Query 022219
Match_columns 300
No_of_seqs 145 out of 227
Neff 7.5
Searched_HMMs 46136
Date Fri Mar 29 08:56:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022219.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022219hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd04497 hPOT1_OB1_like hPOT1_O 100.0 3.7E-36 8E-41 248.8 17.5 137 8-146 1-138 (138)
2 PF02765 POT1: Telomeric singl 100.0 1.4E-35 3E-40 247.7 14.2 137 10-146 1-146 (146)
3 KOG4757 Predicted telomere bin 100.0 1.6E-34 3.6E-39 267.7 14.0 266 3-283 2-282 (522)
4 cd04498 hPOT1_OB2 hPOT1_OB2: A 99.9 6.4E-23 1.4E-27 164.4 11.3 102 169-282 1-113 (123)
5 PRK07211 replication factor A; 99.0 9.2E-09 2E-13 100.4 15.8 204 8-290 159-367 (485)
6 PRK12366 replication factor A; 98.9 3.6E-07 7.8E-12 93.1 22.8 210 6-291 275-497 (637)
7 PRK15491 replication factor A; 98.9 2.1E-07 4.5E-12 89.0 19.3 205 6-287 162-373 (374)
8 PRK07218 replication factor A; 98.9 7.1E-07 1.5E-11 86.3 22.5 196 10-291 58-257 (423)
9 PRK12366 replication factor A; 98.7 2.7E-06 6E-11 86.7 20.6 205 8-288 61-270 (637)
10 PRK14699 replication factor A; 98.6 4E-06 8.7E-11 82.6 20.5 204 8-288 274-484 (484)
11 PRK06386 replication factor A; 98.6 1.5E-05 3.1E-10 75.6 23.4 193 11-290 3-199 (358)
12 PRK15491 replication factor A; 98.5 2.1E-05 4.6E-10 75.3 20.7 204 9-290 56-268 (374)
13 PRK14699 replication factor A; 98.3 0.00016 3.4E-09 71.5 21.8 204 11-291 167-379 (484)
14 TIGR00617 rpa1 replication fac 98.3 1.6E-05 3.5E-10 80.7 14.7 156 7-200 295-479 (608)
15 PRK07211 replication factor A; 98.2 0.00024 5.2E-09 69.8 20.8 201 11-291 54-262 (485)
16 PRK06461 single-stranded DNA-b 98.2 5.3E-05 1.2E-09 61.9 12.6 91 10-110 4-98 (129)
17 cd04475 RPA1_DBD_B RPA1_DBD_B: 98.1 4.2E-05 9.2E-10 59.5 10.0 74 23-101 1-79 (101)
18 cd04491 SoSSB_OBF SoSSB_OBF: A 97.9 0.00031 6.7E-09 52.5 10.8 72 25-102 1-75 (82)
19 TIGR00617 rpa1 replication fac 97.8 0.0011 2.4E-08 67.6 16.9 212 9-287 179-397 (608)
20 PRK06461 single-stranded DNA-b 97.4 0.002 4.3E-08 52.6 10.1 96 159-291 5-101 (129)
21 PRK08402 replication factor A; 97.4 0.007 1.5E-07 57.6 15.2 139 9-180 61-207 (355)
22 cd04497 hPOT1_OB1_like hPOT1_O 97.2 0.0042 9.1E-08 51.2 10.4 101 157-295 3-110 (138)
23 cd03524 RPA2_OBF_family RPA2_O 97.1 0.0033 7.2E-08 44.3 7.5 70 25-100 1-70 (75)
24 KOG3416 Predicted nucleic acid 96.8 0.007 1.5E-07 48.6 7.9 83 11-101 5-87 (134)
25 PRK07217 replication factor A; 96.7 0.039 8.5E-07 51.3 13.3 92 159-292 73-165 (311)
26 PF02765 POT1: Telomeric singl 96.5 0.096 2.1E-06 43.5 12.9 96 159-288 2-109 (146)
27 PRK07217 replication factor A; 96.4 0.069 1.5E-06 49.7 12.7 91 8-109 70-160 (311)
28 cd04481 RPA1_DBD_B_like RPA1_D 96.4 0.02 4.3E-07 44.9 7.8 82 25-108 1-90 (106)
29 cd04489 ExoVII_LU_OBF ExoVII_L 96.2 0.071 1.5E-06 38.8 9.7 69 24-101 2-72 (78)
30 PF01336 tRNA_anti-codon: OB-f 96.2 0.0091 2E-07 42.9 4.6 68 24-101 1-70 (75)
31 PRK06386 replication factor A; 96.1 0.066 1.4E-06 51.0 10.8 89 8-108 105-195 (358)
32 PRK07218 replication factor A; 95.9 0.1 2.2E-06 50.9 11.8 88 11-109 163-253 (423)
33 cd04474 RPA1_DBD_A RPA1_DBD_A: 95.9 0.035 7.6E-07 43.4 7.0 82 12-97 1-86 (104)
34 cd04491 SoSSB_OBF SoSSB_OBF: A 95.4 0.052 1.1E-06 40.3 6.0 47 238-287 35-81 (82)
35 PRK08402 replication factor A; 95.4 0.15 3.3E-06 48.6 10.5 101 159-291 63-165 (355)
36 cd04478 RPA2_DBD_D RPA2_DBD_D: 95.3 0.24 5.2E-06 37.6 9.5 67 24-101 2-72 (95)
37 PRK13480 3'-5' exoribonuclease 95.1 0.19 4.2E-06 47.1 10.1 82 12-101 4-85 (314)
38 cd04485 DnaE_OBF DnaE_OBF: A s 95.0 0.076 1.6E-06 38.5 5.8 70 26-100 2-71 (84)
39 cd04492 YhaM_OBF_like YhaM_OBF 94.5 0.42 9.1E-06 34.7 8.8 68 27-100 3-70 (83)
40 cd04483 hOBFC1_like hOBFC1_lik 94.1 0.57 1.2E-05 35.8 8.9 65 26-101 2-87 (92)
41 PF13742 tRNA_anti_2: OB-fold 91.6 1.9 4.2E-05 33.2 8.8 78 13-99 11-93 (99)
42 PF01336 tRNA_anti-codon: OB-f 90.7 3.8 8.3E-05 28.8 9.2 66 171-278 2-68 (75)
43 cd04488 RecG_wedge_OBF RecG_we 88.1 4 8.6E-05 28.5 7.6 68 26-100 2-69 (75)
44 cd03524 RPA2_OBF_family RPA2_O 86.5 8.1 0.00018 26.3 9.4 68 171-279 1-70 (75)
45 cd04484 polC_OBF polC_OBF: A s 85.8 9.4 0.0002 28.3 8.7 70 24-98 2-74 (82)
46 cd04487 RecJ_OBF2_like RecJ_OB 85.7 10 0.00022 27.5 8.7 64 26-100 3-67 (73)
47 PRK07373 DNA polymerase III su 85.3 3.1 6.7E-05 41.1 7.5 89 8-101 266-355 (449)
48 cd04490 PolII_SU_OBF PolII_SU_ 84.3 4.2 9.1E-05 30.0 6.2 59 24-91 2-62 (79)
49 PF09104 BRCA-2_OB3: BRCA2, ol 81.1 11 0.00023 31.3 7.8 73 11-90 4-81 (143)
50 KOG3056 Protein required for S 80.9 2.7 5.9E-05 42.0 5.0 69 24-95 188-257 (578)
51 PRK05673 dnaE DNA polymerase I 80.8 4.6 9.9E-05 44.4 7.3 88 9-101 964-1052(1135)
52 cd04482 RPA2_OBF_like RPA2_OBF 80.1 8.3 0.00018 29.2 6.5 60 26-93 3-64 (91)
53 cd04498 hPOT1_OB2 hPOT1_OB2: A 78.6 2.6 5.6E-05 34.1 3.4 34 60-94 62-95 (123)
54 cd04474 RPA1_DBD_A RPA1_DBD_A: 78.3 5.9 0.00013 30.7 5.4 49 237-285 47-102 (104)
55 cd04475 RPA1_DBD_B RPA1_DBD_B: 76.6 7.2 0.00016 29.8 5.4 50 238-290 40-89 (101)
56 TIGR00237 xseA exodeoxyribonuc 76.5 22 0.00049 34.8 10.0 80 13-100 9-89 (432)
57 PRK06920 dnaE DNA polymerase I 75.6 8.3 0.00018 42.3 7.3 89 8-101 930-1018(1107)
58 PF02721 DUF223: Domain of unk 74.8 11 0.00024 28.5 6.0 57 235-291 8-71 (95)
59 PRK00286 xseA exodeoxyribonucl 74.7 27 0.00058 34.2 10.1 71 22-100 24-95 (438)
60 PF09104 BRCA-2_OB3: BRCA2, ol 72.5 55 0.0012 27.2 9.8 64 167-271 18-83 (143)
61 cd04495 BRCA2DBD_OB3 BRCA2DBD_ 72.2 13 0.00029 28.8 5.7 64 25-94 1-65 (100)
62 cd04478 RPA2_DBD_D RPA2_DBD_D: 69.9 43 0.00093 24.9 9.7 26 170-197 2-27 (95)
63 PF12100 DUF3576: Domain of un 67.4 13 0.00027 29.1 4.7 53 9-68 17-70 (103)
64 PRK07374 dnaE DNA polymerase I 67.1 17 0.00036 40.3 7.3 89 8-101 986-1075(1170)
65 PF01245 Ribosomal_L19: Riboso 62.2 33 0.00071 27.3 6.3 40 69-109 13-60 (113)
66 PF15072 DUF4539: Domain of un 62.0 27 0.00059 26.3 5.6 63 23-94 3-66 (86)
67 PRK10917 ATP-dependent DNA hel 60.9 41 0.00089 35.0 8.6 78 12-98 52-129 (681)
68 KOG4757 Predicted telomere bin 60.8 0.87 1.9E-05 44.0 -3.4 44 155-201 174-217 (522)
69 PRK05338 rplS 50S ribosomal pr 60.5 25 0.00054 28.1 5.4 43 70-113 14-64 (116)
70 cd04483 hOBFC1_like hOBFC1_lik 60.3 72 0.0016 24.1 9.3 26 171-198 1-26 (92)
71 TIGR00643 recG ATP-dependent D 58.7 57 0.0012 33.6 9.1 77 12-98 25-102 (630)
72 KOG4792 Crk family adapters [S 57.0 22 0.00048 31.8 4.9 60 230-293 224-289 (293)
73 cd04480 RPA1_DBD_A_like RPA1_D 56.2 14 0.00031 27.2 3.2 37 236-272 30-66 (86)
74 PRK05672 dnaE2 error-prone DNA 55.6 29 0.00062 38.1 6.6 86 9-101 940-1026(1046)
75 PRK06826 dnaE DNA polymerase I 53.8 37 0.0008 37.6 7.1 77 20-101 990-1067(1151)
76 TIGR01024 rplS_bact ribosomal 52.0 40 0.00086 26.8 5.2 43 70-113 14-64 (113)
77 COG1107 Archaea-specific RecJ- 51.9 64 0.0014 33.0 7.7 79 10-99 202-281 (715)
78 cd04486 YhcR_OBF_like YhcR_OBF 50.7 96 0.0021 22.6 8.5 63 26-101 2-69 (78)
79 PRK00448 polC DNA polymerase I 50.3 63 0.0014 36.8 8.2 86 7-98 223-312 (1437)
80 PRK07279 dnaE DNA polymerase I 48.7 46 0.00099 36.5 6.7 86 9-101 874-960 (1034)
81 CHL00084 rpl19 ribosomal prote 46.3 59 0.0013 26.0 5.4 41 70-111 18-66 (117)
82 cd04480 RPA1_DBD_A_like RPA1_D 46.0 37 0.0008 25.0 4.1 56 42-99 17-72 (86)
83 PRK13254 cytochrome c-type bio 45.8 1.5E+02 0.0033 24.6 8.0 66 10-85 37-105 (148)
84 COG2176 PolC DNA polymerase II 44.5 50 0.0011 36.5 6.0 70 156-264 228-301 (1444)
85 COG1599 RFA1 Single-stranded D 43.3 97 0.0021 30.1 7.6 84 21-110 59-146 (407)
86 cd04494 BRCA2DBD_OB2 BRCA2DBD_ 43.1 54 0.0012 29.9 5.3 55 239-294 182-241 (251)
87 cd04494 BRCA2DBD_OB2 BRCA2DBD_ 42.1 54 0.0012 29.8 5.1 67 44-112 165-237 (251)
88 COG2049 DUR1 Allophanate hydro 41.1 12 0.00027 33.3 0.9 39 230-270 177-215 (223)
89 COG1200 RecG RecG-like helicas 38.3 1.7E+02 0.0036 30.5 8.5 73 20-99 59-131 (677)
90 COG1570 XseA Exonuclease VII, 38.0 3.2E+02 0.0069 27.0 10.0 70 22-100 24-95 (440)
91 cd04496 SSB_OBF SSB_OBF: A sub 37.8 28 0.0006 25.9 2.3 27 239-265 46-72 (100)
92 PRK00448 polC DNA polymerase I 37.2 1.5E+02 0.0034 33.8 8.7 40 159-198 227-270 (1437)
93 KOG4348 Adaptor protein CMS/SE 35.8 25 0.00053 34.5 2.0 43 242-287 269-311 (627)
94 PRK07772 single-stranded DNA-b 35.8 74 0.0016 27.6 4.9 74 21-94 4-90 (186)
95 cd02792 MopB_CT_Formate-Dh-Na- 34.5 47 0.001 25.8 3.2 16 251-266 45-60 (122)
96 PF11325 DUF3127: Domain of un 32.8 2.1E+02 0.0046 21.4 7.6 66 28-95 4-73 (84)
97 cd02778 MopB_CT_Thiosulfate-R- 31.4 55 0.0012 25.4 3.2 16 251-266 40-55 (123)
98 cd02790 MopB_CT_Formate-Dh_H F 30.6 55 0.0012 25.1 3.0 16 251-266 45-60 (116)
99 cd02779 MopB_CT_Arsenite-Ox Th 30.5 53 0.0012 25.5 2.9 16 251-266 43-58 (115)
100 KOG3416 Predicted nucleic acid 29.5 1E+02 0.0023 25.0 4.3 28 239-270 50-77 (134)
101 PF03100 CcmE: CcmE; InterPro 28.5 3.1E+02 0.0068 22.0 7.8 68 10-86 36-106 (131)
102 PRK07135 dnaE DNA polymerase I 28.5 1.3E+02 0.0029 32.8 6.2 65 12-84 890-954 (973)
103 cd02783 MopB_CT_2 The MopB_CT_ 28.3 62 0.0014 26.8 3.1 16 251-266 42-57 (156)
104 PF01568 Molydop_binding: Moly 28.2 78 0.0017 24.0 3.5 15 251-265 40-54 (110)
105 cd02786 MopB_CT_3 The MopB_CT_ 27.3 1E+02 0.0022 23.6 4.0 17 251-267 41-57 (116)
106 PRK06752 single-stranded DNA-b 26.1 2.1E+02 0.0045 22.2 5.6 72 23-94 4-84 (112)
107 cd04495 BRCA2DBD_OB3 BRCA2DBD_ 25.9 3.2E+02 0.0069 21.2 6.8 33 239-271 30-63 (100)
108 PRK05813 single-stranded DNA-b 25.9 2.9E+02 0.0063 24.5 7.0 72 23-95 111-185 (219)
109 cd04496 SSB_OBF SSB_OBF: A sub 24.4 1.6E+02 0.0034 21.6 4.5 71 24-95 1-82 (100)
110 cd04317 EcAspRS_like_N EcAspRS 24.1 3.7E+02 0.008 21.3 7.5 61 20-90 13-76 (135)
111 TIGR01405 polC_Gram_pos DNA po 24.0 3.3E+02 0.0072 30.6 8.4 62 165-264 5-69 (1213)
112 cd02780 MopB_CT_Tetrathionate_ 23.8 85 0.0018 25.4 3.1 16 251-266 40-55 (143)
113 PRK06751 single-stranded DNA-b 23.4 2.6E+02 0.0057 23.8 6.1 72 23-94 4-84 (173)
114 PF13567 DUF4131: Domain of un 22.8 3.8E+02 0.0083 21.1 7.5 69 21-94 75-146 (176)
115 PF15489 CTC1: CST, telomere m 22.8 1.1E+02 0.0023 33.8 4.2 51 239-290 889-940 (1144)
116 COG2332 CcmE Cytochrome c-type 22.8 3.6E+02 0.0079 22.6 6.5 57 19-84 49-105 (153)
117 PF04404 ERF: ERF superfamily; 22.3 57 0.0012 27.1 1.8 64 4-67 22-87 (160)
118 cd05790 S1_Rrp40 S1_Rrp40: Rrp 22.1 1.6E+02 0.0035 22.1 4.0 51 25-86 9-60 (86)
119 PRK07459 single-stranded DNA-b 21.3 2.7E+02 0.0059 22.1 5.5 72 23-94 5-81 (121)
120 PRK02801 primosomal replicatio 21.0 3.8E+02 0.0083 20.4 6.6 65 23-87 4-77 (101)
121 PRK07274 single-stranded DNA-b 20.8 2E+02 0.0042 23.2 4.6 70 23-92 4-82 (131)
122 PRK10917 ATP-dependent DNA hel 20.5 4.2E+02 0.0091 27.6 8.0 39 159-197 51-90 (681)
123 PRK06293 single-stranded DNA-b 20.4 2E+02 0.0044 24.3 4.7 72 23-94 3-80 (161)
124 PF10459 Peptidase_S46: Peptid 20.4 3.7E+02 0.008 28.3 7.5 79 171-264 148-247 (698)
125 TIGR00594 polc DNA-directed DN 20.2 2.3E+02 0.0049 31.2 6.2 43 20-65 980-1022(1022)
126 PRK08182 single-stranded DNA-b 20.2 1.9E+02 0.0042 23.9 4.5 73 22-94 3-91 (148)
No 1
>cd04497 hPOT1_OB1_like hPOT1_OB1_like: A subfamily of OB folds similar to the first OB fold (OB1) of human protection of telomeres 1 protein (hPOT1), the single OB fold of the N-terminal domain of Schizosaccharomyces pombe POT1 (SpPOT1), and the first OB fold of the N-terminal domain of the alpha subunit (OB1Nalpha) of Oxytricha nova telomere end binding protein (OnTEBP). POT1 proteins recognize single-stranded (ss) 3-prime ends of the telomere. A 3-prime ss overhang is conserved in ciliated protozoa, yeast, and mammals. SpPOT1 is essential for telomere maintenance. It binds specifically to the ss G-rich telomeric sequence (GGTTAC) of S. pombe. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. Deletion of the S. pombe pot1+ gene results in a rapid loss of telomere sequences, chromosome mis-segregation and chromosome circularization. hPOT1 is implicated in telomere length regulation. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB
Probab=100.00 E-value=3.7e-36 Score=248.78 Aligned_cols=137 Identities=33% Similarity=0.507 Sum_probs=129.8
Q ss_pred cceeehhhhhhccCCEEEEEEEEEecCCceecCCCceEEEEEEEeCCCC-CCCeEEEEecCCCCCCCCCCCCCCEEEEee
Q 022219 8 GGIVRIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQ-SPELLVNIFTSSIDQLPRVLSPRDLILLKN 86 (300)
Q Consensus 8 y~y~~l~~~~~~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~-~~gl~v~iF~~~~~~LP~v~~~GDII~l~r 86 (300)
|.|++|++|....++.|||||||+|+++|++++|+||+|+|+|+|+|.. +.||+|+||++++++||.+ ++||||+|||
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 7899999998888999999999999999999999999999999999997 7899999999999999999 8999999999
Q ss_pred EEEEEEcCeEEEEeecCceEEEEEeCCCCCCccccccCCCCcCCCHHHHHHHHHHHHhhh
Q 022219 87 VMIKKHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCV 146 (300)
Q Consensus 87 ~kv~~~~g~~~~~~~~~~ss~~vf~~~~~~~~~P~~~s~~~~~~~~~e~~~v~~Lr~W~~ 146 (300)
++|+.|+|+.+++++.+.|+||||++..+....|++.+. +++++++|+++++.||+|+.
T Consensus 80 ~kv~~~~g~~~~~~~~~~ss~avf~~~~~~~~~p~~~~~-~~~~~~~e~~~~~~Lr~w~~ 138 (138)
T cd04497 80 VKIQSYNGKPQGISNDRGSSWAVFRGDDGVVPIPQQSSK-PVEFGPEEEPSVEELRKWAS 138 (138)
T ss_pred EEEEEECCceEEEECCCceeEEEEcCCCCCCcCccccCC-CcccCcchHHHHHHHHHhhC
Confidence 999999999999999766999999999999988998877 59999999999999999973
No 2
>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=1.4e-35 Score=247.71 Aligned_cols=137 Identities=35% Similarity=0.617 Sum_probs=126.1
Q ss_pred eeehhhhhhccCCEEEEEEEEEecCCc--eecCCCceEEEEEEEeCCCCC-----CCeEEEEecCCCCCCCCCCCCCCEE
Q 022219 10 IVRIKELAMHVKHKVNLLGVVLEFSIP--RKSQGTDYVCVLKIVDDSQQS-----PELLVNIFTSSIDQLPRVLSPRDLI 82 (300)
Q Consensus 10 y~~l~~~~~~~~~~vnviGVVvd~~~P--~~trG~D~~~tl~I~D~S~~~-----~gl~v~iF~~~~~~LP~v~~~GDII 82 (300)
|++|+++.+..++.|||||||+++++| ++|||+||+|+|+|+|+|+.. .||+|+||+++++.||.+..+||||
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 7999999999999999997779999
Q ss_pred EEeeEEEEEEcCeEEEEeecC-ceEEEEE-eCCCCCCccccccCCCCcCCCHHHHHHHHHHHHhhh
Q 022219 83 LLKNVMIKKHQAELSAVFYKD-SSSFALF-DGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCV 146 (300)
Q Consensus 83 ~l~r~kv~~~~g~~~~~~~~~-~ss~~vf-~~~~~~~~~P~~~s~~~~~~~~~e~~~v~~Lr~W~~ 146 (300)
+|||+||+.|+|+++++++.. .++|+|| ++..+.++.|++.++++++++++|+++++.||+|++
T Consensus 81 ~l~r~kv~~~~~~~~~~~~~~~~ss~~vf~~~~~~~~~~p~~~s~~~~~~~~~e~~~~~~Lr~w~~ 146 (146)
T PF02765_consen 81 RLRRVKVQSYNGKPQGLSNSTSNSSWAVFSSGGSGAPFEPYQKSSNPFEFSDEEKKYVESLRKWAQ 146 (146)
T ss_dssp EEEEEEEEEETTEEEEEEECECTEEEEEECTSSTTTCCCSSCESTSSTT-HHHHHHHHHHHHHHH-
T ss_pred EEEEEEEEEECCEEEEEecCCCcEEEEEEecCCCCCCccccccCCCccCCCHHHHHHHHHHHHhhC
Confidence 999999999999999998754 6999999 888889999988887679999999999999999974
No 3
>KOG4757 consensus Predicted telomere binding protein [General function prediction only]
Probab=100.00 E-value=1.6e-34 Score=267.65 Aligned_cols=266 Identities=26% Similarity=0.328 Sum_probs=198.8
Q ss_pred CCCCCcceeehhhhhhccCCEEEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEE
Q 022219 3 SQRNQGGIVRIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLI 82 (300)
Q Consensus 3 ~~~~~y~y~~l~~~~~~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII 82 (300)
..++.|.|..++++....|+.||+||||++|+||++++|+||+||++|+|+...+.||+|++|+++-++||.|+++||||
T Consensus 2 ~~~ds~k~Iri~da~kk~~tiVNl~GiVkef~pp~qs~g~D~~~tv~IvDp~~ss~gLtv~lfSkt~edLP~Ik~~GDii 81 (522)
T KOG4757|consen 2 DVRDSLKLIRISDALKKKNTIVNLIGIVKEFTPPRQSLGKDWVCTVYIVDPDYSSIGLTVHLFSKTGEDLPVIKQVGDII 81 (522)
T ss_pred CcccchheeechHHHHhcCcEEEEEEEEEeccChhhccCCceEEEEEEeCCCCCCCCcEEEEecCchhhCccccccCcEE
Confidence 45788999999999988999999999999999999999999999999999988889999999999999999999999999
Q ss_pred EEeeEEEEEEcCeEEEEeecCc-eEEEEEeCCCCCCccccccCCCCcCCCHHHHHHHHHHHHhhhcCccccCCccccccc
Q 022219 83 LLKNVMIKKHQAELSAVFYKDS-SSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSL 161 (300)
Q Consensus 83 ~l~r~kv~~~~g~~~~~~~~~~-ss~~vf~~~~~~~~~P~~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~~~~~L 161 (300)
+|||+|+|.|+.+.+|+++..+ |+|++|+|+ +.+..|||+|+. |-++ ..||+|++.+.....+ .+ ..+
T Consensus 82 llhRiKiq~y~~rtqgl~s~~fss~~~~Feg~-svd~i~~qssp~-f~~t-------~nlrew~a~~~s~~w~-c~-t~~ 150 (522)
T KOG4757|consen 82 LLHRIKIQSYRDRTQGLCSDQFSSAWALFEGN-SVDTICYQSSPR-FMKT-------GNLREWFALYKSKIWD-CQ-TNL 150 (522)
T ss_pred EEEEEEEEEhhhhhhhhhhcchhhhhhhhcCC-CCCccCCCCchh-hhcc-------chHHHHHHHHhCcccc-cc-cCH
Confidence 9999999999999999999766 468999999 888899999985 7776 7899999877654443 23 445
Q ss_pred ccccCCceEeEEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCcc-cCCCCCCcccCCCCChhhhhcCCCcccEEE
Q 022219 162 KDISEHRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDE-EHNPLPLHIESSPLDLETLRNFFPVGTVLR 240 (300)
Q Consensus 162 ~di~~~~f~Dl~~qVv~~~~~~~~~~~~L~VwDgT~n~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~p~~G~~l~ 240 (300)
.++.++.--.|.||+++.. ......|. .|||-|.+-..++++-..-. -+.-.|++++. .|...+..||..|.+..
T Consensus 151 ~k~fel~cs~l~~q~v~g~-s~~~~~w~-lv~d~~~h~~~s~~~~~~~~~ySlr~~l~~~~--~~T~~~l~Fp~~g~ts~ 226 (522)
T KOG4757|consen 151 HKNFELLCSSLARQNVTGL-SYPSVSWS-LVSDITPHQRCSFYAQVIKTWYSLRNPLLYVT--DPTENLLFFPMSGYTSS 226 (522)
T ss_pred hHhhhhhcchhhhheeecc-ccccceee-eeecccccccccccccceeeEeeccccccccc--CchHhhhhcccCCceee
Confidence 5555555555556677665 43445666 68886644444333321100 01112455554 45556667775554322
Q ss_pred EE------------ecCchhhhhhcCCCCCcEEEEeccEEEe-eCcEEEEEEeeCC
Q 022219 241 VS------------TDRSYENFGRYFTATGKWVRIRNMSCQV-SSGMWHGLLQSSS 283 (300)
Q Consensus 241 V~------------~~~~~~~~~~~~lk~G~wv~l~Nv~~k~-~~g~leg~l~~~s 283 (300)
.. +|..+..+.++..+.||.+.-.|++++. +-|+.+..+++++
T Consensus 227 ~r~~rv~~e~~i~ilq~~~d~~~~Nl~~e~D~~f~~~~~sl~dh~~lsrc~~~~~s 282 (522)
T KOG4757|consen 227 SRWDRVSEEFSICILQDEHDFYCRNLIKEGDYVFMKNVRSLIDHLGLSRCILHGDS 282 (522)
T ss_pred eeeecccccccchhccccchhhhhhhcccccccccccchhhhHHHHHHHHHHHhhc
Confidence 21 2333444568888999999999998876 4566665555554
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=99.89 E-value=6.4e-23 Score=164.41 Aligned_cols=102 Identities=25% Similarity=0.397 Sum_probs=78.8
Q ss_pred eEeEEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCChhhhhcCC-Cccc-EEEEEecCc
Q 022219 169 YFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFF-PVGT-VLRVSTDRS 246 (300)
Q Consensus 169 f~Dl~~qVv~~~~~~~~~~~~L~VwDgT~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p-~~G~-~l~V~~~~~ 246 (300)
||||+||||+++ +.++++++|||||||+||+..+....++. ...+++ +...+.|+ | |. +++|++|++
T Consensus 1 ~~DLvcqVv~v~-~~d~~~~~L~VwDgT~~p~~~~~~~~~~~------~~~e~d---~~~k~~~~gp-g~~ti~It~yD~ 69 (123)
T cd04498 1 YFDLLCQLLSVV-ETDSSSTLLKVWDGTKFPPPLRKVKVEDD------VVLEGD---RSLKHREEGG-KQLTIDILVYDN 69 (123)
T ss_pred CccEEEEEEEEE-EecCCeEEEEEecCCCCChhHhheecccc------Cccccc---hhhhhhccCC-CeEEEEEEEEcc
Confidence 799999999999 76788999999999999776665544332 122332 33346677 5 74 899998888
Q ss_pred hhhhhhcCCCCCcEEEEeccEEEeeCc--------EEEEEE-eeC
Q 022219 247 YENFGRYFTATGKWVRIRNMSCQVSSG--------MWHGLL-QSS 282 (300)
Q Consensus 247 ~~~~~~~~lk~G~wv~l~Nv~~k~~~g--------~leg~l-~~~ 282 (300)
|+.++++ ||+||||+|+|||+|.... .|||.+ +.-
T Consensus 70 H~~~ar~-lK~GdfV~L~NVhiK~~~~~~~~~~~~~Le~~l~~gg 113 (123)
T cd04498 70 HVELAKS-LKPGDFVRIYNVHAKSYSSKNEHDENDHLHFHLVHGG 113 (123)
T ss_pred hHHHHhh-CCCCCEEEEEEEEEEeccCCcccCCcceEEEEEccCc
Confidence 8888777 9999999999999998422 689998 544
No 5
>PRK07211 replication factor A; Reviewed
Probab=99.01 E-value=9.2e-09 Score=100.43 Aligned_cols=204 Identities=15% Similarity=0.181 Sum_probs=147.0
Q ss_pred cceeehhhhhhccCCEEEEEEEEEecCCcee---cCC-CceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEE
Q 022219 8 GGIVRIKELAMHVKHKVNLLGVVLEFSIPRK---SQG-TDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLIL 83 (300)
Q Consensus 8 y~y~~l~~~~~~~~~~vnviGVVvd~~~P~~---trG-~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~ 83 (300)
..+.+|++|.. ....++|+|+|+...+++. .+| .-.+.++.|.|+|- . |++++|.+..+.++.+ .+||||.
T Consensus 159 ~~~~~I~dL~~-~~~~v~I~grV~~v~~iRtf~r~dGseGkv~sv~L~DeTG-~--IR~TlW~d~Ad~~~~l-e~G~Vv~ 233 (485)
T PRK07211 159 GDTYTVEDLSL-GLSDVTLVGVVLDTDSVRTFDRDDGSEGRVSNLTVGDETG-R--VRVTLWDDRADLAEEL-DAGESVE 233 (485)
T ss_pred cCCccHHHcCC-CCCceEEEEEEEEcCCCeEEECCCCCeeEEEEEEEEcCCC-e--EEEEEechhhhhhccC-CCCCEEE
Confidence 47789999963 3456999999999998754 235 45678899999876 2 9999999887888878 7999999
Q ss_pred EeeEEEEEEcCeEEEEeecCceEEEEEeCCCCCCccccccCCCCcCCCHHHHHHHHHHHHhhhcCccccCCccccccccc
Q 022219 84 LKNVMIKKHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSLKD 163 (300)
Q Consensus 84 l~r~kv~~~~g~~~~~~~~~~ss~~vf~~~~~~~~~P~~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~~~~~L~d 163 (300)
+.+++++.++|.+.+..+.. +...-.+ .... +.+ .+ ..|.+
T Consensus 234 I~~a~Vre~~g~~ELsl~~~-s~I~~~~--dev~----------~vp-------------------------~~-~~I~d 274 (485)
T PRK07211 234 IVDGYVRERDGSLELHVGDR-GAVEEVD--EDVE----------YVP-------------------------DT-TPIES 274 (485)
T ss_pred EEeeEEEecCCcEEEEECCC-ceEEECC--cccc----------ccc-------------------------cc-ccHhh
Confidence 99999999999888876533 3333110 0000 000 12 46888
Q ss_pred ccCCceEeEEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCChhhhhcCCCcccEEEEEe
Q 022219 164 ISEHRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRVST 243 (300)
Q Consensus 164 i~~~~f~Dl~~qVv~~~~~~~~~~~~L~VwDgT~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~G~~l~V~~ 243 (300)
+.++..+|+++.|+.+. + ..++-=-||+......+.. .| --| .++|++
T Consensus 275 l~~g~~vdV~GvV~~v~-~----~rtf~r~dG~~~~vr~l~l--~D------------------------~TG-~IrvTL 322 (485)
T PRK07211 275 LEIDETVDIAGVVRSAD-P----KRTFDRDDGSEGQVRNVRI--QD------------------------DTG-DIRVAL 322 (485)
T ss_pred cCCCCceeEEEEEEEcc-C----cEEEEcCCCCEeEEEEEEE--Ec------------------------CCC-cEEEEE
Confidence 89999999999999887 3 2233223455322211110 00 012 478999
Q ss_pred cCchhhhhhcCCCCCcEEEEeccEEEee-CcEEEEEEeeCCceEEcCC
Q 022219 244 DRSYENFGRYFTATGKWVRIRNMSCQVS-SGMWHGLLQSSSKIRLFSD 290 (300)
Q Consensus 244 ~~~~~~~~~~~lk~G~wv~l~Nv~~k~~-~g~leg~l~~~sk~~~l~~ 290 (300)
|..++.+ .+.+|+.|+|+|++++-. .|-+|..+...|.|.+|+.
T Consensus 323 Wg~~A~~---~i~~GdvV~Ikg~~V~dg~~ggleLS~g~~s~i~~~~~ 367 (485)
T PRK07211 323 WGEKADL---DIGPGDEVVAADVEIQDGWQDDLEASAGWQSTVVVLDD 367 (485)
T ss_pred eCccccC---CCCCCCEEEEEccEEEecCCCCEEEEecCCceEEEccc
Confidence 9998843 699999999999999986 4889999999999999977
No 6
>PRK12366 replication factor A; Reviewed
Probab=98.90 E-value=3.6e-07 Score=93.13 Aligned_cols=210 Identities=15% Similarity=0.162 Sum_probs=143.9
Q ss_pred CCcceeehhhhhhc-cCCEEEEEEEEEecCCcee---cCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCE
Q 022219 6 NQGGIVRIKELAMH-VKHKVNLLGVVLEFSIPRK---SQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDL 81 (300)
Q Consensus 6 ~~y~y~~l~~~~~~-~~~~vnviGVVvd~~~P~~---trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDI 81 (300)
..+.+++|++|... .+..+++-|-|+...+++. .+|+--..++.|.|.+- .+.+++|.+..+.+..+ .+||+
T Consensus 275 ~~~~~~pI~~L~~~~~g~~~~I~grV~~~~~~R~f~~~~g~gkv~s~~l~D~tG---~IR~t~w~~~~d~~~~l-~~G~v 350 (637)
T PRK12366 275 KELEIVNIEELTEFEDGEEVDVKGRIIAISDKREVERDDRTAEVQDIELADGTG---RVRVSFWGEKAKILENL-KEGDA 350 (637)
T ss_pred cccCceeHHHCCcccCCCEEEEEEEEEecCCceEEEcCCCcEEEEEEEEEcCCC---eEEEEEeCchhhhhccc-CCCCE
Confidence 45678999999754 5568999999999987755 36788999999999872 39999999877778877 69999
Q ss_pred EEEeeEEEEEEcC-----eEEEEeecCceEEEEEeCCCCCCccccccCCCCcCCCHHHHHHHHHHHHhhhcCccccCCcc
Q 022219 82 ILLKNVMIKKHQA-----ELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSND 156 (300)
Q Consensus 82 I~l~r~kv~~~~g-----~~~~~~~~~~ss~~vf~~~~~~~~~P~~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~ 156 (300)
+.+.+++++.|+. ++.+.++.. |.... + .... .| ..+..
T Consensus 351 y~is~~~vk~y~~~~~~~~~El~~~~~-s~I~~-d--~~~~-~p-------------------------------~~~~~ 394 (637)
T PRK12366 351 VKIENCKVRTYYDNEGEKRVDLNAGYS-SEIIK-D--ESIS-FE-------------------------------EIEEK 394 (637)
T ss_pred EEEecCEEeeccccCCCcCEEEEcCCc-eEEEe-c--cCCc-cc-------------------------------ceeec
Confidence 9999999998863 233444322 33332 1 1000 01 00112
Q ss_pred ccccccccc----CCceEeEEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCChhhhhcC
Q 022219 157 YLLSLKDIS----EHRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNF 232 (300)
Q Consensus 157 ~~~~L~di~----~~~f~Dl~~qVv~~~~~~~~~~~~L~VwDgT~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 232 (300)
| ..|+||. .+..+|+++.|+.+. + -..++ . -||+...-.. ....| .
T Consensus 395 ~-~~i~dI~~~~~~~~~VdVig~V~~v~-~--~~~i~-~-k~G~~~~~r~--i~l~D--------------------~-- 444 (637)
T PRK12366 395 I-YKIKDILNLEEDDNDITVIARVVEDY-P--VNEFE-R-SDGSKGKVRN--IELAD--------------------G-- 444 (637)
T ss_pred c-ccHHHhhcccCCCcEEEEEEEEEEcc-C--ceEEE-e-cCCCEeEEEE--EEEEe--------------------C--
Confidence 3 4555553 578999999999988 4 11221 1 2444322110 10000 0
Q ss_pred CCcccEEEEEecCchhhhhhcCCCCCcEEEEeccEEEeeCcEEEEEEeeCCceEEcCCC
Q 022219 233 FPVGTVLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDN 291 (300)
Q Consensus 233 p~~G~~l~V~~~~~~~~~~~~~lk~G~wv~l~Nv~~k~~~g~leg~l~~~sk~~~l~~~ 291 (300)
-| .+++++|..++.+ .+.+|+.|.|+|+.++..+|.++-.+..+|++...++.
T Consensus 445 --TG-~I~vtlWg~~a~~---~~~~G~vi~i~~~~V~~~~g~~~Ls~~~~s~i~~~p~~ 497 (637)
T PRK12366 445 --TG-SIRLTLWDDDAEI---EIKEGDAIKILHPYVKENGDYLDLSIGRYGRIEINPEG 497 (637)
T ss_pred --CC-EEEEEEecccccc---CCCCCCEEEEEeeEEEeCCCeeEEEecCcceEEECCCC
Confidence 12 4789999987742 58899999999999999999999999999999876643
No 7
>PRK15491 replication factor A; Provisional
Probab=98.88 E-value=2.1e-07 Score=89.02 Aligned_cols=205 Identities=16% Similarity=0.187 Sum_probs=142.9
Q ss_pred CCcceeehhhhhhccCCEEEEEEEEEecCCceec---CCC-ceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCE
Q 022219 6 NQGGIVRIKELAMHVKHKVNLLGVVLEFSIPRKS---QGT-DYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDL 81 (300)
Q Consensus 6 ~~y~y~~l~~~~~~~~~~vnviGVVvd~~~P~~t---rG~-D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDI 81 (300)
.+|.+++|+++.. ....|++.|.|++..+++.= +|+ -...++.|.|+|- . +++++|.+..+.++.+ .+||+
T Consensus 162 ~~~~~~~I~dl~~-~~~~V~I~g~V~~~~~~r~~~~~~G~~~~v~~~~l~DetG-~--Ir~t~W~~~a~~~~~l-~~Gd~ 236 (374)
T PRK15491 162 ASINSQKISDIKD-GDSDINIVGKVLDISDVRTFQKKDGSQGRVRNITIGDETG-K--IRVTLWDGKTDLADKL-ENGDS 236 (374)
T ss_pred cccCcccHHHcCC-CCccEEEEEEEEEccCceEEEecCCCeEEEEEEEEECCCC-e--EEEEEecchhcccccC-CCCCE
Confidence 4567789999963 23459999999999887542 355 4788899999865 2 9999999876777777 79999
Q ss_pred EEEeeEEEE--EEcCeEEEEeecCceEEEEEeCCCCCCccccccCCCCcCCCHHHHHHHHHHHHhhhcCccccCCccccc
Q 022219 82 ILLKNVMIK--KHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLL 159 (300)
Q Consensus 82 I~l~r~kv~--~~~g~~~~~~~~~~ss~~vf~~~~~~~~~P~~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~~~~ 159 (300)
|.+.+..++ .|+|++.+..+.. +... ..+. . + . +. ..| .
T Consensus 237 V~i~~~~~r~~~~~g~~El~~~~~-s~I~--~~~~--~--~-----e-~~-------------------------~~f-~ 277 (374)
T PRK15491 237 VEIINGYARTNNYSQEVEIQIGNH-GSLR--KTDR--N--V-----E-YE-------------------------EDF-T 277 (374)
T ss_pred EEEEeceEEEeccCCCEEEEeCCC-ceEE--ECCc--c--c-----c-cC-------------------------CCc-c
Confidence 999997655 5678888877644 4433 1110 0 0 0 10 125 6
Q ss_pred ccccccCCceEeEEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCChhhhhcCCCcccEE
Q 022219 160 SLKDISEHRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVL 239 (300)
Q Consensus 160 ~L~di~~~~f~Dl~~qVv~~~~~~~~~~~~L~VwDgT~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~G~~l 239 (300)
.|.||+++..+|+++.|..+. + .-++--.||+......+.. .| + -|+ +
T Consensus 278 ~I~dl~~~~~~dv~G~V~~v~-~----~~~~~~~~G~~~~~r~i~l--~D----------~--------------Tg~-I 325 (374)
T PRK15491 278 PIADIIPGQPYSIKGAVSGLG-D----LKEFTKSDGSENKVSNIYV--SD----------D--------------TGR-I 325 (374)
T ss_pred CHHHcCCCCceeEEEEEEEcC-C----cEEEEccCCCEeEEEeEEE--Ee----------C--------------CCc-E
Confidence 788998999999999999886 2 2222235666432211111 00 0 122 7
Q ss_pred EEEecCchhhhhhcCCCCCcEEEEeccEEEee-CcEEEEEEeeCCceEE
Q 022219 240 RVSTDRSYENFGRYFTATGKWVRIRNMSCQVS-SGMWHGLLQSSSKIRL 287 (300)
Q Consensus 240 ~V~~~~~~~~~~~~~lk~G~wv~l~Nv~~k~~-~g~leg~l~~~sk~~~ 287 (300)
++++|..++.. ...+-+|+.|++.+..+|.. +|.+|......|+|..
T Consensus 326 r~tlWg~~a~~-~~~~~~g~~i~i~~~~~k~g~~~~~e~s~g~~s~~~~ 373 (374)
T PRK15491 326 RIALWGEKAEL-VDKLDIDTPIKIIDAFSKSGYNEDVELSAGNRSRVVV 373 (374)
T ss_pred EEEEccccccc-ccccCCCCeEEEEEEEEeecCCCcEEEEeCCcceEEe
Confidence 89999988864 44578889999999999996 6999999999998853
No 8
>PRK07218 replication factor A; Provisional
Probab=98.86 E-value=7.1e-07 Score=86.34 Aligned_cols=196 Identities=18% Similarity=0.248 Sum_probs=136.7
Q ss_pred eeehhhhhhccCCEEEEEEEEEecCCce-ecCC-CceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeE
Q 022219 10 IVRIKELAMHVKHKVNLLGVVLEFSIPR-KSQG-TDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNV 87 (300)
Q Consensus 10 y~~l~~~~~~~~~~vnviGVVvd~~~P~-~trG-~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~r~ 87 (300)
-+.|+|+... ...|++.|-|++...+. +..| .-...++.|.|+|=. +++.++.+ ++ + .+||+|+|.|+
T Consensus 58 ~~kI~Di~~~-~~~V~v~~kVl~i~~rt~r~dg~~g~v~~~~igDeTG~---Ir~tlW~~----~~-l-~~Gdvv~I~na 127 (423)
T PRK07218 58 SKDIKELSTD-DKNVTVTGRVLTIGERSIRYQGDDHVIYEGILADETGT---ISYTAWKD----FG-L-SPGDTVTIGNA 127 (423)
T ss_pred CccHhhCCCC-CceeEEEEEEEEecceeEecCCCceEEEEEEEECCCCe---EEEEEECC----CC-C-CCCCEEEEecc
Confidence 4568888633 46799999999986531 2234 367788899998652 89999983 23 6 79999999999
Q ss_pred EEEEEcCeEEEEeecCceEEEEEeCCCCCCccccccCCCCcCCCHHHHHHHHHHHHhhhcCccccCCcccccccccccCC
Q 022219 88 MIKKHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSLKDISEH 167 (300)
Q Consensus 88 kv~~~~g~~~~~~~~~~ss~~vf~~~~~~~~~P~~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~~~~~L~di~~~ 167 (300)
.++.|+|++.+..+.. +....-+.. ..| +++ . . .. ..|.|++++
T Consensus 128 ~vre~~g~~el~ig~~-t~I~~~de~----~~~------~~~-----------~-----------~--~~-~kI~DL~~g 171 (423)
T PRK07218 128 GVREWDGRPELNIGES-TTVSLLDDS----SLP------PYS-----------I-----------G--GD-KKLIDLGPG 171 (423)
T ss_pred EeeccCCceEEeccCc-ceEEEcCcc----ccc------Ccc-----------c-----------c--Cc-cchhhccCC
Confidence 9999999999877654 555532221 111 010 0 0 12 568899865
Q ss_pred c-eEeEEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCChhhhhcCCCccc-EEEEEecC
Q 022219 168 R-YFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGT-VLRVSTDR 245 (300)
Q Consensus 168 ~-f~Dl~~qVv~~~~~~~~~~~~L~VwDgT~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~G~-~l~V~~~~ 245 (300)
. .+++.++|+.++ + + .+..-||+. - .......| + | .+++++|.
T Consensus 172 ~~~V~v~g~Vl~~~-~----r-~f~~~dg~~--~-v~~giigD----------e----------------TG~Ir~tlW~ 216 (423)
T PRK07218 172 DRGVNVEARVLELE-H----R-EIDGRDGET--T-ILSGVLAD----------E----------------TGRLPFTDWD 216 (423)
T ss_pred CCceEEEEEEEEec-c----e-eEEcCCCCe--E-EEEEEEEC----------C----------------CceEEEEEec
Confidence 4 589999999885 3 2 333455542 1 11111111 0 1 47899998
Q ss_pred chhhhhhcCCCCCcEEEEeccEEEeeCcEEEEEEeeCCceEEcCCC
Q 022219 246 SYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDN 291 (300)
Q Consensus 246 ~~~~~~~~~lk~G~wv~l~Nv~~k~~~g~leg~l~~~sk~~~l~~~ 291 (300)
.++ .+.+|++|+|.|..++..+|.++-.+...+.|..++.+
T Consensus 217 ~~~-----~l~~Gd~v~I~na~v~e~~G~~elnv~~~t~I~~~d~~ 257 (423)
T PRK07218 217 PLP-----EIEIGASIRIEDAYVREFRGVPSVNVSEFTTVEALDRE 257 (423)
T ss_pred ccc-----cCCCCCEEEEeeeEEeccCCeEEEEECCceEEEECCCC
Confidence 754 48999999999999999999999999999999988754
No 9
>PRK12366 replication factor A; Reviewed
Probab=98.67 E-value=2.7e-06 Score=86.72 Aligned_cols=205 Identities=14% Similarity=0.175 Sum_probs=139.1
Q ss_pred cceeehhhhhhccCC-EEEEEEEEEecCCceec---CC-CceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEE
Q 022219 8 GGIVRIKELAMHVKH-KVNLLGVVLEFSIPRKS---QG-TDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLI 82 (300)
Q Consensus 8 y~y~~l~~~~~~~~~-~vnviGVVvd~~~P~~t---rG-~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII 82 (300)
-.+++|++|. +++ .+++.|-|+...+|+.- +| .-..+++.|.|+|- .+.+.+|.+..+.+|.+ .+|||+
T Consensus 61 ~~~~~I~dl~--p~~~~v~i~arV~~~~~~r~~~~~~G~eGkv~~~~v~DetG---~Ir~t~W~~~~~~~~~l-e~G~v~ 134 (637)
T PRK12366 61 EEDFKISDIE--EGQINVEITGRIIEISNIKTFTRKDGSTGKLANITIADNTG---TIRLTLWNDNAKLLKGL-KEGDVI 134 (637)
T ss_pred cceeEHHHCc--CCCcceEEEEEEEEccCCeEEECCCCCccEEEEEEEEcCCC---EEEEEEEchhhhhhccC-CCCCEE
Confidence 3578999997 444 59999999999888742 35 46789999999875 39999999877778888 799999
Q ss_pred EEeeEEEEEEcCeEEEEeecCceEEEEEeCCCCCCccccccCCCCcCCCHHHHHHHHHHHHhhhcCccccCCcccccccc
Q 022219 83 LLKNVMIKKHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSLK 162 (300)
Q Consensus 83 ~l~r~kv~~~~g~~~~~~~~~~ss~~vf~~~~~~~~~P~~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~~~~~L~ 162 (300)
.+.++.++.|+|++.+..+.. ++....+... ....|. . ...+ .|+
T Consensus 135 ~i~~~~v~~~~~~~el~~~~~-t~I~~~~~~d-~~~i~~----------~---------------------~~~~--~I~ 179 (637)
T PRK12366 135 KIENARSRKWNNDVELNSGSE-TRIDKLEKYD-ESRYPI----------I---------------------KENY--DIP 179 (637)
T ss_pred EEeccEecccCCceEEEcCCc-ceEEEccccc-cccCCc----------c---------------------cccc--ccc
Confidence 999999999999988766544 4444222100 000110 0 0013 588
Q ss_pred cccCCceEeEEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCChhhhhcCCCcccEEEEE
Q 022219 163 DISEHRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRVS 242 (300)
Q Consensus 163 di~~~~f~Dl~~qVv~~~~~~~~~~~~L~VwDgT~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~G~~l~V~ 242 (300)
||+++.++|+++.|+.+. + -..++ --||+.-.... ....| . -| .++|+
T Consensus 180 el~~g~~v~v~G~V~~~~-~--~~~f~--rkdg~~~~~r~--~~l~D--------------------~----TG-~irvT 227 (637)
T PRK12366 180 ELEPNLSATIEGEVTKAY-P--IKEFT--RKDGSEGKLKS--FILKD--------------------D----TG-SIRVT 227 (637)
T ss_pred ccCCCCeEEEEEEEEEcc-C--cEEEE--EcCCCeeEEEE--EEEEc--------------------C----CC-cEEEE
Confidence 889999999999999998 4 12222 11555322211 10000 0 12 47899
Q ss_pred ecCchhhhhhcCCCCCcEEEEeccEEEeeCcEEEEEEeeCCceEEc
Q 022219 243 TDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLF 288 (300)
Q Consensus 243 ~~~~~~~~~~~~lk~G~wv~l~Nv~~k~~~g~leg~l~~~sk~~~l 288 (300)
+|...+. ..+.+|+.|+|.+....-.+|.+|-.+...+.+...
T Consensus 228 lW~~~a~---~~~~~g~vv~i~g~~~~~~~~~~el~~~~~~~i~~~ 270 (637)
T PRK12366 228 LWNDLTD---IEVNKGDIVRVKGYVKQGYRTGLEISANNIEILEKL 270 (637)
T ss_pred EEChhhc---ccCCCCCEEEEEeEEecCcCCceEEEeCCceeeccc
Confidence 9998774 358999999999833333457888888766666544
No 10
>PRK14699 replication factor A; Provisional
Probab=98.65 E-value=4e-06 Score=82.63 Aligned_cols=204 Identities=13% Similarity=0.144 Sum_probs=142.7
Q ss_pred cceeehhhhhhccCCEEEEEEEEEecCCcee---cCC-CceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEE
Q 022219 8 GGIVRIKELAMHVKHKVNLLGVVLEFSIPRK---SQG-TDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLIL 83 (300)
Q Consensus 8 y~y~~l~~~~~~~~~~vnviGVVvd~~~P~~---trG-~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~ 83 (300)
..+++|.++.. ....+++.|.|++..+++. .+| ......+.|.|+|=. +++.+|.+..+.++.+ ..||+|.
T Consensus 274 ~~~~~I~~L~~-~~~~v~I~grV~~~~~~r~~~~~~Gseg~v~~~~l~DeTG~---Ir~T~W~~~a~~~~~i-~~Gd~v~ 348 (484)
T PRK14699 274 EEFTPIEDIKA-DMNNINISGRVLDISEVRTFEKKDGSPGRVGNLLLGDSTGK---IRLTLWDEKTNFLDEI-DFDETVE 348 (484)
T ss_pred ccccCHHHcCC-CCceeEEEEEEEEcCCCeEEEcCCCCeeEEEEEEEECCCCe---EEEEEeCccccccccc-CCCceEE
Confidence 35678888863 3467999999999988754 246 467788999999762 9999999877777877 7999999
Q ss_pred EeeEEEEEE--cCeEEEEeecCceEEEEEeCCCCCCccccccCCCCcCCCHHHHHHHHHHHHhhhcCccccCCccccccc
Q 022219 84 LKNVMIKKH--QAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSL 161 (300)
Q Consensus 84 l~r~kv~~~--~g~~~~~~~~~~ss~~vf~~~~~~~~~P~~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~~~~~L 161 (300)
+.++.++.. ++...+..... +.. ..... +.++ ..+| +.|
T Consensus 349 i~~~y~~~~~~~~~~eL~~~~~-t~I---~~~~~------------------~~e~----------------~~~~-~~I 389 (484)
T PRK14699 349 VLNAYSRENTFSQQVELNLGAR-GII---QKSEK------------------KVEY----------------REKF-TDI 389 (484)
T ss_pred EEeEEEEeccCCccEEEEecCc-eeE---eecCC------------------ccee----------------eecc-ccH
Confidence 999998833 45566666643 311 11100 0000 0136 789
Q ss_pred ccccCCceEeEEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCChhhhhcCCCcccEEEE
Q 022219 162 KDISEHRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRV 241 (300)
Q Consensus 162 ~di~~~~f~Dl~~qVv~~~~~~~~~~~~L~VwDgT~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~G~~l~V 241 (300)
.||++++.+|+++.|..+. +. ..+. --||+.-.-.. ....| --| .++|
T Consensus 390 ~die~~~~vdV~G~V~~v~-~~--~~~~--~~~g~~~~vr~--i~l~D------------------------~TG-~Ir~ 437 (484)
T PRK14699 390 ADIIPGESYSVQGKVSEIG-EL--REFE--REDGTENVVAN--LQLKD------------------------ETG-SIRL 437 (484)
T ss_pred HHccCCCeeEEEEEEEEcC-Cc--ceEE--ecCCCEEEEEE--EEEEc------------------------CCC-eEEE
Confidence 9999999999999999887 31 2222 24444211111 10000 012 5789
Q ss_pred EecCchhhhhhcCCCCCcEEEEeccEEEee-CcEEEEEEeeCCceEEc
Q 022219 242 STDRSYENFGRYFTATGKWVRIRNMSCQVS-SGMWHGLLQSSSKIRLF 288 (300)
Q Consensus 242 ~~~~~~~~~~~~~lk~G~wv~l~Nv~~k~~-~g~leg~l~~~sk~~~l 288 (300)
++|...|. ..+.+.+|+-|.+.|..++.. +|.+|..+...|+|..|
T Consensus 438 tlWg~~A~-~~~~~~~~~~v~~~~~~~~~g~~~~~e~s~g~~s~~~~~ 484 (484)
T PRK14699 438 TLWGEQAY-VIEDLDIDSEIQIIDAYARYGLNEEIELSVGNRSRVIIL 484 (484)
T ss_pred EEcchhhh-hccccCCCCeEEEechhhhhcccccEEEEecCceEEEeC
Confidence 99998875 356899999999999999996 78999999999998664
No 11
>PRK06386 replication factor A; Reviewed
Probab=98.65 E-value=1.5e-05 Score=75.59 Aligned_cols=193 Identities=20% Similarity=0.268 Sum_probs=127.5
Q ss_pred eehhhhhhccCCEEEEEEEEEecCCc-eecC-CCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEE
Q 022219 11 VRIKELAMHVKHKVNLLGVVLEFSIP-RKSQ-GTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVM 88 (300)
Q Consensus 11 ~~l~~~~~~~~~~vnviGVVvd~~~P-~~tr-G~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~r~k 88 (300)
+.|+|+.. .+..||+.|-|++.... .+.+ |.--..+-.|-|+|= . +++.+..+ .|.+ ..||+|+|+|++
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----PDAV-KSGDVIEIKYCY 73 (358)
T ss_pred cchhhcCC-CCCcEEEEEEEEEccceEEecCCCCeEEEEEEEECCcc-e--EEEEecCC----cccC-CCCCEEEEEeEE
Confidence 36778862 24569999999999732 1233 333333445777754 2 77887763 4667 689999999999
Q ss_pred EEEEcCeEEEEeecCceEEEEEeCCCCCCccccccCCCCcCCCHHHHHHHHHHHHhhhcCccccCCcccccccccccCC-
Q 022219 89 IKKHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSLKDISEH- 167 (300)
Q Consensus 89 v~~~~g~~~~~~~~~~ss~~vf~~~~~~~~~P~~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~~~~~L~di~~~- 167 (300)
++.|+|++.+..+.. +.... ..+ ... ...+. . +. ..|+||+++
T Consensus 74 v~~~~G~~~Lnv~~~-t~v~~-~~d--~~i----------ev~~~------------------~---~~-~KI~DL~~g~ 117 (358)
T PRK06386 74 SKEYNGKIRIYFDSR-SEVML-KPD--ENI----------EVKRT------------------Y---KL-VKIRDLSLVT 117 (358)
T ss_pred EeeECCEEEEEEcCc-eEEEe-cCc--ccc----------ccccc------------------c---Cc-cEeEeccCCC
Confidence 999999998877643 43320 111 110 00000 0 13 679999875
Q ss_pred ceEeEEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCChhhhhcCCCccc-EEEEEecCc
Q 022219 168 RYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGT-VLRVSTDRS 246 (300)
Q Consensus 168 ~f~Dl~~qVv~~~~~~~~~~~~L~VwDgT~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~G~-~l~V~~~~~ 246 (300)
.++++.++|+.++ + . ..- .||+. .........| + | .+++++|..
T Consensus 118 ~~v~V~akVle~~-e---~--e~~-~~g~~--~~v~sg~lgD----------e----------------TGrIr~TlW~~ 162 (358)
T PRK06386 118 PYVSVIGKITGIT-K---K--EYD-SDGTS--KIVYQGYIED----------D----------------TARVRISSFGK 162 (358)
T ss_pred CceEEEEEEEEcc-C---c--eEe-cCCCc--cEEEEEEEEc----------C----------------CCeEEEEEccc
Confidence 5679999999876 3 1 222 56652 2111111111 0 1 478898874
Q ss_pred hhhhhhcCCCCCcEEEEeccEEEeeCcEEEEEEeeCCceEEcCC
Q 022219 247 YENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSD 290 (300)
Q Consensus 247 ~~~~~~~~lk~G~wv~l~Nv~~k~~~g~leg~l~~~sk~~~l~~ 290 (300)
.++.|+.|+|.|...+..+|.++-.+...|+|..++.
T Consensus 163 -------~l~eGd~v~i~na~v~e~~G~~el~v~~~t~I~~~~~ 199 (358)
T PRK06386 163 -------PLEDNRFVRIENARVSQYNGYIEISVGNKSVIKEVES 199 (358)
T ss_pred -------cccCCCEEEEeeeEEEccCCeEEEEeCCeEEEEECCC
Confidence 3899999999999999999999999999999988754
No 12
>PRK15491 replication factor A; Provisional
Probab=98.51 E-value=2.1e-05 Score=75.30 Aligned_cols=204 Identities=15% Similarity=0.180 Sum_probs=135.7
Q ss_pred ceeehhhhhhccCCEEEEEEEEEecCCcee-c--CC-CceEEEEEEEeCCCCCCCeEEEEecCCCCCC--CCCCCCCCEE
Q 022219 9 GIVRIKELAMHVKHKVNLLGVVLEFSIPRK-S--QG-TDYVCVLKIVDDSQQSPELLVNIFTSSIDQL--PRVLSPRDLI 82 (300)
Q Consensus 9 ~y~~l~~~~~~~~~~vnviGVVvd~~~P~~-t--rG-~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~L--P~v~~~GDII 82 (300)
.-++|++|... ...|++.|-|+....|+. + +| .-...++.|.|+|=. +++.+|.+..+.+ |.+ .+||++
T Consensus 56 ~~~kI~dL~~~-~~~v~i~arVl~~~~~R~f~r~dGs~g~v~~~~v~DeTG~---ir~tlW~~~a~~~~~~~l-e~G~v~ 130 (374)
T PRK15491 56 DTTKIADINES-SSNVNFTAKVVSIFEPKEFNRNDGTTGRVGNIIVADETGS---IRLTLWDDLADLIKTGDI-EVGKSL 130 (374)
T ss_pred ccccHHHCCCC-CCceEEEEEEeeccCCeeeecCCCCceEEEEEEEEcCCCe---EEEEEECchhhhhccCCc-CCCCEE
Confidence 35588999622 357999999999988865 2 46 467888999998652 9999999766655 678 799999
Q ss_pred EEeeEEEEEEcCeEEEEeecCceEEEEEeCCCCCCccccccCCCCcCCCHHHHHHHHHHHHhhhcCccccCCcccccccc
Q 022219 83 LLKNVMIKKHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSLK 162 (300)
Q Consensus 83 ~l~r~kv~~~~g~~~~~~~~~~ss~~vf~~~~~~~~~P~~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~~~~~L~ 162 (300)
.++..--..|+| +.+..+.. +... +. +++.+ ....| ..|+
T Consensus 131 ~I~~~~~~~y~g-~Ei~i~~~-~~i~-----------~~----------~~~~~----------------~~~~~-~~I~ 170 (374)
T PRK15491 131 NISGYAKEGYSG-IEVNIGRY-GGIS-----------ES----------DENVK----------------ASINS-QKIS 170 (374)
T ss_pred EEeeeeccCccc-EEEEeCCC-ceee-----------ec----------ccccc----------------cccCc-ccHH
Confidence 998875556666 44444432 2211 10 00000 00124 5678
Q ss_pred cccCC-ceEeEEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCChhhhhcCCCcccEEEE
Q 022219 163 DISEH-RYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRV 241 (300)
Q Consensus 163 di~~~-~f~Dl~~qVv~~~~~~~~~~~~L~VwDgT~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~G~~l~V 241 (300)
||.++ ..+|+.++|+.+. + ...+. --||+....+. ....| --| .+++
T Consensus 171 dl~~~~~~V~I~g~V~~~~-~--~r~~~--~~~G~~~~v~~--~~l~D------------------------etG-~Ir~ 218 (374)
T PRK15491 171 DIKDGDSDINIVGKVLDIS-D--VRTFQ--KKDGSQGRVRN--ITIGD------------------------ETG-KIRV 218 (374)
T ss_pred HcCCCCccEEEEEEEEEcc-C--ceEEE--ecCCCeEEEEE--EEEEC------------------------CCC-eEEE
Confidence 88764 4699999999987 3 12222 23454222211 11100 012 3789
Q ss_pred EecCchhhhhhcCCCCCcEEEEeccEEEee--CcEEEEEEeeCCceEEcCC
Q 022219 242 STDRSYENFGRYFTATGKWVRIRNMSCQVS--SGMWHGLLQSSSKIRLFSD 290 (300)
Q Consensus 242 ~~~~~~~~~~~~~lk~G~wv~l~Nv~~k~~--~g~leg~l~~~sk~~~l~~ 290 (300)
++|+..+.. ...+++|+-|++.|-.+|.+ .|.+|-.+..+|.|...++
T Consensus 219 t~W~~~a~~-~~~l~~Gd~V~i~~~~~r~~~~~g~~El~~~~~s~I~~~~~ 268 (374)
T PRK15491 219 TLWDGKTDL-ADKLENGDSVEIINGYARTNNYSQEVEIQIGNHGSLRKTDR 268 (374)
T ss_pred EEecchhcc-cccCCCCCEEEEEeceEEEeccCCCEEEEeCCCceEEECCc
Confidence 999988765 36799999999999888874 5899999999999988754
No 13
>PRK14699 replication factor A; Provisional
Probab=98.31 E-value=0.00016 Score=71.50 Aligned_cols=204 Identities=20% Similarity=0.204 Sum_probs=136.8
Q ss_pred eehhhhhhccCCEEEEEEEEEecCCcee-c--CCCc-eEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEee
Q 022219 11 VRIKELAMHVKHKVNLLGVVLEFSIPRK-S--QGTD-YVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKN 86 (300)
Q Consensus 11 ~~l~~~~~~~~~~vnviGVVvd~~~P~~-t--rG~D-~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~r 86 (300)
..|+++... ...||+.|-|+...+|+. + .|+. -..++.|-|+|= .+++.++.+..+.+|.+ ..||+|++.+
T Consensus 167 ~~I~dL~~~-~~~V~i~gkVl~~~~~R~f~~~dG~~g~v~~~~igDeTG---~ir~tlW~~~a~~~~~l-~~Gd~v~I~~ 241 (484)
T PRK14699 167 QKIKDIKDG-MGDLNLTGKVLEISEIRTFQRKDGTSGKVGNLLLGDETG---TLRVTLWDDKTDFLNQI-EYGDTVELIN 241 (484)
T ss_pred cchhhcCCC-CCceEEEEEEEeccCceEEecCCCCceEEEEEEEEcCCc---eEEEEEECccccccccc-CCCCEEEEec
Confidence 467777532 345999999999988764 2 3543 677889999976 39999999877777888 7999999998
Q ss_pred EEEE--EEcCeEEEEeecCceEEEEEeCCCCCCccccccCCCCcCCCHHHHHHHHHHHHhhhcCccccCCcccccccccc
Q 022219 87 VMIK--KHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSLKDI 164 (300)
Q Consensus 87 ~kv~--~~~g~~~~~~~~~~ss~~vf~~~~~~~~~P~~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~~~~~L~di 164 (300)
+.++ .|+|.+.+..+.. +... ......+ +. .++ ..|.+|
T Consensus 242 a~vr~~~~~~~~el~~~~~-s~i~--~~~~~~e----------~~-------------------------~~~-~~I~~L 282 (484)
T PRK14699 242 AYARENAFTQKVELQVGNR-SIIR--KSEKKVE----------YE-------------------------EEF-TPIEDI 282 (484)
T ss_pred ceEeecccCCceEEEecCc-eEee--ccccccc----------cc-------------------------ccc-cCHHHc
Confidence 8775 4778888877643 3222 1110000 10 013 467777
Q ss_pred cC-CceEeEEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCChhhhhcCCCcccEEEEEe
Q 022219 165 SE-HRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRVST 243 (300)
Q Consensus 165 ~~-~~f~Dl~~qVv~~~~~~~~~~~~L~VwDgT~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~G~~l~V~~ 243 (300)
++ +..+++.++|+++. + -..+. --||+.-.. .+....| + -| .+++++
T Consensus 283 ~~~~~~v~I~grV~~~~-~--~r~~~--~~~Gseg~v--~~~~l~D----------e--------------TG-~Ir~T~ 330 (484)
T PRK14699 283 KADMNNINISGRVLDIS-E--VRTFE--KKDGSPGRV--GNLLLGD----------S--------------TG-KIRLTL 330 (484)
T ss_pred CCCCceeEEEEEEEEcC-C--CeEEE--cCCCCeeEE--EEEEEEC----------C--------------CC-eEEEEE
Confidence 75 48899999999887 3 11221 234432111 1111111 0 11 378999
Q ss_pred cCchhhhhhcCCCCCcEEEEeccEEEee--CcEEEEEEeeCCceEEcCCC
Q 022219 244 DRSYENFGRYFTATGKWVRIRNMSCQVS--SGMWHGLLQSSSKIRLFSDN 291 (300)
Q Consensus 244 ~~~~~~~~~~~lk~G~wv~l~Nv~~k~~--~g~leg~l~~~sk~~~l~~~ 291 (300)
|+..+.+ ...+++|+.+++.|...+.+ ++.+|-.+..++.|...+++
T Consensus 331 W~~~a~~-~~~i~~Gd~v~i~~~y~~~~~~~~~~eL~~~~~t~I~~~~~~ 379 (484)
T PRK14699 331 WDEKTNF-LDEIDFDETVEVLNAYSRENTFSQQVELNLGARGIIQKSEKK 379 (484)
T ss_pred eCccccc-ccccCCCceEEEEeEEEEeccCCccEEEEecCceeEeecCCc
Confidence 9988864 56799999999999999986 47899999999988776544
No 14
>TIGR00617 rpa1 replication factor-a protein 1 (rpa1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.28 E-value=1.6e-05 Score=80.72 Aligned_cols=156 Identities=19% Similarity=0.272 Sum_probs=106.0
Q ss_pred Ccceeehhhhhhc-cCCEEEEEEEEEecCCceec--C--CCc-eEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCC
Q 022219 7 QGGIVRIKELAMH-VKHKVNLLGVVLEFSIPRKS--Q--GTD-YVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRD 80 (300)
Q Consensus 7 ~y~y~~l~~~~~~-~~~~vnviGVVvd~~~P~~t--r--G~D-~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GD 80 (300)
.|.|++|+++... .+..|+|||||+++++...- | |+. .+..|+|.|.|-. .|.|+++.+..+.+. . ..|+
T Consensus 295 ~~~f~~i~dI~~~~~~~~VDVIGvV~~v~~~~~i~~k~~g~~~~kR~i~L~D~sg~--sI~vTLWG~~A~~~~-~-~~~~ 370 (608)
T TIGR00617 295 QFNFVKIDDIGGYEGNSLVDVIGIVQSVSPTQTITSRKNNKEFPKRDITLVDDSGK--SVRVTLWGDDATKFD-V-SVQP 370 (608)
T ss_pred cccceEHHHhhhhcCCCCccEEEEEeEecCceEEEEcCCCCeeeeEEEEEEeCCCC--EEEEEEEhhhhhhcC-C-CCCC
Confidence 6899999999764 34589999999999887552 2 443 5679999999863 499999998766776 3 5799
Q ss_pred EEEEeeEEEEEEcCeEEEEeecCceEEEEEeCCCCCCccccccCCCCcCCCHHHHHHHHHHHHhhhcCccc---------
Q 022219 81 LILLKNVMIKKHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFS--------- 151 (300)
Q Consensus 81 II~l~r~kv~~~~g~~~~~~~~~~ss~~vf~~~~~~~~~P~~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~--------- 151 (300)
||.+..++|+.|+|. .+... ..|.+. .. | |..-+..|+.|+.+....
T Consensus 371 Vva~kg~~V~~f~g~-sLs~~-~~S~i~-iN--------P-------------dipEa~~L~~w~~~~g~~~~~~s~~~~ 426 (608)
T TIGR00617 371 VIAIKGVRVSDFGGK-SLSTG-GSSTII-VN--------P-------------DIPEAEKLKGWYDNEGKGTMASSISDM 426 (608)
T ss_pred EEEEEeEEEEecCCc-eEecc-CCceEE-EC--------C-------------CcHHHHHHHHHHHhcCCCccceeehhc
Confidence 999999999999664 44333 224443 11 1 111256889998653221
Q ss_pred -c----C-CcccccccccccC--------CceEeEEEEEEEEEeeCCCCeEEEEEEcCCCCCC
Q 022219 152 -S----G-SNDYLLSLKDISE--------HRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPP 200 (300)
Q Consensus 152 -~----~-~~~~~~~L~di~~--------~~f~Dl~~qVv~~~~~~~~~~~~L~VwDgT~n~~ 200 (300)
. . .... +.|++|++ +.||.+.|.|.++. . + . .| |+.||.
T Consensus 427 ~~~~~~~~~~~~-ktI~ei~~~~lg~~~k~~~f~v~atI~~Ik-~-d--~----~~-Y~ACp~ 479 (608)
T TIGR00617 427 MSGRVGGSNAER-KTIAEIQAENLGKSDKPDYFSVKATISYLK-P-D--N----AL-YRACPS 479 (608)
T ss_pred cccccCCccccc-ccHHHHhhhccCCCCCCcEEEEEEEEEEEe-c-C--C----eE-eccCCh
Confidence 0 0 1123 45666643 35799999999987 3 2 2 14 788875
No 15
>PRK07211 replication factor A; Reviewed
Probab=98.22 E-value=0.00024 Score=69.81 Aligned_cols=201 Identities=14% Similarity=0.134 Sum_probs=130.7
Q ss_pred eehhhhhhccC-CEEEEEEEEEecCCcee-cC----CCceEEEEEEEeCCCCCCCeEEEEecCCC-CCCCCCCCCCCEEE
Q 022219 11 VRIKELAMHVK-HKVNLLGVVLEFSIPRK-SQ----GTDYVCVLKIVDDSQQSPELLVNIFTSSI-DQLPRVLSPRDLIL 83 (300)
Q Consensus 11 ~~l~~~~~~~~-~~vnviGVVvd~~~P~~-tr----G~D~~~tl~I~D~S~~~~gl~v~iF~~~~-~~LP~v~~~GDII~ 83 (300)
.+|++|. ++ ..|++.|-|+..+.|+. ++ +.--.+++.|.|+|= .|++.+|.... ...|.+ ++|||++
T Consensus 54 ~~I~dL~--pg~~~vtI~aRV~~~~~~Rt~~~~~~~~eGkv~~v~l~DeTG---~Ir~TlW~d~ad~~~~~L-e~GdV~~ 127 (485)
T PRK07211 54 NGIADIE--PGMDEVKFLAKVLSIGDLRTFERDGEDEDGRVINVEVADETG---SVRVAFWDEQAVAAEEEL-EVGQVLR 127 (485)
T ss_pred ccHhhCC--CCCCceEEEEEEeEccCceEEEeCCCCCCcEEEEEEEEcCCC---eEEEEEechHhHhhhccc-CCCCEEE
Confidence 4788886 45 46999999999988765 22 235889999999865 29999997543 346778 7999999
Q ss_pred EeeEEEEEEcCeEEEEeecCceEEEEEeCCCCCCccccccCCCCcCCCHHHHHHHHHHHHhhhcCccccCCccccccccc
Q 022219 84 LKNVMIKKHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSLKD 163 (300)
Q Consensus 84 l~r~kv~~~~g~~~~~~~~~~ss~~vf~~~~~~~~~P~~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~~~~~L~d 163 (300)
+++.-...|++ +.+..+ . ........+ |+ . ...| ..|+|
T Consensus 128 I~~~~~~~ys~-~El~i~----~---ve~~~d~~i-~~-----------------------------~--~~~~-~~I~d 166 (485)
T PRK07211 128 IKGRPKDGYNG-LEVSVD----K---VEPDPDAEI-DV-----------------------------Q--IGDT-YTVED 166 (485)
T ss_pred EeceEeccccc-eEEEEe----e---EEEcccccc-cc-----------------------------c--ccCC-ccHHH
Confidence 98754444443 222221 0 110000000 00 0 0125 67888
Q ss_pred ccCC-ceEeEEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCChhhhhcCCCcccEEEEE
Q 022219 164 ISEH-RYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRVS 242 (300)
Q Consensus 164 i~~~-~f~Dl~~qVv~~~~~~~~~~~~L~VwDgT~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~G~~l~V~ 242 (300)
|+++ ..+|++++|+.+. +. .. +-=-||++-..+ ....-| + -| .++++
T Consensus 167 L~~~~~~v~I~grV~~v~-~i--Rt--f~r~dGseGkv~--sv~L~D----------e--------------TG-~IR~T 214 (485)
T PRK07211 167 LSLGLSDVTLVGVVLDTD-SV--RT--FDRDDGSEGRVS--NLTVGD----------E--------------TG-RVRVT 214 (485)
T ss_pred cCCCCCceEEEEEEEEcC-CC--eE--EECCCCCeeEEE--EEEEEc----------C--------------CC-eEEEE
Confidence 8865 5689999999877 32 01 111133221111 111000 0 12 37899
Q ss_pred ecCchhhhhhcCCCCCcEEEEeccEEEeeCcEEEEEEeeCCceEEcCCC
Q 022219 243 TDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDN 291 (300)
Q Consensus 243 ~~~~~~~~~~~~lk~G~wv~l~Nv~~k~~~g~leg~l~~~sk~~~l~~~ 291 (300)
+|+..+.. ...+.+|+.|+|.|.+++...|.+|-.+..++.|..++++
T Consensus 215 lW~d~Ad~-~~~le~G~Vv~I~~a~Vre~~g~~ELsl~~~s~I~~~~de 262 (485)
T PRK07211 215 LWDDRADL-AEELDAGESVEIVDGYVRERDGSLELHVGDRGAVEEVDED 262 (485)
T ss_pred Eechhhhh-hccCCCCCEEEEEeeEEEecCCcEEEEECCCceEEECCcc
Confidence 99987765 3679999999999999999889999999999999998774
No 16
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=98.16 E-value=5.3e-05 Score=61.87 Aligned_cols=91 Identities=16% Similarity=0.248 Sum_probs=71.2
Q ss_pred eeehhhhhhccC-CEEEEEEEEEecCCce--ecCCC-ceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEe
Q 022219 10 IVRIKELAMHVK-HKVNLLGVVLEFSIPR--KSQGT-DYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLK 85 (300)
Q Consensus 10 y~~l~~~~~~~~-~~vnviGVVvd~~~P~--~trG~-D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~ 85 (300)
.+.|+|+. .+ ..||+.|+|++..+++ +++++ -....++|.|.|=. |.+.++.+.. +.+ ..||||+|+
T Consensus 4 ~~kI~dL~--~g~~~v~~~~~V~~i~~~~~~~~k~~~~~v~~~~l~D~TG~---I~~tlW~~~a---~~l-~~GdvV~I~ 74 (129)
T PRK06461 4 ITKIKDLK--PGMERVNVTVRVLEVGEPKVIQTKGGPRTISEAVVGDETGR---VKLTLWGEQA---GSL-KEGEVVEIE 74 (129)
T ss_pred ceEHHHcC--CCCCceEEEEEEEEcCCceEEEeCCCceEEEEEEEECCCCE---EEEEEeCCcc---ccC-CCCCEEEEE
Confidence 57899997 55 5799999999988754 45654 56889999999863 8999998643 345 689999999
Q ss_pred eEEEEEEcCeEEEEeecCceEEEEE
Q 022219 86 NVMIKKHQAELSAVFYKDSSSFALF 110 (300)
Q Consensus 86 r~kv~~~~g~~~~~~~~~~ss~~vf 110 (300)
+++++.|+|.+++...+. +.....
T Consensus 75 na~v~~f~G~lqL~i~~~-~~i~~~ 98 (129)
T PRK06461 75 NAWTTLYRGKVQLNVGKY-GSISES 98 (129)
T ss_pred CcEEeeeCCEEEEEECCC-EEEEEC
Confidence 999999999999887643 444433
No 17
>cd04475 RPA1_DBD_B RPA1_DBD_B: A subfamily of OB folds corresponding to the third OB fold, the ssDNA-binding domain (DBD)-B, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-B, RPA1 contains three other OB folds: DBD-A, DBD-C, and RPA1N. The major DNA binding activity of human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. Although ScRPA and the hRPA have similar ssDNA-binding properties, they differ functiona
Probab=98.08 E-value=4.2e-05 Score=59.47 Aligned_cols=74 Identities=16% Similarity=0.201 Sum_probs=59.2
Q ss_pred EEEEEEEEEecCCceec--C--C-CceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCeEE
Q 022219 23 KVNLLGVVLEFSIPRKS--Q--G-TDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAELS 97 (300)
Q Consensus 23 ~vnviGVVvd~~~P~~t--r--G-~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~r~kv~~~~g~~~ 97 (300)
.|||+|+|++.++++.- + | .-.+..|+|.|.|.. .+.|.++.+..+.+... .|+||.|++++++.|+| ..
T Consensus 1 ~vDvig~V~~v~~~~~i~~k~~g~~~~~r~v~i~D~t~~--~i~vtLWg~~a~~~~~~--~~~vv~~~~~~i~~~~~-~~ 75 (101)
T cd04475 1 IVDVIGVVKSVGPVTTITTKSTGRELDKREITLVDESGH--SVELTLWGEQAELFDGS--ENPVIAIKGVKVSEFNG-KS 75 (101)
T ss_pred CEeEEEEEeEccCcEEEEEecCCCceeEEEEEEEeCCCC--EEEEEEEHHHhhhcccC--CCCEEEEEeeEEEecCC-eE
Confidence 38999999999998653 2 4 467899999999984 49999999776666654 39999999999999985 45
Q ss_pred EEee
Q 022219 98 AVFY 101 (300)
Q Consensus 98 ~~~~ 101 (300)
+.+.
T Consensus 76 l~~~ 79 (101)
T cd04475 76 LSTG 79 (101)
T ss_pred Eeec
Confidence 5443
No 18
>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=97.85 E-value=0.00031 Score=52.46 Aligned_cols=72 Identities=18% Similarity=0.281 Sum_probs=59.9
Q ss_pred EEEEEEEecCCceec---CCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCeEEEEee
Q 022219 25 NLLGVVLEFSIPRKS---QGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAELSAVFY 101 (300)
Q Consensus 25 nviGVVvd~~~P~~t---rG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~r~kv~~~~g~~~~~~~ 101 (300)
|+.|.|++..+++.. .+.--..+++|.|.|- .+.+.++.+.. .+.+ ..||+|.+++++++.|+|++++..+
T Consensus 1 ~v~~~V~~~~~~~~~~~~g~~~~~~~~~l~D~TG---~i~~~~W~~~~--~~~~-~~G~vv~i~~~~v~~~~g~~ql~i~ 74 (82)
T cd04491 1 SVEGKVLSISEPREFTRDGSEGKVQSGLVGDETG---TIRFTLWDEKA--ADDL-EPGDVVRIENAYVREFNGRLELSVG 74 (82)
T ss_pred CEEEEEEEccCCeEeccCCCeeEEEEEEEECCCC---EEEEEEECchh--cccC-CCCCEEEEEeEEEEecCCcEEEEeC
Confidence 589999999888763 3457788999999974 39999998653 6667 7999999999999999999998766
Q ss_pred c
Q 022219 102 K 102 (300)
Q Consensus 102 ~ 102 (300)
.
T Consensus 75 ~ 75 (82)
T cd04491 75 K 75 (82)
T ss_pred C
Confidence 4
No 19
>TIGR00617 rpa1 replication factor-a protein 1 (rpa1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.79 E-value=0.0011 Score=67.56 Aligned_cols=212 Identities=15% Similarity=0.175 Sum_probs=128.0
Q ss_pred ceeehhhhhhccCCEEEEEEEEEecCCcee---cCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCC-CCCCCCCCEEEE
Q 022219 9 GIVRIKELAMHVKHKVNLLGVVLEFSIPRK---SQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQL-PRVLSPRDLILL 84 (300)
Q Consensus 9 ~y~~l~~~~~~~~~~vnviGVVvd~~~P~~---trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~L-P~v~~~GDII~l 84 (300)
.+++|++|.... ....+-|-|+.....+. .+|.....++.|.|++ ..|.+.+|.+..+.+ |.+ ++|+|..|
T Consensus 179 ~~~pI~~L~py~-~~wtIkaRV~~Ks~ir~~~~~~gegkvfsv~L~Deg---g~Irat~f~~~~dkf~~~l-~eG~VY~I 253 (608)
T TIGR00617 179 RVMPIASLSPYQ-NKWTIKARVTNKSEIRTWSNARGEGKLFNVELLDES---GEIRATAFNEQADKFYDII-QEGKVYYI 253 (608)
T ss_pred ceEEHHHCCCCC-CceEEEEEEEeccccceecCCCCCceeeEEEEecCC---CeEEEEECchHHHHHhhhc-ccCCEEEE
Confidence 589999997443 45999999998776654 2455678889999943 349999999755444 666 79999999
Q ss_pred eeEEEEEEcCeEEEEeecCceEEEEEeCCCCCCccccccCCCCcCCCHHHHHHHHHHHHhhhcCccccCCcccccccccc
Q 022219 85 KNVMIKKHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSLKDI 164 (300)
Q Consensus 85 ~r~kv~~~~g~~~~~~~~~~ss~~vf~~~~~~~~~P~~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~~~~~L~di 164 (300)
.+.+|+..+++...+.+ . .... |... ..+.+.. ++. ........| ..|.||
T Consensus 254 s~~~Vk~an~~y~~~~~-~-yei~-f~~~--T~I~~~~----------d~~-------------~iP~~~~~f-~~i~dI 304 (608)
T TIGR00617 254 SKGSLKPANKQFTNLGN-D-YEMT-LDRD--TVIEECE----------DET-------------AIPKIQFNF-VKIDDI 304 (608)
T ss_pred CceEEEEccccccCCCC-C-EEEE-ECCC--eEEEECC----------Ccc-------------cCCcccccc-eEHHHh
Confidence 99999988776543332 1 1111 2211 0111100 000 000001124 455555
Q ss_pred ---cCCceEeEEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCChhhhhcCCCcccEEEE
Q 022219 165 ---SEHRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRV 241 (300)
Q Consensus 165 ---~~~~f~Dl~~qVv~~~~~~~~~~~~L~VwDgT~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~G~~l~V 241 (300)
..+.++|+++.|..+. +. ..++- =.||+...-.. +.+.. --|..++|
T Consensus 305 ~~~~~~~~VDVIGvV~~v~-~~--~~i~~-k~~g~~~~kR~--------------i~L~D------------~sg~sI~v 354 (608)
T TIGR00617 305 GGYEGNSLVDVIGIVQSVS-PT--QTITS-RKNNKEFPKRD--------------ITLVD------------DSGKSVRV 354 (608)
T ss_pred hhhcCCCCccEEEEEeEec-Cc--eEEEE-cCCCCeeeeEE--------------EEEEe------------CCCCEEEE
Confidence 4567999999999987 31 11111 12333221111 11100 01346789
Q ss_pred EecCchhhhhhcCCCCCcEEEEeccEEEeeCcEEEEEEeeCCceEE
Q 022219 242 STDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRL 287 (300)
Q Consensus 242 ~~~~~~~~~~~~~lk~G~wv~l~Nv~~k~~~g~leg~l~~~sk~~~ 287 (300)
++|..++.. .....|+.|-|++++++-.+|. .......|+|.+
T Consensus 355 TLWG~~A~~--~~~~~~~Vva~kg~~V~~f~g~-sLs~~~~S~i~i 397 (608)
T TIGR00617 355 TLWGDDATK--FDVSVQPVIAIKGVRVSDFGGK-SLSTGGSSTIIV 397 (608)
T ss_pred EEEhhhhhh--cCCCCCCEEEEEeEEEEecCCc-eEeccCCceEEE
Confidence 999988843 2377899999999999887664 455566778754
No 20
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=97.39 E-value=0.002 Score=52.59 Aligned_cols=96 Identities=16% Similarity=0.145 Sum_probs=65.9
Q ss_pred cccccccCC-ceEeEEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCChhhhhcCCCccc
Q 022219 159 LSLKDISEH-RYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGT 237 (300)
Q Consensus 159 ~~L~di~~~-~f~Dl~~qVv~~~~~~~~~~~~L~VwDgT~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~G~ 237 (300)
..|+||+++ .-++++++|+.+. + ...+ -.++. +...+.....| . -|
T Consensus 5 ~kI~dL~~g~~~v~~~~~V~~i~-~--~~~~---~~k~~--~~~v~~~~l~D--------------------~----TG- 51 (129)
T PRK06461 5 TKIKDLKPGMERVNVTVRVLEVG-E--PKVI---QTKGG--PRTISEAVVGD--------------------E----TG- 51 (129)
T ss_pred eEHHHcCCCCCceEEEEEEEEcC-C--ceEE---EeCCC--ceEEEEEEEEC--------------------C----CC-
Confidence 689999998 6999999999776 2 0111 11111 11011111111 0 01
Q ss_pred EEEEEecCchhhhhhcCCCCCcEEEEeccEEEeeCcEEEEEEeeCCceEEcCCC
Q 022219 238 VLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDN 291 (300)
Q Consensus 238 ~l~V~~~~~~~~~~~~~lk~G~wv~l~Nv~~k~~~g~leg~l~~~sk~~~l~~~ 291 (300)
.+++++|+..+ ..+++|+.|+|+|..++...|.++-.+...++++.++.+
T Consensus 52 ~I~~tlW~~~a----~~l~~GdvV~I~na~v~~f~G~lqL~i~~~~~i~~~~~~ 101 (129)
T PRK06461 52 RVKLTLWGEQA----GSLKEGEVVEIENAWTTLYRGKVQLNVGKYGSISESDDE 101 (129)
T ss_pred EEEEEEeCCcc----ccCCCCCEEEEECcEEeeeCCEEEEEECCCEEEEECCcc
Confidence 35788888643 358999999999999999999999999999999998864
No 21
>PRK08402 replication factor A; Reviewed
Probab=97.38 E-value=0.007 Score=57.62 Aligned_cols=139 Identities=15% Similarity=0.210 Sum_probs=93.1
Q ss_pred ceeehhhhhhccC-CEEEEEEEEEecCCcee--cC-CC-ceEEEEEEEeCCCCCCCeEEEEecCCCC-CCCCCCCCCCEE
Q 022219 9 GIVRIKELAMHVK-HKVNLLGVVLEFSIPRK--SQ-GT-DYVCVLKIVDDSQQSPELLVNIFTSSID-QLPRVLSPRDLI 82 (300)
Q Consensus 9 ~y~~l~~~~~~~~-~~vnviGVVvd~~~P~~--tr-G~-D~~~tl~I~D~S~~~~gl~v~iF~~~~~-~LP~v~~~GDII 82 (300)
..++|+|+. ++ ..|++.|-|+....|+. .| |+ ....+++|.|+|-. +.+.++.+..+ .++.+ .+||||
T Consensus 61 ~~~kI~dl~--~g~~~V~v~~rVl~~~~~r~f~rrdG~~~~V~~i~l~DeTG~---ir~TlW~~~a~~~~~~l-~~Gdvi 134 (355)
T PRK08402 61 PLMHISDLV--PGMRGVNIVGRVLRKYPPREYTKKDGSTGRVASLIIYDDTGR---ARVVLWDAKVAKYYNKI-NVGDVI 134 (355)
T ss_pred CccCHHHcc--CCCceeeEEEEEEEccCCceeeccCCCcceEEEEEEEcCCCe---EEEEEechhhhhhcccC-CCCCEE
Confidence 467899997 44 46999999999877654 22 43 56888999998762 79999997644 47888 799999
Q ss_pred EEeeEEEEE-EcCeEEEEeecCceEEEEEeCCCCCCccccccCCCCcCCCHHHHHHHHHHHHhhhcCccccCCccccccc
Q 022219 83 LLKNVMIKK-HQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSL 161 (300)
Q Consensus 83 ~l~r~kv~~-~~g~~~~~~~~~~ss~~vf~~~~~~~~~P~~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~~~~~L 161 (300)
++.+++++. |+|.+.+..+.. |+..+=+..+.. . .+..-.++.. ..... +.|
T Consensus 135 ~I~~a~V~e~~~G~~eLsvg~~-s~i~~~pd~~ea--------~-~i~~~~~~~~----------------~~~~~-k~I 187 (355)
T PRK08402 135 KVIDAQVRESLSGLPELHINFR-ARIILNPDDPRV--------E-EIPPLEEVRS----------------YNYTR-KKI 187 (355)
T ss_pred EEECCEEeecCCCcEEEEECCC-ceEEeCCCcccc--------c-cccccccccc----------------ccccc-cCH
Confidence 999999998 488888877643 444422211100 0 0100000100 01123 678
Q ss_pred ccccCCc-eEeEEEEEEEEE
Q 022219 162 KDISEHR-YFDLVCKVFHVS 180 (300)
Q Consensus 162 ~di~~~~-f~Dl~~qVv~~~ 180 (300)
.|++++. ||.+.+.|+.+.
T Consensus 188 ~ei~~gd~~v~v~g~Iv~i~ 207 (355)
T PRK08402 188 GELEGGERFVEVRGTIAKVY 207 (355)
T ss_pred HHcccCCcEEEEEEEEEEEe
Confidence 8887654 789999999987
No 22
>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=97.22 E-value=0.0042 Score=51.21 Aligned_cols=101 Identities=19% Similarity=0.159 Sum_probs=74.7
Q ss_pred ccccccccc--CCceEeEEEEEEEEEeeCC----CCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCChhhhh
Q 022219 157 YLLSLKDIS--EHRYFDLVCKVFHVSYDDS----KGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLR 230 (300)
Q Consensus 157 ~~~~L~di~--~~~f~Dl~~qVv~~~~~~~----~~~~~L~VwDgT~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 230 (300)
| ..|+++. .++.+|+++-|+....... +-+.+|.|+|=|.++
T Consensus 3 f-~~i~~~~~~~~~~v~vigVV~~~~~p~~s~g~d~~~tl~i~D~S~~~------------------------------- 50 (138)
T cd04497 3 Y-TPLSSALKESGGSVNVIGVVVDAGPPVRSKGTDYCCTLTITDPSLAN------------------------------- 50 (138)
T ss_pred e-EeHHHHHhccCCeEEEEEEEeecCCCcccCCCcEEEEEEEECCCCCC-------------------------------
Confidence 5 6788886 7999999999998773111 135567777766422
Q ss_pred cCCCcccEEEEEecCchhhhhhcCCCCCcEEEEeccEEEeeCcEEEEEEee-CCceEEcCCCCccc
Q 022219 231 NFFPVGTVLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQS-SSKIRLFSDNDNVV 295 (300)
Q Consensus 231 ~~p~~G~~l~V~~~~~~~~~~~~~lk~G~wv~l~Nv~~k~~~g~leg~l~~-~sk~~~l~~~d~~v 295 (300)
+..+.|.++...... ...+.+||.|+|+|++++..+|...|.... .|.+.+.+.++...
T Consensus 51 -----~~~l~v~~F~~~~~~-LP~v~~GDVIll~~~kv~~~~g~~~~~~~~~~ss~avf~~~~~~~ 110 (138)
T cd04497 51 -----SDGLTVKLFRPNEES-LPIVKVGDIILLRRVKIQSYNGKPQGISNDRGSSWAVFRGDDGVV 110 (138)
T ss_pred -----CCcEEEEEECCChhh-CCCCCCCCEEEEEEEEEEEECCceEEEECCCceeEEEEcCCCCCC
Confidence 134578887777653 555799999999999999999998899888 78888877666543
No 23
>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=97.07 E-value=0.0033 Score=44.25 Aligned_cols=70 Identities=19% Similarity=0.386 Sum_probs=53.0
Q ss_pred EEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCeEEEEe
Q 022219 25 NLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAELSAVF 100 (300)
Q Consensus 25 nviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~r~kv~~~~g~~~~~~ 100 (300)
++.|+|++..... | ...+..|+|.|.+. ..+.|.+|.+..+........|++|.++ .+++.++++.++..
T Consensus 1 ~v~g~v~~~~~~~-~--~~~~~~~~l~D~~~--~~i~~~~~~~~~~~~~~~~~~g~~v~v~-g~v~~~~~~~~l~~ 70 (75)
T cd03524 1 TIVGIVVAVEEIR-T--EGKVLIFTLTDGTG--GTIRVTLFGELAEELENLLKEGQVVYIK-GKVKKFRGRLQLIV 70 (75)
T ss_pred CeEEEEEeecccc-c--CCeEEEEEEEcCCC--CEEEEEEEchHHHHHHhhccCCCEEEEE-EEEEecCCeEEEEe
Confidence 3789999987753 3 34589999999872 2399999987655553333789999998 99999887776654
No 24
>KOG3416 consensus Predicted nucleic acid binding protein [General function prediction only]
Probab=96.84 E-value=0.007 Score=48.56 Aligned_cols=83 Identities=20% Similarity=0.296 Sum_probs=65.8
Q ss_pred eehhhhhhccCCEEEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEE
Q 022219 11 VRIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIK 90 (300)
Q Consensus 11 ~~l~~~~~~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~r~kv~ 90 (300)
..|+|+.... +..|+.=+|.+.+.-.+|+-++=.++.++.|+|-. |.+.+..+ +-.+ .++||||+|++--..
T Consensus 5 i~ikdi~P~~-kN~~v~fIvl~~g~~tkTkdg~~v~~~kVaD~Tgs---I~isvW~e-~~~~---~~PGDIirLt~Gy~S 76 (134)
T KOG3416|consen 5 IFIKDIKPGL-KNINVTFIVLEYGRATKTKDGHEVRSCKVADETGS---INISVWDE-EGCL---IQPGDIIRLTGGYAS 76 (134)
T ss_pred hhHhhcChhh-hcceEEEEEEeeceeeeccCCCEEEEEEEecccce---EEEEEecC-cCcc---cCCccEEEecccchh
Confidence 4678886332 34899999999999999998888999999999863 88888873 2222 268999999999999
Q ss_pred EEcCeEEEEee
Q 022219 91 KHQAELSAVFY 101 (300)
Q Consensus 91 ~~~g~~~~~~~ 101 (300)
.|+|.+.+-..
T Consensus 77 i~qg~LtL~~G 87 (134)
T KOG3416|consen 77 IFQGCLTLYVG 87 (134)
T ss_pred hhcCceEEEec
Confidence 99998766544
No 25
>PRK07217 replication factor A; Reviewed
Probab=96.75 E-value=0.039 Score=51.30 Aligned_cols=92 Identities=17% Similarity=0.285 Sum_probs=67.0
Q ss_pred ccccccc-CCceEeEEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCChhhhhcCCCccc
Q 022219 159 LSLKDIS-EHRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGT 237 (300)
Q Consensus 159 ~~L~di~-~~~f~Dl~~qVv~~~~~~~~~~~~L~VwDgT~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~G~ 237 (300)
..|+||. +++.++++++|+.++ + ..+ +.....+...| +. |
T Consensus 73 ~kI~Di~~~~~~VsV~aKVl~l~-e-~~~------------~si~qvGllgD----------ET--------------G- 113 (311)
T PRK07217 73 VNIADIDEPEQWVDVTAKVVQLW-E-PSS------------DSIAQVGLLGD----------ET--------------G- 113 (311)
T ss_pred eeeeecCCCCCcEEEEEEEEEec-C-CCC------------CceEEEEEEEc----------CC--------------c-
Confidence 6799998 589999999999998 4 221 22111111111 00 0
Q ss_pred EEEEEecCchhhhhhcCCCCCcEEEEeccEEEeeCcEEEEEEeeCCceEEcCCCC
Q 022219 238 VLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDND 292 (300)
Q Consensus 238 ~l~V~~~~~~~~~~~~~lk~G~wv~l~Nv~~k~~~g~leg~l~~~sk~~~l~~~d 292 (300)
.++.+.|.... ...+++|++|+|.|+..+..+|..+-.+.+.|.|..++.+-
T Consensus 114 ~IkfT~W~~s~---~~~leeGd~~rI~na~v~ey~G~~~lnlg~~t~I~~~de~I 165 (311)
T PRK07217 114 TIKFTKWAKSD---LPELEEGKSYLLKNVVTDEYQGRFSVKLNRTTSIEELDEDI 165 (311)
T ss_pred eEEEEEccCCC---CCcccCCCEEEEEeEEEeeECCEEEEEeCCceEEEeCCCCc
Confidence 36778888532 34599999999999999999999999999999998877653
No 26
>PF02765 POT1: Telomeric single stranded DNA binding POT1/CDC13; InterPro: IPR011564 This entry represents a domain that binds single stranded telomeric DNA and adopts an OB fold []. It includes the proteins POT1 and CDC13 which have been shown to regulate telomere length, replication and capping [, , ]. ; GO: 0003677 DNA binding, 0000723 telomere maintenance, 0000784 nuclear chromosome, telomeric region; PDB: 1S40_A 1KXL_A 1PH7_A 1PH9_A 1PH2_A 1OTC_A 1PHJ_A 1JB7_A 1PA6_A 1PH1_A ....
Probab=96.47 E-value=0.096 Score=43.47 Aligned_cols=96 Identities=19% Similarity=0.164 Sum_probs=67.6
Q ss_pred cccc--cccCCceEeEEEEEEEEEee--C---CCC-eEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCChhhhh
Q 022219 159 LSLK--DISEHRYFDLVCKVFHVSYD--D---SKG-LWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLR 230 (300)
Q Consensus 159 ~~L~--di~~~~f~Dl~~qVv~~~~~--~---~~~-~~~L~VwDgT~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 230 (300)
..|+ ..+.+.++|+++-|+..... . ..+ ..+|.++|-|-+.. ....
T Consensus 2 ~~l~~~~~~~~~~vnvigVV~~~~~p~~~~t~g~D~~~tl~i~D~S~~~~-~~~~------------------------- 55 (146)
T PF02765_consen 2 TPLSTAKEKFGKFVNVIGVVVDFSPPNPKKTRGTDYMCTLTITDPSLNDS-NQKL------------------------- 55 (146)
T ss_dssp CCGGGSCTTSSEEEEEEEEEEEEEEECTEEESSSCEEEEEEEEBTTCSCS-SCCC-------------------------
T ss_pred ccchhhhhcCCCEEEEEEEEEEccCCcceEcCCCcEEEEEEEECCCCCcc-cccc-------------------------
Confidence 3455 44679999999999987633 1 223 67889998885432 1000
Q ss_pred cCCCcccEEEEEec-CchhhhhhcCCCC-CcEEEEeccEEEeeCcEEEEEEeeC--CceEEc
Q 022219 231 NFFPVGTVLRVSTD-RSYENFGRYFTAT-GKWVRIRNMSCQVSSGMWHGLLQSS--SKIRLF 288 (300)
Q Consensus 231 ~~p~~G~~l~V~~~-~~~~~~~~~~lk~-G~wv~l~Nv~~k~~~g~leg~l~~~--sk~~~l 288 (300)
..+.|.+. ++.+. ...++. ||.|+|++++++..+|...|..+.. +.+.++
T Consensus 56 ------~~l~v~iF~~~~~~--LP~v~~~GDii~l~r~kv~~~~~~~~~~~~~~~~ss~~vf 109 (146)
T PF02765_consen 56 ------SGLTVNIFRPHKES--LPNVKSVGDIIRLRRVKVQSYNGKPQGLSNSTSNSSWAVF 109 (146)
T ss_dssp ------CEEEEEEEESSHHH--SCTTCSTTHEEEEEEEEEEEETTEEEEEEECECTEEEEEE
T ss_pred ------CCEEEEEECCCHHH--CCCCCCCCCEEEEEEEEEEEECCEEEEEecCCCcEEEEEE
Confidence 13456543 44442 566776 9999999999999999999998888 888888
No 27
>PRK07217 replication factor A; Reviewed
Probab=96.42 E-value=0.069 Score=49.70 Aligned_cols=91 Identities=18% Similarity=0.266 Sum_probs=66.9
Q ss_pred cceeehhhhhhccCCEEEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeE
Q 022219 8 GGIVRIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNV 87 (300)
Q Consensus 8 y~y~~l~~~~~~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~r~ 87 (300)
..-+.|+|+. ..++.|+|.|-|+....|+. ++-...- -|-|+|= . |++..+.+ ..+|.+ ..||+++|+++
T Consensus 70 ~~~~kI~Di~-~~~~~VsV~aKVl~l~e~~~--~si~qvG-llgDETG-~--IkfT~W~~--s~~~~l-eeGd~~rI~na 139 (311)
T PRK07217 70 SELVNIADID-EPEQWVDVTAKVVQLWEPSS--DSIAQVG-LLGDETG-T--IKFTKWAK--SDLPEL-EEGKSYLLKNV 139 (311)
T ss_pred CCceeeeecC-CCCCcEEEEEEEEEecCCCC--CceEEEE-EEEcCCc-e--EEEEEccC--CCCCcc-cCCCEEEEEeE
Confidence 3455788886 33577999999999887642 2222211 3566654 2 99999986 369999 78999999999
Q ss_pred EEEEEcCeEEEEeecCceEEEE
Q 022219 88 MIKKHQAELSAVFYKDSSSFAL 109 (300)
Q Consensus 88 kv~~~~g~~~~~~~~~~ss~~v 109 (300)
.+..|+|++++..+. +++...
T Consensus 140 ~v~ey~G~~~lnlg~-~t~I~~ 160 (311)
T PRK07217 140 VTDEYQGRFSVKLNR-TTSIEE 160 (311)
T ss_pred EEeeECCEEEEEeCC-ceEEEe
Confidence 999999999988874 366653
No 28
>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=96.37 E-value=0.02 Score=44.86 Aligned_cols=82 Identities=12% Similarity=0.104 Sum_probs=58.1
Q ss_pred EEEEEEEecCCceecC--C-CceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCC----CCCCCEEEEee-EEEEEEcCeE
Q 022219 25 NLLGVVLEFSIPRKSQ--G-TDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRV----LSPRDLILLKN-VMIKKHQAEL 96 (300)
Q Consensus 25 nviGVVvd~~~P~~tr--G-~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v----~~~GDII~l~r-~kv~~~~g~~ 96 (300)
++||+|++.++..... | ......|+|.|.+.. .++|.++.+..+.+..- ...+=||.+-+ .+|..|+|..
T Consensus 1 DviG~i~~v~~~~~~~~~~~~~~kr~~~i~D~~~~--~l~~tlwG~~A~~f~~~~~~~~~~~~VVav~~~~rV~~~~g~~ 78 (106)
T cd04481 1 DVIGVIVDVGPLEELPPVNKPSRKLDFEIRDLSDE--RLKCTLWGEYAEEFDAKFQSAGNGEPVVAVLRFWKIKEYKGPK 78 (106)
T ss_pred CeeEEEEEecceEecccCCccceEEEEEEEeCCCC--EEEEEEEHHHHHHHHHHHHHhCCCCcEEEEEEeEEEEEEcCCc
Confidence 5899999999876643 3 577899999999954 49999998766666642 13344776655 9999999854
Q ss_pred EEEeecCceEEE
Q 022219 97 SAVFYKDSSSFA 108 (300)
Q Consensus 97 ~~~~~~~~ss~~ 108 (300)
.+....+.|.|.
T Consensus 79 ~ls~~~~~s~v~ 90 (106)
T cd04481 79 SLSNSFGASKVY 90 (106)
T ss_pred EEEcCCCceEEE
Confidence 444332435554
No 29
>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=96.23 E-value=0.071 Score=38.81 Aligned_cols=69 Identities=10% Similarity=0.093 Sum_probs=50.5
Q ss_pred EEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEE--cCeEEEEee
Q 022219 24 VNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKH--QAELSAVFY 101 (300)
Q Consensus 24 vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~r~kv~~~--~g~~~~~~~ 101 (300)
+-+.|+|.+.+. |+++ ++-++|.|.+- .+.+.+|.+..+........|++|.++ .+++.+ ++++++...
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 457899998875 5433 99999999873 399999998666666665889988885 445544 466666554
No 30
>PF01336 tRNA_anti-codon: OB-fold nucleic acid binding domain; InterPro: IPR004365 The OB-fold (oligonucleotide/oligosaccharide-binding fold) is found in all three kingdoms and its common architecture presents a binding face that has adapted to bind different ligands. The OB-fold is a five/six-stranded closed beta-barrel formed by 70-80 amino acid residues. The strands are connected by loops of varying length which form the functional appendages of the protein. The majority of OB-fold proteins use the same face for ligand binding or as an active site. Different OB-fold proteins use this 'fold-related binding face' to, variously, bind oligosaccharides, oligonucleotides, proteins, metal ions and catalytic substrates. This entry contains OB-fold domains that bind to nucleic acids []. It includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl-tRNA synthetases (See IPR004364 from INTERPRO). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule 6.1.1 from EC. This domain is found in RecG helicase involved in DNA repair. Replication factor A is a heterotrimeric complex, that contains a subunit in this family [, ]. This domain is also found at the C terminus of bacterial DNA polymerase III alpha chain.; GO: 0003676 nucleic acid binding; PDB: 1BBU_A 1KRS_A 1BBW_A 1KRT_A 1EQR_B 1IL2_B 1C0A_A 3KFU_A 1EOV_A 1ASY_A ....
Probab=96.19 E-value=0.0091 Score=42.91 Aligned_cols=68 Identities=13% Similarity=0.216 Sum_probs=52.0
Q ss_pred EEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEec-CCCCCCCCCCCCCCEEEEeeEEEEEEcCe-EEEEee
Q 022219 24 VNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFT-SSIDQLPRVLSPRDLILLKNVMIKKHQAE-LSAVFY 101 (300)
Q Consensus 24 vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~-~~~~~LP~v~~~GDII~l~r~kv~~~~g~-~~~~~~ 101 (300)
|.+.|.|.... ++..=.+.++|.|.|- .+.|.+|. ........+ ..||+|+++ -+++.++++ +++..+
T Consensus 1 V~v~G~V~~~~-----~~~~~~~~~~l~D~tg---~i~~~~~~~~~~~~~~~l-~~g~~v~v~-G~v~~~~~~~~~l~~~ 70 (75)
T PF01336_consen 1 VTVEGRVTSIR-----RSGGKIVFFTLEDGTG---SIQVVFFNEEYERFREKL-KEGDIVRVR-GKVKRYNGGELELIVP 70 (75)
T ss_dssp EEEEEEEEEEE-----EEETTEEEEEEEETTE---EEEEEEETHHHHHHHHTS--TTSEEEEE-EEEEEETTSSEEEEEE
T ss_pred CEEEEEEEEEE-----cCCCCEEEEEEEECCc---cEEEEEccHHhhHHhhcC-CCCeEEEEE-EEEEEECCccEEEEEC
Confidence 57889999887 3334466889999983 39999999 444555666 799999999 999999987 877654
No 31
>PRK06386 replication factor A; Reviewed
Probab=96.06 E-value=0.066 Score=51.03 Aligned_cols=89 Identities=18% Similarity=0.279 Sum_probs=68.2
Q ss_pred cceeehhhhhhccCCEEEEEEEEEecCCcee-cCCC-ceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEe
Q 022219 8 GGIVRIKELAMHVKHKVNLLGVVLEFSIPRK-SQGT-DYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLK 85 (300)
Q Consensus 8 y~y~~l~~~~~~~~~~vnviGVVvd~~~P~~-trG~-D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~ 85 (300)
|..++|+|+.. ....|||.|-|++...+.- ++|+ -...++-|-|+|=- |++.+|.+ .+ ..||+|+|.
T Consensus 105 ~~~~KI~DL~~-g~~~v~V~akVle~~e~e~~~~g~~~~v~sg~lgDeTGr---Ir~TlW~~------~l-~eGd~v~i~ 173 (358)
T PRK06386 105 YKLVKIRDLSL-VTPYVSVIGKITGITKKEYDSDGTSKIVYQGYIEDDTAR---VRISSFGK------PL-EDNRFVRIE 173 (358)
T ss_pred cCccEeEeccC-CCCceEEEEEEEEccCceEecCCCccEEEEEEEEcCCCe---EEEEEccc------cc-cCCCEEEEe
Confidence 45678999962 2345999999999755422 3444 77888899998752 99999985 25 689999999
Q ss_pred eEEEEEEcCeEEEEeecCceEEE
Q 022219 86 NVMIKKHQAELSAVFYKDSSSFA 108 (300)
Q Consensus 86 r~kv~~~~g~~~~~~~~~~ss~~ 108 (300)
++.++.|+|.+++..+.. |+..
T Consensus 174 na~v~e~~G~~el~v~~~-t~I~ 195 (358)
T PRK06386 174 NARVSQYNGYIEISVGNK-SVIK 195 (358)
T ss_pred eeEEEccCCeEEEEeCCe-EEEE
Confidence 999999999999988743 5433
No 32
>PRK07218 replication factor A; Provisional
Probab=95.93 E-value=0.1 Score=50.88 Aligned_cols=88 Identities=16% Similarity=0.234 Sum_probs=65.7
Q ss_pred eehhhhhhccCCEEEEEEEEEecCCcee--c-CCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeE
Q 022219 11 VRIKELAMHVKHKVNLLGVVLEFSIPRK--S-QGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNV 87 (300)
Q Consensus 11 ~~l~~~~~~~~~~vnviGVVvd~~~P~~--t-rG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~r~ 87 (300)
.+|.++. .....|||.|.|++.. |+. . .|+-...+..|-|+|=. +.+.++.+ +|.+ ..||+|++.++
T Consensus 163 ~kI~DL~-~g~~~V~v~g~Vl~~~-~r~f~~~dg~~~v~~giigDeTG~---Ir~tlW~~----~~~l-~~Gd~v~I~na 232 (423)
T PRK07218 163 KKLIDLG-PGDRGVNVEARVLELE-HREIDGRDGETTILSGVLADETGR---LPFTDWDP----LPEI-EIGASIRIEDA 232 (423)
T ss_pred cchhhcc-CCCCceEEEEEEEEec-ceeEEcCCCCeEEEEEEEECCCce---EEEEEecc----cccC-CCCCEEEEeee
Confidence 3566664 1234499999999984 422 2 35666888889998752 99999985 4567 78999999999
Q ss_pred EEEEEcCeEEEEeecCceEEEE
Q 022219 88 MIKKHQAELSAVFYKDSSSFAL 109 (300)
Q Consensus 88 kv~~~~g~~~~~~~~~~ss~~v 109 (300)
.++.|+|.+++..+.. +....
T Consensus 233 ~v~e~~G~~elnv~~~-t~I~~ 253 (423)
T PRK07218 233 YVREFRGVPSVNVSEF-TTVEA 253 (423)
T ss_pred EEeccCCeEEEEECCc-eEEEE
Confidence 9999999999988753 55553
No 33
>cd04474 RPA1_DBD_A RPA1_DBD_A: A subfamily of OB folds corresponding to the second OB fold, the ssDNA-binding domain (DBD)-A, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change. Although ScRPA and the hRPA have similar ssDNA-binding properties, they differ funct
Probab=95.90 E-value=0.035 Score=43.40 Aligned_cols=82 Identities=15% Similarity=0.186 Sum_probs=61.1
Q ss_pred ehhhhhhccCCEEEEEEEEEecCCceecC---CCceEEEEEEEeCCCCCCCeEEEEecCCCC-CCCCCCCCCCEEEEeeE
Q 022219 12 RIKELAMHVKHKVNLLGVVLEFSIPRKSQ---GTDYVCVLKIVDDSQQSPELLVNIFTSSID-QLPRVLSPRDLILLKNV 87 (300)
Q Consensus 12 ~l~~~~~~~~~~vnviGVVvd~~~P~~tr---G~D~~~tl~I~D~S~~~~gl~v~iF~~~~~-~LP~v~~~GDII~l~r~ 87 (300)
+|++|... .....+.|-|+..+.++.-+ +.-..++|.|.|+... .+.+.+|.+..+ .-|.+ ..|+|+.+.++
T Consensus 1 pI~~L~p~-~~~~~I~~rV~~k~~~~~f~~~~~~g~~~~~~l~De~~~--~I~~t~~~~~~~~f~~~l-~eG~vy~i~~~ 76 (104)
T cd04474 1 PISSLNPY-QNKWTIKARVTNKSDIRTWSNARGEGKLFSFDLLDEDGG--EIRATFFNDAVDKFYDLL-EVGKVYYISKG 76 (104)
T ss_pred ChhHccCC-CCcEEEEEEEeeccccccccCCCCCcEEEEEEEEECCCC--EEEEEEehHHHHHhhccc-ccccEEEEecc
Confidence 46777632 24589999999877765533 3467789999999653 399999986433 55666 79999999999
Q ss_pred EEEEEcCeEE
Q 022219 88 MIKKHQAELS 97 (300)
Q Consensus 88 kv~~~~g~~~ 97 (300)
+|+.-++...
T Consensus 77 ~V~~a~~~y~ 86 (104)
T cd04474 77 SVKVANKKFN 86 (104)
T ss_pred EEeeccccCC
Confidence 9998876543
No 34
>cd04491 SoSSB_OBF SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus solfataricus single-stranded (ss) DNA-binding protein (SSoSSB). SSoSSB has a single OB fold, and it physically and functionally interacts with RNA polymerase. In vitro, SSoSSB can substitute for the basal transcription factor TBP, stimulating transcription from promoters under conditions in which TBP is limiting, and supporting transcription when TBP is absent. SSoSSB selectively melts the duplex DNA of promoter sequences. It also relieves transcriptional repression by the chromatin Alba. In addition, SSoSSB activates reverse gyrase activity, which involves DNA binding, DNA cleavage, strand passage and ligation. SSoSSB stimulates all these steps in the presence of the chromatin protein, Sul7d. SSoSSB antagonizes the inhibitory effect of Sul7d on reverse gyrase supercoiling activity. It also physically and functionally interacts with Mini-chromosome Maintenance (MCM), stimulating
Probab=95.42 E-value=0.052 Score=40.29 Aligned_cols=47 Identities=19% Similarity=0.093 Sum_probs=40.2
Q ss_pred EEEEEecCchhhhhhcCCCCCcEEEEeccEEEeeCcEEEEEEeeCCceEE
Q 022219 238 VLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRL 287 (300)
Q Consensus 238 ~l~V~~~~~~~~~~~~~lk~G~wv~l~Nv~~k~~~g~leg~l~~~sk~~~ 287 (300)
.+++++|+..+ .+.+++|++|+|+|..++...|.++-.+...+.|..
T Consensus 35 ~i~~~~W~~~~---~~~~~~G~vv~i~~~~v~~~~g~~ql~i~~~~~i~~ 81 (82)
T cd04491 35 TIRFTLWDEKA---ADDLEPGDVVRIENAYVREFNGRLELSVGKNSEIEK 81 (82)
T ss_pred EEEEEEECchh---cccCCCCCEEEEEeEEEEecCCcEEEEeCCceEEEE
Confidence 46788888765 567999999999999999999999999998887754
No 35
>PRK08402 replication factor A; Reviewed
Probab=95.39 E-value=0.15 Score=48.62 Aligned_cols=101 Identities=17% Similarity=0.131 Sum_probs=67.5
Q ss_pred cccccccCC-ceEeEEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCChhhhhcCCCccc
Q 022219 159 LSLKDISEH-RYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGT 237 (300)
Q Consensus 159 ~~L~di~~~-~f~Dl~~qVv~~~~~~~~~~~~L~VwDgT~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~G~ 237 (300)
..|+||.++ ..++++++|+.+. +.. .+ ---||+...- ......| + -|+
T Consensus 63 ~kI~dl~~g~~~V~v~~rVl~~~-~~r--~f--~rrdG~~~~V--~~i~l~D----------e--------------TG~ 111 (355)
T PRK08402 63 MHISDLVPGMRGVNIVGRVLRKY-PPR--EY--TKKDGSTGRV--ASLIIYD----------D--------------TGR 111 (355)
T ss_pred cCHHHccCCCceeeEEEEEEEcc-CCc--ee--eccCCCcceE--EEEEEEc----------C--------------CCe
Confidence 679999987 5899999999987 311 11 1123332111 0011100 0 112
Q ss_pred EEEEEecCchhhhhhcCCCCCcEEEEeccEEEee-CcEEEEEEeeCCceEEcCCC
Q 022219 238 VLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVS-SGMWHGLLQSSSKIRLFSDN 291 (300)
Q Consensus 238 ~l~V~~~~~~~~~~~~~lk~G~wv~l~Nv~~k~~-~g~leg~l~~~sk~~~l~~~ 291 (300)
+++++|+..+.-....+.+|+.|+|.|..++.. +|..+-.+..+|.|.+.++.
T Consensus 112 -ir~TlW~~~a~~~~~~l~~Gdvi~I~~a~V~e~~~G~~eLsvg~~s~i~~~pd~ 165 (355)
T PRK08402 112 -ARVVLWDAKVAKYYNKINVGDVIKVIDAQVRESLSGLPELHINFRARIILNPDD 165 (355)
T ss_pred -EEEEEechhhhhhcccCCCCCEEEEECCEEeecCCCcEEEEECCCceEEeCCCc
Confidence 389999877632235699999999999999985 89999999999999777653
No 36
>cd04478 RPA2_DBD_D RPA2_DBD_D: A subfamily of OB folds corresponding to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle dependent manner in response to DNA dam
Probab=95.28 E-value=0.24 Score=37.58 Aligned_cols=67 Identities=16% Similarity=0.184 Sum_probs=51.3
Q ss_pred EEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCC----CCCCCCCCCCEEEEeeEEEEEEcCeEEEE
Q 022219 24 VNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSID----QLPRVLSPRDLILLKNVMIKKHQAELSAV 99 (300)
Q Consensus 24 vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~----~LP~v~~~GDII~l~r~kv~~~~g~~~~~ 99 (300)
|.++|+|.+...- +=..+++|-|.|- .|.+.++....+ ..+.+ .+|++|++ +-+++.|+|+.++.
T Consensus 2 v~~vG~V~~~~~~------~~~~~~tL~D~TG---~I~~~~W~~~~~~~~~~~~~~-~~g~~v~v-~G~v~~~~g~~ql~ 70 (95)
T cd04478 2 VTLVGVVRNVEEQ------STNITYTIDDGTG---TIEVRQWLDDDNDDSSEVEPI-EEGTYVRV-FGNLKSFQGKKSIM 70 (95)
T ss_pred EEEEEEEEeeeEc------ccEEEEEEECCCC---cEEEEEeCCCCCccccccccc-ccCCEEEE-EEEEcccCCeeEEE
Confidence 6789999997541 2347889999874 399999986653 56666 79999998 56789999998876
Q ss_pred ee
Q 022219 100 FY 101 (300)
Q Consensus 100 ~~ 101 (300)
..
T Consensus 71 i~ 72 (95)
T cd04478 71 AF 72 (95)
T ss_pred EE
Confidence 43
No 37
>PRK13480 3'-5' exoribonuclease YhaM; Provisional
Probab=95.08 E-value=0.19 Score=47.13 Aligned_cols=82 Identities=15% Similarity=0.140 Sum_probs=63.4
Q ss_pred ehhhhhhccCCEEEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEE
Q 022219 12 RIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKK 91 (300)
Q Consensus 12 ~l~~~~~~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~r~kv~~ 91 (300)
.|+++. .|..|+.+.+|.+... +.+|.+.=...++|.|.|-. |..+++....+....+ ..|++|.+. -++..
T Consensus 4 ~i~~l~--~g~~v~~~~lv~~~~~-~~~knG~~yl~l~l~D~tG~---I~ak~W~~~~~~~~~~-~~g~vv~v~-G~v~~ 75 (314)
T PRK13480 4 GIEELE--VGEQVDHFLLIKSATK-GVASNGKPFLTLILQDKSGD---IEAKLWDVSPEDEATY-VPETIVHVK-GDIIN 75 (314)
T ss_pred hHhhcC--CCCEeeEEEEEEEcee-eecCCCCeEEEEEEEcCCcE---EEEEeCCCChhhHhhc-CCCCEEEEE-EEEEE
Confidence 467775 6788999999999866 34553344678999998653 9999998777777777 799999994 56678
Q ss_pred EcCeEEEEee
Q 022219 92 HQAELSAVFY 101 (300)
Q Consensus 92 ~~g~~~~~~~ 101 (300)
|+|++|+...
T Consensus 76 y~g~~Ql~i~ 85 (314)
T PRK13480 76 YRGRKQLKVN 85 (314)
T ss_pred ECCcceEEEE
Confidence 9999887653
No 38
>cd04485 DnaE_OBF DnaE_OBF: A subfamily of OB folds corresponding to the C-terminal OB-fold nucleic acid binding domain of Thermus aquaticus and Escherichia coli type C replicative DNA polymerase III alpha subunit (DnaE). The DNA polymerase holoenzyme of E. coli contains two copies of this replicative polymerase, each of which copies a different DNA strand. This group also contains Bacillus subtilis DnaE. Replication in B. subtilis and Staphylococcus aureus requires two different type C polymerases, polC and DnaE, both of which are thought to be included in the DNA polymerase holoenzyme. At the B. subtilis replication fork, polC appears to be involved in leading strand synthesis and DnaE in lagging strand synthesis.
Probab=95.02 E-value=0.076 Score=38.50 Aligned_cols=70 Identities=14% Similarity=0.301 Sum_probs=49.3
Q ss_pred EEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCeEEEEe
Q 022219 26 LLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAELSAVF 100 (300)
Q Consensus 26 viGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~r~kv~~~~g~~~~~~ 100 (300)
+.|+|.+... +.++.+.-+..++|.|.+-. +.+.+|.+..+.+......|.++.++ -+++.|+|..+...
T Consensus 2 i~g~v~~~~~-~~~k~g~~~~~~~l~D~tg~---~~~~~f~~~~~~~~~~l~~g~~v~v~-G~v~~~~~~~~l~~ 71 (84)
T cd04485 2 VAGLVTSVRR-RRTKKGKRMAFVTLEDLTGS---IEVVVFPETYEKYRDLLKEDALLLVE-GKVERRDGGLRLIA 71 (84)
T ss_pred EEEEEEEeEE-EEcCCCCEEEEEEEEeCCCe---EEEEECHHHHHHHHHHhcCCCEEEEE-EEEEecCCceEEEe
Confidence 6788888755 45554556799999998653 99999975533333333789999886 57787877666554
No 39
>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=94.51 E-value=0.42 Score=34.71 Aligned_cols=68 Identities=12% Similarity=0.238 Sum_probs=49.6
Q ss_pred EEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCeEEEEe
Q 022219 27 LGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAELSAVF 100 (300)
Q Consensus 27 iGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~r~kv~~~~g~~~~~~ 100 (300)
+.+|..++. +.||.+.-++.++|-|.+-. +.+.+|.+.....+.+ ..|.+|.++ .++..++|+.+...
T Consensus 3 ~~~v~~~~~-~~tk~g~~~~~~~l~D~tg~---i~~~~f~~~~~~~~~l-~~g~~v~v~-G~v~~~~~~~~l~~ 70 (83)
T cd04492 3 FFLIKSKEL-RTAKNGKPYLALTLQDKTGE---IEAKLWDASEEDEEKF-KPGDIVHVK-GRVEEYRGRLQLKI 70 (83)
T ss_pred EEEEEEeee-ecccCCCcEEEEEEEcCCCe---EEEEEcCCChhhHhhC-CCCCEEEEE-EEEEEeCCceeEEE
Confidence 567777766 45665556899999998763 9999998555444556 789999997 77777877666554
No 40
>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=94.06 E-value=0.57 Score=35.82 Aligned_cols=65 Identities=15% Similarity=0.121 Sum_probs=48.2
Q ss_pred EEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCC---------------------CCCCCCCCCCCEEEE
Q 022219 26 LLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSI---------------------DQLPRVLSPRDLILL 84 (300)
Q Consensus 26 viGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~---------------------~~LP~v~~~GDII~l 84 (300)
++|+|+.... +.+ +.+|+|-|.|= -|.|.++.... +..+.+ ++|++|++
T Consensus 2 ivG~V~sv~~----~~~--~~~~tLdDgTG---~Ie~~~W~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i-~~G~vvrV 71 (92)
T cd04483 2 ILGTVVSRRE----RET--FYSFGVDDGTG---VVNCVCWKNLSYAEVSSRSDAARILKSALMALKQAKVL-EIGDLLRV 71 (92)
T ss_pred eEEEEEEEEe----cCC--eEEEEEecCCc---eEEEEEEcCcCccccccccccccccccccccccccccc-CCCCEEEE
Confidence 6899998743 212 47888888765 28999997543 345556 79999999
Q ss_pred eeEEEEEEcCeEEEEee
Q 022219 85 KNVMIKKHQAELSAVFY 101 (300)
Q Consensus 85 ~r~kv~~~~g~~~~~~~ 101 (300)
+ -+++.|+|+.++...
T Consensus 72 ~-G~i~~frg~~ql~i~ 87 (92)
T cd04483 72 R-GSIRTYRGEREINAS 87 (92)
T ss_pred E-EEEeccCCeeEEEEE
Confidence 6 789999999887654
No 41
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain
Probab=91.58 E-value=1.9 Score=33.24 Aligned_cols=78 Identities=21% Similarity=0.224 Sum_probs=52.2
Q ss_pred hhhhhhcc--CCEEEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCC-CCCCCCCEEEEeeEEE
Q 022219 13 IKELAMHV--KHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLP-RVLSPRDLILLKNVMI 89 (300)
Q Consensus 13 l~~~~~~~--~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP-~v~~~GDII~l~r~kv 89 (300)
|+++++.. -..+-|.|=|.+++.. ++| .+-|+|+|+. ..+.|.+|+.....++ ...+.||-|++ +.++
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 34444432 2679999999998764 222 3667999965 3499999998777787 44478997766 3455
Q ss_pred EEE--cCeEEEE
Q 022219 90 KKH--QAELSAV 99 (300)
Q Consensus 90 ~~~--~g~~~~~ 99 (300)
.-| .|++++.
T Consensus 82 ~~y~~~G~~sl~ 93 (99)
T PF13742_consen 82 SFYEPRGSLSLI 93 (99)
T ss_pred EEECCCcEEEEE
Confidence 544 4445544
No 42
>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=90.67 E-value=3.8 Score=28.83 Aligned_cols=66 Identities=17% Similarity=0.088 Sum_probs=44.0
Q ss_pred eEEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCChhhhhcCCCcccEEEEEecCchhhh
Q 022219 171 DLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRVSTDRSYENF 250 (300)
Q Consensus 171 Dl~~qVv~~~~~~~~~~~~L~VwDgT~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~G~~l~V~~~~~~~~~ 250 (300)
.+.+.|.++. ...+....+.+.|+|+ .+++.+|+.....
T Consensus 2 ~v~G~V~~~~-~~~~~~~~~~l~D~tg----------------------------------------~i~~~~~~~~~~~ 40 (75)
T PF01336_consen 2 TVEGRVTSIR-RSGGKIVFFTLEDGTG----------------------------------------SIQVVFFNEEYER 40 (75)
T ss_dssp EEEEEEEEEE-EEETTEEEEEEEETTE----------------------------------------EEEEEEETHHHHH
T ss_pred EEEEEEEEEE-cCCCCEEEEEEEECCc----------------------------------------cEEEEEccHHhhH
Confidence 5678888885 3356788888999994 1457777733334
Q ss_pred hhcCCCCCcEEEEeccEEEeeCcE-EEEE
Q 022219 251 GRYFTATGKWVRIRNMSCQVSSGM-WHGL 278 (300)
Q Consensus 251 ~~~~lk~G~wv~l~Nv~~k~~~g~-leg~ 278 (300)
..+.+++|++|+++ =+++...+. +|-.
T Consensus 41 ~~~~l~~g~~v~v~-G~v~~~~~~~~~l~ 68 (75)
T PF01336_consen 41 FREKLKEGDIVRVR-GKVKRYNGGELELI 68 (75)
T ss_dssp HHHTS-TTSEEEEE-EEEEEETTSSEEEE
T ss_pred HhhcCCCCeEEEEE-EEEEEECCccEEEE
Confidence 57889999999999 444544333 5443
No 43
>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=88.13 E-value=4 Score=28.53 Aligned_cols=68 Identities=18% Similarity=0.282 Sum_probs=44.3
Q ss_pred EEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCeEEEEe
Q 022219 26 LLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAELSAVF 100 (300)
Q Consensus 26 viGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~r~kv~~~~g~~~~~~ 100 (300)
+.|.|++.... +++|.. ...+++.|.+- .+.+.+|... ..+......|+.+.+. -|+..|+|+++...
T Consensus 2 i~~~V~~~~~~-~~~~~~-~~~~~~~D~~g---~i~~~~F~~~-~~~~~~~~~G~~~~v~-Gkv~~~~~~~qi~~ 69 (75)
T cd04488 2 VEGTVVSVEVV-PRRGRR-RLKVTLSDGTG---TLTLVFFNFQ-PYLKKQLPPGTRVRVS-GKVKRFRGGLQIVH 69 (75)
T ss_pred EEEEEEEEEec-cCCCcc-EEEEEEEcCCC---EEEEEEECCC-HHHHhcCCCCCEEEEE-EEEeecCCeeEEeC
Confidence 56777775332 223333 78999999854 3999999732 2333434789988885 56777877766554
No 44
>cd03524 RPA2_OBF_family RPA2_OBF_family: A family of oligonucleotide binding (OB) folds with similarity to the OB fold of the single strand (ss) DNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA contains six OB folds, which are involved in ssDNA binding and in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. This family also includes OB folds similar to those found in Escherichia coli SSB, the wedge domain of E. coli RecG (a branched-DNA-specific helicase), E. coli ssDNA specific exodeoxyribonuclease VII large subunit, Pyroco
Probab=86.54 E-value=8.1 Score=26.31 Aligned_cols=68 Identities=18% Similarity=0.137 Sum_probs=42.5
Q ss_pred eEEEEEEEEEeeCC--CCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCChhhhhcCCCcccEEEEEecCchh
Q 022219 171 DLVCKVFHVSYDDS--KGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRVSTDRSYE 248 (300)
Q Consensus 171 Dl~~qVv~~~~~~~--~~~~~L~VwDgT~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~G~~l~V~~~~~~~ 248 (300)
++.|+|+++. ... ...+.+.+.|+|+. .+.+.+|+...
T Consensus 1 ~v~g~v~~~~-~~~~~~~~~~~~l~D~~~~---------------------------------------~i~~~~~~~~~ 40 (75)
T cd03524 1 TIVGIVVAVE-EIRTEGKVLIFTLTDGTGG---------------------------------------TIRVTLFGELA 40 (75)
T ss_pred CeEEEEEeec-ccccCCeEEEEEEEcCCCC---------------------------------------EEEEEEEchHH
Confidence 4678888887 323 35678888888810 12455554433
Q ss_pred hhhhcCCCCCcEEEEeccEEEeeCcEEEEEE
Q 022219 249 NFGRYFTATGKWVRIRNMSCQVSSGMWHGLL 279 (300)
Q Consensus 249 ~~~~~~lk~G~wv~l~Nv~~k~~~g~leg~l 279 (300)
.-....+++|+++.+. .+++..+|.++-.+
T Consensus 41 ~~~~~~~~~g~~v~v~-g~v~~~~~~~~l~~ 70 (75)
T cd03524 41 EELENLLKEGQVVYIK-GKVKKFRGRLQLIV 70 (75)
T ss_pred HHHHhhccCCCEEEEE-EEEEecCCeEEEEe
Confidence 2224569999999998 66666555554443
No 45
>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=85.77 E-value=9.4 Score=28.31 Aligned_cols=70 Identities=17% Similarity=0.258 Sum_probs=47.3
Q ss_pred EEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEec-CCCCCCCCCCC-CCCEEEEeeE-EEEEEcCeEEE
Q 022219 24 VNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFT-SSIDQLPRVLS-PRDLILLKNV-MIKKHQAELSA 98 (300)
Q Consensus 24 vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~-~~~~~LP~v~~-~GDII~l~r~-kv~~~~g~~~~ 98 (300)
|-+-|-|.+... +.+|.+-...+|.|+|-+. ++.|.+|. ...+.+-.+ + .||-|+++.- ...+|.++...
T Consensus 2 v~i~G~Vf~~e~-re~k~g~~i~~~~itD~t~---Si~~K~F~~~~~~~~~~i-k~~G~~v~v~G~v~~D~f~~e~~~ 74 (82)
T cd04484 2 VVVEGEVFDLEI-RELKSGRKILTFKVTDYTS---SITVKKFLRKDEKDKEEL-KSKGDWVRVRGKVQYDTFSKELVL 74 (82)
T ss_pred EEEEEEEEEEEE-EEecCCCEEEEEEEEcCCC---CEEEEEeccCChhHHhhc-ccCCCEEEEEEEEEEccCCCceEE
Confidence 345666665533 5567668899999999654 59999998 344555556 5 8999988654 44456555443
No 46
>cd04487 RecJ_OBF2_like RecJ_OBF2_like: A subfamily of OB folds corresponding to the second OB fold (OBF2) of archaeal-specific proteins with similarity to eubacterial RecJ. RecJ is an ssDNA-specific exonuclease. Although the overall sequence similarity of these proteins to eubacterial RecJ proteins is marginal, they appear to carry motifs, which have been shown to be essential for nuclease function in Escherichia coli RecJ. In addition to this OB fold, most proteins in this subfamily contain: i) an N-terminal OB fold belonging to a different domain family (the ribosomal S1-like RNA-binding family); and ii) a domain, C-terminal to OBF2, characteristic of DHH family proteins. DHH family proteins include E. coli RecJ, and are predicted to have a phosphoesterase function.
Probab=85.68 E-value=10 Score=27.51 Aligned_cols=64 Identities=11% Similarity=0.158 Sum_probs=39.7
Q ss_pred EEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEE-eeEEEEEEcCeEEEEe
Q 022219 26 LLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILL-KNVMIKKHQAELSAVF 100 (300)
Q Consensus 26 viGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l-~r~kv~~~~g~~~~~~ 100 (300)
+-|.|..+.. +|+.+. |+|.|+.. .|.|.+|++....++.-...||-|.+ =++.+ .+|+.|+..
T Consensus 3 v~GeVs~~~~----~~GHvy--fsLkD~~a---~i~cv~f~~~~~~~~~~l~~Gd~V~v~G~v~~--~~G~~ql~v 67 (73)
T cd04487 3 IEGEVVQIKQ----TSGPTI--FTLRDETG---TVWAAAFEEAGVRAYPEVEVGDIVRVTGEVEP--RDGQLQIEV 67 (73)
T ss_pred EEEEEecccc----CCCCEE--EEEEcCCE---EEEEEEEchhccCCcCCCCCCCEEEEEEEEec--CCeEEEEEE
Confidence 4566776652 455544 57788543 39999998755445544478995544 44444 566666544
No 47
>PRK07373 DNA polymerase III subunit alpha; Reviewed
Probab=85.34 E-value=3.1 Score=41.09 Aligned_cols=89 Identities=16% Similarity=0.189 Sum_probs=61.5
Q ss_pred cceeehhhhhh-ccCCEEEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEee
Q 022219 8 GGIVRIKELAM-HVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKN 86 (300)
Q Consensus 8 y~y~~l~~~~~-~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~r 86 (300)
+..+++.++.. ..++.|.+.|+|+..+. ++||.++-|+-++|-|.+-. +.+.+|.+.-+..-.....|.+++++
T Consensus 266 ~~~~~~~~l~~~~~~~~v~vaG~I~~ik~-~~TKkG~~maf~~leD~tG~---ie~vvFp~~y~~~~~~l~~~~~v~v~- 340 (449)
T PRK07373 266 LSPINLSELEEQKEKTKVSAVVMLNEVKK-IVTKKGDPMAFLQLEDLSGQ---SEAVVFPKSYERISELLQVDARLIIW- 340 (449)
T ss_pred cCCcCHHHHhcccCCCEEEEEEEEEEeEe-cccCCCCEEEEEEEEECCCC---EEEEECHHHHHHHHHHhccCCEEEEE-
Confidence 34456777642 24678999999999987 46666678999999999763 99999976444444444678888885
Q ss_pred EEEEEEcCeEEEEee
Q 022219 87 VMIKKHQAELSAVFY 101 (300)
Q Consensus 87 ~kv~~~~g~~~~~~~ 101 (300)
.+++.-.++.+.+.+
T Consensus 341 G~v~~~~~~~~liv~ 355 (449)
T PRK07373 341 GKVDRRDDQVQLIVE 355 (449)
T ss_pred EEEEecCCeEEEEEe
Confidence 466653344555543
No 48
>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=84.34 E-value=4.2 Score=30.03 Aligned_cols=59 Identities=14% Similarity=0.296 Sum_probs=41.5
Q ss_pred EEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCC--CCCCCCCCCCEEEEeeEEEEE
Q 022219 24 VNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSID--QLPRVLSPRDLILLKNVMIKK 91 (300)
Q Consensus 24 vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~--~LP~v~~~GDII~l~r~kv~~ 91 (300)
+.+.|+|.+.+ .||.++- .++|-|.+-. +.|.+|.+..+ ..-.....|.+|.++ .++..
T Consensus 2 v~i~GiI~~v~---~TK~g~~--~~~leD~~G~---~Ev~~F~~~~~~~~~~~~l~~d~~v~v~-g~v~~ 62 (79)
T cd04490 2 VSIIGMVNDVR---STKNGHR--IVELEDTTGR---ITVLLTKDKEELFEEAEDILPDEVIGVS-GTVSK 62 (79)
T ss_pred EEEEEEEeEEE---EcCCCCE--EEEEECCCCE---EEEEEeCchhhhhhhhhhccCCCEEEEE-EEEec
Confidence 56899999998 4543333 7888888653 99999987766 555554667777775 45543
No 49
>PF09104 BRCA-2_OB3: BRCA2, oligonucleotide/oligosaccharide-binding, domain 3; InterPro: IPR015188 This domain assumes an OB fold, which consists of a highly curved five-stranded beta-sheet that closes on itself to form a beta-barrel. OB3 has a pronounced groove formed by one face of the curved sheet and is demarcated by two loops, one between beta 1 and beta 2 and another between beta 4 and beta 5, which allows for strong ssDNA binding []. ; PDB: 1IYJ_D 1MIU_A.
Probab=81.07 E-value=11 Score=31.33 Aligned_cols=73 Identities=18% Similarity=0.286 Sum_probs=42.4
Q ss_pred eehhhhhh----ccCCEEEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCC-CCCCCCCCCCCEEEEe
Q 022219 11 VRIKELAM----HVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSI-DQLPRVLSPRDLILLK 85 (300)
Q Consensus 11 ~~l~~~~~----~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~-~~LP~v~~~GDII~l~ 85 (300)
+.+.++.. .+-+-|+++|+|+.. ++++++.--+-|.|++..- +.|+++..-. =.+-.+..+|-+|-..
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 34555544 234569999999999 4557787778899999865 8888887522 2334444789999999
Q ss_pred eEEEE
Q 022219 86 NVMIK 90 (300)
Q Consensus 86 r~kv~ 90 (300)
|++-+
T Consensus 77 NLqwR 81 (143)
T PF09104_consen 77 NLQWR 81 (143)
T ss_dssp EEEE-
T ss_pred eeEee
Confidence 99887
No 50
>KOG3056 consensus Protein required for S-phase initiation or completion [Cell cycle control, cell division, chromosome partitioning]
Probab=80.88 E-value=2.7 Score=42.04 Aligned_cols=69 Identities=20% Similarity=0.296 Sum_probs=57.0
Q ss_pred EEEEEEEEecCCceecC-CCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCe
Q 022219 24 VNLLGVVLEFSIPRKSQ-GTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAE 95 (300)
Q Consensus 24 vnviGVVvd~~~P~~tr-G~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~r~kv~~~~g~ 95 (300)
--++|||++-..|+.|. |.+|+ .++|.|-... ..|.|-+|.+.-+.+=.+ +.|+||-|-|..|-..++.
T Consensus 188 Wvt~GvI~~K~~~K~t~~G~~y~-iwkL~dLk~~-q~vslfLFG~a~k~~wk~-k~GtVialLNp~v~k~~~g 257 (578)
T KOG3056|consen 188 WVTMGVIVEKSDPKFTSNGNPYS-IWKLTDLKDH-QTVSLFLFGKAHKRYWKI-KLGTVIALLNPEVLKDRPG 257 (578)
T ss_pred eEEEEEEeecCCcccccCCCceE-EEEeeecCcc-ceeEEEEecHHHHHHhhh-ccCcEEEEeCccccCCCCC
Confidence 45899999999999985 66654 5888887764 469999999877888888 6899999999999877654
No 51
>PRK05673 dnaE DNA polymerase III subunit alpha; Validated
Probab=80.82 E-value=4.6 Score=44.45 Aligned_cols=88 Identities=14% Similarity=0.224 Sum_probs=62.4
Q ss_pred ceeehhhhhh-ccCCEEEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeE
Q 022219 9 GIVRIKELAM-HVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNV 87 (300)
Q Consensus 9 ~y~~l~~~~~-~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~r~ 87 (300)
..+++.++.. ..+..|.+.|+|+..+.+ +||.++-++.++|-|.+-. +.+.+|.+.-+..=.....|.+|.+. .
T Consensus 964 ~~~~~~~l~~~~~g~~V~v~G~I~~vk~~-~TKkG~~mafltLeD~TG~---iEvviFp~~ye~~~~~L~~g~iV~V~-G 1038 (1135)
T PRK05673 964 RDTRLADLEPTEGGSVVTVAGLVVSVRRR-VTKRGNKMAIVTLEDLSGR---IEVMLFSEALEKYRDLLEEDRIVVVK-G 1038 (1135)
T ss_pred CCcCHHHHhccccCceEEEEEEEEEEEec-ccCCCCeEEEEEEEeCCCc---EEEEECHHHHHHHHHHhccCCEEEEE-E
Confidence 3456666642 246779999999999875 5655666899999999763 99999986533333333689998884 4
Q ss_pred EEEEEcCeEEEEee
Q 022219 88 MIKKHQAELSAVFY 101 (300)
Q Consensus 88 kv~~~~g~~~~~~~ 101 (300)
+++...++.+++.+
T Consensus 1039 kVe~~~~~~qlii~ 1052 (1135)
T PRK05673 1039 QVSFDDGGLRLTAR 1052 (1135)
T ss_pred EEEecCCeEEEEEe
Confidence 77777677777664
No 52
>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=80.05 E-value=8.3 Score=29.24 Aligned_cols=60 Identities=20% Similarity=0.332 Sum_probs=37.3
Q ss_pred EEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCC--CCCCCCCCCCCCEEEEeeEEEEEEc
Q 022219 26 LLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSS--IDQLPRVLSPRDLILLKNVMIKKHQ 93 (300)
Q Consensus 26 viGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~--~~~LP~v~~~GDII~l~r~kv~~~~ 93 (300)
|-|-|..+.. .-+|.. +-|+|.|++. .|.|.+|++. ...+..-...||-|.+..- +..|.
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 4566665543 214555 4467789763 4999999976 4455554489997777543 44444
No 53
>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=78.64 E-value=2.6 Score=34.11 Aligned_cols=34 Identities=15% Similarity=0.338 Sum_probs=27.9
Q ss_pred eEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcC
Q 022219 60 LLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQA 94 (300)
Q Consensus 60 l~v~iF~~~~~~LP~v~~~GDII~l~r~kv~~~~g 94 (300)
|.|.+|-++.+..-.+ ++||.|+|+||.++....
T Consensus 62 i~It~yD~H~~~ar~l-K~GdfV~L~NVhiK~~~~ 95 (123)
T cd04498 62 IDILVYDNHVELAKSL-KPGDFVRIYNVHAKSYSS 95 (123)
T ss_pred EEEEEEcchHHHHhhC-CCCCEEEEEEEEEEeccC
Confidence 6777887877666667 799999999999987766
No 54
>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=78.32 E-value=5.9 Score=30.71 Aligned_cols=49 Identities=14% Similarity=0.032 Sum_probs=35.4
Q ss_pred cEEEEEecCchhhhhhcCCCCCcEEEEeccEEEee-------CcEEEEEEeeCCce
Q 022219 237 TVLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVS-------SGMWHGLLQSSSKI 285 (300)
Q Consensus 237 ~~l~V~~~~~~~~~~~~~lk~G~wv~l~Nv~~k~~-------~g~leg~l~~~sk~ 285 (300)
..+++++|+..+..-...|++|+|+.|.|.+++.. ..-.|..|..++.+
T Consensus 47 ~~I~~t~~~~~~~~f~~~l~eG~vy~i~~~~V~~a~~~y~~~~~~yeI~f~~~t~~ 102 (104)
T cd04474 47 GEIRATFFNDAVDKFYDLLEVGKVYYISKGSVKVANKKFNTLKNDYEITFNRDTSI 102 (104)
T ss_pred CEEEEEEehHHHHHhhcccccccEEEEeccEEeeccccCCCCCCcEEEEECCCcEE
Confidence 35788888765544467899999999999999873 23466666655443
No 55
>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=76.59 E-value=7.2 Score=29.76 Aligned_cols=50 Identities=14% Similarity=0.016 Sum_probs=35.5
Q ss_pred EEEEEecCchhhhhhcCCCCCcEEEEeccEEEeeCcEEEEEEeeCCceEEcCC
Q 022219 238 VLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSD 290 (300)
Q Consensus 238 ~l~V~~~~~~~~~~~~~lk~G~wv~l~Nv~~k~~~g~leg~l~~~sk~~~l~~ 290 (300)
.+.|++|...+..... ..|+.+.|+|++++..+| .+......|++..-++
T Consensus 40 ~i~vtLWg~~a~~~~~--~~~~vv~~~~~~i~~~~~-~~l~~~~~s~i~~np~ 89 (101)
T cd04475 40 SVELTLWGEQAELFDG--SENPVIAIKGVKVSEFNG-KSLSTGSSSTIIINPD 89 (101)
T ss_pred EEEEEEEHHHhhhccc--CCCCEEEEEeeEEEecCC-eEEeecCceeEEECCC
Confidence 4679999887754332 239999999999988765 4555666778855443
No 56
>TIGR00237 xseA exodeoxyribonuclease VII, large subunit. This family consist of exodeoxyribonuclease VII, large subunit XseA which catalyses exonucleolytic cleavage in either the 5'-3' or 3'-5' direction to yield 5'-phosphomononucleotides. Exonuclease VII consists of one large subunit and four small subunits.
Probab=76.52 E-value=22 Score=34.83 Aligned_cols=80 Identities=15% Similarity=0.267 Sum_probs=52.8
Q ss_pred hhhhhhccCCEEEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEe-eEEEEE
Q 022219 13 IKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLK-NVMIKK 91 (300)
Q Consensus 13 l~~~~~~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~-r~kv~~ 91 (300)
|+.+++..=..|-|-|=|..++.+ +.| .+-|+|+|+.- -|.|.+|+.....|+.-.+.|+=|+++ ++.+-.
T Consensus 9 ik~~le~~~~~v~V~GEisn~~~~--~sG---H~YFtLkD~~a---~i~~vmf~~~~~~l~f~~~~G~~V~v~g~v~~y~ 80 (432)
T TIGR00237 9 IKALLEATFLQVWIQGEISNFTQP--VSG---HWYFTLKDENA---QVRCVMFRGNNNRLKFRPQNGQQVLVRGGISVYE 80 (432)
T ss_pred HHHHHHhhCCcEEEEEEecCCeeC--CCc---eEEEEEEcCCc---EEEEEEEcChhhCCCCCCCCCCEEEEEEEEEEEC
Confidence 445554322368899999998854 334 46678899753 399999998777887756889966663 344443
Q ss_pred EcCeEEEEe
Q 022219 92 HQAELSAVF 100 (300)
Q Consensus 92 ~~g~~~~~~ 100 (300)
-.|+.++..
T Consensus 81 ~~G~~ql~v 89 (432)
T TIGR00237 81 PRGDYQIIC 89 (432)
T ss_pred CCCcEEEEE
Confidence 355566554
No 57
>PRK06920 dnaE DNA polymerase III DnaE; Reviewed
Probab=75.62 E-value=8.3 Score=42.34 Aligned_cols=89 Identities=10% Similarity=0.169 Sum_probs=61.2
Q ss_pred cceeehhhhhhccCCEEEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeE
Q 022219 8 GGIVRIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNV 87 (300)
Q Consensus 8 y~y~~l~~~~~~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~r~ 87 (300)
+..+++.++....+..|.+.|+|+..+.+ +|+.++-+.-++|-|.+-. +.+.+|.+.-+..-.....|.++++. -
T Consensus 930 ~~~~~~~~l~~~~~~~v~v~g~i~~~~~~-~tk~g~~maf~~leD~tg~---~e~~vFp~~y~~~~~~l~~~~~~~v~-G 1004 (1107)
T PRK06920 930 LEIPSLAQAMRHKKKVQRAIVYITSVKVI-RTKKGQKMAFITFCDQNDE---MEAVVFPETYIHFSDKLQEGAIVLVD-G 1004 (1107)
T ss_pred hCCcCHHHHhhcCCCEEEEEEEEEEeEee-cCCCCCeEEEEEEeeCCCc---EEEEECHHHHHHHHHHhccCCEEEEE-E
Confidence 34456777643346689999999999874 5655667899999998763 99999986544444433678888774 4
Q ss_pred EEEEEcCeEEEEee
Q 022219 88 MIKKHQAELSAVFY 101 (300)
Q Consensus 88 kv~~~~g~~~~~~~ 101 (300)
+++.-+++.+.+.+
T Consensus 1005 ~v~~~~~~~~~~~~ 1018 (1107)
T PRK06920 1005 TIELRNHKLQWIVN 1018 (1107)
T ss_pred EEEecCCcEEEEEe
Confidence 66654555565554
No 58
>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=74.83 E-value=11 Score=28.51 Aligned_cols=57 Identities=14% Similarity=0.230 Sum_probs=41.8
Q ss_pred cccEEEEEecCchhhhhhcCCCCCcEEEEeccEEEeeCc-------EEEEEEeeCCceEEcCCC
Q 022219 235 VGTVLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSG-------MWHGLLQSSSKIRLFSDN 291 (300)
Q Consensus 235 ~G~~l~V~~~~~~~~~~~~~lk~G~wv~l~Nv~~k~~~g-------~leg~l~~~sk~~~l~~~ 291 (300)
.|..++.+........-...+++|.|..|.|..+..+.| ...-.|...++|...+..
T Consensus 8 ~G~~I~A~I~~~~~~~f~~~l~Eg~~y~i~~F~V~~~~~~yr~t~h~y~I~f~~~T~V~~~~~~ 71 (95)
T PF02721_consen 8 KGDKIQATIPKELVDKFKDSLKEGSWYTISNFTVSPNSGSYRPTDHKYKINFMPNTKVTEIDPP 71 (95)
T ss_pred CCCEEEEEECHHHHHHHHhhcccCCEEEeEeEEEEeCCCceeccCCCEEEEECCcCeEEECCCC
Confidence 356778888766665557889999999999998876533 355677777887766544
No 59
>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed
Probab=74.73 E-value=27 Score=34.19 Aligned_cols=71 Identities=15% Similarity=0.233 Sum_probs=48.6
Q ss_pred CEEEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEe-eEEEEEEcCeEEEEe
Q 022219 22 HKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLK-NVMIKKHQAELSAVF 100 (300)
Q Consensus 22 ~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~-r~kv~~~~g~~~~~~ 100 (300)
..|-|-|=|..++.+ +.| .|-|+|.|... .++|.+|+.....++.-...|+-|+++ ++.+-.-.|+.++..
T Consensus 24 ~~v~v~gEis~~~~~--~sG---H~Yf~Lkd~~a---~i~~~~~~~~~~~~~~~~~~G~~v~v~g~~~~y~~~g~~ql~v 95 (438)
T PRK00286 24 GQVWVRGEISNFTRH--SSG---HWYFTLKDEIA---QIRCVMFKGSARRLKFKPEEGMKVLVRGKVSLYEPRGDYQLIV 95 (438)
T ss_pred CcEEEEEEeCCCeeC--CCC---eEEEEEEcCCc---EEEEEEEcChhhcCCCCCCCCCEEEEEEEEEEECCCCCEEEEE
Confidence 468888998888764 233 46689999943 499999998777888755789966653 334333344455544
No 60
>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=72.46 E-value=55 Score=27.17 Aligned_cols=64 Identities=17% Similarity=0.208 Sum_probs=34.8
Q ss_pred CceEeEEEEEEEEEeeCCCCeE-EEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCChhhhhcCCCcccEEEEEecC
Q 022219 167 HRYFDLVCKVFHVSYDDSKGLW-MLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRVSTDR 245 (300)
Q Consensus 167 ~~f~Dl~~qVv~~~~~~~~~~~-~L~VwDgT~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~G~~l~V~~~~ 245 (300)
=+-||+++-|+.|. . ..+.. .+|+.|.--| .+.|.+|.
T Consensus 18 ~~EvD~VG~VvsV~-~-~~~f~~~vYLsD~~~N---------------------------------------ll~Ikfw~ 56 (143)
T PF09104_consen 18 YGEVDTVGFVVSVS-K-KQGFQPLVYLSDECHN---------------------------------------LLAIKFWT 56 (143)
T ss_dssp CCEEEEEEEEEEEE----TTS--EEEEE-TTS----------------------------------------EEEEEESS
T ss_pred ccccceEEEEEEEE-e-cCCCceeEEeecCCcc---------------------------------------EEEEEecc
Confidence 35699999999996 4 33443 3777654422 24567777
Q ss_pred chhhhhhcC-CCCCcEEEEeccEEEee
Q 022219 246 SYENFGRYF-TATGKWVRIRNMSCQVS 271 (300)
Q Consensus 246 ~~~~~~~~~-lk~G~wv~l~Nv~~k~~ 271 (300)
.-..++.+. +|+|..|-..|++-+..
T Consensus 57 ~l~~~~~eDilk~~~liA~SNLqwR~~ 83 (143)
T PF09104_consen 57 GLNQYGYEDILKPGSLIAASNLQWRPE 83 (143)
T ss_dssp -------SS---TT-EEEEEEEEE-S-
T ss_pred CccccchhhhcCcceEEEEeeeEeecc
Confidence 766666544 69999999999999863
No 61
>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=72.21 E-value=13 Score=28.78 Aligned_cols=64 Identities=19% Similarity=0.259 Sum_probs=42.4
Q ss_pred EEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCC-CCCCCCCCCCCCEEEEeeEEEEEEcC
Q 022219 25 NLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSS-IDQLPRVLSPRDLILLKNVMIKKHQA 94 (300)
Q Consensus 25 nviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~-~~~LP~v~~~GDII~l~r~kv~~~~g 94 (300)
+++|||+....+. +..+=.+-|.|+++.. +.|+++..- ...+-.+-..+-.|-+.|++.+....
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 4689999987754 4566678999999976 888888731 12222333445666677776665544
No 62
>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=69.93 E-value=43 Score=24.91 Aligned_cols=26 Identities=27% Similarity=0.193 Sum_probs=20.8
Q ss_pred EeEEEEEEEEEeeCCCCeEEEEEEcCCC
Q 022219 170 FDLVCKVFHVSYDDSKGLWMLFVWDGTD 197 (300)
Q Consensus 170 ~Dl~~qVv~~~~~~~~~~~~L~VwDgT~ 197 (300)
+.+++.|.++. . .+..+.+.+-|+|+
T Consensus 2 v~~vG~V~~~~-~-~~~~~~~tL~D~TG 27 (95)
T cd04478 2 VTLVGVVRNVE-E-QSTNITYTIDDGTG 27 (95)
T ss_pred EEEEEEEEeee-E-cccEEEEEEECCCC
Confidence 46788888887 4 46788999999996
No 63
>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=67.38 E-value=13 Score=29.09 Aligned_cols=53 Identities=15% Similarity=0.305 Sum_probs=38.2
Q ss_pred ceeehhhhhhccCCEEEEEEEEEe-cCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCC
Q 022219 9 GIVRIKELAMHVKHKVNLLGVVLE-FSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSS 68 (300)
Q Consensus 9 ~y~~l~~~~~~~~~~vnviGVVvd-~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~ 68 (300)
.|+||..+- ..|+. +|+| +++| .+-+.-|++++.|.|+-+..++|+|.+|+..
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 566666664 22221 4566 4554 4456899999999999998899999999864
No 64
>PRK07374 dnaE DNA polymerase III subunit alpha; Validated
Probab=67.11 E-value=17 Score=40.28 Aligned_cols=89 Identities=15% Similarity=0.220 Sum_probs=62.2
Q ss_pred cceeehhhhhhc-cCCEEEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEee
Q 022219 8 GGIVRIKELAMH-VKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKN 86 (300)
Q Consensus 8 y~y~~l~~~~~~-~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~r 86 (300)
+..+++.++.+. .+..|.+.|+|+..+.+ +|+.++-|.-++|-|.+-. +.+.+|.+.-+..-.....|.++++ .
T Consensus 986 ~~~~~~~~l~~~~~~~~v~v~g~i~~~k~~-~Tk~G~~maf~~leD~tg~---~e~vvFp~~y~~~~~~l~~~~~~~v-~ 1060 (1170)
T PRK07374 986 LAPISLSSLEEQPDKAKVSAIAMIPEMKQV-TTRKGDRMAILQLEDLTGS---CEAVVFPKSYERLSDHLMTDTRLLV-W 1060 (1170)
T ss_pred hCCcCHHHHhcccCCCEEEEEEEEEEeEec-ccCCCCEEEEEEEEECCCC---EEEEECHHHHHHHHHHhccCCEEEE-E
Confidence 344566666432 45679999999999875 5665678999999999764 9999998654544443367888877 4
Q ss_pred EEEEEEcCeEEEEee
Q 022219 87 VMIKKHQAELSAVFY 101 (300)
Q Consensus 87 ~kv~~~~g~~~~~~~ 101 (300)
-+++.-.++.+++.+
T Consensus 1061 g~v~~~~~~~~~~~~ 1075 (1170)
T PRK07374 1061 AKVDRRDDRVQLIID 1075 (1170)
T ss_pred EEEEecCCeEEEEEe
Confidence 466654455666654
No 65
>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=62.18 E-value=33 Score=27.27 Aligned_cols=40 Identities=20% Similarity=0.233 Sum_probs=27.4
Q ss_pred CCCCCCCCCCCCEEEEeeE-------EEEEEcCeEEEEeecC-ceEEEE
Q 022219 69 IDQLPRVLSPRDLILLKNV-------MIKKHQAELSAVFYKD-SSSFAL 109 (300)
Q Consensus 69 ~~~LP~v~~~GDII~l~r~-------kv~~~~g~~~~~~~~~-~ss~~v 109 (300)
...+|.+ .+||+|.++=. ++|.|.|-.-+.-+.+ .++|.|
T Consensus 13 ~~~~p~f-~~GD~v~V~~~i~e~~k~r~q~f~GvvIa~~~~g~~ssftl 60 (113)
T PF01245_consen 13 KKDIPEF-RVGDTVRVTYKISEGNKERIQVFEGVVIARRRRGLNSSFTL 60 (113)
T ss_dssp SSSSSSS-SSSSEEEEEEEEESSSSEEEEEEEEEEEEEEBSSTSSEEEE
T ss_pred hcCCCCc-CCCCEEEEEEEEecCCCceeEEEEEEEEEEECCCCCeeEEE
Confidence 3689999 79999999764 2467777655554433 366775
No 66
>PF15072 DUF4539: Domain of unknown function (DUF4539)
Probab=62.00 E-value=27 Score=26.33 Aligned_cols=63 Identities=22% Similarity=0.287 Sum_probs=43.6
Q ss_pred EEEEEEE-EEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcC
Q 022219 23 KVNLLGV-VLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQA 94 (300)
Q Consensus 23 ~vnviGV-Vvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~r~kv~~~~g 94 (300)
+|...++ |..+.+ .+.|. .+.+.|+|-. +.+.|=++-.+..|....+|=+++|+++.|-.=..
T Consensus 3 KVp~l~v~Iks~~~----~~~D~--~v~l~DpTG~---i~~tiH~~v~~~y~~~l~~GavLlLk~V~Vf~ps~ 66 (86)
T PF15072_consen 3 KVPCLVVIIKSIVP----SSEDA--FVVLKDPTGE---IRGTIHRKVLEEYGDELSPGAVLLLKDVTVFSPSP 66 (86)
T ss_pred ccCEEEEEEEEeec----cCCCe--EEEEECCCCc---EEEEEeHHHHhhcCCccccCEEEEEeeeeEEecCC
Confidence 4444444 444544 23455 6689998763 88888887666677766999999999998866443
No 67
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=60.93 E-value=41 Score=35.01 Aligned_cols=78 Identities=19% Similarity=0.197 Sum_probs=51.3
Q ss_pred ehhhhhhccCCEEEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEE
Q 022219 12 RIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKK 91 (300)
Q Consensus 12 ~l~~~~~~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~r~kv~~ 91 (300)
+|+++. .|..+.+.|.|++.....+ +. -..++++.|.+- .+.+.+|.-+...+.....+|+-+.+.. |++.
T Consensus 52 ~i~~l~--~g~~vtv~g~V~~~~~~~~--~~-~~~~v~l~D~tg---~i~l~~F~~n~~~~~~~l~~G~~~~v~G-kv~~ 122 (681)
T PRK10917 52 PIAELR--PGEKVTVEGEVLSAEVVFG--KR-RRLTVTVSDGTG---NLTLRFFNFNQPYLKKQLKVGKRVAVYG-KVKR 122 (681)
T ss_pred CHHHCC--CCCEEEEEEEEEEEEEccC--Cc-eEEEEEEEECCe---EEEEEEEccCcHHHHhhCCCCCEEEEEE-EEEe
Confidence 455554 6889999999998733222 22 378889999763 3899999422235556557999888865 4444
Q ss_pred EcCeEEE
Q 022219 92 HQAELSA 98 (300)
Q Consensus 92 ~~g~~~~ 98 (300)
++|..+.
T Consensus 123 ~~~~~qm 129 (681)
T PRK10917 123 GKYGLEM 129 (681)
T ss_pred cCCeEEE
Confidence 5555443
No 68
>KOG4757 consensus Predicted telomere binding protein [General function prediction only]
Probab=60.76 E-value=0.87 Score=44.03 Aligned_cols=44 Identities=20% Similarity=0.246 Sum_probs=37.6
Q ss_pred cccccccccccCCceEeEEEEEEEEEeeCCCCeEEEEEEcCCCCCCC
Q 022219 155 NDYLLSLKDISEHRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPL 201 (300)
Q Consensus 155 ~~~~~~L~di~~~~f~Dl~~qVv~~~~~~~~~~~~L~VwDgT~n~~~ 201 (300)
..+ .++.|+.+.+.+.+.+++....|. ....++|++|+|.+..+
T Consensus 174 ~~w-~lv~d~~~h~~~s~~~~~~~~~yS--lr~~l~~~~~~T~~~l~ 217 (522)
T KOG4757|consen 174 VSW-SLVSDITPHQRCSFYAQVIKTWYS--LRNPLLYVTDPTENLLF 217 (522)
T ss_pred cee-eeeecccccccccccccceeeEee--cccccccccCchHhhhh
Confidence 346 789999999999999999999866 46778999999998874
No 69
>PRK05338 rplS 50S ribosomal protein L19; Provisional
Probab=60.52 E-value=25 Score=28.13 Aligned_cols=43 Identities=14% Similarity=0.210 Sum_probs=28.2
Q ss_pred CCCCCCCCCCCEEEEeeE-------EEEEEcCeEEEEeecC-ceEEEEEeCC
Q 022219 70 DQLPRVLSPRDLILLKNV-------MIKKHQAELSAVFYKD-SSSFALFDGN 113 (300)
Q Consensus 70 ~~LP~v~~~GDII~l~r~-------kv~~~~g~~~~~~~~~-~ss~~vf~~~ 113 (300)
.++|.+ .+||+|.++-- ++|.|.|-.-+.-+.+ .++|.|=.-.
T Consensus 14 ~~~p~f-~~GD~V~V~~~i~eg~k~R~q~f~GvvI~~~~~G~~~tftvRki~ 64 (116)
T PRK05338 14 KDIPEF-RPGDTVRVHVKVVEGNKERIQAFEGVVIARRGRGLNETFTVRKIS 64 (116)
T ss_pred cCCCCc-CCCCEEEEEEEEccCCceEeccEEEEEEEEeCCCCCceEEEEEcc
Confidence 569999 79999999642 3556666555554433 3677765543
No 70
>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=60.31 E-value=72 Score=24.11 Aligned_cols=26 Identities=27% Similarity=0.362 Sum_probs=19.8
Q ss_pred eEEEEEEEEEeeCCCCeEEEEEEcCCCC
Q 022219 171 DLVCKVFHVSYDDSKGLWMLFVWDGTDV 198 (300)
Q Consensus 171 Dl~~qVv~~~~~~~~~~~~L~VwDgT~n 198 (300)
||++.|+++. + ....+.+-+=|||+.
T Consensus 1 ~ivG~V~sv~-~-~~~~~~~tLdDgTG~ 26 (92)
T cd04483 1 DILGTVVSRR-E-RETFYSFGVDDGTGV 26 (92)
T ss_pred CeEEEEEEEE-e-cCCeEEEEEecCCce
Confidence 5788999887 4 446777778888874
No 71
>TIGR00643 recG ATP-dependent DNA helicase RecG.
Probab=58.66 E-value=57 Score=33.59 Aligned_cols=77 Identities=18% Similarity=0.226 Sum_probs=51.2
Q ss_pred ehhhhhhccCCEEEEEEEEEecCCceecCCCceEEEEEEEe-CCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEE
Q 022219 12 RIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVD-DSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIK 90 (300)
Q Consensus 12 ~l~~~~~~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D-~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~r~kv~ 90 (300)
+|+++. .|..+.+.|.|++... ..++.--..++++.| .+- .+.+.+|.. ..+......|+-+.+.. |+.
T Consensus 25 ~i~~~~--~g~~~~~~~~v~~~~~--~~~~~~~~~~~~~~d~~~~---~~~~~~F~~--~~~~~~~~~g~~~~~~G-k~~ 94 (630)
T TIGR00643 25 TIGELL--PGERATIVGEVLSHCI--FGFKRRKVLKLRLKDGGYK---KLELRFFNR--AFLKKKFKVGSKVVVYG-KVK 94 (630)
T ss_pred CHHHcC--CCCEEEEEEEEEEeEe--ccCCCCceEEEEEEECCCC---EEEEEEECC--HHHHhhCCCCCEEEEEE-EEE
Confidence 556654 6889999999987422 112222278889999 443 399999972 35556557899888854 556
Q ss_pred EEcCeEEE
Q 022219 91 KHQAELSA 98 (300)
Q Consensus 91 ~~~g~~~~ 98 (300)
.++|..+.
T Consensus 95 ~~~~~~~~ 102 (630)
T TIGR00643 95 SSKFKAYL 102 (630)
T ss_pred eeCCEEEE
Confidence 66676554
No 72
>KOG4792 consensus Crk family adapters [Signal transduction mechanisms]
Probab=57.04 E-value=22 Score=31.82 Aligned_cols=60 Identities=17% Similarity=0.356 Sum_probs=38.0
Q ss_pred hcCCCcccEEEEEecCchhhhhhcCCCCCcEEEEeccEEEeeCcEEEEEEeeC------CceEEcCCCCc
Q 022219 230 RNFFPVGTVLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSS------SKIRLFSDNDN 293 (300)
Q Consensus 230 ~~~p~~G~~l~V~~~~~~~~~~~~~lk~G~wv~l~Nv~~k~~~g~leg~l~~~------sk~~~l~~~d~ 293 (300)
.+.|.+-+++|=..-+.-.+ .+-.|++||.|+.. -+..+|.|||-|.+. +.|++++..++
T Consensus 224 ~~lPa~Arv~q~RVPnAYDk-TaL~levGdiVkVT---k~ninGqwegElnGk~G~fPfThvrf~d~~~~ 289 (293)
T KOG4792|consen 224 QNLPAYARVIQKRVPNAYDK-TALALEVGDIVKVT---KKNINGQWEGELNGKIGHFPFTHVRFTDVQNP 289 (293)
T ss_pred cCCChheeeehhcCCCccCh-hhhhhhcCcEEEEE---eeccCceeeeeecCccccccceeEEeeccCCc
Confidence 55665655554333333332 23358999999853 233489999999875 56888776655
No 73
>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=56.21 E-value=14 Score=27.25 Aligned_cols=37 Identities=19% Similarity=0.333 Sum_probs=27.0
Q ss_pred ccEEEEEecCchhhhhhcCCCCCcEEEEeccEEEeeC
Q 022219 236 GTVLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSS 272 (300)
Q Consensus 236 G~~l~V~~~~~~~~~~~~~lk~G~wv~l~Nv~~k~~~ 272 (300)
|..++.+.....+..-...|++|.|+.|.|..++...
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 4567777655444444788999999999998887643
No 74
>PRK05672 dnaE2 error-prone DNA polymerase; Validated
Probab=55.61 E-value=29 Score=38.08 Aligned_cols=86 Identities=21% Similarity=0.254 Sum_probs=56.7
Q ss_pred ceeehhhhhhc-cCCEEEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeE
Q 022219 9 GIVRIKELAMH-VKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNV 87 (300)
Q Consensus 9 ~y~~l~~~~~~-~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~r~ 87 (300)
.++++.++.+. .+..|.+.|+|+..+.+...+| +.-++|-|.+-. +.+.+|.+.-+..-.....|.++++. -
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 4567999999999877533345 888899998763 99999976444443333678888884 4
Q ss_pred EEEEEcCeEEEEee
Q 022219 88 MIKKHQAELSAVFY 101 (300)
Q Consensus 88 kv~~~~g~~~~~~~ 101 (300)
+++.-+++.+.+.+
T Consensus 1013 ~v~~~~~~~~~~~~ 1026 (1046)
T PRK05672 1013 RVQNAEGVRHLVAD 1026 (1046)
T ss_pred EEEecCCeEEEEEe
Confidence 66655555555543
No 75
>PRK06826 dnaE DNA polymerase III DnaE; Reviewed
Probab=53.84 E-value=37 Score=37.63 Aligned_cols=77 Identities=14% Similarity=0.230 Sum_probs=54.0
Q ss_pred cCCEEEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEE-cCeEEE
Q 022219 20 VKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKH-QAELSA 98 (300)
Q Consensus 20 ~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~r~kv~~~-~g~~~~ 98 (300)
.+..|.+.|+|+..+.+ +|+.++-+.-++|-|.+-. +.+.+|.+.-+..-.....|.+|++ ..+++.. +++.+.
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 35679999999999874 5665677899999998763 9999998644444333366788777 4566643 444565
Q ss_pred Eee
Q 022219 99 VFY 101 (300)
Q Consensus 99 ~~~ 101 (300)
+.+
T Consensus 1065 ~~~ 1067 (1151)
T PRK06826 1065 ICE 1067 (1151)
T ss_pred EEe
Confidence 554
No 76
>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=52.00 E-value=40 Score=26.85 Aligned_cols=43 Identities=14% Similarity=0.098 Sum_probs=28.1
Q ss_pred CCCCCCCCCCCEEEEeeE-------EEEEEcCeEEEEeecC-ceEEEEEeCC
Q 022219 70 DQLPRVLSPRDLILLKNV-------MIKKHQAELSAVFYKD-SSSFALFDGN 113 (300)
Q Consensus 70 ~~LP~v~~~GDII~l~r~-------kv~~~~g~~~~~~~~~-~ss~~vf~~~ 113 (300)
.++|.+ .+||+|.++-. ++|.|.|-.-+..+.+ .++|.|=+-.
T Consensus 14 ~~ip~f-~~GD~v~V~~~i~eg~k~R~q~f~GvvI~~~~~G~~~tftvR~i~ 64 (113)
T TIGR01024 14 KDLPDF-RVGDTVRVHVKIVEGKKERIQVFEGVVIARRGGGIGETFTVRKIS 64 (113)
T ss_pred cCCCcc-CCCCEEEEEEEEccCCceEcccEEEEEEEEeCCCCceEEEEEEec
Confidence 579999 79999999643 3456666555555433 3677765443
No 77
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=51.88 E-value=64 Score=32.97 Aligned_cols=79 Identities=15% Similarity=0.342 Sum_probs=58.8
Q ss_pred eeehhhhhhccCCEEEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEec-CCCCCCCCCCCCCCEEEEeeEE
Q 022219 10 IVRIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFT-SSIDQLPRVLSPRDLILLKNVM 88 (300)
Q Consensus 10 y~~l~~~~~~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~-~~~~~LP~v~~~GDII~l~r~k 88 (300)
-+.+.++-+..|..|-+=|=|+..+ +|.|- ..|||.|++-. +.+.-|- +-.-.-|.| .+||||.+-. .
T Consensus 202 r~~i~~id~~ig~tV~I~GeV~qik---qT~GP---TVFtltDetg~---i~aAAFe~aGvRAyP~I-evGdiV~ViG-~ 270 (715)
T COG1107 202 RTLIDDLDEMIGKTVRIEGEVTQIK---QTSGP---TVFTLTDETGA---IWAAAFEEAGVRAYPEI-EVGDIVEVIG-E 270 (715)
T ss_pred cccHHHHHhhcCceEEEEEEEEEEE---EcCCC---EEEEEecCCCc---eehhhhccCCcccCCCC-CCCceEEEEE-E
Confidence 3456677667889999999998763 44332 46899999764 6677775 566789999 7999999865 5
Q ss_pred EEEEcCeEEEE
Q 022219 89 IKKHQAELSAV 99 (300)
Q Consensus 89 v~~~~g~~~~~ 99 (300)
+....|++|.-
T Consensus 271 V~~r~g~lQiE 281 (715)
T COG1107 271 VTRRDGRLQIE 281 (715)
T ss_pred EeecCCcEEEe
Confidence 66677877763
No 78
>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=50.70 E-value=96 Score=22.65 Aligned_cols=63 Identities=17% Similarity=0.105 Sum_probs=39.1
Q ss_pred EEEEEEecCCceecCCCceEEEEEEEeCCCC-----CCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCeEEEEe
Q 022219 26 LLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQ-----SPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAELSAVF 100 (300)
Q Consensus 26 viGVVvd~~~P~~trG~D~~~tl~I~D~S~~-----~~gl~v~iF~~~~~~LP~v~~~GDII~l~r~kv~~~~g~~~~~~ 100 (300)
+=|||+...+.. ...- |-|-|+... ++| +-+|.+. -+.+ .+||.|++. -++..|+|..++..
T Consensus 2 v~GvVTa~~~~~--~~~G----ffiQd~~~d~~~~ts~g--ifV~~~~---~~~~-~~Gd~V~vt-G~v~ey~g~tql~~ 68 (78)
T cd04486 2 VEGVVTAVFSGG--GLGG----FYIQDEDGDGDPATSEG--IFVYTGS---GADV-AVGDLVRVT-GTVTEYYGLTQLTA 68 (78)
T ss_pred eEEEEEEEcCCC--CcCE----EEEEcCCCCCCCcccce--EEEecCC---CCCC-CCCCEEEEE-EEEEeeCCeEEEcc
Confidence 347787764422 1123 335565222 233 4555543 4566 799999996 89999999888765
Q ss_pred e
Q 022219 101 Y 101 (300)
Q Consensus 101 ~ 101 (300)
.
T Consensus 69 ~ 69 (78)
T cd04486 69 V 69 (78)
T ss_pred C
Confidence 4
No 79
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=50.26 E-value=63 Score=36.75 Aligned_cols=86 Identities=16% Similarity=0.307 Sum_probs=61.1
Q ss_pred CcceeehhhhhhccCCEEEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCC---CCCCCCCCCCCEEE
Q 022219 7 QGGIVRIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSI---DQLPRVLSPRDLIL 83 (300)
Q Consensus 7 ~y~y~~l~~~~~~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~---~~LP~v~~~GDII~ 83 (300)
++..++|+++.+. ...|-+-|-|-+... +.+|.+-...+|.|+|-+ +++.|+.|.++. +.+-.+ +.||-|+
T Consensus 223 ~~~~~~~~~i~~~-~~~v~i~G~if~~e~-~~~k~~~~~~~~~~td~~---~s~~~k~f~~~~~~~~~~~~~-~~g~~v~ 296 (1437)
T PRK00448 223 KEEITPMKEINEE-ERRVVVEGYVFKVEI-KELKSGRHILTFKITDYT---SSIIVKKFSRDKEDLKKFDEI-KKGDWVK 296 (1437)
T ss_pred ccCcccHHHhhcc-CCeEEEEEEEEEEEE-EeccCCCEEEEEEEEcCC---CCEEEEEEecCcchhHHHhcC-CCCCEEE
Confidence 3567788888743 457889999977654 556666788999999976 459999998443 345556 7899998
Q ss_pred EeeE-EEEEEcCeEEE
Q 022219 84 LKNV-MIKKHQAELSA 98 (300)
Q Consensus 84 l~r~-kv~~~~g~~~~ 98 (300)
++.- ....|.++...
T Consensus 297 ~~g~~~~d~~~~~~~~ 312 (1437)
T PRK00448 297 VRGSVQNDTFTRDLVM 312 (1437)
T ss_pred EEEEEeccCCCCceEE
Confidence 8653 33456665443
No 80
>PRK07279 dnaE DNA polymerase III DnaE; Reviewed
Probab=48.67 E-value=46 Score=36.48 Aligned_cols=86 Identities=17% Similarity=0.280 Sum_probs=58.0
Q ss_pred ceeehhhhhhccCCEEEEEEEEEecCCceecC-CCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeE
Q 022219 9 GIVRIKELAMHVKHKVNLLGVVLEFSIPRKSQ-GTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNV 87 (300)
Q Consensus 9 ~y~~l~~~~~~~~~~vnviGVVvd~~~P~~tr-G~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~r~ 87 (300)
..+++.++. .+..+.+.|+|...+. .+|| .++-+.-++|-|.+-. +.+.+|.+.-+..-.....|.++++. -
T Consensus 874 ~~~~~~~l~--~~~~~~~~~~i~~~~~-~~tk~~g~~maf~~leD~~g~---ie~~vFp~~y~~~~~~l~~~~~~~v~-G 946 (1034)
T PRK07279 874 PFTPISQLV--KNSEATILVQIQSIRV-IRTKTKGQQMAFLSVTDTKKK---LDVTLFPETYRQYKDELKEGKFYYLK-G 946 (1034)
T ss_pred cCccHHHHh--cCCcceEEEEEEEEEE-EEEcCCCCeEEEEEEeeCCCc---EEEEECHHHHHHHHHHhccCCEEEEE-E
Confidence 345677774 3556889999998866 4555 4567889999998763 99999976434443333678888884 4
Q ss_pred EEEEEcCeEEEEee
Q 022219 88 MIKKHQAELSAVFY 101 (300)
Q Consensus 88 kv~~~~g~~~~~~~ 101 (300)
+++.-.++.+.+.+
T Consensus 947 ~v~~~~~~~~l~~~ 960 (1034)
T PRK07279 947 KIQERDGRLQMVLQ 960 (1034)
T ss_pred EEEecCCeeEEEEe
Confidence 66654555555544
No 81
>CHL00084 rpl19 ribosomal protein L19
Probab=46.29 E-value=59 Score=26.04 Aligned_cols=41 Identities=10% Similarity=0.169 Sum_probs=25.9
Q ss_pred CCCCCCCCCCCEEEEeeE-------EEEEEcCeEEEEeecC-ceEEEEEe
Q 022219 70 DQLPRVLSPRDLILLKNV-------MIKKHQAELSAVFYKD-SSSFALFD 111 (300)
Q Consensus 70 ~~LP~v~~~GDII~l~r~-------kv~~~~g~~~~~~~~~-~ss~~vf~ 111 (300)
.++|.+ ++||+|+++=. ++|.|.|-.-+.-+.+ .++|.|=.
T Consensus 18 ~~~p~f-~~GDtV~V~~~i~eg~k~R~q~F~GvvI~~r~~G~~~tftvRk 66 (117)
T CHL00084 18 KNLPKI-RVGDTVKVGVLIQEGNKERVQFYEGTVIAKKNSGLNTTITVRK 66 (117)
T ss_pred cCCCcc-CCCCEEEEEEEEecCCeeEeceEEEEEEEEeCCCCCeeEEEEE
Confidence 579999 79999998641 3456666544444432 25676533
No 82
>cd04480 RPA1_DBD_A_like RPA1_DBD_A_like: A subgroup of uncharacterized plant OB folds with similarity to the second OB fold, the ssDNA-binding domain (DBD)-A, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of RPA is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change.
Probab=45.95 E-value=37 Score=25.00 Aligned_cols=56 Identities=9% Similarity=0.125 Sum_probs=42.2
Q ss_pred CceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCeEEEE
Q 022219 42 TDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAELSAV 99 (300)
Q Consensus 42 ~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~r~kv~~~~g~~~~~ 99 (300)
....+.+-|.|+.-. .|.+.+|....+.+-...+.|.+..+.++++..-++.....
T Consensus 17 ~~~~~~miL~De~G~--~I~a~i~~~~~~~f~~~L~eg~vy~is~f~v~~~~~~y~~~ 72 (86)
T cd04480 17 SGESLEMVLVDEKGN--RIHATIPKRLAAKFRPLLKEGKWYTISNFEVAPNTGSYRPT 72 (86)
T ss_pred CCcEEEEEEEcCCCC--EEEEEECHHHHHhhhhhceeCCEEEEeeEEEEcCCCccccc
Confidence 566778889998653 49999998655666555589999999999998776554433
No 83
>PRK13254 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=45.76 E-value=1.5e+02 Score=24.65 Aligned_cols=66 Identities=18% Similarity=0.213 Sum_probs=46.3
Q ss_pred eeehhhhhhc---cCCEEEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEe
Q 022219 10 IVRIKELAMH---VKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLK 85 (300)
Q Consensus 10 y~~l~~~~~~---~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~ 85 (300)
|.+.+++.+. .+..+-+-|.|++=+.-+ +..-.++|+|+|... .+.|.+-. .+|...+.|.-|.+.
T Consensus 37 f~tpse~~~~~~~~g~~vrvgG~V~~gSi~~---~~~~~~~F~ltD~~~---~i~V~Y~G----~lPd~F~eg~~VVv~ 105 (148)
T PRK13254 37 FYTPSEVAEGEAPAGRRFRLGGLVEKGSVQR---GDGLTVRFVVTDGNA---TVPVVYTG----ILPDLFREGQGVVAE 105 (148)
T ss_pred eeCHHHHhcCCccCCCeEEEeEEEecCcEEe---CCCCEEEEEEEeCCe---EEEEEECC----CCCccccCCCEEEEE
Confidence 6777777653 467899999999654422 255678999999832 26665543 489888888876653
No 84
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=44.55 E-value=50 Score=36.52 Aligned_cols=70 Identities=26% Similarity=0.295 Sum_probs=0.0
Q ss_pred ccccccccccCCce-EeEEEEEEEEE-eeCCCC--eEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCChhhhhc
Q 022219 156 DYLLSLKDISEHRY-FDLVCKVFHVS-YDDSKG--LWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRN 231 (300)
Q Consensus 156 ~~~~~L~di~~~~f-~Dl~~qVv~~~-~~~~~~--~~~L~VwDgT~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 231 (300)
++ +.|-++.++.+ +-+.++|-++- .+..++ .+.++|||||+ .+.......++++..
T Consensus 228 ~i-~~~~~i~~~~~~v~v~G~IF~~e~~~~ksGr~l~~i~vTD~t~--Sl~~k~f~~~~ed~~----------------- 287 (1444)
T COG2176 228 EI-KPLIKINEEETRVKVEGYIFKIEIKELKSGRTLLNIKVTDYTS--SLILKKFLRDEEDEK----------------- 287 (1444)
T ss_pred ce-eehhhccccccceEEEEEEEEEeeeecccCcEEEEEEEecCch--heeehhhccccccHH-----------------
Q ss_pred CCCcccEEEEEecCchhhhhhcCCCCCcEEEEe
Q 022219 232 FFPVGTVLRVSTDRSYENFGRYFTATGKWVRIR 264 (300)
Q Consensus 232 ~p~~G~~l~V~~~~~~~~~~~~~lk~G~wv~l~ 264 (300)
....+|.|+||+.+
T Consensus 288 -------------------~~~~ik~g~wvk~~ 301 (1444)
T COG2176 288 -------------------KFDGIKKGMWVKAR 301 (1444)
T ss_pred -------------------HHhhcccCcEEEEE
No 85
>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=43.29 E-value=97 Score=30.06 Aligned_cols=84 Identities=18% Similarity=0.219 Sum_probs=57.9
Q ss_pred CCEEEEEEEEEecCCce--ecC-CC-ceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCeE
Q 022219 21 KHKVNLLGVVLEFSIPR--KSQ-GT-DYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAEL 96 (300)
Q Consensus 21 ~~~vnviGVVvd~~~P~--~tr-G~-D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~r~kv~~~~g~~ 96 (300)
.+.+|+.|-|.++..++ +++ |. .=..+..+.|.+-. +... +..+...+++. ..||++++.+..+..|+|.+
T Consensus 59 ~~~~~v~~~V~~~~e~~~~~~k~g~~~~l~~~~v~Detg~---v~~~-~~~~~~a~~~~-e~Gdv~~i~~~~~~~~~~~~ 133 (407)
T COG1599 59 SSRVNVTGRVLSIGEKKTFDRKRGAEGKLAEVLVGDETGS---VKTV-TLWNIAALEKL-EPGDVIRIRNAYTSLYRGGK 133 (407)
T ss_pred hccccEEEEECccccceeeecccccccceEEEEEecCCCC---EEEE-eeccccccccC-CccceEEecCcccccccCce
Confidence 46799999999988765 453 43 33344457777653 3332 55555556667 79999999999999999998
Q ss_pred EEEeecCceEEEEE
Q 022219 97 SAVFYKDSSSFALF 110 (300)
Q Consensus 97 ~~~~~~~~ss~~vf 110 (300)
++..+.. ++.+..
T Consensus 134 ~~~~~~~-~~v~~~ 146 (407)
T COG1599 134 RLSVGRV-GSVADV 146 (407)
T ss_pred eeecccc-cccccC
Confidence 8877643 444433
No 86
>cd04494 BRCA2DBD_OB2 BRCA2DBD_OB2: A subfamily of OB folds corresponding to the second OB fold (OB2) of the 800-amino acid C-terminal ssDNA binding domain (DBD) of BRCA2 (breast cancer susceptibility gene 2) protein, called BRCA2DBD. BRCA2 participates in homologous recombination-mediated repair of double-strand DNA breaks. It stimulates the displacement of Replication protein A (RPA), the most abundant eukaryotic ssDNA binding protein. It also facilitates filament formation. Mutations that map throughout the BRCA2 protein are associated with breast cancer susceptibility. BRCA2 is a large nuclear protein and its most conserved region is the C-terminal BRCA2DBD. BRCA2DBD binds ssDNA in vitro, and is composed of five structural domains, three of which are OB folds (OB1, OB2, and OB3). BRCA2DBD OB2 and OB3 are arranged in tandem, and their mode of binding can be considered qualitatively similar to two OB folds of RPA1, DBD-A and DBD-B (the major DBDs of RPA).
Probab=43.07 E-value=54 Score=29.86 Aligned_cols=55 Identities=16% Similarity=0.105 Sum_probs=43.5
Q ss_pred EEEEecCchhhhhhcCCCCCcEEEEeccEEEee-----CcEEEEEEeeCCceEEcCCCCcc
Q 022219 239 LRVSTDRSYENFGRYFTATGKWVRIRNMSCQVS-----SGMWHGLLQSSSKIRLFSDNDNV 294 (300)
Q Consensus 239 l~V~~~~~~~~~~~~~lk~G~wv~l~Nv~~k~~-----~g~leg~l~~~sk~~~l~~~d~~ 294 (300)
..+++|.+.+.+ ...|++|.-++++|+..--. .+-++-.=+..+++..|+..+..
T Consensus 182 ~~LTIWrPtedl-~s~L~EG~ry~i~~L~~s~~k~~~~~~~vqLtatk~Tr~~~l~~~~~~ 241 (251)
T cd04494 182 GLLSIWRPTEDL-RSLLTEGKRYRIYGLATSNSKKRSGNEEVQLTATKKTRYQPLPVSQRE 241 (251)
T ss_pred EEEEEeCCCHHH-HhhhcCCcEEEEEeccccCCCCCCCcceEEEEecCcccceECCHHHhc
Confidence 468999999874 66799999999999986542 25677777888999998876543
No 87
>cd04494 BRCA2DBD_OB2 BRCA2DBD_OB2: A subfamily of OB folds corresponding to the second OB fold (OB2) of the 800-amino acid C-terminal ssDNA binding domain (DBD) of BRCA2 (breast cancer susceptibility gene 2) protein, called BRCA2DBD. BRCA2 participates in homologous recombination-mediated repair of double-strand DNA breaks. It stimulates the displacement of Replication protein A (RPA), the most abundant eukaryotic ssDNA binding protein. It also facilitates filament formation. Mutations that map throughout the BRCA2 protein are associated with breast cancer susceptibility. BRCA2 is a large nuclear protein and its most conserved region is the C-terminal BRCA2DBD. BRCA2DBD binds ssDNA in vitro, and is composed of five structural domains, three of which are OB folds (OB1, OB2, and OB3). BRCA2DBD OB2 and OB3 are arranged in tandem, and their mode of binding can be considered qualitatively similar to two OB folds of RPA1, DBD-A and DBD-B (the major DBDs of RPA).
Probab=42.07 E-value=54 Score=29.84 Aligned_cols=67 Identities=12% Similarity=0.118 Sum_probs=48.0
Q ss_pred eEEEEEEEeCCC-CCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcC-----eEEEEeecCceEEEEEeC
Q 022219 44 YVCVLKIVDDSQ-QSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQA-----ELSAVFYKDSSSFALFDG 112 (300)
Q Consensus 44 ~~~tl~I~D~S~-~~~gl~v~iF~~~~~~LP~v~~~GDII~l~r~kv~~~~g-----~~~~~~~~~~ss~~vf~~ 112 (300)
=+..++|+|-.. ......++|.+|..+.+-.+ ..|-+.++.++.....++ .+++.+.++ |.|.--+.
T Consensus 165 p~~klRV~d~~~~~~~~~~LTIWrPtedl~s~L-~EG~ry~i~~L~~s~~k~~~~~~~vqLtatk~-Tr~~~l~~ 237 (251)
T cd04494 165 PVWKLRVTDYRSKPEKSGLLSIWRPTEDLRSLL-TEGKRYRIYGLATSNSKKRSGNEEVQLTATKK-TRYQPLPV 237 (251)
T ss_pred eEEEEEEeecccCCCceEEEEEeCCCHHHHhhh-cCCcEEEEEeccccCCCCCCCcceEEEEecCc-ccceECCH
Confidence 356678888763 34568889999875544445 789999999999887766 467777664 77775443
No 88
>COG2049 DUR1 Allophanate hydrolase subunit 1 [Amino acid transport and metabolism]
Probab=41.06 E-value=12 Score=33.31 Aligned_cols=39 Identities=15% Similarity=0.082 Sum_probs=27.1
Q ss_pred hcCCCcccEEEEEecCchhhhhhcCCCCCcEEEEeccEEEe
Q 022219 230 RNFFPVGTVLRVSTDRSYENFGRYFTATGKWVRIRNMSCQV 270 (300)
Q Consensus 230 ~~~p~~G~~l~V~~~~~~~~~~~~~lk~G~wv~l~Nv~~k~ 270 (300)
..|-.+|++....+|..... --.+++||||||+++..+.
T Consensus 177 GGWqlIGrTp~~lfdp~~~~--p~ll~~Gd~VrF~~i~~~e 215 (223)
T COG2049 177 GGWQLIGRTPLPLFDPDREP--PALLRPGDQVRFVPIKEEE 215 (223)
T ss_pred CceeEeccccccccCCCCCC--CeeccCCCEEEEEecCccc
Confidence 34556777776666644442 3458999999999987654
No 89
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=38.29 E-value=1.7e+02 Score=30.53 Aligned_cols=73 Identities=16% Similarity=0.191 Sum_probs=54.2
Q ss_pred cCCEEEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCeEEEE
Q 022219 20 VKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAELSAV 99 (300)
Q Consensus 20 ~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~r~kv~~~~g~~~~~ 99 (300)
.|..|-+.|.|.....+. .++--..++++.|.+. -+++.+|..+. .+..-..+|--+.+ .=|++.|++..+..
T Consensus 59 ~g~~vti~g~V~~~~~~~--~~~~~~l~v~~~d~~~---~l~l~fFn~~~-~l~~~~~~G~~v~v-~Gk~~~~~~~~~~~ 131 (677)
T COG1200 59 PGEIVTIEGTVLSHEKFP--FGKRKLLKVTLSDGTG---VLTLVFFNFPA-YLKKKLKVGERVIV-YGKVKRFKGGLQIT 131 (677)
T ss_pred CCceEEEEEEEEeeeccC--CCCCceEEEEEecCcE---EEEEEEECccH-HHHhhCCCCCEEEE-EEEEeeccCceEEE
Confidence 678899999999876543 5677788899999433 39999998653 66665578998887 45777787765543
No 90
>COG1570 XseA Exonuclease VII, large subunit [DNA replication, recombination, and repair]
Probab=38.04 E-value=3.2e+02 Score=27.02 Aligned_cols=70 Identities=17% Similarity=0.208 Sum_probs=49.1
Q ss_pred CEEEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCe--EEEE
Q 022219 22 HKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAE--LSAV 99 (300)
Q Consensus 22 ~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~r~kv~~~~g~--~~~~ 99 (300)
+.|=|-|=+..++.| ..| ..-|+|.|+.-. |.|.+|+.....|....+.|+-|+++ -+++.|-++ .|.+
T Consensus 24 ~~V~v~GEISn~t~~--~sg---H~YFtLKD~~A~---i~c~mf~~~~~~l~f~p~eG~~V~v~-G~is~Y~~rG~YQi~ 94 (440)
T COG1570 24 GQVWVRGEISNFTRP--ASG---HLYFTLKDERAQ---IRCVMFKGNNRRLKFRPEEGMQVLVR-GKISLYEPRGDYQIV 94 (440)
T ss_pred CeEEEEEEecCCccC--CCc---cEEEEEccCCce---EEEEEEcCcccccCCCccCCCEEEEE-EEEEEEcCCCceEEE
Confidence 457777777777654 233 555799999553 99999998888888766899988774 466666443 4444
Q ss_pred e
Q 022219 100 F 100 (300)
Q Consensus 100 ~ 100 (300)
.
T Consensus 95 ~ 95 (440)
T COG1570 95 A 95 (440)
T ss_pred E
Confidence 3
No 91
>cd04496 SSB_OBF SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs bind with high affinity to ssDNA. They bind to and protect ssDNA intermediates during DNA metabolic pathways. All bacterial and eukaryotic SSBs studied to date oligomerize to bring together four OB folds in their active state. The majority (e.g. Escherichia coli SSB) have a single OB fold per monomer, which oligomerize to form a homotetramer. However, Deinococcus and Thermus SSB proteins have two OB folds per monomer, which oligomerize to form a homodimer. Mycobacterium tuberculosis SSB varies in quaternary structure from E. coli SSB. It forms a dimer of dimers having a unique dimer interface, which lends the protein greater stability. Included in this group are OB folds similar to Escherichia coli PriB. E.coli PriB is homodimeric with each monomer having a single OB fold. It does not appear to form higher order oligomers. PriB is an essential protein for the replication restart
Probab=37.76 E-value=28 Score=25.92 Aligned_cols=27 Identities=15% Similarity=0.201 Sum_probs=22.9
Q ss_pred EEEEecCchhhhhhcCCCCCcEEEEec
Q 022219 239 LRVSTDRSYENFGRYFTATGKWVRIRN 265 (300)
Q Consensus 239 l~V~~~~~~~~~~~~~lk~G~wv~l~N 265 (300)
++|.+|...+....+.++.|++|.+..
T Consensus 46 ~~v~~~g~~a~~~~~~~~kG~~V~v~G 72 (100)
T cd04496 46 IRVVAFGKLAENAAKYLKKGDLVYVEG 72 (100)
T ss_pred EEEEEEhHHHHHHHHHhCCCCEEEEEE
Confidence 688889888877888999999998754
No 92
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=37.15 E-value=1.5e+02 Score=33.75 Aligned_cols=40 Identities=25% Similarity=0.289 Sum_probs=27.9
Q ss_pred ccccccc-CCceEeEEEEEEEEEe-eCCCC--eEEEEEEcCCCC
Q 022219 159 LSLKDIS-EHRYFDLVCKVFHVSY-DDSKG--LWMLFVWDGTDV 198 (300)
Q Consensus 159 ~~L~di~-~~~f~Dl~~qVv~~~~-~~~~~--~~~L~VwDgT~n 198 (300)
..|+||. ++.-+-+.++|.++-. +..++ .++++|+|||+.
T Consensus 227 ~~~~~i~~~~~~v~i~G~if~~e~~~~k~~~~~~~~~~td~~~s 270 (1437)
T PRK00448 227 TPMKEINEEERRVVVEGYVFKVEIKELKSGRHILTFKITDYTSS 270 (1437)
T ss_pred ccHHHhhccCCeEEEEEEEEEEEEEeccCCCEEEEEEEEcCCCC
Confidence 4577775 4567778889988874 22333 558999999963
No 93
>KOG4348 consensus Adaptor protein CMS/SETA [Signal transduction mechanisms]
Probab=35.82 E-value=25 Score=34.48 Aligned_cols=43 Identities=12% Similarity=0.193 Sum_probs=31.7
Q ss_pred EecCchhhhhhcCCCCCcEEEEeccEEEeeCcEEEEEEeeCCceEE
Q 022219 242 STDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRL 287 (300)
Q Consensus 242 ~~~~~~~~~~~~~lk~G~wv~l~Nv~~k~~~g~leg~l~~~sk~~~ 287 (300)
.|...+.. .--+|+||.+.|.| .=..+.|.|||-|++..-|..
T Consensus 269 ~Ye~qndD--ELt~KEgdil~lIt-K~cgdaGWweGELnGk~GvFP 311 (627)
T KOG4348|consen 269 VYEPQNDD--ELTLKEGDILILIT-KNCGDAGWWEGELNGKKGVFP 311 (627)
T ss_pred eecCCCcc--ceeeccccEEEEec-ccccccceeeeeecCccccCC
Confidence 35666552 33589999999988 333468999999999877754
No 94
>PRK07772 single-stranded DNA-binding protein; Provisional
Probab=35.80 E-value=74 Score=27.57 Aligned_cols=74 Identities=8% Similarity=0.104 Sum_probs=50.0
Q ss_pred CCEEEEEEEEEecCCceecCCCceEEEEEEEeC-C-CC-----C-----CCeEEEEecCCCCCCCCCCCCCCEEEEe-eE
Q 022219 21 KHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDD-S-QQ-----S-----PELLVNIFTSSIDQLPRVLSPRDLILLK-NV 87 (300)
Q Consensus 21 ~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~-S-~~-----~-----~gl~v~iF~~~~~~LP~v~~~GDII~l~-r~ 87 (300)
...|.|+|=++.--.-+.|....-+++|+|.-. . .. + .-+.|.+|.+..+.+-.-.+.||-|.+. |+
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 356888887776544455655567889999732 2 11 0 1389999997666666534789966665 78
Q ss_pred EEEEEcC
Q 022219 88 MIKKHQA 94 (300)
Q Consensus 88 kv~~~~g 94 (300)
+...|.+
T Consensus 84 ~~r~wed 90 (186)
T PRK07772 84 KQRSYET 90 (186)
T ss_pred EcCceEC
Confidence 8888864
No 95
>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=34.48 E-value=47 Score=25.78 Aligned_cols=16 Identities=13% Similarity=0.059 Sum_probs=13.8
Q ss_pred hhcCCCCCcEEEEecc
Q 022219 251 GRYFTATGKWVRIRNM 266 (300)
Q Consensus 251 ~~~~lk~G~wv~l~Nv 266 (300)
....++.||+|++.|=
T Consensus 45 ~~lgi~~Gd~V~v~s~ 60 (122)
T cd02792 45 AERGIKNGDMVWVSSP 60 (122)
T ss_pred HHcCCCCCCEEEEEcC
Confidence 4678999999999993
No 96
>PF11325 DUF3127: Domain of unknown function (DUF3127); InterPro: IPR021474 This bacterial family of proteins has no known function.
Probab=32.81 E-value=2.1e+02 Score=21.44 Aligned_cols=66 Identities=9% Similarity=0.180 Sum_probs=40.1
Q ss_pred EEEEecCCceecCCCc-eEEEEEE--EeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEe-eEEEEEEcCe
Q 022219 28 GVVLEFSIPRKSQGTD-YVCVLKI--VDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLK-NVMIKKHQAE 95 (300)
Q Consensus 28 GVVvd~~~P~~trG~D-~~~tl~I--~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~-r~kv~~~~g~ 95 (300)
|.|+...++.+..|.. |.-.=-+ +++-++ .-+.+.+|.+..+.|-.+ ++||.|.++ +++-+.|+|+
T Consensus 4 Gkii~~l~~~~g~s~~Gw~Kre~Vlet~~qYP-~~i~f~~~~dk~~~l~~~-~~Gd~V~Vsf~i~~RE~~gr 73 (84)
T PF11325_consen 4 GKIIKVLPEQQGVSKNGWKKREFVLETEEQYP-QKICFEFWGDKIDLLDNF-QVGDEVKVSFNIEGREWNGR 73 (84)
T ss_pred cEEEEEecCcccCcCCCcEEEEEEEeCCCcCC-ceEEEEEEcchhhhhccC-CCCCEEEEEEEeeccEecce
Confidence 4555555554432211 5433222 333333 359999999777777888 799988774 6677777765
No 97
>cd02778 MopB_CT_Thiosulfate-R-like The MopB_CT_Thiosulfate-R-like CD contains thiosulfate-, sulfur-, and polysulfide-reductases, and other related proteins. Thiosulfate reductase catalyzes the cleavage of sulfur-sulfur bonds in thiosulfate. Polysulfide reductase is a membrane-bound enzyme that catalyzes the reduction of polysulfide using either hydrogen or formate as the electron donor. Also included in this CD is the phenylacetyl-CoA:acceptor oxidoreductase, large subunit (PadB2), which has been characterized as a membrane-bound molybdenum-iron-sulfur enzyme involved in anaerobic metabolism of phenylalanine in the denitrifying bacterium Thauera aromatica. The MopB_CT_Thiosulfate-R-like CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=31.37 E-value=55 Score=25.44 Aligned_cols=16 Identities=19% Similarity=0.239 Sum_probs=13.8
Q ss_pred hhcCCCCCcEEEEecc
Q 022219 251 GRYFTATGKWVRIRNM 266 (300)
Q Consensus 251 ~~~~lk~G~wv~l~Nv 266 (300)
....++.||||++.|=
T Consensus 40 ~~~gi~~Gd~V~v~s~ 55 (123)
T cd02778 40 ARLGIKDGDRVEVSSA 55 (123)
T ss_pred HHcCCCCCCEEEEEeC
Confidence 5678999999999883
No 98
>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=30.62 E-value=55 Score=25.07 Aligned_cols=16 Identities=25% Similarity=0.258 Sum_probs=14.0
Q ss_pred hhcCCCCCcEEEEecc
Q 022219 251 GRYFTATGKWVRIRNM 266 (300)
Q Consensus 251 ~~~~lk~G~wv~l~Nv 266 (300)
....++.||+|+|.|=
T Consensus 45 ~~lgi~~Gd~V~v~~~ 60 (116)
T cd02790 45 KRLGIEDGEKVRVSSR 60 (116)
T ss_pred HHcCCCCCCEEEEEcC
Confidence 5678999999999995
No 99
>cd02779 MopB_CT_Arsenite-Ox This CD contains the molybdopterin_binding C-terminal (MopB_CT) region of Arsenite oxidase (Arsenite-Ox) and related proteins. Arsenite oxidase oxidizes arsenite to the less toxic arsenate; it transfers the electrons obtained from the oxidation of arsenite towards the soluble periplasmic electron carriers cytochrome c and/or amicyanin.
Probab=30.50 E-value=53 Score=25.49 Aligned_cols=16 Identities=25% Similarity=0.144 Sum_probs=13.9
Q ss_pred hhcCCCCCcEEEEecc
Q 022219 251 GRYFTATGKWVRIRNM 266 (300)
Q Consensus 251 ~~~~lk~G~wv~l~Nv 266 (300)
....++.||+|++.|=
T Consensus 43 ~~lgi~~Gd~V~v~s~ 58 (115)
T cd02779 43 KREGLKNGDLVEVYND 58 (115)
T ss_pred HHcCCCCCCEEEEEeC
Confidence 4678999999999995
No 100
>KOG3416 consensus Predicted nucleic acid binding protein [General function prediction only]
Probab=29.55 E-value=1e+02 Score=25.03 Aligned_cols=28 Identities=11% Similarity=0.200 Sum_probs=19.6
Q ss_pred EEEEecCchhhhhhcCCCCCcEEEEeccEEEe
Q 022219 239 LRVSTDRSYENFGRYFTATGKWVRIRNMSCQV 270 (300)
Q Consensus 239 l~V~~~~~~~~~~~~~lk~G~wv~l~Nv~~k~ 270 (300)
+.+.+|+. ....++|||.|||++==..+
T Consensus 50 I~isvW~e----~~~~~~PGDIirLt~Gy~Si 77 (134)
T KOG3416|consen 50 INISVWDE----EGCLIQPGDIIRLTGGYASI 77 (134)
T ss_pred EEEEEecC----cCcccCCccEEEecccchhh
Confidence 45666662 24579999999999874444
No 101
>PF03100 CcmE: CcmE; InterPro: IPR004329 CcmE is the product of one of a cluster of Ccm genes that are necessary for cytochrome c biosynthesis in eubacteria. Expression of these proteins is induced when the organisms are grown under anaerobic conditions with nitrate or nitrite as the final electron acceptor.; GO: 0017003 protein-heme linkage, 0017004 cytochrome complex assembly, 0005886 plasma membrane; PDB: 1SR3_A 2KCT_A 1J6Q_A 1LM0_A.
Probab=28.48 E-value=3.1e+02 Score=22.01 Aligned_cols=68 Identities=24% Similarity=0.290 Sum_probs=42.6
Q ss_pred eeehhhhhhc---cCCEEEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEee
Q 022219 10 IVRIKELAMH---VKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKN 86 (300)
Q Consensus 10 y~~l~~~~~~---~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~r 86 (300)
|.+.+++.+. .+..+.+-|.|+.-+.-+ ....-..+|.|+|... .+.|.+=. .+|...+.|.-|.+..
T Consensus 36 y~t~se~~~~~~~~~~~vrv~G~V~~gSv~~--~~~~~~~~F~i~D~~~---~i~V~Y~G----~~Pd~F~eg~~VVv~G 106 (131)
T PF03100_consen 36 YLTPSELAAEPQKVGRKVRVGGLVVEGSVEY--DPDGNTLTFTITDGGK---EIPVVYTG----PLPDLFREGQGVVVEG 106 (131)
T ss_dssp EE-TTTTTTTST-TTSEEEEEEEEECTTEEE---TTSSEEEEEEE-SS----EEEEEEES------CTT--TTSEEEEEE
T ss_pred EcCHHHHhhccccCCceEEEeeEEccCCEEE--cCCCCEEEEEEEECCc---EEEEEECC----CCCccccCCCeEEEEE
Confidence 7788888653 468899999999754322 2255677899999942 36666544 4888778898777654
No 102
>PRK07135 dnaE DNA polymerase III DnaE; Validated
Probab=28.46 E-value=1.3e+02 Score=32.81 Aligned_cols=65 Identities=15% Similarity=0.165 Sum_probs=46.9
Q ss_pred ehhhhhhccCCEEEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEE
Q 022219 12 RIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILL 84 (300)
Q Consensus 12 ~l~~~~~~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l 84 (300)
+|.++. .+..+.+.|+|+..+.-+ |.++-|.-+++-|.+-. +.+.+|.+.-+..-.. ..|+++++
T Consensus 890 ~~~~l~--~~~~~~v~g~i~~~~~~~--K~g~~maf~~~eD~~~~---~e~~~F~~~~~~~~~l-~~~~~~~~ 954 (973)
T PRK07135 890 RLKDLR--INTEYRLAIEVKNVKRLR--KANKEYKKVILSDDSVE---ITIFVNDNDYLLFETL-KKGDIYEF 954 (973)
T ss_pred hHHHhc--CCCeEEEEEEEEEEEEEe--eCCCeEEEEEEEECCCc---EEEEEcHHHHHHHHHh-hcCCEEEE
Confidence 455552 456789999999988755 44567999999999763 9999997533333334 57888776
No 103
>cd02783 MopB_CT_2 The MopB_CT_2 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=28.28 E-value=62 Score=26.83 Aligned_cols=16 Identities=19% Similarity=0.464 Sum_probs=14.1
Q ss_pred hhcCCCCCcEEEEecc
Q 022219 251 GRYFTATGKWVRIRNM 266 (300)
Q Consensus 251 ~~~~lk~G~wv~l~Nv 266 (300)
....++.||||++.|-
T Consensus 42 ~~~GI~dGd~V~v~s~ 57 (156)
T cd02783 42 KELGIKDGDWVWVESV 57 (156)
T ss_pred HHcCCCCCCEEEEEcC
Confidence 4678999999999994
No 104
>PF01568 Molydop_binding: Molydopterin dinucleotide binding domain; InterPro: IPR006657 A domain in this entry corresponds to the C-terminal domain IV in dimethyl sulphoxide (DMSO)reductase which interacts with the 2-amino pyrimidone ring of both molybdopterin guanine dinucleotide molecules [].; GO: 0016491 oxidoreductase activity, 0030151 molybdenum ion binding, 0055114 oxidation-reduction process; PDB: 2IVF_A 1OGY_G 3ML1_A 3O5A_A 1TI2_G 1VLE_M 1VLD_U 1VLF_O 1TI4_I 1TI6_E ....
Probab=28.18 E-value=78 Score=23.99 Aligned_cols=15 Identities=27% Similarity=0.671 Sum_probs=11.3
Q ss_pred hhcCCCCCcEEEEec
Q 022219 251 GRYFTATGKWVRIRN 265 (300)
Q Consensus 251 ~~~~lk~G~wv~l~N 265 (300)
....++.||||++.|
T Consensus 40 ~~~Gi~~Gd~V~v~s 54 (110)
T PF01568_consen 40 AKLGIKDGDWVRVSS 54 (110)
T ss_dssp HHCT--TTCEEEEEE
T ss_pred HHhcCcCCCEEEEEe
Confidence 467899999999987
No 105
>cd02786 MopB_CT_3 The MopB_CT_3 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=27.28 E-value=1e+02 Score=23.63 Aligned_cols=17 Identities=24% Similarity=0.061 Sum_probs=14.3
Q ss_pred hhcCCCCCcEEEEeccE
Q 022219 251 GRYFTATGKWVRIRNMS 267 (300)
Q Consensus 251 ~~~~lk~G~wv~l~Nv~ 267 (300)
....++.||||++.|-+
T Consensus 41 ~~lgi~~Gd~V~v~s~~ 57 (116)
T cd02786 41 AARGIADGDLVVVFNDR 57 (116)
T ss_pred HHcCCCCCCEEEEEcCC
Confidence 46789999999999863
No 106
>PRK06752 single-stranded DNA-binding protein; Validated
Probab=26.06 E-value=2.1e+02 Score=22.21 Aligned_cols=72 Identities=7% Similarity=0.043 Sum_probs=47.8
Q ss_pred EEEEEEEEEecCCceecCCCceEEEEEEEeCCCC--------CCCeEEEEecCCCCCCCCCCCCCCEEEEe-eEEEEEEc
Q 022219 23 KVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQ--------SPELLVNIFTSSIDQLPRVLSPRDLILLK-NVMIKKHQ 93 (300)
Q Consensus 23 ~vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~--------~~gl~v~iF~~~~~~LP~v~~~GDII~l~-r~kv~~~~ 93 (300)
.|.++|-+..--..+.|.++.-.++|+|.-...- .+-+.|.+|.+..+.+-.-.+-||-|.+. +++...|.
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 5788887776533455655567778888654321 13489999997656555534789966554 77888885
Q ss_pred C
Q 022219 94 A 94 (300)
Q Consensus 94 g 94 (300)
+
T Consensus 84 ~ 84 (112)
T PRK06752 84 D 84 (112)
T ss_pred C
Confidence 4
No 107
>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=25.88 E-value=3.2e+02 Score=21.25 Aligned_cols=33 Identities=15% Similarity=0.093 Sum_probs=24.2
Q ss_pred EEEEecCchhhhhh-cCCCCCcEEEEeccEEEee
Q 022219 239 LRVSTDRSYENFGR-YFTATGKWVRIRNMSCQVS 271 (300)
Q Consensus 239 l~V~~~~~~~~~~~-~~lk~G~wv~l~Nv~~k~~ 271 (300)
+-|.+|..-..++- +.+|++..+-+.|++.+..
T Consensus 30 l~vkfw~~l~~~~~EDvvk~~~lia~SNLQwR~~ 63 (100)
T cd04495 30 LCVKFWSSLEQYAYEDVVKRRVLLAASNLQWRTE 63 (100)
T ss_pred EEEEEecchHHhhhhhhcccceEEEEecceEecc
Confidence 34667765554554 4468999999999999974
No 108
>PRK05813 single-stranded DNA-binding protein; Provisional
Probab=25.86 E-value=2.9e+02 Score=24.54 Aligned_cols=72 Identities=13% Similarity=0.035 Sum_probs=47.5
Q ss_pred EEEEEEEEEecCCceecCCCceEEEEEEEeC-CCC-CCCeEEEEecCCCCCCCCCCCCCCEEEEe-eEEEEEEcCe
Q 022219 23 KVNLLGVVLEFSIPRKSQGTDYVCVLKIVDD-SQQ-SPELLVNIFTSSIDQLPRVLSPRDLILLK-NVMIKKHQAE 95 (300)
Q Consensus 23 ~vnviGVVvd~~~P~~trG~D~~~tl~I~D~-S~~-~~gl~v~iF~~~~~~LP~v~~~GDII~l~-r~kv~~~~g~ 95 (300)
.|.++|=+..--.-+.|.++.-.++|+|.=. ... .+-+.|.+|.+..+.+-.+ +.||-|.+. |++...|..+
T Consensus 111 ~V~LiGrL~~DPelR~t~~G~~va~f~lAvnr~~~~td~i~~v~wg~~Ae~~~~l-~KG~~V~V~GrL~sr~y~~k 185 (219)
T PRK05813 111 EIFLDGYICKEPVYRTTPFGREIADLLLAVNRPYNKSDYIPCIAWGRNARFCKTL-EVGDNIRVWGRVQSREYQKK 185 (219)
T ss_pred EEEEEEEccCCCeEEECCCCCEEEEEEEEEcCCCCCceEEEEEEEhHHhHHHhhC-CCCCEEEEEEEEEecceEcC
Confidence 4667776655422345555567788888543 332 2459999999877777666 789966664 6777777653
No 109
>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=24.43 E-value=1.6e+02 Score=21.63 Aligned_cols=71 Identities=13% Similarity=0.145 Sum_probs=45.3
Q ss_pred EEEEEEEEecCCceecCCCceEEEEEEEeCCCC---------CCCeEEEEecCCCCC-CCCCCCCCCEEEEe-eEEEEEE
Q 022219 24 VNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQ---------SPELLVNIFTSSIDQ-LPRVLSPRDLILLK-NVMIKKH 92 (300)
Q Consensus 24 vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~---------~~gl~v~iF~~~~~~-LP~v~~~GDII~l~-r~kv~~~ 92 (300)
+.+.|-|...-..+.++...-.+.|+|.=.+.. ..-+.|.+|.+..+. +..+ +.||.|.+. +++...|
T Consensus 1 v~l~G~l~~~p~~~~~~~g~~~~~~~v~~~~~~~~~~~~~~~~~~~~v~~~g~~a~~~~~~~-~kG~~V~v~G~l~~~~~ 79 (100)
T cd04496 1 VILIGRLGKDPELRYTPSGTPVARFSLAVNRRRKDRDEEEEETDWIRVVAFGKLAENAAKYL-KKGDLVYVEGRLRTRSW 79 (100)
T ss_pred CEEEEEecCCCEEEECCCCCEEEEEEEEEcCceecccccccccEEEEEEEEhHHHHHHHHHh-CCCCEEEEEEEEEecee
Confidence 357777777655566665567777777554432 124899999864444 4446 789977664 5566666
Q ss_pred cCe
Q 022219 93 QAE 95 (300)
Q Consensus 93 ~g~ 95 (300)
.++
T Consensus 80 ~~~ 82 (100)
T cd04496 80 EDK 82 (100)
T ss_pred ECC
Confidence 653
No 110
>cd04317 EcAspRS_like_N EcAspRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli aspartyl-tRNA synthetase (AspRS), the human mitochondrial (mt) AspRS-2, the discriminating (D) Thermus thermophilus AspRS-1, and the nondiscriminating (ND) Helicobacter pylori AspRS. These homodimeric enzymes are class2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic synthesis, wh
Probab=24.12 E-value=3.7e+02 Score=21.35 Aligned_cols=61 Identities=15% Similarity=0.141 Sum_probs=41.5
Q ss_pred cCCEEEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCC---CCCCCCCCCCCEEEEeeEEEE
Q 022219 20 VKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSI---DQLPRVLSPRDLILLKNVMIK 90 (300)
Q Consensus 20 ~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~---~~LP~v~~~GDII~l~r~kv~ 90 (300)
.|+.|.+.|-|...+. .|+ .+=+.|.|.+. .+.|.+-.+.. +.+..+ ..||+|.+...-..
T Consensus 13 ~g~~V~i~Gwv~~~R~----~gk--~~Fi~LrD~~g---~~Q~v~~~~~~~~~~~~~~l-~~gs~V~V~G~~~~ 76 (135)
T cd04317 13 VGQEVTLCGWVQRRRD----HGG--LIFIDLRDRYG---IVQVVFDPEEAPEFELAEKL-RNESVIQVTGKVRA 76 (135)
T ss_pred CCCEEEEEEeEehhcc----cCC--EEEEEEecCCe---eEEEEEeCCchhHHHHHhCC-CCccEEEEEEEEEC
Confidence 5788999999976543 344 67778888874 26665544322 244566 68999999996443
No 111
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=23.99 E-value=3.3e+02 Score=30.62 Aligned_cols=62 Identities=23% Similarity=0.244 Sum_probs=0.0
Q ss_pred cCCceEeEEEEEEEEEe---eCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCChhhhhcCCCcccEEEE
Q 022219 165 SEHRYFDLVCKVFHVSY---DDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRV 241 (300)
Q Consensus 165 ~~~~f~Dl~~qVv~~~~---~~~~~~~~L~VwDgT~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~G~~l~V 241 (300)
.++.-+-+.++|.++-. ......++++|+|||+. .+...
T Consensus 5 ~~~~~~~~~g~i~~~~~~~~~~~~~~~~~~~~d~~~s--------------------------------------~~~k~ 46 (1213)
T TIGR01405 5 EEENRVKIEGYIFKIEIKELKSGRTLLKIKVTDYTDS--------------------------------------LILKK 46 (1213)
T ss_pred ccCCeEEEEEEEEEEEeEeccCCCEEEEEEEEcCCCC--------------------------------------EEEEE
Q ss_pred EecCchhhhhhcCCCCCcEEEEe
Q 022219 242 STDRSYENFGRYFTATGKWVRIR 264 (300)
Q Consensus 242 ~~~~~~~~~~~~~lk~G~wv~l~ 264 (300)
........-....+|.|+||+++
T Consensus 47 f~~~~~~~~~~~~~~~g~~~~~~ 69 (1213)
T TIGR01405 47 FLKSEEDPEKFDGIKIGKWVRAR 69 (1213)
T ss_pred ecccccchHHHhhcCCCcEEEEE
No 112
>cd02780 MopB_CT_Tetrathionate_Arsenate-R This CD contains the molybdopterin_binding C-terminal (MopB_CT) region of tetrathionate reductase, subunit A, (TtrA); respiratory arsenate As(V) reductase, catalytic subunit (ArrA); and other related proteins.
Probab=23.76 E-value=85 Score=25.35 Aligned_cols=16 Identities=25% Similarity=0.258 Sum_probs=13.8
Q ss_pred hhcCCCCCcEEEEecc
Q 022219 251 GRYFTATGKWVRIRNM 266 (300)
Q Consensus 251 ~~~~lk~G~wv~l~Nv 266 (300)
.+..++.||||++.|=
T Consensus 40 ~~lgI~~Gd~V~v~s~ 55 (143)
T cd02780 40 AKLGIKTGDRVRVVTP 55 (143)
T ss_pred HHcCCCCCCEEEEEeC
Confidence 4678999999999983
No 113
>PRK06751 single-stranded DNA-binding protein; Provisional
Probab=23.42 E-value=2.6e+02 Score=23.84 Aligned_cols=72 Identities=11% Similarity=0.109 Sum_probs=46.9
Q ss_pred EEEEEEEEEecCCceecCCCceEEEEEEEeCCC-C-------CCCeEEEEecCCCCCCCCCCCCCCEEEE-eeEEEEEEc
Q 022219 23 KVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQ-Q-------SPELLVNIFTSSIDQLPRVLSPRDLILL-KNVMIKKHQ 93 (300)
Q Consensus 23 ~vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~-~-------~~gl~v~iF~~~~~~LP~v~~~GDII~l-~r~kv~~~~ 93 (300)
.|.++|=|+.--.-+.|.+.--+++|+|.-... . .+-+.|.+|.+..+.+-.-.+.||-|.+ =|++...|.
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 477888777543334454444578888853321 1 1249999999876767664478996555 478888886
Q ss_pred C
Q 022219 94 A 94 (300)
Q Consensus 94 g 94 (300)
+
T Consensus 84 d 84 (173)
T PRK06751 84 G 84 (173)
T ss_pred C
Confidence 4
No 114
>PF13567 DUF4131: Domain of unknown function (DUF4131)
Probab=22.79 E-value=3.8e+02 Score=21.09 Aligned_cols=69 Identities=17% Similarity=0.209 Sum_probs=37.6
Q ss_pred CCEEEEEEEEEecCCceecC-CCceEEEEEEEe--CCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcC
Q 022219 21 KHKVNLLGVVLEFSIPRKSQ-GTDYVCVLKIVD--DSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQA 94 (300)
Q Consensus 21 ~~~vnviGVVvd~~~P~~tr-G~D~~~tl~I~D--~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~r~kv~~~~g 94 (300)
+..+.+-|+|.+... .+. +..|.+...-+. .......-++.++.+. +..+.+ ..||.|++ +.+++.-.+
T Consensus 75 ~~~~~v~g~V~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~-~~~~~l-~~Gd~i~~-~g~l~~~~~ 146 (176)
T PF13567_consen 75 GKEVTVQGTVESVPQ--IDGRGQRFTLRVERVLAGGNWIPVSGKILLYLPK-DSQPRL-QPGDRIRV-RGKLKPPSG 146 (176)
T ss_pred CceEEEEEEEccccc--ccCceEEEEEEEEEeeccccccccceeeEEEecc-cccccc-CCCCEEEE-EEEEecCCC
Confidence 567889998866533 222 223444333212 2222334677777754 334456 68999998 445554433
No 115
>PF15489 CTC1: CST, telomere maintenance, complex subunit CTC1
Probab=22.76 E-value=1.1e+02 Score=33.84 Aligned_cols=51 Identities=20% Similarity=0.089 Sum_probs=43.1
Q ss_pred EEEEecCchhhhhhcCCCCCcEEEEeccEEEee-CcEEEEEEeeCCceEEcCC
Q 022219 239 LRVSTDRSYENFGRYFTATGKWVRIRNMSCQVS-SGMWHGLLQSSSKIRLFSD 290 (300)
Q Consensus 239 l~V~~~~~~~~~~~~~lk~G~wv~l~Nv~~k~~-~g~leg~l~~~sk~~~l~~ 290 (300)
|.|=++.+|..+ --.|-+|.-|.|.++..|+. +|+.+..+.++|-|+++|-
T Consensus 889 ldVYi~~~h~p~-plGLLPGA~V~f~~lerkVSRs~nVYC~~~psS~VtVlS~ 940 (1144)
T PF15489_consen 889 LDVYIEDPHLPY-PLGLLPGARVLFSQLERKVSRSHNVYCCFLPSSSVTVLSF 940 (1144)
T ss_pred EEEEecCCCCCC-cccccCCceeeeehhhhhhhccCcEEEEEcCCceEEEEec
Confidence 555556666655 56789999999999999996 7999999999999999986
No 116
>COG2332 CcmE Cytochrome c-type biogenesis protein CcmE [Posttranslational modification, protein turnover, chaperones]
Probab=22.75 E-value=3.6e+02 Score=22.57 Aligned_cols=57 Identities=14% Similarity=0.199 Sum_probs=43.1
Q ss_pred ccCCEEEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEE
Q 022219 19 HVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILL 84 (300)
Q Consensus 19 ~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l 84 (300)
..|+++++=|+|.+-+.- ++ +.+-.++|.++|.-- .++|++=. .||..++.|.-|..
T Consensus 49 ~~G~rlR~GGlV~~GSv~-R~-~~~~~v~F~vtD~~~---~v~V~Y~G----iLPDLFREGQgVVa 105 (153)
T COG2332 49 ETGQRLRLGGLVEAGSVQ-RD-PGSLKVSFVVTDGNK---SVTVSYEG----ILPDLFREGQGVVA 105 (153)
T ss_pred cCCcEEEEeeeEeeceEE-ec-CCCcEEEEEEecCCc---eEEEEEec----cCchhhhcCCeEEE
Confidence 467899999999986552 21 467788999998743 37777755 59999899997765
No 117
>PF04404 ERF: ERF superfamily; InterPro: IPR007499 The DNA single-strand annealing proteins (SSAPs), such as RecT, Red-beta, ERF and Rad52, function in RecA-dependent and RecA-independent DNA recombination pathways. This family includes proteins related to ERF [].
Probab=22.34 E-value=57 Score=27.05 Aligned_cols=64 Identities=9% Similarity=-0.026 Sum_probs=40.7
Q ss_pred CCCCcceeehhhhhhccCCEEEEEEEEEecCCceec--CCCceEEEEEEEeCCCCCCCeEEEEecC
Q 022219 4 QRNQGGIVRIKELAMHVKHKVNLLGVVLEFSIPRKS--QGTDYVCVLKIVDDSQQSPELLVNIFTS 67 (300)
Q Consensus 4 ~~~~y~y~~l~~~~~~~~~~vnviGVVvd~~~P~~t--rG~D~~~tl~I~D~S~~~~gl~v~iF~~ 67 (300)
..-.|.|.+|.|++.......+=.|+.+.+.....+ ......++.+|++.+-....+.+.++..
T Consensus 22 ~~~~y~Y~~l~dI~~av~p~l~k~gl~~~~~~~~~~~~~~~~~~v~~~l~~~~g~~e~~~~~~~~~ 87 (160)
T PF04404_consen 22 KFYKYKYASLDDILDAVKPALSKHGLSLTQEFEEIETEENGIVKVTTTLTHASGPSEWIEFPGPAD 87 (160)
T ss_pred CCCCcccccHHHHHHHHHHHHHHcCCeEEEEeecceecccceEEEEEEEEECCCCcEEEEEEEEee
Confidence 346799999999987554445555665555443222 3456778888999776444455555543
No 118
>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=22.12 E-value=1.6e+02 Score=22.09 Aligned_cols=51 Identities=16% Similarity=0.274 Sum_probs=28.8
Q ss_pred EEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEe-cCCCCCCCCCCCCCCEEEEee
Q 022219 25 NLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIF-TSSIDQLPRVLSPRDLILLKN 86 (300)
Q Consensus 25 nviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF-~~~~~~LP~v~~~GDII~l~r 86 (300)
-|||+|++.. +.-|.+.+ -.+... -|.+.=| ......-|.+ .+||+|..|=
T Consensus 9 ~VIG~V~~~~------~~~~~VdI--~s~~~a--~L~~~~f~gatk~~rp~L-~~GDlV~ArV 60 (86)
T cd05790 9 HVIGIVVAKA------GDFFKVDI--GGSEPA--SLSYLAFEGATKRNRPNL-NVGDLVYARV 60 (86)
T ss_pred EEEEEEEEEc------CCeEEEEc--CCCcce--EechHHcccccccccccC-CCCCEEEEEE
Confidence 4899999964 35566532 222211 1333323 2234445887 7999998643
No 119
>PRK07459 single-stranded DNA-binding protein; Provisional
Probab=21.34 E-value=2.7e+02 Score=22.09 Aligned_cols=72 Identities=14% Similarity=0.168 Sum_probs=47.4
Q ss_pred EEEEEEEEEecCCceecCCCceEEEEEEEeCCCC----CCCeEEEEecCCCCCCCCCCCCCCEEEEe-eEEEEEEcC
Q 022219 23 KVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQ----SPELLVNIFTSSIDQLPRVLSPRDLILLK-NVMIKKHQA 94 (300)
Q Consensus 23 ~vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~----~~gl~v~iF~~~~~~LP~v~~~GDII~l~-r~kv~~~~g 94 (300)
.|.++|=+..--.-+.|.++.-.++|+|.-.... .+-+.|.+|.+..+.+=.-..-|+-|.+. +++...|.+
T Consensus 5 ~v~LiGrL~~DPelr~t~~G~~v~~fslAv~~~~~~~~t~w~~v~~wg~~Ae~~~~~l~KG~~V~V~G~l~~~~~~d 81 (121)
T PRK07459 5 SVTLVGRAGRDPEVRYFESGSVVCNLTLAVNRRSRDDEPDWFNLEIWGKTAQVAADYVKKGSLIGITGSLKFDRWTD 81 (121)
T ss_pred EEEEEEEccCCCEEEEcCCCCEEEEEEEEecccccCCCceEEEEEEehHHHHHHHHHcCCCCEEEEEEEEEecceEc
Confidence 5888998877433344555567888999643211 22499999997555554433789966665 678888854
No 120
>PRK02801 primosomal replication protein N; Provisional
Probab=21.01 E-value=3.8e+02 Score=20.42 Aligned_cols=65 Identities=14% Similarity=0.131 Sum_probs=47.5
Q ss_pred EEEEEEEEEecCCceecCCCceEEEEEEEeCCCCC--CC-------eEEEEecCCCCCCCCCCCCCCEEEEeeE
Q 022219 23 KVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQS--PE-------LLVNIFTSSIDQLPRVLSPRDLILLKNV 87 (300)
Q Consensus 23 ~vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~--~g-------l~v~iF~~~~~~LP~v~~~GDII~l~r~ 87 (300)
+|.++|-++.--.-+.|..+--.++|+|.=.|... ++ +.|..|.+..|.+-.-...|.-|.+...
T Consensus 4 ~v~L~Grl~~dpelr~Tp~G~~v~~f~La~~~~~~ea~~~r~~~~~i~~va~G~~Ae~~~~~l~kGs~v~V~G~ 77 (101)
T PRK02801 4 RLVLSGTVCRTPKRKVSPSGIPHCQFVLEHRSVQEEAGLHRQAWCRMPVIVSGNQFQAITQSITVGSKITVQGF 77 (101)
T ss_pred EEEEEEEECcCcceEECCCCCeEEEEEEEEeCeEecCCCceeEEEEEEEEEEcHHHHHHHhhcCCCCEEEEEEE
Confidence 68899999987776777545556788886555431 23 8899999877888853378999988654
No 121
>PRK07274 single-stranded DNA-binding protein; Provisional
Probab=20.77 E-value=2e+02 Score=23.19 Aligned_cols=70 Identities=17% Similarity=0.164 Sum_probs=48.4
Q ss_pred EEEEEEEEEecCCceecCCCceEEEEEEEeCCCC--------CCCeEEEEecCCCCCCCCCCCCCCEEEEe-eEEEEEE
Q 022219 23 KVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQ--------SPELLVNIFTSSIDQLPRVLSPRDLILLK-NVMIKKH 92 (300)
Q Consensus 23 ~vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~--------~~gl~v~iF~~~~~~LP~v~~~GDII~l~-r~kv~~~ 92 (300)
+|.++|=+..--..+.|.++.-.++|+|.-...- .+-+.|.+|.+..+.+..-...|+-|.+. +++...|
T Consensus 4 ~v~LiGrL~~dPelr~t~~g~~~~~fslAv~~~~k~~~g~~~t~w~~v~~fg~~Ae~v~~~l~KG~~V~V~Grl~~~~y 82 (131)
T PRK07274 4 KVILIGRLTATPELVKTANDKSVARVTLAVNRRFKNQNGEREADFINVVLWGKLAETLASYASKGSLISIDGELRTRKY 82 (131)
T ss_pred EEEEEEEccCCCeEEECCCCCEEEEEEEEEcCceecCCCCEEEEEEEEEEehHHHHHHHHHcCCCCEEEEEEEEEeccC
Confidence 5778888776544445555557788888644311 12499999997667777744789977776 6788888
No 122
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=20.47 E-value=4.2e+02 Score=27.59 Aligned_cols=39 Identities=13% Similarity=0.092 Sum_probs=30.2
Q ss_pred cccccccCCceEeEEEEEEEEEeeC-CCCeEEEEEEcCCC
Q 022219 159 LSLKDISEHRYFDLVCKVFHVSYDD-SKGLWMLFVWDGTD 197 (300)
Q Consensus 159 ~~L~di~~~~f~Dl~~qVv~~~~~~-~~~~~~L~VwDgT~ 197 (300)
..|.++++|+.+-+.++|++..... ....+.+.+.|+|+
T Consensus 51 ~~i~~l~~g~~vtv~g~V~~~~~~~~~~~~~~v~l~D~tg 90 (681)
T PRK10917 51 KPIAELRPGEKVTVEGEVLSAEVVFGKRRRLTVTVSDGTG 90 (681)
T ss_pred CCHHHCCCCCEEEEEEEEEEEEEccCCceEEEEEEEECCe
Confidence 5788999999999999999886221 22457888888885
No 123
>PRK06293 single-stranded DNA-binding protein; Provisional
Probab=20.44 E-value=2e+02 Score=24.28 Aligned_cols=72 Identities=14% Similarity=0.067 Sum_probs=45.9
Q ss_pred EEEEEEEEEecCCceecCCCceEEEEEEEeCCCC-----CCCeEEEEecCCCCCCCCCCCCCCEEEEe-eEEEEEEcC
Q 022219 23 KVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQ-----SPELLVNIFTSSIDQLPRVLSPRDLILLK-NVMIKKHQA 94 (300)
Q Consensus 23 ~vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~-----~~gl~v~iF~~~~~~LP~v~~~GDII~l~-r~kv~~~~g 94 (300)
.|.++|=+..--..+.+.+..=.++|+|.=.... ..-+.|.+|.+..+.+..-..-||-|.+. +++...|.+
T Consensus 3 ~V~LiGrLg~DPElR~t~sG~~v~~FsLAvn~~~~~~~~T~wi~v~awg~~Ae~v~~yL~KG~~V~VeGrL~~~~y~d 80 (161)
T PRK06293 3 FGYIVGRLGADPEERMTSKGKRVVVLRLGVKSRVGSKDETVWCRCNIWGNRYDKMLPYLKKGSGVIVAGEMSPESYVD 80 (161)
T ss_pred EEEEEEEecCCCeEEEcCCCCEEEEEEEEEeCCCCCccceEEEEEEEEhHHHHHHHHhCCCCCEEEEEEEEEeCccCC
Confidence 4788887765433344544455688888643211 12399999997666666633689966654 778888854
No 124
>PF10459 Peptidase_S46: Peptidase S46; InterPro: IPR019500 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This entry represents S46 peptidases, where dipeptidyl-peptidase 7 (DPP-7) is the best-characterised member of this family. It is a serine peptidase that is located on the cell surface and is predicted to have two N-terminal transmembrane domains.
Probab=20.42 E-value=3.7e+02 Score=28.30 Aligned_cols=79 Identities=16% Similarity=0.220 Sum_probs=45.3
Q ss_pred eEEEEEEEEEeeCCCCeEEEEEE-cCCCCCCCCCCCCCCcccCCCCCCcccCCCCChhhhhcCC-Ccc--cEEEEEec--
Q 022219 171 DLVCKVFHVSYDDSKGLWMLFVW-DGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFF-PVG--TVLRVSTD-- 244 (300)
Q Consensus 171 Dl~~qVv~~~~~~~~~~~~L~Vw-DgT~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p-~~G--~~l~V~~~-- 244 (300)
.+.|+|+..+ .++.+.||+. .|++=-.. .-|+...+. |+-+. .-+.|| .-| ..+||=.+
T Consensus 148 ~~~~~V~~fy---~G~~Y~L~~y~~y~DVRLV---~APp~siG~---FGGD~------DNw~wPRhtgDfs~fRvY~~~d 212 (698)
T PF10459_consen 148 GYRCQVVSFY---GGNQYYLFVYRRYKDVRLV---YAPPSSIGK---FGGDT------DNWMWPRHTGDFSFFRVYADKD 212 (698)
T ss_pred CeEEEEEEec---CCceEEEEEEEEecceEEe---cCChHHhcc---cCCCc------ccccCCCCCCceEEEEEEeCCC
Confidence 8999999998 4778888875 45542111 111110000 11111 125566 333 36777555
Q ss_pred ---------------CchhhhhhcCCCCCcEEEEe
Q 022219 245 ---------------RSYENFGRYFTATGKWVRIR 264 (300)
Q Consensus 245 ---------------~~~~~~~~~~lk~G~wv~l~ 264 (300)
+|+-++..+.+|+||+|.+-
T Consensus 213 g~PA~Ys~dnvP~~p~~~l~is~~G~keGD~vmv~ 247 (698)
T PF10459_consen 213 GKPADYSKDNVPYKPKHFLKISLKGVKEGDFVMVA 247 (698)
T ss_pred CCccccCcCCCCCCCccccccCCCCCCCCCeEEEc
Confidence 36666777889999998764
No 125
>TIGR00594 polc DNA-directed DNA polymerase III (polc). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=20.18 E-value=2.3e+02 Score=31.24 Aligned_cols=43 Identities=16% Similarity=0.244 Sum_probs=32.8
Q ss_pred cCCEEEEEEEEEecCCceecCCCceEEEEEEEeCCCCCCCeEEEEe
Q 022219 20 VKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIF 65 (300)
Q Consensus 20 ~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF 65 (300)
.+..|.+.|+|+.++.-.+|+.++-+.-++|-|.+-. +.+.+|
T Consensus 980 ~g~~v~v~G~i~~~~~~~~tkkG~~maf~tleD~tg~---ie~viF 1022 (1022)
T TIGR00594 980 NDSQVRTLGGLNSVKKKITTKNGKPMAFLQLEDETGS---IEVVVF 1022 (1022)
T ss_pred CCCEEEEEEEEEEEEEecccCCCCEEEEEEEEECCCc---EEEEeC
Confidence 3567999999999877445555567899999999764 777776
No 126
>PRK08182 single-stranded DNA-binding protein; Provisional
Probab=20.17 E-value=1.9e+02 Score=23.86 Aligned_cols=73 Identities=12% Similarity=0.096 Sum_probs=46.9
Q ss_pred CEEEEEEEEEecCCceecC-CCc---eEEEEEEE-eCCCC---C-------CCeEEEEecCCCCCCCCCCCCCCEEEEe-
Q 022219 22 HKVNLLGVVLEFSIPRKSQ-GTD---YVCVLKIV-DDSQQ---S-------PELLVNIFTSSIDQLPRVLSPRDLILLK- 85 (300)
Q Consensus 22 ~~vnviGVVvd~~~P~~tr-G~D---~~~tl~I~-D~S~~---~-------~gl~v~iF~~~~~~LP~v~~~GDII~l~- 85 (300)
..|.++|=+..--.-+.+. |+. -.++|+|. |.+.. + .-+.|.+|.+..+.+-.-..-||-|.+.
T Consensus 3 N~V~LiGrLg~DPElr~t~~G~~~~~~va~fslA~~r~~~~~~Ge~~~~~t~w~~V~~wg~~Ae~v~~~l~KG~~V~V~G 82 (148)
T PRK08182 3 THFVGEGNIGSAPEYREFPNGNDEPRRLLRLNVYFDNPVPTKDGEYEDRGGFWAPVELWHRDAEHWARLYQKGMRVLVEG 82 (148)
T ss_pred cEEEEEEECCCCCeEEECCCCCeeeeeEEEEEEEecCceECCCCCEEecCcEEEEEEEEhHHHHHHHHhcCCCCEEEEEE
Confidence 3688888777653334443 443 27888884 33221 0 1388999997667676644789966554
Q ss_pred eEEEEEEcC
Q 022219 86 NVMIKKHQA 94 (300)
Q Consensus 86 r~kv~~~~g 94 (300)
+++...|.+
T Consensus 83 rL~~~~w~d 91 (148)
T PRK08182 83 RMERDEWTD 91 (148)
T ss_pred EEEecccCC
Confidence 688888854
Done!