Query 015600
Match_columns 404
No_of_seqs 156 out of 245
Neff 7.5
Searched_HMMs 46136
Date Fri Mar 29 07:49:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/015600.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/015600hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4757 Predicted telomere bin 100.0 2.2E-43 4.8E-48 340.5 7.9 337 3-368 2-363 (522)
2 cd04497 hPOT1_OB1_like hPOT1_O 100.0 3.5E-34 7.5E-39 248.5 17.6 137 8-146 1-138 (138)
3 PF02765 POT1: Telomeric singl 100.0 1E-33 2.2E-38 248.0 14.7 137 10-146 1-146 (146)
4 cd04498 hPOT1_OB2 hPOT1_OB2: A 99.9 1.9E-24 4.2E-29 180.9 11.8 107 169-288 1-123 (123)
5 PRK12366 replication factor A; 99.5 6E-11 1.3E-15 126.7 28.7 282 6-403 275-590 (637)
6 PRK12366 replication factor A; 99.3 3.3E-09 7.2E-14 113.4 28.8 278 8-403 61-344 (637)
7 TIGR00617 rpa1 replication fac 99.3 2E-09 4.4E-14 114.4 27.0 319 9-403 179-537 (608)
8 PRK07218 replication factor A; 99.1 3E-07 6.5E-12 93.3 30.5 196 10-291 58-257 (423)
9 PRK14699 replication factor A; 99.0 3.2E-07 6.9E-12 94.9 29.0 272 11-401 167-447 (484)
10 PRK15491 replication factor A; 99.0 5.9E-07 1.3E-11 90.3 27.7 272 9-400 56-336 (374)
11 PRK07211 replication factor A; 99.0 4.7E-08 1E-12 100.2 19.5 204 8-290 159-367 (485)
12 PRK06386 replication factor A; 99.0 2.6E-06 5.7E-11 84.5 30.9 277 11-404 3-291 (358)
13 PRK15491 replication factor A; 98.8 4E-07 8.8E-12 91.5 19.9 204 6-286 162-372 (374)
14 PRK14699 replication factor A; 98.7 2.4E-06 5.3E-11 88.4 20.4 203 9-288 275-484 (484)
15 PRK07211 replication factor A; 98.6 5.7E-05 1.2E-09 77.8 27.9 269 10-400 53-329 (485)
16 PRK08402 replication factor A; 98.2 6.4E-05 1.4E-09 75.0 17.4 186 159-403 63-272 (355)
17 cd04475 RPA1_DBD_B RPA1_DBD_B: 98.2 2.7E-05 5.8E-10 63.6 11.1 74 23-101 1-79 (101)
18 TIGR00617 rpa1 replication fac 98.1 5.4E-05 1.2E-09 80.9 14.8 156 7-200 295-479 (608)
19 PRK06461 single-stranded DNA-b 98.1 0.00016 3.5E-09 62.0 14.1 89 10-108 4-96 (129)
20 cd04491 SoSSB_OBF SoSSB_OBF: A 97.7 0.00065 1.4E-08 53.2 10.8 72 25-102 1-75 (82)
21 PRK07218 replication factor A; 97.6 0.0091 2E-07 61.0 20.0 159 159-398 59-219 (423)
22 PRK08402 replication factor A; 97.3 0.0079 1.7E-07 60.2 15.2 139 9-180 61-207 (355)
23 PRK06461 single-stranded DNA-b 97.1 0.0065 1.4E-07 52.0 10.7 95 159-290 5-100 (129)
24 cd04497 hPOT1_OB1_like hPOT1_O 96.9 0.011 2.4E-07 51.1 10.6 96 157-290 3-105 (138)
25 cd03524 RPA2_OBF_family RPA2_O 96.8 0.0067 1.5E-07 44.9 7.5 71 25-101 1-71 (75)
26 KOG3416 Predicted nucleic acid 96.4 0.021 4.6E-07 47.8 8.0 82 11-101 5-87 (134)
27 PRK07217 replication factor A; 96.3 0.07 1.5E-06 52.0 12.7 92 7-109 69-160 (311)
28 PF02765 POT1: Telomeric singl 96.0 0.18 3.8E-06 44.0 12.5 97 159-288 2-109 (146)
29 PRK07217 replication factor A; 95.9 0.19 4E-06 49.1 13.5 90 159-291 73-164 (311)
30 PF01336 tRNA_anti-codon: OB-f 95.9 0.015 3.3E-07 43.8 4.8 68 24-101 1-70 (75)
31 cd04489 ExoVII_LU_OBF ExoVII_L 95.8 0.12 2.6E-06 39.5 9.7 69 24-101 2-72 (78)
32 cd04481 RPA1_DBD_B_like RPA1_D 95.8 0.05 1.1E-06 44.7 7.7 82 25-108 1-90 (106)
33 PRK06386 replication factor A; 95.5 0.13 2.8E-06 51.5 10.9 87 8-106 105-193 (358)
34 cd04476 RPA1_DBD_C RPA1_DBD_C: 95.3 0.049 1.1E-06 48.5 6.5 57 347-403 15-95 (166)
35 cd04474 RPA1_DBD_A RPA1_DBD_A: 95.3 0.057 1.2E-06 44.3 6.4 84 12-99 1-88 (104)
36 PF15489 CTC1: CST, telomere m 95.0 0.16 3.6E-06 56.9 10.6 132 238-402 888-1040(1144)
37 cd04478 RPA2_DBD_D RPA2_DBD_D: 94.6 0.37 8E-06 38.4 9.5 67 24-101 2-72 (95)
38 PRK13480 3'-5' exoribonuclease 94.5 0.3 6.5E-06 48.2 10.3 82 12-101 4-85 (314)
39 cd04485 DnaE_OBF DnaE_OBF: A s 94.4 0.12 2.7E-06 39.3 5.9 71 26-101 2-72 (84)
40 cd04475 RPA1_DBD_B RPA1_DBD_B: 94.3 0.63 1.4E-05 37.6 10.2 63 236-302 38-100 (101)
41 cd04491 SoSSB_OBF SoSSB_OBF: A 93.7 0.22 4.7E-06 38.8 6.1 46 238-286 35-80 (82)
42 cd04492 YhaM_OBF_like YhaM_OBF 93.6 0.68 1.5E-05 35.4 8.9 69 27-101 3-71 (83)
43 cd04483 hOBFC1_like hOBFC1_lik 93.1 0.88 1.9E-05 36.5 8.9 65 26-101 2-87 (92)
44 PF13742 tRNA_anti_2: OB-fold 91.6 1.8 3.8E-05 35.2 9.0 79 13-100 11-94 (99)
45 PF08646 Rep_fac-A_C: Replicat 90.8 0.16 3.5E-06 44.1 2.3 32 372-403 50-81 (146)
46 cd04487 RecJ_OBF2_like RecJ_OB 86.8 7.3 0.00016 29.7 8.7 65 26-101 3-68 (73)
47 cd03524 RPA2_OBF_family RPA2_O 86.1 10 0.00023 27.2 9.5 65 171-276 1-67 (75)
48 cd04488 RecG_wedge_OBF RecG_we 85.6 5.8 0.00013 29.1 7.7 68 26-100 2-69 (75)
49 PF09104 BRCA-2_OB3: BRCA2, ol 84.8 7.9 0.00017 33.6 8.8 62 168-270 19-82 (143)
50 PRK07373 DNA polymerase III su 83.5 4 8.7E-05 42.4 7.8 89 8-101 266-355 (449)
51 cd04484 polC_OBF polC_OBF: A s 81.7 15 0.00033 28.5 8.8 70 24-98 2-74 (82)
52 PF09104 BRCA-2_OB3: BRCA2, ol 80.8 9.9 0.00021 33.0 7.9 73 11-90 4-81 (143)
53 cd04490 PolII_SU_OBF PolII_SU_ 80.6 6.4 0.00014 30.5 6.2 59 24-91 2-62 (79)
54 PF12100 DUF3576: Domain of un 78.4 5.1 0.00011 32.7 5.1 54 8-68 16-70 (103)
55 PRK05673 dnaE DNA polymerase I 78.3 5.9 0.00013 45.9 7.5 88 9-101 964-1052(1135)
56 PF01336 tRNA_anti-codon: OB-f 78.0 25 0.00053 25.8 9.0 59 171-271 2-60 (75)
57 TIGR00237 xseA exodeoxyribonuc 76.0 21 0.00044 37.0 10.1 81 13-101 9-90 (432)
58 cd04498 hPOT1_OB2 hPOT1_OB2: A 75.6 3.3 7.2E-05 35.1 3.5 34 60-94 62-95 (123)
59 PRK00286 xseA exodeoxyribonucl 74.5 23 0.00051 36.4 10.2 80 14-101 16-96 (438)
60 cd04482 RPA2_OBF_like RPA2_OBF 74.4 13 0.00029 29.5 6.5 60 26-93 3-64 (91)
61 KOG1030 Predicted Ca2+-depende 72.7 8 0.00017 34.5 5.2 27 372-398 51-77 (168)
62 cd04474 RPA1_DBD_A RPA1_DBD_A: 71.9 9.4 0.0002 31.1 5.2 36 236-271 46-81 (104)
63 PRK06920 dnaE DNA polymerase I 71.7 12 0.00026 43.2 7.7 89 8-101 930-1018(1107)
64 KOG3056 Protein required for S 71.0 6.8 0.00015 41.1 5.0 69 24-95 188-257 (578)
65 cd04495 BRCA2DBD_OB3 BRCA2DBD_ 70.2 21 0.00045 29.0 6.6 64 26-95 2-66 (100)
66 PRK05338 rplS 50S ribosomal pr 67.5 13 0.00029 31.1 5.3 45 70-115 14-66 (116)
67 PF01245 Ribosomal_L19: Riboso 66.8 20 0.00044 29.9 6.2 40 69-109 13-60 (113)
68 PRK07374 dnaE DNA polymerase I 64.5 20 0.00043 41.8 7.6 89 8-101 986-1075(1170)
69 cd04483 hOBFC1_like hOBFC1_lik 62.2 78 0.0017 25.1 9.4 26 171-198 1-26 (92)
70 TIGR01024 rplS_bact ribosomal 60.8 20 0.00044 29.9 5.1 45 70-115 14-66 (113)
71 PF15072 DUF4539: Domain of un 57.7 38 0.00083 26.8 6.0 63 23-94 3-66 (86)
72 PRK10917 ATP-dependent DNA hel 56.3 52 0.0011 36.1 8.8 79 11-98 51-129 (681)
73 CHL00084 rpl19 ribosomal prote 55.4 30 0.00066 29.0 5.3 41 70-111 18-66 (117)
74 cd04486 YhcR_OBF_like YhcR_OBF 53.4 1E+02 0.0022 23.7 8.3 62 27-101 3-69 (78)
75 TIGR00643 recG ATP-dependent D 53.2 73 0.0016 34.5 9.3 79 11-99 24-103 (630)
76 PF02721 DUF223: Domain of unk 51.8 20 0.00043 28.5 3.6 40 236-275 9-48 (95)
77 PRK05672 dnaE2 error-prone DNA 51.1 38 0.00082 39.1 6.9 86 9-101 940-1026(1046)
78 PRK06826 dnaE DNA polymerase I 50.9 43 0.00094 39.0 7.4 77 20-101 990-1067(1151)
79 cd04478 RPA2_DBD_D RPA2_DBD_D: 50.3 21 0.00045 28.1 3.5 22 377-398 17-38 (95)
80 cd04495 BRCA2DBD_OB3 BRCA2DBD_ 48.7 96 0.0021 25.2 6.9 35 238-272 29-64 (100)
81 PF15072 DUF4539: Domain of un 47.8 18 0.00038 28.7 2.6 21 377-397 20-40 (86)
82 PRK07279 dnaE DNA polymerase I 47.4 47 0.001 38.2 6.9 86 9-101 874-960 (1034)
83 COG1107 Archaea-specific RecJ- 47.1 88 0.0019 33.5 8.2 79 11-100 203-282 (715)
84 COG1570 XseA Exonuclease VII, 45.6 1.9E+02 0.004 30.0 10.2 78 15-101 17-96 (440)
85 PRK00448 polC DNA polymerase I 44.8 83 0.0018 37.6 8.5 86 8-99 224-313 (1437)
86 cd04490 PolII_SU_OBF PolII_SU_ 43.7 26 0.00055 27.1 2.9 21 379-399 20-40 (79)
87 KOG4792 Crk family adapters [S 41.6 43 0.00093 31.4 4.4 61 229-293 223-289 (293)
88 cd04492 YhaM_OBF_like YhaM_OBF 37.6 44 0.00095 25.0 3.5 21 377-397 20-40 (83)
89 cd04494 BRCA2DBD_OB2 BRCA2DBD_ 37.1 1.1E+02 0.0025 29.2 6.7 52 238-290 181-237 (251)
90 PRK07772 single-stranded DNA-b 36.5 66 0.0014 29.3 4.9 74 21-94 4-90 (186)
91 cd04480 RPA1_DBD_A_like RPA1_D 36.3 43 0.00092 25.9 3.2 37 236-272 30-66 (86)
92 cd04489 ExoVII_LU_OBF ExoVII_L 36.0 45 0.00097 24.9 3.2 23 377-399 18-40 (78)
93 cd04496 SSB_OBF SSB_OBF: A sub 36.0 32 0.0007 26.9 2.5 27 238-264 45-71 (100)
94 cd04480 RPA1_DBD_A_like RPA1_D 34.6 67 0.0014 24.8 4.1 57 42-100 17-73 (86)
95 COG1599 RFA1 Single-stranded D 34.4 1.4E+02 0.003 30.6 7.4 92 12-110 51-146 (407)
96 cd04481 RPA1_DBD_B_like RPA1_D 34.2 99 0.0021 24.9 5.2 64 236-300 34-103 (106)
97 COG1200 RecG RecG-like helicas 33.4 2.2E+02 0.0047 31.2 8.8 79 13-100 54-132 (677)
98 COG2176 PolC DNA polymerase II 33.1 97 0.0021 36.0 6.3 70 156-264 228-301 (1444)
99 PRK07274 single-stranded DNA-b 32.4 65 0.0014 27.4 4.0 26 238-263 48-73 (131)
100 PRK08763 single-stranded DNA-b 32.0 58 0.0013 29.0 3.7 26 238-263 53-78 (164)
101 PF11325 DUF3127: Domain of un 31.2 2.6E+02 0.0057 22.0 7.7 66 28-95 4-73 (84)
102 cd06555 ASCH_PF0470_like ASC-1 30.4 90 0.0019 25.9 4.3 27 236-266 16-43 (109)
103 PRK13254 cytochrome c-type bio 28.4 3.7E+02 0.0081 23.5 8.1 67 9-85 36-105 (148)
104 PRK06752 single-stranded DNA-b 27.4 1.7E+02 0.0037 23.9 5.6 72 23-94 4-84 (112)
105 PRK09010 single-stranded DNA-b 27.1 84 0.0018 28.4 3.9 27 238-264 55-81 (177)
106 PF15489 CTC1: CST, telomere m 25.9 1.1E+03 0.024 27.6 16.8 71 20-95 164-235 (1144)
107 cd04496 SSB_OBF SSB_OBF: A sub 25.6 1.3E+02 0.0029 23.2 4.5 71 24-95 1-82 (100)
108 PRK05733 single-stranded DNA-b 25.4 88 0.0019 28.1 3.7 27 238-264 54-80 (172)
109 cd04317 EcAspRS_like_N EcAspRS 25.3 3.6E+02 0.0079 22.5 7.5 62 19-90 12-76 (135)
110 cd04494 BRCA2DBD_OB2 BRCA2DBD_ 25.2 1.5E+02 0.0032 28.4 5.3 66 45-112 166-237 (251)
111 PRK08182 single-stranded DNA-b 25.1 1.3E+02 0.0028 26.2 4.6 73 22-94 3-91 (148)
112 PRK07459 single-stranded DNA-b 25.0 1.9E+02 0.0042 24.1 5.5 73 22-94 4-81 (121)
113 PRK06751 single-stranded DNA-b 24.8 2.2E+02 0.0047 25.6 6.1 72 23-94 4-84 (173)
114 PRK07135 dnaE DNA polymerase I 24.7 1.6E+02 0.0035 33.8 6.4 65 12-84 890-954 (973)
115 PRK07459 single-stranded DNA-b 24.6 1E+02 0.0022 25.8 3.8 26 238-263 45-70 (121)
116 KOG4757 Predicted telomere bin 24.4 4.7 0.0001 41.0 -5.0 46 156-205 175-220 (522)
117 PRK06752 single-stranded DNA-b 24.1 1.2E+02 0.0027 24.8 4.1 26 238-263 48-73 (112)
118 COG0335 RplS Ribosomal protein 23.8 2.1E+02 0.0045 23.9 5.2 45 70-115 16-68 (115)
119 PRK06751 single-stranded DNA-b 23.0 1.3E+02 0.0029 27.0 4.3 26 238-263 48-73 (173)
120 PRK06293 single-stranded DNA-b 22.9 1.6E+02 0.0034 26.2 4.7 72 23-94 3-80 (161)
121 PF07933 DUF1681: Protein of u 22.8 77 0.0017 28.2 2.7 16 377-393 86-101 (160)
122 PRK13732 single-stranded DNA-b 22.7 1.1E+02 0.0024 27.6 3.8 27 238-264 55-81 (175)
123 PRK08486 single-stranded DNA-b 21.3 1.2E+02 0.0027 27.4 3.9 26 238-263 50-75 (182)
124 TIGR00621 ssb single stranded 21.3 1.3E+02 0.0029 26.6 4.0 34 238-283 52-85 (164)
125 COG2049 DUR1 Allophanate hydro 20.7 48 0.0011 31.0 1.1 44 224-269 171-214 (223)
126 PRK05813 single-stranded DNA-b 20.3 4.2E+02 0.009 24.8 7.2 72 23-95 111-185 (219)
No 1
>KOG4757 consensus Predicted telomere binding protein [General function prediction only]
Probab=100.00 E-value=2.2e-43 Score=340.53 Aligned_cols=337 Identities=25% Similarity=0.283 Sum_probs=244.2
Q ss_pred CCCCCcceeehHhhhhccCCEEEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEE
Q 015600 3 SQRNQGGIVRIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLI 82 (404)
Q Consensus 3 ~~~~~y~y~~i~~~~~~~~~~vnv~GVV~d~~~P~~trGtD~~~t~~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII 82 (404)
.-++.+.|..+++++.+.+..||+||||++++||++++|+||+||++|+|+...+.||+|++|+++-++||.|+++||||
T Consensus 2 ~~~ds~k~Iri~da~kk~~tiVNl~GiVkef~pp~qs~g~D~~~tv~IvDp~~ss~gLtv~lfSkt~edLP~Ik~~GDii 81 (522)
T KOG4757|consen 2 DVRDSLKLIRISDALKKKNTIVNLIGIVKEFTPPRQSLGKDWVCTVYIVDPDYSSIGLTVHLFSKTGEDLPVIKQVGDII 81 (522)
T ss_pred CcccchheeechHHHHhcCcEEEEEEEEEeccChhhccCCceEEEEEEeCCCCCCCCcEEEEecCchhhCccccccCcEE
Confidence 45678999999999999999999999999999999999999999999999998889999999999999999999999999
Q ss_pred EEeeEEEEEEcCeeEEEeecCc-eEEEEEeCCCCCCCCCCccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCccccccc
Q 015600 83 LLKNVMIKKHQAELSAVFYKDS-SSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSL 161 (404)
Q Consensus 83 ~l~rvki~~~~g~~~~~~~~~~-ss~~vf~~~~~~~~~P~~~s~~~~~~~~~e~~~v~~Lr~w~~~~~~~~~~~~f~~~L 161 (404)
+|||+|||.|+.+.||+++..+ |+|++|+|+ +.+..|||+|+. |-++ .+||+|++.+.....+ .+ ..+
T Consensus 82 llhRiKiq~y~~rtqgl~s~~fss~~~~Feg~-svd~i~~qssp~-f~~t-------~nlrew~a~~~s~~w~-c~-t~~ 150 (522)
T KOG4757|consen 82 LLHRIKIQSYRDRTQGLCSDQFSSAWALFEGN-SVDTICYQSSPR-FMKT-------GNLREWFALYKSKIWD-CQ-TNL 150 (522)
T ss_pred EEEEEEEEEhhhhhhhhhhcchhhhhhhhcCC-CCCccCCCCchh-hhcc-------chHHHHHHHHhCcccc-cc-cCH
Confidence 9999999999999999998776 459999999 889999999888 8887 7899999988776665 34 566
Q ss_pred ccccCCceEeEEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCC-ccCCCCCccccCCCCChhhhccCCCCceEEE
Q 015600 162 KDISEHRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLED-EEHNPLPLHIESSPLDLETLRNFFPVGTVLR 240 (404)
Q Consensus 162 ~di~~~~f~Dl~~qVv~~~~~~~~~~~~L~VwDgT~~~~~~~~~~~~~-~~~~~~~~~~~~~~l~~~~~~~~pp~G~~l~ 240 (404)
.++.++.--.|-||+++.. ......|. .|||-|.+-.-++.+..-- --++..|++|++ ++-..+..||..|.+..
T Consensus 151 ~k~fel~cs~l~~q~v~g~-s~~~~~w~-lv~d~~~h~~~s~~~~~~~~~ySlr~~l~~~~--~~T~~~l~Fp~~g~ts~ 226 (522)
T KOG4757|consen 151 HKNFELLCSSLARQNVTGL-SYPSVSWS-LVSDITPHQRCSFYAQVIKTWYSLRNPLLYVT--DPTENLLFFPMSGYTSS 226 (522)
T ss_pred hHhhhhhcchhhhheeecc-ccccceee-eeecccccccccccccceeeEeeccccccccc--CchHhhhhcccCCceee
Confidence 6666666666777777776 44455666 6889665544433331100 011234555544 55566788887777777
Q ss_pred EEecCchhhhhhccCCCCcEEEEeceE------------EEE-eCcEEEEEEecCC------ceEEcCCCChHHHHHHHH
Q 015600 241 VSTDRSYENFGRYFTATGKWVRIRNMS------------CQV-SSGMWHGLLQSSS------KIRLFSDNDNVVWDYMRR 301 (404)
Q Consensus 241 V~~~~~~~~~~~~~~k~g~wv~l~Nv~------------~k~-~~g~leG~l~~~s------ki~~l~~~d~~v~~r~r~ 301 (404)
+.-+.+.+++...-+..|.-+..+|+- ... |-|..+..+++++ .+.+...+.+.+.
T Consensus 227 ~r~~rv~~e~~i~ilq~~~d~~~~Nl~~e~D~~f~~~~~sl~dh~~lsrc~~~~~saprl~~sl~lhc~~ehll~----- 301 (522)
T KOG4757|consen 227 SRWDRVSEEFSICILQDEHDFYCRNLIKEGDYVFMKNVRSLIDHLGLSRCILHGDSAPRLNMSLELHCSEEHLLN----- 301 (522)
T ss_pred eeeecccccccchhccccchhhhhhhcccccccccccchhhhHHHHHHHHHHHhhccccccceeEeecCcchhhc-----
Confidence 666665555444444555555555554 333 2232222222221 1111111111110
Q ss_pred HHHHHhCCCCCCCCcCCCCCCCCcccccCCCccccHHHHhcCCCCCceEE-EEEEEEe---ecCCCccccc
Q 015600 302 FRERISGGHGHMPIWTDPSSQFLTEVDWVNVASVTLMKIATQLQGNVRCC-CIVRVVS---IHPFQAEHYS 368 (404)
Q Consensus 302 y~~~~~~~~~~~~~~~~p~~~~~t~~~~~~~p~ttL~~IL~~~~~~~kyr-~~VRVV~---~~P~~l~df~ 368 (404)
+++ |...+-.++..|-+++...|+++|||+++-+.++.||| |.||+|+ .+|..+|.+.
T Consensus 302 -------ev~--~e~r~~~q~~~tgi~~v~a~fvsl~Ds~t~~~vt~k~R~~vvrfva~~~~~P~sve~l~ 363 (522)
T KOG4757|consen 302 -------EVK--PEKRLYVQNCQTGIEAVIAPFVSLMDSETPFIVTEKKRTCVVRFVAHVINYPASVELLT 363 (522)
T ss_pred -------ccC--cccceeecccccCcchhhcccchhhhhccccccchhcceeeeeehhhcccccchhhhhh
Confidence 111 00001123567778888999999999999999999999 9999999 9999999984
No 2
>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=100.00 E-value=3.5e-34 Score=248.49 Aligned_cols=137 Identities=33% Similarity=0.509 Sum_probs=129.5
Q ss_pred cceeehHhhhhccCCEEEEEEEEEecCCceecCCCceEEEEEEEeCCCC-CCCeEEEEecCCCCCCCCCCCCCCEEEEee
Q 015600 8 GGIVRIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQ-SPELLVNIFTSSIDQLPRVLSPRDLILLKN 86 (404)
Q Consensus 8 y~y~~i~~~~~~~~~~vnv~GVV~d~~~P~~trGtD~~~t~~I~D~S~~-~~gl~v~iF~~~~~~LP~v~~~GDII~l~r 86 (404)
|.|++|++|....++.|||||||+|+++|++|+|+||+|+|+|+|+|.. +.||+|+||+++.+.||.+ ++||||+|||
T Consensus 1 ~~f~~i~~~~~~~~~~v~vigVV~~~~~p~~s~g~d~~~tl~i~D~S~~~~~~l~v~~F~~~~~~LP~v-~~GDVIll~~ 79 (138)
T cd04497 1 YKYTPLSSALKESGGSVNVIGVVVDAGPPVRSKGTDYCCTLTITDPSLANSDGLTVKLFRPNEESLPIV-KVGDIILLRR 79 (138)
T ss_pred CceEeHHHHHhccCCeEEEEEEEeecCCCcccCCCcEEEEEEEECCCCCCCCcEEEEEECCChhhCCCC-CCCCEEEEEE
Confidence 7899999998778999999999999999999999999999999999997 6899999999999999999 9999999999
Q ss_pred EEEEEEcCeeEEEeecCceEEEEEeCCCCCCCCCCccCCCCCCCCHHHHHHHHHHHHhhh
Q 015600 87 VMIKKHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCV 146 (404)
Q Consensus 87 vki~~~~g~~~~~~~~~~ss~~vf~~~~~~~~~P~~~s~~~~~~~~~e~~~v~~Lr~w~~ 146 (404)
++|+.|+|+.+++++.+.||||||++..+....|++.+.. ++++++|++++..||+|+.
T Consensus 80 ~kv~~~~g~~~~~~~~~~ss~avf~~~~~~~~~p~~~~~~-~~~~~~e~~~~~~Lr~w~~ 138 (138)
T cd04497 80 VKIQSYNGKPQGISNDRGSSWAVFRGDDGVVPIPQQSSKP-VEFGPEEEPSVEELRKWAS 138 (138)
T ss_pred EEEEEECCceEEEECCCceeEEEEcCCCCCCcCccccCCC-cccCcchHHHHHHHHHhhC
Confidence 9999999999999987669999999999999889887666 9999999999999999973
No 3
>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=100.00 E-value=1e-33 Score=248.00 Aligned_cols=137 Identities=35% Similarity=0.617 Sum_probs=126.7
Q ss_pred eeehHhhhhccCCEEEEEEEEEecCCc--eecCCCceEEEEEEEeCCCCC-----CCeEEEEecCCCCCCCCCCCCCCEE
Q 015600 10 IVRIKELAMHVKHKVNLLGVVLEFSIP--RKSQGTDYVCVLKIVDDSQQS-----PELLVNIFTSSIDQLPRVLSPRDLI 82 (404)
Q Consensus 10 y~~i~~~~~~~~~~vnv~GVV~d~~~P--~~trGtD~~~t~~I~D~S~~~-----~gl~v~iF~~~~~~LP~v~~~GDII 82 (404)
|++|+++....++.|||||||+++++| ++|||+||+|+|+|+|+|+.. .||+|++|+++++.||.+..+||||
T Consensus 1 ~~~l~~~~~~~~~~vnvigVV~~~~~p~~~~t~g~D~~~tl~i~D~S~~~~~~~~~~l~v~iF~~~~~~LP~v~~~GDii 80 (146)
T PF02765_consen 1 YTPLSTAKEKFGKFVNVIGVVVDFSPPNPKKTRGTDYMCTLTITDPSLNDSNQKLSGLTVNIFRPHKESLPNVKSVGDII 80 (146)
T ss_dssp BCCGGGSCTTSSEEEEEEEEEEEEEEECTEEESSSCEEEEEEEEBTTCSCSSCCCCEEEEEEEESSHHHSCTTCSTTHEE
T ss_pred CccchhhhhcCCCEEEEEEEEEEccCCcceEcCCCcEEEEEEEECCCCCccccccCCEEEEEECCCHHHCCCCCCCCCEE
Confidence 789998887889999999999999999 999999999999999999985 7999999999999999997779999
Q ss_pred EEeeEEEEEEcCeeEEEeecC-ceEEEEE-eCCCCCCCCCCccCCCCCCCCHHHHHHHHHHHHhhh
Q 015600 83 LLKNVMIKKHQAELSAVFYKD-SSSFALF-DGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCV 146 (404)
Q Consensus 83 ~l~rvki~~~~g~~~~~~~~~-~ss~~vf-~~~~~~~~~P~~~s~~~~~~~~~e~~~v~~Lr~w~~ 146 (404)
+|||+||+.|+|+++++++.. +++|+|| ++..+.++.||+.++++++++++|+++++.||+|++
T Consensus 81 ~l~r~kv~~~~~~~~~~~~~~~~ss~~vf~~~~~~~~~~p~~~s~~~~~~~~~e~~~~~~Lr~w~~ 146 (146)
T PF02765_consen 81 RLRRVKVQSYNGKPQGLSNSTSNSSWAVFSSGGSGAPFEPYQKSSNPFEFSDEEKKYVESLRKWAQ 146 (146)
T ss_dssp EEEEEEEEEETTEEEEEEECECTEEEEEECTSSTTTCCCSSCESTSSTT-HHHHHHHHHHHHHHH-
T ss_pred EEEEEEEEEECCEEEEEecCCCcEEEEEEecCCCCCCccccccCCCccCCCHHHHHHHHHHHHhhC
Confidence 999999999999999999755 6899999 888889999999888779999999999999999974
No 4
>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=99.91 E-value=1.9e-24 Score=180.92 Aligned_cols=107 Identities=24% Similarity=0.360 Sum_probs=86.8
Q ss_pred eEeEEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCCc-cCCCCCccccCCCCChhhhccCC-CCce-EEEEEecC
Q 015600 169 YFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDE-EHNPLPLHIESSPLDLETLRNFF-PVGT-VLRVSTDR 245 (404)
Q Consensus 169 f~Dl~~qVv~~~~~~~~~~~~L~VwDgT~~~~~~~~~~~~~~-~~~~~~~~~~~~~l~~~~~~~~p-p~G~-~l~V~~~~ 245 (404)
||||+||||+++ +.++++++|||||||+||+..+++..++. ..+++ +..++.|+ | |+ +|+|+||+
T Consensus 1 ~~DLvcqVv~v~-~~d~~~~~L~VwDgT~~p~~~~~~~~~~~~~~e~d----------~~~k~~~~gp-g~~ti~It~yD 68 (123)
T cd04498 1 YFDLLCQLLSVV-ETDSSSTLLKVWDGTKFPPPLRKVKVEDDVVLEGD----------RSLKHREEGG-KQLTIDILVYD 68 (123)
T ss_pred CccEEEEEEEEE-EecCCeEEEEEecCCCCChhHhheeccccCccccc----------hhhhhhccCC-CeEEEEEEEEc
Confidence 799999999999 76888999999999999776677765543 22222 34567899 8 99 99999999
Q ss_pred chhhhhhccCCCCcEEEEeceEEEEe--------CcEEEEEE-ecC----CceEEc
Q 015600 246 SYENFGRYFTATGKWVRIRNMSCQVS--------SGMWHGLL-QSS----SKIRLF 288 (404)
Q Consensus 246 ~~~~~~~~~~k~g~wv~l~Nv~~k~~--------~g~leG~l-~~~----ski~~l 288 (404)
+|++++++ +|+||||+|+|||+|.. +-.|||.+ ++- ++|++|
T Consensus 69 ~H~~~ar~-lK~GdfV~L~NVhiK~~~~~~~~~~~~~Le~~l~~gg~~~~rgi~vl 123 (123)
T cd04498 69 NHVELAKS-LKPGDFVRIYNVHAKSYSSKNEHDENDHLHFHLVHGGTEYGRGIRVL 123 (123)
T ss_pred chHHHHhh-CCCCCEEEEEEEEEEeccCCcccCCcceEEEEEccCceeeccceeeC
Confidence 99999888 99999999999999993 33789988 543 466654
No 5
>PRK12366 replication factor A; Reviewed
Probab=99.45 E-value=6e-11 Score=126.72 Aligned_cols=282 Identities=15% Similarity=0.154 Sum_probs=180.9
Q ss_pred CCcceeehHhhhhc-cCCEEEEEEEEEecCCcee---cCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCE
Q 015600 6 NQGGIVRIKELAMH-VKHKVNLLGVVLEFSIPRK---SQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDL 81 (404)
Q Consensus 6 ~~y~y~~i~~~~~~-~~~~vnv~GVV~d~~~P~~---trGtD~~~t~~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDI 81 (404)
..+.+++|+++... .|..+++-|-|+...+++. .+|+--..++.|.|.+- .+.+.+|.+..+.+..+ ..||+
T Consensus 275 ~~~~~~pI~~L~~~~~g~~~~I~grV~~~~~~R~f~~~~g~gkv~s~~l~D~tG---~IR~t~w~~~~d~~~~l-~~G~v 350 (637)
T PRK12366 275 KELEIVNIEELTEFEDGEEVDVKGRIIAISDKREVERDDRTAEVQDIELADGTG---RVRVSFWGEKAKILENL-KEGDA 350 (637)
T ss_pred cccCceeHHHCCcccCCCEEEEEEEEEecCCceEEEcCCCcEEEEEEEEEcCCC---eEEEEEeCchhhhhccc-CCCCE
Confidence 45678999999543 4568999999999988764 36788899999999873 39999999877788877 79999
Q ss_pred EEEeeEEEEEEcC-----eeEEEeecCceEEEEEeCCCCCCCCCCccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCcc
Q 015600 82 ILLKNVMIKKHQA-----ELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSND 156 (404)
Q Consensus 82 I~l~rvki~~~~g-----~~~~~~~~~~ss~~vf~~~~~~~~~P~~~s~~~~~~~~~e~~~v~~Lr~w~~~~~~~~~~~~ 156 (404)
+.+.+++++.|+. ++.+.++.. |.... +. ... .| .....
T Consensus 351 y~is~~~vk~y~~~~~~~~~El~~~~~-s~I~~-d~--~~~-~p-------------------------------~~~~~ 394 (637)
T PRK12366 351 VKIENCKVRTYYDNEGEKRVDLNAGYS-SEIIK-DE--SIS-FE-------------------------------EIEEK 394 (637)
T ss_pred EEEecCEEeeccccCCCcCEEEEcCCc-eEEEe-cc--CCc-cc-------------------------------ceeec
Confidence 9999999998863 344444432 33332 11 101 11 00011
Q ss_pred ccccccccc----CCceEeEEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCCccCCCCCccccCCCCChhhhccC
Q 015600 157 YLLSLKDIS----EHRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNF 232 (404)
Q Consensus 157 f~~~L~di~----~~~f~Dl~~qVv~~~~~~~~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~ 232 (404)
| ..|+||. .+..+|+++.|+.+. +. ..++ . -||+...- -+..+.| +
T Consensus 395 ~-~~i~dI~~~~~~~~~VdVig~V~~v~-~~--~~i~-~-k~G~~~~~--r~i~l~D-----------------~----- 444 (637)
T PRK12366 395 I-YKIKDILNLEEDDNDITVIARVVEDY-PV--NEFE-R-SDGSKGKV--RNIELAD-----------------G----- 444 (637)
T ss_pred c-ccHHHhhcccCCCcEEEEEEEEEEcc-Cc--eEEE-e-cCCCEeEE--EEEEEEe-----------------C-----
Confidence 3 4455553 578999999999988 42 1221 1 23432211 0110100 0
Q ss_pred CCCceEEEEEecCchhhhhhccCCCCcEEEEeceEEEEeCcEEEEEEecCCceEEcCCCChHHHHHHHHHHHHHhCCCCC
Q 015600 233 FPVGTVLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDNDNVVWDYMRRFRERISGGHGH 312 (404)
Q Consensus 233 pp~G~~l~V~~~~~~~~~~~~~~k~g~wv~l~Nv~~k~~~g~leG~l~~~ski~~l~~~d~~v~~r~r~y~~~~~~~~~~ 312 (404)
-| .+++++|..+|. ..+.+|+.|.++|..++..+|.++..+...+.|.+.|+.. ++. .
T Consensus 445 --TG-~I~vtlWg~~a~---~~~~~G~vi~i~~~~V~~~~g~~~Ls~~~~s~i~~~p~~~-el~-----------~---- 502 (637)
T PRK12366 445 --TG-SIRLTLWDDDAE---IEIKEGDAIKILHPYVKENGDYLDLSIGRYGRIEINPEGE-IIK-----------S---- 502 (637)
T ss_pred --CC-EEEEEEeccccc---cCCCCCCEEEEEeeEEEeCCCeeEEEecCcceEEECCCCc-ccc-----------c----
Confidence 14 789999998775 3578999999999999999998888888888887655322 211 0
Q ss_pred CCCcCCCCCCCCcccccCCCccccHHHHhcCCCCCceEEEEEEEEeecCCCcc----------------ccccC-----C
Q 015600 313 MPIWTDPSSQFLTEVDWVNVASVTLMKIATQLQGNVRCCCIVRVVSIHPFQAE----------------HYSSP-----N 371 (404)
Q Consensus 313 ~~~~~~p~~~~~t~~~~~~~p~ttL~~IL~~~~~~~kyr~~VRVV~~~P~~l~----------------df~~~-----~ 371 (404)
+..+|.+|.... .|.+++.|+.+.+.++- .|.++ .
T Consensus 503 --------------------~~~~I~~i~~~~----~~~v~g~i~~i~~~~~~y~aCp~CnkKv~~~~g~~~C~~c~~~~ 558 (637)
T PRK12366 503 --------------------NRKFIADLEEDD----TVEIRGTVVDIRKQKIILYLCPNCRKRVEEVDGEYICEFCGEVE 558 (637)
T ss_pred --------------------cccCHHHcccCC----eEEEEEEEEEEeCCCEEEecccccCeEeEcCCCcEECCCCCCCC
Confidence 011122222111 02222222222222211 11121 3
Q ss_pred CCcEEEEEEEEeCCCceEEEEEeccccccccc
Q 015600 372 GSSEYTMKLTLEDPTARIHALLCGKEWVRFQL 403 (404)
Q Consensus 372 ~~~~~~f~L~leD~t~~~~~~v~~~da~~f~~ 403 (404)
..|.|++.+.|-|.|+.+.+.++++.|+.+||
T Consensus 559 p~~~~~l~~~i~D~TG~~~~t~f~e~ae~l~G 590 (637)
T PRK12366 559 PNELLMLNFTLDDGTGTINCRFYGKNVEKLLG 590 (637)
T ss_pred CcEEEEEEEEEEcCCCCEEEEEEhHHhHHHhC
Confidence 47889999999999999999999999999986
No 6
>PRK12366 replication factor A; Reviewed
Probab=99.28 E-value=3.3e-09 Score=113.44 Aligned_cols=278 Identities=13% Similarity=0.163 Sum_probs=185.4
Q ss_pred cceeehHhhhhccCC-EEEEEEEEEecCCceec---CC-CceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEE
Q 015600 8 GGIVRIKELAMHVKH-KVNLLGVVLEFSIPRKS---QG-TDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLI 82 (404)
Q Consensus 8 y~y~~i~~~~~~~~~-~vnv~GVV~d~~~P~~t---rG-tD~~~t~~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII 82 (404)
-..++|+++ .++. .+++.|-|+...+|+.- +| .-..+++.|.|+|= .+++.+|.+..+.+|.+ .+|||+
T Consensus 61 ~~~~~I~dl--~p~~~~v~i~arV~~~~~~r~~~~~~G~eGkv~~~~v~DetG---~Ir~t~W~~~~~~~~~l-e~G~v~ 134 (637)
T PRK12366 61 EEDFKISDI--EEGQINVEITGRIIEISNIKTFTRKDGSTGKLANITIADNTG---TIRLTLWNDNAKLLKGL-KEGDVI 134 (637)
T ss_pred cceeEHHHC--cCCCcceEEEEEEEEccCCeEEECCCCCccEEEEEEEEcCCC---EEEEEEEchhhhhhccC-CCCCEE
Confidence 457899999 4555 59999999999988732 35 45689999999775 39999999877778888 899999
Q ss_pred EEeeEEEEEEcCeeEEEeecCceEEEEEeCCCCCCCCCCccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCcccccccc
Q 015600 83 LLKNVMIKKHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSLK 162 (404)
Q Consensus 83 ~l~rvki~~~~g~~~~~~~~~~ss~~vf~~~~~~~~~P~~~s~~~~~~~~~e~~~v~~Lr~w~~~~~~~~~~~~f~~~L~ 162 (404)
.+.++.++.|+|++.+..+.. ++....+.. +....| + . ...+ .|.
T Consensus 135 ~i~~~~v~~~~~~~el~~~~~-t~I~~~~~~-d~~~i~-~---------~---------------------~~~~--~I~ 179 (637)
T PRK12366 135 KIENARSRKWNNDVELNSGSE-TRIDKLEKY-DESRYP-I---------I---------------------KENY--DIP 179 (637)
T ss_pred EEeccEecccCCceEEEcCCc-ceEEEcccc-ccccCC-c---------c---------------------cccc--ccc
Confidence 999999999999998766544 444422210 001111 0 0 0013 578
Q ss_pred cccCCceEeEEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCCccCCCCCccccCCCCChhhhccCCCCceEEEEE
Q 015600 163 DISEHRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRVS 242 (404)
Q Consensus 163 di~~~~f~Dl~~qVv~~~~~~~~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~pp~G~~l~V~ 242 (404)
||+++.++|+++.|+.+. +. ..++ --||++-... +..+.| + -| .+++|
T Consensus 180 el~~g~~v~v~G~V~~~~-~~--~~f~--rkdg~~~~~r--~~~l~D-----------------~-------TG-~irvT 227 (637)
T PRK12366 180 ELEPNLSATIEGEVTKAY-PI--KEFT--RKDGSEGKLK--SFILKD-----------------D-------TG-SIRVT 227 (637)
T ss_pred ccCCCCeEEEEEEEEEcc-Cc--EEEE--EcCCCeeEEE--EEEEEc-----------------C-------CC-cEEEE
Confidence 888999999999999998 42 2222 1255432111 111110 0 15 78999
Q ss_pred ecCchhhhhhccCCCCcEEEEeceEEEEeCcEEEEEEecCCceEEcCCCChHHHHHHHHHHHHHhCCCCCCCCcCCCCCC
Q 015600 243 TDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDNDNVVWDYMRRFRERISGGHGHMPIWTDPSSQ 322 (404)
Q Consensus 243 ~~~~~~~~~~~~~k~g~wv~l~Nv~~k~~~g~leG~l~~~ski~~l~~~d~~v~~r~r~y~~~~~~~~~~~~~~~~p~~~ 322 (404)
+|..+|. ..+.+|+.|++.+....-..|.+|......+-| +..+.
T Consensus 228 lW~~~a~---~~~~~g~vv~i~g~~~~~~~~~~el~~~~~~~i---~~~~~----------------------------- 272 (637)
T PRK12366 228 LWNDLTD---IEVNKGDIVRVKGYVKQGYRTGLEISANNIEIL---EKLEK----------------------------- 272 (637)
T ss_pred EEChhhc---ccCCCCCEEEEEeEEecCcCCceEEEeCCceee---ccccc-----------------------------
Confidence 9998775 358999999998833332445666554222222 11000
Q ss_pred CCcccccCCCccccHHHHhcCCC-CCceEEEEEEEEeecCCCccccccCCCCcEEEEEEEEeCCCceEEEEEeccccccc
Q 015600 323 FLTEVDWVNVASVTLMKIATQLQ-GNVRCCCIVRVVSIHPFQAEHYSSPNGSSEYTMKLTLEDPTARIHALLCGKEWVRF 401 (404)
Q Consensus 323 ~~t~~~~~~~p~ttL~~IL~~~~-~~~kyr~~VRVV~~~P~~l~df~~~~~~~~~~f~L~leD~t~~~~~~v~~~da~~f 401 (404)
.. ...+.++|+++ +|. .+.+..+.+||++..|.+ .|....|. --.|.+.|-|.||++++-++++.|++|
T Consensus 273 ---~~--~~~~~~pI~~L--~~~~~g~~~~I~grV~~~~~~R--~f~~~~g~-gkv~s~~l~D~tG~IR~t~w~~~~d~~ 342 (637)
T PRK12366 273 ---EE--KELEIVNIEEL--TEFEDGEEVDVKGRIIAISDKR--EVERDDRT-AEVQDIELADGTGRVRVSFWGEKAKIL 342 (637)
T ss_pred ---cc--cccCceeHHHC--CcccCCCEEEEEEEEEecCCce--EEEcCCCc-EEEEEEEEEcCCCeEEEEEeCchhhhh
Confidence 00 01234567776 333 456899999999977654 46555565 578999999999999999999988877
Q ss_pred cc
Q 015600 402 QL 403 (404)
Q Consensus 402 ~~ 403 (404)
.+
T Consensus 343 ~~ 344 (637)
T PRK12366 343 EN 344 (637)
T ss_pred cc
Confidence 54
No 7
>TIGR00617 rpa1 replication factor-a protein 1 (rpa1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.27 E-value=2e-09 Score=114.43 Aligned_cols=319 Identities=13% Similarity=0.126 Sum_probs=195.0
Q ss_pred ceeehHhhhhccCCEEEEEEEEEecCCcee---cCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCC-CCCCCCCCEEEE
Q 015600 9 GIVRIKELAMHVKHKVNLLGVVLEFSIPRK---SQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQL-PRVLSPRDLILL 84 (404)
Q Consensus 9 ~y~~i~~~~~~~~~~vnv~GVV~d~~~P~~---trGtD~~~t~~I~D~S~~~~gl~v~iF~~~~~~L-P~v~~~GDII~l 84 (404)
.+++|+++-. ......+-|-|+.....+. .+|.....++.|.|++ ..|.+.+|.+..+.+ |.+ ++|+|+.+
T Consensus 179 ~~~pI~~L~p-y~~~wtIkaRV~~Ks~ir~~~~~~gegkvfsv~L~Deg---g~Irat~f~~~~dkf~~~l-~eG~VY~I 253 (608)
T TIGR00617 179 RVMPIASLSP-YQNKWTIKARVTNKSEIRTWSNARGEGKLFNVELLDES---GEIRATAFNEQADKFYDII-QEGKVYYI 253 (608)
T ss_pred ceEEHHHCCC-CCCceEEEEEEEeccccceecCCCCCceeeEEEEecCC---CeEEEEECchHHHHHhhhc-ccCCEEEE
Confidence 5899999953 2346899999998777654 2455578889999943 349999999755554 666 89999999
Q ss_pred eeEEEEEEcCeeEEEeecC---ceEEEEEeCCCCCCCCCCccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCccccccc
Q 015600 85 KNVMIKKHQAELSAVFYKD---SSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSL 161 (404)
Q Consensus 85 ~rvki~~~~g~~~~~~~~~---~ss~~vf~~~~~~~~~P~~~s~~~~~~~~~e~~~v~~Lr~w~~~~~~~~~~~~f~~~L 161 (404)
.+.+|+..++++..+.+.. +..+.......+..-.|. ..|. | ..|
T Consensus 254 s~~~Vk~an~~y~~~~~~yei~f~~~T~I~~~~d~~~iP~----~~~~---------------------------f-~~i 301 (608)
T TIGR00617 254 SKGSLKPANKQFTNLGNDYEMTLDRDTVIEECEDETAIPK----IQFN---------------------------F-VKI 301 (608)
T ss_pred CceEEEEccccccCCCCCEEEEECCCeEEEECCCcccCCc----cccc---------------------------c-eEH
Confidence 9999998877655433210 011111111111111220 0122 3 444
Q ss_pred ccc---cCCceEeEEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCCccCCCCCccccCCCCChhhhccCCCCceE
Q 015600 162 KDI---SEHRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTV 238 (404)
Q Consensus 162 ~di---~~~~f~Dl~~qVv~~~~~~~~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~pp~G~~ 238 (404)
.|| ..+.++|+++.|..+. +. ..++-+ .||+....- ...+.| --|+.
T Consensus 302 ~dI~~~~~~~~VDVIGvV~~v~-~~--~~i~~k-~~g~~~~kR--~i~L~D------------------------~sg~s 351 (608)
T TIGR00617 302 DDIGGYEGNSLVDVIGIVQSVS-PT--QTITSR-KNNKEFPKR--DITLVD------------------------DSGKS 351 (608)
T ss_pred HHhhhhcCCCCccEEEEEeEec-Cc--eEEEEc-CCCCeeeeE--EEEEEe------------------------CCCCE
Confidence 455 4567999999999987 42 121111 122211110 000000 02668
Q ss_pred EEEEecCchhhhhhccCCCCcEEEEeceEEEEeCcEEEEEEecCCceEEcCCCChHHHHHHHHHHHHHhCCCCCCCCcCC
Q 015600 239 LRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDNDNVVWDYMRRFRERISGGHGHMPIWTD 318 (404)
Q Consensus 239 l~V~~~~~~~~~~~~~~k~g~wv~l~Nv~~k~~~g~leG~l~~~ski~~l~~~d~~v~~r~r~y~~~~~~~~~~~~~~~~ 318 (404)
++|++|..+|.. -....|+.|.|+.++++-.+|. .......|.|. ++++-+++.+.+.-|+..-. .. +..++
T Consensus 352 I~vTLWG~~A~~--~~~~~~~Vva~kg~~V~~f~g~-sLs~~~~S~i~-iNPdipEa~~L~~w~~~~g~-~~---~~~s~ 423 (608)
T TIGR00617 352 VRVTLWGDDATK--FDVSVQPVIAIKGVRVSDFGGK-SLSTGGSSTII-VNPDIPEAEKLKGWYDNEGK-GT---MASSI 423 (608)
T ss_pred EEEEEEhhhhhh--cCCCCCCEEEEEeEEEEecCCc-eEeccCCceEE-ECCCcHHHHHHHHHHHhcCC-Cc---cceee
Confidence 999999998853 3377899999999999988664 33444456774 45567787777666643321 10 00000
Q ss_pred CCCCCCcccccCCCccccHHHHhcCC----CCCceEEEEEEEEeecCCCccccccC------------------------
Q 015600 319 PSSQFLTEVDWVNVASVTLMKIATQL----QGNVRCCCIVRVVSIHPFQAEHYSSP------------------------ 370 (404)
Q Consensus 319 p~~~~~t~~~~~~~p~ttL~~IL~~~----~~~~kyr~~VRVV~~~P~~l~df~~~------------------------ 370 (404)
.. ..............||.||.... +-+..|.|++.|+.+.+.++-=.|+|
T Consensus 424 ~~-~~~~~~~~~~~~~ktI~ei~~~~lg~~~k~~~f~v~atI~~Ik~d~~~Y~ACp~~~CnKKV~~~~~g~~~CekC~~~ 502 (608)
T TIGR00617 424 SD-MMSGRVGGSNAERKTIAEIQAENLGKSDKPDYFSVKATISYLKPDNALYRACPSEDCNKKVVDQGDGTYRCEKCNKN 502 (608)
T ss_pred hh-ccccccCCcccccccHHHHhhhccCCCCCCcEEEEEEEEEEEecCCeEeccCChhhCCCccccCCCCCEECCCCCCC
Confidence 00 00000111234567899998632 34567999999998876533222221
Q ss_pred --CCCcEEEEEEEEeCCCceEEEEEeccccccccc
Q 015600 371 --NGSSEYTMKLTLEDPTARIHALLCGKEWVRFQL 403 (404)
Q Consensus 371 --~~~~~~~f~L~leD~t~~~~~~v~~~da~~f~~ 403 (404)
+-.|.|.+.+.+.|.|+.+.+.++++.|+.+||
T Consensus 503 ~~~~~~RYil~~~i~D~Tg~~~~t~F~~~ae~llG 537 (608)
T TIGR00617 503 FAEFKYRYILQISISDETGQLWVTAFNDQAEQILG 537 (608)
T ss_pred CCCccEEEEEEEEEEeCCCCEEEEEEhHHHHHHcC
Confidence 125778889999999999999999999999986
No 8
>PRK07218 replication factor A; Provisional
Probab=99.08 E-value=3e-07 Score=93.33 Aligned_cols=196 Identities=18% Similarity=0.244 Sum_probs=136.7
Q ss_pred eeehHhhhhccCCEEEEEEEEEecCCce-ecCCC-ceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeE
Q 015600 10 IVRIKELAMHVKHKVNLLGVVLEFSIPR-KSQGT-DYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNV 87 (404)
Q Consensus 10 y~~i~~~~~~~~~~vnv~GVV~d~~~P~-~trGt-D~~~t~~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rv 87 (404)
-+.|+|+.. ....|||.|-|++...+. +..|+ -...++.|-|+|=. +++.++.+. + + ..||+|.+.|+
T Consensus 58 ~~kI~Di~~-~~~~V~v~~kVl~i~~rt~r~dg~~g~v~~~~igDeTG~---Ir~tlW~~~----~-l-~~Gdvv~I~na 127 (423)
T PRK07218 58 SKDIKELST-DDKNVTVTGRVLTIGERSIRYQGDDHVIYEGILADETGT---ISYTAWKDF----G-L-SPGDTVTIGNA 127 (423)
T ss_pred CccHhhCCC-CCceeEEEEEEEEecceeEecCCCceEEEEEEEECCCCe---EEEEEECCC----C-C-CCCCEEEEecc
Confidence 457888843 456799999999996631 22343 57788999998652 999999842 3 5 89999999999
Q ss_pred EEEEEcCeeEEEeecCceEEEEEeCCCCCCCCCCccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCcccccccccccCC
Q 015600 88 MIKKHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSLKDISEH 167 (404)
Q Consensus 88 ki~~~~g~~~~~~~~~~ss~~vf~~~~~~~~~P~~~s~~~~~~~~~e~~~v~~Lr~w~~~~~~~~~~~~f~~~L~di~~~ 167 (404)
.++.|+|++++..+.. +....-+.. ..| . +. . . .. ..|.|++++
T Consensus 128 ~vre~~g~~el~ig~~-t~I~~~de~----~~~-----~-~~-----------~-----------~--~~-~kI~DL~~g 171 (423)
T PRK07218 128 GVREWDGRPELNIGES-TTVSLLDDS----SLP-----P-YS-----------I-----------G--GD-KKLIDLGPG 171 (423)
T ss_pred EeeccCCceEEeccCc-ceEEEcCcc----ccc-----C-cc-----------c-----------c--Cc-cchhhccCC
Confidence 9999999999887644 555432221 111 0 10 0 0 02 568899865
Q ss_pred -ceEeEEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCCccCCCCCccccCCCCChhhhccCCCCce-EEEEEecC
Q 015600 168 -RYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGT-VLRVSTDR 245 (404)
Q Consensus 168 -~f~Dl~~qVv~~~~~~~~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~pp~G~-~l~V~~~~ 245 (404)
..+++.++|+.++ + + .+..-||+. .. .+..+.| .+ .+++++|+
T Consensus 172 ~~~V~v~g~Vl~~~-~----r-~f~~~dg~~--~v-~~giigD--------------------------eTG~Ir~tlW~ 216 (423)
T PRK07218 172 DRGVNVEARVLELE-H----R-EIDGRDGET--TI-LSGVLAD--------------------------ETGRLPFTDWD 216 (423)
T ss_pred CCceEEEEEEEEec-c----e-eEEcCCCCe--EE-EEEEEEC--------------------------CCceEEEEEec
Confidence 5589999999885 3 2 233445431 11 1111111 12 78999999
Q ss_pred chhhhhhccCCCCcEEEEeceEEEEeCcEEEEEEecCCceEEcCCC
Q 015600 246 SYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDN 291 (404)
Q Consensus 246 ~~~~~~~~~~k~g~wv~l~Nv~~k~~~g~leG~l~~~ski~~l~~~ 291 (404)
+++ .+.+|++|++.|...+..+|.++-.+...+.|..++.+
T Consensus 217 ~~~-----~l~~Gd~v~I~na~v~e~~G~~elnv~~~t~I~~~d~~ 257 (423)
T PRK07218 217 PLP-----EIEIGASIRIEDAYVREFRGVPSVNVSEFTTVEALDRE 257 (423)
T ss_pred ccc-----cCCCCCEEEEeeeEEeccCCeEEEEECCceEEEECCCC
Confidence 754 37899999999999999999999999999999887753
No 9
>PRK14699 replication factor A; Provisional
Probab=99.03 E-value=3.2e-07 Score=94.88 Aligned_cols=272 Identities=19% Similarity=0.198 Sum_probs=183.8
Q ss_pred eehHhhhhccCCEEEEEEEEEecCCcee---cCCCc-eEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEee
Q 015600 11 VRIKELAMHVKHKVNLLGVVLEFSIPRK---SQGTD-YVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKN 86 (404)
Q Consensus 11 ~~i~~~~~~~~~~vnv~GVV~d~~~P~~---trGtD-~~~t~~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~r 86 (404)
..|+++.. ...-|||.|-|+...+|+. ..|+. -..++.|-|+|=. +++.++.+..+.+|.+ ..||+|++.+
T Consensus 167 ~~I~dL~~-~~~~V~i~gkVl~~~~~R~f~~~dG~~g~v~~~~igDeTG~---ir~tlW~~~a~~~~~l-~~Gd~v~I~~ 241 (484)
T PRK14699 167 QKIKDIKD-GMGDLNLTGKVLEISEIRTFQRKDGTSGKVGNLLLGDETGT---LRVTLWDDKTDFLNQI-EYGDTVELIN 241 (484)
T ss_pred cchhhcCC-CCCceEEEEEEEeccCceEEecCCCCceEEEEEEEEcCCce---EEEEEECccccccccc-CCCCEEEEec
Confidence 46778742 3445999999999999863 23543 5778899999763 9999999877777888 8999999998
Q ss_pred EEEE--EEcCeeEEEeecCceEEEEEeCCCCCCCCCCccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCcccccccccc
Q 015600 87 VMIK--KHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSLKDI 164 (404)
Q Consensus 87 vki~--~~~g~~~~~~~~~~ss~~vf~~~~~~~~~P~~~s~~~~~~~~~e~~~v~~Lr~w~~~~~~~~~~~~f~~~L~di 164 (404)
+.++ .|+|.+.+..+.. +... ......+ +.. .+ ..|.||
T Consensus 242 a~vr~~~~~~~~el~~~~~-s~i~--~~~~~~e----------~~~-------------------------~~-~~I~~L 282 (484)
T PRK14699 242 AYARENAFTQKVELQVGNR-SIIR--KSEKKVE----------YEE-------------------------EF-TPIEDI 282 (484)
T ss_pred ceEeecccCCceEEEecCc-eEee--ccccccc----------ccc-------------------------cc-cCHHHc
Confidence 8765 5778888877643 3222 1100000 000 13 457777
Q ss_pred cC-CceEeEEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCCccCCCCCccccCCCCChhhhccCCCCceEEEEEe
Q 015600 165 SE-HRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRVST 243 (404)
Q Consensus 165 ~~-~~f~Dl~~qVv~~~~~~~~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~pp~G~~l~V~~ 243 (404)
++ ++.+++.++|+.+. +. ..+. --||+.-.. ++..+.| + -| .+|+++
T Consensus 283 ~~~~~~v~I~grV~~~~-~~--r~~~--~~~Gseg~v--~~~~l~D-----------------e-------TG-~Ir~T~ 330 (484)
T PRK14699 283 KADMNNINISGRVLDIS-EV--RTFE--KKDGSPGRV--GNLLLGD-----------------S-------TG-KIRLTL 330 (484)
T ss_pred CCCCceeEEEEEEEEcC-CC--eEEE--cCCCCeeEE--EEEEEEC-----------------C-------CC-eEEEEE
Confidence 75 48999999999887 31 1221 233321111 1111111 0 14 589999
Q ss_pred cCchhhhhhccCCCCcEEEEeceEEEEeC--cEEEEEEecCCceEEcCCCChHHHHHHHHHHHHHhCCCCCCCCcCCCCC
Q 015600 244 DRSYENFGRYFTATGKWVRIRNMSCQVSS--GMWHGLLQSSSKIRLFSDNDNVVWDYMRRFRERISGGHGHMPIWTDPSS 321 (404)
Q Consensus 244 ~~~~~~~~~~~~k~g~wv~l~Nv~~k~~~--g~leG~l~~~ski~~l~~~d~~v~~r~r~y~~~~~~~~~~~~~~~~p~~ 321 (404)
|...+++ ...+++|+.+++.|...+.+. |.+|..+...+.|...++.. + |
T Consensus 331 W~~~a~~-~~~i~~Gd~v~i~~~y~~~~~~~~~~eL~~~~~t~I~~~~~~~-e-------~------------------- 382 (484)
T PRK14699 331 WDEKTNF-LDEIDFDETVEVLNAYSRENTFSQQVELNLGARGIIQKSEKKV-E-------Y------------------- 382 (484)
T ss_pred eCccccc-ccccCCCceEEEEeEEEEeccCCccEEEEecCceeEeecCCcc-e-------e-------------------
Confidence 9998864 567999999999999988753 67888887777554433211 0 0
Q ss_pred CCCcccccCCCccccHHHHhcCCCCCceEEEEEEEEeecCCCccccccCCCCcEEEEEEEEeCCCceEEEEEeccccccc
Q 015600 322 QFLTEVDWVNVASVTLMKIATQLQGNVRCCCIVRVVSIHPFQAEHYSSPNGSSEYTMKLTLEDPTARIHALLCGKEWVRF 401 (404)
Q Consensus 322 ~~~t~~~~~~~p~ttL~~IL~~~~~~~kyr~~VRVV~~~P~~l~df~~~~~~~~~~f~L~leD~t~~~~~~v~~~da~~f 401 (404)
..++++|.+|- ....+-...+|++..|.+ .|.+-.|.=-+.--|+|.|.|+.+.+-++|+.|+.|
T Consensus 383 ---------~~~~~~I~die----~~~~vdV~G~V~~v~~~~--~~~~~~g~~~~vr~i~l~D~TG~Ir~tlWg~~A~~~ 447 (484)
T PRK14699 383 ---------REKFTDIADII----PGESYSVQGKVSEIGELR--EFEREDGTENVVANLQLKDETGSIRLTLWGEQAYVI 447 (484)
T ss_pred ---------eeccccHHHcc----CCCeeEEEEEEEEcCCcc--eEEecCCCEEEEEEEEEEcCCCeEEEEEcchhhhhc
Confidence 12466688883 233578889999998876 666555544577799999999999999999999854
No 10
>PRK15491 replication factor A; Provisional
Probab=98.98 E-value=5.9e-07 Score=90.29 Aligned_cols=272 Identities=15% Similarity=0.183 Sum_probs=178.6
Q ss_pred ceeehHhhhhccCCEEEEEEEEEecCCcee---cCC-CceEEEEEEEeCCCCCCCeEEEEecCCCCCC--CCCCCCCCEE
Q 015600 9 GIVRIKELAMHVKHKVNLLGVVLEFSIPRK---SQG-TDYVCVLKIVDDSQQSPELLVNIFTSSIDQL--PRVLSPRDLI 82 (404)
Q Consensus 9 ~y~~i~~~~~~~~~~vnv~GVV~d~~~P~~---trG-tD~~~t~~I~D~S~~~~gl~v~iF~~~~~~L--P~v~~~GDII 82 (404)
.-++|+++.. ....|++.|-|+....|+. .+| .-...++.|.|+|=. +++.+|.+..+.+ |.+ .+||++
T Consensus 56 ~~~kI~dL~~-~~~~v~i~arVl~~~~~R~f~r~dGs~g~v~~~~v~DeTG~---ir~tlW~~~a~~~~~~~l-e~G~v~ 130 (374)
T PRK15491 56 DTTKIADINE-SSSNVNFTAKVVSIFEPKEFNRNDGTTGRVGNIIVADETGS---IRLTLWDDLADLIKTGDI-EVGKSL 130 (374)
T ss_pred ccccHHHCCC-CCCceEEEEEEeeccCCeeeecCCCCceEEEEEEEEcCCCe---EEEEEECchhhhhccCCc-CCCCEE
Confidence 3568999942 3467999999999988864 246 456788999997652 9999999766665 667 899999
Q ss_pred EEeeEEEEEEcCeeEEEeecCceEEEEEeCCCCCCCCCCccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCcccccccc
Q 015600 83 LLKNVMIKKHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSLK 162 (404)
Q Consensus 83 ~l~rvki~~~~g~~~~~~~~~~ss~~vf~~~~~~~~~P~~~s~~~~~~~~~e~~~v~~Lr~w~~~~~~~~~~~~f~~~L~ 162 (404)
.++..--..|+| +....+.. +... +. +++.+ . ...| ..|+
T Consensus 131 ~I~~~~~~~y~g-~Ei~i~~~-~~i~-----------~~----------~~~~~----~------------~~~~-~~I~ 170 (374)
T PRK15491 131 NISGYAKEGYSG-IEVNIGRY-GGIS-----------ES----------DENVK----A------------SINS-QKIS 170 (374)
T ss_pred EEeeeeccCccc-EEEEeCCC-ceee-----------ec----------ccccc----c------------ccCc-ccHH
Confidence 999875556766 54444432 2211 10 00000 0 0014 5678
Q ss_pred cccCC-ceEeEEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCCccCCCCCccccCCCCChhhhccCCCCceEEEE
Q 015600 163 DISEH-RYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRV 241 (404)
Q Consensus 163 di~~~-~f~Dl~~qVv~~~~~~~~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~pp~G~~l~V 241 (404)
||.++ ..+|+.++|+.+. +. ..+. --||+....+ +..+.| + -| .+++
T Consensus 171 dl~~~~~~V~I~g~V~~~~-~~--r~~~--~~~G~~~~v~--~~~l~D-----------------e-------tG-~Ir~ 218 (374)
T PRK15491 171 DIKDGDSDINIVGKVLDIS-DV--RTFQ--KKDGSQGRVR--NITIGD-----------------E-------TG-KIRV 218 (374)
T ss_pred HcCCCCccEEEEEEEEEcc-Cc--eEEE--ecCCCeEEEE--EEEEEC-----------------C-------CC-eEEE
Confidence 88654 4699999999887 31 2222 2244322111 111100 0 15 4899
Q ss_pred EecCchhhhhhccCCCCcEEEEeceEEEE--eCcEEEEEEecCCceEEcCCCChHHHHHHHHHHHHHhCCCCCCCCcCCC
Q 015600 242 STDRSYENFGRYFTATGKWVRIRNMSCQV--SSGMWHGLLQSSSKIRLFSDNDNVVWDYMRRFRERISGGHGHMPIWTDP 319 (404)
Q Consensus 242 ~~~~~~~~~~~~~~k~g~wv~l~Nv~~k~--~~g~leG~l~~~ski~~l~~~d~~v~~r~r~y~~~~~~~~~~~~~~~~p 319 (404)
++|..++.. ...+.+|+-|++.|-.++. ..|.+|-.+..++.|...++ +.
T Consensus 219 t~W~~~a~~-~~~l~~Gd~V~i~~~~~r~~~~~g~~El~~~~~s~I~~~~~-~~-------------------------- 270 (374)
T PRK15491 219 TLWDGKTDL-ADKLENGDSVEIINGYARTNNYSQEVEIQIGNHGSLRKTDR-NV-------------------------- 270 (374)
T ss_pred EEecchhcc-cccCCCCCEEEEEeceEEEeccCCCEEEEeCCCceEEECCc-cc--------------------------
Confidence 999998875 3779999999999987776 35788888888888765432 11
Q ss_pred CCCCCcccccCCCccccHHHHhcCCCCCceEEEEEEEEeecCCCccccccCCCCcEEEEEEEEeCCCceEEEEEeccccc
Q 015600 320 SSQFLTEVDWVNVASVTLMKIATQLQGNVRCCCIVRVVSIHPFQAEHYSSPNGSSEYTMKLTLEDPTARIHALLCGKEWV 399 (404)
Q Consensus 320 ~~~~~t~~~~~~~p~ttL~~IL~~~~~~~kyr~~VRVV~~~P~~l~df~~~~~~~~~~f~L~leD~t~~~~~~v~~~da~ 399 (404)
++ ..++++|.||-.. ..+-...+|....|. ..|.+..|.=...=-|+|.|.|+++++-++|++|+
T Consensus 271 --------e~-~~~f~~I~dl~~~----~~~dv~G~V~~v~~~--~~~~~~~G~~~~~r~i~l~D~Tg~Ir~tlWg~~a~ 335 (374)
T PRK15491 271 --------EY-EEDFTPIADIIPG----QPYSIKGAVSGLGDL--KEFTKSDGSENKVSNIYVSDDTGRIRIALWGEKAE 335 (374)
T ss_pred --------cc-CCCccCHHHcCCC----CceeEEEEEEEcCCc--EEEEccCCCEeEEEeEEEEeCCCcEEEEEcccccc
Confidence 00 0135567777532 236777888887664 34545556445666889999999999999999998
Q ss_pred c
Q 015600 400 R 400 (404)
Q Consensus 400 ~ 400 (404)
.
T Consensus 336 ~ 336 (374)
T PRK15491 336 L 336 (374)
T ss_pred c
Confidence 5
No 11
>PRK07211 replication factor A; Reviewed
Probab=98.97 E-value=4.7e-08 Score=100.20 Aligned_cols=204 Identities=16% Similarity=0.200 Sum_probs=145.7
Q ss_pred cceeehHhhhhccCCEEEEEEEEEecCCcee---cCC-CceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEE
Q 015600 8 GGIVRIKELAMHVKHKVNLLGVVLEFSIPRK---SQG-TDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLIL 83 (404)
Q Consensus 8 y~y~~i~~~~~~~~~~vnv~GVV~d~~~P~~---trG-tD~~~t~~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~ 83 (404)
..+.+|+++.. ....++|+|+|+...+++. .+| .-.+.++.|.|+|- . |++++|.+..+.++.+ ..||||.
T Consensus 159 ~~~~~I~dL~~-~~~~v~I~grV~~v~~iRtf~r~dGseGkv~sv~L~DeTG-~--IR~TlW~d~Ad~~~~l-e~G~Vv~ 233 (485)
T PRK07211 159 GDTYTVEDLSL-GLSDVTLVGVVLDTDSVRTFDRDDGSEGRVSNLTVGDETG-R--VRVTLWDDRADLAEEL-DAGESVE 233 (485)
T ss_pred cCCccHHHcCC-CCCceEEEEEEEEcCCCeEEECCCCCeeEEEEEEEEcCCC-e--EEEEEechhhhhhccC-CCCCEEE
Confidence 46789999942 4566999999999998763 235 34678899999876 2 9999999888888877 8999999
Q ss_pred EeeEEEEEEcCeeEEEeecCceEEEEEeCCCCCCCCCCccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCccccccccc
Q 015600 84 LKNVMIKKHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSLKD 163 (404)
Q Consensus 84 l~rvki~~~~g~~~~~~~~~~ss~~vf~~~~~~~~~P~~~s~~~~~~~~~e~~~v~~Lr~w~~~~~~~~~~~~f~~~L~d 163 (404)
+.+++++.++|.+.+..+.. +...-.+. .....| .+ ..|.+
T Consensus 234 I~~a~Vre~~g~~ELsl~~~-s~I~~~~d--ev~~vp-----------------------------------~~-~~I~d 274 (485)
T PRK07211 234 IVDGYVRERDGSLELHVGDR-GAVEEVDE--DVEYVP-----------------------------------DT-TPIES 274 (485)
T ss_pred EEeeEEEecCCcEEEEECCC-ceEEECCc--cccccc-----------------------------------cc-ccHhh
Confidence 99999999999988877543 33331110 001111 12 46788
Q ss_pred ccCCceEeEEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCCccCCCCCccccCCCCChhhhccCCCCceEEEEEe
Q 015600 164 ISEHRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRVST 243 (404)
Q Consensus 164 i~~~~f~Dl~~qVv~~~~~~~~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~pp~G~~l~V~~ 243 (404)
+.++..+|+++.|+.+. + ..++-=-||+...-- +..+.| + -| .+++++
T Consensus 275 l~~g~~vdV~GvV~~v~-~----~rtf~r~dG~~~~vr--~l~l~D-----------------~-------TG-~IrvTL 322 (485)
T PRK07211 275 LEIDETVDIAGVVRSAD-P----KRTFDRDDGSEGQVR--NVRIQD-----------------D-------TG-DIRVAL 322 (485)
T ss_pred cCCCCceeEEEEEEEcc-C----cEEEEcCCCCEeEEE--EEEEEc-----------------C-------CC-cEEEEE
Confidence 89999999999999887 3 222222244422211 110100 0 15 789999
Q ss_pred cCchhhhhhccCCCCcEEEEeceEEEEe-CcEEEEEEecCCceEEcCC
Q 015600 244 DRSYENFGRYFTATGKWVRIRNMSCQVS-SGMWHGLLQSSSKIRLFSD 290 (404)
Q Consensus 244 ~~~~~~~~~~~~k~g~wv~l~Nv~~k~~-~g~leG~l~~~ski~~l~~ 290 (404)
|.+++. ..+.+|+.|+|+|++++-. .|-+|..+...+.|.+|+.
T Consensus 323 Wg~~A~---~~i~~GdvV~Ikg~~V~dg~~ggleLS~g~~s~i~~~~~ 367 (485)
T PRK07211 323 WGEKAD---LDIGPGDEVVAADVEIQDGWQDDLEASAGWQSTVVVLDD 367 (485)
T ss_pred eCcccc---CCCCCCCEEEEEccEEEecCCCCEEEEecCCceEEEccc
Confidence 999885 3699999999999999994 4778888888889988876
No 12
>PRK06386 replication factor A; Reviewed
Probab=98.96 E-value=2.6e-06 Score=84.50 Aligned_cols=277 Identities=16% Similarity=0.136 Sum_probs=164.6
Q ss_pred eehHhhhhccCCEEEEEEEEEecCCc-eecC-CCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEE
Q 015600 11 VRIKELAMHVKHKVNLLGVVLEFSIP-RKSQ-GTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVM 88 (404)
Q Consensus 11 ~~i~~~~~~~~~~vnv~GVV~d~~~P-~~tr-GtD~~~t~~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvk 88 (404)
+.|+|+.. .+..|||.|-|++.... .+.+ |.--..+-.|-|+|=. +++.+..+ .|.+ ..||+|+|.|++
T Consensus 3 ~kI~DI~~-~~~~V~v~akVl~~~~r~i~~~~g~~~~~~gllgDeTG~---I~fT~W~~----~~~l-~~Gd~v~i~na~ 73 (358)
T PRK06386 3 SKISDINA-ARQNVDLKVKVLSLNKRTIKNDRGETIYYYGIIGDETGT---VPFTAWEF----PDAV-KSGDVIEIKYCY 73 (358)
T ss_pred cchhhcCC-CCCcEEEEEEEEEccceEEecCCCCeEEEEEEEECCcce---EEEEecCC----cccC-CCCCEEEEEeEE
Confidence 46788842 45669999999999732 1223 4333444457777542 88888763 4667 789999999999
Q ss_pred EEEEcCeeEEEeecCceEEEEEeCCCCCCCCCCccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCcccccccccccCC-
Q 015600 89 IKKHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSLKDISEH- 167 (404)
Q Consensus 89 i~~~~g~~~~~~~~~~ss~~vf~~~~~~~~~P~~~s~~~~~~~~~e~~~v~~Lr~w~~~~~~~~~~~~f~~~L~di~~~- 167 (404)
++.|+|++++..+.. +... -.. +... + ..+. . +. ..|+||+++
T Consensus 74 v~~~~G~~~Lnv~~~-t~v~-~~~--d~~i-e---------v~~~-------------------~--~~-~KI~DL~~g~ 117 (358)
T PRK06386 74 SKEYNGKIRIYFDSR-SEVM-LKP--DENI-E---------VKRT-------------------Y--KL-VKIRDLSLVT 117 (358)
T ss_pred EeeECCEEEEEEcCc-eEEE-ecC--cccc-c---------cccc-------------------c--Cc-cEeEeccCCC
Confidence 999999999777643 4432 111 1111 0 0000 0 13 679999865
Q ss_pred ceEeEEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCCccCCCCCccccCCCCChhhhccCCCCce-EEEEEecCc
Q 015600 168 RYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGT-VLRVSTDRS 246 (404)
Q Consensus 168 ~f~Dl~~qVv~~~~~~~~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~pp~G~-~l~V~~~~~ 246 (404)
.+++++++|+.++ + . ..- .||+...- ....+.| .+ .+++++|..
T Consensus 118 ~~v~V~akVle~~-e---~--e~~-~~g~~~~v--~sg~lgD--------------------------eTGrIr~TlW~~ 162 (358)
T PRK06386 118 PYVSVIGKITGIT-K---K--EYD-SDGTSKIV--YQGYIED--------------------------DTARVRISSFGK 162 (358)
T ss_pred CceEEEEEEEEcc-C---c--eEe-cCCCccEE--EEEEEEc--------------------------CCCeEEEEEccc
Confidence 6679999999876 3 1 222 55541111 0110100 12 789999985
Q ss_pred hhhhhhccCCCCcEEEEeceEEEEeCcEEEEEEecCCceEEcCCCChHHHHHHHHHHHHHhCCCCCCCCcCCCCCCCCcc
Q 015600 247 YENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDNDNVVWDYMRRFRERISGGHGHMPIWTDPSSQFLTE 326 (404)
Q Consensus 247 ~~~~~~~~~k~g~wv~l~Nv~~k~~~g~leG~l~~~ski~~l~~~d~~v~~r~r~y~~~~~~~~~~~~~~~~p~~~~~t~ 326 (404)
.++.|+.|+|.|...+...|.++-.+...+.|..++.+-. +..+ ...+..... ....++
T Consensus 163 -------~l~eGd~v~i~na~v~e~~G~~el~v~~~t~I~~~~~~ie-v~~~----~~~I~di~~---------~~g~v~ 221 (358)
T PRK06386 163 -------PLEDNRFVRIENARVSQYNGYIEISVGNKSVIKEVESDIN-LESR----NIFIFEIKS---------PVGGIT 221 (358)
T ss_pred -------cccCCCEEEEeeeEEEccCCeEEEEeCCeEEEEECCCCcc-cCcc----ccchhhhhc---------cCCeEE
Confidence 3789999999999999999999999988888887764321 1111 000100000 000000
Q ss_pred cccCCCccccHHHHhc----CCCCCceEEEEEEEEeecCCCccccccCC----CCcEEEEEEEEeCCCceEEEEEecccc
Q 015600 327 VDWVNVASVTLMKIAT----QLQGNVRCCCIVRVVSIHPFQAEHYSSPN----GSSEYTMKLTLEDPTARIHALLCGKEW 398 (404)
Q Consensus 327 ~~~~~~p~ttL~~IL~----~~~~~~kyr~~VRVV~~~P~~l~df~~~~----~~~~~~f~L~leD~t~~~~~~v~~~da 398 (404)
.. =+|-+|-. -..+|. +=|+++- -.|.-+ +.+--|.++.|.|.|+.+.++++++.+
T Consensus 222 i~------G~iv~i~~gsgli~rCP~----C~R~l~~------g~C~~HG~v~~~~dlr~k~vLDDGtg~~~~~l~~e~~ 285 (358)
T PRK06386 222 IM------GFIVSVGQGSRIFTKCSV----CNKIIED------GVCKDHPDAPVYLDIFGYFTISDGTGFVTCYANKDSF 285 (358)
T ss_pred EE------EEEEEEcCCcEeEecCcC----CCeEccC------CcCCCCCCCCCeeEEEEEEEEECCCCeEEEEEChHHh
Confidence 00 00111110 011222 2244441 355543 344457778999999999999999999
Q ss_pred cccccC
Q 015600 399 VRFQLG 404 (404)
Q Consensus 399 ~~f~~g 404 (404)
+.+.|+
T Consensus 286 e~l~G~ 291 (358)
T PRK06386 286 LPYINI 291 (358)
T ss_pred HHHhCC
Confidence 998763
No 13
>PRK15491 replication factor A; Provisional
Probab=98.82 E-value=4e-07 Score=91.46 Aligned_cols=204 Identities=15% Similarity=0.162 Sum_probs=141.0
Q ss_pred CCcceeehHhhhhccCCEEEEEEEEEecCCceec---CCC-ceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCE
Q 015600 6 NQGGIVRIKELAMHVKHKVNLLGVVLEFSIPRKS---QGT-DYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDL 81 (404)
Q Consensus 6 ~~y~y~~i~~~~~~~~~~vnv~GVV~d~~~P~~t---rGt-D~~~t~~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDI 81 (404)
.+|.+++|+++.. ....|+|.|+|+...+++.= +|+ -...++.|.|+|- . +++++|.+..+.++.+ .+||+
T Consensus 162 ~~~~~~~I~dl~~-~~~~V~I~g~V~~~~~~r~~~~~~G~~~~v~~~~l~DetG-~--Ir~t~W~~~a~~~~~l-~~Gd~ 236 (374)
T PRK15491 162 ASINSQKISDIKD-GDSDINIVGKVLDISDVRTFQKKDGSQGRVRNITIGDETG-K--IRVTLWDGKTDLADKL-ENGDS 236 (374)
T ss_pred cccCcccHHHcCC-CCccEEEEEEEEEccCceEEEecCCCeEEEEEEEEECCCC-e--EEEEEecchhcccccC-CCCCE
Confidence 3566789999943 34459999999999987532 355 4788899999865 2 9999999877777777 89999
Q ss_pred EEEeeEEEE--EEcCeeEEEeecCceEEEEEeCCCCCCCCCCccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCccccc
Q 015600 82 ILLKNVMIK--KHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLL 159 (404)
Q Consensus 82 I~l~rvki~--~~~g~~~~~~~~~~ss~~vf~~~~~~~~~P~~~s~~~~~~~~~e~~~v~~Lr~w~~~~~~~~~~~~f~~ 159 (404)
|.+.+..++ .|+|++.+..+.. +.... ..... + +. ..| .
T Consensus 237 V~i~~~~~r~~~~~g~~El~~~~~-s~I~~--~~~~~---e-------~~-------------------------~~f-~ 277 (374)
T PRK15491 237 VEIINGYARTNNYSQEVEIQIGNH-GSLRK--TDRNV---E-------YE-------------------------EDF-T 277 (374)
T ss_pred EEEEeceEEEeccCCCEEEEeCCC-ceEEE--CCccc---c-------cC-------------------------CCc-c
Confidence 999997655 5678888887644 44331 11000 0 10 025 6
Q ss_pred ccccccCCceEeEEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCCccCCCCCccccCCCCChhhhccCCCCceEE
Q 015600 160 SLKDISEHRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVL 239 (404)
Q Consensus 160 ~L~di~~~~f~Dl~~qVv~~~~~~~~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~pp~G~~l 239 (404)
.|.||+++..+|+++.|..+. + .-++--.||+....- +..+.| + -|+ +
T Consensus 278 ~I~dl~~~~~~dv~G~V~~v~-~----~~~~~~~~G~~~~~r--~i~l~D-----------------~-------Tg~-I 325 (374)
T PRK15491 278 PIADIIPGQPYSIKGAVSGLG-D----LKEFTKSDGSENKVS--NIYVSD-----------------D-------TGR-I 325 (374)
T ss_pred CHHHcCCCCceeEEEEEEEcC-C----cEEEEccCCCEeEEE--eEEEEe-----------------C-------CCc-E
Confidence 788898899999999999886 3 222222455422221 100110 0 154 8
Q ss_pred EEEecCchhhhhhccCCCCcEEEEeceEEEE-eCcEEEEEEecCCceE
Q 015600 240 RVSTDRSYENFGRYFTATGKWVRIRNMSCQV-SSGMWHGLLQSSSKIR 286 (404)
Q Consensus 240 ~V~~~~~~~~~~~~~~k~g~wv~l~Nv~~k~-~~g~leG~l~~~ski~ 286 (404)
++++|..+|.. ...+-+|+.|++.+..+|. ..|.+|......|.|.
T Consensus 326 r~tlWg~~a~~-~~~~~~g~~i~i~~~~~k~g~~~~~e~s~g~~s~~~ 372 (374)
T PRK15491 326 RIALWGEKAEL-VDKLDIDTPIKIIDAFSKSGYNEDVELSAGNRSRVV 372 (374)
T ss_pred EEEEccccccc-ccccCCCCeEEEEEEEEeecCCCcEEEEeCCcceEE
Confidence 99999998874 4557789999999999999 4589999888877774
No 14
>PRK14699 replication factor A; Provisional
Probab=98.66 E-value=2.4e-06 Score=88.37 Aligned_cols=203 Identities=13% Similarity=0.152 Sum_probs=141.8
Q ss_pred ceeehHhhhhccCCEEEEEEEEEecCCcee---cCC-CceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEE
Q 015600 9 GIVRIKELAMHVKHKVNLLGVVLEFSIPRK---SQG-TDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILL 84 (404)
Q Consensus 9 ~y~~i~~~~~~~~~~vnv~GVV~d~~~P~~---trG-tD~~~t~~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l 84 (404)
.+++|.++.. .+..+++.|.|++..+|+. .+| ......+.|.|+|=. +++.+|.+..+.++.+ ..||+|.+
T Consensus 275 ~~~~I~~L~~-~~~~v~I~grV~~~~~~r~~~~~~Gseg~v~~~~l~DeTG~---Ir~T~W~~~a~~~~~i-~~Gd~v~i 349 (484)
T PRK14699 275 EFTPIEDIKA-DMNNINISGRVLDISEVRTFEKKDGSPGRVGNLLLGDSTGK---IRLTLWDEKTNFLDEI-DFDETVEV 349 (484)
T ss_pred cccCHHHcCC-CCceeEEEEEEEEcCCCeEEEcCCCCeeEEEEEEEECCCCe---EEEEEeCccccccccc-CCCceEEE
Confidence 5678999842 4578999999999998753 246 467788999999762 9999999877777777 88999999
Q ss_pred eeEEEEEE--cCeeEEEeecCceEEEEEeCCCCCCCCCCccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCcccccccc
Q 015600 85 KNVMIKKH--QAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSLK 162 (404)
Q Consensus 85 ~rvki~~~--~g~~~~~~~~~~ss~~vf~~~~~~~~~P~~~s~~~~~~~~~e~~~v~~Lr~w~~~~~~~~~~~~f~~~L~ 162 (404)
.++.++.. ++++.+..... +.. ....+ +.++ ..+| ..|.
T Consensus 350 ~~~y~~~~~~~~~~eL~~~~~-t~I---~~~~~------------------~~e~----------------~~~~-~~I~ 390 (484)
T PRK14699 350 LNAYSRENTFSQQVELNLGAR-GII---QKSEK------------------KVEY----------------REKF-TDIA 390 (484)
T ss_pred EeEEEEeccCCccEEEEecCc-eeE---eecCC------------------ccee----------------eecc-ccHH
Confidence 99998844 45677777643 321 11100 0000 0126 7899
Q ss_pred cccCCceEeEEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCCccCCCCCccccCCCCChhhhccCCCCceEEEEE
Q 015600 163 DISEHRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRVS 242 (404)
Q Consensus 163 di~~~~f~Dl~~qVv~~~~~~~~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~pp~G~~l~V~ 242 (404)
||++++.+|+++.|..+. +. ..+. --||+.-.- -+..+.| + -| .++++
T Consensus 391 die~~~~vdV~G~V~~v~-~~--~~~~--~~~g~~~~v--r~i~l~D-----------------~-------TG-~Ir~t 438 (484)
T PRK14699 391 DIIPGESYSVQGKVSEIG-EL--REFE--REDGTENVV--ANLQLKD-----------------E-------TG-SIRLT 438 (484)
T ss_pred HccCCCeeEEEEEEEEcC-Cc--ceEE--ecCCCEEEE--EEEEEEc-----------------C-------CC-eEEEE
Confidence 999999999999999887 42 1221 134421111 0111110 0 14 88999
Q ss_pred ecCchhhhhhccCCCCcEEEEeceEEEE-eCcEEEEEEecCCceEEc
Q 015600 243 TDRSYENFGRYFTATGKWVRIRNMSCQV-SSGMWHGLLQSSSKIRLF 288 (404)
Q Consensus 243 ~~~~~~~~~~~~~k~g~wv~l~Nv~~k~-~~g~leG~l~~~ski~~l 288 (404)
+|...|.. .+.+.+|+-|.+.|..++. .+|.+|..+...|.|.+|
T Consensus 439 lWg~~A~~-~~~~~~~~~v~~~~~~~~~g~~~~~e~s~g~~s~~~~~ 484 (484)
T PRK14699 439 LWGEQAYV-IEDLDIDSEIQIIDAYARYGLNEEIELSVGNRSRVIIL 484 (484)
T ss_pred Ecchhhhh-ccccCCCCeEEEechhhhhcccccEEEEecCceEEEeC
Confidence 99987752 4689999999999999999 478999998888887654
No 15
>PRK07211 replication factor A; Reviewed
Probab=98.60 E-value=5.7e-05 Score=77.81 Aligned_cols=269 Identities=15% Similarity=0.158 Sum_probs=170.9
Q ss_pred eeehHhhhhccC-CEEEEEEEEEecCCcee-c-CC---CceEEEEEEEeCCCCCCCeEEEEecCCCC-CCCCCCCCCCEE
Q 015600 10 IVRIKELAMHVK-HKVNLLGVVLEFSIPRK-S-QG---TDYVCVLKIVDDSQQSPELLVNIFTSSID-QLPRVLSPRDLI 82 (404)
Q Consensus 10 y~~i~~~~~~~~-~~vnv~GVV~d~~~P~~-t-rG---tD~~~t~~I~D~S~~~~gl~v~iF~~~~~-~LP~v~~~GDII 82 (404)
..+|++| .++ ..||+.|-|+..+.|+. + +| .--.+++.|.|+|= .|++.+|....+ ..|.+ ++|||+
T Consensus 53 ~~~I~dL--~pg~~~vtI~aRV~~~~~~Rt~~~~~~~~eGkv~~v~l~DeTG---~Ir~TlW~d~ad~~~~~L-e~GdV~ 126 (485)
T PRK07211 53 VNGIADI--EPGMDEVKFLAKVLSIGDLRTFERDGEDEDGRVINVEVADETG---SVRVAFWDEQAVAAEEEL-EVGQVL 126 (485)
T ss_pred cccHhhC--CCCCCceEEEEEEeEccCceEEEeCCCCCCcEEEEEEEEcCCC---eEEEEEechHhHhhhccc-CCCCEE
Confidence 3578999 455 56999999999998864 2 22 35789999999765 299999976433 46777 899999
Q ss_pred EEeeEEEEEEcCeeEEEeecCceEEEEEeCCCCCCCCCCccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCcccccccc
Q 015600 83 LLKNVMIKKHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSLK 162 (404)
Q Consensus 83 ~l~rvki~~~~g~~~~~~~~~~ss~~vf~~~~~~~~~P~~~s~~~~~~~~~e~~~v~~Lr~w~~~~~~~~~~~~f~~~L~ 162 (404)
.+.+.-...|++ +.+..+ . ........+ |+ . . ..| ..|+
T Consensus 127 ~I~~~~~~~ys~-~El~i~----~---ve~~~d~~i-~~-----------------------------~-~-~~~-~~I~ 165 (485)
T PRK07211 127 RIKGRPKDGYNG-LEVSVD----K---VEPDPDAEI-DV-----------------------------Q-I-GDT-YTVE 165 (485)
T ss_pred EEeceEeccccc-eEEEEe----e---EEEcccccc-cc-----------------------------c-c-cCC-ccHH
Confidence 997754444443 222221 1 110000000 00 0 0 125 6788
Q ss_pred cccCC-ceEeEEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCCccCCCCCccccCCCCChhhhccCCCCceEEEE
Q 015600 163 DISEH-RYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRV 241 (404)
Q Consensus 163 di~~~-~f~Dl~~qVv~~~~~~~~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~pp~G~~l~V 241 (404)
||+++ ..+|++++|+.+. +. ..+ -=-||++-..+ +..+-| + -| .+++
T Consensus 166 dL~~~~~~v~I~grV~~v~-~i--Rtf--~r~dGseGkv~--sv~L~D-----------------e-------TG-~IR~ 213 (485)
T PRK07211 166 DLSLGLSDVTLVGVVLDTD-SV--RTF--DRDDGSEGRVS--NLTVGD-----------------E-------TG-RVRV 213 (485)
T ss_pred HcCCCCCceEEEEEEEEcC-CC--eEE--ECCCCCeeEEE--EEEEEc-----------------C-------CC-eEEE
Confidence 88865 5689999999776 42 111 11122211111 111100 0 15 5899
Q ss_pred EecCchhhhhhccCCCCcEEEEeceEEEEeCcEEEEEEecCCceEEcCCCChHHHHHHHHHHHHHhCCCCCCCCcCCCCC
Q 015600 242 STDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDNDNVVWDYMRRFRERISGGHGHMPIWTDPSS 321 (404)
Q Consensus 242 ~~~~~~~~~~~~~~k~g~wv~l~Nv~~k~~~g~leG~l~~~ski~~l~~~d~~v~~r~r~y~~~~~~~~~~~~~~~~p~~ 321 (404)
|+|+.++... ..+.+|+-|+|.|.+++...|.+|..+..++.|..++++-.. +| .
T Consensus 214 TlW~d~Ad~~-~~le~G~Vv~I~~a~Vre~~g~~ELsl~~~s~I~~~~dev~~------------------vp-----~- 268 (485)
T PRK07211 214 TLWDDRADLA-EELDAGESVEIVDGYVRERDGSLELHVGDRGAVEEVDEDVEY------------------VP-----D- 268 (485)
T ss_pred EEechhhhhh-ccCCCCCEEEEEeeEEEecCCcEEEEECCCceEEECCccccc------------------cc-----c-
Confidence 9999988753 679999999999999999878888888888888766542000 01 0
Q ss_pred CCCcccccCCCccccHHHHhcCCCCCceEEEEEEEEeecCCCccccccCCCCcEEEEEEEEeCCCceEEEEEecccccc
Q 015600 322 QFLTEVDWVNVASVTLMKIATQLQGNVRCCCIVRVVSIHPFQAEHYSSPNGSSEYTMKLTLEDPTARIHALLCGKEWVR 400 (404)
Q Consensus 322 ~~~t~~~~~~~p~ttL~~IL~~~~~~~kyr~~VRVV~~~P~~l~df~~~~~~~~~~f~L~leD~t~~~~~~v~~~da~~ 400 (404)
++.|.++- ...-.-...+|.+..|..- |.+..|+=-..--|+|-|.|+++++-++|+.|++
T Consensus 269 ------------~~~I~dl~----~g~~vdV~GvV~~v~~~rt--f~r~dG~~~~vr~l~l~D~TG~IrvTLWg~~A~~ 329 (485)
T PRK07211 269 ------------TTPIESLE----IDETVDIAGVVRSADPKRT--FDRDDGSEGQVRNVRIQDDTGDIRVALWGEKADL 329 (485)
T ss_pred ------------cccHhhcC----CCCceeEEEEEEEccCcEE--EEcCCCCEeEEEEEEEEcCCCcEEEEEeCccccC
Confidence 13344432 1123567788888877654 4444453346778999999999999999999853
No 16
>PRK08402 replication factor A; Reviewed
Probab=98.23 E-value=6.4e-05 Score=74.97 Aligned_cols=186 Identities=14% Similarity=0.096 Sum_probs=110.6
Q ss_pred cccccccCC-ceEeEEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCCccCCCCCccccCCCCChhhhccCCCCce
Q 015600 159 LSLKDISEH-RYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGT 237 (404)
Q Consensus 159 ~~L~di~~~-~f~Dl~~qVv~~~~~~~~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~pp~G~ 237 (404)
..|+||.++ ..++++++|+.+. +. ..+ ---||+...- .+..+.| + -|+
T Consensus 63 ~kI~dl~~g~~~V~v~~rVl~~~-~~--r~f--~rrdG~~~~V--~~i~l~D-----------------e-------TG~ 111 (355)
T PRK08402 63 MHISDLVPGMRGVNIVGRVLRKY-PP--REY--TKKDGSTGRV--ASLIIYD-----------------D-------TGR 111 (355)
T ss_pred cCHHHccCCCceeeEEEEEEEcc-CC--cee--eccCCCcceE--EEEEEEc-----------------C-------CCe
Confidence 679999987 5899999999987 31 111 1113321100 0010100 0 144
Q ss_pred EEEEEecCchhhhhhccCCCCcEEEEeceEEEE-eCcEEEEEEecCCceEEcCCCChHHHHHHHHHHHHHhCCCCCCCCc
Q 015600 238 VLRVSTDRSYENFGRYFTATGKWVRIRNMSCQV-SSGMWHGLLQSSSKIRLFSDNDNVVWDYMRRFRERISGGHGHMPIW 316 (404)
Q Consensus 238 ~l~V~~~~~~~~~~~~~~k~g~wv~l~Nv~~k~-~~g~leG~l~~~ski~~l~~~d~~v~~r~r~y~~~~~~~~~~~~~~ 316 (404)
+ ++++|+.+|.-....+.+|+-|++.|..++- .+|..+..+...+.|.+.|+ ++++-+ +|
T Consensus 112 i-r~TlW~~~a~~~~~~l~~Gdvi~I~~a~V~e~~~G~~eLsvg~~s~i~~~pd-~~ea~~---------------i~-- 172 (355)
T PRK08402 112 A-RVVLWDAKVAKYYNKINVGDVIKVIDAQVRESLSGLPELHINFRARIILNPD-DPRVEE---------------IP-- 172 (355)
T ss_pred E-EEEEechhhhhhcccCCCCCEEEEECCEEeecCCCcEEEEECCCceEEeCCC-cccccc---------------cc--
Confidence 4 9999998765224569999999999999998 58998999999999877664 332211 01
Q ss_pred CCCCCCCCcccccCCCccccHHHHhcCCCCCceEEEEEEEEeecCCCccc-----------------ccc---C--CCCc
Q 015600 317 TDPSSQFLTEVDWVNVASVTLMKIATQLQGNVRCCCIVRVVSIHPFQAEH-----------------YSS---P--NGSS 374 (404)
Q Consensus 317 ~~p~~~~~t~~~~~~~p~ttL~~IL~~~~~~~kyr~~VRVV~~~P~~l~d-----------------f~~---~--~~~~ 374 (404)
....+. .. .-+..+|.+|-... .-|.+.+.|+...+.-+-. +.+ + ...|
T Consensus 173 ---~~~~~~--~~-~~~~k~I~ei~~gd---~~v~v~g~Iv~i~~~~~y~aCp~CnKkv~~~~~~~~~~Ce~~~~v~p~~ 243 (355)
T PRK08402 173 ---PLEEVR--SY-NYTRKKIGELEGGE---RFVEVRGTIAKVYRVLVYDACPECRRKVDYDPATDTWICPEHGEVEPIK 243 (355)
T ss_pred ---cccccc--cc-cccccCHHHcccCC---cEEEEEEEEEEEecCeeEecCCCCCeEEEEecCCCCEeCCCCCCcCcce
Confidence 000000 00 12233344442111 1134444444444310000 111 1 3578
Q ss_pred EEEEEEEEeCCCceEEEEEeccccccccc
Q 015600 375 EYTMKLTLEDPTARIHALLCGKEWVRFQL 403 (404)
Q Consensus 375 ~~~f~L~leD~t~~~~~~v~~~da~~f~~ 403 (404)
.|++.+.|-|.||++.+.++++.|+.++|
T Consensus 244 ryil~~~l~D~TG~~~vt~f~e~ae~llG 272 (355)
T PRK08402 244 ITILDFGLDDGTGYIRVTLFGDDAAELLG 272 (355)
T ss_pred eEEEEEEEEcCCCcEEEEEecHHHHHHhC
Confidence 89999999999999999999999999986
No 17
>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=98.17 E-value=2.7e-05 Score=63.62 Aligned_cols=74 Identities=16% Similarity=0.201 Sum_probs=59.1
Q ss_pred EEEEEEEEEecCCceec--C--C-CceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCeeE
Q 015600 23 KVNLLGVVLEFSIPRKS--Q--G-TDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAELS 97 (404)
Q Consensus 23 ~vnv~GVV~d~~~P~~t--r--G-tD~~~t~~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~~~g~~~ 97 (404)
.|||+|+|++.++|+.- + | .-.+..|+|.|.|.. .+.|.++.+..+.+... .|+||.|++++++.|+| ..
T Consensus 1 ~vDvig~V~~v~~~~~i~~k~~g~~~~~r~v~i~D~t~~--~i~vtLWg~~a~~~~~~--~~~vv~~~~~~i~~~~~-~~ 75 (101)
T cd04475 1 IVDVIGVVKSVGPVTTITTKSTGRELDKREITLVDESGH--SVELTLWGEQAELFDGS--ENPVIAIKGVKVSEFNG-KS 75 (101)
T ss_pred CEeEEEEEeEccCcEEEEEecCCCceeEEEEEEEeCCCC--EEEEEEEHHHhhhcccC--CCCEEEEEeeEEEecCC-eE
Confidence 38999999999998743 2 4 367899999999985 49999999876666654 39999999999999985 44
Q ss_pred EEee
Q 015600 98 AVFY 101 (404)
Q Consensus 98 ~~~~ 101 (404)
+.+.
T Consensus 76 l~~~ 79 (101)
T cd04475 76 LSTG 79 (101)
T ss_pred Eeec
Confidence 4443
No 18
>TIGR00617 rpa1 replication factor-a protein 1 (rpa1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.10 E-value=5.4e-05 Score=80.92 Aligned_cols=156 Identities=18% Similarity=0.256 Sum_probs=105.4
Q ss_pred CcceeehHhhhhc-cCCEEEEEEEEEecCCceec--C--CCc-eEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCC
Q 015600 7 QGGIVRIKELAMH-VKHKVNLLGVVLEFSIPRKS--Q--GTD-YVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRD 80 (404)
Q Consensus 7 ~y~y~~i~~~~~~-~~~~vnv~GVV~d~~~P~~t--r--GtD-~~~t~~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GD 80 (404)
.|.|++|+++... .+..|+|||||+++++...- | |+. .+..|+|+|.|-. .|.|+++.+..+.+. . ..|+
T Consensus 295 ~~~f~~i~dI~~~~~~~~VDVIGvV~~v~~~~~i~~k~~g~~~~kR~i~L~D~sg~--sI~vTLWG~~A~~~~-~-~~~~ 370 (608)
T TIGR00617 295 QFNFVKIDDIGGYEGNSLVDVIGIVQSVSPTQTITSRKNNKEFPKRDITLVDDSGK--SVRVTLWGDDATKFD-V-SVQP 370 (608)
T ss_pred cccceEHHHhhhhcCCCCccEEEEEeEecCceEEEEcCCCCeeeeEEEEEEeCCCC--EEEEEEEhhhhhhcC-C-CCCC
Confidence 6889999999764 35589999999999987652 3 444 4789999999864 499999998766776 3 5799
Q ss_pred EEEEeeEEEEEEcCeeEEEeecCceEEEEEeCCCCCCCCCCccCCCCCCCCHHHHHHHHHHHHhhhcCccc---------
Q 015600 81 LILLKNVMIKKHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFS--------- 151 (404)
Q Consensus 81 II~l~rvki~~~~g~~~~~~~~~~ss~~vf~~~~~~~~~P~~~s~~~~~~~~~e~~~v~~Lr~w~~~~~~~--------- 151 (404)
||.|..++|+.|+|. .+.+. ..|.+. .. | |..-+..|+.|+.+....
T Consensus 371 Vva~kg~~V~~f~g~-sLs~~-~~S~i~-iN--------P-------------dipEa~~L~~w~~~~g~~~~~~s~~~~ 426 (608)
T TIGR00617 371 VIAIKGVRVSDFGGK-SLSTG-GSSTII-VN--------P-------------DIPEAEKLKGWYDNEGKGTMASSISDM 426 (608)
T ss_pred EEEEEeEEEEecCCc-eEecc-CCceEE-EC--------C-------------CcHHHHHHHHHHHhcCCCccceeehhc
Confidence 999999999999664 43332 224443 11 1 112256889997643221
Q ss_pred C----C--CcccccccccccC--------CceEeEEEEEEEEEeeCCCCeEEEEEEcCCCCCC
Q 015600 152 S----G--SNDYLLSLKDISE--------HRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPP 200 (404)
Q Consensus 152 ~----~--~~~f~~~L~di~~--------~~f~Dl~~qVv~~~~~~~~~~~~L~VwDgT~~~~ 200 (404)
. + .... +.|++|++ +.||.+.|.|.++. . + .+ | |+.+|.
T Consensus 427 ~~~~~~~~~~~~-ktI~ei~~~~lg~~~k~~~f~v~atI~~Ik-~-d--~~----~-Y~ACp~ 479 (608)
T TIGR00617 427 MSGRVGGSNAER-KTIAEIQAENLGKSDKPDYFSVKATISYLK-P-D--NA----L-YRACPS 479 (608)
T ss_pred cccccCCccccc-ccHHHHhhhccCCCCCCcEEEEEEEEEEEe-c-C--Ce----E-eccCCh
Confidence 0 0 1122 45666643 34789999999987 4 2 22 3 777765
No 19
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=98.05 E-value=0.00016 Score=61.97 Aligned_cols=89 Identities=17% Similarity=0.278 Sum_probs=70.7
Q ss_pred eeehHhhhhccC-CEEEEEEEEEecCCce--ecCCC-ceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEe
Q 015600 10 IVRIKELAMHVK-HKVNLLGVVLEFSIPR--KSQGT-DYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLK 85 (404)
Q Consensus 10 y~~i~~~~~~~~-~~vnv~GVV~d~~~P~--~trGt-D~~~t~~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~ 85 (404)
.+.|+|+ .++ ..||+.|+|++..+++ +++|+ -....++|.|.|=. |.+.++.+.. +.+ +.||||+|+
T Consensus 4 ~~kI~dL--~~g~~~v~~~~~V~~i~~~~~~~~k~~~~~v~~~~l~D~TG~---I~~tlW~~~a---~~l-~~GdvV~I~ 74 (129)
T PRK06461 4 ITKIKDL--KPGMERVNVTVRVLEVGEPKVIQTKGGPRTISEAVVGDETGR---VKLTLWGEQA---GSL-KEGEVVEIE 74 (129)
T ss_pred ceEHHHc--CCCCCceEEEEEEEEcCCceEEEeCCCceEEEEEEEECCCCE---EEEEEeCCcc---ccC-CCCCEEEEE
Confidence 6789999 456 5799999999998764 45654 45889999999863 8999998643 345 689999999
Q ss_pred eEEEEEEcCeeEEEeecCceEEE
Q 015600 86 NVMIKKHQAELSAVFYKDSSSFA 108 (404)
Q Consensus 86 rvki~~~~g~~~~~~~~~~ss~~ 108 (404)
+++++.|+|.+++..... +...
T Consensus 75 na~v~~f~G~lqL~i~~~-~~i~ 96 (129)
T PRK06461 75 NAWTTLYRGKVQLNVGKY-GSIS 96 (129)
T ss_pred CcEEeeeCCEEEEEECCC-EEEE
Confidence 999999999999888643 4444
No 20
>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=97.69 E-value=0.00065 Score=53.23 Aligned_cols=72 Identities=18% Similarity=0.281 Sum_probs=60.2
Q ss_pred EEEEEEEecCCceec---CCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCeeEEEee
Q 015600 25 NLLGVVLEFSIPRKS---QGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAELSAVFY 101 (404)
Q Consensus 25 nv~GVV~d~~~P~~t---rGtD~~~t~~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~~~g~~~~~~~ 101 (404)
||.|.|+...+++.. .+.--..+++|.|.|- .+.+.++.+.. .+.+ +.||+|.+++++++.|+|.+++..+
T Consensus 1 ~v~~~V~~~~~~~~~~~~g~~~~~~~~~l~D~TG---~i~~~~W~~~~--~~~~-~~G~vv~i~~~~v~~~~g~~ql~i~ 74 (82)
T cd04491 1 SVEGKVLSISEPREFTRDGSEGKVQSGLVGDETG---TIRFTLWDEKA--ADDL-EPGDVVRIENAYVREFNGRLELSVG 74 (82)
T ss_pred CEEEEEEEccCCeEeccCCCeeEEEEEEEECCCC---EEEEEEECchh--cccC-CCCCEEEEEeEEEEecCCcEEEEeC
Confidence 689999999998753 3456789999999974 39999998654 6667 7899999999999999999998876
Q ss_pred c
Q 015600 102 K 102 (404)
Q Consensus 102 ~ 102 (404)
.
T Consensus 75 ~ 75 (82)
T cd04491 75 K 75 (82)
T ss_pred C
Confidence 4
No 21
>PRK07218 replication factor A; Provisional
Probab=97.58 E-value=0.0091 Score=61.02 Aligned_cols=159 Identities=17% Similarity=0.217 Sum_probs=107.0
Q ss_pred cccccccC-CceEeEEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCCccCCCCCccccCCCCChhhhccCCCCce
Q 015600 159 LSLKDISE-HRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGT 237 (404)
Q Consensus 159 ~~L~di~~-~~f~Dl~~qVv~~~~~~~~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~pp~G~ 237 (404)
..|+||++ +..++++++|+.+. + + ++. .||+..... ...+.| .+
T Consensus 59 ~kI~Di~~~~~~V~v~~kVl~i~-~----r-t~r-~dg~~g~v~--~~~igD--------------------------eT 103 (423)
T PRK07218 59 KDIKELSTDDKNVTVTGRVLTIG-E----R-SIR-YQGDDHVIY--EGILAD--------------------------ET 103 (423)
T ss_pred ccHhhCCCCCceeEEEEEEEEec-c----e-eEe-cCCCceEEE--EEEEEC--------------------------CC
Confidence 67999986 57999999999987 3 2 223 777632111 110000 12
Q ss_pred -EEEEEecCchhhhhhccCCCCcEEEEeceEEEEeCcEEEEEEecCCceEEcCCCChHHHHHHHHHHHHHhCCCCCCCCc
Q 015600 238 -VLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDNDNVVWDYMRRFRERISGGHGHMPIW 316 (404)
Q Consensus 238 -~l~V~~~~~~~~~~~~~~k~g~wv~l~Nv~~k~~~g~leG~l~~~ski~~l~~~d~~v~~r~r~y~~~~~~~~~~~~~~ 316 (404)
++++++|+.. .+++||+|+|.|...+...|..+-.+...+.|..++++..
T Consensus 104 G~Ir~tlW~~~------~l~~Gdvv~I~na~vre~~g~~el~ig~~t~I~~~de~~~----------------------- 154 (423)
T PRK07218 104 GTISYTAWKDF------GLSPGDTVTIGNAGVREWDGRPELNIGESTTVSLLDDSSL----------------------- 154 (423)
T ss_pred CeEEEEEECCC------CCCCCCEEEEeccEeeccCCceEEeccCcceEEEcCcccc-----------------------
Confidence 7799999942 2999999999999999999998888888888877664311
Q ss_pred CCCCCCCCcccccCCCccccHHHHhcCCCCCceEEEEEEEEeecCCCccccccCCCCcEEEEEEEEeCCCceEEEEEecc
Q 015600 317 TDPSSQFLTEVDWVNVASVTLMKIATQLQGNVRCCCIVRVVSIHPFQAEHYSSPNGSSEYTMKLTLEDPTARIHALLCGK 396 (404)
Q Consensus 317 ~~p~~~~~t~~~~~~~p~ttL~~IL~~~~~~~kyr~~VRVV~~~P~~l~df~~~~~~~~~~f~L~leD~t~~~~~~v~~~ 396 (404)
|. ++..+...|.||-. -..-....+||++.+|. .|-...|.- ....++|.|.||++++-++++
T Consensus 155 --~~--------~~~~~~~kI~DL~~---g~~~V~v~g~Vl~~~~r---~f~~~dg~~-~v~~giigDeTG~Ir~tlW~~ 217 (423)
T PRK07218 155 --PP--------YSIGGDKKLIDLGP---GDRGVNVEARVLELEHR---EIDGRDGET-TILSGVLADETGRLPFTDWDP 217 (423)
T ss_pred --cC--------ccccCccchhhccC---CCCceEEEEEEEEecce---eEEcCCCCe-EEEEEEEECCCceEEEEEecc
Confidence 00 00112223444321 12235788999999874 465665532 467789999999999999998
Q ss_pred cc
Q 015600 397 EW 398 (404)
Q Consensus 397 da 398 (404)
.|
T Consensus 218 ~~ 219 (423)
T PRK07218 218 LP 219 (423)
T ss_pred cc
Confidence 65
No 22
>PRK08402 replication factor A; Reviewed
Probab=97.30 E-value=0.0079 Score=60.17 Aligned_cols=139 Identities=16% Similarity=0.231 Sum_probs=93.2
Q ss_pred ceeehHhhhhccC-CEEEEEEEEEecCCcee--c-CCC-ceEEEEEEEeCCCCCCCeEEEEecCCCC-CCCCCCCCCCEE
Q 015600 9 GIVRIKELAMHVK-HKVNLLGVVLEFSIPRK--S-QGT-DYVCVLKIVDDSQQSPELLVNIFTSSID-QLPRVLSPRDLI 82 (404)
Q Consensus 9 ~y~~i~~~~~~~~-~~vnv~GVV~d~~~P~~--t-rGt-D~~~t~~I~D~S~~~~gl~v~iF~~~~~-~LP~v~~~GDII 82 (404)
..++|+|+. ++ ..||+.|-|+....|+. . .|+ -...+++|.|+|-. +.+.++.+..+ .++.+ ..||||
T Consensus 61 ~~~kI~dl~--~g~~~V~v~~rVl~~~~~r~f~rrdG~~~~V~~i~l~DeTG~---ir~TlW~~~a~~~~~~l-~~Gdvi 134 (355)
T PRK08402 61 PLMHISDLV--PGMRGVNIVGRVLRKYPPREYTKKDGSTGRVASLIIYDDTGR---ARVVLWDAKVAKYYNKI-NVGDVI 134 (355)
T ss_pred CccCHHHcc--CCCceeeEEEEEEEccCCceeeccCCCcceEEEEEEEcCCCe---EEEEEechhhhhhcccC-CCCCEE
Confidence 467899994 44 57999999999987763 2 243 56888999998763 89999997644 47878 889999
Q ss_pred EEeeEEEEEE-cCeeEEEeecCceEEEEEeCCCCCCCCCCccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCccccccc
Q 015600 83 LLKNVMIKKH-QAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSL 161 (404)
Q Consensus 83 ~l~rvki~~~-~g~~~~~~~~~~ss~~vf~~~~~~~~~P~~~s~~~~~~~~~e~~~v~~Lr~w~~~~~~~~~~~~f~~~L 161 (404)
++.+++++.+ +|.+++..... |+..+=+..+...-.| .-.++.. ... .. +.|
T Consensus 135 ~I~~a~V~e~~~G~~eLsvg~~-s~i~~~pd~~ea~~i~---------~~~~~~~--------------~~~--~~-k~I 187 (355)
T PRK08402 135 KVIDAQVRESLSGLPELHINFR-ARIILNPDDPRVEEIP---------PLEEVRS--------------YNY--TR-KKI 187 (355)
T ss_pred EEECCEEeecCCCcEEEEECCC-ceEEeCCCcccccccc---------ccccccc--------------ccc--cc-cCH
Confidence 9999999984 88878877643 4444222111100001 0000000 011 13 568
Q ss_pred ccccCCc-eEeEEEEEEEEE
Q 015600 162 KDISEHR-YFDLVCKVFHVS 180 (404)
Q Consensus 162 ~di~~~~-f~Dl~~qVv~~~ 180 (404)
.|++++. ||.+.+.|+.+.
T Consensus 188 ~ei~~gd~~v~v~g~Iv~i~ 207 (355)
T PRK08402 188 GELEGGERFVEVRGTIAKVY 207 (355)
T ss_pred HHcccCCcEEEEEEEEEEEe
Confidence 8887654 799999999987
No 23
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=97.10 E-value=0.0065 Score=52.04 Aligned_cols=95 Identities=16% Similarity=0.142 Sum_probs=64.8
Q ss_pred cccccccCC-ceEeEEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCCccCCCCCccccCCCCChhhhccCCCCce
Q 015600 159 LSLKDISEH-RYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGT 237 (404)
Q Consensus 159 ~~L~di~~~-~f~Dl~~qVv~~~~~~~~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~pp~G~ 237 (404)
..|+||+++ .-+|++++|+.+. +. ..+ -.++. ...+ +...+.| + -|
T Consensus 5 ~kI~dL~~g~~~v~~~~~V~~i~-~~--~~~---~~k~~-~~~v-~~~~l~D-----------------~-------TG- 51 (129)
T PRK06461 5 TKIKDLKPGMERVNVTVRVLEVG-EP--KVI---QTKGG-PRTI-SEAVVGD-----------------E-------TG- 51 (129)
T ss_pred eEHHHcCCCCCceEEEEEEEEcC-Cc--eEE---EeCCC-ceEE-EEEEEEC-----------------C-------CC-
Confidence 679999998 6999999999775 21 010 01111 0000 1111111 0 13
Q ss_pred EEEEEecCchhhhhhccCCCCcEEEEeceEEEEeCcEEEEEEecCCceEEcCC
Q 015600 238 VLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSD 290 (404)
Q Consensus 238 ~l~V~~~~~~~~~~~~~~k~g~wv~l~Nv~~k~~~g~leG~l~~~ski~~l~~ 290 (404)
++++++|+..+ ..+++|+.|+++|..++...|.++..+...+.|..+++
T Consensus 52 ~I~~tlW~~~a----~~l~~GdvV~I~na~v~~f~G~lqL~i~~~~~i~~~~~ 100 (129)
T PRK06461 52 RVKLTLWGEQA----GSLKEGEVVEIENAWTTLYRGKVQLNVGKYGSISESDD 100 (129)
T ss_pred EEEEEEeCCcc----ccCCCCCEEEEECcEEeeeCCEEEEEECCCEEEEECCc
Confidence 57899999744 45899999999999999999999888888888888775
No 24
>cd04497 hPOT1_OB1_like hPOT1_OB1_like: A subfamily of OB folds similar to the first OB fold (OB1) of human protection of telomeres 1 protein (hPOT1), the single OB fold of the N-terminal domain of Schizosaccharomyces pombe POT1 (SpPOT1), and the first OB fold of the N-terminal domain of the alpha subunit (OB1Nalpha) of Oxytricha nova telomere end binding protein (OnTEBP). POT1 proteins recognize single-stranded (ss) 3-prime ends of the telomere. A 3-prime ss overhang is conserved in ciliated protozoa, yeast, and mammals. SpPOT1 is essential for telomere maintenance. It binds specifically to the ss G-rich telomeric sequence (GGTTAC) of S. pombe. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. Deletion of the S. pombe pot1+ gene results in a rapid loss of telomere sequences, chromosome mis-segregation and chromosome circularization. hPOT1 is implicated in telomere length regulation. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB
Probab=96.91 E-value=0.011 Score=51.12 Aligned_cols=96 Identities=17% Similarity=0.125 Sum_probs=70.8
Q ss_pred ccccccccc--CCceEeEEEEEEEEEeeC----CCCeEEEEEEcCCCCCCCCCCCCCCCccCCCCCccccCCCCChhhhc
Q 015600 157 YLLSLKDIS--EHRYFDLVCKVFHVSYDD----SKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLR 230 (404)
Q Consensus 157 f~~~L~di~--~~~f~Dl~~qVv~~~~~~----~~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~ 230 (404)
| ..|+++. .++.+|+++-|+...... .+.+.+|.|+|=|.++
T Consensus 3 f-~~i~~~~~~~~~~v~vigVV~~~~~p~~s~g~d~~~tl~i~D~S~~~------------------------------- 50 (138)
T cd04497 3 Y-TPLSSALKESGGSVNVIGVVVDAGPPVRSKGTDYCCTLTITDPSLAN------------------------------- 50 (138)
T ss_pred e-EeHHHHHhccCCeEEEEEEEeecCCCcccCCCcEEEEEEEECCCCCC-------------------------------
Confidence 5 6788886 799999999999876211 1246777777744211
Q ss_pred cCCCCceEEEEEecCchhhhhhccCCCCcEEEEeceEEEEeCcEEEEEEec-CCceEEcCC
Q 015600 231 NFFPVGTVLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQS-SSKIRLFSD 290 (404)
Q Consensus 231 ~~pp~G~~l~V~~~~~~~~~~~~~~k~g~wv~l~Nv~~k~~~g~leG~l~~-~ski~~l~~ 290 (404)
+..|.|.+|.++++. ...+.+||.|+|+|++++..+|...|.... .+.+.+.+.
T Consensus 51 -----~~~l~v~~F~~~~~~-LP~v~~GDVIll~~~kv~~~~g~~~~~~~~~~ss~avf~~ 105 (138)
T cd04497 51 -----SDGLTVKLFRPNEES-LPIVKVGDIILLRRVKIQSYNGKPQGISNDRGSSWAVFRG 105 (138)
T ss_pred -----CCcEEEEEECCChhh-CCCCCCCCEEEEEEEEEEEECCceEEEECCCceeEEEEcC
Confidence 226788899987764 566799999999999999998988888777 556655543
No 25
>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=96.80 E-value=0.0067 Score=44.91 Aligned_cols=71 Identities=18% Similarity=0.368 Sum_probs=54.0
Q ss_pred EEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCeeEEEee
Q 015600 25 NLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAELSAVFY 101 (404)
Q Consensus 25 nv~GVV~d~~~P~~trGtD~~~t~~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~~~g~~~~~~~ 101 (404)
.+.|+|.+..... | ...+..++|.|.+- ..+.|.+|.+..+........|++|.++ .+++.++++.++...
T Consensus 1 ~v~g~v~~~~~~~-~--~~~~~~~~l~D~~~--~~i~~~~~~~~~~~~~~~~~~g~~v~v~-g~v~~~~~~~~l~~~ 71 (75)
T cd03524 1 TIVGIVVAVEEIR-T--EGKVLIFTLTDGTG--GTIRVTLFGELAEELENLLKEGQVVYIK-GKVKKFRGRLQLIVE 71 (75)
T ss_pred CeEEEEEeecccc-c--CCeEEEEEEEcCCC--CEEEEEEEchHHHHHHhhccCCCEEEEE-EEEEecCCeEEEEee
Confidence 3789999988753 3 35589999999882 2399999997655553434889999998 999999887776653
No 26
>KOG3416 consensus Predicted nucleic acid binding protein [General function prediction only]
Probab=96.36 E-value=0.021 Score=47.82 Aligned_cols=82 Identities=21% Similarity=0.287 Sum_probs=65.6
Q ss_pred eehHhhhhccCC-EEEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEE
Q 015600 11 VRIKELAMHVKH-KVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMI 89 (404)
Q Consensus 11 ~~i~~~~~~~~~-~vnv~GVV~d~~~P~~trGtD~~~t~~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki 89 (404)
.+|+|+. ++. ..|+.=+|++.+.-.+|+-.+=.++.++.|+|-. |.+.+..+ +..+ + +.||||+|++---
T Consensus 5 i~ikdi~--P~~kN~~v~fIvl~~g~~tkTkdg~~v~~~kVaD~Tgs---I~isvW~e-~~~~--~-~PGDIirLt~Gy~ 75 (134)
T KOG3416|consen 5 IFIKDIK--PGLKNINVTFIVLEYGRATKTKDGHEVRSCKVADETGS---INISVWDE-EGCL--I-QPGDIIRLTGGYA 75 (134)
T ss_pred hhHhhcC--hhhhcceEEEEEEeeceeeeccCCCEEEEEEEecccce---EEEEEecC-cCcc--c-CCccEEEecccch
Confidence 4678883 433 5899999999999889988888999999999863 88888883 3333 2 6799999999999
Q ss_pred EEEcCeeEEEee
Q 015600 90 KKHQAELSAVFY 101 (404)
Q Consensus 90 ~~~~g~~~~~~~ 101 (404)
..|+|.+.+-+.
T Consensus 76 Si~qg~LtL~~G 87 (134)
T KOG3416|consen 76 SIFQGCLTLYVG 87 (134)
T ss_pred hhhcCceEEEec
Confidence 999998766554
No 27
>PRK07217 replication factor A; Reviewed
Probab=96.33 E-value=0.07 Score=52.02 Aligned_cols=92 Identities=17% Similarity=0.260 Sum_probs=68.1
Q ss_pred CcceeehHhhhhccCCEEEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEee
Q 015600 7 QGGIVRIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKN 86 (404)
Q Consensus 7 ~y~y~~i~~~~~~~~~~vnv~GVV~d~~~P~~trGtD~~~t~~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~r 86 (404)
...-+.|+|+. ..++.|+|.|-|+....|+. ++-...- -|-|+|= . |++..+.+ +.+|.+ ..||+++|++
T Consensus 69 ~~~~~kI~Di~-~~~~~VsV~aKVl~l~e~~~--~si~qvG-llgDETG-~--IkfT~W~~--s~~~~l-eeGd~~rI~n 138 (311)
T PRK07217 69 GSELVNIADID-EPEQWVDVTAKVVQLWEPSS--DSIAQVG-LLGDETG-T--IKFTKWAK--SDLPEL-EEGKSYLLKN 138 (311)
T ss_pred CCCceeeeecC-CCCCcEEEEEEEEEecCCCC--CceEEEE-EEEcCCc-e--EEEEEccC--CCCCcc-cCCCEEEEEe
Confidence 34456788884 26778999999999887652 2222211 3566654 2 99999986 369999 7899999999
Q ss_pred EEEEEEcCeeEEEeecCceEEEE
Q 015600 87 VMIKKHQAELSAVFYKDSSSFAL 109 (404)
Q Consensus 87 vki~~~~g~~~~~~~~~~ss~~v 109 (404)
+.+..|+|++++..+. +|+...
T Consensus 139 a~v~ey~G~~~lnlg~-~t~I~~ 160 (311)
T PRK07217 139 VVTDEYQGRFSVKLNR-TTSIEE 160 (311)
T ss_pred EEEeeECCEEEEEeCC-ceEEEe
Confidence 9999999999988874 365553
No 28
>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=95.98 E-value=0.18 Score=44.04 Aligned_cols=97 Identities=19% Similarity=0.144 Sum_probs=67.6
Q ss_pred cccc--cccCCceEeEEEEEEEEEee------CCCCeEEEEEEcCCCCCCCCCCCCCCCccCCCCCccccCCCCChhhhc
Q 015600 159 LSLK--DISEHRYFDLVCKVFHVSYD------DSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLR 230 (404)
Q Consensus 159 ~~L~--di~~~~f~Dl~~qVv~~~~~------~~~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~ 230 (404)
..|. ..+.++++|+++-|+..... ..+-..+|.|+|-|-+..- +
T Consensus 2 ~~l~~~~~~~~~~vnvigVV~~~~~p~~~~t~g~D~~~tl~i~D~S~~~~~------------~---------------- 53 (146)
T PF02765_consen 2 TPLSTAKEKFGKFVNVIGVVVDFSPPNPKKTRGTDYMCTLTITDPSLNDSN------------Q---------------- 53 (146)
T ss_dssp CCGGGSCTTSSEEEEEEEEEEEEEEECTEEESSSCEEEEEEEEBTTCSCSS------------C----------------
T ss_pred ccchhhhhcCCCEEEEEEEEEEccCCcceEcCCCcEEEEEEEECCCCCccc------------c----------------
Confidence 3455 44678999999999977633 1234788999996532211 0
Q ss_pred cCCCCceEEEEEecCchhhhhhccCCC-CcEEEEeceEEEEeCcEEEEEEecC--CceEEc
Q 015600 231 NFFPVGTVLRVSTDRSYENFGRYFTAT-GKWVRIRNMSCQVSSGMWHGLLQSS--SKIRLF 288 (404)
Q Consensus 231 ~~pp~G~~l~V~~~~~~~~~~~~~~k~-g~wv~l~Nv~~k~~~g~leG~l~~~--ski~~l 288 (404)
....|.|.++.++.+. ...++. ||.|+|++++++.+.|...|..... +.+.+.
T Consensus 54 ----~~~~l~v~iF~~~~~~-LP~v~~~GDii~l~r~kv~~~~~~~~~~~~~~~~ss~~vf 109 (146)
T PF02765_consen 54 ----KLSGLTVNIFRPHKES-LPNVKSVGDIIRLRRVKVQSYNGKPQGLSNSTSNSSWAVF 109 (146)
T ss_dssp ----CCCEEEEEEEESSHHH-SCTTCSTTHEEEEEEEEEEEETTEEEEEEECECTEEEEEE
T ss_pred ----ccCCEEEEEECCCHHH-CCCCCCCCCEEEEEEEEEEEECCEEEEEecCCCcEEEEEE
Confidence 0025677777655554 566776 9999999999999998888877776 566666
No 29
>PRK07217 replication factor A; Reviewed
Probab=95.93 E-value=0.19 Score=49.13 Aligned_cols=90 Identities=18% Similarity=0.249 Sum_probs=66.0
Q ss_pred ccccccc-CCceEeEEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCCccCCCCCccccCCCCChhhhccCCCCce
Q 015600 159 LSLKDIS-EHRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGT 237 (404)
Q Consensus 159 ~~L~di~-~~~f~Dl~~qVv~~~~~~~~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~pp~G~ 237 (404)
..|+||. .++.++++++|+.++ + ..+..+.+| ..+.| .+
T Consensus 73 ~kI~Di~~~~~~VsV~aKVl~l~-e-~~~~si~qv------------GllgD--------------------------ET 112 (311)
T PRK07217 73 VNIADIDEPEQWVDVTAKVVQLW-E-PSSDSIAQV------------GLLGD--------------------------ET 112 (311)
T ss_pred eeeeecCCCCCcEEEEEEEEEec-C-CCCCceEEE------------EEEEc--------------------------CC
Confidence 6799998 589999999999998 5 221111110 00000 12
Q ss_pred -EEEEEecCchhhhhhccCCCCcEEEEeceEEEEeCcEEEEEEecCCceEEcCCC
Q 015600 238 -VLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDN 291 (404)
Q Consensus 238 -~l~V~~~~~~~~~~~~~~k~g~wv~l~Nv~~k~~~g~leG~l~~~ski~~l~~~ 291 (404)
.++.++|.... ...+++|++++|.|+..+.++|..+-.+...+.|..++.+
T Consensus 113 G~IkfT~W~~s~---~~~leeGd~~rI~na~v~ey~G~~~lnlg~~t~I~~~de~ 164 (311)
T PRK07217 113 GTIKFTKWAKSD---LPELEEGKSYLLKNVVTDEYQGRFSVKLNRTTSIEELDED 164 (311)
T ss_pred ceEEEEEccCCC---CCcccCCCEEEEEeEEEeeECCEEEEEeCCceEEEeCCCC
Confidence 67899999521 4569999999999999999999999999998888877754
No 30
>PF01336 tRNA_anti-codon: OB-fold nucleic acid binding domain; InterPro: IPR004365 The OB-fold (oligonucleotide/oligosaccharide-binding fold) is found in all three kingdoms and its common architecture presents a binding face that has adapted to bind different ligands. The OB-fold is a five/six-stranded closed beta-barrel formed by 70-80 amino acid residues. The strands are connected by loops of varying length which form the functional appendages of the protein. The majority of OB-fold proteins use the same face for ligand binding or as an active site. Different OB-fold proteins use this 'fold-related binding face' to, variously, bind oligosaccharides, oligonucleotides, proteins, metal ions and catalytic substrates. This entry contains OB-fold domains that bind to nucleic acids []. It includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl-tRNA synthetases (See IPR004364 from INTERPRO). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule 6.1.1 from EC. This domain is found in RecG helicase involved in DNA repair. Replication factor A is a heterotrimeric complex, that contains a subunit in this family [, ]. This domain is also found at the C terminus of bacterial DNA polymerase III alpha chain.; GO: 0003676 nucleic acid binding; PDB: 1BBU_A 1KRS_A 1BBW_A 1KRT_A 1EQR_B 1IL2_B 1C0A_A 3KFU_A 1EOV_A 1ASY_A ....
Probab=95.88 E-value=0.015 Score=43.84 Aligned_cols=68 Identities=13% Similarity=0.216 Sum_probs=52.3
Q ss_pred EEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEec-CCCCCCCCCCCCCCEEEEeeEEEEEEcCe-eEEEee
Q 015600 24 VNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFT-SSIDQLPRVLSPRDLILLKNVMIKKHQAE-LSAVFY 101 (404)
Q Consensus 24 vnv~GVV~d~~~P~~trGtD~~~t~~I~D~S~~~~gl~v~iF~-~~~~~LP~v~~~GDII~l~rvki~~~~g~-~~~~~~ 101 (404)
|.|.|.|.... ++..-.+.++|.|.|- .+.|.+|. ........+ ..||+|+++ -+++.++++ ++...+
T Consensus 1 V~v~G~V~~~~-----~~~~~~~~~~l~D~tg---~i~~~~~~~~~~~~~~~l-~~g~~v~v~-G~v~~~~~~~~~l~~~ 70 (75)
T PF01336_consen 1 VTVEGRVTSIR-----RSGGKIVFFTLEDGTG---SIQVVFFNEEYERFREKL-KEGDIVRVR-GKVKRYNGGELELIVP 70 (75)
T ss_dssp EEEEEEEEEEE-----EEETTEEEEEEEETTE---EEEEEEETHHHHHHHHTS--TTSEEEEE-EEEEEETTSSEEEEEE
T ss_pred CEEEEEEEEEE-----cCCCCEEEEEEEECCc---cEEEEEccHHhhHHhhcC-CCCeEEEEE-EEEEEECCccEEEEEC
Confidence 56889999887 3334467899999983 39999999 344455556 789999999 999999987 887764
No 31
>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=95.82 E-value=0.12 Score=39.55 Aligned_cols=69 Identities=10% Similarity=0.093 Sum_probs=51.1
Q ss_pred EEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEE--cCeeEEEee
Q 015600 24 VNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKH--QAELSAVFY 101 (404)
Q Consensus 24 vnv~GVV~d~~~P~~trGtD~~~t~~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~~--~g~~~~~~~ 101 (404)
+-+.|+|.+.+. |+++ ++-++|.|.+- .+.+.+|.+..+........|++|.++ .+++.+ +|+++.+.+
T Consensus 2 ~~v~g~v~~i~~---tk~g--~~~~~L~D~~~---~i~~~~f~~~~~~~~~~l~~g~~v~v~-g~v~~~~~~~~~~l~v~ 72 (78)
T cd04489 2 VWVEGEISNLKR---PSSG--HLYFTLKDEDA---SIRCVMWRSNARRLGFPLEEGMEVLVR-GKVSFYEPRGGYQLIVE 72 (78)
T ss_pred EEEEEEEecCEE---CCCc--EEEEEEEeCCe---EEEEEEEcchhhhCCCCCCCCCEEEEE-EEEEEECCCCEEEEEEE
Confidence 458899998875 5433 99999999873 399999998667776666889988884 445544 477776664
No 32
>cd04481 RPA1_DBD_B_like RPA1_DBD_B_like: A subgroup of uncharacterized, plant OB folds with similarity to the third OB fold, the ssDNA-binding domain (DBD)-B, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-B, RPA1 contains three other OB folds: DBD-A, DBD-C, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change.
Probab=95.75 E-value=0.05 Score=44.72 Aligned_cols=82 Identities=12% Similarity=0.104 Sum_probs=57.1
Q ss_pred EEEEEEEecCCceecC--C-CceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCC----CCCCCEEEEee-EEEEEEcCee
Q 015600 25 NLLGVVLEFSIPRKSQ--G-TDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRV----LSPRDLILLKN-VMIKKHQAEL 96 (404)
Q Consensus 25 nv~GVV~d~~~P~~tr--G-tD~~~t~~I~D~S~~~~gl~v~iF~~~~~~LP~v----~~~GDII~l~r-vki~~~~g~~ 96 (404)
++||+|++.++..... | ..-+..|+|.|.+.. .++|.+..+..+.+..- ...+=||.+-+ .+|..|+|..
T Consensus 1 DviG~i~~v~~~~~~~~~~~~~~kr~~~i~D~~~~--~l~~tlwG~~A~~f~~~~~~~~~~~~VVav~~~~rV~~~~g~~ 78 (106)
T cd04481 1 DVIGVIVDVGPLEELPPVNKPSRKLDFEIRDLSDE--RLKCTLWGEYAEEFDAKFQSAGNGEPVVAVLRFWKIKEYKGPK 78 (106)
T ss_pred CeeEEEEEecceEecccCCccceEEEEEEEeCCCC--EEEEEEEHHHHHHHHHHHHHhCCCCcEEEEEEeEEEEEEcCCc
Confidence 4899999999876543 3 567899999999964 49999998766666542 13344776655 9999999843
Q ss_pred EEEeecCceEEE
Q 015600 97 SAVFYKDSSSFA 108 (404)
Q Consensus 97 ~~~~~~~~ss~~ 108 (404)
.+....+.|.|.
T Consensus 79 ~ls~~~~~s~v~ 90 (106)
T cd04481 79 SLSNSFGASKVY 90 (106)
T ss_pred EEEcCCCceEEE
Confidence 333332334444
No 33
>PRK06386 replication factor A; Reviewed
Probab=95.49 E-value=0.13 Score=51.46 Aligned_cols=87 Identities=18% Similarity=0.294 Sum_probs=67.6
Q ss_pred cceeehHhhhhccCCEEEEEEEEEecCCce-ecCCC-ceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEe
Q 015600 8 GGIVRIKELAMHVKHKVNLLGVVLEFSIPR-KSQGT-DYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLK 85 (404)
Q Consensus 8 y~y~~i~~~~~~~~~~vnv~GVV~d~~~P~-~trGt-D~~~t~~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~ 85 (404)
|..++|+|+.. ....|||.|-|++...+. .++|+ -...++-|-|+|=. |++.+|.+ .+ ..||+|++.
T Consensus 105 ~~~~KI~DL~~-g~~~v~V~akVle~~e~e~~~~g~~~~v~sg~lgDeTGr---Ir~TlW~~------~l-~eGd~v~i~ 173 (358)
T PRK06386 105 YKLVKIRDLSL-VTPYVSVIGKITGITKKEYDSDGTSKIVYQGYIEDDTAR---VRISSFGK------PL-EDNRFVRIE 173 (358)
T ss_pred cCccEeEeccC-CCCceEEEEEEEEccCceEecCCCccEEEEEEEEcCCCe---EEEEEccc------cc-cCCCEEEEe
Confidence 45678999942 345699999999975542 23444 77888999998752 99999985 25 789999999
Q ss_pred eEEEEEEcCeeEEEeecCceE
Q 015600 86 NVMIKKHQAELSAVFYKDSSS 106 (404)
Q Consensus 86 rvki~~~~g~~~~~~~~~~ss 106 (404)
++.++.|+|.+++..+.. |+
T Consensus 174 na~v~e~~G~~el~v~~~-t~ 193 (358)
T PRK06386 174 NARVSQYNGYIEISVGNK-SV 193 (358)
T ss_pred eeEEEccCCeEEEEeCCe-EE
Confidence 999999999999988743 54
No 34
>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=95.27 E-value=0.049 Score=48.49 Aligned_cols=57 Identities=18% Similarity=0.069 Sum_probs=44.8
Q ss_pred CceEEEEEEEEeecCCCccccccC------------------------CCCcEEEEEEEEeCCCceEEEEEecccccccc
Q 015600 347 NVRCCCIVRVVSIHPFQAEHYSSP------------------------NGSSEYTMKLTLEDPTARIHALLCGKEWVRFQ 402 (404)
Q Consensus 347 ~~kyr~~VRVV~~~P~~l~df~~~------------------------~~~~~~~f~L~leD~t~~~~~~v~~~da~~f~ 402 (404)
+..|.+++.|+.+.+..+-=.|+| +-.|.|++.+.|.|.|+.+.+.++|+.|+.||
T Consensus 15 ~~~~~v~a~I~~I~~~~~~Y~aC~~C~kkv~~~~~~~~~C~~C~~~~~~~~~ry~l~~~i~D~Tg~~~~~~F~~~ae~l~ 94 (166)
T cd04476 15 PDYFTVKATIVFIKPDNWWYPACPGCNKKVVEEGNGTYRCEKCNKSVPNPEYRYILSLNVADHTGEAWLTLFDEVAEQIF 94 (166)
T ss_pred CCEEEEEEEEEEEcCCCeEEccccccCcccEeCCCCcEECCCCCCcCCCccEEEEEEEEEEeCCCCEEEEEehHHHHHHh
Confidence 567888888888877633222222 23678999999999999999999999999999
Q ss_pred c
Q 015600 403 L 403 (404)
Q Consensus 403 ~ 403 (404)
|
T Consensus 95 G 95 (166)
T cd04476 95 G 95 (166)
T ss_pred C
Confidence 7
No 35
>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=95.26 E-value=0.057 Score=44.30 Aligned_cols=84 Identities=13% Similarity=0.182 Sum_probs=62.1
Q ss_pred ehHhhhhccCCEEEEEEEEEecCCceecC---CCceEEEEEEEeCCCCCCCeEEEEecCCCC-CCCCCCCCCCEEEEeeE
Q 015600 12 RIKELAMHVKHKVNLLGVVLEFSIPRKSQ---GTDYVCVLKIVDDSQQSPELLVNIFTSSID-QLPRVLSPRDLILLKNV 87 (404)
Q Consensus 12 ~i~~~~~~~~~~vnv~GVV~d~~~P~~tr---GtD~~~t~~I~D~S~~~~gl~v~iF~~~~~-~LP~v~~~GDII~l~rv 87 (404)
+|+++.. ....+.+.|-|+....++.-+ |.-..++|.|.|+.-.. |.+.+|.+..+ .-|.+ ..|+|+.+.+.
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 PISSLNP-YQNKWTIKARVTNKSDIRTWSNARGEGKLFSFDLLDEDGGE--IRATFFNDAVDKFYDLL-EVGKVYYISKG 76 (104)
T ss_pred ChhHccC-CCCcEEEEEEEeeccccccccCCCCCcEEEEEEEEECCCCE--EEEEEehHHHHHhhccc-ccccEEEEecc
Confidence 4777742 234589999999877766433 34677899999996533 99999986444 45566 89999999999
Q ss_pred EEEEEcCeeEEE
Q 015600 88 MIKKHQAELSAV 99 (404)
Q Consensus 88 ki~~~~g~~~~~ 99 (404)
+|+.-++...-+
T Consensus 77 ~V~~a~~~y~~~ 88 (104)
T cd04474 77 SVKVANKKFNTL 88 (104)
T ss_pred EEeeccccCCCC
Confidence 999887654433
No 36
>PF15489 CTC1: CST, telomere maintenance, complex subunit CTC1
Probab=94.97 E-value=0.16 Score=56.89 Aligned_cols=132 Identities=17% Similarity=0.098 Sum_probs=97.1
Q ss_pred EEEEEecCchhhhhhccCCCCcEEEEeceEEEE-eCcEEEEEEecCCceEEcCCCChHHHHHHHHHHHHHhCCCCCCCCc
Q 015600 238 VLRVSTDRSYENFGRYFTATGKWVRIRNMSCQV-SSGMWHGLLQSSSKIRLFSDNDNVVWDYMRRFRERISGGHGHMPIW 316 (404)
Q Consensus 238 ~l~V~~~~~~~~~~~~~~k~g~wv~l~Nv~~k~-~~g~leG~l~~~ski~~l~~~d~~v~~r~r~y~~~~~~~~~~~~~~ 316 (404)
.|.|.++.+|.-+ -..+-+|.-|.|.+++.|+ .+|+.|..+..+|.|++++-. ++
T Consensus 888 ~ldVYi~~~h~p~-plGLLPGA~V~f~~lerkVSRs~nVYC~~~psS~VtVlS~p-~~---------------------- 943 (1144)
T PF15489_consen 888 HLDVYIEDPHLPY-PLGLLPGARVLFSQLERKVSRSHNVYCCFLPSSSVTVLSFP-PE---------------------- 943 (1144)
T ss_pred eEEEEecCCCCCC-cccccCCceeeeehhhhhhhccCcEEEEEcCCceEEEEecC-cc----------------------
Confidence 5888888888765 5568899999999999999 679999999999999997640 00
Q ss_pred CCCCCCCCcccccCCCccccHHHHhcCCCCCceEEEEEEEEeecCCCcccccc------------------C--CCCcEE
Q 015600 317 TDPSSQFLTEVDWVNVASVTLMKIATQLQGNVRCCCIVRVVSIHPFQAEHYSS------------------P--NGSSEY 376 (404)
Q Consensus 317 ~~p~~~~~t~~~~~~~p~ttL~~IL~~~~~~~kyr~~VRVV~~~P~~l~df~~------------------~--~~~~~~ 376 (404)
...-...|...|.+.+.....+.+.++.++||+++==.|.=-|. + .+....
T Consensus 944 ---------t~~~~~~P~~~L~~~~~~~~~~~~a~~~chVV~V~~l~L~WvCa~C~si~~qg~Csr~~p~C~s~~sV~qA 1014 (1144)
T PF15489_consen 944 ---------TNVSPPLPHIYLAELLQGSQSPFQARVSCHVVSVLSLQLQWVCAHCGSICPQGRCSRQSPPCPSQTSVFQA 1014 (1144)
T ss_pred ---------cCCCCCCCeEEehhhhCCCCCCceEEEEEEEEEEEEEEeeehhhhccCcccCCcCCCCCCCCCCCcceeeE
Confidence 01112456777888887666777888889999887655532222 1 133456
Q ss_pred EEEEEEeCCCceEEEEEecccccccc
Q 015600 377 TMKLTLEDPTARIHALLCGKEWVRFQ 402 (404)
Q Consensus 377 ~f~L~leD~t~~~~~~v~~~da~~f~ 402 (404)
-.+++|||+||+-++.+.|+-...++
T Consensus 1015 ~ar~~vEDGTaeA~v~~~~~~V~~lL 1040 (1144)
T PF15489_consen 1015 SARLLVEDGTAEAVVWCRGHHVAALL 1040 (1144)
T ss_pred EEEEEEecCCeeEEEEECCcHHHHHh
Confidence 77999999999999999886544443
No 37
>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=94.64 E-value=0.37 Score=38.42 Aligned_cols=67 Identities=18% Similarity=0.198 Sum_probs=51.6
Q ss_pred EEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCC----CCCCCCCCCCEEEEeeEEEEEEcCeeEEE
Q 015600 24 VNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSID----QLPRVLSPRDLILLKNVMIKKHQAELSAV 99 (404)
Q Consensus 24 vnv~GVV~d~~~P~~trGtD~~~t~~I~D~S~~~~gl~v~iF~~~~~----~LP~v~~~GDII~l~rvki~~~~g~~~~~ 99 (404)
|.++|+|++... + +=..+++|-|.|= .|.+.++....+ ..+.+ +.|++|++ .-+++.|+|+.|+.
T Consensus 2 v~~vG~V~~~~~----~--~~~~~~tL~D~TG---~I~~~~W~~~~~~~~~~~~~~-~~g~~v~v-~G~v~~~~g~~ql~ 70 (95)
T cd04478 2 VTLVGVVRNVEE----Q--STNITYTIDDGTG---TIEVRQWLDDDNDDSSEVEPI-EEGTYVRV-FGNLKSFQGKKSIM 70 (95)
T ss_pred EEEEEEEEeeeE----c--ccEEEEEEECCCC---cEEEEEeCCCCCccccccccc-ccCCEEEE-EEEEcccCCeeEEE
Confidence 678999999764 1 2347899999874 399999987653 55656 89999998 56779999998877
Q ss_pred ee
Q 015600 100 FY 101 (404)
Q Consensus 100 ~~ 101 (404)
..
T Consensus 71 i~ 72 (95)
T cd04478 71 AF 72 (95)
T ss_pred EE
Confidence 54
No 38
>PRK13480 3'-5' exoribonuclease YhaM; Provisional
Probab=94.53 E-value=0.3 Score=48.17 Aligned_cols=82 Identities=15% Similarity=0.139 Sum_probs=64.1
Q ss_pred ehHhhhhccCCEEEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEE
Q 015600 12 RIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKK 91 (404)
Q Consensus 12 ~i~~~~~~~~~~vnv~GVV~d~~~P~~trGtD~~~t~~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~ 91 (404)
.|+++ +.|..|+.+.+|++...- .+|.+.=...+++.|.|=. |...++....+....+ ..||||.+. -++..
T Consensus 4 ~i~~l--~~g~~v~~~~lv~~~~~~-~~knG~~yl~l~l~D~tG~---I~ak~W~~~~~~~~~~-~~g~vv~v~-G~v~~ 75 (314)
T PRK13480 4 GIEEL--EVGEQVDHFLLIKSATKG-VASNGKPFLTLILQDKSGD---IEAKLWDVSPEDEATY-VPETIVHVK-GDIIN 75 (314)
T ss_pred hHhhc--CCCCEeeEEEEEEEceee-ecCCCCeEEEEEEEcCCcE---EEEEeCCCChhhHhhc-CCCCEEEEE-EEEEE
Confidence 47777 568899999999998763 4553344678999997653 9999998777777777 889999995 56678
Q ss_pred EcCeeEEEee
Q 015600 92 HQAELSAVFY 101 (404)
Q Consensus 92 ~~g~~~~~~~ 101 (404)
|+|++|....
T Consensus 76 y~g~~Ql~i~ 85 (314)
T PRK13480 76 YRGRKQLKVN 85 (314)
T ss_pred ECCcceEEEE
Confidence 9999997764
No 39
>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=94.37 E-value=0.12 Score=39.31 Aligned_cols=71 Identities=14% Similarity=0.285 Sum_probs=50.3
Q ss_pred EEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCeeEEEee
Q 015600 26 LLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAELSAVFY 101 (404)
Q Consensus 26 v~GVV~d~~~P~~trGtD~~~t~~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~~~g~~~~~~~ 101 (404)
+.|+|.+... +.|+.+.-+..++|.|.+-. +.+.+|.+..+.+......|.+|.++ -+++.|+|..+....
T Consensus 2 i~g~v~~~~~-~~~k~g~~~~~~~l~D~tg~---~~~~~f~~~~~~~~~~l~~g~~v~v~-G~v~~~~~~~~l~~~ 72 (84)
T cd04485 2 VAGLVTSVRR-RRTKKGKRMAFVTLEDLTGS---IEVVVFPETYEKYRDLLKEDALLLVE-GKVERRDGGLRLIAE 72 (84)
T ss_pred EEEEEEEeEE-EEcCCCCEEEEEEEEeCCCe---EEEEECHHHHHHHHHHhcCCCEEEEE-EEEEecCCceEEEee
Confidence 6788888765 45554556799999998653 99999976533344434789999886 477878777666543
No 40
>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=94.28 E-value=0.63 Score=37.64 Aligned_cols=63 Identities=11% Similarity=0.028 Sum_probs=42.4
Q ss_pred ceEEEEEecCchhhhhhccCCCCcEEEEeceEEEEeCcEEEEEEecCCceEEcCCCChHHHHHHHHH
Q 015600 236 GTVLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDNDNVVWDYMRRF 302 (404)
Q Consensus 236 G~~l~V~~~~~~~~~~~~~~k~g~wv~l~Nv~~k~~~g~leG~l~~~ski~~l~~~d~~v~~r~r~y 302 (404)
|..+.|++|..+|.... ...|+.+.|+|++++..+|. .......+.|.+-+ +.|++.+.+.-|
T Consensus 38 ~~~i~vtLWg~~a~~~~--~~~~~vv~~~~~~i~~~~~~-~l~~~~~s~i~~np-~~~e~~~l~~w~ 100 (101)
T cd04475 38 GHSVELTLWGEQAELFD--GSENPVIAIKGVKVSEFNGK-SLSTGSSSTIIINP-DIPEAHKLRGWY 100 (101)
T ss_pred CCEEEEEEEHHHhhhcc--cCCCCEEEEEeeEEEecCCe-EEeecCceeEEECC-CcHHHHHHHHhh
Confidence 44788999998876433 22399999999999886653 33444455665444 577777776543
No 41
>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=93.69 E-value=0.22 Score=38.77 Aligned_cols=46 Identities=20% Similarity=0.110 Sum_probs=39.5
Q ss_pred EEEEEecCchhhhhhccCCCCcEEEEeceEEEEeCcEEEEEEecCCceE
Q 015600 238 VLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIR 286 (404)
Q Consensus 238 ~l~V~~~~~~~~~~~~~~k~g~wv~l~Nv~~k~~~g~leG~l~~~ski~ 286 (404)
.+++++|+..+ ...+++|++|+++|..++...|.++..+...+.|.
T Consensus 35 ~i~~~~W~~~~---~~~~~~G~vv~i~~~~v~~~~g~~ql~i~~~~~i~ 80 (82)
T cd04491 35 TIRFTLWDEKA---ADDLEPGDVVRIENAYVREFNGRLELSVGKNSEIE 80 (82)
T ss_pred EEEEEEECchh---cccCCCCCEEEEEeEEEEecCCcEEEEeCCceEEE
Confidence 78999999865 57799999999999999998898988888776664
No 42
>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=93.65 E-value=0.68 Score=35.37 Aligned_cols=69 Identities=12% Similarity=0.227 Sum_probs=50.3
Q ss_pred EEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCeeEEEee
Q 015600 27 LGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAELSAVFY 101 (404)
Q Consensus 27 ~GVV~d~~~P~~trGtD~~~t~~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~~~g~~~~~~~ 101 (404)
+.+|.+++. +.|+.+.-+..++|-|.+-. +.+.+|.+.....+.+ ..|.+|.++ .++..++|+.+....
T Consensus 3 ~~~v~~~~~-~~tk~g~~~~~~~l~D~tg~---i~~~~f~~~~~~~~~l-~~g~~v~v~-G~v~~~~~~~~l~~~ 71 (83)
T cd04492 3 FFLIKSKEL-RTAKNGKPYLALTLQDKTGE---IEAKLWDASEEDEEKF-KPGDIVHVK-GRVEEYRGRLQLKIQ 71 (83)
T ss_pred EEEEEEeee-ecccCCCcEEEEEEEcCCCe---EEEEEcCCChhhHhhC-CCCCEEEEE-EEEEEeCCceeEEEE
Confidence 457777776 45665556899999998763 9999998655444555 789999997 677778776666543
No 43
>cd04483 hOBFC1_like hOBFC1_like: A subfamily of OB folds similar to that found in human OB fold containing protein 1 (hOBFC1). Members of this group belong to the Replication protein A subunit 2 (RPA2) family of OB folds. RPA is a nuclear ssDNA binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The OB fold domain of RPA2 has dual roles in ssDNA binding and trimerization.
Probab=93.15 E-value=0.88 Score=36.47 Aligned_cols=65 Identities=15% Similarity=0.125 Sum_probs=48.4
Q ss_pred EEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCC---------------------CCCCCCCCCCCEEEE
Q 015600 26 LLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSI---------------------DQLPRVLSPRDLILL 84 (404)
Q Consensus 26 v~GVV~d~~~P~~trGtD~~~t~~I~D~S~~~~gl~v~iF~~~~---------------------~~LP~v~~~GDII~l 84 (404)
++|+|+.... +.+ ..+|+|-|.|= . |.|.++.... +..+.+ ++|++|++
T Consensus 2 ivG~V~sv~~----~~~--~~~~tLdDgTG-~--Ie~~~W~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i-~~G~vvrV 71 (92)
T cd04483 2 ILGTVVSRRE----RET--FYSFGVDDGTG-V--VNCVCWKNLSYAEVSSRSDAARILKSALMALKQAKVL-EIGDLLRV 71 (92)
T ss_pred eEEEEEEEEe----cCC--eEEEEEecCCc-e--EEEEEEcCcCccccccccccccccccccccccccccc-CCCCEEEE
Confidence 6899998753 211 37788888665 2 8999997543 344556 89999999
Q ss_pred eeEEEEEEcCeeEEEee
Q 015600 85 KNVMIKKHQAELSAVFY 101 (404)
Q Consensus 85 ~rvki~~~~g~~~~~~~ 101 (404)
+ -+++.|+|+.|+...
T Consensus 72 ~-G~i~~frg~~ql~i~ 87 (92)
T cd04483 72 R-GSIRTYRGEREINAS 87 (92)
T ss_pred E-EEEeccCCeeEEEEE
Confidence 6 789999999888764
No 44
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain
Probab=91.64 E-value=1.8 Score=35.15 Aligned_cols=79 Identities=20% Similarity=0.221 Sum_probs=54.5
Q ss_pred hHhhhhcc--CCEEEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCC-CCCCCCCEEEEeeEEE
Q 015600 13 IKELAMHV--KHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLP-RVLSPRDLILLKNVMI 89 (404)
Q Consensus 13 i~~~~~~~--~~~vnv~GVV~d~~~P~~trGtD~~~t~~I~D~S~~~~gl~v~iF~~~~~~LP-~v~~~GDII~l~rvki 89 (404)
|+++++.. -..+-|.|=|.+++.. ++| .+-|+|+|+. ..++|.+|+.....++ ...+.||-|++ +.++
T Consensus 11 ik~~le~~~~~~~vwV~GEIs~~~~~--~~g---h~YftLkD~~---a~i~~~~~~~~~~~i~~~~l~~G~~V~v-~g~~ 81 (99)
T PF13742_consen 11 IKDLLERDPPLPNVWVEGEISNLKRH--SSG---HVYFTLKDEE---ASISCVIFRSRARRIRGFDLKDGDKVLV-RGRV 81 (99)
T ss_pred HHHHHhcCCCcCCEEEEEEEeecEEC--CCc---eEEEEEEcCC---cEEEEEEEHHHHhhCCCCCCCCCCEEEE-EEEE
Confidence 45555532 3679999999998864 333 4778999965 3499999998777787 44488996666 3455
Q ss_pred EEE--cCeeEEEe
Q 015600 90 KKH--QAELSAVF 100 (404)
Q Consensus 90 ~~~--~g~~~~~~ 100 (404)
..| .|++++..
T Consensus 82 ~~y~~~G~~sl~v 94 (99)
T PF13742_consen 82 SFYEPRGSLSLIV 94 (99)
T ss_pred EEECCCcEEEEEE
Confidence 555 45566554
No 45
>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=90.75 E-value=0.16 Score=44.13 Aligned_cols=32 Identities=22% Similarity=0.237 Sum_probs=29.1
Q ss_pred CCcEEEEEEEEeCCCceEEEEEeccccccccc
Q 015600 372 GSSEYTMKLTLEDPTARIHALLCGKEWVRFQL 403 (404)
Q Consensus 372 ~~~~~~f~L~leD~t~~~~~~v~~~da~~f~~ 403 (404)
..|.|++.+.|.|.|+.+.+.++|+.|++|||
T Consensus 50 ~~~ry~l~~~i~D~tg~~~~~~F~~~a~~l~G 81 (146)
T PF08646_consen 50 PKYRYRLSLKISDGTGSIWVTLFDEEAEQLLG 81 (146)
T ss_dssp -EEEEEEEEEEEETTEEEEEEEEHHHHHHHHC
T ss_pred eeEEEEEEEEEEeCCCeEEEEEEhHHHHHHhC
Confidence 46789999999999999999999999999995
No 46
>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=86.83 E-value=7.3 Score=29.73 Aligned_cols=65 Identities=11% Similarity=0.120 Sum_probs=41.5
Q ss_pred EEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCC-EEEEeeEEEEEEcCeeEEEee
Q 015600 26 LLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRD-LILLKNVMIKKHQAELSAVFY 101 (404)
Q Consensus 26 v~GVV~d~~~P~~trGtD~~~t~~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GD-II~l~rvki~~~~g~~~~~~~ 101 (404)
|-|.|..+.. +|.. +-|+|.|+.. .|.|.+|+.....++.....|| |+..-++.+ .+|+.|+...
T Consensus 3 v~GeVs~~~~----~~GH--vyfsLkD~~a---~i~cv~f~~~~~~~~~~l~~Gd~V~v~G~v~~--~~G~~ql~v~ 68 (73)
T cd04487 3 IEGEVVQIKQ----TSGP--TIFTLRDETG---TVWAAAFEEAGVRAYPEVEVGDIVRVTGEVEP--RDGQLQIEVE 68 (73)
T ss_pred EEEEEecccc----CCCC--EEEEEEcCCE---EEEEEEEchhccCCcCCCCCCCEEEEEEEEec--CCeEEEEEEe
Confidence 4566776653 3444 4567888653 3999999876545655448899 555555554 6677776653
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=86.10 E-value=10 Score=27.16 Aligned_cols=65 Identities=20% Similarity=0.187 Sum_probs=42.0
Q ss_pred eEEEEEEEEEeeCC--CCeEEEEEEcCCCCCCCCCCCCCCCccCCCCCccccCCCCChhhhccCCCCceEEEEEecCchh
Q 015600 171 DLVCKVFHVSYDDS--KGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRVSTDRSYE 248 (404)
Q Consensus 171 Dl~~qVv~~~~~~~--~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~pp~G~~l~V~~~~~~~ 248 (404)
++.|+|+++. ... .....+.+.|+| |..+.+.+|....
T Consensus 1 ~v~g~v~~~~-~~~~~~~~~~~~l~D~~---------------------------------------~~~i~~~~~~~~~ 40 (75)
T cd03524 1 TIVGIVVAVE-EIRTEGKVLIFTLTDGT---------------------------------------GGTIRVTLFGELA 40 (75)
T ss_pred CeEEEEEeec-ccccCCeEEEEEEEcCC---------------------------------------CCEEEEEEEchHH
Confidence 4678888887 422 356777788866 1144677777654
Q ss_pred hhhhccCCCCcEEEEeceEEEEeCcEEE
Q 015600 249 NFGRYFTATGKWVRIRNMSCQVSSGMWH 276 (404)
Q Consensus 249 ~~~~~~~k~g~wv~l~Nv~~k~~~g~le 276 (404)
.-....+++|+++.+. .+++..+|.++
T Consensus 41 ~~~~~~~~~g~~v~v~-g~v~~~~~~~~ 67 (75)
T cd03524 41 EELENLLKEGQVVYIK-GKVKKFRGRLQ 67 (75)
T ss_pred HHHHhhccCCCEEEEE-EEEEecCCeEE
Confidence 3334568999999887 66665554443
No 48
>cd04488 RecG_wedge_OBF RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal (wedge) domain of Escherichia coli RecG. RecG is a branched-DNA-specific helicase, which catalyzes the interconversion of a DNA replication fork to a four-stranded (Holliday) junction in vivo and in vitro. This interconversion provides a route to repair stalled forks. The RecG monomer contains three domains. The N-terminal domain is named for its wedge structure, and may provide the specificity of RecG for binding branched-DNA structures. During the reversal of fork to Holliday junction, the wedge domain is fixed at the junction of the fork where the leading and lagging strand duplex arms meet, and is thought to promote the unwinding of the nascent leading and lagging strands. In order to form the Holliday junction, these nascent strands would be annealed, and the parental strands reannealed. The wedge domain may also be a processivity factor of RecG on these branched cha
Probab=85.56 E-value=5.8 Score=29.13 Aligned_cols=68 Identities=18% Similarity=0.273 Sum_probs=44.3
Q ss_pred EEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCeeEEEe
Q 015600 26 LLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAELSAVF 100 (404)
Q Consensus 26 v~GVV~d~~~P~~trGtD~~~t~~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~~~g~~~~~~ 100 (404)
+.|.|++.... +++|.. ...+++.|.+- .+.+.+|.... .+......|+.+.+. -|+..|+|+++...
T Consensus 2 i~~~V~~~~~~-~~~~~~-~~~~~~~D~~g---~i~~~~F~~~~-~~~~~~~~G~~~~v~-Gkv~~~~~~~qi~~ 69 (75)
T cd04488 2 VEGTVVSVEVV-PRRGRR-RLKVTLSDGTG---TLTLVFFNFQP-YLKKQLPPGTRVRVS-GKVKRFRGGLQIVH 69 (75)
T ss_pred EEEEEEEEEec-cCCCcc-EEEEEEEcCCC---EEEEEEECCCH-HHHhcCCCCCEEEEE-EEEeecCCeeEEeC
Confidence 56777776432 223333 78999999854 39999997322 333434789988885 56677877766554
No 49
>PF09104 BRCA-2_OB3: BRCA2, oligonucleotide/oligosaccharide-binding, domain 3; InterPro: IPR015188 This domain assumes an OB fold, which consists of a highly curved five-stranded beta-sheet that closes on itself to form a beta-barrel. OB3 has a pronounced groove formed by one face of the curved sheet and is demarcated by two loops, one between beta 1 and beta 2 and another between beta 4 and beta 5, which allows for strong ssDNA binding []. ; PDB: 1IYJ_D 1MIU_A.
Probab=84.80 E-value=7.9 Score=33.62 Aligned_cols=62 Identities=18% Similarity=0.213 Sum_probs=36.1
Q ss_pred ceEeEEEEEEEEEeeCCCCe-EEEEEEcCCCCCCCCCCCCCCCccCCCCCccccCCCCChhhhccCCCCceEEEEEecCc
Q 015600 168 RYFDLVCKVFHVSYDDSKGL-WMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRVSTDRS 246 (404)
Q Consensus 168 ~f~Dl~~qVv~~~~~~~~~~-~~L~VwDgT~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~pp~G~~l~V~~~~~ 246 (404)
+-||+++-|+.|. . ..+- -.+|+.|.--| .|.|.+|..
T Consensus 19 ~EvD~VG~VvsV~-~-~~~f~~~vYLsD~~~N---------------------------------------ll~Ikfw~~ 57 (143)
T PF09104_consen 19 GEVDTVGFVVSVS-K-KQGFQPLVYLSDECHN---------------------------------------LLAIKFWTG 57 (143)
T ss_dssp CEEEEEEEEEEEE----TTS--EEEEE-TTS----------------------------------------EEEEEESS-
T ss_pred cccceEEEEEEEE-e-cCCCceeEEeecCCcc---------------------------------------EEEEEeccC
Confidence 4599999999997 5 3343 45888874211 456889988
Q ss_pred hhhhhhcc-CCCCcEEEEeceEEEE
Q 015600 247 YENFGRYF-TATGKWVRIRNMSCQV 270 (404)
Q Consensus 247 ~~~~~~~~-~k~g~wv~l~Nv~~k~ 270 (404)
-..++.+. +++|..|...||+-+.
T Consensus 58 l~~~~~eDilk~~~liA~SNLqwR~ 82 (143)
T PF09104_consen 58 LNQYGYEDILKPGSLIAASNLQWRP 82 (143)
T ss_dssp ------SS---TT-EEEEEEEEE-S
T ss_pred ccccchhhhcCcceEEEEeeeEeec
Confidence 77777765 6999999999999886
No 50
>PRK07373 DNA polymerase III subunit alpha; Reviewed
Probab=83.54 E-value=4 Score=42.35 Aligned_cols=89 Identities=16% Similarity=0.202 Sum_probs=62.9
Q ss_pred cceeehHhhhh-ccCCEEEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEee
Q 015600 8 GGIVRIKELAM-HVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKN 86 (404)
Q Consensus 8 y~y~~i~~~~~-~~~~~vnv~GVV~d~~~P~~trGtD~~~t~~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~r 86 (404)
++.+++.++.. ..++.|.+.|+|...+.+ +|+.++-++-++|-|.+-. +.+.+|.+.-+..-.....|.+|+++.
T Consensus 266 ~~~~~~~~l~~~~~~~~v~vaG~I~~ik~~-~TKkG~~maf~~leD~tG~---ie~vvFp~~y~~~~~~l~~~~~v~v~G 341 (449)
T PRK07373 266 LSPINLSELEEQKEKTKVSAVVMLNEVKKI-VTKKGDPMAFLQLEDLSGQ---SEAVVFPKSYERISELLQVDARLIIWG 341 (449)
T ss_pred cCCcCHHHHhcccCCCEEEEEEEEEEeEec-ccCCCCEEEEEEEEECCCC---EEEEECHHHHHHHHHHhccCCEEEEEE
Confidence 34456777642 246789999999999874 5665678999999999764 999999865555545447788888854
Q ss_pred EEEEEEcCeeEEEee
Q 015600 87 VMIKKHQAELSAVFY 101 (404)
Q Consensus 87 vki~~~~g~~~~~~~ 101 (404)
+++.-.++.+.+.+
T Consensus 342 -~v~~~~~~~~liv~ 355 (449)
T PRK07373 342 -KVDRRDDQVQLIVE 355 (449)
T ss_pred -EEEecCCeEEEEEe
Confidence 66653455666554
No 51
>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=81.69 E-value=15 Score=28.51 Aligned_cols=70 Identities=17% Similarity=0.259 Sum_probs=47.5
Q ss_pred EEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEec-CCCCCCCCCCC-CCCEEEEeeE-EEEEEcCeeEE
Q 015600 24 VNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFT-SSIDQLPRVLS-PRDLILLKNV-MIKKHQAELSA 98 (404)
Q Consensus 24 vnv~GVV~d~~~P~~trGtD~~~t~~I~D~S~~~~gl~v~iF~-~~~~~LP~v~~-~GDII~l~rv-ki~~~~g~~~~ 98 (404)
|-+-|-|-+... +.+|.+-...+|.|+|-+ +++.|.+|. +..+.+-.+ + .||-|+++.- ....|.++...
T Consensus 2 v~i~G~Vf~~e~-re~k~g~~i~~~~itD~t---~Si~~K~F~~~~~~~~~~i-k~~G~~v~v~G~v~~D~f~~e~~~ 74 (82)
T cd04484 2 VVVEGEVFDLEI-RELKSGRKILTFKVTDYT---SSITVKKFLRKDEKDKEEL-KSKGDWVRVRGKVQYDTFSKELVL 74 (82)
T ss_pred EEEEEEEEEEEE-EEecCCCEEEEEEEEcCC---CCEEEEEeccCChhHHhhc-ccCCCEEEEEEEEEEccCCCceEE
Confidence 345666666543 556666889999999965 459999998 344555556 5 8999988654 44456555443
No 52
>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=80.78 E-value=9.9 Score=33.03 Aligned_cols=73 Identities=18% Similarity=0.286 Sum_probs=42.7
Q ss_pred eehHhhhh----ccCCEEEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCC-CCCCCCCCCCCEEEEe
Q 015600 11 VRIKELAM----HVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSI-DQLPRVLSPRDLILLK 85 (404)
Q Consensus 11 ~~i~~~~~----~~~~~vnv~GVV~d~~~P~~trGtD~~~t~~I~D~S~~~~gl~v~iF~~~~-~~LP~v~~~GDII~l~ 85 (404)
+.+.++.+ .+-+-|+++|+|+.. ++++++.--+-|.|+...- +.|+++..-. -.+-.+..+|-+|-+.
T Consensus 4 ~~f~~l~~p~f~pp~~EvD~VG~VvsV-----~~~~~f~~~vYLsD~~~Nl--l~Ikfw~~l~~~~~eDilk~~~liA~S 76 (143)
T PF09104_consen 4 THFSDLQDPDFQPPYGEVDTVGFVVSV-----SKKQGFQPLVYLSDECHNL--LAIKFWTGLNQYGYEDILKPGSLIAAS 76 (143)
T ss_dssp --CGGGGSTT--TCCCEEEEEEEEEEE-----E--TTS--EEEEE-TTS-E--EEEEESS-------SS---TT-EEEEE
T ss_pred echhhhcCcccCCCccccceEEEEEEE-----EecCCCceeEEeecCCccE--EEEEeccCccccchhhhcCcceEEEEe
Confidence 34455544 234569999999999 4557888888999999864 8888887532 2334455789999999
Q ss_pred eEEEE
Q 015600 86 NVMIK 90 (404)
Q Consensus 86 rvki~ 90 (404)
|++-+
T Consensus 77 NLqwR 81 (143)
T PF09104_consen 77 NLQWR 81 (143)
T ss_dssp EEEE-
T ss_pred eeEee
Confidence 99887
No 53
>cd04490 PolII_SU_OBF PolII_SU_OBF: A subfamily of OB folds corresponding to the OB fold found in Pyrococcus abyssi DNA polymerase II (PolII) small subunit. PolII is a family D DNA polymerase, having a 3-prime to 5-prime exonuclease activity. P. abyssi PolII is heterodimeric. The large subunit appears to be the polymerase, and the small subunit may be the exonuclease. The small subunit contains a calcineurin-like phosphatase superfamily domain C-terminal to this OB-fold domain.
Probab=80.63 E-value=6.4 Score=30.50 Aligned_cols=59 Identities=14% Similarity=0.317 Sum_probs=42.1
Q ss_pred EEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCC--CCCCCCCCCCEEEEeeEEEEE
Q 015600 24 VNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSID--QLPRVLSPRDLILLKNVMIKK 91 (404)
Q Consensus 24 vnv~GVV~d~~~P~~trGtD~~~t~~I~D~S~~~~gl~v~iF~~~~~--~LP~v~~~GDII~l~rvki~~ 91 (404)
+.+.|+|.+.+ .||.++- .++|-|.+-. +.|.+|.+..+ ..-.....|.+|.++. ++..
T Consensus 2 v~i~GiI~~v~---~TK~g~~--~~~leD~~G~---~Ev~~F~~~~~~~~~~~~l~~d~~v~v~g-~v~~ 62 (79)
T cd04490 2 VSIIGMVNDVR---STKNGHR--IVELEDTTGR---ITVLLTKDKEELFEEAEDILPDEVIGVSG-TVSK 62 (79)
T ss_pred EEEEEEEeEEE---EcCCCCE--EEEEECCCCE---EEEEEeCchhhhhhhhhhccCCCEEEEEE-EEec
Confidence 56899999999 4543333 7888888653 99999998777 5555546677777754 5544
No 54
>PF12100 DUF3576: Domain of unknown function (DUF3576); InterPro: IPR021959 This presumed domain is functionally uncharacterised. This domain is found in bacteria. This domain is about 100 amino acids in length. This domain has a single completely conserved residue G that may be functionally important.
Probab=78.42 E-value=5.1 Score=32.70 Aligned_cols=54 Identities=17% Similarity=0.303 Sum_probs=39.6
Q ss_pred cceeehHhhhhccCCEEEEEEEEEe-cCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCC
Q 015600 8 GGIVRIKELAMHVKHKVNLLGVVLE-FSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSS 68 (404)
Q Consensus 8 y~y~~i~~~~~~~~~~vnv~GVV~d-~~~P~~trGtD~~~t~~I~D~S~~~~gl~v~iF~~~ 68 (404)
-.|+||..+- ..|+ | +|.| +++| .+.+.-|+.++.|.|.-+..++|+|.+|++.
T Consensus 16 LsFmPl~saD-~~gG-V----I~TdWY~~p-~~~~er~k~tv~Ild~~Lradal~V~vf~q~ 70 (103)
T PF12100_consen 16 LSFMPLASAD-PFGG-V----IVTDWYSPP-PGPNERFKATVYILDRALRADALRVSVFRQV 70 (103)
T ss_pred HhhcchhhcC-CCCC-E----EEeccccCC-CCCCeeEEEEEEEECccccCCceEEEEEEee
Confidence 3577777773 1332 2 4667 4555 4446799999999999999899999999864
No 55
>PRK05673 dnaE DNA polymerase III subunit alpha; Validated
Probab=78.34 E-value=5.9 Score=45.86 Aligned_cols=88 Identities=14% Similarity=0.224 Sum_probs=63.7
Q ss_pred ceeehHhhhh-ccCCEEEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeE
Q 015600 9 GIVRIKELAM-HVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNV 87 (404)
Q Consensus 9 ~y~~i~~~~~-~~~~~vnv~GVV~d~~~P~~trGtD~~~t~~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rv 87 (404)
+.+++.++.. ..+..|.+.|+|...+.+ +||.++-++.++|-|.+-. +.+.+|.+..+..=.....|.+|.+. .
T Consensus 964 ~~~~~~~l~~~~~g~~V~v~G~I~~vk~~-~TKkG~~mafltLeD~TG~---iEvviFp~~ye~~~~~L~~g~iV~V~-G 1038 (1135)
T PRK05673 964 RDTRLADLEPTEGGSVVTVAGLVVSVRRR-VTKRGNKMAIVTLEDLSGR---IEVMLFSEALEKYRDLLEEDRIVVVK-G 1038 (1135)
T ss_pred CCcCHHHHhccccCceEEEEEEEEEEEec-ccCCCCeEEEEEEEeCCCc---EEEEECHHHHHHHHHHhccCCEEEEE-E
Confidence 3456667642 247789999999999885 5655567899999999763 99999986534333333789999884 4
Q ss_pred EEEEEcCeeEEEee
Q 015600 88 MIKKHQAELSAVFY 101 (404)
Q Consensus 88 ki~~~~g~~~~~~~ 101 (404)
+++...++.+.+.+
T Consensus 1039 kVe~~~~~~qlii~ 1052 (1135)
T PRK05673 1039 QVSFDDGGLRLTAR 1052 (1135)
T ss_pred EEEecCCeEEEEEe
Confidence 77777677777765
No 56
>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=78.02 E-value=25 Score=25.83 Aligned_cols=59 Identities=17% Similarity=0.086 Sum_probs=40.6
Q ss_pred eEEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCCccCCCCCccccCCCCChhhhccCCCCceEEEEEecCchhhh
Q 015600 171 DLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRVSTDRSYENF 250 (404)
Q Consensus 171 Dl~~qVv~~~~~~~~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~pp~G~~l~V~~~~~~~~~ 250 (404)
.+.+.|.++. ...+....+.+.|+|+ .+++.+|......
T Consensus 2 ~v~G~V~~~~-~~~~~~~~~~l~D~tg----------------------------------------~i~~~~~~~~~~~ 40 (75)
T PF01336_consen 2 TVEGRVTSIR-RSGGKIVFFTLEDGTG----------------------------------------SIQVVFFNEEYER 40 (75)
T ss_dssp EEEEEEEEEE-EEETTEEEEEEEETTE----------------------------------------EEEEEEETHHHHH
T ss_pred EEEEEEEEEE-cCCCCEEEEEEEECCc----------------------------------------cEEEEEccHHhhH
Confidence 4678888885 3356778888888772 4577888844444
Q ss_pred hhccCCCCcEEEEeceEEEEe
Q 015600 251 GRYFTATGKWVRIRNMSCQVS 271 (404)
Q Consensus 251 ~~~~~k~g~wv~l~Nv~~k~~ 271 (404)
..+.+++|++|++. =.++..
T Consensus 41 ~~~~l~~g~~v~v~-G~v~~~ 60 (75)
T PF01336_consen 41 FREKLKEGDIVRVR-GKVKRY 60 (75)
T ss_dssp HHHTS-TTSEEEEE-EEEEEE
T ss_pred HhhcCCCCeEEEEE-EEEEEE
Confidence 47889999999987 344443
No 57
>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=76.00 E-value=21 Score=36.96 Aligned_cols=81 Identities=15% Similarity=0.269 Sum_probs=54.7
Q ss_pred hHhhhhccCCEEEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEE-eeEEEEE
Q 015600 13 IKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILL-KNVMIKK 91 (404)
Q Consensus 13 i~~~~~~~~~~vnv~GVV~d~~~P~~trGtD~~~t~~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l-~rvki~~ 91 (404)
|+.+++..=..|-|-|=|..++.+ +.| .+-|+|+|..- -|+|.+|+.....|+.-.+.|+=|++ -++.+-.
T Consensus 9 ik~~le~~~~~v~V~GEisn~~~~--~sG---H~YFtLkD~~a---~i~~vmf~~~~~~l~f~~~~G~~V~v~g~v~~y~ 80 (432)
T TIGR00237 9 IKALLEATFLQVWIQGEISNFTQP--VSG---HWYFTLKDENA---QVRCVMFRGNNNRLKFRPQNGQQVLVRGGISVYE 80 (432)
T ss_pred HHHHHHhhCCcEEEEEEecCCeeC--CCc---eEEEEEEcCCc---EEEEEEEcChhhCCCCCCCCCCEEEEEEEEEEEC
Confidence 455555322368889999998853 344 57788999753 39999999877788776688996655 3344444
Q ss_pred EcCeeEEEee
Q 015600 92 HQAELSAVFY 101 (404)
Q Consensus 92 ~~g~~~~~~~ 101 (404)
-.|++|+...
T Consensus 81 ~~G~~ql~v~ 90 (432)
T TIGR00237 81 PRGDYQIICF 90 (432)
T ss_pred CCCcEEEEEE
Confidence 4555666653
No 58
>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=75.60 E-value=3.3 Score=35.06 Aligned_cols=34 Identities=15% Similarity=0.338 Sum_probs=28.2
Q ss_pred eEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcC
Q 015600 60 LLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQA 94 (404)
Q Consensus 60 l~v~iF~~~~~~LP~v~~~GDII~l~rvki~~~~g 94 (404)
|.|.+|-++.+..-.+ +.||.|+|+||.++....
T Consensus 62 i~It~yD~H~~~ar~l-K~GdfV~L~NVhiK~~~~ 95 (123)
T cd04498 62 IDILVYDNHVELAKSL-KPGDFVRIYNVHAKSYSS 95 (123)
T ss_pred EEEEEEcchHHHHhhC-CCCCEEEEEEEEEEeccC
Confidence 7778888877766666 899999999999987766
No 59
>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed
Probab=74.53 E-value=23 Score=36.44 Aligned_cols=80 Identities=16% Similarity=0.179 Sum_probs=53.1
Q ss_pred HhhhhccCCEEEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEE-eeEEEEEE
Q 015600 14 KELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILL-KNVMIKKH 92 (404)
Q Consensus 14 ~~~~~~~~~~vnv~GVV~d~~~P~~trGtD~~~t~~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l-~rvki~~~ 92 (404)
+.+++..-..|-|-|=|..++.+ +.| .+-|+|+|... .|+|.+|+.....++.-.+.|+-|.+ -++.+-.-
T Consensus 16 k~~le~~~~~v~v~gEis~~~~~--~sG---H~Yf~Lkd~~a---~i~~~~~~~~~~~~~~~~~~G~~v~v~g~~~~y~~ 87 (438)
T PRK00286 16 KSLLERDLGQVWVRGEISNFTRH--SSG---HWYFTLKDEIA---QIRCVMFKGSARRLKFKPEEGMKVLVRGKVSLYEP 87 (438)
T ss_pred HHHHHhhCCcEEEEEEeCCCeeC--CCC---eEEEEEEcCCc---EEEEEEEcChhhcCCCCCCCCCEEEEEEEEEEECC
Confidence 34443324468888988888764 334 56789999943 49999999887888875588996665 33444333
Q ss_pred cCeeEEEee
Q 015600 93 QAELSAVFY 101 (404)
Q Consensus 93 ~g~~~~~~~ 101 (404)
.|+++....
T Consensus 88 ~g~~ql~v~ 96 (438)
T PRK00286 88 RGDYQLIVE 96 (438)
T ss_pred CCCEEEEEE
Confidence 455666553
No 60
>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=74.41 E-value=13 Score=29.54 Aligned_cols=60 Identities=20% Similarity=0.332 Sum_probs=37.7
Q ss_pred EEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCC--CCCCCCCCCCCCEEEEeeEEEEEEc
Q 015600 26 LLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSS--IDQLPRVLSPRDLILLKNVMIKKHQ 93 (404)
Q Consensus 26 v~GVV~d~~~P~~trGtD~~~t~~I~D~S~~~~gl~v~iF~~~--~~~LP~v~~~GDII~l~rvki~~~~ 93 (404)
|-|-|..+.. .-+|.. +-|+|.|++. .|.|.+|+++ ...+..-.+.||-|.+..- +..|.
T Consensus 3 v~GeVs~~~~--~~~sGH--~yFtlkD~~~---~i~cv~f~~~g~~~~~~~~l~~Gd~V~v~G~-v~~y~ 64 (91)
T cd04482 3 VTGKVVEEPR--TIEGGH--VFFKISDGTG---EIDCAAYEPTKEFRDVVRLLIPGDEVTVYGS-VRPGT 64 (91)
T ss_pred EEEEEeCCee--cCCCCC--EEEEEECCCc---EEEEEEECcccccccccCCCCCCCEEEEEEE-EecCC
Confidence 4566666553 213344 5568889763 4999999976 4456554489997777543 45444
No 61
>KOG1030 consensus Predicted Ca2+-dependent phospholipid-binding protein [General function prediction only]
Probab=72.71 E-value=8 Score=34.50 Aligned_cols=27 Identities=15% Similarity=0.277 Sum_probs=25.4
Q ss_pred CCcEEEEEEEEeCCCceEEEEEecccc
Q 015600 372 GSSEYTMKLTLEDPTARIHALLCGKEW 398 (404)
Q Consensus 372 ~~~~~~f~L~leD~t~~~~~~v~~~da 398 (404)
-+|.+.|-|+|.|+...+.+-||++|-
T Consensus 51 PeWNe~ltf~v~d~~~~lkv~VyD~D~ 77 (168)
T KOG1030|consen 51 PEWNEELTFTVKDPNTPLKVTVYDKDT 77 (168)
T ss_pred CcccceEEEEecCCCceEEEEEEeCCC
Confidence 489999999999999999999999994
No 62
>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=71.85 E-value=9.4 Score=31.06 Aligned_cols=36 Identities=19% Similarity=0.059 Sum_probs=30.3
Q ss_pred ceEEEEEecCchhhhhhccCCCCcEEEEeceEEEEe
Q 015600 236 GTVLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVS 271 (404)
Q Consensus 236 G~~l~V~~~~~~~~~~~~~~k~g~wv~l~Nv~~k~~ 271 (404)
|..+++++|...+..-...+++|+++.+.|-+++..
T Consensus 46 ~~~I~~t~~~~~~~~f~~~l~eG~vy~i~~~~V~~a 81 (104)
T cd04474 46 GGEIRATFFNDAVDKFYDLLEVGKVYYISKGSVKVA 81 (104)
T ss_pred CCEEEEEEehHHHHHhhcccccccEEEEeccEEeec
Confidence 558899999876654467899999999999999884
No 63
>PRK06920 dnaE DNA polymerase III DnaE; Reviewed
Probab=71.74 E-value=12 Score=43.20 Aligned_cols=89 Identities=10% Similarity=0.169 Sum_probs=62.4
Q ss_pred cceeehHhhhhccCCEEEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeE
Q 015600 8 GGIVRIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNV 87 (404)
Q Consensus 8 y~y~~i~~~~~~~~~~vnv~GVV~d~~~P~~trGtD~~~t~~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rv 87 (404)
++.+++.++....+..|.+.|+|+..+.+ +|+..+-+.-++|-|.+-. +.+.+|.+.-+..-.....|.+|++. -
T Consensus 930 ~~~~~~~~l~~~~~~~v~v~g~i~~~~~~-~tk~g~~maf~~leD~tg~---~e~~vFp~~y~~~~~~l~~~~~~~v~-G 1004 (1107)
T PRK06920 930 LEIPSLAQAMRHKKKVQRAIVYITSVKVI-RTKKGQKMAFITFCDQNDE---MEAVVFPETYIHFSDKLQEGAIVLVD-G 1004 (1107)
T ss_pred hCCcCHHHHhhcCCCEEEEEEEEEEeEee-cCCCCCeEEEEEEeeCCCc---EEEEECHHHHHHHHHHhccCCEEEEE-E
Confidence 34456777743346689999999999874 5555577899999998763 99999986545544444678888884 4
Q ss_pred EEEEEcCeeEEEee
Q 015600 88 MIKKHQAELSAVFY 101 (404)
Q Consensus 88 ki~~~~g~~~~~~~ 101 (404)
+++.-.++.+.+.+
T Consensus 1005 ~v~~~~~~~~~~~~ 1018 (1107)
T PRK06920 1005 TIELRNHKLQWIVN 1018 (1107)
T ss_pred EEEecCCcEEEEEe
Confidence 66654555666654
No 64
>KOG3056 consensus Protein required for S-phase initiation or completion [Cell cycle control, cell division, chromosome partitioning]
Probab=70.98 E-value=6.8 Score=41.15 Aligned_cols=69 Identities=20% Similarity=0.296 Sum_probs=56.5
Q ss_pred EEEEEEEEecCCceecC-CCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCe
Q 015600 24 VNLLGVVLEFSIPRKSQ-GTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAE 95 (404)
Q Consensus 24 vnv~GVV~d~~~P~~tr-GtD~~~t~~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~~~g~ 95 (404)
--++|||++-..|+.|. |.+|+ .++|.|-... .-|.|-+|.+.-+.+=.+ +.|+||-|-|..|-..++.
T Consensus 188 Wvt~GvI~~K~~~K~t~~G~~y~-iwkL~dLk~~-q~vslfLFG~a~k~~wk~-k~GtVialLNp~v~k~~~g 257 (578)
T KOG3056|consen 188 WVTMGVIVEKSDPKFTSNGNPYS-IWKLTDLKDH-QTVSLFLFGKAHKRYWKI-KLGTVIALLNPEVLKDRPG 257 (578)
T ss_pred eEEEEEEeecCCcccccCCCceE-EEEeeecCcc-ceeEEEEecHHHHHHhhh-ccCcEEEEeCccccCCCCC
Confidence 44899999999999885 66654 5788887664 459999999877888888 7899999999999877654
No 65
>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=70.21 E-value=21 Score=29.03 Aligned_cols=64 Identities=19% Similarity=0.249 Sum_probs=44.1
Q ss_pred EEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCC-CCCCCCCCCCCCEEEEeeEEEEEEcCe
Q 015600 26 LLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSS-IDQLPRVLSPRDLILLKNVMIKKHQAE 95 (404)
Q Consensus 26 v~GVV~d~~~P~~trGtD~~~t~~I~D~S~~~~gl~v~iF~~~-~~~LP~v~~~GDII~l~rvki~~~~g~ 95 (404)
++|||+....+. +-.+-.+.|.|+++.. +.|+++..- +..+-.+.+.+-.|-+.|++.+.....
T Consensus 2 ~VGvVvsV~~~~----~g~~~~vYLaDe~~nl--l~vkfw~~l~~~~~EDvvk~~~lia~SNLQwR~~s~~ 66 (100)
T cd04495 2 TVGVVISVGKPI----EGKFPAVYLADECLNL--LCVKFWSSLEQYAYEDVVKRRVLLAASNLQWRTESTS 66 (100)
T ss_pred ceEEEEEEcccc----cCccceEEEecCCcCE--EEEEEecchHHhhhhhhcccceEEEEecceEeccccC
Confidence 689999988754 4567788999999976 888888742 122333334566777777777755443
No 66
>PRK05338 rplS 50S ribosomal protein L19; Provisional
Probab=67.53 E-value=13 Score=31.08 Aligned_cols=45 Identities=16% Similarity=0.235 Sum_probs=30.1
Q ss_pred CCCCCCCCCCCEEEEeeE-------EEEEEcCeeEEEeecC-ceEEEEEeCCCC
Q 015600 70 DQLPRVLSPRDLILLKNV-------MIKKHQAELSAVFYKD-SSSFALFDGNSG 115 (404)
Q Consensus 70 ~~LP~v~~~GDII~l~rv-------ki~~~~g~~~~~~~~~-~ss~~vf~~~~~ 115 (404)
.++|.+ ++||+|.++-- ++|.|.|-.-+.-+.+ .++|.|=+-..+
T Consensus 14 ~~~p~f-~~GD~V~V~~~i~eg~k~R~q~f~GvvI~~~~~G~~~tftvRki~~g 66 (116)
T PRK05338 14 KDIPEF-RPGDTVRVHVKVVEGNKERIQAFEGVVIARRGRGLNETFTVRKISYG 66 (116)
T ss_pred cCCCCc-CCCCEEEEEEEEccCCceEeccEEEEEEEEeCCCCCceEEEEEcccC
Confidence 569999 89999999642 3566766655555544 467887554433
No 67
>PF01245 Ribosomal_L19: Ribosomal protein L19; InterPro: IPR001857 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 [, ]. Ribosomal protein L19 is one of the proteins from the large ribosomal subunit [, ]. In Escherichia coli, L19 is known to be located at the 30S-50S ribosomal subunit interface [] and may play a role in the structure and function of the aminoacyl-tRNA binding site. It belongs to a family of ribosomal proteins, including L19 from bacteria and the chloroplasts of red algae. L19 is a protein of 120 to 130 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3HUZ_T 3V2D_T 3I8I_R 2XG2_T 2V49_T 2XUX_T 3HUX_T 3I9C_R 3V25_T 3UZ2_R ....
Probab=66.80 E-value=20 Score=29.87 Aligned_cols=40 Identities=20% Similarity=0.233 Sum_probs=28.3
Q ss_pred CCCCCCCCCCCCEEEEeeE-------EEEEEcCeeEEEeecC-ceEEEE
Q 015600 69 IDQLPRVLSPRDLILLKNV-------MIKKHQAELSAVFYKD-SSSFAL 109 (404)
Q Consensus 69 ~~~LP~v~~~GDII~l~rv-------ki~~~~g~~~~~~~~~-~ss~~v 109 (404)
...+|.+ .+||+|.++=. ++|.|.|-+.+.-+.+ .++|.|
T Consensus 13 ~~~~p~f-~~GD~v~V~~~i~e~~k~r~q~f~GvvIa~~~~g~~ssftl 60 (113)
T PF01245_consen 13 KKDIPEF-RVGDTVRVTYKISEGNKERIQVFEGVVIARRRRGLNSSFTL 60 (113)
T ss_dssp SSSSSSS-SSSSEEEEEEEEESSSSEEEEEEEEEEEEEEBSSTSSEEEE
T ss_pred hcCCCCc-CCCCEEEEEEEEecCCCceeEEEEEEEEEEECCCCCeeEEE
Confidence 3679999 89999999764 3467777666655544 466776
No 68
>PRK07374 dnaE DNA polymerase III subunit alpha; Validated
Probab=64.51 E-value=20 Score=41.76 Aligned_cols=89 Identities=15% Similarity=0.212 Sum_probs=63.6
Q ss_pred cceeehHhhhh-ccCCEEEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEee
Q 015600 8 GGIVRIKELAM-HVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKN 86 (404)
Q Consensus 8 y~y~~i~~~~~-~~~~~vnv~GVV~d~~~P~~trGtD~~~t~~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~r 86 (404)
++.+++.++.. ..+..|.+.|+|+..+.+ +|+.++-+.-++|-|.+-. +.+.+|.+.-+..-.....|.++++.
T Consensus 986 ~~~~~~~~l~~~~~~~~v~v~g~i~~~k~~-~Tk~G~~maf~~leD~tg~---~e~vvFp~~y~~~~~~l~~~~~~~v~- 1060 (1170)
T PRK07374 986 LAPISLSSLEEQPDKAKVSAIAMIPEMKQV-TTRKGDRMAILQLEDLTGS---CEAVVFPKSYERLSDHLMTDTRLLVW- 1060 (1170)
T ss_pred hCCcCHHHHhcccCCCEEEEEEEEEEeEec-ccCCCCEEEEEEEEECCCC---EEEEECHHHHHHHHHHhccCCEEEEE-
Confidence 34456777642 246679999999999875 5655678999999999764 99999987555554444778888884
Q ss_pred EEEEEEcCeeEEEee
Q 015600 87 VMIKKHQAELSAVFY 101 (404)
Q Consensus 87 vki~~~~g~~~~~~~ 101 (404)
-+++.-.++.+.+.+
T Consensus 1061 g~v~~~~~~~~~~~~ 1075 (1170)
T PRK07374 1061 AKVDRRDDRVQLIID 1075 (1170)
T ss_pred EEEEecCCeEEEEEe
Confidence 466654466676664
No 69
>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=62.20 E-value=78 Score=25.14 Aligned_cols=26 Identities=27% Similarity=0.362 Sum_probs=19.3
Q ss_pred eEEEEEEEEEeeCCCCeEEEEEEcCCCC
Q 015600 171 DLVCKVFHVSYDDSKGLWMLFVWDGTDV 198 (404)
Q Consensus 171 Dl~~qVv~~~~~~~~~~~~L~VwDgT~~ 198 (404)
|+++.|+.+. + ....+.+.+=|||+.
T Consensus 1 ~ivG~V~sv~-~-~~~~~~~tLdDgTG~ 26 (92)
T cd04483 1 DILGTVVSRR-E-RETFYSFGVDDGTGV 26 (92)
T ss_pred CeEEEEEEEE-e-cCCeEEEEEecCCce
Confidence 5788999887 5 345677777888874
No 70
>TIGR01024 rplS_bact ribosomal protein L19, bacterial type. This model describes bacterial ribosomoal protein L19 and its chloroplast equivalent. Putative mitochondrial L19 are found in several species (but not Saccharomyces cerevisiae) and score between trusted and noise cutoffs.
Probab=60.79 E-value=20 Score=29.89 Aligned_cols=45 Identities=16% Similarity=0.128 Sum_probs=30.1
Q ss_pred CCCCCCCCCCCEEEEeeE-------EEEEEcCeeEEEeecC-ceEEEEEeCCCC
Q 015600 70 DQLPRVLSPRDLILLKNV-------MIKKHQAELSAVFYKD-SSSFALFDGNSG 115 (404)
Q Consensus 70 ~~LP~v~~~GDII~l~rv-------ki~~~~g~~~~~~~~~-~ss~~vf~~~~~ 115 (404)
.++|.+ .+||+|.++-. ++|.|.|-.-+.-+.+ .++|.|=+-..+
T Consensus 14 ~~ip~f-~~GD~v~V~~~i~eg~k~R~q~f~GvvI~~~~~G~~~tftvR~i~~g 66 (113)
T TIGR01024 14 KDLPDF-RVGDTVRVHVKIVEGKKERIQVFEGVVIARRGGGIGETFTVRKISYG 66 (113)
T ss_pred cCCCcc-CCCCEEEEEEEEccCCceEcccEEEEEEEEeCCCCceEEEEEEeccC
Confidence 579999 89999999643 3456666665655544 467877554433
No 71
>PF15072 DUF4539: Domain of unknown function (DUF4539)
Probab=57.73 E-value=38 Score=26.77 Aligned_cols=63 Identities=19% Similarity=0.274 Sum_probs=43.8
Q ss_pred EEEE-EEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcC
Q 015600 23 KVNL-LGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQA 94 (404)
Q Consensus 23 ~vnv-~GVV~d~~~P~~trGtD~~~t~~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~~~g 94 (404)
+|.. .|+|..+.. .+.|. .+.+.|+|=. +.+.+=++-.+..|....+|=+++|+++.+=.=..
T Consensus 3 KVp~l~v~Iks~~~----~~~D~--~v~l~DpTG~---i~~tiH~~v~~~y~~~l~~GavLlLk~V~Vf~ps~ 66 (86)
T PF15072_consen 3 KVPCLVVIIKSIVP----SSEDA--FVVLKDPTGE---IRGTIHRKVLEEYGDELSPGAVLLLKDVTVFSPSP 66 (86)
T ss_pred ccCEEEEEEEEeec----cCCCe--EEEEECCCCc---EEEEEeHHHHhhcCCccccCEEEEEeeeeEEecCC
Confidence 3444 445555554 23354 7789998763 88888887666677776999999999998865443
No 72
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=56.26 E-value=52 Score=36.11 Aligned_cols=79 Identities=19% Similarity=0.192 Sum_probs=52.4
Q ss_pred eehHhhhhccCCEEEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEE
Q 015600 11 VRIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIK 90 (404)
Q Consensus 11 ~~i~~~~~~~~~~vnv~GVV~d~~~P~~trGtD~~~t~~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~ 90 (404)
++|+++ ..|+.+.+.|.|++...... + --..++++.|.+- .+.+.+|.-+...+.....+|+-+.+.. |++
T Consensus 51 ~~i~~l--~~g~~vtv~g~V~~~~~~~~--~-~~~~~v~l~D~tg---~i~l~~F~~n~~~~~~~l~~G~~~~v~G-kv~ 121 (681)
T PRK10917 51 KPIAEL--RPGEKVTVEGEVLSAEVVFG--K-RRRLTVTVSDGTG---NLTLRFFNFNQPYLKKQLKVGKRVAVYG-KVK 121 (681)
T ss_pred CCHHHC--CCCCEEEEEEEEEEEEEccC--C-ceEEEEEEEECCe---EEEEEEEccCcHHHHhhCCCCCEEEEEE-EEE
Confidence 356666 46899999999998743222 2 2378889999763 3899999422335556558899888765 344
Q ss_pred EEcCeeEE
Q 015600 91 KHQAELSA 98 (404)
Q Consensus 91 ~~~g~~~~ 98 (404)
.++|..+.
T Consensus 122 ~~~~~~qm 129 (681)
T PRK10917 122 RGKYGLEM 129 (681)
T ss_pred ecCCeEEE
Confidence 45555444
No 73
>CHL00084 rpl19 ribosomal protein L19
Probab=55.42 E-value=30 Score=29.04 Aligned_cols=41 Identities=10% Similarity=0.169 Sum_probs=27.1
Q ss_pred CCCCCCCCCCCEEEEeeE-------EEEEEcCeeEEEeecC-ceEEEEEe
Q 015600 70 DQLPRVLSPRDLILLKNV-------MIKKHQAELSAVFYKD-SSSFALFD 111 (404)
Q Consensus 70 ~~LP~v~~~GDII~l~rv-------ki~~~~g~~~~~~~~~-~ss~~vf~ 111 (404)
.++|.+ ++||+|.++=. ++|.|.|-.-+.-+.+ .++|.|=.
T Consensus 18 ~~~p~f-~~GDtV~V~~~i~eg~k~R~q~F~GvvI~~r~~G~~~tftvRk 66 (117)
T CHL00084 18 KNLPKI-RVGDTVKVGVLIQEGNKERVQFYEGTVIAKKNSGLNTTITVRK 66 (117)
T ss_pred cCCCcc-CCCCEEEEEEEEecCCeeEeceEEEEEEEEeCCCCCeeEEEEE
Confidence 479999 89999999642 3556666655554444 36677633
No 74
>cd04486 YhcR_OBF_like YhcR_OBF_like: A subfamily of OB-fold domains similar to the OB folds of Bacillus subtilis YhcR. YhcR is a sugar-nonspecific nuclease, which is active in the presence of Ca2+ and Mn2+. It cleaves RNA endonucleolytically, producing 3'-monophosphate nucleosides. YhcR appears to be the major Ca2+ activated nuclease of B. subtilis. YhcR may be localized in the cell wall.
Probab=53.44 E-value=1e+02 Score=23.69 Aligned_cols=62 Identities=19% Similarity=0.148 Sum_probs=39.3
Q ss_pred EEEEEecCCceecCCCceEEEEEEEeCCCC-----CCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCeeEEEee
Q 015600 27 LGVVLEFSIPRKSQGTDYVCVLKIVDDSQQ-----SPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAELSAVFY 101 (404)
Q Consensus 27 ~GVV~d~~~P~~trGtD~~~t~~I~D~S~~-----~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~~~g~~~~~~~ 101 (404)
=|||+...+.. | .-.|-|-|+.-. ++| +-+|.+. -+.+ ++||.|++. -++..|+|..|+...
T Consensus 3 ~GvVTa~~~~~---~---~~GffiQd~~~d~~~~ts~g--ifV~~~~---~~~~-~~Gd~V~vt-G~v~ey~g~tql~~~ 69 (78)
T cd04486 3 EGVVTAVFSGG---G---LGGFYIQDEDGDGDPATSEG--IFVYTGS---GADV-AVGDLVRVT-GTVTEYYGLTQLTAV 69 (78)
T ss_pred EEEEEEEcCCC---C---cCEEEEEcCCCCCCCcccce--EEEecCC---CCCC-CCCCEEEEE-EEEEeeCCeEEEccC
Confidence 47777765422 1 123456666322 234 4455543 4556 889999996 899999998887654
No 75
>TIGR00643 recG ATP-dependent DNA helicase RecG.
Probab=53.16 E-value=73 Score=34.55 Aligned_cols=79 Identities=18% Similarity=0.222 Sum_probs=52.5
Q ss_pred eehHhhhhccCCEEEEEEEEEecCCceecCCCceEEEEEEEe-CCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEE
Q 015600 11 VRIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVD-DSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMI 89 (404)
Q Consensus 11 ~~i~~~~~~~~~~vnv~GVV~d~~~P~~trGtD~~~t~~I~D-~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki 89 (404)
++|+++ ..|..+.+.|.|++.... .++.--..++.+.| .+- .+.+.+|.. ..+......|+-+.+.. |+
T Consensus 24 ~~i~~~--~~g~~~~~~~~v~~~~~~--~~~~~~~~~~~~~d~~~~---~~~~~~F~~--~~~~~~~~~g~~~~~~G-k~ 93 (630)
T TIGR00643 24 QTIGEL--LPGERATIVGEVLSHCIF--GFKRRKVLKLRLKDGGYK---KLELRFFNR--AFLKKKFKVGSKVVVYG-KV 93 (630)
T ss_pred cCHHHc--CCCCEEEEEEEEEEeEec--cCCCCceEEEEEEECCCC---EEEEEEECC--HHHHhhCCCCCEEEEEE-EE
Confidence 356776 478999999999874221 12222278889999 443 399999973 35555557899888855 55
Q ss_pred EEEcCeeEEE
Q 015600 90 KKHQAELSAV 99 (404)
Q Consensus 90 ~~~~g~~~~~ 99 (404)
..++|..+..
T Consensus 94 ~~~~~~~~~~ 103 (630)
T TIGR00643 94 KSSKFKAYLI 103 (630)
T ss_pred EeeCCEEEEE
Confidence 5667765543
No 76
>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=51.84 E-value=20 Score=28.52 Aligned_cols=40 Identities=18% Similarity=0.340 Sum_probs=32.5
Q ss_pred ceEEEEEecCchhhhhhccCCCCcEEEEeceEEEEeCcEE
Q 015600 236 GTVLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMW 275 (404)
Q Consensus 236 G~~l~V~~~~~~~~~~~~~~k~g~wv~l~Nv~~k~~~g~l 275 (404)
|..|+.+........-...+++|.|..|.|..+..+.|..
T Consensus 9 G~~I~A~I~~~~~~~f~~~l~Eg~~y~i~~F~V~~~~~~y 48 (95)
T PF02721_consen 9 GDKIQATIPKELVDKFKDSLKEGSWYTISNFTVSPNSGSY 48 (95)
T ss_pred CCEEEEEECHHHHHHHHhhcccCCEEEeEeEEEEeCCCce
Confidence 7788999887665555678999999999999988876643
No 77
>PRK05672 dnaE2 error-prone DNA polymerase; Validated
Probab=51.12 E-value=38 Score=39.12 Aligned_cols=86 Identities=21% Similarity=0.264 Sum_probs=58.3
Q ss_pred ceeehHhhhh-ccCCEEEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeE
Q 015600 9 GIVRIKELAM-HVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNV 87 (404)
Q Consensus 9 ~y~~i~~~~~-~~~~~vnv~GVV~d~~~P~~trGtD~~~t~~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rv 87 (404)
+++++.++.. ..+..|-|.|+|+..+.+...+| +.-++|-|.+-. +.+.+|.+..+..-.....|.++++. -
T Consensus 940 ~~~~~~~l~~~~~~~~v~v~g~i~~~~~~~TkkG---maf~~leD~~g~---~e~~ifp~~~~~~~~~l~~~~~~~v~-g 1012 (1046)
T PRK05672 940 GVVSAAELLDVEDGRRVRVAGVVTHRQRPGTASG---VTFLTLEDETGM---VNVVVWPGLWERQRREALGARLLLVR-G 1012 (1046)
T ss_pred cCcCHHHHhhccCCCEEEEEEEEEEEEEecCCCc---eEEEEEecCCCC---EEEEECHHHHHHHHHHhccCCEEEEE-E
Confidence 3456666643 24667999999999887533346 888899998763 99999986444443433678888884 4
Q ss_pred EEEEEcCeeEEEee
Q 015600 88 MIKKHQAELSAVFY 101 (404)
Q Consensus 88 ki~~~~g~~~~~~~ 101 (404)
+++.-+++.+.+.+
T Consensus 1013 ~v~~~~~~~~~~~~ 1026 (1046)
T PRK05672 1013 RVQNAEGVRHLVAD 1026 (1046)
T ss_pred EEEecCCeEEEEEe
Confidence 66655665666554
No 78
>PRK06826 dnaE DNA polymerase III DnaE; Reviewed
Probab=50.89 E-value=43 Score=39.03 Aligned_cols=77 Identities=14% Similarity=0.230 Sum_probs=55.1
Q ss_pred cCCEEEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEE-cCeeEE
Q 015600 20 VKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKH-QAELSA 98 (404)
Q Consensus 20 ~~~~vnv~GVV~d~~~P~~trGtD~~~t~~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~~-~g~~~~ 98 (404)
.+..|.+.|+|+..+.+ +|+.++-+.-++|-|.+-. +.+.+|.+..+..-.....|.+|++ ..+++.. +++.+.
T Consensus 990 ~~~~v~v~g~i~~~~~~-~tk~G~~maf~~leD~~g~---~e~~vfp~~~~~~~~~l~~~~~~~v-~g~v~~~~~~~~~~ 1064 (1151)
T PRK06826 990 DGDKVIIGGIITEVKRK-TTRNNEMMAFLTLEDLYGT---VEVIVFPKVYEKYRSLLNEDNIVLI-KGRVSLREDEEPKL 1064 (1151)
T ss_pred CCcEEEEEEEEEEeEee-ccCCCCeEEEEEEEECCCc---EEEEECHHHHHHHHHHhccCCEEEE-EEEEEecCCCceEE
Confidence 46679999999999875 5665677899999998763 9999998654444333367888887 4466643 454666
Q ss_pred Eee
Q 015600 99 VFY 101 (404)
Q Consensus 99 ~~~ 101 (404)
+.+
T Consensus 1065 ~~~ 1067 (1151)
T PRK06826 1065 ICE 1067 (1151)
T ss_pred EEe
Confidence 654
No 79
>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=50.32 E-value=21 Score=28.10 Aligned_cols=22 Identities=18% Similarity=0.158 Sum_probs=19.4
Q ss_pred EEEEEEeCCCceEEEEEecccc
Q 015600 377 TMKLTLEDPTARIHALLCGKEW 398 (404)
Q Consensus 377 ~f~L~leD~t~~~~~~v~~~da 398 (404)
.+.|+|+|.||+|.+.++..+.
T Consensus 17 ~~~~tL~D~TG~I~~~~W~~~~ 38 (95)
T cd04478 17 NITYTIDDGTGTIEVRQWLDDD 38 (95)
T ss_pred EEEEEEECCCCcEEEEEeCCCC
Confidence 4899999999999999997664
No 80
>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=48.67 E-value=96 Score=25.24 Aligned_cols=35 Identities=17% Similarity=0.083 Sum_probs=27.4
Q ss_pred EEEEEecCchhhhhhcc-CCCCcEEEEeceEEEEeC
Q 015600 238 VLRVSTDRSYENFGRYF-TATGKWVRIRNMSCQVSS 272 (404)
Q Consensus 238 ~l~V~~~~~~~~~~~~~-~k~g~wv~l~Nv~~k~~~ 272 (404)
.|-|.+|..-+.++.+. +|++..+.+.|++.+..+
T Consensus 29 ll~vkfw~~l~~~~~EDvvk~~~lia~SNLQwR~~s 64 (100)
T cd04495 29 LLCVKFWSSLEQYAYEDVVKRRVLLAASNLQWRTES 64 (100)
T ss_pred EEEEEEecchHHhhhhhhcccceEEEEecceEeccc
Confidence 45678888666666665 689999999999998844
No 81
>PF15072 DUF4539: Domain of unknown function (DUF4539)
Probab=47.82 E-value=18 Score=28.70 Aligned_cols=21 Identities=29% Similarity=0.387 Sum_probs=17.7
Q ss_pred EEEEEEeCCCceEEEEEeccc
Q 015600 377 TMKLTLEDPTARIHALLCGKE 397 (404)
Q Consensus 377 ~f~L~leD~t~~~~~~v~~~d 397 (404)
-..++|.||||+|++.++.+-
T Consensus 20 D~~v~l~DpTG~i~~tiH~~v 40 (86)
T PF15072_consen 20 DAFVVLKDPTGEIRGTIHRKV 40 (86)
T ss_pred CeEEEEECCCCcEEEEEeHHH
Confidence 457899999999999998653
No 82
>PRK07279 dnaE DNA polymerase III DnaE; Reviewed
Probab=47.37 E-value=47 Score=38.18 Aligned_cols=86 Identities=17% Similarity=0.294 Sum_probs=59.4
Q ss_pred ceeehHhhhhccCCEEEEEEEEEecCCceecC-CCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeE
Q 015600 9 GIVRIKELAMHVKHKVNLLGVVLEFSIPRKSQ-GTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNV 87 (404)
Q Consensus 9 ~y~~i~~~~~~~~~~vnv~GVV~d~~~P~~tr-GtD~~~t~~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rv 87 (404)
+.+++.++. .+..+.+.|+|...+. .+|| ..+-+..++|-|.+-. +.+.+|.+.-+..-.....|.++++..
T Consensus 874 ~~~~~~~l~--~~~~~~~~~~i~~~~~-~~tk~~g~~maf~~leD~~g~---ie~~vFp~~y~~~~~~l~~~~~~~v~G- 946 (1034)
T PRK07279 874 PFTPISQLV--KNSEATILVQIQSIRV-IRTKTKGQQMAFLSVTDTKKK---LDVTLFPETYRQYKDELKEGKFYYLKG- 946 (1034)
T ss_pred cCccHHHHh--cCCcceEEEEEEEEEE-EEEcCCCCeEEEEEEeeCCCc---EEEEECHHHHHHHHHHhccCCEEEEEE-
Confidence 345677773 3566889999998876 4555 4567899999998764 999999865444433336788888854
Q ss_pred EEEEEcCeeEEEee
Q 015600 88 MIKKHQAELSAVFY 101 (404)
Q Consensus 88 ki~~~~g~~~~~~~ 101 (404)
+++.-.++.+.+.+
T Consensus 947 ~v~~~~~~~~l~~~ 960 (1034)
T PRK07279 947 KIQERDGRLQMVLQ 960 (1034)
T ss_pred EEEecCCeeEEEEe
Confidence 66654565666654
No 83
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=47.14 E-value=88 Score=33.50 Aligned_cols=79 Identities=15% Similarity=0.348 Sum_probs=58.9
Q ss_pred eehHhhhhccCCEEEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEec-CCCCCCCCCCCCCCEEEEeeEEE
Q 015600 11 VRIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFT-SSIDQLPRVLSPRDLILLKNVMI 89 (404)
Q Consensus 11 ~~i~~~~~~~~~~vnv~GVV~d~~~P~~trGtD~~~t~~I~D~S~~~~gl~v~iF~-~~~~~LP~v~~~GDII~l~rvki 89 (404)
+.+.++-+..|..|.+=|-|+..+ +|.| -..|||.|++-. +.+.-|- +-.-.-|.| ++||||.+-. .+
T Consensus 203 ~~i~~id~~ig~tV~I~GeV~qik---qT~G---PTVFtltDetg~---i~aAAFe~aGvRAyP~I-evGdiV~ViG-~V 271 (715)
T COG1107 203 TLIDDLDEMIGKTVRIEGEVTQIK---QTSG---PTVFTLTDETGA---IWAAAFEEAGVRAYPEI-EVGDIVEVIG-EV 271 (715)
T ss_pred ccHHHHHhhcCceEEEEEEEEEEE---EcCC---CEEEEEecCCCc---eehhhhccCCcccCCCC-CCCceEEEEE-EE
Confidence 446666666899999999998864 4444 246899999764 6677775 456789999 8999999865 45
Q ss_pred EEEcCeeEEEe
Q 015600 90 KKHQAELSAVF 100 (404)
Q Consensus 90 ~~~~g~~~~~~ 100 (404)
....|++|.=.
T Consensus 272 ~~r~g~lQiE~ 282 (715)
T COG1107 272 TRRDGRLQIEI 282 (715)
T ss_pred eecCCcEEEee
Confidence 66778887644
No 84
>COG1570 XseA Exonuclease VII, large subunit [DNA replication, recombination, and repair]
Probab=45.58 E-value=1.9e+02 Score=30.04 Aligned_cols=78 Identities=17% Similarity=0.172 Sum_probs=53.0
Q ss_pred hhhhccCCEEEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcC
Q 015600 15 ELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQA 94 (404)
Q Consensus 15 ~~~~~~~~~vnv~GVV~d~~~P~~trGtD~~~t~~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~~~g 94 (404)
..++..=+.|=|-|=|..++.| ..| ..-|+|.|+.-. |.|.+|+.+...|....+.|+-|.++ -+++.|-+
T Consensus 17 ~llE~~~~~V~v~GEISn~t~~--~sg---H~YFtLKD~~A~---i~c~mf~~~~~~l~f~p~eG~~V~v~-G~is~Y~~ 87 (440)
T COG1570 17 RLLERDLGQVWVRGEISNFTRP--ASG---HLYFTLKDERAQ---IRCVMFKGNNRRLKFRPEEGMQVLVR-GKISLYEP 87 (440)
T ss_pred HHHHhcCCeEEEEEEecCCccC--CCc---cEEEEEccCCce---EEEEEEcCcccccCCCccCCCEEEEE-EEEEEEcC
Confidence 3333333457777877777754 233 666799999553 99999999888888766889977773 46666644
Q ss_pred --eeEEEee
Q 015600 95 --ELSAVFY 101 (404)
Q Consensus 95 --~~~~~~~ 101 (404)
..|.++.
T Consensus 88 rG~YQi~~~ 96 (440)
T COG1570 88 RGDYQIVAE 96 (440)
T ss_pred CCceEEEEe
Confidence 3555553
No 85
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=44.83 E-value=83 Score=37.65 Aligned_cols=86 Identities=16% Similarity=0.284 Sum_probs=61.3
Q ss_pred cceeehHhhhhccCCEEEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCC---CCCCCCCCCCCEEEE
Q 015600 8 GGIVRIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSI---DQLPRVLSPRDLILL 84 (404)
Q Consensus 8 y~y~~i~~~~~~~~~~vnv~GVV~d~~~P~~trGtD~~~t~~I~D~S~~~~gl~v~iF~~~~---~~LP~v~~~GDII~l 84 (404)
+..++|+++.. ....|-+-|-|-+... +.+|..-...+|.|+|-+ +++.|..|.++. +.+-.+ +.||-|++
T Consensus 224 ~~~~~~~~i~~-~~~~v~i~G~if~~e~-~~~k~~~~~~~~~~td~~---~s~~~k~f~~~~~~~~~~~~~-~~g~~v~~ 297 (1437)
T PRK00448 224 EEITPMKEINE-EERRVVVEGYVFKVEI-KELKSGRHILTFKITDYT---SSIIVKKFSRDKEDLKKFDEI-KKGDWVKV 297 (1437)
T ss_pred cCcccHHHhhc-cCCeEEEEEEEEEEEE-EeccCCCEEEEEEEEcCC---CCEEEEEEecCcchhHHHhcC-CCCCEEEE
Confidence 46788999864 4557889999987765 456656788999999975 459999998543 345556 78999888
Q ss_pred eeE-EEEEEcCeeEEE
Q 015600 85 KNV-MIKKHQAELSAV 99 (404)
Q Consensus 85 ~rv-ki~~~~g~~~~~ 99 (404)
+.- ....|.++....
T Consensus 298 ~g~~~~d~~~~~~~~~ 313 (1437)
T PRK00448 298 RGSVQNDTFTRDLVMN 313 (1437)
T ss_pred EEEEeccCCCCceEEE
Confidence 653 334566654443
No 86
>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=43.69 E-value=26 Score=27.09 Aligned_cols=21 Identities=38% Similarity=0.405 Sum_probs=19.4
Q ss_pred EEEEeCCCceEEEEEeccccc
Q 015600 379 KLTLEDPTARIHALLCGKEWV 399 (404)
Q Consensus 379 ~L~leD~t~~~~~~v~~~da~ 399 (404)
.++|||.+|++.+.++.+..+
T Consensus 20 ~~~leD~~G~~Ev~~F~~~~~ 40 (79)
T cd04490 20 IVELEDTTGRITVLLTKDKEE 40 (79)
T ss_pred EEEEECCCCEEEEEEeCchhh
Confidence 899999999999999988766
No 87
>KOG4792 consensus Crk family adapters [Signal transduction mechanisms]
Probab=41.58 E-value=43 Score=31.43 Aligned_cols=61 Identities=16% Similarity=0.327 Sum_probs=39.4
Q ss_pred hccCCCCceEEEEEecCchhhhhhccCCCCcEEEEeceEEEEeCcEEEEEEecCC------ceEEcCCCCh
Q 015600 229 LRNFFPVGTVLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSS------KIRLFSDNDN 293 (404)
Q Consensus 229 ~~~~pp~G~~l~V~~~~~~~~~~~~~~k~g~wv~l~Nv~~k~~~g~leG~l~~~s------ki~~l~~~d~ 293 (404)
..+.|-+.+++|=..-..-.+- .-.++.||.|+. .-+..+|.|||-+.+.. .++.++..++
T Consensus 223 ~~~lPa~Arv~q~RVPnAYDkT-aL~levGdiVkV---Tk~ninGqwegElnGk~G~fPfThvrf~d~~~~ 289 (293)
T KOG4792|consen 223 QQNLPAYARVIQKRVPNAYDKT-ALALEVGDIVKV---TKKNINGQWEGELNGKIGHFPFTHVRFTDVQNP 289 (293)
T ss_pred ccCCChheeeehhcCCCccChh-hhhhhcCcEEEE---EeeccCceeeeeecCccccccceeEEeeccCCc
Confidence 3556666776665544433332 445899999984 34446899999998863 6666665444
No 88
>cd04492 YhaM_OBF_like YhaM_OBF_like: A subfamily of OB folds similar to that found in Bacillus subtilis YhaM and Staphylococcus aureus cmp-binding factor-1 (SaCBF1). Both these proteins are 3'-to-5'exoribonucleases. YhaM requires Mn2+ or Co2+ for activity and is inactive in the presence of Mg2+. YhaM also has a Mn2+ dependent 3'-to-5'single-stranded DNA exonuclease activity. SaCBF is also a double-stranded DNA binding protein, binding specifically to cmp, the replication enhancer found in S. aureus plasmid pT181. Proteins in this group combine an N-terminal OB fold with a C-terminal HD domain. The HD domain is found in metal-dependent phosphohydrolases.
Probab=37.65 E-value=44 Score=25.00 Aligned_cols=21 Identities=38% Similarity=0.442 Sum_probs=18.7
Q ss_pred EEEEEEeCCCceEEEEEeccc
Q 015600 377 TMKLTLEDPTARIHALLCGKE 397 (404)
Q Consensus 377 ~f~L~leD~t~~~~~~v~~~d 397 (404)
.+.++|+|.|+++.+.++++.
T Consensus 20 ~~~~~l~D~tg~i~~~~f~~~ 40 (83)
T cd04492 20 YLALTLQDKTGEIEAKLWDAS 40 (83)
T ss_pred EEEEEEEcCCCeEEEEEcCCC
Confidence 589999999999999999854
No 89
>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=37.05 E-value=1.1e+02 Score=29.15 Aligned_cols=52 Identities=17% Similarity=0.098 Sum_probs=37.0
Q ss_pred EEEEEecCchhhhhhccCCCCcEEEEeceEEEEe-C----cEEEEEEecCCceEEcCC
Q 015600 238 VLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVS-S----GMWHGLLQSSSKIRLFSD 290 (404)
Q Consensus 238 ~l~V~~~~~~~~~~~~~~k~g~wv~l~Nv~~k~~-~----g~leG~l~~~ski~~l~~ 290 (404)
+..+++|+|-++. ...+++|.-+++.|+...-. + +.++..=+..++.+.|+.
T Consensus 181 ~~~LTIWrPtedl-~s~L~EG~ry~i~~L~~s~~k~~~~~~~vqLtatk~Tr~~~l~~ 237 (251)
T cd04494 181 SGLLSIWRPTEDL-RSLLTEGKRYRIYGLATSNSKKRSGNEEVQLTATKKTRYQPLPV 237 (251)
T ss_pred eEEEEEeCCCHHH-HhhhcCCcEEEEEeccccCCCCCCCcceEEEEecCcccceECCH
Confidence 5578999998874 67899999999999996552 1 344444444556665654
No 90
>PRK07772 single-stranded DNA-binding protein; Provisional
Probab=36.53 E-value=66 Score=29.27 Aligned_cols=74 Identities=8% Similarity=0.135 Sum_probs=49.7
Q ss_pred CCEEEEEEEEEecCCceecCCCceEEEEEEEeC-CC-C----------CCCeEEEEecCCCCCCCCCCCCCCEEEEe-eE
Q 015600 21 KHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDD-SQ-Q----------SPELLVNIFTSSIDQLPRVLSPRDLILLK-NV 87 (404)
Q Consensus 21 ~~~vnv~GVV~d~~~P~~trGtD~~~t~~I~D~-S~-~----------~~gl~v~iF~~~~~~LP~v~~~GDII~l~-rv 87 (404)
...|.|+|=+..--.-+.|....-+++|+|.-. .. . ..-++|.+|.+..+.+-.-.+.||-|.+. |+
T Consensus 4 ~~~VtLiGrL~~DPElR~t~sG~~va~FrVAv~~r~~~~~~g~~~d~~t~fi~V~~Wg~~Ae~va~~L~KGd~V~V~GrL 83 (186)
T PRK07772 4 DTTITVVGNLTADPELRFTPSGAAVANFTVASTPRTFDRQTNEWKDGEALFLRCSIWRQAAENVAESLTKGMRVIVTGRL 83 (186)
T ss_pred cCEEEEEEEeCCCCeEEEcCCCCEEEEEEEEecCcceecCCCcEeccCceEEEEEEecHHHHHHHHhcCCCCEEEEEEEE
Confidence 456788887776544455655567889998732 21 1 11389999998666666544789965554 78
Q ss_pred EEEEEcC
Q 015600 88 MIKKHQA 94 (404)
Q Consensus 88 ki~~~~g 94 (404)
+.+.|.+
T Consensus 84 ~~r~wed 90 (186)
T PRK07772 84 KQRSYET 90 (186)
T ss_pred EcCceEC
Confidence 9998864
No 91
>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=36.35 E-value=43 Score=25.94 Aligned_cols=37 Identities=19% Similarity=0.333 Sum_probs=29.6
Q ss_pred ceEEEEEecCchhhhhhccCCCCcEEEEeceEEEEeC
Q 015600 236 GTVLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSS 272 (404)
Q Consensus 236 G~~l~V~~~~~~~~~~~~~~k~g~wv~l~Nv~~k~~~ 272 (404)
|..++.++....++.-...+++|.|..|.|-.++...
T Consensus 30 G~~I~a~i~~~~~~~f~~~L~eg~vy~is~f~v~~~~ 66 (86)
T cd04480 30 GNRIHATIPKRLAAKFRPLLKEGKWYTISNFEVAPNT 66 (86)
T ss_pred CCEEEEEECHHHHHhhhhhceeCCEEEEeeEEEEcCC
Confidence 7788888888665554788999999999998776644
No 92
>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=35.99 E-value=45 Score=24.92 Aligned_cols=23 Identities=22% Similarity=0.286 Sum_probs=20.0
Q ss_pred EEEEEEeCCCceEEEEEeccccc
Q 015600 377 TMKLTLEDPTARIHALLCGKEWV 399 (404)
Q Consensus 377 ~f~L~leD~t~~~~~~v~~~da~ 399 (404)
+.-++|+|.++++++.++.+-..
T Consensus 18 ~~~~~L~D~~~~i~~~~f~~~~~ 40 (78)
T cd04489 18 HLYFTLKDEDASIRCVMWRSNAR 40 (78)
T ss_pred EEEEEEEeCCeEEEEEEEcchhh
Confidence 77899999999999999987544
No 93
>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=35.98 E-value=32 Score=26.92 Aligned_cols=27 Identities=15% Similarity=0.164 Sum_probs=23.6
Q ss_pred EEEEEecCchhhhhhccCCCCcEEEEe
Q 015600 238 VLRVSTDRSYENFGRYFTATGKWVRIR 264 (404)
Q Consensus 238 ~l~V~~~~~~~~~~~~~~k~g~wv~l~ 264 (404)
.++|.+|...|+.+.+.++.|++|.+.
T Consensus 45 ~~~v~~~g~~a~~~~~~~~kG~~V~v~ 71 (100)
T cd04496 45 WIRVVAFGKLAENAAKYLKKGDLVYVE 71 (100)
T ss_pred EEEEEEEhHHHHHHHHHhCCCCEEEEE
Confidence 789999999888888899999999743
No 94
>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=34.58 E-value=67 Score=24.82 Aligned_cols=57 Identities=9% Similarity=0.096 Sum_probs=43.4
Q ss_pred CceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCeeEEEe
Q 015600 42 TDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAELSAVF 100 (404)
Q Consensus 42 tD~~~t~~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~~~g~~~~~~ 100 (404)
.-..+.+-|.|+.-. -|.+.++....+.+-...+.|.+..+.+.++..-++......
T Consensus 17 ~~~~~~miL~De~G~--~I~a~i~~~~~~~f~~~L~eg~vy~is~f~v~~~~~~y~~~~ 73 (86)
T cd04480 17 SGESLEMVLVDEKGN--RIHATIPKRLAAKFRPLLKEGKWYTISNFEVAPNTGSYRPTD 73 (86)
T ss_pred CCcEEEEEEEcCCCC--EEEEEECHHHHHhhhhhceeCCEEEEeeEEEEcCCCcccccC
Confidence 566788889998653 389999987666666655899999999999987766544443
No 95
>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=34.35 E-value=1.4e+02 Score=30.57 Aligned_cols=92 Identities=17% Similarity=0.250 Sum_probs=61.6
Q ss_pred ehHhhhhccCCEEEEEEEEEecCCce--ecC-CC-ceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeE
Q 015600 12 RIKELAMHVKHKVNLLGVVLEFSIPR--KSQ-GT-DYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNV 87 (404)
Q Consensus 12 ~i~~~~~~~~~~vnv~GVV~d~~~P~--~tr-Gt-D~~~t~~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rv 87 (404)
.+.++. ...+.+|+.|-|.++..++ +++ |. .=..+..+.|.+-. +... +..+...+++. +.||++++.+.
T Consensus 51 ~i~~~~-~~~~~~~v~~~V~~~~e~~~~~~k~g~~~~l~~~~v~Detg~---v~~~-~~~~~~a~~~~-e~Gdv~~i~~~ 124 (407)
T COG1599 51 KISDIS-EASSRVNVTGRVLSIGEKKTFDRKRGAEGKLAEVLVGDETGS---VKTV-TLWNIAALEKL-EPGDVIRIRNA 124 (407)
T ss_pred cccccc-hhhccccEEEEECccccceeeecccccccceEEEEEecCCCC---EEEE-eeccccccccC-CccceEEecCc
Confidence 344442 2456799999999998766 454 43 33344557777653 3332 55555556566 78999999999
Q ss_pred EEEEEcCeeEEEeecCceEEEEE
Q 015600 88 MIKKHQAELSAVFYKDSSSFALF 110 (404)
Q Consensus 88 ki~~~~g~~~~~~~~~~ss~~vf 110 (404)
.+..|+|..++..+.. ++.+..
T Consensus 125 ~~~~~~~~~~~~~~~~-~~v~~~ 146 (407)
T COG1599 125 YTSLYRGGKRLSVGRV-GSVADV 146 (407)
T ss_pred ccccccCceeeecccc-cccccC
Confidence 9999999999887644 344433
No 96
>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=34.23 E-value=99 Score=24.93 Aligned_cols=64 Identities=13% Similarity=-0.078 Sum_probs=37.6
Q ss_pred ceEEEEEecCchhhhhhcc----CCCCcEEEE-eceEEEEeCc-EEEEEEecCCceEEcCCCChHHHHHHH
Q 015600 236 GTVLRVSTDRSYENFGRYF----TATGKWVRI-RNMSCQVSSG-MWHGLLQSSSKIRLFSDNDNVVWDYMR 300 (404)
Q Consensus 236 G~~l~V~~~~~~~~~~~~~----~k~g~wv~l-~Nv~~k~~~g-~leG~l~~~ski~~l~~~d~~v~~r~r 300 (404)
|..|.+++|..+|...... -+.+-.|.+ +..+++...| ..-......|++. ++++-|++.+.+.
T Consensus 34 ~~~l~~tlwG~~A~~f~~~~~~~~~~~~VVav~~~~rV~~~~g~~~ls~~~~~s~v~-inp~ipe~~~~~~ 103 (106)
T cd04481 34 DERLKCTLWGEYAEEFDAKFQSAGNGEPVVAVLRFWKIKEYKGPKSLSNSFGASKVY-INPDIPEVPEIKM 103 (106)
T ss_pred CCEEEEEEEHHHHHHHHHHHHHhCCCCcEEEEEEeEEEEEEcCCcEEEcCCCceEEE-ECCCcHHHHHHHh
Confidence 6689999999888654322 345556655 4488888765 2211111334653 4445666666543
No 97
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=33.35 E-value=2.2e+02 Score=31.17 Aligned_cols=79 Identities=18% Similarity=0.201 Sum_probs=57.4
Q ss_pred hHhhhhccCCEEEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEE
Q 015600 13 IKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKH 92 (404)
Q Consensus 13 i~~~~~~~~~~vnv~GVV~d~~~P~~trGtD~~~t~~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~~ 92 (404)
|.++ ..|..|-+.|.|..+..+. .++.-..++++.|.+. -+++.+|..+. .+..-..+|--+.+. =|++.|
T Consensus 54 i~~~--~~g~~vti~g~V~~~~~~~--~~~~~~l~v~~~d~~~---~l~l~fFn~~~-~l~~~~~~G~~v~v~-Gk~~~~ 124 (677)
T COG1200 54 IAEA--RPGEIVTIEGTVLSHEKFP--FGKRKLLKVTLSDGTG---VLTLVFFNFPA-YLKKKLKVGERVIVY-GKVKRF 124 (677)
T ss_pred hhhc--CCCceEEEEEEEEeeeccC--CCCCceEEEEEecCcE---EEEEEEECccH-HHHhhCCCCCEEEEE-EEEeec
Confidence 4444 3678999999999876643 6677888999999433 39999998653 666655789988874 467777
Q ss_pred cCeeEEEe
Q 015600 93 QAELSAVF 100 (404)
Q Consensus 93 ~g~~~~~~ 100 (404)
++..+..-
T Consensus 125 ~~~~~~~h 132 (677)
T COG1200 125 KGGLQITH 132 (677)
T ss_pred cCceEEEc
Confidence 77765543
No 98
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=33.13 E-value=97 Score=36.01 Aligned_cols=70 Identities=20% Similarity=0.210 Sum_probs=0.0
Q ss_pred ccccccccccCCce-EeEEEEEEEEE-eeCCCCe--EEEEEEcCCCCCCCCCCCCCCCccCCCCCccccCCCCChhhhcc
Q 015600 156 DYLLSLKDISEHRY-FDLVCKVFHVS-YDDSKGL--WMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRN 231 (404)
Q Consensus 156 ~f~~~L~di~~~~f-~Dl~~qVv~~~-~~~~~~~--~~L~VwDgT~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ 231 (404)
++ ..|-++.++.+ +-+.++|-.+- .+..+++ +.++|||||+ .+
T Consensus 228 ~i-~~~~~i~~~~~~v~v~G~IF~~e~~~~ksGr~l~~i~vTD~t~--Sl------------------------------ 274 (1444)
T COG2176 228 EI-KPLIKINEEETRVKVEGYIFKIEIKELKSGRTLLNIKVTDYTS--SL------------------------------ 274 (1444)
T ss_pred ce-eehhhccccccceEEEEEEEEEeeeecccCcEEEEEEEecCch--he------------------------------
Q ss_pred CCCCceEEEEEecCchhhhhhccCCCCcEEEEe
Q 015600 232 FFPVGTVLRVSTDRSYENFGRYFTATGKWVRIR 264 (404)
Q Consensus 232 ~pp~G~~l~V~~~~~~~~~~~~~~k~g~wv~l~ 264 (404)
+++..+.+....-..+.++.|+||+.+
T Consensus 275 ------~~k~f~~~~ed~~~~~~ik~g~wvk~~ 301 (1444)
T COG2176 275 ------ILKKFLRDEEDEKKFDGIKKGMWVKAR 301 (1444)
T ss_pred ------eehhhccccccHHHHhhcccCcEEEEE
No 99
>PRK07274 single-stranded DNA-binding protein; Provisional
Probab=32.40 E-value=65 Score=27.37 Aligned_cols=26 Identities=12% Similarity=0.128 Sum_probs=23.1
Q ss_pred EEEEEecCchhhhhhccCCCCcEEEE
Q 015600 238 VLRVSTDRSYENFGRYFTATGKWVRI 263 (404)
Q Consensus 238 ~l~V~~~~~~~~~~~~~~k~g~wv~l 263 (404)
.++|++|...|+.+...++.|+.|.+
T Consensus 48 w~~v~~fg~~Ae~v~~~l~KG~~V~V 73 (131)
T PRK07274 48 FINVVLWGKLAETLASYASKGSLISI 73 (131)
T ss_pred EEEEEEehHHHHHHHHHcCCCCEEEE
Confidence 57899999999988899999999964
No 100
>PRK08763 single-stranded DNA-binding protein; Provisional
Probab=31.98 E-value=58 Score=29.02 Aligned_cols=26 Identities=15% Similarity=0.047 Sum_probs=23.1
Q ss_pred EEEEEecCchhhhhhccCCCCcEEEE
Q 015600 238 VLRVSTDRSYENFGRYFTATGKWVRI 263 (404)
Q Consensus 238 ~l~V~~~~~~~~~~~~~~k~g~wv~l 263 (404)
.++|.+|...|+.+.+.++.|+.|.+
T Consensus 53 w~~Vv~fgk~Ae~v~~~L~KGs~V~V 78 (164)
T PRK08763 53 WHRVKFFGKLGEIAGEYLRKGSQCYI 78 (164)
T ss_pred EEEEEEehHHHHHHHHhcCCCCEEEE
Confidence 57899999999988899999999974
No 101
>PF11325 DUF3127: Domain of unknown function (DUF3127); InterPro: IPR021474 This bacterial family of proteins has no known function.
Probab=31.15 E-value=2.6e+02 Score=21.99 Aligned_cols=66 Identities=9% Similarity=0.202 Sum_probs=40.7
Q ss_pred EEEEecCCceecCCCc-eEE-EEEEE-eCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEe-eEEEEEEcCe
Q 015600 28 GVVLEFSIPRKSQGTD-YVC-VLKIV-DDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLK-NVMIKKHQAE 95 (404)
Q Consensus 28 GVV~d~~~P~~trGtD-~~~-t~~I~-D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~-rvki~~~~g~ 95 (404)
|.|+...++.+.-|.. |.- .|-|- ++-++ .-+.+.+|.+..+.|-.+ ++||.|.++ +++-+.|+|+
T Consensus 4 Gkii~~l~~~~g~s~~Gw~Kre~Vlet~~qYP-~~i~f~~~~dk~~~l~~~-~~Gd~V~Vsf~i~~RE~~gr 73 (84)
T PF11325_consen 4 GKIIKVLPEQQGVSKNGWKKREFVLETEEQYP-QKICFEFWGDKIDLLDNF-QVGDEVKVSFNIEGREWNGR 73 (84)
T ss_pred cEEEEEecCcccCcCCCcEEEEEEEeCCCcCC-ceEEEEEEcchhhhhccC-CCCCEEEEEEEeeccEecce
Confidence 5555555554432211 543 23332 23333 359999999877777888 799987764 7777888865
No 102
>cd06555 ASCH_PF0470_like ASC-1 homology domain, subfamily similar to Pyrococcus furiosus Pf0470. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation.
Probab=30.38 E-value=90 Score=25.86 Aligned_cols=27 Identities=11% Similarity=0.305 Sum_probs=23.2
Q ss_pred ce-EEEEEecCchhhhhhccCCCCcEEEEece
Q 015600 236 GT-VLRVSTDRSYENFGRYFTATGKWVRIRNM 266 (404)
Q Consensus 236 G~-~l~V~~~~~~~~~~~~~~k~g~wv~l~Nv 266 (404)
|+ ++-|.+.+. + ++.+++||.+.|.|.
T Consensus 16 G~KtiEiRlnD~--k--r~~ikvGD~I~f~~~ 43 (109)
T cd06555 16 GKKTIEIRLNDE--K--RQQIKVGDKILFNDL 43 (109)
T ss_pred CCCEEEEEeccc--c--hhcCCCCCEEEEEEc
Confidence 77 999999886 3 678999999999885
No 103
>PRK13254 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=28.43 E-value=3.7e+02 Score=23.46 Aligned_cols=67 Identities=16% Similarity=0.168 Sum_probs=46.2
Q ss_pred ceeehHhhhhc---cCCEEEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEe
Q 015600 9 GIVRIKELAMH---VKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLK 85 (404)
Q Consensus 9 ~y~~i~~~~~~---~~~~vnv~GVV~d~~~P~~trGtD~~~t~~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~ 85 (404)
-|.+.+++... .+..+.+-|.|++=+.- ++..-.++|+|.|... .+.|.+-. .+|...+.|.-|.+.
T Consensus 36 yf~tpse~~~~~~~~g~~vrvgG~V~~gSi~---~~~~~~~~F~ltD~~~---~i~V~Y~G----~lPd~F~eg~~VVv~ 105 (148)
T PRK13254 36 FFYTPSEVAEGEAPAGRRFRLGGLVEKGSVQ---RGDGLTVRFVVTDGNA---TVPVVYTG----ILPDLFREGQGVVAE 105 (148)
T ss_pred eeeCHHHHhcCCccCCCeEEEeEEEecCcEE---eCCCCEEEEEEEeCCe---EEEEEECC----CCCccccCCCEEEEE
Confidence 36777777653 47789999999965442 2255678999999832 26665543 489877888866653
No 104
>PRK06752 single-stranded DNA-binding protein; Validated
Probab=27.39 E-value=1.7e+02 Score=23.90 Aligned_cols=72 Identities=7% Similarity=0.019 Sum_probs=47.5
Q ss_pred EEEEEEEEEecCCceecCCCceEEEEEEEeCCCC--------CCCeEEEEecCCCCCCCCCCCCCCEEE-EeeEEEEEEc
Q 015600 23 KVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQ--------SPELLVNIFTSSIDQLPRVLSPRDLIL-LKNVMIKKHQ 93 (404)
Q Consensus 23 ~vnv~GVV~d~~~P~~trGtD~~~t~~I~D~S~~--------~~gl~v~iF~~~~~~LP~v~~~GDII~-l~rvki~~~~ 93 (404)
.|.++|-+..--..+.|.+..-.++|+|.-...- .+-+.|.+|.+..+.+-.-.+-||-|. --+++...|.
T Consensus 4 ~v~liGrl~~dPelr~t~~G~~~~~f~lAv~~~~~~~~g~~~t~~~~v~~wg~~Ae~~~~~l~KG~~V~V~G~l~~~~~~ 83 (112)
T PRK06752 4 RVVLIGRLTKEPELYYTKQGVAYARVCVAVNRGFRNSLGEQQVDFINCVVWRKSAENVTEYCTKGSLVGITGRIHTRNYE 83 (112)
T ss_pred EEEEEEECcCCCEEEECCCCCEEEEEEEEECCCeEcCCCCEEEEEEEEEEehHHHHHHHHhcCCCCEEEEEEEEEeCccC
Confidence 5778887775433355555567778888654321 134999999976565555347799664 4578888885
Q ss_pred C
Q 015600 94 A 94 (404)
Q Consensus 94 g 94 (404)
+
T Consensus 84 ~ 84 (112)
T PRK06752 84 D 84 (112)
T ss_pred C
Confidence 4
No 105
>PRK09010 single-stranded DNA-binding protein; Provisional
Probab=27.14 E-value=84 Score=28.38 Aligned_cols=27 Identities=19% Similarity=0.089 Sum_probs=23.5
Q ss_pred EEEEEecCchhhhhhccCCCCcEEEEe
Q 015600 238 VLRVSTDRSYENFGRYFTATGKWVRIR 264 (404)
Q Consensus 238 ~l~V~~~~~~~~~~~~~~k~g~wv~l~ 264 (404)
.++|++|...|+.+.+.++.|+.|.+.
T Consensus 55 w~~V~~fgk~Ae~~~~~L~KGs~V~Ve 81 (177)
T PRK09010 55 WHRVVLFGKLAEVAGEYLRKGSQVYIE 81 (177)
T ss_pred EEEEEEehhHHHHHHHhcCCCCEEEEE
Confidence 679999999888888999999999743
No 106
>PF15489 CTC1: CST, telomere maintenance, complex subunit CTC1
Probab=25.86 E-value=1.1e+03 Score=27.57 Aligned_cols=71 Identities=21% Similarity=0.279 Sum_probs=48.0
Q ss_pred cCCEEEEEEEEEecCCceecCCCceEE-EEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCe
Q 015600 20 VKHKVNLLGVVLEFSIPRKSQGTDYVC-VLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAE 95 (404)
Q Consensus 20 ~~~~vnv~GVV~d~~~P~~trGtD~~~-t~~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~~~g~ 95 (404)
.+..+||.|.|+..++-.+++|+-|.| ++. |.. ..+.|.+=-+..-.-=....+|+-+.|.+++|.+.+|.
T Consensus 164 ~~~~~~v~G~v~~ls~l~~~~~k~fF~l~L~--~~~---~~v~viVq~pa~l~Wh~~L~~G~~yvlT~Lrvs~irg~ 235 (1144)
T PF15489_consen 164 RGRQLNVAGKVVRLSALVKSHGKTFFILSLG--DAG---SHVPVIVQEPAQLVWHRALRPGRAYVLTSLRVSKIRGH 235 (1144)
T ss_pred ccCceeeeeEEEEeeceEEEcceEEEEEEeC--CCC---ceeEEEEEecchhhhhhhcccCCeEEEeeeEEEEecCc
Confidence 467799999999999999998876554 444 222 22553332222211223448999999999999988884
No 107
>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=25.55 E-value=1.3e+02 Score=23.24 Aligned_cols=71 Identities=13% Similarity=0.145 Sum_probs=45.6
Q ss_pred EEEEEEEEecCCceecCCCceEEEEEEEeCCCC---------CCCeEEEEecCCCCC-CCCCCCCCCEEEEe-eEEEEEE
Q 015600 24 VNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQ---------SPELLVNIFTSSIDQ-LPRVLSPRDLILLK-NVMIKKH 92 (404)
Q Consensus 24 vnv~GVV~d~~~P~~trGtD~~~t~~I~D~S~~---------~~gl~v~iF~~~~~~-LP~v~~~GDII~l~-rvki~~~ 92 (404)
+.++|-|...-..+.++...-.+.|+|.=.+.. ...+.|.+|.+..+. +..+ +.||.|.+. +++...|
T Consensus 1 v~l~G~l~~~p~~~~~~~g~~~~~~~v~~~~~~~~~~~~~~~~~~~~v~~~g~~a~~~~~~~-~kG~~V~v~G~l~~~~~ 79 (100)
T cd04496 1 VILIGRLGKDPELRYTPSGTPVARFSLAVNRRRKDRDEEEEETDWIRVVAFGKLAENAAKYL-KKGDLVYVEGRLRTRSW 79 (100)
T ss_pred CEEEEEecCCCEEEECCCCCEEEEEEEEEcCceecccccccccEEEEEEEEhHHHHHHHHHh-CCCCEEEEEEEEEecee
Confidence 357777777655566665566677777544432 234899999874444 4446 789966664 5677777
Q ss_pred cCe
Q 015600 93 QAE 95 (404)
Q Consensus 93 ~g~ 95 (404)
.++
T Consensus 80 ~~~ 82 (100)
T cd04496 80 EDK 82 (100)
T ss_pred ECC
Confidence 654
No 108
>PRK05733 single-stranded DNA-binding protein; Provisional
Probab=25.45 E-value=88 Score=28.09 Aligned_cols=27 Identities=22% Similarity=0.126 Sum_probs=23.5
Q ss_pred EEEEEecCchhhhhhccCCCCcEEEEe
Q 015600 238 VLRVSTDRSYENFGRYFTATGKWVRIR 264 (404)
Q Consensus 238 ~l~V~~~~~~~~~~~~~~k~g~wv~l~ 264 (404)
.++|.+|...|+.+.+.++.|+.|.+.
T Consensus 54 w~~Vv~fgk~Ae~v~~~l~KGs~V~Ve 80 (172)
T PRK05733 54 WHRVSLFGKVAEIAGEYLRKGSQVYIE 80 (172)
T ss_pred EEEEEEehHHHHHHHHHhCCCCEEEEE
Confidence 679999998888888999999999743
No 109
>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=25.31 E-value=3.6e+02 Score=22.54 Aligned_cols=62 Identities=16% Similarity=0.171 Sum_probs=42.6
Q ss_pred ccCCEEEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCC---CCCCCCCCCCCEEEEeeEEEE
Q 015600 19 HVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSI---DQLPRVLSPRDLILLKNVMIK 90 (404)
Q Consensus 19 ~~~~~vnv~GVV~d~~~P~~trGtD~~~t~~I~D~S~~~~gl~v~iF~~~~---~~LP~v~~~GDII~l~rvki~ 90 (404)
..|+.|.+.|-|...+. .|+ .+=+.|.|.+. .+.|.+-.+.. +.+..+ ..||+|.+...-..
T Consensus 12 ~~g~~V~i~Gwv~~~R~----~gk--~~Fi~LrD~~g---~~Q~v~~~~~~~~~~~~~~l-~~gs~V~V~G~~~~ 76 (135)
T cd04317 12 HVGQEVTLCGWVQRRRD----HGG--LIFIDLRDRYG---IVQVVFDPEEAPEFELAEKL-RNESVIQVTGKVRA 76 (135)
T ss_pred HCCCEEEEEEeEehhcc----cCC--EEEEEEecCCe---eEEEEEeCCchhHHHHHhCC-CCccEEEEEEEEEC
Confidence 35788999999977553 344 67788888874 27776644322 244556 78999999996443
No 110
>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=25.17 E-value=1.5e+02 Score=28.39 Aligned_cols=66 Identities=12% Similarity=0.135 Sum_probs=46.1
Q ss_pred EEEEEEEeCCC-CCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcC-----eeEEEeecCceEEEEEeC
Q 015600 45 VCVLKIVDDSQ-QSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQA-----ELSAVFYKDSSSFALFDG 112 (404)
Q Consensus 45 ~~t~~I~D~S~-~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~~~g-----~~~~~~~~~~ss~~vf~~ 112 (404)
+..++|+|-.. ......++|.+++.+.+-.+ ..|-+.++.++.....++ .+++.+.++ |.|.-.+.
T Consensus 166 ~~klRV~d~~~~~~~~~~LTIWrPtedl~s~L-~EG~ry~i~~L~~s~~k~~~~~~~vqLtatk~-Tr~~~l~~ 237 (251)
T cd04494 166 VWKLRVTDYRSKPEKSGLLSIWRPTEDLRSLL-TEGKRYRIYGLATSNSKKRSGNEEVQLTATKK-TRYQPLPV 237 (251)
T ss_pred EEEEEEeecccCCCceEEEEEeCCCHHHHhhh-cCCcEEEEEeccccCCCCCCCcceEEEEecCc-ccceECCH
Confidence 56677777663 34568888888865444445 789999999999887666 467777654 77774443
No 111
>PRK08182 single-stranded DNA-binding protein; Provisional
Probab=25.13 E-value=1.3e+02 Score=26.24 Aligned_cols=73 Identities=12% Similarity=0.069 Sum_probs=46.7
Q ss_pred CEEEEEEEEEecCCceec-CCCc---eEEEEEEE-eCCCC----------CCCeEEEEecCCCCCCCCCCCCCCEEE-Ee
Q 015600 22 HKVNLLGVVLEFSIPRKS-QGTD---YVCVLKIV-DDSQQ----------SPELLVNIFTSSIDQLPRVLSPRDLIL-LK 85 (404)
Q Consensus 22 ~~vnv~GVV~d~~~P~~t-rGtD---~~~t~~I~-D~S~~----------~~gl~v~iF~~~~~~LP~v~~~GDII~-l~ 85 (404)
..|+++|=+..--.-+.+ .|+. -.++|+|. |.+.. ..-+.|.+|.+..+.+-.-.+-||-|. --
T Consensus 3 N~V~LiGrLg~DPElr~t~~G~~~~~~va~fslA~~r~~~~~~Ge~~~~~t~w~~V~~wg~~Ae~v~~~l~KG~~V~V~G 82 (148)
T PRK08182 3 THFVGEGNIGSAPEYREFPNGNDEPRRLLRLNVYFDNPVPTKDGEYEDRGGFWAPVELWHRDAEHWARLYQKGMRVLVEG 82 (148)
T ss_pred cEEEEEEECCCCCeEEECCCCCeeeeeEEEEEEEecCceECCCCCEEecCcEEEEEEEEhHHHHHHHHhcCCCCEEEEEE
Confidence 368888877664333444 3543 27888884 32221 013899999976676766447899555 45
Q ss_pred eEEEEEEcC
Q 015600 86 NVMIKKHQA 94 (404)
Q Consensus 86 rvki~~~~g 94 (404)
+++...|.+
T Consensus 83 rL~~~~w~d 91 (148)
T PRK08182 83 RMERDEWTD 91 (148)
T ss_pred EEEecccCC
Confidence 788888854
No 112
>PRK07459 single-stranded DNA-binding protein; Provisional
Probab=25.03 E-value=1.9e+02 Score=24.15 Aligned_cols=73 Identities=14% Similarity=0.165 Sum_probs=47.4
Q ss_pred CEEEEEEEEEecCCceecCCCceEEEEEEEeCCCC----CCCeEEEEecCCCCCCCCCCCCCCEEEE-eeEEEEEEcC
Q 015600 22 HKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQ----SPELLVNIFTSSIDQLPRVLSPRDLILL-KNVMIKKHQA 94 (404)
Q Consensus 22 ~~vnv~GVV~d~~~P~~trGtD~~~t~~I~D~S~~----~~gl~v~iF~~~~~~LP~v~~~GDII~l-~rvki~~~~g 94 (404)
..|.++|=+..--.-+.|.+..-.++|+|.-.... .+-+.|.+|.+..+.+=.-.+-|+-|.+ -+++...|.+
T Consensus 4 N~v~LiGrL~~DPelr~t~~G~~v~~fslAv~~~~~~~~t~w~~v~~wg~~Ae~~~~~l~KG~~V~V~G~l~~~~~~d 81 (121)
T PRK07459 4 NSVTLVGRAGRDPEVRYFESGSVVCNLTLAVNRRSRDDEPDWFNLEIWGKTAQVAADYVKKGSLIGITGSLKFDRWTD 81 (121)
T ss_pred cEEEEEEEccCCCEEEEcCCCCEEEEEEEEecccccCCCceEEEEEEehHHHHHHHHHcCCCCEEEEEEEEEecceEc
Confidence 36888998776322344555567888998643211 2349999999755555443377996655 5788888854
No 113
>PRK06751 single-stranded DNA-binding protein; Provisional
Probab=24.84 E-value=2.2e+02 Score=25.60 Aligned_cols=72 Identities=11% Similarity=0.111 Sum_probs=46.8
Q ss_pred EEEEEEEEEecCCceecCCCceEEEEEEEeCCC-C-------CCCeEEEEecCCCCCCCCCCCCCCEE-EEeeEEEEEEc
Q 015600 23 KVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQ-Q-------SPELLVNIFTSSIDQLPRVLSPRDLI-LLKNVMIKKHQ 93 (404)
Q Consensus 23 ~vnv~GVV~d~~~P~~trGtD~~~t~~I~D~S~-~-------~~gl~v~iF~~~~~~LP~v~~~GDII-~l~rvki~~~~ 93 (404)
.|.|+|=|+.--.-+.|.+.--+++|+|.-... . .+-+.|.+|.+..+.+-.-.+.||-| +--|++...|.
T Consensus 4 ~V~LiGrL~~DpelR~t~sG~~v~~fslAvnr~~~~~~ge~~tdwi~~v~wgk~Ae~~~~~l~KG~~V~VeGrL~~r~ye 83 (173)
T PRK06751 4 RVILVGRLTKDPDLRYTPNGVAVATFTLAVNRAFANQQGEREADFINCVIWRKQAENVANYLKKGSLAGVDGRLQTRNYE 83 (173)
T ss_pred EEEEEEEECCCCcEEECCCCCEEEEEEEEEccceecCCCCEEEEEEEEEEeCcHHHHHHHHcCCCCEEEEEEEEEeCccC
Confidence 577888776532234444444577888853321 1 12499999998767676644789955 45588999996
Q ss_pred C
Q 015600 94 A 94 (404)
Q Consensus 94 g 94 (404)
+
T Consensus 84 d 84 (173)
T PRK06751 84 G 84 (173)
T ss_pred C
Confidence 4
No 114
>PRK07135 dnaE DNA polymerase III DnaE; Validated
Probab=24.66 E-value=1.6e+02 Score=33.76 Aligned_cols=65 Identities=15% Similarity=0.171 Sum_probs=47.9
Q ss_pred ehHhhhhccCCEEEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEE
Q 015600 12 RIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILL 84 (404)
Q Consensus 12 ~i~~~~~~~~~~vnv~GVV~d~~~P~~trGtD~~~t~~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l 84 (404)
+|.++ ..+..+.+.|+|+..+.-+ |.++-|..+++-|.+-. +.+.+|.+..+..-.. ..|+++.+
T Consensus 890 ~~~~l--~~~~~~~v~g~i~~~~~~~--K~g~~maf~~~eD~~~~---~e~~~F~~~~~~~~~l-~~~~~~~~ 954 (973)
T PRK07135 890 RLKDL--RINTEYRLAIEVKNVKRLR--KANKEYKKVILSDDSVE---ITIFVNDNDYLLFETL-KKGDIYEF 954 (973)
T ss_pred hHHHh--cCCCeEEEEEEEEEEEEEe--eCCCeEEEEEEEECCCc---EEEEEcHHHHHHHHHh-hcCCEEEE
Confidence 45666 3566789999999988755 44577999999999764 9999997644333334 67888776
No 115
>PRK07459 single-stranded DNA-binding protein; Provisional
Probab=24.56 E-value=1e+02 Score=25.81 Aligned_cols=26 Identities=8% Similarity=0.104 Sum_probs=22.8
Q ss_pred EEEEEecCchhhhhhccCCCCcEEEE
Q 015600 238 VLRVSTDRSYENFGRYFTATGKWVRI 263 (404)
Q Consensus 238 ~l~V~~~~~~~~~~~~~~k~g~wv~l 263 (404)
.++|.+|...|+.+.+.++.|+.|.+
T Consensus 45 w~~v~~wg~~Ae~~~~~l~KG~~V~V 70 (121)
T PRK07459 45 WFNLEIWGKTAQVAADYVKKGSLIGI 70 (121)
T ss_pred EEEEEEehHHHHHHHHHcCCCCEEEE
Confidence 57899999988888889999999863
No 116
>KOG4757 consensus Predicted telomere binding protein [General function prediction only]
Probab=24.41 E-value=4.7 Score=40.96 Aligned_cols=46 Identities=22% Similarity=0.288 Sum_probs=38.7
Q ss_pred ccccccccccCCceEeEEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCC
Q 015600 156 DYLLSLKDISEHRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPG 205 (404)
Q Consensus 156 ~f~~~L~di~~~~f~Dl~~qVv~~~~~~~~~~~~L~VwDgT~~~~~~~~~ 205 (404)
.+ .++.|+.+.+-+.+.+++....|. ....++||+|+|.+..+ |+.
T Consensus 175 ~w-~lv~d~~~h~~~s~~~~~~~~~yS--lr~~l~~~~~~T~~~l~-Fp~ 220 (522)
T KOG4757|consen 175 SW-SLVSDITPHQRCSFYAQVIKTWYS--LRNPLLYVTDPTENLLF-FPM 220 (522)
T ss_pred ee-eeeecccccccccccccceeeEee--cccccccccCchHhhhh-ccc
Confidence 46 789999999999999999998865 36788999999999887 663
No 117
>PRK06752 single-stranded DNA-binding protein; Validated
Probab=24.11 E-value=1.2e+02 Score=24.80 Aligned_cols=26 Identities=15% Similarity=0.120 Sum_probs=22.9
Q ss_pred EEEEEecCchhhhhhccCCCCcEEEE
Q 015600 238 VLRVSTDRSYENFGRYFTATGKWVRI 263 (404)
Q Consensus 238 ~l~V~~~~~~~~~~~~~~k~g~wv~l 263 (404)
.++|.+|...|+.+.+.++.|+.|.+
T Consensus 48 ~~~v~~wg~~Ae~~~~~l~KG~~V~V 73 (112)
T PRK06752 48 FINCVVWRKSAENVTEYCTKGSLVGI 73 (112)
T ss_pred EEEEEEehHHHHHHHHhcCCCCEEEE
Confidence 67899999988888899999999963
No 118
>COG0335 RplS Ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=23.79 E-value=2.1e+02 Score=23.95 Aligned_cols=45 Identities=16% Similarity=0.254 Sum_probs=27.6
Q ss_pred CCCCCCCCCCCEEEEe-------eEEEEEEcCeeEEEeecC-ceEEEEEeCCCC
Q 015600 70 DQLPRVLSPRDLILLK-------NVMIKKHQAELSAVFYKD-SSSFALFDGNSG 115 (404)
Q Consensus 70 ~~LP~v~~~GDII~l~-------rvki~~~~g~~~~~~~~~-~ss~~vf~~~~~ 115 (404)
.++|.+ .+||-|+++ +-.+|.|.|-..+.-+.+ .++|.|=.-..|
T Consensus 16 ~~iP~f-~~GDtvrv~vki~Eg~keR~Q~FeGvVia~r~~G~~~tftvRkis~G 68 (115)
T COG0335 16 KDIPSF-RPGDTVRVHVKIVEGSKERVQAFEGVVIARRGRGISETFTVRKISYG 68 (115)
T ss_pred hhCCCC-CCCCEEEEEEEEEeCCeEEEeeeeEEEEEECCCCccceEEEEEeecC
Confidence 459999 899999964 224456666554444444 356776554444
No 119
>PRK06751 single-stranded DNA-binding protein; Provisional
Probab=23.00 E-value=1.3e+02 Score=27.00 Aligned_cols=26 Identities=8% Similarity=0.050 Sum_probs=23.2
Q ss_pred EEEEEecCchhhhhhccCCCCcEEEE
Q 015600 238 VLRVSTDRSYENFGRYFTATGKWVRI 263 (404)
Q Consensus 238 ~l~V~~~~~~~~~~~~~~k~g~wv~l 263 (404)
.++|++|...|+.+.+.++.|+.|.+
T Consensus 48 wi~~v~wgk~Ae~~~~~l~KG~~V~V 73 (173)
T PRK06751 48 FINCVIWRKQAENVANYLKKGSLAGV 73 (173)
T ss_pred EEEEEEeCcHHHHHHHHcCCCCEEEE
Confidence 67999999999888899999999963
No 120
>PRK06293 single-stranded DNA-binding protein; Provisional
Probab=22.90 E-value=1.6e+02 Score=26.21 Aligned_cols=72 Identities=14% Similarity=0.064 Sum_probs=45.6
Q ss_pred EEEEEEEEEecCCceecCCCceEEEEEEEeCCCC-----CCCeEEEEecCCCCCCCCCCCCCCEEEE-eeEEEEEEcC
Q 015600 23 KVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQ-----SPELLVNIFTSSIDQLPRVLSPRDLILL-KNVMIKKHQA 94 (404)
Q Consensus 23 ~vnv~GVV~d~~~P~~trGtD~~~t~~I~D~S~~-----~~gl~v~iF~~~~~~LP~v~~~GDII~l-~rvki~~~~g 94 (404)
.|.|+|=+..=-..+.+.+..-.++|+|.=.... ..-+.|.+|.+..+.+..-.+-||-|.+ -+++...|.+
T Consensus 3 ~V~LiGrLg~DPElR~t~sG~~v~~FsLAvn~~~~~~~~T~wi~v~awg~~Ae~v~~yL~KG~~V~VeGrL~~~~y~d 80 (161)
T PRK06293 3 FGYIVGRLGADPEERMTSKGKRVVVLRLGVKSRVGSKDETVWCRCNIWGNRYDKMLPYLKKGSGVIVAGEMSPESYVD 80 (161)
T ss_pred EEEEEEEecCCCeEEEcCCCCEEEEEEEEEeCCCCCccceEEEEEEEEhHHHHHHHHhCCCCCEEEEEEEEEeCccCC
Confidence 5778887765333344544455678888643211 1249999999766666653377995555 5788888854
No 121
>PF07933 DUF1681: Protein of unknown function (DUF1681); InterPro: IPR012466 NECAP 1 localises to clathrin-coated pits and direct binding to the globular ear domain of the alpha-adaptin subunit (alpha-ear) of the adaptor protein 2 (AP-2) complex. This interaction is mediated by a specific motif, WVQF, that uses a distinct alpha-ear interface relative to known alpha-ear-binding partners. Disruption of this interaction blocks clathrin-mediated endocytosis [].; GO: 0006897 endocytosis, 0016020 membrane; PDB: 1TQZ_A.
Probab=22.76 E-value=77 Score=28.15 Aligned_cols=16 Identities=38% Similarity=0.781 Sum_probs=13.2
Q ss_pred EEEEEEeCCCceEEEEE
Q 015600 377 TMKLTLEDPTARIHALL 393 (404)
Q Consensus 377 ~f~L~leD~t~~~~~~v 393 (404)
-|.|.|+|+++| ||||
T Consensus 86 YFvlRv~d~~Gr-~Afi 101 (160)
T PF07933_consen 86 YFVLRVQDPSGR-HAFI 101 (160)
T ss_dssp -EEEEEEETTTE-EEEE
T ss_pred eEEEEEEcCCCc-EEEE
Confidence 589999999886 8876
No 122
>PRK13732 single-stranded DNA-binding protein; Provisional
Probab=22.71 E-value=1.1e+02 Score=27.57 Aligned_cols=27 Identities=19% Similarity=0.083 Sum_probs=23.7
Q ss_pred EEEEEecCchhhhhhccCCCCcEEEEe
Q 015600 238 VLRVSTDRSYENFGRYFTATGKWVRIR 264 (404)
Q Consensus 238 ~l~V~~~~~~~~~~~~~~k~g~wv~l~ 264 (404)
.++|++|...|+.+.+.++.|+.|.+.
T Consensus 55 w~~Vv~wgk~Ae~v~~~L~KG~~V~Ve 81 (175)
T PRK13732 55 WHRVVLFGKLAEVAGEYLRKGAQVYIE 81 (175)
T ss_pred EEEEEEecHHHHHHHHhcCCCCEEEEE
Confidence 678999999888888999999999744
No 123
>PRK08486 single-stranded DNA-binding protein; Provisional
Probab=21.31 E-value=1.2e+02 Score=27.37 Aligned_cols=26 Identities=12% Similarity=0.143 Sum_probs=22.7
Q ss_pred EEEEEecCchhhhhhccCCCCcEEEE
Q 015600 238 VLRVSTDRSYENFGRYFTATGKWVRI 263 (404)
Q Consensus 238 ~l~V~~~~~~~~~~~~~~k~g~wv~l 263 (404)
.++|++|..-|+.+.+.++.|+.|.+
T Consensus 50 fi~v~~fg~~AE~~~~~l~KG~~V~V 75 (182)
T PRK08486 50 FIDIRLFGRTAEIANQYLSKGSKVLI 75 (182)
T ss_pred EEEEEEEhHHHHHHHHHcCCCCEEEE
Confidence 67899999888888889999999964
No 124
>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=21.30 E-value=1.3e+02 Score=26.56 Aligned_cols=34 Identities=12% Similarity=0.120 Sum_probs=0.0
Q ss_pred EEEEEecCchhhhhhccCCCCcEEEEeceEEEEeCcEEEEEEecCC
Q 015600 238 VLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSS 283 (404)
Q Consensus 238 ~l~V~~~~~~~~~~~~~~k~g~wv~l~Nv~~k~~~g~leG~l~~~s 283 (404)
.++|.+|...|+.+.+.++.|+.| ..+|.|+.++
T Consensus 52 ~~~v~~wg~~Ae~~~~~l~KG~~V------------~V~G~L~~~~ 85 (164)
T TIGR00621 52 WHDIVIFGRLAEVAAQYLKKGSLV------------YVEGRLRTRK 85 (164)
T ss_pred EEEEEEehHHHHHHHHhCCCCCEE------------EEEEEEEece
No 125
>COG2049 DUR1 Allophanate hydrolase subunit 1 [Amino acid transport and metabolism]
Probab=20.75 E-value=48 Score=31.04 Aligned_cols=44 Identities=9% Similarity=0.027 Sum_probs=0.0
Q ss_pred CChhhhccCCCCceEEEEEecCchhhhhhccCCCCcEEEEeceEEE
Q 015600 224 LDLETLRNFFPVGTVLRVSTDRSYENFGRYFTATGKWVRIRNMSCQ 269 (404)
Q Consensus 224 l~~~~~~~~pp~G~~l~V~~~~~~~~~~~~~~k~g~wv~l~Nv~~k 269 (404)
+|.+.---|-.+|++ ...+|++..+. --.+++||||||+.+..+
T Consensus 171 Yp~~sPGGWqlIGrT-p~~lfdp~~~~-p~ll~~Gd~VrF~~i~~~ 214 (223)
T COG2049 171 YPSASPGGWQLIGRT-PLPLFDPDREP-PALLRPGDQVRFVPIKEE 214 (223)
T ss_pred eccCCCCceeEeccc-cccccCCCCCC-CeeccCCCEEEEEecCcc
No 126
>PRK05813 single-stranded DNA-binding protein; Provisional
Probab=20.28 E-value=4.2e+02 Score=24.77 Aligned_cols=72 Identities=13% Similarity=0.046 Sum_probs=47.7
Q ss_pred EEEEEEEEEecCCceecCCCceEEEEEEEeC-CCC-CCCeEEEEecCCCCCCCCCCCCCCEEEE-eeEEEEEEcCe
Q 015600 23 KVNLLGVVLEFSIPRKSQGTDYVCVLKIVDD-SQQ-SPELLVNIFTSSIDQLPRVLSPRDLILL-KNVMIKKHQAE 95 (404)
Q Consensus 23 ~vnv~GVV~d~~~P~~trGtD~~~t~~I~D~-S~~-~~gl~v~iF~~~~~~LP~v~~~GDII~l-~rvki~~~~g~ 95 (404)
.|.++|=+..--.-+.|.+..-.++|+|.=. ... .+-+.|.+|.+..+.+-.+ +.||-|.+ -|++...|..+
T Consensus 111 ~V~LiGrL~~DPelR~t~~G~~va~f~lAvnr~~~~td~i~~v~wg~~Ae~~~~l-~KG~~V~V~GrL~sr~y~~k 185 (219)
T PRK05813 111 EIFLDGYICKEPVYRTTPFGREIADLLLAVNRPYNKSDYIPCIAWGRNARFCKTL-EVGDNIRVWGRVQSREYQKK 185 (219)
T ss_pred EEEEEEEccCCCeEEECCCCCEEEEEEEEEcCCCCCceEEEEEEEhHHhHHHhhC-CCCCEEEEEEEEEecceEcC
Confidence 4667776654322245555567788888643 322 2459999999877777676 78995555 57888888653
Done!