Query 012503
Match_columns 462
No_of_seqs 170 out of 231
Neff 7.3
Searched_HMMs 46136
Date Fri Mar 29 03:19:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/012503.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/012503hhsearch_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 5.4E-51 1.2E-55 402.4 12.7 424 3-460 2-462 (522)
2 cd04497 hPOT1_OB1_like hPOT1_O 100.0 2.3E-33 5E-38 249.3 17.6 137 8-146 1-138 (138)
3 PF02765 POT1: Telomeric singl 100.0 6.8E-33 1.5E-37 248.7 14.1 137 10-146 1-146 (146)
4 cd04498 hPOT1_OB2 hPOT1_OB2: A 99.9 3.3E-23 7.1E-28 177.9 12.0 100 169-281 1-112 (123)
5 PRK12366 replication factor A; 99.4 1.5E-10 3.1E-15 126.9 30.9 299 6-401 275-591 (637)
6 TIGR00617 rpa1 replication fac 99.2 1.1E-08 2.3E-13 111.7 28.0 319 9-400 179-537 (608)
7 PRK12366 replication factor A; 99.2 1.6E-08 3.4E-13 111.0 28.9 279 8-400 61-344 (637)
8 PRK07218 replication factor A; 99.1 1.7E-07 3.7E-12 97.5 31.9 284 10-401 58-352 (423)
9 PRK14699 replication factor A; 99.0 3.8E-07 8.3E-12 96.6 29.4 272 11-398 167-447 (484)
10 PRK06386 replication factor A; 99.0 3.1E-06 6.6E-11 86.1 32.3 275 11-401 3-291 (358)
11 PRK07211 replication factor A; 98.9 5.8E-08 1.2E-12 102.0 19.8 204 8-290 159-367 (485)
12 PRK15491 replication factor A; 98.9 8E-07 1.7E-11 91.6 27.7 271 10-397 57-336 (374)
13 PRK15491 replication factor A; 98.8 3.8E-07 8.3E-12 93.9 20.0 204 6-286 162-372 (374)
14 PRK14699 replication factor A; 98.7 1.9E-06 4.1E-11 91.4 20.1 203 9-288 275-484 (484)
15 KOG4757 Predicted telomere bin 98.5 3.6E-09 7.8E-14 106.4 -4.7 117 344-460 378-522 (522)
16 PRK07211 replication factor A; 98.5 0.00016 3.5E-09 76.3 27.9 269 10-397 53-329 (485)
17 PRK08402 replication factor A; 98.3 3.8E-05 8.3E-10 78.5 19.2 195 159-411 63-281 (355)
18 cd04475 RPA1_DBD_B RPA1_DBD_B: 98.0 9E-05 2E-09 62.0 10.9 74 23-101 1-79 (101)
19 TIGR00617 rpa1 replication fac 97.9 0.00019 4.1E-09 78.7 14.5 156 7-200 295-479 (608)
20 PRK06461 single-stranded DNA-b 97.9 0.00041 8.8E-09 61.0 13.7 92 10-111 4-99 (129)
21 PRK07218 replication factor A; 97.6 0.008 1.7E-07 63.0 20.6 160 159-395 59-219 (423)
22 cd04491 SoSSB_OBF SoSSB_OBF: A 97.5 0.0013 2.8E-08 52.8 10.8 72 25-102 1-75 (82)
23 PRK06386 replication factor A; 97.3 0.01 2.2E-07 60.7 16.9 114 238-394 49-163 (358)
24 PRK06461 single-stranded DNA-b 97.2 0.0045 9.8E-08 54.4 10.7 88 159-291 5-101 (129)
25 PRK08402 replication factor A; 97.1 0.018 3.9E-07 59.1 15.4 139 9-180 61-207 (355)
26 cd04497 hPOT1_OB1_like hPOT1_O 96.8 0.014 3E-07 51.8 10.9 96 157-290 3-105 (138)
27 cd03524 RPA2_OBF_family RPA2_O 96.4 0.016 3.5E-07 43.9 7.2 70 25-100 1-70 (75)
28 KOG3416 Predicted nucleic acid 96.3 0.02 4.4E-07 49.2 7.8 84 11-102 5-88 (134)
29 PF02765 POT1: Telomeric singl 96.3 0.12 2.6E-06 46.3 13.2 97 159-288 2-109 (146)
30 PRK07217 replication factor A; 96.2 1.4 3E-05 44.2 21.6 168 159-401 73-245 (311)
31 PRK07217 replication factor A; 96.0 0.12 2.6E-06 51.7 12.9 92 7-109 69-160 (311)
32 PF01336 tRNA_anti-codon: OB-f 95.2 0.034 7.5E-07 43.0 4.6 68 24-101 1-70 (75)
33 cd04489 ExoVII_LU_OBF ExoVII_L 95.1 0.24 5.3E-06 38.8 9.5 69 24-101 2-72 (78)
34 PF15489 CTC1: CST, telomere m 95.0 0.23 5E-06 57.1 12.1 145 238-412 888-1054(1144)
35 cd04481 RPA1_DBD_B_like RPA1_D 94.9 0.12 2.7E-06 43.5 7.6 82 25-108 1-90 (106)
36 cd04476 RPA1_DBD_C RPA1_DBD_C: 94.7 0.16 3.4E-06 46.4 8.3 32 370-401 65-96 (166)
37 cd04474 RPA1_DBD_A RPA1_DBD_A: 94.2 0.16 3.4E-06 42.8 6.6 84 12-99 1-88 (104)
38 cd04478 RPA2_DBD_D RPA2_DBD_D: 94.1 0.48 1E-05 38.8 9.3 67 24-101 2-72 (95)
39 cd04491 SoSSB_OBF SoSSB_OBF: A 93.6 0.23 5.1E-06 39.6 6.3 46 238-286 35-80 (82)
40 cd04475 RPA1_DBD_B RPA1_DBD_B: 93.3 1.1 2.4E-05 37.2 10.1 59 236-298 38-96 (101)
41 PRK13480 3'-5' exoribonuclease 93.2 0.6 1.3E-05 47.3 9.9 82 12-101 4-85 (314)
42 cd04485 DnaE_OBF DnaE_OBF: A s 93.1 0.24 5.1E-06 38.7 5.6 70 26-100 2-71 (84)
43 cd04492 YhaM_OBF_like YhaM_OBF 92.3 1.2 2.6E-05 34.9 8.6 68 27-100 3-70 (83)
44 cd04483 hOBFC1_like hOBFC1_lik 91.6 1.5 3.4E-05 36.0 8.7 65 26-101 2-87 (92)
45 PF08646 Rep_fac-A_C: Replicat 90.5 0.21 4.6E-06 44.5 2.8 32 369-400 50-81 (146)
46 cd04474 RPA1_DBD_A RPA1_DBD_A: 88.9 3.8 8.1E-05 34.3 9.1 49 236-284 46-101 (104)
47 cd03524 RPA2_OBF_family RPA2_O 86.7 9.5 0.0002 28.1 9.5 65 171-276 1-67 (75)
48 PF01336 tRNA_anti-codon: OB-f 86.3 9.3 0.0002 29.0 9.4 62 170-273 1-62 (75)
49 PF13742 tRNA_anti_2: OB-fold 85.5 7.3 0.00016 32.4 8.8 79 13-100 11-94 (99)
50 cd04488 RecG_wedge_OBF RecG_we 82.7 8.6 0.00019 28.9 7.7 69 26-101 2-70 (75)
51 cd04484 polC_OBF polC_OBF: A s 77.8 20 0.00043 28.7 8.4 71 24-98 2-74 (82)
52 cd04487 RecJ_OBF2_like RecJ_OB 76.9 24 0.00053 27.5 8.5 64 26-100 3-67 (73)
53 PF09104 BRCA-2_OB3: BRCA2, ol 76.8 16 0.00035 32.6 8.2 63 167-270 18-82 (143)
54 PRK07373 DNA polymerase III su 75.6 8.9 0.00019 40.9 7.5 88 9-101 267-355 (449)
55 cd04483 hOBFC1_like hOBFC1_lik 75.0 41 0.00088 27.5 9.7 26 171-198 1-26 (92)
56 cd04490 PolII_SU_OBF PolII_SU_ 74.7 11 0.00023 30.0 6.1 59 24-91 2-62 (79)
57 PF09104 BRCA-2_OB3: BRCA2, ol 71.6 23 0.00051 31.6 7.9 63 21-90 18-81 (143)
58 PRK05673 dnaE DNA polymerase I 68.9 13 0.00027 44.3 7.4 87 10-101 965-1052(1135)
59 KOG3056 Protein required for S 67.5 8.6 0.00019 41.4 5.1 70 24-95 188-257 (578)
60 cd04498 hPOT1_OB2 hPOT1_OB2: A 65.8 7.3 0.00016 33.9 3.5 34 60-94 62-95 (123)
61 KOG1030 Predicted Ca2+-depende 65.4 14 0.0003 33.9 5.3 26 369-394 51-76 (168)
62 cd04482 RPA2_OBF_like RPA2_OBF 62.7 32 0.00069 28.1 6.6 60 26-93 3-64 (91)
63 cd04495 BRCA2DBD_OB3 BRCA2DBD_ 62.5 33 0.00072 28.6 6.5 64 26-95 2-66 (100)
64 PRK06920 dnaE DNA polymerase I 61.9 21 0.00045 42.4 7.3 88 9-101 931-1018(1107)
65 PRK00286 xseA exodeoxyribonucl 57.0 72 0.0016 33.7 9.9 77 15-100 17-95 (438)
66 PF12100 DUF3576: Domain of un 56.7 23 0.00049 29.8 4.7 53 9-68 17-70 (103)
67 PF02721 DUF223: Domain of unk 56.4 37 0.0008 27.7 6.0 39 236-274 9-47 (95)
68 TIGR00237 xseA exodeoxyribonuc 56.1 77 0.0017 33.6 9.9 78 13-100 9-89 (432)
69 PF01245 Ribosomal_L19: Riboso 52.5 45 0.00097 28.6 6.0 41 70-111 14-62 (113)
70 PRK05338 rplS 50S ribosomal pr 52.0 34 0.00074 29.4 5.2 45 70-115 14-66 (116)
71 PRK07374 dnaE DNA polymerase I 50.9 40 0.00087 40.3 7.3 88 9-101 987-1075(1170)
72 PRK10917 ATP-dependent DNA hel 48.2 74 0.0016 35.8 8.7 78 12-98 52-129 (681)
73 PF15072 DUF4539: Domain of un 47.4 58 0.0013 26.5 5.6 63 23-94 3-66 (86)
74 COG1107 Archaea-specific RecJ- 46.5 87 0.0019 34.3 8.2 79 11-100 203-282 (715)
75 TIGR00643 recG ATP-dependent D 46.0 1E+02 0.0023 34.2 9.3 79 12-99 25-103 (630)
76 cd04486 YhcR_OBF_like YhcR_OBF 45.8 1.5E+02 0.0032 23.4 8.3 62 27-101 3-69 (78)
77 cd04480 RPA1_DBD_A_like RPA1_D 45.2 44 0.00096 26.6 4.7 37 236-272 30-66 (86)
78 PF15072 DUF4539: Domain of un 43.0 23 0.00049 28.8 2.6 24 374-397 20-43 (86)
79 COG1200 RecG RecG-like helicas 42.9 2.8E+02 0.006 31.2 11.6 80 13-101 54-133 (677)
80 TIGR01024 rplS_bact ribosomal 42.1 57 0.0012 28.0 5.0 45 70-115 14-66 (113)
81 cd04478 RPA2_DBD_D RPA2_DBD_D: 41.3 1.8E+02 0.004 23.2 11.2 26 170-197 2-27 (95)
82 CHL00084 rpl19 ribosomal prote 40.6 67 0.0015 27.7 5.3 42 70-112 18-67 (117)
83 PRK05672 dnaE2 error-prone DNA 38.9 66 0.0014 38.1 6.6 85 10-101 941-1026(1046)
84 PRK06826 dnaE DNA polymerase I 38.9 73 0.0016 38.1 7.0 77 20-101 990-1067(1151)
85 KOG2708 Predicted metalloprote 37.3 19 0.00042 34.7 1.6 48 406-460 90-154 (336)
86 PF11325 DUF3127: Domain of un 36.3 2.3E+02 0.005 22.9 7.5 66 28-95 4-73 (84)
87 cd04490 PolII_SU_OBF PolII_SU_ 34.8 42 0.00092 26.6 3.0 21 376-396 20-40 (79)
88 cd04495 BRCA2DBD_OB3 BRCA2DBD_ 34.5 1.9E+02 0.0042 24.2 6.8 34 239-272 30-64 (100)
89 PRK00448 polC DNA polymerase I 34.4 1.3E+02 0.0028 37.0 8.2 85 8-98 224-312 (1437)
90 PF14535 AMP-binding_C_2: AMP- 33.8 29 0.00063 28.4 2.0 63 354-418 2-70 (96)
91 cd04492 YhaM_OBF_like YhaM_OBF 31.6 60 0.0013 24.9 3.4 21 374-394 20-40 (83)
92 PRK07279 dnaE DNA polymerase I 31.6 98 0.0021 36.6 6.4 85 10-101 875-960 (1034)
93 cd04489 ExoVII_LU_OBF ExoVII_L 30.7 61 0.0013 24.9 3.3 24 374-397 18-41 (78)
94 cd04496 SSB_OBF SSB_OBF: A sub 29.8 40 0.00087 27.1 2.2 27 237-263 44-70 (100)
95 COG1599 RFA1 Single-stranded D 29.4 1.7E+02 0.0038 30.6 7.4 78 21-103 59-140 (407)
96 COG2049 DUR1 Allophanate hydro 28.3 29 0.00062 33.4 1.1 39 230-270 177-215 (223)
97 PRK13254 cytochrome c-type bio 28.0 3.8E+02 0.0082 24.0 8.2 66 10-85 37-105 (148)
98 PF15489 CTC1: CST, telomere m 27.7 1.1E+03 0.024 28.2 16.3 71 20-95 164-235 (1144)
99 KOG4792 Crk family adapters [S 27.2 1.8E+02 0.0038 28.2 6.1 61 229-293 223-289 (293)
100 cd04480 RPA1_DBD_A_like RPA1_D 26.4 1.1E+02 0.0025 24.1 4.3 57 42-100 17-73 (86)
101 cd04481 RPA1_DBD_B_like RPA1_D 26.0 1.9E+02 0.0041 23.9 5.7 62 236-298 34-101 (106)
102 PRK00448 polC DNA polymerase I 25.5 2.5E+02 0.0054 34.7 8.5 40 159-198 227-270 (1437)
103 COG1570 XseA Exonuclease VII, 24.3 6.7E+02 0.015 26.7 10.4 65 22-95 24-88 (440)
104 COG2176 PolC DNA polymerase II 24.1 1.7E+02 0.0036 35.1 6.3 70 156-264 228-301 (1444)
105 KOG3416 Predicted nucleic acid 23.6 78 0.0017 27.7 2.8 32 238-273 49-80 (134)
106 cd04317 EcAspRS_like_N EcAspRS 23.2 4E+02 0.0087 22.9 7.5 68 13-90 5-76 (135)
107 PRK07772 single-stranded DNA-b 20.9 1.8E+02 0.0039 27.2 4.9 75 21-95 4-91 (186)
108 PRK08763 single-stranded DNA-b 20.5 1.2E+02 0.0026 27.8 3.6 26 238-263 53-78 (164)
No 1
>KOG4757 consensus Predicted telomere binding protein [General function prediction only]
Probab=100.00 E-value=5.4e-51 Score=402.42 Aligned_cols=424 Identities=22% Similarity=0.214 Sum_probs=327.7
Q ss_pred CCCCCcceeehhhhhhccCCeEEEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEE
Q 012503 3 SQRNQGGIVRIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLI 82 (462)
Q Consensus 3 ~~~~~y~y~~i~d~~~~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII 82 (462)
.-++.|+|..+++++...+..||+||||+++++|++++|+||+||++|+||.+.+.||+|++|+++-++||.|+++||||
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 45678999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEeeEEEEEEcCeeEEEecCCce-EEEEEeCCCCCCCCccccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCccccccc
Q 012503 83 LLKNVMIKKHQAELSAVFYKDSS-SFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSL 161 (462)
Q Consensus 83 ~l~rvki~~~~g~~~~~~~~~~s-s~~lf~~~~~~~~~Py~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~f~~~L 161 (462)
+|||+|||.|+.+.+|+++..++ +|++|+|+ +.+..|||+|+. |-++ .+||+|++-+.....+ ++ ..+
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 99999999999999999987764 59999999 889999999888 8777 7899999988877776 56 788
Q ss_pred ccccCCceeeeEEEEEEEeeeCCCCeEEEEEEcCCCCCCCCCCCCCCc-ccCCCCCCcccCCCCChhccccCCCcceEEE
Q 012503 162 KDISEHRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLED-EEHNPLPLHIESSPLDLETLRNFFPVGTVLR 240 (462)
Q Consensus 162 ~di~~~~f~Dlv~qVv~v~~~~~~~~~~L~VwDgT~~~~~~~~~~~~~-~~~~~~p~~~~~~~l~~~~~~~~p~~G~~l~ 240 (462)
+++.++..-.|.||+++.. ......|. .|||-|.+-...+++..-- --++..|++|++ .+.+.+..||..|.+..
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 9998998889999999887 54567777 7999555544442221000 011235666654 55666788999998888
Q ss_pred EEecccchhhhcccCCCCCEEEEEceEEEEeCcEEEEEEeeCCceEEcCCCChhHHHH--------------Hh-----h
Q 012503 241 VSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDNDNVVWDY--------------MR-----E 301 (462)
Q Consensus 241 V~~~~~~~~~~~~~~k~g~wV~l~Nv~~k~~~g~leG~l~~~ski~~l~~~d~~v~~~--------------~r-----e 301 (462)
...+.+.+++..+.+.+|.-+..+|+...-+. +|.++ ++.+. |+.-..| ++ |
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 88888777776777777777777777652211 22221 11110 1111111 00 2
Q ss_pred hhcCCCCCCCCcCCCCCCcccccccCCCCcccHHHHhhCCCCCceEE-EEEEEEe---ecCCcccccccCCCceEEEEEE
Q 012503 302 RISGGHGHMPIWTDPSSQFLTEVDWVNVASVTLMKIATQLQGNVRCC-CIVRVVS---IHPFQAEHYSSPNGSSEYTMKL 377 (462)
Q Consensus 302 r~~~~~~~~~~~~~p~~~~it~~~~~~~p~ttL~dIL~~p~v~~kfr-~~VRVV~---~~P~~~edf~~~~~~w~~~f~L 377 (462)
.+..+++.... +-.++..|.+++..+|+++|||+++.+.++.||| |.||+|+ .+|.++|.+.-.+ -...-
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 HLLNEVKPEKR--LYVQNCQTGIEAVIAPFVSLMDSETPFIVTEKKRTCVVRFVAHVINYPASVELLTIIT----ILLAP 371 (522)
T ss_pred hhhcccCcccc--eeecccccCcchhhcccchhhhhccccccchhcceeeeeehhhcccccchhhhhhhhh----hhhHH
Confidence 22222222111 1135778889999999999999999999999999 9999999 9999999885432 13445
Q ss_pred EEeCCCceEEEEEecccccc-----ccCCC-CChHHHHHHHHHHcCCCCCCCCCCCCcCCCcceeEeeeeeeecCCc---
Q 012503 378 TLEDPTARIHALLCGKEWVK-----FFGGS-PPPDVLTKKIKMLLGMPEHEDGNDDMVRNPPWIKCFLHLKESDGGR--- 448 (462)
Q Consensus 378 ~lED~t~ri~~~v~~~da~~-----f~~~~-~~~~~l~~kl~~L~G~~e~~~~~~~~~~~~p~~~cCi~sY~v~~~~--- 448 (462)
+.+|+++|.|+.++..|... +||-. .+..++..+|+.|+|+.+ .+. .|+++||++||....+-.+-+
T Consensus 372 ic~l~n~r~H~~l~~le~s~p~s~~~fgc~~~~~~~~v~~ln~Lv~~e~--~~~--vP~~~~~v~~~~l~~~s~~l~~~l 447 (522)
T KOG4757|consen 372 ICNLLNPRKHRLLVQLEDSWPKSLTQFGCLSQPPSSYVWMLNLLVRDES--NVT--VPVIFFDVDAAELINSSKKLPCNL 447 (522)
T ss_pred HhhhhchhhhhhhhhhcccCcccceeeeeccCCHHHHHHHHHHHhcccc--ccc--cccccchhheeeeccccccccchh
Confidence 57889999999888888775 77744 567888999999999722 222 689999999999999888743
Q ss_pred ---eEEEEEeeeEEc
Q 012503 449 ---NRVYYIRWTKLV 460 (462)
Q Consensus 449 ---~r~f~~F~T~i~ 460 (462)
.|+||||++-|.
T Consensus 448 ~d~~~~fqi~ds~il 462 (522)
T KOG4757|consen 448 ADHQMTFQIKDSLIL 462 (522)
T ss_pred ccccceEEecceeee
Confidence 799999999886
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=2.3e-33 Score=249.32 Aligned_cols=137 Identities=33% Similarity=0.509 Sum_probs=129.8
Q ss_pred cceeehhhhhhccCCeEEEEEEEEecCCccccCCCceEEEEEEEeCCCC-CCCeEEEEecCCCCCCCCCCCCCCEEEEee
Q 012503 8 GGIVRIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQ-SPELLVNIFTSSIDQLPRVLSPRDLILLKN 86 (462)
Q Consensus 8 y~y~~i~d~~~~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~-~~gl~v~iF~~~~~~LP~v~~~GDII~l~r 86 (462)
|.|++|++|.+..++.|||||||+|+++|++|+|+||+|+|+|+|+|.. +.||+|+||+++.++||.+ ++||||+|||
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 7899999999888999999999999999999999999999999999997 7899999999999999999 8999999999
Q ss_pred EEEEEEcCeeEEEecCCceEEEEEeCCCCCCCCccccCCCCCCCCHHHHHHHHHHHHhhh
Q 012503 87 VMIKKHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCV 146 (462)
Q Consensus 87 vki~~~~g~~~~~~~~~~ss~~lf~~~~~~~~~Py~~s~~~~~~~~~e~~~v~~Lr~W~~ 146 (462)
++|+.|+|+.+++++.+.||||||++..+....||+.+.. ++++++|++++..||+|+.
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 9999999999999987679999999999999889887766 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=6.8e-33 Score=248.73 Aligned_cols=137 Identities=35% Similarity=0.617 Sum_probs=126.9
Q ss_pred eeehhhhhhccCCeEEEEEEEEecCCc--cccCCCceEEEEEEEeCCCCC-----CCeEEEEecCCCCCCCCCCCCCCEE
Q 012503 10 IVRIKELAMHVKHKVNLLGVVLEFSIP--RKSQGTDYVCVLKIVDDSQQS-----PELLVNIFTSSIDQLPRVLSPRDLI 82 (462)
Q Consensus 10 y~~i~d~~~~~~~~vnviGVVvd~~~P--~~trG~D~~~tl~I~D~s~~~-----~gl~v~iF~~~~~~LP~v~~~GDII 82 (462)
|++|+++....+..|||||||+++++| ++|||+||+|+|+|+|+|+.. .||+|++|+++++.||.+..+||||
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 789998888899999999999999999 999999999999999999985 7999999999999999998779999
Q ss_pred EEeeEEEEEEcCeeEEEecCC-ceEEEEE-eCCCCCCCCccccCCCCCCCCHHHHHHHHHHHHhhh
Q 012503 83 LLKNVMIKKHQAELSAVFYKD-SSSFALF-DGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCV 146 (462)
Q Consensus 83 ~l~rvki~~~~g~~~~~~~~~-~ss~~lf-~~~~~~~~~Py~~s~~~~~~~~~e~~~v~~Lr~W~~ 146 (462)
+|||+||+.|+|+++++++.. .++|+|| ++..+.++.||+.++++++++++|+++++.||+|++
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 999999999999999998754 6899999 888888999999888889999999999999999974
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=99.90 E-value=3.3e-23 Score=177.86 Aligned_cols=100 Identities=25% Similarity=0.346 Sum_probs=80.7
Q ss_pred eeeeEEEEEEEeeeCCCCeEEEEEEcCCCCCCCCCCCCCCcc-cCCCCCCcccCCCCChhccccCC-Ccc-eEEEEEecc
Q 012503 169 YFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDE-EHNPLPLHIESSPLDLETLRNFF-PVG-TVLRVSTDR 245 (462)
Q Consensus 169 f~Dlv~qVv~v~~~~~~~~~~L~VwDgT~~~~~~~~~~~~~~-~~~~~p~~~~~~~l~~~~~~~~p-~~G-~~l~V~~~~ 245 (462)
||||+||||+++ +.++++++|||||||+||+..+.+..++. ..+++ +..++.|+ | | |+|+|+||+
T Consensus 1 ~~DLvcqVv~v~-~~d~~~~~L~VwDgT~~p~~~~~~~~~~~~~~e~d----------~~~k~~~~gp-g~~ti~It~yD 68 (123)
T cd04498 1 YFDLLCQLLSVV-ETDSSSTLLKVWDGTKFPPPLRKVKVEDDVVLEGD----------RSLKHREEGG-KQLTIDILVYD 68 (123)
T ss_pred CccEEEEEEEEE-EecCCeEEEEEecCCCCChhHhheeccccCccccc----------hhhhhhccCC-CeEEEEEEEEc
Confidence 799999999999 76888999999999999765545544332 11211 33467899 8 9 999999999
Q ss_pred cchhhhcccCCCCCEEEEEceEEEEeC--------cEEEEEE-ee
Q 012503 246 SYENFGRYFTATGKWVRIRNMSCQVSS--------GMWHGLL-QS 281 (462)
Q Consensus 246 ~~~~~~~~~~k~g~wV~l~Nv~~k~~~--------g~leG~l-~~ 281 (462)
+|+++|++ +|+||||+|+|||+|... -.|||.+ +.
T Consensus 69 ~H~~~ar~-lK~GdfV~L~NVhiK~~~~~~~~~~~~~Le~~l~~g 112 (123)
T cd04498 69 NHVELAKS-LKPGDFVRIYNVHAKSYSSKNEHDENDHLHFHLVHG 112 (123)
T ss_pred chHHHHhh-CCCCCEEEEEEEEEEeccCCcccCCcceEEEEEccC
Confidence 99999888 999999999999999932 3788888 44
No 5
>PRK12366 replication factor A; Reviewed
Probab=99.43 E-value=1.5e-10 Score=126.89 Aligned_cols=299 Identities=16% Similarity=0.191 Sum_probs=183.1
Q ss_pred CCcceeehhhhhhc-cCCeEEEEEEEEecCCccc---cCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCE
Q 012503 6 NQGGIVRIKELAMH-VKHKVNLLGVVLEFSIPRK---SQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDL 81 (462)
Q Consensus 6 ~~y~y~~i~d~~~~-~~~~vnviGVVvd~~~P~~---trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDI 81 (462)
..+.+++|+++... .|..+++-|.|+...+++. .+|+--..++.|.|.+- .+.+.+|.+..+.+..+ ..||+
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 45678899999754 5678999999999988754 36788999999999872 39999999877778777 69999
Q ss_pred EEEeeEEEEEEcC-----eeEEEecCCceEEEEEeCCCCCCCCccccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCcc
Q 012503 82 ILLKNVMIKKHQA-----ELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSND 156 (462)
Q Consensus 82 I~l~rvki~~~~g-----~~~~~~~~~~ss~~lf~~~~~~~~~Py~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~ 156 (462)
+.+.+++++.|+. ++.+.++.. |.... .. ... .| .. ...
T Consensus 351 y~is~~~vk~y~~~~~~~~~El~~~~~-s~I~~-d~--~~~-~p----~~---------------------------~~~ 394 (637)
T PRK12366 351 VKIENCKVRTYYDNEGEKRVDLNAGYS-SEIIK-DE--SIS-FE----EI---------------------------EEK 394 (637)
T ss_pred EEEecCEEeeccccCCCcCEEEEcCCc-eEEEe-cc--CCc-cc----ce---------------------------eec
Confidence 9999999998863 344444433 33432 11 100 11 00 002
Q ss_pred ccccccccc----CCceeeeEEEEEEEeeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCChhccccC
Q 012503 157 YLLSLKDIS----EHRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNF 232 (462)
Q Consensus 157 f~~~L~di~----~~~f~Dlv~qVv~v~~~~~~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~ 232 (462)
| ..|+||. .+..+|+++.|+.+. + -..++ . -||+...--. ..+.|+
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-SDGSKGKVRN--IELADG---------------------- 444 (637)
T ss_pred c-ccHHHhhcccCCCcEEEEEEEEEEcc-C--ceEEE-e-cCCCEeEEEE--EEEEeC----------------------
Confidence 3 4555553 578999999999887 3 11111 1 2333211100 000000
Q ss_pred CCcceEEEEEecccchhhhcccCCCCCEEEEEceEEEEeCcEEEEEEeeCCceEEcCCCChhHHHHHhhhhcCCCCCCCC
Q 012503 233 FPVGTVLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDNDNVVWDYMRERISGGHGHMPI 312 (462)
Q Consensus 233 p~~G~~l~V~~~~~~~~~~~~~~k~g~wV~l~Nv~~k~~~g~leG~l~~~ski~~l~~~d~~v~~~~rer~~~~~~~~~~ 312 (462)
=| ++++++|..++.+ .+.+|+.|.+.|..++..+|.++-.+...+.|.+.++ .+. ++ +.
T Consensus 445 --TG-~I~vtlWg~~a~~---~~~~G~vi~i~~~~V~~~~g~~~Ls~~~~s~i~~~p~-~~e----l~----~~------ 503 (637)
T PRK12366 445 --TG-SIRLTLWDDDAEI---EIKEGDAIKILHPYVKENGDYLDLSIGRYGRIEINPE-GEI----IK----SN------ 503 (637)
T ss_pred --CC-EEEEEEecccccc---CCCCCCEEEEEeeEEEeCCCeeEEEecCcceEEECCC-Ccc----cc----cc------
Confidence 05 6799999988863 5789999999999999999988888888888876443 222 11 00
Q ss_pred cCCCCCCcccccccCCCCcc---cHHHHhhCCC-CCceEEEEEEEEeecCCccccccc-CCCceEEEEEEEEeCCCceEE
Q 012503 313 WTDPSSQFLTEVDWVNVASV---TLMKIATQLQ-GNVRCCCIVRVVSIHPFQAEHYSS-PNGSSEYTMKLTLEDPTARIH 387 (462)
Q Consensus 313 ~~~p~~~~it~~~~~~~p~t---tL~dIL~~p~-v~~kfr~~VRVV~~~P~~~edf~~-~~~~w~~~f~L~lED~t~ri~ 387 (462)
+..+.++..... ++ +|..|..... .+++=.|.=+|+.---.-..+-|. ....|.|++.+.|-|.|+.++
T Consensus 504 -----~~~I~~i~~~~~-~~v~g~i~~i~~~~~~y~aCp~CnkKv~~~~g~~~C~~c~~~~p~~~~~l~~~i~D~TG~~~ 577 (637)
T PRK12366 504 -----RKFIADLEEDDT-VEIRGTVVDIRKQKIILYLCPNCRKRVEEVDGEYICEFCGEVEPNELLMLNFTLDDGTGTIN 577 (637)
T ss_pred -----ccCHHHcccCCe-EEEEEEEEEEeCCCEEEecccccCeEeEcCCCcEECCCCCCCCCcEEEEEEEEEEcCCCCEE
Confidence 001111100000 00 1111111100 011112333444210000011121 134788999999999999999
Q ss_pred EEEeccccccccCC
Q 012503 388 ALLCGKEWVKFFGG 401 (462)
Q Consensus 388 ~~v~~~da~~f~~~ 401 (462)
+.++++.|+.|||.
T Consensus 578 ~t~f~e~ae~l~G~ 591 (637)
T PRK12366 578 CRFYGKNVEKLLGM 591 (637)
T ss_pred EEEEhHHhHHHhCC
Confidence 99999999999974
No 6
>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=99.19 E-value=1.1e-08 Score=111.65 Aligned_cols=319 Identities=14% Similarity=0.136 Sum_probs=189.6
Q ss_pred ceeehhhhhhccCCeEEEEEEEEecCCccc---cCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCC-CCCCCCCCEEEE
Q 012503 9 GIVRIKELAMHVKHKVNLLGVVLEFSIPRK---SQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQL-PRVLSPRDLILL 84 (462)
Q Consensus 9 ~y~~i~d~~~~~~~~vnviGVVvd~~~P~~---trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~L-P~v~~~GDII~l 84 (462)
.+++|+++.... ....+-|-|+.....+. .+|.....++.|.|++ ..|.+.+|.+..+.+ |.+ ++|+|+.+
T Consensus 179 ~~~pI~~L~py~-~~wtIkaRV~~Ks~ir~~~~~~gegkvfsv~L~Deg---g~Irat~f~~~~dkf~~~l-~eG~VY~I 253 (608)
T TIGR00617 179 RVMPIASLSPYQ-NKWTIKARVTNKSEIRTWSNARGEGKLFNVELLDES---GEIRATAFNEQADKFYDII-QEGKVYYI 253 (608)
T ss_pred ceEEHHHCCCCC-CceEEEEEEEeccccceecCCCCCceeeEEEEecCC---CeEEEEECchHHHHHhhhc-ccCCEEEE
Confidence 589999998543 35899999998776654 2455678899999943 349999999755444 666 79999999
Q ss_pred eeEEEEEEcCeeEEEecCC---ceEEEEEeCCCCCCCCccccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCccccccc
Q 012503 85 KNVMIKKHQAELSAVFYKD---SSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSL 161 (462)
Q Consensus 85 ~rvki~~~~g~~~~~~~~~---~ss~~lf~~~~~~~~~Py~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~f~~~L 161 (462)
.+.+|+..+++...+.+.. +..+.......+..-.| ...| .| ..|
T Consensus 254 s~~~Vk~an~~y~~~~~~yei~f~~~T~I~~~~d~~~iP----~~~~---------------------------~f-~~i 301 (608)
T TIGR00617 254 SKGSLKPANKQFTNLGNDYEMTLDRDTVIEECEDETAIP----KIQF---------------------------NF-VKI 301 (608)
T ss_pred CceEEEEccccccCCCCCEEEEECCCeEEEECCCcccCC----cccc---------------------------cc-eEH
Confidence 9999998877655433310 11111121111111122 0002 23 445
Q ss_pred ccc---cCCceeeeEEEEEEEeeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCChhccccCCCcceE
Q 012503 162 KDI---SEHRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTV 238 (462)
Q Consensus 162 ~di---~~~~f~Dlv~qVv~v~~~~~~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~p~~G~~ 238 (462)
.|| ..+.++|+++.|..+. +. ..++- =.||++..--. ..+.| --|..
T Consensus 302 ~dI~~~~~~~~VDVIGvV~~v~-~~--~~i~~-k~~g~~~~kR~--i~L~D------------------------~sg~s 351 (608)
T TIGR00617 302 DDIGGYEGNSLVDVIGIVQSVS-PT--QTITS-RKNNKEFPKRD--ITLVD------------------------DSGKS 351 (608)
T ss_pred HHhhhhcCCCCccEEEEEeEec-Cc--eEEEE-cCCCCeeeeEE--EEEEe------------------------CCCCE
Confidence 555 4567999999999887 31 11111 11222111100 00000 01567
Q ss_pred EEEEecccchhhhcccCCCCCEEEEEceEEEEeCcEEEEEEeeCCceEEcCCCChhHHHHHhhhhcCCCCCCCCcCCCCC
Q 012503 239 LRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDNDNVVWDYMRERISGGHGHMPIWTDPSS 318 (462)
Q Consensus 239 l~V~~~~~~~~~~~~~~k~g~wV~l~Nv~~k~~~g~leG~l~~~ski~~l~~~d~~v~~~~rer~~~~~~~~~~~~~p~~ 318 (462)
++||+|..+|.. -....|+.|.|+.++++-.+|. .......|+|. ++++-+.+.++ |....++-...+...+ +.
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-VNPDIPEAEKL-KGWYDNEGKGTMASSI-SD 425 (608)
T ss_pred EEEEEEhhhhhh--cCCCCCCEEEEEeEEEEecCCc-eEeccCCceEE-ECCCcHHHHHH-HHHHHhcCCCccceee-hh
Confidence 899999999864 2367899999999999988664 34445566673 45544554433 3223221111110010 00
Q ss_pred CcccccccCCCCcccHHHHhhC----CCCCceEEEEEEEEeecCCcccccccC--------------------------C
Q 012503 319 QFLTEVDWVNVASVTLMKIATQ----LQGNVRCCCIVRVVSIHPFQAEHYSSP--------------------------N 368 (462)
Q Consensus 319 ~~it~~~~~~~p~ttL~dIL~~----p~v~~kfr~~VRVV~~~P~~~edf~~~--------------------------~ 368 (462)
...+..........||.||... .+-+..|.|.+.|+.+-+.+.-=.++| +
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 0000011123456789999853 133456888888887765432111111 1
Q ss_pred CceEEEEEEEEeCCCceEEEEEeccccccccC
Q 012503 369 GSSEYTMKLTLEDPTARIHALLCGKEWVKFFG 400 (462)
Q Consensus 369 ~~w~~~f~L~lED~t~ri~~~v~~~da~~f~~ 400 (462)
-.|.|.+.+.+.|.|+.+|+.++++.|+.+||
T Consensus 506 ~~~RYil~~~i~D~Tg~~~~t~F~~~ae~llG 537 (608)
T TIGR00617 506 FKYRYILQISISDETGQLWVTAFNDQAEQILG 537 (608)
T ss_pred ccEEEEEEEEEEeCCCCEEEEEEhHHHHHHcC
Confidence 25788899999999999999999999999996
No 7
>PRK12366 replication factor A; Reviewed
Probab=99.18 E-value=1.6e-08 Score=110.99 Aligned_cols=279 Identities=14% Similarity=0.164 Sum_probs=187.0
Q ss_pred cceeehhhhhhccCC-eEEEEEEEEecCCcccc---CC-CceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEE
Q 012503 8 GGIVRIKELAMHVKH-KVNLLGVVLEFSIPRKS---QG-TDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLI 82 (462)
Q Consensus 8 y~y~~i~d~~~~~~~-~vnviGVVvd~~~P~~t---rG-~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII 82 (462)
-.+++|+++. +++ .+++.|-|+..+.|+.- +| .-..+++.|.|.+- .+++.+|.+..+.+|.+ .+|||+
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 3578999997 554 59999999999988742 35 46789999999765 39999999877778888 799999
Q ss_pred EEeeEEEEEEcCeeEEEecCCceEEEEEeCCCCCCCCccccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCcccccccc
Q 012503 83 LLKNVMIKKHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSLK 162 (462)
Q Consensus 83 ~l~rvki~~~~g~~~~~~~~~~ss~~lf~~~~~~~~~Py~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~f~~~L~ 162 (462)
.+.++.++.|+|++.+..+.. ++........ ..-.| + .++ .| .|.
T Consensus 135 ~i~~~~v~~~~~~~el~~~~~-t~I~~~~~~d-~~~i~-~---------~~~---------------------~~--~I~ 179 (637)
T PRK12366 135 KIENARSRKWNNDVELNSGSE-TRIDKLEKYD-ESRYP-I---------IKE---------------------NY--DIP 179 (637)
T ss_pred EEeccEecccCCceEEEcCCc-ceEEEccccc-cccCC-c---------ccc---------------------cc--ccc
Confidence 999999999999998766644 4444332100 01111 0 000 12 588
Q ss_pred cccCCceeeeEEEEEEEeeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCChhccccCCCcceEEEEE
Q 012503 163 DISEHRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRVS 242 (462)
Q Consensus 163 di~~~~f~Dlv~qVv~v~~~~~~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~p~~G~~l~V~ 242 (462)
||.++.++|+++.|+++. + -..++ --||++-.-.. ..+.| + =| ++++|
T Consensus 180 el~~g~~v~v~G~V~~~~-~--~~~f~--rkdg~~~~~r~--~~l~D-----------------~-------TG-~irvT 227 (637)
T PRK12366 180 ELEPNLSATIEGEVTKAY-P--IKEFT--RKDGSEGKLKS--FILKD-----------------D-------TG-SIRVT 227 (637)
T ss_pred ccCCCCeEEEEEEEEEcc-C--cEEEE--EcCCCeeEEEE--EEEEc-----------------C-------CC-cEEEE
Confidence 888999999999999988 3 11211 12554321111 10100 0 15 68999
Q ss_pred ecccchhhhcccCCCCCEEEEEceEEEEeCcEEEEEEeeCCceEEcCCCChhHHHHHhhhhcCCCCCCCCcCCCCCCccc
Q 012503 243 TDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDNDNVVWDYMRERISGGHGHMPIWTDPSSQFLT 322 (462)
Q Consensus 243 ~~~~~~~~~~~~~k~g~wV~l~Nv~~k~~~g~leG~l~~~ski~~l~~~d~~v~~~~rer~~~~~~~~~~~~~p~~~~it 322 (462)
+|..++.. .+.+|+.|++.+....-+.|.+|-.....+.|..... .
T Consensus 228 lW~~~a~~---~~~~g~vv~i~g~~~~~~~~~~el~~~~~~~i~~~~~------------------------------~- 273 (637)
T PRK12366 228 LWNDLTDI---EVNKGDIVRVKGYVKQGYRTGLEISANNIEILEKLEK------------------------------E- 273 (637)
T ss_pred EEChhhcc---cCCCCCEEEEEeEEecCcCCceEEEeCCceeeccccc------------------------------c-
Confidence 99988853 5899999999883333354667665533232221000 0
Q ss_pred ccccCCCCcccHHHHhhCCCCCceEEEEEEEEeecCCcccccccCCCceEEEEEEEEeCCCceEEEEEeccccccccC
Q 012503 323 EVDWVNVASVTLMKIATQLQGNVRCCCIVRVVSIHPFQAEHYSSPNGSSEYTMKLTLEDPTARIHALLCGKEWVKFFG 400 (462)
Q Consensus 323 ~~~~~~~p~ttL~dIL~~p~v~~kfr~~VRVV~~~P~~~edf~~~~~~w~~~f~L~lED~t~ri~~~v~~~da~~f~~ 400 (462)
. ...++++|+++-.+- .+.+....+||++..| ++.|....|. --.|.+.|-|.|++|.+-++++.|.+|.+
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 -E--KELEIVNIEELTEFE-DGEEVDVKGRIIAISD--KREVERDDRT-AEVQDIELADGTGRVRVSFWGEKAKILEN 344 (637)
T ss_pred -c--cccCceeHHHCCccc-CCCEEEEEEEEEecCC--ceEEEcCCCc-EEEEEEEEEcCCCeEEEEEeCchhhhhcc
Confidence 0 011334566665321 3457888899999765 4557666675 57899999999999999999999988876
No 8
>PRK07218 replication factor A; Provisional
Probab=99.13 E-value=1.7e-07 Score=97.47 Aligned_cols=284 Identities=18% Similarity=0.209 Sum_probs=173.1
Q ss_pred eeehhhhhhccCCeEEEEEEEEecCCcc-ccCC-CceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeE
Q 012503 10 IVRIKELAMHVKHKVNLLGVVLEFSIPR-KSQG-TDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNV 87 (462)
Q Consensus 10 y~~i~d~~~~~~~~vnviGVVvd~~~P~-~trG-~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rv 87 (462)
-+.|+|+... ...|+|.|-|++...+. +..| .-...++.|-|++=. +++.++.+ ++ + ..||+|.+.|+
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 SKDIKELSTD-DKNVTVTGRVLTIGERSIRYQGDDHVIYEGILADETGT---ISYTAWKD----FG-L-SPGDTVTIGNA 127 (423)
T ss_pred CccHhhCCCC-CceeEEEEEEEEecceeEecCCCceEEEEEEEECCCCe---EEEEEECC----CC-C-CCCCEEEEecc
Confidence 4568888633 45799999999996521 2234 367889999998652 89999984 23 6 79999999999
Q ss_pred EEEEEcCeeEEEecCCceEEEEEeCCCCCCCCccccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCcccccccccccCC
Q 012503 88 MIKKHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSLKDISEH 167 (462)
Q Consensus 88 ki~~~~g~~~~~~~~~~ss~~lf~~~~~~~~~Py~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~f~~~L~di~~~ 167 (462)
.++.|+|++.+..+.. +....-+.. ..| . +. . . .. ..|.|++++
T Consensus 128 ~vre~~g~~el~ig~~-t~I~~~de~----~~~-~-----~~-----------~-----------~--~~-~kI~DL~~g 171 (423)
T PRK07218 128 GVREWDGRPELNIGES-TTVSLLDDS----SLP-P-----YS-----------I-----------G--GD-KKLIDLGPG 171 (423)
T ss_pred EeeccCCceEEeccCc-ceEEEcCcc----ccc-C-----cc-----------c-----------c--Cc-cchhhccCC
Confidence 9999999999887754 545532221 111 0 10 0 0 11 468899865
Q ss_pred -ceeeeEEEEEEEeeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCChhccccCCCcceEEEEEeccc
Q 012503 168 -RYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRVSTDRS 246 (462)
Q Consensus 168 -~f~Dlv~qVv~v~~~~~~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~p~~G~~l~V~~~~~ 246 (462)
..+++.++|+.++ + + .+..-||+. ... ...+.|+ . | ++++++|.+
T Consensus 172 ~~~V~v~g~Vl~~~-~----r-~f~~~dg~~--~v~-~giigDe-----------------T-------G-~Ir~tlW~~ 217 (423)
T PRK07218 172 DRGVNVEARVLELE-H----R-EIDGRDGET--TIL-SGVLADE-----------------T-------G-RLPFTDWDP 217 (423)
T ss_pred CCceEEEEEEEEec-c----e-eEEcCCCCe--EEE-EEEEECC-----------------C-------c-eEEEEEecc
Confidence 4589999999885 3 1 233445432 111 1111110 0 2 569999997
Q ss_pred chhhhcccCCCCCEEEEEceEEEEeCcEEEEEEeeCCceEEcCCCChhHHH-HHhhhhcCCCCCCCCcCCCCCCcccc--
Q 012503 247 YENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDNDNVVWD-YMRERISGGHGHMPIWTDPSSQFLTE-- 323 (462)
Q Consensus 247 ~~~~~~~~~k~g~wV~l~Nv~~k~~~g~leG~l~~~ski~~l~~~d~~v~~-~~rer~~~~~~~~~~~~~p~~~~it~-- 323 (462)
++ .+.+|++|+|.|...+.++|.++-.+...+.|..++.+ ..+.. ..+..+..-.. +...+ ...++.
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-----EIEIGASIRIEDAYVREFRGVPSVNVSEFTTVEALDRE-VSVSKDPPRLKIREAVE--RGGIF--DVELVGNI 287 (423)
T ss_pred cc-----cCCCCCEEEEeeeEEeccCCeEEEEECCceEEEECCCC-ccccCCccccchhhhhc--cCCcc--eEEEEEEE
Confidence 65 37899999999999999999999999999999876643 11110 00000000000 00000 000110
Q ss_pred cccCCCCcccHHHHh-hCCCCCceEEEEEEEEeecCCcccccccC----CCceEEEEEEEEeCCCceEEEEEeccccccc
Q 012503 324 VDWVNVASVTLMKIA-TQLQGNVRCCCIVRVVSIHPFQAEHYSSP----NGSSEYTMKLTLEDPTARIHALLCGKEWVKF 398 (462)
Q Consensus 324 ~~~~~~p~ttL~dIL-~~p~v~~kfr~~VRVV~~~P~~~edf~~~----~~~w~~~f~L~lED~t~ri~~~v~~~da~~f 398 (462)
++...- +=++ .+|. +=||++- -.|.. .+.+-=|....|.|.|+.+.+++..+.++.+
T Consensus 288 v~i~~g-----sgli~rCP~-------C~r~v~~------~~C~~hG~ve~~~dlrik~vLDDGtg~~~~~~~~e~~e~l 349 (423)
T PRK07218 288 ISVRDG-----SGLIERCPE-------CGRVIQK------GQCRSHGAVEGEDDLRIKAILDDGTGSVTVILDRELTEIV 349 (423)
T ss_pred EEeccC-----CcceecCcC-------ccccccC------CcCCCCCCcCCeeeeEEEEEEECCCCeEEEEEChhhhHhH
Confidence 010000 0011 1332 1133321 22332 3456678999999999999999999999999
Q ss_pred cCC
Q 012503 399 FGG 401 (462)
Q Consensus 399 ~~~ 401 (462)
.|.
T Consensus 350 ~G~ 352 (423)
T PRK07218 350 YGG 352 (423)
T ss_pred hCC
Confidence 986
No 9
>PRK14699 replication factor A; Provisional
Probab=99.02 E-value=3.8e-07 Score=96.64 Aligned_cols=272 Identities=19% Similarity=0.211 Sum_probs=181.5
Q ss_pred eehhhhhhccCCeEEEEEEEEecCCccc---cCCCc-eEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEee
Q 012503 11 VRIKELAMHVKHKVNLLGVVLEFSIPRK---SQGTD-YVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKN 86 (462)
Q Consensus 11 ~~i~d~~~~~~~~vnviGVVvd~~~P~~---trG~D-~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~r 86 (462)
..|+|+... ...||+.|-|+...+|+. ..|+. -..++.|-|+|= .+++.++.+..+.+|.+ ..||+|++.+
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 QKIKDIKDG-MGDLNLTGKVLEISEIRTFQRKDGTSGKVGNLLLGDETG---TLRVTLWDDKTDFLNQI-EYGDTVELIN 241 (484)
T ss_pred cchhhcCCC-CCceEEEEEEEeccCceEEecCCCCceEEEEEEEEcCCc---eEEEEEECccccccccc-CCCCEEEEec
Confidence 467776532 235999999999988864 23533 677889999976 39999999877777888 7999999998
Q ss_pred EEEE--EEcCeeEEEecCCceEEEEEeCCCCCCCCccccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCcccccccccc
Q 012503 87 VMIK--KHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSLKDI 164 (462)
Q Consensus 87 vki~--~~~g~~~~~~~~~~ss~~lf~~~~~~~~~Py~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~f~~~L~di 164 (462)
+.++ .|+|.+.+..+.. +... ......+ +.. .+ ..|.+|
T Consensus 242 a~vr~~~~~~~~el~~~~~-s~i~--~~~~~~e----------~~~-------------------------~~-~~I~~L 282 (484)
T PRK14699 242 AYARENAFTQKVELQVGNR-SIIR--KSEKKVE----------YEE-------------------------EF-TPIEDI 282 (484)
T ss_pred ceEeecccCCceEEEecCc-eEee--ccccccc----------ccc-------------------------cc-cCHHHc
Confidence 8765 5788888877643 3222 1100000 000 13 457777
Q ss_pred cC-CceeeeEEEEEEEeeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCChhccccCCCcceEEEEEe
Q 012503 165 SE-HRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRVST 243 (462)
Q Consensus 165 ~~-~~f~Dlv~qVv~v~~~~~~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~p~~G~~l~V~~ 243 (462)
++ +..+++.++|+++. + -..+. --||++-.-+ +..+.++ =| .+|+|+
T Consensus 283 ~~~~~~v~I~grV~~~~-~--~r~~~--~~~Gseg~v~--~~~l~De------------------------TG-~Ir~T~ 330 (484)
T PRK14699 283 KADMNNINISGRVLDIS-E--VRTFE--KKDGSPGRVG--NLLLGDS------------------------TG-KIRLTL 330 (484)
T ss_pred CCCCceeEEEEEEEEcC-C--CeEEE--cCCCCeeEEE--EEEEECC------------------------CC-eEEEEE
Confidence 75 48899999999776 3 11211 2233211111 1111110 15 479999
Q ss_pred cccchhhhcccCCCCCEEEEEceEEEEe--CcEEEEEEeeCCceEEcCCCChhHHHHHhhhhcCCCCCCCCcCCCCCCcc
Q 012503 244 DRSYENFGRYFTATGKWVRIRNMSCQVS--SGMWHGLLQSSSKIRLFSDNDNVVWDYMRERISGGHGHMPIWTDPSSQFL 321 (462)
Q Consensus 244 ~~~~~~~~~~~~k~g~wV~l~Nv~~k~~--~g~leG~l~~~ski~~l~~~d~~v~~~~rer~~~~~~~~~~~~~p~~~~i 321 (462)
|++.+.+ ...+++|+.+++.|...+.+ +|.+|-.+...+.|...+++ .
T Consensus 331 W~~~a~~-~~~i~~Gd~v~i~~~y~~~~~~~~~~eL~~~~~t~I~~~~~~-~---------------------------- 380 (484)
T PRK14699 331 WDEKTNF-LDEIDFDETVEVLNAYSRENTFSQQVELNLGARGIIQKSEKK-V---------------------------- 380 (484)
T ss_pred eCccccc-ccccCCCceEEEEeEEEEeccCCccEEEEecCceeEeecCCc-c----------------------------
Confidence 9999865 67799999999999998875 36788888877766432211 0
Q ss_pred cccccCCCCcccHHHHhhCCCCCceEEEEEEEEeecCCcccccccCCCceEEEEEEEEeCCCceEEEEEeccccccc
Q 012503 322 TEVDWVNVASVTLMKIATQLQGNVRCCCIVRVVSIHPFQAEHYSSPNGSSEYTMKLTLEDPTARIHALLCGKEWVKF 398 (462)
Q Consensus 322 t~~~~~~~p~ttL~dIL~~p~v~~kfr~~VRVV~~~P~~~edf~~~~~~w~~~f~L~lED~t~ri~~~v~~~da~~f 398 (462)
++ ..+++.|.||-. ...+-..-+|+++.|.. .|.+.+|.=-++--|+|.|.|+++.+-++|+.|+.|
T Consensus 381 ---e~-~~~~~~I~die~----~~~vdV~G~V~~v~~~~--~~~~~~g~~~~vr~i~l~D~TG~Ir~tlWg~~A~~~ 447 (484)
T PRK14699 381 ---EY-REKFTDIADIIP----GESYSVQGKVSEIGELR--EFEREDGTENVVANLQLKDETGSIRLTLWGEQAYVI 447 (484)
T ss_pred ---ee-eeccccHHHccC----CCeeEEEEEEEEcCCcc--eEEecCCCEEEEEEEEEEcCCCeEEEEEcchhhhhc
Confidence 00 124666888832 33567777888888865 666655644467789999999999999999999865
No 10
>PRK06386 replication factor A; Reviewed
Probab=98.96 E-value=3.1e-06 Score=86.15 Aligned_cols=275 Identities=16% Similarity=0.144 Sum_probs=163.6
Q ss_pred eehhhhhhccCCeEEEEEEEEecCCc-ccc-CCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEE
Q 012503 11 VRIKELAMHVKHKVNLLGVVLEFSIP-RKS-QGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVM 88 (462)
Q Consensus 11 ~~i~d~~~~~~~~vnviGVVvd~~~P-~~t-rG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvk 88 (462)
+.|+|+... +..||+.|-|++.... .++ +|.--..+-.|-|++=. +++.+..+ .|.+ ..||+|+|.|++
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 SKISDINAA-RQNVDLKVKVLSLNKRTIKNDRGETIYYYGIIGDETGT---VPFTAWEF----PDAV-KSGDVIEIKYCY 73 (358)
T ss_pred cchhhcCCC-CCcEEEEEEEEEccceEEecCCCCeEEEEEEEECCcce---EEEEecCC----cccC-CCCCEEEEEeEE
Confidence 357777622 4469999999999731 112 34334445557777542 77887763 4667 689999999999
Q ss_pred EEEEcCeeEEEecCCceEEEEEeCCCCCCCCccccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCcccccccccccCC-
Q 012503 89 IKKHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSLKDISEH- 167 (462)
Q Consensus 89 i~~~~g~~~~~~~~~~ss~~lf~~~~~~~~~Py~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~f~~~L~di~~~- 167 (462)
++.|+|++.+..+.. +.... .. +... + ..+. . +. ..|+||+++
T Consensus 74 v~~~~G~~~Lnv~~~-t~v~~-~~--d~~i-e---------v~~~------------------~---~~-~KI~DL~~g~ 117 (358)
T PRK06386 74 SKEYNGKIRIYFDSR-SEVML-KP--DENI-E---------VKRT------------------Y---KL-VKIRDLSLVT 117 (358)
T ss_pred EeeECCEEEEEEcCc-eEEEe-cC--cccc-c---------cccc------------------c---Cc-cEeEeccCCC
Confidence 999999998877744 43321 11 1110 0 0000 0 12 579999865
Q ss_pred ceeeeEEEEEEEeeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCChhccccCCCcceEEEEEecccc
Q 012503 168 RYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRVSTDRSY 247 (462)
Q Consensus 168 ~f~Dlv~qVv~v~~~~~~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~p~~G~~l~V~~~~~~ 247 (462)
.++++.++|+.++ + . .+- .||+..--. ...+.|+ . | .+++++|..
T Consensus 118 ~~v~V~akVle~~-e---~--e~~-~~g~~~~v~--sg~lgDe-----------------T-------G-rIr~TlW~~- 162 (358)
T PRK06386 118 PYVSVIGKITGIT-K---K--EYD-SDGTSKIVY--QGYIEDD-----------------T-------A-RVRISSFGK- 162 (358)
T ss_pred CceEEEEEEEEcc-C---c--eEe-cCCCccEEE--EEEEEcC-----------------C-------C-eEEEEEccc-
Confidence 5679999999876 3 1 222 455421110 1101110 0 2 568999985
Q ss_pred hhhhcccCCCCCEEEEEceEEEEeCcEEEEEEeeCCceEEcCCCChhHHHHHhhhhcCCCCCCCCcCCCCCCcccccccC
Q 012503 248 ENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDNDNVVWDYMRERISGGHGHMPIWTDPSSQFLTEVDWV 327 (462)
Q Consensus 248 ~~~~~~~~k~g~wV~l~Nv~~k~~~g~leG~l~~~ski~~l~~~d~~v~~~~rer~~~~~~~~~~~~~p~~~~it~~~~~ 327 (462)
.++.|+.|+|.|...+.+.|.++-.+...+.|..++.+- .+... +..+. .+-.....+++.
T Consensus 163 ------~l~eGd~v~i~na~v~e~~G~~el~v~~~t~I~~~~~~i-ev~~~-~~~I~---------di~~~~g~v~i~-- 223 (358)
T PRK06386 163 ------PLEDNRFVRIENARVSQYNGYIEISVGNKSVIKEVESDI-NLESR-NIFIF---------EIKSPVGGITIM-- 223 (358)
T ss_pred ------cccCCCEEEEeeeEEEccCCeEEEEeCCeEEEEECCCCc-ccCcc-ccchh---------hhhccCCeEEEE--
Confidence 378999999999999999999999999988887665421 11110 00000 000000000000
Q ss_pred CCCcccHHHHh-------hCCCCCceEEEEEEEEeecCCcccccccCCC----ceEEEEEEEEeCCCceEEEEEeccccc
Q 012503 328 NVASVTLMKIA-------TQLQGNVRCCCIVRVVSIHPFQAEHYSSPNG----SSEYTMKLTLEDPTARIHALLCGKEWV 396 (462)
Q Consensus 328 ~~p~ttL~dIL-------~~p~v~~kfr~~VRVV~~~P~~~edf~~~~~----~w~~~f~L~lED~t~ri~~~v~~~da~ 396 (462)
=+|-+|- .+|. +=||++- -.|..+| .+--|..+.|-|.|+.+.+.++++.++
T Consensus 224 ----G~iv~i~~gsgli~rCP~-------C~R~l~~------g~C~~HG~v~~~~dlr~k~vLDDGtg~~~~~l~~e~~e 286 (358)
T PRK06386 224 ----GFIVSVGQGSRIFTKCSV-------CNKIIED------GVCKDHPDAPVYLDIFGYFTISDGTGFVTCYANKDSFL 286 (358)
T ss_pred ----EEEEEEcCCcEeEecCcC-------CCeEccC------CcCCCCCCCCCeeEEEEEEEEECCCCeEEEEEChHHhH
Confidence 0011111 1231 1244441 3565443 444567789999999999999999999
Q ss_pred cccCC
Q 012503 397 KFFGG 401 (462)
Q Consensus 397 ~f~~~ 401 (462)
.++|.
T Consensus 287 ~l~G~ 291 (358)
T PRK06386 287 PYINI 291 (358)
T ss_pred HHhCC
Confidence 99986
No 11
>PRK07211 replication factor A; Reviewed
Probab=98.95 E-value=5.8e-08 Score=102.00 Aligned_cols=204 Identities=16% Similarity=0.195 Sum_probs=145.1
Q ss_pred cceeehhhhhhccCCeEEEEEEEEecCCccc---cCC-CceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEE
Q 012503 8 GGIVRIKELAMHVKHKVNLLGVVLEFSIPRK---SQG-TDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLIL 83 (462)
Q Consensus 8 y~y~~i~d~~~~~~~~vnviGVVvd~~~P~~---trG-~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~ 83 (462)
..+.+|+++.. ....++|+|+|++..+++. .+| .-.+.++.|.|+|- . +++.+|.+..+.++.+ ..||||.
T Consensus 159 ~~~~~I~dL~~-~~~~v~I~grV~~v~~iRtf~r~dGseGkv~sv~L~DeTG-~--IR~TlW~d~Ad~~~~l-e~G~Vv~ 233 (485)
T PRK07211 159 GDTYTVEDLSL-GLSDVTLVGVVLDTDSVRTFDRDDGSEGRVSNLTVGDETG-R--VRVTLWDDRADLAEEL-DAGESVE 233 (485)
T ss_pred cCCccHHHcCC-CCCceEEEEEEEEcCCCeEEECCCCCeeEEEEEEEEcCCC-e--EEEEEechhhhhhccC-CCCCEEE
Confidence 36778999973 2456999999999998763 235 45678999999876 2 9999999887888878 7999999
Q ss_pred EeeEEEEEEcCeeEEEecCCceEEEEEeCCCCCCCCccccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCccccccccc
Q 012503 84 LKNVMIKKHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSLKD 163 (462)
Q Consensus 84 l~rvki~~~~g~~~~~~~~~~ss~~lf~~~~~~~~~Py~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~f~~~L~d 163 (462)
+.+++++.++|.+.+..+.. +...-... .....| .+ ..|.+
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 12 46788
Q ss_pred ccCCceeeeEEEEEEEeeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCChhccccCCCcceEEEEEe
Q 012503 164 ISEHRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRVST 243 (462)
Q Consensus 164 i~~~~f~Dlv~qVv~v~~~~~~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~p~~G~~l~V~~ 243 (462)
+.++..+|+++.|+.+. + ..++-=-||+...--. ..+.+ -=| .+||++
T Consensus 275 l~~g~~vdV~GvV~~v~-~----~rtf~r~dG~~~~vr~--l~l~D------------------------~TG-~IrvTL 322 (485)
T PRK07211 275 LEIDETVDIAGVVRSAD-P----KRTFDRDDGSEGQVRN--VRIQD------------------------DTG-DIRVAL 322 (485)
T ss_pred cCCCCceeEEEEEEEcc-C----cEEEEcCCCCEeEEEE--EEEEc------------------------CCC-cEEEEE
Confidence 88999999999999886 2 2222222344222111 00000 015 679999
Q ss_pred cccchhhhcccCCCCCEEEEEceEEEE-eCcEEEEEEeeCCceEEcCC
Q 012503 244 DRSYENFGRYFTATGKWVRIRNMSCQV-SSGMWHGLLQSSSKIRLFSD 290 (462)
Q Consensus 244 ~~~~~~~~~~~~k~g~wV~l~Nv~~k~-~~g~leG~l~~~ski~~l~~ 290 (462)
|.+++.+ .+.+|+.|+|.|++++- +.|-+|..+...+.|.+++.
T Consensus 323 Wg~~A~~---~i~~GdvV~Ikg~~V~dg~~ggleLS~g~~s~i~~~~~ 367 (485)
T PRK07211 323 WGEKADL---DIGPGDEVVAADVEIQDGWQDDLEASAGWQSTVVVLDD 367 (485)
T ss_pred eCccccC---CCCCCCEEEEEccEEEecCCCCEEEEecCCceEEEccc
Confidence 9999953 68999999999999999 44778888888888988765
No 12
>PRK15491 replication factor A; Provisional
Probab=98.94 E-value=8e-07 Score=91.57 Aligned_cols=271 Identities=15% Similarity=0.194 Sum_probs=177.5
Q ss_pred eeehhhhhhccCCeEEEEEEEEecCCccc---cCC-CceEEEEEEEeCCCCCCCeEEEEecCCCCCC--CCCCCCCCEEE
Q 012503 10 IVRIKELAMHVKHKVNLLGVVLEFSIPRK---SQG-TDYVCVLKIVDDSQQSPELLVNIFTSSIDQL--PRVLSPRDLIL 83 (462)
Q Consensus 10 y~~i~d~~~~~~~~vnviGVVvd~~~P~~---trG-~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~L--P~v~~~GDII~ 83 (462)
-++|+|+... ...|++.|-|+....|+. .+| .-...++.|.|+|=. +++.+|.+..+.+ |.+ .+||++.
T Consensus 57 ~~kI~dL~~~-~~~v~i~arVl~~~~~R~f~r~dGs~g~v~~~~v~DeTG~---ir~tlW~~~a~~~~~~~l-e~G~v~~ 131 (374)
T PRK15491 57 TTKIADINES-SSNVNFTAKVVSIFEPKEFNRNDGTTGRVGNIIVADETGS---IRLTLWDDLADLIKTGDI-EVGKSLN 131 (374)
T ss_pred cccHHHCCCC-CCceEEEEEEeeccCCeeeecCCCCceEEEEEEEEcCCCe---EEEEEECchhhhhccCCc-CCCCEEE
Confidence 4578998632 256999999999988864 246 467889999997652 9999999765555 678 6999999
Q ss_pred EeeEEEEEEcCeeEEEecCCceEEEEEeCCCCCCCCccccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCccccccccc
Q 012503 84 LKNVMIKKHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSLKD 163 (462)
Q Consensus 84 l~rvki~~~~g~~~~~~~~~~ss~~lf~~~~~~~~~Py~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~f~~~L~d 163 (462)
++..--..|+| +.+..+.. +... ... ... + . ...| ..|+|
T Consensus 132 I~~~~~~~y~g-~Ei~i~~~-~~i~---~~~-~~~-~-------~-------------------------~~~~-~~I~d 171 (374)
T PRK15491 132 ISGYAKEGYSG-IEVNIGRY-GGIS---ESD-ENV-K-------A-------------------------SINS-QKISD 171 (374)
T ss_pred EeeeeccCccc-EEEEeCCC-ceee---ecc-ccc-c-------c-------------------------ccCc-ccHHH
Confidence 99875556766 55555533 3221 000 000 0 0 0024 56777
Q ss_pred ccCC-ceeeeEEEEEEEeeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCChhccccCCCcceEEEEE
Q 012503 164 ISEH-RYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRVS 242 (462)
Q Consensus 164 i~~~-~f~Dlv~qVv~v~~~~~~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~p~~G~~l~V~ 242 (462)
|..+ ..+|+.++|+.+. + ...+. --||+....+. ..+.+ + =|. ++++
T Consensus 172 l~~~~~~V~I~g~V~~~~-~--~r~~~--~~~G~~~~v~~--~~l~D-----------------e-------tG~-Ir~t 219 (374)
T PRK15491 172 IKDGDSDINIVGKVLDIS-D--VRTFQ--KKDGSQGRVRN--ITIGD-----------------E-------TGK-IRVT 219 (374)
T ss_pred cCCCCccEEEEEEEEEcc-C--ceEEE--ecCCCeEEEEE--EEEEC-----------------C-------CCe-EEEE
Confidence 7654 5699999999887 3 12222 12343211111 10000 0 154 7999
Q ss_pred ecccchhhhcccCCCCCEEEEEceEEEE--eCcEEEEEEeeCCceEEcCCCChhHHHHHhhhhcCCCCCCCCcCCCCCCc
Q 012503 243 TDRSYENFGRYFTATGKWVRIRNMSCQV--SSGMWHGLLQSSSKIRLFSDNDNVVWDYMRERISGGHGHMPIWTDPSSQF 320 (462)
Q Consensus 243 ~~~~~~~~~~~~~k~g~wV~l~Nv~~k~--~~g~leG~l~~~ski~~l~~~d~~v~~~~rer~~~~~~~~~~~~~p~~~~ 320 (462)
+|+.++.. ...+++|+-|++.|-.++. ..|.+|-.+..++.|...+. +.
T Consensus 220 ~W~~~a~~-~~~l~~Gd~V~i~~~~~r~~~~~g~~El~~~~~s~I~~~~~-~~--------------------------- 270 (374)
T PRK15491 220 LWDGKTDL-ADKLENGDSVEIINGYARTNNYSQEVEIQIGNHGSLRKTDR-NV--------------------------- 270 (374)
T ss_pred Eecchhcc-cccCCCCCEEEEEeceEEEeccCCCEEEEeCCCceEEECCc-cc---------------------------
Confidence 99999886 4779999999999987776 45788888888888764322 11
Q ss_pred ccccccCCCCcccHHHHhhCCCCCceEEEEEEEEeecCCcccccccCCCceEEEEEEEEeCCCceEEEEEecccccc
Q 012503 321 LTEVDWVNVASVTLMKIATQLQGNVRCCCIVRVVSIHPFQAEHYSSPNGSSEYTMKLTLEDPTARIHALLCGKEWVK 397 (462)
Q Consensus 321 it~~~~~~~p~ttL~dIL~~p~v~~kfr~~VRVV~~~P~~~edf~~~~~~w~~~f~L~lED~t~ri~~~v~~~da~~ 397 (462)
++ ...+++|.||-.. ..+-...+|....|. ..|.+.+|.=...=-|+|.|.|++|++-++|+.|+.
T Consensus 271 ----e~-~~~f~~I~dl~~~----~~~dv~G~V~~v~~~--~~~~~~~G~~~~~r~i~l~D~Tg~Ir~tlWg~~a~~ 336 (374)
T PRK15491 271 ----EY-EEDFTPIADIIPG----QPYSIKGAVSGLGDL--KEFTKSDGSENKVSNIYVSDDTGRIRIALWGEKAEL 336 (374)
T ss_pred ----cc-CCCccCHHHcCCC----CceeEEEEEEEcCCc--EEEEccCCCEeEEEeEEEEeCCCcEEEEEccccccc
Confidence 00 0134557777632 235666777777664 455555564456668899999999999999999985
No 13
>PRK15491 replication factor A; Provisional
Probab=98.81 E-value=3.8e-07 Score=93.93 Aligned_cols=204 Identities=16% Similarity=0.183 Sum_probs=141.5
Q ss_pred CCcceeehhhhhhccCCeEEEEEEEEecCCcccc---CCC-ceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCE
Q 012503 6 NQGGIVRIKELAMHVKHKVNLLGVVLEFSIPRKS---QGT-DYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDL 81 (462)
Q Consensus 6 ~~y~y~~i~d~~~~~~~~vnviGVVvd~~~P~~t---rG~-D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDI 81 (462)
.+|.+++|+++... ...|+|.|+|++..+++.= +|+ -...++.|.|.|- .+++.+|.+..+.++.+ .+||+
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 ASINSQKISDIKDG-DSDINIVGKVLDISDVRTFQKKDGSQGRVRNITIGDETG---KIRVTLWDGKTDLADKL-ENGDS 236 (374)
T ss_pred cccCcccHHHcCCC-CccEEEEEEEEEccCceEEEecCCCeEEEEEEEEECCCC---eEEEEEecchhcccccC-CCCCE
Confidence 34667899998642 3359999999999887532 355 4788899999865 29999999876777777 79999
Q ss_pred EEEeeEEEE--EEcCeeEEEecCCceEEEEEeCCCCCCCCccccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCccccc
Q 012503 82 ILLKNVMIK--KHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLL 159 (462)
Q Consensus 82 I~l~rvki~--~~~g~~~~~~~~~~ss~~lf~~~~~~~~~Py~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~f~~ 159 (462)
|.+.+..++ .|+|++.+..+.. +.... ..... + +. ..| .
T Consensus 237 V~i~~~~~r~~~~~g~~El~~~~~-s~I~~--~~~~~---e-------~~-------------------------~~f-~ 277 (374)
T PRK15491 237 VEIINGYARTNNYSQEVEIQIGNH-GSLRK--TDRNV---E-------YE-------------------------EDF-T 277 (374)
T ss_pred EEEEeceEEEeccCCCEEEEeCCC-ceEEE--CCccc---c-------cC-------------------------CCc-c
Confidence 999997655 5778888887644 44331 11000 0 10 025 6
Q ss_pred ccccccCCceeeeEEEEEEEeeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCChhccccCCCcceEE
Q 012503 160 SLKDISEHRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVL 239 (462)
Q Consensus 160 ~L~di~~~~f~Dlv~qVv~v~~~~~~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~p~~G~~l 239 (462)
.|.||.++..+|+++.|..+. + .-++--.||+...--.+. +.| + =|. +
T Consensus 278 ~I~dl~~~~~~dv~G~V~~v~-~----~~~~~~~~G~~~~~r~i~--l~D-----------------~-------Tg~-I 325 (374)
T PRK15491 278 PIADIIPGQPYSIKGAVSGLG-D----LKEFTKSDGSENKVSNIY--VSD-----------------D-------TGR-I 325 (374)
T ss_pred CHHHcCCCCceeEEEEEEEcC-C----cEEEEccCCCEeEEEeEE--EEe-----------------C-------CCc-E
Confidence 788898899999999999885 2 112222444432111100 000 0 154 7
Q ss_pred EEEecccchhhhcccCCCCCEEEEEceEEEE-eCcEEEEEEeeCCceE
Q 012503 240 RVSTDRSYENFGRYFTATGKWVRIRNMSCQV-SSGMWHGLLQSSSKIR 286 (462)
Q Consensus 240 ~V~~~~~~~~~~~~~~k~g~wV~l~Nv~~k~-~~g~leG~l~~~ski~ 286 (462)
++++|..+|.. ...+-+|+.|++.+..+|. +.|-+|......|+|.
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 99999999985 5567889999999999999 6699999988888874
No 14
>PRK14699 replication factor A; Provisional
Probab=98.66 E-value=1.9e-06 Score=91.39 Aligned_cols=203 Identities=13% Similarity=0.161 Sum_probs=141.7
Q ss_pred ceeehhhhhhccCCeEEEEEEEEecCCccc---cCC-CceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEE
Q 012503 9 GIVRIKELAMHVKHKVNLLGVVLEFSIPRK---SQG-TDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILL 84 (462)
Q Consensus 9 ~y~~i~d~~~~~~~~vnviGVVvd~~~P~~---trG-~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l 84 (462)
.+++|.++.. -...+++.|.|++..+++. .+| .....++.|.|.|=. +++.+|.+..+.++.+ ..||+|.+
T Consensus 275 ~~~~I~~L~~-~~~~v~I~grV~~~~~~r~~~~~~Gseg~v~~~~l~DeTG~---Ir~T~W~~~a~~~~~i-~~Gd~v~i 349 (484)
T PRK14699 275 EFTPIEDIKA-DMNNINISGRVLDISEVRTFEKKDGSPGRVGNLLLGDSTGK---IRLTLWDEKTNFLDEI-DFDETVEV 349 (484)
T ss_pred cccCHHHcCC-CCceeEEEEEEEEcCCCeEEEcCCCCeeEEEEEEEECCCCe---EEEEEeCccccccccc-CCCceEEE
Confidence 5678888863 3467999999999988753 246 467789999999762 9999999877777877 79999999
Q ss_pred eeEEEEEE--cCeeEEEecCCceEEEEEeCCCCCCCCccccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCcccccccc
Q 012503 85 KNVMIKKH--QAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSLK 162 (462)
Q Consensus 85 ~rvki~~~--~g~~~~~~~~~~ss~~lf~~~~~~~~~Py~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~f~~~L~ 162 (462)
.++.++.. ++.+.+..+.. +.. ....+.. . + ...| +.|.
T Consensus 350 ~~~y~~~~~~~~~~eL~~~~~-t~I---~~~~~~~--------e-~-------------------------~~~~-~~I~ 390 (484)
T PRK14699 350 LNAYSRENTFSQQVELNLGAR-GII---QKSEKKV--------E-Y-------------------------REKF-TDIA 390 (484)
T ss_pred EeEEEEeccCCccEEEEecCc-eeE---eecCCcc--------e-e-------------------------eecc-ccHH
Confidence 99998833 45677777644 311 1111000 0 0 0036 7899
Q ss_pred cccCCceeeeEEEEEEEeeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCChhccccCCCcceEEEEE
Q 012503 163 DISEHRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRVS 242 (462)
Q Consensus 163 di~~~~f~Dlv~qVv~v~~~~~~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~p~~G~~l~V~ 242 (462)
||.+++.+|+++.|..+. + -..+. -.||+.-.--. ..+.| -=| .+|++
T Consensus 391 die~~~~vdV~G~V~~v~-~--~~~~~--~~~g~~~~vr~--i~l~D------------------------~TG-~Ir~t 438 (484)
T PRK14699 391 DIIPGESYSVQGKVSEIG-E--LREFE--REDGTENVVAN--LQLKD------------------------ETG-SIRLT 438 (484)
T ss_pred HccCCCeeEEEEEEEEcC-C--cceEE--ecCCCEEEEEE--EEEEc------------------------CCC-eEEEE
Confidence 999999999999999887 3 11111 13433211100 00000 015 78999
Q ss_pred ecccchhhhcccCCCCCEEEEEceEEEE-eCcEEEEEEeeCCceEEc
Q 012503 243 TDRSYENFGRYFTATGKWVRIRNMSCQV-SSGMWHGLLQSSSKIRLF 288 (462)
Q Consensus 243 ~~~~~~~~~~~~~k~g~wV~l~Nv~~k~-~~g~leG~l~~~ski~~l 288 (462)
+|...|.. .+.+.+|+-|.+.|..++. .+|.+|..+-..|+|.+|
T Consensus 439 lWg~~A~~-~~~~~~~~~v~~~~~~~~~g~~~~~e~s~g~~s~~~~~ 484 (484)
T PRK14699 439 LWGEQAYV-IEDLDIDSEIQIIDAYARYGLNEEIELSVGNRSRVIIL 484 (484)
T ss_pred Ecchhhhh-ccccCCCCeEEEechhhhhcccccEEEEecCceEEEeC
Confidence 99988874 5789999999999999999 578999999888887543
No 15
>KOG4757 consensus Predicted telomere binding protein [General function prediction only]
Probab=98.53 E-value=3.6e-09 Score=106.44 Aligned_cols=117 Identities=12% Similarity=0.207 Sum_probs=80.9
Q ss_pred CceEEEEEEEEeecCCcccccccC---CCceEEEEEEEEeCC-CceEEEEEeccccccccCC---CCC-h------HHHH
Q 012503 344 NVRCCCIVRVVSIHPFQAEHYSSP---NGSSEYTMKLTLEDP-TARIHALLCGKEWVKFFGG---SPP-P------DVLT 409 (462)
Q Consensus 344 ~~kfr~~VRVV~~~P~~~edf~~~---~~~w~~~f~L~lED~-t~ri~~~v~~~da~~f~~~---~~~-~------~~l~ 409 (462)
+.+++..+.+++++|..+..|.+. ..+++|+|.++|-|. .+.+++.-..-||.-|-++ ++. + -++.
T Consensus 378 ~r~H~~l~~le~s~p~s~~~fgc~~~~~~~~v~~ln~Lv~~e~~~~vP~~~~~v~~~~l~~~s~~l~~~l~d~~~~fqi~ 457 (522)
T KOG4757|consen 378 PRKHRLLVQLEDSWPKSLTQFGCLSQPPSSYVWMLNLLVRDESNVTVPVIFFDVDAAELINSSKKLPCNLADHQMTFQIK 457 (522)
T ss_pred hhhhhhhhhhcccCcccceeeeeccCCHHHHHHHHHHHhccccccccccccchhheeeeccccccccchhccccceEEec
Confidence 447999999999999999999873 335677777777774 3455555555554433332 121 1 1566
Q ss_pred HHHHHHcCCCCCC------CCC--CCCcCCCcceeEeeeeeeecCCc------eEEEEEeeeEEc
Q 012503 410 KKIKMLLGMPEHE------DGN--DDMVRNPPWIKCFLHLKESDGGR------NRVYYIRWTKLV 460 (462)
Q Consensus 410 ~kl~~L~G~~e~~------~~~--~~~~~~~p~~~cCi~sY~v~~~~------~r~f~~F~T~i~ 460 (462)
+.+...||+||++ ++. .......|||+|-||||.+..+. +.|++-|||+|+
T Consensus 458 ds~il~~~~l~~~i~~~~~~~~~p~~~~~~~pw~~~~vk~y~i~n~~d~q~~~q~~~~~~~~~iv 522 (522)
T KOG4757|consen 458 DSLILIWGNLEERIQHHISKGESPTLAAEETPWFDIYVKEYIIGNTKDHQSLLQKRWRGFGTKIV 522 (522)
T ss_pred ceeeeecccHHHHHHHHHhcCCCCcccccccccceeeeeeeeecCCcchHHHHHHHhhccccccC
Confidence 7788888888864 232 11224789999999999988654 888888888874
No 16
>PRK07211 replication factor A; Reviewed
Probab=98.47 E-value=0.00016 Score=76.32 Aligned_cols=269 Identities=15% Similarity=0.154 Sum_probs=169.0
Q ss_pred eeehhhhhhccC-CeEEEEEEEEecCCcccc-C----CCceEEEEEEEeCCCCCCCeEEEEecCCCC-CCCCCCCCCCEE
Q 012503 10 IVRIKELAMHVK-HKVNLLGVVLEFSIPRKS-Q----GTDYVCVLKIVDDSQQSPELLVNIFTSSID-QLPRVLSPRDLI 82 (462)
Q Consensus 10 y~~i~d~~~~~~-~~vnviGVVvd~~~P~~t-r----G~D~~~tl~I~D~s~~~~gl~v~iF~~~~~-~LP~v~~~GDII 82 (462)
..+|+++. ++ ..|++.|-|+..+.|+.= + +.--.+++.|.|+|= .|++.+|....+ ..|.+ ++|||+
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 VNGIADIE--PGMDEVKFLAKVLSIGDLRTFERDGEDEDGRVINVEVADETG---SVRVAFWDEQAVAAEEEL-EVGQVL 126 (485)
T ss_pred cccHhhCC--CCCCceEEEEEEeEccCceEEEeCCCCCCcEEEEEEEEcCCC---eEEEEEechHhHhhhccc-CCCCEE
Confidence 34788886 55 459999999999987642 2 235899999999765 399999975432 46778 799999
Q ss_pred EEeeEEEEEEcCeeEEEecCCceEEEEEeCCCCCCCCccccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCcccccccc
Q 012503 83 LLKNVMIKKHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSLK 162 (462)
Q Consensus 83 ~l~rvki~~~~g~~~~~~~~~~ss~~lf~~~~~~~~~Py~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~f~~~L~ 162 (462)
.+++.-...|++ +.+..+ . ........+ |++ .. .| ..|+
T Consensus 127 ~I~~~~~~~ys~-~El~i~----~---ve~~~d~~i-~~~------------------------------~~-~~-~~I~ 165 (485)
T PRK07211 127 RIKGRPKDGYNG-LEVSVD----K---VEPDPDAEI-DVQ------------------------------IG-DT-YTVE 165 (485)
T ss_pred EEeceEeccccc-eEEEEe----e---EEEcccccc-ccc------------------------------cc-CC-ccHH
Confidence 998754444444 222222 0 111000010 000 00 24 6788
Q ss_pred cccCC-ceeeeEEEEEEEeeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCChhccccCCCcceEEEE
Q 012503 163 DISEH-RYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRV 241 (462)
Q Consensus 163 di~~~-~f~Dlv~qVv~v~~~~~~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~p~~G~~l~V 241 (462)
||+++ ..+|++++|+.+. +. ..+ -=-||++-.-+. ..+-+ + =| .+|+
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-------TG-RVRV 213 (485)
T ss_pred HcCCCCCceEEEEEEEEcC-CC--eEE--ECCCCCeeEEEE--EEEEc-----------------C-------CC-eEEE
Confidence 88865 5689999999776 31 010 011222111111 00000 0 15 4799
Q ss_pred EecccchhhhcccCCCCCEEEEEceEEEEeCcEEEEEEeeCCceEEcCCCChhHHHHHhhhhcCCCCCCCCcCCCCCCcc
Q 012503 242 STDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDNDNVVWDYMRERISGGHGHMPIWTDPSSQFL 321 (462)
Q Consensus 242 ~~~~~~~~~~~~~~k~g~wV~l~Nv~~k~~~g~leG~l~~~ski~~l~~~d~~v~~~~rer~~~~~~~~~~~~~p~~~~i 321 (462)
|+|+.++... ..+.+|+-|+|.|.+++...|-+|-.+..++.|..++.+-. .+ |.
T Consensus 214 TlW~d~Ad~~-~~le~G~Vv~I~~a~Vre~~g~~ELsl~~~s~I~~~~dev~---------------~v-----p~---- 268 (485)
T PRK07211 214 TLWDDRADLA-EELDAGESVEIVDGYVRERDGSLELHVGDRGAVEEVDEDVE---------------YV-----PD---- 268 (485)
T ss_pred EEechhhhhh-ccCCCCCEEEEEeeEEEecCCcEEEEECCCceEEECCcccc---------------cc-----cc----
Confidence 9999998873 77999999999999999988888888888888876543200 00 00
Q ss_pred cccccCCCCcccHHHHhhCCCCCceEEEEEEEEeecCCcccccccCCCceEEEEEEEEeCCCceEEEEEecccccc
Q 012503 322 TEVDWVNVASVTLMKIATQLQGNVRCCCIVRVVSIHPFQAEHYSSPNGSSEYTMKLTLEDPTARIHALLCGKEWVK 397 (462)
Q Consensus 322 t~~~~~~~p~ttL~dIL~~p~v~~kfr~~VRVV~~~P~~~edf~~~~~~w~~~f~L~lED~t~ri~~~v~~~da~~ 397 (462)
++.|.++-. ..-.-...+|.+..|... |.+.+|+=-..--++|-|.|+++++-++|+.|..
T Consensus 269 ---------~~~I~dl~~----g~~vdV~GvV~~v~~~rt--f~r~dG~~~~vr~l~l~D~TG~IrvTLWg~~A~~ 329 (485)
T PRK07211 269 ---------TTPIESLEI----DETVDIAGVVRSADPKRT--FDRDDGSEGQVRNVRIQDDTGDIRVALWGEKADL 329 (485)
T ss_pred ---------cccHhhcCC----CCceeEEEEEEEccCcEE--EEcCCCCEeEEEEEEEEcCCCcEEEEEeCccccC
Confidence 123333321 112456677888777654 4455563346778999999999999999999853
No 17
>PRK08402 replication factor A; Reviewed
Probab=98.35 E-value=3.8e-05 Score=78.45 Aligned_cols=195 Identities=15% Similarity=0.151 Sum_probs=113.6
Q ss_pred cccccccCC-ceeeeEEEEEEEeeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCChhccccCCCcce
Q 012503 159 LSLKDISEH-RYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGT 237 (462)
Q Consensus 159 ~~L~di~~~-~f~Dlv~qVv~v~~~~~~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~p~~G~ 237 (462)
..|+||.++ ..++++++|+.+. +.. .+ ---||+...-. +..+.| + -|+
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--EY--TKKDGSTGRVA--SLIIYD-----------------D-------TGR 111 (355)
T ss_pred cCHHHccCCCceeeEEEEEEEcc-CCc--ee--eccCCCcceEE--EEEEEc-----------------C-------CCe
Confidence 679999987 5899999999887 311 10 00122211000 000000 0 044
Q ss_pred EEEEEecccchhhhcccCCCCCEEEEEceEEEE-eCcEEEEEEeeCCceEEcCCCChhHHHHHhhhhcCCCCCCCCcCCC
Q 012503 238 VLRVSTDRSYENFGRYFTATGKWVRIRNMSCQV-SSGMWHGLLQSSSKIRLFSDNDNVVWDYMRERISGGHGHMPIWTDP 316 (462)
Q Consensus 238 ~l~V~~~~~~~~~~~~~~k~g~wV~l~Nv~~k~-~~g~leG~l~~~ski~~l~~~d~~v~~~~rer~~~~~~~~~~~~~p 316 (462)
+ ++++|+.++.-....+.+|+-|+|.|..++. ++|..+-.+...|.|.+.++ ++.+.+ + |
T Consensus 112 i-r~TlW~~~a~~~~~~l~~Gdvi~I~~a~V~e~~~G~~eLsvg~~s~i~~~pd-~~ea~~-----i-------~----- 172 (355)
T PRK08402 112 A-RVVLWDAKVAKYYNKINVGDVIKVIDAQVRESLSGLPELHINFRARIILNPD-DPRVEE-----I-------P----- 172 (355)
T ss_pred E-EEEEechhhhhhcccCCCCCEEEEECCEEeecCCCcEEEEECCCceEEeCCC-cccccc-----c-------c-----
Confidence 4 8999998876334669999999999999998 69998999999898865443 332211 0 0
Q ss_pred CCCcccccccCCCCcccHHHHhhCCCCCceEEEEEEEEeecCCcc--------cc---------c-cc--C--CCceEEE
Q 012503 317 SSQFLTEVDWVNVASVTLMKIATQLQGNVRCCCIVRVVSIHPFQA--------EH---------Y-SS--P--NGSSEYT 374 (462)
Q Consensus 317 ~~~~it~~~~~~~p~ttL~dIL~~p~v~~kfr~~VRVV~~~P~~~--------ed---------f-~~--~--~~~w~~~ 374 (462)
....+. .. ..+..+|.||-... .=|.+...|+.+.+..+ +. + |. + ...|.|+
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 12233344442110 00233333333333000 00 0 11 1 3578899
Q ss_pred EEEEEeCCCceEEEEEeccccccccCCCCChHHHHHH
Q 012503 375 MKLTLEDPTARIHALLCGKEWVKFFGGSPPPDVLTKK 411 (462)
Q Consensus 375 f~L~lED~t~ri~~~v~~~da~~f~~~~~~~~~l~~k 411 (462)
+.+.|-|.|+++++.++++.|+.++|. +.+.|.+.
T Consensus 247 l~~~l~D~TG~~~vt~f~e~ae~llG~--sa~el~~~ 281 (355)
T PRK08402 247 LDFGLDDGTGYIRVTLFGDDAAELLGV--EPEEIAEK 281 (355)
T ss_pred EEEEEEcCCCcEEEEEecHHHHHHhCC--CHHHHHHH
Confidence 999999999999999999999999974 34555544
No 18
>cd04475 RPA1_DBD_B RPA1_DBD_B: A subfamily of OB folds corresponding to the third OB fold, the ssDNA-binding domain (DBD)-B, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-B, RPA1 contains three other OB folds: DBD-A, DBD-C, and RPA1N. The major DNA binding activity of human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. Although ScRPA and the hRPA have similar ssDNA-binding properties, they differ functiona
Probab=97.97 E-value=9e-05 Score=62.04 Aligned_cols=74 Identities=16% Similarity=0.201 Sum_probs=58.9
Q ss_pred eEEEEEEEEecCCcccc--C--C-CceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCeeE
Q 012503 23 KVNLLGVVLEFSIPRKS--Q--G-TDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAELS 97 (462)
Q Consensus 23 ~vnviGVVvd~~~P~~t--r--G-~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~~~g~~~ 97 (462)
.|||+|+|++.++|+.- + | .-.+.+|+|.|.|.. .+.|.++.+..+.+... .|+||.+++++++.|+| ..
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 38999999999998653 2 4 367899999999974 59999999766666654 39999999999999995 45
Q ss_pred EEec
Q 012503 98 AVFY 101 (462)
Q Consensus 98 ~~~~ 101 (462)
+.+.
T Consensus 76 l~~~ 79 (101)
T cd04475 76 LSTG 79 (101)
T ss_pred Eeec
Confidence 5444
No 19
>TIGR00617 rpa1 replication factor-a protein 1 (rpa1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.89 E-value=0.00019 Score=78.72 Aligned_cols=156 Identities=18% Similarity=0.261 Sum_probs=104.9
Q ss_pred Ccceeehhhhhhc-cCCeEEEEEEEEecCCcccc----CCCc-eEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCC
Q 012503 7 QGGIVRIKELAMH-VKHKVNLLGVVLEFSIPRKS----QGTD-YVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRD 80 (462)
Q Consensus 7 ~y~y~~i~d~~~~-~~~~vnviGVVvd~~~P~~t----rG~D-~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GD 80 (462)
.|.|++|+++... .+..|+|||||++.++...- .|+. .+.+|+|+|.|-. .|.|.++.+..+.+. . ..|+
T Consensus 295 ~~~f~~i~dI~~~~~~~~VDVIGvV~~v~~~~~i~~k~~g~~~~kR~i~L~D~sg~--sI~vTLWG~~A~~~~-~-~~~~ 370 (608)
T TIGR00617 295 QFNFVKIDDIGGYEGNSLVDVIGIVQSVSPTQTITSRKNNKEFPKRDITLVDDSGK--SVRVTLWGDDATKFD-V-SVQP 370 (608)
T ss_pred cccceEHHHhhhhcCCCCccEEEEEeEecCceEEEEcCCCCeeeeEEEEEEeCCCC--EEEEEEEhhhhhhcC-C-CCCC
Confidence 6889999999865 34589999999999887552 2443 5789999999853 499999998766666 3 5799
Q ss_pred EEEEeeEEEEEEcCeeEEEecCCceEEEEEeCCCCCCCCccccCCCCCCCCHHHHHHHHHHHHhhhcCcccC--------
Q 012503 81 LILLKNVMIKKHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSS-------- 152 (462)
Q Consensus 81 II~l~rvki~~~~g~~~~~~~~~~ss~~lf~~~~~~~~~Py~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~-------- 152 (462)
||.+..++|+.|+|. .+... ..|.+. .+ | |..-+..|+.|+.+.....
T Consensus 371 Vva~kg~~V~~f~g~-sLs~~-~~S~i~-iN--------P-------------dipEa~~L~~w~~~~g~~~~~~s~~~~ 426 (608)
T TIGR00617 371 VIAIKGVRVSDFGGK-SLSTG-GSSTII-VN--------P-------------DIPEAEKLKGWYDNEGKGTMASSISDM 426 (608)
T ss_pred EEEEEeEEEEecCCc-eEecc-CCceEE-EC--------C-------------CcHHHHHHHHHHHhcCCCccceeehhc
Confidence 999999999999664 44433 224443 11 1 1122568899976432210
Q ss_pred ------C-CcccccccccccC--------CceeeeEEEEEEEeeeCCCCeEEEEEEcCCCCCC
Q 012503 153 ------G-SNDYLLSLKDISE--------HRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPP 200 (462)
Q Consensus 153 ------~-~~~f~~~L~di~~--------~~f~Dlv~qVv~v~~~~~~~~~~L~VwDgT~~~~ 200 (462)
+ .... +.|.+|++ +.+|.+.|.|.++. . + .+ | |+.+|.
T Consensus 427 ~~~~~~~~~~~~-ktI~ei~~~~lg~~~k~~~f~v~atI~~Ik-~-d--~~----~-Y~ACp~ 479 (608)
T TIGR00617 427 MSGRVGGSNAER-KTIAEIQAENLGKSDKPDYFSVKATISYLK-P-D--NA----L-YRACPS 479 (608)
T ss_pred cccccCCccccc-ccHHHHhhhccCCCCCCcEEEEEEEEEEEe-c-C--Ce----E-eccCCh
Confidence 0 1122 45666643 34789999999987 3 2 22 3 677765
No 20
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=97.88 E-value=0.00041 Score=60.99 Aligned_cols=92 Identities=17% Similarity=0.262 Sum_probs=71.7
Q ss_pred eeehhhhhhccC-CeEEEEEEEEecCCcc--ccCCC-ceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEe
Q 012503 10 IVRIKELAMHVK-HKVNLLGVVLEFSIPR--KSQGT-DYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLK 85 (462)
Q Consensus 10 y~~i~d~~~~~~-~~vnviGVVvd~~~P~--~trG~-D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~ 85 (462)
++.|+|+. ++ ..||+.|+|++..+++ +++|+ -...+++|.|.|=. |.+.++.+.. +.+ ..||||+|+
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 67899997 55 5799999999988764 45554 56889999999863 8999998643 345 689999999
Q ss_pred eEEEEEEcCeeEEEecCCceEEEEEe
Q 012503 86 NVMIKKHQAELSAVFYKDSSSFALFD 111 (462)
Q Consensus 86 rvki~~~~g~~~~~~~~~~ss~~lf~ 111 (462)
+++++.|+|.+++...+. +.....+
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 21
>PRK07218 replication factor A; Provisional
Probab=97.61 E-value=0.008 Score=62.95 Aligned_cols=160 Identities=16% Similarity=0.209 Sum_probs=105.6
Q ss_pred cccccccC-CceeeeEEEEEEEeeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCChhccccCCCcce
Q 012503 159 LSLKDISE-HRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGT 237 (462)
Q Consensus 159 ~~L~di~~-~~f~Dlv~qVv~v~~~~~~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~p~~G~ 237 (462)
..|+||++ ++.++++++|+.+. + + ++. .||+..... ...+.| . =|
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 67999985 57899999999886 3 2 223 777632111 111111 0 03
Q ss_pred EEEEEecccchhhhcccCCCCCEEEEEceEEEEeCcEEEEEEeeCCceEEcCCCChhHHHHHhhhhcCCCCCCCCcCCCC
Q 012503 238 VLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDNDNVVWDYMRERISGGHGHMPIWTDPS 317 (462)
Q Consensus 238 ~l~V~~~~~~~~~~~~~~k~g~wV~l~Nv~~k~~~g~leG~l~~~ski~~l~~~d~~v~~~~rer~~~~~~~~~~~~~p~ 317 (462)
++++++|+.. .+++||+|+|.|...+...|..+-.+...+.|..++++.. |.
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 4589999933 2999999999999999999998888888888876554311 00
Q ss_pred CCcccccccCCCCcccHHHHhhCCCCCceEEEEEEEEeecCCcccccccCCCceEEEEEEEEeCCCceEEEEEecccc
Q 012503 318 SQFLTEVDWVNVASVTLMKIATQLQGNVRCCCIVRVVSIHPFQAEHYSSPNGSSEYTMKLTLEDPTARIHALLCGKEW 395 (462)
Q Consensus 318 ~~~it~~~~~~~p~ttL~dIL~~p~v~~kfr~~VRVV~~~P~~~edf~~~~~~w~~~f~L~lED~t~ri~~~v~~~da 395 (462)
++..+...|.||-.. ..-....+||++.+|. .|-...|.- ....++|.|.||+|++-++++.|
T Consensus 157 --------~~~~~~~kI~DL~~g---~~~V~v~g~Vl~~~~r---~f~~~dg~~-~v~~giigDeTG~Ir~tlW~~~~ 219 (423)
T PRK07218 157 --------YSIGGDKKLIDLGPG---DRGVNVEARVLELEHR---EIDGRDGET-TILSGVLADETGRLPFTDWDPLP 219 (423)
T ss_pred --------ccccCccchhhccCC---CCceEEEEEEEEecce---eEEcCCCCe-EEEEEEEECCCceEEEEEecccc
Confidence 001112223333311 1224667999999874 466666632 36778999999999999999865
No 22
>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=97.53 E-value=0.0013 Score=52.79 Aligned_cols=72 Identities=18% Similarity=0.281 Sum_probs=60.0
Q ss_pred EEEEEEEecCCcccc---CCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCeeEEEec
Q 012503 25 NLLGVVLEFSIPRKS---QGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAELSAVFY 101 (462)
Q Consensus 25 nviGVVvd~~~P~~t---rG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~~~g~~~~~~~ 101 (462)
||.|.|++..+++.. .+.--..+++|.|.|- .+.+.++.+.. .+.+ ..||+|.+++++++.|+|.+++..+
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 589999999988753 3457789999999974 39999998653 6667 6899999999999999999998876
Q ss_pred C
Q 012503 102 K 102 (462)
Q Consensus 102 ~ 102 (462)
.
T Consensus 75 ~ 75 (82)
T cd04491 75 K 75 (82)
T ss_pred C
Confidence 4
No 23
>PRK06386 replication factor A; Reviewed
Probab=97.34 E-value=0.01 Score=60.74 Aligned_cols=114 Identities=19% Similarity=0.206 Sum_probs=75.0
Q ss_pred EEEEEecccchhhhcccCCCCCEEEEEceEEEEeCcEEEEEEeeCCceEEcCCCChhHHHHHhhhhcCCCCCCCCcCCCC
Q 012503 238 VLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDNDNVVWDYMRERISGGHGHMPIWTDPS 317 (462)
Q Consensus 238 ~l~V~~~~~~~~~~~~~~k~g~wV~l~Nv~~k~~~g~leG~l~~~ski~~l~~~d~~v~~~~rer~~~~~~~~~~~~~p~ 317 (462)
.+++|+|+.. ..+++|++|+|.|...+.+.|.++-.+...+.|...++.+..+
T Consensus 49 ~I~fT~W~~~-----~~l~~Gd~v~i~na~v~~~~G~~~Lnv~~~t~v~~~~d~~iev---------------------- 101 (358)
T PRK06386 49 TVPFTAWEFP-----DAVKSGDVIEIKYCYSKEYNGKIRIYFDSRSEVMLKPDENIEV---------------------- 101 (358)
T ss_pred eEEEEecCCc-----ccCCCCCEEEEEeEEEeeECCEEEEEEcCceEEEecCcccccc----------------------
Confidence 4578999842 3589999999999999999999988787777775333222100
Q ss_pred CCcccccccCCCCcccHHHHhhCCCCCceE-EEEEEEEeecCCcccccccCCCceEEEEEEEEeCCCceEEEEEeccc
Q 012503 318 SQFLTEVDWVNVASVTLMKIATQLQGNVRC-CCIVRVVSIHPFQAEHYSSPNGSSEYTMKLTLEDPTARIHALLCGKE 394 (462)
Q Consensus 318 ~~~it~~~~~~~p~ttL~dIL~~p~v~~kf-r~~VRVV~~~P~~~edf~~~~~~w~~~f~L~lED~t~ri~~~v~~~d 394 (462)
. +.+|.+.|.||- | ...+ ...+||++..++ .|- ..|.=.---.++|.|.||||++-+++++
T Consensus 102 ----~----~~~~~~KI~DL~--~--g~~~v~V~akVle~~e~---e~~-~~g~~~~v~sg~lgDeTGrIr~TlW~~~ 163 (358)
T PRK06386 102 ----K----RTYKLVKIRDLS--L--VTPYVSVIGKITGITKK---EYD-SDGTSKIVYQGYIEDDTARVRISSFGKP 163 (358)
T ss_pred ----c----cccCccEeEecc--C--CCCceEEEEEEEEccCc---eEe-cCCCccEEEEEEEEcCCCeEEEEEcccc
Confidence 0 112445566663 1 2222 356888987654 332 3232123457899999999999999863
No 24
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=97.17 E-value=0.0045 Score=54.36 Aligned_cols=88 Identities=18% Similarity=0.166 Sum_probs=65.1
Q ss_pred cccccccCC-ceeeeEEEEEEEeee-----CCCC---eEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCChhcc
Q 012503 159 LSLKDISEH-RYFDLVCKVFHVSYD-----DSKG---LWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETL 229 (462)
Q Consensus 159 ~~L~di~~~-~f~Dlv~qVv~v~~~-----~~~~---~~~L~VwDgT~~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~ 229 (462)
..|+||+++ .-+|++++|+.+. + ..++ .+.+.|=|.|
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 679999998 6999999999775 2 0111 1222222222
Q ss_pred ccCCCcceEEEEEecccchhhhcccCCCCCEEEEEceEEEEeCcEEEEEEeeCCceEEcCCC
Q 012503 230 RNFFPVGTVLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDN 291 (462)
Q Consensus 230 ~~~p~~G~~l~V~~~~~~~~~~~~~~k~g~wV~l~Nv~~k~~~g~leG~l~~~ski~~l~~~ 291 (462)
| ++++++|+..+ ..+++||.|+++|..++.+.|.++-.+...++|..++++
T Consensus 51 ------G-~I~~tlW~~~a----~~l~~GdvV~I~na~v~~f~G~lqL~i~~~~~i~~~~~~ 101 (129)
T PRK06461 51 ------G-RVKLTLWGEQA----GSLKEGEVVEIENAWTTLYRGKVQLNVGKYGSISESDDE 101 (129)
T ss_pred ------C-EEEEEEeCCcc----ccCCCCCEEEEECcEEeeeCCEEEEEECCCEEEEECCcc
Confidence 3 36899999754 358999999999999999999998888888888877653
No 25
>PRK08402 replication factor A; Reviewed
Probab=97.06 E-value=0.018 Score=59.08 Aligned_cols=139 Identities=16% Similarity=0.233 Sum_probs=93.4
Q ss_pred ceeehhhhhhccC-CeEEEEEEEEecCCccc--c-CCC-ceEEEEEEEeCCCCCCCeEEEEecCCCC-CCCCCCCCCCEE
Q 012503 9 GIVRIKELAMHVK-HKVNLLGVVLEFSIPRK--S-QGT-DYVCVLKIVDDSQQSPELLVNIFTSSID-QLPRVLSPRDLI 82 (462)
Q Consensus 9 ~y~~i~d~~~~~~-~~vnviGVVvd~~~P~~--t-rG~-D~~~tl~I~D~s~~~~gl~v~iF~~~~~-~LP~v~~~GDII 82 (462)
..+.|+|+. ++ ..|++.|-|+....|+. . .|+ ....++.|.|+|-. +++.++.+..+ .++.+ ..||||
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 467899997 44 46999999999987763 1 243 57888999998762 79999997644 47878 689999
Q ss_pred EEeeEEEEE-EcCeeEEEecCCceEEEEEeCCCCCCCCccccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCccccccc
Q 012503 83 LLKNVMIKK-HQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSL 161 (462)
Q Consensus 83 ~l~rvki~~-~~g~~~~~~~~~~ss~~lf~~~~~~~~~Py~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~f~~~L 161 (462)
.+.+++++. |+|.+.+..+.. |+..+=+..+...-.| .-.++.. . ...+ +.|
T Consensus 135 ~I~~a~V~e~~~G~~eLsvg~~-s~i~~~pd~~ea~~i~---------~~~~~~~---------------~-~~~~-k~I 187 (355)
T PRK08402 135 KVIDAQVRESLSGLPELHINFR-ARIILNPDDPRVEEIP---------PLEEVRS---------------Y-NYTR-KKI 187 (355)
T ss_pred EEECCEEeecCCCcEEEEECCC-ceEEeCCCcccccccc---------ccccccc---------------c-cccc-cCH
Confidence 999999998 488878877644 4444222111100011 0000000 0 0123 568
Q ss_pred ccccCCc-eeeeEEEEEEEe
Q 012503 162 KDISEHR-YFDLVCKVFHVS 180 (462)
Q Consensus 162 ~di~~~~-f~Dlv~qVv~v~ 180 (462)
.|++++. ||.+.+.|+.+.
T Consensus 188 ~ei~~gd~~v~v~g~Iv~i~ 207 (355)
T PRK08402 188 GELEGGERFVEVRGTIAKVY 207 (355)
T ss_pred HHcccCCcEEEEEEEEEEEe
Confidence 8887654 789999999987
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=96.83 E-value=0.014 Score=51.85 Aligned_cols=96 Identities=17% Similarity=0.125 Sum_probs=71.5
Q ss_pred ccccccccc--CCceeeeEEEEEEEeeeC----CCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCChhccc
Q 012503 157 YLLSLKDIS--EHRYFDLVCKVFHVSYDD----SKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLR 230 (462)
Q Consensus 157 f~~~L~di~--~~~f~Dlv~qVv~v~~~~----~~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~ 230 (462)
| ..|+++. .++.+|+++-|+.+.... .+.+.+|.|+|-|.++
T Consensus 3 f-~~i~~~~~~~~~~v~vigVV~~~~~p~~s~g~d~~~tl~i~D~S~~~------------------------------- 50 (138)
T cd04497 3 Y-TPLSSALKESGGSVNVIGVVVDAGPPVRSKGTDYCCTLTITDPSLAN------------------------------- 50 (138)
T ss_pred e-EeHHHHHhccCCeEEEEEEEeecCCCcccCCCcEEEEEEEECCCCCC-------------------------------
Confidence 5 6788886 799999999999876211 1347778888844211
Q ss_pred cCCCcceEEEEEecccchhhhcccCCCCCEEEEEceEEEEeCcEEEEEEee-CCceEEcCC
Q 012503 231 NFFPVGTVLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQS-SSKIRLFSD 290 (462)
Q Consensus 231 ~~p~~G~~l~V~~~~~~~~~~~~~~k~g~wV~l~Nv~~k~~~g~leG~l~~-~ski~~l~~ 290 (462)
+..|+|.+|.++++. ...+.+||.|+|+|++++..+|...|.... .+.+.+.+.
T Consensus 51 -----~~~l~v~~F~~~~~~-LP~v~~GDVIll~~~kv~~~~g~~~~~~~~~~ss~avf~~ 105 (138)
T cd04497 51 -----SDGLTVKLFRPNEES-LPIVKVGDIILLRRVKIQSYNGKPQGISNDRGSSWAVFRG 105 (138)
T ss_pred -----CCcEEEEEECCChhh-CCCCCCCCEEEEEEEEEEEECCceEEEECCCceeEEEEcC
Confidence 235678999988775 666799999999999999988988887776 566665444
No 27
>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=96.37 E-value=0.016 Score=43.87 Aligned_cols=70 Identities=19% Similarity=0.386 Sum_probs=53.1
Q ss_pred EEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCeeEEEe
Q 012503 25 NLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAELSAVF 100 (462)
Q Consensus 25 nviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~~~g~~~~~~ 100 (462)
.+.|+|++..... | ...+..|+|.|.+- ..+.+.+|.+..+........|++|.++ .+++.++++.++..
T Consensus 1 ~v~g~v~~~~~~~-~--~~~~~~~~l~D~~~--~~i~~~~~~~~~~~~~~~~~~g~~v~v~-g~v~~~~~~~~l~~ 70 (75)
T cd03524 1 TIVGIVVAVEEIR-T--EGKVLIFTLTDGTG--GTIRVTLFGELAEELENLLKEGQVVYIK-GKVKKFRGRLQLIV 70 (75)
T ss_pred CeEEEEEeecccc-c--CCeEEEEEEEcCCC--CEEEEEEEchHHHHHHhhccCCCEEEEE-EEEEecCCeEEEEe
Confidence 3789999987753 3 35589999999872 2399999997655553334789999998 99999887766654
No 28
>KOG3416 consensus Predicted nucleic acid binding protein [General function prediction only]
Probab=96.30 E-value=0.02 Score=49.18 Aligned_cols=84 Identities=21% Similarity=0.307 Sum_probs=66.3
Q ss_pred eehhhhhhccCCeEEEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEE
Q 012503 11 VRIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIK 90 (462)
Q Consensus 11 ~~i~d~~~~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~ 90 (462)
+.|+|+.... +..|++=+|++.+...+|+-.+=.++.++.|+|-. |.+.+..+ +..+ + ++||||+|++---+
T Consensus 5 i~ikdi~P~~-kN~~v~fIvl~~g~~tkTkdg~~v~~~kVaD~Tgs---I~isvW~e-~~~~--~-~PGDIirLt~Gy~S 76 (134)
T KOG3416|consen 5 IFIKDIKPGL-KNINVTFIVLEYGRATKTKDGHEVRSCKVADETGS---INISVWDE-EGCL--I-QPGDIIRLTGGYAS 76 (134)
T ss_pred hhHhhcChhh-hcceEEEEEEeeceeeeccCCCEEEEEEEecccce---EEEEEecC-cCcc--c-CCccEEEecccchh
Confidence 4677887332 24889999999999999987888999999999864 88888873 3333 2 67999999999999
Q ss_pred EEcCeeEEEecC
Q 012503 91 KHQAELSAVFYK 102 (462)
Q Consensus 91 ~~~g~~~~~~~~ 102 (462)
.|+|.+.+...+
T Consensus 77 i~qg~LtL~~GK 88 (134)
T KOG3416|consen 77 IFQGCLTLYVGK 88 (134)
T ss_pred hhcCceEEEecC
Confidence 999987766543
No 29
>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=96.26 E-value=0.12 Score=46.32 Aligned_cols=97 Identities=19% Similarity=0.144 Sum_probs=68.3
Q ss_pred cccc--cccCCceeeeEEEEEEEeee------CCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCChhccc
Q 012503 159 LSLK--DISEHRYFDLVCKVFHVSYD------DSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLR 230 (462)
Q Consensus 159 ~~L~--di~~~~f~Dlv~qVv~v~~~------~~~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~ 230 (462)
..|. ..+.++++|+++-|+..... ..+-..+|.|+|-|-+..-. .
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 34679999999999987633 12348899999955321100 0
Q ss_pred cCCCcceEEEEEecccchhhhcccCCC-CCEEEEEceEEEEeCcEEEEEEeeC--CceEEc
Q 012503 231 NFFPVGTVLRVSTDRSYENFGRYFTAT-GKWVRIRNMSCQVSSGMWHGLLQSS--SKIRLF 288 (462)
Q Consensus 231 ~~p~~G~~l~V~~~~~~~~~~~~~~k~-g~wV~l~Nv~~k~~~g~leG~l~~~--ski~~l 288 (462)
...|.|.++.++.+. ...++. ||.|+|++++++.+.|...|..... +.+.+.
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 035567777666665 567776 9999999999999999888877776 666666
No 30
>PRK07217 replication factor A; Reviewed
Probab=96.24 E-value=1.4 Score=44.22 Aligned_cols=168 Identities=18% Similarity=0.207 Sum_probs=100.6
Q ss_pred ccccccc-CCceeeeEEEEEEEeeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCChhccccCCCcce
Q 012503 159 LSLKDIS-EHRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGT 237 (462)
Q Consensus 159 ~~L~di~-~~~f~Dlv~qVv~v~~~~~~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~p~~G~ 237 (462)
..|+||+ .++.+++.++|+.++ + ..+..+.+| ..+.|+ . |
T Consensus 73 ~kI~Di~~~~~~VsV~aKVl~l~-e-~~~~si~qv------------GllgDE-----------------T-------G- 113 (311)
T PRK07217 73 VNIADIDEPEQWVDVTAKVVQLW-E-PSSDSIAQV------------GLLGDE-----------------T-------G- 113 (311)
T ss_pred eeeeecCCCCCcEEEEEEEEEec-C-CCCCceEEE------------EEEEcC-----------------C-------c-
Confidence 5799998 589999999999998 5 221111110 001110 0 2
Q ss_pred EEEEEecccchhhhcccCCCCCEEEEEceEEEEeCcEEEEEEeeCCceEEcCCCChhHHHHHhhhhcCCCCCCCCcCCCC
Q 012503 238 VLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDNDNVVWDYMRERISGGHGHMPIWTDPS 317 (462)
Q Consensus 238 ~l~V~~~~~~~~~~~~~~k~g~wV~l~Nv~~k~~~g~leG~l~~~ski~~l~~~d~~v~~~~rer~~~~~~~~~~~~~p~ 317 (462)
.++.|+|.... ...+++|++|+|.|+..+.++|..+-.+...+.|..++.+- .|.... ..+...+=.+. +.
T Consensus 114 ~IkfT~W~~s~---~~~leeGd~~rI~na~v~ey~G~~~lnlg~~t~I~~~de~I-eV~~~~-vei~G~lVdi~----~G 184 (311)
T PRK07217 114 TIKFTKWAKSD---LPELEEGKSYLLKNVVTDEYQGRFSVKLNRTTSIEELDEDI-EVGDDE-VEVEGALVDIQ----SG 184 (311)
T ss_pred eEEEEEccCCC---CCcccCCCEEEEEeEEEeeECCEEEEEeCCceEEEeCCCCc-cccCcc-ccceeEEEEEe----CC
Confidence 45789998432 35589999999999999999999999999988887665432 111100 00000000000 00
Q ss_pred CCcccccccCCCCcccHHHHhhCCCCCceEEEEEEEEeecCCcccccccC----CCceEEEEEEEEeCCCceEEEEEecc
Q 012503 318 SQFLTEVDWVNVASVTLMKIATQLQGNVRCCCIVRVVSIHPFQAEHYSSP----NGSSEYTMKLTLEDPTARIHALLCGK 393 (462)
Q Consensus 318 ~~~it~~~~~~~p~ttL~dIL~~p~v~~kfr~~VRVV~~~P~~~edf~~~----~~~w~~~f~L~lED~t~ri~~~v~~~ 393 (462)
.-.|..|+.+ .| =||++ + -.|.. .|.+--|....|-|.|+.+.++++.+
T Consensus 185 sglI~rCP~~--~C-------------------~Rvl~----~--g~C~~HG~ve~~~DLrik~vlDDGt~~~~~~~~~e 237 (311)
T PRK07217 185 SGLIKRCPEE--DC-------------------TRVLQ----N--GRCSEHGKVEGEFDLRIKGVLDDGEEVQEVIFNRE 237 (311)
T ss_pred CCCeecCCcc--cc-------------------Ccccc----C--CCCCCCCCcCCceeeEEEEEEECCCCeEEEEEChH
Confidence 0111111100 00 03331 1 23332 34566799999999999999999999
Q ss_pred ccccccCC
Q 012503 394 EWVKFFGG 401 (462)
Q Consensus 394 da~~f~~~ 401 (462)
-.+.+.|.
T Consensus 238 ~te~l~G~ 245 (311)
T PRK07217 238 ATEELTGI 245 (311)
T ss_pred HhHHHhCC
Confidence 99999985
No 31
>PRK07217 replication factor A; Reviewed
Probab=96.03 E-value=0.12 Score=51.72 Aligned_cols=92 Identities=17% Similarity=0.254 Sum_probs=67.3
Q ss_pred CcceeehhhhhhccCCeEEEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEee
Q 012503 7 QGGIVRIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKN 86 (462)
Q Consensus 7 ~y~y~~i~d~~~~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~r 86 (462)
...-+.|+|+. ..++.|+|.|-|+....|+. ++-...- -|-|+|= . |++..+.+ +.+|.+ ..||+++|++
T Consensus 69 ~~~~~kI~Di~-~~~~~VsV~aKVl~l~e~~~--~si~qvG-llgDETG-~--IkfT~W~~--s~~~~l-eeGd~~rI~n 138 (311)
T PRK07217 69 GSELVNIADID-EPEQWVDVTAKVVQLWEPSS--DSIAQVG-LLGDETG-T--IKFTKWAK--SDLPEL-EEGKSYLLKN 138 (311)
T ss_pred CCCceeeeecC-CCCCcEEEEEEEEEecCCCC--CceEEEE-EEEcCCc-e--EEEEEccC--CCCCcc-cCCCEEEEEe
Confidence 34456788886 33567999999999988652 2222211 3566643 2 99999986 369999 6899999999
Q ss_pred EEEEEEcCeeEEEecCCceEEEE
Q 012503 87 VMIKKHQAELSAVFYKDSSSFAL 109 (462)
Q Consensus 87 vki~~~~g~~~~~~~~~~ss~~l 109 (462)
+.+..|+|++++..++. |+...
T Consensus 139 a~v~ey~G~~~lnlg~~-t~I~~ 160 (311)
T PRK07217 139 VVTDEYQGRFSVKLNRT-TSIEE 160 (311)
T ss_pred EEEeeECCEEEEEeCCc-eEEEe
Confidence 99999999999888853 55553
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=95.16 E-value=0.034 Score=42.97 Aligned_cols=68 Identities=13% Similarity=0.216 Sum_probs=52.3
Q ss_pred EEEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEec-CCCCCCCCCCCCCCEEEEeeEEEEEEcCe-eEEEec
Q 012503 24 VNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFT-SSIDQLPRVLSPRDLILLKNVMIKKHQAE-LSAVFY 101 (462)
Q Consensus 24 vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~-~~~~~LP~v~~~GDII~l~rvki~~~~g~-~~~~~~ 101 (462)
|.|.|.|.... ++..-.+.++|.|.|- .+.+.+|. ........+ ..||+|+++ -+++.++++ +++..+
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 57889999987 2334567889999983 39999999 444555566 689999998 999999987 877664
No 33
>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=95.12 E-value=0.24 Score=38.78 Aligned_cols=69 Identities=10% Similarity=0.093 Sum_probs=50.8
Q ss_pred EEEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEE--cCeeEEEec
Q 012503 24 VNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKH--QAELSAVFY 101 (462)
Q Consensus 24 vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~~--~g~~~~~~~ 101 (462)
+.+.|+|.+.+. |++. ++-++|.|.+- .+.+.+|.+..+........|++|.++ .+++.+ +|++++..+
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 458899999876 4433 99999999873 399999998677776666889988884 455545 466666554
No 34
>PF15489 CTC1: CST, telomere maintenance, complex subunit CTC1
Probab=95.01 E-value=0.23 Score=57.13 Aligned_cols=145 Identities=17% Similarity=0.123 Sum_probs=104.3
Q ss_pred EEEEEecccchhhhcccCCCCCEEEEEceEEEE-eCcEEEEEEeeCCceEEcCCCChhHHHHHhhhhcCCCCCCCCcCCC
Q 012503 238 VLRVSTDRSYENFGRYFTATGKWVRIRNMSCQV-SSGMWHGLLQSSSKIRLFSDNDNVVWDYMRERISGGHGHMPIWTDP 316 (462)
Q Consensus 238 ~l~V~~~~~~~~~~~~~~k~g~wV~l~Nv~~k~-~~g~leG~l~~~ski~~l~~~d~~v~~~~rer~~~~~~~~~~~~~p 316 (462)
.|.|.++.+|.-+ --.+-||.-|.|.++..|+ .+|+.|..+.++|.|++++-...
T Consensus 888 ~ldVYi~~~h~p~-plGLLPGA~V~f~~lerkVSRs~nVYC~~~psS~VtVlS~p~~----------------------- 943 (1144)
T PF15489_consen 888 HLDVYIEDPHLPY-PLGLLPGARVLFSQLERKVSRSHNVYCCFLPSSSVTVLSFPPE----------------------- 943 (1144)
T ss_pred eEEEEecCCCCCC-cccccCCceeeeehhhhhhhccCcEEEEEcCCceEEEEecCcc-----------------------
Confidence 4677777777776 5678899999999999999 78999999999999998664110
Q ss_pred CCCcccccccCCCCcccHHHHhhCCCCCceEEEEEEEEeecCCccccccc---C-----------------CCceEEEEE
Q 012503 317 SSQFLTEVDWVNVASVTLMKIATQLQGNVRCCCIVRVVSIHPFQAEHYSS---P-----------------NGSSEYTMK 376 (462)
Q Consensus 317 ~~~~it~~~~~~~p~ttL~dIL~~p~v~~kfr~~VRVV~~~P~~~edf~~---~-----------------~~~w~~~f~ 376 (462)
. ..-+.+|...|.+.+.....+.+.++.++||.++==.+.=-|. + .+......+
T Consensus 944 --t----~~~~~~P~~~L~~~~~~~~~~~~a~~~chVV~V~~l~L~WvCa~C~si~~qg~Csr~~p~C~s~~sV~qA~ar 1017 (1144)
T PF15489_consen 944 --T----NVSPPLPHIYLAELLQGSQSPFQARVSCHVVSVLSLQLQWVCAHCGSICPQGRCSRQSPPCPSQTSVFQASAR 1017 (1144)
T ss_pred --c----CCCCCCCeEEehhhhCCCCCCceEEEEEEEEEEEEEEeeehhhhccCcccCCcCCCCCCCCCCCcceeeEEEE
Confidence 0 0112346666777777666666888889999887655543332 0 234456779
Q ss_pred EEEeCCCceEEEEEeccccccccCCCCC-hHHHHHHH
Q 012503 377 LTLEDPTARIHALLCGKEWVKFFGGSPP-PDVLTKKI 412 (462)
Q Consensus 377 L~lED~t~ri~~~v~~~da~~f~~~~~~-~~~l~~kl 412 (462)
++|||.||+-+|.+.|+....+++.-+. -+.|.++.
T Consensus 1018 ~~vEDGTaeA~v~~~~~~V~~lLgL~~~eW~~L~~~v 1054 (1144)
T PF15489_consen 1018 LLVEDGTAEAVVWCRGHHVAALLGLSPSEWESLLEMV 1054 (1144)
T ss_pred EEEecCCeeEEEEECCcHHHHHhCCCHHHHHHHHHHh
Confidence 9999999999999999877788753232 15555444
No 35
>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=94.90 E-value=0.12 Score=43.46 Aligned_cols=82 Identities=12% Similarity=0.095 Sum_probs=57.2
Q ss_pred EEEEEEEecCCccccC--C-CceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCC----CCCCCEEEEee-EEEEEEcCee
Q 012503 25 NLLGVVLEFSIPRKSQ--G-TDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRV----LSPRDLILLKN-VMIKKHQAEL 96 (462)
Q Consensus 25 nviGVVvd~~~P~~tr--G-~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v----~~~GDII~l~r-vki~~~~g~~ 96 (462)
++||+|++.++..... | ..-...|+|.|.+- ..++|.+..+..+.+..- ...+=||.+-+ .+|..|+|..
T Consensus 1 DviG~i~~v~~~~~~~~~~~~~~kr~~~i~D~~~--~~l~~tlwG~~A~~f~~~~~~~~~~~~VVav~~~~rV~~~~g~~ 78 (106)
T cd04481 1 DVIGVIVDVGPLEELPPVNKPSRKLDFEIRDLSD--ERLKCTLWGEYAEEFDAKFQSAGNGEPVVAVLRFWKIKEYKGPK 78 (106)
T ss_pred CeeEEEEEecceEecccCCccceEEEEEEEeCCC--CEEEEEEEHHHHHHHHHHHHHhCCCCcEEEEEEeEEEEEEcCCc
Confidence 4899999999876543 3 56789999999995 349999998766666542 12344776655 9999999854
Q ss_pred EEEecCCceEEE
Q 012503 97 SAVFYKDSSSFA 108 (462)
Q Consensus 97 ~~~~~~~~ss~~ 108 (462)
.+....+.|.|.
T Consensus 79 ~ls~~~~~s~v~ 90 (106)
T cd04481 79 SLSNSFGASKVY 90 (106)
T ss_pred EEEcCCCceEEE
Confidence 444432434444
No 36
>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=94.69 E-value=0.16 Score=46.38 Aligned_cols=32 Identities=22% Similarity=0.315 Sum_probs=30.3
Q ss_pred ceEEEEEEEEeCCCceEEEEEeccccccccCC
Q 012503 370 SSEYTMKLTLEDPTARIHALLCGKEWVKFFGG 401 (462)
Q Consensus 370 ~w~~~f~L~lED~t~ri~~~v~~~da~~f~~~ 401 (462)
.|.|++.+.|.|.|+.+++.++|+.|+.|||.
T Consensus 65 ~~ry~l~~~i~D~Tg~~~~~~F~~~ae~l~G~ 96 (166)
T cd04476 65 EYRYILSLNVADHTGEAWLTLFDEVAEQIFGK 96 (166)
T ss_pred cEEEEEEEEEEeCCCCEEEEEehHHHHHHhCC
Confidence 67899999999999999999999999999985
No 37
>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=94.20 E-value=0.16 Score=42.80 Aligned_cols=84 Identities=14% Similarity=0.180 Sum_probs=61.8
Q ss_pred ehhhhhhccCCeEEEEEEEEecCCccccC---CCceEEEEEEEeCCCCCCCeEEEEecCCCC-CCCCCCCCCCEEEEeeE
Q 012503 12 RIKELAMHVKHKVNLLGVVLEFSIPRKSQ---GTDYVCVLKIVDDSQQSPELLVNIFTSSID-QLPRVLSPRDLILLKNV 87 (462)
Q Consensus 12 ~i~d~~~~~~~~vnviGVVvd~~~P~~tr---G~D~~~tl~I~D~s~~~~gl~v~iF~~~~~-~LP~v~~~GDII~l~rv 87 (462)
+|+++.... ..+.+.|-|+..+.++.-+ |....++|.|.|+... .|.+.+|.+..+ .-|.+ ..|+|+.+.+.
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 PISSLNPYQ-NKWTIKARVTNKSDIRTWSNARGEGKLFSFDLLDEDGG--EIRATFFNDAVDKFYDLL-EVGKVYYISKG 76 (104)
T ss_pred ChhHccCCC-CcEEEEEEEeeccccccccCCCCCcEEEEEEEEECCCC--EEEEEEehHHHHHhhccc-ccccEEEEecc
Confidence 466776332 3589999999887766433 3477889999999643 499999986433 45666 79999999999
Q ss_pred EEEEEcCeeEEE
Q 012503 88 MIKKHQAELSAV 99 (462)
Q Consensus 88 ki~~~~g~~~~~ 99 (462)
+|+.-++...-.
T Consensus 77 ~V~~a~~~y~~~ 88 (104)
T cd04474 77 SVKVANKKFNTL 88 (104)
T ss_pred EEeeccccCCCC
Confidence 999887664433
No 38
>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=94.13 E-value=0.48 Score=38.76 Aligned_cols=67 Identities=18% Similarity=0.198 Sum_probs=51.5
Q ss_pred EEEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCC----CCCCCCCCCCEEEEeeEEEEEEcCeeEEE
Q 012503 24 VNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSID----QLPRVLSPRDLILLKNVMIKKHQAELSAV 99 (462)
Q Consensus 24 vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~----~LP~v~~~GDII~l~rvki~~~~g~~~~~ 99 (462)
|.+.|+|.+... + +=..+++|-|.|- .|.+.++....+ ..+.+ ..|++|++ .-+++.|+|+.++.
T Consensus 2 v~~vG~V~~~~~----~--~~~~~~tL~D~TG---~I~~~~W~~~~~~~~~~~~~~-~~g~~v~v-~G~v~~~~g~~ql~ 70 (95)
T cd04478 2 VTLVGVVRNVEE----Q--STNITYTIDDGTG---TIEVRQWLDDDNDDSSEVEPI-EEGTYVRV-FGNLKSFQGKKSIM 70 (95)
T ss_pred EEEEEEEEeeeE----c--ccEEEEEEECCCC---cEEEEEeCCCCCccccccccc-ccCCEEEE-EEEEcccCCeeEEE
Confidence 779999999764 1 2347889999874 399999987653 56666 79999999 56789999998776
Q ss_pred ec
Q 012503 100 FY 101 (462)
Q Consensus 100 ~~ 101 (462)
..
T Consensus 71 i~ 72 (95)
T cd04478 71 AF 72 (95)
T ss_pred EE
Confidence 43
No 39
>cd04491 SoSSB_OBF SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus solfataricus single-stranded (ss) DNA-binding protein (SSoSSB). SSoSSB has a single OB fold, and it physically and functionally interacts with RNA polymerase. In vitro, SSoSSB can substitute for the basal transcription factor TBP, stimulating transcription from promoters under conditions in which TBP is limiting, and supporting transcription when TBP is absent. SSoSSB selectively melts the duplex DNA of promoter sequences. It also relieves transcriptional repression by the chromatin Alba. In addition, SSoSSB activates reverse gyrase activity, which involves DNA binding, DNA cleavage, strand passage and ligation. SSoSSB stimulates all these steps in the presence of the chromatin protein, Sul7d. SSoSSB antagonizes the inhibitory effect of Sul7d on reverse gyrase supercoiling activity. It also physically and functionally interacts with Mini-chromosome Maintenance (MCM), stimulating
Probab=93.57 E-value=0.23 Score=39.57 Aligned_cols=46 Identities=20% Similarity=0.110 Sum_probs=39.7
Q ss_pred EEEEEecccchhhhcccCCCCCEEEEEceEEEEeCcEEEEEEeeCCceE
Q 012503 238 VLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIR 286 (462)
Q Consensus 238 ~l~V~~~~~~~~~~~~~~k~g~wV~l~Nv~~k~~~g~leG~l~~~ski~ 286 (462)
.+++++|+..+ ...+++|++|++.|..++.+.|.++..+...+.|.
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 67899999776 46799999999999999999899988888877664
No 40
>cd04475 RPA1_DBD_B RPA1_DBD_B: A subfamily of OB folds corresponding to the third OB fold, the ssDNA-binding domain (DBD)-B, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-B, RPA1 contains three other OB folds: DBD-A, DBD-C, and RPA1N. The major DNA binding activity of human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. Although ScRPA and the hRPA have similar ssDNA-binding properties, they differ functiona
Probab=93.31 E-value=1.1 Score=37.18 Aligned_cols=59 Identities=12% Similarity=0.003 Sum_probs=39.2
Q ss_pred ceEEEEEecccchhhhcccCCCCCEEEEEceEEEEeCcEEEEEEeeCCceEEcCCCChhHHHH
Q 012503 236 GTVLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDNDNVVWDY 298 (462)
Q Consensus 236 G~~l~V~~~~~~~~~~~~~~k~g~wV~l~Nv~~k~~~g~leG~l~~~ski~~l~~~d~~v~~~ 298 (462)
|..+.|++|..++....+. .|+.+.|.|++++.++|. .......|+|.+ +++.+.+.+.
T Consensus 38 ~~~i~vtLWg~~a~~~~~~--~~~vv~~~~~~i~~~~~~-~l~~~~~s~i~~-np~~~e~~~l 96 (101)
T cd04475 38 GHSVELTLWGEQAELFDGS--ENPVIAIKGVKVSEFNGK-SLSTGSSSTIII-NPDIPEAHKL 96 (101)
T ss_pred CCEEEEEEEHHHhhhcccC--CCCEEEEEeeEEEecCCe-EEeecCceeEEE-CCCcHHHHHH
Confidence 3467899999888763332 399999999999886663 344445566643 4445555443
No 41
>PRK13480 3'-5' exoribonuclease YhaM; Provisional
Probab=93.21 E-value=0.6 Score=47.26 Aligned_cols=82 Identities=15% Similarity=0.140 Sum_probs=63.5
Q ss_pred ehhhhhhccCCeEEEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEE
Q 012503 12 RIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKK 91 (462)
Q Consensus 12 ~i~d~~~~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~ 91 (462)
.|+++. .|+.|+.+.+|.+... +.++...=...+++.|.|-. |..+++....+....+ ..||||.+. -++..
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 GIEELE--VGEQVDHFLLIKSATK-GVASNGKPFLTLILQDKSGD---IEAKLWDVSPEDEATY-VPETIVHVK-GDIIN 75 (314)
T ss_pred hHhhcC--CCCEeeEEEEEEEcee-eecCCCCeEEEEEEEcCCcE---EEEEeCCCChhhHhhc-CCCCEEEEE-EEEEE
Confidence 467775 6788999999999876 34553344779999998653 8999998777777777 799999994 56678
Q ss_pred EcCeeEEEec
Q 012503 92 HQAELSAVFY 101 (462)
Q Consensus 92 ~~g~~~~~~~ 101 (462)
|+|++|+...
T Consensus 76 y~g~~Ql~i~ 85 (314)
T PRK13480 76 YRGRKQLKVN 85 (314)
T ss_pred ECCcceEEEE
Confidence 9999887654
No 42
>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=93.10 E-value=0.24 Score=38.69 Aligned_cols=70 Identities=14% Similarity=0.301 Sum_probs=49.4
Q ss_pred EEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCeeEEEe
Q 012503 26 LLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAELSAVF 100 (462)
Q Consensus 26 viGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~~~g~~~~~~ 100 (462)
+.|+|.+... +.|+...-+..++|.|.+-. +.+.+|.+..+.+......|.++.++ -+++.|+|..+...
T Consensus 2 i~g~v~~~~~-~~~k~g~~~~~~~l~D~tg~---~~~~~f~~~~~~~~~~l~~g~~v~v~-G~v~~~~~~~~l~~ 71 (84)
T cd04485 2 VAGLVTSVRR-RRTKKGKRMAFVTLEDLTGS---IEVVVFPETYEKYRDLLKEDALLLVE-GKVERRDGGLRLIA 71 (84)
T ss_pred EEEEEEEeEE-EEcCCCCEEEEEEEEeCCCe---EEEEECHHHHHHHHHHhcCCCEEEEE-EEEEecCCceEEEe
Confidence 6788888755 44554456799999998653 99999976533344434689999886 47787877666554
No 43
>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=92.25 E-value=1.2 Score=34.86 Aligned_cols=68 Identities=12% Similarity=0.238 Sum_probs=49.7
Q ss_pred EEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCeeEEEe
Q 012503 27 LGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAELSAVF 100 (462)
Q Consensus 27 iGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~~~g~~~~~~ 100 (462)
+.+|.+++. +.|+...-+..++|-|.+-. +.+.+|.+.....+.+ ..|.+|.++ .++..++|+.+...
T Consensus 3 ~~~v~~~~~-~~tk~g~~~~~~~l~D~tg~---i~~~~f~~~~~~~~~l-~~g~~v~v~-G~v~~~~~~~~l~~ 70 (83)
T cd04492 3 FFLIKSKEL-RTAKNGKPYLALTLQDKTGE---IEAKLWDASEEDEEKF-KPGDIVHVK-GRVEEYRGRLQLKI 70 (83)
T ss_pred EEEEEEeee-ecccCCCcEEEEEEEcCCCe---EEEEEcCCChhhHhhC-CCCCEEEEE-EEEEEeCCceeEEE
Confidence 457777766 45655556899999998763 9999998655444555 689999997 67777877666554
No 44
>cd04483 hOBFC1_like hOBFC1_like: A subfamily of OB folds similar to that found in human OB fold containing protein 1 (hOBFC1). Members of this group belong to the Replication protein A subunit 2 (RPA2) family of OB folds. RPA is a nuclear ssDNA binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The OB fold domain of RPA2 has dual roles in ssDNA binding and trimerization.
Probab=91.55 E-value=1.5 Score=35.99 Aligned_cols=65 Identities=14% Similarity=0.108 Sum_probs=48.1
Q ss_pred EEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCC---------------------CCCCCCCCCCCEEEE
Q 012503 26 LLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSI---------------------DQLPRVLSPRDLILL 84 (462)
Q Consensus 26 viGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~---------------------~~LP~v~~~GDII~l 84 (462)
++|+|+.... +. - ..+|+|-|.|= -|.|+++.... +..+.+ ++|++|++
T Consensus 2 ivG~V~sv~~----~~-~-~~~~tLdDgTG---~Ie~~~W~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i-~~G~vvrV 71 (92)
T cd04483 2 ILGTVVSRRE----RE-T-FYSFGVDDGTG---VVNCVCWKNLSYAEVSSRSDAARILKSALMALKQAKVL-EIGDLLRV 71 (92)
T ss_pred eEEEEEEEEe----cC-C-eEEEEEecCCc---eEEEEEEcCcCccccccccccccccccccccccccccc-CCCCEEEE
Confidence 6899998853 21 2 37888888654 28999997543 345556 79999999
Q ss_pred eeEEEEEEcCeeEEEec
Q 012503 85 KNVMIKKHQAELSAVFY 101 (462)
Q Consensus 85 ~rvki~~~~g~~~~~~~ 101 (462)
+ -+++.|+|+.++...
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 45
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=90.47 E-value=0.21 Score=44.53 Aligned_cols=32 Identities=25% Similarity=0.389 Sum_probs=29.6
Q ss_pred CceEEEEEEEEeCCCceEEEEEeccccccccC
Q 012503 369 GSSEYTMKLTLEDPTARIHALLCGKEWVKFFG 400 (462)
Q Consensus 369 ~~w~~~f~L~lED~t~ri~~~v~~~da~~f~~ 400 (462)
-.|.|++.+.|.|.|+.+++.++|++|+.|||
T Consensus 50 ~~~ry~l~~~i~D~tg~~~~~~F~~~a~~l~G 81 (146)
T PF08646_consen 50 PKYRYRLSLKISDGTGSIWVTLFDEEAEQLLG 81 (146)
T ss_dssp -EEEEEEEEEEEETTEEEEEEEEHHHHHHHHC
T ss_pred eeEEEEEEEEEEeCCCeEEEEEEhHHHHHHhC
Confidence 46889999999999999999999999999996
No 46
>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=88.89 E-value=3.8 Score=34.34 Aligned_cols=49 Identities=14% Similarity=0.055 Sum_probs=36.5
Q ss_pred ceEEEEEecccchhhhcccCCCCCEEEEEceEEEEeC-------cEEEEEEeeCCc
Q 012503 236 GTVLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSS-------GMWHGLLQSSSK 284 (462)
Q Consensus 236 G~~l~V~~~~~~~~~~~~~~k~g~wV~l~Nv~~k~~~-------g~leG~l~~~sk 284 (462)
|..+++++|...+..-...+++|+++.|.|-.++... .-.|..|..++.
T Consensus 46 ~~~I~~t~~~~~~~~f~~~l~eG~vy~i~~~~V~~a~~~y~~~~~~yeI~f~~~t~ 101 (104)
T cd04474 46 GGEIRATFFNDAVDKFYDLLEVGKVYYISKGSVKVANKKFNTLKNDYEITFNRDTS 101 (104)
T ss_pred CCEEEEEEehHHHHHhhcccccccEEEEeccEEeeccccCCCCCCcEEEEECCCcE
Confidence 5678999998776654678999999999999998843 235555555443
No 47
>cd03524 RPA2_OBF_family RPA2_OBF_family: A family of oligonucleotide binding (OB) folds with similarity to the OB fold of the single strand (ss) DNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA contains six OB folds, which are involved in ssDNA binding and in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. This family also includes OB folds similar to those found in Escherichia coli SSB, the wedge domain of E. coli RecG (a branched-DNA-specific helicase), E. coli ssDNA specific exodeoxyribonuclease VII large subunit, Pyroco
Probab=86.74 E-value=9.5 Score=28.13 Aligned_cols=65 Identities=18% Similarity=0.154 Sum_probs=42.6
Q ss_pred eeEEEEEEEeeeCC--CCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCChhccccCCCcceEEEEEecccch
Q 012503 171 DLVCKVFHVSYDDS--KGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRVSTDRSYE 248 (462)
Q Consensus 171 Dlv~qVv~v~~~~~--~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~p~~G~~l~V~~~~~~~ 248 (462)
++.|+|+++. ... .....+.+.|+|+ ..+.+.+|....
T Consensus 1 ~v~g~v~~~~-~~~~~~~~~~~~l~D~~~---------------------------------------~~i~~~~~~~~~ 40 (75)
T cd03524 1 TIVGIVVAVE-EIRTEGKVLIFTLTDGTG---------------------------------------GTIRVTLFGELA 40 (75)
T ss_pred CeEEEEEeec-ccccCCeEEEEEEEcCCC---------------------------------------CEEEEEEEchHH
Confidence 4678888887 323 3567888888771 133577777554
Q ss_pred hhhcccCCCCCEEEEEceEEEEeCcEEE
Q 012503 249 NFGRYFTATGKWVRIRNMSCQVSSGMWH 276 (462)
Q Consensus 249 ~~~~~~~k~g~wV~l~Nv~~k~~~g~le 276 (462)
......+++|+++.+. .+++..+|.++
T Consensus 41 ~~~~~~~~~g~~v~v~-g~v~~~~~~~~ 67 (75)
T cd03524 41 EELENLLKEGQVVYIK-GKVKKFRGRLQ 67 (75)
T ss_pred HHHHhhccCCCEEEEE-EEEEecCCeEE
Confidence 4334678999999887 66665555443
No 48
>PF01336 tRNA_anti-codon: OB-fold nucleic acid binding domain; InterPro: IPR004365 The OB-fold (oligonucleotide/oligosaccharide-binding fold) is found in all three kingdoms and its common architecture presents a binding face that has adapted to bind different ligands. The OB-fold is a five/six-stranded closed beta-barrel formed by 70-80 amino acid residues. The strands are connected by loops of varying length which form the functional appendages of the protein. The majority of OB-fold proteins use the same face for ligand binding or as an active site. Different OB-fold proteins use this 'fold-related binding face' to, variously, bind oligosaccharides, oligonucleotides, proteins, metal ions and catalytic substrates. This entry contains OB-fold domains that bind to nucleic acids []. It includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl-tRNA synthetases (See IPR004364 from INTERPRO). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule 6.1.1 from EC. This domain is found in RecG helicase involved in DNA repair. Replication factor A is a heterotrimeric complex, that contains a subunit in this family [, ]. This domain is also found at the C terminus of bacterial DNA polymerase III alpha chain.; GO: 0003676 nucleic acid binding; PDB: 1BBU_A 1KRS_A 1BBW_A 1KRT_A 1EQR_B 1IL2_B 1C0A_A 3KFU_A 1EOV_A 1ASY_A ....
Probab=86.33 E-value=9.3 Score=28.98 Aligned_cols=62 Identities=18% Similarity=0.123 Sum_probs=43.0
Q ss_pred eeeEEEEEEEeeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCChhccccCCCcceEEEEEecccchh
Q 012503 170 FDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRVSTDRSYEN 249 (462)
Q Consensus 170 ~Dlv~qVv~v~~~~~~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~p~~G~~l~V~~~~~~~~ 249 (462)
+.+.+.|.++. ...+....+.+.|+|+ .+++.+|.....
T Consensus 1 V~v~G~V~~~~-~~~~~~~~~~l~D~tg----------------------------------------~i~~~~~~~~~~ 39 (75)
T PF01336_consen 1 VTVEGRVTSIR-RSGGKIVFFTLEDGTG----------------------------------------SIQVVFFNEEYE 39 (75)
T ss_dssp EEEEEEEEEEE-EEETTEEEEEEEETTE----------------------------------------EEEEEEETHHHH
T ss_pred CEEEEEEEEEE-cCCCCEEEEEEEECCc----------------------------------------cEEEEEccHHhh
Confidence 35778888885 4467788888999883 346788884444
Q ss_pred hhcccCCCCCEEEEEceEEEEeCc
Q 012503 250 FGRYFTATGKWVRIRNMSCQVSSG 273 (462)
Q Consensus 250 ~~~~~~k~g~wV~l~Nv~~k~~~g 273 (462)
...+.+++|++|++. =.++...|
T Consensus 40 ~~~~~l~~g~~v~v~-G~v~~~~~ 62 (75)
T PF01336_consen 40 RFREKLKEGDIVRVR-GKVKRYNG 62 (75)
T ss_dssp HHHHTS-TTSEEEEE-EEEEEETT
T ss_pred HHhhcCCCCeEEEEE-EEEEEECC
Confidence 447889999999988 34444433
No 49
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain
Probab=85.49 E-value=7.3 Score=32.38 Aligned_cols=79 Identities=20% Similarity=0.221 Sum_probs=54.1
Q ss_pred hhhhhhcc--CCeEEEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCC-CCCCCCCEEEEeeEEE
Q 012503 13 IKELAMHV--KHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLP-RVLSPRDLILLKNVMI 89 (462)
Q Consensus 13 i~d~~~~~--~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP-~v~~~GDII~l~rvki 89 (462)
|+++++.. -..+-|.|=|.+++.. ++| .+-|+|+|+. ..++|.+|+.....++ ...+.||-|++ +.++
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 2578999999998764 333 5778899965 4499999998777787 44478997776 4555
Q ss_pred EEE--cCeeEEEe
Q 012503 90 KKH--QAELSAVF 100 (462)
Q Consensus 90 ~~~--~g~~~~~~ 100 (462)
.-| .|++++..
T Consensus 82 ~~y~~~G~~sl~v 94 (99)
T PF13742_consen 82 SFYEPRGSLSLIV 94 (99)
T ss_pred EEECCCcEEEEEE
Confidence 555 44455443
No 50
>cd04488 RecG_wedge_OBF RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal (wedge) domain of Escherichia coli RecG. RecG is a branched-DNA-specific helicase, which catalyzes the interconversion of a DNA replication fork to a four-stranded (Holliday) junction in vivo and in vitro. This interconversion provides a route to repair stalled forks. The RecG monomer contains three domains. The N-terminal domain is named for its wedge structure, and may provide the specificity of RecG for binding branched-DNA structures. During the reversal of fork to Holliday junction, the wedge domain is fixed at the junction of the fork where the leading and lagging strand duplex arms meet, and is thought to promote the unwinding of the nascent leading and lagging strands. In order to form the Holliday junction, these nascent strands would be annealed, and the parental strands reannealed. The wedge domain may also be a processivity factor of RecG on these branched cha
Probab=82.74 E-value=8.6 Score=28.94 Aligned_cols=69 Identities=17% Similarity=0.252 Sum_probs=44.6
Q ss_pred EEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCeeEEEec
Q 012503 26 LLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAELSAVFY 101 (462)
Q Consensus 26 viGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~~~g~~~~~~~ 101 (462)
+.|.|++..... ++|.. ...+++.|.+- .+.+.+|.... .+......|+.+.+. -|+..|+|+++....
T Consensus 2 i~~~V~~~~~~~-~~~~~-~~~~~~~D~~g---~i~~~~F~~~~-~~~~~~~~G~~~~v~-Gkv~~~~~~~qi~~P 70 (75)
T cd04488 2 VEGTVVSVEVVP-RRGRR-RLKVTLSDGTG---TLTLVFFNFQP-YLKKQLPPGTRVRVS-GKVKRFRGGLQIVHP 70 (75)
T ss_pred EEEEEEEEEecc-CCCcc-EEEEEEEcCCC---EEEEEEECCCH-HHHhcCCCCCEEEEE-EEEeecCCeeEEeCC
Confidence 567777764322 23333 78999999854 39999997322 333333789988885 567778887665543
No 51
>cd04484 polC_OBF polC_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold nucleic acid binding domain of Bacillus subtilis type C replicative DNA polymerase III alpha subunit (polC). Replication in B. subtilis and Staphylococcus aureus requires two different polymerases, polC and DnaE. The holoenzyme is thought to include the two different polymerases. At the B. subtilis replication fork, polC appears to be involved in leading strand synthesis and DnaE in lagging strand synthesis.
Probab=77.77 E-value=20 Score=28.68 Aligned_cols=71 Identities=18% Similarity=0.256 Sum_probs=47.6
Q ss_pred EEEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEec-CCCCCCCCCCCCCCEEEEeeE-EEEEEcCeeEE
Q 012503 24 VNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFT-SSIDQLPRVLSPRDLILLKNV-MIKKHQAELSA 98 (462)
Q Consensus 24 vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~-~~~~~LP~v~~~GDII~l~rv-ki~~~~g~~~~ 98 (462)
|-+-|-|.+... +.++......+|.|.|-+ +++.|..|. +..+.+-.+++.||-|+++.- ....|.++...
T Consensus 2 v~i~G~Vf~~e~-re~k~g~~i~~~~itD~t---~Si~~K~F~~~~~~~~~~ik~~G~~v~v~G~v~~D~f~~e~~~ 74 (82)
T cd04484 2 VVVEGEVFDLEI-RELKSGRKILTFKVTDYT---SSITVKKFLRKDEKDKEELKSKGDWVRVRGKVQYDTFSKELVL 74 (82)
T ss_pred EEEEEEEEEEEE-EEecCCCEEEEEEEEcCC---CCEEEEEeccCChhHHhhcccCCCEEEEEEEEEEccCCCceEE
Confidence 346677766643 556666889999999964 469999998 344555556228999988654 34455555443
No 52
>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=76.89 E-value=24 Score=27.54 Aligned_cols=64 Identities=11% Similarity=0.165 Sum_probs=39.6
Q ss_pred EEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEE-eeEEEEEEcCeeEEEe
Q 012503 26 LLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILL-KNVMIKKHQAELSAVF 100 (462)
Q Consensus 26 viGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l-~rvki~~~~g~~~~~~ 100 (462)
+-|.|..+.. +|.. +-|+|.|... .|.|.+|+.+...++.-...||-|.+ =++.+ .+|+.|+..
T Consensus 3 v~GeVs~~~~----~~GH--vyfsLkD~~a---~i~cv~f~~~~~~~~~~l~~Gd~V~v~G~v~~--~~G~~ql~v 67 (73)
T cd04487 3 IEGEVVQIKQ----TSGP--TIFTLRDETG---TVWAAAFEEAGVRAYPEVEVGDIVRVTGEVEP--RDGQLQIEV 67 (73)
T ss_pred EEEEEecccc----CCCC--EEEEEEcCCE---EEEEEEEchhccCCcCCCCCCCEEEEEEEEec--CCeEEEEEE
Confidence 4577776652 4445 4456788543 39999998755455544478995444 44444 566666554
No 53
>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=76.79 E-value=16 Score=32.58 Aligned_cols=63 Identities=17% Similarity=0.212 Sum_probs=36.2
Q ss_pred CceeeeEEEEEEEeeeCCCCe-EEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCChhccccCCCcceEEEEEecc
Q 012503 167 HRYFDLVCKVFHVSYDDSKGL-WMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRVSTDR 245 (462)
Q Consensus 167 ~~f~Dlv~qVv~v~~~~~~~~-~~L~VwDgT~~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~p~~G~~l~V~~~~ 245 (462)
=+-||+++-|+.|. . ..+. -.+|+.|.-- ..|.|.+|.
T Consensus 18 ~~EvD~VG~VvsV~-~-~~~f~~~vYLsD~~~---------------------------------------Nll~Ikfw~ 56 (143)
T PF09104_consen 18 YGEVDTVGFVVSVS-K-KQGFQPLVYLSDECH---------------------------------------NLLAIKFWT 56 (143)
T ss_dssp CCEEEEEEEEEEEE----TTS--EEEEE-TTS----------------------------------------EEEEEESS
T ss_pred ccccceEEEEEEEE-e-cCCCceeEEeecCCc---------------------------------------cEEEEEecc
Confidence 35699999999997 4 3343 4488877321 135688999
Q ss_pred cchhhhccc-CCCCCEEEEEceEEEE
Q 012503 246 SYENFGRYF-TATGKWVRIRNMSCQV 270 (462)
Q Consensus 246 ~~~~~~~~~-~k~g~wV~l~Nv~~k~ 270 (462)
.-..++.+. +|+|..|-..|++-+.
T Consensus 57 ~l~~~~~eDilk~~~liA~SNLqwR~ 82 (143)
T PF09104_consen 57 GLNQYGYEDILKPGSLIAASNLQWRP 82 (143)
T ss_dssp -------SS---TT-EEEEEEEEE-S
T ss_pred CccccchhhhcCcceEEEEeeeEeec
Confidence 888888765 6999999999999875
No 54
>PRK07373 DNA polymerase III subunit alpha; Reviewed
Probab=75.61 E-value=8.9 Score=40.86 Aligned_cols=88 Identities=16% Similarity=0.221 Sum_probs=61.1
Q ss_pred ceeehhhhhh-ccCCeEEEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeE
Q 012503 9 GIVRIKELAM-HVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNV 87 (462)
Q Consensus 9 ~y~~i~d~~~-~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rv 87 (462)
+..+++++.. ..++.|.+.|+|...+.+ +|+..+-++-++|-|.+-. +.+.+|.+.-+..-.....|.+++++.
T Consensus 267 ~~~~~~~l~~~~~~~~v~vaG~I~~ik~~-~TKkG~~maf~~leD~tG~---ie~vvFp~~y~~~~~~l~~~~~v~v~G- 341 (449)
T PRK07373 267 SPINLSELEEQKEKTKVSAVVMLNEVKKI-VTKKGDPMAFLQLEDLSGQ---SEAVVFPKSYERISELLQVDARLIIWG- 341 (449)
T ss_pred CCcCHHHHhcccCCCEEEEEEEEEEeEec-ccCCCCEEEEEEEEECCCC---EEEEECHHHHHHHHHHhccCCEEEEEE-
Confidence 3456676642 246689999999999874 5665678999999999763 999999865555544446788888854
Q ss_pred EEEEEcCeeEEEec
Q 012503 88 MIKKHQAELSAVFY 101 (462)
Q Consensus 88 ki~~~~g~~~~~~~ 101 (462)
+++.-.++.+.+.+
T Consensus 342 ~v~~~~~~~~liv~ 355 (449)
T PRK07373 342 KVDRRDDQVQLIVE 355 (449)
T ss_pred EEEecCCeEEEEEe
Confidence 56543354555544
No 55
>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=74.96 E-value=41 Score=27.55 Aligned_cols=26 Identities=27% Similarity=0.362 Sum_probs=19.0
Q ss_pred eeEEEEEEEeeeCCCCeEEEEEEcCCCC
Q 012503 171 DLVCKVFHVSYDDSKGLWMLFVWDGTDV 198 (462)
Q Consensus 171 Dlv~qVv~v~~~~~~~~~~L~VwDgT~~ 198 (462)
||++.|+.+. + ......+-+=|||+.
T Consensus 1 ~ivG~V~sv~-~-~~~~~~~tLdDgTG~ 26 (92)
T cd04483 1 DILGTVVSRR-E-RETFYSFGVDDGTGV 26 (92)
T ss_pred CeEEEEEEEE-e-cCCeEEEEEecCCce
Confidence 5788999887 4 345677777788874
No 56
>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=74.74 E-value=11 Score=30.01 Aligned_cols=59 Identities=14% Similarity=0.317 Sum_probs=41.4
Q ss_pred EEEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCC--CCCCCCCCCCEEEEeeEEEEE
Q 012503 24 VNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSID--QLPRVLSPRDLILLKNVMIKK 91 (462)
Q Consensus 24 vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~--~LP~v~~~GDII~l~rvki~~ 91 (462)
+.+.|+|.+.+ .|+.++- .++|-|.+-. +.+.+|.+..+ ..-.....|.+|.++. ++..
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 56899999998 4543333 7788888653 99999998777 5555546677777754 5543
No 57
>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=71.61 E-value=23 Score=31.56 Aligned_cols=63 Identities=19% Similarity=0.319 Sum_probs=38.8
Q ss_pred CCeEEEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCC-CCCCCCCCCCCEEEEeeEEEE
Q 012503 21 KHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSI-DQLPRVLSPRDLILLKNVMIK 90 (462)
Q Consensus 21 ~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~-~~LP~v~~~GDII~l~rvki~ 90 (462)
=.-|+++|+|+.. ++++++.--+-|.|....- +.|+++..-. -.+-.+-.+|-+|-+.|++-+
T Consensus 18 ~~EvD~VG~VvsV-----~~~~~f~~~vYLsD~~~Nl--l~Ikfw~~l~~~~~eDilk~~~liA~SNLqwR 81 (143)
T PF09104_consen 18 YGEVDTVGFVVSV-----SKKQGFQPLVYLSDECHNL--LAIKFWTGLNQYGYEDILKPGSLIAASNLQWR 81 (143)
T ss_dssp CCEEEEEEEEEEE-----E--TTS--EEEEE-TTS-E--EEEEESS-------SS---TT-EEEEEEEEE-
T ss_pred ccccceEEEEEEE-----EecCCCceeEEeecCCccE--EEEEeccCccccchhhhcCcceEEEEeeeEee
Confidence 3469999999999 4556788778899999865 8888887522 233445578999999999887
No 58
>PRK05673 dnaE DNA polymerase III subunit alpha; Validated
Probab=68.93 E-value=13 Score=44.31 Aligned_cols=87 Identities=14% Similarity=0.230 Sum_probs=62.0
Q ss_pred eeehhhhhh-ccCCeEEEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEE
Q 012503 10 IVRIKELAM-HVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVM 88 (462)
Q Consensus 10 y~~i~d~~~-~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvk 88 (462)
.+++.++.. ..+..|.+.|+|.+.+.+ +|+.++-++.++|-|.+-. +.+.+|.+..+..=.....|.+|.+. .+
T Consensus 965 ~~~~~~l~~~~~g~~V~v~G~I~~vk~~-~TKkG~~mafltLeD~TG~---iEvviFp~~ye~~~~~L~~g~iV~V~-Gk 1039 (1135)
T PRK05673 965 DTRLADLEPTEGGSVVTVAGLVVSVRRR-VTKRGNKMAIVTLEDLSGR---IEVMLFSEALEKYRDLLEEDRIVVVK-GQ 1039 (1135)
T ss_pred CcCHHHHhccccCceEEEEEEEEEEEec-ccCCCCeEEEEEEEeCCCc---EEEEECHHHHHHHHHHhccCCEEEEE-EE
Confidence 345666642 246779999999999875 4554567899999999763 99999986534333333679999884 46
Q ss_pred EEEEcCeeEEEec
Q 012503 89 IKKHQAELSAVFY 101 (462)
Q Consensus 89 i~~~~g~~~~~~~ 101 (462)
++...++.+++.+
T Consensus 1040 Ve~~~~~~qlii~ 1052 (1135)
T PRK05673 1040 VSFDDGGLRLTAR 1052 (1135)
T ss_pred EEecCCeEEEEEe
Confidence 7776676776665
No 59
>KOG3056 consensus Protein required for S-phase initiation or completion [Cell cycle control, cell division, chromosome partitioning]
Probab=67.46 E-value=8.6 Score=41.39 Aligned_cols=70 Identities=17% Similarity=0.217 Sum_probs=56.6
Q ss_pred EEEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCe
Q 012503 24 VNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAE 95 (462)
Q Consensus 24 vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~~~g~ 95 (462)
--++|||++-+.|+.|...+=.+.++|.|-... .-|.+-+|.+-.+.+=.+ ..|+||-|-|..|-..++.
T Consensus 188 Wvt~GvI~~K~~~K~t~~G~~y~iwkL~dLk~~-q~vslfLFG~a~k~~wk~-k~GtVialLNp~v~k~~~g 257 (578)
T KOG3056|consen 188 WVTMGVIVEKSDPKFTSNGNPYSIWKLTDLKDH-QTVSLFLFGKAHKRYWKI-KLGTVIALLNPEVLKDRPG 257 (578)
T ss_pred eEEEEEEeecCCcccccCCCceEEEEeeecCcc-ceeEEEEecHHHHHHhhh-ccCcEEEEeCccccCCCCC
Confidence 448999999999999854444456788887664 459999999877888888 6899999999999877654
No 60
>cd04498 hPOT1_OB2 hPOT1_OB2: A subfamily of OB folds similar to the second OB fold (OB2) of human protection of telomeres 1 protein (hPOT1). POT1 proteins bind to the single-stranded (ss) 3-prime ends of the telomere. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB2) which cooperate to bind telomeric ssDNA. OB1 makes more extensive contact with the ssDNA than OB2. OB2 protects the 3' end of the ssDNA. hPOT1 is implicated in telomere length regulation.
Probab=65.81 E-value=7.3 Score=33.91 Aligned_cols=34 Identities=15% Similarity=0.338 Sum_probs=27.9
Q ss_pred eEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcC
Q 012503 60 LLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQA 94 (462)
Q Consensus 60 l~v~iF~~~~~~LP~v~~~GDII~l~rvki~~~~g 94 (462)
|.|.+|-++.+..-.+ .+||.|+|+||.+.....
T Consensus 62 i~It~yD~H~~~ar~l-K~GdfV~L~NVhiK~~~~ 95 (123)
T cd04498 62 IDILVYDNHVELAKSL-KPGDFVRIYNVHAKSYSS 95 (123)
T ss_pred EEEEEEcchHHHHhhC-CCCCEEEEEEEEEEeccC
Confidence 7778888777666667 699999999999987766
No 61
>KOG1030 consensus Predicted Ca2+-dependent phospholipid-binding protein [General function prediction only]
Probab=65.39 E-value=14 Score=33.88 Aligned_cols=26 Identities=15% Similarity=0.332 Sum_probs=24.9
Q ss_pred CceEEEEEEEEeCCCceEEEEEeccc
Q 012503 369 GSSEYTMKLTLEDPTARIHALLCGKE 394 (462)
Q Consensus 369 ~~w~~~f~L~lED~t~ri~~~v~~~d 394 (462)
-+|.+.|-|+|.|+..-+.+-||++|
T Consensus 51 PeWNe~ltf~v~d~~~~lkv~VyD~D 76 (168)
T KOG1030|consen 51 PEWNEELTFTVKDPNTPLKVTVYDKD 76 (168)
T ss_pred CcccceEEEEecCCCceEEEEEEeCC
Confidence 38999999999999999999999999
No 62
>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=62.73 E-value=32 Score=28.08 Aligned_cols=60 Identities=20% Similarity=0.332 Sum_probs=37.5
Q ss_pred EEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCC--CCCCCCCCCCCCEEEEeeEEEEEEc
Q 012503 26 LLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSS--IDQLPRVLSPRDLILLKNVMIKKHQ 93 (462)
Q Consensus 26 viGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~--~~~LP~v~~~GDII~l~rvki~~~~ 93 (462)
|-|-|+.+.. .-+|.. +-|+|.|.+. .|.|.+|.++ ...+..-...||-|.+..- +..|.
T Consensus 3 v~GeVs~~~~--~~~sGH--~yFtlkD~~~---~i~cv~f~~~g~~~~~~~~l~~Gd~V~v~G~-v~~y~ 64 (91)
T cd04482 3 VTGKVVEEPR--TIEGGH--VFFKISDGTG---EIDCAAYEPTKEFRDVVRLLIPGDEVTVYGS-VRPGT 64 (91)
T ss_pred EEEEEeCCee--cCCCCC--EEEEEECCCc---EEEEEEECcccccccccCCCCCCCEEEEEEE-EecCC
Confidence 4566666543 213344 5566789763 4999999876 4455554479997777543 45444
No 63
>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=62.47 E-value=33 Score=28.60 Aligned_cols=64 Identities=19% Similarity=0.245 Sum_probs=43.6
Q ss_pred EEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCC-CCCCCCCCCCCEEEEeeEEEEEEcCe
Q 012503 26 LLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSI-DQLPRVLSPRDLILLKNVMIKKHQAE 95 (462)
Q Consensus 26 viGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~-~~LP~v~~~GDII~l~rvki~~~~g~ 95 (462)
++|||+....+. +..+-.+.|.|+++.. +.|+++..-. ..+-.+-..+-.|-+.|++.+.....
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 689999998753 4567788999999976 8888888311 22223334456777777777655444
No 64
>PRK06920 dnaE DNA polymerase III DnaE; Reviewed
Probab=61.91 E-value=21 Score=42.35 Aligned_cols=88 Identities=10% Similarity=0.188 Sum_probs=60.7
Q ss_pred ceeehhhhhhccCCeEEEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEE
Q 012503 9 GIVRIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVM 88 (462)
Q Consensus 9 ~y~~i~d~~~~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvk 88 (462)
+.+++.++....+..|.+.|+|+..+.+ +|+..+-+.-++|-|.+-. +.+.+|.+.-+..-.....|.++++. .+
T Consensus 931 ~~~~~~~l~~~~~~~v~v~g~i~~~~~~-~tk~g~~maf~~leD~tg~---~e~~vFp~~y~~~~~~l~~~~~~~v~-G~ 1005 (1107)
T PRK06920 931 EIPSLAQAMRHKKKVQRAIVYITSVKVI-RTKKGQKMAFITFCDQNDE---MEAVVFPETYIHFSDKLQEGAIVLVD-GT 1005 (1107)
T ss_pred CCcCHHHHhhcCCCEEEEEEEEEEeEee-cCCCCCeEEEEEEeeCCCc---EEEEECHHHHHHHHHHhccCCEEEEE-EE
Confidence 4456666643346689999999999874 4554567899999998653 99999986555544434678888874 46
Q ss_pred EEEEcCeeEEEec
Q 012503 89 IKKHQAELSAVFY 101 (462)
Q Consensus 89 i~~~~g~~~~~~~ 101 (462)
++.-+++.+.+.+
T Consensus 1006 v~~~~~~~~~~~~ 1018 (1107)
T PRK06920 1006 IELRNHKLQWIVN 1018 (1107)
T ss_pred EEecCCcEEEEEe
Confidence 6654555565554
No 65
>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed
Probab=56.99 E-value=72 Score=33.69 Aligned_cols=77 Identities=14% Similarity=0.149 Sum_probs=51.5
Q ss_pred hhhhccCCeEEEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEE--
Q 012503 15 ELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKH-- 92 (462)
Q Consensus 15 d~~~~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~~-- 92 (462)
.+++..-..|-|-|=|..++.+ +.| .|-|+|+|... .|+|.+|+.....++.-...|+-|.+ ..++..|
T Consensus 17 ~~le~~~~~v~v~gEis~~~~~--~sG---H~Yf~Lkd~~a---~i~~~~~~~~~~~~~~~~~~G~~v~v-~g~~~~y~~ 87 (438)
T PRK00286 17 SLLERDLGQVWVRGEISNFTRH--SSG---HWYFTLKDEIA---QIRCVMFKGSARRLKFKPEEGMKVLV-RGKVSLYEP 87 (438)
T ss_pred HHHHhhCCcEEEEEEeCCCeeC--CCC---eEEEEEEcCCc---EEEEEEEcChhhcCCCCCCCCCEEEE-EEEEEEECC
Confidence 3333323468889998888764 334 56788999943 49999999877888875578996666 3344444
Q ss_pred cCeeEEEe
Q 012503 93 QAELSAVF 100 (462)
Q Consensus 93 ~g~~~~~~ 100 (462)
.|++++..
T Consensus 88 ~g~~ql~v 95 (438)
T PRK00286 88 RGDYQLIV 95 (438)
T ss_pred CCCEEEEE
Confidence 44455544
No 66
>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=56.70 E-value=23 Score=29.77 Aligned_cols=53 Identities=17% Similarity=0.328 Sum_probs=38.2
Q ss_pred ceeehhhhhhccCCeEEEEEEEEe-cCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCC
Q 012503 9 GIVRIKELAMHVKHKVNLLGVVLE-FSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSS 68 (462)
Q Consensus 9 ~y~~i~d~~~~~~~~vnviGVVvd-~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~ 68 (462)
.|++|+.+-. .|+ | +|.| +++| .+.+.-|+.++.|.|+-+..++|+|.+|++.
T Consensus 17 sFmPl~saD~-~gG-V----I~TdWY~~p-~~~~er~k~tv~Ild~~Lradal~V~vf~q~ 70 (103)
T PF12100_consen 17 SFMPLASADP-FGG-V----IVTDWYSPP-PGPNERFKATVYILDRALRADALRVSVFRQV 70 (103)
T ss_pred hhcchhhcCC-CCC-E----EEeccccCC-CCCCeeEEEEEEEECccccCCceEEEEEEee
Confidence 4666666642 221 2 4566 5555 3445799999999999999999999999864
No 67
>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=56.36 E-value=37 Score=27.71 Aligned_cols=39 Identities=18% Similarity=0.313 Sum_probs=32.0
Q ss_pred ceEEEEEecccchhhhcccCCCCCEEEEEceEEEEeCcE
Q 012503 236 GTVLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGM 274 (462)
Q Consensus 236 G~~l~V~~~~~~~~~~~~~~k~g~wV~l~Nv~~k~~~g~ 274 (462)
|..|+.++.......-...+++|.|..|.|..+..+.|.
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 778899988766655568899999999999998887664
No 68
>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=56.05 E-value=77 Score=33.60 Aligned_cols=78 Identities=17% Similarity=0.235 Sum_probs=53.2
Q ss_pred hhhhhhc-cCCeEEEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEE
Q 012503 13 IKELAMH-VKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKK 91 (462)
Q Consensus 13 i~d~~~~-~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~ 91 (462)
|+.+++. .+ .|-|-|=|..++.+ +.| .+-|+|+|..- -|+|.+|+.....|+.-.+.|+=|++ ..++..
T Consensus 9 ik~~le~~~~-~v~V~GEisn~~~~--~sG---H~YFtLkD~~a---~i~~vmf~~~~~~l~f~~~~G~~V~v-~g~v~~ 78 (432)
T TIGR00237 9 IKALLEATFL-QVWIQGEISNFTQP--VSG---HWYFTLKDENA---QVRCVMFRGNNNRLKFRPQNGQQVLV-RGGISV 78 (432)
T ss_pred HHHHHHhhCC-cEEEEEEecCCeeC--CCc---eEEEEEEcCCc---EEEEEEEcChhhCCCCCCCCCCEEEE-EEEEEE
Confidence 4555543 33 68899999998854 334 57788899753 39999999877788775578996666 344444
Q ss_pred E--cCeeEEEe
Q 012503 92 H--QAELSAVF 100 (462)
Q Consensus 92 ~--~g~~~~~~ 100 (462)
| .|+.++..
T Consensus 79 y~~~G~~ql~v 89 (432)
T TIGR00237 79 YEPRGDYQIIC 89 (432)
T ss_pred ECCCCcEEEEE
Confidence 4 44455554
No 69
>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=52.49 E-value=45 Score=28.59 Aligned_cols=41 Identities=20% Similarity=0.270 Sum_probs=28.2
Q ss_pred CCCCCCCCCCCEEEEeeEE-------EEEEcCeeEEEecCC-ceEEEEEe
Q 012503 70 DQLPRVLSPRDLILLKNVM-------IKKHQAELSAVFYKD-SSSFALFD 111 (462)
Q Consensus 70 ~~LP~v~~~GDII~l~rvk-------i~~~~g~~~~~~~~~-~ss~~lf~ 111 (462)
..+|.+ .+||+|.++=.. +|.|.|-+.+.-+.+ .++|.|=+
T Consensus 14 ~~~p~f-~~GD~v~V~~~i~e~~k~r~q~f~GvvIa~~~~g~~ssftlR~ 62 (113)
T PF01245_consen 14 KDIPEF-RVGDTVRVTYKISEGNKERIQVFEGVVIARRRRGLNSSFTLRN 62 (113)
T ss_dssp SSSSSS-SSSSEEEEEEEEESSSSEEEEEEEEEEEEEEBSSTSSEEEEEE
T ss_pred cCCCCc-CCCCEEEEEEEEecCCCceeEEEEEEEEEEECCCCCeeEEEEE
Confidence 679999 799999997642 467777665555533 35676633
No 70
>PRK05338 rplS 50S ribosomal protein L19; Provisional
Probab=52.04 E-value=34 Score=29.44 Aligned_cols=45 Identities=16% Similarity=0.235 Sum_probs=29.9
Q ss_pred CCCCCCCCCCCEEEEeeE-------EEEEEcCeeEEEecCC-ceEEEEEeCCCC
Q 012503 70 DQLPRVLSPRDLILLKNV-------MIKKHQAELSAVFYKD-SSSFALFDGNSG 115 (462)
Q Consensus 70 ~~LP~v~~~GDII~l~rv-------ki~~~~g~~~~~~~~~-~ss~~lf~~~~~ 115 (462)
.++|.+ ++||+|.++-- ++|.|.|-+.+.-+.+ .++|.|=+-..+
T Consensus 14 ~~~p~f-~~GD~V~V~~~i~eg~k~R~q~f~GvvI~~~~~G~~~tftvRki~~g 66 (116)
T PRK05338 14 KDIPEF-RPGDTVRVHVKVVEGNKERIQAFEGVVIARRGRGLNETFTVRKISYG 66 (116)
T ss_pred cCCCCc-CCCCEEEEEEEEccCCceEeccEEEEEEEEeCCCCCceEEEEEcccC
Confidence 569999 79999999642 3566777655555543 367887555443
No 71
>PRK07374 dnaE DNA polymerase III subunit alpha; Validated
Probab=50.90 E-value=40 Score=40.33 Aligned_cols=88 Identities=15% Similarity=0.239 Sum_probs=61.8
Q ss_pred ceeehhhhhhc-cCCeEEEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeE
Q 012503 9 GIVRIKELAMH-VKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNV 87 (462)
Q Consensus 9 ~y~~i~d~~~~-~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rv 87 (462)
+.++++++... .+..|.+.|+|+..+.+ +|+..+-+.-++|-|.+-. +.+.+|.+.-+..-.....|.++++. .
T Consensus 987 ~~~~~~~l~~~~~~~~v~v~g~i~~~k~~-~Tk~G~~maf~~leD~tg~---~e~vvFp~~y~~~~~~l~~~~~~~v~-g 1061 (1170)
T PRK07374 987 APISLSSLEEQPDKAKVSAIAMIPEMKQV-TTRKGDRMAILQLEDLTGS---CEAVVFPKSYERLSDHLMTDTRLLVW-A 1061 (1170)
T ss_pred CCcCHHHHhcccCCCEEEEEEEEEEeEec-ccCCCCEEEEEEEEECCCC---EEEEECHHHHHHHHHHhccCCEEEEE-E
Confidence 34566666422 45679999999999875 5555578999999999764 99999987555554444678888884 4
Q ss_pred EEEEEcCeeEEEec
Q 012503 88 MIKKHQAELSAVFY 101 (462)
Q Consensus 88 ki~~~~g~~~~~~~ 101 (462)
+++.-.++.+++.+
T Consensus 1062 ~v~~~~~~~~~~~~ 1075 (1170)
T PRK07374 1062 KVDRRDDRVQLIID 1075 (1170)
T ss_pred EEEecCCeEEEEEe
Confidence 66654455666654
No 72
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=48.20 E-value=74 Score=35.79 Aligned_cols=78 Identities=19% Similarity=0.196 Sum_probs=51.8
Q ss_pred ehhhhhhccCCeEEEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEE
Q 012503 12 RIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKK 91 (462)
Q Consensus 12 ~i~d~~~~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~ 91 (462)
+|+++. .|+.|.+.|.|++...... + --..++++.|.+- .+.+.+|.-+...+.....+|+-+.+.. |++.
T Consensus 52 ~i~~l~--~g~~vtv~g~V~~~~~~~~--~-~~~~~v~l~D~tg---~i~l~~F~~n~~~~~~~l~~G~~~~v~G-kv~~ 122 (681)
T PRK10917 52 PIAELR--PGEKVTVEGEVLSAEVVFG--K-RRRLTVTVSDGTG---NLTLRFFNFNQPYLKKQLKVGKRVAVYG-KVKR 122 (681)
T ss_pred CHHHCC--CCCEEEEEEEEEEEEEccC--C-ceEEEEEEEECCe---EEEEEEEccCcHHHHhhCCCCCEEEEEE-EEEe
Confidence 455554 6889999999999743222 2 2378888999763 3899999422335555557899888865 4444
Q ss_pred EcCeeEE
Q 012503 92 HQAELSA 98 (462)
Q Consensus 92 ~~g~~~~ 98 (462)
++|..+.
T Consensus 123 ~~~~~qm 129 (681)
T PRK10917 123 GKYGLEM 129 (681)
T ss_pred cCCeEEE
Confidence 5565544
No 73
>PF15072 DUF4539: Domain of unknown function (DUF4539)
Probab=47.35 E-value=58 Score=26.48 Aligned_cols=63 Identities=22% Similarity=0.318 Sum_probs=43.6
Q ss_pred eEEEEEEEEe-cCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcC
Q 012503 23 KVNLLGVVLE-FSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQA 94 (462)
Q Consensus 23 ~vnviGVVvd-~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~~~g 94 (462)
+|...+|+++ +.. .+.|. .+.+.|||-. +...+=++-.+..|....+|=+++|+++.+-.=..
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 4444444444 544 33455 6779998763 88888887666677777999999999998865443
No 74
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=46.45 E-value=87 Score=34.34 Aligned_cols=79 Identities=15% Similarity=0.348 Sum_probs=58.7
Q ss_pred eehhhhhhccCCeEEEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEec-CCCCCCCCCCCCCCEEEEeeEEE
Q 012503 11 VRIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFT-SSIDQLPRVLSPRDLILLKNVMI 89 (462)
Q Consensus 11 ~~i~d~~~~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~-~~~~~LP~v~~~GDII~l~rvki 89 (462)
+.|.++-+..|..|.+=|-|+-.+ +|.| -.-|||.|++-. +.+.-|- +-.-.-|.| .+||||.+.. .+
T Consensus 203 ~~i~~id~~ig~tV~I~GeV~qik---qT~G---PTVFtltDetg~---i~aAAFe~aGvRAyP~I-evGdiV~ViG-~V 271 (715)
T COG1107 203 TLIDDLDEMIGKTVRIEGEVTQIK---QTSG---PTVFTLTDETGA---IWAAAFEEAGVRAYPEI-EVGDIVEVIG-EV 271 (715)
T ss_pred ccHHHHHhhcCceEEEEEEEEEEE---EcCC---CEEEEEecCCCc---eehhhhccCCcccCCCC-CCCceEEEEE-EE
Confidence 446666667899999999998763 4544 356889999764 6666775 566789999 7999999965 46
Q ss_pred EEEcCeeEEEe
Q 012503 90 KKHQAELSAVF 100 (462)
Q Consensus 90 ~~~~g~~~~~~ 100 (462)
....|++|.-.
T Consensus 272 ~~r~g~lQiE~ 282 (715)
T COG1107 272 TRRDGRLQIEI 282 (715)
T ss_pred eecCCcEEEee
Confidence 66788877643
No 75
>TIGR00643 recG ATP-dependent DNA helicase RecG.
Probab=46.02 E-value=1e+02 Score=34.25 Aligned_cols=79 Identities=18% Similarity=0.213 Sum_probs=52.0
Q ss_pred ehhhhhhccCCeEEEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEE
Q 012503 12 RIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKK 91 (462)
Q Consensus 12 ~i~d~~~~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~ 91 (462)
+|+++. .|..+.+.|.|++..... ++.--..++.+.|. ....+.+.+|.. ..+......|+-+.+.. |+..
T Consensus 25 ~i~~~~--~g~~~~~~~~v~~~~~~~--~~~~~~~~~~~~d~--~~~~~~~~~F~~--~~~~~~~~~g~~~~~~G-k~~~ 95 (630)
T TIGR00643 25 TIGELL--PGERATIVGEVLSHCIFG--FKRRKVLKLRLKDG--GYKKLELRFFNR--AFLKKKFKVGSKVVVYG-KVKS 95 (630)
T ss_pred CHHHcC--CCCEEEEEEEEEEeEecc--CCCCceEEEEEEEC--CCCEEEEEEECC--HHHHhhCCCCCEEEEEE-EEEe
Confidence 566664 788999999998742211 22222788889994 123399999973 25555557899888865 5566
Q ss_pred EcCeeEEE
Q 012503 92 HQAELSAV 99 (462)
Q Consensus 92 ~~g~~~~~ 99 (462)
++|+.+..
T Consensus 96 ~~~~~~~~ 103 (630)
T TIGR00643 96 SKFKAYLI 103 (630)
T ss_pred eCCEEEEE
Confidence 77766544
No 76
>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=45.76 E-value=1.5e+02 Score=23.40 Aligned_cols=62 Identities=18% Similarity=0.079 Sum_probs=39.0
Q ss_pred EEEEEecCCccccCCCceEEEEEEEeCCCC-----CCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCeeEEEec
Q 012503 27 LGVVLEFSIPRKSQGTDYVCVLKIVDDSQQ-----SPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAELSAVFY 101 (462)
Q Consensus 27 iGVVvd~~~P~~trG~D~~~tl~I~D~s~~-----~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~~~g~~~~~~~ 101 (462)
=|||+...... ... .|-|-|+... ++| +-+|.+. -+.+ .+||.|++. -++..|+|..++...
T Consensus 3 ~GvVTa~~~~~--~~~----GffiQd~~~d~~~~ts~g--ifV~~~~---~~~~-~~Gd~V~vt-G~v~ey~g~tql~~~ 69 (78)
T cd04486 3 EGVVTAVFSGG--GLG----GFYIQDEDGDGDPATSEG--IFVYTGS---GADV-AVGDLVRVT-GTVTEYYGLTQLTAV 69 (78)
T ss_pred EEEEEEEcCCC--CcC----EEEEEcCCCCCCCcccce--EEEecCC---CCCC-CCCCEEEEE-EEEEeeCCeEEEccC
Confidence 47777764422 112 3446666322 233 4555543 4566 789999996 899999998876654
No 77
>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=45.21 E-value=44 Score=26.56 Aligned_cols=37 Identities=19% Similarity=0.333 Sum_probs=29.9
Q ss_pred ceEEEEEecccchhhhcccCCCCCEEEEEceEEEEeC
Q 012503 236 GTVLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSS 272 (462)
Q Consensus 236 G~~l~V~~~~~~~~~~~~~~k~g~wV~l~Nv~~k~~~ 272 (462)
|..++.+++...+..-...+++|.|..|.|-.++...
T Consensus 30 G~~I~a~i~~~~~~~f~~~L~eg~vy~is~f~v~~~~ 66 (86)
T cd04480 30 GNRIHATIPKRLAAKFRPLLKEGKWYTISNFEVAPNT 66 (86)
T ss_pred CCEEEEEECHHHHHhhhhhceeCCEEEEeeEEEEcCC
Confidence 6778899888766655788999999999998877654
No 78
>PF15072 DUF4539: Domain of unknown function (DUF4539)
Probab=42.98 E-value=23 Score=28.84 Aligned_cols=24 Identities=25% Similarity=0.320 Sum_probs=19.7
Q ss_pred EEEEEEeCCCceEEEEEecccccc
Q 012503 374 TMKLTLEDPTARIHALLCGKEWVK 397 (462)
Q Consensus 374 ~f~L~lED~t~ri~~~v~~~da~~ 397 (462)
-..++|.||||+|++.++.+--+.
T Consensus 20 D~~v~l~DpTG~i~~tiH~~v~~~ 43 (86)
T PF15072_consen 20 DAFVVLKDPTGEIRGTIHRKVLEE 43 (86)
T ss_pred CeEEEEECCCCcEEEEEeHHHHhh
Confidence 457899999999999999765444
No 79
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=42.95 E-value=2.8e+02 Score=31.18 Aligned_cols=80 Identities=18% Similarity=0.181 Sum_probs=57.7
Q ss_pred hhhhhhccCCeEEEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEE
Q 012503 13 IKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKH 92 (462)
Q Consensus 13 i~d~~~~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~~ 92 (462)
|.++. .|..|.+-|.|.....+. .++.-..++++.|.+. -+++.+|..+. .+..-..+|--+.+. =|++.|
T Consensus 54 i~~~~--~g~~vti~g~V~~~~~~~--~~~~~~l~v~~~d~~~---~l~l~fFn~~~-~l~~~~~~G~~v~v~-Gk~~~~ 124 (677)
T COG1200 54 IAEAR--PGEIVTIEGTVLSHEKFP--FGKRKLLKVTLSDGTG---VLTLVFFNFPA-YLKKKLKVGERVIVY-GKVKRF 124 (677)
T ss_pred hhhcC--CCceEEEEEEEEeeeccC--CCCCceEEEEEecCcE---EEEEEEECccH-HHHhhCCCCCEEEEE-EEEeec
Confidence 44443 678899999999876543 5567788999999332 39999998653 666655789988884 477778
Q ss_pred cCeeEEEec
Q 012503 93 QAELSAVFY 101 (462)
Q Consensus 93 ~g~~~~~~~ 101 (462)
++..+....
T Consensus 125 ~~~~~~~hp 133 (677)
T COG1200 125 KGGLQITHP 133 (677)
T ss_pred cCceEEEcc
Confidence 887665544
No 80
>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=42.14 E-value=57 Score=27.95 Aligned_cols=45 Identities=16% Similarity=0.128 Sum_probs=29.9
Q ss_pred CCCCCCCCCCCEEEEeeE-------EEEEEcCeeEEEecCC-ceEEEEEeCCCC
Q 012503 70 DQLPRVLSPRDLILLKNV-------MIKKHQAELSAVFYKD-SSSFALFDGNSG 115 (462)
Q Consensus 70 ~~LP~v~~~GDII~l~rv-------ki~~~~g~~~~~~~~~-~ss~~lf~~~~~ 115 (462)
.++|.+ .+||+|.++-- ++|.|.|-+-+.-+.+ .++|.|=+-..+
T Consensus 14 ~~ip~f-~~GD~v~V~~~i~eg~k~R~q~f~GvvI~~~~~G~~~tftvR~i~~g 66 (113)
T TIGR01024 14 KDLPDF-RVGDTVRVHVKIVEGKKERIQVFEGVVIARRGGGIGETFTVRKISYG 66 (113)
T ss_pred cCCCcc-CCCCEEEEEEEEccCCceEcccEEEEEEEEeCCCCceEEEEEEeccC
Confidence 579999 79999999642 3456777655555543 366777555433
No 81
>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=41.34 E-value=1.8e+02 Score=23.17 Aligned_cols=26 Identities=27% Similarity=0.193 Sum_probs=20.5
Q ss_pred eeeEEEEEEEeeeCCCCeEEEEEEcCCC
Q 012503 170 FDLVCKVFHVSYDDSKGLWMLFVWDGTD 197 (462)
Q Consensus 170 ~Dlv~qVv~v~~~~~~~~~~L~VwDgT~ 197 (462)
+.+++.|.++. . .+..+.+.+-|+|+
T Consensus 2 v~~vG~V~~~~-~-~~~~~~~tL~D~TG 27 (95)
T cd04478 2 VTLVGVVRNVE-E-QSTNITYTIDDGTG 27 (95)
T ss_pred EEEEEEEEeee-E-cccEEEEEEECCCC
Confidence 46788999887 4 46788888999885
No 82
>CHL00084 rpl19 ribosomal protein L19
Probab=40.64 E-value=67 Score=27.72 Aligned_cols=42 Identities=10% Similarity=0.150 Sum_probs=27.1
Q ss_pred CCCCCCCCCCCEEEEee-E------EEEEEcCeeEEEecCC-ceEEEEEeC
Q 012503 70 DQLPRVLSPRDLILLKN-V------MIKKHQAELSAVFYKD-SSSFALFDG 112 (462)
Q Consensus 70 ~~LP~v~~~GDII~l~r-v------ki~~~~g~~~~~~~~~-~ss~~lf~~ 112 (462)
.++|.+ ++||+|.++= + .+|.|.|-+-+.-+.+ .++|.|=+-
T Consensus 18 ~~~p~f-~~GDtV~V~~~i~eg~k~R~q~F~GvvI~~r~~G~~~tftvRki 67 (117)
T CHL00084 18 KNLPKI-RVGDTVKVGVLIQEGNKERVQFYEGTVIAKKNSGLNTTITVRKV 67 (117)
T ss_pred cCCCcc-CCCCEEEEEEEEecCCeeEeceEEEEEEEEeCCCCCeeEEEEEe
Confidence 479999 7999999964 1 3556777655554433 356776443
No 83
>PRK05672 dnaE2 error-prone DNA polymerase; Validated
Probab=38.95 E-value=66 Score=38.11 Aligned_cols=85 Identities=20% Similarity=0.232 Sum_probs=56.8
Q ss_pred eeehhhhhhc-cCCeEEEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEE
Q 012503 10 IVRIKELAMH-VKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVM 88 (462)
Q Consensus 10 y~~i~d~~~~-~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvk 88 (462)
++++.++... .+..|.+.|+|+....+...+| +.-++|-|.+-. +.+.+|.+..+..-.....|.++++. -+
T Consensus 941 ~~~~~~l~~~~~~~~v~v~g~i~~~~~~~TkkG---maf~~leD~~g~---~e~~ifp~~~~~~~~~l~~~~~~~v~-g~ 1013 (1046)
T PRK05672 941 VVSAAELLDVEDGRRVRVAGVVTHRQRPGTASG---VTFLTLEDETGM---VNVVVWPGLWERQRREALGARLLLVR-GR 1013 (1046)
T ss_pred CcCHHHHhhccCCCEEEEEEEEEEEEEecCCCc---eEEEEEecCCCC---EEEEECHHHHHHHHHHhccCCEEEEE-EE
Confidence 4556665432 4667999999999877543346 888889888653 99999986444443433678888884 46
Q ss_pred EEEEcCeeEEEec
Q 012503 89 IKKHQAELSAVFY 101 (462)
Q Consensus 89 i~~~~g~~~~~~~ 101 (462)
++.-+|+.+.+.+
T Consensus 1014 v~~~~~~~~~~~~ 1026 (1046)
T PRK05672 1014 VQNAEGVRHLVAD 1026 (1046)
T ss_pred EEecCCeEEEEEe
Confidence 6654555555554
No 84
>PRK06826 dnaE DNA polymerase III DnaE; Reviewed
Probab=38.91 E-value=73 Score=38.13 Aligned_cols=77 Identities=14% Similarity=0.230 Sum_probs=54.2
Q ss_pred cCCeEEEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEE-cCeeEE
Q 012503 20 VKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKH-QAELSA 98 (462)
Q Consensus 20 ~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~~-~g~~~~ 98 (462)
.+..|.+.|+|+..+.+ +|+..+-+.-++|-|.+-. +.+.+|.+..+..-.....|.+|++ ..+++.. ++..+.
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 45679999999999875 5555577899999998763 9999998654444333367888887 4566643 454565
Q ss_pred Eec
Q 012503 99 VFY 101 (462)
Q Consensus 99 ~~~ 101 (462)
+.+
T Consensus 1065 ~~~ 1067 (1151)
T PRK06826 1065 ICE 1067 (1151)
T ss_pred EEe
Confidence 554
No 85
>KOG2708 consensus Predicted metalloprotease with chaperone activity (RNAse H/HSP70 fold) [Posttranslational modification, protein turnover, chaperones]
Probab=37.30 E-value=19 Score=34.70 Aligned_cols=48 Identities=21% Similarity=0.288 Sum_probs=28.6
Q ss_pred HHHHHHHHHHcCCCCCC---------CCC-CCCcCCCcceeEeeeeeeecCCc-------eEEEEEeeeEEc
Q 012503 406 DVLTKKIKMLLGMPEHE---------DGN-DDMVRNPPWIKCFLHLKESDGGR-------NRVYYIRWTKLV 460 (462)
Q Consensus 406 ~~l~~kl~~L~G~~e~~---------~~~-~~~~~~~p~~~cCi~sY~v~~~~-------~r~f~~F~T~i~ 460 (462)
+..-+-|..||..+--. .|. -....||- =-||.+++ ++||||||-+|-
T Consensus 90 aivaRtlsllw~kPlv~VNHCigHIEMGR~iTgA~nPv-------vLYvSGGNTQvIAYse~rYrIFGETlD 154 (336)
T KOG2708|consen 90 AIVARTLSLLWNKPLVGVNHCIGHIEMGREITGAQNPV-------VLYVSGGNTQVIAYSEKRYRIFGETLD 154 (336)
T ss_pred HHHHHHHHHHhCCCcccchhhhhhhhhcceeccCCCCE-------EEEEeCCceEEEEEccceeeeecceeh
Confidence 45556788888643210 111 12234544 24677766 999999999873
No 86
>PF11325 DUF3127: Domain of unknown function (DUF3127); InterPro: IPR021474 This bacterial family of proteins has no known function.
Probab=36.32 E-value=2.3e+02 Score=22.92 Aligned_cols=66 Identities=9% Similarity=0.202 Sum_probs=40.7
Q ss_pred EEEEecCCccccCCCc-eEE-EEEEE-eCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEe-eEEEEEEcCe
Q 012503 28 GVVLEFSIPRKSQGTD-YVC-VLKIV-DDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLK-NVMIKKHQAE 95 (462)
Q Consensus 28 GVVvd~~~P~~trG~D-~~~-tl~I~-D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~-rvki~~~~g~ 95 (462)
|.|+...++.+..|.. |.- .|-|- ++-++ .-+.+.+|.+..+.|-.+ ++||.|.++ +++-+.|+|+
T Consensus 4 Gkii~~l~~~~g~s~~Gw~Kre~Vlet~~qYP-~~i~f~~~~dk~~~l~~~-~~Gd~V~Vsf~i~~RE~~gr 73 (84)
T PF11325_consen 4 GKIIKVLPEQQGVSKNGWKKREFVLETEEQYP-QKICFEFWGDKIDLLDNF-QVGDEVKVSFNIEGREWNGR 73 (84)
T ss_pred cEEEEEecCcccCcCCCcEEEEEEEeCCCcCC-ceEEEEEEcchhhhhccC-CCCCEEEEEEEeeccEecce
Confidence 5555555554432211 543 33332 22232 459999999877777888 699988774 6777788865
No 87
>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=34.84 E-value=42 Score=26.56 Aligned_cols=21 Identities=38% Similarity=0.405 Sum_probs=19.5
Q ss_pred EEEEeCCCceEEEEEeccccc
Q 012503 376 KLTLEDPTARIHALLCGKEWV 396 (462)
Q Consensus 376 ~L~lED~t~ri~~~v~~~da~ 396 (462)
.++|||.++++.+.++.+..+
T Consensus 20 ~~~leD~~G~~Ev~~F~~~~~ 40 (79)
T cd04490 20 IVELEDTTGRITVLLTKDKEE 40 (79)
T ss_pred EEEEECCCCEEEEEEeCchhh
Confidence 899999999999999988766
No 88
>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=34.50 E-value=1.9e+02 Score=24.16 Aligned_cols=34 Identities=18% Similarity=0.068 Sum_probs=27.3
Q ss_pred EEEEecccchhhhccc-CCCCCEEEEEceEEEEeC
Q 012503 239 LRVSTDRSYENFGRYF-TATGKWVRIRNMSCQVSS 272 (462)
Q Consensus 239 l~V~~~~~~~~~~~~~-~k~g~wV~l~Nv~~k~~~ 272 (462)
|-|.+|..-+.++.+. +|++..+.+.|++.+..+
T Consensus 30 l~vkfw~~l~~~~~EDvvk~~~lia~SNLQwR~~s 64 (100)
T cd04495 30 LCVKFWSSLEQYAYEDVVKRRVLLAASNLQWRTES 64 (100)
T ss_pred EEEEEecchHHhhhhhhcccceEEEEecceEeccc
Confidence 3588888777777765 689999999999988844
No 89
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=34.39 E-value=1.3e+02 Score=36.96 Aligned_cols=85 Identities=16% Similarity=0.305 Sum_probs=60.3
Q ss_pred cceeehhhhhhccCCeEEEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCC---CCCCCCCCCCCEEEE
Q 012503 8 GGIVRIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSI---DQLPRVLSPRDLILL 84 (462)
Q Consensus 8 y~y~~i~d~~~~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~---~~LP~v~~~GDII~l 84 (462)
+..++|+++... ...|-+-|-|.+... +.+++.-...+|.|+|-+ +++.|+.|.++. +.+-.+ +.||-|++
T Consensus 224 ~~~~~~~~i~~~-~~~v~i~G~if~~e~-~~~k~~~~~~~~~~td~~---~s~~~k~f~~~~~~~~~~~~~-~~g~~v~~ 297 (1437)
T PRK00448 224 EEITPMKEINEE-ERRVVVEGYVFKVEI-KELKSGRHILTFKITDYT---SSIIVKKFSRDKEDLKKFDEI-KKGDWVKV 297 (1437)
T ss_pred cCcccHHHhhcc-CCeEEEEEEEEEEEE-EeccCCCEEEEEEEEcCC---CCEEEEEEecCcchhHHHhcC-CCCCEEEE
Confidence 466788888743 347889999988755 556656789999999965 459999998443 345556 68999888
Q ss_pred eeE-EEEEEcCeeEE
Q 012503 85 KNV-MIKKHQAELSA 98 (462)
Q Consensus 85 ~rv-ki~~~~g~~~~ 98 (462)
+.- ....|.++...
T Consensus 298 ~g~~~~d~~~~~~~~ 312 (1437)
T PRK00448 298 RGSVQNDTFTRDLVM 312 (1437)
T ss_pred EEEEeccCCCCceEE
Confidence 653 33456665443
No 90
>PF14535 AMP-binding_C_2: AMP-binding enzyme C-terminal domain; PDB: 2Y27_A 2Y4N_A 3QOV_B 3S89_D 3LAX_A 2Y4O_B.
Probab=33.83 E-value=29 Score=28.39 Aligned_cols=63 Identities=21% Similarity=0.269 Sum_probs=41.5
Q ss_pred EeecCCcccccccCC-C-ceEEEEEEEEeCCCceEEEEEeccccccccCCCCC----hHHHHHHHHHHcCC
Q 012503 354 VSIHPFQAEHYSSPN-G-SSEYTMKLTLEDPTARIHALLCGKEWVKFFGGSPP----PDVLTKKIKMLLGM 418 (462)
Q Consensus 354 V~~~P~~~edf~~~~-~-~w~~~f~L~lED~t~ri~~~v~~~da~~f~~~~~~----~~~l~~kl~~L~G~ 418 (462)
|.+||.++|+....- + .=+|++.+.=++...+|.+-|--.+ .+..+... .+.|++++..-+|.
T Consensus 2 vnvfP~~Ie~vl~~~~~~~~~y~i~v~~~~~~D~l~v~vE~~~--~~~~~~~~~~~l~~~i~~~lk~~lgv 70 (96)
T PF14535_consen 2 VNVFPSQIEEVLREFPEVSPEYQIVVTREGGLDELTVRVELRP--GFSDDAEDLEALAERIAERLKERLGV 70 (96)
T ss_dssp EEE-HHHHHHHHCTSTTEEEEEEEEEEEETTEEEEEEEEEEST--TCCTTHHHHHHHHHHHHHHHHHHHSS
T ss_pred cEECHHHHHHHHHhCcCCCCcEEEEEEcCCCCcEEEEEEEECC--ccCcchHHHHHHHHHHHHHHHhhcCc
Confidence 578999999876542 2 2278888888899999999887766 22221111 35666677777775
No 91
>cd04492 YhaM_OBF_like YhaM_OBF_like: A subfamily of OB folds similar to that found in Bacillus subtilis YhaM and Staphylococcus aureus cmp-binding factor-1 (SaCBF1). Both these proteins are 3'-to-5'exoribonucleases. YhaM requires Mn2+ or Co2+ for activity and is inactive in the presence of Mg2+. YhaM also has a Mn2+ dependent 3'-to-5'single-stranded DNA exonuclease activity. SaCBF is also a double-stranded DNA binding protein, binding specifically to cmp, the replication enhancer found in S. aureus plasmid pT181. Proteins in this group combine an N-terminal OB fold with a C-terminal HD domain. The HD domain is found in metal-dependent phosphohydrolases.
Probab=31.64 E-value=60 Score=24.87 Aligned_cols=21 Identities=38% Similarity=0.442 Sum_probs=18.6
Q ss_pred EEEEEEeCCCceEEEEEeccc
Q 012503 374 TMKLTLEDPTARIHALLCGKE 394 (462)
Q Consensus 374 ~f~L~lED~t~ri~~~v~~~d 394 (462)
.+.++|+|.|+++.+.++++.
T Consensus 20 ~~~~~l~D~tg~i~~~~f~~~ 40 (83)
T cd04492 20 YLALTLQDKTGEIEAKLWDAS 40 (83)
T ss_pred EEEEEEEcCCCeEEEEEcCCC
Confidence 589999999999999998754
No 92
>PRK07279 dnaE DNA polymerase III DnaE; Reviewed
Probab=31.58 E-value=98 Score=36.59 Aligned_cols=85 Identities=18% Similarity=0.304 Sum_probs=57.6
Q ss_pred eeehhhhhhccCCeEEEEEEEEecCCccccC-CCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEE
Q 012503 10 IVRIKELAMHVKHKVNLLGVVLEFSIPRKSQ-GTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVM 88 (462)
Q Consensus 10 y~~i~d~~~~~~~~vnviGVVvd~~~P~~tr-G~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvk 88 (462)
.+++.++. .+..+.+.|+|...+. ++|+ ..+-+.-++|-|.+-. +.+.+|.+..+..-.....|.++++.. +
T Consensus 875 ~~~~~~l~--~~~~~~~~~~i~~~~~-~~tk~~g~~maf~~leD~~g~---ie~~vFp~~y~~~~~~l~~~~~~~v~G-~ 947 (1034)
T PRK07279 875 FTPISQLV--KNSEATILVQIQSIRV-IRTKTKGQQMAFLSVTDTKKK---LDVTLFPETYRQYKDELKEGKFYYLKG-K 947 (1034)
T ss_pred CccHHHHh--cCCcceEEEEEEEEEE-EEEcCCCCeEEEEEEeeCCCc---EEEEECHHHHHHHHHHhccCCEEEEEE-E
Confidence 45666664 3556889999998776 4555 3467899999998763 999999865444433336788888854 5
Q ss_pred EEEEcCeeEEEec
Q 012503 89 IKKHQAELSAVFY 101 (462)
Q Consensus 89 i~~~~g~~~~~~~ 101 (462)
++.-.++.+.+.+
T Consensus 948 v~~~~~~~~l~~~ 960 (1034)
T PRK07279 948 IQERDGRLQMVLQ 960 (1034)
T ss_pred EEecCCeeEEEEe
Confidence 6654555565554
No 93
>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=30.71 E-value=61 Score=24.85 Aligned_cols=24 Identities=21% Similarity=0.311 Sum_probs=20.4
Q ss_pred EEEEEEeCCCceEEEEEecccccc
Q 012503 374 TMKLTLEDPTARIHALLCGKEWVK 397 (462)
Q Consensus 374 ~f~L~lED~t~ri~~~v~~~da~~ 397 (462)
+..++|+|.++++.+.++.+-...
T Consensus 18 ~~~~~L~D~~~~i~~~~f~~~~~~ 41 (78)
T cd04489 18 HLYFTLKDEDASIRCVMWRSNARR 41 (78)
T ss_pred EEEEEEEeCCeEEEEEEEcchhhh
Confidence 778999999999999999875443
No 94
>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=29.81 E-value=40 Score=27.07 Aligned_cols=27 Identities=15% Similarity=0.159 Sum_probs=23.4
Q ss_pred eEEEEEecccchhhhcccCCCCCEEEE
Q 012503 237 TVLRVSTDRSYENFGRYFTATGKWVRI 263 (462)
Q Consensus 237 ~~l~V~~~~~~~~~~~~~~k~g~wV~l 263 (462)
..++|.+|...++.+.+.++.|++|.+
T Consensus 44 ~~~~v~~~g~~a~~~~~~~~kG~~V~v 70 (100)
T cd04496 44 DWIRVVAFGKLAENAAKYLKKGDLVYV 70 (100)
T ss_pred EEEEEEEEhHHHHHHHHHhCCCCEEEE
Confidence 467899999988888889999999964
No 95
>COG1599 RFA1 Single-stranded DNA-binding replication protein A (RPA), large (70 kD) subunit and related ssDNA-binding proteins [DNA replication, recombination, and repair]
Probab=29.36 E-value=1.7e+02 Score=30.58 Aligned_cols=78 Identities=17% Similarity=0.230 Sum_probs=55.9
Q ss_pred CCeEEEEEEEEecCCcc--ccC-CC-ceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCee
Q 012503 21 KHKVNLLGVVLEFSIPR--KSQ-GT-DYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAEL 96 (462)
Q Consensus 21 ~~~vnviGVVvd~~~P~--~tr-G~-D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~~~g~~ 96 (462)
.+.+|+.|-|.++..++ .++ |. .=..+..+.|.+-. +... +..+...+++. ..||++.+.+..+..|+|.+
T Consensus 59 ~~~~~v~~~V~~~~e~~~~~~k~g~~~~l~~~~v~Detg~---v~~~-~~~~~~a~~~~-e~Gdv~~i~~~~~~~~~~~~ 133 (407)
T COG1599 59 SSRVNVTGRVLSIGEKKTFDRKRGAEGKLAEVLVGDETGS---VKTV-TLWNIAALEKL-EPGDVIRIRNAYTSLYRGGK 133 (407)
T ss_pred hccccEEEEECccccceeeecccccccceEEEEEecCCCC---EEEE-eeccccccccC-CccceEEecCcccccccCce
Confidence 45799999999998766 443 43 33445557777653 3332 55555566677 68999999999999999999
Q ss_pred EEEecCC
Q 012503 97 SAVFYKD 103 (462)
Q Consensus 97 ~~~~~~~ 103 (462)
++..+..
T Consensus 134 ~~~~~~~ 140 (407)
T COG1599 134 RLSVGRV 140 (407)
T ss_pred eeecccc
Confidence 8887754
No 96
>COG2049 DUR1 Allophanate hydrolase subunit 1 [Amino acid transport and metabolism]
Probab=28.28 E-value=29 Score=33.40 Aligned_cols=39 Identities=10% Similarity=0.033 Sum_probs=27.4
Q ss_pred ccCCCcceEEEEEecccchhhhcccCCCCCEEEEEceEEEE
Q 012503 230 RNFFPVGTVLRVSTDRSYENFGRYFTATGKWVRIRNMSCQV 270 (462)
Q Consensus 230 ~~~p~~G~~l~V~~~~~~~~~~~~~~k~g~wV~l~Nv~~k~ 270 (462)
--|-.+|+|- +.+|++..+. --.+++||||+|+++..+.
T Consensus 177 GGWqlIGrTp-~~lfdp~~~~-p~ll~~Gd~VrF~~i~~~e 215 (223)
T COG2049 177 GGWQLIGRTP-LPLFDPDREP-PALLRPGDQVRFVPIKEEE 215 (223)
T ss_pred CceeEecccc-ccccCCCCCC-CeeccCCCEEEEEecCccc
Confidence 3466678663 3566666654 4679999999999987554
No 97
>PRK13254 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=27.98 E-value=3.8e+02 Score=24.05 Aligned_cols=66 Identities=18% Similarity=0.213 Sum_probs=46.3
Q ss_pred eeehhhhhhc---cCCeEEEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEe
Q 012503 10 IVRIKELAMH---VKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLK 85 (462)
Q Consensus 10 y~~i~d~~~~---~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~ 85 (462)
|.+.+++... .+..+.+-|.|++=+.-+ +.+-..+|.|.|... .+.|.+-. .+|...+.|.-|.+.
T Consensus 37 f~tpse~~~~~~~~g~~vrvgG~V~~gSi~~---~~~~~~~F~ltD~~~---~i~V~Y~G----~lPd~F~eg~~VVv~ 105 (148)
T PRK13254 37 FYTPSEVAEGEAPAGRRFRLGGLVEKGSVQR---GDGLTVRFVVTDGNA---TVPVVYTG----ILPDLFREGQGVVAE 105 (148)
T ss_pred eeCHHHHhcCCccCCCeEEEeEEEecCcEEe---CCCCEEEEEEEeCCe---EEEEEECC----CCCccccCCCEEEEE
Confidence 6777777663 477899999999654422 255678999999732 26665543 489877888876653
No 98
>PF15489 CTC1: CST, telomere maintenance, complex subunit CTC1
Probab=27.74 E-value=1.1e+03 Score=28.23 Aligned_cols=71 Identities=21% Similarity=0.277 Sum_probs=47.6
Q ss_pred cCCeEEEEEEEEecCCccccCCCceE-EEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCe
Q 012503 20 VKHKVNLLGVVLEFSIPRKSQGTDYV-CVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAE 95 (462)
Q Consensus 20 ~~~~vnviGVVvd~~~P~~trG~D~~-~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~~~g~ 95 (462)
.+..+||.|.|+..++-.+++|+-|. +++. |. ...+.|.+=-+..-.-=...++|+-..|.+++|...+|.
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 46679999999999999999887654 4444 22 223553322222211123448999999999999988884
No 99
>KOG4792 consensus Crk family adapters [Signal transduction mechanisms]
Probab=27.21 E-value=1.8e+02 Score=28.16 Aligned_cols=61 Identities=16% Similarity=0.327 Sum_probs=38.3
Q ss_pred cccCCCcceEEEEEecccchhhhcccCCCCCEEEEEceEEEEeCcEEEEEEeeCC------ceEEcCCCCh
Q 012503 229 LRNFFPVGTVLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSS------KIRLFSDNDN 293 (462)
Q Consensus 229 ~~~~p~~G~~l~V~~~~~~~~~~~~~~k~g~wV~l~Nv~~k~~~g~leG~l~~~s------ki~~l~~~d~ 293 (462)
..+-|.+..++|=.+-+...+- .-.+++||.|+. .-+..+|.|||-+.... .++.++..++
T Consensus 223 ~~~lPa~Arv~q~RVPnAYDkT-aL~levGdiVkV---Tk~ninGqwegElnGk~G~fPfThvrf~d~~~~ 289 (293)
T KOG4792|consen 223 QQNLPAYARVIQKRVPNAYDKT-ALALEVGDIVKV---TKKNINGQWEGELNGKIGHFPFTHVRFTDVQNP 289 (293)
T ss_pred ccCCChheeeehhcCCCccChh-hhhhhcCcEEEE---EeeccCceeeeeecCccccccceeEEeeccCCc
Confidence 3455666677665555444443 234889999963 33447899999887754 3555665443
No 100
>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=26.39 E-value=1.1e+02 Score=24.11 Aligned_cols=57 Identities=9% Similarity=0.096 Sum_probs=43.0
Q ss_pred CceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCeeEEEe
Q 012503 42 TDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAELSAVF 100 (462)
Q Consensus 42 ~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~~~g~~~~~~ 100 (462)
....+.+-|.|+.-. .|.+.++....+.+-...+.|.+..+.+.++..-++......
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 566788889998643 489999987566666655899999999999987776544443
No 101
>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=26.00 E-value=1.9e+02 Score=23.88 Aligned_cols=62 Identities=13% Similarity=-0.069 Sum_probs=36.1
Q ss_pred ceEEEEEecccchhhhccc----CCCCCEEEE-EceEEEEeCcE-EEEEEeeCCceEEcCCCChhHHHH
Q 012503 236 GTVLRVSTDRSYENFGRYF----TATGKWVRI-RNMSCQVSSGM-WHGLLQSSSKIRLFSDNDNVVWDY 298 (462)
Q Consensus 236 G~~l~V~~~~~~~~~~~~~----~k~g~wV~l-~Nv~~k~~~g~-leG~l~~~ski~~l~~~d~~v~~~ 298 (462)
|..|.+++|..+|...... -+.+-.|.+ +..+++.+.|. .-......|++. ++++-+.+.+.
T Consensus 34 ~~~l~~tlwG~~A~~f~~~~~~~~~~~~VVav~~~~rV~~~~g~~~ls~~~~~s~v~-inp~ipe~~~~ 101 (106)
T cd04481 34 DERLKCTLWGEYAEEFDAKFQSAGNGEPVVAVLRFWKIKEYKGPKSLSNSFGASKVY-INPDIPEVPEI 101 (106)
T ss_pred CCEEEEEEEHHHHHHHHHHHHHhCCCCcEEEEEEeEEEEEEcCCcEEEcCCCceEEE-ECCCcHHHHHH
Confidence 6788999999988764322 245556655 44888887762 211111345553 45444555444
No 102
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=25.55 E-value=2.5e+02 Score=34.66 Aligned_cols=40 Identities=25% Similarity=0.271 Sum_probs=27.7
Q ss_pred ccccccc-CCceeeeEEEEEEEeee-CCCC--eEEEEEEcCCCC
Q 012503 159 LSLKDIS-EHRYFDLVCKVFHVSYD-DSKG--LWMLFVWDGTDV 198 (462)
Q Consensus 159 ~~L~di~-~~~f~Dlv~qVv~v~~~-~~~~--~~~L~VwDgT~~ 198 (462)
..|+||. ++..+-+.++|.++-.. ..++ -.+++|+|||+.
T Consensus 227 ~~~~~i~~~~~~v~i~G~if~~e~~~~k~~~~~~~~~~td~~~s 270 (1437)
T PRK00448 227 TPMKEINEEERRVVVEGYVFKVEIKELKSGRHILTFKITDYTSS 270 (1437)
T ss_pred ccHHHhhccCCeEEEEEEEEEEEEEeccCCCEEEEEEEEcCCCC
Confidence 4577774 45677788899888732 2233 567899999964
No 103
>COG1570 XseA Exonuclease VII, large subunit [DNA replication, recombination, and repair]
Probab=24.29 E-value=6.7e+02 Score=26.75 Aligned_cols=65 Identities=17% Similarity=0.209 Sum_probs=47.6
Q ss_pred CeEEEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCe
Q 012503 22 HKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAE 95 (462)
Q Consensus 22 ~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~~~g~ 95 (462)
+.|=|-|=|..++.| ..| ..-|+|.|+.-. |.|.+|+.+...|....+.|+-|.+ +-+|+.|-++
T Consensus 24 ~~V~v~GEISn~t~~--~sg---H~YFtLKD~~A~---i~c~mf~~~~~~l~f~p~eG~~V~v-~G~is~Y~~r 88 (440)
T COG1570 24 GQVWVRGEISNFTRP--ASG---HLYFTLKDERAQ---IRCVMFKGNNRRLKFRPEEGMQVLV-RGKISLYEPR 88 (440)
T ss_pred CeEEEEEEecCCccC--CCc---cEEEEEccCCce---EEEEEEcCcccccCCCccCCCEEEE-EEEEEEEcCC
Confidence 357777877777754 233 666889999553 9999999888888876688998877 3466666443
No 104
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=24.11 E-value=1.7e+02 Score=35.07 Aligned_cols=70 Identities=19% Similarity=0.202 Sum_probs=0.0
Q ss_pred ccccccccccCCce-eeeEEEEEEEee---eCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCChhcccc
Q 012503 156 DYLLSLKDISEHRY-FDLVCKVFHVSY---DDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRN 231 (462)
Q Consensus 156 ~f~~~L~di~~~~f-~Dlv~qVv~v~~---~~~~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~ 231 (462)
++ ..|-++.++.+ +-+.++|-.+-- ..+..-+.++|||||+.
T Consensus 228 ~i-~~~~~i~~~~~~v~v~G~IF~~e~~~~ksGr~l~~i~vTD~t~S--------------------------------- 273 (1444)
T COG2176 228 EI-KPLIKINEEETRVKVEGYIFKIEIKELKSGRTLLNIKVTDYTSS--------------------------------- 273 (1444)
T ss_pred ce-eehhhccccccceEEEEEEEEEeeeecccCcEEEEEEEecCchh---------------------------------
Q ss_pred CCCcceEEEEEecccchhhhcccCCCCCEEEEE
Q 012503 232 FFPVGTVLRVSTDRSYENFGRYFTATGKWVRIR 264 (462)
Q Consensus 232 ~p~~G~~l~V~~~~~~~~~~~~~~k~g~wV~l~ 264 (462)
++++..+.+....-..+.++.|+||+.+
T Consensus 274 -----l~~k~f~~~~ed~~~~~~ik~g~wvk~~ 301 (1444)
T COG2176 274 -----LILKKFLRDEEDEKKFDGIKKGMWVKAR 301 (1444)
T ss_pred -----eeehhhccccccHHHHhhcccCcEEEEE
No 105
>KOG3416 consensus Predicted nucleic acid binding protein [General function prediction only]
Probab=23.55 E-value=78 Score=27.65 Aligned_cols=32 Identities=13% Similarity=0.186 Sum_probs=24.0
Q ss_pred EEEEEecccchhhhcccCCCCCEEEEEceEEEEeCc
Q 012503 238 VLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSG 273 (462)
Q Consensus 238 ~l~V~~~~~~~~~~~~~~k~g~wV~l~Nv~~k~~~g 273 (462)
++.|.+|+.. -..++|||.|+|++=-..+..|
T Consensus 49 sI~isvW~e~----~~~~~PGDIirLt~Gy~Si~qg 80 (134)
T KOG3416|consen 49 SINISVWDEE----GCLIQPGDIIRLTGGYASIFQG 80 (134)
T ss_pred eEEEEEecCc----CcccCCccEEEecccchhhhcC
Confidence 4578889832 3569999999999877777555
No 106
>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=23.20 E-value=4e+02 Score=22.88 Aligned_cols=68 Identities=18% Similarity=0.173 Sum_probs=44.6
Q ss_pred hhhhh-hccCCeEEEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCC---CCCCCCCCCCCEEEEeeEE
Q 012503 13 IKELA-MHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSI---DQLPRVLSPRDLILLKNVM 88 (462)
Q Consensus 13 i~d~~-~~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~---~~LP~v~~~GDII~l~rvk 88 (462)
+.++. ...|+.|.+.|-|...+. .|+ .+=+.|.|.+. .+.+.+-.+.. +.+..+ ..||+|.+...-
T Consensus 5 ~~~~~~~~~g~~V~i~Gwv~~~R~----~gk--~~Fi~LrD~~g---~~Q~v~~~~~~~~~~~~~~l-~~gs~V~V~G~~ 74 (135)
T cd04317 5 CGELRESHVGQEVTLCGWVQRRRD----HGG--LIFIDLRDRYG---IVQVVFDPEEAPEFELAEKL-RNESVIQVTGKV 74 (135)
T ss_pred hhhCChhHCCCEEEEEEeEehhcc----cCC--EEEEEEecCCe---eEEEEEeCCchhHHHHHhCC-CCccEEEEEEEE
Confidence 34443 236788999999977554 344 67778888874 26666644322 244556 689999999964
Q ss_pred EE
Q 012503 89 IK 90 (462)
Q Consensus 89 i~ 90 (462)
..
T Consensus 75 ~~ 76 (135)
T cd04317 75 RA 76 (135)
T ss_pred EC
Confidence 43
No 107
>PRK07772 single-stranded DNA-binding protein; Provisional
Probab=20.88 E-value=1.8e+02 Score=27.18 Aligned_cols=75 Identities=8% Similarity=0.135 Sum_probs=50.1
Q ss_pred CCeEEEEEEEEecCCccccCCCceEEEEEEEeC-CC-C----------CCCeEEEEecCCCCCCCCCCCCCCEEEEe-eE
Q 012503 21 KHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDD-SQ-Q----------SPELLVNIFTSSIDQLPRVLSPRDLILLK-NV 87 (462)
Q Consensus 21 ~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~-s~-~----------~~gl~v~iF~~~~~~LP~v~~~GDII~l~-rv 87 (462)
...|.|+|=++.--.-+.|....-+++|+|.-. .. . ..-++|.+|.+..+.+-.-.+.||-|.+. |+
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 346888888776533355555567889999732 21 1 11489999997666666534789966665 78
Q ss_pred EEEEEcCe
Q 012503 88 MIKKHQAE 95 (462)
Q Consensus 88 ki~~~~g~ 95 (462)
+.+.|.++
T Consensus 84 ~~r~wedk 91 (186)
T PRK07772 84 KQRSYETR 91 (186)
T ss_pred EcCceECC
Confidence 88888643
No 108
>PRK08763 single-stranded DNA-binding protein; Provisional
Probab=20.55 E-value=1.2e+02 Score=27.76 Aligned_cols=26 Identities=15% Similarity=0.047 Sum_probs=22.7
Q ss_pred EEEEEecccchhhhcccCCCCCEEEE
Q 012503 238 VLRVSTDRSYENFGRYFTATGKWVRI 263 (462)
Q Consensus 238 ~l~V~~~~~~~~~~~~~~k~g~wV~l 263 (462)
-++|++|...++.+.+.++.|+.|.+
T Consensus 53 w~~Vv~fgk~Ae~v~~~L~KGs~V~V 78 (164)
T PRK08763 53 WHRVKFFGKLGEIAGEYLRKGSQCYI 78 (164)
T ss_pred EEEEEEehHHHHHHHHhcCCCCEEEE
Confidence 46899999999988899999999953
Done!