Query 012425
Match_columns 464
No_of_seqs 167 out of 234
Neff 7.1
Searched_HMMs 46136
Date Fri Mar 29 02:30:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/012425.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/012425hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4757 Predicted telomere bin 100.0 3.6E-52 7.8E-57 412.4 16.5 427 5-461 4-516 (522)
2 cd04497 hPOT1_OB1_like hPOT1_O 100.0 1E-33 2.2E-38 252.4 17.4 137 8-145 1-138 (138)
3 PF02765 POT1: Telomeric singl 100.0 1.6E-32 3.4E-37 247.1 13.5 136 10-145 1-146 (146)
4 cd04498 hPOT1_OB2 hPOT1_OB2: A 99.9 1.8E-21 3.9E-26 167.9 12.1 109 167-285 1-123 (123)
5 PRK12366 replication factor A; 99.3 9.9E-10 2.1E-14 120.7 30.5 292 6-399 275-590 (637)
6 PRK07218 replication factor A; 99.1 7.7E-08 1.7E-12 100.3 28.0 198 9-288 57-257 (423)
7 PRK12366 replication factor A; 99.1 5.2E-08 1.1E-12 107.2 27.0 278 8-399 61-344 (637)
8 TIGR00617 rpa1 replication fac 99.0 2.4E-07 5.1E-12 101.5 29.5 314 9-399 179-537 (608)
9 PRK06386 replication factor A; 99.0 3.9E-07 8.5E-12 92.9 28.3 275 11-399 3-290 (358)
10 PRK14699 replication factor A; 99.0 2.2E-07 4.7E-12 98.8 27.5 271 11-398 167-448 (484)
11 PRK15491 replication factor A; 99.0 2.8E-07 6E-12 95.2 26.5 270 9-396 56-336 (374)
12 PRK07211 replication factor A; 98.9 6.6E-08 1.4E-12 101.9 19.5 204 8-287 159-367 (485)
13 PRK15491 replication factor A; 98.8 2.9E-07 6.2E-12 95.1 19.3 204 6-283 162-372 (374)
14 PRK14699 replication factor A; 98.6 4.3E-06 9.4E-11 89.0 19.1 203 9-285 275-484 (484)
15 PRK07211 replication factor A; 98.5 0.00011 2.4E-09 77.9 26.6 266 10-395 53-328 (485)
16 PRK08402 replication factor A; 98.3 9.2E-05 2E-09 75.9 19.5 101 156-287 62-164 (355)
17 TIGR00617 rpa1 replication fac 98.0 0.00011 2.5E-09 80.6 14.4 159 4-197 292-479 (608)
18 cd04475 RPA1_DBD_B RPA1_DBD_B: 97.9 9.4E-05 2E-09 62.1 10.0 74 23-101 1-79 (101)
19 PRK06461 single-stranded DNA-b 97.8 0.00022 4.9E-09 62.8 11.2 85 10-103 4-92 (129)
20 PRK07218 replication factor A; 97.6 0.0082 1.8E-07 63.1 19.8 161 155-394 57-219 (423)
21 cd04491 SoSSB_OBF SoSSB_OBF: A 97.4 0.0016 3.4E-08 52.5 9.5 72 25-102 1-75 (82)
22 PRK07217 replication factor A; 97.0 0.14 2.9E-06 51.5 20.9 166 155-399 71-244 (311)
23 PRK06461 single-stranded DNA-b 96.9 0.0081 1.8E-07 53.0 9.9 96 156-287 4-100 (129)
24 PRK08402 replication factor A; 96.8 0.033 7.1E-07 57.4 14.6 140 9-179 61-208 (355)
25 cd04497 hPOT1_OB1_like hPOT1_O 96.7 0.017 3.7E-07 51.4 10.2 95 155-286 2-104 (138)
26 KOG4757 Predicted telomere bin 96.7 0.0012 2.5E-08 67.7 3.0 80 378-463 373-462 (522)
27 cd03524 RPA2_OBF_family RPA2_O 96.3 0.02 4.2E-07 43.5 7.5 70 25-100 1-70 (75)
28 KOG3416 Predicted nucleic acid 96.3 0.02 4.3E-07 49.5 7.7 83 11-102 5-88 (134)
29 PRK07217 replication factor A; 95.6 0.12 2.7E-06 51.8 11.3 91 8-109 70-160 (311)
30 PF02765 POT1: Telomeric singl 95.6 0.37 8.1E-06 43.2 13.3 97 156-285 1-109 (146)
31 PF01336 tRNA_anti-codon: OB-f 95.0 0.054 1.2E-06 41.9 5.4 68 24-101 1-70 (75)
32 PF15489 CTC1: CST, telomere m 94.9 0.19 4.2E-06 57.9 11.3 142 235-411 888-1054(1144)
33 cd04489 ExoVII_LU_OBF ExoVII_L 94.8 0.32 6.8E-06 38.2 9.3 69 24-101 2-72 (78)
34 cd04481 RPA1_DBD_B_like RPA1_D 94.7 0.17 3.6E-06 42.8 7.8 82 25-108 1-90 (106)
35 PRK06386 replication factor A; 94.4 0.25 5.4E-06 50.9 9.9 85 8-103 105-191 (358)
36 cd04474 RPA1_DBD_A RPA1_DBD_A: 93.9 0.21 4.6E-06 42.1 6.8 84 12-99 1-88 (104)
37 cd04475 RPA1_DBD_B RPA1_DBD_B: 93.2 1.3 2.8E-05 36.8 10.4 63 233-299 38-100 (101)
38 cd04491 SoSSB_OBF SoSSB_OBF: A 93.1 0.31 6.8E-06 39.0 6.3 46 235-283 35-80 (82)
39 cd04478 RPA2_DBD_D RPA2_DBD_D: 92.9 0.9 1.9E-05 37.2 8.9 65 24-99 2-70 (95)
40 cd04485 DnaE_OBF DnaE_OBF: A s 92.5 0.36 7.9E-06 37.7 5.9 70 26-100 2-71 (84)
41 PRK13480 3'-5' exoribonuclease 92.4 1.9 4.1E-05 43.9 12.1 79 12-99 4-83 (314)
42 cd04476 RPA1_DBD_C RPA1_DBD_C: 91.3 0.31 6.6E-06 44.6 4.8 29 372-400 68-96 (166)
43 cd04492 YhaM_OBF_like YhaM_OBF 90.8 2.1 4.5E-05 33.5 8.7 67 27-99 3-69 (83)
44 PF08646 Rep_fac-A_C: Replicat 89.8 0.29 6.2E-06 43.8 3.1 28 372-399 54-81 (146)
45 cd04483 hOBFC1_like hOBFC1_lik 89.6 2.7 5.8E-05 34.7 8.4 64 26-100 2-86 (92)
46 cd04474 RPA1_DBD_A RPA1_DBD_A: 89.0 1.3 2.7E-05 37.4 6.3 53 346-400 10-64 (104)
47 cd04488 RecG_wedge_OBF RecG_we 82.8 9.8 0.00021 28.7 8.1 67 26-99 2-68 (75)
48 PF13742 tRNA_anti_2: OB-fold 80.0 16 0.00035 30.4 8.8 77 13-98 11-92 (99)
49 cd04484 polC_OBF polC_OBF: A s 78.6 18 0.00038 29.1 8.4 71 24-98 2-74 (82)
50 cd03524 RPA2_OBF_family RPA2_O 78.6 24 0.00051 25.9 10.1 66 169-274 1-68 (75)
51 PRK07373 DNA polymerase III su 74.5 11 0.00023 40.4 7.8 88 9-101 267-355 (449)
52 cd04487 RecJ_OBF2_like RecJ_OB 73.3 30 0.00065 27.1 8.2 64 26-100 3-67 (73)
53 PF01336 tRNA_anti-codon: OB-f 71.9 40 0.00087 25.4 11.3 61 168-269 1-61 (75)
54 PRK05673 dnaE DNA polymerase I 69.3 13 0.00029 44.2 7.7 86 10-101 965-1052(1135)
55 cd04490 PolII_SU_OBF PolII_SU_ 67.0 20 0.00044 28.5 6.1 59 24-91 2-62 (79)
56 PF09104 BRCA-2_OB3: BRCA2, ol 63.6 33 0.00071 30.8 7.2 73 11-90 4-81 (143)
57 PF02721 DUF223: Domain of unk 63.6 29 0.00063 28.5 6.6 55 232-286 8-69 (95)
58 cd04478 RPA2_DBD_D RPA2_DBD_D: 63.1 8.8 0.00019 31.2 3.4 21 373-393 17-37 (95)
59 KOG3056 Protein required for S 62.6 13 0.00027 40.4 5.2 69 23-94 187-256 (578)
60 cd04480 RPA1_DBD_A_like RPA1_D 61.6 18 0.0004 28.9 5.0 45 350-399 2-47 (86)
61 PRK06920 dnaE DNA polymerase I 60.1 26 0.00056 41.7 7.7 88 9-101 931-1018(1107)
62 cd04498 hPOT1_OB2 hPOT1_OB2: A 59.6 11 0.00024 33.0 3.5 34 60-94 62-95 (123)
63 cd04495 BRCA2DBD_OB3 BRCA2DBD_ 58.4 44 0.00096 28.0 6.6 64 25-94 1-65 (100)
64 cd04482 RPA2_OBF_like RPA2_OBF 58.1 40 0.00088 27.6 6.5 60 26-93 3-64 (91)
65 PF12100 DUF3576: Domain of un 58.1 20 0.00044 30.2 4.7 53 9-68 17-70 (103)
66 PRK07374 dnaE DNA polymerase I 54.2 37 0.0008 40.7 7.7 88 9-101 987-1075(1170)
67 cd04483 hOBFC1_like hOBFC1_lik 52.9 17 0.00037 29.9 3.4 21 373-393 15-35 (92)
68 PF09104 BRCA-2_OB3: BRCA2, ol 50.1 1.3E+02 0.0027 27.1 8.6 33 236-268 50-83 (143)
69 cd04496 SSB_OBF SSB_OBF: A sub 49.4 31 0.00067 27.8 4.5 26 235-260 45-70 (100)
70 TIGR00237 xseA exodeoxyribonuc 48.2 1.1E+02 0.0025 32.4 9.7 78 13-99 9-88 (432)
71 PRK00286 xseA exodeoxyribonucl 48.1 1.2E+02 0.0025 32.2 9.8 68 22-98 24-93 (438)
72 cd04490 PolII_SU_OBF PolII_SU_ 47.4 23 0.00049 28.3 3.2 21 375-395 20-40 (79)
73 TIGR00643 recG ATP-dependent D 46.8 1.2E+02 0.0026 33.8 10.0 78 12-99 25-103 (630)
74 PF01245 Ribosomal_L19: Riboso 46.3 58 0.0013 28.0 5.8 39 70-109 14-60 (113)
75 PRK05338 rplS 50S ribosomal pr 46.2 44 0.00095 28.9 5.0 42 70-112 14-63 (116)
76 PF15072 DUF4539: Domain of un 46.1 67 0.0015 26.2 5.8 61 23-91 3-63 (86)
77 PF15072 DUF4539: Domain of un 45.3 19 0.00041 29.4 2.5 23 373-395 20-42 (86)
78 cd04480 RPA1_DBD_A_like RPA1_D 44.1 54 0.0012 26.2 5.1 37 233-269 30-66 (86)
79 PRK10917 ATP-dependent DNA hel 43.9 94 0.002 35.1 8.7 79 11-98 51-129 (681)
80 PF11325 DUF3127: Domain of un 43.2 1.8E+02 0.0038 23.7 7.8 66 28-95 4-73 (84)
81 cd04492 YhaM_OBF_like YhaM_OBF 42.7 35 0.00076 26.3 3.7 25 369-393 16-40 (83)
82 COG1107 Archaea-specific RecJ- 41.4 1.3E+02 0.0029 33.1 8.7 78 10-98 202-280 (715)
83 PRK06826 dnaE DNA polymerase I 40.3 73 0.0016 38.2 7.3 77 20-101 990-1067(1151)
84 CHL00084 rpl19 ribosomal prote 40.0 61 0.0013 28.1 4.9 39 70-109 18-64 (117)
85 COG1200 RecG RecG-like helicas 39.0 3.4E+02 0.0074 30.6 11.6 78 13-99 54-131 (677)
86 PRK00448 polC DNA polymerase I 38.1 1.3E+02 0.0028 37.0 9.0 86 7-98 223-312 (1437)
87 TIGR01024 rplS_bact ribosomal 37.9 62 0.0013 27.9 4.6 42 70-112 14-63 (113)
88 cd04489 ExoVII_LU_OBF ExoVII_L 36.1 47 0.001 25.6 3.5 22 373-394 18-39 (78)
89 PF14535 AMP-binding_C_2: AMP- 36.1 29 0.00063 28.5 2.3 61 355-417 2-70 (96)
90 PRK05672 dnaE2 error-prone DNA 35.4 91 0.002 37.1 7.0 86 9-101 940-1026(1046)
91 cd04485 DnaE_OBF DnaE_OBF: A s 34.0 49 0.0011 25.2 3.3 25 369-393 16-40 (84)
92 COG1570 XseA Exonuclease VII, 32.2 4.1E+02 0.0089 28.4 10.5 64 22-94 24-87 (440)
93 PRK08763 single-stranded DNA-b 31.3 82 0.0018 28.9 4.7 26 235-260 53-78 (164)
94 PRK07772 single-stranded DNA-b 31.2 77 0.0017 29.7 4.5 74 21-94 4-90 (186)
95 PRK07274 single-stranded DNA-b 30.0 93 0.002 27.3 4.6 25 235-259 48-72 (131)
96 COG1599 RFA1 Single-stranded D 29.7 1.4E+02 0.0031 31.3 6.8 87 11-103 50-140 (407)
97 KOG2971 RNA-binding protein re 29.0 1.2E+02 0.0025 30.0 5.3 50 398-457 162-212 (299)
98 PRK09010 single-stranded DNA-b 27.4 1.1E+02 0.0023 28.5 4.7 26 235-260 55-80 (177)
99 cd04486 YhcR_OBF_like YhcR_OBF 27.3 3.1E+02 0.0068 21.6 8.7 62 27-101 3-69 (78)
100 PRK07459 single-stranded DNA-b 27.1 1.2E+02 0.0026 26.2 4.7 73 22-94 4-81 (121)
101 PF00436 SSB: Single-strand bi 26.5 97 0.0021 25.1 4.0 27 235-261 49-75 (104)
102 cd04481 RPA1_DBD_B_like RPA1_D 26.2 2.7E+02 0.0059 23.0 6.7 64 233-297 34-103 (106)
103 PRK13732 single-stranded DNA-b 25.0 1.2E+02 0.0026 28.1 4.6 27 235-261 55-81 (175)
104 PRK05733 single-stranded DNA-b 24.8 1.2E+02 0.0027 28.0 4.6 27 234-260 53-79 (172)
105 PRK07279 dnaE DNA polymerase I 24.5 1.7E+02 0.0038 34.7 6.8 85 10-101 875-960 (1034)
106 PRK07459 single-stranded DNA-b 24.1 1.4E+02 0.0031 25.7 4.7 25 235-259 45-69 (121)
107 KOG4792 Crk family adapters [S 23.8 2.2E+02 0.0048 27.6 6.1 38 250-290 246-289 (293)
108 PRK06752 single-stranded DNA-b 23.6 1.5E+02 0.0033 25.0 4.7 25 235-259 48-72 (112)
109 PRK06752 single-stranded DNA-b 22.9 2E+02 0.0044 24.3 5.3 72 23-94 4-84 (112)
110 TIGR00621 ssb single stranded 22.5 1.5E+02 0.0032 27.1 4.7 27 235-261 52-78 (164)
111 cd04496 SSB_OBF SSB_OBF: A sub 22.0 1.7E+02 0.0036 23.4 4.6 71 24-95 1-82 (100)
112 PRK08486 single-stranded DNA-b 22.0 1.5E+02 0.0032 27.7 4.6 25 235-259 50-74 (182)
113 PRK06751 single-stranded DNA-b 21.8 2.3E+02 0.0049 26.3 5.8 72 23-94 4-84 (173)
114 PRK07738 flagellar protein Fla 21.1 2E+02 0.0043 25.0 4.8 47 372-418 64-112 (117)
115 PRK07135 dnaE DNA polymerase I 21.0 2.2E+02 0.0048 33.6 6.7 65 12-84 890-954 (973)
116 PRK06958 single-stranded DNA-b 20.9 1.9E+02 0.0041 27.1 5.1 74 22-95 5-90 (182)
117 cd02792 MopB_CT_Formate-Dh-Na- 20.8 1.3E+02 0.0028 25.2 3.8 18 246-263 43-60 (122)
118 cd02790 MopB_CT_Formate-Dh_H F 20.4 1.2E+02 0.0027 25.0 3.5 20 245-264 42-61 (116)
119 COG0335 RplS Ribosomal protein 20.0 2.5E+02 0.0055 24.2 5.1 41 70-111 16-64 (115)
120 PRK06751 single-stranded DNA-b 20.0 1.9E+02 0.0042 26.7 4.9 26 235-260 48-73 (173)
No 1
>KOG4757 consensus Predicted telomere binding protein [General function prediction only]
Probab=100.00 E-value=3.6e-52 Score=412.37 Aligned_cols=427 Identities=24% Similarity=0.296 Sum_probs=327.7
Q ss_pred CCceeeEehHHHhhccCCeEEEEEEEEeeCCcccccCCceEEEEEEEeCCCCCCCeEEEEeccCcCCCCCCCCCCCEEEE
Q 012425 5 GEDYRFLKIKDAILSINQKVSFVGVILEVGSPKQSKGTDSFCTIKVTDESHTKDGISVNIFAESMEKLPYIVSVGDIILL 84 (464)
Q Consensus 5 ~~~y~y~~i~d~~~~~~~~vnviGVVvd~~~P~~trGtD~~~tl~I~D~S~~~~gl~v~iF~~~~e~LP~v~~~GDII~l 84 (464)
.+.|+|..+++++...|+.||+||||+++++|++++|+||+||++|+|+.+.+.||+|++|+++-++||.|.++||||+|
T Consensus 4 ~ds~k~Iri~da~kk~~tiVNl~GiVkef~pp~qs~g~D~~~tv~IvDp~~ss~gLtv~lfSkt~edLP~Ik~~GDiill 83 (522)
T KOG4757|consen 4 RDSLKLIRISDALKKKNTIVNLIGIVKEFTPPRQSLGKDWVCTVYIVDPDYSSIGLTVHLFSKTGEDLPVIKQVGDIILL 83 (522)
T ss_pred ccchheeechHHHHhcCcEEEEEEEEEeccChhhccCCceEEEEEEeCCCCCCCCcEEEEecCchhhCccccccCcEEEE
Confidence 46899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeEEEEEECCeeEEeecCCc-eeEEEEeCCCCCCccccccCCCcccChhHHHHHHHHHHHHhhcccccCCccccccccCC
Q 012425 85 SHVVMKAHNKQAYALFNKKF-SSFALYDGKGGEDFLPYQVSSRFFVRDQDKRIIAAVRKWLLNFQFKEDSKKFLLLREIK 163 (464)
Q Consensus 85 ~rvkv~~~~g~~~~~~~~~~-ss~~lf~g~~~~~~~P~~~s~~~~~~~~e~~~v~~Lr~w~~~~~~~~~~~~f~~L~di~ 163 (464)
||+|||.|+.+.+|+++..+ |+|++|+|+ +.+..|||+|+.|-++ .+||+|++.+.+...+ ++..+.++.
T Consensus 84 hRiKiq~y~~rtqgl~s~~fss~~~~Feg~-svd~i~~qssp~f~~t-------~nlrew~a~~~s~~w~-c~t~~~k~f 154 (522)
T KOG4757|consen 84 HRIKIQSYRDRTQGLCSDQFSSAWALFEGN-SVDTICYQSSPRFMKT-------GNLREWFALYKSKIWD-CQTNLHKNF 154 (522)
T ss_pred EEEEEEEhhhhhhhhhhcchhhhhhhhcCC-CCCccCCCCchhhhcc-------chHHHHHHHHhCcccc-cccCHhHhh
Confidence 99999999999999999776 448999999 8889999999998777 7899999988776555 577788888
Q ss_pred CCCeEeEEEEEeEEEeeCCCeEEEEEEeCCCCCCCccccccccc-ccCCCCCcccCCCCcccccccCCCcccEEEEEEcc
Q 012425 164 DGQRINMACKVFHICEVAKGEWMAFVWDGTDAPPAQISKKLEDE-MDHELPLQVEPLPLSRDILCSFPAVGSILRVIIDK 242 (464)
Q Consensus 164 ~~~f~Dl~~qVv~~~~~~~~~~~L~VwDgT~~p~~~~~~~~~~~-~~~~~~~~~e~~~l~~~~l~~~p~~G~~l~V~~~~ 242 (464)
++..-.|.||+++........|. .|||-|-+....+++...-- -..-.|+++++ .+...+..||..|.+.+...+.
T Consensus 155 el~cs~l~~q~v~g~s~~~~~w~-lv~d~~~h~~~s~~~~~~~~~ySlr~~l~~~~--~~T~~~l~Fp~~g~ts~~r~~r 231 (522)
T KOG4757|consen 155 ELLCSSLARQNVTGLSYPSVSWS-LVSDITPHQRCSFYAQVIKTWYSLRNPLLYVT--DPTENLLFFPMSGYTSSSRWDR 231 (522)
T ss_pred hhhcchhhhheeeccccccceee-eeecccccccccccccceeeEeeccccccccc--CchHhhhhcccCCceeeeeeec
Confidence 88888888899988777778888 59996655554443321100 01224666665 5677778899999888888888
Q ss_pred chhHHHhhccCCCCEEEEeceEEEEeCcEEEEEEecccceEEcCCCChHHHHHHHHHHH---Hhh-------ccC---CC
Q 012425 243 GIEKHILHLLKIGKWVKLQNVLCQVDAGLWFGVLTHFTRLRYVPTNDNLIVERQRSYDE---RLS-------WEH---SR 309 (464)
Q Consensus 243 ~~~~~~~~~lk~G~wV~l~Nv~~k~~~G~leG~l~~~ski~~l~~~d~~v~~r~r~y~~---r~~-------~~~---~~ 309 (464)
+.++++.+.+.+|.-+..+|+...-+ .+|.++ ++.+ .|..-..|.-++.. |+. ++. ++
T Consensus 232 v~~e~~i~ilq~~~d~~~~Nl~~e~D-----~~f~~~--~~sl--~dh~~lsrc~~~~~saprl~~sl~lhc~~ehll~e 302 (522)
T KOG4757|consen 232 VSEEFSICILQDEHDFYCRNLIKEGD-----YVFMKN--VRSL--IDHLGLSRCILHGDSAPRLNMSLELHCSEEHLLNE 302 (522)
T ss_pred ccccccchhccccchhhhhhhccccc-----cccccc--chhh--hHHHHHHHHHHHhhccccccceeEeecCcchhhcc
Confidence 88888788888888888888876211 122222 2111 13333333222221 110 000 11
Q ss_pred CCc--ccCCCCCccccCCCCCCCCcccHHhhhcCcccCceeE-EEEEEEe---ecCCCcccc----------cc------
Q 012425 310 MPY--WCFPWTSEVTDIDYSEDGPFVTLKDVLTHSQVTAKFK-CVVRVVA---ALPWRSEDF----------CS------ 367 (464)
Q Consensus 310 ~~~--~~~p~~~~it~~~~~~~~p~~Tl~diLt~~~v~~kfr-~~VRVV~---~~P~~~edf----------~~------ 367 (464)
.+- +.. ..+..|.+++. .+|+++|||+++.+.++.||| |+||+|+ .+|.++|.+ |.
T Consensus 303 v~~e~r~~-~q~~~tgi~~v-~a~fvsl~Ds~t~~~vt~k~R~~vvrfva~~~~~P~sve~l~~i~i~l~~ic~l~n~r~ 380 (522)
T KOG4757|consen 303 VKPEKRLY-VQNCQTGIEAV-IAPFVSLMDSETPFIVTEKKRTCVVRFVAHVINYPASVELLTIITILLAPICNLLNPRK 380 (522)
T ss_pred cCccccee-ecccccCcchh-hcccchhhhhccccccchhcceeeeeehhhcccccchhhhhhhhhhhhHHHhhhhchhh
Confidence 110 111 12566778888 999999999999999999999 9999999 999999988 20
Q ss_pred -----------------------C----------------Cc------cEEEEEEEecCCceEEEEEecCchhhhcC---
Q 012425 368 -----------------------P----------------LG------NYRIRLTLEDPTARIHAFVYAEDGEKLFG--- 399 (464)
Q Consensus 368 -----------------------~----------------~g------~~~~~l~leD~t~~l~~~v~~~da~~f~~--- 399 (464)
+ .+ .|..+++|.|.++.|++++.+. ..+|+
T Consensus 381 H~~l~~le~s~p~s~~~fgc~~~~~~~~v~~ln~Lv~~e~~~~vP~~~~~v~~~~l~~~s~~l~~~l~d~--~~~fqi~d 458 (522)
T KOG4757|consen 381 HRLLVQLEDSWPKSLTQFGCLSQPPSSYVWMLNLLVRDESNVTVPVIFFDVDAAELINSSKKLPCNLADH--QMTFQIKD 458 (522)
T ss_pred hhhhhhhcccCcccceeeeeccCCHHHHHHHHHHHhccccccccccccchhheeeeccccccccchhccc--cceEEecc
Confidence 0 11 1788999999999999999875 78887
Q ss_pred -CCCchHHHHHHHHHHhcCCCCCCccccCCCCCCcceeEeEEeeeeCCCCcceeeEEEeeeee
Q 012425 400 -GYPFVDVLKRKINKLLGVAVSDGQEIKDAPRNPPWVQCCLKSYYIDRNDIWGSRQYRIFDTK 461 (464)
Q Consensus 400 -~~~~~~~l~~kl~~l~g~~e~~~~~~~~~~~~~pw~~cci~sY~~~~~~~~~~r~y~iF~T~ 461 (464)
.+..-+.|+|+..+.+.+-|++.. +....||++|.||||.+. +.+-.+.+||+|+|.
T Consensus 459 s~il~~~~l~~~i~~~~~~~~~p~~----~~~~~pw~~~~vk~y~i~-n~~d~q~~~q~~~~~ 516 (522)
T KOG4757|consen 459 SLILIWGNLEERIQHHISKGESPTL----AAEETPWFDIYVKEYIIG-NTKDHQSLLQKRWRG 516 (522)
T ss_pred eeeeecccHHHHHHHHHhcCCCCcc----cccccccceeeeeeeeec-CCcchHHHHHHHhhc
Confidence 234568899999999998888755 557899999999999987 444456556555443
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=1e-33 Score=252.40 Aligned_cols=137 Identities=33% Similarity=0.592 Sum_probs=130.7
Q ss_pred eeeEehHHHhhccCCeEEEEEEEEeeCCcccccCCceEEEEEEEeCCCC-CCCeEEEEeccCcCCCCCCCCCCCEEEEee
Q 012425 8 YRFLKIKDAILSINQKVSFVGVILEVGSPKQSKGTDSFCTIKVTDESHT-KDGISVNIFAESMEKLPYIVSVGDIILLSH 86 (464)
Q Consensus 8 y~y~~i~d~~~~~~~~vnviGVVvd~~~P~~trGtD~~~tl~I~D~S~~-~~gl~v~iF~~~~e~LP~v~~~GDII~l~r 86 (464)
|.|++|++|....++.|||||||+|+++|++++|+||+|+|+|+|+|.. +.||+|+||+++.++||.+ ++||||+|||
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 5999999999
Q ss_pred EEEEEECCeeEEeecCCceeEEEEeCCCCCCccccccCCCcccChhHHHHHHHHHHHHh
Q 012425 87 VVMKAHNKQAYALFNKKFSSFALYDGKGGEDFLPYQVSSRFFVRDQDKRIIAAVRKWLL 145 (464)
Q Consensus 87 vkv~~~~g~~~~~~~~~~ss~~lf~g~~~~~~~P~~~s~~~~~~~~e~~~v~~Lr~w~~ 145 (464)
+||+.|||+.+++++.+.||||||++..+....|++.+++++++++|++++..||+|+.
T Consensus 80 ~kv~~~~g~~~~~~~~~~ss~avf~~~~~~~~~p~~~~~~~~~~~~e~~~~~~Lr~w~~ 138 (138)
T cd04497 80 VKIQSYNGKPQGISNDRGSSWAVFRGDDGVVPIPQQSSKPVEFGPEEEPSVEELRKWAS 138 (138)
T ss_pred EEEEEECCceEEEECCCceeEEEEcCCCCCCcCccccCCCcccCcchHHHHHHHHHhhC
Confidence 99999999999999986799999999999888899999999999999999999999973
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=1.6e-32 Score=247.11 Aligned_cols=136 Identities=37% Similarity=0.645 Sum_probs=125.6
Q ss_pred eEehHHHhhccCCeEEEEEEEEeeCCc--ccccCCceEEEEEEEeCCCCC-----CCeEEEEeccCcCCCCCCCCCCCEE
Q 012425 10 FLKIKDAILSINQKVSFVGVILEVGSP--KQSKGTDSFCTIKVTDESHTK-----DGISVNIFAESMEKLPYIVSVGDII 82 (464)
Q Consensus 10 y~~i~d~~~~~~~~vnviGVVvd~~~P--~~trGtD~~~tl~I~D~S~~~-----~gl~v~iF~~~~e~LP~v~~~GDII 82 (464)
|++|+++....++.|||||||+|+++| ++|||+||+|+|+|+|+|+.. .||+|+||+++.+.||.+..+||||
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 789998888889999999999999999 999999999999999999985 7999999999999999999889999
Q ss_pred EEeeEEEEEECCeeEEeecCC-ceeEEEE-eCCCCCCccccccCCC-cccChhHHHHHHHHHHHHh
Q 012425 83 LLSHVVMKAHNKQAYALFNKK-FSSFALY-DGKGGEDFLPYQVSSR-FFVRDQDKRIIAAVRKWLL 145 (464)
Q Consensus 83 ~l~rvkv~~~~g~~~~~~~~~-~ss~~lf-~g~~~~~~~P~~~s~~-~~~~~~e~~~v~~Lr~w~~ 145 (464)
+|||+||+.|+|+++++++.. .++|+|| ++..+.++.|++.+++ ++++++|+++++.||+|++
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 999999999999999998855 6899999 7888888999988876 9999999999999999974
No 4
>cd04498 hPOT1_OB2 hPOT1_OB2: A subfamily of OB folds similar to the second OB fold (OB2) of human protection of telomeres 1 protein (hPOT1). POT1 proteins bind to the single-stranded (ss) 3-prime ends of the telomere. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB2) which cooperate to bind telomeric ssDNA. OB1 makes more extensive contact with the ssDNA than OB2. OB2 protects the 3' end of the ssDNA. hPOT1 is implicated in telomere length regulation.
Probab=99.86 E-value=1.8e-21 Score=167.88 Aligned_cols=109 Identities=20% Similarity=0.289 Sum_probs=82.7
Q ss_pred eEeEEEEEeEEEeeCCCeEEEEEEeCCCCCCCcccccccccccCCCCCcccCCCCcccccccCCCcc-cEEEEEEccchh
Q 012425 167 RINMACKVFHICEVAKGEWMAFVWDGTDAPPAQISKKLEDEMDHELPLQVEPLPLSRDILCSFPAVG-SILRVIIDKGIE 245 (464)
Q Consensus 167 f~Dl~~qVv~~~~~~~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~~~~~e~~~l~~~~l~~~p~~G-~~l~V~~~~~~~ 245 (464)
||||+||||++++.++++++|||||||+||+..+....++. +..|++ +...+.|+-.| ++|+|++|++|+
T Consensus 1 ~~DLvcqVv~v~~~d~~~~~L~VwDgT~~p~~~~~~~~~~~------~~~e~d---~~~k~~~~gpg~~ti~It~yD~H~ 71 (123)
T cd04498 1 YFDLLCQLLSVVETDSSSTLLKVWDGTKFPPPLRKVKVEDD------VVLEGD---RSLKHREEGGKQLTIDILVYDNHV 71 (123)
T ss_pred CccEEEEEEEEEEecCCeEEEEEecCCCCChhHhheecccc------Cccccc---hhhhhhccCCCeEEEEEEEEcchH
Confidence 79999999999998889999999999999876555443321 123333 22224566227 799999999999
Q ss_pred HHHhhccCCCCEEEEeceEEEEeCc--------EEEEEE-ecc----cceEEc
Q 012425 246 KHILHLLKIGKWVKLQNVLCQVDAG--------LWFGVL-THF----TRLRYV 285 (464)
Q Consensus 246 ~~~~~~lk~G~wV~l~Nv~~k~~~G--------~leG~l-~~~----ski~~l 285 (464)
++|++ +|+||||+|+|||+|.... .|||.+ ++- |+|++|
T Consensus 72 ~~ar~-lK~GdfV~L~NVhiK~~~~~~~~~~~~~Le~~l~~gg~~~~rgi~vl 123 (123)
T cd04498 72 ELAKS-LKPGDFVRIYNVHAKSYSSKNEHDENDHLHFHLVHGGTEYGRGIRVL 123 (123)
T ss_pred HHHhh-CCCCCEEEEEEEEEEeccCCcccCCcceEEEEEccCceeeccceeeC
Confidence 99988 9999999999999998532 688888 543 355543
No 5
>PRK12366 replication factor A; Reviewed
Probab=99.35 E-value=9.9e-10 Score=120.71 Aligned_cols=292 Identities=18% Similarity=0.275 Sum_probs=179.3
Q ss_pred CceeeEehHHHhhc-cCCeEEEEEEEEeeCCccc---ccCCceEEEEEEEeCCCCCCCeEEEEeccCcCCCCCCCCCCCE
Q 012425 6 EDYRFLKIKDAILS-INQKVSFVGVILEVGSPKQ---SKGTDSFCTIKVTDESHTKDGISVNIFAESMEKLPYIVSVGDI 81 (464)
Q Consensus 6 ~~y~y~~i~d~~~~-~~~~vnviGVVvd~~~P~~---trGtD~~~tl~I~D~S~~~~gl~v~iF~~~~e~LP~v~~~GDI 81 (464)
..+.+++|+++..- .+..+++-|-|+...+++. .+|+--..++.|.|++- .|.+.+|.+..+.+..+. .||+
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---RVRVSFWGEKAKILENLK-EGDA 350 (637)
T ss_pred cccCceeHHHCCcccCCCEEEEEEEEEecCCceEEEcCCCcEEEEEEEEEcCCC---eEEEEEeCchhhhhcccC-CCCE
Confidence 45688999999743 3568999999999988754 36788999999999872 399999998777777775 8999
Q ss_pred EEEeeEEEEEECC-----eeEEeecCCceeEEEEeCCCCCCccccccCCCcccChhHHHHHHHHHHHHhhcccccCCccc
Q 012425 82 ILLSHVVMKAHNK-----QAYALFNKKFSSFALYDGKGGEDFLPYQVSSRFFVRDQDKRIIAAVRKWLLNFQFKEDSKKF 156 (464)
Q Consensus 82 I~l~rvkv~~~~g-----~~~~~~~~~~ss~~lf~g~~~~~~~P~~~s~~~~~~~~e~~~v~~Lr~w~~~~~~~~~~~~f 156 (464)
+.+.+++++.|+. ++.+.++.. +.... ..+ .. .| . ...+|
T Consensus 351 y~is~~~vk~y~~~~~~~~~El~~~~~-s~I~~-d~~--~~-~p-----~-------------------------~~~~~ 395 (637)
T PRK12366 351 VKIENCKVRTYYDNEGEKRVDLNAGYS-SEIIK-DES--IS-FE-----E-------------------------IEEKI 395 (637)
T ss_pred EEEecCEEeeccccCCCcCEEEEcCCc-eEEEe-ccC--Cc-cc-----c-------------------------eeecc
Confidence 9999999998863 233333322 22221 100 00 00 0 01135
Q ss_pred cccccCC----CCCeEeEEEEEeEEEeeCCCeEEEEEEeCCCCCCCcccccccccccCCCCCcccCCCCcccccccCCCc
Q 012425 157 LLLREIK----DGQRINMACKVFHICEVAKGEWMAFVWDGTDAPPAQISKKLEDEMDHELPLQVEPLPLSRDILCSFPAV 232 (464)
Q Consensus 157 ~~L~di~----~~~f~Dl~~qVv~~~~~~~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~~~~~e~~~l~~~~l~~~p~~ 232 (464)
..|+||. .+..+|+++.|+.+.+.. .++ . -||+...--.+. .. -. -
T Consensus 396 ~~i~dI~~~~~~~~~VdVig~V~~v~~~~--~i~-~-k~G~~~~~r~i~--l~-----------------------D~-T 445 (637)
T PRK12366 396 YKIKDILNLEEDDNDITVIARVVEDYPVN--EFE-R-SDGSKGKVRNIE--LA-----------------------DG-T 445 (637)
T ss_pred ccHHHhhcccCCCcEEEEEEEEEEccCce--EEE-e-cCCCEeEEEEEE--EE-----------------------eC-C
Confidence 5566663 578999999999886521 111 1 244421111100 00 01 2
Q ss_pred ccEEEEEEccchhHHHhhccCCCCEEEEeceEEEEeCcEEEEEEecccceEEcCCCChHHHHHHHHHHHHhhccCCCCCc
Q 012425 233 GSILRVIIDKGIEKHILHLLKIGKWVKLQNVLCQVDAGLWFGVLTHFTRLRYVPTNDNLIVERQRSYDERLSWEHSRMPY 312 (464)
Q Consensus 233 G~~l~V~~~~~~~~~~~~~lk~G~wV~l~Nv~~k~~~G~leG~l~~~ski~~l~~~d~~v~~r~r~y~~r~~~~~~~~~~ 312 (464)
| .+++|+|..++. ..+.+|+-|.+.|+.++..+|.++..+...+.|.+.|+.. ++. +..
T Consensus 446 G-~I~vtlWg~~a~---~~~~~G~vi~i~~~~V~~~~g~~~Ls~~~~s~i~~~p~~~-el~-----------~~~----- 504 (637)
T PRK12366 446 G-SIRLTLWDDDAE---IEIKEGDAIKILHPYVKENGDYLDLSIGRYGRIEINPEGE-IIK-----------SNR----- 504 (637)
T ss_pred C-EEEEEEeccccc---cCCCCCCEEEEEeeEEEeCCCeeEEEecCcceEEECCCCc-ccc-----------ccc-----
Confidence 5 579999998876 3589999999999999998999988888888887655322 211 000
Q ss_pred ccCCCCCccccCCCCCCCCcccHH----hhhcCc-ccCceeEEEEEEEeecCCCccccccCCc----c--EEEEEEEecC
Q 012425 313 WCFPWTSEVTDIDYSEDGPFVTLK----DVLTHS-QVTAKFKCVVRVVAALPWRSEDFCSPLG----N--YRIRLTLEDP 381 (464)
Q Consensus 313 ~~~p~~~~it~~~~~~~~p~~Tl~----diLt~~-~v~~kfr~~VRVV~~~P~~~edf~~~~g----~--~~~~l~leD~ 381 (464)
..|.++..+ +. .++. .|-... --+++=.|.=+|+.- .-.=.|..+| . |++.+.|.|.
T Consensus 505 ------~~I~~i~~~-~~--~~v~g~i~~i~~~~~~y~aCp~CnkKv~~~---~g~~~C~~c~~~~p~~~~~l~~~i~D~ 572 (637)
T PRK12366 505 ------KFIADLEED-DT--VEIRGTVVDIRKQKIILYLCPNCRKRVEEV---DGEYICEFCGEVEPNELLMLNFTLDDG 572 (637)
T ss_pred ------cCHHHcccC-Ce--EEEEEEEEEEeCCCEEEecccccCeEeEcC---CCcEECCCCCCCCCcEEEEEEEEEEcC
Confidence 011111111 10 1111 111000 001111243344421 1111233333 2 6778999999
Q ss_pred CceEEEEEecCchhhhcC
Q 012425 382 TARIHAFVYAEDGEKLFG 399 (464)
Q Consensus 382 t~~l~~~v~~~da~~f~~ 399 (464)
||.+++.++++.|+.+||
T Consensus 573 TG~~~~t~f~e~ae~l~G 590 (637)
T PRK12366 573 TGTINCRFYGKNVEKLLG 590 (637)
T ss_pred CCCEEEEEEhHHhHHHhC
Confidence 999999999999999998
No 6
>PRK07218 replication factor A; Provisional
Probab=99.10 E-value=7.7e-08 Score=100.31 Aligned_cols=198 Identities=17% Similarity=0.250 Sum_probs=135.5
Q ss_pred eeEehHHHhhccCCeEEEEEEEEeeCCcc-cccCC-ceEEEEEEEeCCCCCCCeEEEEeccCcCCCCCCCCCCCEEEEee
Q 012425 9 RFLKIKDAILSINQKVSFVGVILEVGSPK-QSKGT-DSFCTIKVTDESHTKDGISVNIFAESMEKLPYIVSVGDIILLSH 86 (464)
Q Consensus 9 ~y~~i~d~~~~~~~~vnviGVVvd~~~P~-~trGt-D~~~tl~I~D~S~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~r 86 (464)
.-++|+|+.. ....||+.|-|++...+. +..|+ --..++.|.|++= -+++.++.+ ++ +. +||+|.|.|
T Consensus 57 ~~~kI~Di~~-~~~~V~v~~kVl~i~~rt~r~dg~~g~v~~~~igDeTG---~Ir~tlW~~----~~-l~-~Gdvv~I~n 126 (423)
T PRK07218 57 SSKDIKELST-DDKNVTVTGRVLTIGERSIRYQGDDHVIYEGILADETG---TISYTAWKD----FG-LS-PGDTVTIGN 126 (423)
T ss_pred CCccHhhCCC-CCceeEEEEEEEEecceeEecCCCceEEEEEEEECCCC---eEEEEEECC----CC-CC-CCCEEEEec
Confidence 3567889863 357799999999996631 22243 5778889999874 289999973 34 66 899999999
Q ss_pred EEEEEECCeeEEeecCCceeEEEEeCCCCCCccccccCCCcccChhHHHHHHHHHHHHhhcccccCCccccccccCCCCC
Q 012425 87 VVMKAHNKQAYALFNKKFSSFALYDGKGGEDFLPYQVSSRFFVRDQDKRIIAAVRKWLLNFQFKEDSKKFLLLREIKDGQ 166 (464)
Q Consensus 87 vkv~~~~g~~~~~~~~~~ss~~lf~g~~~~~~~P~~~s~~~~~~~~e~~~v~~Lr~w~~~~~~~~~~~~f~~L~di~~~~ 166 (464)
+.+..|+|++.+..+.. +....-+... ..|+. ......|.|++++.
T Consensus 127 a~vre~~g~~el~ig~~-t~I~~~de~~---~~~~~------------------------------~~~~~kI~DL~~g~ 172 (423)
T PRK07218 127 AGVREWDGRPELNIGES-TTVSLLDDSS---LPPYS------------------------------IGGDKKLIDLGPGD 172 (423)
T ss_pred cEeeccCCceEEeccCc-ceEEEcCccc---ccCcc------------------------------ccCccchhhccCCC
Confidence 99999999998866644 4444322111 00110 00133488998754
Q ss_pred -eEeEEEEEeEEEeeCCCeEEEEEEeCCCCCCCcccccccccccCCCCCcccCCCCcccccccCCCcccEEEEEEccchh
Q 012425 167 -RINMACKVFHICEVAKGEWMAFVWDGTDAPPAQISKKLEDEMDHELPLQVEPLPLSRDILCSFPAVGSILRVIIDKGIE 245 (464)
Q Consensus 167 -f~Dl~~qVv~~~~~~~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~~~~~e~~~l~~~~l~~~p~~G~~l~V~~~~~~~ 245 (464)
.+++.++|+.+.. + .+-.-||+. ........| . .| .+++++|..++
T Consensus 173 ~~V~v~g~Vl~~~~----r-~f~~~dg~~---~v~~giigD----e--------------------TG-~Ir~tlW~~~~ 219 (423)
T PRK07218 173 RGVNVEARVLELEH----R-EIDGRDGET---TILSGVLAD----E--------------------TG-RLPFTDWDPLP 219 (423)
T ss_pred CceEEEEEEEEecc----e-eEEcCCCCe---EEEEEEEEC----C--------------------Cc-eEEEEEecccc
Confidence 5999999998732 2 333444432 111111111 0 13 36999999764
Q ss_pred HHHhhccCCCCEEEEeceEEEEeCcEEEEEEecccceEEcCCC
Q 012425 246 KHILHLLKIGKWVKLQNVLCQVDAGLWFGVLTHFTRLRYVPTN 288 (464)
Q Consensus 246 ~~~~~~lk~G~wV~l~Nv~~k~~~G~leG~l~~~ski~~l~~~ 288 (464)
.+.+|++|++.|...+...|.++-.+...+.|..++.+
T Consensus 220 -----~l~~Gd~v~I~na~v~e~~G~~elnv~~~t~I~~~d~~ 257 (423)
T PRK07218 220 -----EIEIGASIRIEDAYVREFRGVPSVNVSEFTTVEALDRE 257 (423)
T ss_pred -----cCCCCCEEEEeeeEEeccCCeEEEEECCceEEEECCCC
Confidence 48999999999999999999999999999999887743
No 7
>PRK12366 replication factor A; Reviewed
Probab=99.08 E-value=5.2e-08 Score=107.25 Aligned_cols=278 Identities=15% Similarity=0.174 Sum_probs=181.4
Q ss_pred eeeEehHHHhhccCC-eEEEEEEEEeeCCccc---ccC-CceEEEEEEEeCCCCCCCeEEEEeccCcCCCCCCCCCCCEE
Q 012425 8 YRFLKIKDAILSINQ-KVSFVGVILEVGSPKQ---SKG-TDSFCTIKVTDESHTKDGISVNIFAESMEKLPYIVSVGDII 82 (464)
Q Consensus 8 y~y~~i~d~~~~~~~-~vnviGVVvd~~~P~~---trG-tD~~~tl~I~D~S~~~~gl~v~iF~~~~e~LP~v~~~GDII 82 (464)
-.+++|+|+. ++. .+++.|-|+..+.|+. .+| .-..+++.|.|++= .+++.+|.+..+.+|.++ +|||+
T Consensus 61 ~~~~~I~dl~--p~~~~v~i~arV~~~~~~r~~~~~~G~eGkv~~~~v~DetG---~Ir~t~W~~~~~~~~~le-~G~v~ 134 (637)
T PRK12366 61 EEDFKISDIE--EGQINVEITGRIIEISNIKTFTRKDGSTGKLANITIADNTG---TIRLTLWNDNAKLLKGLK-EGDVI 134 (637)
T ss_pred cceeEHHHCc--CCCcceEEEEEEEEccCCeEEECCCCCccEEEEEEEEcCCC---EEEEEEEchhhhhhccCC-CCCEE
Confidence 3578999997 554 5999999999998863 235 46789999999874 399999998777788887 89999
Q ss_pred EEeeEEEEEECCeeEEeecCCceeEEEEeCCCCCCccccccCCCcccChhHHHHHHHHHHHHhhcccccCCccccccccC
Q 012425 83 LLSHVVMKAHNKQAYALFNKKFSSFALYDGKGGEDFLPYQVSSRFFVRDQDKRIIAAVRKWLLNFQFKEDSKKFLLLREI 162 (464)
Q Consensus 83 ~l~rvkv~~~~g~~~~~~~~~~ss~~lf~g~~~~~~~P~~~s~~~~~~~~e~~~v~~Lr~w~~~~~~~~~~~~f~~L~di 162 (464)
.+.++.++.|+|++.+..+.. ++.....-. .....|.. ...| .|+||
T Consensus 135 ~i~~~~v~~~~~~~el~~~~~-t~I~~~~~~-d~~~i~~~------------------------------~~~~-~I~el 181 (637)
T PRK12366 135 KIENARSRKWNNDVELNSGSE-TRIDKLEKY-DESRYPII------------------------------KENY-DIPEL 181 (637)
T ss_pred EEeccEecccCCceEEEcCCc-ceEEEcccc-ccccCCcc------------------------------cccc-ccccc
Confidence 999999999999988755544 333322200 00001100 0013 38899
Q ss_pred CCCCeEeEEEEEeEEEeeCCCeEEEEEEeCCCCCCCcccccccccccCCCCCcccCCCCcccccccCCCcccEEEEEEcc
Q 012425 163 KDGQRINMACKVFHICEVAKGEWMAFVWDGTDAPPAQISKKLEDEMDHELPLQVEPLPLSRDILCSFPAVGSILRVIIDK 242 (464)
Q Consensus 163 ~~~~f~Dl~~qVv~~~~~~~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~~~~~e~~~l~~~~l~~~p~~G~~l~V~~~~ 242 (464)
.+|.++|+++.|+.+.+.. .++ --||+.-.-..+.. . | . .| .++||+|.
T Consensus 182 ~~g~~v~v~G~V~~~~~~~--~f~--rkdg~~~~~r~~~l--~----D-------------------~-TG-~irvTlW~ 230 (637)
T PRK12366 182 EPNLSATIEGEVTKAYPIK--EFT--RKDGSEGKLKSFIL--K----D-------------------D-TG-SIRVTLWN 230 (637)
T ss_pred CCCCeEEEEEEEEEccCcE--EEE--EcCCCeeEEEEEEE--E----c-------------------C-CC-cEEEEEEC
Confidence 9999999999999887532 111 11555322211100 0 0 0 25 48999999
Q ss_pred chhHHHhhccCCCCEEEEeceEEEEeCcEEEEEEecccceEEcCCCChHHHHHHHHHHHHhhccCCCCCcccCCCCCccc
Q 012425 243 GIEKHILHLLKIGKWVKLQNVLCQVDAGLWFGVLTHFTRLRYVPTNDNLIVERQRSYDERLSWEHSRMPYWCFPWTSEVT 322 (464)
Q Consensus 243 ~~~~~~~~~lk~G~wV~l~Nv~~k~~~G~leG~l~~~ski~~l~~~d~~v~~r~r~y~~r~~~~~~~~~~~~~p~~~~it 322 (464)
.++. ..+.+|+.|++.+....-..|.+|-.+...+- ++..+. + .
T Consensus 231 ~~a~---~~~~~g~vv~i~g~~~~~~~~~~el~~~~~~~---i~~~~~--------~----------------------~ 274 (637)
T PRK12366 231 DLTD---IEVNKGDIVRVKGYVKQGYRTGLEISANNIEI---LEKLEK--------E----------------------E 274 (637)
T ss_pred hhhc---ccCCCCCEEEEEeEEecCcCCceEEEeCCcee---eccccc--------c----------------------c
Confidence 8875 36899999999883222234666665532222 221110 0 0
Q ss_pred cCCCCCCCCcccHHhhhcCcccCceeEEEEEEEeecCCCccccccCCcc-EEEEEEEecCCceEEEEEecCchhhhcC
Q 012425 323 DIDYSEDGPFVTLKDVLTHSQVTAKFKCVVRVVAALPWRSEDFCSPLGN-YRIRLTLEDPTARIHAFVYAEDGEKLFG 399 (464)
Q Consensus 323 ~~~~~~~~p~~Tl~diLt~~~v~~kfr~~VRVV~~~P~~~edf~~~~g~-~~~~l~leD~t~~l~~~v~~~da~~f~~ 399 (464)
. ..++..|.++-.+. .+.+....+||++..|.+- |....|. -.|.+.|-|.||+|.|.++++.|++|.+
T Consensus 275 -~----~~~~~pI~~L~~~~-~g~~~~I~grV~~~~~~R~--f~~~~g~gkv~s~~l~D~tG~IR~t~w~~~~d~~~~ 344 (637)
T PRK12366 275 -K----ELEIVNIEELTEFE-DGEEVDVKGRIIAISDKRE--VERDDRTAEVQDIELADGTGRVRVSFWGEKAKILEN 344 (637)
T ss_pred -c----ccCceeHHHCCccc-CCCEEEEEEEEEecCCceE--EEcCCCcEEEEEEEEEcCCCeEEEEEeCchhhhhcc
Confidence 0 11223355553331 3457888899999776544 5444443 7899999999999999999998888876
No 8
>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=99.03 E-value=2.4e-07 Score=101.53 Aligned_cols=314 Identities=15% Similarity=0.200 Sum_probs=188.4
Q ss_pred eeEehHHHhhccCCeEEEEEEEEeeCCccc---ccCCceEEEEEEEeCCCCCCCeEEEEeccCcCCC-CCCCCCCCEEEE
Q 012425 9 RFLKIKDAILSINQKVSFVGVILEVGSPKQ---SKGTDSFCTIKVTDESHTKDGISVNIFAESMEKL-PYIVSVGDIILL 84 (464)
Q Consensus 9 ~y~~i~d~~~~~~~~vnviGVVvd~~~P~~---trGtD~~~tl~I~D~S~~~~gl~v~iF~~~~e~L-P~v~~~GDII~l 84 (464)
.+++|+++.- ......+-|-|+.....+. .+|.....++.|.|++ ..|.+.+|....+.+ |.++ +|+|+.+
T Consensus 179 ~~~pI~~L~p-y~~~wtIkaRV~~Ks~ir~~~~~~gegkvfsv~L~Deg---g~Irat~f~~~~dkf~~~l~-eG~VY~I 253 (608)
T TIGR00617 179 RVMPIASLSP-YQNKWTIKARVTNKSEIRTWSNARGEGKLFNVELLDES---GEIRATAFNEQADKFYDIIQ-EGKVYYI 253 (608)
T ss_pred ceEEHHHCCC-CCCceEEEEEEEeccccceecCCCCCceeeEEEEecCC---CeEEEEECchHHHHHhhhcc-cCCEEEE
Confidence 5899999973 2356999999998776643 3455678888999943 349999998755444 6676 8999999
Q ss_pred eeEEEEEECCeeEEeecCCceeEEEEeCC------CCCCccccccCCCcccChhHHHHHHHHHHHHhhcccccCCccccc
Q 012425 85 SHVVMKAHNKQAYALFNKKFSSFALYDGK------GGEDFLPYQVSSRFFVRDQDKRIIAAVRKWLLNFQFKEDSKKFLL 158 (464)
Q Consensus 85 ~rvkv~~~~g~~~~~~~~~~ss~~lf~g~------~~~~~~P~~~s~~~~~~~~e~~~v~~Lr~w~~~~~~~~~~~~f~~ 158 (464)
.+.+|+..++....+.| .+- .. |... .+..-.|.. .-+|..
T Consensus 254 s~~~Vk~an~~y~~~~~-~ye-i~-f~~~T~I~~~~d~~~iP~~------------------------------~~~f~~ 300 (608)
T TIGR00617 254 SKGSLKPANKQFTNLGN-DYE-MT-LDRDTVIEECEDETAIPKI------------------------------QFNFVK 300 (608)
T ss_pred CceEEEEccccccCCCC-CEE-EE-ECCCeEEEECCCcccCCcc------------------------------cccceE
Confidence 99999988776554433 211 11 2211 111001100 113444
Q ss_pred cccC---CCCCeEeEEEEEeEEEeeCCCeEEEEEEeCCCCCCCcccccccccccCCCCCcccCCCCcccccccCCCcccE
Q 012425 159 LREI---KDGQRINMACKVFHICEVAKGEWMAFVWDGTDAPPAQISKKLEDEMDHELPLQVEPLPLSRDILCSFPAVGSI 235 (464)
Q Consensus 159 L~di---~~~~f~Dl~~qVv~~~~~~~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~~~~~e~~~l~~~~l~~~p~~G~~ 235 (464)
|.|| ..+.++|+++.|..+..... ++- =.||+...-..+. + .| --|..
T Consensus 301 i~dI~~~~~~~~VDVIGvV~~v~~~~~--i~~-k~~g~~~~kR~i~--------------L------~D------~sg~s 351 (608)
T TIGR00617 301 IDDIGGYEGNSLVDVIGIVQSVSPTQT--ITS-RKNNKEFPKRDIT--------------L------VD------DSGKS 351 (608)
T ss_pred HHHhhhhcCCCCccEEEEEeEecCceE--EEE-cCCCCeeeeEEEE--------------E------Ee------CCCCE
Confidence 5555 45679999999998865321 110 1123321111110 0 00 12566
Q ss_pred EEEEEccchhHHHhhccCCCCEEEEeceEEEEeCcEEEEEEecccceEEcCCCChHHHHHHHHHHHHhhccCCCCCcccC
Q 012425 236 LRVIIDKGIEKHILHLLKIGKWVKLQNVLCQVDAGLWFGVLTHFTRLRYVPTNDNLIVERQRSYDERLSWEHSRMPYWCF 315 (464)
Q Consensus 236 l~V~~~~~~~~~~~~~lk~G~wV~l~Nv~~k~~~G~leG~l~~~ski~~l~~~d~~v~~r~r~y~~r~~~~~~~~~~~~~ 315 (464)
++||||..+|.. -....|+.|.|++++++-.+|. .......+.| +++.+-+++.+.+.-|+..-. ..+..++
T Consensus 352 I~vTLWG~~A~~--~~~~~~~Vva~kg~~V~~f~g~-sLs~~~~S~i-~iNPdipEa~~L~~w~~~~g~----~~~~~s~ 423 (608)
T TIGR00617 352 VRVTLWGDDATK--FDVSVQPVIAIKGVRVSDFGGK-SLSTGGSSTI-IVNPDIPEAEKLKGWYDNEGK----GTMASSI 423 (608)
T ss_pred EEEEEEhhhhhh--cCCCCCCEEEEEeEEEEecCCc-eEeccCCceE-EECCCcHHHHHHHHHHHhcCC----Cccceee
Confidence 899999998863 3478899999999999877664 4444556677 455566777766666643321 1110111
Q ss_pred CCCCccccCCCCCCCCcccHHhhhcC----cccCceeEEEEEEEeecCCCc------cc--------------cccCCc-
Q 012425 316 PWTSEVTDIDYSEDGPFVTLKDVLTH----SQVTAKFKCVVRVVAALPWRS------ED--------------FCSPLG- 370 (464)
Q Consensus 316 p~~~~it~~~~~~~~p~~Tl~diLt~----~~v~~kfr~~VRVV~~~P~~~------ed--------------f~~~~g- 370 (464)
.... ....... .....||.||... .+.+..|.|.+.|+.+-+.++ .. .|..++
T Consensus 424 ~~~~-~~~~~~~-~~~~ktI~ei~~~~lg~~~k~~~f~v~atI~~Ik~d~~~Y~ACp~~~CnKKV~~~~~g~~~CekC~~ 501 (608)
T TIGR00617 424 SDMM-SGRVGGS-NAERKTIAEIQAENLGKSDKPDYFSVKATISYLKPDNALYRACPSEDCNKKVVDQGDGTYRCEKCNK 501 (608)
T ss_pred hhcc-ccccCCc-ccccccHHHHhhhccCCCCCCcEEEEEEEEEEEecCCeEeccCChhhCCCccccCCCCCEECCCCCC
Confidence 0000 0000111 2345789998732 233456778777776654321 11 121122
Q ss_pred -------cEEEEEEEecCCceEEEEEecCchhhhcC
Q 012425 371 -------NYRIRLTLEDPTARIHAFVYAEDGEKLFG 399 (464)
Q Consensus 371 -------~~~~~l~leD~t~~l~~~v~~~da~~f~~ 399 (464)
.|.+.+.+.|.||.+++.++++.|+++||
T Consensus 502 ~~~~~~~RYil~~~i~D~Tg~~~~t~F~~~ae~llG 537 (608)
T TIGR00617 502 NFAEFKYRYILQISISDETGQLWVTAFNDQAEQILG 537 (608)
T ss_pred CCCCccEEEEEEEEEEeCCCCEEEEEEhHHHHHHcC
Confidence 26678889999999999999999999998
No 9
>PRK06386 replication factor A; Reviewed
Probab=99.01 E-value=3.9e-07 Score=92.90 Aligned_cols=275 Identities=16% Similarity=0.182 Sum_probs=163.9
Q ss_pred EehHHHhhccCCeEEEEEEEEeeCCc-cccc-CCceEEEEEEEeCCCCCCCeEEEEeccCcCCCCCCCCCCCEEEEeeEE
Q 012425 11 LKIKDAILSINQKVSFVGVILEVGSP-KQSK-GTDSFCTIKVTDESHTKDGISVNIFAESMEKLPYIVSVGDIILLSHVV 88 (464)
Q Consensus 11 ~~i~d~~~~~~~~vnviGVVvd~~~P-~~tr-GtD~~~tl~I~D~S~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~rvk 88 (464)
++|+|+.. .++.||+.|-|++.... .+.+ |.--..+-.|-|++= . +++.+..+ .|.+. .||+|+|+|++
T Consensus 3 ~kI~DI~~-~~~~V~v~akVl~~~~r~i~~~~g~~~~~~gllgDeTG-~--I~fT~W~~----~~~l~-~Gd~v~i~na~ 73 (358)
T PRK06386 3 SKISDINA-ARQNVDLKVKVLSLNKRTIKNDRGETIYYYGIIGDETG-T--VPFTAWEF----PDAVK-SGDVIEIKYCY 73 (358)
T ss_pred cchhhcCC-CCCcEEEEEEEEEccceEEecCCCCeEEEEEEEECCcc-e--EEEEecCC----cccCC-CCCEEEEEeEE
Confidence 46888862 35669999999999732 1222 333334445677653 2 78888752 46676 79999999999
Q ss_pred EEEECCeeEEeecCCceeEEEEeCCCCCCccccccCCCcccChhHHHHHHHHHHHHhhcccccCCccccccccCCCC-Ce
Q 012425 89 MKAHNKQAYALFNKKFSSFALYDGKGGEDFLPYQVSSRFFVRDQDKRIIAAVRKWLLNFQFKEDSKKFLLLREIKDG-QR 167 (464)
Q Consensus 89 v~~~~g~~~~~~~~~~ss~~lf~g~~~~~~~P~~~s~~~~~~~~e~~~v~~Lr~w~~~~~~~~~~~~f~~L~di~~~-~f 167 (464)
++.|+|++.+..+.. +.... . ..... ...+ .-+...|+||+++ .+
T Consensus 74 v~~~~G~~~Lnv~~~-t~v~~-~--~d~~i---------ev~~---------------------~~~~~KI~DL~~g~~~ 119 (358)
T PRK06386 74 SKEYNGKIRIYFDSR-SEVML-K--PDENI---------EVKR---------------------TYKLVKIRDLSLVTPY 119 (358)
T ss_pred EeeECCEEEEEEcCc-eEEEe-c--Ccccc---------cccc---------------------ccCccEeEeccCCCCc
Confidence 999999988766644 32321 0 11110 0000 0124559999876 56
Q ss_pred EeEEEEEeEEEeeCCCeEEEEEEeCCCCCCCcccccccccccCCCCCcccCCCCcccccccCCCcccEEEEEEccchhHH
Q 012425 168 INMACKVFHICEVAKGEWMAFVWDGTDAPPAQISKKLEDEMDHELPLQVEPLPLSRDILCSFPAVGSILRVIIDKGIEKH 247 (464)
Q Consensus 168 ~Dl~~qVv~~~~~~~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~~~~~e~~~l~~~~l~~~p~~G~~l~V~~~~~~~~~ 247 (464)
+++.++|+.+++ . .+- .||+. .........| + .|+ +++|+|..
T Consensus 120 v~V~akVle~~e---~--e~~-~~g~~--~~v~sg~lgD----e--------------------TGr-Ir~TlW~~---- 162 (358)
T PRK06386 120 VSVIGKITGITK---K--EYD-SDGTS--KIVYQGYIED----D--------------------TAR-VRISSFGK---- 162 (358)
T ss_pred eEEEEEEEEccC---c--eEe-cCCCc--cEEEEEEEEc----C--------------------CCe-EEEEEccc----
Confidence 899999997643 1 222 55542 2111111111 0 133 69999974
Q ss_pred HhhccCCCCEEEEeceEEEEeCcEEEEEEecccceEEcCCCChHHHHHHHHHHHHhhccCCCCCcccCCCCCccccCCCC
Q 012425 248 ILHLLKIGKWVKLQNVLCQVDAGLWFGVLTHFTRLRYVPTNDNLIVERQRSYDERLSWEHSRMPYWCFPWTSEVTDIDYS 327 (464)
Q Consensus 248 ~~~~lk~G~wV~l~Nv~~k~~~G~leG~l~~~ski~~l~~~d~~v~~r~r~y~~r~~~~~~~~~~~~~p~~~~it~~~~~ 327 (464)
.++.|+-|+|.|+..+...|.++-.+...+.|..++.+-. +..+ +.+-..+....+.. .++.
T Consensus 163 ---~l~eGd~v~i~na~v~e~~G~~el~v~~~t~I~~~~~~ie-v~~~-~~~I~di~~~~g~v---------~i~G---- 224 (358)
T PRK06386 163 ---PLEDNRFVRIENARVSQYNGYIEISVGNKSVIKEVESDIN-LESR-NIFIFEIKSPVGGI---------TIMG---- 224 (358)
T ss_pred ---cccCCCEEEEeeeEEEccCCeEEEEeCCeEEEEECCCCcc-cCcc-ccchhhhhccCCeE---------EEEE----
Confidence 4899999999999999999999999999999987764321 1111 00000000000000 0000
Q ss_pred CCCCcccHH--hhh--cCcccCceeEEEEEEEeecCCCccccccCCcc----E--EEEEEEecCCceEEEEEecCchhhh
Q 012425 328 EDGPFVTLK--DVL--THSQVTAKFKCVVRVVAALPWRSEDFCSPLGN----Y--RIRLTLEDPTARIHAFVYAEDGEKL 397 (464)
Q Consensus 328 ~~~p~~Tl~--diL--t~~~v~~kfr~~VRVV~~~P~~~edf~~~~g~----~--~~~l~leD~t~~l~~~v~~~da~~f 397 (464)
-++.+. ..| .+|. | =||++- ..|..+|. + |.++.|.|+||.+.++++++.++.+
T Consensus 225 ---~iv~i~~gsgli~rCP~------C-~R~l~~------g~C~~HG~v~~~~dlr~k~vLDDGtg~~~~~l~~e~~e~l 288 (358)
T PRK06386 225 ---FIVSVGQGSRIFTKCSV------C-NKIIED------GVCKDHPDAPVYLDIFGYFTISDGTGFVTCYANKDSFLPY 288 (358)
T ss_pred ---EEEEEcCCcEeEecCcC------C-CeEccC------CcCCCCCCCCCeeEEEEEEEEECCCCeEEEEEChHHhHHH
Confidence 000000 000 1221 1 155551 47776663 4 6677999999999999999999999
Q ss_pred cC
Q 012425 398 FG 399 (464)
Q Consensus 398 ~~ 399 (464)
.|
T Consensus 289 ~G 290 (358)
T PRK06386 289 IN 290 (358)
T ss_pred hC
Confidence 99
No 10
>PRK14699 replication factor A; Provisional
Probab=99.01 E-value=2.2e-07 Score=98.76 Aligned_cols=271 Identities=19% Similarity=0.248 Sum_probs=179.1
Q ss_pred EehHHHhhccCCeEEEEEEEEeeCCccc---ccCCc-eEEEEEEEeCCCCCCCeEEEEeccCcCCCCCCCCCCCEEEEee
Q 012425 11 LKIKDAILSINQKVSFVGVILEVGSPKQ---SKGTD-SFCTIKVTDESHTKDGISVNIFAESMEKLPYIVSVGDIILLSH 86 (464)
Q Consensus 11 ~~i~d~~~~~~~~vnviGVVvd~~~P~~---trGtD-~~~tl~I~D~S~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~r 86 (464)
.+|+|+.. ....||+.|-|+....|+. ..|+. -..++.|-|+|= .+++.++.+..+.+|.+. .||+|++.+
T Consensus 167 ~~I~dL~~-~~~~V~i~gkVl~~~~~R~f~~~dG~~g~v~~~~igDeTG---~ir~tlW~~~a~~~~~l~-~Gd~v~I~~ 241 (484)
T PRK14699 167 QKIKDIKD-GMGDLNLTGKVLEISEIRTFQRKDGTSGKVGNLLLGDETG---TLRVTLWDDKTDFLNQIE-YGDTVELIN 241 (484)
T ss_pred cchhhcCC-CCCceEEEEEEEeccCceEEecCCCCceEEEEEEEEcCCc---eEEEEEECcccccccccC-CCCEEEEec
Confidence 46777752 2355999999999999853 23543 577789999985 399999998777778887 899999998
Q ss_pred EEEE--EECCeeEEeecCCceeEEEEeCCCCCCccccccCCCcccChhHHHHHHHHHHHHhhcccccCCccccccccCCC
Q 012425 87 VVMK--AHNKQAYALFNKKFSSFALYDGKGGEDFLPYQVSSRFFVRDQDKRIIAAVRKWLLNFQFKEDSKKFLLLREIKD 164 (464)
Q Consensus 87 vkv~--~~~g~~~~~~~~~~ss~~lf~g~~~~~~~P~~~s~~~~~~~~e~~~v~~Lr~w~~~~~~~~~~~~f~~L~di~~ 164 (464)
+.++ .|+|.+.+..+.. +... ....... + ..++..|.||++
T Consensus 242 a~vr~~~~~~~~el~~~~~-s~i~--~~~~~~e---------~-------------------------~~~~~~I~~L~~ 284 (484)
T PRK14699 242 AYARENAFTQKVELQVGNR-SIIR--KSEKKVE---------Y-------------------------EEEFTPIEDIKA 284 (484)
T ss_pred ceEeecccCCceEEEecCc-eEee--ccccccc---------c-------------------------cccccCHHHcCC
Confidence 8665 4888888766633 2111 0000000 0 012455888876
Q ss_pred C-CeEeEEEEEeEEEeeCCCeEEEEEEeCCCCCCCcccccccccccCCCCCcccCCCCcccccccCCCcccEEEEEEccc
Q 012425 165 G-QRINMACKVFHICEVAKGEWMAFVWDGTDAPPAQISKKLEDEMDHELPLQVEPLPLSRDILCSFPAVGSILRVIIDKG 243 (464)
Q Consensus 165 ~-~f~Dl~~qVv~~~~~~~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~~~~~e~~~l~~~~l~~~p~~G~~l~V~~~~~ 243 (464)
+ ..+++.++|+++... ..|. --||+.-.. .+....| --|+ +|+|+|..
T Consensus 285 ~~~~v~I~grV~~~~~~--r~~~--~~~Gseg~v--~~~~l~D------------------------eTG~-Ir~T~W~~ 333 (484)
T PRK14699 285 DMNNINISGRVLDISEV--RTFE--KKDGSPGRV--GNLLLGD------------------------STGK-IRLTLWDE 333 (484)
T ss_pred CCceeEEEEEEEEcCCC--eEEE--cCCCCeeEE--EEEEEEC------------------------CCCe-EEEEEeCc
Confidence 4 899999999987642 1111 223332111 1111111 0243 79999999
Q ss_pred hhHHHhhccCCCCEEEEeceEEEEe--CcEEEEEEecccceEEcCCCChHHHHHHHHHHHHhhccCCCCCcccCCCCCcc
Q 012425 244 IEKHILHLLKIGKWVKLQNVLCQVD--AGLWFGVLTHFTRLRYVPTNDNLIVERQRSYDERLSWEHSRMPYWCFPWTSEV 321 (464)
Q Consensus 244 ~~~~~~~~lk~G~wV~l~Nv~~k~~--~G~leG~l~~~ski~~l~~~d~~v~~r~r~y~~r~~~~~~~~~~~~~p~~~~i 321 (464)
.+++ ...+++|+-+++.|...+.+ ++.+|..+..++.|...++.. +|
T Consensus 334 ~a~~-~~~i~~Gd~v~i~~~y~~~~~~~~~~eL~~~~~t~I~~~~~~~--------e~---------------------- 382 (484)
T PRK14699 334 KTNF-LDEIDFDETVEVLNAYSRENTFSQQVELNLGARGIIQKSEKKV--------EY---------------------- 382 (484)
T ss_pred cccc-ccccCCCceEEEEeEEEEeccCCccEEEEecCceeEeecCCcc--------ee----------------------
Confidence 9865 56799999999999999986 467888888777665433211 11
Q ss_pred ccCCCCCCCCcccHHhhhcCcccCceeEEEEEEEeecCCCccccccCCcc--EEEEEEEecCCceEEEEEecCchhhhc
Q 012425 322 TDIDYSEDGPFVTLKDVLTHSQVTAKFKCVVRVVAALPWRSEDFCSPLGN--YRIRLTLEDPTARIHAFVYAEDGEKLF 398 (464)
Q Consensus 322 t~~~~~~~~p~~Tl~diLt~~~v~~kfr~~VRVV~~~P~~~edf~~~~g~--~~~~l~leD~t~~l~~~v~~~da~~f~ 398 (464)
..+++.|.||- -...+-..-+|++..|.+ .|.+.+|. .+-.++|.|.||++.+-|||+.|++|=
T Consensus 383 -------~~~~~~I~die----~~~~vdV~G~V~~v~~~~--~~~~~~g~~~~vr~i~l~D~TG~Ir~tlWg~~A~~~~ 448 (484)
T PRK14699 383 -------REKFTDIADII----PGESYSVQGKVSEIGELR--EFEREDGTENVVANLQLKDETGSIRLTLWGEQAYVIE 448 (484)
T ss_pred -------eeccccHHHcc----CCCeeEEEEEEEEcCCcc--eEEecCCCEEEEEEEEEEcCCCeEEEEEcchhhhhcc
Confidence 11234455552 123456666788887765 56554564 678999999999999999999998654
No 11
>PRK15491 replication factor A; Provisional
Probab=98.99 E-value=2.8e-07 Score=95.23 Aligned_cols=270 Identities=20% Similarity=0.267 Sum_probs=175.2
Q ss_pred eeEehHHHhhccCCeEEEEEEEEeeCCccc---ccC-CceEEEEEEEeCCCCCCCeEEEEeccCcCCC--CCCCCCCCEE
Q 012425 9 RFLKIKDAILSINQKVSFVGVILEVGSPKQ---SKG-TDSFCTIKVTDESHTKDGISVNIFAESMEKL--PYIVSVGDII 82 (464)
Q Consensus 9 ~y~~i~d~~~~~~~~vnviGVVvd~~~P~~---trG-tD~~~tl~I~D~S~~~~gl~v~iF~~~~e~L--P~v~~~GDII 82 (464)
.-++|+|+. .....|++.|-|+....|+. .+| .-...++.|.|++= .+.+.+|.+..+.+ |.++ +||++
T Consensus 56 ~~~kI~dL~-~~~~~v~i~arVl~~~~~R~f~r~dGs~g~v~~~~v~DeTG---~ir~tlW~~~a~~~~~~~le-~G~v~ 130 (374)
T PRK15491 56 DTTKIADIN-ESSSNVNFTAKVVSIFEPKEFNRNDGTTGRVGNIIVADETG---SIRLTLWDDLADLIKTGDIE-VGKSL 130 (374)
T ss_pred ccccHHHCC-CCCCceEEEEEEeeccCCeeeecCCCCceEEEEEEEEcCCC---eEEEEEECchhhhhccCCcC-CCCEE
Confidence 456899996 23467999999999988864 246 46778899999774 29999998775555 6787 89999
Q ss_pred EEeeEEEEEECCeeEEeecCCceeEEEEeCCCCCCccccccCCCcccChhHHHHHHHHHHHHhhcccccCCccccccccC
Q 012425 83 LLSHVVMKAHNKQAYALFNKKFSSFALYDGKGGEDFLPYQVSSRFFVRDQDKRIIAAVRKWLLNFQFKEDSKKFLLLREI 162 (464)
Q Consensus 83 ~l~rvkv~~~~g~~~~~~~~~~ss~~lf~g~~~~~~~P~~~s~~~~~~~~e~~~v~~Lr~w~~~~~~~~~~~~f~~L~di 162 (464)
.++..--..|+| +.+..+.. +... +. +.+.+ ....|..|+||
T Consensus 131 ~I~~~~~~~y~g-~Ei~i~~~-~~i~-----------~~---------~~~~~----------------~~~~~~~I~dl 172 (374)
T PRK15491 131 NISGYAKEGYSG-IEVNIGRY-GGIS-----------ES---------DENVK----------------ASINSQKISDI 172 (374)
T ss_pred EEeeeeccCccc-EEEEeCCC-ceee-----------ec---------ccccc----------------cccCcccHHHc
Confidence 998875556766 54444422 2111 00 00000 00125568888
Q ss_pred CCC-CeEeEEEEEeEEEeeCCCeEEEEEEeCCCCCCCcccccccccccCCCCCcccCCCCcccccccCCCcccEEEEEEc
Q 012425 163 KDG-QRINMACKVFHICEVAKGEWMAFVWDGTDAPPAQISKKLEDEMDHELPLQVEPLPLSRDILCSFPAVGSILRVIID 241 (464)
Q Consensus 163 ~~~-~f~Dl~~qVv~~~~~~~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~~~~~e~~~l~~~~l~~~p~~G~~l~V~~~ 241 (464)
.++ ..+|+.++|+.+... ..+. --||+....+.. ... .--|+ +++|+|
T Consensus 173 ~~~~~~V~I~g~V~~~~~~--r~~~--~~~G~~~~v~~~--~l~------------------------DetG~-Ir~t~W 221 (374)
T PRK15491 173 KDGDSDINIVGKVLDISDV--RTFQ--KKDGSQGRVRNI--TIG------------------------DETGK-IRVTLW 221 (374)
T ss_pred CCCCccEEEEEEEEEccCc--eEEE--ecCCCeEEEEEE--EEE------------------------CCCCe-EEEEEe
Confidence 765 469999999988641 1111 124442111111 000 01254 799999
Q ss_pred cchhHHHhhccCCCCEEEEeceEEEEe--CcEEEEEEecccceEEcCCCChHHHHHHHHHHHHhhccCCCCCcccCCCCC
Q 012425 242 KGIEKHILHLLKIGKWVKLQNVLCQVD--AGLWFGVLTHFTRLRYVPTNDNLIVERQRSYDERLSWEHSRMPYWCFPWTS 319 (464)
Q Consensus 242 ~~~~~~~~~~lk~G~wV~l~Nv~~k~~--~G~leG~l~~~ski~~l~~~d~~v~~r~r~y~~r~~~~~~~~~~~~~p~~~ 319 (464)
..++... ..+++|+-|++.|-.++.+ .|.+|-.+..++.|...+. +. +
T Consensus 222 ~~~a~~~-~~l~~Gd~V~i~~~~~r~~~~~g~~El~~~~~s~I~~~~~-~~-------e--------------------- 271 (374)
T PRK15491 222 DGKTDLA-DKLENGDSVEIINGYARTNNYSQEVEIQIGNHGSLRKTDR-NV-------E--------------------- 271 (374)
T ss_pred cchhccc-ccCCCCCEEEEEeceEEEeccCCCEEEEeCCCceEEECCc-cc-------c---------------------
Confidence 9988763 6799999999999888875 5789988888888865432 11 0
Q ss_pred ccccCCCCCCCCcccHHhhhcCcccCceeEEEEEEEeecCCCccccccCCcc--EEEEEEEecCCceEEEEEecCchhh
Q 012425 320 EVTDIDYSEDGPFVTLKDVLTHSQVTAKFKCVVRVVAALPWRSEDFCSPLGN--YRIRLTLEDPTARIHAFVYAEDGEK 396 (464)
Q Consensus 320 ~it~~~~~~~~p~~Tl~diLt~~~v~~kfr~~VRVV~~~P~~~edf~~~~g~--~~~~l~leD~t~~l~~~v~~~da~~ 396 (464)
..+ .|++|.||-.. ..+-...+|....|.. .|...+|. ..=.|+|.|.||+|.+-|+|++|+.
T Consensus 272 ----~~~----~f~~I~dl~~~----~~~dv~G~V~~v~~~~--~~~~~~G~~~~~r~i~l~D~Tg~Ir~tlWg~~a~~ 336 (374)
T PRK15491 272 ----YEE----DFTPIADIIPG----QPYSIKGAVSGLGDLK--EFTKSDGSENKVSNIYVSDDTGRIRIALWGEKAEL 336 (374)
T ss_pred ----cCC----CccCHHHcCCC----CceeEEEEEEEcCCcE--EEEccCCCEeEEEeEEEEeCCCcEEEEEccccccc
Confidence 111 13446666422 2246666777766643 44444564 5668899999999999999999875
No 12
>PRK07211 replication factor A; Reviewed
Probab=98.93 E-value=6.6e-08 Score=101.87 Aligned_cols=204 Identities=13% Similarity=0.126 Sum_probs=146.0
Q ss_pred eeeEehHHHhhccCCeEEEEEEEEeeCCccc---ccC-CceEEEEEEEeCCCCCCCeEEEEeccCcCCCCCCCCCCCEEE
Q 012425 8 YRFLKIKDAILSINQKVSFVGVILEVGSPKQ---SKG-TDSFCTIKVTDESHTKDGISVNIFAESMEKLPYIVSVGDIIL 83 (464)
Q Consensus 8 y~y~~i~d~~~~~~~~vnviGVVvd~~~P~~---trG-tD~~~tl~I~D~S~~~~gl~v~iF~~~~e~LP~v~~~GDII~ 83 (464)
..+.+|+++. .....++|+|+|++..+++. .+| .-.+.++.|.|+|- .|++.+|.+..+.++.+. +||||.
T Consensus 159 ~~~~~I~dL~-~~~~~v~I~grV~~v~~iRtf~r~dGseGkv~sv~L~DeTG---~IR~TlW~d~Ad~~~~le-~G~Vv~ 233 (485)
T PRK07211 159 GDTYTVEDLS-LGLSDVTLVGVVLDTDSVRTFDRDDGSEGRVSNLTVGDETG---RVRVTLWDDRADLAEELD-AGESVE 233 (485)
T ss_pred cCCccHHHcC-CCCCceEEEEEEEEcCCCeEEECCCCCeeEEEEEEEEcCCC---eEEEEEechhhhhhccCC-CCCEEE
Confidence 4778999996 23567999999999998753 235 45678899999885 299999998878888787 899999
Q ss_pred EeeEEEEEECCeeEEeecCCceeEEEEeCCCCCCccccccCCCcccChhHHHHHHHHHHHHhhcccccCCccccccccCC
Q 012425 84 LSHVVMKAHNKQAYALFNKKFSSFALYDGKGGEDFLPYQVSSRFFVRDQDKRIIAAVRKWLLNFQFKEDSKKFLLLREIK 163 (464)
Q Consensus 84 l~rvkv~~~~g~~~~~~~~~~ss~~lf~g~~~~~~~P~~~s~~~~~~~~e~~~v~~Lr~w~~~~~~~~~~~~f~~L~di~ 163 (464)
+.+++++.++|.+.+..+.. +...--. ......| .+..|.++.
T Consensus 234 I~~a~Vre~~g~~ELsl~~~-s~I~~~~--dev~~vp----------------------------------~~~~I~dl~ 276 (485)
T PRK07211 234 IVDGYVRERDGSLELHVGDR-GAVEEVD--EDVEYVP----------------------------------DTTPIESLE 276 (485)
T ss_pred EEeeEEEecCCcEEEEECCC-ceEEECC--ccccccc----------------------------------ccccHhhcC
Confidence 99999999999888865533 2222110 0000111 134588899
Q ss_pred CCCeEeEEEEEeEEEeeCCCeEEEEEEeCCCCCCCcccccccccccCCCCCcccCCCCcccccccCCCcccEEEEEEccc
Q 012425 164 DGQRINMACKVFHICEVAKGEWMAFVWDGTDAPPAQISKKLEDEMDHELPLQVEPLPLSRDILCSFPAVGSILRVIIDKG 243 (464)
Q Consensus 164 ~~~f~Dl~~qVv~~~~~~~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~~~~~e~~~l~~~~l~~~p~~G~~l~V~~~~~ 243 (464)
++..+|+++.|+.+.+ .-++-=-||+...-..+.. . | --| .+||++|.+
T Consensus 277 ~g~~vdV~GvV~~v~~----~rtf~r~dG~~~~vr~l~l--~----D--------------------~TG-~IrvTLWg~ 325 (485)
T PRK07211 277 IDETVDIAGVVRSADP----KRTFDRDDGSEGQVRNVRI--Q----D--------------------DTG-DIRVALWGE 325 (485)
T ss_pred CCCceeEEEEEEEccC----cEEEEcCCCCEeEEEEEEE--E----c--------------------CCC-cEEEEEeCc
Confidence 9999999999997754 2233222444322211110 0 0 125 479999999
Q ss_pred hhHHHhhccCCCCEEEEeceEEEEe-CcEEEEEEecccceEEcCC
Q 012425 244 IEKHILHLLKIGKWVKLQNVLCQVD-AGLWFGVLTHFTRLRYVPT 287 (464)
Q Consensus 244 ~~~~~~~~lk~G~wV~l~Nv~~k~~-~G~leG~l~~~ski~~l~~ 287 (464)
++. ..+.+|+.|+|.|++++-. .|-+|..+...+.|.+|+.
T Consensus 326 ~A~---~~i~~GdvV~Ikg~~V~dg~~ggleLS~g~~s~i~~~~~ 367 (485)
T PRK07211 326 KAD---LDIGPGDEVVAADVEIQDGWQDDLEASAGWQSTVVVLDD 367 (485)
T ss_pred ccc---CCCCCCCEEEEEccEEEecCCCCEEEEecCCceEEEccc
Confidence 985 3699999999999999986 4788899999999998875
No 13
>PRK15491 replication factor A; Provisional
Probab=98.82 E-value=2.9e-07 Score=95.14 Aligned_cols=204 Identities=14% Similarity=0.163 Sum_probs=141.8
Q ss_pred CceeeEehHHHhhccCCeEEEEEEEEeeCCccc-c--cCC-ceEEEEEEEeCCCCCCCeEEEEeccCcCCCCCCCCCCCE
Q 012425 6 EDYRFLKIKDAILSINQKVSFVGVILEVGSPKQ-S--KGT-DSFCTIKVTDESHTKDGISVNIFAESMEKLPYIVSVGDI 81 (464)
Q Consensus 6 ~~y~y~~i~d~~~~~~~~vnviGVVvd~~~P~~-t--rGt-D~~~tl~I~D~S~~~~gl~v~iF~~~~e~LP~v~~~GDI 81 (464)
..|.|.+|+++.. ....|++.|.|++..+++. + +|+ -...++.|.|+|- .+++.+|.+..+.++.+. +||+
T Consensus 162 ~~~~~~~I~dl~~-~~~~V~I~g~V~~~~~~r~~~~~~G~~~~v~~~~l~DetG---~Ir~t~W~~~a~~~~~l~-~Gd~ 236 (374)
T PRK15491 162 ASINSQKISDIKD-GDSDINIVGKVLDISDVRTFQKKDGSQGRVRNITIGDETG---KIRVTLWDGKTDLADKLE-NGDS 236 (374)
T ss_pred cccCcccHHHcCC-CCccEEEEEEEEEccCceEEEecCCCeEEEEEEEEECCCC---eEEEEEecchhcccccCC-CCCE
Confidence 3567789999963 3455999999999998753 1 355 4778899999874 299999998766777777 8999
Q ss_pred EEEeeEEEE--EECCeeEEeecCCceeEEEEeCCCCCCccccccCCCcccChhHHHHHHHHHHHHhhcccccCCcccccc
Q 012425 82 ILLSHVVMK--AHNKQAYALFNKKFSSFALYDGKGGEDFLPYQVSSRFFVRDQDKRIIAAVRKWLLNFQFKEDSKKFLLL 159 (464)
Q Consensus 82 I~l~rvkv~--~~~g~~~~~~~~~~ss~~lf~g~~~~~~~P~~~s~~~~~~~~e~~~v~~Lr~w~~~~~~~~~~~~f~~L 159 (464)
|.+.+..++ .|+|++.+..+.. +.... ..... .+ ..+|..|
T Consensus 237 V~i~~~~~r~~~~~g~~El~~~~~-s~I~~--~~~~~---------e~-------------------------~~~f~~I 279 (374)
T PRK15491 237 VEIINGYARTNNYSQEVEIQIGNH-GSLRK--TDRNV---------EY-------------------------EEDFTPI 279 (374)
T ss_pred EEEEeceEEEeccCCCEEEEeCCC-ceEEE--CCccc---------cc-------------------------CCCccCH
Confidence 999987655 5678887765644 33221 10000 00 1136678
Q ss_pred ccCCCCCeEeEEEEEeEEEeeCCCeEEEEEEeCCCCCCCcccccccccccCCCCCcccCCCCcccccccCCCcccEEEEE
Q 012425 160 REIKDGQRINMACKVFHICEVAKGEWMAFVWDGTDAPPAQISKKLEDEMDHELPLQVEPLPLSRDILCSFPAVGSILRVI 239 (464)
Q Consensus 160 ~di~~~~f~Dl~~qVv~~~~~~~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~~~~~e~~~l~~~~l~~~p~~G~~l~V~ 239 (464)
.||.++..+|+++.|..+.+ .-++-.-||+...--.+.. . | --|+ +|+|
T Consensus 280 ~dl~~~~~~dv~G~V~~v~~----~~~~~~~~G~~~~~r~i~l--~----D--------------------~Tg~-Ir~t 328 (374)
T PRK15491 280 ADIIPGQPYSIKGAVSGLGD----LKEFTKSDGSENKVSNIYV--S----D--------------------DTGR-IRIA 328 (374)
T ss_pred HHcCCCCceeEEEEEEEcCC----cEEEEccCCCEeEEEeEEE--E----e--------------------CCCc-EEEE
Confidence 99999999999999998754 2222234555322211111 0 0 0255 8999
Q ss_pred EccchhHHHhhccCCCCEEEEeceEEEEe-CcEEEEEEecccceE
Q 012425 240 IDKGIEKHILHLLKIGKWVKLQNVLCQVD-AGLWFGVLTHFTRLR 283 (464)
Q Consensus 240 ~~~~~~~~~~~~lk~G~wV~l~Nv~~k~~-~G~leG~l~~~ski~ 283 (464)
+|..+|.. ...+-+|+.|++.|..+|.. .|.+|......|+|.
T Consensus 329 lWg~~a~~-~~~~~~g~~i~i~~~~~k~g~~~~~e~s~g~~s~~~ 372 (374)
T PRK15491 329 LWGEKAEL-VDKLDIDTPIKIIDAFSKSGYNEDVELSAGNRSRVV 372 (374)
T ss_pred Eccccccc-ccccCCCCeEEEEEEEEeecCCCcEEEEeCCcceEE
Confidence 99999875 45678889999999999997 599999888877774
No 14
>PRK14699 replication factor A; Provisional
Probab=98.55 E-value=4.3e-06 Score=88.97 Aligned_cols=203 Identities=15% Similarity=0.206 Sum_probs=142.0
Q ss_pred eeEehHHHhhccCCeEEEEEEEEeeCCccc---ccC-CceEEEEEEEeCCCCCCCeEEEEeccCcCCCCCCCCCCCEEEE
Q 012425 9 RFLKIKDAILSINQKVSFVGVILEVGSPKQ---SKG-TDSFCTIKVTDESHTKDGISVNIFAESMEKLPYIVSVGDIILL 84 (464)
Q Consensus 9 ~y~~i~d~~~~~~~~vnviGVVvd~~~P~~---trG-tD~~~tl~I~D~S~~~~gl~v~iF~~~~e~LP~v~~~GDII~l 84 (464)
.+++|.++. ..+..+++.|.|++..+++. .+| ......+.|.|+|= -+++.+|.+..+.++.+. .||+|.+
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 EFTPIEDIK-ADMNNINISGRVLDISEVRTFEKKDGSPGRVGNLLLGDSTG---KIRLTLWDEKTNFLDEID-FDETVEV 349 (484)
T ss_pred cccCHHHcC-CCCceeEEEEEEEEcCCCeEEEcCCCCeeEEEEEEEECCCC---eEEEEEeCcccccccccC-CCceEEE
Confidence 567888886 23578999999999988753 246 46778899999985 299999998876777777 8999999
Q ss_pred eeEEEEE--ECCeeEEeecCCceeEEEEeCCCCCCccccccCCCcccChhHHHHHHHHHHHHhhcccccCCccccccccC
Q 012425 85 SHVVMKA--HNKQAYALFNKKFSSFALYDGKGGEDFLPYQVSSRFFVRDQDKRIIAAVRKWLLNFQFKEDSKKFLLLREI 162 (464)
Q Consensus 85 ~rvkv~~--~~g~~~~~~~~~~ss~~lf~g~~~~~~~P~~~s~~~~~~~~e~~~v~~Lr~w~~~~~~~~~~~~f~~L~di 162 (464)
.++.++. +++.+.+..+.. +. ........ .+ ..+|..|.||
T Consensus 350 ~~~y~~~~~~~~~~eL~~~~~-t~---I~~~~~~~--------e~-------------------------~~~~~~I~di 392 (484)
T PRK14699 350 LNAYSRENTFSQQVELNLGAR-GI---IQKSEKKV--------EY-------------------------REKFTDIADI 392 (484)
T ss_pred EeEEEEeccCCccEEEEecCc-ee---EeecCCcc--------ee-------------------------eeccccHHHc
Confidence 9999884 345566665544 21 11111000 00 1147789999
Q ss_pred CCCCeEeEEEEEeEEEeeCCCeEEEEEEeCCCCCCCcccccccccccCCCCCcccCCCCcccccccCCCcccEEEEEEcc
Q 012425 163 KDGQRINMACKVFHICEVAKGEWMAFVWDGTDAPPAQISKKLEDEMDHELPLQVEPLPLSRDILCSFPAVGSILRVIIDK 242 (464)
Q Consensus 163 ~~~~f~Dl~~qVv~~~~~~~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~~~~~e~~~l~~~~l~~~p~~G~~l~V~~~~ 242 (464)
++++.+|+++.|+.+.+.. .+. --||+.-.-..+. .. | -.| .+|+++|.
T Consensus 393 e~~~~vdV~G~V~~v~~~~--~~~--~~~g~~~~vr~i~--l~----D--------------------~TG-~Ir~tlWg 441 (484)
T PRK14699 393 IPGESYSVQGKVSEIGELR--EFE--REDGTENVVANLQ--LK----D--------------------ETG-SIRLTLWG 441 (484)
T ss_pred cCCCeeEEEEEEEEcCCcc--eEE--ecCCCEEEEEEEE--EE----c--------------------CCC-eEEEEEcc
Confidence 9999999999999886522 111 2344321111000 00 0 125 68999999
Q ss_pred chhHHHhhccCCCCEEEEeceEEEEe-CcEEEEEEecccceEEc
Q 012425 243 GIEKHILHLLKIGKWVKLQNVLCQVD-AGLWFGVLTHFTRLRYV 285 (464)
Q Consensus 243 ~~~~~~~~~lk~G~wV~l~Nv~~k~~-~G~leG~l~~~ski~~l 285 (464)
..|.. .+.+.+|+-|.+.|..++.. .|.+|..+-..|.|.+|
T Consensus 442 ~~A~~-~~~~~~~~~v~~~~~~~~~g~~~~~e~s~g~~s~~~~~ 484 (484)
T PRK14699 442 EQAYV-IEDLDIDSEIQIIDAYARYGLNEEIELSVGNRSRVIIL 484 (484)
T ss_pred hhhhh-ccccCCCCeEEEechhhhhcccccEEEEecCceEEEeC
Confidence 88763 46899999999999999997 78999988888887654
No 15
>PRK07211 replication factor A; Reviewed
Probab=98.46 E-value=0.00011 Score=77.87 Aligned_cols=266 Identities=15% Similarity=0.179 Sum_probs=167.6
Q ss_pred eEehHHHhhccC-CeEEEEEEEEeeCCccc-cc----CCceEEEEEEEeCCCCCCCeEEEEeccCcC-CCCCCCCCCCEE
Q 012425 10 FLKIKDAILSIN-QKVSFVGVILEVGSPKQ-SK----GTDSFCTIKVTDESHTKDGISVNIFAESME-KLPYIVSVGDII 82 (464)
Q Consensus 10 y~~i~d~~~~~~-~~vnviGVVvd~~~P~~-tr----GtD~~~tl~I~D~S~~~~gl~v~iF~~~~e-~LP~v~~~GDII 82 (464)
..+|+++. ++ ..|++.|-|+..+.|+. ++ +.--.+++.|.|+|= .|++.+|....+ ..|.++ +|||+
T Consensus 53 ~~~I~dL~--pg~~~vtI~aRV~~~~~~Rt~~~~~~~~eGkv~~v~l~DeTG---~Ir~TlW~d~ad~~~~~Le-~GdV~ 126 (485)
T PRK07211 53 VNGIADIE--PGMDEVKFLAKVLSIGDLRTFERDGEDEDGRVINVEVADETG---SVRVAFWDEQAVAAEEELE-VGQVL 126 (485)
T ss_pred cccHhhCC--CCCCceEEEEEEeEccCceEEEeCCCCCCcEEEEEEEEcCCC---eEEEEEechHhHhhhcccC-CCCEE
Confidence 35899996 55 56999999999999864 22 235889999999775 399999976432 367787 89999
Q ss_pred EEeeEEEEEECCeeEEeecCCceeEEEEeCCCCCCccccccCCCcccChhHHHHHHHHHHHHhhcccccCCccccccccC
Q 012425 83 LLSHVVMKAHNKQAYALFNKKFSSFALYDGKGGEDFLPYQVSSRFFVRDQDKRIIAAVRKWLLNFQFKEDSKKFLLLREI 162 (464)
Q Consensus 83 ~l~rvkv~~~~g~~~~~~~~~~ss~~lf~g~~~~~~~P~~~s~~~~~~~~e~~~v~~Lr~w~~~~~~~~~~~~f~~L~di 162 (464)
.+.+.-...|++ +.+..+ . ........+ |. ....|..|+||
T Consensus 127 ~I~~~~~~~ys~-~El~i~----~---ve~~~d~~i-~~------------------------------~~~~~~~I~dL 167 (485)
T PRK07211 127 RIKGRPKDGYNG-LEVSVD----K---VEPDPDAEI-DV------------------------------QIGDTYTVEDL 167 (485)
T ss_pred EEeceEeccccc-eEEEEe----e---EEEcccccc-cc------------------------------cccCCccHHHc
Confidence 998754444544 222111 0 000000000 00 01146779999
Q ss_pred CCC-CeEeEEEEEeEEEeeCCCeEEEEEEeCCCCCCCcccccccccccCCCCCcccCCCCcccccccCCCcccEEEEEEc
Q 012425 163 KDG-QRINMACKVFHICEVAKGEWMAFVWDGTDAPPAQISKKLEDEMDHELPLQVEPLPLSRDILCSFPAVGSILRVIID 241 (464)
Q Consensus 163 ~~~-~f~Dl~~qVv~~~~~~~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~~~~~e~~~l~~~~l~~~p~~G~~l~V~~~ 241 (464)
+++ ..+|+.++|+.+.... . +-=-||++-..+. ...-| --|+ +|+|+|
T Consensus 168 ~~~~~~v~I~grV~~v~~iR--t--f~r~dGseGkv~s--v~L~D------------------------eTG~-IR~TlW 216 (485)
T PRK07211 168 SLGLSDVTLVGVVLDTDSVR--T--FDRDDGSEGRVSN--LTVGD------------------------ETGR-VRVTLW 216 (485)
T ss_pred CCCCCceEEEEEEEEcCCCe--E--EECCCCCeeEEEE--EEEEc------------------------CCCe-EEEEEe
Confidence 876 5689999999776420 0 0011232111111 10000 1254 899999
Q ss_pred cchhHHHhhccCCCCEEEEeceEEEEeCcEEEEEEecccceEEcCCCChHHHHHHHHHHHHhhccCCCCCcccCCCCCcc
Q 012425 242 KGIEKHILHLLKIGKWVKLQNVLCQVDAGLWFGVLTHFTRLRYVPTNDNLIVERQRSYDERLSWEHSRMPYWCFPWTSEV 321 (464)
Q Consensus 242 ~~~~~~~~~~lk~G~wV~l~Nv~~k~~~G~leG~l~~~ski~~l~~~d~~v~~r~r~y~~r~~~~~~~~~~~~~p~~~~i 321 (464)
..++... ..+.+|+-|++.|.+++...|.+|..+..++.|..++.+- ++ +| ....
T Consensus 217 ~d~Ad~~-~~le~G~Vv~I~~a~Vre~~g~~ELsl~~~s~I~~~~dev--------~~----------vp-----~~~~- 271 (485)
T PRK07211 217 DDRADLA-EELDAGESVEIVDGYVRERDGSLELHVGDRGAVEEVDEDV--------EY----------VP-----DTTP- 271 (485)
T ss_pred chhhhhh-ccCCCCCEEEEEeeEEEecCCcEEEEECCCceEEECCccc--------cc----------cc-----cccc-
Confidence 9888764 6799999999999999988888999999999998776421 00 11 0001
Q ss_pred ccCCCCCCCCcccHHhhhcCcccCceeEEEEEEEeecCCCccccccCCcc--EEEEEEEecCCceEEEEEecCchh
Q 012425 322 TDIDYSEDGPFVTLKDVLTHSQVTAKFKCVVRVVAALPWRSEDFCSPLGN--YRIRLTLEDPTARIHAFVYAEDGE 395 (464)
Q Consensus 322 t~~~~~~~~p~~Tl~diLt~~~v~~kfr~~VRVV~~~P~~~edf~~~~g~--~~~~l~leD~t~~l~~~v~~~da~ 395 (464)
|.++- + ..-.-...+|.+..|...=. ..+|. .+-.++|.|.||+|.+-++|+.|+
T Consensus 272 -------------I~dl~--~--g~~vdV~GvV~~v~~~rtf~--r~dG~~~~vr~l~l~D~TG~IrvTLWg~~A~ 328 (485)
T PRK07211 272 -------------IESLE--I--DETVDIAGVVRSADPKRTFD--RDDGSEGQVRNVRIQDDTGDIRVALWGEKAD 328 (485)
T ss_pred -------------HhhcC--C--CCceeEEEEEEEccCcEEEE--cCCCCEeEEEEEEEEcCCCcEEEEEeCcccc
Confidence 11110 0 01134556777776665433 33454 677999999999999999999884
No 16
>PRK08402 replication factor A; Reviewed
Probab=98.25 E-value=9.2e-05 Score=75.94 Aligned_cols=101 Identities=16% Similarity=0.220 Sum_probs=68.9
Q ss_pred ccccccCCCC-CeEeEEEEEeEEEeeCCCeEEEEEEeCCCCCCCcccccccccccCCCCCcccCCCCcccccccCCCccc
Q 012425 156 FLLLREIKDG-QRINMACKVFHICEVAKGEWMAFVWDGTDAPPAQISKKLEDEMDHELPLQVEPLPLSRDILCSFPAVGS 234 (464)
Q Consensus 156 f~~L~di~~~-~f~Dl~~qVv~~~~~~~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~~~~~e~~~l~~~~l~~~p~~G~ 234 (464)
...|+||.++ ..++++++|+.+..... +---||+...- .+....| -.|+
T Consensus 62 ~~kI~dl~~g~~~V~v~~rVl~~~~~r~----f~rrdG~~~~V--~~i~l~D------------------------eTG~ 111 (355)
T PRK08402 62 LMHISDLVPGMRGVNIVGRVLRKYPPRE----YTKKDGSTGRV--ASLIIYD------------------------DTGR 111 (355)
T ss_pred ccCHHHccCCCceeeEEEEEEEccCCce----eeccCCCcceE--EEEEEEc------------------------CCCe
Confidence 5679999987 58999999998864211 00113331111 1110000 0244
Q ss_pred EEEEEEccchhHHHhhccCCCCEEEEeceEEEEe-CcEEEEEEecccceEEcCC
Q 012425 235 ILRVIIDKGIEKHILHLLKIGKWVKLQNVLCQVD-AGLWFGVLTHFTRLRYVPT 287 (464)
Q Consensus 235 ~l~V~~~~~~~~~~~~~lk~G~wV~l~Nv~~k~~-~G~leG~l~~~ski~~l~~ 287 (464)
+ ++|+|..++.-....+.+|+-|++.|..++-. +|..+-.+...+.|.+.|+
T Consensus 112 i-r~TlW~~~a~~~~~~l~~Gdvi~I~~a~V~e~~~G~~eLsvg~~s~i~~~pd 164 (355)
T PRK08402 112 A-RVVLWDAKVAKYYNKINVGDVIKVIDAQVRESLSGLPELHINFRARIILNPD 164 (355)
T ss_pred E-EEEEechhhhhhcccCCCCCEEEEECCEEeecCCCcEEEEECCCceEEeCCC
Confidence 4 99999988653245699999999999999985 9999999999999977664
No 17
>TIGR00617 rpa1 replication factor-a protein 1 (rpa1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.96 E-value=0.00011 Score=80.63 Aligned_cols=159 Identities=15% Similarity=0.199 Sum_probs=106.5
Q ss_pred CCCceeeEehHHHhhc-cCCeEEEEEEEEeeCCcccc--c--CCc-eEEEEEEEeCCCCCCCeEEEEeccCcCCCCCCCC
Q 012425 4 NGEDYRFLKIKDAILS-INQKVSFVGVILEVGSPKQS--K--GTD-SFCTIKVTDESHTKDGISVNIFAESMEKLPYIVS 77 (464)
Q Consensus 4 ~~~~y~y~~i~d~~~~-~~~~vnviGVVvd~~~P~~t--r--GtD-~~~tl~I~D~S~~~~gl~v~iF~~~~e~LP~v~~ 77 (464)
+.-.|.|++|+++... .+..|+|||||++.++...- | |+. .+.+|+|.|.|- ..|.|.++.+..+.+. ..
T Consensus 292 P~~~~~f~~i~dI~~~~~~~~VDVIGvV~~v~~~~~i~~k~~g~~~~kR~i~L~D~sg--~sI~vTLWG~~A~~~~-~~- 367 (608)
T TIGR00617 292 PKIQFNFVKIDDIGGYEGNSLVDVIGIVQSVSPTQTITSRKNNKEFPKRDITLVDDSG--KSVRVTLWGDDATKFD-VS- 367 (608)
T ss_pred CcccccceEHHHhhhhcCCCCccEEEEEeEecCceEEEEcCCCCeeeeEEEEEEeCCC--CEEEEEEEhhhhhhcC-CC-
Confidence 4446899999999754 34589999999999987542 2 443 567999999995 4599999998766666 33
Q ss_pred CCCEEEEeeEEEEEECCeeEEeecCCceeEEEEeCCCCCCccccccCCCcccChhHHHHHHHHHHHHhhcccc-------
Q 012425 78 VGDIILLSHVVMKAHNKQAYALFNKKFSSFALYDGKGGEDFLPYQVSSRFFVRDQDKRIIAAVRKWLLNFQFK------- 150 (464)
Q Consensus 78 ~GDII~l~rvkv~~~~g~~~~~~~~~~ss~~lf~g~~~~~~~P~~~s~~~~~~~~e~~~v~~Lr~w~~~~~~~------- 150 (464)
.|+||.+..++|+.|+|. .+... ..|.+. .+ | |..-+..|+.|+.+....
T Consensus 368 ~~~Vva~kg~~V~~f~g~-sLs~~-~~S~i~-iN--------P------------dipEa~~L~~w~~~~g~~~~~~s~~ 424 (608)
T TIGR00617 368 VQPVIAIKGVRVSDFGGK-SLSTG-GSSTII-VN--------P------------DIPEAEKLKGWYDNEGKGTMASSIS 424 (608)
T ss_pred CCCEEEEEeEEEEecCCc-eEecc-CCceEE-EC--------C------------CcHHHHHHHHHHHhcCCCccceeeh
Confidence 699999999999999663 44322 224443 11 1 122356899998654221
Q ss_pred -c------C-CccccccccCCC--------CCeEeEEEEEeEEEeeCCCeEEEEEEeCCCCCC
Q 012425 151 -E------D-SKKFLLLREIKD--------GQRINMACKVFHICEVAKGEWMAFVWDGTDAPP 197 (464)
Q Consensus 151 -~------~-~~~f~~L~di~~--------~~f~Dl~~qVv~~~~~~~~~~~L~VwDgT~~p~ 197 (464)
. + ......|++|++ +.||.+.|.|.++..+ . .| |..+|.
T Consensus 425 ~~~~~~~~~~~~~~ktI~ei~~~~lg~~~k~~~f~v~atI~~Ik~d---~----~~-Y~ACp~ 479 (608)
T TIGR00617 425 DMMSGRVGGSNAERKTIAEIQAENLGKSDKPDYFSVKATISYLKPD---N----AL-YRACPS 479 (608)
T ss_pred hccccccCCcccccccHHHHhhhccCCCCCCcEEEEEEEEEEEecC---C----eE-eccCCh
Confidence 0 0 112344555543 3479999999988642 2 24 777765
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=97.92 E-value=9.4e-05 Score=62.13 Aligned_cols=74 Identities=22% Similarity=0.250 Sum_probs=58.6
Q ss_pred eEEEEEEEEeeCCcccc--c--C-CceEEEEEEEeCCCCCCCeEEEEeccCcCCCCCCCCCCCEEEEeeEEEEEECCeeE
Q 012425 23 KVSFVGVILEVGSPKQS--K--G-TDSFCTIKVTDESHTKDGISVNIFAESMEKLPYIVSVGDIILLSHVVMKAHNKQAY 97 (464)
Q Consensus 23 ~vnviGVVvd~~~P~~t--r--G-tD~~~tl~I~D~S~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~rvkv~~~~g~~~ 97 (464)
.|||+|+|++.++++.- + | .-.+..|+|.|.|.. ++.|.++.+..+.+... .|+||.+++++++.|+| ..
T Consensus 1 ~vDvig~V~~v~~~~~i~~k~~g~~~~~r~v~i~D~t~~--~i~vtLWg~~a~~~~~~--~~~vv~~~~~~i~~~~~-~~ 75 (101)
T cd04475 1 IVDVIGVVKSVGPVTTITTKSTGRELDKREITLVDESGH--SVELTLWGEQAELFDGS--ENPVIAIKGVKVSEFNG-KS 75 (101)
T ss_pred CEeEEEEEeEccCcEEEEEecCCCceeEEEEEEEeCCCC--EEEEEEEHHHhhhcccC--CCCEEEEEeeEEEecCC-eE
Confidence 38999999999998642 2 4 467899999999974 59999998876555543 39999999999999985 45
Q ss_pred Eeec
Q 012425 98 ALFN 101 (464)
Q Consensus 98 ~~~~ 101 (464)
+.++
T Consensus 76 l~~~ 79 (101)
T cd04475 76 LSTG 79 (101)
T ss_pred Eeec
Confidence 5433
No 19
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=97.82 E-value=0.00022 Score=62.85 Aligned_cols=85 Identities=24% Similarity=0.336 Sum_probs=68.5
Q ss_pred eEehHHHhhccC-CeEEEEEEEEeeCCcc--cccCC-ceEEEEEEEeCCCCCCCeEEEEeccCcCCCCCCCCCCCEEEEe
Q 012425 10 FLKIKDAILSIN-QKVSFVGVILEVGSPK--QSKGT-DSFCTIKVTDESHTKDGISVNIFAESMEKLPYIVSVGDIILLS 85 (464)
Q Consensus 10 y~~i~d~~~~~~-~~vnviGVVvd~~~P~--~trGt-D~~~tl~I~D~S~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~ 85 (464)
+++|+|+. ++ ..||+.|+|++..+++ +++|+ -...+++|.|.|=. |.+.++.+. .+.+. .||||.|+
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---VKLTLWGEQ---AGSLK-EGEVVEIE 74 (129)
T ss_pred ceEHHHcC--CCCCceEEEEEEEEcCCceEEEeCCCceEEEEEEEECCCCE---EEEEEeCCc---cccCC-CCCEEEEE
Confidence 67899997 56 5799999999988764 45554 45889999999852 999999764 33455 79999999
Q ss_pred eEEEEEECCeeEEeecCC
Q 012425 86 HVVMKAHNKQAYALFNKK 103 (464)
Q Consensus 86 rvkv~~~~g~~~~~~~~~ 103 (464)
+++++.|+|.+++..++.
T Consensus 75 na~v~~f~G~lqL~i~~~ 92 (129)
T PRK06461 75 NAWTTLYRGKVQLNVGKY 92 (129)
T ss_pred CcEEeeeCCEEEEEECCC
Confidence 999999999999876643
No 20
>PRK07218 replication factor A; Provisional
Probab=97.55 E-value=0.0082 Score=63.07 Aligned_cols=161 Identities=17% Similarity=0.089 Sum_probs=105.6
Q ss_pred cccccccCCC-CCeEeEEEEEeEEEeeCCCeEEEEEEeCCCCCCCcccccccccccCCCCCcccCCCCcccccccCCCcc
Q 012425 155 KFLLLREIKD-GQRINMACKVFHICEVAKGEWMAFVWDGTDAPPAQISKKLEDEMDHELPLQVEPLPLSRDILCSFPAVG 233 (464)
Q Consensus 155 ~f~~L~di~~-~~f~Dl~~qVv~~~~~~~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~~~~~e~~~l~~~~l~~~p~~G 233 (464)
....|+||++ ++.++++++|+.+.. + ++. .||+. ......... | -.|
T Consensus 57 ~~~kI~Di~~~~~~V~v~~kVl~i~~----r-t~r-~dg~~--g~v~~~~ig----D--------------------eTG 104 (423)
T PRK07218 57 SSKDIKELSTDDKNVTVTGRVLTIGE----R-SIR-YQGDD--HVIYEGILA----D--------------------ETG 104 (423)
T ss_pred CCccHhhCCCCCceeEEEEEEEEecc----e-eEe-cCCCc--eEEEEEEEE----C--------------------CCC
Confidence 4667999986 579999999998843 2 222 77763 211111110 0 024
Q ss_pred cEEEEEEccchhHHHhhccCCCCEEEEeceEEEEeCcEEEEEEecccceEEcCCCChHHHHHHHHHHHHhhccCCCCCcc
Q 012425 234 SILRVIIDKGIEKHILHLLKIGKWVKLQNVLCQVDAGLWFGVLTHFTRLRYVPTNDNLIVERQRSYDERLSWEHSRMPYW 313 (464)
Q Consensus 234 ~~l~V~~~~~~~~~~~~~lk~G~wV~l~Nv~~k~~~G~leG~l~~~ski~~l~~~d~~v~~r~r~y~~r~~~~~~~~~~~ 313 (464)
+ +++++|... .+++||+|++.|...+...|..+-.+...+.|..++++..- .|
T Consensus 105 ~-Ir~tlW~~~------~l~~Gdvv~I~na~vre~~g~~el~ig~~t~I~~~de~~~~------~~-------------- 157 (423)
T PRK07218 105 T-ISYTAWKDF------GLSPGDTVTIGNAGVREWDGRPELNIGESTTVSLLDDSSLP------PY-------------- 157 (423)
T ss_pred e-EEEEEECCC------CCCCCCEEEEeccEeeccCCceEEeccCcceEEEcCccccc------Cc--------------
Confidence 4 599999833 39999999999999999999999888888888876643110 00
Q ss_pred cCCCCCccccCCCCCCCCcccHHhhhcCcccCceeEEEEEEEeecCCCccccccCCcc-EEEEEEEecCCceEEEEEecC
Q 012425 314 CFPWTSEVTDIDYSEDGPFVTLKDVLTHSQVTAKFKCVVRVVAALPWRSEDFCSPLGN-YRIRLTLEDPTARIHAFVYAE 392 (464)
Q Consensus 314 ~~p~~~~it~~~~~~~~p~~Tl~diLt~~~v~~kfr~~VRVV~~~P~~~edf~~~~g~-~~~~l~leD~t~~l~~~v~~~ 392 (464)
. -.+...|.|+-.- .......+||++.+|. .|-...|. ....++|.|.||+|+..+|++
T Consensus 158 -----~---------~~~~~kI~DL~~g---~~~V~v~g~Vl~~~~r---~f~~~dg~~~v~~giigDeTG~Ir~tlW~~ 217 (423)
T PRK07218 158 -----S---------IGGDKKLIDLGPG---DRGVNVEARVLELEHR---EIDGRDGETTILSGVLADETGRLPFTDWDP 217 (423)
T ss_pred -----c---------ccCccchhhccCC---CCceEEEEEEEEecce---eEEcCCCCeEEEEEEEECCCceEEEEEecc
Confidence 0 0001113333211 1234667899999874 35455553 577889999999999999997
Q ss_pred ch
Q 012425 393 DG 394 (464)
Q Consensus 393 da 394 (464)
.+
T Consensus 218 ~~ 219 (423)
T PRK07218 218 LP 219 (423)
T ss_pred cc
Confidence 54
No 21
>cd04491 SoSSB_OBF SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus solfataricus single-stranded (ss) DNA-binding protein (SSoSSB). SSoSSB has a single OB fold, and it physically and functionally interacts with RNA polymerase. In vitro, SSoSSB can substitute for the basal transcription factor TBP, stimulating transcription from promoters under conditions in which TBP is limiting, and supporting transcription when TBP is absent. SSoSSB selectively melts the duplex DNA of promoter sequences. It also relieves transcriptional repression by the chromatin Alba. In addition, SSoSSB activates reverse gyrase activity, which involves DNA binding, DNA cleavage, strand passage and ligation. SSoSSB stimulates all these steps in the presence of the chromatin protein, Sul7d. SSoSSB antagonizes the inhibitory effect of Sul7d on reverse gyrase supercoiling activity. It also physically and functionally interacts with Mini-chromosome Maintenance (MCM), stimulating
Probab=97.38 E-value=0.0016 Score=52.51 Aligned_cols=72 Identities=18% Similarity=0.272 Sum_probs=59.3
Q ss_pred EEEEEEEeeCCcccc---cCCceEEEEEEEeCCCCCCCeEEEEeccCcCCCCCCCCCCCEEEEeeEEEEEECCeeEEeec
Q 012425 25 SFVGVILEVGSPKQS---KGTDSFCTIKVTDESHTKDGISVNIFAESMEKLPYIVSVGDIILLSHVVMKAHNKQAYALFN 101 (464)
Q Consensus 25 nviGVVvd~~~P~~t---rGtD~~~tl~I~D~S~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~rvkv~~~~g~~~~~~~ 101 (464)
||.|.|++..+++.- .+.--..+++|.|.|- .+.+.++.+.. .+.++ .||+|.+++.+++.|+|.+++..+
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--ADDLE-PGDVVRIENAYVREFNGRLELSVG 74 (82)
T ss_pred CEEEEEEEccCCeEeccCCCeeEEEEEEEECCCC---EEEEEEECchh--cccCC-CCCEEEEEeEEEEecCCcEEEEeC
Confidence 589999999988653 3457788999999973 39999997653 66676 899999999999999999998655
Q ss_pred C
Q 012425 102 K 102 (464)
Q Consensus 102 ~ 102 (464)
.
T Consensus 75 ~ 75 (82)
T cd04491 75 K 75 (82)
T ss_pred C
Confidence 3
No 22
>PRK07217 replication factor A; Reviewed
Probab=97.04 E-value=0.14 Score=51.52 Aligned_cols=166 Identities=20% Similarity=0.235 Sum_probs=102.3
Q ss_pred cccccccCCC-CCeEeEEEEEeEEEeeCCCeEEEEEEeCCCCCCCcccccccccccCCCCCcccCCCCcccccccCCCcc
Q 012425 155 KFLLLREIKD-GQRINMACKVFHICEVAKGEWMAFVWDGTDAPPAQISKKLEDEMDHELPLQVEPLPLSRDILCSFPAVG 233 (464)
Q Consensus 155 ~f~~L~di~~-~~f~Dl~~qVv~~~~~~~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~~~~~e~~~l~~~~l~~~p~~G 233 (464)
+...|+||.+ ++.+++.++|+.+++... +.....+...| + .|
T Consensus 71 ~~~kI~Di~~~~~~VsV~aKVl~l~e~~~-------------~si~qvGllgD----E--------------------TG 113 (311)
T PRK07217 71 ELVNIADIDEPEQWVDVTAKVVQLWEPSS-------------DSIAQVGLLGD----E--------------------TG 113 (311)
T ss_pred CceeeeecCCCCCcEEEEEEEEEecCCCC-------------CceEEEEEEEc----C--------------------Cc
Confidence 3556999984 899999999998875221 11111111111 0 13
Q ss_pred cEEEEEEccchhHHHhhccCCCCEEEEeceEEEEeCcEEEEEEecccceEEcCCCChHHHHHHHHHHHHhhccCCCCCcc
Q 012425 234 SILRVIIDKGIEKHILHLLKIGKWVKLQNVLCQVDAGLWFGVLTHFTRLRYVPTNDNLIVERQRSYDERLSWEHSRMPYW 313 (464)
Q Consensus 234 ~~l~V~~~~~~~~~~~~~lk~G~wV~l~Nv~~k~~~G~leG~l~~~ski~~l~~~d~~v~~r~r~y~~r~~~~~~~~~~~ 313 (464)
+ ++.|+|...+ ...+++|++++|.|+..+...|..+-.+...+.|..++.+-+ |...- .+... .+-
T Consensus 114 ~-IkfT~W~~s~---~~~leeGd~~rI~na~v~ey~G~~~lnlg~~t~I~~~de~Ie-V~~~~--------vei~G-~lV 179 (311)
T PRK07217 114 T-IKFTKWAKSD---LPELEEGKSYLLKNVVTDEYQGRFSVKLNRTTSIEELDEDIE-VGDDE--------VEVEG-ALV 179 (311)
T ss_pred e-EEEEEccCCC---CCcccCCCEEEEEeEEEeeECCEEEEEeCCceEEEeCCCCcc-ccCcc--------cccee-EEE
Confidence 3 5888887532 346999999999999999999999999999999987775332 11000 00000 000
Q ss_pred cC-CCCCccccCCCCCCCCcccHHhhhcCcccCceeEEEEEEEeecCCCccccccCCc----c--EEEEEEEecCCceEE
Q 012425 314 CF-PWTSEVTDIDYSEDGPFVTLKDVLTHSQVTAKFKCVVRVVAALPWRSEDFCSPLG----N--YRIRLTLEDPTARIH 386 (464)
Q Consensus 314 ~~-p~~~~it~~~~~~~~p~~Tl~diLt~~~v~~kfr~~VRVV~~~P~~~edf~~~~g----~--~~~~l~leD~t~~l~ 386 (464)
.+ |..-.|..|+.+ . |. ||++ ...|..+| . -|.++.|.|+|+.+.
T Consensus 180 di~~GsglI~rCP~~-~--C~-------------------Rvl~------~g~C~~HG~ve~~~DLrik~vlDDGt~~~~ 231 (311)
T PRK07217 180 DIQSGSGLIKRCPEE-D--CT-------------------RVLQ------NGRCSEHGKVEGEFDLRIKGVLDDGEEVQE 231 (311)
T ss_pred EEeCCCCCeecCCcc-c--cC-------------------cccc------CCCCCCCCCcCCceeeEEEEEEECCCCeEE
Confidence 00 111123334332 0 11 3331 12345444 2 488999999999999
Q ss_pred EEEecCchhhhcC
Q 012425 387 AFVYAEDGEKLFG 399 (464)
Q Consensus 387 ~~v~~~da~~f~~ 399 (464)
++++.+-.+.+.|
T Consensus 232 ~~~~~e~te~l~G 244 (311)
T PRK07217 232 VIFNREATEELTG 244 (311)
T ss_pred EEEChHHhHHHhC
Confidence 9999998899988
No 23
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=96.91 E-value=0.0081 Score=52.96 Aligned_cols=96 Identities=17% Similarity=0.235 Sum_probs=65.9
Q ss_pred ccccccCCCC-CeEeEEEEEeEEEeeCCCeEEEEEEeCCCCCCCcccccccccccCCCCCcccCCCCcccccccCCCccc
Q 012425 156 FLLLREIKDG-QRINMACKVFHICEVAKGEWMAFVWDGTDAPPAQISKKLEDEMDHELPLQVEPLPLSRDILCSFPAVGS 234 (464)
Q Consensus 156 f~~L~di~~~-~f~Dl~~qVv~~~~~~~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~~~~~e~~~l~~~~l~~~p~~G~ 234 (464)
+..|+||+++ .-+|++++|+.+.... .+ -.++. +.........| -.|+
T Consensus 4 ~~kI~dL~~g~~~v~~~~~V~~i~~~~--~~---~~k~~--~~~v~~~~l~D------------------------~TG~ 52 (129)
T PRK06461 4 ITKIKDLKPGMERVNVTVRVLEVGEPK--VI---QTKGG--PRTISEAVVGD------------------------ETGR 52 (129)
T ss_pred ceEHHHcCCCCCceEEEEEEEEcCCce--EE---EeCCC--ceEEEEEEEEC------------------------CCCE
Confidence 5679999999 6999999999765311 00 11111 11111111111 0243
Q ss_pred EEEEEEccchhHHHhhccCCCCEEEEeceEEEEeCcEEEEEEecccceEEcCC
Q 012425 235 ILRVIIDKGIEKHILHLLKIGKWVKLQNVLCQVDAGLWFGVLTHFTRLRYVPT 287 (464)
Q Consensus 235 ~l~V~~~~~~~~~~~~~lk~G~wV~l~Nv~~k~~~G~leG~l~~~ski~~l~~ 287 (464)
+++++|...+ ..+++||.|+++|..++...|.++..+...+.|..+++
T Consensus 53 -I~~tlW~~~a----~~l~~GdvV~I~na~v~~f~G~lqL~i~~~~~i~~~~~ 100 (129)
T PRK06461 53 -VKLTLWGEQA----GSLKEGEVVEIENAWTTLYRGKVQLNVGKYGSISESDD 100 (129)
T ss_pred -EEEEEeCCcc----ccCCCCCEEEEECcEEeeeCCEEEEEECCCEEEEECCc
Confidence 6899998653 46899999999999999999999999998889988774
No 24
>PRK08402 replication factor A; Reviewed
Probab=96.78 E-value=0.033 Score=57.38 Aligned_cols=140 Identities=14% Similarity=0.226 Sum_probs=92.3
Q ss_pred eeEehHHHhhccC-CeEEEEEEEEeeCCccc--c-cCC-ceEEEEEEEeCCCCCCCeEEEEeccCcC-CCCCCCCCCCEE
Q 012425 9 RFLKIKDAILSIN-QKVSFVGVILEVGSPKQ--S-KGT-DSFCTIKVTDESHTKDGISVNIFAESME-KLPYIVSVGDII 82 (464)
Q Consensus 9 ~y~~i~d~~~~~~-~~vnviGVVvd~~~P~~--t-rGt-D~~~tl~I~D~S~~~~gl~v~iF~~~~e-~LP~v~~~GDII 82 (464)
...+|+|+. ++ ..||+.|-|+....|+. . .|+ ....++.|.|+|-. +.+.++.+..+ .++.+. .||||
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---ARVVLWDAKVAKYYNKIN-VGDVI 134 (355)
T ss_pred CccCHHHcc--CCCceeeEEEEEEEccCCceeeccCCCcceEEEEEEEcCCCe---EEEEEechhhhhhcccCC-CCCEE
Confidence 478899997 44 57999999999987753 1 243 56788999998852 79999987644 367777 89999
Q ss_pred EEeeEEEEE-ECCeeEEeecCCceeEEEEeCCCCCCccccccCCCcccChhHHHHHHHHHHHHhhcccccCCcccccccc
Q 012425 83 LLSHVVMKA-HNKQAYALFNKKFSSFALYDGKGGEDFLPYQVSSRFFVRDQDKRIIAAVRKWLLNFQFKEDSKKFLLLRE 161 (464)
Q Consensus 83 ~l~rvkv~~-~~g~~~~~~~~~~ss~~lf~g~~~~~~~P~~~s~~~~~~~~e~~~v~~Lr~w~~~~~~~~~~~~f~~L~d 161 (464)
.+.+++++. |+|.+.+..+.. |+..+ ....... .++..-.++.. .......|.|
T Consensus 135 ~I~~a~V~e~~~G~~eLsvg~~-s~i~~-~pd~~ea-------~~i~~~~~~~~----------------~~~~~k~I~e 189 (355)
T PRK08402 135 KVIDAQVRESLSGLPELHINFR-ARIIL-NPDDPRV-------EEIPPLEEVRS----------------YNYTRKKIGE 189 (355)
T ss_pred EEECCEEeecCCCcEEEEECCC-ceEEe-CCCcccc-------ccccccccccc----------------ccccccCHHH
Confidence 999999998 588878765544 33332 1111100 00100000000 0123556888
Q ss_pred CCCCC-eEeEEEEEeEEEe
Q 012425 162 IKDGQ-RINMACKVFHICE 179 (464)
Q Consensus 162 i~~~~-f~Dl~~qVv~~~~ 179 (464)
+++|. ||.+.+.|+.+..
T Consensus 190 i~~gd~~v~v~g~Iv~i~~ 208 (355)
T PRK08402 190 LEGGERFVEVRGTIAKVYR 208 (355)
T ss_pred cccCCcEEEEEEEEEEEec
Confidence 87765 7999999998753
No 25
>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=96.67 E-value=0.017 Score=51.45 Aligned_cols=95 Identities=19% Similarity=0.109 Sum_probs=68.2
Q ss_pred cccccccCC--CCCeEeEEEEEeEEEeeC-----CCeEEEEEEeCCCCCCCcccccccccccCCCCCcccCCCCcccccc
Q 012425 155 KFLLLREIK--DGQRINMACKVFHICEVA-----KGEWMAFVWDGTDAPPAQISKKLEDEMDHELPLQVEPLPLSRDILC 227 (464)
Q Consensus 155 ~f~~L~di~--~~~f~Dl~~qVv~~~~~~-----~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~~~~~e~~~l~~~~l~ 227 (464)
+|..|++++ .++.+|+++-|+...... +-+.+|.++|-|.++
T Consensus 2 ~f~~i~~~~~~~~~~v~vigVV~~~~~p~~s~g~d~~~tl~i~D~S~~~------------------------------- 50 (138)
T cd04497 2 KYTPLSSALKESGGSVNVIGVVVDAGPPVRSKGTDYCCTLTITDPSLAN------------------------------- 50 (138)
T ss_pred ceEeHHHHHhccCCeEEEEEEEeecCCCcccCCCcEEEEEEEECCCCCC-------------------------------
Confidence 367788886 799999999999776421 234455555544211
Q ss_pred cCCCcccEEEEEEccchhHHHhhccCCCCEEEEeceEEEEeCcEEEEEEec-ccceEEcC
Q 012425 228 SFPAVGSILRVIIDKGIEKHILHLLKIGKWVKLQNVLCQVDAGLWFGVLTH-FTRLRYVP 286 (464)
Q Consensus 228 ~~p~~G~~l~V~~~~~~~~~~~~~lk~G~wV~l~Nv~~k~~~G~leG~l~~-~ski~~l~ 286 (464)
+..++|.+|.++++. +..+.+||.|+|+|++++..+|...|.... .+.+.+-+
T Consensus 51 -----~~~l~v~~F~~~~~~-LP~v~~GDVIll~~~kv~~~~g~~~~~~~~~~ss~avf~ 104 (138)
T cd04497 51 -----SDGLTVKLFRPNEES-LPIVKVGDIILLRRVKIQSYNGKPQGISNDRGSSWAVFR 104 (138)
T ss_pred -----CCcEEEEEECCChhh-CCCCCCCCEEEEEEEEEEEECCceEEEECCCceeEEEEc
Confidence 234688888888765 555799999999999999998888888777 55555544
No 26
>KOG4757 consensus Predicted telomere binding protein [General function prediction only]
Probab=96.67 E-value=0.0012 Score=67.72 Aligned_cols=80 Identities=15% Similarity=-0.047 Sum_probs=65.9
Q ss_pred EecCCceEEEEEecCchhh-----hcC-CCCchHHHHHHHHHHhcCCCCCCccc-cCCCCCCcceeEeEEeeeeCCCCcc
Q 012425 378 LEDPTARIHAFVYAEDGEK-----LFG-GYPFVDVLKRKINKLLGVAVSDGQEI-KDAPRNPPWVQCCLKSYYIDRNDIW 450 (464)
Q Consensus 378 leD~t~~l~~~v~~~da~~-----f~~-~~~~~~~l~~kl~~l~g~~e~~~~~~-~~~~~~~pw~~cci~sY~~~~~~~~ 450 (464)
.+|.++|.|+.++-.|... +|| .-.+...+-.+|+.|+++ |+ ...|.++||++||.-+.+..+-..|
T Consensus 373 c~l~n~r~H~~l~~le~s~p~s~~~fgc~~~~~~~~v~~ln~Lv~~------e~~~~vP~~~~~v~~~~l~~~s~~l~~~ 446 (522)
T KOG4757|consen 373 CNLLNPRKHRLLVQLEDSWPKSLTQFGCLSQPPSSYVWMLNLLVRD------ESNVTVPVIFFDVDAAELINSSKKLPCN 446 (522)
T ss_pred hhhhchhhhhhhhhhcccCcccceeeeeccCCHHHHHHHHHHHhcc------ccccccccccchhheeeeccccccccch
Confidence 7889999999999877765 888 446678889999999995 33 3468999999999999998876655
Q ss_pred e---eeEEEeeeeeEC
Q 012425 451 G---SRQYRIFDTKIS 463 (464)
Q Consensus 451 ~---~r~y~iF~T~i~ 463 (464)
. +|+||||++-|.
T Consensus 447 l~d~~~~fqi~ds~il 462 (522)
T KOG4757|consen 447 LADHQMTFQIKDSLIL 462 (522)
T ss_pred hccccceEEecceeee
Confidence 4 599999999874
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=96.33 E-value=0.02 Score=43.51 Aligned_cols=70 Identities=19% Similarity=0.353 Sum_probs=52.5
Q ss_pred EEEEEEEeeCCcccccCCceEEEEEEEeCCCCCCCeEEEEeccCcCCCCCCCCCCCEEEEeeEEEEEECCeeEEee
Q 012425 25 SFVGVILEVGSPKQSKGTDSFCTIKVTDESHTKDGISVNIFAESMEKLPYIVSVGDIILLSHVVMKAHNKQAYALF 100 (464)
Q Consensus 25 nviGVVvd~~~P~~trGtD~~~tl~I~D~S~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~rvkv~~~~g~~~~~~ 100 (464)
++.|+|++...+.. ...+..|+|.|.+- ..+.+.+|.+..+........|++|.++ .+++.+++..++..
T Consensus 1 ~v~g~v~~~~~~~~---~~~~~~~~l~D~~~--~~i~~~~~~~~~~~~~~~~~~g~~v~v~-g~v~~~~~~~~l~~ 70 (75)
T cd03524 1 TIVGIVVAVEEIRT---EGKVLIFTLTDGTG--GTIRVTLFGELAEELENLLKEGQVVYIK-GKVKKFRGRLQLIV 70 (75)
T ss_pred CeEEEEEeeccccc---CCeEEEEEEEcCCC--CEEEEEEEchHHHHHHhhccCCCEEEEE-EEEEecCCeEEEEe
Confidence 37899999887633 35589999999882 2399999987655543333489999998 99998887777654
No 28
>KOG3416 consensus Predicted nucleic acid binding protein [General function prediction only]
Probab=96.28 E-value=0.02 Score=49.48 Aligned_cols=83 Identities=25% Similarity=0.324 Sum_probs=66.6
Q ss_pred EehHHHhhccC-CeEEEEEEEEeeCCcccccCCceEEEEEEEeCCCCCCCeEEEEeccCcCCCCCCCCCCCEEEEeeEEE
Q 012425 11 LKIKDAILSIN-QKVSFVGVILEVGSPKQSKGTDSFCTIKVTDESHTKDGISVNIFAESMEKLPYIVSVGDIILLSHVVM 89 (464)
Q Consensus 11 ~~i~d~~~~~~-~~vnviGVVvd~~~P~~trGtD~~~tl~I~D~S~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~rvkv 89 (464)
+.|+|+. ++ +..|++=+|++.+...+|+-.+=.++.++.|+|-. |.+.+..+. -.+ ++ +||||+|++---
T Consensus 5 i~ikdi~--P~~kN~~v~fIvl~~g~~tkTkdg~~v~~~kVaD~Tgs---I~isvW~e~-~~~--~~-PGDIirLt~Gy~ 75 (134)
T KOG3416|consen 5 IFIKDIK--PGLKNINVTFIVLEYGRATKTKDGHEVRSCKVADETGS---INISVWDEE-GCL--IQ-PGDIIRLTGGYA 75 (134)
T ss_pred hhHhhcC--hhhhcceEEEEEEeeceeeeccCCCEEEEEEEecccce---EEEEEecCc-Ccc--cC-CccEEEecccch
Confidence 4678886 44 45999999999999999998888999999999863 888888632 222 33 899999999999
Q ss_pred EEECCeeEEeecC
Q 012425 90 KAHNKQAYALFNK 102 (464)
Q Consensus 90 ~~~~g~~~~~~~~ 102 (464)
+.|+|.+.+-..+
T Consensus 76 Si~qg~LtL~~GK 88 (134)
T KOG3416|consen 76 SIFQGCLTLYVGK 88 (134)
T ss_pred hhhcCceEEEecC
Confidence 9999987776554
No 29
>PRK07217 replication factor A; Reviewed
Probab=95.64 E-value=0.12 Score=51.83 Aligned_cols=91 Identities=20% Similarity=0.229 Sum_probs=66.5
Q ss_pred eeeEehHHHhhccCCeEEEEEEEEeeCCcccccCCceEEEEEEEeCCCCCCCeEEEEeccCcCCCCCCCCCCCEEEEeeE
Q 012425 8 YRFLKIKDAILSINQKVSFVGVILEVGSPKQSKGTDSFCTIKVTDESHTKDGISVNIFAESMEKLPYIVSVGDIILLSHV 87 (464)
Q Consensus 8 y~y~~i~d~~~~~~~~vnviGVVvd~~~P~~trGtD~~~tl~I~D~S~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~rv 87 (464)
..-++|+|+. ..++.|+|.|-|+....|+. ++-...- -|-|+|= . |++..+.+ +.+|.+. .||+++|+++
T Consensus 70 ~~~~kI~Di~-~~~~~VsV~aKVl~l~e~~~--~si~qvG-llgDETG-~--IkfT~W~~--s~~~~le-eGd~~rI~na 139 (311)
T PRK07217 70 SELVNIADID-EPEQWVDVTAKVVQLWEPSS--DSIAQVG-LLGDETG-T--IKFTKWAK--SDLPELE-EGKSYLLKNV 139 (311)
T ss_pred CCceeeeecC-CCCCcEEEEEEEEEecCCCC--CceEEEE-EEEcCCc-e--EEEEEccC--CCCCccc-CCCEEEEEeE
Confidence 4456788886 34678999999999988742 2222211 3556553 2 88999975 3699998 7999999999
Q ss_pred EEEEECCeeEEeecCCceeEEE
Q 012425 88 VMKAHNKQAYALFNKKFSSFAL 109 (464)
Q Consensus 88 kv~~~~g~~~~~~~~~~ss~~l 109 (464)
.+..|+|.+++..++ +++...
T Consensus 140 ~v~ey~G~~~lnlg~-~t~I~~ 160 (311)
T PRK07217 140 VTDEYQGRFSVKLNR-TTSIEE 160 (311)
T ss_pred EEeeECCEEEEEeCC-ceEEEe
Confidence 999999999987674 354543
No 30
>PF02765 POT1: Telomeric single stranded DNA binding POT1/CDC13; InterPro: IPR011564 This entry represents a domain that binds single stranded telomeric DNA and adopts an OB fold []. It includes the proteins POT1 and CDC13 which have been shown to regulate telomere length, replication and capping [, , ]. ; GO: 0003677 DNA binding, 0000723 telomere maintenance, 0000784 nuclear chromosome, telomeric region; PDB: 1S40_A 1KXL_A 1PH7_A 1PH9_A 1PH2_A 1OTC_A 1PHJ_A 1JB7_A 1PA6_A 1PH1_A ....
Probab=95.58 E-value=0.37 Score=43.21 Aligned_cols=97 Identities=20% Similarity=0.080 Sum_probs=67.0
Q ss_pred ccccc--cCCCCCeEeEEEEEeEEEee-------CCCeEEEEEEeCCCCCCCcccccccccccCCCCCcccCCCCccccc
Q 012425 156 FLLLR--EIKDGQRINMACKVFHICEV-------AKGEWMAFVWDGTDAPPAQISKKLEDEMDHELPLQVEPLPLSRDIL 226 (464)
Q Consensus 156 f~~L~--di~~~~f~Dl~~qVv~~~~~-------~~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~~~~~e~~~l~~~~l 226 (464)
|..|. ..+.++++|+++-|+..... .+-..+|.++|-|-+.... .
T Consensus 1 ~~~l~~~~~~~~~~vnvigVV~~~~~p~~~~t~g~D~~~tl~i~D~S~~~~~~--------------~------------ 54 (146)
T PF02765_consen 1 YTPLSTAKEKFGKFVNVIGVVVDFSPPNPKKTRGTDYMCTLTITDPSLNDSNQ--------------K------------ 54 (146)
T ss_dssp BCCGGGSCTTSSEEEEEEEEEEEEEEECTEEESSSCEEEEEEEEBTTCSCSSC--------------C------------
T ss_pred CccchhhhhcCCCEEEEEEEEEEccCCcceEcCCCcEEEEEEEECCCCCcccc--------------c------------
Confidence 34566 44678999999999977543 1236778887777322210 0
Q ss_pred ccCCCcccEEEEEEccchhHHHhhccCC-CCEEEEeceEEEEeCcEEEEEEecc--cceEEc
Q 012425 227 CSFPAVGSILRVIIDKGIEKHILHLLKI-GKWVKLQNVLCQVDAGLWFGVLTHF--TRLRYV 285 (464)
Q Consensus 227 ~~~p~~G~~l~V~~~~~~~~~~~~~lk~-G~wV~l~Nv~~k~~~G~leG~l~~~--ski~~l 285 (464)
...|.|.+...+.+. ...++. ||.|+|++++++...|...|..... +.+.+.
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 023566666555554 566777 9999999999999999988888777 667666
No 31
>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=95.02 E-value=0.054 Score=41.94 Aligned_cols=68 Identities=18% Similarity=0.187 Sum_probs=51.7
Q ss_pred EEEEEEEEeeCCcccccCCceEEEEEEEeCCCCCCCeEEEEec-cCcCCCCCCCCCCCEEEEeeEEEEEECCe-eEEeec
Q 012425 24 VSFVGVILEVGSPKQSKGTDSFCTIKVTDESHTKDGISVNIFA-ESMEKLPYIVSVGDIILLSHVVMKAHNKQ-AYALFN 101 (464)
Q Consensus 24 vnviGVVvd~~~P~~trGtD~~~tl~I~D~S~~~~gl~v~iF~-~~~e~LP~v~~~GDII~l~rvkv~~~~g~-~~~~~~ 101 (464)
|.|.|.|.... ++..=.+.++|.|.|- .+.+.+|. ........+. .||+|+++ -+++.+++. +++..+
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---SIQVVFFNEEYERFREKLK-EGDIVRVR-GKVKRYNGGELELIVP 70 (75)
T ss_dssp EEEEEEEEEEE-----EEETTEEEEEEEETTE---EEEEEEETHHHHHHHHTS--TTSEEEEE-EEEEEETTSSEEEEEE
T ss_pred CEEEEEEEEEE-----cCCCCEEEEEEEECCc---cEEEEEccHHhhHHhhcCC-CCeEEEEE-EEEEEECCccEEEEEC
Confidence 57889999987 3334466889999993 39999998 3344555566 89999998 999999987 877544
No 32
>PF15489 CTC1: CST, telomere maintenance, complex subunit CTC1
Probab=94.92 E-value=0.19 Score=57.92 Aligned_cols=142 Identities=18% Similarity=0.152 Sum_probs=100.8
Q ss_pred EEEEEEccchhHHHhhccCCCCEEEEeceEEEEe-CcEEEEEEecccceEEcCCCChHHHHHHHHHHHHhhccCCCCCcc
Q 012425 235 ILRVIIDKGIEKHILHLLKIGKWVKLQNVLCQVD-AGLWFGVLTHFTRLRYVPTNDNLIVERQRSYDERLSWEHSRMPYW 313 (464)
Q Consensus 235 ~l~V~~~~~~~~~~~~~lk~G~wV~l~Nv~~k~~-~G~leG~l~~~ski~~l~~~d~~v~~r~r~y~~r~~~~~~~~~~~ 313 (464)
.|.|.++.+|..+ -..+-||.-|.|.++..|+. +|+.|..+.++|.|++++- ++ +.
T Consensus 888 ~ldVYi~~~h~p~-plGLLPGA~V~f~~lerkVSRs~nVYC~~~psS~VtVlS~-p~---------------~t------ 944 (1144)
T PF15489_consen 888 HLDVYIEDPHLPY-PLGLLPGARVLFSQLERKVSRSHNVYCCFLPSSSVTVLSF-PP---------------ET------ 944 (1144)
T ss_pred eEEEEecCCCCCC-cccccCCceeeeehhhhhhhccCcEEEEEcCCceEEEEec-Cc---------------cc------
Confidence 4888899999887 56899999999999999997 8999999999999999874 00 00
Q ss_pred cCCCCCccccCCCCCCCCcccHHhhhcCcccCceeEEEEEEEeecCCCcccccc------------C--------Ccc--
Q 012425 314 CFPWTSEVTDIDYSEDGPFVTLKDVLTHSQVTAKFKCVVRVVAALPWRSEDFCS------------P--------LGN-- 371 (464)
Q Consensus 314 ~~p~~~~it~~~~~~~~p~~Tl~diLt~~~v~~kfr~~VRVV~~~P~~~edf~~------------~--------~g~-- 371 (464)
+ . -. .+|...|.+.+.....+.+.++..+||+++==.+.=-|+ . .+.
T Consensus 945 --------~-~-~~-~~P~~~L~~~~~~~~~~~~a~~~chVV~V~~l~L~WvCa~C~si~~qg~Csr~~p~C~s~~sV~q 1013 (1144)
T PF15489_consen 945 --------N-V-SP-PLPHIYLAELLQGSQSPFQARVSCHVVSVLSLQLQWVCAHCGSICPQGRCSRQSPPCPSQTSVFQ 1013 (1144)
T ss_pred --------C-C-CC-CCCeEEehhhhCCCCCCceEEEEEEEEEEEEEEeeehhhhccCcccCCcCCCCCCCCCCCcceee
Confidence 0 0 01 344555666664444445777778899887555543331 1 122
Q ss_pred EEEEEEEecCCceEEEEEecCchhhhcCCCCc--hHHHHHHH
Q 012425 372 YRIRLTLEDPTARIHAFVYAEDGEKLFGGYPF--VDVLKRKI 411 (464)
Q Consensus 372 ~~~~l~leD~t~~l~~~v~~~da~~f~~~~~~--~~~l~~kl 411 (464)
.-.++++||+||+-+|.+.|+-...+++ +.. -+.|.++.
T Consensus 1014 A~ar~~vEDGTaeA~v~~~~~~V~~lLg-L~~~eW~~L~~~v 1054 (1144)
T PF15489_consen 1014 ASARLLVEDGTAEAVVWCRGHHVAALLG-LSPSEWESLLEMV 1054 (1144)
T ss_pred EEEEEEEecCCeeEEEEECCcHHHHHhC-CCHHHHHHHHHHh
Confidence 4579999999999999999987777877 322 25555544
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=94.80 E-value=0.32 Score=38.25 Aligned_cols=69 Identities=13% Similarity=0.139 Sum_probs=49.9
Q ss_pred EEEEEEEEeeCCcccccCCceEEEEEEEeCCCCCCCeEEEEeccCcCCCCCCCCCCCEEEEeeEEEEEE--CCeeEEeec
Q 012425 24 VSFVGVILEVGSPKQSKGTDSFCTIKVTDESHTKDGISVNIFAESMEKLPYIVSVGDIILLSHVVMKAH--NKQAYALFN 101 (464)
Q Consensus 24 vnviGVVvd~~~P~~trGtD~~~tl~I~D~S~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~rvkv~~~--~g~~~~~~~ 101 (464)
+-+.|+|.+.+. |++. ++-++|.|.+- .+.+.+|.+..+........|++|.++ .+++.+ ++++++..+
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 399999988666666655589988885 344444 466766544
No 34
>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=94.66 E-value=0.17 Score=42.82 Aligned_cols=82 Identities=13% Similarity=0.132 Sum_probs=57.2
Q ss_pred EEEEEEEeeCCccccc---CCceEEEEEEEeCCCCCCCeEEEEeccCcCCCCCC----CCCCCEEEEee-EEEEEECCee
Q 012425 25 SFVGVILEVGSPKQSK---GTDSFCTIKVTDESHTKDGISVNIFAESMEKLPYI----VSVGDIILLSH-VVMKAHNKQA 96 (464)
Q Consensus 25 nviGVVvd~~~P~~tr---GtD~~~tl~I~D~S~~~~gl~v~iF~~~~e~LP~v----~~~GDII~l~r-vkv~~~~g~~ 96 (464)
++||+|++.++..... ....+..|+|.|.+. ..++|....+..+.+..- ...+=||.|-+ .+|..|+|..
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 5899999999876433 357789999999995 449999998866665532 12344776655 9999999854
Q ss_pred EEeecCCceeEE
Q 012425 97 YALFNKKFSSFA 108 (464)
Q Consensus 97 ~~~~~~~~ss~~ 108 (464)
.+......|.|.
T Consensus 79 ~ls~~~~~s~v~ 90 (106)
T cd04481 79 SLSNSFGASKVY 90 (106)
T ss_pred EEEcCCCceEEE
Confidence 443332445454
No 35
>PRK06386 replication factor A; Reviewed
Probab=94.45 E-value=0.25 Score=50.91 Aligned_cols=85 Identities=19% Similarity=0.297 Sum_probs=66.0
Q ss_pred eeeEehHHHhhccCCeEEEEEEEEeeCCcc-cccCC-ceEEEEEEEeCCCCCCCeEEEEeccCcCCCCCCCCCCCEEEEe
Q 012425 8 YRFLKIKDAILSINQKVSFVGVILEVGSPK-QSKGT-DSFCTIKVTDESHTKDGISVNIFAESMEKLPYIVSVGDIILLS 85 (464)
Q Consensus 8 y~y~~i~d~~~~~~~~vnviGVVvd~~~P~-~trGt-D~~~tl~I~D~S~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~ 85 (464)
|..++|+|+.. ....|||.|-|++...+. .++|+ -...++-|-|++= .|++..|.+ .+. .||+|+|.
T Consensus 105 ~~~~KI~DL~~-g~~~v~V~akVle~~e~e~~~~g~~~~v~sg~lgDeTG---rIr~TlW~~------~l~-eGd~v~i~ 173 (358)
T PRK06386 105 YKLVKIRDLSL-VTPYVSVIGKITGITKKEYDSDGTSKIVYQGYIEDDTA---RVRISSFGK------PLE-DNRFVRIE 173 (358)
T ss_pred cCccEeEeccC-CCCceEEEEEEEEccCceEecCCCccEEEEEEEEcCCC---eEEEEEccc------ccc-CCCEEEEe
Confidence 45678999962 245699999999976542 23444 7778888999884 299999975 255 79999999
Q ss_pred eEEEEEECCeeEEeecCC
Q 012425 86 HVVMKAHNKQAYALFNKK 103 (464)
Q Consensus 86 rvkv~~~~g~~~~~~~~~ 103 (464)
++.++.|+|.+++..|..
T Consensus 174 na~v~e~~G~~el~v~~~ 191 (358)
T PRK06386 174 NARVSQYNGYIEISVGNK 191 (358)
T ss_pred eeEEEccCCeEEEEeCCe
Confidence 999999999999877744
No 36
>cd04474 RPA1_DBD_A RPA1_DBD_A: A subfamily of OB folds corresponding to the second OB fold, the ssDNA-binding domain (DBD)-A, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change. Although ScRPA and the hRPA have similar ssDNA-binding properties, they differ funct
Probab=93.88 E-value=0.21 Score=42.11 Aligned_cols=84 Identities=17% Similarity=0.235 Sum_probs=61.9
Q ss_pred ehHHHhhccCCeEEEEEEEEeeCCccccc---CCceEEEEEEEeCCCCCCCeEEEEeccCcC-CCCCCCCCCCEEEEeeE
Q 012425 12 KIKDAILSINQKVSFVGVILEVGSPKQSK---GTDSFCTIKVTDESHTKDGISVNIFAESME-KLPYIVSVGDIILLSHV 87 (464)
Q Consensus 12 ~i~d~~~~~~~~vnviGVVvd~~~P~~tr---GtD~~~tl~I~D~S~~~~gl~v~iF~~~~e-~LP~v~~~GDII~l~rv 87 (464)
+|+++.. ....+.+.|-|+..+.++.-+ |.-..++|.|.|+... .|.+.+|.+..+ .-|.++ .|+|+.+.+.
T Consensus 1 pI~~L~p-~~~~~~I~~rV~~k~~~~~f~~~~~~g~~~~~~l~De~~~--~I~~t~~~~~~~~f~~~l~-eG~vy~i~~~ 76 (104)
T cd04474 1 PISSLNP-YQNKWTIKARVTNKSDIRTWSNARGEGKLFSFDLLDEDGG--EIRATFFNDAVDKFYDLLE-VGKVYYISKG 76 (104)
T ss_pred ChhHccC-CCCcEEEEEEEeeccccccccCCCCCcEEEEEEEEECCCC--EEEEEEehHHHHHhhcccc-cccEEEEecc
Confidence 4677752 234599999999877775433 3467789999999643 499999976433 456676 8999999999
Q ss_pred EEEEECCeeEEe
Q 012425 88 VMKAHNKQAYAL 99 (464)
Q Consensus 88 kv~~~~g~~~~~ 99 (464)
+|+.-++...-+
T Consensus 77 ~V~~a~~~y~~~ 88 (104)
T cd04474 77 SVKVANKKFNTL 88 (104)
T ss_pred EEeeccccCCCC
Confidence 999887654443
No 37
>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=93.16 E-value=1.3 Score=36.83 Aligned_cols=63 Identities=8% Similarity=-0.091 Sum_probs=42.6
Q ss_pred ccEEEEEEccchhHHHhhccCCCCEEEEeceEEEEeCcEEEEEEecccceEEcCCCChHHHHHHHHH
Q 012425 233 GSILRVIIDKGIEKHILHLLKIGKWVKLQNVLCQVDAGLWFGVLTHFTRLRYVPTNDNLIVERQRSY 299 (464)
Q Consensus 233 G~~l~V~~~~~~~~~~~~~lk~G~wV~l~Nv~~k~~~G~leG~l~~~ski~~l~~~d~~v~~r~r~y 299 (464)
|..+.|+||..++.... ...|+.|.|+|++++..+| ........+.|.+-| +.+++.+.+.-|
T Consensus 38 ~~~i~vtLWg~~a~~~~--~~~~~vv~~~~~~i~~~~~-~~l~~~~~s~i~~np-~~~e~~~l~~w~ 100 (101)
T cd04475 38 GHSVELTLWGEQAELFD--GSENPVIAIKGVKVSEFNG-KSLSTGSSSTIIINP-DIPEAHKLRGWY 100 (101)
T ss_pred CCEEEEEEEHHHhhhcc--cCCCCEEEEEeeEEEecCC-eEEeecCceeEEECC-CcHHHHHHHHhh
Confidence 34579999998877433 3339999999999987665 344445566775444 477777666544
No 38
>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=93.08 E-value=0.31 Score=38.98 Aligned_cols=46 Identities=13% Similarity=0.081 Sum_probs=39.6
Q ss_pred EEEEEEccchhHHHhhccCCCCEEEEeceEEEEeCcEEEEEEecccceE
Q 012425 235 ILRVIIDKGIEKHILHLLKIGKWVKLQNVLCQVDAGLWFGVLTHFTRLR 283 (464)
Q Consensus 235 ~l~V~~~~~~~~~~~~~lk~G~wV~l~Nv~~k~~~G~leG~l~~~ski~ 283 (464)
.+++++|+..+ ...+++|++|+++|..++...|.++..+...+.|.
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 47999998776 57799999999999999999999999888877664
No 39
>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=92.88 E-value=0.9 Score=37.22 Aligned_cols=65 Identities=18% Similarity=0.260 Sum_probs=50.3
Q ss_pred EEEEEEEEeeCCcccccCCceEEEEEEEeCCCCCCCeEEEEeccCcC----CCCCCCCCCCEEEEeeEEEEEECCeeEEe
Q 012425 24 VSFVGVILEVGSPKQSKGTDSFCTIKVTDESHTKDGISVNIFAESME----KLPYIVSVGDIILLSHVVMKAHNKQAYAL 99 (464)
Q Consensus 24 vnviGVVvd~~~P~~trGtD~~~tl~I~D~S~~~~gl~v~iF~~~~e----~LP~v~~~GDII~l~rvkv~~~~g~~~~~ 99 (464)
|.++|+|.+...- +-..+++|-|.|= .|.+.++....+ ..+.++ +|++|++ +-+++.|+|+.++.
T Consensus 2 v~~vG~V~~~~~~------~~~~~~tL~D~TG---~I~~~~W~~~~~~~~~~~~~~~-~g~~v~v-~G~v~~~~g~~ql~ 70 (95)
T cd04478 2 VTLVGVVRNVEEQ------STNITYTIDDGTG---TIEVRQWLDDDNDDSSEVEPIE-EGTYVRV-FGNLKSFQGKKSIM 70 (95)
T ss_pred EEEEEEEEeeeEc------ccEEEEEEECCCC---cEEEEEeCCCCCcccccccccc-cCCEEEE-EEEEcccCCeeEEE
Confidence 7899999997542 2448899999873 399999987653 566665 8999999 55678899998875
No 40
>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=92.51 E-value=0.36 Score=37.70 Aligned_cols=70 Identities=16% Similarity=0.272 Sum_probs=48.5
Q ss_pred EEEEEEeeCCcccccCCceEEEEEEEeCCCCCCCeEEEEeccCcCCCCCCCCCCCEEEEeeEEEEEECCeeEEee
Q 012425 26 FVGVILEVGSPKQSKGTDSFCTIKVTDESHTKDGISVNIFAESMEKLPYIVSVGDIILLSHVVMKAHNKQAYALF 100 (464)
Q Consensus 26 viGVVvd~~~P~~trGtD~~~tl~I~D~S~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~rvkv~~~~g~~~~~~ 100 (464)
+.|+|.+.... .++...-+..++|-|.+-. +.+.+|.+..+.+......|.++.++ -+++.|+|..+...
T Consensus 2 i~g~v~~~~~~-~~k~g~~~~~~~l~D~tg~---~~~~~f~~~~~~~~~~l~~g~~v~v~-G~v~~~~~~~~l~~ 71 (84)
T cd04485 2 VAGLVTSVRRR-RTKKGKRMAFVTLEDLTGS---IEVVVFPETYEKYRDLLKEDALLLVE-GKVERRDGGLRLIA 71 (84)
T ss_pred EEEEEEEeEEE-EcCCCCEEEEEEEEeCCCe---EEEEECHHHHHHHHHHhcCCCEEEEE-EEEEecCCceEEEe
Confidence 67888887653 4554556799999998753 99999976533333333479999886 47777877666643
No 41
>PRK13480 3'-5' exoribonuclease YhaM; Provisional
Probab=92.35 E-value=1.9 Score=43.86 Aligned_cols=79 Identities=16% Similarity=0.156 Sum_probs=61.8
Q ss_pred ehHHHhhccCCeEEEEEEEEeeCCccccc-CCceEEEEEEEeCCCCCCCeEEEEeccCcCCCCCCCCCCCEEEEeeEEEE
Q 012425 12 KIKDAILSINQKVSFVGVILEVGSPKQSK-GTDSFCTIKVTDESHTKDGISVNIFAESMEKLPYIVSVGDIILLSHVVMK 90 (464)
Q Consensus 12 ~i~d~~~~~~~~vnviGVVvd~~~P~~tr-GtD~~~tl~I~D~S~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~rvkv~ 90 (464)
.|+++. .|..|+.+.+|.+.... .++ |+. ...|++.|.|=. |..+++....+....+. .||||.+. -++.
T Consensus 4 ~i~~l~--~g~~v~~~~lv~~~~~~-~~knG~~-yl~l~l~D~tG~---I~ak~W~~~~~~~~~~~-~g~vv~v~-G~v~ 74 (314)
T PRK13480 4 GIEELE--VGEQVDHFLLIKSATKG-VASNGKP-FLTLILQDKSGD---IEAKLWDVSPEDEATYV-PETIVHVK-GDII 74 (314)
T ss_pred hHhhcC--CCCEeeEEEEEEEceee-ecCCCCe-EEEEEEEcCCcE---EEEEeCCCChhhHhhcC-CCCEEEEE-EEEE
Confidence 467775 58889999999998764 344 555 678999997742 99999988767777776 89999995 4567
Q ss_pred EECCeeEEe
Q 012425 91 AHNKQAYAL 99 (464)
Q Consensus 91 ~~~g~~~~~ 99 (464)
.|+|++|+.
T Consensus 75 ~y~g~~Ql~ 83 (314)
T PRK13480 75 NYRGRKQLK 83 (314)
T ss_pred EECCcceEE
Confidence 899998875
No 42
>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=91.33 E-value=0.31 Score=44.59 Aligned_cols=29 Identities=28% Similarity=0.512 Sum_probs=27.6
Q ss_pred EEEEEEEecCCceEEEEEecCchhhhcCC
Q 012425 372 YRIRLTLEDPTARIHAFVYAEDGEKLFGG 400 (464)
Q Consensus 372 ~~~~l~leD~t~~l~~~v~~~da~~f~~~ 400 (464)
|++.+.+.|.||.+++.++|+.|+++||.
T Consensus 68 y~l~~~i~D~Tg~~~~~~F~~~ae~l~G~ 96 (166)
T cd04476 68 YILSLNVADHTGEAWLTLFDEVAEQIFGK 96 (166)
T ss_pred EEEEEEEEeCCCCEEEEEehHHHHHHhCC
Confidence 88899999999999999999999999993
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=90.84 E-value=2.1 Score=33.53 Aligned_cols=67 Identities=13% Similarity=0.161 Sum_probs=48.5
Q ss_pred EEEEEeeCCcccccCCceEEEEEEEeCCCCCCCeEEEEeccCcCCCCCCCCCCCEEEEeeEEEEEECCeeEEe
Q 012425 27 VGVILEVGSPKQSKGTDSFCTIKVTDESHTKDGISVNIFAESMEKLPYIVSVGDIILLSHVVMKAHNKQAYAL 99 (464)
Q Consensus 27 iGVVvd~~~P~~trGtD~~~tl~I~D~S~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~rvkv~~~~g~~~~~ 99 (464)
+.+|.++.. +.|+.+.-+..++|-|.+-. +.+.+|.+.....+.+. .|.+|.++ .++..++|+.+..
T Consensus 3 ~~~v~~~~~-~~tk~g~~~~~~~l~D~tg~---i~~~~f~~~~~~~~~l~-~g~~v~v~-G~v~~~~~~~~l~ 69 (83)
T cd04492 3 FFLIKSKEL-RTAKNGKPYLALTLQDKTGE---IEAKLWDASEEDEEKFK-PGDIVHVK-GRVEEYRGRLQLK 69 (83)
T ss_pred EEEEEEeee-ecccCCCcEEEEEEEcCCCe---EEEEEcCCChhhHhhCC-CCCEEEEE-EEEEEeCCceeEE
Confidence 557777766 35555556899999998753 99999976554445555 79999997 6677787766654
No 44
>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=89.82 E-value=0.29 Score=43.82 Aligned_cols=28 Identities=36% Similarity=0.718 Sum_probs=26.8
Q ss_pred EEEEEEEecCCceEEEEEecCchhhhcC
Q 012425 372 YRIRLTLEDPTARIHAFVYAEDGEKLFG 399 (464)
Q Consensus 372 ~~~~l~leD~t~~l~~~v~~~da~~f~~ 399 (464)
|++.+.+.|.||.+++.++|+.|++|||
T Consensus 54 y~l~~~i~D~tg~~~~~~F~~~a~~l~G 81 (146)
T PF08646_consen 54 YRLSLKISDGTGSIWVTLFDEEAEQLLG 81 (146)
T ss_dssp EEEEEEEEETTEEEEEEEEHHHHHHHHC
T ss_pred EEEEEEEEeCCCeEEEEEEhHHHHHHhC
Confidence 7888899999999999999999999998
No 45
>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=89.58 E-value=2.7 Score=34.74 Aligned_cols=64 Identities=9% Similarity=0.199 Sum_probs=46.6
Q ss_pred EEEEEEeeCCcccccCCceEEEEEEEeCCCCCCCeEEEEeccCc---------------------CCCCCCCCCCCEEEE
Q 012425 26 FVGVILEVGSPKQSKGTDSFCTIKVTDESHTKDGISVNIFAESM---------------------EKLPYIVSVGDIILL 84 (464)
Q Consensus 26 viGVVvd~~~P~~trGtD~~~tl~I~D~S~~~~gl~v~iF~~~~---------------------e~LP~v~~~GDII~l 84 (464)
++|+|+.... +. - ..+|+|-|.+= -|.++++.... +..+.+. +|++|++
T Consensus 2 ivG~V~sv~~----~~-~-~~~~tLdDgTG---~Ie~~~W~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~-~G~vvrV 71 (92)
T cd04483 2 ILGTVVSRRE----RE-T-FYSFGVDDGTG---VVNCVCWKNLSYAEVSSRSDAARILKSALMALKQAKVLE-IGDLLRV 71 (92)
T ss_pred eEEEEEEEEe----cC-C-eEEEEEecCCc---eEEEEEEcCcCcccccccccccccccccccccccccccC-CCCEEEE
Confidence 6899998743 21 2 47788888664 28999997643 3444565 8999999
Q ss_pred eeEEEEEECCeeEEee
Q 012425 85 SHVVMKAHNKQAYALF 100 (464)
Q Consensus 85 ~rvkv~~~~g~~~~~~ 100 (464)
+ -+++.|+|+.++..
T Consensus 72 ~-G~i~~frg~~ql~i 86 (92)
T cd04483 72 R-GSIRTYRGEREINA 86 (92)
T ss_pred E-EEEeccCCeeEEEE
Confidence 6 78899999988753
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=89.01 E-value=1.3 Score=37.37 Aligned_cols=53 Identities=17% Similarity=0.243 Sum_probs=40.9
Q ss_pred ceeEEEEEEEeecCCCccccccCCc-cEEEEEEEecC-CceEEEEEecCchhhhcCC
Q 012425 346 AKFKCVVRVVAALPWRSEDFCSPLG-NYRIRLTLEDP-TARIHAFVYAEDGEKLFGG 400 (464)
Q Consensus 346 ~kfr~~VRVV~~~P~~~edf~~~~g-~~~~~l~leD~-t~~l~~~v~~~da~~f~~~ 400 (464)
.+++..+||+... ++..|....| ...|.|.|.|. ++.|+|.++++.+++|++.
T Consensus 10 ~~~~I~~rV~~k~--~~~~f~~~~~~g~~~~~~l~De~~~~I~~t~~~~~~~~f~~~ 64 (104)
T cd04474 10 NKWTIKARVTNKS--DIRTWSNARGEGKLFSFDLLDEDGGEIRATFFNDAVDKFYDL 64 (104)
T ss_pred CcEEEEEEEeecc--ccccccCCCCCcEEEEEEEEECCCCEEEEEEehHHHHHhhcc
Confidence 4689999999863 3455554333 26789999999 9999999999888888863
No 47
>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=82.79 E-value=9.8 Score=28.71 Aligned_cols=67 Identities=12% Similarity=0.116 Sum_probs=43.8
Q ss_pred EEEEEEeeCCcccccCCceEEEEEEEeCCCCCCCeEEEEeccCcCCCCCCCCCCCEEEEeeEEEEEECCeeEEe
Q 012425 26 FVGVILEVGSPKQSKGTDSFCTIKVTDESHTKDGISVNIFAESMEKLPYIVSVGDIILLSHVVMKAHNKQAYAL 99 (464)
Q Consensus 26 viGVVvd~~~P~~trGtD~~~tl~I~D~S~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~rvkv~~~~g~~~~~ 99 (464)
+.|.|++.... +++|.. ...+++.|.+- .+.+.+|.........+. .|+.+.+. =|+..|+|.++..
T Consensus 2 i~~~V~~~~~~-~~~~~~-~~~~~~~D~~g---~i~~~~F~~~~~~~~~~~-~G~~~~v~-Gkv~~~~~~~qi~ 68 (75)
T cd04488 2 VEGTVVSVEVV-PRRGRR-RLKVTLSDGTG---TLTLVFFNFQPYLKKQLP-PGTRVRVS-GKVKRFRGGLQIV 68 (75)
T ss_pred EEEEEEEEEec-cCCCcc-EEEEEEEcCCC---EEEEEEECCCHHHHhcCC-CCCEEEEE-EEEeecCCeeEEe
Confidence 56777776432 223333 78899999854 399999973322233344 89988885 5667788877664
No 48
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain
Probab=79.99 E-value=16 Score=30.43 Aligned_cols=77 Identities=22% Similarity=0.230 Sum_probs=52.6
Q ss_pred hHHHhhcc--CCeEEEEEEEEeeCCcccccCCceEEEEEEEeCCCCCCCeEEEEeccCcCCCC-CCCCCCCEEEEeeEEE
Q 012425 13 IKDAILSI--NQKVSFVGVILEVGSPKQSKGTDSFCTIKVTDESHTKDGISVNIFAESMEKLP-YIVSVGDIILLSHVVM 89 (464)
Q Consensus 13 i~d~~~~~--~~~vnviGVVvd~~~P~~trGtD~~~tl~I~D~S~~~~gl~v~iF~~~~e~LP-~v~~~GDII~l~rvkv 89 (464)
|+++++.. -..+-|.|=|.+++.. ++| .+-|+|+|+. ..++|.+|+.....++ ...+.||-|++ +.++
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 45555432 2679999999998765 233 3667999955 4499999998878787 44458998777 4555
Q ss_pred EEE--CCeeEE
Q 012425 90 KAH--NKQAYA 98 (464)
Q Consensus 90 ~~~--~g~~~~ 98 (464)
..| .|++++
T Consensus 82 ~~y~~~G~~sl 92 (99)
T PF13742_consen 82 SFYEPRGSLSL 92 (99)
T ss_pred EEECCCcEEEE
Confidence 555 444554
No 49
>cd04484 polC_OBF polC_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold nucleic acid binding domain of Bacillus subtilis type C replicative DNA polymerase III alpha subunit (polC). Replication in B. subtilis and Staphylococcus aureus requires two different polymerases, polC and DnaE. The holoenzyme is thought to include the two different polymerases. At the B. subtilis replication fork, polC appears to be involved in leading strand synthesis and DnaE in lagging strand synthesis.
Probab=78.63 E-value=18 Score=29.09 Aligned_cols=71 Identities=23% Similarity=0.280 Sum_probs=47.1
Q ss_pred EEEEEEEEeeCCcccccCCceEEEEEEEeCCCCCCCeEEEEecc-CcCCCCCCCCCCCEEEEee-EEEEEECCeeEE
Q 012425 24 VSFVGVILEVGSPKQSKGTDSFCTIKVTDESHTKDGISVNIFAE-SMEKLPYIVSVGDIILLSH-VVMKAHNKQAYA 98 (464)
Q Consensus 24 vnviGVVvd~~~P~~trGtD~~~tl~I~D~S~~~~gl~v~iF~~-~~e~LP~v~~~GDII~l~r-vkv~~~~g~~~~ 98 (464)
|-+-|-|.+... +.++..-...+|.|+|-+ +++.|..|.. ..+.+-.+.+.||-|+++. +....|.++...
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 345666766533 456666888999999966 4599999983 3344444543699999874 345566666444
No 50
>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=78.60 E-value=24 Score=25.94 Aligned_cols=66 Identities=20% Similarity=0.159 Sum_probs=39.3
Q ss_pred eEEEEEeEEEeeC--CCeEEEEEEeCCCCCCCcccccccccccCCCCCcccCCCCcccccccCCCcccEEEEEEccchhH
Q 012425 169 NMACKVFHICEVA--KGEWMAFVWDGTDAPPAQISKKLEDEMDHELPLQVEPLPLSRDILCSFPAVGSILRVIIDKGIEK 246 (464)
Q Consensus 169 Dl~~qVv~~~~~~--~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~~~~~e~~~l~~~~l~~~p~~G~~l~V~~~~~~~~ 246 (464)
++.|+|+++.... ...+.+.+.|+|+ ..+.+.+|.....
T Consensus 1 ~v~g~v~~~~~~~~~~~~~~~~l~D~~~---------------------------------------~~i~~~~~~~~~~ 41 (75)
T cd03524 1 TIVGIVVAVEEIRTEGKVLIFTLTDGTG---------------------------------------GTIRVTLFGELAE 41 (75)
T ss_pred CeEEEEEeecccccCCeEEEEEEEcCCC---------------------------------------CEEEEEEEchHHH
Confidence 4678888876533 3567777777771 1134445544333
Q ss_pred HHhhccCCCCEEEEeceEEEEeCcEEEE
Q 012425 247 HILHLLKIGKWVKLQNVLCQVDAGLWFG 274 (464)
Q Consensus 247 ~~~~~lk~G~wV~l~Nv~~k~~~G~leG 274 (464)
-....+++|+++.+. .+++...|.++.
T Consensus 42 ~~~~~~~~g~~v~v~-g~v~~~~~~~~l 68 (75)
T cd03524 42 ELENLLKEGQVVYIK-GKVKKFRGRLQL 68 (75)
T ss_pred HHHhhccCCCEEEEE-EEEEecCCeEEE
Confidence 224568999988887 666655444443
No 51
>PRK07373 DNA polymerase III subunit alpha; Reviewed
Probab=74.55 E-value=11 Score=40.37 Aligned_cols=88 Identities=17% Similarity=0.212 Sum_probs=60.4
Q ss_pred eeEehHHHhh-ccCCeEEEEEEEEeeCCcccccCCceEEEEEEEeCCCCCCCeEEEEeccCcCCCCCCCCCCCEEEEeeE
Q 012425 9 RFLKIKDAIL-SINQKVSFVGVILEVGSPKQSKGTDSFCTIKVTDESHTKDGISVNIFAESMEKLPYIVSVGDIILLSHV 87 (464)
Q Consensus 9 ~y~~i~d~~~-~~~~~vnviGVVvd~~~P~~trGtD~~~tl~I~D~S~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~rv 87 (464)
...+++++.. ..++.|.+.|+|+..+.+ +|+.++-|+-++|-|.+-. +.+.+|.+.-+..-..-..|.+++++.
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 3456777642 246789999999999875 6666678999999999853 999999765444434334688888854
Q ss_pred EEEEECCeeEEeec
Q 012425 88 VMKAHNKQAYALFN 101 (464)
Q Consensus 88 kv~~~~g~~~~~~~ 101 (464)
+++.-.++++.+.+
T Consensus 342 ~v~~~~~~~~liv~ 355 (449)
T PRK07373 342 KVDRRDDQVQLIVE 355 (449)
T ss_pred EEEecCCeEEEEEe
Confidence 55543344555544
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=73.35 E-value=30 Score=27.14 Aligned_cols=64 Identities=19% Similarity=0.232 Sum_probs=39.4
Q ss_pred EEEEEEeeCCcccccCCceEEEEEEEeCCCCCCCeEEEEeccCcCCCCCCCCCCCEEEE-eeEEEEEECCeeEEee
Q 012425 26 FVGVILEVGSPKQSKGTDSFCTIKVTDESHTKDGISVNIFAESMEKLPYIVSVGDIILL-SHVVMKAHNKQAYALF 100 (464)
Q Consensus 26 viGVVvd~~~P~~trGtD~~~tl~I~D~S~~~~gl~v~iF~~~~e~LP~v~~~GDII~l-~rvkv~~~~g~~~~~~ 100 (464)
|-|.|..+.. +|..+ -|+|.|+. ..|.|.+|+.+...++.-...||-|.+ -++.+ .+|+.|+..
T Consensus 3 v~GeVs~~~~----~~GHv--yfsLkD~~---a~i~cv~f~~~~~~~~~~l~~Gd~V~v~G~v~~--~~G~~ql~v 67 (73)
T cd04487 3 IEGEVVQIKQ----TSGPT--IFTLRDET---GTVWAAAFEEAGVRAYPEVEVGDIVRVTGEVEP--RDGQLQIEV 67 (73)
T ss_pred EEEEEecccc----CCCCE--EEEEEcCC---EEEEEEEEchhccCCcCCCCCCCEEEEEEEEec--CCeEEEEEE
Confidence 4566776652 44444 45778855 339999998765445543448995544 45554 566666643
No 53
>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=71.92 E-value=40 Score=25.40 Aligned_cols=61 Identities=16% Similarity=0.121 Sum_probs=40.8
Q ss_pred EeEEEEEeEEEeeCCCeEEEEEEeCCCCCCCcccccccccccCCCCCcccCCCCcccccccCCCcccEEEEEEccchhHH
Q 012425 168 INMACKVFHICEVAKGEWMAFVWDGTDAPPAQISKKLEDEMDHELPLQVEPLPLSRDILCSFPAVGSILRVIIDKGIEKH 247 (464)
Q Consensus 168 ~Dl~~qVv~~~~~~~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~~~~~e~~~l~~~~l~~~p~~G~~l~V~~~~~~~~~ 247 (464)
+-+.+.|.++....+....+-+.|+|+. +++.+|......
T Consensus 1 V~v~G~V~~~~~~~~~~~~~~l~D~tg~----------------------------------------i~~~~~~~~~~~ 40 (75)
T PF01336_consen 1 VTVEGRVTSIRRSGGKIVFFTLEDGTGS----------------------------------------IQVVFFNEEYER 40 (75)
T ss_dssp EEEEEEEEEEEEEETTEEEEEEEETTEE----------------------------------------EEEEEETHHHHH
T ss_pred CEEEEEEEEEEcCCCCEEEEEEEECCcc----------------------------------------EEEEEccHHhhH
Confidence 3567888888655677888888888841 355666633334
Q ss_pred HhhccCCCCEEEEeceEEEEeC
Q 012425 248 ILHLLKIGKWVKLQNVLCQVDA 269 (464)
Q Consensus 248 ~~~~lk~G~wV~l~Nv~~k~~~ 269 (464)
....+++|++|++. =+++...
T Consensus 41 ~~~~l~~g~~v~v~-G~v~~~~ 61 (75)
T PF01336_consen 41 FREKLKEGDIVRVR-GKVKRYN 61 (75)
T ss_dssp HHHTS-TTSEEEEE-EEEEEET
T ss_pred HhhcCCCCeEEEEE-EEEEEEC
Confidence 46889999999888 4444443
No 54
>PRK05673 dnaE DNA polymerase III subunit alpha; Validated
Probab=69.32 E-value=13 Score=44.22 Aligned_cols=86 Identities=16% Similarity=0.202 Sum_probs=61.8
Q ss_pred eEehHHHhh-ccCCeEEEEEEEEeeCCcccccCCceEEEEEEEeCCCCCCCeEEEEeccCcCCC-CCCCCCCCEEEEeeE
Q 012425 10 FLKIKDAIL-SINQKVSFVGVILEVGSPKQSKGTDSFCTIKVTDESHTKDGISVNIFAESMEKL-PYIVSVGDIILLSHV 87 (464)
Q Consensus 10 y~~i~d~~~-~~~~~vnviGVVvd~~~P~~trGtD~~~tl~I~D~S~~~~gl~v~iF~~~~e~L-P~v~~~GDII~l~rv 87 (464)
.+++.++.. ..+..|.+.|+|...+.+ +|+.++-++.++|-|.+-. +.+.+|.+.-+.. +.+. .|.+|.+. .
T Consensus 965 ~~~~~~l~~~~~g~~V~v~G~I~~vk~~-~TKkG~~mafltLeD~TG~---iEvviFp~~ye~~~~~L~-~g~iV~V~-G 1038 (1135)
T PRK05673 965 DTRLADLEPTEGGSVVTVAGLVVSVRRR-VTKRGNKMAIVTLEDLSGR---IEVMLFSEALEKYRDLLE-EDRIVVVK-G 1038 (1135)
T ss_pred CcCHHHHhccccCceEEEEEEEEEEEec-ccCCCCeEEEEEEEeCCCc---EEEEECHHHHHHHHHHhc-cCCEEEEE-E
Confidence 456666642 246779999999999886 5655667899999999863 9999997653333 3344 79999885 4
Q ss_pred EEEEECCeeEEeec
Q 012425 88 VMKAHNKQAYALFN 101 (464)
Q Consensus 88 kv~~~~g~~~~~~~ 101 (464)
+++...++.+.+.+
T Consensus 1039 kVe~~~~~~qlii~ 1052 (1135)
T PRK05673 1039 QVSFDDGGLRLTAR 1052 (1135)
T ss_pred EEEecCCeEEEEEe
Confidence 67766677777655
No 55
>cd04490 PolII_SU_OBF PolII_SU_OBF: A subfamily of OB folds corresponding to the OB fold found in Pyrococcus abyssi DNA polymerase II (PolII) small subunit. PolII is a family D DNA polymerase, having a 3-prime to 5-prime exonuclease activity. P. abyssi PolII is heterodimeric. The large subunit appears to be the polymerase, and the small subunit may be the exonuclease. The small subunit contains a calcineurin-like phosphatase superfamily domain C-terminal to this OB-fold domain.
Probab=67.04 E-value=20 Score=28.54 Aligned_cols=59 Identities=19% Similarity=0.272 Sum_probs=40.3
Q ss_pred EEEEEEEEeeCCcccccCCceEEEEEEEeCCCCCCCeEEEEeccCcC--CCCCCCCCCCEEEEeeEEEEE
Q 012425 24 VSFVGVILEVGSPKQSKGTDSFCTIKVTDESHTKDGISVNIFAESME--KLPYIVSVGDIILLSHVVMKA 91 (464)
Q Consensus 24 vnviGVVvd~~~P~~trGtD~~~tl~I~D~S~~~~gl~v~iF~~~~e--~LP~v~~~GDII~l~rvkv~~ 91 (464)
+.+.|+|.+.+ .|+.++- .++|-|.+- .+.+.+|.+..+ ..-.....|.+|.++. ++..
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--IVELEDTTG---RITVLLTKDKEELFEEAEDILPDEVIGVSG-TVSK 62 (79)
T ss_pred EEEEEEEeEEE---EcCCCCE--EEEEECCCC---EEEEEEeCchhhhhhhhhhccCCCEEEEEE-EEec
Confidence 56899999998 4443332 778888774 399999987766 4444444577777753 5543
No 56
>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=63.59 E-value=33 Score=30.78 Aligned_cols=73 Identities=19% Similarity=0.223 Sum_probs=42.4
Q ss_pred EehHHHhh----ccCCeEEEEEEEEeeCCcccccCCceEEEEEEEeCCCCCCCeEEEEeccCc-CCCCCCCCCCCEEEEe
Q 012425 11 LKIKDAIL----SINQKVSFVGVILEVGSPKQSKGTDSFCTIKVTDESHTKDGISVNIFAESM-EKLPYIVSVGDIILLS 85 (464)
Q Consensus 11 ~~i~d~~~----~~~~~vnviGVVvd~~~P~~trGtD~~~tl~I~D~S~~~~gl~v~iF~~~~-e~LP~v~~~GDII~l~ 85 (464)
+.+.++.. .+-+-|+++|+|+.. ++++++.--+-|.|+++.- +.|+++..-. -.+-.+-.+|-+|-+.
T Consensus 4 ~~f~~l~~p~f~pp~~EvD~VG~VvsV-----~~~~~f~~~vYLsD~~~Nl--l~Ikfw~~l~~~~~eDilk~~~liA~S 76 (143)
T PF09104_consen 4 THFSDLQDPDFQPPYGEVDTVGFVVSV-----SKKQGFQPLVYLSDECHNL--LAIKFWTGLNQYGYEDILKPGSLIAAS 76 (143)
T ss_dssp --CGGGGSTT--TCCCEEEEEEEEEEE-----E--TTS--EEEEE-TTS-E--EEEEESS-------SS---TT-EEEEE
T ss_pred echhhhcCcccCCCccccceEEEEEEE-----EecCCCceeEEeecCCccE--EEEEeccCccccchhhhcCcceEEEEe
Confidence 34455542 234669999999999 4557887778899999865 8889886522 2233454589999999
Q ss_pred eEEEE
Q 012425 86 HVVMK 90 (464)
Q Consensus 86 rvkv~ 90 (464)
|+.-+
T Consensus 77 NLqwR 81 (143)
T PF09104_consen 77 NLQWR 81 (143)
T ss_dssp EEEE-
T ss_pred eeEee
Confidence 99886
No 57
>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=63.56 E-value=29 Score=28.45 Aligned_cols=55 Identities=18% Similarity=0.280 Sum_probs=39.4
Q ss_pred cccEEEEEEccchhHHHhhccCCCCEEEEeceEEEEeCcE-------EEEEEecccceEEcC
Q 012425 232 VGSILRVIIDKGIEKHILHLLKIGKWVKLQNVLCQVDAGL-------WFGVLTHFTRLRYVP 286 (464)
Q Consensus 232 ~G~~l~V~~~~~~~~~~~~~lk~G~wV~l~Nv~~k~~~G~-------leG~l~~~ski~~l~ 286 (464)
-|..|+.+........-...+++|.|..|.|..+..+.|. ..-.|...++|...+
T Consensus 8 ~G~~I~A~I~~~~~~~f~~~l~Eg~~y~i~~F~V~~~~~~yr~t~h~y~I~f~~~T~V~~~~ 69 (95)
T PF02721_consen 8 KGDKIQATIPKELVDKFKDSLKEGSWYTISNFTVSPNSGSYRPTDHKYKINFMPNTKVTEID 69 (95)
T ss_pred CCCEEEEEECHHHHHHHHhhcccCCEEEeEeEEEEeCCCceeccCCCEEEEECCcCeEEECC
Confidence 3777888887655554578899999999999998887654 334455556665544
No 58
>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=63.10 E-value=8.8 Score=31.24 Aligned_cols=21 Identities=29% Similarity=0.447 Sum_probs=18.9
Q ss_pred EEEEEEecCCceEEEEEecCc
Q 012425 373 RIRLTLEDPTARIHAFVYAED 393 (464)
Q Consensus 373 ~~~l~leD~t~~l~~~v~~~d 393 (464)
.+.|+|+|.||+|.|.++..+
T Consensus 17 ~~~~tL~D~TG~I~~~~W~~~ 37 (95)
T cd04478 17 NITYTIDDGTGTIEVRQWLDD 37 (95)
T ss_pred EEEEEEECCCCcEEEEEeCCC
Confidence 489999999999999999765
No 59
>KOG3056 consensus Protein required for S-phase initiation or completion [Cell cycle control, cell division, chromosome partitioning]
Probab=62.63 E-value=13 Score=40.37 Aligned_cols=69 Identities=23% Similarity=0.310 Sum_probs=56.1
Q ss_pred eEEEEEEEEeeCCccccc-CCceEEEEEEEeCCCCCCCeEEEEeccCcCCCCCCCCCCCEEEEeeEEEEEECC
Q 012425 23 KVSFVGVILEVGSPKQSK-GTDSFCTIKVTDESHTKDGISVNIFAESMEKLPYIVSVGDIILLSHVVMKAHNK 94 (464)
Q Consensus 23 ~vnviGVVvd~~~P~~tr-GtD~~~tl~I~D~S~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~rvkv~~~~g 94 (464)
.--++|||++-+.|+.|. |.+| +.++|.|-... .-|.+-+|.+--+.+=.++ .|+||-|-|..|-..++
T Consensus 187 ~Wvt~GvI~~K~~~K~t~~G~~y-~iwkL~dLk~~-q~vslfLFG~a~k~~wk~k-~GtVialLNp~v~k~~~ 256 (578)
T KOG3056|consen 187 NWVTMGVIVEKSDPKFTSNGNPY-SIWKLTDLKDH-QTVSLFLFGKAHKRYWKIK-LGTVIALLNPEVLKDRP 256 (578)
T ss_pred CeEEEEEEeecCCcccccCCCce-EEEEeeecCcc-ceeEEEEecHHHHHHhhhc-cCcEEEEeCccccCCCC
Confidence 355899999999999886 5555 56888887764 4599999998778888888 79999999999877655
No 60
>cd04480 RPA1_DBD_A_like RPA1_DBD_A_like: A subgroup of uncharacterized plant OB folds with similarity to the second OB fold, the ssDNA-binding domain (DBD)-A, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of RPA is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change.
Probab=61.65 E-value=18 Score=28.93 Aligned_cols=45 Identities=24% Similarity=0.242 Sum_probs=33.1
Q ss_pred EEEEEEeecCCCccccccCCccEEEEEEEecCCc-eEEEEEecCchhhhcC
Q 012425 350 CVVRVVAALPWRSEDFCSPLGNYRIRLTLEDPTA-RIHAFVYAEDGEKLFG 399 (464)
Q Consensus 350 ~~VRVV~~~P~~~edf~~~~g~~~~~l~leD~t~-~l~~~v~~~da~~f~~ 399 (464)
..|||+..|=..... .| ..+.+.|-|..| +|+|.+..+.+++|..
T Consensus 2 I~Vrv~r~W~~~~~~----~~-~~~~miL~De~G~~I~a~i~~~~~~~f~~ 47 (86)
T cd04480 2 ICVRVLRLWDVYNNA----SG-ESLEMVLVDEKGNRIHATIPKRLAAKFRP 47 (86)
T ss_pred EEEEEEEEEcCcCCC----CC-cEEEEEEEcCCCCEEEEEECHHHHHhhhh
Confidence 468888776322221 22 578999999999 9999999988777765
No 61
>PRK06920 dnaE DNA polymerase III DnaE; Reviewed
Probab=60.06 E-value=26 Score=41.72 Aligned_cols=88 Identities=15% Similarity=0.203 Sum_probs=60.1
Q ss_pred eeEehHHHhhccCCeEEEEEEEEeeCCcccccCCceEEEEEEEeCCCCCCCeEEEEeccCcCCCCCCCCCCCEEEEeeEE
Q 012425 9 RFLKIKDAILSINQKVSFVGVILEVGSPKQSKGTDSFCTIKVTDESHTKDGISVNIFAESMEKLPYIVSVGDIILLSHVV 88 (464)
Q Consensus 9 ~y~~i~d~~~~~~~~vnviGVVvd~~~P~~trGtD~~~tl~I~D~S~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~rvk 88 (464)
..+++.++....++.|.+.|+|+..+.+ +|+..+-|.-++|-|.+-. +.+.+|.+.-+..-..-..|.++++. -+
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 4456777643346689999999999875 5555567899999998753 99999976544443333368888874 45
Q ss_pred EEEECCeeEEeec
Q 012425 89 MKAHNKQAYALFN 101 (464)
Q Consensus 89 v~~~~g~~~~~~~ 101 (464)
++.-+++.+.+.+
T Consensus 1006 v~~~~~~~~~~~~ 1018 (1107)
T PRK06920 1006 IELRNHKLQWIVN 1018 (1107)
T ss_pred EEecCCcEEEEEe
Confidence 6654555666544
No 62
>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=59.60 E-value=11 Score=32.97 Aligned_cols=34 Identities=18% Similarity=0.305 Sum_probs=26.4
Q ss_pred eEEEEeccCcCCCCCCCCCCCEEEEeeEEEEEECC
Q 012425 60 ISVNIFAESMEKLPYIVSVGDIILLSHVVMKAHNK 94 (464)
Q Consensus 60 l~v~iF~~~~e~LP~v~~~GDII~l~rvkv~~~~g 94 (464)
|.|.+|-++.+-.-.+. +||.|+|+||.+.....
T Consensus 62 i~It~yD~H~~~ar~lK-~GdfV~L~NVhiK~~~~ 95 (123)
T cd04498 62 IDILVYDNHVELAKSLK-PGDFVRIYNVHAKSYSS 95 (123)
T ss_pred EEEEEEcchHHHHhhCC-CCCEEEEEEEEEEeccC
Confidence 66777777665555565 89999999999987766
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=58.38 E-value=44 Score=28.04 Aligned_cols=64 Identities=19% Similarity=0.320 Sum_probs=43.1
Q ss_pred EEEEEEEeeCCcccccCCceEEEEEEEeCCCCCCCeEEEEeccC-cCCCCCCCCCCCEEEEeeEEEEEECC
Q 012425 25 SFVGVILEVGSPKQSKGTDSFCTIKVTDESHTKDGISVNIFAES-MEKLPYIVSVGDIILLSHVVMKAHNK 94 (464)
Q Consensus 25 nviGVVvd~~~P~~trGtD~~~tl~I~D~S~~~~gl~v~iF~~~-~e~LP~v~~~GDII~l~rvkv~~~~g 94 (464)
+++|||+....+. +..+-.+-|.|+++.. +.|+++..- ...+-.+-..+-.|-+.|++.+....
T Consensus 1 D~VGvVvsV~~~~----~g~~~~vYLaDe~~nl--l~vkfw~~l~~~~~EDvvk~~~lia~SNLQwR~~s~ 65 (100)
T cd04495 1 DTVGVVISVGKPI----EGKFPAVYLADECLNL--LCVKFWSSLEQYAYEDVVKRRVLLAASNLQWRTEST 65 (100)
T ss_pred CceEEEEEEcccc----cCccceEEEecCCcCE--EEEEEecchHHhhhhhhcccceEEEEecceEecccc
Confidence 3689999998763 4567778999999976 888888731 11222233345667777777765544
No 64
>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=58.10 E-value=40 Score=27.56 Aligned_cols=60 Identities=13% Similarity=0.267 Sum_probs=36.7
Q ss_pred EEEEEEeeCCcccccCCceEEEEEEEeCCCCCCCeEEEEeccC--cCCCCCCCCCCCEEEEeeEEEEEEC
Q 012425 26 FVGVILEVGSPKQSKGTDSFCTIKVTDESHTKDGISVNIFAES--MEKLPYIVSVGDIILLSHVVMKAHN 93 (464)
Q Consensus 26 viGVVvd~~~P~~trGtD~~~tl~I~D~S~~~~gl~v~iF~~~--~e~LP~v~~~GDII~l~rvkv~~~~ 93 (464)
|-|-|+.+.. .-+|.. +-|+|.|++- .|.+.+|.++ ...+..-...||-|.+..- +..|.
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 213444 4467889763 4999999887 4455554458997777543 44443
No 65
>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=58.08 E-value=20 Score=30.19 Aligned_cols=53 Identities=15% Similarity=0.315 Sum_probs=39.3
Q ss_pred eeEehHHHhhccCCeEEEEEEEEe-eCCcccccCCceEEEEEEEeCCCCCCCeEEEEeccC
Q 012425 9 RFLKIKDAILSINQKVSFVGVILE-VGSPKQSKGTDSFCTIKVTDESHTKDGISVNIFAES 68 (464)
Q Consensus 9 ~y~~i~d~~~~~~~~vnviGVVvd-~~~P~~trGtD~~~tl~I~D~S~~~~gl~v~iF~~~ 68 (464)
.|++|..+- ..|+. +|+| ++.| ++.+.-|+.++.|.|.-...++|+|.+|++.
T Consensus 17 sFmPl~saD-~~gGV-----I~TdWY~~p-~~~~er~k~tv~Ild~~Lradal~V~vf~q~ 70 (103)
T PF12100_consen 17 SFMPLASAD-PFGGV-----IVTDWYSPP-PGPNERFKATVYILDRALRADALRVSVFRQV 70 (103)
T ss_pred hhcchhhcC-CCCCE-----EEeccccCC-CCCCeeEEEEEEEECccccCCceEEEEEEee
Confidence 567777664 22331 4567 5555 5556899999999999999899999999865
No 66
>PRK07374 dnaE DNA polymerase III subunit alpha; Validated
Probab=54.18 E-value=37 Score=40.74 Aligned_cols=88 Identities=14% Similarity=0.203 Sum_probs=61.3
Q ss_pred eeEehHHHhhc-cCCeEEEEEEEEeeCCcccccCCceEEEEEEEeCCCCCCCeEEEEeccCcCCCCCCCCCCCEEEEeeE
Q 012425 9 RFLKIKDAILS-INQKVSFVGVILEVGSPKQSKGTDSFCTIKVTDESHTKDGISVNIFAESMEKLPYIVSVGDIILLSHV 87 (464)
Q Consensus 9 ~y~~i~d~~~~-~~~~vnviGVVvd~~~P~~trGtD~~~tl~I~D~S~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~rv 87 (464)
..+++.++... .+..|.+.|+|+..+.+ +|+.++-|.-++|-|.+-. +.+.+|.+.-+..-..-..|.++++. -
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 35679999999999876 5665678999999999863 99999976544444433468888884 4
Q ss_pred EEEEECCeeEEeec
Q 012425 88 VMKAHNKQAYALFN 101 (464)
Q Consensus 88 kv~~~~g~~~~~~~ 101 (464)
+++.-.++.+.+.+
T Consensus 1062 ~v~~~~~~~~~~~~ 1075 (1170)
T PRK07374 1062 KVDRRDDRVQLIID 1075 (1170)
T ss_pred EEEecCCeEEEEEe
Confidence 66654455666654
No 67
>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=52.92 E-value=17 Score=29.94 Aligned_cols=21 Identities=10% Similarity=0.175 Sum_probs=18.6
Q ss_pred EEEEEEecCCceEEEEEecCc
Q 012425 373 RIRLTLEDPTARIHAFVYAED 393 (464)
Q Consensus 373 ~~~l~leD~t~~l~~~v~~~d 393 (464)
.+.|+|+|+||.|.+.++..+
T Consensus 15 ~~~~tLdDgTG~Ie~~~W~~~ 35 (92)
T cd04483 15 FYSFGVDDGTGVVNCVCWKNL 35 (92)
T ss_pred eEEEEEecCCceEEEEEEcCc
Confidence 388999999999999999754
No 68
>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=50.06 E-value=1.3e+02 Score=27.13 Aligned_cols=33 Identities=18% Similarity=0.267 Sum_probs=16.3
Q ss_pred EEEEEccchhHHHh-hccCCCCEEEEeceEEEEe
Q 012425 236 LRVIIDKGIEKHIL-HLLKIGKWVKLQNVLCQVD 268 (464)
Q Consensus 236 l~V~~~~~~~~~~~-~~lk~G~wV~l~Nv~~k~~ 268 (464)
+.|-+|..-..++. +.+++|..|-..|++-+..
T Consensus 50 l~Ikfw~~l~~~~~eDilk~~~liA~SNLqwR~~ 83 (143)
T PF09104_consen 50 LAIKFWTGLNQYGYEDILKPGSLIAASNLQWRPE 83 (143)
T ss_dssp EEEEESS-------SS---TT-EEEEEEEEE-S-
T ss_pred EEEEeccCccccchhhhcCcceEEEEeeeEeecc
Confidence 45666766666665 4579999999999999864
No 69
>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=49.44 E-value=31 Score=27.85 Aligned_cols=26 Identities=23% Similarity=0.298 Sum_probs=22.9
Q ss_pred EEEEEEccchhHHHhhccCCCCEEEE
Q 012425 235 ILRVIIDKGIEKHILHLLKIGKWVKL 260 (464)
Q Consensus 235 ~l~V~~~~~~~~~~~~~lk~G~wV~l 260 (464)
.++|++|...++.+.+.++.|++|.+
T Consensus 45 ~~~v~~~g~~a~~~~~~~~kG~~V~v 70 (100)
T cd04496 45 WIRVVAFGKLAENAAKYLKKGDLVYV 70 (100)
T ss_pred EEEEEEEhHHHHHHHHHhCCCCEEEE
Confidence 58999999988888899999999954
No 70
>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=48.24 E-value=1.1e+02 Score=32.38 Aligned_cols=78 Identities=17% Similarity=0.215 Sum_probs=52.1
Q ss_pred hHHHhhccCCeEEEEEEEEeeCCcccccCCceEEEEEEEeCCCCCCCeEEEEeccCcCCCCCCCCCCCEEEEeeEEEEEE
Q 012425 13 IKDAILSINQKVSFVGVILEVGSPKQSKGTDSFCTIKVTDESHTKDGISVNIFAESMEKLPYIVSVGDIILLSHVVMKAH 92 (464)
Q Consensus 13 i~d~~~~~~~~vnviGVVvd~~~P~~trGtD~~~tl~I~D~S~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~rvkv~~~ 92 (464)
|+.+++..=..|-|-|=|..++.+ +.| .+-|+|+|+.- -|+|.+|+.....|+.-.+.|+=|+++ .++..|
T Consensus 9 ik~~le~~~~~v~V~GEisn~~~~--~sG---H~YFtLkD~~a---~i~~vmf~~~~~~l~f~~~~G~~V~v~-g~v~~y 79 (432)
T TIGR00237 9 IKALLEATFLQVWIQGEISNFTQP--VSG---HWYFTLKDENA---QVRCVMFRGNNNRLKFRPQNGQQVLVR-GGISVY 79 (432)
T ss_pred HHHHHHhhCCcEEEEEEecCCeeC--CCc---eEEEEEEcCCc---EEEEEEEcChhhCCCCCCCCCCEEEEE-EEEEEE
Confidence 455554311368899999998854 334 46678899653 499999998877887766689977773 445545
Q ss_pred --CCeeEEe
Q 012425 93 --NKQAYAL 99 (464)
Q Consensus 93 --~g~~~~~ 99 (464)
.|+.++.
T Consensus 80 ~~~G~~ql~ 88 (432)
T TIGR00237 80 EPRGDYQII 88 (432)
T ss_pred CCCCcEEEE
Confidence 3445553
No 71
>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed
Probab=48.14 E-value=1.2e+02 Score=32.23 Aligned_cols=68 Identities=19% Similarity=0.168 Sum_probs=47.7
Q ss_pred CeEEEEEEEEeeCCcccccCCceEEEEEEEeCCCCCCCeEEEEeccCcCCCCCCCCCCCEEEEeeEEEEEE--CCeeEE
Q 012425 22 QKVSFVGVILEVGSPKQSKGTDSFCTIKVTDESHTKDGISVNIFAESMEKLPYIVSVGDIILLSHVVMKAH--NKQAYA 98 (464)
Q Consensus 22 ~~vnviGVVvd~~~P~~trGtD~~~tl~I~D~S~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~rvkv~~~--~g~~~~ 98 (464)
..|-|.|=|..++.+ ++| .+-|+|+|.. ..|+|.+|+.....++.-...|+-|+++ .++..| +|..++
T Consensus 24 ~~v~v~gEis~~~~~--~sG---H~Yf~Lkd~~---a~i~~~~~~~~~~~~~~~~~~G~~v~v~-g~~~~y~~~g~~ql 93 (438)
T PRK00286 24 GQVWVRGEISNFTRH--SSG---HWYFTLKDEI---AQIRCVMFKGSARRLKFKPEEGMKVLVR-GKVSLYEPRGDYQL 93 (438)
T ss_pred CcEEEEEEeCCCeeC--CCC---eEEEEEEcCC---cEEEEEEEcChhhcCCCCCCCCCEEEEE-EEEEEECCCCCEEE
Confidence 458888998888764 233 4668999984 3499999998877888755689977763 344445 333444
No 72
>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=47.36 E-value=23 Score=28.28 Aligned_cols=21 Identities=33% Similarity=0.488 Sum_probs=19.3
Q ss_pred EEEEecCCceEEEEEecCchh
Q 012425 375 RLTLEDPTARIHAFVYAEDGE 395 (464)
Q Consensus 375 ~l~leD~t~~l~~~v~~~da~ 395 (464)
.++|||.||++++.++.+..+
T Consensus 20 ~~~leD~~G~~Ev~~F~~~~~ 40 (79)
T cd04490 20 IVELEDTTGRITVLLTKDKEE 40 (79)
T ss_pred EEEEECCCCEEEEEEeCchhh
Confidence 899999999999999987665
No 73
>TIGR00643 recG ATP-dependent DNA helicase RecG.
Probab=46.77 E-value=1.2e+02 Score=33.82 Aligned_cols=78 Identities=15% Similarity=0.238 Sum_probs=52.0
Q ss_pred ehHHHhhccCCeEEEEEEEEeeCCcccccCCceEEEEEEEe-CCCCCCCeEEEEeccCcCCCCCCCCCCCEEEEeeEEEE
Q 012425 12 KIKDAILSINQKVSFVGVILEVGSPKQSKGTDSFCTIKVTD-ESHTKDGISVNIFAESMEKLPYIVSVGDIILLSHVVMK 90 (464)
Q Consensus 12 ~i~d~~~~~~~~vnviGVVvd~~~P~~trGtD~~~tl~I~D-~S~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~rvkv~ 90 (464)
+|+++. .|..+.+.|.|++..... ++.--..++++.| .+ ..+.+.+|.. ..+......|+-+.+.. |+.
T Consensus 25 ~i~~~~--~g~~~~~~~~v~~~~~~~--~~~~~~~~~~~~d~~~---~~~~~~~F~~--~~~~~~~~~g~~~~~~G-k~~ 94 (630)
T TIGR00643 25 TIGELL--PGERATIVGEVLSHCIFG--FKRRKVLKLRLKDGGY---KKLELRFFNR--AFLKKKFKVGSKVVVYG-KVK 94 (630)
T ss_pred CHHHcC--CCCEEEEEEEEEEeEecc--CCCCceEEEEEEECCC---CEEEEEEECC--HHHHhhCCCCCEEEEEE-EEE
Confidence 677775 688999999998742211 2222278889999 44 3399999962 24545455899888864 555
Q ss_pred EECCeeEEe
Q 012425 91 AHNKQAYAL 99 (464)
Q Consensus 91 ~~~g~~~~~ 99 (464)
.++|..+..
T Consensus 95 ~~~~~~~~~ 103 (630)
T TIGR00643 95 SSKFKAYLI 103 (630)
T ss_pred eeCCEEEEE
Confidence 677766653
No 74
>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=46.33 E-value=58 Score=28.02 Aligned_cols=39 Identities=23% Similarity=0.338 Sum_probs=28.1
Q ss_pred CCCCCCCCCCCEEEEeeE-------EEEEECCeeEEeecCCc-eeEEE
Q 012425 70 EKLPYIVSVGDIILLSHV-------VMKAHNKQAYALFNKKF-SSFAL 109 (464)
Q Consensus 70 e~LP~v~~~GDII~l~rv-------kv~~~~g~~~~~~~~~~-ss~~l 109 (464)
..+|.+. +||+|.++=. ++|.|.|-+.+.-+.+. ++|.|
T Consensus 14 ~~~p~f~-~GD~v~V~~~i~e~~k~r~q~f~GvvIa~~~~g~~ssftl 60 (113)
T PF01245_consen 14 KDIPEFR-VGDTVRVTYKISEGNKERIQVFEGVVIARRRRGLNSSFTL 60 (113)
T ss_dssp SSSSSSS-SSSEEEEEEEEESSSSEEEEEEEEEEEEEEBSSTSSEEEE
T ss_pred cCCCCcC-CCCEEEEEEEEecCCCceeEEEEEEEEEEECCCCCeeEEE
Confidence 6799998 8999999843 35778887666655433 56665
No 75
>PRK05338 rplS 50S ribosomal protein L19; Provisional
Probab=46.20 E-value=44 Score=28.94 Aligned_cols=42 Identities=14% Similarity=0.155 Sum_probs=29.2
Q ss_pred CCCCCCCCCCCEEEEeeE-------EEEEECCeeEEeecCC-ceeEEEEeC
Q 012425 70 EKLPYIVSVGDIILLSHV-------VMKAHNKQAYALFNKK-FSSFALYDG 112 (464)
Q Consensus 70 e~LP~v~~~GDII~l~rv-------kv~~~~g~~~~~~~~~-~ss~~lf~g 112 (464)
.++|.+. +||+|.++-- ++|.|.|-+-+.-+.+ .++|.|=+-
T Consensus 14 ~~~p~f~-~GD~V~V~~~i~eg~k~R~q~f~GvvI~~~~~G~~~tftvRki 63 (116)
T PRK05338 14 KDIPEFR-PGDTVRVHVKVVEGNKERIQAFEGVVIARRGRGLNETFTVRKI 63 (116)
T ss_pred cCCCCcC-CCCEEEEEEEEccCCceEeccEEEEEEEEeCCCCCceEEEEEc
Confidence 5699997 8999999632 4667888766665543 366776443
No 76
>PF15072 DUF4539: Domain of unknown function (DUF4539)
Probab=46.07 E-value=67 Score=26.22 Aligned_cols=61 Identities=25% Similarity=0.322 Sum_probs=41.8
Q ss_pred eEEEEEEEEeeCCcccccCCceEEEEEEEeCCCCCCCeEEEEeccCcCCCCCCCCCCCEEEEeeEEEEE
Q 012425 23 KVSFVGVILEVGSPKQSKGTDSFCTIKVTDESHTKDGISVNIFAESMEKLPYIVSVGDIILLSHVVMKA 91 (464)
Q Consensus 23 ~vnviGVVvd~~~P~~trGtD~~~tl~I~D~S~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~rvkv~~ 91 (464)
+|...+|+++.-.+ .+.|. .+.+.|+|- .+...|=++-.+..|..-.+|=+++|+++.+=.
T Consensus 3 KVp~l~v~Iks~~~---~~~D~--~v~l~DpTG---~i~~tiH~~v~~~y~~~l~~GavLlLk~V~Vf~ 63 (86)
T PF15072_consen 3 KVPCLVVIIKSIVP---SSEDA--FVVLKDPTG---EIRGTIHRKVLEEYGDELSPGAVLLLKDVTVFS 63 (86)
T ss_pred ccCEEEEEEEEeec---cCCCe--EEEEECCCC---cEEEEEeHHHHhhcCCccccCEEEEEeeeeEEe
Confidence 44555555553333 33455 668899875 377877777666677767799999999998854
No 77
>PF15072 DUF4539: Domain of unknown function (DUF4539)
Probab=45.35 E-value=19 Score=29.42 Aligned_cols=23 Identities=26% Similarity=0.278 Sum_probs=18.9
Q ss_pred EEEEEEecCCceEEEEEecCchh
Q 012425 373 RIRLTLEDPTARIHAFVYAEDGE 395 (464)
Q Consensus 373 ~~~l~leD~t~~l~~~v~~~da~ 395 (464)
-..++|.||||+|++.++.+--+
T Consensus 20 D~~v~l~DpTG~i~~tiH~~v~~ 42 (86)
T PF15072_consen 20 DAFVVLKDPTGEIRGTIHRKVLE 42 (86)
T ss_pred CeEEEEECCCCcEEEEEeHHHHh
Confidence 45789999999999999875433
No 78
>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=44.12 E-value=54 Score=26.16 Aligned_cols=37 Identities=27% Similarity=0.457 Sum_probs=28.7
Q ss_pred ccEEEEEEccchhHHHhhccCCCCEEEEeceEEEEeC
Q 012425 233 GSILRVIIDKGIEKHILHLLKIGKWVKLQNVLCQVDA 269 (464)
Q Consensus 233 G~~l~V~~~~~~~~~~~~~lk~G~wV~l~Nv~~k~~~ 269 (464)
|..|+.+.....++.-...+++|.|..|.|-.++...
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 6678888866555544788999999999998877654
No 79
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=43.90 E-value=94 Score=35.06 Aligned_cols=79 Identities=16% Similarity=0.130 Sum_probs=52.2
Q ss_pred EehHHHhhccCCeEEEEEEEEeeCCcccccCCceEEEEEEEeCCCCCCCeEEEEeccCcCCCCCCCCCCCEEEEeeEEEE
Q 012425 11 LKIKDAILSINQKVSFVGVILEVGSPKQSKGTDSFCTIKVTDESHTKDGISVNIFAESMEKLPYIVSVGDIILLSHVVMK 90 (464)
Q Consensus 11 ~~i~d~~~~~~~~vnviGVVvd~~~P~~trGtD~~~tl~I~D~S~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~rvkv~ 90 (464)
.+|+++. .|..|.+.|.|++...... +. -..++++.|.+- .+.+.+|.-+...+.....+|+-+.+.. |++
T Consensus 51 ~~i~~l~--~g~~vtv~g~V~~~~~~~~--~~-~~~~v~l~D~tg---~i~l~~F~~n~~~~~~~l~~G~~~~v~G-kv~ 121 (681)
T PRK10917 51 KPIAELR--PGEKVTVEGEVLSAEVVFG--KR-RRLTVTVSDGTG---NLTLRFFNFNQPYLKKQLKVGKRVAVYG-KVK 121 (681)
T ss_pred CCHHHCC--CCCEEEEEEEEEEEEEccC--Cc-eEEEEEEEECCe---EEEEEEEccCcHHHHhhCCCCCEEEEEE-EEE
Confidence 3566664 6889999999999743322 22 378889999763 3899999422234555455899888865 344
Q ss_pred EECCeeEE
Q 012425 91 AHNKQAYA 98 (464)
Q Consensus 91 ~~~g~~~~ 98 (464)
.++|..+.
T Consensus 122 ~~~~~~qm 129 (681)
T PRK10917 122 RGKYGLEM 129 (681)
T ss_pred ecCCeEEE
Confidence 46565555
No 80
>PF11325 DUF3127: Domain of unknown function (DUF3127); InterPro: IPR021474 This bacterial family of proteins has no known function.
Probab=43.16 E-value=1.8e+02 Score=23.73 Aligned_cols=66 Identities=21% Similarity=0.258 Sum_probs=41.7
Q ss_pred EEEEeeCCcccccCCc-eEEEEEE--EeCCCCCCCeEEEEeccCcCCCCCCCCCCCEEEEe-eEEEEEECCe
Q 012425 28 GVILEVGSPKQSKGTD-SFCTIKV--TDESHTKDGISVNIFAESMEKLPYIVSVGDIILLS-HVVMKAHNKQ 95 (464)
Q Consensus 28 GVVvd~~~P~~trGtD-~~~tl~I--~D~S~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~-rvkv~~~~g~ 95 (464)
|.|+...++.+.-|.. |.-.=-| .++-+ ..-+.+.+|.+..+.|-.+. +||.|.++ +++-+.|+|+
T Consensus 4 Gkii~~l~~~~g~s~~Gw~Kre~Vlet~~qY-P~~i~f~~~~dk~~~l~~~~-~Gd~V~Vsf~i~~RE~~gr 73 (84)
T PF11325_consen 4 GKIIKVLPEQQGVSKNGWKKREFVLETEEQY-PQKICFEFWGDKIDLLDNFQ-VGDEVKVSFNIEGREWNGR 73 (84)
T ss_pred cEEEEEecCcccCcCCCcEEEEEEEeCCCcC-CceEEEEEEcchhhhhccCC-CCCEEEEEEEeeccEecce
Confidence 4555555554332211 5433223 23333 34599999998877778887 89998886 7888888876
No 81
>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=42.69 E-value=35 Score=26.34 Aligned_cols=25 Identities=32% Similarity=0.414 Sum_probs=20.7
Q ss_pred CccEEEEEEEecCCceEEEEEecCc
Q 012425 369 LGNYRIRLTLEDPTARIHAFVYAED 393 (464)
Q Consensus 369 ~g~~~~~l~leD~t~~l~~~v~~~d 393 (464)
.|.-.+.++|+|.||++.+.++++.
T Consensus 16 ~g~~~~~~~l~D~tg~i~~~~f~~~ 40 (83)
T cd04492 16 NGKPYLALTLQDKTGEIEAKLWDAS 40 (83)
T ss_pred CCCcEEEEEEEcCCCeEEEEEcCCC
Confidence 3545689999999999999999843
No 82
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=41.43 E-value=1.3e+02 Score=33.14 Aligned_cols=78 Identities=23% Similarity=0.296 Sum_probs=58.1
Q ss_pred eEehHHHhhccCCeEEEEEEEEeeCCcccccCCceEEEEEEEeCCCCCCCeEEEEec-cCcCCCCCCCCCCCEEEEeeEE
Q 012425 10 FLKIKDAILSINQKVSFVGVILEVGSPKQSKGTDSFCTIKVTDESHTKDGISVNIFA-ESMEKLPYIVSVGDIILLSHVV 88 (464)
Q Consensus 10 y~~i~d~~~~~~~~vnviGVVvd~~~P~~trGtD~~~tl~I~D~S~~~~gl~v~iF~-~~~e~LP~v~~~GDII~l~rvk 88 (464)
-+.|+++-+..|..|.+=|=|+..+ +|.|- .-|||.|++-. +.+.-|- +-.-.-|.|+ +||||.+-. .
T Consensus 202 r~~i~~id~~ig~tV~I~GeV~qik---qT~GP---TVFtltDetg~---i~aAAFe~aGvRAyP~Ie-vGdiV~ViG-~ 270 (715)
T COG1107 202 RTLIDDLDEMIGKTVRIEGEVTQIK---QTSGP---TVFTLTDETGA---IWAAAFEEAGVRAYPEIE-VGDIVEVIG-E 270 (715)
T ss_pred cccHHHHHhhcCceEEEEEEEEEEE---EcCCC---EEEEEecCCCc---eehhhhccCCcccCCCCC-CCceEEEEE-E
Confidence 3456777777899999999999874 44442 46799999864 6677774 4567899999 999999865 4
Q ss_pred EEEECCeeEE
Q 012425 89 MKAHNKQAYA 98 (464)
Q Consensus 89 v~~~~g~~~~ 98 (464)
+....|++|.
T Consensus 271 V~~r~g~lQi 280 (715)
T COG1107 271 VTRRDGRLQI 280 (715)
T ss_pred EeecCCcEEE
Confidence 5557777776
No 83
>PRK06826 dnaE DNA polymerase III DnaE; Reviewed
Probab=40.33 E-value=73 Score=38.23 Aligned_cols=77 Identities=18% Similarity=0.300 Sum_probs=53.7
Q ss_pred cCCeEEEEEEEEeeCCcccccCCceEEEEEEEeCCCCCCCeEEEEeccCcCCCCCCCCCCCEEEEeeEEEEEE-CCeeEE
Q 012425 20 INQKVSFVGVILEVGSPKQSKGTDSFCTIKVTDESHTKDGISVNIFAESMEKLPYIVSVGDIILLSHVVMKAH-NKQAYA 98 (464)
Q Consensus 20 ~~~~vnviGVVvd~~~P~~trGtD~~~tl~I~D~S~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~rvkv~~~-~g~~~~ 98 (464)
.+..|.+.|+|+..+.+ +|+..+-+.-++|-|.+-. +.+.+|.+.-+..-.....|.+|++ ..+++.. ++..+.
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 35679999999999876 5665677899999998853 9999997654443332336888887 4466643 344666
Q ss_pred eec
Q 012425 99 LFN 101 (464)
Q Consensus 99 ~~~ 101 (464)
+.+
T Consensus 1065 ~~~ 1067 (1151)
T PRK06826 1065 ICE 1067 (1151)
T ss_pred EEe
Confidence 544
No 84
>CHL00084 rpl19 ribosomal protein L19
Probab=40.03 E-value=61 Score=28.09 Aligned_cols=39 Identities=21% Similarity=0.222 Sum_probs=26.8
Q ss_pred CCCCCCCCCCCEEEEee-------EEEEEECCeeEEeecCC-ceeEEE
Q 012425 70 EKLPYIVSVGDIILLSH-------VVMKAHNKQAYALFNKK-FSSFAL 109 (464)
Q Consensus 70 e~LP~v~~~GDII~l~r-------vkv~~~~g~~~~~~~~~-~ss~~l 109 (464)
.++|.+. +||+|.++= =++|.|.|-+-+.-+.+ .++|.|
T Consensus 18 ~~~p~f~-~GDtV~V~~~i~eg~k~R~q~F~GvvI~~r~~G~~~tftv 64 (117)
T CHL00084 18 KNLPKIR-VGDTVKVGVLIQEGNKERVQFYEGTVIAKKNSGLNTTITV 64 (117)
T ss_pred cCCCccC-CCCEEEEEEEEecCCeeEeceEEEEEEEEeCCCCCeeEEE
Confidence 4799988 899999964 24667777766655533 255665
No 85
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=38.97 E-value=3.4e+02 Score=30.59 Aligned_cols=78 Identities=15% Similarity=0.176 Sum_probs=57.1
Q ss_pred hHHHhhccCCeEEEEEEEEeeCCcccccCCceEEEEEEEeCCCCCCCeEEEEeccCcCCCCCCCCCCCEEEEeeEEEEEE
Q 012425 13 IKDAILSINQKVSFVGVILEVGSPKQSKGTDSFCTIKVTDESHTKDGISVNIFAESMEKLPYIVSVGDIILLSHVVMKAH 92 (464)
Q Consensus 13 i~d~~~~~~~~vnviGVVvd~~~P~~trGtD~~~tl~I~D~S~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~rvkv~~~ 92 (464)
|.++. .|..|-+.|.|.....+. .++--..++++.|.+. -+++.+|.... .+..-..+|--+.+. =|++.|
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 44554 678899999999876653 6677888899999332 39999998763 566655589988884 467778
Q ss_pred CCeeEEe
Q 012425 93 NKQAYAL 99 (464)
Q Consensus 93 ~g~~~~~ 99 (464)
++..+..
T Consensus 125 ~~~~~~~ 131 (677)
T COG1200 125 KGGLQIT 131 (677)
T ss_pred cCceEEE
Confidence 8877765
No 86
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=38.11 E-value=1.3e+02 Score=37.03 Aligned_cols=86 Identities=21% Similarity=0.249 Sum_probs=61.2
Q ss_pred ceeeEehHHHhhccCCeEEEEEEEEeeCCcccccCCceEEEEEEEeCCCCCCCeEEEEeccCc---CCCCCCCCCCCEEE
Q 012425 7 DYRFLKIKDAILSINQKVSFVGVILEVGSPKQSKGTDSFCTIKVTDESHTKDGISVNIFAESM---EKLPYIVSVGDIIL 83 (464)
Q Consensus 7 ~y~y~~i~d~~~~~~~~vnviGVVvd~~~P~~trGtD~~~tl~I~D~S~~~~gl~v~iF~~~~---e~LP~v~~~GDII~ 83 (464)
.+..++|+++.. ....|-+-|-|-+... +.+++.-...+|.|+|-+ +++.|+.|.++. +.+-.+. .||-|+
T Consensus 223 ~~~~~~~~~i~~-~~~~v~i~G~if~~e~-~~~k~~~~~~~~~~td~~---~s~~~k~f~~~~~~~~~~~~~~-~g~~v~ 296 (1437)
T PRK00448 223 KEEITPMKEINE-EERRVVVEGYVFKVEI-KELKSGRHILTFKITDYT---SSIIVKKFSRDKEDLKKFDEIK-KGDWVK 296 (1437)
T ss_pred ccCcccHHHhhc-cCCeEEEEEEEEEEEE-EeccCCCEEEEEEEEcCC---CCEEEEEEecCcchhHHHhcCC-CCCEEE
Confidence 356788999874 3567899999988755 355655788899999976 459999998543 3355566 799999
Q ss_pred Eee-EEEEEECCeeEE
Q 012425 84 LSH-VVMKAHNKQAYA 98 (464)
Q Consensus 84 l~r-vkv~~~~g~~~~ 98 (464)
++. +....|.++...
T Consensus 297 ~~g~~~~d~~~~~~~~ 312 (1437)
T PRK00448 297 VRGSVQNDTFTRDLVM 312 (1437)
T ss_pred EEEEEeccCCCCceEE
Confidence 874 344456666444
No 87
>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=37.89 E-value=62 Score=27.87 Aligned_cols=42 Identities=17% Similarity=0.140 Sum_probs=29.0
Q ss_pred CCCCCCCCCCCEEEEeeE-------EEEEECCeeEEeecCC-ceeEEEEeC
Q 012425 70 EKLPYIVSVGDIILLSHV-------VMKAHNKQAYALFNKK-FSSFALYDG 112 (464)
Q Consensus 70 e~LP~v~~~GDII~l~rv-------kv~~~~g~~~~~~~~~-~ss~~lf~g 112 (464)
.++|.+. +||+|.++-- ++|.|.|-+-+..+.+ .++|.|=+-
T Consensus 14 ~~ip~f~-~GD~v~V~~~i~eg~k~R~q~f~GvvI~~~~~G~~~tftvR~i 63 (113)
T TIGR01024 14 KDLPDFR-VGDTVRVHVKIVEGKKERIQVFEGVVIARRGGGIGETFTVRKI 63 (113)
T ss_pred cCCCccC-CCCEEEEEEEEccCCceEcccEEEEEEEEeCCCCceEEEEEEe
Confidence 5799998 8999999732 4567877766666543 356776443
No 88
>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=36.14 E-value=47 Score=25.57 Aligned_cols=22 Identities=23% Similarity=0.469 Sum_probs=19.2
Q ss_pred EEEEEEecCCceEEEEEecCch
Q 012425 373 RIRLTLEDPTARIHAFVYAEDG 394 (464)
Q Consensus 373 ~~~l~leD~t~~l~~~v~~~da 394 (464)
..-++|+|.+|++++.++.+-.
T Consensus 18 ~~~~~L~D~~~~i~~~~f~~~~ 39 (78)
T cd04489 18 HLYFTLKDEDASIRCVMWRSNA 39 (78)
T ss_pred EEEEEEEeCCeEEEEEEEcchh
Confidence 6789999999999999998643
No 89
>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=36.13 E-value=29 Score=28.50 Aligned_cols=61 Identities=18% Similarity=0.207 Sum_probs=40.7
Q ss_pred EeecCCCccccccC----CccEEEEEEEecCCceEEEEEecCchhhhcCCCCc----hHHHHHHHHHHhcC
Q 012425 355 VAALPWRSEDFCSP----LGNYRIRLTLEDPTARIHAFVYAEDGEKLFGGYPF----VDVLKRKINKLLGV 417 (464)
Q Consensus 355 V~~~P~~~edf~~~----~g~~~~~l~leD~t~~l~~~v~~~da~~f~~~~~~----~~~l~~kl~~l~g~ 417 (464)
|.+||.++|+.... .+.|++.++=++.+..|.+.|--.+ .+..+... .+.+.+++..-+|.
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 56889999877542 2359999999999999999997654 22322112 35666667677775
No 90
>PRK05672 dnaE2 error-prone DNA polymerase; Validated
Probab=35.41 E-value=91 Score=37.08 Aligned_cols=86 Identities=12% Similarity=0.168 Sum_probs=56.4
Q ss_pred eeEehHHHhhc-cCCeEEEEEEEEeeCCcccccCCceEEEEEEEeCCCCCCCeEEEEeccCcCCCCCCCCCCCEEEEeeE
Q 012425 9 RFLKIKDAILS-INQKVSFVGVILEVGSPKQSKGTDSFCTIKVTDESHTKDGISVNIFAESMEKLPYIVSVGDIILLSHV 87 (464)
Q Consensus 9 ~y~~i~d~~~~-~~~~vnviGVVvd~~~P~~trGtD~~~tl~I~D~S~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~rv 87 (464)
.++++.++... .+..|.|.|+|+....+...+| |.-++|-|.+-. +.+.+|.+.-+..-..-..|.++++. -
T Consensus 940 ~~~~~~~l~~~~~~~~v~v~g~i~~~~~~~TkkG---maf~~leD~~g~---~e~~ifp~~~~~~~~~l~~~~~~~v~-g 1012 (1046)
T PRK05672 940 GVVSAAELLDVEDGRRVRVAGVVTHRQRPGTASG---VTFLTLEDETGM---VNVVVWPGLWERQRREALGARLLLVR-G 1012 (1046)
T ss_pred cCcCHHHHhhccCCCEEEEEEEEEEEEEecCCCc---eEEEEEecCCCC---EEEEECHHHHHHHHHHhccCCEEEEE-E
Confidence 34566666432 4567999999999887643345 888899888753 99999976443333323368888884 4
Q ss_pred EEEEECCeeEEeec
Q 012425 88 VMKAHNKQAYALFN 101 (464)
Q Consensus 88 kv~~~~g~~~~~~~ 101 (464)
+++.-+++.+.+.+
T Consensus 1013 ~v~~~~~~~~~~~~ 1026 (1046)
T PRK05672 1013 RVQNAEGVRHLVAD 1026 (1046)
T ss_pred EEEecCCeEEEEEe
Confidence 56654555555544
No 91
>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=33.99 E-value=49 Score=25.21 Aligned_cols=25 Identities=36% Similarity=0.426 Sum_probs=20.3
Q ss_pred CccEEEEEEEecCCceEEEEEecCc
Q 012425 369 LGNYRIRLTLEDPTARIHAFVYAED 393 (464)
Q Consensus 369 ~g~~~~~l~leD~t~~l~~~v~~~d 393 (464)
.|.-.+.++|+|.||.+.+.++++.
T Consensus 16 ~g~~~~~~~l~D~tg~~~~~~f~~~ 40 (84)
T cd04485 16 KGKRMAFVTLEDLTGSIEVVVFPET 40 (84)
T ss_pred CCCEEEEEEEEeCCCeEEEEECHHH
Confidence 3544588999999999999999743
No 92
>COG1570 XseA Exonuclease VII, large subunit [DNA replication, recombination, and repair]
Probab=32.19 E-value=4.1e+02 Score=28.40 Aligned_cols=64 Identities=19% Similarity=0.238 Sum_probs=47.1
Q ss_pred CeEEEEEEEEeeCCcccccCCceEEEEEEEeCCCCCCCeEEEEeccCcCCCCCCCCCCCEEEEeeEEEEEECC
Q 012425 22 QKVSFVGVILEVGSPKQSKGTDSFCTIKVTDESHTKDGISVNIFAESMEKLPYIVSVGDIILLSHVVMKAHNK 94 (464)
Q Consensus 22 ~~vnviGVVvd~~~P~~trGtD~~~tl~I~D~S~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~rvkv~~~~g 94 (464)
+.|=|-|=|..++.| ..| ..-|+|.|+.- -|.|.+|+.+...|......|+-|+++ -+++.|-+
T Consensus 24 ~~V~v~GEISn~t~~--~sg---H~YFtLKD~~A---~i~c~mf~~~~~~l~f~p~eG~~V~v~-G~is~Y~~ 87 (440)
T COG1570 24 GQVWVRGEISNFTRP--ASG---HLYFTLKDERA---QIRCVMFKGNNRRLKFRPEEGMQVLVR-GKISLYEP 87 (440)
T ss_pred CeEEEEEEecCCccC--CCc---cEEEEEccCCc---eEEEEEEcCcccccCCCccCCCEEEEE-EEEEEEcC
Confidence 457777877777755 233 55579999964 399999999888898766789988874 46666644
No 93
>PRK08763 single-stranded DNA-binding protein; Provisional
Probab=31.27 E-value=82 Score=28.91 Aligned_cols=26 Identities=15% Similarity=0.029 Sum_probs=22.9
Q ss_pred EEEEEEccchhHHHhhccCCCCEEEE
Q 012425 235 ILRVIIDKGIEKHILHLLKIGKWVKL 260 (464)
Q Consensus 235 ~l~V~~~~~~~~~~~~~lk~G~wV~l 260 (464)
.++|++|...++.+.+.++.|+.|.+
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 57999999999998999999999953
No 94
>PRK07772 single-stranded DNA-binding protein; Provisional
Probab=31.23 E-value=77 Score=29.74 Aligned_cols=74 Identities=9% Similarity=0.214 Sum_probs=49.8
Q ss_pred CCeEEEEEEEEeeCCcccccCCceEEEEEEEeC-C-CC-C-----C----CeEEEEeccCcCCCCCCCCCCCEEEEe-eE
Q 012425 21 NQKVSFVGVILEVGSPKQSKGTDSFCTIKVTDE-S-HT-K-----D----GISVNIFAESMEKLPYIVSVGDIILLS-HV 87 (464)
Q Consensus 21 ~~~vnviGVVvd~~~P~~trGtD~~~tl~I~D~-S-~~-~-----~----gl~v~iF~~~~e~LP~v~~~GDII~l~-rv 87 (464)
...|.|+|=++.--.-+.+....-+++|+|.-. . .. . + =++|.+|.+..+.+-.-.+.||-|.+. |+
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 356888898777544455555567889999732 2 11 0 1 279999988666665533479977776 78
Q ss_pred EEEEECC
Q 012425 88 VMKAHNK 94 (464)
Q Consensus 88 kv~~~~g 94 (464)
+...|.+
T Consensus 84 ~~r~wed 90 (186)
T PRK07772 84 KQRSYET 90 (186)
T ss_pred EcCceEC
Confidence 9888864
No 95
>PRK07274 single-stranded DNA-binding protein; Provisional
Probab=29.95 E-value=93 Score=27.26 Aligned_cols=25 Identities=8% Similarity=0.230 Sum_probs=22.4
Q ss_pred EEEEEEccchhHHHhhccCCCCEEE
Q 012425 235 ILRVIIDKGIEKHILHLLKIGKWVK 259 (464)
Q Consensus 235 ~l~V~~~~~~~~~~~~~lk~G~wV~ 259 (464)
+++|++|...|+.+.+.++.|+.|.
T Consensus 48 w~~v~~fg~~Ae~v~~~l~KG~~V~ 72 (131)
T PRK07274 48 FINVVLWGKLAETLASYASKGSLIS 72 (131)
T ss_pred EEEEEEehHHHHHHHHHcCCCCEEE
Confidence 5799999999998889999999984
No 96
>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=29.68 E-value=1.4e+02 Score=31.32 Aligned_cols=87 Identities=20% Similarity=0.258 Sum_probs=59.9
Q ss_pred EehHHHhhccCCeEEEEEEEEeeCCcc--ccc-CC-ceEEEEEEEeCCCCCCCeEEEEeccCcCCCCCCCCCCCEEEEee
Q 012425 11 LKIKDAILSINQKVSFVGVILEVGSPK--QSK-GT-DSFCTIKVTDESHTKDGISVNIFAESMEKLPYIVSVGDIILLSH 86 (464)
Q Consensus 11 ~~i~d~~~~~~~~vnviGVVvd~~~P~--~tr-Gt-D~~~tl~I~D~S~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~r 86 (464)
..|.++.. ..+.+|+.|-|.++..++ +++ |. .=..+..+.|++-. +... +..+...++..+ .||++.+.+
T Consensus 50 ~~i~~~~~-~~~~~~v~~~V~~~~e~~~~~~k~g~~~~l~~~~v~Detg~---v~~~-~~~~~~a~~~~e-~Gdv~~i~~ 123 (407)
T COG1599 50 GKISDISE-ASSRVNVTGRVLSIGEKKTFDRKRGAEGKLAEVLVGDETGS---VKTV-TLWNIAALEKLE-PGDVIRIRN 123 (407)
T ss_pred ccccccch-hhccccEEEEECccccceeeecccccccceEEEEEecCCCC---EEEE-eeccccccccCC-ccceEEecC
Confidence 34555542 256799999999998775 443 43 33445557777642 3332 566655666666 899999999
Q ss_pred EEEEEECCeeEEeecCC
Q 012425 87 VVMKAHNKQAYALFNKK 103 (464)
Q Consensus 87 vkv~~~~g~~~~~~~~~ 103 (464)
..+..|+|.+++..+..
T Consensus 124 ~~~~~~~~~~~~~~~~~ 140 (407)
T COG1599 124 AYTSLYRGGKRLSVGRV 140 (407)
T ss_pred cccccccCceeeecccc
Confidence 99999999988875543
No 97
>KOG2971 consensus RNA-binding protein required for biogenesis of the ribosomal 60S subunit [Translation, ribosomal structure and biogenesis]
Probab=29.00 E-value=1.2e+02 Score=29.96 Aligned_cols=50 Identities=28% Similarity=0.646 Sum_probs=37.9
Q ss_pred cCCCCchHHHHHHHHHHhcCCCCCCccccCCCCCCccee-EeEEeeeeCCCCcceeeEEEe
Q 012425 398 FGGYPFVDVLKRKINKLLGVAVSDGQEIKDAPRNPPWVQ-CCLKSYYIDRNDIWGSRQYRI 457 (464)
Q Consensus 398 ~~~~~~~~~l~~kl~~l~g~~e~~~~~~~~~~~~~pw~~-cci~sY~~~~~~~~~~r~y~i 457 (464)
|.+++-+.-|++-|-...|++.. .+++.|+++ .|..+| ++ +.-| -|+|||
T Consensus 162 Fd~~pHlkl~Kell~q~fgiP~~-------hrkSkpf~Dhvf~Fsi-~D-~~IW-fRnyqI 212 (299)
T KOG2971|consen 162 FDELPHLKLLKELLEQIFGIPKH-------HRKSKPFVDHVFTFSI-LD-GKIW-FRNYQI 212 (299)
T ss_pred cccchHHHHHHHHHHHHcCCCCC-------CcccCCccceEEEEEE-ec-CeEE-EEEeEe
Confidence 44567788888988999998655 356779877 556677 55 5689 999999
No 98
>PRK09010 single-stranded DNA-binding protein; Provisional
Probab=27.35 E-value=1.1e+02 Score=28.55 Aligned_cols=26 Identities=19% Similarity=0.175 Sum_probs=22.9
Q ss_pred EEEEEEccchhHHHhhccCCCCEEEE
Q 012425 235 ILRVIIDKGIEKHILHLLKIGKWVKL 260 (464)
Q Consensus 235 ~l~V~~~~~~~~~~~~~lk~G~wV~l 260 (464)
.++|++|...++.+.+.|+.|+.|.+
T Consensus 55 w~~V~~fgk~Ae~~~~~L~KGs~V~V 80 (177)
T PRK09010 55 WHRVVLFGKLAEVAGEYLRKGSQVYI 80 (177)
T ss_pred EEEEEEehhHHHHHHHhcCCCCEEEE
Confidence 57999999999988899999999954
No 99
>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=27.26 E-value=3.1e+02 Score=21.62 Aligned_cols=62 Identities=18% Similarity=0.168 Sum_probs=37.7
Q ss_pred EEEEEeeCCcccccCCceEEEEEEEeCCCC-----CCCeEEEEeccCcCCCCCCCCCCCEEEEeeEEEEEECCeeEEeec
Q 012425 27 VGVILEVGSPKQSKGTDSFCTIKVTDESHT-----KDGISVNIFAESMEKLPYIVSVGDIILLSHVVMKAHNKQAYALFN 101 (464)
Q Consensus 27 iGVVvd~~~P~~trGtD~~~tl~I~D~S~~-----~~gl~v~iF~~~~e~LP~v~~~GDII~l~rvkv~~~~g~~~~~~~ 101 (464)
=|||+-..... ... .|-|-|+.-. ++| +-+|.+. -+.+. +||.|++. -++..|+|..++...
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---GADVA-VGDLVRVT-GTVTEYYGLTQLTAV 69 (78)
T ss_pred EEEEEEEcCCC--CcC----EEEEEcCCCCCCCcccce--EEEecCC---CCCCC-CCCEEEEE-EEEEeeCCeEEEccC
Confidence 47777764432 112 3345665222 234 4445443 45565 89999996 899999998887543
No 100
>PRK07459 single-stranded DNA-binding protein; Provisional
Probab=27.12 E-value=1.2e+02 Score=26.24 Aligned_cols=73 Identities=12% Similarity=0.221 Sum_probs=46.6
Q ss_pred CeEEEEEEEEeeCCcccccCCceEEEEEEEeCCCC----CCCeEEEEeccCcCCCCCCCCCCCEEEEe-eEEEEEECC
Q 012425 22 QKVSFVGVILEVGSPKQSKGTDSFCTIKVTDESHT----KDGISVNIFAESMEKLPYIVSVGDIILLS-HVVMKAHNK 94 (464)
Q Consensus 22 ~~vnviGVVvd~~~P~~trGtD~~~tl~I~D~S~~----~~gl~v~iF~~~~e~LP~v~~~GDII~l~-rvkv~~~~g 94 (464)
..|.++|-+..--.-+.+.+..-.++|+|.=.... .+=+.|.+|.+..+.+=.-..-|+-|.+. +++...|.+
T Consensus 4 N~v~LiGrL~~DPelr~t~~G~~v~~fslAv~~~~~~~~t~w~~v~~wg~~Ae~~~~~l~KG~~V~V~G~l~~~~~~d 81 (121)
T PRK07459 4 NSVTLVGRAGRDPEVRYFESGSVVCNLTLAVNRRSRDDEPDWFNLEIWGKTAQVAADYVKKGSLIGITGSLKFDRWTD 81 (121)
T ss_pred cEEEEEEEccCCCEEEEcCCCCEEEEEEEEecccccCCCceEEEEEEehHHHHHHHHHcCCCCEEEEEEEEEecceEc
Confidence 35888998876433344545557888888643211 11289999987544443323469987776 788888854
No 101
>PF00436 SSB: Single-strand binding protein family; InterPro: IPR000424 The Escherichia coli single-strand binding protein [] (gene ssb), also known as the helix-destabilising protein, is a protein of 177 amino acids. It binds tightly, as a homotetramer, to single-stranded DNA (ss-DNA) and plays an important role in DNA replication, recombination and repair. Closely related variants of SSB are encoded in the genome of a variety of large self-transmissible plasmids. SSB has also been characterised in bacteria such as Proteus mirabilis or Serratia marcescens. Eukaryotic mitochondrial proteins that bind ss-DNA and are probably involved in mitochondrial DNA replication are structurally and evolutionary related to prokaryotic SSB.; GO: 0003697 single-stranded DNA binding; PDB: 3UDG_B 1SE8_A 2CWA_A 3ULL_B 1S3O_A 2DUD_A 3AFP_A 3AFQ_A 3VDY_A 3EIV_C ....
Probab=26.53 E-value=97 Score=25.14 Aligned_cols=27 Identities=19% Similarity=0.280 Sum_probs=20.2
Q ss_pred EEEEEEccchhHHHhhccCCCCEEEEe
Q 012425 235 ILRVIIDKGIEKHILHLLKIGKWVKLQ 261 (464)
Q Consensus 235 ~l~V~~~~~~~~~~~~~lk~G~wV~l~ 261 (464)
.++|.+|...|+.+.+.++.|+-|.+.
T Consensus 49 ~~~v~~~g~~A~~~~~~l~kG~~V~V~ 75 (104)
T PF00436_consen 49 WINVVAWGKLAENVAEYLKKGDRVYVE 75 (104)
T ss_dssp EEEEEEEHHHHHHHHHH--TT-EEEEE
T ss_pred EEEEEeeeecccccceEEcCCCEEEEE
Confidence 579999999999988999999988543
No 102
>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=26.18 E-value=2.7e+02 Score=23.01 Aligned_cols=64 Identities=8% Similarity=-0.053 Sum_probs=37.6
Q ss_pred ccEEEEEEccchhHHHhhcc----CCCCEEEE-eceEEEEeCc-EEEEEEecccceEEcCCCChHHHHHHH
Q 012425 233 GSILRVIIDKGIEKHILHLL----KIGKWVKL-QNVLCQVDAG-LWFGVLTHFTRLRYVPTNDNLIVERQR 297 (464)
Q Consensus 233 G~~l~V~~~~~~~~~~~~~l----k~G~wV~l-~Nv~~k~~~G-~leG~l~~~ski~~l~~~d~~v~~r~r 297 (464)
|..|.+++|..+|....... +.+--|-+ +..+++...| ..-......|++ +++.+-+++.+.+.
T Consensus 34 ~~~l~~tlwG~~A~~f~~~~~~~~~~~~VVav~~~~rV~~~~g~~~ls~~~~~s~v-~inp~ipe~~~~~~ 103 (106)
T cd04481 34 DERLKCTLWGEYAEEFDAKFQSAGNGEPVVAVLRFWKIKEYKGPKSLSNSFGASKV-YINPDIPEVPEIKM 103 (106)
T ss_pred CCEEEEEEEHHHHHHHHHHHHHhCCCCcEEEEEEeEEEEEEcCCcEEEcCCCceEE-EECCCcHHHHHHHh
Confidence 56789999999887644332 45555655 5588888765 221111134455 34555666665543
No 103
>PRK13732 single-stranded DNA-binding protein; Provisional
Probab=24.98 E-value=1.2e+02 Score=28.12 Aligned_cols=27 Identities=19% Similarity=0.183 Sum_probs=23.5
Q ss_pred EEEEEEccchhHHHhhccCCCCEEEEe
Q 012425 235 ILRVIIDKGIEKHILHLLKIGKWVKLQ 261 (464)
Q Consensus 235 ~l~V~~~~~~~~~~~~~lk~G~wV~l~ 261 (464)
+++|++|...++.+.+.++.|+.|.+.
T Consensus 55 w~~Vv~wgk~Ae~v~~~L~KG~~V~Ve 81 (175)
T PRK13732 55 WHRVVLFGKLAEVAGEYLRKGAQVYIE 81 (175)
T ss_pred EEEEEEecHHHHHHHHhcCCCCEEEEE
Confidence 579999999899989999999999643
No 104
>PRK05733 single-stranded DNA-binding protein; Provisional
Probab=24.82 E-value=1.2e+02 Score=28.02 Aligned_cols=27 Identities=19% Similarity=0.112 Sum_probs=23.3
Q ss_pred cEEEEEEccchhHHHhhccCCCCEEEE
Q 012425 234 SILRVIIDKGIEKHILHLLKIGKWVKL 260 (464)
Q Consensus 234 ~~l~V~~~~~~~~~~~~~lk~G~wV~l 260 (464)
.+++|++|...++.+.+.++.|+.|.+
T Consensus 53 ~w~~Vv~fgk~Ae~v~~~l~KGs~V~V 79 (172)
T PRK05733 53 EWHRVSLFGKVAEIAGEYLRKGSQVYI 79 (172)
T ss_pred eEEEEEEehHHHHHHHHHhCCCCEEEE
Confidence 357999999888888899999999954
No 105
>PRK07279 dnaE DNA polymerase III DnaE; Reviewed
Probab=24.46 E-value=1.7e+02 Score=34.71 Aligned_cols=85 Identities=15% Similarity=0.267 Sum_probs=56.5
Q ss_pred eEehHHHhhccCCeEEEEEEEEeeCCccccc-CCceEEEEEEEeCCCCCCCeEEEEeccCcCCCCCCCCCCCEEEEeeEE
Q 012425 10 FLKIKDAILSINQKVSFVGVILEVGSPKQSK-GTDSFCTIKVTDESHTKDGISVNIFAESMEKLPYIVSVGDIILLSHVV 88 (464)
Q Consensus 10 y~~i~d~~~~~~~~vnviGVVvd~~~P~~tr-GtD~~~tl~I~D~S~~~~gl~v~iF~~~~e~LP~v~~~GDII~l~rvk 88 (464)
.+++.++. .+..+.+.|+|.....- +|+ ..+-+.-++|-|.+-. +.+.+|.+.-+..-..-..|.++++. -+
T Consensus 875 ~~~~~~l~--~~~~~~~~~~i~~~~~~-~tk~~g~~maf~~leD~~g~---ie~~vFp~~y~~~~~~l~~~~~~~v~-G~ 947 (1034)
T PRK07279 875 FTPISQLV--KNSEATILVQIQSIRVI-RTKTKGQQMAFLSVTDTKKK---LDVTLFPETYRQYKDELKEGKFYYLK-GK 947 (1034)
T ss_pred CccHHHHh--cCCcceEEEEEEEEEEE-EEcCCCCeEEEEEEeeCCCc---EEEEECHHHHHHHHHHhccCCEEEEE-EE
Confidence 45677764 35568899999887663 455 4567889999998863 99999976434333323368888885 45
Q ss_pred EEEECCeeEEeec
Q 012425 89 MKAHNKQAYALFN 101 (464)
Q Consensus 89 v~~~~g~~~~~~~ 101 (464)
++.-+++.+.+.+
T Consensus 948 v~~~~~~~~l~~~ 960 (1034)
T PRK07279 948 IQERDGRLQMVLQ 960 (1034)
T ss_pred EEecCCeeEEEEe
Confidence 5554555665544
No 106
>PRK07459 single-stranded DNA-binding protein; Provisional
Probab=24.05 E-value=1.4e+02 Score=25.73 Aligned_cols=25 Identities=12% Similarity=0.061 Sum_probs=22.2
Q ss_pred EEEEEEccchhHHHhhccCCCCEEE
Q 012425 235 ILRVIIDKGIEKHILHLLKIGKWVK 259 (464)
Q Consensus 235 ~l~V~~~~~~~~~~~~~lk~G~wV~ 259 (464)
+++|++|...|+.+.+.++.|+-|.
T Consensus 45 w~~v~~wg~~Ae~~~~~l~KG~~V~ 69 (121)
T PRK07459 45 WFNLEIWGKTAQVAADYVKKGSLIG 69 (121)
T ss_pred EEEEEEehHHHHHHHHHcCCCCEEE
Confidence 5799999999998889999999884
No 107
>KOG4792 consensus Crk family adapters [Signal transduction mechanisms]
Probab=23.76 E-value=2.2e+02 Score=27.63 Aligned_cols=38 Identities=24% Similarity=0.387 Sum_probs=26.4
Q ss_pred hccCCCCEEEEeceEEEEeCcEEEEEEeccc------ceEEcCCCCh
Q 012425 250 HLLKIGKWVKLQNVLCQVDAGLWFGVLTHFT------RLRYVPTNDN 290 (464)
Q Consensus 250 ~~lk~G~wV~l~Nv~~k~~~G~leG~l~~~s------ki~~l~~~d~ 290 (464)
-.++.||.|+.. -+..+|.|||-+.+.. .+++++..++
T Consensus 246 L~levGdiVkVT---k~ninGqwegElnGk~G~fPfThvrf~d~~~~ 289 (293)
T KOG4792|consen 246 LALEVGDIVKVT---KKNINGQWEGELNGKIGHFPFTHVRFTDVQNP 289 (293)
T ss_pred hhhhcCcEEEEE---eeccCceeeeeecCccccccceeEEeeccCCc
Confidence 359999998753 2234899999888764 5677765443
No 108
>PRK06752 single-stranded DNA-binding protein; Validated
Probab=23.61 E-value=1.5e+02 Score=24.97 Aligned_cols=25 Identities=8% Similarity=0.193 Sum_probs=22.2
Q ss_pred EEEEEEccchhHHHhhccCCCCEEE
Q 012425 235 ILRVIIDKGIEKHILHLLKIGKWVK 259 (464)
Q Consensus 235 ~l~V~~~~~~~~~~~~~lk~G~wV~ 259 (464)
+++|.+|...|+.+.+.++.|+.|.
T Consensus 48 ~~~v~~wg~~Ae~~~~~l~KG~~V~ 72 (112)
T PRK06752 48 FINCVVWRKSAENVTEYCTKGSLVG 72 (112)
T ss_pred EEEEEEehHHHHHHHHhcCCCCEEE
Confidence 5789999998998889999999884
No 109
>PRK06752 single-stranded DNA-binding protein; Validated
Probab=22.91 E-value=2e+02 Score=24.25 Aligned_cols=72 Identities=13% Similarity=0.197 Sum_probs=47.1
Q ss_pred eEEEEEEEEeeCCcccccCCceEEEEEEEeCCCC--C------CCeEEEEeccCcCCCCCCCCCCCEEEEe-eEEEEEEC
Q 012425 23 KVSFVGVILEVGSPKQSKGTDSFCTIKVTDESHT--K------DGISVNIFAESMEKLPYIVSVGDIILLS-HVVMKAHN 93 (464)
Q Consensus 23 ~vnviGVVvd~~~P~~trGtD~~~tl~I~D~S~~--~------~gl~v~iF~~~~e~LP~v~~~GDII~l~-rvkv~~~~ 93 (464)
.|.++|-+..--..+.+.+..-.++|+|.-...- . +=+.|.+|.+..+.+-.-.+-||-|.+. +++...|.
T Consensus 4 ~v~liGrl~~dPelr~t~~G~~~~~f~lAv~~~~~~~~g~~~t~~~~v~~wg~~Ae~~~~~l~KG~~V~V~G~l~~~~~~ 83 (112)
T PRK06752 4 RVVLIGRLTKEPELYYTKQGVAYARVCVAVNRGFRNSLGEQQVDFINCVVWRKSAENVTEYCTKGSLVGITGRIHTRNYE 83 (112)
T ss_pred EEEEEEECcCCCEEEECCCCCEEEEEEEEECCCeEcCCCCEEEEEEEEEEehHHHHHHHHhcCCCCEEEEEEEEEeCccC
Confidence 4788887776433445555567788888754321 1 1288999987655554433479977665 88888885
Q ss_pred C
Q 012425 94 K 94 (464)
Q Consensus 94 g 94 (464)
+
T Consensus 84 ~ 84 (112)
T PRK06752 84 D 84 (112)
T ss_pred C
Confidence 4
No 110
>TIGR00621 ssb single stranded DNA-binding protein (ssb). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=22.49 E-value=1.5e+02 Score=27.08 Aligned_cols=27 Identities=19% Similarity=0.208 Sum_probs=23.2
Q ss_pred EEEEEEccchhHHHhhccCCCCEEEEe
Q 012425 235 ILRVIIDKGIEKHILHLLKIGKWVKLQ 261 (464)
Q Consensus 235 ~l~V~~~~~~~~~~~~~lk~G~wV~l~ 261 (464)
.++|++|...++.+.+.++.|+.|.+.
T Consensus 52 ~~~v~~wg~~Ae~~~~~l~KG~~V~V~ 78 (164)
T TIGR00621 52 WHDIVIFGRLAEVAAQYLKKGSLVYVE 78 (164)
T ss_pred EEEEEEehHHHHHHHHhCCCCCEEEEE
Confidence 589999998888888999999999543
No 111
>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=22.02 E-value=1.7e+02 Score=23.38 Aligned_cols=71 Identities=14% Similarity=0.253 Sum_probs=45.9
Q ss_pred EEEEEEEEeeCCcccccCCceEEEEEEEeCCCC---------CCCeEEEEeccCcCC-CCCCCCCCCEEEEe-eEEEEEE
Q 012425 24 VSFVGVILEVGSPKQSKGTDSFCTIKVTDESHT---------KDGISVNIFAESMEK-LPYIVSVGDIILLS-HVVMKAH 92 (464)
Q Consensus 24 vnviGVVvd~~~P~~trGtD~~~tl~I~D~S~~---------~~gl~v~iF~~~~e~-LP~v~~~GDII~l~-rvkv~~~ 92 (464)
+.++|-|...-..+.++...-.+.|+|.=.+.. ..-+.|.+|.+..+. +..+. .||.|.+. +++...|
T Consensus 1 v~l~G~l~~~p~~~~~~~g~~~~~~~v~~~~~~~~~~~~~~~~~~~~v~~~g~~a~~~~~~~~-kG~~V~v~G~l~~~~~ 79 (100)
T cd04496 1 VILIGRLGKDPELRYTPSGTPVARFSLAVNRRRKDRDEEEEETDWIRVVAFGKLAENAAKYLK-KGDLVYVEGRLRTRSW 79 (100)
T ss_pred CEEEEEecCCCEEEECCCCCEEEEEEEEEcCceecccccccccEEEEEEEEhHHHHHHHHHhC-CCCEEEEEEEEEecee
Confidence 357777777666666665566777777554432 123889999874344 44465 79988776 6677777
Q ss_pred CCe
Q 012425 93 NKQ 95 (464)
Q Consensus 93 ~g~ 95 (464)
.++
T Consensus 80 ~~~ 82 (100)
T cd04496 80 EDK 82 (100)
T ss_pred ECC
Confidence 653
No 112
>PRK08486 single-stranded DNA-binding protein; Provisional
Probab=21.98 E-value=1.5e+02 Score=27.71 Aligned_cols=25 Identities=12% Similarity=0.038 Sum_probs=22.2
Q ss_pred EEEEEEccchhHHHhhccCCCCEEE
Q 012425 235 ILRVIIDKGIEKHILHLLKIGKWVK 259 (464)
Q Consensus 235 ~l~V~~~~~~~~~~~~~lk~G~wV~ 259 (464)
+++|++|..-|+.+.+.++.|+.|.
T Consensus 50 fi~v~~fg~~AE~~~~~l~KG~~V~ 74 (182)
T PRK08486 50 FIDIRLFGRTAEIANQYLSKGSKVL 74 (182)
T ss_pred EEEEEEEhHHHHHHHHHcCCCCEEE
Confidence 4899999998998889999999884
No 113
>PRK06751 single-stranded DNA-binding protein; Provisional
Probab=21.83 E-value=2.3e+02 Score=26.27 Aligned_cols=72 Identities=13% Similarity=0.176 Sum_probs=46.4
Q ss_pred eEEEEEEEEeeCCcccccCCceEEEEEEEeCCC-C-C------CCeEEEEeccCcCCCCCCCCCCCEEEEe-eEEEEEEC
Q 012425 23 KVSFVGVILEVGSPKQSKGTDSFCTIKVTDESH-T-K------DGISVNIFAESMEKLPYIVSVGDIILLS-HVVMKAHN 93 (464)
Q Consensus 23 ~vnviGVVvd~~~P~~trGtD~~~tl~I~D~S~-~-~------~gl~v~iF~~~~e~LP~v~~~GDII~l~-rvkv~~~~ 93 (464)
.|.++|=|+.--.-+.|.+.--.++|+|.-... . . +=+.|.+|.+..+.+-.-.+.||-|.+. |++...|.
T Consensus 4 ~V~LiGrL~~DpelR~t~sG~~v~~fslAvnr~~~~~~ge~~tdwi~~v~wgk~Ae~~~~~l~KG~~V~VeGrL~~r~ye 83 (173)
T PRK06751 4 RVILVGRLTKDPDLRYTPNGVAVATFTLAVNRAFANQQGEREADFINCVIWRKQAENVANYLKKGSLAGVDGRLQTRNYE 83 (173)
T ss_pred EEEEEEEECCCCcEEECCCCCEEEEEEEEEccceecCCCCEEEEEEEEEEeCcHHHHHHHHcCCCCEEEEEEEEEeCccC
Confidence 477888777533333444444578888853322 1 1 1299999998766666544479977776 89999996
Q ss_pred C
Q 012425 94 K 94 (464)
Q Consensus 94 g 94 (464)
+
T Consensus 84 d 84 (173)
T PRK06751 84 G 84 (173)
T ss_pred C
Confidence 4
No 114
>PRK07738 flagellar protein FlaG; Provisional
Probab=21.11 E-value=2e+02 Score=24.97 Aligned_cols=47 Identities=11% Similarity=0.170 Sum_probs=40.2
Q ss_pred EEEEEEEecCCceEEEEEecCchhhhcCCCCchH--HHHHHHHHHhcCC
Q 012425 372 YRIRLTLEDPTARIHAFVYAEDGEKLFGGYPFVD--VLKRKINKLLGVA 418 (464)
Q Consensus 372 ~~~~l~leD~t~~l~~~v~~~da~~f~~~~~~~~--~l~~kl~~l~g~~ 418 (464)
..+.|.+.+.++++-+-|.+.+-......+|+.+ .|-++|..+.|.+
T Consensus 64 ~~L~F~vdeet~~~vVkVvD~~T~EVIRQIPpEe~L~l~~~m~e~~GlL 112 (117)
T PRK07738 64 TSLKFELHEKLNEYYVQVVDERTNEVIREIPPKKLLDMYAAMMEFVGLL 112 (117)
T ss_pred CceEEEEecCCCcEEEEEEECCCCeeeeeCCCHHHHHHHHHHHHHhcce
Confidence 5789999999999999999999888888888854 4458899999976
No 115
>PRK07135 dnaE DNA polymerase III DnaE; Validated
Probab=21.00 E-value=2.2e+02 Score=33.61 Aligned_cols=65 Identities=18% Similarity=0.263 Sum_probs=47.1
Q ss_pred ehHHHhhccCCeEEEEEEEEeeCCcccccCCceEEEEEEEeCCCCCCCeEEEEeccCcCCCCCCCCCCCEEEE
Q 012425 12 KIKDAILSINQKVSFVGVILEVGSPKQSKGTDSFCTIKVTDESHTKDGISVNIFAESMEKLPYIVSVGDIILL 84 (464)
Q Consensus 12 ~i~d~~~~~~~~vnviGVVvd~~~P~~trGtD~~~tl~I~D~S~~~~gl~v~iF~~~~e~LP~v~~~GDII~l 84 (464)
+|.++. .+..+.+.|+|+..+.-+ +.++-|.-+++-|.+-. +.+.+|.+.-+..-... .|+++++
T Consensus 890 ~~~~l~--~~~~~~v~g~i~~~~~~~--K~g~~maf~~~eD~~~~---~e~~~F~~~~~~~~~l~-~~~~~~~ 954 (973)
T PRK07135 890 RLKDLR--INTEYRLAIEVKNVKRLR--KANKEYKKVILSDDSVE---ITIFVNDNDYLLFETLK-KGDIYEF 954 (973)
T ss_pred hHHHhc--CCCeEEEEEEEEEEEEEe--eCCCeEEEEEEEECCCc---EEEEEcHHHHHHHHHhh-cCCEEEE
Confidence 455652 466789999999988765 44567999999999863 99999966433333344 6888776
No 116
>PRK06958 single-stranded DNA-binding protein; Provisional
Probab=20.94 E-value=1.9e+02 Score=27.08 Aligned_cols=74 Identities=18% Similarity=0.235 Sum_probs=0.0
Q ss_pred CeEEEEEEEEeeCCcccccCCceEEEEEE-EeCCCC--CCC--------eEEEEeccCcCCCCCCCCCCCEEEEe-eEEE
Q 012425 22 QKVSFVGVILEVGSPKQSKGTDSFCTIKV-TDESHT--KDG--------ISVNIFAESMEKLPYIVSVGDIILLS-HVVM 89 (464)
Q Consensus 22 ~~vnviGVVvd~~~P~~trGtD~~~tl~I-~D~S~~--~~g--------l~v~iF~~~~e~LP~v~~~GDII~l~-rvkv 89 (464)
..|.|||=|..--..+.+....-.++|+| +..... .+| +.|.+|.+..+.+-.-.+.||.|.+. +++.
T Consensus 5 N~V~LiGrLg~DPElr~t~nG~~va~fsVAv~~~~kdk~sGe~~e~T~w~~V~~fGk~AE~v~~~LkKGs~V~VeGrL~~ 84 (182)
T PRK06958 5 NKVILVGNLGADPEVRYLPSGDAVANIRLATTDRYKDKASGEFKEATEWHRVAFFGRLAEIVGEYLKKGSSVYIEGRIRT 84 (182)
T ss_pred cEEEEEEEecCCCeEEEcCCCCEEEEEEEEeccccccccCCcccccceEEEEEEehHHHHHHHHHhCCCCEEEEEEEEEe
Q ss_pred EEECCe
Q 012425 90 KAHNKQ 95 (464)
Q Consensus 90 ~~~~g~ 95 (464)
..|.++
T Consensus 85 ~~yeDk 90 (182)
T PRK06958 85 RKWQGQ 90 (182)
T ss_pred CceECC
No 117
>cd02792 MopB_CT_Formate-Dh-Na-like Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the major electron donor to the nitrate respiratory chain. Also included in this CD is the Desulfovibrio gigas tungsten formate dehydrogenase, DgW-FDH. In contrast to Fdh-N, which is a functional heterotrimer, DgW-FDH is a heterodimer. The DgW-FDH complex is composed of a large subunit carrying the W active site and one [4Fe-4S] center, and a small subunit that harbors a series of three [4Fe-4S] clusters as well as a putative vacant binding site for a fourth cluster. The smaller subunit is not included in this alignment. This CD (MopB_CT_Formate-Dh-Na-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=20.78 E-value=1.3e+02 Score=25.21 Aligned_cols=18 Identities=17% Similarity=0.003 Sum_probs=14.2
Q ss_pred HHHhhccCCCCEEEEece
Q 012425 246 KHILHLLKIGKWVKLQNV 263 (464)
Q Consensus 246 ~~~~~~lk~G~wV~l~Nv 263 (464)
......++.||||++.|=
T Consensus 43 dA~~lgi~~Gd~V~v~s~ 60 (122)
T cd02792 43 LAAERGIKNGDMVWVSSP 60 (122)
T ss_pred HHHHcCCCCCCEEEEEcC
Confidence 334678999999998883
No 118
>cd02790 MopB_CT_Formate-Dh_H Formate dehydrogenase H (Formate-Dh-H) catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. It is a component of the anaerobic formate hydrogen lyase complex. The E. coli formate dehydrogenase H (Fdh-H) is a monomer composed of a single polypeptide chain with a Mo active site region and a [4Fe-4S] center. This CD (MopB_CT_Formate-Dh_H) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=20.42 E-value=1.2e+02 Score=25.05 Aligned_cols=20 Identities=15% Similarity=0.036 Sum_probs=15.3
Q ss_pred hHHHhhccCCCCEEEEeceE
Q 012425 245 EKHILHLLKIGKWVKLQNVL 264 (464)
Q Consensus 245 ~~~~~~~lk~G~wV~l~Nv~ 264 (464)
+......++.||+|++.|=.
T Consensus 42 ~dA~~lgi~~Gd~V~v~~~~ 61 (116)
T cd02790 42 EDAKRLGIEDGEKVRVSSRR 61 (116)
T ss_pred HHHHHcCCCCCCEEEEEcCC
Confidence 33446789999999999843
No 119
>COG0335 RplS Ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=20.05 E-value=2.5e+02 Score=24.21 Aligned_cols=41 Identities=15% Similarity=0.247 Sum_probs=27.0
Q ss_pred CCCCCCCCCCCEEEEe-------eEEEEEECCeeEEeecCCc-eeEEEEe
Q 012425 70 EKLPYIVSVGDIILLS-------HVVMKAHNKQAYALFNKKF-SSFALYD 111 (464)
Q Consensus 70 e~LP~v~~~GDII~l~-------rvkv~~~~g~~~~~~~~~~-ss~~lf~ 111 (464)
.++|.+. +||-|+++ +-.+|.|.|-+.+.-+.+. ++|.|=.
T Consensus 16 ~~iP~f~-~GDtvrv~vki~Eg~keR~Q~FeGvVia~r~~G~~~tftvRk 64 (115)
T COG0335 16 KDIPSFR-PGDTVRVHVKIVEGSKERVQAFEGVVIARRGRGISETFTVRK 64 (115)
T ss_pred hhCCCCC-CCCEEEEEEEEEeCCeEEEeeeeEEEEEECCCCccceEEEEE
Confidence 4599988 89999976 4456777776666555332 4466543
No 120
>PRK06751 single-stranded DNA-binding protein; Provisional
Probab=20.04 E-value=1.9e+02 Score=26.71 Aligned_cols=26 Identities=15% Similarity=0.298 Sum_probs=22.8
Q ss_pred EEEEEEccchhHHHhhccCCCCEEEE
Q 012425 235 ILRVIIDKGIEKHILHLLKIGKWVKL 260 (464)
Q Consensus 235 ~l~V~~~~~~~~~~~~~lk~G~wV~l 260 (464)
+++|++|...|+.+.+.++.|+.|.+
T Consensus 48 wi~~v~wgk~Ae~~~~~l~KG~~V~V 73 (173)
T PRK06751 48 FINCVIWRKQAENVANYLKKGSLAGV 73 (173)
T ss_pred EEEEEEeCcHHHHHHHHcCCCCEEEE
Confidence 58999999999988899999998843
Done!