~ 525 (786)
..+|.|||.++ |. .| ++.=++|.|.+|.|++++-.+. .+.+...|..|+++.+.+.-.+.
T Consensus 134 ~v~v~Grv~~~---R~------~G~k~~F~~L~d~~g~iQv~~~~~~~~~~~~~~~~~~~~l~~Gd~V~V~G~~~~t--- 201 (585)
T PTZ00417 134 ILNVTGRIMRV---SA------SGQKLRFFDLVGDGAKIQVLANFAFHDHTKSNFAECYDKIRRGDIVGIVGFPGKS--- 201 (585)
T ss_pred eEEEEEEEEee---ec------CCCCCEEEEEEeCCeeEEEEEECCccCCCHHHHHHHHhcCCCCCEEEEEeEEcCC---
Confidence 47899999853 43 35 5666778899999999986431 22234569999999999973221
Q ss_pred cccccCCceEEEEccccEEEEc
Q psy15132 526 KFSSINNDYEMSFTHSTTVIPC 547 (786)
Q Consensus 526 ~y~~~~~~yei~f~~~T~I~~~ 547 (786)
-.+.++|....-+.+.++
T Consensus 202 ----~~gel~i~~~~i~llsk~ 219 (585)
T PTZ00417 202 ----KKGELSIFPKETIILSPC 219 (585)
T ss_pred ----CCceEEEEEEEEEEEecC
Confidence 134566666555444433
No 153
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain
Probab=54.16 E-value=58 Score=28.92 Aligned_cols=68 Identities=19% Similarity=0.204 Sum_probs=41.6
Q ss_pred CceEEEEEEEEeccceeEeeccCCceeeEEEEEEEeCCCCEEEEEeccccccccc---CCCCc-EEEEEeEEEeeeCCce
Q psy15132 58 ENIDVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWGKEAETFD---ASNKP-VIAVKAARVSEFQGGK 133 (786)
Q Consensus 58 ~~vDViGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~s~~~i~~tLWg~~a~~~~---~~~~~-Vi~i~~~kv~~f~g~~ 133 (786)
..+=|.|.|.++ +..++|. .=|+|.|.. .++.|++|...+.... ...|. |++.-...+..-.|..
T Consensus 22 ~~vwV~GEIs~~------~~~~~gh----~YftLkD~~-a~i~~~~~~~~~~~i~~~~l~~G~~V~v~g~~~~y~~~G~~ 90 (99)
T PF13742_consen 22 PNVWVEGEISNL------KRHSSGH----VYFTLKDEE-ASISCVIFRSRARRIRGFDLKDGDKVLVRGRVSFYEPRGSL 90 (99)
T ss_pred CCEEEEEEEeec------EECCCce----EEEEEEcCC-cEEEEEEEHHHHhhCCCCCCCCCCEEEEEEEEEEECCCcEE
Confidence 456676665554 4433343 238899966 7999999999987654 34454 5544444554444544
Q ss_pred eee
Q psy15132 134 TLS 136 (786)
Q Consensus 134 ~ls 136 (786)
+|.
T Consensus 91 sl~ 93 (99)
T PF13742_consen 91 SLI 93 (99)
T ss_pred EEE
Confidence 554
No 154
>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=54.08 E-value=91 Score=37.00 Aligned_cols=95 Identities=17% Similarity=0.160 Sum_probs=60.5
Q ss_pred eecccCCC--CCceEEEEEEeecCCcceecCCCCCceEEEEEEEcCCCcEEEEEcch-hHHHhhhhccCCcEEEEcceEE
Q psy15132 444 PIVSLSPY--QNKWTIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFND-ECNRFHDMIEKDKVYYISNCTL 520 (786)
Q Consensus 444 ~I~~L~p~--~~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~G~I~at~~~~-~~~kf~~~l~~G~vy~is~~~V 520 (786)
.+.+|+.. ....+|+|||.++ |. .|++.=++|.|.+|.|++++-.+ ..-+....|..|+++.+.+.-.
T Consensus 5 ~~~~l~~~~~g~~V~l~GwV~~~---R~------~Gkl~Fi~LrD~sg~iQvv~~~~~~~~~~~~~L~~esvV~V~G~v~ 75 (583)
T TIGR00459 5 YCGQLRTEHLGQTVTLAGWVNRR---RD------LGGLIFIDLRDRSGIVQVVCDPDADALKLAKGLRNEDVVQVKGKVS 75 (583)
T ss_pred eHhhcchhhCCCEEEEEEEEEEE---Ec------CCCcEEEEEEeCCccEEEEEeCCHHHHHHHhcCCCCCEEEEEEEEE
Confidence 34455432 3468899999843 43 35677788999999999988544 2223345689999999988544
Q ss_pred eccCCccc--ccCCceEEEEccccEEEEc
Q psy15132 521 KPANKKFS--SINNDYEMSFTHSTTVIPC 547 (786)
Q Consensus 521 ~~a~~~y~--~~~~~yei~f~~~T~I~~~ 547 (786)
....+.-+ .....+||....-..+..+
T Consensus 76 ~r~~~~~n~~~~tg~iEl~~~~i~iL~~a 104 (583)
T TIGR00459 76 ARPEGNINRNLDTGEIEILAESITLLNKS 104 (583)
T ss_pred eCCccccCccCCCCcEEEEEeEEEEeecC
Confidence 32211111 2356788888765555544
No 155
>PRK02983 lysS lysyl-tRNA synthetase; Provisional
Probab=54.08 E-value=53 Score=42.09 Aligned_cols=79 Identities=18% Similarity=0.245 Sum_probs=57.3
Q ss_pred CceEEEEEEeecCCcceecCCCCCceEEEEEEEcCCCcEEEEEcchh-----HHHhhhhccCCcEEEEcceEEeccCCcc
Q psy15132 453 NKWTIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFNDE-----CNRFHDMIEKDKVYYISNCTLKPANKKF 527 (786)
Q Consensus 453 ~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~G~I~at~~~~~-----~~kf~~~l~~G~vy~is~~~V~~a~~~y 527 (786)
...+|.|||.++ |. .|++.=++|.|.+|.|++.+-.+. .+.|...|..|+++.+.+.-.+..
T Consensus 652 ~~V~v~Grv~~~---R~------~G~~~F~~lrD~~g~iQ~v~~~~~~~~~~~~~~~~~l~~gd~V~v~G~v~~t~---- 718 (1094)
T PRK02983 652 EEVSVSGRVLRI---RD------YGGVLFADLRDWSGELQVLLDASRLEQGSLADFRAAVDLGDLVEVTGTMGTSR---- 718 (1094)
T ss_pred CEEEEEEEEEEE---ee------CCCeEEEEEEeCCeeEEEEEECCccchhhHHHHHhcCCCCCEEEEEEEEEEcC----
Confidence 358999999953 43 367777889999999999885542 244556799999999999654432
Q ss_pred cccCCceEEEEccccEEEEc
Q psy15132 528 SSINNDYEMSFTHSTTVIPC 547 (786)
Q Consensus 528 ~~~~~~yei~f~~~T~I~~~ 547 (786)
...++|..+..+.+.++
T Consensus 719 ---~ge~ei~~~~i~ll~k~ 735 (1094)
T PRK02983 719 ---NGTLSLLVTSWRLAGKC 735 (1094)
T ss_pred ---CCCEEEEEeEEEEEecc
Confidence 25688888776666555
No 156
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=54.07 E-value=7 Score=33.99 Aligned_cols=28 Identities=32% Similarity=0.924 Sum_probs=22.0
Q ss_pred CCCCCCCCcc-eeeCCCceeecccCCCcCCc
Q psy15132 223 ACPSQDCNKK-VIDQNNGMYRCEKCNKEFNT 252 (786)
Q Consensus 223 aC~~~~C~kK-v~~~~~~~~~C~~C~~~~~~ 252 (786)
.|| .|.|. |.....|.|.|.+|+..+.-
T Consensus 38 ~Cp--fCgk~~vkR~a~GIW~C~~C~~~~AG 66 (90)
T PRK03976 38 VCP--VCGRPKVKRVGTGIWECRKCGAKFAG 66 (90)
T ss_pred cCC--CCCCCceEEEEEEEEEcCCCCCEEeC
Confidence 799 89764 65667889999999987643
No 157
>PRK02801 primosomal replication protein N; Provisional
Probab=52.42 E-value=46 Score=29.71 Aligned_cols=63 Identities=6% Similarity=0.054 Sum_probs=38.4
Q ss_pred eeeEEEEEEEcccceeEEeecCCceeeEEEEEEe---ecccc------EEEEEEecccccccc--CCCCCEEEEEeE
Q psy15132 576 NIDVLGVCIDAAELSSVTGKTNQKTYMKRDITLV---DQSQA------SVTMTLWGKEAETFD--ASNKPVIAVKAA 641 (786)
Q Consensus 576 ~vDViGvV~~V~~~~~i~~k~~g~~~~kr~i~l~---D~s~~------~i~~tLWg~~a~~~~--~~~~~vv~i~~~ 641 (786)
.|-++|.++.--++... . .|.+...-.|-.. ++.+. .|.|++||+.|+.+. ...|..|.+.|-
T Consensus 4 ~v~L~Grl~~dpelr~T--p-~G~~v~~f~La~~~~~~ea~~~r~~~~~i~~va~G~~Ae~~~~~l~kGs~v~V~G~ 77 (101)
T PRK02801 4 RLVLSGTVCRTPKRKVS--P-SGIPHCQFVLEHRSVQEEAGLHRQAWCRMPVIVSGNQFQAITQSITVGSKITVQGF 77 (101)
T ss_pred EEEEEEEECcCcceEEC--C-CCCeEEEEEEEEeCeEecCCCceeEEEEEEEEEEcHHHHHHHhhcCCCCEEEEEEE
Confidence 35677888776555422 2 2654433333221 12222 399999999999876 578888888763
No 158
>PRK10220 hypothetical protein; Provisional
Probab=52.17 E-value=11 Score=33.89 Aligned_cols=30 Identities=40% Similarity=0.991 Sum_probs=24.4
Q ss_pred EeCCCCccccccccccCCceeeeCCCCCcCCc
Q psy15132 686 YKACPSQDCNKKVIDQNNGMYRCEKCNKEFNT 717 (786)
Q Consensus 686 Y~aC~~~~C~kkv~~~~~g~~~C~~C~~~~~~ 717 (786)
+|+|| .|...-+-+++..|.|+.|+..+..
T Consensus 3 lP~CP--~C~seytY~d~~~~vCpeC~hEW~~ 32 (111)
T PRK10220 3 LPHCP--KCNSEYTYEDNGMYICPECAHEWND 32 (111)
T ss_pred CCcCC--CCCCcceEcCCCeEECCcccCcCCc
Confidence 58999 7999876667779999999887643
No 159
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=51.94 E-value=77 Score=37.79 Aligned_cols=74 Identities=19% Similarity=0.226 Sum_probs=54.4
Q ss_pred ceeeecccCCCCCceEEEEEEeecCCcceecCCCCCceEEEEEEEcCCCcEEEEEcchhHHHhhhhccCCcEEEEcceEE
Q psy15132 441 QTHPIVSLSPYQNKWTIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFNDECNRFHDMIEKDKVYYISNCTL 520 (786)
Q Consensus 441 ~~~~I~~L~p~~~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~G~I~at~~~~~~~kf~~~l~~G~vy~is~~~V 520 (786)
...+|.++.++ ...+|.++|....... .+..+.+.+.+.|.+|.|.+++|+..+ -....|++|..+.+++ .+
T Consensus 50 ~~~~i~~~~~g-~~vti~g~V~~~~~~~-----~~~~~~l~v~~~d~~~~l~l~fFn~~~-~l~~~~~~G~~v~v~G-k~ 121 (677)
T COG1200 50 LLPGIAEARPG-EIVTIEGTVLSHEKFP-----FGKRKLLKVTLSDGTGVLTLVFFNFPA-YLKKKLKVGERVIVYG-KV 121 (677)
T ss_pred ccCChhhcCCC-ceEEEEEEEEeeeccC-----CCCCceEEEEEecCcEEEEEEEECccH-HHHhhCCCCCEEEEEE-EE
Confidence 34567777754 3568999998543321 334688999999988999999999875 5567899999998875 44
Q ss_pred ec
Q psy15132 521 KP 522 (786)
Q Consensus 521 ~~ 522 (786)
+.
T Consensus 122 ~~ 123 (677)
T COG1200 122 KR 123 (677)
T ss_pred ee
Confidence 43
No 160
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=51.54 E-value=8.7 Score=33.44 Aligned_cols=32 Identities=34% Similarity=0.751 Sum_probs=23.8
Q ss_pred CCCCCCCCcc-eeeCCCceeecccCCCcCCceeEe
Q psy15132 223 ACPSQDCNKK-VIDQNNGMYRCEKCNKEFNTFTYR 256 (786)
Q Consensus 223 aC~~~~C~kK-v~~~~~~~~~C~~C~~~~~~~~~r 256 (786)
.|| -|.+. |.....|.|.|.+|+..+.--.|.
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 799 89754 666677899999999876543433
No 161
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=51.29 E-value=7.9 Score=41.01 Aligned_cols=14 Identities=43% Similarity=1.096 Sum_probs=10.5
Q ss_pred ceeeeCCCCCcCCc
Q psy15132 704 GMYRCEKCNKEFNT 717 (786)
Q Consensus 704 g~~~C~~C~~~~~~ 717 (786)
..|+||.|++.+.+
T Consensus 397 KPYrCevC~KRYKN 410 (423)
T COG5189 397 KPYRCEVCDKRYKN 410 (423)
T ss_pred Cceeccccchhhcc
Confidence 46899999986543
No 162
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=49.61 E-value=8.9 Score=42.86 Aligned_cols=31 Identities=23% Similarity=0.664 Sum_probs=23.8
Q ss_pred eCCCCccccccccccCCceeeeCCCCCcCCcee
Q psy15132 687 KACPSQDCNKKVIDQNNGMYRCEKCNKEFNTFT 719 (786)
Q Consensus 687 ~aC~~~~C~kkv~~~~~g~~~C~~C~~~~~~~~ 719 (786)
+.|| .|++.+...+.+-|+|.+|+...+...
T Consensus 351 p~Cp--~Cg~~m~S~G~~g~rC~kCg~~~~~~~ 381 (421)
T COG1571 351 PVCP--RCGGRMKSAGRNGFRCKKCGTRARETL 381 (421)
T ss_pred CCCC--ccCCchhhcCCCCcccccccccCCccc
Confidence 6899 799988654444599999999876643
No 163
>PRK06826 dnaE DNA polymerase III DnaE; Reviewed
Probab=49.17 E-value=48 Score=42.59 Aligned_cols=60 Identities=15% Similarity=0.316 Sum_probs=46.3
Q ss_pred ceEEEEEEeecCCcceecCCCCCceEEEEEEEcCCCcEEEEEcchhHHHhhhhccCCcEEEEcc
Q psy15132 454 KWTIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFNDECNRFHDMIEKDKVYYISN 517 (786)
Q Consensus 454 ~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~G~I~at~~~~~~~kf~~~l~~G~vy~is~ 517 (786)
...|.|-|+. +|.....+|+ .+.-+.|-|++|.+.+++|.+...++.+.|++|.++.+.+
T Consensus 993 ~v~v~g~i~~---~~~~~tk~G~-~maf~~leD~~g~~e~~vfp~~~~~~~~~l~~~~~~~v~g 1052 (1151)
T PRK06826 993 KVIIGGIITE---VKRKTTRNNE-MMAFLTLEDLYGTVEVIVFPKVYEKYRSLLNEDNIVLIKG 1052 (1151)
T ss_pred EEEEEEEEEE---eEeeccCCCC-eEEEEEEEECCCcEEEEECHHHHHHHHHHhccCCEEEEEE
Confidence 3466667764 3444444432 4566789999999999999999999999999999998865
No 164
>PRK03932 asnC asparaginyl-tRNA synthetase; Validated
Probab=48.85 E-value=1.1e+02 Score=35.17 Aligned_cols=81 Identities=19% Similarity=0.225 Sum_probs=53.7
Q ss_pred CceEEEEEEeecCCcceecCCCCCceEEEEEEEcCCCcEEEEEcch---hHHHhhhhccCCcEEEEcceEEeccCCcccc
Q psy15132 453 NKWTIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFND---ECNRFHDMIEKDKVYYISNCTLKPANKKFSS 529 (786)
Q Consensus 453 ~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~G~I~at~~~~---~~~kf~~~l~~G~vy~is~~~V~~a~~~y~~ 529 (786)
...+|+|||.++ |. .|++.=++|.|.+|.|++.+-.+ ..-++...|..|+++.+.+.-.+ ...
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------SGKIAFLQLRDGSCFKQLQVVKDNGEEYFEEIKKLTTGSSVIVTGTVVE-SPR---- 82 (450)
T ss_pred CEEEEEEEEEEE---Ee------CCCeEEEEEECCCCcEEEEEEcCCChHHHHHHhcCCCCcEEEEEEEEEc-CCC----
Confidence 568999999843 43 26777788999999887776432 11122345999999999884443 221
Q ss_pred cCCceEEEEccccEEEEc
Q psy15132 530 INNDYEMSFTHSTTVIPC 547 (786)
Q Consensus 530 ~~~~yei~f~~~T~I~~~ 547 (786)
....+||....-+.+.++
T Consensus 83 ~~~~~el~~~~i~vl~~~ 100 (450)
T PRK03932 83 AGQGYELQATKIEVIGED 100 (450)
T ss_pred CCCCEEEEEEEEEEccCC
Confidence 235788888765555443
No 165
>PRK07374 dnaE DNA polymerase III subunit alpha; Validated
Probab=47.89 E-value=37 Score=43.64 Aligned_cols=74 Identities=16% Similarity=0.239 Sum_probs=52.6
Q ss_pred cCccchhccCCCCceEEEEEEEEeccceeEeeccCCceeeEEEEEEEeCCCCEEEEEecccccccccC--CCCcEEEEEe
Q psy15132 46 VPLKTIAEISPDENIDVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWGKEAETFDA--SNKPVIAVKA 123 (786)
Q Consensus 46 ~~~~~i~~~~~~~~vDViGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~s~~~i~~tLWg~~a~~~~~--~~~~Vi~i~~ 123 (786)
.++++|.+...+..|-|+|+|.++.. +.+|+ |+. .--++|.|.+| ++++++|-+..+.+.. ..+.++.++|
T Consensus 989 ~~~~~l~~~~~~~~v~v~g~i~~~k~---~~Tk~-G~~--maf~~leD~tg-~~e~vvFp~~y~~~~~~l~~~~~~~v~g 1061 (1170)
T PRK07374 989 ISLSSLEEQPDKAKVSAIAMIPEMKQ---VTTRK-GDR--MAILQLEDLTG-SCEAVVFPKSYERLSDHLMTDTRLLVWA 1061 (1170)
T ss_pred cCHHHHhcccCCCEEEEEEEEEEeEe---cccCC-CCE--EEEEEEEECCC-CEEEEECHHHHHHHHHHhccCCEEEEEE
Confidence 45556554445678889999998754 45564 543 45689999998 8999999998777643 5667777776
Q ss_pred EEEe
Q psy15132 124 ARVS 127 (786)
Q Consensus 124 ~kv~ 127 (786)
+|.
T Consensus 1062 -~v~ 1064 (1170)
T PRK07374 1062 -KVD 1064 (1170)
T ss_pred -EEE
Confidence 554
No 166
>PRK10220 hypothetical protein; Provisional
Probab=47.60 E-value=15 Score=32.90 Aligned_cols=28 Identities=39% Similarity=1.017 Sum_probs=24.1
Q ss_pred EeCCCCCCCCcceeeCCCceeecccCCCcC
Q psy15132 221 YKACPSQDCNKKVIDQNNGMYRCEKCNKEF 250 (786)
Q Consensus 221 Y~aC~~~~C~kKv~~~~~~~~~C~~C~~~~ 250 (786)
+|+|| +|..--+-+++..|-|+.|.-..
T Consensus 3 lP~CP--~C~seytY~d~~~~vCpeC~hEW 30 (111)
T PRK10220 3 LPHCP--KCNSEYTYEDNGMYICPECAHEW 30 (111)
T ss_pred CCcCC--CCCCcceEcCCCeEECCcccCcC
Confidence 58999 99999887778899999998654
No 167
>PRK05813 single-stranded DNA-binding protein; Provisional
Probab=47.54 E-value=63 Score=33.22 Aligned_cols=61 Identities=10% Similarity=0.096 Sum_probs=47.2
Q ss_pred CceEEEEEEeecCCcceecCCCCCceEEEEEEEcCC--C--c-EEEEEcchhHHHhhhhccCCcEEEEcc
Q psy15132 453 NKWTIKARVTNKTPIREWNNARGSGKLFSIDLLDES--G--E-IRATMFNDECNRFHDMIEKDKVYYISN 517 (786)
Q Consensus 453 ~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~--G--~-I~at~~~~~~~kf~~~l~~G~vy~is~ 517 (786)
+...+.||+++...+|...+ | ..+.+|.|+=.. + + |.+++|+..++... .|+.|+-+.+.+
T Consensus 110 N~V~LiGrL~~DPelR~t~~--G-~~va~f~lAvnr~~~~td~i~~v~wg~~Ae~~~-~l~KG~~V~V~G 175 (219)
T PRK05813 110 NEIFLDGYICKEPVYRTTPF--G-REIADLLLAVNRPYNKSDYIPCIAWGRNARFCK-TLEVGDNIRVWG 175 (219)
T ss_pred cEEEEEEEccCCCeEEECCC--C-CEEEEEEEEEcCCCCCceEEEEEEEhHHhHHHh-hCCCCCEEEEEE
Confidence 67899999999888886532 2 367788776432 2 3 99999999987655 599999998887
No 168
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=46.59 E-value=9.9 Score=24.95 Aligned_cols=23 Identities=22% Similarity=0.743 Sum_probs=15.6
Q ss_pred eCCCCccccccccccCCceeeeCCCCCc
Q psy15132 687 KACPSQDCNKKVIDQNNGMYRCEKCNKE 714 (786)
Q Consensus 687 ~aC~~~~C~kkv~~~~~g~~~C~~C~~~ 714 (786)
..|| .|++.+. .+-. +|++||..
T Consensus 3 ~~Cp--~Cg~~~~--~~~~-fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCP--NCGAEID--PDAK-FCPNCGAK 25 (26)
T ss_pred CCCc--ccCCcCC--cccc-cChhhCCC
Confidence 4699 6999643 2334 49999974
No 169
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=46.05 E-value=21 Score=26.41 Aligned_cols=26 Identities=31% Similarity=0.836 Sum_probs=19.6
Q ss_pred CCCCCCCCcce--eeCCCceeecccCCCcC
Q psy15132 223 ACPSQDCNKKV--IDQNNGMYRCEKCNKEF 250 (786)
Q Consensus 223 aC~~~~C~kKv--~~~~~~~~~C~~C~~~~ 250 (786)
.|| .|+.+. .+...|.+.|..|+...
T Consensus 2 ~Cp--~Cg~~~~~~D~~~g~~vC~~CG~Vl 29 (43)
T PF08271_consen 2 KCP--NCGSKEIVFDPERGELVCPNCGLVL 29 (43)
T ss_dssp SBT--TTSSSEEEEETTTTEEEETTT-BBE
T ss_pred CCc--CCcCCceEEcCCCCeEECCCCCCEe
Confidence 699 899874 45667899999998753
No 170
>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=46.00 E-value=9 Score=33.34 Aligned_cols=26 Identities=38% Similarity=1.101 Sum_probs=19.6
Q ss_pred CCCCcccccccc-ccCCceeeeCCCCCcC
Q psy15132 688 ACPSQDCNKKVI-DQNNGMYRCEKCNKEF 715 (786)
Q Consensus 688 aC~~~~C~kkv~-~~~~g~~~C~~C~~~~ 715 (786)
.|| .|.|.-+ -...|.|.|.+|+..+
T Consensus 37 ~Cp--~Cgk~~vkR~a~GIW~C~~C~~~~ 63 (90)
T PF01780_consen 37 TCP--FCGKTSVKRVATGIWKCKKCGKKF 63 (90)
T ss_dssp EES--SSSSSEEEEEETTEEEETTTTEEE
T ss_pred cCC--CCCCceeEEeeeEEeecCCCCCEE
Confidence 588 6988643 3457899999998764
No 171
>KOG3056|consensus
Probab=45.89 E-value=57 Score=37.69 Aligned_cols=74 Identities=24% Similarity=0.344 Sum_probs=52.9
Q ss_pred EEEEEEEeccceeEeeccCCceeeEEEEEEEeCCC-CEEEEEeccccccccc-CCCCcEEEEEeEEEeeeCCce----ee
Q psy15132 62 VLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQ-ASVTMTLWGKEAETFD-ASNKPVIAVKAARVSEFQGGK----TL 135 (786)
Q Consensus 62 ViGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~s~-~~i~~tLWg~~a~~~~-~~~~~Vi~i~~~kv~~f~g~~----~l 135 (786)
++|+|++-++++... +|..+. -..|-|..+ ..|.|-|+|+....++ ...|.||||-++-|-+.+++. +|
T Consensus 190 t~GvI~~K~~~K~t~---~G~~y~--iwkL~dLk~~q~vslfLFG~a~k~~wk~k~GtVialLNp~v~k~~~gs~~~f~L 264 (578)
T KOG3056|consen 190 TMGVIVEKSDPKFTS---NGNPYS--IWKLTDLKDHQTVSLFLFGKAHKRYWKIKLGTVIALLNPEVLKDRPGSRKSFSL 264 (578)
T ss_pred EEEEEeecCCccccc---CCCceE--EEEeeecCccceeEEEEecHHHHHHhhhccCcEEEEeCccccCCCCCCcceEEE
Confidence 899999999887642 365543 355566665 5999999999555544 588999999999887666543 45
Q ss_pred eecce
Q psy15132 136 SLSMS 140 (786)
Q Consensus 136 s~~~~ 140 (786)
++.+.
T Consensus 265 sIds~ 269 (578)
T KOG3056|consen 265 SIDSS 269 (578)
T ss_pred EecCc
Confidence 55544
No 172
>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=45.52 E-value=39 Score=31.43 Aligned_cols=36 Identities=14% Similarity=0.203 Sum_probs=28.7
Q ss_pred cEEEEEcchhHHHhhhhccCCcEEEEcceEEeccCCc
Q psy15132 490 EIRATMFNDECNRFHDMIEKDKVYYISNCTLKPANKK 526 (786)
Q Consensus 490 ~I~at~~~~~~~kf~~~l~~G~vy~is~~~V~~a~~~ 526 (786)
.|++++|++.+.--.+ |++|+.+.|.|..++....+
T Consensus 61 ti~It~yD~H~~~ar~-lK~GdfV~L~NVhiK~~~~~ 96 (123)
T cd04498 61 TIDILVYDNHVELAKS-LKPGDFVRIYNVHAKSYSSK 96 (123)
T ss_pred EEEEEEEcchHHHHhh-CCCCCEEEEEEEEEEeccCC
Confidence 3788899998864444 99999999999999776543
No 173
>KOG2593|consensus
Probab=45.04 E-value=13 Score=41.50 Aligned_cols=29 Identities=38% Similarity=0.983 Sum_probs=22.0
Q ss_pred EEeCCCCccccccc--------cccCCceeeeCCCCCcC
Q psy15132 685 TYKACPSQDCNKKV--------IDQNNGMYRCEKCNKEF 715 (786)
Q Consensus 685 ~Y~aC~~~~C~kkv--------~~~~~g~~~C~~C~~~~ 715 (786)
--..|| .|+||- .+...|.|+|+.|+...
T Consensus 127 ~~Y~Cp--~C~kkyt~Lea~~L~~~~~~~F~C~~C~gel 163 (436)
T KOG2593|consen 127 AGYVCP--NCQKKYTSLEALQLLDNETGEFHCENCGGEL 163 (436)
T ss_pred ccccCC--ccccchhhhHHHHhhcccCceEEEecCCCch
Confidence 456899 599993 23457899999998764
No 174
>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=44.72 E-value=80 Score=33.09 Aligned_cols=58 Identities=16% Similarity=0.222 Sum_probs=43.3
Q ss_pred cEEEEEcchhHHHhhhhccCCcEEEEcceEEeccCCcccccCCceEEEEccccEEEEccCC
Q psy15132 490 EIRATMFNDECNRFHDMIEKDKVYYISNCTLKPANKKFSSINNDYEMSFTHSTTVIPCNED 550 (786)
Q Consensus 490 ~I~at~~~~~~~kf~~~l~~G~vy~is~~~V~~a~~~y~~~~~~yei~f~~~T~I~~~~d~ 550 (786)
....|+|+.. +.+.+.|+||+.|.|.+.......++ +......|+-...|.-.+++..
T Consensus 181 ~~~LTIWrPt-edl~s~L~EG~ry~i~~L~~s~~k~~--~~~~~vqLtatk~Tr~~~l~~~ 238 (251)
T cd04494 181 SGLLSIWRPT-EDLRSLLTEGKRYRIYGLATSNSKKR--SGNEEVQLTATKKTRYQPLPVS 238 (251)
T ss_pred eEEEEEeCCC-HHHHhhhcCCcEEEEEeccccCCCCC--CCcceEEEEecCcccceECCHH
Confidence 4667899975 45778999999999999775443332 3356788888899999887543
No 175
>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=44.14 E-value=14 Score=33.05 Aligned_cols=30 Identities=27% Similarity=0.657 Sum_probs=24.0
Q ss_pred EeCCCCccccccccccCCceeeeCCCCCcCCc
Q psy15132 686 YKACPSQDCNKKVIDQNNGMYRCEKCNKEFNT 717 (786)
Q Consensus 686 Y~aC~~~~C~kkv~~~~~g~~~C~~C~~~~~~ 717 (786)
.|+|| .|+.--+-+++..|.|+.|+..+..
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 47999 7998766666778999999987644
No 176
>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=43.95 E-value=14 Score=32.83 Aligned_cols=37 Identities=22% Similarity=0.234 Sum_probs=31.7
Q ss_pred CccccCCCcceeeEEEeecccccccccCCcccceEEEE
Q psy15132 321 GTKKIPDGVNINSFAMLATQLNDIITDGTLSEFTIVQI 358 (786)
Q Consensus 321 ~~~~~sDG~~~~~~~~la~~ln~~v~~~~L~~~~iikl 358 (786)
..+.++||=|++ .+.+-.+|+.++++|.|..|.=+++
T Consensus 23 ~~lEltDGWYsi-~a~lD~~L~~~l~~gkl~vGqKL~i 59 (100)
T cd04493 23 PIIELTDGWYSI-RAQLDPPLTNLVRKGKLRVGQKLRI 59 (100)
T ss_pred cEEEEecCeEEE-EEEeCHHHHHHHHcCCeecccEEEE
Confidence 478899999975 8999999999999999987665555
No 177
>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=41.86 E-value=13 Score=32.34 Aligned_cols=32 Identities=38% Similarity=0.853 Sum_probs=22.4
Q ss_pred eCCCCcccccc-ccccCCceeeeCCCCCcCCceeE
Q psy15132 687 KACPSQDCNKK-VIDQNNGMYRCEKCNKEFNTFTY 720 (786)
Q Consensus 687 ~aC~~~~C~kk-v~~~~~g~~~C~~C~~~~~~~~~ 720 (786)
..|| -|.|. |.-..-|.|.|.+|+..+.--.|
T Consensus 36 y~Cp--fCgk~~vkR~a~GIW~C~~C~~~~AGGAy 68 (91)
T TIGR00280 36 YVCP--FCGKKTVKRGSTGIWTCRKCGAKFAGGAY 68 (91)
T ss_pred ccCC--CCCCCceEEEeeEEEEcCCCCCEEeCCcc
Confidence 4689 69764 44446789999999987654443
No 178
>PRK05672 dnaE2 error-prone DNA polymerase; Validated
Probab=41.63 E-value=61 Score=41.27 Aligned_cols=41 Identities=12% Similarity=0.205 Sum_probs=36.6
Q ss_pred EEEEEEEcCCCcEEEEEcchhHHHhhhhccCCcEEEEcceEE
Q psy15132 479 LFSIDLLDESGEIRATMFNDECNRFHDMIEKDKVYYISNCTL 520 (786)
Q Consensus 479 ~~~~~L~D~~G~I~at~~~~~~~kf~~~l~~G~vy~is~~~V 520 (786)
+.-+.|-|++|.+.+++|.+..+++...|++|.++.+.+ +|
T Consensus 974 maf~~leD~~g~~e~~ifp~~~~~~~~~l~~~~~~~v~g-~v 1014 (1046)
T PRK05672 974 VTFLTLEDETGMVNVVVWPGLWERQRREALGARLLLVRG-RV 1014 (1046)
T ss_pred eEEEEEecCCCCEEEEECHHHHHHHHHHhccCCEEEEEE-EE
Confidence 556789999999999999999999999999999999965 44
No 179
>PRK12820 bifunctional aspartyl-tRNA synthetase/aspartyl/glutamyl-tRNA amidotransferase subunit C; Provisional
Probab=41.53 E-value=1.9e+02 Score=35.10 Aligned_cols=95 Identities=16% Similarity=0.124 Sum_probs=60.7
Q ss_pred eecccCCC--CCceEEEEEEeecCCcceecCCCCCceEEEEEEEcCCCcEEEEEcchh----HHHhhhhccCCcEEEEcc
Q psy15132 444 PIVSLSPY--QNKWTIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFNDE----CNRFHDMIEKDKVYYISN 517 (786)
Q Consensus 444 ~I~~L~p~--~~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~G~I~at~~~~~----~~kf~~~l~~G~vy~is~ 517 (786)
-..+|++. ....+|+|||.++ |. .|++.=++|.|.+|.|++++-.+. .-++...|..|+++.+.+
T Consensus 8 ~cg~l~~~~~g~~V~l~GWV~~~---R~------~G~l~FidLRD~~G~iQvV~~~~~~~~~~~~~~~~L~~EsvV~V~G 78 (706)
T PRK12820 8 FCGHLSLDDTGREVCLAGWVDAF---RD------HGELLFIHLRDRNGFIQAVFSPEAAPADVYELAASLRAEFCVALQG 78 (706)
T ss_pred ccccCChhhCCCEEEEEEEEEEE---Ec------CCCcEEEEEEeCCccEEEEEeCCcCCHHHHHHHhcCCCCCEEEEEe
Confidence 34455543 2357899999843 43 356777889999999999886432 122335699999999999
Q ss_pred eEEeccCCcccc--cCCceEEEEccccEEEEc
Q psy15132 518 CTLKPANKKFSS--INNDYEMSFTHSTTVIPC 547 (786)
Q Consensus 518 ~~V~~a~~~y~~--~~~~yei~f~~~T~I~~~ 547 (786)
--.....+.-++ ....+||....-..+..+
T Consensus 79 ~v~~r~~~~~n~~~~tg~iEl~~~~i~iL~~a 110 (706)
T PRK12820 79 EVQKRLEETENPHIETGDIEVFVRELSILAAS 110 (706)
T ss_pred EEeccCccccCCCCCCCcEEEEeeEEEEEecC
Confidence 544422121111 236789988776666554
No 180
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=41.47 E-value=14 Score=41.46 Aligned_cols=31 Identities=23% Similarity=0.664 Sum_probs=23.6
Q ss_pred eCCCCCCCCcceeeCCCceeecccCCCcCCcee
Q psy15132 222 KACPSQDCNKKVIDQNNGMYRCEKCNKEFNTFT 254 (786)
Q Consensus 222 ~aC~~~~C~kKv~~~~~~~~~C~~C~~~~~~~~ 254 (786)
|-|| .|++.+..-+.+-|+|.+|+...+...
T Consensus 351 p~Cp--~Cg~~m~S~G~~g~rC~kCg~~~~~~~ 381 (421)
T COG1571 351 PVCP--RCGGRMKSAGRNGFRCKKCGTRARETL 381 (421)
T ss_pred CCCC--ccCCchhhcCCCCcccccccccCCccc
Confidence 7899 999998754443599999998765433
No 181
>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=40.76 E-value=18 Score=32.53 Aligned_cols=28 Identities=25% Similarity=0.660 Sum_probs=23.6
Q ss_pred EeCCCCCCCCcceeeCCCceeecccCCCcC
Q psy15132 221 YKACPSQDCNKKVIDQNNGMYRCEKCNKEF 250 (786)
Q Consensus 221 Y~aC~~~~C~kKv~~~~~~~~~C~~C~~~~ 250 (786)
.|+|| +|+.--+-+++..|-|+.|.-..
T Consensus 2 lp~CP--~C~seytY~dg~~~iCpeC~~EW 29 (109)
T TIGR00686 2 LPPCP--KCNSEYTYHDGTQLICPSCLYEW 29 (109)
T ss_pred CCcCC--cCCCcceEecCCeeECccccccc
Confidence 48999 99998877778899999998654
No 182
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=40.74 E-value=14 Score=32.22 Aligned_cols=30 Identities=30% Similarity=0.812 Sum_probs=21.1
Q ss_pred eCCCCcccccc-ccccCCceeeeCCCCCcCCce
Q psy15132 687 KACPSQDCNKK-VIDQNNGMYRCEKCNKEFNTF 718 (786)
Q Consensus 687 ~aC~~~~C~kk-v~~~~~g~~~C~~C~~~~~~~ 718 (786)
..|| -|.|. |.-..-|.|.|.+|+..+.--
T Consensus 37 y~Cp--fCgk~~vkR~a~GIW~C~~C~~~~AGG 67 (90)
T PRK03976 37 HVCP--VCGRPKVKRVGTGIWECRKCGAKFAGG 67 (90)
T ss_pred ccCC--CCCCCceEEEEEEEEEcCCCCCEEeCC
Confidence 4688 69764 433456899999999875443
No 183
>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=40.06 E-value=95 Score=26.47 Aligned_cols=53 Identities=17% Similarity=0.181 Sum_probs=36.3
Q ss_pred eeeeeEEEEecCCcEEEEeehHHHHHHhCCChhhhhccCCChHHHHHh--cCCEEEEEEeeecccccCcccc
Q psy15132 256 RLILPVMIGDWTNSVWVTLFQNEAESILGVTAQEVGESTEDHPALKKA--LFTQYIFRLRAKLEHYNGTKKI 325 (786)
Q Consensus 256 ry~l~~~v~D~Tg~~~~~~F~~~a~~ilg~sa~el~~~~e~~~~~~~~--~~k~~~f~v~~k~e~y~~~~~~ 325 (786)
|+++++.++|.|+++.+-.|.. ...+ .+..+ .+.-..++.++..|+|..+..+
T Consensus 20 ~~i~~~~itD~t~Si~~K~F~~-------~~~~----------~~~~ik~~G~~v~v~G~v~~D~f~~e~~~ 74 (82)
T cd04484 20 RKILTFKVTDYTSSITVKKFLR-------KDEK----------DKEELKSKGDWVRVRGKVQYDTFSKELVL 74 (82)
T ss_pred CEEEEEEEEcCCCCEEEEEecc-------CChh----------HHhhcccCCCEEEEEEEEEEccCCCceEE
Confidence 6888999999999999999963 1111 11111 3566777777778888765443
No 184
>KOG0556|consensus
Probab=40.05 E-value=2.4e+02 Score=31.54 Aligned_cols=101 Identities=15% Similarity=0.174 Sum_probs=73.8
Q ss_pred CCCceeeecccCCCC--CceEEEEEEeecCCcceecCCCCCceEEEEEEEcCCCcEEEEEcc-------hhHHHhhhhcc
Q psy15132 438 PVVQTHPIVSLSPYQ--NKWTIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFN-------DECNRFHDMIE 508 (786)
Q Consensus 438 ~~~~~~~I~~L~p~~--~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~G~I~at~~~-------~~~~kf~~~l~ 508 (786)
+.++.+++++|+... ....|+|||-. .+-.|++.-++|.+..-+|+|.+.- ...-||...|.
T Consensus 66 ~~~~~~~v~dl~~~~~~~~V~vRgrVht---------sr~~GK~~FlvLRq~~~tVQ~~~~~~~~~~isk~Mvkf~~~is 136 (533)
T KOG0556|consen 66 EGRELTDVSDLDESNDGSEVLVRGRVHT---------SRLKGKLCFLVLRQQGSTVQCLVAVNEDGTISKQMVKFAGSIS 136 (533)
T ss_pred cccceeehhhhhhhcCCceEEEEEEEee---------ccccceEEEEEEeccCceEEEEEEcCCCchHHHHHHHHHhhcC
Confidence 356789999998643 44568888762 2345788778888877789998842 24578998899
Q ss_pred CCcEEEEcceEEeccCCcccccCCceEEEEccccEEEEc
Q psy15132 509 KDKVYYISNCTLKPANKKFSSINNDYEMSFTHSTTVIPC 547 (786)
Q Consensus 509 ~G~vy~is~~~V~~a~~~y~~~~~~yei~f~~~T~I~~~ 547 (786)
.-.++.+.+.-+++..+--..+..+.||....--.|...
T Consensus 137 ~ESiV~v~g~v~k~~~~i~scT~qdvEi~v~~iyviS~a 175 (533)
T KOG0556|consen 137 KESIVDVRGVVVKVKEPIKSCTVQDVEIHVRKIYVISIA 175 (533)
T ss_pred cceEEEEEEEEecCCCcccccccceeEEEEEEEEEEecc
Confidence 989998888777776666666778899988875445443
No 185
>cd04321 ScAspRS_mt_like_N ScAspRS_mt_like_N: N-terminal, anticodon recognition domain of the type found in Saccharomyces cerevisiae mitochondrial (mt) aspartyl-tRNA synthetase (AspRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this fungal group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein synthesis. Mutations in the gene for
Probab=40.01 E-value=2.4e+02 Score=24.08 Aligned_cols=75 Identities=21% Similarity=0.246 Sum_probs=44.1
Q ss_pred eEEEEEEeecCCcceecCCCCCceEEEEEEEcCCC-cEEEEEcchhHHHhh--hhccCCcEEEEcceEEeccCCcccccC
Q psy15132 455 WTIKARVTNKTPIREWNNARGSGKLFSIDLLDESG-EIRATMFNDECNRFH--DMIEKDKVYYISNCTLKPANKKFSSIN 531 (786)
Q Consensus 455 w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~G-~I~at~~~~~~~kf~--~~l~~G~vy~is~~~V~~a~~~y~~~~ 531 (786)
.+|.|+|.++ |.. .|++.=++|.|.+| .|++++-.+. +.|. ..|..|+++.+.+- +....+.-..-.
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 3577777732 221 24666678999999 4998775432 3333 34889999999774 433221110112
Q ss_pred CceEEEEc
Q psy15132 532 NDYEMSFT 539 (786)
Q Consensus 532 ~~yei~f~ 539 (786)
..+||...
T Consensus 72 ~~~Ei~~~ 79 (86)
T cd04321 72 DEWELVVD 79 (86)
T ss_pred CCEEEEEE
Confidence 56777664
No 186
>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=39.66 E-value=1.4e+02 Score=34.36 Aligned_cols=82 Identities=17% Similarity=0.232 Sum_probs=56.2
Q ss_pred CceEEEEEEeecCCcceecCCCCCceEEEEEEEcCC--CcEEEEEcchh---HHHhhhhccCCcEEEEcceEEeccCCcc
Q psy15132 453 NKWTIKARVTNKTPIREWNNARGSGKLFSIDLLDES--GEIRATMFNDE---CNRFHDMIEKDKVYYISNCTLKPANKKF 527 (786)
Q Consensus 453 ~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~--G~I~at~~~~~---~~kf~~~l~~G~vy~is~~~V~~a~~~y 527 (786)
...+|+|||.++ |. .|++.=++|.|.+ |.|++++-... ..++...|..|+++.+.+.-.+.. +
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------SKKIIFLELNDGSSLGPIQAVINGEDNPYLFQLLKSLTTGSSVSVTGKVVESP-G-- 84 (453)
T ss_pred CEEEEEEEeEEE---Ec------CCCeEEEEEECCCCCccEEEEEeCCcChHHHHHHHcCCCCcEEEEEEEEEcCC-C--
Confidence 457899999843 41 2577777899999 99999886542 223335699999999988644321 1
Q ss_pred cccCCceEEEEccccEEEEcc
Q psy15132 528 SSINNDYEMSFTHSTTVIPCN 548 (786)
Q Consensus 528 ~~~~~~yei~f~~~T~I~~~~ 548 (786)
....+||....-..+.++.
T Consensus 85 --~~~~~El~~~~i~vl~~~~ 103 (453)
T TIGR00457 85 --KGQPVELQVKKIEVVGEAE 103 (453)
T ss_pred --CCCCEEEEEeEEEEEecCC
Confidence 1367899887665555553
No 187
>PRK06751 single-stranded DNA-binding protein; Provisional
Probab=39.63 E-value=85 Score=31.05 Aligned_cols=67 Identities=16% Similarity=0.306 Sum_probs=39.6
Q ss_pred ceEEEEEEEEeccceeEeeccCCceeeEEEEEEE------eCCC----CEEEEEecccccccccC--CCCcEEEEEe-EE
Q psy15132 59 NIDVLGVCIDAAELSSVTGKTNQKTYMKRDITLV------DQSQ----ASVTMTLWGKEAETFDA--SNKPVIAVKA-AR 125 (786)
Q Consensus 59 ~vDViGvV~~v~~~~~i~~k~~g~~~~kr~i~l~------D~s~----~~i~~tLWg~~a~~~~~--~~~~Vi~i~~-~k 125 (786)
.|-++|.|..--+++. +. +|..+ ..|.|+ +..| .-+.|++||++|+.+.. ..|.-|+|.| .+
T Consensus 4 ~V~LiGrL~~DpelR~--t~-sG~~v--~~fslAvnr~~~~~~ge~~tdwi~~v~wgk~Ae~~~~~l~KG~~V~VeGrL~ 78 (173)
T PRK06751 4 RVILVGRLTKDPDLRY--TP-NGVAV--ATFTLAVNRAFANQQGEREADFINCVIWRKQAENVANYLKKGSLAGVDGRLQ 78 (173)
T ss_pred EEEEEEEECCCCcEEE--CC-CCCEE--EEEEEEEccceecCCCCEEEEEEEEEEeCcHHHHHHHHcCCCCEEEEEEEEE
Confidence 3557787776433332 22 34433 234442 2223 36899999999988753 5666666655 57
Q ss_pred EeeeC
Q psy15132 126 VSEFQ 130 (786)
Q Consensus 126 v~~f~ 130 (786)
...|.
T Consensus 79 ~r~ye 83 (173)
T PRK06751 79 TRNYE 83 (173)
T ss_pred eCccC
Confidence 77884
No 188
>PLN02903 aminoacyl-tRNA ligase
Probab=39.15 E-value=2e+02 Score=34.60 Aligned_cols=95 Identities=16% Similarity=0.143 Sum_probs=60.4
Q ss_pred eecccCCC--CCceEEEEEEeecCCcceecCCCCCceEEEEEEEcCCCcEEEEEcchhHH---HhhhhccCCcEEEEcce
Q psy15132 444 PIVSLSPY--QNKWTIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFNDECN---RFHDMIEKDKVYYISNC 518 (786)
Q Consensus 444 ~I~~L~p~--~~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~G~I~at~~~~~~~---kf~~~l~~G~vy~is~~ 518 (786)
...+|+.. ....+|+|+|-++ |. .|++.=++|.|.+|.|++++-.+... +.-..|..|+++.+.+-
T Consensus 62 ~cg~l~~~~~gk~V~l~GWV~~~---R~------~G~l~FidLRD~~G~iQvV~~~~~~~~~~~~~~~L~~esvV~V~G~ 132 (652)
T PLN02903 62 LCGALSVNDVGSRVTLCGWVDLH---RD------MGGLTFLDVRDHTGIVQVVTLPDEFPEAHRTANRLRNEYVVAVEGT 132 (652)
T ss_pred chhhcchhhCCCEEEEEEEEEEE---ec------CCCcEEEEEEcCCccEEEEEeCCccHHHHHHHhcCCCCCEEEEEEE
Confidence 44555442 2457899999842 33 35677788999999999988643211 22356999999999885
Q ss_pred EEeccCCccc--ccCCceEEEEccccEEEEc
Q psy15132 519 TLKPANKKFS--SINNDYEMSFTHSTTVIPC 547 (786)
Q Consensus 519 ~V~~a~~~y~--~~~~~yei~f~~~T~I~~~ 547 (786)
-.....+.-+ .....+||....-..+..+
T Consensus 133 V~~r~~~~~n~~~~tGeiEl~~~~i~VL~~a 163 (652)
T PLN02903 133 VRSRPQESPNKKMKTGSVEVVAESVDILNVV 163 (652)
T ss_pred EEeCCCcCcCCCCCCCCEEEEEeEEEEEecC
Confidence 4322111111 1236799998876666555
No 189
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=38.97 E-value=23 Score=37.79 Aligned_cols=28 Identities=21% Similarity=0.657 Sum_probs=21.1
Q ss_pred eEE----eCCCCCCCCcceee---CCCceeecccCCC
Q psy15132 219 TTY----KACPSQDCNKKVID---QNNGMYRCEKCNK 248 (786)
Q Consensus 219 ~~Y----~aC~~~~C~kKv~~---~~~~~~~C~~C~~ 248 (786)
|.| ..|| .|+.++.. .+-+.|+|+.|++
T Consensus 238 ~Vy~R~g~pCp--rCG~~I~~~~~~gR~t~~CP~CQ~ 272 (272)
T PRK14810 238 RVYQRTGEPCL--NCKTPIRRVVVAGRSSHYCPHCQK 272 (272)
T ss_pred eecCCCCCcCC--CCCCeeEEEEECCCccEECcCCcC
Confidence 556 5899 99987753 2456899999974
No 190
>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=38.88 E-value=18 Score=29.90 Aligned_cols=24 Identities=42% Similarity=1.091 Sum_probs=15.4
Q ss_pred CCCCCCCCcceeeCCCceeecccCCCc
Q psy15132 223 ACPSQDCNKKVIDQNNGMYRCEKCNKE 249 (786)
Q Consensus 223 aC~~~~C~kKv~~~~~~~~~C~~C~~~ 249 (786)
-|| .|..-+... ++.|+|+.|++.
T Consensus 3 ~CP--~C~~~L~~~-~~~~~C~~C~~~ 26 (70)
T PF07191_consen 3 TCP--KCQQELEWQ-GGHYHCEACQKD 26 (70)
T ss_dssp B-S--SS-SBEEEE-TTEEEETTT--E
T ss_pred cCC--CCCCccEEe-CCEEECcccccc
Confidence 488 898888764 468999999875
No 191
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=38.84 E-value=16 Score=31.87 Aligned_cols=32 Identities=34% Similarity=0.731 Sum_probs=22.4
Q ss_pred eCCCCcccccc-ccccCCceeeeCCCCCcCCceeE
Q psy15132 687 KACPSQDCNKK-VIDQNNGMYRCEKCNKEFNTFTY 720 (786)
Q Consensus 687 ~aC~~~~C~kk-v~~~~~g~~~C~~C~~~~~~~~~ 720 (786)
..|| -|.|. |.-..-|.|.|.+|++.+.--.|
T Consensus 37 y~Cp--fCgk~~vkR~a~GIW~C~~C~~~~AGGAy 69 (90)
T PTZ00255 37 YFCP--FCGKHAVKRQAVGIWRCKGCKKTVAGGAW 69 (90)
T ss_pred ccCC--CCCCCceeeeeeEEEEcCCCCCEEeCCcc
Confidence 4688 69764 43345689999999987654444
No 192
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=38.78 E-value=25 Score=37.69 Aligned_cols=28 Identities=25% Similarity=0.644 Sum_probs=21.0
Q ss_pred eEE----eCCCCCCCCcceee---CCCceeecccCCC
Q psy15132 219 TTY----KACPSQDCNKKVID---QNNGMYRCEKCNK 248 (786)
Q Consensus 219 ~~Y----~aC~~~~C~kKv~~---~~~~~~~C~~C~~ 248 (786)
|.| ..|+ .|+.++.. .+-+.|||+.|++
T Consensus 248 ~Vy~R~g~pC~--~Cg~~I~~~~~~gR~t~~CP~CQ~ 282 (282)
T PRK13945 248 WVYRRTGKPCR--KCGTPIERIKLAGRSTHWCPNCQK 282 (282)
T ss_pred EEeCCCcCCCC--cCCCeeEEEEECCCccEECCCCcC
Confidence 566 5799 89987753 2456899999974
No 193
>COG1570 XseA Exonuclease VII, large subunit [DNA replication, recombination, and repair]
Probab=38.66 E-value=30 Score=39.11 Aligned_cols=55 Identities=22% Similarity=0.309 Sum_probs=43.8
Q ss_pred EEEEEEEcCCCcEEEEEcchhHHHhhhhccCCcEEEEcc-eEEeccCCcccccCCceEEEEcc
Q psy15132 479 LFSIDLLDESGEIRATMFNDECNRFHDMIEKDKVYYISN-CTLKPANKKFSSINNDYEMSFTH 540 (786)
Q Consensus 479 ~~~~~L~D~~G~I~at~~~~~~~kf~~~l~~G~vy~is~-~~V~~a~~~y~~~~~~yei~f~~ 540 (786)
...|.|.|+...|+|++|.....++.-.+++|.=+.+.+ .++-+. .++|.|..+.
T Consensus 42 H~YFtLKD~~A~i~c~mf~~~~~~l~f~p~eG~~V~v~G~is~Y~~-------rG~YQi~~~~ 97 (440)
T COG1570 42 HLYFTLKDERAQIRCVMFKGNNRRLKFRPEEGMQVLVRGKISLYEP-------RGDYQIVAES 97 (440)
T ss_pred cEEEEEccCCceEEEEEEcCcccccCCCccCCCEEEEEEEEEEEcC-------CCceEEEEec
Confidence 789999999999999999998888777799998776665 455443 4677887764
No 194
>PRK06826 dnaE DNA polymerase III DnaE; Reviewed
Probab=38.38 E-value=66 Score=41.39 Aligned_cols=65 Identities=18% Similarity=0.292 Sum_probs=46.6
Q ss_pred CCCCceEEEEEEEEeccceeEeeccCCceeeEEEEEEEeCCCCEEEEEeccccccccc--CCCCcEEEEEeEEEe
Q psy15132 55 SPDENIDVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWGKEAETFD--ASNKPVIAVKAARVS 127 (786)
Q Consensus 55 ~~~~~vDViGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~s~~~i~~tLWg~~a~~~~--~~~~~Vi~i~~~kv~ 127 (786)
..+..+-|.|+|+++.. +.+|+ |+. .--++|.|.+| ++++++|.+..+.+. ...+.++.++| +|.
T Consensus 989 ~~~~~v~v~g~i~~~~~---~~tk~-G~~--maf~~leD~~g-~~e~~vfp~~~~~~~~~l~~~~~~~v~g-~v~ 1055 (1151)
T PRK06826 989 KDGDKVIIGGIITEVKR---KTTRN-NEM--MAFLTLEDLYG-TVEVIVFPKVYEKYRSLLNEDNIVLIKG-RVS 1055 (1151)
T ss_pred cCCcEEEEEEEEEEeEe---eccCC-CCe--EEEEEEEECCC-cEEEEECHHHHHHHHHHhccCCEEEEEE-EEE
Confidence 34567889999998753 45554 542 44688999998 899999999876654 25666777766 554
No 195
>PRK00420 hypothetical protein; Validated
Probab=37.75 E-value=22 Score=32.36 Aligned_cols=27 Identities=26% Similarity=0.544 Sum_probs=21.4
Q ss_pred EeCCCCccccccccccCCceeeeCCCCCc
Q psy15132 686 YKACPSQDCNKKVIDQNNGMYRCEKCNKE 714 (786)
Q Consensus 686 Y~aC~~~~C~kkv~~~~~g~~~C~~C~~~ 714 (786)
-..|| .|+--+....+|..+|+.|+..
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 46899 6998776545788889999984
No 196
>PRK07459 single-stranded DNA-binding protein; Provisional
Probab=37.65 E-value=1.2e+02 Score=28.07 Aligned_cols=66 Identities=14% Similarity=0.299 Sum_probs=38.4
Q ss_pred eeeEEEEEEEcccceeEEeecCCceeeEEEEEEeec------cccEEEEEEecccccccc--CCCCCEEEEEe-EEEeec
Q psy15132 576 NIDVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQ------SQASVTMTLWGKEAETFD--ASNKPVIAVKA-ARVSEF 646 (786)
Q Consensus 576 ~vDViGvV~~V~~~~~i~~k~~g~~~~kr~i~l~D~------s~~~i~~tLWg~~a~~~~--~~~~~vv~i~~-~~V~~f 646 (786)
.|-++|.+..--++. .+. +|+.+. .+.|.-. ...-+.|++||..|+.+. ...|.-|.+.| .+.+.|
T Consensus 5 ~v~LiGrL~~DPelr--~t~-~G~~v~--~fslAv~~~~~~~~t~w~~v~~wg~~Ae~~~~~l~KG~~V~V~G~l~~~~~ 79 (121)
T PRK07459 5 SVTLVGRAGRDPEVR--YFE-SGSVVC--NLTLAVNRRSRDDEPDWFNLEIWGKTAQVAADYVKKGSLIGITGSLKFDRW 79 (121)
T ss_pred EEEEEEEccCCCEEE--EcC-CCCEEE--EEEEEecccccCCCceEEEEEEehHHHHHHHHHcCCCCEEEEEEEEEecce
Confidence 466888887632221 122 355443 3433321 223699999999998765 57777777765 344445
No 197
>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=37.60 E-value=84 Score=27.22 Aligned_cols=34 Identities=18% Similarity=0.272 Sum_probs=24.0
Q ss_pred ccEEEEEEecccccccc--CCCCCEEEEEeE-EEeec
Q psy15132 613 QASVTMTLWGKEAETFD--ASNKPVIAVKAA-RVSEF 646 (786)
Q Consensus 613 ~~~i~~tLWg~~a~~~~--~~~~~vv~i~~~-~V~~f 646 (786)
...+.|++||+.|+.+. ...|..|.+.|- +.+.|
T Consensus 43 ~~~~~v~~~g~~a~~~~~~~~kG~~V~v~G~l~~~~~ 79 (100)
T cd04496 43 TDWIRVVAFGKLAENAAKYLKKGDLVYVEGRLRTRSW 79 (100)
T ss_pred cEEEEEEEEhHHHHHHHHHhCCCCEEEEEEEEEecee
Confidence 34799999999988754 567777777653 33444
No 198
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=37.22 E-value=22 Score=28.30 Aligned_cols=28 Identities=32% Similarity=0.756 Sum_probs=15.9
Q ss_pred ceEEeCCCCCCCCcceee------CCCceeecccCC
Q psy15132 218 NTTYKACPSQDCNKKVID------QNNGMYRCEKCN 247 (786)
Q Consensus 218 ~~~Y~aC~~~~C~kKv~~------~~~~~~~C~~C~ 247 (786)
...-..|| +|..-++. ..+..|.|++|+
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 34445788 78855431 123457777765
No 199
>PRK00476 aspS aspartyl-tRNA synthetase; Validated
Probab=37.13 E-value=2.4e+02 Score=33.68 Aligned_cols=86 Identities=16% Similarity=0.241 Sum_probs=56.1
Q ss_pred CceEEEEEEeecCCcceecCCCCCceEEEEEEEcCCCcEEEEEcchhHHHh--hhhccCCcEEEEcceEEeccCCcccc-
Q psy15132 453 NKWTIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFNDECNRF--HDMIEKDKVYYISNCTLKPANKKFSS- 529 (786)
Q Consensus 453 ~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~G~I~at~~~~~~~kf--~~~l~~G~vy~is~~~V~~a~~~y~~- 529 (786)
...+|+|||.++ |. .|++.=++|.|.+|.|++++-.. .+.| ...|..|+++.+.+--.+...+.-++
T Consensus 18 ~~V~l~GwV~~~---R~------~g~l~Fi~LrD~~g~iQ~v~~~~-~~~~~~~~~l~~es~V~V~G~v~~~~~~~~n~~ 87 (588)
T PRK00476 18 QTVTLCGWVHRR---RD------HGGLIFIDLRDREGIVQVVFDPD-AEAFEVAESLRSEYVIQVTGTVRARPEGTVNPN 87 (588)
T ss_pred CEEEEEEEEEEE---Ee------CCCeEEEEEEeCCceEEEEEeCC-HHHHHHHhCCCCCCEEEEEEEEEecCCcccCcc
Confidence 357899999843 43 25677788999999999987542 2222 24589999999988544321111121
Q ss_pred -cCCceEEEEccccEEEEcc
Q psy15132 530 -INNDYEMSFTHSTTVIPCN 548 (786)
Q Consensus 530 -~~~~yei~f~~~T~I~~~~ 548 (786)
....+||....-..+.++.
T Consensus 88 ~~~g~~El~~~~i~il~~a~ 107 (588)
T PRK00476 88 LPTGEIEVLASELEVLNKSK 107 (588)
T ss_pred CCCCcEEEEEeEEEEEecCC
Confidence 2467999887766665554
No 200
>KOG2593|consensus
Probab=37.03 E-value=17 Score=40.43 Aligned_cols=26 Identities=42% Similarity=1.123 Sum_probs=20.8
Q ss_pred CCCCCCCCccee--------eCCCceeecccCCCcC
Q psy15132 223 ACPSQDCNKKVI--------DQNNGMYRCEKCNKEF 250 (786)
Q Consensus 223 aC~~~~C~kKv~--------~~~~~~~~C~~C~~~~ 250 (786)
.|| .|+||-+ +...|.|+|+.|+..+
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 899 8999954 2346899999999864
No 201
>COG0587 DnaE DNA polymerase III, alpha subunit [DNA replication, recombination, and repair]
Probab=36.75 E-value=90 Score=39.92 Aligned_cols=71 Identities=15% Similarity=0.335 Sum_probs=51.7
Q ss_pred eeecccCCCCCceEEEEEEeecCCcceecCCCCCc-eEEEEEEEcCCCcEEEEEcchhHHHhhhhccCCcEEEEcc
Q psy15132 443 HPIVSLSPYQNKWTIKARVTNKTPIREWNNARGSG-KLFSIDLLDESGEIRATMFNDECNRFHDMIEKDKVYYISN 517 (786)
Q Consensus 443 ~~I~~L~p~~~~w~I~~RV~~k~~~r~~~~~~~~g-~~~~~~L~D~~G~I~at~~~~~~~kf~~~l~~G~vy~is~ 517 (786)
.++.++.+....|.+-+-|+.. |.-... ..| ++.-+.|-|++|.+.+++|.....+++..+.+|+.|.+.+
T Consensus 967 ~~~~~~~~~~~~~~~~~~i~~v---r~~~tk-~~G~~~~f~tl~D~~g~~e~v~f~~~~~~~~~~l~~~~~~~v~g 1038 (1139)
T COG0587 967 IRLLDLVEDGRRVVLAGGIVAV---RQRPTK-AKGNKMAFLTLEDETGILEVVVFPSEYERYRRLLLEGRLLIVKG 1038 (1139)
T ss_pred cchhhhccccceeEEEEEEEEE---EEeecc-CCCCEEEEEEEecCCCcEEEEEcHHHHHHHHHHhccCcEEEEEE
Confidence 4555555554457777777743 333222 124 4566789999999999999999999999999998888875
No 202
>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=36.19 E-value=22 Score=32.27 Aligned_cols=31 Identities=35% Similarity=0.749 Sum_probs=22.7
Q ss_pred EeCCCCccccccccccCCceeeeCCCCCcCCce
Q psy15132 686 YKACPSQDCNKKVIDQNNGMYRCEKCNKEFNTF 718 (786)
Q Consensus 686 Y~aC~~~~C~kkv~~~~~g~~~C~~C~~~~~~~ 718 (786)
=..|| .|.+|-.+..-..-.|++||..++.-
T Consensus 9 KR~Cp--~CG~kFYDLnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 9 KRTCP--SCGAKFYDLNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred cccCC--CCcchhccCCCCCccCCCCCCccCcc
Confidence 45799 59999876444445699999987543
No 203
>PF14353 CpXC: CpXC protein
Probab=35.00 E-value=49 Score=30.77 Aligned_cols=33 Identities=24% Similarity=0.619 Sum_probs=22.1
Q ss_pred eeecccCCCcCCceeEeeeeeEEEEecCCcEEEEeehH
Q psy15132 240 MYRCEKCNKEFNTFTYRLILPVMIGDWTNSVWVTLFQN 277 (786)
Q Consensus 240 ~~~C~~C~~~~~~~~~ry~l~~~v~D~Tg~~~~~~F~~ 277 (786)
.|.|++|+..+ +..-.+...|......+.++-+
T Consensus 38 ~~~CP~Cg~~~-----~~~~p~lY~D~~~~~~i~~~P~ 70 (128)
T PF14353_consen 38 SFTCPSCGHKF-----RLEYPLLYHDPEKKFMIYYFPD 70 (128)
T ss_pred EEECCCCCCce-----ecCCCEEEEcCCCCEEEEEcCC
Confidence 79999999864 2333445667777666655554
No 204
>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=34.80 E-value=23 Score=32.80 Aligned_cols=31 Identities=23% Similarity=0.349 Sum_probs=22.9
Q ss_pred EEeCCCCccccccccccCCceeeeCCCCCcCCc
Q psy15132 685 TYKACPSQDCNKKVIDQNNGMYRCEKCNKEFNT 717 (786)
Q Consensus 685 ~Y~aC~~~~C~kkv~~~~~g~~~C~~C~~~~~~ 717 (786)
.=..|| .|.+|-.+.....-.|++||..++.
T Consensus 8 tKr~Cp--~cg~kFYDLnk~p~vcP~cg~~~~~ 38 (129)
T TIGR02300 8 TKRICP--NTGSKFYDLNRRPAVSPYTGEQFPP 38 (129)
T ss_pred ccccCC--CcCccccccCCCCccCCCcCCccCc
Confidence 346799 6999987654445679999998643
No 205
>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=34.61 E-value=46 Score=35.27 Aligned_cols=46 Identities=20% Similarity=0.195 Sum_probs=37.2
Q ss_pred CCCcceeeCCCceeecccCCCcCCceeEeeeeeEEEEecCCcEEEEeehHHH
Q psy15132 228 DCNKKVIDQNNGMYRCEKCNKEFNTFTYRLILPVMIGDWTNSVWVTLFQNEA 279 (786)
Q Consensus 228 ~C~kKv~~~~~~~~~C~~C~~~~~~~~~ry~l~~~v~D~Tg~~~~~~F~~~a 279 (786)
.||||++ .+|..-.-.-+-|..||-=++++.-.-|..-+++|+.-.
T Consensus 66 ~cNkK~t------l~C~EKeLvGdvP~aRYGHt~~vV~SrGKta~VlFGGRS 111 (337)
T PF03089_consen 66 GCNKKVT------LCCQEKELVGDVPEARYGHTINVVHSRGKTACVLFGGRS 111 (337)
T ss_pred CCCceeE------EEEecceecCCCCcccccceEEEEEECCcEEEEEECCcc
Confidence 7999996 677655444456888999999999999999999998544
No 206
>PRK00036 primosomal replication protein N; Reviewed
Probab=34.13 E-value=2.2e+02 Score=25.84 Aligned_cols=68 Identities=19% Similarity=0.181 Sum_probs=49.3
Q ss_pred CceEEEEEEeecCCcceecCCCCCceEEEEEEEc-----CCC-------cEEEEEcchhHHHhhhhccCCcEEEEcceEE
Q psy15132 453 NKWTIKARVTNKTPIREWNNARGSGKLFSIDLLD-----ESG-------EIRATMFNDECNRFHDMIEKDKVYYISNCTL 520 (786)
Q Consensus 453 ~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D-----~~G-------~I~at~~~~~~~kf~~~l~~G~vy~is~~~V 520 (786)
|.+.+.|+|+....+| |+.++ -...+|.|-- |-| +|.|.+.++.+.++.. +..|..+.+++|--
T Consensus 2 N~l~Ltg~v~~~~~lr-yTPAG--Ip~~~~~LeH~S~q~EAG~~Rqv~~~i~ava~G~~a~~~~~-l~~Gs~v~v~GFLa 77 (107)
T PRK00036 2 NTLELSARVLECGAMR-HTPAG--LPALELLLVHESEVVEAGHPRRVELTISAVALGDLALLLAD-TPLGTEMQVQGFLA 77 (107)
T ss_pred CEEEEEEEEeccCccc-cCCCC--CceEEEEEEEeEEeEeCCCcceEEEEEEEEEEhhHHHHhcc-cCCCCEEEEEEEEE
Confidence 6788999999766644 44332 2556666633 234 5999999998888876 99999999999976
Q ss_pred eccC
Q psy15132 521 KPAN 524 (786)
Q Consensus 521 ~~a~ 524 (786)
+..+
T Consensus 78 ~~~~ 81 (107)
T PRK00036 78 PARK 81 (107)
T ss_pred ECCC
Confidence 5433
No 207
>PRK10445 endonuclease VIII; Provisional
Probab=33.81 E-value=29 Score=36.82 Aligned_cols=25 Identities=28% Similarity=0.757 Sum_probs=19.1
Q ss_pred eCCCCCCCCcceee---CCCceeecccCCC
Q psy15132 222 KACPSQDCNKKVID---QNNGMYRCEKCNK 248 (786)
Q Consensus 222 ~aC~~~~C~kKv~~---~~~~~~~C~~C~~ 248 (786)
..|| .|+.++.. .+-+.|+|+.|++
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 99987652 3456899999974
No 208
>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=33.48 E-value=1.4e+02 Score=29.27 Aligned_cols=32 Identities=16% Similarity=0.297 Sum_probs=24.2
Q ss_pred EEEEEEecccccccc--CCCCCEEEEEe-EEEeec
Q psy15132 615 SVTMTLWGKEAETFD--ASNKPVIAVKA-ARVSEF 646 (786)
Q Consensus 615 ~i~~tLWg~~a~~~~--~~~~~vv~i~~-~~V~~f 646 (786)
-++|++||+.|+.+. ...|..|.+.| .+.+.|
T Consensus 52 ~~~v~~wg~~Ae~~~~~l~KG~~V~V~G~L~~~~~ 86 (164)
T TIGR00621 52 WHDIVIFGRLAEVAAQYLKKGSLVYVEGRLRTRKW 86 (164)
T ss_pred EEEEEEehHHHHHHHHhCCCCCEEEEEEEEEeceE
Confidence 799999999998765 57788787776 344445
No 209
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=33.45 E-value=27 Score=26.94 Aligned_cols=25 Identities=28% Similarity=0.757 Sum_probs=19.2
Q ss_pred eCCCCCCCCc-ceeeCCCceeecccCCCc
Q psy15132 222 KACPSQDCNK-KVIDQNNGMYRCEKCNKE 249 (786)
Q Consensus 222 ~aC~~~~C~k-Kv~~~~~~~~~C~~C~~~ 249 (786)
.-|| .|+. -+.. ..+.|.|.+|+-+
T Consensus 21 ~fCP--~Cg~~~m~~-~~~r~~C~~Cgyt 46 (50)
T PRK00432 21 KFCP--RCGSGFMAE-HLDRWHCGKCGYT 46 (50)
T ss_pred CcCc--CCCcchhec-cCCcEECCCcCCE
Confidence 4799 8988 5553 4578999999865
No 210
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=33.42 E-value=30 Score=24.27 Aligned_cols=28 Identities=25% Similarity=0.574 Sum_probs=19.9
Q ss_pred eCCCCccccccccc-cCCceeeeCCCCCcCC
Q psy15132 687 KACPSQDCNKKVID-QNNGMYRCEKCNKEFN 716 (786)
Q Consensus 687 ~aC~~~~C~kkv~~-~~~g~~~C~~C~~~~~ 716 (786)
..|+ .|+.-++- ..++.+.|..|+..++
T Consensus 4 ~~C~--~C~~~~i~~~~~~~~~C~~Cg~~~~ 32 (33)
T PF08792_consen 4 KKCS--KCGGNGIVNKEDDYEVCIFCGSSFP 32 (33)
T ss_pred eEcC--CCCCCeEEEecCCeEEcccCCcEee
Confidence 4677 68875543 5677889999998643
No 211
>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=33.41 E-value=1.5e+02 Score=25.94 Aligned_cols=67 Identities=15% Similarity=0.238 Sum_probs=36.6
Q ss_pred eeEEEEEEEcccceeEEeecCCceeeEEEEEEee----cc------ccEEEEEEecccccccc--CCCCCEEEEEeE-EE
Q psy15132 577 IDVLGVCIDAAELSSVTGKTNQKTYMKRDITLVD----QS------QASVTMTLWGKEAETFD--ASNKPVIAVKAA-RV 643 (786)
Q Consensus 577 vDViGvV~~V~~~~~i~~k~~g~~~~kr~i~l~D----~s------~~~i~~tLWg~~a~~~~--~~~~~vv~i~~~-~V 643 (786)
|-++|.|.. +++.-..+ +|+....-.|...+ +. ..-+.|++||+.|+.+. ...|..|.+.|- +.
T Consensus 4 v~l~G~l~~--~p~~~~~~-~g~~~~~f~la~~~~~~~~~~~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l~~ 80 (104)
T PF00436_consen 4 VTLIGRLGK--DPELRYTK-NGTPVARFSLAVNRRFKDDGGEGDEKTDWINVVAWGKLAENVAEYLKKGDRVYVEGRLRT 80 (104)
T ss_dssp EEEEEEESS--SEEEEEET-TSEEEEEEEEEEEEEEEETTSCEEEEEEEEEEEEEHHHHHHHHHH--TT-EEEEEEEEEE
T ss_pred EEEEEEECC--CcEEEECC-CCCEEEEEEEEEecEEeeeeccCccceEEEEEEeeeecccccceEEcCCCEEEEEEEEEe
Confidence 456676654 23222233 36655444444443 11 13799999999998764 577887877762 33
Q ss_pred eec
Q psy15132 644 SEF 646 (786)
Q Consensus 644 ~~f 646 (786)
..|
T Consensus 81 ~~~ 83 (104)
T PF00436_consen 81 RTY 83 (104)
T ss_dssp EEE
T ss_pred eEE
Confidence 444
No 212
>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed
Probab=33.21 E-value=1.4e+02 Score=34.22 Aligned_cols=90 Identities=17% Similarity=0.211 Sum_probs=51.9
Q ss_pred EEEEEeccceeEeeccCCceeeEEEEEEEeCCCCEEEEEeccccccccc--CCCCc-EEEEEeEEEeeeCCceeeeecce
Q psy15132 64 GVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWGKEAETFD--ASNKP-VIAVKAARVSEFQGGKTLSLSMS 140 (786)
Q Consensus 64 GvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~s~~~i~~tLWg~~a~~~~--~~~~~-Vi~i~~~kv~~f~g~~~ls~~~~ 140 (786)
+.|.=.|++.+++..+.|.- =|+|.|+. ..|.|++|...+..+. ...|. |++...+.+.+-+|..+|.+.
T Consensus 24 ~~v~v~gEis~~~~~~sGH~----Yf~Lkd~~-a~i~~~~~~~~~~~~~~~~~~G~~v~v~g~~~~y~~~g~~ql~v~-- 96 (438)
T PRK00286 24 GQVWVRGEISNFTRHSSGHW----YFTLKDEI-AQIRCVMFKGSARRLKFKPEEGMKVLVRGKVSLYEPRGDYQLIVE-- 96 (438)
T ss_pred CcEEEEEEeCCCeeCCCCeE----EEEEEcCC-cEEEEEEEcChhhcCCCCCCCCCEEEEEEEEEEECCCCCEEEEEE--
Confidence 33444455555555444642 38899986 5999999998876643 34444 555555555555566666432
Q ss_pred eEEEECCCc-----hHHHHHHhhhhccC
Q psy15132 141 SVLSLNPDI-----PECHKLQGWFSTQT 163 (786)
Q Consensus 141 s~i~~npd~-----pe~~~l~~w~~~~~ 163 (786)
.+.|.- -+-.++++-+..+|
T Consensus 97 ---~i~~~g~G~l~~~~~~lk~~L~~eG 121 (438)
T PRK00286 97 ---EIEPAGIGALAAAFEQLKEKLAAEG 121 (438)
T ss_pred ---EeeeCCccHHHHHHHHHHHHHHHCC
Confidence 233421 23445565555554
No 213
>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=32.69 E-value=40 Score=24.01 Aligned_cols=27 Identities=33% Similarity=0.829 Sum_probs=19.1
Q ss_pred eCCCCCCCCcceee------CCCceeecccCCCcC
Q psy15132 222 KACPSQDCNKKVID------QNNGMYRCEKCNKEF 250 (786)
Q Consensus 222 ~aC~~~~C~kKv~~------~~~~~~~C~~C~~~~ 250 (786)
..|| .|+.+..- ..++..+|++|+..+
T Consensus 3 ~~CP--~C~~~~~v~~~~~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCP--NCKTSFRVVDSQLGANGGKVRCGKCGHVW 35 (38)
T ss_pred EECC--CCCCEEEeCHHHcCCCCCEEECCCCCCEE
Confidence 4799 89996541 123478999998754
No 214
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=32.57 E-value=30 Score=36.87 Aligned_cols=25 Identities=20% Similarity=0.728 Sum_probs=18.9
Q ss_pred eCCCCCCCCcceee---CCCceeecccCCC
Q psy15132 222 KACPSQDCNKKVID---QNNGMYRCEKCNK 248 (786)
Q Consensus 222 ~aC~~~~C~kKv~~---~~~~~~~C~~C~~ 248 (786)
..|+ .|+.++.. .+-+.|+|+.|++
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 3599 99987652 2456899999985
No 215
>PRK05733 single-stranded DNA-binding protein; Provisional
Probab=32.49 E-value=1.3e+02 Score=29.81 Aligned_cols=68 Identities=18% Similarity=0.262 Sum_probs=39.5
Q ss_pred eeeEEEEEEEcccceeEEeecCCceeeEEEEEEe----ec-cc------cEEEEEEecccccccc--CCCCCEEEEEe-E
Q psy15132 576 NIDVLGVCIDAAELSSVTGKTNQKTYMKRDITLV----DQ-SQ------ASVTMTLWGKEAETFD--ASNKPVIAVKA-A 641 (786)
Q Consensus 576 ~vDViGvV~~V~~~~~i~~k~~g~~~~kr~i~l~----D~-s~------~~i~~tLWg~~a~~~~--~~~~~vv~i~~-~ 641 (786)
.|-++|.|..--++. ... +|..+.+-.|-.. |. +| .-+.|++||..|+.+. ...|..|.|.| .
T Consensus 7 kV~LiGrlg~DPElr--~t~-nG~~va~fsVAv~~~~k~~~~Ge~~e~T~w~~Vv~fgk~Ae~v~~~l~KGs~V~VeGrL 83 (172)
T PRK05733 7 KVILVGTCGQDPEVR--YLP-NGNAVTNLSLATSEQWTDKQSGQKVERTEWHRVSLFGKVAEIAGEYLRKGSQVYIEGKL 83 (172)
T ss_pred EEEEEEEecCCCEEE--ECC-CCCEEEEEEEEEcCccccCCCCcccccceEEEEEEehHHHHHHHHHhCCCCEEEEEEEE
Confidence 466888887632221 222 3655544333331 21 22 2499999999998765 57888887775 3
Q ss_pred EEeec
Q psy15132 642 RVSEF 646 (786)
Q Consensus 642 ~V~~f 646 (786)
+.+.|
T Consensus 84 r~~~y 88 (172)
T PRK05733 84 QTREW 88 (172)
T ss_pred EeCcE
Confidence 44445
No 216
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=32.46 E-value=1.1e+02 Score=40.43 Aligned_cols=74 Identities=14% Similarity=0.239 Sum_probs=56.7
Q ss_pred ceeeecccCCCCCceEEEEEEeecCCcceecCCCCCceEEEEEEEcCCCcEEEEEcchh--HHHhhhhccCCcEEEEcce
Q psy15132 441 QTHPIVSLSPYQNKWTIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFNDE--CNRFHDMIEKDKVYYISNC 518 (786)
Q Consensus 441 ~~~~I~~L~p~~~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~G~I~at~~~~~--~~kf~~~l~~G~vy~is~~ 518 (786)
.++||+++.....+..|.|.|... +.|...+ ...++++.+.|.++.|.+..|... -.+....|+.|+|+.+.+-
T Consensus 225 ~~~~~~~i~~~~~~v~i~G~if~~-e~~~~k~---~~~~~~~~~td~~~s~~~k~f~~~~~~~~~~~~~~~g~~v~~~g~ 300 (1437)
T PRK00448 225 EITPMKEINEEERRVVVEGYVFKV-EIKELKS---GRHILTFKITDYTSSIIVKKFSRDKEDLKKFDEIKKGDWVKVRGS 300 (1437)
T ss_pred CcccHHHhhccCCeEEEEEEEEEE-EEEeccC---CCEEEEEEEEcCCCCEEEEEEecCcchhHHHhcCCCCCEEEEEEE
Confidence 467899999888899999999864 3355433 247889999999999999988732 2244577999999988763
No 217
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=32.33 E-value=2.7e+02 Score=33.90 Aligned_cols=87 Identities=21% Similarity=0.292 Sum_probs=53.2
Q ss_pred CCCceeEeecCccchhccCCCCceEEEEEEEEeccceeEeeccCCceeeEEEEEEEeCCCCEEEEEecc--cc--ccccc
Q psy15132 37 NMPSVKYCFVPLKTIAEISPDENIDVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWG--KE--AETFD 112 (786)
Q Consensus 37 ~iP~~~~~f~~~~~i~~~~~~~~vDViGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~s~~~i~~tLWg--~~--a~~~~ 112 (786)
.+|.-.-++..+..|.+...|..+-|.|.|.++... .+ ++ ....+.+.|.+| .+.+++++ .- +..|
T Consensus 39 ~~P~~y~d~~~~~~i~~l~~g~~vtv~g~V~~~~~~----~~--~~--~~~~v~l~D~tg-~i~l~~F~~n~~~~~~~l- 108 (681)
T PRK10917 39 HLPRRYEDRTRLKPIAELRPGEKVTVEGEVLSAEVV----FG--KR--RRLTVTVSDGTG-NLTLRFFNFNQPYLKKQL- 108 (681)
T ss_pred cCCCceEEcCCcCCHHHCCCCCEEEEEEEEEEEEEc----cC--Cc--eEEEEEEEECCe-EEEEEEEccCcHHHHhhC-
Confidence 345433345545566666778899999999887321 11 22 356889999998 79999993 22 2222
Q ss_pred CCCCcEEEEEeEEEeeeCCceee
Q psy15132 113 ASNKPVIAVKAARVSEFQGGKTL 135 (786)
Q Consensus 113 ~~~~~Vi~i~~~kv~~f~g~~~l 135 (786)
..|.-+++.| ||+.++|..++
T Consensus 109 -~~G~~~~v~G-kv~~~~~~~qm 129 (681)
T PRK10917 109 -KVGKRVAVYG-KVKRGKYGLEM 129 (681)
T ss_pred -CCCCEEEEEE-EEEecCCeEEE
Confidence 4555555555 66666554333
No 218
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=32.21 E-value=22 Score=34.51 Aligned_cols=28 Identities=36% Similarity=1.004 Sum_probs=19.5
Q ss_pred EeCCCCcccccccccc----------------CCceeeeCCCCCcC
Q psy15132 686 YKACPSQDCNKKVIDQ----------------NNGMYRCEKCNKEF 715 (786)
Q Consensus 686 Y~aC~~~~C~kkv~~~----------------~~g~~~C~~C~~~~ 715 (786)
+..|| .||-.+... .+..|+|++|++.+
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 67899 699755321 12367899999975
No 219
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=32.13 E-value=31 Score=33.03 Aligned_cols=26 Identities=31% Similarity=0.953 Sum_probs=19.4
Q ss_pred CCCCCCCCcceee-------CCCceeecccCCCcC
Q psy15132 223 ACPSQDCNKKVID-------QNNGMYRCEKCNKEF 250 (786)
Q Consensus 223 aC~~~~C~kKv~~-------~~~~~~~C~~C~~~~ 250 (786)
-|| .|+++... ..+|.|.|+.|+...
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 89998762 124569999999854
No 220
>PRK08182 single-stranded DNA-binding protein; Provisional
Probab=31.58 E-value=1.4e+02 Score=28.76 Aligned_cols=69 Identities=14% Similarity=0.151 Sum_probs=40.3
Q ss_pred ceEEEEEEEEeccceeEeeccCCcee--eEEEEEEE------eCCC-------CEEEEEeccccccccc--CCCCcEEEE
Q psy15132 59 NIDVLGVCIDAAELSSVTGKTNQKTY--MKRDITLV------DQSQ-------ASVTMTLWGKEAETFD--ASNKPVIAV 121 (786)
Q Consensus 59 ~vDViGvV~~v~~~~~i~~k~~g~~~--~kr~i~l~------D~s~-------~~i~~tLWg~~a~~~~--~~~~~Vi~i 121 (786)
.|-++|.+..-=+++.. . +|... ....+.|. +..| .-+.|++||..|+.+. ...|.-|++
T Consensus 4 ~V~LiGrLg~DPElr~t--~-~G~~~~~~va~fslA~~r~~~~~~Ge~~~~~t~w~~V~~wg~~Ae~v~~~l~KG~~V~V 80 (148)
T PRK08182 4 HFVGEGNIGSAPEYREF--P-NGNDEPRRLLRLNVYFDNPVPTKDGEYEDRGGFWAPVELWHRDAEHWARLYQKGMRVLV 80 (148)
T ss_pred EEEEEEECCCCCeEEEC--C-CCCeeeeeEEEEEEEecCceECCCCCEEecCcEEEEEEEEhHHHHHHHHhcCCCCEEEE
Confidence 45677777664333322 2 34321 14456664 2222 2589999999998764 356666665
Q ss_pred Ee-EEEeeeC
Q psy15132 122 KA-ARVSEFQ 130 (786)
Q Consensus 122 ~~-~kv~~f~ 130 (786)
.| .+...|.
T Consensus 81 ~GrL~~~~w~ 90 (148)
T PRK08182 81 EGRMERDEWT 90 (148)
T ss_pred EEEEEecccC
Confidence 55 5777784
No 221
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=31.51 E-value=39 Score=35.95 Aligned_cols=26 Identities=23% Similarity=0.699 Sum_probs=20.0
Q ss_pred eCCCCCCCCcceee---CCCceeecccCCCc
Q psy15132 222 KACPSQDCNKKVID---QNNGMYRCEKCNKE 249 (786)
Q Consensus 222 ~aC~~~~C~kKv~~---~~~~~~~C~~C~~~ 249 (786)
..|+ .|+.++.. .+-+.|+|+.|+.-
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 4799 99987652 24568999999874
No 222
>KOG0402|consensus
Probab=31.51 E-value=25 Score=29.84 Aligned_cols=33 Identities=30% Similarity=0.708 Sum_probs=23.6
Q ss_pred CCCCCCCCcc-eeeCCCceeecccCCCcCCceeEee
Q psy15132 223 ACPSQDCNKK-VIDQNNGMYRCEKCNKEFNTFTYRL 257 (786)
Q Consensus 223 aC~~~~C~kK-v~~~~~~~~~C~~C~~~~~~~~~ry 257 (786)
-|+ -|.|+ |....-|.|.|..|.+.+.--.|-|
T Consensus 38 ~Cs--fCGK~~vKR~AvGiW~C~~C~kv~agga~~~ 71 (92)
T KOG0402|consen 38 TCS--FCGKKTVKRKAVGIWKCGSCKKVVAGGAYTV 71 (92)
T ss_pred hhh--hcchhhhhhhceeEEecCCccceeccceEEe
Confidence 477 79887 4445678999999999875544433
No 223
>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=31.31 E-value=29 Score=31.47 Aligned_cols=28 Identities=39% Similarity=0.899 Sum_probs=21.5
Q ss_pred eCCCCCCCCcceeeCCCceeecccCCCcCC
Q psy15132 222 KACPSQDCNKKVIDQNNGMYRCEKCNKEFN 251 (786)
Q Consensus 222 ~aC~~~~C~kKv~~~~~~~~~C~~C~~~~~ 251 (786)
..|| .|++|...-+-..=.|++|+..++
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 4799 899998764444557999999864
No 224
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=31.27 E-value=28 Score=28.56 Aligned_cols=18 Identities=22% Similarity=0.730 Sum_probs=13.9
Q ss_pred cccCCceeeeCCCCCcCC
Q psy15132 699 IDQNNGMYRCEKCNKEFN 716 (786)
Q Consensus 699 ~~~~~g~~~C~~C~~~~~ 716 (786)
.+..+|...|+.|++.+|
T Consensus 47 ~~i~eg~L~Cp~c~r~YP 64 (68)
T PF03966_consen 47 VEIVEGELICPECGREYP 64 (68)
T ss_dssp EETTTTEEEETTTTEEEE
T ss_pred ccccCCEEEcCCCCCEEe
Confidence 355678899999998653
No 225
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=31.22 E-value=22 Score=35.28 Aligned_cols=26 Identities=23% Similarity=0.703 Sum_probs=19.5
Q ss_pred CCCCCCCCcceeeC--CCceeecccCCCcC
Q psy15132 223 ACPSQDCNKKVIDQ--NNGMYRCEKCNKEF 250 (786)
Q Consensus 223 aC~~~~C~kKv~~~--~~~~~~C~~C~~~~ 250 (786)
-|| .|+++.+-. .+..|.|+.|+...
T Consensus 119 ~Cp--~C~~rytf~eA~~~~F~Cp~Cg~~L 146 (178)
T PRK06266 119 FCP--NCHIRFTFDEAMEYGFRCPQCGEML 146 (178)
T ss_pred ECC--CCCcEEeHHHHhhcCCcCCCCCCCC
Confidence 789 899998721 22359999999864
No 226
>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=31.04 E-value=29 Score=28.80 Aligned_cols=24 Identities=38% Similarity=1.063 Sum_probs=14.8
Q ss_pred CCCCccccccccccCCceeeeCCCCCc
Q psy15132 688 ACPSQDCNKKVIDQNNGMYRCEKCNKE 714 (786)
Q Consensus 688 aC~~~~C~kkv~~~~~g~~~C~~C~~~ 714 (786)
.|| .|..-+.. .+|.|+|+.|++.
T Consensus 3 ~CP--~C~~~L~~-~~~~~~C~~C~~~ 26 (70)
T PF07191_consen 3 TCP--KCQQELEW-QGGHYHCEACQKD 26 (70)
T ss_dssp B-S--SS-SBEEE-ETTEEEETTT--E
T ss_pred cCC--CCCCccEE-eCCEEECcccccc
Confidence 488 69887654 4578999999875
No 227
>PRK05672 dnaE2 error-prone DNA polymerase; Validated
Probab=31.00 E-value=81 Score=40.23 Aligned_cols=73 Identities=19% Similarity=0.262 Sum_probs=50.6
Q ss_pred ccCcccccccCCCceeeEEEEEEEcccceeEEeecCCceeeEEEEEEeeccccEEEEEEecccccccc--CCCCCEEEEE
Q psy15132 562 FVPLKTIAEISPDENIDVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWGKEAETFD--ASNKPVIAVK 639 (786)
Q Consensus 562 f~~i~dl~~~~~~~~vDViGvV~~V~~~~~i~~k~~g~~~~kr~i~l~D~s~~~i~~tLWg~~a~~~~--~~~~~vv~i~ 639 (786)
..++++|.+...+..|-|.|+|..+... .+|+ | .--++|.|.+| ++++++|.+..+.+. ...+.++.++
T Consensus 941 ~~~~~~l~~~~~~~~v~v~g~i~~~~~~---~Tkk-G----maf~~leD~~g-~~e~~ifp~~~~~~~~~l~~~~~~~v~ 1011 (1046)
T PRK05672 941 VVSAAELLDVEDGRRVRVAGVVTHRQRP---GTAS-G----VTFLTLEDETG-MVNVVVWPGLWERQRREALGARLLLVR 1011 (1046)
T ss_pred CcCHHHHhhccCCCEEEEEEEEEEEEEe---cCCC-c----eEEEEEecCCC-CEEEEECHHHHHHHHHHhccCCEEEEE
Confidence 3455566554345568899999886543 3443 5 45689999999 899999998766554 4677788777
Q ss_pred eEEEe
Q psy15132 640 AARVS 644 (786)
Q Consensus 640 ~~~V~ 644 (786)
| +|.
T Consensus 1012 g-~v~ 1015 (1046)
T PRK05672 1012 G-RVQ 1015 (1046)
T ss_pred E-EEE
Confidence 6 444
No 228
>KOG3108|consensus
Probab=30.88 E-value=2e+02 Score=30.52 Aligned_cols=89 Identities=15% Similarity=0.234 Sum_probs=52.0
Q ss_pred ceEEEEEEEEeccceeEeeccCCceeeEEEEEEEeCCCCEEEEEecccccccccC----CCCcEEEEEe-EEEeeeCCce
Q psy15132 59 NIDVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWGKEAETFDA----SNKPVIAVKA-ARVSEFQGGK 133 (786)
Q Consensus 59 ~vDViGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~s~~~i~~tLWg~~a~~~~~----~~~~Vi~i~~-~kv~~f~g~~ 133 (786)
.|-++|+|..+... ..+..++|.|-+| .|.|..|-........ ..+.- +|. ..++.|+|.+
T Consensus 70 ~v~~VGivr~~e~~-----------~t~i~y~I~D~tg-~id~r~W~~~~~~~~e~~~l~~~~y--Vkv~G~Lk~f~Gk~ 135 (265)
T KOG3108|consen 70 AVSIVGIVRNIEKS-----------ATNITYEIEDGTG-QIDVRQWFHDNAESEEMPALETGTY--VKVYGHLKPFQGKK 135 (265)
T ss_pred EEEEEEEEEeceec-----------CcceEEEEecCcc-cEEEEEeccccchhhhCcccccCcE--EEeeecccCCCCce
Confidence 45677777665422 2345789999998 6999999887654321 12222 232 2567898989
Q ss_pred eeeecceeEE-EECC---CchHHHHHHhhhhc
Q psy15132 134 TLSLSMSSVL-SLNP---DIPECHKLQGWFST 161 (786)
Q Consensus 134 ~ls~~~~s~i-~~np---d~pe~~~l~~w~~~ 161 (786)
+|......-+ ..|+ .+-|+......+..
T Consensus 136 sl~~fkI~pv~D~Nevt~h~LE~i~~hl~~s~ 167 (265)
T KOG3108|consen 136 SLQVFKIRPVEDFNEVTTHFLEVINAHLSLSK 167 (265)
T ss_pred eEEEEeeeeeecCCceeEEeehhhHHHHHhhh
Confidence 8877654443 2343 13344444444433
No 229
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=30.87 E-value=42 Score=25.17 Aligned_cols=25 Identities=24% Similarity=0.555 Sum_probs=18.6
Q ss_pred CCCCCCCCcceeeC-CCceeecccCCCc
Q psy15132 223 ACPSQDCNKKVIDQ-NNGMYRCEKCNKE 249 (786)
Q Consensus 223 aC~~~~C~kKv~~~-~~~~~~C~~C~~~ 249 (786)
.|+ .|+..+.-. .....+|+.|+..
T Consensus 5 ~C~--~CG~~~~~~~~~~~~~Cp~CG~~ 30 (46)
T PRK00398 5 KCA--RCGREVELDEYGTGVRCPYCGYR 30 (46)
T ss_pred ECC--CCCCEEEECCCCCceECCCCCCe
Confidence 699 899987633 2337899999864
No 230
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=30.70 E-value=45 Score=23.77 Aligned_cols=27 Identities=33% Similarity=0.764 Sum_probs=19.2
Q ss_pred eCCCCCCCCcceee------CCCceeecccCCCcC
Q psy15132 222 KACPSQDCNKKVID------QNNGMYRCEKCNKEF 250 (786)
Q Consensus 222 ~aC~~~~C~kKv~~------~~~~~~~C~~C~~~~ 250 (786)
..|| .|+++-.- +.+..-+|.+|+..+
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 89987541 234478999998753
No 231
>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=30.47 E-value=31 Score=32.02 Aligned_cols=28 Identities=21% Similarity=0.380 Sum_probs=22.0
Q ss_pred eCCCCCCCCcceeeCCCceeecccCCCcCC
Q psy15132 222 KACPSQDCNKKVIDQNNGMYRCEKCNKEFN 251 (786)
Q Consensus 222 ~aC~~~~C~kKv~~~~~~~~~C~~C~~~~~ 251 (786)
..|| .|.+|..+-+...-.|++|+..++
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 4799 999998765555678999998753
No 232
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=30.43 E-value=48 Score=24.88 Aligned_cols=25 Identities=36% Similarity=0.923 Sum_probs=17.3
Q ss_pred eCCCCCCCCcc-eeeC-CCceeecccCCC
Q psy15132 222 KACPSQDCNKK-VIDQ-NNGMYRCEKCNK 248 (786)
Q Consensus 222 ~aC~~~~C~kK-v~~~-~~~~~~C~~C~~ 248 (786)
+.|| .|+.. +... ..+.|+|..|..
T Consensus 19 ~~CP--~Cg~~~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCP--HCGSTKHYRLKTRGRYRCKACRK 45 (46)
T ss_pred CCCC--CCCCeeeEEeCCCCeEECCCCCC
Confidence 4699 89863 3322 347999999975
No 233
>PHA00626 hypothetical protein
Probab=30.24 E-value=44 Score=26.33 Aligned_cols=25 Identities=24% Similarity=0.711 Sum_probs=16.7
Q ss_pred CCCCCCCCcc-eee-----CCCceeecccCCCc
Q psy15132 223 ACPSQDCNKK-VID-----QNNGMYRCEKCNKE 249 (786)
Q Consensus 223 aC~~~~C~kK-v~~-----~~~~~~~C~~C~~~ 249 (786)
.|| .|+.- +.. ...+.|.|.+|+-.
T Consensus 2 ~CP--~CGS~~Ivrcg~cr~~snrYkCkdCGY~ 32 (59)
T PHA00626 2 SCP--KCGSGNIAKEKTMRGWSDDYVCCDCGYN 32 (59)
T ss_pred CCC--CCCCceeeeeceecccCcceEcCCCCCe
Confidence 689 89873 332 22457999999854
No 234
>PF15072 DUF4539: Domain of unknown function (DUF4539)
Probab=30.07 E-value=78 Score=27.46 Aligned_cols=39 Identities=23% Similarity=0.235 Sum_probs=31.6
Q ss_pred EEEEeeccccEEEEEEecccccccc--CCCCCEEEEEeEEEe
Q psy15132 605 DITLVDQSQASVTMTLWGKEAETFD--ASNKPVIAVKAARVS 644 (786)
Q Consensus 605 ~i~l~D~s~~~i~~tLWg~~a~~~~--~~~~~vv~i~~~~V~ 644 (786)
.+.|.|.|| +|+.++-.+--+++. ...|.++.++.+-|-
T Consensus 22 ~v~l~DpTG-~i~~tiH~~v~~~y~~~l~~GavLlLk~V~Vf 62 (86)
T PF15072_consen 22 FVVLKDPTG-EIRGTIHRKVLEEYGDELSPGAVLLLKDVTVF 62 (86)
T ss_pred EEEEECCCC-cEEEEEeHHHHhhcCCccccCEEEEEeeeeEE
Confidence 689999999 999999988666543 578889999886553
No 235
>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=29.96 E-value=24 Score=24.19 Aligned_cols=26 Identities=19% Similarity=0.664 Sum_probs=13.3
Q ss_pred EeCCCCCCCCcceeeCCCceeecccCCC
Q psy15132 221 YKACPSQDCNKKVIDQNNGMYRCEKCNK 248 (786)
Q Consensus 221 Y~aC~~~~C~kKv~~~~~~~~~C~~C~~ 248 (786)
.++|| .|+.--+-.++..|-|+.|..
T Consensus 2 ~p~Cp--~C~se~~y~D~~~~vCp~C~~ 27 (30)
T PF08274_consen 2 LPKCP--LCGSEYTYEDGELLVCPECGH 27 (30)
T ss_dssp S---T--TT-----EE-SSSEEETTTTE
T ss_pred CCCCC--CCCCcceeccCCEEeCCcccc
Confidence 47899 898776555677899999964
No 236
>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=29.70 E-value=44 Score=25.50 Aligned_cols=26 Identities=35% Similarity=0.767 Sum_probs=18.1
Q ss_pred eCCCCCCCCcce--eeCCCceeecccCCC
Q psy15132 222 KACPSQDCNKKV--IDQNNGMYRCEKCNK 248 (786)
Q Consensus 222 ~aC~~~~C~kKv--~~~~~~~~~C~~C~~ 248 (786)
.-||++.|.--| .+ -.++|.|-+|+-
T Consensus 19 k~CP~~~CG~GvFMA~-H~dR~~CGKCg~ 46 (47)
T PF01599_consen 19 KECPSPRCGAGVFMAE-HKDRHYCGKCGY 46 (47)
T ss_dssp EE-TSTTTTSSSEEEE--SSEEEETTTSS
T ss_pred hcCCCcccCCceEeee-cCCCccCCCccc
Confidence 468888898854 44 356899999974
No 237
>PF13695 zf-3CxxC: Zinc-binding domain
Probab=29.52 E-value=93 Score=27.59 Aligned_cols=39 Identities=15% Similarity=0.505 Sum_probs=29.4
Q ss_pred ceeeeCCCCCcCCceeEEEEEEEEEEecCCcEEEEEehhhHH
Q psy15132 704 GMYRCEKCNKEFNTFTYRLILPVMIGDWTNSVWVTLFQNEAE 745 (786)
Q Consensus 704 g~~~C~~C~~~~~~~~~ry~l~~~i~D~Tg~~~~~~F~~~ae 745 (786)
|.|.|.+|++......-...+++. ..|...+.+|+..-+
T Consensus 4 grF~C~~C~~~W~S~~v~i~f~~~---~~g~v~~rv~~Q~C~ 42 (98)
T PF13695_consen 4 GRFQCSKCSRGWTSAKVWILFHMY---RGGQVNMRVFGQRCK 42 (98)
T ss_pred EEEECCCCCCCCccCEEEEEEEEc---CCCeEEEEEECCCCC
Confidence 678999998887776665555555 558889999987654
No 238
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=29.16 E-value=24 Score=35.10 Aligned_cols=31 Identities=19% Similarity=0.618 Sum_probs=21.5
Q ss_pred eEEeCCCCcccccccccc--CCceeeeCCCCCcCC
Q psy15132 684 TTYKACPSQDCNKKVIDQ--NNGMYRCEKCNKEFN 716 (786)
Q Consensus 684 ~~Y~aC~~~~C~kkv~~~--~~g~~~C~~C~~~~~ 716 (786)
..|.-|| .|+++.+-. .+..|.|+.||....
T Consensus 115 ~~~Y~Cp--~C~~rytf~eA~~~~F~Cp~Cg~~L~ 147 (178)
T PRK06266 115 NMFFFCP--NCHIRFTFDEAMEYGFRCPQCGEMLE 147 (178)
T ss_pred CCEEECC--CCCcEEeHHHHhhcCCcCCCCCCCCe
Confidence 3566799 599987521 234589999998643
No 239
>TIGR00643 recG ATP-dependent DNA helicase RecG.
Probab=29.13 E-value=2.5e+02 Score=33.81 Aligned_cols=86 Identities=15% Similarity=0.179 Sum_probs=48.5
Q ss_pred CCCcceeeccCcccccccCCCceeeEEEEEEEcccceeEEeecCCceeeEEEEEEee-ccccEEEEEEeccccccccCCC
Q psy15132 554 NMPSVKYCFVPLKTIAEISPDENIDVLGVCIDAAELSSVTGKTNQKTYMKRDITLVD-QSQASVTMTLWGKEAETFDASN 632 (786)
Q Consensus 554 ~iP~~~~~f~~i~dl~~~~~~~~vDViGvV~~V~~~~~i~~k~~g~~~~kr~i~l~D-~s~~~i~~tLWg~~a~~~~~~~ 632 (786)
.+|.-.-++..+..|.+...+..+-|.|.|..+. .. .+ .++ ....+.+.| .+| .+.+++|+...-.=....
T Consensus 12 ~~P~~y~d~~~~~~i~~~~~g~~~~~~~~v~~~~---~~-~~-~~~--~~~~~~~~d~~~~-~~~~~~F~~~~~~~~~~~ 83 (630)
T TIGR00643 12 YFPRRYEDRTLLQTIGELLPGERATIVGEVLSHC---IF-GF-KRR--KVLKLRLKDGGYK-KLELRFFNRAFLKKKFKV 83 (630)
T ss_pred cCCCceEecCcccCHHHcCCCCEEEEEEEEEEeE---ec-cC-CCC--ceEEEEEEECCCC-EEEEEEECCHHHHhhCCC
Confidence 3565433443233344444567889999988742 11 11 122 256789999 888 799999983211101456
Q ss_pred CCEEEEEeEEEeecCC
Q psy15132 633 KPVIAVKAARVSEFQG 648 (786)
Q Consensus 633 ~~vv~i~~~~V~~f~G 648 (786)
|..+.+.| +|..|+|
T Consensus 84 g~~~~~~G-k~~~~~~ 98 (630)
T TIGR00643 84 GSKVVVYG-KVKSSKF 98 (630)
T ss_pred CCEEEEEE-EEEeeCC
Confidence 66665544 5555544
No 240
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=29.00 E-value=36 Score=32.63 Aligned_cols=29 Identities=31% Similarity=0.927 Sum_probs=20.2
Q ss_pred EEeCCCCccccccccc-------cCCceeeeCCCCCcC
Q psy15132 685 TYKACPSQDCNKKVID-------QNNGMYRCEKCNKEF 715 (786)
Q Consensus 685 ~Y~aC~~~~C~kkv~~-------~~~g~~~C~~C~~~~ 715 (786)
.+.-|| .|+++... ..+|.|.|+.||...
T Consensus 98 ~~Y~Cp--~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~l 133 (147)
T smart00531 98 AYYKCP--NCQSKYTFLEANQLLDMDGTFTCPRCGEEL 133 (147)
T ss_pred cEEECc--CCCCEeeHHHHHHhcCCCCcEECCCCCCEE
Confidence 455689 69987642 124569999999863
No 241
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=28.97 E-value=37 Score=27.68 Aligned_cols=38 Identities=24% Similarity=0.460 Sum_probs=25.4
Q ss_pred EeCCCCCCCCcceeeCCCceeecccCCCcCCceeEeeeeeEEEEecC
Q psy15132 221 YKACPSQDCNKKVIDQNNGMYRCEKCNKEFNTFTYRLILPVMIGDWT 267 (786)
Q Consensus 221 Y~aC~~~~C~kKv~~~~~~~~~C~~C~~~~~~~~~ry~l~~~v~D~T 267 (786)
+.||. .|+.-+.+ + .|+.|+.+..++.+.=+| .|.|..
T Consensus 5 ~~AC~--~C~~i~~~--~---~Cp~Cgs~~~S~~w~G~v--~i~dPe 42 (64)
T PRK06393 5 YRACK--KCKRLTPE--K---TCPVHGDEKTTTEWFGFL--IITEPE 42 (64)
T ss_pred hhhHh--hCCcccCC--C---cCCCCCCCcCCcCcceEE--EEECCc
Confidence 67999 99998842 2 799999875555554333 344544
No 242
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=28.61 E-value=69 Score=24.38 Aligned_cols=27 Identities=30% Similarity=0.748 Sum_probs=18.4
Q ss_pred CCCCccccccccccCC---ceeeeCCCCCcCC
Q psy15132 688 ACPSQDCNKKVIDQNN---GMYRCEKCNKEFN 716 (786)
Q Consensus 688 aC~~~~C~kkv~~~~~---g~~~C~~C~~~~~ 716 (786)
-|| .|+.-+....+ ..|.|+.|+-...
T Consensus 2 FCp--~Cg~~l~~~~~~~~~~~vC~~Cg~~~~ 31 (52)
T smart00661 2 FCP--KCGNMLIPKEGKEKRRFVCRKCGYEEP 31 (52)
T ss_pred CCC--CCCCccccccCCCCCEEECCcCCCeEE
Confidence 388 69886643322 2789999997644
No 243
>PRK06752 single-stranded DNA-binding protein; Validated
Probab=28.41 E-value=1.3e+02 Score=27.15 Aligned_cols=33 Identities=12% Similarity=0.434 Sum_probs=24.5
Q ss_pred EEEEEecccccccccC--CCCcEEEEEe-EEEeeeC
Q psy15132 98 SVTMTLWGKEAETFDA--SNKPVIAVKA-ARVSEFQ 130 (786)
Q Consensus 98 ~i~~tLWg~~a~~~~~--~~~~Vi~i~~-~kv~~f~ 130 (786)
-+.|++||+.|+.+.. ..|.-|++.| .+...|.
T Consensus 48 ~~~v~~wg~~Ae~~~~~l~KG~~V~V~G~l~~~~~~ 83 (112)
T PRK06752 48 FINCVVWRKSAENVTEYCTKGSLVGITGRIHTRNYE 83 (112)
T ss_pred EEEEEEehHHHHHHHHhcCCCCEEEEEEEEEeCccC
Confidence 6899999999988753 5677666665 4667774
No 244
>PRK06920 dnaE DNA polymerase III DnaE; Reviewed
Probab=28.33 E-value=95 Score=39.76 Aligned_cols=79 Identities=10% Similarity=0.090 Sum_probs=53.5
Q ss_pred eccCcccccccCCCceeeEEEEEEEcccceeEEeecCCceeeEEEEEEeeccccEEEEEEecccccccc--CCCCCEEEE
Q psy15132 561 CFVPLKTIAEISPDENIDVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWGKEAETFD--ASNKPVIAV 638 (786)
Q Consensus 561 ~f~~i~dl~~~~~~~~vDViGvV~~V~~~~~i~~k~~g~~~~kr~i~l~D~s~~~i~~tLWg~~a~~~~--~~~~~vv~i 638 (786)
...++.+|.. ..+..|-|.|+|+.+.. +++|+ |+. .--++|.|.+| .+++++|.+..+.+. ...+.++.+
T Consensus 931 ~~~~~~~l~~-~~~~~v~v~g~i~~~~~---~~tk~-g~~--maf~~leD~tg-~~e~~vFp~~y~~~~~~l~~~~~~~v 1002 (1107)
T PRK06920 931 EIPSLAQAMR-HKKKVQRAIVYITSVKV---IRTKK-GQK--MAFITFCDQND-EMEAVVFPETYIHFSDKLQEGAIVLV 1002 (1107)
T ss_pred CCcCHHHHhh-cCCCEEEEEEEEEEeEe---ecCCC-CCe--EEEEEEeeCCC-cEEEEECHHHHHHHHHHhccCCEEEE
Confidence 3456666643 23557889999998754 34453 653 34689999999 899999998665554 466777777
Q ss_pred EeEEEeecCC
Q psy15132 639 KAARVSEFQG 648 (786)
Q Consensus 639 ~~~~V~~f~G 648 (786)
+| +|..-+|
T Consensus 1003 ~G-~v~~~~~ 1011 (1107)
T PRK06920 1003 DG-TIELRNH 1011 (1107)
T ss_pred EE-EEEecCC
Confidence 76 5543234
No 245
>PRK11827 hypothetical protein; Provisional
Probab=28.01 E-value=45 Score=26.87 Aligned_cols=28 Identities=32% Similarity=0.516 Sum_probs=20.6
Q ss_pred eCCCCCCCCcceeeC-CCceeecccCCCcCC
Q psy15132 222 KACPSQDCNKKVIDQ-NNGMYRCEKCNKEFN 251 (786)
Q Consensus 222 ~aC~~~~C~kKv~~~-~~~~~~C~~C~~~~~ 251 (786)
.+|| .|+..+... +.....|..|+..++
T Consensus 9 LaCP--~ckg~L~~~~~~~~Lic~~~~laYP 37 (60)
T PRK11827 9 IACP--VCNGKLWYNQEKQELICKLDNLAFP 37 (60)
T ss_pred eECC--CCCCcCeEcCCCCeEECCccCeecc
Confidence 4899 999988632 334688999987654
No 246
>PRK08486 single-stranded DNA-binding protein; Provisional
Probab=27.94 E-value=1.8e+02 Score=29.07 Aligned_cols=32 Identities=16% Similarity=0.350 Sum_probs=24.1
Q ss_pred EEEEEEecccccccc--CCCCCEEEEEe-EEEeec
Q psy15132 615 SVTMTLWGKEAETFD--ASNKPVIAVKA-ARVSEF 646 (786)
Q Consensus 615 ~i~~tLWg~~a~~~~--~~~~~vv~i~~-~~V~~f 646 (786)
-++|++||..|+.+. ...|.-|+|.| .+.+.|
T Consensus 50 fi~v~~fg~~AE~~~~~l~KG~~V~VeGrL~~~~y 84 (182)
T PRK08486 50 FIDIRLFGRTAEIANQYLSKGSKVLIEGRLTFESW 84 (182)
T ss_pred EEEEEEEhHHHHHHHHHcCCCCEEEEEEEEEeCcE
Confidence 699999999998764 57788777775 344556
No 247
>PRK07274 single-stranded DNA-binding protein; Provisional
Probab=27.02 E-value=1.8e+02 Score=27.26 Aligned_cols=32 Identities=31% Similarity=0.644 Sum_probs=24.0
Q ss_pred EEEEEecccccccccC--CCCcEEEEEe-EEEeee
Q psy15132 98 SVTMTLWGKEAETFDA--SNKPVIAVKA-ARVSEF 129 (786)
Q Consensus 98 ~i~~tLWg~~a~~~~~--~~~~Vi~i~~-~kv~~f 129 (786)
-+.|++||.+|+.+.. ..|.-|.+.| .+...|
T Consensus 48 w~~v~~fg~~Ae~v~~~l~KG~~V~V~Grl~~~~y 82 (131)
T PRK07274 48 FINVVLWGKLAETLASYASKGSLISIDGELRTRKY 82 (131)
T ss_pred EEEEEEehHHHHHHHHHcCCCCEEEEEEEEEeccC
Confidence 6899999999987653 5666666665 467777
No 248
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=26.98 E-value=56 Score=23.38 Aligned_cols=27 Identities=33% Similarity=0.874 Sum_probs=19.2
Q ss_pred eCCCCCCCCccee--e----CCCceeecccCCCcC
Q psy15132 222 KACPSQDCNKKVI--D----QNNGMYRCEKCNKEF 250 (786)
Q Consensus 222 ~aC~~~~C~kKv~--~----~~~~~~~C~~C~~~~ 250 (786)
..|| .|..... + ..++.-+|++|+..+
T Consensus 3 i~CP--~C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 3 ITCP--NCQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EECC--CCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 4799 8987643 1 245689999998653
No 249
>PRK07279 dnaE DNA polymerase III DnaE; Reviewed
Probab=26.96 E-value=2.6e+02 Score=35.65 Aligned_cols=64 Identities=11% Similarity=0.206 Sum_probs=44.7
Q ss_pred CCceEEEEEEEEeccceeEeeccCCceeeEEEEEEEeCCCCEEEEEecccccccccC--CCCcEEEEEeEEEe
Q psy15132 57 DENIDVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWGKEAETFDA--SNKPVIAVKAARVS 127 (786)
Q Consensus 57 ~~~vDViGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~s~~~i~~tLWg~~a~~~~~--~~~~Vi~i~~~kv~ 127 (786)
+..+-++|+|.++. .+++|.+|+. .--++|.|.+| ++++++|.+..+.+.. ..+.++.++| +|.
T Consensus 884 ~~~~~~~~~i~~~~---~~~tk~~g~~--maf~~leD~~g-~ie~~vFp~~y~~~~~~l~~~~~~~v~G-~v~ 949 (1034)
T PRK07279 884 NSEATILVQIQSIR---VIRTKTKGQQ--MAFLSVTDTKK-KLDVTLFPETYRQYKDELKEGKFYYLKG-KIQ 949 (1034)
T ss_pred CCcceEEEEEEEEE---EEEEcCCCCe--EEEEEEeeCCC-cEEEEECHHHHHHHHHHhccCCEEEEEE-EEE
Confidence 45567888888764 3445523543 45688999998 8999999997766542 5667777776 454
No 250
>PRK00420 hypothetical protein; Validated
Probab=26.91 E-value=47 Score=30.31 Aligned_cols=26 Identities=27% Similarity=0.589 Sum_probs=21.2
Q ss_pred eCCCCCCCCcceeeCCCceeecccCCCc
Q psy15132 222 KACPSQDCNKKVIDQNNGMYRCEKCNKE 249 (786)
Q Consensus 222 ~aC~~~~C~kKv~~~~~~~~~C~~C~~~ 249 (786)
..|| .|+--+....+|..+|+.|+..
T Consensus 24 ~~CP--~Cg~pLf~lk~g~~~Cp~Cg~~ 49 (112)
T PRK00420 24 KHCP--VCGLPLFELKDGEVVCPVHGKV 49 (112)
T ss_pred CCCC--CCCCcceecCCCceECCCCCCe
Confidence 4899 8998877545778899999974
No 251
>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=26.77 E-value=34 Score=32.74 Aligned_cols=31 Identities=26% Similarity=0.737 Sum_probs=20.2
Q ss_pred EEeCCCCcccccccccc----------------CCceeeeCCCCCcCCc
Q psy15132 685 TYKACPSQDCNKKVIDQ----------------NNGMYRCEKCNKEFNT 717 (786)
Q Consensus 685 ~Y~aC~~~~C~kkv~~~----------------~~g~~~C~~C~~~~~~ 717 (786)
....|+ .||..+... .+--|+|++|++.+-.
T Consensus 90 ~~sRC~--~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW~ 136 (147)
T PF01927_consen 90 IFSRCP--KCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIYWE 136 (147)
T ss_pred CCCccC--CCCcEeeechhhccccccCccccccCCeEEECCCCCCEecc
Confidence 456788 588755321 1236899999997644
No 252
>PRK07275 single-stranded DNA-binding protein; Provisional
Probab=26.69 E-value=1.8e+02 Score=28.40 Aligned_cols=33 Identities=18% Similarity=0.489 Sum_probs=25.1
Q ss_pred EEEEEeccccccccc--CCCCcEEEEEe-EEEeeeC
Q psy15132 98 SVTMTLWGKEAETFD--ASNKPVIAVKA-ARVSEFQ 130 (786)
Q Consensus 98 ~i~~tLWg~~a~~~~--~~~~~Vi~i~~-~kv~~f~ 130 (786)
-|.|++||+.|+.+. ...|.-|++.| .+...|.
T Consensus 48 fi~vv~wgk~Ae~~~~~l~KG~~V~VeGrl~~r~y~ 83 (162)
T PRK07275 48 FINCVIWRQQAENLANWAKKGALIGVTGRIQTRNYE 83 (162)
T ss_pred EEEEEEEcHHHHHHHHHcCCCCEEEEEEEEEeceEE
Confidence 689999999998864 36777777776 3667773
No 253
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=26.68 E-value=62 Score=26.14 Aligned_cols=28 Identities=25% Similarity=0.555 Sum_probs=19.7
Q ss_pred EeCCCCCCCCcceeeCCCceeecccCCCcCCceeE
Q psy15132 221 YKACPSQDCNKKVIDQNNGMYRCEKCNKEFNTFTY 255 (786)
Q Consensus 221 Y~aC~~~~C~kKv~~~~~~~~~C~~C~~~~~~~~~ 255 (786)
+.||. .|+.-+.. + .|+.|+....+..|
T Consensus 3 ~kAC~--~C~~i~~~--~---~CP~Cgs~~~T~~W 30 (61)
T PRK08351 3 EKACR--HCHYITTE--D---RCPVCGSRDLSDEW 30 (61)
T ss_pred hhhhh--hCCcccCC--C---cCCCCcCCcccccc
Confidence 35999 99998843 2 59999986533333
No 254
>KOG3108|consensus
Probab=26.60 E-value=1.6e+02 Score=31.17 Aligned_cols=61 Identities=11% Similarity=0.284 Sum_probs=38.2
Q ss_pred eeeEEEEEEEcccceeEEeecCCceeeEEEEEEeeccccEEEEEEecccccccc----CCCCCEEEEEeEEEeecCCc
Q psy15132 576 NIDVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWGKEAETFD----ASNKPVIAVKAARVSEFQGN 649 (786)
Q Consensus 576 ~vDViGvV~~V~~~~~i~~k~~g~~~~kr~i~l~D~s~~~i~~tLWg~~a~~~~----~~~~~vv~i~~~~V~~f~G~ 649 (786)
.|-++|+|..+... .....+.|.|.+| .|.+..|-....... ...+..|-+ ...++.|+|+
T Consensus 70 ~v~~VGivr~~e~~-----------~t~i~y~I~D~tg-~id~r~W~~~~~~~~e~~~l~~~~yVkv-~G~Lk~f~Gk 134 (265)
T KOG3108|consen 70 AVSIVGIVRNIEKS-----------ATNITYEIEDGTG-QIDVRQWFHDNAESEEMPALETGTYVKV-YGHLKPFQGK 134 (265)
T ss_pred EEEEEEEEEeceec-----------CcceEEEEecCcc-cEEEEEeccccchhhhCcccccCcEEEe-eecccCCCCc
Confidence 46778888776432 2345789999999 699999998664431 223332222 2244667876
No 255
>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=26.31 E-value=40 Score=22.29 Aligned_cols=23 Identities=30% Similarity=0.925 Sum_probs=17.2
Q ss_pred CCCCCCCCcceeeCCCceeecccCCCcC
Q psy15132 223 ACPSQDCNKKVIDQNNGMYRCEKCNKEF 250 (786)
Q Consensus 223 aC~~~~C~kKv~~~~~~~~~C~~C~~~~ 250 (786)
.|| .|.+.|... .-.|+.|+-.+
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 999999632 34699998654
No 256
>KOG3084|consensus
Probab=25.85 E-value=66 Score=34.58 Aligned_cols=49 Identities=20% Similarity=0.490 Sum_probs=31.9
Q ss_pred EEeCCCCccccccccccCCc-eee-----eCCCCCcCCceeEEEEEEEEEEecCCcEEE
Q psy15132 685 TYKACPSQDCNKKVIDQNNG-MYR-----CEKCNKEFNTFTYRLILPVMIGDWTNSVWV 737 (786)
Q Consensus 685 ~Y~aC~~~~C~kkv~~~~~g-~~~-----C~~C~~~~~~~~~ry~l~~~i~D~Tg~~~~ 737 (786)
-|.-|| .|.++......| .-. |+.|+..+|...+ .+-+.|.|++|+.-+
T Consensus 149 kykFCp--~CG~~tkp~e~g~k~~Cs~~~C~~~n~~yPr~dP--vVIm~li~~d~~~~L 203 (345)
T KOG3084|consen 149 KYKFCP--GCGSPTKPEEAGTKLQCSDETCPSCNVIYPRTDP--VVIMLLIDHDGKHAL 203 (345)
T ss_pred HhccCc--ccCCCcccccCCccceeecccCCcCCeeccCCCC--eEEEEEEcCCCCEee
Confidence 499999 799987543333 333 4455566666555 455678899888644
No 257
>KOG1885|consensus
Probab=25.52 E-value=2.4e+02 Score=32.18 Aligned_cols=58 Identities=17% Similarity=0.320 Sum_probs=41.9
Q ss_pred CceEEEEEEeecCCcceecCCCCCceEEEEEEEcCCCcEEEEEcch------hHHHhhhhccCCcEEEEcce
Q psy15132 453 NKWTIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFND------ECNRFHDMIEKDKVYYISNC 518 (786)
Q Consensus 453 ~~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~G~I~at~~~~------~~~kf~~~l~~G~vy~is~~ 518 (786)
...+|.+||..+ |.. .+|++-++|.++.+.+++.+=.. .-....+.|+-||++-+++.
T Consensus 105 ~~~svaGRI~s~---R~s-----GsKL~Fydl~~~g~klQvm~~~~~~~~~~~F~~~~~~lkrGDiig~~G~ 168 (560)
T KOG1885|consen 105 EIVSVAGRIHSK---RES-----GSKLVFYDLHGDGVKLQVMANAKKITSEEDFEQLHKFLKRGDIIGVSGY 168 (560)
T ss_pred ceeeeeeeEeee---ecc-----CCceEEEEEecCCeEEEEEEehhhcCCHHHHHHHHhhhhccCEEeeecC
Confidence 347899999964 432 24888889999877788876433 23455677999999988874
No 258
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=25.37 E-value=72 Score=37.12 Aligned_cols=67 Identities=24% Similarity=0.260 Sum_probs=50.7
Q ss_pred eeeecccCCCCC-ceEEEEEEeecCCcceecCCCCCceEEEEEEEcCCCcEEEEEcchhHHHhhhhccCCcEEEEcc
Q psy15132 442 THPIVSLSPYQN-KWTIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFNDECNRFHDMIEKDKVYYISN 517 (786)
Q Consensus 442 ~~~I~~L~p~~~-~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~G~I~at~~~~~~~kf~~~l~~G~vy~is~ 517 (786)
.+.|.+|..+.. ...|++.|++. ++- .|. . -|+|.|++|.|-|.+|.+.=-+-|+-+++|+++.+.+
T Consensus 202 r~~i~~id~~ig~tV~I~GeV~qi---kqT---~GP-T--VFtltDetg~i~aAAFe~aGvRAyP~IevGdiV~ViG 269 (715)
T COG1107 202 RTLIDDLDEMIGKTVRIEGEVTQI---KQT---SGP-T--VFTLTDETGAIWAAAFEEAGVRAYPEIEVGDIVEVIG 269 (715)
T ss_pred cccHHHHHhhcCceEEEEEEEEEE---EEc---CCC-E--EEEEecCCCceehhhhccCCcccCCCCCCCceEEEEE
Confidence 345666666543 46899999953 332 121 3 3578999999999999998888999999999999887
No 259
>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=25.36 E-value=27 Score=33.96 Aligned_cols=25 Identities=16% Similarity=0.464 Sum_probs=18.6
Q ss_pred CCCCCCCCcceeeC--CCceeecccCCCc
Q psy15132 223 ACPSQDCNKKVIDQ--NNGMYRCEKCNKE 249 (786)
Q Consensus 223 aC~~~~C~kKv~~~--~~~~~~C~~C~~~ 249 (786)
-|| .|+++.+-. .+..|.|+.|+..
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 899998721 1235999999975
No 260
>PRK11827 hypothetical protein; Provisional
Probab=25.10 E-value=52 Score=26.51 Aligned_cols=29 Identities=31% Similarity=0.490 Sum_probs=20.6
Q ss_pred EeCCCCcccccccccc-CCceeeeCCCCCcCC
Q psy15132 686 YKACPSQDCNKKVIDQ-NNGMYRCEKCNKEFN 716 (786)
Q Consensus 686 Y~aC~~~~C~kkv~~~-~~g~~~C~~C~~~~~ 716 (786)
.-+|| .|+..+... ......|..|+..+|
T Consensus 8 ILaCP--~ckg~L~~~~~~~~Lic~~~~laYP 37 (60)
T PRK11827 8 IIACP--VCNGKLWYNQEKQELICKLDNLAFP 37 (60)
T ss_pred heECC--CCCCcCeEcCCCCeEECCccCeecc
Confidence 35899 699887532 234577999988765
No 261
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=25.06 E-value=44 Score=30.55 Aligned_cols=28 Identities=25% Similarity=0.697 Sum_probs=20.7
Q ss_pred CCCCCCCcceeeCCCceeecccCCCcCCceeEeeee
Q psy15132 224 CPSQDCNKKVIDQNNGMYRCEKCNKEFNTFTYRLIL 259 (786)
Q Consensus 224 C~~~~C~kKv~~~~~~~~~C~~C~~~~~~~~~ry~l 259 (786)
|| .|+.++.-. .+.|+.|+..+ .-+|.+
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 899987632 68999999754 445654
No 262
>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=24.51 E-value=38 Score=31.27 Aligned_cols=39 Identities=15% Similarity=0.181 Sum_probs=24.3
Q ss_pred cCccccCCCcceeeEEEeecccccccccCCcccceEEEEc
Q psy15132 320 NGTKKIPDGVNINSFAMLATQLNDIITDGTLSEFTIVQIK 359 (786)
Q Consensus 320 ~~~~~~sDG~~~~~~~~la~~ln~~v~~~~L~~~~iikl~ 359 (786)
+..+.++||=|.+ .+.+-..|..+++.|.|..|.=+.+.
T Consensus 34 ~~~lelTDGWY~I-ka~lD~~L~~~l~~gki~vG~KL~v~ 72 (118)
T PF09103_consen 34 SAILELTDGWYSI-KAQLDPPLTRLLRKGKIRVGQKLRVC 72 (118)
T ss_dssp ---EEEE-SS-EE-EE---HHHHHHHHTT-S-TT-EEEES
T ss_pred cCEEEEecCCEEE-EEEeCHHHHHHHHhCCccCCccEEEE
Confidence 3478899999975 89999999999999999888777763
No 263
>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=24.36 E-value=2.1e+02 Score=32.74 Aligned_cols=89 Identities=17% Similarity=0.167 Sum_probs=52.7
Q ss_pred EEEEeccceeEeeccCCceeeEEEEEEEeCCCCEEEEEecccccccc--cCCCCc-EEEEEeEEEeeeCCceeeeeccee
Q psy15132 65 VCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWGKEAETF--DASNKP-VIAVKAARVSEFQGGKTLSLSMSS 141 (786)
Q Consensus 65 vV~~v~~~~~i~~k~~g~~~~kr~i~l~D~s~~~i~~tLWg~~a~~~--~~~~~~-Vi~i~~~kv~~f~g~~~ls~~~~s 141 (786)
-|.=.||+.+++..++|.- =|+|.|+. ..|.|++|...+..+ ...+|. |++.-.+.+.+-+|..+|.+.
T Consensus 19 ~v~V~GEisn~~~~~sGH~----YFtLkD~~-a~i~~vmf~~~~~~l~f~~~~G~~V~v~g~v~~y~~~G~~ql~v~--- 90 (432)
T TIGR00237 19 QVWIQGEISNFTQPVSGHW----YFTLKDEN-AQVRCVMFRGNNNRLKFRPQNGQQVLVRGGISVYEPRGDYQIICF--- 90 (432)
T ss_pred cEEEEEEecCCeeCCCceE----EEEEEcCC-cEEEEEEEcChhhCCCCCCCCCCEEEEEEEEEEECCCCcEEEEEE---
Confidence 3444456666655445642 38899976 599999999887654 444554 555555556555666666543
Q ss_pred EEEECCCc-----hHHHHHHhhhhccC
Q psy15132 142 VLSLNPDI-----PECHKLQGWFSTQT 163 (786)
Q Consensus 142 ~i~~npd~-----pe~~~l~~w~~~~~ 163 (786)
.+.|.- -+-.+|++-+..+|
T Consensus 91 --~i~~~G~G~l~~~~~~lk~~L~~eG 115 (432)
T TIGR00237 91 --EMQPAGEGLLQLAYEQLKEKLAAEG 115 (432)
T ss_pred --EeccCChHHHHHHHHHHHHHHHHCC
Confidence 344532 23445566565554
No 264
>PRK08763 single-stranded DNA-binding protein; Provisional
Probab=24.32 E-value=2.6e+02 Score=27.44 Aligned_cols=32 Identities=16% Similarity=0.213 Sum_probs=23.2
Q ss_pred EEEEEEecccccccc--CCCCCEEEEEe-EEEeec
Q psy15132 615 SVTMTLWGKEAETFD--ASNKPVIAVKA-ARVSEF 646 (786)
Q Consensus 615 ~i~~tLWg~~a~~~~--~~~~~vv~i~~-~~V~~f 646 (786)
-++|++||..|+.+. ...|.-|.+.| .+...|
T Consensus 53 w~~Vv~fgk~Ae~v~~~L~KGs~V~VeGrL~~~~y 87 (164)
T PRK08763 53 WHRVKFFGKLGEIAGEYLRKGSQCYIEGSIRYDKF 87 (164)
T ss_pred EEEEEEehHHHHHHHHhcCCCCEEEEEEEEEecee
Confidence 499999999987654 57788777765 344456
No 265
>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=23.94 E-value=51 Score=35.11 Aligned_cols=23 Identities=22% Similarity=0.694 Sum_probs=17.8
Q ss_pred CCCCCCCCcceee---CCCceeecccCC
Q psy15132 223 ACPSQDCNKKVID---QNNGMYRCEKCN 247 (786)
Q Consensus 223 aC~~~~C~kKv~~---~~~~~~~C~~C~ 247 (786)
.|+ .|+..+.. .+-+.|+|+.|+
T Consensus 247 pC~--~Cg~~I~~~~~~gR~t~~CP~CQ 272 (272)
T TIGR00577 247 PCR--RCGTPIEKIKVGGRGTHFCPQCQ 272 (272)
T ss_pred CCC--CCCCeeEEEEECCCCCEECCCCC
Confidence 799 89987652 245689999996
No 266
>PF08772 NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon like; InterPro: IPR014881 This entry corresponds to a zinc ribbon and is found on the RNA binding protein NOB1. ; PDB: 2CON_A.
Probab=23.82 E-value=49 Score=27.76 Aligned_cols=45 Identities=20% Similarity=0.237 Sum_probs=14.7
Q ss_pred eEEeCCCCccccccccccCCceeeeCCCCCcCCceeEEEEEEEEEEecCCcEEEE
Q psy15132 684 TTYKACPSQDCNKKVIDQNNGMYRCEKCNKEFNTFTYRLILPVMIGDWTNSVWVT 738 (786)
Q Consensus 684 ~~Y~aC~~~~C~kkv~~~~~g~~~C~~C~~~~~~~~~ry~l~~~i~D~Tg~~~~~ 738 (786)
-|-..|- .|.+-.. +....+|++||...- .++.+.+ |..|.+.+.
T Consensus 7 ~~vlrC~--aCf~~t~--~~~k~FCp~CGn~TL-----~rvsvsv-~~~G~~~~~ 51 (73)
T PF08772_consen 7 TWVLRCH--ACFKITK--DMTKQFCPKCGNATL-----KRVSVSV-DEDGKIKLH 51 (73)
T ss_dssp -EEEE-S--SS--EES---SS--S-SSS--S-------EEEE-B---SS---B--
T ss_pred eeeEEcc--ccccCcC--CCCceeCcccCCCcc-----eEEEEEE-CCCCCEEEE
Confidence 3556677 5888443 345667999998632 1334433 466665543
No 267
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=23.79 E-value=51 Score=27.01 Aligned_cols=17 Identities=24% Similarity=0.790 Sum_probs=13.5
Q ss_pred eeCCCceeecccCCCcC
Q psy15132 234 IDQNNGMYRCEKCNKEF 250 (786)
Q Consensus 234 ~~~~~~~~~C~~C~~~~ 250 (786)
.+...|...|++|+..+
T Consensus 47 ~~i~eg~L~Cp~c~r~Y 63 (68)
T PF03966_consen 47 VEIVEGELICPECGREY 63 (68)
T ss_dssp EETTTTEEEETTTTEEE
T ss_pred ccccCCEEEcCCCCCEE
Confidence 46678899999998764
No 268
>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed
Probab=23.78 E-value=1.3e+02 Score=34.35 Aligned_cols=56 Identities=20% Similarity=0.341 Sum_probs=41.4
Q ss_pred ceEEEEEEeecCCcceecCCCCCceEEEEEEEcCCCcEEEEEcchhHHHhhhhccCCcEEEEcc
Q psy15132 454 KWTIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFNDECNRFHDMIEKDKVYYISN 517 (786)
Q Consensus 454 ~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~G~I~at~~~~~~~kf~~~l~~G~vy~is~ 517 (786)
+..|+|=|. .|+.. ..| .+.|+|.|+...|+|++|...+.+..-.++.|.-+.+.+
T Consensus 25 ~v~v~gEis------~~~~~-~sG-H~Yf~Lkd~~a~i~~~~~~~~~~~~~~~~~~G~~v~v~g 80 (438)
T PRK00286 25 QVWVRGEIS------NFTRH-SSG-HWYFTLKDEIAQIRCVMFKGSARRLKFKPEEGMKVLVRG 80 (438)
T ss_pred cEEEEEEeC------CCeeC-CCC-eEEEEEEcCCcEEEEEEEcChhhcCCCCCCCCCEEEEEE
Confidence 445666666 23322 123 477999999999999999998877777799999887766
No 269
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=23.62 E-value=56 Score=26.22 Aligned_cols=29 Identities=24% Similarity=0.714 Sum_probs=21.5
Q ss_pred EeCCCCcccccccc-ccCCceeeeCCCCCcCC
Q psy15132 686 YKACPSQDCNKKVI-DQNNGMYRCEKCNKEFN 716 (786)
Q Consensus 686 Y~aC~~~~C~kkv~-~~~~g~~~C~~C~~~~~ 716 (786)
.-||| .|+-.+. .++.+...|+.|+..++
T Consensus 8 iLaCP--~~kg~L~~~~~~~~L~c~~~~~aYp 37 (60)
T COG2835 8 ILACP--VCKGPLVYDEEKQELICPRCKLAYP 37 (60)
T ss_pred eeecc--CcCCcceEeccCCEEEecccCceee
Confidence 46899 6988763 44556788999998764
No 270
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.52 E-value=57 Score=29.10 Aligned_cols=31 Identities=23% Similarity=0.667 Sum_probs=22.8
Q ss_pred eCCCCCCCCcceeeCCCceeecccCCCcCCceeEeeeee
Q psy15132 222 KACPSQDCNKKVIDQNNGMYRCEKCNKEFNTFTYRLILP 260 (786)
Q Consensus 222 ~aC~~~~C~kKv~~~~~~~~~C~~C~~~~~~~~~ry~l~ 260 (786)
+.|| .|.+++.-. ..+|+.|..++ +-+|.++
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 5799 999997632 57999998764 4566654
No 271
>PRK02935 hypothetical protein; Provisional
Probab=23.50 E-value=51 Score=29.46 Aligned_cols=25 Identities=28% Similarity=0.743 Sum_probs=16.9
Q ss_pred CCCCccccccccccCCceeeeCCCCCcC
Q psy15132 688 ACPSQDCNKKVIDQNNGMYRCEKCNKEF 715 (786)
Q Consensus 688 aC~~~~C~kkv~~~~~g~~~C~~C~~~~ 715 (786)
-|| .|+|- ++.-+....|..|++..
T Consensus 72 ~CP--~C~K~-TKmLGrvD~CM~C~~PL 96 (110)
T PRK02935 72 ICP--SCEKP-TKMLGRVDACMHCNQPL 96 (110)
T ss_pred ECC--CCCch-hhhccceeecCcCCCcC
Confidence 599 59983 33233456799999864
No 272
>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=23.21 E-value=40 Score=20.81 Aligned_cols=12 Identities=42% Similarity=1.223 Sum_probs=9.0
Q ss_pred eeeCCCCCcCCc
Q psy15132 706 YRCEKCNKEFNT 717 (786)
Q Consensus 706 ~~C~~C~~~~~~ 717 (786)
|.|+.|++.+..
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 679999887654
No 273
>PLN02221 asparaginyl-tRNA synthetase
Probab=23.20 E-value=5.1e+02 Score=30.77 Aligned_cols=84 Identities=17% Similarity=0.222 Sum_probs=53.7
Q ss_pred CceEEEEEEeecCCcceecCCCCCce--EEEEEEEcCC--CcEEEEEcchhHHHhhhhccCCcEEEEcceEEeccCCccc
Q psy15132 453 NKWTIKARVTNKTPIREWNNARGSGK--LFSIDLLDES--GEIRATMFNDECNRFHDMIEKDKVYYISNCTLKPANKKFS 528 (786)
Q Consensus 453 ~~w~I~~RV~~k~~~r~~~~~~~~g~--~~~~~L~D~~--G~I~at~~~~~~~kf~~~l~~G~vy~is~~~V~~a~~~y~ 528 (786)
...+|+|+|-++ |. .|+ +.=++|.|.+ |.|++++-.+.. .....|..|.++.+.+- |+..... .
T Consensus 51 ~~V~I~GWV~~i---R~------~Gk~~i~Fl~LRDgs~~g~iQvVv~~~~~-~~~~~L~~ES~V~V~G~-V~~~~~~-~ 118 (572)
T PLN02221 51 QKVRIGGWVKTG---RE------QGKGTFAFLEVNDGSCPANLQVMVDSSLY-DLSTLVATGTCVTVDGV-LKVPPEG-K 118 (572)
T ss_pred CEEEEEEEEEeh---hh------CCCceEEEEEEeCCcccccEEEEEcCchh-hHHhcCCCceEEEEEEE-EEeCCcc-C
Confidence 457888888742 32 243 5556899999 889998865422 22236889999999874 4332211 1
Q ss_pred ccCCceEEEEccccEEEEcc
Q psy15132 529 SINNDYEMSFTHSTTVIPCN 548 (786)
Q Consensus 529 ~~~~~yei~f~~~T~I~~~~ 548 (786)
...+.+||....-..+.++.
T Consensus 119 ~~~~~iEl~v~~i~vl~~a~ 138 (572)
T PLN02221 119 GTKQKIELSVEKVIDVGTVD 138 (572)
T ss_pred CCCccEEEEEeEEEEEecCC
Confidence 12468999998765555553
No 274
>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=22.89 E-value=61 Score=21.75 Aligned_cols=20 Identities=30% Similarity=0.808 Sum_probs=10.1
Q ss_pred CCCCCCCcceeeC-CCceeeccc
Q psy15132 224 CPSQDCNKKVIDQ-NNGMYRCEK 245 (786)
Q Consensus 224 C~~~~C~kKv~~~-~~~~~~C~~ 245 (786)
|| .|+.++... ++-.|+|.+
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 88 899998743 333688854
No 275
>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=22.89 E-value=2.4e+02 Score=29.76 Aligned_cols=58 Identities=16% Similarity=0.118 Sum_probs=0.0
Q ss_pred eeEEEEEEEcccceeEEeecCCceeeEEEEEEeecccc-EEEEEEecc----ccccccCCCCCEEEEEeE
Q psy15132 577 IDVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQA-SVTMTLWGK----EAETFDASNKPVIAVKAA 641 (786)
Q Consensus 577 vDViGvV~~V~~~~~i~~k~~g~~~~kr~i~l~D~s~~-~i~~tLWg~----~a~~~~~~~~~vv~i~~~ 641 (786)
|.|+|+|+.+.... =+...+.-++|=|.||. .|.|.+|.+ .+..+....|.+|.++|.
T Consensus 69 v~i~G~Vv~~~~~~-------~~~~~~~~l~iDD~Sg~~~i~~~~~~~~~~~~~l~~~~~~G~~V~VkG~ 131 (256)
T PF10451_consen 69 VRIVGVVVGIDYKW-------IENEDRIILTIDDSSGANTIECKCSKSSYLSMGLPINDLIGKVVEVKGT 131 (256)
T ss_dssp EEEEEEEEEEEEEE--------BBTCEEEEEEE-SSCS-EEEEEEEHHHHHCCCHHCTT-TT-EEEEEEE
T ss_pred EEEEEEEEEEEEEe-------ecccceEEEEEeCCCCceeEEEEEEcccccccCCCccCCCCcEEEEEEE
No 276
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=22.73 E-value=59 Score=34.84 Aligned_cols=25 Identities=24% Similarity=0.664 Sum_probs=18.1
Q ss_pred eCCCCccccccccc---cCCceeeeCCCCC
Q psy15132 687 KACPSQDCNKKVID---QNNGMYRCEKCNK 713 (786)
Q Consensus 687 ~aC~~~~C~kkv~~---~~~g~~~C~~C~~ 713 (786)
..|| .|+.++.. .+-++|+|+.|++
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 5799 69987642 2346899999974
No 277
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=22.61 E-value=85 Score=28.16 Aligned_cols=48 Identities=21% Similarity=0.505 Sum_probs=29.5
Q ss_pred EeCCCCccccccccccCCceeeeCCCCCcCCceeE--EEEEEEEEEecCCcE
Q psy15132 686 YKACPSQDCNKKVIDQNNGMYRCEKCNKEFNTFTY--RLILPVMIGDWTNSV 735 (786)
Q Consensus 686 Y~aC~~~~C~kkv~~~~~g~~~C~~C~~~~~~~~~--ry~l~~~i~D~Tg~~ 735 (786)
-+-|| .|+.--+-.+.+.|.|+.|.....+... -=.-...+-|..|..
T Consensus 3 lp~cp--~c~sEytYed~~~~~cpec~~ew~~~~~~~~~~~~~~v~DsnGn~ 52 (112)
T COG2824 3 LPPCP--KCNSEYTYEDGGQLICPECAHEWNENEAAEEADEALIVKDSNGNL 52 (112)
T ss_pred CCCCC--ccCCceEEecCceEeCchhccccccccccccccCceEEEcCCCcE
Confidence 36799 7988655556778999999887552211 001124566666654
No 278
>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=22.51 E-value=34 Score=33.31 Aligned_cols=29 Identities=14% Similarity=0.419 Sum_probs=20.1
Q ss_pred eEEeCCCCcccccccccc--CCceeeeCCCCCc
Q psy15132 684 TTYKACPSQDCNKKVIDQ--NNGMYRCEKCNKE 714 (786)
Q Consensus 684 ~~Y~aC~~~~C~kkv~~~--~~g~~~C~~C~~~ 714 (786)
..|.-|| .|+++.+-. -+..|.|+.||..
T Consensus 107 ~~~Y~Cp--~c~~r~tf~eA~~~~F~Cp~Cg~~ 137 (158)
T TIGR00373 107 NMFFICP--NMCVRFTFNEAMELNFTCPRCGAM 137 (158)
T ss_pred CCeEECC--CCCcEeeHHHHHHcCCcCCCCCCE
Confidence 4566789 699987521 1234899999986
No 279
>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=22.36 E-value=89 Score=25.42 Aligned_cols=29 Identities=24% Similarity=0.768 Sum_probs=21.5
Q ss_pred EEeCCCCccccccccc-cCCceeeeCCCCCcC
Q psy15132 685 TYKACPSQDCNKKVID-QNNGMYRCEKCNKEF 715 (786)
Q Consensus 685 ~Y~aC~~~~C~kkv~~-~~~g~~~C~~C~~~~ 715 (786)
.-..|| .|+..... .....|.|+.||...
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 357899 69987654 345689999998753
No 280
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=22.32 E-value=37 Score=27.32 Aligned_cols=34 Identities=24% Similarity=0.390 Sum_probs=24.0
Q ss_pred EeCCCCCCCCcceeeCCCceeecccCCCcCCceeEeeee
Q psy15132 221 YKACPSQDCNKKVIDQNNGMYRCEKCNKEFNTFTYRLIL 259 (786)
Q Consensus 221 Y~aC~~~~C~kKv~~~~~~~~~C~~C~~~~~~~~~ry~l 259 (786)
|.||. +|++-+.+. .-.|+.|+.+-..-.|+=+|
T Consensus 4 ~kAC~--~Ck~l~~~d---~e~CP~Cgs~~~te~W~G~~ 37 (64)
T COG2093 4 EKACK--NCKRLTPED---TEICPVCGSTDLTEEWFGLL 37 (64)
T ss_pred hHHHh--hccccCCCC---CccCCCCCCcccchhhccEE
Confidence 67999 999998642 33699999875445555443
No 281
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=22.19 E-value=58 Score=34.56 Aligned_cols=25 Identities=20% Similarity=0.688 Sum_probs=18.3
Q ss_pred eCCCCCCCCcceee---CCCceeecccCCC
Q psy15132 222 KACPSQDCNKKVID---QNNGMYRCEKCNK 248 (786)
Q Consensus 222 ~aC~~~~C~kKv~~---~~~~~~~C~~C~~ 248 (786)
..|+ .|+-.+.. .+-+.|||+.|++
T Consensus 246 epC~--~CGt~I~k~~~~gR~t~~CP~CQ~ 273 (273)
T COG0266 246 EPCR--RCGTPIEKIKLGGRSTFYCPVCQK 273 (273)
T ss_pred CCCC--ccCCEeEEEEEcCCcCEeCCCCCC
Confidence 4688 89865542 3567899999974
No 282
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=22.10 E-value=65 Score=25.85 Aligned_cols=28 Identities=25% Similarity=0.748 Sum_probs=21.6
Q ss_pred eCCCCCCCCccee-eCCCceeecccCCCcCC
Q psy15132 222 KACPSQDCNKKVI-DQNNGMYRCEKCNKEFN 251 (786)
Q Consensus 222 ~aC~~~~C~kKv~-~~~~~~~~C~~C~~~~~ 251 (786)
.||| .|+-.+. .+..+...|+.|+..++
T Consensus 9 LaCP--~~kg~L~~~~~~~~L~c~~~~~aYp 37 (60)
T COG2835 9 LACP--VCKGPLVYDEEKQELICPRCKLAYP 37 (60)
T ss_pred eecc--CcCCcceEeccCCEEEecccCceee
Confidence 4899 9998865 34556889999998753
No 283
>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=22.02 E-value=1.5e+02 Score=33.88 Aligned_cols=72 Identities=19% Similarity=0.344 Sum_probs=48.6
Q ss_pred ceEEEEEEeecCCcceecCCCCCceEEEEEEEcCCCcEEEEEcchhHHHhhhhccCCcEEEEcc-eEEeccCCcccccCC
Q psy15132 454 KWTIKARVTNKTPIREWNNARGSGKLFSIDLLDESGEIRATMFNDECNRFHDMIEKDKVYYISN-CTLKPANKKFSSINN 532 (786)
Q Consensus 454 ~w~I~~RV~~k~~~r~~~~~~~~g~~~~~~L~D~~G~I~at~~~~~~~kf~~~l~~G~vy~is~-~~V~~a~~~y~~~~~ 532 (786)
+.-|+|=|.+ |+.. ..| .+.|+|.|+...|+|++|...+.++.-.++.|.=+.+.+ ..+-+. .+
T Consensus 19 ~v~V~GEisn------~~~~-~sG-H~YFtLkD~~a~i~~vmf~~~~~~l~f~~~~G~~V~v~g~v~~y~~-------~G 83 (432)
T TIGR00237 19 QVWIQGEISN------FTQP-VSG-HWYFTLKDENAQVRCVMFRGNNNRLKFRPQNGQQVLVRGGISVYEP-------RG 83 (432)
T ss_pred cEEEEEEecC------CeeC-CCc-eEEEEEEcCCcEEEEEEEcChhhCCCCCCCCCCEEEEEEEEEEECC-------CC
Confidence 4456676663 3322 123 478889999999999999998877766789998877765 334332 34
Q ss_pred ceEEEEcc
Q psy15132 533 DYEMSFTH 540 (786)
Q Consensus 533 ~yei~f~~ 540 (786)
.|.|....
T Consensus 84 ~~ql~v~~ 91 (432)
T TIGR00237 84 DYQIICFE 91 (432)
T ss_pred cEEEEEEE
Confidence 56666553
No 284
>PRK13732 single-stranded DNA-binding protein; Provisional
Probab=22.01 E-value=2.8e+02 Score=27.47 Aligned_cols=32 Identities=19% Similarity=0.256 Sum_probs=23.5
Q ss_pred EEEEEEecccccccc--CCCCCEEEEEe-EEEeec
Q psy15132 615 SVTMTLWGKEAETFD--ASNKPVIAVKA-ARVSEF 646 (786)
Q Consensus 615 ~i~~tLWg~~a~~~~--~~~~~vv~i~~-~~V~~f 646 (786)
-++|++||..|+.+. ...|..|++.| .+.+.|
T Consensus 55 w~~Vv~wgk~Ae~v~~~L~KG~~V~VeGrL~~r~y 89 (175)
T PRK13732 55 WHRVVLFGKLAEVAGEYLRKGAQVYIEGQLRTRSW 89 (175)
T ss_pred EEEEEEecHHHHHHHHhcCCCCEEEEEEEEEeeeE
Confidence 589999999988765 57788777765 344445
No 285
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=21.96 E-value=4.5e+02 Score=31.65 Aligned_cols=83 Identities=20% Similarity=0.259 Sum_probs=53.2
Q ss_pred ecCccchhccCCCCceEEEEEEEEeccceeEeeccCCceeeEEEEEEEeCCCCEEEEEecccccccc-cCCCCcEEEEEe
Q psy15132 45 FVPLKTIAEISPDENIDVLGVCIDAAELSSVTGKTNQKTYMKRDITLVDQSQASVTMTLWGKEAETF-DASNKPVIAVKA 123 (786)
Q Consensus 45 f~~~~~i~~~~~~~~vDViGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~s~~~i~~tLWg~~a~~~-~~~~~~Vi~i~~ 123 (786)
+.....|.....|..+-+.|.|.+..... ++......+.+.|.++ .+.+++++..|-.. ..+.|.-+.+.
T Consensus 48 ~~~~~~i~~~~~g~~vti~g~V~~~~~~~-------~~~~~~l~v~~~d~~~-~l~l~fFn~~~~l~~~~~~G~~v~v~- 118 (677)
T COG1200 48 RTLLPGIAEARPGEIVTIEGTVLSHEKFP-------FGKRKLLKVTLSDGTG-VLTLVFFNFPAYLKKKLKVGERVIVY- 118 (677)
T ss_pred ccccCChhhcCCCceEEEEEEEEeeeccC-------CCCCceEEEEEecCcE-EEEEEEECccHHHHhhCCCCCEEEEE-
Confidence 44444444556678888999998875443 1122456789999554 99999999886221 12555555444
Q ss_pred EEEeeeCCceeee
Q psy15132 124 ARVSEFQGGKTLS 136 (786)
Q Consensus 124 ~kv~~f~g~~~ls 136 (786)
+|++.|+|+.+++
T Consensus 119 Gk~~~~~~~~~~~ 131 (677)
T COG1200 119 GKVKRFKGGLQIT 131 (677)
T ss_pred EEEeeccCceEEE
Confidence 4777787766655
No 286
>PRK10445 endonuclease VIII; Provisional
Probab=21.77 E-value=55 Score=34.71 Aligned_cols=25 Identities=28% Similarity=0.757 Sum_probs=18.1
Q ss_pred eCCCCccccccccc---cCCceeeeCCCCC
Q psy15132 687 KACPSQDCNKKVID---QNNGMYRCEKCNK 713 (786)
Q Consensus 687 ~aC~~~~C~kkv~~---~~~g~~~C~~C~~ 713 (786)
..|| .|+-++.. .+-++|+|+.|++
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 69876632 2446899999974
No 287
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=21.62 E-value=1e+02 Score=27.62 Aligned_cols=28 Identities=29% Similarity=0.834 Sum_probs=22.2
Q ss_pred EeCCCCCCCCcceeeCCCceeecccCCCcC
Q psy15132 221 YKACPSQDCNKKVIDQNNGMYRCEKCNKEF 250 (786)
Q Consensus 221 Y~aC~~~~C~kKv~~~~~~~~~C~~C~~~~ 250 (786)
-|-|| +|+.--+-++.+.|.|+.|....
T Consensus 3 lp~cp--~c~sEytYed~~~~~cpec~~ew 30 (112)
T COG2824 3 LPPCP--KCNSEYTYEDGGQLICPECAHEW 30 (112)
T ss_pred CCCCC--ccCCceEEecCceEeCchhcccc
Confidence 46799 89887766677799999997654
No 288
>PRK06863 single-stranded DNA-binding protein; Provisional
Probab=21.27 E-value=2.8e+02 Score=27.26 Aligned_cols=68 Identities=10% Similarity=0.151 Sum_probs=38.9
Q ss_pred eeeEEEEEEEcccceeEEeecCCceeeEEEEEEe----ec-cc------cEEEEEEecccccccc--CCCCCEEEEEe-E
Q psy15132 576 NIDVLGVCIDAAELSSVTGKTNQKTYMKRDITLV----DQ-SQ------ASVTMTLWGKEAETFD--ASNKPVIAVKA-A 641 (786)
Q Consensus 576 ~vDViGvV~~V~~~~~i~~k~~g~~~~kr~i~l~----D~-s~------~~i~~tLWg~~a~~~~--~~~~~vv~i~~-~ 641 (786)
.|-++|.+.. +.+.-.+. +|+.+.+-.|-.- |. +| .-++|++||..|+.+. ...|.-|.+.| .
T Consensus 6 ~V~LiGrLg~--DPElR~t~-nG~~va~fsVAvn~~~~d~~~Ge~~e~t~w~~Vv~fgk~AE~v~~~LkKGs~V~VeGrL 82 (168)
T PRK06863 6 KVIIVGHLGN--DPEIRTMP-NGEAVANISVATSESWTDKNTGERREVTEWHRIVFYRRQAEVAGEYLRKGSQVYVEGRL 82 (168)
T ss_pred EEEEEEEcCC--CCEEEEcC-CCCEEEEEEEEecCcccccCCCcccccceEEEEEEEhHHHHHHHHHCCCCCEEEEEEEE
Confidence 4667787776 22221222 4655444333332 11 12 2689999999988764 57788777765 3
Q ss_pred EEeec
Q psy15132 642 RVSEF 646 (786)
Q Consensus 642 ~V~~f 646 (786)
+.+.|
T Consensus 83 ~~r~w 87 (168)
T PRK06863 83 KTRKW 87 (168)
T ss_pred EeCCc
Confidence 44445
No 289
>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=21.06 E-value=95 Score=25.36 Aligned_cols=28 Identities=25% Similarity=0.362 Sum_probs=14.6
Q ss_pred eeeCCCCCcCCceeEEEEEEEEEEecCCcEEEEEeh
Q psy15132 706 YRCEKCNKEFNTFTYRLILPVMIGDWTNSVWVTLFQ 741 (786)
Q Consensus 706 ~~C~~C~~~~~~~~~ry~l~~~i~D~Tg~~~~~~F~ 741 (786)
|.|+||+...-+ ..-...||..+-.+||
T Consensus 1 y~C~KCg~~~~e--------~~~v~~tgg~~skiFd 28 (64)
T PF09855_consen 1 YKCPKCGNEEYE--------SGEVRATGGGLSKIFD 28 (64)
T ss_pred CCCCCCCCccee--------cceEEccCCeeEEEEE
Confidence 568888775211 1122245665555566
No 290
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=20.92 E-value=57 Score=34.78 Aligned_cols=25 Identities=20% Similarity=0.728 Sum_probs=17.9
Q ss_pred eCCCCccccccccc---cCCceeeeCCCCC
Q psy15132 687 KACPSQDCNKKVID---QNNGMYRCEKCNK 713 (786)
Q Consensus 687 ~aC~~~~C~kkv~~---~~~g~~~C~~C~~ 713 (786)
..|| .|+.++.. .+-++|+|+.|++
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 3599 69976532 2346899999986
No 291
>PRK07772 single-stranded DNA-binding protein; Provisional
Probab=20.85 E-value=2.4e+02 Score=28.21 Aligned_cols=33 Identities=12% Similarity=0.324 Sum_probs=23.7
Q ss_pred EEEEEeccccccccc--CCCCcEEEEEe-EEEeeeC
Q psy15132 98 SVTMTLWGKEAETFD--ASNKPVIAVKA-ARVSEFQ 130 (786)
Q Consensus 98 ~i~~tLWg~~a~~~~--~~~~~Vi~i~~-~kv~~f~ 130 (786)
-++|++|++.|+.+. ...+.-|.+.+ .+...|.
T Consensus 54 fi~V~~Wg~~Ae~va~~L~KGd~V~V~GrL~~r~we 89 (186)
T PRK07772 54 FLRCSIWRQAAENVAESLTKGMRVIVTGRLKQRSYE 89 (186)
T ss_pred EEEEEEecHHHHHHHHhcCCCCEEEEEEEEEcCceE
Confidence 679999999998874 35566555554 5777785
No 292
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=20.81 E-value=82 Score=23.62 Aligned_cols=25 Identities=20% Similarity=0.676 Sum_probs=19.7
Q ss_pred CCCCCCCCcceeeCCCceeecccCCCc
Q psy15132 223 ACPSQDCNKKVIDQNNGMYRCEKCNKE 249 (786)
Q Consensus 223 aC~~~~C~kKv~~~~~~~~~C~~C~~~ 249 (786)
-|. .|+..+.....+.-+|+.|+..
T Consensus 4 ~C~--~Cg~~~~~~~~~~irC~~CG~r 28 (44)
T smart00659 4 ICG--ECGRENEIKSKDVVRCRECGYR 28 (44)
T ss_pred ECC--CCCCEeecCCCCceECCCCCce
Confidence 588 8999987555567899999864
No 293
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=20.69 E-value=50 Score=35.25 Aligned_cols=14 Identities=43% Similarity=1.096 Sum_probs=10.7
Q ss_pred ceeecccCCCcCCc
Q psy15132 239 GMYRCEKCNKEFNT 252 (786)
Q Consensus 239 ~~~~C~~C~~~~~~ 252 (786)
..|+||-|++.+.+
T Consensus 397 KPYrCevC~KRYKN 410 (423)
T COG5189 397 KPYRCEVCDKRYKN 410 (423)
T ss_pred Cceeccccchhhcc
Confidence 47999999986543
No 294
>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=20.67 E-value=2.9e+02 Score=28.12 Aligned_cols=56 Identities=27% Similarity=0.346 Sum_probs=35.5
Q ss_pred EEEEeCCCCEEEEEecccccccccCCCCcEEEEEeEEEeeeCCceeeeecc-eeEEEECCCc
Q psy15132 89 ITLVDQSQASVTMTLWGKEAETFDASNKPVIAVKAARVSEFQGGKTLSLSM-SSVLSLNPDI 149 (786)
Q Consensus 89 i~l~D~s~~~i~~tLWg~~a~~~~~~~~~Vi~i~~~kv~~f~g~~~ls~~~-~s~i~~npd~ 149 (786)
++..|.++....|.|||+-+.. ....|++|-+-+ +|.+.-...+.. .--++++||.
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 4566788899999999998754 346677776555 443322222222 2367888873
No 295
>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=20.67 E-value=60 Score=31.06 Aligned_cols=29 Identities=28% Similarity=0.795 Sum_probs=20.4
Q ss_pred EeCCCCCCCCcceeeC----------------CCceeecccCCCcCC
Q psy15132 221 YKACPSQDCNKKVIDQ----------------NNGMYRCEKCNKEFN 251 (786)
Q Consensus 221 Y~aC~~~~C~kKv~~~----------------~~~~~~C~~C~~~~~ 251 (786)
...|+ .||..+... .+.-|+|++|++-+-
T Consensus 91 ~sRC~--~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW 135 (147)
T PF01927_consen 91 FSRCP--KCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIYW 135 (147)
T ss_pred CCccC--CCCcEeeechhhccccccCccccccCCeEEECCCCCCEec
Confidence 45899 899766421 233799999998653
No 296
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=20.60 E-value=62 Score=34.40 Aligned_cols=27 Identities=22% Similarity=0.634 Sum_probs=19.5
Q ss_pred eCCCCccccccccc---cCCceeeeCCCCCcC
Q psy15132 687 KACPSQDCNKKVID---QNNGMYRCEKCNKEF 715 (786)
Q Consensus 687 ~aC~~~~C~kkv~~---~~~g~~~C~~C~~~~ 715 (786)
..|| .|+.++.. .+-++|+|+.|++-.
T Consensus 236 ~pC~--~Cg~~I~~~~~~gR~ty~Cp~CQ~~~ 265 (269)
T PRK14811 236 QPCP--RCGTPIEKIVVGGRGTHFCPQCQPLR 265 (269)
T ss_pred CCCC--cCCCeeEEEEECCCCcEECCCCcCCC
Confidence 4699 69986642 234689999998753
No 297
>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=20.51 E-value=61 Score=26.41 Aligned_cols=28 Identities=21% Similarity=0.765 Sum_probs=21.2
Q ss_pred EeCCCCCCCCcceee-CCCceeecccCCCcC
Q psy15132 221 YKACPSQDCNKKVID-QNNGMYRCEKCNKEF 250 (786)
Q Consensus 221 Y~aC~~~~C~kKv~~-~~~~~~~C~~C~~~~ 250 (786)
=..|| .|+..... .....|.|+.|+...
T Consensus 28 Sq~C~--~CG~~~~~~~~~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 28 SQTCP--RCGHRNKKRRSGRVFTCPNCGFEM 56 (69)
T ss_pred ccCcc--CcccccccccccceEEcCCCCCEE
Confidence 45799 89988765 345589999998753
No 298
>COG4085 Predicted RNA-binding protein, contains TRAM domain [General function prediction only]
Probab=20.47 E-value=1.1e+02 Score=30.52 Aligned_cols=26 Identities=19% Similarity=0.254 Sum_probs=23.7
Q ss_pred EEEEEEEecCCcEEEEEehhhHHHHh
Q psy15132 723 ILPVMIGDWTNSVWVTLFQNEAESIL 748 (786)
Q Consensus 723 ~l~~~i~D~Tg~~~~~~F~~~ae~ll 748 (786)
+.++.+.|+||++.+.+|...++.|+
T Consensus 71 i~~l~lndgtGti~vva~~~tee~l~ 96 (204)
T COG4085 71 IESLVLNDGTGTITVVASRSTEETLE 96 (204)
T ss_pred eEEEEEECCCCcEEEEEecChhHhHh
Confidence 45788999999999999999999988
No 299
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=20.43 E-value=58 Score=34.72 Aligned_cols=25 Identities=20% Similarity=0.635 Sum_probs=18.2
Q ss_pred eCCCCccccccccc---cCCceeeeCCCCC
Q psy15132 687 KACPSQDCNKKVID---QNNGMYRCEKCNK 713 (786)
Q Consensus 687 ~aC~~~~C~kkv~~---~~~g~~~C~~C~~ 713 (786)
..|| .|+.++.. .+-++|+|+.|++
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 5799 69876632 2346899999974
No 300
>PF12773 DZR: Double zinc ribbon
Probab=20.29 E-value=44 Score=25.34 Aligned_cols=32 Identities=19% Similarity=0.495 Sum_probs=19.8
Q ss_pred CCCCCCCCcceeeCCCceeecccCCCcCCceeEee
Q psy15132 223 ACPSQDCNKKVIDQNNGMYRCEKCNKEFNTFTYRL 257 (786)
Q Consensus 223 aC~~~~C~kKv~~~~~~~~~C~~C~~~~~~~~~ry 257 (786)
-|+ .|..++.......+.|++|+..+ .+..+|
T Consensus 14 fC~--~CG~~l~~~~~~~~~C~~Cg~~~-~~~~~f 45 (50)
T PF12773_consen 14 FCP--HCGTPLPPPDQSKKICPNCGAEN-PPNAKF 45 (50)
T ss_pred CCh--hhcCChhhccCCCCCCcCCcCCC-cCCcCc
Confidence 577 78888763233457788888764 334444
No 301
>PF13695 zf-3CxxC: Zinc-binding domain
Probab=20.23 E-value=1.1e+02 Score=27.00 Aligned_cols=40 Identities=15% Similarity=0.493 Sum_probs=28.4
Q ss_pred ceeecccCCCcCCceeEeeeeeEEEEecCCcEEEEeehHHHHH
Q psy15132 239 GMYRCEKCNKEFNTFTYRLILPVMIGDWTNSVWVTLFQNEAES 281 (786)
Q Consensus 239 ~~~~C~~C~~~~~~~~~ry~l~~~v~D~Tg~~~~~~F~~~a~~ 281 (786)
|.|.|.+|+..-.+..-.-.+.+. ..|...+.+|++..+.
T Consensus 4 grF~C~~C~~~W~S~~v~i~f~~~---~~g~v~~rv~~Q~C~~ 43 (98)
T PF13695_consen 4 GRFQCSKCSRGWTSAKVWILFHMY---RGGQVNMRVFGQRCKK 43 (98)
T ss_pred EEEECCCCCCCCccCEEEEEEEEc---CCCeEEEEEECCCCCC
Confidence 579999998876654444333333 6688999999988864
No 302
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=20.18 E-value=56 Score=25.15 Aligned_cols=24 Identities=33% Similarity=0.789 Sum_probs=18.0
Q ss_pred CCCCCCCCccee-eCCCceeecccCCC
Q psy15132 223 ACPSQDCNKKVI-DQNNGMYRCEKCNK 248 (786)
Q Consensus 223 aC~~~~C~kKv~-~~~~~~~~C~~C~~ 248 (786)
-|. .|++++. .+.....+|+.|+-
T Consensus 8 ~C~--~Cg~~~~~~~~~~~irCp~Cg~ 32 (49)
T COG1996 8 KCA--RCGREVELDQETRGIRCPYCGS 32 (49)
T ss_pred Ehh--hcCCeeehhhccCceeCCCCCc
Confidence 688 8999996 33344689999975
No 303
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=20.05 E-value=1.5e+02 Score=29.59 Aligned_cols=40 Identities=20% Similarity=0.562 Sum_probs=0.0
Q ss_pred EEEEEEEEEecCce-----------EEeCCCCccccccccccCCceeeeCCCCCc
Q psy15132 671 SVRGIIQVFRGSNT-----------TYKACPSQDCNKKVIDQNNGMYRCEKCNKE 714 (786)
Q Consensus 671 ~v~a~I~~i~~~~~-----------~Y~aC~~~~C~kkv~~~~~g~~~C~~C~~~ 714 (786)
.|+|.|.... ++. .|..|+ .|.--+.. .+-+.+|++|+.+
T Consensus 124 ivrA~Vis~~-~~~~Lst~~~dlGVI~A~Cs--rC~~~L~~-~~~~l~Cp~Cg~t 174 (188)
T COG1096 124 IVRARVISTG-DPIQLSTKGNDLGVIYARCS--RCRAPLVK-KGNMLKCPNCGNT 174 (188)
T ss_pred EEEEEEEecC-CCeEEEecCCcceEEEEEcc--CCCcceEE-cCcEEECCCCCCE
Done!