Query 030281
Match_columns 180
No_of_seqs 126 out of 1056
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 11:20:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030281.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030281hhsearch_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 5.2E-32 1.1E-36 203.4 15.5 109 49-167 1-109 (112)
2 PRK07275 single-stranded DNA-b 100.0 1E-31 2.3E-36 214.1 16.1 108 49-166 1-108 (162)
3 PRK09010 single-stranded DNA-b 100.0 1E-31 2.2E-36 216.8 16.1 116 48-167 4-119 (177)
4 PRK06642 single-stranded DNA-b 100.0 1.3E-31 2.7E-36 211.7 16.3 119 47-168 1-121 (152)
5 PRK06863 single-stranded DNA-b 100.0 1.1E-31 2.4E-36 215.0 15.7 114 47-167 1-114 (168)
6 PRK06958 single-stranded DNA-b 100.0 2.6E-31 5.6E-36 215.0 16.3 114 47-167 1-114 (182)
7 PRK13732 single-stranded DNA-b 100.0 4.6E-31 1E-35 212.6 17.1 117 48-169 4-120 (175)
8 PRK08763 single-stranded DNA-b 100.0 5.6E-31 1.2E-35 210.2 16.4 111 49-167 4-114 (164)
9 PRK07459 single-stranded DNA-b 100.0 7.9E-31 1.7E-35 199.9 15.7 106 50-169 3-109 (121)
10 PRK08486 single-stranded DNA-b 100.0 1.1E-30 2.4E-35 211.6 16.2 111 49-167 1-111 (182)
11 PRK05733 single-stranded DNA-b 100.0 2.8E-30 6.1E-35 207.6 16.5 114 48-166 3-116 (172)
12 PRK07274 single-stranded DNA-b 100.0 2.3E-30 5E-35 199.6 15.1 107 49-166 1-107 (131)
13 PRK06751 single-stranded DNA-b 100.0 3.4E-30 7.4E-35 207.3 15.4 109 49-167 1-109 (173)
14 TIGR00621 ssb single stranded 100.0 6.7E-30 1.4E-34 203.8 16.3 111 47-165 1-111 (164)
15 PRK06341 single-stranded DNA-b 100.0 1.2E-29 2.5E-34 203.0 16.6 115 49-166 4-119 (166)
16 PRK08182 single-stranded DNA-b 100.0 2E-29 4.4E-34 198.3 15.4 111 49-166 1-115 (148)
17 PRK06293 single-stranded DNA-b 100.0 2.4E-28 5.1E-33 194.5 14.9 104 50-166 1-104 (161)
18 PF00436 SSB: Single-strand bi 100.0 2.7E-27 5.8E-32 172.7 13.7 104 50-161 1-104 (104)
19 KOG1653 Single-stranded DNA-bi 100.0 3.3E-28 7.1E-33 191.8 9.1 141 19-164 27-167 (175)
20 PRK07772 single-stranded DNA-b 100.0 3.1E-27 6.6E-32 192.1 14.9 112 47-161 1-113 (186)
21 COG0629 Ssb Single-stranded DN 99.9 1.7E-26 3.6E-31 184.5 13.2 114 48-166 1-116 (167)
22 PRK05813 single-stranded DNA-b 99.9 5.6E-25 1.2E-29 182.8 14.9 102 48-166 107-212 (219)
23 PRK05853 hypothetical protein; 99.9 1.1E-24 2.4E-29 173.5 13.0 95 55-154 1-95 (161)
24 PRK02801 primosomal replicatio 99.9 3.9E-24 8.5E-29 158.3 14.3 101 49-162 1-101 (101)
25 cd04496 SSB_OBF SSB_OBF: A sub 99.9 1.4E-22 3E-27 146.4 14.5 100 53-161 1-100 (100)
26 PRK05813 single-stranded DNA-b 99.8 2.5E-19 5.3E-24 149.1 14.6 99 49-166 7-105 (219)
27 PRK00036 primosomal replicatio 98.5 1.9E-06 4.1E-11 64.6 10.7 96 50-161 1-96 (107)
28 COG2965 PriB Primosomal replic 98.4 6.8E-06 1.5E-10 60.5 11.0 100 47-161 1-102 (103)
29 PF01336 tRNA_anti-codon: OB-f 97.5 0.00084 1.8E-08 45.1 7.9 75 53-161 1-75 (75)
30 cd04484 polC_OBF polC_OBF: A s 96.4 0.03 6.6E-07 39.6 7.9 68 53-138 2-70 (82)
31 cd04487 RecJ_OBF2_like RecJ_OB 96.3 0.034 7.3E-07 38.6 7.8 73 53-161 1-73 (73)
32 cd04474 RPA1_DBD_A RPA1_DBD_A: 96.3 0.025 5.5E-07 41.5 7.4 70 48-133 7-80 (104)
33 cd04492 YhaM_OBF_like YhaM_OBF 96.2 0.087 1.9E-06 35.8 9.4 72 61-163 7-78 (83)
34 cd04489 ExoVII_LU_OBF ExoVII_L 96.1 0.15 3.2E-06 34.7 10.0 62 53-136 2-63 (78)
35 cd04485 DnaE_OBF DnaE_OBF: A s 95.9 0.098 2.1E-06 35.1 8.4 61 55-133 2-62 (84)
36 PRK13480 3'-5' exoribonuclease 95.8 0.075 1.6E-06 46.8 9.5 57 59-133 19-75 (314)
37 PRK15491 replication factor A; 95.6 0.17 3.6E-06 45.6 10.9 90 50-163 176-268 (374)
38 PRK07211 replication factor A; 95.4 0.06 1.3E-06 50.0 7.5 68 48-132 61-133 (485)
39 PRK15491 replication factor A; 95.4 0.19 4.2E-06 45.2 10.6 91 48-163 65-158 (374)
40 cd04482 RPA2_OBF_like RPA2_OBF 95.1 0.2 4.3E-06 36.1 8.2 61 54-135 2-64 (91)
41 PRK07211 replication factor A; 94.1 0.52 1.1E-05 43.9 10.2 90 49-163 170-261 (485)
42 PF11325 DUF3127: Domain of un 93.7 0.58 1.3E-05 33.6 7.8 78 55-153 2-81 (84)
43 cd04488 RecG_wedge_OBF RecG_we 93.2 0.57 1.2E-05 30.7 6.7 31 102-134 31-61 (75)
44 cd03524 RPA2_OBF_family RPA2_O 92.8 0.3 6.5E-06 31.3 4.8 32 101-133 30-61 (75)
45 PRK06461 single-stranded DNA-b 92.7 1.8 3.9E-05 33.0 9.7 84 49-163 13-100 (129)
46 cd04490 PolII_SU_OBF PolII_SU_ 91.7 3.3 7.2E-05 28.9 9.9 57 53-131 2-60 (79)
47 PRK14699 replication factor A; 91.6 1.3 2.9E-05 41.2 9.2 73 48-137 65-140 (484)
48 PRK00286 xseA exodeoxyribonucl 91.4 0.68 1.5E-05 42.0 6.9 80 50-162 23-102 (438)
49 cd04491 SoSSB_OBF SoSSB_OBF: A 91.3 3.4 7.5E-05 28.4 9.1 59 55-133 2-64 (82)
50 PRK12366 replication factor A; 90.9 1.8 4E-05 41.5 9.6 89 51-160 292-382 (637)
51 PF13742 tRNA_anti_2: OB-fold 90.6 0.66 1.4E-05 33.8 5.0 63 50-134 21-84 (99)
52 COG3390 Uncharacterized protei 90.3 2.6 5.6E-05 34.7 8.7 76 48-144 43-118 (196)
53 TIGR00617 rpa1 replication fac 89.7 3.1 6.7E-05 39.8 10.0 92 49-162 189-286 (608)
54 TIGR00237 xseA exodeoxyribonuc 88.9 1.1 2.3E-05 41.0 6.1 79 50-161 17-95 (432)
55 PRK12366 replication factor A; 88.2 1.5 3.3E-05 42.1 6.8 73 48-137 71-145 (637)
56 PRK07373 DNA polymerase III su 88.1 3.5 7.7E-05 38.0 8.9 64 52-133 282-345 (449)
57 PRK08402 replication factor A; 88.1 4 8.8E-05 36.6 9.1 91 49-162 71-163 (355)
58 PRK14699 replication factor A; 87.4 5.5 0.00012 37.2 9.8 89 49-161 285-376 (484)
59 cd04475 RPA1_DBD_B RPA1_DBD_B: 87.3 4.8 0.0001 28.7 7.6 67 54-137 3-72 (101)
60 PF11506 DUF3217: Protein of u 86.3 11 0.00023 27.5 11.1 86 49-149 1-86 (104)
61 PRK05673 dnaE DNA polymerase I 86.1 4.3 9.4E-05 41.6 9.0 65 51-133 978-1042(1135)
62 PRK06826 dnaE DNA polymerase I 83.6 11 0.00023 38.9 10.5 65 52-134 993-1057(1151)
63 TIGR01405 polC_Gram_pos DNA po 83.4 12 0.00027 38.7 10.9 73 49-138 6-79 (1213)
64 PRK06920 dnaE DNA polymerase I 83.0 11 0.00023 38.8 10.2 65 52-134 945-1009(1107)
65 PRK00448 polC DNA polymerase I 80.5 7.6 0.00017 40.9 8.3 72 50-138 236-308 (1437)
66 PRK07279 dnaE DNA polymerase I 78.6 20 0.00044 36.6 10.4 65 52-134 886-951 (1034)
67 PRK07218 replication factor A; 78.5 24 0.00052 32.5 10.1 85 49-164 171-257 (423)
68 cd04317 EcAspRS_like_N EcAspRS 77.4 28 0.00061 26.2 9.6 87 52-164 16-104 (135)
69 PRK07374 dnaE DNA polymerase I 76.9 14 0.00031 38.1 8.9 65 51-133 1001-1065(1170)
70 PRK10917 ATP-dependent DNA hel 76.6 12 0.00025 36.2 7.8 89 51-164 60-154 (681)
71 cd04321 ScAspRS_mt_like_N ScAs 76.0 19 0.00041 25.1 7.0 55 102-163 31-86 (86)
72 COG1570 XseA Exonuclease VII, 75.0 11 0.00023 34.9 6.8 78 50-160 23-100 (440)
73 cd04478 RPA2_DBD_D RPA2_DBD_D: 73.9 22 0.00048 24.8 6.9 59 53-134 2-63 (95)
74 KOG3416 Predicted nucleic acid 72.2 12 0.00027 29.0 5.5 72 59-152 23-100 (134)
75 PRK05672 dnaE2 error-prone DNA 71.9 34 0.00073 35.0 10.0 79 52-163 955-1033(1046)
76 COG1200 RecG RecG-like helicas 71.9 16 0.00036 35.5 7.4 77 52-153 62-138 (677)
77 PRK06386 replication factor A; 71.3 41 0.00089 30.3 9.5 86 48-164 115-200 (358)
78 TIGR00643 recG ATP-dependent D 69.9 36 0.00077 32.5 9.3 64 51-134 33-96 (630)
79 PF13567 DUF4131: Domain of un 69.1 38 0.00083 25.0 7.7 71 51-136 76-146 (176)
80 cd04320 AspRS_cyto_N AspRS_cyt 67.0 38 0.00083 24.1 7.0 58 102-164 30-92 (102)
81 cd04323 AsnRS_cyto_like_N AsnR 66.9 37 0.00081 23.3 6.8 53 102-162 29-83 (84)
82 PF02765 POT1: Telomeric singl 64.4 58 0.0013 25.0 8.0 77 52-139 14-93 (146)
83 smart00350 MCM minichromosome 64.3 26 0.00057 32.5 7.1 60 98-165 102-164 (509)
84 PLN02903 aminoacyl-tRNA ligase 61.3 90 0.0019 30.4 10.2 59 102-164 102-163 (652)
85 TIGR00459 aspS_bact aspartyl-t 61.2 1.3E+02 0.0028 28.9 11.2 87 52-164 17-104 (583)
86 cd04481 RPA1_DBD_B_like RPA1_D 61.0 18 0.0004 26.1 4.4 37 101-138 36-76 (106)
87 COG1571 Predicted DNA-binding 60.2 45 0.00098 30.8 7.6 70 45-135 261-332 (421)
88 cd04318 EcAsnRS_like_N EcAsnRS 59.6 35 0.00076 23.2 5.5 51 102-162 31-81 (82)
89 cd04316 ND_PkAspRS_like_N ND_P 59.0 65 0.0014 23.2 7.4 53 102-164 42-97 (108)
90 TIGR00458 aspS_arch aspartyl-t 59.0 87 0.0019 28.6 9.3 82 51-164 13-97 (428)
91 COG0017 AsnS Aspartyl/asparagi 54.5 34 0.00074 31.7 5.9 82 51-164 17-100 (435)
92 PRK07218 replication factor A; 53.7 50 0.0011 30.4 6.8 66 49-137 67-133 (423)
93 cd04100 Asp_Lys_Asn_RS_N Asp_L 53.1 27 0.00059 24.0 4.0 54 102-162 29-84 (85)
94 PTZ00385 lysyl-tRNA synthetase 51.7 2.3E+02 0.005 27.7 11.2 78 52-163 109-191 (659)
95 KOG0479 DNA replication licens 50.6 22 0.00048 34.6 4.1 55 115-175 223-279 (818)
96 COG3111 Periplasmic protein wi 50.2 72 0.0016 24.7 6.1 77 44-161 51-127 (128)
97 cd04497 hPOT1_OB1_like hPOT1_O 50.0 1.1E+02 0.0024 23.2 8.0 73 52-139 16-88 (138)
98 PF03983 SHD1: SLA1 homology d 49.5 43 0.00092 23.3 4.4 32 132-164 11-42 (70)
99 PF08021 FAD_binding_9: Sidero 47.9 31 0.00068 25.6 3.9 32 98-129 80-112 (117)
100 TIGR00457 asnS asparaginyl-tRN 46.8 2.4E+02 0.0051 26.0 11.0 53 102-165 48-103 (453)
101 cd04319 PhAsnRS_like_N PhAsnRS 46.5 1.1E+02 0.0023 21.9 7.5 52 102-164 29-83 (103)
102 COG4097 Predicted ferric reduc 46.0 33 0.00072 31.5 4.3 38 100-138 276-313 (438)
103 COG2176 PolC DNA polymerase II 45.8 72 0.0016 33.5 7.0 73 48-138 237-311 (1444)
104 COG0587 DnaE DNA polymerase II 45.6 99 0.0021 32.1 8.1 68 52-136 978-1045(1139)
105 PRK12820 bifunctional aspartyl 45.5 3E+02 0.0065 27.2 11.1 60 102-164 48-110 (706)
106 PF12101 DUF3577: Protein of u 43.9 1.6E+02 0.0034 23.1 9.8 77 52-138 13-96 (137)
107 cd04322 LysRS_N LysRS_N: N-ter 43.1 1.2E+02 0.0027 21.7 7.1 36 117-164 48-83 (108)
108 cd04498 hPOT1_OB2 hPOT1_OB2: A 42.9 39 0.00085 25.9 3.8 27 100-128 60-86 (123)
109 PF00970 FAD_binding_6: Oxidor 41.9 65 0.0014 22.2 4.6 33 99-133 62-96 (99)
110 PLN02850 aspartate-tRNA ligase 41.3 3.2E+02 0.0068 25.9 11.9 43 116-164 130-172 (530)
111 PF04076 BOF: Bacterial OB fol 40.8 1.5E+02 0.0032 21.9 6.5 58 47-132 31-88 (103)
112 PLN02532 asparagine-tRNA synth 37.8 1.1E+02 0.0025 29.6 6.8 54 101-164 148-201 (633)
113 PTZ00111 DNA replication licen 36.5 1.3E+02 0.0028 30.6 7.2 57 100-164 346-405 (915)
114 PF02367 UPF0079: Uncharacteri 35.8 23 0.00049 27.0 1.5 22 111-132 4-25 (123)
115 COG0802 Predicted ATPase or ki 33.6 38 0.00081 26.9 2.5 23 111-133 14-36 (149)
116 PRK10646 ADP-binding protein; 32.7 37 0.00079 26.9 2.3 22 111-132 17-38 (153)
117 PRK03065 hutP anti-terminator 32.6 65 0.0014 25.5 3.6 29 73-109 100-128 (148)
118 PRK07135 dnaE DNA polymerase I 30.8 2.4E+02 0.0051 28.9 8.0 64 52-135 899-962 (973)
119 PLN02603 asparaginyl-tRNA synt 30.4 4.9E+02 0.011 24.9 11.7 53 102-165 139-194 (565)
120 cd04483 hOBFC1_like hOBFC1_lik 30.4 59 0.0013 23.2 2.9 20 115-134 59-78 (92)
121 TIGR01077 L13_A_E ribosomal pr 29.5 43 0.00094 26.2 2.2 23 106-129 9-31 (142)
122 COG3651 Uncharacterized protei 29.0 31 0.00067 26.0 1.2 23 25-47 62-84 (125)
123 COG3649 CRISPR system related 27.8 53 0.0012 28.0 2.5 50 98-153 98-147 (283)
124 PRK06394 rpl13p 50S ribosomal 27.5 48 0.001 26.1 2.1 25 106-131 13-37 (146)
125 PTZ00401 aspartyl-tRNA synthet 24.7 3.1E+02 0.0068 26.1 7.3 45 116-165 126-170 (550)
126 PF12869 tRNA_anti-like: tRNA_ 24.5 95 0.0021 23.2 3.2 35 101-135 99-133 (144)
127 TIGR00150 HI0065_YjeE ATPase, 24.5 70 0.0015 24.6 2.5 22 111-132 11-32 (133)
128 COG1838 FumA Tartrate dehydrat 24.4 78 0.0017 26.0 2.8 21 114-134 11-31 (184)
129 COG1908 FrhD Coenzyme F420-red 23.8 1.2E+02 0.0026 23.5 3.6 43 95-137 26-70 (132)
130 TIGR00617 rpa1 replication fac 23.6 6.1E+02 0.013 24.4 9.1 68 52-136 312-382 (608)
131 PRK10053 hypothetical protein; 23.5 2.5E+02 0.0055 21.6 5.4 60 47-134 58-117 (130)
132 PF06557 DUF1122: Protein of u 22.7 3E+02 0.0065 22.3 5.8 47 69-128 25-85 (170)
133 TIGR00156 conserved hypothetic 21.7 3.4E+02 0.0074 20.8 5.8 61 47-136 54-114 (126)
134 PF05309 TraE: TraE protein; 21.2 4.1E+02 0.0088 21.1 6.5 44 121-165 138-182 (187)
135 PLN02221 asparaginyl-tRNA synt 21.1 4.6E+02 0.0099 25.2 7.7 55 101-164 83-137 (572)
136 PF06523 DUF1106: Protein of u 21.1 1.4E+02 0.0031 21.0 3.3 30 53-82 27-56 (91)
137 PRK08395 fumarate hydratase; P 20.6 1.4E+02 0.003 24.0 3.5 21 114-134 10-30 (162)
138 PF05683 Fumerase_C: Fumarase 20.5 1.9E+02 0.0041 24.1 4.5 31 103-134 28-58 (205)
139 TIGR00723 ttdB_fumA_fumB hydro 20.2 1.1E+02 0.0025 24.6 3.0 20 116-135 3-22 (168)
No 1
>PRK06752 single-stranded DNA-binding protein; Validated
Probab=100.00 E-value=5.2e-32 Score=203.37 Aligned_cols=109 Identities=18% Similarity=0.310 Sum_probs=102.2
Q ss_pred cccEEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEEEE
Q 030281 49 GVHKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVYVE 128 (180)
Q Consensus 49 ~mN~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~Ve 128 (180)
|||+|+|+|||++||+++++++|+.+++|+||+++.|++.. |++ .++||+|++||+ +|+.++++|+||++|+|+
T Consensus 1 MmN~v~liGrl~~dPelr~t~~G~~~~~f~lAv~~~~~~~~-g~~----~t~~~~v~~wg~-~Ae~~~~~l~KG~~V~V~ 74 (112)
T PRK06752 1 MMNRVVLIGRLTKEPELYYTKQGVAYARVCVAVNRGFRNSL-GEQ----QVDFINCVVWRK-SAENVTEYCTKGSLVGIT 74 (112)
T ss_pred CceEEEEEEECcCCCEEEECCCCCEEEEEEEEECCCeEcCC-CCE----EEEEEEEEEehH-HHHHHHHhcCCCCEEEEE
Confidence 69999999999999999999999999999999999998763 653 689999999999 999999999999999999
Q ss_pred EEeEEeeeecCCCCeEEEEEEEEEEeCCceEEecCCCCC
Q 030281 129 GDIEIRVYNDSINGEVKNIPEICIRRDGTLRLVKSGESI 167 (180)
Q Consensus 129 GrL~~~~y~d~~dG~~~~~~eI~v~~~g~i~~l~~k~~~ 167 (180)
|+|+++.|+++ +|++++.++|+|+ +|.||+++...
T Consensus 75 G~l~~~~~~~~-~G~~~~~~ei~a~---~i~~l~~~~~~ 109 (112)
T PRK06752 75 GRIHTRNYEDD-QGKRIYITEVVIE---SITFLERRREG 109 (112)
T ss_pred EEEEeCccCCC-CCcEEEEEEEEEE---EEEECCCCCcc
Confidence 99999999998 9999999999999 99999988643
No 2
>PRK07275 single-stranded DNA-binding protein; Provisional
Probab=99.98 E-value=1e-31 Score=214.11 Aligned_cols=108 Identities=13% Similarity=0.297 Sum_probs=102.1
Q ss_pred cccEEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEEEE
Q 030281 49 GVHKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVYVE 128 (180)
Q Consensus 49 ~mN~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~Ve 128 (180)
|||+|+|+|||++||++|++++|..+++|+||+++.|++.+ |+ ..++||+|++||+ +|+.++++|+||++|+|+
T Consensus 1 M~N~v~LiGrL~~DPElr~t~sG~~v~~ftlAv~r~~~~~~-ge----~~tdfi~vv~wgk-~Ae~~~~~l~KG~~V~Ve 74 (162)
T PRK07275 1 MINNVVLVGRMTRDAELRYTPSNVAVATFTLAVNRTFKSQN-GE----READFINCVIWRQ-QAENLANWAKKGALIGVT 74 (162)
T ss_pred CeeEEEEEEEECCCCeEEECCCCCEEEEEEEEEcCceecCC-CC----EeeeEEEEEEEcH-HHHHHHHHcCCCCEEEEE
Confidence 68999999999999999999999999999999999998763 65 3699999999999 999999999999999999
Q ss_pred EEeEEeeeecCCCCeEEEEEEEEEEeCCceEEecCCCC
Q 030281 129 GDIEIRVYNDSINGEVKNIPEICIRRDGTLRLVKSGES 166 (180)
Q Consensus 129 GrL~~~~y~d~~dG~~~~~~eI~v~~~g~i~~l~~k~~ 166 (180)
|+|+++.|+++ +|++++.++|+|+ +|+||+++.+
T Consensus 75 Grl~~r~y~dk-dG~k~~~~evva~---~i~~l~~~~~ 108 (162)
T PRK07275 75 GRIQTRNYENQ-QGQRVYVTEVVAD---NFQMLESRAT 108 (162)
T ss_pred EEEEeceEECC-CCCEEEEEEEEEe---EEEECCCCCc
Confidence 99999999998 9999999999999 9999998874
No 3
>PRK09010 single-stranded DNA-binding protein; Provisional
Probab=99.98 E-value=1e-31 Score=216.80 Aligned_cols=116 Identities=26% Similarity=0.526 Sum_probs=108.4
Q ss_pred ccccEEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEEE
Q 030281 48 RGVHKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVYV 127 (180)
Q Consensus 48 ~~mN~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~V 127 (180)
++||+|+|+|||++||++|+++||..+++|+||+++.|+++.+|++ .+.++||+|++|++ +|+.+.++|+||++|+|
T Consensus 4 r~~N~V~LiGrLg~DPelR~t~nG~~v~~fsVAvn~~~kd~~~Ge~--~e~t~w~~V~~fgk-~Ae~~~~~L~KGs~V~V 80 (177)
T PRK09010 4 RGVNKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKQTGEM--KEQTEWHRVVLFGK-LAEVAGEYLRKGSQVYI 80 (177)
T ss_pred cCceEEEEEEEeCCCceEEEcCCCCEEEEEEEEEcCccccCccccc--ccceEEEEEEEehh-HHHHHHHhcCCCCEEEE
Confidence 5899999999999999999999999999999999999988766775 57899999999998 99999999999999999
Q ss_pred EEEeEEeeeecCCCCeEEEEEEEEEEeCCceEEecCCCCC
Q 030281 128 EGDIEIRVYNDSINGEVKNIPEICIRRDGTLRLVKSGESI 167 (180)
Q Consensus 128 eGrL~~~~y~d~~dG~~~~~~eI~v~~~g~i~~l~~k~~~ 167 (180)
+|+|+++.|+|+ +|++++.++|+|+..++++||+++...
T Consensus 81 eGrL~~~~yedk-dG~~r~~~eVvv~~~~~~~~l~~r~~~ 119 (177)
T PRK09010 81 EGQLRTRKWTDQ-SGQDRYTTEVVVNVGGTMQMLGGRQGG 119 (177)
T ss_pred EEEEEeccccCC-CCCEEEEEEEEEecCCcEEEccCCCCC
Confidence 999999999998 999999999999888899999988543
No 4
>PRK06642 single-stranded DNA-binding protein; Provisional
Probab=99.98 E-value=1.3e-31 Score=211.65 Aligned_cols=119 Identities=28% Similarity=0.515 Sum_probs=106.0
Q ss_pred ccc-ccEEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeE
Q 030281 47 FRG-VHKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSV 125 (180)
Q Consensus 47 m~~-mN~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V 125 (180)
|+. ||+|+|+||||+||++|++++|+.+++|+||+++.|+++.+|++ ...|+||+|++|++.+|+.++++|+||++|
T Consensus 1 Ma~~~N~V~LiGrLg~DPElr~t~~G~~v~~fslAv~~~~k~~~~G~~--~~~T~w~~v~~~g~~~Ae~~~~~l~KG~~V 78 (152)
T PRK06642 1 MAGSLNKVILIGNVGRDPEIRTTGEGKKIINLSLATTETWKDRITSER--KERTEWHRVVIFSEGLVSVVERYVTKGSKL 78 (152)
T ss_pred CCCcceEEEEEEEccCCceEEECCCCCEEEEEEEEeccccccccCCcc--ccceeEEEEEEeChHHHHHHHHhCCCCCEE
Confidence 554 99999999999999999999999999999999999987655775 568999999999965899999999999999
Q ss_pred EEEEEeEEeeeecCCCCeEEEEEEEEEEe-CCceEEecCCCCCC
Q 030281 126 YVEGDIEIRVYNDSINGEVKNIPEICIRR-DGTLRLVKSGESIS 168 (180)
Q Consensus 126 ~VeGrL~~~~y~d~~dG~~~~~~eI~v~~-~g~i~~l~~k~~~~ 168 (180)
+|+|+|+++.|+++ +|++++.++|+|++ ...|+||+++.+.+
T Consensus 79 ~V~GrL~~~~y~dk-dG~~r~~~eVvv~~~~~~i~fl~~k~~~~ 121 (152)
T PRK06642 79 YIEGSLQTRKWNDN-SGQEKYTTEVVLQNFNSQLILLDSKNSNN 121 (152)
T ss_pred EEEEEEEeCeeECC-CCCEEEEEEEEEEecccceEeccCCCCcc
Confidence 99999999999998 99999999999994 23458999886533
No 5
>PRK06863 single-stranded DNA-binding protein; Provisional
Probab=99.98 E-value=1.1e-31 Score=214.96 Aligned_cols=114 Identities=29% Similarity=0.486 Sum_probs=106.7
Q ss_pred cccccEEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEE
Q 030281 47 FRGVHKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVY 126 (180)
Q Consensus 47 m~~mN~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~ 126 (180)
|++||+|+|+||||+||++|+++||+.+++|+||+++.|++++.|++ .+.++||+|++|++ +|+.+.++|+||++|+
T Consensus 1 M~~~N~V~LiGrLg~DPElR~t~nG~~va~fsVAvn~~~~d~~~Ge~--~e~t~w~~Vv~fgk-~AE~v~~~LkKGs~V~ 77 (168)
T PRK06863 1 MAGINKVIIVGHLGNDPEIRTMPNGEAVANISVATSESWTDKNTGER--REVTEWHRIVFYRR-QAEVAGEYLRKGSQVY 77 (168)
T ss_pred CCCccEEEEEEEcCCCCEEEEcCCCCEEEEEEEEecCcccccCCCcc--cccceEEEEEEEhH-HHHHHHHHCCCCCEEE
Confidence 88999999999999999999999999999999999999887655765 46799999999998 9999999999999999
Q ss_pred EEEEeEEeeeecCCCCeEEEEEEEEEEeCCceEEecCCCCC
Q 030281 127 VEGDIEIRVYNDSINGEVKNIPEICIRRDGTLRLVKSGESI 167 (180)
Q Consensus 127 VeGrL~~~~y~d~~dG~~~~~~eI~v~~~g~i~~l~~k~~~ 167 (180)
|+|+|+++.|+|+ +|++++.++|+|+ +|+||+++...
T Consensus 78 VeGrL~~r~w~Dk-dG~~r~~~eI~a~---~i~~L~~r~~~ 114 (168)
T PRK06863 78 VEGRLKTRKWQDQ-NGQDRYTTEIQGD---VLQMLGGRNQR 114 (168)
T ss_pred EEEEEEeCCccCC-CCCEEEEEEEEEe---EEEECCCCCcc
Confidence 9999999999998 9999999999999 99999988653
No 6
>PRK06958 single-stranded DNA-binding protein; Provisional
Probab=99.98 E-value=2.6e-31 Score=215.02 Aligned_cols=114 Identities=25% Similarity=0.456 Sum_probs=107.3
Q ss_pred cccccEEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEE
Q 030281 47 FRGVHKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVY 126 (180)
Q Consensus 47 m~~mN~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~ 126 (180)
|++||+|+|+|||++||+++++++|+.+++|+||++++|+++.+|++ .+.|+||+|++|++ +|+.++++|+||++|+
T Consensus 1 Mas~N~V~LiGrLg~DPElr~t~nG~~va~fsVAv~~~~kdk~sGe~--~e~T~w~~V~~fGk-~AE~v~~~LkKGs~V~ 77 (182)
T PRK06958 1 MASVNKVILVGNLGADPEVRYLPSGDAVANIRLATTDRYKDKASGEF--KEATEWHRVAFFGR-LAEIVGEYLKKGSSVY 77 (182)
T ss_pred CCcccEEEEEEEecCCCeEEEcCCCCEEEEEEEEeccccccccCCcc--cccceEEEEEEehH-HHHHHHHHhCCCCEEE
Confidence 78899999999999999999999999999999999999988766775 56899999999999 9999999999999999
Q ss_pred EEEEeEEeeeecCCCCeEEEEEEEEEEeCCceEEecCCCCC
Q 030281 127 VEGDIEIRVYNDSINGEVKNIPEICIRRDGTLRLVKSGESI 167 (180)
Q Consensus 127 VeGrL~~~~y~d~~dG~~~~~~eI~v~~~g~i~~l~~k~~~ 167 (180)
|+|+|+++.|+|+ +|++++.++|+|+ .|+||.++...
T Consensus 78 VeGrL~~~~yeDk-dG~kr~~~eVvA~---~V~fL~sr~~~ 114 (182)
T PRK06958 78 IEGRIRTRKWQGQ-DGQDRYSTEIVAD---QMQMLGGRGGS 114 (182)
T ss_pred EEEEEEeCceECC-CCcEEEEEEEEEe---EEEECCCCccC
Confidence 9999999999998 9999999999999 99999988643
No 7
>PRK13732 single-stranded DNA-binding protein; Provisional
Probab=99.97 E-value=4.6e-31 Score=212.64 Aligned_cols=117 Identities=26% Similarity=0.556 Sum_probs=108.5
Q ss_pred ccccEEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEEE
Q 030281 48 RGVHKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVYV 127 (180)
Q Consensus 48 ~~mN~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~V 127 (180)
++||+|+|+||||+||++|++++|..+++|+||+++.|+++.+|++ .+.++||+|++||+ +|+.+.++|+||++|+|
T Consensus 4 r~mN~V~LiGrLg~DPElR~t~nG~~va~fslAvn~~~kd~~~Ge~--~e~t~w~~Vv~wgk-~Ae~v~~~L~KG~~V~V 80 (175)
T PRK13732 4 RGINKVILVGRLGKDPEVRYIPNGGAVANLQVATSESWRDKQTGEM--REQTEWHRVVLFGK-LAEVAGEYLRKGAQVYI 80 (175)
T ss_pred cCceEEEEEEEecCCCEEEEcCCCCEEEEEEEEEcCccccCCCCce--ecceeEEEEEEecH-HHHHHHHhcCCCCEEEE
Confidence 3799999999999999999999999999999999999987656775 57899999999998 99999999999999999
Q ss_pred EEEeEEeeeecCCCCeEEEEEEEEEEeCCceEEecCCCCCCC
Q 030281 128 EGDIEIRVYNDSINGEVKNIPEICIRRDGTLRLVKSGESISK 169 (180)
Q Consensus 128 eGrL~~~~y~d~~dG~~~~~~eI~v~~~g~i~~l~~k~~~~~ 169 (180)
+|+|+++.|++ +|++++.++|+|+..|+|+||+++.....
T Consensus 81 eGrL~~r~ye~--dG~kr~~~eIiv~~~g~~~fL~~~~~~~~ 120 (175)
T PRK13732 81 EGQLRTRSWED--NGITRYVTEILVKTTGTMQMLGRAPQQNA 120 (175)
T ss_pred EEEEEeeeEcc--CCeEEEEEEEEEeecCeEEEecCCCCCCC
Confidence 99999999986 69999999999998889999999976554
No 8
>PRK08763 single-stranded DNA-binding protein; Provisional
Probab=99.97 E-value=5.6e-31 Score=210.23 Aligned_cols=111 Identities=26% Similarity=0.493 Sum_probs=104.2
Q ss_pred cccEEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEEEE
Q 030281 49 GVHKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVYVE 128 (180)
Q Consensus 49 ~mN~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~Ve 128 (180)
+||+|+|+||||+||+++++++|..+++|+||+++.|+++. |++ .+.++||+|++||+ +|+++.++|+||++|+|+
T Consensus 4 ~~Nkv~LiGrLg~DPelr~t~~G~~va~fsVA~~~~~k~~~-G~~--~e~t~w~~Vv~fgk-~Ae~v~~~L~KGs~V~Ve 79 (164)
T PRK08763 4 GINKVILVGNLGNDPDIKYTQSGMTITRISLATTSVRKDRE-GNT--QERTEWHRVKFFGK-LGEIAGEYLRKGSQCYIE 79 (164)
T ss_pred cceEEEEEEEecCCCeEEEcCCCCeEEEEEEEeccceecCC-CCe--eccceEEEEEEehH-HHHHHHHhcCCCCEEEEE
Confidence 79999999999999999999999999999999999998874 765 46899999999998 999999999999999999
Q ss_pred EEeEEeeeecCCCCeEEEEEEEEEEeCCceEEecCCCCC
Q 030281 129 GDIEIRVYNDSINGEVKNIPEICIRRDGTLRLVKSGESI 167 (180)
Q Consensus 129 GrL~~~~y~d~~dG~~~~~~eI~v~~~g~i~~l~~k~~~ 167 (180)
|+|+++.|+++ +|++++.++|+|+ +|+||+++..+
T Consensus 80 GrL~~~~y~dk-dG~kr~~~eIva~---~i~~L~~~~~~ 114 (164)
T PRK08763 80 GSIRYDKFTGQ-DGQERYVTEIVAD---EMQMLGGRGEG 114 (164)
T ss_pred EEEEeceeECC-CCCEEEEEEEEEe---EEEECCCCCCC
Confidence 99999999998 9999999999999 99999988543
No 9
>PRK07459 single-stranded DNA-binding protein; Provisional
Probab=99.97 E-value=7.9e-31 Score=199.94 Aligned_cols=106 Identities=17% Similarity=0.335 Sum_probs=98.2
Q ss_pred ccEEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEEEEE
Q 030281 50 VHKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVYVEG 129 (180)
Q Consensus 50 mN~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~VeG 129 (180)
||+|+|+||||+||+++++++|+.+++|+||+++.|++ ..++||+|++||+ +|+.+.++|+||++|+|+|
T Consensus 3 ~N~v~LiGrL~~DPelr~t~~G~~v~~fslAv~~~~~~---------~~t~w~~v~~wg~-~Ae~~~~~l~KG~~V~V~G 72 (121)
T PRK07459 3 LNSVTLVGRAGRDPEVRYFESGSVVCNLTLAVNRRSRD---------DEPDWFNLEIWGK-TAQVAADYVKKGSLIGITG 72 (121)
T ss_pred ccEEEEEEEccCCCEEEEcCCCCEEEEEEEEecccccC---------CCceEEEEEEehH-HHHHHHHHcCCCCEEEEEE
Confidence 89999999999999999999999999999999987753 2688999999998 9999999999999999999
Q ss_pred EeEEeeeecCCC-CeEEEEEEEEEEeCCceEEecCCCCCCC
Q 030281 130 DIEIRVYNDSIN-GEVKNIPEICIRRDGTLRLVKSGESISK 169 (180)
Q Consensus 130 rL~~~~y~d~~d-G~~~~~~eI~v~~~g~i~~l~~k~~~~~ 169 (180)
+|+++.|+++ + |++++.++|+|+ +|++|+++...+.
T Consensus 73 ~l~~~~~~d~-d~G~~r~~~ei~a~---~i~~L~~k~~~~~ 109 (121)
T PRK07459 73 SLKFDRWTDR-NTGEDRSKPVIRVD---RLELLGSKRDSEG 109 (121)
T ss_pred EEEecceEcC-CCCeEEEEEEEEEe---EEEECcCCCcccc
Confidence 9999999998 6 999999999999 9999998865433
No 10
>PRK08486 single-stranded DNA-binding protein; Provisional
Probab=99.97 E-value=1.1e-30 Score=211.64 Aligned_cols=111 Identities=21% Similarity=0.343 Sum_probs=104.2
Q ss_pred cccEEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEEEE
Q 030281 49 GVHKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVYVE 128 (180)
Q Consensus 49 ~mN~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~Ve 128 (180)
|||+|+|+|||++||++|++++|+.+|+|+||++++|++. +|++ .+.++||+|++||+ +|+.+.++|+||++|+|+
T Consensus 1 m~N~V~LvGrL~~DPElr~t~sG~~va~fslAv~r~~~~~-~Ge~--~e~t~fi~v~~fg~-~AE~~~~~l~KG~~V~Ve 76 (182)
T PRK08486 1 MFNKVILVGNLTRDVELRYLPSGSAIATIGLATSRRFKKQ-DGEK--GEEVCFIDIRLFGR-TAEIANQYLSKGSKVLIE 76 (182)
T ss_pred CeeEEEEEEEecCCCEEEECCCCCEEEEEEEEEecceecC-CCCC--cccceEEEEEEEhH-HHHHHHHHcCCCCEEEEE
Confidence 6899999999999999999999999999999999999876 4775 57899999999999 999999999999999999
Q ss_pred EEeEEeeeecCCCCeEEEEEEEEEEeCCceEEecCCCCC
Q 030281 129 GDIEIRVYNDSINGEVKNIPEICIRRDGTLRLVKSGESI 167 (180)
Q Consensus 129 GrL~~~~y~d~~dG~~~~~~eI~v~~~g~i~~l~~k~~~ 167 (180)
|+|+++.|+++ +|++++.++|+|+ .|+||.++...
T Consensus 77 GrL~~~~y~dk-dG~~r~~~eI~a~---~v~~L~~~~~~ 111 (182)
T PRK08486 77 GRLTFESWMDQ-NGQKRSKHTITAE---SMQMLDSKSDN 111 (182)
T ss_pred EEEEeCcEECC-CCcEEEEEEEEEe---EEEECCCCCCC
Confidence 99999999999 9999999999999 99999988653
No 11
>PRK05733 single-stranded DNA-binding protein; Provisional
Probab=99.97 E-value=2.8e-30 Score=207.56 Aligned_cols=114 Identities=30% Similarity=0.550 Sum_probs=106.4
Q ss_pred ccccEEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEEE
Q 030281 48 RGVHKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVYV 127 (180)
Q Consensus 48 ~~mN~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~V 127 (180)
++||+|+|+||||+||++++++||..+++|+||+++.|++..+|++ .+.++||+|++||+ +|+.+.++|+||++|+|
T Consensus 3 ~~mNkV~LiGrlg~DPElr~t~nG~~va~fsVAv~~~~k~~~~Ge~--~e~T~w~~Vv~fgk-~Ae~v~~~l~KGs~V~V 79 (172)
T PRK05733 3 RGVNKVILVGTCGQDPEVRYLPNGNAVTNLSLATSEQWTDKQSGQK--VERTEWHRVSLFGK-VAEIAGEYLRKGSQVYI 79 (172)
T ss_pred CcceEEEEEEEecCCCEEEECCCCCEEEEEEEEEcCccccCCCCcc--cccceEEEEEEehH-HHHHHHHHhCCCCEEEE
Confidence 4799999999999999999999999999999999998887656775 56899999999998 99999999999999999
Q ss_pred EEEeEEeeeecCCCCeEEEEEEEEEEeCCceEEecCCCC
Q 030281 128 EGDIEIRVYNDSINGEVKNIPEICIRRDGTLRLVKSGES 166 (180)
Q Consensus 128 eGrL~~~~y~d~~dG~~~~~~eI~v~~~g~i~~l~~k~~ 166 (180)
+|+|+++.|+ + +|++++.++|+|+..|.|+||+++..
T Consensus 80 eGrLr~~~y~-k-dG~~r~~~eVvvd~~g~v~~L~~~~~ 116 (172)
T PRK05733 80 EGKLQTREWE-K-DGIKRYTTEIVVDMQGTMQLLGGRPQ 116 (172)
T ss_pred EEEEEeCcEe-c-CCEEEEEEEEEEeecCeEEECcCCCC
Confidence 9999999999 6 89999999999998889999997765
No 12
>PRK07274 single-stranded DNA-binding protein; Provisional
Probab=99.97 E-value=2.3e-30 Score=199.64 Aligned_cols=107 Identities=19% Similarity=0.374 Sum_probs=100.0
Q ss_pred cccEEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEEEE
Q 030281 49 GVHKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVYVE 128 (180)
Q Consensus 49 ~mN~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~Ve 128 (180)
|||+|+|+||||+||+++++++|+.+++|+||++++|++. +|++ .++||+|++||+ +|++++++|+||++|+|+
T Consensus 1 mmN~v~LiGrL~~dPelr~t~~g~~~~~fslAv~~~~k~~-~g~~----~t~w~~v~~fg~-~Ae~v~~~l~KG~~V~V~ 74 (131)
T PRK07274 1 MYNKVILIGRLTATPELVKTANDKSVARVTLAVNRRFKNQ-NGER----EADFINVVLWGK-LAETLASYASKGSLISID 74 (131)
T ss_pred CeeEEEEEEEccCCCeEEECCCCCEEEEEEEEEcCceecC-CCCE----EEEEEEEEEehH-HHHHHHHHcCCCCEEEEE
Confidence 6999999999999999999999999999999999999876 3753 589999999998 999999999999999999
Q ss_pred EEeEEeeeecCCCCeEEEEEEEEEEeCCceEEecCCCC
Q 030281 129 GDIEIRVYNDSINGEVKNIPEICIRRDGTLRLVKSGES 166 (180)
Q Consensus 129 GrL~~~~y~d~~dG~~~~~~eI~v~~~g~i~~l~~k~~ 166 (180)
|+|+++.| ++ +|++++.++|+|+ +|++|+++..
T Consensus 75 Grl~~~~y-~k-dG~~~~~~eviv~---~i~~l~~k~~ 107 (131)
T PRK07274 75 GELRTRKY-EK-DGQTHYVTEVLCQ---SFQLLESRAQ 107 (131)
T ss_pred EEEEeccC-cc-CCcEEEEEEEEEE---EEEECcCCCc
Confidence 99999999 77 9999999999999 9999997743
No 13
>PRK06751 single-stranded DNA-binding protein; Provisional
Probab=99.97 E-value=3.4e-30 Score=207.31 Aligned_cols=109 Identities=17% Similarity=0.347 Sum_probs=102.0
Q ss_pred cccEEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEEEE
Q 030281 49 GVHKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVYVE 128 (180)
Q Consensus 49 ~mN~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~Ve 128 (180)
|||+|+|+|||++||++|++++|.++++|+||+++.|++. .|++ .++||+|++||+ +|+.++++|+||++|+|+
T Consensus 1 MmN~V~LiGrL~~DpelR~t~sG~~v~~fslAvnr~~~~~-~ge~----~tdwi~~v~wgk-~Ae~~~~~l~KG~~V~Ve 74 (173)
T PRK06751 1 MMNRVILVGRLTKDPDLRYTPNGVAVATFTLAVNRAFANQ-QGER----EADFINCVIWRK-QAENVANYLKKGSLAGVD 74 (173)
T ss_pred CceEEEEEEEECCCCcEEECCCCCEEEEEEEEEccceecC-CCCE----EEEEEEEEEeCc-HHHHHHHHcCCCCEEEEE
Confidence 6899999999999999999999999999999999988866 3653 689999999999 999999999999999999
Q ss_pred EEeEEeeeecCCCCeEEEEEEEEEEeCCceEEecCCCCC
Q 030281 129 GDIEIRVYNDSINGEVKNIPEICIRRDGTLRLVKSGESI 167 (180)
Q Consensus 129 GrL~~~~y~d~~dG~~~~~~eI~v~~~g~i~~l~~k~~~ 167 (180)
|+|+++.|+++ +|++++.++|+|+ .|+||.++...
T Consensus 75 GrL~~r~yedk-dG~~~~~~eVva~---~i~~l~~r~~~ 109 (173)
T PRK06751 75 GRLQTRNYEGQ-DGKRVYVTEVLAE---SVQFLEPRNGG 109 (173)
T ss_pred EEEEeCccCCC-CCcEEEEEEEEEE---EEEeCcCCCCC
Confidence 99999999998 9999999999999 99999988654
No 14
>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=99.97 E-value=6.7e-30 Score=203.84 Aligned_cols=111 Identities=28% Similarity=0.483 Sum_probs=105.2
Q ss_pred cccccEEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEE
Q 030281 47 FRGVHKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVY 126 (180)
Q Consensus 47 m~~mN~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~ 126 (180)
|+|||+|+|+|||++||++|++++|+.+++|+||++++|+++. |++ .+.++||+|++||+ +|++++++|+||++|+
T Consensus 1 m~m~N~V~L~G~l~~dPe~r~t~~G~~v~~fsvA~~~~~~~~~-G~~--~~~t~~~~v~~wg~-~Ae~~~~~l~KG~~V~ 76 (164)
T TIGR00621 1 MRMVNKVILVGRLTRDPELRYTPSGNAVANFTLATNRRWKDQD-GEW--KEETEWHDIVIFGR-LAEVAAQYLKKGSLVY 76 (164)
T ss_pred CCcccEEEEEEEeCCCCEEEECCCCCEEEEEEEEEcCceecCC-CCE--eccceEEEEEEehH-HHHHHHHhCCCCCEEE
Confidence 8999999999999999999999999999999999999998874 775 57899999999999 9999999999999999
Q ss_pred EEEEeEEeeeecCCCCeEEEEEEEEEEeCCceEEecCCC
Q 030281 127 VEGDIEIRVYNDSINGEVKNIPEICIRRDGTLRLVKSGE 165 (180)
Q Consensus 127 VeGrL~~~~y~d~~dG~~~~~~eI~v~~~g~i~~l~~k~ 165 (180)
|+|+|+++.|+++ +|++++.++|+|+ +|.+|..+.
T Consensus 77 V~G~L~~~~~~~k-dG~~~~~~ev~a~---~i~~L~~~~ 111 (164)
T TIGR00621 77 VEGRLRTRKWEDQ-NGQKRSKTEIIAD---NVQLLDLLG 111 (164)
T ss_pred EEEEEEeceEECC-CCcEEEEEEEEEE---EEeeccccC
Confidence 9999999999998 9999999999999 899998774
No 15
>PRK06341 single-stranded DNA-binding protein; Provisional
Probab=99.97 E-value=1.2e-29 Score=202.95 Aligned_cols=115 Identities=24% Similarity=0.498 Sum_probs=104.7
Q ss_pred cccEEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEEEE
Q 030281 49 GVHKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVYVE 128 (180)
Q Consensus 49 ~mN~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~Ve 128 (180)
+||+|+|+|||++||++|++++|+++++|+||+++.|+++++|++ .+.|+||+|++|++.+|+.+.++|+||++|+|+
T Consensus 4 ~mN~V~LiGrLg~DPElR~t~sG~~v~~fsVAvn~~~kd~~~Ge~--~e~T~w~~Vv~fg~~~Ae~~~~~LkKG~~V~Ve 81 (166)
T PRK06341 4 SVNKVILIGNLGADPEIRRTQDGRPIANLRIATSETWRDRNSGER--KEKTEWHRVVIFNEGLCKVAEQYLKKGAKVYIE 81 (166)
T ss_pred cceEEEEEEEecCCCEEEEcCCCCEEEEEEEEEccceecCCCCcc--cccceEEEEEEeChHHHHHHHHhcCCCCEEEEE
Confidence 499999999999999999999999999999999999988766765 578999999999965899999999999999999
Q ss_pred EEeEEeeeecCCCCeEEEEEEEEEEe-CCceEEecCCCC
Q 030281 129 GDIEIRVYNDSINGEVKNIPEICIRR-DGTLRLVKSGES 166 (180)
Q Consensus 129 GrL~~~~y~d~~dG~~~~~~eI~v~~-~g~i~~l~~k~~ 166 (180)
|+|+++.|+++ +|++++.++|+|+. ...++||+++.+
T Consensus 82 GrL~~r~w~dk-dG~~r~~~eIiv~~~~~~l~~l~~~~~ 119 (166)
T PRK06341 82 GQLQTRKWTDQ-SGVERYSTEVVLQGFNSTLTMLDGRGE 119 (166)
T ss_pred EEEEeCcEECC-CCCEEEEEEEEEEecccceEEcccCCc
Confidence 99999999998 99999999999984 345799988753
No 16
>PRK08182 single-stranded DNA-binding protein; Provisional
Probab=99.97 E-value=2e-29 Score=198.30 Aligned_cols=111 Identities=14% Similarity=0.161 Sum_probs=101.5
Q ss_pred cccEEEEEEEeCCCCeEEEecCCeE----EEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCe
Q 030281 49 GVHKAIICGKVKDTPVQKILRNGKT----VTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSS 124 (180)
Q Consensus 49 ~mN~v~L~Grlg~dPe~r~t~nG~~----v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~ 124 (180)
|||+|+|+||||+||+++++++|.. +++|+||+++.|++. +|++. ...++||+|++||+ +|+++.++|+||++
T Consensus 1 M~N~V~LiGrLg~DPElr~t~~G~~~~~~va~fslA~~r~~~~~-~Ge~~-~~~t~w~~V~~wg~-~Ae~v~~~l~KG~~ 77 (148)
T PRK08182 1 MSTHFVGEGNIGSAPEYREFPNGNDEPRRLLRLNVYFDNPVPTK-DGEYE-DRGGFWAPVELWHR-DAEHWARLYQKGMR 77 (148)
T ss_pred CccEEEEEEECCCCCeEEECCCCCeeeeeEEEEEEEecCceECC-CCCEE-ecCcEEEEEEEEhH-HHHHHHHhcCCCCE
Confidence 6899999999999999999999986 999999999999876 47752 23689999999999 99999999999999
Q ss_pred EEEEEEeEEeeeecCCCCeEEEEEEEEEEeCCceEEecCCCC
Q 030281 125 VYVEGDIEIRVYNDSINGEVKNIPEICIRRDGTLRLVKSGES 166 (180)
Q Consensus 125 V~VeGrL~~~~y~d~~dG~~~~~~eI~v~~~g~i~~l~~k~~ 166 (180)
|+|+|+|+++.|+++ +|++++.++|+|+ .|.||.++..
T Consensus 78 V~V~GrL~~~~w~dk-dG~~r~~~eI~a~---~i~~l~~r~~ 115 (148)
T PRK08182 78 VLVEGRMERDEWTDN-EDNERVTFKVEAR---RVGILPYRIE 115 (148)
T ss_pred EEEEEEEEecccCCC-CCCEEEEEEEEEe---EEEEcCCccc
Confidence 999999999999999 9999999999999 8999876654
No 17
>PRK06293 single-stranded DNA-binding protein; Provisional
Probab=99.96 E-value=2.4e-28 Score=194.46 Aligned_cols=104 Identities=21% Similarity=0.387 Sum_probs=96.7
Q ss_pred ccEEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEEEEE
Q 030281 50 VHKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVYVEG 129 (180)
Q Consensus 50 mN~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~VeG 129 (180)
||+|+|+||||+||++|++++|+.+++|+||+++++ |. ...|+||+|++|++ +|++++++|+||++|+|+|
T Consensus 1 MN~V~LiGrLg~DPElR~t~sG~~v~~FsLAvn~~~-----~~---~~~T~wi~v~awg~-~Ae~v~~yL~KG~~V~VeG 71 (161)
T PRK06293 1 MMFGYIVGRLGADPEERMTSKGKRVVVLRLGVKSRV-----GS---KDETVWCRCNIWGN-RYDKMLPYLKKGSGVIVAG 71 (161)
T ss_pred CeEEEEEEEecCCCeEEEcCCCCEEEEEEEEEeCCC-----CC---ccceEEEEEEEEhH-HHHHHHHhCCCCCEEEEEE
Confidence 899999999999999999999999999999999764 22 25799999999998 9999999999999999999
Q ss_pred EeEEeeeecCCCCeEEEEEEEEEEeCCceEEecCCCC
Q 030281 130 DIEIRVYNDSINGEVKNIPEICIRRDGTLRLVKSGES 166 (180)
Q Consensus 130 rL~~~~y~d~~dG~~~~~~eI~v~~~g~i~~l~~k~~ 166 (180)
+|+++.|+++ +|++++.++|+|+ +|.||..+..
T Consensus 72 rL~~~~y~dk-dG~kr~~~eIva~---~I~fl~~~~~ 104 (161)
T PRK06293 72 EMSPESYVDK-DGSPQSSLVVSVD---TIKFSPFGRN 104 (161)
T ss_pred EEEeCccCCC-CCCEEEEEEEEEe---EEEECcCCCc
Confidence 9999999999 9999999999999 9999977754
No 18
>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=99.95 E-value=2.7e-27 Score=172.70 Aligned_cols=104 Identities=24% Similarity=0.472 Sum_probs=93.5
Q ss_pred ccEEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEEEEE
Q 030281 50 VHKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVYVEG 129 (180)
Q Consensus 50 mN~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~VeG 129 (180)
||+|+|+|+|++||+++++++|+.++.|+||++++|++. .+.. ...++||+|++||+ +|+.++++|+||++|+|+|
T Consensus 1 mN~v~l~G~l~~~p~~~~~~~g~~~~~f~la~~~~~~~~-~~~~--~~~~~~~~v~~~g~-~A~~~~~~l~kG~~V~V~G 76 (104)
T PF00436_consen 1 MNKVTLIGRLGKDPELRYTKNGTPVARFSLAVNRRFKDD-GGEG--DEKTDWINVVAWGK-LAENVAEYLKKGDRVYVEG 76 (104)
T ss_dssp EEEEEEEEEESSSEEEEEETTSEEEEEEEEEEEEEEEET-TSCE--EEEEEEEEEEEEHH-HHHHHHHH--TT-EEEEEE
T ss_pred CcEEEEEEEECCCcEEEECCCCCEEEEEEEEEecEEeee-eccC--ccceEEEEEEeeee-cccccceEEcCCCEEEEEE
Confidence 899999999999999999999999999999999998873 2333 46899999999999 9999999999999999999
Q ss_pred EeEEeeeecCCCCeEEEEEEEEEEeCCceEEe
Q 030281 130 DIEIRVYNDSINGEVKNIPEICIRRDGTLRLV 161 (180)
Q Consensus 130 rL~~~~y~d~~dG~~~~~~eI~v~~~g~i~~l 161 (180)
+|+++.|+++ +|++++.++|.|+ +|.||
T Consensus 77 ~l~~~~~~~~-~G~~~~~~~i~a~---~i~fl 104 (104)
T PF00436_consen 77 RLRTRTYEDK-DGQKRYRVEIIAD---NIEFL 104 (104)
T ss_dssp EEEEEEEEST-TSSEEEEEEEEEE---EEEE-
T ss_pred EEEeeEEECC-CCCEEEEEEEEEE---EEEeC
Confidence 9999999998 8999999999999 89986
No 19
>KOG1653 consensus Single-stranded DNA-binding protein [Replication, recombination and repair]
Probab=99.95 E-value=3.3e-28 Score=191.81 Aligned_cols=141 Identities=50% Similarity=0.821 Sum_probs=119.4
Q ss_pred ccccccchhhccccccCCCCCCCCCCcccccccEEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCC
Q 030281 19 EVDDVFDDFVVEKQELQPQGVDPRRGWGFRGVHKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKP 98 (180)
Q Consensus 19 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~m~~mN~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~ 98 (180)
-.+...+|++.++++ +..+++|+| ..+++|+++|+|+||+||.+|..+||++|+.|+|+++.+|+++--+...+..+
T Consensus 27 Pi~~~v~d~~a~~~~-~~~~~~p~k--~~~~vnkv~lvG~VGqdPl~k~~rngrpVtiFsv~T~~~~k~r~~q~g~~~~~ 103 (175)
T KOG1653|consen 27 PILQGVRDLFAENSE-TTTGEDPRK--LERGVNKVILVGRVGQDPLQKILRNGRPVTIFSVGTGGMFKQRLYQAGDQPQP 103 (175)
T ss_pred chhhhhhhhHhhccc-ccCccchhh--hhcccceEEEEcccccchHHHhhcCCCeEEEEEeecCccccccccccCCcCCc
Confidence 345678999999986 578999988 55999999999999999999999999999999999999998432222234889
Q ss_pred ceEEEEEecCchhHHHHHHhcCCCCeEEEEEEeEEeeeecCCCCeEEEEEEEEEEeCCceEEecCC
Q 030281 99 VQWHRIAVHNEILGSYAVKQLVKNSSVYVEGDIEIRVYNDSINGEVKNIPEICIRRDGTLRLVKSG 164 (180)
Q Consensus 99 t~w~~V~~~gk~~Ae~~~~~l~KG~~V~VeGrL~~~~y~d~~dG~~~~~~eI~v~~~g~i~~l~~k 164 (180)
++||+|++|++.+|+++.++|+||++|||+|+|+++.+.++++|..+.+.++++.+ .+.||...
T Consensus 104 tqWHRVsVf~~~L~d~~~k~lkKGsriyveG~iey~g~~~d~~g~~~r~~t~iIa~--~v~Fl~~a 167 (175)
T KOG1653|consen 104 TQWHRVSVFNEVLADYALKYLKKGSRIYVEGKIEYRGENDDIQGNVKRIPTIIIAR--DVSFLIDA 167 (175)
T ss_pred ceeEEEEeeCchHHHHHHHHhcCCCEEEEeeeEEeeeeeccccCceeecceEEEec--hhHHHHHH
Confidence 99999999998899999999999999999999999999988899986665555543 67776543
No 20
>PRK07772 single-stranded DNA-binding protein; Provisional
Probab=99.95 E-value=3.1e-27 Score=192.05 Aligned_cols=112 Identities=20% Similarity=0.317 Sum_probs=98.6
Q ss_pred cccccEEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEE
Q 030281 47 FRGVHKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVY 126 (180)
Q Consensus 47 m~~mN~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~ 126 (180)
|.++|.|+|+|||++||++|++++|+.+++|+||++.++.++++|++. ...+.||+|++|++ +|++++++|+||++|+
T Consensus 1 m~~~~~VtLiGrL~~DPElR~t~sG~~va~FrVAv~~r~~~~~~g~~~-d~~t~fi~V~~Wg~-~Ae~va~~L~KGd~V~ 78 (186)
T PRK07772 1 MAGDTTITVVGNLTADPELRFTPSGAAVANFTVASTPRTFDRQTNEWK-DGEALFLRCSIWRQ-AAENVAESLTKGMRVI 78 (186)
T ss_pred CCccCEEEEEEEeCCCCeEEEcCCCCEEEEEEEEecCcceecCCCcEe-ccCceEEEEEEecH-HHHHHHHhcCCCCEEE
Confidence 778999999999999999999999999999999998655455457652 34799999999999 9999999999999999
Q ss_pred EEEEeEEeeeecCCCCeEEEEEEEEEEeCC-ceEEe
Q 030281 127 VEGDIEIRVYNDSINGEVKNIPEICIRRDG-TLRLV 161 (180)
Q Consensus 127 VeGrL~~~~y~d~~dG~~~~~~eI~v~~~g-~i~~l 161 (180)
|+|+|+++.|+++ +|++++.++|+|++-| .|.+.
T Consensus 79 V~GrL~~r~wedk-dG~~rt~~eV~a~~Vg~~L~~~ 113 (186)
T PRK07772 79 VTGRLKQRSYETR-EGEKRTVVELEVDEIGPSLRYA 113 (186)
T ss_pred EEEEEEcCceECC-CCCEEEEEEEEEEEcccceeee
Confidence 9999999999999 9999999999999433 34444
No 21
>COG0629 Ssb Single-stranded DNA-binding protein [DNA replication, recombination, and repair]
Probab=99.94 E-value=1.7e-26 Score=184.45 Aligned_cols=114 Identities=26% Similarity=0.478 Sum_probs=91.7
Q ss_pred ccccEEEEEEEeCCCCeEEEecCC-eEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEE
Q 030281 48 RGVHKAIICGKVKDTPVQKILRNG-KTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVY 126 (180)
Q Consensus 48 ~~mN~v~L~Grlg~dPe~r~t~nG-~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~ 126 (180)
.+||+|+|+|||++||++|++++| ..++.|++++++.+ ++.+|+. ...++||+|++||+ +|+.+.+||+||++|+
T Consensus 1 ~~~Nkv~LvG~l~~DPE~r~t~~g~~~v~~~~~a~~r~~-~~~~~~~--~~~t~~~~vv~wgk-~Ae~~~~yl~KG~~V~ 76 (167)
T COG0629 1 MMMNKVILVGRLTRDPELRYTPNGGAVVALFSAAVNRRF-DNQSGER--DEETDWIRVVIWGK-LAENAAEYLKKGSLVY 76 (167)
T ss_pred CCcceEEEEeecccCcceeecCCCCeeeEEEEEEecccc-ccCCccc--ccccceEEEEEehH-HHHHHHHHhcCCCEEE
Confidence 089999999999999999999955 55666666666654 4434554 56899999999999 9999999999999999
Q ss_pred EEEEeEEeeeecCCCCeEEEEEEEEEEe-CCceEEecCCCC
Q 030281 127 VEGDIEIRVYNDSINGEVKNIPEICIRR-DGTLRLVKSGES 166 (180)
Q Consensus 127 VeGrL~~~~y~d~~dG~~~~~~eI~v~~-~g~i~~l~~k~~ 166 (180)
|+|+|+++.|+++ +|.++|..++.++. ...+++|.++..
T Consensus 77 VeG~l~~~~~~~~-~G~~r~~~~~~~~~v~~~~~~l~~~~~ 116 (167)
T COG0629 77 VEGRLQTRKWEDQ-EGQKRYQTEIVTEIVADSVQMLGSRKS 116 (167)
T ss_pred EEEEEEeeeeecC-CCcceeeEEEEEEEeehhhhhccCccc
Confidence 9999999999999 99666666654442 227788888754
No 22
>PRK05813 single-stranded DNA-binding protein; Provisional
Probab=99.93 E-value=5.6e-25 Score=182.84 Aligned_cols=102 Identities=14% Similarity=0.209 Sum_probs=93.8
Q ss_pred ccccEEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEEE
Q 030281 48 RGVHKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVYV 127 (180)
Q Consensus 48 ~~mN~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~V 127 (180)
..||+|+|+|||++||++|++++|+++++|+||+++.|+ .++||+|++||+ +|+++. +|+||++|+|
T Consensus 107 ~~~N~V~LiGrL~~DPelR~t~~G~~va~f~lAvnr~~~-----------~td~i~~v~wg~-~Ae~~~-~l~KG~~V~V 173 (219)
T PRK05813 107 KNPNEIFLDGYICKEPVYRTTPFGREIADLLLAVNRPYN-----------KSDYIPCIAWGR-NARFCK-TLEVGDNIRV 173 (219)
T ss_pred CCccEEEEEEEccCCCeEEECCCCCEEEEEEEEEcCCCC-----------CceEEEEEEEhH-HhHHHh-hCCCCCEEEE
Confidence 459999999999999999999999999999999998652 468999999999 999875 6999999999
Q ss_pred EEEeEEeeeecCCC----CeEEEEEEEEEEeCCceEEecCCCC
Q 030281 128 EGDIEIRVYNDSIN----GEVKNIPEICIRRDGTLRLVKSGES 166 (180)
Q Consensus 128 eGrL~~~~y~d~~d----G~~~~~~eI~v~~~g~i~~l~~k~~ 166 (180)
+|+|+++.|+++ + |++++.++|.|+ +|++|++++.
T Consensus 174 ~GrL~sr~y~~k-~g~~~g~kr~~~eV~v~---~i~~l~~~~~ 212 (219)
T PRK05813 174 WGRVQSREYQKK-LSEGEVVTKVAYEVSIS---KMEKVEKEEA 212 (219)
T ss_pred EEEEEecceEcC-CCCccceEEEEEEEEEE---EEEEcCChhh
Confidence 999999999997 6 489999999999 9999988875
No 23
>PRK05853 hypothetical protein; Validated
Probab=99.92 E-value=1.1e-24 Score=173.49 Aligned_cols=95 Identities=18% Similarity=0.267 Sum_probs=87.3
Q ss_pred EEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEEEEEEeEEe
Q 030281 55 ICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVYVEGDIEIR 134 (180)
Q Consensus 55 L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~VeGrL~~~ 134 (180)
|+|||++||+++++ +|..+++|+||++++|++. +|+++ ...++||+|++||+ +|+++.++|+||++|+|+|+|+++
T Consensus 1 ivGrLg~DPelr~~-~g~~va~F~lAvn~r~~~~-~Ge~~-d~~T~wi~V~~wg~-lAe~v~~~L~KG~~V~V~GrL~~~ 76 (161)
T PRK05853 1 VVGHIVNDPQRRKV-GDQEVIKFRVASNSRRRTA-DGGWE-PGNSLFITVNCWGR-LVTGVGAALGKGAPVIVVGHVYTS 76 (161)
T ss_pred CeEcccCCCEEEEE-CCceEEEEEEEECCCeECC-CCCEe-ccCccEEEEEEEhH-HHHHHHHHcCCCCEEEEEEEEEcc
Confidence 68999999999998 4789999999999999766 48763 34799999999998 999999999999999999999999
Q ss_pred eeecCCCCeEEEEEEEEEEe
Q 030281 135 VYNDSINGEVKNIPEICIRR 154 (180)
Q Consensus 135 ~y~d~~dG~~~~~~eI~v~~ 154 (180)
.|+++ +|++++.++|.++.
T Consensus 77 ~wedk-dG~~r~~~eV~a~~ 95 (161)
T PRK05853 77 EYEDR-DGNRRSSLEMRATS 95 (161)
T ss_pred ceECC-CCCEEEEEEEEEEE
Confidence 99999 99999999999994
No 24
>PRK02801 primosomal replication protein N; Provisional
Probab=99.92 E-value=3.9e-24 Score=158.34 Aligned_cols=101 Identities=16% Similarity=0.179 Sum_probs=87.2
Q ss_pred cccEEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEEEE
Q 030281 49 GVHKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVYVE 128 (180)
Q Consensus 49 ~mN~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~Ve 128 (180)
|||+++|+|||++||++|+|++|.++++|+||+.+ +....+++ ...+.||+|++||+ +|+.+.+||+||++|.|+
T Consensus 1 mmN~v~L~Grl~~dpelr~Tp~G~~v~~f~La~~~-~~~ea~~~---r~~~~~i~~va~G~-~Ae~~~~~l~kGs~v~V~ 75 (101)
T PRK02801 1 MTNRLVLSGTVCRTPKRKVSPSGIPHCQFVLEHRS-VQEEAGLH---RQAWCRMPVIVSGN-QFQAITQSITVGSKITVQ 75 (101)
T ss_pred CccEEEEEEEECcCcceEECCCCCeEEEEEEEEeC-eEecCCCc---eeEEEEEEEEEEcH-HHHHHHhhcCCCCEEEEE
Confidence 58999999999999999999999999999999964 33332222 24569999999999 999999999999999999
Q ss_pred EEeEEeeeecCCCCeEEEEEEEEEEeCCceEEec
Q 030281 129 GDIEIRVYNDSINGEVKNIPEICIRRDGTLRLVK 162 (180)
Q Consensus 129 GrL~~~~y~d~~dG~~~~~~eI~v~~~g~i~~l~ 162 (180)
|+|++ |+++ +|++++. |+++ .|+||+
T Consensus 76 G~L~~--~~~~-~g~~~~~--v~~~---~i~~l~ 101 (101)
T PRK02801 76 GFISC--HQGR-NGLSKLV--LHAE---QIELID 101 (101)
T ss_pred EEEEE--eECC-CCCEEEE--EEEE---EEEECC
Confidence 99999 6887 8988866 8888 898874
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=99.90 E-value=1.4e-22 Score=146.39 Aligned_cols=100 Identities=24% Similarity=0.440 Sum_probs=91.9
Q ss_pred EEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEEEEEEeE
Q 030281 53 AIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVYVEGDIE 132 (180)
Q Consensus 53 v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~VeGrL~ 132 (180)
|+|+|+|+++|+++++++|..++.|+|++++.+++.. .. ...++||+|.+||+ +|+.++++|+||++|+|+|+|+
T Consensus 1 v~l~G~l~~~p~~~~~~~g~~~~~~~v~~~~~~~~~~--~~--~~~~~~~~v~~~g~-~a~~~~~~~~kG~~V~v~G~l~ 75 (100)
T cd04496 1 VILIGRLGKDPELRYTPSGTPVARFSLAVNRRRKDRD--EE--EEETDWIRVVAFGK-LAENAAKYLKKGDLVYVEGRLR 75 (100)
T ss_pred CEEEEEecCCCEEEECCCCCEEEEEEEEEcCceeccc--cc--ccccEEEEEEEEhH-HHHHHHHHhCCCCEEEEEEEEE
Confidence 5799999999999999999999999999999887642 22 46899999999999 9999999999999999999999
Q ss_pred EeeeecCCCCeEEEEEEEEEEeCCceEEe
Q 030281 133 IRVYNDSINGEVKNIPEICIRRDGTLRLV 161 (180)
Q Consensus 133 ~~~y~d~~dG~~~~~~eI~v~~~g~i~~l 161 (180)
++.|+++ +|..++.++|.++ +|.++
T Consensus 76 ~~~~~~~-~g~~~~~~~i~~~---~i~~~ 100 (100)
T cd04496 76 TRSWEDK-DGQKRYGTEVVAD---RIEFL 100 (100)
T ss_pred eceeECC-CCCEEEEEEEEEE---EEEEC
Confidence 9999998 8999999999999 88775
No 26
>PRK05813 single-stranded DNA-binding protein; Provisional
Probab=99.82 E-value=2.5e-19 Score=149.11 Aligned_cols=99 Identities=19% Similarity=0.194 Sum_probs=91.0
Q ss_pred cccEEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEEEE
Q 030281 49 GVHKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVYVE 128 (180)
Q Consensus 49 ~mN~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~Ve 128 (180)
-.|+|+|+|+|++||+++++..|..+..|+||+++ +. ..++||+|++|++ +|+.+. |+||+.|+|+
T Consensus 7 ~~NkV~L~Grl~~d~e~~~~~~G~~~~~f~laV~R-~s----------~~~D~i~v~v~~r-lae~~~--l~kG~~v~Ve 72 (219)
T PRK05813 7 ENNKVYLEGKVVSELEFSHEMYGEGFYNFKLEVPR-LS----------DSKDILPVTVSER-LLAGMD--LKVGTLVIVE 72 (219)
T ss_pred hcCEEEEEEEEcCCceEEEEeCCeEEEEEEEEeec-cC----------CCccEEEEEEEhh-hhhhhc--ccCCCEEEEE
Confidence 37999999999999999999999999999999998 54 3678999999999 999877 9999999999
Q ss_pred EEeEEeeeecCCCCeEEEEEEEEEEeCCceEEecCCCC
Q 030281 129 GDIEIRVYNDSINGEVKNIPEICIRRDGTLRLVKSGES 166 (180)
Q Consensus 129 GrL~~~~y~d~~dG~~~~~~eI~v~~~g~i~~l~~k~~ 166 (180)
|+|| +|++.++|++++.++|.|+ +|++|++++.
T Consensus 73 Gqlr--sy~~~~~G~~R~vl~V~a~---~i~~l~~~~~ 105 (219)
T PRK05813 73 GQLR--SYNKFIDGKNRLILTVFAR---NIEYCDERSD 105 (219)
T ss_pred EEEE--EeccCCCCcEEEEEEEEEE---EEEEccCCCc
Confidence 9999 8887646999999999999 9999999864
No 27
>PRK00036 primosomal replication protein N; Reviewed
Probab=98.51 E-value=1.9e-06 Score=64.61 Aligned_cols=96 Identities=7% Similarity=0.026 Sum_probs=75.2
Q ss_pred ccEEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEEEEE
Q 030281 50 VHKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVYVEG 129 (180)
Q Consensus 50 mN~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~VeG 129 (180)
||++.|+|.|.+.|.+|+||.|-+++.|.|.-.+... + .|-. ...-.-+.+++.|+ +|+.+. .+..|+.|.|+|
T Consensus 1 mN~l~Ltg~v~~~~~lryTPAGIp~~~~~LeH~S~q~-E-AG~~--Rqv~~~i~ava~G~-~a~~~~-~l~~Gs~v~v~G 74 (107)
T PRK00036 1 MNTLELSARVLECGAMRHTPAGLPALELLLVHESEVV-E-AGHP--RRVELTISAVALGD-LALLLA-DTPLGTEMQVQG 74 (107)
T ss_pred CCEEEEEEEEeccCccccCCCCCceEEEEEEEeEEeE-e-CCCc--ceEEEEEEEEEEhh-HHHHhc-ccCCCCEEEEEE
Confidence 6999999999999999999999999999998776432 2 3542 22234467889997 888766 599999999999
Q ss_pred EeEEeeeecCCCCeEEEEEEEEEEeCCceEEe
Q 030281 130 DIEIRVYNDSINGEVKNIPEICIRRDGTLRLV 161 (180)
Q Consensus 130 rL~~~~y~d~~dG~~~~~~eI~v~~~g~i~~l 161 (180)
-|.. +. .|. ..+-+.++ .|+++
T Consensus 75 FLa~----~~-~~~--~~LVLHi~---~Ie~i 96 (107)
T PRK00036 75 FLAP----AR-KDS--VKVKLHLQ---QARRI 96 (107)
T ss_pred EEEE----CC-CCC--CcEEEEhH---HeEEc
Confidence 9998 22 344 45667777 88888
No 28
>COG2965 PriB Primosomal replication protein N [DNA replication, recombination, and repair]
Probab=98.40 E-value=6.8e-06 Score=60.54 Aligned_cols=100 Identities=13% Similarity=0.241 Sum_probs=76.3
Q ss_pred cccccEEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEE--EEecCchhHHHHHHhcCCCCe
Q 030281 47 FRGVHKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHR--IAVHNEILGSYAVKQLVKNSS 124 (180)
Q Consensus 47 m~~mN~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~--V~~~gk~~Ae~~~~~l~KG~~ 124 (180)
|.+.|++.|.|-|.+.|..+++|+|-+.|.|-+.-.. +.-+ .|. ..-.|.+ +.+-|+ +|+.+.+.+..|+.
T Consensus 1 ~~~~Nrl~L~g~vak~~~r~~sPsGIphc~f~Lehrs-~q~E-ag~----~RQv~~~mpv~vsG~-qa~~lt~~i~~Gs~ 73 (103)
T COG2965 1 MNMTNRLSLSGTVAKVPVRRYSPSGIPHCQFVLEHRS-WQEE-AGF----QRQVWCEMPVRVSGR-QAEELTQSITVGSY 73 (103)
T ss_pred CCccceEEEEEEeeccceeeeCCCCCeeEEEEEeecc-hhhh-CCc----ceeEEEEccEEeech-hhhhhhhccccccE
Confidence 4567999999999999999999999999999887765 3222 343 3555644 677888 89998888999999
Q ss_pred EEEEEEeEEeeeecCCCCeEEEEEEEEEEeCCceEEe
Q 030281 125 VYVEGDIEIRVYNDSINGEVKNIPEICIRRDGTLRLV 161 (180)
Q Consensus 125 V~VeGrL~~~~y~d~~dG~~~~~~eI~v~~~g~i~~l 161 (180)
|.|+|-|....-.. |- ..+-|.++ .|.++
T Consensus 74 i~v~GFla~~~~~s---g~--~~lvlha~---qi~~i 102 (103)
T COG2965 74 ILVVGFLACHKRRS---GL--SKLVLHAE---QIEFI 102 (103)
T ss_pred EEEEEEEEeecccC---Cc--cEEEEEee---EEEec
Confidence 99999998766543 43 44555555 56554
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=97.51 E-value=0.00084 Score=45.11 Aligned_cols=75 Identities=20% Similarity=0.355 Sum_probs=53.5
Q ss_pred EEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEEEEEEeE
Q 030281 53 AIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVYVEGDIE 132 (180)
Q Consensus 53 v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~VeGrL~ 132 (180)
|+|.|+|.+-. +++..++.|+|.-. +| -++|.+|++ .+....+.|+.|+.|.|.|.++
T Consensus 1 V~v~G~V~~~~-----~~~~~~~~~~l~D~-------tg---------~i~~~~~~~-~~~~~~~~l~~g~~v~v~G~v~ 58 (75)
T PF01336_consen 1 VTVEGRVTSIR-----RSGGKIVFFTLEDG-------TG---------SIQVVFFNE-EYERFREKLKEGDIVRVRGKVK 58 (75)
T ss_dssp EEEEEEEEEEE-----EEETTEEEEEEEET-------TE---------EEEEEEETH-HHHHHHHTS-TTSEEEEEEEEE
T ss_pred CEEEEEEEEEE-----cCCCCEEEEEEEEC-------Cc---------cEEEEEccH-HhhHHhhcCCCCeEEEEEEEEE
Confidence 57888888755 34566777765332 23 389999996 6778899999999999999999
Q ss_pred EeeeecCCCCeEEEEEEEEEEeCCceEEe
Q 030281 133 IRVYNDSINGEVKNIPEICIRRDGTLRLV 161 (180)
Q Consensus 133 ~~~y~d~~dG~~~~~~eI~v~~~g~i~~l 161 (180)
.. + ++ .++|.+. ++++|
T Consensus 59 ~~----~-~~----~~~l~~~---~i~~l 75 (75)
T PF01336_consen 59 RY----N-GG----ELELIVP---KIEIL 75 (75)
T ss_dssp EE----T-TS----SEEEEEE---EEEEE
T ss_pred EE----C-Cc----cEEEEEC---EEEEC
Confidence 87 2 34 4666666 56554
No 30
>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=96.37 E-value=0.03 Score=39.57 Aligned_cols=68 Identities=18% Similarity=0.273 Sum_probs=51.7
Q ss_pred EEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcC-CCCeEEEEEEe
Q 030281 53 AIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLV-KNSSVYVEGDI 131 (180)
Q Consensus 53 v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~-KG~~V~VeGrL 131 (180)
|+|.|.|-. .+.|.+.+|+.++.|.|.= | ++-+.|..|.+..-+ ....++ +|+-|.|.|++
T Consensus 2 v~i~G~Vf~-~e~re~k~g~~i~~~~itD---~-------------t~Si~~K~F~~~~~~-~~~~ik~~G~~v~v~G~v 63 (82)
T cd04484 2 VVVEGEVFD-LEIRELKSGRKILTFKVTD---Y-------------TSSITVKKFLRKDEK-DKEELKSKGDWVRVRGKV 63 (82)
T ss_pred EEEEEEEEE-EEEEEecCCCEEEEEEEEc---C-------------CCCEEEEEeccCChh-HHhhcccCCCEEEEEEEE
Confidence 789999965 7889999999888886652 1 112788888731333 346799 99999999999
Q ss_pred EEeeeec
Q 030281 132 EIRVYND 138 (180)
Q Consensus 132 ~~~~y~d 138 (180)
++..|..
T Consensus 64 ~~D~f~~ 70 (82)
T cd04484 64 QYDTFSK 70 (82)
T ss_pred EEccCCC
Confidence 9999964
No 31
>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=96.33 E-value=0.034 Score=38.64 Aligned_cols=73 Identities=22% Similarity=0.277 Sum_probs=50.8
Q ss_pred EEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEEEEEEeE
Q 030281 53 AIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVYVEGDIE 132 (180)
Q Consensus 53 v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~VeGrL~ 132 (180)
|.+.|-|.+.+. ++|+.|.++ +|. + .=++|++|.. .+..+...++.||.|.|.|++.
T Consensus 1 v~v~GeVs~~~~----~~GHvyfsL--------kD~--~--------a~i~cv~f~~-~~~~~~~~l~~Gd~V~v~G~v~ 57 (73)
T cd04487 1 VHIEGEVVQIKQ----TSGPTIFTL--------RDE--T--------GTVWAAAFEE-AGVRAYPEVEVGDIVRVTGEVE 57 (73)
T ss_pred CEEEEEEecccc----CCCCEEEEE--------EcC--C--------EEEEEEEEch-hccCCcCCCCCCCEEEEEEEEe
Confidence 357888888773 678866544 232 1 1289999987 5555777899999999999987
Q ss_pred EeeeecCCCCeEEEEEEEEEEeCCceEEe
Q 030281 133 IRVYNDSINGEVKNIPEICIRRDGTLRLV 161 (180)
Q Consensus 133 ~~~y~d~~dG~~~~~~eI~v~~~g~i~~l 161 (180)
. + .|+ +++.|+ .++.|
T Consensus 58 ~-----~-~G~----~ql~v~---~i~~~ 73 (73)
T cd04487 58 P-----R-DGQ----LQIEVE---SLEVL 73 (73)
T ss_pred c-----C-CeE----EEEEEe---eEEEC
Confidence 4 2 354 666776 56543
No 32
>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=96.29 E-value=0.025 Score=41.52 Aligned_cols=70 Identities=14% Similarity=0.107 Sum_probs=52.0
Q ss_pred ccccEEEEEEEeCCCCeEEEecCC---eEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCe
Q 030281 48 RGVHKAIICGKVKDTPVQKILRNG---KTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSS 124 (180)
Q Consensus 48 ~~mN~v~L~Grlg~dPe~r~t~nG---~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~ 124 (180)
.+++.+.|+|||..--+++.+++. ..+..|.|+ |.. |. -++|++|++ .|+.....|+.|+-
T Consensus 7 p~~~~~~I~~rV~~k~~~~~f~~~~~~g~~~~~~l~------De~-~~--------~I~~t~~~~-~~~~f~~~l~eG~v 70 (104)
T cd04474 7 PYQNKWTIKARVTNKSDIRTWSNARGEGKLFSFDLL------DED-GG--------EIRATFFND-AVDKFYDLLEVGKV 70 (104)
T ss_pred CCCCcEEEEEEEeeccccccccCCCCCcEEEEEEEE------ECC-CC--------EEEEEEehH-HHHHhhcccccccE
Confidence 457789999999987677776663 455555442 321 22 389999998 89999999999999
Q ss_pred EEEEE-EeEE
Q 030281 125 VYVEG-DIEI 133 (180)
Q Consensus 125 V~VeG-rL~~ 133 (180)
++|.+ +++.
T Consensus 71 y~i~~~~V~~ 80 (104)
T cd04474 71 YYISKGSVKV 80 (104)
T ss_pred EEEeccEEee
Confidence 99998 4433
No 33
>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=96.21 E-value=0.087 Score=35.76 Aligned_cols=72 Identities=19% Similarity=0.278 Sum_probs=50.2
Q ss_pred CCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEEEEEEeEEeeeecCC
Q 030281 61 DTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVYVEGDIEIRVYNDSI 140 (180)
Q Consensus 61 ~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~VeGrL~~~~y~d~~ 140 (180)
.....+.+++|+.++.|+|.-. +| -+.|.+|++ .- .....++.|..|+|.|+++. +.
T Consensus 7 ~~~~~~~tk~g~~~~~~~l~D~-------tg---------~i~~~~f~~-~~-~~~~~l~~g~~v~v~G~v~~--~~--- 63 (83)
T cd04492 7 KSKELRTAKNGKPYLALTLQDK-------TG---------EIEAKLWDA-SE-EDEEKFKPGDIVHVKGRVEE--YR--- 63 (83)
T ss_pred EEeeeecccCCCcEEEEEEEcC-------CC---------eEEEEEcCC-Ch-hhHhhCCCCCEEEEEEEEEE--eC---
Confidence 3456677888988888876543 24 279999996 33 44789999999999999954 21
Q ss_pred CCeEEEEEEEEEEeCCceEEecC
Q 030281 141 NGEVKNIPEICIRRDGTLRLVKS 163 (180)
Q Consensus 141 dG~~~~~~eI~v~~~g~i~~l~~ 163 (180)
| ..++.+. ++..|..
T Consensus 64 -~----~~~l~~~---~i~~l~~ 78 (83)
T cd04492 64 -G----RLQLKIQ---RIRLVTE 78 (83)
T ss_pred -C----ceeEEEE---EEEECCc
Confidence 2 2455566 6666653
No 34
>cd04489 ExoVII_LU_OBF ExoVII_LU_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of Escherichia coli exodeoxyribonuclease VII (ExoVII) large subunit. E. coli ExoVII is composed of two non-identical subunits. E. coli ExoVII is a single-strand-specific exonuclease which degrades ssDNA from both 3-prime and 5-prime ends. ExoVII plays a role in methyl-directed mismatch repair in vivo. ExoVII may also guard the genome from mutagenesis by removing excess ssDNA, since the build up of ssDNA would lead to SOS induction and PolIV-dependent mutagenesis.
Probab=96.07 E-value=0.15 Score=34.67 Aligned_cols=62 Identities=13% Similarity=0.075 Sum_probs=44.1
Q ss_pred EEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEEEEEEeE
Q 030281 53 AIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVYVEGDIE 132 (180)
Q Consensus 53 v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~VeGrL~ 132 (180)
+.+.|-|.. .. .+++| .+-|+|.-. +| -+.|++|.+ ..+.+...|++|+.|.|+|++.
T Consensus 2 ~~v~g~v~~-i~--~tk~g--~~~~~L~D~-------~~---------~i~~~~f~~-~~~~~~~~l~~g~~v~v~g~v~ 59 (78)
T cd04489 2 VWVEGEISN-LK--RPSSG--HLYFTLKDE-------DA---------SIRCVMWRS-NARRLGFPLEEGMEVLVRGKVS 59 (78)
T ss_pred EEEEEEEec-CE--ECCCc--EEEEEEEeC-------Ce---------EEEEEEEcc-hhhhCCCCCCCCCEEEEEEEEE
Confidence 457777774 33 36677 555544332 13 289999998 6777788999999999999999
Q ss_pred Eeee
Q 030281 133 IRVY 136 (180)
Q Consensus 133 ~~~y 136 (180)
.+.|
T Consensus 60 ~~~~ 63 (78)
T cd04489 60 FYEP 63 (78)
T ss_pred EECC
Confidence 7544
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=95.89 E-value=0.098 Score=35.08 Aligned_cols=61 Identities=21% Similarity=0.297 Sum_probs=44.1
Q ss_pred EEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEEEEEEeEE
Q 030281 55 ICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVYVEGDIEI 133 (180)
Q Consensus 55 L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~VeGrL~~ 133 (180)
+.|.|.. ...+.+.+|+.++.++|.- . +|. +.|.+|+. .-+.+...+++|..|.|.|++..
T Consensus 2 i~g~v~~-~~~~~~k~g~~~~~~~l~D------~-tg~---------~~~~~f~~-~~~~~~~~l~~g~~v~v~G~v~~ 62 (84)
T cd04485 2 VAGLVTS-VRRRRTKKGKRMAFVTLED------L-TGS---------IEVVVFPE-TYEKYRDLLKEDALLLVEGKVER 62 (84)
T ss_pred EEEEEEE-eEEEEcCCCCEEEEEEEEe------C-CCe---------EEEEECHH-HHHHHHHHhcCCCEEEEEEEEEe
Confidence 5666655 3446778898888886532 2 242 79999987 43446889999999999999965
No 36
>PRK13480 3'-5' exoribonuclease YhaM; Provisional
Probab=95.84 E-value=0.075 Score=46.76 Aligned_cols=57 Identities=18% Similarity=0.228 Sum_probs=46.1
Q ss_pred eCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEEEEEEeEE
Q 030281 59 VKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVYVEGDIEI 133 (180)
Q Consensus 59 lg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~VeGrL~~ 133 (180)
+.+..+++.++||++|+.++++- + +|+ ++..+|.. .+.....+..|+.|.|.|++..
T Consensus 19 lv~~~~~~~~knG~~yl~l~l~D------~-tG~---------I~ak~W~~--~~~~~~~~~~g~vv~v~G~v~~ 75 (314)
T PRK13480 19 LIKSATKGVASNGKPFLTLILQD------K-SGD---------IEAKLWDV--SPEDEATYVPETIVHVKGDIIN 75 (314)
T ss_pred EEEEceeeecCCCCeEEEEEEEc------C-CcE---------EEEEeCCC--ChhhHhhcCCCCEEEEEEEEEE
Confidence 45678889999999999997753 3 465 78999997 3455788999999999999974
No 37
>PRK15491 replication factor A; Provisional
Probab=95.59 E-value=0.17 Score=45.56 Aligned_cols=90 Identities=22% Similarity=0.295 Sum_probs=63.2
Q ss_pred ccEEEEEEEeCCCCeEEEe--cCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEEE
Q 030281 50 VHKAIICGKVKDTPVQKIL--RNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVYV 127 (180)
Q Consensus 50 mN~v~L~Grlg~dPe~r~t--~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~V 127 (180)
...|.|.|+|..--.+|.. ..|...-.+++... |. +|. +++++|+. .|+.+ ..|..|+.|+|
T Consensus 176 ~~~V~I~g~V~~~~~~r~~~~~~G~~~~v~~~~l~----De-tG~---------Ir~t~W~~-~a~~~-~~l~~Gd~V~i 239 (374)
T PRK15491 176 DSDINIVGKVLDISDVRTFQKKDGSQGRVRNITIG----DE-TGK---------IRVTLWDG-KTDLA-DKLENGDSVEI 239 (374)
T ss_pred CccEEEEEEEEEccCceEEEecCCCeEEEEEEEEE----CC-CCe---------EEEEEecc-hhccc-ccCCCCCEEEE
Confidence 4469999999998766655 46765444554443 22 352 89999999 88875 67999999999
Q ss_pred EE-EeEEeeeecCCCCeEEEEEEEEEEeCCceEEecC
Q 030281 128 EG-DIEIRVYNDSINGEVKNIPEICIRRDGTLRLVKS 163 (180)
Q Consensus 128 eG-rL~~~~y~d~~dG~~~~~~eI~v~~~g~i~~l~~ 163 (180)
.+ ..+.+.|.. .++|.+...+.|...+.
T Consensus 240 ~~~~~r~~~~~g--------~~El~~~~~s~I~~~~~ 268 (374)
T PRK15491 240 INGYARTNNYSQ--------EVEIQIGNHGSLRKTDR 268 (374)
T ss_pred EeceEEEeccCC--------CEEEEeCCCceEEECCc
Confidence 66 677766642 46777766666766543
No 38
>PRK07211 replication factor A; Reviewed
Probab=95.39 E-value=0.06 Score=50.01 Aligned_cols=68 Identities=19% Similarity=0.232 Sum_probs=53.2
Q ss_pred ccccEEEEEEEeCCCCeEEEecC---Ce--EEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCC
Q 030281 48 RGVHKAIICGKVKDTPVQKILRN---GK--TVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKN 122 (180)
Q Consensus 48 ~~mN~v~L~Grlg~dPe~r~t~n---G~--~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG 122 (180)
.+|++++|.|||..--.+|+..+ +. .++++.|+ |. +|+ +++++|+. .|+.++..|.+|
T Consensus 61 pg~~~vtI~aRV~~~~~~Rt~~~~~~~~eGkv~~v~l~------De-TG~---------Ir~TlW~d-~ad~~~~~Le~G 123 (485)
T PRK07211 61 PGMDEVKFLAKVLSIGDLRTFERDGEDEDGRVINVEVA------DE-TGS---------VRVAFWDE-QAVAAEEELEVG 123 (485)
T ss_pred CCCCceEEEEEEeEccCceEEEeCCCCCCcEEEEEEEE------cC-CCe---------EEEEEech-HhHhhhcccCCC
Confidence 57899999999999988887754 23 44444433 22 564 89999999 898889999999
Q ss_pred CeEEEEEEeE
Q 030281 123 SSVYVEGDIE 132 (180)
Q Consensus 123 ~~V~VeGrL~ 132 (180)
+.++|.|+..
T Consensus 124 dV~~I~~~~~ 133 (485)
T PRK07211 124 QVLRIKGRPK 133 (485)
T ss_pred CEEEEeceEe
Confidence 9999998763
No 39
>PRK15491 replication factor A; Provisional
Probab=95.38 E-value=0.19 Score=45.16 Aligned_cols=91 Identities=18% Similarity=0.192 Sum_probs=61.0
Q ss_pred ccccEEEEEEEeCCCCeEEEec--CCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHH-HhcCCCCe
Q 030281 48 RGVHKAIICGKVKDTPVQKILR--NGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAV-KQLVKNSS 124 (180)
Q Consensus 48 ~~mN~v~L~Grlg~dPe~r~t~--nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~-~~l~KG~~ 124 (180)
.+++.+.|.|||.+--.+|++. .|...-.+++... |. +|. +++++|++ .|+.+. ..|..|+.
T Consensus 65 ~~~~~v~i~arVl~~~~~R~f~r~dGs~g~v~~~~v~----De-TG~---------ir~tlW~~-~a~~~~~~~le~G~v 129 (374)
T PRK15491 65 ESSSNVNFTAKVVSIFEPKEFNRNDGTTGRVGNIIVA----DE-TGS---------IRLTLWDD-LADLIKTGDIEVGKS 129 (374)
T ss_pred CCCCceEEEEEEeeccCCeeeecCCCCceEEEEEEEE----cC-CCe---------EEEEEECc-hhhhhccCCcCCCCE
Confidence 4678999999999987777653 4643333433332 22 464 89999998 888776 46999999
Q ss_pred EEEEEEeEEeeeecCCCCeEEEEEEEEEEeCCceEEecC
Q 030281 125 VYVEGDIEIRVYNDSINGEVKNIPEICIRRDGTLRLVKS 163 (180)
Q Consensus 125 V~VeGrL~~~~y~d~~dG~~~~~~eI~v~~~g~i~~l~~ 163 (180)
+.|.|. +. +|. ..++|.+.+.+.|...+.
T Consensus 130 ~~I~~~-----~~---~~y--~g~Ei~i~~~~~i~~~~~ 158 (374)
T PRK15491 130 LNISGY-----AK---EGY--SGIEVNIGRYGGISESDE 158 (374)
T ss_pred EEEeee-----ec---cCc--ccEEEEeCCCceeeeccc
Confidence 999985 21 122 125888876656655543
No 40
>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=95.14 E-value=0.2 Score=36.08 Aligned_cols=61 Identities=21% Similarity=0.286 Sum_probs=42.9
Q ss_pred EEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchh--HHHHHHhcCCCCeEEEEEEe
Q 030281 54 IICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEIL--GSYAVKQLVKNSSVYVEGDI 131 (180)
Q Consensus 54 ~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~--Ae~~~~~l~KG~~V~VeGrL 131 (180)
.+.|.|.+-|. ..++|+.| |+| +|. ++ -++|++|.. . +..+...|+.||.|.|.|++
T Consensus 2 ~v~GeVs~~~~--~~~sGH~y--Ftl------kD~-~~---------~i~cv~f~~-~g~~~~~~~~l~~Gd~V~v~G~v 60 (91)
T cd04482 2 RVTGKVVEEPR--TIEGGHVF--FKI------SDG-TG---------EIDCAAYEP-TKEFRDVVRLLIPGDEVTVYGSV 60 (91)
T ss_pred EEEEEEeCCee--cCCCCCEE--EEE------ECC-Cc---------EEEEEEECc-ccccccccCCCCCCCEEEEEEEE
Confidence 46788887664 22567765 433 232 12 379999987 5 56788899999999999997
Q ss_pred EEee
Q 030281 132 EIRV 135 (180)
Q Consensus 132 ~~~~ 135 (180)
+...
T Consensus 61 ~~y~ 64 (91)
T cd04482 61 RPGT 64 (91)
T ss_pred ecCC
Confidence 6543
No 41
>PRK07211 replication factor A; Reviewed
Probab=94.08 E-value=0.52 Score=43.91 Aligned_cols=90 Identities=19% Similarity=0.302 Sum_probs=60.4
Q ss_pred cccEEEEEEEeCCCCeEEEec--CCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEE
Q 030281 49 GVHKAIICGKVKDTPVQKILR--NGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVY 126 (180)
Q Consensus 49 ~mN~v~L~Grlg~dPe~r~t~--nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~ 126 (180)
+++.+.|.|+|..--.+|.+. +|+.--.+++... |. +|. +++++|++ .|+.+ ..|.+|+.|.
T Consensus 170 ~~~~v~I~grV~~v~~iRtf~r~dGseGkv~sv~L~----De-TG~---------IR~TlW~d-~Ad~~-~~le~G~Vv~ 233 (485)
T PRK07211 170 GLSDVTLVGVVLDTDSVRTFDRDDGSEGRVSNLTVG----DE-TGR---------VRVTLWDD-RADLA-EELDAGESVE 233 (485)
T ss_pred CCCceEEEEEEEEcCCCeEEECCCCCeeEEEEEEEE----cC-CCe---------EEEEEech-hhhhh-ccCCCCCEEE
Confidence 578899999999887777664 4644444544442 22 342 89999999 88887 6799999999
Q ss_pred EEEEeEEeeeecCCCCeEEEEEEEEEEeCCceEEecC
Q 030281 127 VEGDIEIRVYNDSINGEVKNIPEICIRRDGTLRLVKS 163 (180)
Q Consensus 127 VeGrL~~~~y~d~~dG~~~~~~eI~v~~~g~i~~l~~ 163 (180)
|.+ -+.+.|. ..++|.+...+.|..+..
T Consensus 234 I~~-a~Vre~~--------g~~ELsl~~~s~I~~~~d 261 (485)
T PRK07211 234 IVD-GYVRERD--------GSLELHVGDRGAVEEVDE 261 (485)
T ss_pred EEe-eEEEecC--------CcEEEEECCCceEEECCc
Confidence 975 2333442 235666655556666544
No 42
>PF11325 DUF3127: Domain of unknown function (DUF3127); InterPro: IPR021474 This bacterial family of proteins has no known function.
Probab=93.72 E-value=0.58 Score=33.64 Aligned_cols=78 Identities=23% Similarity=0.164 Sum_probs=52.3
Q ss_pred EEEE-eCCCCeEEE-ecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEEEEEEeE
Q 030281 55 ICGK-VKDTPVQKI-LRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVYVEGDIE 132 (180)
Q Consensus 55 L~Gr-lg~dPe~r~-t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~VeGrL~ 132 (180)
|.|+ |..-|+... ++||=.--.|-|.+.. ..+..+.+.+|++ .++. ...++.|+.|.|.=.|+
T Consensus 2 i~Gkii~~l~~~~g~s~~Gw~Kre~Vlet~~-------------qYP~~i~f~~~~d-k~~~-l~~~~~Gd~V~Vsf~i~ 66 (84)
T PF11325_consen 2 ITGKIIKVLPEQQGVSKNGWKKREFVLETEE-------------QYPQKICFEFWGD-KIDL-LDNFQVGDEVKVSFNIE 66 (84)
T ss_pred cccEEEEEecCcccCcCCCcEEEEEEEeCCC-------------cCCceEEEEEEcc-hhhh-hccCCCCCEEEEEEEee
Confidence 5677 444455543 3477333334444332 2555689999998 5553 56899999999999999
Q ss_pred EeeeecCCCCeEEEEEEEEEE
Q 030281 133 IRVYNDSINGEVKNIPEICIR 153 (180)
Q Consensus 133 ~~~y~d~~dG~~~~~~eI~v~ 153 (180)
.|.|+. ++..+|.+=
T Consensus 67 ~RE~~g------r~fn~i~aW 81 (84)
T PF11325_consen 67 GREWNG------RWFNSIRAW 81 (84)
T ss_pred ccEecc------eEeeEeEEE
Confidence 999983 466666653
No 43
>cd04488 RecG_wedge_OBF RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal (wedge) domain of Escherichia coli RecG. RecG is a branched-DNA-specific helicase, which catalyzes the interconversion of a DNA replication fork to a four-stranded (Holliday) junction in vivo and in vitro. This interconversion provides a route to repair stalled forks. The RecG monomer contains three domains. The N-terminal domain is named for its wedge structure, and may provide the specificity of RecG for binding branched-DNA structures. During the reversal of fork to Holliday junction, the wedge domain is fixed at the junction of the fork where the leading and lagging strand duplex arms meet, and is thought to promote the unwinding of the nascent leading and lagging strands. In order to form the Holliday junction, these nascent strands would be annealed, and the parental strands reannealed. The wedge domain may also be a processivity factor of RecG on these branched cha
Probab=93.18 E-value=0.57 Score=30.67 Aligned_cols=31 Identities=26% Similarity=0.273 Sum_probs=25.7
Q ss_pred EEEEecCchhHHHHHHhcCCCCeEEEEEEeEEe
Q 030281 102 HRIAVHNEILGSYAVKQLVKNSSVYVEGDIEIR 134 (180)
Q Consensus 102 ~~V~~~gk~~Ae~~~~~l~KG~~V~VeGrL~~~ 134 (180)
+.|+.|+. ..++.+.+++|+.++|.|++...
T Consensus 31 i~~~~F~~--~~~~~~~~~~G~~~~v~Gkv~~~ 61 (75)
T cd04488 31 LTLVFFNF--QPYLKKQLPPGTRVRVSGKVKRF 61 (75)
T ss_pred EEEEEECC--CHHHHhcCCCCCEEEEEEEEeec
Confidence 78999983 14678899999999999999763
No 44
>cd03524 RPA2_OBF_family RPA2_OBF_family: A family of oligonucleotide binding (OB) folds with similarity to the OB fold of the single strand (ss) DNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA contains six OB folds, which are involved in ssDNA binding and in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. This family also includes OB folds similar to those found in Escherichia coli SSB, the wedge domain of E. coli RecG (a branched-DNA-specific helicase), E. coli ssDNA specific exodeoxyribonuclease VII large subunit, Pyroco
Probab=92.83 E-value=0.3 Score=31.30 Aligned_cols=32 Identities=22% Similarity=0.360 Sum_probs=28.1
Q ss_pred EEEEEecCchhHHHHHHhcCCCCeEEEEEEeEE
Q 030281 101 WHRIAVHNEILGSYAVKQLVKNSSVYVEGDIEI 133 (180)
Q Consensus 101 w~~V~~~gk~~Ae~~~~~l~KG~~V~VeGrL~~ 133 (180)
.+.|.+|.+ ..+.....+.+|+.|.|+|++..
T Consensus 30 ~i~~~~~~~-~~~~~~~~~~~g~~v~v~g~v~~ 61 (75)
T cd03524 30 TIRVTLFGE-LAEELENLLKEGQVVYIKGKVKK 61 (75)
T ss_pred EEEEEEEch-HHHHHHhhccCCCEEEEEEEEEe
Confidence 589999998 66767789999999999999965
No 45
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=92.68 E-value=1.8 Score=33.02 Aligned_cols=84 Identities=18% Similarity=0.321 Sum_probs=55.2
Q ss_pred cccEEEEEEEeCCC--CeEEEecCCe-EEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeE
Q 030281 49 GVHKAIICGKVKDT--PVQKILRNGK-TVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSV 125 (180)
Q Consensus 49 ~mN~v~L~Grlg~d--Pe~r~t~nG~-~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V 125 (180)
+++.|.+.|.|..- +....+++|. .+..+.|+ |+ +|. +++++|++ .|+ .|++|+.|
T Consensus 13 g~~~v~~~~~V~~i~~~~~~~~k~~~~~v~~~~l~------D~-TG~---------I~~tlW~~-~a~----~l~~GdvV 71 (129)
T PRK06461 13 GMERVNVTVRVLEVGEPKVIQTKGGPRTISEAVVG------DE-TGR---------VKLTLWGE-QAG----SLKEGEVV 71 (129)
T ss_pred CCCceEEEEEEEEcCCceEEEeCCCceEEEEEEEE------CC-CCE---------EEEEEeCC-ccc----cCCCCCEE
Confidence 35677888888863 4444555663 36555442 33 352 89999998 554 68999999
Q ss_pred EEE-EEeEEeeeecCCCCeEEEEEEEEEEeCCceEEecC
Q 030281 126 YVE-GDIEIRVYNDSINGEVKNIPEICIRRDGTLRLVKS 163 (180)
Q Consensus 126 ~Ve-GrL~~~~y~d~~dG~~~~~~eI~v~~~g~i~~l~~ 163 (180)
.|. |..+ .|. | .++|.+.+.|.|..++.
T Consensus 72 ~I~na~v~--~f~----G----~lqL~i~~~~~i~~~~~ 100 (129)
T PRK06461 72 EIENAWTT--LYR----G----KVQLNVGKYGSISESDD 100 (129)
T ss_pred EEECcEEe--eeC----C----EEEEEECCCEEEEECCc
Confidence 999 5555 343 3 36677776677877764
No 46
>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=91.70 E-value=3.3 Score=28.90 Aligned_cols=57 Identities=18% Similarity=0.331 Sum_probs=39.7
Q ss_pred EEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHH--HHHHhcCCCCeEEEEEE
Q 030281 53 AIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGS--YAVKQLVKNSSVYVEGD 130 (180)
Q Consensus 53 v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae--~~~~~l~KG~~V~VeGr 130 (180)
+.++|-|..-- .+.+|+. .++|. |. +|. +.|.+|.+ .-+ .....|..|..|+|.|+
T Consensus 2 v~i~GiI~~v~---~TK~g~~--~~~le------D~-~G~---------~Ev~~F~~-~~~~~~~~~~l~~d~~v~v~g~ 59 (79)
T cd04490 2 VSIIGMVNDVR---STKNGHR--IVELE------DT-TGR---------ITVLLTKD-KEELFEEAEDILPDEVIGVSGT 59 (79)
T ss_pred EEEEEEEeEEE---EcCCCCE--EEEEE------CC-CCE---------EEEEEeCc-hhhhhhhhhhccCCCEEEEEEE
Confidence 45666665422 6677876 33222 22 343 79999999 555 57889999999999999
Q ss_pred e
Q 030281 131 I 131 (180)
Q Consensus 131 L 131 (180)
+
T Consensus 60 v 60 (79)
T cd04490 60 V 60 (79)
T ss_pred E
Confidence 9
No 47
>PRK14699 replication factor A; Provisional
Probab=91.62 E-value=1.3 Score=41.18 Aligned_cols=73 Identities=8% Similarity=0.114 Sum_probs=50.8
Q ss_pred ccccEEEEEEEeCCCCeEEEec--CCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHH-hcCCCCe
Q 030281 48 RGVHKAIICGKVKDTPVQKILR--NGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVK-QLVKNSS 124 (180)
Q Consensus 48 ~~mN~v~L~Grlg~dPe~r~t~--nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~-~l~KG~~ 124 (180)
.++..|.|.|+|..-...|++. .|...-..++... |. +|. +++++|.+ +|+.+.. .|++||.
T Consensus 65 ~~~~~v~i~~rVl~i~~~r~f~r~dG~~g~v~~~~ia----De-TG~---------ir~tlW~~-~a~~~~~g~l~~GDv 129 (484)
T PRK14699 65 PESGPVNFIARVVSVFDTKEFTRNDGTIGRVGNLIVG----DE-TGK---------IKLTLWDN-MADLIKAGKIKAGQT 129 (484)
T ss_pred CCCceEEEEEEEEEecCceEEecCCCCceEEEEEEEe----cC-CCe---------EEEEEecC-ccchhhhcCCCCCCE
Confidence 4677899999999997777663 4543222222222 22 464 89999998 7876665 5999999
Q ss_pred EEEEEEeEEeeee
Q 030281 125 VYVEGDIEIRVYN 137 (180)
Q Consensus 125 V~VeGrL~~~~y~ 137 (180)
|.|.|. .+.|.
T Consensus 130 v~I~~~--~r~~~ 140 (484)
T PRK14699 130 LQISGY--AKQGY 140 (484)
T ss_pred EEEcce--eccCC
Confidence 999994 55554
No 48
>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed
Probab=91.37 E-value=0.68 Score=42.00 Aligned_cols=80 Identities=10% Similarity=0.187 Sum_probs=56.2
Q ss_pred ccEEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEEEEE
Q 030281 50 VHKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVYVEG 129 (180)
Q Consensus 50 mN~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~VeG 129 (180)
+..|-+.|-|.. ++...+|+.|..+ +|. ..-++|++|.. .+..+.-.++.|+.|.|.|
T Consensus 23 ~~~v~v~gEis~---~~~~~sGH~Yf~L--------kd~----------~a~i~~~~~~~-~~~~~~~~~~~G~~v~v~g 80 (438)
T PRK00286 23 LGQVWVRGEISN---FTRHSSGHWYFTL--------KDE----------IAQIRCVMFKG-SARRLKFKPEEGMKVLVRG 80 (438)
T ss_pred CCcEEEEEEeCC---CeeCCCCeEEEEE--------EcC----------CcEEEEEEEcC-hhhcCCCCCCCCCEEEEEE
Confidence 457889999877 3333578877433 222 12389999997 7777777799999999999
Q ss_pred EeEEeeeecCCCCeEEEEEEEEEEeCCceEEec
Q 030281 130 DIEIRVYNDSINGEVKNIPEICIRRDGTLRLVK 162 (180)
Q Consensus 130 rL~~~~y~d~~dG~~~~~~eI~v~~~g~i~~l~ 162 (180)
++.. |+. .|. +.+.|+ .|...+
T Consensus 81 ~~~~--y~~--~g~----~ql~v~---~i~~~g 102 (438)
T PRK00286 81 KVSL--YEP--RGD----YQLIVE---EIEPAG 102 (438)
T ss_pred EEEE--ECC--CCC----EEEEEE---EeeeCC
Confidence 9987 554 354 556666 566543
No 49
>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=91.31 E-value=3.4 Score=28.40 Aligned_cols=59 Identities=22% Similarity=0.294 Sum_probs=37.7
Q ss_pred EEEEeCCCCeEEEec-CC--eEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEEEE-EE
Q 030281 55 ICGKVKDTPVQKILR-NG--KTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVYVE-GD 130 (180)
Q Consensus 55 L~Grlg~dPe~r~t~-nG--~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~Ve-Gr 130 (180)
|.|+|-.--..+.+. +| ..+..+.|+ |. +|. +++++|+. .+ ...+..|+.|.+. |.
T Consensus 2 v~~~V~~~~~~~~~~~~g~~~~~~~~~l~------D~-TG~---------i~~~~W~~-~~---~~~~~~G~vv~i~~~~ 61 (82)
T cd04491 2 VEGKVLSISEPREFTRDGSEGKVQSGLVG------DE-TGT---------IRFTLWDE-KA---ADDLEPGDVVRIENAY 61 (82)
T ss_pred EEEEEEEccCCeEeccCCCeeEEEEEEEE------CC-CCE---------EEEEEECc-hh---cccCCCCCEEEEEeEE
Confidence 566666554444432 33 345544433 22 353 89999998 55 6789999999999 55
Q ss_pred eEE
Q 030281 131 IEI 133 (180)
Q Consensus 131 L~~ 133 (180)
++.
T Consensus 62 v~~ 64 (82)
T cd04491 62 VRE 64 (82)
T ss_pred EEe
Confidence 543
No 50
>PRK12366 replication factor A; Reviewed
Probab=90.93 E-value=1.8 Score=41.52 Aligned_cols=89 Identities=13% Similarity=0.239 Sum_probs=59.9
Q ss_pred cEEEEEEEeCCCCeEEEecC--CeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEEEE
Q 030281 51 HKAIICGKVKDTPVQKILRN--GKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVYVE 128 (180)
Q Consensus 51 N~v~L~Grlg~dPe~r~t~n--G~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~Ve 128 (180)
+.++|.|||..-..+|.+++ |. --.|++... |. +|+ +++++|++ .|+.+.. |..|+.++|.
T Consensus 292 ~~~~I~grV~~~~~~R~f~~~~g~-gkv~s~~l~----D~-tG~---------IR~t~w~~-~~d~~~~-l~~G~vy~is 354 (637)
T PRK12366 292 EEVDVKGRIIAISDKREVERDDRT-AEVQDIELA----DG-TGR---------VRVSFWGE-KAKILEN-LKEGDAVKIE 354 (637)
T ss_pred CEEEEEEEEEecCCceEEEcCCCc-EEEEEEEEE----cC-CCe---------EEEEEeCc-hhhhhcc-cCCCCEEEEe
Confidence 48999999999988888753 33 334555443 22 353 89999999 7876654 6899999998
Q ss_pred EEeEEeeeecCCCCeEEEEEEEEEEeCCceEE
Q 030281 129 GDIEIRVYNDSINGEVKNIPEICIRRDGTLRL 160 (180)
Q Consensus 129 GrL~~~~y~d~~dG~~~~~~eI~v~~~g~i~~ 160 (180)
+ -+.+.|.+. .|. +.+++.+.....|..
T Consensus 355 ~-~~vk~y~~~-~~~--~~~El~~~~~s~I~~ 382 (637)
T PRK12366 355 N-CKVRTYYDN-EGE--KRVDLNAGYSSEIIK 382 (637)
T ss_pred c-CEEeecccc-CCC--cCEEEEcCCceEEEe
Confidence 8 223356543 453 447777765444544
No 51
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain
Probab=90.59 E-value=0.66 Score=33.80 Aligned_cols=63 Identities=11% Similarity=0.131 Sum_probs=45.7
Q ss_pred ccEEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHH-HhcCCCCeEEEE
Q 030281 50 VHKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAV-KQLVKNSSVYVE 128 (180)
Q Consensus 50 mN~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~-~~l~KG~~V~Ve 128 (180)
+..+-+.|-|.. ++...+|..|.++ . |. + .-++|++|.. .+..+. ..++.|++|.|.
T Consensus 21 ~~~vwV~GEIs~---~~~~~~gh~YftL--k------D~---~-------a~i~~~~~~~-~~~~i~~~~l~~G~~V~v~ 78 (99)
T PF13742_consen 21 LPNVWVEGEISN---LKRHSSGHVYFTL--K------DE---E-------ASISCVIFRS-RARRIRGFDLKDGDKVLVR 78 (99)
T ss_pred cCCEEEEEEEee---cEECCCceEEEEE--E------cC---C-------cEEEEEEEHH-HHhhCCCCCCCCCCEEEEE
Confidence 467889999876 2232567766433 2 21 1 2389999998 777777 789999999999
Q ss_pred EEeEEe
Q 030281 129 GDIEIR 134 (180)
Q Consensus 129 GrL~~~ 134 (180)
|++...
T Consensus 79 g~~~~y 84 (99)
T PF13742_consen 79 GRVSFY 84 (99)
T ss_pred EEEEEE
Confidence 998754
No 52
>COG3390 Uncharacterized protein conserved in archaea [Function unknown]
Probab=90.34 E-value=2.6 Score=34.73 Aligned_cols=76 Identities=16% Similarity=0.130 Sum_probs=54.3
Q ss_pred ccccEEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEEE
Q 030281 48 RGVHKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVYV 127 (180)
Q Consensus 48 ~~mN~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~V 127 (180)
..+|++.|+|-|..-+-+-+ ...+.+++|+- + +| +.|+-.=-|.+ -|..+.+.+.+++.|.|
T Consensus 43 ~k~nRifivGtltek~~i~e---d~~~~R~rVvD------p-TG-------sF~Vyag~yqP-Ea~a~l~~ve~~~~VaV 104 (196)
T COG3390 43 LKVNRIFIVGTLTEKEGIGE---DREYWRIRVVD------P-TG-------SFYVYAGQYQP-EAKAFLEDVEVPDLVAV 104 (196)
T ss_pred hheeEEEEEEEEEeccCcCC---cccEEEEEEec------C-Cc-------eEEEEcCCCCh-HHHHHHHhccCCceEEE
Confidence 34899999999998776521 25577776642 2 24 34554445666 67788999999999999
Q ss_pred EEEeEEeeeecCCCCeE
Q 030281 128 EGDIEIRVYNDSINGEV 144 (180)
Q Consensus 128 eGrL~~~~y~d~~dG~~ 144 (180)
.|.++ .|++. +|..
T Consensus 105 iGKi~--~y~~d-~g~~ 118 (196)
T COG3390 105 IGKIR--TYRTD-EGVV 118 (196)
T ss_pred ecccc--eeecC-CCce
Confidence 99886 46665 6763
No 53
>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=89.71 E-value=3.1 Score=39.76 Aligned_cols=92 Identities=15% Similarity=0.173 Sum_probs=63.0
Q ss_pred cccEEEEEEEeCCCCeEEEecC--C-eEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeE
Q 030281 49 GVHKAIICGKVKDTPVQKILRN--G-KTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSV 125 (180)
Q Consensus 49 ~mN~v~L~Grlg~dPe~r~t~n--G-~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V 125 (180)
++++.+|.|||..-..+|...+ | ..+..+.| .| .+|+ |++++|+. .|+.+...|+.|+-.
T Consensus 189 y~~~wtIkaRV~~Ks~ir~~~~~~gegkvfsv~L------~D-egg~---------Irat~f~~-~~dkf~~~l~eG~VY 251 (608)
T TIGR00617 189 YQNKWTIKARVTNKSEIRTWSNARGEGKLFNVEL------LD-ESGE---------IRATAFNE-QADKFYDIIQEGKVY 251 (608)
T ss_pred CCCceEEEEEEEeccccceecCCCCCceeeEEEE------ec-CCCe---------EEEEECch-HHHHHhhhcccCCEE
Confidence 4578999999999988887654 2 13444433 23 2343 89999999 899999999999999
Q ss_pred EEEE-EeEEe--eeecCCCCeEEEEEEEEEEeCCceEEec
Q 030281 126 YVEG-DIEIR--VYNDSINGEVKNIPEICIRRDGTLRLVK 162 (180)
Q Consensus 126 ~VeG-rL~~~--~y~d~~dG~~~~~~eI~v~~~g~i~~l~ 162 (180)
+|.+ +++.. .|.. ....++|..++...|+...
T Consensus 252 ~Is~~~Vk~an~~y~~-----~~~~yei~f~~~T~I~~~~ 286 (608)
T TIGR00617 252 YISKGSLKPANKQFTN-----LGNDYEMTLDRDTVIEECE 286 (608)
T ss_pred EECceEEEEccccccC-----CCCCEEEEECCCeEEEECC
Confidence 9965 55543 2321 1235777777555566554
No 54
>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=88.87 E-value=1.1 Score=40.99 Aligned_cols=79 Identities=14% Similarity=0.161 Sum_probs=55.8
Q ss_pred ccEEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEEEEE
Q 030281 50 VHKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVYVEG 129 (180)
Q Consensus 50 mN~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~VeG 129 (180)
+..|-+.|-|.. ++..++|+.|.++ +|. +. -++|++|.. .+..+.-.++-|+.|+|.|
T Consensus 17 ~~~v~V~GEisn---~~~~~sGH~YFtL--------kD~--~a--------~i~~vmf~~-~~~~l~f~~~~G~~V~v~g 74 (432)
T TIGR00237 17 FLQVWIQGEISN---FTQPVSGHWYFTL--------KDE--NA--------QVRCVMFRG-NNNRLKFRPQNGQQVLVRG 74 (432)
T ss_pred CCcEEEEEEecC---CeeCCCceEEEEE--------EcC--Cc--------EEEEEEEcC-hhhCCCCCCCCCCEEEEEE
Confidence 457899999987 2233678877544 332 12 389999998 7777777799999999999
Q ss_pred EeEEeeeecCCCCeEEEEEEEEEEeCCceEEe
Q 030281 130 DIEIRVYNDSINGEVKNIPEICIRRDGTLRLV 161 (180)
Q Consensus 130 rL~~~~y~d~~dG~~~~~~eI~v~~~g~i~~l 161 (180)
++.. |+. .|. +.+.|+ .|+.-
T Consensus 75 ~v~~--y~~--~G~----~ql~v~---~i~~~ 95 (432)
T TIGR00237 75 GISV--YEP--RGD----YQIICF---EMQPA 95 (432)
T ss_pred EEEE--ECC--CCc----EEEEEE---EeccC
Confidence 9974 554 354 566666 56543
No 55
>PRK12366 replication factor A; Reviewed
Probab=88.19 E-value=1.5 Score=42.09 Aligned_cols=73 Identities=19% Similarity=0.342 Sum_probs=50.9
Q ss_pred ccccEEEEEEEeCCCCeEEEec--CCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeE
Q 030281 48 RGVHKAIICGKVKDTPVQKILR--NGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSV 125 (180)
Q Consensus 48 ~~mN~v~L~Grlg~dPe~r~t~--nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V 125 (180)
.+++.+.|.|||.+--.+|.+. .|..--.|++... |. +|+ +++++|++ .|+. ...|.+|+.+
T Consensus 71 p~~~~v~i~arV~~~~~~r~~~~~~G~eGkv~~~~v~----De-tG~---------Ir~t~W~~-~~~~-~~~le~G~v~ 134 (637)
T PRK12366 71 EGQINVEITGRIIEISNIKTFTRKDGSTGKLANITIA----DN-TGT---------IRLTLWND-NAKL-LKGLKEGDVI 134 (637)
T ss_pred CCCcceEEEEEEEEccCCeEEECCCCCccEEEEEEEE----cC-CCE---------EEEEEEch-hhhh-hccCCCCCEE
Confidence 4678999999999887777653 4533222333332 22 463 89999999 7875 5789999999
Q ss_pred EEEEEeEEeeee
Q 030281 126 YVEGDIEIRVYN 137 (180)
Q Consensus 126 ~VeGrL~~~~y~ 137 (180)
.|.+. ..+.|.
T Consensus 135 ~i~~~-~v~~~~ 145 (637)
T PRK12366 135 KIENA-RSRKWN 145 (637)
T ss_pred EEecc-EecccC
Confidence 99985 344454
No 56
>PRK07373 DNA polymerase III subunit alpha; Reviewed
Probab=88.08 E-value=3.5 Score=38.03 Aligned_cols=64 Identities=9% Similarity=0.132 Sum_probs=49.1
Q ss_pred EEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEEEEEEe
Q 030281 52 KAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVYVEGDI 131 (180)
Q Consensus 52 ~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~VeGrL 131 (180)
+|.+.|-|.. ...+.|.+|...+.+++.-. +|. +.|++|.+ .-+.....|+.|..|+|+|++
T Consensus 282 ~v~vaG~I~~-ik~~~TKkG~~maf~~leD~-------tG~---------ie~vvFp~-~y~~~~~~l~~~~~v~v~G~v 343 (449)
T PRK07373 282 KVSAVVMLNE-VKKIVTKKGDPMAFLQLEDL-------SGQ---------SEAVVFPK-SYERISELLQVDARLIIWGKV 343 (449)
T ss_pred EEEEEEEEEE-eEecccCCCCEEEEEEEEEC-------CCC---------EEEEECHH-HHHHHHHHhccCCEEEEEEEE
Confidence 5777777776 55567788887776655432 354 79999998 777788999999999999999
Q ss_pred EE
Q 030281 132 EI 133 (180)
Q Consensus 132 ~~ 133 (180)
..
T Consensus 344 ~~ 345 (449)
T PRK07373 344 DR 345 (449)
T ss_pred Ee
Confidence 54
No 57
>PRK08402 replication factor A; Reviewed
Probab=88.08 E-value=4 Score=36.57 Aligned_cols=91 Identities=16% Similarity=0.179 Sum_probs=54.6
Q ss_pred cccEEEEEEEeCCCCeEEEe--cCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEE
Q 030281 49 GVHKAIICGKVKDTPVQKIL--RNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVY 126 (180)
Q Consensus 49 ~mN~v~L~Grlg~dPe~r~t--~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~ 126 (180)
++..|.+.|+|.+--..|.+ .+|..--..++... |. +| .+++++|++ .|......+..|+.|.
T Consensus 71 g~~~V~v~~rVl~~~~~r~f~rrdG~~~~V~~i~l~----De-TG---------~ir~TlW~~-~a~~~~~~l~~Gdvi~ 135 (355)
T PRK08402 71 GMRGVNIVGRVLRKYPPREYTKKDGSTGRVASLIIY----DD-TG---------RARVVLWDA-KVAKYYNKINVGDVIK 135 (355)
T ss_pred CCceeeEEEEEEEccCCceeeccCCCcceEEEEEEE----cC-CC---------eEEEEEech-hhhhhcccCCCCCEEE
Confidence 56789999999986443433 35543222222222 22 34 479999998 7775566799999999
Q ss_pred EEEEeEEeeeecCCCCeEEEEEEEEEEeCCceEEec
Q 030281 127 VEGDIEIRVYNDSINGEVKNIPEICIRRDGTLRLVK 162 (180)
Q Consensus 127 VeGrL~~~~y~d~~dG~~~~~~eI~v~~~g~i~~l~ 162 (180)
|.+---...|. | .++|.+.+.+.|.+..
T Consensus 136 I~~a~V~e~~~----G----~~eLsvg~~s~i~~~p 163 (355)
T PRK08402 136 VIDAQVRESLS----G----LPELHINFRARIILNP 163 (355)
T ss_pred EECCEEeecCC----C----cEEEEECCCceEEeCC
Confidence 97533323232 3 3456665555555443
No 58
>PRK14699 replication factor A; Provisional
Probab=87.41 E-value=5.5 Score=37.18 Aligned_cols=89 Identities=15% Similarity=0.227 Sum_probs=57.8
Q ss_pred cccEEEEEEEeCCCCeEEEec--CCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEE
Q 030281 49 GVHKAIICGKVKDTPVQKILR--NGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVY 126 (180)
Q Consensus 49 ~mN~v~L~Grlg~dPe~r~t~--nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~ 126 (180)
+++.++|.|+|..--.+|+.. +|...-.+++.... . +|. +++++|++ .|. +...+..|+.|.
T Consensus 285 ~~~~v~I~grV~~~~~~r~~~~~~Gseg~v~~~~l~D----e-TG~---------Ir~T~W~~-~a~-~~~~i~~Gd~v~ 348 (484)
T PRK14699 285 DMNNINISGRVLDISEVRTFEKKDGSPGRVGNLLLGD----S-TGK---------IRLTLWDE-KTN-FLDEIDFDETVE 348 (484)
T ss_pred CCceeEEEEEEEEcCCCeEEEcCCCCeeEEEEEEEEC----C-CCe---------EEEEEeCc-ccc-cccccCCCceEE
Confidence 578999999999776666654 56666666665543 2 453 89999999 774 566788999776
Q ss_pred EEEEe-EEeeeecCCCCeEEEEEEEEEEeCCceEEe
Q 030281 127 VEGDI-EIRVYNDSINGEVKNIPEICIRRDGTLRLV 161 (180)
Q Consensus 127 VeGrL-~~~~y~d~~dG~~~~~~eI~v~~~g~i~~l 161 (180)
|..-- +.+.| ...++|.+.+.+.|...
T Consensus 349 i~~~y~~~~~~--------~~~~eL~~~~~t~I~~~ 376 (484)
T PRK14699 349 VLNAYSRENTF--------SQQVELNLGARGIIQKS 376 (484)
T ss_pred EEeEEEEeccC--------CccEEEEecCceeEeec
Confidence 65422 22222 12567777655555444
No 59
>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=87.33 E-value=4.8 Score=28.74 Aligned_cols=67 Identities=13% Similarity=0.197 Sum_probs=41.9
Q ss_pred EEEEEeCCCCeEEE--ecC-CeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEEEEEE
Q 030281 54 IICGKVKDTPVQKI--LRN-GKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVYVEGD 130 (180)
Q Consensus 54 ~L~Grlg~dPe~r~--t~n-G~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~VeGr 130 (180)
-|+|.|..--..+. +.+ |+...+..|.... . +|. -+.|++||+ .|+.+.... |+-|.+.+
T Consensus 3 Dvig~V~~v~~~~~i~~k~~g~~~~~r~v~i~D----~-t~~--------~i~vtLWg~-~a~~~~~~~--~~vv~~~~- 65 (101)
T cd04475 3 DVIGVVKSVGPVTTITTKSTGRELDKREITLVD----E-SGH--------SVELTLWGE-QAELFDGSE--NPVIAIKG- 65 (101)
T ss_pred eEEEEEeEccCcEEEEEecCCCceeEEEEEEEe----C-CCC--------EEEEEEEHH-HhhhcccCC--CCEEEEEe-
Confidence 36777765544332 233 7665555554432 2 232 379999999 888765444 89998888
Q ss_pred eEEeeee
Q 030281 131 IEIRVYN 137 (180)
Q Consensus 131 L~~~~y~ 137 (180)
++.+.|.
T Consensus 66 ~~i~~~~ 72 (101)
T cd04475 66 VKVSEFN 72 (101)
T ss_pred eEEEecC
Confidence 6666664
No 60
>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=86.26 E-value=11 Score=27.47 Aligned_cols=86 Identities=16% Similarity=0.190 Sum_probs=54.5
Q ss_pred cccEEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEEEE
Q 030281 49 GVHKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVYVE 128 (180)
Q Consensus 49 ~mN~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~Ve 128 (180)
|+|.|.|.|-|-.- +-+.+ +.-.-.+|...+.| |+. .-|+|+-+-+-|+ +|=.+.+|.+|=.-+.|+
T Consensus 1 MLN~V~LEG~IeS~---kWS~~-KTGF~VTI~QkR~F-----G~r---~FTDyyViYAN~Q-L~~ELEky~~k~k~isie 67 (104)
T PF11506_consen 1 MLNTVFLEGEIESY---KWSKK-KTGFLVTIKQKRKF-----GER---TFTDYYVIYANGQ-LAFELEKYTQKHKTISIE 67 (104)
T ss_dssp --EEEEEEEEEEEE---EE-TT-SSEEEEEEEEEEEE-----TTE---EEEEEEEEEEEHH-HHHHHHHHHTT-SEEEEE
T ss_pred CcceEEEeceeehh---ccccc-CceEEEEEeehhhh-----ccc---cceeEEEEEECCe-eehhHHHhhhhceEEEEe
Confidence 57999999988542 12222 22222334444433 443 5788988888887 998999999999999999
Q ss_pred EEeEEeeeecCCCCeEEEEEE
Q 030281 129 GDIEIRVYNDSINGEVKNIPE 149 (180)
Q Consensus 129 GrL~~~~y~d~~dG~~~~~~e 149 (180)
|.|++.. ++..+.-++..+
T Consensus 68 G~L~TY~--ekkS~iWKT~I~ 86 (104)
T PF11506_consen 68 GILRTYL--EKKSKIWKTTIE 86 (104)
T ss_dssp EEEEEEE--ETTTTEEEEEEE
T ss_pred eehhhHH--HHhcccceeeEE
Confidence 9998754 432565444433
No 61
>PRK05673 dnaE DNA polymerase III subunit alpha; Validated
Probab=86.11 E-value=4.3 Score=41.64 Aligned_cols=65 Identities=15% Similarity=0.241 Sum_probs=50.4
Q ss_pred cEEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEEEEEE
Q 030281 51 HKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVYVEGD 130 (180)
Q Consensus 51 N~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~VeGr 130 (180)
..|.++|-|.. ...+.|++|+.++.++|.-. +|+ +.+++|.+ .-+.+...|..|..|+|+|+
T Consensus 978 ~~V~v~G~I~~-vk~~~TKkG~~mafltLeD~-------TG~---------iEvviFp~-~ye~~~~~L~~g~iV~V~Gk 1039 (1135)
T PRK05673 978 SVVTVAGLVVS-VRRRVTKRGNKMAIVTLEDL-------SGR---------IEVMLFSE-ALEKYRDLLEEDRIVVVKGQ 1039 (1135)
T ss_pred ceEEEEEEEEE-EEecccCCCCeEEEEEEEeC-------CCc---------EEEEECHH-HHHHHHHHhccCCEEEEEEE
Confidence 35777777765 66667889998888776543 354 79999998 55667889999999999999
Q ss_pred eEE
Q 030281 131 IEI 133 (180)
Q Consensus 131 L~~ 133 (180)
+..
T Consensus 1040 Ve~ 1042 (1135)
T PRK05673 1040 VSF 1042 (1135)
T ss_pred EEe
Confidence 964
No 62
>PRK06826 dnaE DNA polymerase III DnaE; Reviewed
Probab=83.62 E-value=11 Score=38.94 Aligned_cols=65 Identities=20% Similarity=0.321 Sum_probs=49.3
Q ss_pred EEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEEEEEEe
Q 030281 52 KAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVYVEGDI 131 (180)
Q Consensus 52 ~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~VeGrL 131 (180)
.+.+.|-|.. ...+.|++|...+.++|.-. +|. +.|++|.+ .-+.+...|..|..|+|+|++
T Consensus 993 ~v~v~g~i~~-~~~~~tk~G~~maf~~leD~-------~g~---------~e~~vfp~-~~~~~~~~l~~~~~~~v~g~v 1054 (1151)
T PRK06826 993 KVIIGGIITE-VKRKTTRNNEMMAFLTLEDL-------YGT---------VEVIVFPK-VYEKYRSLLNEDNIVLIKGRV 1054 (1151)
T ss_pred EEEEEEEEEE-eEeeccCCCCeEEEEEEEEC-------CCc---------EEEEECHH-HHHHHHHHhccCCEEEEEEEE
Confidence 5777777776 45556788887777766532 353 79999998 666778899999999999999
Q ss_pred EEe
Q 030281 132 EIR 134 (180)
Q Consensus 132 ~~~ 134 (180)
+.+
T Consensus 1055 ~~~ 1057 (1151)
T PRK06826 1055 SLR 1057 (1151)
T ss_pred Eec
Confidence 653
No 63
>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=83.35 E-value=12 Score=38.70 Aligned_cols=73 Identities=15% Similarity=0.134 Sum_probs=54.7
Q ss_pred cccEEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchh-HHHHHHhcCCCCeEEE
Q 030281 49 GVHKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEIL-GSYAVKQLVKNSSVYV 127 (180)
Q Consensus 49 ~mN~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~-Ae~~~~~l~KG~~V~V 127 (180)
.++.|+|.|.|-. .+.+.+.+|+.+..|.|.- | ++-+.|..|.+.. -......+++|+-|.|
T Consensus 6 ~~~~~~~~g~i~~-~~~~~~~~~~~~~~~~~~d---~-------------~~s~~~k~f~~~~~~~~~~~~~~~g~~~~~ 68 (1213)
T TIGR01405 6 EENRVKIEGYIFK-IEIKELKSGRTLLKIKVTD---Y-------------TDSLILKKFLKSEEDPEKFDGIKIGKWVRA 68 (1213)
T ss_pred cCCeEEEEEEEEE-EEeEeccCCCEEEEEEEEc---C-------------CCCEEEEEecccccchHHHhhcCCCcEEEE
Confidence 3678999999955 7788999999988887652 1 1126788887411 1123467999999999
Q ss_pred EEEeEEeeeec
Q 030281 128 EGDIEIRVYND 138 (180)
Q Consensus 128 eGrL~~~~y~d 138 (180)
.|++.+..|..
T Consensus 69 ~g~~~~d~~~~ 79 (1213)
T TIGR01405 69 RGKIELDNFSR 79 (1213)
T ss_pred EEEEeccCCCC
Confidence 99999999875
No 64
>PRK06920 dnaE DNA polymerase III DnaE; Reviewed
Probab=82.97 E-value=11 Score=38.80 Aligned_cols=65 Identities=15% Similarity=0.117 Sum_probs=49.1
Q ss_pred EEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEEEEEEe
Q 030281 52 KAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVYVEGDI 131 (180)
Q Consensus 52 ~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~VeGrL 131 (180)
.|.+.|-|.. ...+.|++|+..+.+++.-. +|. +.|++|.+ .-+.+...|..|..|+|+|++
T Consensus 945 ~v~v~g~i~~-~~~~~tk~g~~maf~~leD~-------tg~---------~e~~vFp~-~y~~~~~~l~~~~~~~v~G~v 1006 (1107)
T PRK06920 945 VQRAIVYITS-VKVIRTKKGQKMAFITFCDQ-------NDE---------MEAVVFPE-TYIHFSDKLQEGAIVLVDGTI 1006 (1107)
T ss_pred EEEEEEEEEE-eEeecCCCCCeEEEEEEeeC-------CCc---------EEEEECHH-HHHHHHHHhccCCEEEEEEEE
Confidence 5778887776 44456778887776655432 353 79999998 667788899999999999999
Q ss_pred EEe
Q 030281 132 EIR 134 (180)
Q Consensus 132 ~~~ 134 (180)
..+
T Consensus 1007 ~~~ 1009 (1107)
T PRK06920 1007 ELR 1009 (1107)
T ss_pred Eec
Confidence 653
No 65
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=80.51 E-value=7.6 Score=40.86 Aligned_cols=72 Identities=14% Similarity=0.207 Sum_probs=54.2
Q ss_pred ccEEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchh-HHHHHHhcCCCCeEEEE
Q 030281 50 VHKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEIL-GSYAVKQLVKNSSVYVE 128 (180)
Q Consensus 50 mN~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~-Ae~~~~~l~KG~~V~Ve 128 (180)
.+.|+|.|.|-. .+.|.+.+|+.++.|.|. . | ++-+.|..|.+.. -......+++|+-|.|.
T Consensus 236 ~~~v~i~G~if~-~e~~~~k~~~~~~~~~~t-d--~-------------~~s~~~k~f~~~~~~~~~~~~~~~g~~v~~~ 298 (1437)
T PRK00448 236 ERRVVVEGYVFK-VEIKELKSGRHILTFKIT-D--Y-------------TSSIIVKKFSRDKEDLKKFDEIKKGDWVKVR 298 (1437)
T ss_pred CCeEEEEEEEEE-EEEEeccCCCEEEEEEEE-c--C-------------CCCEEEEEEecCcchhHHHhcCCCCCEEEEE
Confidence 468999999955 788899999999888773 1 1 1226777777411 12345779999999999
Q ss_pred EEeEEeeeec
Q 030281 129 GDIEIRVYND 138 (180)
Q Consensus 129 GrL~~~~y~d 138 (180)
|++.+..|..
T Consensus 299 g~~~~d~~~~ 308 (1437)
T PRK00448 299 GSVQNDTFTR 308 (1437)
T ss_pred EEEeccCCCC
Confidence 9999999875
No 66
>PRK07279 dnaE DNA polymerase III DnaE; Reviewed
Probab=78.55 E-value=20 Score=36.58 Aligned_cols=65 Identities=18% Similarity=0.233 Sum_probs=48.2
Q ss_pred EEEEEEEeCCCCeEEEec-CCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEEEEEE
Q 030281 52 KAIICGKVKDTPVQKILR-NGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVYVEGD 130 (180)
Q Consensus 52 ~v~L~Grlg~dPe~r~t~-nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~VeGr 130 (180)
.+.+.|.|..--. +.+. +|+..+.+++.-. +|+ +.|++|.+ .-+.....|..|..|+|+|+
T Consensus 886 ~~~~~~~i~~~~~-~~tk~~g~~maf~~leD~-------~g~---------ie~~vFp~-~y~~~~~~l~~~~~~~v~G~ 947 (1034)
T PRK07279 886 EATILVQIQSIRV-IRTKTKGQQMAFLSVTDT-------KKK---------LDVTLFPE-TYRQYKDELKEGKFYYLKGK 947 (1034)
T ss_pred cceEEEEEEEEEE-EEEcCCCCeEEEEEEeeC-------CCc---------EEEEECHH-HHHHHHHHhccCCEEEEEEE
Confidence 4678888876443 4455 8888777765432 353 79999998 66667889999999999999
Q ss_pred eEEe
Q 030281 131 IEIR 134 (180)
Q Consensus 131 L~~~ 134 (180)
++.+
T Consensus 948 v~~~ 951 (1034)
T PRK07279 948 IQER 951 (1034)
T ss_pred EEec
Confidence 9663
No 67
>PRK07218 replication factor A; Provisional
Probab=78.51 E-value=24 Score=32.47 Aligned_cols=85 Identities=15% Similarity=0.264 Sum_probs=54.9
Q ss_pred cccEEEEEEEeCCCCeEEEe--cCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEE
Q 030281 49 GVHKAIICGKVKDTPVQKIL--RNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVY 126 (180)
Q Consensus 49 ~mN~v~L~Grlg~dPe~r~t--~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~ 126 (180)
+++.|.|.|+|.+... |.+ ++|... ..+. ...|. +|. +++++|+. +| .|..|+.|.
T Consensus 171 g~~~V~v~g~Vl~~~~-r~f~~~dg~~~-v~~g----iigDe-TG~---------Ir~tlW~~-~~-----~l~~Gd~v~ 228 (423)
T PRK07218 171 GDRGVNVEARVLELEH-REIDGRDGETT-ILSG----VLADE-TGR---------LPFTDWDP-LP-----EIEIGASIR 228 (423)
T ss_pred CCCceEEEEEEEEecc-eeEEcCCCCeE-EEEE----EEECC-Cce---------EEEEEecc-cc-----cCCCCCEEE
Confidence 4667889999987633 332 455432 1111 23333 453 89999998 65 389999999
Q ss_pred EEEEeEEeeeecCCCCeEEEEEEEEEEeCCceEEecCC
Q 030281 127 VEGDIEIRVYNDSINGEVKNIPEICIRRDGTLRLVKSG 164 (180)
Q Consensus 127 VeGrL~~~~y~d~~dG~~~~~~eI~v~~~g~i~~l~~k 164 (180)
|.+--... |.. .++|.+.+.+.|..++..
T Consensus 229 I~na~v~e-~~G--------~~elnv~~~t~I~~~d~~ 257 (423)
T PRK07218 229 IEDAYVRE-FRG--------VPSVNVSEFTTVEALDRE 257 (423)
T ss_pred EeeeEEec-cCC--------eEEEEECCceEEEECCCC
Confidence 99854333 432 577888777778877654
No 68
>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=77.42 E-value=28 Score=26.16 Aligned_cols=87 Identities=18% Similarity=0.235 Sum_probs=51.4
Q ss_pred EEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHH--HHHHhcCCCCeEEEEE
Q 030281 52 KAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGS--YAVKQLVKNSSVYVEG 129 (180)
Q Consensus 52 ~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae--~~~~~l~KG~~V~VeG 129 (180)
.|+|.|+|..--. .|+ + .|-... |. +| .+.|++-.+ ... ...+.|+.|+.|.|+|
T Consensus 16 ~V~i~Gwv~~~R~-----~gk-~-~Fi~Lr-----D~-~g---------~~Q~v~~~~-~~~~~~~~~~l~~gs~V~V~G 72 (135)
T cd04317 16 EVTLCGWVQRRRD-----HGG-L-IFIDLR-----DR-YG---------IVQVVFDPE-EAPEFELAEKLRNESVIQVTG 72 (135)
T ss_pred EEEEEEeEehhcc-----cCC-E-EEEEEe-----cC-Ce---------eEEEEEeCC-chhHHHHHhCCCCccEEEEEE
Confidence 6999999977322 344 3 343322 21 12 266666443 222 2346799999999999
Q ss_pred EeEEeeeecCCCCeEEEEEEEEEEeCCceEEecCC
Q 030281 130 DIEIRVYNDSINGEVKNIPEICIRRDGTLRLVKSG 164 (180)
Q Consensus 130 rL~~~~y~d~~dG~~~~~~eI~v~~~g~i~~l~~k 164 (180)
.+....-..++........||.+. .|++|..-
T Consensus 73 ~~~~~~~~~~~~~~~~~~~El~~~---~i~vl~~~ 104 (135)
T cd04317 73 KVRARPEGTVNPKLPTGEIEVVAS---ELEVLNKA 104 (135)
T ss_pred EEECCCccccCCCCCCCcEEEEEe---EEEEEECC
Confidence 988654210101111234899999 89999855
No 69
>PRK07374 dnaE DNA polymerase III subunit alpha; Validated
Probab=76.95 E-value=14 Score=38.11 Aligned_cols=65 Identities=15% Similarity=0.169 Sum_probs=49.2
Q ss_pred cEEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEEEEEE
Q 030281 51 HKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVYVEGD 130 (180)
Q Consensus 51 N~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~VeGr 130 (180)
..|.+.|-|.. ...+.|++|...+.++|.-. +|. +.|++|.+ .-+.+...|..|..|+|+|+
T Consensus 1001 ~~v~v~g~i~~-~k~~~Tk~G~~maf~~leD~-------tg~---------~e~vvFp~-~y~~~~~~l~~~~~~~v~g~ 1062 (1170)
T PRK07374 1001 AKVSAIAMIPE-MKQVTTRKGDRMAILQLEDL-------TGS---------CEAVVFPK-SYERLSDHLMTDTRLLVWAK 1062 (1170)
T ss_pred CEEEEEEEEEE-eEecccCCCCEEEEEEEEEC-------CCC---------EEEEECHH-HHHHHHHHhccCCEEEEEEE
Confidence 35778888876 44556778887776655432 353 79999998 66778889999999999999
Q ss_pred eEE
Q 030281 131 IEI 133 (180)
Q Consensus 131 L~~ 133 (180)
++.
T Consensus 1063 v~~ 1065 (1170)
T PRK07374 1063 VDR 1065 (1170)
T ss_pred EEe
Confidence 964
No 70
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=76.61 E-value=12 Score=36.19 Aligned_cols=89 Identities=22% Similarity=0.154 Sum_probs=54.5
Q ss_pred cEEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEEEEEE
Q 030281 51 HKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVYVEGD 130 (180)
Q Consensus 51 N~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~VeGr 130 (180)
..+++.|.|...+..+. ++.++.+.+. |. +| -+.|+.|+- ...++.+.+++|..++|.|+
T Consensus 60 ~~vtv~g~V~~~~~~~~---~~~~~~v~l~------D~-tg---------~i~l~~F~~-n~~~~~~~l~~G~~~~v~Gk 119 (681)
T PRK10917 60 EKVTVEGEVLSAEVVFG---KRRRLTVTVS------DG-TG---------NLTLRFFNF-NQPYLKKQLKVGKRVAVYGK 119 (681)
T ss_pred CEEEEEEEEEEEEEccC---CceEEEEEEE------EC-Ce---------EEEEEEEcc-CcHHHHhhCCCCCEEEEEEE
Confidence 47999999987644332 4555555443 21 23 268888841 11478899999999999999
Q ss_pred eEEeeeecCCCCeEEEEEEEEE-E-----eCCceEEecCC
Q 030281 131 IEIRVYNDSINGEVKNIPEICI-R-----RDGTLRLVKSG 164 (180)
Q Consensus 131 L~~~~y~d~~dG~~~~~~eI~v-~-----~~g~i~~l~~k 164 (180)
+.... .+.....+++.+ + ..+.|.++.+.
T Consensus 120 v~~~~-----~~~qm~~P~~~~~~~~~~~~~~~i~PvY~~ 154 (681)
T PRK10917 120 VKRGK-----YGLEMVHPEYEVLEEESPELEGRLTPVYPL 154 (681)
T ss_pred EEecC-----CeEEEEcCEEEecccccccccCceEeecCC
Confidence 98621 122234444432 1 13567777754
No 71
>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=76.03 E-value=19 Score=25.07 Aligned_cols=55 Identities=11% Similarity=0.234 Sum_probs=35.2
Q ss_pred EEEEecCchhHH-HHHHhcCCCCeEEEEEEeEEeeeecCCCCeEEEEEEEEEEeCCceEEecC
Q 030281 102 HRIAVHNEILGS-YAVKQLVKNSSVYVEGDIEIRVYNDSINGEVKNIPEICIRRDGTLRLVKS 163 (180)
Q Consensus 102 ~~V~~~gk~~Ae-~~~~~l~KG~~V~VeGrL~~~~y~d~~dG~~~~~~eI~v~~~g~i~~l~~ 163 (180)
+.|++-.+ ... ...+.|..|+.|.|+|.+..+.-.. .+ .....||.++ +|++|.+
T Consensus 31 iQvv~~~~-~~~~~~~~~l~~~s~V~V~G~v~~~~~~~--~~-~~~~~Ei~~~---~i~il~~ 86 (86)
T cd04321 31 IQLVSTAK-KDAFSLLKSITAESPVQVRGKLQLKEAKS--SE-KNDEWELVVD---DIQTLNA 86 (86)
T ss_pred EEEEECCC-HHHHHHHhcCCCCcEEEEEEEEEeCCCcC--CC-CCCCEEEEEE---EEEEecC
Confidence 56755433 221 1345799999999999998865322 11 1124788898 8988853
No 72
>COG1570 XseA Exonuclease VII, large subunit [DNA replication, recombination, and repair]
Probab=74.98 E-value=11 Score=34.91 Aligned_cols=78 Identities=13% Similarity=0.176 Sum_probs=54.9
Q ss_pred ccEEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEEEEE
Q 030281 50 VHKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVYVEG 129 (180)
Q Consensus 50 mN~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~VeG 129 (180)
+-.|-+.|-|.. ++.-++|+.|.++ +| ...-++|++|.. ....+.-.++-|+.|+|.|
T Consensus 23 ~~~V~v~GEISn---~t~~~sgH~YFtL--------KD----------~~A~i~c~mf~~-~~~~l~f~p~eG~~V~v~G 80 (440)
T COG1570 23 LGQVWVRGEISN---FTRPASGHLYFTL--------KD----------ERAQIRCVMFKG-NNRRLKFRPEEGMQVLVRG 80 (440)
T ss_pred CCeEEEEEEecC---CccCCCccEEEEE--------cc----------CCceEEEEEEcC-cccccCCCccCCCEEEEEE
Confidence 557889999976 2233567666433 22 233499999998 6777777899999999999
Q ss_pred EeEEeeeecCCCCeEEEEEEEEEEeCCceEE
Q 030281 130 DIEIRVYNDSINGEVKNIPEICIRRDGTLRL 160 (180)
Q Consensus 130 rL~~~~y~d~~dG~~~~~~eI~v~~~g~i~~ 160 (180)
++.. |+. .|. +.|+++ .+++
T Consensus 81 ~is~--Y~~--rG~----YQi~~~---~~~p 100 (440)
T COG1570 81 KISL--YEP--RGD----YQIVAE---SMEP 100 (440)
T ss_pred EEEE--EcC--CCc----eEEEEe---cCCc
Confidence 9875 554 354 667777 5553
No 73
>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=73.86 E-value=22 Score=24.79 Aligned_cols=59 Identities=14% Similarity=0.211 Sum_probs=38.6
Q ss_pred EEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHH---HHHHhcCCCCeEEEEE
Q 030281 53 AIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGS---YAVKQLVKNSSVYVEG 129 (180)
Q Consensus 53 v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae---~~~~~l~KG~~V~VeG 129 (180)
|.++|.|..--. . ..++.|+|. |+ +|. +.|..|.. ..+ .....+..|+.|.|.|
T Consensus 2 v~~vG~V~~~~~---~---~~~~~~tL~------D~-TG~---------I~~~~W~~-~~~~~~~~~~~~~~g~~v~v~G 58 (95)
T cd04478 2 VTLVGVVRNVEE---Q---STNITYTID------DG-TGT---------IEVRQWLD-DDNDDSSEVEPIEEGTYVRVFG 58 (95)
T ss_pred EEEEEEEEeeeE---c---ccEEEEEEE------CC-CCc---------EEEEEeCC-CCCcccccccccccCCEEEEEE
Confidence 567887766211 1 244555442 33 454 78889976 322 3577899999999999
Q ss_pred EeEEe
Q 030281 130 DIEIR 134 (180)
Q Consensus 130 rL~~~ 134 (180)
+++..
T Consensus 59 ~v~~~ 63 (95)
T cd04478 59 NLKSF 63 (95)
T ss_pred EEccc
Confidence 99654
No 74
>KOG3416 consensus Predicted nucleic acid binding protein [General function prediction only]
Probab=72.16 E-value=12 Score=28.99 Aligned_cols=72 Identities=24% Similarity=0.344 Sum_probs=46.9
Q ss_pred eCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEEEEEEe------E
Q 030281 59 VKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVYVEGDI------E 132 (180)
Q Consensus 59 lg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~VeGrL------~ 132 (180)
|-.+-..+.|++|+.|..+.||-. +|. |++.+|++ . -..++.||-|.+.|-. .
T Consensus 23 vl~~g~~tkTkdg~~v~~~kVaD~-------Tgs---------I~isvW~e-~----~~~~~PGDIirLt~Gy~Si~qg~ 81 (134)
T KOG3416|consen 23 VLEYGRATKTKDGHEVRSCKVADE-------TGS---------INISVWDE-E----GCLIQPGDIIRLTGGYASIFQGC 81 (134)
T ss_pred EEeeceeeeccCCCEEEEEEEecc-------cce---------EEEEEecC-c----CcccCCccEEEecccchhhhcCc
Confidence 334444556889999999877632 353 89999997 3 3477888888776532 2
Q ss_pred EeeeecCCCCeEEEEEEEEE
Q 030281 133 IRVYNDSINGEVKNIPEICI 152 (180)
Q Consensus 133 ~~~y~d~~dG~~~~~~eI~v 152 (180)
..-|..+ .|.....-|+++
T Consensus 82 LtL~~GK-~Ge~~KiGef~~ 100 (134)
T KOG3416|consen 82 LTLYVGK-GGEVQKIGEFCM 100 (134)
T ss_pred eEEEecC-CceEeEeeeeEE
Confidence 3345555 676666555544
No 75
>PRK05672 dnaE2 error-prone DNA polymerase; Validated
Probab=71.91 E-value=34 Score=35.03 Aligned_cols=79 Identities=15% Similarity=0.225 Sum_probs=53.1
Q ss_pred EEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEEEEEEe
Q 030281 52 KAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVYVEGDI 131 (180)
Q Consensus 52 ~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~VeGrL 131 (180)
.|.+.|-|.. ...+.|++| .+-+++. |. +|. +.|++|.+ .-+.....|+.|..|+|+|++
T Consensus 955 ~v~v~g~i~~-~~~~~TkkG--maf~~le------D~-~g~---------~e~~ifp~-~~~~~~~~l~~~~~~~v~g~v 1014 (1046)
T PRK05672 955 RVRVAGVVTH-RQRPGTASG--VTFLTLE------DE-TGM---------VNVVVWPG-LWERQRREALGARLLLVRGRV 1014 (1046)
T ss_pred EEEEEEEEEE-EEEecCCCc--eEEEEEe------cC-CCC---------EEEEECHH-HHHHHHHHhccCCEEEEEEEE
Confidence 4667676665 444556777 3333222 22 343 79999998 778888899999999999999
Q ss_pred EEeeeecCCCCeEEEEEEEEEEeCCceEEecC
Q 030281 132 EIRVYNDSINGEVKNIPEICIRRDGTLRLVKS 163 (180)
Q Consensus 132 ~~~~y~d~~dG~~~~~~eI~v~~~g~i~~l~~ 163 (180)
+.+ +|. ..|+|+ +|..|..
T Consensus 1015 ~~~------~~~----~~~~~~---~i~~~~~ 1033 (1046)
T PRK05672 1015 QNA------EGV----RHLVAD---RLEDLSP 1033 (1046)
T ss_pred Eec------CCe----EEEEEe---eeechHH
Confidence 653 232 457777 6766643
No 76
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=71.87 E-value=16 Score=35.49 Aligned_cols=77 Identities=19% Similarity=0.163 Sum_probs=54.0
Q ss_pred EEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEEEEEEe
Q 030281 52 KAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVYVEGDI 131 (180)
Q Consensus 52 ~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~VeGrL 131 (180)
.|++.|.|....... ..++..+++.+..+ +| -+.++.|+. .| ++.+.+++|..|.|.|.+
T Consensus 62 ~vti~g~V~~~~~~~--~~~~~~l~v~~~d~-------~~---------~l~l~fFn~-~~-~l~~~~~~G~~v~v~Gk~ 121 (677)
T COG1200 62 IVTIEGTVLSHEKFP--FGKRKLLKVTLSDG-------TG---------VLTLVFFNF-PA-YLKKKLKVGERVIVYGKV 121 (677)
T ss_pred eEEEEEEEEeeeccC--CCCCceEEEEEecC-------cE---------EEEEEEECc-cH-HHHhhCCCCCEEEEEEEE
Confidence 689999998865542 34456666654432 12 378999998 55 899999999999999999
Q ss_pred EEeeeecCCCCeEEEEEEEEEE
Q 030281 132 EIRVYNDSINGEVKNIPEICIR 153 (180)
Q Consensus 132 ~~~~y~d~~dG~~~~~~eI~v~ 153 (180)
....+ +-....+++.+.
T Consensus 122 ~~~~~-----~~~~~hpe~~~~ 138 (677)
T COG1200 122 KRFKG-----GLQITHPEYIVN 138 (677)
T ss_pred eeccC-----ceEEEcceEEec
Confidence 88332 344555666553
No 77
>PRK06386 replication factor A; Reviewed
Probab=71.33 E-value=41 Score=30.30 Aligned_cols=86 Identities=17% Similarity=0.264 Sum_probs=51.6
Q ss_pred ccccEEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEEE
Q 030281 48 RGVHKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVYV 127 (180)
Q Consensus 48 ~~mN~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~V 127 (180)
.++..+.+.|+|..-|+-.+...|..-..-++ ...|. +| -+++++|++ .|..|+.|.|
T Consensus 115 ~g~~~v~V~akVle~~e~e~~~~g~~~~v~sg----~lgDe-TG---------rIr~TlW~~--------~l~eGd~v~i 172 (358)
T PRK06386 115 LVTPYVSVIGKITGITKKEYDSDGTSKIVYQG----YIEDD-TA---------RVRISSFGK--------PLEDNRFVRI 172 (358)
T ss_pred CCCCceEEEEEEEEccCceEecCCCccEEEEE----EEEcC-CC---------eEEEEEccc--------cccCCCEEEE
Confidence 34556779999987766323233321111111 12233 45 489999986 3789999999
Q ss_pred EEEeEEeeeecCCCCeEEEEEEEEEEeCCceEEecCC
Q 030281 128 EGDIEIRVYNDSINGEVKNIPEICIRRDGTLRLVKSG 164 (180)
Q Consensus 128 eGrL~~~~y~d~~dG~~~~~~eI~v~~~g~i~~l~~k 164 (180)
.+- ..+.|. -.++|.+.+.+.|..++..
T Consensus 173 ~na-~v~e~~--------G~~el~v~~~t~I~~~~~~ 200 (358)
T PRK06386 173 ENA-RVSQYN--------GYIEISVGNKSVIKEVESD 200 (358)
T ss_pred eee-EEEccC--------CeEEEEeCCeEEEEECCCC
Confidence 983 355553 2577777766666666444
No 78
>TIGR00643 recG ATP-dependent DNA helicase RecG.
Probab=69.94 E-value=36 Score=32.51 Aligned_cols=64 Identities=19% Similarity=0.227 Sum_probs=42.6
Q ss_pred cEEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEEEEEE
Q 030281 51 HKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVYVEGD 130 (180)
Q Consensus 51 N~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~VeGr 130 (180)
..+++.|.|..... ....+...+.+.+... . +| -+.|+.|+. .++.+.+++|..|+|.|+
T Consensus 33 ~~~~~~~~v~~~~~--~~~~~~~~~~~~~~d~-----~-~~---------~~~~~~F~~---~~~~~~~~~g~~~~~~Gk 92 (630)
T TIGR00643 33 ERATIVGEVLSHCI--FGFKRRKVLKLRLKDG-----G-YK---------KLELRFFNR---AFLKKKFKVGSKVVVYGK 92 (630)
T ss_pred CEEEEEEEEEEeEe--ccCCCCceEEEEEEEC-----C-CC---------EEEEEEECC---HHHHhhCCCCCEEEEEEE
Confidence 36899999877322 1123344555544221 1 23 278899985 388899999999999999
Q ss_pred eEEe
Q 030281 131 IEIR 134 (180)
Q Consensus 131 L~~~ 134 (180)
+...
T Consensus 93 ~~~~ 96 (630)
T TIGR00643 93 VKSS 96 (630)
T ss_pred EEee
Confidence 9753
No 79
>PF13567 DUF4131: Domain of unknown function (DUF4131)
Probab=69.06 E-value=38 Score=24.96 Aligned_cols=71 Identities=13% Similarity=0.150 Sum_probs=42.3
Q ss_pred cEEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEEEEEE
Q 030281 51 HKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVYVEGD 130 (180)
Q Consensus 51 N~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~VeGr 130 (180)
..+++.|.|...|... +.. .+|.+.+.+- ... +.. .....-+.+.+-.+ ... .++.||.+.++|+
T Consensus 76 ~~~~v~g~V~~~~~~~----~~~-~~~~~~~~~~-~~~--~~~--~~~~~~i~~~~~~~-~~~----~l~~Gd~i~~~g~ 140 (176)
T PF13567_consen 76 KEVTVQGTVESVPQID----GRG-QRFTLRVERV-LAG--GNW--IPVSGKILLYLPKD-SQP----RLQPGDRIRVRGK 140 (176)
T ss_pred ceEEEEEEEccccccc----Cce-EEEEEEEEEe-ecc--ccc--cccceeeEEEeccc-ccc----ccCCCCEEEEEEE
Confidence 3688999999988753 222 2666665432 111 221 22334445545444 111 7999999999999
Q ss_pred eEEeee
Q 030281 131 IEIRVY 136 (180)
Q Consensus 131 L~~~~y 136 (180)
|+.=.-
T Consensus 141 l~~~~~ 146 (176)
T PF13567_consen 141 LKPPSG 146 (176)
T ss_pred EecCCC
Confidence 986443
No 80
>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=66.97 E-value=38 Score=24.10 Aligned_cols=58 Identities=17% Similarity=0.076 Sum_probs=37.1
Q ss_pred EEEEecCch---hHH--HHHHhcCCCCeEEEEEEeEEeeeecCCCCeEEEEEEEEEEeCCceEEecCC
Q 030281 102 HRIAVHNEI---LGS--YAVKQLVKNSSVYVEGDIEIRVYNDSINGEVKNIPEICIRRDGTLRLVKSG 164 (180)
Q Consensus 102 ~~V~~~gk~---~Ae--~~~~~l~KG~~V~VeGrL~~~~y~d~~dG~~~~~~eI~v~~~g~i~~l~~k 164 (180)
+.|++-.+. ..+ ..++.|+.|+.|.|+|.+....- .. ++.....+||.++ +|++|..-
T Consensus 30 iQ~v~~~~~~~~~~~~~~~~~~l~~es~V~V~G~v~~~~~-~~-~~~~~~~~El~~~---~i~il~~~ 92 (102)
T cd04320 30 IQGVLAASAEGVSKQMVKWAGSLSKESIVDVEGTVKKPEE-PI-KSCTQQDVELHIE---KIYVVSEA 92 (102)
T ss_pred EEEEEeCCcccCCHHHHHHHhcCCCccEEEEEEEEECCCC-cc-cCCCcCcEEEEEE---EEEEEecC
Confidence 677665331 011 12457999999999999986421 11 2222246899999 99999744
No 81
>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=66.94 E-value=37 Score=23.30 Aligned_cols=53 Identities=21% Similarity=0.288 Sum_probs=34.4
Q ss_pred EEEEecCchhHH--HHHHhcCCCCeEEEEEEeEEeeeecCCCCeEEEEEEEEEEeCCceEEec
Q 030281 102 HRIAVHNEILGS--YAVKQLVKNSSVYVEGDIEIRVYNDSINGEVKNIPEICIRRDGTLRLVK 162 (180)
Q Consensus 102 ~~V~~~gk~~Ae--~~~~~l~KG~~V~VeGrL~~~~y~d~~dG~~~~~~eI~v~~~g~i~~l~ 162 (180)
+.|++-.+ ... ...+.|..|+.|.|+|.+..+.-.. ......||.++ +|++|.
T Consensus 29 iQ~v~~~~-~~~~~~~~~~l~~es~V~V~G~v~~~~~~~----~~~~~~Ei~~~---~i~vl~ 83 (84)
T cd04323 29 LQCVLSKK-LVTEFYDAKSLTQESSVEVTGEVKEDPRAK----QAPGGYELQVD---YLEIIG 83 (84)
T ss_pred EEEEEcCC-cchhHHHHhcCCCcCEEEEEEEEEECCccc----CCCCCEEEEEE---EEEEEc
Confidence 66766544 221 2345799999999999998754221 00124789998 888874
No 82
>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=64.36 E-value=58 Score=24.96 Aligned_cols=77 Identities=10% Similarity=0.155 Sum_probs=50.7
Q ss_pred EEEEEEEeCCCCeE--EEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCC-CCeEEEE
Q 030281 52 KAIICGKVKDTPVQ--KILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVK-NSSVYVE 128 (180)
Q Consensus 52 ~v~L~Grlg~dPe~--r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~K-G~~V~Ve 128 (180)
.+.++|-|...-.. +.+....-.+.|+| +...+... . .....+.|.+|.+ ..+.+- .++. ||.|.+.
T Consensus 14 ~vnvigVV~~~~~p~~~~t~g~D~~~tl~i-~D~S~~~~---~----~~~~~l~v~iF~~-~~~~LP-~v~~~GDii~l~ 83 (146)
T PF02765_consen 14 FVNVIGVVVDFSPPNPKKTRGTDYMCTLTI-TDPSLNDS---N----QKLSGLTVNIFRP-HKESLP-NVKSVGDIIRLR 83 (146)
T ss_dssp EEEEEEEEEEEEEECTEEESSSCEEEEEEE-EBTTCSCS---S----CCCCEEEEEEEES-SHHHSC-TTCSTTHEEEEE
T ss_pred EEEEEEEEEEccCCcceEcCCCcEEEEEEE-ECCCCCcc---c----cccCCEEEEEECC-CHHHCC-CCCCCCCEEEEE
Confidence 56688888776444 55555667788888 33322211 0 0116899999987 566654 5555 9988887
Q ss_pred EEeEEeeeecC
Q 030281 129 GDIEIRVYNDS 139 (180)
Q Consensus 129 GrL~~~~y~d~ 139 (180)
+++...|+++
T Consensus 84 -r~kv~~~~~~ 93 (146)
T PF02765_consen 84 -RVKVQSYNGK 93 (146)
T ss_dssp -EEEEEEETTE
T ss_pred -EEEEEEECCE
Confidence 8889999764
No 83
>smart00350 MCM minichromosome maintenance proteins.
Probab=64.28 E-value=26 Score=32.54 Aligned_cols=60 Identities=15% Similarity=0.063 Sum_probs=42.3
Q ss_pred CceEEEEEecCchhHHHHHHhcCCCCeEEEEEEeEEeeeecCC---CCeEEEEEEEEEEeCCceEEecCCC
Q 030281 98 PVQWHRIAVHNEILGSYAVKQLVKNSSVYVEGDIEIRVYNDSI---NGEVKNIPEICIRRDGTLRLVKSGE 165 (180)
Q Consensus 98 ~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~VeGrL~~~~y~d~~---dG~~~~~~eI~v~~~g~i~~l~~k~ 165 (180)
.+..+.|.+.+. + +..++.||+|.|.|-++.+.|..+. .+...+.+.|.+. .|+.++.+.
T Consensus 102 ~Prsi~v~l~~d-L----vd~~~PGD~V~i~Gi~~~~~~~~~~~~~~~~~~~~~~l~a~---~i~~~~~~~ 164 (509)
T smart00350 102 LPRSVDVILDGD-L----VDKAKPGDRVEVTGIYRNIPYGFKLNTVKGLPVFATYIEAN---HVRKLDYKR 164 (509)
T ss_pred CCcEEEEEEccc-c----cCcccCCCEEEEEEEEEeeccccccccCCCcceeeEEEEEe---EEEEccccc
Confidence 466789999988 4 5589999999999999988663321 1222355667776 777776543
No 84
>PLN02903 aminoacyl-tRNA ligase
Probab=61.34 E-value=90 Score=30.44 Aligned_cols=59 Identities=15% Similarity=0.199 Sum_probs=37.9
Q ss_pred EEEEecCch--hHHHHHHhcCCCCeEEEEEEeEEeeeecCCCCeEE-EEEEEEEEeCCceEEecCC
Q 030281 102 HRIAVHNEI--LGSYAVKQLVKNSSVYVEGDIEIRVYNDSINGEVK-NIPEICIRRDGTLRLVKSG 164 (180)
Q Consensus 102 ~~V~~~gk~--~Ae~~~~~l~KG~~V~VeGrL~~~~y~d~~dG~~~-~~~eI~v~~~g~i~~l~~k 164 (180)
+.|++-.+. .+-..++.|+.|+.|.|+|.++.+.-... +.+.. -..||.|+ +|++|...
T Consensus 102 iQvV~~~~~~~~~~~~~~~L~~esvV~V~G~V~~r~~~~~-n~~~~tGeiEl~~~---~i~VL~~a 163 (652)
T PLN02903 102 VQVVTLPDEFPEAHRTANRLRNEYVVAVEGTVRSRPQESP-NKKMKTGSVEVVAE---SVDILNVV 163 (652)
T ss_pred EEEEEeCCccHHHHHHHhcCCCCCEEEEEEEEEeCCCcCc-CCCCCCCCEEEEEe---EEEEEecC
Confidence 577665331 12223568999999999999987632221 11111 24899999 89999764
No 85
>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=61.16 E-value=1.3e+02 Score=28.90 Aligned_cols=87 Identities=20% Similarity=0.191 Sum_probs=51.2
Q ss_pred EEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEEEEEEe
Q 030281 52 KAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVYVEGDI 131 (180)
Q Consensus 52 ~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~VeGrL 131 (180)
+|+|+|+|-+ +|. .|+ +.|-.. +|. +| -+.|++-.+..+-...+.|+.|+.|.|+|.+
T Consensus 17 ~V~l~GwV~~---~R~--~Gk--l~Fi~L-----rD~-sg---------~iQvv~~~~~~~~~~~~~L~~esvV~V~G~v 74 (583)
T TIGR00459 17 TVTLAGWVNR---RRD--LGG--LIFIDL-----RDR-SG---------IVQVVCDPDADALKLAKGLRNEDVVQVKGKV 74 (583)
T ss_pred EEEEEEEEEE---EEc--CCC--cEEEEE-----EeC-Cc---------cEEEEEeCCHHHHHHHhcCCCCCEEEEEEEE
Confidence 7999999954 332 344 344332 222 23 2677664331122245679999999999999
Q ss_pred EEeeeecCCCC-eEEEEEEEEEEeCCceEEecCC
Q 030281 132 EIRVYNDSING-EVKNIPEICIRRDGTLRLVKSG 164 (180)
Q Consensus 132 ~~~~y~d~~dG-~~~~~~eI~v~~~g~i~~l~~k 164 (180)
..+.=... +- ...-..||.+. ++++|...
T Consensus 75 ~~r~~~~~-n~~~~tg~iEl~~~---~i~iL~~a 104 (583)
T TIGR00459 75 SARPEGNI-NRNLDTGEIEILAE---SITLLNKS 104 (583)
T ss_pred EeCCcccc-CccCCCCcEEEEEe---EEEEeecC
Confidence 86532111 10 11225889998 89998743
No 86
>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=60.95 E-value=18 Score=26.09 Aligned_cols=37 Identities=14% Similarity=0.094 Sum_probs=27.8
Q ss_pred EEEEEecCchhHHHHHHhcC---CCCeEE-EEEEeEEeeeec
Q 030281 101 WHRIAVHNEILGSYAVKQLV---KNSSVY-VEGDIEIRVYND 138 (180)
Q Consensus 101 w~~V~~~gk~~Ae~~~~~l~---KG~~V~-VeGrL~~~~y~d 138 (180)
-+.|++||+ .|+.+...+. ++..|. |-+-.+...|..
T Consensus 36 ~l~~tlwG~-~A~~f~~~~~~~~~~~~VVav~~~~rV~~~~g 76 (106)
T cd04481 36 RLKCTLWGE-YAEEFDAKFQSAGNGEPVVAVLRFWKIKEYKG 76 (106)
T ss_pred EEEEEEEHH-HHHHHHHHHHHhCCCCcEEEEEEeEEEEEEcC
Confidence 489999999 9998877763 555555 445588999964
No 87
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=60.22 E-value=45 Score=30.76 Aligned_cols=70 Identities=14% Similarity=0.179 Sum_probs=51.3
Q ss_pred cccccccEEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHH--HHHHhcCCC
Q 030281 45 WGFRGVHKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGS--YAVKQLVKN 122 (180)
Q Consensus 45 ~~m~~mN~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae--~~~~~l~KG 122 (180)
..++...+..+.|++..+|... ++|..++.+ .+. .| -+.|++|-. ..+ .++..|.+|
T Consensus 261 ~d~~~~~~~~v~g~v~~~p~~i--eGghv~v~i--------~d~-~G---------~I~~~A~ep-tk~fr~~a~~L~pG 319 (421)
T COG1571 261 NDIEDYSKYRVVGRVEAEPRAI--EGGHVVVEI--------TDG-EG---------EIGAVAFEP-TKEFRELARKLIPG 319 (421)
T ss_pred hhhhhccceEEEEEEecccEEe--eCCEEEEEe--------cCC-Cc---------eEEEEEecc-cccchHHHHhcCCC
Confidence 3456778899999999999853 567766533 122 13 388999887 554 367899999
Q ss_pred CeEEEEEEeEEee
Q 030281 123 SSVYVEGDIEIRV 135 (180)
Q Consensus 123 ~~V~VeGrL~~~~ 135 (180)
|.|.+-|.++...
T Consensus 320 D~i~~~G~~~~~~ 332 (421)
T COG1571 320 DEITVYGSVKPGT 332 (421)
T ss_pred CEEEEecCccccc
Confidence 9999999886554
No 88
>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=59.65 E-value=35 Score=23.22 Aligned_cols=51 Identities=18% Similarity=0.170 Sum_probs=33.3
Q ss_pred EEEEecCchhHHHHHHhcCCCCeEEEEEEeEEeeeecCCCCeEEEEEEEEEEeCCceEEec
Q 030281 102 HRIAVHNEILGSYAVKQLVKNSSVYVEGDIEIRVYNDSINGEVKNIPEICIRRDGTLRLVK 162 (180)
Q Consensus 102 ~~V~~~gk~~Ae~~~~~l~KG~~V~VeGrL~~~~y~d~~dG~~~~~~eI~v~~~g~i~~l~ 162 (180)
+.|++-....+-...+.|..|+.|.|+|.+....-. .| ..||.+. +++++.
T Consensus 31 lQvv~~~~~~~~~~~~~l~~gs~V~v~G~v~~~~~~---~~----~~El~~~---~i~il~ 81 (82)
T cd04318 31 LQVVVDKELTNFKEILKLSTGSSIRVEGVLVKSPGA---KQ----PFELQAE---KIEVLG 81 (82)
T ss_pred EEEEEeCcccCHHHHhcCCCceEEEEEEEEEeCCCC---CC----CEEEEEE---EEEEec
Confidence 566654431111245679999999999998875421 12 5788888 787764
No 89
>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=58.99 E-value=65 Score=23.20 Aligned_cols=53 Identities=15% Similarity=0.229 Sum_probs=36.1
Q ss_pred EEEEecCchh-HH--HHHHhcCCCCeEEEEEEeEEeeeecCCCCeEEEEEEEEEEeCCceEEecCC
Q 030281 102 HRIAVHNEIL-GS--YAVKQLVKNSSVYVEGDIEIRVYNDSINGEVKNIPEICIRRDGTLRLVKSG 164 (180)
Q Consensus 102 ~~V~~~gk~~-Ae--~~~~~l~KG~~V~VeGrL~~~~y~d~~dG~~~~~~eI~v~~~g~i~~l~~k 164 (180)
+.|++-.+.. .+ ...+.|..|+.|.|+|.+..+.-. . ...||.+. .|++|...
T Consensus 42 iQ~v~~~~~~~~~~~~~~~~l~~es~V~V~G~v~~~~~~---~----~~~Ei~~~---~i~il~~~ 97 (108)
T cd04316 42 VQVTAPKKKVDKELFKTVRKLSRESVISVTGTVKAEPKA---P----NGVEIIPE---EIEVLSEA 97 (108)
T ss_pred EEEEEeCCCCCHHHHHHHhCCCCcCEEEEEEEEEeCCCC---C----CCEEEEEe---EEEEEeCC
Confidence 6776654311 11 124579999999999998875311 1 24899999 89999854
No 90
>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=58.95 E-value=87 Score=28.60 Aligned_cols=82 Identities=22% Similarity=0.245 Sum_probs=49.0
Q ss_pred cEEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHH---HHHhcCCCCeEEE
Q 030281 51 HKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSY---AVKQLVKNSSVYV 127 (180)
Q Consensus 51 N~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~---~~~~l~KG~~V~V 127 (180)
..|+|.|+|-+ .-..|+ + .|-... |. +| -+.|++-.+..... ....|..||.|.|
T Consensus 13 ~~v~i~G~v~~-----~R~~g~-~-~Fi~lr-----d~-~g---------~iQ~v~~~~~~~~~~~~~~~~l~~~s~v~v 70 (428)
T TIGR00458 13 QEVTFMGWVHE-----IRDLGG-L-IFVLLR-----DR-EG---------LIQITAPAKKVSKNLFKWAKKLNLESVVAV 70 (428)
T ss_pred CEEEEEEEEEE-----EecCCC-c-EEEEEE-----eC-Ce---------eEEEEEECCcCCHHHHHHHhCCCCCcEEEE
Confidence 46999999954 222354 2 343222 21 12 26766653211111 2357999999999
Q ss_pred EEEeEEeeeecCCCCeEEEEEEEEEEeCCceEEecCC
Q 030281 128 EGDIEIRVYNDSINGEVKNIPEICIRRDGTLRLVKSG 164 (180)
Q Consensus 128 eGrL~~~~y~d~~dG~~~~~~eI~v~~~g~i~~l~~k 164 (180)
+|.+....- .....+|.+. +|++|...
T Consensus 71 ~G~v~~~~~-------~~~~~el~~~---~i~vl~~~ 97 (428)
T TIGR00458 71 RGIVKIKEK-------APGGFEIIPT---KIEVINEA 97 (428)
T ss_pred EEEEEecCC-------CCCcEEEEEe---EEEEEecC
Confidence 999984321 1124888898 89988765
No 91
>COG0017 AsnS Aspartyl/asparaginyl-tRNA synthetases [Translation, ribosomal structure and biogenesis]
Probab=54.54 E-value=34 Score=31.65 Aligned_cols=82 Identities=20% Similarity=0.187 Sum_probs=51.6
Q ss_pred cEEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHH--HHhcCCCCeEEEE
Q 030281 51 HKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYA--VKQLVKNSSVYVE 128 (180)
Q Consensus 51 N~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~--~~~l~KG~~V~Ve 128 (180)
.+|+|.|-|-.-= ..|+ +.|-+. +| .+.+++|++-.+...+.+ ++.|..++.|.|+
T Consensus 17 ~~V~v~GWV~~~R-----~~g~--i~Fi~l-----rD----------gsg~iQ~v~~~~~~~~~~~~~~~L~~es~v~V~ 74 (435)
T COG0017 17 QEVTVRGWVHNKR-----DLGK--IIFLVL-----RD----------GSGFIQAVVPKNKVYEELFKAKKLTLESSVVVT 74 (435)
T ss_pred cEEEEEEEeeeec-----ccCC--eEEEEE-----Ec----------CCcEEEEEEECCCCcHHHhhhhcCCCccEEEEE
Confidence 5899999886522 2333 334222 22 222589998752133333 4589999999999
Q ss_pred EEeEEeeeecCCCCeEEEEEEEEEEeCCceEEecCC
Q 030281 129 GDIEIRVYNDSINGEVKNIPEICIRRDGTLRLVKSG 164 (180)
Q Consensus 129 GrL~~~~y~d~~dG~~~~~~eI~v~~~g~i~~l~~k 164 (180)
|.+....-.. ..+||.|. .|.+|...
T Consensus 75 G~v~~~~~a~-------~g~El~v~---~i~Vl~~a 100 (435)
T COG0017 75 GIVKASPKAP-------QGFELQVE---KIEVLGEA 100 (435)
T ss_pred EEEEcCCCCC-------CCEEEEEE---EEEEeecc
Confidence 9998765432 25677777 67777655
No 92
>PRK07218 replication factor A; Provisional
Probab=53.66 E-value=50 Score=30.41 Aligned_cols=66 Identities=14% Similarity=0.270 Sum_probs=41.9
Q ss_pred cccEEEEEEEeCCCCeEEEe-cCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEEE
Q 030281 49 GVHKAIICGKVKDTPVQKIL-RNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVYV 127 (180)
Q Consensus 49 ~mN~v~L~Grlg~dPe~r~t-~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~V 127 (180)
++..|.|.|+|..-.+ |++ ..|..-...++.. -|. +|. +++++|++ .+ |..|+.|.|
T Consensus 67 ~~~~V~v~~kVl~i~~-rt~r~dg~~g~v~~~~i----gDe-TG~---------Ir~tlW~~-~~------l~~Gdvv~I 124 (423)
T PRK07218 67 DDKNVTVTGRVLTIGE-RSIRYQGDDHVIYEGIL----ADE-TGT---------ISYTAWKD-FG------LSPGDTVTI 124 (423)
T ss_pred CCceeEEEEEEEEecc-eeEecCCCceEEEEEEE----ECC-CCe---------EEEEEECC-CC------CCCCCEEEE
Confidence 4567889999988766 433 3454322222222 233 464 89999997 53 999999999
Q ss_pred EEEeEEeeee
Q 030281 128 EGDIEIRVYN 137 (180)
Q Consensus 128 eGrL~~~~y~ 137 (180)
.+- .++.|.
T Consensus 125 ~na-~vre~~ 133 (423)
T PRK07218 125 GNA-GVREWD 133 (423)
T ss_pred ecc-EeeccC
Confidence 863 334453
No 93
>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=53.06 E-value=27 Score=23.98 Aligned_cols=54 Identities=22% Similarity=0.245 Sum_probs=34.6
Q ss_pred EEEEecCchhHH--HHHHhcCCCCeEEEEEEeEEeeeecCCCCeEEEEEEEEEEeCCceEEec
Q 030281 102 HRIAVHNEILGS--YAVKQLVKNSSVYVEGDIEIRVYNDSINGEVKNIPEICIRRDGTLRLVK 162 (180)
Q Consensus 102 ~~V~~~gk~~Ae--~~~~~l~KG~~V~VeGrL~~~~y~d~~dG~~~~~~eI~v~~~g~i~~l~ 162 (180)
+.|++-.....+ ...+.|+.|+.|.|+|.+....-.. ......||.++ .+++|.
T Consensus 29 iQ~v~~~~~~~~~~~~~~~l~~~s~V~v~G~~~~~~~~~----~~~~~~El~~~---~i~il~ 84 (85)
T cd04100 29 VQVVVNKEELGEFFEEAEKLRTESVVGVTGTVVKRPEGN----LATGEIELQAE---ELEVLS 84 (85)
T ss_pred EEEEEECCcChHHHHHHhCCCCCCEEEEEeEEEECCCCC----CCCCCEEEEEe---EEEEEC
Confidence 566554431121 2356899999999999998755311 01134788888 888874
No 94
>PTZ00385 lysyl-tRNA synthetase; Provisional
Probab=51.67 E-value=2.3e+02 Score=27.74 Aligned_cols=78 Identities=13% Similarity=0.057 Sum_probs=48.1
Q ss_pred EEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCc-----hhHHHHHHhcCCCCeEE
Q 030281 52 KAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNE-----ILGSYAVKQLVKNSSVY 126 (180)
Q Consensus 52 ~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk-----~~Ae~~~~~l~KG~~V~ 126 (180)
.|.|.|+|.. +| ..|+ +.|-.. +|. +| -+.|++-.+ .....+.+.|..||.|.
T Consensus 109 ~V~vaGrV~~---~R--~~Gk--~~F~~L-----rD~-~G---------~IQvv~~~~~~~~~~~~~~~~~~l~~gdiV~ 166 (659)
T PTZ00385 109 TVRVAGRVTS---VR--DIGK--IIFVTI-----RSN-GN---------ELQVVGQVGEHFTREDLKKLKVSLRVGDIIG 166 (659)
T ss_pred EEEEEEEEEe---ee--ccCC--eEEEEE-----EEC-Cc---------eEEEEEECCccCCHHHHHHHHhCCCCCCEEE
Confidence 4999999965 22 2454 234332 222 24 256665432 11223445799999999
Q ss_pred EEEEeEEeeeecCCCCeEEEEEEEEEEeCCceEEecC
Q 030281 127 VEGDIEIRVYNDSINGEVKNIPEICIRRDGTLRLVKS 163 (180)
Q Consensus 127 VeGrL~~~~y~d~~dG~~~~~~eI~v~~~g~i~~l~~ 163 (180)
|+|.+... + .|. .+|.|. +|++|..
T Consensus 167 V~G~v~~t----~-~Ge----leI~~~---~i~lLsk 191 (659)
T PTZ00385 167 ADGVPCRM----Q-RGE----LSVAAS---RMLILSP 191 (659)
T ss_pred EEEEEEec----C-Cce----EEEEee---EEEEech
Confidence 99988742 2 343 688888 8888875
No 95
>KOG0479 consensus DNA replication licensing factor, MCM3 component [Replication, recombination and repair]
Probab=50.58 E-value=22 Score=34.62 Aligned_cols=55 Identities=13% Similarity=0.148 Sum_probs=40.3
Q ss_pred HHHhcCCCCeEEEEEEeEEeeeecCCCCeE--EEEEEEEEEeCCceEEecCCCCCCCCChhhh
Q 030281 115 AVKQLVKNSSVYVEGDIEIRVYNDSINGEV--KNIPEICIRRDGTLRLVKSGESISKISFDDL 175 (180)
Q Consensus 115 ~~~~l~KG~~V~VeGrL~~~~y~d~~dG~~--~~~~eI~v~~~g~i~~l~~k~~~~~~~~~~~ 175 (180)
+++.+|+||+|-|.|..+.-.... +|.. ...+-|+++ +|.+|.... ....+.+++
T Consensus 223 LVD~~KPGDRV~ivG~yr~Lp~k~--~g~tsg~FRTvliaN---ni~~l~ke~-~~~~t~~Di 279 (818)
T KOG0479|consen 223 LVDRVKPGDRVNIVGIYRSLPGKS--NGNTSGTFRTVLIAN---NIELLSKEA-APDFTDEDI 279 (818)
T ss_pred ccccCCCCCeeEEEEEEeeccCcc--CCcccceeEEEEEec---cHHhhcccc-cccCChhhH
Confidence 678899999999999988877743 5655 567778888 899995543 444444443
No 96
>COG3111 Periplasmic protein with OB-fold [Function unknown]
Probab=50.16 E-value=72 Score=24.68 Aligned_cols=77 Identities=10% Similarity=0.250 Sum_probs=48.6
Q ss_pred CcccccccEEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCC
Q 030281 44 GWGFRGVHKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNS 123 (180)
Q Consensus 44 ~~~m~~mN~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~ 123 (180)
-.+|++-..|+|.|+|.+-. .+..| .|+|. +|+ |+|.+=.+ ...-+.+..-+
T Consensus 51 Ak~~~Dda~V~l~GnIv~qi------~~D~y---------~FrD~-sGe---------I~VeIdd~---~w~g~tv~P~d 102 (128)
T COG3111 51 AKTLHDDAWVSLEGNIVRQI------GDDRY---------VFRDA-SGE---------INVDIDDK---VWNGQTVTPKD 102 (128)
T ss_pred hhccccCCeEEEEeeEEEee------CCceE---------EEEcC-Ccc---------EEEEeccc---ccCCcccCccc
Confidence 34566667899999997622 12222 26665 465 45554322 12234788999
Q ss_pred eEEEEEEeEEeeeecCCCCeEEEEEEEEEEeCCceEEe
Q 030281 124 SVYVEGDIEIRVYNDSINGEVKNIPEICIRRDGTLRLV 161 (180)
Q Consensus 124 ~V~VeGrL~~~~y~d~~dG~~~~~~eI~v~~~g~i~~l 161 (180)
+|.|+|++... |. .++|-|. +|+.+
T Consensus 103 kV~I~GevDk~-~~---------~~eIdV~---~I~k~ 127 (128)
T COG3111 103 KVRIQGEVDKD-WN---------SVEIDVK---HIEKL 127 (128)
T ss_pred EEEEEeEEcCC-Cc---------cceeEhh---heEec
Confidence 99999999765 53 4577777 67665
No 97
>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=50.02 E-value=1.1e+02 Score=23.19 Aligned_cols=73 Identities=8% Similarity=0.053 Sum_probs=47.7
Q ss_pred EEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEEEEEEe
Q 030281 52 KAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVYVEGDI 131 (180)
Q Consensus 52 ~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~VeGrL 131 (180)
.|-++|-|..-...+.+......+.|+|.=.. +. ...-+.|.+|++ .++.+= .+..||.|.+.+ +
T Consensus 16 ~v~vigVV~~~~~p~~s~g~d~~~tl~i~D~S-------~~-----~~~~l~v~~F~~-~~~~LP-~v~~GDVIll~~-~ 80 (138)
T cd04497 16 SVNVIGVVVDAGPPVRSKGTDYCCTLTITDPS-------LA-----NSDGLTVKLFRP-NEESLP-IVKVGDIILLRR-V 80 (138)
T ss_pred eEEEEEEEeecCCCcccCCCcEEEEEEEECCC-------CC-----CCCcEEEEEECC-ChhhCC-CCCCCCEEEEEE-E
Confidence 45588888776555554332345566554332 11 022389999999 677654 359999999997 8
Q ss_pred EEeeeecC
Q 030281 132 EIRVYNDS 139 (180)
Q Consensus 132 ~~~~y~d~ 139 (180)
+...|.++
T Consensus 81 kv~~~~g~ 88 (138)
T cd04497 81 KIQSYNGK 88 (138)
T ss_pred EEEEECCc
Confidence 88888765
No 98
>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=49.46 E-value=43 Score=23.26 Aligned_cols=32 Identities=28% Similarity=0.425 Sum_probs=22.0
Q ss_pred EEeeeecCCCCeEEEEEEEEEEeCCceEEecCC
Q 030281 132 EIRVYNDSINGEVKNIPEICIRRDGTLRLVKSG 164 (180)
Q Consensus 132 ~~~~y~d~~dG~~~~~~eI~v~~~g~i~~l~~k 164 (180)
..|.|+|. +|.-+--.+++.-.+|+|++....
T Consensus 11 ~~RtWtD~-tG~f~VeA~fv~~~dgkV~L~k~n 42 (70)
T PF03983_consen 11 KTRTWTDR-TGKFKVEAEFVGVNDGKVHLHKTN 42 (70)
T ss_dssp -SEEEEBS-SS--EEEEEEEEEETTEEEEE-TT
T ss_pred cceEEEeC-CCCEEEEEEEEEeeCCEEEEEecC
Confidence 57999999 999666666655568999998654
No 99
>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=47.94 E-value=31 Score=25.65 Aligned_cols=32 Identities=16% Similarity=-0.009 Sum_probs=22.3
Q ss_pred CceEEEEEecCc-hhHHHHHHhcCCCCeEEEEE
Q 030281 98 PVQWHRIAVHNE-ILGSYAVKQLVKNSSVYVEG 129 (180)
Q Consensus 98 ~t~w~~V~~~gk-~~Ae~~~~~l~KG~~V~VeG 129 (180)
..-.|.+++++. +.|..-+..++.||.|.|.|
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 455799999997 78999999999999999988
No 100
>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=46.81 E-value=2.4e+02 Score=26.03 Aligned_cols=53 Identities=21% Similarity=0.264 Sum_probs=35.7
Q ss_pred EEEEecCchhHH---HHHHhcCCCCeEEEEEEeEEeeeecCCCCeEEEEEEEEEEeCCceEEecCCC
Q 030281 102 HRIAVHNEILGS---YAVKQLVKNSSVYVEGDIEIRVYNDSINGEVKNIPEICIRRDGTLRLVKSGE 165 (180)
Q Consensus 102 ~~V~~~gk~~Ae---~~~~~l~KG~~V~VeGrL~~~~y~d~~dG~~~~~~eI~v~~~g~i~~l~~k~ 165 (180)
+.|++-.. ... ...+.|..||.|.|+|.+.... .+ . ...||.+. +|++|....
T Consensus 48 iQ~v~~~~-~~~~~~~~~~~l~~gs~V~v~G~v~~~~--~~-~----~~~El~~~---~i~vl~~~~ 103 (453)
T TIGR00457 48 IQAVINGE-DNPYLFQLLKSLTTGSSVSVTGKVVESP--GK-G----QPVELQVK---KIEVVGEAE 103 (453)
T ss_pred EEEEEeCC-cChHHHHHHHcCCCCcEEEEEEEEEcCC--CC-C----CCEEEEEe---EEEEEecCC
Confidence 67766543 211 2346799999999999998632 12 2 24788888 888887543
No 101
>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=46.45 E-value=1.1e+02 Score=21.88 Aligned_cols=52 Identities=21% Similarity=0.259 Sum_probs=35.1
Q ss_pred EEEEecCchhH-HH--HHHhcCCCCeEEEEEEeEEeeeecCCCCeEEEEEEEEEEeCCceEEecCC
Q 030281 102 HRIAVHNEILG-SY--AVKQLVKNSSVYVEGDIEIRVYNDSINGEVKNIPEICIRRDGTLRLVKSG 164 (180)
Q Consensus 102 ~~V~~~gk~~A-e~--~~~~l~KG~~V~VeGrL~~~~y~d~~dG~~~~~~eI~v~~~g~i~~l~~k 164 (180)
+.|++-.+ .+ +. ....|..|+.|.|+|.+..+.- . .+ ..||.++ .|++|...
T Consensus 29 iQ~v~~~~-~~~~~~~~~~~l~~~s~v~V~G~v~~~~~--~-~~----~~Ei~~~---~i~vl~~a 83 (103)
T cd04319 29 VQAVFSKD-LNEEAYREAKKVGIESSVIVEGAVKADPR--A-PG----GAEVHGE---KLEIIQNV 83 (103)
T ss_pred EEEEEeCC-CCHHHHHHHhCCCCCCEEEEEEEEEECCC--C-CC----CEEEEEE---EEEEEecC
Confidence 67766543 21 11 2356899999999999987531 1 11 4899999 89998754
No 102
>COG4097 Predicted ferric reductase [Inorganic ion transport and metabolism]
Probab=45.99 E-value=33 Score=31.48 Aligned_cols=38 Identities=11% Similarity=0.077 Sum_probs=31.5
Q ss_pred eEEEEEecCchhHHHHHHhcCCCCeEEEEEEeEEeeeec
Q 030281 100 QWHRIAVHNEILGSYAVKQLVKNSSVYVEGDIEIRVYND 138 (180)
Q Consensus 100 ~w~~V~~~gk~~Ae~~~~~l~KG~~V~VeGrL~~~~y~d 138 (180)
-.+.|.+-|+ -...+.+.|+.|++|.|+|-----.++.
T Consensus 276 l~FsIK~LGD-~Tk~l~dnLk~G~k~~vdGPYG~F~~~~ 313 (438)
T COG4097 276 LRFSIKALGD-FTKTLKDNLKVGTKLEVDGPYGKFDFER 313 (438)
T ss_pred EEEEehhhhh-hhHHHHHhccCCceEEEecCcceeeccc
Confidence 4678899999 8899999999999999999765555553
No 103
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=45.78 E-value=72 Score=33.50 Aligned_cols=73 Identities=12% Similarity=0.097 Sum_probs=55.3
Q ss_pred ccccEEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchh--HHHHHHhcCCCCeE
Q 030281 48 RGVHKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEIL--GSYAVKQLVKNSSV 125 (180)
Q Consensus 48 ~~mN~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~--Ae~~~~~l~KG~~V 125 (180)
..+++|.+.|.|=. -+.+.+.+|+.++.|.|.-- ++-+.|..|-+ . -+...+.+++|+-|
T Consensus 237 ~~~~~v~v~G~IF~-~e~~~~ksGr~l~~i~vTD~----------------t~Sl~~k~f~~-~~ed~~~~~~ik~g~wv 298 (1444)
T COG2176 237 EEETRVKVEGYIFK-IEIKELKSGRTLLNIKVTDY----------------TSSLILKKFLR-DEEDEKKFDGIKKGMWV 298 (1444)
T ss_pred ccccceEEEEEEEE-EeeeecccCcEEEEEEEecC----------------chheeehhhcc-ccccHHHHhhcccCcEE
Confidence 45678999999977 78889999999888865321 11356666665 2 23367899999999
Q ss_pred EEEEEeEEeeeec
Q 030281 126 YVEGDIEIRVYND 138 (180)
Q Consensus 126 ~VeGrL~~~~y~d 138 (180)
-+.|.++...+..
T Consensus 299 k~~g~v~~d~f~~ 311 (1444)
T COG2176 299 KARGNVQLDTFTR 311 (1444)
T ss_pred EEEEEEEeccccc
Confidence 9999999998765
No 104
>COG0587 DnaE DNA polymerase III, alpha subunit [DNA replication, recombination, and repair]
Probab=45.60 E-value=99 Score=32.15 Aligned_cols=68 Identities=12% Similarity=0.218 Sum_probs=50.9
Q ss_pred EEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEEEEEEe
Q 030281 52 KAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVYVEGDI 131 (180)
Q Consensus 52 ~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~VeGrL 131 (180)
..++.|-|..-...++.++|..++.+++.-. +| -+.|++|.. ..+.....+..+..++|.|++
T Consensus 978 ~~~~~~~i~~vr~~~tk~~G~~~~f~tl~D~-------~g---------~~e~v~f~~-~~~~~~~~l~~~~~~~v~g~v 1040 (1139)
T COG0587 978 RVVLAGGIVAVRQRPTKAKGNKMAFLTLEDE-------TG---------ILEVVVFPS-EYERYRRLLLEGRLLIVKGKV 1040 (1139)
T ss_pred eeEEEEEEEEEEEeeccCCCCEEEEEEEecC-------CC---------cEEEEEcHH-HHHHHHHHhccCcEEEEEEEE
Confidence 4778888887666555557887776655432 24 269999987 777788899999999999999
Q ss_pred EEeee
Q 030281 132 EIRVY 136 (180)
Q Consensus 132 ~~~~y 136 (180)
+.+..
T Consensus 1041 ~~~~~ 1045 (1139)
T COG0587 1041 QRRED 1045 (1139)
T ss_pred Eeccc
Confidence 98544
No 105
>PRK12820 bifunctional aspartyl-tRNA synthetase/aspartyl/glutamyl-tRNA amidotransferase subunit C; Provisional
Probab=45.54 E-value=3e+02 Score=27.16 Aligned_cols=60 Identities=13% Similarity=0.142 Sum_probs=37.5
Q ss_pred EEEEecCchh-HH--HHHHhcCCCCeEEEEEEeEEeeeecCCCCeEEEEEEEEEEeCCceEEecCC
Q 030281 102 HRIAVHNEIL-GS--YAVKQLVKNSSVYVEGDIEIRVYNDSINGEVKNIPEICIRRDGTLRLVKSG 164 (180)
Q Consensus 102 ~~V~~~gk~~-Ae--~~~~~l~KG~~V~VeGrL~~~~y~d~~dG~~~~~~eI~v~~~g~i~~l~~k 164 (180)
+.|++-.+.. .+ ..++.|+.|+.|.|+|.++.+.-.....+...-..||.+. +|.+|...
T Consensus 48 iQvV~~~~~~~~~~~~~~~~L~~EsvV~V~G~v~~r~~~~~n~~~~tg~iEl~~~---~i~iL~~a 110 (706)
T PRK12820 48 IQAVFSPEAAPADVYELAASLRAEFCVALQGEVQKRLEETENPHIETGDIEVFVR---ELSILAAS 110 (706)
T ss_pred EEEEEeCCcCCHHHHHHHhcCCCCCEEEEEeEEeccCccccCCCCCCCcEEEEee---EEEEEecC
Confidence 6776653311 11 2356899999999999998864222101111234788998 89888654
No 106
>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=43.91 E-value=1.6e+02 Score=23.11 Aligned_cols=77 Identities=12% Similarity=0.107 Sum_probs=54.1
Q ss_pred EEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHh----cCCCCeEEE
Q 030281 52 KAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQ----LVKNSSVYV 127 (180)
Q Consensus 52 ~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~----l~KG~~V~V 127 (180)
.+.=+|+|-+.=++. .++|.+++..+|+.=..-.| ...-.+|.|.+=|+ .|..+.+. +..+.+|+|
T Consensus 13 ht~GiGYLnriR~V~-~~kg~pFlac~I~AL~G~~d--------~~ey~~fD~~V~G~-eA~~Lv~r~~~av~~~~KVli 82 (137)
T PF12101_consen 13 HTTGIGYLNRIREVT-PRKGDPFLACTIAALRGPAD--------NPEYRYFDCRVVGE-EAKELVRRCQKAVDEDKKVLI 82 (137)
T ss_pred EEeeEEEeccceEcc-CCCCCeeEEEEeeeeecCCC--------CccEEEEEEEEecH-HHHHHHHHHHhhcccCCcEEE
Confidence 356788888865553 56899999999987642111 13567899999999 88876555 455888887
Q ss_pred E---EEeEEeeeec
Q 030281 128 E---GDIEIRVYND 138 (180)
Q Consensus 128 e---GrL~~~~y~d 138 (180)
. |.|....|+-
T Consensus 83 ~FrlgDl~~d~f~~ 96 (137)
T PF12101_consen 83 GFRLGDLWADTFTY 96 (137)
T ss_pred EEEecCCceeeEEe
Confidence 6 5667777773
No 107
>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=43.09 E-value=1.2e+02 Score=21.68 Aligned_cols=36 Identities=22% Similarity=0.240 Sum_probs=27.4
Q ss_pred HhcCCCCeEEEEEEeEEeeeecCCCCeEEEEEEEEEEeCCceEEecCC
Q 030281 117 KQLVKNSSVYVEGDIEIRVYNDSINGEVKNIPEICIRRDGTLRLVKSG 164 (180)
Q Consensus 117 ~~l~KG~~V~VeGrL~~~~y~d~~dG~~~~~~eI~v~~~g~i~~l~~k 164 (180)
+.|..|+.|.|+|.+... + .|. .||.+. .+++|...
T Consensus 48 ~~l~~g~~V~v~G~v~~~----~-~g~----~El~~~---~~~ils~~ 83 (108)
T cd04322 48 KLLDLGDIIGVTGTPFKT----K-TGE----LSIFVK---EFTLLSKS 83 (108)
T ss_pred hcCCCCCEEEEEEEEEec----C-CCC----EEEEeC---EeEEeecc
Confidence 349999999999998754 2 233 688888 88888754
No 108
>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=42.87 E-value=39 Score=25.86 Aligned_cols=27 Identities=19% Similarity=-0.033 Sum_probs=22.7
Q ss_pred eEEEEEecCchhHHHHHHhcCCCCeEEEE
Q 030281 100 QWHRIAVHNEILGSYAVKQLVKNSSVYVE 128 (180)
Q Consensus 100 ~w~~V~~~gk~~Ae~~~~~l~KG~~V~Ve 128 (180)
--+.|.+|.+ -|+++.+ |+.||-|.+.
T Consensus 60 ~ti~It~yD~-H~~~ar~-lK~GdfV~L~ 86 (123)
T cd04498 60 LTIDILVYDN-HVELAKS-LKPGDFVRIY 86 (123)
T ss_pred EEEEEEEEcc-hHHHHhh-CCCCCEEEEE
Confidence 3488999999 8887666 9999999876
No 109
>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=41.87 E-value=65 Score=22.23 Aligned_cols=33 Identities=18% Similarity=0.133 Sum_probs=24.5
Q ss_pred ceEEEEEec--CchhHHHHHHhcCCCCeEEEEEEeEE
Q 030281 99 VQWHRIAVH--NEILGSYAVKQLVKNSSVYVEGDIEI 133 (180)
Q Consensus 99 t~w~~V~~~--gk~~Ae~~~~~l~KG~~V~VeGrL~~ 133 (180)
.--+.|... |. ...++ ..|+.||.|.|.|-+-.
T Consensus 62 ~~~~~ik~~~~G~-~S~~L-~~l~~Gd~v~i~gP~G~ 96 (99)
T PF00970_consen 62 YLEFAIKRYPNGR-VSRYL-HQLKPGDEVEIRGPYGN 96 (99)
T ss_dssp EEEEEEEECTTSH-HHHHH-HTSCTTSEEEEEEEESS
T ss_pred cEEEEEEeccCCH-HHHHH-HhCCCCCEEEEEEcccc
Confidence 345677777 65 66777 56999999999996643
No 110
>PLN02850 aspartate-tRNA ligase
Probab=41.34 E-value=3.2e+02 Score=25.90 Aligned_cols=43 Identities=30% Similarity=0.405 Sum_probs=31.0
Q ss_pred HHhcCCCCeEEEEEEeEEeeeecCCCCeEEEEEEEEEEeCCceEEecCC
Q 030281 116 VKQLVKNSSVYVEGDIEIRVYNDSINGEVKNIPEICIRRDGTLRLVKSG 164 (180)
Q Consensus 116 ~~~l~KG~~V~VeGrL~~~~y~d~~dG~~~~~~eI~v~~~g~i~~l~~k 164 (180)
+..|.+|+.|.|+|.+....- +..+... ..||.+. +|.+|...
T Consensus 130 ~~~l~~es~V~V~G~v~~~~~--~~~~~t~-~~El~~~---~i~vls~a 172 (530)
T PLN02850 130 AKQLSRESVVDVEGVVSVPKK--PVKGTTQ-QVEIQVR---KIYCVSKA 172 (530)
T ss_pred HhCCCCCCEEEEEEEEEccCc--CCCCCCc-cEEEEEe---EEEEEeCC
Confidence 467999999999999985321 1123322 7889998 89888755
No 111
>PF04076 BOF: Bacterial OB fold (BOF) protein; InterPro: IPR005220 Proteins in this entry have an OB-fold fold (oligonucleotide/oligosaccharide binding motif). Analysis of the predicted nucleotide-binding site of the OB-fold suggests that they lack nucleic acid-binding properties. They contain an predicted N-terminal signal peptide which indicates that they localise to the periplasm where they may function to bind proteins, small molecules, or other typical OB-fold ligands. As hypothesised for the distantly related OB-fold containing bacterial enterotoxins, the loss of nucleotide-binding function and the rapid evolution of the OB-fold ligand-binding site may be associated with the presence of members in mobile genetic elements and their potential role in bacterial pathogenicity [].; PDB: 1NNX_A.
Probab=40.76 E-value=1.5e+02 Score=21.89 Aligned_cols=58 Identities=12% Similarity=0.371 Sum_probs=33.4
Q ss_pred cccccEEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEE
Q 030281 47 FRGVHKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVY 126 (180)
Q Consensus 47 m~~mN~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~ 126 (180)
|..=..|+|.|+|.+- . .+..| .|+|. +|+ +.|.+=.+ . .--..+..+++|.
T Consensus 31 ~~Dd~~V~L~G~Iv~~-----l-~~d~Y---------~F~D~-TG~---------I~VeId~~-~--w~g~~vt~~~~Vr 82 (103)
T PF04076_consen 31 AKDDTPVTLEGNIVKQ-----L-GDDKY---------LFRDA-TGE---------IEVEIDDD-V--WRGQTVTPDDKVR 82 (103)
T ss_dssp S-SSEEEEEEEEEEEE-----E-ETTEE---------EEEET-TEE---------EEEE--GG-G--STT----TTSEEE
T ss_pred CcCCCeEEEEEEEEEE-----e-cCCEE---------EEECC-CCc---------EEEEEChh-h--cCCcccCCCCEEE
Confidence 4556789999999872 2 13333 26666 464 56664333 1 1124678999999
Q ss_pred EEEEeE
Q 030281 127 VEGDIE 132 (180)
Q Consensus 127 VeGrL~ 132 (180)
|.|++.
T Consensus 83 i~GeVD 88 (103)
T PF04076_consen 83 ISGEVD 88 (103)
T ss_dssp EEEEEE
T ss_pred EEEEEe
Confidence 999998
No 112
>PLN02532 asparagine-tRNA synthetase
Probab=37.82 E-value=1.1e+02 Score=29.65 Aligned_cols=54 Identities=11% Similarity=0.220 Sum_probs=38.4
Q ss_pred EEEEEecCchhHHHHHHhcCCCCeEEEEEEeEEeeeecCCCCeEEEEEEEEEEeCCceEEecCC
Q 030281 101 WHRIAVHNEILGSYAVKQLVKNSSVYVEGDIEIRVYNDSINGEVKNIPEICIRRDGTLRLVKSG 164 (180)
Q Consensus 101 w~~V~~~gk~~Ae~~~~~l~KG~~V~VeGrL~~~~y~d~~dG~~~~~~eI~v~~~g~i~~l~~k 164 (180)
.+.|++-.. .+.. .+.|+.|+.|.|+|.++.+.- .+ .....||.|+ .|.+|...
T Consensus 148 ~lQvVv~~~-~~~~-~~~L~~Es~V~V~G~V~~~~~----~~-~~g~iEl~v~---~i~VLg~a 201 (633)
T PLN02532 148 SLQVVVDSA-LAPL-TQLMATGTCILAEGVLKLPLP----AQ-GKHVIELEVE---KILHIGTV 201 (633)
T ss_pred ceEEEEeCC-cccH-hhcCCCceEEEEEEEEEecCC----CC-CCCcEEEEee---EEEEEecC
Confidence 378888765 4433 378999999999999987621 11 1235888898 89888853
No 113
>PTZ00111 DNA replication licensing factor MCM4; Provisional
Probab=36.51 E-value=1.3e+02 Score=30.58 Aligned_cols=57 Identities=9% Similarity=0.107 Sum_probs=38.5
Q ss_pred eEEEEEecCchhHHHHHHhcCCCCeEEEEEEeEEeeeecCC---CCeEEEEEEEEEEeCCceEEecCC
Q 030281 100 QWHRIAVHNEILGSYAVKQLVKNSSVYVEGDIEIRVYNDSI---NGEVKNIPEICIRRDGTLRLVKSG 164 (180)
Q Consensus 100 ~w~~V~~~gk~~Ae~~~~~l~KG~~V~VeGrL~~~~y~d~~---dG~~~~~~eI~v~~~g~i~~l~~k 164 (180)
.-+.|.+.+. ++..++.||+|.|.|-++...-.... .....+.+.|.|. .|+.+.+.
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 6688888887 45689999999999999876422100 1223456667666 67776543
No 114
>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=35.78 E-value=23 Score=26.97 Aligned_cols=22 Identities=18% Similarity=0.320 Sum_probs=19.0
Q ss_pred hHHHHHHhcCCCCeEEEEEEeE
Q 030281 111 LGSYAVKQLVKNSSVYVEGDIE 132 (180)
Q Consensus 111 ~Ae~~~~~l~KG~~V~VeGrL~ 132 (180)
+|+.+++.|++|+.|++.|.|-
T Consensus 4 la~~l~~~l~~g~vi~L~GdLG 25 (123)
T PF02367_consen 4 LAKKLAQILKPGDVILLSGDLG 25 (123)
T ss_dssp HHHHHHHHHSS-EEEEEEESTT
T ss_pred HHHHHHHhCCCCCEEEEECCCC
Confidence 7889999999999999999873
No 115
>COG0802 Predicted ATPase or kinase [General function prediction only]
Probab=33.64 E-value=38 Score=26.86 Aligned_cols=23 Identities=26% Similarity=0.416 Sum_probs=20.3
Q ss_pred hHHHHHHhcCCCCeEEEEEEeEE
Q 030281 111 LGSYAVKQLVKNSSVYVEGDIEI 133 (180)
Q Consensus 111 ~Ae~~~~~l~KG~~V~VeGrL~~ 133 (180)
+|+.+++.|++|+.|+++|.|-.
T Consensus 14 lg~~l~~~l~~g~Vv~L~GdLGA 36 (149)
T COG0802 14 LGERLAEALKAGDVVLLSGDLGA 36 (149)
T ss_pred HHHHHHhhCCCCCEEEEEcCCcC
Confidence 67888999999999999999853
No 116
>PRK10646 ADP-binding protein; Provisional
Probab=32.67 E-value=37 Score=26.86 Aligned_cols=22 Identities=27% Similarity=0.472 Sum_probs=19.9
Q ss_pred hHHHHHHhcCCCCeEEEEEEeE
Q 030281 111 LGSYAVKQLVKNSSVYVEGDIE 132 (180)
Q Consensus 111 ~Ae~~~~~l~KG~~V~VeGrL~ 132 (180)
+|+.+++.|+.|+.|++.|.|-
T Consensus 17 l~~~la~~l~~g~vi~L~GdLG 38 (153)
T PRK10646 17 LGARVAKACDGATVIYLYGDLG 38 (153)
T ss_pred HHHHHHHhCCCCcEEEEECCCC
Confidence 6888999999999999999874
No 117
>PRK03065 hutP anti-terminator HutP; Provisional
Probab=32.58 E-value=65 Score=25.54 Aligned_cols=29 Identities=21% Similarity=0.384 Sum_probs=22.3
Q ss_pred EEEEEEEEECCceeccCCCcccCCCCceEEEEEecCc
Q 030281 73 TVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNE 109 (180)
Q Consensus 73 ~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk 109 (180)
.-++|.|..+..|.+. ...+|+.|.+||+
T Consensus 100 vglk~aIVrg~~~~~~--------~dg~WIaVa~yG~ 128 (148)
T PRK03065 100 VGLRFAIVRGTPYDGK--------KEGEWIAVALYGT 128 (148)
T ss_pred cceEEEEEecCCCCCC--------CCCcEEEEEEecc
Confidence 4578888888777544 3566999999998
No 118
>PRK07135 dnaE DNA polymerase III DnaE; Validated
Probab=30.83 E-value=2.4e+02 Score=28.94 Aligned_cols=64 Identities=11% Similarity=-0.079 Sum_probs=42.5
Q ss_pred EEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEEEEEEe
Q 030281 52 KAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVYVEGDI 131 (180)
Q Consensus 52 ~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~VeGrL 131 (180)
.+.+.|-|..--..+ .+|...+.+++.-. +|+ +.|++|.+ .-+.+.. +.+|+.++|+|+.
T Consensus 899 ~~~v~g~i~~~~~~~--K~g~~maf~~~eD~-------~~~---------~e~~~F~~-~~~~~~~-l~~~~~~~~~~~~ 958 (973)
T PRK07135 899 EYRLAIEVKNVKRLR--KANKEYKKVILSDD-------SVE---------ITIFVNDN-DYLLFET-LKKGDIYEFLISK 958 (973)
T ss_pred eEEEEEEEEEEEEEe--eCCCeEEEEEEEEC-------CCc---------EEEEEcHH-HHHHHHH-hhcCCEEEEEEEE
Confidence 356777666644433 66776665544322 243 79999998 5555554 9999999999987
Q ss_pred EEee
Q 030281 132 EIRV 135 (180)
Q Consensus 132 ~~~~ 135 (180)
+.+.
T Consensus 959 ~~~~ 962 (973)
T PRK07135 959 SKNN 962 (973)
T ss_pred cCCC
Confidence 7654
No 119
>PLN02603 asparaginyl-tRNA synthetase
Probab=30.44 E-value=4.9e+02 Score=24.92 Aligned_cols=53 Identities=17% Similarity=0.318 Sum_probs=35.2
Q ss_pred EEEEecCchhHHH-HHH--hcCCCCeEEEEEEeEEeeeecCCCCeEEEEEEEEEEeCCceEEecCCC
Q 030281 102 HRIAVHNEILGSY-AVK--QLVKNSSVYVEGDIEIRVYNDSINGEVKNIPEICIRRDGTLRLVKSGE 165 (180)
Q Consensus 102 ~~V~~~gk~~Ae~-~~~--~l~KG~~V~VeGrL~~~~y~d~~dG~~~~~~eI~v~~~g~i~~l~~k~ 165 (180)
+.|++-.. ...+ ... .|..|+.|.|+|.+.... .+. ...||.|+ +|++|..-.
T Consensus 139 lQ~v~~~~-~~~~~~l~~~~l~~gs~V~V~G~v~~~~-----~~~--~~~EL~v~---~i~vlg~a~ 194 (565)
T PLN02603 139 MQCVMTPD-AEGYDQVESGLITTGASVLVQGTVVSSQ-----GGK--QKVELKVS---KIVVVGKSD 194 (565)
T ss_pred EEEEEECc-HHHHHHHhhcCCCCCCEEEEEEEEEecC-----CCC--ccEEEEEe---EEEEEECCC
Confidence 67766433 2221 122 488999999999998542 232 36899999 899987654
No 120
>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=30.40 E-value=59 Score=23.21 Aligned_cols=20 Identities=25% Similarity=0.223 Sum_probs=17.0
Q ss_pred HHHhcCCCCeEEEEEEeEEe
Q 030281 115 AVKQLVKNSSVYVEGDIEIR 134 (180)
Q Consensus 115 ~~~~l~KG~~V~VeGrL~~~ 134 (180)
....+..|+-|.|.|+|++.
T Consensus 59 ~~~~i~~G~vvrV~G~i~~f 78 (92)
T cd04483 59 QAKVLEIGDLLRVRGSIRTY 78 (92)
T ss_pred cccccCCCCEEEEEEEEecc
Confidence 45569999999999999875
No 121
>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=29.47 E-value=43 Score=26.21 Aligned_cols=23 Identities=30% Similarity=0.367 Sum_probs=20.3
Q ss_pred ecCchhHHHHHHhcCCCCeEEEEE
Q 030281 106 VHNEILGSYAVKQLVKNSSVYVEG 129 (180)
Q Consensus 106 ~~gk~~Ae~~~~~l~KG~~V~VeG 129 (180)
+.|+ +|..+++.|..||.|.|.-
T Consensus 9 vlGR-LAs~IA~~L~~Gd~VvViN 31 (142)
T TIGR01077 9 ILGR-LASVVAKQLLNGEKVVVVN 31 (142)
T ss_pred chHH-HHHHHHHHHhcCCEEEEEe
Confidence 5677 9999999999999999865
No 122
>COG3651 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.00 E-value=31 Score=26.03 Aligned_cols=23 Identities=17% Similarity=0.452 Sum_probs=20.3
Q ss_pred chhhccccccCCCCCCCCCCccc
Q 030281 25 DDFVVEKQELQPQGVDPRRGWGF 47 (180)
Q Consensus 25 ~~~~~~~~~~~~~~~~~~~~~~m 47 (180)
||++..+|+++..|+.|--+|-.
T Consensus 62 NDLSt~rP~~~fpglkpgdrwcl 84 (125)
T COG3651 62 NDLSTPRPPYWFPGLKPGDRWCL 84 (125)
T ss_pred CCCCCCCCcccCCCCCCCCeeee
Confidence 78999999999999999988853
No 123
>COG3649 CRISPR system related protein [Defense mechanisms]
Probab=27.78 E-value=53 Score=28.02 Aligned_cols=50 Identities=18% Similarity=0.141 Sum_probs=35.7
Q ss_pred CceEEEEEecCchhHHHHHHhcCCCCeEEEEEEeEEeeeecCCCCeEEEEEEEEEE
Q 030281 98 PVQWHRIAVHNEILGSYAVKQLVKNSSVYVEGDIEIRVYNDSINGEVKNIPEICIR 153 (180)
Q Consensus 98 ~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~VeGrL~~~~y~d~~dG~~~~~~eI~v~ 153 (180)
-..|+.|.+||. +..+.+||..+.|.|-..-+.-+-= +-.+...++|.+.
T Consensus 98 cq~w~DvR~FGq-----Vf~~~kk~ms~gvrGPVsi~~atSl-~pi~i~s~QiT~s 147 (283)
T COG3649 98 CQKWIDVRLFGQ-----VFPQSKKGMSSGVRGPVSIRYATSL-HPIKIMSIQITAS 147 (283)
T ss_pred HHHHhhHHHhhh-----hhhhhccCcccccccceEEEeeccc-cceEEEEEEEeee
Confidence 357999999997 5668999999999998776655432 4444455555543
No 124
>PRK06394 rpl13p 50S ribosomal protein L13P; Reviewed
Probab=27.49 E-value=48 Score=26.09 Aligned_cols=25 Identities=24% Similarity=0.403 Sum_probs=21.2
Q ss_pred ecCchhHHHHHHhcCCCCeEEEEEEe
Q 030281 106 VHNEILGSYAVKQLVKNSSVYVEGDI 131 (180)
Q Consensus 106 ~~gk~~Ae~~~~~l~KG~~V~VeGrL 131 (180)
+.|+ +|..++..|.-||.|+|.---
T Consensus 13 vlGR-LAs~IA~~L~~Gd~VVViNa~ 37 (146)
T PRK06394 13 ILGR-LASYVAKRLLEGEEVVIVNAE 37 (146)
T ss_pred chHH-HHHHHHHHHhCCCEEEEEech
Confidence 5677 999999999999999987543
No 125
>PTZ00401 aspartyl-tRNA synthetase; Provisional
Probab=24.67 E-value=3.1e+02 Score=26.09 Aligned_cols=45 Identities=16% Similarity=0.082 Sum_probs=32.3
Q ss_pred HHhcCCCCeEEEEEEeEEeeeecCCCCeEEEEEEEEEEeCCceEEecCCC
Q 030281 116 VKQLVKNSSVYVEGDIEIRVYNDSINGEVKNIPEICIRRDGTLRLVKSGE 165 (180)
Q Consensus 116 ~~~l~KG~~V~VeGrL~~~~y~d~~dG~~~~~~eI~v~~~g~i~~l~~k~ 165 (180)
...|.+|+.|.|+|.+....-.- ........||.+. +|.+|..-.
T Consensus 126 ~~~l~~esiV~V~G~v~~~~~~~--~~~~~~~~El~v~---~i~vls~a~ 170 (550)
T PTZ00401 126 IGQIPTESIVDVEATVCKVEQPI--TSTSHSDIELKVK---KIHTVTESL 170 (550)
T ss_pred HhcCCCCCEEEEEEEEEecCccC--CCCCCccEEEEee---EEEEEeCCC
Confidence 45699999999999998753221 2333446889998 888887553
No 126
>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=24.47 E-value=95 Score=23.15 Aligned_cols=35 Identities=17% Similarity=0.024 Sum_probs=17.0
Q ss_pred EEEEEecCchhHHHHHHhcCCCCeEEEEEEeEEee
Q 030281 101 WHRIAVHNEILGSYAVKQLVKNSSVYVEGDIEIRV 135 (180)
Q Consensus 101 w~~V~~~gk~~Ae~~~~~l~KG~~V~VeGrL~~~~ 135 (180)
.+.|..-...........|+||+.|.|.|...-..
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 45665555511222355799999999999987553
No 127
>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=24.46 E-value=70 Score=24.58 Aligned_cols=22 Identities=27% Similarity=0.391 Sum_probs=19.6
Q ss_pred hHHHHHHhcCCCCeEEEEEEeE
Q 030281 111 LGSYAVKQLVKNSSVYVEGDIE 132 (180)
Q Consensus 111 ~Ae~~~~~l~KG~~V~VeGrL~ 132 (180)
+|+.+++.|++|+.|.+.|.+-
T Consensus 11 l~~~l~~~l~~~~~i~l~G~lG 32 (133)
T TIGR00150 11 FGKAFAKPLDFGTVVLLKGDLG 32 (133)
T ss_pred HHHHHHHhCCCCCEEEEEcCCC
Confidence 6888999999999999999874
No 128
>COG1838 FumA Tartrate dehydratase beta subunit/Fumarate hydratase class I, C-terminal domain [Energy production and conversion]
Probab=24.41 E-value=78 Score=26.00 Aligned_cols=21 Identities=24% Similarity=0.363 Sum_probs=18.3
Q ss_pred HHHHhcCCCCeEEEEEEeEEe
Q 030281 114 YAVKQLVKNSSVYVEGDIEIR 134 (180)
Q Consensus 114 ~~~~~l~KG~~V~VeGrL~~~ 134 (180)
...+.|+.||.|++.|.|-+-
T Consensus 11 e~i~~LkvGd~v~lsG~I~t~ 31 (184)
T COG1838 11 EEIAKLKVGDVVYLSGKIVTG 31 (184)
T ss_pred HHHHhccCCCEEEEeeEEEEe
Confidence 456789999999999999886
No 129
>COG1908 FrhD Coenzyme F420-reducing hydrogenase, delta subunit [Energy production and conversion]
Probab=23.79 E-value=1.2e+02 Score=23.48 Aligned_cols=43 Identities=26% Similarity=0.351 Sum_probs=34.7
Q ss_pred CCCCceEEEEEecCchhHHHHHHhcCCC-CeEEEEE-EeEEeeee
Q 030281 95 LPKPVQWHRIAVHNEILGSYAVKQLVKN-SSVYVEG-DIEIRVYN 137 (180)
Q Consensus 95 ~~~~t~w~~V~~~gk~~Ae~~~~~l~KG-~~V~VeG-rL~~~~y~ 137 (180)
|+...--++|-+-|+-.++++.+.|++| |-|+|.| ++---.|.
T Consensus 26 yp~~vRiIrv~CsGrvn~~fvl~Al~~GaDGV~v~GC~~geCHy~ 70 (132)
T COG1908 26 YPPNVRIIRVMCSGRVNPEFVLKALRKGADGVLVAGCKIGECHYI 70 (132)
T ss_pred CCCceEEEEeeccCccCHHHHHHHHHcCCCeEEEecccccceeee
Confidence 3556667899999997799999999998 7899988 66666665
No 130
>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=23.61 E-value=6.1e+02 Score=24.39 Aligned_cols=68 Identities=10% Similarity=0.149 Sum_probs=40.7
Q ss_pred EEEEEEEeCCCCeEEE---ecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEEEE
Q 030281 52 KAIICGKVKDTPVQKI---LRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVYVE 128 (180)
Q Consensus 52 ~v~L~Grlg~dPe~r~---t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~Ve 128 (180)
-|-++|-|..--.+.. -.+|+...+-.|..- |. +|. -++|++||+ .|..+. ..+|..|.+.
T Consensus 312 ~VDVIGvV~~v~~~~~i~~k~~g~~~~kR~i~L~----D~-sg~--------sI~vTLWG~-~A~~~~--~~~~~Vva~k 375 (608)
T TIGR00617 312 LVDVIGIVQSVSPTQTITSRKNNKEFPKRDITLV----DD-SGK--------SVRVTLWGD-DATKFD--VSVQPVIAIK 375 (608)
T ss_pred CccEEEEEeEecCceEEEEcCCCCeeeeEEEEEE----eC-CCC--------EEEEEEEhh-hhhhcC--CCCCCEEEEE
Confidence 4567777776533322 235555443333332 22 232 389999999 887654 6788888887
Q ss_pred EEeEEeee
Q 030281 129 GDIEIRVY 136 (180)
Q Consensus 129 GrL~~~~y 136 (180)
| ++...|
T Consensus 376 g-~~V~~f 382 (608)
T TIGR00617 376 G-VRVSDF 382 (608)
T ss_pred e-EEEEec
Confidence 7 555566
No 131
>PRK10053 hypothetical protein; Provisional
Probab=23.55 E-value=2.5e+02 Score=21.63 Aligned_cols=60 Identities=8% Similarity=0.292 Sum_probs=38.9
Q ss_pred cccccEEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEE
Q 030281 47 FRGVHKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVY 126 (180)
Q Consensus 47 m~~mN~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~ 126 (180)
|..=..|+|.|+|.+-. .+..| .|+|. +|+ |.|.+=.+ ...-+.+...++|.
T Consensus 58 ~~Dd~~V~L~G~Iv~~l------g~d~Y---------~F~D~-tG~---------I~VeID~~---~w~G~~v~p~~kV~ 109 (130)
T PRK10053 58 MHDGATVSLRGNLIDHK------GDDRY---------VFRDK-SGE---------INVIIPAA---VFDGREVQPDQMIN 109 (130)
T ss_pred CcCCCeEEEEEEEEEEe------CCceE---------EEECC-CCc---------EEEEeCHH---HcCCCcCCCCCEEE
Confidence 55566799999987732 22333 26666 465 56665333 12234789999999
Q ss_pred EEEEeEEe
Q 030281 127 VEGDIEIR 134 (180)
Q Consensus 127 VeGrL~~~ 134 (180)
|.|++...
T Consensus 110 I~GevDk~ 117 (130)
T PRK10053 110 INGSLDKK 117 (130)
T ss_pred EEEEECCC
Confidence 99998743
No 132
>PF06557 DUF1122: Protein of unknown function (DUF1122); InterPro: IPR008304 There are currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.; PDB: 2ARH_C.
Probab=22.75 E-value=3e+02 Score=22.33 Aligned_cols=47 Identities=17% Similarity=0.190 Sum_probs=24.1
Q ss_pred cCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEe---------cCchhHH-----HHHHhcCCCCeEEEE
Q 030281 69 RNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAV---------HNEILGS-----YAVKQLVKNSSVYVE 128 (180)
Q Consensus 69 ~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~---------~gk~~Ae-----~~~~~l~KG~~V~Ve 128 (180)
-+++.++...|-..+.| .+-|+.+.= |+. .++ .++.+|.+|++++|+
T Consensus 25 ~~~~~l~~~kvF~GR~y------------Y~pW~EiFni~p~~~~~~~~s-~~E~~l~~~~~~~l~pg~~lfVe 85 (170)
T PF06557_consen 25 LGGRHLCHVKVFFGRPY------------YRPWAEIFNINPWLRVVFFGS-PLEDELYKLFSRYLEPGGRLFVE 85 (170)
T ss_dssp ETTEEEEEEEEE--BTT------------B--EEEEE---GGGHHHHTTS-HHHHHHHHHHHTT----SEEEEE
T ss_pred ECCeeEEEEEEecCCCC------------CcchheeecccchhcccccCC-hHHHHHHHHHHHHhhhcCeEEEE
Confidence 47777777776666543 444766622 243 232 357899999999997
No 133
>TIGR00156 conserved hypothetical protein TIGR00156. As of the last revision, this family consists only of two proteins from Escherichia coli and one from the related species Haemophilus influenzae.
Probab=21.72 E-value=3.4e+02 Score=20.82 Aligned_cols=61 Identities=8% Similarity=0.250 Sum_probs=38.3
Q ss_pred cccccEEEEEEEeCCCCeEEEecCCeEEEEEEEEECCceeccCCCcccCCCCceEEEEEecCchhHHHHHHhcCCCCeEE
Q 030281 47 FRGVHKAIICGKVKDTPVQKILRNGKTVTIFSVGTGGLFDQRIVGSKDLPKPVQWHRIAVHNEILGSYAVKQLVKNSSVY 126 (180)
Q Consensus 47 m~~mN~v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~~~~~d~~~Ge~~~~~~t~w~~V~~~gk~~Ae~~~~~l~KG~~V~ 126 (180)
|+.=..|+|.|+|.+-. .+..| .|+|. +|+ |.|.+=.+ ..--..+..+++|.
T Consensus 54 ~~Ddt~V~L~G~Iv~~l------~~d~Y---------~F~D~-TG~---------I~VeId~~---~w~G~~v~p~d~V~ 105 (126)
T TIGR00156 54 MHDGASVTLRGNIISHI------GDDRY---------VFRDK-SGE---------INVVIPAA---VWNGREVQPKDMVN 105 (126)
T ss_pred CCCCCEEEEEEEEEEEe------CCceE---------EEECC-CCC---------EEEEECHH---HcCCCcCCCCCEEE
Confidence 44556799999997732 12333 26666 464 56665322 11234688999999
Q ss_pred EEEEeEEeee
Q 030281 127 VEGDIEIRVY 136 (180)
Q Consensus 127 VeGrL~~~~y 136 (180)
|.|++. ..|
T Consensus 106 I~GeVD-k~~ 114 (126)
T TIGR00156 106 ISGSLD-KKS 114 (126)
T ss_pred EEEEEC-CCC
Confidence 999997 334
No 134
>PF05309 TraE: TraE protein; InterPro: IPR007973 This family consists of several bacterial sex pilus assembly and synthesis proteins (TraE). Conjugal transfer of plasmids from donor to recipient cells is a complex process in which a cell-to-cell contact plays a key role. Many genes encoded by self-transmissible plasmids are required for various processes of conjugation, including pilus formation, stabilisation of mating pairs, conjugative DNA metabolism, surface exclusion and regulation of transfer gene expression []. The exact function of the TraE protein is unknown.; GO: 0000746 conjugation
Probab=21.19 E-value=4.1e+02 Score=21.10 Aligned_cols=44 Identities=18% Similarity=0.302 Sum_probs=29.0
Q ss_pred CCCeEEEEEEeEEeeeecCCCCeEEEEEEEEEE-eCCceEEecCCC
Q 030281 121 KNSSVYVEGDIEIRVYNDSINGEVKNIPEICIR-RDGTLRLVKSGE 165 (180)
Q Consensus 121 KG~~V~VeGrL~~~~y~d~~dG~~~~~~eI~v~-~~g~i~~l~~k~ 165 (180)
....|.|.|.+++..-... --.....++|... ++|.+.+..-++
T Consensus 138 ~~~~V~V~G~l~t~~g~~~-~~~~~~~y~~~~~~~~g~~~L~~f~e 182 (187)
T PF05309_consen 138 ETLTVFVTGTLKTWIGDKK-VSSEDKTYRLQFKYRNGRLWLKSFKE 182 (187)
T ss_pred CCCEEEEEEEEEEEECCcc-ccceeEEEEEEEEEeCCEEEEeeeEe
Confidence 4789999999987665443 2333455566655 478888766544
No 135
>PLN02221 asparaginyl-tRNA synthetase
Probab=21.14 E-value=4.6e+02 Score=25.21 Aligned_cols=55 Identities=15% Similarity=0.134 Sum_probs=37.7
Q ss_pred EEEEEecCchhHHHHHHhcCCCCeEEEEEEeEEeeeecCCCCeEEEEEEEEEEeCCceEEecCC
Q 030281 101 WHRIAVHNEILGSYAVKQLVKNSSVYVEGDIEIRVYNDSINGEVKNIPEICIRRDGTLRLVKSG 164 (180)
Q Consensus 101 w~~V~~~gk~~Ae~~~~~l~KG~~V~VeGrL~~~~y~d~~dG~~~~~~eI~v~~~g~i~~l~~k 164 (180)
.++|++-.. .. ...+.|+.|+.|.|+|.+..+.-. .+.. ...||.++ +|.+|...
T Consensus 83 ~iQvVv~~~-~~-~~~~~L~~ES~V~V~G~V~~~~~~---~~~~-~~iEl~v~---~i~vl~~a 137 (572)
T PLN02221 83 NLQVMVDSS-LY-DLSTLVATGTCVTVDGVLKVPPEG---KGTK-QKIELSVE---KVIDVGTV 137 (572)
T ss_pred cEEEEEcCc-hh-hHHhcCCCceEEEEEEEEEeCCcc---CCCC-ccEEEEEe---EEEEEecC
Confidence 378877543 22 233468999999999999865431 1221 27899999 89998754
No 136
>PF06523 DUF1106: Protein of unknown function (DUF1106); InterPro: IPR009490 This family consists of several hypothetical bacterial proteins found in Escherichia coli and Citrobacter rodentium. The function of this family is unknown.
Probab=21.10 E-value=1.4e+02 Score=21.04 Aligned_cols=30 Identities=23% Similarity=0.411 Sum_probs=20.4
Q ss_pred EEEEEEeCCCCeEEEecCCeEEEEEEEEEC
Q 030281 53 AIICGKVKDTPVQKILRNGKTVTIFSVGTG 82 (180)
Q Consensus 53 v~L~Grlg~dPe~r~t~nG~~v~~fsVa~~ 82 (180)
-+|||+|-.-...-.-+||.-+++.+|..+
T Consensus 27 siicgrlrgiv~t~kcs~g~iylsi~v~pn 56 (91)
T PF06523_consen 27 SIICGRLRGIVLTIKCSNGIIYLSIKVNPN 56 (91)
T ss_pred EEEeeceeeEEEEEEecCcEEEEEEEeCCC
Confidence 368999977544444578888877666544
No 137
>PRK08395 fumarate hydratase; Provisional
Probab=20.57 E-value=1.4e+02 Score=24.00 Aligned_cols=21 Identities=29% Similarity=0.283 Sum_probs=17.8
Q ss_pred HHHHhcCCCCeEEEEEEeEEe
Q 030281 114 YAVKQLVKNSSVYVEGDIEIR 134 (180)
Q Consensus 114 ~~~~~l~KG~~V~VeGrL~~~ 134 (180)
...+.|+.||.|++.|.|-+-
T Consensus 10 e~i~~L~~GD~V~LsG~i~ta 30 (162)
T PRK08395 10 EDVLKLKAGDVVYLSGIIYTA 30 (162)
T ss_pred HHHhhCCCCCEEEEEEEEEEE
Confidence 346799999999999998764
No 138
>PF05683 Fumerase_C: Fumarase C-terminus; InterPro: IPR004647 This entry represents various Fe-S type hydro-lyases, including the beta subunit from both L-tartrate dehydratase (TtdB; EC:4.2.1.32) and class 2 fumarate hydratase (FumC; (4.2.1.2 from EC) []. A number of Fe-S cluster-containing hydro-lyases share a conserved motif, including argininosuccinate lyase, adenylosuccinate lyase, aspartase, class I fumarate hydratase (fumarase), and tartrate dehydratase (see IPR000362 from INTERPRO). Proteins in this group represent a subset of closely related proteins or modules, including the Escherichia coli tartrate dehydratase beta chain and the C-terminal region of the class I fumarase (where the N-terminal region is homologous to the tartrate dehydratase alpha chain). The activity of the archaeal proteins in this group is unknown.; GO: 0016836 hydro-lyase activity; PDB: 2ISB_A.
Probab=20.47 E-value=1.9e+02 Score=24.11 Aligned_cols=31 Identities=23% Similarity=0.390 Sum_probs=18.8
Q ss_pred EEEecCchhHHHHHHhcCCCCeEEEEEEeEEe
Q 030281 103 RIAVHNEILGSYAVKQLVKNSSVYVEGDIEIR 134 (180)
Q Consensus 103 ~V~~~gk~~Ae~~~~~l~KG~~V~VeGrL~~~ 134 (180)
++.+--. +.+...+.|+.||.|++.|.|-+-
T Consensus 28 ~~~L~tP-lt~e~i~~L~vGD~V~LsG~i~ta 58 (205)
T PF05683_consen 28 EIELTTP-LTEEDIRKLKVGDTVYLSGTIYTA 58 (205)
T ss_dssp EEEEESS---HHHHHH--TT-EEEEEEEEEE-
T ss_pred EEEcCCC-CCHHHHhhCCCCCEEEEeeEEEEE
Confidence 4444444 555667899999999999998763
No 139
>TIGR00723 ttdB_fumA_fumB hydro-lyases, Fe-S type, tartrate/fumarate subfamily, beta region. A number of Fe-S cluster-containing hydro-lyases share a conserved motif, including argininosuccinate lyase, adenylosuccinate lyase, aspartase, class I fumarate hydratase (fumarase), and tartrate dehydratase. This model represents a subset of closely related proteins or modules, including the E. coli tartrate dehydratase beta chain and the C-terminal region of the class I fumarase (where the N-terminal region is homologous to the tartrate dehydratase alpha chain). The activity of archaeal proteins in this subfamily has not been established.
Probab=20.22 E-value=1.1e+02 Score=24.63 Aligned_cols=20 Identities=25% Similarity=0.325 Sum_probs=16.8
Q ss_pred HHhcCCCCeEEEEEEeEEee
Q 030281 116 VKQLVKNSSVYVEGDIEIRV 135 (180)
Q Consensus 116 ~~~l~KG~~V~VeGrL~~~~ 135 (180)
.+.|+.||.|++.|.|-+-.
T Consensus 3 i~~L~vGD~V~LsG~i~taR 22 (168)
T TIGR00723 3 ILKLKVGDVVYLTGTIFTAR 22 (168)
T ss_pred hHhCCCCCEEEEEEEEEEEE
Confidence 45799999999999997643
Done!