Query 012376
Match_columns 465
No_of_seqs 179 out of 234
Neff 7.3
Searched_HMMs 46136
Date Fri Mar 29 01:59:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/012376.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/012376hhsearch_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 1.2E-52 2.6E-57 414.2 11.9 430 3-464 2-463 (522)
2 cd04497 hPOT1_OB1_like hPOT1_O 100.0 1.6E-33 3.4E-38 250.5 17.7 137 8-146 1-138 (138)
3 PF02765 POT1: Telomeric singl 100.0 4.7E-33 1E-37 249.9 14.0 137 10-146 1-146 (146)
4 cd04498 hPOT1_OB2 hPOT1_OB2: A 99.9 2.9E-23 6.4E-28 178.2 11.5 106 169-287 1-122 (123)
5 PRK12366 replication factor A; 99.4 1.8E-10 3.9E-15 126.3 30.7 298 6-403 275-590 (637)
6 TIGR00617 rpa1 replication fac 99.2 1.6E-08 3.5E-13 110.3 27.9 319 9-403 179-537 (608)
7 PRK12366 replication factor A; 99.1 2.6E-08 5.7E-13 109.4 28.6 279 8-403 61-344 (637)
8 PRK07218 replication factor A; 99.0 4.3E-07 9.4E-12 94.5 30.9 279 10-404 58-352 (423)
9 PRK14699 replication factor A; 99.0 6.4E-07 1.4E-11 95.0 28.9 272 11-401 167-447 (484)
10 PRK07211 replication factor A; 98.9 6.4E-08 1.4E-12 101.7 19.7 204 8-290 159-367 (485)
11 PRK15491 replication factor A; 98.9 1.2E-06 2.5E-11 90.4 27.8 272 9-400 56-336 (374)
12 PRK06386 replication factor A; 98.9 6.6E-06 1.4E-10 83.8 31.8 274 11-404 3-291 (358)
13 PRK15491 replication factor A; 98.8 4.8E-07 1E-11 93.3 19.5 204 6-286 162-372 (374)
14 PRK14699 replication factor A; 98.6 3.6E-06 7.7E-11 89.4 20.4 204 8-288 274-484 (484)
15 PRK07211 replication factor A; 98.4 0.00025 5.4E-09 75.0 27.5 269 10-400 53-329 (485)
16 PRK08402 replication factor A; 98.4 4.1E-05 9E-10 78.3 19.6 195 159-414 63-281 (355)
17 KOG4757 Predicted telomere bin 98.3 6.1E-08 1.3E-12 97.8 -3.3 117 347-463 378-522 (522)
18 TIGR00617 rpa1 replication fac 97.9 0.00019 4.1E-09 78.8 14.4 157 6-200 294-479 (608)
19 PRK06461 single-stranded DNA-b 97.9 0.0004 8.7E-09 61.1 13.8 92 10-111 4-99 (129)
20 cd04475 RPA1_DBD_B RPA1_DBD_B: 97.7 0.00027 5.9E-09 59.1 9.8 73 24-101 2-79 (101)
21 cd04491 SoSSB_OBF SoSSB_OBF: A 97.5 0.0014 3E-08 52.7 10.8 72 25-102 1-75 (82)
22 PRK07218 replication factor A; 97.5 0.014 3.1E-07 61.2 20.5 159 159-398 59-219 (423)
23 PRK06461 single-stranded DNA-b 97.1 0.0047 1E-07 54.3 10.5 87 159-290 5-100 (129)
24 PRK08402 replication factor A; 97.1 0.016 3.6E-07 59.4 15.3 139 9-180 61-207 (355)
25 cd04497 hPOT1_OB1_like hPOT1_O 96.6 0.022 4.9E-07 50.5 10.5 96 157-290 3-105 (138)
26 cd03524 RPA2_OBF_family RPA2_O 96.4 0.015 3.3E-07 44.1 7.2 70 25-100 1-70 (75)
27 KOG3416 Predicted nucleic acid 96.4 0.018 4E-07 49.5 7.8 83 11-101 5-87 (134)
28 PF02765 POT1: Telomeric singl 95.9 0.19 4E-06 45.0 12.8 97 159-288 2-109 (146)
29 PRK07217 replication factor A; 95.8 0.16 3.5E-06 50.8 12.7 93 7-110 69-161 (311)
30 PRK07217 replication factor A; 95.4 0.31 6.7E-06 48.8 13.2 167 159-404 73-245 (311)
31 cd04489 ExoVII_LU_OBF ExoVII_L 95.2 0.22 4.7E-06 39.1 9.5 69 24-101 2-72 (78)
32 PRK06386 replication factor A; 95.1 0.17 3.8E-06 51.9 10.6 87 8-106 105-193 (358)
33 PF01336 tRNA_anti-codon: OB-f 95.0 0.039 8.4E-07 42.7 4.5 68 24-101 1-70 (75)
34 cd04481 RPA1_DBD_B_like RPA1_D 94.9 0.11 2.3E-06 43.9 7.2 82 25-108 1-90 (106)
35 cd04474 RPA1_DBD_A RPA1_DBD_A: 94.6 0.12 2.5E-06 43.6 6.7 84 12-99 1-88 (104)
36 cd04476 RPA1_DBD_C RPA1_DBD_C: 94.6 0.17 3.8E-06 46.1 8.3 32 373-404 65-96 (166)
37 PF15489 CTC1: CST, telomere m 94.4 0.4 8.7E-06 55.3 12.3 145 238-416 888-1055(1144)
38 cd04478 RPA2_DBD_D RPA2_DBD_D: 94.1 0.49 1.1E-05 38.7 9.2 67 24-101 2-72 (95)
39 cd04491 SoSSB_OBF SoSSB_OBF: A 93.8 0.19 4.1E-06 40.1 6.1 46 238-286 35-80 (82)
40 cd04475 RPA1_DBD_B RPA1_DBD_B: 93.7 0.81 1.8E-05 38.0 10.0 61 236-300 38-98 (101)
41 cd04485 DnaE_OBF DnaE_OBF: A s 93.2 0.23 5E-06 38.8 5.6 70 26-100 2-71 (84)
42 PRK13480 3'-5' exoribonuclease 92.6 0.77 1.7E-05 46.5 9.7 82 12-101 4-85 (314)
43 cd04492 YhaM_OBF_like YhaM_OBF 92.4 1.1 2.4E-05 35.1 8.6 68 27-100 3-70 (83)
44 cd04483 hOBFC1_like hOBFC1_lik 91.6 1.5 3.3E-05 36.1 8.7 65 26-101 2-87 (92)
45 PF08646 Rep_fac-A_C: Replicat 90.6 0.22 4.8E-06 44.4 3.0 32 372-403 50-81 (146)
46 cd03524 RPA2_OBF_family RPA2_O 85.5 11 0.00024 27.8 9.3 65 171-276 1-67 (75)
47 PF13742 tRNA_anti_2: OB-fold 85.0 8 0.00017 32.1 8.9 78 13-99 11-93 (99)
48 PF01336 tRNA_anti-codon: OB-f 84.4 12 0.00026 28.4 9.2 60 171-272 2-61 (75)
49 cd04488 RecG_wedge_OBF RecG_we 82.3 9.1 0.0002 28.8 7.7 68 26-100 2-69 (75)
50 cd04484 polC_OBF polC_OBF: A s 78.6 18 0.00039 28.9 8.4 71 24-98 2-74 (82)
51 PRK07373 DNA polymerase III su 78.0 7.1 0.00015 41.6 7.5 89 8-101 266-355 (449)
52 cd04490 PolII_SU_OBF PolII_SU_ 77.1 8.6 0.00019 30.6 6.1 59 24-91 2-62 (79)
53 cd04487 RecJ_OBF2_like RecJ_OB 75.4 28 0.00062 27.2 8.5 64 26-100 3-67 (73)
54 PF09104 BRCA-2_OB3: BRCA2, ol 74.6 17 0.00038 32.4 7.8 62 168-270 19-82 (143)
55 cd04474 RPA1_DBD_A RPA1_DBD_A: 73.3 8.2 0.00018 32.3 5.3 48 236-283 46-100 (104)
56 PRK05673 dnaE DNA polymerase I 71.3 11 0.00023 44.9 7.5 88 9-101 964-1052(1135)
57 PF09104 BRCA-2_OB3: BRCA2, ol 70.8 18 0.00038 32.4 6.9 63 21-90 18-81 (143)
58 cd04483 hOBFC1_like hOBFC1_lik 68.8 58 0.0012 26.7 9.3 26 171-198 1-26 (92)
59 KOG3056 Protein required for S 68.2 8.2 0.00018 41.6 5.1 70 24-95 188-257 (578)
60 cd04495 BRCA2DBD_OB3 BRCA2DBD_ 67.5 17 0.00036 30.3 5.7 64 26-95 2-66 (100)
61 cd04482 RPA2_OBF_like RPA2_OBF 65.7 26 0.00057 28.6 6.7 60 26-93 3-64 (91)
62 PRK06920 dnaE DNA polymerase I 64.6 18 0.00039 42.9 7.4 89 8-101 930-1018(1107)
63 cd04498 hPOT1_OB2 hPOT1_OB2: A 64.3 8.1 0.00017 33.7 3.5 34 60-94 62-95 (123)
64 PF02721 DUF223: Domain of unk 62.8 23 0.0005 28.9 5.9 39 236-274 9-47 (95)
65 KOG1030 Predicted Ca2+-depende 62.8 16 0.00034 33.5 5.2 26 372-397 51-76 (168)
66 PRK00286 xseA exodeoxyribonucl 56.9 75 0.0016 33.6 10.0 70 22-100 24-95 (438)
67 TIGR00237 xseA exodeoxyribonuc 55.3 83 0.0018 33.4 10.0 78 13-100 9-89 (432)
68 PF12100 DUF3576: Domain of un 54.8 26 0.00056 29.5 4.7 54 8-68 16-70 (103)
69 PRK07374 dnaE DNA polymerase I 54.8 34 0.00073 41.0 7.5 88 9-101 987-1075(1170)
70 PF01245 Ribosomal_L19: Riboso 53.3 43 0.00093 28.7 6.0 41 70-111 14-62 (113)
71 PRK05338 rplS 50S ribosomal pr 53.2 32 0.0007 29.6 5.2 45 70-115 14-66 (116)
72 PF15072 DUF4539: Domain of un 52.1 44 0.00094 27.2 5.6 63 23-94 3-66 (86)
73 cd04480 RPA1_DBD_A_like RPA1_D 49.8 33 0.00072 27.3 4.6 37 236-272 30-66 (86)
74 PRK10917 ATP-dependent DNA hel 49.5 70 0.0015 36.0 8.7 78 12-98 52-129 (681)
75 cd04478 RPA2_DBD_D RPA2_DBD_D: 49.3 92 0.002 25.0 7.3 26 170-197 2-27 (95)
76 TIGR00643 recG ATP-dependent D 47.0 95 0.0021 34.6 9.2 78 12-99 25-103 (630)
77 COG1107 Archaea-specific RecJ- 46.2 91 0.002 34.2 8.3 78 11-99 203-281 (715)
78 PRK06826 dnaE DNA polymerase I 42.8 60 0.0013 38.8 7.1 77 20-101 990-1067(1151)
79 TIGR01024 rplS_bact ribosomal 42.8 46 0.00099 28.6 4.5 45 70-115 14-66 (113)
80 PRK05672 dnaE2 error-prone DNA 42.0 57 0.0012 38.7 6.7 86 9-101 940-1026(1046)
81 CHL00084 rpl19 ribosomal prote 41.0 66 0.0014 27.8 5.2 42 70-112 18-67 (117)
82 cd04486 YhcR_OBF_like YhcR_OBF 39.9 1.9E+02 0.004 22.8 8.3 62 27-101 3-69 (78)
83 PF15072 DUF4539: Domain of un 39.7 27 0.00059 28.4 2.6 24 377-400 20-43 (86)
84 PRK00448 polC DNA polymerase I 36.3 1.2E+02 0.0025 37.4 8.2 85 8-98 224-312 (1437)
85 PRK07279 dnaE DNA polymerase I 35.4 79 0.0017 37.4 6.4 86 9-101 874-960 (1034)
86 KOG4792 Crk family adapters [S 34.9 89 0.0019 30.1 5.5 61 229-293 223-289 (293)
87 cd04495 BRCA2DBD_OB3 BRCA2DBD_ 34.6 2E+02 0.0043 24.1 6.9 34 239-272 30-64 (100)
88 cd04490 PolII_SU_OBF PolII_SU_ 34.1 45 0.00098 26.4 3.1 21 379-399 20-40 (79)
89 PF14535 AMP-binding_C_2: AMP- 33.9 28 0.00061 28.5 1.9 63 357-421 2-70 (96)
90 KOG2708 Predicted metalloprote 33.0 25 0.00054 34.0 1.6 47 409-462 90-153 (336)
91 COG2049 DUR1 Allophanate hydro 31.5 22 0.00048 34.2 1.0 39 230-270 177-215 (223)
92 PRK13254 cytochrome c-type bio 31.0 2.8E+02 0.0061 24.9 7.9 67 9-85 36-105 (148)
93 cd04496 SSB_OBF SSB_OBF: A sub 30.9 40 0.00086 27.1 2.3 27 238-264 45-71 (100)
94 cd04489 ExoVII_LU_OBF ExoVII_L 30.7 61 0.0013 24.8 3.3 24 377-400 18-41 (78)
95 cd04492 YhaM_OBF_like YhaM_OBF 29.9 67 0.0014 24.6 3.4 21 377-397 20-40 (83)
96 cd04481 RPA1_DBD_B_like RPA1_D 28.9 1.2E+02 0.0027 25.0 5.1 63 236-299 34-102 (106)
97 COG1599 RFA1 Single-stranded D 28.8 1.8E+02 0.0039 30.5 7.4 78 21-103 59-140 (407)
98 COG1570 XseA Exonuclease VII, 27.9 5.7E+02 0.012 27.3 10.6 64 22-94 24-87 (440)
99 cd04317 EcAspRS_like_N EcAspRS 26.6 3.2E+02 0.007 23.5 7.5 68 13-90 5-76 (135)
100 COG1200 RecG RecG-like helicas 26.5 3E+02 0.0066 30.9 8.7 79 13-100 54-132 (677)
101 cd04480 RPA1_DBD_A_like RPA1_D 26.5 1.2E+02 0.0025 24.1 4.3 57 42-100 17-73 (86)
102 PF15489 CTC1: CST, telomere m 24.1 1.3E+03 0.028 27.7 15.9 71 20-95 164-235 (1144)
103 cd04494 BRCA2DBD_OB2 BRCA2DBD_ 21.4 1.5E+02 0.0033 29.1 4.7 53 236-289 179-236 (251)
104 PF11325 DUF3127: Domain of un 20.6 4.6E+02 0.01 21.2 7.7 66 28-95 4-73 (84)
105 PRK00448 polC DNA polymerase I 20.2 3.3E+02 0.0071 33.7 8.1 40 159-198 227-270 (1437)
No 1
>KOG4757 consensus Predicted telomere binding protein [General function prediction only]
Probab=100.00 E-value=1.2e-52 Score=414.21 Aligned_cols=430 Identities=22% Similarity=0.201 Sum_probs=333.5
Q ss_pred CCCCCcceeehHhhhhccCCEEEEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEE
Q 012376 3 SQRNQGGIVRIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLI 82 (465)
Q Consensus 3 ~~~~~y~y~~i~~~~~~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII 82 (465)
.-++.|+|..+++++...|+.||+||||++++||++++|+||+||++|+||++.+.||+|++|+++-++||.|+++||||
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 EEeeEEEEEEcCeeeEEecCCce-EEEEEeCCCCCCCCccccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCccccccc
Q 012376 83 LLKNVMIKKHQAELSAVFYKDSS-SFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSL 161 (465)
Q Consensus 83 ~l~rvki~~~~g~~~~~~~~~~s-s~~lf~~~~~~~~~Py~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~f~~~L 161 (465)
+|||+|||.|+.+.+|+|+..++ +|++|+|+ +.+..|||+|+. |-++ .+||+|++.+.....+ ++ ..+
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 889999999987 8777 7899999988877766 56 789
Q ss_pred ccccCCceEeEEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCc-ccCCCCCCccccCCCChhccccCCCcceEEE
Q 012376 162 KDISEHRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLED-EEHNPLPLHIESSPLDLETLRNFFPVGTVLR 240 (465)
Q Consensus 162 kdi~~~~f~Dlv~qVv~v~~~~~~~~~~L~VwDgT~~p~~~~~~~~~~-~~~~~~p~~~~~~~l~~~~~~~~p~~G~vL~ 240 (465)
+++.++..-.|.||+++.. ......|. .|||-|.+-..++++..-- --++..|++|++ .+.+.+..||..|.|..
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 7999555544442221000 011235777764 56677889999999999
Q ss_pred EEeccchhhhhccCCCCCcEEEEeCcEEEEeCcEEEEEEecCCceEEcCCCChhHHHHHHHHHHHHh----------CC-
Q 012376 241 VSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDNDNVVWDYMRRFRERIS----------GG- 309 (465)
Q Consensus 241 V~~~~~~~~~~~~~~k~G~wV~l~Nv~~k~~~g~leG~l~~~ski~~l~~~d~~v~~r~r~y~~r~~----------~~- 309 (465)
+..+.+.+++..+.+++|.-+..+|+...-+. +|.++ ++.+ -|+.-..|.-+...... ++
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 99988888887888888888888888762221 33332 1111 12322233111111000 00
Q ss_pred --CCCCC-CcCCCCCCCCcccccCCCccccHHHHhhCCCCCcceE-EEEEEEe---ecCCCccccccCCCCeEEEEEEEE
Q 012376 310 --HGHMP-IWTDPSSQFLTEVDWVNVASVTLMKIATQLQGNVRCC-CIVRVVS---IHPFQAEHYSSPNGSSEYTMKLTL 382 (465)
Q Consensus 310 --~~~~~-~~~~~~~~~~t~~~~~~~p~ttL~dIL~~p~v~~kfr-~~VRVV~---~~P~~~edf~~~~~~w~~rf~L~l 382 (465)
.++.+ ...+-.+...|.+++..+|+++|||+++.+.++.||| |.||+|+ .+|.++|.+.-.+ -...-+.
T Consensus 298 hll~ev~~e~r~~~q~~~tgi~~v~a~fvsl~Ds~t~~~vt~k~R~~vvrfva~~~~~P~sve~l~~i~----i~l~~ic 373 (522)
T KOG4757|consen 298 HLLNEVKPEKRLYVQNCQTGIEAVIAPFVSLMDSETPFIVTEKKRTCVVRFVAHVINYPASVELLTIIT----ILLAPIC 373 (522)
T ss_pred hhhcccCcccceeecccccCcchhhcccchhhhhccccccchhcceeeeeehhhcccccchhhhhhhhh----hhhHHHh
Confidence 00111 0001124677888899999999999999999999999 9999999 9999999985331 1344457
Q ss_pred eCCCceEEEEEeccccch-----hcCCC-CChHHHHHHHHHHhCCCCCCCCCCCCccCCcceeeeeeeeeecCCc-----
Q 012376 383 EDPTARIHALLCGKEWVK-----FFGGS-PPPDVLTKKIKMLLGMPEHEDGNDDMVRNPPWIKCFLHLKESDGGR----- 451 (465)
Q Consensus 383 ED~t~ri~~~v~~~da~~-----f~~~~-~~~~~L~~kl~~L~G~~e~~~~~~~~~~n~pw~~CCi~sY~v~~~~----- 451 (465)
+|+++|.|+.++..|... +||-. .+..++..+|+.|+|+.+. + ..|+++||++||....|-.+-+
T Consensus 374 ~l~n~r~H~~l~~le~s~p~s~~~fgc~~~~~~~~v~~ln~Lv~~e~~--~--~vP~~~~~v~~~~l~~~s~~l~~~l~d 449 (522)
T KOG4757|consen 374 NLLNPRKHRLLVQLEDSWPKSLTQFGCLSQPPSSYVWMLNLLVRDESN--V--TVPVIFFDVDAAELINSSKKLPCNLAD 449 (522)
T ss_pred hhhchhhhhhhhhhcccCcccceeeeeccCCHHHHHHHHHHHhccccc--c--ccccccchhheeeeccccccccchhcc
Confidence 889999999888888775 77744 5678899999999998333 2 2689999999999999888643
Q ss_pred -eEEEEEeeeEEcC
Q 012376 452 -NRVYYIRWTKLVT 464 (465)
Q Consensus 452 -~r~f~~F~T~i~~ 464 (465)
+|+||||++-|.-
T Consensus 450 ~~~~fqi~ds~il~ 463 (522)
T KOG4757|consen 450 HQMTFQIKDSLILI 463 (522)
T ss_pred ccceEEecceeeee
Confidence 7999999998864
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=1.6e-33 Score=250.51 Aligned_cols=137 Identities=33% Similarity=0.509 Sum_probs=129.9
Q ss_pred cceeehHhhhhccCCEEEEEEEEEecCCccccCCCceEEEEEEEeCCCC-CCCeEEEEecCCCCCCCCCCCCCCEEEEee
Q 012376 8 GGIVRIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQ-SPELLVNIFTSSIDQLPRVLSPRDLILLKN 86 (465)
Q Consensus 8 y~y~~i~~~~~~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~-~~gl~v~iF~~~~~~LP~v~~~GDII~l~r 86 (465)
|.|++|++|.+..++.|||||||+|+++|++|+|+||+|+|+|+|+|.. +.||+|+||+++.++||.+ ++||||+|||
T Consensus 1 ~~f~~i~~~~~~~~~~v~vigVV~~~~~p~~s~g~d~~~tl~i~D~S~~~~~~l~v~~F~~~~~~LP~v-~~GDVIll~~ 79 (138)
T cd04497 1 YKYTPLSSALKESGGSVNVIGVVVDAGPPVRSKGTDYCCTLTITDPSLANSDGLTVKLFRPNEESLPIV-KVGDIILLRR 79 (138)
T ss_pred CceEeHHHHHhccCCeEEEEEEEeecCCCcccCCCcEEEEEEEECCCCCCCCcEEEEEECCChhhCCCC-CCCCEEEEEE
Confidence 7899999999888999999999999999999999999999999999997 7899999999999999999 8999999999
Q ss_pred EEEEEEcCeeeEEecCCceEEEEEeCCCCCCCCccccCCCCCCCCHHHHHHHHHHHHhhh
Q 012376 87 VMIKKHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCV 146 (465)
Q Consensus 87 vki~~~~g~~~~~~~~~~ss~~lf~~~~~~~~~Py~~s~~~~~~~~~e~~~v~~Lr~W~~ 146 (465)
++|+.|+|+.+++++.+.||||||++..+....||+.++. ++++++|++++..||+|+.
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=4.7e-33 Score=249.89 Aligned_cols=137 Identities=35% Similarity=0.617 Sum_probs=127.1
Q ss_pred eeehHhhhhccCCEEEEEEEEEecCCc--cccCCCceEEEEEEEeCCCCC-----CCeEEEEecCCCCCCCCCCCCCCEE
Q 012376 10 IVRIKELAMHVKHKVNLLGVVLEFSIP--RKSQGTDYVCVLKIVDDSQQS-----PELLVNIFTSSIDQLPRVLSPRDLI 82 (465)
Q Consensus 10 y~~i~~~~~~~~~~vnviGVVvd~~~P--~~trG~D~~~tl~I~D~s~~~-----~gl~v~iF~~~~~~LP~v~~~GDII 82 (465)
|++|+++....+..|||||||+++++| ++|||+||+|+|+|+|+|+.. .||+|++|+++++.||.+..+||||
T Consensus 1 ~~~l~~~~~~~~~~vnvigVV~~~~~p~~~~t~g~D~~~tl~i~D~S~~~~~~~~~~l~v~iF~~~~~~LP~v~~~GDii 80 (146)
T PF02765_consen 1 YTPLSTAKEKFGKFVNVIGVVVDFSPPNPKKTRGTDYMCTLTITDPSLNDSNQKLSGLTVNIFRPHKESLPNVKSVGDII 80 (146)
T ss_dssp BCCGGGSCTTSSEEEEEEEEEEEEEEECTEEESSSCEEEEEEEEBTTCSCSSCCCCEEEEEEEESSHHHSCTTCSTTHEE
T ss_pred CccchhhhhcCCCEEEEEEEEEEccCCcceEcCCCcEEEEEEEECCCCCccccccCCEEEEEECCCHHHCCCCCCCCCEE
Confidence 789998888899999999999999999 999999999999999999985 7999999999999999998779999
Q ss_pred EEeeEEEEEEcCeeeEEecCC-ceEEEEE-eCCCCCCCCccccCCCCCCCCHHHHHHHHHHHHhhh
Q 012376 83 LLKNVMIKKHQAELSAVFYKD-SSSFALF-DGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCV 146 (465)
Q Consensus 83 ~l~rvki~~~~g~~~~~~~~~-~ss~~lf-~~~~~~~~~Py~~s~~~~~~~~~e~~~v~~Lr~W~~ 146 (465)
+|||+||+.|+|+++++++.. .++|+|| ++..+.++.||+.++++++++++|+++++.||+|++
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=2.9e-23 Score=178.19 Aligned_cols=106 Identities=25% Similarity=0.357 Sum_probs=84.0
Q ss_pred eEeEEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCcc-cCCCCCCccccCCCChhccccCC-Ccce-EEEEEecc
Q 012376 169 YFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDE-EHNPLPLHIESSPLDLETLRNFF-PVGT-VLRVSTDR 245 (465)
Q Consensus 169 f~Dlv~qVv~v~~~~~~~~~~L~VwDgT~~p~~~~~~~~~~~-~~~~~p~~~~~~~l~~~~~~~~p-~~G~-vL~V~~~~ 245 (465)
||||+||||+++ +.++++++|||||||+||+..+.+..++. ..+++ +...+.|+ | |+ +|+|+||+
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 76888999999999999765555544432 11221 33467899 8 99 99999999
Q ss_pred chhhhhccCCCCCcEEEEeCcEEEEe--------CcEEEEEE-ecC----CceEE
Q 012376 246 SYENFGRYFTATGKWVRIRNMSCQVS--------SGMWHGLL-QSS----SKIRL 287 (465)
Q Consensus 246 ~~~~~~~~~~k~G~wV~l~Nv~~k~~--------~g~leG~l-~~~----ski~~ 287 (465)
+|++++++ +|+||||+|+|||+|.. +-.|||.+ +.- ++|++
T Consensus 69 ~H~~~ar~-lK~GdfV~L~NVhiK~~~~~~~~~~~~~Le~~l~~gg~~~~rgi~v 122 (123)
T cd04498 69 NHVELAKS-LKPGDFVRIYNVHAKSYSSKNEHDENDHLHFHLVHGGTEYGRGIRV 122 (123)
T ss_pred chHHHHhh-CCCCCEEEEEEEEEEeccCCcccCCcceEEEEEccCceeeccceee
Confidence 99999999 99999999999999993 23788888 543 45554
No 5
>PRK12366 replication factor A; Reviewed
Probab=99.42 E-value=1.8e-10 Score=126.27 Aligned_cols=298 Identities=16% Similarity=0.188 Sum_probs=182.8
Q ss_pred CCcceeehHhhhhc-cCCEEEEEEEEEecCCccc---cCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCE
Q 012376 6 NQGGIVRIKELAMH-VKHKVNLLGVVLEFSIPRK---SQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDL 81 (465)
Q Consensus 6 ~~y~y~~i~~~~~~-~~~~vnviGVVvd~~~P~~---trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDI 81 (465)
..+.+++|+++... .|..+++-|.|+...+++. .+|+--..++.|.|.+- .+.+.+|.+..+.+..+ ..||+
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 45688999999754 5678999999999988754 36788999999999873 39999999877778877 69999
Q ss_pred EEEeeEEEEEEcC-----eeeEEecCCceEEEEEeCCCCCCCCccccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCcc
Q 012376 82 ILLKNVMIKKHQA-----ELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSND 156 (465)
Q Consensus 82 I~l~rvki~~~~g-----~~~~~~~~~~ss~~lf~~~~~~~~~Py~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~ 156 (465)
+.+.+++++.|+. ++.+.++.. |.... .. ... .| . ..+ .
T Consensus 351 y~is~~~vk~y~~~~~~~~~El~~~~~-s~I~~-d~--~~~-~p-~---~~~---------------------------~ 394 (637)
T PRK12366 351 VKIENCKVRTYYDNEGEKRVDLNAGYS-SEIIK-DE--SIS-FE-E---IEE---------------------------K 394 (637)
T ss_pred EEEecCEEeeccccCCCcCEEEEcCCc-eEEEe-cc--CCc-cc-c---eee---------------------------c
Confidence 9999999998863 344444433 33432 11 100 11 0 001 2
Q ss_pred ccccccccc----CCceEeEEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCccccCCCChhccccC
Q 012376 157 YLLSLKDIS----EHRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNF 232 (465)
Q Consensus 157 f~~~Lkdi~----~~~f~Dlv~qVv~v~~~~~~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~ 232 (465)
| ..|+||. .+..+|+++.|+.+. + -..++ . -||++..--. ..+.|+
T Consensus 395 ~-~~i~dI~~~~~~~~~VdVig~V~~v~-~--~~~i~-~-k~G~~~~~r~--i~l~D~---------------------- 444 (637)
T PRK12366 395 I-YKIKDILNLEEDDNDITVIARVVEDY-P--VNEFE-R-SDGSKGKVRN--IELADG---------------------- 444 (637)
T ss_pred c-ccHHHhhcccCCCcEEEEEEEEEEcc-C--ceEEE-e-cCCCEeEEEE--EEEEeC----------------------
Confidence 3 4555553 578999999999887 3 11111 1 2333221100 000000
Q ss_pred CCcceEEEEEeccchhhhhccCCCCCcEEEEeCcEEEEeCcEEEEEEecCCceEEcCCCChhHHHHHHHHHHHHhCCCCC
Q 012376 233 FPVGTVLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDNDNVVWDYMRRFRERISGGHGH 312 (465)
Q Consensus 233 p~~G~vL~V~~~~~~~~~~~~~~k~G~wV~l~Nv~~k~~~g~leG~l~~~ski~~l~~~d~~v~~r~r~y~~r~~~~~~~ 312 (465)
-| .+++++|..++.+ .+.+|+.|.+.|..++..+|.++..+...+.|.+.++ .+++. +.
T Consensus 445 --TG-~I~vtlWg~~a~~---~~~~G~vi~i~~~~V~~~~g~~~Ls~~~~s~i~~~p~-~~el~-----------~~--- 503 (637)
T PRK12366 445 --TG-SIRLTLWDDDAEI---EIKEGDAIKILHPYVKENGDYLDLSIGRYGRIEINPE-GEIIK-----------SN--- 503 (637)
T ss_pred --CC-EEEEEEecccccc---CCCCCCEEEEEeeEEEeCCCeeEEEecCcceEEECCC-Ccccc-----------cc---
Confidence 04 6899999988863 5789999999999999988988888888888876443 22211 00
Q ss_pred CCCcCCCCCCCCcccccCCCccc---cHHHHhhCCC-CCcceEEEEEEEeecCCCccccccC-CCCeEEEEEEEEeCCCc
Q 012376 313 MPIWTDPSSQFLTEVDWVNVASV---TLMKIATQLQ-GNVRCCCIVRVVSIHPFQAEHYSSP-NGSSEYTMKLTLEDPTA 387 (465)
Q Consensus 313 ~~~~~~~~~~~~t~~~~~~~p~t---tL~dIL~~p~-v~~kfr~~VRVV~~~P~~~edf~~~-~~~w~~rf~L~lED~t~ 387 (465)
+..+.++..... ++ +|..|-.... .+++=.|.=+|+.---.-...-|.. ...|.|++.+.|-|.|+
T Consensus 504 --------~~~I~~i~~~~~-~~v~g~i~~i~~~~~~y~aCp~CnkKv~~~~g~~~C~~c~~~~p~~~~~l~~~i~D~TG 574 (637)
T PRK12366 504 --------RKFIADLEEDDT-VEIRGTVVDIRKQKIILYLCPNCRKRVEEVDGEYICEFCGEVEPNELLMLNFTLDDGTG 574 (637)
T ss_pred --------ccCHHHcccCCe-EEEEEEEEEEeCCCEEEecccccCeEeEcCCCcEECCCCCCCCCcEEEEEEEEEEcCCC
Confidence 001111100000 00 1111111100 0111124334442100000111211 35788999999999999
Q ss_pred eEEEEEeccccchhcC
Q 012376 388 RIHALLCGKEWVKFFG 403 (465)
Q Consensus 388 ri~~~v~~~da~~f~~ 403 (465)
.+++.++++.|+.|||
T Consensus 575 ~~~~t~f~e~ae~l~G 590 (637)
T PRK12366 575 TINCRFYGKNVEKLLG 590 (637)
T ss_pred CEEEEEEhHHhHHHhC
Confidence 9999999999999996
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=99.17 E-value=1.6e-08 Score=110.34 Aligned_cols=319 Identities=14% Similarity=0.145 Sum_probs=192.0
Q ss_pred ceeehHhhhhccCCEEEEEEEEEecCCccc---cCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCC-CCCCCCCCEEEE
Q 012376 9 GIVRIKELAMHVKHKVNLLGVVLEFSIPRK---SQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQL-PRVLSPRDLILL 84 (465)
Q Consensus 9 ~y~~i~~~~~~~~~~vnviGVVvd~~~P~~---trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~L-P~v~~~GDII~l 84 (465)
.+++|+++.... ....+-|-|+.....+. .+|.....++.|.|++ ..|.+.+|.+..+.+ |.+ .+|+|+.+
T Consensus 179 ~~~pI~~L~py~-~~wtIkaRV~~Ks~ir~~~~~~gegkvfsv~L~Deg---g~Irat~f~~~~dkf~~~l-~eG~VY~I 253 (608)
T TIGR00617 179 RVMPIASLSPYQ-NKWTIKARVTNKSEIRTWSNARGEGKLFNVELLDES---GEIRATAFNEQADKFYDII-QEGKVYYI 253 (608)
T ss_pred ceEEHHHCCCCC-CceEEEEEEEeccccceecCCCCCceeeEEEEecCC---CeEEEEECchHHHHHhhhc-ccCCEEEE
Confidence 589999998543 35899999998776654 2455678889999943 349999999755454 666 79999999
Q ss_pred eeEEEEEEcCeeeEEecCC---ceEEEEEeCCCCCCCCccccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCccccccc
Q 012376 85 KNVMIKKHQAELSAVFYKD---SSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSL 161 (465)
Q Consensus 85 ~rvki~~~~g~~~~~~~~~---~ss~~lf~~~~~~~~~Py~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~f~~~L 161 (465)
.+.+|+..+++...+.+.. +..+.......+..-.| ...| .| ..|
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 9999998877655443310 11111121111111122 0012 23 444
Q ss_pred ccc---cCCceEeEEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCccccCCCChhccccCCCcceE
Q 012376 162 KDI---SEHRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTV 238 (465)
Q Consensus 162 kdi---~~~~f~Dlv~qVv~v~~~~~~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~p~~G~v 238 (465)
.|| ..+.++|+++.|..+. +. ..++- =.||++..--. ..+.| --|+.
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 554 4567999999999887 31 11110 11222211100 00000 01667
Q ss_pred EEEEeccchhhhhccCCCCCcEEEEeCcEEEEeCcEEEEEEecCCceEEcCCCChhHHHHHHHHHHHHhCCCCCCCCcCC
Q 012376 239 LRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDNDNVVWDYMRRFRERISGGHGHMPIWTD 318 (465)
Q Consensus 239 L~V~~~~~~~~~~~~~~k~G~wV~l~Nv~~k~~~g~leG~l~~~ski~~l~~~d~~v~~r~r~y~~r~~~~~~~~~~~~~ 318 (465)
++||+|..+|.. -....|+.|.|+.++++-.+|. .......|+|. ++++-+++.+.+.-|...-. .. +..++
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-SLSTGGSSTII-VNPDIPEAEKLKGWYDNEGK-GT---MASSI 423 (608)
T ss_pred EEEEEEhhhhhh--cCCCCCCEEEEEeEEEEecCCc-eEeccCCceEE-ECCCcHHHHHHHHHHHhcCC-Cc---cceee
Confidence 899999998864 2377899999999999888664 34444556774 55566776666544432211 11 00000
Q ss_pred CCCCCCcccccCCCccccHHHHhhCC----CCCcceEEEEEEEeecCCCccccccC------------------------
Q 012376 319 PSSQFLTEVDWVNVASVTLMKIATQL----QGNVRCCCIVRVVSIHPFQAEHYSSP------------------------ 370 (465)
Q Consensus 319 ~~~~~~t~~~~~~~p~ttL~dIL~~p----~v~~kfr~~VRVV~~~P~~~edf~~~------------------------ 370 (465)
+....+..........||.||.... +-+..|.|.+.|+.+-+.+.-=.++|
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 0000000111234567899998632 23445888888887765432111111
Q ss_pred --CCCeEEEEEEEEeCCCceEEEEEeccccchhcC
Q 012376 371 --NGSSEYTMKLTLEDPTARIHALLCGKEWVKFFG 403 (465)
Q Consensus 371 --~~~w~~rf~L~lED~t~ri~~~v~~~da~~f~~ 403 (465)
+-.|.|.+.+.+.|.|+.+|+.++++.|+.+||
T Consensus 503 ~~~~~~RYil~~~i~D~Tg~~~~t~F~~~ae~llG 537 (608)
T TIGR00617 503 FAEFKYRYILQISISDETGQLWVTAFNDQAEQILG 537 (608)
T ss_pred CCCccEEEEEEEEEEeCCCCEEEEEEhHHHHHHcC
Confidence 125788899999999999999999999999995
No 7
>PRK12366 replication factor A; Reviewed
Probab=99.15 E-value=2.6e-08 Score=109.36 Aligned_cols=279 Identities=14% Similarity=0.165 Sum_probs=185.8
Q ss_pred cceeehHhhhhccCC-EEEEEEEEEecCCcccc---CC-CceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEE
Q 012376 8 GGIVRIKELAMHVKH-KVNLLGVVLEFSIPRKS---QG-TDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLI 82 (465)
Q Consensus 8 y~y~~i~~~~~~~~~-~vnviGVVvd~~~P~~t---rG-~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII 82 (465)
-.+++|+++. +++ .+++.|-|+..+.|+.- +| .-..+++.|.|++- .+++.+|.+..+.+|.+ .+|||+
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 4578999997 555 59999999999988742 35 46789999999865 39999999877778888 799999
Q ss_pred EEeeEEEEEEcCeeeEEecCCceEEEEEeCCCCCCCCccccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCcccccccc
Q 012376 83 LLKNVMIKKHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSLK 162 (465)
Q Consensus 83 ~l~rvki~~~~g~~~~~~~~~~ss~~lf~~~~~~~~~Py~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~f~~~Lk 162 (465)
.+.++.++.|+|++.+..+.. ++....... +..-.| + .++ .| .|.
T Consensus 135 ~i~~~~v~~~~~~~el~~~~~-t~I~~~~~~-d~~~i~-~---------~~~---------------------~~--~I~ 179 (637)
T PRK12366 135 KIENARSRKWNNDVELNSGSE-TRIDKLEKY-DESRYP-I---------IKE---------------------NY--DIP 179 (637)
T ss_pred EEeccEecccCCceEEEcCCc-ceEEEcccc-ccccCC-c---------ccc---------------------cc--ccc
Confidence 999999999999988766644 444433210 001111 0 000 12 588
Q ss_pred cccCCceEeEEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCccccCCCChhccccCCCcceEEEEE
Q 012376 163 DISEHRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRVS 242 (465)
Q Consensus 163 di~~~~f~Dlv~qVv~v~~~~~~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~p~~G~vL~V~ 242 (465)
||.+|.++|+++.|+.+. + -..++ --||++-.-.. ..+.| + -| .+++|
T Consensus 180 el~~g~~v~v~G~V~~~~-~--~~~f~--rkdg~~~~~r~--~~l~D-----------------~-------TG-~irvT 227 (637)
T PRK12366 180 ELEPNLSATIEGEVTKAY-P--IKEFT--RKDGSEGKLKS--FILKD-----------------D-------TG-SIRVT 227 (637)
T ss_pred ccCCCCeEEEEEEEEEcc-C--cEEEE--EcCCCeeEEEE--EEEEc-----------------C-------CC-cEEEE
Confidence 889999999999999887 4 11211 12554321111 10100 0 15 68999
Q ss_pred eccchhhhhccCCCCCcEEEEeCcEEEEeCcEEEEEEecCCceEEcCCCChhHHHHHHHHHHHHhCCCCCCCCcCCCCCC
Q 012376 243 TDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDNDNVVWDYMRRFRERISGGHGHMPIWTDPSSQ 322 (465)
Q Consensus 243 ~~~~~~~~~~~~~k~G~wV~l~Nv~~k~~~g~leG~l~~~ski~~l~~~d~~v~~r~r~y~~r~~~~~~~~~~~~~~~~~ 322 (465)
+|..++.. .+.+|+.|++.+....-..|.+|-.....+.|... +.
T Consensus 228 lW~~~a~~---~~~~g~vv~i~g~~~~~~~~~~el~~~~~~~i~~~---~~----------------------------- 272 (637)
T PRK12366 228 LWNDLTDI---EVNKGDIVRVKGYVKQGYRTGLEISANNIEILEKL---EK----------------------------- 272 (637)
T ss_pred EEChhhcc---cCCCCCEEEEEeEEecCcCCceEEEeCCceeeccc---cc-----------------------------
Confidence 99988863 58999999998833332446666655332222111 00
Q ss_pred CCcccccCCCccccHHHHhhCCCCCcceEEEEEEEeecCCCccccccCCCCeEEEEEEEEeCCCceEEEEEeccccchhc
Q 012376 323 FLTEVDWVNVASVTLMKIATQLQGNVRCCCIVRVVSIHPFQAEHYSSPNGSSEYTMKLTLEDPTARIHALLCGKEWVKFF 402 (465)
Q Consensus 323 ~~t~~~~~~~p~ttL~dIL~~p~v~~kfr~~VRVV~~~P~~~edf~~~~~~w~~rf~L~lED~t~ri~~~v~~~da~~f~ 402 (465)
.. ...++++|+++-.+- .+.+....+||++..|. +.|....|. --.|.+.|-|.|++|.|.++++.|.+|.
T Consensus 273 -~~----~~~~~~pI~~L~~~~-~g~~~~I~grV~~~~~~--R~f~~~~g~-gkv~s~~l~D~tG~IR~t~w~~~~d~~~ 343 (637)
T PRK12366 273 -EE----KELEIVNIEELTEFE-DGEEVDVKGRIIAISDK--REVERDDRT-AEVQDIELADGTGRVRVSFWGEKAKILE 343 (637)
T ss_pred -cc----cccCceeHHHCCccc-CCCEEEEEEEEEecCCc--eEEEcCCCc-EEEEEEEEEcCCCeEEEEEeCchhhhhc
Confidence 00 011334566654321 34578888999997654 456666665 5788999999999999999999998887
Q ss_pred C
Q 012376 403 G 403 (465)
Q Consensus 403 ~ 403 (465)
+
T Consensus 344 ~ 344 (637)
T PRK12366 344 N 344 (637)
T ss_pred c
Confidence 5
No 8
>PRK07218 replication factor A; Provisional
Probab=99.05 E-value=4.3e-07 Score=94.51 Aligned_cols=279 Identities=18% Similarity=0.214 Sum_probs=172.7
Q ss_pred eeehHhhhhccCCEEEEEEEEEecCCcc-ccCC-CceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeE
Q 012376 10 IVRIKELAMHVKHKVNLLGVVLEFSIPR-KSQG-TDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNV 87 (465)
Q Consensus 10 y~~i~~~~~~~~~~vnviGVVvd~~~P~-~trG-~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rv 87 (465)
-+.|+|+... ...|+|.|-|++...+. +..| .-...++.|.|++=. +++.++.+ ++ + .+||+|.+.++
T Consensus 58 ~~kI~Di~~~-~~~V~v~~kVl~i~~rt~r~dg~~g~v~~~~igDeTG~---Ir~tlW~~----~~-l-~~Gdvv~I~na 127 (423)
T PRK07218 58 SKDIKELSTD-DKNVTVTGRVLTIGERSIRYQGDDHVIYEGILADETGT---ISYTAWKD----FG-L-SPGDTVTIGNA 127 (423)
T ss_pred CccHhhCCCC-CceeEEEEEEEEecceeEecCCCceEEEEEEEECCCCe---EEEEEECC----CC-C-CCCCEEEEecc
Confidence 4568888633 45799999999996521 2234 367889999999653 99999984 23 6 79999999999
Q ss_pred EEEEEcCeeeEEecCCceEEEEEeCCCCCCCCccccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCcccccccccccCC
Q 012376 88 MIKKHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSLKDISEH 167 (465)
Q Consensus 88 ki~~~~g~~~~~~~~~~ss~~lf~~~~~~~~~Py~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~f~~~Lkdi~~~ 167 (465)
.++.|+|++.+..+.. +....-+.. ..| . +.. . .. ..|.|++++
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 9999999998887754 555533321 111 0 100 0 11 468899865
Q ss_pred -ceEeEEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCccccCCCChhccccCCCcce-EEEEEecc
Q 012376 168 -RYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGT-VLRVSTDR 245 (465)
Q Consensus 168 -~f~Dlv~qVv~v~~~~~~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~p~~G~-vL~V~~~~ 245 (465)
..+++.++|+.++ . + .+-.-||+. ... +..+.| .+ ++++++|+
T Consensus 172 ~~~V~v~g~Vl~~~-~----r-~f~~~dg~~--~v~-~giigD--------------------------eTG~Ir~tlW~ 216 (423)
T PRK07218 172 DRGVNVEARVLELE-H----R-EIDGRDGET--TIL-SGVLAD--------------------------ETGRLPFTDWD 216 (423)
T ss_pred CCceEEEEEEEEec-c----e-eEEcCCCCe--EEE-EEEEEC--------------------------CCceEEEEEec
Confidence 4589999999875 3 1 233444431 111 111111 22 67999999
Q ss_pred chhhhhccCCCCCcEEEEeCcEEEEeCcEEEEEEecCCceEEcCCCChhHHHHHHHHHHHHhCCCCCCCCcCCCCCC---
Q 012376 246 SYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDNDNVVWDYMRRFRERISGGHGHMPIWTDPSSQ--- 322 (465)
Q Consensus 246 ~~~~~~~~~~k~G~wV~l~Nv~~k~~~g~leG~l~~~ski~~l~~~d~~v~~r~r~y~~r~~~~~~~~~~~~~~~~~--- 322 (465)
+++ .+.+|++|++.|...+.+.|.++-.+...+.|..++.+- ++.. ...++.........
T Consensus 217 ~~~-----~l~~Gd~v~I~na~v~e~~G~~elnv~~~t~I~~~d~~i-~v~~-----------~~~~~~I~e~~~~~g~~ 279 (423)
T PRK07218 217 PLP-----EIEIGASIRIEDAYVREFRGVPSVNVSEFTTVEALDREV-SVSK-----------DPPRLKIREAVERGGIF 279 (423)
T ss_pred ccc-----cCCCCCEEEEeeeEEeccCCeEEEEECCceEEEECCCCc-cccC-----------CccccchhhhhccCCcc
Confidence 765 379999999999999999999999999999998876431 1000 00000000000000
Q ss_pred --CCcc--cccCCCccccHHHHh-hCCCCCcceEEEEEEEeecCCCccccccCC----CCeEEEEEEEEeCCCceEEEEE
Q 012376 323 --FLTE--VDWVNVASVTLMKIA-TQLQGNVRCCCIVRVVSIHPFQAEHYSSPN----GSSEYTMKLTLEDPTARIHALL 393 (465)
Q Consensus 323 --~~t~--~~~~~~p~ttL~dIL-~~p~v~~kfr~~VRVV~~~P~~~edf~~~~----~~w~~rf~L~lED~t~ri~~~v 393 (465)
.++. ++.. .=+=++ -.|. +=||++- -.|..+ +.+-=|....|.|.|+.+.+++
T Consensus 280 ~Vev~G~Iv~i~-----~gsgli~rCP~-------C~r~v~~------~~C~~hG~ve~~~dlrik~vLDDGtg~~~~~~ 341 (423)
T PRK07218 280 DVELVGNIISVR-----DGSGLIERCPE-------CGRVIQK------GQCRSHGAVEGEDDLRIKAILDDGTGSVTVIL 341 (423)
T ss_pred eEEEEEEEEEec-----cCCcceecCcC-------ccccccC------CcCCCCCCcCCeeeeEEEEEEECCCCeEEEEE
Confidence 0000 0000 000001 1232 1133321 233323 4556789999999999999999
Q ss_pred eccccchhcCC
Q 012376 394 CGKEWVKFFGG 404 (465)
Q Consensus 394 ~~~da~~f~~~ 404 (465)
..+.++.+.|.
T Consensus 342 ~~e~~e~l~G~ 352 (423)
T PRK07218 342 DRELTEIVYGG 352 (423)
T ss_pred ChhhhHhHhCC
Confidence 99999999985
No 9
>PRK14699 replication factor A; Provisional
Probab=98.97 E-value=6.4e-07 Score=94.99 Aligned_cols=272 Identities=19% Similarity=0.197 Sum_probs=181.3
Q ss_pred eehHhhhhccCCEEEEEEEEEecCCccc---cCCCc-eEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEee
Q 012376 11 VRIKELAMHVKHKVNLLGVVLEFSIPRK---SQGTD-YVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKN 86 (465)
Q Consensus 11 ~~i~~~~~~~~~~vnviGVVvd~~~P~~---trG~D-~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~r 86 (465)
..|+++... ...||+.|-|+...+|+. ..|+. -..++.|-|+|=. +++.++.+..+.+|.+ ..||+|++.+
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-MGDLNLTGKVLEISEIRTFQRKDGTSGKVGNLLLGDETGT---LRVTLWDDKTDFLNQI-EYGDTVELIN 241 (484)
T ss_pred cchhhcCCC-CCceEEEEEEEeccCceEEecCCCCceEEEEEEEEcCCce---EEEEEECccccccccc-CCCCEEEEec
Confidence 467776532 235999999999998863 23533 6778899999763 9999999877777888 6999999998
Q ss_pred EEEE--EEcCeeeEEecCCceEEEEEeCCCCCCCCccccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCcccccccccc
Q 012376 87 VMIK--KHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSLKDI 164 (465)
Q Consensus 87 vki~--~~~g~~~~~~~~~~ss~~lf~~~~~~~~~Py~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~f~~~Lkdi 164 (465)
+.++ .|+|.+.+..+.. +... ......+ +.. .+ ..|.+|
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-CceEeEEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCccccCCCChhccccCCCcceEEEEEe
Q 012376 165 SE-HRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRVST 243 (465)
Q Consensus 165 ~~-~~f~Dlv~qVv~v~~~~~~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~p~~G~vL~V~~ 243 (465)
++ +..+++.++|+++. + -..|. --||++-.-+ +..+.|+ -| .+|+|+
T Consensus 283 ~~~~~~v~I~grV~~~~-~--~r~~~--~~~Gseg~v~--~~~l~De------------------------TG-~Ir~T~ 330 (484)
T PRK14699 283 KADMNNINISGRVLDIS-E--VRTFE--KKDGSPGRVG--NLLLGDS------------------------TG-KIRLTL 330 (484)
T ss_pred CCCCceeEEEEEEEEcC-C--CeEEE--cCCCCeeEEE--EEEEECC------------------------CC-eEEEEE
Confidence 75 48899999999776 3 11211 2233211111 1111110 04 589999
Q ss_pred ccchhhhhccCCCCCcEEEEeCcEEEEe--CcEEEEEEecCCceEEcCCCChhHHHHHHHHHHHHhCCCCCCCCcCCCCC
Q 012376 244 DRSYENFGRYFTATGKWVRIRNMSCQVS--SGMWHGLLQSSSKIRLFSDNDNVVWDYMRRFRERISGGHGHMPIWTDPSS 321 (465)
Q Consensus 244 ~~~~~~~~~~~~k~G~wV~l~Nv~~k~~--~g~leG~l~~~ski~~l~~~d~~v~~r~r~y~~r~~~~~~~~~~~~~~~~ 321 (465)
|++.+++ ...+.+|+.+++.|...+.+ +|.+|..+...+.|...++. .+
T Consensus 331 W~~~a~~-~~~i~~Gd~v~i~~~y~~~~~~~~~~eL~~~~~t~I~~~~~~-~e--------------------------- 381 (484)
T PRK14699 331 WDEKTNF-LDEIDFDETVEVLNAYSRENTFSQQVELNLGARGIIQKSEKK-VE--------------------------- 381 (484)
T ss_pred eCccccc-ccccCCCceEEEEeEEEEeccCCccEEEEecCceeEeecCCc-ce---------------------------
Confidence 9999865 56789999999999998875 36788888887766443221 10
Q ss_pred CCCcccccCCCccccHHHHhhCCCCCcceEEEEEEEeecCCCccccccCCCCeEEEEEEEEeCCCceEEEEEeccccchh
Q 012376 322 QFLTEVDWVNVASVTLMKIATQLQGNVRCCCIVRVVSIHPFQAEHYSSPNGSSEYTMKLTLEDPTARIHALLCGKEWVKF 401 (465)
Q Consensus 322 ~~~t~~~~~~~p~ttL~dIL~~p~v~~kfr~~VRVV~~~P~~~edf~~~~~~w~~rf~L~lED~t~ri~~~v~~~da~~f 401 (465)
. ..+++.|.||- -...+-..-+|+++.|.+ .|.+.+|.=-++--|+|.|.|+++.+-++|+.|+.|
T Consensus 382 -----~---~~~~~~I~die----~~~~vdV~G~V~~v~~~~--~~~~~~g~~~~vr~i~l~D~TG~Ir~tlWg~~A~~~ 447 (484)
T PRK14699 382 -----Y---REKFTDIADII----PGESYSVQGKVSEIGELR--EFEREDGTENVVANLQLKDETGSIRLTLWGEQAYVI 447 (484)
T ss_pred -----e---eeccccHHHcc----CCCeeEEEEEEEEcCCcc--eEEecCCCEEEEEEEEEEcCCCeEEEEEcchhhhhc
Confidence 0 11456677773 233567777888888865 666655644477789999999999999999999875
No 10
>PRK07211 replication factor A; Reviewed
Probab=98.94 E-value=6.4e-08 Score=101.69 Aligned_cols=204 Identities=16% Similarity=0.208 Sum_probs=145.1
Q ss_pred cceeehHhhhhccCCEEEEEEEEEecCCccc---cCC-CceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEE
Q 012376 8 GGIVRIKELAMHVKHKVNLLGVVLEFSIPRK---SQG-TDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLIL 83 (465)
Q Consensus 8 y~y~~i~~~~~~~~~~vnviGVVvd~~~P~~---trG-~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~ 83 (465)
..+.+|+++.. ....++|+|+|++..+++. .+| .-.+.++.|.|+|-. +++.+|.+..+.++.+ .+||||.
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 47789999973 2346999999999998763 235 456789999998762 9999999888888878 7999999
Q ss_pred EeeEEEEEEcCeeeEEecCCceEEEEEeCCCCCCCCccccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCccccccccc
Q 012376 84 LKNVMIKKHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSLKD 163 (465)
Q Consensus 84 l~rvki~~~~g~~~~~~~~~~ss~~lf~~~~~~~~~Py~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~f~~~Lkd 163 (465)
+.+++++.++|.+.+..+.. +...-... .....| .+ ..|.+
T Consensus 234 I~~a~Vre~~g~~ELsl~~~-s~I~~~~d--ev~~vp-----------------------------------~~-~~I~d 274 (485)
T PRK07211 234 IVDGYVRERDGSLELHVGDR-GAVEEVDE--DVEYVP-----------------------------------DT-TPIES 274 (485)
T ss_pred EEeeEEEecCCcEEEEECCC-ceEEECCc--cccccc-----------------------------------cc-ccHhh
Confidence 99999999999988877643 33331111 001111 12 46788
Q ss_pred ccCCceEeEEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCccccCCCChhccccCCCcceEEEEEe
Q 012376 164 ISEHRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRVST 243 (465)
Q Consensus 164 i~~~~f~Dlv~qVv~v~~~~~~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~p~~G~vL~V~~ 243 (465)
+.++..+|+++.|+.+. + .-++-=-||+...--.+. +.+ --| .+||++
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 88999999999999876 2 222222234422211100 000 014 689999
Q ss_pred ccchhhhhccCCCCCcEEEEeCcEEEEe-CcEEEEEEecCCceEEcCC
Q 012376 244 DRSYENFGRYFTATGKWVRIRNMSCQVS-SGMWHGLLQSSSKIRLFSD 290 (465)
Q Consensus 244 ~~~~~~~~~~~~k~G~wV~l~Nv~~k~~-~g~leG~l~~~ski~~l~~ 290 (465)
|.+++.+ .+.+|+.|+|.|++++-. .|-+|..+...+.|.+|+.
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 9999854 689999999999999994 4778888888889988865
No 11
>PRK15491 replication factor A; Provisional
Probab=98.92 E-value=1.2e-06 Score=90.42 Aligned_cols=272 Identities=15% Similarity=0.172 Sum_probs=177.6
Q ss_pred ceeehHhhhhccCCEEEEEEEEEecCCccc---cCC-CceEEEEEEEeCCCCCCCeEEEEecCCCCCC--CCCCCCCCEE
Q 012376 9 GIVRIKELAMHVKHKVNLLGVVLEFSIPRK---SQG-TDYVCVLKIVDDSQQSPELLVNIFTSSIDQL--PRVLSPRDLI 82 (465)
Q Consensus 9 ~y~~i~~~~~~~~~~vnviGVVvd~~~P~~---trG-~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~L--P~v~~~GDII 82 (465)
.-++|+|+... ...|++.|-|+....|+. .+| .-...++.|.|++=. +++.+|.+..+.+ |.+ .+||++
T Consensus 56 ~~~kI~dL~~~-~~~v~i~arVl~~~~~R~f~r~dGs~g~v~~~~v~DeTG~---ir~tlW~~~a~~~~~~~l-e~G~v~ 130 (374)
T PRK15491 56 DTTKIADINES-SSNVNFTAKVVSIFEPKEFNRNDGTTGRVGNIIVADETGS---IRLTLWDDLADLIKTGDI-EVGKSL 130 (374)
T ss_pred ccccHHHCCCC-CCceEEEEEEeeccCCeeeecCCCCceEEEEEEEEcCCCe---EEEEEECchhhhhccCCc-CCCCEE
Confidence 35578998622 256999999999988864 246 467889999998653 9999999766665 678 699999
Q ss_pred EEeeEEEEEEcCeeeEEecCCceEEEEEeCCCCCCCCccccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCcccccccc
Q 012376 83 LLKNVMIKKHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSLK 162 (465)
Q Consensus 83 ~l~rvki~~~~g~~~~~~~~~~ss~~lf~~~~~~~~~Py~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~f~~~Lk 162 (465)
.++..--..|+| +....+.. +...-.. ... + .. ..| ..|+
T Consensus 131 ~I~~~~~~~y~g-~Ei~i~~~-~~i~~~~----~~~-~-------~~-------------------------~~~-~~I~ 170 (374)
T PRK15491 131 NISGYAKEGYSG-IEVNIGRY-GGISESD----ENV-K-------AS-------------------------INS-QKIS 170 (374)
T ss_pred EEeeeeccCccc-EEEEeCCC-ceeeecc----ccc-c-------cc-------------------------cCc-ccHH
Confidence 999875556766 55544432 2221000 000 0 00 024 5677
Q ss_pred cccCC-ceEeEEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCccccCCCChhccccCCCcceEEEE
Q 012376 163 DISEH-RYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRV 241 (465)
Q Consensus 163 di~~~-~f~Dlv~qVv~v~~~~~~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~p~~G~vL~V 241 (465)
||..+ ..+|+.++|+.+. + ...+. --||+...-+. ..+.+ --| .+++
T Consensus 171 dl~~~~~~V~I~g~V~~~~-~--~r~~~--~~~G~~~~v~~--~~l~D------------------------etG-~Ir~ 218 (374)
T PRK15491 171 DIKDGDSDINIVGKVLDIS-D--VRTFQ--KKDGSQGRVRN--ITIGD------------------------ETG-KIRV 218 (374)
T ss_pred HcCCCCccEEEEEEEEEcc-C--ceEEE--ecCCCeEEEEE--EEEEC------------------------CCC-eEEE
Confidence 77654 4699999999887 3 11221 22443211111 10000 015 4899
Q ss_pred EeccchhhhhccCCCCCcEEEEeCcEEEE--eCcEEEEEEecCCceEEcCCCChhHHHHHHHHHHHHhCCCCCCCCcCCC
Q 012376 242 STDRSYENFGRYFTATGKWVRIRNMSCQV--SSGMWHGLLQSSSKIRLFSDNDNVVWDYMRRFRERISGGHGHMPIWTDP 319 (465)
Q Consensus 242 ~~~~~~~~~~~~~~k~G~wV~l~Nv~~k~--~~g~leG~l~~~ski~~l~~~d~~v~~r~r~y~~r~~~~~~~~~~~~~~ 319 (465)
++|..++.. ...+++|+-|++.|-.++. ..|.+|-.+..++.|...+. +.+
T Consensus 219 t~W~~~a~~-~~~l~~Gd~V~i~~~~~r~~~~~g~~El~~~~~s~I~~~~~-~~e------------------------- 271 (374)
T PRK15491 219 TLWDGKTDL-ADKLENGDSVEIINGYARTNNYSQEVEIQIGNHGSLRKTDR-NVE------------------------- 271 (374)
T ss_pred EEecchhcc-cccCCCCCEEEEEeceEEEeccCCCEEEEeCCCceEEECCc-ccc-------------------------
Confidence 999999887 3779999999999988876 35788888888888865432 110
Q ss_pred CCCCCcccccCCCccccHHHHhhCCCCCcceEEEEEEEeecCCCccccccCCCCeEEEEEEEEeCCCceEEEEEeccccc
Q 012376 320 SSQFLTEVDWVNVASVTLMKIATQLQGNVRCCCIVRVVSIHPFQAEHYSSPNGSSEYTMKLTLEDPTARIHALLCGKEWV 399 (465)
Q Consensus 320 ~~~~~t~~~~~~~p~ttL~dIL~~p~v~~kfr~~VRVV~~~P~~~edf~~~~~~w~~rf~L~lED~t~ri~~~v~~~da~ 399 (465)
.. .++++|.||-.. ..+-...+|....|. ..|.+.+|.=...=-|+|.|.|++|++-++|+.|+
T Consensus 272 -------~~---~~f~~I~dl~~~----~~~dv~G~V~~v~~~--~~~~~~~G~~~~~r~i~l~D~Tg~Ir~tlWg~~a~ 335 (374)
T PRK15491 272 -------YE---EDFTPIADIIPG----QPYSIKGAVSGLGDL--KEFTKSDGSENKVSNIYVSDDTGRIRIALWGEKAE 335 (374)
T ss_pred -------cC---CCccCHHHcCCC----CceeEEEEEEEcCCc--EEEEccCCCEeEEEeEEEEeCCCcEEEEEcccccc
Confidence 00 134557777532 235666777777664 45555556444666789999999999999999998
Q ss_pred h
Q 012376 400 K 400 (465)
Q Consensus 400 ~ 400 (465)
.
T Consensus 336 ~ 336 (374)
T PRK15491 336 L 336 (374)
T ss_pred c
Confidence 5
No 12
>PRK06386 replication factor A; Reviewed
Probab=98.89 E-value=6.6e-06 Score=83.78 Aligned_cols=274 Identities=16% Similarity=0.161 Sum_probs=165.0
Q ss_pred eehHhhhhccCCEEEEEEEEEecCCc-ccc-CCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEE
Q 012376 11 VRIKELAMHVKHKVNLLGVVLEFSIP-RKS-QGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVM 88 (465)
Q Consensus 11 ~~i~~~~~~~~~~vnviGVVvd~~~P-~~t-rG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvk 88 (465)
+.|+|+.. .+..||+.|-|++.... .+. +|.--..+-.|-|++=- +++.+..+ .|.+ ..||+|+|.|++
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 35777762 24469999999999731 122 34444445557777542 78888763 4667 689999999999
Q ss_pred EEEEcCeeeEEecCCceEEEEEeCCCCCCCCccccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCcccccccccccCC-
Q 012376 89 IKKHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSLKDISEH- 167 (465)
Q Consensus 89 i~~~~g~~~~~~~~~~ss~~lf~~~~~~~~~Py~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~f~~~Lkdi~~~- 167 (465)
++.|+|++.+..+.. +.... .. +... + ..+. -+. ..|+||+++
T Consensus 74 v~~~~G~~~Lnv~~~-t~v~~-~~--d~~i-e---------v~~~---------------------~~~-~KI~DL~~g~ 117 (358)
T PRK06386 74 SKEYNGKIRIYFDSR-SEVML-KP--DENI-E---------VKRT---------------------YKL-VKIRDLSLVT 117 (358)
T ss_pred EeeECCEEEEEEcCc-eEEEe-cC--cccc-c---------cccc---------------------cCc-cEeEeccCCC
Confidence 999999998877644 43321 11 1111 0 0000 012 579999875
Q ss_pred ceEeEEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCccccCCCChhccccCCCcce-EEEEEeccc
Q 012376 168 RYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGT-VLRVSTDRS 246 (465)
Q Consensus 168 ~f~Dlv~qVv~v~~~~~~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~p~~G~-vL~V~~~~~ 246 (465)
.++++.++|+.++ + . .+- .||+. .......+.| .+ .+++++|..
T Consensus 118 ~~v~V~akVle~~-e---~--e~~-~~g~~--~~v~sg~lgD--------------------------eTGrIr~TlW~~ 162 (358)
T PRK06386 118 PYVSVIGKITGIT-K---K--EYD-SDGTS--KIVYQGYIED--------------------------DTARVRISSFGK 162 (358)
T ss_pred CceEEEEEEEEcc-C---c--eEe-cCCCc--cEEEEEEEEc--------------------------CCCeEEEEEccc
Confidence 5679999999876 3 1 222 45541 1110110111 12 679999974
Q ss_pred hhhhhccCCCCCcEEEEeCcEEEEeCcEEEEEEecCCceEEcCCCChhHHHHHHHHHHHHhCCCCCCCCcCCCCCCCCcc
Q 012376 247 YENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDNDNVVWDYMRRFRERISGGHGHMPIWTDPSSQFLTE 326 (465)
Q Consensus 247 ~~~~~~~~~k~G~wV~l~Nv~~k~~~g~leG~l~~~ski~~l~~~d~~v~~r~r~y~~r~~~~~~~~~~~~~~~~~~~t~ 326 (465)
.++.|+.|+|.|...+.+.|.++-.+...+.|..++.+- ++..+ +.+-..+.. ....++
T Consensus 163 -------~l~eGd~v~i~na~v~e~~G~~el~v~~~t~I~~~~~~i-ev~~~-~~~I~di~~------------~~g~v~ 221 (358)
T PRK06386 163 -------PLEDNRFVRIENARVSQYNGYIEISVGNKSVIKEVESDI-NLESR-NIFIFEIKS------------PVGGIT 221 (358)
T ss_pred -------cccCCCEEEEeeeEEEccCCeEEEEeCCeEEEEECCCCc-ccCcc-ccchhhhhc------------cCCeEE
Confidence 378999999999999999999999999888887765422 11111 000000100 000011
Q ss_pred cccCCCccccHHHHh-------hCCCCCcceEEEEEEEeecCCCccccccCC----CCeEEEEEEEEeCCCceEEEEEec
Q 012376 327 VDWVNVASVTLMKIA-------TQLQGNVRCCCIVRVVSIHPFQAEHYSSPN----GSSEYTMKLTLEDPTARIHALLCG 395 (465)
Q Consensus 327 ~~~~~~p~ttL~dIL-------~~p~v~~kfr~~VRVV~~~P~~~edf~~~~----~~w~~rf~L~lED~t~ri~~~v~~ 395 (465)
+. =+|-+|- ..|. +=||++- -.|..+ +.+--|..+.|.|.|+.+.+.+++
T Consensus 222 i~------G~iv~i~~gsgli~rCP~-------C~R~l~~------g~C~~HG~v~~~~dlr~k~vLDDGtg~~~~~l~~ 282 (358)
T PRK06386 222 IM------GFIVSVGQGSRIFTKCSV-------CNKIIED------GVCKDHPDAPVYLDIFGYFTISDGTGFVTCYANK 282 (358)
T ss_pred EE------EEEEEEcCCcEeEecCcC-------CCeEccC------CcCCCCCCCCCeeEEEEEEEEECCCCeEEEEECh
Confidence 00 0011111 1331 1244541 366544 444456777999999999999999
Q ss_pred cccchhcCC
Q 012376 396 KEWVKFFGG 404 (465)
Q Consensus 396 ~da~~f~~~ 404 (465)
+.++.++|.
T Consensus 283 e~~e~l~G~ 291 (358)
T PRK06386 283 DSFLPYINI 291 (358)
T ss_pred HHhHHHhCC
Confidence 999999985
No 13
>PRK15491 replication factor A; Provisional
Probab=98.78 E-value=4.8e-07 Score=93.27 Aligned_cols=204 Identities=16% Similarity=0.181 Sum_probs=141.0
Q ss_pred CCcceeehHhhhhccCCEEEEEEEEEecCCcccc---CCC-ceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCE
Q 012376 6 NQGGIVRIKELAMHVKHKVNLLGVVLEFSIPRKS---QGT-DYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDL 81 (465)
Q Consensus 6 ~~y~y~~i~~~~~~~~~~vnviGVVvd~~~P~~t---rG~-D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDI 81 (465)
..|.|++|+++... ...|++.|+|++..+++.= +|+ -...++.|.|+|- .+++.+|.+..+.++.+ .+||+
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 35677899998632 3359999999999887532 355 4788899999865 29999999876777777 69999
Q ss_pred EEEeeEEEE--EEcCeeeEEecCCceEEEEEeCCCCCCCCccccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCccccc
Q 012376 82 ILLKNVMIK--KHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLL 159 (465)
Q Consensus 82 I~l~rvki~--~~~g~~~~~~~~~~ss~~lf~~~~~~~~~Py~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~f~~ 159 (465)
|.+.+..++ .|+|++.+..+.. ++...- .... + +. ..| .
T Consensus 237 V~i~~~~~r~~~~~g~~El~~~~~-s~I~~~--~~~~---e-------~~-------------------------~~f-~ 277 (374)
T PRK15491 237 VEIINGYARTNNYSQEVEIQIGNH-GSLRKT--DRNV---E-------YE-------------------------EDF-T 277 (374)
T ss_pred EEEEeceEEEeccCCCEEEEeCCC-ceEEEC--Cccc---c-------cC-------------------------CCc-c
Confidence 999997655 5678888877644 443311 1000 0 10 025 6
Q ss_pred ccccccCCceEeEEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCccccCCCChhccccCCCcceEE
Q 012376 160 SLKDISEHRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVL 239 (465)
Q Consensus 160 ~Lkdi~~~~f~Dlv~qVv~v~~~~~~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~p~~G~vL 239 (465)
.|.||.++..+|+++.|..+. + .-++--.||+...--.+. +.| + -|+ +
T Consensus 278 ~I~dl~~~~~~dv~G~V~~v~-~----~~~~~~~~G~~~~~r~i~--l~D-----------------~-------Tg~-I 325 (374)
T PRK15491 278 PIADIIPGQPYSIKGAVSGLG-D----LKEFTKSDGSENKVSNIY--VSD-----------------D-------TGR-I 325 (374)
T ss_pred CHHHcCCCCceeEEEEEEEcC-C----cEEEEccCCCEeEEEeEE--EEe-----------------C-------CCc-E
Confidence 788898899999999999885 2 112222454432211100 000 0 143 8
Q ss_pred EEEeccchhhhhccCCCCCcEEEEeCcEEEE-eCcEEEEEEecCCceE
Q 012376 240 RVSTDRSYENFGRYFTATGKWVRIRNMSCQV-SSGMWHGLLQSSSKIR 286 (465)
Q Consensus 240 ~V~~~~~~~~~~~~~~k~G~wV~l~Nv~~k~-~~g~leG~l~~~ski~ 286 (465)
++++|..+|.. ...+-+|+.|++.+..+|. ..|.+|......|.|.
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 5567889999999999998 5589999888877774
No 14
>PRK14699 replication factor A; Provisional
Probab=98.61 E-value=3.6e-06 Score=89.40 Aligned_cols=204 Identities=13% Similarity=0.157 Sum_probs=141.3
Q ss_pred cceeehHhhhhccCCEEEEEEEEEecCCccc---cCC-CceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEE
Q 012376 8 GGIVRIKELAMHVKHKVNLLGVVLEFSIPRK---SQG-TDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLIL 83 (465)
Q Consensus 8 y~y~~i~~~~~~~~~~vnviGVVvd~~~P~~---trG-~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~ 83 (465)
..+++|.++.. -...+++.|.|++..+|+. .+| .....++.|.|.|=. +++.+|.+..+.++.+ ..||+|.
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--cCeeeEEecCCceEEEEEeCCCCCCCCccccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCccccccc
Q 012376 84 LKNVMIKKH--QAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSL 161 (465)
Q Consensus 84 l~rvki~~~--~g~~~~~~~~~~ss~~lf~~~~~~~~~Py~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~f~~~L 161 (465)
+.++.++.. ++.+.+..+.. +.. ....+.. . +. ..| ..|
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 45677776644 311 1111000 0 00 036 789
Q ss_pred ccccCCceEeEEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCccccCCCChhccccCCCcceEEEE
Q 012376 162 KDISEHRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRV 241 (465)
Q Consensus 162 kdi~~~~f~Dlv~qVv~v~~~~~~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~p~~G~vL~V 241 (465)
.||.+++.+|+++.|..+. +. ..+. -.||+.-.--. ..+.| --| .+|+
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 13433211100 00000 014 7899
Q ss_pred EeccchhhhhccCCCCCcEEEEeCcEEEE-eCcEEEEEEecCCceEEc
Q 012376 242 STDRSYENFGRYFTATGKWVRIRNMSCQV-SSGMWHGLLQSSSKIRLF 288 (465)
Q Consensus 242 ~~~~~~~~~~~~~~k~G~wV~l~Nv~~k~-~~g~leG~l~~~ski~~l 288 (465)
++|...|.. .+.+.+|+-|.+.|..++. .+|.+|..+-..|.|.+|
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 999988864 5689999999999999999 478999988888877554
No 15
>PRK07211 replication factor A; Reviewed
Probab=98.41 E-value=0.00025 Score=75.02 Aligned_cols=269 Identities=14% Similarity=0.160 Sum_probs=169.2
Q ss_pred eeehHhhhhccC-CEEEEEEEEEecCCcccc-C----CCceEEEEEEEeCCCCCCCeEEEEecCCCC-CCCCCCCCCCEE
Q 012376 10 IVRIKELAMHVK-HKVNLLGVVLEFSIPRKS-Q----GTDYVCVLKIVDDSQQSPELLVNIFTSSID-QLPRVLSPRDLI 82 (465)
Q Consensus 10 y~~i~~~~~~~~-~~vnviGVVvd~~~P~~t-r----G~D~~~tl~I~D~s~~~~gl~v~iF~~~~~-~LP~v~~~GDII 82 (465)
..+|+++. ++ ..|++.|-|+..+.|+.= + +.--.+++.|.|+|= .|++.+|....+ ..|.+ ++|||+
T Consensus 53 ~~~I~dL~--pg~~~vtI~aRV~~~~~~Rt~~~~~~~~eGkv~~v~l~DeTG---~Ir~TlW~d~ad~~~~~L-e~GdV~ 126 (485)
T PRK07211 53 VNGIADIE--PGMDEVKFLAKVLSIGDLRTFERDGEDEDGRVINVEVADETG---SVRVAFWDEQAVAAEEEL-EVGQVL 126 (485)
T ss_pred cccHhhCC--CCCCceEEEEEEeEccCceEEEeCCCCCCcEEEEEEEEcCCC---eEEEEEechHhHhhhccc-CCCCEE
Confidence 34788886 55 459999999999987642 2 235899999999765 399999975433 46778 799999
Q ss_pred EEeeEEEEEEcCeeeEEecCCceEEEEEeCCCCCCCCccccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCcccccccc
Q 012376 83 LLKNVMIKKHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSLK 162 (465)
Q Consensus 83 ~l~rvki~~~~g~~~~~~~~~~ss~~lf~~~~~~~~~Py~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~f~~~Lk 162 (465)
.+.+.-...|++ +.+..+ . ........+ |++ . ..| ..|+
T Consensus 127 ~I~~~~~~~ys~-~El~i~----~---ve~~~d~~i-~~~------------------------------~-~~~-~~I~ 165 (485)
T PRK07211 127 RIKGRPKDGYNG-LEVSVD----K---VEPDPDAEI-DVQ------------------------------I-GDT-YTVE 165 (485)
T ss_pred EEeceEeccccc-eEEEEe----e---EEEcccccc-ccc------------------------------c-cCC-ccHH
Confidence 997754444443 222222 0 111000000 000 0 024 6788
Q ss_pred cccCC-ceEeEEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCccccCCCChhccccCCCcceEEEE
Q 012376 163 DISEH-RYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRV 241 (465)
Q Consensus 163 di~~~-~f~Dlv~qVv~v~~~~~~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~p~~G~vL~V 241 (465)
||+++ ..+|++++|+.+. +. ..| -=-||++-.-+. ..+-+ --| .+|+
T Consensus 166 dL~~~~~~v~I~grV~~v~-~i--Rtf--~r~dGseGkv~s--v~L~D------------------------eTG-~IR~ 213 (485)
T PRK07211 166 DLSLGLSDVTLVGVVLDTD-SV--RTF--DRDDGSEGRVSN--LTVGD------------------------ETG-RVRV 213 (485)
T ss_pred HcCCCCCceEEEEEEEEcC-CC--eEE--ECCCCCeeEEEE--EEEEc------------------------CCC-eEEE
Confidence 88865 5689999999776 31 010 011222111111 10000 015 4899
Q ss_pred EeccchhhhhccCCCCCcEEEEeCcEEEEeCcEEEEEEecCCceEEcCCCChhHHHHHHHHHHHHhCCCCCCCCcCCCCC
Q 012376 242 STDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDNDNVVWDYMRRFRERISGGHGHMPIWTDPSS 321 (465)
Q Consensus 242 ~~~~~~~~~~~~~~k~G~wV~l~Nv~~k~~~g~leG~l~~~ski~~l~~~d~~v~~r~r~y~~r~~~~~~~~~~~~~~~~ 321 (465)
|+|+.++... ..+.+|+-|++.|.+++...|.+|..+..++.|..++.+ .+ + +| .
T Consensus 214 TlW~d~Ad~~-~~le~G~Vv~I~~a~Vre~~g~~ELsl~~~s~I~~~~de-v~-------~----------vp-----~- 268 (485)
T PRK07211 214 TLWDDRADLA-EELDAGESVEIVDGYVRERDGSLELHVGDRGAVEEVDED-VE-------Y----------VP-----D- 268 (485)
T ss_pred EEechhhhhh-ccCCCCCEEEEEeeEEEecCCcEEEEECCCceEEECCcc-cc-------c----------cc-----c-
Confidence 9999988874 779999999999999999878888888888888765542 10 0 01 0
Q ss_pred CCCcccccCCCccccHHHHhhCCCCCcceEEEEEEEeecCCCccccccCCCCeEEEEEEEEeCCCceEEEEEeccccch
Q 012376 322 QFLTEVDWVNVASVTLMKIATQLQGNVRCCCIVRVVSIHPFQAEHYSSPNGSSEYTMKLTLEDPTARIHALLCGKEWVK 400 (465)
Q Consensus 322 ~~~t~~~~~~~p~ttL~dIL~~p~v~~kfr~~VRVV~~~P~~~edf~~~~~~w~~rf~L~lED~t~ri~~~v~~~da~~ 400 (465)
++.|.++- + ..-.-...+|.+..|... |.+.+|+=-..--++|-|.|+++++-++|+.|..
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 12333322 1 112456678888877654 4454553346778999999999999999999853
No 16
>PRK08402 replication factor A; Reviewed
Probab=98.35 E-value=4.1e-05 Score=78.26 Aligned_cols=195 Identities=15% Similarity=0.143 Sum_probs=113.4
Q ss_pred cccccccCC-ceEeEEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCccccCCCChhccccCCCcce
Q 012376 159 LSLKDISEH-RYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGT 237 (465)
Q Consensus 159 ~~Lkdi~~~-~f~Dlv~qVv~v~~~~~~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~p~~G~ 237 (465)
..|+||.++ ..++++++|+.+. +.. . +---||+...-. +..+.| --|+
T Consensus 63 ~kI~dl~~g~~~V~v~~rVl~~~-~~r--~--f~rrdG~~~~V~--~i~l~D------------------------eTG~ 111 (355)
T PRK08402 63 MHISDLVPGMRGVNIVGRVLRKY-PPR--E--YTKKDGSTGRVA--SLIIYD------------------------DTGR 111 (355)
T ss_pred cCHHHccCCCceeeEEEEEEEcc-CCc--e--eeccCCCcceEE--EEEEEc------------------------CCCe
Confidence 679999987 5899999999886 311 1 001122211000 000000 0144
Q ss_pred EEEEEeccchhhhhccCCCCCcEEEEeCcEEEE-eCcEEEEEEecCCceEEcCCCChhHHHHHHHHHHHHhCCCCCCCCc
Q 012376 238 VLRVSTDRSYENFGRYFTATGKWVRIRNMSCQV-SSGMWHGLLQSSSKIRLFSDNDNVVWDYMRRFRERISGGHGHMPIW 316 (465)
Q Consensus 238 vL~V~~~~~~~~~~~~~~k~G~wV~l~Nv~~k~-~~g~leG~l~~~ski~~l~~~d~~v~~r~r~y~~r~~~~~~~~~~~ 316 (465)
+ ++++|+.++.-....+.+|+-|++.|..++- .+|..+..+...|.|.+.++ ++++.+ +|
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 9999998876334569999999999999998 59998999999999876553 332211 11
Q ss_pred CCCCCCCCcccccCCCccccHHHHhhCCCCCcceEEEEEEEeecCCCc--------cc---------c-cc--C--CCCe
Q 012376 317 TDPSSQFLTEVDWVNVASVTLMKIATQLQGNVRCCCIVRVVSIHPFQA--------EH---------Y-SS--P--NGSS 374 (465)
Q Consensus 317 ~~~~~~~~t~~~~~~~p~ttL~dIL~~p~v~~kfr~~VRVV~~~P~~~--------ed---------f-~~--~--~~~w 374 (465)
....+.. . ..+..+|.||-.. . .-|.+...|+.+.+.-+ +. + |. + ...|
T Consensus 173 ---~~~~~~~--~-~~~~k~I~ei~~g-d--~~v~v~g~Iv~i~~~~~y~aCp~CnKkv~~~~~~~~~~Ce~~~~v~p~~ 243 (355)
T PRK08402 173 ---PLEEVRS--Y-NYTRKKIGELEGG-E--RFVEVRGTIAKVYRVLVYDACPECRRKVDYDPATDTWICPEHGEVEPIK 243 (355)
T ss_pred ---ccccccc--c-cccccCHHHcccC-C--cEEEEEEEEEEEecCeeEecCCCCCeEEEEecCCCCEeCCCCCCcCcce
Confidence 1000000 0 1223334444211 0 00233333333333000 00 0 10 1 3578
Q ss_pred EEEEEEEEeCCCceEEEEEeccccchhcCCCCChHHHHHH
Q 012376 375 EYTMKLTLEDPTARIHALLCGKEWVKFFGGSPPPDVLTKK 414 (465)
Q Consensus 375 ~~rf~L~lED~t~ri~~~v~~~da~~f~~~~~~~~~L~~k 414 (465)
.|++.+.|-|.|+++|+.++++.|+.++|. +.+.|.+.
T Consensus 244 ryil~~~l~D~TG~~~vt~f~e~ae~llG~--sa~el~~~ 281 (355)
T PRK08402 244 ITILDFGLDDGTGYIRVTLFGDDAAELLGV--EPEEIAEK 281 (355)
T ss_pred eEEEEEEEEcCCCcEEEEEecHHHHHHhCC--CHHHHHHH
Confidence 899999999999999999999999999963 33445443
No 17
>KOG4757 consensus Predicted telomere binding protein [General function prediction only]
Probab=98.26 E-value=6.1e-08 Score=97.78 Aligned_cols=117 Identities=12% Similarity=0.207 Sum_probs=78.8
Q ss_pred CcceEEEEEEEeecCCCccccccC---CCCeEEEEEEEEeCC-CceEEEEEeccccchhcCC---CCC-h------HHHH
Q 012376 347 NVRCCCIVRVVSIHPFQAEHYSSP---NGSSEYTMKLTLEDP-TARIHALLCGKEWVKFFGG---SPP-P------DVLT 412 (465)
Q Consensus 347 ~~kfr~~VRVV~~~P~~~edf~~~---~~~w~~rf~L~lED~-t~ri~~~v~~~da~~f~~~---~~~-~------~~L~ 412 (465)
+.+++..+.+++++|..+..|.+. ..+++|+|.++|-|. .+.+++.-..-||..|-++ ++. + -++.
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 235667777777663 3444544444443333221 111 1 1566
Q ss_pred HHHHHHhCCCCCC------CCC--CCCccCCcceeeeeeeeeecCCc------eEEEEEeeeEEc
Q 012376 413 KKIKMLLGMPEHE------DGN--DDMVRNPPWIKCFLHLKESDGGR------NRVYYIRWTKLV 463 (465)
Q Consensus 413 ~kl~~L~G~~e~~------~~~--~~~~~n~pw~~CCi~sY~v~~~~------~r~f~~F~T~i~ 463 (465)
+.+...||+||++ +++ .......|||+|-||||.+..+. +.|++-|||+|+
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 7788888888763 333 11224789999999999988653 888888888874
No 18
>TIGR00617 rpa1 replication factor-a protein 1 (rpa1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.89 E-value=0.00019 Score=78.81 Aligned_cols=157 Identities=18% Similarity=0.257 Sum_probs=105.5
Q ss_pred CCcceeehHhhhhc-cCCEEEEEEEEEecCCccc----cCCCc-eEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCC
Q 012376 6 NQGGIVRIKELAMH-VKHKVNLLGVVLEFSIPRK----SQGTD-YVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPR 79 (465)
Q Consensus 6 ~~y~y~~i~~~~~~-~~~~vnviGVVvd~~~P~~----trG~D-~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~G 79 (465)
..|.|++|+++... .+..|+|||||+++++... +.|+. .+.+|+|+|.|-. .|.|.++.+....+. . ..|
T Consensus 294 ~~~~f~~i~dI~~~~~~~~VDVIGvV~~v~~~~~i~~k~~g~~~~kR~i~L~D~sg~--sI~vTLWG~~A~~~~-~-~~~ 369 (608)
T TIGR00617 294 IQFNFVKIDDIGGYEGNSLVDVIGIVQSVSPTQTITSRKNNKEFPKRDITLVDDSGK--SVRVTLWGDDATKFD-V-SVQ 369 (608)
T ss_pred ccccceEHHHhhhhcCCCCccEEEEEeEecCceEEEEcCCCCeeeeEEEEEEeCCCC--EEEEEEEhhhhhhcC-C-CCC
Confidence 36899999999865 3457999999999988754 22443 4679999999853 499999998776776 3 579
Q ss_pred CEEEEeeEEEEEEcCeeeEEecCCceEEEEEeCCCCCCCCccccCCCCCCCCHHHHHHHHHHHHhhhcCcccC-------
Q 012376 80 DLILLKNVMIKKHQAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSS------- 152 (465)
Q Consensus 80 DII~l~rvki~~~~g~~~~~~~~~~ss~~lf~~~~~~~~~Py~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~------- 152 (465)
+||.+..++|+.|+|. .+... ..|.+. .+ | |..-+..|+.|+.+.....
T Consensus 370 ~Vva~kg~~V~~f~g~-sLs~~-~~S~i~-iN--------P-------------dipEa~~L~~w~~~~g~~~~~~s~~~ 425 (608)
T TIGR00617 370 PVIAIKGVRVSDFGGK-SLSTG-GSSTII-VN--------P-------------DIPEAEKLKGWYDNEGKGTMASSISD 425 (608)
T ss_pred CEEEEEeEEEEecCCc-eEecc-CCceEE-EC--------C-------------CcHHHHHHHHHHHhcCCCccceeehh
Confidence 9999999999999664 44333 224443 11 1 1112568899976432210
Q ss_pred -------C-CcccccccccccC--------CceEeEEEEEEEEEeeCCCCeEEEEEEcCCCCCC
Q 012376 153 -------G-SNDYLLSLKDISE--------HRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPP 200 (465)
Q Consensus 153 -------~-~~~f~~~Lkdi~~--------~~f~Dlv~qVv~v~~~~~~~~~~L~VwDgT~~p~ 200 (465)
+ .... +.|.+|++ +.+|.+.|.|.++. . + .+ | |+.+|.
T Consensus 426 ~~~~~~~~~~~~~-ktI~ei~~~~lg~~~k~~~f~v~atI~~Ik-~-d--~~----~-Y~ACp~ 479 (608)
T TIGR00617 426 MMSGRVGGSNAER-KTIAEIQAENLGKSDKPDYFSVKATISYLK-P-D--NA----L-YRACPS 479 (608)
T ss_pred ccccccCCccccc-ccHHHHhhhccCCCCCCcEEEEEEEEEEEe-c-C--Ce----E-eccCCh
Confidence 0 1122 45666643 35799999999987 3 2 22 3 777765
No 19
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=97.88 E-value=0.0004 Score=61.06 Aligned_cols=92 Identities=17% Similarity=0.262 Sum_probs=71.7
Q ss_pred eeehHhhhhccC-CEEEEEEEEEecCCcc--ccCCC-ceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEe
Q 012376 10 IVRIKELAMHVK-HKVNLLGVVLEFSIPR--KSQGT-DYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLK 85 (465)
Q Consensus 10 y~~i~~~~~~~~-~~vnviGVVvd~~~P~--~trG~-D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~ 85 (465)
++.|+|+. ++ ..||+.|+|++..+++ +++|+ -...+++|.|.|=. |.+.++.+.. +.+ ..||||.|+
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 eEEEEEEcCeeeEEecCCceEEEEEe
Q 012376 86 NVMIKKHQAELSAVFYKDSSSFALFD 111 (465)
Q Consensus 86 rvki~~~~g~~~~~~~~~~ss~~lf~ 111 (465)
+++++.|+|.+++..++. +.....+
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 999999999999887743 4444333
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=0.00027 Score=59.14 Aligned_cols=73 Identities=16% Similarity=0.213 Sum_probs=58.5
Q ss_pred EEEEEEEEecCCcccc--C--C-CceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCeeeE
Q 012376 24 VNLLGVVLEFSIPRKS--Q--G-TDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAELSA 98 (465)
Q Consensus 24 vnviGVVvd~~~P~~t--r--G-~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~~~g~~~~ 98 (465)
|||+|+|++.++|+.- + | .-.+.+|+|.|.|.. .+.|.++.+..+.+... .|+||.+++++++.|+| ..+
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 4 367899999999974 59999999766666654 39999999999999985 444
Q ss_pred Eec
Q 012376 99 VFY 101 (465)
Q Consensus 99 ~~~ 101 (465)
.+.
T Consensus 77 ~~~ 79 (101)
T cd04475 77 STG 79 (101)
T ss_pred eec
Confidence 443
No 21
>cd04491 SoSSB_OBF SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus solfataricus single-stranded (ss) DNA-binding protein (SSoSSB). SSoSSB has a single OB fold, and it physically and functionally interacts with RNA polymerase. In vitro, SSoSSB can substitute for the basal transcription factor TBP, stimulating transcription from promoters under conditions in which TBP is limiting, and supporting transcription when TBP is absent. SSoSSB selectively melts the duplex DNA of promoter sequences. It also relieves transcriptional repression by the chromatin Alba. In addition, SSoSSB activates reverse gyrase activity, which involves DNA binding, DNA cleavage, strand passage and ligation. SSoSSB stimulates all these steps in the presence of the chromatin protein, Sul7d. SSoSSB antagonizes the inhibitory effect of Sul7d on reverse gyrase supercoiling activity. It also physically and functionally interacts with Mini-chromosome Maintenance (MCM), stimulating
Probab=97.52 E-value=0.0014 Score=52.69 Aligned_cols=72 Identities=18% Similarity=0.281 Sum_probs=59.9
Q ss_pred EEEEEEEecCCcccc---CCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCeeeEEec
Q 012376 25 NLLGVVLEFSIPRKS---QGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAELSAVFY 101 (465)
Q Consensus 25 nviGVVvd~~~P~~t---rG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~~~g~~~~~~~ 101 (465)
|+.|.|++..+++.. .+.--..+++|.|.|- .+.+.++.+.. .+.+ ..||+|.+++.+++.|+|.+++..+
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 2457789999999974 39999998654 6667 6899999999999999999998776
Q ss_pred C
Q 012376 102 K 102 (465)
Q Consensus 102 ~ 102 (465)
.
T Consensus 75 ~ 75 (82)
T cd04491 75 K 75 (82)
T ss_pred C
Confidence 4
No 22
>PRK07218 replication factor A; Provisional
Probab=97.49 E-value=0.014 Score=61.18 Aligned_cols=159 Identities=16% Similarity=0.201 Sum_probs=105.8
Q ss_pred cccccccC-CceEeEEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCccccCCCChhccccCCCcce
Q 012376 159 LSLKDISE-HRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGT 237 (465)
Q Consensus 159 ~~Lkdi~~-~~f~Dlv~qVv~v~~~~~~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~p~~G~ 237 (465)
..|+||++ +..++++++|+.+. + + ++. .||+..... ...+.| .+
T Consensus 59 ~kI~Di~~~~~~V~v~~kVl~i~-~----r-t~r-~dg~~g~v~--~~~igD--------------------------eT 103 (423)
T PRK07218 59 KDIKELSTDDKNVTVTGRVLTIG-E----R-SIR-YQGDDHVIY--EGILAD--------------------------ET 103 (423)
T ss_pred ccHhhCCCCCceeEEEEEEEEec-c----e-eEe-cCCCceEEE--EEEEEC--------------------------CC
Confidence 67999986 57899999999886 3 2 223 777632111 110100 12
Q ss_pred -EEEEEeccchhhhhccCCCCCcEEEEeCcEEEEeCcEEEEEEecCCceEEcCCCChhHHHHHHHHHHHHhCCCCCCCCc
Q 012376 238 -VLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDNDNVVWDYMRRFRERISGGHGHMPIW 316 (465)
Q Consensus 238 -vL~V~~~~~~~~~~~~~~k~G~wV~l~Nv~~k~~~g~leG~l~~~ski~~l~~~d~~v~~r~r~y~~r~~~~~~~~~~~ 316 (465)
++++++|+.. .+++||+|++.|...+...|..+-.+...+.|..++++..
T Consensus 104 G~Ir~tlW~~~------~l~~Gdvv~I~na~vre~~g~~el~ig~~t~I~~~de~~~----------------------- 154 (423)
T PRK07218 104 GTISYTAWKDF------GLSPGDTVTIGNAGVREWDGRPELNIGESTTVSLLDDSSL----------------------- 154 (423)
T ss_pred CeEEEEEECCC------CCCCCCEEEEeccEeeccCCceEEeccCcceEEEcCcccc-----------------------
Confidence 6799999933 2999999999999999999999888888888876664311
Q ss_pred CCCCCCCCcccccCCCccccHHHHhhCCCCCcceEEEEEEEeecCCCccccccCCCCeEEEEEEEEeCCCceEEEEEecc
Q 012376 317 TDPSSQFLTEVDWVNVASVTLMKIATQLQGNVRCCCIVRVVSIHPFQAEHYSSPNGSSEYTMKLTLEDPTARIHALLCGK 396 (465)
Q Consensus 317 ~~~~~~~~t~~~~~~~p~ttL~dIL~~p~v~~kfr~~VRVV~~~P~~~edf~~~~~~w~~rf~L~lED~t~ri~~~v~~~ 396 (465)
+. ++..+...|.||-.. ..-....+||++.+|. .|-...|.- ....++|.|.|++|++.++++
T Consensus 155 --~~--------~~~~~~~kI~DL~~g---~~~V~v~g~Vl~~~~r---~f~~~dg~~-~v~~giigDeTG~Ir~tlW~~ 217 (423)
T PRK07218 155 --PP--------YSIGGDKKLIDLGPG---DRGVNVEARVLELEHR---EIDGRDGET-TILSGVLADETGRLPFTDWDP 217 (423)
T ss_pred --cC--------ccccCccchhhccCC---CCceEEEEEEEEecce---eEEcCCCCe-EEEEEEEECCCceEEEEEecc
Confidence 00 001112223333311 1225667999999874 465666632 366789999999999999997
Q ss_pred cc
Q 012376 397 EW 398 (465)
Q Consensus 397 da 398 (465)
.|
T Consensus 218 ~~ 219 (423)
T PRK07218 218 LP 219 (423)
T ss_pred cc
Confidence 65
No 23
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=97.14 E-value=0.0047 Score=54.27 Aligned_cols=87 Identities=18% Similarity=0.165 Sum_probs=64.5
Q ss_pred cccccccCC-ceEeEEEEEEEEEee-----CCCC---eEEEEEEcCCCCCCCCCCCCCCcccCCCCCCccccCCCChhcc
Q 012376 159 LSLKDISEH-RYFDLVCKVFHVSYD-----DSKG---LWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETL 229 (465)
Q Consensus 159 ~~Lkdi~~~-~f~Dlv~qVv~v~~~-----~~~~---~~~L~VwDgT~~p~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~ 229 (465)
..|+||+++ .-+|++++|+.+. + ..++ .+.+.|=|.|
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 6999999999765 2 0111 1112222211
Q ss_pred ccCCCcceEEEEEeccchhhhhccCCCCCcEEEEeCcEEEEeCcEEEEEEecCCceEEcCC
Q 012376 230 RNFFPVGTVLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSD 290 (465)
Q Consensus 230 ~~~p~~G~vL~V~~~~~~~~~~~~~~k~G~wV~l~Nv~~k~~~g~leG~l~~~ski~~l~~ 290 (465)
| ++++++|+..+ ..+++||.|+++|..++...|.++..+...++|..+++
T Consensus 51 ------G-~I~~tlW~~~a----~~l~~GdvV~I~na~v~~f~G~lqL~i~~~~~i~~~~~ 100 (129)
T PRK06461 51 ------G-RVKLTLWGEQA----GSLKEGEVVEIENAWTTLYRGKVQLNVGKYGSISESDD 100 (129)
T ss_pred ------C-EEEEEEeCCcc----ccCCCCCEEEEECcEEeeeCCEEEEEECCCEEEEECCc
Confidence 3 47899999654 35899999999999999999999888888888987775
No 24
>PRK08402 replication factor A; Reviewed
Probab=97.08 E-value=0.016 Score=59.40 Aligned_cols=139 Identities=16% Similarity=0.232 Sum_probs=93.4
Q ss_pred ceeehHhhhhccC-CEEEEEEEEEecCCccc--c-CCC-ceEEEEEEEeCCCCCCCeEEEEecCCCC-CCCCCCCCCCEE
Q 012376 9 GIVRIKELAMHVK-HKVNLLGVVLEFSIPRK--S-QGT-DYVCVLKIVDDSQQSPELLVNIFTSSID-QLPRVLSPRDLI 82 (465)
Q Consensus 9 ~y~~i~~~~~~~~-~~vnviGVVvd~~~P~~--t-rG~-D~~~tl~I~D~s~~~~gl~v~iF~~~~~-~LP~v~~~GDII 82 (465)
..++|+|+. ++ ..|++.|-|+....|+. . .|+ ....++.|.|+|-. +++.++.+..+ .++.+ ..||||
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 477899997 44 46999999999987763 1 243 57888999998763 79999997644 47878 689999
Q ss_pred EEeeEEEEEE-cCeeeEEecCCceEEEEEeCCCCCCCCccccCCCCCCCCHHHHHHHHHHHHhhhcCcccCCCccccccc
Q 012376 83 LLKNVMIKKH-QAELSAVFYKDSSSFALFDGNSGSNLLPYQSSPQRFEITEAEERRINVLRQWCVGFEFSSGSNDYLLSL 161 (465)
Q Consensus 83 ~l~rvki~~~-~g~~~~~~~~~~ss~~lf~~~~~~~~~Py~~s~~~~~~~~~e~~~v~~Lr~W~~~~~~~~~~~~f~~~L 161 (465)
.+.+++++.+ +|.+.+..+.. |+..+=+..+...-.| .-.+... ..... +.|
T Consensus 135 ~I~~a~V~e~~~G~~eLsvg~~-s~i~~~pd~~ea~~i~---------~~~~~~~----------------~~~~~-k~I 187 (355)
T PRK08402 135 KVIDAQVRESLSGLPELHINFR-ARIILNPDDPRVEEIP---------PLEEVRS----------------YNYTR-KKI 187 (355)
T ss_pred EEECCEEeecCCCcEEEEECCC-ceEEeCCCcccccccc---------ccccccc----------------ccccc-cCH
Confidence 9999999984 88878877644 4444222111100011 0000100 00123 578
Q ss_pred ccccCCc-eEeEEEEEEEEE
Q 012376 162 KDISEHR-YFDLVCKVFHVS 180 (465)
Q Consensus 162 kdi~~~~-f~Dlv~qVv~v~ 180 (465)
.|++++. ||.+.+.|+.+.
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=96.60 E-value=0.022 Score=50.55 Aligned_cols=96 Identities=17% Similarity=0.125 Sum_probs=70.6
Q ss_pred ccccccccc--CCceEeEEEEEEEEEeeC----CCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCccccCCCChhccc
Q 012376 157 YLLSLKDIS--EHRYFDLVCKVFHVSYDD----SKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLR 230 (465)
Q Consensus 157 f~~~Lkdi~--~~~f~Dlv~qVv~v~~~~----~~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~ 230 (465)
| ..|+++. .++.+|+++-|+.+.... .+.+.+|.|+|=|.++
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 1246777777744211
Q ss_pred cCCCcceEEEEEeccchhhhhccCCCCCcEEEEeCcEEEEeCcEEEEEEec-CCceEEcCC
Q 012376 231 NFFPVGTVLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQS-SSKIRLFSD 290 (465)
Q Consensus 231 ~~p~~G~vL~V~~~~~~~~~~~~~~k~G~wV~l~Nv~~k~~~g~leG~l~~-~ski~~l~~ 290 (465)
+..|+|.+|.++++. ...+++||.|+|+|++++..+|...|.... .+.+.+.+.
T Consensus 51 -----~~~l~v~~F~~~~~~-LP~v~~GDVIll~~~kv~~~~g~~~~~~~~~~ss~avf~~ 105 (138)
T cd04497 51 -----SDGLTVKLFRPNEES-LPIVKVGDIILLRRVKIQSYNGKPQGISNDRGSSWAVFRG 105 (138)
T ss_pred -----CCcEEEEEECCChhh-CCCCCCCCEEEEEEEEEEEECCceEEEECCCceeEEEEcC
Confidence 235689999988776 565799999999999999988988887777 556655443
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=96.40 E-value=0.015 Score=44.07 Aligned_cols=70 Identities=19% Similarity=0.386 Sum_probs=53.2
Q ss_pred EEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCeeeEEe
Q 012376 25 NLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAELSAVF 100 (465)
Q Consensus 25 nviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~~~g~~~~~~ 100 (465)
.+.|+|++..... | ...+..|+|.|.+- ..+.+.+|.+..+........|++|.++ .+++.++++.+...
T Consensus 1 ~v~g~v~~~~~~~-~--~~~~~~~~l~D~~~--~~i~~~~~~~~~~~~~~~~~~g~~v~v~-g~v~~~~~~~~l~~ 70 (75)
T cd03524 1 TIVGIVVAVEEIR-T--EGKVLIFTLTDGTG--GTIRVTLFGELAEELENLLKEGQVVYIK-GKVKKFRGRLQLIV 70 (75)
T ss_pred CeEEEEEeecccc-c--CCeEEEEEEEcCCC--CEEEEEEEchHHHHHHhhccCCCEEEEE-EEEEecCCeEEEEe
Confidence 3789999997753 3 35689999999872 2399999997666553434789999998 99998887766654
No 27
>KOG3416 consensus Predicted nucleic acid binding protein [General function prediction only]
Probab=96.35 E-value=0.018 Score=49.45 Aligned_cols=83 Identities=20% Similarity=0.297 Sum_probs=66.0
Q ss_pred eehHhhhhccCCEEEEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEE
Q 012376 11 VRIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIK 90 (465)
Q Consensus 11 ~~i~~~~~~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~ 90 (465)
+.|+|+.... +..|++=+|++.+...+|+-++=.++.++.|+|-. |.+.+..+ +..+ + ++||||+|++---+
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 24889999999999999988889999999999864 88888883 3333 2 67999999999999
Q ss_pred EEcCeeeEEec
Q 012376 91 KHQAELSAVFY 101 (465)
Q Consensus 91 ~~~g~~~~~~~ 101 (465)
.|+|.+.+...
T Consensus 77 i~qg~LtL~~G 87 (134)
T KOG3416|consen 77 IFQGCLTLYVG 87 (134)
T ss_pred hhcCceEEEec
Confidence 99998766554
No 28
>PF02765 POT1: Telomeric single stranded DNA binding POT1/CDC13; InterPro: IPR011564 This entry represents a domain that binds single stranded telomeric DNA and adopts an OB fold []. It includes the proteins POT1 and CDC13 which have been shown to regulate telomere length, replication and capping [, , ]. ; GO: 0003677 DNA binding, 0000723 telomere maintenance, 0000784 nuclear chromosome, telomeric region; PDB: 1S40_A 1KXL_A 1PH7_A 1PH9_A 1PH2_A 1OTC_A 1PHJ_A 1JB7_A 1PA6_A 1PH1_A ....
Probab=95.93 E-value=0.19 Score=45.05 Aligned_cols=97 Identities=19% Similarity=0.144 Sum_probs=68.3
Q ss_pred cccc--cccCCceEeEEEEEEEEEee------CCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCccccCCCChhccc
Q 012376 159 LSLK--DISEHRYFDLVCKVFHVSYD------DSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLR 230 (465)
Q Consensus 159 ~~Lk--di~~~~f~Dlv~qVv~v~~~------~~~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~ 230 (465)
..|. ..+.++++|+++-|+..... ..+-.++|.|+|-|-+.... .
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 4455 44679999999999977633 12348889999955321100 0
Q ss_pred cCCCcceEEEEEeccchhhhhccCCCC-CcEEEEeCcEEEEeCcEEEEEEecC--CceEEc
Q 012376 231 NFFPVGTVLRVSTDRSYENFGRYFTAT-GKWVRIRNMSCQVSSGMWHGLLQSS--SKIRLF 288 (465)
Q Consensus 231 ~~p~~G~vL~V~~~~~~~~~~~~~~k~-G~wV~l~Nv~~k~~~g~leG~l~~~--ski~~l 288 (465)
...|.|.++.++.+. ...++. ||.|+|++++++.+.|...|..... +.+.+.
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 035677887666765 566766 9999999999999999888877776 566666
No 29
>PRK07217 replication factor A; Reviewed
Probab=95.80 E-value=0.16 Score=50.84 Aligned_cols=93 Identities=17% Similarity=0.253 Sum_probs=67.7
Q ss_pred CcceeehHhhhhccCCEEEEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEee
Q 012376 7 QGGIVRIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKN 86 (465)
Q Consensus 7 ~y~y~~i~~~~~~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~r 86 (465)
...-+.|+|+. ..++.|+|.|-|+....|+. ++-...- -|-|+|=. |++..+.+ +.+|.+ ..||+++|++
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-LLGDETGT---IKFTKWAK--SDLPEL-EEGKSYLLKN 138 (311)
T ss_pred CCCceeeeecC-CCCCcEEEEEEEEEecCCCC--CceEEEE-EEEcCCce---EEEEEccC--CCCCcc-cCCCEEEEEe
Confidence 34456788886 33567999999999988642 2222211 36666542 99999986 369999 6899999999
Q ss_pred EEEEEEcCeeeEEecCCceEEEEE
Q 012376 87 VMIKKHQAELSAVFYKDSSSFALF 110 (465)
Q Consensus 87 vki~~~~g~~~~~~~~~~ss~~lf 110 (465)
+.+..|+|++++..++. |+...-
T Consensus 139 a~v~ey~G~~~lnlg~~-t~I~~~ 161 (311)
T PRK07217 139 VVTDEYQGRFSVKLNRT-TSIEEL 161 (311)
T ss_pred EEEeeECCEEEEEeCCc-eEEEeC
Confidence 99999999999988743 655543
No 30
>PRK07217 replication factor A; Reviewed
Probab=95.43 E-value=0.31 Score=48.83 Aligned_cols=167 Identities=17% Similarity=0.192 Sum_probs=100.9
Q ss_pred ccccccc-CCceEeEEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCccccCCCChhccccCCCcce
Q 012376 159 LSLKDIS-EHRYFDLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGT 237 (465)
Q Consensus 159 ~~Lkdi~-~~~f~Dlv~qVv~v~~~~~~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~p~~G~ 237 (465)
..|+||+ .++.+++.++|+.++ + ..+..+.+| ..+.| .+
T Consensus 73 ~kI~Di~~~~~~VsV~aKVl~l~-e-~~~~si~qv------------GllgD--------------------------ET 112 (311)
T PRK07217 73 VNIADIDEPEQWVDVTAKVVQLW-E-PSSDSIAQV------------GLLGD--------------------------ET 112 (311)
T ss_pred eeeeecCCCCCcEEEEEEEEEec-C-CCCCceEEE------------EEEEc--------------------------CC
Confidence 5799998 589999999999998 5 221111110 00001 12
Q ss_pred -EEEEEeccchhhhhccCCCCCcEEEEeCcEEEEeCcEEEEEEecCCceEEcCCCChhHHHHHHHHHHHHhCCCCCCCCc
Q 012376 238 -VLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDNDNVVWDYMRRFRERISGGHGHMPIW 316 (465)
Q Consensus 238 -vL~V~~~~~~~~~~~~~~k~G~wV~l~Nv~~k~~~g~leG~l~~~ski~~l~~~d~~v~~r~r~y~~r~~~~~~~~~~~ 316 (465)
.++.|+|.... ...+++|++|+|.|+..+.+.|..+-.+...+.|..++.+-. +...- -.+...+=.+.
T Consensus 113 G~IkfT~W~~s~---~~~leeGd~~rI~na~v~ey~G~~~lnlg~~t~I~~~de~Ie-V~~~~----vei~G~lVdi~-- 182 (311)
T PRK07217 113 GTIKFTKWAKSD---LPELEEGKSYLLKNVVTDEYQGRFSVKLNRTTSIEELDEDIE-VGDDE----VEVEGALVDIQ-- 182 (311)
T ss_pred ceEEEEEccCCC---CCcccCCCEEEEEeEEEeeECCEEEEEeCCceEEEeCCCCcc-ccCcc----ccceeEEEEEe--
Confidence 56889998421 345899999999999999999999999999998877664321 11000 00000000000
Q ss_pred CCCCCCCCcccccCCCccccHHHHhhCCCCCcceEEEEEEEeecCCCccccccC----CCCeEEEEEEEEeCCCceEEEE
Q 012376 317 TDPSSQFLTEVDWVNVASVTLMKIATQLQGNVRCCCIVRVVSIHPFQAEHYSSP----NGSSEYTMKLTLEDPTARIHAL 392 (465)
Q Consensus 317 ~~~~~~~~t~~~~~~~p~ttL~dIL~~p~v~~kfr~~VRVV~~~P~~~edf~~~----~~~w~~rf~L~lED~t~ri~~~ 392 (465)
+..-.+..|+. -.| =||++ + -.|.. .|.+--|....|-|.|+.+.++
T Consensus 183 --~GsglI~rCP~--~~C-------------------~Rvl~----~--g~C~~HG~ve~~~DLrik~vlDDGt~~~~~~ 233 (311)
T PRK07217 183 --SGSGLIKRCPE--EDC-------------------TRVLQ----N--GRCSEHGKVEGEFDLRIKGVLDDGEEVQEVI 233 (311)
T ss_pred --CCCCCeecCCc--ccc-------------------Ccccc----C--CCCCCCCCcCCceeeEEEEEEECCCCeEEEE
Confidence 00011111110 000 13331 1 23332 2456679999999999999999
Q ss_pred EeccccchhcCC
Q 012376 393 LCGKEWVKFFGG 404 (465)
Q Consensus 393 v~~~da~~f~~~ 404 (465)
++.+-.+.+.|.
T Consensus 234 ~~~e~te~l~G~ 245 (311)
T PRK07217 234 FNREATEELTGI 245 (311)
T ss_pred EChHHhHHHhCC
Confidence 999999999875
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=95.24 E-value=0.22 Score=39.11 Aligned_cols=69 Identities=10% Similarity=0.093 Sum_probs=50.9
Q ss_pred EEEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEE--cCeeeEEec
Q 012376 24 VNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKH--QAELSAVFY 101 (465)
Q Consensus 24 vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~~--~g~~~~~~~ 101 (465)
+.+.|+|.+.+. |+++ ++-++|.|.+- .+.+.+|.+..+........|++|.++ .+++.+ +|+++...+
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 399999998677776666789988885 455545 466666554
No 32
>PRK06386 replication factor A; Reviewed
Probab=95.09 E-value=0.17 Score=51.88 Aligned_cols=87 Identities=17% Similarity=0.273 Sum_probs=67.3
Q ss_pred cceeehHhhhhccCCEEEEEEEEEecCCcc-ccCCC-ceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEe
Q 012376 8 GGIVRIKELAMHVKHKVNLLGVVLEFSIPR-KSQGT-DYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLK 85 (465)
Q Consensus 8 y~y~~i~~~~~~~~~~vnviGVVvd~~~P~-~trG~-D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~ 85 (465)
|..++|+|+... ...|||.|-|++...+. .++|+ -...++-|-|++=. |++.+|.+ .+ ..||+|++.
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 456789998622 34599999999985542 23444 77888999998753 99999985 25 689999999
Q ss_pred eEEEEEEcCeeeEEecCCceE
Q 012376 86 NVMIKKHQAELSAVFYKDSSS 106 (465)
Q Consensus 86 rvki~~~~g~~~~~~~~~~ss 106 (465)
++.++.|+|.+++..+.. |+
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 999999999999988754 44
No 33
>PF01336 tRNA_anti-codon: OB-fold nucleic acid binding domain; InterPro: IPR004365 The OB-fold (oligonucleotide/oligosaccharide-binding fold) is found in all three kingdoms and its common architecture presents a binding face that has adapted to bind different ligands. The OB-fold is a five/six-stranded closed beta-barrel formed by 70-80 amino acid residues. The strands are connected by loops of varying length which form the functional appendages of the protein. The majority of OB-fold proteins use the same face for ligand binding or as an active site. Different OB-fold proteins use this 'fold-related binding face' to, variously, bind oligosaccharides, oligonucleotides, proteins, metal ions and catalytic substrates. This entry contains OB-fold domains that bind to nucleic acids []. It includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl-tRNA synthetases (See IPR004364 from INTERPRO). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule 6.1.1 from EC. This domain is found in RecG helicase involved in DNA repair. Replication factor A is a heterotrimeric complex, that contains a subunit in this family [, ]. This domain is also found at the C terminus of bacterial DNA polymerase III alpha chain.; GO: 0003676 nucleic acid binding; PDB: 1BBU_A 1KRS_A 1BBW_A 1KRT_A 1EQR_B 1IL2_B 1C0A_A 3KFU_A 1EOV_A 1ASY_A ....
Probab=95.02 E-value=0.039 Score=42.70 Aligned_cols=68 Identities=13% Similarity=0.216 Sum_probs=52.2
Q ss_pred EEEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEec-CCCCCCCCCCCCCCEEEEeeEEEEEEcCe-eeEEec
Q 012376 24 VNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFT-SSIDQLPRVLSPRDLILLKNVMIKKHQAE-LSAVFY 101 (465)
Q Consensus 24 vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~-~~~~~LP~v~~~GDII~l~rvki~~~~g~-~~~~~~ 101 (465)
|.+.|.|.... ++..-.+.++|.|.|- .+.+.+|. ........+ ..||+|+++ -+++.+++. ++...+
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 777654
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=94.91 E-value=0.11 Score=43.91 Aligned_cols=82 Identities=12% Similarity=0.095 Sum_probs=57.0
Q ss_pred EEEEEEEecCCccccC--C-CceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCC----CCCCCEEEEee-EEEEEEcCee
Q 012376 25 NLLGVVLEFSIPRKSQ--G-TDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRV----LSPRDLILLKN-VMIKKHQAEL 96 (465)
Q Consensus 25 nviGVVvd~~~P~~tr--G-~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v----~~~GDII~l~r-vki~~~~g~~ 96 (465)
++||+|++.++..... | ..-...|+|.|.+- ..++|.+..+..+.+..- ...+=||.+-+ .+|..|+|..
T Consensus 1 DviG~i~~v~~~~~~~~~~~~~~kr~~~i~D~~~--~~l~~tlwG~~A~~f~~~~~~~~~~~~VVav~~~~rV~~~~g~~ 78 (106)
T cd04481 1 DVIGVIVDVGPLEELPPVNKPSRKLDFEIRDLSD--ERLKCTLWGEYAEEFDAKFQSAGNGEPVVAVLRFWKIKEYKGPK 78 (106)
T ss_pred CeeEEEEEecceEecccCCccceEEEEEEEeCCC--CEEEEEEEHHHHHHHHHHHHHhCCCCcEEEEEEeEEEEEEcCCc
Confidence 4899999999876543 3 56789999999985 349999998766666542 12344776655 9999999854
Q ss_pred eEEecCCceEEE
Q 012376 97 SAVFYKDSSSFA 108 (465)
Q Consensus 97 ~~~~~~~~ss~~ 108 (465)
.+....+.|.|.
T Consensus 79 ~ls~~~~~s~v~ 90 (106)
T cd04481 79 SLSNSFGASKVY 90 (106)
T ss_pred EEEcCCCceEEE
Confidence 443332434444
No 35
>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=94.60 E-value=0.12 Score=43.59 Aligned_cols=84 Identities=14% Similarity=0.180 Sum_probs=61.9
Q ss_pred ehHhhhhccCCEEEEEEEEEecCCccccC---CCceEEEEEEEeCCCCCCCeEEEEecCCCC-CCCCCCCCCCEEEEeeE
Q 012376 12 RIKELAMHVKHKVNLLGVVLEFSIPRKSQ---GTDYVCVLKIVDDSQQSPELLVNIFTSSID-QLPRVLSPRDLILLKNV 87 (465)
Q Consensus 12 ~i~~~~~~~~~~vnviGVVvd~~~P~~tr---G~D~~~tl~I~D~s~~~~gl~v~iF~~~~~-~LP~v~~~GDII~l~rv 87 (465)
+|+++.... ..+.+.|-|+..+.++.-+ |....++|.|.|+... .|.+.+|.+..+ .-|.+ ..|+|+.+.+.
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 466776322 3589999999887766433 3467789999999643 499999986444 45666 69999999999
Q ss_pred EEEEEcCeeeEE
Q 012376 88 MIKKHQAELSAV 99 (465)
Q Consensus 88 ki~~~~g~~~~~ 99 (465)
+|+.-++...-+
T Consensus 77 ~V~~a~~~y~~~ 88 (104)
T cd04474 77 SVKVANKKFNTL 88 (104)
T ss_pred EEeeccccCCCC
Confidence 999887664443
No 36
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=94.58 E-value=0.17 Score=46.12 Aligned_cols=32 Identities=22% Similarity=0.315 Sum_probs=30.2
Q ss_pred CeEEEEEEEEeCCCceEEEEEeccccchhcCC
Q 012376 373 SSEYTMKLTLEDPTARIHALLCGKEWVKFFGG 404 (465)
Q Consensus 373 ~w~~rf~L~lED~t~ri~~~v~~~da~~f~~~ 404 (465)
.|.|++.+.|.|.|+.+++.++|+.|+.|||.
T Consensus 65 ~~ry~l~~~i~D~Tg~~~~~~F~~~ae~l~G~ 96 (166)
T cd04476 65 EYRYILSLNVADHTGEAWLTLFDEVAEQIFGK 96 (166)
T ss_pred cEEEEEEEEEEeCCCCEEEEEehHHHHHHhCC
Confidence 67899999999999999999999999999974
No 37
>PF15489 CTC1: CST, telomere maintenance, complex subunit CTC1
Probab=94.45 E-value=0.4 Score=55.26 Aligned_cols=145 Identities=17% Similarity=0.137 Sum_probs=103.4
Q ss_pred EEEEEeccchhhhhccCCCCCcEEEEeCcEEEE-eCcEEEEEEecCCceEEcCCCChhHHHHHHHHHHHHhCCCCCCCCc
Q 012376 238 VLRVSTDRSYENFGRYFTATGKWVRIRNMSCQV-SSGMWHGLLQSSSKIRLFSDNDNVVWDYMRRFRERISGGHGHMPIW 316 (465)
Q Consensus 238 vL~V~~~~~~~~~~~~~~k~G~wV~l~Nv~~k~-~~g~leG~l~~~ski~~l~~~d~~v~~r~r~y~~r~~~~~~~~~~~ 316 (465)
.|.|-++.+|.-+ --.+-||.-|.|.++..|+ .+|+.+..+.++|.|++++-.. +
T Consensus 888 ~ldVYi~~~h~p~-plGLLPGA~V~f~~lerkVSRs~nVYC~~~psS~VtVlS~p~-~---------------------- 943 (1144)
T PF15489_consen 888 HLDVYIEDPHLPY-PLGLLPGARVLFSQLERKVSRSHNVYCCFLPSSSVTVLSFPP-E---------------------- 943 (1144)
T ss_pred eEEEEecCCCCCC-cccccCCceeeeehhhhhhhccCcEEEEEcCCceEEEEecCc-c----------------------
Confidence 4677777777766 5568899999999999999 7889999999999999976410 0
Q ss_pred CCCCCCCCcccccCCCccccHHHHhhCCCCCcceEEEEEEEeecCCCccccccC--------------------CCCeEE
Q 012376 317 TDPSSQFLTEVDWVNVASVTLMKIATQLQGNVRCCCIVRVVSIHPFQAEHYSSP--------------------NGSSEY 376 (465)
Q Consensus 317 ~~~~~~~~t~~~~~~~p~ttL~dIL~~p~v~~kfr~~VRVV~~~P~~~edf~~~--------------------~~~w~~ 376 (465)
| ..-..+|...|.+.+.....+.+.++.++||.++==.+.=-|.. .+....
T Consensus 944 --------t-~~~~~~P~~~L~~~~~~~~~~~~a~~~chVV~V~~l~L~WvCa~C~si~~qg~Csr~~p~C~s~~sV~qA 1014 (1144)
T PF15489_consen 944 --------T-NVSPPLPHIYLAELLQGSQSPFQARVSCHVVSVLSLQLQWVCAHCGSICPQGRCSRQSPPCPSQTSVFQA 1014 (1144)
T ss_pred --------c-CCCCCCCeEEehhhhCCCCCCceEEEEEEEEEEEEEEeeehhhhccCcccCCcCCCCCCCCCCCcceeeE
Confidence 0 01123466667777766666668888889998776555433320 134456
Q ss_pred EEEEEEeCCCceEEEEEeccccchhcCCCCCh--HHHHHHHH
Q 012376 377 TMKLTLEDPTARIHALLCGKEWVKFFGGSPPP--DVLTKKIK 416 (465)
Q Consensus 377 rf~L~lED~t~ri~~~v~~~da~~f~~~~~~~--~~L~~kl~ 416 (465)
..+++|||.||+-+|.+.|+....+++ ++.. +.|.++..
T Consensus 1015 ~ar~~vEDGTaeA~v~~~~~~V~~lLg-L~~~eW~~L~~~v~ 1055 (1144)
T PF15489_consen 1015 SARLLVEDGTAEAVVWCRGHHVAALLG-LSPSEWESLLEMVR 1055 (1144)
T ss_pred EEEEEEecCCeeEEEEECCcHHHHHhC-CCHHHHHHHHHHhh
Confidence 779999999999999999977777775 4432 55555443
No 38
>cd04478 RPA2_DBD_D RPA2_DBD_D: A subfamily of OB folds corresponding to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle dependent manner in response to DNA dam
Probab=94.07 E-value=0.49 Score=38.72 Aligned_cols=67 Identities=18% Similarity=0.198 Sum_probs=51.4
Q ss_pred EEEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCC----CCCCCCCCCCEEEEeeEEEEEEcCeeeEE
Q 012376 24 VNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSID----QLPRVLSPRDLILLKNVMIKKHQAELSAV 99 (465)
Q Consensus 24 vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~----~LP~v~~~GDII~l~rvki~~~~g~~~~~ 99 (465)
|.++|+|.+... + +=..+++|-|.|- .|.+.++....+ ..+.+ ..|++|++ .-+++.|+|+.+..
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 789999999764 1 2348889999874 399999987654 55666 79999998 56779999998776
Q ss_pred ec
Q 012376 100 FY 101 (465)
Q Consensus 100 ~~ 101 (465)
..
T Consensus 71 i~ 72 (95)
T cd04478 71 AF 72 (95)
T ss_pred EE
Confidence 43
No 39
>cd04491 SoSSB_OBF SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus solfataricus single-stranded (ss) DNA-binding protein (SSoSSB). SSoSSB has a single OB fold, and it physically and functionally interacts with RNA polymerase. In vitro, SSoSSB can substitute for the basal transcription factor TBP, stimulating transcription from promoters under conditions in which TBP is limiting, and supporting transcription when TBP is absent. SSoSSB selectively melts the duplex DNA of promoter sequences. It also relieves transcriptional repression by the chromatin Alba. In addition, SSoSSB activates reverse gyrase activity, which involves DNA binding, DNA cleavage, strand passage and ligation. SSoSSB stimulates all these steps in the presence of the chromatin protein, Sul7d. SSoSSB antagonizes the inhibitory effect of Sul7d on reverse gyrase supercoiling activity. It also physically and functionally interacts with Mini-chromosome Maintenance (MCM), stimulating
Probab=93.77 E-value=0.19 Score=40.14 Aligned_cols=46 Identities=20% Similarity=0.110 Sum_probs=39.8
Q ss_pred EEEEEeccchhhhhccCCCCCcEEEEeCcEEEEeCcEEEEEEecCCceE
Q 012376 238 VLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIR 286 (465)
Q Consensus 238 vL~V~~~~~~~~~~~~~~k~G~wV~l~Nv~~k~~~g~leG~l~~~ski~ 286 (465)
.+++++|+..+ ...+++|++|++.|..++...|.++..+...+.|.
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 68999999776 56799999999999999998899988888877664
No 40
>cd04475 RPA1_DBD_B RPA1_DBD_B: A subfamily of OB folds corresponding to the third OB fold, the ssDNA-binding domain (DBD)-B, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-B, RPA1 contains three other OB folds: DBD-A, DBD-C, and RPA1N. The major DNA binding activity of human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. Although ScRPA and the hRPA have similar ssDNA-binding properties, they differ functiona
Probab=93.72 E-value=0.81 Score=37.98 Aligned_cols=61 Identities=11% Similarity=-0.012 Sum_probs=41.4
Q ss_pred ceEEEEEeccchhhhhccCCCCCcEEEEeCcEEEEeCcEEEEEEecCCceEEcCCCChhHHHHHH
Q 012376 236 GTVLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSSSKIRLFSDNDNVVWDYMR 300 (465)
Q Consensus 236 G~vL~V~~~~~~~~~~~~~~k~G~wV~l~Nv~~k~~~g~leG~l~~~ski~~l~~~d~~v~~r~r 300 (465)
|..+.|++|..++....+. .|+.+.|.|++++..+|. .......|+|.+ +++.+++.+.+.
T Consensus 38 ~~~i~vtLWg~~a~~~~~~--~~~vv~~~~~~i~~~~~~-~l~~~~~s~i~~-np~~~e~~~l~~ 98 (101)
T cd04475 38 GHSVELTLWGEQAELFDGS--ENPVIAIKGVKVSEFNGK-SLSTGSSSTIII-NPDIPEAHKLRG 98 (101)
T ss_pred CCEEEEEEEHHHhhhcccC--CCCEEEEEeeEEEecCCe-EEeecCceeEEE-CCCcHHHHHHHH
Confidence 3467999999888763332 399999999999886653 344444567754 445667666543
No 41
>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=93.16 E-value=0.23 Score=38.78 Aligned_cols=70 Identities=14% Similarity=0.301 Sum_probs=49.4
Q ss_pred EEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCeeeEEe
Q 012376 26 LLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAELSAVF 100 (465)
Q Consensus 26 viGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~~~g~~~~~~ 100 (465)
+.|+|.+... +.|+.+.-+..++|.|.+-. +.+.+|.+..+.+......|.++.++ -+++.++|..+...
T Consensus 2 i~g~v~~~~~-~~~k~g~~~~~~~l~D~tg~---~~~~~f~~~~~~~~~~l~~g~~v~v~-G~v~~~~~~~~l~~ 71 (84)
T cd04485 2 VAGLVTSVRR-RRTKKGKRMAFVTLEDLTGS---IEVVVFPETYEKYRDLLKEDALLLVE-GKVERRDGGLRLIA 71 (84)
T ss_pred EEEEEEEeEE-EEcCCCCEEEEEEEEeCCCe---EEEEECHHHHHHHHHHhcCCCEEEEE-EEEEecCCceEEEe
Confidence 6788888755 45554456799999998653 99999976533344434689999886 47777877666554
No 42
>PRK13480 3'-5' exoribonuclease YhaM; Provisional
Probab=92.62 E-value=0.77 Score=46.49 Aligned_cols=82 Identities=15% Similarity=0.140 Sum_probs=63.6
Q ss_pred ehHhhhhccCCEEEEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEE
Q 012376 12 RIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKK 91 (465)
Q Consensus 12 ~i~~~~~~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~ 91 (465)
.|+++. .|+.|+.+.+|.+... +.++.+.-...+++.|.|-. |..+++....+....+ ..||||.+. -++..
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 6889999999999876 34553344789999998653 9999998777777777 789999995 56678
Q ss_pred EcCeeeEEec
Q 012376 92 HQAELSAVFY 101 (465)
Q Consensus 92 ~~g~~~~~~~ 101 (465)
|+|++|....
T Consensus 76 y~g~~Ql~i~ 85 (314)
T PRK13480 76 YRGRKQLKVN 85 (314)
T ss_pred ECCcceEEEE
Confidence 9999887654
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=92.42 E-value=1.1 Score=35.06 Aligned_cols=68 Identities=12% Similarity=0.238 Sum_probs=49.7
Q ss_pred EEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCeeeEEe
Q 012376 27 LGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAELSAVF 100 (465)
Q Consensus 27 iGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~~~g~~~~~~ 100 (465)
+.+|.+++. +.|+++.-+..++|-|.+-. +.+.+|.+.....+.+ ..|.+|.++ .++..++|+.+...
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 55655556899999998763 9999998655444556 689999997 67777877665554
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=91.61 E-value=1.5 Score=36.06 Aligned_cols=65 Identities=15% Similarity=0.121 Sum_probs=48.1
Q ss_pred EEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCC---------------------CCCCCCCCCCCEEEE
Q 012376 26 LLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSI---------------------DQLPRVLSPRDLILL 84 (465)
Q Consensus 26 viGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~---------------------~~LP~v~~~GDII~l 84 (465)
++|+|+.... +.+ ..+|+|-|.+= -|.|+++.... +..+.+ ++|++|++
T Consensus 2 ivG~V~sv~~----~~~--~~~~tLdDgTG---~Ie~~~W~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i-~~G~vvrV 71 (92)
T cd04483 2 ILGTVVSRRE----RET--FYSFGVDDGTG---VVNCVCWKNLSYAEVSSRSDAARILKSALMALKQAKVL-EIGDLLRV 71 (92)
T ss_pred eEEEEEEEEe----cCC--eEEEEEecCCc---eEEEEEEcCcCccccccccccccccccccccccccccc-CCCCEEEE
Confidence 6899998854 222 37888888665 28999997543 345556 79999999
Q ss_pred eeEEEEEEcCeeeEEec
Q 012376 85 KNVMIKKHQAELSAVFY 101 (465)
Q Consensus 85 ~rvki~~~~g~~~~~~~ 101 (465)
+ -+++.|+|+.++...
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=90.57 E-value=0.22 Score=44.43 Aligned_cols=32 Identities=25% Similarity=0.389 Sum_probs=29.4
Q ss_pred CCeEEEEEEEEeCCCceEEEEEeccccchhcC
Q 012376 372 GSSEYTMKLTLEDPTARIHALLCGKEWVKFFG 403 (465)
Q Consensus 372 ~~w~~rf~L~lED~t~ri~~~v~~~da~~f~~ 403 (465)
-.|.|++.+.|.|.|+.+++.++|+.|+.|||
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 47889999999999999999999999999995
No 46
>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=85.52 E-value=11 Score=27.79 Aligned_cols=65 Identities=18% Similarity=0.154 Sum_probs=42.2
Q ss_pred eEEEEEEEEEeeCC--CCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCccccCCCChhccccCCCcceEEEEEeccchh
Q 012376 171 DLVCKVFHVSYDDS--KGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRVSTDRSYE 248 (465)
Q Consensus 171 Dlv~qVv~v~~~~~--~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~p~~G~vL~V~~~~~~~ 248 (465)
++.|+|+++. ... .....+.+.|+|+ ..+.+.+|+...
T Consensus 1 ~v~g~v~~~~-~~~~~~~~~~~~l~D~~~---------------------------------------~~i~~~~~~~~~ 40 (75)
T cd03524 1 TIVGIVVAVE-EIRTEGKVLIFTLTDGTG---------------------------------------GTIRVTLFGELA 40 (75)
T ss_pred CeEEEEEeec-ccccCCeEEEEEEEcCCC---------------------------------------CEEEEEEEchHH
Confidence 4678888887 323 3567788888771 134667777554
Q ss_pred hhhccCCCCCcEEEEeCcEEEEeCcEEE
Q 012376 249 NFGRYFTATGKWVRIRNMSCQVSSGMWH 276 (465)
Q Consensus 249 ~~~~~~~k~G~wV~l~Nv~~k~~~g~le 276 (465)
.-....+++|+++.+. .+++..+|.++
T Consensus 41 ~~~~~~~~~g~~v~v~-g~v~~~~~~~~ 67 (75)
T cd03524 41 EELENLLKEGQVVYIK-GKVKKFRGRLQ 67 (75)
T ss_pred HHHHhhccCCCEEEEE-EEEEecCCeEE
Confidence 4334668999999887 66665554443
No 47
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain
Probab=85.02 E-value=8 Score=32.14 Aligned_cols=78 Identities=21% Similarity=0.224 Sum_probs=53.7
Q ss_pred hHhhhhcc--CCEEEEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCC-CCCCCCCEEEEeeEEE
Q 012376 13 IKELAMHV--KHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLP-RVLSPRDLILLKNVMI 89 (465)
Q Consensus 13 i~~~~~~~--~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP-~v~~~GDII~l~rvki 89 (465)
|+++++.. -..+-|.|=|.+++.. ++| .+-|+|+|+. ..|+|.+|+.....++ ...+.||-|++ +.++
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 2579999999998764 233 5778899965 4499999998878887 44478997777 4555
Q ss_pred EEE--cCeeeEE
Q 012376 90 KKH--QAELSAV 99 (465)
Q Consensus 90 ~~~--~g~~~~~ 99 (465)
..| .|++++.
T Consensus 82 ~~y~~~G~~sl~ 93 (99)
T PF13742_consen 82 SFYEPRGSLSLI 93 (99)
T ss_pred EEECCCcEEEEE
Confidence 555 4445544
No 48
>PF01336 tRNA_anti-codon: OB-fold nucleic acid binding domain; InterPro: IPR004365 The OB-fold (oligonucleotide/oligosaccharide-binding fold) is found in all three kingdoms and its common architecture presents a binding face that has adapted to bind different ligands. The OB-fold is a five/six-stranded closed beta-barrel formed by 70-80 amino acid residues. The strands are connected by loops of varying length which form the functional appendages of the protein. The majority of OB-fold proteins use the same face for ligand binding or as an active site. Different OB-fold proteins use this 'fold-related binding face' to, variously, bind oligosaccharides, oligonucleotides, proteins, metal ions and catalytic substrates. This entry contains OB-fold domains that bind to nucleic acids []. It includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl-tRNA synthetases (See IPR004364 from INTERPRO). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule 6.1.1 from EC. This domain is found in RecG helicase involved in DNA repair. Replication factor A is a heterotrimeric complex, that contains a subunit in this family [, ]. This domain is also found at the C terminus of bacterial DNA polymerase III alpha chain.; GO: 0003676 nucleic acid binding; PDB: 1BBU_A 1KRS_A 1BBW_A 1KRT_A 1EQR_B 1IL2_B 1C0A_A 3KFU_A 1EOV_A 1ASY_A ....
Probab=84.43 E-value=12 Score=28.41 Aligned_cols=60 Identities=17% Similarity=0.090 Sum_probs=41.9
Q ss_pred eEEEEEEEEEeeCCCCeEEEEEEcCCCCCCCCCCCCCCcccCCCCCCccccCCCChhccccCCCcceEEEEEeccchhhh
Q 012376 171 DLVCKVFHVSYDDSKGLWMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRVSTDRSYENF 250 (465)
Q Consensus 171 Dlv~qVv~v~~~~~~~~~~L~VwDgT~~p~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~p~~G~vL~V~~~~~~~~~ 250 (465)
.+.+.|.++. ...+....+.+.|+|+ .+++.+|......
T Consensus 2 ~v~G~V~~~~-~~~~~~~~~~l~D~tg----------------------------------------~i~~~~~~~~~~~ 40 (75)
T PF01336_consen 2 TVEGRVTSIR-RSGGKIVFFTLEDGTG----------------------------------------SIQVVFFNEEYER 40 (75)
T ss_dssp EEEEEEEEEE-EEETTEEEEEEEETTE----------------------------------------EEEEEEETHHHHH
T ss_pred EEEEEEEEEE-cCCCCEEEEEEEECCc----------------------------------------cEEEEEccHHhhH
Confidence 5678888885 4367788888999873 3578888844444
Q ss_pred hccCCCCCcEEEEeCcEEEEeC
Q 012376 251 GRYFTATGKWVRIRNMSCQVSS 272 (465)
Q Consensus 251 ~~~~~k~G~wV~l~Nv~~k~~~ 272 (465)
..+.+++|++|++. =.++...
T Consensus 41 ~~~~l~~g~~v~v~-G~v~~~~ 61 (75)
T PF01336_consen 41 FREKLKEGDIVRVR-GKVKRYN 61 (75)
T ss_dssp HHHTS-TTSEEEEE-EEEEEET
T ss_pred HhhcCCCCeEEEEE-EEEEEEC
Confidence 47889999999888 3444433
No 49
>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=82.35 E-value=9.1 Score=28.83 Aligned_cols=68 Identities=18% Similarity=0.273 Sum_probs=44.1
Q ss_pred EEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCeeeEEe
Q 012376 26 LLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAELSAVF 100 (465)
Q Consensus 26 viGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~~~g~~~~~~ 100 (465)
+.|.|++.... +++|.. ...+++.|.+- .+.+.+|.... .+......|+.+.+. -|+..|+|+++...
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 56677877766544
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=78.60 E-value=18 Score=28.92 Aligned_cols=71 Identities=18% Similarity=0.256 Sum_probs=47.5
Q ss_pred EEEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEec-CCCCCCCCCCCCCCEEEEeeE-EEEEEcCeeeE
Q 012376 24 VNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFT-SSIDQLPRVLSPRDLILLKNV-MIKKHQAELSA 98 (465)
Q Consensus 24 vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~-~~~~~LP~v~~~GDII~l~rv-ki~~~~g~~~~ 98 (465)
|-+-|-|.+... +.++.+-...+|.|.|-+ +++.|+.|. +..+.+-.+++.||-|+++.- ....|.++...
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 469999998 344555556328999988654 34455555433
No 51
>PRK07373 DNA polymerase III subunit alpha; Reviewed
Probab=77.97 E-value=7.1 Score=41.62 Aligned_cols=89 Identities=16% Similarity=0.203 Sum_probs=62.0
Q ss_pred cceeehHhhhh-ccCCEEEEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEee
Q 012376 8 GGIVRIKELAM-HVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKN 86 (465)
Q Consensus 8 y~y~~i~~~~~-~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~r 86 (465)
+...+++++.. ..++.|.+.|+|...+. ++|+.++-++-++|-|.+-. +.+.+|.+.-+..-.....|.+++++.
T Consensus 266 ~~~~~~~~l~~~~~~~~v~vaG~I~~ik~-~~TKkG~~maf~~leD~tG~---ie~vvFp~~y~~~~~~l~~~~~v~v~G 341 (449)
T PRK07373 266 LSPINLSELEEQKEKTKVSAVVMLNEVKK-IVTKKGDPMAFLQLEDLSGQ---SEAVVFPKSYERISELLQVDARLIIWG 341 (449)
T ss_pred cCCcCHHHHhcccCCCEEEEEEEEEEeEe-cccCCCCEEEEEEEEECCCC---EEEEECHHHHHHHHHHhccCCEEEEEE
Confidence 34456777642 24668999999999987 45665678999999999764 999999865555545446788888854
Q ss_pred EEEEEEcCeeeEEec
Q 012376 87 VMIKKHQAELSAVFY 101 (465)
Q Consensus 87 vki~~~~g~~~~~~~ 101 (465)
+++.-.++.+.+.+
T Consensus 342 -~v~~~~~~~~liv~ 355 (449)
T PRK07373 342 -KVDRRDDQVQLIVE 355 (449)
T ss_pred -EEEecCCeEEEEEe
Confidence 56543354555544
No 52
>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=77.14 E-value=8.6 Score=30.58 Aligned_cols=59 Identities=14% Similarity=0.317 Sum_probs=41.7
Q ss_pred EEEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCC--CCCCCCCCCCEEEEeeEEEEE
Q 012376 24 VNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSID--QLPRVLSPRDLILLKNVMIKK 91 (465)
Q Consensus 24 vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~--~LP~v~~~GDII~l~rvki~~ 91 (465)
+.+.|+|.+.+ .|+.++- .++|-|.+-. +.+.+|.+..+ ..-.....|.+|.++. ++..
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 7788888653 99999998777 6555545677777754 5543
No 53
>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=75.43 E-value=28 Score=27.17 Aligned_cols=64 Identities=11% Similarity=0.164 Sum_probs=39.6
Q ss_pred EEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEe-eEEEEEEcCeeeEEe
Q 012376 26 LLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLK-NVMIKKHQAELSAVF 100 (465)
Q Consensus 26 viGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~-rvki~~~~g~~~~~~ 100 (465)
+-|.|..+.. +|..+ -|+|.|... .|.|.+|+.+...++.-...||-|.++ ++.+ .+|+.|+..
T Consensus 3 v~GeVs~~~~----~~GHv--yfsLkD~~a---~i~cv~f~~~~~~~~~~l~~Gd~V~v~G~v~~--~~G~~ql~v 67 (73)
T cd04487 3 IEGEVVQIKQ----TSGPT--IFTLRDETG---TVWAAAFEEAGVRAYPEVEVGDIVRVTGEVEP--RDGQLQIEV 67 (73)
T ss_pred EEEEEecccc----CCCCE--EEEEEcCCE---EEEEEEEchhccCCcCCCCCCCEEEEEEEEec--CCeEEEEEE
Confidence 4577776652 44454 456788543 399999987654555444789955554 4443 566666554
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=74.56 E-value=17 Score=32.39 Aligned_cols=62 Identities=18% Similarity=0.213 Sum_probs=36.0
Q ss_pred ceEeEEEEEEEEEeeCCCCe-EEEEEEcCCCCCCCCCCCCCCcccCCCCCCccccCCCChhccccCCCcceEEEEEeccc
Q 012376 168 RYFDLVCKVFHVSYDDSKGL-WMLFVWDGTDVPPLSIPGKLEDEEHNPLPLHIESSPLDLETLRNFFPVGTVLRVSTDRS 246 (465)
Q Consensus 168 ~f~Dlv~qVv~v~~~~~~~~-~~L~VwDgT~~p~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~p~~G~vL~V~~~~~ 246 (465)
+-||+++-|+.|. . ..+. ..+|+.|.--| .|.|.+|..
T Consensus 19 ~EvD~VG~VvsV~-~-~~~f~~~vYLsD~~~N---------------------------------------ll~Ikfw~~ 57 (143)
T PF09104_consen 19 GEVDTVGFVVSVS-K-KQGFQPLVYLSDECHN---------------------------------------LLAIKFWTG 57 (143)
T ss_dssp CEEEEEEEEEEEE----TTS--EEEEE-TTS----------------------------------------EEEEEESS-
T ss_pred cccceEEEEEEEE-e-cCCCceeEEeecCCcc---------------------------------------EEEEEeccC
Confidence 5599999999997 5 3444 44888773211 357889998
Q ss_pred hhhhhccC-CCCCcEEEEeCcEEEE
Q 012376 247 YENFGRYF-TATGKWVRIRNMSCQV 270 (465)
Q Consensus 247 ~~~~~~~~-~k~G~wV~l~Nv~~k~ 270 (465)
-..++.+. +|+|..|...|++-+.
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 88888776 6999999999999876
No 55
>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=73.28 E-value=8.2 Score=32.28 Aligned_cols=48 Identities=15% Similarity=0.055 Sum_probs=36.2
Q ss_pred ceEEEEEeccchhhhhccCCCCCcEEEEeCcEEEEeC-------cEEEEEEecCC
Q 012376 236 GTVLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSS-------GMWHGLLQSSS 283 (465)
Q Consensus 236 G~vL~V~~~~~~~~~~~~~~k~G~wV~l~Nv~~k~~~-------g~leG~l~~~s 283 (465)
|..+++++|...+..-...+++|+++.+.|-+++... .-.|..|..++
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 5578999998776655678999999999999998843 23555555444
No 56
>PRK05673 dnaE DNA polymerase III subunit alpha; Validated
Probab=71.34 E-value=11 Score=44.94 Aligned_cols=88 Identities=14% Similarity=0.224 Sum_probs=62.8
Q ss_pred ceeehHhhhh-ccCCEEEEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeE
Q 012376 9 GIVRIKELAM-HVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNV 87 (465)
Q Consensus 9 ~y~~i~~~~~-~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rv 87 (465)
+.+++.++.. ..+..|.+.|+|.+.+.+ +|+.++-++.++|-|.+-. +.+.+|.+..+..=.....|.+|.+. .
T Consensus 964 ~~~~~~~l~~~~~g~~V~v~G~I~~vk~~-~TKkG~~mafltLeD~TG~---iEvviFp~~ye~~~~~L~~g~iV~V~-G 1038 (1135)
T PRK05673 964 RDTRLADLEPTEGGSVVTVAGLVVSVRRR-VTKRGNKMAIVTLEDLSGR---IEVMLFSEALEKYRDLLEEDRIVVVK-G 1038 (1135)
T ss_pred CCcCHHHHhccccCceEEEEEEEEEEEec-ccCCCCeEEEEEEEeCCCc---EEEEECHHHHHHHHHHhccCCEEEEE-E
Confidence 3456666642 246779999999999874 5555567999999999764 99999986534443333679998884 4
Q ss_pred EEEEEcCeeeEEec
Q 012376 88 MIKKHQAELSAVFY 101 (465)
Q Consensus 88 ki~~~~g~~~~~~~ 101 (465)
+++...++.+.+.+
T Consensus 1039 kVe~~~~~~qlii~ 1052 (1135)
T PRK05673 1039 QVSFDDGGLRLTAR 1052 (1135)
T ss_pred EEEecCCeEEEEEe
Confidence 67776676776665
No 57
>PF09104 BRCA-2_OB3: BRCA2, oligonucleotide/oligosaccharide-binding, domain 3; InterPro: IPR015188 This domain assumes an OB fold, which consists of a highly curved five-stranded beta-sheet that closes on itself to form a beta-barrel. OB3 has a pronounced groove formed by one face of the curved sheet and is demarcated by two loops, one between beta 1 and beta 2 and another between beta 4 and beta 5, which allows for strong ssDNA binding []. ; PDB: 1IYJ_D 1MIU_A.
Probab=70.83 E-value=18 Score=32.36 Aligned_cols=63 Identities=19% Similarity=0.319 Sum_probs=38.8
Q ss_pred CCEEEEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCC-CCCCCCCCCCCEEEEeeEEEE
Q 012376 21 KHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSI-DQLPRVLSPRDLILLKNVMIK 90 (465)
Q Consensus 21 ~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~-~~LP~v~~~GDII~l~rvki~ 90 (465)
=.-|+++|+|+.. ++++++.--+-|.|.++.- +.|+++..-. -.+-.+..+|-+|-+.|++-+
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 4556787778899999865 8889887522 233445578999999999887
No 58
>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=68.81 E-value=58 Score=26.65 Aligned_cols=26 Identities=27% Similarity=0.362 Sum_probs=19.0
Q ss_pred eEEEEEEEEEeeCCCCeEEEEEEcCCCC
Q 012376 171 DLVCKVFHVSYDDSKGLWMLFVWDGTDV 198 (465)
Q Consensus 171 Dlv~qVv~v~~~~~~~~~~L~VwDgT~~ 198 (465)
||++.|+.+. + ......+-+=|||+.
T Consensus 1 ~ivG~V~sv~-~-~~~~~~~tLdDgTG~ 26 (92)
T cd04483 1 DILGTVVSRR-E-RETFYSFGVDDGTGV 26 (92)
T ss_pred CeEEEEEEEE-e-cCCeEEEEEecCCce
Confidence 5788899887 4 345677777788874
No 59
>KOG3056 consensus Protein required for S-phase initiation or completion [Cell cycle control, cell division, chromosome partitioning]
Probab=68.21 E-value=8.2 Score=41.56 Aligned_cols=70 Identities=17% Similarity=0.217 Sum_probs=56.4
Q ss_pred EEEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCe
Q 012376 24 VNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAE 95 (465)
Q Consensus 24 vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~~~g~ 95 (465)
--++|||++-+.|+.|...+=.+.++|.|-.-. .-|.+-+|.+-.+.+=.+ ..|+||-|-|..|-..++.
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 448999999999999854444456788877664 459999999877888888 5899999999999877654
No 60
>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=67.48 E-value=17 Score=30.33 Aligned_cols=64 Identities=19% Similarity=0.245 Sum_probs=43.9
Q ss_pred EEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCC-CCCCCCCCCCCEEEEeeEEEEEEcCe
Q 012376 26 LLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSI-DQLPRVLSPRDLILLKNVMIKKHQAE 95 (465)
Q Consensus 26 viGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~-~~LP~v~~~GDII~l~rvki~~~~g~ 95 (465)
++|||+....+. +..+-.+.|.|+++.. +.|+++..-. ..+-.+-..+-.|-+.|++.+.....
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 8888888311 22233334456777777777755444
No 61
>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=65.75 E-value=26 Score=28.59 Aligned_cols=60 Identities=20% Similarity=0.332 Sum_probs=37.7
Q ss_pred EEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCC--CCCCCCCCCCCCEEEEeeEEEEEEc
Q 012376 26 LLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSS--IDQLPRVLSPRDLILLKNVMIKKHQ 93 (465)
Q Consensus 26 viGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~--~~~LP~v~~~GDII~l~rvki~~~~ 93 (465)
|-|-|+.+.. .-+|.. +-|+|.|.+. .|.+.+|.++ ...+..-...||.|.+..- +..|.
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 213445 4566789763 4999999976 4455554479998777554 45444
No 62
>PRK06920 dnaE DNA polymerase III DnaE; Reviewed
Probab=64.58 E-value=18 Score=42.92 Aligned_cols=89 Identities=10% Similarity=0.169 Sum_probs=61.6
Q ss_pred cceeehHhhhhccCCEEEEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeE
Q 012376 8 GGIVRIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNV 87 (465)
Q Consensus 8 y~y~~i~~~~~~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rv 87 (465)
++.+++.++....+..|.+.|+|+..+.+ +|+.++-+.-++|-|.+-. +.+.+|.+.-+..-.....|.++++. .
T Consensus 930 ~~~~~~~~l~~~~~~~v~v~g~i~~~~~~-~tk~g~~maf~~leD~tg~---~e~~vFp~~y~~~~~~l~~~~~~~v~-G 1004 (1107)
T PRK06920 930 LEIPSLAQAMRHKKKVQRAIVYITSVKVI-RTKKGQKMAFITFCDQNDE---MEAVVFPETYIHFSDKLQEGAIVLVD-G 1004 (1107)
T ss_pred hCCcCHHHHhhcCCCEEEEEEEEEEeEee-cCCCCCeEEEEEEeeCCCc---EEEEECHHHHHHHHHHhccCCEEEEE-E
Confidence 34456777643346689999999999874 5554577899999998663 99999987555554444678888874 4
Q ss_pred EEEEEcCeeeEEec
Q 012376 88 MIKKHQAELSAVFY 101 (465)
Q Consensus 88 ki~~~~g~~~~~~~ 101 (465)
+++.-+++.+.+.+
T Consensus 1005 ~v~~~~~~~~~~~~ 1018 (1107)
T PRK06920 1005 TIELRNHKLQWIVN 1018 (1107)
T ss_pred EEEecCCcEEEEEe
Confidence 66654555565554
No 63
>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=64.32 E-value=8.1 Score=33.65 Aligned_cols=34 Identities=15% Similarity=0.338 Sum_probs=27.8
Q ss_pred eEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcC
Q 012376 60 LLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQA 94 (465)
Q Consensus 60 l~v~iF~~~~~~LP~v~~~GDII~l~rvki~~~~g 94 (465)
|.|.+|-++.+..-.+ .+||.|+|+||.++....
T Consensus 62 i~It~yD~H~~~ar~l-K~GdfV~L~NVhiK~~~~ 95 (123)
T cd04498 62 IDILVYDNHVELAKSL-KPGDFVRIYNVHAKSYSS 95 (123)
T ss_pred EEEEEEcchHHHHhhC-CCCCEEEEEEEEEEeccC
Confidence 7778888777666667 689999999999987766
No 64
>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=62.83 E-value=23 Score=28.93 Aligned_cols=39 Identities=18% Similarity=0.313 Sum_probs=32.1
Q ss_pred ceEEEEEeccchhhhhccCCCCCcEEEEeCcEEEEeCcE
Q 012376 236 GTVLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGM 274 (465)
Q Consensus 236 G~vL~V~~~~~~~~~~~~~~k~G~wV~l~Nv~~k~~~g~ 274 (465)
|..|+.++.......-...+++|.|..|.|..+..+.|.
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 778899998766655578899999999999998887654
No 65
>KOG1030 consensus Predicted Ca2+-dependent phospholipid-binding protein [General function prediction only]
Probab=62.82 E-value=16 Score=33.50 Aligned_cols=26 Identities=15% Similarity=0.332 Sum_probs=25.0
Q ss_pred CCeEEEEEEEEeCCCceEEEEEeccc
Q 012376 372 GSSEYTMKLTLEDPTARIHALLCGKE 397 (465)
Q Consensus 372 ~~w~~rf~L~lED~t~ri~~~v~~~d 397 (465)
-+|.+.|-|+|.|+..-+.+-||++|
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 66
>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed
Probab=56.89 E-value=75 Score=33.60 Aligned_cols=70 Identities=14% Similarity=0.180 Sum_probs=48.9
Q ss_pred CEEEEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEE--cCeeeEE
Q 012376 22 HKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKH--QAELSAV 99 (465)
Q Consensus 22 ~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~~--~g~~~~~ 99 (465)
..|-|.|=|..++.+ +.| .|-|+|+|... .|+|.+|+.....++.-...|+-|++ ..++..| .|.++..
T Consensus 24 ~~v~v~gEis~~~~~--~sG---H~Yf~Lkd~~a---~i~~~~~~~~~~~~~~~~~~G~~v~v-~g~~~~y~~~g~~ql~ 94 (438)
T PRK00286 24 GQVWVRGEISNFTRH--SSG---HWYFTLKDEIA---QIRCVMFKGSARRLKFKPEEGMKVLV-RGKVSLYEPRGDYQLI 94 (438)
T ss_pred CcEEEEEEeCCCeeC--CCC---eEEEEEEcCCc---EEEEEEEcChhhcCCCCCCCCCEEEE-EEEEEEECCCCCEEEE
Confidence 468888988888764 234 56788999943 49999999877888875578997766 3344444 3445554
Q ss_pred e
Q 012376 100 F 100 (465)
Q Consensus 100 ~ 100 (465)
.
T Consensus 95 v 95 (438)
T PRK00286 95 V 95 (438)
T ss_pred E
Confidence 4
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=55.34 E-value=83 Score=33.38 Aligned_cols=78 Identities=17% Similarity=0.235 Sum_probs=53.1
Q ss_pred hHhhhhc-cCCEEEEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEE
Q 012376 13 IKELAMH-VKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKK 91 (465)
Q Consensus 13 i~~~~~~-~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~ 91 (465)
|+.+++. .+ .|-|-|=|..++.+ +.| .+-|+|+|..- -|+|.+|+.....|+.-.+.|+=|++ ..++..
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 57778899753 39999999877788776578997666 344555
Q ss_pred E--cCeeeEEe
Q 012376 92 H--QAELSAVF 100 (465)
Q Consensus 92 ~--~g~~~~~~ 100 (465)
| .|+++...
T Consensus 79 y~~~G~~ql~v 89 (432)
T TIGR00237 79 YEPRGDYQIIC 89 (432)
T ss_pred ECCCCcEEEEE
Confidence 5 44455544
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=54.84 E-value=26 Score=29.45 Aligned_cols=54 Identities=17% Similarity=0.295 Sum_probs=38.9
Q ss_pred cceeehHhhhhccCCEEEEEEEEEe-cCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCC
Q 012376 8 GGIVRIKELAMHVKHKVNLLGVVLE-FSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSS 68 (465)
Q Consensus 8 y~y~~i~~~~~~~~~~vnviGVVvd-~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~ 68 (465)
-.|+||+.+-. .|+ | +|.| +++| .+.+.-|+.++.|.|+-+..++|+|.+|++.
T Consensus 16 LsFmPl~saD~-~gG-V----I~TdWY~~p-~~~~er~k~tv~Ild~~Lradal~V~vf~q~ 70 (103)
T PF12100_consen 16 LSFMPLASADP-FGG-V----IVTDWYSPP-PGPNERFKATVYILDRALRADALRVSVFRQV 70 (103)
T ss_pred HhhcchhhcCC-CCC-E----EEeccccCC-CCCCeeEEEEEEEECccccCCceEEEEEEee
Confidence 35777777642 221 1 3566 5555 3445789999999999999999999999864
No 69
>PRK07374 dnaE DNA polymerase III subunit alpha; Validated
Probab=54.82 E-value=34 Score=40.96 Aligned_cols=88 Identities=15% Similarity=0.239 Sum_probs=62.3
Q ss_pred ceeehHhhhhc-cCCEEEEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeE
Q 012376 9 GIVRIKELAMH-VKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNV 87 (465)
Q Consensus 9 ~y~~i~~~~~~-~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rv 87 (465)
..++++++... .+..|.+.|+|+..+.+ +|+.++-+.-++|-|.+-. +.+.+|.+.-+..-.....|.++++. .
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 44566666432 46679999999999875 5555678999999999764 99999987655554544678888884 4
Q ss_pred EEEEEcCeeeEEec
Q 012376 88 MIKKHQAELSAVFY 101 (465)
Q Consensus 88 ki~~~~g~~~~~~~ 101 (465)
+++.-.++.+.+.+
T Consensus 1062 ~v~~~~~~~~~~~~ 1075 (1170)
T PRK07374 1062 KVDRRDDRVQLIID 1075 (1170)
T ss_pred EEEecCCeEEEEEe
Confidence 66654455666654
No 70
>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=53.34 E-value=43 Score=28.70 Aligned_cols=41 Identities=20% Similarity=0.236 Sum_probs=28.6
Q ss_pred CCCCCCCCCCCEEEEeeE-------EEEEEcCeeeEEecCC-ceEEEEEe
Q 012376 70 DQLPRVLSPRDLILLKNV-------MIKKHQAELSAVFYKD-SSSFALFD 111 (465)
Q Consensus 70 ~~LP~v~~~GDII~l~rv-------ki~~~~g~~~~~~~~~-~ss~~lf~ 111 (465)
..+|.+ .+||+|.++=. ++|.|.|-+.+.-+.+ .++|.|=+
T Consensus 14 ~~~p~f-~~GD~v~V~~~i~e~~k~r~q~f~GvvIa~~~~g~~ssftlR~ 62 (113)
T PF01245_consen 14 KDIPEF-RVGDTVRVTYKISEGNKERIQVFEGVVIARRRRGLNSSFTLRN 62 (113)
T ss_dssp SSSSSS-SSSSEEEEEEEEESSSSEEEEEEEEEEEEEEBSSTSSEEEEEE
T ss_pred cCCCCc-CCCCEEEEEEEEecCCCceeEEEEEEEEEEECCCCCeeEEEEE
Confidence 679999 79999999764 2467777666665533 36677633
No 71
>PRK05338 rplS 50S ribosomal protein L19; Provisional
Probab=53.16 E-value=32 Score=29.62 Aligned_cols=45 Identities=16% Similarity=0.235 Sum_probs=30.4
Q ss_pred CCCCCCCCCCCEEEEeeE-------EEEEEcCeeeEEecCC-ceEEEEEeCCCC
Q 012376 70 DQLPRVLSPRDLILLKNV-------MIKKHQAELSAVFYKD-SSSFALFDGNSG 115 (465)
Q Consensus 70 ~~LP~v~~~GDII~l~rv-------ki~~~~g~~~~~~~~~-~ss~~lf~~~~~ 115 (465)
.++|.+ .+||+|.++-- ++|.|.|-+.+.-+.+ .++|.|=+-..+
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 3567777666655543 367887555444
No 72
>PF15072 DUF4539: Domain of unknown function (DUF4539)
Probab=52.12 E-value=44 Score=27.20 Aligned_cols=63 Identities=22% Similarity=0.318 Sum_probs=43.8
Q ss_pred EEEEEEEEEe-cCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcC
Q 012376 23 KVNLLGVVLE-FSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQA 94 (465)
Q Consensus 23 ~vnviGVVvd-~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~~~g 94 (465)
+|...+|+++ +.. .+.|. .+.+.|||-. +...+=++-.+..|....+|=+++|++|.+=.=..
T Consensus 3 KVp~l~v~Iks~~~----~~~D~--~v~l~DpTG~---i~~tiH~~v~~~y~~~l~~GavLlLk~V~Vf~ps~ 66 (86)
T PF15072_consen 3 KVPCLVVIIKSIVP----SSEDA--FVVLKDPTGE---IRGTIHRKVLEEYGDELSPGAVLLLKDVTVFSPSP 66 (86)
T ss_pred ccCEEEEEEEEeec----cCCCe--EEEEECCCCc---EEEEEeHHHHhhcCCccccCEEEEEeeeeEEecCC
Confidence 4444444444 544 33455 6779998763 88888887666778877999999999998765433
No 73
>cd04480 RPA1_DBD_A_like RPA1_DBD_A_like: A subgroup of uncharacterized plant OB folds with similarity to the second OB fold, the ssDNA-binding domain (DBD)-A, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of RPA is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change.
Probab=49.77 E-value=33 Score=27.33 Aligned_cols=37 Identities=19% Similarity=0.333 Sum_probs=29.9
Q ss_pred ceEEEEEeccchhhhhccCCCCCcEEEEeCcEEEEeC
Q 012376 236 GTVLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSS 272 (465)
Q Consensus 236 G~vL~V~~~~~~~~~~~~~~k~G~wV~l~Nv~~k~~~ 272 (465)
|..++.++....++.-...+++|.|..|.|-.++...
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 6778999887666655788999999999998876644
No 74
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=49.51 E-value=70 Score=36.03 Aligned_cols=78 Identities=19% Similarity=0.196 Sum_probs=52.0
Q ss_pred ehHhhhhccCCEEEEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEE
Q 012376 12 RIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKK 91 (465)
Q Consensus 12 ~i~~~~~~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~ 91 (465)
+|+++. .|+.|.+.|.|++.....+ + --..++++.|.+- .+.+.+|.-+...+.....+|+-+.+.. |++.
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 3899999422235555557899888865 4444
Q ss_pred EcCeeeE
Q 012376 92 HQAELSA 98 (465)
Q Consensus 92 ~~g~~~~ 98 (465)
++|..+.
T Consensus 123 ~~~~~qm 129 (681)
T PRK10917 123 GKYGLEM 129 (681)
T ss_pred cCCeEEE
Confidence 5555444
No 75
>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=49.28 E-value=92 Score=24.98 Aligned_cols=26 Identities=27% Similarity=0.193 Sum_probs=20.3
Q ss_pred EeEEEEEEEEEeeCCCCeEEEEEEcCCC
Q 012376 170 FDLVCKVFHVSYDDSKGLWMLFVWDGTD 197 (465)
Q Consensus 170 ~Dlv~qVv~v~~~~~~~~~~L~VwDgT~ 197 (465)
+.+++.|.++. . .+..+.+.+-|+|+
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 46788888899885
No 76
>TIGR00643 recG ATP-dependent DNA helicase RecG.
Probab=47.01 E-value=95 Score=34.58 Aligned_cols=78 Identities=18% Similarity=0.229 Sum_probs=52.2
Q ss_pred ehHhhhhccCCEEEEEEEEEecCCccccCCCceEEEEEEEe-CCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEE
Q 012376 12 RIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVD-DSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIK 90 (465)
Q Consensus 12 ~i~~~~~~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D-~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~ 90 (465)
+|+++. .|+.+.+.|.|++..... ++.--..++.+.| .+- .+.+.+|.. ..+......|+-+.+.. |+.
T Consensus 25 ~i~~~~--~g~~~~~~~~v~~~~~~~--~~~~~~~~~~~~d~~~~---~~~~~~F~~--~~~~~~~~~g~~~~~~G-k~~ 94 (630)
T TIGR00643 25 TIGELL--PGERATIVGEVLSHCIFG--FKRRKVLKLRLKDGGYK---KLELRFFNR--AFLKKKFKVGSKVVVYG-KVK 94 (630)
T ss_pred CHHHcC--CCCEEEEEEEEEEeEecc--CCCCceEEEEEEECCCC---EEEEEEECC--HHHHhhCCCCCEEEEEE-EEE
Confidence 566665 788999999998742211 2222278888999 433 399999973 25555557899988865 556
Q ss_pred EEcCeeeEE
Q 012376 91 KHQAELSAV 99 (465)
Q Consensus 91 ~~~g~~~~~ 99 (465)
.++|..+..
T Consensus 95 ~~~~~~~~~ 103 (630)
T TIGR00643 95 SSKFKAYLI 103 (630)
T ss_pred eeCCEEEEE
Confidence 677766543
No 77
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=46.25 E-value=91 Score=34.23 Aligned_cols=78 Identities=15% Similarity=0.348 Sum_probs=58.3
Q ss_pred eehHhhhhccCCEEEEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEec-CCCCCCCCCCCCCCEEEEeeEEE
Q 012376 11 VRIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFT-SSIDQLPRVLSPRDLILLKNVMI 89 (465)
Q Consensus 11 ~~i~~~~~~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~-~~~~~LP~v~~~GDII~l~rvki 89 (465)
+.|.++-+..|..|.+=|-|+..+ +|.| -.-|||.|++-. +.+.-|- +-.-.-|.| .+||||.+.. .+
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 6677775 566789999 7999999965 46
Q ss_pred EEEcCeeeEE
Q 012376 90 KKHQAELSAV 99 (465)
Q Consensus 90 ~~~~g~~~~~ 99 (465)
..+.|++|.-
T Consensus 272 ~~r~g~lQiE 281 (715)
T COG1107 272 TRRDGRLQIE 281 (715)
T ss_pred eecCCcEEEe
Confidence 6677887763
No 78
>PRK06826 dnaE DNA polymerase III DnaE; Reviewed
Probab=42.84 E-value=60 Score=38.85 Aligned_cols=77 Identities=14% Similarity=0.230 Sum_probs=54.5
Q ss_pred cCCEEEEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEE-cCeeeE
Q 012376 20 VKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKH-QAELSA 98 (465)
Q Consensus 20 ~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~~-~g~~~~ 98 (465)
.+..|.+.|+|+..+.+ +|+.++-+.-++|-|.+-. +.+.+|.+..+..-.....|.+|++ ..+++.. ++..+.
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 46679999999999874 5555677999999998763 9999998654444343356888887 4566643 454565
Q ss_pred Eec
Q 012376 99 VFY 101 (465)
Q Consensus 99 ~~~ 101 (465)
+.+
T Consensus 1065 ~~~ 1067 (1151)
T PRK06826 1065 ICE 1067 (1151)
T ss_pred EEe
Confidence 554
No 79
>TIGR01024 rplS_bact ribosomal protein L19, bacterial type. This model describes bacterial ribosomoal protein L19 and its chloroplast equivalent. Putative mitochondrial L19 are found in several species (but not Saccharomyces cerevisiae) and score between trusted and noise cutoffs.
Probab=42.81 E-value=46 Score=28.56 Aligned_cols=45 Identities=16% Similarity=0.128 Sum_probs=30.3
Q ss_pred CCCCCCCCCCCEEEEeeE-------EEEEEcCeeeEEecCC-ceEEEEEeCCCC
Q 012376 70 DQLPRVLSPRDLILLKNV-------MIKKHQAELSAVFYKD-SSSFALFDGNSG 115 (465)
Q Consensus 70 ~~LP~v~~~GDII~l~rv-------ki~~~~g~~~~~~~~~-~ss~~lf~~~~~ 115 (465)
.++|.+ .+||+|.++-- ++|.|.|-+.+.-+.+ .++|.|=+-..+
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 3456777666665543 366877555433
No 80
>PRK05672 dnaE2 error-prone DNA polymerase; Validated
Probab=41.95 E-value=57 Score=38.67 Aligned_cols=86 Identities=21% Similarity=0.254 Sum_probs=57.5
Q ss_pred ceeehHhhhhc-cCCEEEEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeE
Q 012376 9 GIVRIKELAMH-VKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNV 87 (465)
Q Consensus 9 ~y~~i~~~~~~-~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rv 87 (465)
.++++.++... .+..|.+.|+|+....+...+| +.-++|-|.+-. +.+.+|.+..+..-.....|.++++. -
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 34566666542 4667999999999877533345 888899988663 99999986544443433678888884 4
Q ss_pred EEEEEcCeeeEEec
Q 012376 88 MIKKHQAELSAVFY 101 (465)
Q Consensus 88 ki~~~~g~~~~~~~ 101 (465)
+++.-+|+.+.+.+
T Consensus 1013 ~v~~~~~~~~~~~~ 1026 (1046)
T PRK05672 1013 RVQNAEGVRHLVAD 1026 (1046)
T ss_pred EEEecCCeEEEEEe
Confidence 66654555555544
No 81
>CHL00084 rpl19 ribosomal protein L19
Probab=40.96 E-value=66 Score=27.79 Aligned_cols=42 Identities=10% Similarity=0.150 Sum_probs=27.6
Q ss_pred CCCCCCCCCCCEEEEee-E------EEEEEcCeeeEEecCC-ceEEEEEeC
Q 012376 70 DQLPRVLSPRDLILLKN-V------MIKKHQAELSAVFYKD-SSSFALFDG 112 (465)
Q Consensus 70 ~~LP~v~~~GDII~l~r-v------ki~~~~g~~~~~~~~~-~ss~~lf~~ 112 (465)
.++|.+ .+||+|.++= + ++|.|.|-+.+.-+.+ .++|.|=+-
T Consensus 18 ~~~p~f-~~GDtV~V~~~i~eg~k~R~q~F~GvvI~~r~~G~~~tftvRki 67 (117)
T CHL00084 18 KNLPKI-RVGDTVKVGVLIQEGNKERVQFYEGTVIAKKNSGLNTTITVRKV 67 (117)
T ss_pred cCCCcc-CCCCEEEEEEEEecCCeeEeceEEEEEEEEeCCCCCeeEEEEEe
Confidence 479999 7999999864 2 3566777655554433 356776443
No 82
>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=39.87 E-value=1.9e+02 Score=22.84 Aligned_cols=62 Identities=18% Similarity=0.079 Sum_probs=38.8
Q ss_pred EEEEEecCCccccCCCceEEEEEEEeCCCC-----CCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCeeeEEec
Q 012376 27 LGVVLEFSIPRKSQGTDYVCVLKIVDDSQQ-----SPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAELSAVFY 101 (465)
Q Consensus 27 iGVVvd~~~P~~trG~D~~~tl~I~D~s~~-----~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~~~g~~~~~~~ 101 (465)
=|||+...... ... .|-|-|+... ++| +-+|.+. -+.+ .+||.|++. -++..|+|..++...
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 47777765432 112 3446666322 234 4455543 4566 789999996 899999998776554
No 83
>PF15072 DUF4539: Domain of unknown function (DUF4539)
Probab=39.70 E-value=27 Score=28.40 Aligned_cols=24 Identities=25% Similarity=0.320 Sum_probs=19.5
Q ss_pred EEEEEEeCCCceEEEEEeccccch
Q 012376 377 TMKLTLEDPTARIHALLCGKEWVK 400 (465)
Q Consensus 377 rf~L~lED~t~ri~~~v~~~da~~ 400 (465)
-..++|.|||++|++.|+.+--+.
T Consensus 20 D~~v~l~DpTG~i~~tiH~~v~~~ 43 (86)
T PF15072_consen 20 DAFVVLKDPTGEIRGTIHRKVLEE 43 (86)
T ss_pred CeEEEEECCCCcEEEEEeHHHHhh
Confidence 457899999999999999665443
No 84
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=36.27 E-value=1.2e+02 Score=37.38 Aligned_cols=85 Identities=16% Similarity=0.305 Sum_probs=60.5
Q ss_pred cceeehHhhhhccCCEEEEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCC---CCCCCCCCCCCEEEE
Q 012376 8 GGIVRIKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSI---DQLPRVLSPRDLILL 84 (465)
Q Consensus 8 y~y~~i~~~~~~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~---~~LP~v~~~GDII~l 84 (465)
+..++|+++... ...|-+-|-|.+... +.++++-...+|.|+|-+ +++.|+.|.++. +.+-.+ +.||-|++
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 467888988743 347889999988755 556656789999999975 459999998443 345556 68999988
Q ss_pred eeE-EEEEEcCeeeE
Q 012376 85 KNV-MIKKHQAELSA 98 (465)
Q Consensus 85 ~rv-ki~~~~g~~~~ 98 (465)
+.- ....|.++...
T Consensus 298 ~g~~~~d~~~~~~~~ 312 (1437)
T PRK00448 298 RGSVQNDTFTRDLVM 312 (1437)
T ss_pred EEEEeccCCCCceEE
Confidence 653 33456555443
No 85
>PRK07279 dnaE DNA polymerase III DnaE; Reviewed
Probab=35.37 E-value=79 Score=37.39 Aligned_cols=86 Identities=17% Similarity=0.294 Sum_probs=58.5
Q ss_pred ceeehHhhhhccCCEEEEEEEEEecCCccccC-CCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeE
Q 012376 9 GIVRIKELAMHVKHKVNLLGVVLEFSIPRKSQ-GTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNV 87 (465)
Q Consensus 9 ~y~~i~~~~~~~~~~vnviGVVvd~~~P~~tr-G~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rv 87 (465)
..+++.++. .+..+.+.|+|...+. .+|+ .++-+..++|-|.+-. +.+.+|.+..+..-.....|.++++..
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 4567899999998764 999999865444433336788888854
Q ss_pred EEEEEcCeeeEEec
Q 012376 88 MIKKHQAELSAVFY 101 (465)
Q Consensus 88 ki~~~~g~~~~~~~ 101 (465)
+++.-.++.+.+.+
T Consensus 947 ~v~~~~~~~~l~~~ 960 (1034)
T PRK07279 947 KIQERDGRLQMVLQ 960 (1034)
T ss_pred EEEecCCeeEEEEe
Confidence 56654555555554
No 86
>KOG4792 consensus Crk family adapters [Signal transduction mechanisms]
Probab=34.91 E-value=89 Score=30.13 Aligned_cols=61 Identities=16% Similarity=0.336 Sum_probs=40.0
Q ss_pred cccCCCcceEEEEEeccchhhhhccCCCCCcEEEEeCcEEEEeCcEEEEEEecC------CceEEcCCCCh
Q 012376 229 LRNFFPVGTVLRVSTDRSYENFGRYFTATGKWVRIRNMSCQVSSGMWHGLLQSS------SKIRLFSDNDN 293 (465)
Q Consensus 229 ~~~~p~~G~vL~V~~~~~~~~~~~~~~k~G~wV~l~Nv~~k~~~g~leG~l~~~------ski~~l~~~d~ 293 (465)
..+-|.+.+++|=.+-+...+- .-.++.||.|+.. -+..+|+|||-+.+. +.|+.++..++
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 4556777777776655444443 2348999999643 344689999988875 46677665444
No 87
>cd04495 BRCA2DBD_OB3 BRCA2DBD_OB3: A subfamily of OB folds corresponding to the third OB fold (OB3) of the 800-amino acid C-terminal ssDNA binding domain (DBD) of BRCA2 (breast cancer susceptibility gene 2) protein, called BRCA2DBD. BRCA2 participates in homologous recombination-mediated repair of double-strand DNA breaks. It stimulates the displacement of Replication protein A (RPA), the most abundant eukaryotic ssDNA binding protein. It also facilitates filament formation. Mutations that map throughout the BRCA2 protein are associated with breast cancer susceptibility. BRCA2 is a large nuclear protein and its most conserved region is the C-terminal BRCA2DBD. BRCA2DBD binds ssDNA in vitro, and is composed of five structural domains, three of which are OB folds (OB1, OB2, and OB3). BRCA2DBD OB2 and OB3 are arranged in tandem, and their mode of binding can be considered qualitatively similar to two OB folds of RPA1, DBD-A and DBD-B (the major DBDs of RPA).
Probab=34.65 E-value=2e+02 Score=24.11 Aligned_cols=34 Identities=18% Similarity=0.068 Sum_probs=27.6
Q ss_pred EEEEeccchhhhhccC-CCCCcEEEEeCcEEEEeC
Q 012376 239 LRVSTDRSYENFGRYF-TATGKWVRIRNMSCQVSS 272 (465)
Q Consensus 239 L~V~~~~~~~~~~~~~-~k~G~wV~l~Nv~~k~~~ 272 (465)
|-|.+|..-+.++.+. +|++..+...|++.+..+
T Consensus 30 l~vkfw~~l~~~~~EDvvk~~~lia~SNLQwR~~s 64 (100)
T cd04495 30 LCVKFWSSLEQYAYEDVVKRRVLLAASNLQWRTES 64 (100)
T ss_pred EEEEEecchHHhhhhhhcccceEEEEecceEeccc
Confidence 4688888777777765 689999999999998844
No 88
>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=34.14 E-value=45 Score=26.40 Aligned_cols=21 Identities=38% Similarity=0.405 Sum_probs=19.5
Q ss_pred EEEEeCCCceEEEEEeccccc
Q 012376 379 KLTLEDPTARIHALLCGKEWV 399 (465)
Q Consensus 379 ~L~lED~t~ri~~~v~~~da~ 399 (465)
.++|||.++++.+.++.+..+
T Consensus 20 ~~~leD~~G~~Ev~~F~~~~~ 40 (79)
T cd04490 20 IVELEDTTGRITVLLTKDKEE 40 (79)
T ss_pred EEEEECCCCEEEEEEeCchhh
Confidence 899999999999999988766
No 89
>PF14535 AMP-binding_C_2: AMP-binding enzyme C-terminal domain; PDB: 2Y27_A 2Y4N_A 3QOV_B 3S89_D 3LAX_A 2Y4O_B.
Probab=33.86 E-value=28 Score=28.49 Aligned_cols=63 Identities=21% Similarity=0.274 Sum_probs=41.8
Q ss_pred EeecCCCccccccCC-C-CeEEEEEEEEeCCCceEEEEEeccccchhcCCC---CC-hHHHHHHHHHHhCC
Q 012376 357 VSIHPFQAEHYSSPN-G-SSEYTMKLTLEDPTARIHALLCGKEWVKFFGGS---PP-PDVLTKKIKMLLGM 421 (465)
Q Consensus 357 V~~~P~~~edf~~~~-~-~w~~rf~L~lED~t~ri~~~v~~~da~~f~~~~---~~-~~~L~~kl~~L~G~ 421 (465)
|.+||.++|+-...- + .=+|++.+.=++...+|.+.|--.+ .+..+. .. .+.|++++..-+|.
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 578999999866532 1 2278888888899999999887766 222211 11 35667777777775
No 90
>KOG2708 consensus Predicted metalloprotease with chaperone activity (RNAse H/HSP70 fold) [Posttranslational modification, protein turnover, chaperones]
Probab=33.01 E-value=25 Score=33.98 Aligned_cols=47 Identities=23% Similarity=0.346 Sum_probs=28.0
Q ss_pred HHHHHHHHHHhCCCCC---------CCCC-CCCccCCcceeeeeeeeeecCCc-------eEEEEEeeeEE
Q 012376 409 DVLTKKIKMLLGMPEH---------EDGN-DDMVRNPPWIKCFLHLKESDGGR-------NRVYYIRWTKL 462 (465)
Q Consensus 409 ~~L~~kl~~L~G~~e~---------~~~~-~~~~~n~pw~~CCi~sY~v~~~~-------~r~f~~F~T~i 462 (465)
+..-+-+..||..+-- +.|. -+...||- =-||.+++ ++||||||-+|
T Consensus 90 aivaRtlsllw~kPlv~VNHCigHIEMGR~iTgA~nPv-------vLYvSGGNTQvIAYse~rYrIFGETl 153 (336)
T KOG2708|consen 90 AIVARTLSLLWNKPLVGVNHCIGHIEMGREITGAQNPV-------VLYVSGGNTQVIAYSEKRYRIFGETL 153 (336)
T ss_pred HHHHHHHHHHhCCCcccchhhhhhhhhcceeccCCCCE-------EEEEeCCceEEEEEccceeeeeccee
Confidence 4555678888864321 0110 12234544 24677665 99999999987
No 91
>COG2049 DUR1 Allophanate hydrolase subunit 1 [Amino acid transport and metabolism]
Probab=31.51 E-value=22 Score=34.18 Aligned_cols=39 Identities=10% Similarity=-0.001 Sum_probs=27.9
Q ss_pred ccCCCcceEEEEEeccchhhhhccCCCCCcEEEEeCcEEEE
Q 012376 230 RNFFPVGTVLRVSTDRSYENFGRYFTATGKWVRIRNMSCQV 270 (465)
Q Consensus 230 ~~~p~~G~vL~V~~~~~~~~~~~~~~k~G~wV~l~Nv~~k~ 270 (465)
-.|--+|+|-. .+|++..+. --.+++||||+|+++..+.
T Consensus 177 GGWqlIGrTp~-~lfdp~~~~-p~ll~~Gd~VrF~~i~~~e 215 (223)
T COG2049 177 GGWQLIGRTPL-PLFDPDREP-PALLRPGDQVRFVPIKEEE 215 (223)
T ss_pred CceeEeccccc-cccCCCCCC-CeeccCCCEEEEEecCccc
Confidence 45777888743 456666654 4568999999999987554
No 92
>PRK13254 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=30.95 E-value=2.8e+02 Score=24.90 Aligned_cols=67 Identities=16% Similarity=0.168 Sum_probs=46.8
Q ss_pred ceeehHhhhhc---cCCEEEEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEe
Q 012376 9 GIVRIKELAMH---VKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLK 85 (465)
Q Consensus 9 ~y~~i~~~~~~---~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~ 85 (465)
-|.+.+++... .+..+.+-|.|++=+.- ++.+-..+|.|.|... .+.|.+-. .+|...+.|.-|.+.
T Consensus 36 yf~tpse~~~~~~~~g~~vrvgG~V~~gSi~---~~~~~~~~F~ltD~~~---~i~V~Y~G----~lPd~F~eg~~VVv~ 105 (148)
T PRK13254 36 FFYTPSEVAEGEAPAGRRFRLGGLVEKGSVQ---RGDGLTVRFVVTDGNA---TVPVVYTG----ILPDLFREGQGVVAE 105 (148)
T ss_pred eeeCHHHHhcCCccCCCeEEEeEEEecCcEE---eCCCCEEEEEEEeCCe---EEEEEECC----CCCccccCCCEEEEE
Confidence 36677777663 47789999999965442 2256678999999833 26666544 489877888876653
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=30.88 E-value=40 Score=27.13 Aligned_cols=27 Identities=15% Similarity=0.164 Sum_probs=23.4
Q ss_pred EEEEEeccchhhhhccCCCCCcEEEEe
Q 012376 238 VLRVSTDRSYENFGRYFTATGKWVRIR 264 (465)
Q Consensus 238 vL~V~~~~~~~~~~~~~~k~G~wV~l~ 264 (465)
.++|.+|...++.+.+.++.|++|.+.
T Consensus 45 ~~~v~~~g~~a~~~~~~~~kG~~V~v~ 71 (100)
T cd04496 45 WIRVVAFGKLAENAAKYLKKGDLVYVE 71 (100)
T ss_pred EEEEEEEhHHHHHHHHHhCCCCEEEEE
Confidence 679999999888888899999999543
No 94
>cd04489 ExoVII_LU_OBF ExoVII_LU_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of Escherichia coli exodeoxyribonuclease VII (ExoVII) large subunit. E. coli ExoVII is composed of two non-identical subunits. E. coli ExoVII is a single-strand-specific exonuclease which degrades ssDNA from both 3-prime and 5-prime ends. ExoVII plays a role in methyl-directed mismatch repair in vivo. ExoVII may also guard the genome from mutagenesis by removing excess ssDNA, since the build up of ssDNA would lead to SOS induction and PolIV-dependent mutagenesis.
Probab=30.69 E-value=61 Score=24.85 Aligned_cols=24 Identities=21% Similarity=0.311 Sum_probs=20.4
Q ss_pred EEEEEEeCCCceEEEEEeccccch
Q 012376 377 TMKLTLEDPTARIHALLCGKEWVK 400 (465)
Q Consensus 377 rf~L~lED~t~ri~~~v~~~da~~ 400 (465)
+..++|+|.++++.+.++.+-...
T Consensus 18 ~~~~~L~D~~~~i~~~~f~~~~~~ 41 (78)
T cd04489 18 HLYFTLKDEDASIRCVMWRSNARR 41 (78)
T ss_pred EEEEEEEeCCeEEEEEEEcchhhh
Confidence 778999999999999999875443
No 95
>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=29.92 E-value=67 Score=24.63 Aligned_cols=21 Identities=38% Similarity=0.442 Sum_probs=18.6
Q ss_pred EEEEEEeCCCceEEEEEeccc
Q 012376 377 TMKLTLEDPTARIHALLCGKE 397 (465)
Q Consensus 377 rf~L~lED~t~ri~~~v~~~d 397 (465)
.+.++|+|.|+++.+.++++.
T Consensus 20 ~~~~~l~D~tg~i~~~~f~~~ 40 (83)
T cd04492 20 YLALTLQDKTGEIEAKLWDAS 40 (83)
T ss_pred EEEEEEEcCCCeEEEEEcCCC
Confidence 589999999999999998754
No 96
>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=28.89 E-value=1.2e+02 Score=25.02 Aligned_cols=63 Identities=11% Similarity=-0.094 Sum_probs=37.1
Q ss_pred ceEEEEEeccchhhhhccC----CCCCcEEEEeC-cEEEEeCcE-EEEEEecCCceEEcCCCChhHHHHH
Q 012376 236 GTVLRVSTDRSYENFGRYF----TATGKWVRIRN-MSCQVSSGM-WHGLLQSSSKIRLFSDNDNVVWDYM 299 (465)
Q Consensus 236 G~vL~V~~~~~~~~~~~~~----~k~G~wV~l~N-v~~k~~~g~-leG~l~~~ski~~l~~~d~~v~~r~ 299 (465)
|..|.+++|..+|...... -+.+-.|.+.. .+++...|. .-......|++. ++++-+++...+
T Consensus 34 ~~~l~~tlwG~~A~~f~~~~~~~~~~~~VVav~~~~rV~~~~g~~~ls~~~~~s~v~-inp~ipe~~~~~ 102 (106)
T cd04481 34 DERLKCTLWGEYAEEFDAKFQSAGNGEPVVAVLRFWKIKEYKGPKSLSNSFGASKVY-INPDIPEVPEIK 102 (106)
T ss_pred CCEEEEEEEHHHHHHHHHHHHHhCCCCcEEEEEEeEEEEEEcCCcEEEcCCCceEEE-ECCCcHHHHHHH
Confidence 6689999999988764432 25556666544 888887662 111111345663 455555655543
No 97
>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=28.80 E-value=1.8e+02 Score=30.48 Aligned_cols=78 Identities=17% Similarity=0.230 Sum_probs=56.2
Q ss_pred CCEEEEEEEEEecCCcc--ccC-CC-ceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCee
Q 012376 21 KHKVNLLGVVLEFSIPR--KSQ-GT-DYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAEL 96 (465)
Q Consensus 21 ~~~vnviGVVvd~~~P~--~tr-G~-D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~~~g~~ 96 (465)
.+.+|+.|-|..+..++ .++ |. .=..+..+.|.+-. +... +..+...+++. ..||++.+.+..+..|+|.+
T Consensus 59 ~~~~~v~~~V~~~~e~~~~~~k~g~~~~l~~~~v~Detg~---v~~~-~~~~~~a~~~~-e~Gdv~~i~~~~~~~~~~~~ 133 (407)
T COG1599 59 SSRVNVTGRVLSIGEKKTFDRKRGAEGKLAEVLVGDETGS---VKTV-TLWNIAALEKL-EPGDVIRIRNAYTSLYRGGK 133 (407)
T ss_pred hccccEEEEECccccceeeecccccccceEEEEEecCCCC---EEEE-eeccccccccC-CccceEEecCcccccccCce
Confidence 45799999999998766 443 43 33445557777653 3332 56555666677 68999999999999999999
Q ss_pred eEEecCC
Q 012376 97 SAVFYKD 103 (465)
Q Consensus 97 ~~~~~~~ 103 (465)
++..+..
T Consensus 134 ~~~~~~~ 140 (407)
T COG1599 134 RLSVGRV 140 (407)
T ss_pred eeecccc
Confidence 8887644
No 98
>COG1570 XseA Exonuclease VII, large subunit [DNA replication, recombination, and repair]
Probab=27.89 E-value=5.7e+02 Score=27.28 Aligned_cols=64 Identities=17% Similarity=0.223 Sum_probs=47.2
Q ss_pred CEEEEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcC
Q 012376 22 HKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQA 94 (465)
Q Consensus 22 ~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~~~g 94 (465)
+.|=|-|=|..++.| ..| ..-|+|.|+.-. |.|.+|+.+...|....+.|+-|+++ -+|+.|-+
T Consensus 24 ~~V~v~GEISn~t~~--~sg---H~YFtLKD~~A~---i~c~mf~~~~~~l~f~p~eG~~V~v~-G~is~Y~~ 87 (440)
T COG1570 24 GQVWVRGEISNFTRP--ASG---HLYFTLKDERAQ---IRCVMFKGNNRRLKFRPEEGMQVLVR-GKISLYEP 87 (440)
T ss_pred CeEEEEEEecCCccC--CCc---cEEEEEccCCce---EEEEEEcCcccccCCCccCCCEEEEE-EEEEEEcC
Confidence 357777777777754 133 667889999553 99999998888888766889988774 46666644
No 99
>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=26.64 E-value=3.2e+02 Score=23.54 Aligned_cols=68 Identities=18% Similarity=0.173 Sum_probs=44.9
Q ss_pred hHhhh-hccCCEEEEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCC---CCCCCCCCCCCEEEEeeEE
Q 012376 13 IKELA-MHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSI---DQLPRVLSPRDLILLKNVM 88 (465)
Q Consensus 13 i~~~~-~~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~---~~LP~v~~~GDII~l~rvk 88 (465)
+.++. ...|+.|.+.|-|...+. .|+ .+=+.|.|.+. .+.+.+-.+.. +.+..+ ..||+|.+...-
T Consensus 5 ~~~~~~~~~g~~V~i~Gwv~~~R~----~gk--~~Fi~LrD~~g---~~Q~v~~~~~~~~~~~~~~l-~~gs~V~V~G~~ 74 (135)
T cd04317 5 CGELRESHVGQEVTLCGWVQRRRD----HGG--LIFIDLRDRYG---IVQVVFDPEEAPEFELAEKL-RNESVIQVTGKV 74 (135)
T ss_pred hhhCChhHCCCEEEEEEeEehhcc----cCC--EEEEEEecCCe---eEEEEEeCCchhHHHHHhCC-CCccEEEEEEEE
Confidence 34443 236788999999977654 344 67788888874 26766644322 244556 689999999964
Q ss_pred EE
Q 012376 89 IK 90 (465)
Q Consensus 89 i~ 90 (465)
..
T Consensus 75 ~~ 76 (135)
T cd04317 75 RA 76 (135)
T ss_pred EC
Confidence 43
No 100
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=26.54 E-value=3e+02 Score=30.88 Aligned_cols=79 Identities=18% Similarity=0.196 Sum_probs=56.9
Q ss_pred hHhhhhccCCEEEEEEEEEecCCccccCCCceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEE
Q 012376 13 IKELAMHVKHKVNLLGVVLEFSIPRKSQGTDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKH 92 (465)
Q Consensus 13 i~~~~~~~~~~vnviGVVvd~~~P~~trG~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~~ 92 (465)
|.++. .|..|.+.|.|.....+. .++.-..++++.|.+. -+++.+|.... .+..-..+|--+.+. =|++.+
T Consensus 54 i~~~~--~g~~vti~g~V~~~~~~~--~~~~~~l~v~~~d~~~---~l~l~fFn~~~-~l~~~~~~G~~v~v~-Gk~~~~ 124 (677)
T COG1200 54 IAEAR--PGEIVTIEGTVLSHEKFP--FGKRKLLKVTLSDGTG---VLTLVFFNFPA-YLKKKLKVGERVIVY-GKVKRF 124 (677)
T ss_pred hhhcC--CCceEEEEEEEEeeeccC--CCCCceEEEEEecCcE---EEEEEEECccH-HHHhhCCCCCEEEEE-EEEeec
Confidence 44443 678999999999876543 5567788999999433 39999998653 566655789988874 467778
Q ss_pred cCeeeEEe
Q 012376 93 QAELSAVF 100 (465)
Q Consensus 93 ~g~~~~~~ 100 (465)
++..+...
T Consensus 125 ~~~~~~~h 132 (677)
T COG1200 125 KGGLQITH 132 (677)
T ss_pred cCceEEEc
Confidence 77766544
No 101
>cd04480 RPA1_DBD_A_like RPA1_DBD_A_like: A subgroup of uncharacterized plant OB folds with similarity to the second OB fold, the ssDNA-binding domain (DBD)-A, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of RPA is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change.
Probab=26.46 E-value=1.2e+02 Score=24.10 Aligned_cols=57 Identities=9% Similarity=0.096 Sum_probs=43.2
Q ss_pred CceEEEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCeeeEEe
Q 012376 42 TDYVCVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAELSAVF 100 (465)
Q Consensus 42 ~D~~~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~~~g~~~~~~ 100 (465)
....+++-|.|+.-. -|.+.++....+.+-.....|.+..+.+.++..-++......
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 488999987666666655899999999999987776544443
No 102
>PF15489 CTC1: CST, telomere maintenance, complex subunit CTC1
Probab=24.13 E-value=1.3e+03 Score=27.74 Aligned_cols=71 Identities=21% Similarity=0.277 Sum_probs=47.5
Q ss_pred cCCEEEEEEEEEecCCccccCCCceE-EEEEEEeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEeeEEEEEEcCe
Q 012376 20 VKHKVNLLGVVLEFSIPRKSQGTDYV-CVLKIVDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLKNVMIKKHQAE 95 (465)
Q Consensus 20 ~~~~vnviGVVvd~~~P~~trG~D~~-~tl~I~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~rvki~~~~g~ 95 (465)
.+..+||.|.|+..++-.+++|+-|. +++. |. ...++|.+=-+..-.-=....+|+-..|.+++|...+|.
T Consensus 164 ~~~~~~v~G~v~~ls~l~~~~~k~fF~l~L~--~~---~~~v~viVq~pa~l~Wh~~L~~G~~yvlT~Lrvs~irg~ 235 (1144)
T PF15489_consen 164 RGRQLNVAGKVVRLSALVKSHGKTFFILSLG--DA---GSHVPVIVQEPAQLVWHRALRPGRAYVLTSLRVSKIRGH 235 (1144)
T ss_pred ccCceeeeeEEEEeeceEEEcceEEEEEEeC--CC---CceeEEEEEecchhhhhhhcccCCeEEEeeeEEEEecCc
Confidence 46679999999999999999887654 4444 22 223553332222111123347999999999999988874
No 103
>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=21.41 E-value=1.5e+02 Score=29.09 Aligned_cols=53 Identities=15% Similarity=0.097 Sum_probs=0.0
Q ss_pred ceEEEEEeccchhhhhccCCCCCcEEEEeCcEEEE-eC----cEEEEEEecCCceEEcC
Q 012376 236 GTVLRVSTDRSYENFGRYFTATGKWVRIRNMSCQV-SS----GMWHGLLQSSSKIRLFS 289 (465)
Q Consensus 236 G~vL~V~~~~~~~~~~~~~~k~G~wV~l~Nv~~k~-~~----g~leG~l~~~ski~~l~ 289 (465)
.++..+++|+|.++. ...+++|.-+++.|+...- .+ +.++..=+..++.+-|+
T Consensus 179 ~~~~~LTIWrPtedl-~s~L~EG~ry~i~~L~~s~~k~~~~~~~vqLtatk~Tr~~~l~ 236 (251)
T cd04494 179 EKSGLLSIWRPTEDL-RSLLTEGKRYRIYGLATSNSKKRSGNEEVQLTATKKTRYQPLP 236 (251)
T ss_pred CceEEEEEeCCCHHH-HhhhcCCcEEEEEeccccCCCCCCCcceEEEEecCcccceECC
No 104
>PF11325 DUF3127: Domain of unknown function (DUF3127); InterPro: IPR021474 This bacterial family of proteins has no known function.
Probab=20.56 E-value=4.6e+02 Score=21.20 Aligned_cols=66 Identities=9% Similarity=0.211 Sum_probs=40.8
Q ss_pred EEEEecCCccccCCCc-eEE-EEEE-EeCCCCCCCeEEEEecCCCCCCCCCCCCCCEEEEe-eEEEEEEcCe
Q 012376 28 GVVLEFSIPRKSQGTD-YVC-VLKI-VDDSQQSPELLVNIFTSSIDQLPRVLSPRDLILLK-NVMIKKHQAE 95 (465)
Q Consensus 28 GVVvd~~~P~~trG~D-~~~-tl~I-~D~s~~~~gl~v~iF~~~~~~LP~v~~~GDII~l~-rvki~~~~g~ 95 (465)
|.|+...++.+..|.. |.- .|-| .++-++ .-+.+.+|.+..+.|-.+ ++||.|.++ +++-+.|+|+
T Consensus 4 Gkii~~l~~~~g~s~~Gw~Kre~Vlet~~qYP-~~i~f~~~~dk~~~l~~~-~~Gd~V~Vsf~i~~RE~~gr 73 (84)
T PF11325_consen 4 GKIIKVLPEQQGVSKNGWKKREFVLETEEQYP-QKICFEFWGDKIDLLDNF-QVGDEVKVSFNIEGREWNGR 73 (84)
T ss_pred cEEEEEecCcccCcCCCcEEEEEEEeCCCcCC-ceEEEEEEcchhhhhccC-CCCCEEEEEEEeeccEecce
Confidence 5555555554432211 543 2222 333333 359999999877777888 699988774 6777788765
No 105
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=20.25 E-value=3.3e+02 Score=33.65 Aligned_cols=40 Identities=25% Similarity=0.289 Sum_probs=27.8
Q ss_pred ccccccc-CCceEeEEEEEEEEEe-eCCCC--eEEEEEEcCCCC
Q 012376 159 LSLKDIS-EHRYFDLVCKVFHVSY-DDSKG--LWMLFVWDGTDV 198 (465)
Q Consensus 159 ~~Lkdi~-~~~f~Dlv~qVv~v~~-~~~~~--~~~L~VwDgT~~ 198 (465)
..|+||. ++..+=+.++|.++-. +..++ -.+++|+|||+.
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 4567778889988873 22233 567899999964
Done!