Query 012401
Match_columns 464
No_of_seqs 179 out of 233
Neff 7.3
Searched_HMMs 46136
Date Fri Mar 29 02:15:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/012401.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/012401hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4757 Predicted telomere bin 100.0 8E-52 1.7E-56 408.8 13.2 426 3-462 2-462 (522)
2 cd04497 hPOT1_OB1_like hPOT1_O 100.0 1.8E-33 3.9E-38 250.3 17.6 137 8-146 1-138 (138)
3 PF02765 POT1: Telomeric singl 100.0 4.9E-33 1.1E-37 250.0 14.0 137 10-146 1-146 (146)
4 cd04498 hPOT1_OB2 hPOT1_OB2: A 99.9 1.9E-23 4.1E-28 179.6 11.3 101 169-282 1-113 (123)
5 PRK12366 replication factor A; 99.4 1.2E-10 2.7E-15 127.5 30.5 299 6-403 275-591 (637)
6 TIGR00617 rpa1 replication fac 99.2 6.4E-09 1.4E-13 113.5 27.2 318 9-402 179-537 (608)
7 PRK12366 replication factor A; 99.2 2.1E-08 4.6E-13 110.1 28.5 279 8-402 61-344 (637)
8 PRK07218 replication factor A; 99.1 3.9E-07 8.4E-12 94.9 31.6 282 10-403 58-352 (423)
9 PRK14699 replication factor A; 99.0 5E-07 1.1E-11 95.9 29.1 272 11-400 167-447 (484)
10 PRK07211 replication factor A; 98.9 5.6E-08 1.2E-12 102.2 19.8 204 8-290 159-367 (485)
11 PRK15491 replication factor A; 98.9 1E-06 2.3E-11 90.8 27.7 271 10-399 57-336 (374)
12 PRK06386 replication factor A; 98.9 7.5E-06 1.6E-10 83.4 31.7 275 11-403 3-291 (358)
13 PRK15491 replication factor A; 98.8 4.3E-07 9.4E-12 93.6 19.6 204 6-286 162-372 (374)
14 PRK14699 replication factor A; 98.6 2.7E-06 5.9E-11 90.4 20.6 204 8-288 274-484 (484)
15 KOG4757 Predicted telomere bin 98.4 1.2E-08 2.5E-13 103.0 -4.2 117 346-462 378-522 (522)
16 PRK07211 replication factor A; 98.4 0.0003 6.5E-09 74.4 27.7 269 10-399 53-329 (485)
17 PRK08402 replication factor A; 98.3 5.7E-05 1.2E-09 77.3 19.3 195 159-413 63-281 (355)
18 PRK06461 single-stranded DNA-b 97.9 0.0004 8.6E-09 61.1 13.6 92 10-111 4-99 (129)
19 TIGR00617 rpa1 replication fac 97.9 0.00021 4.5E-09 78.5 14.4 145 7-180 295-468 (608)
20 cd04475 RPA1_DBD_B RPA1_DBD_B: 97.7 0.00026 5.6E-09 59.3 9.7 73 24-101 2-79 (101)
21 PRK07218 replication factor A; 97.5 0.011 2.3E-07 62.1 20.4 160 159-397 59-219 (423)
22 cd04491 SoSSB_OBF SoSSB_OBF: A 97.5 0.0014 2.9E-08 52.8 10.6 72 25-102 1-75 (82)
23 PRK06461 single-stranded DNA-b 97.1 0.0049 1.1E-07 54.2 10.7 88 159-291 5-101 (129)
24 PRK08402 replication factor A; 97.0 0.019 4.1E-07 59.0 15.3 139 9-180 61-207 (355)
25 cd04497 hPOT1_OB1_like hPOT1_O 96.6 0.02 4.4E-07 50.9 10.5 97 157-291 3-106 (138)
26 cd03524 RPA2_OBF_family RPA2_O 96.4 0.014 3.1E-07 44.2 7.2 71 25-101 1-71 (75)
27 PRK07217 replication factor A; 96.3 0.3 6.5E-06 49.0 17.6 168 159-403 73-245 (311)
28 KOG3416 Predicted nucleic acid 96.3 0.019 4.1E-07 49.4 7.8 84 11-102 5-88 (134)
29 PF02765 POT1: Telomeric singl 96.1 0.16 3.4E-06 45.6 12.9 97 159-288 2-109 (146)
30 PRK07217 replication factor A; 95.9 0.14 3E-06 51.3 12.8 92 7-109 69-160 (311)
31 cd04489 ExoVII_LU_OBF ExoVII_L 95.2 0.23 4.9E-06 39.0 9.5 69 24-101 2-72 (78)
32 PF01336 tRNA_anti-codon: OB-f 95.2 0.035 7.6E-07 43.0 4.7 68 24-101 1-70 (75)
33 PRK06386 replication factor A; 95.1 0.18 3.8E-06 51.9 10.6 87 8-106 105-193 (358)
34 cd04481 RPA1_DBD_B_like RPA1_D 94.9 0.099 2.2E-06 44.1 7.1 82 25-108 1-90 (106)
35 cd04476 RPA1_DBD_C RPA1_DBD_C: 94.7 0.15 3.3E-06 46.5 8.3 58 346-403 15-96 (166)
36 cd04475 RPA1_DBD_B RPA1_DBD_B: 94.4 0.42 9E-06 39.8 9.6 61 236-300 38-98 (101)
37 PF15489 CTC1: CST, telomere m 94.2 0.44 9.6E-06 55.0 12.0 145 238-415 888-1055(1144)
38 cd04474 RPA1_DBD_A RPA1_DBD_A: 94.1 0.16 3.5E-06 42.7 6.6 83 12-98 1-87 (104)
39 cd04478 RPA2_DBD_D RPA2_DBD_D: 94.0 0.52 1.1E-05 38.6 9.3 67 24-101 2-72 (95)
40 cd04491 SoSSB_OBF SoSSB_OBF: A 93.6 0.21 4.6E-06 39.9 6.0 46 238-286 35-80 (82)
41 PRK13480 3'-5' exoribonuclease 93.3 1.4 3E-05 44.7 12.7 82 12-101 4-85 (314)
42 cd04485 DnaE_OBF DnaE_OBF: A s 93.2 0.23 5.1E-06 38.8 5.6 71 26-101 2-72 (84)
43 cd04492 YhaM_OBF_like YhaM_OBF 92.3 1.2 2.6E-05 34.9 8.7 68 27-100 3-70 (83)
44 cd04483 hOBFC1_like hOBFC1_lik 91.4 1.6 3.5E-05 35.9 8.7 65 26-101 2-87 (92)
45 PF08646 Rep_fac-A_C: Replicat 90.4 0.22 4.7E-06 44.5 2.8 32 371-402 50-81 (146)
46 PF13742 tRNA_anti_2: OB-fold 86.5 6.1 0.00013 32.9 8.9 79 13-100 11-94 (99)
47 cd03524 RPA2_OBF_family RPA2_O 85.2 11 0.00023 27.9 9.1 65 171-276 1-67 (75)
48 cd04488 RecG_wedge_OBF RecG_we 82.6 8.9 0.00019 28.9 7.8 68 26-100 2-69 (75)
49 PF01336 tRNA_anti-codon: OB-f 79.7 24 0.00052 26.7 9.4 62 170-273 1-62 (75)
50 cd04484 polC_OBF polC_OBF: A s 78.5 18 0.00039 28.9 8.4 71 24-98 2-74 (82)
51 cd04487 RecJ_OBF2_like RecJ_OB 78.2 21 0.00046 27.9 8.6 64 26-100 3-67 (73)
52 PRK07373 DNA polymerase III su 77.3 7.5 0.00016 41.5 7.5 88 9-101 267-355 (449)
53 cd04490 PolII_SU_OBF PolII_SU_ 75.5 10 0.00022 30.2 6.1 59 24-91 2-62 (79)
54 PF09104 BRCA-2_OB3: BRCA2, ol 74.8 17 0.00037 32.5 7.8 62 168-270 19-82 (143)
55 PF09104 BRCA-2_OB3: BRCA2, ol 73.3 20 0.00043 32.1 7.8 63 21-90 18-81 (143)
56 cd04474 RPA1_DBD_A RPA1_DBD_A: 72.8 8.1 0.00018 32.3 5.2 48 236-283 46-100 (104)
57 cd04483 hOBFC1_like hOBFC1_lik 71.3 47 0.001 27.2 9.3 26 171-198 1-26 (92)
58 PRK05673 dnaE DNA polymerase I 70.6 11 0.00025 44.7 7.5 87 10-101 965-1052(1135)
59 KOG3056 Protein required for S 67.8 8.5 0.00018 41.5 5.1 70 24-95 188-257 (578)
60 cd04482 RPA2_OBF_like RPA2_OBF 66.0 25 0.00055 28.7 6.6 60 26-93 3-64 (91)
61 cd04495 BRCA2DBD_OB3 BRCA2DBD_ 65.9 26 0.00057 29.3 6.5 64 26-95 2-66 (100)
62 KOG1030 Predicted Ca2+-depende 65.3 13 0.00029 34.0 5.2 26 371-396 51-76 (168)
63 PRK06920 dnaE DNA polymerase I 64.6 18 0.00039 42.9 7.4 88 9-101 931-1018(1107)
64 cd04498 hPOT1_OB2 hPOT1_OB2: A 64.4 8 0.00017 33.7 3.5 34 60-94 62-95 (123)
65 PF02721 DUF223: Domain of unk 61.3 24 0.00052 28.9 5.7 39 236-274 9-47 (95)
66 PRK00286 xseA exodeoxyribonucl 60.1 60 0.0013 34.4 9.9 78 14-100 16-95 (438)
67 TIGR00237 xseA exodeoxyribonuc 58.7 65 0.0014 34.2 9.9 79 13-101 9-90 (432)
68 PF12100 DUF3576: Domain of un 54.5 26 0.00056 29.5 4.7 53 9-68 17-70 (103)
69 PRK07374 dnaE DNA polymerase I 53.6 37 0.0008 40.7 7.5 88 9-101 987-1075(1170)
70 PRK05338 rplS 50S ribosomal pr 53.3 33 0.00071 29.6 5.3 45 70-115 14-66 (116)
71 PF01245 Ribosomal_L19: Riboso 52.7 49 0.0011 28.4 6.3 42 69-111 13-62 (113)
72 cd04478 RPA2_DBD_D RPA2_DBD_D: 52.5 75 0.0016 25.5 7.3 26 170-197 2-27 (95)
73 PF15072 DUF4539: Domain of un 49.3 52 0.0011 26.8 5.6 63 23-94 3-66 (86)
74 PRK10917 ATP-dependent DNA hel 49.2 72 0.0016 35.9 8.8 78 12-98 52-129 (681)
75 COG1107 Archaea-specific RecJ- 48.0 82 0.0018 34.6 8.3 79 11-100 203-282 (715)
76 TIGR00643 recG ATP-dependent D 46.5 1E+02 0.0022 34.4 9.3 78 12-99 25-103 (630)
77 cd04480 RPA1_DBD_A_like RPA1_D 46.0 37 0.00081 27.0 4.4 37 236-272 30-66 (86)
78 TIGR01024 rplS_bact ribosomal 45.0 48 0.0011 28.4 5.0 45 70-115 14-66 (113)
79 cd04486 YhcR_OBF_like YhcR_OBF 42.1 1.7E+02 0.0037 23.1 8.4 62 27-101 3-69 (78)
80 PRK06826 dnaE DNA polymerase I 41.8 64 0.0014 38.7 7.1 77 20-101 990-1067(1151)
81 PRK05672 dnaE2 error-prone DNA 41.8 58 0.0013 38.6 6.7 86 9-101 940-1026(1046)
82 PF15072 DUF4539: Domain of un 41.2 25 0.00054 28.7 2.6 24 376-399 20-43 (86)
83 CHL00084 rpl19 ribosomal prote 40.3 68 0.0015 27.7 5.2 43 70-113 18-68 (117)
84 PRK00448 polC DNA polymerase I 35.8 1.2E+02 0.0026 37.2 8.2 85 8-98 224-312 (1437)
85 PF14535 AMP-binding_C_2: AMP- 35.1 26 0.00057 28.7 1.9 63 356-420 2-70 (96)
86 KOG2708 Predicted metalloprote 34.8 22 0.00049 34.3 1.6 48 408-462 90-154 (336)
87 cd04490 PolII_SU_OBF PolII_SU_ 34.8 42 0.00092 26.6 3.0 21 378-398 20-40 (79)
88 PRK07279 dnaE DNA polymerase I 34.5 84 0.0018 37.2 6.4 86 9-101 874-960 (1034)
89 KOG4792 Crk family adapters [S 33.3 1.1E+02 0.0023 29.7 5.8 61 229-293 223-289 (293)
90 cd04495 BRCA2DBD_OB3 BRCA2DBD_ 32.9 2.1E+02 0.0046 24.0 6.8 34 239-272 30-64 (100)
91 cd04489 ExoVII_LU_OBF ExoVII_L 31.4 58 0.0013 25.0 3.3 24 376-399 18-41 (78)
92 cd04492 YhaM_OBF_like YhaM_OBF 30.9 63 0.0014 24.8 3.4 21 376-396 20-40 (83)
93 cd04496 SSB_OBF SSB_OBF: A sub 29.8 39 0.00086 27.2 2.1 28 237-264 44-71 (100)
94 PRK13254 cytochrome c-type bio 29.6 3.5E+02 0.0076 24.3 8.3 66 10-85 37-105 (148)
95 COG2049 DUR1 Allophanate hydro 29.4 26 0.00057 33.7 1.1 39 230-270 177-215 (223)
96 COG1599 RFA1 Single-stranded D 28.1 1.9E+02 0.0041 30.4 7.4 78 21-103 59-140 (407)
97 COG1200 RecG RecG-like helicas 27.2 2.9E+02 0.0064 31.0 8.7 80 13-101 54-133 (677)
98 COG1570 XseA Exonuclease VII, 26.5 5.8E+02 0.013 27.2 10.4 70 22-100 24-95 (440)
99 PF15489 CTC1: CST, telomere m 26.0 1.2E+03 0.026 28.0 16.0 71 20-95 164-235 (1144)
100 cd04481 RPA1_DBD_B_like RPA1_D 25.9 1.4E+02 0.003 24.8 4.8 63 236-299 34-102 (106)
101 cd04317 EcAspRS_like_N EcAspRS 25.4 3.5E+02 0.0075 23.3 7.5 68 13-90 5-76 (135)
102 PRK00448 polC DNA polymerase I 25.1 2.5E+02 0.0054 34.7 8.4 40 159-198 227-270 (1437)
103 cd04480 RPA1_DBD_A_like RPA1_D 24.9 1.3E+02 0.0028 23.9 4.3 57 42-100 17-73 (86)
104 COG2176 PolC DNA polymerase II 22.6 1.7E+02 0.0036 35.1 5.9 69 156-264 228-301 (1444)
105 PRK07772 single-stranded DNA-b 20.4 1.9E+02 0.0041 27.1 4.9 74 21-94 4-90 (186)
106 cd04494 BRCA2DBD_OB2 BRCA2DBD_ 20.2 1.6E+02 0.0035 28.9 4.6 52 237-289 180-236 (251)
No 1
>KOG4757 consensus Predicted telomere binding protein [General function prediction only]
Probab=100.00 E-value=8e-52 Score=408.81 Aligned_cols=426 Identities=22% Similarity=0.207 Sum_probs=331.6
Q ss_pred CCCCCcceeehhhhhhccCCEEEEEEEEEEcCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEE
Q 012401 3 SQRNQGGIVRIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLI 82 (464)
Q Consensus 3 ~~~~~y~y~~i~d~~~~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII 82 (464)
.-++.++|..+++++...+..||+||||++++||++++|+||+||++|+||++.+.||+|++|+++-++||.|+++||||
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 45788999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEeeEEEEEEcCeeEEEeccCcc-EEEEEeCCCCCCCCccccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCccccccc
Q 012401 83 LLKNVMIKKHQAELSAVFYKDSS-SFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSL 161 (464)
Q Consensus 83 ~l~rvkv~~~~g~~~~~~~~~~s-s~~lf~~~~~~~~~Py~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~f~~~L 161 (464)
+|||+|||.|+.+.+|+++..++ +|++|+|+ +.+..|||+|+. |-++ .+||+|++.+.....+ ++ ..+
T Consensus 82 llhRiKiq~y~~rtqgl~s~~fss~~~~Feg~-svd~i~~qssp~-f~~t-------~nlrew~a~~~s~~w~-c~-t~~ 150 (522)
T KOG4757|consen 82 LLHRIKIQSYRDRTQGLCSDQFSSAWALFEGN-SVDTICYQSSPR-FMKT-------GNLREWFALYKSKIWD-CQ-TNL 150 (522)
T ss_pred EEEEEEEEEhhhhhhhhhhcchhhhhhhhcCC-CCCccCCCCchh-hhcc-------chHHHHHHHHhCcccc-cc-cCH
Confidence 99999999999999999987764 59999999 889999999887 8777 7899999988877766 56 789
Q ss_pred ccccCCceEeeEEEEEEeeeeCCCCeEEEEEEcCCCCCCCCCCCCCCc-ccCCCCCCcccCCCCCccccccCCCcceEEE
Q 012401 162 KDISEHRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLED-EEHNPLPLHIESSPLDLETLRNFFPVGTVLR 240 (464)
Q Consensus 162 kdi~~~~f~Dlv~qVv~v~~~~~~~~~~L~VwDgT~~~~~~~~~~~~~-~~~~~~p~~~~~~~l~~~~~~~~p~~G~vl~ 240 (464)
+++.++..-.|.||+++.. ......|. .|||-|.+-...+++..-- --+.-.|++|++ .+.+.+..||..|.|..
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 9999999999999999887 54567777 7999554444332221000 001235677754 56667889999998889
Q ss_pred EEecccchhhhccCCCCCcEEEEeCcEEEEeCcEEEEEEecCcceEEcCCCChhHHHHHH-HH----------------H
Q 012401 241 VSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDNDNVVWDYMR-FR----------------E 303 (464)
Q Consensus 241 V~~~~~~~~~~~~~~k~G~wV~l~Nv~~k~~~g~leG~l~~~ski~~l~~~d~~v~~r~r-y~----------------~ 303 (464)
...+.+.+++..+.+++|.-+..+|+...-+. +|.++ ++.+ .|+.-..|.- .. +
T Consensus 227 ~r~~rv~~e~~i~ilq~~~d~~~~Nl~~e~D~-----~f~~~--~~sl--~dh~~lsrc~~~~~saprl~~sl~lhc~~e 297 (522)
T KOG4757|consen 227 SRWDRVSEEFSICILQDEHDFYCRNLIKEGDY-----VFMKN--VRSL--IDHLGLSRCILHGDSAPRLNMSLELHCSEE 297 (522)
T ss_pred eeeecccccccchhccccchhhhhhhcccccc-----ccccc--chhh--hHHHHHHHHHHHhhccccccceeEeecCcc
Confidence 88888888887778888888888888752211 33332 1111 1222222211 00 0
Q ss_pred HHhCCCCCCCCccCCCCCCCcccccCCCccccHHHHhhCCCCCceeE-EEEEEEe---ecCCCccccccCCCCeEEEEEE
Q 012401 304 RISGGHGHMPIWTDPSSQFLTEVDWVNVASVTLMKIATQLQGNVRCC-CIVRVVS---IHPFQAEHYSSPNGSSEYTMKL 379 (464)
Q Consensus 304 r~~~~~~~~~~~~~~~~~~~t~~~~~~~p~ttL~dIL~~p~v~~kfr-~~VRVV~---~~P~~~edf~~~~~~w~~rf~L 379 (464)
.+..+++... .+-.++..|.+++..+|+++|||+++.+.++.||| |.||+|+ .+|.++|.+.-.+ -...-
T Consensus 298 hll~ev~~e~--r~~~q~~~tgi~~v~a~fvsl~Ds~t~~~vt~k~R~~vvrfva~~~~~P~sve~l~~i~----i~l~~ 371 (522)
T KOG4757|consen 298 HLLNEVKPEK--RLYVQNCQTGIEAVIAPFVSLMDSETPFIVTEKKRTCVVRFVAHVINYPASVELLTIIT----ILLAP 371 (522)
T ss_pred hhhcccCccc--ceeecccccCcchhhcccchhhhhccccccchhcceeeeeehhhcccccchhhhhhhhh----hhhHH
Confidence 0111111110 01124677888999999999999999999999999 9999999 9999999986432 13445
Q ss_pred EEeCCCceEEEEEecccccc-----ccCCC-CChHHHHHHHHHHcCCCCCCCCCCCCccCCcceeEeeeeeeecCCc---
Q 012401 380 TLEDPTARIHALLCGKEWVK-----FFGGS-PPPDVLTKKIKMLLGMPEHEDGNDDMVRNPPWIKCFLHLKESDGGR--- 450 (464)
Q Consensus 380 ~lED~t~ri~~~v~~~da~~-----f~~~~-~~~~~L~~kl~~L~G~~e~~~~~~~~~~~~pw~~CCi~sY~v~~~~--- 450 (464)
+.+|+++|.|+.++..|... +||-. .+..++..+|+.|+|+.+. + ..|+++||++||....+-.+-.
T Consensus 372 ic~l~n~r~H~~l~~le~s~p~s~~~fgc~~~~~~~~v~~ln~Lv~~e~~--~--~vP~~~~~v~~~~l~~~s~~l~~~l 447 (522)
T KOG4757|consen 372 ICNLLNPRKHRLLVQLEDSWPKSLTQFGCLSQPPSSYVWMLNLLVRDESN--V--TVPVIFFDVDAAELINSSKKLPCNL 447 (522)
T ss_pred HhhhhchhhhhhhhhhcccCcccceeeeeccCCHHHHHHHHHHHhccccc--c--ccccccchhheeeeccccccccchh
Confidence 67899999999998888775 77743 5678889999999998332 2 2689999999999999888743
Q ss_pred ---eEEEEEeeeEEc
Q 012401 451 ---NRVYYIRWTKLV 462 (464)
Q Consensus 451 ---~r~f~~F~T~i~ 462 (464)
+|+||||++-|.
T Consensus 448 ~d~~~~fqi~ds~il 462 (522)
T KOG4757|consen 448 ADHQMTFQIKDSLIL 462 (522)
T ss_pred ccccceEEecceeee
Confidence 799999999886
No 2
>cd04497 hPOT1_OB1_like hPOT1_OB1_like: A subfamily of OB folds similar to the first OB fold (OB1) of human protection of telomeres 1 protein (hPOT1), the single OB fold of the N-terminal domain of Schizosaccharomyces pombe POT1 (SpPOT1), and the first OB fold of the N-terminal domain of the alpha subunit (OB1Nalpha) of Oxytricha nova telomere end binding protein (OnTEBP). POT1 proteins recognize single-stranded (ss) 3-prime ends of the telomere. A 3-prime ss overhang is conserved in ciliated protozoa, yeast, and mammals. SpPOT1 is essential for telomere maintenance. It binds specifically to the ss G-rich telomeric sequence (GGTTAC) of S. pombe. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. Deletion of the S. pombe pot1+ gene results in a rapid loss of telomere sequences, chromosome mis-segregation and chromosome circularization. hPOT1 is implicated in telomere length regulation. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB
Probab=100.00 E-value=1.8e-33 Score=250.32 Aligned_cols=137 Identities=33% Similarity=0.509 Sum_probs=129.8
Q ss_pred cceeehhhhhhccCCEEEEEEEEEEcCCccccCCCceEEEEEEEeCCCC-CCCeEEEEecCCCCCCCCCCCCCCEEEEee
Q 012401 8 GGIVRIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQ-SPELLVNIFTSSIDQLPRVLSPRDLILLKN 86 (464)
Q Consensus 8 y~y~~i~d~~~~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~-~~gl~v~iF~~~~~~LP~v~~~GDII~l~r 86 (464)
|.|++|++|.+..++.|||||||+|+++|++|+|+||+|+|+|+|+|.. +.||+|+||+++.++||.+ ++||||+|||
T Consensus 1 ~~f~~i~~~~~~~~~~v~vigVV~~~~~p~~s~g~d~~~tl~i~D~S~~~~~~l~v~~F~~~~~~LP~v-~~GDVIll~~ 79 (138)
T cd04497 1 YKYTPLSSALKESGGSVNVIGVVVDAGPPVRSKGTDYCCTLTITDPSLANSDGLTVKLFRPNEESLPIV-KVGDIILLRR 79 (138)
T ss_pred CceEeHHHHHhccCCeEEEEEEEeecCCCcccCCCcEEEEEEEECCCCCCCCcEEEEEECCChhhCCCC-CCCCEEEEEE
Confidence 6899999999888999999999999999999999999999999999997 7899999999999999999 8999999999
Q ss_pred EEEEEEcCeeEEEeccCccEEEEEeCCCCCCCCccccCCCCCCCCHHHHHHHHHHHHhhh
Q 012401 87 VMIKKHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCV 146 (464)
Q Consensus 87 vkv~~~~g~~~~~~~~~~ss~~lf~~~~~~~~~Py~~s~~~~~~~~~e~~~v~~Lr~W~~ 146 (464)
++|+.|+|+.+++++.+.||||||++..+....||+.+.+ ++++++|++++..||+|+.
T Consensus 80 ~kv~~~~g~~~~~~~~~~ss~avf~~~~~~~~~p~~~~~~-~~~~~~e~~~~~~Lr~w~~ 138 (138)
T cd04497 80 VKIQSYNGKPQGISNDRGSSWAVFRGDDGVVPIPQQSSKP-VEFGPEEEPSVEELRKWAS 138 (138)
T ss_pred EEEEEECCceEEEECCCceeEEEEcCCCCCCcCccccCCC-cccCcchHHHHHHHHHhhC
Confidence 9999999999999987679999999999999889887766 9999999999999999973
No 3
>PF02765 POT1: Telomeric single stranded DNA binding POT1/CDC13; InterPro: IPR011564 This entry represents a domain that binds single stranded telomeric DNA and adopts an OB fold []. It includes the proteins POT1 and CDC13 which have been shown to regulate telomere length, replication and capping [, , ]. ; GO: 0003677 DNA binding, 0000723 telomere maintenance, 0000784 nuclear chromosome, telomeric region; PDB: 1S40_A 1KXL_A 1PH7_A 1PH9_A 1PH2_A 1OTC_A 1PHJ_A 1JB7_A 1PA6_A 1PH1_A ....
Probab=100.00 E-value=4.9e-33 Score=249.96 Aligned_cols=137 Identities=35% Similarity=0.617 Sum_probs=127.0
Q ss_pred eeehhhhhhccCCEEEEEEEEEEcCCc--cccCCCceEEEEEEEeCCCCC-----CCeEEEEecCCCCCCCCCCCCCCEE
Q 012401 10 IVRIKELAMHVKHKVNLLGVVLEFSIP--RKSQGTDYVCVLKIVDDSQQS-----PELLVNIFTSSIDQLPRVLSPRDLI 82 (464)
Q Consensus 10 y~~i~d~~~~~~~~vnviGVVvd~~~P--~~trG~D~~~tl~I~D~S~~~-----~gl~v~iF~~~~~~LP~v~~~GDII 82 (464)
|++|+++....+..|||||||+++++| ++|||+||+|+|+|+|+|+.. .||+|++|+++++.||.+..+||||
T Consensus 1 ~~~l~~~~~~~~~~vnvigVV~~~~~p~~~~t~g~D~~~tl~i~D~S~~~~~~~~~~l~v~iF~~~~~~LP~v~~~GDii 80 (146)
T PF02765_consen 1 YTPLSTAKEKFGKFVNVIGVVVDFSPPNPKKTRGTDYMCTLTITDPSLNDSNQKLSGLTVNIFRPHKESLPNVKSVGDII 80 (146)
T ss_dssp BCCGGGSCTTSSEEEEEEEEEEEEEEECTEEESSSCEEEEEEEEBTTCSCSSCCCCEEEEEEEESSHHHSCTTCSTTHEE
T ss_pred CccchhhhhcCCCEEEEEEEEEEccCCcceEcCCCcEEEEEEEECCCCCccccccCCEEEEEECCCHHHCCCCCCCCCEE
Confidence 789998888899999999999999999 999999999999999999985 7999999999999999998779999
Q ss_pred EEeeEEEEEEcCeeEEEeccC-ccEEEEE-eCCCCCCCCccccCCCCCCCCHHHHHHHHHHHHhhh
Q 012401 83 LLKNVMIKKHQAELSAVFYKD-SSSFALF-DGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCV 146 (464)
Q Consensus 83 ~l~rvkv~~~~g~~~~~~~~~-~ss~~lf-~~~~~~~~~Py~~s~~~~~~~~~e~~~v~~Lr~W~~ 146 (464)
+|||+||+.|+|+++++++.. .++|+|| ++..+.++.||+.++++++++++|+++++.||+|++
T Consensus 81 ~l~r~kv~~~~~~~~~~~~~~~~ss~~vf~~~~~~~~~~p~~~s~~~~~~~~~e~~~~~~Lr~w~~ 146 (146)
T PF02765_consen 81 RLRRVKVQSYNGKPQGLSNSTSNSSWAVFSSGGSGAPFEPYQKSSNPFEFSDEEKKYVESLRKWAQ 146 (146)
T ss_dssp EEEEEEEEEETTEEEEEEECECTEEEEEECTSSTTTCCCSSCESTSSTT-HHHHHHHHHHHHHHH-
T ss_pred EEEEEEEEEECCEEEEEecCCCcEEEEEEecCCCCCCccccccCCCccCCCHHHHHHHHHHHHhhC
Confidence 999999999999999998754 6899999 888889999999888889999999999999999974
No 4
>cd04498 hPOT1_OB2 hPOT1_OB2: A subfamily of OB folds similar to the second OB fold (OB2) of human protection of telomeres 1 protein (hPOT1). POT1 proteins bind to the single-stranded (ss) 3-prime ends of the telomere. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB2) which cooperate to bind telomeric ssDNA. OB1 makes more extensive contact with the ssDNA than OB2. OB2 protects the 3' end of the ssDNA. hPOT1 is implicated in telomere length regulation.
Probab=99.90 E-value=1.9e-23 Score=179.60 Aligned_cols=101 Identities=24% Similarity=0.340 Sum_probs=81.1
Q ss_pred eEeeEEEEEEeeeeCCCCeEEEEEEcCCCCCCCCCCCCCCcc-cCCCCCCcccCCCCCccccccCC-Ccc-eEEEEEecc
Q 012401 169 YFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDE-EHNPLPLHIESSPLDLETLRNFF-PVG-TVLRVSTDR 245 (464)
Q Consensus 169 f~Dlv~qVv~v~~~~~~~~~~L~VwDgT~~~~~~~~~~~~~~-~~~~~p~~~~~~~l~~~~~~~~p-~~G-~vl~V~~~~ 245 (464)
||||+||||+++ +.++++++|||||||+||+-.+.+..++. ..+++ +..++.|+ | | |+|||+||+
T Consensus 1 ~~DLvcqVv~v~-~~d~~~~~L~VwDgT~~p~~~~~~~~~~~~~~e~d----------~~~k~~~~gp-g~~ti~It~yD 68 (123)
T cd04498 1 YFDLLCQLLSVV-ETDSSSTLLKVWDGTKFPPPLRKVKVEDDVVLEGD----------RSLKHREEGG-KQLTIDILVYD 68 (123)
T ss_pred CccEEEEEEEEE-EecCCeEEEEEecCCCCChhHhheeccccCccccc----------hhhhhhccCC-CeEEEEEEEEc
Confidence 799999999999 76888999999999999765545544332 11211 33467899 8 9 999999999
Q ss_pred cchhhhccCCCCCcEEEEeCcEEEEe--------CcEEEEEE-ecC
Q 012401 246 SYENFGRYFTATGKWVRIRNMSCQVS--------SGMWHGLL-QSS 282 (464)
Q Consensus 246 ~~~~~~~~~~k~G~wV~l~Nv~~k~~--------~g~leG~l-~~~ 282 (464)
+|++++++ +|+||||+|+|||+|.. +-.|||.+ +.-
T Consensus 69 ~H~~~ar~-lK~GdfV~L~NVhiK~~~~~~~~~~~~~Le~~l~~gg 113 (123)
T cd04498 69 NHVELAKS-LKPGDFVRIYNVHAKSYSSKNEHDENDHLHFHLVHGG 113 (123)
T ss_pred chHHHHhh-CCCCCEEEEEEEEEEeccCCcccCCcceEEEEEccCc
Confidence 99999888 99999999999999993 23788888 543
No 5
>PRK12366 replication factor A; Reviewed
Probab=99.43 E-value=1.2e-10 Score=127.55 Aligned_cols=299 Identities=16% Similarity=0.185 Sum_probs=182.9
Q ss_pred CCcceeehhhhhhc-cCCEEEEEEEEEEcCCccc---cCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCE
Q 012401 6 NQGGIVRIKELAMH-VKHKVNLLGVVLEFSIPRK---SQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDL 81 (464)
Q Consensus 6 ~~y~y~~i~d~~~~-~~~~vnviGVVvd~~~P~~---trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDI 81 (464)
..+.+++|+++... .|..+++-|.|+...+++. .+|+--..++.|.|.+- .+.+.+|.+..+.+..+ ..||+
T Consensus 275 ~~~~~~pI~~L~~~~~g~~~~I~grV~~~~~~R~f~~~~g~gkv~s~~l~D~tG---~IR~t~w~~~~d~~~~l-~~G~v 350 (637)
T PRK12366 275 KELEIVNIEELTEFEDGEEVDVKGRIIAISDKREVERDDRTAEVQDIELADGTG---RVRVSFWGEKAKILENL-KEGDA 350 (637)
T ss_pred cccCceeHHHCCcccCCCEEEEEEEEEecCCceEEEcCCCcEEEEEEEEEcCCC---eEEEEEeCchhhhhccc-CCCCE
Confidence 45678999999754 5678999999999988754 36788999999999872 39999999877778777 69999
Q ss_pred EEEeeEEEEEEcC-----eeEEEeccCccEEEEEeCCCCCCCCccccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCcc
Q 012401 82 ILLKNVMIKKHQA-----ELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSND 156 (464)
Q Consensus 82 I~l~rvkv~~~~g-----~~~~~~~~~~ss~~lf~~~~~~~~~Py~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~ 156 (464)
+.+.+++++.|+. ++.+.++.. |.... .. ... .| ...+ .
T Consensus 351 y~is~~~vk~y~~~~~~~~~El~~~~~-s~I~~-d~--~~~-~p----~~~~---------------------------~ 394 (637)
T PRK12366 351 VKIENCKVRTYYDNEGEKRVDLNAGYS-SEIIK-DE--SIS-FE----EIEE---------------------------K 394 (637)
T ss_pred EEEecCEEeeccccCCCcCEEEEcCCc-eEEEe-cc--CCc-cc----ceee---------------------------c
Confidence 9999999998863 344444433 33432 11 101 11 0001 2
Q ss_pred ccccccccc----CCceEeeEEEEEEeeeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCCccccccC
Q 012401 157 YLLSLKDIS----EHRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNF 232 (464)
Q Consensus 157 f~~~Lkdi~----~~~f~Dlv~qVv~v~~~~~~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~ 232 (464)
| ..|+||. .+..+|+++.|+.+. +. ..++ . -||+...--. ..+.| +
T Consensus 395 ~-~~i~dI~~~~~~~~~VdVig~V~~v~-~~--~~i~-~-k~G~~~~~r~--i~l~D-----------------~----- 444 (637)
T PRK12366 395 I-YKIKDILNLEEDDNDITVIARVVEDY-PV--NEFE-R-SDGSKGKVRN--IELAD-----------------G----- 444 (637)
T ss_pred c-ccHHHhhcccCCCcEEEEEEEEEEcc-Cc--eEEE-e-cCCCEeEEEE--EEEEe-----------------C-----
Confidence 3 4455553 578999999999887 41 1111 1 2333221100 00000 0
Q ss_pred CCcceEEEEEecccchhhhccCCCCCcEEEEeCcEEEEeCcEEEEEEecCcceEEcCCCChhHHHHHHHHHHHhCCCCCC
Q 012401 233 FPVGTVLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDNDNVVWDYMRFRERISGGHGHM 312 (464)
Q Consensus 233 p~~G~vl~V~~~~~~~~~~~~~~k~G~wV~l~Nv~~k~~~g~leG~l~~~ski~~l~~~d~~v~~r~ry~~r~~~~~~~~ 312 (464)
=| .+++++|..++.+ .+.+|+.|.+.|..++..+|.++..+...|.|.+.++. +++ +-.+
T Consensus 445 --TG-~I~vtlWg~~a~~---~~~~G~vi~i~~~~V~~~~g~~~Ls~~~~s~i~~~p~~-~el-~~~~------------ 504 (637)
T PRK12366 445 --TG-SIRLTLWDDDAEI---EIKEGDAIKILHPYVKENGDYLDLSIGRYGRIEINPEG-EII-KSNR------------ 504 (637)
T ss_pred --CC-EEEEEEecccccc---CCCCCCEEEEEeeEEEeCCCeeEEEecCcceEEECCCC-ccc-cccc------------
Confidence 15 6799999988863 57899999999999999889888888888888765432 221 1000
Q ss_pred CCccCCCCCCCcccccCCCccc---cHHHHhhCCC-CCceeEEEEEEEeecCCCccccccC-CCCeEEEEEEEEeCCCce
Q 012401 313 PIWTDPSSQFLTEVDWVNVASV---TLMKIATQLQ-GNVRCCCIVRVVSIHPFQAEHYSSP-NGSSEYTMKLTLEDPTAR 387 (464)
Q Consensus 313 ~~~~~~~~~~~t~~~~~~~p~t---tL~dIL~~p~-v~~kfr~~VRVV~~~P~~~edf~~~-~~~w~~rf~L~lED~t~r 387 (464)
..+.++..... ++ +|..|-.... .+++=.|.=+|+.---.-...-|.. ...|.|++.+.|-|.|+.
T Consensus 505 --------~~I~~i~~~~~-~~v~g~i~~i~~~~~~y~aCp~CnkKv~~~~g~~~C~~c~~~~p~~~~~l~~~i~D~TG~ 575 (637)
T PRK12366 505 --------KFIADLEEDDT-VEIRGTVVDIRKQKIILYLCPNCRKRVEEVDGEYICEFCGEVEPNELLMLNFTLDDGTGT 575 (637)
T ss_pred --------cCHHHcccCCe-EEEEEEEEEEeCCCEEEecccccCeEeEcCCCcEECCCCCCCCCcEEEEEEEEEEcCCCC
Confidence 00111000000 00 1111111100 0111123334442100000111111 347889999999999999
Q ss_pred EEEEEeccccccccCC
Q 012401 388 IHALLCGKEWVKFFGG 403 (464)
Q Consensus 388 i~~~v~~~da~~f~~~ 403 (464)
+++.++++.|+.+||.
T Consensus 576 ~~~t~f~e~ae~l~G~ 591 (637)
T PRK12366 576 INCRFYGKNVEKLLGM 591 (637)
T ss_pred EEEEEEhHHhHHHhCC
Confidence 9999999999999963
No 6
>TIGR00617 rpa1 replication factor-a protein 1 (rpa1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.21 E-value=6.4e-09 Score=113.53 Aligned_cols=318 Identities=14% Similarity=0.152 Sum_probs=193.1
Q ss_pred ceeehhhhhhccCCEEEEEEEEEEcCCccc---cCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCC-CCCCCCCCEEEE
Q 012401 9 GIVRIKELAMHVKHKVNLLGVVLEFSIPRK---SQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQL-PRVLSPRDLILL 84 (464)
Q Consensus 9 ~y~~i~d~~~~~~~~vnviGVVvd~~~P~~---trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~L-P~v~~~GDII~l 84 (464)
.+++|+++.... ....+-|-|+.....+. .+|.....++.|.|++ ..|.+.+|.+..+.+ |.+ +.|+|+.+
T Consensus 179 ~~~pI~~L~py~-~~wtIkaRV~~Ks~ir~~~~~~gegkvfsv~L~Deg---g~Irat~f~~~~dkf~~~l-~eG~VY~I 253 (608)
T TIGR00617 179 RVMPIASLSPYQ-NKWTIKARVTNKSEIRTWSNARGEGKLFNVELLDES---GEIRATAFNEQADKFYDII-QEGKVYYI 253 (608)
T ss_pred ceEEHHHCCCCC-CceEEEEEEEeccccceecCCCCCceeeEEEEecCC---CeEEEEECchHHHHHhhhc-ccCCEEEE
Confidence 589999998543 35889999998776654 2455678889999943 349999999755444 666 79999999
Q ss_pred eeEEEEEEcCeeEEEeccC---ccEEEEEeCCCCCCCCccccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCccccccc
Q 012401 85 KNVMIKKHQAELSAVFYKD---SSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSL 161 (464)
Q Consensus 85 ~rvkv~~~~g~~~~~~~~~---~ss~~lf~~~~~~~~~Py~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~f~~~L 161 (464)
.+.+|+..+++...+.+.. +..+.......+..-.| ...| .| ..|
T Consensus 254 s~~~Vk~an~~y~~~~~~yei~f~~~T~I~~~~d~~~iP----~~~~---------------------------~f-~~i 301 (608)
T TIGR00617 254 SKGSLKPANKQFTNLGNDYEMTLDRDTVIEECEDETAIP----KIQF---------------------------NF-VKI 301 (608)
T ss_pred CceEEEEccccccCCCCCEEEEECCCeEEEECCCcccCC----cccc---------------------------cc-eEH
Confidence 9999998877654433310 11111222111111122 0012 23 344
Q ss_pred ccc---cCCceEeeEEEEEEeeeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCCccccccCCCcceE
Q 012401 162 KDI---SEHRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTV 238 (464)
Q Consensus 162 kdi---~~~~f~Dlv~qVv~v~~~~~~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~p~~G~v 238 (464)
.|| ..+.++|+++.|..+. +. ..++- =.||++..--. ..+.| --|..
T Consensus 302 ~dI~~~~~~~~VDVIGvV~~v~-~~--~~i~~-k~~g~~~~kR~--i~L~D------------------------~sg~s 351 (608)
T TIGR00617 302 DDIGGYEGNSLVDVIGIVQSVS-PT--QTITS-RKNNKEFPKRD--ITLVD------------------------DSGKS 351 (608)
T ss_pred HHhhhhcCCCCccEEEEEeEec-Cc--eEEEE-cCCCCeeeeEE--EEEEe------------------------CCCCE
Confidence 444 4567999999999887 31 11110 11222111100 00000 01567
Q ss_pred EEEEecccchhhhccCCCCCcEEEEeCcEEEEeCcEEEEEEecCcceEEcCCCChhHHHHHH-HHHHHhCCCCCCCCccC
Q 012401 239 LRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDNDNVVWDYMR-FRERISGGHGHMPIWTD 317 (464)
Q Consensus 239 l~V~~~~~~~~~~~~~~k~G~wV~l~Nv~~k~~~g~leG~l~~~ski~~l~~~d~~v~~r~r-y~~r~~~~~~~~~~~~~ 317 (464)
++||+|..+|.. -....|+.|.|+.++++-.+|. .......|.| +++++-+++.+.+. |+..-.. . +..++
T Consensus 352 I~vTLWG~~A~~--~~~~~~~Vva~kg~~V~~f~g~-sLs~~~~S~i-~iNPdipEa~~L~~w~~~~g~~-~---~~~s~ 423 (608)
T TIGR00617 352 VRVTLWGDDATK--FDVSVQPVIAIKGVRVSDFGGK-SLSTGGSSTI-IVNPDIPEAEKLKGWYDNEGKG-T---MASSI 423 (608)
T ss_pred EEEEEEhhhhhh--cCCCCCCEEEEEeEEEEecCCc-eEeccCCceE-EECCCcHHHHHHHHHHHhcCCC-c---cceee
Confidence 899999999864 2377899999999999987664 3444456777 45666677766666 6543211 0 10000
Q ss_pred CCCCCCcccccCCCccccHHHHhhCC----CCCceeEEEEEEEeecCCCccccccC------------------------
Q 012401 318 PSSQFLTEVDWVNVASVTLMKIATQL----QGNVRCCCIVRVVSIHPFQAEHYSSP------------------------ 369 (464)
Q Consensus 318 ~~~~~~t~~~~~~~p~ttL~dIL~~p----~v~~kfr~~VRVV~~~P~~~edf~~~------------------------ 369 (464)
+....+..........||.||.... +-+..|.|.+.|+.+-+.+.-=.++|
T Consensus 424 -~~~~~~~~~~~~~~~ktI~ei~~~~lg~~~k~~~f~v~atI~~Ik~d~~~Y~ACp~~~CnKKV~~~~~g~~~CekC~~~ 502 (608)
T TIGR00617 424 -SDMMSGRVGGSNAERKTIAEIQAENLGKSDKPDYFSVKATISYLKPDNALYRACPSEDCNKKVVDQGDGTYRCEKCNKN 502 (608)
T ss_pred -hhccccccCCcccccccHHHHhhhccCCCCCCcEEEEEEEEEEEecCCeEeccCChhhCCCccccCCCCCEECCCCCCC
Confidence 0000000111234567899998631 23455888888887765432111111
Q ss_pred --CCCeEEEEEEEEeCCCceEEEEEeccccccccC
Q 012401 370 --NGSSEYTMKLTLEDPTARIHALLCGKEWVKFFG 402 (464)
Q Consensus 370 --~~~w~~rf~L~lED~t~ri~~~v~~~da~~f~~ 402 (464)
.-.|.|.+.+.+.|.|+.+|+.++++.|+.+||
T Consensus 503 ~~~~~~RYil~~~i~D~Tg~~~~t~F~~~ae~llG 537 (608)
T TIGR00617 503 FAEFKYRYILQISISDETGQLWVTAFNDQAEQILG 537 (608)
T ss_pred CCCccEEEEEEEEEEeCCCCEEEEEEhHHHHHHcC
Confidence 125788899999999999999999999999996
No 7
>PRK12366 replication factor A; Reviewed
Probab=99.16 E-value=2.1e-08 Score=110.10 Aligned_cols=279 Identities=14% Similarity=0.160 Sum_probs=186.4
Q ss_pred cceeehhhhhhccCC-EEEEEEEEEEcCCcccc---CC-CceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEE
Q 012401 8 GGIVRIKELAMHVKH-KVNLLGVVLEFSIPRKS---QG-TDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLI 82 (464)
Q Consensus 8 y~y~~i~d~~~~~~~-~vnviGVVvd~~~P~~t---rG-~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII 82 (464)
-.+++|+++. +++ .+++.|-|+..+.|+.- +| .-..+++.|.|.+= .+++.+|.+..+.+|.+ .+|||+
T Consensus 61 ~~~~~I~dl~--p~~~~v~i~arV~~~~~~r~~~~~~G~eGkv~~~~v~DetG---~Ir~t~W~~~~~~~~~l-e~G~v~ 134 (637)
T PRK12366 61 EEDFKISDIE--EGQINVEITGRIIEISNIKTFTRKDGSTGKLANITIADNTG---TIRLTLWNDNAKLLKGL-KEGDVI 134 (637)
T ss_pred cceeEHHHCc--CCCcceEEEEEEEEccCCeEEECCCCCccEEEEEEEEcCCC---EEEEEEEchhhhhhccC-CCCCEE
Confidence 3578999997 554 59999999999988742 35 46789999999764 39999999877778888 699999
Q ss_pred EEeeEEEEEEcCeeEEEeccCccEEEEEeCCCCCCCCccccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCcccccccc
Q 012401 83 LLKNVMIKKHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSLK 162 (464)
Q Consensus 83 ~l~rvkv~~~~g~~~~~~~~~~ss~~lf~~~~~~~~~Py~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~f~~~Lk 162 (464)
.+.++.++.|+|++.+..+.. ++........ ..-.| + .++ .| .|.
T Consensus 135 ~i~~~~v~~~~~~~el~~~~~-t~I~~~~~~d-~~~i~-~---------~~~---------------------~~--~I~ 179 (637)
T PRK12366 135 KIENARSRKWNNDVELNSGSE-TRIDKLEKYD-ESRYP-I---------IKE---------------------NY--DIP 179 (637)
T ss_pred EEeccEecccCCceEEEcCCc-ceEEEccccc-cccCC-c---------ccc---------------------cc--ccc
Confidence 999999999999998766644 5454332100 01111 0 000 12 578
Q ss_pred cccCCceEeeEEEEEEeeeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCCccccccCCCcceEEEEE
Q 012401 163 DISEHRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRVS 242 (464)
Q Consensus 163 di~~~~f~Dlv~qVv~v~~~~~~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~p~~G~vl~V~ 242 (464)
||.++.++|+++.|+++. +. ..++ --||++-.... ..+.| + =| .+++|
T Consensus 180 el~~g~~v~v~G~V~~~~-~~--~~f~--rkdg~~~~~r~--~~l~D-----------------~-------TG-~irvT 227 (637)
T PRK12366 180 ELEPNLSATIEGEVTKAY-PI--KEFT--RKDGSEGKLKS--FILKD-----------------D-------TG-SIRVT 227 (637)
T ss_pred ccCCCCeEEEEEEEEEcc-Cc--EEEE--EcCCCeeEEEE--EEEEc-----------------C-------CC-cEEEE
Confidence 888999999999999987 41 1211 12544322211 10100 0 15 68999
Q ss_pred ecccchhhhccCCCCCcEEEEeCcEEEEeCcEEEEEEecCcceEEcCCCChhHHHHHHHHHHHhCCCCCCCCccCCCCCC
Q 012401 243 TDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDNDNVVWDYMRFRERISGGHGHMPIWTDPSSQF 322 (464)
Q Consensus 243 ~~~~~~~~~~~~~k~G~wV~l~Nv~~k~~~g~leG~l~~~ski~~l~~~d~~v~~r~ry~~r~~~~~~~~~~~~~~~~~~ 322 (464)
+|..++.. .+.+|+.|++.+....-+.|.+|-.....+.|.....
T Consensus 228 lW~~~a~~---~~~~g~vv~i~g~~~~~~~~~~el~~~~~~~i~~~~~-------------------------------- 272 (637)
T PRK12366 228 LWNDLTDI---EVNKGDIVRVKGYVKQGYRTGLEISANNIEILEKLEK-------------------------------- 272 (637)
T ss_pred EEChhhcc---cCCCCCEEEEEeEEecCcCCceEEEeCCceeeccccc--------------------------------
Confidence 99988853 5899999999883333344666665533222211100
Q ss_pred CcccccCCCccccHHHHhhCCCCCceeEEEEEEEeecCCCccccccCCCCeEEEEEEEEeCCCceEEEEEeccccccccC
Q 012401 323 LTEVDWVNVASVTLMKIATQLQGNVRCCCIVRVVSIHPFQAEHYSSPNGSSEYTMKLTLEDPTARIHALLCGKEWVKFFG 402 (464)
Q Consensus 323 ~t~~~~~~~p~ttL~dIL~~p~v~~kfr~~VRVV~~~P~~~edf~~~~~~w~~rf~L~lED~t~ri~~~v~~~da~~f~~ 402 (464)
.. ...++.+|+++-.+- .+.+....+||++..|. +.|....|. --.|.+.|-|.|++|.+.++++.|.+|.+
T Consensus 273 ~~----~~~~~~pI~~L~~~~-~g~~~~I~grV~~~~~~--R~f~~~~g~-gkv~s~~l~D~tG~IR~t~w~~~~d~~~~ 344 (637)
T PRK12366 273 EE----KELEIVNIEELTEFE-DGEEVDVKGRIIAISDK--REVERDDRT-AEVQDIELADGTGRVRVSFWGEKAKILEN 344 (637)
T ss_pred cc----cccCceeHHHCCccc-CCCEEEEEEEEEecCCc--eEEEcCCCc-EEEEEEEEEcCCCeEEEEEeCchhhhhcc
Confidence 00 011334566664321 35578888999997654 557666665 57889999999999999999999988876
No 8
>PRK07218 replication factor A; Provisional
Probab=99.07 E-value=3.9e-07 Score=94.92 Aligned_cols=282 Identities=19% Similarity=0.245 Sum_probs=173.4
Q ss_pred eeehhhhhhccCCEEEEEEEEEEcCCcc-ccCCC-ceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeE
Q 012401 10 IVRIKELAMHVKHKVNLLGVVLEFSIPR-KSQGT-DYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNV 87 (464)
Q Consensus 10 y~~i~d~~~~~~~~vnviGVVvd~~~P~-~trG~-D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rv 87 (464)
-+.|+|+... ...|+|.|-|++...+. +..|+ -...++.|-|++=. +++.++.+ ++ + ..||+|.+.++
T Consensus 58 ~~kI~Di~~~-~~~V~v~~kVl~i~~rt~r~dg~~g~v~~~~igDeTG~---Ir~tlW~~----~~-l-~~Gdvv~I~na 127 (423)
T PRK07218 58 SKDIKELSTD-DKNVTVTGRVLTIGERSIRYQGDDHVIYEGILADETGT---ISYTAWKD----FG-L-SPGDTVTIGNA 127 (423)
T ss_pred CccHhhCCCC-CceeEEEEEEEEecceeEecCCCceEEEEEEEECCCCe---EEEEEECC----CC-C-CCCCEEEEecc
Confidence 4568888633 45799999999996521 22343 67889999998653 89999984 23 6 79999999999
Q ss_pred EEEEEcCeeEEEeccCccEEEEEeCCCCCCCCccccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCcccccccccccCC
Q 012401 88 MIKKHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSLKDISEH 167 (464)
Q Consensus 88 kv~~~~g~~~~~~~~~~ss~~lf~~~~~~~~~Py~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~f~~~Lkdi~~~ 167 (464)
.++.|+|++.+..+.. +....-+.. ..| . +.. . .. ..|.|++++
T Consensus 128 ~vre~~g~~el~ig~~-t~I~~~de~----~~~-~-----~~~----------------------~--~~-~kI~DL~~g 171 (423)
T PRK07218 128 GVREWDGRPELNIGES-TTVSLLDDS----SLP-P-----YSI----------------------G--GD-KKLIDLGPG 171 (423)
T ss_pred EeeccCCceEEeccCc-ceEEEcCcc----ccc-C-----ccc----------------------c--Cc-cchhhccCC
Confidence 9999999999887754 555533221 111 0 100 0 11 468889865
Q ss_pred -ceEeeEEEEEEeeeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCCccccccCCCcceEEEEEeccc
Q 012401 168 -RYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRVSTDRS 246 (464)
Q Consensus 168 -~f~Dlv~qVv~v~~~~~~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~p~~G~vl~V~~~~~ 246 (464)
..+++.++|+.++ . + .+-.-||+.. .. ...+.|+ . | ++++++|++
T Consensus 172 ~~~V~v~g~Vl~~~-~----r-~f~~~dg~~~--v~-~giigDe-----------------T-------G-~Ir~tlW~~ 217 (423)
T PRK07218 172 DRGVNVEARVLELE-H----R-EIDGRDGETT--IL-SGVLADE-----------------T-------G-RLPFTDWDP 217 (423)
T ss_pred CCceEEEEEEEEec-c----e-eEEcCCCCeE--EE-EEEEECC-----------------C-------c-eEEEEEecc
Confidence 4589999999875 3 2 2334454311 11 1111110 0 2 569999997
Q ss_pred chhhhccCCCCCcEEEEeCcEEEEeCcEEEEEEecCcceEEcCCCChhHH---HHHHHHHHHhCCCCCCCCccCCCCCCC
Q 012401 247 YENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDNDNVVW---DYMRFRERISGGHGHMPIWTDPSSQFL 323 (464)
Q Consensus 247 ~~~~~~~~~k~G~wV~l~Nv~~k~~~g~leG~l~~~ski~~l~~~d~~v~---~r~ry~~r~~~~~~~~~~~~~~~~~~~ 323 (464)
++ .+.+|++|++.|...+.++|.++-.+...+.|..++.+-. +. .++.-.+.+.. -+ .+ ...+
T Consensus 218 ~~-----~l~~Gd~v~I~na~v~e~~G~~elnv~~~t~I~~~d~~i~-v~~~~~~~~I~e~~~~-~g-----~~--~Vev 283 (423)
T PRK07218 218 LP-----EIEIGASIRIEDAYVREFRGVPSVNVSEFTTVEALDREVS-VSKDPPRLKIREAVER-GG-----IF--DVEL 283 (423)
T ss_pred cc-----cCCCCCEEEEeeeEEeccCCeEEEEECCceEEEECCCCcc-ccCCccccchhhhhcc-CC-----cc--eEEE
Confidence 65 3799999999999999999999999999999988765311 10 00000000000 00 00 0000
Q ss_pred cc--cccCCCccccHHHHh-hCCCCCceeEEEEEEEeecCCCccccccCC----CCeEEEEEEEEeCCCceEEEEEeccc
Q 012401 324 TE--VDWVNVASVTLMKIA-TQLQGNVRCCCIVRVVSIHPFQAEHYSSPN----GSSEYTMKLTLEDPTARIHALLCGKE 396 (464)
Q Consensus 324 t~--~~~~~~p~ttL~dIL-~~p~v~~kfr~~VRVV~~~P~~~edf~~~~----~~w~~rf~L~lED~t~ri~~~v~~~d 396 (464)
+. ++... =+=++ -+|. +=||++- -.|..+ +.+-=|..+.|.|.|+.+.+++..+.
T Consensus 284 ~G~Iv~i~~-----gsgli~rCP~-------C~r~v~~------~~C~~hG~ve~~~dlrik~vLDDGtg~~~~~~~~e~ 345 (423)
T PRK07218 284 VGNIISVRD-----GSGLIERCPE-------CGRVIQK------GQCRSHGAVEGEDDLRIKAILDDGTGSVTVILDREL 345 (423)
T ss_pred EEEEEEecc-----CCcceecCcC-------ccccccC------CcCCCCCCcCCeeeeEEEEEEECCCCeEEEEEChhh
Confidence 00 01000 00011 1232 1133321 233333 45567899999999999999999999
Q ss_pred cccccCC
Q 012401 397 WVKFFGG 403 (464)
Q Consensus 397 a~~f~~~ 403 (464)
++.+.|.
T Consensus 346 ~e~l~G~ 352 (423)
T PRK07218 346 TEIVYGG 352 (423)
T ss_pred hHhHhCC
Confidence 9999985
No 9
>PRK14699 replication factor A; Provisional
Probab=98.99 E-value=5e-07 Score=95.86 Aligned_cols=272 Identities=19% Similarity=0.208 Sum_probs=181.9
Q ss_pred eehhhhhhccCCEEEEEEEEEEcCCccc---cCCCc-eEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEee
Q 012401 11 VRIKELAMHVKHKVNLLGVVLEFSIPRK---SQGTD-YVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKN 86 (464)
Q Consensus 11 ~~i~d~~~~~~~~vnviGVVvd~~~P~~---trG~D-~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~r 86 (464)
..|+|+... ...||+.|-|+...+|+. ..|+. -..++.|-|+|= .+++.++.+..+.+|.+ ..||+|++.+
T Consensus 167 ~~I~dL~~~-~~~V~i~gkVl~~~~~R~f~~~dG~~g~v~~~~igDeTG---~ir~tlW~~~a~~~~~l-~~Gd~v~I~~ 241 (484)
T PRK14699 167 QKIKDIKDG-MGDLNLTGKVLEISEIRTFQRKDGTSGKVGNLLLGDETG---TLRVTLWDDKTDFLNQI-EYGDTVELIN 241 (484)
T ss_pred cchhhcCCC-CCceEEEEEEEeccCceEEecCCCCceEEEEEEEEcCCc---eEEEEEECccccccccc-CCCCEEEEec
Confidence 467777532 235999999999998863 23543 677889999976 39999999877777888 6999999998
Q ss_pred EEEE--EEcCeeEEEeccCccEEEEEeCCCCCCCCccccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCcccccccccc
Q 012401 87 VMIK--KHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSLKDI 164 (464)
Q Consensus 87 vkv~--~~~g~~~~~~~~~~ss~~lf~~~~~~~~~Py~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~f~~~Lkdi 164 (464)
+.++ .|+|.+.+..+.. +... ......+ +.. .+ ..|.+|
T Consensus 242 a~vr~~~~~~~~el~~~~~-s~i~--~~~~~~e----------~~~-------------------------~~-~~I~~L 282 (484)
T PRK14699 242 AYARENAFTQKVELQVGNR-SIIR--KSEKKVE----------YEE-------------------------EF-TPIEDI 282 (484)
T ss_pred ceEeecccCCceEEEecCc-eEee--ccccccc----------ccc-------------------------cc-cCHHHc
Confidence 8765 4778888877643 3222 1100000 000 13 457777
Q ss_pred cC-CceEeeEEEEEEeeeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCCccccccCCCcceEEEEEe
Q 012401 165 SE-HRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRVST 243 (464)
Q Consensus 165 ~~-~~f~Dlv~qVv~v~~~~~~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~p~~G~vl~V~~ 243 (464)
++ +..+++.++|+++. + -..|. --||++-.-+ +..+.|+ =| .+|+|+
T Consensus 283 ~~~~~~v~I~grV~~~~-~--~r~~~--~~~Gseg~v~--~~~l~De------------------------TG-~Ir~T~ 330 (484)
T PRK14699 283 KADMNNINISGRVLDIS-E--VRTFE--KKDGSPGRVG--NLLLGDS------------------------TG-KIRLTL 330 (484)
T ss_pred CCCCceeEEEEEEEEcC-C--CeEEE--cCCCCeeEEE--EEEEECC------------------------CC-eEEEEE
Confidence 75 48899999999876 3 11211 2233211111 1111110 15 479999
Q ss_pred cccchhhhccCCCCCcEEEEeCcEEEEe--CcEEEEEEecCcceEEcCCCChhHHHHHHHHHHHhCCCCCCCCccCCCCC
Q 012401 244 DRSYENFGRYFTATGKWVRIRNMSCQVS--SGMWHGLLQSSSKIRLFSDNDNVVWDYMRFRERISGGHGHMPIWTDPSSQ 321 (464)
Q Consensus 244 ~~~~~~~~~~~~k~G~wV~l~Nv~~k~~--~g~leG~l~~~ski~~l~~~d~~v~~r~ry~~r~~~~~~~~~~~~~~~~~ 321 (464)
|++.+.+ ...+++|+.+++.|...+.+ +|.+|..+...+.|...+++.
T Consensus 331 W~~~a~~-~~~i~~Gd~v~i~~~y~~~~~~~~~~eL~~~~~t~I~~~~~~~----------------------------- 380 (484)
T PRK14699 331 WDEKTNF-LDEIDFDETVEVLNAYSRENTFSQQVELNLGARGIIQKSEKKV----------------------------- 380 (484)
T ss_pred eCccccc-ccccCCCceEEEEeEEEEeccCCccEEEEecCceeEeecCCcc-----------------------------
Confidence 9999865 67799999999999998875 367888888777664422111
Q ss_pred CCcccccCCCccccHHHHhhCCCCCceeEEEEEEEeecCCCccccccCCCCeEEEEEEEEeCCCceEEEEEeccccccc
Q 012401 322 FLTEVDWVNVASVTLMKIATQLQGNVRCCCIVRVVSIHPFQAEHYSSPNGSSEYTMKLTLEDPTARIHALLCGKEWVKF 400 (464)
Q Consensus 322 ~~t~~~~~~~p~ttL~dIL~~p~v~~kfr~~VRVV~~~P~~~edf~~~~~~w~~rf~L~lED~t~ri~~~v~~~da~~f 400 (464)
++ ..+++.|.||- -...+-..-+|+++.|.+ .|.+.+|.=-++--|+|.|.|+++.+-++|+.|+.|
T Consensus 381 -----e~-~~~~~~I~die----~~~~vdV~G~V~~v~~~~--~~~~~~g~~~~vr~i~l~D~TG~Ir~tlWg~~A~~~ 447 (484)
T PRK14699 381 -----EY-REKFTDIADII----PGESYSVQGKVSEIGELR--EFEREDGTENVVANLQLKDETGSIRLTLWGEQAYVI 447 (484)
T ss_pred -----ee-eeccccHHHcc----CCCeeEEEEEEEEcCCcc--eEEecCCCEEEEEEEEEEcCCCeEEEEEcchhhhhc
Confidence 00 12466677773 233567778888888865 666655644477799999999999999999999875
No 10
>PRK07211 replication factor A; Reviewed
Probab=98.95 E-value=5.6e-08 Score=102.19 Aligned_cols=204 Identities=16% Similarity=0.202 Sum_probs=145.4
Q ss_pred cceeehhhhhhccCCEEEEEEEEEEcCCccc---cCC-CceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEE
Q 012401 8 GGIVRIKELAMHVKHKVNLLGVVLEFSIPRK---SQG-TDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLIL 83 (464)
Q Consensus 8 y~y~~i~d~~~~~~~~vnviGVVvd~~~P~~---trG-~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~ 83 (464)
..+.+|+++.. ....++|+|+|++..+++. .+| .-.+.++.|.|+|=. +++.+|.+..+.++.+ ..||||.
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-GLSDVTLVGVVLDTDSVRTFDRDDGSEGRVSNLTVGDETGR---VRVTLWDDRADLAEEL-DAGESVE 233 (485)
T ss_pred cCCccHHHcCC-CCCceEEEEEEEEcCCCeEEECCCCCeeEEEEEEEEcCCCe---EEEEEechhhhhhccC-CCCCEEE
Confidence 36788999973 2456999999999998763 235 456789999998762 9999999887888878 7999999
Q ss_pred EeeEEEEEEcCeeEEEeccCccEEEEEeCCCCCCCCccccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCccccccccc
Q 012401 84 LKNVMIKKHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSLKD 163 (464)
Q Consensus 84 l~rvkv~~~~g~~~~~~~~~~ss~~lf~~~~~~~~~Py~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~f~~~Lkd 163 (464)
+.+++++.++|.+.+..+.. +...--.. .....| .+ ..|.+
T Consensus 234 I~~a~Vre~~g~~ELsl~~~-s~I~~~~d--ev~~vp-----------------------------------~~-~~I~d 274 (485)
T PRK07211 234 IVDGYVRERDGSLELHVGDR-GAVEEVDE--DVEYVP-----------------------------------DT-TPIES 274 (485)
T ss_pred EEeeEEEecCCcEEEEECCC-ceEEECCc--cccccc-----------------------------------cc-ccHhh
Confidence 99999999999988877643 43331111 001111 12 46788
Q ss_pred ccCCceEeeEEEEEEeeeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCCccccccCCCcceEEEEEe
Q 012401 164 ISEHRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRVST 243 (464)
Q Consensus 164 i~~~~f~Dlv~qVv~v~~~~~~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~p~~G~vl~V~~ 243 (464)
+.++..+|+++.|+.+. + ..++-=-||+...--.+. +.+ -=| .+||++
T Consensus 275 l~~g~~vdV~GvV~~v~-~----~rtf~r~dG~~~~vr~l~--l~D------------------------~TG-~IrvTL 322 (485)
T PRK07211 275 LEIDETVDIAGVVRSAD-P----KRTFDRDDGSEGQVRNVR--IQD------------------------DTG-DIRVAL 322 (485)
T ss_pred cCCCCceeEEEEEEEcc-C----cEEEEcCCCCEeEEEEEE--EEc------------------------CCC-cEEEEE
Confidence 88999999999999886 3 222222234422221100 000 015 679999
Q ss_pred cccchhhhccCCCCCcEEEEeCcEEEE-eCcEEEEEEecCcceEEcCC
Q 012401 244 DRSYENFGRYFTATGKWVRIRNMSCQV-SSGMWHGLLQSSSKIRLFSD 290 (464)
Q Consensus 244 ~~~~~~~~~~~~k~G~wV~l~Nv~~k~-~~g~leG~l~~~ski~~l~~ 290 (464)
|.+++.+ .+.+|+.|+|.|++++- +.|-+|..+...+.|.+|+.
T Consensus 323 Wg~~A~~---~i~~GdvV~Ikg~~V~dg~~ggleLS~g~~s~i~~~~~ 367 (485)
T PRK07211 323 WGEKADL---DIGPGDEVVAADVEIQDGWQDDLEASAGWQSTVVVLDD 367 (485)
T ss_pred eCccccC---CCCCCCEEEEEccEEEecCCCCEEEEecCCceEEEccc
Confidence 9999953 68999999999999999 44778888888889988875
No 11
>PRK15491 replication factor A; Provisional
Probab=98.92 E-value=1e-06 Score=90.82 Aligned_cols=271 Identities=15% Similarity=0.189 Sum_probs=177.7
Q ss_pred eeehhhhhhccCCEEEEEEEEEEcCCccc---cCC-CceEEEEEEEeCCCCCCCeEEEEecCCCCCC--CCCCCCCCEEE
Q 012401 10 IVRIKELAMHVKHKVNLLGVVLEFSIPRK---SQG-TDYVCVLKIVDDSQQSPELLVNIFTSSIDQL--PRVLSPRDLIL 83 (464)
Q Consensus 10 y~~i~d~~~~~~~~vnviGVVvd~~~P~~---trG-~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~L--P~v~~~GDII~ 83 (464)
-++|+|+... ...|++.|-|+....|+. .+| .-...++.|.|+|=. +++.+|.+..+.+ |.+ .+||++.
T Consensus 57 ~~kI~dL~~~-~~~v~i~arVl~~~~~R~f~r~dGs~g~v~~~~v~DeTG~---ir~tlW~~~a~~~~~~~l-e~G~v~~ 131 (374)
T PRK15491 57 TTKIADINES-SSNVNFTAKVVSIFEPKEFNRNDGTTGRVGNIIVADETGS---IRLTLWDDLADLIKTGDI-EVGKSLN 131 (374)
T ss_pred cccHHHCCCC-CCceEEEEEEeeccCCeeeecCCCCceEEEEEEEEcCCCe---EEEEEECchhhhhccCCc-CCCCEEE
Confidence 5579999732 256999999999988864 246 467889999997652 9999999766555 678 6999999
Q ss_pred EeeEEEEEEcCeeEEEeccCccEEEEEeCCCCCCCCccccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCccccccccc
Q 012401 84 LKNVMIKKHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSLKD 163 (464)
Q Consensus 84 l~rvkv~~~~g~~~~~~~~~~ss~~lf~~~~~~~~~Py~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~f~~~Lkd 163 (464)
++..--..|+| +.+..+.. +... ... ... + .. ..| ..|+|
T Consensus 132 I~~~~~~~y~g-~Ei~i~~~-~~i~---~~~-~~~-~-------~~-------------------------~~~-~~I~d 171 (374)
T PRK15491 132 ISGYAKEGYSG-IEVNIGRY-GGIS---ESD-ENV-K-------AS-------------------------INS-QKISD 171 (374)
T ss_pred EeeeeccCccc-EEEEeCCC-ceee---ecc-ccc-c-------cc-------------------------cCc-ccHHH
Confidence 99875556766 55555533 3221 000 000 0 00 024 56777
Q ss_pred ccCC-ceEeeEEEEEEeeeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCCccccccCCCcceEEEEE
Q 012401 164 ISEH-RYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRVS 242 (464)
Q Consensus 164 i~~~-~f~Dlv~qVv~v~~~~~~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~p~~G~vl~V~ 242 (464)
|..+ ..+|+.++|+.+. + ...+. --||+....+. ..+.+ + =|. ++++
T Consensus 172 l~~~~~~V~I~g~V~~~~-~--~r~~~--~~~G~~~~v~~--~~l~D-----------------e-------tG~-Ir~t 219 (374)
T PRK15491 172 IKDGDSDINIVGKVLDIS-D--VRTFQ--KKDGSQGRVRN--ITIGD-----------------E-------TGK-IRVT 219 (374)
T ss_pred cCCCCccEEEEEEEEEcc-C--ceEEE--ecCCCeEEEEE--EEEEC-----------------C-------CCe-EEEE
Confidence 7654 4699999999887 3 11221 12343221111 10000 0 154 7999
Q ss_pred ecccchhhhccCCCCCcEEEEeCcEEEE--eCcEEEEEEecCcceEEcCCCChhHHHHHHHHHHHhCCCCCCCCccCCCC
Q 012401 243 TDRSYENFGRYFTATGKWVRIRNMSCQV--SSGMWHGLLQSSSKIRLFSDNDNVVWDYMRFRERISGGHGHMPIWTDPSS 320 (464)
Q Consensus 243 ~~~~~~~~~~~~~k~G~wV~l~Nv~~k~--~~g~leG~l~~~ski~~l~~~d~~v~~r~ry~~r~~~~~~~~~~~~~~~~ 320 (464)
+|+.++.. ...+++|+-|++.|-.++. ..|.+|-.+..++.|...++ +.
T Consensus 220 ~W~~~a~~-~~~l~~Gd~V~i~~~~~r~~~~~g~~El~~~~~s~I~~~~~-~~--------------------------- 270 (374)
T PRK15491 220 LWDGKTDL-ADKLENGDSVEIINGYARTNNYSQEVEIQIGNHGSLRKTDR-NV--------------------------- 270 (374)
T ss_pred Eecchhcc-cccCCCCCEEEEEeceEEEeccCCCEEEEeCCCceEEECCc-cc---------------------------
Confidence 99999886 4779999999999988876 35788888888888865432 11
Q ss_pred CCCcccccCCCccccHHHHhhCCCCCceeEEEEEEEeecCCCccccccCCCCeEEEEEEEEeCCCceEEEEEecccccc
Q 012401 321 QFLTEVDWVNVASVTLMKIATQLQGNVRCCCIVRVVSIHPFQAEHYSSPNGSSEYTMKLTLEDPTARIHALLCGKEWVK 399 (464)
Q Consensus 321 ~~~t~~~~~~~p~ttL~dIL~~p~v~~kfr~~VRVV~~~P~~~edf~~~~~~w~~rf~L~lED~t~ri~~~v~~~da~~ 399 (464)
+.. .++++|.||-.. ..+-...+|....|. ..|.+.+|.=...=-|+|.|.|++|++-++|+.|+.
T Consensus 271 ----e~~---~~f~~I~dl~~~----~~~dv~G~V~~v~~~--~~~~~~~G~~~~~r~i~l~D~Tg~Ir~tlWg~~a~~ 336 (374)
T PRK15491 271 ----EYE---EDFTPIADIIPG----QPYSIKGAVSGLGDL--KEFTKSDGSENKVSNIYVSDDTGRIRIALWGEKAEL 336 (374)
T ss_pred ----ccC---CCccCHHHcCCC----CceeEEEEEEEcCCc--EEEEccCCCEeEEEeEEEEeCCCcEEEEEccccccc
Confidence 011 134557777532 235667777777664 455555564446668899999999999999999986
No 12
>PRK06386 replication factor A; Reviewed
Probab=98.88 E-value=7.5e-06 Score=83.43 Aligned_cols=275 Identities=16% Similarity=0.168 Sum_probs=165.4
Q ss_pred eehhhhhhccCCEEEEEEEEEEcCCc-ccc-CCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEE
Q 012401 11 VRIKELAMHVKHKVNLLGVVLEFSIP-RKS-QGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVM 88 (464)
Q Consensus 11 ~~i~d~~~~~~~~vnviGVVvd~~~P-~~t-rG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvk 88 (464)
+.|+|+.. .+..||+.|-|++.... .+. +|.--..+-.|-|++=- +++.+..+ .|.+ ..||+|++.+++
T Consensus 3 ~kI~DI~~-~~~~V~v~akVl~~~~r~i~~~~g~~~~~~gllgDeTG~---I~fT~W~~----~~~l-~~Gd~v~i~na~ 73 (358)
T PRK06386 3 SKISDINA-ARQNVDLKVKVLSLNKRTIKNDRGETIYYYGIIGDETGT---VPFTAWEF----PDAV-KSGDVIEIKYCY 73 (358)
T ss_pred cchhhcCC-CCCcEEEEEEEEEccceEEecCCCCeEEEEEEEECCcce---EEEEecCC----cccC-CCCCEEEEEeEE
Confidence 45778762 24469999999999731 122 34344445557777542 78888763 4667 689999999999
Q ss_pred EEEEcCeeEEEeccCccEEEEEeCCCCCCCCccccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCcccccccccccCC-
Q 012401 89 IKKHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSLKDISEH- 167 (464)
Q Consensus 89 v~~~~g~~~~~~~~~~ss~~lf~~~~~~~~~Py~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~f~~~Lkdi~~~- 167 (464)
++.|+|++.+..+.. +.... . .+... + ..+. . +. ..|+||+++
T Consensus 74 v~~~~G~~~Lnv~~~-t~v~~-~--~d~~i-e---------v~~~------------------~---~~-~KI~DL~~g~ 117 (358)
T PRK06386 74 SKEYNGKIRIYFDSR-SEVML-K--PDENI-E---------VKRT------------------Y---KL-VKIRDLSLVT 117 (358)
T ss_pred EeeECCEEEEEEcCc-eEEEe-c--Ccccc-c---------cccc------------------c---Cc-cEeEeccCCC
Confidence 999999998877744 43321 1 11111 0 0000 0 12 579999875
Q ss_pred ceEeeEEEEEEeeeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCCccccccCCCcceEEEEEecccc
Q 012401 168 RYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRVSTDRSY 247 (464)
Q Consensus 168 ~f~Dlv~qVv~v~~~~~~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~p~~G~vl~V~~~~~~ 247 (464)
.++++.++|+.++ + . .+- .||+..--. ...+.|+ . | .+++++|..
T Consensus 118 ~~v~V~akVle~~-e---~--e~~-~~g~~~~v~--sg~lgDe-----------------T-------G-rIr~TlW~~- 162 (358)
T PRK06386 118 PYVSVIGKITGIT-K---K--EYD-SDGTSKIVY--QGYIEDD-----------------T-------A-RVRISSFGK- 162 (358)
T ss_pred CceEEEEEEEEcc-C---c--eEe-cCCCccEEE--EEEEEcC-----------------C-------C-eEEEEEccc-
Confidence 5679999999876 3 1 222 455411110 1111110 0 2 569999985
Q ss_pred hhhhccCCCCCcEEEEeCcEEEEeCcEEEEEEecCcceEEcCCCChhHHHHHHHHHHHhCCCCCCCCccCCCCCCCcccc
Q 012401 248 ENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDNDNVVWDYMRFRERISGGHGHMPIWTDPSSQFLTEVD 327 (464)
Q Consensus 248 ~~~~~~~~k~G~wV~l~Nv~~k~~~g~leG~l~~~ski~~l~~~d~~v~~r~ry~~r~~~~~~~~~~~~~~~~~~~t~~~ 327 (464)
.++.|+.|+|.|...+.+.|.++-.+...+.|..++.+- ++..+..+-..+....+ .+++.
T Consensus 163 ------~l~eGd~v~i~na~v~e~~G~~el~v~~~t~I~~~~~~i-ev~~~~~~I~di~~~~g------------~v~i~ 223 (358)
T PRK06386 163 ------PLEDNRFVRIENARVSQYNGYIEISVGNKSVIKEVESDI-NLESRNIFIFEIKSPVG------------GITIM 223 (358)
T ss_pred ------cccCCCEEEEeeeEEEccCCeEEEEeCCeEEEEECCCCc-ccCccccchhhhhccCC------------eEEEE
Confidence 378999999999999999999999999989988775432 11111001111111000 00000
Q ss_pred cCCCccccHHHHh-------hCCCCCceeEEEEEEEeecCCCccccccCCC----CeEEEEEEEEeCCCceEEEEEeccc
Q 012401 328 WVNVASVTLMKIA-------TQLQGNVRCCCIVRVVSIHPFQAEHYSSPNG----SSEYTMKLTLEDPTARIHALLCGKE 396 (464)
Q Consensus 328 ~~~~p~ttL~dIL-------~~p~v~~kfr~~VRVV~~~P~~~edf~~~~~----~w~~rf~L~lED~t~ri~~~v~~~d 396 (464)
=+|-+|- .+|. +=||++- -.|..+| .+--|..+.|.|.|+.+.+.++++.
T Consensus 224 ------G~iv~i~~gsgli~rCP~-------C~R~l~~------g~C~~HG~v~~~~dlr~k~vLDDGtg~~~~~l~~e~ 284 (358)
T PRK06386 224 ------GFIVSVGQGSRIFTKCSV-------CNKIIED------GVCKDHPDAPVYLDIFGYFTISDGTGFVTCYANKDS 284 (358)
T ss_pred ------EEEEEEcCCcEeEecCcC-------CCeEccC------CcCCCCCCCCCeeEEEEEEEEECCCCeEEEEEChHH
Confidence 0011111 1332 2245551 3666544 4445677799999999999999999
Q ss_pred cccccCC
Q 012401 397 WVKFFGG 403 (464)
Q Consensus 397 a~~f~~~ 403 (464)
++.++|.
T Consensus 285 ~e~l~G~ 291 (358)
T PRK06386 285 FLPYINI 291 (358)
T ss_pred hHHHhCC
Confidence 9999986
No 13
>PRK15491 replication factor A; Provisional
Probab=98.79 E-value=4.3e-07 Score=93.64 Aligned_cols=204 Identities=16% Similarity=0.183 Sum_probs=141.4
Q ss_pred CCcceeehhhhhhccCCEEEEEEEEEEcCCcccc---CCC-ceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCE
Q 012401 6 NQGGIVRIKELAMHVKHKVNLLGVVLEFSIPRKS---QGT-DYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDL 81 (464)
Q Consensus 6 ~~y~y~~i~d~~~~~~~~vnviGVVvd~~~P~~t---rG~-D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDI 81 (464)
..|.|++|+++... ...|++.|+|++..+++.= +|+ -...++.|.|.|- .+++.+|.+..+.++.+ .+||+
T Consensus 162 ~~~~~~~I~dl~~~-~~~V~I~g~V~~~~~~r~~~~~~G~~~~v~~~~l~DetG---~Ir~t~W~~~a~~~~~l-~~Gd~ 236 (374)
T PRK15491 162 ASINSQKISDIKDG-DSDINIVGKVLDISDVRTFQKKDGSQGRVRNITIGDETG---KIRVTLWDGKTDLADKL-ENGDS 236 (374)
T ss_pred cccCcccHHHcCCC-CccEEEEEEEEEccCceEEEecCCCeEEEEEEEEECCCC---eEEEEEecchhcccccC-CCCCE
Confidence 35677899998642 3359999999999987532 355 4788899999865 29999999876777777 69999
Q ss_pred EEEeeEEEE--EEcCeeEEEeccCccEEEEEeCCCCCCCCccccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCccccc
Q 012401 82 ILLKNVMIK--KHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLL 159 (464)
Q Consensus 82 I~l~rvkv~--~~~g~~~~~~~~~~ss~~lf~~~~~~~~~Py~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~f~~ 159 (464)
|.+.+..++ .|+|++.+..+.. ++... ..... + +. ..| .
T Consensus 237 V~i~~~~~r~~~~~g~~El~~~~~-s~I~~--~~~~~---e-------~~-------------------------~~f-~ 277 (374)
T PRK15491 237 VEIINGYARTNNYSQEVEIQIGNH-GSLRK--TDRNV---E-------YE-------------------------EDF-T 277 (374)
T ss_pred EEEEeceEEEeccCCCEEEEeCCC-ceEEE--CCccc---c-------cC-------------------------CCc-c
Confidence 999997655 5678888887644 44331 11100 0 10 025 6
Q ss_pred ccccccCCceEeeEEEEEEeeeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCCccccccCCCcceEE
Q 012401 160 SLKDISEHRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVL 239 (464)
Q Consensus 160 ~Lkdi~~~~f~Dlv~qVv~v~~~~~~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~p~~G~vl 239 (464)
.|.||.++..+|+++.|..+. + .-++--.||+...--.+. +.| + =|. +
T Consensus 278 ~I~dl~~~~~~dv~G~V~~v~-~----~~~~~~~~G~~~~~r~i~--l~D-----------------~-------Tg~-I 325 (374)
T PRK15491 278 PIADIIPGQPYSIKGAVSGLG-D----LKEFTKSDGSENKVSNIY--VSD-----------------D-------TGR-I 325 (374)
T ss_pred CHHHcCCCCceeEEEEEEEcC-C----cEEEEccCCCEeEEEeEE--EEe-----------------C-------CCc-E
Confidence 788888899999999999886 2 122222444432221100 000 0 154 7
Q ss_pred EEEecccchhhhccCCCCCcEEEEeCcEEEE-eCcEEEEEEecCcceE
Q 012401 240 RVSTDRSYENFGRYFTATGKWVRIRNMSCQV-SSGMWHGLLQSSSKIR 286 (464)
Q Consensus 240 ~V~~~~~~~~~~~~~~k~G~wV~l~Nv~~k~-~~g~leG~l~~~ski~ 286 (464)
++++|..+|.. ...+-+|+.|++.+..+|. ..|.+|......|+|.
T Consensus 326 r~tlWg~~a~~-~~~~~~g~~i~i~~~~~k~g~~~~~e~s~g~~s~~~ 372 (374)
T PRK15491 326 RIALWGEKAEL-VDKLDIDTPIKIIDAFSKSGYNEDVELSAGNRSRVV 372 (374)
T ss_pred EEEEccccccc-ccccCCCCeEEEEEEEEeecCCCcEEEEeCCcceEE
Confidence 99999999986 5567889999999999999 5699999888888774
No 14
>PRK14699 replication factor A; Provisional
Probab=98.64 E-value=2.7e-06 Score=90.36 Aligned_cols=204 Identities=13% Similarity=0.157 Sum_probs=141.9
Q ss_pred cceeehhhhhhccCCEEEEEEEEEEcCCccc---cCC-CceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEE
Q 012401 8 GGIVRIKELAMHVKHKVNLLGVVLEFSIPRK---SQG-TDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLIL 83 (464)
Q Consensus 8 y~y~~i~d~~~~~~~~vnviGVVvd~~~P~~---trG-~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~ 83 (464)
..+++|.++.. -...+++.|.|++..+|+. .+| ......+.|.|.|=. +++.+|.+..+.++.+ ..||+|.
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 3467999999999988753 246 467789999999763 9999999877777877 6899999
Q ss_pred EeeEEEEEE--cCeeEEEeccCccEEEEEeCCCCCCCCccccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCccccccc
Q 012401 84 LKNVMIKKH--QAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSL 161 (464)
Q Consensus 84 l~rvkv~~~--~g~~~~~~~~~~ss~~lf~~~~~~~~~Py~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~f~~~L 161 (464)
+.++.++.. ++.+.+..+.. +.. ....+.. . +. ..| +.|
T Consensus 349 i~~~y~~~~~~~~~~eL~~~~~-t~I---~~~~~~~--------e-~~-------------------------~~~-~~I 389 (484)
T PRK14699 349 VLNAYSRENTFSQQVELNLGAR-GII---QKSEKKV--------E-YR-------------------------EKF-TDI 389 (484)
T ss_pred EEeEEEEeccCCccEEEEecCc-eeE---eecCCcc--------e-ee-------------------------ecc-ccH
Confidence 999998843 45677777644 311 1111000 0 00 036 789
Q ss_pred ccccCCceEeeEEEEEEeeeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCCccccccCCCcceEEEE
Q 012401 162 KDISEHRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRV 241 (464)
Q Consensus 162 kdi~~~~f~Dlv~qVv~v~~~~~~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~p~~G~vl~V 241 (464)
.||.+++.+|+++.|..+. +. ..+. -.||+.-.--. ..+.| -=| .+|+
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 1111 13333111100 00000 015 7899
Q ss_pred EecccchhhhccCCCCCcEEEEeCcEEEE-eCcEEEEEEecCcceEEc
Q 012401 242 STDRSYENFGRYFTATGKWVRIRNMSCQV-SSGMWHGLLQSSSKIRLF 288 (464)
Q Consensus 242 ~~~~~~~~~~~~~~k~G~wV~l~Nv~~k~-~~g~leG~l~~~ski~~l 288 (464)
++|...|.. .+.+.+|+-|.+.|..++. .+|.+|..+-..|.|.+|
T Consensus 438 tlWg~~A~~-~~~~~~~~~v~~~~~~~~~g~~~~~e~s~g~~s~~~~~ 484 (484)
T PRK14699 438 TLWGEQAYV-IEDLDIDSEIQIIDAYARYGLNEEIELSVGNRSRVIIL 484 (484)
T ss_pred EEcchhhhh-ccccCCCCeEEEechhhhhcccccEEEEecCceEEEeC
Confidence 999988874 5789999999999999999 578999988888887554
No 15
>KOG4757 consensus Predicted telomere binding protein [General function prediction only]
Probab=98.42 E-value=1.2e-08 Score=102.95 Aligned_cols=117 Identities=12% Similarity=0.207 Sum_probs=81.8
Q ss_pred CceeEEEEEEEeecCCCccccccC---CCCeEEEEEEEEeCC-CceEEEEEeccccccccCC---CCC-h------HHHH
Q 012401 346 NVRCCCIVRVVSIHPFQAEHYSSP---NGSSEYTMKLTLEDP-TARIHALLCGKEWVKFFGG---SPP-P------DVLT 411 (464)
Q Consensus 346 ~~kfr~~VRVV~~~P~~~edf~~~---~~~w~~rf~L~lED~-t~ri~~~v~~~da~~f~~~---~~~-~------~~L~ 411 (464)
+.+++..+.+++++|..+..|.+. ..+++|+|.++|-|. .+.+++.-..-||..|-++ ++. + -++.
T Consensus 378 ~r~H~~l~~le~s~p~s~~~fgc~~~~~~~~v~~ln~Lv~~e~~~~vP~~~~~v~~~~l~~~s~~l~~~l~d~~~~fqi~ 457 (522)
T KOG4757|consen 378 PRKHRLLVQLEDSWPKSLTQFGCLSQPPSSYVWMLNLLVRDESNVTVPVIFFDVDAAELINSSKKLPCNLADHQMTFQIK 457 (522)
T ss_pred hhhhhhhhhhcccCcccceeeeeccCCHHHHHHHHHHHhccccccccccccchhheeeeccccccccchhccccceEEec
Confidence 447999999999999999999884 335677777777774 3455555555554444322 121 1 2567
Q ss_pred HHHHHHcCCCCCC------CCC--CCCccCCcceeEeeeeeeecCCc------eEEEEEeeeEEc
Q 012401 412 KKIKMLLGMPEHE------DGN--DDMVRNPPWIKCFLHLKESDGGR------NRVYYIRWTKLV 462 (464)
Q Consensus 412 ~kl~~L~G~~e~~------~~~--~~~~~~~pw~~CCi~sY~v~~~~------~r~f~~F~T~i~ 462 (464)
+.+...||+||++ +++ .......|||+|-||||.+..+. +.|++-|||+|+
T Consensus 458 ds~il~~~~l~~~i~~~~~~~~~p~~~~~~~pw~~~~vk~y~i~n~~d~q~~~q~~~~~~~~~iv 522 (522)
T KOG4757|consen 458 DSLILIWGNLEERIQHHISKGESPTLAAEETPWFDIYVKEYIIGNTKDHQSLLQKRWRGFGTKIV 522 (522)
T ss_pred ceeeeecccHHHHHHHHHhcCCCCcccccccccceeeeeeeeecCCcchHHHHHHHhhccccccC
Confidence 7888889999874 333 11224789999999999987653 888888998874
No 16
>PRK07211 replication factor A; Reviewed
Probab=98.39 E-value=0.0003 Score=74.45 Aligned_cols=269 Identities=15% Similarity=0.159 Sum_probs=169.5
Q ss_pred eeehhhhhhccC-CEEEEEEEEEEcCCcccc-C----CCceEEEEEEEeCCCCCCCeEEEEecCCCC-CCCCCCCCCCEE
Q 012401 10 IVRIKELAMHVK-HKVNLLGVVLEFSIPRKS-Q----GTDYVCVLKIVDDSQQSPELLVNIFTSSID-QLPRVLSPRDLI 82 (464)
Q Consensus 10 y~~i~d~~~~~~-~~vnviGVVvd~~~P~~t-r----G~D~~~tl~I~D~S~~~~gl~v~iF~~~~~-~LP~v~~~GDII 82 (464)
..+|+++. ++ ..|++.|-|+..+.|+.= + +.--.+++.|.|+|= .|++.+|....+ ..|.+ ++|||+
T Consensus 53 ~~~I~dL~--pg~~~vtI~aRV~~~~~~Rt~~~~~~~~eGkv~~v~l~DeTG---~Ir~TlW~d~ad~~~~~L-e~GdV~ 126 (485)
T PRK07211 53 VNGIADIE--PGMDEVKFLAKVLSIGDLRTFERDGEDEDGRVINVEVADETG---SVRVAFWDEQAVAAEEEL-EVGQVL 126 (485)
T ss_pred cccHhhCC--CCCCceEEEEEEeEccCceEEEeCCCCCCcEEEEEEEEcCCC---eEEEEEechHhHhhhccc-CCCCEE
Confidence 34788886 55 469999999999987642 2 235899999999765 399999975432 46778 799999
Q ss_pred EEeeEEEEEEcCeeEEEeccCccEEEEEeCCCCCCCCccccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCcccccccc
Q 012401 83 LLKNVMIKKHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSLK 162 (464)
Q Consensus 83 ~l~rvkv~~~~g~~~~~~~~~~ss~~lf~~~~~~~~~Py~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~f~~~Lk 162 (464)
.+.+.-...|++ +.+..+ . ........+ |++ .. .| ..|+
T Consensus 127 ~I~~~~~~~ys~-~El~i~----~---ve~~~d~~i-~~~------------------------------~~-~~-~~I~ 165 (485)
T PRK07211 127 RIKGRPKDGYNG-LEVSVD----K---VEPDPDAEI-DVQ------------------------------IG-DT-YTVE 165 (485)
T ss_pred EEeceEeccccc-eEEEEe----e---EEEcccccc-ccc------------------------------cc-CC-ccHH
Confidence 998754444444 222222 0 111010010 000 00 24 6788
Q ss_pred cccCC-ceEeeEEEEEEeeeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCCccccccCCCcceEEEE
Q 012401 163 DISEH-RYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRV 241 (464)
Q Consensus 163 di~~~-~f~Dlv~qVv~v~~~~~~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~p~~G~vl~V 241 (464)
||+++ ..+|++++|+.+. +. ..| -=-||++-.-+. ..+-| + =| .+|+
T Consensus 166 dL~~~~~~v~I~grV~~v~-~i--Rtf--~r~dGseGkv~s--v~L~D-----------------e-------TG-~IR~ 213 (485)
T PRK07211 166 DLSLGLSDVTLVGVVLDTD-SV--RTF--DRDDGSEGRVSN--LTVGD-----------------E-------TG-RVRV 213 (485)
T ss_pred HcCCCCCceEEEEEEEEcC-CC--eEE--ECCCCCeeEEEE--EEEEc-----------------C-------CC-eEEE
Confidence 88865 5689999999776 31 010 011222111111 00000 0 15 4799
Q ss_pred EecccchhhhccCCCCCcEEEEeCcEEEEeCcEEEEEEecCcceEEcCCCChhHHHHHHHHHHHhCCCCCCCCccCCCCC
Q 012401 242 STDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDNDNVVWDYMRFRERISGGHGHMPIWTDPSSQ 321 (464)
Q Consensus 242 ~~~~~~~~~~~~~~k~G~wV~l~Nv~~k~~~g~leG~l~~~ski~~l~~~d~~v~~r~ry~~r~~~~~~~~~~~~~~~~~ 321 (464)
|+|+.++... ..+.+|+-|++.|.+++...|.+|..+..++.|..++.+-. .+| .
T Consensus 214 TlW~d~Ad~~-~~le~G~Vv~I~~a~Vre~~g~~ELsl~~~s~I~~~~dev~-----------------~vp-----~-- 268 (485)
T PRK07211 214 TLWDDRADLA-EELDAGESVEIVDGYVRERDGSLELHVGDRGAVEEVDEDVE-----------------YVP-----D-- 268 (485)
T ss_pred EEechhhhhh-ccCCCCCEEEEEeeEEEecCCcEEEEECCCceEEECCcccc-----------------ccc-----c--
Confidence 9999998874 77999999999999999987888888888888877654210 001 0
Q ss_pred CCcccccCCCccccHHHHhhCCCCCceeEEEEEEEeecCCCccccccCCCCeEEEEEEEEeCCCceEEEEEecccccc
Q 012401 322 FLTEVDWVNVASVTLMKIATQLQGNVRCCCIVRVVSIHPFQAEHYSSPNGSSEYTMKLTLEDPTARIHALLCGKEWVK 399 (464)
Q Consensus 322 ~~t~~~~~~~p~ttL~dIL~~p~v~~kfr~~VRVV~~~P~~~edf~~~~~~w~~rf~L~lED~t~ri~~~v~~~da~~ 399 (464)
++.|.++- + ..-.-...+|.+..|... |.+.+|+=-..--++|-|.|+++++-++|+.|..
T Consensus 269 -----------~~~I~dl~--~--g~~vdV~GvV~~v~~~rt--f~r~dG~~~~vr~l~l~D~TG~IrvTLWg~~A~~ 329 (485)
T PRK07211 269 -----------TTPIESLE--I--DETVDIAGVVRSADPKRT--FDRDDGSEGQVRNVRIQDDTGDIRVALWGEKADL 329 (485)
T ss_pred -----------cccHhhcC--C--CCceeEEEEEEEccCcEE--EEcCCCCEeEEEEEEEEcCCCcEEEEEeCccccC
Confidence 12233322 1 112456678888877654 4454453346778999999999999999999853
No 17
>PRK08402 replication factor A; Reviewed
Probab=98.30 E-value=5.7e-05 Score=77.28 Aligned_cols=195 Identities=15% Similarity=0.149 Sum_probs=113.5
Q ss_pred cccccccCC-ceEeeEEEEEEeeeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCCccccccCCCcce
Q 012401 159 LSLKDISEH-RYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGT 237 (464)
Q Consensus 159 ~~Lkdi~~~-~f~Dlv~qVv~v~~~~~~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~p~~G~ 237 (464)
..|+||.++ ..++++++|+.+. +.. .+ ---||+...-. +..+.| + -|+
T Consensus 63 ~kI~dl~~g~~~V~v~~rVl~~~-~~r--~f--~rrdG~~~~V~--~i~l~D-----------------e-------TG~ 111 (355)
T PRK08402 63 MHISDLVPGMRGVNIVGRVLRKY-PPR--EY--TKKDGSTGRVA--SLIIYD-----------------D-------TGR 111 (355)
T ss_pred cCHHHccCCCceeeEEEEEEEcc-CCc--ee--eccCCCcceEE--EEEEEc-----------------C-------CCe
Confidence 579999987 5899999999887 311 10 01122211000 000000 0 144
Q ss_pred EEEEEecccchhhhccCCCCCcEEEEeCcEEEE-eCcEEEEEEecCcceEEcCCCChhHHHHHHHHHHHhCCCCCCCCcc
Q 012401 238 VLRVSTDRSYENFGRYFTATGKWVRIRNMSCQV-SSGMWHGLLQSSSKIRLFSDNDNVVWDYMRFRERISGGHGHMPIWT 316 (464)
Q Consensus 238 vl~V~~~~~~~~~~~~~~k~G~wV~l~Nv~~k~-~~g~leG~l~~~ski~~l~~~d~~v~~r~ry~~r~~~~~~~~~~~~ 316 (464)
+ ++++|+.++.-....+.+|+-|++.|..++. .+|..+..+...|.|.+.++ ++++-+ +|
T Consensus 112 i-r~TlW~~~a~~~~~~l~~Gdvi~I~~a~V~e~~~G~~eLsvg~~s~i~~~pd-~~ea~~--------------i~--- 172 (355)
T PRK08402 112 A-RVVLWDAKVAKYYNKINVGDVIKVIDAQVRESLSGLPELHINFRARIILNPD-DPRVEE--------------IP--- 172 (355)
T ss_pred E-EEEEechhhhhhcccCCCCCEEEEECCEEeecCCCcEEEEECCCceEEeCCC-cccccc--------------cc---
Confidence 4 9999998876334669999999999999998 59998999999999876553 332211 11
Q ss_pred CCCCCCCcccccCCCccccHHHHhhCCCCCceeEEEEEEEeecCCCc--------cc---------c-cc--C--CCCeE
Q 012401 317 DPSSQFLTEVDWVNVASVTLMKIATQLQGNVRCCCIVRVVSIHPFQA--------EH---------Y-SS--P--NGSSE 374 (464)
Q Consensus 317 ~~~~~~~t~~~~~~~p~ttL~dIL~~p~v~~kfr~~VRVV~~~P~~~--------ed---------f-~~--~--~~~w~ 374 (464)
....+. .. ..+..+|.||-... .=|.+...|+.+.+.-+ +. + |. + ...|.
T Consensus 173 --~~~~~~--~~-~~~~k~I~ei~~gd---~~v~v~g~Iv~i~~~~~y~aCp~CnKkv~~~~~~~~~~Ce~~~~v~p~~r 244 (355)
T PRK08402 173 --PLEEVR--SY-NYTRKKIGELEGGE---RFVEVRGTIAKVYRVLVYDACPECRRKVDYDPATDTWICPEHGEVEPIKI 244 (355)
T ss_pred --cccccc--cc-cccccCHHHcccCC---cEEEEEEEEEEEecCeeEecCCCCCeEEEEecCCCCEeCCCCCCcCccee
Confidence 000000 00 12233344442110 00233333333333000 00 0 10 1 35788
Q ss_pred EEEEEEEeCCCceEEEEEeccccccccCCCCChHHHHHH
Q 012401 375 YTMKLTLEDPTARIHALLCGKEWVKFFGGSPPPDVLTKK 413 (464)
Q Consensus 375 ~rf~L~lED~t~ri~~~v~~~da~~f~~~~~~~~~L~~k 413 (464)
|++.+.|-|.|+++|+.++++.|+.++|. +.+.|.+.
T Consensus 245 yil~~~l~D~TG~~~vt~f~e~ae~llG~--sa~el~~~ 281 (355)
T PRK08402 245 TILDFGLDDGTGYIRVTLFGDDAAELLGV--EPEEIAEK 281 (355)
T ss_pred EEEEEEEEcCCCcEEEEEecHHHHHHhCC--CHHHHHHH
Confidence 99999999999999999999999999974 33455444
No 18
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=97.88 E-value=0.0004 Score=61.12 Aligned_cols=92 Identities=17% Similarity=0.262 Sum_probs=71.7
Q ss_pred eeehhhhhhccC-CEEEEEEEEEEcCCcc--ccCCC-ceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEe
Q 012401 10 IVRIKELAMHVK-HKVNLLGVVLEFSIPR--KSQGT-DYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLK 85 (464)
Q Consensus 10 y~~i~d~~~~~~-~~vnviGVVvd~~~P~--~trG~-D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~ 85 (464)
++.|+|+. ++ ..||+.|+|++..+++ +++|+ ....+++|.|.|=. |.+.++.+.. +.+ ..||||.|+
T Consensus 4 ~~kI~dL~--~g~~~v~~~~~V~~i~~~~~~~~k~~~~~v~~~~l~D~TG~---I~~tlW~~~a---~~l-~~GdvV~I~ 74 (129)
T PRK06461 4 ITKIKDLK--PGMERVNVTVRVLEVGEPKVIQTKGGPRTISEAVVGDETGR---VKLTLWGEQA---GSL-KEGEVVEIE 74 (129)
T ss_pred ceEHHHcC--CCCCceEEEEEEEEcCCceEEEeCCCceEEEEEEEECCCCE---EEEEEeCCcc---ccC-CCCCEEEEE
Confidence 67899997 55 5799999999988764 45554 56889999999863 8999998643 345 589999999
Q ss_pred eEEEEEEcCeeEEEeccCccEEEEEe
Q 012401 86 NVMIKKHQAELSAVFYKDSSSFALFD 111 (464)
Q Consensus 86 rvkv~~~~g~~~~~~~~~~ss~~lf~ 111 (464)
+++++.|+|.+++..++. +.....+
T Consensus 75 na~v~~f~G~lqL~i~~~-~~i~~~~ 99 (129)
T PRK06461 75 NAWTTLYRGKVQLNVGKY-GSISESD 99 (129)
T ss_pred CcEEeeeCCEEEEEECCC-EEEEECC
Confidence 999999999999888743 4444333
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=97.87 E-value=0.00021 Score=78.48 Aligned_cols=145 Identities=19% Similarity=0.294 Sum_probs=99.3
Q ss_pred Ccceeehhhhhhc-cCCEEEEEEEEEEcCCccc----cCCCc-eEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCC
Q 012401 7 QGGIVRIKELAMH-VKHKVNLLGVVLEFSIPRK----SQGTD-YVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRD 80 (464)
Q Consensus 7 ~y~y~~i~d~~~~-~~~~vnviGVVvd~~~P~~----trG~D-~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GD 80 (464)
.|.|++|+++... .+..|+|||||+++++... +.|+. .+.+|+|+|.|-. .|.|.++.+..+.+. . ..|+
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 6899999999864 3457999999999988765 22443 5789999999853 499999998766776 3 5799
Q ss_pred EEEEeeEEEEEEcCeeEEEeccCccEEEEEeCCCCCCCCccccCCCCCCCCHHHHHHHHHHHHhhhcCcccC--------
Q 012401 81 LILLKNVMIKKHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSS-------- 152 (464)
Q Consensus 81 II~l~rvkv~~~~g~~~~~~~~~~ss~~lf~~~~~~~~~Py~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~-------- 152 (464)
||.+..++|+.|+|. .+... ..|.+. .+ | |..-+..|+.|+.+.....
T Consensus 371 Vva~kg~~V~~f~g~-sLs~~-~~S~i~-iN--------P-------------dipEa~~L~~w~~~~g~~~~~~s~~~~ 426 (608)
T TIGR00617 371 VIAIKGVRVSDFGGK-SLSTG-GSSTII-VN--------P-------------DIPEAEKLKGWYDNEGKGTMASSISDM 426 (608)
T ss_pred EEEEEeEEEEecCCc-eEecc-CCceEE-EC--------C-------------CcHHHHHHHHHHHhcCCCccceeehhc
Confidence 999999999999664 44433 224443 11 1 1112568889976432210
Q ss_pred ------C-CcccccccccccC--------CceEeeEEEEEEee
Q 012401 153 ------G-SNDYLLSLKDISE--------HRYFDLVCKVFHVS 180 (464)
Q Consensus 153 ------~-~~~f~~~Lkdi~~--------~~f~Dlv~qVv~v~ 180 (464)
+ .... +.|.+|++ +.+|.+.|.|.++.
T Consensus 427 ~~~~~~~~~~~~-ktI~ei~~~~lg~~~k~~~f~v~atI~~Ik 468 (608)
T TIGR00617 427 MSGRVGGSNAER-KTIAEIQAENLGKSDKPDYFSVKATISYLK 468 (608)
T ss_pred cccccCCccccc-ccHHHHhhhccCCCCCCcEEEEEEEEEEEe
Confidence 0 1122 45666643 35789999999987
No 20
>cd04475 RPA1_DBD_B RPA1_DBD_B: A subfamily of OB folds corresponding to the third OB fold, the ssDNA-binding domain (DBD)-B, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-B, RPA1 contains three other OB folds: DBD-A, DBD-C, and RPA1N. The major DNA binding activity of human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. Although ScRPA and the hRPA have similar ssDNA-binding properties, they differ functiona
Probab=97.73 E-value=0.00026 Score=59.33 Aligned_cols=73 Identities=16% Similarity=0.213 Sum_probs=58.7
Q ss_pred EEEEEEEEEcCCcccc--C--CC-ceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCeeEE
Q 012401 24 VNLLGVVLEFSIPRKS--Q--GT-DYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAELSA 98 (464)
Q Consensus 24 vnviGVVvd~~~P~~t--r--G~-D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvkv~~~~g~~~~ 98 (464)
|||+|+|++.++|+.- + |+ -.+.+|+|.|.|.. .+.|.++.+..+.+... .|+||.+++++++.|+| ..+
T Consensus 2 vDvig~V~~v~~~~~i~~k~~g~~~~~r~v~i~D~t~~--~i~vtLWg~~a~~~~~~--~~~vv~~~~~~i~~~~~-~~l 76 (101)
T cd04475 2 VDVIGVVKSVGPVTTITTKSTGRELDKREITLVDESGH--SVELTLWGEQAELFDGS--ENPVIAIKGVKVSEFNG-KSL 76 (101)
T ss_pred EeEEEEEeEccCcEEEEEecCCCceeEEEEEEEeCCCC--EEEEEEEHHHhhhcccC--CCCEEEEEeeEEEecCC-eEE
Confidence 8999999999998643 2 43 67899999999974 59999999766666654 39999999999999985 454
Q ss_pred Eec
Q 012401 99 VFY 101 (464)
Q Consensus 99 ~~~ 101 (464)
.+.
T Consensus 77 ~~~ 79 (101)
T cd04475 77 STG 79 (101)
T ss_pred eec
Confidence 443
No 21
>PRK07218 replication factor A; Provisional
Probab=97.54 E-value=0.011 Score=62.11 Aligned_cols=160 Identities=17% Similarity=0.218 Sum_probs=105.7
Q ss_pred cccccccC-CceEeeEEEEEEeeeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCCccccccCCCcce
Q 012401 159 LSLKDISE-HRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGT 237 (464)
Q Consensus 159 ~~Lkdi~~-~~f~Dlv~qVv~v~~~~~~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~p~~G~ 237 (464)
..|+||++ ++.++++++|+.+. + + ++. .||+..... ...+.|+ =|
T Consensus 59 ~kI~Di~~~~~~V~v~~kVl~i~-~----r-t~r-~dg~~g~v~--~~~igDe------------------------TG- 104 (423)
T PRK07218 59 KDIKELSTDDKNVTVTGRVLTIG-E----R-SIR-YQGDDHVIY--EGILADE------------------------TG- 104 (423)
T ss_pred ccHhhCCCCCceeEEEEEEEEec-c----e-eEe-cCCCceEEE--EEEEECC------------------------CC-
Confidence 67999986 57899999999886 3 2 223 777632111 1111110 03
Q ss_pred EEEEEecccchhhhccCCCCCcEEEEeCcEEEEeCcEEEEEEecCcceEEcCCCChhHHHHHHHHHHHhCCCCCCCCccC
Q 012401 238 VLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDNDNVVWDYMRFRERISGGHGHMPIWTD 317 (464)
Q Consensus 238 vl~V~~~~~~~~~~~~~~k~G~wV~l~Nv~~k~~~g~leG~l~~~ski~~l~~~d~~v~~r~ry~~r~~~~~~~~~~~~~ 317 (464)
++++++|+.. .+++||+|+|.|...+...|..+-.+...+.|..++++..
T Consensus 105 ~Ir~tlW~~~------~l~~Gdvv~I~na~vre~~g~~el~ig~~t~I~~~de~~~------------------------ 154 (423)
T PRK07218 105 TISYTAWKDF------GLSPGDTVTIGNAGVREWDGRPELNIGESTTVSLLDDSSL------------------------ 154 (423)
T ss_pred eEEEEEECCC------CCCCCCEEEEeccEeeccCCceEEeccCcceEEEcCcccc------------------------
Confidence 4599999933 2999999999999999999998888888888876664321
Q ss_pred CCCCCCcccccCCCccccHHHHhhCCCCCceeEEEEEEEeecCCCccccccCCCCeEEEEEEEEeCCCceEEEEEecccc
Q 012401 318 PSSQFLTEVDWVNVASVTLMKIATQLQGNVRCCCIVRVVSIHPFQAEHYSSPNGSSEYTMKLTLEDPTARIHALLCGKEW 397 (464)
Q Consensus 318 ~~~~~~t~~~~~~~p~ttL~dIL~~p~v~~kfr~~VRVV~~~P~~~edf~~~~~~w~~rf~L~lED~t~ri~~~v~~~da 397 (464)
+. ++..+...|.||-.. ..-....+||++.+|. .|-...|.- ....++|.|.|++|++-++++.|
T Consensus 155 ~~--------~~~~~~~kI~DL~~g---~~~V~v~g~Vl~~~~r---~f~~~dg~~-~v~~giigDeTG~Ir~tlW~~~~ 219 (423)
T PRK07218 155 PP--------YSIGGDKKLIDLGPG---DRGVNVEARVLELEHR---EIDGRDGET-TILSGVLADETGRLPFTDWDPLP 219 (423)
T ss_pred cC--------ccccCccchhhccCC---CCceEEEEEEEEecce---eEEcCCCCe-EEEEEEEECCCceEEEEEecccc
Confidence 00 001112223333311 1224667999999874 465666632 36778999999999999999865
No 22
>cd04491 SoSSB_OBF SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus solfataricus single-stranded (ss) DNA-binding protein (SSoSSB). SSoSSB has a single OB fold, and it physically and functionally interacts with RNA polymerase. In vitro, SSoSSB can substitute for the basal transcription factor TBP, stimulating transcription from promoters under conditions in which TBP is limiting, and supporting transcription when TBP is absent. SSoSSB selectively melts the duplex DNA of promoter sequences. It also relieves transcriptional repression by the chromatin Alba. In addition, SSoSSB activates reverse gyrase activity, which involves DNA binding, DNA cleavage, strand passage and ligation. SSoSSB stimulates all these steps in the presence of the chromatin protein, Sul7d. SSoSSB antagonizes the inhibitory effect of Sul7d on reverse gyrase supercoiling activity. It also physically and functionally interacts with Mini-chromosome Maintenance (MCM), stimulating
Probab=97.52 E-value=0.0014 Score=52.76 Aligned_cols=72 Identities=18% Similarity=0.281 Sum_probs=59.9
Q ss_pred EEEEEEEEcCCcccc---CCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCeeEEEec
Q 012401 25 NLLGVVLEFSIPRKS---QGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAELSAVFY 101 (464)
Q Consensus 25 nviGVVvd~~~P~~t---rG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvkv~~~~g~~~~~~~ 101 (464)
|+.|.|++..+++.. .+.--..+++|.|.|= .+.+.++.+.. .+.+ ..||+|.+++++++.|+|.+++..+
T Consensus 1 ~v~~~V~~~~~~~~~~~~g~~~~~~~~~l~D~TG---~i~~~~W~~~~--~~~~-~~G~vv~i~~~~v~~~~g~~ql~i~ 74 (82)
T cd04491 1 SVEGKVLSISEPREFTRDGSEGKVQSGLVGDETG---TIRFTLWDEKA--ADDL-EPGDVVRIENAYVREFNGRLELSVG 74 (82)
T ss_pred CEEEEEEEccCCeEeccCCCeeEEEEEEEECCCC---EEEEEEECchh--cccC-CCCCEEEEEeEEEEecCCcEEEEeC
Confidence 589999999988753 3457789999999874 39999998654 6667 6899999999999999999998776
Q ss_pred c
Q 012401 102 K 102 (464)
Q Consensus 102 ~ 102 (464)
.
T Consensus 75 ~ 75 (82)
T cd04491 75 K 75 (82)
T ss_pred C
Confidence 4
No 23
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=97.15 E-value=0.0049 Score=54.20 Aligned_cols=88 Identities=18% Similarity=0.164 Sum_probs=65.1
Q ss_pred cccccccCC-ceEeeEEEEEEeeeeC-----CCC---eEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCCcccc
Q 012401 159 LSLKDISEH-RYFDLVCKVFHVSYDD-----SKG---LWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETL 229 (464)
Q Consensus 159 ~~Lkdi~~~-~f~Dlv~qVv~v~~~~-----~~~---~~~L~VwDgT~~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~ 229 (464)
..|+||+++ .-+|++++|+.+. +. .++ .+.+.|=|.|
T Consensus 5 ~kI~dL~~g~~~v~~~~~V~~i~-~~~~~~~k~~~~~v~~~~l~D~T--------------------------------- 50 (129)
T PRK06461 5 TKIKDLKPGMERVNVTVRVLEVG-EPKVIQTKGGPRTISEAVVGDET--------------------------------- 50 (129)
T ss_pred eEHHHcCCCCCceEEEEEEEEcC-CceEEEeCCCceEEEEEEEECCC---------------------------------
Confidence 679999998 6999999999775 20 111 1112222211
Q ss_pred ccCCCcceEEEEEecccchhhhccCCCCCcEEEEeCcEEEEeCcEEEEEEecCcceEEcCCC
Q 012401 230 RNFFPVGTVLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDN 291 (464)
Q Consensus 230 ~~~p~~G~vl~V~~~~~~~~~~~~~~k~G~wV~l~Nv~~k~~~g~leG~l~~~ski~~l~~~ 291 (464)
| ++++++|+..+ ..+++|+.|+++|..++...|.++..+...++|..++++
T Consensus 51 ------G-~I~~tlW~~~a----~~l~~GdvV~I~na~v~~f~G~lqL~i~~~~~i~~~~~~ 101 (129)
T PRK06461 51 ------G-RVKLTLWGEQA----GSLKEGEVVEIENAWTTLYRGKVQLNVGKYGSISESDDE 101 (129)
T ss_pred ------C-EEEEEEeCCcc----ccCCCCCEEEEECcEEeeeCCEEEEEECCCEEEEECCcc
Confidence 3 36899999754 358999999999999999999998888888899887753
No 24
>PRK08402 replication factor A; Reviewed
Probab=97.04 E-value=0.019 Score=59.00 Aligned_cols=139 Identities=16% Similarity=0.233 Sum_probs=93.5
Q ss_pred ceeehhhhhhccC-CEEEEEEEEEEcCCccc--c-CCC-ceEEEEEEEeCCCCCCCeEEEEecCCCC-CCCCCCCCCCEE
Q 012401 9 GIVRIKELAMHVK-HKVNLLGVVLEFSIPRK--S-QGT-DYVCVLKIVDDSQQSPELLVNIFTSSID-QLPRVLSPRDLI 82 (464)
Q Consensus 9 ~y~~i~d~~~~~~-~~vnviGVVvd~~~P~~--t-rG~-D~~~tl~I~D~S~~~~gl~v~iF~~~~~-~LP~v~~~GDII 82 (464)
..++|+|+. ++ ..|++.|-|+....|+. . .|+ ....++.|.|+|-. +++.++.+..+ .++.+ ..||||
T Consensus 61 ~~~kI~dl~--~g~~~V~v~~rVl~~~~~r~f~rrdG~~~~V~~i~l~DeTG~---ir~TlW~~~a~~~~~~l-~~Gdvi 134 (355)
T PRK08402 61 PLMHISDLV--PGMRGVNIVGRVLRKYPPREYTKKDGSTGRVASLIIYDDTGR---ARVVLWDAKVAKYYNKI-NVGDVI 134 (355)
T ss_pred CccCHHHcc--CCCceeeEEEEEEEccCCceeeccCCCcceEEEEEEEcCCCe---EEEEEechhhhhhcccC-CCCCEE
Confidence 467899997 44 46999999999987763 1 243 57888999998763 79999997644 47878 689999
Q ss_pred EEeeEEEEE-EcCeeEEEeccCccEEEEEeCCCCCCCCccccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCccccccc
Q 012401 83 LLKNVMIKK-HQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSL 161 (464)
Q Consensus 83 ~l~rvkv~~-~~g~~~~~~~~~~ss~~lf~~~~~~~~~Py~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~f~~~L 161 (464)
.+.+++++. |+|.+.+..+.. |+..+=+..+...-.| .-.++.. . .... ..|
T Consensus 135 ~I~~a~V~e~~~G~~eLsvg~~-s~i~~~pd~~ea~~i~---------~~~~~~~---------------~-~~~~-k~I 187 (355)
T PRK08402 135 KVIDAQVRESLSGLPELHINFR-ARIILNPDDPRVEEIP---------PLEEVRS---------------Y-NYTR-KKI 187 (355)
T ss_pred EEECCEEeecCCCcEEEEECCC-ceEEeCCCcccccccc---------ccccccc---------------c-cccc-cCH
Confidence 999999998 488878877644 4444222111100011 0000100 0 0123 568
Q ss_pred ccccCCc-eEeeEEEEEEee
Q 012401 162 KDISEHR-YFDLVCKVFHVS 180 (464)
Q Consensus 162 kdi~~~~-f~Dlv~qVv~v~ 180 (464)
.|++++. ||.+.+.|+.+.
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 25
>cd04497 hPOT1_OB1_like hPOT1_OB1_like: A subfamily of OB folds similar to the first OB fold (OB1) of human protection of telomeres 1 protein (hPOT1), the single OB fold of the N-terminal domain of Schizosaccharomyces pombe POT1 (SpPOT1), and the first OB fold of the N-terminal domain of the alpha subunit (OB1Nalpha) of Oxytricha nova telomere end binding protein (OnTEBP). POT1 proteins recognize single-stranded (ss) 3-prime ends of the telomere. A 3-prime ss overhang is conserved in ciliated protozoa, yeast, and mammals. SpPOT1 is essential for telomere maintenance. It binds specifically to the ss G-rich telomeric sequence (GGTTAC) of S. pombe. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. Deletion of the S. pombe pot1+ gene results in a rapid loss of telomere sequences, chromosome mis-segregation and chromosome circularization. hPOT1 is implicated in telomere length regulation. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB
Probab=96.65 E-value=0.02 Score=50.86 Aligned_cols=97 Identities=16% Similarity=0.131 Sum_probs=71.4
Q ss_pred ccccccccc--CCceEeeEEEEEEeeeeC----CCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCCccccc
Q 012401 157 YLLSLKDIS--EHRYFDLVCKVFHVSYDD----SKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLR 230 (464)
Q Consensus 157 f~~~Lkdi~--~~~f~Dlv~qVv~v~~~~----~~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~ 230 (464)
| ..|+++. .++.+|+++-|+.+.... .+.+.+|.|+|=|.++
T Consensus 3 f-~~i~~~~~~~~~~v~vigVV~~~~~p~~s~g~d~~~tl~i~D~S~~~------------------------------- 50 (138)
T cd04497 3 Y-TPLSSALKESGGSVNVIGVVVDAGPPVRSKGTDYCCTLTITDPSLAN------------------------------- 50 (138)
T ss_pred e-EeHHHHHhccCCeEEEEEEEeecCCCcccCCCcEEEEEEEECCCCCC-------------------------------
Confidence 5 6788886 799999999999876211 1346777777744211
Q ss_pred cCCCcceEEEEEecccchhhhccCCCCCcEEEEeCcEEEEeCcEEEEEEec-CcceEEcCCC
Q 012401 231 NFFPVGTVLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQS-SSKIRLFSDN 291 (464)
Q Consensus 231 ~~p~~G~vl~V~~~~~~~~~~~~~~k~G~wV~l~Nv~~k~~~g~leG~l~~-~ski~~l~~~ 291 (464)
+..|+|.+|.++++. ...+++||.|+|+|++++..+|...|.... .+.+.+.+..
T Consensus 51 -----~~~l~v~~F~~~~~~-LP~v~~GDVIll~~~kv~~~~g~~~~~~~~~~ss~avf~~~ 106 (138)
T cd04497 51 -----SDGLTVKLFRPNEES-LPIVKVGDIILLRRVKIQSYNGKPQGISNDRGSSWAVFRGD 106 (138)
T ss_pred -----CCcEEEEEECCChhh-CCCCCCCCEEEEEEEEEEEECCceEEEECCCceeEEEEcCC
Confidence 235688999988775 566799999999999999988888887776 5666655443
No 26
>cd03524 RPA2_OBF_family RPA2_OBF_family: A family of oligonucleotide binding (OB) folds with similarity to the OB fold of the single strand (ss) DNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA contains six OB folds, which are involved in ssDNA binding and in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. This family also includes OB folds similar to those found in Escherichia coli SSB, the wedge domain of E. coli RecG (a branched-DNA-specific helicase), E. coli ssDNA specific exodeoxyribonuclease VII large subunit, Pyroco
Probab=96.43 E-value=0.014 Score=44.22 Aligned_cols=71 Identities=18% Similarity=0.368 Sum_probs=53.6
Q ss_pred EEEEEEEEcCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCeeEEEec
Q 012401 25 NLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAELSAVFY 101 (464)
Q Consensus 25 nviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvkv~~~~g~~~~~~~ 101 (464)
.+.|+|++..... | ...+..|+|.|.+- ..+.+.+|.+..+........|++|.++ .+++.++++.++...
T Consensus 1 ~v~g~v~~~~~~~-~--~~~~~~~~l~D~~~--~~i~~~~~~~~~~~~~~~~~~g~~v~v~-g~v~~~~~~~~l~~~ 71 (75)
T cd03524 1 TIVGIVVAVEEIR-T--EGKVLIFTLTDGTG--GTIRVTLFGELAEELENLLKEGQVVYIK-GKVKKFRGRLQLIVE 71 (75)
T ss_pred CeEEEEEeecccc-c--CCeEEEEEEEcCCC--CEEEEEEEchHHHHHHhhccCCCEEEEE-EEEEecCCeEEEEee
Confidence 3789999998753 3 35589999999872 2399999997666553434789999998 999998877766543
No 27
>PRK07217 replication factor A; Reviewed
Probab=96.35 E-value=0.3 Score=48.97 Aligned_cols=168 Identities=18% Similarity=0.213 Sum_probs=101.3
Q ss_pred ccccccc-CCceEeeEEEEEEeeeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCCccccccCCCcce
Q 012401 159 LSLKDIS-EHRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGT 237 (464)
Q Consensus 159 ~~Lkdi~-~~~f~Dlv~qVv~v~~~~~~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~p~~G~ 237 (464)
..|+||+ .++.+++.++|+.++ + ..+..+.+| ..+.|+ . |
T Consensus 73 ~kI~Di~~~~~~VsV~aKVl~l~-e-~~~~si~qv------------GllgDE-----------------T-------G- 113 (311)
T PRK07217 73 VNIADIDEPEQWVDVTAKVVQLW-E-PSSDSIAQV------------GLLGDE-----------------T-------G- 113 (311)
T ss_pred eeeeecCCCCCcEEEEEEEEEec-C-CCCCceEEE------------EEEEcC-----------------C-------c-
Confidence 5699998 589999999999998 5 222111110 001110 0 2
Q ss_pred EEEEEecccchhhhccCCCCCcEEEEeCcEEEEeCcEEEEEEecCcceEEcCCCChhHHHHHHHHHHHhCCCCCCCCccC
Q 012401 238 VLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDNDNVVWDYMRFRERISGGHGHMPIWTD 317 (464)
Q Consensus 238 vl~V~~~~~~~~~~~~~~k~G~wV~l~Nv~~k~~~g~leG~l~~~ski~~l~~~d~~v~~r~ry~~r~~~~~~~~~~~~~ 317 (464)
.++.|+|.... ...+++|++|+|.|+..+.++|..+-.+...+.|..++.+-. +-... -.+...+=.+.
T Consensus 114 ~IkfT~W~~s~---~~~leeGd~~rI~na~v~ey~G~~~lnlg~~t~I~~~de~Ie-V~~~~---vei~G~lVdi~---- 182 (311)
T PRK07217 114 TIKFTKWAKSD---LPELEEGKSYLLKNVVTDEYQGRFSVKLNRTTSIEELDEDIE-VGDDE---VEVEGALVDIQ---- 182 (311)
T ss_pred eEEEEEccCCC---CCcccCCCEEEEEeEEEeeECCEEEEEeCCceEEEeCCCCcc-ccCcc---ccceeEEEEEe----
Confidence 45889998432 345899999999999999999999999999999877665321 10000 00000000000
Q ss_pred CCCCCCcccccCCCccccHHHHhhCCCCCceeEEEEEEEeecCCCccccccC----CCCeEEEEEEEEeCCCceEEEEEe
Q 012401 318 PSSQFLTEVDWVNVASVTLMKIATQLQGNVRCCCIVRVVSIHPFQAEHYSSP----NGSSEYTMKLTLEDPTARIHALLC 393 (464)
Q Consensus 318 ~~~~~~t~~~~~~~p~ttL~dIL~~p~v~~kfr~~VRVV~~~P~~~edf~~~----~~~w~~rf~L~lED~t~ri~~~v~ 393 (464)
+..-.+..|.. -.| =||++ + -.|.. .|.+--|....|-|.|+.+.++++
T Consensus 183 ~GsglI~rCP~--~~C-------------------~Rvl~----~--g~C~~HG~ve~~~DLrik~vlDDGt~~~~~~~~ 235 (311)
T PRK07217 183 SGSGLIKRCPE--EDC-------------------TRVLQ----N--GRCSEHGKVEGEFDLRIKGVLDDGEEVQEVIFN 235 (311)
T ss_pred CCCCCeecCCc--ccc-------------------Ccccc----C--CCCCCCCCcCCceeeEEEEEEECCCCeEEEEEC
Confidence 00001111110 000 13331 1 23333 345667999999999999999999
Q ss_pred ccccccccCC
Q 012401 394 GKEWVKFFGG 403 (464)
Q Consensus 394 ~~da~~f~~~ 403 (464)
.+-.+.+.|.
T Consensus 236 ~e~te~l~G~ 245 (311)
T PRK07217 236 REATEELTGI 245 (311)
T ss_pred hHHhHHHhCC
Confidence 9999999885
No 28
>KOG3416 consensus Predicted nucleic acid binding protein [General function prediction only]
Probab=96.33 E-value=0.019 Score=49.41 Aligned_cols=84 Identities=21% Similarity=0.307 Sum_probs=66.5
Q ss_pred eehhhhhhccCCEEEEEEEEEEcCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEE
Q 012401 11 VRIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIK 90 (464)
Q Consensus 11 ~~i~d~~~~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvkv~ 90 (464)
+.|+|+.... +..|++=+|++.+...+|+-.+=.++.++.|+|-. |.+.+..+ +..+ + ++||||+|++---+
T Consensus 5 i~ikdi~P~~-kN~~v~fIvl~~g~~tkTkdg~~v~~~kVaD~Tgs---I~isvW~e-~~~~--~-~PGDIirLt~Gy~S 76 (134)
T KOG3416|consen 5 IFIKDIKPGL-KNINVTFIVLEYGRATKTKDGHEVRSCKVADETGS---INISVWDE-EGCL--I-QPGDIIRLTGGYAS 76 (134)
T ss_pred hhHhhcChhh-hcceEEEEEEeeceeeeccCCCEEEEEEEecccce---EEEEEecC-cCcc--c-CCccEEEecccchh
Confidence 4678887332 24889999999999999987889999999999864 88888873 3333 2 67999999999999
Q ss_pred EEcCeeEEEecc
Q 012401 91 KHQAELSAVFYK 102 (464)
Q Consensus 91 ~~~g~~~~~~~~ 102 (464)
.|+|.+.+...+
T Consensus 77 i~qg~LtL~~GK 88 (134)
T KOG3416|consen 77 IFQGCLTLYVGK 88 (134)
T ss_pred hhcCceEEEecC
Confidence 999987766543
No 29
>PF02765 POT1: Telomeric single stranded DNA binding POT1/CDC13; InterPro: IPR011564 This entry represents a domain that binds single stranded telomeric DNA and adopts an OB fold []. It includes the proteins POT1 and CDC13 which have been shown to regulate telomere length, replication and capping [, , ]. ; GO: 0003677 DNA binding, 0000723 telomere maintenance, 0000784 nuclear chromosome, telomeric region; PDB: 1S40_A 1KXL_A 1PH7_A 1PH9_A 1PH2_A 1OTC_A 1PHJ_A 1JB7_A 1PA6_A 1PH1_A ....
Probab=96.06 E-value=0.16 Score=45.59 Aligned_cols=97 Identities=19% Similarity=0.144 Sum_probs=68.4
Q ss_pred cccc--cccCCceEeeEEEEEEeeee------CCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCCccccc
Q 012401 159 LSLK--DISEHRYFDLVCKVFHVSYD------DSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLR 230 (464)
Q Consensus 159 ~~Lk--di~~~~f~Dlv~qVv~v~~~------~~~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~ 230 (464)
..|. ..+.++++|+++-|+..... ..+-..+|.|+|-|-+..-. .
T Consensus 2 ~~l~~~~~~~~~~vnvigVV~~~~~p~~~~t~g~D~~~tl~i~D~S~~~~~~------------~--------------- 54 (146)
T PF02765_consen 2 TPLSTAKEKFGKFVNVIGVVVDFSPPNPKKTRGTDYMCTLTITDPSLNDSNQ------------K--------------- 54 (146)
T ss_dssp CCGGGSCTTSSEEEEEEEEEEEEEEECTEEESSSCEEEEEEEEBTTCSCSSC------------C---------------
T ss_pred ccchhhhhcCCCEEEEEEEEEEccCCcceEcCCCcEEEEEEEECCCCCcccc------------c---------------
Confidence 4555 44679999999999987633 12348889999955221100 0
Q ss_pred cCCCcceEEEEEecccchhhhccCCCC-CcEEEEeCcEEEEeCcEEEEEEecC--cceEEc
Q 012401 231 NFFPVGTVLRVSTDRSYENFGRYFTAT-GKWVRIRNMSCQVSSGMWHGLLQSS--SKIRLF 288 (464)
Q Consensus 231 ~~p~~G~vl~V~~~~~~~~~~~~~~k~-G~wV~l~Nv~~k~~~g~leG~l~~~--ski~~l 288 (464)
...|.|.++.++.+. ...++. ||.|+|++++++.+.|...|..... +.+.+.
T Consensus 55 -----~~~l~v~iF~~~~~~-LP~v~~~GDii~l~r~kv~~~~~~~~~~~~~~~~ss~~vf 109 (146)
T PF02765_consen 55 -----LSGLTVNIFRPHKES-LPNVKSVGDIIRLRRVKVQSYNGKPQGLSNSTSNSSWAVF 109 (146)
T ss_dssp -----CCEEEEEEEESSHHH-SCTTCSTTHEEEEEEEEEEEETTEEEEEEECECTEEEEEE
T ss_pred -----cCCEEEEEECCCHHH-CCCCCCCCCEEEEEEEEEEEECCEEEEEecCCCcEEEEEE
Confidence 035567777666665 566776 9999999999999999888877766 677776
No 30
>PRK07217 replication factor A; Reviewed
Probab=95.90 E-value=0.14 Score=51.31 Aligned_cols=92 Identities=17% Similarity=0.248 Sum_probs=67.2
Q ss_pred CcceeehhhhhhccCCEEEEEEEEEEcCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEee
Q 012401 7 QGGIVRIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKN 86 (464)
Q Consensus 7 ~y~y~~i~d~~~~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~r 86 (464)
...-+.|+|+. ..++.|+|.|-|+....|+. ++-...- -|-|+|= -|++..+.+ +.+|.+ ..||++++++
T Consensus 69 ~~~~~kI~Di~-~~~~~VsV~aKVl~l~e~~~--~si~qvG-llgDETG---~IkfT~W~~--s~~~~l-eeGd~~rI~n 138 (311)
T PRK07217 69 GSELVNIADID-EPEQWVDVTAKVVQLWEPSS--DSIAQVG-LLGDETG---TIKFTKWAK--SDLPEL-EEGKSYLLKN 138 (311)
T ss_pred CCCceeeeecC-CCCCcEEEEEEEEEecCCCC--CceEEEE-EEEcCCc---eEEEEEccC--CCCCcc-cCCCEEEEEe
Confidence 34456788886 33567999999999988642 2222211 3566643 299999986 369999 6899999999
Q ss_pred EEEEEEcCeeEEEeccCccEEEE
Q 012401 87 VMIKKHQAELSAVFYKDSSSFAL 109 (464)
Q Consensus 87 vkv~~~~g~~~~~~~~~~ss~~l 109 (464)
+.+..|+|++++..++. |+...
T Consensus 139 a~v~ey~G~~~lnlg~~-t~I~~ 160 (311)
T PRK07217 139 VVTDEYQGRFSVKLNRT-TSIEE 160 (311)
T ss_pred EEEeeECCEEEEEeCCc-eEEEe
Confidence 99999999999888743 55553
No 31
>cd04489 ExoVII_LU_OBF ExoVII_LU_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of Escherichia coli exodeoxyribonuclease VII (ExoVII) large subunit. E. coli ExoVII is composed of two non-identical subunits. E. coli ExoVII is a single-strand-specific exonuclease which degrades ssDNA from both 3-prime and 5-prime ends. ExoVII plays a role in methyl-directed mismatch repair in vivo. ExoVII may also guard the genome from mutagenesis by removing excess ssDNA, since the build up of ssDNA would lead to SOS induction and PolIV-dependent mutagenesis.
Probab=95.20 E-value=0.23 Score=39.01 Aligned_cols=69 Identities=10% Similarity=0.093 Sum_probs=50.9
Q ss_pred EEEEEEEEEcCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEE--cCeeEEEec
Q 012401 24 VNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKH--QAELSAVFY 101 (464)
Q Consensus 24 vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvkv~~~--~g~~~~~~~ 101 (464)
+.+.|+|.+.+. |++. ++-++|.|.+- .+.+.+|.+..+........|++|.++ .+++.+ +|++++..+
T Consensus 2 ~~v~g~v~~i~~---tk~g--~~~~~L~D~~~---~i~~~~f~~~~~~~~~~l~~g~~v~v~-g~v~~~~~~~~~~l~v~ 72 (78)
T cd04489 2 VWVEGEISNLKR---PSSG--HLYFTLKDEDA---SIRCVMWRSNARRLGFPLEEGMEVLVR-GKVSFYEPRGGYQLIVE 72 (78)
T ss_pred EEEEEEEecCEE---CCCc--EEEEEEEeCCe---EEEEEEEcchhhhCCCCCCCCCEEEEE-EEEEEECCCCEEEEEEE
Confidence 458899999876 4433 99999999873 399999998677776666789988884 455545 466666654
No 32
>PF01336 tRNA_anti-codon: OB-fold nucleic acid binding domain; InterPro: IPR004365 The OB-fold (oligonucleotide/oligosaccharide-binding fold) is found in all three kingdoms and its common architecture presents a binding face that has adapted to bind different ligands. The OB-fold is a five/six-stranded closed beta-barrel formed by 70-80 amino acid residues. The strands are connected by loops of varying length which form the functional appendages of the protein. The majority of OB-fold proteins use the same face for ligand binding or as an active site. Different OB-fold proteins use this 'fold-related binding face' to, variously, bind oligosaccharides, oligonucleotides, proteins, metal ions and catalytic substrates. This entry contains OB-fold domains that bind to nucleic acids []. It includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl-tRNA synthetases (See IPR004364 from INTERPRO). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule 6.1.1 from EC. This domain is found in RecG helicase involved in DNA repair. Replication factor A is a heterotrimeric complex, that contains a subunit in this family [, ]. This domain is also found at the C terminus of bacterial DNA polymerase III alpha chain.; GO: 0003676 nucleic acid binding; PDB: 1BBU_A 1KRS_A 1BBW_A 1KRT_A 1EQR_B 1IL2_B 1C0A_A 3KFU_A 1EOV_A 1ASY_A ....
Probab=95.16 E-value=0.035 Score=42.96 Aligned_cols=68 Identities=13% Similarity=0.216 Sum_probs=52.4
Q ss_pred EEEEEEEEEcCCccccCCCceEEEEEEEeCCCCCCCeEEEEec-CCCCCCCCCCCCCCEEEEeeEEEEEEcCe-eEEEec
Q 012401 24 VNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFT-SSIDQLPRVLSPRDLILLKNVMIKKHQAE-LSAVFY 101 (464)
Q Consensus 24 vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~-~~~~~LP~v~~~GDII~l~rvkv~~~~g~-~~~~~~ 101 (464)
|.+.|.|.... ++..-.+.++|.|.|- .+.+.+|. ........+ ..||+|+++ -+++.++++ +++..+
T Consensus 1 V~v~G~V~~~~-----~~~~~~~~~~l~D~tg---~i~~~~~~~~~~~~~~~l-~~g~~v~v~-G~v~~~~~~~~~l~~~ 70 (75)
T PF01336_consen 1 VTVEGRVTSIR-----RSGGKIVFFTLEDGTG---SIQVVFFNEEYERFREKL-KEGDIVRVR-GKVKRYNGGELELIVP 70 (75)
T ss_dssp EEEEEEEEEEE-----EEETTEEEEEEEETTE---EEEEEEETHHHHHHHHTS--TTSEEEEE-EEEEEETTSSEEEEEE
T ss_pred CEEEEEEEEEE-----cCCCCEEEEEEEECCc---cEEEEEccHHhhHHhhcC-CCCeEEEEE-EEEEEECCccEEEEEC
Confidence 57889999987 2334567889999983 39999999 444555556 689999998 999999987 877664
No 33
>PRK06386 replication factor A; Reviewed
Probab=95.08 E-value=0.18 Score=51.90 Aligned_cols=87 Identities=17% Similarity=0.273 Sum_probs=67.3
Q ss_pred cceeehhhhhhccCCEEEEEEEEEEcCCcc-ccCCC-ceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEe
Q 012401 8 GGIVRIKELAMHVKHKVNLLGVVLEFSIPR-KSQGT-DYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLK 85 (464)
Q Consensus 8 y~y~~i~d~~~~~~~~vnviGVVvd~~~P~-~trG~-D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~ 85 (464)
|..++|+|+... ...|||.|-|++...+. .++|+ -...++-|-|++=. |++.+|.+ .+ ..||+|++.
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 YKLVKIRDLSLV-TPYVSVIGKITGITKKEYDSDGTSKIVYQGYIEDDTAR---VRISSFGK------PL-EDNRFVRIE 173 (358)
T ss_pred cCccEeEeccCC-CCceEEEEEEEEccCceEecCCCccEEEEEEEEcCCCe---EEEEEccc------cc-cCCCEEEEe
Confidence 456788998622 34599999999985542 23444 77888999998753 99999985 25 689999999
Q ss_pred eEEEEEEcCeeEEEeccCccE
Q 012401 86 NVMIKKHQAELSAVFYKDSSS 106 (464)
Q Consensus 86 rvkv~~~~g~~~~~~~~~~ss 106 (464)
++.++.|+|.+++..+.. |+
T Consensus 174 na~v~e~~G~~el~v~~~-t~ 193 (358)
T PRK06386 174 NARVSQYNGYIEISVGNK-SV 193 (358)
T ss_pred eeEEEccCCeEEEEeCCe-EE
Confidence 999999999999988854 44
No 34
>cd04481 RPA1_DBD_B_like RPA1_DBD_B_like: A subgroup of uncharacterized, plant OB folds with similarity to the third OB fold, the ssDNA-binding domain (DBD)-B, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-B, RPA1 contains three other OB folds: DBD-A, DBD-C, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change.
Probab=94.92 E-value=0.099 Score=44.10 Aligned_cols=82 Identities=12% Similarity=0.104 Sum_probs=57.1
Q ss_pred EEEEEEEEcCCccccC--C-CceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCC----CCCCCEEEEee-EEEEEEcCee
Q 012401 25 NLLGVVLEFSIPRKSQ--G-TDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRV----LSPRDLILLKN-VMIKKHQAEL 96 (464)
Q Consensus 25 nviGVVvd~~~P~~tr--G-~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v----~~~GDII~l~r-vkv~~~~g~~ 96 (464)
++||+|++.++..... | ..-...|+|.|.+-. .++|.+..+..+.+..- ...+=||.+-+ .+|..|+|..
T Consensus 1 DviG~i~~v~~~~~~~~~~~~~~kr~~~i~D~~~~--~l~~tlwG~~A~~f~~~~~~~~~~~~VVav~~~~rV~~~~g~~ 78 (106)
T cd04481 1 DVIGVIVDVGPLEELPPVNKPSRKLDFEIRDLSDE--RLKCTLWGEYAEEFDAKFQSAGNGEPVVAVLRFWKIKEYKGPK 78 (106)
T ss_pred CeeEEEEEecceEecccCCccceEEEEEEEeCCCC--EEEEEEEHHHHHHHHHHHHHhCCCCcEEEEEEeEEEEEEcCCc
Confidence 4899999999876543 3 477899999999953 49999998766666542 12344776655 9999999854
Q ss_pred EEEeccCccEEE
Q 012401 97 SAVFYKDSSSFA 108 (464)
Q Consensus 97 ~~~~~~~~ss~~ 108 (464)
.+....+.|.|.
T Consensus 79 ~ls~~~~~s~v~ 90 (106)
T cd04481 79 SLSNSFGASKVY 90 (106)
T ss_pred EEEcCCCceEEE
Confidence 444332434444
No 35
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=94.69 E-value=0.15 Score=46.50 Aligned_cols=58 Identities=21% Similarity=0.179 Sum_probs=43.6
Q ss_pred CceeEEEEEEEeecCCCccccccC------------------------CCCeEEEEEEEEeCCCceEEEEEecccccccc
Q 012401 346 NVRCCCIVRVVSIHPFQAEHYSSP------------------------NGSSEYTMKLTLEDPTARIHALLCGKEWVKFF 401 (464)
Q Consensus 346 ~~kfr~~VRVV~~~P~~~edf~~~------------------------~~~w~~rf~L~lED~t~ri~~~v~~~da~~f~ 401 (464)
...|.+.+.|+.+.+...-=.++| +-.|.|++.+.|.|.|+.+++.++|+.|+.||
T Consensus 15 ~~~~~v~a~I~~I~~~~~~Y~aC~~C~kkv~~~~~~~~~C~~C~~~~~~~~~ry~l~~~i~D~Tg~~~~~~F~~~ae~l~ 94 (166)
T cd04476 15 PDYFTVKATIVFIKPDNWWYPACPGCNKKVVEEGNGTYRCEKCNKSVPNPEYRYILSLNVADHTGEAWLTLFDEVAEQIF 94 (166)
T ss_pred CCEEEEEEEEEEEcCCCeEEccccccCcccEeCCCCcEECCCCCCcCCCccEEEEEEEEEEeCCCCEEEEEehHHHHHHh
Confidence 456777777777776632211111 23678999999999999999999999999999
Q ss_pred CC
Q 012401 402 GG 403 (464)
Q Consensus 402 ~~ 403 (464)
|.
T Consensus 95 G~ 96 (166)
T cd04476 95 GK 96 (166)
T ss_pred CC
Confidence 85
No 36
>cd04475 RPA1_DBD_B RPA1_DBD_B: A subfamily of OB folds corresponding to the third OB fold, the ssDNA-binding domain (DBD)-B, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-B, RPA1 contains three other OB folds: DBD-A, DBD-C, and RPA1N. The major DNA binding activity of human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. Although ScRPA and the hRPA have similar ssDNA-binding properties, they differ functiona
Probab=94.43 E-value=0.42 Score=39.77 Aligned_cols=61 Identities=11% Similarity=-0.021 Sum_probs=41.9
Q ss_pred ceEEEEEecccchhhhccCCCCCcEEEEeCcEEEEeCcEEEEEEecCcceEEcCCCChhHHHHHH
Q 012401 236 GTVLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDNDNVVWDYMR 300 (464)
Q Consensus 236 G~vl~V~~~~~~~~~~~~~~k~G~wV~l~Nv~~k~~~g~leG~l~~~ski~~l~~~d~~v~~r~r 300 (464)
|..+.|++|..++...... .|+.+.|.|++++.++|. .......|+|. ++++.+++.+.+.
T Consensus 38 ~~~i~vtLWg~~a~~~~~~--~~~vv~~~~~~i~~~~~~-~l~~~~~s~i~-~np~~~e~~~l~~ 98 (101)
T cd04475 38 GHSVELTLWGEQAELFDGS--ENPVIAIKGVKVSEFNGK-SLSTGSSSTII-INPDIPEAHKLRG 98 (101)
T ss_pred CCEEEEEEEHHHhhhcccC--CCCEEEEEeeEEEecCCe-EEeecCceeEE-ECCCcHHHHHHHH
Confidence 3467899999888763332 399999999999886653 34444556774 4445677766654
No 37
>PF15489 CTC1: CST, telomere maintenance, complex subunit CTC1
Probab=94.21 E-value=0.44 Score=54.96 Aligned_cols=145 Identities=17% Similarity=0.147 Sum_probs=103.2
Q ss_pred EEEEEecccchhhhccCCCCCcEEEEeCcEEEE-eCcEEEEEEecCcceEEcCCCChhHHHHHHHHHHHhCCCCCCCCcc
Q 012401 238 VLRVSTDRSYENFGRYFTATGKWVRIRNMSCQV-SSGMWHGLLQSSSKIRLFSDNDNVVWDYMRFRERISGGHGHMPIWT 316 (464)
Q Consensus 238 vl~V~~~~~~~~~~~~~~k~G~wV~l~Nv~~k~-~~g~leG~l~~~ski~~l~~~d~~v~~r~ry~~r~~~~~~~~~~~~ 316 (464)
.|.|-++.+|.-+ --.+-||.-|.|.++..|+ .+|+.+..+.++|.|++++-...
T Consensus 888 ~ldVYi~~~h~p~-plGLLPGA~V~f~~lerkVSRs~nVYC~~~psS~VtVlS~p~~----------------------- 943 (1144)
T PF15489_consen 888 HLDVYIEDPHLPY-PLGLLPGARVLFSQLERKVSRSHNVYCCFLPSSSVTVLSFPPE----------------------- 943 (1144)
T ss_pred eEEEEecCCCCCC-cccccCCceeeeehhhhhhhccCcEEEEEcCCceEEEEecCcc-----------------------
Confidence 4667777777766 5668899999999999999 78999999999999998764110
Q ss_pred CCCCCCCcccccCCCccccHHHHhhCCCCCceeEEEEEEEeecCCCcccccc---C-----------------CCCeEEE
Q 012401 317 DPSSQFLTEVDWVNVASVTLMKIATQLQGNVRCCCIVRVVSIHPFQAEHYSS---P-----------------NGSSEYT 376 (464)
Q Consensus 317 ~~~~~~~t~~~~~~~p~ttL~dIL~~p~v~~kfr~~VRVV~~~P~~~edf~~---~-----------------~~~w~~r 376 (464)
| ..-..+|...|.+.+.....+.+.++.++||.++==.+.=-|. + .+.....
T Consensus 944 -------t-~~~~~~P~~~L~~~~~~~~~~~~a~~~chVV~V~~l~L~WvCa~C~si~~qg~Csr~~p~C~s~~sV~qA~ 1015 (1144)
T PF15489_consen 944 -------T-NVSPPLPHIYLAELLQGSQSPFQARVSCHVVSVLSLQLQWVCAHCGSICPQGRCSRQSPPCPSQTSVFQAS 1015 (1144)
T ss_pred -------c-CCCCCCCeEEehhhhCCCCCCceEEEEEEEEEEEEEEeeehhhhccCcccCCcCCCCCCCCCCCcceeeEE
Confidence 1 0112346666777776655666888888999887655543332 0 1334466
Q ss_pred EEEEEeCCCceEEEEEeccccccccCCCCCh--HHHHHHHH
Q 012401 377 MKLTLEDPTARIHALLCGKEWVKFFGGSPPP--DVLTKKIK 415 (464)
Q Consensus 377 f~L~lED~t~ri~~~v~~~da~~f~~~~~~~--~~L~~kl~ 415 (464)
-+++|||.||+-+|.+.|+....+++ ++.. +.|.++..
T Consensus 1016 ar~~vEDGTaeA~v~~~~~~V~~lLg-L~~~eW~~L~~~v~ 1055 (1144)
T PF15489_consen 1016 ARLLVEDGTAEAVVWCRGHHVAALLG-LSPSEWESLLEMVR 1055 (1144)
T ss_pred EEEEEecCCeeEEEEECCcHHHHHhC-CCHHHHHHHHHHhh
Confidence 79999999999999999987778875 4332 55554443
No 38
>cd04474 RPA1_DBD_A RPA1_DBD_A: A subfamily of OB folds corresponding to the second OB fold, the ssDNA-binding domain (DBD)-A, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change. Although ScRPA and the hRPA have similar ssDNA-binding properties, they differ funct
Probab=94.15 E-value=0.16 Score=42.72 Aligned_cols=83 Identities=14% Similarity=0.175 Sum_probs=61.3
Q ss_pred ehhhhhhccCCEEEEEEEEEEcCCccccC---CCceEEEEEEEeCCCCCCCeEEEEecCCCC-CCCCCCCCCCEEEEeeE
Q 012401 12 RIKELAMHVKHKVNLLGVVLEFSIPRKSQ---GTDYVCVLKIVDDSQQSPELLVNIFTSSID-QLPRVLSPRDLILLKNV 87 (464)
Q Consensus 12 ~i~d~~~~~~~~vnviGVVvd~~~P~~tr---G~D~~~tl~I~D~S~~~~gl~v~iF~~~~~-~LP~v~~~GDII~l~rv 87 (464)
+|+++.... ..+.+.|-|+..+.++.-+ |....++|.|.|+.-. .|.+.+|.+..+ .-|.+ ..|+|+.+.+.
T Consensus 1 pI~~L~p~~-~~~~I~~rV~~k~~~~~f~~~~~~g~~~~~~l~De~~~--~I~~t~~~~~~~~f~~~l-~eG~vy~i~~~ 76 (104)
T cd04474 1 PISSLNPYQ-NKWTIKARVTNKSDIRTWSNARGEGKLFSFDLLDEDGG--EIRATFFNDAVDKFYDLL-EVGKVYYISKG 76 (104)
T ss_pred ChhHccCCC-CcEEEEEEEeeccccccccCCCCCcEEEEEEEEECCCC--EEEEEEehHHHHHhhccc-ccccEEEEecc
Confidence 466776332 3588999999887766433 3467889999999643 499999986443 45666 69999999999
Q ss_pred EEEEEcCeeEE
Q 012401 88 MIKKHQAELSA 98 (464)
Q Consensus 88 kv~~~~g~~~~ 98 (464)
+|+.-++...-
T Consensus 77 ~V~~a~~~y~~ 87 (104)
T cd04474 77 SVKVANKKFNT 87 (104)
T ss_pred EEeeccccCCC
Confidence 99988765443
No 39
>cd04478 RPA2_DBD_D RPA2_DBD_D: A subfamily of OB folds corresponding to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle dependent manner in response to DNA dam
Probab=94.00 E-value=0.52 Score=38.59 Aligned_cols=67 Identities=18% Similarity=0.198 Sum_probs=51.4
Q ss_pred EEEEEEEEEcCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCC----CCCCCCCCCCEEEEeeEEEEEEcCeeEEE
Q 012401 24 VNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSID----QLPRVLSPRDLILLKNVMIKKHQAELSAV 99 (464)
Q Consensus 24 vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~----~LP~v~~~GDII~l~rvkv~~~~g~~~~~ 99 (464)
|.++|+|.+... + +=..+++|-|.|= .|.+.++....+ ..+.+ ..|++|++ .-+++.|+|+.++.
T Consensus 2 v~~vG~V~~~~~----~--~~~~~~tL~D~TG---~I~~~~W~~~~~~~~~~~~~~-~~g~~v~v-~G~v~~~~g~~ql~ 70 (95)
T cd04478 2 VTLVGVVRNVEE----Q--STNITYTIDDGTG---TIEVRQWLDDDNDDSSEVEPI-EEGTYVRV-FGNLKSFQGKKSIM 70 (95)
T ss_pred EEEEEEEEeeeE----c--ccEEEEEEECCCC---cEEEEEeCCCCCccccccccc-ccCCEEEE-EEEEcccCCeeEEE
Confidence 779999999764 1 2348889999874 399999987653 56666 79999998 56779999998766
Q ss_pred ec
Q 012401 100 FY 101 (464)
Q Consensus 100 ~~ 101 (464)
..
T Consensus 71 i~ 72 (95)
T cd04478 71 AF 72 (95)
T ss_pred EE
Confidence 43
No 40
>cd04491 SoSSB_OBF SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus solfataricus single-stranded (ss) DNA-binding protein (SSoSSB). SSoSSB has a single OB fold, and it physically and functionally interacts with RNA polymerase. In vitro, SSoSSB can substitute for the basal transcription factor TBP, stimulating transcription from promoters under conditions in which TBP is limiting, and supporting transcription when TBP is absent. SSoSSB selectively melts the duplex DNA of promoter sequences. It also relieves transcriptional repression by the chromatin Alba. In addition, SSoSSB activates reverse gyrase activity, which involves DNA binding, DNA cleavage, strand passage and ligation. SSoSSB stimulates all these steps in the presence of the chromatin protein, Sul7d. SSoSSB antagonizes the inhibitory effect of Sul7d on reverse gyrase supercoiling activity. It also physically and functionally interacts with Mini-chromosome Maintenance (MCM), stimulating
Probab=93.61 E-value=0.21 Score=39.91 Aligned_cols=46 Identities=20% Similarity=0.110 Sum_probs=39.8
Q ss_pred EEEEEecccchhhhccCCCCCcEEEEeCcEEEEeCcEEEEEEecCcceE
Q 012401 238 VLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIR 286 (464)
Q Consensus 238 vl~V~~~~~~~~~~~~~~k~G~wV~l~Nv~~k~~~g~leG~l~~~ski~ 286 (464)
.+++++|+..+ ...+++|++|++.|..++...|.++..+...+.|.
T Consensus 35 ~i~~~~W~~~~---~~~~~~G~vv~i~~~~v~~~~g~~ql~i~~~~~i~ 80 (82)
T cd04491 35 TIRFTLWDEKA---ADDLEPGDVVRIENAYVREFNGRLELSVGKNSEIE 80 (82)
T ss_pred EEEEEEECchh---cccCCCCCEEEEEeEEEEecCCcEEEEeCCceEEE
Confidence 67999999776 56799999999999999998899988888877764
No 41
>PRK13480 3'-5' exoribonuclease YhaM; Provisional
Probab=93.29 E-value=1.4 Score=44.71 Aligned_cols=82 Identities=15% Similarity=0.140 Sum_probs=63.5
Q ss_pred ehhhhhhccCCEEEEEEEEEEcCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEE
Q 012401 12 RIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKK 91 (464)
Q Consensus 12 ~i~d~~~~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvkv~~ 91 (464)
.|+++. .|+.|+.+.+|.+... +.++...=...+++.|.|=. |..+++....+....+ ..||||.+. -++..
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 6888999999999876 34553344779999998653 9999998777777777 789999994 56678
Q ss_pred EcCeeEEEec
Q 012401 92 HQAELSAVFY 101 (464)
Q Consensus 92 ~~g~~~~~~~ 101 (464)
|+|++|+...
T Consensus 76 y~g~~Ql~i~ 85 (314)
T PRK13480 76 YRGRKQLKVN 85 (314)
T ss_pred ECCcceEEEE
Confidence 9999887654
No 42
>cd04485 DnaE_OBF DnaE_OBF: A subfamily of OB folds corresponding to the C-terminal OB-fold nucleic acid binding domain of Thermus aquaticus and Escherichia coli type C replicative DNA polymerase III alpha subunit (DnaE). The DNA polymerase holoenzyme of E. coli contains two copies of this replicative polymerase, each of which copies a different DNA strand. This group also contains Bacillus subtilis DnaE. Replication in B. subtilis and Staphylococcus aureus requires two different type C polymerases, polC and DnaE, both of which are thought to be included in the DNA polymerase holoenzyme. At the B. subtilis replication fork, polC appears to be involved in leading strand synthesis and DnaE in lagging strand synthesis.
Probab=93.15 E-value=0.23 Score=38.78 Aligned_cols=71 Identities=14% Similarity=0.285 Sum_probs=49.8
Q ss_pred EEEEEEEcCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCeeEEEec
Q 012401 26 LLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAELSAVFY 101 (464)
Q Consensus 26 viGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvkv~~~~g~~~~~~~ 101 (464)
+.|+|.+... +.|+...-+..++|.|.+-. +.+.+|.+..+.+......|.++.++ -+++.|+|..+...+
T Consensus 2 i~g~v~~~~~-~~~k~g~~~~~~~l~D~tg~---~~~~~f~~~~~~~~~~l~~g~~v~v~-G~v~~~~~~~~l~~~ 72 (84)
T cd04485 2 VAGLVTSVRR-RRTKKGKRMAFVTLEDLTGS---IEVVVFPETYEKYRDLLKEDALLLVE-GKVERRDGGLRLIAE 72 (84)
T ss_pred EEEEEEEeEE-EEcCCCCEEEEEEEEeCCCe---EEEEECHHHHHHHHHHhcCCCEEEEE-EEEEecCCceEEEee
Confidence 6788888755 44554456799999998653 99999986533344434689999886 477878776665543
No 43
>cd04492 YhaM_OBF_like YhaM_OBF_like: A subfamily of OB folds similar to that found in Bacillus subtilis YhaM and Staphylococcus aureus cmp-binding factor-1 (SaCBF1). Both these proteins are 3'-to-5'exoribonucleases. YhaM requires Mn2+ or Co2+ for activity and is inactive in the presence of Mg2+. YhaM also has a Mn2+ dependent 3'-to-5'single-stranded DNA exonuclease activity. SaCBF is also a double-stranded DNA binding protein, binding specifically to cmp, the replication enhancer found in S. aureus plasmid pT181. Proteins in this group combine an N-terminal OB fold with a C-terminal HD domain. The HD domain is found in metal-dependent phosphohydrolases.
Probab=92.27 E-value=1.2 Score=34.90 Aligned_cols=68 Identities=12% Similarity=0.238 Sum_probs=49.6
Q ss_pred EEEEEEcCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCeeEEEe
Q 012401 27 LGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAELSAVF 100 (464)
Q Consensus 27 iGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvkv~~~~g~~~~~~ 100 (464)
+.+|.+++. +.|+...-+..++|-|.+-. +.+.+|.+.....+.+ ..|.+|.++ .++..++|+.+...
T Consensus 3 ~~~v~~~~~-~~tk~g~~~~~~~l~D~tg~---i~~~~f~~~~~~~~~l-~~g~~v~v~-G~v~~~~~~~~l~~ 70 (83)
T cd04492 3 FFLIKSKEL-RTAKNGKPYLALTLQDKTGE---IEAKLWDASEEDEEKF-KPGDIVHVK-GRVEEYRGRLQLKI 70 (83)
T ss_pred EEEEEEeee-ecccCCCcEEEEEEEcCCCe---EEEEEcCCChhhHhhC-CCCCEEEEE-EEEEEeCCceeEEE
Confidence 457777766 45654556899999998763 9999998655444556 689999997 67777877666554
No 44
>cd04483 hOBFC1_like hOBFC1_like: A subfamily of OB folds similar to that found in human OB fold containing protein 1 (hOBFC1). Members of this group belong to the Replication protein A subunit 2 (RPA2) family of OB folds. RPA is a nuclear ssDNA binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The OB fold domain of RPA2 has dual roles in ssDNA binding and trimerization.
Probab=91.45 E-value=1.6 Score=35.91 Aligned_cols=65 Identities=14% Similarity=0.108 Sum_probs=48.0
Q ss_pred EEEEEEEcCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCC---------------------CCCCCCCCCCCEEEE
Q 012401 26 LLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSI---------------------DQLPRVLSPRDLILL 84 (464)
Q Consensus 26 viGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~---------------------~~LP~v~~~GDII~l 84 (464)
++|+|+.... +. - ..+|+|-|.|= -|.|+++.... +..+.+ ++|++|++
T Consensus 2 ivG~V~sv~~----~~-~-~~~~tLdDgTG---~Ie~~~W~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i-~~G~vvrV 71 (92)
T cd04483 2 ILGTVVSRRE----RE-T-FYSFGVDDGTG---VVNCVCWKNLSYAEVSSRSDAARILKSALMALKQAKVL-EIGDLLRV 71 (92)
T ss_pred eEEEEEEEEe----cC-C-eEEEEEecCCc---eEEEEEEcCcCccccccccccccccccccccccccccc-CCCCEEEE
Confidence 6899998853 21 2 37788888654 28999997543 345556 79999999
Q ss_pred eeEEEEEEcCeeEEEec
Q 012401 85 KNVMIKKHQAELSAVFY 101 (464)
Q Consensus 85 ~rvkv~~~~g~~~~~~~ 101 (464)
+ -+++.|+|+.++...
T Consensus 72 ~-G~i~~frg~~ql~i~ 87 (92)
T cd04483 72 R-GSIRTYRGEREINAS 87 (92)
T ss_pred E-EEEeccCCeeEEEEE
Confidence 6 789999999887654
No 45
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=90.43 E-value=0.22 Score=44.51 Aligned_cols=32 Identities=25% Similarity=0.389 Sum_probs=29.5
Q ss_pred CCeEEEEEEEEeCCCceEEEEEeccccccccC
Q 012401 371 GSSEYTMKLTLEDPTARIHALLCGKEWVKFFG 402 (464)
Q Consensus 371 ~~w~~rf~L~lED~t~ri~~~v~~~da~~f~~ 402 (464)
-.|.|++.+.|.|.|+.+++.++|+.|+.|||
T Consensus 50 ~~~ry~l~~~i~D~tg~~~~~~F~~~a~~l~G 81 (146)
T PF08646_consen 50 PKYRYRLSLKISDGTGSIWVTLFDEEAEQLLG 81 (146)
T ss_dssp -EEEEEEEEEEEETTEEEEEEEEHHHHHHHHC
T ss_pred eeEEEEEEEEEEeCCCeEEEEEEhHHHHHHhC
Confidence 46889999999999999999999999999996
No 46
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain
Probab=86.52 E-value=6.1 Score=32.86 Aligned_cols=79 Identities=20% Similarity=0.221 Sum_probs=54.2
Q ss_pred hhhhhhcc--CCEEEEEEEEEEcCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCC-CCCCCCCEEEEeeEEE
Q 012401 13 IKELAMHV--KHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLP-RVLSPRDLILLKNVMI 89 (464)
Q Consensus 13 i~d~~~~~--~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP-~v~~~GDII~l~rvkv 89 (464)
|+++++.. -..+-|.|=|.+++.. ++| .+-|+|+|+. ..|+|.+|+.....++ ...+.||-|++ +.++
T Consensus 11 ik~~le~~~~~~~vwV~GEIs~~~~~--~~g---h~YftLkD~~---a~i~~~~~~~~~~~i~~~~l~~G~~V~v-~g~~ 81 (99)
T PF13742_consen 11 IKDLLERDPPLPNVWVEGEISNLKRH--SSG---HVYFTLKDEE---ASISCVIFRSRARRIRGFDLKDGDKVLV-RGRV 81 (99)
T ss_pred HHHHHhcCCCcCCEEEEEEEeecEEC--CCc---eEEEEEEcCC---cEEEEEEEHHHHhhCCCCCCCCCCEEEE-EEEE
Confidence 45555442 2578999999998764 233 5778899965 4499999998878887 44478997776 4555
Q ss_pred EEE--cCeeEEEe
Q 012401 90 KKH--QAELSAVF 100 (464)
Q Consensus 90 ~~~--~g~~~~~~ 100 (464)
..| .|++++..
T Consensus 82 ~~y~~~G~~sl~v 94 (99)
T PF13742_consen 82 SFYEPRGSLSLIV 94 (99)
T ss_pred EEECCCcEEEEEE
Confidence 555 44455443
No 47
>cd03524 RPA2_OBF_family RPA2_OBF_family: A family of oligonucleotide binding (OB) folds with similarity to the OB fold of the single strand (ss) DNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA contains six OB folds, which are involved in ssDNA binding and in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. This family also includes OB folds similar to those found in Escherichia coli SSB, the wedge domain of E. coli RecG (a branched-DNA-specific helicase), E. coli ssDNA specific exodeoxyribonuclease VII large subunit, Pyroco
Probab=85.22 E-value=11 Score=27.90 Aligned_cols=65 Identities=20% Similarity=0.187 Sum_probs=42.1
Q ss_pred eeEEEEEEeeeeCC--CCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCCccccccCCCcceEEEEEecccch
Q 012401 171 DLVCKVFHVSYDDS--KGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRVSTDRSYE 248 (464)
Q Consensus 171 Dlv~qVv~v~~~~~--~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~p~~G~vl~V~~~~~~~ 248 (464)
++.++|+++. ... .....+.+.|+| |..+.+.+|....
T Consensus 1 ~v~g~v~~~~-~~~~~~~~~~~~l~D~~---------------------------------------~~~i~~~~~~~~~ 40 (75)
T cd03524 1 TIVGIVVAVE-EIRTEGKVLIFTLTDGT---------------------------------------GGTIRVTLFGELA 40 (75)
T ss_pred CeEEEEEeec-ccccCCeEEEEEEEcCC---------------------------------------CCEEEEEEEchHH
Confidence 4678888887 423 356777788866 1133567777554
Q ss_pred hhhccCCCCCcEEEEeCcEEEEeCcEEE
Q 012401 249 NFGRYFTATGKWVRIRNMSCQVSSGMWH 276 (464)
Q Consensus 249 ~~~~~~~k~G~wV~l~Nv~~k~~~g~le 276 (464)
......+++|+++.+. .+++..+|.++
T Consensus 41 ~~~~~~~~~g~~v~v~-g~v~~~~~~~~ 67 (75)
T cd03524 41 EELENLLKEGQVVYIK-GKVKKFRGRLQ 67 (75)
T ss_pred HHHHhhccCCCEEEEE-EEEEecCCeEE
Confidence 4334678999999887 66665554443
No 48
>cd04488 RecG_wedge_OBF RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal (wedge) domain of Escherichia coli RecG. RecG is a branched-DNA-specific helicase, which catalyzes the interconversion of a DNA replication fork to a four-stranded (Holliday) junction in vivo and in vitro. This interconversion provides a route to repair stalled forks. The RecG monomer contains three domains. The N-terminal domain is named for its wedge structure, and may provide the specificity of RecG for binding branched-DNA structures. During the reversal of fork to Holliday junction, the wedge domain is fixed at the junction of the fork where the leading and lagging strand duplex arms meet, and is thought to promote the unwinding of the nascent leading and lagging strands. In order to form the Holliday junction, these nascent strands would be annealed, and the parental strands reannealed. The wedge domain may also be a processivity factor of RecG on these branched cha
Probab=82.65 E-value=8.9 Score=28.91 Aligned_cols=68 Identities=18% Similarity=0.273 Sum_probs=44.2
Q ss_pred EEEEEEEcCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCeeEEEe
Q 012401 26 LLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAELSAVF 100 (464)
Q Consensus 26 viGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvkv~~~~g~~~~~~ 100 (464)
+.|.|++.... +++|.. ...+++.|.+- .+.+.+|.... .+......|+.+.+. -|+..|+|+++...
T Consensus 2 i~~~V~~~~~~-~~~~~~-~~~~~~~D~~g---~i~~~~F~~~~-~~~~~~~~G~~~~v~-Gkv~~~~~~~qi~~ 69 (75)
T cd04488 2 VEGTVVSVEVV-PRRGRR-RLKVTLSDGTG---TLTLVFFNFQP-YLKKQLPPGTRVRVS-GKVKRFRGGLQIVH 69 (75)
T ss_pred EEEEEEEEEec-cCCCcc-EEEEEEEcCCC---EEEEEEECCCH-HHHhcCCCCCEEEEE-EEEeecCCeeEEeC
Confidence 56777776432 223333 78999999854 39999997322 333333689988885 56777887766554
No 49
>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=79.75 E-value=24 Score=26.65 Aligned_cols=62 Identities=18% Similarity=0.123 Sum_probs=42.8
Q ss_pred EeeEEEEEEeeeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCCccccccCCCcceEEEEEecccchh
Q 012401 170 FDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRVSTDRSYEN 249 (464)
Q Consensus 170 ~Dlv~qVv~v~~~~~~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~p~~G~vl~V~~~~~~~~ 249 (464)
+.+.+.|.++. ...+....+.+.|+|+ .+++.+|.....
T Consensus 1 V~v~G~V~~~~-~~~~~~~~~~l~D~tg----------------------------------------~i~~~~~~~~~~ 39 (75)
T PF01336_consen 1 VTVEGRVTSIR-RSGGKIVFFTLEDGTG----------------------------------------SIQVVFFNEEYE 39 (75)
T ss_dssp EEEEEEEEEEE-EEETTEEEEEEEETTE----------------------------------------EEEEEEETHHHH
T ss_pred CEEEEEEEEEE-cCCCCEEEEEEEECCc----------------------------------------cEEEEEccHHhh
Confidence 35778888885 4467788888999872 347788884444
Q ss_pred hhccCCCCCcEEEEeCcEEEEeCc
Q 012401 250 FGRYFTATGKWVRIRNMSCQVSSG 273 (464)
Q Consensus 250 ~~~~~~k~G~wV~l~Nv~~k~~~g 273 (464)
...+.+++|++|++. =.++...|
T Consensus 40 ~~~~~l~~g~~v~v~-G~v~~~~~ 62 (75)
T PF01336_consen 40 RFREKLKEGDIVRVR-GKVKRYNG 62 (75)
T ss_dssp HHHHTS-TTSEEEEE-EEEEEETT
T ss_pred HHhhcCCCCeEEEEE-EEEEEECC
Confidence 447889999999988 34444333
No 50
>cd04484 polC_OBF polC_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold nucleic acid binding domain of Bacillus subtilis type C replicative DNA polymerase III alpha subunit (polC). Replication in B. subtilis and Staphylococcus aureus requires two different polymerases, polC and DnaE. The holoenzyme is thought to include the two different polymerases. At the B. subtilis replication fork, polC appears to be involved in leading strand synthesis and DnaE in lagging strand synthesis.
Probab=78.50 E-value=18 Score=28.91 Aligned_cols=71 Identities=18% Similarity=0.256 Sum_probs=47.5
Q ss_pred EEEEEEEEEcCCccccCCCceEEEEEEEeCCCCCCCeEEEEec-CCCCCCCCCCCCCCEEEEeeE-EEEEEcCeeEE
Q 012401 24 VNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFT-SSIDQLPRVLSPRDLILLKNV-MIKKHQAELSA 98 (464)
Q Consensus 24 vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~-~~~~~LP~v~~~GDII~l~rv-kv~~~~g~~~~ 98 (464)
|-+-|-|.+... +.++......+|.|.|-+ +++.|..|. +..+.+-.+++.||-|+++.- ....|.++...
T Consensus 2 v~i~G~Vf~~e~-re~k~g~~i~~~~itD~t---~Si~~K~F~~~~~~~~~~ik~~G~~v~v~G~v~~D~f~~e~~~ 74 (82)
T cd04484 2 VVVEGEVFDLEI-RELKSGRKILTFKVTDYT---SSITVKKFLRKDEKDKEELKSKGDWVRVRGKVQYDTFSKELVL 74 (82)
T ss_pred EEEEEEEEEEEE-EEecCCCEEEEEEEEcCC---CCEEEEEeccCChhHHhhcccCCCEEEEEEEEEEccCCCceEE
Confidence 446677766643 556666889999999965 459999998 344555556228999988654 34455555443
No 51
>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=78.23 E-value=21 Score=27.90 Aligned_cols=64 Identities=11% Similarity=0.149 Sum_probs=39.8
Q ss_pred EEEEEEEcCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEE-EeeEEEEEEcCeeEEEe
Q 012401 26 LLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLIL-LKNVMIKKHQAELSAVF 100 (464)
Q Consensus 26 viGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~-l~rvkv~~~~g~~~~~~ 100 (464)
+-|.|..+.. +|.. +-|+|.|... .|.|.+|+.+...++.-...||-|. .=++.+ .+|+.|+..
T Consensus 3 v~GeVs~~~~----~~GH--vyfsLkD~~a---~i~cv~f~~~~~~~~~~l~~Gd~V~v~G~v~~--~~G~~ql~v 67 (73)
T cd04487 3 IEGEVVQIKQ----TSGP--TIFTLRDETG---TVWAAAFEEAGVRAYPEVEVGDIVRVTGEVEP--RDGQLQIEV 67 (73)
T ss_pred EEEEEecccc----CCCC--EEEEEEcCCE---EEEEEEEchhccCCcCCCCCCCEEEEEEEEec--CCeEEEEEE
Confidence 4577776652 4445 4466788543 3999999876545554447899544 444544 566666554
No 52
>PRK07373 DNA polymerase III subunit alpha; Reviewed
Probab=77.34 E-value=7.5 Score=41.45 Aligned_cols=88 Identities=16% Similarity=0.222 Sum_probs=61.6
Q ss_pred ceeehhhhhh-ccCCEEEEEEEEEEcCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeE
Q 012401 9 GIVRIKELAM-HVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNV 87 (464)
Q Consensus 9 ~y~~i~d~~~-~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rv 87 (464)
...++.++.. ..++.|.+.|+|...+. ++|+..+-++-++|-|.+-. +.+.+|.+..+..-.....|.+++++.
T Consensus 267 ~~~~~~~l~~~~~~~~v~vaG~I~~ik~-~~TKkG~~maf~~leD~tG~---ie~vvFp~~y~~~~~~l~~~~~v~v~G- 341 (449)
T PRK07373 267 SPINLSELEEQKEKTKVSAVVMLNEVKK-IVTKKGDPMAFLQLEDLSGQ---SEAVVFPKSYERISELLQVDARLIIWG- 341 (449)
T ss_pred CCcCHHHHhcccCCCEEEEEEEEEEeEe-cccCCCCEEEEEEEEECCCC---EEEEECHHHHHHHHHHhccCCEEEEEE-
Confidence 3456776642 24668999999999987 45665678999999999764 999999865555545446788888854
Q ss_pred EEEEEcCeeEEEec
Q 012401 88 MIKKHQAELSAVFY 101 (464)
Q Consensus 88 kv~~~~g~~~~~~~ 101 (464)
+++.-.++.+.+.+
T Consensus 342 ~v~~~~~~~~liv~ 355 (449)
T PRK07373 342 KVDRRDDQVQLIVE 355 (449)
T ss_pred EEEecCCeEEEEEe
Confidence 66653454555554
No 53
>cd04490 PolII_SU_OBF PolII_SU_OBF: A subfamily of OB folds corresponding to the OB fold found in Pyrococcus abyssi DNA polymerase II (PolII) small subunit. PolII is a family D DNA polymerase, having a 3-prime to 5-prime exonuclease activity. P. abyssi PolII is heterodimeric. The large subunit appears to be the polymerase, and the small subunit may be the exonuclease. The small subunit contains a calcineurin-like phosphatase superfamily domain C-terminal to this OB-fold domain.
Probab=75.49 E-value=10 Score=30.20 Aligned_cols=59 Identities=14% Similarity=0.317 Sum_probs=41.5
Q ss_pred EEEEEEEEEcCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCC--CCCCCCCCCCEEEEeeEEEEE
Q 012401 24 VNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSID--QLPRVLSPRDLILLKNVMIKK 91 (464)
Q Consensus 24 vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~--~LP~v~~~GDII~l~rvkv~~ 91 (464)
+.+.|+|.+.+ .|+.++- .++|-|.+-. +.+.+|.+..+ ..-.....|.+|.++. ++..
T Consensus 2 v~i~GiI~~v~---~TK~g~~--~~~leD~~G~---~Ev~~F~~~~~~~~~~~~l~~d~~v~v~g-~v~~ 62 (79)
T cd04490 2 VSIIGMVNDVR---STKNGHR--IVELEDTTGR---ITVLLTKDKEELFEEAEDILPDEVIGVSG-TVSK 62 (79)
T ss_pred EEEEEEEeEEE---EcCCCCE--EEEEECCCCE---EEEEEeCchhhhhhhhhhccCCCEEEEEE-EEec
Confidence 56899999999 4543333 7788887653 99999998777 6655545677777754 5543
No 54
>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=74.84 E-value=17 Score=32.47 Aligned_cols=62 Identities=18% Similarity=0.227 Sum_probs=35.9
Q ss_pred ceEeeEEEEEEeeeeCCCCe-EEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCCccccccCCCcceEEEEEeccc
Q 012401 168 RYFDLVCKVFHVSYDDSKGL-WMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRVSTDRS 246 (464)
Q Consensus 168 ~f~Dlv~qVv~v~~~~~~~~-~~L~VwDgT~~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~p~~G~vl~V~~~~~ 246 (464)
+-||+++-|+.|. . ..+. ..+|+.|.-- ..|.|.+|..
T Consensus 19 ~EvD~VG~VvsV~-~-~~~f~~~vYLsD~~~---------------------------------------Nll~Ikfw~~ 57 (143)
T PF09104_consen 19 GEVDTVGFVVSVS-K-KQGFQPLVYLSDECH---------------------------------------NLLAIKFWTG 57 (143)
T ss_dssp CEEEEEEEEEEEE----TTS--EEEEE-TTS----------------------------------------EEEEEESS-
T ss_pred cccceEEEEEEEE-e-cCCCceeEEeecCCc---------------------------------------cEEEEEeccC
Confidence 5599999999996 5 3444 4488777321 1356889998
Q ss_pred chhhhccC-CCCCcEEEEeCcEEEE
Q 012401 247 YENFGRYF-TATGKWVRIRNMSCQV 270 (464)
Q Consensus 247 ~~~~~~~~-~k~G~wV~l~Nv~~k~ 270 (464)
-..++.+. +|+|..|...|++-+.
T Consensus 58 l~~~~~eDilk~~~liA~SNLqwR~ 82 (143)
T PF09104_consen 58 LNQYGYEDILKPGSLIAASNLQWRP 82 (143)
T ss_dssp ------SS---TT-EEEEEEEEE-S
T ss_pred ccccchhhhcCcceEEEEeeeEeec
Confidence 88888765 6999999999999876
No 55
>PF09104 BRCA-2_OB3: BRCA2, oligonucleotide/oligosaccharide-binding, domain 3; InterPro: IPR015188 This domain assumes an OB fold, which consists of a highly curved five-stranded beta-sheet that closes on itself to form a beta-barrel. OB3 has a pronounced groove formed by one face of the curved sheet and is demarcated by two loops, one between beta 1 and beta 2 and another between beta 4 and beta 5, which allows for strong ssDNA binding []. ; PDB: 1IYJ_D 1MIU_A.
Probab=73.33 E-value=20 Score=32.08 Aligned_cols=63 Identities=19% Similarity=0.319 Sum_probs=38.7
Q ss_pred CCEEEEEEEEEEcCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCC-CCCCCCCCCCCEEEEeeEEEE
Q 012401 21 KHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSI-DQLPRVLSPRDLILLKNVMIK 90 (464)
Q Consensus 21 ~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~-~~LP~v~~~GDII~l~rvkv~ 90 (464)
=.-|+++|+|+.. ++++++.--+-|.|.+..- +.|+++..-. -.+-.+..+|-+|-+.|+.-+
T Consensus 18 ~~EvD~VG~VvsV-----~~~~~f~~~vYLsD~~~Nl--l~Ikfw~~l~~~~~eDilk~~~liA~SNLqwR 81 (143)
T PF09104_consen 18 YGEVDTVGFVVSV-----SKKQGFQPLVYLSDECHNL--LAIKFWTGLNQYGYEDILKPGSLIAASNLQWR 81 (143)
T ss_dssp CCEEEEEEEEEEE-----E--TTS--EEEEE-TTS-E--EEEEESS-------SS---TT-EEEEEEEEE-
T ss_pred ccccceEEEEEEE-----EecCCCceeEEeecCCccE--EEEEeccCccccchhhhcCcceEEEEeeeEee
Confidence 3469999999999 4556787778899999864 8888887522 233445578999999999887
No 56
>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=72.82 E-value=8.1 Score=32.34 Aligned_cols=48 Identities=15% Similarity=0.055 Sum_probs=36.3
Q ss_pred ceEEEEEecccchhhhccCCCCCcEEEEeCcEEEEeC-------cEEEEEEecCc
Q 012401 236 GTVLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSS-------GMWHGLLQSSS 283 (464)
Q Consensus 236 G~vl~V~~~~~~~~~~~~~~k~G~wV~l~Nv~~k~~~-------g~leG~l~~~s 283 (464)
|..+++++|...+..-...+++|+++.+.|-+++... .-.|..|..++
T Consensus 46 ~~~I~~t~~~~~~~~f~~~l~eG~vy~i~~~~V~~a~~~y~~~~~~yeI~f~~~t 100 (104)
T cd04474 46 GGEIRATFFNDAVDKFYDLLEVGKVYYISKGSVKVANKKFNTLKNDYEITFNRDT 100 (104)
T ss_pred CCEEEEEEehHHHHHhhcccccccEEEEeccEEeeccccCCCCCCcEEEEECCCc
Confidence 6688999998776654678999999999999998843 23555555443
No 57
>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=71.29 E-value=47 Score=27.19 Aligned_cols=26 Identities=27% Similarity=0.362 Sum_probs=18.9
Q ss_pred eeEEEEEEeeeeCCCCeEEEEEEcCCCC
Q 012401 171 DLVCKVFHVSYDDSKGLWMLFVWDGTDV 198 (464)
Q Consensus 171 Dlv~qVv~v~~~~~~~~~~L~VwDgT~~ 198 (464)
||++.|+.+. + ......+-+=|||+.
T Consensus 1 ~ivG~V~sv~-~-~~~~~~~tLdDgTG~ 26 (92)
T cd04483 1 DILGTVVSRR-E-RETFYSFGVDDGTGV 26 (92)
T ss_pred CeEEEEEEEE-e-cCCeEEEEEecCCce
Confidence 5788898887 4 345677777788874
No 58
>PRK05673 dnaE DNA polymerase III subunit alpha; Validated
Probab=70.58 E-value=11 Score=44.72 Aligned_cols=87 Identities=14% Similarity=0.230 Sum_probs=62.3
Q ss_pred eeehhhhhh-ccCCEEEEEEEEEEcCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEE
Q 012401 10 IVRIKELAM-HVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVM 88 (464)
Q Consensus 10 y~~i~d~~~-~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvk 88 (464)
.+++.++.. ..+..|.+.|+|.+.+.+ +|+.++-++.++|-|.+-. +.+.+|.+..+..=.....|.+|.+. .+
T Consensus 965 ~~~~~~l~~~~~g~~V~v~G~I~~vk~~-~TKkG~~mafltLeD~TG~---iEvviFp~~ye~~~~~L~~g~iV~V~-Gk 1039 (1135)
T PRK05673 965 DTRLADLEPTEGGSVVTVAGLVVSVRRR-VTKRGNKMAIVTLEDLSGR---IEVMLFSEALEKYRDLLEEDRIVVVK-GQ 1039 (1135)
T ss_pred CcCHHHHhccccCceEEEEEEEEEEEec-ccCCCCeEEEEEEEeCCCc---EEEEECHHHHHHHHHHhccCCEEEEE-EE
Confidence 345666642 246779999999999875 5554567899999999764 99999986534443333679998884 47
Q ss_pred EEEEcCeeEEEec
Q 012401 89 IKKHQAELSAVFY 101 (464)
Q Consensus 89 v~~~~g~~~~~~~ 101 (464)
++...++.+++.+
T Consensus 1040 Ve~~~~~~qlii~ 1052 (1135)
T PRK05673 1040 VSFDDGGLRLTAR 1052 (1135)
T ss_pred EEecCCeEEEEEe
Confidence 7776677777665
No 59
>KOG3056 consensus Protein required for S-phase initiation or completion [Cell cycle control, cell division, chromosome partitioning]
Probab=67.76 E-value=8.5 Score=41.50 Aligned_cols=70 Identities=17% Similarity=0.217 Sum_probs=56.3
Q ss_pred EEEEEEEEEcCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCe
Q 012401 24 VNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAE 95 (464)
Q Consensus 24 vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvkv~~~~g~ 95 (464)
--++|||++-+.|+.|...+=.+.++|.|-.-. .-|.+-+|.+-.+.+=.+ ..|+||-|-|..|-..++.
T Consensus 188 Wvt~GvI~~K~~~K~t~~G~~y~iwkL~dLk~~-q~vslfLFG~a~k~~wk~-k~GtVialLNp~v~k~~~g 257 (578)
T KOG3056|consen 188 WVTMGVIVEKSDPKFTSNGNPYSIWKLTDLKDH-QTVSLFLFGKAHKRYWKI-KLGTVIALLNPEVLKDRPG 257 (578)
T ss_pred eEEEEEEeecCCcccccCCCceEEEEeeecCcc-ceeEEEEecHHHHHHhhh-ccCcEEEEeCccccCCCCC
Confidence 348999999999999853444456788887664 459999999877888888 6899999999999877654
No 60
>cd04482 RPA2_OBF_like RPA2_OBF_like: A subgroup of uncharacterized archaeal OB folds with similarity to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle depende
Probab=66.01 E-value=25 Score=28.71 Aligned_cols=60 Identities=20% Similarity=0.332 Sum_probs=37.5
Q ss_pred EEEEEEEcCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCC--CCCCCCCCCCCCEEEEeeEEEEEEc
Q 012401 26 LLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSS--IDQLPRVLSPRDLILLKNVMIKKHQ 93 (464)
Q Consensus 26 viGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~--~~~LP~v~~~GDII~l~rvkv~~~~ 93 (464)
|-|-|+.+.. .-+|.. +-|+|.|.+. .|.+.+|+++ ...+..-...||.|.+..- +..|.
T Consensus 3 v~GeVs~~~~--~~~sGH--~yFtlkD~~~---~i~cv~f~~~g~~~~~~~~l~~Gd~V~v~G~-v~~y~ 64 (91)
T cd04482 3 VTGKVVEEPR--TIEGGH--VFFKISDGTG---EIDCAAYEPTKEFRDVVRLLIPGDEVTVYGS-VRPGT 64 (91)
T ss_pred EEEEEeCCee--cCCCCC--EEEEEECCCc---EEEEEEECcccccccccCCCCCCCEEEEEEE-EecCC
Confidence 4566666543 213444 5566889763 4999999976 4455554479997777543 44444
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=65.88 E-value=26 Score=29.26 Aligned_cols=64 Identities=19% Similarity=0.245 Sum_probs=43.4
Q ss_pred EEEEEEEcCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCC-CCCCCCCCCCCEEEEeeEEEEEEcCe
Q 012401 26 LLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSI-DQLPRVLSPRDLILLKNVMIKKHQAE 95 (464)
Q Consensus 26 viGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~-~~LP~v~~~GDII~l~rvkv~~~~g~ 95 (464)
++|||+....+. +..+-.+.|.|+++.. +.|+++..-. ..+-.+-..+-.|-+.|++.+.....
T Consensus 2 ~VGvVvsV~~~~----~g~~~~vYLaDe~~nl--l~vkfw~~l~~~~~EDvvk~~~lia~SNLQwR~~s~~ 66 (100)
T cd04495 2 TVGVVISVGKPI----EGKFPAVYLADECLNL--LCVKFWSSLEQYAYEDVVKRRVLLAASNLQWRTESTS 66 (100)
T ss_pred ceEEEEEEcccc----cCccceEEEecCCcCE--EEEEEecchHHhhhhhhcccceEEEEecceEeccccC
Confidence 689999998763 4567788999999976 8888887311 22223334456677777777655443
No 62
>KOG1030 consensus Predicted Ca2+-dependent phospholipid-binding protein [General function prediction only]
Probab=65.31 E-value=13 Score=34.02 Aligned_cols=26 Identities=15% Similarity=0.332 Sum_probs=24.9
Q ss_pred CCeEEEEEEEEeCCCceEEEEEeccc
Q 012401 371 GSSEYTMKLTLEDPTARIHALLCGKE 396 (464)
Q Consensus 371 ~~w~~rf~L~lED~t~ri~~~v~~~d 396 (464)
-+|.+.|-|+|.|+..-+.+-||++|
T Consensus 51 PeWNe~ltf~v~d~~~~lkv~VyD~D 76 (168)
T KOG1030|consen 51 PEWNEELTFTVKDPNTPLKVTVYDKD 76 (168)
T ss_pred CcccceEEEEecCCCceEEEEEEeCC
Confidence 38999999999999999999999999
No 63
>PRK06920 dnaE DNA polymerase III DnaE; Reviewed
Probab=64.55 E-value=18 Score=42.92 Aligned_cols=88 Identities=10% Similarity=0.188 Sum_probs=61.2
Q ss_pred ceeehhhhhhccCCEEEEEEEEEEcCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEE
Q 012401 9 GIVRIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVM 88 (464)
Q Consensus 9 ~y~~i~d~~~~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvk 88 (464)
+.+++.++....+..|.+.|+|+..+.+ +|+..+-+.-++|-|.+-. +.+.+|.+..+..-.....|.++++. .+
T Consensus 931 ~~~~~~~l~~~~~~~v~v~g~i~~~~~~-~tk~g~~maf~~leD~tg~---~e~~vFp~~y~~~~~~l~~~~~~~v~-G~ 1005 (1107)
T PRK06920 931 EIPSLAQAMRHKKKVQRAIVYITSVKVI-RTKKGQKMAFITFCDQNDE---MEAVVFPETYIHFSDKLQEGAIVLVD-GT 1005 (1107)
T ss_pred CCcCHHHHhhcCCCEEEEEEEEEEeEee-cCCCCCeEEEEEEeeCCCc---EEEEECHHHHHHHHHHhccCCEEEEE-EE
Confidence 4456676643346689999999999874 4554567899999998653 99999986555554444678888874 46
Q ss_pred EEEEcCeeEEEec
Q 012401 89 IKKHQAELSAVFY 101 (464)
Q Consensus 89 v~~~~g~~~~~~~ 101 (464)
++.-+++.+.+.+
T Consensus 1006 v~~~~~~~~~~~~ 1018 (1107)
T PRK06920 1006 IELRNHKLQWIVN 1018 (1107)
T ss_pred EEecCCcEEEEEe
Confidence 6654555666654
No 64
>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=64.37 E-value=8 Score=33.70 Aligned_cols=34 Identities=15% Similarity=0.338 Sum_probs=27.8
Q ss_pred eEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcC
Q 012401 60 LLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQA 94 (464)
Q Consensus 60 l~v~iF~~~~~~LP~v~~~GDII~l~rvkv~~~~g 94 (464)
|.|.+|-++.+..-.+ .+||.|+|+||.++....
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 7778887777666667 689999999999987766
No 65
>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=61.29 E-value=24 Score=28.88 Aligned_cols=39 Identities=18% Similarity=0.313 Sum_probs=32.1
Q ss_pred ceEEEEEecccchhhhccCCCCCcEEEEeCcEEEEeCcE
Q 012401 236 GTVLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGM 274 (464)
Q Consensus 236 G~vl~V~~~~~~~~~~~~~~k~G~wV~l~Nv~~k~~~g~ 274 (464)
|..|+.++.......-...+++|.|..|.|..+..+.|.
T Consensus 9 G~~I~A~I~~~~~~~f~~~l~Eg~~y~i~~F~V~~~~~~ 47 (95)
T PF02721_consen 9 GDKIQATIPKELVDKFKDSLKEGSWYTISNFTVSPNSGS 47 (95)
T ss_pred CCEEEEEECHHHHHHHHhhcccCCEEEeEeEEEEeCCCc
Confidence 778899998766655578899999999999998887653
No 66
>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed
Probab=60.06 E-value=60 Score=34.35 Aligned_cols=78 Identities=15% Similarity=0.161 Sum_probs=52.0
Q ss_pred hhhhhccCCEEEEEEEEEEcCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEE-
Q 012401 14 KELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKH- 92 (464)
Q Consensus 14 ~d~~~~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvkv~~~- 92 (464)
+.+++..-..|-|.|=|..++.+ +.| .|-|+|+|... .|+|.+|+.....++.-...|+-|++ ..++..|
T Consensus 16 k~~le~~~~~v~v~gEis~~~~~--~sG---H~Yf~Lkd~~a---~i~~~~~~~~~~~~~~~~~~G~~v~v-~g~~~~y~ 86 (438)
T PRK00286 16 KSLLERDLGQVWVRGEISNFTRH--SSG---HWYFTLKDEIA---QIRCVMFKGSARRLKFKPEEGMKVLV-RGKVSLYE 86 (438)
T ss_pred HHHHHhhCCcEEEEEEeCCCeeC--CCC---eEEEEEEcCCc---EEEEEEEcChhhcCCCCCCCCCEEEE-EEEEEEEC
Confidence 33443323468889998888764 334 57788999943 49999999877888875578996666 3344444
Q ss_pred -cCeeEEEe
Q 012401 93 -QAELSAVF 100 (464)
Q Consensus 93 -~g~~~~~~ 100 (464)
.|++++..
T Consensus 87 ~~g~~ql~v 95 (438)
T PRK00286 87 PRGDYQLIV 95 (438)
T ss_pred CCCCEEEEE
Confidence 44455544
No 67
>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=58.74 E-value=65 Score=34.17 Aligned_cols=79 Identities=16% Similarity=0.254 Sum_probs=53.7
Q ss_pred hhhhhhc-cCCEEEEEEEEEEcCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEE
Q 012401 13 IKELAMH-VKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKK 91 (464)
Q Consensus 13 i~d~~~~-~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvkv~~ 91 (464)
|+.+++. .+ .|-|-|=|..++.+ +.| .+-|+|+|..- -|+|.+|+.....|+.-.+.|+=|++ ..++..
T Consensus 9 ik~~le~~~~-~v~V~GEisn~~~~--~sG---H~YFtLkD~~a---~i~~vmf~~~~~~l~f~~~~G~~V~v-~g~v~~ 78 (432)
T TIGR00237 9 IKALLEATFL-QVWIQGEISNFTQP--VSG---HWYFTLKDENA---QVRCVMFRGNNNRLKFRPQNGQQVLV-RGGISV 78 (432)
T ss_pred HHHHHHhhCC-cEEEEEEecCCeeC--CCc---eEEEEEEcCCc---EEEEEEEcChhhCCCCCCCCCCEEEE-EEEEEE
Confidence 4555543 33 68899999998854 334 57788899753 49999999877788776578996666 344444
Q ss_pred E--cCeeEEEec
Q 012401 92 H--QAELSAVFY 101 (464)
Q Consensus 92 ~--~g~~~~~~~ 101 (464)
| .|+.++...
T Consensus 79 y~~~G~~ql~v~ 90 (432)
T TIGR00237 79 YEPRGDYQIICF 90 (432)
T ss_pred ECCCCcEEEEEE
Confidence 5 444555543
No 68
>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=54.48 E-value=26 Score=29.48 Aligned_cols=53 Identities=17% Similarity=0.328 Sum_probs=38.5
Q ss_pred ceeehhhhhhccCCEEEEEEEEEE-cCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCC
Q 012401 9 GIVRIKELAMHVKHKVNLLGVVLE-FSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSS 68 (464)
Q Consensus 9 ~y~~i~d~~~~~~~~vnviGVVvd-~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~ 68 (464)
.|+||..+-. .|+ | +|.| +++| .+.+.-|+.++.|.|+-+..++|+|.+|++.
T Consensus 17 sFmPl~saD~-~gG-V----I~TdWY~~p-~~~~er~k~tv~Ild~~Lradal~V~vf~q~ 70 (103)
T PF12100_consen 17 SFMPLASADP-FGG-V----IVTDWYSPP-PGPNERFKATVYILDRALRADALRVSVFRQV 70 (103)
T ss_pred hhcchhhcCC-CCC-E----EEeccccCC-CCCCeeEEEEEEEECccccCCceEEEEEEee
Confidence 5677776642 221 2 3566 5555 3445799999999999999999999999864
No 69
>PRK07374 dnaE DNA polymerase III subunit alpha; Validated
Probab=53.60 E-value=37 Score=40.66 Aligned_cols=88 Identities=15% Similarity=0.239 Sum_probs=62.2
Q ss_pred ceeehhhhhhc-cCCEEEEEEEEEEcCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeE
Q 012401 9 GIVRIKELAMH-VKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNV 87 (464)
Q Consensus 9 ~y~~i~d~~~~-~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rv 87 (464)
..++++++... .+..|.+.|+|+..+.+ +|+..+-+.-++|-|.+-. +.+.+|.+..+..-.....|.++++. .
T Consensus 987 ~~~~~~~l~~~~~~~~v~v~g~i~~~k~~-~Tk~G~~maf~~leD~tg~---~e~vvFp~~y~~~~~~l~~~~~~~v~-g 1061 (1170)
T PRK07374 987 APISLSSLEEQPDKAKVSAIAMIPEMKQV-TTRKGDRMAILQLEDLTGS---CEAVVFPKSYERLSDHLMTDTRLLVW-A 1061 (1170)
T ss_pred CCcCHHHHhcccCCCEEEEEEEEEEeEec-ccCCCCEEEEEEEEECCCC---EEEEECHHHHHHHHHHhccCCEEEEE-E
Confidence 34566666422 46679999999999875 5555578999999999764 99999987655554544678888884 4
Q ss_pred EEEEEcCeeEEEec
Q 012401 88 MIKKHQAELSAVFY 101 (464)
Q Consensus 88 kv~~~~g~~~~~~~ 101 (464)
+++.-.++.+++.+
T Consensus 1062 ~v~~~~~~~~~~~~ 1075 (1170)
T PRK07374 1062 KVDRRDDRVQLIID 1075 (1170)
T ss_pred EEEecCCeEEEEEe
Confidence 66654455666665
No 70
>PRK05338 rplS 50S ribosomal protein L19; Provisional
Probab=53.30 E-value=33 Score=29.63 Aligned_cols=45 Identities=16% Similarity=0.235 Sum_probs=30.5
Q ss_pred CCCCCCCCCCCEEEEeeE-------EEEEEcCeeEEEeccC-ccEEEEEeCCCC
Q 012401 70 DQLPRVLSPRDLILLKNV-------MIKKHQAELSAVFYKD-SSSFALFDGNSG 115 (464)
Q Consensus 70 ~~LP~v~~~GDII~l~rv-------kv~~~~g~~~~~~~~~-~ss~~lf~~~~~ 115 (464)
.++|.+ .+||+|.++-- ++|.|.|-+.+.-+.+ .++|.|=+-..+
T Consensus 14 ~~~p~f-~~GD~V~V~~~i~eg~k~R~q~f~GvvI~~~~~G~~~tftvRki~~g 66 (116)
T PRK05338 14 KDIPEF-RPGDTVRVHVKVVEGNKERIQAFEGVVIARRGRGLNETFTVRKISYG 66 (116)
T ss_pred cCCCCc-CCCCEEEEEEEEccCCceEeccEEEEEEEEeCCCCCceEEEEEcccC
Confidence 569999 79999999642 3567777665555543 367887655444
No 71
>PF01245 Ribosomal_L19: Ribosomal protein L19; InterPro: IPR001857 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L19 is one of the proteins from the large ribosomal subunit [, ]. In Escherichia coli, L19 is known to be located at the 30S-50S ribosomal subunit interface [] and may play a role in the structure and function of the aminoacyl-tRNA binding site. It belongs to a family of ribosomal proteins, including L19 from bacteria and the chloroplasts of red algae. L19 is a protein of 120 to 130 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3HUZ_T 3V2D_T 3I8I_R 2XG2_T 2V49_T 2XUX_T 3HUX_T 3I9C_R 3V25_T 3UZ2_R ....
Probab=52.66 E-value=49 Score=28.41 Aligned_cols=42 Identities=19% Similarity=0.214 Sum_probs=28.9
Q ss_pred CCCCCCCCCCCCEEEEeeE-------EEEEEcCeeEEEeccC-ccEEEEEe
Q 012401 69 IDQLPRVLSPRDLILLKNV-------MIKKHQAELSAVFYKD-SSSFALFD 111 (464)
Q Consensus 69 ~~~LP~v~~~GDII~l~rv-------kv~~~~g~~~~~~~~~-~ss~~lf~ 111 (464)
...+|.+ .+||+|.++=. ++|.|.|-+.+.-+.+ .++|.|=+
T Consensus 13 ~~~~p~f-~~GD~v~V~~~i~e~~k~r~q~f~GvvIa~~~~g~~ssftlR~ 62 (113)
T PF01245_consen 13 KKDIPEF-RVGDTVRVTYKISEGNKERIQVFEGVVIARRRRGLNSSFTLRN 62 (113)
T ss_dssp SSSSSSS-SSSSEEEEEEEEESSSSEEEEEEEEEEEEEEBSSTSSEEEEEE
T ss_pred hcCCCCc-CCCCEEEEEEEEecCCCceeEEEEEEEEEEECCCCCeeEEEEE
Confidence 3689999 79999999764 2467777666655543 36677633
No 72
>cd04478 RPA2_DBD_D RPA2_DBD_D: A subfamily of OB folds corresponding to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle dependent manner in response to DNA dam
Probab=52.48 E-value=75 Score=25.54 Aligned_cols=26 Identities=27% Similarity=0.193 Sum_probs=20.2
Q ss_pred EeeEEEEEEeeeeCCCCeEEEEEEcCCC
Q 012401 170 FDLVCKVFHVSYDDSKGLWMLFVWDGTD 197 (464)
Q Consensus 170 ~Dlv~qVv~v~~~~~~~~~~L~VwDgT~ 197 (464)
+.+++.|.++. . .+..+.+.+-|+|+
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 46788899887 4 46788888889884
No 73
>PF15072 DUF4539: Domain of unknown function (DUF4539)
Probab=49.32 E-value=52 Score=26.80 Aligned_cols=63 Identities=22% Similarity=0.313 Sum_probs=43.6
Q ss_pred EEEEEEEEE-EcCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcC
Q 012401 23 KVNLLGVVL-EFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQA 94 (464)
Q Consensus 23 ~vnviGVVv-d~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvkv~~~~g 94 (464)
+|...+|++ .+.. .+.|. .+.+.|||=. +...+=++-.+..|....+|=+++|++|.|=.=..
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 444444444 4544 33455 6779998763 88888887666777777999999999998865443
No 74
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=49.18 E-value=72 Score=35.92 Aligned_cols=78 Identities=19% Similarity=0.196 Sum_probs=51.8
Q ss_pred ehhhhhhccCCEEEEEEEEEEcCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEE
Q 012401 12 RIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKK 91 (464)
Q Consensus 12 ~i~d~~~~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvkv~~ 91 (464)
+|+++. .|+.|.+.|.|++.....+ + --..++++.|.+- .+.+.+|.-+...+.....+|+-+.+.. |++.
T Consensus 52 ~i~~l~--~g~~vtv~g~V~~~~~~~~--~-~~~~~v~l~D~tg---~i~l~~F~~n~~~~~~~l~~G~~~~v~G-kv~~ 122 (681)
T PRK10917 52 PIAELR--PGEKVTVEGEVLSAEVVFG--K-RRRLTVTVSDGTG---NLTLRFFNFNQPYLKKQLKVGKRVAVYG-KVKR 122 (681)
T ss_pred CHHHCC--CCCEEEEEEEEEEEEEccC--C-ceEEEEEEEECCe---EEEEEEEccCcHHHHhhCCCCCEEEEEE-EEEe
Confidence 556654 6889999999999743222 2 2378888999763 3899999422335555557899888865 4444
Q ss_pred EcCeeEE
Q 012401 92 HQAELSA 98 (464)
Q Consensus 92 ~~g~~~~ 98 (464)
++|..+.
T Consensus 123 ~~~~~qm 129 (681)
T PRK10917 123 GKYGLEM 129 (681)
T ss_pred cCCeEEE
Confidence 5555444
No 75
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=47.96 E-value=82 Score=34.59 Aligned_cols=79 Identities=15% Similarity=0.348 Sum_probs=58.8
Q ss_pred eehhhhhhccCCEEEEEEEEEEcCCccccCCCceEEEEEEEeCCCCCCCeEEEEec-CCCCCCCCCCCCCCEEEEeeEEE
Q 012401 11 VRIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFT-SSIDQLPRVLSPRDLILLKNVMI 89 (464)
Q Consensus 11 ~~i~d~~~~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~-~~~~~LP~v~~~GDII~l~rvkv 89 (464)
+.|.++-+..|..|.+=|-|+..+ +|.| -.-|||.|++-. +.+.-|- .-.-.-|.| .+||||.+.. .+
T Consensus 203 ~~i~~id~~ig~tV~I~GeV~qik---qT~G---PTVFtltDetg~---i~aAAFe~aGvRAyP~I-evGdiV~ViG-~V 271 (715)
T COG1107 203 TLIDDLDEMIGKTVRIEGEVTQIK---QTSG---PTVFTLTDETGA---IWAAAFEEAGVRAYPEI-EVGDIVEVIG-EV 271 (715)
T ss_pred ccHHHHHhhcCceEEEEEEEEEEE---EcCC---CEEEEEecCCCc---eehhhhccCCcccCCCC-CCCceEEEEE-EE
Confidence 446666667899999999998863 4444 356889999764 6667775 566789999 7999999965 56
Q ss_pred EEEcCeeEEEe
Q 012401 90 KKHQAELSAVF 100 (464)
Q Consensus 90 ~~~~g~~~~~~ 100 (464)
....|++|.-.
T Consensus 272 ~~r~g~lQiE~ 282 (715)
T COG1107 272 TRRDGRLQIEI 282 (715)
T ss_pred eecCCcEEEee
Confidence 66788877543
No 76
>TIGR00643 recG ATP-dependent DNA helicase RecG.
Probab=46.50 E-value=1e+02 Score=34.43 Aligned_cols=78 Identities=18% Similarity=0.227 Sum_probs=52.0
Q ss_pred ehhhhhhccCCEEEEEEEEEEcCCccccCCCceEEEEEEEe-CCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEE
Q 012401 12 RIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVD-DSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIK 90 (464)
Q Consensus 12 ~i~d~~~~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D-~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvkv~ 90 (464)
+|+++. .|..+.+.|.|++..... .++ --..++.+.| .+ ..+.+.+|.. ..+......|+-+.+.. |+.
T Consensus 25 ~i~~~~--~g~~~~~~~~v~~~~~~~-~~~-~~~~~~~~~d~~~---~~~~~~~F~~--~~~~~~~~~g~~~~~~G-k~~ 94 (630)
T TIGR00643 25 TIGELL--PGERATIVGEVLSHCIFG-FKR-RKVLKLRLKDGGY---KKLELRFFNR--AFLKKKFKVGSKVVVYG-KVK 94 (630)
T ss_pred CHHHcC--CCCEEEEEEEEEEeEecc-CCC-CceEEEEEEECCC---CEEEEEEECC--HHHHhhCCCCCEEEEEE-EEE
Confidence 566665 788999999998742211 122 2278888999 43 3399999973 25555557899888865 556
Q ss_pred EEcCeeEEE
Q 012401 91 KHQAELSAV 99 (464)
Q Consensus 91 ~~~g~~~~~ 99 (464)
.++|+.+..
T Consensus 95 ~~~~~~~~~ 103 (630)
T TIGR00643 95 SSKFKAYLI 103 (630)
T ss_pred eeCCEEEEE
Confidence 677765543
No 77
>cd04480 RPA1_DBD_A_like RPA1_DBD_A_like: A subgroup of uncharacterized plant OB folds with similarity to the second OB fold, the ssDNA-binding domain (DBD)-A, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of RPA is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change.
Probab=45.99 E-value=37 Score=27.04 Aligned_cols=37 Identities=19% Similarity=0.333 Sum_probs=30.1
Q ss_pred ceEEEEEecccchhhhccCCCCCcEEEEeCcEEEEeC
Q 012401 236 GTVLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSS 272 (464)
Q Consensus 236 G~vl~V~~~~~~~~~~~~~~k~G~wV~l~Nv~~k~~~ 272 (464)
|..++.+++...+..-...+++|.|..|.|-.++...
T Consensus 30 G~~I~a~i~~~~~~~f~~~L~eg~vy~is~f~v~~~~ 66 (86)
T cd04480 30 GNRIHATIPKRLAAKFRPLLKEGKWYTISNFEVAPNT 66 (86)
T ss_pred CCEEEEEECHHHHHhhhhhceeCCEEEEeeEEEEcCC
Confidence 7788999988766655788999999999998876644
No 78
>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=45.02 E-value=48 Score=28.44 Aligned_cols=45 Identities=16% Similarity=0.128 Sum_probs=30.4
Q ss_pred CCCCCCCCCCCEEEEeeE-------EEEEEcCeeEEEeccC-ccEEEEEeCCCC
Q 012401 70 DQLPRVLSPRDLILLKNV-------MIKKHQAELSAVFYKD-SSSFALFDGNSG 115 (464)
Q Consensus 70 ~~LP~v~~~GDII~l~rv-------kv~~~~g~~~~~~~~~-~ss~~lf~~~~~ 115 (464)
.++|.+ .+||+|.++-- ++|.|.|-+.+.-+.+ .++|.|=+-..+
T Consensus 14 ~~ip~f-~~GD~v~V~~~i~eg~k~R~q~f~GvvI~~~~~G~~~tftvR~i~~g 66 (113)
T TIGR01024 14 KDLPDF-RVGDTVRVHVKIVEGKKERIQVFEGVVIARRGGGIGETFTVRKISYG 66 (113)
T ss_pred cCCCcc-CCCCEEEEEEEEccCCceEcccEEEEEEEEeCCCCceEEEEEEeccC
Confidence 579999 79999999642 3566777666665543 366877555444
No 79
>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=42.09 E-value=1.7e+02 Score=23.07 Aligned_cols=62 Identities=18% Similarity=0.079 Sum_probs=38.9
Q ss_pred EEEEEEcCCccccCCCceEEEEEEEeCCCC-----CCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCeeEEEec
Q 012401 27 LGVVLEFSIPRKSQGTDYVCVLKIVDDSQQ-----SPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAELSAVFY 101 (464)
Q Consensus 27 iGVVvd~~~P~~trG~D~~~tl~I~D~S~~-----~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvkv~~~~g~~~~~~~ 101 (464)
=|||+...... ... .|-|-|+.-. ++| +-+|.+. -+.+ .+||.|++. -++..|+|..++...
T Consensus 3 ~GvVTa~~~~~--~~~----GffiQd~~~d~~~~ts~g--ifV~~~~---~~~~-~~Gd~V~vt-G~v~ey~g~tql~~~ 69 (78)
T cd04486 3 EGVVTAVFSGG--GLG----GFYIQDEDGDGDPATSEG--IFVYTGS---GADV-AVGDLVRVT-GTVTEYYGLTQLTAV 69 (78)
T ss_pred EEEEEEEcCCC--CcC----EEEEEcCCCCCCCcccce--EEEecCC---CCCC-CCCCEEEEE-EEEEeeCCeEEEccC
Confidence 47777765422 112 3446666322 234 4455543 4566 789999996 899999998776654
No 80
>PRK06826 dnaE DNA polymerase III DnaE; Reviewed
Probab=41.80 E-value=64 Score=38.66 Aligned_cols=77 Identities=14% Similarity=0.230 Sum_probs=54.5
Q ss_pred cCCEEEEEEEEEEcCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEE-cCeeEE
Q 012401 20 VKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKH-QAELSA 98 (464)
Q Consensus 20 ~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvkv~~~-~g~~~~ 98 (464)
.+..|.+.|+|+..+.+ +|+..+-+.-++|-|.+-. +.+.+|.+..+..-.....|.+|++ ..+++.. ++..+.
T Consensus 990 ~~~~v~v~g~i~~~~~~-~tk~G~~maf~~leD~~g~---~e~~vfp~~~~~~~~~l~~~~~~~v-~g~v~~~~~~~~~~ 1064 (1151)
T PRK06826 990 DGDKVIIGGIITEVKRK-TTRNNEMMAFLTLEDLYGT---VEVIVFPKVYEKYRSLLNEDNIVLI-KGRVSLREDEEPKL 1064 (1151)
T ss_pred CCcEEEEEEEEEEeEee-ccCCCCeEEEEEEEECCCc---EEEEECHHHHHHHHHHhccCCEEEE-EEEEEecCCCceEE
Confidence 46679999999999875 5555577899999998763 9999998654444343356888877 4566643 454666
Q ss_pred Eec
Q 012401 99 VFY 101 (464)
Q Consensus 99 ~~~ 101 (464)
+.+
T Consensus 1065 ~~~ 1067 (1151)
T PRK06826 1065 ICE 1067 (1151)
T ss_pred EEe
Confidence 554
No 81
>PRK05672 dnaE2 error-prone DNA polymerase; Validated
Probab=41.79 E-value=58 Score=38.61 Aligned_cols=86 Identities=21% Similarity=0.254 Sum_probs=57.6
Q ss_pred ceeehhhhhhc-cCCEEEEEEEEEEcCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeE
Q 012401 9 GIVRIKELAMH-VKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNV 87 (464)
Q Consensus 9 ~y~~i~d~~~~-~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rv 87 (464)
+++++.++... .+..|.+.|+|+....+...+| +.-++|-|.+-. +.+.+|.+..+..-.....|.++++. -
T Consensus 940 ~~~~~~~l~~~~~~~~v~v~g~i~~~~~~~TkkG---maf~~leD~~g~---~e~~ifp~~~~~~~~~l~~~~~~~v~-g 1012 (1046)
T PRK05672 940 GVVSAAELLDVEDGRRVRVAGVVTHRQRPGTASG---VTFLTLEDETGM---VNVVVWPGLWERQRREALGARLLLVR-G 1012 (1046)
T ss_pred cCcCHHHHhhccCCCEEEEEEEEEEEEEecCCCc---eEEEEEecCCCC---EEEEECHHHHHHHHHHhccCCEEEEE-E
Confidence 34556666442 4667999999999877533346 888899988653 99999986544443433678888884 4
Q ss_pred EEEEEcCeeEEEec
Q 012401 88 MIKKHQAELSAVFY 101 (464)
Q Consensus 88 kv~~~~g~~~~~~~ 101 (464)
+++.-+|+.+.+.+
T Consensus 1013 ~v~~~~~~~~~~~~ 1026 (1046)
T PRK05672 1013 RVQNAEGVRHLVAD 1026 (1046)
T ss_pred EEEecCCeEEEEEe
Confidence 66655555565554
No 82
>PF15072 DUF4539: Domain of unknown function (DUF4539)
Probab=41.21 E-value=25 Score=28.67 Aligned_cols=24 Identities=25% Similarity=0.320 Sum_probs=19.7
Q ss_pred EEEEEEeCCCceEEEEEecccccc
Q 012401 376 TMKLTLEDPTARIHALLCGKEWVK 399 (464)
Q Consensus 376 rf~L~lED~t~ri~~~v~~~da~~ 399 (464)
-..++|.||||+|++.|+.+--+.
T Consensus 20 D~~v~l~DpTG~i~~tiH~~v~~~ 43 (86)
T PF15072_consen 20 DAFVVLKDPTGEIRGTIHRKVLEE 43 (86)
T ss_pred CeEEEEECCCCcEEEEEeHHHHhh
Confidence 457899999999999999765444
No 83
>CHL00084 rpl19 ribosomal protein L19
Probab=40.32 E-value=68 Score=27.73 Aligned_cols=43 Identities=9% Similarity=0.122 Sum_probs=28.0
Q ss_pred CCCCCCCCCCCEEEEee-E------EEEEEcCeeEEEeccC-ccEEEEEeCC
Q 012401 70 DQLPRVLSPRDLILLKN-V------MIKKHQAELSAVFYKD-SSSFALFDGN 113 (464)
Q Consensus 70 ~~LP~v~~~GDII~l~r-v------kv~~~~g~~~~~~~~~-~ss~~lf~~~ 113 (464)
.++|.+ ++||+|.++= + ++|.|.|-+.+.-+.+ .++|.|=+-.
T Consensus 18 ~~~p~f-~~GDtV~V~~~i~eg~k~R~q~F~GvvI~~r~~G~~~tftvRki~ 68 (117)
T CHL00084 18 KNLPKI-RVGDTVKVGVLIQEGNKERVQFYEGTVIAKKNSGLNTTITVRKVF 68 (117)
T ss_pred cCCCcc-CCCCEEEEEEEEecCCeeEeceEEEEEEEEeCCCCCeeEEEEEec
Confidence 479999 7999999965 2 3566777655554433 3567764433
No 84
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=35.79 E-value=1.2e+02 Score=37.23 Aligned_cols=85 Identities=16% Similarity=0.305 Sum_probs=60.3
Q ss_pred cceeehhhhhhccCCEEEEEEEEEEcCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCC---CCCCCCCCCCCEEEE
Q 012401 8 GGIVRIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSI---DQLPRVLSPRDLILL 84 (464)
Q Consensus 8 y~y~~i~d~~~~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~---~~LP~v~~~GDII~l 84 (464)
+..++|+++... ...|-+-|-|.+... +.+++.-...+|.|+|-+ +++.|+.|.++. +.+-.+ +.||-|++
T Consensus 224 ~~~~~~~~i~~~-~~~v~i~G~if~~e~-~~~k~~~~~~~~~~td~~---~s~~~k~f~~~~~~~~~~~~~-~~g~~v~~ 297 (1437)
T PRK00448 224 EEITPMKEINEE-ERRVVVEGYVFKVEI-KELKSGRHILTFKITDYT---SSIIVKKFSRDKEDLKKFDEI-KKGDWVKV 297 (1437)
T ss_pred cCcccHHHhhcc-CCeEEEEEEEEEEEE-EeccCCCEEEEEEEEcCC---CCEEEEEEecCcchhHHHhcC-CCCCEEEE
Confidence 467788888743 347889999988755 556655789999999975 459999998543 345556 68999888
Q ss_pred eeE-EEEEEcCeeEE
Q 012401 85 KNV-MIKKHQAELSA 98 (464)
Q Consensus 85 ~rv-kv~~~~g~~~~ 98 (464)
+.- ....|.++...
T Consensus 298 ~g~~~~d~~~~~~~~ 312 (1437)
T PRK00448 298 RGSVQNDTFTRDLVM 312 (1437)
T ss_pred EEEEeccCCCCceEE
Confidence 653 33456665443
No 85
>PF14535 AMP-binding_C_2: AMP-binding enzyme C-terminal domain; PDB: 2Y27_A 2Y4N_A 3QOV_B 3S89_D 3LAX_A 2Y4O_B.
Probab=35.14 E-value=26 Score=28.70 Aligned_cols=63 Identities=21% Similarity=0.269 Sum_probs=41.7
Q ss_pred EeecCCCccccccCC-C-CeEEEEEEEEeCCCceEEEEEeccccccccCCCCC----hHHHHHHHHHHcCC
Q 012401 356 VSIHPFQAEHYSSPN-G-SSEYTMKLTLEDPTARIHALLCGKEWVKFFGGSPP----PDVLTKKIKMLLGM 420 (464)
Q Consensus 356 V~~~P~~~edf~~~~-~-~w~~rf~L~lED~t~ri~~~v~~~da~~f~~~~~~----~~~L~~kl~~L~G~ 420 (464)
|.+||.++|+-.... + .=+|++.+.=++...+|.+.|--.+ .+..+... .+.|++++..-+|.
T Consensus 2 vnvfP~~Ie~vl~~~~~~~~~y~i~v~~~~~~D~l~v~vE~~~--~~~~~~~~~~~l~~~i~~~lk~~lgv 70 (96)
T PF14535_consen 2 VNVFPSQIEEVLREFPEVSPEYQIVVTREGGLDELTVRVELRP--GFSDDAEDLEALAERIAERLKERLGV 70 (96)
T ss_dssp EEE-HHHHHHHHCTSTTEEEEEEEEEEEETTEEEEEEEEEEST--TCCTTHHHHHHHHHHHHHHHHHHHSS
T ss_pred cEECHHHHHHHHHhCcCCCCcEEEEEEcCCCCcEEEEEEEECC--ccCcchHHHHHHHHHHHHHHHhhcCc
Confidence 578999999876642 1 2268888888899999999887766 22221111 35667777777775
No 86
>KOG2708 consensus Predicted metalloprotease with chaperone activity (RNAse H/HSP70 fold) [Posttranslational modification, protein turnover, chaperones]
Probab=34.85 E-value=22 Score=34.34 Aligned_cols=48 Identities=21% Similarity=0.288 Sum_probs=28.8
Q ss_pred HHHHHHHHHHcCCCCCC---------CCC-CCCccCCcceeEeeeeeeecCCc-------eEEEEEeeeEEc
Q 012401 408 DVLTKKIKMLLGMPEHE---------DGN-DDMVRNPPWIKCFLHLKESDGGR-------NRVYYIRWTKLV 462 (464)
Q Consensus 408 ~~L~~kl~~L~G~~e~~---------~~~-~~~~~~~pw~~CCi~sY~v~~~~-------~r~f~~F~T~i~ 462 (464)
+..-+-+..||..+--. .|. -+...||- =-||.+++ ++||||||-+|-
T Consensus 90 aivaRtlsllw~kPlv~VNHCigHIEMGR~iTgA~nPv-------vLYvSGGNTQvIAYse~rYrIFGETlD 154 (336)
T KOG2708|consen 90 AIVARTLSLLWNKPLVGVNHCIGHIEMGREITGAQNPV-------VLYVSGGNTQVIAYSEKRYRIFGETLD 154 (336)
T ss_pred HHHHHHHHHHhCCCcccchhhhhhhhhcceeccCCCCE-------EEEEeCCceEEEEEccceeeeecceeh
Confidence 45556788888643210 010 12335544 24677766 999999999873
No 87
>cd04490 PolII_SU_OBF PolII_SU_OBF: A subfamily of OB folds corresponding to the OB fold found in Pyrococcus abyssi DNA polymerase II (PolII) small subunit. PolII is a family D DNA polymerase, having a 3-prime to 5-prime exonuclease activity. P. abyssi PolII is heterodimeric. The large subunit appears to be the polymerase, and the small subunit may be the exonuclease. The small subunit contains a calcineurin-like phosphatase superfamily domain C-terminal to this OB-fold domain.
Probab=34.78 E-value=42 Score=26.60 Aligned_cols=21 Identities=38% Similarity=0.405 Sum_probs=19.6
Q ss_pred EEEEeCCCceEEEEEeccccc
Q 012401 378 KLTLEDPTARIHALLCGKEWV 398 (464)
Q Consensus 378 ~L~lED~t~ri~~~v~~~da~ 398 (464)
.++|||.++++.+.++.+..+
T Consensus 20 ~~~leD~~G~~Ev~~F~~~~~ 40 (79)
T cd04490 20 IVELEDTTGRITVLLTKDKEE 40 (79)
T ss_pred EEEEECCCCEEEEEEeCchhh
Confidence 899999999999999988776
No 88
>PRK07279 dnaE DNA polymerase III DnaE; Reviewed
Probab=34.52 E-value=84 Score=37.19 Aligned_cols=86 Identities=17% Similarity=0.294 Sum_probs=58.5
Q ss_pred ceeehhhhhhccCCEEEEEEEEEEcCCccccC-CCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeE
Q 012401 9 GIVRIKELAMHVKHKVNLLGVVLEFSIPRKSQ-GTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNV 87 (464)
Q Consensus 9 ~y~~i~d~~~~~~~~vnviGVVvd~~~P~~tr-G~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rv 87 (464)
+.+++.++. .+..+.+.|+|...+. .+|+ ..+-+..++|-|.+-. +.+.+|.+..+..-.....|.++++..
T Consensus 874 ~~~~~~~l~--~~~~~~~~~~i~~~~~-~~tk~~g~~maf~~leD~~g~---ie~~vFp~~y~~~~~~l~~~~~~~v~G- 946 (1034)
T PRK07279 874 PFTPISQLV--KNSEATILVQIQSIRV-IRTKTKGQQMAFLSVTDTKKK---LDVTLFPETYRQYKDELKEGKFYYLKG- 946 (1034)
T ss_pred cCccHHHHh--cCCcceEEEEEEEEEE-EEEcCCCCeEEEEEEeeCCCc---EEEEECHHHHHHHHHHhccCCEEEEEE-
Confidence 345667764 3556889999998876 4555 3467899999998764 999999865444434336788888854
Q ss_pred EEEEEcCeeEEEec
Q 012401 88 MIKKHQAELSAVFY 101 (464)
Q Consensus 88 kv~~~~g~~~~~~~ 101 (464)
+++.-.++.+.+.+
T Consensus 947 ~v~~~~~~~~l~~~ 960 (1034)
T PRK07279 947 KIQERDGRLQMVLQ 960 (1034)
T ss_pred EEEecCCeeEEEEe
Confidence 66654555665554
No 89
>KOG4792 consensus Crk family adapters [Signal transduction mechanisms]
Probab=33.29 E-value=1.1e+02 Score=29.65 Aligned_cols=61 Identities=16% Similarity=0.336 Sum_probs=39.6
Q ss_pred cccCCCcceEEEEEecccchhhhccCCCCCcEEEEeCcEEEEeCcEEEEEEecC------cceEEcCCCCh
Q 012401 229 LRNFFPVGTVLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSS------SKIRLFSDNDN 293 (464)
Q Consensus 229 ~~~~p~~G~vl~V~~~~~~~~~~~~~~k~G~wV~l~Nv~~k~~~g~leG~l~~~------ski~~l~~~d~ 293 (464)
..+-|.+..++|=.+-+...+- .-.+++||.|+.. -+..+|+|||-+.+. +.++.++..++
T Consensus 223 ~~~lPa~Arv~q~RVPnAYDkT-aL~levGdiVkVT---k~ninGqwegElnGk~G~fPfThvrf~d~~~~ 289 (293)
T KOG4792|consen 223 QQNLPAYARVIQKRVPNAYDKT-ALALEVGDIVKVT---KKNINGQWEGELNGKIGHFPFTHVRFTDVQNP 289 (293)
T ss_pred ccCCChheeeehhcCCCccChh-hhhhhcCcEEEEE---eeccCceeeeeecCccccccceeEEeeccCCc
Confidence 3456666777776655444443 2348999999643 344689999988875 56777665443
No 90
>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=32.90 E-value=2.1e+02 Score=23.97 Aligned_cols=34 Identities=18% Similarity=0.068 Sum_probs=27.3
Q ss_pred EEEEecccchhhhccC-CCCCcEEEEeCcEEEEeC
Q 012401 239 LRVSTDRSYENFGRYF-TATGKWVRIRNMSCQVSS 272 (464)
Q Consensus 239 l~V~~~~~~~~~~~~~-~k~G~wV~l~Nv~~k~~~ 272 (464)
+-|.+|..-+.++.+. +|++..+...|++.+..+
T Consensus 30 l~vkfw~~l~~~~~EDvvk~~~lia~SNLQwR~~s 64 (100)
T cd04495 30 LCVKFWSSLEQYAYEDVVKRRVLLAASNLQWRTES 64 (100)
T ss_pred EEEEEecchHHhhhhhhcccceEEEEecceEeccc
Confidence 4578888777777665 689999999999988844
No 91
>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=31.36 E-value=58 Score=24.98 Aligned_cols=24 Identities=21% Similarity=0.311 Sum_probs=20.5
Q ss_pred EEEEEEeCCCceEEEEEecccccc
Q 012401 376 TMKLTLEDPTARIHALLCGKEWVK 399 (464)
Q Consensus 376 rf~L~lED~t~ri~~~v~~~da~~ 399 (464)
+..++|+|.++++.+.++.+-...
T Consensus 18 ~~~~~L~D~~~~i~~~~f~~~~~~ 41 (78)
T cd04489 18 HLYFTLKDEDASIRCVMWRSNARR 41 (78)
T ss_pred EEEEEEEeCCeEEEEEEEcchhhh
Confidence 778999999999999999875444
No 92
>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=30.91 E-value=63 Score=24.79 Aligned_cols=21 Identities=38% Similarity=0.442 Sum_probs=18.6
Q ss_pred EEEEEEeCCCceEEEEEeccc
Q 012401 376 TMKLTLEDPTARIHALLCGKE 396 (464)
Q Consensus 376 rf~L~lED~t~ri~~~v~~~d 396 (464)
.+.++|+|.|+++.+.++++.
T Consensus 20 ~~~~~l~D~tg~i~~~~f~~~ 40 (83)
T cd04492 20 YLALTLQDKTGEIEAKLWDAS 40 (83)
T ss_pred EEEEEEEcCCCeEEEEEcCCC
Confidence 589999999999999998754
No 93
>cd04496 SSB_OBF SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs bind with high affinity to ssDNA. They bind to and protect ssDNA intermediates during DNA metabolic pathways. All bacterial and eukaryotic SSBs studied to date oligomerize to bring together four OB folds in their active state. The majority (e.g. Escherichia coli SSB) have a single OB fold per monomer, which oligomerize to form a homotetramer. However, Deinococcus and Thermus SSB proteins have two OB folds per monomer, which oligomerize to form a homodimer. Mycobacterium tuberculosis SSB varies in quaternary structure from E. coli SSB. It forms a dimer of dimers having a unique dimer interface, which lends the protein greater stability. Included in this group are OB folds similar to Escherichia coli PriB. E.coli PriB is homodimeric with each monomer having a single OB fold. It does not appear to form higher order oligomers. PriB is an essential protein for the replication restart
Probab=29.80 E-value=39 Score=27.16 Aligned_cols=28 Identities=14% Similarity=0.158 Sum_probs=23.9
Q ss_pred eEEEEEecccchhhhccCCCCCcEEEEe
Q 012401 237 TVLRVSTDRSYENFGRYFTATGKWVRIR 264 (464)
Q Consensus 237 ~vl~V~~~~~~~~~~~~~~k~G~wV~l~ 264 (464)
..++|.+|...++.+.+.++.|++|.+.
T Consensus 44 ~~~~v~~~g~~a~~~~~~~~kG~~V~v~ 71 (100)
T cd04496 44 DWIRVVAFGKLAENAAKYLKKGDLVYVE 71 (100)
T ss_pred EEEEEEEEhHHHHHHHHHhCCCCEEEEE
Confidence 4679999999888888899999999643
No 94
>PRK13254 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=29.61 E-value=3.5e+02 Score=24.31 Aligned_cols=66 Identities=17% Similarity=0.197 Sum_probs=46.4
Q ss_pred eeehhhhhhc---cCCEEEEEEEEEEcCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEe
Q 012401 10 IVRIKELAMH---VKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLK 85 (464)
Q Consensus 10 y~~i~d~~~~---~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~ 85 (464)
|.+.+++... .+..+.+-|.|++=+.- ++.+-..+|.|.|... .+.|.+-. .+|...+.|.-|.+.
T Consensus 37 f~tpse~~~~~~~~g~~vrvgG~V~~gSi~---~~~~~~~~F~ltD~~~---~i~V~Y~G----~lPd~F~eg~~VVv~ 105 (148)
T PRK13254 37 FYTPSEVAEGEAPAGRRFRLGGLVEKGSVQ---RGDGLTVRFVVTDGNA---TVPVVYTG----ILPDLFREGQGVVAE 105 (148)
T ss_pred eeCHHHHhcCCccCCCeEEEeEEEecCcEE---eCCCCEEEEEEEeCCe---EEEEEECC----CCCccccCCCEEEEE
Confidence 6777777663 47789999999965442 2256678999999843 26665543 489877888866653
No 95
>COG2049 DUR1 Allophanate hydrolase subunit 1 [Amino acid transport and metabolism]
Probab=29.39 E-value=26 Score=33.72 Aligned_cols=39 Identities=10% Similarity=0.033 Sum_probs=27.5
Q ss_pred ccCCCcceEEEEEecccchhhhccCCCCCcEEEEeCcEEEE
Q 012401 230 RNFFPVGTVLRVSTDRSYENFGRYFTATGKWVRIRNMSCQV 270 (464)
Q Consensus 230 ~~~p~~G~vl~V~~~~~~~~~~~~~~k~G~wV~l~Nv~~k~ 270 (464)
--|-.+|+|- +.+|++..+. --.+++||||||+++..+.
T Consensus 177 GGWqlIGrTp-~~lfdp~~~~-p~ll~~Gd~VrF~~i~~~e 215 (223)
T COG2049 177 GGWQLIGRTP-LPLFDPDREP-PALLRPGDQVRFVPIKEEE 215 (223)
T ss_pred CceeEecccc-ccccCCCCCC-CeeccCCCEEEEEecCccc
Confidence 3466778663 3566666654 4579999999999987544
No 96
>COG1599 RFA1 Single-stranded DNA-binding replication protein A (RPA), large (70 kD) subunit and related ssDNA-binding proteins [DNA replication, recombination, and repair]
Probab=28.09 E-value=1.9e+02 Score=30.35 Aligned_cols=78 Identities=17% Similarity=0.230 Sum_probs=56.1
Q ss_pred CCEEEEEEEEEEcCCcc--ccC-CC-ceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCee
Q 012401 21 KHKVNLLGVVLEFSIPR--KSQ-GT-DYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAEL 96 (464)
Q Consensus 21 ~~~vnviGVVvd~~~P~--~tr-G~-D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvkv~~~~g~~ 96 (464)
.+.+|+.|-|.++..++ +++ |. .=..+..+.|.+-. +... +..+...+++. ..||++.+.+..+..|+|.+
T Consensus 59 ~~~~~v~~~V~~~~e~~~~~~k~g~~~~l~~~~v~Detg~---v~~~-~~~~~~a~~~~-e~Gdv~~i~~~~~~~~~~~~ 133 (407)
T COG1599 59 SSRVNVTGRVLSIGEKKTFDRKRGAEGKLAEVLVGDETGS---VKTV-TLWNIAALEKL-EPGDVIRIRNAYTSLYRGGK 133 (407)
T ss_pred hccccEEEEECccccceeeecccccccceEEEEEecCCCC---EEEE-eeccccccccC-CccceEEecCcccccccCce
Confidence 45799999999998766 443 44 33445557777653 3332 55555666677 68999999999999999999
Q ss_pred EEEeccC
Q 012401 97 SAVFYKD 103 (464)
Q Consensus 97 ~~~~~~~ 103 (464)
++..+..
T Consensus 134 ~~~~~~~ 140 (407)
T COG1599 134 RLSVGRV 140 (407)
T ss_pred eeecccc
Confidence 8887754
No 97
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=27.20 E-value=2.9e+02 Score=31.00 Aligned_cols=80 Identities=18% Similarity=0.181 Sum_probs=57.4
Q ss_pred hhhhhhccCCEEEEEEEEEEcCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEE
Q 012401 13 IKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKH 92 (464)
Q Consensus 13 i~d~~~~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvkv~~~ 92 (464)
|.++. .|..|.+.|.|..+..+. .+..-..++++.|.+. -+++.+|..+. .+..-..+|--+.+. =|++.+
T Consensus 54 i~~~~--~g~~vti~g~V~~~~~~~--~~~~~~l~v~~~d~~~---~l~l~fFn~~~-~l~~~~~~G~~v~v~-Gk~~~~ 124 (677)
T COG1200 54 IAEAR--PGEIVTIEGTVLSHEKFP--FGKRKLLKVTLSDGTG---VLTLVFFNFPA-YLKKKLKVGERVIVY-GKVKRF 124 (677)
T ss_pred hhhcC--CCceEEEEEEEEeeeccC--CCCCceEEEEEecCcE---EEEEEEECccH-HHHhhCCCCCEEEEE-EEEeec
Confidence 44444 678899999999876543 5567788999999433 39999998653 566655789988874 467778
Q ss_pred cCeeEEEec
Q 012401 93 QAELSAVFY 101 (464)
Q Consensus 93 ~g~~~~~~~ 101 (464)
++..+....
T Consensus 125 ~~~~~~~hp 133 (677)
T COG1200 125 KGGLQITHP 133 (677)
T ss_pred cCceEEEcc
Confidence 777665543
No 98
>COG1570 XseA Exonuclease VII, large subunit [DNA replication, recombination, and repair]
Probab=26.51 E-value=5.8e+02 Score=27.25 Aligned_cols=70 Identities=17% Similarity=0.208 Sum_probs=49.8
Q ss_pred CEEEEEEEEEEcCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCe--eEEE
Q 012401 22 HKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAE--LSAV 99 (464)
Q Consensus 22 ~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvkv~~~~g~--~~~~ 99 (464)
+.|=|-|=|..++.| ..| ..-|+|.|+.-. |.|.+|+.+...|....+.|+-|+++ -+|+.|-++ .|.+
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 357777877777754 233 667889999553 99999998888888766889988773 466666443 4444
Q ss_pred e
Q 012401 100 F 100 (464)
Q Consensus 100 ~ 100 (464)
.
T Consensus 95 ~ 95 (440)
T COG1570 95 A 95 (440)
T ss_pred E
Confidence 3
No 99
>PF15489 CTC1: CST, telomere maintenance, complex subunit CTC1
Probab=25.95 E-value=1.2e+03 Score=28.00 Aligned_cols=71 Identities=21% Similarity=0.277 Sum_probs=47.5
Q ss_pred cCCEEEEEEEEEEcCCccccCCCceE-EEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCe
Q 012401 20 VKHKVNLLGVVLEFSIPRKSQGTDYV-CVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAE 95 (464)
Q Consensus 20 ~~~~vnviGVVvd~~~P~~trG~D~~-~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvkv~~~~g~ 95 (464)
.+..+||.|.|+..++-.+++|+-|. +++. |. ...++|.+=-+..-.-=....+|+-..|.+++|...+|.
T Consensus 164 ~~~~~~v~G~v~~ls~l~~~~~k~fF~l~L~--~~---~~~v~viVq~pa~l~Wh~~L~~G~~yvlT~Lrvs~irg~ 235 (1144)
T PF15489_consen 164 RGRQLNVAGKVVRLSALVKSHGKTFFILSLG--DA---GSHVPVIVQEPAQLVWHRALRPGRAYVLTSLRVSKIRGH 235 (1144)
T ss_pred ccCceeeeeEEEEeeceEEEcceEEEEEEeC--CC---CceeEEEEEecchhhhhhhcccCCeEEEeeeEEEEecCc
Confidence 46679999999999999899887554 4444 22 223553322222111123347999999999999988874
No 100
>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=25.93 E-value=1.4e+02 Score=24.79 Aligned_cols=63 Identities=13% Similarity=-0.066 Sum_probs=37.1
Q ss_pred ceEEEEEecccchhhhccC----CCCCcEEEE-eCcEEEEeCcE-EEEEEecCcceEEcCCCChhHHHHH
Q 012401 236 GTVLRVSTDRSYENFGRYF----TATGKWVRI-RNMSCQVSSGM-WHGLLQSSSKIRLFSDNDNVVWDYM 299 (464)
Q Consensus 236 G~vl~V~~~~~~~~~~~~~----~k~G~wV~l-~Nv~~k~~~g~-leG~l~~~ski~~l~~~d~~v~~r~ 299 (464)
|..|.+++|..+|...... -+.+-.|.+ +..+++...|. .-......|++ +++++-+++...+
T Consensus 34 ~~~l~~tlwG~~A~~f~~~~~~~~~~~~VVav~~~~rV~~~~g~~~ls~~~~~s~v-~inp~ipe~~~~~ 102 (106)
T cd04481 34 DERLKCTLWGEYAEEFDAKFQSAGNGEPVVAVLRFWKIKEYKGPKSLSNSFGASKV-YINPDIPEVPEIK 102 (106)
T ss_pred CCEEEEEEEHHHHHHHHHHHHHhCCCCcEEEEEEeEEEEEEcCCcEEEcCCCceEE-EECCCcHHHHHHH
Confidence 6788999999988764332 245556655 44888887662 11111134566 4555555555443
No 101
>cd04317 EcAspRS_like_N EcAspRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli aspartyl-tRNA synthetase (AspRS), the human mitochondrial (mt) AspRS-2, the discriminating (D) Thermus thermophilus AspRS-1, and the nondiscriminating (ND) Helicobacter pylori AspRS. These homodimeric enzymes are class2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic synthesis, wh
Probab=25.43 E-value=3.5e+02 Score=23.33 Aligned_cols=68 Identities=18% Similarity=0.173 Sum_probs=44.8
Q ss_pred hhhhh-hccCCEEEEEEEEEEcCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCC---CCCCCCCCCCCEEEEeeEE
Q 012401 13 IKELA-MHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSI---DQLPRVLSPRDLILLKNVM 88 (464)
Q Consensus 13 i~d~~-~~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~S~~~~gl~v~iF~~~~---~~LP~v~~~GDII~l~rvk 88 (464)
+.++. ...|+.|.+.|-|...+. .|+ .+=+.|.|.+. .+.+.+-.+.. +.+..+ ..||+|.+...-
T Consensus 5 ~~~~~~~~~g~~V~i~Gwv~~~R~----~gk--~~Fi~LrD~~g---~~Q~v~~~~~~~~~~~~~~l-~~gs~V~V~G~~ 74 (135)
T cd04317 5 CGELRESHVGQEVTLCGWVQRRRD----HGG--LIFIDLRDRYG---IVQVVFDPEEAPEFELAEKL-RNESVIQVTGKV 74 (135)
T ss_pred hhhCChhHCCCEEEEEEeEehhcc----cCC--EEEEEEecCCe---eEEEEEeCCchhHHHHHhCC-CCccEEEEEEEE
Confidence 44443 236788999999977554 344 67788888874 26666644322 244556 689999999964
Q ss_pred EE
Q 012401 89 IK 90 (464)
Q Consensus 89 v~ 90 (464)
..
T Consensus 75 ~~ 76 (135)
T cd04317 75 RA 76 (135)
T ss_pred EC
Confidence 43
No 102
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=25.07 E-value=2.5e+02 Score=34.67 Aligned_cols=40 Identities=25% Similarity=0.271 Sum_probs=27.7
Q ss_pred ccccccc-CCceEeeEEEEEEeeee-CCCC--eEEEEEEcCCCC
Q 012401 159 LSLKDIS-EHRYFDLVCKVFHVSYD-DSKG--LWMLFVWDGTDV 198 (464)
Q Consensus 159 ~~Lkdi~-~~~f~Dlv~qVv~v~~~-~~~~--~~~L~VwDgT~~ 198 (464)
..|+||. ++..+=+.++|.++-.. ..++ -.+++|+|||+.
T Consensus 227 ~~~~~i~~~~~~v~i~G~if~~e~~~~k~~~~~~~~~~td~~~s 270 (1437)
T PRK00448 227 TPMKEINEEERRVVVEGYVFKVEIKELKSGRHILTFKITDYTSS 270 (1437)
T ss_pred ccHHHhhccCCeEEEEEEEEEEEEEeccCCCEEEEEEEEcCCCC
Confidence 4577774 45677788899888732 1233 567899999955
No 103
>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=24.86 E-value=1.3e+02 Score=23.88 Aligned_cols=57 Identities=9% Similarity=0.096 Sum_probs=42.9
Q ss_pred CceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCeeEEEe
Q 012401 42 TDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAELSAVF 100 (464)
Q Consensus 42 ~D~~~tl~I~D~S~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvkv~~~~g~~~~~~ 100 (464)
....+.+-|.|+.-. -|.+.++....+.+-.....|.+..+.+.++..-++......
T Consensus 17 ~~~~~~miL~De~G~--~I~a~i~~~~~~~f~~~L~eg~vy~is~f~v~~~~~~y~~~~ 73 (86)
T cd04480 17 SGESLEMVLVDEKGN--RIHATIPKRLAAKFRPLLKEGKWYTISNFEVAPNTGSYRPTD 73 (86)
T ss_pred CCcEEEEEEEcCCCC--EEEEEECHHHHHhhhhhceeCCEEEEeeEEEEcCCCcccccC
Confidence 566788889998643 488999987666666655899999999999987766544433
No 104
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=22.62 E-value=1.7e+02 Score=35.13 Aligned_cols=69 Identities=19% Similarity=0.187 Sum_probs=0.0
Q ss_pred ccccccccccCCce-EeeEEEEEEeeeeCC----CCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCcccCCCCCccccc
Q 012401 156 DYLLSLKDISEHRY-FDLVCKVFHVSYDDS----KGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLR 230 (464)
Q Consensus 156 ~f~~~Lkdi~~~~f-~Dlv~qVv~v~~~~~----~~~~~L~VwDgT~~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~ 230 (464)
++ ..|-++.++.+ +-+.++|-.+- ... ..-..++|||||+.
T Consensus 228 ~i-~~~~~i~~~~~~v~v~G~IF~~e-~~~~ksGr~l~~i~vTD~t~S-------------------------------- 273 (1444)
T COG2176 228 EI-KPLIKINEEETRVKVEGYIFKIE-IKELKSGRTLLNIKVTDYTSS-------------------------------- 273 (1444)
T ss_pred ce-eehhhccccccceEEEEEEEEEe-eeecccCcEEEEEEEecCchh--------------------------------
Q ss_pred cCCCcceEEEEEecccchhhhccCCCCCcEEEEe
Q 012401 231 NFFPVGTVLRVSTDRSYENFGRYFTATGKWVRIR 264 (464)
Q Consensus 231 ~~p~~G~vl~V~~~~~~~~~~~~~~k~G~wV~l~ 264 (464)
++++..+.+....-..+.++.|+||+.+
T Consensus 274 ------l~~k~f~~~~ed~~~~~~ik~g~wvk~~ 301 (1444)
T COG2176 274 ------LILKKFLRDEEDEKKFDGIKKGMWVKAR 301 (1444)
T ss_pred ------eeehhhccccccHHHHhhcccCcEEEEE
No 105
>PRK07772 single-stranded DNA-binding protein; Provisional
Probab=20.42 E-value=1.9e+02 Score=27.10 Aligned_cols=74 Identities=8% Similarity=0.124 Sum_probs=49.6
Q ss_pred CCEEEEEEEEEEcCCccccCCCceEEEEEEEeC-C-CC----------CCCeEEEEecCCCCCCCCCCCCCCEEEEe-eE
Q 012401 21 KHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDD-S-QQ----------SPELLVNIFTSSIDQLPRVLSPRDLILLK-NV 87 (464)
Q Consensus 21 ~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~-S-~~----------~~gl~v~iF~~~~~~LP~v~~~GDII~l~-rv 87 (464)
...|.|+|=++.--.-+.|....-+++|+|.-. . .. ..-++|.+|.+..+.+-.-.+.||-|.+. |+
T Consensus 4 ~~~VtLiGrL~~DPElR~t~sG~~va~FrVAv~~r~~~~~~g~~~d~~t~fi~V~~Wg~~Ae~va~~L~KGd~V~V~GrL 83 (186)
T PRK07772 4 DTTITVVGNLTADPELRFTPSGAAVANFTVASTPRTFDRQTNEWKDGEALFLRCSIWRQAAENVAESLTKGMRVIVTGRL 83 (186)
T ss_pred cCEEEEEEEeCCCCeEEEcCCCCEEEEEEEEecCcceecCCCcEeccCceEEEEEEecHHHHHHHHhcCCCCEEEEEEEE
Confidence 346888887776533345555567889999732 2 11 11489999998666666534789966665 78
Q ss_pred EEEEEcC
Q 012401 88 MIKKHQA 94 (464)
Q Consensus 88 kv~~~~g 94 (464)
+.+.|.+
T Consensus 84 ~~r~wed 90 (186)
T PRK07772 84 KQRSYET 90 (186)
T ss_pred EcCceEC
Confidence 8888864
No 106
>cd04494 BRCA2DBD_OB2 BRCA2DBD_OB2: A subfamily of OB folds corresponding to the second OB fold (OB2) of the 800-amino acid C-terminal ssDNA binding domain (DBD) of BRCA2 (breast cancer susceptibility gene 2) protein, called BRCA2DBD. BRCA2 participates in homologous recombination-mediated repair of double-strand DNA breaks. It stimulates the displacement of Replication protein A (RPA), the most abundant eukaryotic ssDNA binding protein. It also facilitates filament formation. Mutations that map throughout the BRCA2 protein are associated with breast cancer susceptibility. BRCA2 is a large nuclear protein and its most conserved region is the C-terminal BRCA2DBD. BRCA2DBD binds ssDNA in vitro, and is composed of five structural domains, three of which are OB folds (OB1, OB2, and OB3). BRCA2DBD OB2 and OB3 are arranged in tandem, and their mode of binding can be considered qualitatively similar to two OB folds of RPA1, DBD-A and DBD-B (the major DBDs of RPA).
Probab=20.23 E-value=1.6e+02 Score=28.93 Aligned_cols=52 Identities=15% Similarity=0.104 Sum_probs=0.0
Q ss_pred eEEEEEecccchhhhccCCCCCcEEEEeCcEEEE-eC----cEEEEEEecCcceEEcC
Q 012401 237 TVLRVSTDRSYENFGRYFTATGKWVRIRNMSCQV-SS----GMWHGLLQSSSKIRLFS 289 (464)
Q Consensus 237 ~vl~V~~~~~~~~~~~~~~k~G~wV~l~Nv~~k~-~~----g~leG~l~~~ski~~l~ 289 (464)
.+..+++|+|.++. ...+++|.-+++.|+...- .+ +.++..=+..++.+.|+
T Consensus 180 ~~~~LTIWrPtedl-~s~L~EG~ry~i~~L~~s~~k~~~~~~~vqLtatk~Tr~~~l~ 236 (251)
T cd04494 180 KSGLLSIWRPTEDL-RSLLTEGKRYRIYGLATSNSKKRSGNEEVQLTATKKTRYQPLP 236 (251)
T ss_pred ceEEEEEeCCCHHH-HhhhcCCcEEEEEeccccCCCCCCCcceEEEEecCcccceECC
Done!