Query 032583
Match_columns 137
No_of_seqs 107 out of 448
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 03:19:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032583.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032583hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK06461 single-stranded DNA-b 100.0 6.1E-28 1.3E-32 176.8 13.5 114 12-131 3-116 (129)
2 KOG3416 Predicted nucleic acid 99.9 6.5E-27 1.4E-31 170.0 10.5 109 14-130 5-113 (134)
3 PRK06386 replication factor A; 99.9 8.1E-23 1.8E-27 171.4 12.9 104 13-122 2-105 (358)
4 PRK07218 replication factor A; 99.9 7.1E-23 1.5E-27 175.0 12.1 98 10-114 55-152 (423)
5 PRK07217 replication factor A; 99.9 1E-21 2.2E-26 161.7 13.3 113 9-134 68-181 (311)
6 PRK08402 replication factor A; 99.9 5.3E-22 1.1E-26 166.5 11.3 101 11-114 60-165 (355)
7 PRK06386 replication factor A; 99.9 1.9E-21 4.1E-26 163.2 13.6 100 12-120 106-205 (358)
8 PRK07218 replication factor A; 99.9 2.8E-21 6E-26 165.3 13.6 102 12-120 161-262 (423)
9 PRK15491 replication factor A; 99.9 4.4E-21 9.6E-26 161.9 11.7 101 9-113 53-158 (374)
10 PRK14699 replication factor A; 99.8 1.1E-20 2.3E-25 163.9 11.7 114 10-128 54-173 (484)
11 PRK07211 replication factor A; 99.8 1.5E-20 3.3E-25 162.7 11.7 100 11-113 159-261 (485)
12 PRK14699 replication factor A; 99.8 2.2E-20 4.9E-25 162.0 12.2 98 12-112 165-267 (484)
13 PRK12366 replication factor A; 99.8 5.3E-20 1.2E-24 164.0 12.2 100 10-112 60-162 (637)
14 cd04491 SoSSB_OBF SoSSB_OBF: A 99.8 1.1E-18 2.5E-23 117.5 11.4 80 27-110 1-81 (82)
15 PRK15491 replication factor A; 99.8 8.8E-19 1.9E-23 147.9 11.6 100 11-113 164-268 (374)
16 PRK07211 replication factor A; 99.7 9.3E-18 2E-22 145.5 11.2 98 7-111 47-149 (485)
17 PRK12366 replication factor A; 99.7 5.8E-17 1.2E-21 144.6 11.5 99 11-112 393-495 (637)
18 cd04475 RPA1_DBD_B RPA1_DBD_B: 99.5 7.1E-13 1.5E-17 92.2 9.9 84 26-113 2-89 (101)
19 cd04474 RPA1_DBD_A RPA1_DBD_A: 99.5 6.1E-13 1.3E-17 93.7 9.4 90 15-108 1-102 (104)
20 COG1599 RFA1 Single-stranded D 99.4 2.4E-13 5.1E-18 115.7 8.0 111 7-120 43-155 (407)
21 TIGR00617 rpa1 replication fac 99.2 1.8E-10 3.8E-15 102.8 10.9 98 12-113 179-287 (608)
22 TIGR00617 rpa1 replication fac 99.0 2E-09 4.3E-14 96.1 10.0 98 11-112 296-399 (608)
23 PF01336 tRNA_anti-codon: OB-f 98.5 6.2E-07 1.3E-11 57.7 7.5 67 26-105 1-72 (75)
24 cd04497 hPOT1_OB1_like hPOT1_O 98.4 2.2E-06 4.7E-11 63.2 9.5 86 12-104 2-95 (138)
25 cd04483 hOBFC1_like hOBFC1_lik 98.0 5.6E-05 1.2E-09 52.3 8.6 62 28-103 2-87 (92)
26 cd04478 RPA2_DBD_D RPA2_DBD_D: 97.9 0.0002 4.3E-09 48.7 9.8 70 26-112 2-78 (95)
27 cd03524 RPA2_OBF_family RPA2_O 97.9 0.00013 2.8E-09 45.3 7.9 65 28-103 2-71 (75)
28 PRK13480 3'-5' exoribonuclease 97.8 0.00012 2.5E-09 61.1 7.8 80 15-104 4-86 (314)
29 cd04481 RPA1_DBD_B_like RPA1_D 97.7 0.00034 7.4E-09 48.9 7.9 82 27-112 1-93 (106)
30 cd04492 YhaM_OBF_like YhaM_OBF 97.7 0.00037 8E-09 45.4 7.5 51 52-103 18-71 (83)
31 cd04480 RPA1_DBD_A_like RPA1_D 97.4 0.0006 1.3E-08 45.9 6.2 63 28-98 2-69 (86)
32 COG1599 RFA1 Single-stranded D 97.4 0.0012 2.6E-08 56.4 8.9 65 29-101 173-238 (407)
33 cd04488 RecG_wedge_OBF RecG_we 97.3 0.0029 6.2E-08 39.9 7.8 64 28-101 2-68 (75)
34 PF02765 POT1: Telomeric singl 97.2 0.0045 9.8E-08 45.8 9.5 83 22-111 11-109 (146)
35 cd04485 DnaE_OBF DnaE_OBF: A s 97.2 0.0033 7.1E-08 40.4 7.8 51 52-103 18-72 (84)
36 cd04489 ExoVII_LU_OBF ExoVII_L 96.7 0.02 4.3E-07 37.1 8.4 65 27-103 3-72 (78)
37 PRK08402 replication factor A; 95.2 0.037 8E-07 47.0 5.1 67 11-77 182-269 (355)
38 PRK10917 ATP-dependent DNA hel 95.0 0.13 2.9E-06 46.7 8.4 77 12-100 49-129 (681)
39 cd04484 polC_OBF polC_OBF: A s 94.8 0.57 1.2E-05 31.4 9.1 71 25-103 1-77 (82)
40 cd04498 hPOT1_OB2 hPOT1_OB2: A 94.7 0.079 1.7E-06 38.8 5.1 32 65-96 61-95 (123)
41 COG4085 Predicted RNA-binding 94.7 0.15 3.3E-06 40.1 6.8 93 12-116 36-141 (204)
42 TIGR00643 recG ATP-dependent D 94.3 0.27 5.9E-06 44.2 8.5 79 12-101 22-103 (630)
43 cd04487 RecJ_OBF2_like RecJ_OB 93.5 0.48 1E-05 31.2 6.7 46 57-103 19-68 (73)
44 cd04490 PolII_SU_OBF PolII_SU_ 93.1 1 2.3E-05 30.0 7.8 54 26-91 2-61 (79)
45 PRK05673 dnaE DNA polymerase I 92.0 0.38 8.3E-06 46.5 6.3 86 14-108 966-1057(1135)
46 PRK07373 DNA polymerase III su 91.7 0.49 1.1E-05 41.4 6.1 83 14-105 269-357 (449)
47 PF02760 HIN: HIN-200/IF120x d 91.5 3.5 7.6E-05 31.7 9.8 83 28-117 5-89 (170)
48 PF02721 DUF223: Domain of unk 91.0 0.95 2.1E-05 30.8 5.8 57 56-112 1-69 (95)
49 PRK05159 aspC aspartyl-tRNA sy 90.8 1.7 3.8E-05 37.6 8.5 86 14-112 5-101 (437)
50 PF10451 Stn1: Telomere regula 89.0 3 6.6E-05 33.9 8.2 73 23-108 66-147 (256)
51 COG5235 RFA2 Single-stranded D 88.4 3.1 6.8E-05 33.5 7.6 45 57-102 87-137 (258)
52 PF13742 tRNA_anti_2: OB-fold 87.5 7.3 0.00016 26.8 8.3 69 23-103 21-95 (99)
53 cd04494 BRCA2DBD_OB2 BRCA2DBD_ 87.5 1.9 4.2E-05 35.1 6.1 59 54-112 166-236 (251)
54 PRK00448 polC DNA polymerase I 87.4 4.4 9.5E-05 40.4 9.5 88 11-106 224-318 (1437)
55 PRK07459 single-stranded DNA-b 87.4 1.7 3.7E-05 31.3 5.2 62 23-91 3-75 (121)
56 PF08646 Rep_fac-A_C: Replicat 87.2 0.31 6.6E-06 35.7 1.2 25 52-76 53-77 (146)
57 PF04076 BOF: Bacterial OB fol 87.1 3.2 6.9E-05 29.3 6.3 66 21-103 32-99 (103)
58 COG1200 RecG RecG-like helicas 86.5 5.1 0.00011 37.0 8.7 79 11-100 49-130 (677)
59 cd04322 LysRS_N LysRS_N: N-ter 85.3 9.9 0.00021 26.2 9.3 59 53-111 16-83 (108)
60 cd04316 ND_PkAspRS_like_N ND_P 85.3 10 0.00022 26.2 8.8 75 24-111 13-97 (108)
61 cd04317 EcAspRS_like_N EcAspRS 85.2 11 0.00025 26.9 8.9 84 24-120 15-113 (135)
62 cd04482 RPA2_OBF_like RPA2_OBF 84.9 3.4 7.4E-05 28.1 5.5 38 57-95 21-64 (91)
63 TIGR00499 lysS_bact lysyl-tRNA 84.9 9.7 0.00021 33.7 9.6 74 25-111 55-137 (496)
64 PF11325 DUF3127: Domain of un 84.9 7.5 0.00016 26.6 7.0 67 28-99 2-75 (84)
65 PRK02801 primosomal replicatio 84.7 3.5 7.5E-05 28.7 5.5 63 23-92 2-80 (101)
66 PLN02850 aspartate-tRNA ligase 84.2 14 0.0003 33.1 10.4 95 11-118 67-180 (530)
67 PRK00484 lysS lysyl-tRNA synth 84.1 12 0.00026 33.1 9.9 75 24-111 55-137 (491)
68 PRK12445 lysyl-tRNA synthetase 83.4 6.1 0.00013 35.1 7.7 74 25-111 67-149 (505)
69 PTZ00401 aspartyl-tRNA synthet 83.3 15 0.00032 33.2 10.1 95 11-118 63-177 (550)
70 PRK05733 single-stranded DNA-b 83.2 10 0.00022 29.1 8.0 84 22-112 4-112 (172)
71 PRK07374 dnaE DNA polymerase I 82.3 3.5 7.6E-05 40.3 6.1 84 14-106 989-1078(1170)
72 PRK09010 single-stranded DNA-b 81.8 16 0.00035 28.2 8.6 84 22-112 5-114 (177)
73 TIGR00156 conserved hypothetic 81.6 8.8 0.00019 28.2 6.8 65 21-102 55-121 (126)
74 TIGR00621 ssb single stranded 81.3 4.2 9.1E-05 30.6 5.2 62 23-91 4-82 (164)
75 PRK06752 single-stranded DNA-b 80.9 4.1 9E-05 28.6 4.8 63 23-92 2-79 (112)
76 cd04320 AspRS_cyto_N AspRS_cyt 80.8 15 0.00032 24.9 9.3 59 53-111 17-92 (102)
77 PLN02502 lysyl-tRNA synthetase 80.6 8.6 0.00019 34.7 7.7 73 26-111 111-194 (553)
78 PRK07274 single-stranded DNA-b 80.3 4.3 9.3E-05 29.5 4.8 62 23-91 2-78 (131)
79 PRK07279 dnaE DNA polymerase I 80.1 7.3 0.00016 37.7 7.4 84 13-105 875-962 (1034)
80 PRK06826 dnaE DNA polymerase I 79.3 8.5 0.00018 37.6 7.7 75 24-106 992-1070(1151)
81 PRK05813 single-stranded DNA-b 79.2 7.7 0.00017 30.9 6.3 65 22-93 108-180 (219)
82 COG1107 Archaea-specific RecJ- 79.2 6.3 0.00014 36.1 6.3 69 26-108 216-288 (715)
83 PRK06751 single-stranded DNA-b 78.8 5.3 0.00011 30.7 5.1 66 23-95 2-83 (173)
84 PRK07275 single-stranded DNA-b 78.8 4.9 0.00011 30.5 4.8 61 24-91 3-78 (162)
85 KOG3108 Single-stranded DNA-bi 78.8 10 0.00022 31.2 7.0 52 57-109 89-146 (265)
86 PRK08763 single-stranded DNA-b 78.6 5.7 0.00012 30.3 5.2 64 22-92 4-84 (164)
87 PRK10053 hypothetical protein; 78.4 16 0.00036 26.9 7.4 44 58-102 80-125 (130)
88 cd04476 RPA1_DBD_C RPA1_DBD_C: 78.3 1.5 3.2E-05 32.6 1.9 25 52-76 67-91 (166)
89 cd04496 SSB_OBF SSB_OBF: A sub 78.1 7.6 0.00017 25.6 5.2 31 62-92 42-76 (100)
90 PF00436 SSB: Single-strand bi 78.1 2.6 5.7E-05 28.3 2.9 62 24-92 2-80 (104)
91 cd01491 Ube1_repeat1 Ubiquitin 77.2 10 0.00023 31.2 6.7 67 54-127 167-233 (286)
92 PRK05672 dnaE2 error-prone DNA 77.0 5.8 0.00012 38.4 5.8 69 25-104 955-1027(1046)
93 PTZ00385 lysyl-tRNA synthetase 76.5 25 0.00053 32.6 9.4 73 25-110 109-191 (659)
94 cd04486 YhcR_OBF_like YhcR_OBF 75.8 6.6 0.00014 26.0 4.3 36 67-104 35-70 (78)
95 PRK06920 dnaE DNA polymerase I 75.5 7 0.00015 38.1 5.9 84 14-106 933-1021(1107)
96 PRK06958 single-stranded DNA-b 75.0 8.7 0.00019 29.9 5.4 62 23-91 4-83 (182)
97 PRK06293 single-stranded DNA-b 74.9 7.6 0.00017 29.6 4.9 64 23-93 1-76 (161)
98 TIGR00458 aspS_arch aspartyl-t 74.1 24 0.00052 30.5 8.4 83 16-111 3-97 (428)
99 PF02760 HIN: HIN-200/IF120x d 74.0 22 0.00047 27.4 7.1 64 13-87 101-165 (170)
100 cd04100 Asp_Lys_Asn_RS_N Asp_L 73.1 23 0.0005 23.1 8.1 51 53-103 16-78 (85)
101 PRK13732 single-stranded DNA-b 73.1 9.8 0.00021 29.3 5.2 83 22-111 5-112 (175)
102 PRK03932 asnC asparaginyl-tRNA 72.8 24 0.00052 30.8 8.1 75 23-110 16-99 (450)
103 PRK08486 single-stranded DNA-b 72.3 10 0.00022 29.3 5.2 61 24-91 3-80 (182)
104 PRK02983 lysS lysyl-tRNA synth 71.7 35 0.00076 33.3 9.6 74 25-111 653-735 (1094)
105 PF07680 DoxA: TQO small subun 71.4 39 0.00084 25.0 8.3 98 16-134 21-120 (133)
106 COG1571 Predicted DNA-binding 71.1 18 0.0004 31.6 6.9 75 16-107 260-340 (421)
107 cd04321 ScAspRS_mt_like_N ScAs 70.7 28 0.0006 23.0 7.3 50 53-102 17-78 (86)
108 PRK08182 single-stranded DNA-b 69.5 11 0.00025 28.0 4.8 65 24-91 3-85 (148)
109 TIGR00457 asnS asparaginyl-tRN 68.6 30 0.00065 30.2 7.8 76 24-112 17-103 (453)
110 cd04318 EcAsnRS_like_N EcAsnRS 67.0 32 0.00068 22.3 7.4 52 53-104 16-76 (82)
111 TIGR01405 polC_Gram_pos DNA po 66.3 71 0.0015 31.7 10.5 83 18-108 2-91 (1213)
112 PRK07772 single-stranded DNA-b 66.0 20 0.00043 27.9 5.6 63 23-92 4-85 (186)
113 PTZ00417 lysine-tRNA ligase; P 65.8 29 0.00063 31.5 7.4 74 26-111 135-219 (585)
114 PF15072 DUF4539: Domain of un 65.6 19 0.00042 24.6 4.9 52 55-106 21-77 (86)
115 cd03583 NTR_complement_C3 NTR/ 63.2 60 0.0013 24.2 8.5 82 26-113 31-121 (149)
116 PRK06863 single-stranded DNA-b 62.3 22 0.00048 27.2 5.2 65 22-93 3-85 (168)
117 TIGR00459 aspS_bact aspartyl-t 62.2 58 0.0013 29.7 8.6 81 25-118 17-111 (583)
118 COG0017 AsnS Aspartyl/asparagi 61.7 95 0.0021 27.4 9.5 87 13-112 4-101 (435)
119 PF09104 BRCA-2_OB3: BRCA2, ol 61.7 66 0.0014 24.1 8.6 83 19-113 14-104 (143)
120 PRK07135 dnaE DNA polymerase I 61.1 28 0.0006 33.6 6.6 79 14-104 889-970 (973)
121 COG3481 Predicted HD-superfami 60.4 8 0.00017 32.2 2.6 59 53-112 21-82 (287)
122 PRK06642 single-stranded DNA-b 60.4 34 0.00073 25.5 5.8 62 23-91 5-85 (152)
123 COG1190 LysU Lysyl-tRNA synthe 60.2 52 0.0011 29.5 7.7 59 52-110 77-144 (502)
124 PRK00476 aspS aspartyl-tRNA sy 59.8 82 0.0018 28.6 9.1 81 25-118 19-113 (588)
125 cd04319 PhAsnRS_like_N PhAsnRS 56.3 61 0.0013 22.0 8.7 60 53-112 16-84 (103)
126 PRK05813 single-stranded DNA-b 56.0 1E+02 0.0022 24.5 8.9 82 23-111 8-100 (219)
127 PRK10260 L,D-transpeptidase; P 54.3 8.2 0.00018 32.4 1.7 42 61-102 206-252 (306)
128 KOG2012 Ubiquitin activating e 53.5 17 0.00038 34.7 3.8 58 67-129 196-253 (1013)
129 PRK09919 anti-adapter protein 53.2 55 0.0012 23.7 5.6 38 65-102 26-63 (114)
130 cd03582 NTR_complement_C5 NTR/ 52.4 95 0.0021 23.1 7.1 81 27-113 34-124 (150)
131 PLN02603 asparaginyl-tRNA synt 51.3 1.5E+02 0.0033 26.9 9.4 88 12-112 88-194 (565)
132 PRK12820 bifunctional aspartyl 50.7 1.4E+02 0.0031 27.9 9.2 89 17-118 10-117 (706)
133 PF11183 PmrD: Polymyxin resis 50.7 22 0.00049 24.3 3.1 38 54-91 16-55 (82)
134 PRK10190 L,D-transpeptidase; P 48.4 11 0.00024 31.6 1.7 43 61-103 203-250 (310)
135 COG1376 ErfK Uncharacterized p 48.3 9 0.00019 29.9 1.0 30 60-89 200-231 (232)
136 cd03584 NTR_complement_C4 NTR/ 46.5 1.2E+02 0.0026 22.6 7.0 82 26-113 36-125 (153)
137 COG1097 RRP4 RNA-binding prote 46.5 66 0.0014 26.1 5.7 61 51-111 117-190 (239)
138 PRK00286 xseA exodeoxyribonucl 46.3 83 0.0018 27.0 6.7 69 23-103 23-96 (438)
139 PLN02221 asparaginyl-tRNA synt 45.6 1.5E+02 0.0032 27.0 8.4 59 54-112 70-138 (572)
140 PF04775 Bile_Hydr_Trans: Acyl 44.6 57 0.0012 23.4 4.7 48 9-69 2-49 (126)
141 smart00643 C345C Netrin C-term 43.8 1E+02 0.0022 21.0 8.4 50 64-113 49-103 (114)
142 PRK06341 single-stranded DNA-b 42.4 64 0.0014 24.6 4.9 65 23-94 5-89 (166)
143 COG1570 XseA Exonuclease VII, 42.2 1.3E+02 0.0028 26.6 7.3 69 23-103 23-96 (440)
144 PF05113 DUF693: Protein of un 39.9 79 0.0017 26.5 5.3 33 64-96 61-96 (314)
145 PF12869 tRNA_anti-like: tRNA_ 38.6 96 0.0021 21.9 5.1 66 23-100 67-140 (144)
146 TIGR00237 xseA exodeoxyribonuc 38.5 1.3E+02 0.0028 26.1 6.8 48 56-103 38-90 (432)
147 KOG1816 Ubiquitin fusion-degra 37.2 28 0.0006 29.2 2.3 31 61-91 81-111 (308)
148 COG1917 Uncharacterized conser 36.8 36 0.00077 23.9 2.6 28 63-91 72-99 (131)
149 PLN02903 aminoacyl-tRNA ligase 36.4 2.7E+02 0.0058 25.9 8.6 59 53-111 89-163 (652)
150 COG0587 DnaE DNA polymerase II 36.2 1.2E+02 0.0026 30.0 6.7 72 14-92 967-1042(1139)
151 COG2176 PolC DNA polymerase II 35.2 2E+02 0.0043 29.1 7.8 91 11-109 227-324 (1444)
152 cd05694 S1_Rrp5_repeat_hs2_sc2 35.1 1.2E+02 0.0027 19.4 5.9 69 18-103 1-69 (74)
153 PF00575 S1: S1 RNA binding do 34.9 83 0.0018 19.4 3.9 62 27-102 7-73 (74)
154 PRK04036 DNA polymerase II sma 34.4 1.4E+02 0.003 26.5 6.3 67 13-91 143-215 (504)
155 COG4013 Uncharacterized protei 33.7 1E+02 0.0022 21.4 4.2 32 77-108 20-61 (91)
156 TIGR02656 cyanin_plasto plasto 33.2 58 0.0013 22.0 3.1 30 57-89 3-32 (99)
157 PF01957 NfeD: NfeD-like C-ter 32.5 79 0.0017 22.1 3.8 37 52-89 94-133 (144)
158 KOG0851 Single-stranded DNA-bi 31.8 1.3E+02 0.0029 22.8 5.3 81 12-100 3-88 (246)
159 COG4880 Secreted protein conta 31.4 58 0.0013 29.2 3.4 54 59-112 488-542 (603)
160 cd04461 S1_Rrp5_repeat_hs8_sc7 30.7 1.4E+02 0.003 19.1 4.5 77 14-102 7-83 (83)
161 cd03574 NTR_complement_C345C N 30.4 2.1E+02 0.0047 20.7 8.1 38 76-113 77-119 (147)
162 PF01759 NTR: UNC-6/NTR/C345C 29.9 1.8E+02 0.0038 19.6 5.5 50 63-112 44-99 (111)
163 COG4043 Preprotein translocase 29.7 69 0.0015 22.9 3.0 28 65-92 21-48 (111)
164 COG3111 Periplasmic protein wi 28.2 1.8E+02 0.0038 21.5 5.0 44 58-102 76-121 (128)
165 PF09356 Phage_BR0599: Phage c 27.7 81 0.0017 21.0 3.0 23 66-88 29-51 (80)
166 PF03459 TOBE: TOBE domain; I 26.3 1.5E+02 0.0032 17.8 3.9 50 27-87 6-56 (64)
167 cd04323 AsnRS_cyto_like_N AsnR 25.2 2E+02 0.0042 18.6 8.0 41 53-93 16-62 (84)
168 PF00333 Ribosomal_S5: Ribosom 25.1 2E+02 0.0043 18.5 4.5 39 28-70 2-41 (67)
169 PF03100 CcmE: CcmE; InterPro 24.6 2.7E+02 0.0058 19.9 7.0 69 13-90 36-108 (131)
170 PF11213 DUF3006: Protein of u 24.4 1.8E+02 0.0039 18.7 4.1 32 53-86 10-42 (71)
171 smart00739 KOW KOW (Kyprides, 24.0 63 0.0014 16.2 1.5 15 78-92 2-16 (28)
172 smart00350 MCM minichromosome 23.8 1E+02 0.0022 27.2 3.6 29 65-93 105-133 (509)
173 cd05706 S1_Rrp5_repeat_sc10 S1 23.2 1.9E+02 0.0042 17.7 7.0 27 76-102 46-72 (73)
174 COG2049 DUR1 Allophanate hydro 23.0 52 0.0011 26.4 1.6 31 64-94 183-216 (223)
175 PF02563 Poly_export: Polysacc 22.7 39 0.00085 22.1 0.7 32 77-110 12-43 (82)
176 PRK13159 cytochrome c-type bio 22.6 3.5E+02 0.0075 20.5 6.3 38 54-91 73-110 (155)
177 PF13296 T6SS_Vgr: Putative ty 21.9 97 0.0021 22.1 2.6 57 54-110 9-67 (109)
178 PF08696 Dna2: DNA replication 21.1 2.5E+02 0.0054 21.8 5.0 24 65-88 11-35 (209)
179 PLN02532 asparagine-tRNA synth 20.2 5.4E+02 0.012 23.9 7.6 67 52-118 133-208 (633)
180 TIGR00594 polc DNA-directed DN 20.2 2.4E+02 0.0053 27.4 5.6 39 26-71 984-1022(1022)
No 1
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=99.96 E-value=6.1e-28 Score=176.75 Aligned_cols=114 Identities=29% Similarity=0.452 Sum_probs=106.2
Q ss_pred eeeeeccCCCCCCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecCCcCCCCCCCEEEEeceEE
Q 032583 12 VFTKVDQLRPGTSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARNDQVDLMKEGTTVILRNAKI 91 (137)
Q Consensus 12 ~~~kI~dL~p~~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~~~~~i~~Gd~v~I~na~~ 91 (137)
.++||+||+|++.+++++++|+++++++.+.+++| ...+.+++|||+||+|+|++|+++++.+++||+|+|.||++
T Consensus 3 ~~~kI~dL~~g~~~v~~~~~V~~i~~~~~~~~k~~----~~~v~~~~l~D~TG~I~~tlW~~~a~~l~~GdvV~I~na~v 78 (129)
T PRK06461 3 MITKIKDLKPGMERVNVTVRVLEVGEPKVIQTKGG----PRTISEAVVGDETGRVKLTLWGEQAGSLKEGEVVEIENAWT 78 (129)
T ss_pred CceEHHHcCCCCCceEEEEEEEEcCCceEEEeCCC----ceEEEEEEEECCCCEEEEEEeCCccccCCCCCEEEEECcEE
Confidence 47899999999999999999999999888877654 36899999999999999999999998999999999999999
Q ss_pred cccCCeEEEEeCCcEeEEEcCCCceEEcCCCCccccceee
Q 032583 92 DMFKGSMRLAVDKWGRVEVAEPANFTVKEDNNLSLIEYEL 131 (137)
Q Consensus 92 ~~~~g~~~L~vg~~g~I~~~~~~~~~vn~~~n~S~~eye~ 131 (137)
++|+|+++|+++++|.|..+++. +|+..++||+.+||.
T Consensus 79 ~~f~G~lqL~i~~~~~i~~~~~~--~v~~~~~i~~~~~~~ 116 (129)
T PRK06461 79 TLYRGKVQLNVGKYGSISESDDE--EVPEAEEIPEETPEA 116 (129)
T ss_pred eeeCCEEEEEECCCEEEEECCcc--ccCCCCccCccCccc
Confidence 99999999999999999999765 899999999999985
No 2
>KOG3416 consensus Predicted nucleic acid binding protein [General function prediction only]
Probab=99.94 E-value=6.5e-27 Score=169.96 Aligned_cols=109 Identities=25% Similarity=0.409 Sum_probs=102.3
Q ss_pred eeeccCCCCCCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecCCcCCCCCCCEEEEeceEEcc
Q 032583 14 TKVDQLRPGTSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARNDQVDLMKEGTTVILRNAKIDM 93 (137)
Q Consensus 14 ~kI~dL~p~~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~~~~~i~~Gd~v~I~na~~~~ 93 (137)
..|+||+|+++|+++++.||+.+..+.++ || +.|+.++|||+||+|.+++|+|..+.+++||+|+++++|+++
T Consensus 5 i~ikdi~P~~kN~~v~fIvl~~g~~tkTk--dg-----~~v~~~kVaD~TgsI~isvW~e~~~~~~PGDIirLt~Gy~Si 77 (134)
T KOG3416|consen 5 IFIKDIKPGLKNINVTFIVLEYGRATKTK--DG-----HEVRSCKVADETGSINISVWDEEGCLIQPGDIIRLTGGYASI 77 (134)
T ss_pred hhHhhcChhhhcceEEEEEEeeceeeecc--CC-----CEEEEEEEecccceEEEEEecCcCcccCCccEEEecccchhh
Confidence 46899999999999999999999887653 76 799999999999999999999999999999999999999999
Q ss_pred cCCeEEEEeCCcEeEEEcCCCceEEcCCCCcccccee
Q 032583 94 FKGSMRLAVDKWGRVEVAEPANFTVKEDNNLSLIEYE 130 (137)
Q Consensus 94 ~~g~~~L~vg~~g~I~~~~~~~~~vn~~~n~S~~eye 130 (137)
|+|++.|++||.|.++++++|++.|++++|+| +.|-
T Consensus 78 ~qg~LtL~~GK~Ge~~KiGef~~vf~etpn~S-~~~~ 113 (134)
T KOG3416|consen 78 FQGCLTLYVGKGGEVQKIGEFCMVFSETPNIS-IQWA 113 (134)
T ss_pred hcCceEEEecCCceEeEeeeeEEeeecCCCcc-cccc
Confidence 99999999999999999999999999999999 5554
No 3
>PRK06386 replication factor A; Reviewed
Probab=99.89 E-value=8.1e-23 Score=171.42 Aligned_cols=104 Identities=24% Similarity=0.347 Sum_probs=93.9
Q ss_pred eeeeccCCCCCCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecCCcCCCCCCCEEEEeceEEc
Q 032583 13 FTKVDQLRPGTSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARNDQVDLMKEGTTVILRNAKID 92 (137)
Q Consensus 13 ~~kI~dL~p~~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~~~~~i~~Gd~v~I~na~~~ 92 (137)
..||+||.|++.+++++||||+++ .++|.++||+ ..+.+++|||+||+|+||+|+ +++.+++||+|+|.||+++
T Consensus 2 ~~kI~DI~~~~~~V~v~akVl~~~-~r~i~~~~g~----~~~~~gllgDeTG~I~fT~W~-~~~~l~~Gd~v~i~na~v~ 75 (358)
T PRK06386 2 LSKISDINAARQNVDLKVKVLSLN-KRTIKNDRGE----TIYYYGIIGDETGTVPFTAWE-FPDAVKSGDVIEIKYCYSK 75 (358)
T ss_pred CcchhhcCCCCCcEEEEEEEEEcc-ceEEecCCCC----eEEEEEEEECCcceEEEEecC-CcccCCCCCEEEEEeEEEe
Confidence 468999999999999999999998 6899999985 588899999999999999999 4567899999999999999
Q ss_pred ccCCeEEEEeCCcEeEEEcCCCceEEcCCC
Q 032583 93 MFKGSMRLAVDKWGRVEVAEPANFTVKEDN 122 (137)
Q Consensus 93 ~~~g~~~L~vg~~g~I~~~~~~~~~vn~~~ 122 (137)
+|+|.++|+++++++|...++..+++++..
T Consensus 76 ~~~G~~~Lnv~~~t~v~~~~d~~iev~~~~ 105 (358)
T PRK06386 76 EYNGKIRIYFDSRSEVMLKPDENIEVKRTY 105 (358)
T ss_pred eECCEEEEEEcCceEEEecCcccccccccc
Confidence 999999999999999987766777776653
No 4
>PRK07218 replication factor A; Provisional
Probab=99.89 E-value=7.1e-23 Score=174.99 Aligned_cols=98 Identities=26% Similarity=0.342 Sum_probs=90.8
Q ss_pred CCeeeeeccCCCCCCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecCCcCCCCCCCEEEEece
Q 032583 10 KPVFTKVDQLRPGTSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARNDQVDLMKEGTTVILRNA 89 (137)
Q Consensus 10 ~~~~~kI~dL~p~~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~~~~~i~~Gd~v~I~na 89 (137)
.+..+||+||.|++.+|+|+||||++++ ++| |+||+. +.|++++|||+||+|+||+|+++. +++||+|+|.||
T Consensus 55 ~~~~~kI~Di~~~~~~V~v~~kVl~i~~-rt~-r~dg~~---g~v~~~~igDeTG~Ir~tlW~~~~--l~~Gdvv~I~na 127 (423)
T PRK07218 55 TPSSKDIKELSTDDKNVTVTGRVLTIGE-RSI-RYQGDD---HVIYEGILADETGTISYTAWKDFG--LSPGDTVTIGNA 127 (423)
T ss_pred CCCCccHhhCCCCCceeEEEEEEEEecc-eeE-ecCCCc---eEEEEEEEECCCCeEEEEEECCCC--CCCCCEEEEecc
Confidence 4678999999999999999999999998 777 688874 999999999999999999999774 999999999999
Q ss_pred EEcccCCeEEEEeCCcEeEEEcCCC
Q 032583 90 KIDMFKGSMRLAVDKWGRVEVAEPA 114 (137)
Q Consensus 90 ~~~~~~g~~~L~vg~~g~I~~~~~~ 114 (137)
++++|+|+++|++|+++.|...++.
T Consensus 128 ~vre~~g~~el~ig~~t~I~~~de~ 152 (423)
T PRK07218 128 GVREWDGRPELNIGESTTVSLLDDS 152 (423)
T ss_pred EeeccCCceEEeccCcceEEEcCcc
Confidence 9999999999999999999988744
No 5
>PRK07217 replication factor A; Reviewed
Probab=99.87 E-value=1e-21 Score=161.68 Aligned_cols=113 Identities=22% Similarity=0.312 Sum_probs=94.8
Q ss_pred CCCeeeeeccCCCCCCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecC-CcCCCCCCCEEEEe
Q 032583 9 RKPVFTKVDQLRPGTSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARND-QVDLMKEGTTVILR 87 (137)
Q Consensus 9 ~~~~~~kI~dL~p~~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~-~~~~i~~Gd~v~I~ 87 (137)
..+..+||+||.|+..+|+|+|||+++++++. + .....++|||+||+|+||+|+. .+..+++|++|+|.
T Consensus 68 ~~~~~~kI~Di~~~~~~VsV~aKVl~l~e~~~-----~-----si~qvGllgDETG~IkfT~W~~s~~~~leeGd~~rI~ 137 (311)
T PRK07217 68 GGSELVNIADIDEPEQWVDVTAKVVQLWEPSS-----D-----SIAQVGLLGDETGTIKFTKWAKSDLPELEEGKSYLLK 137 (311)
T ss_pred CCCCceeeeecCCCCCcEEEEEEEEEecCCCC-----C-----ceEEEEEEEcCCceEEEEEccCCCCCcccCCCEEEEE
Confidence 35678899999999999999999999999752 2 2344589999999999999995 66679999999999
Q ss_pred ceEEcccCCeEEEEeCCcEeEEEcCCCceEEcCCCCccccceeeeee
Q 032583 88 NAKIDMFKGSMRLAVDKWGRVEVAEPANFTVKEDNNLSLIEYELVNV 134 (137)
Q Consensus 88 na~~~~~~g~~~L~vg~~g~I~~~~~~~~~vn~~~n~S~~eye~~~~ 134 (137)
||++++|+|+++|++++++.|..+ +..++|.+.. ..+.-.++.|
T Consensus 138 na~v~ey~G~~~lnlg~~t~I~~~-de~IeV~~~~--vei~G~lVdi 181 (311)
T PRK07217 138 NVVTDEYQGRFSVKLNRTTSIEEL-DEDIEVGDDE--VEVEGALVDI 181 (311)
T ss_pred eEEEeeECCEEEEEeCCceEEEeC-CCCccccCcc--ccceeEEEEE
Confidence 999999999999999999999999 5566776543 4555556655
No 6
>PRK08402 replication factor A; Reviewed
Probab=99.87 E-value=5.3e-22 Score=166.49 Aligned_cols=101 Identities=18% Similarity=0.273 Sum_probs=93.3
Q ss_pred CeeeeeccCCCCCCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecCCcC----CCCCCCEEEE
Q 032583 11 PVFTKVDQLRPGTSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARNDQVD----LMKEGTTVIL 86 (137)
Q Consensus 11 ~~~~kI~dL~p~~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~~~~----~i~~Gd~v~I 86 (137)
..+.||+||.|++++++++++|++++++++|.|+||+. ++|++++|||+||+|+||||++++. .+++||+|+|
T Consensus 60 ~~~~kI~dl~~g~~~V~v~~rVl~~~~~r~f~rrdG~~---~~V~~i~l~DeTG~ir~TlW~~~a~~~~~~l~~Gdvi~I 136 (355)
T PRK08402 60 APLMHISDLVPGMRGVNIVGRVLRKYPPREYTKKDGST---GRVASLIIYDDTGRARVVLWDAKVAKYYNKINVGDVIKV 136 (355)
T ss_pred cCccCHHHccCCCceeeEEEEEEEccCCceeeccCCCc---ceEEEEEEEcCCCeEEEEEechhhhhhcccCCCCCEEEE
Confidence 35889999999999999999999999999999999975 9999999999999999999998764 4899999999
Q ss_pred eceEEccc-CCeEEEEeCCcEeEEEcCCC
Q 032583 87 RNAKIDMF-KGSMRLAVDKWGRVEVAEPA 114 (137)
Q Consensus 87 ~na~~~~~-~g~~~L~vg~~g~I~~~~~~ 114 (137)
.||+++.| +|.++|++|++|+|...|+.
T Consensus 137 ~~a~V~e~~~G~~eLsvg~~s~i~~~pd~ 165 (355)
T PRK08402 137 IDAQVRESLSGLPELHINFRARIILNPDD 165 (355)
T ss_pred ECCEEeecCCCcEEEEECCCceEEeCCCc
Confidence 99999985 89999999999999888643
No 7
>PRK06386 replication factor A; Reviewed
Probab=99.87 E-value=1.9e-21 Score=163.19 Aligned_cols=100 Identities=14% Similarity=0.245 Sum_probs=89.3
Q ss_pred eeeeeccCCCCCCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecCCcCCCCCCCEEEEeceEE
Q 032583 12 VFTKVDQLRPGTSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARNDQVDLMKEGTTVILRNAKI 91 (137)
Q Consensus 12 ~~~kI~dL~p~~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~~~~~i~~Gd~v~I~na~~ 91 (137)
..+||+||.|++.+++++|||+++++ ++|. .||+ .+.+++++|||+||+||||+|++ .+++||+|+|.||++
T Consensus 106 ~~~KI~DL~~g~~~v~V~akVle~~e-~e~~-~~g~---~~~v~sg~lgDeTGrIr~TlW~~---~l~eGd~v~i~na~v 177 (358)
T PRK06386 106 KLVKIRDLSLVTPYVSVIGKITGITK-KEYD-SDGT---SKIVYQGYIEDDTARVRISSFGK---PLEDNRFVRIENARV 177 (358)
T ss_pred CccEeEeccCCCCceEEEEEEEEccC-ceEe-cCCC---ccEEEEEEEEcCCCeEEEEEccc---cccCCCEEEEeeeEE
Confidence 46799999999999999999999987 5776 4554 48999999999999999999997 479999999999999
Q ss_pred cccCCeEEEEeCCcEeEEEcCCCceEEcC
Q 032583 92 DMFKGSMRLAVDKWGRVEVAEPANFTVKE 120 (137)
Q Consensus 92 ~~~~g~~~L~vg~~g~I~~~~~~~~~vn~ 120 (137)
++|+|+++|+++++++|+.+ +..+++..
T Consensus 178 ~e~~G~~el~v~~~t~I~~~-~~~iev~~ 205 (358)
T PRK06386 178 SQYNGYIEISVGNKSVIKEV-ESDINLES 205 (358)
T ss_pred EccCCeEEEEeCCeEEEEEC-CCCcccCc
Confidence 99999999999999999999 55555544
No 8
>PRK07218 replication factor A; Provisional
Probab=99.86 E-value=2.8e-21 Score=165.25 Aligned_cols=102 Identities=23% Similarity=0.354 Sum_probs=91.5
Q ss_pred eeeeeccCCCCCCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecCCcCCCCCCCEEEEeceEE
Q 032583 12 VFTKVDQLRPGTSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARNDQVDLMKEGTTVILRNAKI 91 (137)
Q Consensus 12 ~~~kI~dL~p~~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~~~~~i~~Gd~v~I~na~~ 91 (137)
...+|.||.|++.+++++|+|++++ +++|.|+||+ ..|.+++|||+||+||||+|++++ .+++||+|+|.||++
T Consensus 161 ~~~kI~DL~~g~~~V~v~g~Vl~~~-~r~f~~~dg~----~~v~~giigDeTG~Ir~tlW~~~~-~l~~Gd~v~I~na~v 234 (423)
T PRK07218 161 GDKKLIDLGPGDRGVNVEARVLELE-HREIDGRDGE----TTILSGVLADETGRLPFTDWDPLP-EIEIGASIRIEDAYV 234 (423)
T ss_pred CccchhhccCCCCceEEEEEEEEec-ceeEEcCCCC----eEEEEEEEECCCceEEEEEecccc-cCCCCCEEEEeeeEE
Confidence 4568999999999999999999996 5899999985 579999999999999999999875 589999999999999
Q ss_pred cccCCeEEEEeCCcEeEEEcCCCceEEcC
Q 032583 92 DMFKGSMRLAVDKWGRVEVAEPANFTVKE 120 (137)
Q Consensus 92 ~~~~g~~~L~vg~~g~I~~~~~~~~~vn~ 120 (137)
++|+|+++|+++++++|+.++ ...++..
T Consensus 235 ~e~~G~~elnv~~~t~I~~~d-~~i~v~~ 262 (423)
T PRK07218 235 REFRGVPSVNVSEFTTVEALD-REVSVSK 262 (423)
T ss_pred eccCCeEEEEECCceEEEECC-CCccccC
Confidence 999999999999999999995 3445543
No 9
>PRK15491 replication factor A; Provisional
Probab=99.85 E-value=4.4e-21 Score=161.86 Aligned_cols=101 Identities=25% Similarity=0.368 Sum_probs=90.9
Q ss_pred CCCeeeeeccCCCCCCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecCCcC-----CCCCCCE
Q 032583 9 RKPVFTKVDQLRPGTSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARNDQVD-----LMKEGTT 83 (137)
Q Consensus 9 ~~~~~~kI~dL~p~~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~~~~-----~i~~Gd~ 83 (137)
..+.+.||+||.|++.+++|+|||++++++++|.|+||+. +++.+++|||+||+||||||+++++ .+++|++
T Consensus 53 ~~~~~~kI~dL~~~~~~v~i~arVl~~~~~R~f~r~dGs~---g~v~~~~v~DeTG~ir~tlW~~~a~~~~~~~le~G~v 129 (374)
T PRK15491 53 TGVDTTKIADINESSSNVNFTAKVVSIFEPKEFNRNDGTT---GRVGNIIVADETGSIRLTLWDDLADLIKTGDIEVGKS 129 (374)
T ss_pred cccccccHHHCCCCCCceEEEEEEeeccCCeeeecCCCCc---eEEEEEEEEcCCCeEEEEEECchhhhhccCCcCCCCE
Confidence 3567889999999999999999999999999999999975 9999999999999999999998763 4788999
Q ss_pred EEEeceEEcccCCeEEEEeCCcEeEEEcCC
Q 032583 84 VILRNAKIDMFKGSMRLAVDKWGRVEVAEP 113 (137)
Q Consensus 84 v~I~na~~~~~~g~~~L~vg~~g~I~~~~~ 113 (137)
|+|.++..+.|+| ++|++++.+.|.+.++
T Consensus 130 ~~I~~~~~~~y~g-~Ei~i~~~~~i~~~~~ 158 (374)
T PRK15491 130 LNISGYAKEGYSG-IEVNIGRYGGISESDE 158 (374)
T ss_pred EEEeeeeccCccc-EEEEeCCCceeeeccc
Confidence 9998776667777 8999999999998863
No 10
>PRK14699 replication factor A; Provisional
Probab=99.84 E-value=1.1e-20 Score=163.95 Aligned_cols=114 Identities=24% Similarity=0.323 Sum_probs=96.3
Q ss_pred CCeeeeeccCCCCCCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecCCcCC-----CCCCCEE
Q 032583 10 KPVFTKVDQLRPGTSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARNDQVDL-----MKEGTTV 84 (137)
Q Consensus 10 ~~~~~kI~dL~p~~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~~~~~-----i~~Gd~v 84 (137)
.+...||+||.|++.+++|+|||++++++++|.|+||+. ++++++.|||+||+||||||++.++. +++||+|
T Consensus 54 ~~~~~kI~di~~~~~~v~i~~rVl~i~~~r~f~r~dG~~---g~v~~~~iaDeTG~ir~tlW~~~a~~~~~g~l~~GDvv 130 (484)
T PRK14699 54 GRDSVKIENITPESGPVNFIARVVSVFDTKEFTRNDGTI---GRVGNLIVGDETGKIKLTLWDNMADLIKAGKIKAGQTL 130 (484)
T ss_pred ccccccHhHccCCCceEEEEEEEEEecCceEEecCCCCc---eEEEEEEEecCCCeEEEEEecCccchhhhcCCCCCCEE
Confidence 356789999999999999999999999999999999975 99999999999999999999988764 8999999
Q ss_pred EEeceEEcccCCeEEEEeCCcEeEEEcCCCceEEcC-CCCccccc
Q 032583 85 ILRNAKIDMFKGSMRLAVDKWGRVEVAEPANFTVKE-DNNLSLIE 128 (137)
Q Consensus 85 ~I~na~~~~~~g~~~L~vg~~g~I~~~~~~~~~vn~-~~n~S~~e 128 (137)
+|.|+ ++.+.+.++|++++.+.+...+ ..+++.. ..+++++.
T Consensus 131 ~I~~~-~r~~~~g~el~~~~~~~i~~~~-~~i~v~~~~~~I~dL~ 173 (484)
T PRK14699 131 QISGY-AKQGYSGVEVNIGNNGVLTESE-EEIDVAANSQKIKDIK 173 (484)
T ss_pred EEcce-eccCCCCceEEeCCCceeeccC-cccccCCCCcchhhcC
Confidence 99995 6666666999999999998874 3344422 34555554
No 11
>PRK07211 replication factor A; Reviewed
Probab=99.84 E-value=1.5e-20 Score=162.68 Aligned_cols=100 Identities=32% Similarity=0.405 Sum_probs=93.8
Q ss_pred CeeeeeccCCCCCCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecCCcCC---CCCCCEEEEe
Q 032583 11 PVFTKVDQLRPGTSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARNDQVDL---MKEGTTVILR 87 (137)
Q Consensus 11 ~~~~kI~dL~p~~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~~~~~---i~~Gd~v~I~ 87 (137)
..+.+|++|.|++.+++|+++|++++++++|.|+||+. ++++++.|+|+||+||||||+++++. +++|++|+|.
T Consensus 159 ~~~~~I~dL~~~~~~v~I~grV~~v~~iRtf~r~dGse---Gkv~sv~L~DeTG~IR~TlW~d~Ad~~~~le~G~Vv~I~ 235 (485)
T PRK07211 159 GDTYTVEDLSLGLSDVTLVGVVLDTDSVRTFDRDDGSE---GRVSNLTVGDETGRVRVTLWDDRADLAEELDAGESVEIV 235 (485)
T ss_pred cCCccHHHcCCCCCceEEEEEEEEcCCCeEEECCCCCe---eEEEEEEEEcCCCeEEEEEechhhhhhccCCCCCEEEEE
Confidence 37789999999999999999999999999999999975 99999999999999999999987654 6899999999
Q ss_pred ceEEcccCCeEEEEeCCcEeEEEcCC
Q 032583 88 NAKIDMFKGSMRLAVDKWGRVEVAEP 113 (137)
Q Consensus 88 na~~~~~~g~~~L~vg~~g~I~~~~~ 113 (137)
||+++.|+|.++|+++..+.|.+.++
T Consensus 236 ~a~Vre~~g~~ELsl~~~s~I~~~~d 261 (485)
T PRK07211 236 DGYVRERDGSLELHVGDRGAVEEVDE 261 (485)
T ss_pred eeEEEecCCcEEEEECCCceEEECCc
Confidence 99999999999999999999999865
No 12
>PRK14699 replication factor A; Provisional
Probab=99.84 E-value=2.2e-20 Score=161.97 Aligned_cols=98 Identities=30% Similarity=0.394 Sum_probs=90.2
Q ss_pred eeeeeccCCCCCCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecCCcCC---CCCCCEEEEec
Q 032583 12 VFTKVDQLRPGTSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARNDQVDL---MKEGTTVILRN 88 (137)
Q Consensus 12 ~~~kI~dL~p~~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~~~~~---i~~Gd~v~I~n 88 (137)
...+|+||.|++.++++.|||++++++++|.|+||+. ++|.+++|||+||+||||+|+++++. +++||+|+|.|
T Consensus 165 ~~~~I~dL~~~~~~V~i~gkVl~~~~~R~f~~~dG~~---g~v~~~~igDeTG~ir~tlW~~~a~~~~~l~~Gd~v~I~~ 241 (484)
T PRK14699 165 NSQKIKDIKDGMGDLNLTGKVLEISEIRTFQRKDGTS---GKVGNLLLGDETGTLRVTLWDDKTDFLNQIEYGDTVELIN 241 (484)
T ss_pred CCcchhhcCCCCCceEEEEEEEeccCceEEecCCCCc---eEEEEEEEEcCCceEEEEEECcccccccccCCCCEEEEec
Confidence 3469999999999999999999999999999999974 99999999999999999999987555 79999999999
Q ss_pred eEEcc--cCCeEEEEeCCcEeEEEcC
Q 032583 89 AKIDM--FKGSMRLAVDKWGRVEVAE 112 (137)
Q Consensus 89 a~~~~--~~g~~~L~vg~~g~I~~~~ 112 (137)
||++. |+|.++|++++.+.|...+
T Consensus 242 a~vr~~~~~~~~el~~~~~s~i~~~~ 267 (484)
T PRK14699 242 AYARENAFTQKVELQVGNRSIIRKSE 267 (484)
T ss_pred ceEeecccCCceEEEecCceEeeccc
Confidence 99975 7799999999999998875
No 13
>PRK12366 replication factor A; Reviewed
Probab=99.83 E-value=5.3e-20 Score=163.98 Aligned_cols=100 Identities=23% Similarity=0.356 Sum_probs=94.0
Q ss_pred CCeeeeeccCCCCCCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecCCcCC---CCCCCEEEE
Q 032583 10 KPVFTKVDQLRPGTSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARNDQVDL---MKEGTTVIL 86 (137)
Q Consensus 10 ~~~~~kI~dL~p~~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~~~~~---i~~Gd~v~I 86 (137)
.+.+.+|+||.|++.+++|+|||++++++++|.|+||+. ++|.++.|+|+||+||||+|++.++. +++||+|+|
T Consensus 60 ~~~~~~I~dl~p~~~~v~i~arV~~~~~~r~~~~~~G~e---Gkv~~~~v~DetG~Ir~t~W~~~~~~~~~le~G~v~~i 136 (637)
T PRK12366 60 EEEDFKISDIEEGQINVEITGRIIEISNIKTFTRKDGST---GKLANITIADNTGTIRLTLWNDNAKLLKGLKEGDVIKI 136 (637)
T ss_pred ccceeEHHHCcCCCcceEEEEEEEEccCCeEEECCCCCc---cEEEEEEEEcCCCEEEEEEEchhhhhhccCCCCCEEEE
Confidence 357899999999999999999999999999999999964 99999999999999999999987654 799999999
Q ss_pred eceEEcccCCeEEEEeCCcEeEEEcC
Q 032583 87 RNAKIDMFKGSMRLAVDKWGRVEVAE 112 (137)
Q Consensus 87 ~na~~~~~~g~~~L~vg~~g~I~~~~ 112 (137)
.||+++.|++.++|+++..++|.+.+
T Consensus 137 ~~~~v~~~~~~~el~~~~~t~I~~~~ 162 (637)
T PRK12366 137 ENARSRKWNNDVELNSGSETRIDKLE 162 (637)
T ss_pred eccEecccCCceEEEcCCcceEEEcc
Confidence 99999999999999999999999886
No 14
>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=99.80 E-value=1.1e-18 Score=117.45 Aligned_cols=80 Identities=33% Similarity=0.468 Sum_probs=74.1
Q ss_pred eEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecCC-cCCCCCCCEEEEeceEEcccCCeEEEEeCCc
Q 032583 27 TLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARNDQ-VDLMKEGTTVILRNAKIDMFKGSMRLAVDKW 105 (137)
Q Consensus 27 ~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~~-~~~i~~Gd~v~I~na~~~~~~g~~~L~vg~~ 105 (137)
++.|+|++++++++|. +||+ .+++.++.|+|+||+|++++|++. ...+++|++|+|.||+++.|+|.++|+++++
T Consensus 1 ~v~~~V~~~~~~~~~~-~~g~---~~~~~~~~l~D~TG~i~~~~W~~~~~~~~~~G~vv~i~~~~v~~~~g~~ql~i~~~ 76 (82)
T cd04491 1 SVEGKVLSISEPREFT-RDGS---EGKVQSGLVGDETGTIRFTLWDEKAADDLEPGDVVRIENAYVREFNGRLELSVGKN 76 (82)
T ss_pred CEEEEEEEccCCeEec-cCCC---eeEEEEEEEECCCCEEEEEEECchhcccCCCCCEEEEEeEEEEecCCcEEEEeCCc
Confidence 5899999999999998 6876 499999999999999999999976 5668999999999999999999999999999
Q ss_pred EeEEE
Q 032583 106 GRVEV 110 (137)
Q Consensus 106 g~I~~ 110 (137)
|.|+.
T Consensus 77 ~~i~~ 81 (82)
T cd04491 77 SEIEK 81 (82)
T ss_pred eEEEE
Confidence 99875
No 15
>PRK15491 replication factor A; Provisional
Probab=99.79 E-value=8.8e-19 Score=147.94 Aligned_cols=100 Identities=22% Similarity=0.344 Sum_probs=91.2
Q ss_pred CeeeeeccCCCCCCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecCCcC---CCCCCCEEEEe
Q 032583 11 PVFTKVDQLRPGTSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARNDQVD---LMKEGTTVILR 87 (137)
Q Consensus 11 ~~~~kI~dL~p~~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~~~~---~i~~Gd~v~I~ 87 (137)
..|.+|+||.+++.+++++|+|++++++++|.|++|+. ++++++.++|+||.||+|||+++++ .+++||+|+|.
T Consensus 164 ~~~~~I~dl~~~~~~V~I~g~V~~~~~~r~~~~~~G~~---~~v~~~~l~DetG~Ir~t~W~~~a~~~~~l~~Gd~V~i~ 240 (374)
T PRK15491 164 INSQKISDIKDGDSDINIVGKVLDISDVRTFQKKDGSQ---GRVRNITIGDETGKIRVTLWDGKTDLADKLENGDSVEII 240 (374)
T ss_pred cCcccHHHcCCCCccEEEEEEEEEccCceEEEecCCCe---EEEEEEEEECCCCeEEEEEecchhcccccCCCCCEEEEE
Confidence 35789999999999999999999999999999999864 8999999999999999999998766 47899999999
Q ss_pred ceEEcc--cCCeEEEEeCCcEeEEEcCC
Q 032583 88 NAKIDM--FKGSMRLAVDKWGRVEVAEP 113 (137)
Q Consensus 88 na~~~~--~~g~~~L~vg~~g~I~~~~~ 113 (137)
|||++. |+|.++|++++++.|.+.++
T Consensus 241 ~~~~r~~~~~g~~El~~~~~s~I~~~~~ 268 (374)
T PRK15491 241 NGYARTNNYSQEVEIQIGNHGSLRKTDR 268 (374)
T ss_pred eceEEEeccCCCEEEEeCCCceEEECCc
Confidence 999874 67999999999999998863
No 16
>PRK07211 replication factor A; Reviewed
Probab=99.75 E-value=9.3e-18 Score=145.47 Aligned_cols=98 Identities=22% Similarity=0.357 Sum_probs=84.8
Q ss_pred CCCCCeeeeeccCCCCCCCceEEEEEEEcceeeeeccCC-CccccceeEEEEEEeeCcceEEEEEecCCc----CCCCCC
Q 032583 7 GLRKPVFTKVDQLRPGTSGHTLTVKVVSTKMVLQKGRGD-GTQVRQMRIAECLVGDETGMIIFTARNDQV----DLMKEG 81 (137)
Q Consensus 7 ~l~~~~~~kI~dL~p~~~~v~l~~kVl~~~~~~~~~R~D-Gs~~~~~~v~~~~VgDeTG~I~ltlW~~~~----~~i~~G 81 (137)
+|......||++|.|++++++|+|||++++++++|.|+| |+ .++|+++.|+|+||.||+|||++++ +.+++|
T Consensus 47 elg~~e~~~I~dL~pg~~~vtI~aRV~~~~~~Rt~~~~~~~~---eGkv~~v~l~DeTG~Ir~TlW~d~ad~~~~~Le~G 123 (485)
T PRK07211 47 ELRDEEVNGIADIEPGMDEVKFLAKVLSIGDLRTFERDGEDE---DGRVINVEVADETGSVRVAFWDEQAVAAEEELEVG 123 (485)
T ss_pred HhCccccccHhhCCCCCCceEEEEEEeEccCceEEEeCCCCC---CcEEEEEEEEcCCCeEEEEEechHhHhhhcccCCC
Confidence 355567789999999999999999999999999999976 34 4999999999999999999999885 568999
Q ss_pred CEEEEeceEEcccCCeEEEEeCCcEeEEEc
Q 032583 82 TTVILRNAKIDMFKGSMRLAVDKWGRVEVA 111 (137)
Q Consensus 82 d~v~I~na~~~~~~g~~~L~vg~~g~I~~~ 111 (137)
|+|+|.|++.+.|++ ++|+++ .++.-
T Consensus 124 dV~~I~~~~~~~ys~-~El~i~---~ve~~ 149 (485)
T PRK07211 124 QVLRIKGRPKDGYNG-LEVSVD---KVEPD 149 (485)
T ss_pred CEEEEeceEeccccc-eEEEEe---eEEEc
Confidence 999999988777776 699999 35543
No 17
>PRK12366 replication factor A; Reviewed
Probab=99.71 E-value=5.8e-17 Score=144.63 Aligned_cols=99 Identities=21% Similarity=0.373 Sum_probs=90.5
Q ss_pred CeeeeeccCC---CCCCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecCCcCC-CCCCCEEEE
Q 032583 11 PVFTKVDQLR---PGTSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARNDQVDL-MKEGTTVIL 86 (137)
Q Consensus 11 ~~~~kI~dL~---p~~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~~~~~-i~~Gd~v~I 86 (137)
..|++|++|. ++...+++.|+|+++++++++.|+||++ ..+++++|+|+||+|+||||++++.. +.+|++|.|
T Consensus 393 ~~~~~i~dI~~~~~~~~~VdVig~V~~v~~~~~i~~k~G~~---~~~r~i~l~D~TG~I~vtlWg~~a~~~~~~G~vi~i 469 (637)
T PRK12366 393 EKIYKIKDILNLEEDDNDITVIARVVEDYPVNEFERSDGSK---GKVRNIELADGTGSIRLTLWDDDAEIEIKEGDAIKI 469 (637)
T ss_pred eccccHHHhhcccCCCcEEEEEEEEEEccCceEEEecCCCE---eEEEEEEEEeCCCEEEEEEeccccccCCCCCCEEEE
Confidence 4578888887 5677899999999999999999999864 89999999999999999999998865 789999999
Q ss_pred eceEEcccCCeEEEEeCCcEeEEEcC
Q 032583 87 RNAKIDMFKGSMRLAVDKWGRVEVAE 112 (137)
Q Consensus 87 ~na~~~~~~g~~~L~vg~~g~I~~~~ 112 (137)
.||+++.|+|+++|+++++|+|...|
T Consensus 470 ~~~~V~~~~g~~~Ls~~~~s~i~~~p 495 (637)
T PRK12366 470 LHPYVKENGDYLDLSIGRYGRIEINP 495 (637)
T ss_pred EeeEEEeCCCeeEEEecCcceEEECC
Confidence 99999999999999999999999886
No 18
>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=99.46 E-value=7.1e-13 Score=92.18 Aligned_cols=84 Identities=17% Similarity=0.223 Sum_probs=75.4
Q ss_pred ceEEEEEEEcceeeeeccCC-CccccceeEEEEEEeeCcc-eEEEEEecCCcCCCCC--CCEEEEeceEEcccCCeEEEE
Q 032583 26 HTLTVKVVSTKMVLQKGRGD-GTQVRQMRIAECLVGDETG-MIIFTARNDQVDLMKE--GTTVILRNAKIDMFKGSMRLA 101 (137)
Q Consensus 26 v~l~~kVl~~~~~~~~~R~D-Gs~~~~~~v~~~~VgDeTG-~I~ltlW~~~~~~i~~--Gd~v~I~na~~~~~~g~~~L~ 101 (137)
+++.|.|.++++++++.+++ |+ ....++..|+|+|| .+++|||++++..+.. |+++.|.|++++.|+ +.+|+
T Consensus 2 vDvig~V~~v~~~~~i~~k~~g~---~~~~r~v~i~D~t~~~i~vtLWg~~a~~~~~~~~~vv~~~~~~i~~~~-~~~l~ 77 (101)
T cd04475 2 VDVIGVVKSVGPVTTITTKSTGR---ELDKREITLVDESGHSVELTLWGEQAELFDGSENPVIAIKGVKVSEFN-GKSLS 77 (101)
T ss_pred EeEEEEEeEccCcEEEEEecCCC---ceeEEEEEEEeCCCCEEEEEEEHHHhhhcccCCCCEEEEEeeEEEecC-CeEEe
Confidence 68999999999999988777 75 48999999999999 9999999998877643 999999999999999 58999
Q ss_pred eCCcEeEEEcCC
Q 032583 102 VDKWGRVEVAEP 113 (137)
Q Consensus 102 vg~~g~I~~~~~ 113 (137)
.+..+.|...|+
T Consensus 78 ~~~~s~i~~np~ 89 (101)
T cd04475 78 TGSSSTIIINPD 89 (101)
T ss_pred ecCceeEEECCC
Confidence 999999988864
No 19
>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=99.46 E-value=6.1e-13 Score=93.73 Aligned_cols=90 Identities=18% Similarity=0.254 Sum_probs=74.7
Q ss_pred eeccCCCCCCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeC-cceEEEEEecCCcC----CCCCCCEEEEece
Q 032583 15 KVDQLRPGTSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDE-TGMIIFTARNDQVD----LMKEGTTVILRNA 89 (137)
Q Consensus 15 kI~dL~p~~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDe-TG~I~ltlW~~~~~----~i~~Gd~v~I~na 89 (137)
+|++|.|++.+..|+|||+.+++++.|...+| .+++.++.|.|+ +|.|+.++|++.++ .|++|+++.|.++
T Consensus 1 pI~~L~p~~~~~~I~~rV~~k~~~~~f~~~~~----~g~~~~~~l~De~~~~I~~t~~~~~~~~f~~~l~eG~vy~i~~~ 76 (104)
T cd04474 1 PISSLNPYQNKWTIKARVTNKSDIRTWSNARG----EGKLFSFDLLDEDGGEIRATFFNDAVDKFYDLLEVGKVYYISKG 76 (104)
T ss_pred ChhHccCCCCcEEEEEEEeeccccccccCCCC----CcEEEEEEEEECCCCEEEEEEehHHHHHhhcccccccEEEEecc
Confidence 48999999999999999999999999976654 389999999999 99999999987654 6899999999999
Q ss_pred EEcccC-------CeEEEEeCCcEeE
Q 032583 90 KIDMFK-------GSMRLAVDKWGRV 108 (137)
Q Consensus 90 ~~~~~~-------g~~~L~vg~~g~I 108 (137)
.++..+ .-.++.+++++.|
T Consensus 77 ~V~~a~~~y~~~~~~yeI~f~~~t~~ 102 (104)
T cd04474 77 SVKVANKKFNTLKNDYEITFNRDTSI 102 (104)
T ss_pred EEeeccccCCCCCCcEEEEECCCcEE
Confidence 997753 2345555554443
No 20
>COG1599 RFA1 Single-stranded DNA-binding replication protein A (RPA), large (70 kD) subunit and related ssDNA-binding proteins [DNA replication, recombination, and repair]
Probab=99.45 E-value=2.4e-13 Score=115.68 Aligned_cols=111 Identities=27% Similarity=0.347 Sum_probs=99.9
Q ss_pred CCCCCeeeeeccCCCCCCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEE-EEecCCcC-CCCCCCEE
Q 032583 7 GLRKPVFTKVDQLRPGTSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIF-TARNDQVD-LMKEGTTV 84 (137)
Q Consensus 7 ~l~~~~~~kI~dL~p~~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~l-tlW~~~~~-~i~~Gd~v 84 (137)
.+..+...+|.++.+++.+++++++|++++++..+.|++|.. +.+.+.++||+||++++ ++|...+. ..++||++
T Consensus 43 ~~~~~~~~~i~~~~~~~~~~~v~~~V~~~~e~~~~~~k~g~~---~~l~~~~v~Detg~v~~~~~~~~~a~~~~e~Gdv~ 119 (407)
T COG1599 43 VLAMESIGKISDISEASSRVNVTGRVLSIGEKKTFDRKRGAE---GKLAEVLVGDETGSVKTVTLWNIAALEKLEPGDVI 119 (407)
T ss_pred hhchhhcccccccchhhccccEEEEECccccceeeecccccc---cceEEEEEecCCCCEEEEeeccccccccCCccceE
Confidence 356678899999999999999999999999999999999974 89999999999999999 79998776 68999999
Q ss_pred EEeceEEcccCCeEEEEeCCcEeEEEcCCCceEEcC
Q 032583 85 ILRNAKIDMFKGSMRLAVDKWGRVEVAEPANFTVKE 120 (137)
Q Consensus 85 ~I~na~~~~~~g~~~L~vg~~g~I~~~~~~~~~vn~ 120 (137)
+|.|++++.|.|++++++++.+.+...+++...+..
T Consensus 120 ~i~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~ 155 (407)
T COG1599 120 RIRNAYTSLYRGGKRLSVGRVGSVADVDDEEDEARE 155 (407)
T ss_pred EecCcccccccCceeeecccccccccCchhhccccc
Confidence 999999999999999999999999988765544433
No 21
>TIGR00617 rpa1 replication factor-a protein 1 (rpa1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.18 E-value=1.8e-10 Score=102.78 Aligned_cols=98 Identities=19% Similarity=0.275 Sum_probs=87.0
Q ss_pred eeeeeccCCCCCCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecCCc----CCCCCCCEEEEe
Q 032583 12 VFTKVDQLRPGTSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARNDQV----DLMKEGTTVILR 87 (137)
Q Consensus 12 ~~~kI~dL~p~~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~~~----~~i~~Gd~v~I~ 87 (137)
.+.+|++|.|.+.+..|+|||+.+++.++|...+| .+++.++.+.|++|.|+.++|++.+ +.|++|++|.|.
T Consensus 179 ~~~pI~~L~py~~~wtIkaRV~~Ks~ir~~~~~~g----egkvfsv~L~Degg~Irat~f~~~~dkf~~~l~eG~VY~Is 254 (608)
T TIGR00617 179 RVMPIASLSPYQNKWTIKARVTNKSEIRTWSNARG----EGKLFNVELLDESGEIRATAFNEQADKFYDIIQEGKVYYIS 254 (608)
T ss_pred ceEEHHHCCCCCCceEEEEEEEeccccceecCCCC----CceeeEEEEecCCCeEEEEECchHHHHHhhhcccCCEEEEC
Confidence 58999999999999999999999999999987776 3799999999999999999999865 557999999999
Q ss_pred ceEEcccC-------CeEEEEeCCcEeEEEcCC
Q 032583 88 NAKIDMFK-------GSMRLAVDKWGRVEVAEP 113 (137)
Q Consensus 88 na~~~~~~-------g~~~L~vg~~g~I~~~~~ 113 (137)
++.++..+ ...+|.+++++.|++.++
T Consensus 255 ~~~Vk~an~~y~~~~~~yei~f~~~T~I~~~~d 287 (608)
T TIGR00617 255 KGSLKPANKQFTNLGNDYEMTLDRDTVIEECED 287 (608)
T ss_pred ceEEEEccccccCCCCCEEEEECCCeEEEECCC
Confidence 99987643 358999999999998753
No 22
>TIGR00617 rpa1 replication factor-a protein 1 (rpa1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.01 E-value=2e-09 Score=96.09 Aligned_cols=98 Identities=15% Similarity=0.162 Sum_probs=84.0
Q ss_pred CeeeeeccCCCC--CCCceEEEEEEEcceeeeec-cCCCccccceeEEEEEEeeCcc-eEEEEEecCCcCCC--CCCCEE
Q 032583 11 PVFTKVDQLRPG--TSGHTLTVKVVSTKMVLQKG-RGDGTQVRQMRIAECLVGDETG-MIIFTARNDQVDLM--KEGTTV 84 (137)
Q Consensus 11 ~~~~kI~dL~p~--~~~v~l~~kVl~~~~~~~~~-R~DGs~~~~~~v~~~~VgDeTG-~I~ltlW~~~~~~i--~~Gd~v 84 (137)
-.|++|.||... ...++|.|.|.+++++.++. |.+|+ ....+++.|.|+|| +|++|||++++..+ .+|++|
T Consensus 296 ~~f~~i~dI~~~~~~~~VDVIGvV~~v~~~~~i~~k~~g~---~~~kR~i~L~D~sg~sI~vTLWG~~A~~~~~~~~~Vv 372 (608)
T TIGR00617 296 FNFVKIDDIGGYEGNSLVDVIGIVQSVSPTQTITSRKNNK---EFPKRDITLVDDSGKSVRVTLWGDDATKFDVSVQPVI 372 (608)
T ss_pred ccceEHHHhhhhcCCCCccEEEEEeEecCceEEEEcCCCC---eeeeEEEEEEeCCCCEEEEEEEhhhhhhcCCCCCCEE
Confidence 468899999754 34689999999999998876 77876 48889999999999 69999999987554 689999
Q ss_pred EEeceEEcccCCeEEEEeCCcEeEEEcC
Q 032583 85 ILRNAKIDMFKGSMRLAVDKWGRVEVAE 112 (137)
Q Consensus 85 ~I~na~~~~~~g~~~L~vg~~g~I~~~~ 112 (137)
.|.++.++.|+| .+|+.+..+.|...+
T Consensus 373 a~kg~~V~~f~g-~sLs~~~~S~i~iNP 399 (608)
T TIGR00617 373 AIKGVRVSDFGG-KSLSTGGSSTIIVNP 399 (608)
T ss_pred EEEeEEEEecCC-ceEeccCCceEEECC
Confidence 999999999955 699999999997765
No 23
>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=98.52 E-value=6.2e-07 Score=57.70 Aligned_cols=67 Identities=28% Similarity=0.322 Sum_probs=53.8
Q ss_pred ceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEec----CCcCCCCCCCEEEEeceEEcccCCe-EEE
Q 032583 26 HTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARN----DQVDLMKEGTTVILRNAKIDMFKGS-MRL 100 (137)
Q Consensus 26 v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~----~~~~~i~~Gd~v~I~na~~~~~~g~-~~L 100 (137)
|.+.|+|.++. +. .+.+..+.+.|+||++.+.+|+ ...+.+++|+.|++. |.++.+++. ++|
T Consensus 1 V~v~G~V~~~~--~~----------~~~~~~~~l~D~tg~i~~~~~~~~~~~~~~~l~~g~~v~v~-G~v~~~~~~~~~l 67 (75)
T PF01336_consen 1 VTVEGRVTSIR--RS----------GGKIVFFTLEDGTGSIQVVFFNEEYERFREKLKEGDIVRVR-GKVKRYNGGELEL 67 (75)
T ss_dssp EEEEEEEEEEE--EE----------ETTEEEEEEEETTEEEEEEEETHHHHHHHHTS-TTSEEEEE-EEEEEETTSSEEE
T ss_pred CEEEEEEEEEE--cC----------CCCEEEEEEEECCccEEEEEccHHhhHHhhcCCCCeEEEEE-EEEEEECCccEEE
Confidence 46888998876 11 2578889999999999999999 245678999999999 888888887 999
Q ss_pred EeCCc
Q 032583 101 AVDKW 105 (137)
Q Consensus 101 ~vg~~ 105 (137)
.+.+.
T Consensus 68 ~~~~i 72 (75)
T PF01336_consen 68 IVPKI 72 (75)
T ss_dssp EEEEE
T ss_pred EECEE
Confidence 87653
No 24
>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=98.44 E-value=2.2e-06 Score=63.16 Aligned_cols=86 Identities=15% Similarity=0.194 Sum_probs=71.0
Q ss_pred eeeeeccCC-CCCCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcce----EEEEEecCC---cCCCCCCCE
Q 032583 12 VFTKVDQLR-PGTSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGM----IIFTARNDQ---VDLMKEGTT 83 (137)
Q Consensus 12 ~~~kI~dL~-p~~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~----I~ltlW~~~---~~~i~~Gd~ 83 (137)
.|++|++|. .....+|+.|-|++..++... .|+ .-+++..|.|+|+. +++.+|.+. ...+.+||+
T Consensus 2 ~f~~i~~~~~~~~~~v~vigVV~~~~~p~~s---~g~----d~~~tl~i~D~S~~~~~~l~v~~F~~~~~~LP~v~~GDV 74 (138)
T cd04497 2 KYTPLSSALKESGGSVNVIGVVVDAGPPVRS---KGT----DYCCTLTITDPSLANSDGLTVKLFRPNEESLPIVKVGDI 74 (138)
T ss_pred ceEeHHHHHhccCCeEEEEEEEeecCCCccc---CCC----cEEEEEEEECCCCCCCCcEEEEEECCChhhCCCCCCCCE
Confidence 578899988 445568999999999987643 342 48889999999875 999999864 343589999
Q ss_pred EEEeceEEcccCCeEEEEeCC
Q 032583 84 VILRNAKIDMFKGSMRLAVDK 104 (137)
Q Consensus 84 v~I~na~~~~~~g~~~L~vg~ 104 (137)
|.++++.++.|+|++.+..+.
T Consensus 75 Ill~~~kv~~~~g~~~~~~~~ 95 (138)
T cd04497 75 ILLRRVKIQSYNGKPQGISND 95 (138)
T ss_pred EEEEEEEEEEECCceEEEECC
Confidence 999999999999999988887
No 25
>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=98.02 E-value=5.6e-05 Score=52.33 Aligned_cols=62 Identities=18% Similarity=0.272 Sum_probs=48.6
Q ss_pred EEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecCC------------------------cCCCCCCCE
Q 032583 28 LTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARNDQ------------------------VDLMKEGTT 83 (137)
Q Consensus 28 l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~~------------------------~~~i~~Gd~ 83 (137)
|.+.|.++.+. ..-....|.|.||+|...+|+.. ++.+++|+.
T Consensus 2 ivG~V~sv~~~-------------~~~~~~tLdDgTG~Ie~~~W~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~G~v 68 (92)
T cd04483 2 ILGTVVSRRER-------------ETFYSFGVDDGTGVVNCVCWKNLSYAEVSSRSDAARILKSALMALKQAKVLEIGDL 68 (92)
T ss_pred eEEEEEEEEec-------------CCeEEEEEecCCceEEEEEEcCcCcccccccccccccccccccccccccccCCCCE
Confidence 67788887543 23356789999999999999842 234799999
Q ss_pred EEEeceEEcccCCeEEEEeC
Q 032583 84 VILRNAKIDMFKGSMRLAVD 103 (137)
Q Consensus 84 v~I~na~~~~~~g~~~L~vg 103 (137)
++++ |.++.|+|.++|++.
T Consensus 69 vrV~-G~i~~frg~~ql~i~ 87 (92)
T cd04483 69 LRVR-GSIRTYRGEREINAS 87 (92)
T ss_pred EEEE-EEEeccCCeeEEEEE
Confidence 9999 566899999999875
No 26
>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=97.92 E-value=0.0002 Score=48.72 Aligned_cols=70 Identities=21% Similarity=0.182 Sum_probs=52.8
Q ss_pred ceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecCC-------cCCCCCCCEEEEeceEEcccCCeE
Q 032583 26 HTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARNDQ-------VDLMKEGTTVILRNAKIDMFKGSM 98 (137)
Q Consensus 26 v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~~-------~~~i~~Gd~v~I~na~~~~~~g~~ 98 (137)
+.+.+.|.++... ..-....+.|.||+|....|+.. .+.+++|+.+++.+-. +.|+|.+
T Consensus 2 v~~vG~V~~~~~~-------------~~~~~~tL~D~TG~I~~~~W~~~~~~~~~~~~~~~~g~~v~v~G~v-~~~~g~~ 67 (95)
T cd04478 2 VTLVGVVRNVEEQ-------------STNITYTIDDGTGTIEVRQWLDDDNDDSSEVEPIEEGTYVRVFGNL-KSFQGKK 67 (95)
T ss_pred EEEEEEEEeeeEc-------------ccEEEEEEECCCCcEEEEEeCCCCCcccccccccccCCEEEEEEEE-cccCCee
Confidence 5677888876543 23466789999999999999732 3447999999998766 7889999
Q ss_pred EEEeCCcEeEEEcC
Q 032583 99 RLAVDKWGRVEVAE 112 (137)
Q Consensus 99 ~L~vg~~g~I~~~~ 112 (137)
+|.+. .|.+++
T Consensus 68 ql~i~---~i~~v~ 78 (95)
T cd04478 68 SIMAF---SIRPVT 78 (95)
T ss_pred EEEEE---EEEEeC
Confidence 99865 444443
No 27
>cd03524 RPA2_OBF_family RPA2_OBF_family: A family of oligonucleotide binding (OB) folds with similarity to the OB fold of the single strand (ss) DNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA contains six OB folds, which are involved in ssDNA binding and in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. This family also includes OB folds similar to those found in Escherichia coli SSB, the wedge domain of E. coli RecG (a branched-DNA-specific helicase), E. coli ssDNA specific exodeoxyribonuclease VII large subunit, Pyroco
Probab=97.89 E-value=0.00013 Score=45.34 Aligned_cols=65 Identities=26% Similarity=0.420 Sum_probs=52.1
Q ss_pred EEEEEEEcceeeeeccCCCccccceeEEEEEEeeCc-ceEEEEEecCCc----CCCCCCCEEEEeceEEcccCCeEEEEe
Q 032583 28 LTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDET-GMIIFTARNDQV----DLMKEGTTVILRNAKIDMFKGSMRLAV 102 (137)
Q Consensus 28 l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeT-G~I~ltlW~~~~----~~i~~Gd~v~I~na~~~~~~g~~~L~v 102 (137)
+.+.|.++..... | ..+..+.|.|.| |.+.+.+|.+.. ..+++|+.+.+. +.++.+++.++|.+
T Consensus 2 v~g~v~~~~~~~~-----~-----~~~~~~~l~D~~~~~i~~~~~~~~~~~~~~~~~~g~~v~v~-g~v~~~~~~~~l~~ 70 (75)
T cd03524 2 IVGIVVAVEEIRT-----E-----GKVLIFTLTDGTGGTIRVTLFGELAEELENLLKEGQVVYIK-GKVKKFRGRLQLIV 70 (75)
T ss_pred eEEEEEeeccccc-----C-----CeEEEEEEEcCCCCEEEEEEEchHHHHHHhhccCCCEEEEE-EEEEecCCeEEEEe
Confidence 6788888766542 3 357889999999 999999998653 357999999999 77777888888876
Q ss_pred C
Q 032583 103 D 103 (137)
Q Consensus 103 g 103 (137)
.
T Consensus 71 ~ 71 (75)
T cd03524 71 E 71 (75)
T ss_pred e
Confidence 5
No 28
>PRK13480 3'-5' exoribonuclease YhaM; Provisional
Probab=97.76 E-value=0.00012 Score=61.11 Aligned_cols=80 Identities=15% Similarity=0.172 Sum_probs=61.9
Q ss_pred eeccCCCCCCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecC---CcCCCCCCCEEEEeceEE
Q 032583 15 KVDQLRPGTSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARND---QVDLMKEGTTVILRNAKI 91 (137)
Q Consensus 15 kI~dL~p~~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~---~~~~i~~Gd~v~I~na~~ 91 (137)
+|++|++|.. ++..+.|-++.. ++ . ++| .....+.++|.||+|+..+|+. ....+++|++|++.+-.
T Consensus 4 ~i~~l~~g~~-v~~~~lv~~~~~-~~-~-knG-----~~yl~l~l~D~tG~I~ak~W~~~~~~~~~~~~g~vv~v~G~v- 73 (314)
T PRK13480 4 GIEELEVGEQ-VDHFLLIKSATK-GV-A-SNG-----KPFLTLILQDKSGDIEAKLWDVSPEDEATYVPETIVHVKGDI- 73 (314)
T ss_pred hHhhcCCCCE-eeEEEEEEEcee-ee-c-CCC-----CeEEEEEEEcCCcEEEEEeCCCChhhHhhcCCCCEEEEEEEE-
Confidence 7999999864 677776666543 22 2 355 3578899999999999999994 34558999999998776
Q ss_pred cccCCeEEEEeCC
Q 032583 92 DMFKGSMRLAVDK 104 (137)
Q Consensus 92 ~~~~g~~~L~vg~ 104 (137)
..|+|.++|+|.+
T Consensus 74 ~~y~g~~Ql~i~~ 86 (314)
T PRK13480 74 INYRGRKQLKVNQ 86 (314)
T ss_pred EEECCcceEEEEE
Confidence 5799999998763
No 29
>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=97.66 E-value=0.00034 Score=48.95 Aligned_cols=82 Identities=13% Similarity=0.087 Sum_probs=65.0
Q ss_pred eEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcc-eEEEEEecCCcCCC--------CCCCEEEEec-eEEcccCC
Q 032583 27 TLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETG-MIIFTARNDQVDLM--------KEGTTVILRN-AKIDMFKG 96 (137)
Q Consensus 27 ~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG-~I~ltlW~~~~~~i--------~~Gd~v~I~n-a~~~~~~g 96 (137)
++.+.|.++++...+.++ |. ...-++..|-|.+| ++.++||+++|..+ ..+-+|-|.. +.++.|+|
T Consensus 1 DviG~i~~v~~~~~~~~~-~~---~~~kr~~~i~D~~~~~l~~tlwG~~A~~f~~~~~~~~~~~~VVav~~~~rV~~~~g 76 (106)
T cd04481 1 DVIGVIVDVGPLEELPPV-NK---PSRKLDFEIRDLSDERLKCTLWGEYAEEFDAKFQSAGNGEPVVAVLRFWKIKEYKG 76 (106)
T ss_pred CeeEEEEEecceEecccC-Cc---cceEEEEEEEeCCCCEEEEEEEHHHHHHHHHHHHHhCCCCcEEEEEEeEEEEEEcC
Confidence 478899999998877665 53 47888999999996 99999999887653 3566776755 99999999
Q ss_pred eEEEEeC-CcEeEEEcC
Q 032583 97 SMRLAVD-KWGRVEVAE 112 (137)
Q Consensus 97 ~~~L~vg-~~g~I~~~~ 112 (137)
...|+-. ..+++...|
T Consensus 77 ~~~ls~~~~~s~v~inp 93 (106)
T cd04481 77 PKSLSNSFGASKVYINP 93 (106)
T ss_pred CcEEEcCCCceEEEECC
Confidence 7888887 667776664
No 30
>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=97.66 E-value=0.00037 Score=45.38 Aligned_cols=51 Identities=18% Similarity=0.347 Sum_probs=41.5
Q ss_pred eeEEEEEEeeCcceEEEEEecCC---cCCCCCCCEEEEeceEEcccCCeEEEEeC
Q 032583 52 MRIAECLVGDETGMIIFTARNDQ---VDLMKEGTTVILRNAKIDMFKGSMRLAVD 103 (137)
Q Consensus 52 ~~v~~~~VgDeTG~I~ltlW~~~---~~~i~~Gd~v~I~na~~~~~~g~~~L~vg 103 (137)
..+..+.+.|.||.+.+++|++. ...+++|..+.+.+ .++.++|.+++.+.
T Consensus 18 ~~~~~~~l~D~tg~i~~~~f~~~~~~~~~l~~g~~v~v~G-~v~~~~~~~~l~~~ 71 (83)
T cd04492 18 KPYLALTLQDKTGEIEAKLWDASEEDEEKFKPGDIVHVKG-RVEEYRGRLQLKIQ 71 (83)
T ss_pred CcEEEEEEEcCCCeEEEEEcCCChhhHhhCCCCCEEEEEE-EEEEeCCceeEEEE
Confidence 36899999999999999999954 24579999999994 55667888888754
No 31
>cd04480 RPA1_DBD_A_like RPA1_DBD_A_like: A subgroup of uncharacterized plant OB folds with similarity to the second OB fold, the ssDNA-binding domain (DBD)-A, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of RPA is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change.
Probab=97.42 E-value=0.0006 Score=45.92 Aligned_cols=63 Identities=25% Similarity=0.236 Sum_probs=51.8
Q ss_pred EEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcc-eEEEEEecCC----cCCCCCCCEEEEeceEEcccCCeE
Q 032583 28 LTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETG-MIIFTARNDQ----VDLMKEGTTVILRNAKIDMFKGSM 98 (137)
Q Consensus 28 l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG-~I~ltlW~~~----~~~i~~Gd~v~I~na~~~~~~g~~ 98 (137)
|.+||+.+|...... .+...++++.|+.| .|..+.+.+. .+.+++|.++.|.|..+...++..
T Consensus 2 I~Vrv~r~W~~~~~~--------~~~~~~miL~De~G~~I~a~i~~~~~~~f~~~L~eg~vy~is~f~v~~~~~~y 69 (86)
T cd04480 2 ICVRVLRLWDVYNNA--------SGESLEMVLVDEKGNRIHATIPKRLAAKFRPLLKEGKWYTISNFEVAPNTGSY 69 (86)
T ss_pred EEEEEEEEEcCcCCC--------CCcEEEEEEEcCCCCEEEEEECHHHHHhhhhhceeCCEEEEeeEEEEcCCCcc
Confidence 789999999876532 26889999999999 9999999864 456799999999998887765433
No 32
>COG1599 RFA1 Single-stranded DNA-binding replication protein A (RPA), large (70 kD) subunit and related ssDNA-binding proteins [DNA replication, recombination, and repair]
Probab=97.36 E-value=0.0012 Score=56.43 Aligned_cols=65 Identities=17% Similarity=0.265 Sum_probs=54.6
Q ss_pred EEEEEEcceeeeeccCCCccccceeEEEEEEeeCc-ceEEEEEecCCcCCCCCCCEEEEeceEEcccCCeEEEE
Q 032583 29 TVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDET-GMIIFTARNDQVDLMKEGTTVILRNAKIDMFKGSMRLA 101 (137)
Q Consensus 29 ~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeT-G~I~ltlW~~~~~~i~~Gd~v~I~na~~~~~~g~~~L~ 101 (137)
.++|+.-.+.++|.+++|. +.+.+..+.|+| |.++|+.|++. +.|+++.+.++.++++++.++.+
T Consensus 173 ~~~v~~g~~ik~~~~~~ge----~~~~~~~~~d~~~~~~~~~~~~~~----~~g~~~~ie~~~v~~~~~~~~~~ 238 (407)
T COG1599 173 KARVVVGSEIKTFDNQGGE----SKVFSNELEDEERGVIVFTDWDPS----QDGDVYRIEGARVKTKNKQPEEN 238 (407)
T ss_pred eEEEEecccceeEecCCCc----cceEeeeecccceeEEEeccCccc----ccceeeeecCcEEEEeccccccc
Confidence 7899999999999887774 778888888887 99999999976 67888888888888887776664
No 33
>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=97.27 E-value=0.0029 Score=39.94 Aligned_cols=64 Identities=25% Similarity=0.360 Sum_probs=46.9
Q ss_pred EEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEec-C--CcCCCCCCCEEEEeceEEcccCCeEEEE
Q 032583 28 LTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARN-D--QVDLMKEGTTVILRNAKIDMFKGSMRLA 101 (137)
Q Consensus 28 l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~-~--~~~~i~~Gd~v~I~na~~~~~~g~~~L~ 101 (137)
+.|+|++..... .+ | ..+..+.+.|++|.+.++.|+ . ....+++|+.+.+.|-. +.++|.+++.
T Consensus 2 i~~~V~~~~~~~--~~--~-----~~~~~~~~~D~~g~i~~~~F~~~~~~~~~~~~G~~~~v~Gkv-~~~~~~~qi~ 68 (75)
T cd04488 2 VEGTVVSVEVVP--RR--G-----RRRLKVTLSDGTGTLTLVFFNFQPYLKKQLPPGTRVRVSGKV-KRFRGGLQIV 68 (75)
T ss_pred EEEEEEEEEecc--CC--C-----ccEEEEEEEcCCCEEEEEEECCCHHHHhcCCCCCEEEEEEEE-eecCCeeEEe
Confidence 677887764322 11 2 357889999999999999998 3 24568999999998666 5567777663
No 34
>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=97.21 E-value=0.0045 Score=45.75 Aligned_cols=83 Identities=16% Similarity=0.096 Sum_probs=63.8
Q ss_pred CCCCceEEEEEEEccee--eeeccCCCccccceeEEEEEEeeCc--------ceEEEEEecC---CcCCCCC-CCEEEEe
Q 032583 22 GTSGHTLTVKVVSTKMV--LQKGRGDGTQVRQMRIAECLVGDET--------GMIIFTARND---QVDLMKE-GTTVILR 87 (137)
Q Consensus 22 ~~~~v~l~~kVl~~~~~--~~~~R~DGs~~~~~~v~~~~VgDeT--------G~I~ltlW~~---~~~~i~~-Gd~v~I~ 87 (137)
...-+|+.|-|++...+ ... | |+ .-+.+..|-|.| -.+.+.++.. ....++. ||+|.++
T Consensus 11 ~~~~vnvigVV~~~~~p~~~~t-~--g~----D~~~tl~i~D~S~~~~~~~~~~l~v~iF~~~~~~LP~v~~~GDii~l~ 83 (146)
T PF02765_consen 11 FGKFVNVIGVVVDFSPPNPKKT-R--GT----DYMCTLTITDPSLNDSNQKLSGLTVNIFRPHKESLPNVKSVGDIIRLR 83 (146)
T ss_dssp SSEEEEEEEEEEEEEEECTEEE-S--SS----CEEEEEEEEBTTCSCSSCCCCEEEEEEEESSHHHSCTTCSTTHEEEEE
T ss_pred CCCEEEEEEEEEEccCCcceEc-C--CC----cEEEEEEEECCCCCccccccCCEEEEEECCCHHHCCCCCCCCCEEEEE
Confidence 34568999999999888 443 2 32 688899999998 4799999953 3444555 9999999
Q ss_pred ceEEcccCCeEEEEeCCc--EeEEEc
Q 032583 88 NAKIDMFKGSMRLAVDKW--GRVEVA 111 (137)
Q Consensus 88 na~~~~~~g~~~L~vg~~--g~I~~~ 111 (137)
+..++.|+|++.+..+.. .....-
T Consensus 84 r~kv~~~~~~~~~~~~~~~~ss~~vf 109 (146)
T PF02765_consen 84 RVKVQSYNGKPQGLSNSTSNSSWAVF 109 (146)
T ss_dssp EEEEEEETTEEEEEEECECTEEEEEE
T ss_pred EEEEEEECCEEEEEecCCCcEEEEEE
Confidence 999999999999888776 444333
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=97.21 E-value=0.0033 Score=40.37 Aligned_cols=51 Identities=25% Similarity=0.350 Sum_probs=41.2
Q ss_pred eeEEEEEEeeCcceEEEEEecCC----cCCCCCCCEEEEeceEEcccCCeEEEEeC
Q 032583 52 MRIAECLVGDETGMIIFTARNDQ----VDLMKEGTTVILRNAKIDMFKGSMRLAVD 103 (137)
Q Consensus 52 ~~v~~~~VgDeTG~I~ltlW~~~----~~~i~~Gd~v~I~na~~~~~~g~~~L~vg 103 (137)
..+..+.+.|.||.+.+++|++. .+.+++|..+.+.+-. +.++|.++|.+.
T Consensus 18 ~~~~~~~l~D~tg~~~~~~f~~~~~~~~~~l~~g~~v~v~G~v-~~~~~~~~l~~~ 72 (84)
T cd04485 18 KRMAFVTLEDLTGSIEVVVFPETYEKYRDLLKEDALLLVEGKV-ERRDGGLRLIAE 72 (84)
T ss_pred CEEEEEEEEeCCCeEEEEECHHHHHHHHHHhcCCCEEEEEEEE-EecCCceEEEee
Confidence 36889999999999999999843 3457999999998655 557788888765
No 36
>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=96.75 E-value=0.02 Score=37.11 Aligned_cols=65 Identities=17% Similarity=0.088 Sum_probs=48.6
Q ss_pred eEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecCC----cCCCCCCCEEEEeceEEc-ccCCeEEEE
Q 032583 27 TLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARNDQ----VDLMKEGTTVILRNAKID-MFKGSMRLA 101 (137)
Q Consensus 27 ~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~~----~~~i~~Gd~v~I~na~~~-~~~g~~~L~ 101 (137)
.+.+.|.++.. .| .+ ++-+.+-|.+|.+.+++|.+. ...+++|+.|.+.+.... .+++.++|.
T Consensus 3 ~v~g~v~~i~~----tk-------~g-~~~~~L~D~~~~i~~~~f~~~~~~~~~~l~~g~~v~v~g~v~~~~~~~~~~l~ 70 (78)
T cd04489 3 WVEGEISNLKR----PS-------SG-HLYFTLKDEDASIRCVMWRSNARRLGFPLEEGMEVLVRGKVSFYEPRGGYQLI 70 (78)
T ss_pred EEEEEEecCEE----CC-------Cc-EEEEEEEeCCeEEEEEEEcchhhhCCCCCCCCCEEEEEEEEEEECCCCEEEEE
Confidence 45666666543 11 25 888999999999999999863 245799999999988773 346788887
Q ss_pred eC
Q 032583 102 VD 103 (137)
Q Consensus 102 vg 103 (137)
+.
T Consensus 71 v~ 72 (78)
T cd04489 71 VE 72 (78)
T ss_pred EE
Confidence 74
No 37
>PRK08402 replication factor A; Reviewed
Probab=95.19 E-value=0.037 Score=47.02 Aligned_cols=67 Identities=18% Similarity=0.114 Sum_probs=48.4
Q ss_pred CeeeeeccCCCCCCCceEEEEEEEccee----------eeeccCCCc-----------cccceeEEEEEEeeCcceEEEE
Q 032583 11 PVFTKVDQLRPGTSGHTLTVKVVSTKMV----------LQKGRGDGT-----------QVRQMRIAECLVGDETGMIIFT 69 (137)
Q Consensus 11 ~~~~kI~dL~p~~~~v~l~~kVl~~~~~----------~~~~R~DGs-----------~~~~~~v~~~~VgDeTG~I~lt 69 (137)
....+|+++.++...++++|.|+.+... +.+.+.+|+ .....-+.++.|.|.||.++++
T Consensus 182 ~~~k~I~ei~~gd~~v~v~g~Iv~i~~~~~y~aCp~CnKkv~~~~~~~~~~Ce~~~~v~p~~ryil~~~l~D~TG~~~vt 261 (355)
T PRK08402 182 YTRKKIGELEGGERFVEVRGTIAKVYRVLVYDACPECRRKVDYDPATDTWICPEHGEVEPIKITILDFGLDDGTGYIRVT 261 (355)
T ss_pred ccccCHHHcccCCcEEEEEEEEEEEecCeeEecCCCCCeEEEEecCCCCEeCCCCCCcCcceeEEEEEEEEcCCCcEEEE
Confidence 4568899999998889999999998861 222211111 1123456679999999999999
Q ss_pred EecCCcCC
Q 032583 70 ARNDQVDL 77 (137)
Q Consensus 70 lW~~~~~~ 77 (137)
||++++..
T Consensus 262 ~f~e~ae~ 269 (355)
T PRK08402 262 LFGDDAAE 269 (355)
T ss_pred EecHHHHH
Confidence 99987643
No 38
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=94.98 E-value=0.13 Score=46.72 Aligned_cols=77 Identities=23% Similarity=0.263 Sum_probs=57.9
Q ss_pred eeeeeccCCCCCCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEe--c-CC-cCCCCCCCEEEEe
Q 032583 12 VFTKVDQLRPGTSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTAR--N-DQ-VDLMKEGTTVILR 87 (137)
Q Consensus 12 ~~~kI~dL~p~~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW--~-~~-~~~i~~Gd~v~I~ 87 (137)
...+|.++.+|.. +.+.++|.+..... + + ..+..+.+.|+||.+.++.+ + .. ...+++|+.+.+.
T Consensus 49 ~~~~i~~l~~g~~-vtv~g~V~~~~~~~---~--~-----~~~~~v~l~D~tg~i~l~~F~~n~~~~~~~l~~G~~~~v~ 117 (681)
T PRK10917 49 RLKPIAELRPGEK-VTVEGEVLSAEVVF---G--K-----RRRLTVTVSDGTGNLTLRFFNFNQPYLKKQLKVGKRVAVY 117 (681)
T ss_pred CcCCHHHCCCCCE-EEEEEEEEEEEEcc---C--C-----ceEEEEEEEECCeEEEEEEEccCcHHHHhhCCCCCEEEEE
Confidence 3568899999864 89999999873321 1 2 35888999999999999999 3 22 4668999999999
Q ss_pred ceEEcccCCeEEE
Q 032583 88 NAKIDMFKGSMRL 100 (137)
Q Consensus 88 na~~~~~~g~~~L 100 (137)
|-... ++|.+++
T Consensus 118 Gkv~~-~~~~~qm 129 (681)
T PRK10917 118 GKVKR-GKYGLEM 129 (681)
T ss_pred EEEEe-cCCeEEE
Confidence 87754 5555555
No 39
>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=94.78 E-value=0.57 Score=31.36 Aligned_cols=71 Identities=20% Similarity=0.209 Sum_probs=52.4
Q ss_pred CceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecC-C---cCCCC-CCCEEEEeceEE-cccCCeE
Q 032583 25 GHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARND-Q---VDLMK-EGTTVILRNAKI-DMFKGSM 98 (137)
Q Consensus 25 ~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~-~---~~~i~-~Gd~v~I~na~~-~~~~g~~ 98 (137)
++.+.|.|..+.. ++.+ .| ..+...-|.|.|++|.+-.|.. . .+.++ +|+.|++++-.. ..|.+.+
T Consensus 1 ~v~i~G~Vf~~e~-re~k--~g-----~~i~~~~itD~t~Si~~K~F~~~~~~~~~~ik~~G~~v~v~G~v~~D~f~~e~ 72 (82)
T cd04484 1 NVVVEGEVFDLEI-RELK--SG-----RKILTFKVTDYTSSITVKKFLRKDEKDKEELKSKGDWVRVRGKVQYDTFSKEL 72 (82)
T ss_pred CEEEEEEEEEEEE-EEec--CC-----CEEEEEEEEcCCCCEEEEEeccCChhHHhhcccCCCEEEEEEEEEEccCCCce
Confidence 3678999999744 5542 34 5788899999999999999983 2 24578 999999999843 4466766
Q ss_pred EEEeC
Q 032583 99 RLAVD 103 (137)
Q Consensus 99 ~L~vg 103 (137)
.+.+.
T Consensus 73 ~~~i~ 77 (82)
T cd04484 73 VLMIN 77 (82)
T ss_pred EEEee
Confidence 66553
No 40
>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=94.72 E-value=0.079 Score=38.77 Aligned_cols=32 Identities=19% Similarity=0.265 Sum_probs=27.6
Q ss_pred eEEEEEecCCc---CCCCCCCEEEEeceEEcccCC
Q 032583 65 MIIFTARNDQV---DLMKEGTTVILRNAKIDMFKG 96 (137)
Q Consensus 65 ~I~ltlW~~~~---~~i~~Gd~v~I~na~~~~~~g 96 (137)
+|.+++||+++ ..+++||.|+|+|..++..+.
T Consensus 61 ti~It~yD~H~~~ar~lK~GdfV~L~NVhiK~~~~ 95 (123)
T cd04498 61 TIDILVYDNHVELAKSLKPGDFVRIYNVHAKSYSS 95 (123)
T ss_pred EEEEEEEcchHHHHhhCCCCCEEEEEEEEEEeccC
Confidence 89999999764 347999999999999988766
No 41
>COG4085 Predicted RNA-binding protein, contains TRAM domain [General function prediction only]
Probab=94.69 E-value=0.15 Score=40.14 Aligned_cols=93 Identities=18% Similarity=0.210 Sum_probs=66.3
Q ss_pred eeeeeccCCCCC----CCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecCCc---------CCC
Q 032583 12 VFTKVDQLRPGT----SGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARNDQV---------DLM 78 (137)
Q Consensus 12 ~~~kI~dL~p~~----~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~~~---------~~i 78 (137)
...+++.+..+. +.+.+++.|.+.... +| .-+....+-|+||+|.+.+...-+ ..+
T Consensus 36 ~~~~~a~i~eg~G~l~e~v~vkg~V~~~~n~------~~-----~gi~~l~lndgtGti~vva~~~tee~l~~n~~~p~~ 104 (204)
T COG4085 36 VAEQIATINEGDGRLNEEVTVKGEVTADQNA------IG-----GGIESLVLNDGTGTITVVASRSTEETLELNEGMPVT 104 (204)
T ss_pred CccceeEEecCCceeeccceeeeEEEeeecc------cc-----cceEEEEEECCCCcEEEEEecChhHhHhhcCCCCcc
Confidence 344456665443 334566777666542 34 456778999999999988886432 234
Q ss_pred CCCCEEEEeceEEcccCCeEEEEeCCcEeEEEcCCCce
Q 032583 79 KEGTTVILRNAKIDMFKGSMRLAVDKWGRVEVAEPANF 116 (137)
Q Consensus 79 ~~Gd~v~I~na~~~~~~g~~~L~vg~~g~I~~~~~~~~ 116 (137)
.+|+.+.+.+.. ++|+|..++.++.--.+.+.+...+
T Consensus 105 ~eGe~veVtGrv-~~yrG~~eVkvnq~~d~~~l~k~~~ 141 (204)
T COG4085 105 VEGEIVEVTGRV-EEYRGSSEVKVNQPNDSRPLPKHLT 141 (204)
T ss_pred ccCcEEEEEEEE-EEeCCCceeeccCcccccccccccc
Confidence 699999999765 7999999999999888888865544
No 42
>TIGR00643 recG ATP-dependent DNA helicase RecG.
Probab=94.26 E-value=0.27 Score=44.24 Aligned_cols=79 Identities=18% Similarity=0.177 Sum_probs=58.2
Q ss_pred eeeeeccCCCCCCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEee-CcceEEEEEecC--CcCCCCCCCEEEEec
Q 032583 12 VFTKVDQLRPGTSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGD-ETGMIIFTARND--QVDLMKEGTTVILRN 88 (137)
Q Consensus 12 ~~~kI~dL~p~~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgD-eTG~I~ltlW~~--~~~~i~~Gd~v~I~n 88 (137)
...+|.++.+|.. +.+.++|++.... .+ + ...+..+.+.| ++|.+.++.|+. ....+++|+.+.+.|
T Consensus 22 ~~~~i~~~~~g~~-~~~~~~v~~~~~~---~~--~----~~~~~~~~~~d~~~~~~~~~~F~~~~~~~~~~~g~~~~~~G 91 (630)
T TIGR00643 22 LLQTIGELLPGER-ATIVGEVLSHCIF---GF--K----RRKVLKLRLKDGGYKKLELRFFNRAFLKKKFKVGSKVVVYG 91 (630)
T ss_pred cccCHHHcCCCCE-EEEEEEEEEeEec---cC--C----CCceEEEEEEECCCCEEEEEEECCHHHHhhCCCCCEEEEEE
Confidence 3468999999865 7899999884221 11 1 13578899999 999999999973 245689999999998
Q ss_pred eEEcccCCeEEEE
Q 032583 89 AKIDMFKGSMRLA 101 (137)
Q Consensus 89 a~~~~~~g~~~L~ 101 (137)
-.. .+++.+++.
T Consensus 92 k~~-~~~~~~~~~ 103 (630)
T TIGR00643 92 KVK-SSKFKAYLI 103 (630)
T ss_pred EEE-eeCCEEEEE
Confidence 774 456666553
No 43
>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=93.55 E-value=0.48 Score=31.19 Aligned_cols=46 Identities=20% Similarity=0.244 Sum_probs=36.0
Q ss_pred EEEeeCcceEEEEEecCC----cCCCCCCCEEEEeceEEcccCCeEEEEeC
Q 032583 57 CLVGDETGMIIFTARNDQ----VDLMKEGTTVILRNAKIDMFKGSMRLAVD 103 (137)
Q Consensus 57 ~~VgDeTG~I~ltlW~~~----~~~i~~Gd~v~I~na~~~~~~g~~~L~vg 103 (137)
.-+-|+++.|++..|... ...+++||-|.+.+... ..+|.++|.+.
T Consensus 19 fsLkD~~a~i~cv~f~~~~~~~~~~l~~Gd~V~v~G~v~-~~~G~~ql~v~ 68 (73)
T cd04487 19 FTLRDETGTVWAAAFEEAGVRAYPEVEVGDIVRVTGEVE-PRDGQLQIEVE 68 (73)
T ss_pred EEEEcCCEEEEEEEEchhccCCcCCCCCCCEEEEEEEEe-cCCeEEEEEEe
Confidence 456899999999999743 23368999999999865 47788888764
No 44
>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=93.09 E-value=1 Score=29.96 Aligned_cols=54 Identities=15% Similarity=0.156 Sum_probs=41.0
Q ss_pred ceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecCCcC------CCCCCCEEEEeceEE
Q 032583 26 HTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARNDQVD------LMKEGTTVILRNAKI 91 (137)
Q Consensus 26 v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~~~~------~i~~Gd~v~I~na~~ 91 (137)
+.+.|.|.++. ++| .| .. -+.+-|.||++.+++|.+..+ .+++|..|.|.+-.-
T Consensus 2 v~i~GiI~~v~----~TK-~g-----~~--~~~leD~~G~~Ev~~F~~~~~~~~~~~~l~~d~~v~v~g~v~ 61 (79)
T cd04490 2 VSIIGMVNDVR----STK-NG-----HR--IVELEDTTGRITVLLTKDKEELFEEAEDILPDEVIGVSGTVS 61 (79)
T ss_pred EEEEEEEeEEE----EcC-CC-----CE--EEEEECCCCEEEEEEeCchhhhhhhhhhccCCCEEEEEEEEe
Confidence 45677887776 233 23 12 779999999999999986555 678999999998773
No 45
>PRK05673 dnaE DNA polymerase III subunit alpha; Validated
Probab=92.05 E-value=0.38 Score=46.52 Aligned_cols=86 Identities=26% Similarity=0.334 Sum_probs=62.6
Q ss_pred eeeccCCC--CCCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecCC----cCCCCCCCEEEEe
Q 032583 14 TKVDQLRP--GTSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARNDQ----VDLMKEGTTVILR 87 (137)
Q Consensus 14 ~kI~dL~p--~~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~~----~~~i~~Gd~v~I~ 87 (137)
.++.+|.. ....+.+.+.|.++....+. .| ..|+-+.+.|.||.+.+++|.+. ...+++|.+|.|.
T Consensus 966 ~~~~~l~~~~~g~~V~v~G~I~~vk~~~TK---kG-----~~mafltLeD~TG~iEvviFp~~ye~~~~~L~~g~iV~V~ 1037 (1135)
T PRK05673 966 TRLADLEPTEGGSVVTVAGLVVSVRRRVTK---RG-----NKMAIVTLEDLSGRIEVMLFSEALEKYRDLLEEDRIVVVK 1037 (1135)
T ss_pred cCHHHHhccccCceEEEEEEEEEEEecccC---CC-----CeEEEEEEEeCCCcEEEEECHHHHHHHHHHhccCCEEEEE
Confidence 35666642 34557888888888765542 24 47999999999999999999753 3457999999998
Q ss_pred ceEEcccCCeEEEEeCCcEeE
Q 032583 88 NAKIDMFKGSMRLAVDKWGRV 108 (137)
Q Consensus 88 na~~~~~~g~~~L~vg~~g~I 108 (137)
+-.. .+++.++|.+.+--.+
T Consensus 1038 GkVe-~~~~~~qlii~~I~~L 1057 (1135)
T PRK05673 1038 GQVS-FDDGGLRLTAREVMDL 1057 (1135)
T ss_pred EEEE-ecCCeEEEEEeecccH
Confidence 8664 4567888888755444
No 46
>PRK07373 DNA polymerase III subunit alpha; Reviewed
Probab=91.72 E-value=0.49 Score=41.41 Aligned_cols=83 Identities=14% Similarity=0.144 Sum_probs=59.3
Q ss_pred eeeccCC--CCCCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecCC----cCCCCCCCEEEEe
Q 032583 14 TKVDQLR--PGTSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARNDQ----VDLMKEGTTVILR 87 (137)
Q Consensus 14 ~kI~dL~--p~~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~~----~~~i~~Gd~v~I~ 87 (137)
.++.+|. ++...+.+-+.|.++....++ .| ..|+-+.+-|.||.+.+++|-+. ...+++|.++.|.
T Consensus 269 ~~~~~l~~~~~~~~v~vaG~I~~ik~~~TK---kG-----~~maf~~leD~tG~ie~vvFp~~y~~~~~~l~~~~~v~v~ 340 (449)
T PRK07373 269 INLSELEEQKEKTKVSAVVMLNEVKKIVTK---KG-----DPMAFLQLEDLSGQSEAVVFPKSYERISELLQVDARLIIW 340 (449)
T ss_pred cCHHHHhcccCCCEEEEEEEEEEeEecccC---CC-----CEEEEEEEEECCCCEEEEECHHHHHHHHHHhccCCEEEEE
Confidence 4566664 233457788888888765542 23 47999999999999999999753 3457999999998
Q ss_pred ceEEcccCCeEEEEeCCc
Q 032583 88 NAKIDMFKGSMRLAVDKW 105 (137)
Q Consensus 88 na~~~~~~g~~~L~vg~~ 105 (137)
+-.-+ ..+.+++.+.+-
T Consensus 341 G~v~~-~~~~~~liv~~i 357 (449)
T PRK07373 341 GKVDR-RDDQVQLIVEDA 357 (449)
T ss_pred EEEEe-cCCeEEEEEeEe
Confidence 87643 346677776543
No 47
>PF02760 HIN: HIN-200/IF120x domain; InterPro: IPR004021 This domain has no known function. It is found in one or two copies per protein, and is found associated with the PAAD/DAPIN domain IPR004020 from INTERPRO.; PDB: 3RN2_A 3RN5_C 2OQ0_A 3B6Y_A 3RLN_A 3RNU_A 3RLO_A.
Probab=91.49 E-value=3.5 Score=31.69 Aligned_cols=83 Identities=11% Similarity=0.070 Sum_probs=55.3
Q ss_pred EEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecC-CcCCCCCCCEEEEeceEEcccCCeEEEEeCCcE
Q 032583 28 LTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARND-QVDLMKEGTTVILRNAKIDMFKGSMRLAVDKWG 106 (137)
Q Consensus 28 l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~-~~~~i~~Gd~v~I~na~~~~~~g~~~L~vg~~g 106 (137)
+.+.||...+|=++.-.. .+..+|..+.||-+|--.++-+.+- +-+.+-+..+|.|.|.+ .++|.+++ .+.+
T Consensus 5 ~~VmVLkaTepF~Ye~~e---~gkk~MFHATVATet~fF~VKVfn~~LKeKF~~kkiI~IS~Y~--~~~gfLEi--~~aS 77 (170)
T PF02760_consen 5 KTVMVLKATEPFEYESPE---EGKKKMFHATVATETEFFRVKVFNINLKEKFIPKKIIAISDYF--GRNGFLEI--NEAS 77 (170)
T ss_dssp EEEEEEEE---EEEECTT---TCEEEEEEEEEE-SS-EEEEEES-GGGCCTCSTTSEEEEESEE--EETTEEEE---TTS
T ss_pred eEEEEEeccCCeEEeCcc---cCcceEEEEEEeccccEEEEEEecchhHhhcCCCcEEEEehhh--cccceEEE--eecc
Confidence 678899998887663323 1247999999999999999999994 55668999999999988 45887665 5678
Q ss_pred eEEEcC-CCceE
Q 032583 107 RVEVAE-PANFT 117 (137)
Q Consensus 107 ~I~~~~-~~~~~ 117 (137)
++..++ +..++
T Consensus 78 sVse~~~dq~~e 89 (170)
T PF02760_consen 78 SVSEVNPDQKME 89 (170)
T ss_dssp EEEE--TTC---
T ss_pred EEEecCCCceEE
Confidence 887775 33444
No 48
>PF02721 DUF223: Domain of unknown function DUF223; InterPro: IPR003871 The function of this domain has not been characterised, but may be involved in nucleic acid or nucleotide binding.
Probab=90.99 E-value=0.95 Score=30.82 Aligned_cols=57 Identities=26% Similarity=0.303 Sum_probs=43.8
Q ss_pred EEEEeeCcc-eEEEEEecCCc----CCCCCCCEEEEeceEEcccCCe-------EEEEeCCcEeEEEcC
Q 032583 56 ECLVGDETG-MIIFTARNDQV----DLMKEGTTVILRNAKIDMFKGS-------MRLAVDKWGRVEVAE 112 (137)
Q Consensus 56 ~~~VgDeTG-~I~ltlW~~~~----~~i~~Gd~v~I~na~~~~~~g~-------~~L~vg~~g~I~~~~ 112 (137)
++++.|+.| .|..+.+.+.+ ..++||.++.|.|-.+....|. ..|....++.|..++
T Consensus 1 emvL~De~G~~I~A~I~~~~~~~f~~~l~Eg~~y~i~~F~V~~~~~~yr~t~h~y~I~f~~~T~V~~~~ 69 (95)
T PF02721_consen 1 EMVLVDEKGDKIQATIPKELVDKFKDSLKEGSWYTISNFTVSPNSGSYRPTDHKYKINFMPNTKVTEID 69 (95)
T ss_pred CEEEEecCCCEEEEEECHHHHHHHHhhcccCCEEEeEeEEEEeCCCceeccCCCEEEEECCcCeEEECC
Confidence 468899988 57788887543 5579999999999999776654 457777777777775
No 49
>PRK05159 aspC aspartyl-tRNA synthetase; Provisional
Probab=90.76 E-value=1.7 Score=37.58 Aligned_cols=86 Identities=20% Similarity=0.200 Sum_probs=61.8
Q ss_pred eeeccCCCCC--CCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecC-------CcCCCCCCCEE
Q 032583 14 TKVDQLRPGT--SGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARND-------QVDLMKEGTTV 84 (137)
Q Consensus 14 ~kI~dL~p~~--~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~-------~~~~i~~Gd~v 84 (137)
..|++|.+.. +.|.|.|+|.++ |.- +.+.=+.|-|.+|.|.+++=.. .+..+..||+|
T Consensus 5 ~~~~~l~~~~~g~~V~i~GrV~~~-------R~~------gk~~Fl~LrD~~g~iQ~v~~~~~~~~~~~~~~~L~~gs~V 71 (437)
T PRK05159 5 HLTSELTPELDGEEVTLAGWVHEI-------RDL------GGIAFLILRDRSGIIQVVVKKKVDEELFETIKKLKRESVV 71 (437)
T ss_pred eEhhhCChhhCCCEEEEEEEeEee-------ecC------CCeEEEEEEcCCcEEEEEEeCCccHHHHHHHhCCCCCcEE
Confidence 4688888755 456777777554 222 3566678899999999977432 23467899999
Q ss_pred EEeceEEcccC--CeEEEEeCCcEeEEEcC
Q 032583 85 ILRNAKIDMFK--GSMRLAVDKWGRVEVAE 112 (137)
Q Consensus 85 ~I~na~~~~~~--g~~~L~vg~~g~I~~~~ 112 (137)
.|.|-.....+ |.++|.+.+.--+.+..
T Consensus 72 ~v~G~v~~~~~~~~~~el~~~~i~vls~a~ 101 (437)
T PRK05159 72 SVTGTVKANPKAPGGVEVIPEEIEVLNKAE 101 (437)
T ss_pred EEEEEEEcCCCCCCCEEEEEeEEEEEeCCC
Confidence 99997776554 78999998777766664
No 50
>PF10451 Stn1: Telomere regulation protein Stn1; InterPro: IPR018856 The budding yeast protein Stn1 is a DNA-binding protein which has specificity for telomeric DNA. Structural profiling has predicted an OB-fold []. This entry represents the N-terminal part of the molecule, which adopts the OB fold. Protection of telomeres by multiple proteins with OB-fold domains is conserved in eukaryotic evolution [].; PDB: 3KF6_A 3KF8_A.
Probab=89.03 E-value=3 Score=33.93 Aligned_cols=73 Identities=14% Similarity=0.106 Sum_probs=49.0
Q ss_pred CCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcc--eEEEEEecCC-------cCCCCCCCEEEEeceEEcc
Q 032583 23 TSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETG--MIIFTARNDQ-------VDLMKEGTTVILRNAKIDM 93 (137)
Q Consensus 23 ~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG--~I~ltlW~~~-------~~~i~~Gd~v~I~na~~~~ 93 (137)
.+.+.|.|+|++.... ...+ ....-..|-|.|| .|...+|.+. +..+ .|++|.|.|...
T Consensus 66 I~~v~i~G~Vv~~~~~-~~~~--------~~~~~l~iDD~Sg~~~i~~~~~~~~~~~~~l~~~~~-~G~~V~VkG~vs-- 133 (256)
T PF10451_consen 66 IRWVRIVGVVVGIDYK-WIEN--------EDRIILTIDDSSGANTIECKCSKSSYLSMGLPINDL-IGKVVEVKGTVS-- 133 (256)
T ss_dssp E-EEEEEEEEEEEEEE-E-BB--------TCEEEEEEE-SSCS-EEEEEEEHHHHHCCCHHCTT--TT-EEEEEEEEE--
T ss_pred cEEEEEEEEEEEEEEE-eecc--------cceEEEEEeCCCCceeEEEEEEcccccccCCCccCC-CCcEEEEEEEEc--
Confidence 3567899999998653 2221 1234457999999 8999999752 2223 999999999987
Q ss_pred cCCeEEEEeCCcEeE
Q 032583 94 FKGSMRLAVDKWGRV 108 (137)
Q Consensus 94 ~~g~~~L~vg~~g~I 108 (137)
++..+|.+.+-+.+
T Consensus 134 -r~~~ql~ve~i~~~ 147 (256)
T PF10451_consen 134 -RNERQLDVERIELV 147 (256)
T ss_dssp -SSSEEEEEEEEEEE
T ss_pred -cCcEEEEEEEEEcc
Confidence 77788877666543
No 51
>COG5235 RFA2 Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [DNA replication, recombination, and repair]
Probab=88.44 E-value=3.1 Score=33.48 Aligned_cols=45 Identities=18% Similarity=0.247 Sum_probs=35.4
Q ss_pred EEEeeCcceEEEEEecCC------cCCCCCCCEEEEeceEEcccCCeEEEEe
Q 032583 57 CLVGDETGMIIFTARNDQ------VDLMKEGTTVILRNAKIDMFKGSMRLAV 102 (137)
Q Consensus 57 ~~VgDeTG~I~ltlW~~~------~~~i~~Gd~v~I~na~~~~~~g~~~L~v 102 (137)
..|-|.||.|.++.|... +...++|.-|++.++. +.|+|+..+.-
T Consensus 87 ~~iEDGTG~Ievr~W~~~~~~~e~~~d~~~~~yvkV~G~l-k~F~GK~~I~~ 137 (258)
T COG5235 87 FVIEDGTGSIEVRFWPGNSYEEEQCKDLEEQNYVKVNGSL-KTFNGKRSISA 137 (258)
T ss_pred EEEecCCceEEEEecCCCchHHHhccccccccEEEEecce-eeeCCeeEEeh
Confidence 478999999999999743 3345788888887765 89999888753
No 52
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain
Probab=87.51 E-value=7.3 Score=26.81 Aligned_cols=69 Identities=17% Similarity=0.123 Sum_probs=49.1
Q ss_pred CCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecCC---c--CCCCCCCEEEEeceEEcc-cCC
Q 032583 23 TSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARNDQ---V--DLMKEGTTVILRNAKIDM-FKG 96 (137)
Q Consensus 23 ~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~~---~--~~i~~Gd~v~I~na~~~~-~~g 96 (137)
..++-+.|-|.++...+ .--....+-|+...|+.++|... + ..++.|+-|.+.+...-. -+|
T Consensus 21 ~~~vwV~GEIs~~~~~~------------~gh~YftLkD~~a~i~~~~~~~~~~~i~~~~l~~G~~V~v~g~~~~y~~~G 88 (99)
T PF13742_consen 21 LPNVWVEGEISNLKRHS------------SGHVYFTLKDEEASISCVIFRSRARRIRGFDLKDGDKVLVRGRVSFYEPRG 88 (99)
T ss_pred cCCEEEEEEEeecEECC------------CceEEEEEEcCCcEEEEEEEHHHHhhCCCCCCCCCCEEEEEEEEEEECCCc
Confidence 47788888888775531 12255677888899999999843 2 357999999998776533 346
Q ss_pred eEEEEeC
Q 032583 97 SMRLAVD 103 (137)
Q Consensus 97 ~~~L~vg 103 (137)
.++|.+.
T Consensus 89 ~~sl~v~ 95 (99)
T PF13742_consen 89 SLSLIVE 95 (99)
T ss_pred EEEEEEE
Confidence 7888764
No 53
>cd04494 BRCA2DBD_OB2 BRCA2DBD_OB2: A subfamily of OB folds corresponding to the second OB fold (OB2) of the 800-amino acid C-terminal ssDNA binding domain (DBD) of BRCA2 (breast cancer susceptibility gene 2) protein, called BRCA2DBD. BRCA2 participates in homologous recombination-mediated repair of double-strand DNA breaks. It stimulates the displacement of Replication protein A (RPA), the most abundant eukaryotic ssDNA binding protein. It also facilitates filament formation. Mutations that map throughout the BRCA2 protein are associated with breast cancer susceptibility. BRCA2 is a large nuclear protein and its most conserved region is the C-terminal BRCA2DBD. BRCA2DBD binds ssDNA in vitro, and is composed of five structural domains, three of which are OB folds (OB1, OB2, and OB3). BRCA2DBD OB2 and OB3 are arranged in tandem, and their mode of binding can be considered qualitatively similar to two OB folds of RPA1, DBD-A and DBD-B (the major DBDs of RPA).
Probab=87.50 E-value=1.9 Score=35.12 Aligned_cols=59 Identities=15% Similarity=0.086 Sum_probs=46.2
Q ss_pred EEEEEEeeCc----ceEEEEEecCC---cCCCCCCCEEEEeceEEcccCC-----eEEEEeCCcEeEEEcC
Q 032583 54 IAECLVGDET----GMIIFTARNDQ---VDLMKEGTTVILRNAKIDMFKG-----SMRLAVDKWGRVEVAE 112 (137)
Q Consensus 54 v~~~~VgDeT----G~I~ltlW~~~---~~~i~~Gd~v~I~na~~~~~~g-----~~~L~vg~~g~I~~~~ 112 (137)
+..+.|.|-. ....||+|+.- ...+++|..++|+|-.++-.++ .++|.-++.++-.+++
T Consensus 166 ~~klRV~d~~~~~~~~~~LTIWrPtedl~s~L~EG~ry~i~~L~~s~~k~~~~~~~vqLtatk~Tr~~~l~ 236 (251)
T cd04494 166 VWKLRVTDYRSKPEKSGLLSIWRPTEDLRSLLTEGKRYRIYGLATSNSKKRSGNEEVQLTATKKTRYQPLP 236 (251)
T ss_pred EEEEEEeecccCCCceEEEEEeCCCHHHHhhhcCCcEEEEEeccccCCCCCCCcceEEEEecCcccceECC
Confidence 3445555555 67889999953 3468999999999998877554 9999999999988886
No 54
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=87.42 E-value=4.4 Score=40.42 Aligned_cols=88 Identities=17% Similarity=0.199 Sum_probs=67.4
Q ss_pred CeeeeeccCCCCCCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecCC------cCCCCCCCEE
Q 032583 11 PVFTKVDQLRPGTSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARNDQ------VDLMKEGTTV 84 (137)
Q Consensus 11 ~~~~kI~dL~p~~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~~------~~~i~~Gd~v 84 (137)
..+.+|+++.....++.+.|.|..+.. ++.+ .| ..+...-|.|-|++|.+..|... .+.++.|+.|
T Consensus 224 ~~~~~~~~i~~~~~~v~i~G~if~~e~-~~~k--~~-----~~~~~~~~td~~~s~~~k~f~~~~~~~~~~~~~~~g~~v 295 (1437)
T PRK00448 224 EEITPMKEINEEERRVVVEGYVFKVEI-KELK--SG-----RHILTFKITDYTSSIIVKKFSRDKEDLKKFDEIKKGDWV 295 (1437)
T ss_pred cCcccHHHhhccCCeEEEEEEEEEEEE-Eecc--CC-----CEEEEEEEEcCCCCEEEEEEecCcchhHHHhcCCCCCEE
Confidence 467789999998999999999999755 4432 34 46778999999999999999722 2558999999
Q ss_pred EEeceEE-cccCCeEEEEeCCcE
Q 032583 85 ILRNAKI-DMFKGSMRLAVDKWG 106 (137)
Q Consensus 85 ~I~na~~-~~~~g~~~L~vg~~g 106 (137)
++++-.. ..|.+.+.+.+..-.
T Consensus 296 ~~~g~~~~d~~~~~~~~~~~~~~ 318 (1437)
T PRK00448 296 KVRGSVQNDTFTRDLVMNAQDIN 318 (1437)
T ss_pred EEEEEEeccCCCCceEEEeeeee
Confidence 9998764 446777777665433
No 55
>PRK07459 single-stranded DNA-binding protein; Provisional
Probab=87.37 E-value=1.7 Score=31.28 Aligned_cols=62 Identities=13% Similarity=0.107 Sum_probs=46.2
Q ss_pred CCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEe-------eCcceEEEEEecCCcC----CCCCCCEEEEeceEE
Q 032583 23 TSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVG-------DETGMIIFTARNDQVD----LMKEGTTVILRNAKI 91 (137)
Q Consensus 23 ~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~Vg-------DeTG~I~ltlW~~~~~----~i~~Gd~v~I~na~~ 91 (137)
++.+.|.+++-.-.+.+.+. +| ..+++..|| ++|-=+++++|+.+|+ .++.|+.|.|.|-..
T Consensus 3 ~N~v~LiGrL~~DPelr~t~--~G-----~~v~~fslAv~~~~~~~~t~w~~v~~wg~~Ae~~~~~l~KG~~V~V~G~l~ 75 (121)
T PRK07459 3 LNSVTLVGRAGRDPEVRYFE--SG-----SVVCNLTLAVNRRSRDDEPDWFNLEIWGKTAQVAADYVKKGSLIGITGSLK 75 (121)
T ss_pred ccEEEEEEEccCCCEEEEcC--CC-----CEEEEEEEEecccccCCCceEEEEEEehHHHHHHHHHcCCCCEEEEEEEEE
Confidence 35578889888865555442 44 467777777 5688899999996543 368999999999865
No 56
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=87.17 E-value=0.31 Score=35.66 Aligned_cols=25 Identities=20% Similarity=0.194 Sum_probs=21.1
Q ss_pred eeEEEEEEeeCcceEEEEEecCCcC
Q 032583 52 MRIAECLVGDETGMIIFTARNDQVD 76 (137)
Q Consensus 52 ~~v~~~~VgDeTG~I~ltlW~~~~~ 76 (137)
.-+.++.|+|.||.+++++|++.+.
T Consensus 53 ry~l~~~i~D~tg~~~~~~F~~~a~ 77 (146)
T PF08646_consen 53 RYRLSLKISDGTGSIWVTLFDEEAE 77 (146)
T ss_dssp EEEEEEEEEETTEEEEEEEEHHHHH
T ss_pred EEEEEEEEEeCCCeEEEEEEhHHHH
Confidence 4556899999999999999997653
No 57
>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=87.14 E-value=3.2 Score=29.32 Aligned_cols=66 Identities=18% Similarity=0.129 Sum_probs=42.1
Q ss_pred CCCCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecCC--cCCCCCCCEEEEeceEEcccCCeE
Q 032583 21 PGTSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARNDQ--VDLMKEGTTVILRNAKIDMFKGSM 98 (137)
Q Consensus 21 p~~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~~--~~~i~~Gd~v~I~na~~~~~~g~~ 98 (137)
++...|.|+++|++--.-. .-++.|.||.|++-+=++. ...+.+.+.|+|.+-.-+.++ ..
T Consensus 32 ~Dd~~V~L~G~Iv~~l~~d----------------~Y~F~D~TG~I~VeId~~~w~g~~vt~~~~Vri~GeVDk~~~-~~ 94 (103)
T PF04076_consen 32 KDDTPVTLEGNIVKQLGDD----------------KYLFRDATGEIEVEIDDDVWRGQTVTPDDKVRISGEVDKDWN-KT 94 (103)
T ss_dssp -SSEEEEEEEEEEEEEETT----------------EEEEEETTEEEEEE--GGGSTT----TTSEEEEEEEEEEETT-EE
T ss_pred cCCCeEEEEEEEEEEecCC----------------EEEEECCCCcEEEEEChhhcCCcccCCCCEEEEEEEEeCCCC-ce
Confidence 3455678888887632211 2378999999999875542 224789999999998887775 47
Q ss_pred EEEeC
Q 032583 99 RLAVD 103 (137)
Q Consensus 99 ~L~vg 103 (137)
+|.+.
T Consensus 95 ~IdV~ 99 (103)
T PF04076_consen 95 EIDVD 99 (103)
T ss_dssp EEEEE
T ss_pred EEEEE
Confidence 76653
No 58
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=86.48 E-value=5.1 Score=37.00 Aligned_cols=79 Identities=23% Similarity=0.363 Sum_probs=59.0
Q ss_pred CeeeeeccCCCCCCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecCC---cCCCCCCCEEEEe
Q 032583 11 PVFTKVDQLRPGTSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARNDQ---VDLMKEGTTVILR 87 (137)
Q Consensus 11 ~~~~kI~dL~p~~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~~---~~~i~~Gd~v~I~ 87 (137)
.....|.++.+|.. +.+.+.|.+..... +. ......+.+.|.||.+.+++++.. ...++.|..+.+.
T Consensus 49 ~~~~~i~~~~~g~~-vti~g~V~~~~~~~-~~--------~~~~l~v~~~d~~~~l~l~fFn~~~~l~~~~~~G~~v~v~ 118 (677)
T COG1200 49 TLLPGIAEARPGEI-VTIEGTVLSHEKFP-FG--------KRKLLKVTLSDGTGVLTLVFFNFPAYLKKKLKVGERVIVY 118 (677)
T ss_pred cccCChhhcCCCce-EEEEEEEEeeeccC-CC--------CCceEEEEEecCcEEEEEEEECccHHHHhhCCCCCEEEEE
Confidence 34456788887765 78999998876543 21 257788999999999999999954 3557999999988
Q ss_pred ceEEcccCCeEEE
Q 032583 88 NAKIDMFKGSMRL 100 (137)
Q Consensus 88 na~~~~~~g~~~L 100 (137)
|-. +.+++.+++
T Consensus 119 Gk~-~~~~~~~~~ 130 (677)
T COG1200 119 GKV-KRFKGGLQI 130 (677)
T ss_pred EEE-eeccCceEE
Confidence 655 557766665
No 59
>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=85.30 E-value=9.9 Score=26.17 Aligned_cols=59 Identities=15% Similarity=0.274 Sum_probs=43.6
Q ss_pred eEEEEEEeeCcceEEEEEecCC--------c-CCCCCCCEEEEeceEEcccCCeEEEEeCCcEeEEEc
Q 032583 53 RIAECLVGDETGMIIFTARNDQ--------V-DLMKEGTTVILRNAKIDMFKGSMRLAVDKWGRVEVA 111 (137)
Q Consensus 53 ~v~~~~VgDeTG~I~ltlW~~~--------~-~~i~~Gd~v~I~na~~~~~~g~~~L~vg~~g~I~~~ 111 (137)
.++=+.+-|.||.+.+++=... . ..+..||+|.+.|-..+.-.|.++|.+.+.--+.+.
T Consensus 16 ~~~Fi~lrd~~~~lQ~v~~~~~~~~~~~~~~~~~l~~g~~V~v~G~v~~~~~g~~El~~~~~~ils~~ 83 (108)
T cd04322 16 KLSFADLQDESGKIQVYVNKDDLGEEEFEDFKKLLDLGDIIGVTGTPFKTKTGELSIFVKEFTLLSKS 83 (108)
T ss_pred CeEEEEEEECCeEEEEEEECCCCCHHHHHHHHhcCCCCCEEEEEEEEEecCCCCEEEEeCEeEEeecc
Confidence 4666788999999998663221 1 127899999999988877778899988776555544
No 60
>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=85.27 E-value=10 Score=26.20 Aligned_cols=75 Identities=15% Similarity=0.115 Sum_probs=49.7
Q ss_pred CCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecCC--------cCCCCCCCEEEEeceEEcccC
Q 032583 24 SGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARNDQ--------VDLMKEGTTVILRNAKIDMFK 95 (137)
Q Consensus 24 ~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~~--------~~~i~~Gd~v~I~na~~~~~~ 95 (137)
..+.+.|.|-.+ |.- +.+.=+.+-|.+|.+...+=++. +..+..|++|.+.|...+.-+
T Consensus 13 ~~V~v~Gwv~~~-------R~~------g~~~Fi~LrD~~g~iQ~v~~~~~~~~~~~~~~~~l~~es~V~V~G~v~~~~~ 79 (108)
T cd04316 13 EEVTVAGWVHEI-------RDL------GGIKFVILRDREGIVQVTAPKKKVDKELFKTVRKLSRESVISVTGTVKAEPK 79 (108)
T ss_pred CEEEEEEEEEee-------ecc------CCeEEEEEecCCeeEEEEEeCCCCCHHHHHHHhCCCCcCEEEEEEEEEeCCC
Confidence 346777777543 222 23556678899998888664331 234789999999998776433
Q ss_pred --CeEEEEeCCcEeEEEc
Q 032583 96 --GSMRLAVDKWGRVEVA 111 (137)
Q Consensus 96 --g~~~L~vg~~g~I~~~ 111 (137)
+.++|.+.+.--+.+.
T Consensus 80 ~~~~~Ei~~~~i~il~~~ 97 (108)
T cd04316 80 APNGVEIIPEEIEVLSEA 97 (108)
T ss_pred CCCCEEEEEeEEEEEeCC
Confidence 4688888766666555
No 61
>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=85.22 E-value=11 Score=26.86 Aligned_cols=84 Identities=11% Similarity=0.122 Sum_probs=55.4
Q ss_pred CCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecC------CcCCCCCCCEEEEeceEEcc----
Q 032583 24 SGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARND------QVDLMKEGTTVILRNAKIDM---- 93 (137)
Q Consensus 24 ~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~------~~~~i~~Gd~v~I~na~~~~---- 93 (137)
..+.+.|.|-.+ |.- +.++=+.+-|.+|.+...+=.. .+..+..|++|.+.|-...-
T Consensus 15 ~~V~i~Gwv~~~-------R~~------gk~~Fi~LrD~~g~~Q~v~~~~~~~~~~~~~~l~~gs~V~V~G~~~~~~~~~ 81 (135)
T cd04317 15 QEVTLCGWVQRR-------RDH------GGLIFIDLRDRYGIVQVVFDPEEAPEFELAEKLRNESVIQVTGKVRARPEGT 81 (135)
T ss_pred CEEEEEEeEehh-------ccc------CCEEEEEEecCCeeEEEEEeCCchhHHHHHhCCCCccEEEEEEEEECCCccc
Confidence 347777777543 222 2356667789999888766432 22357899999999977642
Q ss_pred -----cCCeEEEEeCCcEeEEEcCCCceEEcC
Q 032583 94 -----FKGSMRLAVDKWGRVEVAEPANFTVKE 120 (137)
Q Consensus 94 -----~~g~~~L~vg~~g~I~~~~~~~~~vn~ 120 (137)
-.|.++|.+...--+.+.++..+.++.
T Consensus 82 ~~~~~~~~~~El~~~~i~vl~~~~~lP~~~~~ 113 (135)
T cd04317 82 VNPKLPTGEIEVVASELEVLNKAKTLPFEIDD 113 (135)
T ss_pred cCCCCCCCcEEEEEeEEEEEECCCCCCCcccc
Confidence 246799998887666666555555443
No 62
>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=84.93 E-value=3.4 Score=28.13 Aligned_cols=38 Identities=21% Similarity=0.157 Sum_probs=29.2
Q ss_pred EEEeeCcceEEEEEecCC--c----CCCCCCCEEEEeceEEcccC
Q 032583 57 CLVGDETGMIIFTARNDQ--V----DLMKEGTTVILRNAKIDMFK 95 (137)
Q Consensus 57 ~~VgDeTG~I~ltlW~~~--~----~~i~~Gd~v~I~na~~~~~~ 95 (137)
..+-|+++.|++.+|.+. + ..+++||.|.+.+.. +.|.
T Consensus 21 FtlkD~~~~i~cv~f~~~g~~~~~~~~l~~Gd~V~v~G~v-~~y~ 64 (91)
T cd04482 21 FKISDGTGEIDCAAYEPTKEFRDVVRLLIPGDEVTVYGSV-RPGT 64 (91)
T ss_pred EEEECCCcEEEEEEECcccccccccCCCCCCCEEEEEEEE-ecCC
Confidence 356899999999999753 2 336899999999985 4444
No 63
>TIGR00499 lysS_bact lysyl-tRNA synthetase, eukaryotic and non-spirochete bacterial. This model represents the lysyl-tRNA synthetases that are class II amino-acyl tRNA synthetases. It includes all eukaryotic and most bacterial examples of the enzyme, but not archaeal or spirochete forms.
Probab=84.90 E-value=9.7 Score=33.71 Aligned_cols=74 Identities=14% Similarity=0.196 Sum_probs=55.1
Q ss_pred CceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecCCc---------CCCCCCCEEEEeceEEcccC
Q 032583 25 GHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARNDQV---------DLMKEGTTVILRNAKIDMFK 95 (137)
Q Consensus 25 ~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~~~---------~~i~~Gd~v~I~na~~~~~~ 95 (137)
.+.|.|+|.++- .+ ++++=+.|-|.||.|.+.+=.+.. ..+..||+|.+.|-..+...
T Consensus 55 ~v~v~Grv~~~R--------~~-----gk~~F~~l~D~~g~iQ~~~~~~~~~~~~~~~~~~~l~~gd~V~v~G~~~~t~~ 121 (496)
T TIGR00499 55 EVSIAGRIMARR--------SM-----GKATFITLQDESGQIQLYVNKDDLPEDFYEFDEYLLDLGDIIGVTGYPFKTKT 121 (496)
T ss_pred EEEEEEEEEEEe--------cC-----CCeEEEEEEcCCccEEEEEECCcCcHHHHHHHHhcCCCCCEEEEEEEEEECCC
Confidence 367777776642 11 456677899999999987753321 13689999999998888888
Q ss_pred CeEEEEeCCcEeEEEc
Q 032583 96 GSMRLAVDKWGRVEVA 111 (137)
Q Consensus 96 g~~~L~vg~~g~I~~~ 111 (137)
|.++|.+.+..-+.+.
T Consensus 122 gelel~~~~i~ilsk~ 137 (496)
T TIGR00499 122 GELSVHVTELQILTKA 137 (496)
T ss_pred CcEEEEeeEEEEEecC
Confidence 9999999888666655
No 64
>PF11325 DUF3127: Domain of unknown function (DUF3127); InterPro: IPR021474 This bacterial family of proteins has no known function.
Probab=84.86 E-value=7.5 Score=26.60 Aligned_cols=67 Identities=22% Similarity=0.270 Sum_probs=42.0
Q ss_pred EEEEEEEcceeeeeccCCCccccceeEEEEEEeeCc---ceEEEEEecCCcCC---CCCCCEEEEe-ceEEcccCCeEE
Q 032583 28 LTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDET---GMIIFTARNDQVDL---MKEGTTVILR-NAKIDMFKGSMR 99 (137)
Q Consensus 28 l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeT---G~I~ltlW~~~~~~---i~~Gd~v~I~-na~~~~~~g~~~ 99 (137)
+++||+.+-++.+..-+.| =+-++.+|--+. -.|.|.+|.+.++. +++||.|.+. |...++|+|+--
T Consensus 2 i~Gkii~~l~~~~g~s~~G-----w~Kre~Vlet~~qYP~~i~f~~~~dk~~~l~~~~~Gd~V~Vsf~i~~RE~~gr~f 75 (84)
T PF11325_consen 2 ITGKIIKVLPEQQGVSKNG-----WKKREFVLETEEQYPQKICFEFWGDKIDLLDNFQVGDEVKVSFNIEGREWNGRWF 75 (84)
T ss_pred cccEEEEEecCcccCcCCC-----cEEEEEEEeCCCcCCceEEEEEEcchhhhhccCCCCCEEEEEEEeeccEecceEe
Confidence 6788777666543211122 233455555322 47999999987655 6899999986 555577776443
No 65
>PRK02801 primosomal replication protein N; Provisional
Probab=84.68 E-value=3.5 Score=28.67 Aligned_cols=63 Identities=14% Similarity=0.178 Sum_probs=47.1
Q ss_pred CCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEee-----Ccce-------EEEEEecCCcC----CCCCCCEEEE
Q 032583 23 TSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGD-----ETGM-------IIFTARNDQVD----LMKEGTTVIL 86 (137)
Q Consensus 23 ~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgD-----eTG~-------I~ltlW~~~~~----~i~~Gd~v~I 86 (137)
++.+.|.|++..-.+.+.+. .| ..+++..+|= ++|- |++++|...|+ .+..|+.|.|
T Consensus 2 mN~v~L~Grl~~dpelr~Tp--~G-----~~v~~f~La~~~~~~ea~~~r~~~~~i~~va~G~~Ae~~~~~l~kGs~v~V 74 (101)
T PRK02801 2 TNRLVLSGTVCRTPKRKVSP--SG-----IPHCQFVLEHRSVQEEAGLHRQAWCRMPVIVSGNQFQAITQSITVGSKITV 74 (101)
T ss_pred ccEEEEEEEECcCcceEECC--CC-----CeEEEEEEEEeCeEecCCCceeEEEEEEEEEEcHHHHHHHhhcCCCCEEEE
Confidence 56788999999988877653 55 4566666653 3455 99999996553 3689999999
Q ss_pred eceEEc
Q 032583 87 RNAKID 92 (137)
Q Consensus 87 ~na~~~ 92 (137)
.|-...
T Consensus 75 ~G~L~~ 80 (101)
T PRK02801 75 QGFISC 80 (101)
T ss_pred EEEEEE
Confidence 998875
No 66
>PLN02850 aspartate-tRNA ligase
Probab=84.24 E-value=14 Score=33.08 Aligned_cols=95 Identities=16% Similarity=0.064 Sum_probs=64.8
Q ss_pred CeeeeeccCCCCC--CCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecCC----------cCCC
Q 032583 11 PVFTKVDQLRPGT--SGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARNDQ----------VDLM 78 (137)
Q Consensus 11 ~~~~kI~dL~p~~--~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~~----------~~~i 78 (137)
..+++|.+|.+.. +.|.|.|+|-.+ |.- +.++=+.+-|.+|+|..++=... +..+
T Consensus 67 ~~~~~i~~l~~~~~g~~V~v~Grv~~~-------R~~------gk~~Fl~Lrd~~~~iQ~v~~~~~~~~~~~~~~~~~~l 133 (530)
T PLN02850 67 REWTDVSDLGEELAGSEVLIRGRVHTI-------RGK------GKSAFLVLRQSGFTVQCVVFVSEVTVSKGMVKYAKQL 133 (530)
T ss_pred ceEeEhhhcchhhCCCEEEEEEEEEEE-------ccC------CCeEEEEEEeCCcCEEEEEECCccccCHHHHHHHhCC
Confidence 5789999998743 346666666443 333 34566788999999998775432 3457
Q ss_pred CCCCEEEEeceEEc------ccCCeEEEEeCCcEeEEEcC-CCceEE
Q 032583 79 KEGTTVILRNAKID------MFKGSMRLAVDKWGRVEVAE-PANFTV 118 (137)
Q Consensus 79 ~~Gd~v~I~na~~~------~~~g~~~L~vg~~g~I~~~~-~~~~~v 118 (137)
..|++|.|.|-..+ .-.+.++|.+.+.--|.+.. +..+.+
T Consensus 134 ~~es~V~V~G~v~~~~~~~~~~t~~~El~~~~i~vls~a~~~lP~~~ 180 (530)
T PLN02850 134 SRESVVDVEGVVSVPKKPVKGTTQQVEIQVRKIYCVSKALATLPFNV 180 (530)
T ss_pred CCCCEEEEEEEEEccCcCCCCCCccEEEEEeEEEEEeCCCCCCCCCh
Confidence 89999999997762 22346999998887776663 333444
No 67
>PRK00484 lysS lysyl-tRNA synthetase; Reviewed
Probab=84.14 E-value=12 Score=33.05 Aligned_cols=75 Identities=11% Similarity=0.118 Sum_probs=55.0
Q ss_pred CCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecCC--------cCCCCCCCEEEEeceEEcccC
Q 032583 24 SGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARNDQ--------VDLMKEGTTVILRNAKIDMFK 95 (137)
Q Consensus 24 ~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~~--------~~~i~~Gd~v~I~na~~~~~~ 95 (137)
..|.|.|+|.++ |.- +.++=+.|-|.+|.|.+.+=.+. ...+..||+|.|.|-..+...
T Consensus 55 ~~v~v~G~v~~~-------R~~------g~~~Fi~lrD~~g~iQ~v~~~~~~~~~~~~~~~~l~~g~~v~v~G~v~~t~~ 121 (491)
T PRK00484 55 IEVSVAGRVMLK-------RVM------GKASFATLQDGSGRIQLYVSKDDVGEEALEAFKKLDLGDIIGVEGTLFKTKT 121 (491)
T ss_pred cEEEEEEEEEEE-------ecC------CceEEEEEEcCCccEEEEEECCcCCHHHHHHHhcCCCCCEEEEEEEEEEcCC
Confidence 346777777654 222 35666788999999998775332 123789999999998888778
Q ss_pred CeEEEEeCCcEeEEEc
Q 032583 96 GSMRLAVDKWGRVEVA 111 (137)
Q Consensus 96 g~~~L~vg~~g~I~~~ 111 (137)
|.++|.+.+.--+.+.
T Consensus 122 ge~el~~~~~~vls~~ 137 (491)
T PRK00484 122 GELSVKATELTLLTKS 137 (491)
T ss_pred CcEEEEEeEEEEEecc
Confidence 9999999888666655
No 68
>PRK12445 lysyl-tRNA synthetase; Reviewed
Probab=83.39 E-value=6.1 Score=35.09 Aligned_cols=74 Identities=12% Similarity=0.104 Sum_probs=54.5
Q ss_pred CceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecCC---------cCCCCCCCEEEEeceEEcccC
Q 032583 25 GHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARNDQ---------VDLMKEGTTVILRNAKIDMFK 95 (137)
Q Consensus 25 ~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~~---------~~~i~~Gd~v~I~na~~~~~~ 95 (137)
.|.|.|+|.++ |.- +.++=+.|-|.+|.|.+.+=.+. ...+..||+|.+.|-..+...
T Consensus 67 ~v~v~Grv~~~-------R~~------Gk~~F~~lrD~~g~iQ~~~~~~~~~~~~~~~~~~~l~~Gd~V~v~G~~~~t~~ 133 (505)
T PRK12445 67 EVSVAGRMMTR-------RIM------GKASFVTLQDVGGRIQLYVARDSLPEGVYNDQFKKWDLGDIIGARGTLFKTQT 133 (505)
T ss_pred EEEEEEEEEEE-------ecC------CCcEEEEEEeCCccEEEEEECCccchhhHHHHHhcCCCCCEEEEEEEEEecCC
Confidence 37777777664 222 34556788999999998775321 234679999999998888888
Q ss_pred CeEEEEeCCcEeEEEc
Q 032583 96 GSMRLAVDKWGRVEVA 111 (137)
Q Consensus 96 g~~~L~vg~~g~I~~~ 111 (137)
|.++|.+.+.--+.+.
T Consensus 134 gelel~~~~~~llsk~ 149 (505)
T PRK12445 134 GELSIHCTELRLLTKA 149 (505)
T ss_pred CcEEEEEeEEEEEecC
Confidence 9999999888766655
No 69
>PTZ00401 aspartyl-tRNA synthetase; Provisional
Probab=83.29 E-value=15 Score=33.17 Aligned_cols=95 Identities=18% Similarity=0.177 Sum_probs=65.5
Q ss_pred CeeeeeccCCCCC---CCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEe--cCC-------cCCC
Q 032583 11 PVFTKVDQLRPGT---SGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTAR--NDQ-------VDLM 78 (137)
Q Consensus 11 ~~~~kI~dL~p~~---~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW--~~~-------~~~i 78 (137)
..+++|++|.+.. +.|.|.|+|-.+ |.- +.++=+.|-|.+|.|..++= ++. +..+
T Consensus 63 ~~~~~i~~l~~~~~~g~~V~v~Grv~~~-------R~~------Gk~~Fl~LRd~~~~iQ~v~~~~~~~~~~~~~~~~~l 129 (550)
T PTZ00401 63 RTFIPVAVLSKPELVDKTVLIRARVSTT-------RKK------GKMAFMVLRDGSDSVQAMAAVEGDVPKEMIDFIGQI 129 (550)
T ss_pred CceEEHHHCCccccCCCEEEEEEEEEEE-------ecC------CCeEEEEEEeCCcCEEEEEECCCccCHHHHHHHhcC
Confidence 5789999998654 446677777543 322 34566788999999998873 211 2347
Q ss_pred CCCCEEEEeceEEc-------ccCCeEEEEeCCcEeEEEcC-CCceEE
Q 032583 79 KEGTTVILRNAKID-------MFKGSMRLAVDKWGRVEVAE-PANFTV 118 (137)
Q Consensus 79 ~~Gd~v~I~na~~~-------~~~g~~~L~vg~~g~I~~~~-~~~~~v 118 (137)
..|++|.|.|-..+ .-.+.++|.+.+.--|.+.. +..+.+
T Consensus 130 ~~esiV~V~G~v~~~~~~~~~~~~~~~El~v~~i~vls~a~~~lP~~~ 177 (550)
T PTZ00401 130 PTESIVDVEATVCKVEQPITSTSHSDIELKVKKIHTVTESLRTLPFTL 177 (550)
T ss_pred CCCCEEEEEEEEEecCccCCCCCCccEEEEeeEEEEEeCCCCCCCCCc
Confidence 89999999996654 23577999999887776663 334444
No 70
>PRK05733 single-stranded DNA-binding protein; Provisional
Probab=83.17 E-value=10 Score=29.10 Aligned_cols=84 Identities=13% Similarity=0.207 Sum_probs=53.9
Q ss_pred CCCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEee-------Ccce-------EEEEEecCCc----CCCCCCCE
Q 032583 22 GTSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGD-------ETGM-------IIFTARNDQV----DLMKEGTT 83 (137)
Q Consensus 22 ~~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgD-------eTG~-------I~ltlW~~~~----~~i~~Gd~ 83 (137)
+++.+.|+++|..--+.+.+. +| ..+++..||= ++|. +++++|...+ +.++.|+.
T Consensus 4 ~mNkV~LiGrlg~DPElr~t~--nG-----~~va~fsVAv~~~~k~~~~Ge~~e~T~w~~Vv~fgk~Ae~v~~~l~KGs~ 76 (172)
T PRK05733 4 GVNKVILVGTCGQDPEVRYLP--NG-----NAVTNLSLATSEQWTDKQSGQKVERTEWHRVSLFGKVAEIAGEYLRKGSQ 76 (172)
T ss_pred cceEEEEEEEecCCCEEEECC--CC-----CEEEEEEEEEcCccccCCCCcccccceEEEEEEehHHHHHHHHHhCCCCE
Confidence 467788999998865665542 44 3566655552 2343 8999999654 44689999
Q ss_pred EEEeceEEcc-cC--C----eEEEEeCCcEeEEEcC
Q 032583 84 VILRNAKIDM-FK--G----SMRLAVDKWGRVEVAE 112 (137)
Q Consensus 84 v~I~na~~~~-~~--g----~~~L~vg~~g~I~~~~ 112 (137)
|.|.+-.... |. | .+++.++..|.+..++
T Consensus 77 V~VeGrLr~~~y~kdG~~r~~~eVvvd~~g~v~~L~ 112 (172)
T PRK05733 77 VYIEGKLQTREWEKDGIKRYTTEIVVDMQGTMQLLG 112 (172)
T ss_pred EEEEEEEEeCcEecCCEEEEEEEEEEeecCeEEECc
Confidence 9999865432 32 2 4556655555555543
No 71
>PRK07374 dnaE DNA polymerase III subunit alpha; Validated
Probab=82.26 E-value=3.5 Score=40.28 Aligned_cols=84 Identities=17% Similarity=0.165 Sum_probs=59.5
Q ss_pred eeeccCC--CCCCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecCC----cCCCCCCCEEEEe
Q 032583 14 TKVDQLR--PGTSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARNDQ----VDLMKEGTTVILR 87 (137)
Q Consensus 14 ~kI~dL~--p~~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~~----~~~i~~Gd~v~I~ 87 (137)
..+.+|. ++...+.+.+.|.++..++++ .| ..|+-+.+-|+||.+.+++|-+. ...+.+|..+.|.
T Consensus 989 ~~~~~l~~~~~~~~v~v~g~i~~~k~~~Tk---~G-----~~maf~~leD~tg~~e~vvFp~~y~~~~~~l~~~~~~~v~ 1060 (1170)
T PRK07374 989 ISLSSLEEQPDKAKVSAIAMIPEMKQVTTR---KG-----DRMAILQLEDLTGSCEAVVFPKSYERLSDHLMTDTRLLVW 1060 (1170)
T ss_pred cCHHHHhcccCCCEEEEEEEEEEeEecccC---CC-----CEEEEEEEEECCCCEEEEECHHHHHHHHHHhccCCEEEEE
Confidence 3455554 233457888888888776543 24 47999999999999999999753 3457899999998
Q ss_pred ceEEcccCCeEEEEeCCcE
Q 032583 88 NAKIDMFKGSMRLAVDKWG 106 (137)
Q Consensus 88 na~~~~~~g~~~L~vg~~g 106 (137)
+-.-+ ..+.++|.+.+--
T Consensus 1061 g~v~~-~~~~~~~~~~~i~ 1078 (1170)
T PRK07374 1061 AKVDR-RDDRVQLIIDDCR 1078 (1170)
T ss_pred EEEEe-cCCeEEEEEeeee
Confidence 86643 3466777765443
No 72
>PRK09010 single-stranded DNA-binding protein; Provisional
Probab=81.75 E-value=16 Score=28.15 Aligned_cols=84 Identities=13% Similarity=0.172 Sum_probs=53.0
Q ss_pred CCCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEee-------Ccc-------eEEEEEecCCc----CCCCCCCE
Q 032583 22 GTSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGD-------ETG-------MIIFTARNDQV----DLMKEGTT 83 (137)
Q Consensus 22 ~~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgD-------eTG-------~I~ltlW~~~~----~~i~~Gd~ 83 (137)
+++.+.|++++..-.+.+.+. +| ..+++..||= .+| -+++++|...+ ..++.|+-
T Consensus 5 ~~N~V~LiGrLg~DPelR~t~--nG-----~~v~~fsVAvn~~~kd~~~Ge~~e~t~w~~V~~fgk~Ae~~~~~L~KGs~ 77 (177)
T PRK09010 5 GVNKVILVGNLGQDPEVRYMP--NG-----GAVANITLATSESWRDKQTGEMKEQTEWHRVVLFGKLAEVAGEYLRKGSQ 77 (177)
T ss_pred CceEEEEEEEeCCCceEEEcC--CC-----CEEEEEEEEEcCccccCcccccccceEEEEEEEehhHHHHHHHhcCCCCE
Confidence 356678888888865665542 34 4566655552 133 46999999654 34799999
Q ss_pred EEEeceEEcc-cCC-------eEEEEeCCcEeEEEcC
Q 032583 84 VILRNAKIDM-FKG-------SMRLAVDKWGRVEVAE 112 (137)
Q Consensus 84 v~I~na~~~~-~~g-------~~~L~vg~~g~I~~~~ 112 (137)
|.|.+-.... |.+ .++|.+...+.+..++
T Consensus 78 V~VeGrL~~~~yedkdG~~r~~~eVvv~~~~~~~~l~ 114 (177)
T PRK09010 78 VYIEGQLRTRKWTDQSGQDRYTTEVVVNVGGTMQMLG 114 (177)
T ss_pred EEEEEEEEeccccCCCCCEEEEEEEEEecCCcEEEcc
Confidence 9999977533 532 4555555555555443
No 73
>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=81.64 E-value=8.8 Score=28.16 Aligned_cols=65 Identities=12% Similarity=-0.001 Sum_probs=42.2
Q ss_pred CCCCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecCC--cCCCCCCCEEEEeceEEcccCCeE
Q 032583 21 PGTSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARNDQ--VDLMKEGTTVILRNAKIDMFKGSM 98 (137)
Q Consensus 21 p~~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~~--~~~i~~Gd~v~I~na~~~~~~g~~ 98 (137)
++...|.|++.|++--.-. .-++.|.||.|.+-.=++. .-.+.|+|.|+|.+-.=+.|++ .
T Consensus 55 ~Ddt~V~L~G~Iv~~l~~d----------------~Y~F~D~TG~I~VeId~~~w~G~~v~p~d~V~I~GeVDk~~~~-~ 117 (126)
T TIGR00156 55 HDGASVTLRGNIISHIGDD----------------RYVFRDKSGEINVVIPAAVWNGREVQPKDMVNISGSLDKKSAP-A 117 (126)
T ss_pred CCCCEEEEEEEEEEEeCCc----------------eEEEECCCCCEEEEECHHHcCCCcCCCCCEEEEEEEECCCCCC-e
Confidence 3455577777776532111 1267899999999763322 2247899999999988777764 4
Q ss_pred EEEe
Q 032583 99 RLAV 102 (137)
Q Consensus 99 ~L~v 102 (137)
++.+
T Consensus 118 ~IdV 121 (126)
T TIGR00156 118 EVDV 121 (126)
T ss_pred EEEE
Confidence 5433
No 74
>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=81.31 E-value=4.2 Score=30.64 Aligned_cols=62 Identities=13% Similarity=0.126 Sum_probs=41.2
Q ss_pred CCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEe-------------eCcceEEEEEecCCcC----CCCCCCEEE
Q 032583 23 TSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVG-------------DETGMIIFTARNDQVD----LMKEGTTVI 85 (137)
Q Consensus 23 ~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~Vg-------------DeTG~I~ltlW~~~~~----~i~~Gd~v~ 85 (137)
++.+.|.++|..--+.+.+. +|. .++...|+ |.|--+++++|..+++ .++.|+.|.
T Consensus 4 ~N~V~L~G~l~~dPe~r~t~--~G~-----~v~~fsvA~~~~~~~~~G~~~~~t~~~~v~~wg~~Ae~~~~~l~KG~~V~ 76 (164)
T TIGR00621 4 VNKVILVGRLTRDPELRYTP--SGN-----AVANFTLATNRRWKDQDGEWKEETEWHDIVIFGRLAEVAAQYLKKGSLVY 76 (164)
T ss_pred ccEEEEEEEeCCCCEEEECC--CCC-----EEEEEEEEEcCceecCCCCEeccceEEEEEEehHHHHHHHHhCCCCCEEE
Confidence 45577888887755555432 442 34443333 3466899999987543 469999999
Q ss_pred EeceEE
Q 032583 86 LRNAKI 91 (137)
Q Consensus 86 I~na~~ 91 (137)
|.+...
T Consensus 77 V~G~L~ 82 (164)
T TIGR00621 77 VEGRLR 82 (164)
T ss_pred EEEEEE
Confidence 999765
No 75
>PRK06752 single-stranded DNA-binding protein; Validated
Probab=80.93 E-value=4.1 Score=28.58 Aligned_cols=63 Identities=11% Similarity=0.102 Sum_probs=42.0
Q ss_pred CCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEee-----------CcceEEEEEecCCcC----CCCCCCEEEEe
Q 032583 23 TSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGD-----------ETGMIIFTARNDQVD----LMKEGTTVILR 87 (137)
Q Consensus 23 ~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgD-----------eTG~I~ltlW~~~~~----~i~~Gd~v~I~ 87 (137)
|+.+.|.+++..-.+.+.+ .+| ..++...||- +|--+++++|..+|+ .++.|+.|.|.
T Consensus 2 mN~v~liGrl~~dPelr~t--~~G-----~~~~~f~lAv~~~~~~~~g~~~t~~~~v~~wg~~Ae~~~~~l~KG~~V~V~ 74 (112)
T PRK06752 2 MNRVVLIGRLTKEPELYYT--KQG-----VAYARVCVAVNRGFRNSLGEQQVDFINCVVWRKSAENVTEYCTKGSLVGIT 74 (112)
T ss_pred ceEEEEEEECcCCCEEEEC--CCC-----CEEEEEEEEECCCeEcCCCCEEEEEEEEEEehHHHHHHHHhcCCCCEEEEE
Confidence 3456777777765555543 244 3566655652 255688999996553 46899999999
Q ss_pred ceEEc
Q 032583 88 NAKID 92 (137)
Q Consensus 88 na~~~ 92 (137)
|-...
T Consensus 75 G~l~~ 79 (112)
T PRK06752 75 GRIHT 79 (112)
T ss_pred EEEEe
Confidence 88653
No 76
>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=80.82 E-value=15 Score=24.94 Aligned_cols=59 Identities=12% Similarity=0.024 Sum_probs=41.8
Q ss_pred eEEEEEEeeCcceEEEEEecCC----------cCCCCCCCEEEEeceEEcccC-------CeEEEEeCCcEeEEEc
Q 032583 53 RIAECLVGDETGMIIFTARNDQ----------VDLMKEGTTVILRNAKIDMFK-------GSMRLAVDKWGRVEVA 111 (137)
Q Consensus 53 ~v~~~~VgDeTG~I~ltlW~~~----------~~~i~~Gd~v~I~na~~~~~~-------g~~~L~vg~~g~I~~~ 111 (137)
.+.=+.+-|.+|.+...+=... +..+..|++|.+.|...+.-+ +.++|.+.+.--+.+.
T Consensus 17 k~~Fi~LrD~sg~iQ~v~~~~~~~~~~~~~~~~~~l~~es~V~V~G~v~~~~~~~~~~~~~~~El~~~~i~il~~~ 92 (102)
T cd04320 17 KLAFLVLRQQGYTIQGVLAASAEGVSKQMVKWAGSLSKESIVDVEGTVKKPEEPIKSCTQQDVELHIEKIYVVSEA 92 (102)
T ss_pred ceEEEEEecCCceEEEEEeCCcccCCHHHHHHHhcCCCccEEEEEEEEECCCCcccCCCcCcEEEEEEEEEEEecC
Confidence 4556678899999888885332 234789999999998776433 6688887766555444
No 77
>PLN02502 lysyl-tRNA synthetase
Probab=80.56 E-value=8.6 Score=34.65 Aligned_cols=73 Identities=15% Similarity=0.202 Sum_probs=52.4
Q ss_pred ceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecCCc-----------CCCCCCCEEEEeceEEccc
Q 032583 26 HTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARNDQV-----------DLMKEGTTVILRNAKIDMF 94 (137)
Q Consensus 26 v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~~~-----------~~i~~Gd~v~I~na~~~~~ 94 (137)
|.|.|+|.++ |.- +++.=+.|-|.+|.|.+.+=.+.. ..+..||+|.+.|-..+..
T Consensus 111 V~v~GrV~~~-------R~~------Gk~~F~~LrD~~g~iQv~~~~~~~~~~~~~~~~~~~~l~~gdiV~V~G~~~~t~ 177 (553)
T PLN02502 111 VSVAGRIMAK-------RAF------GKLAFYDLRDDGGKIQLYADKKRLDLDEEEFEKLHSLVDRGDIVGVTGTPGKTK 177 (553)
T ss_pred EEEEEEEEEE-------ecC------CCeEEEEEecCCccEEEEEECccccchhHHHHHHHhCCCCCcEEEEEEEEEecC
Confidence 5666666654 222 355667888999998887643211 2478999999999888888
Q ss_pred CCeEEEEeCCcEeEEEc
Q 032583 95 KGSMRLAVDKWGRVEVA 111 (137)
Q Consensus 95 ~g~~~L~vg~~g~I~~~ 111 (137)
.|.++|.+.+.--+.+.
T Consensus 178 ~gelel~~~~i~vLs~~ 194 (553)
T PLN02502 178 KGELSIFPTSFEVLTKC 194 (553)
T ss_pred CCCEEEEEeEEEEEecc
Confidence 89999999887666554
No 78
>PRK07274 single-stranded DNA-binding protein; Provisional
Probab=80.25 E-value=4.3 Score=29.45 Aligned_cols=62 Identities=8% Similarity=0.146 Sum_probs=39.2
Q ss_pred CCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEe------eC-----cceEEEEEecCCcCC----CCCCCEEEEe
Q 032583 23 TSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVG------DE-----TGMIIFTARNDQVDL----MKEGTTVILR 87 (137)
Q Consensus 23 ~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~Vg------De-----TG~I~ltlW~~~~~~----i~~Gd~v~I~ 87 (137)
|+.+.|.+++-+-.+.+.+ .+| ..++...|| |+ |--+++++|..+++. ++.|+.|.|.
T Consensus 2 mN~v~LiGrL~~dPelr~t--~~g-----~~~~~fslAv~~~~k~~~g~~~t~w~~v~~fg~~Ae~v~~~l~KG~~V~V~ 74 (131)
T PRK07274 2 YNKVILIGRLTATPELVKT--AND-----KSVARVTLAVNRRFKNQNGEREADFINVVLWGKLAETLASYASKGSLISID 74 (131)
T ss_pred eeEEEEEEEccCCCeEEEC--CCC-----CEEEEEEEEEcCceecCCCCEEEEEEEEEEehHHHHHHHHHcCCCCEEEEE
Confidence 3446677777665444432 133 345555554 32 447899999976543 6899999999
Q ss_pred ceEE
Q 032583 88 NAKI 91 (137)
Q Consensus 88 na~~ 91 (137)
+-..
T Consensus 75 Grl~ 78 (131)
T PRK07274 75 GELR 78 (131)
T ss_pred EEEE
Confidence 8655
No 79
>PRK07279 dnaE DNA polymerase III DnaE; Reviewed
Probab=80.14 E-value=7.3 Score=37.70 Aligned_cols=84 Identities=24% Similarity=0.306 Sum_probs=59.9
Q ss_pred eeeeccCCCCCCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecCC----cCCCCCCCEEEEec
Q 032583 13 FTKVDQLRPGTSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARNDQ----VDLMKEGTTVILRN 88 (137)
Q Consensus 13 ~~kI~dL~p~~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~~----~~~i~~Gd~v~I~n 88 (137)
...+.+|.. ...+.+.+.|.++...++. ..| ..|+-+.+.|+||.+.+++|-+. ...+.+|..+.|.+
T Consensus 875 ~~~~~~l~~-~~~~~~~~~i~~~~~~~tk--~~g-----~~maf~~leD~~g~ie~~vFp~~y~~~~~~l~~~~~~~v~G 946 (1034)
T PRK07279 875 FTPISQLVK-NSEATILVQIQSIRVIRTK--TKG-----QQMAFLSVTDTKKKLDVTLFPETYRQYKDELKEGKFYYLKG 946 (1034)
T ss_pred CccHHHHhc-CCcceEEEEEEEEEEEEEc--CCC-----CeEEEEEEeeCCCcEEEEECHHHHHHHHHHhccCCEEEEEE
Confidence 345666654 3456788888887775543 123 47899999999999999999753 34578999999988
Q ss_pred eEEcccCCeEEEEeCCc
Q 032583 89 AKIDMFKGSMRLAVDKW 105 (137)
Q Consensus 89 a~~~~~~g~~~L~vg~~ 105 (137)
-.-+ .++.++|.+.+-
T Consensus 947 ~v~~-~~~~~~l~~~~i 962 (1034)
T PRK07279 947 KIQE-RDGRLQMVLQQI 962 (1034)
T ss_pred EEEe-cCCeeEEEEeee
Confidence 7654 366677765443
No 80
>PRK06826 dnaE DNA polymerase III DnaE; Reviewed
Probab=79.33 E-value=8.5 Score=37.63 Aligned_cols=75 Identities=11% Similarity=0.044 Sum_probs=54.5
Q ss_pred CCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecCC----cCCCCCCCEEEEeceEEcccCCeEE
Q 032583 24 SGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARNDQ----VDLMKEGTTVILRNAKIDMFKGSMR 99 (137)
Q Consensus 24 ~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~~----~~~i~~Gd~v~I~na~~~~~~g~~~ 99 (137)
..+.+.+.|.++..+++. .| ..|+-+.+.|+||.+.+++|-+. ...+++|..|.|.+-.-...++.++
T Consensus 992 ~~v~v~g~i~~~~~~~tk---~G-----~~maf~~leD~~g~~e~~vfp~~~~~~~~~l~~~~~~~v~g~v~~~~~~~~~ 1063 (1151)
T PRK06826 992 DKVIIGGIITEVKRKTTR---NN-----EMMAFLTLEDLYGTVEVIVFPKVYEKYRSLLNEDNIVLIKGRVSLREDEEPK 1063 (1151)
T ss_pred cEEEEEEEEEEeEeeccC---CC-----CeEEEEEEEECCCcEEEEECHHHHHHHHHHhccCCEEEEEEEEEecCCCceE
Confidence 457788888887765542 23 47999999999999999999753 3457899999998876433356677
Q ss_pred EEeCCcE
Q 032583 100 LAVDKWG 106 (137)
Q Consensus 100 L~vg~~g 106 (137)
|.+.+--
T Consensus 1064 ~~~~~~~ 1070 (1151)
T PRK06826 1064 LICEEIE 1070 (1151)
T ss_pred EEEeeee
Confidence 7765443
No 81
>PRK05813 single-stranded DNA-binding protein; Provisional
Probab=79.21 E-value=7.7 Score=30.91 Aligned_cols=65 Identities=12% Similarity=0.073 Sum_probs=48.4
Q ss_pred CCCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEee-----CcceEEEEEecCCcC---CCCCCCEEEEeceEEcc
Q 032583 22 GTSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGD-----ETGMIIFTARNDQVD---LMKEGTTVILRNAKIDM 93 (137)
Q Consensus 22 ~~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgD-----eTG~I~ltlW~~~~~---~i~~Gd~v~I~na~~~~ 93 (137)
+++.+.|.+++..-.+.+.+. .| ..++...||= .|--|++++|..+|+ .++.|+.|.|.|.....
T Consensus 108 ~~N~V~LiGrL~~DPelR~t~--~G-----~~va~f~lAvnr~~~~td~i~~v~wg~~Ae~~~~l~KG~~V~V~GrL~sr 180 (219)
T PRK05813 108 NPNEIFLDGYICKEPVYRTTP--FG-----REIADLLLAVNRPYNKSDYIPCIAWGRNARFCKTLEVGDNIRVWGRVQSR 180 (219)
T ss_pred CccEEEEEEEccCCCeEEECC--CC-----CEEEEEEEEEcCCCCCceEEEEEEEhHHhHHHhhCCCCCEEEEEEEEEec
Confidence 466778888888876666543 45 4788888873 367899999996543 36899999999987643
No 82
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=79.17 E-value=6.3 Score=36.13 Aligned_cols=69 Identities=17% Similarity=0.227 Sum_probs=47.7
Q ss_pred ceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecCC----cCCCCCCCEEEEeceEEcccCCeEEEE
Q 032583 26 HTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARNDQ----VDLMKEGTTVILRNAKIDMFKGSMRLA 101 (137)
Q Consensus 26 v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~~----~~~i~~Gd~v~I~na~~~~~~g~~~L~ 101 (137)
|.+.++|+.+... -| ..|. .+-|+||.|-..++.+. -..+++||+|++.+-.. ...|.+++-
T Consensus 216 V~I~GeV~qikqT------~G-----PTVF--tltDetg~i~aAAFe~aGvRAyP~IevGdiV~ViG~V~-~r~g~lQiE 281 (715)
T COG1107 216 VRIEGEVTQIKQT------SG-----PTVF--TLTDETGAIWAAAFEEAGVRAYPEIEVGDIVEVIGEVT-RRDGRLQIE 281 (715)
T ss_pred EEEEEEEEEEEEc------CC-----CEEE--EEecCCCceehhhhccCCcccCCCCCCCceEEEEEEEe-ecCCcEEEe
Confidence 5666666665432 23 3444 68899999999888843 25589999999998664 567888887
Q ss_pred eCCcEeE
Q 032583 102 VDKWGRV 108 (137)
Q Consensus 102 vg~~g~I 108 (137)
+-.--++
T Consensus 282 ~~~me~L 288 (715)
T COG1107 282 IEAMEKL 288 (715)
T ss_pred ehhhHHh
Confidence 6554443
No 83
>PRK06751 single-stranded DNA-binding protein; Provisional
Probab=78.80 E-value=5.3 Score=30.69 Aligned_cols=66 Identities=12% Similarity=0.172 Sum_probs=43.1
Q ss_pred CCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEe------e-----CcceEEEEEecCCcC----CCCCCCEEEEe
Q 032583 23 TSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVG------D-----ETGMIIFTARNDQVD----LMKEGTTVILR 87 (137)
Q Consensus 23 ~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~Vg------D-----eTG~I~ltlW~~~~~----~i~~Gd~v~I~ 87 (137)
|..+.|.++|..-.+.+.+. .| ..|+...|| + +|--+++++|..+|+ .++.|+.|.|.
T Consensus 2 mN~V~LiGrL~~DpelR~t~--sG-----~~v~~fslAvnr~~~~~~ge~~tdwi~~v~wgk~Ae~~~~~l~KG~~V~Ve 74 (173)
T PRK06751 2 MNRVILVGRLTKDPDLRYTP--NG-----VAVATFTLAVNRAFANQQGEREADFINCVIWRKQAENVANYLKKGSLAGVD 74 (173)
T ss_pred ceEEEEEEEECCCCcEEECC--CC-----CEEEEEEEEEccceecCCCCEEEEEEEEEEeCcHHHHHHHHcCCCCEEEEE
Confidence 34567778877655555432 33 346665554 2 245799999997654 36899999999
Q ss_pred ceEEc-ccC
Q 032583 88 NAKID-MFK 95 (137)
Q Consensus 88 na~~~-~~~ 95 (137)
+.... .|.
T Consensus 75 GrL~~r~ye 83 (173)
T PRK06751 75 GRLQTRNYE 83 (173)
T ss_pred EEEEeCccC
Confidence 88763 353
No 84
>PRK07275 single-stranded DNA-binding protein; Provisional
Probab=78.78 E-value=4.9 Score=30.50 Aligned_cols=61 Identities=11% Similarity=0.103 Sum_probs=42.4
Q ss_pred CCceEEEEEEEcceeeeeccCCCccccceeEEEEEEe-----------eCcceEEEEEecCCcCC----CCCCCEEEEec
Q 032583 24 SGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVG-----------DETGMIIFTARNDQVDL----MKEGTTVILRN 88 (137)
Q Consensus 24 ~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~Vg-----------DeTG~I~ltlW~~~~~~----i~~Gd~v~I~n 88 (137)
+.+.|.+++..-.+.+.+. .| ..|++..|| .+|--|++++|...|+. ++.|+-|.|.+
T Consensus 3 N~v~LiGrL~~DPElr~t~--sG-----~~v~~ftlAv~r~~~~~~ge~~tdfi~vv~wgk~Ae~~~~~l~KG~~V~VeG 75 (162)
T PRK07275 3 NNVVLVGRMTRDAELRYTP--SN-----VAVATFTLAVNRTFKSQNGEREADFINCVIWRQQAENLANWAKKGALIGVTG 75 (162)
T ss_pred eEEEEEEEECCCCeEEECC--CC-----CEEEEEEEEEcCceecCCCCEeeeEEEEEEEcHHHHHHHHHcCCCCEEEEEE
Confidence 4567777777655555442 44 366666664 24667999999976544 68999999999
Q ss_pred eEE
Q 032583 89 AKI 91 (137)
Q Consensus 89 a~~ 91 (137)
...
T Consensus 76 rl~ 78 (162)
T PRK07275 76 RIQ 78 (162)
T ss_pred EEE
Confidence 875
No 85
>KOG3108 consensus Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [Replication, recombination and repair]
Probab=78.77 E-value=10 Score=31.21 Aligned_cols=52 Identities=27% Similarity=0.231 Sum_probs=39.9
Q ss_pred EEEeeCcceEEEEEecCC--cC----CCCCCCEEEEeceEEcccCCeEEEEeCCcEeEE
Q 032583 57 CLVGDETGMIIFTARNDQ--VD----LMKEGTTVILRNAKIDMFKGSMRLAVDKWGRVE 109 (137)
Q Consensus 57 ~~VgDeTG~I~ltlW~~~--~~----~i~~Gd~v~I~na~~~~~~g~~~L~vg~~g~I~ 109 (137)
-.|.|-||.|-...|... .. .+++|.-|++.|+. +.|+|...|.+-+---|+
T Consensus 89 y~I~D~tg~id~r~W~~~~~~~~e~~~l~~~~yVkv~G~L-k~f~Gk~sl~~fkI~pv~ 146 (265)
T KOG3108|consen 89 YEIEDGTGQIDVRQWFHDNAESEEMPALETGTYVKVYGHL-KPFQGKKSLQVFKIRPVE 146 (265)
T ss_pred EEEecCcccEEEEEeccccchhhhCcccccCcEEEeeecc-cCCCCceeEEEEeeeeee
Confidence 479999999999999743 22 46889999998877 789998888765444433
No 86
>PRK08763 single-stranded DNA-binding protein; Provisional
Probab=78.65 E-value=5.7 Score=30.27 Aligned_cols=64 Identities=13% Similarity=0.133 Sum_probs=43.5
Q ss_pred CCCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEe------eCcc-------eEEEEEecCCcC----CCCCCCEE
Q 032583 22 GTSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVG------DETG-------MIIFTARNDQVD----LMKEGTTV 84 (137)
Q Consensus 22 ~~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~Vg------DeTG-------~I~ltlW~~~~~----~i~~Gd~v 84 (137)
+++.+.|.+++..-.+.+.+ .+| ..++...|| |..| -+++++|+.+++ .++.|+.|
T Consensus 4 ~~Nkv~LiGrLg~DPelr~t--~~G-----~~va~fsVA~~~~~k~~~G~~~e~t~w~~Vv~fgk~Ae~v~~~L~KGs~V 76 (164)
T PRK08763 4 GINKVILVGNLGNDPDIKYT--QSG-----MTITRISLATTSVRKDREGNTQERTEWHRVKFFGKLGEIAGEYLRKGSQC 76 (164)
T ss_pred cceEEEEEEEecCCCeEEEc--CCC-----CeEEEEEEEeccceecCCCCeeccceEEEEEEehHHHHHHHHhcCCCCEE
Confidence 46667888888875555543 245 356666665 3233 489999986543 36899999
Q ss_pred EEeceEEc
Q 032583 85 ILRNAKID 92 (137)
Q Consensus 85 ~I~na~~~ 92 (137)
.|.+-...
T Consensus 77 ~VeGrL~~ 84 (164)
T PRK08763 77 YIEGSIRY 84 (164)
T ss_pred EEEEEEEe
Confidence 99998653
No 87
>PRK10053 hypothetical protein; Provisional
Probab=78.39 E-value=16 Score=26.86 Aligned_cols=44 Identities=9% Similarity=-0.005 Sum_probs=32.4
Q ss_pred EEeeCcceEEEEEecCC--cCCCCCCCEEEEeceEEcccCCeEEEEe
Q 032583 58 LVGDETGMIIFTARNDQ--VDLMKEGTTVILRNAKIDMFKGSMRLAV 102 (137)
Q Consensus 58 ~VgDeTG~I~ltlW~~~--~~~i~~Gd~v~I~na~~~~~~g~~~L~v 102 (137)
++.|.||.|.+-+=++. ...+.|.|.|+|.+-.=+.|.. .++-|
T Consensus 80 ~F~D~tG~I~VeID~~~w~G~~v~p~~kV~I~GevDk~~~~-~~IdV 125 (130)
T PRK10053 80 VFRDKSGEINVIIPAAVFDGREVQPDQMININGSLDKKSAP-PVVRV 125 (130)
T ss_pred EEECCCCcEEEEeCHHHcCCCcCCCCCEEEEEEEECCCCCC-eEEEE
Confidence 67899999999763321 1257999999999998887764 44443
No 88
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=78.33 E-value=1.5 Score=32.63 Aligned_cols=25 Identities=24% Similarity=0.199 Sum_probs=21.0
Q ss_pred eeEEEEEEeeCcceEEEEEecCCcC
Q 032583 52 MRIAECLVGDETGMIIFTARNDQVD 76 (137)
Q Consensus 52 ~~v~~~~VgDeTG~I~ltlW~~~~~ 76 (137)
.-+..+.|.|.||.+.++++++.+.
T Consensus 67 ry~l~~~i~D~Tg~~~~~~F~~~ae 91 (166)
T cd04476 67 RYILSLNVADHTGEAWLTLFDEVAE 91 (166)
T ss_pred EEEEEEEEEeCCCCEEEEEehHHHH
Confidence 3556799999999999999997653
No 89
>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=78.14 E-value=7.6 Score=25.60 Aligned_cols=31 Identities=23% Similarity=0.203 Sum_probs=24.3
Q ss_pred CcceEEEEEecCCc----CCCCCCCEEEEeceEEc
Q 032583 62 ETGMIIFTARNDQV----DLMKEGTTVILRNAKID 92 (137)
Q Consensus 62 eTG~I~ltlW~~~~----~~i~~Gd~v~I~na~~~ 92 (137)
.+=-+++++|++++ ..+++||.|.|.+-...
T Consensus 42 ~~~~~~v~~~g~~a~~~~~~~~kG~~V~v~G~l~~ 76 (100)
T cd04496 42 ETDWIRVVAFGKLAENAAKYLKKGDLVYVEGRLRT 76 (100)
T ss_pred ccEEEEEEEEhHHHHHHHHHhCCCCEEEEEEEEEe
Confidence 55678999999754 33689999999987753
No 90
>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=78.12 E-value=2.6 Score=28.26 Aligned_cols=62 Identities=18% Similarity=0.191 Sum_probs=37.3
Q ss_pred CCceEEEEEEEcceeeeeccCCCccccceeEEEEEEe-------------eCcceEEEEEecCCcC----CCCCCCEEEE
Q 032583 24 SGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVG-------------DETGMIIFTARNDQVD----LMKEGTTVIL 86 (137)
Q Consensus 24 ~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~Vg-------------DeTG~I~ltlW~~~~~----~i~~Gd~v~I 86 (137)
+.+.|.++|..-.+.+.+. +|+ .++...|+ +.+--+++++|.++|+ .++.||.|.|
T Consensus 2 N~v~l~G~l~~~p~~~~~~--~g~-----~~~~f~la~~~~~~~~~~~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V 74 (104)
T PF00436_consen 2 NKVTLIGRLGKDPELRYTK--NGT-----PVARFSLAVNRRFKDDGGEGDEKTDWINVVAWGKLAENVAEYLKKGDRVYV 74 (104)
T ss_dssp EEEEEEEEESSSEEEEEET--TSE-----EEEEEEEEEEEEEEETTSCEEEEEEEEEEEEEHHHHHHHHHH--TT-EEEE
T ss_pred cEEEEEEEECCCcEEEECC--CCC-----EEEEEEEEEecEEeeeeccCccceEEEEEEeeeecccccceEEcCCCEEEE
Confidence 3467777777765555543 442 34433332 3345789999997553 3689999999
Q ss_pred eceEEc
Q 032583 87 RNAKID 92 (137)
Q Consensus 87 ~na~~~ 92 (137)
.+....
T Consensus 75 ~G~l~~ 80 (104)
T PF00436_consen 75 EGRLRT 80 (104)
T ss_dssp EEEEEE
T ss_pred EEEEEe
Confidence 987653
No 91
>cd01491 Ube1_repeat1 Ubiquitin activating enzyme (E1), repeat 1. E1, a highly conserved small protein present universally in eukaryotic cells, is part of cascade to attach ubiquitin (Ub) covalently to substrate proteins. This cascade consists of activating (E1), conjugating (E2), and/or ligating (E3) enzymes and then targets them for degradation by the 26S proteasome. E1 activates ubiquitin by C-terminal adenylation, and subsequently forms a highly reactive thioester bond between its catalytic cysteine and ubiquitin's C-terminus. E1 also associates with E2 and promotes ubiquitin transfer to the E2's catalytic cysteine. Ubiquitin-E1 is a single-chain protein with a weakly conserved two-fold repeat. This CD represents the first repeat of Ub-E1.
Probab=77.20 E-value=10 Score=31.23 Aligned_cols=67 Identities=16% Similarity=0.323 Sum_probs=50.2
Q ss_pred EEEEEEeeCcceEEEEEecCCcCCCCCCCEEEEeceEEcccCCeEEEEeCCcEeEEEcCCCceEEcCCCCcccc
Q 032583 54 IAECLVGDETGMIIFTARNDQVDLMKEGTTVILRNAKIDMFKGSMRLAVDKWGRVEVAEPANFTVKEDNNLSLI 127 (137)
Q Consensus 54 v~~~~VgDeTG~I~ltlW~~~~~~i~~Gd~v~I~na~~~~~~g~~~L~vg~~g~I~~~~~~~~~vn~~~n~S~~ 127 (137)
+...+.+|..|.| ++.+++.-.++.||.|++.+. +|..+||=++-=+|+..+++.|++.++..+|..
T Consensus 167 ~i~~I~~~~~g~V--~~~~~~~h~l~~gd~V~f~ev-----~gm~~lN~~~~~~v~~~~~~~f~i~d~~~~~~y 233 (286)
T cd01491 167 MISSISKDNPGVV--TCLDETRHGFEDGDYVTFSEV-----EGMTELNGCEPRKIKVKGPYTFSIGDTSSFSEY 233 (286)
T ss_pred ceeeeecCCceEE--EEECCcccCCcCCCEEEEecc-----CcchhhCCCccEEEEECCCCeEEECcCcCcCcc
Confidence 4455667788876 567877778999999999763 466667655556888888888998887777764
No 92
>PRK05672 dnaE2 error-prone DNA polymerase; Validated
Probab=77.04 E-value=5.8 Score=38.35 Aligned_cols=69 Identities=14% Similarity=0.090 Sum_probs=48.4
Q ss_pred CceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecCC----cCCCCCCCEEEEeceEEcccCCeEEE
Q 032583 25 GHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARNDQ----VDLMKEGTTVILRNAKIDMFKGSMRL 100 (137)
Q Consensus 25 ~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~~----~~~i~~Gd~v~I~na~~~~~~g~~~L 100 (137)
.+.+-+.|..+..+.++ ++ |+-+.+.|+||.+.+++|-+. ...+++|..+.|.+-.-+ .++.+++
T Consensus 955 ~v~v~g~i~~~~~~~Tk---------kG-maf~~leD~~g~~e~~ifp~~~~~~~~~l~~~~~~~v~g~v~~-~~~~~~~ 1023 (1046)
T PRK05672 955 RVRVAGVVTHRQRPGTA---------SG-VTFLTLEDETGMVNVVVWPGLWERQRREALGARLLLVRGRVQN-AEGVRHL 1023 (1046)
T ss_pred EEEEEEEEEEEEEecCC---------Cc-eEEEEEecCCCCEEEEECHHHHHHHHHHhccCCEEEEEEEEEe-cCCeEEE
Confidence 35565555555444321 25 889999999999999999753 345789999999886654 4566777
Q ss_pred EeCC
Q 032583 101 AVDK 104 (137)
Q Consensus 101 ~vg~ 104 (137)
.+.+
T Consensus 1024 ~~~~ 1027 (1046)
T PRK05672 1024 VADR 1027 (1046)
T ss_pred EEee
Confidence 6643
No 93
>PTZ00385 lysyl-tRNA synthetase; Provisional
Probab=76.52 E-value=25 Score=32.55 Aligned_cols=73 Identities=11% Similarity=0.084 Sum_probs=54.0
Q ss_pred CceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecCC----------cCCCCCCCEEEEeceEEccc
Q 032583 25 GHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARNDQ----------VDLMKEGTTVILRNAKIDMF 94 (137)
Q Consensus 25 ~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~~----------~~~i~~Gd~v~I~na~~~~~ 94 (137)
.|.|.|+|..+ |.- ++++=+.|-|.||.|.+.+-.+. ...+..||+|.+.|-..+..
T Consensus 109 ~V~vaGrV~~~-------R~~------Gk~~F~~LrD~~G~IQvv~~~~~~~~~~~~~~~~~~l~~gdiV~V~G~v~~t~ 175 (659)
T PTZ00385 109 TVRVAGRVTSV-------RDI------GKIIFVTIRSNGNELQVVGQVGEHFTREDLKKLKVSLRVGDIIGADGVPCRMQ 175 (659)
T ss_pred EEEEEEEEEee-------ecc------CCeEEEEEEECCceEEEEEECCccCCHHHHHHHHhCCCCCCEEEEEEEEEecC
Confidence 37777777654 222 34566778899999999885422 12478999999999888777
Q ss_pred CCeEEEEeCCcEeEEE
Q 032583 95 KGSMRLAVDKWGRVEV 110 (137)
Q Consensus 95 ~g~~~L~vg~~g~I~~ 110 (137)
.|.++|.+.+.--+.+
T Consensus 176 ~GeleI~~~~i~lLsk 191 (659)
T PTZ00385 176 RGELSVAASRMLILSP 191 (659)
T ss_pred CceEEEEeeEEEEech
Confidence 8999998888866665
No 94
>cd04486 YhcR_OBF_like YhcR_OBF_like: A subfamily of OB-fold domains similar to the OB folds of Bacillus subtilis YhcR. YhcR is a sugar-nonspecific nuclease, which is active in the presence of Ca2+ and Mn2+. It cleaves RNA endonucleolytically, producing 3'-monophosphate nucleosides. YhcR appears to be the major Ca2+ activated nuclease of B. subtilis. YhcR may be localized in the cell wall.
Probab=75.85 E-value=6.6 Score=26.04 Aligned_cols=36 Identities=17% Similarity=0.197 Sum_probs=26.5
Q ss_pred EEEEecCCcCCCCCCCEEEEeceEEcccCCeEEEEeCC
Q 032583 67 IFTARNDQVDLMKEGTTVILRNAKIDMFKGSMRLAVDK 104 (137)
Q Consensus 67 ~ltlW~~~~~~i~~Gd~v~I~na~~~~~~g~~~L~vg~ 104 (137)
-|..... ...+++||.|+|. +.+++|.|..+|.-..
T Consensus 35 ifV~~~~-~~~~~~Gd~V~vt-G~v~ey~g~tql~~~~ 70 (78)
T cd04486 35 IFVYTGS-GADVAVGDLVRVT-GTVTEYYGLTQLTAVS 70 (78)
T ss_pred EEEecCC-CCCCCCCCEEEEE-EEEEeeCCeEEEccCC
Confidence 3433333 5568999999998 8889999988876543
No 95
>PRK06920 dnaE DNA polymerase III DnaE; Reviewed
Probab=75.54 E-value=7 Score=38.07 Aligned_cols=84 Identities=15% Similarity=0.132 Sum_probs=58.8
Q ss_pred eeeccCCC-CCCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecCC----cCCCCCCCEEEEec
Q 032583 14 TKVDQLRP-GTSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARNDQ----VDLMKEGTTVILRN 88 (137)
Q Consensus 14 ~kI~dL~p-~~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~~----~~~i~~Gd~v~I~n 88 (137)
..+.+|.. ....+.+.+.|.++...++. .| ..|+-+.+-|+||.+.+++|-+. ...+.+|..+.|.+
T Consensus 933 ~~~~~l~~~~~~~v~v~g~i~~~~~~~tk---~g-----~~maf~~leD~tg~~e~~vFp~~y~~~~~~l~~~~~~~v~G 1004 (1107)
T PRK06920 933 PSLAQAMRHKKKVQRAIVYITSVKVIRTK---KG-----QKMAFITFCDQNDEMEAVVFPETYIHFSDKLQEGAIVLVDG 1004 (1107)
T ss_pred cCHHHHhhcCCCEEEEEEEEEEeEeecCC---CC-----CeEEEEEEeeCCCcEEEEECHHHHHHHHHHhccCCEEEEEE
Confidence 45666642 22357788888887765542 23 47999999999999999999643 35578999999988
Q ss_pred eEEcccCCeEEEEeCCcE
Q 032583 89 AKIDMFKGSMRLAVDKWG 106 (137)
Q Consensus 89 a~~~~~~g~~~L~vg~~g 106 (137)
-.-. .++.++|.+.+--
T Consensus 1005 ~v~~-~~~~~~~~~~~i~ 1021 (1107)
T PRK06920 1005 TIEL-RNHKLQWIVNGLY 1021 (1107)
T ss_pred EEEe-cCCcEEEEEeecc
Confidence 6643 4566777665443
No 96
>PRK06958 single-stranded DNA-binding protein; Provisional
Probab=75.04 E-value=8.7 Score=29.86 Aligned_cols=62 Identities=13% Similarity=0.076 Sum_probs=43.1
Q ss_pred CCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEe--------------eCcceEEEEEecCCcC----CCCCCCEE
Q 032583 23 TSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVG--------------DETGMIIFTARNDQVD----LMKEGTTV 84 (137)
Q Consensus 23 ~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~Vg--------------DeTG~I~ltlW~~~~~----~i~~Gd~v 84 (137)
++.|.|++++.+-.+.+.+. +| ..++...|| +.|--+++++|..+++ .++.|+.|
T Consensus 4 ~N~V~LiGrLg~DPElr~t~--nG-----~~va~fsVAv~~~~kdk~sGe~~e~T~w~~V~~fGk~AE~v~~~LkKGs~V 76 (182)
T PRK06958 4 VNKVILVGNLGADPEVRYLP--SG-----DAVANIRLATTDRYKDKASGEFKEATEWHRVAFFGRLAEIVGEYLKKGSSV 76 (182)
T ss_pred ccEEEEEEEecCCCeEEEcC--CC-----CEEEEEEEEeccccccccCCcccccceEEEEEEehHHHHHHHHHhCCCCEE
Confidence 45678888888765555442 44 356665554 2356789999986553 46899999
Q ss_pred EEeceEE
Q 032583 85 ILRNAKI 91 (137)
Q Consensus 85 ~I~na~~ 91 (137)
.|.+...
T Consensus 77 ~VeGrL~ 83 (182)
T PRK06958 77 YIEGRIR 83 (182)
T ss_pred EEEEEEE
Confidence 9998765
No 97
>PRK06293 single-stranded DNA-binding protein; Provisional
Probab=74.86 E-value=7.6 Score=29.57 Aligned_cols=64 Identities=17% Similarity=0.137 Sum_probs=44.8
Q ss_pred CCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEe--------eCcceEEEEEecCCcC----CCCCCCEEEEeceE
Q 032583 23 TSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVG--------DETGMIIFTARNDQVD----LMKEGTTVILRNAK 90 (137)
Q Consensus 23 ~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~Vg--------DeTG~I~ltlW~~~~~----~i~~Gd~v~I~na~ 90 (137)
|+.+.|.+++-.-.+.+.+. .| ..++...|| ++|-=+++++|...++ .++.|+.|.|.+-.
T Consensus 1 MN~V~LiGrLg~DPElR~t~--sG-----~~v~~FsLAvn~~~~~~~~T~wi~v~awg~~Ae~v~~yL~KG~~V~VeGrL 73 (161)
T PRK06293 1 MMFGYIVGRLGADPEERMTS--KG-----KRVVVLRLGVKSRVGSKDETVWCRCNIWGNRYDKMLPYLKKGSGVIVAGEM 73 (161)
T ss_pred CeEEEEEEEecCCCeEEEcC--CC-----CEEEEEEEEEeCCCCCccceEEEEEEEEhHHHHHHHHhCCCCCEEEEEEEE
Confidence 45577888887755555432 34 356666666 3677899999996543 37999999999987
Q ss_pred Ecc
Q 032583 91 IDM 93 (137)
Q Consensus 91 ~~~ 93 (137)
...
T Consensus 74 ~~~ 76 (161)
T PRK06293 74 SPE 76 (161)
T ss_pred EeC
Confidence 643
No 98
>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=74.12 E-value=24 Score=30.54 Aligned_cols=83 Identities=19% Similarity=0.148 Sum_probs=55.3
Q ss_pred eccCCCCC--CCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecC--------CcCCCCCCCEEE
Q 032583 16 VDQLRPGT--SGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARND--------QVDLMKEGTTVI 85 (137)
Q Consensus 16 I~dL~p~~--~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~--------~~~~i~~Gd~v~ 85 (137)
+++|.+.. +.+.|.|+|-++ |.- +.+.=+.|-|.+|.|.+++=.. .+..+..||+|.
T Consensus 3 ~~~l~~~~~g~~v~i~G~v~~~-------R~~------g~~~Fi~lrd~~g~iQ~v~~~~~~~~~~~~~~~~l~~~s~v~ 69 (428)
T TIGR00458 3 SADIKPEMDGQEVTFMGWVHEI-------RDL------GGLIFVLLRDREGLIQITAPAKKVSKNLFKWAKKLNLESVVA 69 (428)
T ss_pred hhhCchhhCCCEEEEEEEEEEE-------ecC------CCcEEEEEEeCCeeEEEEEECCcCCHHHHHHHhCCCCCcEEE
Confidence 45555422 335666666543 222 3466678899999999877532 123578999999
Q ss_pred EeceEEcccC--CeEEEEeCCcEeEEEc
Q 032583 86 LRNAKIDMFK--GSMRLAVDKWGRVEVA 111 (137)
Q Consensus 86 I~na~~~~~~--g~~~L~vg~~g~I~~~ 111 (137)
+.|-.....+ |.++|.+.+.--+.+.
T Consensus 70 v~G~v~~~~~~~~~~el~~~~i~vl~~~ 97 (428)
T TIGR00458 70 VRGIVKIKEKAPGGFEIIPTKIEVINEA 97 (428)
T ss_pred EEEEEEecCCCCCcEEEEEeEEEEEecC
Confidence 9997765433 7899999887666655
No 99
>PF02760 HIN: HIN-200/IF120x domain; InterPro: IPR004021 This domain has no known function. It is found in one or two copies per protein, and is found associated with the PAAD/DAPIN domain IPR004020 from INTERPRO.; PDB: 3RN2_A 3RN5_C 2OQ0_A 3B6Y_A 3RLN_A 3RNU_A 3RLO_A.
Probab=74.02 E-value=22 Score=27.43 Aligned_cols=64 Identities=17% Similarity=0.213 Sum_probs=37.4
Q ss_pred eeeeccCCCCCCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecCCcCC-CCCCCEEEEe
Q 032583 13 FTKVDQLRPGTSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARNDQVDL-MKEGTTVILR 87 (137)
Q Consensus 13 ~~kI~dL~p~~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~~~~~-i~~Gd~v~I~ 87 (137)
-.||.+|.....+- +.--+..+...... + ...+. -|.|.||.+.+......... .++||-+++.
T Consensus 101 TpKI~~L~~q~~Gt-~V~G~F~v~KK~v~--~------~~~~Y--eI~DnTG~MeVvv~G~~~ni~CEeGDKLrL~ 165 (170)
T PF02760_consen 101 TPKINDLQKQASGT-FVNGLFTVHKKTVN--K------KNTIY--EIQDNTGKMEVVVYGKWHNIKCEEGDKLRLF 165 (170)
T ss_dssp ---HHHHTTSSTTE-EEEEEEEEEEEEEE--S------SEEEE--EEEETTEEEEEEEEGGGCGCC--TT-EEEEE
T ss_pred CCchhHHhcCCCCc-EEeEEEEEEEEEEc--C------CeEEE--EEecCCCcEEEEEeccCcccccCCCCeEEEE
Confidence 35788998888774 44334444433221 1 12333 68999999999877755443 4899999874
No 100
>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=73.15 E-value=23 Score=23.11 Aligned_cols=51 Identities=10% Similarity=0.233 Sum_probs=35.4
Q ss_pred eEEEEEEeeCcceEEEEEecCC-------cCCCCCCCEEEEeceEEccc-----CCeEEEEeC
Q 032583 53 RIAECLVGDETGMIIFTARNDQ-------VDLMKEGTTVILRNAKIDMF-----KGSMRLAVD 103 (137)
Q Consensus 53 ~v~~~~VgDeTG~I~ltlW~~~-------~~~i~~Gd~v~I~na~~~~~-----~g~~~L~vg 103 (137)
.++=+.+-|.||.+...+=... ...+..||+|.+.|-..+.- .+.++|.+.
T Consensus 16 ~~~Fi~Lrd~~~~iQ~v~~~~~~~~~~~~~~~l~~~s~V~v~G~~~~~~~~~~~~~~~El~~~ 78 (85)
T cd04100 16 GLIFIDLRDGSGIVQVVVNKEELGEFFEEAEKLRTESVVGVTGTVVKRPEGNLATGEIELQAE 78 (85)
T ss_pred CEEEEEEEeCCeeEEEEEECCcChHHHHHHhCCCCCCEEEEEeEEEECCCCCCCCCCEEEEEe
Confidence 4566778899999888664332 23578999999999776532 455666553
No 101
>PRK13732 single-stranded DNA-binding protein; Provisional
Probab=73.07 E-value=9.8 Score=29.29 Aligned_cols=83 Identities=16% Similarity=0.199 Sum_probs=51.9
Q ss_pred CCCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEee-------Ccc-------eEEEEEecCCc----CCCCCCCE
Q 032583 22 GTSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGD-------ETG-------MIIFTARNDQV----DLMKEGTT 83 (137)
Q Consensus 22 ~~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgD-------eTG-------~I~ltlW~~~~----~~i~~Gd~ 83 (137)
+++.+.|.+++..--+.+.+. +| ..+++..||- ++| -+++++|+..+ ..++.|+.
T Consensus 5 ~mN~V~LiGrLg~DPElR~t~--nG-----~~va~fslAvn~~~kd~~~Ge~~e~t~w~~Vv~wgk~Ae~v~~~L~KG~~ 77 (175)
T PRK13732 5 GINKVILVGRLGKDPEVRYIP--NG-----GAVANLQVATSESWRDKQTGEMREQTEWHRVVLFGKLAEVAGEYLRKGAQ 77 (175)
T ss_pred CceEEEEEEEecCCCEEEEcC--CC-----CEEEEEEEEEcCccccCCCCceecceeEEEEEEecHHHHHHHHhcCCCCE
Confidence 466788889888865655542 44 3566666652 244 46899999654 34689999
Q ss_pred EEEeceEEcc-c--CC----eEEEEeCCcEeEEEc
Q 032583 84 VILRNAKIDM-F--KG----SMRLAVDKWGRVEVA 111 (137)
Q Consensus 84 v~I~na~~~~-~--~g----~~~L~vg~~g~I~~~ 111 (137)
|.|.+-.... | +| ..++.+...|.|..+
T Consensus 78 V~VeGrL~~r~ye~dG~kr~~~eIiv~~~g~~~fL 112 (175)
T PRK13732 78 VYIEGQLRTRSWEDNGITRYVTEILVKTTGTMQML 112 (175)
T ss_pred EEEEEEEEeeeEccCCeEEEEEEEEEeecCeEEEe
Confidence 9999875422 3 23 344545544455444
No 102
>PRK03932 asnC asparaginyl-tRNA synthetase; Validated
Probab=72.79 E-value=24 Score=30.76 Aligned_cols=75 Identities=15% Similarity=0.130 Sum_probs=51.6
Q ss_pred CCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecC-------CcCCCCCCCEEEEeceEEccc-
Q 032583 23 TSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARND-------QVDLMKEGTTVILRNAKIDMF- 94 (137)
Q Consensus 23 ~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~-------~~~~i~~Gd~v~I~na~~~~~- 94 (137)
.+.|.|.|+|-++-. - +.++=+.|-|.||.+.+.+-.+ .+..+..||+|.+.|-..+.-
T Consensus 16 ~~~V~i~G~v~~~R~-------~------g~~~Fi~lrD~~g~iq~~~~~~~~~~~~~~~~~l~~~s~v~v~G~v~~~~~ 82 (450)
T PRK03932 16 GQEVTVRGWVRTKRD-------S------GKIAFLQLRDGSCFKQLQVVKDNGEEYFEEIKKLTTGSSVIVTGTVVESPR 82 (450)
T ss_pred CCEEEEEEEEEEEEe-------C------CCeEEEEEECCCCcEEEEEEcCCChHHHHHHhcCCCCcEEEEEEEEEcCCC
Confidence 345788888866522 1 3556678899999887776432 223578999999999777543
Q ss_pred -CCeEEEEeCCcEeEEE
Q 032583 95 -KGSMRLAVDKWGRVEV 110 (137)
Q Consensus 95 -~g~~~L~vg~~g~I~~ 110 (137)
.+.++|.+.+.--+.+
T Consensus 83 ~~~~~el~~~~i~vl~~ 99 (450)
T PRK03932 83 AGQGYELQATKIEVIGE 99 (450)
T ss_pred CCCCEEEEEEEEEEccC
Confidence 3578998876655544
No 103
>PRK08486 single-stranded DNA-binding protein; Provisional
Probab=72.33 E-value=10 Score=29.32 Aligned_cols=61 Identities=13% Similarity=0.129 Sum_probs=39.8
Q ss_pred CCceEEEEEEEcceeeeeccCCCccccceeEEEEEEe-------------eCcceEEEEEecCCcC----CCCCCCEEEE
Q 032583 24 SGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVG-------------DETGMIIFTARNDQVD----LMKEGTTVIL 86 (137)
Q Consensus 24 ~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~Vg-------------DeTG~I~ltlW~~~~~----~i~~Gd~v~I 86 (137)
..|.|++++..-.+.+.+. .| ..++...|| ++|--+++++|...|+ .++.|+-|.|
T Consensus 3 N~V~LvGrL~~DPElr~t~--sG-----~~va~fslAv~r~~~~~~Ge~~e~t~fi~v~~fg~~AE~~~~~l~KG~~V~V 75 (182)
T PRK08486 3 NKVILVGNLTRDVELRYLP--SG-----SAIATIGLATSRRFKKQDGEKGEEVCFIDIRLFGRTAEIANQYLSKGSKVLI 75 (182)
T ss_pred eEEEEEEEecCCCEEEECC--CC-----CEEEEEEEEEecceecCCCCCcccceEEEEEEEhHHHHHHHHHcCCCCEEEE
Confidence 3456666666654544432 34 245554443 3577899999986543 3689999999
Q ss_pred eceEE
Q 032583 87 RNAKI 91 (137)
Q Consensus 87 ~na~~ 91 (137)
.+...
T Consensus 76 eGrL~ 80 (182)
T PRK08486 76 EGRLT 80 (182)
T ss_pred EEEEE
Confidence 99876
No 104
>PRK02983 lysS lysyl-tRNA synthetase; Provisional
Probab=71.65 E-value=35 Score=33.31 Aligned_cols=74 Identities=14% Similarity=0.136 Sum_probs=55.0
Q ss_pred CceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecCCc---------CCCCCCCEEEEeceEEcccC
Q 032583 25 GHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARNDQV---------DLMKEGTTVILRNAKIDMFK 95 (137)
Q Consensus 25 ~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~~~---------~~i~~Gd~v~I~na~~~~~~ 95 (137)
.|.+.++|..+ |.- +++.=+.|-|.||.|.+.+=.+.. ..+..||+|.+.|-..+...
T Consensus 653 ~V~v~Grv~~~-------R~~------G~~~F~~lrD~~g~iQ~v~~~~~~~~~~~~~~~~~l~~gd~V~v~G~v~~t~~ 719 (1094)
T PRK02983 653 EVSVSGRVLRI-------RDY------GGVLFADLRDWSGELQVLLDASRLEQGSLADFRAAVDLGDLVEVTGTMGTSRN 719 (1094)
T ss_pred EEEEEEEEEEE-------eeC------CCeEEEEEEeCCeeEEEEEECCccchhhHHHHHhcCCCCCEEEEEEEEEEcCC
Confidence 37777887664 211 356667889999999997754321 23789999999999988888
Q ss_pred CeEEEEeCCcEeEEEc
Q 032583 96 GSMRLAVDKWGRVEVA 111 (137)
Q Consensus 96 g~~~L~vg~~g~I~~~ 111 (137)
|.++|.+.++--+.+.
T Consensus 720 ge~ei~~~~i~ll~k~ 735 (1094)
T PRK02983 720 GTLSLLVTSWRLAGKC 735 (1094)
T ss_pred CCEEEEEeEEEEEecc
Confidence 9999999887666544
No 105
>PF07680 DoxA: TQO small subunit DoxA; InterPro: IPR011636 Thiosulphate:quinone oxidoreductase (TQO) catalyses one of the early steps in elemental sulphur oxidation. A novel TQO enzyme was purified from the thermo-acidophilic archaeon Acidianus ambivalens and shown to consist of a large subunit (DoxD) and a smaller subunit (DoxA). The DoxD- and DoxA-like two subunits are fused together in a single polypeptide in Q8AAF0 from SWISSPROT.
Probab=71.44 E-value=39 Score=25.02 Aligned_cols=98 Identities=15% Similarity=0.113 Sum_probs=60.9
Q ss_pred eccCCCCCCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecC-CcCCCCCCCEEEEeceEEccc
Q 032583 16 VDQLRPGTSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARND-QVDLMKEGTTVILRNAKIDMF 94 (137)
Q Consensus 16 I~dL~p~~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~-~~~~i~~Gd~v~I~na~~~~~ 94 (137)
|.+..-... +|.+.|..+.-+... ...+..+.+-|+||.+ +--|+. +...+..- .|.|-|+.-
T Consensus 21 is~~~~~~~--~L~f~vyr~~G~D~Y---------gsfl~~i~l~d~~g~v-v~~~~~~~L~~lP~~---~i~N~Yv~~- 84 (133)
T PF07680_consen 21 ISDALIENG--TLSFHVYRVEGPDVY---------GSFLIGIQLKDSTGHV-VLNWDQEKLSSLPKS---NIKNDYVAK- 84 (133)
T ss_pred EeeeEEeCC--eEEEEEEEcCCCccC---------CceeeEEEEECCCCCE-EEEeCHHHhhhCChh---HcCccEEcc-
Confidence 554443333 366666555554432 2577889999999999 457883 33333332 356777633
Q ss_pred CCeEEEEeCCcEeEEEcC-CCceEEcCCCCccccceeeeee
Q 032583 95 KGSMRLAVDKWGRVEVAE-PANFTVKEDNNLSLIEYELVNV 134 (137)
Q Consensus 95 ~g~~~L~vg~~g~I~~~~-~~~~~vn~~~n~S~~eye~~~~ 134 (137)
+..|++|-+.+++ +..+.+...-+|+.-.|.++-.
T Consensus 85 -----~~~g~~gl~vpLGakA~i~L~~~~~l~~g~Y~l~L~ 120 (133)
T PF07680_consen 85 -----VKPGKHGLVVPLGAKATITLPLPDHLPPGTYTLKLY 120 (133)
T ss_pred -----ccCCceeEEEEcCCcEEEEecCCCccCCCcEEEEEE
Confidence 2367777777776 5556666667888888877643
No 106
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=71.11 E-value=18 Score=31.64 Aligned_cols=75 Identities=12% Similarity=0.133 Sum_probs=51.0
Q ss_pred eccCCCCCCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecCC------cCCCCCCCEEEEece
Q 032583 16 VDQLRPGTSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARNDQ------VDLMKEGTTVILRNA 89 (137)
Q Consensus 16 I~dL~p~~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~~------~~~i~~Gd~v~I~na 89 (137)
++|+.+..+ ..+.++|.+.....+ .| +.+ ..+.|++|.|.+.+.... +..+.+||.|.+.|+
T Consensus 260 l~d~~~~~~-~~v~g~v~~~p~~ie----Gg-----hv~--v~i~d~~G~I~~~A~eptk~fr~~a~~L~pGD~i~~~G~ 327 (421)
T COG1571 260 LNDIEDYSK-YRVVGRVEAEPRAIE----GG-----HVV--VEITDGEGEIGAVAFEPTKEFRELARKLIPGDEITVYGS 327 (421)
T ss_pred hhhhhhccc-eEEEEEEecccEEee----CC-----EEE--EEecCCCceEEEEEecccccchHHHHhcCCCCEEEEecC
Confidence 567777654 678888887554432 11 344 478999999988887632 234679999999999
Q ss_pred EEcccCCeEEEEeCCcEe
Q 032583 90 KIDMFKGSMRLAVDKWGR 107 (137)
Q Consensus 90 ~~~~~~g~~~L~vg~~g~ 107 (137)
....- |++.+.--
T Consensus 328 ~~~~~-----~n~ek~~v 340 (421)
T COG1571 328 VKPGT-----LNLEKFQV 340 (421)
T ss_pred ccccc-----eeEEEEEE
Confidence 86543 55555443
No 107
>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=70.67 E-value=28 Score=23.00 Aligned_cols=50 Identities=14% Similarity=0.152 Sum_probs=33.0
Q ss_pred eEEEEEEeeCcc-eEEEEEecC-----CcCCCCCCCEEEEeceEEcccC------CeEEEEe
Q 032583 53 RIAECLVGDETG-MIIFTARND-----QVDLMKEGTTVILRNAKIDMFK------GSMRLAV 102 (137)
Q Consensus 53 ~v~~~~VgDeTG-~I~ltlW~~-----~~~~i~~Gd~v~I~na~~~~~~------g~~~L~v 102 (137)
.++=+.+-|.|| .+.+++=.+ .+..+..|++|.+.+-....-+ |.++|.+
T Consensus 17 ~~~Fi~LrD~~g~~iQvv~~~~~~~~~~~~~l~~~s~V~V~G~v~~~~~~~~~~~~~~Ei~~ 78 (86)
T cd04321 17 KLSFADLRDPNGDIIQLVSTAKKDAFSLLKSITAESPVQVRGKLQLKEAKSSEKNDEWELVV 78 (86)
T ss_pred ceEEEEEECCCCCEEEEEECCCHHHHHHHhcCCCCcEEEEEEEEEeCCCcCCCCCCCEEEEE
Confidence 456667899999 577644222 2245789999999997665432 5566655
No 108
>PRK08182 single-stranded DNA-binding protein; Provisional
Probab=69.52 E-value=11 Score=27.95 Aligned_cols=65 Identities=12% Similarity=0.081 Sum_probs=41.2
Q ss_pred CCceEEEEEEEcceeeeeccCCCccccceeEEEEEEe------eCcc--------eEEEEEecCCc----CCCCCCCEEE
Q 032583 24 SGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVG------DETG--------MIIFTARNDQV----DLMKEGTTVI 85 (137)
Q Consensus 24 ~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~Vg------DeTG--------~I~ltlW~~~~----~~i~~Gd~v~ 85 (137)
+.|.|.+++..-.+.+.+. .|.. -.-.+++..|+ +.+| -+++++|..++ ..++.|+.|.
T Consensus 3 N~V~LiGrLg~DPElr~t~--~G~~-~~~~va~fslA~~r~~~~~~Ge~~~~~t~w~~V~~wg~~Ae~v~~~l~KG~~V~ 79 (148)
T PRK08182 3 THFVGEGNIGSAPEYREFP--NGND-EPRRLLRLNVYFDNPVPTKDGEYEDRGGFWAPVELWHRDAEHWARLYQKGMRVL 79 (148)
T ss_pred cEEEEEEECCCCCeEEECC--CCCe-eeeeEEEEEEEecCceECCCCCEEecCcEEEEEEEEhHHHHHHHHhcCCCCEEE
Confidence 4567777777755555442 3420 00136776665 3333 47899999654 3368999999
Q ss_pred EeceEE
Q 032583 86 LRNAKI 91 (137)
Q Consensus 86 I~na~~ 91 (137)
|.|-..
T Consensus 80 V~GrL~ 85 (148)
T PRK08182 80 VEGRME 85 (148)
T ss_pred EEEEEE
Confidence 999765
No 109
>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=68.64 E-value=30 Score=30.24 Aligned_cols=76 Identities=18% Similarity=0.180 Sum_probs=52.5
Q ss_pred CCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCc--ceEEEEEecC-------CcCCCCCCCEEEEeceEEcc-
Q 032583 24 SGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDET--GMIIFTARND-------QVDLMKEGTTVILRNAKIDM- 93 (137)
Q Consensus 24 ~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeT--G~I~ltlW~~-------~~~~i~~Gd~v~I~na~~~~- 93 (137)
+.|.|.|.|-++- ++ +.+.=+.|-|.+ |.|.+++=.. .+..+..||+|.+.|-..+.
T Consensus 17 ~~v~v~Gwv~~~R--------~~-----~~~~F~~lrD~~~~g~iQ~v~~~~~~~~~~~~~~~l~~gs~V~v~G~v~~~~ 83 (453)
T TIGR00457 17 DEVTVSGWVRTKR--------SS-----KKIIFLELNDGSSLGPIQAVINGEDNPYLFQLLKSLTTGSSVSVTGKVVESP 83 (453)
T ss_pred CEEEEEEEeEEEE--------cC-----CCeEEEEEECCCCCccEEEEEeCCcChHHHHHHHcCCCCcEEEEEEEEEcCC
Confidence 4577888886642 11 355667789999 9999876443 12347899999999987653
Q ss_pred -cCCeEEEEeCCcEeEEEcC
Q 032583 94 -FKGSMRLAVDKWGRVEVAE 112 (137)
Q Consensus 94 -~~g~~~L~vg~~g~I~~~~ 112 (137)
..+.++|.+.+.--+.+.+
T Consensus 84 ~~~~~~El~~~~i~vl~~~~ 103 (453)
T TIGR00457 84 GKGQPVELQVKKIEVVGEAE 103 (453)
T ss_pred CCCCCEEEEEeEEEEEecCC
Confidence 4577999987665555553
No 110
>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=67.01 E-value=32 Score=22.26 Aligned_cols=52 Identities=10% Similarity=0.217 Sum_probs=34.9
Q ss_pred eEEEEEEeeCcce--EEEEEecC-----CcCCCCCCCEEEEeceEEcccC--CeEEEEeCC
Q 032583 53 RIAECLVGDETGM--IIFTARND-----QVDLMKEGTTVILRNAKIDMFK--GSMRLAVDK 104 (137)
Q Consensus 53 ~v~~~~VgDeTG~--I~ltlW~~-----~~~~i~~Gd~v~I~na~~~~~~--g~~~L~vg~ 104 (137)
.++=+.+-|.||. +.+++=.+ .+..+..|++|.+.|.....-. +.++|.+.+
T Consensus 16 ~~~Fi~LrD~s~~~~lQvv~~~~~~~~~~~~~l~~gs~V~v~G~v~~~~~~~~~~El~~~~ 76 (82)
T cd04318 16 KISFIELNDGSCLKNLQVVVDKELTNFKEILKLSTGSSIRVEGVLVKSPGAKQPFELQAEK 76 (82)
T ss_pred cEEEEEEECCCCccCEEEEEeCcccCHHHHhcCCCceEEEEEEEEEeCCCCCCCEEEEEEE
Confidence 4555677788874 77765332 2345789999999998776544 667776643
No 111
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=66.29 E-value=71 Score=31.66 Aligned_cols=83 Identities=14% Similarity=0.168 Sum_probs=61.4
Q ss_pred cCCCCCCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecCC------cCCCCCCCEEEEeceEE
Q 032583 18 QLRPGTSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARNDQ------VDLMKEGTTVILRNAKI 91 (137)
Q Consensus 18 dL~p~~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~~------~~~i~~Gd~v~I~na~~ 91 (137)
++.....++.|.+.|..+.. ++.+ .| ..+...-|-|-|++|.+..|... .+.+++|+.|++++-..
T Consensus 2 ~~~~~~~~~~~~g~i~~~~~-~~~~--~~-----~~~~~~~~~d~~~s~~~k~f~~~~~~~~~~~~~~~g~~~~~~g~~~ 73 (1213)
T TIGR01405 2 KINEEENRVKIEGYIFKIEI-KELK--SG-----RTLLKIKVTDYTDSLILKKFLKSEEDPEKFDGIKIGKWVRARGKIE 73 (1213)
T ss_pred cccccCCeEEEEEEEEEEEe-Eecc--CC-----CEEEEEEEEcCCCCEEEEEecccccchHHHhhcCCCcEEEEEEEEe
Confidence 46677888999999999755 4432 34 47778999999999999999721 24579999999998853
Q ss_pred -cccCCeEEEEeCCcEeE
Q 032583 92 -DMFKGSMRLAVDKWGRV 108 (137)
Q Consensus 92 -~~~~g~~~L~vg~~g~I 108 (137)
..|.+.+.+.+..-..+
T Consensus 74 ~d~~~~~~~~~~~~~~~~ 91 (1213)
T TIGR01405 74 LDNFSRDLQMIIKDIEEI 91 (1213)
T ss_pred ccCCCCceEEEeeeeeec
Confidence 45667777777654433
No 112
>PRK07772 single-stranded DNA-binding protein; Provisional
Probab=66.02 E-value=20 Score=27.89 Aligned_cols=63 Identities=13% Similarity=0.148 Sum_probs=41.3
Q ss_pred CCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEee---------------CcceEEEEEecCCc----CCCCCCCE
Q 032583 23 TSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGD---------------ETGMIIFTARNDQV----DLMKEGTT 83 (137)
Q Consensus 23 ~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgD---------------eTG~I~ltlW~~~~----~~i~~Gd~ 83 (137)
+..|.|++++..-.+.+.+. +| ..|++..||- +|=-+++++|..++ ..++.||.
T Consensus 4 ~~~VtLiGrL~~DPElR~t~--sG-----~~va~FrVAv~~r~~~~~~g~~~d~~t~fi~V~~Wg~~Ae~va~~L~KGd~ 76 (186)
T PRK07772 4 DTTITVVGNLTADPELRFTP--SG-----AAVANFTVASTPRTFDRQTNEWKDGEALFLRCSIWRQAAENVAESLTKGMR 76 (186)
T ss_pred cCEEEEEEEeCCCCeEEEcC--CC-----CEEEEEEEEecCcceecCCCcEeccCceEEEEEEecHHHHHHHHhcCCCCE
Confidence 44567777777665555432 33 3555555551 23467899999654 34689999
Q ss_pred EEEeceEEc
Q 032583 84 VILRNAKID 92 (137)
Q Consensus 84 v~I~na~~~ 92 (137)
|.|.+....
T Consensus 77 V~V~GrL~~ 85 (186)
T PRK07772 77 VIVTGRLKQ 85 (186)
T ss_pred EEEEEEEEc
Confidence 999997763
No 113
>PTZ00417 lysine-tRNA ligase; Provisional
Probab=65.81 E-value=29 Score=31.55 Aligned_cols=74 Identities=12% Similarity=0.053 Sum_probs=51.7
Q ss_pred ceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecCC-----------cCCCCCCCEEEEeceEEccc
Q 032583 26 HTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARNDQ-----------VDLMKEGTTVILRNAKIDMF 94 (137)
Q Consensus 26 v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~~-----------~~~i~~Gd~v~I~na~~~~~ 94 (137)
+.|.|+|.++ |.-| ..+.=+.|-|++|.|.+.+=.+. ...+..||+|.+.|...+..
T Consensus 135 v~v~Grv~~~-------R~~G-----~k~~F~~L~d~~g~iQv~~~~~~~~~~~~~~~~~~~~l~~Gd~V~V~G~~~~t~ 202 (585)
T PTZ00417 135 LNVTGRIMRV-------SASG-----QKLRFFDLVGDGAKIQVLANFAFHDHTKSNFAECYDKIRRGDIVGIVGFPGKSK 202 (585)
T ss_pred EEEEEEEEee-------ecCC-----CCCEEEEEEeCCeeEEEEEECCccCCCHHHHHHHHhcCCCCCEEEEEeEEcCCC
Confidence 6677777554 3223 13555677888999998885321 23478999999999987777
Q ss_pred CCeEEEEeCCcEeEEEc
Q 032583 95 KGSMRLAVDKWGRVEVA 111 (137)
Q Consensus 95 ~g~~~L~vg~~g~I~~~ 111 (137)
.|.++|.+.+.--+.+.
T Consensus 203 ~gel~i~~~~i~llsk~ 219 (585)
T PTZ00417 203 KGELSIFPKETIILSPC 219 (585)
T ss_pred CceEEEEEEEEEEEecC
Confidence 89999988877655544
No 114
>PF15072 DUF4539: Domain of unknown function (DUF4539)
Probab=65.58 E-value=19 Score=24.56 Aligned_cols=52 Identities=21% Similarity=0.165 Sum_probs=38.5
Q ss_pred EEEEEeeCcceEEEEEecC----CcCCCCCCCEEEEeceEEcc-cCCeEEEEeCCcE
Q 032583 55 AECLVGDETGMIIFTARND----QVDLMKEGTTVILRNAKIDM-FKGSMRLAVDKWG 106 (137)
Q Consensus 55 ~~~~VgDeTG~I~ltlW~~----~~~~i~~Gd~v~I~na~~~~-~~g~~~L~vg~~g 106 (137)
+.+++.|.||.|+-++=.+ ..+.+.+|.++-+++..+=. -.....|+|...-
T Consensus 21 ~~v~l~DpTG~i~~tiH~~v~~~y~~~l~~GavLlLk~V~Vf~ps~~~~yLnIt~~N 77 (86)
T PF15072_consen 21 AFVVLKDPTGEIRGTIHRKVLEEYGDELSPGAVLLLKDVTVFSPSPRSHYLNITLNN 77 (86)
T ss_pred eEEEEECCCCcEEEEEeHHHHhhcCCccccCEEEEEeeeeEEecCCCccEEEEehhH
Confidence 4678999999999999863 45668999999999987632 2345666665443
No 115
>cd03583 NTR_complement_C3 NTR/C345C domain, complement C3 subfamily; The NTR domain found in complement C3 is also known as the C345C domain because it occurs at the C-terminus of complement C3, C4 and C5. Complement C3 plays a pivotal role in the activation of the complement systems, as all pathways (classical, alternative, and lectin) result in the processing of C3 by C3 convertase. The larger fragment, activated C3b, contains the NTR/C345C domain and binds covalently, via a reactive thioester, to cell surface carbohydrates including components of bacterial cell walls and immune aggregates. The smaller cleavage product, C3a, acts independently as a diffusible signal to mediate local inflammatory processes. The structure of C3 shows that the NTR/C345C domain is located in an exposed position relative to the rest of the molecule. The function of the domain in complement C3 is poorly understood.
Probab=63.16 E-value=60 Score=24.16 Aligned_cols=82 Identities=16% Similarity=0.165 Sum_probs=53.5
Q ss_pred ceEEEEEEEcceeeeeccCCCccccceeEEEEEE-ee---CcceEEEEEecCC---cCCCCCCCEEEEeceEEcccC--C
Q 032583 26 HTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLV-GD---ETGMIIFTARNDQ---VDLMKEGTTVILRNAKIDMFK--G 96 (137)
Q Consensus 26 v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~V-gD---eTG~I~ltlW~~~---~~~i~~Gd~v~I~na~~~~~~--g 96 (137)
.=.+++|+++.+...|..+. .+|.+++= |. -.|.+|.-++-.. +..+++|..+-|.|.....++ |
T Consensus 31 Yvykv~v~~~~~~~~f~~Y~------~~I~~ViK~G~D~~~~~~~r~F~~r~sCr~~l~l~~gk~YLIMG~~~~~~~~~~ 104 (149)
T cd03583 31 YVYKVKLVNVELSDSYDIYT------MEILQVIKEGTDEGPEGKTRTFISHPKCREALNLKEGKDYLIMGLSSDLWRIKD 104 (149)
T ss_pred EEEEEEEEEEeccCCeEEEE------EEEEEEEecccccCcCCCeEEEEecCCCcchhccCCCCEEEEEeCCCCccccCC
Confidence 34778888877655553322 33443321 11 2667775444432 334679999999999876654 5
Q ss_pred eEEEEeCCcEeEEEcCC
Q 032583 97 SMRLAVDKWGRVEVAEP 113 (137)
Q Consensus 97 ~~~L~vg~~g~I~~~~~ 113 (137)
.+++.+|+.+-|+.-|.
T Consensus 105 ~~~YvL~~~TWvE~wP~ 121 (149)
T cd03583 105 KYSYVIGKDTWIEYWPT 121 (149)
T ss_pred cEEEEeCCCeEEEECCC
Confidence 79999999999998863
No 116
>PRK06863 single-stranded DNA-binding protein; Provisional
Probab=62.32 E-value=22 Score=27.17 Aligned_cols=65 Identities=12% Similarity=0.112 Sum_probs=43.3
Q ss_pred CCCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEee--------------CcceEEEEEecCCc----CCCCCCCE
Q 032583 22 GTSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGD--------------ETGMIIFTARNDQV----DLMKEGTT 83 (137)
Q Consensus 22 ~~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgD--------------eTG~I~ltlW~~~~----~~i~~Gd~ 83 (137)
+++.+.|.+++-.-.+.+.+ .+| ..++...||= .|=-+++++|..++ ..++.|+.
T Consensus 3 ~~N~V~LiGrLg~DPElR~t--~nG-----~~va~fsVAvn~~~~d~~~Ge~~e~t~w~~Vv~fgk~AE~v~~~LkKGs~ 75 (168)
T PRK06863 3 GINKVIIVGHLGNDPEIRTM--PNG-----EAVANISVATSESWTDKNTGERREVTEWHRIVFYRRQAEVAGEYLRKGSQ 75 (168)
T ss_pred CccEEEEEEEcCCCCEEEEc--CCC-----CEEEEEEEEecCcccccCCCcccccceEEEEEEEhHHHHHHHHHCCCCCE
Confidence 35667888888775555554 245 3455555541 13368999999654 34799999
Q ss_pred EEEeceEEcc
Q 032583 84 VILRNAKIDM 93 (137)
Q Consensus 84 v~I~na~~~~ 93 (137)
|.|.+.....
T Consensus 76 V~VeGrL~~r 85 (168)
T PRK06863 76 VYVEGRLKTR 85 (168)
T ss_pred EEEEEEEEeC
Confidence 9999987643
No 117
>TIGR00459 aspS_bact aspartyl-tRNA synthetase, bacterial type. In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, aspS_bact, represents aspartyl-tRNA synthetases from the Bacteria and from mitochondria. In some species, this enzyme aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently transamidated to Asn-tRNA(asn). This model generates very low scores for the archaeal type of aspS and for asnS; scores between the trusted and noise cutoffs represent fragmentary sequences.
Probab=62.20 E-value=58 Score=29.67 Aligned_cols=81 Identities=11% Similarity=0.110 Sum_probs=55.3
Q ss_pred CceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecC-----CcCCCCCCCEEEEeceEEc-------
Q 032583 25 GHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARND-----QVDLMKEGTTVILRNAKID------- 92 (137)
Q Consensus 25 ~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~-----~~~~i~~Gd~v~I~na~~~------- 92 (137)
.|.|.|.|-.+ |.- +.+.=+.|-|.||.|.+++=.+ .+..+..|++|.|.|-..+
T Consensus 17 ~V~l~GwV~~~-------R~~------Gkl~Fi~LrD~sg~iQvv~~~~~~~~~~~~~L~~esvV~V~G~v~~r~~~~~n 83 (583)
T TIGR00459 17 TVTLAGWVNRR-------RDL------GGLIFIDLRDRSGIVQVVCDPDADALKLAKGLRNEDVVQVKGKVSARPEGNIN 83 (583)
T ss_pred EEEEEEEEEEE-------EcC------CCcEEEEEEeCCccEEEEEeCCHHHHHHHhcCCCCCEEEEEEEEEeCCccccC
Confidence 46777777543 222 3466678899999999876432 2345789999999997764
Q ss_pred --ccCCeEEEEeCCcEeEEEcCCCceEE
Q 032583 93 --MFKGSMRLAVDKWGRVEVAEPANFTV 118 (137)
Q Consensus 93 --~~~g~~~L~vg~~g~I~~~~~~~~~v 118 (137)
.-.|.++|.+.+.--+.+.....+..
T Consensus 84 ~~~~tg~iEl~~~~i~iL~~a~~~P~~~ 111 (583)
T TIGR00459 84 RNLDTGEIEILAESITLLNKSKTPPLII 111 (583)
T ss_pred ccCCCCcEEEEEeEEEEeecCCCCCCcc
Confidence 34578999888777666654444444
No 118
>COG0017 AsnS Aspartyl/asparaginyl-tRNA synthetases [Translation, ribosomal structure and biogenesis]
Probab=61.67 E-value=95 Score=27.40 Aligned_cols=87 Identities=16% Similarity=0.141 Sum_probs=62.8
Q ss_pred eeeeccCCCCCC--CceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEec-CC------cCCCCCCCE
Q 032583 13 FTKVDQLRPGTS--GHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARN-DQ------VDLMKEGTT 83 (137)
Q Consensus 13 ~~kI~dL~p~~~--~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~-~~------~~~i~~Gd~ 83 (137)
...|+|+.+... .|.|.|-|-++ |.- +.++=+++-|.||.|..++-. +. +..+..+++
T Consensus 4 ~~~i~di~~~~~~~~V~v~GWV~~~-------R~~------g~i~Fi~lrDgsg~iQ~v~~~~~~~~~~~~~~~L~~es~ 70 (435)
T COG0017 4 RTYIKDIKPHVGGQEVTVRGWVHNK-------RDL------GKIIFLVLRDGSGFIQAVVPKNKVYEELFKAKKLTLESS 70 (435)
T ss_pred eeeHHhhhccCCCcEEEEEEEeeee-------ccc------CCeEEEEEEcCCcEEEEEEECCCCcHHHhhhhcCCCccE
Confidence 345778877553 55555555432 322 468888999999999999974 12 335789999
Q ss_pred EEEeceEEccc--CCeEEEEeCCcEeEEEcC
Q 032583 84 VILRNAKIDMF--KGSMRLAVDKWGRVEVAE 112 (137)
Q Consensus 84 v~I~na~~~~~--~g~~~L~vg~~g~I~~~~ 112 (137)
|.+.|.....- .+.++|.+.+---+..++
T Consensus 71 v~V~G~v~~~~~a~~g~El~v~~i~Vl~~a~ 101 (435)
T COG0017 71 VVVTGIVKASPKAPQGFELQVEKIEVLGEAD 101 (435)
T ss_pred EEEEEEEEcCCCCCCCEEEEEEEEEEeeccC
Confidence 99999988664 368999998877777774
No 119
>PF09104 BRCA-2_OB3: BRCA2, oligonucleotide/oligosaccharide-binding, domain 3; InterPro: IPR015188 This domain assumes an OB fold, which consists of a highly curved five-stranded beta-sheet that closes on itself to form a beta-barrel. OB3 has a pronounced groove formed by one face of the curved sheet and is demarcated by two loops, one between beta 1 and beta 2 and another between beta 4 and beta 5, which allows for strong ssDNA binding []. ; PDB: 1IYJ_D 1MIU_A.
Probab=61.67 E-value=66 Score=24.13 Aligned_cols=83 Identities=14% Similarity=0.077 Sum_probs=52.8
Q ss_pred CCCCCCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcc-eEEEEEecCC-----cCCCCCCCEEEEeceEEc
Q 032583 19 LRPGTSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETG-MIIFTARNDQ-----VDLMKEGTTVILRNAKID 92 (137)
Q Consensus 19 L~p~~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG-~I~ltlW~~~-----~~~i~~Gd~v~I~na~~~ 92 (137)
.+|.=.-++++|-|+++... - +...-+.++|+.- -+-+.+|.+. -+.+++|..|...|-.-|
T Consensus 14 f~pp~~EvD~VG~VvsV~~~------~------~f~~~vYLsD~~~Nll~Ikfw~~l~~~~~eDilk~~~liA~SNLqwR 81 (143)
T PF09104_consen 14 FQPPYGEVDTVGFVVSVSKK------Q------GFQPLVYLSDECHNLLAIKFWTGLNQYGYEDILKPGSLIAASNLQWR 81 (143)
T ss_dssp --TCCCEEEEEEEEEEEE--------T------TS--EEEEE-TTS-EEEEEESS-------SS---TT-EEEEEEEEE-
T ss_pred cCCCccccceEEEEEEEEec------C------CCceeEEeecCCccEEEEEeccCccccchhhhcCcceEEEEeeeEee
Confidence 34667779999999999221 1 2222356789977 6778899864 356799999999999885
Q ss_pred cc--CCeEEEEeCCcEeEEEcCC
Q 032583 93 MF--KGSMRLAVDKWGRVEVAEP 113 (137)
Q Consensus 93 ~~--~g~~~L~vg~~g~I~~~~~ 113 (137)
-. .+-+.+..+..+.+...|.
T Consensus 82 ~~s~s~iP~~~A~d~S~FS~nPK 104 (143)
T PF09104_consen 82 PESTSGIPTLFATDLSVFSANPK 104 (143)
T ss_dssp S-TTSSS-EEEEECCEEEESS-S
T ss_pred cccccCCCeeEeccceeeecCcc
Confidence 42 4789999999999988763
No 120
>PRK07135 dnaE DNA polymerase III DnaE; Validated
Probab=61.08 E-value=28 Score=33.63 Aligned_cols=79 Identities=14% Similarity=0.232 Sum_probs=53.0
Q ss_pred eeeccCCCCCCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecCC---cCCCCCCCEEEEeceE
Q 032583 14 TKVDQLRPGTSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARNDQ---VDLMKEGTTVILRNAK 90 (137)
Q Consensus 14 ~kI~dL~p~~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~~---~~~i~~Gd~v~I~na~ 90 (137)
.++.+|.. ...+.+.+.|.++...+ + .| ..|+-+.+.|.||.+.+++|.+. ...+.+|+.+.+.+-.
T Consensus 889 ~~~~~l~~-~~~~~v~g~i~~~~~~~--K--~g-----~~maf~~~eD~~~~~e~~~F~~~~~~~~~l~~~~~~~~~~~~ 958 (973)
T PRK07135 889 IRLKDLRI-NTEYRLAIEVKNVKRLR--K--AN-----KEYKKVILSDDSVEITIFVNDNDYLLFETLKKGDIYEFLISK 958 (973)
T ss_pred hhHHHhcC-CCeEEEEEEEEEEEEEe--e--CC-----CeEEEEEEEECCCcEEEEEcHHHHHHHHHhhcCCEEEEEEEE
Confidence 35777743 34567788777776654 2 34 47999999999999999999742 2337788888886655
Q ss_pred EcccCCeEEEEeCC
Q 032583 91 IDMFKGSMRLAVDK 104 (137)
Q Consensus 91 ~~~~~g~~~L~vg~ 104 (137)
.+ ++...|..-+
T Consensus 959 ~~--~~~~~~~~~~ 970 (973)
T PRK07135 959 SK--NNKFYIINNK 970 (973)
T ss_pred cC--CCceEecccc
Confidence 43 3344443333
No 121
>COG3481 Predicted HD-superfamily hydrolase [General function prediction only]
Probab=60.40 E-value=8 Score=32.19 Aligned_cols=59 Identities=15% Similarity=0.224 Sum_probs=46.7
Q ss_pred eEEEEEEeeCcceEEEEEecCC---cCCCCCCCEEEEeceEEcccCCeEEEEeCCcEeEEEcC
Q 032583 53 RIAECLVGDETGMIIFTARNDQ---VDLMKEGTTVILRNAKIDMFKGSMRLAVDKWGRVEVAE 112 (137)
Q Consensus 53 ~v~~~~VgDeTG~I~ltlW~~~---~~~i~~Gd~v~I~na~~~~~~g~~~L~vg~~g~I~~~~ 112 (137)
.-..+...|.||.|+-.+|+.. .+.+.+|.++.+.+.. ..|++..++.+.+.+.++..+
T Consensus 21 ~~l~l~~~d~~gei~~~~wd~~~~~~~~~~~~~Vv~~~g~~-~~~~~~~q~ki~~~r~~~~~~ 82 (287)
T COG3481 21 DKLKLTLQDKTGEIEAKLWDALKNDEEAFKPGMVVHVEGVK-EVYRGRKQHKIIRIRLITDSD 82 (287)
T ss_pred hhheeeeccccceecccccccccccHhhhCcCceeccccce-ecccccchheeeecccccccC
Confidence 3346789999999999999943 3457999999987665 678888999888887776553
No 122
>PRK06642 single-stranded DNA-binding protein; Provisional
Probab=60.37 E-value=34 Score=25.54 Aligned_cols=62 Identities=15% Similarity=0.170 Sum_probs=42.9
Q ss_pred CCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEe------e--------CcceEEEEEecC-CcC----CCCCCCE
Q 032583 23 TSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVG------D--------ETGMIIFTARND-QVD----LMKEGTT 83 (137)
Q Consensus 23 ~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~Vg------D--------eTG~I~ltlW~~-~~~----~i~~Gd~ 83 (137)
++.+.|.+++-.-.+.+.+ .+| ..++...|| | +|-=+++++|.. +++ .++.|+.
T Consensus 5 ~N~V~LiGrLg~DPElr~t--~~G-----~~v~~fslAv~~~~k~~~~G~~~~~T~w~~v~~~g~~~Ae~~~~~l~KG~~ 77 (152)
T PRK06642 5 LNKVILIGNVGRDPEIRTT--GEG-----KKIINLSLATTETWKDRITSERKERTEWHRVVIFSEGLVSVVERYVTKGSK 77 (152)
T ss_pred ceEEEEEEEccCCceEEEC--CCC-----CEEEEEEEEeccccccccCCccccceeEEEEEEeChHHHHHHHHhCCCCCE
Confidence 5667888888875555543 244 356666666 2 244688999985 443 3689999
Q ss_pred EEEeceEE
Q 032583 84 VILRNAKI 91 (137)
Q Consensus 84 v~I~na~~ 91 (137)
|.|.+...
T Consensus 78 V~V~GrL~ 85 (152)
T PRK06642 78 LYIEGSLQ 85 (152)
T ss_pred EEEEEEEE
Confidence 99999865
No 123
>COG1190 LysU Lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]
Probab=60.21 E-value=52 Score=29.54 Aligned_cols=59 Identities=14% Similarity=0.198 Sum_probs=46.5
Q ss_pred eeEEEEEEeeCcceEEEEEecCCc---------CCCCCCCEEEEeceEEcccCCeEEEEeCCcEeEEE
Q 032583 52 MRIAECLVGDETGMIIFTARNDQV---------DLMKEGTTVILRNAKIDMFKGSMRLAVDKWGRVEV 110 (137)
Q Consensus 52 ~~v~~~~VgDeTG~I~ltlW~~~~---------~~i~~Gd~v~I~na~~~~~~g~~~L~vg~~g~I~~ 110 (137)
|+++=+.|-|.+|.|.+-+-.+.. ..+.-||+|.+.|...+...|.+++++..+--+.+
T Consensus 77 GK~~F~~i~d~~gkiQ~yi~k~~~~~~~~~~~~~~~dlGDiigv~G~~~~T~~GelSv~v~~~~lLsK 144 (502)
T COG1190 77 GKASFADLQDGSGKIQLYVNKDEVGEEVFEALFKKLDLGDIIGVEGPLFKTKTGELSVSVEELRLLSK 144 (502)
T ss_pred CceeEEEEecCCceEEEEEeccccchhhHHHHHhccccCCEEeeeeeeeecCCCceEEEEEEEeeecc
Confidence 466667899999999887765421 22357999999999999999999999999866543
No 124
>PRK00476 aspS aspartyl-tRNA synthetase; Validated
Probab=59.84 E-value=82 Score=28.63 Aligned_cols=81 Identities=11% Similarity=0.103 Sum_probs=54.5
Q ss_pred CceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecC-----CcCCCCCCCEEEEeceEEccc-----
Q 032583 25 GHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARND-----QVDLMKEGTTVILRNAKIDMF----- 94 (137)
Q Consensus 25 ~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~-----~~~~i~~Gd~v~I~na~~~~~----- 94 (137)
.|.+.|.|-.+ |.- +.+.=+.+-|.+|.+.+++=.. .+..+..|++|.|.|...+.-
T Consensus 19 ~V~l~GwV~~~-------R~~------g~l~Fi~LrD~~g~iQ~v~~~~~~~~~~~~~l~~es~V~V~G~v~~~~~~~~n 85 (588)
T PRK00476 19 TVTLCGWVHRR-------RDH------GGLIFIDLRDREGIVQVVFDPDAEAFEVAESLRSEYVIQVTGTVRARPEGTVN 85 (588)
T ss_pred EEEEEEEEEEE-------EeC------CCeEEEEEEeCCceEEEEEeCCHHHHHHHhCCCCCCEEEEEEEEEecCCcccC
Confidence 36677766443 222 3466678899999998876321 234578999999999777532
Q ss_pred ----CCeEEEEeCCcEeEEEcCCCceEE
Q 032583 95 ----KGSMRLAVDKWGRVEVAEPANFTV 118 (137)
Q Consensus 95 ----~g~~~L~vg~~g~I~~~~~~~~~v 118 (137)
.|.++|.+.+.--+.+..+..+.+
T Consensus 86 ~~~~~g~~El~~~~i~il~~a~~lP~~~ 113 (588)
T PRK00476 86 PNLPTGEIEVLASELEVLNKSKTLPFPI 113 (588)
T ss_pred ccCCCCcEEEEEeEEEEEecCCCCCCcc
Confidence 567999988887666664334444
No 125
>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=56.26 E-value=61 Score=21.98 Aligned_cols=60 Identities=18% Similarity=0.184 Sum_probs=40.0
Q ss_pred eEEEEEEeeCcceEEEEEecC-------CcCCCCCCCEEEEeceEEccc--CCeEEEEeCCcEeEEEcC
Q 032583 53 RIAECLVGDETGMIIFTARND-------QVDLMKEGTTVILRNAKIDMF--KGSMRLAVDKWGRVEVAE 112 (137)
Q Consensus 53 ~v~~~~VgDeTG~I~ltlW~~-------~~~~i~~Gd~v~I~na~~~~~--~g~~~L~vg~~g~I~~~~ 112 (137)
.+.=+.+-|.+|.+.+.+=.+ ++..+..|++|.+.|...+.- .+.+||.+.+.--+...+
T Consensus 16 k~~Fi~lrD~~g~iQ~v~~~~~~~~~~~~~~~l~~~s~v~V~G~v~~~~~~~~~~Ei~~~~i~vl~~a~ 84 (103)
T cd04319 16 KKAFIVLRDSTGIVQAVFSKDLNEEAYREAKKVGIESSVIVEGAVKADPRAPGGAEVHGEKLEIIQNVE 84 (103)
T ss_pred CeEEEEEecCCeeEEEEEeCCCCHHHHHHHhCCCCCCEEEEEEEEEECCCCCCCEEEEEEEEEEEecCC
Confidence 345567889999988866432 123468999999999766432 245888886665555543
No 126
>PRK05813 single-stranded DNA-binding protein; Provisional
Probab=56.05 E-value=1e+02 Score=24.52 Aligned_cols=82 Identities=22% Similarity=0.230 Sum_probs=55.2
Q ss_pred CCCceEEEEEEEcceeeeeccCCCccccceeEEEEEE-----eeCcceEEEEEecCCcCC--CCCCCEEEEeceEEcc--
Q 032583 23 TSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLV-----GDETGMIIFTARNDQVDL--MKEGTTVILRNAKIDM-- 93 (137)
Q Consensus 23 ~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~V-----gDeTG~I~ltlW~~~~~~--i~~Gd~v~I~na~~~~-- 93 (137)
.+.|.|.+++.+-.+.+... .| ..++...| .|++--|++++|..+++. +..|+.|.|.|-.-++
T Consensus 8 ~NkV~L~Grl~~d~e~~~~~--~G-----~~~~~f~laV~R~s~~~D~i~v~v~~rlae~~~l~kG~~v~VeGqlrsy~~ 80 (219)
T PRK05813 8 NNKVYLEGKVVSELEFSHEM--YG-----EGFYNFKLEVPRLSDSKDILPVTVSERLLAGMDLKVGTLVIVEGQLRSYNK 80 (219)
T ss_pred cCEEEEEEEEcCCceEEEEe--CC-----eEEEEEEEEeeccCCCccEEEEEEEhhhhhhhcccCCCEEEEEEEEEEecc
Confidence 45688999998877766532 34 34444444 499999999999987765 6899999999988744
Q ss_pred c-CCeEEEEeCCcE-eEEEc
Q 032583 94 F-KGSMRLAVDKWG-RVEVA 111 (137)
Q Consensus 94 ~-~g~~~L~vg~~g-~I~~~ 111 (137)
+ .|.-+|.+.=.+ .|+..
T Consensus 81 ~~~G~~R~vl~V~a~~i~~l 100 (219)
T PRK05813 81 FIDGKNRLILTVFARNIEYC 100 (219)
T ss_pred CCCCcEEEEEEEEEEEEEEc
Confidence 2 354444443333 33334
No 127
>PRK10260 L,D-transpeptidase; Provisional
Probab=54.35 E-value=8.2 Score=32.40 Aligned_cols=42 Identities=17% Similarity=0.204 Sum_probs=33.7
Q ss_pred eCcceEEEEEec--CCcCCCCCCCEEEEeceEEccc---CCeEEEEe
Q 032583 61 DETGMIIFTARN--DQVDLMKEGTTVILRNAKIDMF---KGSMRLAV 102 (137)
Q Consensus 61 DeTG~I~ltlW~--~~~~~i~~Gd~v~I~na~~~~~---~g~~~L~v 102 (137)
=+.|||||.-|| ...+.+..|..|+|.|.-++.- +|.+.|.+
T Consensus 206 vShGCIRl~n~Di~~L~~~V~~Gt~V~ii~~pvk~~~~~~g~~~lEv 252 (306)
T PRK10260 206 VSHGCVRLRNEDIKFLFEKVPVGTRVQFIDEPVKATTEPDGSRYIEV 252 (306)
T ss_pred CCCCeeCCCHHHHHHHHhcCCCCCEEEEecCceeccccCCCeEEEEE
Confidence 468999999999 4667789999999999988762 46666644
No 128
>KOG2012 consensus Ubiquitin activating enzyme UBA1 [Posttranslational modification, protein turnover, chaperones]
Probab=53.51 E-value=17 Score=34.68 Aligned_cols=58 Identities=16% Similarity=0.235 Sum_probs=48.3
Q ss_pred EEEEecCCcCCCCCCCEEEEeceEEcccCCeEEEEeCCcEeEEEcCCCceEEcCCCCccccce
Q 032583 67 IFTARNDQVDLMKEGTTVILRNAKIDMFKGSMRLAVDKWGRVEVAEPANFTVKEDNNLSLIEY 129 (137)
Q Consensus 67 ~ltlW~~~~~~i~~Gd~v~I~na~~~~~~g~~~L~vg~~g~I~~~~~~~~~vn~~~n~S~~ey 129 (137)
-+|+-++..-.++-||.|.+. +.+|..+||=+.=-+|+..+++.|++.++.++++.-+
T Consensus 196 vvT~ld~~rH~lEdGd~V~Fs-----EveGm~eLN~~~P~kI~v~~p~sf~Igdt~~f~~y~~ 253 (1013)
T KOG2012|consen 196 VVTCLDGARHGFEDGDLVTFS-----EVEGMTELNDCKPRKITVLGPYSFSIGDTTEFGEYKK 253 (1013)
T ss_pred eEEEecCccccCccCCEEEEE-----eeccccccCCCCceEEEEecCceEEeccccchhhhhc
Confidence 345667666678999999987 7788999998888999999999999999888887654
No 129
>PRK09919 anti-adapter protein IraM; Provisional
Probab=53.16 E-value=55 Score=23.68 Aligned_cols=38 Identities=3% Similarity=0.037 Sum_probs=29.2
Q ss_pred eEEEEEecCCcCCCCCCCEEEEeceEEcccCCeEEEEe
Q 032583 65 MIIFTARNDQVDLMKEGTTVILRNAKIDMFKGSMRLAV 102 (137)
Q Consensus 65 ~I~ltlW~~~~~~i~~Gd~v~I~na~~~~~~g~~~L~v 102 (137)
..+|++|-.---.+.+||++.+.+.-+-..+..+.+.|
T Consensus 26 nlKlilWY~~d~~L~pG~~i~~~~~gvliNdk~~pItI 63 (114)
T PRK09919 26 NLKLILWYQADIFLPPGSIITPVKSGVLLNDKPYPITI 63 (114)
T ss_pred cceEEEEEeeeEEeCCCCEEEEcCCeEEECCcEeEEEE
Confidence 57899998432236999999999999888777676643
No 130
>cd03582 NTR_complement_C5 NTR/C345C domain, complement C5 subfamily; The NTR domain found in complement C5 is also known as C345C because it occurs at the C-terminus of complement C3, C4 and C5. Complement C5 is activated by C5 convertase, which itself is a complex between C3b and C3 convertase. The small cleavage fragment, C5a, is the most important small peptide mediator of inflammation, and the larger active fragment, C5b, initiates late events of complement activation. The NTR/C345C domain is important in the function of C5 as it interacts with enzymes that convert C5 to the active form, C5b. The domain has also been found to bind to complement components C6 and C7, and may specifically interact with their factor I modules.
Probab=52.44 E-value=95 Score=23.07 Aligned_cols=81 Identities=11% Similarity=0.045 Sum_probs=48.8
Q ss_pred eEEEEEEEcceeeeeccCCCccccceeEEEEEE----eeCcceEEEEEecC--CcCCCCCCCEEEEeceEEcccC---C-
Q 032583 27 TLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLV----GDETGMIIFTARND--QVDLMKEGTTVILRNAKIDMFK---G- 96 (137)
Q Consensus 27 ~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~V----gDeTG~I~ltlW~~--~~~~i~~Gd~v~I~na~~~~~~---g- 96 (137)
=++++|++......|.++. ..|.+++= ....|..|.-+... ....+++|..+-|.|.....++ +
T Consensus 34 aykv~V~~~~~~~~~~~y~------~~I~~V~K~g~d~~~~g~~r~f~~~~~Cr~~~l~~gk~YLImG~~~~~~~~~~~~ 107 (150)
T cd03582 34 AYKVMIKSSAAEGDFVTYK------ATVLDVLKNGQAELEKDSEVTLVKKATCTSVELQEGQQYLIMGKEALKIRLNRSF 107 (150)
T ss_pred EEEEEEEEEEecCCeEEEE------EEEEEeEecCCccccCCCeEEEeecCCCCCCcccCCCEEEEeeCCCCccccCCCc
Confidence 4666677666544443322 22222111 11245555323332 2345789999999999765443 3
Q ss_pred eEEEEeCCcEeEEEcCC
Q 032583 97 SMRLAVDKWGRVEVAEP 113 (137)
Q Consensus 97 ~~~L~vg~~g~I~~~~~ 113 (137)
++++.+|+.+-|+.-|.
T Consensus 108 ~~~Y~L~~~TWvE~WP~ 124 (150)
T cd03582 108 RYRYPLDSEAWIEWWPT 124 (150)
T ss_pred eeEEEcCCceeEEECCC
Confidence 59999999999998763
No 131
>PLN02603 asparaginyl-tRNA synthetase
Probab=51.33 E-value=1.5e+02 Score=26.87 Aligned_cols=88 Identities=15% Similarity=0.183 Sum_probs=55.5
Q ss_pred eeeeeccCCCC--------CCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcce--EEEEEecCCc-----C
Q 032583 12 VFTKVDQLRPG--------TSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGM--IIFTARNDQV-----D 76 (137)
Q Consensus 12 ~~~kI~dL~p~--------~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~--I~ltlW~~~~-----~ 76 (137)
....|+++.+. .+.|.|.|.|-++ |.. +.++=+.|-|.||. +.+++=.+.. .
T Consensus 88 ~~~~~~~~~~~~~~~~~~~g~~V~v~GwV~~i-------R~~------g~~~Fi~l~Dgs~~~~lQ~v~~~~~~~~~~l~ 154 (565)
T PLN02603 88 KKLRIADVKGGEDEGLARVGKTLNVMGWVRTL-------RAQ------SSVTFIEVNDGSCLSNMQCVMTPDAEGYDQVE 154 (565)
T ss_pred CceEhhhcccccccccccCCCEEEEEEEEEEE-------EeC------CCeEEEEEECCCCCEeEEEEEECcHHHHHHHh
Confidence 44578888742 2445666666433 222 35566788898874 7776632211 1
Q ss_pred --CCCCCCEEEEeceEEcccC--CeEEEEeCCcEeEEEcC
Q 032583 77 --LMKEGTTVILRNAKIDMFK--GSMRLAVDKWGRVEVAE 112 (137)
Q Consensus 77 --~i~~Gd~v~I~na~~~~~~--g~~~L~vg~~g~I~~~~ 112 (137)
.+..|++|.|.|-..+.-. +.++|.+.+---+.+.+
T Consensus 155 ~~~l~~gs~V~V~G~v~~~~~~~~~~EL~v~~i~vlg~a~ 194 (565)
T PLN02603 155 SGLITTGASVLVQGTVVSSQGGKQKVELKVSKIVVVGKSD 194 (565)
T ss_pred hcCCCCCCEEEEEEEEEecCCCCccEEEEEeEEEEEECCC
Confidence 3789999999998775433 34899987765555554
No 132
>PRK12820 bifunctional aspartyl-tRNA synthetase/aspartyl/glutamyl-tRNA amidotransferase subunit C; Provisional
Probab=50.68 E-value=1.4e+02 Score=27.90 Aligned_cols=89 Identities=15% Similarity=0.132 Sum_probs=57.7
Q ss_pred ccCCCCCC--CceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecCC--------cCCCCCCCEEEE
Q 032583 17 DQLRPGTS--GHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARNDQ--------VDLMKEGTTVIL 86 (137)
Q Consensus 17 ~dL~p~~~--~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~~--------~~~i~~Gd~v~I 86 (137)
.+|.+... .|.|.|.|-.+ |.- +.+.=+.+-|.+|.|.+++=.+. +..+..|++|.|
T Consensus 10 g~l~~~~~g~~V~l~GWV~~~-------R~~------G~l~FidLRD~~G~iQvV~~~~~~~~~~~~~~~~L~~EsvV~V 76 (706)
T PRK12820 10 GHLSLDDTGREVCLAGWVDAF-------RDH------GELLFIHLRDRNGFIQAVFSPEAAPADVYELAASLRAEFCVAL 76 (706)
T ss_pred ccCChhhCCCEEEEEEEEEEE-------EcC------CCcEEEEEEeCCccEEEEEeCCcCCHHHHHHHhcCCCCCEEEE
Confidence 45554332 36677776443 222 34666788999999998774321 245789999999
Q ss_pred eceEEcc---------cCCeEEEEeCCcEeEEEcCCCceEE
Q 032583 87 RNAKIDM---------FKGSMRLAVDKWGRVEVAEPANFTV 118 (137)
Q Consensus 87 ~na~~~~---------~~g~~~L~vg~~g~I~~~~~~~~~v 118 (137)
.|-..+. -.|.++|.+.+.--+.+.....|.+
T Consensus 77 ~G~v~~r~~~~~n~~~~tg~iEl~~~~i~iL~~a~~lP~~i 117 (706)
T PRK12820 77 QGEVQKRLEETENPHIETGDIEVFVRELSILAASEALPFAI 117 (706)
T ss_pred EeEEeccCccccCCCCCCCcEEEEeeEEEEEecCCCCCCCC
Confidence 9976542 2377999988887776664334444
No 133
>PF11183 PmrD: Polymyxin resistance protein PmrD; InterPro: IPR020146 The Salmonella PmrA/PmrB two-component system is required for resistance to the cationic peptide antibiotic olymyxin B, resistance to Fe(3+)-mediated killing, growth in soil, virulence in mice, and infection of chicken macrophages. PmrA-activated genes encode periplasmic and integral membrane proteins as well as cytoplasmic products mediating the modification of the lipopolysaccharide, suggesting a role for the PmrA/PmrB system in remodeling of the Gram-negative envelope. The PmrA/PmrB two-component system of Salmonella enterica is activated by Fe(3+), which is sensed by the PmrB protein, and by low Mg(2+), which is sensed by the PhoQ protein. The low Mg(2+) activation requires pmrD, a PhoPPhoQ-activated gene that activates the response regulator PmrA at a posttranscriptional level. However, under conditions that activate the PmrA protein independently of pmrD, such as exposure to Fe3, lower levels of pmrD transcription occur. It has been demonstrated that PmrA binds to the pmrD promoter, suppressing transcription. Negative regulation of the PhoP/PhoQ-activated pmrD gene by the PmrA/ PmrB system closes a regulatory circuit designed to maintain proper cellular levels of activated PmrA protein, and constitutes a singular example of a multicomponent feedback loop []. ; PDB: 2RQX_A 2JSO_A.
Probab=50.67 E-value=22 Score=24.27 Aligned_cols=38 Identities=21% Similarity=0.209 Sum_probs=27.7
Q ss_pred EEEEEEeeCcceEEEEEecCCcCCCCCCCEEE-Eece-EE
Q 032583 54 IAECLVGDETGMIIFTARNDQVDLMKEGTTVI-LRNA-KI 91 (137)
Q Consensus 54 v~~~~VgDeTG~I~ltlW~~~~~~i~~Gd~v~-I~na-~~ 91 (137)
..-.++-|.-|.+.|.+|-...-.+++||.+. +.|| |.
T Consensus 16 ~~~l~l~~a~g~LkmIAEv~s~~~l~~GD~LtPl~dA~Yc 55 (82)
T PF11183_consen 16 CHVLLLCDAGGALKMIAEVTSDFRLQEGDKLTPLQDALYC 55 (82)
T ss_dssp EEEEEEEETTTTCEEEEEEEESS---TT-EEEESSSSEEE
T ss_pred EEEEEEecCCCCeEEEEEeecCcccCCCCCccccccceEE
Confidence 34468899999999999986555689999999 9998 44
No 134
>PRK10190 L,D-transpeptidase; Provisional
Probab=48.37 E-value=11 Score=31.63 Aligned_cols=43 Identities=23% Similarity=0.247 Sum_probs=34.0
Q ss_pred eCcceEEEEEec--CCcCCCCCCCEEEEeceEEccc---CCeEEEEeC
Q 032583 61 DETGMIIFTARN--DQVDLMKEGTTVILRNAKIDMF---KGSMRLAVD 103 (137)
Q Consensus 61 DeTG~I~ltlW~--~~~~~i~~Gd~v~I~na~~~~~---~g~~~L~vg 103 (137)
-+.|||||.-|| +..+.+..|..|.|.|..++.. +|.+.|-+-
T Consensus 203 vShGCIRm~n~Di~~Lf~~V~~GT~V~ii~~pvk~~~~~~g~~ylEvH 250 (310)
T PRK10190 203 VSQGCIRLRNDDIKYLFDNVPVGTRVQIIDQPVKYTTEPDGSRWLEVH 250 (310)
T ss_pred CCCceeCcCHHHHHHHHhhCCCCCEEEEecccEEEEEcCCCEEEEEEe
Confidence 368999999999 4667789999999999998873 466655443
No 135
>COG1376 ErfK Uncharacterized protein conserved in bacteria [Function unknown]
Probab=48.28 E-value=9 Score=29.86 Aligned_cols=30 Identities=20% Similarity=0.342 Sum_probs=24.9
Q ss_pred eeCcceEEEEEec--CCcCCCCCCCEEEEece
Q 032583 60 GDETGMIIFTARN--DQVDLMKEGTTVILRNA 89 (137)
Q Consensus 60 gDeTG~I~ltlW~--~~~~~i~~Gd~v~I~na 89 (137)
.-+.|||||.-|| +..+.+..|+.|.|.+.
T Consensus 200 ~~ShGCIRL~n~Da~~ly~~v~~Gt~V~v~~~ 231 (232)
T COG1376 200 AVSHGCIRLSNQDAKDLYNRVPVGTPVVVIDT 231 (232)
T ss_pred ccCCceEecCchhHHHHHhhCCCCCEEEEeeC
Confidence 3468999999999 56778899999998763
No 136
>cd03584 NTR_complement_C4 NTR/C345C domain, complement C4 subfamily; The NTR domain found in complement C4 is also known as the C345C domain because it occurs at the C-terminus of complement C3, C4 and C5. Complement C4 is a key player in the activation of the component classical pathway. C4 is cleaved by activated C1 to yield C4a anaphylatoxin, and the larger fragment C4b, an essential component of the C3- and C5-convertase enzymes. C4b binds covalently to the surface of pathogens through a reactive thioester. The role of the NTR/C345C domain in C4 (C4b) is unclear.
Probab=46.51 E-value=1.2e+02 Score=22.55 Aligned_cols=82 Identities=15% Similarity=0.061 Sum_probs=53.1
Q ss_pred ceEEEEEEEcceeeeeccCCCccccceeEEEEEE-----eeCcceEEEEEecCCc-CCCCCCCEEEEeceEEccc--CCe
Q 032583 26 HTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLV-----GDETGMIIFTARNDQV-DLMKEGTTVILRNAKIDMF--KGS 97 (137)
Q Consensus 26 v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~V-----gDeTG~I~ltlW~~~~-~~i~~Gd~v~I~na~~~~~--~g~ 97 (137)
.=+.++|++......|.++. ..|.+++= ++.-|..|.-+....- ..+++|..+-|.|.-...+ +|.
T Consensus 36 Yaykv~V~~~~~~~~~~~y~------~~I~~ViK~g~d~~~~~g~~r~f~~~~~Cr~~l~~gk~YLImG~~~~~~~~~~~ 109 (153)
T cd03584 36 YAYVVKVLNISEKSNFELYE------TSITDVLQTTGDVSVKPEETRVFLKRLSCKLELKKGKEYLIMGKDGATSDSNGH 109 (153)
T ss_pred EEEEEEEEEEEecCCEEEEE------EEEEEEEEcCCcCcccCCCeEEEEecCCccCcccCCCEEEEEcCCCCCcCcCCc
Confidence 45888888887765554332 23333211 2336777743444321 2567999999999875544 457
Q ss_pred EEEEeCCcEeEEEcCC
Q 032583 98 MRLAVDKWGRVEVAEP 113 (137)
Q Consensus 98 ~~L~vg~~g~I~~~~~ 113 (137)
+++.+|+.+-|+.-|.
T Consensus 110 ~~Y~L~~~tWvE~wP~ 125 (153)
T cd03584 110 MQYLLDSKTWVEKIPS 125 (153)
T ss_pred EEEEeCCCceEEECCC
Confidence 9999999999998863
No 137
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=46.47 E-value=66 Score=26.14 Aligned_cols=61 Identities=21% Similarity=0.323 Sum_probs=47.5
Q ss_pred ceeEEEEEEeeCcceEEEEEecCCcCCCCCCCEEEEeceEEccc-------------CCeEEEEeCCcEeEEEc
Q 032583 51 QMRIAECLVGDETGMIIFTARNDQVDLMKEGTTVILRNAKIDMF-------------KGSMRLAVDKWGRVEVA 111 (137)
Q Consensus 51 ~~~v~~~~VgDeTG~I~ltlW~~~~~~i~~Gd~v~I~na~~~~~-------------~g~~~L~vg~~g~I~~~ 111 (137)
+..++.+.-.|.++.+.|++-++....++-|-+|.|.-+.+... ....++.+|.+|.|=..
T Consensus 117 D~v~AkV~~vd~~~~~~L~~k~~~~GkL~~G~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~NG~IWV~ 190 (239)
T COG1097 117 DLVYAKVVDVDRDGEVELTLKDEGLGKLKNGQIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQNGRIWVD 190 (239)
T ss_pred CEEEEEEEEccCCCceEEEeecCCCccccCCEEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEecCCEEEec
Confidence 35677778899999999999888777889999999987766332 23568888888888544
No 138
>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed
Probab=46.26 E-value=83 Score=26.96 Aligned_cols=69 Identities=14% Similarity=0.049 Sum_probs=45.6
Q ss_pred CCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecCCcCC----CCCCCEEEEeceEEcc-cCCe
Q 032583 23 TSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARNDQVDL----MKEGTTVILRNAKIDM-FKGS 97 (137)
Q Consensus 23 ~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~~~~~----i~~Gd~v~I~na~~~~-~~g~ 97 (137)
..++-|.|-|-...... +|. ....+-|+++.|+.++|...+.. ++.|+-|.+.+...-. -+|.
T Consensus 23 ~~~v~v~gEis~~~~~~-----------sGH-~Yf~Lkd~~a~i~~~~~~~~~~~~~~~~~~G~~v~v~g~~~~y~~~g~ 90 (438)
T PRK00286 23 LGQVWVRGEISNFTRHS-----------SGH-WYFTLKDEIAQIRCVMFKGSARRLKFKPEEGMKVLVRGKVSLYEPRGD 90 (438)
T ss_pred CCcEEEEEEeCCCeeCC-----------CCe-EEEEEEcCCcEEEEEEEcChhhcCCCCCCCCCEEEEEEEEEEECCCCC
Confidence 45566666655543221 133 44678999999999999854322 5899999998776532 3567
Q ss_pred EEEEeC
Q 032583 98 MRLAVD 103 (137)
Q Consensus 98 ~~L~vg 103 (137)
++|++.
T Consensus 91 ~ql~v~ 96 (438)
T PRK00286 91 YQLIVE 96 (438)
T ss_pred EEEEEE
Confidence 888663
No 139
>PLN02221 asparaginyl-tRNA synthetase
Probab=45.61 E-value=1.5e+02 Score=27.04 Aligned_cols=59 Identities=20% Similarity=0.141 Sum_probs=41.5
Q ss_pred EEEEEEeeCc--ceEEEEEecCC---cCCCCCCCEEEEeceEEccc-----CCeEEEEeCCcEeEEEcC
Q 032583 54 IAECLVGDET--GMIIFTARNDQ---VDLMKEGTTVILRNAKIDMF-----KGSMRLAVDKWGRVEVAE 112 (137)
Q Consensus 54 v~~~~VgDeT--G~I~ltlW~~~---~~~i~~Gd~v~I~na~~~~~-----~g~~~L~vg~~g~I~~~~ 112 (137)
+.=+.|-|.| |.|.+++=.+. ...+..|.+|.|.|..+..- .+.++|.+.+.--|...+
T Consensus 70 i~Fl~LRDgs~~g~iQvVv~~~~~~~~~~L~~ES~V~V~G~V~~~~~~~~~~~~iEl~v~~i~vl~~a~ 138 (572)
T PLN02221 70 FAFLEVNDGSCPANLQVMVDSSLYDLSTLVATGTCVTVDGVLKVPPEGKGTKQKIELSVEKVIDVGTVD 138 (572)
T ss_pred EEEEEEeCCcccccEEEEEcCchhhHHhcCCCceEEEEEEEEEeCCccCCCCccEEEEEeEEEEEecCC
Confidence 5556888888 88888664321 12478999999999776432 347999998776666554
No 140
>PF04775 Bile_Hydr_Trans: Acyl-CoA thioester hydrolase/BAAT N-terminal region; InterPro: IPR006862 This entry presents the N-termini of acyl-CoA thioester hydrolase and bile acid-CoA:amino acid N-acetyltransferase (BAAT) []. This region is not thought to contain the active site of either enzyme. Thioesterase isoforms have been identified in peroxisomes, cytoplasm and mitochondria, where they are thought to have distinct functions in lipid metabolism []. For example, in peroxisomes, the hydrolase acts on bile-CoA esters [].; GO: 0016290 palmitoyl-CoA hydrolase activity, 0006629 lipid metabolic process; PDB: 3HLK_B 3K2I_B.
Probab=44.64 E-value=57 Score=23.39 Aligned_cols=48 Identities=27% Similarity=0.473 Sum_probs=25.0
Q ss_pred CCCeeeeeccCCCCCCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEE
Q 032583 9 RKPVFTKVDQLRPGTSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFT 69 (137)
Q Consensus 9 ~~~~~~kI~dL~p~~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~lt 69 (137)
..|..++|..|.|+.. ++|.++..+- .|. .=+-.-...||++|.|-|.
T Consensus 2 De~~~I~v~GL~p~~~-vtl~a~~~~~---------~g~---~w~S~A~f~Ad~~G~VDl~ 49 (126)
T PF04775_consen 2 DEPVDIRVSGLPPGQE-VTLRARLTDD---------NGV---QWQSYATFRADENGIVDLS 49 (126)
T ss_dssp TS--EEEEES--TT-E-EEEEEEEE-T---------TS----EEEEEEEEE--TTS-EETT
T ss_pred CCCeEEEEeCCCCCCE-EEEEEEEEeC---------CCC---EEEEEEEEEcCCCCeEEec
Confidence 3567788999999876 7888887752 111 0122235779999999874
No 141
>smart00643 C345C Netrin C-terminal Domain.
Probab=43.75 E-value=1e+02 Score=21.02 Aligned_cols=50 Identities=20% Similarity=0.259 Sum_probs=34.8
Q ss_pred ceEEEEEecCCc---CCCCCCCEEEEeceEEccc--CCeEEEEeCCcEeEEEcCC
Q 032583 64 GMIIFTARNDQV---DLMKEGTTVILRNAKIDMF--KGSMRLAVDKWGRVEVAEP 113 (137)
Q Consensus 64 G~I~ltlW~~~~---~~i~~Gd~v~I~na~~~~~--~g~~~L~vg~~g~I~~~~~ 113 (137)
+..++-.|.... ..+++|..+-|.+-....+ ++..+|.++..+-|++-+.
T Consensus 49 ~~~~~~~~~~~C~cp~~l~~g~~YLImG~~~~~~~~~~~~~~~l~~~s~v~~W~~ 103 (114)
T smart00643 49 GKLRLFISRASCRCPLLLKKGKSYLIMGKSGDLWDVKGRGQYVLGKNSWVEEWPT 103 (114)
T ss_pred CcEEEEeeccccCCccccCCCCEEEEecCCCCccccCCccEEEeCCCeEEEECCC
Confidence 555555554322 2467999999999764443 3468899999999987753
No 142
>PRK06341 single-stranded DNA-binding protein; Provisional
Probab=42.41 E-value=64 Score=24.60 Aligned_cols=65 Identities=15% Similarity=0.185 Sum_probs=41.2
Q ss_pred CCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeC-------cc-------eEEEEEecC-Cc----CCCCCCCE
Q 032583 23 TSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDE-------TG-------MIIFTARND-QV----DLMKEGTT 83 (137)
Q Consensus 23 ~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDe-------TG-------~I~ltlW~~-~~----~~i~~Gd~ 83 (137)
++.+.|.+++..-.+.+.+ .+| ..+++..||=. +| -+++++|.+ ++ ..++.|+.
T Consensus 5 mN~V~LiGrLg~DPElR~t--~sG-----~~v~~fsVAvn~~~kd~~~Ge~~e~T~w~~Vv~fg~~~Ae~~~~~LkKG~~ 77 (166)
T PRK06341 5 VNKVILIGNLGADPEIRRT--QDG-----RPIANLRIATSETWRDRNSGERKEKTEWHRVVIFNEGLCKVAEQYLKKGAK 77 (166)
T ss_pred ceEEEEEEEecCCCEEEEc--CCC-----CEEEEEEEEEccceecCCCCcccccceEEEEEEeChHHHHHHHHhcCCCCE
Confidence 4567788888775455443 244 35555554432 33 468999985 33 34699999
Q ss_pred EEEeceEE-ccc
Q 032583 84 VILRNAKI-DMF 94 (137)
Q Consensus 84 v~I~na~~-~~~ 94 (137)
|.|.+... +.|
T Consensus 78 V~VeGrL~~r~w 89 (166)
T PRK06341 78 VYIEGQLQTRKW 89 (166)
T ss_pred EEEEEEEEeCcE
Confidence 99998864 335
No 143
>COG1570 XseA Exonuclease VII, large subunit [DNA replication, recombination, and repair]
Probab=42.16 E-value=1.3e+02 Score=26.62 Aligned_cols=69 Identities=12% Similarity=0.026 Sum_probs=45.7
Q ss_pred CCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecCCcCC----CCCCCEEEEeceEEcc-cCCe
Q 032583 23 TSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARNDQVDL----MKEGTTVILRNAKIDM-FKGS 97 (137)
Q Consensus 23 ~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~~~~~----i~~Gd~v~I~na~~~~-~~g~ 97 (137)
..+|-|+|-|-.+..+. ++ =....+.|+.+.|+.++|...... +++|+-|.+.+-..-+ -+|.
T Consensus 23 ~~~V~v~GEISn~t~~~-----------sg-H~YFtLKD~~A~i~c~mf~~~~~~l~f~p~eG~~V~v~G~is~Y~~rG~ 90 (440)
T COG1570 23 LGQVWVRGEISNFTRPA-----------SG-HLYFTLKDERAQIRCVMFKGNNRRLKFRPEEGMQVLVRGKISLYEPRGD 90 (440)
T ss_pred CCeEEEEEEecCCccCC-----------Cc-cEEEEEccCCceEEEEEEcCcccccCCCccCCCEEEEEEEEEEEcCCCc
Confidence 35566666555544322 13 345689999999999999854322 4799999998766533 2567
Q ss_pred EEEEeC
Q 032583 98 MRLAVD 103 (137)
Q Consensus 98 ~~L~vg 103 (137)
.+|++.
T Consensus 91 YQi~~~ 96 (440)
T COG1570 91 YQIVAE 96 (440)
T ss_pred eEEEEe
Confidence 777664
No 144
>PF05113 DUF693: Protein of unknown function (DUF693); InterPro: IPR007800 This family consists of uncharacterised proteins from Borrelia burgdorferi.
Probab=39.94 E-value=79 Score=26.51 Aligned_cols=33 Identities=24% Similarity=0.153 Sum_probs=24.0
Q ss_pred ceEEEEEec---CCcCCCCCCCEEEEeceEEcccCC
Q 032583 64 GMIIFTARN---DQVDLMKEGTTVILRNAKIDMFKG 96 (137)
Q Consensus 64 G~I~ltlW~---~~~~~i~~Gd~v~I~na~~~~~~g 96 (137)
-...+++|+ +..+.+++||+|+|+.-.-..-+.
T Consensus 61 Kqaki~lwNlPLdFt~~ik~gDIVKIYYKKFa~~k~ 96 (314)
T PF05113_consen 61 KQAKIVLWNLPLDFTDNIKTGDIVKIYYKKFAHEKD 96 (314)
T ss_pred eeeEEEEEecCcccccccCcCcEEEEEeeccccccc
Confidence 356788999 345668999999998765544444
No 145
>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=38.64 E-value=96 Score=21.92 Aligned_cols=66 Identities=23% Similarity=0.161 Sum_probs=30.3
Q ss_pred CCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEee--CcceEEEEEecCC-----cCCCCCCCEEEEeceEEccc-
Q 032583 23 TSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGD--ETGMIIFTARNDQ-----VDLMKEGTTVILRNAKIDMF- 94 (137)
Q Consensus 23 ~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgD--eTG~I~ltlW~~~-----~~~i~~Gd~v~I~na~~~~~- 94 (137)
.+.+.++++|.++.. . ++. ..+. +.++ ..+.|++.+=++. ...+++||.|.|.+.....-
T Consensus 67 gK~i~vtG~V~~I~~-~-----~~~----~~~~--~~~~~~~~~~v~~~~~~~~~~~~~~~~l~~G~~Vti~G~~~g~~~ 134 (144)
T PF12869_consen 67 GKIIEVTGTVSSIDK-G-----FGD----NYVV--LLGTENGFAGVQCYFSNDQEKRASVAKLKKGQKVTIKGICTGYSL 134 (144)
T ss_dssp T-EEEEEEEEEEEEE-------STT-----EEE--EEE-TT-S-S--EEEEEEGGGHHHHHH--TTSEEEEEEE-----S
T ss_pred CCEEEEEEEEEEEEE-c-----CCC----cEEE--EccCCCCceeEEEEEccchhhhhhHhcCCCCCEEEEEEEEEeeec
Confidence 466889999988754 1 121 2222 2333 3444555444543 22389999999999887663
Q ss_pred CCeEEE
Q 032583 95 KGSMRL 100 (137)
Q Consensus 95 ~g~~~L 100 (137)
.+.+-|
T Consensus 135 ~~~v~l 140 (144)
T PF12869_consen 135 MGVVML 140 (144)
T ss_dssp SS-EEE
T ss_pred CCcEEe
Confidence 555544
No 146
>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=38.52 E-value=1.3e+02 Score=26.07 Aligned_cols=48 Identities=13% Similarity=0.121 Sum_probs=35.5
Q ss_pred EEEEeeCcceEEEEEecCCcCC----CCCCCEEEEeceEEcc-cCCeEEEEeC
Q 032583 56 ECLVGDETGMIIFTARNDQVDL----MKEGTTVILRNAKIDM-FKGSMRLAVD 103 (137)
Q Consensus 56 ~~~VgDeTG~I~ltlW~~~~~~----i~~Gd~v~I~na~~~~-~~g~~~L~vg 103 (137)
...+-|+...|+.+.|...+.. ++.|+-|.+.+...-+ -+|.++|++.
T Consensus 38 YFtLkD~~a~i~~vmf~~~~~~l~f~~~~G~~V~v~g~v~~y~~~G~~ql~v~ 90 (432)
T TIGR00237 38 YFTLKDENAQVRCVMFRGNNNRLKFRPQNGQQVLVRGGISVYEPRGDYQIICF 90 (432)
T ss_pred EEEEEcCCcEEEEEEEcChhhCCCCCCCCCCEEEEEEEEEEECCCCcEEEEEE
Confidence 4556899999999999854322 4899999998876433 3577888764
No 147
>KOG1816 consensus Ubiquitin fusion-degradation protein [Posttranslational modification, protein turnover, chaperones]
Probab=37.16 E-value=28 Score=29.24 Aligned_cols=31 Identities=26% Similarity=0.318 Sum_probs=25.7
Q ss_pred eCcceEEEEEecCCcCCCCCCCEEEEeceEE
Q 032583 61 DETGMIIFTARNDQVDLMKEGTTVILRNAKI 91 (137)
Q Consensus 61 DeTG~I~ltlW~~~~~~i~~Gd~v~I~na~~ 91 (137)
=|.|.|-|=.|--+-..+++||.|+|++...
T Consensus 81 AeEG~vyLP~WMmq~L~le~gdlv~i~~v~l 111 (308)
T KOG1816|consen 81 AEEGRVYLPYWMMQNLLLEEGDLVRIRSVTL 111 (308)
T ss_pred ecCceEEeehHhhhhccCCCCCeEEEEEeec
Confidence 4568999999996666789999999998653
No 148
>COG1917 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]
Probab=36.78 E-value=36 Score=23.88 Aligned_cols=28 Identities=14% Similarity=0.229 Sum_probs=20.9
Q ss_pred cceEEEEEecCCcCCCCCCCEEEEeceEE
Q 032583 63 TGMIIFTARNDQVDLMKEGTTVILRNAKI 91 (137)
Q Consensus 63 TG~I~ltlW~~~~~~i~~Gd~v~I~na~~ 91 (137)
.|.++++++ .+.-.+++||++.|-=+..
T Consensus 72 ~G~~~~~~~-g~~~~l~~Gd~i~ip~g~~ 99 (131)
T COG1917 72 EGEGTVQLE-GEKKELKAGDVIIIPPGVV 99 (131)
T ss_pred ecEEEEEec-CCceEecCCCEEEECCCCe
Confidence 477888888 5556789999998865443
No 149
>PLN02903 aminoacyl-tRNA ligase
Probab=36.42 E-value=2.7e+02 Score=25.92 Aligned_cols=59 Identities=15% Similarity=0.201 Sum_probs=43.1
Q ss_pred eEEEEEEeeCcceEEEEEecCC-------cCCCCCCCEEEEeceEEcc---------cCCeEEEEeCCcEeEEEc
Q 032583 53 RIAECLVGDETGMIIFTARNDQ-------VDLMKEGTTVILRNAKIDM---------FKGSMRLAVDKWGRVEVA 111 (137)
Q Consensus 53 ~v~~~~VgDeTG~I~ltlW~~~-------~~~i~~Gd~v~I~na~~~~---------~~g~~~L~vg~~g~I~~~ 111 (137)
.+.=+.+-|.+|.+.+++=.+. +..+..|++|.+.|-.... -.|.++|.+.+.--+.+.
T Consensus 89 ~l~FidLRD~~G~iQvV~~~~~~~~~~~~~~~L~~esvV~V~G~V~~r~~~~~n~~~~tGeiEl~~~~i~VL~~a 163 (652)
T PLN02903 89 GLTFLDVRDHTGIVQVVTLPDEFPEAHRTANRLRNEYVVAVEGTVRSRPQESPNKKMKTGSVEVVAESVDILNVV 163 (652)
T ss_pred CcEEEEEEcCCccEEEEEeCCccHHHHHHHhcCCCCCEEEEEEEEEeCCCcCcCCCCCCCCEEEEEeEEEEEecC
Confidence 4566788999999988764321 2458899999999976632 137799999888666665
No 150
>COG0587 DnaE DNA polymerase III, alpha subunit [DNA replication, recombination, and repair]
Probab=36.24 E-value=1.2e+02 Score=30.01 Aligned_cols=72 Identities=18% Similarity=0.213 Sum_probs=46.7
Q ss_pred eeeccCCCCCCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecC----CcCCCCCCCEEEEece
Q 032583 14 TKVDQLRPGTSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARND----QVDLMKEGTTVILRNA 89 (137)
Q Consensus 14 ~kI~dL~p~~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~----~~~~i~~Gd~v~I~na 89 (137)
....++.+......+.+.|..+..... +..| ..++-+.+.|+||.+.+++|-. +...+.+|..+.|.+.
T Consensus 967 ~~~~~~~~~~~~~~~~~~i~~vr~~~t--k~~G-----~~~~f~tl~D~~g~~e~v~f~~~~~~~~~~l~~~~~~~v~g~ 1039 (1139)
T COG0587 967 IRLLDLVEDGRRVVLAGGIVAVRQRPT--KAKG-----NKMAFLTLEDETGILEVVVFPSEYERYRRLLLEGRLLIVKGK 1039 (1139)
T ss_pred cchhhhccccceeEEEEEEEEEEEeec--cCCC-----CEEEEEEEecCCCcEEEEEcHHHHHHHHHHhccCcEEEEEEE
Confidence 344555554442456666666654332 2244 5788899999999999999942 3345678888877765
Q ss_pred EEc
Q 032583 90 KID 92 (137)
Q Consensus 90 ~~~ 92 (137)
...
T Consensus 1040 v~~ 1042 (1139)
T COG0587 1040 VQR 1042 (1139)
T ss_pred EEe
Confidence 544
No 151
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=35.16 E-value=2e+02 Score=29.07 Aligned_cols=91 Identities=13% Similarity=0.141 Sum_probs=68.5
Q ss_pred CeeeeeccCCCCCCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecC------CcCCCCCCCEE
Q 032583 11 PVFTKVDQLRPGTSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARND------QVDLMKEGTTV 84 (137)
Q Consensus 11 ~~~~kI~dL~p~~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~------~~~~i~~Gd~v 84 (137)
.+++++-++.+.+.++.+.+.|.++... + .+-| ..+.+.-|-|-|-+..+-.|-. ..+.++.|+.|
T Consensus 227 ~~i~~~~~i~~~~~~v~v~G~IF~~e~~-~--~ksG-----r~l~~i~vTD~t~Sl~~k~f~~~~ed~~~~~~ik~g~wv 298 (1444)
T COG2176 227 EEIKPLIKINEEETRVKVEGYIFKIEIK-E--LKSG-----RTLLNIKVTDYTSSLILKKFLRDEEDEKKFDGIKKGMWV 298 (1444)
T ss_pred cceeehhhccccccceEEEEEEEEEeee-e--cccC-----cEEEEEEEecCchheeehhhccccccHHHHhhcccCcEE
Confidence 4677888888888889999999997543 2 2234 4677899999999999988863 24567999999
Q ss_pred EEeceEEcc-cCCeEEEEeCCcEeEE
Q 032583 85 ILRNAKIDM-FKGSMRLAVDKWGRVE 109 (137)
Q Consensus 85 ~I~na~~~~-~~g~~~L~vg~~g~I~ 109 (137)
+.++-.-.. +.+.+.+.++.--.|.
T Consensus 299 k~~g~v~~d~f~~~l~m~i~~I~ei~ 324 (1444)
T COG2176 299 KARGNVQLDTFTRDLTMIINDINEIE 324 (1444)
T ss_pred EEEEEEEecccccceEEEhhhhhhhh
Confidence 999876544 5667777776655554
No 152
>cd05694 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=35.12 E-value=1.2e+02 Score=19.41 Aligned_cols=69 Identities=19% Similarity=0.127 Sum_probs=40.2
Q ss_pred cCCCCCCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecCCcCCCCCCCEEEEeceEEcccCCe
Q 032583 18 QLRPGTSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARNDQVDLMKEGTTVILRNAKIDMFKGS 97 (137)
Q Consensus 18 dL~p~~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~~~~~i~~Gd~v~I~na~~~~~~g~ 97 (137)
||+.|+ -+.|.|-++.+- +-+.+.-+++=+|-++.+--... ..+++|+.+...=-.+...+++
T Consensus 1 dl~~G~---~v~g~V~si~d~-------------G~~v~~g~~gv~Gfl~~~~~~~~-~~~~~Gq~v~~~V~~vd~~~~~ 63 (74)
T cd05694 1 DLVEGM---VLSGCVSSVEDH-------------GYILDIGIPGTTGFLPKKDAGNF-SKLKVGQLLLCVVEKVKDDGRV 63 (74)
T ss_pred CCCCCC---EEEEEEEEEeCC-------------EEEEEeCCCCcEEEEEHHHCCcc-cccCCCCEEEEEEEEEECCCCE
Confidence 455554 388888887652 23333211122455543221111 5689999998886666666778
Q ss_pred EEEEeC
Q 032583 98 MRLAVD 103 (137)
Q Consensus 98 ~~L~vg 103 (137)
+.|++.
T Consensus 64 v~ls~k 69 (74)
T cd05694 64 VSLSAD 69 (74)
T ss_pred EEEEEe
Confidence 888764
No 153
>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....
Probab=34.93 E-value=83 Score=19.43 Aligned_cols=62 Identities=26% Similarity=0.298 Sum_probs=41.1
Q ss_pred eEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecC-----CcCCCCCCCEEEEeceEEcccCCeEEEE
Q 032583 27 TLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARND-----QVDLMKEGTTVILRNAKIDMFKGSMRLA 101 (137)
Q Consensus 27 ~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~-----~~~~i~~Gd~v~I~na~~~~~~g~~~L~ 101 (137)
-+.|+|.++.+- +-..+.- +.-+|-|.++-+.. ....+.+|+.+++.=-.++..++++.|+
T Consensus 7 iv~g~V~~v~~~-------------g~~V~l~-~~~~g~ip~~~l~~~~~~~~~~~~~~G~~v~v~v~~vd~~~~~i~lS 72 (74)
T PF00575_consen 7 IVEGKVTSVEDF-------------GVFVDLG-NGIEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKVDKEKGRIRLS 72 (74)
T ss_dssp EEEEEEEEEETT-------------EEEEEES-TSSEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEEETTTTEEEEE
T ss_pred EEEEEEEEEECC-------------EEEEEEC-CcEEEEEEeehhcCccccccccccCCCCEEEEEEEEEECCCCeEEEE
Confidence 478888877652 1222111 24556666666653 3355789999999988888888888886
Q ss_pred e
Q 032583 102 V 102 (137)
Q Consensus 102 v 102 (137)
+
T Consensus 73 ~ 73 (74)
T PF00575_consen 73 L 73 (74)
T ss_dssp S
T ss_pred E
Confidence 4
No 154
>PRK04036 DNA polymerase II small subunit; Validated
Probab=34.38 E-value=1.4e+02 Score=26.49 Aligned_cols=67 Identities=13% Similarity=0.152 Sum_probs=43.5
Q ss_pred eeeeccCCCCCCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecCC------cCCCCCCCEEEE
Q 032583 13 FTKVDQLRPGTSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARNDQ------VDLMKEGTTVIL 86 (137)
Q Consensus 13 ~~kI~dL~p~~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~~------~~~i~~Gd~v~I 86 (137)
..+|.+++-+...+.+.|.|-++ ++. .+| .. ...+-|+||+|++..-.+. .+.+-.|.+|-+
T Consensus 143 i~~l~~~~~~~~~~~viG~v~~~---~~~--~~g-----~~--~~~LED~sgrv~l~~~~~~~~~~~~~~~lvtg~vv~v 210 (504)
T PRK04036 143 IESLKKLKRGGEEVSIIGMVSDI---RST--KNG-----HK--IVELEDTTGTFPVLIMKDREDLAELADELLLDEVIGV 210 (504)
T ss_pred HHHHhcCccCCceEEEEEEEEEe---ecc--cCC-----ce--EEEEECCCCeEEEEeecchhhhhhhhhcccCceEEEE
Confidence 45566666233557788888654 222 133 11 3689999999999875432 245788999988
Q ss_pred eceEE
Q 032583 87 RNAKI 91 (137)
Q Consensus 87 ~na~~ 91 (137)
.|-+.
T Consensus 211 ~G~~~ 215 (504)
T PRK04036 211 EGTLS 215 (504)
T ss_pred EEEEc
Confidence 88654
No 155
>COG4013 Uncharacterized protein conserved in archaea [Function unknown]
Probab=33.66 E-value=1e+02 Score=21.35 Aligned_cols=32 Identities=22% Similarity=0.357 Sum_probs=23.9
Q ss_pred CCCCCCEEEEeceEE-------cccCCeEEEEeCC---cEeE
Q 032583 77 LMKEGTTVILRNAKI-------DMFKGSMRLAVDK---WGRV 108 (137)
Q Consensus 77 ~i~~Gd~v~I~na~~-------~~~~g~~~L~vg~---~g~I 108 (137)
.+++||.+++.-|.+ ...+|.++|.+.+ .|-+
T Consensus 20 eV~~gd~vel~~grVhIpG~vv~~n~g~l~l~~esdmi~Gi~ 61 (91)
T COG4013 20 EVDVGDYVELYFGRVHIPGRVVHYNDGLLRLVHESDMIYGII 61 (91)
T ss_pred cCCCCCEEEEEEEEEEeccEEEEeeccEEEEEEeccccCceE
Confidence 468999988876654 5567889998888 5544
No 156
>TIGR02656 cyanin_plasto plastocyanin. Members of this family are plastocyanin, a blue copper protein related to pseudoazurin, halocyanin, amicyanin, etc. This protein, located in the thylakoid luman, performs electron transport to photosystem I in Cyanobacteria and chloroplasts.
Probab=33.25 E-value=58 Score=22.00 Aligned_cols=30 Identities=23% Similarity=0.363 Sum_probs=20.6
Q ss_pred EEEeeCcceEEEEEecCCcCCCCCCCEEEEece
Q 032583 57 CLVGDETGMIIFTARNDQVDLMKEGTTVILRNA 89 (137)
Q Consensus 57 ~~VgDeTG~I~ltlW~~~~~~i~~Gd~v~I~na 89 (137)
+.+|.+.|...| +...-.+++||.|++.|.
T Consensus 3 v~~g~~~g~~~F---~P~~i~v~~G~~V~~~N~ 32 (99)
T TIGR02656 3 VKMGADKGALVF---EPAKISIAAGDTVEWVNN 32 (99)
T ss_pred EEEecCCCceeE---eCCEEEECCCCEEEEEEC
Confidence 456777777766 333334689999999875
No 157
>PF01957 NfeD: NfeD-like C-terminal, partner-binding; InterPro: IPR002810 The nfe genes (nfeA, nfeB, and nfeD) are involved in the nodulation efficiency and competitiveness of Rhizobium meliloti (Sinorhizobium meliloti) (Rhizobium meliloti) on alfalfa roots []. The specific function of this family is unknown although it is unlikely that NfeD is specifically involved in nodulation as the family contains several different archaeal and bacterial species most of which are not symbionts. This entry describes archaeal and bacterial proteins which are variously described, examples are: nodulation protein, nodulation efficiency protein D (nfeD), hypothetical protein and membrane-bound serine protease (ClpP class). A number of these proteins are classified in MEROPS peptidase family S49 as non-peptidase homologues or as unassigned peptidases. ; PDB: 2K5H_A 3CP0_A 2EXD_A.
Probab=32.55 E-value=79 Score=22.06 Aligned_cols=37 Identities=8% Similarity=0.092 Sum_probs=19.8
Q ss_pred eeEEEEEEeeCcceEEE--EEecCCcC-CCCCCCEEEEece
Q 032583 52 MRIAECLVGDETGMIIF--TARNDQVD-LMKEGTTVILRNA 89 (137)
Q Consensus 52 ~~v~~~~VgDeTG~I~l--tlW~~~~~-~i~~Gd~v~I~na 89 (137)
+.+. -...+.+|.+++ ..|+...+ .+++|+.|+|...
T Consensus 94 g~v~-~~~~~~~G~V~~~G~~w~A~s~~~i~~G~~V~Vv~v 133 (144)
T PF01957_consen 94 GTVI-EIPLNGSGRVKVDGERWRARSEDEIPKGDRVRVVGV 133 (144)
T ss_dssp EEEE-EEBSSS-EEEEETTEEEEEEESSTB-TT-EEEEEEE
T ss_pred EEEE-EeecCCcEEEEECCeEEEEEeCCCCCCCCEEEEEEE
Confidence 4443 344555666655 46774322 2899999988654
No 158
>KOG0851 consensus Single-stranded DNA-binding replication protein A (RPA), large (70 kD) subunit and related ssDNA-binding proteins [Replication, recombination and repair]
Probab=31.80 E-value=1.3e+02 Score=22.84 Aligned_cols=81 Identities=21% Similarity=0.242 Sum_probs=55.9
Q ss_pred eeeeeccCCCCCCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcc-eEEEEEecCCc----CCCCCCCEEEE
Q 032583 12 VFTKVDQLRPGTSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETG-MIIFTARNDQV----DLMKEGTTVIL 86 (137)
Q Consensus 12 ~~~kI~dL~p~~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG-~I~ltlW~~~~----~~i~~Gd~v~I 86 (137)
.+..+.+|.|...+-.+.++|+.++...... .+....++++|++| .|..+....+. ..+.+|..+.|
T Consensus 3 ~~~~l~~l~~~~t~w~i~~~vl~v~~~~~~~--------~~~~~~~il~D~~~~~i~a~i~~~~~~~~~~~l~~~~w~~i 74 (246)
T KOG0851|consen 3 GFHRLRDLSPSITGWRIQVKVLRVWKKYSNP--------NGEELRLVLADEHGVKIEATVGRRLSSKYEDNLIENEWKII 74 (246)
T ss_pred cccchhhcCcCceeeEEEEEEEEEEEecCCC--------CccEEEEEEEecCCcEEEEEcchHHHhhhhhheecceeEEe
Confidence 4667889999887778999999999865421 24677788899985 34444444322 34578888888
Q ss_pred eceEEcccCCeEEE
Q 032583 87 RNAKIDMFKGSMRL 100 (137)
Q Consensus 87 ~na~~~~~~g~~~L 100 (137)
.+-.+....+.++.
T Consensus 75 ~~f~v~~~~~~~~~ 88 (246)
T KOG0851|consen 75 TTFGVNPNSGQVRA 88 (246)
T ss_pred eeeeecccccceee
Confidence 88777766654444
No 159
>COG4880 Secreted protein containing C-terminal beta-propeller domain distantly related to WD-40 repeats [General function prediction only]
Probab=31.43 E-value=58 Score=29.23 Aligned_cols=54 Identities=19% Similarity=0.132 Sum_probs=46.6
Q ss_pred EeeCcceEEEEEec-CCcCCCCCCCEEEEeceEEcccCCeEEEEeCCcEeEEEcC
Q 032583 59 VGDETGMIIFTARN-DQVDLMKEGTTVILRNAKIDMFKGSMRLAVDKWGRVEVAE 112 (137)
Q Consensus 59 VgDeTG~I~ltlW~-~~~~~i~~Gd~v~I~na~~~~~~g~~~L~vg~~g~I~~~~ 112 (137)
||-+.|.+.++|+| ......++=+.+.+.+++...|.+++-...+....|--.+
T Consensus 488 vG~~~g~vKiSLFdiSdl~~PkEv~~y~l~~~wspvf~dhHAFl~d~~~~ifFlP 542 (603)
T COG4880 488 VGAYQGGVKISLFDISDLAAPKEVSNYTLSNAWSPVFYDHHAFLYDPEAEIFFLP 542 (603)
T ss_pred eecccCCceEEEEeccCCCCchhhhheehhhhcchhhhccceeecCCcccEEEec
Confidence 45556999999999 5666679999999999999999999999999888887776
No 160
>cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=30.65 E-value=1.4e+02 Score=19.14 Aligned_cols=77 Identities=19% Similarity=0.116 Sum_probs=41.6
Q ss_pred eeeccCCCCCCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecCCcCCCCCCCEEEEeceEEcc
Q 032583 14 TKVDQLRPGTSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARNDQVDLMKEGTTVILRNAKIDM 93 (137)
Q Consensus 14 ~kI~dL~p~~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~~~~~i~~Gd~v~I~na~~~~ 93 (137)
.++.++++|+ -+.|+|..+.+---|-.-.+. -.+.+-.--++++- ..+..+.++.||.+++.=-.+..
T Consensus 7 ~~~~~~~~G~---i~~g~V~~v~~~G~fv~l~~~--~~g~v~~~el~~~~-------~~~~~~~~~~Gd~v~vkV~~id~ 74 (83)
T cd04461 7 TNFSDLKPGM---VVHGYVRNITPYGVFVEFLGG--LTGLAPKSYISDEF-------VTDPSFGFKKGQSVTAKVTSVDE 74 (83)
T ss_pred hhHHhCCCCC---EEEEEEEEEeeceEEEEcCCC--CEEEEEHHHCCccc-------ccCHHHhcCCCCEEEEEEEEEcC
Confidence 3467777776 488898888764333211110 01111111111110 11223457899999998666666
Q ss_pred cCCeEEEEe
Q 032583 94 FKGSMRLAV 102 (137)
Q Consensus 94 ~~g~~~L~v 102 (137)
.++++.|++
T Consensus 75 ~~~~i~lsl 83 (83)
T cd04461 75 EKQRFLLSL 83 (83)
T ss_pred CCCEEEEeC
Confidence 678887753
No 161
>cd03574 NTR_complement_C345C NTR/C345C domain; The NTR domains that are found in the C-termini of complement C3, C4 and C5, are also called C345C domains. In C5, the domain interacts with various partners during the formation of the membrane attack complex, a fundamental process in the mammalian defense against infection. It's role in component C3 and C4 is not well understood.
Probab=30.37 E-value=2.1e+02 Score=20.72 Aligned_cols=38 Identities=16% Similarity=0.172 Sum_probs=31.2
Q ss_pred CCCCCCCEEEEeceEEcccC-----CeEEEEeCCcEeEEEcCC
Q 032583 76 DLMKEGTTVILRNAKIDMFK-----GSMRLAVDKWGRVEVAEP 113 (137)
Q Consensus 76 ~~i~~Gd~v~I~na~~~~~~-----g~~~L~vg~~g~I~~~~~ 113 (137)
..+++|..+-|.|.....++ +..+|.+|..+-|+.-+.
T Consensus 77 ~~l~~g~~YLImG~~~~~~~~~~~~~~~~yvl~~~t~Ve~Wp~ 119 (147)
T cd03574 77 LRLKEGRHYLIMGSDGAFYDDRNGEDRYQYVLDSNTWVEEWPT 119 (147)
T ss_pred hcCCCCCEEEEeccCcCcccccCCCcceEEEeCCCcEEEECCC
Confidence 45689999999999766654 378999999999998763
No 162
>PF01759 NTR: UNC-6/NTR/C345C module; InterPro: IPR018933 The netrin (NTR) module is an about 130-residue domain found in the C-terminal parts of netrins, complement proteins C3, C4, and C5, secreted frizzled-related proteins, and type I procollagen C-proteinase enhancer proteins (PCOLCEs), as well as in the N-terminal parts of tissue inhibitors of metalloproteinases (TIMPs). The proteins harboring the NTR domain fulfill diverse biological roles ranging from axon guidance, regulation of Wnt signalling, to the control of the activity of metalloproteinases. The NTR domain can be found associated to other domains such as CUB, WAP, Kazal, Kunitz, Ig-like, laminin N-terminal, laminin-type EGF or frizzled. The NTR domain is implicated in inhibition of zinc metalloproteinases of the metzincin family [, ]. The NTR module is a basic domain containing six conserved cysteines, which are likely to form internal disulphide bonds, and several conserved blocks of hydrophobic residues (including an YLLLG-like motif). The NTR module consists of a beta-barrel with two terminal alpha-helices packed side by side against the face of the beta-barrel (see P16035 from SWISSPROT) []. This entry includes most netrin modules, but excludes those found in TIMPs.; PDB: 2B39_B 3HS0_C 3PRX_B 3PVM_D 3HRZ_C 3FRP_B 2WIN_H 2I07_B 2ICF_B 2XWJ_D ....
Probab=29.90 E-value=1.8e+02 Score=19.59 Aligned_cols=50 Identities=18% Similarity=0.086 Sum_probs=32.4
Q ss_pred cceEEEEEecC----CcCCCCC-CCEEEEeceEEcc-cCCeEEEEeCCcEeEEEcC
Q 032583 63 TGMIIFTARND----QVDLMKE-GTTVILRNAKIDM-FKGSMRLAVDKWGRVEVAE 112 (137)
Q Consensus 63 TG~I~ltlW~~----~~~~i~~-Gd~v~I~na~~~~-~~g~~~L~vg~~g~I~~~~ 112 (137)
.|..++..... ....+++ |..+-|.+..... ..+..+|.++..+-|.+=+
T Consensus 44 ~~~~~~~~~~~~~~C~Cp~l~~~g~~YLImG~~~~~~~~~~~~~~l~~~s~v~~W~ 99 (111)
T PF01759_consen 44 RGRRRLFVKRNDCRCPCPDLKVIGKEYLIMGKDGDTDGKDRGRYVLDSDSFVEPWP 99 (111)
T ss_dssp STSEEEEEEEGS-S-GGHHHHTTTCEEEEEEEGGGECSTTSEEEE-STTSEEEEE-
T ss_pred CCceEEEEEcccccccCcccccCCCEEEEEEeecccCCCCccEEEECCCcEEEECC
Confidence 45555544444 4455666 9999999954222 5677899999998887663
No 163
>COG4043 Preprotein translocase subunit Sec61beta [Intracellular trafficking, secretion, and vesicular transport]
Probab=29.67 E-value=69 Score=22.93 Aligned_cols=28 Identities=18% Similarity=0.299 Sum_probs=21.6
Q ss_pred eEEEEEecCCcCCCCCCCEEEEeceEEc
Q 032583 65 MIIFTARNDQVDLMKEGTTVILRNAKID 92 (137)
Q Consensus 65 ~I~ltlW~~~~~~i~~Gd~v~I~na~~~ 92 (137)
+|-..+-|++.-.+++||.|.+.+...+
T Consensus 21 ~iEvRl~d~krr~ik~GD~IiF~~~~l~ 48 (111)
T COG4043 21 KIEVRLADPKRRQIKPGDKIIFNGDKLK 48 (111)
T ss_pred eEEEEecCHhhcCCCCCCEEEEcCCeeE
Confidence 4566677888888999999999875443
No 164
>COG3111 Periplasmic protein with OB-fold [Function unknown]
Probab=28.16 E-value=1.8e+02 Score=21.52 Aligned_cols=44 Identities=11% Similarity=0.154 Sum_probs=32.0
Q ss_pred EEeeCcceEEEEEecCC--cCCCCCCCEEEEeceEEcccCCeEEEEe
Q 032583 58 LVGDETGMIIFTARNDQ--VDLMKEGTTVILRNAKIDMFKGSMRLAV 102 (137)
Q Consensus 58 ~VgDeTG~I~ltlW~~~--~~~i~~Gd~v~I~na~~~~~~g~~~L~v 102 (137)
++-|.||+|++.+=+.- ...+.|-|.|+|.+-.=+.|+. +++.|
T Consensus 76 ~FrD~sGeI~VeIdd~~w~g~tv~P~dkV~I~GevDk~~~~-~eIdV 121 (128)
T COG3111 76 VFRDASGEINVDIDDKVWNGQTVTPKDKVRIQGEVDKDWNS-VEIDV 121 (128)
T ss_pred EEEcCCccEEEEecccccCCcccCcccEEEEEeEEcCCCcc-ceeEh
Confidence 56789999999764432 2247899999999988777765 45544
No 165
>PF09356 Phage_BR0599: Phage conserved hypothetical protein BR0599; InterPro: IPR018964 This entry describes the C-terminal region of a family of proteins found almost exclusively in phage or in prophage regions of bacterial genomes, including the phage-like Rhodobacter capsulatus (Rhodopseudomonas capsulata) gene transfer agent, which packages DNA. An apparent exception is Wolbachia pipientis wMel, a bacterial endosymbiont of the fruit fly, which has several candidate phage-related genes physically separate from obvious prophage regions.
Probab=27.73 E-value=81 Score=20.99 Aligned_cols=23 Identities=22% Similarity=0.029 Sum_probs=18.8
Q ss_pred EEEEEecCCcCCCCCCCEEEEec
Q 032583 66 IIFTARNDQVDLMKEGTTVILRN 88 (137)
Q Consensus 66 I~ltlW~~~~~~i~~Gd~v~I~n 88 (137)
-.|+||......+..||.++|.=
T Consensus 29 ~~l~L~~p~~~~~~~G~~v~l~~ 51 (80)
T PF09356_consen 29 GTLTLWRPLPAGLAVGDTVTLYP 51 (80)
T ss_pred CEEEEeccCcccCCCCCEEEEEe
Confidence 67888987766789999999873
No 166
>PF03459 TOBE: TOBE domain; InterPro: IPR005116 The TOBE domain [] (Transport-associated OB) always occurs as a dimer as the C-terminal strand of each domain is supplied by the partner. It is probably involved in the recognition of small ligands such as molybdenum (P46930 from SWISSPROT) and sulphate (P16676 from SWISSPROT), and is found in ABC transporters immediately after the ATPase domain.; GO: 0005215 transporter activity, 0005524 ATP binding, 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0006810 transport, 0043190 ATP-binding cassette (ABC) transporter complex; PDB: 1G29_2 1H9M_B 1H9J_A 1H9K_A 1H9R_B 1O7L_C 1H9S_A 1B9N_A 1B9M_A 1GUS_C ....
Probab=26.25 E-value=1.5e+02 Score=17.83 Aligned_cols=50 Identities=18% Similarity=0.066 Sum_probs=29.1
Q ss_pred eEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCc-ceEEEEEecCCcCCCCCCCEEEEe
Q 032583 27 TLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDET-GMIIFTARNDQVDLMKEGTTVILR 87 (137)
Q Consensus 27 ~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeT-G~I~ltlW~~~~~~i~~Gd~v~I~ 87 (137)
.+.++|..+..- |. .....+.+++.. =+++++.+.-....+++||.+.+.
T Consensus 6 ~l~g~V~~ie~~-------g~----~~~v~~~~~~~~~l~a~it~~~~~~L~L~~G~~V~~~ 56 (64)
T PF03459_consen 6 QLPGTVESIENL-------GS----EVEVTLDLGGGETLTARITPESAEELGLKPGDEVYAS 56 (64)
T ss_dssp EEEEEEEEEEES-------SS----EEEEEEEETTSEEEEEEEEHHHHHHCT-STT-EEEEE
T ss_pred EEEEEEEEEEEC-------CC----eEEEEEEECCCCEEEEEEcHHHHHHcCCCCCCEEEEE
Confidence 477888776432 21 345566777776 455555555444458999998763
No 167
>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=25.19 E-value=2e+02 Score=18.56 Aligned_cols=41 Identities=10% Similarity=0.156 Sum_probs=27.8
Q ss_pred eEEEEEEeeCcceEEEEEecCC------cCCCCCCCEEEEeceEEcc
Q 032583 53 RIAECLVGDETGMIIFTARNDQ------VDLMKEGTTVILRNAKIDM 93 (137)
Q Consensus 53 ~v~~~~VgDeTG~I~ltlW~~~------~~~i~~Gd~v~I~na~~~~ 93 (137)
.++=+.+-|.+|.+...+=... +..+..|++|.+.+-..+.
T Consensus 16 ~~~Fi~LrD~~~~iQ~v~~~~~~~~~~~~~~l~~es~V~V~G~v~~~ 62 (84)
T cd04323 16 KLMFLVLRDGTGFLQCVLSKKLVTEFYDAKSLTQESSVEVTGEVKED 62 (84)
T ss_pred CcEEEEEEcCCeEEEEEEcCCcchhHHHHhcCCCcCEEEEEEEEEEC
Confidence 4455677888888877553221 2347889999999876653
No 168
>PF00333 Ribosomal_S5: Ribosomal protein S5, N-terminal domain; InterPro: IPR013810 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S5 is one of the proteins from the small ribosomal subunit, and is a protein of 166 to 254 amino-acid residues. In Escherichia coli, S5 is known to be important in the assembly and function of the 30S ribosomal subunit. Mutations in S5 have been shown to increase translational error frequencies. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, ], groups bacterial, cyanelle, red algal chloroplast, archaeal and fungal mitochondrial S5; mammalian, Caenorhabditis elegans, Drosophila and plant S2; and yeast S4 (SUP44). This entry represents the N-terminal domain of ribosomal protein S5, which has an alpha-beta(3)-alpha structure that folds into two layers, alpha/beta.; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2ZKQ_e 2XZN_E 2XZM_E 3O30_B 1S1H_E 3IZB_E 3U5C_C 3U5G_C 3O2Z_B 3BBN_E ....
Probab=25.06 E-value=2e+02 Score=18.55 Aligned_cols=39 Identities=26% Similarity=0.398 Sum_probs=25.6
Q ss_pred EEEEEEEcceeeeeccCCCccccceeEE-EEEEeeCcceEEEEE
Q 032583 28 LTVKVVSTKMVLQKGRGDGTQVRQMRIA-ECLVGDETGMIIFTA 70 (137)
Q Consensus 28 l~~kVl~~~~~~~~~R~DGs~~~~~~v~-~~~VgDeTG~I~ltl 70 (137)
+.-+||++.-+....+ -|. ..++. -+++||..|.+=|=.
T Consensus 2 l~~~vl~v~rv~k~tk-~Gr---~~~~~alvvvGn~~G~vG~G~ 41 (67)
T PF00333_consen 2 LEEKVLEVKRVSKMTK-GGR---IFSFRALVVVGNGNGLVGFGV 41 (67)
T ss_dssp HEEEEEEEEEEEEEET-TEE---EEEEEEEEEEECSSSEEEEEE
T ss_pred ceEEEEEEEEEEEEec-CCc---eeEEEEEEEEecCCCcEecCc
Confidence 4568888887666553 232 34444 377899999987743
No 169
>PF03100 CcmE: CcmE; InterPro: IPR004329 CcmE is the product of one of a cluster of Ccm genes that are necessary for cytochrome c biosynthesis in eubacteria. Expression of these proteins is induced when the organisms are grown under anaerobic conditions with nitrate or nitrite as the final electron acceptor.; GO: 0017003 protein-heme linkage, 0017004 cytochrome complex assembly, 0005886 plasma membrane; PDB: 1SR3_A 2KCT_A 1J6Q_A 1LM0_A.
Probab=24.58 E-value=2.7e+02 Score=19.95 Aligned_cols=69 Identities=16% Similarity=0.095 Sum_probs=40.3
Q ss_pred eeeeccCCCC----CCCceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEecCCcCCCCCCCEEEEec
Q 032583 13 FTKVDQLRPG----TSGHTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTARNDQVDLMKEGTTVILRN 88 (137)
Q Consensus 13 ~~kI~dL~p~----~~~v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW~~~~~~i~~Gd~v~I~n 88 (137)
|....++... .+.+.+.+.|.. +... +..+ ..-.+..|-|....+++.-=+...+.+++|..|.+.+
T Consensus 36 y~t~se~~~~~~~~~~~vrv~G~V~~-gSv~---~~~~-----~~~~~F~i~D~~~~i~V~Y~G~~Pd~F~eg~~VVv~G 106 (131)
T PF03100_consen 36 YLTPSELAAEPQKVGRKVRVGGLVVE-GSVE---YDPD-----GNTLTFTITDGGKEIPVVYTGPLPDLFREGQGVVVEG 106 (131)
T ss_dssp EE-TTTTTTTST-TTSEEEEEEEEEC-TTEE---E-TT-----SSEEEEEEE-SS-EEEEEEES--CTT--TTSEEEEEE
T ss_pred EcCHHHHhhccccCCceEEEeeEEcc-CCEE---EcCC-----CCEEEEEEEECCcEEEEEECCCCCccccCCCeEEEEE
Confidence 4555666532 355677776664 3322 1111 3445577889988988877778888999999999999
Q ss_pred eE
Q 032583 89 AK 90 (137)
Q Consensus 89 a~ 90 (137)
.+
T Consensus 107 ~~ 108 (131)
T PF03100_consen 107 RL 108 (131)
T ss_dssp EE
T ss_pred EE
Confidence 76
No 170
>PF11213 DUF3006: Protein of unknown function (DUF3006); InterPro: IPR021377 This family of proteins has no known function.
Probab=24.40 E-value=1.8e+02 Score=18.66 Aligned_cols=32 Identities=16% Similarity=0.053 Sum_probs=19.1
Q ss_pred eEEEEEEeeCcceEEEEEec-CCcCCCCCCCEEEE
Q 032583 53 RIAECLVGDETGMIIFTARN-DQVDLMKEGTTVIL 86 (137)
Q Consensus 53 ~v~~~~VgDeTG~I~ltlW~-~~~~~i~~Gd~v~I 86 (137)
..+-+++.|.. ..+.+=- .....+++||++.+
T Consensus 10 ~~AVl~~~~~~--~~~~vp~~~LP~~~keGDvl~i 42 (71)
T PF11213_consen 10 DYAVLELEDGE--KEIDVPRSRLPEGAKEGDVLEI 42 (71)
T ss_pred CEEEEEECCCe--EEEEEEHHHCCCCCCcccEEEE
Confidence 44544555554 2232222 35667899999999
No 171
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=23.96 E-value=63 Score=16.19 Aligned_cols=15 Identities=20% Similarity=0.257 Sum_probs=11.4
Q ss_pred CCCCCEEEEeceEEc
Q 032583 78 MKEGTTVILRNAKID 92 (137)
Q Consensus 78 i~~Gd~v~I~na~~~ 92 (137)
+++||.|+|.++.-+
T Consensus 2 ~~~G~~V~I~~G~~~ 16 (28)
T smart00739 2 FEVGDTVRVIAGPFK 16 (28)
T ss_pred CCCCCEEEEeECCCC
Confidence 578999998887643
No 172
>smart00350 MCM minichromosome maintenance proteins.
Probab=23.77 E-value=1e+02 Score=27.22 Aligned_cols=29 Identities=21% Similarity=0.185 Sum_probs=25.4
Q ss_pred eEEEEEecCCcCCCCCCCEEEEeceEEcc
Q 032583 65 MIIFTARNDQVDLMKEGTTVILRNAKIDM 93 (137)
Q Consensus 65 ~I~ltlW~~~~~~i~~Gd~v~I~na~~~~ 93 (137)
++.+.|-++..+.++|||.|.|.|-+...
T Consensus 105 si~v~l~~dLvd~~~PGD~V~i~Gi~~~~ 133 (509)
T smart00350 105 SVDVILDGDLVDKAKPGDRVEVTGIYRNI 133 (509)
T ss_pred EEEEEEcccccCcccCCCEEEEEEEEEee
Confidence 57888888999999999999999999754
No 173
>cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=23.18 E-value=1.9e+02 Score=17.73 Aligned_cols=27 Identities=15% Similarity=0.118 Sum_probs=20.7
Q ss_pred CCCCCCCEEEEeceEEcccCCeEEEEe
Q 032583 76 DLMKEGTTVILRNAKIDMFKGSMRLAV 102 (137)
Q Consensus 76 ~~i~~Gd~v~I~na~~~~~~g~~~L~v 102 (137)
+.+++||.+++.=..++..++.++|++
T Consensus 46 ~~~~~Gd~v~~~V~~~d~~~~~i~ls~ 72 (73)
T cd05706 46 YKFKKNDIVRACVLSVDVPNKKIALSL 72 (73)
T ss_pred cccCCCCEEEEEEEEEeCCCCEEEEEE
Confidence 447999999998777776677777764
No 174
>COG2049 DUR1 Allophanate hydrolase subunit 1 [Amino acid transport and metabolism]
Probab=22.97 E-value=52 Score=26.42 Aligned_cols=31 Identities=19% Similarity=0.235 Sum_probs=23.7
Q ss_pred ceEEEEEecC---CcCCCCCCCEEEEeceEEccc
Q 032583 64 GMIIFTARND---QVDLMKEGTTVILRNAKIDMF 94 (137)
Q Consensus 64 G~I~ltlW~~---~~~~i~~Gd~v~I~na~~~~~ 94 (137)
|...+.+||. ..-.+++||.|++......++
T Consensus 183 GrTp~~lfdp~~~~p~ll~~Gd~VrF~~i~~~e~ 216 (223)
T COG2049 183 GRTPLPLFDPDREPPALLRPGDQVRFVPIKEEEF 216 (223)
T ss_pred ccccccccCCCCCCCeeccCCCEEEEEecCcccc
Confidence 6778899993 344579999999998776554
No 175
>PF02563 Poly_export: Polysaccharide biosynthesis/export protein; InterPro: IPR003715 The extracellular polysaccharide colanic acid (CA) is produced by species of the family Enterobacteriaceae. In Escherichia coli (strain K12) the CA cluster comprises 19 genes. The wzx gene encodes a protein with multiple transmembrane segments that may function in export of the CA repeat unit from the cytoplasm into the periplasm in a process analogous to O-unit export. The CA gene clusters may be involved in the export of polysaccharide from the cell [].; GO: 0015159 polysaccharide transmembrane transporter activity, 0015774 polysaccharide transport, 0016020 membrane; PDB: 2W8I_E 2W8H_E 2J58_D.
Probab=22.71 E-value=39 Score=22.12 Aligned_cols=32 Identities=16% Similarity=0.221 Sum_probs=17.4
Q ss_pred CCCCCCEEEEeceEEcccCCeEEEEeCCcEeEEE
Q 032583 77 LMKEGTTVILRNAKIDMFKGSMRLAVDKWGRVEV 110 (137)
Q Consensus 77 ~i~~Gd~v~I~na~~~~~~g~~~L~vg~~g~I~~ 110 (137)
.+.+||.+.|.=-.....++ .+.|+..|.|..
T Consensus 12 ~l~pGD~l~i~v~~~~~l~~--~~~V~~dG~I~l 43 (82)
T PF02563_consen 12 RLGPGDVLRISVFGWPELSG--EYTVDPDGTISL 43 (82)
T ss_dssp ---TT-EEEEEETT-HHHCC--SEE--TTSEEEE
T ss_pred EECCCCEEEEEEecCCCccc--ceEECCCCcEee
Confidence 46788888887655555544 677788888764
No 176
>PRK13159 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=22.60 E-value=3.5e+02 Score=20.51 Aligned_cols=38 Identities=16% Similarity=0.091 Sum_probs=31.9
Q ss_pred EEEEEEeeCcceEEEEEecCCcCCCCCCCEEEEeceEE
Q 032583 54 IAECLVGDETGMIIFTARNDQVDLMKEGTTVILRNAKI 91 (137)
Q Consensus 54 v~~~~VgDeTG~I~ltlW~~~~~~i~~Gd~v~I~na~~ 91 (137)
-....|.|..+.++++-=.-..|++++|.-+...+.+.
T Consensus 73 ~v~F~vtD~~~~v~V~Y~GilPDlFrEGqgVVaeG~~~ 110 (155)
T PRK13159 73 KVSFTVIDKNAATQVEYTGILPDLFRDNQSVIANGRMQ 110 (155)
T ss_pred EEEEEEEcCCcEEEEEEccCCCccccCCCeEEEEEEEc
Confidence 34567889999998877777889999999999999875
No 177
>PF13296 T6SS_Vgr: Putative type VI secretion system Rhs element Vgr
Probab=21.91 E-value=97 Score=22.07 Aligned_cols=57 Identities=23% Similarity=0.339 Sum_probs=44.4
Q ss_pred EEEEEEeeCcceEEEEEecCCc-CCCCCCCEEEEeceEEcccCC-eEEEEeCCcEeEEE
Q 032583 54 IAECLVGDETGMIIFTARNDQV-DLMKEGTTVILRNAKIDMFKG-SMRLAVDKWGRVEV 110 (137)
Q Consensus 54 v~~~~VgDeTG~I~ltlW~~~~-~~i~~Gd~v~I~na~~~~~~g-~~~L~vg~~g~I~~ 110 (137)
--+.++-|.+|.++.-|-.++. ..+.-|=.+.+.+..-..++| ..+|..+.||-|.-
T Consensus 9 ~Nql~~DDt~gQ~~~qL~S~~~~SqLnLG~l~~~~~~~R~~~RG~GfELrTD~~gavRa 67 (109)
T PF13296_consen 9 YNQLVFDDTPGQIRAQLSSDHGASQLNLGHLVDQRDNGRGAPRGEGFELRTDAWGAVRA 67 (109)
T ss_pred CCEEEEecCCCcceEEEecccchhhhhcccccCcccccccCccccceEEecchhhhhhc
Confidence 3457788899999999998754 447899999996555555555 89999999998753
No 178
>PF08696 Dna2: DNA replication factor Dna2; InterPro: IPR014808 Dna2 is a DNA replication factor with single-stranded DNA-dependent ATPase, ATP-dependent nuclease, (5'-flap endonuclease) and helicase activities. It is required for Okazaki fragment processing and is involved in DNA repair pathways []. ; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication
Probab=21.06 E-value=2.5e+02 Score=21.81 Aligned_cols=24 Identities=8% Similarity=0.167 Sum_probs=17.9
Q ss_pred eEEEEEecCCcCC-CCCCCEEEEec
Q 032583 65 MIIFTARNDQVDL-MKEGTTVILRN 88 (137)
Q Consensus 65 ~I~ltlW~~~~~~-i~~Gd~v~I~n 88 (137)
...+.||++=.+. +++||+|.|.+
T Consensus 11 ~~~v~L~~~W~~t~v~~Gd~I~ii~ 35 (209)
T PF08696_consen 11 TRTVILRDEWCETPVSPGDIIHIIG 35 (209)
T ss_pred eEEEEEeCCcccCCCcCCCEEEEEE
Confidence 4556677764333 79999999999
No 179
>PLN02532 asparagine-tRNA synthetase
Probab=20.19 E-value=5.4e+02 Score=23.89 Aligned_cols=67 Identities=18% Similarity=0.287 Sum_probs=46.6
Q ss_pred eeEEEEEEeeCcce--EEEEEecCCc---CCCCCCCEEEEeceEEccc----CCeEEEEeCCcEeEEEcCCCceEE
Q 032583 52 MRIAECLVGDETGM--IIFTARNDQV---DLMKEGTTVILRNAKIDMF----KGSMRLAVDKWGRVEVAEPANFTV 118 (137)
Q Consensus 52 ~~v~~~~VgDeTG~--I~ltlW~~~~---~~i~~Gd~v~I~na~~~~~----~g~~~L~vg~~g~I~~~~~~~~~v 118 (137)
+.+.=+.|-|.||. +.+++=.... ..+..|.+|.|.|...... .|.++|.+.+.--+...++..+.+
T Consensus 133 g~i~FI~LrDGSg~~~lQvVv~~~~~~~~~~L~~Es~V~V~G~V~~~~~~~~~g~iEl~v~~i~VLg~a~~~p~Pi 208 (633)
T PLN02532 133 PSVAYLLISDGSCVASLQVVVDSALAPLTQLMATGTCILAEGVLKLPLPAQGKHVIELEVEKILHIGTVDPEKYPL 208 (633)
T ss_pred CCcEEEEEECCCCccceEEEEeCCcccHhhcCCCceEEEEEEEEEecCCCCCCCcEEEEeeEEEEEecCCCCCCcc
Confidence 56777899999998 8887754322 3578899999999877541 467999887765555443233433
No 180
>TIGR00594 polc DNA-directed DNA polymerase III (polc). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=20.18 E-value=2.4e+02 Score=27.44 Aligned_cols=39 Identities=23% Similarity=0.123 Sum_probs=26.9
Q ss_pred ceEEEEEEEcceeeeeccCCCccccceeEEEEEEeeCcceEEEEEe
Q 032583 26 HTLTVKVVSTKMVLQKGRGDGTQVRQMRIAECLVGDETGMIIFTAR 71 (137)
Q Consensus 26 v~l~~kVl~~~~~~~~~R~DGs~~~~~~v~~~~VgDeTG~I~ltlW 71 (137)
+.+-+.|.++.....++ .| ..|+-+.+.|+||.+.+++|
T Consensus 984 v~v~G~i~~~~~~~~tk--kG-----~~maf~tleD~tg~ie~viF 1022 (1022)
T TIGR00594 984 VRTLGGLNSVKKKITTK--NG-----KPMAFLQLEDETGSIEVVVF 1022 (1022)
T ss_pred EEEEEEEEEEEEecccC--CC-----CEEEEEEEEECCCcEEEEeC
Confidence 55666665554432222 23 37899999999999999987
Done!