Query 015760
Match_columns 401
No_of_seqs 174 out of 243
Neff 7.4
Searched_HMMs 46136
Date Fri Mar 29 09:19:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/015760.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/015760hhsearch_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 3.2E-46 6.9E-51 360.8 9.8 364 3-396 2-390 (522)
2 cd04497 hPOT1_OB1_like hPOT1_O 100.0 1.7E-34 3.6E-39 250.7 17.5 137 8-146 1-138 (138)
3 PF02765 POT1: Telomeric singl 100.0 5.6E-34 1.2E-38 249.9 14.3 137 10-146 1-146 (146)
4 cd04498 hPOT1_OB2 hPOT1_OB2: A 99.9 2.7E-21 5.8E-26 162.3 12.3 109 169-288 1-123 (123)
5 PRK12366 replication factor A; 99.4 3.7E-10 7.9E-15 120.8 29.8 295 6-400 275-590 (637)
6 PRK12366 replication factor A; 99.2 8.4E-09 1.8E-13 110.4 29.1 279 8-400 61-344 (637)
7 TIGR00617 rpa1 replication fac 99.2 2.3E-08 5E-13 106.5 27.8 319 9-400 179-537 (608)
8 PRK07218 replication factor A; 99.1 1.8E-07 4E-12 94.9 31.3 285 10-401 58-352 (423)
9 PRK14699 replication factor A; 99.0 3.7E-07 7.9E-12 94.5 29.4 272 11-398 167-447 (484)
10 PRK15491 replication factor A; 99.0 5.7E-07 1.2E-11 90.5 28.0 272 9-397 56-336 (374)
11 PRK06386 replication factor A; 99.0 2.8E-06 6E-11 84.4 31.6 276 11-401 3-291 (358)
12 PRK07211 replication factor A; 98.9 2.3E-07 5.1E-12 95.2 20.0 204 8-290 159-367 (485)
13 PRK15491 replication factor A; 98.8 9E-07 2E-11 89.0 20.3 204 6-286 162-372 (374)
14 PRK07211 replication factor A; 98.5 6.8E-05 1.5E-09 77.3 26.8 269 10-397 53-329 (485)
15 PRK14699 replication factor A; 98.5 9.9E-06 2.2E-10 84.0 20.6 204 8-288 274-484 (484)
16 cd04475 RPA1_DBD_B RPA1_DBD_B: 98.2 2.8E-05 6.1E-10 63.6 11.1 74 23-101 1-79 (101)
17 TIGR00617 rpa1 replication fac 98.1 7.3E-05 1.6E-09 80.0 15.0 157 6-200 294-479 (608)
18 PRK08402 replication factor A; 98.0 0.00044 9.5E-09 69.1 18.5 187 159-401 63-273 (355)
19 PRK06461 single-stranded DNA-b 98.0 0.00024 5.1E-09 61.0 14.0 92 10-111 4-99 (129)
20 PRK07218 replication factor A; 97.7 0.0068 1.5E-07 62.0 20.6 161 159-396 59-220 (423)
21 cd04491 SoSSB_OBF SoSSB_OBF: A 97.7 0.00084 1.8E-08 52.6 11.0 72 25-102 1-75 (82)
22 PRK08402 replication factor A; 97.2 0.012 2.5E-07 59.0 15.6 139 9-180 61-207 (355)
23 PRK06461 single-stranded DNA-b 96.8 0.013 2.8E-07 50.2 10.2 88 159-291 5-101 (129)
24 cd03524 RPA2_OBF_family RPA2_O 96.8 0.0068 1.5E-07 44.9 7.5 71 25-101 1-71 (75)
25 KOG3416 Predicted nucleic acid 96.5 0.018 3.9E-07 48.4 8.1 83 11-102 5-88 (134)
26 cd04497 hPOT1_OB1_like hPOT1_O 96.4 0.044 9.5E-07 47.5 11.1 97 157-291 3-106 (138)
27 PRK07217 replication factor A; 96.3 0.075 1.6E-06 51.9 12.7 93 7-111 69-162 (311)
28 cd04489 ExoVII_LU_OBF ExoVII_L 95.8 0.12 2.6E-06 39.5 9.6 69 24-101 2-72 (78)
29 cd04481 RPA1_DBD_B_like RPA1_D 95.8 0.05 1.1E-06 44.8 7.7 82 25-108 1-90 (106)
30 PRK07217 replication factor A; 95.6 0.31 6.6E-06 47.7 13.6 165 159-400 73-244 (311)
31 PRK06386 replication factor A; 95.5 0.13 2.7E-06 51.6 10.9 88 8-107 105-194 (358)
32 PF01336 tRNA_anti-codon: OB-f 95.5 0.023 5.1E-07 42.8 4.6 68 24-101 1-70 (75)
33 PF02765 POT1: Telomeric singl 95.4 0.49 1.1E-05 41.3 13.0 97 159-288 2-109 (146)
34 cd04474 RPA1_DBD_A RPA1_DBD_A: 95.0 0.078 1.7E-06 43.5 6.6 84 12-99 1-88 (104)
35 cd04476 RPA1_DBD_C RPA1_DBD_C: 94.8 0.081 1.8E-06 47.1 6.7 58 344-401 15-96 (166)
36 cd04478 RPA2_DBD_D RPA2_DBD_D: 94.7 0.35 7.5E-06 38.6 9.4 67 24-101 2-72 (95)
37 PF15489 CTC1: CST, telomere m 94.7 0.25 5.4E-06 55.6 11.0 133 238-400 888-1041(1144)
38 cd04485 DnaE_OBF DnaE_OBF: A s 94.2 0.14 3E-06 39.0 5.9 71 26-101 2-72 (84)
39 PRK13480 3'-5' exoribonuclease 94.0 0.39 8.3E-06 47.5 9.8 82 12-101 4-85 (314)
40 cd04492 YhaM_OBF_like YhaM_OBF 93.2 0.87 1.9E-05 34.8 8.8 69 27-101 3-71 (83)
41 cd04483 hOBFC1_like hOBFC1_lik 92.8 1 2.2E-05 36.1 8.9 65 26-101 2-87 (92)
42 PF08646 Rep_fac-A_C: Replicat 91.9 0.11 2.3E-06 45.3 2.3 31 370-400 51-81 (146)
43 cd04491 SoSSB_OBF SoSSB_OBF: A 90.6 0.96 2.1E-05 35.1 6.3 46 238-286 35-80 (82)
44 PF13742 tRNA_anti_2: OB-fold 90.5 2.4 5.1E-05 34.5 8.8 79 13-100 11-94 (99)
45 cd04475 RPA1_DBD_B RPA1_DBD_B: 89.7 5.4 0.00012 32.1 10.3 60 236-299 38-97 (101)
46 cd04487 RecJ_OBF2_like RecJ_OB 85.8 8.7 0.00019 29.3 8.7 65 26-101 3-68 (73)
47 cd04474 RPA1_DBD_A RPA1_DBD_A: 85.7 2 4.4E-05 35.1 5.5 52 346-400 11-63 (104)
48 cd04488 RecG_wedge_OBF RecG_we 84.7 6.7 0.00014 28.8 7.7 68 26-100 2-69 (75)
49 PRK07373 DNA polymerase III su 82.0 4.9 0.00011 41.8 7.7 89 8-101 266-355 (449)
50 cd04484 polC_OBF polC_OBF: A s 80.7 17 0.00038 28.2 8.7 69 25-98 3-74 (82)
51 cd04490 PolII_SU_OBF PolII_SU_ 80.0 6.8 0.00015 30.4 6.2 59 24-91 2-62 (79)
52 PF12100 DUF3576: Domain of un 78.2 5.3 0.00011 32.7 5.1 53 9-68 17-70 (103)
53 KOG4757 Predicted telomere bin 78.0 0.079 1.7E-06 53.3 -6.6 214 156-393 175-450 (522)
54 cd04482 RPA2_OBF_like RPA2_OBF 77.2 9.8 0.00021 30.3 6.5 60 26-93 3-64 (91)
55 PF09104 BRCA-2_OB3: BRCA2, ol 76.5 12 0.00025 32.7 7.0 64 20-90 17-81 (143)
56 PRK05673 dnaE DNA polymerase I 76.2 7.2 0.00016 45.2 7.4 88 9-101 964-1052(1135)
57 TIGR00237 xseA exodeoxyribonuc 75.2 22 0.00047 36.8 10.1 80 13-101 9-90 (432)
58 cd04498 hPOT1_OB2 hPOT1_OB2: A 74.2 3.7 8.1E-05 34.8 3.4 35 60-95 62-96 (123)
59 PF09104 BRCA-2_OB3: BRCA2, ol 73.7 33 0.00071 29.9 9.1 64 168-271 19-83 (143)
60 PRK00286 xseA exodeoxyribonucl 73.3 26 0.00056 36.2 10.1 72 21-101 23-96 (438)
61 cd03524 RPA2_OBF_family RPA2_O 72.9 31 0.00067 24.5 9.3 25 171-196 1-27 (75)
62 cd04495 BRCA2DBD_OB3 BRCA2DBD_ 71.7 13 0.00028 30.3 5.7 64 26-95 2-66 (100)
63 PRK06920 dnaE DNA polymerase I 69.0 14 0.0003 42.8 7.4 89 8-101 930-1018(1107)
64 PF01336 tRNA_anti-codon: OB-f 68.4 44 0.00095 24.4 9.1 60 171-272 2-61 (75)
65 KOG1030 Predicted Ca2+-depende 67.7 12 0.00026 33.4 5.3 26 370-395 52-77 (168)
66 KOG3056 Protein required for S 67.7 8.8 0.00019 40.4 5.1 70 23-95 187-257 (578)
67 PRK07374 dnaE DNA polymerase I 64.6 19 0.00041 41.9 7.5 89 8-101 986-1075(1170)
68 PF01245 Ribosomal_L19: Riboso 64.5 23 0.00051 29.5 6.2 40 70-110 14-61 (113)
69 PRK05338 rplS 50S ribosomal pr 64.3 17 0.00037 30.5 5.3 43 70-113 14-64 (116)
70 cd04480 RPA1_DBD_A_like RPA1_D 62.0 15 0.00033 28.6 4.4 45 348-399 1-46 (86)
71 PF15072 DUF4539: Domain of un 58.8 9.1 0.0002 30.4 2.6 21 374-394 20-40 (86)
72 cd04478 RPA2_DBD_D RPA2_DBD_D: 57.1 14 0.0003 29.2 3.5 22 374-395 17-38 (95)
73 TIGR01024 rplS_bact ribosomal 56.5 27 0.00058 29.2 5.1 43 70-113 14-64 (113)
74 PRK10917 ATP-dependent DNA hel 54.5 58 0.0013 35.7 8.9 79 11-98 51-129 (681)
75 PF15072 DUF4539: Domain of un 54.4 40 0.00087 26.7 5.6 63 23-94 3-66 (86)
76 CHL00084 rpl19 ribosomal prote 53.4 34 0.00074 28.8 5.3 41 70-111 18-66 (117)
77 TIGR00643 recG ATP-dependent D 51.0 84 0.0018 34.1 9.3 77 12-98 25-102 (630)
78 PRK06826 dnaE DNA polymerase I 50.3 43 0.00093 39.1 7.2 77 20-101 990-1067(1151)
79 KOG4792 Crk family adapters [S 49.3 25 0.00055 33.0 4.2 60 230-293 224-289 (293)
80 cd04486 YhcR_OBF_like YhcR_OBF 48.6 1.2E+02 0.0027 23.3 8.3 62 27-101 3-69 (78)
81 cd04490 PolII_SU_OBF PolII_SU_ 48.2 18 0.00039 28.0 2.7 21 376-396 20-40 (79)
82 COG1200 RecG RecG-like helicas 48.1 2.3E+02 0.0051 31.0 11.7 80 13-101 54-133 (677)
83 COG1570 XseA Exonuclease VII, 47.3 1.7E+02 0.0037 30.3 10.2 71 22-101 24-96 (440)
84 PRK05672 dnaE2 error-prone DNA 45.5 50 0.0011 38.1 6.8 86 9-101 940-1026(1046)
85 PF02721 DUF223: Domain of unk 45.2 66 0.0014 25.5 5.7 39 236-274 9-47 (95)
86 cd04492 YhaM_OBF_like YhaM_OBF 43.4 32 0.00068 25.8 3.5 22 373-394 19-40 (83)
87 COG1107 Archaea-specific RecJ- 41.9 1.1E+02 0.0023 32.9 7.9 80 10-100 202-282 (715)
88 PRK00448 polC DNA polymerase I 41.2 1E+02 0.0022 36.9 8.5 87 7-99 223-313 (1437)
89 PRK07279 dnaE DNA polymerase I 41.1 66 0.0014 37.1 6.8 86 9-101 874-960 (1034)
90 cd04489 ExoVII_LU_OBF ExoVII_L 38.1 40 0.00086 25.3 3.3 23 374-396 18-40 (78)
91 COG1599 RFA1 Single-stranded D 35.5 1.3E+02 0.0028 30.8 7.4 93 12-111 51-147 (407)
92 cd04480 RPA1_DBD_A_like RPA1_D 34.6 66 0.0014 24.9 4.1 57 42-100 17-73 (86)
93 cd04483 hOBFC1_like hOBFC1_lik 32.4 2.5E+02 0.0055 22.2 9.6 26 171-198 1-26 (92)
94 PRK07772 single-stranded DNA-b 32.1 81 0.0018 28.8 4.7 74 21-94 4-90 (186)
95 PRK13254 cytochrome c-type bio 29.1 3.5E+02 0.0076 23.6 8.0 66 10-85 37-105 (148)
96 cd04495 BRCA2DBD_OB3 BRCA2DBD_ 27.6 3E+02 0.0064 22.5 6.6 33 240-272 31-64 (100)
97 cd04317 EcAspRS_like_N EcAspRS 25.3 3.6E+02 0.0079 22.6 7.5 61 20-90 13-76 (135)
98 PF07933 DUF1681: Protein of u 24.9 64 0.0014 28.7 2.6 16 374-390 86-101 (160)
99 PF11325 DUF3127: Domain of un 23.5 3.7E+02 0.0081 21.2 7.6 66 28-95 4-73 (84)
100 cd04496 SSB_OBF SSB_OBF: A sub 23.2 1.5E+02 0.0032 23.0 4.4 71 24-95 1-82 (100)
101 PRK07135 dnaE DNA polymerase I 23.1 1.8E+02 0.0039 33.4 6.4 65 12-84 890-954 (973)
102 COG0335 RplS Ribosomal protein 23.0 2.2E+02 0.0047 23.8 5.2 45 70-115 16-68 (115)
103 PRK06752 single-stranded DNA-b 22.6 2.3E+02 0.005 23.2 5.5 73 23-95 4-85 (112)
104 PF15489 CTC1: CST, telomere m 22.5 1.3E+03 0.028 27.1 17.0 71 20-95 164-235 (1144)
105 PRK06751 single-stranded DNA-b 22.1 2.5E+02 0.0055 25.2 6.0 72 23-94 4-84 (173)
106 smart00800 uDENN Domain always 20.6 1.5E+02 0.0032 23.2 3.7 13 357-369 42-54 (89)
107 PRK07459 single-stranded DNA-b 20.3 2.5E+02 0.0055 23.5 5.3 72 23-94 5-81 (121)
108 PRK08182 single-stranded DNA-b 20.2 1.7E+02 0.0037 25.5 4.4 72 23-94 4-91 (148)
109 cd04494 BRCA2DBD_OB2 BRCA2DBD_ 20.1 2.1E+02 0.0045 27.4 5.2 66 45-112 166-237 (251)
No 1
>KOG4757 consensus Predicted telomere binding protein [General function prediction only]
Probab=100.00 E-value=3.2e-46 Score=360.82 Aligned_cols=364 Identities=24% Similarity=0.243 Sum_probs=273.4
Q ss_pred CCCCCcceeeHHhhhhccCCEEEEEEEEEEcCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEE
Q 015760 3 SQRNQGGIVRIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLI 82 (401)
Q Consensus 3 ~~~~~y~y~~i~~~~~~~~~~vnviGVVvd~~~P~~trGtD~~~tl~I~D~s~~~~gl~v~iF~~~~e~LP~v~~~GDII 82 (401)
.-++.|+|..+++++.+.+..||+||||++++||++++|+||+||++|+||...+.||+|++|+++.++||.|+++||||
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 34688999999999999999999999999999999999999999999999999889999999999999999999999999
Q ss_pred EEeeEEEEEecCeeEEEeecCce-EEEEEeCCCCCCccccccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCccccccc
Q 015760 83 LLKNVMIKKHQAELSAVFYKDSS-SFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSL 161 (401)
Q Consensus 83 ~l~rvki~~~~g~~~~~~~~~~s-s~~lf~~~~~~~~~P~~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~f~~~L 161 (401)
+|||+|||.|+.+.+|+++..|+ +|++|+|+ +.+..|||+|+. |-++ .+||+|++.+.....+ ++ ..+
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 99999999999999999998764 59999999 889999999987 8777 8999999999887776 46 778
Q ss_pred ccccCCceeeeEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCcc-cCCCCCccccCCCCcHHhhhcCCCCccEEE
Q 015760 162 KDISEHRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDE-EHNPLPLHIESSPLDLETLRNFFPVGTVLR 240 (401)
Q Consensus 162 ~di~~~~f~Dl~~qVv~~~~~~~~~~~~L~VwDgT~~p~~~~~~~~~~~-~~~~~~~~~e~~~l~~~~~~~~p~~G~~l~ 240 (401)
.++.++..-.|.||+++.. ......|. .|||-|.+...++++...-- -+.-.|++.+. ++...+..||..|.+.+
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 8888888888888888887 55567777 79996655554444321100 01124566655 66677889998899888
Q ss_pred EEecCcchhhhcccCCCCCEEEEeeeEEEEeCcEEEEEeecCcceEEccCCChHHH-H--Hhh----------------h
Q 015760 241 VSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDNDNVVW-D--YMR----------------E 301 (401)
Q Consensus 241 V~~~~~~~~~~~~~~k~g~wv~l~Nv~~k~~~G~leG~l~~~s~i~~l~~~d~~v~-~--l~r----------------~ 301 (401)
+..+...++...+.+.+|.-+..+|+....+. .|.++ ++.+. |..-. + ++. |
T Consensus 227 ~r~~rv~~e~~i~ilq~~~d~~~~Nl~~e~D~-----~f~~~--~~sl~--dh~~lsrc~~~~~saprl~~sl~lhc~~e 297 (522)
T KOG4757|consen 227 SRWDRVSEEFSICILQDEHDFYCRNLIKEGDY-----VFMKN--VRSLI--DHLGLSRCILHGDSAPRLNMSLELHCSEE 297 (522)
T ss_pred eeeecccccccchhccccchhhhhhhcccccc-----ccccc--chhhh--HHHHHHHHHHHhhccccccceeEeecCcc
Confidence 88777777777777888888888888763222 22221 11111 11100 0 000 1
Q ss_pred hhcCCCCCCCCcCCCCCCcccccccCCCccccHHHHhcCCCCCceEE-EEEEEEE---eeCCCccccccCCCceEEEEEE
Q 015760 302 RISGGHGHMPIWTDPSSQFLTEVDWVNVASVTLMKIATQLQGNVRCC-CIVRVVS---IHPFQAEHYSSPNGSSEYTMKL 377 (401)
Q Consensus 302 r~~~~~~~~p~~~~p~~~~~t~~~~~~~p~ttL~dIL~~~~~~~kfr-~~VRVv~---~~P~~~~df~~~~g~~~~~~~L 377 (401)
.+..++..+. .+-.++..|.+++..+|+++|||+++...++.||| |.||+|+ .+|..+|.+.--+ -.+.-
T Consensus 298 hll~ev~~e~--r~~~q~~~tgi~~v~a~fvsl~Ds~t~~~vt~k~R~~vvrfva~~~~~P~sve~l~~i~----i~l~~ 371 (522)
T KOG4757|consen 298 HLLNEVKPEK--RLYVQNCQTGIEAVIAPFVSLMDSETPFIVTEKKRTCVVRFVAHVINYPASVELLTIIT----ILLAP 371 (522)
T ss_pred hhhcccCccc--ceeecccccCcchhhcccchhhhhccccccchhcceeeeeehhhcccccchhhhhhhhh----hhhHH
Confidence 1111221111 11245778889999999999999999888999999 9999999 9999999985331 12333
Q ss_pred EEeCCCceEEEEEeccccc
Q 015760 378 TLEDPTARIHALLCGKEWV 396 (401)
Q Consensus 378 ~leD~t~~i~~~v~~~da~ 396 (401)
+.+|.++|.|+.++..|..
T Consensus 372 ic~l~n~r~H~~l~~le~s 390 (522)
T KOG4757|consen 372 ICNLLNPRKHRLLVQLEDS 390 (522)
T ss_pred Hhhhhchhhhhhhhhhccc
Confidence 4555566666655555544
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=1.7e-34 Score=250.74 Aligned_cols=137 Identities=33% Similarity=0.509 Sum_probs=130.0
Q ss_pred cceeeHHhhhhccCCEEEEEEEEEEcCCceecCCCceEEEEEEEeCCCC-CCCeEEEEecCCCCCCCCCCCCCCEEEEee
Q 015760 8 GGIVRIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQ-SPELLVNIFTSSIDQLPRVLSPRDLILLKN 86 (401)
Q Consensus 8 y~y~~i~~~~~~~~~~vnviGVVvd~~~P~~trGtD~~~tl~I~D~s~~-~~gl~v~iF~~~~e~LP~v~~~GDII~l~r 86 (401)
|.|++|++|.+..++.|||||||+|+++|++++|+||+|+|+|+|+|.. +.||+|+||+++.+.||.+ ++||||+|||
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 015760 87 VMIKKHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCV 146 (401)
Q Consensus 87 vki~~~~g~~~~~~~~~~ss~~lf~~~~~~~~~P~~~s~~~~~~~~~e~~~v~~Lr~W~~ 146 (401)
++|+.|+|+.+++++.+.||||||++..+....|+++++. ++++++|++++..||+|+.
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 9999999999999998678999999999999999987775 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=5.6e-34 Score=249.86 Aligned_cols=137 Identities=35% Similarity=0.617 Sum_probs=127.0
Q ss_pred eeeHHhhhhccCCEEEEEEEEEEcCCc--eecCCCceEEEEEEEeCCCCC-----CCeEEEEecCCCCCCCCCCCCCCEE
Q 015760 10 IVRIKELAMHVKHKVNLLGVVLEFSIP--RKSQGTDYVCVLKIVDDSQQS-----PELLVNIFTSSIDQLPRVLSPRDLI 82 (401)
Q Consensus 10 y~~i~~~~~~~~~~vnviGVVvd~~~P--~~trGtD~~~tl~I~D~s~~~-----~gl~v~iF~~~~e~LP~v~~~GDII 82 (401)
|++|+++....+..|||||||+++++| ++|||+||+|+|+|+|+|+.. .||+|++|+++++.||.+..+||||
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 015760 83 LLKNVMIKKHQAELSAVFYKD-SSSFALF-DGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCV 146 (401)
Q Consensus 83 ~l~rvki~~~~g~~~~~~~~~-~ss~~lf-~~~~~~~~~P~~~s~~~~~~~~~e~~~v~~Lr~W~~ 146 (401)
+|||+||+.|+|+++++++.. .++|+|| ++..+.++.||+.++++++++++|+++++.||+|++
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 999999999999999999865 6899999 888889999998888779999999999999999974
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=99.86 E-value=2.7e-21 Score=162.34 Aligned_cols=109 Identities=26% Similarity=0.396 Sum_probs=84.0
Q ss_pred eeeeEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCccccCCCCcHHhhhcCCCCcc-EEEEEecCcc
Q 015760 169 YFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGT-VLRVSTDRSY 247 (401)
Q Consensus 169 f~Dl~~qVv~~~~~~~~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~~~~~e~~~l~~~~~~~~p~~G~-~l~V~~~~~~ 247 (401)
||||+||||+++ +.++++++|||||||+||+..+....+++ ...|++ +...+.|+++|+ .++|++|++|
T Consensus 1 ~~DLvcqVv~v~-~~d~~~~~L~VwDgT~~p~~~~~~~~~~~------~~~e~d---~~~k~~~~gpg~~ti~It~yD~H 70 (123)
T cd04498 1 YFDLLCQLLSVV-ETDSSSTLLKVWDGTKFPPPLRKVKVEDD------VVLEGD---RSLKHREEGGKQLTIDILVYDNH 70 (123)
T ss_pred CccEEEEEEEEE-EecCCeEEEEEecCCCCChhHhheecccc------Cccccc---hhhhhhccCCCeEEEEEEEEcch
Confidence 799999999999 77889999999999999877766654432 112333 334567777777 6899999999
Q ss_pred hhhhcccCCCCCEEEEeeeEEEEeCc--------EEEEEe-ecC----cceEEc
Q 015760 248 ENFGRYFTATGKWVRIRNMSCQVSSG--------MWHGLL-QSS----SKIRLF 288 (401)
Q Consensus 248 ~~~~~~~~k~g~wv~l~Nv~~k~~~G--------~leG~l-~~~----s~i~~l 288 (401)
+.++++ +|+||||+|+|||+|.... .|||.+ +.- ++|+++
T Consensus 71 ~~~ar~-lK~GdfV~L~NVhiK~~~~~~~~~~~~~Le~~l~~gg~~~~rgi~vl 123 (123)
T cd04498 71 VELAKS-LKPGDFVRIYNVHAKSYSSKNEHDENDHLHFHLVHGGTEYGRGIRVL 123 (123)
T ss_pred HHHHhh-CCCCCEEEEEEEEEEeccCCcccCCcceEEEEEccCceeeccceeeC
Confidence 998888 9999999999999998543 678777 432 456553
No 5
>PRK12366 replication factor A; Reviewed
Probab=99.39 E-value=3.7e-10 Score=120.80 Aligned_cols=295 Identities=17% Similarity=0.189 Sum_probs=181.1
Q ss_pred CCcceeeHHhhhhc-cCCEEEEEEEEEEcCCcee---cCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCE
Q 015760 6 NQGGIVRIKELAMH-VKHKVNLLGVVLEFSIPRK---SQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDL 81 (401)
Q Consensus 6 ~~y~y~~i~~~~~~-~~~~vnviGVVvd~~~P~~---trGtD~~~tl~I~D~s~~~~gl~v~iF~~~~e~LP~v~~~GDI 81 (401)
..+.+++|+++-.- .+..+++-|-|+...+++. .+|+--..++.|.|.+- .+.+++|.+..+.+..+ ..||+
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 45678999999532 3568999999999988754 36888999999999872 39999999877778877 79999
Q ss_pred EEEeeEEEEEecC-----eeEEEeecCceEEEEEeCCCCCCccccccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCcc
Q 015760 82 ILLKNVMIKKHQA-----ELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSND 156 (401)
Q Consensus 82 I~l~rvki~~~~g-----~~~~~~~~~~ss~~lf~~~~~~~~~P~~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~ 156 (401)
+.+.+++++.|+. ++.+.++.. |.... + .... .| ...+ +
T Consensus 351 y~is~~~vk~y~~~~~~~~~El~~~~~-s~I~~-d--~~~~-~p----~~~~---------------------------~ 394 (637)
T PRK12366 351 VKIENCKVRTYYDNEGEKRVDLNAGYS-SEIIK-D--ESIS-FE----EIEE---------------------------K 394 (637)
T ss_pred EEEecCEEeeccccCCCcCEEEEcCCc-eEEEe-c--cCCc-cc----ceee---------------------------c
Confidence 9999999998863 344444433 33432 1 1111 11 0001 1
Q ss_pred ccccccccc----CCceeeeEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCccccCCCCcHHhhhcC
Q 015760 157 YLLSLKDIS----EHRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNF 232 (401)
Q Consensus 157 f~~~L~di~----~~~f~Dl~~qVv~~~~~~~~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~~~~~e~~~l~~~~~~~~ 232 (401)
| ..|+||. .+..+|+++.|+.+. + -..++ . -||+...-.... +.| +
T Consensus 395 ~-~~i~dI~~~~~~~~~VdVig~V~~v~-~--~~~i~-~-k~G~~~~~r~i~--l~D----------~------------ 444 (637)
T PRK12366 395 I-YKIKDILNLEEDDNDITVIARVVEDY-P--VNEFE-R-SDGSKGKVRNIE--LAD----------G------------ 444 (637)
T ss_pred c-ccHHHhhcccCCCcEEEEEEEEEEcc-C--ceEEE-e-cCCCEeEEEEEE--EEe----------C------------
Confidence 4 4555553 578999999999887 4 11211 1 234322111000 000 0
Q ss_pred CCCccEEEEEecCcchhhhcccCCCCCEEEEeeeEEEEeCcEEEEEeecCcceEEccCCChHHHHHhh-hhhcCCCCCCC
Q 015760 233 FPVGTVLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDNDNVVWDYMR-ERISGGHGHMP 311 (401)
Q Consensus 233 p~~G~~l~V~~~~~~~~~~~~~~k~g~wv~l~Nv~~k~~~G~leG~l~~~s~i~~l~~~d~~v~~l~r-~r~~~~~~~~p 311 (401)
-| .+++++|..++. ..+.+|+.|.+.|..++..+|.++..+...+.|.+.++... +| .|
T Consensus 445 --TG-~I~vtlWg~~a~---~~~~~G~vi~i~~~~V~~~~g~~~Ls~~~~s~i~~~p~~~e-----l~~~~--------- 504 (637)
T PRK12366 445 --TG-SIRLTLWDDDAE---IEIKEGDAIKILHPYVKENGDYLDLSIGRYGRIEINPEGEI-----IKSNR--------- 504 (637)
T ss_pred --CC-EEEEEEeccccc---cCCCCCCEEEEEeeEEEeCCCeeEEEecCcceEEECCCCcc-----ccccc---------
Confidence 15 578999997654 35789999999999999999988888888888876554332 21 00
Q ss_pred CcCCCCCCcccccccCC-Cccc-cHHHHhcCCC-CCceEEEEEEEEEeeCCCccccccCC----CceEEEEEEEEeCCCc
Q 015760 312 IWTDPSSQFLTEVDWVN-VASV-TLMKIATQLQ-GNVRCCCIVRVVSIHPFQAEHYSSPN----GSSEYTMKLTLEDPTA 384 (401)
Q Consensus 312 ~~~~p~~~~~t~~~~~~-~p~t-tL~dIL~~~~-~~~kfr~~VRVv~~~P~~~~df~~~~----g~~~~~~~L~leD~t~ 384 (401)
..+.++.... .-++ +|..|..... .++|=-|.=+|+.- +-.=.|..+ ..|.|++.+.|-|.|+
T Consensus 505 -------~~I~~i~~~~~~~v~g~i~~i~~~~~~y~aCp~CnkKv~~~---~g~~~C~~c~~~~p~~~~~l~~~i~D~TG 574 (637)
T PRK12366 505 -------KFIADLEEDDTVEIRGTVVDIRKQKIILYLCPNCRKRVEEV---DGEYICEFCGEVEPNELLMLNFTLDDGTG 574 (637)
T ss_pred -------cCHHHcccCCeEEEEEEEEEEeCCCEEEecccccCeEeEcC---CCcEECCCCCCCCCcEEEEEEEEEEcCCC
Confidence 0000000000 0000 1111111100 01111244444421 000022222 3788999999999999
Q ss_pred eEEEEEeccccccccc
Q 015760 385 RIHALLCGKEWVRFQL 400 (401)
Q Consensus 385 ~i~~~v~~~da~~f~~ 400 (401)
.+.+.++++.|+.+||
T Consensus 575 ~~~~t~f~e~ae~l~G 590 (637)
T PRK12366 575 TINCRFYGKNVEKLLG 590 (637)
T ss_pred CEEEEEEhHHhHHHhC
Confidence 9999999999999997
No 6
>PRK12366 replication factor A; Reviewed
Probab=99.23 E-value=8.4e-09 Score=110.43 Aligned_cols=279 Identities=13% Similarity=0.163 Sum_probs=184.7
Q ss_pred cceeeHHhhhhccCC-EEEEEEEEEEcCCcee---cCC-CceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEE
Q 015760 8 GGIVRIKELAMHVKH-KVNLLGVVLEFSIPRK---SQG-TDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLI 82 (401)
Q Consensus 8 y~y~~i~~~~~~~~~-~vnviGVVvd~~~P~~---trG-tD~~~tl~I~D~s~~~~gl~v~iF~~~~e~LP~v~~~GDII 82 (401)
-.+++|+++. +++ .+++.|-|+....|+. .+| .-..+++.|.|.+= .+++.+|.+..+.+|.+ .+||||
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 EEDFKISDIE--EGQINVEITGRIIEISNIKTFTRKDGSTGKLANITIADNTG---TIRLTLWNDNAKLLKGL-KEGDVI 134 (637)
T ss_pred cceeEHHHCc--CCCcceEEEEEEEEccCCeEEECCCCCccEEEEEEEEcCCC---EEEEEEEchhhhhhccC-CCCCEE
Confidence 3578999994 555 5999999999998873 236 46789999999765 29999999877778888 899999
Q ss_pred EEeeEEEEEecCeeEEEeecCceEEEEEeCCCCCCccccccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCcccccccc
Q 015760 83 LLKNVMIKKHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSLK 162 (401)
Q Consensus 83 ~l~rvki~~~~g~~~~~~~~~~ss~~lf~~~~~~~~~P~~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~f~~~L~ 162 (401)
.+.++.++.|+|++.+..+.. ++....+-. .....|-. . + .| .|.
T Consensus 135 ~i~~~~v~~~~~~~el~~~~~-t~I~~~~~~-d~~~i~~~---~-~---------------------------~~--~I~ 179 (637)
T PRK12366 135 KIENARSRKWNNDVELNSGSE-TRIDKLEKY-DESRYPII---K-E---------------------------NY--DIP 179 (637)
T ss_pred EEeccEecccCCceEEEcCCc-ceEEEcccc-ccccCCcc---c-c---------------------------cc--ccc
Confidence 999999999999998766644 444433210 01111100 0 0 13 688
Q ss_pred cccCCceeeeEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCccccCCCCcHHhhhcCCCCccEEEEE
Q 015760 163 DISEHRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRVS 242 (401)
Q Consensus 163 di~~~~f~Dl~~qVv~~~~~~~~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~~~~~e~~~l~~~~~~~~p~~G~~l~V~ 242 (401)
|+.++.++|+++.|+++. + -..+. --||++-.-..+. +.| + -| .++++
T Consensus 180 el~~g~~v~v~G~V~~~~-~--~~~f~--rkdg~~~~~r~~~--l~D----------~--------------TG-~irvT 227 (637)
T PRK12366 180 ELEPNLSATIEGEVTKAY-P--IKEFT--RKDGSEGKLKSFI--LKD----------D--------------TG-SIRVT 227 (637)
T ss_pred ccCCCCeEEEEEEEEEcc-C--cEEEE--EcCCCeeEEEEEE--EEc----------C--------------CC-cEEEE
Confidence 889999999999999988 4 12222 1155422111100 000 0 15 57999
Q ss_pred ecCcchhhhcccCCCCCEEEEeeeEEEEeCcEEEEEeecCcceEEccCCChHHHHHhhhhhcCCCCCCCCcCCCCCCccc
Q 015760 243 TDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDNDNVVWDYMRERISGGHGHMPIWTDPSSQFLT 322 (401)
Q Consensus 243 ~~~~~~~~~~~~~k~g~wv~l~Nv~~k~~~G~leG~l~~~s~i~~l~~~d~~v~~l~r~r~~~~~~~~p~~~~p~~~~~t 322 (401)
+|...+. ..+.+|+.|++.+....-..|.+|-.....+.|..... .
T Consensus 228 lW~~~a~---~~~~~g~vv~i~g~~~~~~~~~~el~~~~~~~i~~~~~------------~------------------- 273 (637)
T PRK12366 228 LWNDLTD---IEVNKGDIVRVKGYVKQGYRTGLEISANNIEILEKLEK------------E------------------- 273 (637)
T ss_pred EEChhhc---ccCCCCCEEEEEeEEecCcCCceEEEeCCceeeccccc------------c-------------------
Confidence 9997664 35899999999883333233556554322222211000 0
Q ss_pred ccccCCCccccHHHHhcCCCCCceEEEEEEEEEeeCCCccccccCCCceEEEEEEEEeCCCceEEEEEeccccccccc
Q 015760 323 EVDWVNVASVTLMKIATQLQGNVRCCCIVRVVSIHPFQAEHYSSPNGSSEYTMKLTLEDPTARIHALLCGKEWVRFQL 400 (401)
Q Consensus 323 ~~~~~~~p~ttL~dIL~~~~~~~kfr~~VRVv~~~P~~~~df~~~~g~~~~~~~L~leD~t~~i~~~v~~~da~~f~~ 400 (401)
-...+.++|.++-... +..+..+.+||++..|. +.|....|. --.|.+.|-|.||+|++-++++.|++|.+
T Consensus 274 ---~~~~~~~pI~~L~~~~-~g~~~~I~grV~~~~~~--R~f~~~~g~-gkv~s~~l~D~tG~IR~t~w~~~~d~~~~ 344 (637)
T PRK12366 274 ---EKELEIVNIEELTEFE-DGEEVDVKGRIIAISDK--REVERDDRT-AEVQDIELADGTGRVRVSFWGEKAKILEN 344 (637)
T ss_pred ---ccccCceeHHHCCccc-CCCEEEEEEEEEecCCc--eEEEcCCCc-EEEEEEEEEcCCCeEEEEEeCchhhhhcc
Confidence 0012456677763332 45589999999997654 456666665 57889999999999999999999887764
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=99.16 E-value=2.3e-08 Score=106.49 Aligned_cols=319 Identities=13% Similarity=0.112 Sum_probs=190.2
Q ss_pred ceeeHHhhhhccCCEEEEEEEEEEcCCcee---cCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCC-CCCCCCCCEEEE
Q 015760 9 GIVRIKELAMHVKHKVNLLGVVLEFSIPRK---SQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQL-PRVLSPRDLILL 84 (401)
Q Consensus 9 ~y~~i~~~~~~~~~~vnviGVVvd~~~P~~---trGtD~~~tl~I~D~s~~~~gl~v~iF~~~~e~L-P~v~~~GDII~l 84 (401)
.+++|+++-- ......+-|-|+.....+. .+|.....++.|.|++ ..|.+.+|.+..+.+ |.+ ++|+|+.+
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 5899999942 2346899999998776543 2455678889999943 349999999755554 566 89999999
Q ss_pred eeEEEEEecCeeEEEeecC---ceEEEEEeCCCCCCccccccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCccccccc
Q 015760 85 KNVMIKKHQAELSAVFYKD---SSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSL 161 (401)
Q Consensus 85 ~rvki~~~~g~~~~~~~~~---~ss~~lf~~~~~~~~~P~~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~f~~~L 161 (401)
.+.+++..+++...+.+.. +..+.......+..-.|- ..| +| ..|
T Consensus 254 s~~~Vk~an~~y~~~~~~yei~f~~~T~I~~~~d~~~iP~----~~~---------------------------~f-~~i 301 (608)
T TIGR00617 254 SKGSLKPANKQFTNLGNDYEMTLDRDTVIEECEDETAIPK----IQF---------------------------NF-VKI 301 (608)
T ss_pred CceEEEEccccccCCCCCEEEEECCCeEEEECCCcccCCc----ccc---------------------------cc-eEH
Confidence 9999998877654433310 111111211111111220 012 24 455
Q ss_pred ccc---cCCceeeeEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCccccCCCCcHHhhhcCCCCccE
Q 015760 162 KDI---SEHRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTV 238 (401)
Q Consensus 162 ~di---~~~~f~Dl~~qVv~~~~~~~~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~~~~~e~~~l~~~~~~~~p~~G~~ 238 (401)
.|| ..+.++|+++.|..+. +.. .++-+ .||+...-..+. +..- -|..
T Consensus 302 ~dI~~~~~~~~VDVIGvV~~v~-~~~--~i~~k-~~g~~~~kR~i~------------------------L~D~--sg~s 351 (608)
T TIGR00617 302 DDIGGYEGNSLVDVIGIVQSVS-PTQ--TITSR-KNNKEFPKRDIT------------------------LVDD--SGKS 351 (608)
T ss_pred HHhhhhcCCCCccEEEEEeEec-Cce--EEEEc-CCCCeeeeEEEE------------------------EEeC--CCCE
Confidence 555 4567999999999887 311 11111 122211111100 0111 1667
Q ss_pred EEEEecCcchhhhcccCCCCCEEEEeeeEEEEeCcEEEEEeecCcceEEccCCChHHHHHhhhhhcCCCCCCCCcCCCCC
Q 015760 239 LRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDNDNVVWDYMRERISGGHGHMPIWTDPSS 318 (401)
Q Consensus 239 l~V~~~~~~~~~~~~~~k~g~wv~l~Nv~~k~~~G~leG~l~~~s~i~~l~~~d~~v~~l~r~r~~~~~~~~p~~~~p~~ 318 (401)
++|++|..++.. -....|+.|.|++++++-.+|. .......|.|. ++.+-+.+.+|.. ...++-...+..++..
T Consensus 352 I~vTLWG~~A~~--~~~~~~~Vva~kg~~V~~f~g~-sLs~~~~S~i~-iNPdipEa~~L~~-w~~~~g~~~~~~s~~~- 425 (608)
T TIGR00617 352 VRVTLWGDDATK--FDVSVQPVIAIKGVRVSDFGGK-SLSTGGSSTII-VNPDIPEAEKLKG-WYDNEGKGTMASSISD- 425 (608)
T ss_pred EEEEEEhhhhhh--cCCCCCCEEEEEeEEEEecCCc-eEeccCCceEE-ECCCcHHHHHHHH-HHHhcCCCccceeehh-
Confidence 899999987642 2367899999999999888775 34445566774 4445565555532 2221111111001000
Q ss_pred CcccccccCCCccccHHHHhcCC----CCCceEEEEEEEEEeeCCCccc--------------------cccCCC-----
Q 015760 319 QFLTEVDWVNVASVTLMKIATQL----QGNVRCCCIVRVVSIHPFQAEH--------------------YSSPNG----- 369 (401)
Q Consensus 319 ~~~t~~~~~~~p~ttL~dIL~~~----~~~~kfr~~VRVv~~~P~~~~d--------------------f~~~~g----- 369 (401)
...+..........||.||.... +-+..|.|++.|+.+-+.+.-= +|-.++
T Consensus 426 ~~~~~~~~~~~~~ktI~ei~~~~lg~~~k~~~f~v~atI~~Ik~d~~~Y~ACp~~~CnKKV~~~~~g~~~CekC~~~~~~ 505 (608)
T TIGR00617 426 MMSGRVGGSNAERKTIAEIQAENLGKSDKPDYFSVKATISYLKPDNALYRACPSEDCNKKVVDQGDGTYRCEKCNKNFAE 505 (608)
T ss_pred ccccccCCcccccccHHHHhhhccCCCCCCcEEEEEEEEEEEecCCeEeccCChhhCCCccccCCCCCEECCCCCCCCCC
Confidence 00000111234567899998532 3456799999998877643211 111122
Q ss_pred -ceEEEEEEEEeCCCceEEEEEeccccccccc
Q 015760 370 -SSEYTMKLTLEDPTARIHALLCGKEWVRFQL 400 (401)
Q Consensus 370 -~~~~~~~L~leD~t~~i~~~v~~~da~~f~~ 400 (401)
.|.|++.+.+.|.|+.+.+.++++.|+.+||
T Consensus 506 ~~~RYil~~~i~D~Tg~~~~t~F~~~ae~llG 537 (608)
T TIGR00617 506 FKYRYILQISISDETGQLWVTAFNDQAEQILG 537 (608)
T ss_pred ccEEEEEEEEEEeCCCCEEEEEEhHHHHHHcC
Confidence 5788899999999999999999999999997
No 8
>PRK07218 replication factor A; Provisional
Probab=99.12 E-value=1.8e-07 Score=94.91 Aligned_cols=285 Identities=18% Similarity=0.174 Sum_probs=172.4
Q ss_pred eeeHHhhhhccCCEEEEEEEEEEcCCce-ecCC-CceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeE
Q 015760 10 IVRIKELAMHVKHKVNLLGVVLEFSIPR-KSQG-TDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNV 87 (401)
Q Consensus 10 y~~i~~~~~~~~~~vnviGVVvd~~~P~-~trG-tD~~~tl~I~D~s~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~rv 87 (401)
-+.|+|+.. ....|||.|-|++...+. +..| .-...++.|-|++=. +++.++.+. + + ..||+|.+.|+
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 456888853 356799999999996631 2234 357788999998653 999999842 3 5 89999999999
Q ss_pred EEEEecCeeEEEeecCceEEEEEeCCCCCCccccccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCcccccccccccCC
Q 015760 88 MIKKHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSLKDISEH 167 (401)
Q Consensus 88 ki~~~~g~~~~~~~~~~ss~~lf~~~~~~~~~P~~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~f~~~L~di~~~ 167 (401)
.++.|+|++++..+.. +....-+.. ..| ++. + . .. ..|.|++++
T Consensus 128 ~vre~~g~~el~ig~~-t~I~~~de~----~~~------~~~--------~--------------~--~~-~kI~DL~~g 171 (423)
T PRK07218 128 GVREWDGRPELNIGES-TTVSLLDDS----SLP------PYS--------I--------------G--GD-KKLIDLGPG 171 (423)
T ss_pred EeeccCCceEEeccCc-ceEEEcCcc----ccc------Ccc--------c--------------c--Cc-cchhhccCC
Confidence 9999999999888754 555533321 111 010 0 0 12 568899865
Q ss_pred -ceeeeEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCccccCCCCcHHhhhcCCCCccEEEEEecCc
Q 015760 168 -RYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRVSTDRS 246 (401)
Q Consensus 168 -~f~Dl~~qVv~~~~~~~~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~~~~~e~~~l~~~~~~~~p~~G~~l~V~~~~~ 246 (401)
..+++.++|+.++ + + .+..-||+. ......+.| | -| .+|+++|..
T Consensus 172 ~~~V~v~g~Vl~~~-~----r-~f~~~dg~~---~v~~giigD----------e--------------TG-~Ir~tlW~~ 217 (423)
T PRK07218 172 DRGVNVEARVLELE-H----R-EIDGRDGET---TILSGVLAD----------E--------------TG-RLPFTDWDP 217 (423)
T ss_pred CCceEEEEEEEEec-c----e-eEEcCCCCe---EEEEEEEEC----------C--------------Cc-eEEEEEecc
Confidence 4589999999885 3 1 233444431 110110111 0 12 458899996
Q ss_pred chhhhcccCCCCCEEEEeeeEEEEeCcEEEEEeecCcceEEccCCChHHHHHh-hhhhcCCCCCCCCcCCCCCCccc--c
Q 015760 247 YENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDNDNVVWDYM-RERISGGHGHMPIWTDPSSQFLT--E 323 (401)
Q Consensus 247 ~~~~~~~~~k~g~wv~l~Nv~~k~~~G~leG~l~~~s~i~~l~~~d~~v~~l~-r~r~~~~~~~~p~~~~p~~~~~t--~ 323 (401)
++ .+.+|++|++.|...+..+|.++-.+...+.|..++.+-. +...- +..+..... +...+ ...++ .
T Consensus 218 ~~-----~l~~Gd~v~I~na~v~e~~G~~elnv~~~t~I~~~d~~i~-v~~~~~~~~I~e~~~--~~g~~--~Vev~G~I 287 (423)
T PRK07218 218 LP-----EIEIGASIRIEDAYVREFRGVPSVNVSEFTTVEALDREVS-VSKDPPRLKIREAVE--RGGIF--DVELVGNI 287 (423)
T ss_pred cc-----cCCCCCEEEEeeeEEeccCCeEEEEECCceEEEECCCCcc-ccCCccccchhhhhc--cCCcc--eEEEEEEE
Confidence 43 3789999999999999999999999999999987765421 11100 000000000 00000 00000 0
Q ss_pred cccCCCccccHHHHhcCCCCCceEEEEEEEEEeeCCCccccccCCC----ceEEEEEEEEeCCCceEEEEEecccccccc
Q 015760 324 VDWVNVASVTLMKIATQLQGNVRCCCIVRVVSIHPFQAEHYSSPNG----SSEYTMKLTLEDPTARIHALLCGKEWVRFQ 399 (401)
Q Consensus 324 ~~~~~~p~ttL~dIL~~~~~~~kfr~~VRVv~~~P~~~~df~~~~g----~~~~~~~L~leD~t~~i~~~v~~~da~~f~ 399 (401)
++-..- +=+++ .+|.|- |+++- -.|..+| .+-=|..+.|.|.|+.+.+++.++.++.+.
T Consensus 288 v~i~~g-----sgli~--rCP~C~----r~v~~------~~C~~hG~ve~~~dlrik~vLDDGtg~~~~~~~~e~~e~l~ 350 (423)
T PRK07218 288 ISVRDG-----SGLIE--RCPECG----RVIQK------GQCRSHGAVEGEDDLRIKAILDDGTGSVTVILDRELTEIVY 350 (423)
T ss_pred EEeccC-----Cccee--cCcCcc----ccccC------CcCCCCCCcCCeeeeEEEEEEECCCCeEEEEEChhhhHhHh
Confidence 110000 00111 123222 22221 2344444 556788999999999999999999999887
Q ss_pred cC
Q 015760 400 LG 401 (401)
Q Consensus 400 ~~ 401 (401)
|+
T Consensus 351 G~ 352 (423)
T PRK07218 351 GG 352 (423)
T ss_pred CC
Confidence 73
No 9
>PRK14699 replication factor A; Provisional
Probab=99.03 E-value=3.7e-07 Score=94.51 Aligned_cols=272 Identities=19% Similarity=0.208 Sum_probs=181.9
Q ss_pred eeHHhhhhccCCEEEEEEEEEEcCCcee---cCCCc-eEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEee
Q 015760 11 VRIKELAMHVKHKVNLLGVVLEFSIPRK---SQGTD-YVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKN 86 (401)
Q Consensus 11 ~~i~~~~~~~~~~vnviGVVvd~~~P~~---trGtD-~~~tl~I~D~s~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~r 86 (401)
..|+++.. ....||+.|-|+...+|+. ..|+. -..++.|-|++=. +++.++.+..+.+|.+ ..||+|++.+
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 46777742 3445999999999998853 23543 6778899999763 9999999877777888 8999999998
Q ss_pred EEEE--EecCeeEEEeecCceEEEEEeCCCCCCccccccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCcccccccccc
Q 015760 87 VMIK--KHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSLKDI 164 (401)
Q Consensus 87 vki~--~~~g~~~~~~~~~~ss~~lf~~~~~~~~~P~~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~f~~~L~di 164 (401)
+.++ .|+|.+.+..+.. +... ......+ +.. ++ ..|.||
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 8665 4788888887743 3222 1110000 000 13 567777
Q ss_pred cC-CceeeeEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCccccCCCCcHHhhhcCCCCccEEEEEe
Q 015760 165 SE-HRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRVST 243 (401)
Q Consensus 165 ~~-~~f~Dl~~qVv~~~~~~~~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~~~~~e~~~l~~~~~~~~p~~G~~l~V~~ 243 (401)
++ ++.+++.++|+++. + -..|. --||+. .......+.| + -| .+|+++
T Consensus 283 ~~~~~~v~I~grV~~~~-~--~r~~~--~~~Gse--g~v~~~~l~D----------e--------------TG-~Ir~T~ 330 (484)
T PRK14699 283 KADMNNINISGRVLDIS-E--VRTFE--KKDGSP--GRVGNLLLGD----------S--------------TG-KIRLTL 330 (484)
T ss_pred CCCCceeEEEEEEEEcC-C--CeEEE--cCCCCe--eEEEEEEEEC----------C--------------CC-eEEEEE
Confidence 75 48999999999887 3 11211 123321 1111110111 0 15 378999
Q ss_pred cCcchhhhcccCCCCCEEEEeeeEEEEeC--cEEEEEeecCcceEEccCCChHHHHHhhhhhcCCCCCCCCcCCCCCCcc
Q 015760 244 DRSYENFGRYFTATGKWVRIRNMSCQVSS--GMWHGLLQSSSKIRLFSDNDNVVWDYMRERISGGHGHMPIWTDPSSQFL 321 (401)
Q Consensus 244 ~~~~~~~~~~~~k~g~wv~l~Nv~~k~~~--G~leG~l~~~s~i~~l~~~d~~v~~l~r~r~~~~~~~~p~~~~p~~~~~ 321 (401)
|...+.+ ...+++|+.+++.|...+.+. |.+|..|...+.|...+++. +
T Consensus 331 W~~~a~~-~~~i~~Gd~v~i~~~y~~~~~~~~~~eL~~~~~t~I~~~~~~~----e------------------------ 381 (484)
T PRK14699 331 WDEKTNF-LDEIDFDETVEVLNAYSRENTFSQQVELNLGARGIIQKSEKKV----E------------------------ 381 (484)
T ss_pred eCccccc-ccccCCCceEEEEeEEEEeccCCccEEEEecCceeEeecCCcc----e------------------------
Confidence 9987754 566899999999999988763 67888777777554322211 0
Q ss_pred cccccCCCccccHHHHhcCCCCCceEEEEEEEEEeeCCCccccccCCCceEEEEEEEEeCCCceEEEEEeccccccc
Q 015760 322 TEVDWVNVASVTLMKIATQLQGNVRCCCIVRVVSIHPFQAEHYSSPNGSSEYTMKLTLEDPTARIHALLCGKEWVRF 398 (401)
Q Consensus 322 t~~~~~~~p~ttL~dIL~~~~~~~kfr~~VRVv~~~P~~~~df~~~~g~~~~~~~L~leD~t~~i~~~v~~~da~~f 398 (401)
+ ..++++|.||-. ..-+-..-+|.++.|.+ .|.+-.|+=..+--++|.|.|+++.+-++|+.|+.|
T Consensus 382 ----~-~~~~~~I~die~----~~~vdV~G~V~~v~~~~--~~~~~~g~~~~vr~i~l~D~TG~Ir~tlWg~~A~~~ 447 (484)
T PRK14699 382 ----Y-REKFTDIADIIP----GESYSVQGKVSEIGELR--EFEREDGTENVVANLQLKDETGSIRLTLWGEQAYVI 447 (484)
T ss_pred ----e-eeccccHHHccC----CCeeEEEEEEEEcCCcc--eEEecCCCEEEEEEEEEEcCCCeEEEEEcchhhhhc
Confidence 0 124677888832 33578889999998876 666655643467789999999999999999999864
No 10
>PRK15491 replication factor A; Provisional
Probab=98.99 E-value=5.7e-07 Score=90.48 Aligned_cols=272 Identities=15% Similarity=0.180 Sum_probs=177.0
Q ss_pred ceeeHHhhhhccCCEEEEEEEEEEcCCcee---cCC-CceEEEEEEEeCCCCCCCeEEEEecCCCCCC--CCCCCCCCEE
Q 015760 9 GIVRIKELAMHVKHKVNLLGVVLEFSIPRK---SQG-TDYVCVLKIVDDSQQSPELLVNIFTSSIDQL--PRVLSPRDLI 82 (401)
Q Consensus 9 ~y~~i~~~~~~~~~~vnviGVVvd~~~P~~---trG-tD~~~tl~I~D~s~~~~gl~v~iF~~~~e~L--P~v~~~GDII 82 (401)
.-++|+++. .....|++.|-|+....|+. .+| .-...++.|.|++=. +++++|.+..+.+ |.+ .+||++
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 DTTKIADIN-ESSSNVNFTAKVVSIFEPKEFNRNDGTTGRVGNIIVADETGS---IRLTLWDDLADLIKTGDI-EVGKSL 130 (374)
T ss_pred ccccHHHCC-CCCCceEEEEEEeeccCCeeeecCCCCceEEEEEEEEcCCCe---EEEEEECchhhhhccCCc-CCCCEE
Confidence 356799994 23467999999999988864 247 467888999997652 9999999766665 677 799999
Q ss_pred EEeeEEEEEecCeeEEEeecCceEEEEEeCCCCCCccccccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCcccccccc
Q 015760 83 LLKNVMIKKHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSLK 162 (401)
Q Consensus 83 ~l~rvki~~~~g~~~~~~~~~~ss~~lf~~~~~~~~~P~~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~f~~~L~ 162 (401)
.++..--..|+| +.+..+.. +...-.. . .. + .. -.| ..|+
T Consensus 131 ~I~~~~~~~y~g-~Ei~i~~~-~~i~~~~--~--~~-~-------~~-------------------------~~~-~~I~ 170 (374)
T PRK15491 131 NISGYAKEGYSG-IEVNIGRY-GGISESD--E--NV-K-------AS-------------------------INS-QKIS 170 (374)
T ss_pred EEeeeeccCccc-EEEEeCCC-ceeeecc--c--cc-c-------cc-------------------------cCc-ccHH
Confidence 998875556766 55555433 2221000 0 00 0 00 014 5678
Q ss_pred cccCC-ceeeeEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCccccCCCCcHHhhhcCCCCccEEEE
Q 015760 163 DISEH-RYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRV 241 (401)
Q Consensus 163 di~~~-~f~Dl~~qVv~~~~~~~~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~~~~~e~~~l~~~~~~~~p~~G~~l~V 241 (401)
||.++ ..+|+.+.|+.+. + ...+. --||+...... ..+ .. --|+ +++
T Consensus 171 dl~~~~~~V~I~g~V~~~~-~--~r~~~--~~~G~~~~v~~--~~l----------------------~D--etG~-Ir~ 218 (374)
T PRK15491 171 DIKDGDSDINIVGKVLDIS-D--VRTFQ--KKDGSQGRVRN--ITI----------------------GD--ETGK-IRV 218 (374)
T ss_pred HcCCCCccEEEEEEEEEcc-C--ceEEE--ecCCCeEEEEE--EEE----------------------EC--CCCe-EEE
Confidence 88654 4699999999887 3 12222 12333111111 000 00 0254 789
Q ss_pred EecCcchhhhcccCCCCCEEEEeeeEEEEe--CcEEEEEeecCcceEEccCCChHHHHHhhhhhcCCCCCCCCcCCCCCC
Q 015760 242 STDRSYENFGRYFTATGKWVRIRNMSCQVS--SGMWHGLLQSSSKIRLFSDNDNVVWDYMRERISGGHGHMPIWTDPSSQ 319 (401)
Q Consensus 242 ~~~~~~~~~~~~~~k~g~wv~l~Nv~~k~~--~G~leG~l~~~s~i~~l~~~d~~v~~l~r~r~~~~~~~~p~~~~p~~~ 319 (401)
++|...+.. ...+++|+-|++.|-.++.+ .|.+|-.+..++.|...++ +. + +
T Consensus 219 t~W~~~a~~-~~~l~~Gd~V~i~~~~~r~~~~~g~~El~~~~~s~I~~~~~-~~---e-----~---------------- 272 (374)
T PRK15491 219 TLWDGKTDL-ADKLENGDSVEIINGYARTNNYSQEVEIQIGNHGSLRKTDR-NV---E-----Y---------------- 272 (374)
T ss_pred EEecchhcc-cccCCCCCEEEEEeceEEEeccCCCEEEEeCCCceEEECCc-cc---c-----c----------------
Confidence 999987654 36799999999999877764 5788888888888765422 11 0 0
Q ss_pred cccccccCCCccccHHHHhcCCCCCceEEEEEEEEEeeCCCccccccCCCceEEEEEEEEeCCCceEEEEEecccccc
Q 015760 320 FLTEVDWVNVASVTLMKIATQLQGNVRCCCIVRVVSIHPFQAEHYSSPNGSSEYTMKLTLEDPTARIHALLCGKEWVR 397 (401)
Q Consensus 320 ~~t~~~~~~~p~ttL~dIL~~~~~~~kfr~~VRVv~~~P~~~~df~~~~g~~~~~~~L~leD~t~~i~~~v~~~da~~ 397 (401)
..++++|.||-... .+-+..+|....|. ..|.+..|+=...=.|+|.|.|++|++-++|++|+.
T Consensus 273 --------~~~f~~I~dl~~~~----~~dv~G~V~~v~~~--~~~~~~~G~~~~~r~i~l~D~Tg~Ir~tlWg~~a~~ 336 (374)
T PRK15491 273 --------EEDFTPIADIIPGQ----PYSIKGAVSGLGDL--KEFTKSDGSENKVSNIYVSDDTGRIRIALWGEKAEL 336 (374)
T ss_pred --------CCCccCHHHcCCCC----ceeEEEEEEEcCCc--EEEEccCCCEeEEEeEEEEeCCCcEEEEEccccccc
Confidence 01355688875322 36778888887764 345455564345667899999999999999999985
No 11
>PRK06386 replication factor A; Reviewed
Probab=98.97 E-value=2.8e-06 Score=84.42 Aligned_cols=276 Identities=16% Similarity=0.167 Sum_probs=164.4
Q ss_pred eeHHhhhhccCCEEEEEEEEEEcCCc-eec-CCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEE
Q 015760 11 VRIKELAMHVKHKVNLLGVVLEFSIP-RKS-QGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVM 88 (401)
Q Consensus 11 ~~i~~~~~~~~~~vnviGVVvd~~~P-~~t-rGtD~~~tl~I~D~s~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~rvk 88 (401)
+.|+|+. ..+..||+.|-|++.... .+. +|.--..+-.|-|++=. +++++..+ .|.+ ..||+|+|.|++
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 SKISDIN-AARQNVDLKVKVLSLNKRTIKNDRGETIYYYGIIGDETGT---VPFTAWEF----PDAV-KSGDVIEIKYCY 73 (358)
T ss_pred cchhhcC-CCCCcEEEEEEEEEccceEEecCCCCeEEEEEEEECCcce---EEEEecCC----cccC-CCCCEEEEEeEE
Confidence 4578884 246679999999999732 122 34333444457777442 88888763 4667 789999999999
Q ss_pred EEEecCeeEEEeecCceEEEEEeCCCCCCccccccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCcccccccccccCC-
Q 015760 89 IKKHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSLKDISEH- 167 (401)
Q Consensus 89 i~~~~g~~~~~~~~~~ss~~lf~~~~~~~~~P~~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~f~~~L~di~~~- 167 (401)
++.|+|++.+..+.. +... -..+....+.+ + . +. ..|+||+++
T Consensus 74 v~~~~G~~~Lnv~~~-t~v~-~~~d~~iev~~----------~--------------------~---~~-~KI~DL~~g~ 117 (358)
T PRK06386 74 SKEYNGKIRIYFDSR-SEVM-LKPDENIEVKR----------T--------------------Y---KL-VKIRDLSLVT 117 (358)
T ss_pred EeeECCEEEEEEcCc-eEEE-ecCcccccccc----------c--------------------c---Cc-cEeEeccCCC
Confidence 999999998877644 4332 11111011000 0 0 13 689999865
Q ss_pred ceeeeEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCccccCCCCcHHhhhcCCCCccEEEEEecCcc
Q 015760 168 RYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRVSTDRSY 247 (401)
Q Consensus 168 ~f~Dl~~qVv~~~~~~~~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~~~~~e~~~l~~~~~~~~p~~G~~l~V~~~~~~ 247 (401)
.+++++++|+.++ + . ..- .||+. ...-...+.| | -| .+|+++|..
T Consensus 118 ~~v~V~akVle~~-e---~--e~~-~~g~~--~~v~sg~lgD----------e--------------TG-rIr~TlW~~- 162 (358)
T PRK06386 118 PYVSVIGKITGIT-K---K--EYD-SDGTS--KIVYQGYIED----------D--------------TA-RVRISSFGK- 162 (358)
T ss_pred CceEEEEEEEEcc-C---c--eEe-cCCCc--cEEEEEEEEc----------C--------------CC-eEEEEEccc-
Confidence 6679999999876 3 1 222 45541 1110110111 0 12 358889974
Q ss_pred hhhhcccCCCCCEEEEeeeEEEEeCcEEEEEeecCcceEEccCCChHHHHH-hh-hhhcCCCCCCCCcCCCCCCcccccc
Q 015760 248 ENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDNDNVVWDY-MR-ERISGGHGHMPIWTDPSSQFLTEVD 325 (401)
Q Consensus 248 ~~~~~~~~k~g~wv~l~Nv~~k~~~G~leG~l~~~s~i~~l~~~d~~v~~l-~r-~r~~~~~~~~p~~~~p~~~~~t~~~ 325 (401)
.++.|+.+++.|...+...|.++-.+...+.|..++.+-. +... .. .-+....+ ...+.
T Consensus 163 ------~l~eGd~v~i~na~v~e~~G~~el~v~~~t~I~~~~~~ie-v~~~~~~I~di~~~~g---------~v~i~--- 223 (358)
T PRK06386 163 ------PLEDNRFVRIENARVSQYNGYIEISVGNKSVIKEVESDIN-LESRNIFIFEIKSPVG---------GITIM--- 223 (358)
T ss_pred ------cccCCCEEEEeeeEEEccCCeEEEEeCCeEEEEECCCCcc-cCccccchhhhhccCC---------eEEEE---
Confidence 3789999999999999999999999888888887654321 1100 00 00100000 00000
Q ss_pred cCCCccccHHHHhc----CCCCCceEEEEEEEEEeeCCCccccccCCC----ceEEEEEEEEeCCCceEEEEEecccccc
Q 015760 326 WVNVASVTLMKIAT----QLQGNVRCCCIVRVVSIHPFQAEHYSSPNG----SSEYTMKLTLEDPTARIHALLCGKEWVR 397 (401)
Q Consensus 326 ~~~~p~ttL~dIL~----~~~~~~kfr~~VRVv~~~P~~~~df~~~~g----~~~~~~~L~leD~t~~i~~~v~~~da~~ 397 (401)
=+|-+|-. -..+|.| =|+++- ..|..+| .+--|..+.|-|.|+.+.++++++.++.
T Consensus 224 ------G~iv~i~~gsgli~rCP~C----~R~l~~------g~C~~HG~v~~~~dlr~k~vLDDGtg~~~~~l~~e~~e~ 287 (358)
T PRK06386 224 ------GFIVSVGQGSRIFTKCSVC----NKIIED------GVCKDHPDAPVYLDIFGYFTISDGTGFVTCYANKDSFLP 287 (358)
T ss_pred ------EEEEEEcCCcEeEecCcCC----CeEccC------CcCCCCCCCCCeeEEEEEEEEECCCCeEEEEEChHHhHH
Confidence 00111110 0113332 234441 3666555 3445667799999999999999999999
Q ss_pred cccC
Q 015760 398 FQLG 401 (401)
Q Consensus 398 f~~~ 401 (401)
+.|.
T Consensus 288 l~G~ 291 (358)
T PRK06386 288 YINI 291 (358)
T ss_pred HhCC
Confidence 8873
No 12
>PRK07211 replication factor A; Reviewed
Probab=98.86 E-value=2.3e-07 Score=95.21 Aligned_cols=204 Identities=16% Similarity=0.183 Sum_probs=144.7
Q ss_pred cceeeHHhhhhccCCEEEEEEEEEEcCCcee---cCC-CceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEE
Q 015760 8 GGIVRIKELAMHVKHKVNLLGVVLEFSIPRK---SQG-TDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLIL 83 (401)
Q Consensus 8 y~y~~i~~~~~~~~~~vnviGVVvd~~~P~~---trG-tD~~~tl~I~D~s~~~~gl~v~iF~~~~e~LP~v~~~GDII~ 83 (401)
..+.+|+++. .....++|+|+|+...+++. .+| .-.+.++.|.|+|- . +++++|.+..+.++.+ ..||+|.
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 GDTYTVEDLS-LGLSDVTLVGVVLDTDSVRTFDRDDGSEGRVSNLTVGDETG-R--VRVTLWDDRADLAEEL-DAGESVE 233 (485)
T ss_pred cCCccHHHcC-CCCCceEEEEEEEEcCCCeEEECCCCCeeEEEEEEEEcCCC-e--EEEEEechhhhhhccC-CCCCEEE
Confidence 4678999994 23566999999999998753 235 45678899999876 2 9999999888888877 8999999
Q ss_pred EeeEEEEEecCeeEEEeecCceEEEEEeCCCCCCccccccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCccccccccc
Q 015760 84 LKNVMIKKHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSLKD 163 (401)
Q Consensus 84 l~rvki~~~~g~~~~~~~~~~ss~~lf~~~~~~~~~P~~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~f~~~L~d 163 (401)
+.+++++.++|.+.+..+.. +....... .....| .+ ..|.+
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 99999999999988877643 33331111 001111 02 46888
Q ss_pred ccCCceeeeEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCccccCCCCcHHhhhcCCCCccEEEEEe
Q 015760 164 ISEHRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRVST 243 (401)
Q Consensus 164 i~~~~f~Dl~~qVv~~~~~~~~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~~~~~e~~~l~~~~~~~~p~~G~~l~V~~ 243 (401)
+.++..+|+++.|+.+. + ..++-=-||+...-..+.. .| + -| .+|+++
T Consensus 275 l~~g~~vdV~GvV~~v~-~----~rtf~r~dG~~~~vr~l~l--~D----------~--------------TG-~IrvTL 322 (485)
T PRK07211 275 LEIDETVDIAGVVRSAD-P----KRTFDRDDGSEGQVRNVRI--QD----------D--------------TG-DIRVAL 322 (485)
T ss_pred cCCCCceeEEEEEEEcc-C----cEEEEcCCCCEeEEEEEEE--Ec----------C--------------CC-cEEEEE
Confidence 89999999999999887 3 2222222344222211000 00 0 25 579999
Q ss_pred cCcchhhhcccCCCCCEEEEeeeEEEEeC-cEEEEEeecCcceEEccC
Q 015760 244 DRSYENFGRYFTATGKWVRIRNMSCQVSS-GMWHGLLQSSSKIRLFSD 290 (401)
Q Consensus 244 ~~~~~~~~~~~~k~g~wv~l~Nv~~k~~~-G~leG~l~~~s~i~~l~~ 290 (401)
|..++. ..+.+|+.|+|.|++++-.. |-+|..+...+.|.+++.
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 998764 36899999999999999863 677788888889988866
No 13
>PRK15491 replication factor A; Provisional
Probab=98.76 E-value=9e-07 Score=89.03 Aligned_cols=204 Identities=16% Similarity=0.149 Sum_probs=140.8
Q ss_pred CCcceeeHHhhhhccCCEEEEEEEEEEcCCceec---CCC-ceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCE
Q 015760 6 NQGGIVRIKELAMHVKHKVNLLGVVLEFSIPRKS---QGT-DYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDL 81 (401)
Q Consensus 6 ~~y~y~~i~~~~~~~~~~vnviGVVvd~~~P~~t---rGt-D~~~tl~I~D~s~~~~gl~v~iF~~~~e~LP~v~~~GDI 81 (401)
.+|.+++|+++.. ....|+|.|+|+...+++.= +|+ -...++.|.|.|- . +++++|.+..+.++.+ .+||+
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 4567789999953 34459999999999987531 355 4788899999865 2 9999999877777777 89999
Q ss_pred EEEeeEEEE--EecCeeEEEeecCceEEEEEeCCCCCCccccccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCccccc
Q 015760 82 ILLKNVMIK--KHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLL 159 (401)
Q Consensus 82 I~l~rvki~--~~~g~~~~~~~~~~ss~~lf~~~~~~~~~P~~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~f~~ 159 (401)
|.+.+..++ .|+|++.+..+.. +....- +... + +.+ .| .
T Consensus 237 V~i~~~~~r~~~~~g~~El~~~~~-s~I~~~--~~~~---e-------~~~-------------------------~f-~ 277 (374)
T PRK15491 237 VEIINGYARTNNYSQEVEIQIGNH-GSLRKT--DRNV---E-------YEE-------------------------DF-T 277 (374)
T ss_pred EEEEeceEEEeccCCCEEEEeCCC-ceEEEC--Cccc---c-------cCC-------------------------Cc-c
Confidence 999997655 5678888887644 443311 1100 0 110 26 6
Q ss_pred ccccccCCceeeeEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCccccCCCCcHHhhhcCCCCccEE
Q 015760 160 SLKDISEHRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVL 239 (401)
Q Consensus 160 ~L~di~~~~f~Dl~~qVv~~~~~~~~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~~~~~e~~~l~~~~~~~~p~~G~~l 239 (401)
.|.||+++..+|+++.|..+. + .-++--.||+...-..+.. .| - -|+ +
T Consensus 278 ~I~dl~~~~~~dv~G~V~~v~-~----~~~~~~~~G~~~~~r~i~l--~D----------------------~--Tg~-I 325 (374)
T PRK15491 278 PIADIIPGQPYSIKGAVSGLG-D----LKEFTKSDGSENKVSNIYV--SD----------------------D--TGR-I 325 (374)
T ss_pred CHHHcCCCCceeEEEEEEEcC-C----cEEEEccCCCEeEEEeEEE--Ee----------------------C--CCc-E
Confidence 788999999999999999886 2 1122224554322211110 00 0 155 7
Q ss_pred EEEecCcchhhhcccCCCCCEEEEeeeEEEEeC-cEEEEEeecCcceE
Q 015760 240 RVSTDRSYENFGRYFTATGKWVRIRNMSCQVSS-GMWHGLLQSSSKIR 286 (401)
Q Consensus 240 ~V~~~~~~~~~~~~~~k~g~wv~l~Nv~~k~~~-G~leG~l~~~s~i~ 286 (401)
|+++|..++.. ...+-+|+.|++.+...|... |-+|......|+|.
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 99999987764 445678899999999999864 89998888777774
No 14
>PRK07211 replication factor A; Reviewed
Probab=98.54 E-value=6.8e-05 Score=77.30 Aligned_cols=269 Identities=15% Similarity=0.147 Sum_probs=169.4
Q ss_pred eeeHHhhhhccC-CEEEEEEEEEEcCCcee-c-C---CCceEEEEEEEeCCCCCCCeEEEEecCCCC-CCCCCCCCCCEE
Q 015760 10 IVRIKELAMHVK-HKVNLLGVVLEFSIPRK-S-Q---GTDYVCVLKIVDDSQQSPELLVNIFTSSID-QLPRVLSPRDLI 82 (401)
Q Consensus 10 y~~i~~~~~~~~-~~vnviGVVvd~~~P~~-t-r---GtD~~~tl~I~D~s~~~~gl~v~iF~~~~e-~LP~v~~~GDII 82 (401)
..+|+++ .++ ..||+.|-|+..+.|+. + + +.--.+++.|.|+|=. |++.+|.+..+ ..|.+ ++|||+
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--EPGMDEVKFLAKVLSIGDLRTFERDGEDEDGRVINVEVADETGS---VRVAFWDEQAVAAEEEL-EVGQVL 126 (485)
T ss_pred cccHhhC--CCCCCceEEEEEEeEccCceEEEeCCCCCCcEEEEEEEEcCCCe---EEEEEechHhHhhhccc-CCCCEE
Confidence 3478888 455 56999999999998764 2 2 2358899999997652 99999976433 46777 899999
Q ss_pred EEeeEEEEEecCeeEEEeecCceEEEEEeCCCCCCccccccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCcccccccc
Q 015760 83 LLKNVMIKKHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSLK 162 (401)
Q Consensus 83 ~l~rvki~~~~g~~~~~~~~~~ss~~lf~~~~~~~~~P~~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~f~~~L~ 162 (401)
++.+.-...|++ +.+..+ . ........+ |++ . ..| ..|+
T Consensus 127 ~I~~~~~~~ys~-~El~i~----~---ve~~~d~~i-~~~------------------------------~-~~~-~~I~ 165 (485)
T PRK07211 127 RIKGRPKDGYNG-LEVSVD----K---VEPDPDAEI-DVQ------------------------------I-GDT-YTVE 165 (485)
T ss_pred EEeceEeccccc-eEEEEe----e---EEEcccccc-ccc------------------------------c-cCC-ccHH
Confidence 997754444444 222222 1 111110111 100 0 025 6888
Q ss_pred cccCC-ceeeeEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCccccCCCCcHHhhhcCCCCccEEEE
Q 015760 163 DISEH-RYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRV 241 (401)
Q Consensus 163 di~~~-~f~Dl~~qVv~~~~~~~~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~~~~~e~~~l~~~~~~~~p~~G~~l~V 241 (401)
||+++ ..+|++++|+.+. +. ..| -=-||++-.-.. ..+-| + -|+ +|+
T Consensus 166 dL~~~~~~v~I~grV~~v~-~i--Rtf--~r~dGseGkv~s--v~L~D----------e--------------TG~-IR~ 213 (485)
T PRK07211 166 DLSLGLSDVTLVGVVLDTD-SV--RTF--DRDDGSEGRVSN--LTVGD----------E--------------TGR-VRV 213 (485)
T ss_pred HcCCCCCceEEEEEEEEcC-CC--eEE--ECCCCCeeEEEE--EEEEc----------C--------------CCe-EEE
Confidence 99865 5689999999776 32 000 011222110000 00000 0 154 799
Q ss_pred EecCcchhhhcccCCCCCEEEEeeeEEEEeCcEEEEEeecCcceEEccCCChHHHHHhhhhhcCCCCCCCCcCCCCCCcc
Q 015760 242 STDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDNDNVVWDYMRERISGGHGHMPIWTDPSSQFL 321 (401)
Q Consensus 242 ~~~~~~~~~~~~~~k~g~wv~l~Nv~~k~~~G~leG~l~~~s~i~~l~~~d~~v~~l~r~r~~~~~~~~p~~~~p~~~~~ 321 (401)
++|+..+.. ...+.+|+.|+|.|.+++...|.+|..+..++.|..++++-.. +| .
T Consensus 214 TlW~d~Ad~-~~~le~G~Vv~I~~a~Vre~~g~~ELsl~~~s~I~~~~dev~~---------------vp-----~---- 268 (485)
T PRK07211 214 TLWDDRADL-AEELDAGESVEIVDGYVRERDGSLELHVGDRGAVEEVDEDVEY---------------VP-----D---- 268 (485)
T ss_pred EEechhhhh-hccCCCCCEEEEEeeEEEecCCcEEEEECCCceEEECCccccc---------------cc-----c----
Confidence 999977654 3669999999999999998888888888888888765542100 01 0
Q ss_pred cccccCCCccccHHHHhcCCCCCceEEEEEEEEEeeCCCccccccCCCceEEEEEEEEeCCCceEEEEEecccccc
Q 015760 322 TEVDWVNVASVTLMKIATQLQGNVRCCCIVRVVSIHPFQAEHYSSPNGSSEYTMKLTLEDPTARIHALLCGKEWVR 397 (401)
Q Consensus 322 t~~~~~~~p~ttL~dIL~~~~~~~kfr~~VRVv~~~P~~~~df~~~~g~~~~~~~L~leD~t~~i~~~v~~~da~~ 397 (401)
++.|.++-.. .-.-+..+|.+..|..-- ....|+=...--++|.|.|+++++-++|+.|++
T Consensus 269 ---------~~~I~dl~~g----~~vdV~GvV~~v~~~rtf--~r~dG~~~~vr~l~l~D~TG~IrvTLWg~~A~~ 329 (485)
T PRK07211 269 ---------TTPIESLEID----ETVDIAGVVRSADPKRTF--DRDDGSEGQVRNVRIQDDTGDIRVALWGEKADL 329 (485)
T ss_pred ---------cccHhhcCCC----CceeEEEEEEEccCcEEE--EcCCCCEeEEEEEEEEcCCCcEEEEEeCccccC
Confidence 1334443211 125677888888876554 344463336778999999999999999999863
No 15
>PRK14699 replication factor A; Provisional
Probab=98.53 E-value=9.9e-06 Score=83.98 Aligned_cols=204 Identities=13% Similarity=0.170 Sum_probs=140.7
Q ss_pred cceeeHHhhhhccCCEEEEEEEEEEcCCcee---cCC-CceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEE
Q 015760 8 GGIVRIKELAMHVKHKVNLLGVVLEFSIPRK---SQG-TDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLIL 83 (401)
Q Consensus 8 y~y~~i~~~~~~~~~~vnviGVVvd~~~P~~---trG-tD~~~tl~I~D~s~~~~gl~v~iF~~~~e~LP~v~~~GDII~ 83 (401)
..+++|.++. .....+++.|.|++..+++. .+| ......+.|.|.|=. +++.+|.+..+.++.+ ..||+|.
T Consensus 274 ~~~~~I~~L~-~~~~~v~I~grV~~~~~~r~~~~~~Gseg~v~~~~l~DeTG~---Ir~T~W~~~a~~~~~i-~~Gd~v~ 348 (484)
T PRK14699 274 EEFTPIEDIK-ADMNNINISGRVLDISEVRTFEKKDGSPGRVGNLLLGDSTGK---IRLTLWDEKTNFLDEI-DFDETVE 348 (484)
T ss_pred ccccCHHHcC-CCCceeEEEEEEEEcCCCeEEEcCCCCeeEEEEEEEECCCCe---EEEEEeCccccccccc-CCCceEE
Confidence 3567899984 23578999999999998753 246 467788999999763 9999999877777877 8899999
Q ss_pred EeeEEEEEe--cCeeEEEeecCceEEEEEeCCCCCCccccccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCccccccc
Q 015760 84 LKNVMIKKH--QAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSL 161 (401)
Q Consensus 84 l~rvki~~~--~g~~~~~~~~~~ss~~lf~~~~~~~~~P~~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~f~~~L 161 (401)
+.++..+.. ++++.+..+.+ +.. ....+.. . +. .+| +.|
T Consensus 349 i~~~y~~~~~~~~~~eL~~~~~-t~I---~~~~~~~--------e-~~-------------------------~~~-~~I 389 (484)
T PRK14699 349 VLNAYSRENTFSQQVELNLGAR-GII---QKSEKKV--------E-YR-------------------------EKF-TDI 389 (484)
T ss_pred EEeEEEEeccCCccEEEEecCc-eeE---eecCCcc--------e-ee-------------------------ecc-ccH
Confidence 999998843 45677777644 311 1111000 0 10 026 789
Q ss_pred ccccCCceeeeEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCccccCCCCcHHhhhcCCCCccEEEE
Q 015760 162 KDISEHRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRV 241 (401)
Q Consensus 162 ~di~~~~f~Dl~~qVv~~~~~~~~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~~~~~e~~~l~~~~~~~~p~~G~~l~V 241 (401)
.||+++..+|+++.|..+. +. ..+. --||+.-.-.... +.| .-| .+|+
T Consensus 390 ~die~~~~vdV~G~V~~v~-~~--~~~~--~~~g~~~~vr~i~--l~D------------------------~TG-~Ir~ 437 (484)
T PRK14699 390 ADIIPGESYSVQGKVSEIG-EL--REFE--REDGTENVVANLQ--LKD------------------------ETG-SIRL 437 (484)
T ss_pred HHccCCCeeEEEEEEEEcC-Cc--ceEE--ecCCCEEEEEEEE--EEc------------------------CCC-eEEE
Confidence 9999999999999999887 41 1211 1344311110000 000 025 6799
Q ss_pred EecCcchhhhcccCCCCCEEEEeeeEEEEe-CcEEEEEeecCcceEEc
Q 015760 242 STDRSYENFGRYFTATGKWVRIRNMSCQVS-SGMWHGLLQSSSKIRLF 288 (401)
Q Consensus 242 ~~~~~~~~~~~~~~k~g~wv~l~Nv~~k~~-~G~leG~l~~~s~i~~l 288 (401)
++|...+.. .+.+.+||-|.+.|...+.. +|.+|......|+|.+|
T Consensus 438 tlWg~~A~~-~~~~~~~~~v~~~~~~~~~g~~~~~e~s~g~~s~~~~~ 484 (484)
T PRK14699 438 TLWGEQAYV-IEDLDIDSEIQIIDAYARYGLNEEIELSVGNRSRVIIL 484 (484)
T ss_pred EEcchhhhh-ccccCCCCeEEEechhhhhcccccEEEEecCceEEEeC
Confidence 999976642 46799999999999999996 68999988888887654
No 16
>cd04475 RPA1_DBD_B RPA1_DBD_B: A subfamily of OB folds corresponding to the third OB fold, the ssDNA-binding domain (DBD)-B, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-B, RPA1 contains three other OB folds: DBD-A, DBD-C, and RPA1N. The major DNA binding activity of human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. Although ScRPA and the hRPA have similar ssDNA-binding properties, they differ functiona
Probab=98.16 E-value=2.8e-05 Score=63.56 Aligned_cols=74 Identities=16% Similarity=0.201 Sum_probs=59.3
Q ss_pred EEEEEEEEEEcCCceec--C--C-CceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEecCeeE
Q 015760 23 KVNLLGVVLEFSIPRKS--Q--G-TDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAELS 97 (401)
Q Consensus 23 ~vnviGVVvd~~~P~~t--r--G-tD~~~tl~I~D~s~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~rvki~~~~g~~~ 97 (401)
.|||+|+|++.++|+.- + | .-.+..|+|.|.|.. .+.|+++.+..+.+... .|+||.|++++++.|+| ..
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 38999999999998642 2 4 367899999999985 49999999766666654 39999999999999985 45
Q ss_pred EEee
Q 015760 98 AVFY 101 (401)
Q Consensus 98 ~~~~ 101 (401)
+.+.
T Consensus 76 l~~~ 79 (101)
T cd04475 76 LSTG 79 (101)
T ss_pred Eeec
Confidence 5444
No 17
>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=98.07 E-value=7.3e-05 Score=79.96 Aligned_cols=157 Identities=18% Similarity=0.237 Sum_probs=106.2
Q ss_pred CCcceeeHHhhhhc-cCCEEEEEEEEEEcCCceec--C--CCc-eEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCC
Q 015760 6 NQGGIVRIKELAMH-VKHKVNLLGVVLEFSIPRKS--Q--GTD-YVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPR 79 (401)
Q Consensus 6 ~~y~y~~i~~~~~~-~~~~vnviGVVvd~~~P~~t--r--GtD-~~~tl~I~D~s~~~~gl~v~iF~~~~e~LP~v~~~G 79 (401)
..|.|++|+++... .+..|+|||||+++++...- | |+. .+..|+|.|.|-. .|.|+++.+..+.+. . ..|
T Consensus 294 ~~~~f~~i~dI~~~~~~~~VDVIGvV~~v~~~~~i~~k~~g~~~~kR~i~L~D~sg~--sI~vTLWG~~A~~~~-~-~~~ 369 (608)
T TIGR00617 294 IQFNFVKIDDIGGYEGNSLVDVIGIVQSVSPTQTITSRKNNKEFPKRDITLVDDSGK--SVRVTLWGDDATKFD-V-SVQ 369 (608)
T ss_pred ccccceEHHHhhhhcCCCCccEEEEEeEecCceEEEEcCCCCeeeeEEEEEEeCCCC--EEEEEEEhhhhhhcC-C-CCC
Confidence 46899999999753 34589999999999987652 2 444 4779999999864 499999998766776 3 579
Q ss_pred CEEEEeeEEEEEecCeeEEEeecCceEEEEEeCCCCCCccccccCCCCCCCCHHHHHHHHHHHHhhhcCccc--------
Q 015760 80 DLILLKNVMIKKHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFS-------- 151 (401)
Q Consensus 80 DII~l~rvki~~~~g~~~~~~~~~~ss~~lf~~~~~~~~~P~~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~-------- 151 (401)
+||.+..++++.|+|. .+... ..|.+. .+. |..-+..||.|+.+....
T Consensus 370 ~Vva~kg~~V~~f~g~-sLs~~-~~S~i~-iNP---------------------dipEa~~L~~w~~~~g~~~~~~s~~~ 425 (608)
T TIGR00617 370 PVIAIKGVRVSDFGGK-SLSTG-GSSTII-VNP---------------------DIPEAEKLKGWYDNEGKGTMASSISD 425 (608)
T ss_pred CEEEEEeEEEEecCCc-eEecc-CCceEE-ECC---------------------CcHHHHHHHHHHHhcCCCccceeehh
Confidence 9999999999999663 44433 224443 221 112256889998653221
Q ss_pred --C---C--CcccccccccccC--------CceeeeEEEEEEEEeeCCCCeEEEEEEcCCCCCC
Q 015760 152 --S---G--SNDYLLSLKDISE--------HRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPP 200 (401)
Q Consensus 152 --~---~--~~~f~~~L~di~~--------~~f~Dl~~qVv~~~~~~~~~~~~L~VwDgT~~p~ 200 (401)
. + .... +.|.||++ +.||.+.|.|.++. . + .+ | |+.||.
T Consensus 426 ~~~~~~~~~~~~~-ktI~ei~~~~lg~~~k~~~f~v~atI~~Ik-~-d--~~----~-Y~ACp~ 479 (608)
T TIGR00617 426 MMSGRVGGSNAER-KTIAEIQAENLGKSDKPDYFSVKATISYLK-P-D--NA----L-YRACPS 479 (608)
T ss_pred ccccccCCccccc-ccHHHHhhhccCCCCCCcEEEEEEEEEEEe-c-C--Ce----E-eccCCh
Confidence 0 0 1123 45666643 34799999999987 4 2 21 3 777776
No 18
>PRK08402 replication factor A; Reviewed
Probab=98.02 E-value=0.00044 Score=69.11 Aligned_cols=187 Identities=14% Similarity=0.074 Sum_probs=109.4
Q ss_pred cccccccCC-ceeeeEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCccccCCCCcHHhhhcCCCCcc
Q 015760 159 LSLKDISEH-RYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGT 237 (401)
Q Consensus 159 ~~L~di~~~-~f~Dl~~qVv~~~~~~~~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~~~~~e~~~l~~~~~~~~p~~G~ 237 (401)
..|+||.++ ..++++++|+.+. +.. .+. --||+...-. ...+.| + -|+
T Consensus 63 ~kI~dl~~g~~~V~v~~rVl~~~-~~r--~f~--rrdG~~~~V~--~i~l~D----------e--------------TG~ 111 (355)
T PRK08402 63 MHISDLVPGMRGVNIVGRVLRKY-PPR--EYT--KKDGSTGRVA--SLIIYD----------D--------------TGR 111 (355)
T ss_pred cCHHHccCCCceeeEEEEEEEcc-CCc--eee--ccCCCcceEE--EEEEEc----------C--------------CCe
Confidence 689999987 5899999999987 311 110 0122210000 000000 0 144
Q ss_pred EEEEEecCcchhhhcccCCCCCEEEEeeeEEEEe-CcEEEEEeecCcceEEccCCChHHHHHhhhhhcCCCCCCCCcCCC
Q 015760 238 VLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVS-SGMWHGLLQSSSKIRLFSDNDNVVWDYMRERISGGHGHMPIWTDP 316 (401)
Q Consensus 238 ~l~V~~~~~~~~~~~~~~k~g~wv~l~Nv~~k~~-~G~leG~l~~~s~i~~l~~~d~~v~~l~r~r~~~~~~~~p~~~~p 316 (401)
+ ++++|...+.-....+.+|+.|++.|..++.. +|..+..+...|.|.+.|+ ++.+.++-
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-DPRVEEIP----------------- 172 (355)
T ss_pred E-EEEEechhhhhhcccCCCCCEEEEECCEEeecCCCcEEEEECCCceEEeCCC-cccccccc-----------------
Confidence 5 89999976431235699999999999999984 8998989889999976664 33222111
Q ss_pred CCCcccccccCCCccccHHHHhcCCCCCceEEEEEEEEEeeCCCccc------------------cccC----CCceEEE
Q 015760 317 SSQFLTEVDWVNVASVTLMKIATQLQGNVRCCCIVRVVSIHPFQAEH------------------YSSP----NGSSEYT 374 (401)
Q Consensus 317 ~~~~~t~~~~~~~p~ttL~dIL~~~~~~~kfr~~VRVv~~~P~~~~d------------------f~~~----~g~~~~~ 374 (401)
+...+. .. ..+..+|.||-... .-|.+.+.|+.+.+.-+-. .|.. .+.|.|+
T Consensus 173 ~~~~~~--~~-~~~~k~I~ei~~gd---~~v~v~g~Iv~i~~~~~y~aCp~CnKkv~~~~~~~~~~Ce~~~~v~p~~ryi 246 (355)
T PRK08402 173 PLEEVR--SY-NYTRKKIGELEGGE---RFVEVRGTIAKVYRVLVYDACPECRRKVDYDPATDTWICPEHGEVEPIKITI 246 (355)
T ss_pred cccccc--cc-cccccCHHHcccCC---cEEEEEEEEEEEecCeeEecCCCCCeEEEEecCCCCEeCCCCCCcCcceeEE
Confidence 000000 00 12233444442111 1134444444444310000 1111 2478899
Q ss_pred EEEEEeCCCceEEEEEecccccccccC
Q 015760 375 MKLTLEDPTARIHALLCGKEWVRFQLG 401 (401)
Q Consensus 375 ~~L~leD~t~~i~~~v~~~da~~f~~~ 401 (401)
+.+.|-|.||++.+.++++.|+.++|.
T Consensus 247 l~~~l~D~TG~~~vt~f~e~ae~llG~ 273 (355)
T PRK08402 247 LDFGLDDGTGYIRVTLFGDDAAELLGV 273 (355)
T ss_pred EEEEEEcCCCcEEEEEecHHHHHHhCC
Confidence 999999999999999999999999873
No 19
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=98.00 E-value=0.00024 Score=61.00 Aligned_cols=92 Identities=17% Similarity=0.262 Sum_probs=71.9
Q ss_pred eeeHHhhhhccC-CEEEEEEEEEEcCCce--ecCCC-ceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEe
Q 015760 10 IVRIKELAMHVK-HKVNLLGVVLEFSIPR--KSQGT-DYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLK 85 (401)
Q Consensus 10 y~~i~~~~~~~~-~~vnviGVVvd~~~P~--~trGt-D~~~tl~I~D~s~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~ 85 (401)
++.|+|+. ++ ..||+.|+|++..+++ +++|+ -....++|.|.|=. +.+.++.+.. +.+ +.||||+++
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 ITKIKDLK--PGMERVNVTVRVLEVGEPKVIQTKGGPRTISEAVVGDETGR---VKLTLWGEQA---GSL-KEGEVVEIE 74 (129)
T ss_pred ceEHHHcC--CCCCceEEEEEEEEcCCceEEEeCCCceEEEEEEEECCCCE---EEEEEeCCcc---ccC-CCCCEEEEE
Confidence 67899994 56 5799999999998764 45554 56889999999863 9999998643 345 689999999
Q ss_pred eEEEEEecCeeEEEeecCceEEEEEe
Q 015760 86 NVMIKKHQAELSAVFYKDSSSFALFD 111 (401)
Q Consensus 86 rvki~~~~g~~~~~~~~~~ss~~lf~ 111 (401)
+++++.|+|.+++..+.. +.....+
T Consensus 75 na~v~~f~G~lqL~i~~~-~~i~~~~ 99 (129)
T PRK06461 75 NAWTTLYRGKVQLNVGKY-GSISESD 99 (129)
T ss_pred CcEEeeeCCEEEEEECCC-EEEEECC
Confidence 999999999999888744 4444333
No 20
>PRK07218 replication factor A; Provisional
Probab=97.67 E-value=0.0068 Score=61.97 Aligned_cols=161 Identities=17% Similarity=0.212 Sum_probs=106.1
Q ss_pred cccccccC-CceeeeEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCccccCCCCcHHhhhcCCCCcc
Q 015760 159 LSLKDISE-HRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGT 237 (401)
Q Consensus 159 ~~L~di~~-~~f~Dl~~qVv~~~~~~~~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~~~~~e~~~l~~~~~~~~p~~G~ 237 (401)
..|+||++ +..++++++|+.+. + + ++. .||+..-.. ...+-| + -|
T Consensus 59 ~kI~Di~~~~~~V~v~~kVl~i~-~----r-t~r-~dg~~g~v~--~~~igD----------e--------------TG- 104 (423)
T PRK07218 59 KDIKELSTDDKNVTVTGRVLTIG-E----R-SIR-YQGDDHVIY--EGILAD----------E--------------TG- 104 (423)
T ss_pred ccHhhCCCCCceeEEEEEEEEec-c----e-eEe-cCCCceEEE--EEEEEC----------C--------------CC-
Confidence 67999986 57999999999886 3 2 223 777632111 110000 0 13
Q ss_pred EEEEEecCcchhhhcccCCCCCEEEEeeeEEEEeCcEEEEEeecCcceEEccCCChHHHHHhhhhhcCCCCCCCCcCCCC
Q 015760 238 VLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDNDNVVWDYMRERISGGHGHMPIWTDPS 317 (401)
Q Consensus 238 ~l~V~~~~~~~~~~~~~~k~g~wv~l~Nv~~k~~~G~leG~l~~~s~i~~l~~~d~~v~~l~r~r~~~~~~~~p~~~~p~ 317 (401)
.+++++|... .+++||+|++.|...+...|..+-.+...+.|..++++.. |.
T Consensus 105 ~Ir~tlW~~~------~l~~Gdvv~I~na~vre~~g~~el~ig~~t~I~~~de~~~----------------------~~ 156 (423)
T PRK07218 105 TISYTAWKDF------GLSPGDTVTIGNAGVREWDGRPELNIGESTTVSLLDDSSL----------------------PP 156 (423)
T ss_pred eEEEEEECCC------CCCCCCEEEEeccEeeccCCceEEeccCcceEEEcCcccc----------------------cC
Confidence 3488999832 2999999999999999999998888888888876555321 00
Q ss_pred CCcccccccCCCccccHHHHhcCCCCCceEEEEEEEEEeeCCCccccccCCCceEEEEEEEEeCCCceEEEEEeccccc
Q 015760 318 SQFLTEVDWVNVASVTLMKIATQLQGNVRCCCIVRVVSIHPFQAEHYSSPNGSSEYTMKLTLEDPTARIHALLCGKEWV 396 (401)
Q Consensus 318 ~~~~t~~~~~~~p~ttL~dIL~~~~~~~kfr~~VRVv~~~P~~~~df~~~~g~~~~~~~L~leD~t~~i~~~v~~~da~ 396 (401)
.+..+...|.||-.. ..-....+||++.+|. .|-...|.- ....++|.|.||+|+.-++++.|+
T Consensus 157 --------~~~~~~~kI~DL~~g---~~~V~v~g~Vl~~~~r---~f~~~dg~~-~v~~giigDeTG~Ir~tlW~~~~~ 220 (423)
T PRK07218 157 --------YSIGGDKKLIDLGPG---DRGVNVEARVLELEHR---EIDGRDGET-TILSGVLADETGRLPFTDWDPLPE 220 (423)
T ss_pred --------ccccCccchhhccCC---CCceEEEEEEEEecce---eEEcCCCCe-EEEEEEEECCCceEEEEEeccccc
Confidence 001122334444211 1225788999999874 466666632 366789999999999999998653
No 21
>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=97.66 E-value=0.00084 Score=52.62 Aligned_cols=72 Identities=18% Similarity=0.281 Sum_probs=60.2
Q ss_pred EEEEEEEEcCCceec---CCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEecCeeEEEee
Q 015760 25 NLLGVVLEFSIPRKS---QGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAELSAVFY 101 (401)
Q Consensus 25 nviGVVvd~~~P~~t---rGtD~~~tl~I~D~s~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~rvki~~~~g~~~~~~~ 101 (401)
||.|.|+...+++.- .+.--..+++|.|.|- .+.+.++.+.. .+.+ +.||+|.+++++++.|+|.+++..+
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 3457789999999974 39999998653 6667 7899999999999999999998876
Q ss_pred c
Q 015760 102 K 102 (401)
Q Consensus 102 ~ 102 (401)
.
T Consensus 75 ~ 75 (82)
T cd04491 75 K 75 (82)
T ss_pred C
Confidence 4
No 22
>PRK08402 replication factor A; Reviewed
Probab=97.23 E-value=0.012 Score=59.00 Aligned_cols=139 Identities=16% Similarity=0.230 Sum_probs=93.7
Q ss_pred ceeeHHhhhhccC-CEEEEEEEEEEcCCcee--c-CCC-ceEEEEEEEeCCCCCCCeEEEEecCCCC-CCCCCCCCCCEE
Q 015760 9 GIVRIKELAMHVK-HKVNLLGVVLEFSIPRK--S-QGT-DYVCVLKIVDDSQQSPELLVNIFTSSID-QLPRVLSPRDLI 82 (401)
Q Consensus 9 ~y~~i~~~~~~~~-~~vnviGVVvd~~~P~~--t-rGt-D~~~tl~I~D~s~~~~gl~v~iF~~~~e-~LP~v~~~GDII 82 (401)
...+|+|+. ++ ..||+.|-|+....|+. . .|+ ....+++|.|.|-. +.+.++.+..+ .++.+ ..||||
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 57999999999987753 2 243 56888999998763 89999997644 47878 789999
Q ss_pred EEeeEEEEEe-cCeeEEEeecCceEEEEEeCCCCCCccccccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCccccccc
Q 015760 83 LLKNVMIKKH-QAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSL 161 (401)
Q Consensus 83 ~l~rvki~~~-~g~~~~~~~~~~ss~~lf~~~~~~~~~P~~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~f~~~L 161 (401)
++.+++++.+ +|.+.+..+.. |+..+=+..+...-.|. -.++.. ... .. ..|
T Consensus 135 ~I~~a~V~e~~~G~~eLsvg~~-s~i~~~pd~~ea~~i~~---------~~~~~~--------------~~~--~~-k~I 187 (355)
T PRK08402 135 KVIDAQVRESLSGLPELHINFR-ARIILNPDDPRVEEIPP---------LEEVRS--------------YNY--TR-KKI 187 (355)
T ss_pred EEECCEEeecCCCcEEEEECCC-ceEEeCCCccccccccc---------cccccc--------------ccc--cc-cCH
Confidence 9999999984 88878887744 44442221111100110 000000 001 23 578
Q ss_pred ccccCCc-eeeeEEEEEEEE
Q 015760 162 KDISEHR-YFDLVCKVFHVS 180 (401)
Q Consensus 162 ~di~~~~-f~Dl~~qVv~~~ 180 (401)
.|++++. ||.+.+.|+.+.
T Consensus 188 ~ei~~gd~~v~v~g~Iv~i~ 207 (355)
T PRK08402 188 GELEGGERFVEVRGTIAKVY 207 (355)
T ss_pred HHcccCCcEEEEEEEEEEEe
Confidence 8887655 799999999987
No 23
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=96.82 E-value=0.013 Score=50.20 Aligned_cols=88 Identities=18% Similarity=0.171 Sum_probs=64.2
Q ss_pred cccccccCC-ceeeeEEEEEEEEee-----CCCC---eEEEEEEcCCCCCCCCCCCCCCcccCCCCCccccCCCCcHHhh
Q 015760 159 LSLKDISEH-RYFDLVCKVFHVSYD-----DSKG---LWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETL 229 (401)
Q Consensus 159 ~~L~di~~~-~f~Dl~~qVv~~~~~-----~~~~---~~~L~VwDgT~~p~~~~~~~~~~~~~~~~~~~~e~~~l~~~~~ 229 (401)
..|+||+++ .-+|++++|+.+. + ..++ .+.+.|=|.|
T Consensus 5 ~kI~dL~~g~~~v~~~~~V~~i~-~~~~~~~k~~~~~v~~~~l~D~T--------------------------------- 50 (129)
T PRK06461 5 TKIKDLKPGMERVNVTVRVLEVG-EPKVIQTKGGPRTISEAVVGDET--------------------------------- 50 (129)
T ss_pred eEHHHcCCCCCceEEEEEEEEcC-CceEEEeCCCceEEEEEEEECCC---------------------------------
Confidence 689999998 6999999999775 2 0111 1112222211
Q ss_pred hcCCCCccEEEEEecCcchhhhcccCCCCCEEEEeeeEEEEeCcEEEEEeecCcceEEccCC
Q 015760 230 RNFFPVGTVLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDN 291 (401)
Q Consensus 230 ~~~p~~G~~l~V~~~~~~~~~~~~~~k~g~wv~l~Nv~~k~~~G~leG~l~~~s~i~~l~~~ 291 (401)
|+ +++++|... ...+++||.|+++|..++...|.++..+...+.|..++++
T Consensus 51 ------G~-I~~tlW~~~----a~~l~~GdvV~I~na~v~~f~G~lqL~i~~~~~i~~~~~~ 101 (129)
T PRK06461 51 ------GR-VKLTLWGEQ----AGSLKEGEVVEIENAWTTLYRGKVQLNVGKYGSISESDDE 101 (129)
T ss_pred ------CE-EEEEEeCCc----cccCCCCCEEEEECcEEeeeCCEEEEEECCCEEEEECCcc
Confidence 43 578888863 3458999999999999999999998888888889877764
No 24
>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=0.0068 Score=44.91 Aligned_cols=71 Identities=18% Similarity=0.364 Sum_probs=54.1
Q ss_pred EEEEEEEEcCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEecCeeEEEee
Q 015760 25 NLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAELSAVFY 101 (401)
Q Consensus 25 nviGVVvd~~~P~~trGtD~~~tl~I~D~s~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~rvki~~~~g~~~~~~~ 101 (401)
.+.|+|+++..... ...+..++|.|.+.. .+.|.+|.+..+........|++|.++ .+++.++++.++...
T Consensus 1 ~v~g~v~~~~~~~~---~~~~~~~~l~D~~~~--~i~~~~~~~~~~~~~~~~~~g~~v~v~-g~v~~~~~~~~l~~~ 71 (75)
T cd03524 1 TIVGIVVAVEEIRT---EGKVLIFTLTDGTGG--TIRVTLFGELAEELENLLKEGQVVYIK-GKVKKFRGRLQLIVE 71 (75)
T ss_pred CeEEEEEeeccccc---CCeEEEEEEEcCCCC--EEEEEEEchHHHHHHhhccCCCEEEEE-EEEEecCCeEEEEee
Confidence 37899999887533 355899999998822 399999997666553444889999998 999998877766553
No 25
>KOG3416 consensus Predicted nucleic acid binding protein [General function prediction only]
Probab=96.46 E-value=0.018 Score=48.40 Aligned_cols=83 Identities=22% Similarity=0.307 Sum_probs=66.5
Q ss_pred eeHHhhhhccC-CEEEEEEEEEEcCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEE
Q 015760 11 VRIKELAMHVK-HKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMI 89 (401)
Q Consensus 11 ~~i~~~~~~~~-~~vnviGVVvd~~~P~~trGtD~~~tl~I~D~s~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~rvki 89 (401)
..|+|+. ++ +..|++=+|++.+...+|+-.+=.++.++.|+|-. |.+.+..+ +..+ + ++||||+|++---
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 4678884 33 35899999999999999988888999999999874 88888873 3333 2 6799999999999
Q ss_pred EEecCeeEEEeec
Q 015760 90 KKHQAELSAVFYK 102 (401)
Q Consensus 90 ~~~~g~~~~~~~~ 102 (401)
..|+|.+.+-..+
T Consensus 76 Si~qg~LtL~~GK 88 (134)
T KOG3416|consen 76 SIFQGCLTLYVGK 88 (134)
T ss_pred hhhcCceEEEecC
Confidence 9999987666654
No 26
>cd04497 hPOT1_OB1_like hPOT1_OB1_like: A subfamily of OB folds similar to the first OB fold (OB1) of human protection of telomeres 1 protein (hPOT1), the single OB fold of the N-terminal domain of Schizosaccharomyces pombe POT1 (SpPOT1), and the first OB fold of the N-terminal domain of the alpha subunit (OB1Nalpha) of Oxytricha nova telomere end binding protein (OnTEBP). POT1 proteins recognize single-stranded (ss) 3-prime ends of the telomere. A 3-prime ss overhang is conserved in ciliated protozoa, yeast, and mammals. SpPOT1 is essential for telomere maintenance. It binds specifically to the ss G-rich telomeric sequence (GGTTAC) of S. pombe. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. Deletion of the S. pombe pot1+ gene results in a rapid loss of telomere sequences, chromosome mis-segregation and chromosome circularization. hPOT1 is implicated in telomere length regulation. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB
Probab=96.44 E-value=0.044 Score=47.45 Aligned_cols=97 Identities=16% Similarity=0.131 Sum_probs=70.1
Q ss_pred ccccccccc--CCceeeeEEEEEEEEeeC----CCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCccccCCCCcHHhhh
Q 015760 157 YLLSLKDIS--EHRYFDLVCKVFHVSYDD----SKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLR 230 (401)
Q Consensus 157 f~~~L~di~--~~~f~Dl~~qVv~~~~~~----~~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~~~~~e~~~l~~~~~~ 230 (401)
| ..|+++. .++.+|+++-|+...... .+.+.+|.|+|-|.++
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 899999999999876211 1347778888855221
Q ss_pred cCCCCccEEEEEecCcchhhhcccCCCCCEEEEeeeEEEEeCcEEEEEeec-CcceEEccCC
Q 015760 231 NFFPVGTVLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQS-SSKIRLFSDN 291 (401)
Q Consensus 231 ~~p~~G~~l~V~~~~~~~~~~~~~~k~g~wv~l~Nv~~k~~~G~leG~l~~-~s~i~~l~~~ 291 (401)
+..++|.++....+. ...+++||.|+|+|++++..+|...|.... .+.+.+.+.+
T Consensus 51 -----~~~l~v~~F~~~~~~-LP~v~~GDVIll~~~kv~~~~g~~~~~~~~~~ss~avf~~~ 106 (138)
T cd04497 51 -----SDGLTVKLFRPNEES-LPIVKVGDIILLRRVKIQSYNGKPQGISNDRGSSWAVFRGD 106 (138)
T ss_pred -----CCcEEEEEECCChhh-CCCCCCCCEEEEEEEEEEEECCceEEEECCCceeEEEEcCC
Confidence 224567777766543 555799999999999999999998888777 5666665543
No 27
>PRK07217 replication factor A; Reviewed
Probab=96.29 E-value=0.075 Score=51.87 Aligned_cols=93 Identities=19% Similarity=0.338 Sum_probs=68.6
Q ss_pred CcceeeHHhhhhccCCEEEEEEEEEEcCCceecCCCceEEEE-EEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEe
Q 015760 7 QGGIVRIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVL-KIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLK 85 (401)
Q Consensus 7 ~y~y~~i~~~~~~~~~~vnviGVVvd~~~P~~trGtD~~~tl-~I~D~s~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~ 85 (401)
...-+.|+|+. ..++.|+|.|-|+....|+. +-.... -|-|+|= . |+++.+.+ +.+|.+ ..||+++|+
T Consensus 69 ~~~~~kI~Di~-~~~~~VsV~aKVl~l~e~~~----~si~qvGllgDETG-~--IkfT~W~~--s~~~~l-eeGd~~rI~ 137 (311)
T PRK07217 69 GSELVNIADID-EPEQWVDVTAKVVQLWEPSS----DSIAQVGLLGDETG-T--IKFTKWAK--SDLPEL-EEGKSYLLK 137 (311)
T ss_pred CCCceeeeecC-CCCCcEEEEEEEEEecCCCC----CceEEEEEEEcCCc-e--EEEEEccC--CCCCcc-cCCCEEEEE
Confidence 34456788885 35778999999999988642 222222 3555543 3 99999986 369999 789999999
Q ss_pred eEEEEEecCeeEEEeecCceEEEEEe
Q 015760 86 NVMIKKHQAELSAVFYKDSSSFALFD 111 (401)
Q Consensus 86 rvki~~~~g~~~~~~~~~~ss~~lf~ 111 (401)
++.+..|+|++++..+. +|+....+
T Consensus 138 na~v~ey~G~~~lnlg~-~t~I~~~d 162 (311)
T PRK07217 138 NVVTDEYQGRFSVKLNR-TTSIEELD 162 (311)
T ss_pred eEEEeeECCEEEEEeCC-ceEEEeCC
Confidence 99999999999998884 35555433
No 28
>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=95.80 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 015760 24 VNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKH--QAELSAVFY 101 (401)
Q Consensus 24 vnviGVVvd~~~P~~trGtD~~~tl~I~D~s~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~rvki~~~--~g~~~~~~~ 101 (401)
+-+.|+|.+.+. |++. ++-++|.|.+- .+.+.+|.+..+........|++|.++ .+++.+ ++++++...
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 457899999876 4433 99999999873 399999998777777766889988884 445544 466766654
No 29
>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=95.76 E-value=0.05 Score=44.78 Aligned_cols=82 Identities=12% Similarity=0.130 Sum_probs=57.9
Q ss_pred EEEEEEEEcCCceecC--C-CceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCC----CCCCEEEEee-EEEEEecCee
Q 015760 25 NLLGVVLEFSIPRKSQ--G-TDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVL----SPRDLILLKN-VMIKKHQAEL 96 (401)
Q Consensus 25 nviGVVvd~~~P~~tr--G-tD~~~tl~I~D~s~~~~gl~v~iF~~~~e~LP~v~----~~GDII~l~r-vki~~~~g~~ 96 (401)
++||+|+++++..... | ..-...|+|.|.+.. .++|.+..+..+.+..-. ..+=||.+-+ .+|..|+|..
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 5899999999876543 3 567899999999964 499999987666665421 3344776655 9999999854
Q ss_pred EEEeecCceEEE
Q 015760 97 SAVFYKDSSSFA 108 (401)
Q Consensus 97 ~~~~~~~~ss~~ 108 (401)
.+....+.|.|.
T Consensus 79 ~ls~~~~~s~v~ 90 (106)
T cd04481 79 SLSNSFGASKVY 90 (106)
T ss_pred EEEcCCCceEEE
Confidence 444432434454
No 30
>PRK07217 replication factor A; Reviewed
Probab=95.61 E-value=0.31 Score=47.70 Aligned_cols=165 Identities=16% Similarity=0.191 Sum_probs=97.6
Q ss_pred ccccccc-CCceeeeEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCccccCCCCcHHhhhcCCCCcc
Q 015760 159 LSLKDIS-EHRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGT 237 (401)
Q Consensus 159 ~~L~di~-~~~f~Dl~~qVv~~~~~~~~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~~~~~e~~~l~~~~~~~~p~~G~ 237 (401)
..|+||. .++.++++++|+.++ + ..+.-+.+ .+.+.|+ -|
T Consensus 73 ~kI~Di~~~~~~VsV~aKVl~l~-e-~~~~si~q------------vGllgDE------------------------TG- 113 (311)
T PRK07217 73 VNIADIDEPEQWVDVTAKVVQLW-E-PSSDSIAQ------------VGLLGDE------------------------TG- 113 (311)
T ss_pred eeeeecCCCCCcEEEEEEEEEec-C-CCCCceEE------------EEEEEcC------------------------Cc-
Confidence 6799998 589999999999998 4 22111111 0101110 02
Q ss_pred EEEEEecCcchhhhcccCCCCCEEEEeeeEEEEeCcEEEEEeecCcceEEccCCChHHHHHhhhhhcCCCCCCCCcCCCC
Q 015760 238 VLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDNDNVVWDYMRERISGGHGHMPIWTDPS 317 (401)
Q Consensus 238 ~l~V~~~~~~~~~~~~~~k~g~wv~l~Nv~~k~~~G~leG~l~~~s~i~~l~~~d~~v~~l~r~r~~~~~~~~p~~~~p~ 317 (401)
.++.++|.-.. ...+++|++++|.|+..+..+|..+-.+...+.|..++++-+ |...-- .+...+=.+. +.
T Consensus 114 ~IkfT~W~~s~---~~~leeGd~~rI~na~v~ey~G~~~lnlg~~t~I~~~de~Ie-V~~~~v-ei~G~lVdi~----~G 184 (311)
T PRK07217 114 TIKFTKWAKSD---LPELEEGKSYLLKNVVTDEYQGRFSVKLNRTTSIEELDEDIE-VGDDEV-EVEGALVDIQ----SG 184 (311)
T ss_pred eEEEEEccCCC---CCcccCCCEEEEEeEEEeeECCEEEEEeCCceEEEeCCCCcc-ccCccc-cceeEEEEEe----CC
Confidence 34678888422 455899999999999999999999999999898877665432 111000 0000000000 00
Q ss_pred CCcccccccCCCccccHHHHhcCCCCCc--eEEEEEEEEEeeCCCccccccCC----CceEEEEEEEEeCCCceEEEEEe
Q 015760 318 SQFLTEVDWVNVASVTLMKIATQLQGNV--RCCCIVRVVSIHPFQAEHYSSPN----GSSEYTMKLTLEDPTARIHALLC 391 (401)
Q Consensus 318 ~~~~t~~~~~~~p~ttL~dIL~~~~~~~--kfr~~VRVv~~~P~~~~df~~~~----g~~~~~~~L~leD~t~~i~~~v~ 391 (401)
.-.|.. +|. |- ||++ ...|..+ |.+--|....|-|.|+.+.++++
T Consensus 185 sglI~r-------------------CP~~~C~----Rvl~------~g~C~~HG~ve~~~DLrik~vlDDGt~~~~~~~~ 235 (311)
T PRK07217 185 SGLIKR-------------------CPEEDCT----RVLQ------NGRCSEHGKVEGEFDLRIKGVLDDGEEVQEVIFN 235 (311)
T ss_pred CCCeec-------------------CCccccC----cccc------CCCCCCCCCcCCceeeEEEEEEECCCCeEEEEEC
Confidence 000111 111 11 2221 1234433 35667899999999999999999
Q ss_pred ccccccccc
Q 015760 392 GKEWVRFQL 400 (401)
Q Consensus 392 ~~da~~f~~ 400 (401)
.+-.+.+.|
T Consensus 236 ~e~te~l~G 244 (311)
T PRK07217 236 REATEELTG 244 (311)
T ss_pred hHHhHHHhC
Confidence 888887765
No 31
>PRK06386 replication factor A; Reviewed
Probab=95.52 E-value=0.13 Score=51.60 Aligned_cols=88 Identities=18% Similarity=0.276 Sum_probs=68.5
Q ss_pred cceeeHHhhhhccCCEEEEEEEEEEcCCce-ecCCC-ceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEe
Q 015760 8 GGIVRIKELAMHVKHKVNLLGVVLEFSIPR-KSQGT-DYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLK 85 (401)
Q Consensus 8 y~y~~i~~~~~~~~~~vnviGVVvd~~~P~-~trGt-D~~~tl~I~D~s~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~ 85 (401)
|..++|+|+. ....-|||.|-|++...+. .++|+ -...++-|-|++=. |++.+|.+ .+ ..||+|++.
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 YKLVKIRDLS-LVTPYVSVIGKITGITKKEYDSDGTSKIVYQGYIEDDTAR---VRISSFGK------PL-EDNRFVRIE 173 (358)
T ss_pred cCccEeEecc-CCCCceEEEEEEEEccCceEecCCCccEEEEEEEEcCCCe---EEEEEccc------cc-cCCCEEEEe
Confidence 4567899994 2345699999999986542 23444 77888999998753 99999985 25 789999999
Q ss_pred eEEEEEecCeeEEEeecCceEE
Q 015760 86 NVMIKKHQAELSAVFYKDSSSF 107 (401)
Q Consensus 86 rvki~~~~g~~~~~~~~~~ss~ 107 (401)
++.++.|+|.+++..+.. |+.
T Consensus 174 na~v~e~~G~~el~v~~~-t~I 194 (358)
T PRK06386 174 NARVSQYNGYIEISVGNK-SVI 194 (358)
T ss_pred eeEEEccCCeEEEEeCCe-EEE
Confidence 999999999999988844 443
No 32
>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=95.51 E-value=0.023 Score=42.84 Aligned_cols=68 Identities=13% Similarity=0.216 Sum_probs=52.1
Q ss_pred EEEEEEEEEcCCceecCCCceEEEEEEEeCCCCCCCeEEEEec-CCCCCCCCCCCCCCEEEEeeEEEEEecCe-eEEEee
Q 015760 24 VNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFT-SSIDQLPRVLSPRDLILLKNVMIKKHQAE-LSAVFY 101 (401)
Q Consensus 24 vnviGVVvd~~~P~~trGtD~~~tl~I~D~s~~~~gl~v~iF~-~~~e~LP~v~~~GDII~l~rvki~~~~g~-~~~~~~ 101 (401)
|.|.|.|.... ++..-.+.++|.|.+- .+.|.+|. ........+ ..||+|+++ -+++.++++ +++...
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 3344466889999983 39999999 334455556 789999998 999999987 877665
No 33
>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=95.36 E-value=0.49 Score=41.27 Aligned_cols=97 Identities=19% Similarity=0.149 Sum_probs=64.0
Q ss_pred cccc--cccCCceeeeEEEEEEEEee------CCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCccccCCCCcHHhhh
Q 015760 159 LSLK--DISEHRYFDLVCKVFHVSYD------DSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLR 230 (401)
Q Consensus 159 ~~L~--di~~~~f~Dl~~qVv~~~~~------~~~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~~~~~e~~~l~~~~~~ 230 (401)
..|. ..+.++++|+++-|+..... ..+-.++|.|+|-|-+.... .
T Consensus 2 ~~l~~~~~~~~~~vnvigVV~~~~~p~~~~t~g~D~~~tl~i~D~S~~~~~~-~-------------------------- 54 (146)
T PF02765_consen 2 TPLSTAKEKFGKFVNVIGVVVDFSPPNPKKTRGTDYMCTLTITDPSLNDSNQ-K-------------------------- 54 (146)
T ss_dssp CCGGGSCTTSSEEEEEEEEEEEEEEECTEEESSSCEEEEEEEEBTTCSCSSC-C--------------------------
T ss_pred ccchhhhhcCCCEEEEEEEEEEccCCcceEcCCCcEEEEEEEECCCCCcccc-c--------------------------
Confidence 4555 44678999999999987633 12348899999966221100 0
Q ss_pred cCCCCccEEEEEecCcchhhhcccCCC-CCEEEEeeeEEEEeCcEEEEEeecC--cceEEc
Q 015760 231 NFFPVGTVLRVSTDRSYENFGRYFTAT-GKWVRIRNMSCQVSSGMWHGLLQSS--SKIRLF 288 (401)
Q Consensus 231 ~~p~~G~~l~V~~~~~~~~~~~~~~k~-g~wv~l~Nv~~k~~~G~leG~l~~~--s~i~~l 288 (401)
...+.|.+...+.+. ...++. ||.|+|++++++...|...|..... +.+.+.
T Consensus 55 -----~~~l~v~iF~~~~~~-LP~v~~~GDii~l~r~kv~~~~~~~~~~~~~~~~ss~~vf 109 (146)
T PF02765_consen 55 -----LSGLTVNIFRPHKES-LPNVKSVGDIIRLRRVKVQSYNGKPQGLSNSTSNSSWAVF 109 (146)
T ss_dssp -----CCEEEEEEEESSHHH-SCTTCSTTHEEEEEEEEEEEETTEEEEEEECECTEEEEEE
T ss_pred -----cCCEEEEEECCCHHH-CCCCCCCCCEEEEEEEEEEEECCEEEEEecCCCcEEEEEE
Confidence 023344333222222 566776 9999999999999999888877766 667666
No 34
>cd04474 RPA1_DBD_A RPA1_DBD_A: A subfamily of OB folds corresponding to the second OB fold, the ssDNA-binding domain (DBD)-A, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change. Although ScRPA and the hRPA have similar ssDNA-binding properties, they differ funct
Probab=95.04 E-value=0.078 Score=43.54 Aligned_cols=84 Identities=13% Similarity=0.182 Sum_probs=61.7
Q ss_pred eHHhhhhccCCEEEEEEEEEEcCCceecC---CCceEEEEEEEeCCCCCCCeEEEEecCCCC-CCCCCCCCCCEEEEeeE
Q 015760 12 RIKELAMHVKHKVNLLGVVLEFSIPRKSQ---GTDYVCVLKIVDDSQQSPELLVNIFTSSID-QLPRVLSPRDLILLKNV 87 (401)
Q Consensus 12 ~i~~~~~~~~~~vnviGVVvd~~~P~~tr---GtD~~~tl~I~D~s~~~~gl~v~iF~~~~e-~LP~v~~~GDII~l~rv 87 (401)
+|+++.. ......+.|-|+....++.-+ |....++|.|.|+.... |.+.+|.+..+ .-|.+ ..|+|+.+.+.
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 4677732 234589999999877765432 45777899999996533 99999986444 45566 79999999999
Q ss_pred EEEEecCeeEEE
Q 015760 88 MIKKHQAELSAV 99 (401)
Q Consensus 88 ki~~~~g~~~~~ 99 (401)
+|+.-++...-.
T Consensus 77 ~V~~a~~~y~~~ 88 (104)
T cd04474 77 SVKVANKKFNTL 88 (104)
T ss_pred EEeeccccCCCC
Confidence 999887654433
No 35
>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=94.84 E-value=0.081 Score=47.10 Aligned_cols=58 Identities=16% Similarity=0.017 Sum_probs=44.0
Q ss_pred CceEEEEEEEEEeeCCCccc------------------cccC------CCceEEEEEEEEeCCCceEEEEEecccccccc
Q 015760 344 NVRCCCIVRVVSIHPFQAEH------------------YSSP------NGSSEYTMKLTLEDPTARIHALLCGKEWVRFQ 399 (401)
Q Consensus 344 ~~kfr~~VRVv~~~P~~~~d------------------f~~~------~g~~~~~~~L~leD~t~~i~~~v~~~da~~f~ 399 (401)
+..|.+.+.|+.+.+...-= +|.. +-.|.|++.+.|.|.|+.+.+.++|+.|+.||
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 56788888888877763211 1111 12678999999999999999999999999999
Q ss_pred cC
Q 015760 400 LG 401 (401)
Q Consensus 400 ~~ 401 (401)
|.
T Consensus 95 G~ 96 (166)
T cd04476 95 GK 96 (166)
T ss_pred CC
Confidence 83
No 36
>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=94.70 E-value=0.35 Score=38.62 Aligned_cols=67 Identities=16% Similarity=0.184 Sum_probs=51.5
Q ss_pred EEEEEEEEEcCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCC----CCCCCCCCCCEEEEeeEEEEEecCeeEEE
Q 015760 24 VNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSID----QLPRVLSPRDLILLKNVMIKKHQAELSAV 99 (401)
Q Consensus 24 vnviGVVvd~~~P~~trGtD~~~tl~I~D~s~~~~gl~v~iF~~~~e----~LP~v~~~GDII~l~rvki~~~~g~~~~~ 99 (401)
|.+.|+|+++..- +=..+++|-|.|= .|.+.++....+ ..+.+ +.|++|++ +-+++.|+|+.++.
T Consensus 2 v~~vG~V~~~~~~------~~~~~~tL~D~TG---~I~~~~W~~~~~~~~~~~~~~-~~g~~v~v-~G~v~~~~g~~ql~ 70 (95)
T cd04478 2 VTLVGVVRNVEEQ------STNITYTIDDGTG---TIEVRQWLDDDNDDSSEVEPI-EEGTYVRV-FGNLKSFQGKKSIM 70 (95)
T ss_pred EEEEEEEEeeeEc------ccEEEEEEECCCC---cEEEEEeCCCCCccccccccc-ccCCEEEE-EEEEcccCCeeEEE
Confidence 6789999997641 2347889999874 399999987654 55555 89999998 56789999998876
Q ss_pred ee
Q 015760 100 FY 101 (401)
Q Consensus 100 ~~ 101 (401)
..
T Consensus 71 i~ 72 (95)
T cd04478 71 AF 72 (95)
T ss_pred EE
Confidence 54
No 37
>PF15489 CTC1: CST, telomere maintenance, complex subunit CTC1
Probab=94.66 E-value=0.25 Score=55.58 Aligned_cols=133 Identities=17% Similarity=0.082 Sum_probs=95.8
Q ss_pred EEEEEecCcchhhhcccCCCCCEEEEeeeEEEEe-CcEEEEEeecCcceEEccCCChHHHHHhhhhhcCCCCCCCCcCCC
Q 015760 238 VLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVS-SGMWHGLLQSSSKIRLFSDNDNVVWDYMRERISGGHGHMPIWTDP 316 (401)
Q Consensus 238 ~l~V~~~~~~~~~~~~~~k~g~wv~l~Nv~~k~~-~G~leG~l~~~s~i~~l~~~d~~v~~l~r~r~~~~~~~~p~~~~p 316 (401)
.|.|+++.+|.-+ -..+-||.-|.|.++..|+. +|..|..+.++|.|++++-... .
T Consensus 888 ~ldVYi~~~h~p~-plGLLPGA~V~f~~lerkVSRs~nVYC~~~psS~VtVlS~p~~----------t------------ 944 (1144)
T PF15489_consen 888 HLDVYIEDPHLPY-PLGLLPGARVLFSQLERKVSRSHNVYCCFLPSSSVTVLSFPPE----------T------------ 944 (1144)
T ss_pred eEEEEecCCCCCC-cccccCCceeeeehhhhhhhccCcEEEEEcCCceEEEEecCcc----------c------------
Confidence 3678888877765 55678999999999999997 6999999999999998765110 0
Q ss_pred CCCcccccccCCCccccHHHHhcCCCCCceEEEEEEEEEeeCCCccccccC--------------------CCceEEEEE
Q 015760 317 SSQFLTEVDWVNVASVTLMKIATQLQGNVRCCCIVRVVSIHPFQAEHYSSP--------------------NGSSEYTMK 376 (401)
Q Consensus 317 ~~~~~t~~~~~~~p~ttL~dIL~~~~~~~kfr~~VRVv~~~P~~~~df~~~--------------------~g~~~~~~~ 376 (401)
+.-..+|...|.+.+.....+.+.++.++||+++=-.+.=-|.. .+.....-+
T Consensus 945 -------~~~~~~P~~~L~~~~~~~~~~~~a~~~chVV~V~~l~L~WvCa~C~si~~qg~Csr~~p~C~s~~sV~qA~ar 1017 (1144)
T PF15489_consen 945 -------NVSPPLPHIYLAELLQGSQSPFQARVSCHVVSVLSLQLQWVCAHCGSICPQGRCSRQSPPCPSQTSVFQASAR 1017 (1144)
T ss_pred -------CCCCCCCeEEehhhhCCCCCCceEEEEEEEEEEEEEEeeehhhhccCcccCCcCCCCCCCCCCCcceeeEEEE
Confidence 00113456667777776667778888899998776555433331 123345679
Q ss_pred EEEeCCCceEEEEEeccccccccc
Q 015760 377 LTLEDPTARIHALLCGKEWVRFQL 400 (401)
Q Consensus 377 L~leD~t~~i~~~v~~~da~~f~~ 400 (401)
++|||.||+-++.+.|+-...++|
T Consensus 1018 ~~vEDGTaeA~v~~~~~~V~~lLg 1041 (1144)
T PF15489_consen 1018 LLVEDGTAEAVVWCRGHHVAALLG 1041 (1144)
T ss_pred EEEecCCeeEEEEECCcHHHHHhC
Confidence 999999999999999965555443
No 38
>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=94.18 E-value=0.14 Score=39.03 Aligned_cols=71 Identities=14% Similarity=0.285 Sum_probs=50.2
Q ss_pred EEEEEEEcCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEecCeeEEEee
Q 015760 26 LLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAELSAVFY 101 (401)
Q Consensus 26 viGVVvd~~~P~~trGtD~~~tl~I~D~s~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~rvki~~~~g~~~~~~~ 101 (401)
+.|+|.+... +.++...-+..++|.|.+-. +.+.+|.+..+.+......|.++.++ -+++.|+|..+....
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 44554556799999998663 99999986543344444789999886 477778776665543
No 39
>PRK13480 3'-5' exoribonuclease YhaM; Provisional
Probab=93.99 E-value=0.39 Score=47.46 Aligned_cols=82 Identities=16% Similarity=0.171 Sum_probs=63.9
Q ss_pred eHHhhhhccCCEEEEEEEEEEcCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEE
Q 015760 12 RIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKK 91 (401)
Q Consensus 12 ~i~~~~~~~~~~vnviGVVvd~~~P~~trGtD~~~tl~I~D~s~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~rvki~~ 91 (401)
.|+++ ..|..|+.+.+|.+...-...+|+. ...+++.|.|=. |..+++....+....+ ..||||.+ +-++..
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--EVGEQVDHFLLIKSATKGVASNGKP-FLTLILQDKSGD---IEAKLWDVSPEDEATY-VPETIVHV-KGDIIN 75 (314)
T ss_pred hHhhc--CCCCEeeEEEEEEEceeeecCCCCe-EEEEEEEcCCcE---EEEEeCCCChhhHhhc-CCCCEEEE-EEEEEE
Confidence 47777 4688999999999987643333555 678999998653 9999998877777777 88999999 456678
Q ss_pred ecCeeEEEee
Q 015760 92 HQAELSAVFY 101 (401)
Q Consensus 92 ~~g~~~~~~~ 101 (401)
|+|++|+...
T Consensus 76 y~g~~Ql~i~ 85 (314)
T PRK13480 76 YRGRKQLKVN 85 (314)
T ss_pred ECCcceEEEE
Confidence 9999887654
No 40
>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=93.20 E-value=0.87 Score=34.77 Aligned_cols=69 Identities=12% Similarity=0.227 Sum_probs=50.0
Q ss_pred EEEEEEcCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEecCeeEEEee
Q 015760 27 LGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAELSAVFY 101 (401)
Q Consensus 27 iGVVvd~~~P~~trGtD~~~tl~I~D~s~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~rvki~~~~g~~~~~~~ 101 (401)
+.+|.+++. +.|+...-+..++|-|.+-. +.+.+|.+.....+.+ ..|.+|.++ .++..++|+.+....
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 45555556899999998763 9999998655444555 789999997 677778776665543
No 41
>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=92.82 E-value=1 Score=36.12 Aligned_cols=65 Identities=15% Similarity=0.125 Sum_probs=47.9
Q ss_pred EEEEEEEcCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCC---------------------CCCCCCCCCCCEEEE
Q 015760 26 LLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSI---------------------DQLPRVLSPRDLILL 84 (401)
Q Consensus 26 viGVVvd~~~P~~trGtD~~~tl~I~D~s~~~~gl~v~iF~~~~---------------------e~LP~v~~~GDII~l 84 (401)
++|+|+.... +.+ ..+|+|-|.+= . |.|.++.... +..+.+ ++|++|++
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 212 37788888655 2 8999997543 344456 89999999
Q ss_pred eeEEEEEecCeeEEEee
Q 015760 85 KNVMIKKHQAELSAVFY 101 (401)
Q Consensus 85 ~rvki~~~~g~~~~~~~ 101 (401)
+ -+++.|+|+.|+...
T Consensus 72 ~-G~i~~frg~~ql~i~ 87 (92)
T cd04483 72 R-GSIRTYRGEREINAS 87 (92)
T ss_pred E-EEEeccCCeeEEEEE
Confidence 6 789999999887654
No 42
>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=91.94 E-value=0.11 Score=45.30 Aligned_cols=31 Identities=23% Similarity=0.262 Sum_probs=29.4
Q ss_pred ceEEEEEEEEeCCCceEEEEEeccccccccc
Q 015760 370 SSEYTMKLTLEDPTARIHALLCGKEWVRFQL 400 (401)
Q Consensus 370 ~~~~~~~L~leD~t~~i~~~v~~~da~~f~~ 400 (401)
.|.|++.+.|.|.|+.+.+.++|+.|+.|||
T Consensus 51 ~~ry~l~~~i~D~tg~~~~~~F~~~a~~l~G 81 (146)
T PF08646_consen 51 KYRYRLSLKISDGTGSIWVTLFDEEAEQLLG 81 (146)
T ss_dssp EEEEEEEEEEEETTEEEEEEEEHHHHHHHHC
T ss_pred eEEEEEEEEEEeCCCeEEEEEEhHHHHHHhC
Confidence 6889999999999999999999999999996
No 43
>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=90.61 E-value=0.96 Score=35.08 Aligned_cols=46 Identities=20% Similarity=0.110 Sum_probs=38.1
Q ss_pred EEEEEecCcchhhhcccCCCCCEEEEeeeEEEEeCcEEEEEeecCcceE
Q 015760 238 VLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIR 286 (401)
Q Consensus 238 ~l~V~~~~~~~~~~~~~~k~g~wv~l~Nv~~k~~~G~leG~l~~~s~i~ 286 (401)
.+++.+|+..+ ...+++|++|++.|..++...|.++..+...+.|.
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 46788888654 56799999999999999999999988888777664
No 44
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain
Probab=90.53 E-value=2.4 Score=34.46 Aligned_cols=79 Identities=20% Similarity=0.221 Sum_probs=53.9
Q ss_pred HHhhhhcc--CCEEEEEEEEEEcCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCC-CCCCCCCEEEEeeEEE
Q 015760 13 IKELAMHV--KHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLP-RVLSPRDLILLKNVMI 89 (401)
Q Consensus 13 i~~~~~~~--~~~vnviGVVvd~~~P~~trGtD~~~tl~I~D~s~~~~gl~v~iF~~~~e~LP-~v~~~GDII~l~rvki 89 (401)
|+++++.. -..+-|.|=|.+++.. ++| .+-|+|+|+. ..|+|.+|+.....++ ...+.||-|.+ +.++
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 45555442 2679999999998874 222 4778999965 3499999998878887 54488997766 4455
Q ss_pred EEe--cCeeEEEe
Q 015760 90 KKH--QAELSAVF 100 (401)
Q Consensus 90 ~~~--~g~~~~~~ 100 (401)
..| .|++++..
T Consensus 82 ~~y~~~G~~sl~v 94 (99)
T PF13742_consen 82 SFYEPRGSLSLIV 94 (99)
T ss_pred EEECCCcEEEEEE
Confidence 555 44455443
No 45
>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=89.71 E-value=5.4 Score=32.12 Aligned_cols=60 Identities=12% Similarity=0.031 Sum_probs=39.1
Q ss_pred ccEEEEEecCcchhhhcccCCCCCEEEEeeeEEEEeCcEEEEEeecCcceEEccCCChHHHHHh
Q 015760 236 GTVLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDNDNVVWDYM 299 (401)
Q Consensus 236 G~~l~V~~~~~~~~~~~~~~k~g~wv~l~Nv~~k~~~G~leG~l~~~s~i~~l~~~d~~v~~l~ 299 (401)
|..+.|++|...+.... ...|+.+.|.|++++..+|. .......|.|.+ +++.+++.++.
T Consensus 38 ~~~i~vtLWg~~a~~~~--~~~~~vv~~~~~~i~~~~~~-~l~~~~~s~i~~-np~~~e~~~l~ 97 (101)
T cd04475 38 GHSVELTLWGEQAELFD--GSENPVIAIKGVKVSEFNGK-SLSTGSSSTIII-NPDIPEAHKLR 97 (101)
T ss_pred CCEEEEEEEHHHhhhcc--cCCCCEEEEEeeEEEecCCe-EEeecCceeEEE-CCCcHHHHHHH
Confidence 44567899987665322 22399999999999877653 344445566654 44466666654
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=85.78 E-value=8.7 Score=29.34 Aligned_cols=65 Identities=11% Similarity=0.120 Sum_probs=40.8
Q ss_pred EEEEEEEcCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCC-EEEEeeEEEEEecCeeEEEee
Q 015760 26 LLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRD-LILLKNVMIKKHQAELSAVFY 101 (401)
Q Consensus 26 viGVVvd~~~P~~trGtD~~~tl~I~D~s~~~~gl~v~iF~~~~e~LP~v~~~GD-II~l~rvki~~~~g~~~~~~~ 101 (401)
+-|.|..+.. +|.. +-|+|.|... .|.|.+|+.+...++.-...|| |+..-++.+ .+|+.|+...
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 4567788543 3999999875545655447899 555545554 5666666543
No 47
>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=85.72 E-value=2 Score=35.08 Aligned_cols=52 Identities=17% Similarity=0.198 Sum_probs=39.0
Q ss_pred eEEEEEEEEEeeCCCccccccCCCceEEEEEEEEeCC-CceEEEEEeccccccccc
Q 015760 346 RCCCIVRVVSIHPFQAEHYSSPNGSSEYTMKLTLEDP-TARIHALLCGKEWVRFQL 400 (401)
Q Consensus 346 kfr~~VRVv~~~P~~~~df~~~~g~~~~~~~L~leD~-t~~i~~~v~~~da~~f~~ 400 (401)
.+++.|||+... ++..|....+ =.-.|.|.|-|. +++|+|-++++.|++|..
T Consensus 11 ~~~I~~rV~~k~--~~~~f~~~~~-~g~~~~~~l~De~~~~I~~t~~~~~~~~f~~ 63 (104)
T cd04474 11 KWTIKARVTNKS--DIRTWSNARG-EGKLFSFDLLDEDGGEIRATFFNDAVDKFYD 63 (104)
T ss_pred cEEEEEEEeecc--ccccccCCCC-CcEEEEEEEEECCCCEEEEEEehHHHHHhhc
Confidence 589999999763 3455555422 024678899999 999999999999988764
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=84.75 E-value=6.7 Score=28.82 Aligned_cols=68 Identities=18% Similarity=0.280 Sum_probs=44.2
Q ss_pred EEEEEEEcCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEecCeeEEEe
Q 015760 26 LLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAELSAVF 100 (401)
Q Consensus 26 viGVVvd~~~P~~trGtD~~~tl~I~D~s~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~rvki~~~~g~~~~~~ 100 (401)
+.|.|++..... ++|.. ...+++.|.+- .+.+.+|... ..+......|+.+.+. -|+..|+|+++...
T Consensus 2 i~~~V~~~~~~~-~~~~~-~~~~~~~D~~g---~i~~~~F~~~-~~~~~~~~~G~~~~v~-Gkv~~~~~~~qi~~ 69 (75)
T cd04488 2 VEGTVVSVEVVP-RRGRR-RLKVTLSDGTG---TLTLVFFNFQ-PYLKKQLPPGTRVRVS-GKVKRFRGGLQIVH 69 (75)
T ss_pred EEEEEEEEEecc-CCCcc-EEEEEEEcCCC---EEEEEEECCC-HHHHhcCCCCCEEEEE-EEEeecCCeeEEeC
Confidence 567777764321 22333 78999999854 3999999732 2334434789988885 56677877666544
No 49
>PRK07373 DNA polymerase III subunit alpha; Reviewed
Probab=81.96 E-value=4.9 Score=41.77 Aligned_cols=89 Identities=16% Similarity=0.202 Sum_probs=63.2
Q ss_pred cceeeHHhhhh-ccCCEEEEEEEEEEcCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEee
Q 015760 8 GGIVRIKELAM-HVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKN 86 (401)
Q Consensus 8 y~y~~i~~~~~-~~~~~vnviGVVvd~~~P~~trGtD~~~tl~I~D~s~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~r 86 (401)
+...+++++.. ..++.|.+.|+|...+.+ +|+..+-++-++|-|.+-. +.+.+|.+..+..-.....|.+++++.
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 6666678999999999764 999999876555555447788888854
Q ss_pred EEEEEecCeeEEEee
Q 015760 87 VMIKKHQAELSAVFY 101 (401)
Q Consensus 87 vki~~~~g~~~~~~~ 101 (401)
+++.-.++.+.+.+
T Consensus 342 -~v~~~~~~~~liv~ 355 (449)
T PRK07373 342 -KVDRRDDQVQLIVE 355 (449)
T ss_pred -EEEecCCeEEEEEe
Confidence 55543344555554
No 50
>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=80.65 E-value=17 Score=28.24 Aligned_cols=69 Identities=16% Similarity=0.247 Sum_probs=46.5
Q ss_pred EEEEEEEEcCCceecCCCceEEEEEEEeCCCCCCCeEEEEec-CCCCCCCCCCC-CCCEEEEeeE-EEEEecCeeEE
Q 015760 25 NLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFT-SSIDQLPRVLS-PRDLILLKNV-MIKKHQAELSA 98 (401)
Q Consensus 25 nviGVVvd~~~P~~trGtD~~~tl~I~D~s~~~~gl~v~iF~-~~~e~LP~v~~-~GDII~l~rv-ki~~~~g~~~~ 98 (401)
-+-|-|-+... +.+|..-...+|.|+|-+ +++.|..|. +..+.+-.+ + .||-|+++.- ....|.++...
T Consensus 3 ~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 3 VVEGEVFDLEI-RELKSGRKILTFKVTDYT---SSITVKKFLRKDEKDKEEL-KSKGDWVRVRGKVQYDTFSKELVL 74 (82)
T ss_pred EEEEEEEEEEE-EEecCCCEEEEEEEEcCC---CCEEEEEeccCChhHHhhc-ccCCCEEEEEEEEEEccCCCceEE
Confidence 35566665543 455666889999999965 459999998 344555556 5 8999988654 34455555443
No 51
>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=79.97 E-value=6.8 Score=30.38 Aligned_cols=59 Identities=14% Similarity=0.317 Sum_probs=42.2
Q ss_pred EEEEEEEEEcCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCC--CCCCCCCCCCEEEEeeEEEEE
Q 015760 24 VNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSID--QLPRVLSPRDLILLKNVMIKK 91 (401)
Q Consensus 24 vnviGVVvd~~~P~~trGtD~~~tl~I~D~s~~~~gl~v~iF~~~~e--~LP~v~~~GDII~l~rvki~~ 91 (401)
+.+.|+|.+.+ .||.++- .++|-|.+-. +.|.+|.+..+ ..-.....|.+|.++. ++..
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 6655556677777754 5543
No 52
>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=78.15 E-value=5.3 Score=32.68 Aligned_cols=53 Identities=17% Similarity=0.337 Sum_probs=39.7
Q ss_pred ceeeHHhhhhccCCEEEEEEEEEE-cCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCC
Q 015760 9 GIVRIKELAMHVKHKVNLLGVVLE-FSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSS 68 (401)
Q Consensus 9 ~y~~i~~~~~~~~~~vnviGVVvd-~~~P~~trGtD~~~tl~I~D~s~~~~gl~v~iF~~~ 68 (401)
.|+||+.+- ..|+ | +|.| +++| .+.+.-|+.++.|.|+-+..++|+|.+|++.
T Consensus 17 sFmPl~saD-~~gG-V----I~TdWY~~p-~~~~er~k~tv~Ild~~Lradal~V~vf~q~ 70 (103)
T PF12100_consen 17 SFMPLASAD-PFGG-V----IVTDWYSPP-PGPNERFKATVYILDRALRADALRVSVFRQV 70 (103)
T ss_pred hhcchhhcC-CCCC-E----EEeccccCC-CCCCeeEEEEEEEECccccCCceEEEEEEee
Confidence 577777773 2233 2 4677 5555 4456899999999999999899999999864
No 53
>KOG4757 consensus Predicted telomere binding protein [General function prediction only]
Probab=77.96 E-value=0.079 Score=53.32 Aligned_cols=214 Identities=13% Similarity=0.177 Sum_probs=117.9
Q ss_pred ccccccccccCCceeeeEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCccccCCCCcHHhhhcCCCC
Q 015760 156 DYLLSLKDISEHRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPV 235 (401)
Q Consensus 156 ~f~~~L~di~~~~f~Dl~~qVv~~~~~~~~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~~~~~e~~~l~~~~~~~~p~~ 235 (401)
.+ .++.|+.+.+...+.+++....|. ....++|++|+|.+...+ .+..- .. +++ |-.+
T Consensus 175 ~w-~lv~d~~~h~~~s~~~~~~~~~yS--lr~~l~~~~~~T~~~l~F-p~~g~------ts-------~~r-----~~rv 232 (522)
T KOG4757|consen 175 SW-SLVSDITPHQRCSFYAQVIKTWYS--LRNPLLYVTDPTENLLFF-PMSGY------TS-------SSR-----WDRV 232 (522)
T ss_pred ee-eeeecccccccccccccceeeEee--cccccccccCchHhhhhc-ccCCc------ee-------eee-----eecc
Confidence 36 789999999999999999988865 567889999999886643 32100 00 000 0001
Q ss_pred -cc-EEEEEecCcchhhhcccCCCCCEEEEeeeEEEE-eCcEEEEEeecCc------ceEEccCCChHHHHHh-hhhhc-
Q 015760 236 -GT-VLRVSTDRSYENFGRYFTATGKWVRIRNMSCQV-SSGMWHGLLQSSS------KIRLFSDNDNVVWDYM-RERIS- 304 (401)
Q Consensus 236 -G~-~l~V~~~~~~~~~~~~~~k~g~wv~l~Nv~~k~-~~G~leG~l~~~s------~i~~l~~~d~~v~~l~-r~r~~- 304 (401)
|. .+- +++..+.-+.++..+.||.+-..|++... |-|+.+..+++++ .+.+...+.+...+.. +.|+.
T Consensus 233 ~~e~~i~-ilq~~~d~~~~Nl~~e~D~~f~~~~~sl~dh~~lsrc~~~~~saprl~~sl~lhc~~ehll~ev~~e~r~~~ 311 (522)
T KOG4757|consen 233 SEEFSIC-ILQDEHDFYCRNLIKEGDYVFMKNVRSLIDHLGLSRCILHGDSAPRLNMSLELHCSEEHLLNEVKPEKRLYV 311 (522)
T ss_pred cccccch-hccccchhhhhhhcccccccccccchhhhHHHHHHHHHHHhhccccccceeEeecCcchhhcccCcccceee
Confidence 11 122 33444444568888999999999988765 4454433333333 2333334444332222 12221
Q ss_pred -CCCCCCC---------CcCCC-------CC---Cccc--ccccC-CCccccHHH-----HhcCCCCCceEEEEEEEEEe
Q 015760 305 -GGHGHMP---------IWTDP-------SS---QFLT--EVDWV-NVASVTLMK-----IATQLQGNVRCCCIVRVVSI 356 (401)
Q Consensus 305 -~~~~~~p---------~~~~p-------~~---~~~t--~~~~~-~~p~ttL~d-----IL~~~~~~~kfr~~VRVv~~ 356 (401)
+....++ |.+.. .+ ..+. ...+| ++.+.+|.- |.... -+.+++.++.+.++
T Consensus 312 q~~~tgi~~v~a~fvsl~Ds~t~~~vt~k~R~~vvrfva~~~~~P~sve~l~~i~i~l~~ic~l~-n~r~H~~l~~le~s 390 (522)
T KOG4757|consen 312 QNCQTGIEAVIAPFVSLMDSETPFIVTEKKRTCVVRFVAHVINYPASVELLTIITILLAPICNLL-NPRKHRLLVQLEDS 390 (522)
T ss_pred cccccCcchhhcccchhhhhccccccchhcceeeeeehhhcccccchhhhhhhhhhhhHHHhhhh-chhhhhhhhhhccc
Confidence 1111111 10100 00 0000 11333 345554443 33322 46689999999999
Q ss_pred eCCCccccccCC---C--------------------ceEEEEEEEEeCCCceEEEEEecc
Q 015760 357 HPFQAEHYSSPN---G--------------------SSEYTMKLTLEDPTARIHALLCGK 393 (401)
Q Consensus 357 ~P~~~~df~~~~---g--------------------~~~~~~~L~leD~t~~i~~~v~~~ 393 (401)
+|..+..|.+.. . .+.|-.+.++-|.+.-|++++.+.
T Consensus 391 ~p~s~~~fgc~~~~~~~~v~~ln~Lv~~e~~~~vP~~~~~v~~~~l~~~s~~l~~~l~d~ 450 (522)
T KOG4757|consen 391 WPKSLTQFGCLSQPPSSYVWMLNLLVRDESNVTVPVIFFDVDAAELINSSKKLPCNLADH 450 (522)
T ss_pred CcccceeeeeccCCHHHHHHHHHHHhccccccccccccchhheeeeccccccccchhccc
Confidence 999999998731 1 344556666666677777765544
No 54
>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=77.22 E-value=9.8 Score=30.33 Aligned_cols=60 Identities=20% Similarity=0.329 Sum_probs=37.6
Q ss_pred EEEEEEEcCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCC--CCCCCCCCCCCCEEEEeeEEEEEec
Q 015760 26 LLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSS--IDQLPRVLSPRDLILLKNVMIKKHQ 93 (401)
Q Consensus 26 viGVVvd~~~P~~trGtD~~~tl~I~D~s~~~~gl~v~iF~~~--~e~LP~v~~~GDII~l~rvki~~~~ 93 (401)
|-|-|..+..+. +|.. +-|+|.|.+. .|.|.+|.++ ...+..-.+.||-|.+..- +..|.
T Consensus 3 v~GeVs~~~~~~--~sGH--~yFtlkD~~~---~i~cv~f~~~g~~~~~~~~l~~Gd~V~v~G~-v~~y~ 64 (91)
T cd04482 3 VTGKVVEEPRTI--EGGH--VFFKISDGTG---EIDCAAYEPTKEFRDVVRLLIPGDEVTVYGS-VRPGT 64 (91)
T ss_pred EEEEEeCCeecC--CCCC--EEEEEECCCc---EEEEEEECcccccccccCCCCCCCEEEEEEE-EecCC
Confidence 456666655321 3344 5568889763 3999999876 4456554489997777543 45444
No 55
>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=76.52 E-value=12 Score=32.68 Aligned_cols=64 Identities=19% Similarity=0.305 Sum_probs=39.6
Q ss_pred cCCEEEEEEEEEEcCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCC-CCCCCCCCCCCEEEEeeEEEE
Q 015760 20 VKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSI-DQLPRVLSPRDLILLKNVMIK 90 (401)
Q Consensus 20 ~~~~vnviGVVvd~~~P~~trGtD~~~tl~I~D~s~~~~gl~v~iF~~~~-e~LP~v~~~GDII~l~rvki~ 90 (401)
+=.-|+++|+|+.. ++++++.--+-|.|.+..- +.|+++..-. -.+-.+..+|-+|-+.|+.-+
T Consensus 17 p~~EvD~VG~VvsV-----~~~~~f~~~vYLsD~~~Nl--l~Ikfw~~l~~~~~eDilk~~~liA~SNLqwR 81 (143)
T PF09104_consen 17 PYGEVDTVGFVVSV-----SKKQGFQPLVYLSDECHNL--LAIKFWTGLNQYGYEDILKPGSLIAASNLQWR 81 (143)
T ss_dssp CCCEEEEEEEEEEE-----E--TTS--EEEEE-TTS-E--EEEEESS-------SS---TT-EEEEEEEEE-
T ss_pred CccccceEEEEEEE-----EecCCCceeEEeecCCccE--EEEEeccCccccchhhhcCcceEEEEeeeEee
Confidence 34459999999999 4567888888999999865 8888887532 233445578999999999887
No 56
>PRK05673 dnaE DNA polymerase III subunit alpha; Validated
Probab=76.23 E-value=7.2 Score=45.20 Aligned_cols=88 Identities=14% Similarity=0.224 Sum_probs=63.8
Q ss_pred ceeeHHhhhh-ccCCEEEEEEEEEEcCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeE
Q 015760 9 GIVRIKELAM-HVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNV 87 (401)
Q Consensus 9 ~y~~i~~~~~-~~~~~vnviGVVvd~~~P~~trGtD~~~tl~I~D~s~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~rv 87 (401)
+.+++.++.. ..+..|.+.|+|...+.+ +|+.++-++.++|-|.+-. +.+.+|.+..+..=.....|.+|.+. .
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 3456666632 246789999999999885 5655666899999999764 99999986544443333789999884 4
Q ss_pred EEEEecCeeEEEee
Q 015760 88 MIKKHQAELSAVFY 101 (401)
Q Consensus 88 ki~~~~g~~~~~~~ 101 (401)
+++...++.+.+.+
T Consensus 1039 kVe~~~~~~qlii~ 1052 (1135)
T PRK05673 1039 QVSFDDGGLRLTAR 1052 (1135)
T ss_pred EEEecCCeEEEEEe
Confidence 67776677777765
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=75.18 E-value=22 Score=36.78 Aligned_cols=80 Identities=16% Similarity=0.237 Sum_probs=54.0
Q ss_pred HHhhhhccCCEEEEEEEEEEcCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEe
Q 015760 13 IKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKH 92 (401)
Q Consensus 13 i~~~~~~~~~~vnviGVVvd~~~P~~trGtD~~~tl~I~D~s~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~rvki~~~ 92 (401)
|+.+++..=..|-|-|=|..++.+ +.| .+-|+|+|..- -|+|.+|+.....|+.-.+.|+=|.+ ..++..|
T Consensus 9 ik~~le~~~~~v~V~GEisn~~~~--~sG---H~YFtLkD~~a---~i~~vmf~~~~~~l~f~~~~G~~V~v-~g~v~~y 79 (432)
T TIGR00237 9 IKALLEATFLQVWIQGEISNFTQP--VSG---HWYFTLKDENA---QVRCVMFRGNNNRLKFRPQNGQQVLV-RGGISVY 79 (432)
T ss_pred HHHHHHhhCCcEEEEEEecCCeeC--CCc---eEEEEEEcCCc---EEEEEEEcChhhCCCCCCCCCCEEEE-EEEEEEE
Confidence 455554322368889999988854 334 67788999753 39999999877788876688996666 3444444
Q ss_pred --cCeeEEEee
Q 015760 93 --QAELSAVFY 101 (401)
Q Consensus 93 --~g~~~~~~~ 101 (401)
.|+.++...
T Consensus 80 ~~~G~~ql~v~ 90 (432)
T TIGR00237 80 EPRGDYQIICF 90 (432)
T ss_pred CCCCcEEEEEE
Confidence 454665553
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=74.21 E-value=3.7 Score=34.83 Aligned_cols=35 Identities=14% Similarity=0.339 Sum_probs=28.4
Q ss_pred eEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEecCe
Q 015760 60 LLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAE 95 (401)
Q Consensus 60 l~v~iF~~~~e~LP~v~~~GDII~l~rvki~~~~g~ 95 (401)
|.|.+|-++.+..-.+ ++||.|+|+||.++.....
T Consensus 62 i~It~yD~H~~~ar~l-K~GdfV~L~NVhiK~~~~~ 96 (123)
T cd04498 62 IDILVYDNHVELAKSL-KPGDFVRIYNVHAKSYSSK 96 (123)
T ss_pred EEEEEEcchHHHHhhC-CCCCEEEEEEEEEEeccCC
Confidence 7778888777666666 7899999999999877663
No 59
>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=73.70 E-value=33 Score=29.90 Aligned_cols=64 Identities=16% Similarity=0.145 Sum_probs=33.9
Q ss_pred ceeeeEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCccccCCCCcHHhhhcCCCCccEEEEEecCcc
Q 015760 168 RYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRVSTDRSY 247 (401)
Q Consensus 168 ~f~Dl~~qVv~~~~~~~~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~~~~~e~~~l~~~~~~~~p~~G~~l~V~~~~~~ 247 (401)
+-||+++-|+.|. ...+-...+|+.|.--| .+-|.+|..-
T Consensus 19 ~EvD~VG~VvsV~-~~~~f~~~vYLsD~~~N---------------------------------------ll~Ikfw~~l 58 (143)
T PF09104_consen 19 GEVDTVGFVVSVS-KKQGFQPLVYLSDECHN---------------------------------------LLAIKFWTGL 58 (143)
T ss_dssp CEEEEEEEEEEEE---TTS--EEEEE-TTS----------------------------------------EEEEEESS--
T ss_pred cccceEEEEEEEE-ecCCCceeEEeecCCcc---------------------------------------EEEEEeccCc
Confidence 5699999999997 42223445787773311 3457777766
Q ss_pred hhhhcc-cCCCCCEEEEeeeEEEEe
Q 015760 248 ENFGRY-FTATGKWVRIRNMSCQVS 271 (401)
Q Consensus 248 ~~~~~~-~~k~g~wv~l~Nv~~k~~ 271 (401)
..++.+ .+|+|..|-..||+-+..
T Consensus 59 ~~~~~eDilk~~~liA~SNLqwR~~ 83 (143)
T PF09104_consen 59 NQYGYEDILKPGSLIAASNLQWRPE 83 (143)
T ss_dssp -----SS---TT-EEEEEEEEE-S-
T ss_pred cccchhhhcCcceEEEEeeeEeecc
Confidence 655544 469999999999998854
No 60
>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed
Probab=73.25 E-value=26 Score=36.16 Aligned_cols=72 Identities=14% Similarity=0.153 Sum_probs=50.0
Q ss_pred CCEEEEEEEEEEcCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEe--cCeeEE
Q 015760 21 KHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKH--QAELSA 98 (401)
Q Consensus 21 ~~~vnviGVVvd~~~P~~trGtD~~~tl~I~D~s~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~rvki~~~--~g~~~~ 98 (401)
-..|-|-|=|..++.+ +.| .|-|+|+|... .|+|.+|+.....++.-.+.|+-|.+ ..++..| .|++++
T Consensus 23 ~~~v~v~gEis~~~~~--~sG---H~Yf~Lkd~~a---~i~~~~~~~~~~~~~~~~~~G~~v~v-~g~~~~y~~~g~~ql 93 (438)
T PRK00286 23 LGQVWVRGEISNFTRH--SSG---HWYFTLKDEIA---QIRCVMFKGSARRLKFKPEEGMKVLV-RGKVSLYEPRGDYQL 93 (438)
T ss_pred CCcEEEEEEeCCCeeC--CCC---eEEEEEEcCCc---EEEEEEEcChhhcCCCCCCCCCEEEE-EEEEEEECCCCCEEE
Confidence 3457888888888764 233 56789999943 49999999888888875688996666 3344444 444555
Q ss_pred Eee
Q 015760 99 VFY 101 (401)
Q Consensus 99 ~~~ 101 (401)
...
T Consensus 94 ~v~ 96 (438)
T PRK00286 94 IVE 96 (438)
T ss_pred EEE
Confidence 443
No 61
>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=72.90 E-value=31 Score=24.53 Aligned_cols=25 Identities=24% Similarity=0.274 Sum_probs=18.2
Q ss_pred eeEEEEEEEEeeCC--CCeEEEEEEcCC
Q 015760 171 DLVCKVFHVSYDDS--KGLWMLFVWDGT 196 (401)
Q Consensus 171 Dl~~qVv~~~~~~~--~~~~~L~VwDgT 196 (401)
++.|+|+++. ... .....+.+.|+|
T Consensus 1 ~v~g~v~~~~-~~~~~~~~~~~~l~D~~ 27 (75)
T cd03524 1 TIVGIVVAVE-EIRTEGKVLIFTLTDGT 27 (75)
T ss_pred CeEEEEEeec-ccccCCeEEEEEEEcCC
Confidence 4678888887 423 357888888877
No 62
>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=71.66 E-value=13 Score=30.27 Aligned_cols=64 Identities=19% Similarity=0.249 Sum_probs=45.2
Q ss_pred EEEEEEEcCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCC-CCCCCCCCCCCCEEEEeeEEEEEecCe
Q 015760 26 LLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSS-IDQLPRVLSPRDLILLKNVMIKKHQAE 95 (401)
Q Consensus 26 viGVVvd~~~P~~trGtD~~~tl~I~D~s~~~~gl~v~iF~~~-~e~LP~v~~~GDII~l~rvki~~~~g~ 95 (401)
++|||+....+. +..+-.+.|.|+++.. +.|+++..- ...+-.+...+-.|-+.|++.+.....
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 689999998763 5667788999999976 888888831 122333435567777888877765544
No 63
>PRK06920 dnaE DNA polymerase III DnaE; Reviewed
Probab=68.99 E-value=14 Score=42.81 Aligned_cols=89 Identities=10% Similarity=0.169 Sum_probs=62.6
Q ss_pred cceeeHHhhhhccCCEEEEEEEEEEcCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeE
Q 015760 8 GGIVRIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNV 87 (401)
Q Consensus 8 y~y~~i~~~~~~~~~~vnviGVVvd~~~P~~trGtD~~~tl~I~D~s~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~rv 87 (401)
++.+++.++....+..|.+.|+|+..+.+ +|+..+-+.-++|-|.+-. +.+.+|.+..+..-.....|.++++. -
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 34556777643346689999999999874 5555667899999998663 99999987655554444678888884 4
Q ss_pred EEEEecCeeEEEee
Q 015760 88 MIKKHQAELSAVFY 101 (401)
Q Consensus 88 ki~~~~g~~~~~~~ 101 (401)
+++.-+++.+.+.+
T Consensus 1005 ~v~~~~~~~~~~~~ 1018 (1107)
T PRK06920 1005 TIELRNHKLQWIVN 1018 (1107)
T ss_pred EEEecCCcEEEEEe
Confidence 56654555666654
No 64
>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=68.39 E-value=44 Score=24.44 Aligned_cols=60 Identities=17% Similarity=0.090 Sum_probs=38.6
Q ss_pred eeEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCccccCCCCcHHhhhcCCCCccEEEEEecCcchhh
Q 015760 171 DLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRVSTDRSYENF 250 (401)
Q Consensus 171 Dl~~qVv~~~~~~~~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~~~~~e~~~l~~~~~~~~p~~G~~l~V~~~~~~~~~ 250 (401)
.+.+.|.++. ...+....+.+.|+|+. +++.+|......
T Consensus 2 ~v~G~V~~~~-~~~~~~~~~~l~D~tg~----------------------------------------i~~~~~~~~~~~ 40 (75)
T PF01336_consen 2 TVEGRVTSIR-RSGGKIVFFTLEDGTGS----------------------------------------IQVVFFNEEYER 40 (75)
T ss_dssp EEEEEEEEEE-EEETTEEEEEEEETTEE----------------------------------------EEEEEETHHHHH
T ss_pred EEEEEEEEEE-cCCCCEEEEEEEECCcc----------------------------------------EEEEEccHHhhH
Confidence 5678888885 43677888889998832 245555522223
Q ss_pred hcccCCCCCEEEEeeeEEEEeC
Q 015760 251 GRYFTATGKWVRIRNMSCQVSS 272 (401)
Q Consensus 251 ~~~~~k~g~wv~l~Nv~~k~~~ 272 (401)
....+++|++|++. =.++...
T Consensus 41 ~~~~l~~g~~v~v~-G~v~~~~ 61 (75)
T PF01336_consen 41 FREKLKEGDIVRVR-GKVKRYN 61 (75)
T ss_dssp HHHTS-TTSEEEEE-EEEEEET
T ss_pred HhhcCCCCeEEEEE-EEEEEEC
Confidence 46779999999877 3344443
No 65
>KOG1030 consensus Predicted Ca2+-dependent phospholipid-binding protein [General function prediction only]
Probab=67.74 E-value=12 Score=33.44 Aligned_cols=26 Identities=15% Similarity=0.308 Sum_probs=25.0
Q ss_pred ceEEEEEEEEeCCCceEEEEEecccc
Q 015760 370 SSEYTMKLTLEDPTARIHALLCGKEW 395 (401)
Q Consensus 370 ~~~~~~~L~leD~t~~i~~~v~~~da 395 (401)
+|...|-|+|.|+..-+.+-||++|-
T Consensus 52 eWNe~ltf~v~d~~~~lkv~VyD~D~ 77 (168)
T KOG1030|consen 52 EWNEELTFTVKDPNTPLKVTVYDKDT 77 (168)
T ss_pred cccceEEEEecCCCceEEEEEEeCCC
Confidence 89999999999999999999999984
No 66
>KOG3056 consensus Protein required for S-phase initiation or completion [Cell cycle control, cell division, chromosome partitioning]
Probab=67.73 E-value=8.8 Score=40.40 Aligned_cols=70 Identities=20% Similarity=0.296 Sum_probs=57.1
Q ss_pred EEEEEEEEEEcCCceecC-CCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEecCe
Q 015760 23 KVNLLGVVLEFSIPRKSQ-GTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAE 95 (401)
Q Consensus 23 ~vnviGVVvd~~~P~~tr-GtD~~~tl~I~D~s~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~rvki~~~~g~ 95 (401)
.--++|||++-..|+.|. |.+|+ .++|.|-... .-|.|-+|.+..+.+=.+ +.|+||-|-|..|-..++.
T Consensus 187 ~Wvt~GvI~~K~~~K~t~~G~~y~-iwkL~dLk~~-q~vslfLFG~a~k~~wk~-k~GtVialLNp~v~k~~~g 257 (578)
T KOG3056|consen 187 NWVTMGVIVEKSDPKFTSNGNPYS-IWKLTDLKDH-QTVSLFLFGKAHKRYWKI-KLGTVIALLNPEVLKDRPG 257 (578)
T ss_pred CeEEEEEEeecCCcccccCCCceE-EEEeeecCcc-ceeEEEEecHHHHHHhhh-ccCcEEEEeCccccCCCCC
Confidence 345899999999999885 66665 5788887664 459999999888888888 7899999999998877654
No 67
>PRK07374 dnaE DNA polymerase III subunit alpha; Validated
Probab=64.64 E-value=19 Score=41.92 Aligned_cols=89 Identities=15% Similarity=0.212 Sum_probs=63.9
Q ss_pred cceeeHHhhhh-ccCCEEEEEEEEEEcCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEee
Q 015760 8 GGIVRIKELAM-HVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKN 86 (401)
Q Consensus 8 y~y~~i~~~~~-~~~~~vnviGVVvd~~~P~~trGtD~~~tl~I~D~s~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~r 86 (401)
+..++++++.. ..+..|.+.|+|+..+.+ +|+..+-+.-++|-|.+-. +.+.+|.+..+..-.....|.++++.
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 5665678999999999764 99999987666555544778888884
Q ss_pred EEEEEecCeeEEEee
Q 015760 87 VMIKKHQAELSAVFY 101 (401)
Q Consensus 87 vki~~~~g~~~~~~~ 101 (401)
-+++.-.++.+.+.+
T Consensus 1061 g~v~~~~~~~~~~~~ 1075 (1170)
T PRK07374 1061 AKVDRRDDRVQLIID 1075 (1170)
T ss_pred EEEEecCCeEEEEEe
Confidence 466654455666665
No 68
>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=64.47 E-value=23 Score=29.55 Aligned_cols=40 Identities=20% Similarity=0.223 Sum_probs=28.8
Q ss_pred CCCCCCCCCCCEEEEeeE-------EEEEecCeeEEEeecC-ceEEEEE
Q 015760 70 DQLPRVLSPRDLILLKNV-------MIKKHQAELSAVFYKD-SSSFALF 110 (401)
Q Consensus 70 e~LP~v~~~GDII~l~rv-------ki~~~~g~~~~~~~~~-~ss~~lf 110 (401)
..+|.+ ++||+|.++=. ++|.|.|-+-+.-+.+ .++|.|=
T Consensus 14 ~~~p~f-~~GD~v~V~~~i~e~~k~r~q~f~GvvIa~~~~g~~ssftlR 61 (113)
T PF01245_consen 14 KDIPEF-RVGDTVRVTYKISEGNKERIQVFEGVVIARRRRGLNSSFTLR 61 (113)
T ss_dssp SSSSSS-SSSSEEEEEEEEESSSSEEEEEEEEEEEEEEBSSTSSEEEEE
T ss_pred cCCCCc-CCCCEEEEEEEEecCCCceeEEEEEEEEEEECCCCCeeEEEE
Confidence 679999 89999999764 3577777666665544 3667763
No 69
>PRK05338 rplS 50S ribosomal protein L19; Provisional
Probab=64.27 E-value=17 Score=30.51 Aligned_cols=43 Identities=14% Similarity=0.210 Sum_probs=29.9
Q ss_pred CCCCCCCCCCCEEEEeeE-------EEEEecCeeEEEeecC-ceEEEEEeCC
Q 015760 70 DQLPRVLSPRDLILLKNV-------MIKKHQAELSAVFYKD-SSSFALFDGN 113 (401)
Q Consensus 70 e~LP~v~~~GDII~l~rv-------ki~~~~g~~~~~~~~~-~ss~~lf~~~ 113 (401)
.++|.+ ++||+|.++-- ++|.|.|-+-+.-+.+ .++|.|=+-.
T Consensus 14 ~~~p~f-~~GD~V~V~~~i~eg~k~R~q~f~GvvI~~~~~G~~~tftvRki~ 64 (116)
T PRK05338 14 KDIPEF-RPGDTVRVHVKVVEGNKERIQAFEGVVIARRGRGLNETFTVRKIS 64 (116)
T ss_pred cCCCCc-CCCCEEEEEEEEccCCceEeccEEEEEEEEeCCCCCceEEEEEcc
Confidence 569999 89999999642 3667777666665554 3678865543
No 70
>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=61.97 E-value=15 Score=28.58 Aligned_cols=45 Identities=22% Similarity=0.310 Sum_probs=32.8
Q ss_pred EEEEEEEEeeCCCccccccCCCceEEEEEEEEeCCCc-eEEEEEecccccccc
Q 015760 348 CCIVRVVSIHPFQAEHYSSPNGSSEYTMKLTLEDPTA-RIHALLCGKEWVRFQ 399 (401)
Q Consensus 348 r~~VRVv~~~P~~~~df~~~~g~~~~~~~L~leD~t~-~i~~~v~~~da~~f~ 399 (401)
++.|||...|=..... . ...+.|.|-|..| +|+|.+..+.+++|.
T Consensus 1 ~I~Vrv~r~W~~~~~~-----~--~~~~~miL~De~G~~I~a~i~~~~~~~f~ 46 (86)
T cd04480 1 KICVRVLRLWDVYNNA-----S--GESLEMVLVDEKGNRIHATIPKRLAAKFR 46 (86)
T ss_pred CEEEEEEEEEcCcCCC-----C--CcEEEEEEEcCCCCEEEEEECHHHHHhhh
Confidence 3678888765332221 1 3478899999988 999999999888775
No 71
>PF15072 DUF4539: Domain of unknown function (DUF4539)
Probab=58.80 E-value=9.1 Score=30.38 Aligned_cols=21 Identities=29% Similarity=0.387 Sum_probs=17.9
Q ss_pred EEEEEEeCCCceEEEEEeccc
Q 015760 374 TMKLTLEDPTARIHALLCGKE 394 (401)
Q Consensus 374 ~~~L~leD~t~~i~~~v~~~d 394 (401)
-..++|.||||+|++.++.+-
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 72
>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=57.08 E-value=14 Score=29.17 Aligned_cols=22 Identities=18% Similarity=0.158 Sum_probs=19.6
Q ss_pred EEEEEEeCCCceEEEEEecccc
Q 015760 374 TMKLTLEDPTARIHALLCGKEW 395 (401)
Q Consensus 374 ~~~L~leD~t~~i~~~v~~~da 395 (401)
.+.++|+|.||+|.|.++..+.
T Consensus 17 ~~~~tL~D~TG~I~~~~W~~~~ 38 (95)
T cd04478 17 NITYTIDDGTGTIEVRQWLDDD 38 (95)
T ss_pred EEEEEEECCCCcEEEEEeCCCC
Confidence 4899999999999999998664
No 73
>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=56.51 E-value=27 Score=29.24 Aligned_cols=43 Identities=14% Similarity=0.098 Sum_probs=29.9
Q ss_pred CCCCCCCCCCCEEEEeeE-------EEEEecCeeEEEeecC-ceEEEEEeCC
Q 015760 70 DQLPRVLSPRDLILLKNV-------MIKKHQAELSAVFYKD-SSSFALFDGN 113 (401)
Q Consensus 70 e~LP~v~~~GDII~l~rv-------ki~~~~g~~~~~~~~~-~ss~~lf~~~ 113 (401)
.++|.+ ++||+|.++-- ++|.|.|-+-+.-+.+ .++|.|=+-.
T Consensus 14 ~~ip~f-~~GD~v~V~~~i~eg~k~R~q~f~GvvI~~~~~G~~~tftvR~i~ 64 (113)
T TIGR01024 14 KDLPDF-RVGDTVRVHVKIVEGKKERIQVFEGVVIARRGGGIGETFTVRKIS 64 (113)
T ss_pred cCCCcc-CCCCEEEEEEEEccCCceEcccEEEEEEEEeCCCCceEEEEEEec
Confidence 579999 89999999642 3566777666666554 3678765543
No 74
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=54.48 E-value=58 Score=35.72 Aligned_cols=79 Identities=19% Similarity=0.192 Sum_probs=52.2
Q ss_pred eeHHhhhhccCCEEEEEEEEEEcCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEE
Q 015760 11 VRIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIK 90 (401)
Q Consensus 11 ~~i~~~~~~~~~~vnviGVVvd~~~P~~trGtD~~~tl~I~D~s~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~rvki~ 90 (401)
.+|+++ ..|+.+.+.|.|++...... +. -..++++.|.+- .+.+.+|.-+...+.....+|+-+.+.. |++
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--KR-RRLTVTVSDGTG---NLTLRFFNFNQPYLKKQLKVGKRVAVYG-KVK 121 (681)
T ss_pred CCHHHC--CCCCEEEEEEEEEEEEEccC--Cc-eEEEEEEEECCe---EEEEEEEccCcHHHHhhCCCCCEEEEEE-EEE
Confidence 356666 46889999999998743222 22 378889999763 3899999522345666568999888765 344
Q ss_pred EecCeeEE
Q 015760 91 KHQAELSA 98 (401)
Q Consensus 91 ~~~g~~~~ 98 (401)
.++|..+.
T Consensus 122 ~~~~~~qm 129 (681)
T PRK10917 122 RGKYGLEM 129 (681)
T ss_pred ecCCeEEE
Confidence 45555443
No 75
>PF15072 DUF4539: Domain of unknown function (DUF4539)
Probab=54.39 E-value=40 Score=26.70 Aligned_cols=63 Identities=22% Similarity=0.287 Sum_probs=43.9
Q ss_pred EEEEEEEE-EEcCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEecC
Q 015760 23 KVNLLGVV-LEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQA 94 (401)
Q Consensus 23 ~vnviGVV-vd~~~P~~trGtD~~~tl~I~D~s~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~rvki~~~~g 94 (401)
+|...+|+ ..+.. .+.|. .+.+.|||=. +.+.+=++-.+..|....+|=+++|+++.+=.=..
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 34444444 44544 33454 6789998763 88888887666778777999999999998765443
No 76
>CHL00084 rpl19 ribosomal protein L19
Probab=53.37 E-value=34 Score=28.76 Aligned_cols=41 Identities=10% Similarity=0.180 Sum_probs=27.7
Q ss_pred CCCCCCCCCCCEEEEee-E------EEEEecCeeEEEeecC-ceEEEEEe
Q 015760 70 DQLPRVLSPRDLILLKN-V------MIKKHQAELSAVFYKD-SSSFALFD 111 (401)
Q Consensus 70 e~LP~v~~~GDII~l~r-v------ki~~~~g~~~~~~~~~-~ss~~lf~ 111 (401)
.++|.+ ++||+|+++= + ++|.|.|-+-+.-+.+ .++|.|=+
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 8999999965 2 3667777655555544 35677533
No 77
>TIGR00643 recG ATP-dependent DNA helicase RecG.
Probab=51.01 E-value=84 Score=34.12 Aligned_cols=77 Identities=18% Similarity=0.215 Sum_probs=51.6
Q ss_pred eHHhhhhccCCEEEEEEEEEEcCCceecCCCceEEEEEEEe-CCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEE
Q 015760 12 RIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVD-DSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIK 90 (401)
Q Consensus 12 ~i~~~~~~~~~~vnviGVVvd~~~P~~trGtD~~~tl~I~D-~s~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~rvki~ 90 (401)
+|+++ ..|..+.+.|.|++..... ++.--..++++.| .+- .+.+.+|.. ..+......|+-+.+.. |+.
T Consensus 25 ~i~~~--~~g~~~~~~~~v~~~~~~~--~~~~~~~~~~~~d~~~~---~~~~~~F~~--~~~~~~~~~g~~~~~~G-k~~ 94 (630)
T TIGR00643 25 TIGEL--LPGERATIVGEVLSHCIFG--FKRRKVLKLRLKDGGYK---KLELRFFNR--AFLKKKFKVGSKVVVYG-KVK 94 (630)
T ss_pred CHHHc--CCCCEEEEEEEEEEeEecc--CCCCceEEEEEEECCCC---EEEEEEECC--HHHHhhCCCCCEEEEEE-EEE
Confidence 56666 4688999999998742211 2222278889999 433 399999972 35556558899888854 555
Q ss_pred EecCeeEE
Q 015760 91 KHQAELSA 98 (401)
Q Consensus 91 ~~~g~~~~ 98 (401)
.++|..+.
T Consensus 95 ~~~~~~~~ 102 (630)
T TIGR00643 95 SSKFKAYL 102 (630)
T ss_pred eeCCEEEE
Confidence 66676554
No 78
>PRK06826 dnaE DNA polymerase III DnaE; Reviewed
Probab=50.33 E-value=43 Score=39.09 Aligned_cols=77 Identities=14% Similarity=0.230 Sum_probs=55.5
Q ss_pred cCCEEEEEEEEEEcCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEe-cCeeEE
Q 015760 20 VKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKH-QAELSA 98 (401)
Q Consensus 20 ~~~~vnviGVVvd~~~P~~trGtD~~~tl~I~D~s~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~rvki~~~-~g~~~~ 98 (401)
.+..|.+.|+|+..+.+ +|+..+-+.-++|-|.+-. +.+.+|.+..+..-.....|.+|++ ..+++.. +++.+.
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 5665677899999998764 9999998755554443367888888 4466643 344666
Q ss_pred Eee
Q 015760 99 VFY 101 (401)
Q Consensus 99 ~~~ 101 (401)
+..
T Consensus 1065 ~~~ 1067 (1151)
T PRK06826 1065 ICE 1067 (1151)
T ss_pred EEe
Confidence 654
No 79
>KOG4792 consensus Crk family adapters [Signal transduction mechanisms]
Probab=49.35 E-value=25 Score=32.97 Aligned_cols=60 Identities=17% Similarity=0.324 Sum_probs=36.5
Q ss_pred hcCCCCccEEEEEecCcchhhhcccCCCCCEEEEeeeEEEEeCcEEEEEeecCcc------eEEccCCCh
Q 015760 230 RNFFPVGTVLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSK------IRLFSDNDN 293 (401)
Q Consensus 230 ~~~p~~G~~l~V~~~~~~~~~~~~~~k~g~wv~l~Nv~~k~~~G~leG~l~~~s~------i~~l~~~d~ 293 (401)
.+.|...+++|=..-+...+- +-.++.||.|+ |.-+..+|.|||-+.+..+ ++.++..++
T Consensus 224 ~~lPa~Arv~q~RVPnAYDkT-aL~levGdiVk---VTk~ninGqwegElnGk~G~fPfThvrf~d~~~~ 289 (293)
T KOG4792|consen 224 QNLPAYARVIQKRVPNAYDKT-ALALEVGDIVK---VTKKNINGQWEGELNGKIGHFPFTHVRFTDVQNP 289 (293)
T ss_pred cCCChheeeehhcCCCccChh-hhhhhcCcEEE---EEeeccCceeeeeecCccccccceeEEeeccCCc
Confidence 445545555543333333332 33488999997 3444468999999887643 566666554
No 80
>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=48.64 E-value=1.2e+02 Score=23.26 Aligned_cols=62 Identities=19% Similarity=0.148 Sum_probs=38.9
Q ss_pred EEEEEEcCCceecCCCceEEEEEEEeCCCC-----CCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEecCeeEEEee
Q 015760 27 LGVVLEFSIPRKSQGTDYVCVLKIVDDSQQ-----SPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAELSAVFY 101 (401)
Q Consensus 27 iGVVvd~~~P~~trGtD~~~tl~I~D~s~~-----~~gl~v~iF~~~~e~LP~v~~~GDII~l~rvki~~~~g~~~~~~~ 101 (401)
=|||+...... | .-.|-|-|+.-. ++| +-+|.+. -+.+ ++||.|++. -++..|+|..++...
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 47777765432 1 123446666322 233 4445543 4556 789999995 899999998887654
No 81
>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=48.15 E-value=18 Score=27.99 Aligned_cols=21 Identities=38% Similarity=0.405 Sum_probs=19.5
Q ss_pred EEEEeCCCceEEEEEeccccc
Q 015760 376 KLTLEDPTARIHALLCGKEWV 396 (401)
Q Consensus 376 ~L~leD~t~~i~~~v~~~da~ 396 (401)
.++|||.+|++.+.++++..+
T Consensus 20 ~~~leD~~G~~Ev~~F~~~~~ 40 (79)
T cd04490 20 IVELEDTTGRITVLLTKDKEE 40 (79)
T ss_pred EEEEECCCCEEEEEEeCchhh
Confidence 899999999999999998766
No 82
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=48.08 E-value=2.3e+02 Score=30.98 Aligned_cols=80 Identities=18% Similarity=0.189 Sum_probs=58.1
Q ss_pred HHhhhhccCCEEEEEEEEEEcCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEe
Q 015760 13 IKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKH 92 (401)
Q Consensus 13 i~~~~~~~~~~vnviGVVvd~~~P~~trGtD~~~tl~I~D~s~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~rvki~~~ 92 (401)
|.++ ..|..|-+-|.|.....+. .+..-..++++.|.+. . +++.+|..+. .+..-..+|--+.+. =|++.|
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-V--LTLVFFNFPA-YLKKKLKVGERVIVY-GKVKRF 124 (677)
T ss_pred hhhc--CCCceEEEEEEEEeeeccC--CCCCceEEEEEecCcE-E--EEEEEECccH-HHHhhCCCCCEEEEE-EEEeec
Confidence 4444 3678999999999876543 6677888999999333 2 9999998653 666666789988874 467778
Q ss_pred cCeeEEEee
Q 015760 93 QAELSAVFY 101 (401)
Q Consensus 93 ~g~~~~~~~ 101 (401)
++..+....
T Consensus 125 ~~~~~~~hp 133 (677)
T COG1200 125 KGGLQITHP 133 (677)
T ss_pred cCceEEEcc
Confidence 777665543
No 83
>COG1570 XseA Exonuclease VII, large subunit [DNA replication, recombination, and repair]
Probab=47.25 E-value=1.7e+02 Score=30.31 Aligned_cols=71 Identities=17% Similarity=0.192 Sum_probs=51.5
Q ss_pred CEEEEEEEEEEcCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEecC--eeEEE
Q 015760 22 HKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQA--ELSAV 99 (401)
Q Consensus 22 ~~vnviGVVvd~~~P~~trGtD~~~tl~I~D~s~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~rvki~~~~g--~~~~~ 99 (401)
+.|=|-|=|..++.| ..| ..-|+|.|+.-. |.|.+|+.+...|....+.|+-|.+ +-+++.|-+ +.|.+
T Consensus 24 ~~V~v~GEISn~t~~--~sg---H~YFtLKD~~A~---i~c~mf~~~~~~l~f~p~eG~~V~v-~G~is~Y~~rG~YQi~ 94 (440)
T COG1570 24 GQVWVRGEISNFTRP--ASG---HLYFTLKDERAQ---IRCVMFKGNNRRLKFRPEEGMQVLV-RGKISLYEPRGDYQIV 94 (440)
T ss_pred CeEEEEEEecCCccC--CCc---cEEEEEccCCce---EEEEEEcCcccccCCCccCCCEEEE-EEEEEEEcCCCceEEE
Confidence 457788888877765 233 667899999553 9999999988889876689997777 346666644 34554
Q ss_pred ee
Q 015760 100 FY 101 (401)
Q Consensus 100 ~~ 101 (401)
+.
T Consensus 95 ~~ 96 (440)
T COG1570 95 AE 96 (440)
T ss_pred Ee
Confidence 43
No 84
>PRK05672 dnaE2 error-prone DNA polymerase; Validated
Probab=45.51 E-value=50 Score=38.15 Aligned_cols=86 Identities=21% Similarity=0.264 Sum_probs=58.1
Q ss_pred ceeeHHhhhh-ccCCEEEEEEEEEEcCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeE
Q 015760 9 GIVRIKELAM-HVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNV 87 (401)
Q Consensus 9 ~y~~i~~~~~-~~~~~vnviGVVvd~~~P~~trGtD~~~tl~I~D~s~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~rv 87 (401)
+++++.++.. ..+..|-+.|+|+..+.+...+| +.-++|-|.+-. +.+.+|.+..+..-.....|.++++. -
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 24667999999999887633345 888899998663 99999986555444434678888884 4
Q ss_pred EEEEecCeeEEEee
Q 015760 88 MIKKHQAELSAVFY 101 (401)
Q Consensus 88 ki~~~~g~~~~~~~ 101 (401)
+++.-+++.+.+.+
T Consensus 1013 ~v~~~~~~~~~~~~ 1026 (1046)
T PRK05672 1013 RVQNAEGVRHLVAD 1026 (1046)
T ss_pred EEEecCCeEEEEEe
Confidence 56654555555554
No 85
>PF02721 DUF223: Domain of unknown function DUF223; InterPro: IPR003871 The function of this domain has not been characterised, but may be involved in nucleic acid or nucleotide binding.
Probab=45.19 E-value=66 Score=25.49 Aligned_cols=39 Identities=18% Similarity=0.313 Sum_probs=30.3
Q ss_pred ccEEEEEecCcchhhhcccCCCCCEEEEeeeEEEEeCcE
Q 015760 236 GTVLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGM 274 (401)
Q Consensus 236 G~~l~V~~~~~~~~~~~~~~k~g~wv~l~Nv~~k~~~G~ 274 (401)
|..++.+........-...+++|.|..|.|..+..+.|.
T Consensus 9 G~~I~A~I~~~~~~~f~~~l~Eg~~y~i~~F~V~~~~~~ 47 (95)
T PF02721_consen 9 GDKIQATIPKELVDKFKDSLKEGSWYTISNFTVSPNSGS 47 (95)
T ss_pred CCEEEEEECHHHHHHHHhhcccCCEEEeEeEEEEeCCCc
Confidence 777787776655443467899999999999998887664
No 86
>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=43.39 E-value=32 Score=25.83 Aligned_cols=22 Identities=36% Similarity=0.375 Sum_probs=19.3
Q ss_pred EEEEEEEeCCCceEEEEEeccc
Q 015760 373 YTMKLTLEDPTARIHALLCGKE 394 (401)
Q Consensus 373 ~~~~L~leD~t~~i~~~v~~~d 394 (401)
-.+.++|+|.|+++.+.++++.
T Consensus 19 ~~~~~~l~D~tg~i~~~~f~~~ 40 (83)
T cd04492 19 PYLALTLQDKTGEIEAKLWDAS 40 (83)
T ss_pred cEEEEEEEcCCCeEEEEEcCCC
Confidence 3689999999999999999854
No 87
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=41.86 E-value=1.1e+02 Score=32.90 Aligned_cols=80 Identities=15% Similarity=0.334 Sum_probs=58.9
Q ss_pred eeeHHhhhhccCCEEEEEEEEEEcCCceecCCCceEEEEEEEeCCCCCCCeEEEEec-CCCCCCCCCCCCCCEEEEeeEE
Q 015760 10 IVRIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFT-SSIDQLPRVLSPRDLILLKNVM 88 (401)
Q Consensus 10 y~~i~~~~~~~~~~vnviGVVvd~~~P~~trGtD~~~tl~I~D~s~~~~gl~v~iF~-~~~e~LP~v~~~GDII~l~rvk 88 (401)
-+.+.++-+..|..|.+=|-|+-.+ +|.| -..|||.|++-. +.+.-|- .-.-.-|.| ++||||.+-. .
T Consensus 202 r~~i~~id~~ig~tV~I~GeV~qik---qT~G---PTVFtltDetg~---i~aAAFe~aGvRAyP~I-evGdiV~ViG-~ 270 (715)
T COG1107 202 RTLIDDLDEMIGKTVRIEGEVTQIK---QTSG---PTVFTLTDETGA---IWAAAFEEAGVRAYPEI-EVGDIVEVIG-E 270 (715)
T ss_pred cccHHHHHhhcCceEEEEEEEEEEE---EcCC---CEEEEEecCCCc---eehhhhccCCcccCCCC-CCCceEEEEE-E
Confidence 3456777667899999999998864 3333 246899999764 7777785 566789999 8999999865 4
Q ss_pred EEEecCeeEEEe
Q 015760 89 IKKHQAELSAVF 100 (401)
Q Consensus 89 i~~~~g~~~~~~ 100 (401)
+....|++|.-.
T Consensus 271 V~~r~g~lQiE~ 282 (715)
T COG1107 271 VTRRDGRLQIEI 282 (715)
T ss_pred EeecCCcEEEee
Confidence 556677777543
No 88
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=41.18 E-value=1e+02 Score=36.91 Aligned_cols=87 Identities=16% Similarity=0.287 Sum_probs=61.0
Q ss_pred CcceeeHHhhhhccCCEEEEEEEEEEcCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCC---CCCCCCCCCCCEEE
Q 015760 7 QGGIVRIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSI---DQLPRVLSPRDLIL 83 (401)
Q Consensus 7 ~y~y~~i~~~~~~~~~~vnviGVVvd~~~P~~trGtD~~~tl~I~D~s~~~~gl~v~iF~~~~---e~LP~v~~~GDII~ 83 (401)
++..++|+++.. ....|-+-|-|-+... +.++..-...+|.|+|-+ +++.|..|.++. +.+-.+ +.||-|+
T Consensus 223 ~~~~~~~~~i~~-~~~~v~i~G~if~~e~-~~~k~~~~~~~~~~td~~---~s~~~k~f~~~~~~~~~~~~~-~~g~~v~ 296 (1437)
T PRK00448 223 KEEITPMKEINE-EERRVVVEGYVFKVEI-KELKSGRHILTFKITDYT---SSIIVKKFSRDKEDLKKFDEI-KKGDWVK 296 (1437)
T ss_pred ccCcccHHHhhc-cCCeEEEEEEEEEEEE-EeccCCCEEEEEEEEcCC---CCEEEEEEecCcchhHHHhcC-CCCCEEE
Confidence 356788898864 3557889999977765 455656788999999975 459999998543 345556 7899988
Q ss_pred EeeE-EEEEecCeeEEE
Q 015760 84 LKNV-MIKKHQAELSAV 99 (401)
Q Consensus 84 l~rv-ki~~~~g~~~~~ 99 (401)
++.- ....|.++....
T Consensus 297 ~~g~~~~d~~~~~~~~~ 313 (1437)
T PRK00448 297 VRGSVQNDTFTRDLVMN 313 (1437)
T ss_pred EEEEEeccCCCCceEEE
Confidence 8643 334566554433
No 89
>PRK07279 dnaE DNA polymerase III DnaE; Reviewed
Probab=41.07 E-value=66 Score=37.09 Aligned_cols=86 Identities=17% Similarity=0.294 Sum_probs=59.3
Q ss_pred ceeeHHhhhhccCCEEEEEEEEEEcCCceecC-CCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeE
Q 015760 9 GIVRIKELAMHVKHKVNLLGVVLEFSIPRKSQ-GTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNV 87 (401)
Q Consensus 9 ~y~~i~~~~~~~~~~vnviGVVvd~~~P~~tr-GtD~~~tl~I~D~s~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~rv 87 (401)
..++++++. .+..+.+.|+|...+. .+|| ..+-+..++|-|.+-. +.+.+|.+..+..-.....|.++++..
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 3556889999998876 4555 4567899999998764 999999865554444346788888854
Q ss_pred EEEEecCeeEEEee
Q 015760 88 MIKKHQAELSAVFY 101 (401)
Q Consensus 88 ki~~~~g~~~~~~~ 101 (401)
+++.-.++.+.+.+
T Consensus 947 ~v~~~~~~~~l~~~ 960 (1034)
T PRK07279 947 KIQERDGRLQMVLQ 960 (1034)
T ss_pred EEEecCCeeEEEEe
Confidence 55654555666554
No 90
>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=38.14 E-value=40 Score=25.25 Aligned_cols=23 Identities=22% Similarity=0.286 Sum_probs=20.1
Q ss_pred EEEEEEeCCCceEEEEEeccccc
Q 015760 374 TMKLTLEDPTARIHALLCGKEWV 396 (401)
Q Consensus 374 ~~~L~leD~t~~i~~~v~~~da~ 396 (401)
+.-++|+|.+++|++.++.+-.+
T Consensus 18 ~~~~~L~D~~~~i~~~~f~~~~~ 40 (78)
T cd04489 18 HLYFTLKDEDASIRCVMWRSNAR 40 (78)
T ss_pred EEEEEEEeCCeEEEEEEEcchhh
Confidence 77899999999999999987544
No 91
>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=35.46 E-value=1.3e+02 Score=30.79 Aligned_cols=93 Identities=18% Similarity=0.264 Sum_probs=62.9
Q ss_pred eHHhhhhccCCEEEEEEEEEEcCCce--ecC-CC-ceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeE
Q 015760 12 RIKELAMHVKHKVNLLGVVLEFSIPR--KSQ-GT-DYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNV 87 (401)
Q Consensus 12 ~i~~~~~~~~~~vnviGVVvd~~~P~--~tr-Gt-D~~~tl~I~D~s~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~rv 87 (401)
.+.++. ...+.+|+.|-|.++..++ .++ |. .=..+..+.|.+-. +... +..+...+++. ..||++++.+.
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 344443 2356799999999998776 443 44 33444557777653 3332 56555666677 78999999999
Q ss_pred EEEEecCeeEEEeecCceEEEEEe
Q 015760 88 MIKKHQAELSAVFYKDSSSFALFD 111 (401)
Q Consensus 88 ki~~~~g~~~~~~~~~~ss~~lf~ 111 (401)
.+..|+|..++..+.. ++.+..+
T Consensus 125 ~~~~~~~~~~~~~~~~-~~v~~~~ 147 (407)
T COG1599 125 YTSLYRGGKRLSVGRV-GSVADVD 147 (407)
T ss_pred ccccccCceeeecccc-cccccCc
Confidence 9999999998888754 3444333
No 92
>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=34.61 E-value=66 Score=24.89 Aligned_cols=57 Identities=9% Similarity=0.096 Sum_probs=43.7
Q ss_pred CceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEecCeeEEEe
Q 015760 42 TDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAELSAVF 100 (401)
Q Consensus 42 tD~~~tl~I~D~s~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~rvki~~~~g~~~~~~ 100 (401)
....+.+-|.|+.-. .|.+.++....+.+-...+.|.+..+.+.++..-++......
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 666788889998653 499999987666666666899999999999987766544433
No 93
>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=32.40 E-value=2.5e+02 Score=22.20 Aligned_cols=26 Identities=27% Similarity=0.362 Sum_probs=18.8
Q ss_pred eeEEEEEEEEeeCCCCeEEEEEEcCCCC
Q 015760 171 DLVCKVFHVSYDDSKGLWMLFVWDGTDV 198 (401)
Q Consensus 171 Dl~~qVv~~~~~~~~~~~~L~VwDgT~~ 198 (401)
||++.|+++. + ....+.+.+=|||+.
T Consensus 1 ~ivG~V~sv~-~-~~~~~~~tLdDgTG~ 26 (92)
T cd04483 1 DILGTVVSRR-E-RETFYSFGVDDGTGV 26 (92)
T ss_pred CeEEEEEEEE-e-cCCeEEEEEecCCce
Confidence 5788899887 4 345677777788774
No 94
>PRK07772 single-stranded DNA-binding protein; Provisional
Probab=32.09 E-value=81 Score=28.75 Aligned_cols=74 Identities=8% Similarity=0.135 Sum_probs=49.1
Q ss_pred CCEEEEEEEEEEcCCceecCCCceEEEEEEEeC-CC-C----------CCCeEEEEecCCCCCCCCCCCCCCEEEEe-eE
Q 015760 21 KHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDD-SQ-Q----------SPELLVNIFTSSIDQLPRVLSPRDLILLK-NV 87 (401)
Q Consensus 21 ~~~vnviGVVvd~~~P~~trGtD~~~tl~I~D~-s~-~----------~~gl~v~iF~~~~e~LP~v~~~GDII~l~-rv 87 (401)
...|.|+|=+..--.-+.+....-+++|+|.-. .. . ..-++|.+|.+..+.+-.-.+.||-|.+. |+
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 346788887776533344555567788998732 21 1 11489999998666666544789965554 78
Q ss_pred EEEEecC
Q 015760 88 MIKKHQA 94 (401)
Q Consensus 88 ki~~~~g 94 (401)
+.+.|.+
T Consensus 84 ~~r~wed 90 (186)
T PRK07772 84 KQRSYET 90 (186)
T ss_pred EcCceEC
Confidence 9998864
No 95
>PRK13254 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=29.14 E-value=3.5e+02 Score=23.64 Aligned_cols=66 Identities=17% Similarity=0.197 Sum_probs=45.8
Q ss_pred eeeHHhhhhc---cCCEEEEEEEEEEcCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEe
Q 015760 10 IVRIKELAMH---VKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLK 85 (401)
Q Consensus 10 y~~i~~~~~~---~~~~vnviGVVvd~~~P~~trGtD~~~tl~I~D~s~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~ 85 (401)
|.+.+++.+. .+..+.+-|.|++=+.- ++..-..+|.|.|... .+.|.+-. .+|...+.|.-|.+.
T Consensus 37 f~tpse~~~~~~~~g~~vrvgG~V~~gSi~---~~~~~~~~F~ltD~~~---~i~V~Y~G----~lPd~F~eg~~VVv~ 105 (148)
T PRK13254 37 FYTPSEVAEGEAPAGRRFRLGGLVEKGSVQ---RGDGLTVRFVVTDGNA---TVPVVYTG----ILPDLFREGQGVVAE 105 (148)
T ss_pred eeCHHHHhcCCccCCCeEEEeEEEecCcEE---eCCCCEEEEEEEeCCe---EEEEEECC----CCCccccCCCEEEEE
Confidence 6667777653 47789999999964432 2256678999999833 26665543 489888888866653
No 96
>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=27.58 E-value=3e+02 Score=22.51 Aligned_cols=33 Identities=15% Similarity=0.075 Sum_probs=23.7
Q ss_pred EEEecCcchhhhc-ccCCCCCEEEEeeeEEEEeC
Q 015760 240 RVSTDRSYENFGR-YFTATGKWVRIRNMSCQVSS 272 (401)
Q Consensus 240 ~V~~~~~~~~~~~-~~~k~g~wv~l~Nv~~k~~~ 272 (401)
-|.+|..-..++. +.+|++..+-..|++.+..+
T Consensus 31 ~vkfw~~l~~~~~EDvvk~~~lia~SNLQwR~~s 64 (100)
T cd04495 31 CVKFWSSLEQYAYEDVVKRRVLLAASNLQWRTES 64 (100)
T ss_pred EEEEecchHHhhhhhhcccceEEEEecceEeccc
Confidence 4666664444444 44689999999999998864
No 97
>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=25.30 E-value=3.6e+02 Score=22.56 Aligned_cols=61 Identities=15% Similarity=0.141 Sum_probs=42.2
Q ss_pred cCCEEEEEEEEEEcCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCC---CCCCCCCCCCCEEEEeeEEEE
Q 015760 20 VKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSI---DQLPRVLSPRDLILLKNVMIK 90 (401)
Q Consensus 20 ~~~~vnviGVVvd~~~P~~trGtD~~~tl~I~D~s~~~~gl~v~iF~~~~---e~LP~v~~~GDII~l~rvki~ 90 (401)
.|+.|.+.|-|...+. .|+ .+=+.|.|.+. .+.|.+-.+.. +.+..+ ..||+|.+...-..
T Consensus 13 ~g~~V~i~Gwv~~~R~----~gk--~~Fi~LrD~~g---~~Q~v~~~~~~~~~~~~~~l-~~gs~V~V~G~~~~ 76 (135)
T cd04317 13 VGQEVTLCGWVQRRRD----HGG--LIFIDLRDRYG---IVQVVFDPEEAPEFELAEKL-RNESVIQVTGKVRA 76 (135)
T ss_pred CCCEEEEEEeEehhcc----cCC--EEEEEEecCCe---eEEEEEeCCchhHHHHHhCC-CCccEEEEEEEEEC
Confidence 5788999999976554 344 67788888874 27776644322 244556 68999999996443
No 98
>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=24.90 E-value=64 Score=28.69 Aligned_cols=16 Identities=38% Similarity=0.781 Sum_probs=13.6
Q ss_pred EEEEEEeCCCceEEEEE
Q 015760 374 TMKLTLEDPTARIHALL 390 (401)
Q Consensus 374 ~~~L~leD~t~~i~~~v 390 (401)
-|.|.|+|+++| ||||
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 589999999887 8987
No 99
>PF11325 DUF3127: Domain of unknown function (DUF3127); InterPro: IPR021474 This bacterial family of proteins has no known function.
Probab=23.45 E-value=3.7e+02 Score=21.18 Aligned_cols=66 Identities=9% Similarity=0.205 Sum_probs=40.7
Q ss_pred EEEEEcCCceecCCCc-eEE-EEEEE-eCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEe-eEEEEEecCe
Q 015760 28 GVVLEFSIPRKSQGTD-YVC-VLKIV-DDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLK-NVMIKKHQAE 95 (401)
Q Consensus 28 GVVvd~~~P~~trGtD-~~~-tl~I~-D~s~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~-rvki~~~~g~ 95 (401)
|.|+...++.+..|.. |.- .|-|- ++-+ ..-+.+.+|.+..+.|-.+ ++||-|.++ +++-+.|+|+
T Consensus 4 Gkii~~l~~~~g~s~~Gw~Kre~Vlet~~qY-P~~i~f~~~~dk~~~l~~~-~~Gd~V~Vsf~i~~RE~~gr 73 (84)
T PF11325_consen 4 GKIIKVLPEQQGVSKNGWKKREFVLETEEQY-PQKICFEFWGDKIDLLDNF-QVGDEVKVSFNIEGREWNGR 73 (84)
T ss_pred cEEEEEecCcccCcCCCcEEEEEEEeCCCcC-CceEEEEEEcchhhhhccC-CCCCEEEEEEEeeccEecce
Confidence 5555555554432211 543 23332 2223 2459999999877777888 799987764 7777788865
No 100
>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=23.18 E-value=1.5e+02 Score=22.99 Aligned_cols=71 Identities=13% Similarity=0.145 Sum_probs=44.6
Q ss_pred EEEEEEEEEcCCceecCCCceEEEEEEEeCCCC---------CCCeEEEEecCCCCC-CCCCCCCCCEEEEe-eEEEEEe
Q 015760 24 VNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQ---------SPELLVNIFTSSIDQ-LPRVLSPRDLILLK-NVMIKKH 92 (401)
Q Consensus 24 vnviGVVvd~~~P~~trGtD~~~tl~I~D~s~~---------~~gl~v~iF~~~~e~-LP~v~~~GDII~l~-rvki~~~ 92 (401)
+.++|-|..--..+.++...-.+.|+|.=.+.. ...+.|.+|.+..+. +..+ +.||.|.+. +++...|
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 356777776655555664566666776544432 234999999874444 4446 789966654 5677777
Q ss_pred cCe
Q 015760 93 QAE 95 (401)
Q Consensus 93 ~g~ 95 (401)
.++
T Consensus 80 ~~~ 82 (100)
T cd04496 80 EDK 82 (100)
T ss_pred ECC
Confidence 654
No 101
>PRK07135 dnaE DNA polymerase III DnaE; Validated
Probab=23.09 E-value=1.8e+02 Score=33.44 Aligned_cols=65 Identities=15% Similarity=0.171 Sum_probs=48.0
Q ss_pred eHHhhhhccCCEEEEEEEEEEcCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEE
Q 015760 12 RIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILL 84 (401)
Q Consensus 12 ~i~~~~~~~~~~vnviGVVvd~~~P~~trGtD~~~tl~I~D~s~~~~gl~v~iF~~~~e~LP~v~~~GDII~l 84 (401)
+|.++ ..+..+.+.|+|+..+.-+ |.++-|..+++-|.+-. +.|.+|.+..+..-.. ..|+++.+
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 45665 2466789999999988755 44567999999999764 9999997644444344 67888776
No 102
>COG0335 RplS Ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=23.01 E-value=2.2e+02 Score=23.85 Aligned_cols=45 Identities=16% Similarity=0.254 Sum_probs=27.3
Q ss_pred CCCCCCCCCCCEEEEe-------eEEEEEecCeeEEEeecC-ceEEEEEeCCCC
Q 015760 70 DQLPRVLSPRDLILLK-------NVMIKKHQAELSAVFYKD-SSSFALFDGNSG 115 (401)
Q Consensus 70 e~LP~v~~~GDII~l~-------rvki~~~~g~~~~~~~~~-~ss~~lf~~~~~ 115 (401)
.++|.+ .+||-|+++ +-.+|.|.|-+-+.-+.+ .++|.|=.-..|
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 223566666555554544 245665444333
No 103
>PRK06752 single-stranded DNA-binding protein; Validated
Probab=22.62 E-value=2.3e+02 Score=23.16 Aligned_cols=73 Identities=7% Similarity=0.031 Sum_probs=46.9
Q ss_pred EEEEEEEEEEcCCceecCCCceEEEEEEEeCCCC--------CCCeEEEEecCCCCCCCCCCCCCCEEE-EeeEEEEEec
Q 015760 23 KVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQ--------SPELLVNIFTSSIDQLPRVLSPRDLIL-LKNVMIKKHQ 93 (401)
Q Consensus 23 ~vnviGVVvd~~~P~~trGtD~~~tl~I~D~s~~--------~~gl~v~iF~~~~e~LP~v~~~GDII~-l~rvki~~~~ 93 (401)
.|.++|-+..--.-+.+.+..-.++|+|.-.... .+-+.|.+|.+..+.+-.-.+-||-|. --+++...|.
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 4778887765433344555566777888654321 134999999976565555447899664 4578888886
Q ss_pred Ce
Q 015760 94 AE 95 (401)
Q Consensus 94 g~ 95 (401)
++
T Consensus 84 ~~ 85 (112)
T PRK06752 84 DD 85 (112)
T ss_pred CC
Confidence 43
No 104
>PF15489 CTC1: CST, telomere maintenance, complex subunit CTC1
Probab=22.54 E-value=1.3e+03 Score=27.12 Aligned_cols=71 Identities=21% Similarity=0.277 Sum_probs=47.9
Q ss_pred cCCEEEEEEEEEEcCCceecCCCceE-EEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEecCe
Q 015760 20 VKHKVNLLGVVLEFSIPRKSQGTDYV-CVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAE 95 (401)
Q Consensus 20 ~~~~vnviGVVvd~~~P~~trGtD~~-~tl~I~D~s~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~rvki~~~~g~ 95 (401)
-+..+||-|.|+..++-.+++|+-|. +++. |. ...+.|.+=-+..-.-=...++|+-..|.+++|...+|.
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--DA---GSHVPVIVQEPAQLVWHRALRPGRAYVLTSLRVSKIRGH 235 (1144)
T ss_pred ccCceeeeeEEEEeeceEEEcceEEEEEEeC--CC---CceeEEEEEecchhhhhhhcccCCeEEEeeeEEEEecCc
Confidence 46679999999999999899887655 4444 22 222553322222222223448999999999999988884
No 105
>PRK06751 single-stranded DNA-binding protein; Provisional
Probab=22.08 E-value=2.5e+02 Score=25.22 Aligned_cols=72 Identities=11% Similarity=0.082 Sum_probs=45.8
Q ss_pred EEEEEEEEEEcCCceecCCCceEEEEEEEeCCC-C-------CCCeEEEEecCCCCCCCCCCCCCCEEE-EeeEEEEEec
Q 015760 23 KVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQ-Q-------SPELLVNIFTSSIDQLPRVLSPRDLIL-LKNVMIKKHQ 93 (401)
Q Consensus 23 ~vnviGVVvd~~~P~~trGtD~~~tl~I~D~s~-~-------~~gl~v~iF~~~~e~LP~v~~~GDII~-l~rvki~~~~ 93 (401)
.|.|+|=|+.=-.-+.|.+.--.++|+|.-... . .+-+.|.+|.+..+.+-.-.+.||-|. --|++...|.
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 467788776432223343344577888853321 1 124999999987676766557899554 4588999996
Q ss_pred C
Q 015760 94 A 94 (401)
Q Consensus 94 g 94 (401)
+
T Consensus 84 d 84 (173)
T PRK06751 84 G 84 (173)
T ss_pred C
Confidence 4
No 106
>smart00800 uDENN Domain always found upstream of DENN domain, found in a variety of signalling proteins. The uDENN domain is part of the tripartite DENN domain. It is always found upstream of the DENN domain itself, which is found in a variety of signalling proteins involved in Rab-mediated processes or regulation of MAPKs signalling pathways. The DENN domain is always encircled on both sides by more divergent domains, called uDENN (for upstream DENN) and dDENN (for downstream DENN). The function of the DENN domain remains to date unclear, although it appears to represent a good candidate for a GTP/GDP exchange activity.
Probab=20.63 E-value=1.5e+02 Score=23.19 Aligned_cols=13 Identities=23% Similarity=0.404 Sum_probs=9.3
Q ss_pred eCCCccccccCCC
Q 015760 357 HPFQAEHYSSPNG 369 (401)
Q Consensus 357 ~P~~~~df~~~~g 369 (401)
.|..|..||-|.|
T Consensus 42 ~~~~i~~FCfP~G 54 (89)
T smart00800 42 LPDSIPLFCFPEG 54 (89)
T ss_pred CccCCCeeECCCC
Confidence 3455777888877
No 107
>PRK07459 single-stranded DNA-binding protein; Provisional
Probab=20.33 E-value=2.5e+02 Score=23.47 Aligned_cols=72 Identities=14% Similarity=0.162 Sum_probs=46.3
Q ss_pred EEEEEEEEEEcCCceecCCCceEEEEEEEeCCCC----CCCeEEEEecCCCCCCCCCCCCCCEEEE-eeEEEEEecC
Q 015760 23 KVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQ----SPELLVNIFTSSIDQLPRVLSPRDLILL-KNVMIKKHQA 94 (401)
Q Consensus 23 ~vnviGVVvd~~~P~~trGtD~~~tl~I~D~s~~----~~gl~v~iF~~~~e~LP~v~~~GDII~l-~rvki~~~~g 94 (401)
.|.++|=+..--.-+.+.+..-.++|+|.=.... .+-+.|.+|.+..+.+=.-.+-|+-|.+ -+++...|.+
T Consensus 5 ~v~LiGrL~~DPelr~t~~G~~v~~fslAv~~~~~~~~t~w~~v~~wg~~Ae~~~~~l~KG~~V~V~G~l~~~~~~d 81 (121)
T PRK07459 5 SVTLVGRAGRDPEVRYFESGSVVCNLTLAVNRRSRDDEPDWFNLEIWGKTAQVAADYVKKGSLIGITGSLKFDRWTD 81 (121)
T ss_pred EEEEEEEccCCCEEEEcCCCCEEEEEEEEecccccCCCceEEEEEEehHHHHHHHHHcCCCCEEEEEEEEEecceEc
Confidence 5788887776322234444556888888643211 2349999999755555443478996655 5788888854
No 108
>PRK08182 single-stranded DNA-binding protein; Provisional
Probab=20.19 E-value=1.7e+02 Score=25.48 Aligned_cols=72 Identities=13% Similarity=0.071 Sum_probs=45.8
Q ss_pred EEEEEEEEEEcCCceec-CCCc---eEEEEEEE-eCCCC----------CCCeEEEEecCCCCCCCCCCCCCCEEE-Eee
Q 015760 23 KVNLLGVVLEFSIPRKS-QGTD---YVCVLKIV-DDSQQ----------SPELLVNIFTSSIDQLPRVLSPRDLIL-LKN 86 (401)
Q Consensus 23 ~vnviGVVvd~~~P~~t-rGtD---~~~tl~I~-D~s~~----------~~gl~v~iF~~~~e~LP~v~~~GDII~-l~r 86 (401)
.|+++|=+..--.-+.+ .|+. -.++|+|. |.+.. ..-+.|.+|.+..+.+-.-.+-||-|. --+
T Consensus 4 ~V~LiGrLg~DPElr~t~~G~~~~~~va~fslA~~r~~~~~~Ge~~~~~t~w~~V~~wg~~Ae~v~~~l~KG~~V~V~Gr 83 (148)
T PRK08182 4 HFVGEGNIGSAPEYREFPNGNDEPRRLLRLNVYFDNPVPTKDGEYEDRGGFWAPVELWHRDAEHWARLYQKGMRVLVEGR 83 (148)
T ss_pred EEEEEEECCCCCeEEECCCCCeeeeeEEEEEEEecCceECCCCCEEecCcEEEEEEEEhHHHHHHHHhcCCCCEEEEEEE
Confidence 57888877654222334 3543 37888884 32221 013899999976676766557899555 457
Q ss_pred EEEEEecC
Q 015760 87 VMIKKHQA 94 (401)
Q Consensus 87 vki~~~~g 94 (401)
++...|.+
T Consensus 84 L~~~~w~d 91 (148)
T PRK08182 84 MERDEWTD 91 (148)
T ss_pred EEecccCC
Confidence 88888854
No 109
>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=20.12 E-value=2.1e+02 Score=27.40 Aligned_cols=66 Identities=12% Similarity=0.142 Sum_probs=45.4
Q ss_pred EEEEEEEeCC-CCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEecC-----eeEEEeecCceEEEEEeC
Q 015760 45 VCVLKIVDDS-QQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQA-----ELSAVFYKDSSSFALFDG 112 (401)
Q Consensus 45 ~~tl~I~D~s-~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~rvki~~~~g-----~~~~~~~~~~ss~~lf~~ 112 (401)
+..++|+|-. .......++|..++.+.+-.+ ..|-+.++.++.....++ .+++.+.++ |.|.-.+.
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 5566777766 334567788888764444444 789999999998877666 467777764 67774443
Done!