Query 027819
Match_columns 218
No_of_seqs 126 out of 1062
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 15:40:50 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027819.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027819hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK06752 single-stranded DNA-b 100.0 2.1E-30 4.5E-35 202.2 16.1 111 80-206 1-111 (112)
2 PRK07459 single-stranded DNA-b 100.0 8E-30 1.7E-34 202.0 16.4 113 80-212 2-119 (121)
3 PRK07275 single-stranded DNA-b 100.0 7.5E-30 1.6E-34 211.5 16.9 108 80-203 1-108 (162)
4 PRK09010 single-stranded DNA-b 100.0 9.3E-30 2E-34 213.5 16.9 117 79-205 4-120 (177)
5 PRK06642 single-stranded DNA-b 100.0 1.3E-29 2.7E-34 208.1 17.3 118 80-206 4-122 (152)
6 PRK08763 single-stranded DNA-b 100.0 1.3E-29 2.9E-34 210.3 17.0 113 79-205 3-115 (164)
7 PRK06863 single-stranded DNA-b 100.0 1.3E-29 2.9E-34 211.0 16.4 114 78-204 1-114 (168)
8 PRK06958 single-stranded DNA-b 100.0 2.1E-29 4.5E-34 212.1 16.7 118 78-208 1-118 (182)
9 PRK13732 single-stranded DNA-b 100.0 6E-29 1.3E-33 208.3 17.5 116 80-206 5-120 (175)
10 PRK08486 single-stranded DNA-b 100.0 4.3E-29 9.3E-34 210.4 16.5 111 80-204 1-111 (182)
11 PRK05733 single-stranded DNA-b 100.0 1E-28 2.2E-33 206.4 17.3 118 78-206 2-119 (172)
12 PRK06751 single-stranded DNA-b 100.0 1.4E-28 3.1E-33 205.7 16.0 110 80-205 1-110 (173)
13 PRK06341 single-stranded DNA-b 100.0 3.8E-28 8.2E-33 201.9 18.2 126 80-214 4-132 (166)
14 PRK07274 single-stranded DNA-b 100.0 1.7E-28 3.8E-33 196.5 15.6 108 80-204 1-108 (131)
15 TIGR00621 ssb single stranded 100.0 1E-27 2.2E-32 198.7 17.2 111 78-202 1-111 (164)
16 PRK08182 single-stranded DNA-b 100.0 7.6E-28 1.7E-32 196.8 15.5 111 80-203 1-115 (148)
17 PRK06293 single-stranded DNA-b 100.0 9.8E-28 2.1E-32 198.5 15.9 106 81-205 1-106 (161)
18 KOG1653 Single-stranded DNA-bi 99.9 4.3E-27 9.2E-32 193.0 8.6 132 65-207 41-173 (175)
19 PF00436 SSB: Single-strand bi 99.9 6.1E-26 1.3E-30 171.6 13.6 104 81-198 1-104 (104)
20 PRK07772 single-stranded DNA-b 99.9 1.1E-25 2.4E-30 190.2 15.9 114 78-200 1-115 (186)
21 COG0629 Ssb Single-stranded DN 99.9 8.6E-25 1.9E-29 181.3 13.6 113 80-203 2-116 (167)
22 PRK05813 single-stranded DNA-b 99.9 3E-24 6.5E-29 185.6 15.6 104 79-205 107-214 (219)
23 PRK05853 hypothetical protein; 99.9 7E-24 1.5E-28 175.6 13.1 104 86-200 1-105 (161)
24 PRK02801 primosomal replicatio 99.9 2.1E-22 4.6E-27 154.9 15.1 101 80-199 1-101 (101)
25 cd04496 SSB_OBF SSB_OBF: A sub 99.9 2E-21 4.3E-26 145.4 14.9 100 84-198 1-100 (100)
26 PRK05813 single-stranded DNA-b 99.8 6.7E-19 1.5E-23 152.3 13.7 100 80-204 7-106 (219)
27 PRK00036 primosomal replicatio 98.3 1.5E-05 3.3E-10 62.2 11.7 96 81-198 1-96 (107)
28 COG2965 PriB Primosomal replic 98.1 9.3E-05 2E-09 56.9 11.9 100 78-198 1-102 (103)
29 PF01336 tRNA_anti-codon: OB-f 97.0 0.011 2.5E-07 41.0 9.2 75 84-198 1-75 (75)
30 cd04474 RPA1_DBD_A RPA1_DBD_A: 96.1 0.04 8.6E-07 42.1 8.1 72 76-169 4-78 (104)
31 cd04484 polC_OBF polC_OBF: A s 96.0 0.061 1.3E-06 39.6 8.4 69 83-175 1-70 (82)
32 cd04487 RecJ_OBF2_like RecJ_OB 95.5 0.15 3.2E-06 36.9 8.5 73 84-198 1-73 (73)
33 cd04489 ExoVII_LU_OBF ExoVII_L 95.4 0.37 8E-06 34.0 10.3 62 84-173 2-63 (78)
34 cd04492 YhaM_OBF_like YhaM_OBF 95.0 0.51 1.1E-05 33.1 10.0 71 92-199 7-77 (83)
35 cd04485 DnaE_OBF DnaE_OBF: A s 94.5 0.44 9.5E-06 33.1 8.6 61 86-170 2-62 (84)
36 cd03524 RPA2_OBF_family RPA2_O 93.8 0.71 1.5E-05 30.6 8.2 33 137-170 29-61 (75)
37 PRK07211 replication factor A; 93.1 0.38 8.3E-06 46.6 7.9 71 76-169 58-133 (485)
38 PF11506 DUF3217: Protein of u 92.3 4 8.6E-05 31.0 11.2 87 80-187 1-87 (104)
39 PRK15491 replication factor A; 92.1 1.6 3.5E-05 40.9 10.5 90 79-198 174-266 (374)
40 COG3390 Uncharacterized protei 90.9 2 4.3E-05 36.9 8.8 78 79-183 43-120 (196)
41 cd04482 RPA2_OBF_like RPA2_OBF 90.7 0.64 1.4E-05 34.8 5.1 75 85-202 2-78 (91)
42 PRK07211 replication factor A; 90.5 2.8 6E-05 40.8 10.5 98 70-199 161-260 (485)
43 PF11325 DUF3127: Domain of un 89.5 4.2 9.1E-05 30.5 8.6 47 136-190 35-81 (84)
44 PRK15491 replication factor A; 87.4 2.6 5.6E-05 39.5 7.8 93 75-198 61-156 (374)
45 PRK13480 3'-5' exoribonuclease 87.2 4.1 8.8E-05 37.4 8.8 60 90-175 19-78 (314)
46 PF13742 tRNA_anti_2: OB-fold 86.2 2.5 5.5E-05 32.0 5.8 63 81-171 21-84 (99)
47 cd04488 RecG_wedge_OBF RecG_we 85.9 5.1 0.00011 27.0 6.8 31 139-171 31-61 (75)
48 TIGR00617 rpa1 replication fac 85.8 6.8 0.00015 39.0 10.1 101 70-199 180-286 (608)
49 PRK06461 single-stranded DNA-b 85.2 17 0.00037 28.8 11.6 88 76-200 9-100 (129)
50 PRK00286 xseA exodeoxyribonucl 85.1 7.2 0.00016 36.8 9.6 80 81-199 23-102 (438)
51 TIGR00237 xseA exodeoxyribonuc 83.6 3.3 7.1E-05 39.4 6.6 74 81-190 17-90 (432)
52 KOG3416 Predicted nucleic acid 83.1 23 0.0005 28.7 10.7 108 79-216 12-129 (134)
53 PRK14699 replication factor A; 81.1 6.1 0.00013 38.4 7.5 76 76-174 62-140 (484)
54 PRK07373 DNA polymerase III su 81.0 9.1 0.0002 36.8 8.6 64 83-170 282-345 (449)
55 TIGR01405 polC_Gram_pos DNA po 80.1 9.7 0.00021 41.1 9.2 73 80-176 6-80 (1213)
56 cd04490 PolII_SU_OBF PolII_SU_ 79.3 12 0.00025 27.2 6.9 30 138-168 29-60 (79)
57 PRK05673 dnaE DNA polymerase I 78.3 11 0.00023 40.5 8.7 65 82-170 978-1042(1135)
58 PRK00448 polC DNA polymerase I 78.2 10 0.00022 41.6 8.7 75 79-176 234-309 (1437)
59 PRK12366 replication factor A; 77.8 8.5 0.00018 38.5 7.5 77 76-175 68-146 (637)
60 cd04475 RPA1_DBD_B RPA1_DBD_B: 77.4 19 0.00041 26.7 7.7 68 84-174 2-72 (101)
61 PRK12366 replication factor A; 77.2 18 0.00038 36.3 9.6 93 71-191 280-376 (637)
62 PRK08402 replication factor A; 75.6 11 0.00024 35.2 7.2 77 76-173 67-145 (355)
63 PLN02903 aminoacyl-tRNA ligase 74.7 47 0.001 33.7 11.7 46 152-201 117-163 (652)
64 cd04491 SoSSB_OBF SoSSB_OBF: A 74.5 28 0.0006 24.8 7.7 29 138-170 35-64 (82)
65 PF02765 POT1: Telomeric singl 72.5 39 0.00085 27.0 8.9 79 81-176 12-93 (146)
66 PRK14699 replication factor A; 72.5 37 0.00081 33.0 10.2 76 77-174 172-250 (484)
67 cd04321 ScAspRS_mt_like_N ScAs 72.2 25 0.00054 25.5 7.1 41 153-199 45-85 (86)
68 cd04320 AspRS_cyto_N AspRS_cyt 70.5 16 0.00034 27.3 5.8 43 154-201 50-92 (102)
69 COG1570 XseA Exonuclease VII, 68.7 14 0.00031 35.6 6.3 75 80-190 22-96 (440)
70 PRK06826 dnaE DNA polymerase I 66.0 31 0.00067 37.1 8.8 65 83-171 993-1057(1151)
71 PRK06920 dnaE DNA polymerase I 65.0 33 0.00072 36.8 8.7 65 83-171 945-1009(1107)
72 PRK07374 dnaE DNA polymerase I 64.3 33 0.00071 37.0 8.6 65 82-170 1001-1065(1170)
73 cd04498 hPOT1_OB2 hPOT1_OB2: A 58.8 14 0.00031 29.5 3.7 33 136-171 59-91 (123)
74 cd04481 RPA1_DBD_B_like RPA1_D 58.2 32 0.00069 25.9 5.5 38 137-175 35-76 (106)
75 PRK07279 dnaE DNA polymerase I 58.0 86 0.0019 33.5 10.2 65 83-171 886-951 (1034)
76 cd04323 AsnRS_cyto_like_N AsnR 56.8 70 0.0015 22.8 7.1 39 154-199 45-83 (84)
77 cd04100 Asp_Lys_Asn_RS_N Asp_L 55.5 23 0.00051 25.3 4.2 41 152-199 44-84 (85)
78 cd04319 PhAsnRS_like_N PhAsnRS 55.2 42 0.0009 25.1 5.7 39 154-202 46-84 (103)
79 cd04322 LysRS_N LysRS_N: N-ter 55.1 71 0.0015 23.9 7.0 36 155-202 49-84 (108)
80 cd04316 ND_PkAspRS_like_N ND_P 54.6 90 0.0019 23.4 8.7 38 154-201 60-97 (108)
81 PF13567 DUF4131: Domain of un 54.5 49 0.0011 25.3 6.2 71 82-173 76-146 (176)
82 PRK07218 replication factor A; 53.9 1.3E+02 0.0028 28.8 10.0 88 76-200 167-256 (423)
83 cd04317 EcAspRS_like_N EcAspRS 53.7 82 0.0018 24.5 7.4 47 152-201 58-104 (135)
84 cd04318 EcAsnRS_like_N EcAsnRS 53.1 69 0.0015 22.7 6.3 38 152-199 44-81 (82)
85 PF12869 tRNA_anti-like: tRNA_ 52.9 83 0.0018 24.5 7.3 35 138-172 99-133 (144)
86 COG2176 PolC DNA polymerase II 51.9 36 0.00079 36.9 6.3 82 71-176 230-312 (1444)
87 COG1200 RecG RecG-like helicas 51.3 78 0.0017 32.3 8.3 63 83-171 62-124 (677)
88 PF12342 DUF3640: Protein of u 51.2 9.4 0.0002 22.5 1.1 16 1-16 1-16 (26)
89 TIGR00499 lysS_bact lysyl-tRNA 50.8 2.5E+02 0.0054 27.4 11.9 38 152-201 100-137 (496)
90 PRK05672 dnaE2 error-prone DNA 50.7 1.1E+02 0.0024 32.7 9.7 49 138-200 985-1033(1046)
91 PRK10917 ATP-dependent DNA hel 49.7 79 0.0017 31.8 8.2 63 82-170 60-122 (681)
92 cd04478 RPA2_DBD_D RPA2_DBD_D: 49.1 29 0.00063 25.2 3.9 32 139-171 29-63 (95)
93 COG0017 AsnS Aspartyl/asparagi 43.8 80 0.0017 30.5 6.8 82 82-201 17-100 (435)
94 PF12101 DUF3577: Protein of u 42.9 1.9E+02 0.004 23.7 12.1 86 83-185 13-109 (137)
95 cd04497 hPOT1_OB1_like hPOT1_O 41.5 1.8E+02 0.0038 23.0 7.9 73 83-176 16-88 (138)
96 TIGR00643 recG ATP-dependent D 41.1 2.1E+02 0.0046 28.4 9.6 64 82-171 33-96 (630)
97 PRK10646 ADP-binding protein; 39.3 22 0.00048 29.3 2.1 24 147-170 16-39 (153)
98 PRK06386 replication factor A; 39.2 3E+02 0.0066 25.8 9.8 67 76-174 112-181 (358)
99 PF02367 UPF0079: Uncharacteri 39.1 17 0.00038 28.8 1.4 23 147-169 3-25 (123)
100 PF03983 SHD1: SLA1 homology d 38.5 80 0.0017 22.9 4.6 31 169-200 11-41 (70)
101 smart00350 MCM minichromosome 37.7 90 0.0019 30.2 6.3 59 135-201 102-163 (509)
102 PRK07218 replication factor A; 36.7 1.4E+02 0.0029 28.7 7.2 71 76-175 63-134 (423)
103 COG0802 Predicted ATPase or ki 36.4 30 0.00065 28.6 2.4 24 147-170 13-36 (149)
104 PF08021 FAD_binding_9: Sidero 35.4 78 0.0017 24.5 4.5 32 135-166 80-112 (117)
105 cd04483 hOBFC1_like hOBFC1_lik 35.3 46 0.001 24.8 3.1 20 152-171 59-78 (92)
106 PF00970 FAD_binding_6: Oxidor 35.2 95 0.0021 22.3 4.8 33 136-170 62-96 (99)
107 PLN02603 asparaginyl-tRNA synt 34.5 4.8E+02 0.01 26.0 12.3 38 155-202 157-194 (565)
108 COG4097 Predicted ferric reduc 33.8 61 0.0013 31.1 4.2 38 136-174 275-312 (438)
109 TIGR01077 L13_A_E ribosomal pr 33.4 32 0.0007 28.1 2.1 23 143-166 9-31 (142)
110 COG0587 DnaE DNA polymerase II 30.7 2.1E+02 0.0045 31.1 8.0 68 83-173 978-1045(1139)
111 PRK06394 rpl13p 50S ribosomal 30.3 37 0.00081 27.9 2.0 26 143-169 13-38 (146)
112 COG1862 YajC Preprotein transl 30.0 1.6E+02 0.0034 22.6 5.3 24 150-173 38-61 (97)
113 TIGR00458 aspS_arch aspartyl-t 28.4 1.3E+02 0.0028 28.7 5.6 39 154-202 60-98 (428)
114 TIGR00150 HI0065_YjeE ATPase, 28.0 49 0.0011 26.5 2.3 23 147-169 10-32 (133)
115 COG1838 FumA Tartrate dehydrat 27.7 69 0.0015 27.4 3.2 21 150-171 11-31 (184)
116 KOG4101 Cysteine-rich hydropho 26.3 60 0.0013 27.0 2.5 19 33-51 4-22 (175)
117 TIGR00459 aspS_bact aspartyl-t 25.7 2.2E+02 0.0048 28.5 6.8 59 139-201 45-104 (583)
118 PF15285 BH3: Beclin-1 BH3 dom 25.7 23 0.00051 20.7 0.0 9 1-9 5-13 (25)
119 TIGR00617 rpa1 replication fac 24.2 3.1E+02 0.0067 27.5 7.6 69 83-174 312-383 (608)
120 PLN02532 asparagine-tRNA synth 24.1 2.9E+02 0.0063 28.1 7.3 56 137-202 147-202 (633)
121 PTZ00385 lysyl-tRNA synthetase 24.0 2.9E+02 0.0064 28.2 7.4 38 151-200 154-191 (659)
122 PF11948 DUF3465: Protein of u 23.7 1E+02 0.0023 25.0 3.4 32 143-179 74-105 (131)
123 PLN02850 aspartate-tRNA ligase 23.6 2E+02 0.0044 28.3 6.1 44 153-202 130-173 (530)
124 TIGR00457 asnS asparaginyl-tRN 22.5 3.3E+02 0.0072 26.1 7.2 41 152-202 63-103 (453)
125 PTZ00401 aspartyl-tRNA synthet 22.1 4.3E+02 0.0092 26.3 8.0 44 154-202 127-170 (550)
126 TIGR01066 rplM_bact ribosomal 22.0 68 0.0015 26.2 2.1 32 135-167 10-57 (140)
127 PTZ00111 DNA replication licen 21.6 2.7E+02 0.0058 29.6 6.7 57 137-201 346-405 (915)
128 PF00572 Ribosomal_L13: Riboso 21.6 64 0.0014 25.8 1.8 22 143-165 10-43 (128)
129 PRK00484 lysS lysyl-tRNA synth 20.5 2.4E+02 0.0053 27.4 5.9 35 155-201 103-137 (491)
No 1
>PRK06752 single-stranded DNA-binding protein; Validated
Probab=99.97 E-value=2.1e-30 Score=202.16 Aligned_cols=111 Identities=17% Similarity=0.263 Sum_probs=102.0
Q ss_pred CCceEEEEEEeCcCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHhhcCCC
Q 027819 80 GIFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLVPG 159 (218)
Q Consensus 80 ~~N~v~LiGrIg~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~~LkKG 159 (218)
+||+|+|+|||++|||++++++|.++++|+||+++.|+++. |+ ..++||+|++|| ++|+.+.++|+||
T Consensus 1 MmN~v~liGrl~~dPelr~t~~G~~~~~f~lAv~~~~~~~~----g~-------~~t~~~~v~~wg-~~Ae~~~~~l~KG 68 (112)
T PRK06752 1 MMNRVVLIGRLTKEPELYYTKQGVAYARVCVAVNRGFRNSL----GE-------QQVDFINCVVWR-KSAENVTEYCTKG 68 (112)
T ss_pred CceEEEEEEECcCCCEEEECCCCCEEEEEEEEECCCeEcCC----CC-------EEEEEEEEEEeh-HHHHHHHHhcCCC
Confidence 48999999999999999999999999999999999998652 32 269999999998 8999999999999
Q ss_pred CEEEEEEEeEeeeeeCCCCCeEEEEEEEEEEeCCcEEEeeCCCCCCC
Q 027819 160 STIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGRLVFLGKGGDAQP 206 (218)
Q Consensus 160 ~~V~VeG~L~t~~~~d~~dG~~r~~~eI~v~~~g~i~~L~~k~~~~~ 206 (218)
+.|+|+|+|+++.|+++ +|++++.++|+|+ +|+||+++...+.
T Consensus 69 ~~V~V~G~l~~~~~~~~-~G~~~~~~ei~a~---~i~~l~~~~~~~~ 111 (112)
T PRK06752 69 SLVGITGRIHTRNYEDD-QGKRIYITEVVIE---SITFLERRREGAS 111 (112)
T ss_pred CEEEEEEEEEeCccCCC-CCcEEEEEEEEEE---EEEECCCCCcccC
Confidence 99999999999999999 9999999999999 9999998875543
No 2
>PRK07459 single-stranded DNA-binding protein; Provisional
Probab=99.97 E-value=8e-30 Score=201.96 Aligned_cols=113 Identities=25% Similarity=0.436 Sum_probs=101.1
Q ss_pred CCceEEEEEEeCcCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHhhcCCC
Q 027819 80 GIFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLVPG 159 (218)
Q Consensus 80 ~~N~v~LiGrIg~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~~LkKG 159 (218)
.||+|+|+||||+|||++++++|.++++|+||+++.|++. .++||+|++|| ++|+.+.++|+||
T Consensus 2 ~~N~v~LiGrL~~DPelr~t~~G~~v~~fslAv~~~~~~~---------------~t~w~~v~~wg-~~Ae~~~~~l~KG 65 (121)
T PRK07459 2 SLNSVTLVGRAGRDPEVRYFESGSVVCNLTLAVNRRSRDD---------------EPDWFNLEIWG-KTAQVAADYVKKG 65 (121)
T ss_pred CccEEEEEEEccCCCEEEEcCCCCEEEEEEEEecccccCC---------------CceEEEEEEeh-HHHHHHHHHcCCC
Confidence 4899999999999999999999999999999999887631 58999999998 8999999999999
Q ss_pred CEEEEEEEeEeeeeeCCCC-CeEEEEEEEEEEeCCcEEEeeCCCCCC----CCCCccC
Q 027819 160 STIYVEGNLEQKVFNDPIT-GLVRRIREIAIRRNGRLVFLGKGGDAQ----PPSPSEV 212 (218)
Q Consensus 160 ~~V~VeG~L~t~~~~d~~d-G~~r~~~eI~v~~~g~i~~L~~k~~~~----~~~~~e~ 212 (218)
++|+|+|+|+++.|+|+ + |++++.++|+|+ +|+||++++..+ .+.++|+
T Consensus 66 ~~V~V~G~l~~~~~~d~-d~G~~r~~~ei~a~---~i~~L~~k~~~~~~~~~~~~~~~ 119 (121)
T PRK07459 66 SLIGITGSLKFDRWTDR-NTGEDRSKPVIRVD---RLELLGSKRDSEGNANPSNSSEI 119 (121)
T ss_pred CEEEEEEEEEecceEcC-CCCeEEEEEEEEEe---EEEECcCCCccccccCcCCCCCC
Confidence 99999999999999998 6 999999999999 999998775433 4444444
No 3
>PRK07275 single-stranded DNA-binding protein; Provisional
Probab=99.97 E-value=7.5e-30 Score=211.47 Aligned_cols=108 Identities=14% Similarity=0.231 Sum_probs=100.7
Q ss_pred CCceEEEEEEeCcCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHhhcCCC
Q 027819 80 GIFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLVPG 159 (218)
Q Consensus 80 ~~N~v~LiGrIg~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~~LkKG 159 (218)
|||+|+|+|||++|||+|++++|.+++.|+||+++.|++.. |+ ..++||+|++|| ++|+.+.++|+||
T Consensus 1 M~N~v~LiGrL~~DPElr~t~sG~~v~~ftlAv~r~~~~~~----ge-------~~tdfi~vv~wg-k~Ae~~~~~l~KG 68 (162)
T PRK07275 1 MINNVVLVGRMTRDAELRYTPSNVAVATFTLAVNRTFKSQN----GE-------READFINCVIWR-QQAENLANWAKKG 68 (162)
T ss_pred CeeEEEEEEEECCCCeEEECCCCCEEEEEEEEEcCceecCC----CC-------EeeeEEEEEEEc-HHHHHHHHHcCCC
Confidence 58999999999999999999999999999999999998642 32 269999999998 8999999999999
Q ss_pred CEEEEEEEeEeeeeeCCCCCeEEEEEEEEEEeCCcEEEeeCCCC
Q 027819 160 STIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGRLVFLGKGGD 203 (218)
Q Consensus 160 ~~V~VeG~L~t~~~~d~~dG~~r~~~eI~v~~~g~i~~L~~k~~ 203 (218)
++|+|+|+|+++.|+++ +|++++.+||+|+ +|+||+++..
T Consensus 69 ~~V~VeGrl~~r~y~dk-dG~k~~~~evva~---~i~~l~~~~~ 108 (162)
T PRK07275 69 ALIGVTGRIQTRNYENQ-QGQRVYVTEVVAD---NFQMLESRAT 108 (162)
T ss_pred CEEEEEEEEEeceEECC-CCCEEEEEEEEEe---EEEECCCCCc
Confidence 99999999999999999 9999999999999 9999998873
No 4
>PRK09010 single-stranded DNA-binding protein; Provisional
Probab=99.97 E-value=9.3e-30 Score=213.54 Aligned_cols=117 Identities=28% Similarity=0.531 Sum_probs=106.1
Q ss_pred CCCceEEEEEEeCcCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHhhcCC
Q 027819 79 PGIFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLVP 158 (218)
Q Consensus 79 ~~~N~v~LiGrIg~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~~LkK 158 (218)
++||+|+|+||||+||++|++++|..|++|+||+++.|+++. .|+ | +..++||+|++|+ ++|+.+.++|+|
T Consensus 4 r~~N~V~LiGrLg~DPelR~t~nG~~v~~fsVAvn~~~kd~~---~Ge---~--~e~t~w~~V~~fg-k~Ae~~~~~L~K 74 (177)
T PRK09010 4 RGVNKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKQ---TGE---M--KEQTEWHRVVLFG-KLAEVAGEYLRK 74 (177)
T ss_pred cCceEEEEEEEeCCCceEEEcCCCCEEEEEEEEEcCccccCc---ccc---c--ccceEEEEEEEeh-hHHHHHHHhcCC
Confidence 489999999999999999999999999999999999998764 232 2 2379999999998 899999999999
Q ss_pred CCEEEEEEEeEeeeeeCCCCCeEEEEEEEEEEeCCcEEEeeCCCCCC
Q 027819 159 GSTIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGRLVFLGKGGDAQ 205 (218)
Q Consensus 159 G~~V~VeG~L~t~~~~d~~dG~~r~~~eI~v~~~g~i~~L~~k~~~~ 205 (218)
|++|+|+|+|+++.|+|+ +|++++.++|+|+.+++|+||+++....
T Consensus 75 Gs~V~VeGrL~~~~yedk-dG~~r~~~eVvv~~~~~~~~l~~r~~~~ 120 (177)
T PRK09010 75 GSQVYIEGQLRTRKWTDQ-SGQDRYTTEVVVNVGGTMQMLGGRQGGG 120 (177)
T ss_pred CCEEEEEEEEEeccccCC-CCCEEEEEEEEEecCCcEEEccCCCCCC
Confidence 999999999999999999 9999999999998788999999885544
No 5
>PRK06642 single-stranded DNA-binding protein; Provisional
Probab=99.97 E-value=1.3e-29 Score=208.09 Aligned_cols=118 Identities=28% Similarity=0.543 Sum_probs=103.0
Q ss_pred CCceEEEEEEeCcCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHhhcCCC
Q 027819 80 GIFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLVPG 159 (218)
Q Consensus 80 ~~N~v~LiGrIg~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~~LkKG 159 (218)
.||+|+|+||||+||++|++++|.++++|+||+++.|+++. +|+ | ...|+||+|++||+++|+.+.+||+||
T Consensus 4 ~~N~V~LiGrLg~DPElr~t~~G~~v~~fslAv~~~~k~~~---~G~---~--~~~T~w~~v~~~g~~~Ae~~~~~l~KG 75 (152)
T PRK06642 4 SLNKVILIGNVGRDPEIRTTGEGKKIINLSLATTETWKDRI---TSE---R--KERTEWHRVVIFSEGLVSVVERYVTKG 75 (152)
T ss_pred cceEEEEEEEccCCceEEECCCCCEEEEEEEEecccccccc---CCc---c--ccceeEEEEEEeChHHHHHHHHhCCCC
Confidence 38999999999999999999999999999999999998753 232 2 237999999999844999999999999
Q ss_pred CEEEEEEEeEeeeeeCCCCCeEEEEEEEEEEe-CCcEEEeeCCCCCCC
Q 027819 160 STIYVEGNLEQKVFNDPITGLVRRIREIAIRR-NGRLVFLGKGGDAQP 206 (218)
Q Consensus 160 ~~V~VeG~L~t~~~~d~~dG~~r~~~eI~v~~-~g~i~~L~~k~~~~~ 206 (218)
++|+|+|+|+++.|+++ +|++++.++|+|+. +..|.||+++...+.
T Consensus 76 ~~V~V~GrL~~~~y~dk-dG~~r~~~eVvv~~~~~~i~fl~~k~~~~~ 122 (152)
T PRK06642 76 SKLYIEGSLQTRKWNDN-SGQEKYTTEVVLQNFNSQLILLDSKNSNNH 122 (152)
T ss_pred CEEEEEEEEEeCeeECC-CCCEEEEEEEEEEecccceEeccCCCCccc
Confidence 99999999999999998 99999999999993 334589998765544
No 6
>PRK08763 single-stranded DNA-binding protein; Provisional
Probab=99.97 E-value=1.3e-29 Score=210.35 Aligned_cols=113 Identities=35% Similarity=0.595 Sum_probs=103.4
Q ss_pred CCCceEEEEEEeCcCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHhhcCC
Q 027819 79 PGIFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLVP 158 (218)
Q Consensus 79 ~~~N~v~LiGrIg~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~~LkK 158 (218)
++||+|+|+||||+||++|++++|..|++|+||+++.|+++. |++ .+.++||+|++|| ++|+.+.++|+|
T Consensus 3 r~~Nkv~LiGrLg~DPelr~t~~G~~va~fsVA~~~~~k~~~----G~~-----~e~t~w~~Vv~fg-k~Ae~v~~~L~K 72 (164)
T PRK08763 3 RGINKVILVGNLGNDPDIKYTQSGMTITRISLATTSVRKDRE----GNT-----QERTEWHRVKFFG-KLGEIAGEYLRK 72 (164)
T ss_pred CcceEEEEEEEecCCCeEEEcCCCCeEEEEEEEeccceecCC----CCe-----eccceEEEEEEeh-HHHHHHHHhcCC
Confidence 379999999999999999999999999999999999998763 432 1379999999998 899999999999
Q ss_pred CCEEEEEEEeEeeeeeCCCCCeEEEEEEEEEEeCCcEEEeeCCCCCC
Q 027819 159 GSTIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGRLVFLGKGGDAQ 205 (218)
Q Consensus 159 G~~V~VeG~L~t~~~~d~~dG~~r~~~eI~v~~~g~i~~L~~k~~~~ 205 (218)
|+.|+|+|+|+++.|+++ +|++++.++|+|+ +|+||+++...+
T Consensus 73 Gs~V~VeGrL~~~~y~dk-dG~kr~~~eIva~---~i~~L~~~~~~~ 115 (164)
T PRK08763 73 GSQCYIEGSIRYDKFTGQ-DGQERYVTEIVAD---EMQMLGGRGEGG 115 (164)
T ss_pred CCEEEEEEEEEeceeECC-CCCEEEEEEEEEe---EEEECCCCCCCC
Confidence 999999999999999998 9999999999999 999999886544
No 7
>PRK06863 single-stranded DNA-binding protein; Provisional
Probab=99.97 E-value=1.3e-29 Score=211.01 Aligned_cols=114 Identities=32% Similarity=0.506 Sum_probs=104.3
Q ss_pred CCCCceEEEEEEeCcCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHhhcC
Q 027819 78 DPGIFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLV 157 (218)
Q Consensus 78 ~~~~N~v~LiGrIg~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~~Lk 157 (218)
|++||+|+|+||||+|||+|++++|..+++|+||+++.|+++.. | +| .+.++||+|++|| ++|+.+.++|+
T Consensus 1 M~~~N~V~LiGrLg~DPElR~t~nG~~va~fsVAvn~~~~d~~~---G---e~--~e~t~w~~Vv~fg-k~AE~v~~~Lk 71 (168)
T PRK06863 1 MAGINKVIIVGHLGNDPEIRTMPNGEAVANISVATSESWTDKNT---G---ER--REVTEWHRIVFYR-RQAEVAGEYLR 71 (168)
T ss_pred CCCccEEEEEEEcCCCCEEEEcCCCCEEEEEEEEecCcccccCC---C---cc--cccceEEEEEEEh-HHHHHHHHHCC
Confidence 77899999999999999999999999999999999999987642 3 22 1369999999998 89999999999
Q ss_pred CCCEEEEEEEeEeeeeeCCCCCeEEEEEEEEEEeCCcEEEeeCCCCC
Q 027819 158 PGSTIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGRLVFLGKGGDA 204 (218)
Q Consensus 158 KG~~V~VeG~L~t~~~~d~~dG~~r~~~eI~v~~~g~i~~L~~k~~~ 204 (218)
||++|+|+|+|+++.|+|+ +|++++.++|+|+ +|+||+++...
T Consensus 72 KGs~V~VeGrL~~r~w~Dk-dG~~r~~~eI~a~---~i~~L~~r~~~ 114 (168)
T PRK06863 72 KGSQVYVEGRLKTRKWQDQ-NGQDRYTTEIQGD---VLQMLGGRNQR 114 (168)
T ss_pred CCCEEEEEEEEEeCCccCC-CCCEEEEEEEEEe---EEEECCCCCcc
Confidence 9999999999999999999 9999999999999 99999988763
No 8
>PRK06958 single-stranded DNA-binding protein; Provisional
Probab=99.97 E-value=2.1e-29 Score=212.07 Aligned_cols=118 Identities=30% Similarity=0.506 Sum_probs=106.2
Q ss_pred CCCCceEEEEEEeCcCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHhhcC
Q 027819 78 DPGIFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLV 157 (218)
Q Consensus 78 ~~~~N~v~LiGrIg~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~~Lk 157 (218)
|+.||+|+|+|||++||+++++++|..|++|+||++++|+++. .+ +|. +.|+||+|++|+ ++|+.+.++|+
T Consensus 1 Mas~N~V~LiGrLg~DPElr~t~nG~~va~fsVAv~~~~kdk~---sG---e~~--e~T~w~~V~~fG-k~AE~v~~~Lk 71 (182)
T PRK06958 1 MASVNKVILVGNLGADPEVRYLPSGDAVANIRLATTDRYKDKA---SG---EFK--EATEWHRVAFFG-RLAEIVGEYLK 71 (182)
T ss_pred CCcccEEEEEEEecCCCeEEEcCCCCEEEEEEEEecccccccc---CC---ccc--ccceEEEEEEeh-HHHHHHHHHhC
Confidence 6779999999999999999999999999999999999998764 23 332 369999999998 89999999999
Q ss_pred CCCEEEEEEEeEeeeeeCCCCCeEEEEEEEEEEeCCcEEEeeCCCCCCCCC
Q 027819 158 PGSTIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGRLVFLGKGGDAQPPS 208 (218)
Q Consensus 158 KG~~V~VeG~L~t~~~~d~~dG~~r~~~eI~v~~~g~i~~L~~k~~~~~~~ 208 (218)
||++|+|+|+|+++.|+|+ +|++++.++|+|+ +|+||..+....+.+
T Consensus 72 KGs~V~VeGrL~~~~yeDk-dG~kr~~~eVvA~---~V~fL~sr~~~~~~~ 118 (182)
T PRK06958 72 KGSSVYIEGRIRTRKWQGQ-DGQDRYSTEIVAD---QMQMLGGRGGSGGGG 118 (182)
T ss_pred CCCEEEEEEEEEeCceECC-CCcEEEEEEEEEe---EEEECCCCccCcCcc
Confidence 9999999999999999998 9999999999999 999999876554333
No 9
>PRK13732 single-stranded DNA-binding protein; Provisional
Probab=99.96 E-value=6e-29 Score=208.32 Aligned_cols=116 Identities=28% Similarity=0.591 Sum_probs=105.3
Q ss_pred CCceEEEEEEeCcCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHhhcCCC
Q 027819 80 GIFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLVPG 159 (218)
Q Consensus 80 ~~N~v~LiGrIg~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~~LkKG 159 (218)
+||+|+|+||||+|||+|++++|..|++|+||+++.|+++. .| +|. +.++||+|++|| ++|+.+.++|+||
T Consensus 5 ~mN~V~LiGrLg~DPElR~t~nG~~va~fslAvn~~~kd~~---~G---e~~--e~t~w~~Vv~wg-k~Ae~v~~~L~KG 75 (175)
T PRK13732 5 GINKVILVGRLGKDPEVRYIPNGGAVANLQVATSESWRDKQ---TG---EMR--EQTEWHRVVLFG-KLAEVAGEYLRKG 75 (175)
T ss_pred CceEEEEEEEecCCCEEEEcCCCCEEEEEEEEEcCccccCC---CC---cee--cceeEEEEEEec-HHHHHHHHhcCCC
Confidence 79999999999999999999999999999999999998753 24 342 379999999998 8999999999999
Q ss_pred CEEEEEEEeEeeeeeCCCCCeEEEEEEEEEEeCCcEEEeeCCCCCCC
Q 027819 160 STIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGRLVFLGKGGDAQP 206 (218)
Q Consensus 160 ~~V~VeG~L~t~~~~d~~dG~~r~~~eI~v~~~g~i~~L~~k~~~~~ 206 (218)
+.|+|+|+|+++.|++ +|++++.+||+|+..|+|+||+++...+.
T Consensus 76 ~~V~VeGrL~~r~ye~--dG~kr~~~eIiv~~~g~~~fL~~~~~~~~ 120 (175)
T PRK13732 76 AQVYIEGQLRTRSWED--NGITRYVTEILVKTTGTMQMLGRAPQQNA 120 (175)
T ss_pred CEEEEEEEEEeeeEcc--CCeEEEEEEEEEeecCeEEEecCCCCCCC
Confidence 9999999999999976 69999999999998889999999887553
No 10
>PRK08486 single-stranded DNA-binding protein; Provisional
Probab=99.96 E-value=4.3e-29 Score=210.40 Aligned_cols=111 Identities=22% Similarity=0.299 Sum_probs=102.0
Q ss_pred CCceEEEEEEeCcCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHhhcCCC
Q 027819 80 GIFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLVPG 159 (218)
Q Consensus 80 ~~N~v~LiGrIg~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~~LkKG 159 (218)
+||+|+|+|||++|||+|++++|..+++|+||++++|+++. |+ | .+.++||+|++|| ++|+.+.++|+||
T Consensus 1 m~N~V~LvGrL~~DPElr~t~sG~~va~fslAv~r~~~~~~----Ge---~--~e~t~fi~v~~fg-~~AE~~~~~l~KG 70 (182)
T PRK08486 1 MFNKVILVGNLTRDVELRYLPSGSAIATIGLATSRRFKKQD----GE---K--GEEVCFIDIRLFG-RTAEIANQYLSKG 70 (182)
T ss_pred CeeEEEEEEEecCCCEEEECCCCCEEEEEEEEEecceecCC----CC---C--cccceEEEEEEEh-HHHHHHHHHcCCC
Confidence 57999999999999999999999999999999999987552 43 2 2379999999998 8999999999999
Q ss_pred CEEEEEEEeEeeeeeCCCCCeEEEEEEEEEEeCCcEEEeeCCCCC
Q 027819 160 STIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGRLVFLGKGGDA 204 (218)
Q Consensus 160 ~~V~VeG~L~t~~~~d~~dG~~r~~~eI~v~~~g~i~~L~~k~~~ 204 (218)
++|+|+|+|+++.|+++ +|++++.++|+|+ +|+||.++...
T Consensus 71 ~~V~VeGrL~~~~y~dk-dG~~r~~~eI~a~---~v~~L~~~~~~ 111 (182)
T PRK08486 71 SKVLIEGRLTFESWMDQ-NGQKRSKHTITAE---SMQMLDSKSDN 111 (182)
T ss_pred CEEEEEEEEEeCcEECC-CCcEEEEEEEEEe---EEEECCCCCCC
Confidence 99999999999999999 9999999999999 99999887654
No 11
>PRK05733 single-stranded DNA-binding protein; Provisional
Probab=99.96 E-value=1e-28 Score=206.39 Aligned_cols=118 Identities=30% Similarity=0.537 Sum_probs=105.5
Q ss_pred CCCCceEEEEEEeCcCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHhhcC
Q 027819 78 DPGIFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLV 157 (218)
Q Consensus 78 ~~~~N~v~LiGrIg~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~~Lk 157 (218)
.++||+|+|+||||+||+++++++|..|++|+||+++.|+++. .| +|. +.++||+|++|| ++|+.+.++|+
T Consensus 2 a~~mNkV~LiGrlg~DPElr~t~nG~~va~fsVAv~~~~k~~~---~G---e~~--e~T~w~~Vv~fg-k~Ae~v~~~l~ 72 (172)
T PRK05733 2 ARGVNKVILVGTCGQDPEVRYLPNGNAVTNLSLATSEQWTDKQ---SG---QKV--ERTEWHRVSLFG-KVAEIAGEYLR 72 (172)
T ss_pred CCcceEEEEEEEecCCCEEEECCCCCEEEEEEEEEcCccccCC---CC---ccc--ccceEEEEEEeh-HHHHHHHHHhC
Confidence 3579999999999999999999999999999999999988653 23 332 369999999998 89999999999
Q ss_pred CCCEEEEEEEeEeeeeeCCCCCeEEEEEEEEEEeCCcEEEeeCCCCCCC
Q 027819 158 PGSTIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGRLVFLGKGGDAQP 206 (218)
Q Consensus 158 KG~~V~VeG~L~t~~~~d~~dG~~r~~~eI~v~~~g~i~~L~~k~~~~~ 206 (218)
||+.|+|+|+|+++.|+ + +|++++.++|+|+..|+|+||+.+...+.
T Consensus 73 KGs~V~VeGrLr~~~y~-k-dG~~r~~~eVvvd~~g~v~~L~~~~~~~~ 119 (172)
T PRK05733 73 KGSQVYIEGKLQTREWE-K-DGIKRYTTEIVVDMQGTMQLLGGRPQGDD 119 (172)
T ss_pred CCCEEEEEEEEEeCcEe-c-CCEEEEEEEEEEeecCeEEECcCCCCCcC
Confidence 99999999999999999 6 99999999999998899999987765443
No 12
>PRK06751 single-stranded DNA-binding protein; Provisional
Probab=99.96 E-value=1.4e-28 Score=205.70 Aligned_cols=110 Identities=19% Similarity=0.297 Sum_probs=101.2
Q ss_pred CCceEEEEEEeCcCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHhhcCCC
Q 027819 80 GIFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLVPG 159 (218)
Q Consensus 80 ~~N~v~LiGrIg~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~~LkKG 159 (218)
|||+|+|+|||++||++|++++|.+|+.|+||+++.|+++. |+ + .++||+|++|| ++|+.++++|+||
T Consensus 1 MmN~V~LiGrL~~DpelR~t~sG~~v~~fslAvnr~~~~~~----ge---~----~tdwi~~v~wg-k~Ae~~~~~l~KG 68 (173)
T PRK06751 1 MMNRVILVGRLTKDPDLRYTPNGVAVATFTLAVNRAFANQQ----GE---R----EADFINCVIWR-KQAENVANYLKKG 68 (173)
T ss_pred CceEEEEEEEECCCCcEEECCCCCEEEEEEEEEccceecCC----CC---E----EEEEEEEEEeC-cHHHHHHHHcCCC
Confidence 58999999999999999999999999999999999987542 32 2 68999999998 8999999999999
Q ss_pred CEEEEEEEeEeeeeeCCCCCeEEEEEEEEEEeCCcEEEeeCCCCCC
Q 027819 160 STIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGRLVFLGKGGDAQ 205 (218)
Q Consensus 160 ~~V~VeG~L~t~~~~d~~dG~~r~~~eI~v~~~g~i~~L~~k~~~~ 205 (218)
++|+|+|+|+++.|+++ +|++++.++|+|+ .|+||..++..+
T Consensus 69 ~~V~VeGrL~~r~yedk-dG~~~~~~eVva~---~i~~l~~r~~~~ 110 (173)
T PRK06751 69 SLAGVDGRLQTRNYEGQ-DGKRVYVTEVLAE---SVQFLEPRNGGG 110 (173)
T ss_pred CEEEEEEEEEeCccCCC-CCcEEEEEEEEEE---EEEeCcCCCCCc
Confidence 99999999999999998 9999999999999 999999886544
No 13
>PRK06341 single-stranded DNA-binding protein; Provisional
Probab=99.96 E-value=3.8e-28 Score=201.94 Aligned_cols=126 Identities=25% Similarity=0.514 Sum_probs=106.9
Q ss_pred CCceEEEEEEeCcCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHhhcCCC
Q 027819 80 GIFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLVPG 159 (218)
Q Consensus 80 ~~N~v~LiGrIg~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~~LkKG 159 (218)
.||+|+|+|||++||++|++++|+++++|+||++++|++++. |+ | .+.|+||+|++|++++|+.+.++|+||
T Consensus 4 ~mN~V~LiGrLg~DPElR~t~sG~~v~~fsVAvn~~~kd~~~---Ge---~--~e~T~w~~Vv~fg~~~Ae~~~~~LkKG 75 (166)
T PRK06341 4 SVNKVILIGNLGADPEIRRTQDGRPIANLRIATSETWRDRNS---GE---R--KEKTEWHRVVIFNEGLCKVAEQYLKKG 75 (166)
T ss_pred cceEEEEEEEecCCCEEEEcCCCCEEEEEEEEEccceecCCC---Cc---c--cccceEEEEEEeChHHHHHHHHhcCCC
Confidence 489999999999999999999999999999999999987642 32 3 237999999999855999999999999
Q ss_pred CEEEEEEEeEeeeeeCCCCCeEEEEEEEEEEe-CCcEEEeeCCCCCC--CCCCccCCC
Q 027819 160 STIYVEGNLEQKVFNDPITGLVRRIREIAIRR-NGRLVFLGKGGDAQ--PPSPSEVRG 214 (218)
Q Consensus 160 ~~V~VeG~L~t~~~~d~~dG~~r~~~eI~v~~-~g~i~~L~~k~~~~--~~~~~e~~~ 214 (218)
++|+|+|+|+++.|+++ +|++++.++|+|+. +..|+||+.+.+.. .-..++..|
T Consensus 76 ~~V~VeGrL~~r~w~dk-dG~~r~~~eIiv~~~~~~l~~l~~~~~~~~~~~~~~~~~~ 132 (166)
T PRK06341 76 AKVYIEGQLQTRKWTDQ-SGVERYSTEVVLQGFNSTLTMLDGRGEGGGGGGGGDDGGG 132 (166)
T ss_pred CEEEEEEEEEeCcEECC-CCCEEEEEEEEEEecccceEEcccCCcCCCCCCCCCccCC
Confidence 99999999999999999 99999999999983 44579998886433 333444444
No 14
>PRK07274 single-stranded DNA-binding protein; Provisional
Probab=99.96 E-value=1.7e-28 Score=196.54 Aligned_cols=108 Identities=18% Similarity=0.305 Sum_probs=99.1
Q ss_pred CCceEEEEEEeCcCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHhhcCCC
Q 027819 80 GIFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLVPG 159 (218)
Q Consensus 80 ~~N~v~LiGrIg~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~~LkKG 159 (218)
|||+|+|+|+||+||+++++++|..+++|+||++++|+++. |+ | .++||+|++|| ++|+.+.++|+||
T Consensus 1 mmN~v~LiGrL~~dPelr~t~~g~~~~~fslAv~~~~k~~~----g~---~----~t~w~~v~~fg-~~Ae~v~~~l~KG 68 (131)
T PRK07274 1 MYNKVILIGRLTATPELVKTANDKSVARVTLAVNRRFKNQN----GE---R----EADFINVVLWG-KLAETLASYASKG 68 (131)
T ss_pred CeeEEEEEEEccCCCeEEECCCCCEEEEEEEEEcCceecCC----CC---E----EEEEEEEEEeh-HHHHHHHHHcCCC
Confidence 58999999999999999999999999999999999997642 32 2 69999999998 8999999999999
Q ss_pred CEEEEEEEeEeeeeeCCCCCeEEEEEEEEEEeCCcEEEeeCCCCC
Q 027819 160 STIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGRLVFLGKGGDA 204 (218)
Q Consensus 160 ~~V~VeG~L~t~~~~d~~dG~~r~~~eI~v~~~g~i~~L~~k~~~ 204 (218)
++|+|+|+|+++.| ++ +|++++.++|+|+ +|+||..+...
T Consensus 69 ~~V~V~Grl~~~~y-~k-dG~~~~~~eviv~---~i~~l~~k~~~ 108 (131)
T PRK07274 69 SLISIDGELRTRKY-EK-DGQTHYVTEVLCQ---SFQLLESRAQR 108 (131)
T ss_pred CEEEEEEEEEeccC-cc-CCcEEEEEEEEEE---EEEECcCCCcc
Confidence 99999999999999 77 9999999999999 99999876543
No 15
>TIGR00621 ssb single stranded DNA-binding protein (ssb). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.96 E-value=1e-27 Score=198.73 Aligned_cols=111 Identities=30% Similarity=0.475 Sum_probs=102.5
Q ss_pred CCCCceEEEEEEeCcCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHhhcC
Q 027819 78 DPGIFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLV 157 (218)
Q Consensus 78 ~~~~N~v~LiGrIg~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~~Lk 157 (218)
|+++|+|+|+|+|++||++|++++|+.+++|+||++++|+++. | +|. ..++||+|++|| ++|+.+.++|+
T Consensus 1 m~m~N~V~L~G~l~~dPe~r~t~~G~~v~~fsvA~~~~~~~~~----G---~~~--~~t~~~~v~~wg-~~Ae~~~~~l~ 70 (164)
T TIGR00621 1 MRMVNKVILVGRLTRDPELRYTPSGNAVANFTLATNRRWKDQD----G---EWK--EETEWHDIVIFG-RLAEVAAQYLK 70 (164)
T ss_pred CCcccEEEEEEEeCCCCEEEECCCCCEEEEEEEEEcCceecCC----C---CEe--ccceEEEEEEeh-HHHHHHHHhCC
Confidence 7889999999999999999999999999999999999998653 3 332 369999999998 89999999999
Q ss_pred CCCEEEEEEEeEeeeeeCCCCCeEEEEEEEEEEeCCcEEEeeCCC
Q 027819 158 PGSTIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGRLVFLGKGG 202 (218)
Q Consensus 158 KG~~V~VeG~L~t~~~~d~~dG~~r~~~eI~v~~~g~i~~L~~k~ 202 (218)
||+.|+|+|+|+++.|+++ +|++++.++|+|+ +|.||..+.
T Consensus 71 KG~~V~V~G~L~~~~~~~k-dG~~~~~~ev~a~---~i~~L~~~~ 111 (164)
T TIGR00621 71 KGSLVYVEGRLRTRKWEDQ-NGQKRSKTEIIAD---NVQLLDLLG 111 (164)
T ss_pred CCCEEEEEEEEEeceEECC-CCcEEEEEEEEEE---EEeeccccC
Confidence 9999999999999999999 9999999999999 999998764
No 16
>PRK08182 single-stranded DNA-binding protein; Provisional
Probab=99.96 E-value=7.6e-28 Score=196.75 Aligned_cols=111 Identities=17% Similarity=0.243 Sum_probs=100.2
Q ss_pred CCceEEEEEEeCcCCeEEEcCCCcE----EEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHhh
Q 027819 80 GIFKAILVGQVGQSPVQKKLKSGRT----VTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKH 155 (218)
Q Consensus 80 ~~N~v~LiGrIg~dPelr~~~nG~~----v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~~ 155 (218)
|+|+|+|+||||+||++|++++|.. |++|+||+++.|++. +| +|.+ ..++||+|++|| ++|+.+.++
T Consensus 1 M~N~V~LiGrLg~DPElr~t~~G~~~~~~va~fslA~~r~~~~~----~G---e~~~-~~t~w~~V~~wg-~~Ae~v~~~ 71 (148)
T PRK08182 1 MSTHFVGEGNIGSAPEYREFPNGNDEPRRLLRLNVYFDNPVPTK----DG---EYED-RGGFWAPVELWH-RDAEHWARL 71 (148)
T ss_pred CccEEEEEEECCCCCeEEECCCCCeeeeeEEEEEEEecCceECC----CC---CEEe-cCcEEEEEEEEh-HHHHHHHHh
Confidence 5799999999999999999999986 999999999999754 23 3432 268999999998 899999999
Q ss_pred cCCCCEEEEEEEeEeeeeeCCCCCeEEEEEEEEEEeCCcEEEeeCCCC
Q 027819 156 LVPGSTIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGRLVFLGKGGD 203 (218)
Q Consensus 156 LkKG~~V~VeG~L~t~~~~d~~dG~~r~~~eI~v~~~g~i~~L~~k~~ 203 (218)
|+||++|+|+|+|+++.|+++ +|++++.++|+|+ +|.||..+..
T Consensus 72 l~KG~~V~V~GrL~~~~w~dk-dG~~r~~~eI~a~---~i~~l~~r~~ 115 (148)
T PRK08182 72 YQKGMRVLVEGRMERDEWTDN-EDNERVTFKVEAR---RVGILPYRIE 115 (148)
T ss_pred cCCCCEEEEEEEEEecccCCC-CCCEEEEEEEEEe---EEEEcCCccc
Confidence 999999999999999999999 9999999999999 9999976654
No 17
>PRK06293 single-stranded DNA-binding protein; Provisional
Probab=99.95 E-value=9.8e-28 Score=198.49 Aligned_cols=106 Identities=18% Similarity=0.365 Sum_probs=97.3
Q ss_pred CceEEEEEEeCcCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHhhcCCCC
Q 027819 81 IFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLVPGS 160 (218)
Q Consensus 81 ~N~v~LiGrIg~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~~LkKG~ 160 (218)
||+|+|+||||+||++|++++|+++++|+||+++++.+ ...++||+|++|+ ++|+.+.++|+||+
T Consensus 1 MN~V~LiGrLg~DPElR~t~sG~~v~~FsLAvn~~~~~--------------~~~T~wi~v~awg-~~Ae~v~~yL~KG~ 65 (161)
T PRK06293 1 MMFGYIVGRLGADPEERMTSKGKRVVVLRLGVKSRVGS--------------KDETVWCRCNIWG-NRYDKMLPYLKKGS 65 (161)
T ss_pred CeEEEEEEEecCCCeEEEcCCCCEEEEEEEEEeCCCCC--------------ccceEEEEEEEEh-HHHHHHHHhCCCCC
Confidence 79999999999999999999999999999999976421 1269999999998 89999999999999
Q ss_pred EEEEEEEeEeeeeeCCCCCeEEEEEEEEEEeCCcEEEeeCCCCCC
Q 027819 161 TIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGRLVFLGKGGDAQ 205 (218)
Q Consensus 161 ~V~VeG~L~t~~~~d~~dG~~r~~~eI~v~~~g~i~~L~~k~~~~ 205 (218)
+|+|+|+|+++.|+++ +|++++.++|+|+ +|+||..+..++
T Consensus 66 ~V~VeGrL~~~~y~dk-dG~kr~~~eIva~---~I~fl~~~~~~~ 106 (161)
T PRK06293 66 GVIVAGEMSPESYVDK-DGSPQSSLVVSVD---TIKFSPFGRNEG 106 (161)
T ss_pred EEEEEEEEEeCccCCC-CCCEEEEEEEEEe---EEEECcCCCccc
Confidence 9999999999999999 9999999999999 999997776543
No 18
>KOG1653 consensus Single-stranded DNA-binding protein [Replication, recombination and repair]
Probab=99.94 E-value=4.3e-27 Score=192.96 Aligned_cols=132 Identities=42% Similarity=0.600 Sum_probs=110.5
Q ss_pred CcccccccccCCCCCCCceEEEEEEeCcCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEe
Q 027819 65 QRESFDRPLENGLDPGIFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVY 144 (218)
Q Consensus 65 ~r~~~~r~~~~~~~~~~N~v~LiGrIg~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~w 144 (218)
++....+|++ +..++|+|+|+|+||+||.+|...||++|+.|+|+++.+|+++.. ++|++ ...++||+|.+|
T Consensus 41 ~~~~~~~p~k--~~~~vnkv~lvG~VGqdPl~k~~rngrpVtiFsv~T~~~~k~r~~-q~g~~-----~~~tqWHRVsVf 112 (175)
T KOG1653|consen 41 ETTTGEDPRK--LERGVNKVILVGRVGQDPLQKILRNGRPVTIFSVGTGGMFKQRLY-QAGDQ-----PQPTQWHRVSVF 112 (175)
T ss_pred cccCccchhh--hhcccceEEEEcccccchHHHhhcCCCeEEEEEeecCcccccccc-ccCCc-----CCcceeEEEEee
Confidence 4555567766 667889999999999999999999999999999999999997643 23432 358999999999
Q ss_pred CchhHHHHHhhcCCCCEEEEEEEeEeeeeeCCCCCeE-EEEEEEEEEeCCcEEEeeCCCCCCCC
Q 027819 145 PERLGGVVMKHLVPGSTIYVEGNLEQKVFNDPITGLV-RRIREIAIRRNGRLVFLGKGGDAQPP 207 (218)
Q Consensus 145 g~k~Ae~v~~~LkKG~~V~VeG~L~t~~~~d~~dG~~-r~~~eI~v~~~g~i~~L~~k~~~~~~ 207 (218)
++++|+++.++|+||+.|||+|+|+++-+.+.++|.. +..+.|+++ ++.||......+++
T Consensus 113 ~~~L~d~~~k~lkKGsriyveG~iey~g~~~d~~g~~~r~~t~iIa~---~v~Fl~~a~~ek~~ 173 (175)
T KOG1653|consen 113 NEVLADYALKYLKKGSRIYVEGKIEYRGENDDIQGNVKRIPTIIIAR---DVSFLIDAIFEKKK 173 (175)
T ss_pred CchHHHHHHHHhcCCCEEEEeeeEEeeeeeccccCceeecceEEEec---hhHHHHHHhhhccC
Confidence 9999999999999999999999999998888779987 444555566 89999876655544
No 19
>PF00436 SSB: Single-strand binding protein family; InterPro: IPR000424 The Escherichia coli single-strand binding protein [] (gene ssb), also known as the helix-destabilising protein, is a protein of 177 amino acids. It binds tightly, as a homotetramer, to single-stranded DNA (ss-DNA) and plays an important role in DNA replication, recombination and repair. Closely related variants of SSB are encoded in the genome of a variety of large self-transmissible plasmids. SSB has also been characterised in bacteria such as Proteus mirabilis or Serratia marcescens. Eukaryotic mitochondrial proteins that bind ss-DNA and are probably involved in mitochondrial DNA replication are structurally and evolutionary related to prokaryotic SSB.; GO: 0003697 single-stranded DNA binding; PDB: 3UDG_B 1SE8_A 2CWA_A 3ULL_B 1S3O_A 2DUD_A 3AFP_A 3AFQ_A 3VDY_A 3EIV_C ....
Probab=99.94 E-value=6.1e-26 Score=171.55 Aligned_cols=104 Identities=28% Similarity=0.456 Sum_probs=92.2
Q ss_pred CceEEEEEEeCcCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHhhcCCCC
Q 027819 81 IFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLVPGS 160 (218)
Q Consensus 81 ~N~v~LiGrIg~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~~LkKG~ 160 (218)
||+|+|+|+|++||+++++++|++++.|+|+++++|++.. +.. ...++||+|++|| ++|+.+.++|+||+
T Consensus 1 mN~v~l~G~l~~~p~~~~~~~g~~~~~f~la~~~~~~~~~----~~~-----~~~~~~~~v~~~g-~~A~~~~~~l~kG~ 70 (104)
T PF00436_consen 1 MNKVTLIGRLGKDPELRYTKNGTPVARFSLAVNRRFKDDG----GEG-----DEKTDWINVVAWG-KLAENVAEYLKKGD 70 (104)
T ss_dssp EEEEEEEEEESSSEEEEEETTSEEEEEEEEEEEEEEEETT----SCE-----EEEEEEEEEEEEH-HHHHHHHHH--TT-
T ss_pred CcEEEEEEEECCCcEEEECCCCCEEEEEEEEEecEEeeee----ccC-----ccceEEEEEEeee-ecccccceEEcCCC
Confidence 7999999999999999999999999999999999998621 211 2489999999998 79999999999999
Q ss_pred EEEEEEEeEeeeeeCCCCCeEEEEEEEEEEeCCcEEEe
Q 027819 161 TIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGRLVFL 198 (218)
Q Consensus 161 ~V~VeG~L~t~~~~d~~dG~~r~~~eI~v~~~g~i~~L 198 (218)
.|+|+|+|+++.|+++ +|++++.++|.|+ +|+||
T Consensus 71 ~V~V~G~l~~~~~~~~-~G~~~~~~~i~a~---~i~fl 104 (104)
T PF00436_consen 71 RVYVEGRLRTRTYEDK-DGQKRYRVEIIAD---NIEFL 104 (104)
T ss_dssp EEEEEEEEEEEEEEST-TSSEEEEEEEEEE---EEEE-
T ss_pred EEEEEEEEEeeEEECC-CCCEEEEEEEEEE---EEEeC
Confidence 9999999999999999 8999999999999 99997
No 20
>PRK07772 single-stranded DNA-binding protein; Provisional
Probab=99.94 E-value=1.1e-25 Score=190.21 Aligned_cols=114 Identities=20% Similarity=0.333 Sum_probs=99.4
Q ss_pred CCCCceEEEEEEeCcCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHhhcC
Q 027819 78 DPGIFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLV 157 (218)
Q Consensus 78 ~~~~N~v~LiGrIg~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~~Lk 157 (218)
|.++|+|+|+|||++||++|++++|..|++|+||++.++.+++ .+ +|.| ..++||+|++|+ ++|++++++|+
T Consensus 1 m~~~~~VtLiGrL~~DPElR~t~sG~~va~FrVAv~~r~~~~~---~g---~~~d-~~t~fi~V~~Wg-~~Ae~va~~L~ 72 (186)
T PRK07772 1 MAGDTTITVVGNLTADPELRFTPSGAAVANFTVASTPRTFDRQ---TN---EWKD-GEALFLRCSIWR-QAAENVAESLT 72 (186)
T ss_pred CCccCEEEEEEEeCCCCeEEEcCCCCEEEEEEEEecCcceecC---CC---cEec-cCceEEEEEEec-HHHHHHHHhcC
Confidence 6678999999999999999999999999999999986554443 23 4544 379999999998 89999999999
Q ss_pred CCCEEEEEEEeEeeeeeCCCCCeEEEEEEEEEEe-CCcEEEeeC
Q 027819 158 PGSTIYVEGNLEQKVFNDPITGLVRRIREIAIRR-NGRLVFLGK 200 (218)
Q Consensus 158 KG~~V~VeG~L~t~~~~d~~dG~~r~~~eI~v~~-~g~i~~L~~ 200 (218)
|||+|+|+|+|+++.|+++ +|++++.++|+|+. +..|.++..
T Consensus 73 KGd~V~V~GrL~~r~wedk-dG~~rt~~eV~a~~Vg~~L~~~~a 115 (186)
T PRK07772 73 KGMRVIVTGRLKQRSYETR-EGEKRTVVELEVDEIGPSLRYATA 115 (186)
T ss_pred CCCEEEEEEEEEcCceECC-CCCEEEEEEEEEEEcccceeeeec
Confidence 9999999999999999999 99999999999995 556666643
No 21
>COG0629 Ssb Single-stranded DNA-binding protein [DNA replication, recombination, and repair]
Probab=99.92 E-value=8.6e-25 Score=181.33 Aligned_cols=113 Identities=27% Similarity=0.412 Sum_probs=90.6
Q ss_pred CCceEEEEEEeCcCCeEEEcCCC-cEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHhhcCC
Q 027819 80 GIFKAILVGQVGQSPVQKKLKSG-RTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLVP 158 (218)
Q Consensus 80 ~~N~v~LiGrIg~dPelr~~~nG-~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~~LkK 158 (218)
+||+|+|+|||++|||+|++++| ..++.|++++++.++ +.. ++. ...++||+|++|| ++|+.+.+||+|
T Consensus 2 ~~Nkv~LvG~l~~DPE~r~t~~g~~~v~~~~~a~~r~~~-~~~---~~~-----~~~t~~~~vv~wg-k~Ae~~~~yl~K 71 (167)
T COG0629 2 MMNKVILVGRLTRDPELRYTPNGGAVVALFSAAVNRRFD-NQS---GER-----DEETDWIRVVIWG-KLAENAAEYLKK 71 (167)
T ss_pred CcceEEEEeecccCcceeecCCCCeeeEEEEEEeccccc-cCC---ccc-----ccccceEEEEEeh-HHHHHHHHHhcC
Confidence 79999999999999999999955 566666666666544 331 211 2479999999999 899999999999
Q ss_pred CCEEEEEEEeEeeeeeCCCCCeEEEEEEEEEEe-CCcEEEeeCCCC
Q 027819 159 GSTIYVEGNLEQKVFNDPITGLVRRIREIAIRR-NGRLVFLGKGGD 203 (218)
Q Consensus 159 G~~V~VeG~L~t~~~~d~~dG~~r~~~eI~v~~-~g~i~~L~~k~~ 203 (218)
|++|+|+|+|+++.|+++ +|..++..++++.. ...+++|+.++.
T Consensus 72 G~~V~VeG~l~~~~~~~~-~G~~r~~~~~~~~~v~~~~~~l~~~~~ 116 (167)
T COG0629 72 GSLVYVEGRLQTRKWEDQ-EGQKRYQTEIVTEIVADSVQMLGSRKS 116 (167)
T ss_pred CCEEEEEEEEEeeeeecC-CCcceeeEEEEEEEeehhhhhccCccc
Confidence 999999999999999999 99666666664443 338899988864
No 22
>PRK05813 single-stranded DNA-binding protein; Provisional
Probab=99.92 E-value=3e-24 Score=185.60 Aligned_cols=104 Identities=16% Similarity=0.203 Sum_probs=95.2
Q ss_pred CCCceEEEEEEeCcCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHhhcCC
Q 027819 79 PGIFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLVP 158 (218)
Q Consensus 79 ~~~N~v~LiGrIg~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~~LkK 158 (218)
..||+|+|+|||++||++|++++|+++++|+||+++.|+ .++||+|++|| ++|+.+. +|+|
T Consensus 107 ~~~N~V~LiGrL~~DPelR~t~~G~~va~f~lAvnr~~~-----------------~td~i~~v~wg-~~Ae~~~-~l~K 167 (219)
T PRK05813 107 KNPNEIFLDGYICKEPVYRTTPFGREIADLLLAVNRPYN-----------------KSDYIPCIAWG-RNARFCK-TLEV 167 (219)
T ss_pred CCccEEEEEEEccCCCeEEECCCCCEEEEEEEEEcCCCC-----------------CceEEEEEEEh-HHhHHHh-hCCC
Confidence 579999999999999999999999999999999998653 47999999998 8999876 6999
Q ss_pred CCEEEEEEEeEeeeeeCCCC----CeEEEEEEEEEEeCCcEEEeeCCCCCC
Q 027819 159 GSTIYVEGNLEQKVFNDPIT----GLVRRIREIAIRRNGRLVFLGKGGDAQ 205 (218)
Q Consensus 159 G~~V~VeG~L~t~~~~d~~d----G~~r~~~eI~v~~~g~i~~L~~k~~~~ 205 (218)
|++|.|+|+|+++.|+++ + |++++.+||.|+ +|+||+.+...+
T Consensus 168 G~~V~V~GrL~sr~y~~k-~g~~~g~kr~~~eV~v~---~i~~l~~~~~~~ 214 (219)
T PRK05813 168 GDNIRVWGRVQSREYQKK-LSEGEVVTKVAYEVSIS---KMEKVEKEEANN 214 (219)
T ss_pred CCEEEEEEEEEecceEcC-CCCccceEEEEEEEEEE---EEEEcCChhhcc
Confidence 999999999999999997 6 489999999999 999998877633
No 23
>PRK05853 hypothetical protein; Validated
Probab=99.91 E-value=7e-24 Score=175.63 Aligned_cols=104 Identities=19% Similarity=0.233 Sum_probs=91.2
Q ss_pred EEEEeCcCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHhhcCCCCEEEEE
Q 027819 86 LVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLVPGSTIYVE 165 (218)
Q Consensus 86 LiGrIg~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~~LkKG~~V~Ve 165 (218)
|+|||++||+++++. |..+++|+||++++|+++. | +|.+ ..++||+|++|| ++|+++.++|+||++|+|+
T Consensus 1 ivGrLg~DPelr~~~-g~~va~F~lAvn~r~~~~~----G---e~~d-~~T~wi~V~~wg-~lAe~v~~~L~KG~~V~V~ 70 (161)
T PRK05853 1 VVGHIVNDPQRRKVG-DQEVIKFRVASNSRRRTAD----G---GWEP-GNSLFITVNCWG-RLVTGVGAALGKGAPVIVV 70 (161)
T ss_pred CeEcccCCCEEEEEC-CceEEEEEEEECCCeECCC----C---CEec-cCccEEEEEEEh-HHHHHHHHHcCCCCEEEEE
Confidence 689999999999984 7899999999999997542 4 4543 269999999998 8999999999999999999
Q ss_pred EEeEeeeeeCCCCCeEEEEEEEEEEe-CCcEEEeeC
Q 027819 166 GNLEQKVFNDPITGLVRRIREIAIRR-NGRLVFLGK 200 (218)
Q Consensus 166 G~L~t~~~~d~~dG~~r~~~eI~v~~-~g~i~~L~~ 200 (218)
|+|+++.|+++ +|++++.++|.++. +..+.++..
T Consensus 71 GrL~~~~wedk-dG~~r~~~eV~a~~Vg~dL~~~~a 105 (161)
T PRK05853 71 GHVYTSEYEDR-DGNRRSSLEMRATSVGPDLSRCIV 105 (161)
T ss_pred EEEEccceECC-CCCEEEEEEEEEEEecccccccee
Confidence 99999999999 99999999999995 665666644
No 24
>PRK02801 primosomal replication protein N; Provisional
Probab=99.90 E-value=2.1e-22 Score=154.86 Aligned_cols=101 Identities=20% Similarity=0.229 Sum_probs=86.4
Q ss_pred CCceEEEEEEeCcCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHhhcCCC
Q 027819 80 GIFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLVPG 159 (218)
Q Consensus 80 ~~N~v~LiGrIg~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~~LkKG 159 (218)
+||+|+|+|+|++||++|++++|.++++|+||+... ... .+ +. ++.++|++|++|| ++|+.+.+||+||
T Consensus 1 mmN~v~L~Grl~~dpelr~Tp~G~~v~~f~La~~~~-~~e----a~----~~-r~~~~~i~~va~G-~~Ae~~~~~l~kG 69 (101)
T PRK02801 1 MTNRLVLSGTVCRTPKRKVSPSGIPHCQFVLEHRSV-QEE----AG----LH-RQAWCRMPVIVSG-NQFQAITQSITVG 69 (101)
T ss_pred CccEEEEEEEECcCcceEECCCCCeEEEEEEEEeCe-Eec----CC----Cc-eeEEEEEEEEEEc-HHHHHHHhhcCCC
Confidence 479999999999999999999999999999999533 211 11 11 2367999999999 8999999999999
Q ss_pred CEEEEEEEeEeeeeeCCCCCeEEEEEEEEEEeCCcEEEee
Q 027819 160 STIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGRLVFLG 199 (218)
Q Consensus 160 ~~V~VeG~L~t~~~~d~~dG~~r~~~eI~v~~~g~i~~L~ 199 (218)
+.|.|+|+|++ |+++ +|++++. |.++ +|+||+
T Consensus 70 s~v~V~G~L~~--~~~~-~g~~~~~--v~~~---~i~~l~ 101 (101)
T PRK02801 70 SKITVQGFISC--HQGR-NGLSKLV--LHAE---QIELID 101 (101)
T ss_pred CEEEEEEEEEE--eECC-CCCEEEE--EEEE---EEEECC
Confidence 99999999998 7888 8988866 8899 999874
No 25
>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=99.88 E-value=2e-21 Score=145.38 Aligned_cols=100 Identities=32% Similarity=0.532 Sum_probs=91.1
Q ss_pred EEEEEEeCcCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHhhcCCCCEEE
Q 027819 84 AILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLVPGSTIY 163 (218)
Q Consensus 84 v~LiGrIg~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~~LkKG~~V~ 163 (218)
|+|+|+|+++|+++++++|..++.|+|++++.+++.. |. ...++||+|++|| ++|+.+.++|+|||.|+
T Consensus 1 v~l~G~l~~~p~~~~~~~g~~~~~~~v~~~~~~~~~~---------~~-~~~~~~~~v~~~g-~~a~~~~~~~~kG~~V~ 69 (100)
T cd04496 1 VILIGRLGKDPELRYTPSGTPVARFSLAVNRRRKDRD---------EE-EEETDWIRVVAFG-KLAENAAKYLKKGDLVY 69 (100)
T ss_pred CEEEEEecCCCEEEECCCCCEEEEEEEEEcCceeccc---------cc-ccccEEEEEEEEh-HHHHHHHHHhCCCCEEE
Confidence 5799999999999999999999999999999987542 00 2379999999999 79999999999999999
Q ss_pred EEEEeEeeeeeCCCCCeEEEEEEEEEEeCCcEEEe
Q 027819 164 VEGNLEQKVFNDPITGLVRRIREIAIRRNGRLVFL 198 (218)
Q Consensus 164 VeG~L~t~~~~d~~dG~~r~~~eI~v~~~g~i~~L 198 (218)
|+|+|+.+.|+++ +|..++.++|.++ +|.++
T Consensus 70 v~G~l~~~~~~~~-~g~~~~~~~i~~~---~i~~~ 100 (100)
T cd04496 70 VEGRLRTRSWEDK-DGQKRYGTEVVAD---RIEFL 100 (100)
T ss_pred EEEEEEeceeECC-CCCEEEEEEEEEE---EEEEC
Confidence 9999999999998 8999999999999 98875
No 26
>PRK05813 single-stranded DNA-binding protein; Provisional
Probab=99.80 E-value=6.7e-19 Score=152.34 Aligned_cols=100 Identities=24% Similarity=0.213 Sum_probs=91.3
Q ss_pred CCceEEEEEEeCcCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHhhcCCC
Q 027819 80 GIFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLVPG 159 (218)
Q Consensus 80 ~~N~v~LiGrIg~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~~LkKG 159 (218)
..|+|+|+|+|++||+++++..|..+++|+|||+| +.+ .++||+|++|+ ++|+.+. |+||
T Consensus 7 ~~NkV~L~Grl~~d~e~~~~~~G~~~~~f~laV~R-~s~----------------~~D~i~v~v~~-rlae~~~--l~kG 66 (219)
T PRK05813 7 ENNKVYLEGKVVSELEFSHEMYGEGFYNFKLEVPR-LSD----------------SKDILPVTVSE-RLLAGMD--LKVG 66 (219)
T ss_pred hcCEEEEEEEEcCCceEEEEeCCeEEEEEEEEeec-cCC----------------CccEEEEEEEh-hhhhhhc--ccCC
Confidence 46999999999999999999999999999999998 541 58999999997 9999988 9999
Q ss_pred CEEEEEEEeEeeeeeCCCCCeEEEEEEEEEEeCCcEEEeeCCCCC
Q 027819 160 STIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGRLVFLGKGGDA 204 (218)
Q Consensus 160 ~~V~VeG~L~t~~~~d~~dG~~r~~~eI~v~~~g~i~~L~~k~~~ 204 (218)
+.|+|+|+|+ .|++.++|++|+.++|.|+ +|+||+.+++.
T Consensus 67 ~~v~VeGqlr--sy~~~~~G~~R~vl~V~a~---~i~~l~~~~~~ 106 (219)
T PRK05813 67 TLVIVEGQLR--SYNKFIDGKNRLILTVFAR---NIEYCDERSDI 106 (219)
T ss_pred CEEEEEEEEE--EeccCCCCcEEEEEEEEEE---EEEEccCCCcc
Confidence 9999999999 7877646999999999999 99999997653
No 27
>PRK00036 primosomal replication protein N; Reviewed
Probab=98.31 E-value=1.5e-05 Score=62.22 Aligned_cols=96 Identities=13% Similarity=0.045 Sum_probs=75.6
Q ss_pred CceEEEEEEeCcCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHhhcCCCC
Q 027819 81 IFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLVPGS 160 (218)
Q Consensus 81 ~N~v~LiGrIg~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~~LkKG~ 160 (218)
||++.|+|.|++-|.+|++|.|-+++.|.|.-..... +.|-+ +..-.-+.+++.| .+|+.+.+ +..|+
T Consensus 1 mN~l~Ltg~v~~~~~lryTPAGIp~~~~~LeH~S~q~-----EAG~~-----Rqv~~~i~ava~G-~~a~~~~~-l~~Gs 68 (107)
T PRK00036 1 MNTLELSARVLECGAMRHTPAGLPALELLLVHESEVV-----EAGHP-----RRVELTISAVALG-DLALLLAD-TPLGT 68 (107)
T ss_pred CCEEEEEEEEeccCccccCCCCCceEEEEEEEeEEeE-----eCCCc-----ceEEEEEEEEEEh-hHHHHhcc-cCCCC
Confidence 5999999999999999999999999999998755422 12332 2234456779999 79998886 99999
Q ss_pred EEEEEEEeEeeeeeCCCCCeEEEEEEEEEEeCCcEEEe
Q 027819 161 TIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGRLVFL 198 (218)
Q Consensus 161 ~V~VeG~L~t~~~~d~~dG~~r~~~eI~v~~~g~i~~L 198 (218)
.|.|+|-|.. +. .|. ..+.+.++ .|+++
T Consensus 69 ~v~v~GFLa~----~~-~~~--~~LVLHi~---~Ie~i 96 (107)
T PRK00036 69 EMQVQGFLAP----AR-KDS--VKVKLHLQ---QARRI 96 (107)
T ss_pred EEEEEEEEEE----CC-CCC--CcEEEEhH---HeEEc
Confidence 9999999998 22 333 45667888 99999
No 28
>COG2965 PriB Primosomal replication protein N [DNA replication, recombination, and repair]
Probab=98.10 E-value=9.3e-05 Score=56.86 Aligned_cols=100 Identities=21% Similarity=0.203 Sum_probs=75.5
Q ss_pred CCCCceEEEEEEeCcCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEE--EEEEeCchhHHHHHhh
Q 027819 78 DPGIFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWH--RVSVYPERLGGVVMKH 155 (218)
Q Consensus 78 ~~~~N~v~LiGrIg~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~--~V~~wg~k~Ae~v~~~ 155 (218)
|...|++.|+|.|++-|..+++++|.+++.|-|.-.. +-.. .|- ..--|+ .+.+-| ++|+.+-..
T Consensus 1 ~~~~Nrl~L~g~vak~~~r~~sPsGIphc~f~Lehrs-~q~E----ag~-------~RQv~~~mpv~vsG-~qa~~lt~~ 67 (103)
T COG2965 1 MNMTNRLSLSGTVAKVPVRRYSPSGIPHCQFVLEHRS-WQEE----AGF-------QRQVWCEMPVRVSG-RQAEELTQS 67 (103)
T ss_pred CCccceEEEEEEeeccceeeeCCCCCeeEEEEEeecc-hhhh----CCc-------ceeEEEEccEEeec-hhhhhhhhc
Confidence 4468999999999999999999999999999997643 3211 221 256665 457777 899988888
Q ss_pred cCCCCEEEEEEEeEeeeeeCCCCCeEEEEEEEEEEeCCcEEEe
Q 027819 156 LVPGSTIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGRLVFL 198 (218)
Q Consensus 156 LkKG~~V~VeG~L~t~~~~d~~dG~~r~~~eI~v~~~g~i~~L 198 (218)
+..|+.|.|+|-|....-. +| ...+.|.+. .|.++
T Consensus 68 i~~Gs~i~v~GFla~~~~~---sg--~~~lvlha~---qi~~i 102 (103)
T COG2965 68 ITVGSYILVVGFLACHKRR---SG--LSKLVLHAE---QIEFI 102 (103)
T ss_pred cccccEEEEEEEEEeeccc---CC--ccEEEEEee---EEEec
Confidence 9999999999999877543 33 234456666 66665
No 29
>PF01336 tRNA_anti-codon: OB-fold nucleic acid binding domain; InterPro: IPR004365 The OB-fold (oligonucleotide/oligosaccharide-binding fold) is found in all three kingdoms and its common architecture presents a binding face that has adapted to bind different ligands. The OB-fold is a five/six-stranded closed beta-barrel formed by 70-80 amino acid residues. The strands are connected by loops of varying length which form the functional appendages of the protein. The majority of OB-fold proteins use the same face for ligand binding or as an active site. Different OB-fold proteins use this 'fold-related binding face' to, variously, bind oligosaccharides, oligonucleotides, proteins, metal ions and catalytic substrates. This entry contains OB-fold domains that bind to nucleic acids []. It includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl-tRNA synthetases (See IPR004364 from INTERPRO). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule 6.1.1 from EC. This domain is found in RecG helicase involved in DNA repair. Replication factor A is a heterotrimeric complex, that contains a subunit in this family [, ]. This domain is also found at the C terminus of bacterial DNA polymerase III alpha chain.; GO: 0003676 nucleic acid binding; PDB: 1BBU_A 1KRS_A 1BBW_A 1KRT_A 1EQR_B 1IL2_B 1C0A_A 3KFU_A 1EOV_A 1ASY_A ....
Probab=96.97 E-value=0.011 Score=40.98 Aligned_cols=75 Identities=19% Similarity=0.300 Sum_probs=54.2
Q ss_pred EEEEEEeCcCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHhhcCCCCEEE
Q 027819 84 AILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLVPGSTIY 163 (218)
Q Consensus 84 v~LiGrIg~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~~LkKG~~V~ 163 (218)
|.+.|.|.+-. .++..++.|.|.- .+--+.|.+|+ ..+....+.|+.|+.|.
T Consensus 1 V~v~G~V~~~~-----~~~~~~~~~~l~D----------------------~tg~i~~~~~~-~~~~~~~~~l~~g~~v~ 52 (75)
T PF01336_consen 1 VTVEGRVTSIR-----RSGGKIVFFTLED----------------------GTGSIQVVFFN-EEYERFREKLKEGDIVR 52 (75)
T ss_dssp EEEEEEEEEEE-----EEETTEEEEEEEE----------------------TTEEEEEEEET-HHHHHHHHTS-TTSEEE
T ss_pred CEEEEEEEEEE-----cCCCCEEEEEEEE----------------------CCccEEEEEcc-HHhhHHhhcCCCCeEEE
Confidence 57888887743 4556677777732 23457999997 67888888999999999
Q ss_pred EEEEeEeeeeeCCCCCeEEEEEEEEEEeCCcEEEe
Q 027819 164 VEGNLEQKVFNDPITGLVRRIREIAIRRNGRLVFL 198 (218)
Q Consensus 164 VeG~L~t~~~~d~~dG~~r~~~eI~v~~~g~i~~L 198 (218)
|.|.+... + +| .++|.+. +|+.|
T Consensus 53 v~G~v~~~----~-~~----~~~l~~~---~i~~l 75 (75)
T PF01336_consen 53 VRGKVKRY----N-GG----ELELIVP---KIEIL 75 (75)
T ss_dssp EEEEEEEE----T-TS----SEEEEEE---EEEEE
T ss_pred EEEEEEEE----C-Cc----cEEEEEC---EEEEC
Confidence 99999887 2 33 3567777 77654
No 30
>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=96.12 E-value=0.04 Score=42.11 Aligned_cols=72 Identities=14% Similarity=0.096 Sum_probs=54.6
Q ss_pred CCCCCCceEEEEEEeCcCCeEEEcCCC---cEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHH
Q 027819 76 GLDPGIFKAILVGQVGQSPVQKKLKSG---RTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVV 152 (218)
Q Consensus 76 ~~~~~~N~v~LiGrIg~dPelr~~~nG---~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v 152 (218)
.|.|+++.+.|.|+|..-=+++.+.+. ..+..|.|+ |. .+.-++|++|+ ..|+..
T Consensus 4 ~L~p~~~~~~I~~rV~~k~~~~~f~~~~~~g~~~~~~l~------De---------------~~~~I~~t~~~-~~~~~f 61 (104)
T cd04474 4 SLNPYQNKWTIKARVTNKSDIRTWSNARGEGKLFSFDLL------DE---------------DGGEIRATFFN-DAVDKF 61 (104)
T ss_pred HccCCCCcEEEEEEEeeccccccccCCCCCcEEEEEEEE------EC---------------CCCEEEEEEeh-HHHHHh
Confidence 456788999999999987667777663 445555542 11 24457999998 899999
Q ss_pred HhhcCCCCEEEEEEEeE
Q 027819 153 MKHLVPGSTIYVEGNLE 169 (218)
Q Consensus 153 ~~~LkKG~~V~VeG~L~ 169 (218)
...|+.|+.++|.+-..
T Consensus 62 ~~~l~eG~vy~i~~~~V 78 (104)
T cd04474 62 YDLLEVGKVYYISKGSV 78 (104)
T ss_pred hcccccccEEEEeccEE
Confidence 99999999999998443
No 31
>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=96.03 E-value=0.061 Score=39.56 Aligned_cols=69 Identities=20% Similarity=0.282 Sum_probs=51.6
Q ss_pred eEEEEEEeCcCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHhhcC-CCCE
Q 027819 83 KAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLV-PGST 161 (218)
Q Consensus 83 ~v~LiGrIg~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~~Lk-KG~~ 161 (218)
.|++.|.|-. .+.|.+.+|+.+..|.|.= .++-+.|..|..+.-+ ....|+ +|+-
T Consensus 1 ~v~i~G~Vf~-~e~re~k~g~~i~~~~itD----------------------~t~Si~~K~F~~~~~~-~~~~ik~~G~~ 56 (82)
T cd04484 1 NVVVEGEVFD-LEIRELKSGRKILTFKVTD----------------------YTSSITVKKFLRKDEK-DKEELKSKGDW 56 (82)
T ss_pred CEEEEEEEEE-EEEEEecCCCEEEEEEEEc----------------------CCCCEEEEEeccCChh-HHhhcccCCCE
Confidence 3789999966 7889999999888887742 1334677788621222 335699 9999
Q ss_pred EEEEEEeEeeeeeC
Q 027819 162 IYVEGNLEQKVFND 175 (218)
Q Consensus 162 V~VeG~L~t~~~~d 175 (218)
|.|.|.++...|..
T Consensus 57 v~v~G~v~~D~f~~ 70 (82)
T cd04484 57 VRVRGKVQYDTFSK 70 (82)
T ss_pred EEEEEEEEEccCCC
Confidence 99999999999964
No 32
>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=95.51 E-value=0.15 Score=36.88 Aligned_cols=73 Identities=23% Similarity=0.329 Sum_probs=50.2
Q ss_pred EEEEEEeCcCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHhhcCCCCEEE
Q 027819 84 AILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLVPGSTIY 163 (218)
Q Consensus 84 v~LiGrIg~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~~LkKG~~V~ 163 (218)
|.+.|.|.+.+. ++|+.| |+| +|. ..=++|++|. ..+..+...++.||.|.
T Consensus 1 v~v~GeVs~~~~----~~GHvy--fsL------kD~----------------~a~i~cv~f~-~~~~~~~~~l~~Gd~V~ 51 (73)
T cd04487 1 VHIEGEVVQIKQ----TSGPTI--FTL------RDE----------------TGTVWAAAFE-EAGVRAYPEVEVGDIVR 51 (73)
T ss_pred CEEEEEEecccc----CCCCEE--EEE------EcC----------------CEEEEEEEEc-hhccCCcCCCCCCCEEE
Confidence 357888888762 678754 555 221 1227999996 55555667799999999
Q ss_pred EEEEeEeeeeeCCCCCeEEEEEEEEEEeCCcEEEe
Q 027819 164 VEGNLEQKVFNDPITGLVRRIREIAIRRNGRLVFL 198 (218)
Q Consensus 164 VeG~L~t~~~~d~~dG~~r~~~eI~v~~~g~i~~L 198 (218)
|.|++.. + .| .+++.|+ +|+.|
T Consensus 52 v~G~v~~-----~-~G----~~ql~v~---~i~~~ 73 (73)
T cd04487 52 VTGEVEP-----R-DG----QLQIEVE---SLEVL 73 (73)
T ss_pred EEEEEec-----C-Ce----EEEEEEe---eEEEC
Confidence 9999874 3 45 3567777 66654
No 33
>cd04489 ExoVII_LU_OBF ExoVII_LU_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of Escherichia coli exodeoxyribonuclease VII (ExoVII) large subunit. E. coli ExoVII is composed of two non-identical subunits. E. coli ExoVII is a single-strand-specific exonuclease which degrades ssDNA from both 3-prime and 5-prime ends. ExoVII plays a role in methyl-directed mismatch repair in vivo. ExoVII may also guard the genome from mutagenesis by removing excess ssDNA, since the build up of ssDNA would lead to SOS induction and PolIV-dependent mutagenesis.
Probab=95.44 E-value=0.37 Score=33.98 Aligned_cols=62 Identities=18% Similarity=0.161 Sum_probs=45.0
Q ss_pred EEEEEEeCcCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHhhcCCCCEEE
Q 027819 84 AILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLVPGSTIY 163 (218)
Q Consensus 84 v~LiGrIg~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~~LkKG~~V~ 163 (218)
+.+.|-|.. ++.+++| .+-|+|.-. +.=+.|++|. ...+.+...|++|+.|.
T Consensus 2 ~~v~g~v~~---i~~tk~g--~~~~~L~D~----------------------~~~i~~~~f~-~~~~~~~~~l~~g~~v~ 53 (78)
T cd04489 2 VWVEGEISN---LKRPSSG--HLYFTLKDE----------------------DASIRCVMWR-SNARRLGFPLEEGMEVL 53 (78)
T ss_pred EEEEEEEec---CEECCCc--EEEEEEEeC----------------------CeEEEEEEEc-chhhhCCCCCCCCCEEE
Confidence 467787774 3436676 666666332 2237899997 66777888999999999
Q ss_pred EEEEeEeeee
Q 027819 164 VEGNLEQKVF 173 (218)
Q Consensus 164 VeG~L~t~~~ 173 (218)
|+|++....|
T Consensus 54 v~g~v~~~~~ 63 (78)
T cd04489 54 VRGKVSFYEP 63 (78)
T ss_pred EEEEEEEECC
Confidence 9999997544
No 34
>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=95.00 E-value=0.51 Score=33.12 Aligned_cols=71 Identities=17% Similarity=0.308 Sum_probs=48.9
Q ss_pred cCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHhhcCCCCEEEEEEEeEee
Q 027819 92 QSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLVPGSTIYVEGNLEQK 171 (218)
Q Consensus 92 ~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~~LkKG~~V~VeG~L~t~ 171 (218)
.....+.+.+|+.++.|+|.-. +--+.|.+|++.. .....|++|..|+|.|.+..
T Consensus 7 ~~~~~~~tk~g~~~~~~~l~D~----------------------tg~i~~~~f~~~~--~~~~~l~~g~~v~v~G~v~~- 61 (83)
T cd04492 7 KSKELRTAKNGKPYLALTLQDK----------------------TGEIEAKLWDASE--EDEEKFKPGDIVHVKGRVEE- 61 (83)
T ss_pred EEeeeecccCCCcEEEEEEEcC----------------------CCeEEEEEcCCCh--hhHhhCCCCCEEEEEEEEEE-
Confidence 3455677888988888887432 2237899998433 34778999999999999954
Q ss_pred eeeCCCCCeEEEEEEEEEEeCCcEEEee
Q 027819 172 VFNDPITGLVRRIREIAIRRNGRLVFLG 199 (218)
Q Consensus 172 ~~~d~~dG~~r~~~eI~v~~~g~i~~L~ 199 (218)
+ . | ..++.+. +|..|.
T Consensus 62 -~-~---~----~~~l~~~---~i~~l~ 77 (83)
T cd04492 62 -Y-R---G----RLQLKIQ---RIRLVT 77 (83)
T ss_pred -e-C---C----ceeEEEE---EEEECC
Confidence 3 1 2 2356666 676665
No 35
>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=94.54 E-value=0.44 Score=33.06 Aligned_cols=61 Identities=21% Similarity=0.301 Sum_probs=43.4
Q ss_pred EEEEeCcCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHhhcCCCCEEEEE
Q 027819 86 LVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLVPGSTIYVE 165 (218)
Q Consensus 86 LiGrIg~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~~LkKG~~V~Ve 165 (218)
+.|.|.. ...+.+.+|+.++.+.|.-. +--+.|.+|+ ..-+.+.+.|++|..|.|.
T Consensus 2 i~g~v~~-~~~~~~k~g~~~~~~~l~D~----------------------tg~~~~~~f~-~~~~~~~~~l~~g~~v~v~ 57 (84)
T cd04485 2 VAGLVTS-VRRRRTKKGKRMAFVTLEDL----------------------TGSIEVVVFP-ETYEKYRDLLKEDALLLVE 57 (84)
T ss_pred EEEEEEE-eEEEEcCCCCEEEEEEEEeC----------------------CCeEEEEECH-HHHHHHHHHhcCCCEEEEE
Confidence 5666655 44567788988887776221 2236899997 4434467789999999999
Q ss_pred EEeEe
Q 027819 166 GNLEQ 170 (218)
Q Consensus 166 G~L~t 170 (218)
|.+..
T Consensus 58 G~v~~ 62 (84)
T cd04485 58 GKVER 62 (84)
T ss_pred EEEEe
Confidence 99965
No 36
>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=93.81 E-value=0.71 Score=30.61 Aligned_cols=33 Identities=21% Similarity=0.454 Sum_probs=28.4
Q ss_pred eEEEEEEeCchhHHHHHhhcCCCCEEEEEEEeEe
Q 027819 137 QWHRVSVYPERLGGVVMKHLVPGSTIYVEGNLEQ 170 (218)
Q Consensus 137 ~w~~V~~wg~k~Ae~v~~~LkKG~~V~VeG~L~t 170 (218)
..+.|.+|. ...+.....+++|+.|.|+|++..
T Consensus 29 ~~i~~~~~~-~~~~~~~~~~~~g~~v~v~g~v~~ 61 (75)
T cd03524 29 GTIRVTLFG-ELAEELENLLKEGQVVYIKGKVKK 61 (75)
T ss_pred CEEEEEEEc-hHHHHHHhhccCCCEEEEEEEEEe
Confidence 578999997 677777788999999999999965
No 37
>PRK07211 replication factor A; Reviewed
Probab=93.14 E-value=0.38 Score=46.63 Aligned_cols=71 Identities=14% Similarity=0.234 Sum_probs=54.2
Q ss_pred CCCCCCceEEEEEEeCcCCeEEEcCC-C--c--EEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHH
Q 027819 76 GLDPGIFKAILVGQVGQSPVQKKLKS-G--R--TVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGG 150 (218)
Q Consensus 76 ~~~~~~N~v~LiGrIg~dPelr~~~n-G--~--~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae 150 (218)
.|.|++++|.|.|+|..--++|++.+ | . .++++.|+= .|-=+++++|+ ..|+
T Consensus 58 dL~pg~~~vtI~aRV~~~~~~Rt~~~~~~~~eGkv~~v~l~D----------------------eTG~Ir~TlW~-d~ad 114 (485)
T PRK07211 58 DIEPGMDEVKFLAKVLSIGDLRTFERDGEDEDGRVINVEVAD----------------------ETGSVRVAFWD-EQAV 114 (485)
T ss_pred hCCCCCCceEEEEEEeEccCceEEEeCCCCCCcEEEEEEEEc----------------------CCCeEEEEEec-hHhH
Confidence 56689999999999999988888863 2 2 444444432 12247999998 7888
Q ss_pred HHHhhcCCCCEEEEEEEeE
Q 027819 151 VVMKHLVPGSTIYVEGNLE 169 (218)
Q Consensus 151 ~v~~~LkKG~~V~VeG~L~ 169 (218)
.....|++|+.++|.|+..
T Consensus 115 ~~~~~Le~GdV~~I~~~~~ 133 (485)
T PRK07211 115 AAEEELEVGQVLRIKGRPK 133 (485)
T ss_pred hhhcccCCCCEEEEeceEe
Confidence 8888999999999998763
No 38
>PF11506 DUF3217: Protein of unknown function (DUF3217); InterPro: IPR024506 This family of proteins with unknown function appears to be restricted to Mycoplasma.; PDB: 2HQL_E.
Probab=92.28 E-value=4 Score=30.99 Aligned_cols=87 Identities=17% Similarity=0.111 Sum_probs=56.1
Q ss_pred CCceEEEEEEeCcCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHhhcCCC
Q 027819 80 GIFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLVPG 159 (218)
Q Consensus 80 ~~N~v~LiGrIg~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~~LkKG 159 (218)
++|.|.|.|-|-. .+-..+ +.-.-.++...|.|-+ +.-|+|+-+-+-| ++|--+.+|.+|=
T Consensus 1 MLN~V~LEG~IeS---~kWS~~-KTGF~VTI~QkR~FG~--------------r~FTDyyViYAN~-QL~~ELEky~~k~ 61 (104)
T PF11506_consen 1 MLNTVFLEGEIES---YKWSKK-KTGFLVTIKQKRKFGE--------------RTFTDYYVIYANG-QLAFELEKYTQKH 61 (104)
T ss_dssp --EEEEEEEEEEE---EEE-TT-SSEEEEEEEEEEEETT--------------EEEEEEEEEEEEH-HHHHHHHHHHTT-
T ss_pred CcceEEEeceeeh---hccccc-CceEEEEEeehhhhcc--------------ccceeEEEEEECC-eeehhHHHhhhhc
Confidence 4799999999866 222222 2112233444444422 2369999999997 9999999999999
Q ss_pred CEEEEEEEeEeeeeeCCCCCeEEEEEEE
Q 027819 160 STIYVEGNLEQKVFNDPITGLVRRIREI 187 (218)
Q Consensus 160 ~~V~VeG~L~t~~~~d~~dG~~r~~~eI 187 (218)
..+.|+|.|++.. ++..+-....+++
T Consensus 62 k~isieG~L~TY~--ekkS~iWKT~I~~ 87 (104)
T PF11506_consen 62 KTISIEGILRTYL--EKKSKIWKTTIEA 87 (104)
T ss_dssp SEEEEEEEEEEEE--ETTTTEEEEEEEE
T ss_pred eEEEEeeehhhHH--HHhcccceeeEEE
Confidence 9999999998753 4325655544443
No 39
>PRK15491 replication factor A; Provisional
Probab=92.14 E-value=1.6 Score=40.86 Aligned_cols=90 Identities=18% Similarity=0.217 Sum_probs=61.9
Q ss_pred CCCceEEEEEEeCcCCeEEEc--CCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHhhc
Q 027819 79 PGIFKAILVGQVGQSPVQKKL--KSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHL 156 (218)
Q Consensus 79 ~~~N~v~LiGrIg~dPelr~~--~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~~L 156 (218)
++...|.+.|+|..--+.|.+ ..|...-.|++.... . . . -+++++|+ ..|+.+ ..|
T Consensus 174 ~~~~~V~I~g~V~~~~~~r~~~~~~G~~~~v~~~~l~D----e----t----------G--~Ir~t~W~-~~a~~~-~~l 231 (374)
T PRK15491 174 DGDSDINIVGKVLDISDVRTFQKKDGSQGRVRNITIGD----E----T----------G--KIRVTLWD-GKTDLA-DKL 231 (374)
T ss_pred CCCccEEEEEEEEEccCceEEEecCCCeEEEEEEEEEC----C----C----------C--eEEEEEec-chhccc-ccC
Confidence 345669999999998776666 367755556665532 1 1 1 28999998 688876 569
Q ss_pred CCCCEEEEEE-EeEeeeeeCCCCCeEEEEEEEEEEeCCcEEEe
Q 027819 157 VPGSTIYVEG-NLEQKVFNDPITGLVRRIREIAIRRNGRLVFL 198 (218)
Q Consensus 157 kKG~~V~VeG-~L~t~~~~d~~dG~~r~~~eI~v~~~g~i~~L 198 (218)
..|+.|+|.+ +.+.+.|.. .+||.+...+.|..+
T Consensus 232 ~~Gd~V~i~~~~~r~~~~~g--------~~El~~~~~s~I~~~ 266 (374)
T PRK15491 232 ENGDSVEIINGYARTNNYSQ--------EVEIQIGNHGSLRKT 266 (374)
T ss_pred CCCCEEEEEeceEEEeccCC--------CEEEEeCCCceEEEC
Confidence 9999999966 688777743 346666655555554
No 40
>COG3390 Uncharacterized protein conserved in archaea [Function unknown]
Probab=90.94 E-value=2 Score=36.93 Aligned_cols=78 Identities=10% Similarity=0.115 Sum_probs=56.7
Q ss_pred CCCceEEEEEEeCcCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHhhcCC
Q 027819 79 PGIFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLVP 158 (218)
Q Consensus 79 ~~~N~v~LiGrIg~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~~LkK 158 (218)
.-+|++.|+|.|+..+-+- .+..+.+++|+-. ..+.|.-.--|. ..|..+.+.+.+
T Consensus 43 ~k~nRifivGtltek~~i~---ed~~~~R~rVvDp--------------------TGsF~Vyag~yq-PEa~a~l~~ve~ 98 (196)
T COG3390 43 LKVNRIFIVGTLTEKEGIG---EDREYWRIRVVDP--------------------TGSFYVYAGQYQ-PEAKAFLEDVEV 98 (196)
T ss_pred hheeEEEEEEEEEeccCcC---CcccEEEEEEecC--------------------CceEEEEcCCCC-hHHHHHHHhccC
Confidence 3679999999999966552 2356888888531 146676555565 567778888999
Q ss_pred CCEEEEEEEeEeeeeeCCCCCeEEE
Q 027819 159 GSTIYVEGNLEQKVFNDPITGLVRR 183 (218)
Q Consensus 159 G~~V~VeG~L~t~~~~d~~dG~~r~ 183 (218)
++.|.|.|.+++ |++. +|....
T Consensus 99 ~~~VaViGKi~~--y~~d-~g~~~~ 120 (196)
T COG3390 99 PDLVAVIGKIRT--YRTD-EGVVLF 120 (196)
T ss_pred CceEEEecccce--eecC-CCceEE
Confidence 999999998865 7776 676544
No 41
>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=90.69 E-value=0.64 Score=34.81 Aligned_cols=75 Identities=17% Similarity=0.338 Sum_probs=50.1
Q ss_pred EEEEEeCcCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchh--HHHHHhhcCCCCEE
Q 027819 85 ILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERL--GGVVMKHLVPGSTI 162 (218)
Q Consensus 85 ~LiGrIg~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~--Ae~v~~~LkKG~~V 162 (218)
.+.|.|.+-|. ...+|..+ |+| +|. ..-++|++|. .. +..+...|+.||.|
T Consensus 2 ~v~GeVs~~~~--~~~sGH~y--Ftl------kD~----------------~~~i~cv~f~-~~g~~~~~~~~l~~Gd~V 54 (91)
T cd04482 2 RVTGKVVEEPR--TIEGGHVF--FKI------SDG----------------TGEIDCAAYE-PTKEFRDVVRLLIPGDEV 54 (91)
T ss_pred EEEEEEeCCee--cCCCCCEE--EEE------ECC----------------CcEEEEEEEC-cccccccccCCCCCCCEE
Confidence 47788887552 22577744 555 111 1246899995 55 56777789999999
Q ss_pred EEEEEeEeeeeeCCCCCeEEEEEEEEEEeCCcEEEeeCCC
Q 027819 163 YVEGNLEQKVFNDPITGLVRRIREIAIRRNGRLVFLGKGG 202 (218)
Q Consensus 163 ~VeG~L~t~~~~d~~dG~~r~~~eI~v~~~g~i~~L~~k~ 202 (218)
.|.|.+.... .+.++ +++.++-+.
T Consensus 55 ~v~G~v~~y~-------------ql~ve---~l~~~glg~ 78 (91)
T cd04482 55 TVYGSVRPGT-------------TLNLE---KLRVIRLAR 78 (91)
T ss_pred EEEEEEecCC-------------EEEEE---EEEECCCcc
Confidence 9999976553 46677 666665443
No 42
>PRK07211 replication factor A; Reviewed
Probab=90.48 E-value=2.8 Score=40.83 Aligned_cols=98 Identities=16% Similarity=0.219 Sum_probs=63.8
Q ss_pred cccccCCCCCCCceEEEEEEeCcCCeEEEcC--CCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCch
Q 027819 70 DRPLENGLDPGIFKAILVGQVGQSPVQKKLK--SGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPER 147 (218)
Q Consensus 70 ~r~~~~~~~~~~N~v~LiGrIg~dPelr~~~--nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k 147 (218)
+.|+. .|.++++.+.|+|+|..--++|++. +|..--.|++.... . +--+++++|+ .
T Consensus 161 ~~~I~-dL~~~~~~v~I~grV~~v~~iRtf~r~dGseGkv~sv~L~D----e----------------TG~IR~TlW~-d 218 (485)
T PRK07211 161 TYTVE-DLSLGLSDVTLVGVVLDTDSVRTFDRDDGSEGRVSNLTVGD----E----------------TGRVRVTLWD-D 218 (485)
T ss_pred CccHH-HcCCCCCceEEEEEEEEcCCCeEEECCCCCeeEEEEEEEEc----C----------------CCeEEEEEec-h
Confidence 34544 4456889999999999887777775 45444445555532 1 1138999998 7
Q ss_pred hHHHHHhhcCCCCEEEEEEEeEeeeeeCCCCCeEEEEEEEEEEeCCcEEEee
Q 027819 148 LGGVVMKHLVPGSTIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGRLVFLG 199 (218)
Q Consensus 148 ~Ae~v~~~LkKG~~V~VeG~L~t~~~~d~~dG~~r~~~eI~v~~~g~i~~L~ 199 (218)
.|+.+ ..|.+|+.|.|.+ -+.+.|.. .++|.+...+.|..+.
T Consensus 219 ~Ad~~-~~le~G~Vv~I~~-a~Vre~~g--------~~ELsl~~~s~I~~~~ 260 (485)
T PRK07211 219 RADLA-EELDAGESVEIVD-GYVRERDG--------SLELHVGDRGAVEEVD 260 (485)
T ss_pred hhhhh-ccCCCCCEEEEEe-eEEEecCC--------cEEEEECCCceEEECC
Confidence 88887 5699999999975 23334532 2355555445555553
No 43
>PF11325 DUF3127: Domain of unknown function (DUF3127); InterPro: IPR021474 This bacterial family of proteins has no known function.
Probab=89.53 E-value=4.2 Score=30.46 Aligned_cols=47 Identities=17% Similarity=0.159 Sum_probs=36.0
Q ss_pred eeEEEEEEeCchhHHHHHhhcCCCCEEEEEEEeEeeeeeCCCCCeEEEEEEEEEE
Q 027819 136 VQWHRVSVYPERLGGVVMKHLVPGSTIYVEGNLEQKVFNDPITGLVRRIREIAIR 190 (218)
Q Consensus 136 t~w~~V~~wg~k~Ae~v~~~LkKG~~V~VeG~L~t~~~~d~~dG~~r~~~eI~v~ 190 (218)
+..+.+.+||+ .++.+. .++.|+.|.|.-+|+.+.|+. ++...|.+=
T Consensus 35 P~~i~f~~~~d-k~~~l~-~~~~Gd~V~Vsf~i~~RE~~g------r~fn~i~aW 81 (84)
T PF11325_consen 35 PQKICFEFWGD-KIDLLD-NFQVGDEVKVSFNIEGREWNG------RWFNSIRAW 81 (84)
T ss_pred CceEEEEEEcc-hhhhhc-cCCCCCEEEEEEEeeccEecc------eEeeEeEEE
Confidence 56678999994 455444 599999999999999999963 455666554
No 44
>PRK15491 replication factor A; Provisional
Probab=87.39 E-value=2.6 Score=39.54 Aligned_cols=93 Identities=14% Similarity=0.211 Sum_probs=60.6
Q ss_pred CCCCCCCceEEEEEEeCcCCeEEEcC--CCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHH
Q 027819 75 NGLDPGIFKAILVGQVGQSPVQKKLK--SGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVV 152 (218)
Q Consensus 75 ~~~~~~~N~v~LiGrIg~dPelr~~~--nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v 152 (218)
..|.++++.|.|.|+|.+--+.|++. .|..--.|++-+.. .|--+++++|+ ..|+.+
T Consensus 61 ~dL~~~~~~v~i~arVl~~~~~R~f~r~dGs~g~v~~~~v~D--------------------eTG~ir~tlW~-~~a~~~ 119 (374)
T PRK15491 61 ADINESSSNVNFTAKVVSIFEPKEFNRNDGTTGRVGNIIVAD--------------------ETGSIRLTLWD-DLADLI 119 (374)
T ss_pred HHCCCCCCceEEEEEEeeccCCeeeecCCCCceEEEEEEEEc--------------------CCCeEEEEEEC-chhhhh
Confidence 35667889999999999987777763 45333334443321 12237999998 688877
Q ss_pred H-hhcCCCCEEEEEEEeEeeeeeCCCCCeEEEEEEEEEEeCCcEEEe
Q 027819 153 M-KHLVPGSTIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGRLVFL 198 (218)
Q Consensus 153 ~-~~LkKG~~V~VeG~L~t~~~~d~~dG~~r~~~eI~v~~~g~i~~L 198 (218)
. .-|..|+.|.|.|.. ...| .| +||.+...+.|.-+
T Consensus 120 ~~~~le~G~v~~I~~~~-~~~y----~g-----~Ei~i~~~~~i~~~ 156 (374)
T PRK15491 120 KTGDIEVGKSLNISGYA-KEGY----SG-----IEVNIGRYGGISES 156 (374)
T ss_pred ccCCcCCCCEEEEeeee-ccCc----cc-----EEEEeCCCceeeec
Confidence 6 469999999999851 1112 22 47777744444443
No 45
>PRK13480 3'-5' exoribonuclease YhaM; Provisional
Probab=87.18 E-value=4.1 Score=37.40 Aligned_cols=60 Identities=12% Similarity=0.159 Sum_probs=45.7
Q ss_pred eCcCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHhhcCCCCEEEEEEEeE
Q 027819 90 VGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLVPGSTIYVEGNLE 169 (218)
Q Consensus 90 Ig~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~~LkKG~~V~VeG~L~ 169 (218)
+.++.++++++||++|..++++=. .| -++..+|. . .+.....+++|+.|.|.|.+.
T Consensus 19 lv~~~~~~~~knG~~yl~l~l~D~----------tG------------~I~ak~W~-~-~~~~~~~~~~g~vv~v~G~v~ 74 (314)
T PRK13480 19 LIKSATKGVASNGKPFLTLILQDK----------SG------------DIEAKLWD-V-SPEDEATYVPETIVHVKGDII 74 (314)
T ss_pred EEEEceeeecCCCCeEEEEEEEcC----------Cc------------EEEEEeCC-C-ChhhHhhcCCCCEEEEEEEEE
Confidence 456788999999999999988532 12 26888996 3 444566799999999999997
Q ss_pred eeeeeC
Q 027819 170 QKVFND 175 (218)
Q Consensus 170 t~~~~d 175 (218)
. |.+
T Consensus 75 ~--y~g 78 (314)
T PRK13480 75 N--YRG 78 (314)
T ss_pred E--ECC
Confidence 4 644
No 46
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain
Probab=86.16 E-value=2.5 Score=31.97 Aligned_cols=63 Identities=16% Similarity=0.240 Sum_probs=46.9
Q ss_pred CceEEEEEEeCcCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHH-hhcCCC
Q 027819 81 IFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVM-KHLVPG 159 (218)
Q Consensus 81 ~N~v~LiGrIg~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~-~~LkKG 159 (218)
+..+-+.|.|.. ++...+|.. -|+|.-. ..=++|++|. ..+..+. ..++.|
T Consensus 21 ~~~vwV~GEIs~---~~~~~~gh~--YftLkD~----------------------~a~i~~~~~~-~~~~~i~~~~l~~G 72 (99)
T PF13742_consen 21 LPNVWVEGEISN---LKRHSSGHV--YFTLKDE----------------------EASISCVIFR-SRARRIRGFDLKDG 72 (99)
T ss_pred cCCEEEEEEEee---cEECCCceE--EEEEEcC----------------------CcEEEEEEEH-HHHhhCCCCCCCCC
Confidence 578899999987 444456664 4565321 1347999997 7777777 789999
Q ss_pred CEEEEEEEeEee
Q 027819 160 STIYVEGNLEQK 171 (218)
Q Consensus 160 ~~V~VeG~L~t~ 171 (218)
++|.|.|++...
T Consensus 73 ~~V~v~g~~~~y 84 (99)
T PF13742_consen 73 DKVLVRGRVSFY 84 (99)
T ss_pred CEEEEEEEEEEE
Confidence 999999999764
No 47
>cd04488 RecG_wedge_OBF RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal (wedge) domain of Escherichia coli RecG. RecG is a branched-DNA-specific helicase, which catalyzes the interconversion of a DNA replication fork to a four-stranded (Holliday) junction in vivo and in vitro. This interconversion provides a route to repair stalled forks. The RecG monomer contains three domains. The N-terminal domain is named for its wedge structure, and may provide the specificity of RecG for binding branched-DNA structures. During the reversal of fork to Holliday junction, the wedge domain is fixed at the junction of the fork where the leading and lagging strand duplex arms meet, and is thought to promote the unwinding of the nascent leading and lagging strands. In order to form the Holliday junction, these nascent strands would be annealed, and the parental strands reannealed. The wedge domain may also be a processivity factor of RecG on these branched cha
Probab=85.85 E-value=5.1 Score=27.00 Aligned_cols=31 Identities=19% Similarity=0.346 Sum_probs=25.0
Q ss_pred EEEEEeCchhHHHHHhhcCCCCEEEEEEEeEee
Q 027819 139 HRVSVYPERLGGVVMKHLVPGSTIYVEGNLEQK 171 (218)
Q Consensus 139 ~~V~~wg~k~Ae~v~~~LkKG~~V~VeG~L~t~ 171 (218)
+.|+.|+ . ..++.+.+++|+.|+|.|.+...
T Consensus 31 i~~~~F~-~-~~~~~~~~~~G~~~~v~Gkv~~~ 61 (75)
T cd04488 31 LTLVFFN-F-QPYLKKQLPPGTRVRVSGKVKRF 61 (75)
T ss_pred EEEEEEC-C-CHHHHhcCCCCCEEEEEEEEeec
Confidence 6888886 2 34667889999999999999763
No 48
>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=85.77 E-value=6.8 Score=39.03 Aligned_cols=101 Identities=14% Similarity=0.202 Sum_probs=68.0
Q ss_pred cccccCCCCCCCceEEEEEEeCcCCeEEEcCC--Cc-EEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCc
Q 027819 70 DRPLENGLDPGIFKAILVGQVGQSPVQKKLKS--GR-TVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPE 146 (218)
Q Consensus 70 ~r~~~~~~~~~~N~v~LiGrIg~dPelr~~~n--G~-~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~ 146 (218)
+-|++ .|-+++++++|.|||..--++|.+.+ |. .+ |+|..- | . +.=+++.+|+
T Consensus 180 ~~pI~-~L~py~~~wtIkaRV~~Ks~ir~~~~~~gegkv--fsv~L~----D-e---------------gg~Irat~f~- 235 (608)
T TIGR00617 180 VMPIA-SLSPYQNKWTIKARVTNKSEIRTWSNARGEGKL--FNVELL----D-E---------------SGEIRATAFN- 235 (608)
T ss_pred eEEHH-HCCCCCCceEEEEEEEeccccceecCCCCCcee--eEEEEe----c-C---------------CCeEEEEECc-
Confidence 34555 67788999999999999998888754 22 34 444332 2 1 1136999998
Q ss_pred hhHHHHHhhcCCCCEEEEEE-EeEee--eeeCCCCCeEEEEEEEEEEeCCcEEEee
Q 027819 147 RLGGVVMKHLVPGSTIYVEG-NLEQK--VFNDPITGLVRRIREIAIRRNGRLVFLG 199 (218)
Q Consensus 147 k~Ae~v~~~LkKG~~V~VeG-~L~t~--~~~d~~dG~~r~~~eI~v~~~g~i~~L~ 199 (218)
..|+.....|+.|+.++|.+ +++.. .|.. ....+||....+..|+.+.
T Consensus 236 ~~~dkf~~~l~eG~VY~Is~~~Vk~an~~y~~-----~~~~yei~f~~~T~I~~~~ 286 (608)
T TIGR00617 236 EQADKFYDIIQEGKVYYISKGSLKPANKQFTN-----LGNDYEMTLDRDTVIEECE 286 (608)
T ss_pred hHHHHHhhhcccCCEEEECceEEEEccccccC-----CCCCEEEEECCCeEEEECC
Confidence 79999999999999999965 44432 3332 1224677777544555543
No 49
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=85.19 E-value=17 Score=28.78 Aligned_cols=88 Identities=17% Similarity=0.318 Sum_probs=54.4
Q ss_pred CCCCCCceEEEEEEeCcC--CeEEEcCCCc-EEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHH
Q 027819 76 GLDPGIFKAILVGQVGQS--PVQKKLKSGR-TVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVV 152 (218)
Q Consensus 76 ~~~~~~N~v~LiGrIg~d--Pelr~~~nG~-~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v 152 (218)
.|.++++.|.++|.|-.- +.....++|. .+..+.|+ |+ |--+++.+|+ ..|+
T Consensus 9 dL~~g~~~v~~~~~V~~i~~~~~~~~k~~~~~v~~~~l~------D~----------------TG~I~~tlW~-~~a~-- 63 (129)
T PRK06461 9 DLKPGMERVNVTVRVLEVGEPKVIQTKGGPRTISEAVVG------DE----------------TGRVKLTLWG-EQAG-- 63 (129)
T ss_pred HcCCCCCceEEEEEEEEcCCceEEEeCCCceEEEEEEEE------CC----------------CCEEEEEEeC-Cccc--
Confidence 344566788899999863 3333455553 35555442 11 2237999998 5543
Q ss_pred HhhcCCCCEEEEE-EEeEeeeeeCCCCCeEEEEEEEEEEeCCcEEEeeC
Q 027819 153 MKHLVPGSTIYVE-GNLEQKVFNDPITGLVRRIREIAIRRNGRLVFLGK 200 (218)
Q Consensus 153 ~~~LkKG~~V~Ve-G~L~t~~~~d~~dG~~r~~~eI~v~~~g~i~~L~~ 200 (218)
.|++|+.|.|. |..+ .|. | .++|.+...+.|..++.
T Consensus 64 --~l~~GdvV~I~na~v~--~f~----G----~lqL~i~~~~~i~~~~~ 100 (129)
T PRK06461 64 --SLKEGEVVEIENAWTT--LYR----G----KVQLNVGKYGSISESDD 100 (129)
T ss_pred --cCCCCCEEEEECcEEe--eeC----C----EEEEEECCCEEEEECCc
Confidence 58999999999 5555 353 3 24566665556776654
No 50
>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed
Probab=85.09 E-value=7.2 Score=36.81 Aligned_cols=80 Identities=14% Similarity=0.244 Sum_probs=56.7
Q ss_pred CceEEEEEEeCcCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHhhcCCCC
Q 027819 81 IFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLVPGS 160 (218)
Q Consensus 81 ~N~v~LiGrIg~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~~LkKG~ 160 (218)
+..|.+.|.|.. ++...+|+.| |+|. |. ..-++|++|. ..+..+.-.++.|+
T Consensus 23 ~~~v~v~gEis~---~~~~~sGH~Y--f~Lk------d~----------------~a~i~~~~~~-~~~~~~~~~~~~G~ 74 (438)
T PRK00286 23 LGQVWVRGEISN---FTRHSSGHWY--FTLK------DE----------------IAQIRCVMFK-GSARRLKFKPEEGM 74 (438)
T ss_pred CCcEEEEEEeCC---CeeCCCCeEE--EEEE------cC----------------CcEEEEEEEc-ChhhcCCCCCCCCC
Confidence 578999999988 4545678765 5652 11 2247999997 77777777799999
Q ss_pred EEEEEEEeEeeeeeCCCCCeEEEEEEEEEEeCCcEEEee
Q 027819 161 TIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGRLVFLG 199 (218)
Q Consensus 161 ~V~VeG~L~t~~~~d~~dG~~r~~~eI~v~~~g~i~~L~ 199 (218)
.|.|.|++.. |+. .|. +.+.|. +|+..+
T Consensus 75 ~v~v~g~~~~--y~~--~g~----~ql~v~---~i~~~g 102 (438)
T PRK00286 75 KVLVRGKVSL--YEP--RGD----YQLIVE---EIEPAG 102 (438)
T ss_pred EEEEEEEEEE--ECC--CCC----EEEEEE---EeeeCC
Confidence 9999999987 544 453 456666 555443
No 51
>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=83.57 E-value=3.3 Score=39.40 Aligned_cols=74 Identities=15% Similarity=0.232 Sum_probs=53.6
Q ss_pred CceEEEEEEeCcCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHhhcCCCC
Q 027819 81 IFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLVPGS 160 (218)
Q Consensus 81 ~N~v~LiGrIg~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~~LkKG~ 160 (218)
+..|.+.|.|.. ++...+|+.| |+| +|. ..=++|++|. ..+..+.-.++-|+
T Consensus 17 ~~~v~V~GEisn---~~~~~sGH~Y--FtL------kD~----------------~a~i~~vmf~-~~~~~l~f~~~~G~ 68 (432)
T TIGR00237 17 FLQVWIQGEISN---FTQPVSGHWY--FTL------KDE----------------NAQVRCVMFR-GNNNRLKFRPQNGQ 68 (432)
T ss_pred CCcEEEEEEecC---CeeCCCceEE--EEE------EcC----------------CcEEEEEEEc-ChhhCCCCCCCCCC
Confidence 568999999988 5555788865 555 221 2236999997 77777777799999
Q ss_pred EEEEEEEeEeeeeeCCCCCeEEEEEEEEEE
Q 027819 161 TIYVEGNLEQKVFNDPITGLVRRIREIAIR 190 (218)
Q Consensus 161 ~V~VeG~L~t~~~~d~~dG~~r~~~eI~v~ 190 (218)
.|.|.|++.. |+. .|. +.+.|+
T Consensus 69 ~V~v~g~v~~--y~~--~G~----~ql~v~ 90 (432)
T TIGR00237 69 QVLVRGGISV--YEP--RGD----YQIICF 90 (432)
T ss_pred EEEEEEEEEE--ECC--CCc----EEEEEE
Confidence 9999999975 544 453 456666
No 52
>KOG3416 consensus Predicted nucleic acid binding protein [General function prediction only]
Probab=83.06 E-value=23 Score=28.68 Aligned_cols=108 Identities=20% Similarity=0.242 Sum_probs=66.0
Q ss_pred CCCceEEEEEEeCcCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHhhcCC
Q 027819 79 PGIFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLVP 158 (218)
Q Consensus 79 ~~~N~v~LiGrIg~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~~LkK 158 (218)
|+++.+.++=-|-.+-....+++|+.|..+.||- .|--+++.+|+| ....++.
T Consensus 12 P~~kN~~v~fIvl~~g~~tkTkdg~~v~~~kVaD----------------------~TgsI~isvW~e-----~~~~~~P 64 (134)
T KOG3416|consen 12 PGLKNINVTFIVLEYGRATKTKDGHEVRSCKVAD----------------------ETGSINISVWDE-----EGCLIQP 64 (134)
T ss_pred hhhhcceEEEEEEeeceeeeccCCCEEEEEEEec----------------------ccceEEEEEecC-----cCcccCC
Confidence 3445555554455555567788999999888853 244578999984 4457899
Q ss_pred CCEEEEEEEeE------eeeeeCCCCCeEEEEEEEEEE--e--CCcEEEeeCCCCCCCCCCccCCCCc
Q 027819 159 GSTIYVEGNLE------QKVFNDPITGLVRRIREIAIR--R--NGRLVFLGKGGDAQPPSPSEVRGAG 216 (218)
Q Consensus 159 G~~V~VeG~L~------t~~~~d~~dG~~r~~~eI~v~--~--~g~i~~L~~k~~~~~~~~~e~~~~~ 216 (218)
||.|.+.|-.- ..-|..+ .|+....-|+.+- + +..++.+- .+...+......|+|
T Consensus 65 GDIirLt~Gy~Si~qg~LtL~~GK-~Ge~~KiGef~~vf~etpn~S~~~~p--~n~~n~~~~~psg~~ 129 (134)
T KOG3416|consen 65 GDIIRLTGGYASIFQGCLTLYVGK-GGEVQKIGEFCMVFSETPNISIQWAP--MNPMNPDLLRPSGGG 129 (134)
T ss_pred ccEEEecccchhhhcCceEEEecC-CceEeEeeeeEEeeecCCCccccccC--CCccCccccCCCCCC
Confidence 99998887332 2346666 7876666565433 1 33333332 234455555555554
No 53
>PRK14699 replication factor A; Provisional
Probab=81.08 E-value=6.1 Score=38.41 Aligned_cols=76 Identities=13% Similarity=0.175 Sum_probs=52.7
Q ss_pred CCCCCCceEEEEEEeCcCCeEEEcC--CCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHH
Q 027819 76 GLDPGIFKAILVGQVGQSPVQKKLK--SGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVM 153 (218)
Q Consensus 76 ~~~~~~N~v~LiGrIg~dPelr~~~--nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~ 153 (218)
.+.+++..|.+.|+|-.-...|++. +|..--..++.+.. .|=-+++++|. .+|..+.
T Consensus 62 di~~~~~~v~i~~rVl~i~~~r~f~r~dG~~g~v~~~~iaD--------------------eTG~ir~tlW~-~~a~~~~ 120 (484)
T PRK14699 62 NITPESGPVNFIARVVSVFDTKEFTRNDGTIGRVGNLIVGD--------------------ETGKIKLTLWD-NMADLIK 120 (484)
T ss_pred HccCCCceEEEEEEEEEecCceEEecCCCCceEEEEEEEec--------------------CCCeEEEEEec-Cccchhh
Confidence 4556778999999999987777773 45432222232221 23347999997 6787777
Q ss_pred h-hcCCCCEEEEEEEeEeeeee
Q 027819 154 K-HLVPGSTIYVEGNLEQKVFN 174 (218)
Q Consensus 154 ~-~LkKG~~V~VeG~L~t~~~~ 174 (218)
. .|++||.|.|.|. .+.|.
T Consensus 121 ~g~l~~GDvv~I~~~--~r~~~ 140 (484)
T PRK14699 121 AGKIKAGQTLQISGY--AKQGY 140 (484)
T ss_pred hcCCCCCCEEEEcce--eccCC
Confidence 6 5999999999995 55564
No 54
>PRK07373 DNA polymerase III subunit alpha; Reviewed
Probab=81.02 E-value=9.1 Score=36.81 Aligned_cols=64 Identities=14% Similarity=0.172 Sum_probs=48.1
Q ss_pred eEEEEEEeCcCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHhhcCCCCEE
Q 027819 83 KAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLVPGSTI 162 (218)
Q Consensus 83 ~v~LiGrIg~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~~LkKG~~V 162 (218)
+|.+.|-|.. ...+.+++|..++-+++.-. +--+.|++|. +.-+.....|+.|..|
T Consensus 282 ~v~vaG~I~~-ik~~~TKkG~~maf~~leD~----------------------tG~ie~vvFp-~~y~~~~~~l~~~~~v 337 (449)
T PRK07373 282 KVSAVVMLNE-VKKIVTKKGDPMAFLQLEDL----------------------SGQSEAVVFP-KSYERISELLQVDARL 337 (449)
T ss_pred EEEEEEEEEE-eEecccCCCCEEEEEEEEEC----------------------CCCEEEEECH-HHHHHHHHHhccCCEE
Confidence 5677777776 55566778887776666321 2226899997 7888888999999999
Q ss_pred EEEEEeEe
Q 027819 163 YVEGNLEQ 170 (218)
Q Consensus 163 ~VeG~L~t 170 (218)
+|+|+++.
T Consensus 338 ~v~G~v~~ 345 (449)
T PRK07373 338 IIWGKVDR 345 (449)
T ss_pred EEEEEEEe
Confidence 99999964
No 55
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=80.14 E-value=9.7 Score=41.06 Aligned_cols=73 Identities=16% Similarity=0.141 Sum_probs=54.4
Q ss_pred CCceEEEEEEeCcCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCc--hhHHHHHhhcC
Q 027819 80 GIFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPE--RLGGVVMKHLV 157 (218)
Q Consensus 80 ~~N~v~LiGrIg~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~--k~Ae~v~~~Lk 157 (218)
..+.|++.|.|-. .+.+.+.+|+.+..|.|. . | ++-+.|..|.. +..+ ....|+
T Consensus 6 ~~~~~~~~g~i~~-~~~~~~~~~~~~~~~~~~--d-~-------------------~~s~~~k~f~~~~~~~~-~~~~~~ 61 (1213)
T TIGR01405 6 EENRVKIEGYIFK-IEIKELKSGRTLLKIKVT--D-Y-------------------TDSLILKKFLKSEEDPE-KFDGIK 61 (1213)
T ss_pred cCCeEEEEEEEEE-EEeEeccCCCEEEEEEEE--c-C-------------------CCCEEEEEecccccchH-HHhhcC
Confidence 4589999999965 788899999988888774 2 1 23356666652 1223 335699
Q ss_pred CCCEEEEEEEeEeeeeeCC
Q 027819 158 PGSTIYVEGNLEQKVFNDP 176 (218)
Q Consensus 158 KG~~V~VeG~L~t~~~~d~ 176 (218)
+|+-|.|.|.++...|..+
T Consensus 62 ~g~~~~~~g~~~~d~~~~~ 80 (1213)
T TIGR01405 62 IGKWVRARGKIELDNFSRD 80 (1213)
T ss_pred CCcEEEEEEEEeccCCCCc
Confidence 9999999999999998753
No 56
>cd04490 PolII_SU_OBF PolII_SU_OBF: A subfamily of OB folds corresponding to the OB fold found in Pyrococcus abyssi DNA polymerase II (PolII) small subunit. PolII is a family D DNA polymerase, having a 3-prime to 5-prime exonuclease activity. P. abyssi PolII is heterodimeric. The large subunit appears to be the polymerase, and the small subunit may be the exonuclease. The small subunit contains a calcineurin-like phosphatase superfamily domain C-terminal to this OB-fold domain.
Probab=79.34 E-value=12 Score=27.21 Aligned_cols=30 Identities=17% Similarity=0.165 Sum_probs=25.3
Q ss_pred EEEEEEeCchhHH--HHHhhcCCCCEEEEEEEe
Q 027819 138 WHRVSVYPERLGG--VVMKHLVPGSTIYVEGNL 168 (218)
Q Consensus 138 w~~V~~wg~k~Ae--~v~~~LkKG~~V~VeG~L 168 (218)
-+.|.+|+ +.-+ .....|+.|..|+|.|++
T Consensus 29 ~~Ev~~F~-~~~~~~~~~~~l~~d~~v~v~g~v 60 (79)
T cd04490 29 RITVLLTK-DKEELFEEAEDILPDEVIGVSGTV 60 (79)
T ss_pred EEEEEEeC-chhhhhhhhhhccCCCEEEEEEEE
Confidence 37899998 4555 677889999999999999
No 57
>PRK05673 dnaE DNA polymerase III subunit alpha; Validated
Probab=78.28 E-value=11 Score=40.50 Aligned_cols=65 Identities=14% Similarity=0.111 Sum_probs=49.3
Q ss_pred ceEEEEEEeCcCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHhhcCCCCE
Q 027819 82 FKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLVPGST 161 (218)
Q Consensus 82 N~v~LiGrIg~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~~LkKG~~ 161 (218)
..|.+.|-|.. ...+.+++|++++.++|.-. +--+.|++|. +.-+.....|+.|..
T Consensus 978 ~~V~v~G~I~~-vk~~~TKkG~~mafltLeD~----------------------TG~iEvviFp-~~ye~~~~~L~~g~i 1033 (1135)
T PRK05673 978 SVVTVAGLVVS-VRRRVTKRGNKMAIVTLEDL----------------------SGRIEVMLFS-EALEKYRDLLEEDRI 1033 (1135)
T ss_pred ceEEEEEEEEE-EEecccCCCCeEEEEEEEeC----------------------CCcEEEEECH-HHHHHHHHHhccCCE
Confidence 35777777765 66677889998887777431 2236899997 665777888999999
Q ss_pred EEEEEEeEe
Q 027819 162 IYVEGNLEQ 170 (218)
Q Consensus 162 V~VeG~L~t 170 (218)
|+|+|+++.
T Consensus 1034 V~V~GkVe~ 1042 (1135)
T PRK05673 1034 VVVKGQVSF 1042 (1135)
T ss_pred EEEEEEEEe
Confidence 999999964
No 58
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=78.17 E-value=10 Score=41.60 Aligned_cols=75 Identities=19% Similarity=0.234 Sum_probs=54.9
Q ss_pred CCCceEEEEEEeCcCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCc-hhHHHHHhhcC
Q 027819 79 PGIFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPE-RLGGVVMKHLV 157 (218)
Q Consensus 79 ~~~N~v~LiGrIg~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~-k~Ae~v~~~Lk 157 (218)
...+.|++.|.|-. .+.+.+.+|+.+..|.|. . | ++-+.|..|.+ +.-......|+
T Consensus 234 ~~~~~v~i~G~if~-~e~~~~k~~~~~~~~~~t--d-~-------------------~~s~~~k~f~~~~~~~~~~~~~~ 290 (1437)
T PRK00448 234 EEERRVVVEGYVFK-VEIKELKSGRHILTFKIT--D-Y-------------------TSSIIVKKFSRDKEDLKKFDEIK 290 (1437)
T ss_pred ccCCeEEEEEEEEE-EEEEeccCCCEEEEEEEE--c-C-------------------CCCEEEEEEecCcchhHHHhcCC
Confidence 35578999999966 888899999988888883 1 1 23356666641 11123446699
Q ss_pred CCCEEEEEEEeEeeeeeCC
Q 027819 158 PGSTIYVEGNLEQKVFNDP 176 (218)
Q Consensus 158 KG~~V~VeG~L~t~~~~d~ 176 (218)
+|+-|.|.|.++...|...
T Consensus 291 ~g~~v~~~g~~~~d~~~~~ 309 (1437)
T PRK00448 291 KGDWVKVRGSVQNDTFTRD 309 (1437)
T ss_pred CCCEEEEEEEEeccCCCCc
Confidence 9999999999999999753
No 59
>PRK12366 replication factor A; Reviewed
Probab=77.78 E-value=8.5 Score=38.55 Aligned_cols=77 Identities=17% Similarity=0.301 Sum_probs=52.5
Q ss_pred CCCCCCceEEEEEEeCcCCeEEEcC--CCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHH
Q 027819 76 GLDPGIFKAILVGQVGQSPVQKKLK--SGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVM 153 (218)
Q Consensus 76 ~~~~~~N~v~LiGrIg~dPelr~~~--nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~ 153 (218)
.|.++++.+.|.|+|.+--++|++. .|..--.|++.+.. . .| -+++++|+ ..|+. .
T Consensus 68 dl~p~~~~v~i~arV~~~~~~r~~~~~~G~eGkv~~~~v~D----e----tG------------~Ir~t~W~-~~~~~-~ 125 (637)
T PRK12366 68 DIEEGQINVEITGRIIEISNIKTFTRKDGSTGKLANITIAD----N----TG------------TIRLTLWN-DNAKL-L 125 (637)
T ss_pred HCcCCCcceEEEEEEEEccCCeEEECCCCCccEEEEEEEEc----C----CC------------EEEEEEEc-hhhhh-h
Confidence 5667889999999999887777663 45332223433321 1 11 28999998 67875 5
Q ss_pred hhcCCCCEEEEEEEeEeeeeeC
Q 027819 154 KHLVPGSTIYVEGNLEQKVFND 175 (218)
Q Consensus 154 ~~LkKG~~V~VeG~L~t~~~~d 175 (218)
..|.+|+.+.|.+. ..+.|..
T Consensus 126 ~~le~G~v~~i~~~-~v~~~~~ 146 (637)
T PRK12366 126 KGLKEGDVIKIENA-RSRKWNN 146 (637)
T ss_pred ccCCCCCEEEEecc-EecccCC
Confidence 67999999999985 3344643
No 60
>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=77.42 E-value=19 Score=26.69 Aligned_cols=68 Identities=15% Similarity=0.162 Sum_probs=42.5
Q ss_pred EEEEEEeCcCCeEEEc--CC-CcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHhhcCCCC
Q 027819 84 AILVGQVGQSPVQKKL--KS-GRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLVPGS 160 (218)
Q Consensus 84 v~LiGrIg~dPelr~~--~n-G~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~~LkKG~ 160 (218)
|-++|.|..--+.+.. .+ |....+..|..... ...-+.|++|| ..|+.+.... |+
T Consensus 2 vDvig~V~~v~~~~~i~~k~~g~~~~~r~v~i~D~-------------------t~~~i~vtLWg-~~a~~~~~~~--~~ 59 (101)
T cd04475 2 VDVIGVVKSVGPVTTITTKSTGRELDKREITLVDE-------------------SGHSVELTLWG-EQAELFDGSE--NP 59 (101)
T ss_pred EeEEEEEeEccCcEEEEEecCCCceeEEEEEEEeC-------------------CCCEEEEEEEH-HHhhhcccCC--CC
Confidence 3467777655443332 33 77666666655321 11256899998 7888776543 99
Q ss_pred EEEEEEEeEeeeee
Q 027819 161 TIYVEGNLEQKVFN 174 (218)
Q Consensus 161 ~V~VeG~L~t~~~~ 174 (218)
.|.+.| ++...|.
T Consensus 60 vv~~~~-~~i~~~~ 72 (101)
T cd04475 60 VIAIKG-VKVSEFN 72 (101)
T ss_pred EEEEEe-eEEEecC
Confidence 998888 6666675
No 61
>PRK12366 replication factor A; Reviewed
Probab=77.19 E-value=18 Score=36.30 Aligned_cols=93 Identities=12% Similarity=0.127 Sum_probs=61.3
Q ss_pred ccccCCCCCC-Cc-eEEEEEEeCcCCeEEEcCC--CcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCc
Q 027819 71 RPLENGLDPG-IF-KAILVGQVGQSPVQKKLKS--GRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPE 146 (218)
Q Consensus 71 r~~~~~~~~~-~N-~v~LiGrIg~dPelr~~~n--G~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~ 146 (218)
.|++ .|.+. .+ .++|.|+|..--.+|++.+ |. --.|++.... . .| =+++++|+
T Consensus 280 ~pI~-~L~~~~~g~~~~I~grV~~~~~~R~f~~~~g~-gkv~s~~l~D----~----tG------------~IR~t~w~- 336 (637)
T PRK12366 280 VNIE-ELTEFEDGEEVDVKGRIIAISDKREVERDDRT-AEVQDIELAD----G----TG------------RVRVSFWG- 336 (637)
T ss_pred eeHH-HCCcccCCCEEEEEEEEEecCCceEEEcCCCc-EEEEEEEEEc----C----CC------------eEEEEEeC-
Confidence 4555 45454 44 8999999999988888853 33 3446665532 1 11 28999998
Q ss_pred hhHHHHHhhcCCCCEEEEEEEeEeeeeeCCCCCeEEEEEEEEEEe
Q 027819 147 RLGGVVMKHLVPGSTIYVEGNLEQKVFNDPITGLVRRIREIAIRR 191 (218)
Q Consensus 147 k~Ae~v~~~LkKG~~V~VeG~L~t~~~~d~~dG~~r~~~eI~v~~ 191 (218)
..|+.... |..|+.++|.+--. +.|.+. +|. +.+++.+..
T Consensus 337 ~~~d~~~~-l~~G~vy~is~~~v-k~y~~~-~~~--~~~El~~~~ 376 (637)
T PRK12366 337 EKAKILEN-LKEGDAVKIENCKV-RTYYDN-EGE--KRVDLNAGY 376 (637)
T ss_pred chhhhhcc-cCCCCEEEEecCEE-eecccc-CCC--cCEEEEcCC
Confidence 67887765 78999999998333 356654 443 235666663
No 62
>PRK08402 replication factor A; Reviewed
Probab=75.59 E-value=11 Score=35.19 Aligned_cols=77 Identities=21% Similarity=0.177 Sum_probs=48.9
Q ss_pred CCCCCCceEEEEEEeCcCCeEEEc--CCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHH
Q 027819 76 GLDPGIFKAILVGQVGQSPVQKKL--KSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVM 153 (218)
Q Consensus 76 ~~~~~~N~v~LiGrIg~dPelr~~--~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~ 153 (218)
.+.+++..|.++|+|.+--..|.+ .+|..--.+++.+.. .|-.+++++|+ ..|....
T Consensus 67 dl~~g~~~V~v~~rVl~~~~~r~f~rrdG~~~~V~~i~l~D--------------------eTG~ir~TlW~-~~a~~~~ 125 (355)
T PRK08402 67 DLVPGMRGVNIVGRVLRKYPPREYTKKDGSTGRVASLIIYD--------------------DTGRARVVLWD-AKVAKYY 125 (355)
T ss_pred HccCCCceeeEEEEEEEccCCceeeccCCCcceEEEEEEEc--------------------CCCeEEEEEec-hhhhhhc
Confidence 455677899999999986444444 355432223333321 13345999998 6777555
Q ss_pred hhcCCCCEEEEEEEeEeeee
Q 027819 154 KHLVPGSTIYVEGNLEQKVF 173 (218)
Q Consensus 154 ~~LkKG~~V~VeG~L~t~~~ 173 (218)
..|..|+.|.|.|--....|
T Consensus 126 ~~l~~Gdvi~I~~a~V~e~~ 145 (355)
T PRK08402 126 NKINVGDVIKVIDAQVRESL 145 (355)
T ss_pred ccCCCCCEEEEECCEEeecC
Confidence 56999999999865444434
No 63
>PLN02903 aminoacyl-tRNA ligase
Probab=74.70 E-value=47 Score=33.67 Aligned_cols=46 Identities=15% Similarity=0.191 Sum_probs=32.2
Q ss_pred HHhhcCCCCEEEEEEEeEeeeeeCCCCCeEE-EEEEEEEEeCCcEEEeeCC
Q 027819 152 VMKHLVPGSTIYVEGNLEQKVFNDPITGLVR-RIREIAIRRNGRLVFLGKG 201 (218)
Q Consensus 152 v~~~LkKG~~V~VeG~L~t~~~~d~~dG~~r-~~~eI~v~~~g~i~~L~~k 201 (218)
..+.|..|+.|.|+|.+..+.-... +.+.. -.+||.|. +|++|+..
T Consensus 117 ~~~~L~~esvV~V~G~V~~r~~~~~-n~~~~tGeiEl~~~---~i~VL~~a 163 (652)
T PLN02903 117 TANRLRNEYVVAVEGTVRSRPQESP-NKKMKTGSVEVVAE---SVDILNVV 163 (652)
T ss_pred HHhcCCCCCEEEEEEEEEeCCCcCc-CCCCCCCCEEEEEe---EEEEEecC
Confidence 3457999999999999987632111 11111 24899999 99999875
No 64
>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=74.49 E-value=28 Score=24.75 Aligned_cols=29 Identities=17% Similarity=0.376 Sum_probs=22.7
Q ss_pred EEEEEEeCchhHHHHHhhcCCCCEEEEE-EEeEe
Q 027819 138 WHRVSVYPERLGGVVMKHLVPGSTIYVE-GNLEQ 170 (218)
Q Consensus 138 w~~V~~wg~k~Ae~v~~~LkKG~~V~Ve-G~L~t 170 (218)
-+++.+|+ ..+ ...++.|+.|.|. |.++.
T Consensus 35 ~i~~~~W~-~~~---~~~~~~G~vv~i~~~~v~~ 64 (82)
T cd04491 35 TIRFTLWD-EKA---ADDLEPGDVVRIENAYVRE 64 (82)
T ss_pred EEEEEEEC-chh---cccCCCCCEEEEEeEEEEe
Confidence 47999998 455 6679999999999 66543
No 65
>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=72.52 E-value=39 Score=27.01 Aligned_cols=79 Identities=14% Similarity=0.136 Sum_probs=53.1
Q ss_pred CceEEEEEEeCcCCeE--EEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHhhcCC
Q 027819 81 IFKAILVGQVGQSPVQ--KKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLVP 158 (218)
Q Consensus 81 ~N~v~LiGrIg~dPel--r~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~~LkK 158 (218)
-..+.++|-|...-.. +.+......+.|+| +...+.+. + .....+.|.+|. +..+.+-. ++.
T Consensus 12 ~~~vnvigVV~~~~~p~~~~t~g~D~~~tl~i-~D~S~~~~------~-------~~~~~l~v~iF~-~~~~~LP~-v~~ 75 (146)
T PF02765_consen 12 GKFVNVIGVVVDFSPPNPKKTRGTDYMCTLTI-TDPSLNDS------N-------QKLSGLTVNIFR-PHKESLPN-VKS 75 (146)
T ss_dssp SEEEEEEEEEEEEEEECTEEESSSCEEEEEEE-EBTTCSCS------S-------CCCCEEEEEEEE-SSHHHSCT-TCS
T ss_pred CCEEEEEEEEEEccCCcceEcCCCcEEEEEEE-ECCCCCcc------c-------cccCCEEEEEEC-CCHHHCCC-CCC
Confidence 3467888988876444 55556778888888 33322111 0 011789999996 67777765 566
Q ss_pred -CCEEEEEEEeEeeeeeCC
Q 027819 159 -GSTIYVEGNLEQKVFNDP 176 (218)
Q Consensus 159 -G~~V~VeG~L~t~~~~d~ 176 (218)
||.|.+. +++...|.++
T Consensus 76 ~GDii~l~-r~kv~~~~~~ 93 (146)
T PF02765_consen 76 VGDIIRLR-RVKVQSYNGK 93 (146)
T ss_dssp TTHEEEEE-EEEEEEETTE
T ss_pred CCCEEEEE-EEEEEEECCE
Confidence 9988887 8888889664
No 66
>PRK14699 replication factor A; Provisional
Probab=72.46 E-value=37 Score=33.05 Aligned_cols=76 Identities=16% Similarity=0.220 Sum_probs=50.1
Q ss_pred CCCCCceEEEEEEeCcCCeEEEcC--CCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHh
Q 027819 77 LDPGIFKAILVGQVGQSPVQKKLK--SGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMK 154 (218)
Q Consensus 77 ~~~~~N~v~LiGrIg~dPelr~~~--nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~ 154 (218)
|.+++..|.+.|+|.+--+.|++. +|..--.+++.+.. .|==+++++|+ ..|+ +..
T Consensus 172 L~~~~~~V~i~gkVl~~~~~R~f~~~dG~~g~v~~~~igD--------------------eTG~ir~tlW~-~~a~-~~~ 229 (484)
T PRK14699 172 IKDGMGDLNLTGKVLEISEIRTFQRKDGTSGKVGNLLLGD--------------------ETGTLRVTLWD-DKTD-FLN 229 (484)
T ss_pred cCCCCCceEEEEEEEeccCceEEecCCCCceEEEEEEEEc--------------------CCceEEEEEEC-cccc-ccc
Confidence 445667799999999988888764 55432223333321 13347999998 5676 444
Q ss_pred hcCCCCEEEEEE-EeEeeeee
Q 027819 155 HLVPGSTIYVEG-NLEQKVFN 174 (218)
Q Consensus 155 ~LkKG~~V~VeG-~L~t~~~~ 174 (218)
-|.+|+.|.|.+ ..+.+.|.
T Consensus 230 ~l~~Gd~v~I~~a~vr~~~~~ 250 (484)
T PRK14699 230 QIEYGDTVELINAYARENAFT 250 (484)
T ss_pred ccCCCCEEEEecceEeecccC
Confidence 599999999765 56666563
No 67
>cd04321 ScAspRS_mt_like_N ScAspRS_mt_like_N: N-terminal, anticodon recognition domain of the type found in Saccharomyces cerevisiae mitochondrial (mt) aspartyl-tRNA synthetase (AspRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this fungal group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). 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 protein synthesis, whereas the other exclusively with mitochondrial protein synthesis. Mutations in the gene for
Probab=72.19 E-value=25 Score=25.49 Aligned_cols=41 Identities=20% Similarity=0.280 Sum_probs=29.3
Q ss_pred HhhcCCCCEEEEEEEeEeeeeeCCCCCeEEEEEEEEEEeCCcEEEee
Q 027819 153 MKHLVPGSTIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGRLVFLG 199 (218)
Q Consensus 153 ~~~LkKG~~V~VeG~L~t~~~~d~~dG~~r~~~eI~v~~~g~i~~L~ 199 (218)
.+.|..|+.|.|+|.+..+.-.. .+. ...+||.++ +|++|+
T Consensus 45 ~~~l~~~s~V~V~G~v~~~~~~~--~~~-~~~~Ei~~~---~i~il~ 85 (86)
T cd04321 45 LKSITAESPVQVRGKLQLKEAKS--SEK-NDEWELVVD---DIQTLN 85 (86)
T ss_pred HhcCCCCcEEEEEEEEEeCCCcC--CCC-CCCEEEEEE---EEEEec
Confidence 35699999999999998764221 111 124789999 999886
No 68
>cd04320 AspRS_cyto_N AspRS_cyto_N: N-terminal, anticodon recognition domain of the type found in Saccharomyces cerevisiae and human cytoplasmic aspartyl-tRNA synthetase (AspRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). 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 protein synthesis, whereas the other exclusively with mitochondrial protein synthesis.
Probab=70.50 E-value=16 Score=27.25 Aligned_cols=43 Identities=16% Similarity=0.201 Sum_probs=31.0
Q ss_pred hhcCCCCEEEEEEEeEeeeeeCCCCCeEEEEEEEEEEeCCcEEEeeCC
Q 027819 154 KHLVPGSTIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGRLVFLGKG 201 (218)
Q Consensus 154 ~~LkKG~~V~VeG~L~t~~~~d~~dG~~r~~~eI~v~~~g~i~~L~~k 201 (218)
+.|..|+.|.|+|.+....= .. ++.....+||.+. +|++|+..
T Consensus 50 ~~l~~es~V~V~G~v~~~~~-~~-~~~~~~~~El~~~---~i~il~~~ 92 (102)
T cd04320 50 GSLSKESIVDVEGTVKKPEE-PI-KSCTQQDVELHIE---KIYVVSEA 92 (102)
T ss_pred hcCCCccEEEEEEEEECCCC-cc-cCCCcCcEEEEEE---EEEEEecC
Confidence 46999999999999876421 11 2222245899999 99999864
No 69
>COG1570 XseA Exonuclease VII, large subunit [DNA replication, recombination, and repair]
Probab=68.74 E-value=14 Score=35.58 Aligned_cols=75 Identities=15% Similarity=0.203 Sum_probs=54.5
Q ss_pred CCceEEEEEEeCcCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHhhcCCC
Q 027819 80 GIFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLVPG 159 (218)
Q Consensus 80 ~~N~v~LiGrIg~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~~LkKG 159 (218)
.+-.|.+.|.|.+ ++.-.+|+ .-|+| +| ...-++|++|. .....+.--++-|
T Consensus 22 ~~~~V~v~GEISn---~t~~~sgH--~YFtL------KD----------------~~A~i~c~mf~-~~~~~l~f~p~eG 73 (440)
T COG1570 22 DLGQVWVRGEISN---FTRPASGH--LYFTL------KD----------------ERAQIRCVMFK-GNNRRLKFRPEEG 73 (440)
T ss_pred cCCeEEEEEEecC---CccCCCcc--EEEEE------cc----------------CCceEEEEEEc-CcccccCCCccCC
Confidence 3578999999988 55456775 44555 11 24457999997 6777777779999
Q ss_pred CEEEEEEEeEeeeeeCCCCCeEEEEEEEEEE
Q 027819 160 STIYVEGNLEQKVFNDPITGLVRRIREIAIR 190 (218)
Q Consensus 160 ~~V~VeG~L~t~~~~d~~dG~~r~~~eI~v~ 190 (218)
+.|.|.|++... +. -| .+.|+++
T Consensus 74 ~~V~v~G~is~Y--~~--rG----~YQi~~~ 96 (440)
T COG1570 74 MQVLVRGKISLY--EP--RG----DYQIVAE 96 (440)
T ss_pred CEEEEEEEEEEE--cC--CC----ceEEEEe
Confidence 999999999764 43 35 3567777
No 70
>PRK06826 dnaE DNA polymerase III DnaE; Reviewed
Probab=65.98 E-value=31 Score=37.14 Aligned_cols=65 Identities=15% Similarity=0.250 Sum_probs=48.1
Q ss_pred eEEEEEEeCcCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHhhcCCCCEE
Q 027819 83 KAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLVPGSTI 162 (218)
Q Consensus 83 ~v~LiGrIg~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~~LkKG~~V 162 (218)
.+.+.|-|.. ...+.+++|..++-++|.-. +--+.|++|. +.-+.....|+.|..|
T Consensus 993 ~v~v~g~i~~-~~~~~tk~G~~maf~~leD~----------------------~g~~e~~vfp-~~~~~~~~~l~~~~~~ 1048 (1151)
T PRK06826 993 KVIIGGIITE-VKRKTTRNNEMMAFLTLEDL----------------------YGTVEVIVFP-KVYEKYRSLLNEDNIV 1048 (1151)
T ss_pred EEEEEEEEEE-eEeeccCCCCeEEEEEEEEC----------------------CCcEEEEECH-HHHHHHHHHhccCCEE
Confidence 5677777766 55566778888776666321 2226899997 6777788889999999
Q ss_pred EEEEEeEee
Q 027819 163 YVEGNLEQK 171 (218)
Q Consensus 163 ~VeG~L~t~ 171 (218)
+|+|+++.+
T Consensus 1049 ~v~g~v~~~ 1057 (1151)
T PRK06826 1049 LIKGRVSLR 1057 (1151)
T ss_pred EEEEEEEec
Confidence 999999653
No 71
>PRK06920 dnaE DNA polymerase III DnaE; Reviewed
Probab=64.99 E-value=33 Score=36.77 Aligned_cols=65 Identities=14% Similarity=0.188 Sum_probs=48.5
Q ss_pred eEEEEEEeCcCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHhhcCCCCEE
Q 027819 83 KAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLVPGSTI 162 (218)
Q Consensus 83 ~v~LiGrIg~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~~LkKG~~V 162 (218)
.|.+.|-|.. ...+.+++|+.++-+++.-. +--+.|++|. +.-+.....|..|..|
T Consensus 945 ~v~v~g~i~~-~~~~~tk~g~~maf~~leD~----------------------tg~~e~~vFp-~~y~~~~~~l~~~~~~ 1000 (1107)
T PRK06920 945 VQRAIVYITS-VKVIRTKKGQKMAFITFCDQ----------------------NDEMEAVVFP-ETYIHFSDKLQEGAIV 1000 (1107)
T ss_pred EEEEEEEEEE-eEeecCCCCCeEEEEEEeeC----------------------CCcEEEEECH-HHHHHHHHHhccCCEE
Confidence 5777787776 44556778888776666321 2236899997 7777888899999999
Q ss_pred EEEEEeEee
Q 027819 163 YVEGNLEQK 171 (218)
Q Consensus 163 ~VeG~L~t~ 171 (218)
+|+|+++.+
T Consensus 1001 ~v~G~v~~~ 1009 (1107)
T PRK06920 1001 LVDGTIELR 1009 (1107)
T ss_pred EEEEEEEec
Confidence 999999653
No 72
>PRK07374 dnaE DNA polymerase III subunit alpha; Validated
Probab=64.28 E-value=33 Score=37.04 Aligned_cols=65 Identities=14% Similarity=0.214 Sum_probs=48.8
Q ss_pred ceEEEEEEeCcCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHhhcCCCCE
Q 027819 82 FKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLVPGST 161 (218)
Q Consensus 82 N~v~LiGrIg~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~~LkKG~~ 161 (218)
.+|.+.|-|.. ...+.+++|..++-+++.-. +--+.|++|. +.-+.....|+.|..
T Consensus 1001 ~~v~v~g~i~~-~k~~~Tk~G~~maf~~leD~----------------------tg~~e~vvFp-~~y~~~~~~l~~~~~ 1056 (1170)
T PRK07374 1001 AKVSAIAMIPE-MKQVTTRKGDRMAILQLEDL----------------------TGSCEAVVFP-KSYERLSDHLMTDTR 1056 (1170)
T ss_pred CEEEEEEEEEE-eEecccCCCCEEEEEEEEEC----------------------CCCEEEEECH-HHHHHHHHHhccCCE
Confidence 35778888776 45566778888776666321 2226899997 777778889999999
Q ss_pred EEEEEEeEe
Q 027819 162 IYVEGNLEQ 170 (218)
Q Consensus 162 V~VeG~L~t 170 (218)
|+|+|+++.
T Consensus 1057 ~~v~g~v~~ 1065 (1170)
T PRK07374 1057 LLVWAKVDR 1065 (1170)
T ss_pred EEEEEEEEe
Confidence 999999965
No 73
>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=58.79 E-value=14 Score=29.50 Aligned_cols=33 Identities=21% Similarity=0.232 Sum_probs=25.9
Q ss_pred eeEEEEEEeCchhHHHHHhhcCCCCEEEEEEEeEee
Q 027819 136 VQWHRVSVYPERLGGVVMKHLVPGSTIYVEGNLEQK 171 (218)
Q Consensus 136 t~w~~V~~wg~k~Ae~v~~~LkKG~~V~VeG~L~t~ 171 (218)
..-+.|.+|. ..|+.+.+ |+.||.|.|. +++..
T Consensus 59 ~~ti~It~yD-~H~~~ar~-lK~GdfV~L~-NVhiK 91 (123)
T cd04498 59 QLTIDILVYD-NHVELAKS-LKPGDFVRIY-NVHAK 91 (123)
T ss_pred eEEEEEEEEc-chHHHHhh-CCCCCEEEEE-EEEEE
Confidence 3558999995 89998887 9999999886 34433
No 74
>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=58.19 E-value=32 Score=25.86 Aligned_cols=38 Identities=8% Similarity=0.108 Sum_probs=28.0
Q ss_pred eEEEEEEeCchhHHHHHhhcC---CCCEE-EEEEEeEeeeeeC
Q 027819 137 QWHRVSVYPERLGGVVMKHLV---PGSTI-YVEGNLEQKVFND 175 (218)
Q Consensus 137 ~w~~V~~wg~k~Ae~v~~~Lk---KG~~V-~VeG~L~t~~~~d 175 (218)
.-+.|++|| +.|+.+...+. ++..| .|-+-.+...|.+
T Consensus 35 ~~l~~tlwG-~~A~~f~~~~~~~~~~~~VVav~~~~rV~~~~g 76 (106)
T cd04481 35 ERLKCTLWG-EYAEEFDAKFQSAGNGEPVVAVLRFWKIKEYKG 76 (106)
T ss_pred CEEEEEEEH-HHHHHHHHHHHHhCCCCcEEEEEEeEEEEEEcC
Confidence 357999999 89998887763 44444 4556689999964
No 75
>PRK07279 dnaE DNA polymerase III DnaE; Reviewed
Probab=57.99 E-value=86 Score=33.55 Aligned_cols=65 Identities=17% Similarity=0.314 Sum_probs=47.2
Q ss_pred eEEEEEEeCcCCeEEEcC-CCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHhhcCCCCE
Q 027819 83 KAILVGQVGQSPVQKKLK-SGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLVPGST 161 (218)
Q Consensus 83 ~v~LiGrIg~dPelr~~~-nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~~LkKG~~ 161 (218)
.+.+.|.|..-- .+.+. +|+.++.+++.-. +--+.|++|. +.-+.....|+.|..
T Consensus 886 ~~~~~~~i~~~~-~~~tk~~g~~maf~~leD~----------------------~g~ie~~vFp-~~y~~~~~~l~~~~~ 941 (1034)
T PRK07279 886 EATILVQIQSIR-VIRTKTKGQQMAFLSVTDT----------------------KKKLDVTLFP-ETYRQYKDELKEGKF 941 (1034)
T ss_pred cceEEEEEEEEE-EEEEcCCCCeEEEEEEeeC----------------------CCcEEEEECH-HHHHHHHHHhccCCE
Confidence 467788887633 34455 8888776666331 1226899997 676778888999999
Q ss_pred EEEEEEeEee
Q 027819 162 IYVEGNLEQK 171 (218)
Q Consensus 162 V~VeG~L~t~ 171 (218)
|+|+|+++.+
T Consensus 942 ~~v~G~v~~~ 951 (1034)
T PRK07279 942 YYLKGKIQER 951 (1034)
T ss_pred EEEEEEEEec
Confidence 9999999663
No 76
>cd04323 AsnRS_cyto_like_N AsnRS_cyto_like_N: N-terminal, anticodon recognition domain of the type found in human and Saccharomyces cerevisiae cytoplasmic asparaginyl-tRNA synthetase (AsnRS), in Brugia malayai AsnRs and, in various putative bacterial AsnRSs. This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). 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, whereas the other exclusively with
Probab=56.81 E-value=70 Score=22.84 Aligned_cols=39 Identities=21% Similarity=0.269 Sum_probs=28.3
Q ss_pred hhcCCCCEEEEEEEeEeeeeeCCCCCeEEEEEEEEEEeCCcEEEee
Q 027819 154 KHLVPGSTIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGRLVFLG 199 (218)
Q Consensus 154 ~~LkKG~~V~VeG~L~t~~~~d~~dG~~r~~~eI~v~~~g~i~~L~ 199 (218)
+.|..|+.|.|+|.+....-.. .....+||.++ +|++|+
T Consensus 45 ~~l~~es~V~V~G~v~~~~~~~----~~~~~~Ei~~~---~i~vl~ 83 (84)
T cd04323 45 KSLTQESSVEVTGEVKEDPRAK----QAPGGYELQVD---YLEIIG 83 (84)
T ss_pred hcCCCcCEEEEEEEEEECCccc----CCCCCEEEEEE---EEEEEc
Confidence 4699999999999998754221 00114799999 998885
No 77
>cd04100 Asp_Lys_Asn_RS_N Asp_Lys_Asn_RS_N: N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases (AspRS, AsnRS, and LysRS). 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 protein synthesis, whereas the other exclusively with mitochondrial protein synthesis. Included in this group are archeal and archeal-like A
Probab=55.54 E-value=23 Score=25.34 Aligned_cols=41 Identities=20% Similarity=0.195 Sum_probs=29.6
Q ss_pred HHhhcCCCCEEEEEEEeEeeeeeCCCCCeEEEEEEEEEEeCCcEEEee
Q 027819 152 VMKHLVPGSTIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGRLVFLG 199 (218)
Q Consensus 152 v~~~LkKG~~V~VeG~L~t~~~~d~~dG~~r~~~eI~v~~~g~i~~L~ 199 (218)
..+.|..|+.|.|+|.+....-.. .....+||.++ +|++|+
T Consensus 44 ~~~~l~~~s~V~v~G~~~~~~~~~----~~~~~~El~~~---~i~il~ 84 (85)
T cd04100 44 EAEKLRTESVVGVTGTVVKRPEGN----LATGEIELQAE---ELEVLS 84 (85)
T ss_pred HHhCCCCCCEEEEEeEEEECCCCC----CCCCCEEEEEe---EEEEEC
Confidence 345799999999999998765211 01134789999 898885
No 78
>cd04319 PhAsnRS_like_N PhAsnRS_like_N: N-terminal, anticodon recognition domain of the type found in Pyrococcus horikoshii AsnRS asparaginyl-tRNA synthetase (AsnRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The archeal enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). 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.
Probab=55.16 E-value=42 Score=25.08 Aligned_cols=39 Identities=21% Similarity=0.237 Sum_probs=30.3
Q ss_pred hhcCCCCEEEEEEEeEeeeeeCCCCCeEEEEEEEEEEeCCcEEEeeCCC
Q 027819 154 KHLVPGSTIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGRLVFLGKGG 202 (218)
Q Consensus 154 ~~LkKG~~V~VeG~L~t~~~~d~~dG~~r~~~eI~v~~~g~i~~L~~k~ 202 (218)
..|..|+.|.|+|.+..+. .. .+ .+||.++ +|++|+...
T Consensus 46 ~~l~~~s~v~V~G~v~~~~--~~-~~----~~Ei~~~---~i~vl~~a~ 84 (103)
T cd04319 46 KKVGIESSVIVEGAVKADP--RA-PG----GAEVHGE---KLEIIQNVE 84 (103)
T ss_pred hCCCCCCEEEEEEEEEECC--CC-CC----CEEEEEE---EEEEEecCC
Confidence 4589999999999988763 22 11 4899999 999998753
No 79
>cd04322 LysRS_N LysRS_N: N-terminal, anticodon recognition domain of lysyl-tRNA synthetases (LysRS). These enzymes are homodimeric class 2b 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. Included in this group are E. coli LysS and LysU. These two isoforms of LysRS are encoded by distinct genes which are differently regulated. Eukaryotes contain 2 sets of aaRSs, both of which encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein
Probab=55.06 E-value=71 Score=23.94 Aligned_cols=36 Identities=28% Similarity=0.265 Sum_probs=28.4
Q ss_pred hcCCCCEEEEEEEeEeeeeeCCCCCeEEEEEEEEEEeCCcEEEeeCCC
Q 027819 155 HLVPGSTIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGRLVFLGKGG 202 (218)
Q Consensus 155 ~LkKG~~V~VeG~L~t~~~~d~~dG~~r~~~eI~v~~~g~i~~L~~k~ 202 (218)
.|..|+.|.|+|.+... + .|. +||.+. .+++|++..
T Consensus 49 ~l~~g~~V~v~G~v~~~----~-~g~----~El~~~---~~~ils~~~ 84 (108)
T cd04322 49 LLDLGDIIGVTGTPFKT----K-TGE----LSIFVK---EFTLLSKSL 84 (108)
T ss_pred cCCCCCEEEEEEEEEec----C-CCC----EEEEeC---EeEEeeccC
Confidence 39999999999988764 2 332 689999 999998653
No 80
>cd04316 ND_PkAspRS_like_N ND_PkAspRS_like_N: N-terminal, anticodon recognition domain of the type found in the homodimeric non-discriminating (ND) Pyrococcus kodakaraensis aspartyl-tRNA synthetase (AspRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. P. kodakaraensis AspRS is a class 2b aaRS. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation 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. P. kodakaraensis ND-AspRS can charge both tRNAAsp and tRNAAsn. Some of the enzymes in this group may be discriminating, based on the presence of homologs of asparaginyl-tRNA synthetase (AsnRS) in their completed genomes.
Probab=54.62 E-value=90 Score=23.44 Aligned_cols=38 Identities=21% Similarity=0.218 Sum_probs=29.8
Q ss_pred hhcCCCCEEEEEEEeEeeeeeCCCCCeEEEEEEEEEEeCCcEEEeeCC
Q 027819 154 KHLVPGSTIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGRLVFLGKG 201 (218)
Q Consensus 154 ~~LkKG~~V~VeG~L~t~~~~d~~dG~~r~~~eI~v~~~g~i~~L~~k 201 (218)
+.|..|+.|.|+|.+....- . .+ .+||.+. +|++|+..
T Consensus 60 ~~l~~es~V~V~G~v~~~~~--~-~~----~~Ei~~~---~i~il~~~ 97 (108)
T cd04316 60 RKLSRESVISVTGTVKAEPK--A-PN----GVEIIPE---EIEVLSEA 97 (108)
T ss_pred hCCCCcCEEEEEEEEEeCCC--C-CC----CEEEEEe---EEEEEeCC
Confidence 46999999999999887631 1 11 4799999 99999864
No 81
>PF13567 DUF4131: Domain of unknown function (DUF4131)
Probab=54.48 E-value=49 Score=25.33 Aligned_cols=71 Identities=23% Similarity=0.267 Sum_probs=40.5
Q ss_pred ceEEEEEEeCcCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHhhcCCCCE
Q 027819 82 FKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLVPGST 161 (218)
Q Consensus 82 N~v~LiGrIg~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~~LkKG~~ 161 (218)
..+++.|.|...|+.. +. ..+|.+.+.+-... ++ ....-.++.++-++.... .++.||.
T Consensus 76 ~~~~v~g~V~~~~~~~----~~-~~~~~~~~~~~~~~------~~-------~~~~~~~i~~~~~~~~~~---~l~~Gd~ 134 (176)
T PF13567_consen 76 KEVTVQGTVESVPQID----GR-GQRFTLRVERVLAG------GN-------WIPVSGKILLYLPKDSQP---RLQPGDR 134 (176)
T ss_pred ceEEEEEEEccccccc----Cc-eEEEEEEEEEeecc------cc-------ccccceeeEEEecccccc---ccCCCCE
Confidence 4678999998888764 12 12677765432111 11 012222333332222222 6999999
Q ss_pred EEEEEEeEeeee
Q 027819 162 IYVEGNLEQKVF 173 (218)
Q Consensus 162 V~VeG~L~t~~~ 173 (218)
|.++|+|+.=.=
T Consensus 135 i~~~g~l~~~~~ 146 (176)
T PF13567_consen 135 IRVRGKLKPPSG 146 (176)
T ss_pred EEEEEEEecCCC
Confidence 999999986543
No 82
>PRK07218 replication factor A; Provisional
Probab=53.87 E-value=1.3e+02 Score=28.85 Aligned_cols=88 Identities=15% Similarity=0.215 Sum_probs=54.6
Q ss_pred CCCCCCceEEEEEEeCcCCeEEEc--CCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHH
Q 027819 76 GLDPGIFKAILVGQVGQSPVQKKL--KSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVM 153 (218)
Q Consensus 76 ~~~~~~N~v~LiGrIg~dPelr~~--~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~ 153 (218)
.+.++.+.|.+.|+|.+-.. |.+ ++|... ..+... .| .|=-+++++|+ .+|
T Consensus 167 DL~~g~~~V~v~g~Vl~~~~-r~f~~~dg~~~-v~~gii----gD----------------eTG~Ir~tlW~-~~~---- 219 (423)
T PRK07218 167 DLGPGDRGVNVEARVLELEH-REIDGRDGETT-ILSGVL----AD----------------ETGRLPFTDWD-PLP---- 219 (423)
T ss_pred hccCCCCceEEEEEEEEecc-eeEEcCCCCeE-EEEEEE----EC----------------CCceEEEEEec-ccc----
Confidence 45567788999999997633 443 345432 222222 11 23357999998 454
Q ss_pred hhcCCCCEEEEEEEeEeeeeeCCCCCeEEEEEEEEEEeCCcEEEeeC
Q 027819 154 KHLVPGSTIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGRLVFLGK 200 (218)
Q Consensus 154 ~~LkKG~~V~VeG~L~t~~~~d~~dG~~r~~~eI~v~~~g~i~~L~~ 200 (218)
-|..|+.|.|.+-.... |.+ .++|.+...+.|..++.
T Consensus 220 -~l~~Gd~v~I~na~v~e-~~G--------~~elnv~~~t~I~~~d~ 256 (423)
T PRK07218 220 -EIEIGASIRIEDAYVRE-FRG--------VPSVNVSEFTTVEALDR 256 (423)
T ss_pred -cCCCCCEEEEeeeEEec-cCC--------eEEEEECCceEEEECCC
Confidence 38999999999854443 633 45666665566666644
No 83
>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=53.68 E-value=82 Score=24.55 Aligned_cols=47 Identities=21% Similarity=0.176 Sum_probs=31.6
Q ss_pred HHhhcCCCCEEEEEEEeEeeeeeCCCCCeEEEEEEEEEEeCCcEEEeeCC
Q 027819 152 VMKHLVPGSTIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGRLVFLGKG 201 (218)
Q Consensus 152 v~~~LkKG~~V~VeG~L~t~~~~d~~dG~~r~~~eI~v~~~g~i~~L~~k 201 (218)
..+.|+.|+.|.|+|.+....-..+........+||.+. +|++|+..
T Consensus 58 ~~~~l~~gs~V~V~G~~~~~~~~~~~~~~~~~~~El~~~---~i~vl~~~ 104 (135)
T cd04317 58 LAEKLRNESVIQVTGKVRARPEGTVNPKLPTGEIEVVAS---ELEVLNKA 104 (135)
T ss_pred HHhCCCCccEEEEEEEEECCCccccCCCCCCCcEEEEEe---EEEEEECC
Confidence 335699999999999988753210100111224799999 99999865
No 84
>cd04318 EcAsnRS_like_N EcAsnRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli asparaginyl-tRNA synthetase (AsnRS) and, in Arabidopsis thaliana and Saccharomyces cerevisiae mitochondrial (mt) AsnRS. This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). 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 protein synthesis, whereas the other exclusively with mitochondrial
Probab=53.09 E-value=69 Score=22.67 Aligned_cols=38 Identities=29% Similarity=0.316 Sum_probs=28.1
Q ss_pred HHhhcCCCCEEEEEEEeEeeeeeCCCCCeEEEEEEEEEEeCCcEEEee
Q 027819 152 VMKHLVPGSTIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGRLVFLG 199 (218)
Q Consensus 152 v~~~LkKG~~V~VeG~L~t~~~~d~~dG~~r~~~eI~v~~~g~i~~L~ 199 (218)
..+.|..|+.|.|+|.+....=. .| ..||.+. +|+.+.
T Consensus 44 ~~~~l~~gs~V~v~G~v~~~~~~---~~----~~El~~~---~i~il~ 81 (82)
T cd04318 44 EILKLSTGSSIRVEGVLVKSPGA---KQ----PFELQAE---KIEVLG 81 (82)
T ss_pred HHhcCCCceEEEEEEEEEeCCCC---CC----CEEEEEE---EEEEec
Confidence 34569999999999998875311 12 4789898 888774
No 85
>PF12869 tRNA_anti-like: tRNA_anti-like; InterPro: IPR024422 The function of the proteins in this entry is not known, but they contain a novel variant of the nucleic acid-binding OB fold [].; PDB: 3F1Z_I.
Probab=52.87 E-value=83 Score=24.47 Aligned_cols=35 Identities=9% Similarity=0.034 Sum_probs=16.6
Q ss_pred EEEEEEeCchhHHHHHhhcCCCCEEEEEEEeEeee
Q 027819 138 WHRVSVYPERLGGVVMKHLVPGSTIYVEGNLEQKV 172 (218)
Q Consensus 138 w~~V~~wg~k~Ae~v~~~LkKG~~V~VeG~L~t~~ 172 (218)
.+.|.+-.+.........|+||+.|.|.|.+.-..
T Consensus 99 ~v~~~~~~~~~~~~~~~~l~~G~~Vti~G~~~g~~ 133 (144)
T PF12869_consen 99 GVQCYFSNDQEKRASVAKLKKGQKVTIKGICTGYS 133 (144)
T ss_dssp S--EEEEEEGGGHHHHHH--TTSEEEEEEE-----
T ss_pred eEEEEEccchhhhhhHhcCCCCCEEEEEEEEEeee
Confidence 44555554222233444699999999999886553
No 86
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=51.86 E-value=36 Score=36.92 Aligned_cols=82 Identities=17% Similarity=0.194 Sum_probs=58.7
Q ss_pred ccccCCCCCCCceEEEEEEeCcCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCc-hhH
Q 027819 71 RPLENGLDPGIFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPE-RLG 149 (218)
Q Consensus 71 r~~~~~~~~~~N~v~LiGrIg~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~-k~A 149 (218)
.|+. .....+++|.+.|.|=. -+.+.+.+|+..+.|.|. .+ +.-+.|..|-+ +.-
T Consensus 230 ~~~~-~i~~~~~~v~v~G~IF~-~e~~~~ksGr~l~~i~vT--D~--------------------t~Sl~~k~f~~~~ed 285 (1444)
T COG2176 230 KPLI-KINEEETRVKVEGYIFK-IEIKELKSGRTLLNIKVT--DY--------------------TSSLILKKFLRDEED 285 (1444)
T ss_pred eehh-hccccccceEEEEEEEE-EeeeecccCcEEEEEEEe--cC--------------------chheeehhhcccccc
Confidence 4444 34446788999999987 888999999988888772 21 22345555641 112
Q ss_pred HHHHhhcCCCCEEEEEEEeEeeeeeCC
Q 027819 150 GVVMKHLVPGSTIYVEGNLEQKVFNDP 176 (218)
Q Consensus 150 e~v~~~LkKG~~V~VeG~L~t~~~~d~ 176 (218)
+...+.+++|+-|.|.|.++.+.+...
T Consensus 286 ~~~~~~ik~g~wvk~~g~v~~d~f~~~ 312 (1444)
T COG2176 286 EKKFDGIKKGMWVKARGNVQLDTFTRD 312 (1444)
T ss_pred HHHHhhcccCcEEEEEEEEEecccccc
Confidence 345567999999999999999988663
No 87
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=51.30 E-value=78 Score=32.27 Aligned_cols=63 Identities=14% Similarity=0.111 Sum_probs=46.0
Q ss_pred eEEEEEEeCcCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHhhcCCCCEE
Q 027819 83 KAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLVPGSTI 162 (218)
Q Consensus 83 ~v~LiGrIg~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~~LkKG~~V 162 (218)
.|+++|.|..-.... ..++...++.+.. .+.-+.+++|+ ..| ++.+.+++|..|
T Consensus 62 ~vti~g~V~~~~~~~--~~~~~~l~v~~~d----------------------~~~~l~l~fFn-~~~-~l~~~~~~G~~v 115 (677)
T COG1200 62 IVTIEGTVLSHEKFP--FGKRKLLKVTLSD----------------------GTGVLTLVFFN-FPA-YLKKKLKVGERV 115 (677)
T ss_pred eEEEEEEEEeeeccC--CCCCceEEEEEec----------------------CcEEEEEEEEC-ccH-HHHhhCCCCCEE
Confidence 899999998854432 3445555555533 13456888997 555 899999999999
Q ss_pred EEEEEeEee
Q 027819 163 YVEGNLEQK 171 (218)
Q Consensus 163 ~VeG~L~t~ 171 (218)
.|.|.+...
T Consensus 116 ~v~Gk~~~~ 124 (677)
T COG1200 116 IVYGKVKRF 124 (677)
T ss_pred EEEEEEeec
Confidence 999998873
No 88
>PF12342 DUF3640: Protein of unknown function (DUF3640) ; InterPro: IPR022101 This entry defines the N-terminal domain of the polyprotein of GB virus C; its function is not known.
Probab=51.18 E-value=9.4 Score=22.46 Aligned_cols=16 Identities=31% Similarity=0.397 Sum_probs=12.9
Q ss_pred CchhhHHHHHHhhcCC
Q 027819 1 MAALTRRFYRSLLLNP 16 (218)
Q Consensus 1 ~~~~~~~~~r~~l~~~ 16 (218)
|.+|.-||+|+|=-.+
T Consensus 1 mslLtnr~crrvdkdq 16 (26)
T PF12342_consen 1 MSLLTNRMCRRVDKDQ 16 (26)
T ss_pred ChHHHHHHHhhhcccc
Confidence 7789999999986554
No 89
>TIGR00499 lysS_bact lysyl-tRNA synthetase, eukaryotic and non-spirochete bacterial. This model represents the lysyl-tRNA synthetases that are class II amino-acyl tRNA synthetases. It includes all eukaryotic and most bacterial examples of the enzyme, but not archaeal or spirochete forms.
Probab=50.76 E-value=2.5e+02 Score=27.38 Aligned_cols=38 Identities=26% Similarity=0.174 Sum_probs=29.1
Q ss_pred HHhhcCCCCEEEEEEEeEeeeeeCCCCCeEEEEEEEEEEeCCcEEEeeCC
Q 027819 152 VMKHLVPGSTIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGRLVFLGKG 201 (218)
Q Consensus 152 v~~~LkKG~~V~VeG~L~t~~~~d~~dG~~r~~~eI~v~~~g~i~~L~~k 201 (218)
+...|..||.|.|+|.+.. .+ .|+ ++|.|. +|++|++.
T Consensus 100 ~~~~l~~gd~V~v~G~~~~----t~-~ge----lel~~~---~i~ilsk~ 137 (496)
T TIGR00499 100 DEYLLDLGDIIGVTGYPFK----TK-TGE----LSVHVT---ELQILTKA 137 (496)
T ss_pred HHhcCCCCCEEEEEEEEEE----CC-CCc----EEEEee---EEEEEecC
Confidence 3345899999999999943 33 443 789999 99999865
No 90
>PRK05672 dnaE2 error-prone DNA polymerase; Validated
Probab=50.67 E-value=1.1e+02 Score=32.72 Aligned_cols=49 Identities=22% Similarity=0.325 Sum_probs=37.4
Q ss_pred EEEEEEeCchhHHHHHhhcCCCCEEEEEEEeEeeeeeCCCCCeEEEEEEEEEEeCCcEEEeeC
Q 027819 138 WHRVSVYPERLGGVVMKHLVPGSTIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGRLVFLGK 200 (218)
Q Consensus 138 w~~V~~wg~k~Ae~v~~~LkKG~~V~VeG~L~t~~~~d~~dG~~r~~~eI~v~~~g~i~~L~~ 200 (218)
-+.|++|. +.-+.....|+.|..|+|+|+++.+ +|. ..|+|+ +|.-+..
T Consensus 985 ~~e~~ifp-~~~~~~~~~l~~~~~~~v~g~v~~~------~~~----~~~~~~---~i~~~~~ 1033 (1046)
T PRK05672 985 MVNVVVWP-GLWERQRREALGARLLLVRGRVQNA------EGV----RHLVAD---RLEDLSP 1033 (1046)
T ss_pred CEEEEECH-HHHHHHHHHhccCCEEEEEEEEEec------CCe----EEEEEe---eeechHH
Confidence 37999997 7888888899999999999999653 232 357777 7765533
No 91
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=49.72 E-value=79 Score=31.81 Aligned_cols=63 Identities=16% Similarity=0.112 Sum_probs=42.0
Q ss_pred ceEEEEEEeCcCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHhhcCCCCE
Q 027819 82 FKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLVPGST 161 (218)
Q Consensus 82 N~v~LiGrIg~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~~LkKG~~ 161 (218)
..+++.|.|..-+..+. +..+..+.+.- + +--+.|+.|+ -...++.+.|++|+.
T Consensus 60 ~~vtv~g~V~~~~~~~~---~~~~~~v~l~D------------~----------tg~i~l~~F~-~n~~~~~~~l~~G~~ 113 (681)
T PRK10917 60 EKVTVEGEVLSAEVVFG---KRRRLTVTVSD------------G----------TGNLTLRFFN-FNQPYLKKQLKVGKR 113 (681)
T ss_pred CEEEEEEEEEEEEEccC---CceEEEEEEEE------------C----------CeEEEEEEEc-cCcHHHHhhCCCCCE
Confidence 48999999987644332 45555555531 1 1235777773 113377888999999
Q ss_pred EEEEEEeEe
Q 027819 162 IYVEGNLEQ 170 (218)
Q Consensus 162 V~VeG~L~t 170 (218)
|+|.|.+..
T Consensus 114 ~~v~Gkv~~ 122 (681)
T PRK10917 114 VAVYGKVKR 122 (681)
T ss_pred EEEEEEEEe
Confidence 999999986
No 92
>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=49.06 E-value=29 Score=25.18 Aligned_cols=32 Identities=19% Similarity=0.175 Sum_probs=24.5
Q ss_pred EEEEEeCchhHH---HHHhhcCCCCEEEEEEEeEee
Q 027819 139 HRVSVYPERLGG---VVMKHLVPGSTIYVEGNLEQK 171 (218)
Q Consensus 139 ~~V~~wg~k~Ae---~v~~~LkKG~~V~VeG~L~t~ 171 (218)
+.|.+|. ...+ .....++.|+.|.|.|.++..
T Consensus 29 I~~~~W~-~~~~~~~~~~~~~~~g~~v~v~G~v~~~ 63 (95)
T cd04478 29 IEVRQWL-DDDNDDSSEVEPIEEGTYVRVFGNLKSF 63 (95)
T ss_pred EEEEEeC-CCCCcccccccccccCCEEEEEEEEccc
Confidence 6888886 3322 356779999999999999654
No 93
>COG0017 AsnS Aspartyl/asparaginyl-tRNA synthetases [Translation, ribosomal structure and biogenesis]
Probab=43.78 E-value=80 Score=30.52 Aligned_cols=82 Identities=16% Similarity=0.223 Sum_probs=54.2
Q ss_pred ceEEEEEEeCcCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHH--HhhcCCC
Q 027819 82 FKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVV--MKHLVPG 159 (218)
Q Consensus 82 N~v~LiGrIg~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v--~~~LkKG 159 (218)
.+|+|.|-|-. .| ..|+ ..|-+.-. .+.++.|++-..+..+.+ .+.|..+
T Consensus 17 ~~V~v~GWV~~---~R--~~g~--i~Fi~lrD---------------------gsg~iQ~v~~~~~~~~~~~~~~~L~~e 68 (435)
T COG0017 17 QEVTVRGWVHN---KR--DLGK--IIFLVLRD---------------------GSGFIQAVVPKNKVYEELFKAKKLTLE 68 (435)
T ss_pred cEEEEEEEeee---ec--ccCC--eEEEEEEc---------------------CCcEEEEEEECCCCcHHHhhhhcCCCc
Confidence 68999999866 22 2333 33544321 234488988742222222 4589999
Q ss_pred CEEEEEEEeEeeeeeCCCCCeEEEEEEEEEEeCCcEEEeeCC
Q 027819 160 STIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGRLVFLGKG 201 (218)
Q Consensus 160 ~~V~VeG~L~t~~~~d~~dG~~r~~~eI~v~~~g~i~~L~~k 201 (218)
+.|.|+|.+....= . ....||.+. +|++|+..
T Consensus 69 s~v~V~G~v~~~~~-a------~~g~El~v~---~i~Vl~~a 100 (435)
T COG0017 69 SSVVVTGIVKASPK-A------PQGFELQVE---KIEVLGEA 100 (435)
T ss_pred cEEEEEEEEEcCCC-C------CCCEEEEEE---EEEEeecc
Confidence 99999999987643 2 225689999 99999876
No 94
>PF12101 DUF3577: Protein of unknown function (DUF3577); InterPro: IPR021960 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 143 to 307 amino acids in length.
Probab=42.91 E-value=1.9e+02 Score=23.69 Aligned_cols=86 Identities=10% Similarity=0.094 Sum_probs=58.1
Q ss_pred eEEEEEEeCcCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHH----HHhhcCC
Q 027819 83 KAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGV----VMKHLVP 158 (218)
Q Consensus 83 ~v~LiGrIg~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~----v~~~LkK 158 (218)
++.-+|+|-+--++. .++|.+++..+|+.=.. . ..+ ....+|.|.+=| ..|.. +.+.+..
T Consensus 13 ht~GiGYLnriR~V~-~~kg~pFlac~I~AL~G---~----~d~-------~ey~~fD~~V~G-~eA~~Lv~r~~~av~~ 76 (137)
T PF12101_consen 13 HTTGIGYLNRIREVT-PRKGDPFLACTIAALRG---P----ADN-------PEYRYFDCRVVG-EEAKELVRRCQKAVDE 76 (137)
T ss_pred EEeeEEEeccceEcc-CCCCCeeEEEEeeeeec---C----CCC-------ccEEEEEEEEec-HHHHHHHHHHHhhccc
Confidence 466889998865554 56899998888887542 1 111 257899999999 66664 4445677
Q ss_pred CCEEEEE---EEeEeeeee----CCCCCeEEEEE
Q 027819 159 GSTIYVE---GNLEQKVFN----DPITGLVRRIR 185 (218)
Q Consensus 159 G~~V~Ve---G~L~t~~~~----d~~dG~~r~~~ 185 (218)
+.+|+|. |.|....|+ ++ .|+..-.+
T Consensus 77 ~~KVli~FrlgDl~~d~f~~~~G~~-~Ge~g~sL 109 (137)
T PF12101_consen 77 DKKVLIGFRLGDLWADTFTYKKGER-AGEPGASL 109 (137)
T ss_pred CCcEEEEEEecCCceeeEEeccCCc-CCccceee
Confidence 8888876 556677777 33 56544433
No 95
>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=41.46 E-value=1.8e+02 Score=23.03 Aligned_cols=73 Identities=10% Similarity=0.110 Sum_probs=47.5
Q ss_pred eEEEEEEeCcCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHhhcCCCCEE
Q 027819 83 KAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLVPGSTI 162 (218)
Q Consensus 83 ~v~LiGrIg~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~~LkKG~~V 162 (218)
.|-++|-|..-...+.+......+.|+|.=... . ...-+.|.+|+ +.++.+=. +..||.|
T Consensus 16 ~v~vigVV~~~~~p~~s~g~d~~~tl~i~D~S~----------~--------~~~~l~v~~F~-~~~~~LP~-v~~GDVI 75 (138)
T cd04497 16 SVNVIGVVVDAGPPVRSKGTDYCCTLTITDPSL----------A--------NSDGLTVKLFR-PNEESLPI-VKVGDII 75 (138)
T ss_pred eEEEEEEEeecCCCcccCCCcEEEEEEEECCCC----------C--------CCCcEEEEEEC-CChhhCCC-CCCCCEE
Confidence 566888877665544443333555565533211 0 12347999998 67777665 5999999
Q ss_pred EEEEEeEeeeeeCC
Q 027819 163 YVEGNLEQKVFNDP 176 (218)
Q Consensus 163 ~VeG~L~t~~~~d~ 176 (218)
.+.+ ++...|.++
T Consensus 76 ll~~-~kv~~~~g~ 88 (138)
T cd04497 76 LLRR-VKIQSYNGK 88 (138)
T ss_pred EEEE-EEEEEECCc
Confidence 9998 788888664
No 96
>TIGR00643 recG ATP-dependent DNA helicase RecG.
Probab=41.10 E-value=2.1e+02 Score=28.39 Aligned_cols=64 Identities=22% Similarity=0.260 Sum_probs=41.1
Q ss_pred ceEEEEEEeCcCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHhhcCCCCE
Q 027819 82 FKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLVPGST 161 (218)
Q Consensus 82 N~v~LiGrIg~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~~LkKG~~ 161 (218)
..+++.|.|...... ...+..+..+.+... . +.-+.|+.|+ + .++.+.+++|+.
T Consensus 33 ~~~~~~~~v~~~~~~--~~~~~~~~~~~~~d~-----~----------------~~~~~~~~F~-~--~~~~~~~~~g~~ 86 (630)
T TIGR00643 33 ERATIVGEVLSHCIF--GFKRRKVLKLRLKDG-----G----------------YKKLELRFFN-R--AFLKKKFKVGSK 86 (630)
T ss_pred CEEEEEEEEEEeEec--cCCCCceEEEEEEEC-----C----------------CCEEEEEEEC-C--HHHHhhCCCCCE
Confidence 378999998873221 123344555544221 0 1125788886 2 278888999999
Q ss_pred EEEEEEeEee
Q 027819 162 IYVEGNLEQK 171 (218)
Q Consensus 162 V~VeG~L~t~ 171 (218)
|+|.|.+...
T Consensus 87 ~~~~Gk~~~~ 96 (630)
T TIGR00643 87 VVVYGKVKSS 96 (630)
T ss_pred EEEEEEEEee
Confidence 9999999753
No 97
>PRK10646 ADP-binding protein; Provisional
Probab=39.35 E-value=22 Score=29.30 Aligned_cols=24 Identities=33% Similarity=0.454 Sum_probs=21.3
Q ss_pred hhHHHHHhhcCCCCEEEEEEEeEe
Q 027819 147 RLGGVVMKHLVPGSTIYVEGNLEQ 170 (218)
Q Consensus 147 k~Ae~v~~~LkKG~~V~VeG~L~t 170 (218)
++|+.+++.|+.|+.|++.|.|-.
T Consensus 16 ~l~~~la~~l~~g~vi~L~GdLGa 39 (153)
T PRK10646 16 DLGARVAKACDGATVIYLYGDLGA 39 (153)
T ss_pred HHHHHHHHhCCCCcEEEEECCCCC
Confidence 678899999999999999999853
No 98
>PRK06386 replication factor A; Reviewed
Probab=39.24 E-value=3e+02 Score=25.84 Aligned_cols=67 Identities=15% Similarity=0.156 Sum_probs=42.7
Q ss_pred CCCCCCceEEEEEEeCcCCeEEEcC-CCc--EEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHH
Q 027819 76 GLDPGIFKAILVGQVGQSPVQKKLK-SGR--TVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVV 152 (218)
Q Consensus 76 ~~~~~~N~v~LiGrIg~dPelr~~~-nG~--~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v 152 (218)
.|.+++.-+.+.|+|..-++ +.+. .|. .+...-| . | .|=-+++++|+ .
T Consensus 112 DL~~g~~~v~V~akVle~~e-~e~~~~g~~~~v~sg~l--g----D----------------eTGrIr~TlW~-~----- 162 (358)
T PRK06386 112 DLSLVTPYVSVIGKITGITK-KEYDSDGTSKIVYQGYI--E----D----------------DTARVRISSFG-K----- 162 (358)
T ss_pred eccCCCCceEEEEEEEEccC-ceEecCCCccEEEEEEE--E----c----------------CCCeEEEEEcc-c-----
Confidence 45667788889999987766 3332 332 2222222 1 1 24457899997 3
Q ss_pred HhhcCCCCEEEEEEEeEeeeee
Q 027819 153 MKHLVPGSTIYVEGNLEQKVFN 174 (218)
Q Consensus 153 ~~~LkKG~~V~VeG~L~t~~~~ 174 (218)
.|..|+.|.|.+-. ++.|.
T Consensus 163 --~l~eGd~v~i~na~-v~e~~ 181 (358)
T PRK06386 163 --PLEDNRFVRIENAR-VSQYN 181 (358)
T ss_pred --cccCCCEEEEeeeE-EEccC
Confidence 38999999999843 55563
No 99
>PF02367 UPF0079: Uncharacterised P-loop hydrolase UPF0079; InterPro: IPR003442 This group consists of bacterial proteins, which contain a P-loop. They are probably essential to bacteria as members are found in all genomes so far sequenced and no equivalent genes have been found in the archaea and eukaryotes, suggesting the protein may be involved in cell wall biosynthesis. The sequence of YjeE, from Haemophilus influenzae, has been determined to 1.7-A resolution. The protein has a nucleotide-binding fold with a four-stranded parallel beta-sheet flanked by antiparallel beta-strands on each side. The topology of the beta-sheet is unique among P-loop proteins and has features of different families of enzymes. ADP has been shown to bind to the P-loop in the presence of Mg2+ and ATPase activity has been confirmed by kinetic measurements [].; PDB: 1HTW_A 1FL9_A.
Probab=39.14 E-value=17 Score=28.78 Aligned_cols=23 Identities=35% Similarity=0.606 Sum_probs=19.8
Q ss_pred hhHHHHHhhcCCCCEEEEEEEeE
Q 027819 147 RLGGVVMKHLVPGSTIYVEGNLE 169 (218)
Q Consensus 147 k~Ae~v~~~LkKG~~V~VeG~L~ 169 (218)
++|+.+++.|++|+.|++.|.|-
T Consensus 3 ~la~~l~~~l~~g~vi~L~GdLG 25 (123)
T PF02367_consen 3 RLAKKLAQILKPGDVILLSGDLG 25 (123)
T ss_dssp HHHHHHHHHHSS-EEEEEEESTT
T ss_pred HHHHHHHHhCCCCCEEEEECCCC
Confidence 58899999999999999999873
No 100
>PF03983 SHD1: SLA1 homology domain 1, SHD1 ; InterPro: IPR007131 The SLA1 homology domain is found in the cytoskeleton assembly control protein SLA1, which is responsible for the correct formation of the actin cytoskeleton.; GO: 0008092 cytoskeletal protein binding, 0030674 protein binding, bridging, 0042802 identical protein binding, 0043130 ubiquitin binding; PDB: 2HBP_A.
Probab=38.51 E-value=80 Score=22.88 Aligned_cols=31 Identities=16% Similarity=0.273 Sum_probs=20.7
Q ss_pred EeeeeeCCCCCeEEEEEEEEEEeCCcEEEeeC
Q 027819 169 EQKVFNDPITGLVRRIREIAIRRNGRLVFLGK 200 (218)
Q Consensus 169 ~t~~~~d~~dG~~r~~~eI~v~~~g~i~~L~~ 200 (218)
..+.|+|. +|.-+--.+++.-.+|+|.+...
T Consensus 11 ~~RtWtD~-tG~f~VeA~fv~~~dgkV~L~k~ 41 (70)
T PF03983_consen 11 KTRTWTDR-TGKFKVEAEFVGVNDGKVHLHKT 41 (70)
T ss_dssp -SEEEEBS-SS--EEEEEEEEEETTEEEEE-T
T ss_pred cceEEEeC-CCCEEEEEEEEEeeCCEEEEEec
Confidence 56899999 99855555555555899999865
No 101
>smart00350 MCM minichromosome maintenance proteins.
Probab=37.72 E-value=90 Score=30.23 Aligned_cols=59 Identities=15% Similarity=0.116 Sum_probs=40.4
Q ss_pred ceeEEEEEEeCchhHHHHHhhcCCCCEEEEEEEeEeeeeeCCC---CCeEEEEEEEEEEeCCcEEEeeCC
Q 027819 135 AVQWHRVSVYPERLGGVVMKHLVPGSTIYVEGNLEQKVFNDPI---TGLVRRIREIAIRRNGRLVFLGKG 201 (218)
Q Consensus 135 ~t~w~~V~~wg~k~Ae~v~~~LkKG~~V~VeG~L~t~~~~d~~---dG~~r~~~eI~v~~~g~i~~L~~k 201 (218)
.+..+.|.+.++ +.+.++.||.|.|.|-+....|..+. .+...+.+.|.+. .|+.++.+
T Consensus 102 ~Prsi~v~l~~d-----Lvd~~~PGD~V~i~Gi~~~~~~~~~~~~~~~~~~~~~~l~a~---~i~~~~~~ 163 (509)
T smart00350 102 LPRSVDVILDGD-----LVDKAKPGDRVEVTGIYRNIPYGFKLNTVKGLPVFATYIEAN---HVRKLDYK 163 (509)
T ss_pred CCcEEEEEEccc-----ccCcccCCCEEEEEEEEEeeccccccccCCCcceeeEEEEEe---EEEEcccc
Confidence 467889999873 44578999999999999988663321 1222245666676 77776543
No 102
>PRK07218 replication factor A; Provisional
Probab=36.66 E-value=1.4e+02 Score=28.74 Aligned_cols=71 Identities=13% Similarity=0.216 Sum_probs=43.6
Q ss_pred CCCCCCceEEEEEEeCcCCeEEEcC-CCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHh
Q 027819 76 GLDPGIFKAILVGQVGQSPVQKKLK-SGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMK 154 (218)
Q Consensus 76 ~~~~~~N~v~LiGrIg~dPelr~~~-nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~ 154 (218)
.+.+++..|.++|+|..-.+ |++. +|..-...++.+.. .|=-+++++|+ ..+
T Consensus 63 Di~~~~~~V~v~~kVl~i~~-rt~r~dg~~g~v~~~~igD--------------------eTG~Ir~tlW~-~~~----- 115 (423)
T PRK07218 63 ELSTDDKNVTVTGRVLTIGE-RSIRYQGDDHVIYEGILAD--------------------ETGTISYTAWK-DFG----- 115 (423)
T ss_pred hCCCCCceeEEEEEEEEecc-eeEecCCCceEEEEEEEEC--------------------CCCeEEEEEEC-CCC-----
Confidence 34456678999999987765 4443 45432222332221 23347999997 443
Q ss_pred hcCCCCEEEEEEEeEeeeeeC
Q 027819 155 HLVPGSTIYVEGNLEQKVFND 175 (218)
Q Consensus 155 ~LkKG~~V~VeG~L~t~~~~d 175 (218)
|..||.|.|.+- .++.|.+
T Consensus 116 -l~~Gdvv~I~na-~vre~~g 134 (423)
T PRK07218 116 -LSPGDTVTIGNA-GVREWDG 134 (423)
T ss_pred -CCCCCEEEEecc-EeeccCC
Confidence 999999999863 3444643
No 103
>COG0802 Predicted ATPase or kinase [General function prediction only]
Probab=36.43 E-value=30 Score=28.57 Aligned_cols=24 Identities=25% Similarity=0.491 Sum_probs=21.1
Q ss_pred hhHHHHHhhcCCCCEEEEEEEeEe
Q 027819 147 RLGGVVMKHLVPGSTIYVEGNLEQ 170 (218)
Q Consensus 147 k~Ae~v~~~LkKG~~V~VeG~L~t 170 (218)
++|+.+++.|++|+.|+++|.|-.
T Consensus 13 ~lg~~l~~~l~~g~Vv~L~GdLGA 36 (149)
T COG0802 13 ALGERLAEALKAGDVVLLSGDLGA 36 (149)
T ss_pred HHHHHHHhhCCCCCEEEEEcCCcC
Confidence 578889999999999999999853
No 104
>PF08021 FAD_binding_9: Siderophore-interacting FAD-binding domain; InterPro: IPR013113 Proteins in this entry are siderophore-interacting FAD-binding proteins. This entry includes the vibriobactin utilization protein ViuB, which is involved in the removal of iron from iron-vibriobactin complexes, as well as several hypothetical proteins.; PDB: 2GPJ_A.
Probab=35.40 E-value=78 Score=24.49 Aligned_cols=32 Identities=13% Similarity=0.046 Sum_probs=22.5
Q ss_pred ceeEEEEEEeCc-hhHHHHHhhcCCCCEEEEEE
Q 027819 135 AVQWHRVSVYPE-RLGGVVMKHLVPGSTIYVEG 166 (218)
Q Consensus 135 ~t~w~~V~~wg~-k~Ae~v~~~LkKG~~V~VeG 166 (218)
.+..+.++++++ ..|...+..++.||.|.|.|
T Consensus 80 ~~l~iDfv~Hg~~Gpas~WA~~A~pGd~v~v~g 112 (117)
T PF08021_consen 80 GELDIDFVLHGDEGPASRWARSARPGDRVGVTG 112 (117)
T ss_dssp -EEEEEEE--SS--HHHHHHHH--TT-EEEEEE
T ss_pred CEEEEEEEECCCCCchHHHHhhCCCCCEEEEeC
Confidence 578899999986 68888889999999999988
No 105
>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=35.31 E-value=46 Score=24.80 Aligned_cols=20 Identities=25% Similarity=0.297 Sum_probs=16.8
Q ss_pred HHhhcCCCCEEEEEEEeEee
Q 027819 152 VMKHLVPGSTIYVEGNLEQK 171 (218)
Q Consensus 152 v~~~LkKG~~V~VeG~L~t~ 171 (218)
....+..|+.|.|.|++++.
T Consensus 59 ~~~~i~~G~vvrV~G~i~~f 78 (92)
T cd04483 59 QAKVLEIGDLLRVRGSIRTY 78 (92)
T ss_pred cccccCCCCEEEEEEEEecc
Confidence 44469999999999999875
No 106
>PF00970 FAD_binding_6: Oxidoreductase FAD-binding domain; InterPro: IPR008333 These sequences contain an oxidoreductase FAD-binding domain. To date, the 3D-structures of the flavoprotein domain of Zea mays (Maize) nitrate reductase [] and of pig NADH:cytochrome b5 reductase [] have been solved. The overall fold is similar to that of ferredoxin:NADP+ reductase []: the FAD-binding domain (N-terminal) has the topology of an anti-parallel beta-barrel, while the NAD(P)-binding domain (C-terminal) has the topology of a classical pyridine dinucleotide-binding fold (i.e. a central parallel beta-sheet flanked by 2 helices on each side).; PDB: 1JB9_A 3LVB_A 3LO8_A 1FRN_A 1FND_A 1BX1_A 1FNC_A 1FNB_A 1BX0_A 1FRQ_A ....
Probab=35.22 E-value=95 Score=22.30 Aligned_cols=33 Identities=18% Similarity=0.331 Sum_probs=24.7
Q ss_pred eeEEEEEEe--CchhHHHHHhhcCCCCEEEEEEEeEe
Q 027819 136 VQWHRVSVY--PERLGGVVMKHLVPGSTIYVEGNLEQ 170 (218)
Q Consensus 136 t~w~~V~~w--g~k~Ae~v~~~LkKG~~V~VeG~L~t 170 (218)
..-+-|... | .....+. .|+.||.|.|.|-+-.
T Consensus 62 ~~~~~ik~~~~G-~~S~~L~-~l~~Gd~v~i~gP~G~ 96 (99)
T PF00970_consen 62 YLEFAIKRYPNG-RVSRYLH-QLKPGDEVEIRGPYGN 96 (99)
T ss_dssp EEEEEEEECTTS-HHHHHHH-TSCTTSEEEEEEEESS
T ss_pred cEEEEEEeccCC-HHHHHHH-hCCCCCEEEEEEcccc
Confidence 555677777 5 5677774 5999999999996643
No 107
>PLN02603 asparaginyl-tRNA synthetase
Probab=34.53 E-value=4.8e+02 Score=26.04 Aligned_cols=38 Identities=21% Similarity=0.495 Sum_probs=29.8
Q ss_pred hcCCCCEEEEEEEeEeeeeeCCCCCeEEEEEEEEEEeCCcEEEeeCCC
Q 027819 155 HLVPGSTIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGRLVFLGKGG 202 (218)
Q Consensus 155 ~LkKG~~V~VeG~L~t~~~~d~~dG~~r~~~eI~v~~~g~i~~L~~k~ 202 (218)
.|..|+.|.|+|.+... + .++ ..+||.|+ +|++|+...
T Consensus 157 ~l~~gs~V~V~G~v~~~----~-~~~--~~~EL~v~---~i~vlg~a~ 194 (565)
T PLN02603 157 LITTGASVLVQGTVVSS----Q-GGK--QKVELKVS---KIVVVGKSD 194 (565)
T ss_pred CCCCCCEEEEEEEEEec----C-CCC--ccEEEEEe---EEEEEECCC
Confidence 48899999999998754 2 232 35899999 999998754
No 108
>COG4097 Predicted ferric reductase [Inorganic ion transport and metabolism]
Probab=33.78 E-value=61 Score=31.05 Aligned_cols=38 Identities=13% Similarity=0.185 Sum_probs=31.4
Q ss_pred eeEEEEEEeCchhHHHHHhhcCCCCEEEEEEEeEeeeee
Q 027819 136 VQWHRVSVYPERLGGVVMKHLVPGSTIYVEGNLEQKVFN 174 (218)
Q Consensus 136 t~w~~V~~wg~k~Ae~v~~~LkKG~~V~VeG~L~t~~~~ 174 (218)
.-.+.|++-| .....+.+.|+.|++|.|+|---.-.++
T Consensus 275 el~FsIK~LG-D~Tk~l~dnLk~G~k~~vdGPYG~F~~~ 312 (438)
T COG4097 275 ELRFSIKALG-DFTKTLKDNLKVGTKLEVDGPYGKFDFE 312 (438)
T ss_pred eEEEEehhhh-hhhHHHHHhccCCceEEEecCcceeecc
Confidence 3567999998 6888999999999999999966555554
No 109
>TIGR01077 L13_A_E ribosomal protein L13, archaeal/eukaryotic. This model represents ribosomal protein of L13 from the Archaea and from the eukaryotic cytosol. Bacterial and organellar forms are represented by TIGR01066.
Probab=33.36 E-value=32 Score=28.09 Aligned_cols=23 Identities=35% Similarity=0.541 Sum_probs=20.3
Q ss_pred EeCchhHHHHHhhcCCCCEEEEEE
Q 027819 143 VYPERLGGVVMKHLVPGSTIYVEG 166 (218)
Q Consensus 143 ~wg~k~Ae~v~~~LkKG~~V~VeG 166 (218)
+.| ++|..+++.|..||.|.|.-
T Consensus 9 vlG-RLAs~IA~~L~~Gd~VvViN 31 (142)
T TIGR01077 9 ILG-RLASVVAKQLLNGEKVVVVN 31 (142)
T ss_pred chH-HHHHHHHHHHhcCCEEEEEe
Confidence 456 89999999999999999865
No 110
>COG0587 DnaE DNA polymerase III, alpha subunit [DNA replication, recombination, and repair]
Probab=30.69 E-value=2.1e+02 Score=31.10 Aligned_cols=68 Identities=16% Similarity=0.277 Sum_probs=51.3
Q ss_pred eEEEEEEeCcCCeEEEcCCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHhhcCCCCEE
Q 027819 83 KAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLVPGSTI 162 (218)
Q Consensus 83 ~v~LiGrIg~dPelr~~~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~~LkKG~~V 162 (218)
.+++.|-|..-...++..+|..++.+++.-.. . -+.|++|. ...+.....+..|..+
T Consensus 978 ~~~~~~~i~~vr~~~tk~~G~~~~f~tl~D~~--------------------g--~~e~v~f~-~~~~~~~~~l~~~~~~ 1034 (1139)
T COG0587 978 RVVLAGGIVAVRQRPTKAKGNKMAFLTLEDET--------------------G--ILEVVVFP-SEYERYRRLLLEGRLL 1034 (1139)
T ss_pred eeEEEEEEEEEEEeeccCCCCEEEEEEEecCC--------------------C--cEEEEEcH-HHHHHHHHHhccCcEE
Confidence 47888888886665554588888877663210 1 35899996 7888888899999999
Q ss_pred EEEEEeEeeee
Q 027819 163 YVEGNLEQKVF 173 (218)
Q Consensus 163 ~VeG~L~t~~~ 173 (218)
+|.|.++.+..
T Consensus 1035 ~v~g~v~~~~~ 1045 (1139)
T COG0587 1035 IVKGKVQRRED 1045 (1139)
T ss_pred EEEEEEEeccc
Confidence 99999998543
No 111
>PRK06394 rpl13p 50S ribosomal protein L13P; Reviewed
Probab=30.30 E-value=37 Score=27.86 Aligned_cols=26 Identities=23% Similarity=0.388 Sum_probs=21.5
Q ss_pred EeCchhHHHHHhhcCCCCEEEEEEEeE
Q 027819 143 VYPERLGGVVMKHLVPGSTIYVEGNLE 169 (218)
Q Consensus 143 ~wg~k~Ae~v~~~LkKG~~V~VeG~L~ 169 (218)
+.| ++|..+++.|..||.|+|.---.
T Consensus 13 vlG-RLAs~IA~~L~~Gd~VVViNa~k 38 (146)
T PRK06394 13 ILG-RLASYVAKRLLEGEEVVIVNAEK 38 (146)
T ss_pred chH-HHHHHHHHHHhCCCEEEEEechh
Confidence 456 89999999999999999875433
No 112
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=30.00 E-value=1.6e+02 Score=22.59 Aligned_cols=24 Identities=17% Similarity=0.259 Sum_probs=18.2
Q ss_pred HHHHhhcCCCCEEEEEEEeEeeee
Q 027819 150 GVVMKHLVPGSTIYVEGNLEQKVF 173 (218)
Q Consensus 150 e~v~~~LkKG~~V~VeG~L~t~~~ 173 (218)
+.+.+.|+|||.|.-.|=|.-..=
T Consensus 38 ~~ml~sL~kGD~VvT~gGi~G~V~ 61 (97)
T COG1862 38 QELLNSLKKGDEVVTIGGIVGTVT 61 (97)
T ss_pred HHHHHhccCCCEEEEcCCeEEEEE
Confidence 457778999999998886655533
No 113
>TIGR00458 aspS_arch aspartyl-tRNA synthetase, archaeal type. In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, aspS_arch, represents aspartyl-tRNA synthetases from the eukaryotic cytosol and from the Archaea. In some species, this enzyme aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently transamidated to Asn-tRNA(asn).
Probab=28.44 E-value=1.3e+02 Score=28.66 Aligned_cols=39 Identities=23% Similarity=0.199 Sum_probs=30.1
Q ss_pred hhcCCCCEEEEEEEeEeeeeeCCCCCeEEEEEEEEEEeCCcEEEeeCCC
Q 027819 154 KHLVPGSTIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGRLVFLGKGG 202 (218)
Q Consensus 154 ~~LkKG~~V~VeG~L~t~~~~d~~dG~~r~~~eI~v~~~g~i~~L~~k~ 202 (218)
+.|..||.|.|+|.+....= . .| .+||.+. +|++|+...
T Consensus 60 ~~l~~~s~v~v~G~v~~~~~--~-~~----~~el~~~---~i~vl~~~~ 98 (428)
T TIGR00458 60 KKLNLESVVAVRGIVKIKEK--A-PG----GFEIIPT---KIEVINEAK 98 (428)
T ss_pred hCCCCCcEEEEEEEEEecCC--C-CC----cEEEEEe---EEEEEecCC
Confidence 46999999999999985321 1 22 4899999 999998753
No 114
>TIGR00150 HI0065_YjeE ATPase, YjeE family. Members of this family have a conserved nucleotide-binding motif GXXGXGKT and a nucleotide-binding fold. Member protein YjeE of Haemophilus influenzae (HI0065) was shown to have ATPase activity.
Probab=28.01 E-value=49 Score=26.53 Aligned_cols=23 Identities=26% Similarity=0.512 Sum_probs=20.6
Q ss_pred hhHHHHHhhcCCCCEEEEEEEeE
Q 027819 147 RLGGVVMKHLVPGSTIYVEGNLE 169 (218)
Q Consensus 147 k~Ae~v~~~LkKG~~V~VeG~L~ 169 (218)
++|+.+++.|++|+.|.+.|.+-
T Consensus 10 ~l~~~l~~~l~~~~~i~l~G~lG 32 (133)
T TIGR00150 10 KFGKAFAKPLDFGTVVLLKGDLG 32 (133)
T ss_pred HHHHHHHHhCCCCCEEEEEcCCC
Confidence 67889999999999999999874
No 115
>COG1838 FumA Tartrate dehydratase beta subunit/Fumarate hydratase class I, C-terminal domain [Energy production and conversion]
Probab=27.68 E-value=69 Score=27.42 Aligned_cols=21 Identities=19% Similarity=0.445 Sum_probs=17.5
Q ss_pred HHHHhhcCCCCEEEEEEEeEee
Q 027819 150 GVVMKHLVPGSTIYVEGNLEQK 171 (218)
Q Consensus 150 e~v~~~LkKG~~V~VeG~L~t~ 171 (218)
+.+. .|+.||.|++.|.|-+-
T Consensus 11 e~i~-~LkvGd~v~lsG~I~t~ 31 (184)
T COG1838 11 EEIA-KLKVGDVVYLSGKIVTG 31 (184)
T ss_pred HHHH-hccCCCEEEEeeEEEEe
Confidence 4444 59999999999999876
No 116
>KOG4101 consensus Cysteine-rich hydrophobic proteins [General function prediction only]
Probab=26.34 E-value=60 Score=27.00 Aligned_cols=19 Identities=26% Similarity=0.326 Sum_probs=10.1
Q ss_pred cccccCCCccccccCCCCC
Q 027819 33 SSSRVDSDLDESAIHSDAD 51 (218)
Q Consensus 33 ~~~~~~~~~~~~~~~~~~~ 51 (218)
.|+.+++|.|+..++++.|
T Consensus 4 ~s~~s~ad~d~~~Eeee~d 22 (175)
T KOG4101|consen 4 GSPASSADFDEIYEEEEID 22 (175)
T ss_pred CCCCCCCcccccccchhhh
Confidence 3455555666555554444
No 117
>TIGR00459 aspS_bact aspartyl-tRNA synthetase, bacterial type. In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, aspS_bact, represents aspartyl-tRNA synthetases from the Bacteria and from mitochondria. In some species, this enzyme aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently transamidated to Asn-tRNA(asn). This model generates very low scores for the archaeal type of aspS and for asnS; scores between the trusted and noise cutoffs represent fragmentary sequences.
Probab=25.70 E-value=2.2e+02 Score=28.48 Aligned_cols=59 Identities=19% Similarity=0.160 Sum_probs=36.4
Q ss_pred EEEEEeCchhHHHHHhhcCCCCEEEEEEEeEeeeeeCCCCC-eEEEEEEEEEEeCCcEEEeeCC
Q 027819 139 HRVSVYPERLGGVVMKHLVPGSTIYVEGNLEQKVFNDPITG-LVRRIREIAIRRNGRLVFLGKG 201 (218)
Q Consensus 139 ~~V~~wg~k~Ae~v~~~LkKG~~V~VeG~L~t~~~~d~~dG-~~r~~~eI~v~~~g~i~~L~~k 201 (218)
+.|++-.+..+-...+.|..|+.|.|+|.+..+.=... +- ...-.+||.+. +|++|++.
T Consensus 45 iQvv~~~~~~~~~~~~~L~~esvV~V~G~v~~r~~~~~-n~~~~tg~iEl~~~---~i~iL~~a 104 (583)
T TIGR00459 45 VQVVCDPDADALKLAKGLRNEDVVQVKGKVSARPEGNI-NRNLDTGEIEILAE---SITLLNKS 104 (583)
T ss_pred EEEEEeCCHHHHHHHhcCCCCCEEEEEEEEEeCCcccc-CccCCCCcEEEEEe---EEEEeecC
Confidence 55655432122223467999999999999986531110 00 11125899999 99999864
No 118
>PF15285 BH3: Beclin-1 BH3 domain, Bcl-2-interacting; PDB: 3BL2_C 2P1L_H 3DVU_C 2PON_A.
Probab=25.66 E-value=23 Score=20.69 Aligned_cols=9 Identities=44% Similarity=0.696 Sum_probs=6.6
Q ss_pred CchhhHHHH
Q 027819 1 MAALTRRFY 9 (218)
Q Consensus 1 ~~~~~~~~~ 9 (218)
|..|||||-
T Consensus 5 ~e~ls~rlk 13 (25)
T PF15285_consen 5 MENLSRRLK 13 (25)
T ss_dssp HHHHHHHHH
T ss_pred ccccchhhe
Confidence 567888874
No 119
>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=24.25 E-value=3.1e+02 Score=27.46 Aligned_cols=69 Identities=12% Similarity=0.111 Sum_probs=43.3
Q ss_pred eEEEEEEeCcCCeEEEc---CCCcEEEEEEEEeCceecCCCCCCCCCCccccccCceeEEEEEEeCchhHHHHHhhcCCC
Q 027819 83 KAILVGQVGQSPVQKKL---KSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLVPG 159 (218)
Q Consensus 83 ~v~LiGrIg~dPelr~~---~nG~~v~~FsVav~~~~~dr~~g~~g~~~ey~d~~~t~w~~V~~wg~k~Ae~v~~~LkKG 159 (218)
-|-++|-|..-=++... .+|+...+-.|..-. . ...-++|++|| ..|+.+. ..+|
T Consensus 312 ~VDVIGvV~~v~~~~~i~~k~~g~~~~kR~i~L~D----~---------------sg~sI~vTLWG-~~A~~~~--~~~~ 369 (608)
T TIGR00617 312 LVDVIGIVQSVSPTQTITSRKNNKEFPKRDITLVD----D---------------SGKSVRVTLWG-DDATKFD--VSVQ 369 (608)
T ss_pred CccEEEEEeEecCceEEEEcCCCCeeeeEEEEEEe----C---------------CCCEEEEEEEh-hhhhhcC--CCCC
Confidence 66788888765333332 356665555554432 1 11247999999 7887765 6788
Q ss_pred CEEEEEEEeEeeeee
Q 027819 160 STIYVEGNLEQKVFN 174 (218)
Q Consensus 160 ~~V~VeG~L~t~~~~ 174 (218)
+.|.+.| ++...|.
T Consensus 370 ~Vva~kg-~~V~~f~ 383 (608)
T TIGR00617 370 PVIAIKG-VRVSDFG 383 (608)
T ss_pred CEEEEEe-EEEEecC
Confidence 8888887 4445673
No 120
>PLN02532 asparagine-tRNA synthetase
Probab=24.09 E-value=2.9e+02 Score=28.06 Aligned_cols=56 Identities=18% Similarity=0.303 Sum_probs=39.0
Q ss_pred eEEEEEEeCchhHHHHHhhcCCCCEEEEEEEeEeeeeeCCCCCeEEEEEEEEEEeCCcEEEeeCCC
Q 027819 137 QWHRVSVYPERLGGVVMKHLVPGSTIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGRLVFLGKGG 202 (218)
Q Consensus 137 ~w~~V~~wg~k~Ae~v~~~LkKG~~V~VeG~L~t~~~~d~~dG~~r~~~eI~v~~~g~i~~L~~k~ 202 (218)
..+.|++-. ..+... +.|..|+.|.|+|.+..+.- .+ ....+||.|+ +|++|+...
T Consensus 147 ~~lQvVv~~-~~~~~~-~~L~~Es~V~V~G~V~~~~~----~~-~~g~iEl~v~---~i~VLg~a~ 202 (633)
T PLN02532 147 ASLQVVVDS-ALAPLT-QLMATGTCILAEGVLKLPLP----AQ-GKHVIELEVE---KILHIGTVD 202 (633)
T ss_pred cceEEEEeC-CcccHh-hcCCCceEEEEEEEEEecCC----CC-CCCcEEEEee---EEEEEecCC
Confidence 347887764 444332 67999999999999987621 11 1224799999 999998643
No 121
>PTZ00385 lysyl-tRNA synthetase; Provisional
Probab=24.02 E-value=2.9e+02 Score=28.15 Aligned_cols=38 Identities=21% Similarity=0.225 Sum_probs=29.7
Q ss_pred HHHhhcCCCCEEEEEEEeEeeeeeCCCCCeEEEEEEEEEEeCCcEEEeeC
Q 027819 151 VVMKHLVPGSTIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGRLVFLGK 200 (218)
Q Consensus 151 ~v~~~LkKG~~V~VeG~L~t~~~~d~~dG~~r~~~eI~v~~~g~i~~L~~ 200 (218)
.+.+.|..||.|.|+|.+... + .|. ++|.|. +|++|.+
T Consensus 154 ~~~~~l~~gdiV~V~G~v~~t----~-~Ge----leI~~~---~i~lLsk 191 (659)
T PTZ00385 154 KLKVSLRVGDIIGADGVPCRM----Q-RGE----LSVAAS---RMLILSP 191 (659)
T ss_pred HHHhCCCCCCEEEEEEEEEec----C-Cce----EEEEee---EEEEech
Confidence 344569999999999988743 3 453 689999 9999986
No 122
>PF11948 DUF3465: Protein of unknown function (DUF3465); InterPro: IPR021856 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 131 to 151 amino acids in length. This protein has a conserved HWTH sequence motif.
Probab=23.70 E-value=1e+02 Score=24.96 Aligned_cols=32 Identities=19% Similarity=0.170 Sum_probs=23.1
Q ss_pred EeCchhHHHHHhhcCCCCEEEEEEEeEeeeeeCCCCC
Q 027819 143 VYPERLGGVVMKHLVPGSTIYVEGNLEQKVFNDPITG 179 (218)
Q Consensus 143 ~wg~k~Ae~v~~~LkKG~~V~VeG~L~t~~~~d~~dG 179 (218)
+.+-.+|..+-. |+|||.|.+.|+- .|..+ .|
T Consensus 74 ahNIDlaprip~-l~~GD~V~f~GeY---e~n~k-gg 105 (131)
T PF11948_consen 74 AHNIDLAPRIPW-LQKGDQVEFYGEY---EWNPK-GG 105 (131)
T ss_pred EeccCccccCcC-cCCCCEEEEEEEE---EECCC-CC
Confidence 455457766664 9999999999988 45554 44
No 123
>PLN02850 aspartate-tRNA ligase
Probab=23.55 E-value=2e+02 Score=28.29 Aligned_cols=44 Identities=27% Similarity=0.392 Sum_probs=32.1
Q ss_pred HhhcCCCCEEEEEEEeEeeeeeCCCCCeEEEEEEEEEEeCCcEEEeeCCC
Q 027819 153 MKHLVPGSTIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGRLVFLGKGG 202 (218)
Q Consensus 153 ~~~LkKG~~V~VeG~L~t~~~~d~~dG~~r~~~eI~v~~~g~i~~L~~k~ 202 (218)
...|.+|+.|.|+|.+.... .++.+.+. .+||.+. +|.+|+...
T Consensus 130 ~~~l~~es~V~V~G~v~~~~--~~~~~~t~-~~El~~~---~i~vls~a~ 173 (530)
T PLN02850 130 AKQLSRESVVDVEGVVSVPK--KPVKGTTQ-QVEIQVR---KIYCVSKAL 173 (530)
T ss_pred HhCCCCCCEEEEEEEEEccC--cCCCCCCc-cEEEEEe---EEEEEeCCC
Confidence 35699999999999998532 11133333 7899999 999998753
No 124
>TIGR00457 asnS asparaginyl-tRNA synthetase. In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, asnS, represents asparaginyl-tRNA synthetases from the three domains of life. Some species lack this enzyme and charge tRNA(asn) by misacylation with Asp, followed by transamidation of Asp to Asn.
Probab=22.49 E-value=3.3e+02 Score=26.10 Aligned_cols=41 Identities=20% Similarity=0.421 Sum_probs=31.1
Q ss_pred HHhhcCCCCEEEEEEEeEeeeeeCCCCCeEEEEEEEEEEeCCcEEEeeCCC
Q 027819 152 VMKHLVPGSTIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGRLVFLGKGG 202 (218)
Q Consensus 152 v~~~LkKG~~V~VeG~L~t~~~~d~~dG~~r~~~eI~v~~~g~i~~L~~k~ 202 (218)
..+.|..||.|.|+|.+.... .+ .| ..||.+. +|++|+...
T Consensus 63 ~~~~l~~gs~V~v~G~v~~~~--~~-~~----~~El~~~---~i~vl~~~~ 103 (453)
T TIGR00457 63 LLKSLTTGSSVSVTGKVVESP--GK-GQ----PVELQVK---KIEVVGEAE 103 (453)
T ss_pred HHHcCCCCcEEEEEEEEEcCC--CC-CC----CEEEEEe---EEEEEecCC
Confidence 335699999999999988632 12 22 5789999 999998754
No 125
>PTZ00401 aspartyl-tRNA synthetase; Provisional
Probab=22.12 E-value=4.3e+02 Score=26.27 Aligned_cols=44 Identities=14% Similarity=0.103 Sum_probs=32.4
Q ss_pred hhcCCCCEEEEEEEeEeeeeeCCCCCeEEEEEEEEEEeCCcEEEeeCCC
Q 027819 154 KHLVPGSTIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGRLVFLGKGG 202 (218)
Q Consensus 154 ~~LkKG~~V~VeG~L~t~~~~d~~dG~~r~~~eI~v~~~g~i~~L~~k~ 202 (218)
..|.+|+.|.|+|.+....-. +.......+||.+. +|.+|+...
T Consensus 127 ~~l~~esiV~V~G~v~~~~~~--~~~~~~~~~El~v~---~i~vls~a~ 170 (550)
T PTZ00401 127 GQIPTESIVDVEATVCKVEQP--ITSTSHSDIELKVK---KIHTVTESL 170 (550)
T ss_pred hcCCCCCEEEEEEEEEecCcc--CCCCCCccEEEEee---EEEEEeCCC
Confidence 459999999999998875321 12233446899999 999998754
No 126
>TIGR01066 rplM_bact ribosomal protein L13, bacterial type. This model distinguishes ribosomal protein L13 of bacteria and organelles from its eukarytotic and archaeal counterparts.
Probab=22.01 E-value=68 Score=26.15 Aligned_cols=32 Identities=25% Similarity=0.313 Sum_probs=24.8
Q ss_pred ceeEEEEE----EeCchhHHHHHhhcC------------CCCEEEEEEE
Q 027819 135 AVQWHRVS----VYPERLGGVVMKHLV------------PGSTIYVEGN 167 (218)
Q Consensus 135 ~t~w~~V~----~wg~k~Ae~v~~~Lk------------KG~~V~VeG~ 167 (218)
...||=+- +.| ++|..+++.|. .||.|.|.--
T Consensus 10 ~r~W~viDA~~~~lG-RLAs~iAk~L~GKhKp~y~p~~d~Gd~VvViNa 57 (140)
T TIGR01066 10 KRKWYVVDAAGKTLG-RLASEVARLLRGKHKPTYTPHVDCGDYVIVINA 57 (140)
T ss_pred cccEEEEeCCCCchH-HHHHHHHHHHhccCCCccCCCccCCCEEEEEec
Confidence 35687664 455 79999999999 8999988753
No 127
>PTZ00111 DNA replication licensing factor MCM4; Provisional
Probab=21.62 E-value=2.7e+02 Score=29.59 Aligned_cols=57 Identities=11% Similarity=0.132 Sum_probs=37.7
Q ss_pred eEEEEEEeCchhHHHHHhhcCCCCEEEEEEEeEeeeeeCC---CCCeEEEEEEEEEEeCCcEEEeeCC
Q 027819 137 QWHRVSVYPERLGGVVMKHLVPGSTIYVEGNLEQKVFNDP---ITGLVRRIREIAIRRNGRLVFLGKG 201 (218)
Q Consensus 137 ~w~~V~~wg~k~Ae~v~~~LkKG~~V~VeG~L~t~~~~d~---~dG~~r~~~eI~v~~~g~i~~L~~k 201 (218)
.-+.|.+.++ +.+.+++||.|.|.|-++...-... ......+.+.|.|. .|+.+.+.
T Consensus 346 rsi~v~l~dD-----LVD~v~PGDrV~VtGIl~~~~~~~~~~~~~~~~~~~~yl~~~---~i~~~~~~ 405 (915)
T PTZ00111 346 EVINLNLYDD-----LIDSVKTGDRVTVVGILKVTPIRTSTTRRTLKSLYTYFVNVI---HVKVINST 405 (915)
T ss_pred ceEEEEEecc-----hhccCCCCCEEEEEEEEEeccccccccccccccccceEEEEE---EEEEeccc
Confidence 6688888873 5557899999999999987632110 01223455667777 77776543
No 128
>PF00572 Ribosomal_L13: Ribosomal protein L13; InterPro: IPR005822 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 L13 is one of the proteins from the large ribosomal subunit []. In Escherichia coli, L13 is known to be one of the early assembly proteins of the 50S ribosomal subunit.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 4A17_I 4A1E_I 4A1A_I 4A1C_I 3D5B_N 3MS1_J 1VSP_H 3PYT_J 3PYO_J 3PYV_J ....
Probab=21.57 E-value=64 Score=25.76 Aligned_cols=22 Identities=27% Similarity=0.384 Sum_probs=19.1
Q ss_pred EeCchhHHHHHhhcC------------CCCEEEEE
Q 027819 143 VYPERLGGVVMKHLV------------PGSTIYVE 165 (218)
Q Consensus 143 ~wg~k~Ae~v~~~Lk------------KG~~V~Ve 165 (218)
+-| ++|..+++.|. .||.|.|.
T Consensus 10 ~lG-RLAs~iAk~L~GKhk~~y~p~~d~Gd~VvVi 43 (128)
T PF00572_consen 10 ILG-RLASKIAKLLLGKHKPTYTPNVDCGDHVVVI 43 (128)
T ss_dssp BHH-HHHHHHHHHHCTTSSTSSBTTSSTTEEEEEE
T ss_pred chH-HHHHHHHHHHhCCCCCccCcCccCCCEEEEE
Confidence 345 89999999999 99999886
No 129
>PRK00484 lysS lysyl-tRNA synthetase; Reviewed
Probab=20.49 E-value=2.4e+02 Score=27.38 Aligned_cols=35 Identities=34% Similarity=0.383 Sum_probs=29.0
Q ss_pred hcCCCCEEEEEEEeEeeeeeCCCCCeEEEEEEEEEEeCCcEEEeeCC
Q 027819 155 HLVPGSTIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGRLVFLGKG 201 (218)
Q Consensus 155 ~LkKG~~V~VeG~L~t~~~~d~~dG~~r~~~eI~v~~~g~i~~L~~k 201 (218)
.|..||.|.|+|.+... + .| .++|.|. +|++|++.
T Consensus 103 ~l~~g~~v~v~G~v~~t----~-~g----e~el~~~---~~~vls~~ 137 (491)
T PRK00484 103 KLDLGDIIGVEGTLFKT----K-TG----ELSVKAT---ELTLLTKS 137 (491)
T ss_pred cCCCCCEEEEEEEEEEc----C-CC----cEEEEEe---EEEEEecc
Confidence 49999999999999864 3 45 4889999 99999864
Done!