Query 031443
Match_columns 159
No_of_seqs 106 out of 431
Neff 5.7
Searched_HMMs 46136
Date Fri Mar 29 14:10:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031443.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031443hhsearch_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 99.9 9.6E-27 2.1E-31 176.6 13.1 114 34-153 3-116 (129)
2 KOG3416 Predicted nucleic acid 99.9 4.6E-27 9.9E-32 177.6 9.9 111 35-153 4-114 (134)
3 PRK06386 replication factor A; 99.9 1.2E-21 2.6E-26 170.7 12.5 104 35-144 2-105 (358)
4 PRK07218 replication factor A; 99.9 1E-21 2.2E-26 174.4 11.6 98 32-136 55-152 (423)
5 PRK07217 replication factor A; 99.9 1.2E-20 2.5E-25 161.5 14.2 114 31-157 68-182 (311)
6 PRK06386 replication factor A; 99.9 7.3E-21 1.6E-25 165.8 13.2 101 34-143 106-206 (358)
7 PRK08402 replication factor A; 99.8 5.4E-21 1.2E-25 166.6 11.4 100 34-136 61-165 (355)
8 PRK07218 replication factor A; 99.8 4.6E-20 1E-24 163.8 12.3 102 34-142 161-262 (423)
9 PRK15491 replication factor A; 99.8 5.3E-20 1.2E-24 161.2 11.0 100 32-135 54-158 (374)
10 PRK14699 replication factor A; 99.8 1.1E-19 2.4E-24 163.8 10.7 114 32-150 54-173 (484)
11 PRK07211 replication factor A; 99.8 1.4E-19 3E-24 162.9 11.2 99 34-135 160-261 (485)
12 PRK14699 replication factor A; 99.8 2.3E-19 4.9E-24 161.7 12.4 97 35-134 166-267 (484)
13 PRK12366 replication factor A; 99.8 5.7E-19 1.2E-23 163.4 11.5 99 33-134 61-162 (637)
14 cd04491 SoSSB_OBF SoSSB_OBF: A 99.8 6.4E-18 1.4E-22 117.8 10.9 80 49-132 1-81 (82)
15 PRK15491 replication factor A; 99.8 4.4E-18 9.6E-23 149.1 10.9 100 33-135 164-268 (374)
16 PRK07211 replication factor A; 99.7 2.4E-17 5.2E-22 148.5 10.5 102 27-134 45-150 (485)
17 PRK12366 replication factor A; 99.7 4.9E-16 1.1E-20 144.0 10.7 100 33-135 393-496 (637)
18 COG1599 RFA1 Single-stranded D 99.4 8.6E-13 1.9E-17 116.4 7.6 114 28-144 42-157 (407)
19 cd04475 RPA1_DBD_B RPA1_DBD_B: 99.4 3.5E-12 7.6E-17 91.8 9.2 84 48-135 2-89 (101)
20 cd04474 RPA1_DBD_A RPA1_DBD_A: 99.4 6.5E-12 1.4E-16 91.7 9.7 77 37-117 1-82 (104)
21 TIGR00617 rpa1 replication fac 99.1 9.4E-10 2E-14 102.0 10.6 98 34-135 179-287 (608)
22 TIGR00617 rpa1 replication fac 98.9 6.2E-09 1.3E-13 96.5 9.3 100 32-135 295-400 (608)
23 PF01336 tRNA_anti-codon: OB-f 98.4 1.6E-06 3.5E-11 57.6 7.4 66 48-126 1-71 (75)
24 cd04497 hPOT1_OB1_like hPOT1_O 98.3 6.1E-06 1.3E-10 63.0 9.9 86 34-126 2-95 (138)
25 cd04483 hOBFC1_like hOBFC1_lik 97.9 9.1E-05 2E-09 53.2 8.3 64 49-126 1-88 (92)
26 cd04478 RPA2_DBD_D RPA2_DBD_D: 97.9 0.00016 3.5E-09 50.9 9.0 70 48-134 2-78 (95)
27 cd03524 RPA2_OBF_family RPA2_O 97.8 0.0003 6.5E-09 45.0 8.1 66 49-125 1-71 (75)
28 cd04492 YhaM_OBF_like YhaM_OBF 97.7 0.00065 1.4E-08 45.7 9.3 52 74-126 18-72 (83)
29 PRK13480 3'-5' exoribonuclease 97.7 0.00027 5.8E-09 61.2 9.0 85 37-134 4-91 (314)
30 cd04481 RPA1_DBD_B_like RPA1_D 97.4 0.0009 2E-08 48.5 7.6 83 49-135 1-94 (106)
31 COG1599 RFA1 Single-stranded D 97.2 0.0019 4.1E-08 57.3 9.0 69 51-128 173-242 (407)
32 cd04488 RecG_wedge_OBF RecG_we 97.2 0.0031 6.7E-08 41.2 7.8 64 50-123 2-68 (75)
33 cd04485 DnaE_OBF DnaE_OBF: A s 97.1 0.0026 5.7E-08 42.2 6.9 52 74-126 18-73 (84)
34 PF02765 POT1: Telomeric singl 97.0 0.0059 1.3E-07 46.8 8.9 87 36-127 2-101 (146)
35 cd04480 RPA1_DBD_A_like RPA1_D 97.0 0.0034 7.3E-08 43.8 6.3 62 50-119 2-68 (86)
36 cd04489 ExoVII_LU_OBF ExoVII_L 96.6 0.026 5.7E-07 37.9 8.3 66 49-126 3-73 (78)
37 COG4085 Predicted RNA-binding 94.4 0.2 4.3E-06 41.1 7.1 92 33-136 35-139 (204)
38 PRK10917 ATP-dependent DNA hel 94.1 0.25 5.4E-06 46.7 8.4 76 35-122 50-129 (681)
39 cd04498 hPOT1_OB2 hPOT1_OB2: A 93.8 0.15 3.3E-06 38.8 5.1 38 87-124 61-109 (123)
40 cd04484 polC_OBF polC_OBF: A s 93.0 0.86 1.9E-05 31.7 7.6 71 47-125 1-77 (82)
41 TIGR00643 recG ATP-dependent D 93.0 0.58 1.3E-05 43.7 8.7 80 35-125 23-105 (630)
42 PRK08402 replication factor A; 92.8 0.15 3.1E-06 45.1 4.2 67 33-99 182-269 (355)
43 cd04487 RecJ_OBF2_like RecJ_OB 92.1 0.62 1.3E-05 31.9 5.8 49 77-126 17-69 (73)
44 cd04490 PolII_SU_OBF PolII_SU_ 91.1 1.8 3.9E-05 30.0 7.4 54 48-113 2-61 (79)
45 PRK05673 dnaE DNA polymerase I 90.5 0.6 1.3E-05 46.9 6.2 84 36-128 966-1055(1135)
46 PF02760 HIN: HIN-200/IF120x d 90.4 3.4 7.5E-05 33.1 9.1 92 50-148 5-106 (170)
47 PRK07373 DNA polymerase III su 90.2 0.74 1.6E-05 41.9 6.0 82 36-126 269-356 (449)
48 PRK05159 aspC aspartyl-tRNA sy 90.1 2 4.3E-05 38.6 8.6 87 35-134 4-101 (437)
49 COG5235 RFA2 Single-stranded D 88.7 3.2 7E-05 34.8 8.2 54 78-135 86-145 (258)
50 PLN02850 aspartate-tRNA ligase 88.3 4.1 8.8E-05 37.8 9.5 96 33-141 67-181 (530)
51 PF02721 DUF223: Domain of unk 88.3 1.8 3.8E-05 30.6 5.7 57 78-134 1-69 (95)
52 cd04316 ND_PkAspRS_like_N ND_P 87.6 7.3 0.00016 27.9 8.7 75 46-133 13-97 (108)
53 COG1200 RecG RecG-like helicas 86.7 4.7 0.0001 38.7 9.0 78 35-123 51-131 (677)
54 PF11325 DUF3127: Domain of un 86.6 6.5 0.00014 28.0 7.7 69 50-124 2-78 (84)
55 cd04317 EcAspRS_like_N EcAspRS 86.5 11 0.00024 28.0 9.5 83 47-142 16-113 (135)
56 cd04322 LysRS_N LysRS_N: N-ter 85.7 11 0.00023 27.0 9.2 59 74-132 15-82 (108)
57 PRK00448 polC DNA polymerase I 85.5 4.3 9.2E-05 42.1 8.6 86 33-126 224-316 (1437)
58 cd04494 BRCA2DBD_OB2 BRCA2DBD_ 85.0 2.6 5.6E-05 35.8 5.8 49 86-134 180-236 (251)
59 PF10451 Stn1: Telomere regula 84.9 4.7 0.0001 34.1 7.4 71 46-129 67-146 (256)
60 cd04482 RPA2_OBF_like RPA2_OBF 84.3 9.8 0.00021 26.9 7.8 45 78-126 20-70 (91)
61 PTZ00401 aspartyl-tRNA synthet 84.3 18 0.00038 33.9 11.5 97 33-142 63-179 (550)
62 PF13742 tRNA_anti_2: OB-fold 84.0 13 0.00027 26.6 8.4 70 45-126 21-96 (99)
63 cd04320 AspRS_cyto_N AspRS_cyt 83.9 13 0.00027 26.3 9.2 57 75-131 17-90 (102)
64 PRK02983 lysS lysyl-tRNA synth 82.6 7.8 0.00017 39.1 8.9 85 36-133 640-735 (1094)
65 PF08646 Rep_fac-A_C: Replicat 82.6 0.59 1.3E-05 35.4 0.9 24 74-97 53-76 (146)
66 TIGR00499 lysS_bact lysyl-tRNA 82.4 12 0.00027 34.4 9.6 74 47-133 55-137 (496)
67 PRK00484 lysS lysyl-tRNA synth 81.2 16 0.00034 33.6 9.8 75 46-133 55-137 (491)
68 KOG3108 Single-stranded DNA-bi 80.5 8.8 0.00019 32.8 7.4 56 77-136 87-148 (265)
69 PF04076 BOF: Bacterial OB fol 80.3 7.8 0.00017 28.4 6.2 67 43-126 32-100 (103)
70 PRK12445 lysyl-tRNA synthetase 80.1 8.5 0.00018 35.5 7.7 74 47-133 67-149 (505)
71 cd01491 Ube1_repeat1 Ubiquitin 80.0 7.3 0.00016 33.4 6.9 68 74-148 165-232 (286)
72 TIGR00458 aspS_arch aspartyl-t 78.7 15 0.00034 32.9 8.8 83 38-133 3-97 (428)
73 PRK07459 single-stranded DNA-b 78.3 6.1 0.00013 29.5 5.2 63 45-114 3-76 (121)
74 PRK05733 single-stranded DNA-b 77.9 16 0.00036 29.1 7.8 84 44-134 4-112 (172)
75 PF07680 DoxA: TQO small subun 77.7 11 0.00023 29.1 6.5 98 38-156 21-120 (133)
76 PLN02502 lysyl-tRNA synthetase 77.4 11 0.00023 35.4 7.6 60 74-133 124-194 (553)
77 PRK07374 dnaE DNA polymerase I 77.3 5.6 0.00012 40.4 6.1 81 37-126 990-1076(1170)
78 PRK02801 primosomal replicatio 76.2 8.2 0.00018 27.9 5.2 63 45-114 2-80 (101)
79 PRK09010 single-stranded DNA-b 75.4 23 0.0005 28.4 8.1 83 45-134 6-114 (177)
80 PF15072 DUF4539: Domain of un 75.3 7.8 0.00017 27.6 4.8 51 77-127 21-76 (86)
81 PRK06826 dnaE DNA polymerase I 75.2 9.8 0.00021 38.6 7.1 73 46-126 992-1068(1151)
82 TIGR00621 ssb single stranded 74.9 11 0.00023 29.6 5.9 32 83-114 48-83 (164)
83 PRK13732 single-stranded DNA-b 74.6 30 0.00064 27.7 8.5 83 44-133 5-112 (175)
84 cd04100 Asp_Lys_Asn_RS_N Asp_L 74.3 24 0.00052 23.9 8.4 53 74-126 15-79 (85)
85 cd04486 YhcR_OBF_like YhcR_OBF 74.2 11 0.00023 26.1 5.2 36 89-126 35-70 (78)
86 PTZ00385 lysyl-tRNA synthetase 73.5 29 0.00064 33.3 9.5 73 47-132 109-191 (659)
87 PRK07279 dnaE DNA polymerase I 71.8 9.6 0.00021 38.3 6.1 82 36-126 876-961 (1034)
88 COG1107 Archaea-specific RecJ- 71.7 11 0.00023 36.0 6.0 50 79-129 234-287 (715)
89 PRK05672 dnaE2 error-prone DNA 71.7 8.3 0.00018 38.7 5.6 69 47-126 955-1027(1046)
90 PRK06920 dnaE DNA polymerase I 71.4 9 0.0002 38.8 5.8 82 36-126 933-1019(1107)
91 cd04476 RPA1_DBD_C RPA1_DBD_C: 71.3 2.6 5.5E-05 32.5 1.6 26 74-99 67-92 (166)
92 COG1571 Predicted DNA-binding 69.2 16 0.00034 33.3 6.4 77 37-130 259-341 (421)
93 cd04318 EcAsnRS_like_N EcAsnRS 68.9 32 0.0007 23.1 7.2 53 74-126 15-76 (82)
94 PRK08763 single-stranded DNA-b 68.4 16 0.00034 29.0 5.6 64 44-114 4-84 (164)
95 PRK07274 single-stranded DNA-b 68.2 11 0.00024 28.3 4.6 30 85-114 46-79 (131)
96 cd04321 ScAspRS_mt_like_N ScAs 68.1 36 0.00078 23.3 8.3 53 74-126 16-80 (86)
97 PRK06752 single-stranded DNA-b 67.9 14 0.0003 26.9 4.9 30 85-114 46-79 (112)
98 PRK03932 asnC asparaginyl-tRNA 66.4 30 0.00064 31.3 7.6 73 46-131 17-98 (450)
99 PF00436 SSB: Single-strand bi 65.9 5 0.00011 27.8 2.1 62 46-114 2-80 (104)
100 PRK06751 single-stranded DNA-b 65.6 20 0.00044 28.6 5.7 64 46-116 3-82 (173)
101 PF02760 HIN: HIN-200/IF120x d 64.6 26 0.00057 28.1 6.1 65 34-109 100-165 (170)
102 COG0017 AsnS Aspartyl/asparagi 64.4 58 0.0013 29.8 9.0 86 36-134 5-101 (435)
103 TIGR00457 asnS asparaginyl-tRN 64.3 34 0.00073 31.1 7.6 75 46-133 17-102 (453)
104 cd04496 SSB_OBF SSB_OBF: A sub 64.0 16 0.00034 25.0 4.3 31 84-114 42-76 (100)
105 cd03583 NTR_complement_C3 NTR/ 63.9 67 0.0014 24.9 8.6 81 49-135 32-121 (149)
106 COG2176 PolC DNA polymerase II 63.2 42 0.00092 34.7 8.5 109 33-149 227-348 (1444)
107 PRK07275 single-stranded DNA-b 63.1 16 0.00034 28.8 4.7 74 46-126 3-99 (162)
108 PRK06293 single-stranded DNA-b 62.1 25 0.00054 27.9 5.6 64 45-115 1-76 (161)
109 PTZ00417 lysine-tRNA ligase; P 61.6 35 0.00077 32.2 7.4 74 47-132 134-218 (585)
110 PRK08486 single-stranded DNA-b 61.0 23 0.0005 28.4 5.3 34 83-116 46-84 (182)
111 PRK06958 single-stranded DNA-b 60.9 21 0.00045 28.9 5.1 63 45-114 4-84 (182)
112 TIGR01405 polC_Gram_pos DNA po 60.3 57 0.0012 33.6 9.0 80 40-127 2-88 (1213)
113 cd04319 PhAsnRS_like_N PhAsnRS 59.3 60 0.0013 22.9 8.8 60 74-133 15-83 (103)
114 COG1190 LysU Lysyl-tRNA synthe 58.9 59 0.0013 30.3 8.2 72 48-132 64-144 (502)
115 PRK05813 single-stranded DNA-b 57.6 44 0.00094 27.7 6.5 65 44-115 108-180 (219)
116 PRK00476 aspS aspartyl-tRNA sy 57.6 75 0.0016 30.0 8.8 81 47-140 19-113 (588)
117 COG3481 Predicted HD-superfami 57.0 5.2 0.00011 34.6 1.0 58 76-134 22-82 (287)
118 TIGR00156 conserved hypothetic 57.0 26 0.00057 26.7 4.8 73 36-125 46-122 (126)
119 TIGR00459 aspS_bact aspartyl-t 56.8 67 0.0014 30.4 8.3 81 47-140 17-111 (583)
120 PRK00286 xseA exodeoxyribonucl 55.8 79 0.0017 28.1 8.4 75 45-134 23-102 (438)
121 PRK07772 single-stranded DNA-b 54.4 42 0.00092 27.1 5.8 30 85-114 52-85 (186)
122 PF09104 BRCA-2_OB3: BRCA2, ol 54.0 1E+02 0.0023 24.0 8.2 81 42-134 15-103 (143)
123 PRK08182 single-stranded DNA-b 53.1 28 0.0006 26.9 4.5 66 46-114 3-86 (148)
124 PRK09919 anti-adapter protein 51.4 53 0.0011 24.8 5.5 38 87-124 26-63 (114)
125 PRK06863 single-stranded DNA-b 51.0 52 0.0011 26.1 5.8 64 45-115 4-85 (168)
126 KOG2012 Ubiquitin activating e 49.1 23 0.0005 35.2 4.0 57 90-151 197-253 (1013)
127 PRK12820 bifunctional aspartyl 48.6 1.3E+02 0.0029 29.2 9.0 91 38-141 9-118 (706)
128 PRK10053 hypothetical protein; 48.3 46 0.00099 25.5 4.9 73 36-125 50-126 (130)
129 PRK07135 dnaE DNA polymerase I 48.0 40 0.00087 33.8 5.6 69 36-114 889-960 (973)
130 cd05694 S1_Rrp5_repeat_hs2_sc2 46.6 87 0.0019 21.0 5.8 70 40-126 1-70 (74)
131 PRK06642 single-stranded DNA-b 46.3 69 0.0015 24.8 5.7 63 45-114 5-86 (152)
132 PLN02603 asparaginyl-tRNA synt 46.3 1.7E+02 0.0037 27.6 9.2 87 34-133 88-193 (565)
133 TIGR02656 cyanin_plasto plasto 45.4 25 0.00053 24.8 2.9 31 78-111 2-32 (99)
134 PRK10260 L,D-transpeptidase; P 43.0 15 0.00032 32.1 1.6 41 84-124 207-252 (306)
135 PF12869 tRNA_anti-like: tRNA_ 41.5 59 0.0013 23.9 4.6 66 45-122 67-140 (144)
136 PRK10190 L,D-transpeptidase; P 41.0 18 0.00038 31.7 1.8 42 84-125 204-250 (310)
137 PF11183 PmrD: Polymyxin resis 40.6 30 0.00065 24.7 2.6 37 76-112 16-53 (82)
138 COG1376 ErfK Uncharacterized p 40.2 12 0.00027 30.1 0.7 29 83-111 201-231 (232)
139 cd03584 NTR_complement_C4 NTR/ 39.4 1.3E+02 0.0027 23.4 6.2 82 48-135 36-125 (153)
140 smart00643 C345C Netrin C-term 39.2 1.4E+02 0.003 21.2 7.8 50 86-135 49-103 (114)
141 COG1097 RRP4 RNA-binding prote 38.6 1.1E+02 0.0024 25.9 6.1 61 73-133 117-190 (239)
142 PF05113 DUF693: Protein of un 38.3 37 0.0008 29.6 3.3 28 87-114 62-92 (314)
143 TIGR00237 xseA exodeoxyribonuc 38.2 1.7E+02 0.0037 26.3 7.7 74 45-133 17-95 (432)
144 COG3111 Periplasmic protein wi 36.8 1.4E+02 0.0029 23.1 5.8 47 79-126 75-123 (128)
145 KOG1816 Ubiquitin fusion-degra 36.2 26 0.00057 30.6 2.1 30 83-112 81-110 (308)
146 COG1570 XseA Exonuclease VII, 36.1 2.1E+02 0.0046 26.3 7.9 70 45-126 23-97 (440)
147 cd03582 NTR_complement_C5 NTR/ 35.3 2.1E+02 0.0045 22.1 8.4 51 85-135 68-124 (150)
148 PF13567 DUF4131: Domain of un 34.7 1.7E+02 0.0036 20.9 6.0 29 84-112 113-141 (176)
149 PLN02903 aminoacyl-tRNA ligase 34.4 2.5E+02 0.0053 27.2 8.4 82 47-141 74-172 (652)
150 PF00575 S1: S1 RNA binding do 33.5 65 0.0014 20.7 3.3 62 49-124 7-73 (74)
151 PF11213 DUF3006: Protein of u 33.1 1.2E+02 0.0026 20.4 4.6 32 75-108 10-42 (71)
152 PRK04036 DNA polymerase II sma 31.6 1.6E+02 0.0035 27.1 6.5 67 35-113 143-215 (504)
153 COG4013 Uncharacterized protei 31.4 1.2E+02 0.0026 21.9 4.4 32 99-130 20-61 (91)
154 PF03459 TOBE: TOBE domain; I 31.2 96 0.0021 19.5 3.8 50 49-109 6-56 (64)
155 COG1917 Uncharacterized conser 30.0 50 0.0011 24.0 2.5 28 85-113 72-99 (131)
156 KOG0851 Single-stranded DNA-bi 28.8 1.4E+02 0.0031 23.5 5.2 81 34-122 3-88 (246)
157 cd04495 BRCA2DBD_OB3 BRCA2DBD_ 27.0 2.6E+02 0.0057 20.6 6.8 75 49-134 1-83 (100)
158 cd04454 S1_Rrp4_like S1_Rrp4_l 26.7 2E+02 0.0043 19.1 6.5 64 48-126 8-76 (82)
159 cd05706 S1_Rrp5_repeat_sc10 S1 26.4 1.8E+02 0.0039 18.6 6.6 40 85-124 28-72 (73)
160 smart00350 MCM minichromosome 25.8 83 0.0018 28.8 3.6 29 87-115 105-133 (509)
161 cd04323 AsnRS_cyto_like_N AsnR 24.7 2.2E+02 0.0048 19.0 8.1 42 74-115 15-62 (84)
162 PF01957 NfeD: NfeD-like C-ter 23.9 1.3E+02 0.0027 21.8 3.7 36 74-110 94-132 (144)
163 PLN02221 asparaginyl-tRNA synt 23.5 6.4E+02 0.014 23.9 9.3 90 33-133 30-137 (572)
164 COG4880 Secreted protein conta 23.3 1E+02 0.0023 28.8 3.7 54 81-134 488-542 (603)
165 PF09356 Phage_BR0599: Phage c 22.6 1.1E+02 0.0024 21.2 3.0 23 88-110 29-51 (80)
166 PRK06341 single-stranded DNA-b 22.1 2.2E+02 0.0048 22.5 5.0 65 45-116 5-89 (166)
167 smart00739 KOW KOW (Kyprides, 21.9 71 0.0015 16.7 1.6 14 100-113 2-15 (28)
168 cd03574 NTR_complement_C345C N 21.4 3.6E+02 0.0079 20.3 8.0 38 98-135 77-119 (147)
169 PRK05807 hypothetical protein; 21.3 3.6E+02 0.0079 20.3 6.4 62 49-126 8-74 (136)
170 PF05899 Cupin_3: Protein of u 20.5 71 0.0015 21.4 1.6 32 85-116 33-64 (74)
171 PF08696 Dna2: DNA replication 20.5 3.7E+02 0.0081 21.6 6.1 48 87-138 11-60 (209)
172 PF09696 Ctf8: Ctf8; InterPro 20.2 2.7E+02 0.0058 20.7 4.9 41 115-156 53-108 (122)
No 1
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=99.94 E-value=9.6e-27 Score=176.65 Aligned_cols=114 Identities=29% Similarity=0.452 Sum_probs=105.4
Q ss_pred ceeecccCCCCCCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecCCcCCCCCCCEEEEeceEE
Q 031443 34 VFTKVDQLKPGTNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARNDQVDLMKPGTTVILRNAKI 113 (159)
Q Consensus 34 ~~~kI~dL~P~~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde~~~~i~~Gdvv~I~na~v 113 (159)
.++||+||.|++.+++++++|+++++++++.+++ +...+.+++|+|+||+|+|++|+++++.+++||+|+|.||++
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 MITKIKDLKPGMERVNVTVRVLEVGEPKVIQTKG----GPRTISEAVVGDETGRVKLTLWGEQAGSLKEGEVVEIENAWT 78 (129)
T ss_pred CceEHHHcCCCCCceEEEEEEEEcCCceEEEeCC----CceEEEEEEEECCCCEEEEEEeCCccccCCCCCEEEEECcEE
Confidence 3789999999999999999999999988877653 347899999999999999999999988999999999999999
Q ss_pred ceeCCeEEEEeCCceeEEEcCCCcEEEccCCCccccceee
Q 031443 114 DMFKGSMRIAVDKWGRIEATEPAKFVVKEDNNLSLVEYEL 153 (159)
Q Consensus 114 ~~~~G~~~L~vgk~g~I~~~~~~~~~vne~~N~S~ieye~ 153 (159)
++|+|+++|+++++|.|.++++. +|+..++||+.+||.
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 899999999999996
No 2
>KOG3416 consensus Predicted nucleic acid binding protein [General function prediction only]
Probab=99.94 E-value=4.6e-27 Score=177.64 Aligned_cols=111 Identities=23% Similarity=0.423 Sum_probs=102.5
Q ss_pred eeecccCCCCCCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecCCcCCCCCCCEEEEeceEEc
Q 031443 35 FTKVDQLKPGTNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARNDQVDLMKPGTTVILRNAKID 114 (159)
Q Consensus 35 ~~kI~dL~P~~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde~~~~i~~Gdvv~I~na~v~ 114 (159)
.+.|+||+|+++|++++++||+.+..+.. +|| ..|+.++|||+||+|.+++|||..+.++|||+|++++||++
T Consensus 4 ~i~ikdi~P~~kN~~v~fIvl~~g~~tkT--kdg-----~~v~~~kVaD~TgsI~isvW~e~~~~~~PGDIirLt~Gy~S 76 (134)
T KOG3416|consen 4 MIFIKDIKPGLKNINVTFIVLEYGRATKT--KDG-----HEVRSCKVADETGSINISVWDEEGCLIQPGDIIRLTGGYAS 76 (134)
T ss_pred chhHhhcChhhhcceEEEEEEeeceeeec--cCC-----CEEEEEEEecccceEEEEEecCcCcccCCccEEEecccchh
Confidence 35689999999999999999999987643 366 68999999999999999999999999999999999999999
Q ss_pred eeCCeEEEEeCCceeEEEcCCCcEEEccCCCccccceee
Q 031443 115 MFKGSMRIAVDKWGRIEATEPAKFVVKEDNNLSLVEYEL 153 (159)
Q Consensus 115 ~~~G~~~L~vgk~g~I~~~~~~~~~vne~~N~S~ieye~ 153 (159)
+|+|++.|++||.|.++++++|++.|++++|+| +.|-.
T Consensus 77 i~qg~LtL~~GK~Ge~~KiGef~~vf~etpn~S-~~~~p 114 (134)
T KOG3416|consen 77 IFQGCLTLYVGKGGEVQKIGEFCMVFSETPNIS-IQWAP 114 (134)
T ss_pred hhcCceEEEecCCceEeEeeeeEEeeecCCCcc-ccccC
Confidence 999999999999999999999999999999999 66543
No 3
>PRK06386 replication factor A; Reviewed
Probab=99.87 E-value=1.2e-21 Score=170.73 Aligned_cols=104 Identities=22% Similarity=0.322 Sum_probs=92.9
Q ss_pred eeecccCCCCCCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecCCcCCCCCCCEEEEeceEEc
Q 031443 35 FTKVDQLKPGTNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARNDQVDLMKPGTTVILRNAKID 114 (159)
Q Consensus 35 ~~kI~dL~P~~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde~~~~i~~Gdvv~I~na~v~ 114 (159)
.+||+||.|++.++++++|||+++ .++|.+.||+ ..+.+++|||+||+|+||+|+. .+.+++||+|+|.||+++
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----TIYYYGIIGDETGTVPFTAWEF-PDAVKSGDVIEIKYCYSK 75 (358)
T ss_pred CcchhhcCCCCCcEEEEEEEEEcc-ceEEecCCCC----eEEEEEEEECCcceEEEEecCC-cccCCCCCEEEEEeEEEe
Confidence 368999999999999999999998 6888888873 5788999999999999999994 567999999999999999
Q ss_pred eeCCeEEEEeCCceeEEEcCCCcEEEccCC
Q 031443 115 MFKGSMRIAVDKWGRIEATEPAKFVVKEDN 144 (159)
Q Consensus 115 ~~~G~~~L~vgk~g~I~~~~~~~~~vne~~ 144 (159)
+|+|.++|++++++.|...++..+++++..
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=99.87 E-value=1e-21 Score=174.42 Aligned_cols=98 Identities=23% Similarity=0.336 Sum_probs=90.2
Q ss_pred CCceeecccCCCCCCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecCCcCCCCCCCEEEEece
Q 031443 32 KPVFTKVDQLKPGTNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARNDQVDLMKPGTTVILRNA 111 (159)
Q Consensus 32 ~~~~~kI~dL~P~~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde~~~~i~~Gdvv~I~na 111 (159)
.+..+||+||.|++.+|+|++|||++++ ++| |+||+. +.|++++|||+||+|+||||++.. +++||+|+|.||
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 4668999999999999999999999998 677 678855 999999999999999999999764 999999999999
Q ss_pred EEceeCCeEEEEeCCceeEEEcCCC
Q 031443 112 KIDMFKGSMRIAVDKWGRIEATEPA 136 (159)
Q Consensus 112 ~v~~~~G~~~L~vgk~g~I~~~~~~ 136 (159)
++++|+|+++|++|+.+.|...++.
T Consensus 128 ~vre~~g~~el~ig~~t~I~~~de~ 152 (423)
T PRK07218 128 GVREWDGRPELNIGESTTVSLLDDS 152 (423)
T ss_pred EeeccCCceEEeccCcceEEEcCcc
Confidence 9999999999999999999988643
No 5
>PRK07217 replication factor A; Reviewed
Probab=99.85 E-value=1.2e-20 Score=161.51 Aligned_cols=114 Identities=21% Similarity=0.314 Sum_probs=96.0
Q ss_pred CCCceeecccCCCCCCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecC-CcCCCCCCCEEEEe
Q 031443 31 RKPVFTKVDQLKPGTNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARND-QVDLMKPGTTVILR 109 (159)
Q Consensus 31 ~~~~~~kI~dL~P~~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde-~~~~i~~Gdvv~I~ 109 (159)
..+..+||+||.|+..+|+|++||+++++++. + .....++||||||+|+||+|+. ....+++|++|+|.
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 45678999999999999999999999998641 1 3445599999999999999995 66779999999999
Q ss_pred ceEEceeCCeEEEEeCCceeEEEcCCCcEEEccCCCccccceeeeeee
Q 031443 110 NAKIDMFKGSMRIAVDKWGRIEATEPAKFVVKEDNNLSLVEYELVNVV 157 (159)
Q Consensus 110 na~v~~~~G~~~L~vgk~g~I~~~~~~~~~vne~~N~S~ieye~v~~~ 157 (159)
||++++|+|+++|++++++.|+.+ +..++|++.. ..+.-.+|.+.
T Consensus 138 na~v~ey~G~~~lnlg~~t~I~~~-de~IeV~~~~--vei~G~lVdi~ 182 (311)
T PRK07217 138 NVVTDEYQGRFSVKLNRTTSIEEL-DEDIEVGDDE--VEVEGALVDIQ 182 (311)
T ss_pred eEEEeeECCEEEEEeCCceEEEeC-CCCccccCcc--ccceeEEEEEe
Confidence 999999999999999999999999 5666776544 55666666664
No 6
>PRK06386 replication factor A; Reviewed
Probab=99.85 E-value=7.3e-21 Score=165.81 Aligned_cols=101 Identities=13% Similarity=0.178 Sum_probs=89.6
Q ss_pred ceeecccCCCCCCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecCCcCCCCCCCEEEEeceEE
Q 031443 34 VFTKVDQLKPGTNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARNDQVDLMKPGTTVILRNAKI 113 (159)
Q Consensus 34 ~~~kI~dL~P~~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde~~~~i~~Gdvv~I~na~v 113 (159)
...||+||.|++.+++++++|+++++ ++|. .|| +++.|.+++||||||+|+||+|++ .+++||+|+|.||++
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-SDG---TSKIVYQGYIEDDTARVRISSFGK---PLEDNRFVRIENARV 177 (358)
T ss_pred CccEeEeccCCCCceEEEEEEEEccC-ceEe-cCC---CccEEEEEEEEcCCCeEEEEEccc---cccCCCEEEEeeeEE
Confidence 46899999999999999999999987 4776 565 359999999999999999999996 479999999999999
Q ss_pred ceeCCeEEEEeCCceeEEEcCCCcEEEccC
Q 031443 114 DMFKGSMRIAVDKWGRIEATEPAKFVVKED 143 (159)
Q Consensus 114 ~~~~G~~~L~vgk~g~I~~~~~~~~~vne~ 143 (159)
++|+|+++|++++++.|+.+ +..+++...
T Consensus 178 ~e~~G~~el~v~~~t~I~~~-~~~iev~~~ 206 (358)
T PRK06386 178 SQYNGYIEISVGNKSVIKEV-ESDINLESR 206 (358)
T ss_pred EccCCeEEEEeCCeEEEEEC-CCCcccCcc
Confidence 99999999999999999999 555555443
No 7
>PRK08402 replication factor A; Reviewed
Probab=99.85 E-value=5.4e-21 Score=166.57 Aligned_cols=100 Identities=20% Similarity=0.300 Sum_probs=92.6
Q ss_pred ceeecccCCCCCCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecCCcC----CCCCCCEEEEe
Q 031443 34 VFTKVDQLKPGTNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARNDQVD----LMKPGTTVILR 109 (159)
Q Consensus 34 ~~~kI~dL~P~~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde~~~----~i~~Gdvv~I~ 109 (159)
...||+||.|++++++++++|++++++++|.|+||+. ++|++++|+|+||.|+||||++.++ .+++||+|+|.
T Consensus 61 ~~~kI~dl~~g~~~V~v~~rVl~~~~~r~f~rrdG~~---~~V~~i~l~DeTG~ir~TlW~~~a~~~~~~l~~Gdvi~I~ 137 (355)
T PRK08402 61 PLMHISDLVPGMRGVNIVGRVLRKYPPREYTKKDGST---GRVASLIIYDDTGRARVVLWDAKVAKYYNKINVGDVIKVI 137 (355)
T ss_pred CccCHHHccCCCceeeEEEEEEEccCCceeeccCCCc---ceEEEEEEEcCCCeEEEEEechhhhhhcccCCCCCEEEEE
Confidence 4789999999999999999999999999999999865 9999999999999999999998754 48999999999
Q ss_pred ceEEcee-CCeEEEEeCCceeEEEcCCC
Q 031443 110 NAKIDMF-KGSMRIAVDKWGRIEATEPA 136 (159)
Q Consensus 110 na~v~~~-~G~~~L~vgk~g~I~~~~~~ 136 (159)
||+++.| +|.++|++|++|.|...|+.
T Consensus 138 ~a~V~e~~~G~~eLsvg~~s~i~~~pd~ 165 (355)
T PRK08402 138 DAQVRESLSGLPELHINFRARIILNPDD 165 (355)
T ss_pred CCEEeecCCCcEEEEECCCceEEeCCCc
Confidence 9999985 89999999999999988643
No 8
>PRK07218 replication factor A; Provisional
Probab=99.83 E-value=4.6e-20 Score=163.83 Aligned_cols=102 Identities=24% Similarity=0.356 Sum_probs=91.2
Q ss_pred ceeecccCCCCCCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecCCcCCCCCCCEEEEeceEE
Q 031443 34 VFTKVDQLKPGTNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARNDQVDLMKPGTTVILRNAKI 113 (159)
Q Consensus 34 ~~~kI~dL~P~~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde~~~~i~~Gdvv~I~na~v 113 (159)
...+|.||.|++.+++++++|+++++ ++|.|+||+ +.|.+++|||+||+|+||+|++++ .+++||+|+|.||++
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 GDKKLIDLGPGDRGVNVEARVLELEH-REIDGRDGE----TTILSGVLADETGRLPFTDWDPLP-EIEIGASIRIEDAYV 234 (423)
T ss_pred CccchhhccCCCCceEEEEEEEEecc-eeEEcCCCC----eEEEEEEEECCCceEEEEEecccc-cCCCCCEEEEeeeEE
Confidence 45689999999999999999999965 789988873 579999999999999999999865 589999999999999
Q ss_pred ceeCCeEEEEeCCceeEEEcCCCcEEEcc
Q 031443 114 DMFKGSMRIAVDKWGRIEATEPAKFVVKE 142 (159)
Q Consensus 114 ~~~~G~~~L~vgk~g~I~~~~~~~~~vne 142 (159)
++|+|.++|++++++.|+.++ ..+++..
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 4455544
No 9
>PRK15491 replication factor A; Provisional
Probab=99.82 E-value=5.3e-20 Score=161.21 Aligned_cols=100 Identities=19% Similarity=0.331 Sum_probs=89.7
Q ss_pred CCceeecccCCCCCCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecCCc-----CCCCCCCEE
Q 031443 32 KPVFTKVDQLKPGTNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARNDQV-----DLMKPGTTV 106 (159)
Q Consensus 32 ~~~~~kI~dL~P~~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde~~-----~~i~~Gdvv 106 (159)
.+.+.||+||.|++.+++|++||++++++++|.|+||+. ++|.+++|||+||+||||||++.+ +.|++|++|
T Consensus 54 ~~~~~kI~dL~~~~~~v~i~arVl~~~~~R~f~r~dGs~---g~v~~~~v~DeTG~ir~tlW~~~a~~~~~~~le~G~v~ 130 (374)
T PRK15491 54 GVDTTKIADINESSSNVNFTAKVVSIFEPKEFNRNDGTT---GRVGNIIVADETGSIRLTLWDDLADLIKTGDIEVGKSL 130 (374)
T ss_pred ccccccHHHCCCCCCceEEEEEEeeccCCeeeecCCCCc---eEEEEEEEEcCCCeEEEEEECchhhhhccCCcCCCCEE
Confidence 457889999999999999999999999999999999865 999999999999999999999876 347889999
Q ss_pred EEeceEEceeCCeEEEEeCCceeEEEcCC
Q 031443 107 ILRNAKIDMFKGSMRIAVDKWGRIEATEP 135 (159)
Q Consensus 107 ~I~na~v~~~~G~~~L~vgk~g~I~~~~~ 135 (159)
+|.++....|+| ++|++++.+.|.+.++
T Consensus 131 ~I~~~~~~~y~g-~Ei~i~~~~~i~~~~~ 158 (374)
T PRK15491 131 NISGYAKEGYSG-IEVNIGRYGGISESDE 158 (374)
T ss_pred EEeeeeccCccc-EEEEeCCCceeeeccc
Confidence 998765556777 8999999999998853
No 10
>PRK14699 replication factor A; Provisional
Probab=99.81 E-value=1.1e-19 Score=163.76 Aligned_cols=114 Identities=18% Similarity=0.289 Sum_probs=95.9
Q ss_pred CCceeecccCCCCCCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecCCcCC-----CCCCCEE
Q 031443 32 KPVFTKVDQLKPGTNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARNDQVDL-----MKPGTTV 106 (159)
Q Consensus 32 ~~~~~kI~dL~P~~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde~~~~-----i~~Gdvv 106 (159)
.+...||+||.|++.+++|+++||+++++++|.|+||+. ++++++.|||+||+|+||||++.++. |++||+|
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 356689999999999999999999999999999999965 99999999999999999999988764 8999999
Q ss_pred EEeceEEceeCCeEEEEeCCceeEEEcCCCcEEEc-cCCCccccc
Q 031443 107 ILRNAKIDMFKGSMRIAVDKWGRIEATEPAKFVVK-EDNNLSLVE 150 (159)
Q Consensus 107 ~I~na~v~~~~G~~~L~vgk~g~I~~~~~~~~~vn-e~~N~S~ie 150 (159)
+|.|+ ++.+.+.++|+++..+.|...+ ..+++. ...+++++.
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 7776666999999988888874 434442 234565544
No 11
>PRK07211 replication factor A; Reviewed
Probab=99.81 E-value=1.4e-19 Score=162.93 Aligned_cols=99 Identities=25% Similarity=0.398 Sum_probs=93.3
Q ss_pred ceeecccCCCCCCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecCCcCC---CCCCCEEEEec
Q 031443 34 VFTKVDQLKPGTNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARNDQVDL---MKPGTTVILRN 110 (159)
Q Consensus 34 ~~~kI~dL~P~~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde~~~~---i~~Gdvv~I~n 110 (159)
.+.+|++|.|++.+++|+++|++++++++|.|+||+. ++++++.|+|+||+||||||+++++. +++|++|+|.|
T Consensus 160 ~~~~I~dL~~~~~~v~I~grV~~v~~iRtf~r~dGse---Gkv~sv~L~DeTG~IR~TlW~d~Ad~~~~le~G~Vv~I~~ 236 (485)
T PRK07211 160 DTYTVEDLSLGLSDVTLVGVVLDTDSVRTFDRDDGSE---GRVSNLTVGDETGRVRVTLWDDRADLAEELDAGESVEIVD 236 (485)
T ss_pred CCccHHHcCCCCCceEEEEEEEEcCCCeEEECCCCCe---eEEEEEEEEcCCCeEEEEEechhhhhhccCCCCCEEEEEe
Confidence 6889999999999999999999999999999999855 99999999999999999999987654 78999999999
Q ss_pred eEEceeCCeEEEEeCCceeEEEcCC
Q 031443 111 AKIDMFKGSMRIAVDKWGRIEATEP 135 (159)
Q Consensus 111 a~v~~~~G~~~L~vgk~g~I~~~~~ 135 (159)
|+++.|+|.++|+++..+.|++.++
T Consensus 237 a~Vre~~g~~ELsl~~~s~I~~~~d 261 (485)
T PRK07211 237 GYVRERDGSLELHVGDRGAVEEVDE 261 (485)
T ss_pred eEEEecCCcEEEEECCCceEEECCc
Confidence 9999999999999999999999865
No 12
>PRK14699 replication factor A; Provisional
Probab=99.81 E-value=2.3e-19 Score=161.75 Aligned_cols=97 Identities=29% Similarity=0.404 Sum_probs=89.5
Q ss_pred eeecccCCCCCCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecCCcCC---CCCCCEEEEece
Q 031443 35 FTKVDQLKPGTNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARNDQVDL---MKPGTTVILRNA 111 (159)
Q Consensus 35 ~~kI~dL~P~~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde~~~~---i~~Gdvv~I~na 111 (159)
..+|.||.|++.+++|.++|++++++++|.|+||+. ++|.+++||||||+||||+|+++++. |++||+|+|.||
T Consensus 166 ~~~I~dL~~~~~~V~i~gkVl~~~~~R~f~~~dG~~---g~v~~~~igDeTG~ir~tlW~~~a~~~~~l~~Gd~v~I~~a 242 (484)
T PRK14699 166 SQKIKDIKDGMGDLNLTGKVLEISEIRTFQRKDGTS---GKVGNLLLGDETGTLRVTLWDDKTDFLNQIEYGDTVELINA 242 (484)
T ss_pred CcchhhcCCCCCceEEEEEEEeccCceEEecCCCCc---eEEEEEEEEcCCceEEEEEECcccccccccCCCCEEEEecc
Confidence 479999999999999999999999999999999854 99999999999999999999986555 899999999999
Q ss_pred EEce--eCCeEEEEeCCceeEEEcC
Q 031443 112 KIDM--FKGSMRIAVDKWGRIEATE 134 (159)
Q Consensus 112 ~v~~--~~G~~~L~vgk~g~I~~~~ 134 (159)
|++. |+|.++|++++.+.|...+
T Consensus 243 ~vr~~~~~~~~el~~~~~s~i~~~~ 267 (484)
T PRK14699 243 YARENAFTQKVELQVGNRSIIRKSE 267 (484)
T ss_pred eEeecccCCceEEEecCceEeeccc
Confidence 9975 7799999999999988875
No 13
>PRK12366 replication factor A; Reviewed
Probab=99.79 E-value=5.7e-19 Score=163.43 Aligned_cols=99 Identities=21% Similarity=0.333 Sum_probs=93.1
Q ss_pred CceeecccCCCCCCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecCCcCC---CCCCCEEEEe
Q 031443 33 PVFTKVDQLKPGTNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARNDQVDL---MKPGTTVILR 109 (159)
Q Consensus 33 ~~~~kI~dL~P~~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde~~~~---i~~Gdvv~I~ 109 (159)
+.+.||+||.|++.+++|+|||++++++++|.|.||+. ++|+++.|+|+||+|+|++|++.++. |++||+|+|.
T Consensus 61 ~~~~~I~dl~p~~~~v~i~arV~~~~~~r~~~~~~G~e---Gkv~~~~v~DetG~Ir~t~W~~~~~~~~~le~G~v~~i~ 137 (637)
T PRK12366 61 EEDFKISDIEEGQINVEITGRIIEISNIKTFTRKDGST---GKLANITIADNTGTIRLTLWNDNAKLLKGLKEGDVIKIE 137 (637)
T ss_pred cceeEHHHCcCCCcceEEEEEEEEccCCeEEECCCCCc---cEEEEEEEEcCCCEEEEEEEchhhhhhccCCCCCEEEEe
Confidence 46899999999999999999999999999999999854 99999999999999999999987644 7999999999
Q ss_pred ceEEceeCCeEEEEeCCceeEEEcC
Q 031443 110 NAKIDMFKGSMRIAVDKWGRIEATE 134 (159)
Q Consensus 110 na~v~~~~G~~~L~vgk~g~I~~~~ 134 (159)
||+++.|++.++|+++..+.|.+++
T Consensus 138 ~~~v~~~~~~~el~~~~~t~I~~~~ 162 (637)
T PRK12366 138 NARSRKWNNDVELNSGSETRIDKLE 162 (637)
T ss_pred ccEecccCCceEEEcCCcceEEEcc
Confidence 9999999999999999999999886
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=99.77 E-value=6.4e-18 Score=117.76 Aligned_cols=80 Identities=30% Similarity=0.463 Sum_probs=73.9
Q ss_pred eEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecCC-cCCCCCCCEEEEeceEEceeCCeEEEEeCCc
Q 031443 49 NLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARNDQ-VDLMKPGTTVILRNAKIDMFKGSMRIAVDKW 127 (159)
Q Consensus 49 nv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde~-~~~i~~Gdvv~I~na~v~~~~G~~~L~vgk~ 127 (159)
+|.++|++++++++|. .||+ .+++.++.|+|+||+|++++|++. .+.+++|++|+|.||+++.|+|.++|+++++
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 6774 499999999999999999999975 6678999999999999999999999999999
Q ss_pred eeEEE
Q 031443 128 GRIEA 132 (159)
Q Consensus 128 g~I~~ 132 (159)
|.|+.
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=99.76 E-value=4.4e-18 Score=149.12 Aligned_cols=100 Identities=22% Similarity=0.346 Sum_probs=91.0
Q ss_pred CceeecccCCCCCCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecCCcC---CCCCCCEEEEe
Q 031443 33 PVFTKVDQLKPGTNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARNDQVD---LMKPGTTVILR 109 (159)
Q Consensus 33 ~~~~kI~dL~P~~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde~~~---~i~~Gdvv~I~ 109 (159)
+.|.||+||.+++.+++|+++|++++++++|.+++|+ +++++++.|+|+||.|+||||+++++ .+++||+|+|.
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 INSQKISDIKDGDSDINIVGKVLDISDVRTFQKKDGS---QGRVRNITIGDETGKIRVTLWDGKTDLADKLENGDSVEII 240 (374)
T ss_pred cCcccHHHcCCCCccEEEEEEEEEccCceEEEecCCC---eEEEEEEEEECCCCeEEEEEecchhcccccCCCCCEEEEE
Confidence 3578999999999999999999999999999998885 48999999999999999999998765 57999999999
Q ss_pred ceEEce--eCCeEEEEeCCceeEEEcCC
Q 031443 110 NAKIDM--FKGSMRIAVDKWGRIEATEP 135 (159)
Q Consensus 110 na~v~~--~~G~~~L~vgk~g~I~~~~~ 135 (159)
|||++. |+|.++|+++..+.|.+.++
T Consensus 241 ~~~~r~~~~~g~~El~~~~~s~I~~~~~ 268 (374)
T PRK15491 241 NGYARTNNYSQEVEIQIGNHGSLRKTDR 268 (374)
T ss_pred eceEEEeccCCCEEEEeCCCceEEECCc
Confidence 999875 67999999999999999863
No 16
>PRK07211 replication factor A; Reviewed
Probab=99.72 E-value=2.4e-17 Score=148.48 Aligned_cols=102 Identities=20% Similarity=0.360 Sum_probs=87.8
Q ss_pred ccccCCCceeecccCCCCCCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecCCc----CCCCC
Q 031443 27 VVEKRKPVFTKVDQLKPGTNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARNDQV----DLMKP 102 (159)
Q Consensus 27 ~~~l~~~~~~kI~dL~P~~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde~~----~~i~~ 102 (159)
+++|..+...||++|.|++++++|++||++++++++|.|.++ +++++|+++.|+|+||.||+|||++++ +.|++
T Consensus 45 a~elg~~e~~~I~dL~pg~~~vtI~aRV~~~~~~Rt~~~~~~--~~eGkv~~v~l~DeTG~Ir~TlW~d~ad~~~~~Le~ 122 (485)
T PRK07211 45 AHELRDEEVNGIADIEPGMDEVKFLAKVLSIGDLRTFERDGE--DEDGRVINVEVADETGSVRVAFWDEQAVAAEEELEV 122 (485)
T ss_pred HHHhCccccccHhhCCCCCCceEEEEEEeEccCceEEEeCCC--CCCcEEEEEEEEcCCCeEEEEEechHhHhhhcccCC
Confidence 346777888899999999999999999999999999999762 145999999999999999999999876 56899
Q ss_pred CCEEEEeceEEceeCCeEEEEeCCceeEEEcC
Q 031443 103 GTTVILRNAKIDMFKGSMRIAVDKWGRIEATE 134 (159)
Q Consensus 103 Gdvv~I~na~v~~~~G~~~L~vgk~g~I~~~~ 134 (159)
||+|+|.|++.+.|++ ++|++++ |++-.
T Consensus 123 GdV~~I~~~~~~~ys~-~El~i~~---ve~~~ 150 (485)
T PRK07211 123 GQVLRIKGRPKDGYNG-LEVSVDK---VEPDP 150 (485)
T ss_pred CCEEEEeceEeccccc-eEEEEee---EEEcc
Confidence 9999999988777776 6999993 65543
No 17
>PRK12366 replication factor A; Reviewed
Probab=99.66 E-value=4.9e-16 Score=144.02 Aligned_cols=100 Identities=18% Similarity=0.350 Sum_probs=90.5
Q ss_pred CceeecccCC---CCCCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecCCcCC-CCCCCEEEE
Q 031443 33 PVFTKVDQLK---PGTNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARNDQVDL-MKPGTTVIL 108 (159)
Q Consensus 33 ~~~~kI~dL~---P~~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde~~~~-i~~Gdvv~I 108 (159)
..|++|++|. ++...+++.++|++++++++|.|.+|+ +..+++++|+|+||+|+||||++++.. +.+|++|.|
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 EKIYKIKDILNLEEDDNDITVIARVVEDYPVNEFERSDGS---KGKVRNIELADGTGSIRLTLWDDDAEIEIKEGDAIKI 469 (637)
T ss_pred eccccHHHhhcccCCCcEEEEEEEEEEccCceEEEecCCC---EeEEEEEEEEeCCCEEEEEEeccccccCCCCCCEEEE
Confidence 3478888887 567789999999999999999988885 489999999999999999999988764 799999999
Q ss_pred eceEEceeCCeEEEEeCCceeEEEcCC
Q 031443 109 RNAKIDMFKGSMRIAVDKWGRIEATEP 135 (159)
Q Consensus 109 ~na~v~~~~G~~~L~vgk~g~I~~~~~ 135 (159)
.||++++|+|+++|+++++|.|+..|+
T Consensus 470 ~~~~V~~~~g~~~Ls~~~~s~i~~~p~ 496 (637)
T PRK12366 470 LHPYVKENGDYLDLSIGRYGRIEINPE 496 (637)
T ss_pred EeeEEEeCCCeeEEEecCcceEEECCC
Confidence 999999999999999999999998863
No 18
>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=99.38 E-value=8.6e-13 Score=116.42 Aligned_cols=114 Identities=23% Similarity=0.359 Sum_probs=101.2
Q ss_pred cccCCCceeecccCCCCCCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEE-EEecCCcC-CCCCCCE
Q 031443 28 VEKRKPVFTKVDQLKPGTNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILF-TARNDQVD-LMKPGTT 105 (159)
Q Consensus 28 ~~l~~~~~~kI~dL~P~~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~l-tlWde~~~-~i~~Gdv 105 (159)
..+..+...+|.++.|++.+++++++|++++++..+.|..|.. +.+.+.+|||+||.+.+ ++|...+. .+++||+
T Consensus 42 ~~~~~~~~~~i~~~~~~~~~~~v~~~V~~~~e~~~~~~k~g~~---~~l~~~~v~Detg~v~~~~~~~~~a~~~~e~Gdv 118 (407)
T COG1599 42 LVLAMESIGKISDISEASSRVNVTGRVLSIGEKKTFDRKRGAE---GKLAEVLVGDETGSVKTVTLWNIAALEKLEPGDV 118 (407)
T ss_pred hhhchhhcccccccchhhccccEEEEECccccceeeecccccc---cceEEEEEecCCCCEEEEeeccccccccCCccce
Confidence 4566678899999999999999999999999999999988854 99999999999999999 79998775 7899999
Q ss_pred EEEeceEEceeCCeEEEEeCCceeEEEcCCCcEEEccCC
Q 031443 106 VILRNAKIDMFKGSMRIAVDKWGRIEATEPAKFVVKEDN 144 (159)
Q Consensus 106 v~I~na~v~~~~G~~~L~vgk~g~I~~~~~~~~~vne~~ 144 (159)
++|.|++++.|.|++++++++.+.+...++....+.+..
T Consensus 119 ~~i~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~ 157 (407)
T COG1599 119 IRIRNAYTSLYRGGKRLSVGRVGSVADVDDEEDEARESE 157 (407)
T ss_pred EEecCcccccccCceeeecccccccccCchhhccccccc
Confidence 999999999999999999999999999876554444433
No 19
>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=99.38 E-value=3.5e-12 Score=91.80 Aligned_cols=84 Identities=14% Similarity=0.216 Sum_probs=75.3
Q ss_pred ceEEEEEEecCcccccccCC-CCCCCcceEEEEEEeeCce-eEEEEEecCCcCCCCC--CCEEEEeceEEceeCCeEEEE
Q 031443 48 HNLTVNVLKSEPVLPKNRAA-SPQLRQTRIAECLVGDDTG-TILFTARNDQVDLMKP--GTTVILRNAKIDMFKGSMRIA 123 (159)
Q Consensus 48 vnv~~kVL~i~~~~~~~R~D-G~~~~~~~V~~~lVgDeTG-~I~ltlWde~~~~i~~--Gdvv~I~na~v~~~~G~~~L~ 123 (159)
+++.|.|.++++++++.+++ |+ +...+++.|+|+|| .+.+|||++++..+.+ |++|.|.|+.++.|+ ..+|+
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 68999999999999988877 64 48999999999999 9999999988877643 999999999999999 58999
Q ss_pred eCCceeEEEcCC
Q 031443 124 VDKWGRIEATEP 135 (159)
Q Consensus 124 vgk~g~I~~~~~ 135 (159)
.+..+.|...|+
T Consensus 78 ~~~~s~i~~np~ 89 (101)
T cd04475 78 TGSSSTIIINPD 89 (101)
T ss_pred ecCceeEEECCC
Confidence 999999988865
No 20
>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=99.36 E-value=6.5e-12 Score=91.71 Aligned_cols=77 Identities=19% Similarity=0.263 Sum_probs=68.5
Q ss_pred ecccCCCCCCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeC-ceeEEEEEecCCcC----CCCCCCEEEEece
Q 031443 37 KVDQLKPGTNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDD-TGTILFTARNDQVD----LMKPGTTVILRNA 111 (159)
Q Consensus 37 kI~dL~P~~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDe-TG~I~ltlWde~~~----~i~~Gdvv~I~na 111 (159)
+|++|.|++.+..|.|+|+.+++++.|...+ +++++.++.|.|+ +|.|+.++|++.++ .|++|+++.|.++
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 PISSLNPYQNKWTIKARVTNKSDIRTWSNAR----GEGKLFSFDLLDEDGGEIRATFFNDAVDKFYDLLEVGKVYYISKG 76 (104)
T ss_pred ChhHccCCCCcEEEEEEEeeccccccccCCC----CCcEEEEEEEEECCCCEEEEEEehHHHHHhhcccccccEEEEecc
Confidence 5899999999999999999999999887654 2489999999999 99999999987654 6899999999999
Q ss_pred EEceeC
Q 031443 112 KIDMFK 117 (159)
Q Consensus 112 ~v~~~~ 117 (159)
.++..+
T Consensus 77 ~V~~a~ 82 (104)
T cd04474 77 SVKVAN 82 (104)
T ss_pred EEeecc
Confidence 998764
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=99.06 E-value=9.4e-10 Score=101.96 Aligned_cols=98 Identities=18% Similarity=0.262 Sum_probs=86.8
Q ss_pred ceeecccCCCCCCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecCCc----CCCCCCCEEEEe
Q 031443 34 VFTKVDQLKPGTNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARNDQV----DLMKPGTTVILR 109 (159)
Q Consensus 34 ~~~kI~dL~P~~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde~~----~~i~~Gdvv~I~ 109 (159)
.+++|++|.|.+.+..|+++|+.+++.++|...+| ++++.++.|.|++|.|+.++|++.+ +.|++|+++.|.
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 58999999999999999999999999999887654 4799999999999999999999766 557999999999
Q ss_pred ceEEceeC-------CeEEEEeCCceeEEEcCC
Q 031443 110 NAKIDMFK-------GSMRIAVDKWGRIEATEP 135 (159)
Q Consensus 110 na~v~~~~-------G~~~L~vgk~g~I~~~~~ 135 (159)
++.++..+ ...+|.++.++.|++.++
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 368999999999998764
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=98.90 E-value=6.2e-09 Score=96.54 Aligned_cols=100 Identities=14% Similarity=0.177 Sum_probs=84.7
Q ss_pred CCceeecccCCCCC--CCceEEEEEEecCcccccc-cCCCCCCCcceEEEEEEeeCce-eEEEEEecCCcCCC--CCCCE
Q 031443 32 KPVFTKVDQLKPGT--NGHNLTVNVLKSEPVLPKN-RAASPQLRQTRIAECLVGDDTG-TILFTARNDQVDLM--KPGTT 105 (159)
Q Consensus 32 ~~~~~kI~dL~P~~--~~vnv~~kVL~i~~~~~~~-R~DG~~~~~~~V~~~lVgDeTG-~I~ltlWde~~~~i--~~Gdv 105 (159)
.-.|++|.||.... ..++|.+.|.+++++.++. |.+|+. ...+++.|.|+|| +|++|||++++..+ .+|++
T Consensus 295 ~~~f~~i~dI~~~~~~~~VDVIGvV~~v~~~~~i~~k~~g~~---~~kR~i~L~D~sg~sI~vTLWG~~A~~~~~~~~~V 371 (608)
T TIGR00617 295 QFNFVKIDDIGGYEGNSLVDVIGIVQSVSPTQTITSRKNNKE---FPKRDITLVDDSGKSVRVTLWGDDATKFDVSVQPV 371 (608)
T ss_pred cccceEHHHhhhhcCCCCccEEEEEeEecCceEEEEcCCCCe---eeeEEEEEEeCCCCEEEEEEEhhhhhhcCCCCCCE
Confidence 34689999997543 3689999999999998876 677744 8899999999999 69999999887554 68999
Q ss_pred EEEeceEEceeCCeEEEEeCCceeEEEcCC
Q 031443 106 VILRNAKIDMFKGSMRIAVDKWGRIEATEP 135 (159)
Q Consensus 106 v~I~na~v~~~~G~~~L~vgk~g~I~~~~~ 135 (159)
|.|.++.++.|+| .+|+.+..+.|...++
T Consensus 372 va~kg~~V~~f~g-~sLs~~~~S~i~iNPd 400 (608)
T TIGR00617 372 IAIKGVRVSDFGG-KSLSTGGSSTIIVNPD 400 (608)
T ss_pred EEEEeEEEEecCC-ceEeccCCceEEECCC
Confidence 9999999999955 6999999999987753
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=98.41 E-value=1.6e-06 Score=57.64 Aligned_cols=66 Identities=23% Similarity=0.283 Sum_probs=54.3
Q ss_pred ceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEec----CCcCCCCCCCEEEEeceEEceeCCe-EEE
Q 031443 48 HNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARN----DQVDLMKPGTTVILRNAKIDMFKGS-MRI 122 (159)
Q Consensus 48 vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWd----e~~~~i~~Gdvv~I~na~v~~~~G~-~~L 122 (159)
|.+.++|.++. + +.+.+..+.|.|+||.|.+.+|+ ...+.+++|+.|++. |.++.+++. ++|
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--R----------SGGKIVFFTLEDGTGSIQVVFFNEEYERFREKLKEGDIVRVR-GKVKRYNGGELEL 67 (75)
T ss_dssp EEEEEEEEEEE--E----------EETTEEEEEEEETTEEEEEEEETHHHHHHHHTS-TTSEEEEE-EEEEEETTSSEEE
T ss_pred CEEEEEEEEEE--c----------CCCCEEEEEEEECCccEEEEEccHHhhHHhhcCCCCeEEEEE-EEEEEECCccEEE
Confidence 46888999886 1 12679999999999999999999 244678999999999 888888887 999
Q ss_pred EeCC
Q 031443 123 AVDK 126 (159)
Q Consensus 123 ~vgk 126 (159)
.+.+
T Consensus 68 ~~~~ 71 (75)
T PF01336_consen 68 IVPK 71 (75)
T ss_dssp EEEE
T ss_pred EECE
Confidence 8876
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=98.33 E-value=6.1e-06 Score=63.02 Aligned_cols=86 Identities=14% Similarity=0.212 Sum_probs=70.5
Q ss_pred ceeecccCC-CCCCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCcee----EEEEEecCC---cCCCCCCCE
Q 031443 34 VFTKVDQLK-PGTNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGT----ILFTARNDQ---VDLMKPGTT 105 (159)
Q Consensus 34 ~~~kI~dL~-P~~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~----I~ltlWde~---~~~i~~Gdv 105 (159)
.|++|++|. .....+|+.+.|++..++.. ..| +..++...|.|+|+. +++.+|.+. ...+.+||+
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 KYTPLSSALKESGGSVNVIGVVVDAGPPVR---SKG----TDYCCTLTITDPSLANSDGLTVKLFRPNEESLPIVKVGDI 74 (138)
T ss_pred ceEeHHHHHhccCCeEEEEEEEeecCCCcc---cCC----CcEEEEEEEECCCCCCCCcEEEEEECCChhhCCCCCCCCE
Confidence 578899988 44455999999999998753 223 348899999999875 999999754 354699999
Q ss_pred EEEeceEEceeCCeEEEEeCC
Q 031443 106 VILRNAKIDMFKGSMRIAVDK 126 (159)
Q Consensus 106 v~I~na~v~~~~G~~~L~vgk 126 (159)
|.|++..++.|+|++.+....
T Consensus 75 Ill~~~kv~~~~g~~~~~~~~ 95 (138)
T cd04497 75 ILLRRVKIQSYNGKPQGISND 95 (138)
T ss_pred EEEEEEEEEEECCceEEEECC
Confidence 999999999999998888877
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=97.91 E-value=9.1e-05 Score=53.24 Aligned_cols=64 Identities=16% Similarity=0.257 Sum_probs=50.9
Q ss_pred eEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecCC------------------------cCCCCCCC
Q 031443 49 NLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARNDQ------------------------VDLMKPGT 104 (159)
Q Consensus 49 nv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde~------------------------~~~i~~Gd 104 (159)
+|.+.|.++.+. .......|.|.||+|...+|... .+.+++|+
T Consensus 1 ~ivG~V~sv~~~-------------~~~~~~tLdDgTG~Ie~~~W~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~G~ 67 (92)
T cd04483 1 DILGTVVSRRER-------------ETFYSFGVDDGTGVVNCVCWKNLSYAEVSSRSDAARILKSALMALKQAKVLEIGD 67 (92)
T ss_pred CeEEEEEEEEec-------------CCeEEEEEecCCceEEEEEEcCcCcccccccccccccccccccccccccccCCCC
Confidence 367888888653 23577899999999999999732 23489999
Q ss_pred EEEEeceEEceeCCeEEEEeCC
Q 031443 105 TVILRNAKIDMFKGSMRIAVDK 126 (159)
Q Consensus 105 vv~I~na~v~~~~G~~~L~vgk 126 (159)
.+++. |.++.|+|.++|++..
T Consensus 68 vvrV~-G~i~~frg~~ql~i~~ 88 (92)
T cd04483 68 LLRVR-GSIRTYRGEREINASV 88 (92)
T ss_pred EEEEE-EEEeccCCeeEEEEEE
Confidence 99999 5668999999998763
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=97.87 E-value=0.00016 Score=50.92 Aligned_cols=70 Identities=24% Similarity=0.220 Sum_probs=55.4
Q ss_pred ceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecC-------CcCCCCCCCEEEEeceEEceeCCeE
Q 031443 48 HNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARND-------QVDLMKPGTTVILRNAKIDMFKGSM 120 (159)
Q Consensus 48 vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde-------~~~~i~~Gdvv~I~na~v~~~~G~~ 120 (159)
+.+.+.|.++... +.-....+.|.||+|...+|+. ..+.+++|+.|++.+-. +.|+|.+
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 5788888887753 3467899999999999999973 23458999999998766 7899999
Q ss_pred EEEeCCceeEEEcC
Q 031443 121 RIAVDKWGRIEATE 134 (159)
Q Consensus 121 ~L~vgk~g~I~~~~ 134 (159)
.|.+.+ |.+++
T Consensus 68 ql~i~~---i~~v~ 78 (95)
T cd04478 68 SIMAFS---IRPVT 78 (95)
T ss_pred EEEEEE---EEEeC
Confidence 998774 66664
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=97.75 E-value=0.0003 Score=45.02 Aligned_cols=66 Identities=24% Similarity=0.423 Sum_probs=53.0
Q ss_pred eEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCc-eeEEEEEecCCc----CCCCCCCEEEEeceEEceeCCeEEEE
Q 031443 49 NLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDT-GTILFTARNDQV----DLMKPGTTVILRNAKIDMFKGSMRIA 123 (159)
Q Consensus 49 nv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeT-G~I~ltlWde~~----~~i~~Gdvv~I~na~v~~~~G~~~L~ 123 (159)
++.+.|.++.+..+ | ..+..+.|.|.| |.+.+.+|.+.. ..+++|+.+.+. +.++.+++.++|.
T Consensus 1 ~v~g~v~~~~~~~~-----~-----~~~~~~~l~D~~~~~i~~~~~~~~~~~~~~~~~~g~~v~v~-g~v~~~~~~~~l~ 69 (75)
T cd03524 1 TIVGIVVAVEEIRT-----E-----GKVLIFTLTDGTGGTIRVTLFGELAEELENLLKEGQVVYIK-GKVKKFRGRLQLI 69 (75)
T ss_pred CeEEEEEeeccccc-----C-----CeEEEEEEEcCCCCEEEEEEEchHHHHHHhhccCCCEEEEE-EEEEecCCeEEEE
Confidence 36788888877533 2 458999999999 999999998643 358999999999 7777788888887
Q ss_pred eC
Q 031443 124 VD 125 (159)
Q Consensus 124 vg 125 (159)
+.
T Consensus 70 ~~ 71 (75)
T cd03524 70 VE 71 (75)
T ss_pred ee
Confidence 65
No 28
>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=97.68 E-value=0.00065 Score=45.71 Aligned_cols=52 Identities=17% Similarity=0.419 Sum_probs=42.5
Q ss_pred ceEEEEEEeeCceeEEEEEecCC---cCCCCCCCEEEEeceEEceeCCeEEEEeCC
Q 031443 74 TRIAECLVGDDTGTILFTARNDQ---VDLMKPGTTVILRNAKIDMFKGSMRIAVDK 126 (159)
Q Consensus 74 ~~V~~~lVgDeTG~I~ltlWde~---~~~i~~Gdvv~I~na~v~~~~G~~~L~vgk 126 (159)
..+..+.|.|.||.+.+.+|++. ...+++|..|.|. |.++.++|.++|.+..
T Consensus 18 ~~~~~~~l~D~tg~i~~~~f~~~~~~~~~l~~g~~v~v~-G~v~~~~~~~~l~~~~ 72 (83)
T cd04492 18 KPYLALTLQDKTGEIEAKLWDASEEDEEKFKPGDIVHVK-GRVEEYRGRLQLKIQR 72 (83)
T ss_pred CcEEEEEEEcCCCeEEEEEcCCChhhHhhCCCCCEEEEE-EEEEEeCCceeEEEEE
Confidence 35999999999999999999854 2458999999999 5556688888887654
No 29
>PRK13480 3'-5' exoribonuclease YhaM; Provisional
Probab=97.68 E-value=0.00027 Score=61.21 Aligned_cols=85 Identities=13% Similarity=0.206 Sum_probs=65.1
Q ss_pred ecccCCCCCCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecC---CcCCCCCCCEEEEeceEE
Q 031443 37 KVDQLKPGTNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARND---QVDLMKPGTTVILRNAKI 113 (159)
Q Consensus 37 kI~dL~P~~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde---~~~~i~~Gdvv~I~na~v 113 (159)
+|++|++|.. ++..+-|-++.... . ++| .....+.++|.||+|...+|+. ....+++|++|++.+-.
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-VDHFLLIKSATKGV--A-SNG-----KPFLTLILQDKSGDIEAKLWDVSPEDEATYVPETIVHVKGDI- 73 (314)
T ss_pred hHhhcCCCCE-eeEEEEEEEceeee--c-CCC-----CeEEEEEEEcCCcEEEEEeCCCChhhHhhcCCCCEEEEEEEE-
Confidence 6999999874 77777776655322 1 234 3489999999999999999984 34568999999998766
Q ss_pred ceeCCeEEEEeCCceeEEEcC
Q 031443 114 DMFKGSMRIAVDKWGRIEATE 134 (159)
Q Consensus 114 ~~~~G~~~L~vgk~g~I~~~~ 134 (159)
..|+|.++|+|.+ |.+++
T Consensus 74 ~~y~g~~Ql~i~~---i~~~~ 91 (314)
T PRK13480 74 INYRGRKQLKVNQ---IRLAT 91 (314)
T ss_pred EEECCcceEEEEE---eEECC
Confidence 5799999998875 55553
No 30
>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=97.41 E-value=0.0009 Score=48.51 Aligned_cols=83 Identities=11% Similarity=0.132 Sum_probs=64.6
Q ss_pred eEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCce-eEEEEEecCCcCCC--------CCCCEEEEec-eEEceeCC
Q 031443 49 NLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTG-TILFTARNDQVDLM--------KPGTTVILRN-AKIDMFKG 118 (159)
Q Consensus 49 nv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG-~I~ltlWde~~~~i--------~~Gdvv~I~n-a~v~~~~G 118 (159)
++.+.|.++++...+.+. | ....-++..|-|.+| ++.++||++++..+ ..+-+|-|.. +.++.|+|
T Consensus 1 DviG~i~~v~~~~~~~~~-~---~~~~kr~~~i~D~~~~~l~~tlwG~~A~~f~~~~~~~~~~~~VVav~~~~rV~~~~g 76 (106)
T cd04481 1 DVIGVIVDVGPLEELPPV-N---KPSRKLDFEIRDLSDERLKCTLWGEYAEEFDAKFQSAGNGEPVVAVLRFWKIKEYKG 76 (106)
T ss_pred CeeEEEEEecceEecccC-C---ccceEEEEEEEeCCCCEEEEEEEHHHHHHHHHHHHHhCCCCcEEEEEEeEEEEEEcC
Confidence 467889999987766554 4 458889999999996 99999999877553 3555776655 99999999
Q ss_pred eEEEEeC-CceeEEEcCC
Q 031443 119 SMRIAVD-KWGRIEATEP 135 (159)
Q Consensus 119 ~~~L~vg-k~g~I~~~~~ 135 (159)
...|+-+ ..+++...|+
T Consensus 77 ~~~ls~~~~~s~v~inp~ 94 (106)
T cd04481 77 PKSLSNSFGASKVYINPD 94 (106)
T ss_pred CcEEEcCCCceEEEECCC
Confidence 8888887 6677776653
No 31
>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=97.23 E-value=0.0019 Score=57.34 Aligned_cols=69 Identities=12% Similarity=0.172 Sum_probs=57.0
Q ss_pred EEEEEecCcccccccCCCCCCCcceEEEEEEeeCc-eeEEEEEecCCcCCCCCCCEEEEeceEEceeCCeEEEEeCCce
Q 031443 51 TVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDT-GTILFTARNDQVDLMKPGTTVILRNAKIDMFKGSMRIAVDKWG 128 (159)
Q Consensus 51 ~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeT-G~I~ltlWde~~~~i~~Gdvv~I~na~v~~~~G~~~L~vgk~g 128 (159)
+++|+...+++.|.+.+| ++.+.+..+.|+| |.++|+.|++. ..|+++.+.++.+.++++.++++ +...
T Consensus 173 ~~~v~~g~~ik~~~~~~g----e~~~~~~~~~d~~~~~~~~~~~~~~----~~g~~~~ie~~~v~~~~~~~~~~-~~~e 242 (407)
T COG1599 173 KARVVVGSEIKTFDNQGG----ESKVFSNELEDEERGVIVFTDWDPS----QDGDVYRIEGARVKTKNKQPEEN-LAEE 242 (407)
T ss_pred eEEEEecccceeEecCCC----ccceEeeeecccceeEEEeccCccc----ccceeeeecCcEEEEeccccccc-ccce
Confidence 789999899988887654 4778888888887 99999999976 78999999999999988877775 4433
No 32
>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=97.22 E-value=0.0031 Score=41.15 Aligned_cols=64 Identities=27% Similarity=0.374 Sum_probs=47.1
Q ss_pred EEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEec-C--CcCCCCCCCEEEEeceEEceeCCeEEEE
Q 031443 50 LTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARN-D--QVDLMKPGTTVILRNAKIDMFKGSMRIA 123 (159)
Q Consensus 50 v~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWd-e--~~~~i~~Gdvv~I~na~v~~~~G~~~L~ 123 (159)
+.++|+++..... + | ..+..+.+.|++|.+.++.|+ . ....+++|+.+.+.+-. +.|+|.++|.
T Consensus 2 i~~~V~~~~~~~~--~--~-----~~~~~~~~~D~~g~i~~~~F~~~~~~~~~~~~G~~~~v~Gkv-~~~~~~~qi~ 68 (75)
T cd04488 2 VEGTVVSVEVVPR--R--G-----RRRLKVTLSDGTGTLTLVFFNFQPYLKKQLPPGTRVRVSGKV-KRFRGGLQIV 68 (75)
T ss_pred EEEEEEEEEeccC--C--C-----ccEEEEEEEcCCCEEEEEEECCCHHHHhcCCCCCEEEEEEEE-eecCCeeEEe
Confidence 6778888643221 1 2 358999999999999999998 3 24568999999888665 5567766664
No 33
>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=97.14 E-value=0.0026 Score=42.20 Aligned_cols=52 Identities=21% Similarity=0.346 Sum_probs=41.8
Q ss_pred ceEEEEEEeeCceeEEEEEecCC----cCCCCCCCEEEEeceEEceeCCeEEEEeCC
Q 031443 74 TRIAECLVGDDTGTILFTARNDQ----VDLMKPGTTVILRNAKIDMFKGSMRIAVDK 126 (159)
Q Consensus 74 ~~V~~~lVgDeTG~I~ltlWde~----~~~i~~Gdvv~I~na~v~~~~G~~~L~vgk 126 (159)
..+..+.+.|.||.+.+++|++. .+.+++|..|.|.+-. +.++|.++|.+.+
T Consensus 18 ~~~~~~~l~D~tg~~~~~~f~~~~~~~~~~l~~g~~v~v~G~v-~~~~~~~~l~~~~ 73 (84)
T cd04485 18 KRMAFVTLEDLTGSIEVVVFPETYEKYRDLLKEDALLLVEGKV-ERRDGGLRLIAER 73 (84)
T ss_pred CEEEEEEEEeCCCeEEEEECHHHHHHHHHHhcCCCEEEEEEEE-EecCCceEEEeec
Confidence 35899999999999999999743 3458999999888655 5577888888764
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=97.03 E-value=0.0059 Score=46.82 Aligned_cols=87 Identities=16% Similarity=0.183 Sum_probs=64.4
Q ss_pred eecccCC-CCCCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCc--------eeEEEEEec---CCcCCCCC-
Q 031443 36 TKVDQLK-PGTNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDT--------GTILFTARN---DQVDLMKP- 102 (159)
Q Consensus 36 ~kI~dL~-P~~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeT--------G~I~ltlWd---e~~~~i~~- 102 (159)
.+|.+.. ....-+|+.+.|++...+... +.-| ..-+++..|-|++ -.+.+.++. +....+..
T Consensus 2 ~~l~~~~~~~~~~vnvigVV~~~~~p~~~-~t~g----~D~~~tl~i~D~S~~~~~~~~~~l~v~iF~~~~~~LP~v~~~ 76 (146)
T PF02765_consen 2 TPLSTAKEKFGKFVNVIGVVVDFSPPNPK-KTRG----TDYMCTLTITDPSLNDSNQKLSGLTVNIFRPHKESLPNVKSV 76 (146)
T ss_dssp CCGGGSCTTSSEEEEEEEEEEEEEEECTE-EESS----SCEEEEEEEEBTTCSCSSCCCCEEEEEEEESSHHHSCTTCST
T ss_pred ccchhhhhcCCCEEEEEEEEEEccCCcce-EcCC----CcEEEEEEEECCCCCccccccCCEEEEEECCCHHHCCCCCCC
Confidence 3455222 334458999999999877221 1112 3678999999998 479999994 34455666
Q ss_pred CCEEEEeceEEceeCCeEEEEeCCc
Q 031443 103 GTTVILRNAKIDMFKGSMRIAVDKW 127 (159)
Q Consensus 103 Gdvv~I~na~v~~~~G~~~L~vgk~ 127 (159)
||+|+|++..++.|+|.+.+..+..
T Consensus 77 GDii~l~r~kv~~~~~~~~~~~~~~ 101 (146)
T PF02765_consen 77 GDIIRLRRVKVQSYNGKPQGLSNST 101 (146)
T ss_dssp THEEEEEEEEEEEETTEEEEEEECE
T ss_pred CCEEEEEEEEEEEECCEEEEEecCC
Confidence 9999999999999999999888766
No 35
>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=96.96 E-value=0.0034 Score=43.76 Aligned_cols=62 Identities=24% Similarity=0.253 Sum_probs=50.6
Q ss_pred EEEEEEecCcccccccCCCCCCCcceEEEEEEeeCce-eEEEEEecCCc----CCCCCCCEEEEeceEEceeCCe
Q 031443 50 LTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTG-TILFTARNDQV----DLMKPGTTVILRNAKIDMFKGS 119 (159)
Q Consensus 50 v~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG-~I~ltlWde~~----~~i~~Gdvv~I~na~v~~~~G~ 119 (159)
|.++|+.++...... ++...++++.||.| .|..+++.+.+ +.+++|.++.|.|..+...++.
T Consensus 2 I~Vrv~r~W~~~~~~--------~~~~~~miL~De~G~~I~a~i~~~~~~~f~~~L~eg~vy~is~f~v~~~~~~ 68 (86)
T cd04480 2 ICVRVLRLWDVYNNA--------SGESLEMVLVDEKGNRIHATIPKRLAAKFRPLLKEGKWYTISNFEVAPNTGS 68 (86)
T ss_pred EEEEEEEEEcCcCCC--------CCcEEEEEEEcCCCCEEEEEECHHHHHhhhhhceeCCEEEEeeEEEEcCCCc
Confidence 789999999865422 47899999999999 99999998643 5679999999999888765543
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=96.57 E-value=0.026 Score=37.85 Aligned_cols=66 Identities=12% Similarity=0.140 Sum_probs=49.6
Q ss_pred eEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecCCc----CCCCCCCEEEEeceEEc-eeCCeEEEE
Q 031443 49 NLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARNDQV----DLMKPGTTVILRNAKID-MFKGSMRIA 123 (159)
Q Consensus 49 nv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde~~----~~i~~Gdvv~I~na~v~-~~~G~~~L~ 123 (159)
.+.+.|.++.. + + .+ ++-+.+-|.+|.+.+++|.+.. +.+++|+.|.|.+-... .+++.++|.
T Consensus 3 ~v~g~v~~i~~--t-k--------~g-~~~~~L~D~~~~i~~~~f~~~~~~~~~~l~~g~~v~v~g~v~~~~~~~~~~l~ 70 (78)
T cd04489 3 WVEGEISNLKR--P-S--------SG-HLYFTLKDEDASIRCVMWRSNARRLGFPLEEGMEVLVRGKVSFYEPRGGYQLI 70 (78)
T ss_pred EEEEEEecCEE--C-C--------Cc-EEEEEEEeCCeEEEEEEEcchhhhCCCCCCCCCEEEEEEEEEEECCCCEEEEE
Confidence 46677776654 1 1 14 9999999999999999997522 45799999999988774 346888888
Q ss_pred eCC
Q 031443 124 VDK 126 (159)
Q Consensus 124 vgk 126 (159)
+.+
T Consensus 71 v~~ 73 (78)
T cd04489 71 VEE 73 (78)
T ss_pred EEE
Confidence 753
No 37
>COG4085 Predicted RNA-binding protein, contains TRAM domain [General function prediction only]
Probab=94.35 E-value=0.2 Score=41.12 Aligned_cols=92 Identities=17% Similarity=0.272 Sum_probs=67.5
Q ss_pred CceeecccCCCCC----CCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecCCc---------CC
Q 031443 33 PVFTKVDQLKPGT----NGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARNDQV---------DL 99 (159)
Q Consensus 33 ~~~~kI~dL~P~~----~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde~~---------~~ 99 (159)
|...+++.+..+. +.+.+++.|++.... +| .-+-..++-|+||+|.+.+...-. +.
T Consensus 35 p~~~~~a~i~eg~G~l~e~v~vkg~V~~~~n~------~~-----~gi~~l~lndgtGti~vva~~~tee~l~~n~~~p~ 103 (204)
T COG4085 35 PVAEQIATINEGDGRLNEEVTVKGEVTADQNA------IG-----GGIESLVLNDGTGTITVVASRSTEETLELNEGMPV 103 (204)
T ss_pred CCccceeEEecCCceeeccceeeeEEEeeecc------cc-----cceEEEEEECCCCcEEEEEecChhHhHhhcCCCCc
Confidence 3445566665443 446688888887652 33 447889999999999998886322 24
Q ss_pred CCCCCEEEEeceEEceeCCeEEEEeCCceeEEEcCCC
Q 031443 100 MKPGTTVILRNAKIDMFKGSMRIAVDKWGRIEATEPA 136 (159)
Q Consensus 100 i~~Gdvv~I~na~v~~~~G~~~L~vgk~g~I~~~~~~ 136 (159)
+.+|+++.+.+. +.+|+|..++.+..--.+.+++..
T Consensus 104 ~~eGe~veVtGr-v~~yrG~~eVkvnq~~d~~~l~k~ 139 (204)
T COG4085 104 TVEGEIVEVTGR-VEEYRGSSEVKVNQPNDSRPLPKH 139 (204)
T ss_pred cccCcEEEEEEE-EEEeCCCceeeccCcccccccccc
Confidence 569999999865 579999999999988887777633
No 38
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=94.14 E-value=0.25 Score=46.67 Aligned_cols=76 Identities=22% Similarity=0.281 Sum_probs=57.8
Q ss_pred eeecccCCCCCCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEec---CC-cCCCCCCCEEEEec
Q 031443 35 FTKVDQLKPGTNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARN---DQ-VDLMKPGTTVILRN 110 (159)
Q Consensus 35 ~~kI~dL~P~~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWd---e~-~~~i~~Gdvv~I~n 110 (159)
..+|.++.+|.. +.+.++|++..... + + ..+..+.+.|+||.+.++.+. .. ...+++|..+.+.|
T Consensus 50 ~~~i~~l~~g~~-vtv~g~V~~~~~~~---~--~-----~~~~~v~l~D~tg~i~l~~F~~n~~~~~~~l~~G~~~~v~G 118 (681)
T PRK10917 50 LKPIAELRPGEK-VTVEGEVLSAEVVF---G--K-----RRRLTVTVSDGTGNLTLRFFNFNQPYLKKQLKVGKRVAVYG 118 (681)
T ss_pred cCCHHHCCCCCE-EEEEEEEEEEEEcc---C--C-----ceEEEEEEEECCeEEEEEEEccCcHHHHhhCCCCCEEEEEE
Confidence 468889998865 89999999874432 1 2 358999999999999999983 22 36689999999988
Q ss_pred eEEceeCCeEEE
Q 031443 111 AKIDMFKGSMRI 122 (159)
Q Consensus 111 a~v~~~~G~~~L 122 (159)
-... ++|.+++
T Consensus 119 kv~~-~~~~~qm 129 (681)
T PRK10917 119 KVKR-GKYGLEM 129 (681)
T ss_pred EEEe-cCCeEEE
Confidence 7754 5565555
No 39
>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=93.80 E-value=0.15 Score=38.80 Aligned_cols=38 Identities=21% Similarity=0.365 Sum_probs=31.3
Q ss_pred eEEEEEecCCc---CCCCCCCEEEEeceEEceeCC--------eEEEEe
Q 031443 87 TILFTARNDQV---DLMKPGTTVILRNAKIDMFKG--------SMRIAV 124 (159)
Q Consensus 87 ~I~ltlWde~~---~~i~~Gdvv~I~na~v~~~~G--------~~~L~v 124 (159)
+|.++|||+.+ ..|++||.|+|+|..++..+. ++++.+
T Consensus 61 ti~It~yD~H~~~ar~lK~GdfV~L~NVhiK~~~~~~~~~~~~~Le~~l 109 (123)
T cd04498 61 TIDILVYDNHVELAKSLKPGDFVRIYNVHAKSYSSKNEHDENDHLHFHL 109 (123)
T ss_pred EEEEEEEcchHHHHhhCCCCCEEEEEEEEEEeccCCcccCCcceEEEEE
Confidence 89999999755 338999999999999988766 566665
No 40
>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=93.04 E-value=0.86 Score=31.71 Aligned_cols=71 Identities=18% Similarity=0.165 Sum_probs=51.8
Q ss_pred CceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecC-C---cCCCC-CCCEEEEeceEE-ceeCCeE
Q 031443 47 GHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARND-Q---VDLMK-PGTTVILRNAKI-DMFKGSM 120 (159)
Q Consensus 47 ~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde-~---~~~i~-~Gdvv~I~na~v-~~~~G~~ 120 (159)
++.+.+.|..+.. ++.+ .| ..+...-|.|.|++|.+-.|.. . .+.++ +|+.|++++-.. .-|.+.+
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 3678999999865 3322 23 5688999999999999999972 2 24578 999999998853 3456666
Q ss_pred EEEeC
Q 031443 121 RIAVD 125 (159)
Q Consensus 121 ~L~vg 125 (159)
.|.+.
T Consensus 73 ~~~i~ 77 (82)
T cd04484 73 VLMIN 77 (82)
T ss_pred EEEee
Confidence 66654
No 41
>TIGR00643 recG ATP-dependent DNA helicase RecG.
Probab=93.02 E-value=0.58 Score=43.74 Aligned_cols=80 Identities=14% Similarity=0.119 Sum_probs=58.6
Q ss_pred eeecccCCCCCCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEee-CceeEEEEEecC--CcCCCCCCCEEEEece
Q 031443 35 FTKVDQLKPGTNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGD-DTGTILFTARND--QVDLMKPGTTVILRNA 111 (159)
Q Consensus 35 ~~kI~dL~P~~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgD-eTG~I~ltlWde--~~~~i~~Gdvv~I~na 111 (159)
..+|.++.+|.. +.+.++|++.... .+ + ...+..+.+.| ++|.+.++.|+. ....+++|+.+.+.|-
T Consensus 23 ~~~i~~~~~g~~-~~~~~~v~~~~~~---~~--~----~~~~~~~~~~d~~~~~~~~~~F~~~~~~~~~~~g~~~~~~Gk 92 (630)
T TIGR00643 23 LQTIGELLPGER-ATIVGEVLSHCIF---GF--K----RRKVLKLRLKDGGYKKLELRFFNRAFLKKKFKVGSKVVVYGK 92 (630)
T ss_pred ccCHHHcCCCCE-EEEEEEEEEeEec---cC--C----CCceEEEEEEECCCCEEEEEEECCHHHHhhCCCCCEEEEEEE
Confidence 457999999875 7899999885321 11 1 13488999999 999999999973 2356899999999887
Q ss_pred EEceeCCeEEEEeC
Q 031443 112 KIDMFKGSMRIAVD 125 (159)
Q Consensus 112 ~v~~~~G~~~L~vg 125 (159)
.. .++|.+++.--
T Consensus 93 ~~-~~~~~~~~~~p 105 (630)
T TIGR00643 93 VK-SSKFKAYLIHP 105 (630)
T ss_pred EE-eeCCEEEEECC
Confidence 64 46676655433
No 42
>PRK08402 replication factor A; Reviewed
Probab=92.84 E-value=0.15 Score=45.12 Aligned_cols=67 Identities=18% Similarity=0.105 Sum_probs=47.4
Q ss_pred CceeecccCCCCCCCceEEEEEEecCcc----------cccccCCCC-----------CCCcceEEEEEEeeCceeEEEE
Q 031443 33 PVFTKVDQLKPGTNGHNLTVNVLKSEPV----------LPKNRAASP-----------QLRQTRIAECLVGDDTGTILFT 91 (159)
Q Consensus 33 ~~~~kI~dL~P~~~~vnv~~kVL~i~~~----------~~~~R~DG~-----------~~~~~~V~~~lVgDeTG~I~lt 91 (159)
....+|.+|.++...++++|.|+.+... +...+.+|. ......+.++.|.|.||.+.++
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 3458899999998889999999998751 111111110 1123456779999999999999
Q ss_pred EecCCcCC
Q 031443 92 ARNDQVDL 99 (159)
Q Consensus 92 lWde~~~~ 99 (159)
||++++..
T Consensus 262 ~f~e~ae~ 269 (355)
T PRK08402 262 LFGDDAAE 269 (355)
T ss_pred EecHHHHH
Confidence 99987744
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=92.13 E-value=0.62 Score=31.91 Aligned_cols=49 Identities=20% Similarity=0.232 Sum_probs=37.8
Q ss_pred EEEEEeeCceeEEEEEecCCc----CCCCCCCEEEEeceEEceeCCeEEEEeCC
Q 031443 77 AECLVGDDTGTILFTARNDQV----DLMKPGTTVILRNAKIDMFKGSMRIAVDK 126 (159)
Q Consensus 77 ~~~lVgDeTG~I~ltlWde~~----~~i~~Gdvv~I~na~v~~~~G~~~L~vgk 126 (159)
...-+-|+++.|++.+|.... ..+++||-|.+.+... ..+|.++|.+.+
T Consensus 17 vyfsLkD~~a~i~cv~f~~~~~~~~~~l~~Gd~V~v~G~v~-~~~G~~ql~v~~ 69 (73)
T cd04487 17 TIFTLRDETGTVWAAAFEEAGVRAYPEVEVGDIVRVTGEVE-PRDGQLQIEVES 69 (73)
T ss_pred EEEEEEcCCEEEEEEEEchhccCCcCCCCCCCEEEEEEEEe-cCCeEEEEEEee
Confidence 345568999999999997422 3469999999999865 478888887754
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=91.14 E-value=1.8 Score=29.95 Aligned_cols=54 Identities=15% Similarity=0.116 Sum_probs=40.4
Q ss_pred ceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecCCcC------CCCCCCEEEEeceEE
Q 031443 48 HNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARNDQVD------LMKPGTTVILRNAKI 113 (159)
Q Consensus 48 vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde~~~------~i~~Gdvv~I~na~v 113 (159)
+.+-+.|.++. .+ ++ | .. -+.+-|.||++.+.+|.+..+ .+.+|.+|.|.+-.-
T Consensus 2 v~i~GiI~~v~--~T-K~--g-----~~--~~~leD~~G~~Ev~~F~~~~~~~~~~~~l~~d~~v~v~g~v~ 61 (79)
T cd04490 2 VSIIGMVNDVR--ST-KN--G-----HR--IVELEDTTGRITVLLTKDKEELFEEAEDILPDEVIGVSGTVS 61 (79)
T ss_pred EEEEEEEeEEE--Ec-CC--C-----CE--EEEEECCCCEEEEEEeCchhhhhhhhhhccCCCEEEEEEEEe
Confidence 45677787777 22 21 2 12 889999999999999986544 689999999998773
No 45
>PRK05673 dnaE DNA polymerase III subunit alpha; Validated
Probab=90.53 E-value=0.6 Score=46.95 Aligned_cols=84 Identities=18% Similarity=0.266 Sum_probs=62.4
Q ss_pred eecccCCC--CCCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecCC----cCCCCCCCEEEEe
Q 031443 36 TKVDQLKP--GTNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARNDQ----VDLMKPGTTVILR 109 (159)
Q Consensus 36 ~kI~dL~P--~~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde~----~~~i~~Gdvv~I~ 109 (159)
.++.+|.. ....+.+.+.|.++....+++ | ..++-+.+.|.||.+.+++|.+. ...+.+|.+|.|.
T Consensus 966 ~~~~~l~~~~~g~~V~v~G~I~~vk~~~TKk---G-----~~mafltLeD~TG~iEvviFp~~ye~~~~~L~~g~iV~V~ 1037 (1135)
T PRK05673 966 TRLADLEPTEGGSVVTVAGLVVSVRRRVTKR---G-----NKMAIVTLEDLSGRIEVMLFSEALEKYRDLLEEDRIVVVK 1037 (1135)
T ss_pred cCHHHHhccccCceEEEEEEEEEEEecccCC---C-----CeEEEEEEEeCCCcEEEEECHHHHHHHHHHhccCCEEEEE
Confidence 35666642 344578888888888765432 3 46999999999999999999743 3558999999998
Q ss_pred ceEEceeCCeEEEEeCCce
Q 031443 110 NAKIDMFKGSMRIAVDKWG 128 (159)
Q Consensus 110 na~v~~~~G~~~L~vgk~g 128 (159)
+-.. .+++.++|.+.+--
T Consensus 1038 GkVe-~~~~~~qlii~~I~ 1055 (1135)
T PRK05673 1038 GQVS-FDDGGLRLTAREVM 1055 (1135)
T ss_pred EEEE-ecCCeEEEEEeecc
Confidence 8664 45688888887633
No 46
>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=90.35 E-value=3.4 Score=33.06 Aligned_cols=92 Identities=16% Similarity=0.159 Sum_probs=57.8
Q ss_pred EEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecC-CcCCCCCCCEEEEeceEEceeCCeEEEEeCCce
Q 031443 50 LTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARND-QVDLMKPGTTVILRNAKIDMFKGSMRIAVDKWG 128 (159)
Q Consensus 50 v~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde-~~~~i~~Gdvv~I~na~v~~~~G~~~L~vgk~g 128 (159)
+.+.||...+|-++.- +..+..+|..+.||-||--.++-+.|- +-+.+-+..+|.|.|-+ ..+|.|+++ +.+
T Consensus 5 ~~VmVLkaTepF~Ye~---~e~gkk~MFHATVATet~fF~VKVfn~~LKeKF~~kkiI~IS~Y~--~~~gfLEi~--~aS 77 (170)
T PF02760_consen 5 KTVMVLKATEPFEYES---PEEGKKKMFHATVATETEFFRVKVFNINLKEKFIPKKIIAISDYF--GRNGFLEIN--EAS 77 (170)
T ss_dssp EEEEEEEE---EEEEC---TTTCEEEEEEEEEE-SS-EEEEEES-GGGCCTCSTTSEEEEESEE--EETTEEEE---TTS
T ss_pred eEEEEEeccCCeEEeC---cccCcceEEEEEEeccccEEEEEEecchhHhhcCCCcEEEEehhh--cccceEEEe--ecc
Confidence 6789999888765432 223458999999999999999999995 44668999999999987 458987765 567
Q ss_pred eEEEcC-CCcEEE--------ccCCCccc
Q 031443 129 RIEATE-PAKFVV--------KEDNNLSL 148 (159)
Q Consensus 129 ~I~~~~-~~~~~v--------ne~~N~S~ 148 (159)
.+..++ +-.++| +++|+|+.
T Consensus 78 sVse~~~dq~~eVp~~ii~~A~~TpKI~~ 106 (170)
T PF02760_consen 78 SVSEVNPDQKMEVPNSIIRRANETPKIND 106 (170)
T ss_dssp EEEE--TTC-----HHHHHHHCS---HHH
T ss_pred EEEecCCCceEEccHHHHHhhccCCchhH
Confidence 777775 344443 45555554
No 47
>PRK07373 DNA polymerase III subunit alpha; Reviewed
Probab=90.22 E-value=0.74 Score=41.86 Aligned_cols=82 Identities=11% Similarity=0.120 Sum_probs=59.7
Q ss_pred eecccCC--CCCCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecC----CcCCCCCCCEEEEe
Q 031443 36 TKVDQLK--PGTNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARND----QVDLMKPGTTVILR 109 (159)
Q Consensus 36 ~kI~dL~--P~~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde----~~~~i~~Gdvv~I~ 109 (159)
.++.+|. ++...+.+-+.|.++....+++ | ..|+-+.+-|+||.+-+++|-+ ....+++|.+|.|.
T Consensus 269 ~~~~~l~~~~~~~~v~vaG~I~~ik~~~TKk---G-----~~maf~~leD~tG~ie~vvFp~~y~~~~~~l~~~~~v~v~ 340 (449)
T PRK07373 269 INLSELEEQKEKTKVSAVVMLNEVKKIVTKK---G-----DPMAFLQLEDLSGQSEAVVFPKSYERISELLQVDARLIIW 340 (449)
T ss_pred cCHHHHhcccCCCEEEEEEEEEEeEecccCC---C-----CEEEEEEEEECCCCEEEEECHHHHHHHHHHhccCCEEEEE
Confidence 3556664 2334578888898888765532 3 4699999999999999999964 23558999999998
Q ss_pred ceEEceeCCeEEEEeCC
Q 031443 110 NAKIDMFKGSMRIAVDK 126 (159)
Q Consensus 110 na~v~~~~G~~~L~vgk 126 (159)
+-.-. ..+.++|.+.+
T Consensus 341 G~v~~-~~~~~~liv~~ 356 (449)
T PRK07373 341 GKVDR-RDDQVQLIVED 356 (449)
T ss_pred EEEEe-cCCeEEEEEeE
Confidence 87643 34667887765
No 48
>PRK05159 aspC aspartyl-tRNA synthetase; Provisional
Probab=90.08 E-value=2 Score=38.62 Aligned_cols=87 Identities=16% Similarity=0.168 Sum_probs=63.2
Q ss_pred eeecccCCCCC--CCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecC-------CcCCCCCCCE
Q 031443 35 FTKVDQLKPGT--NGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARND-------QVDLMKPGTT 105 (159)
Q Consensus 35 ~~kI~dL~P~~--~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde-------~~~~i~~Gdv 105 (159)
.+.|+||.+.. +.|.|.+.|.++-. .+.++=+.|-|.+|.|.+++=.. .+..+..||+
T Consensus 4 ~~~~~~l~~~~~g~~V~i~GrV~~~R~-------------~gk~~Fl~LrD~~g~iQ~v~~~~~~~~~~~~~~~L~~gs~ 70 (437)
T PRK05159 4 RHLTSELTPELDGEEVTLAGWVHEIRD-------------LGGIAFLILRDRSGIIQVVVKKKVDEELFETIKKLKRESV 70 (437)
T ss_pred eeEhhhCChhhCCCEEEEEEEeEeeec-------------CCCeEEEEEEcCCcEEEEEEeCCccHHHHHHHhCCCCCcE
Confidence 35688888765 44778888876532 14577788999999999977432 2356899999
Q ss_pred EEEeceEEceeC--CeEEEEeCCceeEEEcC
Q 031443 106 VILRNAKIDMFK--GSMRIAVDKWGRIEATE 134 (159)
Q Consensus 106 v~I~na~v~~~~--G~~~L~vgk~g~I~~~~ 134 (159)
|.|.|-....-+ |.++|.+.+.--+.+..
T Consensus 71 V~v~G~v~~~~~~~~~~el~~~~i~vls~a~ 101 (437)
T PRK05159 71 VSVTGTVKANPKAPGGVEVIPEEIEVLNKAE 101 (437)
T ss_pred EEEEEEEEcCCCCCCCEEEEEeEEEEEeCCC
Confidence 999997776544 78999998766555553
No 49
>COG5235 RFA2 Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [DNA replication, recombination, and repair]
Probab=88.71 E-value=3.2 Score=34.77 Aligned_cols=54 Identities=22% Similarity=0.273 Sum_probs=40.1
Q ss_pred EEEEeeCceeEEEEEecC------CcCCCCCCCEEEEeceEEceeCCeEEEEeCCceeEEEcCC
Q 031443 78 ECLVGDDTGTILFTARND------QVDLMKPGTTVILRNAKIDMFKGSMRIAVDKWGRIEATEP 135 (159)
Q Consensus 78 ~~lVgDeTG~I~ltlWde------~~~~i~~Gdvv~I~na~v~~~~G~~~L~vgk~g~I~~~~~ 135 (159)
-.+|.|.||.|-++.|.. ++...++|.-|++.++. +.|.|+..+... -|..+++
T Consensus 86 ~~~iEDGTG~Ievr~W~~~~~~~e~~~d~~~~~yvkV~G~l-k~F~GK~~I~~~---~i~~I~d 145 (258)
T COG5235 86 MFVIEDGTGSIEVRFWPGNSYEEEQCKDLEEQNYVKVNGSL-KTFNGKRSISAS---HISAIED 145 (258)
T ss_pred EEEEecCCceEEEEecCCCchHHHhccccccccEEEEecce-eeeCCeeEEehh---heeeccc
Confidence 367899999999999963 33446788888887665 899998888543 3555543
No 50
>PLN02850 aspartate-tRNA ligase
Probab=88.31 E-value=4.1 Score=37.84 Aligned_cols=96 Identities=13% Similarity=0.019 Sum_probs=67.1
Q ss_pred CceeecccCCCCC--CCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecCC----------cCCC
Q 031443 33 PVFTKVDQLKPGT--NGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARNDQ----------VDLM 100 (159)
Q Consensus 33 ~~~~kI~dL~P~~--~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde~----------~~~i 100 (159)
..+++|.+|.+.. +.|.|.++|-.+-. .+.++=+.|-|.+|+|..++-... +..+
T Consensus 67 ~~~~~i~~l~~~~~g~~V~v~Grv~~~R~-------------~gk~~Fl~Lrd~~~~iQ~v~~~~~~~~~~~~~~~~~~l 133 (530)
T PLN02850 67 REWTDVSDLGEELAGSEVLIRGRVHTIRG-------------KGKSAFLVLRQSGFTVQCVVFVSEVTVSKGMVKYAKQL 133 (530)
T ss_pred ceEeEhhhcchhhCCCEEEEEEEEEEEcc-------------CCCeEEEEEEeCCcCEEEEEECCccccCHHHHHHHhCC
Confidence 5689999998754 34777888866433 144777889999999998775422 2458
Q ss_pred CCCCEEEEeceEEc------eeCCeEEEEeCCceeEEEc-CCCcEEEc
Q 031443 101 KPGTTVILRNAKID------MFKGSMRIAVDKWGRIEAT-EPAKFVVK 141 (159)
Q Consensus 101 ~~Gdvv~I~na~v~------~~~G~~~L~vgk~g~I~~~-~~~~~~vn 141 (159)
..|++|.|.+-... --.+.++|.+.+.--|.+. .+..+.++
T Consensus 134 ~~es~V~V~G~v~~~~~~~~~~t~~~El~~~~i~vls~a~~~lP~~~~ 181 (530)
T PLN02850 134 SRESVVDVEGVVSVPKKPVKGTTQQVEIQVRKIYCVSKALATLPFNVE 181 (530)
T ss_pred CCCCEEEEEEEEEccCcCCCCCCccEEEEEeEEEEEeCCCCCCCCChh
Confidence 99999999997762 1234699999887666555 23445444
No 51
>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=88.27 E-value=1.8 Score=30.61 Aligned_cols=57 Identities=23% Similarity=0.302 Sum_probs=42.6
Q ss_pred EEEEeeCce-eEEEEEecCCc----CCCCCCCEEEEeceEEceeCCeE-------EEEeCCceeEEEcC
Q 031443 78 ECLVGDDTG-TILFTARNDQV----DLMKPGTTVILRNAKIDMFKGSM-------RIAVDKWGRIEATE 134 (159)
Q Consensus 78 ~~lVgDeTG-~I~ltlWde~~----~~i~~Gdvv~I~na~v~~~~G~~-------~L~vgk~g~I~~~~ 134 (159)
++++.|+.| .|..+.+.+.+ ..+++|.++.|.|-.+....|.. .|....++.|..++
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 478899988 47777776544 55899999999999987766644 46666667777665
No 52
>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=87.60 E-value=7.3 Score=27.94 Aligned_cols=75 Identities=12% Similarity=0.111 Sum_probs=50.8
Q ss_pred CCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecCC--------cCCCCCCCEEEEeceEEceeC
Q 031443 46 NGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARNDQ--------VDLMKPGTTVILRNAKIDMFK 117 (159)
Q Consensus 46 ~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde~--------~~~i~~Gdvv~I~na~v~~~~ 117 (159)
..|.+.+.|-.+-.. +.++=+.|-|.+|.+...+=.+. +..+..|++|.+.+...+.-+
T Consensus 13 ~~V~v~Gwv~~~R~~-------------g~~~Fi~LrD~~g~iQ~v~~~~~~~~~~~~~~~~l~~es~V~V~G~v~~~~~ 79 (108)
T cd04316 13 EEVTVAGWVHEIRDL-------------GGIKFVILRDREGIVQVTAPKKKVDKELFKTVRKLSRESVISVTGTVKAEPK 79 (108)
T ss_pred CEEEEEEEEEeeecc-------------CCeEEEEEecCCeeEEEEEeCCCCCHHHHHHHhCCCCcCEEEEEEEEEeCCC
Confidence 347788888664321 34677888999999888654331 235789999999998776433
Q ss_pred --CeEEEEeCCceeEEEc
Q 031443 118 --GSMRIAVDKWGRIEAT 133 (159)
Q Consensus 118 --G~~~L~vgk~g~I~~~ 133 (159)
+.++|.+...--+.+.
T Consensus 80 ~~~~~Ei~~~~i~il~~~ 97 (108)
T cd04316 80 APNGVEIIPEEIEVLSEA 97 (108)
T ss_pred CCCCEEEEEeEEEEEeCC
Confidence 4688888775444444
No 53
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=86.75 E-value=4.7 Score=38.68 Aligned_cols=78 Identities=22% Similarity=0.330 Sum_probs=58.8
Q ss_pred eeecccCCCCCCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecCC---cCCCCCCCEEEEece
Q 031443 35 FTKVDQLKPGTNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARNDQ---VDLMKPGTTVILRNA 111 (159)
Q Consensus 35 ~~kI~dL~P~~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde~---~~~i~~Gdvv~I~na 111 (159)
...|.++.+|.. +.+.+.|.+..... + +......+.+.|.||.+.+++++.. ...+++|..+.+.+-
T Consensus 51 ~~~i~~~~~g~~-vti~g~V~~~~~~~-~--------~~~~~l~v~~~d~~~~l~l~fFn~~~~l~~~~~~G~~v~v~Gk 120 (677)
T COG1200 51 LPGIAEARPGEI-VTIEGTVLSHEKFP-F--------GKRKLLKVTLSDGTGVLTLVFFNFPAYLKKKLKVGERVIVYGK 120 (677)
T ss_pred cCChhhcCCCce-EEEEEEEEeeeccC-C--------CCCceEEEEEecCcEEEEEEEECccHHHHhhCCCCCEEEEEEE
Confidence 345777777666 78999999877643 2 2267889999999999999999854 256899999998765
Q ss_pred EEceeCCeEEEE
Q 031443 112 KIDMFKGSMRIA 123 (159)
Q Consensus 112 ~v~~~~G~~~L~ 123 (159)
. +.|++.+++.
T Consensus 121 ~-~~~~~~~~~~ 131 (677)
T COG1200 121 V-KRFKGGLQIT 131 (677)
T ss_pred E-eeccCceEEE
Confidence 4 5577766654
No 54
>PF11325 DUF3127: Domain of unknown function (DUF3127); InterPro: IPR021474 This bacterial family of proteins has no known function.
Probab=86.56 E-value=6.5 Score=28.01 Aligned_cols=69 Identities=17% Similarity=0.247 Sum_probs=44.1
Q ss_pred EEEEEEecCcccc-cccCCCCCCCcceEEEEEEeeCc---eeEEEEEecCCcC---CCCCCCEEEEe-ceEEceeCCeEE
Q 031443 50 LTVNVLKSEPVLP-KNRAASPQLRQTRIAECLVGDDT---GTILFTARNDQVD---LMKPGTTVILR-NAKIDMFKGSMR 121 (159)
Q Consensus 50 v~~kVL~i~~~~~-~~R~DG~~~~~~~V~~~lVgDeT---G~I~ltlWde~~~---~i~~Gdvv~I~-na~v~~~~G~~~ 121 (159)
++++|+.+-+..+ +.+ .| =+-++.+|--+. -.|.|.+|.+.++ .+.+||.|.+. |-..++|+|+--
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 ITGKIIKVLPEQQGVSK-NG-----WKKREFVLETEEQYPQKICFEFWGDKIDLLDNFQVGDEVKVSFNIEGREWNGRWF 75 (84)
T ss_pred cccEEEEEecCcccCcC-CC-----cEEEEEEEeCCCcCCceEEEEEEcchhhhhccCCCCCEEEEEEEeeccEecceEe
Confidence 6778766654432 221 11 344666665332 4799999987554 47999999997 666778887554
Q ss_pred EEe
Q 031443 122 IAV 124 (159)
Q Consensus 122 L~v 124 (159)
-++
T Consensus 76 n~i 78 (84)
T PF11325_consen 76 NSI 78 (84)
T ss_pred eEe
Confidence 443
No 55
>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=86.52 E-value=11 Score=27.98 Aligned_cols=83 Identities=7% Similarity=0.085 Sum_probs=56.8
Q ss_pred CceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecC------CcCCCCCCCEEEEeceEEce-----
Q 031443 47 GHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARND------QVDLMKPGTTVILRNAKIDM----- 115 (159)
Q Consensus 47 ~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde------~~~~i~~Gdvv~I~na~v~~----- 115 (159)
.|.+.|.|-.+-.. +.++=+.|-|.+|.+.+.+=.. .+..+..|++|.+.+-...-
T Consensus 16 ~V~i~Gwv~~~R~~-------------gk~~Fi~LrD~~g~~Q~v~~~~~~~~~~~~~~l~~gs~V~V~G~~~~~~~~~~ 82 (135)
T cd04317 16 EVTLCGWVQRRRDH-------------GGLIFIDLRDRYGIVQVVFDPEEAPEFELAEKLRNESVIQVTGKVRARPEGTV 82 (135)
T ss_pred EEEEEEeEehhccc-------------CCEEEEEEecCCeeEEEEEeCCchhHHHHHhCCCCccEEEEEEEEECCCcccc
Confidence 47788888654331 3477788899999988866432 22358999999999977752
Q ss_pred ----eCCeEEEEeCCceeEEEcCCCcEEEcc
Q 031443 116 ----FKGSMRIAVDKWGRIEATEPAKFVVKE 142 (159)
Q Consensus 116 ----~~G~~~L~vgk~g~I~~~~~~~~~vne 142 (159)
-.|.++|.+...--+.+.++.++.++.
T Consensus 83 ~~~~~~~~~El~~~~i~vl~~~~~lP~~~~~ 113 (135)
T cd04317 83 NPKLPTGEIEVVASELEVLNKAKTLPFEIDD 113 (135)
T ss_pred CCCCCCCcEEEEEeEEEEEECCCCCCCcccc
Confidence 246799998887656555555555544
No 56
>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=85.73 E-value=11 Score=26.99 Aligned_cols=59 Identities=15% Similarity=0.289 Sum_probs=43.7
Q ss_pred ceEEEEEEeeCceeEEEEEecCC--------c-CCCCCCCEEEEeceEEceeCCeEEEEeCCceeEEE
Q 031443 74 TRIAECLVGDDTGTILFTARNDQ--------V-DLMKPGTTVILRNAKIDMFKGSMRIAVDKWGRIEA 132 (159)
Q Consensus 74 ~~V~~~lVgDeTG~I~ltlWde~--------~-~~i~~Gdvv~I~na~v~~~~G~~~L~vgk~g~I~~ 132 (159)
+.++=+.+-|.||.+.+.+=... . ..+..||+|.+.+-....-+|.++|.+.+.--+.+
T Consensus 15 g~~~Fi~lrd~~~~lQ~v~~~~~~~~~~~~~~~~~l~~g~~V~v~G~v~~~~~g~~El~~~~~~ils~ 82 (108)
T cd04322 15 GKLSFADLQDESGKIQVYVNKDDLGEEEFEDFKKLLDLGDIIGVTGTPFKTKTGELSIFVKEFTLLSK 82 (108)
T ss_pred CCeEEEEEEECCeEEEEEEECCCCCHHHHHHHHhcCCCCCEEEEEEEEEecCCCCEEEEeCEeEEeec
Confidence 44777889999999998663221 1 12889999999998887777889998877544443
No 57
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=85.47 E-value=4.3 Score=42.08 Aligned_cols=86 Identities=17% Similarity=0.185 Sum_probs=66.7
Q ss_pred CceeecccCCCCCCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecCC------cCCCCCCCEE
Q 031443 33 PVFTKVDQLKPGTNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARNDQ------VDLMKPGTTV 106 (159)
Q Consensus 33 ~~~~kI~dL~P~~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde~------~~~i~~Gdvv 106 (159)
..+++|++|.....+|.|.+.|..+..... + .| ..+...-|.|-|++|.+..|... .+.++.|+.|
T Consensus 224 ~~~~~~~~i~~~~~~v~i~G~if~~e~~~~-k--~~-----~~~~~~~~td~~~s~~~k~f~~~~~~~~~~~~~~~g~~v 295 (1437)
T PRK00448 224 EEITPMKEINEEERRVVVEGYVFKVEIKEL-K--SG-----RHILTFKITDYTSSIIVKKFSRDKEDLKKFDEIKKGDWV 295 (1437)
T ss_pred cCcccHHHhhccCCeEEEEEEEEEEEEEec-c--CC-----CEEEEEEEEcCCCCEEEEEEecCcchhHHHhcCCCCCEE
Confidence 367889999999999999999999876322 1 12 56888999999999999999621 2558999999
Q ss_pred EEeceEE-ceeCCeEEEEeCC
Q 031443 107 ILRNAKI-DMFKGSMRIAVDK 126 (159)
Q Consensus 107 ~I~na~v-~~~~G~~~L~vgk 126 (159)
++++-.. .-|.+.+.+.+..
T Consensus 296 ~~~g~~~~d~~~~~~~~~~~~ 316 (1437)
T PRK00448 296 KVRGSVQNDTFTRDLVMNAQD 316 (1437)
T ss_pred EEEEEEeccCCCCceEEEeee
Confidence 9998764 3466777777655
No 58
>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=84.98 E-value=2.6 Score=35.80 Aligned_cols=49 Identities=12% Similarity=0.104 Sum_probs=40.8
Q ss_pred eeEEEEEecCC---cCCCCCCCEEEEeceEEceeCC-----eEEEEeCCceeEEEcC
Q 031443 86 GTILFTARNDQ---VDLMKPGTTVILRNAKIDMFKG-----SMRIAVDKWGRIEATE 134 (159)
Q Consensus 86 G~I~ltlWde~---~~~i~~Gdvv~I~na~v~~~~G-----~~~L~vgk~g~I~~~~ 134 (159)
....||+|+.. ...+.+|..++|.|-.++-.++ .+.|..++.++-.+++
T Consensus 180 ~~~~LTIWrPtedl~s~L~EG~ry~i~~L~~s~~k~~~~~~~vqLtatk~Tr~~~l~ 236 (251)
T cd04494 180 KSGLLSIWRPTEDLRSLLTEGKRYRIYGLATSNSKKRSGNEEVQLTATKKTRYQPLP 236 (251)
T ss_pred ceEEEEEeCCCHHHHhhhcCCcEEEEEeccccCCCCCCCcceEEEEecCcccceECC
Confidence 57789999853 3468999999999998877554 8999999999988886
No 59
>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=84.85 E-value=4.7 Score=34.10 Aligned_cols=71 Identities=11% Similarity=0.111 Sum_probs=49.3
Q ss_pred CCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCce--eEEEEEecCC-------cCCCCCCCEEEEeceEEcee
Q 031443 46 NGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTG--TILFTARNDQ-------VDLMKPGTTVILRNAKIDMF 116 (159)
Q Consensus 46 ~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG--~I~ltlWde~-------~~~i~~Gdvv~I~na~v~~~ 116 (159)
+.|.|.|+|+.+.... +.+ ....-..|-|.|| .|...+|.+. ...+ .|++|.|.|...
T Consensus 67 ~~v~i~G~Vv~~~~~~-~~~--------~~~~~l~iDD~Sg~~~i~~~~~~~~~~~~~l~~~~~-~G~~V~VkG~vs--- 133 (256)
T PF10451_consen 67 RWVRIVGVVVGIDYKW-IEN--------EDRIILTIDDSSGANTIECKCSKSSYLSMGLPINDL-IGKVVEVKGTVS--- 133 (256)
T ss_dssp -EEEEEEEEEEEEEEE--BB--------TCEEEEEEE-SSCS-EEEEEEEHHHHHCCCHHCTT--TT-EEEEEEEEE---
T ss_pred EEEEEEEEEEEEEEEe-ecc--------cceEEEEEeCCCCceeEEEEEEcccccccCCCccCC-CCcEEEEEEEEc---
Confidence 4578999999986431 111 2356677999999 8999999641 2334 999999999987
Q ss_pred CCeEEEEeCCcee
Q 031443 117 KGSMRIAVDKWGR 129 (159)
Q Consensus 117 ~G~~~L~vgk~g~ 129 (159)
++..+|.+.+.+.
T Consensus 134 r~~~ql~ve~i~~ 146 (256)
T PF10451_consen 134 RNERQLDVERIEL 146 (256)
T ss_dssp SSSEEEEEEEEEE
T ss_pred cCcEEEEEEEEEc
Confidence 8888888877553
No 60
>cd04482 RPA2_OBF_like RPA2_OBF_like: A subgroup of uncharacterized archaeal OB folds with similarity to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle depende
Probab=84.28 E-value=9.8 Score=26.88 Aligned_cols=45 Identities=22% Similarity=0.242 Sum_probs=33.0
Q ss_pred EEEEeeCceeEEEEEecCC--c----CCCCCCCEEEEeceEEceeCCeEEEEeCC
Q 031443 78 ECLVGDDTGTILFTARNDQ--V----DLMKPGTTVILRNAKIDMFKGSMRIAVDK 126 (159)
Q Consensus 78 ~~lVgDeTG~I~ltlWde~--~----~~i~~Gdvv~I~na~v~~~~G~~~L~vgk 126 (159)
-.-+-|+++.|++.+|.+. . ..+++||.|.+.+... .+. +|++.+
T Consensus 20 yFtlkD~~~~i~cv~f~~~g~~~~~~~~l~~Gd~V~v~G~v~-~y~---ql~ve~ 70 (91)
T cd04482 20 FFKISDGTGEIDCAAYEPTKEFRDVVRLLIPGDEVTVYGSVR-PGT---TLNLEK 70 (91)
T ss_pred EEEEECCCcEEEEEEECcccccccccCCCCCCCEEEEEEEEe-cCC---EEEEEE
Confidence 3456899999999999754 2 3369999999999864 333 566555
No 61
>PTZ00401 aspartyl-tRNA synthetase; Provisional
Probab=84.28 E-value=18 Score=33.91 Aligned_cols=97 Identities=12% Similarity=0.173 Sum_probs=67.8
Q ss_pred CceeecccCCCCC---CCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEe--cCC-------cCCC
Q 031443 33 PVFTKVDQLKPGT---NGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTAR--NDQ-------VDLM 100 (159)
Q Consensus 33 ~~~~kI~dL~P~~---~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlW--de~-------~~~i 100 (159)
..+++|++|.+.. +.|.|.+.|-.+-. .+.++=+.|-|.+|.|..++= ++. +..|
T Consensus 63 ~~~~~i~~l~~~~~~g~~V~v~Grv~~~R~-------------~Gk~~Fl~LRd~~~~iQ~v~~~~~~~~~~~~~~~~~l 129 (550)
T PTZ00401 63 RTFIPVAVLSKPELVDKTVLIRARVSTTRK-------------KGKMAFMVLRDGSDSVQAMAAVEGDVPKEMIDFIGQI 129 (550)
T ss_pred CceEEHHHCCccccCCCEEEEEEEEEEEec-------------CCCeEEEEEEeCCcCEEEEEECCCccCHHHHHHHhcC
Confidence 5689999998654 44778888866433 145677889999999998773 211 2357
Q ss_pred CCCCEEEEeceEEc-------eeCCeEEEEeCCceeEEEcC-CCcEEEcc
Q 031443 101 KPGTTVILRNAKID-------MFKGSMRIAVDKWGRIEATE-PAKFVVKE 142 (159)
Q Consensus 101 ~~Gdvv~I~na~v~-------~~~G~~~L~vgk~g~I~~~~-~~~~~vne 142 (159)
..|++|.|.+-... .-.+.++|.+.+.--|.+.. +.++.+.+
T Consensus 130 ~~esiV~V~G~v~~~~~~~~~~~~~~~El~v~~i~vls~a~~~lP~~~~d 179 (550)
T PTZ00401 130 PTESIVDVEATVCKVEQPITSTSHSDIELKVKKIHTVTESLRTLPFTLED 179 (550)
T ss_pred CCCCEEEEEEEEEecCccCCCCCCccEEEEeeEEEEEeCCCCCCCCCccc
Confidence 99999999997664 23577999999876665553 34454433
No 62
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain
Probab=83.95 E-value=13 Score=26.63 Aligned_cols=70 Identities=13% Similarity=0.100 Sum_probs=51.1
Q ss_pred CCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecCC---c--CCCCCCCEEEEeceEEcee-CC
Q 031443 45 TNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARNDQ---V--DLMKPGTTVILRNAKIDMF-KG 118 (159)
Q Consensus 45 ~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde~---~--~~i~~Gdvv~I~na~v~~~-~G 118 (159)
..++-|.+.|.++.... .--...-+-|+...|+.++|... + ..++.|+-|.+.+...-+- +|
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 57889999998877531 12366777889999999999732 2 3579999999987665432 57
Q ss_pred eEEEEeCC
Q 031443 119 SMRIAVDK 126 (159)
Q Consensus 119 ~~~L~vgk 126 (159)
.++|.+..
T Consensus 89 ~~sl~v~~ 96 (99)
T PF13742_consen 89 SLSLIVED 96 (99)
T ss_pred EEEEEEEE
Confidence 78887754
No 63
>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=83.95 E-value=13 Score=26.29 Aligned_cols=57 Identities=9% Similarity=0.018 Sum_probs=40.8
Q ss_pred eEEEEEEeeCceeEEEEEecCC----------cCCCCCCCEEEEeceEEceeC-------CeEEEEeCCceeEE
Q 031443 75 RIAECLVGDDTGTILFTARNDQ----------VDLMKPGTTVILRNAKIDMFK-------GSMRIAVDKWGRIE 131 (159)
Q Consensus 75 ~V~~~lVgDeTG~I~ltlWde~----------~~~i~~Gdvv~I~na~v~~~~-------G~~~L~vgk~g~I~ 131 (159)
.+.=+.|-|.+|.+...+=... +..+..|++|.+.+-..+.-+ +.++|.+.+.--+.
T Consensus 17 k~~Fi~LrD~sg~iQ~v~~~~~~~~~~~~~~~~~~l~~es~V~V~G~v~~~~~~~~~~~~~~~El~~~~i~il~ 90 (102)
T cd04320 17 KLAFLVLRQQGYTIQGVLAASAEGVSKQMVKWAGSLSKESIVDVEGTVKKPEEPIKSCTQQDVELHIEKIYVVS 90 (102)
T ss_pred ceEEEEEecCCceEEEEEeCCcccCCHHHHHHHhcCCCccEEEEEEEEECCCCcccCCCcCcEEEEEEEEEEEe
Confidence 5777888999999888875332 135789999999998776433 66888777644333
No 64
>PRK02983 lysS lysyl-tRNA synthetase; Provisional
Probab=82.59 E-value=7.8 Score=39.10 Aligned_cols=85 Identities=12% Similarity=0.121 Sum_probs=61.5
Q ss_pred eecccCCCC--CCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecCCc---------CCCCCCC
Q 031443 36 TKVDQLKPG--TNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARNDQV---------DLMKPGT 104 (159)
Q Consensus 36 ~kI~dL~P~--~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde~~---------~~i~~Gd 104 (159)
..++++... ...|.|.+.|..+-.. ++++=+.|-|.+|.|.+.+=.+.. ..+..||
T Consensus 640 ~~~~~~~~~~~~~~V~v~Grv~~~R~~-------------G~~~F~~lrD~~g~iQ~v~~~~~~~~~~~~~~~~~l~~gd 706 (1094)
T PRK02983 640 HTVAEALDAPTGEEVSVSGRVLRIRDY-------------GGVLFADLRDWSGELQVLLDASRLEQGSLADFRAAVDLGD 706 (1094)
T ss_pred cCHHHHHHhcCCCEEEEEEEEEEEeeC-------------CCeEEEEEEeCCeeEEEEEECCccchhhHHHHHhcCCCCC
Confidence 445565422 2237888888876431 458888999999999997754321 2378999
Q ss_pred EEEEeceEEceeCCeEEEEeCCceeEEEc
Q 031443 105 TVILRNAKIDMFKGSMRIAVDKWGRIEAT 133 (159)
Q Consensus 105 vv~I~na~v~~~~G~~~L~vgk~g~I~~~ 133 (159)
+|.+.+-..+...|.++|.+.++--+.+.
T Consensus 707 ~V~v~G~v~~t~~ge~ei~~~~i~ll~k~ 735 (1094)
T PRK02983 707 LVEVTGTMGTSRNGTLSLLVTSWRLAGKC 735 (1094)
T ss_pred EEEEEEEEEEcCCCCEEEEEeEEEEEecc
Confidence 99999999888889999998886555433
No 65
>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=82.56 E-value=0.59 Score=35.41 Aligned_cols=24 Identities=21% Similarity=0.253 Sum_probs=21.0
Q ss_pred ceEEEEEEeeCceeEEEEEecCCc
Q 031443 74 TRIAECLVGDDTGTILFTARNDQV 97 (159)
Q Consensus 74 ~~V~~~lVgDeTG~I~ltlWde~~ 97 (159)
..+.++.|.|.||.+.+++|++.+
T Consensus 53 ry~l~~~i~D~tg~~~~~~F~~~a 76 (146)
T PF08646_consen 53 RYRLSLKISDGTGSIWVTLFDEEA 76 (146)
T ss_dssp EEEEEEEEEETTEEEEEEEEHHHH
T ss_pred EEEEEEEEEeCCCeEEEEEEhHHH
Confidence 456889999999999999999765
No 66
>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=82.40 E-value=12 Score=34.35 Aligned_cols=74 Identities=11% Similarity=0.204 Sum_probs=56.3
Q ss_pred CceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecCCc---------CCCCCCCEEEEeceEEceeC
Q 031443 47 GHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARNDQV---------DLMKPGTTVILRNAKIDMFK 117 (159)
Q Consensus 47 ~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde~~---------~~i~~Gdvv~I~na~v~~~~ 117 (159)
.|.|.++|.++-. .++++=+.|-|.+|.|.+.+=.... ..+..||+|.+.+-..+.-.
T Consensus 55 ~v~v~Grv~~~R~-------------~gk~~F~~l~D~~g~iQ~~~~~~~~~~~~~~~~~~~l~~gd~V~v~G~~~~t~~ 121 (496)
T TIGR00499 55 EVSIAGRIMARRS-------------MGKATFITLQDESGQIQLYVNKDDLPEDFYEFDEYLLDLGDIIGVTGYPFKTKT 121 (496)
T ss_pred EEEEEEEEEEEec-------------CCCeEEEEEEcCCccEEEEEECCcCcHHHHHHHHhcCCCCCEEEEEEEEEECCC
Confidence 3788888887542 1567889999999999987753221 13789999999998888778
Q ss_pred CeEEEEeCCceeEEEc
Q 031443 118 GSMRIAVDKWGRIEAT 133 (159)
Q Consensus 118 G~~~L~vgk~g~I~~~ 133 (159)
|.++|.+.+.--+.+.
T Consensus 122 gelel~~~~i~ilsk~ 137 (496)
T TIGR00499 122 GELSVHVTELQILTKA 137 (496)
T ss_pred CcEEEEeeEEEEEecC
Confidence 9999999887555544
No 67
>PRK00484 lysS lysyl-tRNA synthetase; Reviewed
Probab=81.23 E-value=16 Score=33.60 Aligned_cols=75 Identities=9% Similarity=0.145 Sum_probs=56.2
Q ss_pred CCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecCC--------cCCCCCCCEEEEeceEEceeC
Q 031443 46 NGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARNDQ--------VDLMKPGTTVILRNAKIDMFK 117 (159)
Q Consensus 46 ~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde~--------~~~i~~Gdvv~I~na~v~~~~ 117 (159)
..|.|.+.|.++-. .+.++=+.|-|.+|.|.+.+=.+. ...+..||+|.|.+-..+.-.
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 IEVSVAGRVMLKRV-------------MGKASFATLQDGSGRIQLYVSKDDVGEEALEAFKKLDLGDIIGVEGTLFKTKT 121 (491)
T ss_pred cEEEEEEEEEEEec-------------CCceEEEEEEcCCccEEEEEECCcCCHHHHHHHhcCCCCCEEEEEEEEEEcCC
Confidence 34778888877543 145788899999999998765332 124789999999998887778
Q ss_pred CeEEEEeCCceeEEEc
Q 031443 118 GSMRIAVDKWGRIEAT 133 (159)
Q Consensus 118 G~~~L~vgk~g~I~~~ 133 (159)
|.++|.+.+.--+.+.
T Consensus 122 ge~el~~~~~~vls~~ 137 (491)
T PRK00484 122 GELSVKATELTLLTKS 137 (491)
T ss_pred CcEEEEEeEEEEEecc
Confidence 9999999887555444
No 68
>KOG3108 consensus Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [Replication, recombination and repair]
Probab=80.51 E-value=8.8 Score=32.80 Aligned_cols=56 Identities=23% Similarity=0.218 Sum_probs=43.5
Q ss_pred EEEEEeeCceeEEEEEecCC--c----CCCCCCCEEEEeceEEceeCCeEEEEeCCceeEEEcCCC
Q 031443 77 AECLVGDDTGTILFTARNDQ--V----DLMKPGTTVILRNAKIDMFKGSMRIAVDKWGRIEATEPA 136 (159)
Q Consensus 77 ~~~lVgDeTG~I~ltlWde~--~----~~i~~Gdvv~I~na~v~~~~G~~~L~vgk~g~I~~~~~~ 136 (159)
....|.|.||.|-...|... . ..+++|.-|++.+.. +.|.|..+|.+-+ |.++.++
T Consensus 87 i~y~I~D~tg~id~r~W~~~~~~~~e~~~l~~~~yVkv~G~L-k~f~Gk~sl~~fk---I~pv~D~ 148 (265)
T KOG3108|consen 87 ITYEIEDGTGQIDVRQWFHDNAESEEMPALETGTYVKVYGHL-KPFQGKKSLQVFK---IRPVEDF 148 (265)
T ss_pred eEEEEecCcccEEEEEeccccchhhhCcccccCcEEEeeecc-cCCCCceeEEEEe---eeeeecC
Confidence 45679999999999999632 2 257899999998877 7899988887766 6666533
No 69
>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=80.33 E-value=7.8 Score=28.43 Aligned_cols=67 Identities=21% Similarity=0.242 Sum_probs=44.5
Q ss_pred CCCCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecC--CcCCCCCCCEEEEeceEEceeCCeE
Q 031443 43 PGTNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARND--QVDLMKPGTTVILRNAKIDMFKGSM 120 (159)
Q Consensus 43 P~~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde--~~~~i~~Gdvv~I~na~v~~~~G~~ 120 (159)
++...|.|++.|++.-.- -..++.|.||.|.+.+=++ ..-.+.+++.|+|.+-.-+.|+ ..
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 KDDTPVTLEGNIVKQLGD----------------DKYLFRDATGEIEVEIDDDVWRGQTVTPDDKVRISGEVDKDWN-KT 94 (103)
T ss_dssp -SSEEEEEEEEEEEEEET----------------TEEEEEETTEEEEEE--GGGSTT----TTSEEEEEEEEEEETT-EE
T ss_pred cCCCeEEEEEEEEEEecC----------------CEEEEECCCCcEEEEEChhhcCCcccCCCCEEEEEEEEeCCCC-ce
Confidence 445568999999873211 1368899999999987554 2234799999999998887775 47
Q ss_pred EEEeCC
Q 031443 121 RIAVDK 126 (159)
Q Consensus 121 ~L~vgk 126 (159)
+|.+.+
T Consensus 95 ~IdV~~ 100 (103)
T PF04076_consen 95 EIDVDR 100 (103)
T ss_dssp EEEEEE
T ss_pred EEEEEE
Confidence 776654
No 70
>PRK12445 lysyl-tRNA synthetase; Reviewed
Probab=80.15 E-value=8.5 Score=35.52 Aligned_cols=74 Identities=11% Similarity=0.123 Sum_probs=55.9
Q ss_pred CceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecCC---------cCCCCCCCEEEEeceEEceeC
Q 031443 47 GHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARNDQ---------VDLMKPGTTVILRNAKIDMFK 117 (159)
Q Consensus 47 ~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde~---------~~~i~~Gdvv~I~na~v~~~~ 117 (159)
.|.|.++|.++-.. |+++=+.|-|.+|.|.+.+-.+. ...+..||+|.+.+-..+.-.
T Consensus 67 ~v~v~Grv~~~R~~-------------Gk~~F~~lrD~~g~iQ~~~~~~~~~~~~~~~~~~~l~~Gd~V~v~G~~~~t~~ 133 (505)
T PRK12445 67 EVSVAGRMMTRRIM-------------GKASFVTLQDVGGRIQLYVARDSLPEGVYNDQFKKWDLGDIIGARGTLFKTQT 133 (505)
T ss_pred EEEEEEEEEEEecC-------------CCcEEEEEEeCCccEEEEEECCccchhhHHHHHhcCCCCCEEEEEEEEEecCC
Confidence 37888888775431 45777889999999988765321 234789999999998888778
Q ss_pred CeEEEEeCCceeEEEc
Q 031443 118 GSMRIAVDKWGRIEAT 133 (159)
Q Consensus 118 G~~~L~vgk~g~I~~~ 133 (159)
|.++|.+.+.--+.+.
T Consensus 134 gelel~~~~~~llsk~ 149 (505)
T PRK12445 134 GELSIHCTELRLLTKA 149 (505)
T ss_pred CcEEEEEeEEEEEecC
Confidence 9999999887555544
No 71
>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=80.05 E-value=7.3 Score=33.39 Aligned_cols=68 Identities=15% Similarity=0.277 Sum_probs=51.5
Q ss_pred ceEEEEEEeeCceeEEEEEecCCcCCCCCCCEEEEeceEEceeCCeEEEEeCCceeEEEcCCCcEEEccCCCccc
Q 031443 74 TRIAECLVGDDTGTILFTARNDQVDLMKPGTTVILRNAKIDMFKGSMRIAVDKWGRIEATEPAKFVVKEDNNLSL 148 (159)
Q Consensus 74 ~~V~~~lVgDeTG~I~ltlWde~~~~i~~Gdvv~I~na~v~~~~G~~~L~vgk~g~I~~~~~~~~~vne~~N~S~ 148 (159)
.-+...+.+|..|.| +++++.--.++.||.|++.+. +|..+||=++-=+|+..+++.|++.++..+|.
T Consensus 165 ~~~i~~I~~~~~g~V--~~~~~~~h~l~~gd~V~f~ev-----~gm~~lN~~~~~~v~~~~~~~f~i~d~~~~~~ 232 (286)
T cd01491 165 SGMISSISKDNPGVV--TCLDETRHGFEDGDYVTFSEV-----EGMTELNGCEPRKIKVKGPYTFSIGDTSSFSE 232 (286)
T ss_pred ccceeeeecCCceEE--EEECCcccCCcCCCEEEEecc-----CcchhhCCCccEEEEECCCCeEEECcCcCcCc
Confidence 345566677888886 456877677999999999753 56677765555678888899999988887776
No 72
>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=78.72 E-value=15 Score=32.94 Aligned_cols=83 Identities=19% Similarity=0.135 Sum_probs=56.3
Q ss_pred cccCCCCC--CCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecC--------CcCCCCCCCEEE
Q 031443 38 VDQLKPGT--NGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARND--------QVDLMKPGTTVI 107 (159)
Q Consensus 38 I~dL~P~~--~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde--------~~~~i~~Gdvv~ 107 (159)
+++|.+.. +.|.|.+.|-++-. .+.++=+.|-|.+|.|.+.+-.. .+..+..||+|.
T Consensus 3 ~~~l~~~~~g~~v~i~G~v~~~R~-------------~g~~~Fi~lrd~~g~iQ~v~~~~~~~~~~~~~~~~l~~~s~v~ 69 (428)
T TIGR00458 3 SADIKPEMDGQEVTFMGWVHEIRD-------------LGGLIFVLLRDREGLIQITAPAKKVSKNLFKWAKKLNLESVVA 69 (428)
T ss_pred hhhCchhhCCCEEEEEEEEEEEec-------------CCCcEEEEEEeCCeeEEEEEECCcCCHHHHHHHhCCCCCcEEE
Confidence 34555422 33677777766433 14477788999999999877532 123578999999
Q ss_pred EeceEEceeC--CeEEEEeCCceeEEEc
Q 031443 108 LRNAKIDMFK--GSMRIAVDKWGRIEAT 133 (159)
Q Consensus 108 I~na~v~~~~--G~~~L~vgk~g~I~~~ 133 (159)
|.|-....-+ |.++|.+.+.--+.+.
T Consensus 70 v~G~v~~~~~~~~~~el~~~~i~vl~~~ 97 (428)
T TIGR00458 70 VRGIVKIKEKAPGGFEIIPTKIEVINEA 97 (428)
T ss_pred EEEEEEecCCCCCcEEEEEeEEEEEecC
Confidence 9997765433 7899999886555544
No 73
>PRK07459 single-stranded DNA-binding protein; Provisional
Probab=78.29 E-value=6.1 Score=29.50 Aligned_cols=63 Identities=11% Similarity=0.073 Sum_probs=45.4
Q ss_pred CCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEe-------eCceeEEEEEecCCc----CCCCCCCEEEEeceEE
Q 031443 45 TNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVG-------DDTGTILFTARNDQV----DLMKPGTTVILRNAKI 113 (159)
Q Consensus 45 ~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVg-------DeTG~I~ltlWde~~----~~i~~Gdvv~I~na~v 113 (159)
++.+.|.+++-.-.+.+.+. .| ..++...|| ++|-=+++++|+.++ ..++.|+-|.|.+-..
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 34577888887755544332 33 457887777 568889999998654 4479999999998876
Q ss_pred c
Q 031443 114 D 114 (159)
Q Consensus 114 ~ 114 (159)
.
T Consensus 76 ~ 76 (121)
T PRK07459 76 F 76 (121)
T ss_pred e
Confidence 3
No 74
>PRK05733 single-stranded DNA-binding protein; Provisional
Probab=77.86 E-value=16 Score=29.09 Aligned_cols=84 Identities=14% Similarity=0.171 Sum_probs=53.4
Q ss_pred CCCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEee-------Cce-------eEEEEEecCCc----CCCCCCCE
Q 031443 44 GTNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGD-------DTG-------TILFTARNDQV----DLMKPGTT 105 (159)
Q Consensus 44 ~~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgD-------eTG-------~I~ltlWde~~----~~i~~Gdv 105 (159)
+++.+.|.++|-.-.+.+.+. +| ..|++..||= ++| -+++++|+..+ +.++.|+.
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 466778888888865554432 33 3466666652 234 38999998643 44799999
Q ss_pred EEEeceEEce-eC--C----eEEEEeCCceeEEEcC
Q 031443 106 VILRNAKIDM-FK--G----SMRIAVDKWGRIEATE 134 (159)
Q Consensus 106 v~I~na~v~~-~~--G----~~~L~vgk~g~I~~~~ 134 (159)
|.|.+-.... |. | .++|.++..|+|..++
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 9999866532 32 2 4556666555665553
No 75
>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=77.72 E-value=11 Score=29.13 Aligned_cols=98 Identities=13% Similarity=0.169 Sum_probs=64.7
Q ss_pred cccCCCCCCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEec-CCcCCCCCCCEEEEeceEEcee
Q 031443 38 VDQLKPGTNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARN-DQVDLMKPGTTVILRNAKIDMF 116 (159)
Q Consensus 38 I~dL~P~~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWd-e~~~~i~~Gdvv~I~na~v~~~ 116 (159)
|.+..-... +|.+.|..+.-+.. --+.+..+.|-|+||.+-+ -|+ .++..+..- .|.|-|+.-
T Consensus 21 is~~~~~~~--~L~f~vyr~~G~D~---------Ygsfl~~i~l~d~~g~vv~-~~~~~~L~~lP~~---~i~N~Yv~~- 84 (133)
T PF07680_consen 21 ISDALIENG--TLSFHVYRVEGPDV---------YGSFLIGIQLKDSTGHVVL-NWDQEKLSSLPKS---NIKNDYVAK- 84 (133)
T ss_pred EeeeEEeCC--eEEEEEEEcCCCcc---------CCceeeEEEEECCCCCEEE-EeCHHHhhhCChh---HcCccEEcc-
Confidence 555444333 36666665543332 2267899999999999955 687 344344433 356777643
Q ss_pred CCeEEEEeCCceeEEEcC-CCcEEEccCCCccccceeeeee
Q 031443 117 KGSMRIAVDKWGRIEATE-PAKFVVKEDNNLSLVEYELVNV 156 (159)
Q Consensus 117 ~G~~~L~vgk~g~I~~~~-~~~~~vne~~N~S~ieye~v~~ 156 (159)
+..|++|-+.+++ .+++.+...-+|+.-.|.++-.
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 3378888888887 5577777778899888888754
No 76
>PLN02502 lysyl-tRNA synthetase
Probab=77.37 E-value=11 Score=35.37 Aligned_cols=60 Identities=20% Similarity=0.242 Sum_probs=45.6
Q ss_pred ceEEEEEEeeCceeEEEEEecCCc-----------CCCCCCCEEEEeceEEceeCCeEEEEeCCceeEEEc
Q 031443 74 TRIAECLVGDDTGTILFTARNDQV-----------DLMKPGTTVILRNAKIDMFKGSMRIAVDKWGRIEAT 133 (159)
Q Consensus 74 ~~V~~~lVgDeTG~I~ltlWde~~-----------~~i~~Gdvv~I~na~v~~~~G~~~L~vgk~g~I~~~ 133 (159)
|+++=+.|-|.+|.|-+.+-.+.. ..+..||+|.|.+-..+.-.|.++|.+.+.--+.+.
T Consensus 124 Gk~~F~~LrD~~g~iQv~~~~~~~~~~~~~~~~~~~~l~~gdiV~V~G~~~~t~~gelel~~~~i~vLs~~ 194 (553)
T PLN02502 124 GKLAFYDLRDDGGKIQLYADKKRLDLDEEEFEKLHSLVDRGDIVGVTGTPGKTKKGELSIFPTSFEVLTKC 194 (553)
T ss_pred CCeEEEEEecCCccEEEEEECccccchhHHHHHHHhCCCCCcEEEEEEEEEecCCCCEEEEEeEEEEEecc
Confidence 457778889999999887643211 247899999999988887789999999886555444
No 77
>PRK07374 dnaE DNA polymerase III subunit alpha; Validated
Probab=77.25 E-value=5.6 Score=40.39 Aligned_cols=81 Identities=14% Similarity=0.151 Sum_probs=58.8
Q ss_pred ecccCC--CCCCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecC----CcCCCCCCCEEEEec
Q 031443 37 KVDQLK--PGTNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARND----QVDLMKPGTTVILRN 110 (159)
Q Consensus 37 kI~dL~--P~~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde----~~~~i~~Gdvv~I~n 110 (159)
++.+|. ++...+.+-+.|.++..+.+++ | ..|+-+.+-|+||.+.+++|-+ ....+.+|.+|.|.+
T Consensus 990 ~~~~l~~~~~~~~v~v~g~i~~~k~~~Tk~---G-----~~maf~~leD~tg~~e~vvFp~~y~~~~~~l~~~~~~~v~g 1061 (1170)
T PRK07374 990 SLSSLEEQPDKAKVSAIAMIPEMKQVTTRK---G-----DRMAILQLEDLTGSCEAVVFPKSYERLSDHLMTDTRLLVWA 1061 (1170)
T ss_pred CHHHHhcccCCCEEEEEEEEEEeEecccCC---C-----CEEEEEEEEECCCCEEEEECHHHHHHHHHHhccCCEEEEEE
Confidence 455654 2334578888898888766532 3 4699999999999999999964 234579999999987
Q ss_pred eEEceeCCeEEEEeCC
Q 031443 111 AKIDMFKGSMRIAVDK 126 (159)
Q Consensus 111 a~v~~~~G~~~L~vgk 126 (159)
-.-+ ..+.+.|.+.+
T Consensus 1062 ~v~~-~~~~~~~~~~~ 1076 (1170)
T PRK07374 1062 KVDR-RDDRVQLIIDD 1076 (1170)
T ss_pred EEEe-cCCeEEEEEee
Confidence 6643 34667777665
No 78
>PRK02801 primosomal replication protein N; Provisional
Probab=76.24 E-value=8.2 Score=27.85 Aligned_cols=63 Identities=11% Similarity=0.123 Sum_probs=46.2
Q ss_pred CCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEee-----Ccee-------EEEEEecCCcC----CCCCCCEEEE
Q 031443 45 TNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGD-----DTGT-------ILFTARNDQVD----LMKPGTTVIL 108 (159)
Q Consensus 45 ~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgD-----eTG~-------I~ltlWde~~~----~i~~Gdvv~I 108 (159)
|+.+.|.+++..-.+.+.++ .| ..+++..|+= ++|- |+.++|+..++ .+..|+.|.|
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 45688899998887776543 34 4577766654 3454 99999996543 4789999999
Q ss_pred eceEEc
Q 031443 109 RNAKID 114 (159)
Q Consensus 109 ~na~v~ 114 (159)
.+-...
T Consensus 75 ~G~L~~ 80 (101)
T PRK02801 75 QGFISC 80 (101)
T ss_pred EEEEEE
Confidence 998876
No 79
>PRK09010 single-stranded DNA-binding protein; Provisional
Probab=75.43 E-value=23 Score=28.40 Aligned_cols=83 Identities=13% Similarity=0.119 Sum_probs=50.8
Q ss_pred CCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEee--------------CceeEEEEEecCCc----CCCCCCCEE
Q 031443 45 TNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGD--------------DTGTILFTARNDQV----DLMKPGTTV 106 (159)
Q Consensus 45 ~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgD--------------eTG~I~ltlWde~~----~~i~~Gdvv 106 (159)
++.+.|.+++..-.+.+.+. .| ..|++..||= +|=-+++++|+..+ ..|+.|+-|
T Consensus 6 ~N~V~LiGrLg~DPelR~t~--nG-----~~v~~fsVAvn~~~kd~~~Ge~~e~t~w~~V~~fgk~Ae~~~~~L~KGs~V 78 (177)
T PRK09010 6 VNKVILVGNLGQDPEVRYMP--NG-----GAVANITLATSESWRDKQTGEMKEQTEWHRVVLFGKLAEVAGEYLRKGSQV 78 (177)
T ss_pred ceEEEEEEEeCCCceEEEcC--CC-----CEEEEEEEEEcCccccCcccccccceEEEEEEEehhHHHHHHHhcCCCCEE
Confidence 45567777777755544332 23 4566655552 13356999998654 447999999
Q ss_pred EEeceEEce-eC---C----eEEEEeCCceeEEEcC
Q 031443 107 ILRNAKIDM-FK---G----SMRIAVDKWGRIEATE 134 (159)
Q Consensus 107 ~I~na~v~~-~~---G----~~~L~vgk~g~I~~~~ 134 (159)
.|.+-.... |. | .++|.+...+.+..++
T Consensus 79 ~VeGrL~~~~yedkdG~~r~~~eVvv~~~~~~~~l~ 114 (177)
T PRK09010 79 YIEGQLRTRKWTDQSGQDRYTTEVVVNVGGTMQMLG 114 (177)
T ss_pred EEEEEEEeccccCCCCCEEEEEEEEEecCCcEEEcc
Confidence 999877643 53 2 4555555455565554
No 80
>PF15072 DUF4539: Domain of unknown function (DUF4539)
Probab=75.33 E-value=7.8 Score=27.59 Aligned_cols=51 Identities=22% Similarity=0.223 Sum_probs=38.9
Q ss_pred EEEEEeeCceeEEEEEecC----CcCCCCCCCEEEEeceEEce-eCCeEEEEeCCc
Q 031443 77 AECLVGDDTGTILFTARND----QVDLMKPGTTVILRNAKIDM-FKGSMRIAVDKW 127 (159)
Q Consensus 77 ~~~lVgDeTG~I~ltlWde----~~~~i~~Gdvv~I~na~v~~-~~G~~~L~vgk~ 127 (159)
+.+++.|.||.|.-++-.+ ..+.+.+|.++.+++..+-. ......|+|...
T Consensus 21 ~~v~l~DpTG~i~~tiH~~v~~~y~~~l~~GavLlLk~V~Vf~ps~~~~yLnIt~~ 76 (86)
T PF15072_consen 21 AFVVLKDPTGEIRGTIHRKVLEEYGDELSPGAVLLLKDVTVFSPSPRSHYLNITLN 76 (86)
T ss_pred eEEEEECCCCcEEEEEeHHHHhhcCCccccCEEEEEeeeeEEecCCCccEEEEehh
Confidence 5789999999999999863 45778999999999987532 234566666553
No 81
>PRK06826 dnaE DNA polymerase III DnaE; Reviewed
Probab=75.19 E-value=9.8 Score=38.64 Aligned_cols=73 Identities=10% Similarity=0.043 Sum_probs=54.4
Q ss_pred CCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecCC----cCCCCCCCEEEEeceEEceeCCeEE
Q 031443 46 NGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARNDQ----VDLMKPGTTVILRNAKIDMFKGSMR 121 (159)
Q Consensus 46 ~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde~----~~~i~~Gdvv~I~na~v~~~~G~~~ 121 (159)
..+.+.+.|.++..+.+++ | ..++-+.+.|+||.+.+++|-+. ...+.+|.+|.|.+-.-...++.++
T Consensus 992 ~~v~v~g~i~~~~~~~tk~---G-----~~maf~~leD~~g~~e~~vfp~~~~~~~~~l~~~~~~~v~g~v~~~~~~~~~ 1063 (1151)
T PRK06826 992 DKVIIGGIITEVKRKTTRN---N-----EMMAFLTLEDLYGTVEVIVFPKVYEKYRSLLNEDNIVLIKGRVSLREDEEPK 1063 (1151)
T ss_pred cEEEEEEEEEEeEeeccCC---C-----CeEEEEEEEECCCcEEEEECHHHHHHHHHHhccCCEEEEEEEEEecCCCceE
Confidence 4577888888887765432 3 46999999999999999999642 3558999999998876432356677
Q ss_pred EEeCC
Q 031443 122 IAVDK 126 (159)
Q Consensus 122 L~vgk 126 (159)
|.+.+
T Consensus 1064 ~~~~~ 1068 (1151)
T PRK06826 1064 LICEE 1068 (1151)
T ss_pred EEEee
Confidence 77765
No 82
>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=74.87 E-value=11 Score=29.57 Aligned_cols=32 Identities=13% Similarity=0.068 Sum_probs=25.3
Q ss_pred eCceeEEEEEecCCc----CCCCCCCEEEEeceEEc
Q 031443 83 DDTGTILFTARNDQV----DLMKPGTTVILRNAKID 114 (159)
Q Consensus 83 DeTG~I~ltlWde~~----~~i~~Gdvv~I~na~v~ 114 (159)
|+|--+++++|+.++ ..++.|+.|.|.+-...
T Consensus 48 ~~t~~~~v~~wg~~Ae~~~~~l~KG~~V~V~G~L~~ 83 (164)
T TIGR00621 48 EETEWHDIVIFGRLAEVAAQYLKKGSLVYVEGRLRT 83 (164)
T ss_pred ccceEEEEEEehHHHHHHHHhCCCCCEEEEEEEEEe
Confidence 346789999998654 34799999999987763
No 83
>PRK13732 single-stranded DNA-binding protein; Provisional
Probab=74.60 E-value=30 Score=27.70 Aligned_cols=83 Identities=18% Similarity=0.160 Sum_probs=50.8
Q ss_pred CCCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEee-------Cce-------eEEEEEecCCc----CCCCCCCE
Q 031443 44 GTNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGD-------DTG-------TILFTARNDQV----DLMKPGTT 105 (159)
Q Consensus 44 ~~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgD-------eTG-------~I~ltlWde~~----~~i~~Gdv 105 (159)
+++.|.|.+++..-.+.+.+. +| ..|++..||- ++| -+++++|+..+ ..+..|+.
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 456678888887755544332 23 3577766653 234 56899998644 44799999
Q ss_pred EEEeceEEce-e--CC----eEEEEeCCceeEEEc
Q 031443 106 VILRNAKIDM-F--KG----SMRIAVDKWGRIEAT 133 (159)
Q Consensus 106 v~I~na~v~~-~--~G----~~~L~vgk~g~I~~~ 133 (159)
|.|.+-.... | +| ..+|.+...|+|..+
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 9999876532 3 23 344555544455444
No 84
>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=74.32 E-value=24 Score=23.90 Aligned_cols=53 Identities=8% Similarity=0.206 Sum_probs=37.0
Q ss_pred ceEEEEEEeeCceeEEEEEecCC-------cCCCCCCCEEEEeceEEcee-----CCeEEEEeCC
Q 031443 74 TRIAECLVGDDTGTILFTARNDQ-------VDLMKPGTTVILRNAKIDMF-----KGSMRIAVDK 126 (159)
Q Consensus 74 ~~V~~~lVgDeTG~I~ltlWde~-------~~~i~~Gdvv~I~na~v~~~-----~G~~~L~vgk 126 (159)
+.++=+.+-|.||.+...+=... ...+..||+|.+.+-...-- .+.++|.+..
T Consensus 15 g~~~Fi~Lrd~~~~iQ~v~~~~~~~~~~~~~~~l~~~s~V~v~G~~~~~~~~~~~~~~~El~~~~ 79 (85)
T cd04100 15 GGLIFIDLRDGSGIVQVVVNKEELGEFFEEAEKLRTESVVGVTGTVVKRPEGNLATGEIELQAEE 79 (85)
T ss_pred CCEEEEEEEeCCeeEEEEEECCcChHHHHHHhCCCCCCEEEEEeEEEECCCCCCCCCCEEEEEeE
Confidence 34777888999999988664332 23579999999999776532 4556665543
No 85
>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=74.20 E-value=11 Score=26.07 Aligned_cols=36 Identities=11% Similarity=0.176 Sum_probs=27.1
Q ss_pred EEEEecCCcCCCCCCCEEEEeceEEceeCCeEEEEeCC
Q 031443 89 LFTARNDQVDLMKPGTTVILRNAKIDMFKGSMRIAVDK 126 (159)
Q Consensus 89 ~ltlWde~~~~i~~Gdvv~I~na~v~~~~G~~~L~vgk 126 (159)
.|..... ...+++||.|+|. |.+.+|.|..+|....
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 4444443 5678999999997 8889999988876544
No 86
>PTZ00385 lysyl-tRNA synthetase; Provisional
Probab=73.54 E-value=29 Score=33.31 Aligned_cols=73 Identities=8% Similarity=0.111 Sum_probs=54.7
Q ss_pred CceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecCC----------cCCCCCCCEEEEeceEEcee
Q 031443 47 GHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARNDQ----------VDLMKPGTTVILRNAKIDMF 116 (159)
Q Consensus 47 ~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde~----------~~~i~~Gdvv~I~na~v~~~ 116 (159)
.|.|.++|..+-.. |+++=+.|-|.||.|-+.+-.+. ...+..||+|.+.+-..+.-
T Consensus 109 ~V~vaGrV~~~R~~-------------Gk~~F~~LrD~~G~IQvv~~~~~~~~~~~~~~~~~~l~~gdiV~V~G~v~~t~ 175 (659)
T PTZ00385 109 TVRVAGRVTSVRDI-------------GKIIFVTIRSNGNELQVVGQVGEHFTREDLKKLKVSLRVGDIIGADGVPCRMQ 175 (659)
T ss_pred EEEEEEEEEeeecc-------------CCeEEEEEEECCceEEEEEECCccCCHHHHHHHHhCCCCCCEEEEEEEEEecC
Confidence 37788888774331 45777888899999999885322 12478999999999877777
Q ss_pred CCeEEEEeCCceeEEE
Q 031443 117 KGSMRIAVDKWGRIEA 132 (159)
Q Consensus 117 ~G~~~L~vgk~g~I~~ 132 (159)
.|.++|.+.+.--+.+
T Consensus 176 ~GeleI~~~~i~lLsk 191 (659)
T PTZ00385 176 RGELSVAASRMLILSP 191 (659)
T ss_pred CceEEEEeeEEEEech
Confidence 8999998888655554
No 87
>PRK07279 dnaE DNA polymerase III DnaE; Reviewed
Probab=71.85 E-value=9.6 Score=38.33 Aligned_cols=82 Identities=17% Similarity=0.203 Sum_probs=59.1
Q ss_pred eecccCCCCCCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecC----CcCCCCCCCEEEEece
Q 031443 36 TKVDQLKPGTNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARND----QVDLMKPGTTVILRNA 111 (159)
Q Consensus 36 ~kI~dL~P~~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde----~~~~i~~Gdvv~I~na 111 (159)
.++.+|.. ...+.+.+.|.++...+++. -| ..++-+.+.|+||.+.+++|-+ ....+.+|.+|.|.+-
T Consensus 876 ~~~~~l~~-~~~~~~~~~i~~~~~~~tk~--~g-----~~maf~~leD~~g~ie~~vFp~~y~~~~~~l~~~~~~~v~G~ 947 (1034)
T PRK07279 876 TPISQLVK-NSEATILVQIQSIRVIRTKT--KG-----QQMAFLSVTDTKKKLDVTLFPETYRQYKDELKEGKFYYLKGK 947 (1034)
T ss_pred ccHHHHhc-CCcceEEEEEEEEEEEEEcC--CC-----CeEEEEEEeeCCCcEEEEECHHHHHHHHHHhccCCEEEEEEE
Confidence 45666653 34467888888887765431 23 4699999999999999999964 2355899999999887
Q ss_pred EEceeCCeEEEEeCC
Q 031443 112 KIDMFKGSMRIAVDK 126 (159)
Q Consensus 112 ~v~~~~G~~~L~vgk 126 (159)
.-+ .++.++|.+.+
T Consensus 948 v~~-~~~~~~l~~~~ 961 (1034)
T PRK07279 948 IQE-RDGRLQMVLQQ 961 (1034)
T ss_pred EEe-cCCeeEEEEee
Confidence 654 36667776655
No 88
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=71.74 E-value=11 Score=36.05 Aligned_cols=50 Identities=18% Similarity=0.240 Sum_probs=38.5
Q ss_pred EEEeeCceeEEEEEecCCc----CCCCCCCEEEEeceEEceeCCeEEEEeCCcee
Q 031443 79 CLVGDDTGTILFTARNDQV----DLMKPGTTVILRNAKIDMFKGSMRIAVDKWGR 129 (159)
Q Consensus 79 ~lVgDeTG~I~ltlWde~~----~~i~~Gdvv~I~na~v~~~~G~~~L~vgk~g~ 129 (159)
..|-||||.|...++.+.. ..|++||+|++.+-.. ...|.++|-+-..-+
T Consensus 234 FtltDetg~i~aAAFe~aGvRAyP~IevGdiV~ViG~V~-~r~g~lQiE~~~me~ 287 (715)
T COG1107 234 FTLTDETGAIWAAAFEEAGVRAYPEIEVGDIVEVIGEVT-RRDGRLQIEIEAMEK 287 (715)
T ss_pred EEEecCCCceehhhhccCCcccCCCCCCCceEEEEEEEe-ecCCcEEEeehhhHH
Confidence 4578999999999997533 5589999999997664 557888887766443
No 89
>PRK05672 dnaE2 error-prone DNA polymerase; Validated
Probab=71.69 E-value=8.3 Score=38.73 Aligned_cols=69 Identities=12% Similarity=0.084 Sum_probs=49.7
Q ss_pred CceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecC----CcCCCCCCCEEEEeceEEceeCCeEEE
Q 031443 47 GHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARND----QVDLMKPGTTVILRNAKIDMFKGSMRI 122 (159)
Q Consensus 47 ~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde----~~~~i~~Gdvv~I~na~v~~~~G~~~L 122 (159)
.+.+-+.|..+..+.++ + | |+-+.+.|+||.+.+++|-+ ....+++|..+.|.+-.-+ .++.++|
T Consensus 955 ~v~v~g~i~~~~~~~Tk-k--------G-maf~~leD~~g~~e~~ifp~~~~~~~~~l~~~~~~~v~g~v~~-~~~~~~~ 1023 (1046)
T PRK05672 955 RVRVAGVVTHRQRPGTA-S--------G-VTFLTLEDETGMVNVVVWPGLWERQRREALGARLLLVRGRVQN-AEGVRHL 1023 (1046)
T ss_pred EEEEEEEEEEEEEecCC-C--------c-eEEEEEecCCCCEEEEECHHHHHHHHHHhccCCEEEEEEEEEe-cCCeEEE
Confidence 36666666666554432 1 4 99999999999999999964 2245799999999876654 3566777
Q ss_pred EeCC
Q 031443 123 AVDK 126 (159)
Q Consensus 123 ~vgk 126 (159)
.+.+
T Consensus 1024 ~~~~ 1027 (1046)
T PRK05672 1024 VADR 1027 (1046)
T ss_pred EEee
Confidence 7655
No 90
>PRK06920 dnaE DNA polymerase III DnaE; Reviewed
Probab=71.38 E-value=9 Score=38.75 Aligned_cols=82 Identities=11% Similarity=0.076 Sum_probs=59.0
Q ss_pred eecccCCC-CCCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecC----CcCCCCCCCEEEEec
Q 031443 36 TKVDQLKP-GTNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARND----QVDLMKPGTTVILRN 110 (159)
Q Consensus 36 ~kI~dL~P-~~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde----~~~~i~~Gdvv~I~n 110 (159)
.++.+|.. ....+.+-+.|.++...++++ | ..|+-+.+-|+||.+.+++|-+ ....+.+|.+|.|.+
T Consensus 933 ~~~~~l~~~~~~~v~v~g~i~~~~~~~tk~---g-----~~maf~~leD~tg~~e~~vFp~~y~~~~~~l~~~~~~~v~G 1004 (1107)
T PRK06920 933 PSLAQAMRHKKKVQRAIVYITSVKVIRTKK---G-----QKMAFITFCDQNDEMEAVVFPETYIHFSDKLQEGAIVLVDG 1004 (1107)
T ss_pred cCHHHHhhcCCCEEEEEEEEEEeEeecCCC---C-----CeEEEEEEeeCCCcEEEEECHHHHHHHHHHhccCCEEEEEE
Confidence 45666642 223477888888888765532 3 4699999999999999999964 335589999999987
Q ss_pred eEEceeCCeEEEEeCC
Q 031443 111 AKIDMFKGSMRIAVDK 126 (159)
Q Consensus 111 a~v~~~~G~~~L~vgk 126 (159)
-.-. .++.+.|.+.+
T Consensus 1005 ~v~~-~~~~~~~~~~~ 1019 (1107)
T PRK06920 1005 TIEL-RNHKLQWIVNG 1019 (1107)
T ss_pred EEEe-cCCcEEEEEee
Confidence 6643 35667777655
No 91
>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=71.28 E-value=2.6 Score=32.52 Aligned_cols=26 Identities=23% Similarity=0.229 Sum_probs=21.8
Q ss_pred ceEEEEEEeeCceeEEEEEecCCcCC
Q 031443 74 TRIAECLVGDDTGTILFTARNDQVDL 99 (159)
Q Consensus 74 ~~V~~~lVgDeTG~I~ltlWde~~~~ 99 (159)
..+..+.|.|.||.+.++++++.+..
T Consensus 67 ry~l~~~i~D~Tg~~~~~~F~~~ae~ 92 (166)
T cd04476 67 RYILSLNVADHTGEAWLTLFDEVAEQ 92 (166)
T ss_pred EEEEEEEEEeCCCCEEEEEehHHHHH
Confidence 45678999999999999999976633
No 92
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=69.18 E-value=16 Score=33.30 Aligned_cols=77 Identities=12% Similarity=0.127 Sum_probs=54.0
Q ss_pred ecccCCCCCCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecCC------cCCCCCCCEEEEec
Q 031443 37 KVDQLKPGTNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARNDQ------VDLMKPGTTVILRN 110 (159)
Q Consensus 37 kI~dL~P~~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde~------~~~i~~Gdvv~I~n 110 (159)
+++|+.+..+ ..+.++|.+.....+ +-..=+.+.|++|.|.+.+.-.. +..+-+||.|.+.|
T Consensus 259 ~l~d~~~~~~-~~v~g~v~~~p~~ie-----------Gghv~v~i~d~~G~I~~~A~eptk~fr~~a~~L~pGD~i~~~G 326 (421)
T COG1571 259 KLNDIEDYSK-YRVVGRVEAEPRAIE-----------GGHVVVEITDGEGEIGAVAFEPTKEFRELARKLIPGDEITVYG 326 (421)
T ss_pred hhhhhhhccc-eEEEEEEecccEEee-----------CCEEEEEecCCCceEEEEEecccccchHHHHhcCCCCEEEEec
Confidence 3678887655 678888887655432 33555678999998888887532 23478999999999
Q ss_pred eEEceeCCeEEEEeCCceeE
Q 031443 111 AKIDMFKGSMRIAVDKWGRI 130 (159)
Q Consensus 111 a~v~~~~G~~~L~vgk~g~I 130 (159)
+....- |++.+.--+
T Consensus 327 ~~~~~~-----~n~ek~~v~ 341 (421)
T COG1571 327 SVKPGT-----LNLEKFQVL 341 (421)
T ss_pred Cccccc-----eeEEEEEEE
Confidence 987543 676664433
No 93
>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=68.85 E-value=32 Score=23.09 Aligned_cols=53 Identities=8% Similarity=0.189 Sum_probs=36.2
Q ss_pred ceEEEEEEeeCcee--EEEEEecC-----CcCCCCCCCEEEEeceEEceeC--CeEEEEeCC
Q 031443 74 TRIAECLVGDDTGT--ILFTARND-----QVDLMKPGTTVILRNAKIDMFK--GSMRIAVDK 126 (159)
Q Consensus 74 ~~V~~~lVgDeTG~--I~ltlWde-----~~~~i~~Gdvv~I~na~v~~~~--G~~~L~vgk 126 (159)
+.++=+.|-|.+|. +.+.+=.+ .+..+..|++|.+.+-....-. +.++|.+.+
T Consensus 15 g~~~Fi~LrD~s~~~~lQvv~~~~~~~~~~~~~l~~gs~V~v~G~v~~~~~~~~~~El~~~~ 76 (82)
T cd04318 15 KKISFIELNDGSCLKNLQVVVDKELTNFKEILKLSTGSSIRVEGVLVKSPGAKQPFELQAEK 76 (82)
T ss_pred CcEEEEEEECCCCccCEEEEEeCcccCHHHHhcCCCceEEEEEEEEEeCCCCCCCEEEEEEE
Confidence 34666777788884 77765322 2345799999999998776544 667776654
No 94
>PRK08763 single-stranded DNA-binding protein; Provisional
Probab=68.35 E-value=16 Score=28.98 Aligned_cols=64 Identities=13% Similarity=0.058 Sum_probs=42.1
Q ss_pred CCCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEe------eC-------ceeEEEEEecCCc----CCCCCCCEE
Q 031443 44 GTNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVG------DD-------TGTILFTARNDQV----DLMKPGTTV 106 (159)
Q Consensus 44 ~~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVg------De-------TG~I~ltlWde~~----~~i~~Gdvv 106 (159)
+++.+.|.+++-.-.+.+.+. +| ..|+...|| |. |=-+++++|+.++ ..++.|+.|
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 GINKVILVGNLGNDPDIKYTQ--SG-----MTITRISLATTSVRKDREGNTQERTEWHRVKFFGKLGEIAGEYLRKGSQC 76 (164)
T ss_pred cceEEEEEEEecCCCeEEEcC--CC-----CeEEEEEEEeccceecCCCCeeccceEEEEEEehHHHHHHHHhcCCCCEE
Confidence 355677777777754444322 33 456666665 22 2348999998654 347999999
Q ss_pred EEeceEEc
Q 031443 107 ILRNAKID 114 (159)
Q Consensus 107 ~I~na~v~ 114 (159)
.|.+-...
T Consensus 77 ~VeGrL~~ 84 (164)
T PRK08763 77 YIEGSIRY 84 (164)
T ss_pred EEEEEEEe
Confidence 99988754
No 95
>PRK07274 single-stranded DNA-binding protein; Provisional
Probab=68.23 E-value=11 Score=28.31 Aligned_cols=30 Identities=7% Similarity=0.025 Sum_probs=23.4
Q ss_pred ceeEEEEEecCCc----CCCCCCCEEEEeceEEc
Q 031443 85 TGTILFTARNDQV----DLMKPGTTVILRNAKID 114 (159)
Q Consensus 85 TG~I~ltlWde~~----~~i~~Gdvv~I~na~v~ 114 (159)
|--+++++|+.++ ..++.|+.|.|.+-...
T Consensus 46 t~w~~v~~fg~~Ae~v~~~l~KG~~V~V~Grl~~ 79 (131)
T PRK07274 46 ADFINVVLWGKLAETLASYASKGSLISIDGELRT 79 (131)
T ss_pred EEEEEEEEehHHHHHHHHHcCCCCEEEEEEEEEe
Confidence 4478999998655 34799999999986653
No 96
>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=68.08 E-value=36 Score=23.32 Aligned_cols=53 Identities=13% Similarity=0.152 Sum_probs=34.7
Q ss_pred ceEEEEEEeeCce-eEEEEEecC-----CcCCCCCCCEEEEeceEEceeC------CeEEEEeCC
Q 031443 74 TRIAECLVGDDTG-TILFTARND-----QVDLMKPGTTVILRNAKIDMFK------GSMRIAVDK 126 (159)
Q Consensus 74 ~~V~~~lVgDeTG-~I~ltlWde-----~~~~i~~Gdvv~I~na~v~~~~------G~~~L~vgk 126 (159)
+.++=+.|-|.|| .+.+.+=.+ .+..+..|++|.+.+-....-+ |.++|.+..
T Consensus 16 ~~~~Fi~LrD~~g~~iQvv~~~~~~~~~~~~~l~~~s~V~V~G~v~~~~~~~~~~~~~~Ei~~~~ 80 (86)
T cd04321 16 KKLSFADLRDPNGDIIQLVSTAKKDAFSLLKSITAESPVQVRGKLQLKEAKSSEKNDEWELVVDD 80 (86)
T ss_pred CceEEEEEECCCCCEEEEEECCCHHHHHHHhcCCCCcEEEEEEEEEeCCCcCCCCCCCEEEEEEE
Confidence 4577788899999 577643222 2245789999999987665332 556665543
No 97
>PRK06752 single-stranded DNA-binding protein; Validated
Probab=67.93 E-value=14 Score=26.91 Aligned_cols=30 Identities=10% Similarity=0.034 Sum_probs=23.8
Q ss_pred ceeEEEEEecCCc----CCCCCCCEEEEeceEEc
Q 031443 85 TGTILFTARNDQV----DLMKPGTTVILRNAKID 114 (159)
Q Consensus 85 TG~I~ltlWde~~----~~i~~Gdvv~I~na~v~ 114 (159)
|--+++++|+..+ ..++.|+.|.|.+-...
T Consensus 46 t~~~~v~~wg~~Ae~~~~~l~KG~~V~V~G~l~~ 79 (112)
T PRK06752 46 VDFINCVVWRKSAENVTEYCTKGSLVGITGRIHT 79 (112)
T ss_pred EEEEEEEEehHHHHHHHHhcCCCCEEEEEEEEEe
Confidence 5578899998654 34799999999988764
No 98
>PRK03932 asnC asparaginyl-tRNA synthetase; Validated
Probab=66.44 E-value=30 Score=31.35 Aligned_cols=73 Identities=14% Similarity=0.124 Sum_probs=52.1
Q ss_pred CCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecC-------CcCCCCCCCEEEEeceEEcee--
Q 031443 46 NGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARND-------QVDLMKPGTTVILRNAKIDMF-- 116 (159)
Q Consensus 46 ~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde-------~~~~i~~Gdvv~I~na~v~~~-- 116 (159)
+.|.|.+.|-++-.. ++++=+.|-|.||.+.+.+-.+ .+..+..||+|.|.|-....-
T Consensus 17 ~~V~i~G~v~~~R~~-------------g~~~Fi~lrD~~g~iq~~~~~~~~~~~~~~~~~l~~~s~v~v~G~v~~~~~~ 83 (450)
T PRK03932 17 QEVTVRGWVRTKRDS-------------GKIAFLQLRDGSCFKQLQVVKDNGEEYFEEIKKLTTGSSVIVTGTVVESPRA 83 (450)
T ss_pred CEEEEEEEEEEEEeC-------------CCeEEEEEECCCCcEEEEEEcCCChHHHHHHhcCCCCcEEEEEEEEEcCCCC
Confidence 458888988776431 4577889999999987776422 223579999999999777532
Q ss_pred CCeEEEEeCCceeEE
Q 031443 117 KGSMRIAVDKWGRIE 131 (159)
Q Consensus 117 ~G~~~L~vgk~g~I~ 131 (159)
.|.++|.+.+.--+.
T Consensus 84 ~~~~el~~~~i~vl~ 98 (450)
T PRK03932 84 GQGYELQATKIEVIG 98 (450)
T ss_pred CCCEEEEEEEEEEcc
Confidence 357899887754443
No 99
>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=65.92 E-value=5 Score=27.83 Aligned_cols=62 Identities=18% Similarity=0.133 Sum_probs=36.2
Q ss_pred CCceEEEEEEecCcccccccCCCCCCCcceEEEEEEe-------------eCceeEEEEEecCCcC----CCCCCCEEEE
Q 031443 46 NGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVG-------------DDTGTILFTARNDQVD----LMKPGTTVIL 108 (159)
Q Consensus 46 ~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVg-------------DeTG~I~ltlWde~~~----~i~~Gdvv~I 108 (159)
+.+.+.+.|..-.+.+.+. +| ..++...|+ +.+--+++++|++.++ .+++||.|.|
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--NG-----TPVARFSLAVNRRFKDDGGEGDEKTDWINVVAWGKLAENVAEYLKKGDRVYV 74 (104)
T ss_dssp EEEEEEEEESSSEEEEEET--TS-----EEEEEEEEEEEEEEEETTSCEEEEEEEEEEEEEHHHHHHHHHH--TT-EEEE
T ss_pred cEEEEEEEECCCcEEEECC--CC-----CEEEEEEEEEecEEeeeeccCccceEEEEEEeeeecccccceEEcCCCEEEE
Confidence 3466777776655544332 33 334443332 3355789999987553 3799999999
Q ss_pred eceEEc
Q 031443 109 RNAKID 114 (159)
Q Consensus 109 ~na~v~ 114 (159)
.+-...
T Consensus 75 ~G~l~~ 80 (104)
T PF00436_consen 75 EGRLRT 80 (104)
T ss_dssp EEEEEE
T ss_pred EEEEEe
Confidence 987764
No 100
>PRK06751 single-stranded DNA-binding protein; Provisional
Probab=65.61 E-value=20 Score=28.59 Aligned_cols=64 Identities=13% Similarity=0.098 Sum_probs=40.2
Q ss_pred CCceEEEEEEecCcccccccCCCCCCCcceEEEEEEe------e-----CceeEEEEEecCCcC----CCCCCCEEEEec
Q 031443 46 NGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVG------D-----DTGTILFTARNDQVD----LMKPGTTVILRN 110 (159)
Q Consensus 46 ~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVg------D-----eTG~I~ltlWde~~~----~i~~Gdvv~I~n 110 (159)
..+.|.++|..-.+.+.+. .| ..|+...|| + +|--+++++|+.+++ .++.|+.|.|.+
T Consensus 3 N~V~LiGrL~~DpelR~t~--sG-----~~v~~fslAvnr~~~~~~ge~~tdwi~~v~wgk~Ae~~~~~l~KG~~V~VeG 75 (173)
T PRK06751 3 NRVILVGRLTKDPDLRYTP--NG-----VAVATFTLAVNRAFANQQGEREADFINCVIWRKQAENVANYLKKGSLAGVDG 75 (173)
T ss_pred eEEEEEEEECCCCcEEECC--CC-----CEEEEEEEEEccceecCCCCEEEEEEEEEEeCcHHHHHHHHcCCCCEEEEEE
Confidence 4456666666644443221 22 345555554 1 345799999997653 479999999998
Q ss_pred eEEc-ee
Q 031443 111 AKID-MF 116 (159)
Q Consensus 111 a~v~-~~ 116 (159)
.... .|
T Consensus 76 rL~~r~y 82 (173)
T PRK06751 76 RLQTRNY 82 (173)
T ss_pred EEEeCcc
Confidence 8764 35
No 101
>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=64.57 E-value=26 Score=28.10 Aligned_cols=65 Identities=12% Similarity=0.178 Sum_probs=36.8
Q ss_pred ceeecccCCCCCCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecCCcCC-CCCCCEEEEe
Q 031443 34 VFTKVDQLKPGTNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARNDQVDL-MKPGTTVILR 109 (159)
Q Consensus 34 ~~~kI~dL~P~~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde~~~~-i~~Gdvv~I~ 109 (159)
..-||.+|.....|. +.--+..+..... + ..-.---|.|.||.+-+...+..... .++||-++|.
T Consensus 100 ~TpKI~~L~~q~~Gt-~V~G~F~v~KK~v--~--------~~~~~YeI~DnTG~MeVvv~G~~~ni~CEeGDKLrL~ 165 (170)
T PF02760_consen 100 ETPKINDLQKQASGT-FVNGLFTVHKKTV--N--------KKNTIYEIQDNTGKMEVVVYGKWHNIKCEEGDKLRLF 165 (170)
T ss_dssp S---HHHHTTSSTTE-EEEEEEEEEEEEE--E--------SSEEEEEEEETTEEEEEEEEGGGCGCC--TT-EEEEE
T ss_pred cCCchhHHhcCCCCc-EEeEEEEEEEEEE--c--------CCeEEEEEecCCCcEEEEEeccCcccccCCCCeEEEE
Confidence 345788888887773 3322333332211 1 22344568999999999877754433 5899999874
No 102
>COG0017 AsnS Aspartyl/asparaginyl-tRNA synthetases [Translation, ribosomal structure and biogenesis]
Probab=64.43 E-value=58 Score=29.83 Aligned_cols=86 Identities=13% Similarity=0.140 Sum_probs=62.9
Q ss_pred eecccCCCCC--CCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEec-CC------cCCCCCCCEE
Q 031443 36 TKVDQLKPGT--NGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARN-DQ------VDLMKPGTTV 106 (159)
Q Consensus 36 ~kI~dL~P~~--~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWd-e~------~~~i~~Gdvv 106 (159)
+.|+|+.+.. ..|.|.+-|-++-. .+.|+=++|-|.||.|..++-. +. +..+..+++|
T Consensus 5 ~~i~di~~~~~~~~V~v~GWV~~~R~-------------~g~i~Fi~lrDgsg~iQ~v~~~~~~~~~~~~~~~L~~es~v 71 (435)
T COG0017 5 TYIKDIKPHVGGQEVTVRGWVHNKRD-------------LGKIIFLVLRDGSGFIQAVVPKNKVYEELFKAKKLTLESSV 71 (435)
T ss_pred eeHHhhhccCCCcEEEEEEEeeeecc-------------cCCeEEEEEEcCCcEEEEEEECCCCcHHHhhhhcCCCccEE
Confidence 5577888755 45666666655432 2568999999999999999873 12 2357899999
Q ss_pred EEeceEEcee--CCeEEEEeCCceeEEEcC
Q 031443 107 ILRNAKIDMF--KGSMRIAVDKWGRIEATE 134 (159)
Q Consensus 107 ~I~na~v~~~--~G~~~L~vgk~g~I~~~~ 134 (159)
.|.|.....- .+.++|.+.+---+..++
T Consensus 72 ~V~G~v~~~~~a~~g~El~v~~i~Vl~~a~ 101 (435)
T COG0017 72 VVTGIVKASPKAPQGFELQVEKIEVLGEAD 101 (435)
T ss_pred EEEEEEEcCCCCCCCEEEEEEEEEEeeccC
Confidence 9999988654 478999998865555553
No 103
>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=64.34 E-value=34 Score=31.10 Aligned_cols=75 Identities=13% Similarity=0.173 Sum_probs=52.7
Q ss_pred CCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCc--eeEEEEEecC-------CcCCCCCCCEEEEeceEEce-
Q 031443 46 NGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDT--GTILFTARND-------QVDLMKPGTTVILRNAKIDM- 115 (159)
Q Consensus 46 ~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeT--G~I~ltlWde-------~~~~i~~Gdvv~I~na~v~~- 115 (159)
+.|.|.+.|-++-. + +.++=+.|-|.+ |.|.+++=.. .+..+..||+|.+.+-...-
T Consensus 17 ~~v~v~Gwv~~~R~--------~-----~~~~F~~lrD~~~~g~iQ~v~~~~~~~~~~~~~~~l~~gs~V~v~G~v~~~~ 83 (453)
T TIGR00457 17 DEVTVSGWVRTKRS--------S-----KKIIFLELNDGSSLGPIQAVINGEDNPYLFQLLKSLTTGSSVSVTGKVVESP 83 (453)
T ss_pred CEEEEEEEeEEEEc--------C-----CCeEEEEEECCCCCccEEEEEeCCcChHHHHHHHcCCCCcEEEEEEEEEcCC
Confidence 44888888877542 1 457778889999 9999876433 12357999999999977653
Q ss_pred -eCCeEEEEeCCceeEEEc
Q 031443 116 -FKGSMRIAVDKWGRIEAT 133 (159)
Q Consensus 116 -~~G~~~L~vgk~g~I~~~ 133 (159)
-.+.++|.+.+.--+.+.
T Consensus 84 ~~~~~~El~~~~i~vl~~~ 102 (453)
T TIGR00457 84 GKGQPVELQVKKIEVVGEA 102 (453)
T ss_pred CCCCCEEEEEeEEEEEecC
Confidence 347789988765444444
No 104
>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=64.03 E-value=16 Score=24.97 Aligned_cols=31 Identities=19% Similarity=0.149 Sum_probs=24.5
Q ss_pred CceeEEEEEecCCc----CCCCCCCEEEEeceEEc
Q 031443 84 DTGTILFTARNDQV----DLMKPGTTVILRNAKID 114 (159)
Q Consensus 84 eTG~I~ltlWde~~----~~i~~Gdvv~I~na~v~ 114 (159)
++=-+.+++|++.+ ..+++||.|.|.+-...
T Consensus 42 ~~~~~~v~~~g~~a~~~~~~~~kG~~V~v~G~l~~ 76 (100)
T cd04496 42 ETDWIRVVAFGKLAENAAKYLKKGDLVYVEGRLRT 76 (100)
T ss_pred ccEEEEEEEEhHHHHHHHHHhCCCCEEEEEEEEEe
Confidence 45578999999754 34799999999988764
No 105
>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=63.89 E-value=67 Score=24.90 Aligned_cols=81 Identities=15% Similarity=0.123 Sum_probs=51.0
Q ss_pred eEEEEEEecCcccccccCCCCCCCcceEEEEEE-ee---CceeEEEEEecC---CcCCCCCCCEEEEeceEEcee--CCe
Q 031443 49 NLTVNVLKSEPVLPKNRAASPQLRQTRIAECLV-GD---DTGTILFTARND---QVDLMKPGTTVILRNAKIDMF--KGS 119 (159)
Q Consensus 49 nv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lV-gD---eTG~I~ltlWde---~~~~i~~Gdvv~I~na~v~~~--~G~ 119 (159)
=.+++|+++.+...|..+. .+|.+++= |. ..|.+|.-++-. .+..+++|..+-|.+.-...+ +|.
T Consensus 32 vykv~v~~~~~~~~f~~Y~------~~I~~ViK~G~D~~~~~~~r~F~~r~sCr~~l~l~~gk~YLIMG~~~~~~~~~~~ 105 (149)
T cd03583 32 VYKVKLVNVELSDSYDIYT------MEILQVIKEGTDEGPEGKTRTFISHPKCREALNLKEGKDYLIMGLSSDLWRIKDK 105 (149)
T ss_pred EEEEEEEEEeccCCeEEEE------EEEEEEEecccccCcCCCeEEEEecCCCcchhccCCCCEEEEEeCCCCccccCCc
Confidence 4677777776654443322 33333221 11 256666434432 223457999999999887665 467
Q ss_pred EEEEeCCceeEEEcCC
Q 031443 120 MRIAVDKWGRIEATEP 135 (159)
Q Consensus 120 ~~L~vgk~g~I~~~~~ 135 (159)
+++.+|+.+.|+.-|.
T Consensus 106 ~~YvL~~~TWvE~wP~ 121 (149)
T cd03583 106 YSYVIGKDTWIEYWPT 121 (149)
T ss_pred EEEEeCCCeEEEECCC
Confidence 9999999999999863
No 106
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=63.16 E-value=42 Score=34.72 Aligned_cols=109 Identities=13% Similarity=0.121 Sum_probs=77.5
Q ss_pred CceeecccCCCCCCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecC------CcCCCCCCCEE
Q 031443 33 PVFTKVDQLKPGTNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARND------QVDLMKPGTTV 106 (159)
Q Consensus 33 ~~~~kI~dL~P~~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde------~~~~i~~Gdvv 106 (159)
.+++++-++.+.+.++.+.+.|.++..... +-| ..+.+.-|-|-|-++.+-.|-. ..+.++.|+.|
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 EEIKPLIKINEEETRVKVEGYIFKIEIKEL---KSG-----RTLLNIKVTDYTSSLILKKFLRDEEDEKKFDGIKKGMWV 298 (1444)
T ss_pred cceeehhhccccccceEEEEEEEEEeeeec---ccC-----cEEEEEEEecCchheeehhhccccccHHHHhhcccCcEE
Confidence 368888888888888999999999775321 223 5688999999999999998853 23568999999
Q ss_pred EEeceEEce-eCCeEEEEeCCceeEEEcC------CCcEEEccCCCcccc
Q 031443 107 ILRNAKIDM-FKGSMRIAVDKWGRIEATE------PAKFVVKEDNNLSLV 149 (159)
Q Consensus 107 ~I~na~v~~-~~G~~~L~vgk~g~I~~~~------~~~~~vne~~N~S~i 149 (159)
++++-.-.. |.+.+.+.+..=-.|+... +.-+++.-.-+||..
T Consensus 299 k~~g~v~~d~f~~~l~m~i~~I~ei~~~~r~D~~~eKRVELh~HTkMS~m 348 (1444)
T COG2176 299 KARGNVQLDTFTRDLTMIINDINEIENAKRKDLAKEKRVELHFHTKMSQM 348 (1444)
T ss_pred EEEEEEEecccccceEEEhhhhhhhhcccccccCccceEEEEeccchhhh
Confidence 999877653 6677888877744443221 223455555566653
No 107
>PRK07275 single-stranded DNA-binding protein; Provisional
Probab=63.13 E-value=16 Score=28.82 Aligned_cols=74 Identities=12% Similarity=0.151 Sum_probs=45.3
Q ss_pred CCceEEEEEEecCcccccccCCCCCCCcceEEEEEEe-----------eCceeEEEEEecCCc----CCCCCCCEEEEec
Q 031443 46 NGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVG-----------DDTGTILFTARNDQV----DLMKPGTTVILRN 110 (159)
Q Consensus 46 ~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVg-----------DeTG~I~ltlWde~~----~~i~~Gdvv~I~n 110 (159)
+.|.|.+++..-.+.+.+. .| ..|++..|| .+|--|++++|...+ ..++.|+-|.|.+
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 3455666665544443321 23 345555554 246679999999755 4479999999998
Q ss_pred eEEc-eeC---C----eEEEEeCC
Q 031443 111 AKID-MFK---G----SMRIAVDK 126 (159)
Q Consensus 111 a~v~-~~~---G----~~~L~vgk 126 (159)
-... .|. | ..++.++.
T Consensus 76 rl~~r~y~dkdG~k~~~~evva~~ 99 (162)
T PRK07275 76 RIQTRNYENQQGQRVYVTEVVADN 99 (162)
T ss_pred EEEeceEECCCCCEEEEEEEEEeE
Confidence 8763 342 3 45555554
No 108
>PRK06293 single-stranded DNA-binding protein; Provisional
Probab=62.12 E-value=25 Score=27.86 Aligned_cols=64 Identities=13% Similarity=0.032 Sum_probs=42.3
Q ss_pred CCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEe--------eCceeEEEEEecCCc----CCCCCCCEEEEeceE
Q 031443 45 TNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVG--------DDTGTILFTARNDQV----DLMKPGTTVILRNAK 112 (159)
Q Consensus 45 ~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVg--------DeTG~I~ltlWde~~----~~i~~Gdvv~I~na~ 112 (159)
|+.|.|.+++-.-.+.+.+. .| ..++...|| ++|-=+++++|+..+ ..++.|+.|.|.+-.
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 34466777766644443321 22 346666665 467789999998644 347999999999987
Q ss_pred Ece
Q 031443 113 IDM 115 (159)
Q Consensus 113 v~~ 115 (159)
...
T Consensus 74 ~~~ 76 (161)
T PRK06293 74 SPE 76 (161)
T ss_pred EeC
Confidence 743
No 109
>PTZ00417 lysine-tRNA ligase; Provisional
Probab=61.64 E-value=35 Score=32.23 Aligned_cols=74 Identities=15% Similarity=0.059 Sum_probs=52.3
Q ss_pred CceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecCC-----------cCCCCCCCEEEEeceEEce
Q 031443 47 GHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARNDQ-----------VDLMKPGTTVILRNAKIDM 115 (159)
Q Consensus 47 ~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde~-----------~~~i~~Gdvv~I~na~v~~ 115 (159)
.+.|.++|.++-. -| ..+.=+.|-|++|.|.+.+-.+. ...+..||+|.+.|...+.
T Consensus 134 ~v~v~Grv~~~R~-------~G-----~k~~F~~L~d~~g~iQv~~~~~~~~~~~~~~~~~~~~l~~Gd~V~V~G~~~~t 201 (585)
T PTZ00417 134 ILNVTGRIMRVSA-------SG-----QKLRFFDLVGDGAKIQVLANFAFHDHTKSNFAECYDKIRRGDIVGIVGFPGKS 201 (585)
T ss_pred eEEEEEEEEeeec-------CC-----CCCEEEEEEeCCeeEEEEEECCccCCCHHHHHHHHhcCCCCCEEEEEeEEcCC
Confidence 3677777776533 12 14666777899999888875221 2357899999999987776
Q ss_pred eCCeEEEEeCCceeEEE
Q 031443 116 FKGSMRIAVDKWGRIEA 132 (159)
Q Consensus 116 ~~G~~~L~vgk~g~I~~ 132 (159)
-.|.++|.+.+.--+.+
T Consensus 202 ~~gel~i~~~~i~llsk 218 (585)
T PTZ00417 202 KKGELSIFPKETIILSP 218 (585)
T ss_pred CCceEEEEEEEEEEEec
Confidence 67989988888654443
No 110
>PRK08486 single-stranded DNA-binding protein; Provisional
Probab=61.03 E-value=23 Score=28.45 Aligned_cols=34 Identities=9% Similarity=0.133 Sum_probs=26.4
Q ss_pred eCceeEEEEEecCCc----CCCCCCCEEEEeceEEc-ee
Q 031443 83 DDTGTILFTARNDQV----DLMKPGTTVILRNAKID-MF 116 (159)
Q Consensus 83 DeTG~I~ltlWde~~----~~i~~Gdvv~I~na~v~-~~ 116 (159)
++|--+++++|...+ ..++.|+-|.|.+-... .|
T Consensus 46 e~t~fi~v~~fg~~AE~~~~~l~KG~~V~VeGrL~~~~y 84 (182)
T PRK08486 46 EEVCFIDIRLFGRTAEIANQYLSKGSKVLIEGRLTFESW 84 (182)
T ss_pred ccceEEEEEEEhHHHHHHHHHcCCCCEEEEEEEEEeCcE
Confidence 467789999998544 44799999999988763 35
No 111
>PRK06958 single-stranded DNA-binding protein; Provisional
Probab=60.90 E-value=21 Score=28.85 Aligned_cols=63 Identities=14% Similarity=0.051 Sum_probs=41.6
Q ss_pred CCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEe--------------eCceeEEEEEecCCc----CCCCCCCEE
Q 031443 45 TNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVG--------------DDTGTILFTARNDQV----DLMKPGTTV 106 (159)
Q Consensus 45 ~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVg--------------DeTG~I~ltlWde~~----~~i~~Gdvv 106 (159)
++.|.|.+++..-.+.+.+. .| ..|+...|| ++|--+++++|..++ ..++.|+.|
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 45567777777655544322 23 346665554 235678999998655 347999999
Q ss_pred EEeceEEc
Q 031443 107 ILRNAKID 114 (159)
Q Consensus 107 ~I~na~v~ 114 (159)
.|.+-...
T Consensus 77 ~VeGrL~~ 84 (182)
T PRK06958 77 YIEGRIRT 84 (182)
T ss_pred EEEEEEEe
Confidence 99987764
No 112
>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=60.31 E-value=57 Score=33.57 Aligned_cols=80 Identities=16% Similarity=0.166 Sum_probs=60.1
Q ss_pred cCCCCCCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecCC------cCCCCCCCEEEEeceEE
Q 031443 40 QLKPGTNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARNDQ------VDLMKPGTTVILRNAKI 113 (159)
Q Consensus 40 dL~P~~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde~------~~~i~~Gdvv~I~na~v 113 (159)
++.....++.|.+.|..+..... + .| ..+...-|-|-|.+|.+..|... .+.+++|+.|++++-..
T Consensus 2 ~~~~~~~~~~~~g~i~~~~~~~~-~--~~-----~~~~~~~~~d~~~s~~~k~f~~~~~~~~~~~~~~~g~~~~~~g~~~ 73 (1213)
T TIGR01405 2 KINEEENRVKIEGYIFKIEIKEL-K--SG-----RTLLKIKVTDYTDSLILKKFLKSEEDPEKFDGIKIGKWVRARGKIE 73 (1213)
T ss_pred cccccCCeEEEEEEEEEEEeEec-c--CC-----CEEEEEEEEcCCCCEEEEEecccccchHHHhhcCCCcEEEEEEEEe
Confidence 46677888999999999876321 1 23 56888999999999999999621 24589999999998753
Q ss_pred -ceeCCeEEEEeCCc
Q 031443 114 -DMFKGSMRIAVDKW 127 (159)
Q Consensus 114 -~~~~G~~~L~vgk~ 127 (159)
..|.+.+.+.+..-
T Consensus 74 ~d~~~~~~~~~~~~~ 88 (1213)
T TIGR01405 74 LDNFSRDLQMIIKDI 88 (1213)
T ss_pred ccCCCCceEEEeeee
Confidence 35667777777753
No 113
>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=59.30 E-value=60 Score=22.88 Aligned_cols=60 Identities=18% Similarity=0.167 Sum_probs=39.6
Q ss_pred ceEEEEEEeeCceeEEEEEecC-------CcCCCCCCCEEEEeceEEcee--CCeEEEEeCCceeEEEc
Q 031443 74 TRIAECLVGDDTGTILFTARND-------QVDLMKPGTTVILRNAKIDMF--KGSMRIAVDKWGRIEAT 133 (159)
Q Consensus 74 ~~V~~~lVgDeTG~I~ltlWde-------~~~~i~~Gdvv~I~na~v~~~--~G~~~L~vgk~g~I~~~ 133 (159)
+.++=+.|-|.+|.+.+.+=.+ .+..+..|++|.|.+.....- .+.+||.+...--+...
T Consensus 15 gk~~Fi~lrD~~g~iQ~v~~~~~~~~~~~~~~~l~~~s~v~V~G~v~~~~~~~~~~Ei~~~~i~vl~~a 83 (103)
T cd04319 15 GKKAFIVLRDSTGIVQAVFSKDLNEEAYREAKKVGIESSVIVEGAVKADPRAPGGAEVHGEKLEIIQNV 83 (103)
T ss_pred CCeEEEEEecCCeeEEEEEeCCCCHHHHHHHhCCCCCCEEEEEEEEEECCCCCCCEEEEEEEEEEEecC
Confidence 3456678899999988766432 123478999999999766432 24578887664444333
No 114
>COG1190 LysU Lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]
Probab=58.92 E-value=59 Score=30.34 Aligned_cols=72 Identities=11% Similarity=0.210 Sum_probs=54.3
Q ss_pred ceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecCCc---------CCCCCCCEEEEeceEEceeCC
Q 031443 48 HNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARNDQV---------DLMKPGTTVILRNAKIDMFKG 118 (159)
Q Consensus 48 vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde~~---------~~i~~Gdvv~I~na~v~~~~G 118 (159)
|.+-++|+.+-. .|+++=+.|-|.+|.|.+-+-.+.. ..++-||+|-+.+...+...|
T Consensus 64 v~vAGRi~~~R~-------------~GK~~F~~i~d~~gkiQ~yi~k~~~~~~~~~~~~~~~dlGDiigv~G~~~~T~~G 130 (502)
T COG1190 64 VSVAGRIMTIRN-------------MGKASFADLQDGSGKIQLYVNKDEVGEEVFEALFKKLDLGDIIGVEGPLFKTKTG 130 (502)
T ss_pred eEEecceeeecc-------------cCceeEEEEecCCceEEEEEeccccchhhHHHHHhccccCCEEeeeeeeeecCCC
Confidence 666666666432 2577888999999999887764321 234679999999999999999
Q ss_pred eEEEEeCCceeEEE
Q 031443 119 SMRIAVDKWGRIEA 132 (159)
Q Consensus 119 ~~~L~vgk~g~I~~ 132 (159)
.+++++..+--+.+
T Consensus 131 elSv~v~~~~lLsK 144 (502)
T COG1190 131 ELSVSVEELRLLSK 144 (502)
T ss_pred ceEEEEEEEeeecc
Confidence 99999999865533
No 115
>PRK05813 single-stranded DNA-binding protein; Provisional
Probab=57.62 E-value=44 Score=27.70 Aligned_cols=65 Identities=14% Similarity=0.073 Sum_probs=47.5
Q ss_pred CCCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeC-----ceeEEEEEecCCc---CCCCCCCEEEEeceEEce
Q 031443 44 GTNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDD-----TGTILFTARNDQV---DLMKPGTTVILRNAKIDM 115 (159)
Q Consensus 44 ~~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDe-----TG~I~ltlWde~~---~~i~~Gdvv~I~na~v~~ 115 (159)
+++.+.|.+++-.-.+.+.++ .| ..|+...||=. |--|++++|+.++ ..++.||-|.|.+-....
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 356678888888766655433 34 46888888843 6789999998544 347999999999887643
No 116
>PRK00476 aspS aspartyl-tRNA synthetase; Validated
Probab=57.56 E-value=75 Score=29.98 Aligned_cols=81 Identities=9% Similarity=0.095 Sum_probs=55.6
Q ss_pred CceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecC-----CcCCCCCCCEEEEeceEEcee-----
Q 031443 47 GHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARND-----QVDLMKPGTTVILRNAKIDMF----- 116 (159)
Q Consensus 47 ~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde-----~~~~i~~Gdvv~I~na~v~~~----- 116 (159)
.|.+.+.|-.+-. .+.++=+.|-|.+|.+.+++=.. .+..+..|++|.|.+.....-
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 TVTLCGWVHRRRD-------------HGGLIFIDLRDREGIVQVVFDPDAEAFEVAESLRSEYVIQVTGTVRARPEGTVN 85 (588)
T ss_pred EEEEEEEEEEEEe-------------CCCeEEEEEEeCCceEEEEEeCCHHHHHHHhCCCCCCEEEEEEEEEecCCcccC
Confidence 3777777766432 14577788999999998876321 234589999999999777532
Q ss_pred ----CCeEEEEeCCceeEEEcCCCcEEE
Q 031443 117 ----KGSMRIAVDKWGRIEATEPAKFVV 140 (159)
Q Consensus 117 ----~G~~~L~vgk~g~I~~~~~~~~~v 140 (159)
.|.++|.+.+.--+.+..+.++.+
T Consensus 86 ~~~~~g~~El~~~~i~il~~a~~lP~~~ 113 (588)
T PRK00476 86 PNLPTGEIEVLASELEVLNKSKTLPFPI 113 (588)
T ss_pred ccCCCCcEEEEEeEEEEEecCCCCCCcc
Confidence 567999888876555554344444
No 117
>COG3481 Predicted HD-superfamily hydrolase [General function prediction only]
Probab=57.00 E-value=5.2 Score=34.60 Aligned_cols=58 Identities=19% Similarity=0.303 Sum_probs=45.3
Q ss_pred EEEEEEeeCceeEEEEEecCC---cCCCCCCCEEEEeceEEceeCCeEEEEeCCceeEEEcC
Q 031443 76 IAECLVGDDTGTILFTARNDQ---VDLMKPGTTVILRNAKIDMFKGSMRIAVDKWGRIEATE 134 (159)
Q Consensus 76 V~~~lVgDeTG~I~ltlWde~---~~~i~~Gdvv~I~na~v~~~~G~~~L~vgk~g~I~~~~ 134 (159)
.-...+.|.||.|.=.+|+-. .+.+.+|.++.+.+.. ..+++...+++-+-+-++...
T Consensus 22 ~l~l~~~d~~gei~~~~wd~~~~~~~~~~~~~Vv~~~g~~-~~~~~~~q~ki~~~r~~~~~~ 82 (287)
T COG3481 22 KLKLTLQDKTGEIEAKLWDALKNDEEAFKPGMVVHVEGVK-EVYRGRKQHKIIRIRLITDSD 82 (287)
T ss_pred hheeeeccccceecccccccccccHhhhCcCceeccccce-ecccccchheeeecccccccC
Confidence 456889999999999999843 3458999999887654 678888888888866665543
No 118
>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=56.97 E-value=26 Score=26.71 Aligned_cols=73 Identities=15% Similarity=0.099 Sum_probs=48.7
Q ss_pred eecccCC--CCCCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecC--CcCCCCCCCEEEEece
Q 031443 36 TKVDQLK--PGTNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARND--QVDLMKPGTTVILRNA 111 (159)
Q Consensus 36 ~kI~dL~--P~~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde--~~~~i~~Gdvv~I~na 111 (159)
+.|++.. ++...|.|++.|++--.- -..++.|.||.|.+.+=++ ..-.+.|+|.|+|.+-
T Consensus 46 ~tV~~a~~~~Ddt~V~L~G~Iv~~l~~----------------d~Y~F~D~TG~I~VeId~~~w~G~~v~p~d~V~I~Ge 109 (126)
T TIGR00156 46 MTVDFAKSMHDGASVTLRGNIISHIGD----------------DRYVFRDKSGEINVVIPAAVWNGREVQPKDMVNISGS 109 (126)
T ss_pred EeHHHHhhCCCCCEEEEEEEEEEEeCC----------------ceEEEECCCCCEEEEECHHHcCCCcCCCCCEEEEEEE
Confidence 3344433 456668999998873210 1357889999999976332 2234799999999998
Q ss_pred EEceeCCeEEEEeC
Q 031443 112 KIDMFKGSMRIAVD 125 (159)
Q Consensus 112 ~v~~~~G~~~L~vg 125 (159)
.-+.|++ .+|-+.
T Consensus 110 VDk~~~~-~~IdV~ 122 (126)
T TIGR00156 110 LDKKSAP-AEVDVT 122 (126)
T ss_pred ECCCCCC-eEEEEE
Confidence 8777764 555443
No 119
>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=56.76 E-value=67 Score=30.42 Aligned_cols=81 Identities=10% Similarity=0.120 Sum_probs=55.5
Q ss_pred CceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecC-----CcCCCCCCCEEEEeceEEc-------
Q 031443 47 GHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARND-----QVDLMKPGTTVILRNAKID------- 114 (159)
Q Consensus 47 ~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde-----~~~~i~~Gdvv~I~na~v~------- 114 (159)
.|.|.+.|-.+-. .+.+.=+.|-|.+|.|.+.+=.+ .+..+..|++|.|.+-...
T Consensus 17 ~V~l~GwV~~~R~-------------~Gkl~Fi~LrD~sg~iQvv~~~~~~~~~~~~~L~~esvV~V~G~v~~r~~~~~n 83 (583)
T TIGR00459 17 TVTLAGWVNRRRD-------------LGGLIFIDLRDRSGIVQVVCDPDADALKLAKGLRNEDVVQVKGKVSARPEGNIN 83 (583)
T ss_pred EEEEEEEEEEEEc-------------CCCcEEEEEEeCCccEEEEEeCCHHHHHHHhcCCCCCEEEEEEEEEeCCccccC
Confidence 4778888866432 14477788999999999876432 2345899999999997764
Q ss_pred --eeCCeEEEEeCCceeEEEcCCCcEEE
Q 031443 115 --MFKGSMRIAVDKWGRIEATEPAKFVV 140 (159)
Q Consensus 115 --~~~G~~~L~vgk~g~I~~~~~~~~~v 140 (159)
.-.|.++|.+...--+.+.....+.+
T Consensus 84 ~~~~tg~iEl~~~~i~iL~~a~~~P~~~ 111 (583)
T TIGR00459 84 RNLDTGEIEILAESITLLNKSKTPPLII 111 (583)
T ss_pred ccCCCCcEEEEEeEEEEeecCCCCCCcc
Confidence 33577888887765555444334443
No 120
>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed
Probab=55.76 E-value=79 Score=28.12 Aligned_cols=75 Identities=12% Similarity=0.067 Sum_probs=51.2
Q ss_pred CCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecCCcC----CCCCCCEEEEeceEEce-eCCe
Q 031443 45 TNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARNDQVD----LMKPGTTVILRNAKIDM-FKGS 119 (159)
Q Consensus 45 ~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde~~~----~i~~Gdvv~I~na~v~~-~~G~ 119 (159)
..++-|.+.|-+..... .|. +..-+-|++..|+.++|..... .++.|+-|.+.+...-+ -+|.
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 45677777766654321 133 5577899999999999975332 25899999998776532 3577
Q ss_pred EEEEeCCceeEEEcC
Q 031443 120 MRIAVDKWGRIEATE 134 (159)
Q Consensus 120 ~~L~vgk~g~I~~~~ 134 (159)
++|++.. |++.+
T Consensus 91 ~ql~v~~---i~~~g 102 (438)
T PRK00286 91 YQLIVEE---IEPAG 102 (438)
T ss_pred EEEEEEE---eeeCC
Confidence 8888766 55553
No 121
>PRK07772 single-stranded DNA-binding protein; Provisional
Probab=54.39 E-value=42 Score=27.10 Aligned_cols=30 Identities=10% Similarity=0.093 Sum_probs=23.7
Q ss_pred ceeEEEEEecCCc----CCCCCCCEEEEeceEEc
Q 031443 85 TGTILFTARNDQV----DLMKPGTTVILRNAKID 114 (159)
Q Consensus 85 TG~I~ltlWde~~----~~i~~Gdvv~I~na~v~ 114 (159)
|=-+++++|..++ ..++.||.|.|.+-+..
T Consensus 52 t~fi~V~~Wg~~Ae~va~~L~KGd~V~V~GrL~~ 85 (186)
T PRK07772 52 ALFLRCSIWRQAAENVAESLTKGMRVIVTGRLKQ 85 (186)
T ss_pred ceEEEEEEecHHHHHHHHhcCCCCEEEEEEEEEc
Confidence 4468999998644 44799999999987764
No 122
>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=54.02 E-value=1e+02 Score=24.03 Aligned_cols=81 Identities=14% Similarity=0.106 Sum_probs=51.2
Q ss_pred CCCCCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCce-eEEEEEecCCc-----CCCCCCCEEEEeceEEce
Q 031443 42 KPGTNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTG-TILFTARNDQV-----DLMKPGTTVILRNAKIDM 115 (159)
Q Consensus 42 ~P~~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG-~I~ltlWde~~-----~~i~~Gdvv~I~na~v~~ 115 (159)
.|.=.-++++|-|+++... .+...-+.++|+.- -+-+.+|.+.. +.+++|..|-..|=.-|-
T Consensus 15 ~pp~~EvD~VG~VvsV~~~------------~~f~~~vYLsD~~~Nll~Ikfw~~l~~~~~eDilk~~~liA~SNLqwR~ 82 (143)
T PF09104_consen 15 QPPYGEVDTVGFVVSVSKK------------QGFQPLVYLSDECHNLLAIKFWTGLNQYGYEDILKPGSLIAASNLQWRP 82 (143)
T ss_dssp -TCCCEEEEEEEEEEEE--------------TTS--EEEEE-TTS-EEEEEESS-------SS---TT-EEEEEEEEE-S
T ss_pred CCCccccceEEEEEEEEec------------CCCceeEEeecCCccEEEEEeccCccccchhhhcCcceEEEEeeeEeec
Confidence 4555679999999999321 12233377899976 77888997543 667999999999988763
Q ss_pred e--CCeEEEEeCCceeEEEcC
Q 031443 116 F--KGSMRIAVDKWGRIEATE 134 (159)
Q Consensus 116 ~--~G~~~L~vgk~g~I~~~~ 134 (159)
. .+-+.+..|..+.+...|
T Consensus 83 ~s~s~iP~~~A~d~S~FS~nP 103 (143)
T PF09104_consen 83 ESTSGIPTLFATDLSVFSANP 103 (143)
T ss_dssp -TTSSS-EEEEECCEEEESS-
T ss_pred ccccCCCeeEeccceeeecCc
Confidence 2 478999999998887775
No 123
>PRK08182 single-stranded DNA-binding protein; Provisional
Probab=53.13 E-value=28 Score=26.89 Aligned_cols=66 Identities=11% Similarity=-0.002 Sum_probs=39.0
Q ss_pred CCceEEEEEEecCcccccccCCCCCCCcceEEEEEEe------eCce--------eEEEEEecCCc----CCCCCCCEEE
Q 031443 46 NGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVG------DDTG--------TILFTARNDQV----DLMKPGTTVI 107 (159)
Q Consensus 46 ~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVg------DeTG--------~I~ltlWde~~----~~i~~Gdvv~ 107 (159)
+.|.|.+++-.-.+.+.+. .|.. ..-.|++..|+ +.+| -+++++|+..+ ..++.|+.|.
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 3456666666654444332 2210 00126666664 2333 57899998544 4479999999
Q ss_pred EeceEEc
Q 031443 108 LRNAKID 114 (159)
Q Consensus 108 I~na~v~ 114 (159)
|.+-...
T Consensus 80 V~GrL~~ 86 (148)
T PRK08182 80 VEGRMER 86 (148)
T ss_pred EEEEEEe
Confidence 9987764
No 124
>PRK09919 anti-adapter protein IraM; Provisional
Probab=51.36 E-value=53 Score=24.79 Aligned_cols=38 Identities=8% Similarity=0.142 Sum_probs=29.2
Q ss_pred eEEEEEecCCcCCCCCCCEEEEeceEEceeCCeEEEEe
Q 031443 87 TILFTARNDQVDLMKPGTTVILRNAKIDMFKGSMRIAV 124 (159)
Q Consensus 87 ~I~ltlWde~~~~i~~Gdvv~I~na~v~~~~G~~~L~v 124 (159)
..+|.+|-.---.+.+||++.+.+.-+-..+-...|.|
T Consensus 26 nlKlilWY~~d~~L~pG~~i~~~~~gvliNdk~~pItI 63 (114)
T PRK09919 26 NLKLILWYQADIFLPPGSIITPVKSGVLLNDKPYPITI 63 (114)
T ss_pred cceEEEEEeeeEEeCCCCEEEEcCCeEEECCcEeEEEE
Confidence 57899998432347999999999999877776666654
No 125
>PRK06863 single-stranded DNA-binding protein; Provisional
Probab=50.97 E-value=52 Score=26.15 Aligned_cols=64 Identities=11% Similarity=0.034 Sum_probs=40.7
Q ss_pred CCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEee--------------CceeEEEEEecCCc----CCCCCCCEE
Q 031443 45 TNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGD--------------DTGTILFTARNDQV----DLMKPGTTV 106 (159)
Q Consensus 45 ~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgD--------------eTG~I~ltlWde~~----~~i~~Gdvv 106 (159)
+..|.|.+++-.-.+.+.+. +| ..++...||= .|=-+++++|+.++ ..++.|+.|
T Consensus 4 ~N~V~LiGrLg~DPElR~t~--nG-----~~va~fsVAvn~~~~d~~~Ge~~e~t~w~~Vv~fgk~AE~v~~~LkKGs~V 76 (168)
T PRK06863 4 INKVIIVGHLGNDPEIRTMP--NG-----EAVANISVATSESWTDKNTGERREVTEWHRIVFYRRQAEVAGEYLRKGSQV 76 (168)
T ss_pred ccEEEEEEEcCCCCEEEEcC--CC-----CEEEEEEEEecCcccccCCCcccccceEEEEEEEhHHHHHHHHHCCCCCEE
Confidence 45567777776644444322 33 3455555541 23368999998644 447999999
Q ss_pred EEeceEEce
Q 031443 107 ILRNAKIDM 115 (159)
Q Consensus 107 ~I~na~v~~ 115 (159)
.|.+.....
T Consensus 77 ~VeGrL~~r 85 (168)
T PRK06863 77 YVEGRLKTR 85 (168)
T ss_pred EEEEEEEeC
Confidence 999987643
No 126
>KOG2012 consensus Ubiquitin activating enzyme UBA1 [Posttranslational modification, protein turnover, chaperones]
Probab=49.15 E-value=23 Score=35.24 Aligned_cols=57 Identities=14% Similarity=0.158 Sum_probs=45.9
Q ss_pred EEEecCCcCCCCCCCEEEEeceEEceeCCeEEEEeCCceeEEEcCCCcEEEccCCCccccce
Q 031443 90 FTARNDQVDLMKPGTTVILRNAKIDMFKGSMRIAVDKWGRIEATEPAKFVVKEDNNLSLVEY 151 (159)
Q Consensus 90 ltlWde~~~~i~~Gdvv~I~na~v~~~~G~~~L~vgk~g~I~~~~~~~~~vne~~N~S~iey 151 (159)
+|+-++.--.++-||.|.+. +.+|..+||=+.=-+|+..+++.|++.++.++++.-+
T Consensus 197 vT~ld~~rH~lEdGd~V~Fs-----EveGm~eLN~~~P~kI~v~~p~sf~Igdt~~f~~y~~ 253 (1013)
T KOG2012|consen 197 VTCLDGARHGFEDGDLVTFS-----EVEGMTELNDCKPRKITVLGPYSFSIGDTTEFGEYKK 253 (1013)
T ss_pred EEEecCccccCccCCEEEEE-----eeccccccCCCCceEEEEecCceEEeccccchhhhhc
Confidence 34456555568899999886 7788999988888899999999999999888887543
No 127
>PRK12820 bifunctional aspartyl-tRNA synthetase/aspartyl/glutamyl-tRNA amidotransferase subunit C; Provisional
Probab=48.58 E-value=1.3e+02 Score=29.21 Aligned_cols=91 Identities=14% Similarity=0.107 Sum_probs=59.3
Q ss_pred cccCCCCCC--CceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecCC--------cCCCCCCCEEE
Q 031443 38 VDQLKPGTN--GHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARNDQ--------VDLMKPGTTVI 107 (159)
Q Consensus 38 I~dL~P~~~--~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde~--------~~~i~~Gdvv~ 107 (159)
..+|.+... .|.|.+.|-.+-. .+.+.=+.|-|.+|.|.+++=.+. +..+..|++|.
T Consensus 9 cg~l~~~~~g~~V~l~GWV~~~R~-------------~G~l~FidLRD~~G~iQvV~~~~~~~~~~~~~~~~L~~EsvV~ 75 (706)
T PRK12820 9 CGHLSLDDTGREVCLAGWVDAFRD-------------HGELLFIHLRDRNGFIQAVFSPEAAPADVYELAASLRAEFCVA 75 (706)
T ss_pred cccCChhhCCCEEEEEEEEEEEEc-------------CCCcEEEEEEeCCccEEEEEeCCcCCHHHHHHHhcCCCCCEEE
Confidence 345555332 3777777765432 144777889999999998774322 24589999999
Q ss_pred EeceEEce---------eCCeEEEEeCCceeEEEcCCCcEEEc
Q 031443 108 LRNAKIDM---------FKGSMRIAVDKWGRIEATEPAKFVVK 141 (159)
Q Consensus 108 I~na~v~~---------~~G~~~L~vgk~g~I~~~~~~~~~vn 141 (159)
|.|-.... -.|.++|.+.+.--+.+.....|.++
T Consensus 76 V~G~v~~r~~~~~n~~~~tg~iEl~~~~i~iL~~a~~lP~~i~ 118 (706)
T PRK12820 76 LQGEVQKRLEETENPHIETGDIEVFVRELSILAASEALPFAIS 118 (706)
T ss_pred EEeEEeccCccccCCCCCCCcEEEEeeEEEEEecCCCCCCCCc
Confidence 99976652 23778998888666655543344443
No 128
>PRK10053 hypothetical protein; Provisional
Probab=48.32 E-value=46 Score=25.53 Aligned_cols=73 Identities=14% Similarity=0.107 Sum_probs=48.5
Q ss_pred eecccCC--CCCCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecC--CcCCCCCCCEEEEece
Q 031443 36 TKVDQLK--PGTNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARND--QVDLMKPGTTVILRNA 111 (159)
Q Consensus 36 ~kI~dL~--P~~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde--~~~~i~~Gdvv~I~na 111 (159)
+.|++.. .+...|.|++.|+.--.- -..++.|.||.|.+-+=++ ..-.+.|.|.|+|.+-
T Consensus 50 ~tV~~a~~~~Dd~~V~L~G~Iv~~lg~----------------d~Y~F~D~tG~I~VeID~~~w~G~~v~p~~kV~I~Ge 113 (130)
T PRK10053 50 MTVEQAKTMHDGATVSLRGNLIDHKGD----------------DRYVFRDKSGEINVIIPAAVFDGREVQPDQMININGS 113 (130)
T ss_pred EEHHHhhcCcCCCeEEEEEEEEEEeCC----------------ceEEEECCCCcEEEEeCHHHcCCCcCCCCCEEEEEEE
Confidence 3455444 345668888888762210 1357889999999976332 2235899999999998
Q ss_pred EEceeCCeEEEEeC
Q 031443 112 KIDMFKGSMRIAVD 125 (159)
Q Consensus 112 ~v~~~~G~~~L~vg 125 (159)
+-+.|.. .++-+.
T Consensus 114 vDk~~~~-~~IdV~ 126 (130)
T PRK10053 114 LDKKSAP-PVVRVT 126 (130)
T ss_pred ECCCCCC-eEEEEE
Confidence 8877764 455443
No 129
>PRK07135 dnaE DNA polymerase III DnaE; Validated
Probab=47.97 E-value=40 Score=33.83 Aligned_cols=69 Identities=13% Similarity=0.211 Sum_probs=49.2
Q ss_pred eecccCCCCCCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecC---CcCCCCCCCEEEEeceE
Q 031443 36 TKVDQLKPGTNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARND---QVDLMKPGTTVILRNAK 112 (159)
Q Consensus 36 ~kI~dL~P~~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde---~~~~i~~Gdvv~I~na~ 112 (159)
.++.+|. ....+.+-+.|.++...+ ++ | ..++-+.+.|.||.+.+++|.+ ....+.+|+.+.+.+-.
T Consensus 889 ~~~~~l~-~~~~~~v~g~i~~~~~~~--K~--g-----~~maf~~~eD~~~~~e~~~F~~~~~~~~~l~~~~~~~~~~~~ 958 (973)
T PRK07135 889 IRLKDLR-INTEYRLAIEVKNVKRLR--KA--N-----KEYKKVILSDDSVEITIFVNDNDYLLFETLKKGDIYEFLISK 958 (973)
T ss_pred hhHHHhc-CCCeEEEEEEEEEEEEEe--eC--C-----CeEEEEEEEECCCcEEEEEcHHHHHHHHHhhcCCEEEEEEEE
Confidence 4677774 334567888888877654 22 3 4699999999999999999964 22337888888886554
Q ss_pred Ec
Q 031443 113 ID 114 (159)
Q Consensus 113 v~ 114 (159)
.+
T Consensus 959 ~~ 960 (973)
T PRK07135 959 SK 960 (973)
T ss_pred cC
Confidence 43
No 130
>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=46.62 E-value=87 Score=20.98 Aligned_cols=70 Identities=17% Similarity=0.110 Sum_probs=42.3
Q ss_pred cCCCCCCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecCCcCCCCCCCEEEEeceEEceeCCe
Q 031443 40 QLKPGTNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARNDQVDLMKPGTTVILRNAKIDMFKGS 119 (159)
Q Consensus 40 dL~P~~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde~~~~i~~Gdvv~I~na~v~~~~G~ 119 (159)
||+.|+ -+.+.|-++.+- |-+.+.-+++=+|-++.+--... ..+++|+.+...=-.+...++.
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 345554 388888888752 44555322233666664322211 5689999998875555666677
Q ss_pred EEEEeCC
Q 031443 120 MRIAVDK 126 (159)
Q Consensus 120 ~~L~vgk 126 (159)
+.|++..
T Consensus 64 v~ls~k~ 70 (74)
T cd05694 64 VSLSADP 70 (74)
T ss_pred EEEEEee
Confidence 7777643
No 131
>PRK06642 single-stranded DNA-binding protein; Provisional
Probab=46.33 E-value=69 Score=24.81 Aligned_cols=63 Identities=14% Similarity=0.106 Sum_probs=41.6
Q ss_pred CCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEe------e--------CceeEEEEEecC-Cc----CCCCCCCE
Q 031443 45 TNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVG------D--------DTGTILFTARND-QV----DLMKPGTT 105 (159)
Q Consensus 45 ~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVg------D--------eTG~I~ltlWde-~~----~~i~~Gdv 105 (159)
++.|.|.+++-.-.+.+.+. +| ..++..-|| | +|=-+++++|+. .+ ..++.|+.
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 LNKVILIGNVGRDPEIRTTG--EG-----KKIINLSLATTETWKDRITSERKERTEWHRVVIFSEGLVSVVERYVTKGSK 77 (152)
T ss_pred ceEEEEEEEccCCceEEECC--CC-----CEEEEEEEEeccccccccCCccccceeEEEEEEeChHHHHHHHHhCCCCCE
Confidence 45577777777654444322 23 356666666 2 345788999985 33 34799999
Q ss_pred EEEeceEEc
Q 031443 106 VILRNAKID 114 (159)
Q Consensus 106 v~I~na~v~ 114 (159)
|.|.+-...
T Consensus 78 V~V~GrL~~ 86 (152)
T PRK06642 78 LYIEGSLQT 86 (152)
T ss_pred EEEEEEEEe
Confidence 999988763
No 132
>PLN02603 asparaginyl-tRNA synthetase
Probab=46.26 E-value=1.7e+02 Score=27.62 Aligned_cols=87 Identities=15% Similarity=0.173 Sum_probs=56.1
Q ss_pred ceeecccCCCC--------CCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCcee--EEEEEecCCc-----C
Q 031443 34 VFTKVDQLKPG--------TNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGT--ILFTARNDQV-----D 98 (159)
Q Consensus 34 ~~~kI~dL~P~--------~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~--I~ltlWde~~-----~ 98 (159)
....|+++.+. .+.|.|.+.|-++-. .+.++=+.|-|.+|. |.+++=.+.. .
T Consensus 88 ~~~~~~~~~~~~~~~~~~~g~~V~v~GwV~~iR~-------------~g~~~Fi~l~Dgs~~~~lQ~v~~~~~~~~~~l~ 154 (565)
T PLN02603 88 KKLRIADVKGGEDEGLARVGKTLNVMGWVRTLRA-------------QSSVTFIEVNDGSCLSNMQCVMTPDAEGYDQVE 154 (565)
T ss_pred CceEhhhcccccccccccCCCEEEEEEEEEEEEe-------------CCCeEEEEEECCCCCEeEEEEEECcHHHHHHHh
Confidence 44678888743 244677777765432 145777888998874 7776532211 1
Q ss_pred --CCCCCCEEEEeceEEceeC--CeEEEEeCCceeEEEc
Q 031443 99 --LMKPGTTVILRNAKIDMFK--GSMRIAVDKWGRIEAT 133 (159)
Q Consensus 99 --~i~~Gdvv~I~na~v~~~~--G~~~L~vgk~g~I~~~ 133 (159)
.+..|++|.|.+-...--. +.++|.+.+---+.+.
T Consensus 155 ~~~l~~gs~V~V~G~v~~~~~~~~~~EL~v~~i~vlg~a 193 (565)
T PLN02603 155 SGLITTGASVLVQGTVVSSQGGKQKVELKVSKIVVVGKS 193 (565)
T ss_pred hcCCCCCCEEEEEEEEEecCCCCccEEEEEeEEEEEECC
Confidence 2789999999998775433 3489988775444444
No 133
>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=45.43 E-value=25 Score=24.83 Aligned_cols=31 Identities=26% Similarity=0.374 Sum_probs=22.5
Q ss_pred EEEEeeCceeEEEEEecCCcCCCCCCCEEEEece
Q 031443 78 ECLVGDDTGTILFTARNDQVDLMKPGTTVILRNA 111 (159)
Q Consensus 78 ~~lVgDeTG~I~ltlWde~~~~i~~Gdvv~I~na 111 (159)
.+.+|.+.|...| ....-.|++||.|++.|.
T Consensus 2 ~v~~g~~~g~~~F---~P~~i~v~~G~~V~~~N~ 32 (99)
T TIGR02656 2 TVKMGADKGALVF---EPAKISIAAGDTVEWVNN 32 (99)
T ss_pred EEEEecCCCceeE---eCCEEEECCCCEEEEEEC
Confidence 3567777888877 333345799999999875
No 134
>PRK10260 L,D-transpeptidase; Provisional
Probab=42.98 E-value=15 Score=32.15 Aligned_cols=41 Identities=20% Similarity=0.250 Sum_probs=33.0
Q ss_pred CceeEEEEEec--CCcCCCCCCCEEEEeceEEcee---CCeEEEEe
Q 031443 84 DTGTILFTARN--DQVDLMKPGTTVILRNAKIDMF---KGSMRIAV 124 (159)
Q Consensus 84 eTG~I~ltlWd--e~~~~i~~Gdvv~I~na~v~~~---~G~~~L~v 124 (159)
..|||||.-|| ...+.+..|..|.|.|.-++.- .|.+.|-+
T Consensus 207 ShGCIRl~n~Di~~L~~~V~~Gt~V~ii~~pvk~~~~~~g~~~lEv 252 (306)
T PRK10260 207 SHGCVRLRNEDIKFLFEKVPVGTRVQFIDEPVKATTEPDGSRYIEV 252 (306)
T ss_pred CCCeeCCCHHHHHHHHhcCCCCCEEEEecCceeccccCCCeEEEEE
Confidence 58999999998 4667899999999999888763 46665544
No 135
>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=41.52 E-value=59 Score=23.90 Aligned_cols=66 Identities=18% Similarity=0.154 Sum_probs=31.4
Q ss_pred CCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeC--ceeEEEEEecCC-----cCCCCCCCEEEEeceEEcee-
Q 031443 45 TNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDD--TGTILFTARNDQ-----VDLMKPGTTVILRNAKIDMF- 116 (159)
Q Consensus 45 ~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDe--TG~I~ltlWde~-----~~~i~~Gdvv~I~na~v~~~- 116 (159)
.+.+.++++|.++..- + + ... -.+.+++ .+.|.+.+=++. ...+++||.|.|.+.+...-
T Consensus 67 gK~i~vtG~V~~I~~~--~----~----~~~--~~~~~~~~~~~~v~~~~~~~~~~~~~~~~l~~G~~Vti~G~~~g~~~ 134 (144)
T PF12869_consen 67 GKIIEVTGTVSSIDKG--F----G----DNY--VVLLGTENGFAGVQCYFSNDQEKRASVAKLKKGQKVTIKGICTGYSL 134 (144)
T ss_dssp T-EEEEEEEEEEEEE---S----T----T-E--EEEEE-TT-S-S--EEEEEEGGGHHHHHH--TTSEEEEEEE-----S
T ss_pred CCEEEEEEEEEEEEEc--C----C----CcE--EEEccCCCCceeEEEEEccchhhhhhHhcCCCCCEEEEEEEEEeeec
Confidence 5668999999998651 1 1 012 2223443 344444444444 22389999999999887763
Q ss_pred CCeEEE
Q 031443 117 KGSMRI 122 (159)
Q Consensus 117 ~G~~~L 122 (159)
.+.+.|
T Consensus 135 ~~~v~l 140 (144)
T PF12869_consen 135 MGVVML 140 (144)
T ss_dssp SS-EEE
T ss_pred CCcEEe
Confidence 565554
No 136
>PRK10190 L,D-transpeptidase; Provisional
Probab=41.04 E-value=18 Score=31.71 Aligned_cols=42 Identities=21% Similarity=0.275 Sum_probs=33.6
Q ss_pred CceeEEEEEec--CCcCCCCCCCEEEEeceEEcee---CCeEEEEeC
Q 031443 84 DTGTILFTARN--DQVDLMKPGTTVILRNAKIDMF---KGSMRIAVD 125 (159)
Q Consensus 84 eTG~I~ltlWd--e~~~~i~~Gdvv~I~na~v~~~---~G~~~L~vg 125 (159)
.-|||||.-|| +..+.+..|..|.|.|--++.. .|.+.|-+-
T Consensus 204 ShGCIRm~n~Di~~Lf~~V~~GT~V~ii~~pvk~~~~~~g~~ylEvH 250 (310)
T PRK10190 204 SQGCIRLRNDDIKYLFDNVPVGTRVQIIDQPVKYTTEPDGSRWLEVH 250 (310)
T ss_pred CCceeCcCHHHHHHHHhhCCCCCEEEEecccEEEEEcCCCEEEEEEe
Confidence 68999999998 4667799999999999998873 466555443
No 137
>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=40.60 E-value=30 Score=24.68 Aligned_cols=37 Identities=19% Similarity=0.196 Sum_probs=27.4
Q ss_pred EEEEEEeeCceeEEEEEecCCcCCCCCCCEEE-EeceE
Q 031443 76 IAECLVGDDTGTILFTARNDQVDLMKPGTTVI-LRNAK 112 (159)
Q Consensus 76 V~~~lVgDeTG~I~ltlWde~~~~i~~Gdvv~-I~na~ 112 (159)
..-.++-|.-|.+.|.+|-.-.-.+++||.+. |.||.
T Consensus 16 ~~~l~l~~a~g~LkmIAEv~s~~~l~~GD~LtPl~dA~ 53 (82)
T PF11183_consen 16 CHVLLLCDAGGALKMIAEVTSDFRLQEGDKLTPLQDAL 53 (82)
T ss_dssp EEEEEEEETTTTCEEEEEEEESS---TT-EEEESSSSE
T ss_pred EEEEEEecCCCCeEEEEEeecCcccCCCCCccccccce
Confidence 55678899999999999975445689999999 99983
No 138
>COG1376 ErfK Uncharacterized protein conserved in bacteria [Function unknown]
Probab=40.25 E-value=12 Score=30.13 Aligned_cols=29 Identities=21% Similarity=0.360 Sum_probs=24.1
Q ss_pred eCceeEEEEEec--CCcCCCCCCCEEEEece
Q 031443 83 DDTGTILFTARN--DQVDLMKPGTTVILRNA 111 (159)
Q Consensus 83 DeTG~I~ltlWd--e~~~~i~~Gdvv~I~na 111 (159)
-..|||||.-|| ++.+.+..|+.|.|.+.
T Consensus 201 ~ShGCIRL~n~Da~~ly~~v~~Gt~V~v~~~ 231 (232)
T COG1376 201 VSHGCIRLSNQDAKDLYNRVPVGTPVVVIDT 231 (232)
T ss_pred cCCceEecCchhHHHHHhhCCCCCEEEEeeC
Confidence 357999999998 56688999999998763
No 139
>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=39.44 E-value=1.3e+02 Score=23.36 Aligned_cols=82 Identities=15% Similarity=0.050 Sum_probs=49.7
Q ss_pred ceEEEEEEecCcccccccCCCCCCCcceEEEEEE-----eeCceeEEEEEecC-CcCCCCCCCEEEEeceEEcee--CCe
Q 031443 48 HNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLV-----GDDTGTILFTARND-QVDLMKPGTTVILRNAKIDMF--KGS 119 (159)
Q Consensus 48 vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lV-----gDeTG~I~ltlWde-~~~~i~~Gdvv~I~na~v~~~--~G~ 119 (159)
.=++++|+++.....|..+. ..|.+++= ++.-|..|.-+... --..+.+|..+-|.+.-...+ +|.
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 34667777766544443322 22222211 22356666433332 113578999999998865544 467
Q ss_pred EEEEeCCceeEEEcCC
Q 031443 120 MRIAVDKWGRIEATEP 135 (159)
Q Consensus 120 ~~L~vgk~g~I~~~~~ 135 (159)
+++.+|+.+.|+.-|.
T Consensus 110 ~~Y~L~~~tWvE~wP~ 125 (153)
T cd03584 110 MQYLLDSKTWVEKIPS 125 (153)
T ss_pred EEEEeCCCceEEECCC
Confidence 9999999999999863
No 140
>smart00643 C345C Netrin C-terminal Domain.
Probab=39.18 E-value=1.4e+02 Score=21.18 Aligned_cols=50 Identities=18% Similarity=0.287 Sum_probs=34.8
Q ss_pred eeEEEEEecCCc--C-CCCCCCEEEEeceEEcee--CCeEEEEeCCceeEEEcCC
Q 031443 86 GTILFTARNDQV--D-LMKPGTTVILRNAKIDMF--KGSMRIAVDKWGRIEATEP 135 (159)
Q Consensus 86 G~I~ltlWde~~--~-~i~~Gdvv~I~na~v~~~--~G~~~L~vgk~g~I~~~~~ 135 (159)
+.+++-.|.... . .+++|..+-|.+-....+ ++..++.++..+.|++-++
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 455555554322 3 367999999999754444 4468899999999988753
No 141
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=38.63 E-value=1.1e+02 Score=25.93 Aligned_cols=61 Identities=23% Similarity=0.292 Sum_probs=48.0
Q ss_pred cceEEEEEEeeCceeEEEEEecCCcCCCCCCCEEEEeceEEcee-------------CCeEEEEeCCceeEEEc
Q 031443 73 QTRIAECLVGDDTGTILFTARNDQVDLMKPGTTVILRNAKIDMF-------------KGSMRIAVDKWGRIEAT 133 (159)
Q Consensus 73 ~~~V~~~lVgDeTG~I~ltlWde~~~~i~~Gdvv~I~na~v~~~-------------~G~~~L~vgk~g~I~~~ 133 (159)
.-.++.+.-.|.++.+.|++-++....++-|-+|.|.-+.+... ....++.+|.+|.|=..
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 45667788899999999999888778899999999987766432 23568889999988544
No 142
>PF05113 DUF693: Protein of unknown function (DUF693); InterPro: IPR007800 This family consists of uncharacterised proteins from Borrelia burgdorferi.
Probab=38.33 E-value=37 Score=29.58 Aligned_cols=28 Identities=25% Similarity=0.229 Sum_probs=21.1
Q ss_pred eEEEEEec---CCcCCCCCCCEEEEeceEEc
Q 031443 87 TILFTARN---DQVDLMKPGTTVILRNAKID 114 (159)
Q Consensus 87 ~I~ltlWd---e~~~~i~~Gdvv~I~na~v~ 114 (159)
...+++|+ +..+.+++||+|+|.--...
T Consensus 62 qaki~lwNlPLdFt~~ik~gDIVKIYYKKFa 92 (314)
T PF05113_consen 62 QAKIVLWNLPLDFTDNIKTGDIVKIYYKKFA 92 (314)
T ss_pred eeEEEEEecCcccccccCcCcEEEEEeeccc
Confidence 56789998 45566999999999854433
No 143
>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=38.19 E-value=1.7e+02 Score=26.29 Aligned_cols=74 Identities=8% Similarity=0.032 Sum_probs=49.1
Q ss_pred CCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecCCcC----CCCCCCEEEEeceEEce-eCCe
Q 031443 45 TNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARNDQVD----LMKPGTTVILRNAKIDM-FKGS 119 (159)
Q Consensus 45 ~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde~~~----~i~~Gdvv~I~na~v~~-~~G~ 119 (159)
..++-|.+-|-+..... .|. ...-+-|+...|+.++|..... .++.|+-|.+.+...-+ -+|.
T Consensus 17 ~~~v~V~GEisn~~~~~-----------sGH-~YFtLkD~~a~i~~vmf~~~~~~l~f~~~~G~~V~v~g~v~~y~~~G~ 84 (432)
T TIGR00237 17 FLQVWIQGEISNFTQPV-----------SGH-WYFTLKDENAQVRCVMFRGNNNRLKFRPQNGQQVLVRGGISVYEPRGD 84 (432)
T ss_pred CCcEEEEEEecCCeeCC-----------Cce-EEEEEEcCCcEEEEEEEcChhhCCCCCCCCCCEEEEEEEEEEECCCCc
Confidence 34566776666654321 133 4455689999999999975332 25899999998776533 2577
Q ss_pred EEEEeCCceeEEEc
Q 031443 120 MRIAVDKWGRIEAT 133 (159)
Q Consensus 120 ~~L~vgk~g~I~~~ 133 (159)
+.|++.. |++.
T Consensus 85 ~ql~v~~---i~~~ 95 (432)
T TIGR00237 85 YQIICFE---MQPA 95 (432)
T ss_pred EEEEEEE---eccC
Confidence 9998876 5544
No 144
>COG3111 Periplasmic protein with OB-fold [Function unknown]
Probab=36.85 E-value=1.4e+02 Score=23.05 Aligned_cols=47 Identities=15% Similarity=0.239 Sum_probs=34.4
Q ss_pred EEEeeCceeEEEEEecC--CcCCCCCCCEEEEeceEEceeCCeEEEEeCC
Q 031443 79 CLVGDDTGTILFTARND--QVDLMKPGTTVILRNAKIDMFKGSMRIAVDK 126 (159)
Q Consensus 79 ~lVgDeTG~I~ltlWde--~~~~i~~Gdvv~I~na~v~~~~G~~~L~vgk 126 (159)
.++-|.||.|++.+=+. ....+.|-|.|+|.+-.-+.|+. +++-+..
T Consensus 75 y~FrD~sGeI~VeIdd~~w~g~tv~P~dkV~I~GevDk~~~~-~eIdV~~ 123 (128)
T COG3111 75 YVFRDASGEINVDIDDKVWNGQTVTPKDKVRIQGEVDKDWNS-VEIDVKH 123 (128)
T ss_pred EEEEcCCccEEEEecccccCCcccCcccEEEEEeEEcCCCcc-ceeEhhh
Confidence 46779999999976443 22348999999999988887765 5555544
No 145
>KOG1816 consensus Ubiquitin fusion-degradation protein [Posttranslational modification, protein turnover, chaperones]
Probab=36.22 E-value=26 Score=30.57 Aligned_cols=30 Identities=20% Similarity=0.266 Sum_probs=25.3
Q ss_pred eCceeEEEEEecCCcCCCCCCCEEEEeceE
Q 031443 83 DDTGTILFTARNDQVDLMKPGTTVILRNAK 112 (159)
Q Consensus 83 DeTG~I~ltlWde~~~~i~~Gdvv~I~na~ 112 (159)
=|.|.|-|=.|--+...+++||.|+|++..
T Consensus 81 AeEG~vyLP~WMmq~L~le~gdlv~i~~v~ 110 (308)
T KOG1816|consen 81 AEEGRVYLPYWMMQNLLLEEGDLVRIRSVT 110 (308)
T ss_pred ecCceEEeehHhhhhccCCCCCeEEEEEee
Confidence 355899999999777789999999999753
No 146
>COG1570 XseA Exonuclease VII, large subunit [DNA replication, recombination, and repair]
Probab=36.05 E-value=2.1e+02 Score=26.31 Aligned_cols=70 Identities=10% Similarity=0.018 Sum_probs=49.5
Q ss_pred CCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecCCcCC----CCCCCEEEEeceEEce-eCCe
Q 031443 45 TNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARNDQVDL----MKPGTTVILRNAKIDM-FKGS 119 (159)
Q Consensus 45 ~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde~~~~----i~~Gdvv~I~na~v~~-~~G~ 119 (159)
..+|-|++.|-++..+. ++ =...-+.|+.+.|+.++|...... +++|+-|.+.+-..-+ -+|.
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 45577777776665431 13 456788999999999999743322 5899999998776543 2688
Q ss_pred EEEEeCC
Q 031443 120 MRIAVDK 126 (159)
Q Consensus 120 ~~L~vgk 126 (159)
..|++..
T Consensus 91 YQi~~~~ 97 (440)
T COG1570 91 YQIVAES 97 (440)
T ss_pred eEEEEec
Confidence 8888766
No 147
>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=35.27 E-value=2.1e+02 Score=22.07 Aligned_cols=51 Identities=10% Similarity=0.077 Sum_probs=36.0
Q ss_pred ceeEEEEEecC--CcCCCCCCCEEEEeceEEceeC---C-eEEEEeCCceeEEEcCC
Q 031443 85 TGTILFTARND--QVDLMKPGTTVILRNAKIDMFK---G-SMRIAVDKWGRIEATEP 135 (159)
Q Consensus 85 TG~I~ltlWde--~~~~i~~Gdvv~I~na~v~~~~---G-~~~L~vgk~g~I~~~~~ 135 (159)
.|..+.-+... ....+++|..+-|.+.-...++ + ++++.+|+.+.|+.-|.
T Consensus 68 ~g~~r~f~~~~~Cr~~~l~~gk~YLImG~~~~~~~~~~~~~~~Y~L~~~TWvE~WP~ 124 (150)
T cd03582 68 KDSEVTLVKKATCTSVELQEGQQYLIMGKEALKIRLNRSFRYRYPLDSEAWIEWWPT 124 (150)
T ss_pred CCCeEEEeecCCCCCCcccCCCEEEEeeCCCCccccCCCceeEEEcCCceeEEECCC
Confidence 45555323332 2345789999999998755443 3 59999999999999864
No 148
>PF13567 DUF4131: Domain of unknown function (DUF4131)
Probab=34.67 E-value=1.7e+02 Score=20.93 Aligned_cols=29 Identities=24% Similarity=0.415 Sum_probs=21.0
Q ss_pred CceeEEEEEecCCcCCCCCCCEEEEeceE
Q 031443 84 DTGTILFTARNDQVDLMKPGTTVILRNAK 112 (159)
Q Consensus 84 eTG~I~ltlWde~~~~i~~Gdvv~I~na~ 112 (159)
..|.+.+.+-.+....+.+||.+++++-.
T Consensus 113 ~~~~i~~~~~~~~~~~l~~Gd~i~~~g~l 141 (176)
T PF13567_consen 113 VSGKILLYLPKDSQPRLQPGDRIRVRGKL 141 (176)
T ss_pred cceeeEEEeccccccccCCCCEEEEEEEE
Confidence 37888887665544458999999996543
No 149
>PLN02903 aminoacyl-tRNA ligase
Probab=34.38 E-value=2.5e+02 Score=27.17 Aligned_cols=82 Identities=15% Similarity=0.127 Sum_probs=54.4
Q ss_pred CceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecCC-------cCCCCCCCEEEEeceEEce----
Q 031443 47 GHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARNDQ-------VDLMKPGTTVILRNAKIDM---- 115 (159)
Q Consensus 47 ~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde~-------~~~i~~Gdvv~I~na~v~~---- 115 (159)
.|.|.+.|-.+-. - +.+.=+.|-|.+|.+.+++=.+. +..+..|++|.|.+-....
T Consensus 74 ~V~l~GWV~~~R~-------~------G~l~FidLRD~~G~iQvV~~~~~~~~~~~~~~~L~~esvV~V~G~V~~r~~~~ 140 (652)
T PLN02903 74 RVTLCGWVDLHRD-------M------GGLTFLDVRDHTGIVQVVTLPDEFPEAHRTANRLRNEYVVAVEGTVRSRPQES 140 (652)
T ss_pred EEEEEEEEEEEec-------C------CCcEEEEEEcCCccEEEEEeCCccHHHHHHHhcCCCCCEEEEEEEEEeCCCcC
Confidence 3677777765432 1 34777888999999988764321 2458999999999976632
Q ss_pred -----eCCeEEEEeCCceeEEEc-CCCcEEEc
Q 031443 116 -----FKGSMRIAVDKWGRIEAT-EPAKFVVK 141 (159)
Q Consensus 116 -----~~G~~~L~vgk~g~I~~~-~~~~~~vn 141 (159)
-.|.++|.+.+.--+.+. .+..|.++
T Consensus 141 ~n~~~~tGeiEl~~~~i~VL~~a~~~lPf~i~ 172 (652)
T PLN02903 141 PNKKMKTGSVEVVAESVDILNVVTKSLPFLVT 172 (652)
T ss_pred cCCCCCCCCEEEEEeEEEEEecCCCCCCcccc
Confidence 137799998886555554 23344443
No 150
>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=33.48 E-value=65 Score=20.72 Aligned_cols=62 Identities=23% Similarity=0.257 Sum_probs=41.6
Q ss_pred eEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecC-----CcCCCCCCCEEEEeceEEceeCCeEEEE
Q 031443 49 NLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARND-----QVDLMKPGTTVILRNAKIDMFKGSMRIA 123 (159)
Q Consensus 49 nv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde-----~~~~i~~Gdvv~I~na~v~~~~G~~~L~ 123 (159)
-+.++|.++.+- +-..+.- +.-+|.|+++-+.. ....+.+|+.+++.=-.++..++.+.|+
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 478888887752 2222222 35567777766653 3355799999999877777778888876
Q ss_pred e
Q 031443 124 V 124 (159)
Q Consensus 124 v 124 (159)
+
T Consensus 73 ~ 73 (74)
T PF00575_consen 73 L 73 (74)
T ss_dssp S
T ss_pred E
Confidence 4
No 151
>PF11213 DUF3006: Protein of unknown function (DUF3006); InterPro: IPR021377 This family of proteins has no known function.
Probab=33.07 E-value=1.2e+02 Score=20.36 Aligned_cols=32 Identities=13% Similarity=0.025 Sum_probs=19.8
Q ss_pred eEEEEEEeeCceeEEEEEe-cCCcCCCCCCCEEEE
Q 031443 75 RIAECLVGDDTGTILFTAR-NDQVDLMKPGTTVIL 108 (159)
Q Consensus 75 ~V~~~lVgDeTG~I~ltlW-de~~~~i~~Gdvv~I 108 (159)
.++-+++.|.. ..+.+- +.....+++||++.+
T Consensus 10 ~~AVl~~~~~~--~~~~vp~~~LP~~~keGDvl~i 42 (71)
T PF11213_consen 10 DYAVLELEDGE--KEIDVPRSRLPEGAKEGDVLEI 42 (71)
T ss_pred CEEEEEECCCe--EEEEEEHHHCCCCCCcccEEEE
Confidence 45556666555 222222 235567899999999
No 152
>PRK04036 DNA polymerase II small subunit; Validated
Probab=31.59 E-value=1.6e+02 Score=27.07 Aligned_cols=67 Identities=15% Similarity=0.123 Sum_probs=44.0
Q ss_pred eeecccCCCCCCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecCC------cCCCCCCCEEEE
Q 031443 35 FTKVDQLKPGTNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARNDQ------VDLMKPGTTVIL 108 (159)
Q Consensus 35 ~~kI~dL~P~~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde~------~~~i~~Gdvv~I 108 (159)
..+|.+++-+...+.+.+.|-++... .+| . ....+-|+||+|++..-.+. .+.+-.|.+|-+
T Consensus 143 i~~l~~~~~~~~~~~viG~v~~~~~~-----~~g-----~--~~~~LED~sgrv~l~~~~~~~~~~~~~~~lvtg~vv~v 210 (504)
T PRK04036 143 IESLKKLKRGGEEVSIIGMVSDIRST-----KNG-----H--KIVELEDTTGTFPVLIMKDREDLAELADELLLDEVIGV 210 (504)
T ss_pred HHHHhcCccCCceEEEEEEEEEeecc-----cCC-----c--eEEEEECCCCeEEEEeecchhhhhhhhhcccCceEEEE
Confidence 45666666233557788888765432 122 1 24789999999999874322 245788999988
Q ss_pred eceEE
Q 031443 109 RNAKI 113 (159)
Q Consensus 109 ~na~v 113 (159)
.|-+.
T Consensus 211 ~G~~~ 215 (504)
T PRK04036 211 EGTLS 215 (504)
T ss_pred EEEEc
Confidence 88654
No 153
>COG4013 Uncharacterized protein conserved in archaea [Function unknown]
Probab=31.38 E-value=1.2e+02 Score=21.92 Aligned_cols=32 Identities=22% Similarity=0.354 Sum_probs=23.9
Q ss_pred CCCCCCEEEEeceEE-------ceeCCeEEEEeCC---ceeE
Q 031443 99 LMKPGTTVILRNAKI-------DMFKGSMRIAVDK---WGRI 130 (159)
Q Consensus 99 ~i~~Gdvv~I~na~v-------~~~~G~~~L~vgk---~g~I 130 (159)
.+++||.++|.=|++ ...+|.++|.+.+ .|-+
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 478999998876554 5667888988887 5544
No 154
>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=31.20 E-value=96 Score=19.48 Aligned_cols=50 Identities=20% Similarity=0.106 Sum_probs=29.9
Q ss_pred eEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCc-eeEEEEEecCCcCCCCCCCEEEEe
Q 031443 49 NLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDT-GTILFTARNDQVDLMKPGTTVILR 109 (159)
Q Consensus 49 nv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeT-G~I~ltlWde~~~~i~~Gdvv~I~ 109 (159)
.+.++|..+..- +......+.+++.. =+++++.|.-....+++||.|.+.
T Consensus 6 ~l~g~V~~ie~~-----------g~~~~v~~~~~~~~~l~a~it~~~~~~L~L~~G~~V~~~ 56 (64)
T PF03459_consen 6 QLPGTVESIENL-----------GSEVEVTLDLGGGETLTARITPESAEELGLKPGDEVYAS 56 (64)
T ss_dssp EEEEEEEEEEES-----------SSEEEEEEEETTSEEEEEEEEHHHHHHCT-STT-EEEEE
T ss_pred EEEEEEEEEEEC-----------CCeEEEEEEECCCCEEEEEEcHHHHHHcCCCCCCEEEEE
Confidence 477888887652 12445666777766 455555555443458999998763
No 155
>COG1917 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]
Probab=30.03 E-value=50 Score=24.02 Aligned_cols=28 Identities=14% Similarity=0.247 Sum_probs=20.7
Q ss_pred ceeEEEEEecCCcCCCCCCCEEEEeceEE
Q 031443 85 TGTILFTARNDQVDLMKPGTTVILRNAKI 113 (159)
Q Consensus 85 TG~I~ltlWde~~~~i~~Gdvv~I~na~v 113 (159)
.|.++++++ ...-.+++||+|.|--+..
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 467778888 4556689999999875444
No 156
>KOG0851 consensus Single-stranded DNA-binding replication protein A (RPA), large (70 kD) subunit and related ssDNA-binding proteins [Replication, recombination and repair]
Probab=28.76 E-value=1.4e+02 Score=23.48 Aligned_cols=81 Identities=19% Similarity=0.245 Sum_probs=55.3
Q ss_pred ceeecccCCCCCCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCcee-EEEEEecC----CcCCCCCCCEEEE
Q 031443 34 VFTKVDQLKPGTNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGT-ILFTARND----QVDLMKPGTTVIL 108 (159)
Q Consensus 34 ~~~kI~dL~P~~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~-I~ltlWde----~~~~i~~Gdvv~I 108 (159)
.+..+.+|.|...+-.+.++||.+...... ..+....+++.|++|. |..+.... ....+.+|..+.|
T Consensus 3 ~~~~l~~l~~~~t~w~i~~~vl~v~~~~~~--------~~~~~~~~il~D~~~~~i~a~i~~~~~~~~~~~l~~~~w~~i 74 (246)
T KOG0851|consen 3 GFHRLRDLSPSITGWRIQVKVLRVWKKYSN--------PNGEELRLVLADEHGVKIEATVGRRLSSKYEDNLIENEWKII 74 (246)
T ss_pred cccchhhcCcCceeeEEEEEEEEEEEecCC--------CCccEEEEEEEecCCcEEEEEcchHHHhhhhhheecceeEEe
Confidence 467788999988888899999999875321 1256788888999853 33443332 2244688888888
Q ss_pred eceEEceeCCeEEE
Q 031443 109 RNAKIDMFKGSMRI 122 (159)
Q Consensus 109 ~na~v~~~~G~~~L 122 (159)
.+-.+....+.++.
T Consensus 75 ~~f~v~~~~~~~~~ 88 (246)
T KOG0851|consen 75 TTFGVNPNSGQVRA 88 (246)
T ss_pred eeeeecccccceee
Confidence 77777665554443
No 157
>cd04495 BRCA2DBD_OB3 BRCA2DBD_OB3: A subfamily of OB folds corresponding to the third OB fold (OB3) of the 800-amino acid C-terminal ssDNA binding domain (DBD) of BRCA2 (breast cancer susceptibility gene 2) protein, called BRCA2DBD. BRCA2 participates in homologous recombination-mediated repair of double-strand DNA breaks. It stimulates the displacement of Replication protein A (RPA), the most abundant eukaryotic ssDNA binding protein. It also facilitates filament formation. Mutations that map throughout the BRCA2 protein are associated with breast cancer susceptibility. BRCA2 is a large nuclear protein and its most conserved region is the C-terminal BRCA2DBD. BRCA2DBD binds ssDNA in vitro, and is composed of five structural domains, three of which are OB folds (OB1, OB2, and OB3). BRCA2DBD OB2 and OB3 are arranged in tandem, and their mode of binding can be considered qualitatively similar to two OB folds of RPA1, DBD-A and DBD-B (the major DBDs of RPA).
Probab=27.02 E-value=2.6e+02 Score=20.62 Aligned_cols=75 Identities=9% Similarity=0.090 Sum_probs=55.2
Q ss_pred eEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCce-eEEEEEecC-----CcCCCCCCCEEEEeceEEceeC--CeE
Q 031443 49 NLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTG-TILFTARND-----QVDLMKPGTTVILRNAKIDMFK--GSM 120 (159)
Q Consensus 49 nv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG-~I~ltlWde-----~~~~i~~Gdvv~I~na~v~~~~--G~~ 120 (159)
++++.|+++....+ +..--+-++|+.= -+.+-+|.. .-+.++++.-|-+.|=..+-.. |-+
T Consensus 1 D~VGvVvsV~~~~~-----------g~~~~vYLaDe~~nll~vkfw~~l~~~~~EDvvk~~~lia~SNLQwR~~s~~~iP 69 (100)
T cd04495 1 DTVGVVISVGKPIE-----------GKFPAVYLADECLNLLCVKFWSSLEQYAYEDVVKRRVLLAASNLQWRTESTSGVP 69 (100)
T ss_pred CceEEEEEEccccc-----------CccceEEEecCCcCEEEEEEecchHHhhhhhhcccceEEEEecceEeccccCCCc
Confidence 46788999987532 4455678899963 445667872 2255699999999999887654 679
Q ss_pred EEEeCCceeEEEcC
Q 031443 121 RIAVDKWGRIEATE 134 (159)
Q Consensus 121 ~L~vgk~g~I~~~~ 134 (159)
.|..|.++.+...|
T Consensus 70 tl~Age~t~FS~nP 83 (100)
T cd04495 70 TLFAGEYSTFSANP 83 (100)
T ss_pred eeeeecceeecCCc
Confidence 99999988877664
No 158
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=26.67 E-value=2e+02 Score=19.07 Aligned_cols=64 Identities=6% Similarity=0.042 Sum_probs=38.8
Q ss_pred ceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecC-----CcCCCCCCCEEEEeceEEceeCCeEEE
Q 031443 48 HNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARND-----QVDLMKPGTTVILRNAKIDMFKGSMRI 122 (159)
Q Consensus 48 vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde-----~~~~i~~Gdvv~I~na~v~~~~G~~~L 122 (159)
--+.++|.++... +-+..+ -+.-.|.++++-... ..+.+++||.+..+=.....- +.+.|
T Consensus 8 diV~G~V~~v~~~-------------~~~V~i-~~~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~~-~~i~L 72 (82)
T cd04454 8 DIVIGIVTEVNSR-------------FWKVDI-LSRGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDD-MNVLL 72 (82)
T ss_pred CEEEEEEEEEcCC-------------EEEEEe-CCCceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCCC-CCEEE
Confidence 3589999998652 112211 245678888876642 124489999998764444332 56777
Q ss_pred EeCC
Q 031443 123 AVDK 126 (159)
Q Consensus 123 ~vgk 126 (159)
++-.
T Consensus 73 S~~~ 76 (82)
T cd04454 73 TTAD 76 (82)
T ss_pred EECC
Confidence 6644
No 159
>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=26.40 E-value=1.8e+02 Score=18.58 Aligned_cols=40 Identities=18% Similarity=0.141 Sum_probs=25.3
Q ss_pred ceeEEEEEecC-----CcCCCCCCCEEEEeceEEceeCCeEEEEe
Q 031443 85 TGTILFTARND-----QVDLMKPGTTVILRNAKIDMFKGSMRIAV 124 (159)
Q Consensus 85 TG~I~ltlWde-----~~~~i~~Gdvv~I~na~v~~~~G~~~L~v 124 (159)
+|.++.+-..+ ..+.+++||.|++.=..+...++.+.|++
T Consensus 28 ~g~v~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~~d~~~~~i~ls~ 72 (73)
T cd05706 28 TGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIALSL 72 (73)
T ss_pred EEEEEhhhccCccccccccccCCCCEEEEEEEEEeCCCCEEEEEE
Confidence 55665554321 12447999999987666665567777664
No 160
>smart00350 MCM minichromosome maintenance proteins.
Probab=25.83 E-value=83 Score=28.79 Aligned_cols=29 Identities=24% Similarity=0.308 Sum_probs=25.4
Q ss_pred eEEEEEecCCcCCCCCCCEEEEeceEEce
Q 031443 87 TILFTARNDQVDLMKPGTTVILRNAKIDM 115 (159)
Q Consensus 87 ~I~ltlWde~~~~i~~Gdvv~I~na~v~~ 115 (159)
++.+.|-++.++.+.|||.|.|.+-+...
T Consensus 105 si~v~l~~dLvd~~~PGD~V~i~Gi~~~~ 133 (509)
T smart00350 105 SVDVILDGDLVDKAKPGDRVEVTGIYRNI 133 (509)
T ss_pred EEEEEEcccccCcccCCCEEEEEEEEEee
Confidence 57788889999999999999999998754
No 161
>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=24.69 E-value=2.2e+02 Score=19.03 Aligned_cols=42 Identities=10% Similarity=0.117 Sum_probs=29.4
Q ss_pred ceEEEEEEeeCceeEEEEEecCC------cCCCCCCCEEEEeceEEce
Q 031443 74 TRIAECLVGDDTGTILFTARNDQ------VDLMKPGTTVILRNAKIDM 115 (159)
Q Consensus 74 ~~V~~~lVgDeTG~I~ltlWde~------~~~i~~Gdvv~I~na~v~~ 115 (159)
+.++=+.+-|.+|.+...+=.+. +..+..|++|.+.+-..+.
T Consensus 15 g~~~Fi~LrD~~~~iQ~v~~~~~~~~~~~~~~l~~es~V~V~G~v~~~ 62 (84)
T cd04323 15 KKLMFLVLRDGTGFLQCVLSKKLVTEFYDAKSLTQESSVEVTGEVKED 62 (84)
T ss_pred CCcEEEEEEcCCeEEEEEEcCCcchhHHHHhcCCCcCEEEEEEEEEEC
Confidence 44667778899998887553221 2347899999999876653
No 162
>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=23.85 E-value=1.3e+02 Score=21.77 Aligned_cols=36 Identities=8% Similarity=0.122 Sum_probs=19.1
Q ss_pred ceEEEEEEeeCceeEEE--EEecCCcC-CCCCCCEEEEec
Q 031443 74 TRIAECLVGDDTGTILF--TARNDQVD-LMKPGTTVILRN 110 (159)
Q Consensus 74 ~~V~~~lVgDeTG~I~l--tlWde~~~-~i~~Gdvv~I~n 110 (159)
+.+. -...+.+|.|++ ..|+...+ .+++|+.|+|..
T Consensus 94 g~v~-~~~~~~~G~V~~~G~~w~A~s~~~i~~G~~V~Vv~ 132 (144)
T PF01957_consen 94 GTVI-EIPLNGSGRVKVDGERWRARSEDEIPKGDRVRVVG 132 (144)
T ss_dssp EEEE-EEBSSS-EEEEETTEEEEEEESSTB-TT-EEEEEE
T ss_pred EEEE-EeecCCcEEEEECCeEEEEEeCCCCCCCCEEEEEE
Confidence 4443 344555666665 46763222 299999988864
No 163
>PLN02221 asparaginyl-tRNA synthetase
Probab=23.48 E-value=6.4e+02 Score=23.91 Aligned_cols=90 Identities=13% Similarity=0.081 Sum_probs=56.3
Q ss_pred CceeecccCC------CCC--CCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCc--eeEEEEEecCC---cCC
Q 031443 33 PVFTKVDQLK------PGT--NGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDT--GTILFTARNDQ---VDL 99 (159)
Q Consensus 33 ~~~~kI~dL~------P~~--~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeT--G~I~ltlWde~---~~~ 99 (159)
+.+.+|+++. +.. +.|.|.+-|-++-. -| ...++=+.|-|.| |.|.+++=.+. ...
T Consensus 30 ~~~~~~~~~~~~~~~~~~~~g~~V~I~GWV~~iR~-------~G----k~~i~Fl~LRDgs~~g~iQvVv~~~~~~~~~~ 98 (572)
T PLN02221 30 SDRVLIRSILDRPDGGAGLAGQKVRIGGWVKTGRE-------QG----KGTFAFLEVNDGSCPANLQVMVDSSLYDLSTL 98 (572)
T ss_pred cCceEHHHHhccccCChhcCCCEEEEEEEEEehhh-------CC----CceEEEEEEeCCcccccEEEEEcCchhhHHhc
Confidence 4667788875 222 33566666655432 12 1136667888998 88888664321 124
Q ss_pred CCCCCEEEEeceEEcee-----CCeEEEEeCCceeEEEc
Q 031443 100 MKPGTTVILRNAKIDMF-----KGSMRIAVDKWGRIEAT 133 (159)
Q Consensus 100 i~~Gdvv~I~na~v~~~-----~G~~~L~vgk~g~I~~~ 133 (159)
+..|++|.|.|-.+.-- .+.++|.+.+.--|.+.
T Consensus 99 L~~ES~V~V~G~V~~~~~~~~~~~~iEl~v~~i~vl~~a 137 (572)
T PLN02221 99 VATGTCVTVDGVLKVPPEGKGTKQKIELSVEKVIDVGTV 137 (572)
T ss_pred CCCceEEEEEEEEEeCCccCCCCccEEEEEeEEEEEecC
Confidence 78999999999776421 24799999875555444
No 164
>COG4880 Secreted protein containing C-terminal beta-propeller domain distantly related to WD-40 repeats [General function prediction only]
Probab=23.26 E-value=1e+02 Score=28.77 Aligned_cols=54 Identities=19% Similarity=0.105 Sum_probs=45.7
Q ss_pred EeeCceeEEEEEec-CCcCCCCCCCEEEEeceEEceeCCeEEEEeCCceeEEEcC
Q 031443 81 VGDDTGTILFTARN-DQVDLMKPGTTVILRNAKIDMFKGSMRIAVDKWGRIEATE 134 (159)
Q Consensus 81 VgDeTG~I~ltlWd-e~~~~i~~Gdvv~I~na~v~~~~G~~~L~vgk~g~I~~~~ 134 (159)
||-+.|-+.++|+| ......++=+.+.|.+++...|++++-...+....|--+|
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 45566999999999 5666689999999999999999999888888888776665
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=22.61 E-value=1.1e+02 Score=21.17 Aligned_cols=23 Identities=22% Similarity=0.020 Sum_probs=18.9
Q ss_pred EEEEEecCCcCCCCCCCEEEEec
Q 031443 88 ILFTARNDQVDLMKPGTTVILRN 110 (159)
Q Consensus 88 I~ltlWde~~~~i~~Gdvv~I~n 110 (159)
-.|+||......+.+||.++|.=
T Consensus 29 ~~l~L~~p~~~~~~~G~~v~l~~ 51 (80)
T PF09356_consen 29 GTLTLWRPLPAGLAVGDTVTLYP 51 (80)
T ss_pred CEEEEeccCcccCCCCCEEEEEe
Confidence 67788987766789999999973
No 166
>PRK06341 single-stranded DNA-binding protein; Provisional
Probab=22.14 E-value=2.2e+02 Score=22.52 Aligned_cols=65 Identities=15% Similarity=0.091 Sum_probs=39.1
Q ss_pred CCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEee--------------CceeEEEEEecC-Cc----CCCCCCCE
Q 031443 45 TNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGD--------------DTGTILFTARND-QV----DLMKPGTT 105 (159)
Q Consensus 45 ~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgD--------------eTG~I~ltlWde-~~----~~i~~Gdv 105 (159)
++.+.|.+++..-.+.+.+ .+| ..+++..||= +|=-+++++|++ ++ ..++.|+.
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 4456677777664343322 122 3455555543 233568999985 33 34799999
Q ss_pred EEEeceEE-cee
Q 031443 106 VILRNAKI-DMF 116 (159)
Q Consensus 106 v~I~na~v-~~~ 116 (159)
|.|.+-.. +.|
T Consensus 78 V~VeGrL~~r~w 89 (166)
T PRK06341 78 VYIEGQLQTRKW 89 (166)
T ss_pred EEEEEEEEeCcE
Confidence 99998875 335
No 167
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=21.88 E-value=71 Score=16.67 Aligned_cols=14 Identities=21% Similarity=0.266 Sum_probs=11.3
Q ss_pred CCCCCEEEEeceEE
Q 031443 100 MKPGTTVILRNAKI 113 (159)
Q Consensus 100 i~~Gdvv~I~na~v 113 (159)
+++||.|+|.++.-
T Consensus 2 ~~~G~~V~I~~G~~ 15 (28)
T smart00739 2 FEVGDTVRVIAGPF 15 (28)
T ss_pred CCCCCEEEEeECCC
Confidence 57899999988763
No 168
>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=21.42 E-value=3.6e+02 Score=20.28 Aligned_cols=38 Identities=11% Similarity=0.145 Sum_probs=31.2
Q ss_pred CCCCCCCEEEEeceEEceeC-----CeEEEEeCCceeEEEcCC
Q 031443 98 DLMKPGTTVILRNAKIDMFK-----GSMRIAVDKWGRIEATEP 135 (159)
Q Consensus 98 ~~i~~Gdvv~I~na~v~~~~-----G~~~L~vgk~g~I~~~~~ 135 (159)
..+++|..+-|.+.-...++ +.+++.+|..+.|++-+.
T Consensus 77 ~~l~~g~~YLImG~~~~~~~~~~~~~~~~yvl~~~t~Ve~Wp~ 119 (147)
T cd03574 77 LRLKEGRHYLIMGSDGAFYDDRNGEDRYQYVLDSNTWVEEWPT 119 (147)
T ss_pred hcCCCCCEEEEeccCcCcccccCCCcceEEEeCCCcEEEECCC
Confidence 44689999999999766654 378999999999998863
No 169
>PRK05807 hypothetical protein; Provisional
Probab=21.28 E-value=3.6e+02 Score=20.25 Aligned_cols=62 Identities=18% Similarity=0.255 Sum_probs=40.2
Q ss_pred eEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEec-----CCcCCCCCCCEEEEeceEEceeCCeEEEE
Q 031443 49 NLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARN-----DQVDLMKPGTTVILRNAKIDMFKGSMRIA 123 (159)
Q Consensus 49 nv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWd-----e~~~~i~~Gdvv~I~na~v~~~~G~~~L~ 123 (159)
.+.++|..+.+- +..... ...+|.|.++-.. +..+.++.||.|.+.=..+.. .|.+.|+
T Consensus 8 vv~G~Vt~i~~~-------------GafV~L--~~~~Glvhiseis~~~v~~~~~~~kvGd~V~VkV~~id~-~gkI~LS 71 (136)
T PRK05807 8 ILEGTVVNITNF-------------GAFVEV--EGKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDD-NGKISLS 71 (136)
T ss_pred EEEEEEEEEECC-------------eEEEEE--CCEEEEEEhhhcccccccCccccCCCCCEEEEEEEEECC-CCcEEEE
Confidence 588888887653 223322 3346777766432 112457999999988666666 6888888
Q ss_pred eCC
Q 031443 124 VDK 126 (159)
Q Consensus 124 vgk 126 (159)
+-.
T Consensus 72 lk~ 74 (136)
T PRK05807 72 IKQ 74 (136)
T ss_pred EEe
Confidence 755
No 170
>PF05899 Cupin_3: Protein of unknown function (DUF861); InterPro: IPR008579 The function of the proteins in this entry are unknown. They contain the conserved barrel domain of the 'cupin' superfamily and members are specific to plants and bacteria.; PDB: 1RC6_A 3MYX_A 1O5U_A 2K9Z_A 1LKN_A 3ES4_A 1SFN_B 3BCW_A.
Probab=20.48 E-value=71 Score=21.37 Aligned_cols=32 Identities=16% Similarity=0.298 Sum_probs=19.9
Q ss_pred ceeEEEEEecCCcCCCCCCCEEEEeceEEcee
Q 031443 85 TGTILFTARNDQVDLMKPGTTVILRNAKIDMF 116 (159)
Q Consensus 85 TG~I~ltlWde~~~~i~~Gdvv~I~na~v~~~ 116 (159)
.|.+.|+.=+...-.+.+||.+.|-.+..-.|
T Consensus 33 eG~v~it~~~G~~~~~~aGD~~~~p~G~~~~w 64 (74)
T PF05899_consen 33 EGEVTITDEDGETVTFKAGDAFFLPKGWTGTW 64 (74)
T ss_dssp EEEEEEEETTTEEEEEETTEEEEE-TTEEEEE
T ss_pred EeEEEEEECCCCEEEEcCCcEEEECCCCEEEE
Confidence 45666664332233478999999998886554
No 171
>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=20.46 E-value=3.7e+02 Score=21.63 Aligned_cols=48 Identities=13% Similarity=0.122 Sum_probs=27.8
Q ss_pred eEEEEEecCCcC-CCCCCCEEEEeceEEceeCCe-EEEEeCCceeEEEcCCCcE
Q 031443 87 TILFTARNDQVD-LMKPGTTVILRNAKIDMFKGS-MRIAVDKWGRIEATEPAKF 138 (159)
Q Consensus 87 ~I~ltlWde~~~-~i~~Gdvv~I~na~v~~~~G~-~~L~vgk~g~I~~~~~~~~ 138 (159)
...+.||++=.+ .+++||+|.|.+ .+.+. .-+.-+..|-+..-||.-+
T Consensus 11 ~~~v~L~~~W~~t~v~~Gd~I~ii~----~~~~~~~~~v~~~~~~lIl~PD~Li 60 (209)
T PF08696_consen 11 TRTVILRDEWCETPVSPGDIIHIIG----EFDDDDPCIVDNDSNLLILHPDILI 60 (209)
T ss_pred eEEEEEeCCcccCCCcCCCEEEEEE----EeCCCCCEEEeCCCCEEEEcCCcee
Confidence 455667775333 389999999999 33332 3333344445555544443
No 172
>PF09696 Ctf8: Ctf8; InterPro: IPR018607 Ctf8 (chromosome transmissions fidelity 8) is a component of the Ctf18 RFC-like complex which is a DNA clamp loader involved in sister chromatid cohesion.
Probab=20.21 E-value=2.7e+02 Score=20.73 Aligned_cols=41 Identities=22% Similarity=0.382 Sum_probs=26.6
Q ss_pred eeCCeEEEEeCC----ceeEEEcCCCcEEE--cc---------CCCccccceeeeee
Q 031443 115 MFKGSMRIAVDK----WGRIEATEPAKFVV--KE---------DNNLSLVEYELVNV 156 (159)
Q Consensus 115 ~~~G~~~L~vgk----~g~I~~~~~~~~~v--ne---------~~N~S~ieye~v~~ 156 (159)
.+.+++.|+||+ .|++..++ ..+-| +. ...-+..+||++.|
T Consensus 53 ~~~~~~~L~IG~~q~L~Gkv~kL~-kPLaVLrk~~~~~~~~~~~~~~~~~e~evv~I 108 (122)
T PF09696_consen 53 KWMKRVTLYIGKHQRLEGKVVKLK-KPLAVLRKRKSNDDSSDDSEEESSTEYEVVDI 108 (122)
T ss_pred CCCCeEEEEECCCEEEEEEEeccC-CCEEEEEEcccCcccccccCCCCCeEEEEEEe
Confidence 466777888883 47778884 44332 11 23367799999987
Done!