Query psy14498
Match_columns 171
No_of_seqs 208 out of 1267
Neff 8.2
Searched_HMMs 46136
Date Fri Aug 16 21:19:17 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy14498.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/14498hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK09010 single-stranded DNA-b 100.0 3.9E-45 8.5E-50 274.2 21.1 116 1-116 1-121 (177)
2 PRK13732 single-stranded DNA-b 100.0 2.1E-44 4.5E-49 269.9 21.2 117 1-118 1-122 (175)
3 PRK06863 single-stranded DNA-b 100.0 2.5E-44 5.4E-49 267.9 20.2 119 1-119 1-119 (168)
4 PRK06958 single-stranded DNA-b 100.0 1.4E-43 3E-48 266.0 20.9 116 1-116 1-116 (182)
5 PRK08763 single-stranded DNA-b 100.0 1.7E-43 3.6E-48 262.7 20.8 114 1-115 1-115 (164)
6 PRK05733 single-stranded DNA-b 100.0 4.3E-43 9.3E-48 262.1 20.4 115 1-116 1-119 (172)
7 PRK08486 single-stranded DNA-b 100.0 2.5E-42 5.3E-47 260.6 20.7 111 3-114 1-111 (182)
8 PRK07275 single-stranded DNA-b 100.0 6.1E-42 1.3E-46 254.2 20.7 110 3-115 1-110 (162)
9 TIGR00621 ssb single stranded 100.0 1.6E-40 3.4E-45 248.2 20.7 113 1-114 1-113 (164)
10 PRK06751 single-stranded DNA-b 100.0 2.8E-40 6.1E-45 247.3 20.6 110 3-115 1-110 (173)
11 PRK06341 single-stranded DNA-b 100.0 7.8E-40 1.7E-44 243.1 20.1 117 1-117 1-123 (166)
12 PRK06642 single-stranded DNA-b 100.0 8E-39 1.7E-43 235.8 18.4 114 1-114 1-120 (152)
13 PRK07274 single-stranded DNA-b 100.0 8.1E-38 1.8E-42 225.6 18.3 108 3-114 1-108 (131)
14 PRK07459 single-stranded DNA-b 100.0 8.6E-37 1.9E-41 217.3 17.5 106 2-114 1-107 (121)
15 PRK06752 single-stranded DNA-b 100.0 3E-36 6.5E-41 212.2 16.5 108 3-113 1-108 (112)
16 COG0629 Ssb Single-stranded DN 100.0 2.7E-35 5.9E-40 220.7 17.4 111 2-113 1-116 (167)
17 PRK07772 single-stranded DNA-b 100.0 4.2E-34 9.2E-39 216.0 20.5 106 1-106 1-107 (186)
18 PRK06293 single-stranded DNA-b 100.0 3.7E-34 7.9E-39 211.4 18.7 105 4-114 1-105 (161)
19 PRK08182 single-stranded DNA-b 100.0 3.4E-34 7.4E-39 210.3 18.0 111 3-114 1-116 (148)
20 PF00436 SSB: Single-strand bi 100.0 1.3E-30 2.7E-35 180.6 16.3 104 4-108 1-104 (104)
21 PRK05853 hypothetical protein; 100.0 7.5E-29 1.6E-33 183.5 16.5 97 9-107 1-98 (161)
22 PRK02801 primosomal replicatio 100.0 1.6E-28 3.4E-33 169.6 15.2 101 3-109 1-101 (101)
23 PRK05813 single-stranded DNA-b 100.0 1.2E-27 2.6E-32 185.2 14.9 101 3-113 108-212 (219)
24 cd04496 SSB_OBF SSB_OBF: A sub 99.9 2.1E-25 4.6E-30 153.0 14.9 100 7-108 1-100 (100)
25 PRK05813 single-stranded DNA-b 99.9 1.8E-22 3.9E-27 156.4 15.3 98 4-114 8-106 (219)
26 KOG1653|consensus 99.9 8.3E-22 1.8E-26 143.0 8.3 108 3-110 54-166 (175)
27 PRK00036 primosomal replicatio 99.3 6.8E-11 1.5E-15 81.7 10.7 96 4-108 1-96 (107)
28 COG2965 PriB Primosomal replic 99.2 8E-10 1.7E-14 74.2 12.4 103 1-109 1-103 (103)
29 PF01336 tRNA_anti-codon: OB-f 98.1 5.8E-05 1.2E-09 48.2 9.3 75 7-108 1-75 (75)
30 cd04484 polC_OBF polC_OBF: A s 97.5 0.0029 6.2E-08 41.8 10.1 66 7-88 2-69 (82)
31 PF11325 DUF3127: Domain of un 97.4 0.0017 3.6E-08 43.1 8.2 81 9-106 2-84 (84)
32 cd04474 RPA1_DBD_A RPA1_DBD_A: 97.3 0.0019 4E-08 44.6 7.9 69 3-84 8-80 (104)
33 cd04489 ExoVII_LU_OBF ExoVII_L 97.2 0.0075 1.6E-07 38.8 9.7 74 7-106 2-75 (78)
34 PHA01740 putative single-stran 97.2 0.001 2.2E-08 47.5 5.6 9 163-171 150-158 (158)
35 cd04487 RecJ_OBF2_like RecJ_OB 97.2 0.0039 8.4E-08 40.3 7.6 73 7-108 1-73 (73)
36 PRK07211 replication factor A; 97.1 0.0059 1.3E-07 52.9 10.1 67 3-83 62-133 (485)
37 cd03524 RPA2_OBF_family RPA2_O 96.9 0.023 5.1E-07 35.0 9.8 59 9-84 2-61 (75)
38 cd04492 YhaM_OBF_like YhaM_OBF 96.9 0.016 3.5E-07 37.3 9.1 73 14-110 6-78 (83)
39 cd04485 DnaE_OBF DnaE_OBF: A s 96.8 0.019 4.2E-07 36.7 8.8 76 9-108 2-77 (84)
40 PF11506 DUF3217: Protein of u 96.6 0.096 2.1E-06 34.6 12.0 90 3-105 1-90 (104)
41 PF13742 tRNA_anti_2: OB-fold 96.2 0.15 3.3E-06 34.7 10.4 77 4-106 21-98 (99)
42 COG3390 Uncharacterized protei 96.2 0.034 7.4E-07 42.1 7.6 87 3-108 44-130 (196)
43 cd04490 PolII_SU_OBF PolII_SU_ 96.2 0.15 3.2E-06 33.4 9.7 57 7-82 2-60 (79)
44 cd04482 RPA2_OBF_like RPA2_OBF 95.9 0.021 4.6E-07 38.4 5.1 73 8-110 2-76 (91)
45 PRK07373 DNA polymerase III su 95.8 0.18 3.9E-06 43.6 11.2 79 6-108 282-360 (449)
46 PRK15491 replication factor A; 95.7 0.066 1.4E-06 45.2 8.3 72 4-88 176-250 (374)
47 cd04475 RPA1_DBD_B RPA1_DBD_B: 95.6 0.14 3.1E-06 34.6 8.4 67 7-87 2-71 (101)
48 PRK07211 replication factor A; 95.5 0.1 2.2E-06 45.4 8.7 68 3-83 170-240 (485)
49 PF12101 DUF3577: Protein of u 95.5 0.64 1.4E-05 33.6 12.2 96 7-109 14-120 (137)
50 PRK15491 replication factor A; 95.1 0.12 2.6E-06 43.6 7.8 65 3-81 66-135 (374)
51 PRK12366 replication factor A; 95.0 0.21 4.5E-06 45.1 9.6 81 5-103 292-375 (637)
52 PRK05673 dnaE DNA polymerase I 95.0 0.25 5.5E-06 47.3 10.5 80 6-109 979-1058(1135)
53 PRK13480 3'-5' exoribonuclease 94.9 0.17 3.6E-06 41.7 8.1 73 13-109 19-91 (314)
54 TIGR00237 xseA exodeoxyribonuc 94.8 0.21 4.6E-06 42.9 8.7 79 4-108 17-95 (432)
55 PRK14699 replication factor A; 94.5 0.23 5E-06 43.3 8.2 70 3-88 66-140 (484)
56 cd04491 SoSSB_OBF SoSSB_OBF: A 94.4 0.4 8.6E-06 31.1 7.5 61 9-84 2-64 (82)
57 PRK00286 xseA exodeoxyribonucl 93.8 0.44 9.6E-06 40.9 8.6 80 4-109 23-102 (438)
58 PRK06826 dnaE DNA polymerase I 93.7 1 2.2E-05 43.5 11.3 81 6-109 993-1073(1151)
59 cd04488 RecG_wedge_OBF RecG_we 93.6 0.42 9E-06 29.7 6.3 59 9-84 2-60 (75)
60 PRK06920 dnaE DNA polymerase I 93.3 1.1 2.3E-05 43.1 10.8 80 6-109 945-1024(1107)
61 PRK12366 replication factor A; 93.1 0.47 1E-05 42.8 7.8 64 3-81 72-139 (637)
62 PRK00448 polC DNA polymerase I 93.0 0.96 2.1E-05 44.5 10.2 70 4-88 236-307 (1437)
63 PRK07374 dnaE DNA polymerase I 92.9 1.4 3E-05 42.6 11.1 64 6-84 1002-1065(1170)
64 TIGR01405 polC_Gram_pos DNA po 92.8 1.4 2.9E-05 42.8 10.9 69 4-88 7-78 (1213)
65 cd04481 RPA1_DBD_B_like RPA1_D 92.8 2 4.2E-05 29.3 9.1 38 52-89 35-76 (106)
66 cd04317 EcAspRS_like_N EcAspRS 92.5 2.7 5.9E-05 29.9 9.9 87 5-111 15-104 (135)
67 PRK08402 replication factor A; 92.5 0.53 1.2E-05 39.5 6.9 67 3-83 71-142 (355)
68 PRK06461 single-stranded DNA-b 92.3 1.1 2.5E-05 31.9 7.6 63 3-83 13-79 (129)
69 COG1570 XseA Exonuclease VII, 92.0 0.72 1.6E-05 39.6 7.2 78 4-107 23-100 (440)
70 TIGR00617 rpa1 replication fac 91.9 0.64 1.4E-05 41.8 7.1 68 3-84 189-260 (608)
71 PRK07279 dnaE DNA polymerase I 91.7 2.2 4.8E-05 40.6 10.7 80 6-109 886-966 (1034)
72 cd04320 AspRS_cyto_N AspRS_cyt 91.3 1.9 4E-05 29.2 7.5 85 6-110 1-91 (102)
73 PRK14699 replication factor A; 90.8 1.5 3.3E-05 38.3 8.2 65 3-80 285-351 (484)
74 PF02765 POT1: Telomeric singl 90.4 1.8 3.8E-05 31.5 7.1 77 5-89 13-92 (146)
75 cd04100 Asp_Lys_Asn_RS_N Asp_L 89.8 1.8 4E-05 28.1 6.2 81 6-109 1-84 (85)
76 PRK05672 dnaE2 error-prone DNA 89.5 4.2 9.1E-05 39.0 10.5 51 51-110 983-1033(1046)
77 cd04323 AsnRS_cyto_like_N AsnR 89.5 1.6 3.5E-05 28.4 5.7 53 54-109 29-83 (84)
78 cd04321 ScAspRS_mt_like_N ScAs 87.1 3.5 7.6E-05 27.0 6.2 40 68-109 46-85 (86)
79 PHA00458 single-stranded DNA-b 85.8 2.9 6.3E-05 32.6 5.9 82 24-112 100-183 (233)
80 cd04322 LysRS_N LysRS_N: N-ter 85.8 7.8 0.00017 26.4 7.7 76 7-110 2-82 (108)
81 COG1200 RecG RecG-like helicas 85.7 8.5 0.00018 35.0 9.6 62 6-84 62-123 (677)
82 cd04319 PhAsnRS_like_N PhAsnRS 85.7 8.7 0.00019 25.9 7.9 53 53-111 28-83 (103)
83 PF13567 DUF4131: Domain of un 85.2 6.2 0.00013 28.1 7.4 69 5-85 76-144 (176)
84 cd04478 RPA2_DBD_D RPA2_DBD_D: 84.1 9.6 0.00021 25.1 7.5 75 7-110 2-79 (95)
85 TIGR00617 rpa1 replication fac 83.9 6.6 0.00014 35.4 8.2 68 6-87 312-382 (608)
86 TIGR00458 aspS_arch aspartyl-t 83.9 20 0.00044 30.8 10.9 80 5-111 13-97 (428)
87 COG2176 PolC DNA polymerase II 83.7 4.5 9.7E-05 39.1 7.1 71 3-88 238-310 (1444)
88 KOG3416|consensus 83.6 4 8.8E-05 29.1 5.3 75 5-97 15-95 (134)
89 cd04316 ND_PkAspRS_like_N ND_P 83.3 12 0.00026 25.5 8.6 79 6-110 14-96 (108)
90 PLN02850 aspartate-tRNA ligase 82.8 23 0.00049 31.5 11.0 43 67-111 130-172 (530)
91 cd04497 hPOT1_OB1_like hPOT1_O 82.4 7.7 0.00017 27.8 6.7 72 5-88 15-86 (138)
92 PRK05159 aspC aspartyl-tRNA sy 81.8 24 0.00052 30.4 10.6 52 54-111 46-100 (437)
93 smart00350 MCM minichromosome 81.1 8.2 0.00018 33.9 7.6 56 51-110 103-162 (509)
94 COG0017 AsnS Aspartyl/asparagi 80.8 5.5 0.00012 34.4 6.2 55 51-111 43-100 (435)
95 PRK10917 ATP-dependent DNA hel 80.7 8.5 0.00018 35.1 7.8 63 5-84 60-122 (681)
96 TIGR00457 asnS asparaginyl-tRN 79.6 41 0.00088 29.2 11.7 53 53-111 47-102 (453)
97 TIGR00459 aspS_bact aspartyl-t 79.4 31 0.00067 31.1 10.6 58 53-110 44-103 (583)
98 TIGR00643 recG ATP-dependent D 78.5 19 0.0004 32.5 9.2 63 5-84 33-95 (630)
99 KOG3056|consensus 78.4 17 0.00036 32.3 8.4 77 8-100 189-266 (578)
100 COG0587 DnaE DNA polymerase II 78.2 14 0.00031 35.8 8.6 66 7-86 979-1044(1139)
101 PTZ00385 lysyl-tRNA synthetase 77.1 52 0.0011 30.1 11.4 77 6-110 109-191 (659)
102 PLN02903 aminoacyl-tRNA ligase 76.3 12 0.00025 34.2 7.2 58 54-111 102-163 (652)
103 PRK07218 replication factor A; 76.3 12 0.00025 32.3 6.9 62 3-83 171-234 (423)
104 PRK07218 replication factor A; 76.2 14 0.00031 31.8 7.4 58 3-81 67-127 (423)
105 cd04318 EcAsnRS_like_N EcAsnRS 76.0 11 0.00024 24.1 5.4 50 54-109 31-81 (82)
106 KOG1885|consensus 74.1 18 0.0004 31.6 7.4 78 6-110 106-189 (560)
107 cd04498 hPOT1_OB2 hPOT1_OB2: A 72.5 6.9 0.00015 27.8 3.9 32 52-84 60-92 (123)
108 PF10451 Stn1: Telomere regula 72.5 22 0.00047 28.5 7.2 81 4-110 66-149 (256)
109 PTZ00417 lysine-tRNA ligase; P 70.8 82 0.0018 28.5 11.1 36 67-110 183-218 (585)
110 PRK06386 replication factor A; 70.7 52 0.0011 27.8 9.3 44 50-108 151-194 (358)
111 cd04483 hOBFC1_like hOBFC1_lik 68.7 5.4 0.00012 26.7 2.6 20 66-85 59-78 (92)
112 PTZ00401 aspartyl-tRNA synthet 68.5 24 0.00053 31.5 7.3 43 68-111 127-169 (550)
113 PRK00484 lysS lysyl-tRNA synth 68.0 85 0.0018 27.6 11.1 35 69-111 103-137 (491)
114 PLN02502 lysyl-tRNA synthetase 66.9 87 0.0019 28.1 10.4 36 68-111 159-194 (553)
115 COG4097 Predicted ferric reduc 65.6 11 0.00023 32.2 4.2 36 52-87 276-311 (438)
116 KOG0479|consensus 65.2 9.7 0.00021 34.4 4.1 56 51-111 212-269 (818)
117 PLN02532 asparagine-tRNA synth 64.3 22 0.00047 32.3 6.2 53 53-110 148-200 (633)
118 PF12869 tRNA_anti-like: tRNA_ 64.2 48 0.001 23.4 7.3 33 53-85 99-132 (144)
119 PRK07135 dnaE DNA polymerase I 62.3 55 0.0012 31.4 8.7 63 6-85 899-961 (973)
120 COG3111 Periplasmic protein wi 62.1 40 0.00087 24.0 6.0 31 69-108 97-127 (128)
121 PF04076 BOF: Bacterial OB fol 62.1 48 0.001 22.7 8.2 28 70-106 75-102 (103)
122 PRK03932 asnC asparaginyl-tRNA 62.0 1.1E+02 0.0023 26.6 11.3 37 68-110 63-99 (450)
123 COG0802 Predicted ATPase or ki 60.0 9.8 0.00021 28.0 2.7 24 61-84 13-36 (149)
124 TIGR00499 lysS_bact lysyl-tRNA 58.0 30 0.00066 30.4 5.9 36 68-111 102-137 (496)
125 PF02367 UPF0079: Uncharacteri 57.8 7.5 0.00016 27.6 1.8 23 61-83 3-25 (123)
126 PRK00476 aspS aspartyl-tRNA sy 57.6 50 0.0011 29.8 7.3 58 53-111 46-106 (588)
127 PRK10646 ADP-binding protein; 56.9 11 0.00024 27.7 2.6 24 61-84 16-39 (153)
128 PRK06763 F0F1 ATP synthase sub 56.6 3.4 7.3E-05 31.8 -0.2 15 1-16 1-15 (213)
129 COG1571 Predicted DNA-binding 56.1 1E+02 0.0022 26.7 8.5 64 4-86 266-332 (421)
130 PTZ00111 DNA replication licen 56.1 66 0.0014 30.6 7.9 55 52-110 346-404 (915)
131 PLN02603 asparaginyl-tRNA synt 54.9 1.6E+02 0.0035 26.5 12.2 53 53-111 138-193 (565)
132 PRK02983 lysS lysyl-tRNA synth 52.8 2.3E+02 0.0051 27.7 11.5 36 67-110 699-734 (1094)
133 PF11948 DUF3465: Protein of u 52.6 68 0.0015 23.1 5.9 29 61-93 78-106 (131)
134 TIGR01077 L13_A_E ribosomal pr 51.2 14 0.0003 27.0 2.3 23 58-80 9-31 (142)
135 PF03843 Slp: Outer membrane l 49.9 1E+02 0.0022 22.7 9.5 95 6-110 36-131 (160)
136 COG1838 FumA Tartrate dehydrat 49.9 21 0.00045 27.1 3.1 21 64-85 11-31 (184)
137 PF00970 FAD_binding_6: Oxidor 48.8 50 0.0011 21.5 4.7 31 52-83 63-95 (99)
138 PRK12820 bifunctional aspartyl 48.7 84 0.0018 29.1 7.3 59 53-111 47-110 (706)
139 PRK06394 rpl13p 50S ribosomal 48.4 18 0.00038 26.5 2.5 22 59-80 14-35 (146)
140 COG0677 WecC UDP-N-acetyl-D-ma 48.0 20 0.00043 30.8 3.0 45 30-83 87-131 (436)
141 TIGR00150 HI0065_YjeE ATPase, 47.1 21 0.00046 25.6 2.7 24 61-84 10-33 (133)
142 PF11736 DUF3299: Protein of u 47.0 53 0.0011 24.0 4.8 33 73-107 112-144 (146)
143 PLN02221 asparaginyl-tRNA synt 46.0 82 0.0018 28.4 6.7 55 53-111 83-137 (572)
144 COG4085 Predicted RNA-binding 44.8 47 0.001 25.6 4.3 33 53-85 82-119 (204)
145 COG1241 MCM2 Predicted ATPase 44.5 1.4E+02 0.0031 27.5 8.1 58 50-111 194-254 (682)
146 PF08021 FAD_binding_9: Sidero 43.9 83 0.0018 21.8 5.3 30 51-80 81-112 (117)
147 PF12080 GldM_C: GldM C-termin 42.7 79 0.0017 23.8 5.4 22 59-80 153-174 (181)
148 CHL00010 infA translation init 42.6 91 0.002 20.0 7.1 56 1-79 1-56 (78)
149 cd04486 YhcR_OBF_like YhcR_OBF 41.8 32 0.00069 22.1 2.7 19 67-85 42-60 (78)
150 cd04480 RPA1_DBD_A_like RPA1_D 40.7 44 0.00096 21.5 3.3 29 52-80 31-59 (86)
151 PRK12445 lysyl-tRNA synthetase 40.7 82 0.0018 27.8 5.9 36 68-111 114-149 (505)
152 cd00392 Ribosomal_L13 Ribosoma 39.4 31 0.00067 24.1 2.5 14 59-72 11-24 (114)
153 PF10574 UPF0552: Uncharacteri 39.1 97 0.0021 24.3 5.4 40 70-109 29-71 (224)
154 PF13511 DUF4124: Domain of un 38.3 24 0.00051 21.1 1.6 17 83-99 14-30 (60)
155 PF00572 Ribosomal_L13: Riboso 37.7 29 0.00063 24.8 2.2 21 59-79 11-43 (128)
156 TIGR01066 rplM_bact ribosomal 37.1 31 0.00067 25.1 2.3 30 51-80 11-56 (140)
157 COG2087 CobU Adenosyl cobinami 36.9 46 0.001 25.1 3.2 31 50-80 53-83 (175)
158 COG1190 LysU Lysyl-tRNA synthe 36.5 2.9E+02 0.0062 24.6 8.3 41 62-110 104-144 (502)
159 PTZ00425 asparagine-tRNA ligas 36.5 1.2E+02 0.0026 27.4 6.3 58 54-111 115-180 (586)
160 COG3689 Predicted membrane pro 35.8 74 0.0016 25.7 4.4 86 6-111 177-262 (271)
161 KOG0478|consensus 35.3 61 0.0013 29.9 4.2 34 51-88 328-361 (804)
162 PF05683 Fumerase_C: Fumarase 34.5 80 0.0017 24.5 4.3 31 55-85 28-58 (205)
163 PRK08395 fumarate hydratase; P 33.7 62 0.0013 24.2 3.4 19 67-85 12-30 (162)
164 PRK09216 rplM 50S ribosomal pr 33.4 38 0.00082 24.8 2.2 30 51-80 13-58 (144)
165 COG1908 FrhD Coenzyme F420-red 33.3 46 0.00099 23.7 2.5 38 50-87 29-69 (132)
166 TIGR01618 phage_P_loop phage n 33.1 37 0.00079 26.5 2.3 46 56-101 112-163 (220)
167 PRK06043 fumarate hydratase; P 32.8 63 0.0014 24.8 3.4 19 67-85 14-32 (192)
168 PRK06842 fumarate hydratase; P 32.7 64 0.0014 24.6 3.4 19 67-85 14-32 (185)
169 PTZ00068 60S ribosomal protein 32.6 37 0.0008 26.3 2.2 22 59-80 15-36 (202)
170 PRK08228 L(+)-tartrate dehydra 32.0 66 0.0014 25.0 3.4 19 67-85 15-33 (204)
171 TIGR00723 ttdB_fumA_fumB hydro 31.6 56 0.0012 24.5 2.9 18 68-85 4-21 (168)
172 PF02751 TFIIA_gamma_C: Transc 30.6 1.2E+02 0.0027 18.1 5.4 30 74-109 4-33 (52)
173 PF07378 FlbT: Flagellar prote 30.3 64 0.0014 23.0 3.0 34 70-110 5-38 (126)
174 PF06557 DUF1122: Protein of u 30.2 89 0.0019 23.4 3.8 60 11-80 13-86 (170)
175 CHL00159 rpl13 ribosomal prote 30.2 46 0.001 24.3 2.3 30 51-80 14-59 (143)
176 COG1862 YajC Preprotein transl 29.1 63 0.0014 22.0 2.6 23 63-85 37-59 (97)
177 PF02721 DUF223: Domain of unk 29.1 1.1E+02 0.0023 20.2 3.8 32 51-82 9-40 (95)
178 TIGR03853 matur_matur probable 29.0 46 0.00099 21.7 1.8 36 50-85 34-70 (77)
179 PF03734 YkuD: L,D-transpeptid 28.8 72 0.0016 22.1 3.1 25 54-78 119-144 (144)
180 PRK12791 flbT flagellar biosyn 27.3 72 0.0016 22.9 2.8 34 70-110 7-40 (131)
181 PF03658 Ub-RnfH: RnfH family 26.9 26 0.00056 23.2 0.4 30 54-84 47-76 (84)
182 cd04495 BRCA2DBD_OB3 BRCA2DBD_ 26.3 1.5E+02 0.0033 20.2 4.1 54 50-108 26-79 (100)
183 COG1107 Archaea-specific RecJ- 25.6 89 0.0019 28.4 3.5 77 6-111 215-291 (715)
184 TIGR00739 yajC preprotein tran 24.6 81 0.0018 20.7 2.5 23 64-86 32-54 (84)
185 PRK03065 hutP anti-terminator 24.4 1.2E+02 0.0026 22.2 3.5 30 28-63 101-130 (148)
186 KOG3108|consensus 23.5 71 0.0015 25.8 2.4 35 51-85 95-131 (265)
187 COG3649 CRISPR system related 22.8 55 0.0012 25.8 1.6 34 51-88 99-132 (283)
188 PF05037 DUF669: Protein of un 22.6 97 0.0021 22.2 2.8 36 16-58 27-63 (141)
189 PRK05800 cobU adenosylcobinami 22.2 90 0.002 23.1 2.6 30 51-80 55-84 (170)
190 PLN00205 ribisomal protein L13 22.2 79 0.0017 24.3 2.3 30 51-80 15-60 (191)
191 PRK12442 translation initiatio 22.1 2.3E+02 0.005 18.9 4.2 58 1-81 1-58 (87)
192 PF11434 CHIPS: Chemotaxis-inh 21.9 42 0.00092 21.4 0.7 18 59-76 8-25 (91)
193 PRK05585 yajC preprotein trans 21.9 94 0.002 21.4 2.5 23 64-86 47-69 (106)
194 PF03983 SHD1: SLA1 homology d 21.2 1.3E+02 0.0029 19.1 2.8 27 83-109 11-40 (70)
195 KOG1496|consensus 20.0 97 0.0021 25.1 2.5 39 45-83 95-133 (332)
196 smart00110 C1Q Complement comp 20.0 70 0.0015 22.8 1.6 13 69-81 99-111 (135)
No 1
>PRK09010 single-stranded DNA-binding protein; Provisional
Probab=100.00 E-value=3.9e-45 Score=274.24 Aligned_cols=116 Identities=58% Similarity=1.082 Sum_probs=109.3
Q ss_pred CC--CccEEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEE
Q psy14498 1 MA--SVNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYI 78 (171)
Q Consensus 1 M~--~~N~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V 78 (171)
|+ +||+|+|+|||++||++|++++|.++++|+||++++|+++++|++.++++||+|++|+++|+.+.++|+||++|+|
T Consensus 1 m~~r~~N~V~LiGrLg~DPelR~t~nG~~v~~fsVAvn~~~kd~~~Ge~~e~t~w~~V~~fgk~Ae~~~~~L~KGs~V~V 80 (177)
T PRK09010 1 MASRGVNKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKQTGEMKEQTEWHRVVLFGKLAEVAGEYLRKGSQVYI 80 (177)
T ss_pred CCccCceEEEEEEEeCCCceEEEcCCCCEEEEEEEEEcCccccCcccccccceEEEEEEEehhHHHHHHHhcCCCCEEEE
Confidence 65 7999999999999999999999999999999999999987779988899999999999999999999999999999
Q ss_pred EeEeeeeeeecCCCcEEEEEEEEEe---EEEEccCCCCCCC
Q psy14498 79 EGRLQTRKWTNKEGVEKYITEVIAD---NMQMLGSRKNTNE 116 (171)
Q Consensus 79 ~G~l~~~~~~~kdG~~~~~~~i~a~---~i~~l~~~~~~~~ 116 (171)
+|+|++++|+|++|++++.++|+|+ +|+||+++..+..
T Consensus 81 eGrL~~~~yedkdG~~r~~~eVvv~~~~~~~~l~~r~~~~~ 121 (177)
T PRK09010 81 EGQLRTRKWTDQSGQDRYTTEVVVNVGGTMQMLGGRQGGGA 121 (177)
T ss_pred EEEEEeccccCCCCCEEEEEEEEEecCCcEEEccCCCCCCC
Confidence 9999999999999999999999998 8999998855443
No 2
>PRK13732 single-stranded DNA-binding protein; Provisional
Probab=100.00 E-value=2.1e-44 Score=269.89 Aligned_cols=117 Identities=52% Similarity=1.039 Sum_probs=110.2
Q ss_pred CC--CccEEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEE
Q psy14498 1 MA--SVNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYI 78 (171)
Q Consensus 1 M~--~~N~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V 78 (171)
|+ +||+|+|+|||++|||+|++++|..+|+|+||++++|++.++|+|.+.++||+|++||++|+.++++|+||+.|+|
T Consensus 1 m~~r~mN~V~LiGrLg~DPElR~t~nG~~va~fslAvn~~~kd~~~Ge~~e~t~w~~Vv~wgk~Ae~v~~~L~KG~~V~V 80 (175)
T PRK13732 1 MAVRGINKVILVGRLGKDPEVRYIPNGGAVANLQVATSESWRDKQTGEMREQTEWHRVVLFGKLAEVAGEYLRKGAQVYI 80 (175)
T ss_pred CCccCceEEEEEEEecCCCEEEEcCCCCEEEEEEEEEcCccccCCCCceecceeEEEEEEecHHHHHHHHhcCCCCEEEE
Confidence 77 7999999999999999999999999999999999999987679998899999999999999999999999999999
Q ss_pred EeEeeeeeeecCCCcEEEEEEEEEe---EEEEccCCCCCCCCC
Q psy14498 79 EGRLQTRKWTNKEGVEKYITEVIAD---NMQMLGSRKNTNEKN 118 (171)
Q Consensus 79 ~G~l~~~~~~~kdG~~~~~~~i~a~---~i~~l~~~~~~~~~~ 118 (171)
+|+|++++|++ +|++++.++|+|+ +|.||+++...+...
T Consensus 81 eGrL~~r~ye~-dG~kr~~~eIiv~~~g~~~fL~~~~~~~~~~ 122 (175)
T PRK13732 81 EGQLRTRSWED-NGITRYVTEILVKTTGTMQMLGRAPQQNAQP 122 (175)
T ss_pred EEEEEeeeEcc-CCeEEEEEEEEEeecCeEEEecCCCCCCCCC
Confidence 99999999985 7999999999999 999999988776543
No 3
>PRK06863 single-stranded DNA-binding protein; Provisional
Probab=100.00 E-value=2.5e-44 Score=267.86 Aligned_cols=119 Identities=57% Similarity=1.062 Sum_probs=112.1
Q ss_pred CCCccEEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEe
Q psy14498 1 MASVNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEG 80 (171)
Q Consensus 1 M~~~N~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G 80 (171)
|++||+|+|+|||++||++|++++|+.+++|+|+++++|+++++|++.+.++||+|++||++|+.+.++|+||++|+|+|
T Consensus 1 M~~~N~V~LiGrLg~DPElR~t~nG~~va~fsVAvn~~~~d~~~Ge~~e~t~w~~Vv~fgk~AE~v~~~LkKGs~V~VeG 80 (168)
T PRK06863 1 MAGINKVIIVGHLGNDPEIRTMPNGEAVANISVATSESWTDKNTGERREVTEWHRIVFYRRQAEVAGEYLRKGSQVYVEG 80 (168)
T ss_pred CCCccEEEEEEEcCCCCEEEEcCCCCEEEEEEEEecCcccccCCCcccccceEEEEEEEhHHHHHHHHHCCCCCEEEEEE
Confidence 99999999999999999999999999999999999999988766888777999999999999999999999999999999
Q ss_pred EeeeeeeecCCCcEEEEEEEEEeEEEEccCCCCCCCCCc
Q psy14498 81 RLQTRKWTNKEGVEKYITEVIADNMQMLGSRKNTNEKNI 119 (171)
Q Consensus 81 ~l~~~~~~~kdG~~~~~~~i~a~~i~~l~~~~~~~~~~~ 119 (171)
+|++++|+|++|++++.++|+|++|+||.++.+....+.
T Consensus 81 rL~~r~w~DkdG~~r~~~eI~a~~i~~L~~r~~~~~~~~ 119 (168)
T PRK06863 81 RLKTRKWQDQNGQDRYTTEIQGDVLQMLGGRNQRNAGGY 119 (168)
T ss_pred EEEeCCccCCCCCEEEEEEEEEeEEEECCCCCccccccc
Confidence 999999999999999999999999999999987655444
No 4
>PRK06958 single-stranded DNA-binding protein; Provisional
Probab=100.00 E-value=1.4e-43 Score=266.03 Aligned_cols=116 Identities=59% Similarity=1.064 Sum_probs=110.9
Q ss_pred CCCccEEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEe
Q psy14498 1 MASVNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEG 80 (171)
Q Consensus 1 M~~~N~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G 80 (171)
|++||+|+|+|||++||++|++++|.++++|+||++++|+++++|++++.++||+|++|+++|+.++++|+||++|+|+|
T Consensus 1 Mas~N~V~LiGrLg~DPElr~t~nG~~va~fsVAv~~~~kdk~sGe~~e~T~w~~V~~fGk~AE~v~~~LkKGs~V~VeG 80 (182)
T PRK06958 1 MASVNKVILVGNLGADPEVRYLPSGDAVANIRLATTDRYKDKASGEFKEATEWHRVAFFGRLAEIVGEYLKKGSSVYIEG 80 (182)
T ss_pred CCcccEEEEEEEecCCCeEEEcCCCCEEEEEEEEeccccccccCCcccccceEEEEEEehHHHHHHHHHhCCCCEEEEEE
Confidence 99999999999999999999999999999999999999998877998888999999999999999999999999999999
Q ss_pred EeeeeeeecCCCcEEEEEEEEEeEEEEccCCCCCCC
Q psy14498 81 RLQTRKWTNKEGVEKYITEVIADNMQMLGSRKNTNE 116 (171)
Q Consensus 81 ~l~~~~~~~kdG~~~~~~~i~a~~i~~l~~~~~~~~ 116 (171)
+|+++.|+|+||++++.++|+|++|+||.++...+.
T Consensus 81 rL~~~~yeDkdG~kr~~~eVvA~~V~fL~sr~~~~~ 116 (182)
T PRK06958 81 RIRTRKWQGQDGQDRYSTEIVADQMQMLGGRGGSGG 116 (182)
T ss_pred EEEeCceECCCCcEEEEEEEEEeEEEECCCCccCcC
Confidence 999999999999999999999999999998865544
No 5
>PRK08763 single-stranded DNA-binding protein; Provisional
Probab=100.00 E-value=1.7e-43 Score=262.68 Aligned_cols=114 Identities=49% Similarity=0.920 Sum_probs=108.6
Q ss_pred CC-CccEEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEE
Q psy14498 1 MA-SVNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIE 79 (171)
Q Consensus 1 M~-~~N~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~ 79 (171)
|+ +||+|+|+|||++||+||++++|.++++|+||+++.+++++ |++.+.++||+|++||++|+.+.++|+||+.|+|+
T Consensus 1 mar~~Nkv~LiGrLg~DPelr~t~~G~~va~fsVA~~~~~k~~~-G~~~e~t~w~~Vv~fgk~Ae~v~~~L~KGs~V~Ve 79 (164)
T PRK08763 1 MARGINKVILVGNLGNDPDIKYTQSGMTITRISLATTSVRKDRE-GNTQERTEWHRVKFFGKLGEIAGEYLRKGSQCYIE 79 (164)
T ss_pred CCCcceEEEEEEEecCCCeEEEcCCCCeEEEEEEEeccceecCC-CCeeccceEEEEEEehHHHHHHHHhcCCCCEEEEE
Confidence 87 79999999999999999999999999999999999999986 98888899999999999999999999999999999
Q ss_pred eEeeeeeeecCCCcEEEEEEEEEeEEEEccCCCCCC
Q psy14498 80 GRLQTRKWTNKEGVEKYITEVIADNMQMLGSRKNTN 115 (171)
Q Consensus 80 G~l~~~~~~~kdG~~~~~~~i~a~~i~~l~~~~~~~ 115 (171)
|+|++++|++++|++++.++|+|++|.||.++.+.+
T Consensus 80 GrL~~~~y~dkdG~kr~~~eIva~~i~~L~~~~~~~ 115 (164)
T PRK08763 80 GSIRYDKFTGQDGQERYVTEIVADEMQMLGGRGEGG 115 (164)
T ss_pred EEEEeceeECCCCCEEEEEEEEEeEEEECCCCCCCC
Confidence 999999999999999999999999999999885433
No 6
>PRK05733 single-stranded DNA-binding protein; Provisional
Probab=100.00 E-value=4.3e-43 Score=262.12 Aligned_cols=115 Identities=57% Similarity=1.070 Sum_probs=108.1
Q ss_pred CC-CccEEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEE
Q psy14498 1 MA-SVNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIE 79 (171)
Q Consensus 1 M~-~~N~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~ 79 (171)
|+ +||+|+|+|||++||++|++++|.++++|+|+++++|++.++|++.+.++||+|++||++|+.++++|+||++|+|+
T Consensus 1 ma~~mNkV~LiGrlg~DPElr~t~nG~~va~fsVAv~~~~k~~~~Ge~~e~T~w~~Vv~fgk~Ae~v~~~l~KGs~V~Ve 80 (172)
T PRK05733 1 MARGVNKVILVGTCGQDPEVRYLPNGNAVTNLSLATSEQWTDKQSGQKVERTEWHRVSLFGKVAEIAGEYLRKGSQVYIE 80 (172)
T ss_pred CCCcceEEEEEEEecCCCEEEECCCCCEEEEEEEEEcCccccCCCCcccccceEEEEEEehHHHHHHHHHhCCCCEEEEE
Confidence 77 79999999999999999999999999999999999999876799888899999999999999999999999999999
Q ss_pred eEeeeeeeecCCCcEEEEEEEEEe---EEEEccCCCCCCC
Q psy14498 80 GRLQTRKWTNKEGVEKYITEVIAD---NMQMLGSRKNTNE 116 (171)
Q Consensus 80 G~l~~~~~~~kdG~~~~~~~i~a~---~i~~l~~~~~~~~ 116 (171)
|+|++++|+ ++|++++.++|+|+ +|.||+++....+
T Consensus 81 GrLr~~~y~-kdG~~r~~~eVvvd~~g~v~~L~~~~~~~~ 119 (172)
T PRK05733 81 GKLQTREWE-KDGIKRYTTEIVVDMQGTMQLLGGRPQGDD 119 (172)
T ss_pred EEEEeCcEe-cCCEEEEEEEEEEeecCeEEECcCCCCCcC
Confidence 999999999 99999999999999 8999987765444
No 7
>PRK08486 single-stranded DNA-binding protein; Provisional
Probab=100.00 E-value=2.5e-42 Score=260.56 Aligned_cols=111 Identities=38% Similarity=0.705 Sum_probs=106.6
Q ss_pred CccEEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEe
Q psy14498 3 SVNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEGRL 82 (171)
Q Consensus 3 ~~N~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l 82 (171)
|||+|+|+|||++|||+|++++|.++|+|+||++++|++.+ |++.++++||+|++||++||.+.++|+||++|+|+|+|
T Consensus 1 m~N~V~LvGrL~~DPElr~t~sG~~va~fslAv~r~~~~~~-Ge~~e~t~fi~v~~fg~~AE~~~~~l~KG~~V~VeGrL 79 (182)
T PRK08486 1 MFNKVILVGNLTRDVELRYLPSGSAIATIGLATSRRFKKQD-GEKGEEVCFIDIRLFGRTAEIANQYLSKGSKVLIEGRL 79 (182)
T ss_pred CeeEEEEEEEecCCCEEEECCCCCEEEEEEEEEecceecCC-CCCcccceEEEEEEEhHHHHHHHHHcCCCCEEEEEEEE
Confidence 68999999999999999999999999999999999998875 99888999999999999999999999999999999999
Q ss_pred eeeeeecCCCcEEEEEEEEEeEEEEccCCCCC
Q psy14498 83 QTRKWTNKEGVEKYITEVIADNMQMLGSRKNT 114 (171)
Q Consensus 83 ~~~~~~~kdG~~~~~~~i~a~~i~~l~~~~~~ 114 (171)
++++|+|++|++++.++|+|++|+||.++...
T Consensus 80 ~~~~y~dkdG~~r~~~eI~a~~v~~L~~~~~~ 111 (182)
T PRK08486 80 TFESWMDQNGQKRSKHTITAESMQMLDSKSDN 111 (182)
T ss_pred EeCcEECCCCcEEEEEEEEEeEEEECCCCCCC
Confidence 99999999999999999999999999988665
No 8
>PRK07275 single-stranded DNA-binding protein; Provisional
Probab=100.00 E-value=6.1e-42 Score=254.23 Aligned_cols=110 Identities=35% Similarity=0.656 Sum_probs=104.4
Q ss_pred CccEEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEe
Q psy14498 3 SVNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEGRL 82 (171)
Q Consensus 3 ~~N~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l 82 (171)
|||+|+|+|||++|||+|++++|.++|+|+||++++|++.+ |++ +++||+|++||++||.++++|+||++|+|+|+|
T Consensus 1 M~N~v~LiGrL~~DPElr~t~sG~~v~~ftlAv~r~~~~~~-ge~--~tdfi~vv~wgk~Ae~~~~~l~KG~~V~VeGrl 77 (162)
T PRK07275 1 MINNVVLVGRMTRDAELRYTPSNVAVATFTLAVNRTFKSQN-GER--EADFINCVIWRQQAENLANWAKKGALIGVTGRI 77 (162)
T ss_pred CeeEEEEEEEECCCCeEEECCCCCEEEEEEEEEcCceecCC-CCE--eeeEEEEEEEcHHHHHHHHHcCCCCEEEEEEEE
Confidence 69999999999999999999999999999999999999875 775 699999999999999999999999999999999
Q ss_pred eeeeeecCCCcEEEEEEEEEeEEEEccCCCCCC
Q psy14498 83 QTRKWTNKEGVEKYITEVIADNMQMLGSRKNTN 115 (171)
Q Consensus 83 ~~~~~~~kdG~~~~~~~i~a~~i~~l~~~~~~~ 115 (171)
++++|++++|++++.++|+|++|+||+++....
T Consensus 78 ~~r~y~dkdG~k~~~~evva~~i~~l~~~~~~~ 110 (162)
T PRK07275 78 QTRNYENQQGQRVYVTEVVADNFQMLESRATRE 110 (162)
T ss_pred EeceEECCCCCEEEEEEEEEeEEEECCCCCccc
Confidence 999999999999999999999999999886443
No 9
>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=100.00 E-value=1.6e-40 Score=248.23 Aligned_cols=113 Identities=50% Similarity=0.908 Sum_probs=108.5
Q ss_pred CCCccEEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEe
Q psy14498 1 MASVNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEG 80 (171)
Q Consensus 1 M~~~N~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G 80 (171)
|+|||+|+|+|||++||++|++++|+++++|+|++++++++++ |+|.+.++||+|++||++|+.++++|+||++|+|+|
T Consensus 1 m~m~N~V~L~G~l~~dPe~r~t~~G~~v~~fsvA~~~~~~~~~-G~~~~~t~~~~v~~wg~~Ae~~~~~l~KG~~V~V~G 79 (164)
T TIGR00621 1 MRMVNKVILVGRLTRDPELRYTPSGNAVANFTLATNRRWKDQD-GEWKEETEWHDIVIFGRLAEVAAQYLKKGSLVYVEG 79 (164)
T ss_pred CCcccEEEEEEEeCCCCEEEECCCCCEEEEEEEEEcCceecCC-CCEeccceEEEEEEehHHHHHHHHhCCCCCEEEEEE
Confidence 8999999999999999999999999999999999999999886 999888999999999999999999999999999999
Q ss_pred EeeeeeeecCCCcEEEEEEEEEeEEEEccCCCCC
Q psy14498 81 RLQTRKWTNKEGVEKYITEVIADNMQMLGSRKNT 114 (171)
Q Consensus 81 ~l~~~~~~~kdG~~~~~~~i~a~~i~~l~~~~~~ 114 (171)
+|++++|++++|++++.++|+|++|.+|..+...
T Consensus 80 ~L~~~~~~~kdG~~~~~~ev~a~~i~~L~~~~~~ 113 (164)
T TIGR00621 80 RLRTRKWEDQNGQKRSKTEIIADNVQLLDLLGAR 113 (164)
T ss_pred EEEeceEECCCCcEEEEEEEEEEEEeeccccCCc
Confidence 9999999999999999999999999999877544
No 10
>PRK06751 single-stranded DNA-binding protein; Provisional
Probab=100.00 E-value=2.8e-40 Score=247.35 Aligned_cols=110 Identities=37% Similarity=0.687 Sum_probs=103.9
Q ss_pred CccEEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEe
Q psy14498 3 SVNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEGRL 82 (171)
Q Consensus 3 ~~N~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l 82 (171)
|||+|+|+|||++||++|++++|.++|+|+||++++|++.. |++ +++||+|++||++|+.++++|+||++|+|+|+|
T Consensus 1 MmN~V~LiGrL~~DpelR~t~sG~~v~~fslAvnr~~~~~~-ge~--~tdwi~~v~wgk~Ae~~~~~l~KG~~V~VeGrL 77 (173)
T PRK06751 1 MMNRVILVGRLTKDPDLRYTPNGVAVATFTLAVNRAFANQQ-GER--EADFINCVIWRKQAENVANYLKKGSLAGVDGRL 77 (173)
T ss_pred CceEEEEEEEECCCCcEEECCCCCEEEEEEEEEccceecCC-CCE--EEEEEEEEEeCcHHHHHHHHcCCCCEEEEEEEE
Confidence 69999999999999999999999999999999999998774 776 689999999999999999999999999999999
Q ss_pred eeeeeecCCCcEEEEEEEEEeEEEEccCCCCCC
Q psy14498 83 QTRKWTNKEGVEKYITEVIADNMQMLGSRKNTN 115 (171)
Q Consensus 83 ~~~~~~~kdG~~~~~~~i~a~~i~~l~~~~~~~ 115 (171)
+++.|++++|++++.++|+|++|+||+++....
T Consensus 78 ~~r~yedkdG~~~~~~eVva~~i~~l~~r~~~~ 110 (173)
T PRK06751 78 QTRNYEGQDGKRVYVTEVLAESVQFLEPRNGGG 110 (173)
T ss_pred EeCccCCCCCcEEEEEEEEEEEEEeCcCCCCCc
Confidence 999999999999999999999999999886543
No 11
>PRK06341 single-stranded DNA-binding protein; Provisional
Probab=100.00 E-value=7.8e-40 Score=243.10 Aligned_cols=117 Identities=55% Similarity=0.992 Sum_probs=108.5
Q ss_pred CC-CccEEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhH-HHHHHHHHcCCCCEEEE
Q psy14498 1 MA-SVNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRK-LAQIVKQYLKKGSQIYI 78 (171)
Q Consensus 1 M~-~~N~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~-~A~~~~~~l~kG~~V~V 78 (171)
|+ +||+|+|+|||++||++|++++|+++|+|+||++++|+++.+|+|.++++||+|++|++ +|+.++++|+||++|+|
T Consensus 1 Ma~~mN~V~LiGrLg~DPElR~t~sG~~v~~fsVAvn~~~kd~~~Ge~~e~T~w~~Vv~fg~~~Ae~~~~~LkKG~~V~V 80 (166)
T PRK06341 1 MAGSVNKVILIGNLGADPEIRRTQDGRPIANLRIATSETWRDRNSGERKEKTEWHRVVIFNEGLCKVAEQYLKKGAKVYI 80 (166)
T ss_pred CCCcceEEEEEEEecCCCEEEEcCCCCEEEEEEEEEccceecCCCCcccccceEEEEEEeChHHHHHHHHhcCCCCEEEE
Confidence 77 59999999999999999999999999999999999999876799988999999999996 99999999999999999
Q ss_pred EeEeeeeeeecCCCcEEEEEEEEEeE----EEEccCCCCCCCC
Q psy14498 79 EGRLQTRKWTNKEGVEKYITEVIADN----MQMLGSRKNTNEK 117 (171)
Q Consensus 79 ~G~l~~~~~~~kdG~~~~~~~i~a~~----i~~l~~~~~~~~~ 117 (171)
+|+|++++|+|++|++++.++|++++ |.||.++.+.++.
T Consensus 81 eGrL~~r~w~dkdG~~r~~~eIiv~~~~~~l~~l~~~~~~~~~ 123 (166)
T PRK06341 81 EGQLQTRKWTDQSGVERYSTEVVLQGFNSTLTMLDGRGEGGGG 123 (166)
T ss_pred EEEEEeCcEECCCCCEEEEEEEEEEecccceEEcccCCcCCCC
Confidence 99999999999999999999999986 4899888655443
No 12
>PRK06642 single-stranded DNA-binding protein; Provisional
Probab=100.00 E-value=8e-39 Score=235.80 Aligned_cols=114 Identities=51% Similarity=0.952 Sum_probs=106.9
Q ss_pred CC-CccEEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhH-HHHHHHHHcCCCCEEEE
Q psy14498 1 MA-SVNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRK-LAQIVKQYLKKGSQIYI 78 (171)
Q Consensus 1 M~-~~N~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~-~A~~~~~~l~kG~~V~V 78 (171)
|+ +||+|+|+|||++||++|++++|+++++|+||++++|+++++|++.+.++||+|++||+ +|+.+++||+||++|+|
T Consensus 1 Ma~~~N~V~LiGrLg~DPElr~t~~G~~v~~fslAv~~~~k~~~~G~~~~~T~w~~v~~~g~~~Ae~~~~~l~KG~~V~V 80 (152)
T PRK06642 1 MAGSLNKVILIGNVGRDPEIRTTGEGKKIINLSLATTETWKDRITSERKERTEWHRVVIFSEGLVSVVERYVTKGSKLYI 80 (152)
T ss_pred CCCcceEEEEEEEccCCceEEECCCCCEEEEEEEEeccccccccCCccccceeEEEEEEeChHHHHHHHHhCCCCCEEEE
Confidence 88 49999999999999999999999999999999999999876699888899999999996 99999999999999999
Q ss_pred EeEeeeeeeecCCCcEEEEEEEEEeEE----EEccCCCCC
Q psy14498 79 EGRLQTRKWTNKEGVEKYITEVIADNM----QMLGSRKNT 114 (171)
Q Consensus 79 ~G~l~~~~~~~kdG~~~~~~~i~a~~i----~~l~~~~~~ 114 (171)
+|+|++++|++++|++++.++|+|++| .||.++...
T Consensus 81 ~GrL~~~~y~dkdG~~r~~~eVvv~~~~~~i~fl~~k~~~ 120 (152)
T PRK06642 81 EGSLQTRKWNDNSGQEKYTTEVVLQNFNSQLILLDSKNSN 120 (152)
T ss_pred EEEEEeCeeECCCCCEEEEEEEEEEecccceEeccCCCCc
Confidence 999999999999999999999999987 899877544
No 13
>PRK07274 single-stranded DNA-binding protein; Provisional
Probab=100.00 E-value=8.1e-38 Score=225.63 Aligned_cols=108 Identities=37% Similarity=0.657 Sum_probs=102.2
Q ss_pred CccEEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEe
Q psy14498 3 SVNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEGRL 82 (171)
Q Consensus 3 ~~N~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l 82 (171)
|||+|+|+|||++||++|++++|+++|+|+||++++|++++ |++ +++||+|++||++|+.++++|+||++|+|+|+|
T Consensus 1 mmN~v~LiGrL~~dPelr~t~~g~~~~~fslAv~~~~k~~~-g~~--~t~w~~v~~fg~~Ae~v~~~l~KG~~V~V~Grl 77 (131)
T PRK07274 1 MYNKVILIGRLTATPELVKTANDKSVARVTLAVNRRFKNQN-GER--EADFINVVLWGKLAETLASYASKGSLISIDGEL 77 (131)
T ss_pred CeeEEEEEEEccCCCeEEECCCCCEEEEEEEEEcCceecCC-CCE--EEEEEEEEEehHHHHHHHHHcCCCCEEEEEEEE
Confidence 69999999999999999999999999999999999998875 876 699999999999999999999999999999999
Q ss_pred eeeeeecCCCcEEEEEEEEEeEEEEccCCCCC
Q psy14498 83 QTRKWTNKEGVEKYITEVIADNMQMLGSRKNT 114 (171)
Q Consensus 83 ~~~~~~~kdG~~~~~~~i~a~~i~~l~~~~~~ 114 (171)
++++| ++||++++.++|++++|.+|+++...
T Consensus 78 ~~~~y-~kdG~~~~~~eviv~~i~~l~~k~~~ 108 (131)
T PRK07274 78 RTRKY-EKDGQTHYVTEVLCQSFQLLESRAQR 108 (131)
T ss_pred EeccC-ccCCcEEEEEEEEEEEEEECcCCCcc
Confidence 99999 89999999999999999999977543
No 14
>PRK07459 single-stranded DNA-binding protein; Provisional
Probab=100.00 E-value=8.6e-37 Score=217.26 Aligned_cols=106 Identities=35% Similarity=0.714 Sum_probs=98.8
Q ss_pred CCccEEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEeE
Q psy14498 2 ASVNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEGR 81 (171)
Q Consensus 2 ~~~N~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~ 81 (171)
.+||+|+|+|||++|||+|++++|+++++|+||+++++++. .++||+|++||++|+.+.++|+||++|+|+|+
T Consensus 1 M~~N~v~LiGrL~~DPelr~t~~G~~v~~fslAv~~~~~~~-------~t~w~~v~~wg~~Ae~~~~~l~KG~~V~V~G~ 73 (121)
T PRK07459 1 MSLNSVTLVGRAGRDPEVRYFESGSVVCNLTLAVNRRSRDD-------EPDWFNLEIWGKTAQVAADYVKKGSLIGITGS 73 (121)
T ss_pred CCccEEEEEEEccCCCEEEEcCCCCEEEEEEEEecccccCC-------CceEEEEEEehHHHHHHHHHcCCCCEEEEEEE
Confidence 04999999999999999999999999999999999988752 58999999999999999999999999999999
Q ss_pred eeeeeeecCC-CcEEEEEEEEEeEEEEccCCCCC
Q psy14498 82 LQTRKWTNKE-GVEKYITEVIADNMQMLGSRKNT 114 (171)
Q Consensus 82 l~~~~~~~kd-G~~~~~~~i~a~~i~~l~~~~~~ 114 (171)
|++++|+|++ |++++.++|+|++|+||.++...
T Consensus 74 l~~~~~~d~d~G~~r~~~ei~a~~i~~L~~k~~~ 107 (121)
T PRK07459 74 LKFDRWTDRNTGEDRSKPVIRVDRLELLGSKRDS 107 (121)
T ss_pred EEecceEcCCCCeEEEEEEEEEeEEEECcCCCcc
Confidence 9999999987 99999999999999999877543
No 15
>PRK06752 single-stranded DNA-binding protein; Validated
Probab=100.00 E-value=3e-36 Score=212.17 Aligned_cols=108 Identities=33% Similarity=0.625 Sum_probs=103.0
Q ss_pred CccEEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEe
Q psy14498 3 SVNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEGRL 82 (171)
Q Consensus 3 ~~N~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l 82 (171)
|||+|+|+|||++|||+|++++|+++++|+||++++|++.+ |++ +++||+|++||++|+.++++|+||+.|+|+|+|
T Consensus 1 MmN~v~liGrl~~dPelr~t~~G~~~~~f~lAv~~~~~~~~-g~~--~t~~~~v~~wg~~Ae~~~~~l~KG~~V~V~G~l 77 (112)
T PRK06752 1 MMNRVVLIGRLTKEPELYYTKQGVAYARVCVAVNRGFRNSL-GEQ--QVDFINCVVWRKSAENVTEYCTKGSLVGITGRI 77 (112)
T ss_pred CceEEEEEEECcCCCEEEECCCCCEEEEEEEEECCCeEcCC-CCE--EEEEEEEEEehHHHHHHHHhcCCCCEEEEEEEE
Confidence 69999999999999999999999999999999999998875 775 699999999999999999999999999999999
Q ss_pred eeeeeecCCCcEEEEEEEEEeEEEEccCCCC
Q psy14498 83 QTRKWTNKEGVEKYITEVIADNMQMLGSRKN 113 (171)
Q Consensus 83 ~~~~~~~kdG~~~~~~~i~a~~i~~l~~~~~ 113 (171)
++++|+|++|++++.++|+|++|.||+++.+
T Consensus 78 ~~~~~~~~~G~~~~~~ei~a~~i~~l~~~~~ 108 (112)
T PRK06752 78 HTRNYEDDQGKRIYITEVVIESITFLERRRE 108 (112)
T ss_pred EeCccCCCCCcEEEEEEEEEEEEEECCCCCc
Confidence 9999999999999999999999999988753
No 16
>COG0629 Ssb Single-stranded DNA-binding protein [DNA replication, recombination, and repair]
Probab=100.00 E-value=2.7e-35 Score=220.75 Aligned_cols=111 Identities=51% Similarity=0.894 Sum_probs=91.6
Q ss_pred CCccEEEEEEEeCCCCeEEEecCCc-EEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEe
Q psy14498 2 ASVNKVIIIGNLGRDPETRYMSNGD-AVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEG 80 (171)
Q Consensus 2 ~~~N~v~l~G~l~~dp~~~~~~~g~-~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G 80 (171)
+|||+|+|+|||++|||+|++++|. .++.|++++++.++.. +|+..+.++||+|++||++|+.+.+||+||++|+|+|
T Consensus 1 ~~~Nkv~LvG~l~~DPE~r~t~~g~~~v~~~~~a~~r~~~~~-~~~~~~~t~~~~vv~wgk~Ae~~~~yl~KG~~V~VeG 79 (167)
T COG0629 1 MMMNKVILVGRLTRDPELRYTPNGGAVVALFSAAVNRRFDNQ-SGERDEETDWIRVVIWGKLAENAAEYLKKGSLVYVEG 79 (167)
T ss_pred CCcceEEEEeecccCcceeecCCCCeeeEEEEEEeccccccC-CcccccccceEEEEEehHHHHHHHHHhcCCCEEEEEE
Confidence 0899999999999999999999554 5555555555554444 4677678999999999999999999999999999999
Q ss_pred EeeeeeeecCCCcEEEEEEE----EEeEEEEccCCCC
Q psy14498 81 RLQTRKWTNKEGVEKYITEV----IADNMQMLGSRKN 113 (171)
Q Consensus 81 ~l~~~~~~~kdG~~~~~~~i----~a~~i~~l~~~~~ 113 (171)
+|+++.|++++|.+||.+++ ++..+.+|..+..
T Consensus 80 ~l~~~~~~~~~G~~r~~~~~~~~~v~~~~~~l~~~~~ 116 (167)
T COG0629 80 RLQTRKWEDQEGQKRYQTEIVTEIVADSVQMLGSRKS 116 (167)
T ss_pred EEEeeeeecCCCcceeeEEEEEEEeehhhhhccCccc
Confidence 99999999999965555555 6667788887765
No 17
>PRK07772 single-stranded DNA-binding protein; Provisional
Probab=100.00 E-value=4.2e-34 Score=215.96 Aligned_cols=106 Identities=30% Similarity=0.551 Sum_probs=99.5
Q ss_pred CCCccEEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeee-eceEEEEEEEhHHHHHHHHHcCCCCEEEEE
Q psy14498 1 MASVNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRE-LTEWHRITFYRKLAQIVKQYLKKGSQIYIE 79 (171)
Q Consensus 1 M~~~N~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~-~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~ 79 (171)
|+++|.|+|+|||++||+||++++|+++|+|+||+++++.++++|+|++ +++||+|++|+++|+.++++|+||++|+|+
T Consensus 1 m~~~~~VtLiGrL~~DPElR~t~sG~~va~FrVAv~~r~~~~~~g~~~d~~t~fi~V~~Wg~~Ae~va~~L~KGd~V~V~ 80 (186)
T PRK07772 1 MAGDTTITVVGNLTADPELRFTPSGAAVANFTVASTPRTFDRQTNEWKDGEALFLRCSIWRQAAENVAESLTKGMRVIVT 80 (186)
T ss_pred CCccCEEEEEEEeCCCCeEEEcCCCCEEEEEEEEecCcceecCCCcEeccCceEEEEEEecHHHHHHHHhcCCCCEEEEE
Confidence 8999999999999999999999999999999999987666655688876 799999999999999999999999999999
Q ss_pred eEeeeeeeecCCCcEEEEEEEEEeEEE
Q psy14498 80 GRLQTRKWTNKEGVEKYITEVIADNMQ 106 (171)
Q Consensus 80 G~l~~~~~~~kdG~~~~~~~i~a~~i~ 106 (171)
|+|+.++|++++|++++.++|+|++|.
T Consensus 81 GrL~~r~wedkdG~~rt~~eV~a~~Vg 107 (186)
T PRK07772 81 GRLKQRSYETREGEKRTVVELEVDEIG 107 (186)
T ss_pred EEEEcCceECCCCCEEEEEEEEEEEcc
Confidence 999999999999999999999999764
No 18
>PRK06293 single-stranded DNA-binding protein; Provisional
Probab=100.00 E-value=3.7e-34 Score=211.45 Aligned_cols=105 Identities=25% Similarity=0.424 Sum_probs=97.7
Q ss_pred ccEEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEee
Q psy14498 4 VNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEGRLQ 83 (171)
Q Consensus 4 ~N~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l~ 83 (171)
||+|+|+|||++||++|++++|+++++|+||+++++.. .++++||+|++|+++|+.+.++|+||++|+|+|+|+
T Consensus 1 MN~V~LiGrLg~DPElR~t~sG~~v~~FsLAvn~~~~~------~~~T~wi~v~awg~~Ae~v~~yL~KG~~V~VeGrL~ 74 (161)
T PRK06293 1 MMFGYIVGRLGADPEERMTSKGKRVVVLRLGVKSRVGS------KDETVWCRCNIWGNRYDKMLPYLKKGSGVIVAGEMS 74 (161)
T ss_pred CeEEEEEEEecCCCeEEEcCCCCEEEEEEEEEeCCCCC------ccceEEEEEEEEhHHHHHHHHhCCCCCEEEEEEEEE
Confidence 89999999999999999999999999999999987532 136999999999999999999999999999999999
Q ss_pred eeeeecCCCcEEEEEEEEEeEEEEccCCCCC
Q psy14498 84 TRKWTNKEGVEKYITEVIADNMQMLGSRKNT 114 (171)
Q Consensus 84 ~~~~~~kdG~~~~~~~i~a~~i~~l~~~~~~ 114 (171)
++.|+|++|++++.++|+|++|+||..++..
T Consensus 75 ~~~y~dkdG~kr~~~eIva~~I~fl~~~~~~ 105 (161)
T PRK06293 75 PESYVDKDGSPQSSLVVSVDTIKFSPFGRNE 105 (161)
T ss_pred eCccCCCCCCEEEEEEEEEeEEEECcCCCcc
Confidence 9999999999999999999999999777543
No 19
>PRK08182 single-stranded DNA-binding protein; Provisional
Probab=100.00 E-value=3.4e-34 Score=210.32 Aligned_cols=111 Identities=23% Similarity=0.425 Sum_probs=104.2
Q ss_pred CccEEEEEEEeCCCCeEEEecCCcE----EEEEEEEEecccccCCCCeeee-eceEEEEEEEhHHHHHHHHHcCCCCEEE
Q psy14498 3 SVNKVIIIGNLGRDPETRYMSNGDA----VTNVSIATTENWRDKNSGEKRE-LTEWHRITFYRKLAQIVKQYLKKGSQIY 77 (171)
Q Consensus 3 ~~N~v~l~G~l~~dp~~~~~~~g~~----~~~~~la~~~~~~~~~~G~~~~-~~~~~~v~~~g~~A~~~~~~l~kG~~V~ 77 (171)
|||+|+|+|||++||++|++++|.. +++|+|+++++|++.+ |+|.+ .++||+|++||++|+.+.++|+||++|+
T Consensus 1 M~N~V~LiGrLg~DPElr~t~~G~~~~~~va~fslA~~r~~~~~~-Ge~~~~~t~w~~V~~wg~~Ae~v~~~l~KG~~V~ 79 (148)
T PRK08182 1 MSTHFVGEGNIGSAPEYREFPNGNDEPRRLLRLNVYFDNPVPTKD-GEYEDRGGFWAPVELWHRDAEHWARLYQKGMRVL 79 (148)
T ss_pred CccEEEEEEECCCCCeEEECCCCCeeeeeEEEEEEEecCceECCC-CCEEecCcEEEEEEEEhHHHHHHHHhcCCCCEEE
Confidence 6899999999999999999999986 9999999999998874 98865 5899999999999999999999999999
Q ss_pred EEeEeeeeeeecCCCcEEEEEEEEEeEEEEccCCCCC
Q psy14498 78 IEGRLQTRKWTNKEGVEKYITEVIADNMQMLGSRKNT 114 (171)
Q Consensus 78 V~G~l~~~~~~~kdG~~~~~~~i~a~~i~~l~~~~~~ 114 (171)
|+|+|++++|+|+||++++.++|+|++|.||.++...
T Consensus 80 V~GrL~~~~w~dkdG~~r~~~eI~a~~i~~l~~r~~~ 116 (148)
T PRK08182 80 VEGRMERDEWTDNEDNERVTFKVEARRVGILPYRIES 116 (148)
T ss_pred EEEEEEecccCCCCCCEEEEEEEEEeEEEEcCCcccc
Confidence 9999999999999999999999999999999877554
No 20
>PF00436 SSB: Single-strand binding protein family; InterPro: IPR000424 The Escherichia coli single-strand binding protein [] (gene ssb), also known as the helix-destabilising protein, is a protein of 177 amino acids. It binds tightly, as a homotetramer, to single-stranded DNA (ss-DNA) and plays an important role in DNA replication, recombination and repair. Closely related variants of SSB are encoded in the genome of a variety of large self-transmissible plasmids. SSB has also been characterised in bacteria such as Proteus mirabilis or Serratia marcescens. Eukaryotic mitochondrial proteins that bind ss-DNA and are probably involved in mitochondrial DNA replication are structurally and evolutionary related to prokaryotic SSB.; GO: 0003697 single-stranded DNA binding; PDB: 3UDG_B 1SE8_A 2CWA_A 3ULL_B 1S3O_A 2DUD_A 3AFP_A 3AFQ_A 3VDY_A 3EIV_C ....
Probab=99.97 E-value=1.3e-30 Score=180.57 Aligned_cols=104 Identities=46% Similarity=0.871 Sum_probs=95.6
Q ss_pred ccEEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEee
Q psy14498 4 VNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEGRLQ 83 (171)
Q Consensus 4 ~N~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l~ 83 (171)
||+|+|+|+|++||+++++++|+++++|+|++++++++. .++..+.++||+|++||++|+.++++|+||+.|.|+|+|+
T Consensus 1 mN~v~l~G~l~~~p~~~~~~~g~~~~~f~la~~~~~~~~-~~~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l~ 79 (104)
T PF00436_consen 1 MNKVTLIGRLGKDPELRYTKNGTPVARFSLAVNRRFKDD-GGEGDEKTDWINVVAWGKLAENVAEYLKKGDRVYVEGRLR 79 (104)
T ss_dssp EEEEEEEEEESSSEEEEEETTSEEEEEEEEEEEEEEEET-TSCEEEEEEEEEEEEEHHHHHHHHHH--TT-EEEEEEEEE
T ss_pred CcEEEEEEEECCCcEEEECCCCCEEEEEEEEEecEEeee-eccCccceEEEEEEeeeecccccceEEcCCCEEEEEEEEE
Confidence 899999999999999999999999999999999999983 3666678999999999999999999999999999999999
Q ss_pred eeeeecCCCcEEEEEEEEEeEEEEc
Q psy14498 84 TRKWTNKEGVEKYITEVIADNMQML 108 (171)
Q Consensus 84 ~~~~~~kdG~~~~~~~i~a~~i~~l 108 (171)
++.|++++|++++.++|+|++|+||
T Consensus 80 ~~~~~~~~G~~~~~~~i~a~~i~fl 104 (104)
T PF00436_consen 80 TRTYEDKDGQKRYRVEIIADNIEFL 104 (104)
T ss_dssp EEEEESTTSSEEEEEEEEEEEEEE-
T ss_pred eeEEECCCCCEEEEEEEEEEEEEeC
Confidence 9999999999999999999999997
No 21
>PRK05853 hypothetical protein; Validated
Probab=99.96 E-value=7.5e-29 Score=183.48 Aligned_cols=97 Identities=19% Similarity=0.356 Sum_probs=90.9
Q ss_pred EEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeee-eceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEeeeeee
Q psy14498 9 IIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRE-LTEWHRITFYRKLAQIVKQYLKKGSQIYIEGRLQTRKW 87 (171)
Q Consensus 9 l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~-~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l~~~~~ 87 (171)
|+|||++||++|++. |..+++|+||++++|++.+ |+|.+ .++||+|++||++|+.+.++|+||++|+|+|+|++++|
T Consensus 1 ivGrLg~DPelr~~~-g~~va~F~lAvn~r~~~~~-Ge~~d~~T~wi~V~~wg~lAe~v~~~L~KG~~V~V~GrL~~~~w 78 (161)
T PRK05853 1 VVGHIVNDPQRRKVG-DQEVIKFRVASNSRRRTAD-GGWEPGNSLFITVNCWGRLVTGVGAALGKGAPVIVVGHVYTSEY 78 (161)
T ss_pred CeEcccCCCEEEEEC-CceEEEEEEEECCCeECCC-CCEeccCccEEEEEEEhHHHHHHHHHcCCCCEEEEEEEEEccce
Confidence 689999999999985 6899999999999998875 99875 69999999999999999999999999999999999999
Q ss_pred ecCCCcEEEEEEEEEeEEEE
Q psy14498 88 TNKEGVEKYITEVIADNMQM 107 (171)
Q Consensus 88 ~~kdG~~~~~~~i~a~~i~~ 107 (171)
++++|++++.++|+|+.|.+
T Consensus 79 edkdG~~r~~~eV~a~~Vg~ 98 (161)
T PRK05853 79 EDRDGNRRSSLEMRATSVGP 98 (161)
T ss_pred ECCCCCEEEEEEEEEEEecc
Confidence 99999999999999998754
No 22
>PRK02801 primosomal replication protein N; Provisional
Probab=99.96 E-value=1.6e-28 Score=169.63 Aligned_cols=101 Identities=16% Similarity=0.326 Sum_probs=88.7
Q ss_pred CccEEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEe
Q psy14498 3 SVNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEGRL 82 (171)
Q Consensus 3 ~~N~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l 82 (171)
|||+|+|+|||++||++|++++|.++++|+||++ ++.... |-.++.++||+|++||++||.+.+||+||+.|.|+|+|
T Consensus 1 mmN~v~L~Grl~~dpelr~Tp~G~~v~~f~La~~-~~~~ea-~~~r~~~~~i~~va~G~~Ae~~~~~l~kGs~v~V~G~L 78 (101)
T PRK02801 1 MTNRLVLSGTVCRTPKRKVSPSGIPHCQFVLEHR-SVQEEA-GLHRQAWCRMPVIVSGNQFQAITQSITVGSKITVQGFI 78 (101)
T ss_pred CccEEEEEEEECcCcceEECCCCCeEEEEEEEEe-CeEecC-CCceeEEEEEEEEEEcHHHHHHHhhcCCCCEEEEEEEE
Confidence 6899999999999999999999999999999996 344332 32244679999999999999999999999999999999
Q ss_pred eeeeeecCCCcEEEEEEEEEeEEEEcc
Q psy14498 83 QTRKWTNKEGVEKYITEVIADNMQMLG 109 (171)
Q Consensus 83 ~~~~~~~kdG~~~~~~~i~a~~i~~l~ 109 (171)
++ |++++|++++. |++++|+||.
T Consensus 79 ~~--~~~~~g~~~~~--v~~~~i~~l~ 101 (101)
T PRK02801 79 SC--HQGRNGLSKLV--LHAEQIELID 101 (101)
T ss_pred EE--eECCCCCEEEE--EEEEEEEECC
Confidence 98 68899998876 8999999873
No 23
>PRK05813 single-stranded DNA-binding protein; Provisional
Probab=99.95 E-value=1.2e-27 Score=185.21 Aligned_cols=101 Identities=21% Similarity=0.358 Sum_probs=94.1
Q ss_pred CccEEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEe
Q psy14498 3 SVNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEGRL 82 (171)
Q Consensus 3 ~~N~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l 82 (171)
.||+|+|+|||++||++|++++|+++++|+||++++|+ .++||+|++||++|+.+. +|+||+.|.|+|+|
T Consensus 108 ~~N~V~LiGrL~~DPelR~t~~G~~va~f~lAvnr~~~---------~td~i~~v~wg~~Ae~~~-~l~KG~~V~V~GrL 177 (219)
T PRK05813 108 NPNEIFLDGYICKEPVYRTTPFGREIADLLLAVNRPYN---------KSDYIPCIAWGRNARFCK-TLEVGDNIRVWGRV 177 (219)
T ss_pred CccEEEEEEEccCCCeEEECCCCCEEEEEEEEEcCCCC---------CceEEEEEEEhHHhHHHh-hCCCCCEEEEEEEE
Confidence 59999999999999999999999999999999998875 378999999999999876 59999999999999
Q ss_pred eeeeeecCCC----cEEEEEEEEEeEEEEccCCCC
Q psy14498 83 QTRKWTNKEG----VEKYITEVIADNMQMLGSRKN 113 (171)
Q Consensus 83 ~~~~~~~kdG----~~~~~~~i~a~~i~~l~~~~~ 113 (171)
++++|++++| ++|+.++|.+++|++|+.+..
T Consensus 178 ~sr~y~~k~g~~~g~kr~~~eV~v~~i~~l~~~~~ 212 (219)
T PRK05813 178 QSREYQKKLSEGEVVTKVAYEVSISKMEKVEKEEA 212 (219)
T ss_pred EecceEcCCCCccceEEEEEEEEEEEEEEcCChhh
Confidence 9999999875 899999999999999988765
No 24
>cd04496 SSB_OBF SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs bind with high affinity to ssDNA. They bind to and protect ssDNA intermediates during DNA metabolic pathways. All bacterial and eukaryotic SSBs studied to date oligomerize to bring together four OB folds in their active state. The majority (e.g. Escherichia coli SSB) have a single OB fold per monomer, which oligomerize to form a homotetramer. However, Deinococcus and Thermus SSB proteins have two OB folds per monomer, which oligomerize to form a homodimer. Mycobacterium tuberculosis SSB varies in quaternary structure from E. coli SSB. It forms a dimer of dimers having a unique dimer interface, which lends the protein greater stability. Included in this group are OB folds similar to Escherichia coli PriB. E.coli PriB is homodimeric with each monomer having a single OB fold. It does not appear to form higher order oligomers. PriB is an essential protein for the replication restart
Probab=99.94 E-value=2.1e-25 Score=153.05 Aligned_cols=100 Identities=46% Similarity=0.883 Sum_probs=93.1
Q ss_pred EEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEeeeee
Q psy14498 7 VIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEGRLQTRK 86 (171)
Q Consensus 7 v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l~~~~ 86 (171)
|+|+|+|+++|+++++++|.++++|+|++++.+++.+ .....++||+|++||++|+.++++|+||+.|+|+|+|+.+.
T Consensus 1 v~l~G~l~~~p~~~~~~~g~~~~~~~v~~~~~~~~~~--~~~~~~~~~~v~~~g~~a~~~~~~~~kG~~V~v~G~l~~~~ 78 (100)
T cd04496 1 VILIGRLGKDPELRYTPSGTPVARFSLAVNRRRKDRD--EEEEETDWIRVVAFGKLAENAAKYLKKGDLVYVEGRLRTRS 78 (100)
T ss_pred CEEEEEecCCCEEEECCCCCEEEEEEEEEcCceeccc--ccccccEEEEEEEEhHHHHHHHHHhCCCCEEEEEEEEEece
Confidence 5799999999999999999999999999999988752 33347999999999999999999999999999999999999
Q ss_pred eecCCCcEEEEEEEEEeEEEEc
Q psy14498 87 WTNKEGVEKYITEVIADNMQML 108 (171)
Q Consensus 87 ~~~kdG~~~~~~~i~a~~i~~l 108 (171)
|++++|..++.++|++++|.++
T Consensus 79 ~~~~~g~~~~~~~i~~~~i~~~ 100 (100)
T cd04496 79 WEDKDGQKRYGTEVVADRIEFL 100 (100)
T ss_pred eECCCCCEEEEEEEEEEEEEEC
Confidence 9999999999999999999875
No 25
>PRK05813 single-stranded DNA-binding protein; Provisional
Probab=99.90 E-value=1.8e-22 Score=156.37 Aligned_cols=98 Identities=22% Similarity=0.343 Sum_probs=91.4
Q ss_pred ccEEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEee
Q psy14498 4 VNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEGRLQ 83 (171)
Q Consensus 4 ~N~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l~ 83 (171)
.|+|+|+|+|++||+++++..|..+++|+||++| +++ .++||+|++|+++|+.+. |+||+.|+|+|+|+
T Consensus 8 ~NkV~L~Grl~~d~e~~~~~~G~~~~~f~laV~R-~s~--------~~D~i~v~v~~rlae~~~--l~kG~~v~VeGqlr 76 (219)
T PRK05813 8 NNKVYLEGKVVSELEFSHEMYGEGFYNFKLEVPR-LSD--------SKDILPVTVSERLLAGMD--LKVGTLVIVEGQLR 76 (219)
T ss_pred cCEEEEEEEEcCCceEEEEeCCeEEEEEEEEeec-cCC--------CccEEEEEEEhhhhhhhc--ccCCCEEEEEEEEE
Confidence 6999999999999999999999999999999998 652 589999999999999988 99999999999999
Q ss_pred eeeeecC-CCcEEEEEEEEEeEEEEccCCCCC
Q psy14498 84 TRKWTNK-EGVEKYITEVIADNMQMLGSRKNT 114 (171)
Q Consensus 84 ~~~~~~k-dG~~~~~~~i~a~~i~~l~~~~~~ 114 (171)
+|+++ +|++|+.++|+|++|++|+.+...
T Consensus 77 --sy~~~~~G~~R~vl~V~a~~i~~l~~~~~~ 106 (219)
T PRK05813 77 --SYNKFIDGKNRLILTVFARNIEYCDERSDI 106 (219)
T ss_pred --EeccCCCCcEEEEEEEEEEEEEEccCCCcc
Confidence 88877 799999999999999999998543
No 26
>KOG1653|consensus
Probab=99.86 E-value=8.3e-22 Score=142.96 Aligned_cols=108 Identities=35% Similarity=0.647 Sum_probs=96.5
Q ss_pred CccEEEEEEEeCCCCeEEEecCCcEEEEEEEEEeccccc--CCCCeeeeeceEEEEEEEh-HHHHHHHHHcCCCCEEEEE
Q psy14498 3 SVNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRD--KNSGEKRELTEWHRITFYR-KLAQIVKQYLKKGSQIYIE 79 (171)
Q Consensus 3 ~~N~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~--~~~G~~~~~~~~~~v~~~g-~~A~~~~~~l~kG~~V~V~ 79 (171)
++|+|+|.|+|+.||.+|...||++|+-|+|+++..|+. ...|.+...++||+|.+|+ .+|+.+.++|+||++|+|+
T Consensus 54 ~vnkv~lvG~VGqdPl~k~~rngrpVtiFsv~T~~~~k~r~~q~g~~~~~tqWHRVsVf~~~L~d~~~k~lkKGsriyve 133 (175)
T KOG1653|consen 54 GVNKVILVGRVGQDPLQKILRNGRPVTIFSVGTGGMFKQRLYQAGDQPQPTQWHRVSVFNEVLADYALKYLKKGSRIYVE 133 (175)
T ss_pred ccceEEEEcccccchHHHhhcCCCeEEEEEeecCccccccccccCCcCCcceeEEEEeeCchHHHHHHHHhcCCCEEEEe
Confidence 689999999999999999999999999999999999983 2248888899999999999 6999999999999999999
Q ss_pred eEeeeeeee-cCCCcE-EEEEEEEEeEEEEccC
Q psy14498 80 GRLQTRKWT-NKEGVE-KYITEVIADNMQMLGS 110 (171)
Q Consensus 80 G~l~~~~~~-~kdG~~-~~~~~i~a~~i~~l~~ 110 (171)
|+|.++-+. |+.|.. +..+.|++++|.||..
T Consensus 134 G~iey~g~~~d~~g~~~r~~t~iIa~~v~Fl~~ 166 (175)
T KOG1653|consen 134 GKIEYRGENDDIQGNVKRIPTIIIARDVSFLID 166 (175)
T ss_pred eeEEeeeeeccccCceeecceEEEechhHHHHH
Confidence 999996555 568876 7888889999999864
No 27
>PRK00036 primosomal replication protein N; Reviewed
Probab=99.28 E-value=6.8e-11 Score=81.65 Aligned_cols=96 Identities=10% Similarity=0.128 Sum_probs=81.0
Q ss_pred ccEEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEee
Q psy14498 4 VNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEGRLQ 83 (171)
Q Consensus 4 ~N~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l~ 83 (171)
||.+.|+|.|++-|.+||+|.|-++|.|.|......... |-.+.-..-+.+++.|++|+.+.. +..|+.|.|+|.|.
T Consensus 1 mN~l~Ltg~v~~~~~lryTPAGIp~~~~~LeH~S~q~EA--G~~Rqv~~~i~ava~G~~a~~~~~-l~~Gs~v~v~GFLa 77 (107)
T PRK00036 1 MNTLELSARVLECGAMRHTPAGLPALELLLVHESEVVEA--GHPRRVELTISAVALGDLALLLAD-TPLGTEMQVQGFLA 77 (107)
T ss_pred CCEEEEEEEEeccCccccCCCCCceEEEEEEEeEEeEeC--CCcceEEEEEEEEEEhhHHHHhcc-cCCCCEEEEEEEEE
Confidence 599999999999999999999999999999986544433 665555777899999999999887 99999999999999
Q ss_pred eeeeecCCCcEEEEEEEEEeEEEEc
Q psy14498 84 TRKWTNKEGVEKYITEVIADNMQML 108 (171)
Q Consensus 84 ~~~~~~kdG~~~~~~~i~a~~i~~l 108 (171)
.. .+|. ..+-+.+++|+++
T Consensus 78 ~~----~~~~--~~LVLHi~~Ie~i 96 (107)
T PRK00036 78 PA----RKDS--VKVKLHLQQARRI 96 (107)
T ss_pred EC----CCCC--CcEEEEhHHeEEc
Confidence 72 3343 4667889999999
No 28
>COG2965 PriB Primosomal replication protein N [DNA replication, recombination, and repair]
Probab=99.21 E-value=8e-10 Score=74.23 Aligned_cols=103 Identities=19% Similarity=0.343 Sum_probs=83.1
Q ss_pred CCCccEEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEe
Q psy14498 1 MASVNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEG 80 (171)
Q Consensus 1 M~~~N~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G 80 (171)
|.+.|.+.|+|.|.+-|..|++++|.+.|.|-|..+ ++.... |..+....-+.+.+-|+.|+.+-..+..|+.|.|+|
T Consensus 1 ~~~~Nrl~L~g~vak~~~r~~sPsGIphc~f~Lehr-s~q~Ea-g~~RQv~~~mpv~vsG~qa~~lt~~i~~Gs~i~v~G 78 (103)
T COG2965 1 MNMTNRLSLSGTVAKVPVRRYSPSGIPHCQFVLEHR-SWQEEA-GFQRQVWCEMPVRVSGRQAEELTQSITVGSYILVVG 78 (103)
T ss_pred CCccceEEEEEEeeccceeeeCCCCCeeEEEEEeec-chhhhC-CcceeEEEEccEEeechhhhhhhhccccccEEEEEE
Confidence 778999999999999999999999999999999875 444442 654333444566777999999999999999999999
Q ss_pred EeeeeeeecCCCcEEEEEEEEEeEEEEcc
Q psy14498 81 RLQTRKWTNKEGVEKYITEVIADNMQMLG 109 (171)
Q Consensus 81 ~l~~~~~~~kdG~~~~~~~i~a~~i~~l~ 109 (171)
.|....- ++|- ..+.|.++.|++++
T Consensus 79 Fla~~~~--~sg~--~~lvlha~qi~~id 103 (103)
T COG2965 79 FLACHKR--RSGL--SKLVLHAEQIEFID 103 (103)
T ss_pred EEEeecc--cCCc--cEEEEEeeEEEecC
Confidence 9998765 4564 55677888888763
No 29
>PF01336 tRNA_anti-codon: OB-fold nucleic acid binding domain; InterPro: IPR004365 The OB-fold (oligonucleotide/oligosaccharide-binding fold) is found in all three kingdoms and its common architecture presents a binding face that has adapted to bind different ligands. The OB-fold is a five/six-stranded closed beta-barrel formed by 70-80 amino acid residues. The strands are connected by loops of varying length which form the functional appendages of the protein. The majority of OB-fold proteins use the same face for ligand binding or as an active site. Different OB-fold proteins use this 'fold-related binding face' to, variously, bind oligosaccharides, oligonucleotides, proteins, metal ions and catalytic substrates. This entry contains OB-fold domains that bind to nucleic acids []. It includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl-tRNA synthetases (See IPR004364 from INTERPRO). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule 6.1.1 from EC. This domain is found in RecG helicase involved in DNA repair. Replication factor A is a heterotrimeric complex, that contains a subunit in this family [, ]. This domain is also found at the C terminus of bacterial DNA polymerase III alpha chain.; GO: 0003676 nucleic acid binding; PDB: 1BBU_A 1KRS_A 1BBW_A 1KRT_A 1EQR_B 1IL2_B 1C0A_A 3KFU_A 1EOV_A 1ASY_A ....
Probab=98.10 E-value=5.8e-05 Score=48.18 Aligned_cols=75 Identities=17% Similarity=0.339 Sum_probs=56.0
Q ss_pred EEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEeeeee
Q psy14498 7 VIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEGRLQTRK 86 (171)
Q Consensus 7 v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l~~~~ 86 (171)
|+|.|+|.+-. .++..++.|+|.- .+--+.|++|.+......+.|+.|+.|.|+|.++..
T Consensus 1 V~v~G~V~~~~-----~~~~~~~~~~l~D--------------~tg~i~~~~~~~~~~~~~~~l~~g~~v~v~G~v~~~- 60 (75)
T PF01336_consen 1 VTVEGRVTSIR-----RSGGKIVFFTLED--------------GTGSIQVVFFNEEYERFREKLKEGDIVRVRGKVKRY- 60 (75)
T ss_dssp EEEEEEEEEEE-----EEETTEEEEEEEE--------------TTEEEEEEEETHHHHHHHHTS-TTSEEEEEEEEEEE-
T ss_pred CEEEEEEEEEE-----cCCCCEEEEEEEE--------------CCccEEEEEccHHhhHHhhcCCCCeEEEEEEEEEEE-
Confidence 67888888643 3445577777732 245679999998888888889999999999999866
Q ss_pred eecCCCcEEEEEEEEEeEEEEc
Q psy14498 87 WTNKEGVEKYITEVIADNMQML 108 (171)
Q Consensus 87 ~~~kdG~~~~~~~i~a~~i~~l 108 (171)
++| .++|.+.+|++|
T Consensus 61 ---~~~----~~~l~~~~i~~l 75 (75)
T PF01336_consen 61 ---NGG----ELELIVPKIEIL 75 (75)
T ss_dssp ---TTS----SEEEEEEEEEEE
T ss_pred ---CCc----cEEEEECEEEEC
Confidence 233 578888888875
No 30
>cd04484 polC_OBF polC_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold nucleic acid binding domain of Bacillus subtilis type C replicative DNA polymerase III alpha subunit (polC). Replication in B. subtilis and Staphylococcus aureus requires two different polymerases, polC and DnaE. The holoenzyme is thought to include the two different polymerases. At the B. subtilis replication fork, polC appears to be involved in leading strand synthesis and DnaE in lagging strand synthesis.
Probab=97.50 E-value=0.0029 Score=41.80 Aligned_cols=66 Identities=18% Similarity=0.314 Sum_probs=51.0
Q ss_pred EEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhH-HHHHHHHHcC-CCCEEEEEeEeee
Q psy14498 7 VIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRK-LAQIVKQYLK-KGSQIYIEGRLQT 84 (171)
Q Consensus 7 v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~-~A~~~~~~l~-kG~~V~V~G~l~~ 84 (171)
|+|.|.|-. .+.|.+.+|+.+..|.|. . .++-+.|..|.+ .-+.+ ..|+ +|+.|.|.|+++.
T Consensus 2 v~i~G~Vf~-~e~re~k~g~~i~~~~it--D------------~t~Si~~K~F~~~~~~~~-~~ik~~G~~v~v~G~v~~ 65 (82)
T cd04484 2 VVVEGEVFD-LEIRELKSGRKILTFKVT--D------------YTSSITVKKFLRKDEKDK-EELKSKGDWVRVRGKVQY 65 (82)
T ss_pred EEEEEEEEE-EEEEEecCCCEEEEEEEE--c------------CCCCEEEEEeccCChhHH-hhcccCCCEEEEEEEEEE
Confidence 789999976 788999999888777764 1 245667778873 33333 5599 9999999999999
Q ss_pred eeee
Q psy14498 85 RKWT 88 (171)
Q Consensus 85 ~~~~ 88 (171)
..|.
T Consensus 66 D~f~ 69 (82)
T cd04484 66 DTFS 69 (82)
T ss_pred ccCC
Confidence 9985
No 31
>PF11325 DUF3127: Domain of unknown function (DUF3127); InterPro: IPR021474 This bacterial family of proteins has no known function.
Probab=97.42 E-value=0.0017 Score=43.11 Aligned_cols=81 Identities=14% Similarity=0.322 Sum_probs=56.4
Q ss_pred EEEEe-CCCCeEEEe-cCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEeeeee
Q psy14498 9 IIGNL-GRDPETRYM-SNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEGRLQTRK 86 (171)
Q Consensus 9 l~G~l-~~dp~~~~~-~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l~~~~ 86 (171)
|.|.| ..-|+.... ++| +.+-.+.+.. .++ .+..+.+.+|++.++.+.. ++.|+.|.|+-.|+.|.
T Consensus 2 i~Gkii~~l~~~~g~s~~G--w~Kre~Vlet------~~q---YP~~i~f~~~~dk~~~l~~-~~~Gd~V~Vsf~i~~RE 69 (84)
T PF11325_consen 2 ITGKIIKVLPEQQGVSKNG--WKKREFVLET------EEQ---YPQKICFEFWGDKIDLLDN-FQVGDEVKVSFNIEGRE 69 (84)
T ss_pred cccEEEEEecCcccCcCCC--cEEEEEEEeC------CCc---CCceEEEEEEcchhhhhcc-CCCCCEEEEEEEeeccE
Confidence 56773 444555433 467 4444444331 133 3778899999987766444 99999999999999999
Q ss_pred eecCCCcEEEEEEEEEeEEE
Q psy14498 87 WTNKEGVEKYITEVIADNMQ 106 (171)
Q Consensus 87 ~~~kdG~~~~~~~i~a~~i~ 106 (171)
|+ .++..+|.|-+|+
T Consensus 70 ~~-----gr~fn~i~aWrie 84 (84)
T PF11325_consen 70 WN-----GRWFNSIRAWRIE 84 (84)
T ss_pred ec-----ceEeeEeEEEEeC
Confidence 97 4688899887763
No 32
>cd04474 RPA1_DBD_A RPA1_DBD_A: A subfamily of OB folds corresponding to the second OB fold, the ssDNA-binding domain (DBD)-A, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change. Although ScRPA and the hRPA have similar ssDNA-binding properties, they differ funct
Probab=97.32 E-value=0.0019 Score=44.57 Aligned_cols=69 Identities=20% Similarity=0.239 Sum_probs=53.2
Q ss_pred CccEEEEEEEeCCCCeEEEecCC---cEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEE
Q psy14498 3 SVNKVIIIGNLGRDPETRYMSNG---DAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIE 79 (171)
Q Consensus 3 ~~N~v~l~G~l~~dp~~~~~~~g---~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~ 79 (171)
.++.++|.|||.+.=+++.+.+. ..+..|.|. |. .+.-+++++|++.++.+...|++|+.++|+
T Consensus 8 ~~~~~~I~~rV~~k~~~~~f~~~~~~g~~~~~~l~------De-------~~~~I~~t~~~~~~~~f~~~l~eG~vy~i~ 74 (104)
T cd04474 8 YQNKWTIKARVTNKSDIRTWSNARGEGKLFSFDLL------DE-------DGGEIRATFFNDAVDKFYDLLEVGKVYYIS 74 (104)
T ss_pred CCCcEEEEEEEeeccccccccCCCCCcEEEEEEEE------EC-------CCCEEEEEEehHHHHHhhcccccccEEEEe
Confidence 57889999999987777777653 456555542 11 245679999999999999999999999999
Q ss_pred e-Eeee
Q psy14498 80 G-RLQT 84 (171)
Q Consensus 80 G-~l~~ 84 (171)
+ +++.
T Consensus 75 ~~~V~~ 80 (104)
T cd04474 75 KGSVKV 80 (104)
T ss_pred ccEEee
Confidence 7 5543
No 33
>cd04489 ExoVII_LU_OBF ExoVII_LU_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of Escherichia coli exodeoxyribonuclease VII (ExoVII) large subunit. E. coli ExoVII is composed of two non-identical subunits. E. coli ExoVII is a single-strand-specific exonuclease which degrades ssDNA from both 3-prime and 5-prime ends. ExoVII plays a role in methyl-directed mismatch repair in vivo. ExoVII may also guard the genome from mutagenesis by removing excess ssDNA, since the build up of ssDNA would lead to SOS induction and PolIV-dependent mutagenesis.
Probab=97.24 E-value=0.0075 Score=38.79 Aligned_cols=74 Identities=16% Similarity=0.272 Sum_probs=53.2
Q ss_pred EEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEeeeee
Q psy14498 7 VIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEGRLQTRK 86 (171)
Q Consensus 7 v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l~~~~ 86 (171)
+.+.|.|.+ ++.+++| .+-|+|.-. +.-+.|++|.+..+.+...|++|+.|.|+|++..+.
T Consensus 2 ~~v~g~v~~---i~~tk~g--~~~~~L~D~--------------~~~i~~~~f~~~~~~~~~~l~~g~~v~v~g~v~~~~ 62 (78)
T cd04489 2 VWVEGEISN---LKRPSSG--HLYFTLKDE--------------DASIRCVMWRSNARRLGFPLEEGMEVLVRGKVSFYE 62 (78)
T ss_pred EEEEEEEec---CEECCCc--EEEEEEEeC--------------CeEEEEEEEcchhhhCCCCCCCCCEEEEEEEEEEEC
Confidence 567888884 3336666 777777432 234799999997778888899999999999999754
Q ss_pred eecCCCcEEEEEEEEEeEEE
Q psy14498 87 WTNKEGVEKYITEVIADNMQ 106 (171)
Q Consensus 87 ~~~kdG~~~~~~~i~a~~i~ 106 (171)
+. | .+.+.+++|.
T Consensus 63 ~~---~----~~~l~v~~i~ 75 (78)
T cd04489 63 PR---G----GYQLIVEEIE 75 (78)
T ss_pred CC---C----EEEEEEEEEE
Confidence 32 2 3566777664
No 34
>PHA01740 putative single-stranded DNA-binding protein
Probab=97.21 E-value=0.001 Score=47.53 Aligned_cols=9 Identities=56% Similarity=1.294 Sum_probs=7.5
Q ss_pred CCCCCCCCC
Q psy14498 163 LEADDDVPF 171 (171)
Q Consensus 163 ~~~dDdiPF 171 (171)
.+|||||||
T Consensus 150 ~dfdddipf 158 (158)
T PHA01740 150 MDFDDDIPF 158 (158)
T ss_pred cccccCCCC
Confidence 456999999
No 35
>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=97.16 E-value=0.0039 Score=40.28 Aligned_cols=73 Identities=15% Similarity=0.253 Sum_probs=51.4
Q ss_pred EEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEeeeee
Q psy14498 7 VIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEGRLQTRK 86 (171)
Q Consensus 7 v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l~~~~ 86 (171)
|.+.|.|.+.+. .+|- +-|+| +|. ..-++|++|...+..+...++.||.|.|.|++..
T Consensus 1 v~v~GeVs~~~~----~~GH--vyfsL------kD~--------~a~i~cv~f~~~~~~~~~~l~~Gd~V~v~G~v~~-- 58 (73)
T cd04487 1 VHIEGEVVQIKQ----TSGP--TIFTL------RDE--------TGTVWAAAFEEAGVRAYPEVEVGDIVRVTGEVEP-- 58 (73)
T ss_pred CEEEEEEecccc----CCCC--EEEEE------EcC--------CEEEEEEEEchhccCCcCCCCCCCEEEEEEEEec--
Confidence 457888887662 5664 44666 221 2347999998866556666999999999999874
Q ss_pred eecCCCcEEEEEEEEEeEEEEc
Q psy14498 87 WTNKEGVEKYITEVIADNMQML 108 (171)
Q Consensus 87 ~~~kdG~~~~~~~i~a~~i~~l 108 (171)
+. -.+.+.+++|++|
T Consensus 59 ---~~----G~~ql~v~~i~~~ 73 (73)
T cd04487 59 ---RD----GQLQIEVESLEVL 73 (73)
T ss_pred ---CC----eEEEEEEeeEEEC
Confidence 23 3577888888765
No 36
>PRK07211 replication factor A; Reviewed
Probab=97.08 E-value=0.0059 Score=52.90 Aligned_cols=67 Identities=22% Similarity=0.385 Sum_probs=53.1
Q ss_pred CccEEEEEEEeCCCCeEEEecC---C--cEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEE
Q psy14498 3 SVNKVIIIGNLGRDPETRYMSN---G--DAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIY 77 (171)
Q Consensus 3 ~~N~v~l~G~l~~dp~~~~~~~---g--~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~ 77 (171)
.|+.|+|.|||.+--++|+..+ + ..++++.|+= +||+ +++++|+..|+.+...|++|+.|+
T Consensus 62 g~~~vtI~aRV~~~~~~Rt~~~~~~~~eGkv~~v~l~D-------eTG~-------Ir~TlW~d~ad~~~~~Le~GdV~~ 127 (485)
T PRK07211 62 GMDEVKFLAKVLSIGDLRTFERDGEDEDGRVINVEVAD-------ETGS-------VRVAFWDEQAVAAEEELEVGQVLR 127 (485)
T ss_pred CCCceEEEEEEeEccCceEEEeCCCCCCcEEEEEEEEc-------CCCe-------EEEEEechHhHhhhcccCCCCEEE
Confidence 5899999999999888777753 2 2566666542 1454 599999999999899999999999
Q ss_pred EEeEee
Q psy14498 78 IEGRLQ 83 (171)
Q Consensus 78 V~G~l~ 83 (171)
|.|+++
T Consensus 128 I~~~~~ 133 (485)
T PRK07211 128 IKGRPK 133 (485)
T ss_pred EeceEe
Confidence 998764
No 37
>cd03524 RPA2_OBF_family RPA2_OBF_family: A family of oligonucleotide binding (OB) folds with similarity to the OB fold of the single strand (ss) DNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA contains six OB folds, which are involved in ssDNA binding and in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. This family also includes OB folds similar to those found in Escherichia coli SSB, the wedge domain of E. coli RecG (a branched-DNA-specific helicase), E. coli ssDNA specific exodeoxyribonuclease VII large subunit, Pyroco
Probab=96.95 E-value=0.023 Score=34.99 Aligned_cols=59 Identities=25% Similarity=0.412 Sum_probs=42.4
Q ss_pred EEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeec-eEEEEEEEhHHHHHHHHHcCCCCEEEEEeEeee
Q psy14498 9 IIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELT-EWHRITFYRKLAQIVKQYLKKGSQIYIEGRLQT 84 (171)
Q Consensus 9 l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~-~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l~~ 84 (171)
+.|.|.+--.. .+ |+.++.|+|. + .+ ..+.|.+|.+..+.+...+.+|+.|.|+|++..
T Consensus 2 v~g~v~~~~~~-~~--~~~~~~~~l~--D------------~~~~~i~~~~~~~~~~~~~~~~~~g~~v~v~g~v~~ 61 (75)
T cd03524 2 IVGIVVAVEEI-RT--EGKVLIFTLT--D------------GTGGTIRVTLFGELAEELENLLKEGQVVYIKGKVKK 61 (75)
T ss_pred eEEEEEeeccc-cc--CCeEEEEEEE--c------------CCCCEEEEEEEchHHHHHHhhccCCCEEEEEEEEEe
Confidence 45666642222 22 5567777774 1 24 588999999988888888999999999999964
No 38
>cd04492 YhaM_OBF_like YhaM_OBF_like: A subfamily of OB folds similar to that found in Bacillus subtilis YhaM and Staphylococcus aureus cmp-binding factor-1 (SaCBF1). Both these proteins are 3'-to-5'exoribonucleases. YhaM requires Mn2+ or Co2+ for activity and is inactive in the presence of Mg2+. YhaM also has a Mn2+ dependent 3'-to-5'single-stranded DNA exonuclease activity. SaCBF is also a double-stranded DNA binding protein, binding specifically to cmp, the replication enhancer found in S. aureus plasmid pT181. Proteins in this group combine an N-terminal OB fold with a C-terminal HD domain. The HD domain is found in metal-dependent phosphohydrolases.
Probab=96.93 E-value=0.016 Score=37.34 Aligned_cols=73 Identities=14% Similarity=0.262 Sum_probs=51.5
Q ss_pred CCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEeeeeeeecCCCc
Q psy14498 14 GRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEGRLQTRKWTNKEGV 93 (171)
Q Consensus 14 ~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l~~~~~~~kdG~ 93 (171)
......+.+++|+.++.++|.-. +--+.|++|++.- .....|.+|..|.|.|++.. + +|
T Consensus 6 v~~~~~~~tk~g~~~~~~~l~D~--------------tg~i~~~~f~~~~-~~~~~l~~g~~v~v~G~v~~--~---~~- 64 (83)
T cd04492 6 IKSKELRTAKNGKPYLALTLQDK--------------TGEIEAKLWDASE-EDEEKFKPGDIVHVKGRVEE--Y---RG- 64 (83)
T ss_pred EEEeeeecccCCCcEEEEEEEcC--------------CCeEEEEEcCCCh-hhHhhCCCCCEEEEEEEEEE--e---CC-
Confidence 34456777888888888887532 2346899998543 33677999999999999954 2 22
Q ss_pred EEEEEEEEEeEEEEccC
Q psy14498 94 EKYITEVIADNMQMLGS 110 (171)
Q Consensus 94 ~~~~~~i~a~~i~~l~~ 110 (171)
..++.+.+|..|..
T Consensus 65 ---~~~l~~~~i~~l~~ 78 (83)
T cd04492 65 ---RLQLKIQRIRLVTE 78 (83)
T ss_pred ---ceeEEEEEEEECCc
Confidence 35677888887763
No 39
>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=96.82 E-value=0.019 Score=36.71 Aligned_cols=76 Identities=18% Similarity=0.343 Sum_probs=52.9
Q ss_pred EEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEeeeeeee
Q psy14498 9 IIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEGRLQTRKWT 88 (171)
Q Consensus 9 l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l~~~~~~ 88 (171)
+.|.|.. ...+.+.+|+.++.++|.= .+.-+.|++|...-+.+.+.|.+|..|.|.|++.. +
T Consensus 2 i~g~v~~-~~~~~~k~g~~~~~~~l~D--------------~tg~~~~~~f~~~~~~~~~~l~~g~~v~v~G~v~~--~- 63 (84)
T cd04485 2 VAGLVTS-VRRRRTKKGKRMAFVTLED--------------LTGSIEVVVFPETYEKYRDLLKEDALLLVEGKVER--R- 63 (84)
T ss_pred EEEEEEE-eEEEEcCCCCEEEEEEEEe--------------CCCeEEEEECHHHHHHHHHHhcCCCEEEEEEEEEe--c-
Confidence 5666655 4557778888887777631 13346999998765566788999999999999864 2
Q ss_pred cCCCcEEEEEEEEEeEEEEc
Q psy14498 89 NKEGVEKYITEVIADNMQML 108 (171)
Q Consensus 89 ~kdG~~~~~~~i~a~~i~~l 108 (171)
.| ..++.+++|..+
T Consensus 64 --~~----~~~l~~~~i~~~ 77 (84)
T cd04485 64 --DG----GLRLIAERIEDL 77 (84)
T ss_pred --CC----ceEEEeeccccH
Confidence 12 346666766655
No 40
>PF11506 DUF3217: Protein of unknown function (DUF3217); InterPro: IPR024506 This family of proteins with unknown function appears to be restricted to Mycoplasma.; PDB: 2HQL_E.
Probab=96.64 E-value=0.096 Score=34.60 Aligned_cols=90 Identities=24% Similarity=0.306 Sum_probs=57.7
Q ss_pred CccEEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEe
Q psy14498 3 SVNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEGRL 82 (171)
Q Consensus 3 ~~N~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l 82 (171)
|+|.|.|.|.|-+ .+-+.+-+ -.-.+|.-.|.| |+. .-++|+-+-+-|.+|-.+..|..|=..+.|+|.|
T Consensus 1 MLN~V~LEG~IeS---~kWS~~KT-GF~VTI~QkR~F-----G~r-~FTDyyViYAN~QL~~ELEky~~k~k~isieG~L 70 (104)
T PF11506_consen 1 MLNTVFLEGEIES---YKWSKKKT-GFLVTIKQKRKF-----GER-TFTDYYVIYANGQLAFELEKYTQKHKTISIEGIL 70 (104)
T ss_dssp --EEEEEEEEEEE---EEE-TTSS-EEEEEEEEEEEE-----TTE-EEEEEEEEEEEHHHHHHHHHHHTT-SEEEEEEEE
T ss_pred CcceEEEeceeeh---hcccccCc-eEEEEEeehhhh-----ccc-cceeEEEEEECCeeehhHHHhhhhceEEEEeeeh
Confidence 6899999999875 33333322 112333333333 432 2488999999999999999999999999999999
Q ss_pred eeeeeecCCCcEEEEEEEEEeEE
Q psy14498 83 QTRKWTNKEGVEKYITEVIADNM 105 (171)
Q Consensus 83 ~~~~~~~kdG~~~~~~~i~a~~i 105 (171)
++..=. +.+ ...+.|.+..|
T Consensus 71 ~TY~ek-kS~--iWKT~I~~~KI 90 (104)
T PF11506_consen 71 RTYLEK-KSK--IWKTTIEAVKI 90 (104)
T ss_dssp EEEEET-TTT--EEEEEEEEEEE
T ss_pred hhHHHH-hcc--cceeeEEEEEe
Confidence 875432 344 35556665443
No 41
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain
Probab=96.19 E-value=0.15 Score=34.70 Aligned_cols=77 Identities=17% Similarity=0.336 Sum_probs=56.3
Q ss_pred ccEEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHH-HHcCCCCEEEEEeEe
Q psy14498 4 VNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVK-QYLKKGSQIYIEGRL 82 (171)
Q Consensus 4 ~N~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~-~~l~kG~~V~V~G~l 82 (171)
+..+-+.|.|.. ++...+| .+-|+|.= + ..-++|++|...+..+. ..++.|+.|.|.|++
T Consensus 21 ~~~vwV~GEIs~---~~~~~~g--h~YftLkD---------~-----~a~i~~~~~~~~~~~i~~~~l~~G~~V~v~g~~ 81 (99)
T PF13742_consen 21 LPNVWVEGEISN---LKRHSSG--HVYFTLKD---------E-----EASISCVIFRSRARRIRGFDLKDGDKVLVRGRV 81 (99)
T ss_pred cCCEEEEEEEee---cEECCCc--eEEEEEEc---------C-----CcEEEEEEEHHHHhhCCCCCCCCCCEEEEEEEE
Confidence 467889999985 5444455 56677743 1 24679999999888887 779999999999999
Q ss_pred eeeeeecCCCcEEEEEEEEEeEEE
Q psy14498 83 QTRKWTNKEGVEKYITEVIADNMQ 106 (171)
Q Consensus 83 ~~~~~~~kdG~~~~~~~i~a~~i~ 106 (171)
.... +.| .+.+.+++|+
T Consensus 82 ~~y~---~~G----~~sl~v~~i~ 98 (99)
T PF13742_consen 82 SFYE---PRG----SLSLIVEDID 98 (99)
T ss_pred EEEC---CCc----EEEEEEEEeE
Confidence 8554 555 3556666654
No 42
>COG3390 Uncharacterized protein conserved in archaea [Function unknown]
Probab=96.18 E-value=0.034 Score=42.09 Aligned_cols=87 Identities=14% Similarity=0.266 Sum_probs=59.6
Q ss_pred CccEEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEe
Q psy14498 3 SVNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEGRL 82 (171)
Q Consensus 3 ~~N~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l 82 (171)
.+|.+.|+|.|++.+-+-. ...+.+++|+=. ||. +|+=.-.|-.-|..+.+.+.+++.|.|.|.+
T Consensus 44 k~nRifivGtltek~~i~e---d~~~~R~rVvDp-------TGs-----F~Vyag~yqPEa~a~l~~ve~~~~VaViGKi 108 (196)
T COG3390 44 KVNRIFIVGTLTEKEGIGE---DREYWRIRVVDP-------TGS-----FYVYAGQYQPEAKAFLEDVEVPDLVAVIGKI 108 (196)
T ss_pred heeEEEEEEEEEeccCcCC---cccEEEEEEecC-------Cce-----EEEEcCCCChHHHHHHHhccCCceEEEeccc
Confidence 4799999999998765521 145778887632 463 4552333445788888899999999999998
Q ss_pred eeeeeecCCCcEEEEEEEEEeEEEEc
Q psy14498 83 QTRKWTNKEGVEKYITEVIADNMQML 108 (171)
Q Consensus 83 ~~~~~~~kdG~~~~~~~i~a~~i~~l 108 (171)
+ .|++.+|. +.+.|..+.|...
T Consensus 109 ~--~y~~d~g~--~~~siRpE~vs~v 130 (196)
T COG3390 109 R--TYRTDEGV--VLFSIRPELVSKV 130 (196)
T ss_pred c--eeecCCCc--eEEEechhhhhhc
Confidence 7 67766776 4445555555443
No 43
>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=96.16 E-value=0.15 Score=33.36 Aligned_cols=57 Identities=19% Similarity=0.236 Sum_probs=41.4
Q ss_pred EEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHH--HHHHHcCCCCEEEEEeEe
Q psy14498 7 VIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQ--IVKQYLKKGSQIYIEGRL 82 (171)
Q Consensus 7 v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~--~~~~~l~kG~~V~V~G~l 82 (171)
+.+.|-|.. ++.+++|+. .++| .+ .+--+.|++|.+.-+ .+...|..|..|+|.|++
T Consensus 2 v~i~GiI~~---v~~TK~g~~--~~~l--eD------------~~G~~Ev~~F~~~~~~~~~~~~l~~d~~v~v~g~v 60 (79)
T cd04490 2 VSIIGMVND---VRSTKNGHR--IVEL--ED------------TTGRITVLLTKDKEELFEEAEDILPDEVIGVSGTV 60 (79)
T ss_pred EEEEEEEeE---EEEcCCCCE--EEEE--EC------------CCCEEEEEEeCchhhhhhhhhhccCCCEEEEEEEE
Confidence 456676664 226677776 3333 22 133569999999877 888899999999999999
No 44
>cd04482 RPA2_OBF_like RPA2_OBF_like: A subgroup of uncharacterized archaeal OB folds with similarity to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle depende
Probab=95.94 E-value=0.021 Score=38.40 Aligned_cols=73 Identities=15% Similarity=0.255 Sum_probs=50.4
Q ss_pred EEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHH--HHHHHHHcCCCCEEEEEeEeeee
Q psy14498 8 IIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKL--AQIVKQYLKKGSQIYIEGRLQTR 85 (171)
Q Consensus 8 ~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~--A~~~~~~l~kG~~V~V~G~l~~~ 85 (171)
.|.|.|..-+. ...+|- +-|+|. |. ..-++|++|... +..+...|+.||.|.|.|++...
T Consensus 2 ~v~GeVs~~~~--~~~sGH--~yFtlk------D~--------~~~i~cv~f~~~g~~~~~~~~l~~Gd~V~v~G~v~~y 63 (91)
T cd04482 2 RVTGKVVEEPR--TIEGGH--VFFKIS------DG--------TGEIDCAAYEPTKEFRDVVRLLIPGDEVTVYGSVRPG 63 (91)
T ss_pred EEEEEEeCCee--cCCCCC--EEEEEE------CC--------CcEEEEEEECcccccccccCCCCCCCEEEEEEEEecC
Confidence 46788886542 114553 456662 21 235789999876 56777779999999999998654
Q ss_pred eeecCCCcEEEEEEEEEeEEEEccC
Q psy14498 86 KWTNKEGVEKYITEVIADNMQMLGS 110 (171)
Q Consensus 86 ~~~~kdG~~~~~~~i~a~~i~~l~~ 110 (171)
. .+.+++|+.+.-
T Consensus 64 ~------------ql~ve~l~~~gl 76 (91)
T cd04482 64 T------------TLNLEKLRVIRL 76 (91)
T ss_pred C------------EEEEEEEEECCC
Confidence 3 578888887653
No 45
>PRK07373 DNA polymerase III subunit alpha; Reviewed
Probab=95.76 E-value=0.18 Score=43.60 Aligned_cols=79 Identities=14% Similarity=0.260 Sum_probs=55.8
Q ss_pred EEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEeeee
Q psy14498 6 KVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEGRLQTR 85 (171)
Q Consensus 6 ~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l~~~ 85 (171)
.|.+.|-|.. ...+.|++|..++-++|.-. +--+.|++|-+.-+.+...|.+|..|+|+|++..+
T Consensus 282 ~v~vaG~I~~-ik~~~TKkG~~maf~~leD~--------------tG~ie~vvFp~~y~~~~~~l~~~~~v~v~G~v~~~ 346 (449)
T PRK07373 282 KVSAVVMLNE-VKKIVTKKGDPMAFLQLEDL--------------SGQSEAVVFPKSYERISELLQVDARLIIWGKVDRR 346 (449)
T ss_pred EEEEEEEEEE-eEecccCCCCEEEEEEEEEC--------------CCCEEEEECHHHHHHHHHHhccCCEEEEEEEEEec
Confidence 4667777766 45556677777766666422 33469999999999999999999999999999542
Q ss_pred eeecCCCcEEEEEEEEEeEEEEc
Q psy14498 86 KWTNKEGVEKYITEVIADNMQML 108 (171)
Q Consensus 86 ~~~~kdG~~~~~~~i~a~~i~~l 108 (171)
+| .+.|++++|.-|
T Consensus 347 -----~~----~~~liv~~i~~l 360 (449)
T PRK07373 347 -----DD----QVQLIVEDAEPI 360 (449)
T ss_pred -----CC----eEEEEEeEeecH
Confidence 23 245666665544
No 46
>PRK15491 replication factor A; Provisional
Probab=95.73 E-value=0.066 Score=45.16 Aligned_cols=72 Identities=17% Similarity=0.301 Sum_probs=51.6
Q ss_pred ccEEEEEEEeCCCCeEEEec--CCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEe-
Q psy14498 4 VNKVIIIGNLGRDPETRYMS--NGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEG- 80 (171)
Q Consensus 4 ~N~v~l~G~l~~dp~~~~~~--~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G- 80 (171)
...|.|.|+|..--++|... +|.....+++.+-. +|| -+++++|+..|+.+ ..|..|+.|+|.+
T Consensus 176 ~~~V~I~g~V~~~~~~r~~~~~~G~~~~v~~~~l~D-----etG-------~Ir~t~W~~~a~~~-~~l~~Gd~V~i~~~ 242 (374)
T PRK15491 176 DSDINIVGKVLDISDVRTFQKKDGSQGRVRNITIGD-----ETG-------KIRVTLWDGKTDLA-DKLENGDSVEIING 242 (374)
T ss_pred CccEEEEEEEEEccCceEEEecCCCeEEEEEEEEEC-----CCC-------eEEEEEecchhccc-ccCCCCCEEEEEec
Confidence 34589999999876666553 67644445555432 134 37999999999887 5599999999965
Q ss_pred Eeeeeeee
Q psy14498 81 RLQTRKWT 88 (171)
Q Consensus 81 ~l~~~~~~ 88 (171)
..+.+.|.
T Consensus 243 ~~r~~~~~ 250 (374)
T PRK15491 243 YARTNNYS 250 (374)
T ss_pred eEEEeccC
Confidence 67776664
No 47
>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=95.64 E-value=0.14 Score=34.62 Aligned_cols=67 Identities=18% Similarity=0.295 Sum_probs=44.5
Q ss_pred EEEEEEeCCCCeEEEe--cC-CcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEee
Q psy14498 7 VIIIGNLGRDPETRYM--SN-GDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEGRLQ 83 (171)
Q Consensus 7 v~l~G~l~~dp~~~~~--~~-g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l~ 83 (171)
|-|+|.|.+--+++.. ++ |+...+..|.+.+. +| .-+.|++||+.|+.+.... |+.|.+.+ ++
T Consensus 2 vDvig~V~~v~~~~~i~~k~~g~~~~~r~v~i~D~-----t~------~~i~vtLWg~~a~~~~~~~--~~vv~~~~-~~ 67 (101)
T cd04475 2 VDVIGVVKSVGPVTTITTKSTGRELDKREITLVDE-----SG------HSVELTLWGEQAELFDGSE--NPVIAIKG-VK 67 (101)
T ss_pred EeEEEEEeEccCcEEEEEecCCCceeEEEEEEEeC-----CC------CEEEEEEEHHHhhhcccCC--CCEEEEEe-eE
Confidence 4477777765443332 33 77666666666532 22 2678999999998877544 99999998 55
Q ss_pred eeee
Q psy14498 84 TRKW 87 (171)
Q Consensus 84 ~~~~ 87 (171)
.+.|
T Consensus 68 i~~~ 71 (101)
T cd04475 68 VSEF 71 (101)
T ss_pred EEec
Confidence 5666
No 48
>PRK07211 replication factor A; Reviewed
Probab=95.49 E-value=0.1 Score=45.39 Aligned_cols=68 Identities=16% Similarity=0.331 Sum_probs=49.1
Q ss_pred CccEEEEEEEeCCCCeEEEec--CCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEe
Q psy14498 3 SVNKVIIIGNLGRDPETRYMS--NGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEG 80 (171)
Q Consensus 3 ~~N~v~l~G~l~~dp~~~~~~--~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G 80 (171)
.++.|.|+|+|..--++|.+. +|+.-..+++.+-. . +| -+++++|++.|+.+ ..|.+|+.|.|.+
T Consensus 170 ~~~~v~I~grV~~v~~iRtf~r~dGseGkv~sv~L~D----e-TG-------~IR~TlW~d~Ad~~-~~le~G~Vv~I~~ 236 (485)
T PRK07211 170 GLSDVTLVGVVLDTDSVRTFDRDDGSEGRVSNLTVGD----E-TG-------RVRVTLWDDRADLA-EELDAGESVEIVD 236 (485)
T ss_pred CCCceEEEEEEEEcCCCeEEECCCCCeeEEEEEEEEc----C-CC-------eEEEEEechhhhhh-ccCCCCCEEEEEe
Confidence 467899999999877777665 45444444444432 1 34 48999999999998 5699999999975
Q ss_pred -Eee
Q psy14498 81 -RLQ 83 (171)
Q Consensus 81 -~l~ 83 (171)
+++
T Consensus 237 a~Vr 240 (485)
T PRK07211 237 GYVR 240 (485)
T ss_pred eEEE
Confidence 554
No 49
>PF12101 DUF3577: Protein of unknown function (DUF3577); InterPro: IPR021960 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 143 to 307 amino acids in length.
Probab=95.47 E-value=0.64 Score=33.62 Aligned_cols=96 Identities=17% Similarity=0.133 Sum_probs=66.4
Q ss_pred EEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHH----HHcCCCCEEEEEeE-
Q psy14498 7 VIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVK----QYLKKGSQIYIEGR- 81 (171)
Q Consensus 7 v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~----~~l~kG~~V~V~G~- 81 (171)
+.=+|+|-+--++. ..+|.+++..+|+.=..-.|. . +..+|+|.+-|+.|..+. +.+..+.+|+|.-+
T Consensus 14 t~GiGYLnriR~V~-~~kg~pFlac~I~AL~G~~d~--~----ey~~fD~~V~G~eA~~Lv~r~~~av~~~~KVli~Frl 86 (137)
T PF12101_consen 14 TTGIGYLNRIREVT-PRKGDPFLACTIAALRGPADN--P----EYRYFDCRVVGEEAKELVRRCQKAVDEDKKVLIGFRL 86 (137)
T ss_pred EeeEEEeccceEcc-CCCCCeeEEEEeeeeecCCCC--c----cEEEEEEEEecHHHHHHHHHHHhhcccCCcEEEEEEe
Confidence 45689998855554 457888888888775532221 1 578999999998665544 45778999999854
Q ss_pred --eeeeeee----cCCCcEEEEEEEEEeEEEEcc
Q psy14498 82 --LQTRKWT----NKEGVEKYITEVIADNMQMLG 109 (171)
Q Consensus 82 --l~~~~~~----~kdG~~~~~~~i~a~~i~~l~ 109 (171)
|....|+ ++.|+...+++=..-.|.+|.
T Consensus 87 gDl~~d~f~~~~G~~~Ge~g~sLKgRLl~i~~iK 120 (137)
T PF12101_consen 87 GDLWADTFTYKKGERAGEPGASLKGRLLKIKWIK 120 (137)
T ss_pred cCCceeeEEeccCCcCCccceeeEEEEEEEEEEE
Confidence 5566666 467877776666666777764
No 50
>PRK15491 replication factor A; Provisional
Probab=95.08 E-value=0.12 Score=43.62 Aligned_cols=65 Identities=25% Similarity=0.401 Sum_probs=49.0
Q ss_pred CccEEEEEEEeCCCCeEEEec--CCc--EEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHH-HHcCCCCEEE
Q psy14498 3 SVNKVIIIGNLGRDPETRYMS--NGD--AVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVK-QYLKKGSQIY 77 (171)
Q Consensus 3 ~~N~v~l~G~l~~dp~~~~~~--~g~--~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~-~~l~kG~~V~ 77 (171)
.++.|.|.|||.+--.+|.+. +|. .+.++.|+ . +|| -+++++|.+.|+.+. ..|.+|+.|.
T Consensus 66 ~~~~v~i~arVl~~~~~R~f~r~dGs~g~v~~~~v~--D-----eTG-------~ir~tlW~~~a~~~~~~~le~G~v~~ 131 (374)
T PRK15491 66 SSSNVNFTAKVVSIFEPKEFNRNDGTTGRVGNIIVA--D-----ETG-------SIRLTLWDDLADLIKTGDIEVGKSLN 131 (374)
T ss_pred CCCceEEEEEEeeccCCeeeecCCCCceEEEEEEEE--c-----CCC-------eEEEEEECchhhhhccCCcCCCCEEE
Confidence 578999999999886777653 453 45444543 2 145 369999999998877 4699999999
Q ss_pred EEeE
Q psy14498 78 IEGR 81 (171)
Q Consensus 78 V~G~ 81 (171)
|.|.
T Consensus 132 I~~~ 135 (374)
T PRK15491 132 ISGY 135 (374)
T ss_pred Eeee
Confidence 9986
No 51
>PRK12366 replication factor A; Reviewed
Probab=95.04 E-value=0.21 Score=45.07 Aligned_cols=81 Identities=21% Similarity=0.384 Sum_probs=56.2
Q ss_pred cEEEEEEEeCCCCeEEEec--CCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEe-E
Q psy14498 5 NKVIIIGNLGRDPETRYMS--NGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEG-R 81 (171)
Q Consensus 5 N~v~l~G~l~~dp~~~~~~--~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G-~ 81 (171)
+.++|.|||...-.+|.+. +|. ---|++.+... +| -+++++|++.|+.+.. |.+|+.|.|++ +
T Consensus 292 ~~~~I~grV~~~~~~R~f~~~~g~-gkv~s~~l~D~-----tG-------~IR~t~w~~~~d~~~~-l~~G~vy~is~~~ 357 (637)
T PRK12366 292 EEVDVKGRIIAISDKREVERDDRT-AEVQDIELADG-----TG-------RVRVSFWGEKAKILEN-LKEGDAVKIENCK 357 (637)
T ss_pred CEEEEEEEEEecCCceEEEcCCCc-EEEEEEEEEcC-----CC-------eEEEEEeCchhhhhcc-cCCCCEEEEecCE
Confidence 3899999999998888875 333 33455554431 34 3799999999988776 78999999997 5
Q ss_pred eeeeeeecCCCcEEEEEEEEEe
Q psy14498 82 LQTRKWTNKEGVEKYITEVIAD 103 (171)
Q Consensus 82 l~~~~~~~kdG~~~~~~~i~a~ 103 (171)
++ .|.+..|. +.+++.+.
T Consensus 358 vk--~y~~~~~~--~~~El~~~ 375 (637)
T PRK12366 358 VR--TYYDNEGE--KRVDLNAG 375 (637)
T ss_pred Ee--eccccCCC--cCEEEEcC
Confidence 55 45433444 33455554
No 52
>PRK05673 dnaE DNA polymerase III subunit alpha; Validated
Probab=95.00 E-value=0.25 Score=47.34 Aligned_cols=80 Identities=15% Similarity=0.269 Sum_probs=59.3
Q ss_pred EEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEeeee
Q psy14498 6 KVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEGRLQTR 85 (171)
Q Consensus 6 ~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l~~~ 85 (171)
.|.+.|-|.. ...+.|++|+.++.++|.-. +| -+.+++|.+.-+.+...|.+|..|.|+|++..+
T Consensus 979 ~V~v~G~I~~-vk~~~TKkG~~mafltLeD~-------TG-------~iEvviFp~~ye~~~~~L~~g~iV~V~GkVe~~ 1043 (1135)
T PRK05673 979 VVTVAGLVVS-VRRRVTKRGNKMAIVTLEDL-------SG-------RIEVMLFSEALEKYRDLLEEDRIVVVKGQVSFD 1043 (1135)
T ss_pred eEEEEEEEEE-EEecccCCCCeEEEEEEEeC-------CC-------cEEEEECHHHHHHHHHHhccCCEEEEEEEEEec
Confidence 4667777665 66677788888887777532 24 469999999878888899999999999999642
Q ss_pred eeecCCCcEEEEEEEEEeEEEEcc
Q psy14498 86 KWTNKEGVEKYITEVIADNMQMLG 109 (171)
Q Consensus 86 ~~~~kdG~~~~~~~i~a~~i~~l~ 109 (171)
+| .+.+++++|..|.
T Consensus 1044 -----~~----~~qlii~~I~~L~ 1058 (1135)
T PRK05673 1044 -----DG----GLRLTAREVMDLE 1058 (1135)
T ss_pred -----CC----eEEEEEeecccHH
Confidence 22 3467777777664
No 53
>PRK13480 3'-5' exoribonuclease YhaM; Provisional
Probab=94.92 E-value=0.17 Score=41.75 Aligned_cols=73 Identities=11% Similarity=0.215 Sum_probs=53.5
Q ss_pred eCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEeeeeeeecCCC
Q psy14498 13 LGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEGRLQTRKWTNKEG 92 (171)
Q Consensus 13 l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l~~~~~~~kdG 92 (171)
|.++.+++.++||+++..++|.=. ||+ ++..+|+.. +...+.+.+|+.|.|+|++. .|. |
T Consensus 19 lv~~~~~~~~knG~~yl~l~l~D~-------tG~-------I~ak~W~~~-~~~~~~~~~g~vv~v~G~v~--~y~---g 78 (314)
T PRK13480 19 LIKSATKGVASNGKPFLTLILQDK-------SGD-------IEAKLWDVS-PEDEATYVPETIVHVKGDII--NYR---G 78 (314)
T ss_pred EEEEceeeecCCCCeEEEEEEEcC-------CcE-------EEEEeCCCC-hhhHhhcCCCCEEEEEEEEE--EEC---C
Confidence 566788999999999999888632 354 588889864 34466699999999999997 453 2
Q ss_pred cEEEEEEEEEeEEEEcc
Q psy14498 93 VEKYITEVIADNMQMLG 109 (171)
Q Consensus 93 ~~~~~~~i~a~~i~~l~ 109 (171)
...+.+.+|..+.
T Consensus 79 ----~~Ql~i~~i~~~~ 91 (314)
T PRK13480 79 ----RKQLKVNQIRLAT 91 (314)
T ss_pred ----cceEEEEEeEECC
Confidence 2345666776654
No 54
>TIGR00237 xseA exodeoxyribonuclease VII, large subunit. This family consist of exodeoxyribonuclease VII, large subunit XseA which catalyses exonucleolytic cleavage in either the 5'-3' or 3'-5' direction to yield 5'-phosphomononucleotides. Exonuclease VII consists of one large subunit and four small subunits.
Probab=94.79 E-value=0.21 Score=42.90 Aligned_cols=79 Identities=19% Similarity=0.272 Sum_probs=57.7
Q ss_pred ccEEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEee
Q psy14498 4 VNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEGRLQ 83 (171)
Q Consensus 4 ~N~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l~ 83 (171)
+..|-|.|.|.. ++...+| .+.|+| ||. ..-++|++|...+..+.-.++.|+.|.|.|++.
T Consensus 17 ~~~v~V~GEisn---~~~~~sG--H~YFtL------kD~--------~a~i~~vmf~~~~~~l~f~~~~G~~V~v~g~v~ 77 (432)
T TIGR00237 17 FLQVWIQGEISN---FTQPVSG--HWYFTL------KDE--------NAQVRCVMFRGNNNRLKFRPQNGQQVLVRGGIS 77 (432)
T ss_pred CCcEEEEEEecC---CeeCCCc--eEEEEE------EcC--------CcEEEEEEEcChhhCCCCCCCCCCEEEEEEEEE
Confidence 557889999985 4444567 566777 222 345799999988877776699999999999998
Q ss_pred eeeeecCCCcEEEEEEEEEeEEEEc
Q psy14498 84 TRKWTNKEGVEKYITEVIADNMQML 108 (171)
Q Consensus 84 ~~~~~~kdG~~~~~~~i~a~~i~~l 108 (171)
. |+ +.|. +.+.+++|+..
T Consensus 78 ~--y~-~~G~----~ql~v~~i~~~ 95 (432)
T TIGR00237 78 V--YE-PRGD----YQIICFEMQPA 95 (432)
T ss_pred E--EC-CCCc----EEEEEEEeccC
Confidence 4 44 4553 56777777743
No 55
>PRK14699 replication factor A; Provisional
Probab=94.47 E-value=0.23 Score=43.33 Aligned_cols=70 Identities=20% Similarity=0.325 Sum_probs=50.6
Q ss_pred CccEEEEEEEeCCCCeEEEec--CCc--EEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHH-HcCCCCEEE
Q psy14498 3 SVNKVIIIGNLGRDPETRYMS--NGD--AVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQ-YLKKGSQIY 77 (171)
Q Consensus 3 ~~N~v~l~G~l~~dp~~~~~~--~g~--~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~-~l~kG~~V~ 77 (171)
.+..|.|.|+|.+--..|.+. +|. .++++.|+ . +|--+++++|.++|+.+.+ .|++||.|.
T Consensus 66 ~~~~v~i~~rVl~i~~~r~f~r~dG~~g~v~~~~ia--D------------eTG~ir~tlW~~~a~~~~~g~l~~GDvv~ 131 (484)
T PRK14699 66 ESGPVNFIARVVSVFDTKEFTRNDGTIGRVGNLIVG--D------------ETGKIKLTLWDNMADLIKAGKIKAGQTLQ 131 (484)
T ss_pred CCceEEEEEEEEEecCceEEecCCCCceEEEEEEEe--c------------CCCeEEEEEecCccchhhhcCCCCCCEEE
Confidence 467899999999986677663 454 34444443 1 2335699999999988887 499999999
Q ss_pred EEeEeeeeeee
Q psy14498 78 IEGRLQTRKWT 88 (171)
Q Consensus 78 V~G~l~~~~~~ 88 (171)
|.|. .+.|.
T Consensus 132 I~~~--~r~~~ 140 (484)
T PRK14699 132 ISGY--AKQGY 140 (484)
T ss_pred Ecce--eccCC
Confidence 9995 45663
No 56
>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=94.40 E-value=0.4 Score=31.12 Aligned_cols=61 Identities=21% Similarity=0.266 Sum_probs=38.1
Q ss_pred EEEEeCCCCeEEEec-CCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEE-eEeee
Q psy14498 9 IIGNLGRDPETRYMS-NGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIE-GRLQT 84 (171)
Q Consensus 9 l~G~l~~dp~~~~~~-~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~-G~l~~ 84 (171)
|+|+|..--+.+.+. +|.....+++.+.+. || -+++++|+..+ ...+..|+.|.|+ |.++.
T Consensus 2 v~~~V~~~~~~~~~~~~g~~~~~~~~~l~D~-----TG-------~i~~~~W~~~~---~~~~~~G~vv~i~~~~v~~ 64 (82)
T cd04491 2 VEGKVLSISEPREFTRDGSEGKVQSGLVGDE-----TG-------TIRFTLWDEKA---ADDLEPGDVVRIENAYVRE 64 (82)
T ss_pred EEEEEEEccCCeEeccCCCeeEEEEEEEECC-----CC-------EEEEEEECchh---cccCCCCCEEEEEeEEEEe
Confidence 567776554444442 444333333433321 34 47999999877 5669999999999 66643
No 57
>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed
Probab=93.82 E-value=0.44 Score=40.85 Aligned_cols=80 Identities=15% Similarity=0.302 Sum_probs=57.8
Q ss_pred ccEEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEee
Q psy14498 4 VNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEGRLQ 83 (171)
Q Consensus 4 ~N~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l~ 83 (171)
+..|-|.|.|.. ++...+| .+-|+|.= . ..-++|++|...+..+.-.++.|+.|.|.|++.
T Consensus 23 ~~~v~v~gEis~---~~~~~sG--H~Yf~Lkd------~--------~a~i~~~~~~~~~~~~~~~~~~G~~v~v~g~~~ 83 (438)
T PRK00286 23 LGQVWVRGEISN---FTRHSSG--HWYFTLKD------E--------IAQIRCVMFKGSARRLKFKPEEGMKVLVRGKVS 83 (438)
T ss_pred CCcEEEEEEeCC---CeeCCCC--eEEEEEEc------C--------CcEEEEEEEcChhhcCCCCCCCCCEEEEEEEEE
Confidence 456889999885 4444566 56677732 1 345799999987877776799999999999998
Q ss_pred eeeeecCCCcEEEEEEEEEeEEEEcc
Q psy14498 84 TRKWTNKEGVEKYITEVIADNMQMLG 109 (171)
Q Consensus 84 ~~~~~~kdG~~~~~~~i~a~~i~~l~ 109 (171)
. |+ +.| .+.+.+.+|...+
T Consensus 84 ~--y~-~~g----~~ql~v~~i~~~g 102 (438)
T PRK00286 84 L--YE-PRG----DYQLIVEEIEPAG 102 (438)
T ss_pred E--EC-CCC----CEEEEEEEeeeCC
Confidence 6 44 445 3567788887543
No 58
>PRK06826 dnaE DNA polymerase III DnaE; Reviewed
Probab=93.66 E-value=1 Score=43.45 Aligned_cols=81 Identities=19% Similarity=0.322 Sum_probs=56.3
Q ss_pred EEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEeeee
Q psy14498 6 KVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEGRLQTR 85 (171)
Q Consensus 6 ~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l~~~ 85 (171)
.|.+.|-|.. ...+.|++|..++-++|.- .+--+.|++|.+.-+.+...|..|..|+|+|+++.+
T Consensus 993 ~v~v~g~i~~-~~~~~tk~G~~maf~~leD--------------~~g~~e~~vfp~~~~~~~~~l~~~~~~~v~g~v~~~ 1057 (1151)
T PRK06826 993 KVIIGGIITE-VKRKTTRNNEMMAFLTLED--------------LYGTVEVIVFPKVYEKYRSLLNEDNIVLIKGRVSLR 1057 (1151)
T ss_pred EEEEEEEEEE-eEeeccCCCCeEEEEEEEE--------------CCCcEEEEECHHHHHHHHHHhccCCEEEEEEEEEec
Confidence 4566666665 4455666777776666642 233469999999888889999999999999999643
Q ss_pred eeecCCCcEEEEEEEEEeEEEEcc
Q psy14498 86 KWTNKEGVEKYITEVIADNMQMLG 109 (171)
Q Consensus 86 ~~~~kdG~~~~~~~i~a~~i~~l~ 109 (171)
. +| .+.+++++|.-|.
T Consensus 1058 ~----~~----~~~~~~~~~~~l~ 1073 (1151)
T PRK06826 1058 E----DE----EPKLICEEIEPLV 1073 (1151)
T ss_pred C----CC----ceEEEEeeeecHh
Confidence 2 22 2456667666554
No 59
>cd04488 RecG_wedge_OBF RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal (wedge) domain of Escherichia coli RecG. RecG is a branched-DNA-specific helicase, which catalyzes the interconversion of a DNA replication fork to a four-stranded (Holliday) junction in vivo and in vitro. This interconversion provides a route to repair stalled forks. The RecG monomer contains three domains. The N-terminal domain is named for its wedge structure, and may provide the specificity of RecG for binding branched-DNA structures. During the reversal of fork to Holliday junction, the wedge domain is fixed at the junction of the fork where the leading and lagging strand duplex arms meet, and is thought to promote the unwinding of the nascent leading and lagging strands. In order to form the Holliday junction, these nascent strands would be annealed, and the parental strands reannealed. The wedge domain may also be a processivity factor of RecG on these branched cha
Probab=93.60 E-value=0.42 Score=29.65 Aligned_cols=59 Identities=15% Similarity=0.262 Sum_probs=36.6
Q ss_pred EEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEeee
Q psy14498 9 IIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEGRLQT 84 (171)
Q Consensus 9 l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l~~ 84 (171)
+.|+|.+.... ... ++.++++.|.-. +.-+.|+.|+.. ..+.+.+++|+.|.|.|++..
T Consensus 2 i~~~V~~~~~~-~~~-~~~~~~~~~~D~--------------~g~i~~~~F~~~-~~~~~~~~~G~~~~v~Gkv~~ 60 (75)
T cd04488 2 VEGTVVSVEVV-PRR-GRRRLKVTLSDG--------------TGTLTLVFFNFQ-PYLKKQLPPGTRVRVSGKVKR 60 (75)
T ss_pred EEEEEEEEEec-cCC-CccEEEEEEEcC--------------CCEEEEEEECCC-HHHHhcCCCCCEEEEEEEEee
Confidence 56776553222 222 455666655221 224678888732 245667999999999999975
No 60
>PRK06920 dnaE DNA polymerase III DnaE; Reviewed
Probab=93.32 E-value=1.1 Score=43.09 Aligned_cols=80 Identities=10% Similarity=0.145 Sum_probs=57.3
Q ss_pred EEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEeeee
Q psy14498 6 KVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEGRLQTR 85 (171)
Q Consensus 6 ~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l~~~ 85 (171)
.|.+.|-|.. ...+.|++|..++-++|.- .+--+.|++|.+.-+.+...|..|..|+|+|++..+
T Consensus 945 ~v~v~g~i~~-~~~~~tk~g~~maf~~leD--------------~tg~~e~~vFp~~y~~~~~~l~~~~~~~v~G~v~~~ 1009 (1107)
T PRK06920 945 VQRAIVYITS-VKVIRTKKGQKMAFITFCD--------------QNDEMEAVVFPETYIHFSDKLQEGAIVLVDGTIELR 1009 (1107)
T ss_pred EEEEEEEEEE-eEeecCCCCCeEEEEEEee--------------CCCcEEEEECHHHHHHHHHHhccCCEEEEEEEEEec
Confidence 4677777765 4445666777777666642 233469999999888899999999999999999653
Q ss_pred eeecCCCcEEEEEEEEEeEEEEcc
Q psy14498 86 KWTNKEGVEKYITEVIADNMQMLG 109 (171)
Q Consensus 86 ~~~~kdG~~~~~~~i~a~~i~~l~ 109 (171)
+| ...+++++|..|.
T Consensus 1010 -----~~----~~~~~~~~i~~l~ 1024 (1107)
T PRK06920 1010 -----NH----KLQWIVNGLYPLE 1024 (1107)
T ss_pred -----CC----cEEEEEeecccHH
Confidence 22 2456777776664
No 61
>PRK12366 replication factor A; Reviewed
Probab=93.05 E-value=0.47 Score=42.84 Aligned_cols=64 Identities=28% Similarity=0.427 Sum_probs=47.6
Q ss_pred CccEEEEEEEeCCCCeEEEec--CCc--EEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEE
Q psy14498 3 SVNKVIIIGNLGRDPETRYMS--NGD--AVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYI 78 (171)
Q Consensus 3 ~~N~v~l~G~l~~dp~~~~~~--~g~--~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V 78 (171)
.++.+.|.|||.+--++|.+. +|. .++++.|+ . +|| -+++++|++.|+. ...|.+|+.|.|
T Consensus 72 ~~~~v~i~arV~~~~~~r~~~~~~G~eGkv~~~~v~--D-----etG-------~Ir~t~W~~~~~~-~~~le~G~v~~i 136 (637)
T PRK12366 72 GQINVEITGRIIEISNIKTFTRKDGSTGKLANITIA--D-----NTG-------TIRLTLWNDNAKL-LKGLKEGDVIKI 136 (637)
T ss_pred CCcceEEEEEEEEccCCeEEECCCCCccEEEEEEEE--c-----CCC-------EEEEEEEchhhhh-hccCCCCCEEEE
Confidence 578899999999877777653 452 45555554 2 135 3699999999886 467999999999
Q ss_pred EeE
Q psy14498 79 EGR 81 (171)
Q Consensus 79 ~G~ 81 (171)
.+.
T Consensus 137 ~~~ 139 (637)
T PRK12366 137 ENA 139 (637)
T ss_pred ecc
Confidence 984
No 62
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=92.98 E-value=0.96 Score=44.48 Aligned_cols=70 Identities=17% Similarity=0.273 Sum_probs=52.8
Q ss_pred ccEEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhH--HHHHHHHHcCCCCEEEEEeE
Q psy14498 4 VNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRK--LAQIVKQYLKKGSQIYIEGR 81 (171)
Q Consensus 4 ~N~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~--~A~~~~~~l~kG~~V~V~G~ 81 (171)
.+.|+|.|.|-. .+.|.+.+|+.+..|.|. + .++-+.|..|.+ .-......|++|+.|.|.|+
T Consensus 236 ~~~v~i~G~if~-~e~~~~k~~~~~~~~~~t--d------------~~~s~~~k~f~~~~~~~~~~~~~~~g~~v~~~g~ 300 (1437)
T PRK00448 236 ERRVVVEGYVFK-VEIKELKSGRHILTFKIT--D------------YTSSIIVKKFSRDKEDLKKFDEIKKGDWVKVRGS 300 (1437)
T ss_pred CCeEEEEEEEEE-EEEEeccCCCEEEEEEEE--c------------CCCCEEEEEEecCcchhHHHhcCCCCCEEEEEEE
Confidence 468999999976 788899999888777772 1 244566777753 12233455999999999999
Q ss_pred eeeeeee
Q psy14498 82 LQTRKWT 88 (171)
Q Consensus 82 l~~~~~~ 88 (171)
+....|.
T Consensus 301 ~~~d~~~ 307 (1437)
T PRK00448 301 VQNDTFT 307 (1437)
T ss_pred EeccCCC
Confidence 9999886
No 63
>PRK07374 dnaE DNA polymerase III subunit alpha; Validated
Probab=92.94 E-value=1.4 Score=42.56 Aligned_cols=64 Identities=13% Similarity=0.155 Sum_probs=48.6
Q ss_pred EEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEeee
Q psy14498 6 KVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEGRLQT 84 (171)
Q Consensus 6 ~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l~~ 84 (171)
.|.+.|-|.. ...+.|++|..++-++|.-. +--+.|++|-+.-+.+...|..|..|+|+|+++.
T Consensus 1002 ~v~v~g~i~~-~k~~~Tk~G~~maf~~leD~--------------tg~~e~vvFp~~y~~~~~~l~~~~~~~v~g~v~~ 1065 (1170)
T PRK07374 1002 KVSAIAMIPE-MKQVTTRKGDRMAILQLEDL--------------TGSCEAVVFPKSYERLSDHLMTDTRLLVWAKVDR 1065 (1170)
T ss_pred EEEEEEEEEE-eEecccCCCCEEEEEEEEEC--------------CCCEEEEECHHHHHHHHHHhccCCEEEEEEEEEe
Confidence 4677777765 44556677777776666422 3346999999988899999999999999999964
No 64
>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=92.85 E-value=1.4 Score=42.80 Aligned_cols=69 Identities=16% Similarity=0.266 Sum_probs=52.8
Q ss_pred ccEEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhH---HHHHHHHHcCCCCEEEEEe
Q psy14498 4 VNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRK---LAQIVKQYLKKGSQIYIEG 80 (171)
Q Consensus 4 ~N~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~---~A~~~~~~l~kG~~V~V~G 80 (171)
++.|+|.|.|-. .+.|.+.+|+.+..|.|. . .++-+.|..|.+ ..+ ....|++|+.|.|.|
T Consensus 7 ~~~~~~~g~i~~-~~~~~~~~~~~~~~~~~~--d------------~~~s~~~k~f~~~~~~~~-~~~~~~~g~~~~~~g 70 (1213)
T TIGR01405 7 ENRVKIEGYIFK-IEIKELKSGRTLLKIKVT--D------------YTDSLILKKFLKSEEDPE-KFDGIKIGKWVRARG 70 (1213)
T ss_pred CCeEEEEEEEEE-EEeEeccCCCEEEEEEEE--c------------CCCCEEEEEecccccchH-HHhhcCCCcEEEEEE
Confidence 578999999976 788899999887777764 1 244567777763 223 335599999999999
Q ss_pred Eeeeeeee
Q psy14498 81 RLQTRKWT 88 (171)
Q Consensus 81 ~l~~~~~~ 88 (171)
++....|.
T Consensus 71 ~~~~d~~~ 78 (1213)
T TIGR01405 71 KIELDNFS 78 (1213)
T ss_pred EEeccCCC
Confidence 99999886
No 65
>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=92.78 E-value=2 Score=29.35 Aligned_cols=38 Identities=8% Similarity=0.163 Sum_probs=28.8
Q ss_pred eEEEEEEEhHHHHHHHHHcC---C-CCEEEEEeEeeeeeeec
Q psy14498 52 EWHRITFYRKLAQIVKQYLK---K-GSQIYIEGRLQTRKWTN 89 (171)
Q Consensus 52 ~~~~v~~~g~~A~~~~~~l~---k-G~~V~V~G~l~~~~~~~ 89 (171)
.-+.|++||+.|+.+...+. + +-.|.|-+-.+...|.+
T Consensus 35 ~~l~~tlwG~~A~~f~~~~~~~~~~~~VVav~~~~rV~~~~g 76 (106)
T cd04481 35 ERLKCTLWGEYAEEFDAKFQSAGNGEPVVAVLRFWKIKEYKG 76 (106)
T ss_pred CEEEEEEEHHHHHHHHHHHHHhCCCCcEEEEEEeEEEEEEcC
Confidence 47899999999999988763 4 44455666688888853
No 66
>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=92.53 E-value=2.7 Score=29.87 Aligned_cols=87 Identities=18% Similarity=0.242 Sum_probs=51.3
Q ss_pred cEEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHH--HHHHHcCCCCEEEEEeEe
Q psy14498 5 NKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQ--IVKQYLKKGSQIYIEGRL 82 (171)
Q Consensus 5 N~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~--~~~~~l~kG~~V~V~G~l 82 (171)
..|+|.|+|.+ +|.. |+ ++-+.| -+ | +..+.|++-.+... .....|..|+.|.|+|.+
T Consensus 15 ~~V~i~Gwv~~---~R~~--gk-~~Fi~L-rD--------~-----~g~~Q~v~~~~~~~~~~~~~~l~~gs~V~V~G~~ 74 (135)
T cd04317 15 QEVTLCGWVQR---RRDH--GG-LIFIDL-RD--------R-----YGIVQVVFDPEEAPEFELAEKLRNESVIQVTGKV 74 (135)
T ss_pred CEEEEEEeEeh---hccc--CC-EEEEEE-ec--------C-----CeeEEEEEeCCchhHHHHHhCCCCccEEEEEEEE
Confidence 36889999976 3332 33 443333 21 2 12366666543222 233459999999999998
Q ss_pred eeeeeecCCCc-EEEEEEEEEeEEEEccCC
Q psy14498 83 QTRKWTNKEGV-EKYITEVIADNMQMLGSR 111 (171)
Q Consensus 83 ~~~~~~~kdG~-~~~~~~i~a~~i~~l~~~ 111 (171)
....-..++.. ....+||.+++|.+|...
T Consensus 75 ~~~~~~~~~~~~~~~~~El~~~~i~vl~~~ 104 (135)
T cd04317 75 RARPEGTVNPKLPTGEIEVVASELEVLNKA 104 (135)
T ss_pred ECCCccccCCCCCCCcEEEEEeEEEEEECC
Confidence 86542101111 223489999999999743
No 67
>PRK08402 replication factor A; Reviewed
Probab=92.48 E-value=0.53 Score=39.49 Aligned_cols=67 Identities=18% Similarity=0.247 Sum_probs=44.7
Q ss_pred CccEEEEEEEeCCCCeEEEe--cCCc--EEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEE
Q psy14498 3 SVNKVIIIGNLGRDPETRYM--SNGD--AVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYI 78 (171)
Q Consensus 3 ~~N~v~l~G~l~~dp~~~~~--~~g~--~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V 78 (171)
.+..|.++|+|.+--..|.+ .+|. .+.++.|+ . +|-.+++++|++.|......|..|+.|.|
T Consensus 71 g~~~V~v~~rVl~~~~~r~f~rrdG~~~~V~~i~l~--D------------eTG~ir~TlW~~~a~~~~~~l~~Gdvi~I 136 (355)
T PRK08402 71 GMRGVNIVGRVLRKYPPREYTKKDGSTGRVASLIIY--D------------DTGRARVVLWDAKVAKYYNKINVGDVIKV 136 (355)
T ss_pred CCceeeEEEEEEEccCCceeeccCCCcceEEEEEEE--c------------CCCeEEEEEechhhhhhcccCCCCCEEEE
Confidence 45678889998875333333 2453 34444443 1 24466999999998866666999999999
Q ss_pred Ee-Eee
Q psy14498 79 EG-RLQ 83 (171)
Q Consensus 79 ~G-~l~ 83 (171)
.+ +.+
T Consensus 137 ~~a~V~ 142 (355)
T PRK08402 137 IDAQVR 142 (355)
T ss_pred ECCEEe
Confidence 85 443
No 68
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=92.32 E-value=1.1 Score=31.90 Aligned_cols=63 Identities=19% Similarity=0.329 Sum_probs=41.6
Q ss_pred CccEEEEEEEeCCC--CeEEEecCCc-EEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEE
Q psy14498 3 SVNKVIIIGNLGRD--PETRYMSNGD-AVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIE 79 (171)
Q Consensus 3 ~~N~v~l~G~l~~d--p~~~~~~~g~-~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~ 79 (171)
.++.|.++|.|.+- +....+++|. .+..+.|+ |. || -+++++|++.|. .|.+|+.|.|.
T Consensus 13 g~~~v~~~~~V~~i~~~~~~~~k~~~~~v~~~~l~------D~-TG-------~I~~tlW~~~a~----~l~~GdvV~I~ 74 (129)
T PRK06461 13 GMERVNVTVRVLEVGEPKVIQTKGGPRTISEAVVG------DE-TG-------RVKLTLWGEQAG----SLKEGEVVEIE 74 (129)
T ss_pred CCCceEEEEEEEEcCCceEEEeCCCceEEEEEEEE------CC-CC-------EEEEEEeCCccc----cCCCCCEEEEE
Confidence 35678889998863 3333444553 35555552 11 34 478999998654 48999999999
Q ss_pred -eEee
Q psy14498 80 -GRLQ 83 (171)
Q Consensus 80 -G~l~ 83 (171)
|..+
T Consensus 75 na~v~ 79 (129)
T PRK06461 75 NAWTT 79 (129)
T ss_pred CcEEe
Confidence 5655
No 69
>COG1570 XseA Exonuclease VII, large subunit [DNA replication, recombination, and repair]
Probab=92.00 E-value=0.72 Score=39.64 Aligned_cols=78 Identities=15% Similarity=0.306 Sum_probs=56.6
Q ss_pred ccEEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEee
Q psy14498 4 VNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEGRLQ 83 (171)
Q Consensus 4 ~N~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l~ 83 (171)
|-.|-|.|.|.. ++.-.+| ..-|+|. | ..--++|++|......+.-.++.|+.|.|.|++.
T Consensus 23 ~~~V~v~GEISn---~t~~~sg--H~YFtLK------D--------~~A~i~c~mf~~~~~~l~f~p~eG~~V~v~G~is 83 (440)
T COG1570 23 LGQVWVRGEISN---FTRPASG--HLYFTLK------D--------ERAQIRCVMFKGNNRRLKFRPEEGMQVLVRGKIS 83 (440)
T ss_pred CCeEEEEEEecC---CccCCCc--cEEEEEc------c--------CCceEEEEEEcCcccccCCCccCCCEEEEEEEEE
Confidence 456888888875 4444566 4556662 1 2457899999988888887799999999999998
Q ss_pred eeeeecCCCcEEEEEEEEEeEEEE
Q psy14498 84 TRKWTNKEGVEKYITEVIADNMQM 107 (171)
Q Consensus 84 ~~~~~~kdG~~~~~~~i~a~~i~~ 107 (171)
. |+ ..| .+.|++++|+.
T Consensus 84 ~--Y~-~rG----~YQi~~~~~~p 100 (440)
T COG1570 84 L--YE-PRG----DYQIVAESMEP 100 (440)
T ss_pred E--Ec-CCC----ceEEEEecCCc
Confidence 5 44 455 35677777764
No 70
>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=91.85 E-value=0.64 Score=41.78 Aligned_cols=68 Identities=29% Similarity=0.361 Sum_probs=51.4
Q ss_pred CccEEEEEEEeCCCCeEEEecC--C-cEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEE
Q psy14498 3 SVNKVIIIGNLGRDPETRYMSN--G-DAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIE 79 (171)
Q Consensus 3 ~~N~v~l~G~l~~dp~~~~~~~--g-~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~ 79 (171)
.+++++|.|||.+.-++|...+ | ..+..+.| - | ++| -+++++|++.|+.+...|+.|+.++|+
T Consensus 189 y~~~wtIkaRV~~Ks~ir~~~~~~gegkvfsv~L--~----D-egg-------~Irat~f~~~~dkf~~~l~eG~VY~Is 254 (608)
T TIGR00617 189 YQNKWTIKARVTNKSEIRTWSNARGEGKLFNVEL--L----D-ESG-------EIRATAFNEQADKFYDIIQEGKVYYIS 254 (608)
T ss_pred CCCceEEEEEEEeccccceecCCCCCceeeEEEE--e----c-CCC-------eEEEEECchHHHHHhhhcccCCEEEEC
Confidence 4678999999999988887653 2 24444443 2 2 223 469999999999999999999999997
Q ss_pred e-Eeee
Q psy14498 80 G-RLQT 84 (171)
Q Consensus 80 G-~l~~ 84 (171)
+ +++.
T Consensus 255 ~~~Vk~ 260 (608)
T TIGR00617 255 KGSLKP 260 (608)
T ss_pred ceEEEE
Confidence 5 6654
No 71
>PRK07279 dnaE DNA polymerase III DnaE; Reviewed
Probab=91.71 E-value=2.2 Score=40.65 Aligned_cols=80 Identities=19% Similarity=0.324 Sum_probs=56.4
Q ss_pred EEEEEEEeCCCCeEEEec-CCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEeee
Q psy14498 6 KVIIIGNLGRDPETRYMS-NGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEGRLQT 84 (171)
Q Consensus 6 ~v~l~G~l~~dp~~~~~~-~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l~~ 84 (171)
.+.+.|.|.. ...+.++ +|..++.++|.-. +| -+.|++|.+.-+.+...|..|..|+|+|+++.
T Consensus 886 ~~~~~~~i~~-~~~~~tk~~g~~maf~~leD~-------~g-------~ie~~vFp~~y~~~~~~l~~~~~~~v~G~v~~ 950 (1034)
T PRK07279 886 EATILVQIQS-IRVIRTKTKGQQMAFLSVTDT-------KK-------KLDVTLFPETYRQYKDELKEGKFYYLKGKIQE 950 (1034)
T ss_pred cceEEEEEEE-EEEEEEcCCCCeEEEEEEeeC-------CC-------cEEEEECHHHHHHHHHHhccCCEEEEEEEEEe
Confidence 3567788765 3344555 7877777766432 24 46999999988888899999999999999965
Q ss_pred eeeecCCCcEEEEEEEEEeEEEEcc
Q psy14498 85 RKWTNKEGVEKYITEVIADNMQMLG 109 (171)
Q Consensus 85 ~~~~~kdG~~~~~~~i~a~~i~~l~ 109 (171)
+ +| ...+++++|..+.
T Consensus 951 ~-----~~----~~~l~~~~i~~l~ 966 (1034)
T PRK07279 951 R-----DG----RLQMVLQQIQEAS 966 (1034)
T ss_pred c-----CC----eeEEEEeeeeccc
Confidence 3 22 2456677776553
No 72
>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=91.33 E-value=1.9 Score=29.17 Aligned_cols=85 Identities=13% Similarity=0.101 Sum_probs=50.2
Q ss_pred EEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHH----HH--HHHHHcCCCCEEEEE
Q psy14498 6 KVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKL----AQ--IVKQYLKKGSQIYIE 79 (171)
Q Consensus 6 ~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~----A~--~~~~~l~kG~~V~V~ 79 (171)
.|.|.|+|.+ +|.. |+.++-+.| -+ + +..+.|++-.+. .+ ...+.|..|+.|.|+
T Consensus 1 ~V~i~Gwv~~---~R~~--g~k~~Fi~L-rD--------~-----sg~iQ~v~~~~~~~~~~~~~~~~~~l~~es~V~V~ 61 (102)
T cd04320 1 EVLIRARVHT---SRAQ--GAKLAFLVL-RQ--------Q-----GYTIQGVLAASAEGVSKQMVKWAGSLSKESIVDVE 61 (102)
T ss_pred CEEEEEEEEE---eecC--CCceEEEEE-ec--------C-----CceEEEEEeCCcccCCHHHHHHHhcCCCccEEEEE
Confidence 3678899864 3332 323443333 11 1 224666665331 11 223459999999999
Q ss_pred eEeeeeeeecCCCcEEEEEEEEEeEEEEccC
Q psy14498 80 GRLQTRKWTNKEGVEKYITEVIADNMQMLGS 110 (171)
Q Consensus 80 G~l~~~~~~~kdG~~~~~~~i~a~~i~~l~~ 110 (171)
|.+..+.- ..++.....+||.+++|.+|..
T Consensus 62 G~v~~~~~-~~~~~~~~~~El~~~~i~il~~ 91 (102)
T cd04320 62 GTVKKPEE-PIKSCTQQDVELHIEKIYVVSE 91 (102)
T ss_pred EEEECCCC-cccCCCcCcEEEEEEEEEEEec
Confidence 99986532 1222233468999999999963
No 73
>PRK14699 replication factor A; Provisional
Probab=90.84 E-value=1.5 Score=38.28 Aligned_cols=65 Identities=14% Similarity=0.182 Sum_probs=47.1
Q ss_pred CccEEEEEEEeCCCCeEEEec--CCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEe
Q psy14498 3 SVNKVIIIGNLGRDPETRYMS--NGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEG 80 (171)
Q Consensus 3 ~~N~v~l~G~l~~dp~~~~~~--~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G 80 (171)
.++.++|.|+|...-.+|... +|+....+++.+... || -+++++|+..| .+...+..|+.|.|..
T Consensus 285 ~~~~v~I~grV~~~~~~r~~~~~~Gseg~v~~~~l~De-----TG-------~Ir~T~W~~~a-~~~~~i~~Gd~v~i~~ 351 (484)
T PRK14699 285 DMNNINISGRVLDISEVRTFEKKDGSPGRVGNLLLGDS-----TG-------KIRLTLWDEKT-NFLDEIDFDETVEVLN 351 (484)
T ss_pred CCceeEEEEEEEEcCCCeEEEcCCCCeeEEEEEEEECC-----CC-------eEEEEEeCccc-ccccccCCCceEEEEe
Confidence 478999999999776666664 565555566655432 34 47999999999 4445589999888775
No 74
>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=90.44 E-value=1.8 Score=31.48 Aligned_cols=77 Identities=17% Similarity=0.254 Sum_probs=52.4
Q ss_pred cEEEEEEEeCCCCeE--EEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCC-CCEEEEEeE
Q psy14498 5 NKVIIIGNLGRDPET--RYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKK-GSQIYIEGR 81 (171)
Q Consensus 5 N~v~l~G~l~~dp~~--~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~k-G~~V~V~G~ 81 (171)
..|.|+|-|...-.. +.+....-++.|+| ++.+..+.. + ....+.|.+|.+..+.+-. ++. ||.|.+. +
T Consensus 13 ~~vnvigVV~~~~~p~~~~t~g~D~~~tl~i-~D~S~~~~~-~----~~~~l~v~iF~~~~~~LP~-v~~~GDii~l~-r 84 (146)
T PF02765_consen 13 KFVNVIGVVVDFSPPNPKKTRGTDYMCTLTI-TDPSLNDSN-Q----KLSGLTVNIFRPHKESLPN-VKSVGDIIRLR-R 84 (146)
T ss_dssp EEEEEEEEEEEEEEECTEEESSSCEEEEEEE-EBTTCSCSS-C----CCCEEEEEEEESSHHHSCT-TCSTTHEEEEE-E
T ss_pred CEEEEEEEEEEccCCcceEcCCCcEEEEEEE-ECCCCCccc-c----ccCCEEEEEECCCHHHCCC-CCCCCCEEEEE-E
Confidence 367899988876445 55555567777777 444443221 1 1178999999887777766 555 9988887 7
Q ss_pred eeeeeeec
Q psy14498 82 LQTRKWTN 89 (171)
Q Consensus 82 l~~~~~~~ 89 (171)
++...|.+
T Consensus 85 ~kv~~~~~ 92 (146)
T PF02765_consen 85 VKVQSYNG 92 (146)
T ss_dssp EEEEEETT
T ss_pred EEEEEECC
Confidence 77778853
No 75
>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=89.80 E-value=1.8 Score=28.10 Aligned_cols=81 Identities=15% Similarity=0.221 Sum_probs=48.8
Q ss_pred EEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHH---HHHHHcCCCCEEEEEeEe
Q psy14498 6 KVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQ---IVKQYLKKGSQIYIEGRL 82 (171)
Q Consensus 6 ~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~---~~~~~l~kG~~V~V~G~l 82 (171)
+|+|.|+|.+ +|. .|+ ++-+.| -+ | +.-+.|++-.+... .....|..|+.|.|+|.+
T Consensus 1 ~V~i~Gwv~~---~R~--~g~-~~Fi~L-rd--------~-----~~~iQ~v~~~~~~~~~~~~~~~l~~~s~V~v~G~~ 60 (85)
T cd04100 1 EVTLAGWVHS---RRD--HGG-LIFIDL-RD--------G-----SGIVQVVVNKEELGEFFEEAEKLRTESVVGVTGTV 60 (85)
T ss_pred CEEEEEEEeh---hcc--CCC-EEEEEE-Ee--------C-----CeeEEEEEECCcChHHHHHHhCCCCCCEEEEEeEE
Confidence 3788999975 333 343 443333 22 1 22356655433211 233459999999999999
Q ss_pred eeeeeecCCCcEEEEEEEEEeEEEEcc
Q psy14498 83 QTRKWTNKEGVEKYITEVIADNMQMLG 109 (171)
Q Consensus 83 ~~~~~~~kdG~~~~~~~i~a~~i~~l~ 109 (171)
....-. . .....+||.+++|.+|.
T Consensus 61 ~~~~~~--~-~~~~~~El~~~~i~il~ 84 (85)
T cd04100 61 VKRPEG--N-LATGEIELQAEELEVLS 84 (85)
T ss_pred EECCCC--C-CCCCCEEEEEeEEEEEC
Confidence 876531 1 11245799999999884
No 76
>PRK05672 dnaE2 error-prone DNA polymerase; Validated
Probab=89.52 E-value=4.2 Score=38.99 Aligned_cols=51 Identities=20% Similarity=0.344 Sum_probs=41.1
Q ss_pred ceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEeeeeeeecCCCcEEEEEEEEEeEEEEccC
Q psy14498 51 TEWHRITFYRKLAQIVKQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQMLGS 110 (171)
Q Consensus 51 ~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l~~~~~~~kdG~~~~~~~i~a~~i~~l~~ 110 (171)
+--+.|++|.+.-+.+...|+.|..|+|+|+++.+ +| .+.+++++|.-|..
T Consensus 983 ~g~~e~~ifp~~~~~~~~~l~~~~~~~v~g~v~~~-----~~----~~~~~~~~i~~~~~ 1033 (1046)
T PRK05672 983 TGMVNVVVWPGLWERQRREALGARLLLVRGRVQNA-----EG----VRHLVADRLEDLSP 1033 (1046)
T ss_pred CCCEEEEECHHHHHHHHHHhccCCEEEEEEEEEec-----CC----eEEEEEeeeechHH
Confidence 44579999999999999999999999999999642 23 24688888887744
No 77
>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=89.49 E-value=1.6 Score=28.41 Aligned_cols=53 Identities=15% Similarity=0.220 Sum_probs=34.4
Q ss_pred EEEEEEhHHHH--HHHHHcCCCCEEEEEeEeeeeeeecCCCcEEEEEEEEEeEEEEcc
Q psy14498 54 HRITFYRKLAQ--IVKQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQMLG 109 (171)
Q Consensus 54 ~~v~~~g~~A~--~~~~~l~kG~~V~V~G~l~~~~~~~kdG~~~~~~~i~a~~i~~l~ 109 (171)
+.|++-.+... .....|..|+.|.|+|.+..+.-.. .....+||.+++|.+|.
T Consensus 29 iQ~v~~~~~~~~~~~~~~l~~es~V~V~G~v~~~~~~~---~~~~~~Ei~~~~i~vl~ 83 (84)
T cd04323 29 LQCVLSKKLVTEFYDAKSLTQESSVEVTGEVKEDPRAK---QAPGGYELQVDYLEIIG 83 (84)
T ss_pred EEEEEcCCcchhHHHHhcCCCcCEEEEEEEEEECCccc---CCCCCEEEEEEEEEEEc
Confidence 66665443221 2224599999999999998754221 11124799999999884
No 78
>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=87.08 E-value=3.5 Score=26.98 Aligned_cols=40 Identities=20% Similarity=0.344 Sum_probs=29.2
Q ss_pred HHcCCCCEEEEEeEeeeeeeecCCCcEEEEEEEEEeEEEEcc
Q psy14498 68 QYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQMLG 109 (171)
Q Consensus 68 ~~l~kG~~V~V~G~l~~~~~~~kdG~~~~~~~i~a~~i~~l~ 109 (171)
..|..|+.|.|+|.+..+.-.. .+ ....+||.+++|++|.
T Consensus 46 ~~l~~~s~V~V~G~v~~~~~~~-~~-~~~~~Ei~~~~i~il~ 85 (86)
T cd04321 46 KSITAESPVQVRGKLQLKEAKS-SE-KNDEWELVVDDIQTLN 85 (86)
T ss_pred hcCCCCcEEEEEEEEEeCCCcC-CC-CCCCEEEEEEEEEEec
Confidence 4599999999999998765321 11 1134799999999985
No 79
>PHA00458 single-stranded DNA-binding protein
Probab=85.83 E-value=2.9 Score=32.63 Aligned_cols=82 Identities=16% Similarity=0.298 Sum_probs=57.0
Q ss_pred CCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHH--cCCCCEEEEEeEeeeeeeecCCCcEEEEEEEE
Q psy14498 24 NGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQY--LKKGSQIYIEGRLQTRKWTNKEGVEKYITEVI 101 (171)
Q Consensus 24 ~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~--l~kG~~V~V~G~l~~~~~~~kdG~~~~~~~i~ 101 (171)
|+.--+.|...+.-+++++.||+. --+.+.+|...+..+.+- +.-|+.+.|++.|....|..+-| +.+.|.
T Consensus 100 NedG~v~F~FK~~aS~~dkktGe~----~~i~l~v~DskGK~l~~vp~I~gGS~~kVkf~v~pY~~~~~~g---asVkLq 172 (233)
T PHA00458 100 NGDGTVTFKFKCYASYKDKKTGEN----KPIVLRVVDSKGKRIEDVPAIGGGSKLKVKFSLFPYKWNAAVG---ASVKLQ 172 (233)
T ss_pred CCCceEEEEEEeeeecccccCCcc----cccceeEEcCCCcCcCcCccccCCceeEEEEEEeccccCCccc---ceeEEE
Confidence 333355677777788898888863 234566676655555543 77799999999999999865544 567777
Q ss_pred EeEEEEccCCC
Q psy14498 102 ADNMQMLGSRK 112 (171)
Q Consensus 102 a~~i~~l~~~~ 112 (171)
.+.|.+|.-+.
T Consensus 173 L~sv~vieL~e 183 (233)
T PHA00458 173 LESVMLVELAE 183 (233)
T ss_pred eeeEEEEEEEE
Confidence 77777775443
No 80
>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=85.76 E-value=7.8 Score=26.36 Aligned_cols=76 Identities=16% Similarity=0.206 Sum_probs=46.8
Q ss_pred EEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHH--HH---HHHHHcCCCCEEEEEeE
Q psy14498 7 VIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKL--AQ---IVKQYLKKGSQIYIEGR 81 (171)
Q Consensus 7 v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~--A~---~~~~~l~kG~~V~V~G~ 81 (171)
|+|.|+|-+ +|.. |+ ++ |-...+ | +.-+.|++-.+. .+ .+...|..|+.|.|+|.
T Consensus 2 v~v~GwV~~---~R~~--g~-~~-Fi~lrd--------~-----~~~lQ~v~~~~~~~~~~~~~~~~~l~~g~~V~v~G~ 61 (108)
T cd04322 2 VSVAGRIMS---KRGS--GK-LS-FADLQD--------E-----SGKIQVYVNKDDLGEEEFEDFKKLLDLGDIIGVTGT 61 (108)
T ss_pred EEEEEEEEE---EecC--CC-eE-EEEEEE--------C-----CeEEEEEEECCCCCHHHHHHHHhcCCCCCEEEEEEE
Confidence 678888875 4443 43 44 333322 1 234666664321 11 22233999999999999
Q ss_pred eeeeeeecCCCcEEEEEEEEEeEEEEccC
Q psy14498 82 LQTRKWTNKEGVEKYITEVIADNMQMLGS 110 (171)
Q Consensus 82 l~~~~~~~kdG~~~~~~~i~a~~i~~l~~ 110 (171)
+.... .|. +||.++++++|..
T Consensus 62 v~~~~----~g~----~El~~~~~~ils~ 82 (108)
T cd04322 62 PFKTK----TGE----LSIFVKEFTLLSK 82 (108)
T ss_pred EEecC----CCC----EEEEeCEeEEeec
Confidence 87643 232 6899999999963
No 81
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=85.75 E-value=8.5 Score=34.98 Aligned_cols=62 Identities=21% Similarity=0.333 Sum_probs=43.5
Q ss_pred EEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEeee
Q psy14498 6 KVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEGRLQT 84 (171)
Q Consensus 6 ~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l~~ 84 (171)
.|++.|.|.+..... ..++...++.+ .. | +..+.+++|+.-| .+.+.|++|..|.|.|.++.
T Consensus 62 ~vti~g~V~~~~~~~--~~~~~~l~v~~--~d-------~-----~~~l~l~fFn~~~-~l~~~~~~G~~v~v~Gk~~~ 123 (677)
T COG1200 62 IVTIEGTVLSHEKFP--FGKRKLLKVTL--SD-------G-----TGVLTLVFFNFPA-YLKKKLKVGERVIVYGKVKR 123 (677)
T ss_pred eEEEEEEEEeeeccC--CCCCceEEEEE--ec-------C-----cEEEEEEEECccH-HHHhhCCCCCEEEEEEEEee
Confidence 678888887744332 23344444444 32 1 4467888898877 88888999999999999876
No 82
>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=85.72 E-value=8.7 Score=25.92 Aligned_cols=53 Identities=13% Similarity=0.187 Sum_probs=35.4
Q ss_pred EEEEEEEhHHHHH---HHHHcCCCCEEEEEeEeeeeeeecCCCcEEEEEEEEEeEEEEccCC
Q psy14498 53 WHRITFYRKLAQI---VKQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQMLGSR 111 (171)
Q Consensus 53 ~~~v~~~g~~A~~---~~~~l~kG~~V~V~G~l~~~~~~~kdG~~~~~~~i~a~~i~~l~~~ 111 (171)
.+.|++-.+..+. ....|..|+.|.|+|.+..+.- .. ..+||.+++|++|...
T Consensus 28 ~iQ~v~~~~~~~~~~~~~~~l~~~s~v~V~G~v~~~~~--~~----~~~Ei~~~~i~vl~~a 83 (103)
T cd04319 28 IVQAVFSKDLNEEAYREAKKVGIESSVIVEGAVKADPR--AP----GGAEVHGEKLEIIQNV 83 (103)
T ss_pred eEEEEEeCCCCHHHHHHHhCCCCCCEEEEEEEEEECCC--CC----CCEEEEEEEEEEEecC
Confidence 3677665432111 1234899999999999987642 11 2489999999999633
No 83
>PF13567 DUF4131: Domain of unknown function (DUF4131)
Probab=85.24 E-value=6.2 Score=28.11 Aligned_cols=69 Identities=17% Similarity=0.299 Sum_probs=39.5
Q ss_pred cEEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEeee
Q psy14498 5 NKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEGRLQT 84 (171)
Q Consensus 5 N~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l~~ 84 (171)
..+++.|.|...|+.. +. ..+|.+.+.+-... +++ ...-.++.++-+..... .++.||.|.++|+|+.
T Consensus 76 ~~~~v~g~V~~~~~~~----~~-~~~~~~~~~~~~~~---~~~--~~~~~~i~~~~~~~~~~--~l~~Gd~i~~~g~l~~ 143 (176)
T PF13567_consen 76 KEVTVQGTVESVPQID----GR-GQRFTLRVERVLAG---GNW--IPVSGKILLYLPKDSQP--RLQPGDRIRVRGKLKP 143 (176)
T ss_pred ceEEEEEEEccccccc----Cc-eEEEEEEEEEeecc---ccc--cccceeeEEEecccccc--ccCCCCEEEEEEEEec
Confidence 3577999999888663 22 22677765532111 222 22233333332211111 6999999999999986
Q ss_pred e
Q psy14498 85 R 85 (171)
Q Consensus 85 ~ 85 (171)
=
T Consensus 144 ~ 144 (176)
T PF13567_consen 144 P 144 (176)
T ss_pred C
Confidence 4
No 84
>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=84.14 E-value=9.6 Score=25.05 Aligned_cols=75 Identities=12% Similarity=0.224 Sum_probs=46.1
Q ss_pred EEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHH---HHHHHcCCCCEEEEEeEee
Q psy14498 7 VIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQ---IVKQYLKKGSQIYIEGRLQ 83 (171)
Q Consensus 7 v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~---~~~~~l~kG~~V~V~G~l~ 83 (171)
|.++|.|.+ +... + .+..|+|. + + ||. +.+.+|....+ ...+.+..|+.|.|.|+++
T Consensus 2 v~~vG~V~~---~~~~--~-~~~~~tL~--D----~-TG~-------I~~~~W~~~~~~~~~~~~~~~~g~~v~v~G~v~ 61 (95)
T cd04478 2 VTLVGVVRN---VEEQ--S-TNITYTID--D----G-TGT-------IEVRQWLDDDNDDSSEVEPIEEGTYVRVFGNLK 61 (95)
T ss_pred EEEEEEEEe---eeEc--c-cEEEEEEE--C----C-CCc-------EEEEEeCCCCCcccccccccccCCEEEEEEEEc
Confidence 678888876 2222 1 35555553 2 1 343 58888875432 3466699999999999997
Q ss_pred eeeeecCCCcEEEEEEEEEeEEEEccC
Q psy14498 84 TRKWTNKEGVEKYITEVIADNMQMLGS 110 (171)
Q Consensus 84 ~~~~~~kdG~~~~~~~i~a~~i~~l~~ 110 (171)
... | ...|.+..|..+..
T Consensus 62 ~~~-----g----~~ql~i~~i~~v~d 79 (95)
T cd04478 62 SFQ-----G----KKSIMAFSIRPVTD 79 (95)
T ss_pred ccC-----C----eeEEEEEEEEEeCC
Confidence 442 2 23455666666653
No 85
>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=83.93 E-value=6.6 Score=35.41 Aligned_cols=68 Identities=21% Similarity=0.273 Sum_probs=44.0
Q ss_pred EEEEEEEeCCCCeEEE---ecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEe
Q psy14498 6 KVIIIGNLGRDPETRY---MSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEGRL 82 (171)
Q Consensus 6 ~v~l~G~l~~dp~~~~---~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l 82 (171)
.|-|+|-|..-=.+.. ..+|+...+..|.+.+. +| .-++|++||+.|+.+. ..+|+.|.|.| +
T Consensus 312 ~VDVIGvV~~v~~~~~i~~k~~g~~~~kR~i~L~D~-----sg------~sI~vTLWG~~A~~~~--~~~~~Vva~kg-~ 377 (608)
T TIGR00617 312 LVDVIGIVQSVSPTQTITSRKNNKEFPKRDITLVDD-----SG------KSVRVTLWGDDATKFD--VSVQPVIAIKG-V 377 (608)
T ss_pred CccEEEEEeEecCceEEEEcCCCCeeeeEEEEEEeC-----CC------CEEEEEEEhhhhhhcC--CCCCCEEEEEe-E
Confidence 4567777776433333 23566666656655431 12 2589999999998765 78899999988 3
Q ss_pred eeeee
Q psy14498 83 QTRKW 87 (171)
Q Consensus 83 ~~~~~ 87 (171)
+...|
T Consensus 378 ~V~~f 382 (608)
T TIGR00617 378 RVSDF 382 (608)
T ss_pred EEEec
Confidence 33456
No 86
>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=83.86 E-value=20 Score=30.81 Aligned_cols=80 Identities=18% Similarity=0.221 Sum_probs=49.0
Q ss_pred cEEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhH-----HHHHHHHHcCCCCEEEEE
Q psy14498 5 NKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRK-----LAQIVKQYLKKGSQIYIE 79 (171)
Q Consensus 5 N~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~-----~A~~~~~~l~kG~~V~V~ 79 (171)
.+|+|.|+|.+ +|. .|+ ++ |-...+. +| .+.|++-.+ .-+.+ ..|..||.|.|+
T Consensus 13 ~~v~i~G~v~~---~R~--~g~-~~-Fi~lrd~------~g-------~iQ~v~~~~~~~~~~~~~~-~~l~~~s~v~v~ 71 (428)
T TIGR00458 13 QEVTFMGWVHE---IRD--LGG-LI-FVLLRDR------EG-------LIQITAPAKKVSKNLFKWA-KKLNLESVVAVR 71 (428)
T ss_pred CEEEEEEEEEE---Eec--CCC-cE-EEEEEeC------Ce-------eEEEEEECCcCCHHHHHHH-hCCCCCcEEEEE
Confidence 46888899864 333 343 33 3333221 12 366666532 11222 459999999999
Q ss_pred eEeeeeeeecCCCcEEEEEEEEEeEEEEccCC
Q psy14498 80 GRLQTRKWTNKEGVEKYITEVIADNMQMLGSR 111 (171)
Q Consensus 80 G~l~~~~~~~kdG~~~~~~~i~a~~i~~l~~~ 111 (171)
|.+....- ....+||.+.+|++|...
T Consensus 72 G~v~~~~~------~~~~~el~~~~i~vl~~~ 97 (428)
T TIGR00458 72 GIVKIKEK------APGGFEIIPTKIEVINEA 97 (428)
T ss_pred EEEEecCC------CCCcEEEEEeEEEEEecC
Confidence 99985432 122489999999999754
No 87
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=83.70 E-value=4.5 Score=39.10 Aligned_cols=71 Identities=17% Similarity=0.208 Sum_probs=53.1
Q ss_pred CccEEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhH--HHHHHHHHcCCCCEEEEEe
Q psy14498 3 SVNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRK--LAQIVKQYLKKGSQIYIEG 80 (171)
Q Consensus 3 ~~N~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~--~A~~~~~~l~kG~~V~V~G 80 (171)
.++.|.+.|.|-. -+.+.+.+|+.+++|.|-= + ++-+.|..|-+ --+...+.+++|++|.++|
T Consensus 238 ~~~~v~v~G~IF~-~e~~~~ksGr~l~~i~vTD---------~-----t~Sl~~k~f~~~~ed~~~~~~ik~g~wvk~~g 302 (1444)
T COG2176 238 EETRVKVEGYIFK-IEIKELKSGRTLLNIKVTD---------Y-----TSSLILKKFLRDEEDEKKFDGIKKGMWVKARG 302 (1444)
T ss_pred cccceEEEEEEEE-EeeeecccCcEEEEEEEec---------C-----chheeehhhccccccHHHHhhcccCcEEEEEE
Confidence 4678999999987 8889999998888887731 1 33445555644 2234455699999999999
Q ss_pred Eeeeeeee
Q psy14498 81 RLQTRKWT 88 (171)
Q Consensus 81 ~l~~~~~~ 88 (171)
.++...+.
T Consensus 303 ~v~~d~f~ 310 (1444)
T COG2176 303 NVQLDTFT 310 (1444)
T ss_pred EEEecccc
Confidence 99998765
No 88
>KOG3416|consensus
Probab=83.58 E-value=4 Score=29.10 Aligned_cols=75 Identities=15% Similarity=0.158 Sum_probs=47.7
Q ss_pred cEEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEee-
Q psy14498 5 NKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEGRLQ- 83 (171)
Q Consensus 5 N~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l~- 83 (171)
+.+.++=-|..+-+.+.+++|..++.+.|+= +|--+++.+|++.. ..++.||.|.+.|-.-
T Consensus 15 kN~~v~fIvl~~g~~tkTkdg~~v~~~kVaD--------------~TgsI~isvW~e~~----~~~~PGDIirLt~Gy~S 76 (134)
T KOG3416|consen 15 KNINVTFIVLEYGRATKTKDGHEVRSCKVAD--------------ETGSINISVWDEEG----CLIQPGDIIRLTGGYAS 76 (134)
T ss_pred hcceEEEEEEeeceeeeccCCCEEEEEEEec--------------ccceEEEEEecCcC----cccCCccEEEecccchh
Confidence 3334444444555667788888888887762 35567999999533 4489999999886332
Q ss_pred -----eeeeecCCCcEEEE
Q psy14498 84 -----TRKWTNKEGVEKYI 97 (171)
Q Consensus 84 -----~~~~~~kdG~~~~~ 97 (171)
..-|..|.|+....
T Consensus 77 i~qg~LtL~~GK~Ge~~Ki 95 (134)
T KOG3416|consen 77 IFQGCLTLYVGKGGEVQKI 95 (134)
T ss_pred hhcCceEEEecCCceEeEe
Confidence 23455666664433
No 89
>cd04316 ND_PkAspRS_like_N ND_PkAspRS_like_N: N-terminal, anticodon recognition domain of the type found in the homodimeric non-discriminating (ND) Pyrococcus kodakaraensis aspartyl-tRNA synthetase (AspRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. P. kodakaraensis AspRS is a class 2b aaRS. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. P. kodakaraensis ND-AspRS can charge both tRNAAsp and tRNAAsn. Some of the enzymes in this group may be discriminating, based on the presence of homologs of asparaginyl-tRNA synthetase (AsnRS) in their completed genomes.
Probab=83.26 E-value=12 Score=25.47 Aligned_cols=79 Identities=18% Similarity=0.252 Sum_probs=48.8
Q ss_pred EEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHH--HH--HHHHHcCCCCEEEEEeE
Q psy14498 6 KVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKL--AQ--IVKQYLKKGSQIYIEGR 81 (171)
Q Consensus 6 ~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~--A~--~~~~~l~kG~~V~V~G~ 81 (171)
.|+|.|+|.+ +|.. |+ ++-+.| -+ | +..+.|++-.+. .+ .....|..|+.|.|+|.
T Consensus 14 ~V~v~Gwv~~---~R~~--g~-~~Fi~L-rD--------~-----~g~iQ~v~~~~~~~~~~~~~~~~l~~es~V~V~G~ 73 (108)
T cd04316 14 EVTVAGWVHE---IRDL--GG-IKFVIL-RD--------R-----EGIVQVTAPKKKVDKELFKTVRKLSRESVISVTGT 73 (108)
T ss_pred EEEEEEEEEe---eecc--CC-eEEEEE-ec--------C-----CeeEEEEEeCCCCCHHHHHHHhCCCCcCEEEEEEE
Confidence 5888899864 3332 33 443333 11 1 224677665431 11 12245999999999999
Q ss_pred eeeeeeecCCCcEEEEEEEEEeEEEEccC
Q psy14498 82 LQTRKWTNKEGVEKYITEVIADNMQMLGS 110 (171)
Q Consensus 82 l~~~~~~~kdG~~~~~~~i~a~~i~~l~~ 110 (171)
+..+.-. + ..+||.+++|.+|..
T Consensus 74 v~~~~~~-~-----~~~Ei~~~~i~il~~ 96 (108)
T cd04316 74 VKAEPKA-P-----NGVEIIPEEIEVLSE 96 (108)
T ss_pred EEeCCCC-C-----CCEEEEEeEEEEEeC
Confidence 8876421 1 248999999999974
No 90
>PLN02850 aspartate-tRNA ligase
Probab=82.81 E-value=23 Score=31.47 Aligned_cols=43 Identities=16% Similarity=0.244 Sum_probs=30.8
Q ss_pred HHHcCCCCEEEEEeEeeeeeeecCCCcEEEEEEEEEeEEEEccCC
Q psy14498 67 KQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQMLGSR 111 (171)
Q Consensus 67 ~~~l~kG~~V~V~G~l~~~~~~~kdG~~~~~~~i~a~~i~~l~~~ 111 (171)
...|..|+.|.|+|.+....-. ..+.+. .+||.+.+|.+|...
T Consensus 130 ~~~l~~es~V~V~G~v~~~~~~-~~~~t~-~~El~~~~i~vls~a 172 (530)
T PLN02850 130 AKQLSRESVVDVEGVVSVPKKP-VKGTTQ-QVEIQVRKIYCVSKA 172 (530)
T ss_pred HhCCCCCCEEEEEEEEEccCcC-CCCCCc-cEEEEEeEEEEEeCC
Confidence 3559999999999999853211 123222 789999999998654
No 91
>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=82.41 E-value=7.7 Score=27.82 Aligned_cols=72 Identities=13% Similarity=0.180 Sum_probs=46.6
Q ss_pred cEEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEeee
Q psy14498 5 NKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEGRLQT 84 (171)
Q Consensus 5 N~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l~~ 84 (171)
..|.|+|-|..-...+.+......+.|+|.= .+ +. ...-+.|.+|++.++.+-. +..||.|.+.+ ++.
T Consensus 15 ~~v~vigVV~~~~~p~~s~g~d~~~tl~i~D-~S------~~---~~~~l~v~~F~~~~~~LP~-v~~GDVIll~~-~kv 82 (138)
T cd04497 15 GSVNVIGVVVDAGPPVRSKGTDYCCTLTITD-PS------LA---NSDGLTVKLFRPNEESLPI-VKVGDIILLRR-VKI 82 (138)
T ss_pred CeEEEEEEEeecCCCcccCCCcEEEEEEEEC-CC------CC---CCCcEEEEEECCChhhCCC-CCCCCEEEEEE-EEE
Confidence 4677889888765554443222444444432 11 11 0345899999998888666 59999999998 566
Q ss_pred eeee
Q psy14498 85 RKWT 88 (171)
Q Consensus 85 ~~~~ 88 (171)
..|.
T Consensus 83 ~~~~ 86 (138)
T cd04497 83 QSYN 86 (138)
T ss_pred EEEC
Confidence 6774
No 92
>PRK05159 aspC aspartyl-tRNA synthetase; Provisional
Probab=81.84 E-value=24 Score=30.43 Aligned_cols=52 Identities=17% Similarity=0.224 Sum_probs=35.3
Q ss_pred EEEEEEhHH---HHHHHHHcCCCCEEEEEeEeeeeeeecCCCcEEEEEEEEEeEEEEccCC
Q psy14498 54 HRITFYRKL---AQIVKQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQMLGSR 111 (171)
Q Consensus 54 ~~v~~~g~~---A~~~~~~l~kG~~V~V~G~l~~~~~~~kdG~~~~~~~i~a~~i~~l~~~ 111 (171)
+.|++=.+. .-...+.|..||.|.|+|.+....- .. ..++|.+++|.+|...
T Consensus 46 iQ~v~~~~~~~~~~~~~~~L~~gs~V~v~G~v~~~~~--~~----~~~el~~~~i~vls~a 100 (437)
T PRK05159 46 IQVVVKKKVDEELFETIKKLKRESVVSVTGTVKANPK--AP----GGVEVIPEEIEVLNKA 100 (437)
T ss_pred EEEEEeCCccHHHHHHHhCCCCCcEEEEEEEEEcCCC--CC----CCEEEEEeEEEEEeCC
Confidence 666664331 1122345999999999999986532 11 2478999999999754
No 93
>smart00350 MCM minichromosome maintenance proteins.
Probab=81.10 E-value=8.2 Score=33.89 Aligned_cols=56 Identities=16% Similarity=0.242 Sum_probs=42.0
Q ss_pred ceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEeeeeeeecC----CCcEEEEEEEEEeEEEEccC
Q psy14498 51 TEWHRITFYRKLAQIVKQYLKKGSQIYIEGRLQTRKWTNK----EGVEKYITEVIADNMQMLGS 110 (171)
Q Consensus 51 ~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l~~~~~~~k----dG~~~~~~~i~a~~i~~l~~ 110 (171)
+..+.|++.+++++. ++.||.|.|.|-++.+.|.-+ .+...+.+.|.+..|+.+..
T Consensus 103 Prsi~v~l~~dLvd~----~~PGD~V~i~Gi~~~~~~~~~~~~~~~~~~~~~~l~a~~i~~~~~ 162 (509)
T smart00350 103 PRSVDVILDGDLVDK----AKPGDRVEVTGIYRNIPYGFKLNTVKGLPVFATYIEANHVRKLDY 162 (509)
T ss_pred CcEEEEEEcccccCc----ccCCCEEEEEEEEEeeccccccccCCCcceeeEEEEEeEEEEccc
Confidence 678999999988865 889999999999998765322 22223567778888887754
No 94
>COG0017 AsnS Aspartyl/asparaginyl-tRNA synthetases [Translation, ribosomal structure and biogenesis]
Probab=80.80 E-value=5.5 Score=34.38 Aligned_cols=55 Identities=11% Similarity=0.179 Sum_probs=40.2
Q ss_pred ceEEEEEEEhH-HHHHH--HHHcCCCCEEEEEeEeeeeeeecCCCcEEEEEEEEEeEEEEccCC
Q psy14498 51 TEWHRITFYRK-LAQIV--KQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQMLGSR 111 (171)
Q Consensus 51 ~~~~~v~~~g~-~A~~~--~~~l~kG~~V~V~G~l~~~~~~~kdG~~~~~~~i~a~~i~~l~~~ 111 (171)
+.++.|++..+ ..+.+ ++.|..++.|.|+|.+....- ....+||.+.+|++|...
T Consensus 43 sg~iQ~v~~~~~~~~~~~~~~~L~~es~v~V~G~v~~~~~------a~~g~El~v~~i~Vl~~a 100 (435)
T COG0017 43 SGFIQAVVPKNKVYEELFKAKKLTLESSVVVTGIVKASPK------APQGFELQVEKIEVLGEA 100 (435)
T ss_pred CcEEEEEEECCCCcHHHhhhhcCCCccEEEEEEEEEcCCC------CCCCEEEEEEEEEEeecc
Confidence 55799999742 22222 457999999999999986543 234679999999999654
No 95
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=80.72 E-value=8.5 Score=35.08 Aligned_cols=63 Identities=17% Similarity=0.267 Sum_probs=40.5
Q ss_pred cEEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEeee
Q psy14498 5 NKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEGRLQT 84 (171)
Q Consensus 5 N~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l~~ 84 (171)
..+++.|+|.+-...+. ++.+.++.|. . . +| .+.|+.|...-.++.+.|++|+.|+|.|++..
T Consensus 60 ~~vtv~g~V~~~~~~~~---~~~~~~v~l~--D----~-tg-------~i~l~~F~~n~~~~~~~l~~G~~~~v~Gkv~~ 122 (681)
T PRK10917 60 EKVTVEGEVLSAEVVFG---KRRRLTVTVS--D----G-TG-------NLTLRFFNFNQPYLKKQLKVGKRVAVYGKVKR 122 (681)
T ss_pred CEEEEEEEEEEEEEccC---CceEEEEEEE--E----C-Ce-------EEEEEEEccCcHHHHhhCCCCCEEEEEEEEEe
Confidence 36889999887533322 4445555443 1 1 23 35777773112266778999999999999975
No 96
>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=79.62 E-value=41 Score=29.23 Aligned_cols=53 Identities=13% Similarity=0.172 Sum_probs=36.0
Q ss_pred EEEEEEEhHHH---HHHHHHcCCCCEEEEEeEeeeeeeecCCCcEEEEEEEEEeEEEEccCC
Q psy14498 53 WHRITFYRKLA---QIVKQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQMLGSR 111 (171)
Q Consensus 53 ~~~v~~~g~~A---~~~~~~l~kG~~V~V~G~l~~~~~~~kdG~~~~~~~i~a~~i~~l~~~ 111 (171)
.+.|++-.+.. -...+.|..||.|.|+|.+.... .+. ...||.+++|++|...
T Consensus 47 ~iQ~v~~~~~~~~~~~~~~~l~~gs~V~v~G~v~~~~--~~~----~~~El~~~~i~vl~~~ 102 (453)
T TIGR00457 47 PIQAVINGEDNPYLFQLLKSLTTGSSVSVTGKVVESP--GKG----QPVELQVKKIEVVGEA 102 (453)
T ss_pred cEEEEEeCCcChHHHHHHHcCCCCcEEEEEEEEEcCC--CCC----CCEEEEEeEEEEEecC
Confidence 46666654311 12335599999999999998643 122 3578999999999754
No 97
>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=79.40 E-value=31 Score=31.08 Aligned_cols=58 Identities=14% Similarity=0.212 Sum_probs=36.3
Q ss_pred EEEEEEEhH-HHHHHHHHcCCCCEEEEEeEeeeeeeecCCC-cEEEEEEEEEeEEEEccC
Q psy14498 53 WHRITFYRK-LAQIVKQYLKKGSQIYIEGRLQTRKWTNKEG-VEKYITEVIADNMQMLGS 110 (171)
Q Consensus 53 ~~~v~~~g~-~A~~~~~~l~kG~~V~V~G~l~~~~~~~kdG-~~~~~~~i~a~~i~~l~~ 110 (171)
-+.|++-.+ .+-...+.|..|+.|.|+|.+..+.=...+- ...-.+||.+++|.+|..
T Consensus 44 ~iQvv~~~~~~~~~~~~~L~~esvV~V~G~v~~r~~~~~n~~~~tg~iEl~~~~i~iL~~ 103 (583)
T TIGR00459 44 IVQVVCDPDADALKLAKGLRNEDVVQVKGKVSARPEGNINRNLDTGEIEILAESITLLNK 103 (583)
T ss_pred cEEEEEeCCHHHHHHHhcCCCCCEEEEEEEEEeCCccccCccCCCCcEEEEEeEEEEeec
Confidence 356666433 1122345599999999999998653111111 112358999999999964
No 98
>TIGR00643 recG ATP-dependent DNA helicase RecG.
Probab=78.46 E-value=19 Score=32.55 Aligned_cols=63 Identities=14% Similarity=0.325 Sum_probs=39.2
Q ss_pred cEEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEeee
Q psy14498 5 NKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEGRLQT 84 (171)
Q Consensus 5 N~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l~~ 84 (171)
..+++.|.|.+... ....++...++.|.. . . +.-+.++.|+. .++.+.|++|+.|+|.|++..
T Consensus 33 ~~~~~~~~v~~~~~--~~~~~~~~~~~~~~d--~---~--------~~~~~~~~F~~--~~~~~~~~~g~~~~~~Gk~~~ 95 (630)
T TIGR00643 33 ERATIVGEVLSHCI--FGFKRRKVLKLRLKD--G---G--------YKKLELRFFNR--AFLKKKFKVGSKVVVYGKVKS 95 (630)
T ss_pred CEEEEEEEEEEeEe--ccCCCCceEEEEEEE--C---C--------CCEEEEEEECC--HHHHhhCCCCCEEEEEEEEEe
Confidence 36788898876321 112333444444322 1 1 22457888872 267788999999999999974
No 99
>KOG3056|consensus
Probab=78.40 E-value=17 Score=32.35 Aligned_cols=77 Identities=13% Similarity=0.300 Sum_probs=47.2
Q ss_pred EEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEeeeeee
Q psy14498 8 IIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEGRLQTRKW 87 (171)
Q Consensus 8 ~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l~~~~~ 87 (171)
.++|-|...-..+.+.+|.+|+-|.|-.-+ +. .-+.|.+||+.-+..-+ ++-|+.|.| |.-...
T Consensus 189 vt~GvI~~K~~~K~t~~G~~y~iwkL~dLk-----------~~-q~vslfLFG~a~k~~wk-~k~GtVial---LNp~v~ 252 (578)
T KOG3056|consen 189 VTMGVIVEKSDPKFTSNGNPYSIWKLTDLK-----------DH-QTVSLFLFGKAHKRYWK-IKLGTVIAL---LNPEVL 252 (578)
T ss_pred EEEEEEeecCCcccccCCCceEEEEeeecC-----------cc-ceeEEEEecHHHHHHhh-hccCcEEEE---eCcccc
Confidence 345666666666666666666666653221 01 35788899995555444 899998765 555556
Q ss_pred ecCCCc-EEEEEEE
Q psy14498 88 TNKEGV-EKYITEV 100 (171)
Q Consensus 88 ~~kdG~-~~~~~~i 100 (171)
.+++|- ....+.|
T Consensus 253 k~~~gs~~~f~LsI 266 (578)
T KOG3056|consen 253 KDRPGSRKSFSLSI 266 (578)
T ss_pred CCCCCCcceEEEEe
Confidence 666665 4555555
No 100
>COG0587 DnaE DNA polymerase III, alpha subunit [DNA replication, recombination, and repair]
Probab=78.24 E-value=14 Score=35.76 Aligned_cols=66 Identities=14% Similarity=0.339 Sum_probs=48.2
Q ss_pred EEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEeeeee
Q psy14498 7 VIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEGRLQTRK 86 (171)
Q Consensus 7 v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l~~~~ 86 (171)
+++.|-|..-...+...+|..++.++|.-. +| -++|++|-...+.....+.++..++|+|+++.+.
T Consensus 979 ~~~~~~i~~vr~~~tk~~G~~~~f~tl~D~-------~g-------~~e~v~f~~~~~~~~~~l~~~~~~~v~g~v~~~~ 1044 (1139)
T COG0587 979 VVLAGGIVAVRQRPTKAKGNKMAFLTLEDE-------TG-------ILEVVVFPSEYERYRRLLLEGRLLIVKGKVQRRE 1044 (1139)
T ss_pred eEEEEEEEEEEEeeccCCCCEEEEEEEecC-------CC-------cEEEEEcHHHHHHHHHHhccCcEEEEEEEEEecc
Confidence 567777776444444436777776666422 23 4599999888888899999999999999998754
No 101
>PTZ00385 lysyl-tRNA synthetase; Provisional
Probab=77.11 E-value=52 Score=30.11 Aligned_cols=77 Identities=18% Similarity=0.178 Sum_probs=47.6
Q ss_pred EEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEE-----hH-HHHHHHHHcCCCCEEEEE
Q psy14498 6 KVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFY-----RK-LAQIVKQYLKKGSQIYIE 79 (171)
Q Consensus 6 ~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~-----g~-~A~~~~~~l~kG~~V~V~ 79 (171)
.|.|-|+|.+ +|. -|+ ++ |-..-+. +| -+.|++- ++ ....+...|..||.|.|+
T Consensus 109 ~V~vaGrV~~---~R~--~Gk-~~-F~~LrD~------~G-------~IQvv~~~~~~~~~~~~~~~~~~l~~gdiV~V~ 168 (659)
T PTZ00385 109 TVRVAGRVTS---VRD--IGK-II-FVTIRSN------GN-------ELQVVGQVGEHFTREDLKKLKVSLRVGDIIGAD 168 (659)
T ss_pred EEEEEEEEEe---eec--cCC-eE-EEEEEEC------Cc-------eEEEEEECCccCCHHHHHHHHhCCCCCCEEEEE
Confidence 4889999975 333 243 33 3332221 23 3455553 22 233344569999999999
Q ss_pred eEeeeeeeecCCCcEEEEEEEEEeEEEEccC
Q psy14498 80 GRLQTRKWTNKEGVEKYITEVIADNMQMLGS 110 (171)
Q Consensus 80 G~l~~~~~~~kdG~~~~~~~i~a~~i~~l~~ 110 (171)
|.+... +.| .++|.+.+|.+|..
T Consensus 169 G~v~~t----~~G----eleI~~~~i~lLsk 191 (659)
T PTZ00385 169 GVPCRM----QRG----ELSVAASRMLILSP 191 (659)
T ss_pred EEEEec----CCc----eEEEEeeEEEEech
Confidence 988743 334 47899999999974
No 102
>PLN02903 aminoacyl-tRNA ligase
Probab=76.34 E-value=12 Score=34.16 Aligned_cols=58 Identities=17% Similarity=0.212 Sum_probs=37.6
Q ss_pred EEEEEEhH---HHHHHHHHcCCCCEEEEEeEeeeeeeecCCCcEE-EEEEEEEeEEEEccCC
Q psy14498 54 HRITFYRK---LAQIVKQYLKKGSQIYIEGRLQTRKWTNKEGVEK-YITEVIADNMQMLGSR 111 (171)
Q Consensus 54 ~~v~~~g~---~A~~~~~~l~kG~~V~V~G~l~~~~~~~kdG~~~-~~~~i~a~~i~~l~~~ 111 (171)
+.|++-.+ .+-...+.|..|+.|.|+|.++.+.-...+.+.. -.+||.+++|++|...
T Consensus 102 iQvV~~~~~~~~~~~~~~~L~~esvV~V~G~V~~r~~~~~n~~~~tGeiEl~~~~i~VL~~a 163 (652)
T PLN02903 102 VQVVTLPDEFPEAHRTANRLRNEYVVAVEGTVRSRPQESPNKKMKTGSVEVVAESVDILNVV 163 (652)
T ss_pred EEEEEeCCccHHHHHHHhcCCCCCEEEEEEEEEeCCCcCcCCCCCCCCEEEEEeEEEEEecC
Confidence 56766532 1222335699999999999998763222222211 2489999999999754
No 103
>PRK07218 replication factor A; Provisional
Probab=76.34 E-value=12 Score=32.34 Aligned_cols=62 Identities=19% Similarity=0.162 Sum_probs=38.3
Q ss_pred CccEEEEEEEeCCCCeEEEe--cCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEe
Q psy14498 3 SVNKVIIIGNLGRDPETRYM--SNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEG 80 (171)
Q Consensus 3 ~~N~v~l~G~l~~dp~~~~~--~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G 80 (171)
.++.|.|.|+|..-.. |.+ ++|... -.++.+. | +|--+++++|+.+++ |..|+.|.|.+
T Consensus 171 g~~~V~v~g~Vl~~~~-r~f~~~dg~~~-v~~giig----D--------eTG~Ir~tlW~~~~~-----l~~Gd~v~I~n 231 (423)
T PRK07218 171 GDRGVNVEARVLELEH-REIDGRDGETT-ILSGVLA----D--------ETGRLPFTDWDPLPE-----IEIGASIRIED 231 (423)
T ss_pred CCCceEEEEEEEEecc-eeEEcCCCCeE-EEEEEEE----C--------CCceEEEEEeccccc-----CCCCCEEEEee
Confidence 3566888888886532 332 344322 2222222 1 244679999998652 89999999998
Q ss_pred Eee
Q psy14498 81 RLQ 83 (171)
Q Consensus 81 ~l~ 83 (171)
-..
T Consensus 232 a~v 234 (423)
T PRK07218 232 AYV 234 (423)
T ss_pred eEE
Confidence 543
No 104
>PRK07218 replication factor A; Provisional
Probab=76.22 E-value=14 Score=31.83 Aligned_cols=58 Identities=21% Similarity=0.266 Sum_probs=38.1
Q ss_pred CccEEEEEEEeCCCCeEEEec-CCc--EEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEE
Q psy14498 3 SVNKVIIIGNLGRDPETRYMS-NGD--AVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIE 79 (171)
Q Consensus 3 ~~N~v~l~G~l~~dp~~~~~~-~g~--~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~ 79 (171)
.+..|.|+|+|..-.+ |.+. +|. .+....|+ . +|=-+++++|++++ |..|+.|.|.
T Consensus 67 ~~~~V~v~~kVl~i~~-rt~r~dg~~g~v~~~~ig--D------------eTG~Ir~tlW~~~~------l~~Gdvv~I~ 125 (423)
T PRK07218 67 DDKNVTVTGRVLTIGE-RSIRYQGDDHVIYEGILA--D------------ETGTISYTAWKDFG------LSPGDTVTIG 125 (423)
T ss_pred CCceeEEEEEEEEecc-eeEecCCCceEEEEEEEE--C------------CCCeEEEEEECCCC------CCCCCEEEEe
Confidence 3567889999887655 4333 443 23333332 2 23356999999663 9999999999
Q ss_pred eE
Q psy14498 80 GR 81 (171)
Q Consensus 80 G~ 81 (171)
+-
T Consensus 126 na 127 (423)
T PRK07218 126 NA 127 (423)
T ss_pred cc
Confidence 73
No 105
>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=75.98 E-value=11 Score=24.10 Aligned_cols=50 Identities=24% Similarity=0.280 Sum_probs=33.6
Q ss_pred EEEEEEhHHH-HHHHHHcCCCCEEEEEeEeeeeeeecCCCcEEEEEEEEEeEEEEcc
Q psy14498 54 HRITFYRKLA-QIVKQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQMLG 109 (171)
Q Consensus 54 ~~v~~~g~~A-~~~~~~l~kG~~V~V~G~l~~~~~~~kdG~~~~~~~i~a~~i~~l~ 109 (171)
+.|++-.+.. -...+.|..|+.|.|+|.+....-. . ..+||.++++.+|.
T Consensus 31 lQvv~~~~~~~~~~~~~l~~gs~V~v~G~v~~~~~~--~----~~~El~~~~i~il~ 81 (82)
T cd04318 31 LQVVVDKELTNFKEILKLSTGSSIRVEGVLVKSPGA--K----QPFELQAEKIEVLG 81 (82)
T ss_pred EEEEEeCcccCHHHHhcCCCceEEEEEEEEEeCCCC--C----CCEEEEEEEEEEec
Confidence 5665543311 1233459999999999998875421 1 25899999998874
No 106
>KOG1885|consensus
Probab=74.07 E-value=18 Score=31.62 Aligned_cols=78 Identities=19% Similarity=0.291 Sum_probs=49.4
Q ss_pred EEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhH------HHHHHHHHcCCCCEEEEE
Q psy14498 6 KVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRK------LAQIVKQYLKKGSQIYIE 79 (171)
Q Consensus 6 ~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~------~A~~~~~~l~kG~~V~V~ 79 (171)
.+.|.|||-+ +|+ +|.+++-|.|.-. |. -+.|.+--+ .-+...++|++||.|-|.
T Consensus 106 ~~svaGRI~s---~R~--sGsKL~Fydl~~~--------g~------klQvm~~~~~~~~~~~F~~~~~~lkrGDiig~~ 166 (560)
T KOG1885|consen 106 IVSVAGRIHS---KRE--SGSKLVFYDLHGD--------GV------KLQVMANAKKITSEEDFEQLHKFLKRGDIIGVS 166 (560)
T ss_pred eeeeeeeEee---eec--cCCceEEEEEecC--------Ce------EEEEEEehhhcCCHHHHHHHHhhhhccCEEeee
Confidence 4788899875 333 4666776666422 21 144444322 234556779999999999
Q ss_pred eEeeeeeeecCCCcEEEEEEEEEeEEEEccC
Q psy14498 80 GRLQTRKWTNKEGVEKYITEVIADNMQMLGS 110 (171)
Q Consensus 80 G~l~~~~~~~kdG~~~~~~~i~a~~i~~l~~ 110 (171)
|..-.. +.| .++|.+.+|.+|..
T Consensus 167 G~pgrt----~~g----ELSi~~~~~~lLsp 189 (560)
T KOG1885|consen 167 GYPGRT----KSG----ELSIIPNEIILLSP 189 (560)
T ss_pred cCCCcC----CCc----eEEEeecchheecc
Confidence 986432 334 67888888877743
No 107
>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=72.47 E-value=6.9 Score=27.83 Aligned_cols=32 Identities=22% Similarity=0.262 Sum_probs=26.3
Q ss_pred eEEEEEEEhHHHHHHHHHcCCCCEEEEEe-Eeee
Q psy14498 52 EWHRITFYRKLAQIVKQYLKKGSQIYIEG-RLQT 84 (171)
Q Consensus 52 ~~~~v~~~g~~A~~~~~~l~kG~~V~V~G-~l~~ 84 (171)
.-+.|.+|..-|+.+.+ |+.||.|.+.= +++.
T Consensus 60 ~ti~It~yD~H~~~ar~-lK~GdfV~L~NVhiK~ 92 (123)
T cd04498 60 LTIDILVYDNHVELAKS-LKPGDFVRIYNVHAKS 92 (123)
T ss_pred EEEEEEEEcchHHHHhh-CCCCCEEEEEEEEEEe
Confidence 56899999999987777 99999999875 4443
No 108
>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=72.46 E-value=22 Score=28.53 Aligned_cols=81 Identities=12% Similarity=0.185 Sum_probs=45.2
Q ss_pred ccEEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHH---HHHcCCCCEEEEEe
Q psy14498 4 VNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIV---KQYLKKGSQIYIEG 80 (171)
Q Consensus 4 ~N~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~---~~~l~kG~~V~V~G 80 (171)
++.|.|+|.|...- .+...+.. ++.|+ +++. +|. ..+.|.++....-.+ ...+ -|+.|.|.|
T Consensus 66 I~~v~i~G~Vv~~~-~~~~~~~~-~~~l~--iDD~-----Sg~-----~~i~~~~~~~~~~~~~l~~~~~-~G~~V~VkG 130 (256)
T PF10451_consen 66 IRWVRIVGVVVGID-YKWIENED-RIILT--IDDS-----SGA-----NTIECKCSKSSYLSMGLPINDL-IGKVVEVKG 130 (256)
T ss_dssp E-EEEEEEEEEEEE-EEE-BBTC-EEEEE--EE-S-----SCS------EEEEEEEHHHHHCCCHHCTT--TT-EEEEEE
T ss_pred cEEEEEEEEEEEEE-EEeecccc-eEEEE--EeCC-----CCc-----eeEEEEEEcccccccCCCccCC-CCcEEEEEE
Confidence 68899999999853 33333332 33333 3322 353 188899996622111 1224 899999999
Q ss_pred EeeeeeeecCCCcEEEEEEEEEeEEEEccC
Q psy14498 81 RLQTRKWTNKEGVEKYITEVIADNMQMLGS 110 (171)
Q Consensus 81 ~l~~~~~~~kdG~~~~~~~i~a~~i~~l~~ 110 (171)
.+. +...++.++.|.++..
T Consensus 131 ~vs-----------r~~~ql~ve~i~~~~~ 149 (256)
T PF10451_consen 131 TVS-----------RNERQLDVERIELVRD 149 (256)
T ss_dssp EEE-----------SSSEEEEEEEEEEETS
T ss_pred EEc-----------cCcEEEEEEEEEccCC
Confidence 999 1233566777776643
No 109
>PTZ00417 lysine-tRNA ligase; Provisional
Probab=70.77 E-value=82 Score=28.46 Aligned_cols=36 Identities=17% Similarity=0.271 Sum_probs=27.6
Q ss_pred HHHcCCCCEEEEEeEeeeeeeecCCCcEEEEEEEEEeEEEEccC
Q psy14498 67 KQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQMLGS 110 (171)
Q Consensus 67 ~~~l~kG~~V~V~G~l~~~~~~~kdG~~~~~~~i~a~~i~~l~~ 110 (171)
...|..||.|.|+|.+... +.| .++|.+.+|++|..
T Consensus 183 ~~~l~~Gd~V~V~G~~~~t----~~g----el~i~~~~i~llsk 218 (585)
T PTZ00417 183 YDKIRRGDIVGIVGFPGKS----KKG----ELSIFPKETIILSP 218 (585)
T ss_pred HhcCCCCCEEEEEeEEcCC----CCc----eEEEEEEEEEEEec
Confidence 3459999999999995532 334 47889999999864
No 110
>PRK06386 replication factor A; Reviewed
Probab=70.68 E-value=52 Score=27.76 Aligned_cols=44 Identities=23% Similarity=0.302 Sum_probs=29.5
Q ss_pred eceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEeeeeeeecCCCcEEEEEEEEEeEEEEc
Q psy14498 50 LTEWHRITFYRKLAQIVKQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQML 108 (171)
Q Consensus 50 ~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l~~~~~~~kdG~~~~~~~i~a~~i~~l 108 (171)
+|=-+++++|++ .|..|+.|.|.+-. .+.|. | .++|.+.+...+
T Consensus 151 eTGrIr~TlW~~-------~l~eGd~v~i~na~-v~e~~---G----~~el~v~~~t~I 194 (358)
T PRK06386 151 DTARVRISSFGK-------PLEDNRFVRIENAR-VSQYN---G----YIEISVGNKSVI 194 (358)
T ss_pred CCCeEEEEEccc-------cccCCCEEEEeeeE-EEccC---C----eEEEEeCCeEEE
Confidence 455779999986 38999999999944 55552 2 445555544433
No 111
>cd04483 hOBFC1_like hOBFC1_like: A subfamily of OB folds similar to that found in human OB fold containing protein 1 (hOBFC1). Members of this group belong to the Replication protein A subunit 2 (RPA2) family of OB folds. RPA is a nuclear ssDNA binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The OB fold domain of RPA2 has dual roles in ssDNA binding and trimerization.
Probab=68.65 E-value=5.4 Score=26.67 Aligned_cols=20 Identities=20% Similarity=0.384 Sum_probs=16.4
Q ss_pred HHHHcCCCCEEEEEeEeeee
Q psy14498 66 VKQYLKKGSQIYIEGRLQTR 85 (171)
Q Consensus 66 ~~~~l~kG~~V~V~G~l~~~ 85 (171)
....+..|+.|.|.|+|+..
T Consensus 59 ~~~~i~~G~vvrV~G~i~~f 78 (92)
T cd04483 59 QAKVLEIGDLLRVRGSIRTY 78 (92)
T ss_pred cccccCCCCEEEEEEEEecc
Confidence 34459999999999999854
No 112
>PTZ00401 aspartyl-tRNA synthetase; Provisional
Probab=68.46 E-value=24 Score=31.47 Aligned_cols=43 Identities=7% Similarity=0.031 Sum_probs=31.4
Q ss_pred HHcCCCCEEEEEeEeeeeeeecCCCcEEEEEEEEEeEEEEccCC
Q psy14498 68 QYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQMLGSR 111 (171)
Q Consensus 68 ~~l~kG~~V~V~G~l~~~~~~~kdG~~~~~~~i~a~~i~~l~~~ 111 (171)
..|.+|+.|.|+|.+....-. ........+||.+.+|.+|...
T Consensus 127 ~~l~~esiV~V~G~v~~~~~~-~~~~~~~~~El~v~~i~vls~a 169 (550)
T PTZ00401 127 GQIPTESIVDVEATVCKVEQP-ITSTSHSDIELKVKKIHTVTES 169 (550)
T ss_pred hcCCCCCEEEEEEEEEecCcc-CCCCCCccEEEEeeEEEEEeCC
Confidence 459999999999998875321 1223344689999999999654
No 113
>PRK00484 lysS lysyl-tRNA synthetase; Reviewed
Probab=68.02 E-value=85 Score=27.59 Aligned_cols=35 Identities=31% Similarity=0.371 Sum_probs=28.4
Q ss_pred HcCCCCEEEEEeEeeeeeeecCCCcEEEEEEEEEeEEEEccCC
Q psy14498 69 YLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQMLGSR 111 (171)
Q Consensus 69 ~l~kG~~V~V~G~l~~~~~~~kdG~~~~~~~i~a~~i~~l~~~ 111 (171)
.|..||.|.|+|.+..+ +.| .++|.+++|.+|...
T Consensus 103 ~l~~g~~v~v~G~v~~t----~~g----e~el~~~~~~vls~~ 137 (491)
T PRK00484 103 KLDLGDIIGVEGTLFKT----KTG----ELSVKATELTLLTKS 137 (491)
T ss_pred cCCCCCEEEEEEEEEEc----CCC----cEEEEEeEEEEEecc
Confidence 39999999999999864 234 489999999999643
No 114
>PLN02502 lysyl-tRNA synthetase
Probab=66.94 E-value=87 Score=28.07 Aligned_cols=36 Identities=14% Similarity=0.314 Sum_probs=28.3
Q ss_pred HHcCCCCEEEEEeEeeeeeeecCCCcEEEEEEEEEeEEEEccCC
Q psy14498 68 QYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQMLGSR 111 (171)
Q Consensus 68 ~~l~kG~~V~V~G~l~~~~~~~kdG~~~~~~~i~a~~i~~l~~~ 111 (171)
..|..||.|.|+|.+... +.| .++|.+.+|.+|...
T Consensus 159 ~~l~~gdiV~V~G~~~~t----~~g----elel~~~~i~vLs~~ 194 (553)
T PLN02502 159 SLVDRGDIVGVTGTPGKT----KKG----ELSIFPTSFEVLTKC 194 (553)
T ss_pred hCCCCCcEEEEEEEEEec----CCC----CEEEEEeEEEEEecc
Confidence 348999999999998753 334 478999999999643
No 115
>COG4097 Predicted ferric reductase [Inorganic ion transport and metabolism]
Probab=65.56 E-value=11 Score=32.18 Aligned_cols=36 Identities=17% Similarity=0.291 Sum_probs=29.9
Q ss_pred eEEEEEEEhHHHHHHHHHcCCCCEEEEEeEeeeeee
Q psy14498 52 EWHRITFYRKLAQIVKQYLKKGSQIYIEGRLQTRKW 87 (171)
Q Consensus 52 ~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l~~~~~ 87 (171)
-.+.|.+-|+-.+.+.+.|+.|++|.|+|-.---.+
T Consensus 276 l~FsIK~LGD~Tk~l~dnLk~G~k~~vdGPYG~F~~ 311 (438)
T COG4097 276 LRFSIKALGDFTKTLKDNLKVGTKLEVDGPYGKFDF 311 (438)
T ss_pred EEEEehhhhhhhHHHHHhccCCceEEEecCcceeec
Confidence 467888899999999999999999999985444334
No 116
>KOG0479|consensus
Probab=65.22 E-value=9.7 Score=34.40 Aligned_cols=56 Identities=20% Similarity=0.308 Sum_probs=40.9
Q ss_pred ceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEeeeeeeecCCCcE--EEEEEEEEeEEEEccCC
Q psy14498 51 TEWHRITFYRKLAQIVKQYLKKGSQIYIEGRLQTRKWTNKEGVE--KYITEVIADNMQMLGSR 111 (171)
Q Consensus 51 ~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l~~~~~~~kdG~~--~~~~~i~a~~i~~l~~~ 111 (171)
+--+.|++=.+|++. ++.||+|-|.|..+.-..+ .+|.. ...+-|++++|.+|...
T Consensus 212 PRSVDvilddDLVD~----~KPGDRV~ivG~yr~Lp~k-~~g~tsg~FRTvliaNni~~l~ke 269 (818)
T KOG0479|consen 212 PRSVDVILDDDLVDR----VKPGDRVNIVGIYRSLPGK-SNGNTSGTFRTVLIANNIELLSKE 269 (818)
T ss_pred CcceeEEeccccccc----CCCCCeeEEEEEEeeccCc-cCCcccceeEEEEEeccHHhhccc
Confidence 334555555555544 8999999999998876664 46654 66778899999999755
No 117
>PLN02532 asparagine-tRNA synthetase
Probab=64.29 E-value=22 Score=32.34 Aligned_cols=53 Identities=21% Similarity=0.295 Sum_probs=38.3
Q ss_pred EEEEEEEhHHHHHHHHHcCCCCEEEEEeEeeeeeeecCCCcEEEEEEEEEeEEEEccC
Q psy14498 53 WHRITFYRKLAQIVKQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQMLGS 110 (171)
Q Consensus 53 ~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l~~~~~~~kdG~~~~~~~i~a~~i~~l~~ 110 (171)
.+.|++-.+.+.. .+.|..|+.|.|+|.++.+. +.+ ....+||.+++|.+|..
T Consensus 148 ~lQvVv~~~~~~~-~~~L~~Es~V~V~G~V~~~~---~~~-~~g~iEl~v~~i~VLg~ 200 (633)
T PLN02532 148 SLQVVVDSALAPL-TQLMATGTCILAEGVLKLPL---PAQ-GKHVIELEVEKILHIGT 200 (633)
T ss_pred ceEEEEeCCcccH-hhcCCCceEEEEEEEEEecC---CCC-CCCcEEEEeeEEEEEec
Confidence 4888887664432 25699999999999998762 111 12358999999999975
No 118
>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=64.17 E-value=48 Score=23.38 Aligned_cols=33 Identities=21% Similarity=0.174 Sum_probs=15.9
Q ss_pred EEEEEEEhHH-HHHHHHHcCCCCEEEEEeEeeee
Q psy14498 53 WHRITFYRKL-AQIVKQYLKKGSQIYIEGRLQTR 85 (171)
Q Consensus 53 ~~~v~~~g~~-A~~~~~~l~kG~~V~V~G~l~~~ 85 (171)
.+.|.+-... .......|+||+.|.|.|.+...
T Consensus 99 ~v~~~~~~~~~~~~~~~~l~~G~~Vti~G~~~g~ 132 (144)
T PF12869_consen 99 GVQCYFSNDQEKRASVAKLKKGQKVTIKGICTGY 132 (144)
T ss_dssp S--EEEEEEGGGHHHHHH--TTSEEEEEEE----
T ss_pred eEEEEEccchhhhhhHhcCCCCCEEEEEEEEEee
Confidence 4445444333 22334459999999999998755
No 119
>PRK07135 dnaE DNA polymerase III DnaE; Validated
Probab=62.29 E-value=55 Score=31.38 Aligned_cols=63 Identities=11% Similarity=-0.030 Sum_probs=43.4
Q ss_pred EEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEeeee
Q psy14498 6 KVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEGRLQTR 85 (171)
Q Consensus 6 ~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l~~~ 85 (171)
.+.+.|-|..--.++ ++|..++.++|.- .+.-+.|++|.+.-+.+.. |.+|+.++|+|+.+.+
T Consensus 899 ~~~v~g~i~~~~~~~--K~g~~maf~~~eD--------------~~~~~e~~~F~~~~~~~~~-l~~~~~~~~~~~~~~~ 961 (973)
T PRK07135 899 EYRLAIEVKNVKRLR--KANKEYKKVILSD--------------DSVEITIFVNDNDYLLFET-LKKGDIYEFLISKSKN 961 (973)
T ss_pred eEEEEEEEEEEEEEe--eCCCeEEEEEEEE--------------CCCcEEEEEcHHHHHHHHH-hhcCCEEEEEEEEcCC
Confidence 356777666533333 5677666666542 2334699999997777775 9999999999987654
No 120
>COG3111 Periplasmic protein with OB-fold [Function unknown]
Probab=62.15 E-value=40 Score=24.00 Aligned_cols=31 Identities=16% Similarity=0.444 Sum_probs=24.5
Q ss_pred HcCCCCEEEEEeEeeeeeeecCCCcEEEEEEEEEeEEEEc
Q psy14498 69 YLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQML 108 (171)
Q Consensus 69 ~l~kG~~V~V~G~l~~~~~~~kdG~~~~~~~i~a~~i~~l 108 (171)
.+..-++|.|.|.+... |. ..||-|.+|+.+
T Consensus 97 tv~P~dkV~I~GevDk~-~~--------~~eIdV~~I~k~ 127 (128)
T COG3111 97 TVTPKDKVRIQGEVDKD-WN--------SVEIDVKHIEKL 127 (128)
T ss_pred ccCcccEEEEEeEEcCC-Cc--------cceeEhhheEec
Confidence 38899999999999755 53 567888888776
No 121
>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=62.06 E-value=48 Score=22.69 Aligned_cols=28 Identities=21% Similarity=0.553 Sum_probs=19.4
Q ss_pred cCCCCEEEEEeEeeeeeeecCCCcEEEEEEEEEeEEE
Q psy14498 70 LKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQ 106 (171)
Q Consensus 70 l~kG~~V~V~G~l~~~~~~~kdG~~~~~~~i~a~~i~ 106 (171)
+...++|.|.|.+. +.| . .++|-|.+|+
T Consensus 75 vt~~~~Vri~GeVD-k~~-----~---~~~IdV~~I~ 102 (103)
T PF04076_consen 75 VTPDDKVRISGEVD-KDW-----N---KTEIDVDRIE 102 (103)
T ss_dssp --TTSEEEEEEEEE-EET-----T---EEEEEEEEEE
T ss_pred cCCCCEEEEEEEEe-CCC-----C---ceEEEEEEEE
Confidence 88999999999997 334 2 3677777765
No 122
>PRK03932 asnC asparaginyl-tRNA synthetase; Validated
Probab=61.96 E-value=1.1e+02 Score=26.60 Aligned_cols=37 Identities=19% Similarity=0.317 Sum_probs=29.0
Q ss_pred HHcCCCCEEEEEeEeeeeeeecCCCcEEEEEEEEEeEEEEccC
Q psy14498 68 QYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQMLGS 110 (171)
Q Consensus 68 ~~l~kG~~V~V~G~l~~~~~~~kdG~~~~~~~i~a~~i~~l~~ 110 (171)
..|..||.|.|+|.+....- +. ..+||.+.+|.+|..
T Consensus 63 ~~l~~~s~v~v~G~v~~~~~--~~----~~~el~~~~i~vl~~ 99 (450)
T PRK03932 63 KKLTTGSSVIVTGTVVESPR--AG----QGYELQATKIEVIGE 99 (450)
T ss_pred hcCCCCcEEEEEEEEEcCCC--CC----CCEEEEEEEEEEccC
Confidence 45999999999999986432 12 247999999999975
No 123
>COG0802 Predicted ATPase or kinase [General function prediction only]
Probab=59.97 E-value=9.8 Score=27.99 Aligned_cols=24 Identities=25% Similarity=0.455 Sum_probs=21.1
Q ss_pred HHHHHHHHHcCCCCEEEEEeEeee
Q psy14498 61 KLAQIVKQYLKKGSQIYIEGRLQT 84 (171)
Q Consensus 61 ~~A~~~~~~l~kG~~V~V~G~l~~ 84 (171)
++++.+++.|.+|+.|+++|.|-.
T Consensus 13 ~lg~~l~~~l~~g~Vv~L~GdLGA 36 (149)
T COG0802 13 ALGERLAEALKAGDVVLLSGDLGA 36 (149)
T ss_pred HHHHHHHhhCCCCCEEEEEcCCcC
Confidence 478899999999999999998853
No 124
>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=57.99 E-value=30 Score=30.40 Aligned_cols=36 Identities=25% Similarity=0.254 Sum_probs=27.8
Q ss_pred HHcCCCCEEEEEeEeeeeeeecCCCcEEEEEEEEEeEEEEccCC
Q psy14498 68 QYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQMLGSR 111 (171)
Q Consensus 68 ~~l~kG~~V~V~G~l~~~~~~~kdG~~~~~~~i~a~~i~~l~~~ 111 (171)
..|..||.|.|+|.+... +.| .++|.+++|.+|...
T Consensus 102 ~~l~~gd~V~v~G~~~~t----~~g----elel~~~~i~ilsk~ 137 (496)
T TIGR00499 102 YLLDLGDIIGVTGYPFKT----KTG----ELSVHVTELQILTKA 137 (496)
T ss_pred hcCCCCCEEEEEEEEEEC----CCC----cEEEEeeEEEEEecC
Confidence 348999999999999532 334 388999999999744
No 125
>PF02367 UPF0079: Uncharacterised P-loop hydrolase UPF0079; InterPro: IPR003442 This group consists of bacterial proteins, which contain a P-loop. They are probably essential to bacteria as members are found in all genomes so far sequenced and no equivalent genes have been found in the archaea and eukaryotes, suggesting the protein may be involved in cell wall biosynthesis. The sequence of YjeE, from Haemophilus influenzae, has been determined to 1.7-A resolution. The protein has a nucleotide-binding fold with a four-stranded parallel beta-sheet flanked by antiparallel beta-strands on each side. The topology of the beta-sheet is unique among P-loop proteins and has features of different families of enzymes. ADP has been shown to bind to the P-loop in the presence of Mg2+ and ATPase activity has been confirmed by kinetic measurements [].; PDB: 1HTW_A 1FL9_A.
Probab=57.84 E-value=7.5 Score=27.57 Aligned_cols=23 Identities=39% Similarity=0.586 Sum_probs=19.6
Q ss_pred HHHHHHHHHcCCCCEEEEEeEee
Q psy14498 61 KLAQIVKQYLKKGSQIYIEGRLQ 83 (171)
Q Consensus 61 ~~A~~~~~~l~kG~~V~V~G~l~ 83 (171)
++|+.+++.|++|+.|.++|.|-
T Consensus 3 ~la~~l~~~l~~g~vi~L~GdLG 25 (123)
T PF02367_consen 3 RLAKKLAQILKPGDVILLSGDLG 25 (123)
T ss_dssp HHHHHHHHHHSS-EEEEEEESTT
T ss_pred HHHHHHHHhCCCCCEEEEECCCC
Confidence 57889999999999999999874
No 126
>PRK00476 aspS aspartyl-tRNA synthetase; Validated
Probab=57.55 E-value=50 Score=29.76 Aligned_cols=58 Identities=19% Similarity=0.206 Sum_probs=35.9
Q ss_pred EEEEEEEhHHHH--HHHHHcCCCCEEEEEeEeeeeeeecCCCcE-EEEEEEEEeEEEEccCC
Q psy14498 53 WHRITFYRKLAQ--IVKQYLKKGSQIYIEGRLQTRKWTNKEGVE-KYITEVIADNMQMLGSR 111 (171)
Q Consensus 53 ~~~v~~~g~~A~--~~~~~l~kG~~V~V~G~l~~~~~~~kdG~~-~~~~~i~a~~i~~l~~~ 111 (171)
.+.|++-.. .+ .....|..|+.|.|+|.+..+.-...+-.. .-.+||.+++|.+|...
T Consensus 46 ~iQ~v~~~~-~~~~~~~~~l~~es~V~V~G~v~~~~~~~~n~~~~~g~~El~~~~i~il~~a 106 (588)
T PRK00476 46 IVQVVFDPD-AEAFEVAESLRSEYVIQVTGTVRARPEGTVNPNLPTGEIEVLASELEVLNKS 106 (588)
T ss_pred eEEEEEeCC-HHHHHHHhCCCCCCEEEEEEEEEecCCcccCccCCCCcEEEEEeEEEEEecC
Confidence 356655431 11 123459999999999999875421111111 12489999999999654
No 127
>PRK10646 ADP-binding protein; Provisional
Probab=56.90 E-value=11 Score=27.74 Aligned_cols=24 Identities=25% Similarity=0.347 Sum_probs=21.3
Q ss_pred HHHHHHHHHcCCCCEEEEEeEeee
Q psy14498 61 KLAQIVKQYLKKGSQIYIEGRLQT 84 (171)
Q Consensus 61 ~~A~~~~~~l~kG~~V~V~G~l~~ 84 (171)
++|+.+++.|+.|+.|+++|.|-.
T Consensus 16 ~l~~~la~~l~~g~vi~L~GdLGa 39 (153)
T PRK10646 16 DLGARVAKACDGATVIYLYGDLGA 39 (153)
T ss_pred HHHHHHHHhCCCCcEEEEECCCCC
Confidence 588999999999999999998854
No 128
>PRK06763 F0F1 ATP synthase subunit alpha; Validated
Probab=56.58 E-value=3.4 Score=31.83 Aligned_cols=15 Identities=47% Similarity=0.738 Sum_probs=11.2
Q ss_pred CCCccEEEEEEEeCCC
Q psy14498 1 MASVNKVIIIGNLGRD 16 (171)
Q Consensus 1 M~~~N~v~l~G~l~~d 16 (171)
|. |.+|+|.|-|+-.
T Consensus 1 Mn-~kk~ila~alg~~ 15 (213)
T PRK06763 1 MN-MKKVILAGALGIA 15 (213)
T ss_pred CC-cceEEEecchhhe
Confidence 54 7888888888753
No 129
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=56.14 E-value=1e+02 Score=26.69 Aligned_cols=64 Identities=22% Similarity=0.380 Sum_probs=39.3
Q ss_pred ccEEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhH---HHHHHHHHcCCCCEEEEEe
Q psy14498 4 VNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRK---LAQIVKQYLKKGSQIYIEG 80 (171)
Q Consensus 4 ~N~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~---~A~~~~~~l~kG~~V~V~G 80 (171)
..+..|.|++..+|.... +|-.+ |.+. + |+ - -+.|.+|.. ..+. +..|.+||.|.+.|
T Consensus 266 ~~~~~v~g~v~~~p~~ie--Gghv~--v~i~------d---~~----G-~I~~~A~eptk~fr~~-a~~L~pGD~i~~~G 326 (421)
T COG1571 266 YSKYRVVGRVEAEPRAIE--GGHVV--VEIT------D---GE----G-EIGAVAFEPTKEFREL-ARKLIPGDEITVYG 326 (421)
T ss_pred ccceEEEEEEecccEEee--CCEEE--EEec------C---CC----c-eEEEEEecccccchHH-HHhcCCCCEEEEec
Confidence 456778888888775533 44322 2221 1 21 1 567888754 3333 34599999999999
Q ss_pred Eeeeee
Q psy14498 81 RLQTRK 86 (171)
Q Consensus 81 ~l~~~~ 86 (171)
.++...
T Consensus 327 ~~~~~~ 332 (421)
T COG1571 327 SVKPGT 332 (421)
T ss_pred Cccccc
Confidence 986544
No 130
>PTZ00111 DNA replication licensing factor MCM4; Provisional
Probab=56.10 E-value=66 Score=30.64 Aligned_cols=55 Identities=18% Similarity=0.257 Sum_probs=39.9
Q ss_pred eEEEEEEEhHHHHHHHHHcCCCCEEEEEeEeeeeeee----cCCCcEEEEEEEEEeEEEEccC
Q psy14498 52 EWHRITFYRKLAQIVKQYLKKGSQIYIEGRLQTRKWT----NKEGVEKYITEVIADNMQMLGS 110 (171)
Q Consensus 52 ~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l~~~~~~----~kdG~~~~~~~i~a~~i~~l~~ 110 (171)
..+.|++.+++++. ++.||+|.|.|-++...-. .+.....+.+.|.|.+|+.+..
T Consensus 346 rsi~v~l~dDLVD~----v~PGDrV~VtGIl~~~~~~~~~~~~~~~~~~~~yl~~~~i~~~~~ 404 (915)
T PTZ00111 346 EVINLNLYDDLIDS----VKTGDRVTVVGILKVTPIRTSTTRRTLKSLYTYFVNVIHVKVINS 404 (915)
T ss_pred ceEEEEEecchhcc----CCCCCEEEEEEEEEeccccccccccccccccceEEEEEEEEEecc
Confidence 67999999988865 8899999999999865321 0112345667777888887654
No 131
>PLN02603 asparaginyl-tRNA synthetase
Probab=54.91 E-value=1.6e+02 Score=26.48 Aligned_cols=53 Identities=11% Similarity=0.263 Sum_probs=35.4
Q ss_pred EEEEEEEhHHH--HHHHH-HcCCCCEEEEEeEeeeeeeecCCCcEEEEEEEEEeEEEEccCC
Q psy14498 53 WHRITFYRKLA--QIVKQ-YLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQMLGSR 111 (171)
Q Consensus 53 ~~~v~~~g~~A--~~~~~-~l~kG~~V~V~G~l~~~~~~~kdG~~~~~~~i~a~~i~~l~~~ 111 (171)
-+.|++-.+.. +.+.. .|..|+.|.|+|.+.... .++ ..+||.+++|.+|...
T Consensus 138 ~lQ~v~~~~~~~~~~l~~~~l~~gs~V~V~G~v~~~~----~~~--~~~EL~v~~i~vlg~a 193 (565)
T PLN02603 138 NMQCVMTPDAEGYDQVESGLITTGASVLVQGTVVSSQ----GGK--QKVELKVSKIVVVGKS 193 (565)
T ss_pred eEEEEEECcHHHHHHHhhcCCCCCCEEEEEEEEEecC----CCC--ccEEEEEeEEEEEECC
Confidence 46777643321 11111 388999999999987542 232 4689999999999754
No 132
>PRK02983 lysS lysyl-tRNA synthetase; Provisional
Probab=52.75 E-value=2.3e+02 Score=27.69 Aligned_cols=36 Identities=14% Similarity=0.398 Sum_probs=28.2
Q ss_pred HHHcCCCCEEEEEeEeeeeeeecCCCcEEEEEEEEEeEEEEccC
Q psy14498 67 KQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQMLGS 110 (171)
Q Consensus 67 ~~~l~kG~~V~V~G~l~~~~~~~kdG~~~~~~~i~a~~i~~l~~ 110 (171)
...+..||.|.|+|.+... +.| .++|.+++|++|..
T Consensus 699 ~~~l~~gd~V~v~G~v~~t----~~g----e~ei~~~~i~ll~k 734 (1094)
T PRK02983 699 RAAVDLGDLVEVTGTMGTS----RNG----TLSLLVTSWRLAGK 734 (1094)
T ss_pred HhcCCCCCEEEEEEEEEEc----CCC----CEEEEEeEEEEEec
Confidence 3458999999999998753 334 47889999999864
No 133
>PF11948 DUF3465: Protein of unknown function (DUF3465); InterPro: IPR021856 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 131 to 151 amino acids in length. This protein has a conserved HWTH sequence motif.
Probab=52.63 E-value=68 Score=23.06 Aligned_cols=29 Identities=38% Similarity=0.646 Sum_probs=21.3
Q ss_pred HHHHHHHHHcCCCCEEEEEeEeeeeeeecCCCc
Q psy14498 61 KLAQIVKQYLKKGSQIYIEGRLQTRKWTNKEGV 93 (171)
Q Consensus 61 ~~A~~~~~~l~kG~~V~V~G~l~~~~~~~kdG~ 93 (171)
++|.++-. |+|||.|.+.|+.. |.++.|.
T Consensus 78 Dlaprip~-l~~GD~V~f~GeYe---~n~kggv 106 (131)
T PF11948_consen 78 DLAPRIPW-LQKGDQVEFYGEYE---WNPKGGV 106 (131)
T ss_pred CccccCcC-cCCCCEEEEEEEEE---ECCCCCE
Confidence 46666555 99999999999984 5445554
No 134
>TIGR01077 L13_A_E ribosomal protein L13, archaeal/eukaryotic. This model represents ribosomal protein of L13 from the Archaea and from the eukaryotic cytosol. Bacterial and organellar forms are represented by TIGR01066.
Probab=51.17 E-value=14 Score=26.97 Aligned_cols=23 Identities=22% Similarity=0.433 Sum_probs=20.2
Q ss_pred EEhHHHHHHHHHcCCCCEEEEEe
Q psy14498 58 FYRKLAQIVKQYLKKGSQIYIEG 80 (171)
Q Consensus 58 ~~g~~A~~~~~~l~kG~~V~V~G 80 (171)
+.|.+|..++..|.-||.|.|.-
T Consensus 9 vlGRLAs~IA~~L~~Gd~VvViN 31 (142)
T TIGR01077 9 ILGRLASVVAKQLLNGEKVVVVN 31 (142)
T ss_pred chHHHHHHHHHHHhcCCEEEEEe
Confidence 36899999999999999998864
No 135
>PF03843 Slp: Outer membrane lipoprotein Slp family; InterPro: IPR004658 Slp superfamily members are present in the Gram-negative gamma proteobacteria Escherichia coli (which also contains a close paralog), Haemophilus influenzae and Pasteurella multocida and Vibrio cholerae. The known members of the family to date share a motif LX[GA]C near the N terminus, which is compatible with the possibility that the protein is modified into a lipoprotein with Cys as the new N terminus. Slp from E. coli is known to be a lipoprotein of the outer membrane and to be expressed in response to carbon starvation.; GO: 0019867 outer membrane
Probab=49.91 E-value=1e+02 Score=22.74 Aligned_cols=95 Identities=12% Similarity=0.071 Sum_probs=51.0
Q ss_pred EEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEeeee
Q psy14498 6 KVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEGRLQTR 85 (171)
Q Consensus 6 ~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l~~~ 85 (171)
.|.+=|.|. +++-.++++.+--...-.++.-+...+.. ...-|+ + .+...-+-+ -+++|..|.|.|++.-.
T Consensus 36 ~VrwGG~I~---~v~n~~~~T~leV~~~PLd~~grP~~~~~--s~GRFl-a-~~~gFLDP~--~y~~Gr~vTV~G~v~g~ 106 (160)
T PF03843_consen 36 QVRWGGVIV---NVRNLPDQTELEVVQYPLDSSGRPQTDDP--SQGRFL-A-RVPGFLDPA--IYAPGRLVTVVGTVTGM 106 (160)
T ss_pred EEEECCEEE---EEEECCCceEEEEEEccCCCCCCcCCCCC--CCCEEE-E-EeCCCcCHH--HcCCCCEEEEEEEecce
Confidence 566667775 45555555533333333333333221111 122333 2 232222221 18899999999999877
Q ss_pred eeecCCCc-EEEEEEEEEeEEEEccC
Q psy14498 86 KWTNKEGV-EKYITEVIADNMQMLGS 110 (171)
Q Consensus 86 ~~~~kdG~-~~~~~~i~a~~i~~l~~ 110 (171)
.- .+=|+ ......|.+..+.+-..
T Consensus 107 ~~-~~ige~~Y~yPvv~~~~~~lW~~ 131 (160)
T PF03843_consen 107 ET-GKIGEYPYRYPVVDASGIHLWPE 131 (160)
T ss_pred EE-eeeCCCcceeeEEEeeEEEECCC
Confidence 64 34444 44555667888988863
No 136
>COG1838 FumA Tartrate dehydratase beta subunit/Fumarate hydratase class I, C-terminal domain [Energy production and conversion]
Probab=49.85 E-value=21 Score=27.15 Aligned_cols=21 Identities=29% Similarity=0.640 Sum_probs=17.4
Q ss_pred HHHHHHcCCCCEEEEEeEeeee
Q psy14498 64 QIVKQYLKKGSQIYIEGRLQTR 85 (171)
Q Consensus 64 ~~~~~~l~kG~~V~V~G~l~~~ 85 (171)
|.+.+ |+.||.|+++|.|-+-
T Consensus 11 e~i~~-LkvGd~v~lsG~I~t~ 31 (184)
T COG1838 11 EEIAK-LKVGDVVYLSGKIVTG 31 (184)
T ss_pred HHHHh-ccCCCEEEEeeEEEEe
Confidence 45555 9999999999999875
No 137
>PF00970 FAD_binding_6: Oxidoreductase FAD-binding domain; InterPro: IPR008333 These sequences contain an oxidoreductase FAD-binding domain. To date, the 3D-structures of the flavoprotein domain of Zea mays (Maize) nitrate reductase [] and of pig NADH:cytochrome b5 reductase [] have been solved. The overall fold is similar to that of ferredoxin:NADP+ reductase []: the FAD-binding domain (N-terminal) has the topology of an anti-parallel beta-barrel, while the NAD(P)-binding domain (C-terminal) has the topology of a classical pyridine dinucleotide-binding fold (i.e. a central parallel beta-sheet flanked by 2 helices on each side).; PDB: 1JB9_A 3LVB_A 3LO8_A 1FRN_A 1FND_A 1BX1_A 1FNC_A 1FNB_A 1BX0_A 1FRQ_A ....
Probab=48.83 E-value=50 Score=21.49 Aligned_cols=31 Identities=26% Similarity=0.392 Sum_probs=22.9
Q ss_pred eEEEEEEE--hHHHHHHHHHcCCCCEEEEEeEee
Q psy14498 52 EWHRITFY--RKLAQIVKQYLKKGSQIYIEGRLQ 83 (171)
Q Consensus 52 ~~~~v~~~--g~~A~~~~~~l~kG~~V~V~G~l~ 83 (171)
.-+-|... |.....+.+ |+.||.|.|+|-+-
T Consensus 63 ~~~~ik~~~~G~~S~~L~~-l~~Gd~v~i~gP~G 95 (99)
T PF00970_consen 63 LEFAIKRYPNGRVSRYLHQ-LKPGDEVEIRGPYG 95 (99)
T ss_dssp EEEEEEECTTSHHHHHHHT-SCTTSEEEEEEEES
T ss_pred EEEEEEeccCCHHHHHHHh-CCCCCEEEEEEccc
Confidence 34455556 677777755 99999999999654
No 138
>PRK12820 bifunctional aspartyl-tRNA synthetase/aspartyl/glutamyl-tRNA amidotransferase subunit C; Provisional
Probab=48.69 E-value=84 Score=29.07 Aligned_cols=59 Identities=15% Similarity=0.205 Sum_probs=37.7
Q ss_pred EEEEEEEhHH----HHHHHHHcCCCCEEEEEeEeeeeeeecCC-CcEEEEEEEEEeEEEEccCC
Q psy14498 53 WHRITFYRKL----AQIVKQYLKKGSQIYIEGRLQTRKWTNKE-GVEKYITEVIADNMQMLGSR 111 (171)
Q Consensus 53 ~~~v~~~g~~----A~~~~~~l~kG~~V~V~G~l~~~~~~~kd-G~~~~~~~i~a~~i~~l~~~ 111 (171)
.+.|++-.+. .-.....|..|+.|.|+|.++.+.-..++ +...-.+||.+.+|.+|...
T Consensus 47 ~iQvV~~~~~~~~~~~~~~~~L~~EsvV~V~G~v~~r~~~~~n~~~~tg~iEl~~~~i~iL~~a 110 (706)
T PRK12820 47 FIQAVFSPEAAPADVYELAASLRAEFCVALQGEVQKRLEETENPHIETGDIEVFVRELSILAAS 110 (706)
T ss_pred cEEEEEeCCcCCHHHHHHHhcCCCCCEEEEEeEEeccCccccCCCCCCCcEEEEeeEEEEEecC
Confidence 4677665331 11233569999999999999876322111 11123589999999999653
No 139
>PRK06394 rpl13p 50S ribosomal protein L13P; Reviewed
Probab=48.40 E-value=18 Score=26.54 Aligned_cols=22 Identities=27% Similarity=0.401 Sum_probs=19.6
Q ss_pred EhHHHHHHHHHcCCCCEEEEEe
Q psy14498 59 YRKLAQIVKQYLKKGSQIYIEG 80 (171)
Q Consensus 59 ~g~~A~~~~~~l~kG~~V~V~G 80 (171)
.|.+|..++..|.-||.|+|.-
T Consensus 14 lGRLAs~IA~~L~~Gd~VVViN 35 (146)
T PRK06394 14 LGRLASYVAKRLLEGEEVVIVN 35 (146)
T ss_pred hHHHHHHHHHHHhCCCEEEEEe
Confidence 6889999999999999988865
No 140
>COG0677 WecC UDP-N-acetyl-D-mannosaminuronate dehydrogenase [Cell envelope biogenesis, outer membrane]
Probab=47.98 E-value=20 Score=30.83 Aligned_cols=45 Identities=18% Similarity=0.271 Sum_probs=31.8
Q ss_pred EEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEee
Q psy14498 30 NVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEGRLQ 83 (171)
Q Consensus 30 ~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l~ 83 (171)
-|.|++.-..++. .+. ++..-.+.|+.++.+|+||+.|.+|-..-
T Consensus 87 v~iI~VPTPl~~~--~~p-------Dls~v~~aa~sIa~~L~kG~LVIlEST~~ 131 (436)
T COG0677 87 VFIICVPTPLKKY--REP-------DLSYVESAARSIAPVLKKGDLVILESTTP 131 (436)
T ss_pred EEEEEecCCcCCC--CCC-------ChHHHHHHHHHHHHhcCCCCEEEEecCCC
Confidence 4777777666542 222 33445678999999999999999987643
No 141
>TIGR00150 HI0065_YjeE ATPase, YjeE family. Members of this family have a conserved nucleotide-binding motif GXXGXGKT and a nucleotide-binding fold. Member protein YjeE of Haemophilus influenzae (HI0065) was shown to have ATPase activity.
Probab=47.13 E-value=21 Score=25.58 Aligned_cols=24 Identities=21% Similarity=0.408 Sum_probs=20.9
Q ss_pred HHHHHHHHHcCCCCEEEEEeEeee
Q psy14498 61 KLAQIVKQYLKKGSQIYIEGRLQT 84 (171)
Q Consensus 61 ~~A~~~~~~l~kG~~V~V~G~l~~ 84 (171)
++|+.+++.|++|+.|.+.|.+-.
T Consensus 10 ~l~~~l~~~l~~~~~i~l~G~lGa 33 (133)
T TIGR00150 10 KFGKAFAKPLDFGTVVLLKGDLGA 33 (133)
T ss_pred HHHHHHHHhCCCCCEEEEEcCCCC
Confidence 578899999999999999998753
No 142
>PF11736 DUF3299: Protein of unknown function (DUF3299); InterPro: IPR021727 This is a family of bacterial proteins of unknown function.
Probab=47.00 E-value=53 Score=23.99 Aligned_cols=33 Identities=15% Similarity=0.245 Sum_probs=25.4
Q ss_pred CCEEEEEeEeeeeeeecCCCcEEEEEEEEEeEEEE
Q psy14498 73 GSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQM 107 (171)
Q Consensus 73 G~~V~V~G~l~~~~~~~kdG~~~~~~~i~a~~i~~ 107 (171)
-+.|.|+|+|+...... +-....+.+.+..|+-
T Consensus 112 ~~pv~V~G~l~~~~~~~--~~~~~~Y~m~a~~v~~ 144 (146)
T PF11736_consen 112 YDPVWVEGTLKVERSSS--DLGTSGYSMDADSVEP 144 (146)
T ss_pred ceeEEEEEEEEeccccc--hheeEEEEEEeeEEEe
Confidence 36999999999998853 4446777788887764
No 143
>PLN02221 asparaginyl-tRNA synthetase
Probab=46.01 E-value=82 Score=28.37 Aligned_cols=55 Identities=13% Similarity=0.180 Sum_probs=37.9
Q ss_pred EEEEEEEhHHHHHHHHHcCCCCEEEEEeEeeeeeeecCCCcEEEEEEEEEeEEEEccCC
Q psy14498 53 WHRITFYRKLAQIVKQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQMLGSR 111 (171)
Q Consensus 53 ~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l~~~~~~~kdG~~~~~~~i~a~~i~~l~~~ 111 (171)
.+.|++-.+.. ...+.|..|+.|.|+|.+..+.-. .|.+ ..+||.+++|.+|...
T Consensus 83 ~iQvVv~~~~~-~~~~~L~~ES~V~V~G~V~~~~~~--~~~~-~~iEl~v~~i~vl~~a 137 (572)
T PLN02221 83 NLQVMVDSSLY-DLSTLVATGTCVTVDGVLKVPPEG--KGTK-QKIELSVEKVIDVGTV 137 (572)
T ss_pred cEEEEEcCchh-hHHhcCCCceEEEEEEEEEeCCcc--CCCC-ccEEEEEeEEEEEecC
Confidence 57887754422 223358999999999999865431 1222 2789999999999743
No 144
>COG4085 Predicted RNA-binding protein, contains TRAM domain [General function prediction only]
Probab=44.80 E-value=47 Score=25.58 Aligned_cols=33 Identities=12% Similarity=0.177 Sum_probs=26.1
Q ss_pred EEEEEEEhHHHHHHHH-----HcCCCCEEEEEeEeeee
Q psy14498 53 WHRITFYRKLAQIVKQ-----YLKKGSQIYIEGRLQTR 85 (171)
Q Consensus 53 ~~~v~~~g~~A~~~~~-----~l~kG~~V~V~G~l~~~ 85 (171)
-+.+++|+..++.++. -+.+|+.|.|.|+....
T Consensus 82 ti~vva~~~tee~l~~n~~~p~~~eGe~veVtGrv~~y 119 (204)
T COG4085 82 TITVVASRSTEETLELNEGMPVTVEGEIVEVTGRVEEY 119 (204)
T ss_pred cEEEEEecChhHhHhhcCCCCccccCcEEEEEEEEEEe
Confidence 5689999998888772 27789999999987643
No 145
>COG1241 MCM2 Predicted ATPase involved in replication control, Cdc46/Mcm family [DNA replication, recombination, and repair]
Probab=44.54 E-value=1.4e+02 Score=27.48 Aligned_cols=58 Identities=14% Similarity=0.191 Sum_probs=42.7
Q ss_pred eceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEeeeeee-ec--CCCcEEEEEEEEEeEEEEccCC
Q psy14498 50 LTEWHRITFYRKLAQIVKQYLKKGSQIYIEGRLQTRKW-TN--KEGVEKYITEVIADNMQMLGSR 111 (171)
Q Consensus 50 ~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l~~~~~-~~--kdG~~~~~~~i~a~~i~~l~~~ 111 (171)
.+..+.|++++.++.. +..||+|.|.|-++.+.. .. ......+.+.+.+..|..+...
T Consensus 194 ~Prs~~vil~~dlv~~----~~pGdrV~itGi~~~~~~~~~~~~~~~~~~~~~~~a~~v~~~~~~ 254 (682)
T COG1241 194 LPRSIEVILEDDLVDS----VRPGDRVKITGVVRIVPSRSLSGRRKGPVFEIYLEANSVEKLDKR 254 (682)
T ss_pred CCceEEEEEecCcccc----cCCCCEEEEEEEEecccccccccccCCceEEEEEEEEEEEeccch
Confidence 4778899999988766 889999999998887752 21 1234466677778888777654
No 146
>PF08021 FAD_binding_9: Siderophore-interacting FAD-binding domain; InterPro: IPR013113 Proteins in this entry are siderophore-interacting FAD-binding proteins. This entry includes the vibriobactin utilization protein ViuB, which is involved in the removal of iron from iron-vibriobactin complexes, as well as several hypothetical proteins.; PDB: 2GPJ_A.
Probab=43.95 E-value=83 Score=21.76 Aligned_cols=30 Identities=10% Similarity=0.029 Sum_probs=20.5
Q ss_pred ceEEEEEEEhH--HHHHHHHHcCCCCEEEEEe
Q psy14498 51 TEWHRITFYRK--LAQIVKQYLKKGSQIYIEG 80 (171)
Q Consensus 51 ~~~~~v~~~g~--~A~~~~~~l~kG~~V~V~G 80 (171)
...|.+++.+. .|...+..++.||.|.|.|
T Consensus 81 ~l~iDfv~Hg~~Gpas~WA~~A~pGd~v~v~g 112 (117)
T PF08021_consen 81 ELDIDFVLHGDEGPASRWARSARPGDRVGVTG 112 (117)
T ss_dssp EEEEEEE--SS--HHHHHHHH--TT-EEEEEE
T ss_pred EEEEEEEECCCCCchHHHHhhCCCCCEEEEeC
Confidence 55788888875 6777778899999999998
No 147
>PF12080 GldM_C: GldM C-terminal domain; InterPro: IPR022719 This domain is found in bacteria at the C terminus of the GldM protein. This domain is typically between 169 to 182 amino acids in length and has two completely conserved residues (Y and N) that may be functionally important. GldM, is named for the member from Bacteriodetes Flavobacterium johnsoniae, which is required for a type of rapid gliding motility found in certain members of the Bacteriodetes [].
Probab=42.73 E-value=79 Score=23.82 Aligned_cols=22 Identities=27% Similarity=0.474 Sum_probs=16.8
Q ss_pred EhHHHHHHHHHcCCCCEEEEEe
Q psy14498 59 YRKLAQIVKQYLKKGSQIYIEG 80 (171)
Q Consensus 59 ~g~~A~~~~~~l~kG~~V~V~G 80 (171)
|...+..+...+++||+|+|.-
T Consensus 153 ~s~~~~~~l~~~~~Gd~i~I~~ 174 (181)
T PF12080_consen 153 FSARAKSALRKAKRGDRIYISD 174 (181)
T ss_pred ccHHHHHHHHhcCCCCEEEEEE
Confidence 4446667777799999999874
No 148
>CHL00010 infA translation initiation factor 1
Probab=42.64 E-value=91 Score=20.04 Aligned_cols=56 Identities=18% Similarity=0.185 Sum_probs=33.3
Q ss_pred CCCccEEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEE
Q psy14498 1 MASVNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIE 79 (171)
Q Consensus 1 M~~~N~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~ 79 (171)
|+--..+.+.|.|.+ ...+| .|.|.+. +| ..+.|.+-|++-.. .-.+..||.|.|+
T Consensus 1 m~~~~~~~~~G~Vik-----~lg~~----~y~V~~~-------~g------~~~~c~~rGklr~~-~i~~~vGD~V~ve 56 (78)
T CHL00010 1 MKKENKIEMEGLVTE-----SLPNG----MFRVRLD-------NG------CQVLGYISGKIRRN-SIRILPGDRVKVE 56 (78)
T ss_pred CCccceEEEEEEEEE-----EcCCC----EEEEEeC-------CC------CEEEEEeccceecC-CcccCCCCEEEEE
Confidence 666677888887754 33233 3455332 13 24567777765422 2226789999998
No 149
>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=41.79 E-value=32 Score=22.15 Aligned_cols=19 Identities=11% Similarity=0.207 Sum_probs=15.4
Q ss_pred HHHcCCCCEEEEEeEeeee
Q psy14498 67 KQYLKKGSQIYIEGRLQTR 85 (171)
Q Consensus 67 ~~~l~kG~~V~V~G~l~~~ 85 (171)
...++.||+|.|.|++...
T Consensus 42 ~~~~~~Gd~V~vtG~v~ey 60 (78)
T cd04486 42 GADVAVGDLVRVTGTVTEY 60 (78)
T ss_pred CCCCCCCCEEEEEEEEEee
Confidence 3459999999999998743
No 150
>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=40.75 E-value=44 Score=21.52 Aligned_cols=29 Identities=24% Similarity=0.275 Sum_probs=26.3
Q ss_pred eEEEEEEEhHHHHHHHHHcCCCCEEEEEe
Q psy14498 52 EWHRITFYRKLAQIVKQYLKKGSQIYIEG 80 (171)
Q Consensus 52 ~~~~v~~~g~~A~~~~~~l~kG~~V~V~G 80 (171)
.=+.+.++..+++.....|+.|....|++
T Consensus 31 ~~I~a~i~~~~~~~f~~~L~eg~vy~is~ 59 (86)
T cd04480 31 NRIHATIPKRLAAKFRPLLKEGKWYTISN 59 (86)
T ss_pred CEEEEEECHHHHHhhhhhceeCCEEEEee
Confidence 36789999999999999999999999996
No 151
>PRK12445 lysyl-tRNA synthetase; Reviewed
Probab=40.67 E-value=82 Score=27.83 Aligned_cols=36 Identities=17% Similarity=0.239 Sum_probs=28.6
Q ss_pred HHcCCCCEEEEEeEeeeeeeecCCCcEEEEEEEEEeEEEEccCC
Q psy14498 68 QYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQMLGSR 111 (171)
Q Consensus 68 ~~l~kG~~V~V~G~l~~~~~~~kdG~~~~~~~i~a~~i~~l~~~ 111 (171)
..|..||.|.|+|.+... +.| .++|.|.+|.+|...
T Consensus 114 ~~l~~Gd~V~v~G~~~~t----~~g----elel~~~~~~llsk~ 149 (505)
T PRK12445 114 KKWDLGDIIGARGTLFKT----QTG----ELSIHCTELRLLTKA 149 (505)
T ss_pred hcCCCCCEEEEEEEEEec----CCC----cEEEEEeEEEEEecC
Confidence 459999999999998753 334 488999999999643
No 152
>cd00392 Ribosomal_L13 Ribosomal protein L13. Protein L13, a large ribosomal subunit protein, is one of five proteins required for an early folding intermediate of 23S rRNA in the assembly of the large subunit. L13 is situated on the bottom of the large subunit, near the polypeptide exit site. It interacts with proteins L3 and L6, and forms an extensive network of interactions with 23S rRNA. L13 has been identified as a homolog of the human breast basic conserved protein 1 (BBC1), a protein identified through its increased expression in breast cancer. L13 expression is also upregulated in a variety of human gastrointestinal cancers, suggesting it may play a role in the etiology of a variety of human malignancies.
Probab=39.43 E-value=31 Score=24.12 Aligned_cols=14 Identities=29% Similarity=0.275 Sum_probs=12.0
Q ss_pred EhHHHHHHHHHcCC
Q psy14498 59 YRKLAQIVKQYLKK 72 (171)
Q Consensus 59 ~g~~A~~~~~~l~k 72 (171)
.|++|..++..|.-
T Consensus 11 lGRlAs~iA~~L~g 24 (114)
T cd00392 11 LGRLASKVAKLLLG 24 (114)
T ss_pred hHHHHHHHHHHHcC
Confidence 58899999998776
No 153
>PF10574 UPF0552: Uncharacterised protein family UPF0552; InterPro: IPR018889 This family of proteins has no known function.
Probab=39.07 E-value=97 Score=24.31 Aligned_cols=40 Identities=15% Similarity=0.231 Sum_probs=27.2
Q ss_pred cCCCCEEEEEeEeee---eeeecCCCcEEEEEEEEEeEEEEcc
Q psy14498 70 LKKGSQIYIEGRLQT---RKWTNKEGVEKYITEVIADNMQMLG 109 (171)
Q Consensus 70 l~kG~~V~V~G~l~~---~~~~~kdG~~~~~~~i~a~~i~~l~ 109 (171)
++.|+-|++||.|.- ..-.|..|++...+.|.++=-..+.
T Consensus 29 ~q~G~GvilEG~l~~~sRH~I~D~~~~k~Ry~vl~i~~~~~hr 71 (224)
T PF10574_consen 29 HQSGDGVILEGELVDVSRHSITDASGQKERYYVLYIRPSRIHR 71 (224)
T ss_pred hcCCCeEEEEEEEEeeeEEEEEcCCCCceEEEEEEEeechhhh
Confidence 899999999998865 4556778876555545544333333
No 154
>PF13511 DUF4124: Domain of unknown function (DUF4124)
Probab=38.32 E-value=24 Score=21.12 Aligned_cols=17 Identities=29% Similarity=0.710 Sum_probs=13.4
Q ss_pred eeeeeecCCCcEEEEEE
Q psy14498 83 QTRKWTNKEGVEKYITE 99 (171)
Q Consensus 83 ~~~~~~~kdG~~~~~~~ 99 (171)
...+|+|.+|..+|+-.
T Consensus 14 ~vYk~~D~~G~v~ysd~ 30 (60)
T PF13511_consen 14 EVYKWVDENGVVHYSDT 30 (60)
T ss_pred cEEEEECCCCCEEECcc
Confidence 55689999999877654
No 155
>PF00572 Ribosomal_L13: Ribosomal protein L13; InterPro: IPR005822 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L13 is one of the proteins from the large ribosomal subunit []. In Escherichia coli, L13 is known to be one of the early assembly proteins of the 50S ribosomal subunit.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 4A17_I 4A1E_I 4A1A_I 4A1C_I 3D5B_N 3MS1_J 1VSP_H 3PYT_J 3PYO_J 3PYV_J ....
Probab=37.70 E-value=29 Score=24.77 Aligned_cols=21 Identities=19% Similarity=0.322 Sum_probs=18.4
Q ss_pred EhHHHHHHHHHcC------------CCCEEEEE
Q psy14498 59 YRKLAQIVKQYLK------------KGSQIYIE 79 (171)
Q Consensus 59 ~g~~A~~~~~~l~------------kG~~V~V~ 79 (171)
-|++|..++..|. .||.|.|.
T Consensus 11 lGRLAs~iAk~L~GKhk~~y~p~~d~Gd~VvVi 43 (128)
T PF00572_consen 11 LGRLASKIAKLLLGKHKPTYTPNVDCGDHVVVI 43 (128)
T ss_dssp HHHHHHHHHHHHCTTSSTSSBTTSSTTEEEEEE
T ss_pred hHHHHHHHHHHHhCCCCCccCcCccCCCEEEEE
Confidence 4789999999999 89988876
No 156
>TIGR01066 rplM_bact ribosomal protein L13, bacterial type. This model distinguishes ribosomal protein L13 of bacteria and organelles from its eukarytotic and archaeal counterparts.
Probab=37.07 E-value=31 Score=25.09 Aligned_cols=30 Identities=20% Similarity=0.383 Sum_probs=22.7
Q ss_pred ceEEEEEE----EhHHHHHHHHHcC------------CCCEEEEEe
Q psy14498 51 TEWHRITF----YRKLAQIVKQYLK------------KGSQIYIEG 80 (171)
Q Consensus 51 ~~~~~v~~----~g~~A~~~~~~l~------------kG~~V~V~G 80 (171)
-.||=|-+ .|++|..++..|. .||.|.|.-
T Consensus 11 r~W~viDA~~~~lGRLAs~iAk~L~GKhKp~y~p~~d~Gd~VvViN 56 (140)
T TIGR01066 11 RKWYVVDAAGKTLGRLASEVARLLRGKHKPTYTPHVDCGDYVIVIN 56 (140)
T ss_pred ccEEEEeCCCCchHHHHHHHHHHHhccCCCccCCCccCCCEEEEEe
Confidence 34665544 5789999999988 799888764
No 157
>COG2087 CobU Adenosyl cobinamide kinase/adenosyl cobinamide phosphate guanylyltransferase [Coenzyme metabolism]
Probab=36.89 E-value=46 Score=25.10 Aligned_cols=31 Identities=13% Similarity=0.393 Sum_probs=28.4
Q ss_pred eceEEEEEEEhHHHHHHHHHcCCCCEEEEEe
Q psy14498 50 LTEWHRITFYRKLAQIVKQYLKKGSQIYIEG 80 (171)
Q Consensus 50 ~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G 80 (171)
...|..+..+-.+++.+......|+.|+|.+
T Consensus 53 p~~W~tvE~~~~l~~~L~~~~~~~~~VLvDc 83 (175)
T COG2087 53 PEHWRTVEAPLDLATLLEALIEPGDVVLVDC 83 (175)
T ss_pred CCcceEEeccccHHHHHHhcccCCCEEEEEc
Confidence 4779999999999999999888899999997
No 158
>COG1190 LysU Lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]
Probab=36.51 E-value=2.9e+02 Score=24.56 Aligned_cols=41 Identities=24% Similarity=0.346 Sum_probs=28.3
Q ss_pred HHHHHHHHcCCCCEEEEEeEeeeeeeecCCCcEEEEEEEEEeEEEEccC
Q psy14498 62 LAQIVKQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQMLGS 110 (171)
Q Consensus 62 ~A~~~~~~l~kG~~V~V~G~l~~~~~~~kdG~~~~~~~i~a~~i~~l~~ 110 (171)
..+...+.+..||.|.|+|.+-.. +.| .++|.|+.+.+|..
T Consensus 104 ~~~~~~~~~dlGDiigv~G~~~~T----~~G----elSv~v~~~~lLsK 144 (502)
T COG1190 104 VFEALFKKLDLGDIIGVEGPLFKT----KTG----ELSVSVEELRLLSK 144 (502)
T ss_pred hHHHHHhccccCCEEeeeeeeeec----CCC----ceEEEEEEEeeecc
Confidence 344455667889999999987543 445 35677777877753
No 159
>PTZ00425 asparagine-tRNA ligase; Provisional
Probab=36.48 E-value=1.2e+02 Score=27.40 Aligned_cols=58 Identities=19% Similarity=0.186 Sum_probs=35.4
Q ss_pred EEEEEEhHH-HHHHHHHcCCCCEEEEEeEeeeeeee--cCCCcEEEEEEEEE-----eEEEEccCC
Q psy14498 54 HRITFYRKL-AQIVKQYLKKGSQIYIEGRLQTRKWT--NKEGVEKYITEVIA-----DNMQMLGSR 111 (171)
Q Consensus 54 ~~v~~~g~~-A~~~~~~l~kG~~V~V~G~l~~~~~~--~kdG~~~~~~~i~a-----~~i~~l~~~ 111 (171)
+.|++-... +-.....|..|+.|.|+|.+..+.-. ++.|.....+||.+ .+|++|+..
T Consensus 115 iQiVv~~~~~~~~~l~~l~~gs~v~v~G~v~~~~~~~~n~~g~~~~~~El~~~~~~~~~~~ilg~~ 180 (586)
T PTZ00425 115 LQIIVDQSIENYEKLLKCGVGCCFRFTGKLIISPVQNENKKGLLKENVELALKDNSIHNFEIYGEN 180 (586)
T ss_pred eEEEECCchHHHHHHhcCCCccEEEEEEEEEcCCccccCcCCCCCccEEEEEecCCCceEEEEecc
Confidence 566654321 11223458999999999999876533 13343334467766 688888643
No 160
>COG3689 Predicted membrane protein [Function unknown]
Probab=35.82 E-value=74 Score=25.70 Aligned_cols=86 Identities=15% Similarity=0.140 Sum_probs=51.9
Q ss_pred EEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEeeee
Q psy14498 6 KVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEGRLQTR 85 (171)
Q Consensus 6 ~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l~~~ 85 (171)
++-++|-|-+|+.+.. |--.++||-|.|=- -|. | -+-..+-.. . ...++..++|.|+|+|...
T Consensus 177 ~Ie~tGFVy~~~~~~~--N~lflaRFgiicC~--ADa--~-------vygl~v~~~---~-~~~y~ndtWltvkGtl~~e 239 (271)
T COG3689 177 KIEFTGFVYNDESFPK--NYLFLARFGIICCA--ADA--G-------VYGLLVELD---N-QTDYKNDTWLTVKGTLSSE 239 (271)
T ss_pred eEEEEEEEECCCCCCc--ceeehhhhheeeee--ccc--e-------eEEEEEEcc---c-cccCCCCceEEEEeEEEee
Confidence 5677888887664421 22355666655421 111 1 112222221 1 2238999999999999999
Q ss_pred eeecCCCcEEEEEEEEEeEEEEccCC
Q psy14498 86 KWTNKEGVEKYITEVIADNMQMLGSR 111 (171)
Q Consensus 86 ~~~~kdG~~~~~~~i~a~~i~~l~~~ 111 (171)
.+.+. +..-..|.|++++.+..+
T Consensus 240 ~~~~~---~~~ipvi~v~sv~~I~kP 262 (271)
T COG3689 240 YLSDF---KKRIPVIEVDSVEVIPKP 262 (271)
T ss_pred ecCch---hhcCcEEEeeeeeecCCC
Confidence 88653 344566889999988655
No 161
>KOG0478|consensus
Probab=35.28 E-value=61 Score=29.95 Aligned_cols=34 Identities=12% Similarity=0.237 Sum_probs=28.1
Q ss_pred ceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEeeeeeee
Q psy14498 51 TEWHRITFYRKLAQIVKQYLKKGSQIYIEGRLQTRKWT 88 (171)
Q Consensus 51 ~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l~~~~~~ 88 (171)
++-+.|.+.+++++. ++.||+|.|+|-++.....
T Consensus 328 Phtv~v~~~~dLVD~----v~pGDrv~VTGi~ra~p~r 361 (804)
T KOG0478|consen 328 PHTVSVVLHNDLVDK----VRPGDRVEVTGILRATPVR 361 (804)
T ss_pred CceEEEEEehhhhhc----cCCCCeEEEEEEEEeEEec
Confidence 667888888887766 8999999999988876554
No 162
>PF05683 Fumerase_C: Fumarase C-terminus; InterPro: IPR004647 This entry represents various Fe-S type hydro-lyases, including the beta subunit from both L-tartrate dehydratase (TtdB; EC:4.2.1.32) and class 2 fumarate hydratase (FumC; (4.2.1.2 from EC) []. A number of Fe-S cluster-containing hydro-lyases share a conserved motif, including argininosuccinate lyase, adenylosuccinate lyase, aspartase, class I fumarate hydratase (fumarase), and tartrate dehydratase (see IPR000362 from INTERPRO). Proteins in this group represent a subset of closely related proteins or modules, including the Escherichia coli tartrate dehydratase beta chain and the C-terminal region of the class I fumarase (where the N-terminal region is homologous to the tartrate dehydratase alpha chain). The activity of the archaeal proteins in this group is unknown.; GO: 0016836 hydro-lyase activity; PDB: 2ISB_A.
Probab=34.46 E-value=80 Score=24.50 Aligned_cols=31 Identities=26% Similarity=0.404 Sum_probs=17.0
Q ss_pred EEEEEhHHHHHHHHHcCCCCEEEEEeEeeee
Q psy14498 55 RITFYRKLAQIVKQYLKKGSQIYIEGRLQTR 85 (171)
Q Consensus 55 ~v~~~g~~A~~~~~~l~kG~~V~V~G~l~~~ 85 (171)
.+.+--.+.+...+.|+.||.|+++|.|-+-
T Consensus 28 ~~~L~tPlt~e~i~~L~vGD~V~LsG~i~ta 58 (205)
T PF05683_consen 28 EIELTTPLTEEDIRKLKVGDTVYLSGTIYTA 58 (205)
T ss_dssp EEEEESS--HHHHHH--TT-EEEEEEEEEE-
T ss_pred EEEcCCCCCHHHHhhCCCCCEEEEeeEEEEE
Confidence 3333334444555559999999999998763
No 163
>PRK08395 fumarate hydratase; Provisional
Probab=33.73 E-value=62 Score=24.16 Aligned_cols=19 Identities=32% Similarity=0.494 Sum_probs=15.9
Q ss_pred HHHcCCCCEEEEEeEeeee
Q psy14498 67 KQYLKKGSQIYIEGRLQTR 85 (171)
Q Consensus 67 ~~~l~kG~~V~V~G~l~~~ 85 (171)
...|+.||.|+++|.|-+-
T Consensus 12 i~~L~~GD~V~LsG~i~ta 30 (162)
T PRK08395 12 VLKLKAGDVVYLSGIIYTA 30 (162)
T ss_pred HhhCCCCCEEEEEEEEEEE
Confidence 3459999999999998764
No 164
>PRK09216 rplM 50S ribosomal protein L13; Reviewed
Probab=33.40 E-value=38 Score=24.76 Aligned_cols=30 Identities=23% Similarity=0.393 Sum_probs=23.0
Q ss_pred ceEEEEEE----EhHHHHHHHHHcC------------CCCEEEEEe
Q psy14498 51 TEWHRITF----YRKLAQIVKQYLK------------KGSQIYIEG 80 (171)
Q Consensus 51 ~~~~~v~~----~g~~A~~~~~~l~------------kG~~V~V~G 80 (171)
..||=|-+ .|.+|..++..|. .||.|.|--
T Consensus 13 ~~W~viDA~~~~lGRlAs~IAk~L~GKhKp~y~p~~d~Gd~VvViN 58 (144)
T PRK09216 13 RKWYVIDAEGKVLGRLASEVASILRGKHKPTFTPHVDTGDFVIVIN 58 (144)
T ss_pred CCEEEEeCCCCchHHHHHHHHHHHhccCCCCcCCCCCCCCEEEEEe
Confidence 34766655 4779999999998 799888764
No 165
>COG1908 FrhD Coenzyme F420-reducing hydrogenase, delta subunit [Energy production and conversion]
Probab=33.29 E-value=46 Score=23.71 Aligned_cols=38 Identities=16% Similarity=0.316 Sum_probs=29.6
Q ss_pred eceEEEEEEEhH-HHHHHHHHcCCC-CEEEEEe-Eeeeeee
Q psy14498 50 LTEWHRITFYRK-LAQIVKQYLKKG-SQIYIEG-RLQTRKW 87 (171)
Q Consensus 50 ~~~~~~v~~~g~-~A~~~~~~l~kG-~~V~V~G-~l~~~~~ 87 (171)
..--++|.+-|+ .++.+++.|++| |-|+|.| ++-.-.|
T Consensus 29 ~vRiIrv~CsGrvn~~fvl~Al~~GaDGV~v~GC~~geCHy 69 (132)
T COG1908 29 NVRIIRVMCSGRVNPEFVLKALRKGADGVLVAGCKIGECHY 69 (132)
T ss_pred ceEEEEeeccCccCHHHHHHHHHcCCCeEEEecccccceee
Confidence 355688888888 899999999998 7888888 5554455
No 166
>TIGR01618 phage_P_loop phage nucleotide-binding protein. This model represents an uncharacterized family of proteins from a number of phage of Gram-positive bacteria. This protein contains a P-loop motif, G/A-X-X-G-X-G-K-T near its amino end. The function of this protein is unknown.
Probab=33.09 E-value=37 Score=26.54 Aligned_cols=46 Identities=17% Similarity=0.310 Sum_probs=34.2
Q ss_pred EEEEhHHHHHHHHH----cCCCCEEEEEeEeeeeeeecCCCc--EEEEEEEE
Q psy14498 56 ITFYRKLAQIVKQY----LKKGSQIYIEGRLQTRKWTNKEGV--EKYITEVI 101 (171)
Q Consensus 56 v~~~g~~A~~~~~~----l~kG~~V~V~G~l~~~~~~~kdG~--~~~~~~i~ 101 (171)
...||++.+.+... ...|--|++.++...+.+.+.+|+ .++...|.
T Consensus 112 ~~~yg~~~~~fl~~l~~L~~~g~nII~tAhe~~~~~~de~G~~~~r~~P~i~ 163 (220)
T TIGR01618 112 LQHYQKLDLWFLDLLTVLKESNKNIYATAWELTNQSSGESGQIYNRYQPDIR 163 (220)
T ss_pred cccHHHHHHHHHHHHHHHHhCCCcEEEEEeeccccccCCCCCCcceechhhh
Confidence 35577766666554 347999999999988889889999 66655554
No 167
>PRK06043 fumarate hydratase; Provisional
Probab=32.82 E-value=63 Score=24.81 Aligned_cols=19 Identities=32% Similarity=0.545 Sum_probs=15.9
Q ss_pred HHHcCCCCEEEEEeEeeee
Q psy14498 67 KQYLKKGSQIYIEGRLQTR 85 (171)
Q Consensus 67 ~~~l~kG~~V~V~G~l~~~ 85 (171)
...|+.||.|+++|.|-+-
T Consensus 14 i~~L~vGD~V~LsG~Iyta 32 (192)
T PRK06043 14 IEKLNVGDIVYISGEILTA 32 (192)
T ss_pred HhhCCCCCEEEEEEEEEEE
Confidence 3459999999999998764
No 168
>PRK06842 fumarate hydratase; Provisional
Probab=32.72 E-value=64 Score=24.64 Aligned_cols=19 Identities=32% Similarity=0.461 Sum_probs=15.9
Q ss_pred HHHcCCCCEEEEEeEeeee
Q psy14498 67 KQYLKKGSQIYIEGRLQTR 85 (171)
Q Consensus 67 ~~~l~kG~~V~V~G~l~~~ 85 (171)
...|+.||.|+++|.|-+-
T Consensus 14 i~~L~vGD~V~LsG~i~ta 32 (185)
T PRK06842 14 VKDLKAGDSVLISGYIYTA 32 (185)
T ss_pred HhhCCCCCEEEEeEEEEEE
Confidence 3459999999999998764
No 169
>PTZ00068 60S ribosomal protein L13a; Provisional
Probab=32.61 E-value=37 Score=26.29 Aligned_cols=22 Identities=27% Similarity=0.371 Sum_probs=19.7
Q ss_pred EhHHHHHHHHHcCCCCEEEEEe
Q psy14498 59 YRKLAQIVKQYLKKGSQIYIEG 80 (171)
Q Consensus 59 ~g~~A~~~~~~l~kG~~V~V~G 80 (171)
.|.+|..++..|.-||.|.|.-
T Consensus 15 LGRLAS~VAk~Ll~Gd~VVVVN 36 (202)
T PTZ00068 15 LGRLASVVAKELLLGQKIVVVR 36 (202)
T ss_pred HHHHHHHHHHHHhCCCEEEEEe
Confidence 6889999999999999998864
No 170
>PRK08228 L(+)-tartrate dehydratase subunit beta; Validated
Probab=31.99 E-value=66 Score=24.95 Aligned_cols=19 Identities=42% Similarity=0.552 Sum_probs=15.9
Q ss_pred HHHcCCCCEEEEEeEeeee
Q psy14498 67 KQYLKKGSQIYIEGRLQTR 85 (171)
Q Consensus 67 ~~~l~kG~~V~V~G~l~~~ 85 (171)
...|+.||.|+++|.|-+-
T Consensus 15 i~~L~vGD~V~LsG~Iyta 33 (204)
T PRK08228 15 LQDIKVGDVIYLTGTLVTC 33 (204)
T ss_pred HhhCCCCCEEEEEEEEEEE
Confidence 3459999999999998764
No 171
>TIGR00723 ttdB_fumA_fumB hydro-lyases, Fe-S type, tartrate/fumarate subfamily, beta region. A number of Fe-S cluster-containing hydro-lyases share a conserved motif, including argininosuccinate lyase, adenylosuccinate lyase, aspartase, class I fumarate hydratase (fumarase), and tartrate dehydratase. This model represents a subset of closely related proteins or modules, including the E. coli tartrate dehydratase beta chain and the C-terminal region of the class I fumarase (where the N-terminal region is homologous to the tartrate dehydratase alpha chain). The activity of archaeal proteins in this subfamily has not been established.
Probab=31.62 E-value=56 Score=24.54 Aligned_cols=18 Identities=33% Similarity=0.547 Sum_probs=15.4
Q ss_pred HHcCCCCEEEEEeEeeee
Q psy14498 68 QYLKKGSQIYIEGRLQTR 85 (171)
Q Consensus 68 ~~l~kG~~V~V~G~l~~~ 85 (171)
..|+.||.|+++|.|-+-
T Consensus 4 ~~L~vGD~V~LsG~i~ta 21 (168)
T TIGR00723 4 LKLKVGDVVYLTGTIFTA 21 (168)
T ss_pred HhCCCCCEEEEEEEEEEE
Confidence 349999999999998764
No 172
>PF02751 TFIIA_gamma_C: Transcription initiation factor IIA, gamma subunit; InterPro: IPR015871 Transcription factor IIA (TFIIA) is one of several factors that form part of a transcription pre-initiation complex along with RNA polymerase II, the TATA-box-binding protein (TBP) and TBP-associated factors, on the TATA-box sequence upstream of the initiation start site. After initiation, some components of the pre-initiation complex (including TFIIA) remain attached and re-initiate a subsequent round of transcription. TFIIA binds to TBP to stabilise TBP binding to the TATA element. TFIIA also inhibits the cytokine HMGB1 (high mobility group 1 protein) binding to TBP [], and can dissociate HMGB1 already bound to TBP/TATA-box. Human and Drosophila TFIIA have three subunits: two large subunits, LN/alpha and LC/beta, derived from the same gene, and a small subunit, S/gamma. Yeast TFIIA has two subunits: a large TOA1 subunit that shows sequence similarity to the N-terminal of LN/alpha and the C-terminal of LC/beta, and a small subunit, TOA2 that is highly homologous with S/gamma. The conserved regions of the large and small subunits of TFIIA combine to form two domains: a four-helix bundle (helical domain) composed of two helices from each of the N-terminal regions of TOA1 and TOA2 in yeast; and a beta-barrel (beta-barrel domain) composed of beta-sheets from the C-terminal regions of TOA1 and TOA2 []. This entry represents the beta-barrel domain found at the C-terminal of the gamma subunit of transcription factor TFIIA. ; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005672 transcription factor TFIIA complex; PDB: 1NVP_D 1RM1_B 1YTF_D 1NH2_D.
Probab=30.62 E-value=1.2e+02 Score=18.06 Aligned_cols=30 Identities=17% Similarity=0.369 Sum_probs=23.1
Q ss_pred CEEEEEeEeeeeeeecCCCcEEEEEEEEEeEEEEcc
Q psy14498 74 SQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQMLG 109 (171)
Q Consensus 74 ~~V~V~G~l~~~~~~~kdG~~~~~~~i~a~~i~~l~ 109 (171)
+++.+.|+|.+.++-|. .+.+++.+++|-.
T Consensus 4 ~k~~fKG~L~tYrfcDn------VWTFi~kn~~fk~ 33 (52)
T PF02751_consen 4 NKLSFKGHLDTYRFCDN------VWTFILKNVEFKM 33 (52)
T ss_dssp -EEEEEEEEEEEEEETT------EEEEEEEEEEEEE
T ss_pred eeEEEEEeeeEEEeeCc------EEEEEEcCEEEEE
Confidence 46889999999998753 7777888777754
No 173
>PF07378 FlbT: Flagellar protein FlbT; InterPro: IPR009967 This family consists of several FlbT proteins. FlbT is a post-transcriptional repressor function in flagellum biogenesis. FlbT is associated with the 5' untranslated region (UTR) of fljK (25 kDa flagellin) mRNA and that this association requires a predicted loop structure in the transcript. Mutations within this loop abolish FlbT association and result in increased mRNA stability. It is therefore thought that FlbT promotes the degradation of flagellin mRNA by associating with the 5' UTR [].; GO: 0048027 mRNA 5'-UTR binding, 0006402 mRNA catabolic process, 0045718 negative regulation of flagellum assembly
Probab=30.33 E-value=64 Score=22.97 Aligned_cols=34 Identities=29% Similarity=0.471 Sum_probs=24.9
Q ss_pred cCCCCEEEEEeEeeeeeeecCCCcEEEEEEEEEeEEEEccC
Q psy14498 70 LKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQMLGS 110 (171)
Q Consensus 70 l~kG~~V~V~G~l~~~~~~~kdG~~~~~~~i~a~~i~~l~~ 110 (171)
|++|.+|+|.|-+- +||..+.+++|.-+ ..||--
T Consensus 5 LkpgERi~INGAVi------~N~drr~~l~i~n~-a~~Lre 38 (126)
T PF07378_consen 5 LKPGERIIINGAVI------RNGDRRSTLEIEND-APFLRE 38 (126)
T ss_pred ecCCCEEEEcCeEE------EeCCCceEEEEecC-Cceech
Confidence 89999999999865 35556677776655 666643
No 174
>PF06557 DUF1122: Protein of unknown function (DUF1122); InterPro: IPR008304 There are currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.; PDB: 2ARH_C.
Probab=30.22 E-value=89 Score=23.42 Aligned_cols=60 Identities=17% Similarity=0.403 Sum_probs=28.6
Q ss_pred EEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEE---------EhH-----HHHHHHHHcCCCCEE
Q psy14498 11 GNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITF---------YRK-----LAQIVKQYLKKGSQI 76 (171)
Q Consensus 11 G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~---------~g~-----~A~~~~~~l~kG~~V 76 (171)
||+...-.+...-+++.++...|-.-|.|. .-|+.|.- |+. +-+.+..+|.+|+++
T Consensus 13 Grf~Ee~n~~l~~~~~~l~~~kvF~GR~yY----------~pW~EiFni~p~~~~~~~~s~~E~~l~~~~~~~l~pg~~l 82 (170)
T PF06557_consen 13 GRFKEEVNFELYLGGRHLCHVKVFFGRPYY----------RPWAEIFNINPWLRVVFFGSPLEDELYKLFSRYLEPGGRL 82 (170)
T ss_dssp -SSTTEEEEEEEETTEEEEEEEEE--BTTB------------EEEEE---GGGHHHHTTSHHHHHHHHHHHTT----SEE
T ss_pred CcccceeeEEEEECCeeEEEEEEecCCCCC----------cchheeecccchhcccccCChHHHHHHHHHHHHhhhcCeE
Confidence 333333333333367777777777766533 44655521 122 445667789999999
Q ss_pred EEEe
Q psy14498 77 YIEG 80 (171)
Q Consensus 77 ~V~G 80 (171)
+|+-
T Consensus 83 fVeY 86 (170)
T PF06557_consen 83 FVEY 86 (170)
T ss_dssp EEE-
T ss_pred EEEE
Confidence 9984
No 175
>CHL00159 rpl13 ribosomal protein L13; Validated
Probab=30.18 E-value=46 Score=24.28 Aligned_cols=30 Identities=20% Similarity=0.408 Sum_probs=23.1
Q ss_pred ceEEEEEE----EhHHHHHHHHHcC------------CCCEEEEEe
Q psy14498 51 TEWHRITF----YRKLAQIVKQYLK------------KGSQIYIEG 80 (171)
Q Consensus 51 ~~~~~v~~----~g~~A~~~~~~l~------------kG~~V~V~G 80 (171)
..|+=|-+ .|++|..++..|. -||.|+|.-
T Consensus 14 r~W~viDA~~~~lGRlAs~iA~~L~GKhKp~ytP~~d~Gd~VVViN 59 (143)
T CHL00159 14 RKWYIIDAKDQTLGRLATKIASLLRGKNKPSYHPSVDTGDYVIVIN 59 (143)
T ss_pred CCEEEEeCCCCchHHHHHHHHHHHhccCCCCcCCCcCCCCEEEEEe
Confidence 44766655 4679999999988 799888764
No 176
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=29.10 E-value=63 Score=21.97 Aligned_cols=23 Identities=26% Similarity=0.309 Sum_probs=16.5
Q ss_pred HHHHHHHcCCCCEEEEEeEeeee
Q psy14498 63 AQIVKQYLKKGSQIYIEGRLQTR 85 (171)
Q Consensus 63 A~~~~~~l~kG~~V~V~G~l~~~ 85 (171)
-+.+.+.|+|||.|.-.|=|.-.
T Consensus 37 ~~~ml~sL~kGD~VvT~gGi~G~ 59 (97)
T COG1862 37 HQELLNSLKKGDEVVTIGGIVGT 59 (97)
T ss_pred HHHHHHhccCCCEEEEcCCeEEE
Confidence 34556679999999988755443
No 177
>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=29.07 E-value=1.1e+02 Score=20.18 Aligned_cols=32 Identities=25% Similarity=0.191 Sum_probs=27.0
Q ss_pred ceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEe
Q psy14498 51 TEWHRITFYRKLAQIVKQYLKKGSQIYIEGRL 82 (171)
Q Consensus 51 ~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l 82 (171)
..=+.+.+..+++..+...|++|+...++=-.
T Consensus 9 G~~I~A~I~~~~~~~f~~~l~Eg~~y~i~~F~ 40 (95)
T PF02721_consen 9 GDKIQATIPKELVDKFKDSLKEGSWYTISNFT 40 (95)
T ss_pred CCEEEEEECHHHHHHHHhhcccCCEEEeEeEE
Confidence 34578888999999999999999999998643
No 178
>TIGR03853 matur_matur probable metal-binding protein. This protein family was identified by searching with a phylogenetic profile based on an anaerobic sulfatase-maturase enzyme, which contains multiple 4Fe-4S clusters. The linkages by phylogenetic profiling and by iron-sulfur cluster-related motifs together suggest this protein may be an accessory protein to certain maturases in sulfatase/maturase systems.
Probab=29.02 E-value=46 Score=21.67 Aligned_cols=36 Identities=28% Similarity=0.310 Sum_probs=27.8
Q ss_pred eceEEEEEEEhHHHHHHHHH-cCCCCEEEEEeEeeee
Q psy14498 50 LTEWHRITFYRKLAQIVKQY-LKKGSQIYIEGRLQTR 85 (171)
Q Consensus 50 ~~~~~~v~~~g~~A~~~~~~-l~kG~~V~V~G~l~~~ 85 (171)
...||.|.+=+=.|+.+.++ +.||..|..+|-+.++
T Consensus 34 ~arFhTCSa~~m~a~~Li~FL~~kgKfi~~~~gft~~ 70 (77)
T TIGR03853 34 DARFHTCSAEGMTADELLQFLLKKGKFIESDGGFTTN 70 (77)
T ss_pred CceEeecccccCCHHHHHHHHHHCCCEeecCCcEEEC
Confidence 58899999988766666655 7899998887766554
No 179
>PF03734 YkuD: L,D-transpeptidase catalytic domain; InterPro: IPR005490 This family of proteins are found in a range of bacteria. The conserved region contains a conserved histidine and cysteine, suggesting that these proteins have an enzymatic activity. Several members of this family contain peptidoglycan binding domains. So these proteins may use peptidoglycan or a precursor as a substrate. The molecular structure of YkuD protein shows this domain has a novel tertiary fold consisting of a beta-sandwich with two mixed sheets, one containing five strands and the other, six strands. The two beta-sheets form a cradle capped by an alpha-helix. This domain contains a putative catalytic site with a tetrad of invariant His123, Gly124, Cys139, and Arg141. The stereochemistry of this active site shows similarities to peptidotransferases and sortases, and suggests that the enzymes of this family may play an important role in cell wall biology. This family was formerly called the ErfK/YbiS/YcfS/YnhG family, but is now named after the first protein of known structure.; GO: 0016740 transferase activity; PDB: 3ZQD_A 1Y7M_B 4A52_A 2HKL_C 1ZAT_A.
Probab=28.79 E-value=72 Score=22.05 Aligned_cols=25 Identities=16% Similarity=0.171 Sum_probs=18.6
Q ss_pred EEEEEE-hHHHHHHHHHcCCCCEEEE
Q psy14498 54 HRITFY-RKLAQIVKQYLKKGSQIYI 78 (171)
Q Consensus 54 ~~v~~~-g~~A~~~~~~l~kG~~V~V 78 (171)
|-|+-. ...|+.+.+.+..|+.|.|
T Consensus 119 ~GCIrl~~~d~~~l~~~v~~gt~V~I 144 (144)
T PF03734_consen 119 HGCIRLSNEDAKWLYDNVPVGTPVII 144 (144)
T ss_dssp SSSEEE-HHHHHHHHHHS-TTEEEEE
T ss_pred CCEeccCHHHHHHHHhhCCCCCEEeC
Confidence 344444 4589999999999999987
No 180
>PRK12791 flbT flagellar biosynthesis repressor FlbT; Reviewed
Probab=27.31 E-value=72 Score=22.92 Aligned_cols=34 Identities=15% Similarity=0.093 Sum_probs=25.9
Q ss_pred cCCCCEEEEEeEeeeeeeecCCCcEEEEEEEEEeEEEEccC
Q psy14498 70 LKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQMLGS 110 (171)
Q Consensus 70 l~kG~~V~V~G~l~~~~~~~kdG~~~~~~~i~a~~i~~l~~ 110 (171)
|+.|-+|+|.|-+- +||..+.+++| -.+..||.-
T Consensus 7 LKP~ERi~INGaVi------~Ngdrr~~l~i-~n~a~iLre 40 (131)
T PRK12791 7 LKPFERIVIGQSVI------TNSDTRARFLI-DGDAPILRE 40 (131)
T ss_pred eCCCCEEEEcCEEE------EeCCcceEEEE-eCCCceehh
Confidence 89999999999875 35666777777 666777743
No 181
>PF03658 Ub-RnfH: RnfH family Ubiquitin; InterPro: IPR005346 This is a small family of proteins of unknown function.; PDB: 2HJ1_B.
Probab=26.85 E-value=26 Score=23.19 Aligned_cols=30 Identities=20% Similarity=0.459 Sum_probs=13.1
Q ss_pred EEEEEEhHHHHHHHHHcCCCCEEEEEeEeee
Q psy14498 54 HRITFYRKLAQIVKQYLKKGSQIYIEGRLQT 84 (171)
Q Consensus 54 ~~v~~~g~~A~~~~~~l~kG~~V~V~G~l~~ 84 (171)
+.|=+||+.+. +..-|+.||+|.|-=-|..
T Consensus 47 ~~vGIfGk~~~-~d~~L~~GDRVEIYRPL~~ 76 (84)
T PF03658_consen 47 NKVGIFGKLVK-LDTVLRDGDRVEIYRPLTA 76 (84)
T ss_dssp SEEEEEE-S---TT-B--TT-EEEEE-S---
T ss_pred ceeeeeeeEcC-CCCcCCCCCEEEEeccCcc
Confidence 46777888664 4444888888887654443
No 182
>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=26.31 E-value=1.5e+02 Score=20.23 Aligned_cols=54 Identities=17% Similarity=0.227 Sum_probs=37.5
Q ss_pred eceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEeeeeeeecCCCcEEEEEEEEEeEEEEc
Q psy14498 50 LTEWHRITFYRKLAQIVKQYLKKGSQIYIEGRLQTRKWTNKEGVEKYITEVIADNMQML 108 (171)
Q Consensus 50 ~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l~~~~~~~kdG~~~~~~~i~a~~i~~l 108 (171)
.-.++-|.+|..+.+.+.+-+.|...++....|+.|+.. ..| .....|-++...
T Consensus 26 ~~nll~vkfw~~l~~~~~EDvvk~~~lia~SNLQwR~~s-~~~----iPtl~Age~t~F 79 (100)
T cd04495 26 CLNLLCVKFWSSLEQYAYEDVVKRRVLLAASNLQWRTES-TSG----VPTLFAGEYSTF 79 (100)
T ss_pred CcCEEEEEEecchHHhhhhhhcccceEEEEecceEeccc-cCC----Cceeeeecceee
Confidence 367899999999999888888888777777778877654 223 334445555444
No 183
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=25.65 E-value=89 Score=28.36 Aligned_cols=77 Identities=17% Similarity=0.232 Sum_probs=53.6
Q ss_pred EEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEeeee
Q psy14498 6 KVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEGRLQTR 85 (171)
Q Consensus 6 ~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l~~~ 85 (171)
.|.|.|.|++ ++.|+ |= +-|+|- ++|-++.+.+|.....++.-.+..|+.|.|.|....+
T Consensus 215 tV~I~GeV~q---ikqT~-GP--TVFtlt--------------Detg~i~aAAFe~aGvRAyP~IevGdiV~ViG~V~~r 274 (715)
T COG1107 215 TVRIEGEVTQ---IKQTS-GP--TVFTLT--------------DETGAIWAAAFEEAGVRAYPEIEVGDIVEVIGEVTRR 274 (715)
T ss_pred eEEEEEEEEE---EEEcC-CC--EEEEEe--------------cCCCceehhhhccCCcccCCCCCCCceEEEEEEEeec
Confidence 5778888874 66664 32 236552 1355777889988888888889999999999998654
Q ss_pred eeecCCCcEEEEEEEEEeEEEEccCC
Q psy14498 86 KWTNKEGVEKYITEVIADNMQMLGSR 111 (171)
Q Consensus 86 ~~~~kdG~~~~~~~i~a~~i~~l~~~ 111 (171)
+|+ +.|.+..++.|...
T Consensus 275 -----~g~----lQiE~~~me~L~G~ 291 (715)
T COG1107 275 -----DGR----LQIEIEAMEKLTGD 291 (715)
T ss_pred -----CCc----EEEeehhhHHhhCc
Confidence 554 44556667766543
No 184
>TIGR00739 yajC preprotein translocase, YajC subunit. While this protein is part of the preprotein translocase in Escherichia coli, it is not essential for viability or protein secretion. The N-terminus region contains a predicted membrane-spanning region followed by a region consisting almost entirely of residues with charged (acidic, basic, or zwitterionic) side chains. This small protein is about 100 residues in length, and is restricted to bacteria; however, this protein is absent from some lineages, including spirochetes and Mycoplasmas.
Probab=24.56 E-value=81 Score=20.66 Aligned_cols=23 Identities=22% Similarity=0.309 Sum_probs=16.9
Q ss_pred HHHHHHcCCCCEEEEEeEeeeee
Q psy14498 64 QIVKQYLKKGSQIYIEGRLQTRK 86 (171)
Q Consensus 64 ~~~~~~l~kG~~V~V~G~l~~~~ 86 (171)
+.+.+.|++||.|.-.|=+.-..
T Consensus 32 ~~m~~~L~~Gd~VvT~gGi~G~V 54 (84)
T TIGR00739 32 KKLIESLKKGDKVLTIGGIIGTV 54 (84)
T ss_pred HHHHHhCCCCCEEEECCCeEEEE
Confidence 35566699999999887665543
No 185
>PRK03065 hutP anti-terminator HutP; Provisional
Probab=24.36 E-value=1.2e+02 Score=22.22 Aligned_cols=30 Identities=17% Similarity=0.375 Sum_probs=20.8
Q ss_pred EEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHH
Q psy14498 28 VTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLA 63 (171)
Q Consensus 28 ~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A 63 (171)
-++|.|.....|.... +.+|+-|-+||+.+
T Consensus 101 glk~aIVrg~~~~~~~------dg~WIaVa~yG~~~ 130 (148)
T PRK03065 101 GLRFAIVRGTPYDGKK------EGEWIAVALYGTIG 130 (148)
T ss_pred ceEEEEEecCCCCCCC------CCcEEEEEEecccc
Confidence 3566666666665543 46799999999854
No 186
>KOG3108|consensus
Probab=23.46 E-value=71 Score=25.80 Aligned_cols=35 Identities=14% Similarity=0.088 Sum_probs=26.5
Q ss_pred ceEEEEEEEhHHHHHH--HHHcCCCCEEEEEeEeeee
Q psy14498 51 TEWHRITFYRKLAQIV--KQYLKKGSQIYIEGRLQTR 85 (171)
Q Consensus 51 ~~~~~v~~~g~~A~~~--~~~l~kG~~V~V~G~l~~~ 85 (171)
+-++.|..|-...... ...|.+|..|.|.|.|+.-
T Consensus 95 tg~id~r~W~~~~~~~~e~~~l~~~~yVkv~G~Lk~f 131 (265)
T KOG3108|consen 95 TGQIDVRQWFHDNAESEEMPALETGTYVKVYGHLKPF 131 (265)
T ss_pred cccEEEEEeccccchhhhCcccccCcEEEeeecccCC
Confidence 6679999996633333 3359999999999999853
No 187
>COG3649 CRISPR system related protein [Defense mechanisms]
Probab=22.80 E-value=55 Score=25.79 Aligned_cols=34 Identities=24% Similarity=0.370 Sum_probs=25.8
Q ss_pred ceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEeeeeeee
Q psy14498 51 TEWHRITFYRKLAQIVKQYLKKGSQIYIEGRLQTRKWT 88 (171)
Q Consensus 51 ~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l~~~~~~ 88 (171)
..|+.|.+||. +.-+++||..+.|.|-++.+--+
T Consensus 99 q~w~DvR~FGq----Vf~~~kk~ms~gvrGPVsi~~at 132 (283)
T COG3649 99 QKWIDVRLFGQ----VFPQSKKGMSSGVRGPVSIRYAT 132 (283)
T ss_pred HHHhhHHHhhh----hhhhhccCcccccccceEEEeec
Confidence 45899988885 44558999999999977765433
No 188
>PF05037 DUF669: Protein of unknown function (DUF669); InterPro: IPR007731 This entry is represented by Streptococcus phage Sfi11, Gp151. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=22.65 E-value=97 Score=22.17 Aligned_cols=36 Identities=11% Similarity=0.175 Sum_probs=26.4
Q ss_pred CCeEEEecC-CcEEEEEEEEEecccccCCCCeeeeeceEEEEEE
Q psy14498 16 DPETRYMSN-GDAVTNVSIATTENWRDKNSGEKRELTEWHRITF 58 (171)
Q Consensus 16 dp~~~~~~~-g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~ 58 (171)
..+++.+++ |...+.|.+.+.+. +...+..|+++.+
T Consensus 27 ~~e~~~tk~~G~~~l~~~~~I~~g-------~~~Gr~if~~~~~ 63 (141)
T PF05037_consen 27 KAEEKATKNNGNEMLSFDFEIRDG-------EYKGRKIFDNNWV 63 (141)
T ss_pred EeEEeecccCCCceEEEEEEEecC-------CcCCcEehhhhcc
Confidence 467888887 88999999988753 3333567777777
No 189
>PRK05800 cobU adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated
Probab=22.23 E-value=90 Score=23.08 Aligned_cols=30 Identities=13% Similarity=0.352 Sum_probs=26.6
Q ss_pred ceEEEEEEEhHHHHHHHHHcCCCCEEEEEe
Q psy14498 51 TEWHRITFYRKLAQIVKQYLKKGSQIYIEG 80 (171)
Q Consensus 51 ~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G 80 (171)
..|..++...++++.+..+..+|..|.|.+
T Consensus 55 ~~w~t~E~~~~l~~~i~~~~~~~~~VlID~ 84 (170)
T PRK05800 55 AHWQTVEEPLDLAELLRADAAPGRCVLVDC 84 (170)
T ss_pred CCCeEecccccHHHHHHhhcCCCCEEEehh
Confidence 569999999999999888788899999987
No 190
>PLN00205 ribisomal protein L13 family protein; Provisional
Probab=22.15 E-value=79 Score=24.26 Aligned_cols=30 Identities=17% Similarity=0.326 Sum_probs=22.4
Q ss_pred ceEEEEEE----EhHHHHHHHHHcC------------CCCEEEEEe
Q psy14498 51 TEWHRITF----YRKLAQIVKQYLK------------KGSQIYIEG 80 (171)
Q Consensus 51 ~~~~~v~~----~g~~A~~~~~~l~------------kG~~V~V~G 80 (171)
-.||=|-+ .|.+|..++..|. -||.|+|.-
T Consensus 15 r~W~VIDA~~~iLGRLAS~IAk~L~GKhKP~ytP~~D~GD~VVVIN 60 (191)
T PLN00205 15 LRWRVFDAKGQVLGRLASQISTVLQGKDKPTYAPNRDDGDICIVLN 60 (191)
T ss_pred CcEEEEeCCCCchHHHHHHHHHHHhccCCCCcCCCcCCCCEEEEEe
Confidence 34666555 4779999999988 698887754
No 191
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=22.09 E-value=2.3e+02 Score=18.88 Aligned_cols=58 Identities=10% Similarity=0.119 Sum_probs=31.9
Q ss_pred CCCccEEEEEEEeCCCCeEEEecCCcEEEEEEEEEecccccCCCCeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEe
Q psy14498 1 MASVNKVIIIGNLGRDPETRYMSNGDAVTNVSIATTENWRDKNSGEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEG 80 (171)
Q Consensus 1 M~~~N~v~l~G~l~~dp~~~~~~~g~~~~~~~la~~~~~~~~~~G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G 80 (171)
|+--..+.+.|.|.. ..+++ .|.|.+.. |. -+-+-+-|++-..-.. +..||.|.|+=
T Consensus 1 M~ke~~ie~~G~V~e-----~Lp~~----~frV~Len-------G~------~vla~isGKmR~~rIr-Il~GD~V~VE~ 57 (87)
T PRK12442 1 MAKEELIELDGIVDE-----VLPDS----RFRVTLEN-------GV------EVGAYASGRMRKHRIR-ILAGDRVTLEL 57 (87)
T ss_pred CCccceEEEEEEEEE-----ECCCC----EEEEEeCC-------CC------EEEEEeccceeeeeEE-ecCCCEEEEEE
Confidence 555567888888765 33444 57776652 32 1223333543221111 67899999874
Q ss_pred E
Q psy14498 81 R 81 (171)
Q Consensus 81 ~ 81 (171)
.
T Consensus 58 s 58 (87)
T PRK12442 58 S 58 (87)
T ss_pred C
Confidence 4
No 192
>PF11434 CHIPS: Chemotaxis-inhibiting protein CHIPS; InterPro: IPR020986 Chemotaxis inhibitory protein (also knows as CHIPS) is a Staphylococcus aureus-secreted virulence factor that impairs the response of neutrophils and monocytes to FPR and C5a []. CHIPS has been shown to reduce neutrophil recruitment toward C5a in mouse models (its activity is more potent on human than on mouse cells). As such, its properties may make it a candidate new anti-inflammatory therapeutic compound []. CHIPS also plays an key role in bacterial invasion, by inhibiting FMLP- and C5a-induced calcium moblisation []. By influencing 2 related receptors with very different ligand specificities (C5aR and FPR), the protein has a unique role; nevertheless, neither the manner in which it binds such structurally different molecules nor how its expression is regulated are currently unknown []. The structure of a CHIPS fragment (residues 31-121) has been solved by NMR spectroscopy []. This fragment has the same activity in blocking the C5aR relative to full-length CHIPS, but lacks FPR antagonism []. The protein has a compact fold comprising 2 short alpha-helices packed onto a 4-stranded anti-parallel beta-sheet: strands-2 and -3 are joined by a loop with a well-defined conformation []. The protein shares a high degree of structural similarity with a number of proteins, including the C-terminal domain of staphylococcal superantigen-like proteins (SSLs) 5 and 7, staphyloccocal and streptococcal superantigens TSST-1 and SPE-C, and various domains of the staphylococcal extracellullar adherence protein (EAP) [].; PDB: 2K3U_A 1XEE_A.
Probab=21.88 E-value=42 Score=21.36 Aligned_cols=18 Identities=39% Similarity=0.656 Sum_probs=14.5
Q ss_pred EhHHHHHHHHHcCCCCEE
Q psy14498 59 YRKLAQIVKQYLKKGSQI 76 (171)
Q Consensus 59 ~g~~A~~~~~~l~kG~~V 76 (171)
.|++-|++.++|+||..-
T Consensus 8 lgklderlrnylkkgtkn 25 (91)
T PF11434_consen 8 LGKLDERLRNYLKKGTKN 25 (91)
T ss_dssp HHHHHHHHHHHHHCC-S-
T ss_pred hHHHHHHHHHHHHhcccc
Confidence 588999999999999753
No 193
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=21.86 E-value=94 Score=21.37 Aligned_cols=23 Identities=17% Similarity=0.313 Sum_probs=16.3
Q ss_pred HHHHHHcCCCCEEEEEeEeeeee
Q psy14498 64 QIVKQYLKKGSQIYIEGRLQTRK 86 (171)
Q Consensus 64 ~~~~~~l~kG~~V~V~G~l~~~~ 86 (171)
+.+.+.|++||.|.-.|=|.-..
T Consensus 47 ~~~~~~Lk~Gd~VvT~gGi~G~V 69 (106)
T PRK05585 47 KKMLSSLAKGDEVVTNGGIIGKV 69 (106)
T ss_pred HHHHHhcCCCCEEEECCCeEEEE
Confidence 45566699999997776555443
No 194
>PF03983 SHD1: SLA1 homology domain 1, SHD1 ; InterPro: IPR007131 The SLA1 homology domain is found in the cytoskeleton assembly control protein SLA1, which is responsible for the correct formation of the actin cytoskeleton.; GO: 0008092 cytoskeletal protein binding, 0030674 protein binding, bridging, 0042802 identical protein binding, 0043130 ubiquitin binding; PDB: 2HBP_A.
Probab=21.19 E-value=1.3e+02 Score=19.12 Aligned_cols=27 Identities=26% Similarity=0.521 Sum_probs=14.0
Q ss_pred eeeeeecCCCcEEEEEEEEE---eEEEEcc
Q psy14498 83 QTRKWTNKEGVEKYITEVIA---DNMQMLG 109 (171)
Q Consensus 83 ~~~~~~~kdG~~~~~~~i~a---~~i~~l~ 109 (171)
..|.|+|++|.-+-..+++. ..|.+..
T Consensus 11 ~~RtWtD~tG~f~VeA~fv~~~dgkV~L~k 40 (70)
T PF03983_consen 11 KTRTWTDRTGKFKVEAEFVGVNDGKVHLHK 40 (70)
T ss_dssp -SEEEEBSSS--EEEEEEEEEETTEEEEE-
T ss_pred cceEEEeCCCCEEEEEEEEEeeCCEEEEEe
Confidence 57899999998443333332 2455543
No 195
>KOG1496|consensus
Probab=20.03 E-value=97 Score=25.09 Aligned_cols=39 Identities=13% Similarity=0.284 Sum_probs=33.2
Q ss_pred CeeeeeceEEEEEEEhHHHHHHHHHcCCCCEEEEEeEee
Q psy14498 45 GEKRELTEWHRITFYRKLAQIVKQYLKKGSQIYIEGRLQ 83 (171)
Q Consensus 45 G~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G~l~ 83 (171)
|-.+.+..-.+|.+|..++..+.+|.++..+|+|.|...
T Consensus 95 GMERkDll~~NvkIfk~Qg~AL~k~A~~~~KVlVVgNPa 133 (332)
T KOG1496|consen 95 GMERKDLLSANVKIFKSQGAALEKYAKPNVKVLVVGNPA 133 (332)
T ss_pred cchhhhHHhhcceeehhhhHHHHHhcCCCceEEEecCcc
Confidence 655456667899999999999999999999999999654
No 196
>smart00110 C1Q Complement component C1q domain. Globular domain found in many collagens and eponymously in complement C1q. When part of full length proteins these domains form a 'bouquet' due to the multimerization of heterotrimers. The C1q fold is similar to that of tumour necrosis factor.
Probab=20.01 E-value=70 Score=22.83 Aligned_cols=13 Identities=31% Similarity=0.631 Sum_probs=10.9
Q ss_pred HcCCCCEEEEEeE
Q psy14498 69 YLKKGSQIYIEGR 81 (171)
Q Consensus 69 ~l~kG~~V~V~G~ 81 (171)
.|++||.|+|+=.
T Consensus 99 ~L~~GD~Vwl~l~ 111 (135)
T smart00110 99 QLRQGDQVWLELP 111 (135)
T ss_pred EECCCCEEEEEEe
Confidence 3899999999853
Done!