Query 025404
Match_columns 253
No_of_seqs 300 out of 3254
Neff 9.7
Searched_HMMs 46136
Date Fri Mar 29 05:27:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025404.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025404hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2249 3'-5' exonuclease [Rep 100.0 7E-32 1.5E-36 211.7 8.3 208 16-253 2-209 (280)
2 cd06143 PAN2_exo DEDDh 3'-5' e 99.9 3E-23 6.5E-28 156.9 8.5 102 138-252 1-126 (174)
3 cd06149 ISG20 DEDDh 3'-5' exon 99.9 7.8E-23 1.7E-27 155.6 9.5 99 138-251 1-100 (157)
4 cd06145 REX1_like DEDDh 3'-5' 99.9 1E-21 2.2E-26 148.4 8.9 95 138-249 1-97 (150)
5 KOG2462 C2H2-type Zn-finger pr 99.9 2.6E-22 5.6E-27 158.9 4.1 112 11-124 127-264 (279)
6 cd06144 REX4_like DEDDh 3'-5' 99.8 5.2E-21 1.1E-25 145.1 9.8 99 138-251 1-100 (152)
7 KOG2248 3'-5' exonuclease [Rep 99.8 9.5E-20 2.1E-24 154.2 8.4 104 131-250 212-316 (380)
8 cd06137 DEDDh_RNase DEDDh 3'-5 99.8 2.8E-19 6.1E-24 136.8 7.1 95 138-248 1-104 (161)
9 KOG2462 C2H2-type Zn-finger pr 99.7 4.6E-19 9.9E-24 140.5 1.5 101 45-153 132-257 (279)
10 PRK07247 DNA polymerase III su 99.7 8.2E-17 1.8E-21 126.2 8.5 94 135-245 5-102 (195)
11 PRK05711 DNA polymerase III su 99.7 7.6E-17 1.6E-21 130.2 7.7 98 135-247 4-105 (240)
12 TIGR01406 dnaQ_proteo DNA poly 99.7 9.3E-17 2E-21 129.1 7.7 96 137-247 2-101 (225)
13 KOG1074 Transcriptional repres 99.6 1.3E-16 2.9E-21 142.6 5.7 67 11-79 602-681 (958)
14 cd06130 DNA_pol_III_epsilon_li 99.6 3.1E-16 6.8E-21 119.5 6.7 93 137-246 1-95 (156)
15 TIGR00573 dnaq exonuclease, DN 99.6 4.6E-16 1E-20 124.7 7.9 100 133-247 5-106 (217)
16 PRK09146 DNA polymerase III su 99.6 6.5E-16 1.4E-20 125.0 8.6 99 131-246 43-147 (239)
17 PRK06310 DNA polymerase III su 99.6 6E-16 1.3E-20 126.3 7.2 101 134-248 6-108 (250)
18 PRK07740 hypothetical protein; 99.6 1.2E-15 2.6E-20 124.1 8.7 99 132-245 56-158 (244)
19 COG2176 PolC DNA polymerase II 99.6 2.7E-16 5.9E-21 145.3 4.2 104 132-252 418-525 (1444)
20 KOG1074 Transcriptional repres 99.6 3.6E-16 7.7E-21 139.9 4.7 77 81-161 608-690 (958)
21 PRK06195 DNA polymerase III su 99.6 1.2E-15 2.6E-20 128.4 7.4 94 136-246 2-98 (309)
22 PRK05601 DNA polymerase III su 99.6 2.5E-15 5.5E-20 126.1 9.0 98 132-247 43-144 (377)
23 cd06131 DNA_pol_III_epsilon_Ec 99.6 2.7E-15 5.8E-20 115.7 7.1 97 137-248 1-101 (167)
24 PRK09145 DNA polymerase III su 99.6 3.5E-15 7.6E-20 118.5 7.8 96 133-245 27-128 (202)
25 PRK06807 DNA polymerase III su 99.6 5E-15 1.1E-19 124.2 8.2 97 133-246 6-106 (313)
26 PRK07983 exodeoxyribonuclease 99.6 6E-15 1.3E-19 117.8 7.1 88 137-245 2-91 (219)
27 PRK06722 exonuclease; Provisio 99.6 5.4E-15 1.2E-19 121.4 6.8 98 135-247 5-109 (281)
28 PRK08517 DNA polymerase III su 99.6 8.9E-15 1.9E-19 119.5 7.4 97 131-245 64-164 (257)
29 cd06136 TREX1_2 DEDDh 3'-5' ex 99.5 5.8E-15 1.2E-19 114.7 5.0 100 137-247 1-118 (177)
30 PRK06063 DNA polymerase III su 99.5 1.8E-14 3.9E-19 121.2 8.2 97 133-247 13-113 (313)
31 PRK06309 DNA polymerase III su 99.5 2.9E-14 6.3E-19 115.4 7.8 96 136-248 3-101 (232)
32 PRK07246 bifunctional ATP-depe 99.5 2.3E-14 4.9E-19 134.6 8.0 95 134-245 6-103 (820)
33 KOG3608 Zn finger proteins [Ge 99.5 5.6E-15 1.2E-19 120.6 2.8 115 11-127 173-316 (467)
34 PRK07942 DNA polymerase III su 99.5 4.3E-14 9.2E-19 114.3 7.6 105 134-249 5-114 (232)
35 smart00479 EXOIII exonuclease 99.5 2.7E-14 5.7E-19 110.1 6.1 99 137-250 2-103 (169)
36 PRK07748 sporulation inhibitor 99.5 3.9E-14 8.5E-19 112.8 5.9 96 135-247 4-112 (207)
37 PRK05168 ribonuclease T; Provi 99.5 8.4E-14 1.8E-18 111.0 7.5 108 133-246 15-132 (211)
38 PRK07883 hypothetical protein; 99.5 6.1E-14 1.3E-18 126.5 6.6 98 132-246 12-113 (557)
39 COG0847 DnaQ DNA polymerase II 99.5 8.5E-14 1.9E-18 113.8 6.6 98 135-247 13-114 (243)
40 cd06134 RNaseT DEDDh 3'-5' exo 99.5 1.3E-13 2.7E-18 108.2 6.9 105 136-246 6-120 (189)
41 TIGR01298 RNaseT ribonuclease 99.5 1.5E-13 3.1E-18 108.8 7.2 106 135-246 8-123 (200)
42 PRK08074 bifunctional ATP-depe 99.4 1.5E-13 3.3E-18 131.1 7.9 94 135-245 3-101 (928)
43 KOG3623 Homeobox transcription 99.4 3.7E-14 8E-19 125.3 2.3 107 14-124 210-330 (1007)
44 TIGR01405 polC_Gram_pos DNA po 99.4 1.4E-13 3.1E-18 132.4 6.4 99 133-248 188-290 (1213)
45 TIGR01407 dinG_rel DnaQ family 99.4 2.8E-13 6.2E-18 128.5 7.9 92 137-245 2-97 (850)
46 PRK05359 oligoribonuclease; Pr 99.4 5E-13 1.1E-17 103.9 6.2 104 135-248 3-118 (181)
47 cd06127 DEDDh DEDDh 3'-5' exon 99.4 1E-12 2.2E-17 99.8 7.2 95 138-248 1-99 (159)
48 PF00929 RNase_T: Exonuclease; 99.4 7.8E-14 1.7E-18 106.4 0.6 94 138-245 1-100 (164)
49 PRK09182 DNA polymerase III su 99.4 1.4E-12 3E-17 108.6 7.5 98 133-247 35-140 (294)
50 cd06138 ExoI_N N-terminal DEDD 99.4 1.4E-12 3.1E-17 101.9 6.4 95 138-246 1-103 (183)
51 cd06135 Orn DEDDh 3'-5' exonuc 99.3 7.5E-13 1.6E-17 102.4 4.3 101 138-247 2-113 (173)
52 KOG3576 Ovo and related transc 99.3 7.8E-13 1.7E-17 100.5 2.5 67 10-78 113-185 (267)
53 cd06133 ERI-1_3'hExo_like DEDD 99.3 8.9E-12 1.9E-16 96.7 6.7 94 137-245 1-107 (176)
54 KOG3608 Zn finger proteins [Ge 99.3 4.1E-12 8.9E-17 104.1 4.2 130 12-144 235-393 (467)
55 PTZ00315 2'-phosphotransferase 99.2 1.9E-11 4E-16 108.6 7.9 105 135-244 56-170 (582)
56 KOG3623 Homeobox transcription 99.2 9.9E-12 2.1E-16 110.3 2.5 55 7-63 887-942 (1007)
57 KOG3576 Ovo and related transc 99.2 3.2E-12 6.9E-17 97.2 -0.9 97 45-148 119-221 (267)
58 PRK11779 sbcB exonuclease I; P 99.1 1.1E-10 2.3E-15 102.9 7.1 103 134-249 5-115 (476)
59 PRK00448 polC DNA polymerase I 99.1 9.3E-11 2E-15 114.7 5.7 95 134-245 418-516 (1437)
60 PHA02768 hypothetical protein; 98.9 4E-10 8.7E-15 68.2 1.6 43 14-60 5-48 (55)
61 PHA00733 hypothetical protein 98.8 2.6E-09 5.7E-14 77.9 3.9 81 11-103 37-124 (128)
62 KOG1275 PAB-dependent poly(A) 98.8 4.2E-09 9.1E-14 96.1 3.8 110 131-253 906-1039(1118)
63 PHA02768 hypothetical protein; 98.7 7.5E-09 1.6E-13 62.7 2.6 42 80-121 7-49 (55)
64 PHA00733 hypothetical protein 98.6 7.2E-08 1.5E-12 70.4 4.3 53 7-63 66-119 (128)
65 PLN03086 PRLI-interacting fact 98.4 5.5E-07 1.2E-11 80.5 5.5 101 11-123 450-560 (567)
66 PF13465 zf-H2C2_2: Zinc-finge 98.3 4.1E-07 8.9E-12 47.0 1.6 25 29-55 1-26 (26)
67 PHA00616 hypothetical protein 98.2 4.3E-07 9.4E-12 52.3 1.4 33 81-113 4-36 (44)
68 PHA00616 hypothetical protein 98.2 5.6E-07 1.2E-11 51.9 1.5 34 14-49 1-35 (44)
69 PHA00732 hypothetical protein 98.2 1E-06 2.2E-11 58.4 2.6 44 14-63 1-44 (79)
70 KOG3993 Transcription factor ( 98.2 6.4E-07 1.4E-11 75.7 1.4 88 14-103 267-381 (500)
71 PLN03086 PRLI-interacting fact 98.1 5.2E-06 1.1E-10 74.4 5.7 115 14-148 407-550 (567)
72 KOG3993 Transcription factor ( 98.0 2.9E-06 6.3E-11 71.8 3.0 48 14-63 295-376 (500)
73 KOG3242 Oligoribonuclease (3'- 98.0 1.4E-06 3.1E-11 65.1 0.5 107 134-250 25-143 (208)
74 PF13465 zf-H2C2_2: Zinc-finge 97.9 5.5E-06 1.2E-10 42.7 1.4 22 93-114 1-25 (26)
75 cd05160 DEDDy_DNA_polB_exo DED 97.8 6.7E-05 1.5E-09 59.3 6.3 90 138-245 2-97 (199)
76 PF00096 zf-C2H2: Zinc finger, 97.7 1.4E-05 3.1E-10 39.8 1.3 22 15-36 1-22 (23)
77 PF00096 zf-C2H2: Zinc finger, 97.7 2.3E-05 5E-10 39.1 1.8 21 81-101 3-23 (23)
78 COG1949 Orn Oligoribonuclease 97.7 2.5E-05 5.3E-10 58.1 2.6 106 134-249 5-122 (184)
79 PF13912 zf-C2H2_6: C2H2-type 97.4 0.00012 2.7E-09 37.9 1.9 23 14-36 1-23 (27)
80 PF05605 zf-Di19: Drought indu 97.4 0.0002 4.2E-09 44.0 2.9 46 14-63 2-49 (54)
81 PF13894 zf-C2H2_4: C2H2-type 97.3 0.00014 3E-09 36.3 1.8 22 15-36 1-22 (24)
82 PF13894 zf-C2H2_4: C2H2-type 97.2 0.00022 4.7E-09 35.5 1.8 22 81-102 3-24 (24)
83 PHA00732 hypothetical protein 97.2 0.00029 6.2E-09 46.8 2.6 34 81-114 4-38 (79)
84 KOG0542 Predicted exonuclease 97.2 0.00021 4.6E-09 57.0 2.3 77 137-214 58-145 (280)
85 COG5189 SFP1 Putative transcri 97.1 0.00017 3.6E-09 59.2 0.6 28 12-40 347-376 (423)
86 smart00355 ZnF_C2H2 zinc finge 96.7 0.0014 3E-08 33.1 2.1 24 15-40 1-24 (26)
87 PF12756 zf-C2H2_2: C2H2 type 96.7 0.0012 2.6E-08 45.7 2.4 74 16-102 1-74 (100)
88 PF13912 zf-C2H2_6: C2H2-type 96.7 0.00083 1.8E-08 34.7 1.0 22 81-102 4-25 (27)
89 PF09237 GAGA: GAGA factor; I 96.6 0.0016 3.6E-08 38.5 2.2 26 81-106 27-52 (54)
90 smart00355 ZnF_C2H2 zinc finge 96.6 0.002 4.4E-08 32.4 2.2 22 81-102 3-24 (26)
91 cd06125 DnaQ_like_exo DnaQ-lik 96.4 0.0045 9.9E-08 42.8 3.6 21 229-249 45-65 (96)
92 PF09237 GAGA: GAGA factor; I 96.4 0.0032 6.9E-08 37.3 2.3 26 11-36 21-46 (54)
93 PF05605 zf-Di19: Drought indu 96.2 0.0067 1.5E-07 37.1 3.5 44 45-103 4-54 (54)
94 PF01612 DNA_pol_A_exo1: 3'-5' 96.0 0.029 6.3E-07 42.9 6.9 30 204-245 65-94 (176)
95 PF12874 zf-met: Zinc-finger o 96.0 0.0037 8E-08 31.5 1.2 22 15-36 1-22 (25)
96 PF12171 zf-C2H2_jaz: Zinc-fin 95.5 0.0074 1.6E-07 31.1 1.3 22 15-36 2-23 (27)
97 PF12756 zf-C2H2_2: C2H2 type 95.5 0.007 1.5E-07 41.8 1.5 20 44-63 51-70 (100)
98 PRK04860 hypothetical protein; 95.4 0.0045 9.7E-08 46.9 0.3 39 13-57 118-157 (160)
99 PF12874 zf-met: Zinc-finger o 95.1 0.01 2.2E-07 29.9 1.0 21 81-101 3-23 (25)
100 COG5189 SFP1 Putative transcri 94.7 0.013 2.7E-07 48.5 0.8 56 42-97 347-417 (423)
101 PF13909 zf-H2C2_5: C2H2-type 94.5 0.026 5.6E-07 28.1 1.5 22 81-103 3-24 (24)
102 PF13913 zf-C2HC_2: zinc-finge 94.5 0.032 6.9E-07 28.2 1.8 20 81-101 5-24 (25)
103 PF13909 zf-H2C2_5: C2H2-type 94.5 0.021 4.5E-07 28.4 1.1 21 15-36 1-21 (24)
104 COG2925 SbcB Exonuclease I [DN 93.8 0.34 7.4E-06 41.5 7.6 98 134-245 8-114 (475)
105 cd05780 DNA_polB_Kod1_like_exo 93.7 0.24 5.2E-06 38.9 6.4 39 195-244 50-89 (195)
106 cd05785 DNA_polB_like2_exo Unc 93.7 0.26 5.6E-06 39.2 6.5 36 198-244 55-91 (207)
107 PF13913 zf-C2HC_2: zinc-finge 93.3 0.069 1.5E-06 26.9 1.7 21 15-36 3-23 (25)
108 COG5048 FOG: Zn-finger [Genera 93.1 0.036 7.8E-07 48.6 0.8 113 13-127 288-442 (467)
109 PF10571 UPF0547: Uncharacteri 93.0 0.057 1.2E-06 27.5 1.2 22 68-89 2-25 (26)
110 smart00451 ZnF_U1 U1-like zinc 92.9 0.079 1.7E-06 28.9 1.8 23 14-36 3-25 (35)
111 PF12171 zf-C2H2_jaz: Zinc-fin 92.8 0.079 1.7E-06 27.1 1.6 19 45-63 3-21 (27)
112 cd05781 DNA_polB_B3_exo DEDDy 90.7 1.4 3E-05 34.5 7.2 37 198-245 45-82 (188)
113 KOG2231 Predicted E3 ubiquitin 90.4 0.39 8.5E-06 44.4 4.4 72 25-102 125-206 (669)
114 cd06139 DNA_polA_I_Ecoli_like_ 90.2 0.37 7.9E-06 37.4 3.6 37 197-245 48-84 (193)
115 PF09845 DUF2072: Zn-ribbon co 89.0 0.19 4.2E-06 36.3 1.1 25 66-90 1-32 (131)
116 COG4049 Uncharacterized protei 88.9 0.21 4.5E-06 30.2 0.9 28 9-36 12-39 (65)
117 cd05784 DNA_polB_II_exo DEDDy 88.5 1.6 3.5E-05 34.3 6.1 36 198-244 48-84 (193)
118 PF09986 DUF2225: Uncharacteri 88.1 0.23 4.9E-06 39.7 1.1 13 45-57 7-19 (214)
119 PF09538 FYDLN_acid: Protein o 88.0 0.3 6.5E-06 34.5 1.5 10 45-54 11-20 (108)
120 smart00451 ZnF_U1 U1-like zinc 87.9 0.32 7E-06 26.3 1.3 19 81-99 6-24 (35)
121 PRK04860 hypothetical protein; 87.3 0.36 7.9E-06 36.6 1.7 28 80-111 121-148 (160)
122 PF03104 DNA_pol_B_exo1: DNA p 87.2 1.8 3.8E-05 36.7 6.1 41 193-244 214-255 (325)
123 PF13482 RNase_H_2: RNase_H su 87.0 1 2.2E-05 34.1 4.1 21 227-247 56-77 (164)
124 COG5018 KapD Inhibitor of the 86.8 0.21 4.5E-06 37.8 0.1 45 169-213 45-91 (210)
125 cd06146 mut-7_like_exo DEDDy 3 86.5 4.8 0.0001 31.5 7.7 35 202-248 68-102 (193)
126 PRK05755 DNA polymerase I; Pro 86.3 2 4.4E-05 41.9 6.6 31 203-245 357-387 (880)
127 cd05779 DNA_polB_epsilon_exo D 85.9 3.7 7.9E-05 32.6 6.8 37 198-245 70-107 (204)
128 KOG4173 Alpha-SNAP protein [In 85.5 0.47 1E-05 37.0 1.5 88 11-112 76-181 (253)
129 KOG1146 Homeobox protein [Gene 85.3 0.52 1.1E-05 46.6 2.0 115 11-126 462-641 (1406)
130 PF15135 UPF0515: Uncharacteri 85.2 0.33 7.2E-06 38.9 0.5 60 8-78 106-167 (278)
131 KOG2893 Zn finger protein [Gen 84.2 0.38 8.1E-06 38.4 0.4 42 16-63 12-54 (341)
132 cd05776 DNA_polB_alpha_exo ina 84.0 1.3 2.8E-05 35.9 3.5 39 195-244 76-115 (234)
133 cd05783 DNA_polB_B1_exo DEDDy 84.0 11 0.00024 29.9 8.7 36 197-245 69-105 (204)
134 KOG2231 Predicted E3 ubiquitin 82.2 1.3 2.8E-05 41.2 3.0 29 45-73 184-213 (669)
135 COG3364 Zn-ribbon containing p 80.7 0.74 1.6E-05 31.6 0.8 25 66-90 2-33 (112)
136 KOG2785 C2H2-type Zn-finger pr 80.2 3.2 7E-05 35.7 4.5 46 81-126 169-243 (390)
137 TIGR02098 MJ0042_CXXC MJ0042 f 79.6 0.71 1.5E-05 25.7 0.4 13 15-27 3-15 (38)
138 cd06141 WRN_exo DEDDy 3'-5' ex 79.5 6.6 0.00014 29.8 5.9 28 206-245 63-90 (170)
139 PF09538 FYDLN_acid: Protein o 79.4 0.98 2.1E-05 31.9 1.1 25 67-91 10-39 (108)
140 cd06148 Egl_like_exo DEDDy 3'- 79.3 6.2 0.00013 31.0 5.7 27 205-243 54-80 (197)
141 TIGR02300 FYDLN_acid conserved 78.8 1.3 2.8E-05 31.9 1.5 11 81-91 29-39 (129)
142 cd05778 DNA_polB_zeta_exo inac 78.0 7.7 0.00017 31.4 6.1 40 193-243 73-113 (231)
143 cd00007 35EXOc 3'-5' exonuclea 78.0 2.6 5.6E-05 31.0 3.1 32 202-245 40-71 (155)
144 cd05777 DNA_polB_delta_exo DED 77.9 24 0.00052 28.4 9.0 38 196-244 66-104 (230)
145 KOG2893 Zn finger protein [Gen 77.6 1 2.2E-05 36.0 0.8 34 43-76 10-44 (341)
146 PF05443 ROS_MUCR: ROS/MUCR tr 77.4 1.3 2.7E-05 32.5 1.2 23 81-106 75-97 (132)
147 PF09986 DUF2225: Uncharacteri 76.7 0.51 1.1E-05 37.7 -1.1 19 12-30 3-21 (214)
148 PF13240 zinc_ribbon_2: zinc-r 76.1 1.6 3.5E-05 21.4 1.0 18 69-86 2-21 (23)
149 smart00614 ZnF_BED BED zinc fi 75.7 2.2 4.7E-05 25.4 1.7 22 81-102 21-48 (50)
150 PF14353 CpXC: CpXC protein 75.6 1.4 3E-05 32.1 1.0 14 199-212 103-116 (128)
151 PHA00626 hypothetical protein 75.3 0.98 2.1E-05 27.4 0.1 11 66-76 23-33 (59)
152 smart00531 TFIIE Transcription 74.9 3.1 6.7E-05 31.1 2.8 33 45-77 101-134 (147)
153 TIGR00622 ssl1 transcription f 74.9 3 6.6E-05 29.5 2.5 21 12-32 13-33 (112)
154 COG4049 Uncharacterized protei 74.8 1.2 2.6E-05 27.0 0.4 24 40-63 13-37 (65)
155 PRK00398 rpoP DNA-directed RNA 74.8 1 2.2E-05 26.3 0.1 22 67-88 4-31 (46)
156 PF13719 zinc_ribbon_5: zinc-r 74.2 1.6 3.5E-05 24.2 0.8 12 16-27 4-15 (37)
157 COG1997 RPL43A Ribosomal prote 73.7 2.1 4.5E-05 28.6 1.4 28 64-91 33-66 (89)
158 COG5236 Uncharacterized conser 73.6 3.9 8.4E-05 34.7 3.2 102 15-124 152-272 (493)
159 PF13717 zinc_ribbon_4: zinc-r 73.5 1.5 3.3E-05 24.1 0.6 13 16-28 4-16 (36)
160 smart00834 CxxC_CXXC_SSSS Puta 72.7 1.3 2.8E-05 24.9 0.2 10 45-54 7-16 (41)
161 PRK00464 nrdR transcriptional 71.5 1.2 2.7E-05 33.5 -0.1 16 197-212 101-116 (154)
162 COG1198 PriA Primosomal protei 71.2 1.6 3.5E-05 41.3 0.5 42 45-86 437-483 (730)
163 KOG1146 Homeobox protein [Gene 71.2 2.2 4.7E-05 42.5 1.4 84 16-100 438-540 (1406)
164 PF09723 Zn-ribbon_8: Zinc rib 70.4 1.4 3E-05 25.2 -0.0 12 45-56 7-18 (42)
165 PF12013 DUF3505: Protein of u 70.2 7.1 0.00015 27.4 3.6 22 82-103 88-109 (109)
166 PF15269 zf-C2H2_7: Zinc-finge 70.1 4.7 0.0001 23.2 2.1 23 14-36 20-42 (54)
167 PF13248 zf-ribbon_3: zinc-rib 69.9 3.2 6.9E-05 20.9 1.3 20 68-87 4-25 (26)
168 PRK14559 putative protein seri 68.9 4.4 9.4E-05 38.0 2.8 36 45-91 17-54 (645)
169 PF10108 DNA_pol_B_exo2: Predi 68.8 6.4 0.00014 31.3 3.4 34 200-245 36-70 (209)
170 PRK04023 DNA polymerase II lar 68.7 3.4 7.3E-05 40.2 2.1 28 165-195 735-762 (1121)
171 cd00350 rubredoxin_like Rubred 68.6 2.3 5E-05 22.9 0.6 9 45-53 3-11 (33)
172 cd05782 DNA_polB_like1_exo Unc 68.5 6.2 0.00014 31.3 3.3 35 199-245 76-111 (208)
173 COG0068 HypF Hydrogenase matur 68.5 1.3 2.8E-05 41.2 -0.6 55 16-74 125-181 (750)
174 PF02892 zf-BED: BED zinc fing 67.7 3.6 7.7E-05 23.6 1.4 19 81-99 19-41 (45)
175 TIGR02300 FYDLN_acid conserved 67.1 3.4 7.3E-05 29.8 1.3 30 43-78 9-38 (129)
176 PHA02528 43 DNA polymerase; Pr 65.4 29 0.00063 34.0 7.7 36 198-244 175-211 (881)
177 PRK14873 primosome assembly pr 64.4 2.4 5.1E-05 40.0 0.2 43 45-87 385-431 (665)
178 smart00659 RPOLCX RNA polymera 64.3 2.7 5.9E-05 24.3 0.4 11 67-77 3-13 (44)
179 COG4957 Predicted transcriptio 64.3 3.8 8.1E-05 29.8 1.2 23 81-106 79-101 (148)
180 TIGR02605 CxxC_CxxC_SSSS putat 64.0 2.4 5.2E-05 25.3 0.1 11 45-55 7-17 (52)
181 cd06129 RNaseD_like DEDDy 3'-5 63.9 45 0.00098 25.0 7.2 19 227-245 66-84 (161)
182 PRK14873 primosome assembly pr 62.7 2.7 5.9E-05 39.6 0.3 54 8-75 376-431 (665)
183 COG2888 Predicted Zn-ribbon RN 62.6 6.4 0.00014 24.3 1.8 7 45-51 29-35 (61)
184 PF01780 Ribosomal_L37ae: Ribo 61.8 2.5 5.5E-05 28.6 -0.1 26 65-90 34-65 (90)
185 COG1996 RPC10 DNA-directed RNA 61.1 2.4 5.3E-05 25.1 -0.2 9 45-53 8-16 (49)
186 TIGR00373 conserved hypothetic 61.1 9.5 0.00021 28.9 2.9 33 41-77 106-139 (158)
187 PTZ00166 DNA polymerase delta 60.1 24 0.00052 35.4 6.2 39 195-244 324-363 (1054)
188 PTZ00255 60S ribosomal protein 60.1 5.1 0.00011 27.1 1.2 26 65-90 35-66 (90)
189 TIGR00280 L37a ribosomal prote 59.8 4.9 0.00011 27.3 1.0 26 65-90 34-65 (91)
190 PF03604 DNA_RNApol_7kD: DNA d 59.4 4 8.7E-05 21.9 0.5 8 46-53 3-10 (32)
191 COG5236 Uncharacterized conser 59.1 11 0.00024 32.1 3.2 18 86-103 289-306 (493)
192 KOG2186 Cell growth-regulating 58.7 5.2 0.00011 32.4 1.2 45 15-63 4-48 (276)
193 PTZ00303 phosphatidylinositol 58.1 3.1 6.8E-05 39.2 -0.1 71 45-123 462-536 (1374)
194 KOG3657 Mitochondrial DNA poly 58.1 5.7 0.00012 37.8 1.5 19 226-244 239-257 (1075)
195 smart00734 ZnF_Rad18 Rad18-lik 57.8 8.4 0.00018 19.4 1.5 19 16-35 3-21 (26)
196 KOG3362 Predicted BBOX Zn-fing 57.8 3.5 7.7E-05 30.3 0.1 30 69-99 121-150 (156)
197 COG1198 PriA Primosomal protei 57.6 4.1 8.9E-05 38.7 0.5 53 10-75 430-484 (730)
198 PRK05762 DNA polymerase II; Re 57.2 40 0.00088 32.7 7.1 39 195-244 197-236 (786)
199 TIGR00595 priA primosomal prot 57.1 4.2 9.1E-05 37.1 0.5 43 45-87 215-262 (505)
200 smart00486 POLBc DNA polymeras 57.1 22 0.00047 31.6 5.1 35 199-244 67-102 (471)
201 TIGR01206 lysW lysine biosynth 56.7 5.8 0.00013 24.1 0.9 7 81-87 25-31 (54)
202 PF14446 Prok-RING_1: Prokaryo 56.5 6 0.00013 24.0 0.9 22 68-89 7-32 (54)
203 COG5151 SSL1 RNA polymerase II 56.5 3.8 8.1E-05 34.3 0.1 21 81-101 391-411 (421)
204 PRK03976 rpl37ae 50S ribosomal 56.3 6.1 0.00013 26.8 1.0 26 65-90 35-66 (90)
205 PRK12496 hypothetical protein; 56.2 4.6 0.0001 30.8 0.5 24 66-89 127-154 (164)
206 PHA02570 dexA exonuclease; Pro 55.4 26 0.00056 28.1 4.5 39 198-244 85-124 (220)
207 PRK06266 transcription initiat 55.0 15 0.00031 28.5 3.1 29 45-77 119-147 (178)
208 COG3359 Predicted exonuclease 54.7 17 0.00037 29.6 3.5 17 133-149 96-112 (278)
209 COG1592 Rubrerythrin [Energy p 54.1 5.8 0.00013 30.3 0.8 19 67-85 135-156 (166)
210 TIGR00595 priA primosomal prot 54.0 5.2 0.00011 36.5 0.6 47 16-75 215-262 (505)
211 PF07191 zinc-ribbons_6: zinc- 52.8 2.4 5.2E-05 27.2 -1.2 35 45-86 3-38 (70)
212 PF05191 ADK_lid: Adenylate ki 51.7 7.3 0.00016 21.5 0.7 10 16-25 3-12 (36)
213 KOG0978 E3 ubiquitin ligase in 48.9 4.9 0.00011 37.7 -0.4 16 81-96 681-696 (698)
214 KOG3408 U1-like Zn-finger-cont 46.8 15 0.00033 26.2 1.8 26 11-36 54-79 (129)
215 PRK14559 putative protein seri 46.8 9.4 0.0002 35.9 1.1 36 45-89 3-38 (645)
216 COG3357 Predicted transcriptio 46.4 13 0.00028 25.1 1.4 11 45-55 60-70 (97)
217 COG1773 Rubredoxin [Energy pro 45.9 8.9 0.00019 23.4 0.5 10 45-54 5-14 (55)
218 KOG2482 Predicted C2H2-type Zn 44.7 18 0.0004 30.8 2.3 72 27-100 128-217 (423)
219 COG4530 Uncharacterized protei 44.7 13 0.00028 26.0 1.2 10 45-54 11-20 (129)
220 KOG4167 Predicted DNA-binding 44.5 8 0.00017 36.3 0.2 25 12-36 790-814 (907)
221 PRK05580 primosome assembly pr 44.5 9.5 0.00021 36.2 0.7 43 45-87 383-430 (679)
222 smart00474 35EXOc 3'-5' exonuc 44.2 26 0.00056 26.0 3.0 28 205-244 64-91 (172)
223 PF01363 FYVE: FYVE zinc finge 44.1 11 0.00023 23.9 0.7 30 45-85 11-40 (69)
224 PRK05580 primosome assembly pr 44.0 8.8 0.00019 36.4 0.4 8 67-74 422-429 (679)
225 PF04438 zf-HIT: HIT zinc fing 43.9 9.1 0.0002 20.1 0.3 20 69-89 5-24 (30)
226 cd00730 rubredoxin Rubredoxin; 43.9 13 0.00028 22.2 1.0 10 45-54 3-12 (50)
227 COG2331 Uncharacterized protei 43.4 3.9 8.4E-05 26.5 -1.4 31 15-54 13-44 (82)
228 PRK03564 formate dehydrogenase 42.6 24 0.00052 29.9 2.8 7 80-86 228-234 (309)
229 KOG2593 Transcription initiati 41.8 18 0.00039 31.8 1.9 34 45-78 130-165 (436)
230 PF04216 FdhE: Protein involve 41.2 7 0.00015 32.8 -0.6 9 14-22 172-180 (290)
231 cd00065 FYVE FYVE domain; Zinc 41.0 15 0.00032 22.1 1.0 31 45-86 4-34 (57)
232 PF01927 Mut7-C: Mut7-C RNAse 40.9 18 0.0004 26.9 1.7 18 81-98 127-144 (147)
233 PF13878 zf-C2H2_3: zinc-finge 40.7 31 0.00068 19.5 2.2 24 79-102 14-39 (41)
234 PF12773 DZR: Double zinc ribb 40.6 22 0.00049 20.7 1.7 35 45-85 14-50 (50)
235 PF13453 zf-TFIIB: Transcripti 40.5 26 0.00056 19.7 1.9 16 81-96 22-37 (41)
236 PF06524 NOA36: NOA36 protein; 39.9 6.1 0.00013 32.2 -1.1 9 66-74 171-179 (314)
237 COG0068 HypF Hydrogenase matur 39.7 7.8 0.00017 36.3 -0.6 34 45-78 125-163 (750)
238 COG0417 PolB DNA polymerase el 39.3 1.2E+02 0.0026 29.6 7.2 40 195-245 205-245 (792)
239 PF01286 XPA_N: XPA protein N- 39.1 14 0.00031 20.1 0.6 12 45-56 5-16 (34)
240 smart00154 ZnF_AN1 AN1-like Zi 38.0 14 0.0003 20.7 0.5 14 14-27 12-25 (39)
241 COG1571 Predicted DNA-binding 37.7 18 0.00039 31.9 1.3 23 69-91 353-380 (421)
242 PRK03824 hypA hydrogenase nick 37.4 12 0.00027 27.5 0.2 11 45-55 72-82 (135)
243 PF03337 Pox_F12L: Poxvirus F1 37.0 45 0.00098 31.2 3.8 71 169-250 225-298 (651)
244 PF07754 DUF1610: Domain of un 36.6 19 0.00041 17.9 0.8 11 12-22 14-24 (24)
245 PF03833 PolC_DP2: DNA polymer 36.6 12 0.00025 36.0 0.0 28 64-91 678-705 (900)
246 PF00301 Rubredoxin: Rubredoxi 36.0 10 0.00022 22.3 -0.3 11 45-55 3-13 (47)
247 KOG1813 Predicted E3 ubiquitin 35.9 16 0.00035 30.5 0.7 45 65-112 240-284 (313)
248 KOG0978 E3 ubiquitin ligase in 35.6 21 0.00045 33.7 1.4 13 65-77 677-689 (698)
249 smart00064 FYVE Protein presen 35.3 20 0.00044 22.5 1.0 25 45-76 12-36 (68)
250 KOG2186 Cell growth-regulating 35.3 17 0.00037 29.6 0.7 45 45-99 5-49 (276)
251 KOG1280 Uncharacterized conser 34.9 38 0.00083 29.0 2.7 38 12-50 77-116 (381)
252 PF06821 Ser_hydrolase: Serine 34.8 42 0.0009 25.7 2.8 31 197-237 35-65 (171)
253 PF02176 zf-TRAF: TRAF-type zi 34.2 20 0.00044 21.7 0.8 38 14-54 9-53 (60)
254 PF07295 DUF1451: Protein of u 34.2 10 0.00022 28.4 -0.7 14 39-52 103-121 (146)
255 COG5048 FOG: Zn-finger [Genera 33.9 26 0.00056 30.4 1.8 51 11-63 30-83 (467)
256 COG1656 Uncharacterized conser 33.6 29 0.00063 26.4 1.7 18 81-98 133-150 (165)
257 PRK14714 DNA polymerase II lar 33.4 24 0.00052 35.6 1.5 28 165-195 782-809 (1337)
258 COG5152 Uncharacterized conser 33.3 19 0.00042 28.1 0.7 45 65-112 195-239 (259)
259 PF01155 HypA: Hydrogenase exp 33.3 13 0.00029 26.3 -0.1 11 45-55 72-82 (113)
260 PHA02524 43A DNA polymerase su 33.2 39 0.00084 30.8 2.7 35 198-243 177-212 (498)
261 KOG4167 Predicted DNA-binding 33.1 12 0.00026 35.2 -0.5 23 81-103 795-817 (907)
262 PRK12380 hydrogenase nickel in 32.9 19 0.00042 25.5 0.6 10 68-77 72-81 (113)
263 PF04857 CAF1: CAF1 family rib 32.7 29 0.00062 28.6 1.7 18 226-243 147-164 (262)
264 cd01121 Sms Sms (bacterial rad 32.7 26 0.00056 30.7 1.5 25 67-91 1-27 (372)
265 COG1779 C4-type Zn-finger prot 32.5 20 0.00044 28.1 0.7 63 171-234 95-171 (201)
266 KOG2593 Transcription initiati 32.0 29 0.00064 30.6 1.7 39 10-53 124-163 (436)
267 TIGR00244 transcriptional regu 31.8 29 0.00062 25.9 1.4 10 81-90 31-40 (147)
268 COG1327 Predicted transcriptio 31.3 31 0.00067 25.8 1.5 11 81-91 31-41 (156)
269 COG4640 Predicted membrane pro 30.9 33 0.00071 30.0 1.7 28 69-96 4-33 (465)
270 TIGR00593 pola DNA polymerase 30.8 51 0.0011 32.4 3.3 34 200-245 362-395 (887)
271 COG1439 Predicted nucleic acid 30.6 16 0.00036 28.1 -0.0 22 66-87 139-162 (177)
272 PF08271 TF_Zn_Ribbon: TFIIB z 30.3 22 0.00047 20.2 0.5 6 81-86 22-27 (43)
273 PF04959 ARS2: Arsenite-resist 29.9 33 0.00072 27.4 1.6 26 11-36 74-99 (214)
274 TIGR00686 phnA alkylphosphonat 29.6 30 0.00064 24.3 1.1 10 81-90 22-31 (109)
275 cd06142 RNaseD_exo DEDDy 3'-5' 29.6 53 0.0012 24.7 2.7 29 204-244 52-80 (178)
276 PF13451 zf-trcl: Probable zin 29.6 21 0.00046 21.2 0.3 15 12-26 2-16 (49)
277 TIGR01562 FdhE formate dehydro 29.3 27 0.00058 29.6 1.0 20 67-86 211-232 (305)
278 PF01428 zf-AN1: AN1-like Zinc 29.0 18 0.00039 20.6 -0.1 15 13-27 12-26 (43)
279 COG1066 Sms Predicted ATP-depe 28.9 24 0.00053 31.2 0.7 24 66-89 7-32 (456)
280 PRK11823 DNA repair protein Ra 28.4 25 0.00055 31.5 0.8 25 66-90 7-33 (446)
281 PF05290 Baculo_IE-1: Baculovi 28.3 27 0.00058 25.6 0.7 15 41-55 77-92 (140)
282 PRK13130 H/ACA RNA-protein com 28.2 38 0.00082 20.8 1.3 21 69-89 8-28 (56)
283 PRK10829 ribonuclease D; Provi 28.0 66 0.0014 28.2 3.2 27 206-244 64-90 (373)
284 PF12013 DUF3505: Protein of u 27.6 44 0.00096 23.3 1.8 23 14-36 80-106 (109)
285 PRK00564 hypA hydrogenase nick 27.6 27 0.0006 24.9 0.7 9 45-53 73-81 (117)
286 PF09332 Mcm10: Mcm10 replicat 27.6 19 0.00041 31.0 -0.2 13 45-57 254-266 (344)
287 TIGR00416 sms DNA repair prote 27.3 28 0.00061 31.3 0.8 26 66-91 7-34 (454)
288 PRK14890 putative Zn-ribbon RN 27.1 19 0.00041 22.3 -0.2 8 45-52 27-34 (59)
289 COG1545 Predicted nucleic-acid 26.8 28 0.0006 25.8 0.6 17 69-85 32-50 (140)
290 PF07503 zf-HYPF: HypF finger; 26.5 19 0.00041 19.7 -0.2 10 46-55 2-11 (35)
291 PF04959 ARS2: Arsenite-resist 26.5 28 0.0006 27.8 0.6 25 80-104 79-103 (214)
292 KOG0717 Molecular chaperone (D 26.5 38 0.00083 30.2 1.5 19 81-99 295-313 (508)
293 COG4306 Uncharacterized protei 26.2 24 0.00053 25.3 0.2 55 28-92 24-82 (160)
294 KOG0402 60S ribosomal protein 25.8 29 0.00062 23.0 0.5 9 81-89 57-65 (92)
295 COG5151 SSL1 RNA polymerase II 25.7 60 0.0013 27.4 2.4 32 45-76 364-398 (421)
296 cd06140 DNA_polA_I_Bacillus_li 25.7 66 0.0014 24.3 2.6 29 204-244 44-72 (178)
297 PF09889 DUF2116: Uncharacteri 25.6 26 0.00055 21.8 0.2 24 67-90 4-30 (59)
298 KOG0320 Predicted E3 ubiquitin 25.6 46 0.00099 25.7 1.6 20 8-27 125-144 (187)
299 PF11238 DUF3039: Protein of u 25.5 21 0.00046 21.9 -0.2 8 81-88 47-54 (58)
300 PF12083 DUF3560: Domain of un 25.5 52 0.0011 23.9 1.8 27 199-237 26-52 (126)
301 PRK00432 30S ribosomal protein 25.0 36 0.00077 20.3 0.7 7 45-51 22-28 (50)
302 PRK05978 hypothetical protein; 24.9 43 0.00092 25.1 1.3 31 45-79 35-65 (148)
303 PRK00420 hypothetical protein; 24.7 42 0.00091 23.8 1.1 9 45-53 25-33 (112)
304 PRK10220 hypothetical protein; 24.2 45 0.00099 23.4 1.2 9 81-89 23-31 (111)
305 KOG2785 C2H2-type Zn-finger pr 23.8 92 0.002 27.1 3.2 21 81-101 220-243 (390)
306 PF11781 RRN7: RNA polymerase 23.3 42 0.0009 18.4 0.7 7 46-52 11-17 (36)
307 smart00661 RPOL9 RNA polymeras 23.2 47 0.001 19.4 1.1 6 46-51 3-8 (52)
308 PRK00762 hypA hydrogenase nick 23.2 40 0.00088 24.3 0.9 10 45-55 72-81 (124)
309 PF15616 TerY-C: TerY-C metal 23.0 39 0.00086 24.7 0.8 22 68-90 79-100 (131)
310 PF01096 TFIIS_C: Transcriptio 23.0 35 0.00076 19.0 0.4 7 81-87 31-37 (39)
311 PF10013 DUF2256: Uncharacteri 23.0 50 0.0011 18.9 1.0 18 15-32 9-26 (42)
312 PRK07218 replication factor A; 22.9 42 0.00091 29.9 1.1 21 67-87 298-318 (423)
313 TIGR00143 hypF [NiFe] hydrogen 22.9 15 0.00033 35.0 -1.7 13 200-212 301-313 (711)
314 COG3545 Predicted esterase of 22.3 1.7E+02 0.0036 22.7 4.1 30 198-237 40-69 (181)
315 KOG4173 Alpha-SNAP protein [In 22.2 39 0.00084 26.7 0.7 47 16-63 108-166 (253)
316 PF05129 Elf1: Transcription e 22.1 36 0.00078 22.6 0.4 10 81-90 49-58 (81)
317 PF08274 PhnA_Zn_Ribbon: PhnA 21.9 39 0.00085 17.7 0.4 11 45-55 4-14 (30)
318 PRK14892 putative transcriptio 21.8 40 0.00086 23.4 0.6 9 81-89 45-53 (99)
319 COG1571 Predicted DNA-binding 21.8 44 0.00096 29.6 1.0 29 44-78 351-379 (421)
320 PF14803 Nudix_N_2: Nudix N-te 21.8 37 0.0008 18.4 0.3 6 81-86 25-30 (34)
321 KOG4317 Predicted Zn-finger pr 21.7 23 0.00049 29.9 -0.7 26 45-81 9-34 (383)
322 KOG3276 Uncharacterized conser 21.0 1.7E+02 0.0038 20.8 3.6 47 163-213 30-80 (125)
323 KOG2807 RNA polymerase II tran 20.5 98 0.0021 26.4 2.7 58 45-102 292-369 (378)
324 cd09018 DEDDy_polA_RNaseD_like 20.4 1.1E+02 0.0023 22.1 2.7 18 227-244 52-69 (150)
325 KOG0717 Molecular chaperone (D 20.1 55 0.0012 29.3 1.2 22 15-36 293-314 (508)
No 1
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=99.97 E-value=7e-32 Score=211.72 Aligned_cols=208 Identities=40% Similarity=0.719 Sum_probs=152.1
Q ss_pred cccccccccCCHHHHHHhhhhcCCCCCccccccccccccCHHHHhhhhCCCCCCCcCCcccccccccccccccCChHHHH
Q 025404 16 KCVACYKQFKRKDHLIEHMKISYHSVHQPKCAVCQKLSKSFESLREHLTGPLSKAHCSGIFSDRGCNLCMNIFDSPSSLI 95 (253)
Q Consensus 16 ~C~~C~k~f~~~~~l~~H~~~~~H~~~~~~C~~C~~~f~~~~~l~~H~~~~~~C~~C~~~f~~~~C~~C~k~f~~~~~l~ 95 (253)
+|..|.+.|.-...+..|+ +..|....++|..|.+.-.....+..++..+.+- .|...|+...|..|.-.-.......
T Consensus 2 ~~~~~~~~~~~~~~~~~~~-v~~~~~~~~~~~~~k~~~~~~~~~~e~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~ 79 (280)
T KOG2249|consen 2 KASSCAQQFNKKEHLPNHK-VSRHKLHERKCGKCKKVARSFESNEEGLIAPLPK-EGKNIFSQRGNRFKATIKASPGKRR 79 (280)
T ss_pred CccHHHHHhCccccCcccc-chhhccCcchhhhHHHhccCcccccccccCCCCc-ccCccccchhhHHHhhHhhcCCcch
Confidence 3567777787777777777 2114433337888877777777777776444443 6666666665555543322222233
Q ss_pred HHHHHccCCCCCCccccCccchhhhhhccccccccccCCCceeeeecccccCCCCCcccccceeeeecCCCCeEEeeecc
Q 025404 96 KHKEACSLSAPVPFEKTLSNAESQKKISGAIDEKRTCRGPKAVAMDCEMVGGGSNGTLDLCARVCLVDEDENVIFHTYVQ 175 (253)
Q Consensus 96 ~H~~~h~~~~~~~C~~~f~~~~~l~~h~~~~~~~r~~~~~~~~~~dcE~~g~~~~~~~~ll~~v~iv~~~~~~~~~~~v~ 175 (253)
.|+..+.+. |..+ ..+.+ ..+.....+++|+||||+|.|.++..+++|+++|||..|+++||.||+
T Consensus 80 ~~~~~~~~~----~~~~----~~~~k------~s~~~~~~r~vAmDCEMVG~Gp~G~~s~lARvSIVN~~G~VvyDkyVk 145 (280)
T KOG2249|consen 80 IHQGSCQAS----CRMA----ALGSK------DSRMGSLTRVVAMDCEMVGVGPDGRESLLARVSIVNYHGHVVYDKYVK 145 (280)
T ss_pred hhhcccCCC----cccc----ccchh------hccccccceEEEEeeeEeccCCCccceeeeEEEEeeccCcEeeeeecC
Confidence 333222211 1100 00000 011222236899999999999999999999999999999999999999
Q ss_pred CCCCcccceeeeccCCHHhhcCCCCHHHHHHHHHHHHhcCCCCCcccccCCCCeEEEeechhhhhhhhcCCCCCCCCC
Q 025404 176 PQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNYPDHMLR 253 (253)
Q Consensus 176 P~~~i~~~~~~~~Git~~~l~~~~~~~~v~~~l~~~~~~~~~~~~~~~~~~~~~~lv~h~~~~D~~~l~~~~~~~~~~ 253 (253)
|..+|+||+++++||++++|.+|++|+.|+.+++++| .|+|||||.+.+||.+|.+.||+.+||
T Consensus 146 P~~~VtDyRT~vSGIrpehm~~A~pf~~aQ~ev~klL--------------~gRIlVGHaLhnDl~~L~l~hp~s~iR 209 (280)
T KOG2249|consen 146 PTEPVTDYRTRVSGIRPEHMRDAMPFKVAQKEVLKLL--------------KGRILVGHALHNDLQALKLEHPRSMIR 209 (280)
T ss_pred CCcccccceeeecccCHHHhccCccHHHHHHHHHHHH--------------hCCEEeccccccHHHHHhhhCchhhhc
Confidence 9999999999999999999999999999999999999 899999999999999999999999997
No 2
>cd06143 PAN2_exo DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. PAN catalyzes the deadenylation of poly(A) tails, which are initially synthesized to default lengths of 70 to 90, to mRNA-specific lengths of 55 to 71. Pab1p and PAN also play a role in the export and decay of mRNA. PAN2 contains a DEDDh-type DnaQ-like 3'-5' exonuclease domain with three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis.
Probab=99.89 E-value=3e-23 Score=156.94 Aligned_cols=102 Identities=26% Similarity=0.439 Sum_probs=88.8
Q ss_pred eeeecccccCCC-------CCccc-------ccceeeeec----CCCCeEEeeeccCCCCcccceeeeccCCHHhhcCCC
Q 025404 138 VAMDCEMVGGGS-------NGTLD-------LCARVCLVD----EDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAM 199 (253)
Q Consensus 138 ~~~dcE~~g~~~-------~~~~~-------ll~~v~iv~----~~~~~~~~~~v~P~~~i~~~~~~~~Git~~~l~~~~ 199 (253)
+++|||++|.+. ++..+ .++|+++|| .+|+++++.||+|..+|.+|+|+++|||+++|.+++
T Consensus 1 ~a~d~e~v~~~~~~~~~~~~g~~~~~~~~~~~LaRVsiVd~~~~~~g~vllD~~VkP~~~V~DYrT~~SGIt~~~L~~a~ 80 (174)
T cd06143 1 VAIDAEFVKLKPEETEIRSDGTKSTIRPSQMSLARVSVVRGEGELEGVPFIDDYISTTEPVVDYLTRFSGIKPGDLDPKT 80 (174)
T ss_pred CceeeeEEEecchhceecCCCcEeeeccCCceeEEEEEEcCCCCcCCCEEEeeeECCCCCccCcCccccccCHHHcCccc
Confidence 467888887664 44441 249999999 789999999999999999999999999999998874
Q ss_pred ------CHHHHHHHHHHHHhcCCCCCcccccCCCCeEEEeechhhhhhhhcCCCCCCCC
Q 025404 200 ------PLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNYPDHML 252 (253)
Q Consensus 200 ------~~~~v~~~l~~~~~~~~~~~~~~~~~~~~~~lv~h~~~~D~~~l~~~~~~~~~ 252 (253)
++++++.+|++++. .++|||||++++||++|+|.||..++
T Consensus 81 ~~~~~~t~~~v~~~l~~li~-------------~~tILVGHsL~nDL~aL~l~hp~~~v 126 (174)
T cd06143 81 SSKNLTTLKSAYLKLRLLVD-------------LGCIFVGHGLAKDFRVINIQVPKEQV 126 (174)
T ss_pred cccccCCHHHHHHHHHHHcC-------------CCCEEEeccchhHHHHhcCcCCCcce
Confidence 69999999999993 68899999999999999999997654
No 3
>cd06149 ISG20 DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar proteins. Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20) is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. It was also independently identified by its response to estrogen and was called HEM45 (human estrogen regulated transcript). ISG20 is a DEDDh-type DnaQ-like 3'-5' exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ISG20 may be a major effector of innate immunity against pathogens including viruses, bacteria, and parasites. It is located in promyelocytic leukemia (PML) nuclear bodies, sites for oncogenic DNA viral transcription and repli
Probab=99.89 E-value=7.8e-23 Score=155.59 Aligned_cols=99 Identities=39% Similarity=0.788 Sum_probs=91.0
Q ss_pred eeeecccccCCCCC-cccccceeeeecCCCCeEEeeeccCCCCcccceeeeccCCHHhhcCCCCHHHHHHHHHHHHhcCC
Q 025404 138 VAMDCEMVGGGSNG-TLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEILNNGE 216 (253)
Q Consensus 138 ~~~dcE~~g~~~~~-~~~ll~~v~iv~~~~~~~~~~~v~P~~~i~~~~~~~~Git~~~l~~~~~~~~v~~~l~~~~~~~~ 216 (253)
+++||||+|.+..+ ..++ +++.+++.+|.++++.+|+|..+|+++++++||||+++++++|++++|+.++.+++
T Consensus 1 v~~D~EttGl~~~~~~~~i-~~i~~v~~~g~~~~~~lv~P~~~i~~~~~~i~GIt~~~l~~a~~~~~v~~~l~~~l---- 75 (157)
T cd06149 1 VAIDCEMVGTGPGGRESEL-ARCSIVNYHGDVLYDKYIRPEGPVTDYRTRWSGIRRQHLVNATPFAVAQKEILKIL---- 75 (157)
T ss_pred CEEEeEeccccCCCCeEEE-EEEEEEeCCCCEEEEEeECCCCccCccceECCCCCHHHHhcCCCHHHHHHHHHHHc----
Confidence 48999999998653 3455 88999988999999999999999999999999999999999999999999999999
Q ss_pred CCCcccccCCCCeEEEeechhhhhhhhcCCCCCCC
Q 025404 217 STGRLMLDDGKARLLVGHGLEHDLDSLRMNYPDHM 251 (253)
Q Consensus 217 ~~~~~~~~~~~~~~lv~h~~~~D~~~l~~~~~~~~ 251 (253)
+++||||||+.||++||++.++.+.
T Consensus 76 ----------~~~vlV~Hn~~~D~~~l~~~~~~~~ 100 (157)
T cd06149 76 ----------KGKVVVGHAIHNDFKALKYFHPKHM 100 (157)
T ss_pred ----------CCCEEEEeCcHHHHHHhcccCCCcC
Confidence 8899999999999999999988754
No 4
>cd06145 REX1_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins. This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins. In yeast, REX1 and REX3 are required for 5S rRNA and MRP (mitochondrial RNA processing) RNA maturation, respectively. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. REX1 is the major exonuclease responsible for pre-tRNA trail trimming and may also be involved in nuclear CCA turnover. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherichia coli RNase T.
Probab=99.86 E-value=1e-21 Score=148.38 Aligned_cols=95 Identities=37% Similarity=0.687 Sum_probs=86.6
Q ss_pred eeeecccccCCCCCcccccceeeeecCCCCeEEeeeccCCCCcccceeeeccCCHHhhcCCC-CHHHHHHHHHHHHhcCC
Q 025404 138 VAMDCEMVGGGSNGTLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAM-PLKEVKDKILEILNNGE 216 (253)
Q Consensus 138 ~~~dcE~~g~~~~~~~~ll~~v~iv~~~~~~~~~~~v~P~~~i~~~~~~~~Git~~~l~~~~-~~~~v~~~l~~~~~~~~ 216 (253)
+++||||+|.+.+ .++ +++.+++.+|.+.|+++|+|..+|+++++++||||+++|+++| ++++|++++.+++
T Consensus 1 ~~iD~E~~g~~~g--~ei-~~i~~v~~~~~~~f~~lv~P~~~i~~~~t~itGIt~~~l~~a~~~~~~v~~~~~~fl---- 73 (150)
T cd06145 1 FALDCEMCYTTDG--LEL-TRVTVVDENGKVVLDELVKPDGEIVDYNTRFSGITEEMLENVTTTLEDVQKKLLSLI---- 73 (150)
T ss_pred CEEeeeeeeecCC--CEE-EEEEEEeCCCCEEEEEeECCCCccchhccCcCCCCHHHhccCCCCHHHHHHHHHHHh----
Confidence 4799999998654 555 9999999999999999999999999999999999999999995 9999999999999
Q ss_pred CCCcccccCCC-CeEEEeechhhhhhhhcCCCCC
Q 025404 217 STGRLMLDDGK-ARLLVGHGLEHDLDSLRMNYPD 249 (253)
Q Consensus 217 ~~~~~~~~~~~-~~~lv~h~~~~D~~~l~~~~~~ 249 (253)
. +.+|||||+.||++||+..+++
T Consensus 74 ----------~~~~vlVgHn~~fD~~fL~~~~~~ 97 (150)
T cd06145 74 ----------SPDTILVGHSLENDLKALKLIHPR 97 (150)
T ss_pred ----------CCCCEEEEcChHHHHHHhhccCCC
Confidence 5 7899999999999999987654
No 5
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.85 E-value=2.6e-22 Score=158.86 Aligned_cols=112 Identities=26% Similarity=0.407 Sum_probs=93.0
Q ss_pred CCCcccccccccccCCHHHHHHhhhhcCCCC---Ccc-ccccccccccCHHHHhhhh---CCCCCCCcCCcccccc----
Q 025404 11 STARHKCVACYKQFKRKDHLIEHMKISYHSV---HQP-KCAVCQKLSKSFESLREHL---TGPLSKAHCSGIFSDR---- 79 (253)
Q Consensus 11 ~~k~~~C~~C~k~f~~~~~l~~H~~~~~H~~---~~~-~C~~C~~~f~~~~~l~~H~---~~~~~C~~C~~~f~~~---- 79 (253)
..-.|+|+.|+|.|.+.++|.+|+++ |.. .+. .|+.|||.|.+...|+.|+ +-++.|.+|||.|+..
T Consensus 127 ~~~r~~c~eCgk~ysT~snLsrHkQ~--H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaFSRPWLLQ 204 (279)
T KOG2462|consen 127 KHPRYKCPECGKSYSTSSNLSRHKQT--HRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHTLPCECGICGKAFSRPWLLQ 204 (279)
T ss_pred cCCceeccccccccccccccchhhcc--cccccccccccCCCCCceeeehHHHhhHhhccCCCcccccccccccchHHhh
Confidence 44569999999999999999999999 753 333 9999999999999999999 4577888888888743
Q ss_pred ------------cccccccccCChHHHHHHHHHccCCCCCC---ccccCccchhhhhhcc
Q 025404 80 ------------GCNLCMNIFDSPSSLIKHKEACSLSAPVP---FEKTLSNAESQKKISG 124 (253)
Q Consensus 80 ------------~C~~C~k~f~~~~~l~~H~~~h~~~~~~~---C~~~f~~~~~l~~h~~ 124 (253)
+|..|+|+|.++++|+.||++|++.|+|+ |+++|++.+-|.+|.+
T Consensus 205 GHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~E 264 (279)
T KOG2462|consen 205 GHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHSE 264 (279)
T ss_pred cccccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhhh
Confidence 38888888888888888888888888876 7888888888888874
No 6
>cd06144 REX4_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product of 20 kDa, and similar proteins. This subfamily is composed of RNA exonuclease 4 (REX4 or Rex4p), XPMC2, Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20), and similar proteins. REX4 is involved in pre-rRNA processing. It controls the ratio between the two forms of 5.8S rRNA in yeast. XPMC2 is a Xenopus gene which was identified through its ability to correct a mitotic defect in fission yeast. The human homolog of XPMC2 (hPMC2) may be involved in angiotensin II-induced adrenal cell cycle progression and cell proliferation. ISG20 is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. These proteins are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clus
Probab=99.85 E-value=5.2e-21 Score=145.06 Aligned_cols=99 Identities=51% Similarity=0.902 Sum_probs=89.9
Q ss_pred eeeecccccCCCCC-cccccceeeeecCCCCeEEeeeccCCCCcccceeeeccCCHHhhcCCCCHHHHHHHHHHHHhcCC
Q 025404 138 VAMDCEMVGGGSNG-TLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEILNNGE 216 (253)
Q Consensus 138 ~~~dcE~~g~~~~~-~~~ll~~v~iv~~~~~~~~~~~v~P~~~i~~~~~~~~Git~~~l~~~~~~~~v~~~l~~~~~~~~ 216 (253)
+++||||||..... ..++ +.+.+++.++.+.++.+++|..+++++++++||||+++++++|+|.+++.+|.+++
T Consensus 1 v~lD~EttGl~~~~~~~~i-~~v~~v~~~~~~~~~~~v~P~~~i~~~~~~ihGIt~~~v~~a~~~~~~~~~l~~~l---- 75 (152)
T cd06144 1 VALDCEMVGVGPDGSESAL-ARVSIVNEDGNVVYDTYVKPQEPVTDYRTAVSGIRPEHLKDAPDFEEVQKKVAELL---- 75 (152)
T ss_pred CEEEEEeecccCCCCEEEE-EEEEEEeCCCCEEEEEEECCCCCCCcccccCCCCCHHHHcCCCCHHHHHHHHHHHh----
Confidence 47999999987553 4555 88899888899999999999999999999999999999999999999999999999
Q ss_pred CCCcccccCCCCeEEEeechhhhhhhhcCCCCCCC
Q 025404 217 STGRLMLDDGKARLLVGHGLEHDLDSLRMNYPDHM 251 (253)
Q Consensus 217 ~~~~~~~~~~~~~~lv~h~~~~D~~~l~~~~~~~~ 251 (253)
.+.+|||||+.||++||++..|++.
T Consensus 76 ----------~~~vlVgHn~~fD~~~L~~~~~~~~ 100 (152)
T cd06144 76 ----------KGRILVGHALKNDLKVLKLDHPKKL 100 (152)
T ss_pred ----------CCCEEEEcCcHHHHHHhcCcCCCcc
Confidence 7789999999999999999888754
No 7
>KOG2248 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=99.80 E-value=9.5e-20 Score=154.20 Aligned_cols=104 Identities=41% Similarity=0.790 Sum_probs=94.8
Q ss_pred ccCCCceeeeecccccCCCCCcccccceeeeecCCCCeEEeeeccCCCCcccceeeeccCCHHhhcCC-CCHHHHHHHHH
Q 025404 131 TCRGPKAVAMDCEMVGGGSNGTLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNA-MPLKEVKDKIL 209 (253)
Q Consensus 131 ~~~~~~~~~~dcE~~g~~~~~~~~ll~~v~iv~~~~~~~~~~~v~P~~~i~~~~~~~~Git~~~l~~~-~~~~~v~~~l~ 209 (253)
.....+++++|||||....+ .++ +||.+||.+++++++.+|+|..||.||+++++|||+++++++ .++++|+++|.
T Consensus 212 v~~~~~i~AlDCEm~~te~g--~el-~RVt~VD~~~~vi~D~fVkP~~~VvDy~T~~SGIT~~~~e~~t~tl~dvq~~l~ 288 (380)
T KOG2248|consen 212 VSKSPNIFALDCEMVVTENG--LEL-TRVTAVDRDGKVILDTFVKPNKPVVDYNTRYSGITEEDLENSTITLEDVQKELL 288 (380)
T ss_pred CCCCCCeEEEEeeeeeeccc--eee-EEeeeeeccCcEEeEEeecCCCcccccccccccccHHHHhcCccCHHHHHHHHH
Confidence 45567799999999997544 566 999999999999999999999999999999999999999876 79999999999
Q ss_pred HHHhcCCCCCcccccCCCCeEEEeechhhhhhhhcCCCCCC
Q 025404 210 EILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNYPDH 250 (253)
Q Consensus 210 ~~~~~~~~~~~~~~~~~~~~~lv~h~~~~D~~~l~~~~~~~ 250 (253)
.+++ .++|||||+++.||++|++.||.+
T Consensus 289 ~~~~-------------~~TILVGHSLenDL~aLKl~H~~V 316 (380)
T KOG2248|consen 289 ELIS-------------KNTILVGHSLENDLKALKLDHPSV 316 (380)
T ss_pred hhcC-------------cCcEEEeechhhHHHHHhhhCCce
Confidence 9994 889999999999999999999875
No 8
>cd06137 DEDDh_RNase DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX)-1,-3, and -4, ISG20, and similar proteins. This group is composed of eukaryotic exoribonucleases that include PAN2, RNA exonuclease 1 (REX1 or Rex1p), REX3 (Rex3p), REX4 (or Rex4p), ISG20, and similar proteins. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. REX proteins are required for the processing and maturation of many RNA species, and ISG20 is an interferon-induced antiviral exonuclease with a strong prefere
Probab=99.78 E-value=2.8e-19 Score=136.78 Aligned_cols=95 Identities=34% Similarity=0.628 Sum_probs=80.0
Q ss_pred eeeecccccCCCCCcccccceeeeecC-CCCeEEeeeccCCCCcccceeeeccCCHHhhcCCCC-------HHHHHHHHH
Q 025404 138 VAMDCEMVGGGSNGTLDLCARVCLVDE-DENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMP-------LKEVKDKIL 209 (253)
Q Consensus 138 ~~~dcE~~g~~~~~~~~ll~~v~iv~~-~~~~~~~~~v~P~~~i~~~~~~~~Git~~~l~~~~~-------~~~v~~~l~ 209 (253)
+++||||||.+.. ..++ .++.+++. +|++.++.+|+|..+|+++++++||||++++.++|+ |+++++++.
T Consensus 1 v~lD~EttGl~~~-~d~i-i~Ig~V~v~~g~i~~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~~~~~~~~~~~~~~~ 78 (161)
T cd06137 1 VALDCEMVGLADG-DSEV-VRISAVDVLTGEVLIDSLVRPSVRVTDWRTRFSGVTPADLEEAAKAGKTIFGWEAARAALW 78 (161)
T ss_pred CEEEeeeeeEcCC-CCEE-EEEEEEEcCCCeEEEeccccCCCCCCccceeccCCCHHHHhhhhhcCCccccHHHHHHHHH
Confidence 4799999997643 2233 55555554 788899999999999999999999999999998875 469999999
Q ss_pred HHHhcCCCCCcccccCCCC-eEEEeechhhhhhhhcCCCC
Q 025404 210 EILNNGESTGRLMLDDGKA-RLLVGHGLEHDLDSLRMNYP 248 (253)
Q Consensus 210 ~~~~~~~~~~~~~~~~~~~-~~lv~h~~~~D~~~l~~~~~ 248 (253)
+++ ++ .+|||||+.||++||++.++
T Consensus 79 ~~i--------------~~~~vlVgHn~~fD~~fL~~~~~ 104 (161)
T cd06137 79 KFI--------------DPDTILVGHSLQNDLDALRMIHT 104 (161)
T ss_pred Hhc--------------CCCcEEEeccHHHHHHHHhCcCC
Confidence 999 65 89999999999999998654
No 9
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.74 E-value=4.6e-19 Score=140.54 Aligned_cols=101 Identities=18% Similarity=0.315 Sum_probs=90.1
Q ss_pred ccccccccccCHHHHhhhh--------CCCCCCCcCCccccccc--------------ccccccccCChHHHHHHHHHcc
Q 025404 45 KCAVCQKLSKSFESLREHL--------TGPLSKAHCSGIFSDRG--------------CNLCMNIFDSPSSLIKHKEACS 102 (253)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~--------~~~~~C~~C~~~f~~~~--------------C~~C~k~f~~~~~l~~H~~~h~ 102 (253)
+|..||+.+++.++|.+|. .+.+.|+.|+|.|+... |.+|||.|.+..-|+.|+|+|+
T Consensus 132 ~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaFSRPWLLQGHiRTHT 211 (279)
T KOG2462|consen 132 KCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHTLPCECGICGKAFSRPWLLQGHIRTHT 211 (279)
T ss_pred eccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccCCCcccccccccccchHHhhccccccc
Confidence 9999999999999999997 45689999999998752 9999999999999999999999
Q ss_pred CCCCCC---ccccCccchhhhhhccccccccccCCCceeeeecccccCCCCCcc
Q 025404 103 LSAPVP---FEKTLSNAESQKKISGAIDEKRTCRGPKAVAMDCEMVGGGSNGTL 153 (253)
Q Consensus 103 ~~~~~~---C~~~f~~~~~l~~h~~~~~~~r~~~~~~~~~~dcE~~g~~~~~~~ 153 (253)
|||||. |+++|+.+++|+.|+..|.. +..+.|..|++.|....
T Consensus 212 GEKPF~C~hC~kAFADRSNLRAHmQTHS~--------~K~~qC~~C~KsFsl~S 257 (279)
T KOG2462|consen 212 GEKPFSCPHCGKAFADRSNLRAHMQTHSD--------VKKHQCPRCGKSFALKS 257 (279)
T ss_pred CCCCccCCcccchhcchHHHHHHHHhhcC--------CccccCcchhhHHHHHH
Confidence 999997 99999999999999976654 35778999998765543
No 10
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=99.69 E-value=8.2e-17 Score=126.23 Aligned_cols=94 Identities=23% Similarity=0.334 Sum_probs=81.2
Q ss_pred CceeeeecccccCC-CCCcccccceeeeecCCCCe--EEeeeccCCCCcccceeeeccCCHHhhcCCCCHHHHHHHHHHH
Q 025404 135 PKAVAMDCEMVGGG-SNGTLDLCARVCLVDEDENV--IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEI 211 (253)
Q Consensus 135 ~~~~~~dcE~~g~~-~~~~~~ll~~v~iv~~~~~~--~~~~~v~P~~~i~~~~~~~~Git~~~l~~~~~~~~v~~~l~~~ 211 (253)
..++++|+||+|.. .+.++++ +.|.+. +|.+ .++.+|+|..+++++.+++||||+++|+++|++.+|+.++.++
T Consensus 5 ~~~vvlD~EtTGl~~~~eIIeI-gaV~v~--~g~~~~~f~~lv~P~~~i~~~~~~lhGIt~~~v~~ap~~~evl~~f~~f 81 (195)
T PRK07247 5 ETYIAFDLEFNTVNGVSHIIQV-SAVKYD--DHKEVDSFDSYVYTDVPLQSFINGLTGITADKIADAPKVEEVLAAFKEF 81 (195)
T ss_pred CeEEEEEeeCCCCCCCCeEEEE-EEEEEE--CCEEEEEEEEEECCCCCCCccceecCCCCHHHHhCCCCHHHHHHHHHHH
Confidence 46899999999965 3445565 767764 3433 7999999999999999999999999999999999999999999
Q ss_pred HhcCCCCCcccccCCCCeEEEeechh-hhhhhhcC
Q 025404 212 LNNGESTGRLMLDDGKARLLVGHGLE-HDLDSLRM 245 (253)
Q Consensus 212 ~~~~~~~~~~~~~~~~~~~lv~h~~~-~D~~~l~~ 245 (253)
+ ++.+|||||+. ||+.||+-
T Consensus 82 ~--------------~~~~lVaHNa~~fD~~fL~~ 102 (195)
T PRK07247 82 V--------------GELPLIGYNAQKSDLPILAE 102 (195)
T ss_pred H--------------CCCeEEEEeCcHhHHHHHHH
Confidence 9 78899999997 89999975
No 11
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=99.68 E-value=7.6e-17 Score=130.25 Aligned_cols=98 Identities=21% Similarity=0.408 Sum_probs=84.3
Q ss_pred CceeeeecccccCCC---CCcccccceeeeecCCCC-eEEeeeccCCCCcccceeeeccCCHHhhcCCCCHHHHHHHHHH
Q 025404 135 PKAVAMDCEMVGGGS---NGTLDLCARVCLVDEDEN-VIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILE 210 (253)
Q Consensus 135 ~~~~~~dcE~~g~~~---~~~~~ll~~v~iv~~~~~-~~~~~~v~P~~~i~~~~~~~~Git~~~l~~~~~~~~v~~~l~~ 210 (253)
.+++++|+||||... +.++++ +.|.+.+.... ..|+.+++|..+|++...++||||+++|.++|+|.+|+.++.+
T Consensus 4 ~r~vvlDtETTGldp~~~drIIEI-GaV~v~~~~~~~~~f~~~i~P~~~i~~~a~~VHGIT~e~l~~~p~f~ev~~~f~~ 82 (240)
T PRK05711 4 MRQIVLDTETTGLNQREGHRIIEI-GAVELINRRLTGRNFHVYIKPDRLVDPEALAVHGITDEFLADKPTFAEVADEFLD 82 (240)
T ss_pred CeEEEEEeeCCCcCCCCCCeEEEE-EEEEEECCEEeccEEEEEECcCCcCCHHHhhhcCCCHHHHcCCCCHHHHHHHHHH
Confidence 468999999999764 467777 88887643221 1688999999999999999999999999999999999999999
Q ss_pred HHhcCCCCCcccccCCCCeEEEeechhhhhhhhcCCC
Q 025404 211 ILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNY 247 (253)
Q Consensus 211 ~~~~~~~~~~~~~~~~~~~~lv~h~~~~D~~~l~~~~ 247 (253)
++ ++.+|||||+.||+.||+...
T Consensus 83 fi--------------~~~~lVaHNa~FD~~fL~~el 105 (240)
T PRK05711 83 FI--------------RGAELIIHNAPFDIGFMDYEF 105 (240)
T ss_pred Hh--------------CCCEEEEEccHHhHHHHHHHH
Confidence 99 788999999999999998643
No 12
>TIGR01406 dnaQ_proteo DNA polymerase III, epsilon subunit, Proteobacterial. This model represents DnaQ, the DNA polymerase III epsilon subunit, as found in most Proteobacteria. It consists largely of an exonuclease domain as described in pfam model pfam00929. In Gram-positive bacteria, closely related regions are found both in the Gram-positive type DNA polymerase III alpha subunit and as an additional N-terminal domain of a DinG-family helicase. Both are excluded from this model, as are smaller proteins, also outside the Proteobacteria, that are similar in size to the epsilon subunit but as different in sequence as are the epsilon-like regions found in Gram-positive bacteria.
Probab=99.68 E-value=9.3e-17 Score=129.06 Aligned_cols=96 Identities=25% Similarity=0.381 Sum_probs=82.9
Q ss_pred eeeeecccccCCC---CCcccccceeeeecCCCC-eEEeeeccCCCCcccceeeeccCCHHhhcCCCCHHHHHHHHHHHH
Q 025404 137 AVAMDCEMVGGGS---NGTLDLCARVCLVDEDEN-VIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEIL 212 (253)
Q Consensus 137 ~~~~dcE~~g~~~---~~~~~ll~~v~iv~~~~~-~~~~~~v~P~~~i~~~~~~~~Git~~~l~~~~~~~~v~~~l~~~~ 212 (253)
++++|+||+|... +.++++ +.+.+.+.... ..|+.+++|..++++..+++||||+++|+++|+|.+|+.++.+++
T Consensus 2 ~vvlD~ETTGl~p~~~d~IIEI-gav~~~~~~~~~~~f~~~i~P~~~i~~~a~~vhGIt~e~l~~~p~f~ev~~~f~~fi 80 (225)
T TIGR01406 2 QIILDTETTGLDPKGGHRIVEI-GAVELVNRMLTGDNFHVYVNPERDMPAEAAKVHGITDEFLADKPKFKEIADEFLDFI 80 (225)
T ss_pred EEEEEeeCCCcCCCCCCeEEEE-EEEEEECCcEecceEEEEECcCCCCCHHHHhccCCCHHHHhCCCCHHHHHHHHHHHh
Confidence 6899999999764 356777 88877653211 268999999999999999999999999999999999999999999
Q ss_pred hcCCCCCcccccCCCCeEEEeechhhhhhhhcCCC
Q 025404 213 NNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNY 247 (253)
Q Consensus 213 ~~~~~~~~~~~~~~~~~~lv~h~~~~D~~~l~~~~ 247 (253)
++.+|||||+.||+.||+...
T Consensus 81 --------------~~~~lVaHNa~FD~~fL~~el 101 (225)
T TIGR01406 81 --------------GGSELVIHNAAFDVGFLNYEL 101 (225)
T ss_pred --------------CCCEEEEEecHHHHHHHHHHH
Confidence 788999999999999998643
No 13
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.65 E-value=1.3e-16 Score=142.57 Aligned_cols=67 Identities=22% Similarity=0.528 Sum_probs=60.1
Q ss_pred CCCcccccccccccCCHHHHHHhhhhcCCCCCcc-ccccccccccCHHHHhhhh---------CCCCCCC---cCCcccc
Q 025404 11 STARHKCVACYKQFKRKDHLIEHMKISYHSVHQP-KCAVCQKLSKSFESLREHL---------TGPLSKA---HCSGIFS 77 (253)
Q Consensus 11 ~~k~~~C~~C~k~f~~~~~l~~H~~~~~H~~~~~-~C~~C~~~f~~~~~l~~H~---------~~~~~C~---~C~~~f~ 77 (253)
..-|.+|-.|-+..+.++.|+.|.|+ |+|++| +|.+||+.|.++.+|+.|+ ..++.|+ +|-+.|.
T Consensus 602 ~TdPNqCiiC~rVlSC~saLqmHyrt--HtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~~kft 679 (958)
T KOG1074|consen 602 RTDPNQCIICLRVLSCPSALQMHYRT--HTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQKKFT 679 (958)
T ss_pred cCCccceeeeeecccchhhhhhhhhc--ccCcCccccccccchhccccchhhcccccccCccccccccCCchhhhccccc
Confidence 34578999999999999999999999 999999 9999999999999999998 3467888 8888887
Q ss_pred cc
Q 025404 78 DR 79 (253)
Q Consensus 78 ~~ 79 (253)
..
T Consensus 680 n~ 681 (958)
T KOG1074|consen 680 NA 681 (958)
T ss_pred cc
Confidence 64
No 14
>cd06130 DNA_pol_III_epsilon_like an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III. This subfamily is composed of uncharacterized bacterial proteins with similarity to the epsilon subunit of DNA polymerase III (Pol III), a multisubunit polymerase which is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. The Pol III holoenzyme is a complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that ser
Probab=99.64 E-value=3.1e-16 Score=119.47 Aligned_cols=93 Identities=26% Similarity=0.382 Sum_probs=81.6
Q ss_pred eeeeecccccCCCCCcccccceeeeecCCCCe--EEeeeccCCCCcccceeeeccCCHHhhcCCCCHHHHHHHHHHHHhc
Q 025404 137 AVAMDCEMVGGGSNGTLDLCARVCLVDEDENV--IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEILNN 214 (253)
Q Consensus 137 ~~~~dcE~~g~~~~~~~~ll~~v~iv~~~~~~--~~~~~v~P~~~i~~~~~~~~Git~~~l~~~~~~~~v~~~l~~~~~~ 214 (253)
++++|+||+|...+..+++ +.+.+. .+++ .++.+++|..++++...+++|||++++.+++++.+++++|.+++
T Consensus 1 ~v~~D~Ettg~~~~~ii~i-g~v~~~--~~~~~~~~~~~i~p~~~~~~~~~~i~GIt~e~l~~~~~~~~v~~~l~~~l-- 75 (156)
T cd06130 1 FVAIDFETANADRASACSI-GLVKVR--DGQIVDTFYTLIRPPTRFDPFNIAIHGITPEDVADAPTFPEVWPEIKPFL-- 75 (156)
T ss_pred CEEEEEeCCCCCCCceEEE-EEEEEE--CCEEEEEEEEEeCcCCCCChhhccccCcCHHHHhcCCCHHHHHHHHHHHh--
Confidence 4789999999777777776 777763 4444 57899999999999999999999999999999999999999999
Q ss_pred CCCCCcccccCCCCeEEEeechhhhhhhhcCC
Q 025404 215 GESTGRLMLDDGKARLLVGHGLEHDLDSLRMN 246 (253)
Q Consensus 215 ~~~~~~~~~~~~~~~~lv~h~~~~D~~~l~~~ 246 (253)
.+.++||||+.||+.+|+..
T Consensus 76 ------------~~~~lv~hn~~fD~~~l~~~ 95 (156)
T cd06130 76 ------------GGSLVVAHNASFDRSVLRAA 95 (156)
T ss_pred ------------CCCEEEEeChHHhHHHHHHH
Confidence 67899999999999999643
No 15
>TIGR00573 dnaq exonuclease, DNA polymerase III, epsilon subunit family. All proteins in this family for which functions are known are components of the DNA polymerase III complex (epsilon subunit). There is, however, an outgroup that includes paralogs in some gamma-proteobacteria and the n-terminal region of DinG from some low GC gram positive bacteria. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.64 E-value=4.6e-16 Score=124.73 Aligned_cols=100 Identities=20% Similarity=0.367 Sum_probs=84.4
Q ss_pred CCCceeeeecccccCCCC-CcccccceeeeecCCCC-eEEeeeccCCCCcccceeeeccCCHHhhcCCCCHHHHHHHHHH
Q 025404 133 RGPKAVAMDCEMVGGGSN-GTLDLCARVCLVDEDEN-VIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILE 210 (253)
Q Consensus 133 ~~~~~~~~dcE~~g~~~~-~~~~ll~~v~iv~~~~~-~~~~~~v~P~~~i~~~~~~~~Git~~~l~~~~~~~~v~~~l~~ 210 (253)
....++++|+||+|.... .++++ +.+.+.+.... ..+..+++|..++++....++|||++++.++|++.+|+.++.+
T Consensus 5 ~~~~fvv~D~ETTGl~~~~~IIeI-gav~v~~~~~~~~~f~~li~P~~~i~~~a~~ihGIt~e~l~~~p~~~ev~~~~~~ 83 (217)
T TIGR00573 5 VLDTETTGDNETTGLYAGHDIIEI-GAVEIINRRITGNKFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDFAD 83 (217)
T ss_pred EecCEEEEEecCCCCCCCCCEEEE-EEEEEECCCEeeeEEEEEECcCCCCCHHHHhhcCCCHHHHcCCCCHHHHHHHHHH
Confidence 445689999999997632 26666 77776543222 2788999999999999999999999999999999999999999
Q ss_pred HHhcCCCCCcccccCCCCeEEEeechhhhhhhhcCCC
Q 025404 211 ILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNY 247 (253)
Q Consensus 211 ~~~~~~~~~~~~~~~~~~~~lv~h~~~~D~~~l~~~~ 247 (253)
++ ++.++||||+.||+.||+-..
T Consensus 84 ~~--------------~~~~lVaHNa~FD~~fL~~~~ 106 (217)
T TIGR00573 84 YI--------------RGAELVIHNASFDVGFLNYEF 106 (217)
T ss_pred Hh--------------CCCEEEEeccHHHHHHHHHHH
Confidence 99 778999999999999998643
No 16
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=99.64 E-value=6.5e-16 Score=125.04 Aligned_cols=99 Identities=22% Similarity=0.313 Sum_probs=84.7
Q ss_pred ccCCCceeeeecccccCC--CCCcccccceeeeecCCCCe----EEeeeccCCCCcccceeeeccCCHHhhcCCCCHHHH
Q 025404 131 TCRGPKAVAMDCEMVGGG--SNGTLDLCARVCLVDEDENV----IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEV 204 (253)
Q Consensus 131 ~~~~~~~~~~dcE~~g~~--~~~~~~ll~~v~iv~~~~~~----~~~~~v~P~~~i~~~~~~~~Git~~~l~~~~~~~~v 204 (253)
.-....++++|+||+|.. .+.++++ +.+.+.+ +.+ .+..+++|..+|+...+++||||++++.++|++.+|
T Consensus 43 ~~~~~~~vviD~ETTGl~p~~d~IieI-g~v~v~~--~~i~~~~~~~~li~P~~~i~~~~~~IhGIt~e~l~~ap~~~ev 119 (239)
T PRK09146 43 PLSEVPFVALDFETTGLDAEQDAIVSI-GLVPFTL--QRIRCRQARHWVVKPRRPLEEESVVIHGITHSELQDAPDLERI 119 (239)
T ss_pred CcccCCEEEEEeECCCCCCCCCcEEEE-EEEEEEC--CeEeecceEEEEECCCCCCChhhhhhcCCCHHHHhCCCCHHHH
Confidence 444667999999999966 3566777 7777733 332 578899999999999999999999999999999999
Q ss_pred HHHHHHHHhcCCCCCcccccCCCCeEEEeechhhhhhhhcCC
Q 025404 205 KDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMN 246 (253)
Q Consensus 205 ~~~l~~~~~~~~~~~~~~~~~~~~~~lv~h~~~~D~~~l~~~ 246 (253)
+.++.+++ ++.+|||||+.||+.||+..
T Consensus 120 l~~l~~~~--------------~~~~lVaHna~FD~~fL~~~ 147 (239)
T PRK09146 120 LDELLEAL--------------AGKVVVVHYRRIERDFLDQA 147 (239)
T ss_pred HHHHHHHh--------------CCCEEEEECHHHHHHHHHHH
Confidence 99999999 78899999999999999764
No 17
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=99.63 E-value=6e-16 Score=126.31 Aligned_cols=101 Identities=17% Similarity=0.303 Sum_probs=83.2
Q ss_pred CCceeeeecccccCCC--CCcccccceeeeecCCCCeEEeeeccCCCCcccceeeeccCCHHhhcCCCCHHHHHHHHHHH
Q 025404 134 GPKAVAMDCEMVGGGS--NGTLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEI 211 (253)
Q Consensus 134 ~~~~~~~dcE~~g~~~--~~~~~ll~~v~iv~~~~~~~~~~~v~P~~~i~~~~~~~~Git~~~l~~~~~~~~v~~~l~~~ 211 (253)
...++++|+||+|... +.++++ +.+.+........++.+++|..+|+...+++||||+++|+++|+|.+|..++.++
T Consensus 6 ~~~~v~~D~ETTGl~~~~d~IIEI-a~v~v~~~~~~~~~~~li~P~~~I~~~a~~ihgIt~e~v~~~p~~~ev~~~~~~f 84 (250)
T PRK06310 6 DTEFVCLDCETTGLDVKKDRIIEF-AAIRFTFDEVIDSVEFLINPERVVSAESQRIHHISDAMLRDKPKIAEVFPQIKGF 84 (250)
T ss_pred CCcEEEEEEeCCCCCCCCCeEEEE-EEEEEECCeEEEEEEEEECcCCCCCHhhhhccCcCHHHHhCCCCHHHHHHHHHHH
Confidence 3568999999999753 567777 7776643211126889999999999999999999999999999999999999999
Q ss_pred HhcCCCCCcccccCCCCeEEEeechhhhhhhhcCCCC
Q 025404 212 LNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNYP 248 (253)
Q Consensus 212 ~~~~~~~~~~~~~~~~~~~lv~h~~~~D~~~l~~~~~ 248 (253)
+. .+.+|||||+.||+.||+...+
T Consensus 85 l~-------------~~~~lvghn~~FD~~~L~~~~~ 108 (250)
T PRK06310 85 FK-------------EGDYIVGHSVGFDLQVLSQESE 108 (250)
T ss_pred hC-------------CCCEEEEECHHHHHHHHHHHHH
Confidence 92 2379999999999999976443
No 18
>PRK07740 hypothetical protein; Provisional
Probab=99.63 E-value=1.2e-15 Score=124.11 Aligned_cols=99 Identities=29% Similarity=0.378 Sum_probs=82.8
Q ss_pred cCCCceeeeecccccCCC---CCcccccceeeeecCCC-CeEEeeeccCCCCcccceeeeccCCHHhhcCCCCHHHHHHH
Q 025404 132 CRGPKAVAMDCEMVGGGS---NGTLDLCARVCLVDEDE-NVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDK 207 (253)
Q Consensus 132 ~~~~~~~~~dcE~~g~~~---~~~~~ll~~v~iv~~~~-~~~~~~~v~P~~~i~~~~~~~~Git~~~l~~~~~~~~v~~~ 207 (253)
-...+++++|+||+|... +.++++ +.+.+.+..- .-.+..+|+|..+++++..+++|||+++|++++++.+|..+
T Consensus 56 ~~~~~~vv~D~ETTGl~p~~~deIIeI-gaV~~~~~~i~~~~f~~lv~P~~~i~~~~~~ltGIt~e~l~~ap~~~evl~~ 134 (244)
T PRK07740 56 LTDLPFVVFDLETTGFSPQQGDEILSI-GAVKTKGGEVETDTFYSLVKPKRPIPEHILELTGITAEDVAFAPPLAEVLHR 134 (244)
T ss_pred ccCCCEEEEEEeCCCCCCCCCCeEEEE-EEEEEECCEEEEEEEEEEeCcCCCCChhheeccCCCHHHHhCCCCHHHHHHH
Confidence 345679999999999764 456666 7777642211 11477899999999999999999999999999999999999
Q ss_pred HHHHHhcCCCCCcccccCCCCeEEEeechhhhhhhhcC
Q 025404 208 ILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRM 245 (253)
Q Consensus 208 l~~~~~~~~~~~~~~~~~~~~~~lv~h~~~~D~~~l~~ 245 (253)
+.+++ ++.+|||||+.||+.||+-
T Consensus 135 f~~fi--------------~~~~lVahna~fD~~fL~~ 158 (244)
T PRK07740 135 FYAFI--------------GAGVLVAHHAGHDKAFLRH 158 (244)
T ss_pred HHHHh--------------CCCEEEEeCHHHHHHHHHH
Confidence 99999 7889999999999999964
No 19
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=99.61 E-value=2.7e-16 Score=145.33 Aligned_cols=104 Identities=27% Similarity=0.436 Sum_probs=93.0
Q ss_pred cCCCceeeeecccccCC--CCCcccccceeeeecCCCCe--EEeeeccCCCCcccceeeeccCCHHhhcCCCCHHHHHHH
Q 025404 132 CRGPKAVAMDCEMVGGG--SNGTLDLCARVCLVDEDENV--IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDK 207 (253)
Q Consensus 132 ~~~~~~~~~dcE~~g~~--~~~~~~ll~~v~iv~~~~~~--~~~~~v~P~~~i~~~~~~~~Git~~~l~~~~~~~~v~~~ 207 (253)
-....++++|.||||.+ .+..+++ +.+.+ .+|++ .++.+++|..|++...++++|||+++|++++++++|..+
T Consensus 418 l~datyVVfDiETTGLs~~~d~iIE~-aAvKi--kng~iId~f~~Fi~P~~pl~~~~telTgITdeml~~a~~i~~vL~k 494 (1444)
T COG2176 418 LDDATYVVFDIETTGLSPVYDEIIEI-AAVKI--KNGRIIDKFQFFIKPGRPLSATITELTGITDEMLENAPEIEEVLEK 494 (1444)
T ss_pred cccccEEEEEeecCCcCcccchhhhh-eeeee--eCCcchHHHHHhcCCCCcCchhhhhccccCHHHHcCCccHHHHHHH
Confidence 34566999999999976 6778888 88888 56666 789999999999999999999999999999999999999
Q ss_pred HHHHHhcCCCCCcccccCCCCeEEEeechhhhhhhhcCCCCCCCC
Q 025404 208 ILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNYPDHML 252 (253)
Q Consensus 208 l~~~~~~~~~~~~~~~~~~~~~~lv~h~~~~D~~~l~~~~~~~~~ 252 (253)
+.+++ .++||||||+.||++||+..+.++.+
T Consensus 495 f~~~~--------------~d~IlVAHNasFD~gFl~~~~~k~~~ 525 (1444)
T COG2176 495 FREFI--------------GDSILVAHNASFDMGFLNTNYEKYGL 525 (1444)
T ss_pred HHHHh--------------cCcEEEeccCccchhHHHHHHHHhCC
Confidence 99999 89999999999999999987776543
No 20
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.61 E-value=3.6e-16 Score=139.86 Aligned_cols=77 Identities=16% Similarity=0.336 Sum_probs=59.7
Q ss_pred ccccccccCChHHHHHHHHHccCCCCCC---ccccCccchhhhhhccccccccccCCCceeeeecc---cccCCCCCccc
Q 025404 81 CNLCMNIFDSPSSLIKHKEACSLSAPVP---FEKTLSNAESQKKISGAIDEKRTCRGPKAVAMDCE---MVGGGSNGTLD 154 (253)
Q Consensus 81 C~~C~k~f~~~~~l~~H~~~h~~~~~~~---C~~~f~~~~~l~~h~~~~~~~r~~~~~~~~~~dcE---~~g~~~~~~~~ 154 (253)
|-+|-+...-++.|+.|.|+|+||+||+ |++.|+++.+|+.|+..|..+ ...+ +.+.|. .|-..+...+.
T Consensus 608 CiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~---p~~R-~q~ScP~~~ic~~kftn~V~ 683 (958)
T KOG1074|consen 608 CIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAK---PPAR-VQFSCPSTFICQKKFTNAVT 683 (958)
T ss_pred eeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccC---cccc-ccccCCchhhhccccccccc
Confidence 9999999999999999999999999998 999999999999999777432 2222 567787 66554444444
Q ss_pred ccceeee
Q 025404 155 LCARVCL 161 (253)
Q Consensus 155 ll~~v~i 161 (253)
+--+|.+
T Consensus 684 lpQhIri 690 (958)
T KOG1074|consen 684 LPQHIRI 690 (958)
T ss_pred ccceEEe
Confidence 4334444
No 21
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=99.61 E-value=1.2e-15 Score=128.43 Aligned_cols=94 Identities=18% Similarity=0.346 Sum_probs=82.3
Q ss_pred ceeeeecccccCCCCCcccccceeeeecCCCCe--EEeeeccCCC-CcccceeeeccCCHHhhcCCCCHHHHHHHHHHHH
Q 025404 136 KAVAMDCEMVGGGSNGTLDLCARVCLVDEDENV--IFHTYVQPQL-PVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEIL 212 (253)
Q Consensus 136 ~~~~~dcE~~g~~~~~~~~ll~~v~iv~~~~~~--~~~~~v~P~~-~i~~~~~~~~Git~~~l~~~~~~~~v~~~l~~~~ 212 (253)
.++++|+||+|...+.++++ +.+.+. ++.+ .++.+|+|.. .+++..+++||||+++|+++|+|.+|+.+|.+++
T Consensus 2 ~~vviD~ETTg~~~d~IieI-gav~v~--~g~i~~~f~~lv~P~~~~~~~~~~~IhGIT~e~v~~ap~f~ev~~~~~~fl 78 (309)
T PRK06195 2 NFVAIDFETANEKRNSPCSI-GIVVVK--DGEIVEKVHYLIKPKEMRFMPINIGIHGIRPHMVEDELEFDKIWEKIKHYF 78 (309)
T ss_pred cEEEEEEeCCCCCCCceEEE-EEEEEE--CCEEEEEEEEEECCCCCCCChhheeccCcCHHHHhCCCCHHHHHHHHHHHh
Confidence 57899999999777888887 888874 4444 6889999985 5678889999999999999999999999999999
Q ss_pred hcCCCCCcccccCCCCeEEEeechhhhhhhhcCC
Q 025404 213 NNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMN 246 (253)
Q Consensus 213 ~~~~~~~~~~~~~~~~~~lv~h~~~~D~~~l~~~ 246 (253)
.+.+|||||+.||+.||+..
T Consensus 79 --------------~~~~lVaHNa~FD~~fL~~~ 98 (309)
T PRK06195 79 --------------NNNLVIAHNASFDISVLRKT 98 (309)
T ss_pred --------------CCCEEEEECcHHHHHHHHHH
Confidence 78899999999999999754
No 22
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=99.61 E-value=2.5e-15 Score=126.07 Aligned_cols=98 Identities=15% Similarity=0.245 Sum_probs=81.3
Q ss_pred cCCCceeeeecccccCCC--CCcccccceeeeecCCCCe--EEeeeccCCCCcccceeeeccCCHHhhcCCCCHHHHHHH
Q 025404 132 CRGPKAVAMDCEMVGGGS--NGTLDLCARVCLVDEDENV--IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDK 207 (253)
Q Consensus 132 ~~~~~~~~~dcE~~g~~~--~~~~~ll~~v~iv~~~~~~--~~~~~v~P~~~i~~~~~~~~Git~~~l~~~~~~~~v~~~ 207 (253)
.....++++|+||+|... +.++++ +.|.+.. +|.+ .|..+|+|..++.. ..+||||+++|+++|+|.+|+.+
T Consensus 43 ~~~~~fVvlDiETTGLdp~~drIIeI-gAV~i~~-~g~ive~f~tLVnP~~~~~p--~~LHGIT~e~La~AP~f~eVl~e 118 (377)
T PRK05601 43 IEAAPFVAVSIQTSGIHPSTSRLITI-DAVTLTA-DGEEVEHFHAVLNPGEDPGP--FHLHGLSAEEFAQGKRFSQILKP 118 (377)
T ss_pred CCCCCEEEEEEECCCCCCCCCeEEEE-EEEEEEc-CCEEEEEEEEEECcCCCCCC--ccccCCCHHHHhcCCCHHHHHHH
Confidence 344679999999999863 456666 7777742 3444 89999999876554 47999999999999999999999
Q ss_pred HHHHHhcCCCCCcccccCCCCeEEEeechhhhhhhhcCCC
Q 025404 208 ILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNY 247 (253)
Q Consensus 208 l~~~~~~~~~~~~~~~~~~~~~~lv~h~~~~D~~~l~~~~ 247 (253)
|.++| .+.+|||||+.||++||+...
T Consensus 119 l~~fL--------------~g~vLVaHNA~FD~~FL~~e~ 144 (377)
T PRK05601 119 LDRLI--------------DGRTLILHNAPRTWGFIVSEA 144 (377)
T ss_pred HHHHh--------------CCCEEEEECcHHHHHHHHHHH
Confidence 99999 889999999999999997743
No 23
>cd06131 DNA_pol_III_epsilon_Ecoli_like DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins. This subfamily is composed of the epsilon subunit of Escherichia coli DNA polymerase III (Pol III) and similar proteins. Pol III is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. It is a holoenzyme complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The epsilon
Probab=99.59 E-value=2.7e-15 Score=115.65 Aligned_cols=97 Identities=22% Similarity=0.430 Sum_probs=80.4
Q ss_pred eeeeecccccCCC---CCcccccceeeeecCCCC-eEEeeeccCCCCcccceeeeccCCHHhhcCCCCHHHHHHHHHHHH
Q 025404 137 AVAMDCEMVGGGS---NGTLDLCARVCLVDEDEN-VIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEIL 212 (253)
Q Consensus 137 ~~~~dcE~~g~~~---~~~~~ll~~v~iv~~~~~-~~~~~~v~P~~~i~~~~~~~~Git~~~l~~~~~~~~v~~~l~~~~ 212 (253)
++++|+||+|... +.++++ +.+.+.+.... ..+..+++|..++++...+++|||++++++++++.+|+.+|.+++
T Consensus 1 ~v~~D~ETTGl~~~~~~~iiei-g~v~v~~~~~~~~~~~~~v~P~~~i~~~~~~ihGIt~e~l~~~~~~~~v~~~l~~~l 79 (167)
T cd06131 1 QIVLDTETTGLDPREGHRIIEI-GCVELINRRLTGNTFHVYINPERDIPEEAFKVHGITDEFLADKPKFAEIADEFLDFI 79 (167)
T ss_pred CEEEEeeCCCCCCCCCCeEEEE-EEEEEECCcEeccEEEEEECCCCCCCHHHHHHhCCCHHHHhcCCCHHHHHHHHHHHH
Confidence 4789999999764 356666 66666432111 167889999999999999999999999999999999999999999
Q ss_pred hcCCCCCcccccCCCCeEEEeechhhhhhhhcCCCC
Q 025404 213 NNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNYP 248 (253)
Q Consensus 213 ~~~~~~~~~~~~~~~~~~lv~h~~~~D~~~l~~~~~ 248 (253)
.+.++||||+.||+.||+-...
T Consensus 80 --------------~~~~lv~hn~~fD~~~l~~~~~ 101 (167)
T cd06131 80 --------------RGAELVIHNASFDVGFLNAELS 101 (167)
T ss_pred --------------CCCeEEEeChHHhHHHHHHHHH
Confidence 6779999999999999976443
No 24
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=99.59 E-value=3.5e-15 Score=118.46 Aligned_cols=96 Identities=23% Similarity=0.363 Sum_probs=81.8
Q ss_pred CCCceeeeecccccCCC--CCcccccceeeeecCCCCe----EEeeeccCCCCcccceeeeccCCHHhhcCCCCHHHHHH
Q 025404 133 RGPKAVAMDCEMVGGGS--NGTLDLCARVCLVDEDENV----IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKD 206 (253)
Q Consensus 133 ~~~~~~~~dcE~~g~~~--~~~~~ll~~v~iv~~~~~~----~~~~~v~P~~~i~~~~~~~~Git~~~l~~~~~~~~v~~ 206 (253)
....++++|+||+|... +.++++ +.|.+.+ +.+ .++.+++|..+++++.++++|||++++++++++.+|+.
T Consensus 27 ~~~~~vviD~ETTGl~~~~d~IieI-gaV~~~~--~~~~~~~~f~~~i~p~~~i~~~~~~ihGIt~~~l~~~~~~~~vl~ 103 (202)
T PRK09145 27 PPDEWVALDCETTGLDPRRAEIVSI-AAVKIRG--NRILTSERLELLVRPPQSLSAESIKIHRLRHQDLEDGLSEEEALR 103 (202)
T ss_pred CCCCEEEEEeECCCCCCCCCceEEE-EEEEEEC--CEEeecCceEEEECCCCCCCHhHhhhcCcCHHHHhcCCCHHHHHH
Confidence 34578999999999753 566666 6666632 222 47889999999999999999999999999999999999
Q ss_pred HHHHHHhcCCCCCcccccCCCCeEEEeechhhhhhhhcC
Q 025404 207 KILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRM 245 (253)
Q Consensus 207 ~l~~~~~~~~~~~~~~~~~~~~~~lv~h~~~~D~~~l~~ 245 (253)
++.+++ ++.+|||||+.||+.||+-
T Consensus 104 ~~~~~i--------------~~~~lv~hn~~fD~~fL~~ 128 (202)
T PRK09145 104 QLLAFI--------------GNRPLVGYYLEFDVAMLNR 128 (202)
T ss_pred HHHHHH--------------cCCeEEEeCHHHHHHHHHH
Confidence 999999 7889999999999999974
No 25
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=99.58 E-value=5e-15 Score=124.22 Aligned_cols=97 Identities=25% Similarity=0.394 Sum_probs=83.8
Q ss_pred CCCceeeeecccccCCC--CCcccccceeeeecCCCCe--EEeeeccCCCCcccceeeeccCCHHhhcCCCCHHHHHHHH
Q 025404 133 RGPKAVAMDCEMVGGGS--NGTLDLCARVCLVDEDENV--IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKI 208 (253)
Q Consensus 133 ~~~~~~~~dcE~~g~~~--~~~~~ll~~v~iv~~~~~~--~~~~~v~P~~~i~~~~~~~~Git~~~l~~~~~~~~v~~~l 208 (253)
.+..++++|+||+|... +..+++ +.+.+. ++.+ .++.+|+|..++++..++++|||+++|.++++|.+|+.++
T Consensus 6 ~~~~~Vv~DlETTGl~p~~~eIIEI-gaV~v~--~g~i~~~f~~lVkP~~~I~~~a~~ihGIT~e~l~~~~~~~evl~~f 82 (313)
T PRK06807 6 LPLDYVVIDFETTGFNPYNDKIIQV-AAVKYR--NHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLF 82 (313)
T ss_pred CCCCEEEEEEECCCCCCCCCeEEEE-EEEEEE--CCEEEEEEEEEECcCCCCCHhhhccCCCCHHHHhCCCCHHHHHHHH
Confidence 34578999999999764 466676 777663 4555 5888999999999999999999999999999999999999
Q ss_pred HHHHhcCCCCCcccccCCCCeEEEeechhhhhhhhcCC
Q 025404 209 LEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMN 246 (253)
Q Consensus 209 ~~~~~~~~~~~~~~~~~~~~~~lv~h~~~~D~~~l~~~ 246 (253)
.+++ ++.+|||||+.||+.||+-.
T Consensus 83 ~~fl--------------~~~~lVaHNa~FD~~fL~~~ 106 (313)
T PRK06807 83 LAFL--------------HTNVIVAHNASFDMRFLKSN 106 (313)
T ss_pred HHHH--------------cCCeEEEEcHHHHHHHHHHH
Confidence 9999 77899999999999999754
No 26
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=99.56 E-value=6e-15 Score=117.79 Aligned_cols=88 Identities=19% Similarity=0.298 Sum_probs=75.4
Q ss_pred eeeeecccccCCCCCcccccceeeeecCCCCe--EEeeeccCCCCcccceeeeccCCHHhhcCCCCHHHHHHHHHHHHhc
Q 025404 137 AVAMDCEMVGGGSNGTLDLCARVCLVDEDENV--IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEILNN 214 (253)
Q Consensus 137 ~~~~dcE~~g~~~~~~~~ll~~v~iv~~~~~~--~~~~~v~P~~~i~~~~~~~~Git~~~l~~~~~~~~v~~~l~~~~~~ 214 (253)
++++|+||+|.. ..++++ +.+.+. ++.+ .+..+++|..+|+...+++||||+++++++|++.+++.. ++
T Consensus 2 ~~vlD~ETTGl~-~~IieI-g~v~v~--~~~i~~~~~~lv~P~~~i~~~~~~ihgIt~e~v~~ap~~~ev~~~---~~-- 72 (219)
T PRK07983 2 LRVIDTETCGLQ-GGIVEI-ASVDVI--DGKIVNPMSHLVRPDRPISPQAMAIHRITEAMVADKPWIEDVIPH---YY-- 72 (219)
T ss_pred eEEEEEECCCCC-CCCEEE-EEEEEE--CCEEEEEEEEEECcCCCCCHHHhhcCCCCHHHHcCCCCHHHHHHH---Hc--
Confidence 578999999975 347777 777775 4454 689999999999999999999999999999999999876 46
Q ss_pred CCCCCcccccCCCCeEEEeechhhhhhhhcC
Q 025404 215 GESTGRLMLDDGKARLLVGHGLEHDLDSLRM 245 (253)
Q Consensus 215 ~~~~~~~~~~~~~~~~lv~h~~~~D~~~l~~ 245 (253)
++.+|||||+.||.+||..
T Consensus 73 ------------~~~~lVaHNa~FD~~~L~~ 91 (219)
T PRK07983 73 ------------GSEWYVAHNASFDRRVLPE 91 (219)
T ss_pred ------------CCCEEEEeCcHhhHHHHhC
Confidence 6679999999999999964
No 27
>PRK06722 exonuclease; Provisional
Probab=99.56 E-value=5.4e-15 Score=121.45 Aligned_cols=98 Identities=16% Similarity=0.214 Sum_probs=82.9
Q ss_pred CceeeeecccccCC-----CCCcccccceeeeecCCCCe--EEeeeccCCCCcccceeeeccCCHHhhcCCCCHHHHHHH
Q 025404 135 PKAVAMDCEMVGGG-----SNGTLDLCARVCLVDEDENV--IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDK 207 (253)
Q Consensus 135 ~~~~~~dcE~~g~~-----~~~~~~ll~~v~iv~~~~~~--~~~~~v~P~~~i~~~~~~~~Git~~~l~~~~~~~~v~~~ 207 (253)
..++++|.||++.. .+.++++ +.|.+.+..+.+ .|+.+|+|..+|+++++++||||+++|.++|+|.+|+.+
T Consensus 5 ~~~vViD~ETT~~p~~~~~~deIIEI-GAVkV~~g~i~Ivd~F~sLV~P~~~I~~~i~~LTGIT~emV~~AP~f~eVl~e 83 (281)
T PRK06722 5 THFIVFDIERNFRPYKSEDPSEIVDI-GAVKIEASTMKVIGEFSELVKPGARLTRHTTKLTGITKKDLIGVEKFPQIIEK 83 (281)
T ss_pred CEEEEEEeeCCCCCCCCCCCCeEEEE-EEEEEECCceeEEeeEEEEECCCCcCCHhHhhhcCCCHHHHcCCCCHHHHHHH
Confidence 45899999998532 2567777 888885543455 599999999999999999999999999999999999999
Q ss_pred HHHHHhcCCCCCcccccCCCCeEEEeechhhhhhhhcCCC
Q 025404 208 ILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNY 247 (253)
Q Consensus 208 l~~~~~~~~~~~~~~~~~~~~~~lv~h~~~~D~~~l~~~~ 247 (253)
+.+++ ++.++|+||+.||++||+...
T Consensus 84 f~~fi--------------g~~~lvahna~FD~~FL~~~l 109 (281)
T PRK06722 84 FIQFI--------------GEDSIFVTWGKEDYRFLSHDC 109 (281)
T ss_pred HHHHH--------------CCCcEEEEEeHHHHHHHHHHH
Confidence 99999 666778888899999998743
No 28
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=99.55 E-value=8.9e-15 Score=119.53 Aligned_cols=97 Identities=25% Similarity=0.406 Sum_probs=83.2
Q ss_pred ccCCCceeeeecccccCCC--CCcccccceeeeecCCCCe--EEeeeccCCCCcccceeeeccCCHHhhcCCCCHHHHHH
Q 025404 131 TCRGPKAVAMDCEMVGGGS--NGTLDLCARVCLVDEDENV--IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKD 206 (253)
Q Consensus 131 ~~~~~~~~~~dcE~~g~~~--~~~~~ll~~v~iv~~~~~~--~~~~~v~P~~~i~~~~~~~~Git~~~l~~~~~~~~v~~ 206 (253)
......++++|+||+|... +.++++ +.+.+. ++.+ .+..+++|. +++.+.++++|||++++.+++++.+|+.
T Consensus 64 ~~~~~~~vv~DiETTG~~~~~~~IIEI-GAv~v~--~g~i~~~f~~~v~p~-~ip~~~~~itGIt~e~l~~ap~~~evl~ 139 (257)
T PRK08517 64 PIKDQVFCFVDIETNGSKPKKHQIIEI-GAVKVK--NGEIIDRFESFVKAK-EVPEYITELTGITYEDLENAPSLKEVLE 139 (257)
T ss_pred CCCCCCEEEEEEeCCCCCCCCCeEEEE-EEEEEE--CCEEEEEEEEEECCC-CCChhhhhhcCcCHHHHcCCCCHHHHHH
Confidence 3456678999999999764 356776 777774 4444 678899996 8999999999999999999999999999
Q ss_pred HHHHHHhcCCCCCcccccCCCCeEEEeechhhhhhhhcC
Q 025404 207 KILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRM 245 (253)
Q Consensus 207 ~l~~~~~~~~~~~~~~~~~~~~~~lv~h~~~~D~~~l~~ 245 (253)
++.+++ ++.++||||+.||+.||+.
T Consensus 140 ~f~~fl--------------~~~v~VaHNa~FD~~fL~~ 164 (257)
T PRK08517 140 EFRLFL--------------GDSVFVAHNVNFDYNFISR 164 (257)
T ss_pred HHHHHH--------------CCCeEEEECHHHHHHHHHH
Confidence 999999 7789999999999999975
No 29
>cd06136 TREX1_2 DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins. Three prime repair exonuclease (TREX)1 and TREX2 are closely related DEDDh-type DnaQ-like 3'-5' exonucleases. They contain three conserved sequence motifs known as ExoI, II, and III, with a specific Hx(4)D conserved pattern at ExoIII. These motifs contain four conserved acidic residues that participate in coordination of divalent metal ions required for catalysis. Both proteins play a role in the metabolism and clearance of DNA. TREX1 is the major 3'-5' exonuclease activity detected in mammalian cells. Mutations in the human TREX1 gene can cause Aicardi-Goutieres syndrome (AGS), which is characterized by perturbed innate immunity and presents itself as a severe neurological disease. TREX1 degrades ssDNA generated by aberrant replication intermediates to prevent checkpoint activation and autoimmune disease. There are distinct structural differences between TREX1 and TRE
Probab=99.54 E-value=5.8e-15 Score=114.67 Aligned_cols=100 Identities=22% Similarity=0.269 Sum_probs=77.5
Q ss_pred eeeeecccccCC---CCCcccccceeeeecCC---CC--------e--EEeeeccCCCCcccceeeeccCCHHhhcCCCC
Q 025404 137 AVAMDCEMVGGG---SNGTLDLCARVCLVDED---EN--------V--IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMP 200 (253)
Q Consensus 137 ~~~~dcE~~g~~---~~~~~~ll~~v~iv~~~---~~--------~--~~~~~v~P~~~i~~~~~~~~Git~~~l~~~~~ 200 (253)
++++|+||||.. .+.++++ +.+.+.+.. +. + .++.+++|..+|++..+++||||++++.++++
T Consensus 1 ~vv~D~ETTGl~~~~~d~Iiei-~av~v~~~~~~~~~~~~~~~~~~~~~~~~lv~P~~~I~~~a~~IhGIt~e~l~~~~~ 79 (177)
T cd06136 1 FVFLDLETTGLPKHNRPEITEL-CLVAVHRDHLLNTSRDKPALPRVLDKLSLCFNPGRAISPGASEITGLSNDLLEHKAP 79 (177)
T ss_pred CeEEeeecCCCCCCCCCceEEE-EEEEEecccccccccccccccceeeeeeEEeCCCCcCChhHHHHhCcCHHHHhcCCC
Confidence 478999999986 3566777 888774321 11 1 57899999999999999999999999999988
Q ss_pred HHH-HHHHHHHHHhcCCCCCcccccCCCCeEEEeech-hhhhhhhcCCC
Q 025404 201 LKE-VKDKILEILNNGESTGRLMLDDGKARLLVGHGL-EHDLDSLRMNY 247 (253)
Q Consensus 201 ~~~-v~~~l~~~~~~~~~~~~~~~~~~~~~~lv~h~~-~~D~~~l~~~~ 247 (253)
+.+ +++.+.+++... +.+.+|||||+ .||++||+-..
T Consensus 80 ~~~~~~~~l~~f~~~~----------~~~~~lVaHNa~~FD~~fL~~~~ 118 (177)
T cd06136 80 FDSDTANLIKLFLRRQ----------PKPICLVAHNGNRFDFPILRSEL 118 (177)
T ss_pred ccHHHHHHHHHHHHhc----------CCCCEEEEcCCcccCHHHHHHHH
Confidence 874 777777777210 12459999998 89999996544
No 30
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=99.54 E-value=1.8e-14 Score=121.20 Aligned_cols=97 Identities=25% Similarity=0.297 Sum_probs=79.9
Q ss_pred CCCceeeeecccccCCCC--CcccccceeeeecCCCCe--EEeeeccCCCCcccceeeeccCCHHhhcCCCCHHHHHHHH
Q 025404 133 RGPKAVAMDCEMVGGGSN--GTLDLCARVCLVDEDENV--IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKI 208 (253)
Q Consensus 133 ~~~~~~~~dcE~~g~~~~--~~~~ll~~v~iv~~~~~~--~~~~~v~P~~~i~~~~~~~~Git~~~l~~~~~~~~v~~~l 208 (253)
.+..++++|+||+|.... .++++ +.+.+. .+|.+ .+..+++|..+ ...+.+||||+++|.++|+|.+++.+|
T Consensus 13 ~~~~fvvlD~ETTGl~p~~d~IIeI-gav~v~-~~g~i~~~~~~lv~P~~~--~~~~~IhGIt~e~l~~ap~f~ev~~~l 88 (313)
T PRK06063 13 YPRGWAVVDVETSGFRPGQARIISL-AVLGLD-ADGNVEQSVVTLLNPGVD--PGPTHVHGLTAEMLEGQPQFADIAGEV 88 (313)
T ss_pred CCCCEEEEEEECCCCCCCCCEEEEE-EEEEEE-CCceeeeEEEEEECcCCC--CCCeecCCCCHHHHhCCCCHHHHHHHH
Confidence 356789999999997643 56666 555553 34555 68899999753 467899999999999999999999999
Q ss_pred HHHHhcCCCCCcccccCCCCeEEEeechhhhhhhhcCCC
Q 025404 209 LEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNY 247 (253)
Q Consensus 209 ~~~~~~~~~~~~~~~~~~~~~~lv~h~~~~D~~~l~~~~ 247 (253)
.+++ .+.+|||||+.||+.||+-..
T Consensus 89 ~~~l--------------~~~~lVaHNa~FD~~fL~~~~ 113 (313)
T PRK06063 89 AELL--------------RGRTLVAHNVAFDYSFLAAEA 113 (313)
T ss_pred HHHc--------------CCCEEEEeCHHHHHHHHHHHH
Confidence 9999 788999999999999998644
No 31
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=99.52 E-value=2.9e-14 Score=115.41 Aligned_cols=96 Identities=22% Similarity=0.383 Sum_probs=79.2
Q ss_pred ceeeeecccccCCC--CCcccccceeeeecCCCCeEEeeeccCCCCcccceeeeccCCHHhhcCCCCHHHHHHHHHHHHh
Q 025404 136 KAVAMDCEMVGGGS--NGTLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEILN 213 (253)
Q Consensus 136 ~~~~~dcE~~g~~~--~~~~~ll~~v~iv~~~~~~~~~~~v~P~~~i~~~~~~~~Git~~~l~~~~~~~~v~~~l~~~~~ 213 (253)
.++++|+||||... +.++++ +. ++......+..+++|..+|+...+++||||+++|+++|+|.+|++++.+++.
T Consensus 3 ~~vv~D~ETTGl~~~~d~IIei-g~---v~~~~~~~f~~lv~P~~~I~~~a~~IhGIt~e~v~~~p~f~ev~~~~~~fi~ 78 (232)
T PRK06309 3 ALIFYDTETTGTQIDKDRIIEI-AA---YNGVTSESFQTLVNPEIPIPAEASKIHGITTDEVADAPKFPEAYQKFIEFCG 78 (232)
T ss_pred cEEEEEeeCCCCCCCCCEEEEE-EE---EcCccccEEEEEeCCCCCCChhHHhhcCCCHHHHhCCCCHHHHHHHHHHHHc
Confidence 47899999999753 455555 43 4434445899999999999999999999999999999999999999999992
Q ss_pred cCCCCCcccccCCCCeEEEeec-hhhhhhhhcCCCC
Q 025404 214 NGESTGRLMLDDGKARLLVGHG-LEHDLDSLRMNYP 248 (253)
Q Consensus 214 ~~~~~~~~~~~~~~~~~lv~h~-~~~D~~~l~~~~~ 248 (253)
.+.+||||| +.||+.||+-...
T Consensus 79 -------------~~~~lVaHN~~~FD~~~L~~e~~ 101 (232)
T PRK06309 79 -------------TDNILVAHNNDAFDFPLLRKECR 101 (232)
T ss_pred -------------CCCEEEEeCCHHHHHHHHHHHHH
Confidence 346999999 5899999975443
No 32
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.52 E-value=2.3e-14 Score=134.60 Aligned_cols=95 Identities=21% Similarity=0.386 Sum_probs=83.3
Q ss_pred CCceeeeecccccCC-CCCcccccceeeeecCCCCe--EEeeeccCCCCcccceeeeccCCHHhhcCCCCHHHHHHHHHH
Q 025404 134 GPKAVAMDCEMVGGG-SNGTLDLCARVCLVDEDENV--IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILE 210 (253)
Q Consensus 134 ~~~~~~~dcE~~g~~-~~~~~~ll~~v~iv~~~~~~--~~~~~v~P~~~i~~~~~~~~Git~~~l~~~~~~~~v~~~l~~ 210 (253)
...++++|+||+|.. .+.++++ +.+.+. ++.+ .|..+|+|..+|+++++++||||++++.++|+|++|+.++.+
T Consensus 6 ~~~~vvvD~ETTGl~~~d~IIeI-gaV~v~--~g~i~~~f~~lv~P~~~i~~~~~~ltGIt~e~l~~ap~~~ev~~~~~~ 82 (820)
T PRK07246 6 LRKYAVVDLEATGAGPNASIIQV-GIVIIE--GGEIIDSYTTDVNPHEPLDEHIKHLTGITDQQLAQAPDFSQVARHIYD 82 (820)
T ss_pred CCCEEEEEEecCCcCCCCeEEEE-EEEEEE--CCEEEEEEEEEeCcCCCCCHhHhhcCCCCHHHHhcCCCHHHHHHHHHH
Confidence 456899999999975 3566666 777773 4555 688899999999999999999999999999999999999999
Q ss_pred HHhcCCCCCcccccCCCCeEEEeechhhhhhhhcC
Q 025404 211 ILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRM 245 (253)
Q Consensus 211 ~~~~~~~~~~~~~~~~~~~~lv~h~~~~D~~~l~~ 245 (253)
++ ++.++||||+.||+.||+-
T Consensus 83 ~l--------------~~~~lVaHN~~FD~~fL~~ 103 (820)
T PRK07246 83 LI--------------EDCIFVAHNVKFDANLLAE 103 (820)
T ss_pred Hh--------------CCCEEEEECcHHHHHHHHH
Confidence 99 7899999999999999964
No 33
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=99.51 E-value=5.6e-15 Score=120.63 Aligned_cols=115 Identities=26% Similarity=0.399 Sum_probs=102.6
Q ss_pred CCCc-ccc--cccccccCCHHHHHHhhhhcCCCCCcc-ccccccccccCHHHHhhhh-------CCCCCCCcCCcccccc
Q 025404 11 STAR-HKC--VACYKQFKRKDHLIEHMKISYHSVHQP-KCAVCQKLSKSFESLREHL-------TGPLSKAHCSGIFSDR 79 (253)
Q Consensus 11 ~~k~-~~C--~~C~k~f~~~~~l~~H~~~~~H~~~~~-~C~~C~~~f~~~~~l~~H~-------~~~~~C~~C~~~f~~~ 79 (253)
.+|| +.| ..|-+.|..++.|.+|.+. |++++. .|+.||..|+++..|-.|+ +.+|.|..|.|.|...
T Consensus 173 D~~pv~~C~W~~Ct~~~~~k~~LreH~r~--Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTe 250 (467)
T KOG3608|consen 173 DERPVTMCNWAMCTKHMGNKYRLREHIRT--HSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATE 250 (467)
T ss_pred CCCceeeccchhhhhhhccHHHHHHHHHh--cCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHH
Confidence 3444 667 6799999999999999999 999999 9999999999999999997 6799999999999876
Q ss_pred c--------------ccccccccCChHHHHHHHH-HccCCCCCC---ccccCccchhhhhhccccc
Q 025404 80 G--------------CNLCMNIFDSPSSLIKHKE-ACSLSAPVP---FEKTLSNAESQKKISGAID 127 (253)
Q Consensus 80 ~--------------C~~C~k~f~~~~~l~~H~~-~h~~~~~~~---C~~~f~~~~~l~~h~~~~~ 127 (253)
+ |+.|.-+....++|..|+| .|+..|||+ |++.|.+.+.|.+|...|+
T Consensus 251 klL~~Hv~rHvn~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS 316 (467)
T KOG3608|consen 251 KLLKSHVVRHVNCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS 316 (467)
T ss_pred HHHHHHHHHhhhcccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc
Confidence 4 9999999999999999998 588889998 8888999999999986543
No 34
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=99.51 E-value=4.3e-14 Score=114.32 Aligned_cols=105 Identities=22% Similarity=0.214 Sum_probs=80.4
Q ss_pred CCceeeeecccccCCC--CCcccccceeeeecCCCCe--EEeeeccCCCCcccceeeeccCCHHhhcC-CCCHHHHHHHH
Q 025404 134 GPKAVAMDCEMVGGGS--NGTLDLCARVCLVDEDENV--IFHTYVQPQLPVTNYRYEVTGLTEEDIKN-AMPLKEVKDKI 208 (253)
Q Consensus 134 ~~~~~~~dcE~~g~~~--~~~~~ll~~v~iv~~~~~~--~~~~~v~P~~~i~~~~~~~~Git~~~l~~-~~~~~~v~~~l 208 (253)
...++++|+||+|... +.++++ +.+.+ +.+|.+ .+..+++|..+|++..+++||||++++.. ++++.++..++
T Consensus 5 ~~~~vv~D~ETTGl~p~~d~Iiei-g~v~v-~~~g~~~~~~~~lv~P~~~i~~~a~~IhGIt~e~l~~~g~~~~~vl~e~ 82 (232)
T PRK07942 5 PGPLAAFDLETTGVDPETARIVTA-ALVVV-DADGEVVESREWLADPGVEIPEEASAVHGITTEYARAHGRPAAEVLAEI 82 (232)
T ss_pred cCcEEEEEeccCCCCCCCCeeEEE-EEEEE-eCCCccccceEEEECCCCCCCHHHHHHhCCCHHHHHhhCCCHHHHHHHH
Confidence 4568999999999763 445555 55555 333554 57889999999999999999999999975 68888888888
Q ss_pred HHHHhcCCCCCcccccCCCCeEEEeechhhhhhhhcCCCCC
Q 025404 209 LEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNYPD 249 (253)
Q Consensus 209 ~~~~~~~~~~~~~~~~~~~~~~lv~h~~~~D~~~l~~~~~~ 249 (253)
..+|.... ..+.+|||||+.||++||+....+
T Consensus 83 ~~~l~~~~---------~~~~~lVahNa~FD~~fL~~~~~r 114 (232)
T PRK07942 83 ADALREAW---------ARGVPVVVFNAPYDLTVLDRELRR 114 (232)
T ss_pred HHHHHHHh---------hcCCEEEEeCcHhhHHHHHHHHHH
Confidence 88772111 046799999999999999765433
No 35
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=99.51 E-value=2.7e-14 Score=110.13 Aligned_cols=99 Identities=33% Similarity=0.576 Sum_probs=80.9
Q ss_pred eeeeecccccCCCC--CcccccceeeeecCCCCeEEeeeccCCCCcccceeeeccCCHHhhcCCCCHHHHHHHHHHHHhc
Q 025404 137 AVAMDCEMVGGGSN--GTLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEILNN 214 (253)
Q Consensus 137 ~~~~dcE~~g~~~~--~~~~ll~~v~iv~~~~~~~~~~~v~P~~~i~~~~~~~~Git~~~l~~~~~~~~v~~~l~~~~~~ 214 (253)
++++|+||+|.... ..+++ +.+.+-+..-...++.+|+|..+++++.++++|||++++.+++++.+|+.++.+++
T Consensus 2 ~v~~D~Ettg~~~~~~~Iiei-g~v~~~~~~~~~~f~~~v~p~~~i~~~~~~~~Git~~~l~~~~~~~~~~~~~~~~l-- 78 (169)
T smart00479 2 LVVIDCETTGLDPGKDEIIEI-AAVDVDGGRIIVVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFL-- 78 (169)
T ss_pred EEEEEeeCCCCCCCCCeEEEE-EEEEEECCEeEEEEEEEECCCCCCCHHHHHHhCCCHHHHhCCCCHHHHHHHHHHHh--
Confidence 68999999997643 45555 55555322212379999999999999999999999999999999999999999999
Q ss_pred CCCCCcccccCCCCeEEEeech-hhhhhhhcCCCCCC
Q 025404 215 GESTGRLMLDDGKARLLVGHGL-EHDLDSLRMNYPDH 250 (253)
Q Consensus 215 ~~~~~~~~~~~~~~~~lv~h~~-~~D~~~l~~~~~~~ 250 (253)
.+.++||||. .||+.+|+....+.
T Consensus 79 ------------~~~~~v~~n~~~fD~~~L~~~~~~~ 103 (169)
T smart00479 79 ------------KGKILVAGNALNFDLRFLKLEHPRL 103 (169)
T ss_pred ------------cCCEEEEeCCHHHhHHHHHHHHHHh
Confidence 6678888887 99999999865543
No 36
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=99.49 E-value=3.9e-14 Score=112.80 Aligned_cols=96 Identities=22% Similarity=0.323 Sum_probs=77.7
Q ss_pred CceeeeecccccCC--------CCCcccccceeeeecCCCCe--EEeeeccCCC--CcccceeeeccCCHHhhcCCCCHH
Q 025404 135 PKAVAMDCEMVGGG--------SNGTLDLCARVCLVDEDENV--IFHTYVQPQL--PVTNYRYEVTGLTEEDIKNAMPLK 202 (253)
Q Consensus 135 ~~~~~~dcE~~g~~--------~~~~~~ll~~v~iv~~~~~~--~~~~~v~P~~--~i~~~~~~~~Git~~~l~~~~~~~ 202 (253)
..++++|+||+|.. .+.++++ +.|.+. ++.+ .|+.+|+|.. +++++.+++||||+++|.++|+|+
T Consensus 4 ~~~vvlD~EtTg~~~~~~~~~~~~eIIeI-GaV~v~--~~~i~~~f~~lV~P~~~~~i~~~~~~ltGIt~~~l~~ap~~~ 80 (207)
T PRK07748 4 QQFLFLDFEFTMPQHKKKPKGFFPEIIEV-GLVSVV--GCEVEDTFSSYVKPKTFPSLTERCKSFLGITQEDVDKGISFE 80 (207)
T ss_pred ceEEEEEeecCCcCCCCCCCCCCCceEEE-eEEEEe--cCcChhhhcceECCCccCccChhhhhhcCcCHHHHccCCCHH
Confidence 45899999999843 2456777 777774 3344 7999999986 689999999999999999999999
Q ss_pred HHHHHHHHHHhcCCCCCcccccCCCC-eEEEeechhhhhhhhcCCC
Q 025404 203 EVKDKILEILNNGESTGRLMLDDGKA-RLLVGHGLEHDLDSLRMNY 247 (253)
Q Consensus 203 ~v~~~l~~~~~~~~~~~~~~~~~~~~-~~lv~h~~~~D~~~l~~~~ 247 (253)
+|+++|.+++ ++ .++|.|+..||++||+...
T Consensus 81 evl~~f~~~~--------------~~~~~~iv~~~~fD~~fL~~~~ 112 (207)
T PRK07748 81 ELVEKLAEYD--------------KRCKPTIVTWGNMDMKVLKHNC 112 (207)
T ss_pred HHHHHHHHHh--------------CcCCeEEEEECHHHHHHHHHHH
Confidence 9999999999 55 3444456799999997543
No 37
>PRK05168 ribonuclease T; Provisional
Probab=99.48 E-value=8.4e-14 Score=111.04 Aligned_cols=108 Identities=24% Similarity=0.358 Sum_probs=80.6
Q ss_pred CCCceeeeecccccCC--CCCcccccceeeeec-CCCCe----EEeeeccC--CCCcccceeeeccCCHHh-hcCCCCHH
Q 025404 133 RGPKAVAMDCEMVGGG--SNGTLDLCARVCLVD-EDENV----IFHTYVQP--QLPVTNYRYEVTGLTEED-IKNAMPLK 202 (253)
Q Consensus 133 ~~~~~~~~dcE~~g~~--~~~~~~ll~~v~iv~-~~~~~----~~~~~v~P--~~~i~~~~~~~~Git~~~-l~~~~~~~ 202 (253)
....++++|+||+|.. .+.++++ +.+.+.. .+|.+ .|+.+++| ..+|+...++++|||+++ +.+++++.
T Consensus 15 ~~~~~vv~D~ETTGl~~~~d~IieI-gaV~v~~d~~g~i~~~~~f~~lv~P~~~~~i~~~~~~ihGIt~e~~~~~~~~~~ 93 (211)
T PRK05168 15 RGFLPVVIDVETAGFNAKTDALLEI-AAVTLKMDEQGWLYPDETLHFHVEPFEGANLEPEALAFNGIDPDNPLRGAVSEK 93 (211)
T ss_pred cCCceEEEEeeCCCCCCCCCEEEEE-eEEEEEecCCCcEeccceEEEEECCCCCCCCCHHHHhhcCCCchhhhhcCCChH
Confidence 3445799999999976 3566777 8887753 24542 68899999 468999999999999986 78889988
Q ss_pred HHHHHHHHHHhcCCCCCcccccCCCCeEEEeechhhhhhhhcCC
Q 025404 203 EVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMN 246 (253)
Q Consensus 203 ~v~~~l~~~~~~~~~~~~~~~~~~~~~~lv~h~~~~D~~~l~~~ 246 (253)
+++.++.+++..... .....+.+|||||+.||+.||+..
T Consensus 94 ~~l~~~~~~l~~~~~-----~~~~~~~~lVaHNa~FD~~fL~~~ 132 (211)
T PRK05168 94 EALHEIFKMVRKGIK-----ASGCNRAILVAHNAHFDLSFLMAA 132 (211)
T ss_pred HHHHHHHHHHHHHHH-----hcccCCceEEEeccHHhHHHHHHH
Confidence 888888887721000 000026799999999999999754
No 38
>PRK07883 hypothetical protein; Validated
Probab=99.47 E-value=6.1e-14 Score=126.48 Aligned_cols=98 Identities=29% Similarity=0.435 Sum_probs=84.6
Q ss_pred cCCCceeeeecccccCCC--CCcccccceeeeecCCCCe--EEeeeccCCCCcccceeeeccCCHHhhcCCCCHHHHHHH
Q 025404 132 CRGPKAVAMDCEMVGGGS--NGTLDLCARVCLVDEDENV--IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDK 207 (253)
Q Consensus 132 ~~~~~~~~~dcE~~g~~~--~~~~~ll~~v~iv~~~~~~--~~~~~v~P~~~i~~~~~~~~Git~~~l~~~~~~~~v~~~ 207 (253)
.....++++|+||+|... +.++++ +.+.+. ++.+ .+..+|+|..+++++.+++||||++++.+++++.+++.+
T Consensus 12 ~~~~~~Vv~D~ETTGl~p~~~~IIEI-gaV~v~--~g~iv~~f~~lV~P~~~i~~~~~~itGIt~e~l~~ap~~~evl~~ 88 (557)
T PRK07883 12 LRDVTFVVVDLETTGGSPAGDAITEI-GAVKVR--GGEVLGEFATLVNPGRPIPPFITVLTGITTAMVAGAPPIEEVLPA 88 (557)
T ss_pred CcCCCEEEEEEecCCCCCCCCeEEEE-EEEEEE--CCEEEEEEEEEECCCCCCChhHHhhcCCCHHHHhCCCCHHHHHHH
Confidence 344678999999999764 466676 777773 4444 588999999999999999999999999999999999999
Q ss_pred HHHHHhcCCCCCcccccCCCCeEEEeechhhhhhhhcCC
Q 025404 208 ILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMN 246 (253)
Q Consensus 208 l~~~~~~~~~~~~~~~~~~~~~~lv~h~~~~D~~~l~~~ 246 (253)
+.+++ ++.+|||||+.||+.||+..
T Consensus 89 f~~fl--------------~~~~lVaHNa~FD~~fL~~~ 113 (557)
T PRK07883 89 FLEFA--------------RGAVLVAHNAPFDIGFLRAA 113 (557)
T ss_pred HHHHh--------------cCCEEEEeCcHHHHHHHHHH
Confidence 99999 77899999999999999753
No 39
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=99.47 E-value=8.5e-14 Score=113.77 Aligned_cols=98 Identities=29% Similarity=0.466 Sum_probs=85.0
Q ss_pred CceeeeecccccCC--CCCcccccceeeeecCCCC-eEEeeeccCCCCcccceeeeccCCHHhhcCCCCHHHHHHHHHHH
Q 025404 135 PKAVAMDCEMVGGG--SNGTLDLCARVCLVDEDEN-VIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEI 211 (253)
Q Consensus 135 ~~~~~~dcE~~g~~--~~~~~~ll~~v~iv~~~~~-~~~~~~v~P~~~i~~~~~~~~Git~~~l~~~~~~~~v~~~l~~~ 211 (253)
..++++|+|++|.. .+.++++ +.|.+.+..-. ..++.+++|..+|++...+++|||.+++.++|.|.++.+++.++
T Consensus 13 ~~~vv~D~ETtg~~~~~~~iieI-gav~~~~~~i~~~~~~~~v~P~~~i~~~~~~i~git~e~l~~~p~~~~v~~~~~~~ 91 (243)
T COG0847 13 TRFVVIDLETTGLNPKKDRIIEI-GAVTLEDGRIVERSFHTLVNPERPIPPEIFKIHGITDEMLADAPKFAEVLPEFLDF 91 (243)
T ss_pred CcEEEEecccCCCCCCCCceEEE-EeEEEECCeeecceeEEEECCCCCCChhhhhhcCCCHHHHhcCCCHHHHHHHHHHH
Confidence 46799999999975 6777787 88888654222 24889999999999999999999999999999999999999999
Q ss_pred HhcCCCCCcccccCCCC-eEEEeechhhhhhhhcCCC
Q 025404 212 LNNGESTGRLMLDDGKA-RLLVGHGLEHDLDSLRMNY 247 (253)
Q Consensus 212 ~~~~~~~~~~~~~~~~~-~~lv~h~~~~D~~~l~~~~ 247 (253)
+ .+ .++||||+.||+.||+...
T Consensus 92 i--------------~~~~~~Vahna~fD~~fl~~~~ 114 (243)
T COG0847 92 I--------------GGLRLLVAHNAAFDVGFLRVES 114 (243)
T ss_pred H--------------CCCCeEEEEchhhcHHHHHHHH
Confidence 9 66 8999999999999997543
No 40
>cd06134 RNaseT DEDDh 3'-5' exonuclease domain of RNase T. RNase T is a DEDDh-type DnaQ-like 3'-5' exoribonuclease E implicated in the 3' maturation of small stable RNAs and 23srRNA, and in the end turnover of tRNA. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase T is related to the proofreading domain of DNA polymerase III. Despite its important role, RNase T is mainly found only in gammaproteobacteria. It is speculated that it might have originated from DNA polymerase III at the time the gamma division of proteobacteria diverged from other bacteria. RNase T is a homodimer with the catalytic residues of one monomer contacting a large basic patch on the other monomer to form a functional active site.
Probab=99.46 E-value=1.3e-13 Score=108.24 Aligned_cols=105 Identities=24% Similarity=0.309 Sum_probs=74.4
Q ss_pred ceeeeecccccCC--CCCcccccceeeeecC-CCCe----EEeeeccC--CCCcccceeeeccCCHHh-hcCCCCHHHHH
Q 025404 136 KAVAMDCEMVGGG--SNGTLDLCARVCLVDE-DENV----IFHTYVQP--QLPVTNYRYEVTGLTEED-IKNAMPLKEVK 205 (253)
Q Consensus 136 ~~~~~dcE~~g~~--~~~~~~ll~~v~iv~~-~~~~----~~~~~v~P--~~~i~~~~~~~~Git~~~-l~~~~~~~~v~ 205 (253)
..+++|+||+|.. .+.++++ +.+.+.+. +|.+ .++.+++| ..+|+....+++|||+++ +..++...++.
T Consensus 6 ~~vv~D~ETTGl~~~~d~Iiei-gav~v~~~~~~~i~~~~~f~~lv~P~~~~~i~~~~~~ihGIt~~~~~~~~~~~~~~~ 84 (189)
T cd06134 6 LPVVVDVETGGFNPQTDALLEI-AAVTLEMDEQGNLYPDETFHFHILPFEGANLDPAALEFNGIDPFHPFRFAVDEKEAL 84 (189)
T ss_pred eeEEEEecCCCCCCCCCeEEEE-EEEEEEECCCCceeccceEEEEEcCCCCCCCCHHHHhhcCCCchhhhccccchHHHH
Confidence 4689999999965 4567777 88888642 4433 78999999 568999999999999987 55666656655
Q ss_pred HHHHHHHhcCCCCCcccccCCCCeEEEeechhhhhhhhcCC
Q 025404 206 DKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMN 246 (253)
Q Consensus 206 ~~l~~~~~~~~~~~~~~~~~~~~~~lv~h~~~~D~~~l~~~ 246 (253)
.++++++.+-. + .....+.+|||||+.||+.||+..
T Consensus 85 ~~~~~~l~~~~--~---~~~~~~~~lVaHna~FD~~fL~~~ 120 (189)
T cd06134 85 KEIFKPIRKAL--K---AQGCTRAILVGHNAHFDLGFLNAA 120 (189)
T ss_pred HHHHHHHHHHH--h---hcccCCCeEEEecchhhHHHHHHH
Confidence 55555541000 0 000025799999999999999854
No 41
>TIGR01298 RNaseT ribonuclease T. in gamma-subdivision Proteobacteria such as Escherichia coli and Xylella fastidiosa. Ribonuclease T is homologous to the DNA polymerase III alpha chain. It can liberate AMP from the common C-C-A terminus of uncharged tRNA. It appears also to be involved in RNA maturation. It also acts as a 3' to 5' single-strand DNA-specific exonuclease; it is distinctive for its ability to remove residues near a double-stranded stem. Ribonuclease T is a high copy suppressor in E. coli of a uv-repair defect caused by deletion of three other single-stranded DNA exonucleases.
Probab=99.46 E-value=1.5e-13 Score=108.78 Aligned_cols=106 Identities=24% Similarity=0.337 Sum_probs=78.2
Q ss_pred CceeeeecccccCCC--CCcccccceeeee-cCCCCe----EEeeeccC--CCCcccceeeeccCCHH-hhcCCCCHHHH
Q 025404 135 PKAVAMDCEMVGGGS--NGTLDLCARVCLV-DEDENV----IFHTYVQP--QLPVTNYRYEVTGLTEE-DIKNAMPLKEV 204 (253)
Q Consensus 135 ~~~~~~dcE~~g~~~--~~~~~ll~~v~iv-~~~~~~----~~~~~v~P--~~~i~~~~~~~~Git~~-~l~~~~~~~~v 204 (253)
..++++|+||+|... +.++++ +.+.+. +.++.+ .+..+++| ..+|+....+++|||++ ++.+++++.++
T Consensus 8 ~~~vv~D~ETTGl~~~~d~IieI-gav~v~~~~~g~i~~~~~f~~~v~p~p~~~i~~~a~~ihGIt~~~~~~~~~~~~~~ 86 (200)
T TIGR01298 8 YLPVVVDVETGGFNAKTDALLEI-AAITLKMDEQGWLFPDTTLHFHVEPFEGANIQPEALEFTGIDLDHPLRGAVSEYEA 86 (200)
T ss_pred CeeEEEEeeCCCCCCCCCeEEEE-EEEEEEEcCCCcEeecceeEEEEcCCCCCCCCHHHHHccCCChhhhhhcCcchHHH
Confidence 457899999999763 456777 778775 334554 37889997 47899999999999976 58888988888
Q ss_pred HHHHHHHHhcCCCCCcccccCCCCeEEEeechhhhhhhhcCC
Q 025404 205 KDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMN 246 (253)
Q Consensus 205 ~~~l~~~~~~~~~~~~~~~~~~~~~~lv~h~~~~D~~~l~~~ 246 (253)
+.+++.++.... ...-.++.+|||||+.||++||+..
T Consensus 87 ~~~~~~~l~~~~-----~~~~~~~~~lVaHNa~FD~~fL~~~ 123 (200)
T TIGR01298 87 LHEIFKVVRKAM-----KASGCQRAILVGHNANFDLGFLNAA 123 (200)
T ss_pred HHHHHHHHHHHH-----HhcccCCCEEEEECchhhHHHHHHH
Confidence 888877761000 0000035699999999999999753
No 42
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.45 E-value=1.5e-13 Score=131.06 Aligned_cols=94 Identities=29% Similarity=0.536 Sum_probs=83.2
Q ss_pred CceeeeecccccCCC---CCcccccceeeeecCCCCe--EEeeeccCCCCcccceeeeccCCHHhhcCCCCHHHHHHHHH
Q 025404 135 PKAVAMDCEMVGGGS---NGTLDLCARVCLVDEDENV--IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKIL 209 (253)
Q Consensus 135 ~~~~~~dcE~~g~~~---~~~~~ll~~v~iv~~~~~~--~~~~~v~P~~~i~~~~~~~~Git~~~l~~~~~~~~v~~~l~ 209 (253)
.+++++|+||+|... +.++++ +.+.+. ++++ .|..+|+|..+|++++.++||||+++|+++|+|.+|+.+|.
T Consensus 3 ~~~vvvD~ETTG~~p~~~d~IIei-gav~v~--~~~i~~~f~~~v~P~~~i~~~~~~ltGIt~~~l~~ap~f~ev~~~l~ 79 (928)
T PRK08074 3 KRFVVVDLETTGNSPKKGDKIIQI-AAVVVE--DGEILERFSSFVNPERPIPPFITELTGISEEMVKQAPLFEDVAPEIV 79 (928)
T ss_pred CCEEEEEEeCCCCCCCCCCcEEEE-EEEEEE--CCEEEEEEEEEECcCCCCCHHHhhcCCCCHHHHhcCCCHHHHHHHHH
Confidence 458999999999753 456777 777773 4555 68999999999999999999999999999999999999999
Q ss_pred HHHhcCCCCCcccccCCCCeEEEeechhhhhhhhcC
Q 025404 210 EILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRM 245 (253)
Q Consensus 210 ~~~~~~~~~~~~~~~~~~~~~lv~h~~~~D~~~l~~ 245 (253)
+++ ++.++||||+.||+.||+-
T Consensus 80 ~~l--------------~~~~~VaHN~~FD~~fL~~ 101 (928)
T PRK08074 80 ELL--------------EGAYFVAHNVHFDLNFLNE 101 (928)
T ss_pred HHh--------------CCCeEEEEChHHHHHHHHH
Confidence 999 7899999999999999975
No 43
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.43 E-value=3.7e-14 Score=125.33 Aligned_cols=107 Identities=23% Similarity=0.351 Sum_probs=89.2
Q ss_pred cccccccccccCCHHHHHHhhhhcCCCCCcc--ccccccccccCHHHHhhhhCCCCCC---------CcCCccccccccc
Q 025404 14 RHKCVACYKQFKRKDHLIEHMKISYHSVHQP--KCAVCQKLSKSFESLREHLTGPLSK---------AHCSGIFSDRGCN 82 (253)
Q Consensus 14 ~~~C~~C~k~f~~~~~l~~H~~~~~H~~~~~--~C~~C~~~f~~~~~l~~H~~~~~~C---------~~C~~~f~~~~C~ 82 (253)
...|+.|.+.+.+...|+.|++.. |....+ .|..|.++|.+...|.+|+.-..+| ..|.+.|+ |.
T Consensus 210 lltcpycdrgykrltslkeHikyr-hekne~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFK---Ct 285 (1007)
T KOG3623|consen 210 LLTCPYCDRGYKRLTSLKEHIKYR-HEKNEPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFK---CT 285 (1007)
T ss_pred hhcchhHHHHHHHHHHHHHHHHHH-HhhCCCCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhcccc---cc
Confidence 368999999999999999999874 543333 9999999999999999999222222 34555554 99
Q ss_pred ccccccCChHHHHHHHHHccCCCCCC---ccccCccchhhhhhcc
Q 025404 83 LCMNIFDSPSSLIKHKEACSLSAPVP---FEKTLSNAESQKKISG 124 (253)
Q Consensus 83 ~C~k~f~~~~~l~~H~~~h~~~~~~~---C~~~f~~~~~l~~h~~ 124 (253)
+|||+|+.+..|+.|+|+|+|||||. |.++|+...+...|+.
T Consensus 286 ECgKAFKfKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHmS 330 (1007)
T KOG3623|consen 286 ECGKAFKFKHHLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHMS 330 (1007)
T ss_pred ccchhhhhHHHHHhhheeecCCCCcCCcccccccccCCccccccc
Confidence 99999999999999999999999997 8899999888888873
No 44
>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=99.43 E-value=1.4e-13 Score=132.38 Aligned_cols=99 Identities=25% Similarity=0.472 Sum_probs=86.6
Q ss_pred CCCceeeeecccccCC--CCCcccccceeeeecCCCCe--EEeeeccCCCCcccceeeeccCCHHhhcCCCCHHHHHHHH
Q 025404 133 RGPKAVAMDCEMVGGG--SNGTLDLCARVCLVDEDENV--IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKI 208 (253)
Q Consensus 133 ~~~~~~~~dcE~~g~~--~~~~~~ll~~v~iv~~~~~~--~~~~~v~P~~~i~~~~~~~~Git~~~l~~~~~~~~v~~~l 208 (253)
....++++|+||+|.. .+.++++ +.+.+. ++.+ .++.+|+|..+|++..++++|||+++|++++++.+|++++
T Consensus 188 ~~~~~VVfDiETTGL~~~~d~IIEI-GAVkv~--~g~iid~f~~~V~P~~~I~~~~~~ltGIT~e~L~~ap~~~evl~~f 264 (1213)
T TIGR01405 188 DDATYVVFDIETTGLSPQYDEIIEF-GAVKVK--NGRIIDKFQFFIKPHEPLSAFVTELTGITQDMLENAPEIEEVLEKF 264 (1213)
T ss_pred cCCcEEEEEeEecCCCCCCCeEEEE-EEEEEE--CCeEEEEEEEEECCCCCCCHHHHHHhCCCHHHHhCCCCHHHHHHHH
Confidence 3557999999999975 4567777 888874 3455 5899999999999999999999999999999999999999
Q ss_pred HHHHhcCCCCCcccccCCCCeEEEeechhhhhhhhcCCCC
Q 025404 209 LEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNYP 248 (253)
Q Consensus 209 ~~~~~~~~~~~~~~~~~~~~~~lv~h~~~~D~~~l~~~~~ 248 (253)
.+++ ++++|||||+.||+.||+-...
T Consensus 265 ~~fl--------------~~~iLVaHNa~FD~~fL~~~~~ 290 (1213)
T TIGR01405 265 KEFF--------------KDSILVAHNASFDIGFLNTNFE 290 (1213)
T ss_pred HHHh--------------CCCeEEEEChHHHHHHHHHHHH
Confidence 9999 7889999999999999986443
No 45
>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative. This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli.
Probab=99.42 E-value=2.8e-13 Score=128.51 Aligned_cols=92 Identities=26% Similarity=0.482 Sum_probs=82.0
Q ss_pred eeeeecccccCC--CCCcccccceeeeecCCCCe--EEeeeccCCCCcccceeeeccCCHHhhcCCCCHHHHHHHHHHHH
Q 025404 137 AVAMDCEMVGGG--SNGTLDLCARVCLVDEDENV--IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEIL 212 (253)
Q Consensus 137 ~~~~dcE~~g~~--~~~~~~ll~~v~iv~~~~~~--~~~~~v~P~~~i~~~~~~~~Git~~~l~~~~~~~~v~~~l~~~~ 212 (253)
++++|+||+|.. .+.++++ +.+.+ .+|++ .++.+|+|..+|+++.+++||||++++.++|+|.+|..+|.+++
T Consensus 2 ~vvvD~ETTG~~~~~~~IIei-g~v~v--~~~~i~~~f~~~v~P~~~i~~~~~~ltGIt~e~l~~ap~~~ev~~~l~~~l 78 (850)
T TIGR01407 2 YAVVDLETTGTQLSFDKIIQI-GIVVV--EDGEIVDTFHTDVNPNEPIPPFIQELTGISDNMLQQAPYFSQVAQEIYDLL 78 (850)
T ss_pred EEEEEEECCCCCCCCCeEEEE-EEEEE--ECCEEEEEEEEEeCCCCCCChhhhhhcCcCHHHHhCCCCHHHHHHHHHHHh
Confidence 689999999976 4566777 77777 34555 58999999999999999999999999999999999999999999
Q ss_pred hcCCCCCcccccCCCCeEEEeechhhhhhhhcC
Q 025404 213 NNGESTGRLMLDDGKARLLVGHGLEHDLDSLRM 245 (253)
Q Consensus 213 ~~~~~~~~~~~~~~~~~~lv~h~~~~D~~~l~~ 245 (253)
++.++||||+.||+.||+-
T Consensus 79 --------------~~~~~VahN~~fD~~fL~~ 97 (850)
T TIGR01407 79 --------------EDGIFVAHNVHFDLNFLAK 97 (850)
T ss_pred --------------CCCEEEEeCcHHHHHHHHH
Confidence 7889999999999999975
No 46
>PRK05359 oligoribonuclease; Provisional
Probab=99.40 E-value=5e-13 Score=103.90 Aligned_cols=104 Identities=18% Similarity=0.227 Sum_probs=78.7
Q ss_pred CceeeeecccccCC--CCCcccccceeeeecCCCCe---EEeeeccCCCC----cccceeeec---cCCHHhhcCCCCHH
Q 025404 135 PKAVAMDCEMVGGG--SNGTLDLCARVCLVDEDENV---IFHTYVQPQLP----VTNYRYEVT---GLTEEDIKNAMPLK 202 (253)
Q Consensus 135 ~~~~~~dcE~~g~~--~~~~~~ll~~v~iv~~~~~~---~~~~~v~P~~~----i~~~~~~~~---Git~~~l~~~~~~~ 202 (253)
.+++++|+||||.. .+.++++ +.+.+ +.+..+ .+..+++|... ++.+...++ |||++++++++++.
T Consensus 3 ~~~vvlD~ETTGLdp~~d~IieI-gaV~~-~~~~~~~~~~~~~~i~~~~~~l~~~~~~~~~ih~~tGIt~~~l~~~~~~~ 80 (181)
T PRK05359 3 DNLIWIDLEMTGLDPERDRIIEI-ATIVT-DADLNILAEGPVIAIHQSDEALAAMDEWNTRTHTRSGLIDRVRASTVSEA 80 (181)
T ss_pred CcEEEEEeecCCCCCCCCeEEEE-EEEEE-cCCceEcccceEEEECCCHHHhhccChHHHHhcccccCcHHHHhcCCCHH
Confidence 46899999999976 4566777 77755 333333 47788988754 456677776 89999999999999
Q ss_pred HHHHHHHHHHhcCCCCCcccccCCCCeEEEeechhhhhhhhcCCCC
Q 025404 203 EVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNYP 248 (253)
Q Consensus 203 ~v~~~l~~~~~~~~~~~~~~~~~~~~~~lv~h~~~~D~~~l~~~~~ 248 (253)
+|+.++.+++.. |.+ ..+.+|||||+.||+.||+...+
T Consensus 81 e~~~~~l~fl~~----~~~----~~~~~l~g~~v~FD~~FL~~~~~ 118 (181)
T PRK05359 81 EAEAQTLEFLKQ----WVP----AGKSPLCGNSIGQDRRFLARYMP 118 (181)
T ss_pred HHHHHHHHHHHH----hcC----CCCCceeecchhhCHHHHHHHHH
Confidence 999999999921 100 12468999999999999987654
No 47
>cd06127 DEDDh DEDDh 3'-5' exonuclease domain family. DEDDh exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. These proteins contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDh exonucleases are classified as such because of the presence of specific Hx(4)D conserved pattern at the ExoIII motif. The four conserved acidic residues are clustered around the active site and serve as ligands for the two metal ions required for catalysis. Most DEDDh exonucleases are the proofreading subunits (epsilon) or domains of bacterial DNA polymerase III, the main replicating enzyme in bacteria, which functions as the chromosomal replicase. Other members include other DNA and RNA exonucleases such as RNase T, Oligoribonuclease, and RNA exonuclease (REX), among others.
Probab=99.38 E-value=1e-12 Score=99.78 Aligned_cols=95 Identities=28% Similarity=0.436 Sum_probs=79.5
Q ss_pred eeeecccccCC--CCCcccccceeeeecCCCCe--EEeeeccCCCCcccceeeeccCCHHhhcCCCCHHHHHHHHHHHHh
Q 025404 138 VAMDCEMVGGG--SNGTLDLCARVCLVDEDENV--IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEILN 213 (253)
Q Consensus 138 ~~~dcE~~g~~--~~~~~~ll~~v~iv~~~~~~--~~~~~v~P~~~i~~~~~~~~Git~~~l~~~~~~~~v~~~l~~~~~ 213 (253)
+++|+||+|.. ....+++ +.+.+- .++++ .++.+++|...+.++..+++||+++++.+++++.+++.++.+++
T Consensus 1 v~~D~Ettg~~~~~~~iiei-~~v~~~-~~~~~~~~~~~~i~p~~~~~~~~~~~~gi~~~~~~~~~~~~~~~~~~~~~l- 77 (159)
T cd06127 1 VVFDTETTGLDPKKDRIIEI-GAVKVD-GGIEIVERFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFL- 77 (159)
T ss_pred CeEEeeCCCcCCCCCeEEEE-EEEEEE-CCcChhhhhheeeCcCCcCCHhheeccCCCHHHHhcCCCHHHHHHHHHHHH-
Confidence 46899999976 4556666 555553 22233 78999999999999999999999999999999999999999999
Q ss_pred cCCCCCcccccCCCCeEEEeechhhhhhhhcCCCC
Q 025404 214 NGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNYP 248 (253)
Q Consensus 214 ~~~~~~~~~~~~~~~~~lv~h~~~~D~~~l~~~~~ 248 (253)
.+.++||||+.||+.||+...+
T Consensus 78 -------------~~~~~v~~n~~fD~~~l~~~~~ 99 (159)
T cd06127 78 -------------GGRVLVAHNASFDLRFLNRELR 99 (159)
T ss_pred -------------CCCEEEEeCcHhhHHHHHHHHH
Confidence 5689999999999999986544
No 48
>PF00929 RNase_T: Exonuclease; InterPro: IPR013520 This entry includes a variety of exonuclease proteins, such as ribonuclease T [] and the epsilon subunit of DNA polymerase III. Ribonuclease T is responsible for the end-turnover of tRNA,and removes the terminal AMP residue from uncharged tRNA. DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria, and also exhibits 3' to 5' exonuclease activity.; PDB: 3CM6_A 3CM5_A 3CG7_A 1ZBU_B 1ZBH_A 1W0H_A 3NGY_C 2IS3_B 3NH1_C 3NH2_F ....
Probab=99.38 E-value=7.8e-14 Score=106.40 Aligned_cols=94 Identities=30% Similarity=0.542 Sum_probs=81.5
Q ss_pred eeeecccccCCC--CCcccccceeeeecCC--CCeEEeeeccCCCC--cccceeeeccCCHHhhcCCCCHHHHHHHHHHH
Q 025404 138 VAMDCEMVGGGS--NGTLDLCARVCLVDED--ENVIFHTYVQPQLP--VTNYRYEVTGLTEEDIKNAMPLKEVKDKILEI 211 (253)
Q Consensus 138 ~~~dcE~~g~~~--~~~~~ll~~v~iv~~~--~~~~~~~~v~P~~~--i~~~~~~~~Git~~~l~~~~~~~~v~~~l~~~ 211 (253)
+++|+||+|... ...+++ +.+.+.+.. ....++.+++|..+ ++++.++++|||.+++.+++++.+++.++.++
T Consensus 1 v~~D~Ettg~~~~~~~iiei-g~v~~~~~~~~~~~~~~~~i~p~~~~~i~~~~~~~~gIt~~~l~~~~~~~~~~~~~~~~ 79 (164)
T PF00929_consen 1 VVFDTETTGLDPRQDEIIEI-GAVKVDDDENEEVESFNSLIRPEEPPKISPWATKVHGITQEDLEDAPSFEEALDEFEEF 79 (164)
T ss_dssp EEEEEEESSSTTTTCTEEEE-EEEEEETTTTEEEEEEEEEBEHSSHCSSEHHHHHHHHHCHHHHHCHCEHHHHHHHHHHH
T ss_pred cEEEeEcCCCCCCCCeEEEE-EEEEeeCCccccceeeeecccccccccCCHHHeeecCCcccccccCCcHHHHHHhhhhh
Confidence 579999999775 677777 888887655 33489999999988 99999999999999999999999999999999
Q ss_pred HhcCCCCCcccccCCCCeEEEeechhhhhhhhcC
Q 025404 212 LNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRM 245 (253)
Q Consensus 212 ~~~~~~~~~~~~~~~~~~~lv~h~~~~D~~~l~~ 245 (253)
+. .+.++||||+.||..+|+-
T Consensus 80 ~~-------------~~~~~v~~n~~fd~~~l~~ 100 (164)
T PF00929_consen 80 LK-------------KNDILVGHNASFDIGFLRR 100 (164)
T ss_dssp HH-------------HHTEEEETTCCHEEESSHH
T ss_pred hh-------------cccccccccccchhhHHHH
Confidence 93 3679999999999988753
No 49
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=99.37 E-value=1.4e-12 Score=108.55 Aligned_cols=98 Identities=19% Similarity=0.242 Sum_probs=76.9
Q ss_pred CCCceeeeecccccCCC--CCcccccceeeeec-CCCCe-----EEeeeccCCCCcccceeeeccCCHHhhcCCCCHHHH
Q 025404 133 RGPKAVAMDCEMVGGGS--NGTLDLCARVCLVD-EDENV-----IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEV 204 (253)
Q Consensus 133 ~~~~~~~~dcE~~g~~~--~~~~~ll~~v~iv~-~~~~~-----~~~~~v~P~~~i~~~~~~~~Git~~~l~~~~~~~~v 204 (253)
....++++|+||||... +.++++ +.|.+.. .+|.+ .++.+++|..+|+...+++||||++++.+++...
T Consensus 35 ~~~~~vvlD~ETTGLd~~~d~IIEI-g~V~v~~~~~g~i~~v~~~~~~lv~P~~~I~~~~t~IhGIt~e~v~~~~~~~-- 111 (294)
T PRK09182 35 FVRLGVILDTETTGLDPRKDEIIEI-GMVAFEYDDDGRIGDVLDTFGGLQQPSRPIPPEITRLTGITDEMVAGQTIDP-- 111 (294)
T ss_pred CCCeEEEEEeeCCCCCCCCCeEEEE-EEEEEEecCCCceeeeeeEEEEEeCCCCCCCHHHHHhcCCCHHHHhcCCCcH--
Confidence 34567999999999764 567777 7777742 24432 5788999999999999999999999999987643
Q ss_pred HHHHHHHHhcCCCCCcccccCCCCeEEEeechhhhhhhhcCCC
Q 025404 205 KDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNY 247 (253)
Q Consensus 205 ~~~l~~~~~~~~~~~~~~~~~~~~~~lv~h~~~~D~~~l~~~~ 247 (253)
..|.+++. .+.+|||||+.||+.||+...
T Consensus 112 -~~l~~fl~-------------~~~vlVAHNA~FD~~fL~~~~ 140 (294)
T PRK09182 112 -AAVDALIA-------------PADLIIAHNAGFDRPFLERFS 140 (294)
T ss_pred -HHHHHHhc-------------CCCEEEEeCHHHHHHHHHHHH
Confidence 35677782 345999999999999997643
No 50
>cd06138 ExoI_N N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins. This subfamily is composed of the N-terminal domain of Escherichia coli exonuclease I (ExoI) and similar proteins. ExoI is a monomeric enzyme that hydrolyzes single stranded DNA in the 3' to 5' direction. It plays a role in DNA recombination and repair. It primarily functions in repairing frameshift mutations. The N-terminal domain of ExoI is a DEDDh-type DnaQ-like 3'-5 exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The ExoI structure is unique among DnaQ family enzymes in that there is a large distance between the two metal ions required for catalysis and the catalytic histidine is oriented away from the active site.
Probab=99.35 E-value=1.4e-12 Score=101.89 Aligned_cols=95 Identities=23% Similarity=0.283 Sum_probs=74.4
Q ss_pred eeeecccccCC--CCCcccccceeeeecCCCCe--EEeeeccCCC--CcccceeeeccCCHHhhcC-CCCHHHHHHHHHH
Q 025404 138 VAMDCEMVGGG--SNGTLDLCARVCLVDEDENV--IFHTYVQPQL--PVTNYRYEVTGLTEEDIKN-AMPLKEVKDKILE 210 (253)
Q Consensus 138 ~~~dcE~~g~~--~~~~~~ll~~v~iv~~~~~~--~~~~~v~P~~--~i~~~~~~~~Git~~~l~~-~~~~~~v~~~l~~ 210 (253)
.++|+||+|.. .+.++++ +.+.+ +.++.+ .++.+++|.. +++.....++|||+++|.+ ++++.+++.++..
T Consensus 1 ~~~D~ETTGl~~~~d~Iiei-g~v~v-~~~~~~~~~~~~~v~p~~~~~~~~~a~~ihGIt~e~l~~~~~~~~~~l~~~~~ 78 (183)
T cd06138 1 LFYDYETFGLNPSFDQILQF-AAIRT-DENFNEIEPFNIFCRLPPDVLPSPEALIVTGITPQQLLKEGLSEYEFIAKIHR 78 (183)
T ss_pred CEEEeecCCCCCCCCceEEE-EEEEE-CCCCCCccceeEEEeCCCCCCCCHHHHHHhCCCHHHHHhcCCCHHHHHHHHHH
Confidence 36899999975 4466666 66655 223333 5788998874 5677888999999999999 8999999999999
Q ss_pred HHhcCCCCCcccccCCCCeEEEeec-hhhhhhhhcCC
Q 025404 211 ILNNGESTGRLMLDDGKARLLVGHG-LEHDLDSLRMN 246 (253)
Q Consensus 211 ~~~~~~~~~~~~~~~~~~~~lv~h~-~~~D~~~l~~~ 246 (253)
++.. .+.+||||| +.||+.||+..
T Consensus 79 ~~~~------------~~~~lVahn~~~FD~~fL~~~ 103 (183)
T cd06138 79 LFNT------------PGTCIVGYNNIRFDDEFLRFA 103 (183)
T ss_pred HHcc------------CCCcEEeeCchhhHHHHHHHH
Confidence 9921 356999997 89999999753
No 51
>cd06135 Orn DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins. Oligoribonuclease (Orn) is a DEDDh-type DnaQ-like 3'-5' exoribonuclease that is responsible for degrading small oligoribonucleotides to mononucleotides. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Orn is essential for Escherichia coli survival. The human homolog, also called Sfn (small fragment nuclease), is able to hydrolyze short single-stranded RNA and DNA oligomers. It plays a role in cellular nucleotide recycling.
Probab=99.35 E-value=7.5e-13 Score=102.42 Aligned_cols=101 Identities=20% Similarity=0.215 Sum_probs=75.8
Q ss_pred eeeecccccCC--CCCcccccceeeeecCCCCe--EEeeeccCCCCcc----cceeee---ccCCHHhhcCCCCHHHHHH
Q 025404 138 VAMDCEMVGGG--SNGTLDLCARVCLVDEDENV--IFHTYVQPQLPVT----NYRYEV---TGLTEEDIKNAMPLKEVKD 206 (253)
Q Consensus 138 ~~~dcE~~g~~--~~~~~~ll~~v~iv~~~~~~--~~~~~v~P~~~i~----~~~~~~---~Git~~~l~~~~~~~~v~~ 206 (253)
+++|+||+|.. .+.++++ +.+.+.+..+.+ .|+.+++|..+++ .+..++ +||+++++++++++.+++.
T Consensus 2 v~iD~ETTGl~p~~d~IieI-gaV~~~~~~~~i~~~f~~~i~p~~~~~~~~~~~~~~ih~~tgIt~~~l~~~~~~~~vl~ 80 (173)
T cd06135 2 VWIDLEMTGLDPEKDRILEI-ACIITDGDLNIIAEGPELVIHQPDEVLDGMDEWCTEMHTKSGLTERVRASTVTLAQAEA 80 (173)
T ss_pred EEEEEecCCCCCCCCeeEEE-EEEEEeCCCceecCceeEEECCCHHHhhhccHHHHHcccccccHHHHHhCCCCHHHHHH
Confidence 68999999977 3566777 777663322333 6899999987654 344445 6999999999999999999
Q ss_pred HHHHHHhcCCCCCcccccCCCCeEEEeechhhhhhhhcCCC
Q 025404 207 KILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNY 247 (253)
Q Consensus 207 ~l~~~~~~~~~~~~~~~~~~~~~~lv~h~~~~D~~~l~~~~ 247 (253)
++.+++.+.. .....+|||||+.||+.||+-..
T Consensus 81 ~~~~f~~~~~--------~~~~~~lvgh~~~FD~~fL~~~~ 113 (173)
T cd06135 81 ELLEFIKKYV--------PKGKSPLAGNSVHQDRRFLDKYM 113 (173)
T ss_pred HHHHHHHHhc--------CCCCCceeecchhhCHHHHHHHH
Confidence 9999993100 00235999999999999998654
No 52
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.31 E-value=7.8e-13 Score=100.46 Aligned_cols=67 Identities=25% Similarity=0.439 Sum_probs=57.6
Q ss_pred CCCCcccccccccccCCHHHHHHhhhhcCCCCCcc-ccccccccccCHHHHhhhh-----CCCCCCCcCCccccc
Q 025404 10 RSTARHKCVACYKQFKRKDHLIEHMKISYHSVHQP-KCAVCQKLSKSFESLREHL-----TGPLSKAHCSGIFSD 78 (253)
Q Consensus 10 ~~~k~~~C~~C~k~f~~~~~l~~H~~~~~H~~~~~-~C~~C~~~f~~~~~l~~H~-----~~~~~C~~C~~~f~~ 78 (253)
++.-.|.|..|+|.|.....|.+|++. |+..+- .|..||+.|...-.|++|+ .+||.|..|+|+|..
T Consensus 113 sd~d~ftCrvCgK~F~lQRmlnrh~kc--h~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftq 185 (267)
T KOG3576|consen 113 SDQDSFTCRVCGKKFGLQRMLNRHLKC--HSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQ 185 (267)
T ss_pred CCCCeeeeehhhhhhhHHHHHHHHhhh--ccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHh
Confidence 345679999999999999999999999 998888 9999999999999999998 578987665555543
No 53
>cd06133 ERI-1_3'hExo_like DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins. This subfamily is composed of Caenorhabditis elegans ERI-1, human 3' exonuclease (3'hExo), Drosophila exonuclease snipper (snp), and similar proteins from eukaryotes and bacteria. These are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ERI-1 has been implicated in the degradation of small interfering RNAs (RNAi). 3'hExo participates in the degradation of histone mRNAs. Snp is a non-essential exonuclease that efficiently degrades structured RNA and DNA substrates as long as there is a minimum of 2 nucleotides in the 3' overhang to initiate degradation. Snp is not a functional ho
Probab=99.27 E-value=8.9e-12 Score=96.73 Aligned_cols=94 Identities=26% Similarity=0.381 Sum_probs=74.8
Q ss_pred eeeeecccccCCC-------CCcccccceeeeecCCCCe--EEeeeccCCC--CcccceeeeccCCHHhhcCCCCHHHHH
Q 025404 137 AVAMDCEMVGGGS-------NGTLDLCARVCLVDEDENV--IFHTYVQPQL--PVTNYRYEVTGLTEEDIKNAMPLKEVK 205 (253)
Q Consensus 137 ~~~~dcE~~g~~~-------~~~~~ll~~v~iv~~~~~~--~~~~~v~P~~--~i~~~~~~~~Git~~~l~~~~~~~~v~ 205 (253)
++++|+||+|... +.++++ +.+.+....+.+ .++.+|+|.. +++++..+++|||++++.+++++++|+
T Consensus 1 ~vv~D~Ettg~~~~~~~~~~~~IieI-gav~v~~~~~~~~~~f~~~i~P~~~~~i~~~~~~i~gIt~e~l~~~~~~~~vl 79 (176)
T cd06133 1 YLVIDFEATCWEGNSKPDYPNEIIEI-GAVLVDVKTKEIIDTFSSYVKPVINPKLSDFCTELTGITQEDVDNAPSFPEVL 79 (176)
T ss_pred CEEEEeeccccCCCCCCCCCcceEEE-EEEEEEcCCCeEEeeeeeeECCCcCCchhHHHHHhcCcCHHHHhcCCCHHHHH
Confidence 4789999999764 456666 666664333323 7899999998 899999999999999999999999999
Q ss_pred HHHHHHHhcCCCCCcccccCCCCe--EEEeechhhhhhhhcC
Q 025404 206 DKILEILNNGESTGRLMLDDGKAR--LLVGHGLEHDLDSLRM 245 (253)
Q Consensus 206 ~~l~~~~~~~~~~~~~~~~~~~~~--~lv~h~~~~D~~~l~~ 245 (253)
.++.+++ ++. .+++|+..||+.+|.-
T Consensus 80 ~~~~~~l--------------~~~~~~~~v~~~~~d~~~l~~ 107 (176)
T cd06133 80 KEFLEWL--------------GKNGKYAFVTWGDWDLKDLLQ 107 (176)
T ss_pred HHHHHHH--------------HhCCCeEEEeecHhhHHHHHH
Confidence 9999999 454 4555556999887654
No 54
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=99.26 E-value=4.1e-12 Score=104.08 Aligned_cols=130 Identities=19% Similarity=0.329 Sum_probs=94.4
Q ss_pred CCcccccccccccCCHHHHHHhhhhcCCCCCccccccccccccCHHHHhhhh------CCCCCCCcCCccccccc-----
Q 025404 12 TARHKCVACYKQFKRKDHLIEHMKISYHSVHQPKCAVCQKLSKSFESLREHL------TGPLSKAHCSGIFSDRG----- 80 (253)
Q Consensus 12 ~k~~~C~~C~k~f~~~~~l~~H~~~~~H~~~~~~C~~C~~~f~~~~~l~~H~------~~~~~C~~C~~~f~~~~----- 80 (253)
..+|.|..|.|.|.+...|..|+.. |.. -.+|+.|+......++|.+|+ .+||+|..|++.|...+
T Consensus 235 ~n~fqC~~C~KrFaTeklL~~Hv~r--Hvn-~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH 311 (467)
T KOG3608|consen 235 TNSFQCAQCFKRFATEKLLKSHVVR--HVN-CYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKH 311 (467)
T ss_pred CCchHHHHHHHHHhHHHHHHHHHHH--hhh-cccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHH
Confidence 3478888888888888888888877 542 127888888888888888887 67888888888887653
Q ss_pred ----------ccc--cccccCChHHHHHHHHHcc-CCCC--CC---ccccCccchhhhhhccccccccccCCCceeeeec
Q 025404 81 ----------CNL--CMNIFDSPSSLIKHKEACS-LSAP--VP---FEKTLSNAESQKKISGAIDEKRTCRGPKAVAMDC 142 (253)
Q Consensus 81 ----------C~~--C~k~f~~~~~l~~H~~~h~-~~~~--~~---C~~~f~~~~~l~~h~~~~~~~r~~~~~~~~~~dc 142 (253)
|+. |..+|.+..++++|++.++ |..| |. |++.|.+-.+|..|....++-+.+..-+-+.+..
T Consensus 312 ~~~HS~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np~~Y~CH~Cdr~ft~G~~L~~HL~kkH~f~~PsGh~RFtYk~ 391 (467)
T KOG3608|consen 312 VQVHSKTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNPILYACHCCDRFFTSGKSLSAHLMKKHGFRLPSGHKRFTYKV 391 (467)
T ss_pred HHhccccceecCCCCCcHHHHHHHHHHHHHHHhccCCCCCceeeecchhhhccchhHHHHHHHhhcccCCCCCCceeeee
Confidence 776 8888888888888888665 5443 44 8888888888888876555555444444444443
Q ss_pred cc
Q 025404 143 EM 144 (253)
Q Consensus 143 E~ 144 (253)
..
T Consensus 392 ~e 393 (467)
T KOG3608|consen 392 DE 393 (467)
T ss_pred cc
Confidence 33
No 55
>PTZ00315 2'-phosphotransferase; Provisional
Probab=99.24 E-value=1.9e-11 Score=108.65 Aligned_cols=105 Identities=21% Similarity=0.252 Sum_probs=80.3
Q ss_pred CceeeeecccccCC-----CCCcccccceeeeecCCCCe--EEeeeccCCC--CcccceeeeccCCHHhhcCCCCHHHHH
Q 025404 135 PKAVAMDCEMVGGG-----SNGTLDLCARVCLVDEDENV--IFHTYVQPQL--PVTNYRYEVTGLTEEDIKNAMPLKEVK 205 (253)
Q Consensus 135 ~~~~~~dcE~~g~~-----~~~~~~ll~~v~iv~~~~~~--~~~~~v~P~~--~i~~~~~~~~Git~~~l~~~~~~~~v~ 205 (253)
..++++|.|+||.. .+.++++ +.|.+--.++++ .|+.||+|.. +++++++++||||+++|+++++|.+|+
T Consensus 56 d~~IV~DlETTgl~~~~~~~dEIIEI-GaV~Vd~~ng~Ii~~F~~yVkP~~~p~Ls~fct~LTGITqe~V~~Ap~F~eVl 134 (582)
T PTZ00315 56 DAYVVLDFEATCEADRRIEDAEVIEF-PMVLVDARTATPVAEFQRYVRPVKNPVLSRFCTELTGITQSMVSRADPFPVVY 134 (582)
T ss_pred CeEEEEEEecCCCCCCCCCCCceEEE-EEEEEEccCCEEEEEEEEEECCCCCCCCChhHhhhcCcCHHHHhcCCCHHHHH
Confidence 56899999999964 2456676 666663235655 7899999986 699999999999999999999999999
Q ss_pred HHHHHHHhcCCCCCcccccCCCCeEEEeechhhhhh-hhc
Q 025404 206 DKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLD-SLR 244 (253)
Q Consensus 206 ~~l~~~~~~~~~~~~~~~~~~~~~~lv~h~~~~D~~-~l~ 244 (253)
.++.++|.+... +. ....+..+|+||..||+. ||.
T Consensus 135 ~ef~~fL~~~~~-~e---~~~~~~~~vah~g~fDl~~fL~ 170 (582)
T PTZ00315 135 CEALQFLAEAGL-GD---APPLRSYCVVTCGDWDLKTMLP 170 (582)
T ss_pred HHHHHHHhcccc-cc---ccccCceEEEeccHHHHHHHHH
Confidence 999999932110 00 011234799999999995 773
No 56
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.17 E-value=9.9e-12 Score=110.27 Aligned_cols=55 Identities=31% Similarity=0.535 Sum_probs=37.9
Q ss_pred CCCCCCCcccccccccccCCHHHHHHhhhhcCCCCCcc-ccccccccccCHHHHhhhh
Q 025404 7 LPKRSTARHKCVACYKQFKRKDHLIEHMKISYHSVHQP-KCAVCQKLSKSFESLREHL 63 (253)
Q Consensus 7 ~~~~~~k~~~C~~C~k~f~~~~~l~~H~~~~~H~~~~~-~C~~C~~~f~~~~~l~~H~ 63 (253)
+-.+.+.+|.|+.|+|.|...+.|.+|.-. |+|++| +|.+|.|.|..+..|..|.
T Consensus 887 ~~kte~gmyaCDqCDK~FqKqSSLaRHKYE--HsGqRPyqC~iCkKAFKHKHHLtEHk 942 (1007)
T KOG3623|consen 887 HAKTEDGMYACDQCDKAFQKQSSLARHKYE--HSGQRPYQCIICKKAFKHKHHLTEHK 942 (1007)
T ss_pred cccCccccchHHHHHHHHHhhHHHHHhhhh--hcCCCCcccchhhHhhhhhhhhhhhh
Confidence 344556778888888888888888888777 888776 6666555555555444444
No 57
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.16 E-value=3.2e-12 Score=97.17 Aligned_cols=97 Identities=21% Similarity=0.270 Sum_probs=73.1
Q ss_pred ccccccccccCHHHHhhhhCCCCCCCcCCcccccccccccccccCChHHHHHHHHHccCCCCCC---ccccCccchhhhh
Q 025404 45 KCAVCQKLSKSFESLREHLTGPLSKAHCSGIFSDRGCNLCMNIFDSPSSLIKHKEACSLSAPVP---FEKTLSNAESQKK 121 (253)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~~~~~~C~~C~~~f~~~~C~~C~k~f~~~~~l~~H~~~h~~~~~~~---C~~~f~~~~~l~~ 121 (253)
.|.+|+|.|...--|.+|+. | -...+..-|..|||.|.....|++|+|+|+|.+||+ |+++|.+.-+|..
T Consensus 119 tCrvCgK~F~lQRmlnrh~k----c---h~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsles 191 (267)
T KOG3576|consen 119 TCRVCGKKFGLQRMLNRHLK----C---HSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLES 191 (267)
T ss_pred eeehhhhhhhHHHHHHHHhh----h---ccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHH
Confidence 88999999988888888862 1 001111127789999999999999999999999998 9999999999999
Q ss_pred hcccccccc---ccCCCceeeeecccccCC
Q 025404 122 ISGAIDEKR---TCRGPKAVAMDCEMVGGG 148 (253)
Q Consensus 122 h~~~~~~~r---~~~~~~~~~~dcE~~g~~ 148 (253)
|....++.. .+...+...+.||-||..
T Consensus 192 hl~kvhgv~~~yaykerr~kl~vcedcg~t 221 (267)
T KOG3576|consen 192 HLKKVHGVQHQYAYKERRAKLYVCEDCGYT 221 (267)
T ss_pred HHHHHcCchHHHHHHHhhhheeeecccCCC
Confidence 986544322 233444566779999964
No 58
>PRK11779 sbcB exonuclease I; Provisional
Probab=99.13 E-value=1.1e-10 Score=102.93 Aligned_cols=103 Identities=16% Similarity=0.211 Sum_probs=78.5
Q ss_pred CCceeeeecccccCC--CCCcccccceeeeecCCCCe--EEeeeccCCCC--cccceeeeccCCHHhhcC-CCCHHHHHH
Q 025404 134 GPKAVAMDCEMVGGG--SNGTLDLCARVCLVDEDENV--IFHTYVQPQLP--VTNYRYEVTGLTEEDIKN-AMPLKEVKD 206 (253)
Q Consensus 134 ~~~~~~~dcE~~g~~--~~~~~~ll~~v~iv~~~~~~--~~~~~v~P~~~--i~~~~~~~~Git~~~l~~-~~~~~~v~~ 206 (253)
...++++|+||+|.. .+.++++ |.|.+.+....+ .+..+++|..+ +.+..+.+||||++++.. +.+..++..
T Consensus 5 ~~~fvv~D~ETTGLdP~~DrIIei-AaVrvd~~~~~i~e~~~~~~~P~~~~lp~p~a~~IhGIT~e~l~~~g~~e~e~~~ 83 (476)
T PRK11779 5 QPTFLWHDYETFGANPALDRPAQF-AGIRTDADLNIIGEPLVFYCKPADDYLPSPEAVLITGITPQEALEKGLPEAEFAA 83 (476)
T ss_pred CCcEEEEEEECCCCCCCCCeeEEE-EEEEEeCCCceecceeEEEEcCCcCcCCCHHHHHHhCCCHHHHHhcCCCHHHHHH
Confidence 345899999999976 4677777 777764321122 47889999853 356789999999999965 467999999
Q ss_pred HHHHHHhcCCCCCcccccCCCCeEEEeec-hhhhhhhhcCCCCC
Q 025404 207 KILEILNNGESTGRLMLDDGKARLLVGHG-LEHDLDSLRMNYPD 249 (253)
Q Consensus 207 ~l~~~~~~~~~~~~~~~~~~~~~~lv~h~-~~~D~~~l~~~~~~ 249 (253)
++.+++.. .++++|||| +.||+.||+....+
T Consensus 84 ~i~~~l~~------------~~~~lVGhNni~FD~eflr~~~~r 115 (476)
T PRK11779 84 RIHAEFSQ------------PGTCILGYNNIRFDDEVTRYIFYR 115 (476)
T ss_pred HHHHHHhc------------CCCEEEEeCchhhcHHHHHHHHHh
Confidence 99999921 367999997 79999998775433
No 59
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=99.10 E-value=9.3e-11 Score=114.70 Aligned_cols=95 Identities=23% Similarity=0.437 Sum_probs=82.6
Q ss_pred CCceeeeecccccCC--CCCcccccceeeeecCCCCe--EEeeeccCCCCcccceeeeccCCHHhhcCCCCHHHHHHHHH
Q 025404 134 GPKAVAMDCEMVGGG--SNGTLDLCARVCLVDEDENV--IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKIL 209 (253)
Q Consensus 134 ~~~~~~~dcE~~g~~--~~~~~~ll~~v~iv~~~~~~--~~~~~v~P~~~i~~~~~~~~Git~~~l~~~~~~~~v~~~l~ 209 (253)
...++++|+|++|.. .+..+++ +.+.+. +|.+ .++.+++|..+++.+.++++|||++++.+++++.+|+.++.
T Consensus 418 ~~~~VVfDLETTGL~~~~deIIEI-gAV~V~--~G~iie~F~~~V~P~~~I~~~~~~LTGIT~e~L~~aps~~EaL~~f~ 494 (1437)
T PRK00448 418 DATYVVFDVETTGLSAVYDEIIEI-GAVKIK--NGEIIDKFEFFIKPGHPLSAFTTELTGITDDMVKDAPSIEEVLPKFK 494 (1437)
T ss_pred cCcEEEEEhhhcCCCCchhhhhee-eeEEEe--CCeEeeeEEEEECCCCCCCHHHHHHhCCCHHHHcCCCCHHHHHHHHH
Confidence 356899999999965 4566666 776663 4555 68999999999999999999999999999999999999999
Q ss_pred HHHhcCCCCCcccccCCCCeEEEeechhhhhhhhcC
Q 025404 210 EILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRM 245 (253)
Q Consensus 210 ~~~~~~~~~~~~~~~~~~~~~lv~h~~~~D~~~l~~ 245 (253)
+++ ++.+|||||+.||+.||+-
T Consensus 495 ~fi--------------gg~vLVAHNa~FD~~fL~~ 516 (1437)
T PRK00448 495 EFC--------------GDSILVAHNASFDVGFINT 516 (1437)
T ss_pred HHh--------------CCCEEEEeCccccHHHHHH
Confidence 999 7899999999999999853
No 60
>PHA02768 hypothetical protein; Provisional
Probab=98.92 E-value=4e-10 Score=68.17 Aligned_cols=43 Identities=19% Similarity=0.453 Sum_probs=38.9
Q ss_pred cccccccccccCCHHHHHHhhhhcCCCCCcc-ccccccccccCHHHHh
Q 025404 14 RHKCVACYKQFKRKDHLIEHMKISYHSVHQP-KCAVCQKLSKSFESLR 60 (253)
Q Consensus 14 ~~~C~~C~k~f~~~~~l~~H~~~~~H~~~~~-~C~~C~~~f~~~~~l~ 60 (253)
.|+|+.||+.|+..++|..||++ |+ ++ +|..|++.|.+.+.|.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~--H~--k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRK--HN--TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHh--cC--CcccCCcccceecccceeE
Confidence 58999999999999999999999 88 56 9999999999887764
No 61
>PHA00733 hypothetical protein
Probab=98.85 E-value=2.6e-09 Score=77.91 Aligned_cols=81 Identities=19% Similarity=0.199 Sum_probs=56.8
Q ss_pred CCCcccccccccccCCHHHHHHh--hhhc-CCCCCcc-ccccccccccCHHHHhhhhC---CCCCCCcCCcccccccccc
Q 025404 11 STARHKCVACYKQFKRKDHLIEH--MKIS-YHSVHQP-KCAVCQKLSKSFESLREHLT---GPLSKAHCSGIFSDRGCNL 83 (253)
Q Consensus 11 ~~k~~~C~~C~k~f~~~~~l~~H--~~~~-~H~~~~~-~C~~C~~~f~~~~~l~~H~~---~~~~C~~C~~~f~~~~C~~ 83 (253)
.+|++.|..|.+.|.....|..+ ++.+ .+.+.+| .|+.|++.|.+.++|..|+. .+| .|+.
T Consensus 37 ~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h~~~~------------~C~~ 104 (128)
T PHA00733 37 EQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYTEHSK------------VCPV 104 (128)
T ss_pred hhhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcCCcCc------------cCCC
Confidence 46788888888888877666655 1110 0233556 88888888888888888872 333 3677
Q ss_pred cccccCChHHHHHHHHHccC
Q 025404 84 CMNIFDSPSSLIKHKEACSL 103 (253)
Q Consensus 84 C~k~f~~~~~l~~H~~~h~~ 103 (253)
|+++|.....|..|++..++
T Consensus 105 CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 105 CGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred CCCccCCHHHHHHHHHHhcC
Confidence 78888888888888876543
No 62
>KOG1275 consensus PAB-dependent poly(A) ribonuclease, subunit PAN2 [Replication, recombination and repair]
Probab=98.78 E-value=4.2e-09 Score=96.07 Aligned_cols=110 Identities=23% Similarity=0.398 Sum_probs=87.0
Q ss_pred ccCCCceeeeecccccCC-------CCCccc-------ccceeeeecCCCCe----EEeeeccCCCCcccceeeeccCCH
Q 025404 131 TCRGPKAVAMDCEMVGGG-------SNGTLD-------LCARVCLVDEDENV----IFHTYVQPQLPVTNYRYEVTGLTE 192 (253)
Q Consensus 131 ~~~~~~~~~~dcE~~g~~-------~~~~~~-------ll~~v~iv~~~~~~----~~~~~v~P~~~i~~~~~~~~Git~ 192 (253)
....+..+++|-|.+... .+++.. .+||+++++..|.- -.|.||-.+..|.||.++++||-|
T Consensus 906 mPk~g~LVgiDAEFVtLq~Ee~Eir~DG~~stIkP~~msvARiScvRGeGp~eGiPFiDDYv~T~d~VvDYLTqySGI~P 985 (1118)
T KOG1275|consen 906 MPKSGDLVGIDAEFVTLQTEELEIRSDGKTSTIKPSRMSVARISCVRGEGPNEGIPFIDDYVSTDDKVVDYLTQYSGIKP 985 (1118)
T ss_pred cCCCCceeeeehhheecchHHhccccCCceeEeccccceeEEEEEEcccCCCCCCccccceecchhHHHHHHHHhcCCCc
Confidence 344566788887776432 222221 23899998865433 678899999999999999999999
Q ss_pred HhhcCC------CCHHHHHHHHHHHHhcCCCCCcccccCCCCeEEEeechhhhhhhhcCCCCCCCCC
Q 025404 193 EDIKNA------MPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNYPDHMLR 253 (253)
Q Consensus 193 ~~l~~~------~~~~~v~~~l~~~~~~~~~~~~~~~~~~~~~~lv~h~~~~D~~~l~~~~~~~~~~ 253 (253)
.||+.. .++..++.+|.-++. .|.++|||++.+|+++|||.+|+.||+
T Consensus 986 GDLDp~~S~K~Lt~lK~~Y~Kl~~Li~-------------~GviFVGHGL~nDFrvINi~Vp~~Qii 1039 (1118)
T KOG1275|consen 986 GDLDPTTSEKRLTTLKVLYLKLRLLIQ-------------RGVIFVGHGLQNDFRVINIHVPEEQII 1039 (1118)
T ss_pred cccCCccCcceehhHHHHHHHHHHHHH-------------cCcEEEcccccccceEEEEecChhhhe
Confidence 999754 468889999998884 899999999999999999999999874
No 63
>PHA02768 hypothetical protein; Provisional
Probab=98.73 E-value=7.5e-09 Score=62.66 Aligned_cols=42 Identities=14% Similarity=0.200 Sum_probs=35.3
Q ss_pred cccccccccCChHHHHHHHHHcc-CCCCCCccccCccchhhhh
Q 025404 80 GCNLCMNIFDSPSSLIKHKEACS-LSAPVPFEKTLSNAESQKK 121 (253)
Q Consensus 80 ~C~~C~k~f~~~~~l~~H~~~h~-~~~~~~C~~~f~~~~~l~~ 121 (253)
.|+.||+.|.+.++|..|+++|+ +.++..|++.|.+.+.|..
T Consensus 7 ~C~~CGK~Fs~~~~L~~H~r~H~k~~kc~~C~k~f~~~s~l~~ 49 (55)
T PHA02768 7 ECPICGEIYIKRKSMITHLRKHNTNLKLSNCKRISLRTGEYIE 49 (55)
T ss_pred CcchhCCeeccHHHHHHHHHhcCCcccCCcccceecccceeEE
Confidence 48899999999999999999999 5555669999998776654
No 64
>PHA00733 hypothetical protein
Probab=98.57 E-value=7.2e-08 Score=70.39 Aligned_cols=53 Identities=23% Similarity=0.486 Sum_probs=47.7
Q ss_pred CCCCCCCcccccccccccCCHHHHHHhhhhcCCCCCcc-ccccccccccCHHHHhhhh
Q 025404 7 LPKRSTARHKCVACYKQFKRKDHLIEHMKISYHSVHQP-KCAVCQKLSKSFESLREHL 63 (253)
Q Consensus 7 ~~~~~~k~~~C~~C~k~f~~~~~l~~H~~~~~H~~~~~-~C~~C~~~f~~~~~l~~H~ 63 (253)
++..+++||.|+.|++.|.....|..|++. |. .+ .|..|++.|.....|..|+
T Consensus 66 ~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~--h~--~~~~C~~CgK~F~~~~sL~~H~ 119 (128)
T PHA00733 66 LTSKAVSPYVCPLCLMPFSSSVSLKQHIRY--TE--HSKVCPVCGKEFRNTDSTLDHV 119 (128)
T ss_pred cccCCCCCccCCCCCCcCCCHHHHHHHHhc--CC--cCccCCCCCCccCCHHHHHHHH
Confidence 455678999999999999999999999998 63 34 9999999999999999998
No 65
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.37 E-value=5.5e-07 Score=80.47 Aligned_cols=101 Identities=18% Similarity=0.389 Sum_probs=62.3
Q ss_pred CCCcccccccccccCCHHHHHHhhhhcCCCCCcc-ccccccccccCHHHHhhhh-----CCCCCCCcCCccccccccccc
Q 025404 11 STARHKCVACYKQFKRKDHLIEHMKISYHSVHQP-KCAVCQKLSKSFESLREHL-----TGPLSKAHCSGIFSDRGCNLC 84 (253)
Q Consensus 11 ~~k~~~C~~C~k~f~~~~~l~~H~~~~~H~~~~~-~C~~C~~~f~~~~~l~~H~-----~~~~~C~~C~~~f~~~~C~~C 84 (253)
-++.+.|+.|++.|. ...|..|+++ |. .+ .|+ ||+.+ ....|..|+ .+++.|+.|++.|.....
T Consensus 450 l~~H~~C~~Cgk~f~-~s~LekH~~~--~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~--- 519 (567)
T PLN03086 450 AKNHVHCEKCGQAFQ-QGEMEKHMKV--FH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGS--- 519 (567)
T ss_pred cccCccCCCCCCccc-hHHHHHHHHh--cC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCcc---
Confidence 356678999998885 5778899988 53 55 888 98755 568888886 455665555544421000
Q ss_pred cccc-CChHHHHHHHHHccCCCCCC---ccccCccchhhhhhc
Q 025404 85 MNIF-DSPSSLIKHKEACSLSAPVP---FEKTLSNAESQKKIS 123 (253)
Q Consensus 85 ~k~f-~~~~~l~~H~~~h~~~~~~~---C~~~f~~~~~l~~h~ 123 (253)
.-.+ ...+.|..|+..+ |.+++. |++.+... .+..|+
T Consensus 520 ~~d~~d~~s~Lt~HE~~C-G~rt~~C~~Cgk~Vrlr-dm~~H~ 560 (567)
T PLN03086 520 AMDVRDRLRGMSEHESIC-GSRTAPCDSCGRSVMLK-EMDIHQ 560 (567)
T ss_pred ccchhhhhhhHHHHHHhc-CCcceEccccCCeeeeh-hHHHHH
Confidence 0000 0245788888886 888776 44444432 344444
No 66
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.27 E-value=4.1e-07 Score=46.98 Aligned_cols=25 Identities=36% Similarity=0.707 Sum_probs=22.6
Q ss_pred HHHHhhhhcCCCCCcc-ccccccccccC
Q 025404 29 HLIEHMKISYHSVHQP-KCAVCQKLSKS 55 (253)
Q Consensus 29 ~l~~H~~~~~H~~~~~-~C~~C~~~f~~ 55 (253)
+|..|+++ |++++| +|+.|++.|.+
T Consensus 1 ~l~~H~~~--H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRT--HTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHH--HSSSSSEEESSSSEEESS
T ss_pred CHHHHhhh--cCCCCCCCCCCCcCeeCc
Confidence 58899999 999999 99999999964
No 67
>PHA00616 hypothetical protein
Probab=98.24 E-value=4.3e-07 Score=52.34 Aligned_cols=33 Identities=21% Similarity=0.351 Sum_probs=29.7
Q ss_pred ccccccccCChHHHHHHHHHccCCCCCCccccC
Q 025404 81 CNLCMNIFDSPSSLIKHKEACSLSAPVPFEKTL 113 (253)
Q Consensus 81 C~~C~k~f~~~~~l~~H~~~h~~~~~~~C~~~f 113 (253)
|+.||+.|.++++|..|++.|++++|+.|+..+
T Consensus 4 C~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~~y 36 (44)
T PHA00616 4 CLRCGGIFRKKKEVIEHLLSVHKQNKLTLEYFY 36 (44)
T ss_pred cchhhHHHhhHHHHHHHHHHhcCCCccceeEEE
Confidence 788999999999999999999999999877553
No 68
>PHA00616 hypothetical protein
Probab=98.22 E-value=5.6e-07 Score=51.88 Aligned_cols=34 Identities=21% Similarity=0.390 Sum_probs=30.8
Q ss_pred cccccccccccCCHHHHHHhhhhcCCCCCcc-ccccc
Q 025404 14 RHKCVACYKQFKRKDHLIEHMKISYHSVHQP-KCAVC 49 (253)
Q Consensus 14 ~~~C~~C~k~f~~~~~l~~H~~~~~H~~~~~-~C~~C 49 (253)
||+|..||+.|..++.|..|++. |+++++ .|+.-
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~--~hg~~~~~~~~~ 35 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLS--VHKQNKLTLEYF 35 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHH--hcCCCccceeEE
Confidence 79999999999999999999999 888888 77653
No 69
>PHA00732 hypothetical protein
Probab=98.20 E-value=1e-06 Score=58.44 Aligned_cols=44 Identities=30% Similarity=0.519 Sum_probs=35.8
Q ss_pred cccccccccccCCHHHHHHhhhhcCCCCCccccccccccccCHHHHhhhh
Q 025404 14 RHKCVACYKQFKRKDHLIEHMKISYHSVHQPKCAVCQKLSKSFESLREHL 63 (253)
Q Consensus 14 ~~~C~~C~k~f~~~~~l~~H~~~~~H~~~~~~C~~C~~~f~~~~~l~~H~ 63 (253)
||.|+.|++.|.+...|..|++.+ |.+. .|+.|++.|. .|..|.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~-H~~~--~C~~CgKsF~---~l~~H~ 44 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRN-HTLT--KCPVCNKSYR---RLNQHF 44 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcc-cCCC--ccCCCCCEeC---Chhhhh
Confidence 689999999999999999999841 5532 7999999887 477786
No 70
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=98.17 E-value=6.4e-07 Score=75.66 Aligned_cols=88 Identities=18% Similarity=0.261 Sum_probs=63.9
Q ss_pred cccccccccccCCHHHHHHhhhhcCCCC-CccccccccccccCHHHHhhhhCCCCCCCcCCc--------c---------
Q 025404 14 RHKCVACYKQFKRKDHLIEHMKISYHSV-HQPKCAVCQKLSKSFESLREHLTGPLSKAHCSG--------I--------- 75 (253)
Q Consensus 14 ~~~C~~C~k~f~~~~~l~~H~~~~~H~~-~~~~C~~C~~~f~~~~~l~~H~~~~~~C~~C~~--------~--------- 75 (253)
-|.|..|...|.+...|.+|.-. ..- ....|.+|+|.|+-..||..|.....+-..-++ .
T Consensus 267 dyiCqLCK~kYeD~F~LAQHrC~--RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~e 344 (500)
T KOG3993|consen 267 DYICQLCKEKYEDAFALAQHRCP--RIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQE 344 (500)
T ss_pred HHHHHHHHHhhhhHHHHhhccCC--eeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhh
Confidence 38999999999999999999742 221 223899999999999999999822111111000 0
Q ss_pred ---------cccccccccccccCChHHHHHHHHHccC
Q 025404 76 ---------FSDRGCNLCMNIFDSPSSLIKHKEACSL 103 (253)
Q Consensus 76 ---------f~~~~C~~C~k~f~~~~~l~~H~~~h~~ 103 (253)
-.-..|..|+|.|.+...|+.|+.+|+.
T Consensus 345 a~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~ 381 (500)
T KOG3993|consen 345 AERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQR 381 (500)
T ss_pred ccccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhc
Confidence 0001299999999999999999999874
No 71
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.10 E-value=5.2e-06 Score=74.37 Aligned_cols=115 Identities=11% Similarity=0.287 Sum_probs=76.0
Q ss_pred cccccccccccCCHHHHHHhhhhcCCCCCcc-cccc--ccccccCHHHHhhhhCCCCCCCcCCcccccc-----------
Q 025404 14 RHKCVACYKQFKRKDHLIEHMKISYHSVHQP-KCAV--CQKLSKSFESLREHLTGPLSKAHCSGIFSDR----------- 79 (253)
Q Consensus 14 ~~~C~~C~k~f~~~~~l~~H~~~~~H~~~~~-~C~~--C~~~f~~~~~l~~H~~~~~~C~~C~~~f~~~----------- 79 (253)
.-.|+.|..... ...|..|.. +-.... .|+. ||..|.. ..+ ..++.|+.|++.|...
T Consensus 407 ~V~C~NC~~~i~-l~~l~lHe~---~C~r~~V~Cp~~~Cg~v~~r-~el----~~H~~C~~Cgk~f~~s~LekH~~~~Hk 477 (567)
T PLN03086 407 TVECRNCKHYIP-SRSIALHEA---YCSRHNVVCPHDGCGIVLRV-EEA----KNHVHCEKCGQAFQQGEMEKHMKVFHE 477 (567)
T ss_pred eEECCCCCCccc-hhHHHHHHh---hCCCcceeCCcccccceeec-ccc----ccCccCCCCCCccchHHHHHHHHhcCC
Confidence 347999987654 466778874 333344 7774 8887732 233 3446788888877532
Q ss_pred --cccccccccCChHHHHHHHHHccCCCCCC---ccccCc----------cchhhhhhccccccccccCCCceeeeeccc
Q 025404 80 --GCNLCMNIFDSPSSLIKHKEACSLSAPVP---FEKTLS----------NAESQKKISGAIDEKRTCRGPKAVAMDCEM 144 (253)
Q Consensus 80 --~C~~C~k~f~~~~~l~~H~~~h~~~~~~~---C~~~f~----------~~~~l~~h~~~~~~~r~~~~~~~~~~dcE~ 144 (253)
.|+ ||+.+ .+..|..|+++|..++|+. |++.+. ..+.|..|.... ....+.|..
T Consensus 478 pv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C---------G~rt~~C~~ 546 (567)
T PLN03086 478 PLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC---------GSRTAPCDS 546 (567)
T ss_pred CccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc---------CCcceEccc
Confidence 388 98755 5689999999999999987 556553 134677776432 124577888
Q ss_pred ccCC
Q 025404 145 VGGG 148 (253)
Q Consensus 145 ~g~~ 148 (253)
||..
T Consensus 547 Cgk~ 550 (567)
T PLN03086 547 CGRS 550 (567)
T ss_pred cCCe
Confidence 8854
No 72
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=98.04 E-value=2.9e-06 Score=71.82 Aligned_cols=48 Identities=27% Similarity=0.473 Sum_probs=41.2
Q ss_pred cccccccccccCCHHHHHHhhhhcCCCC--------Cc-------------------------c-ccccccccccCHHHH
Q 025404 14 RHKCVACYKQFKRKDHLIEHMKISYHSV--------HQ-------------------------P-KCAVCQKLSKSFESL 59 (253)
Q Consensus 14 ~~~C~~C~k~f~~~~~l~~H~~~~~H~~--------~~-------------------------~-~C~~C~~~f~~~~~l 59 (253)
-|+|+.|+|.|+...+|..|+|- |.. .+ . .|..|+|.|.+...|
T Consensus 295 EYrCPEC~KVFsCPANLASHRRW--HKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYL 372 (500)
T KOG3993|consen 295 EYRCPECDKVFSCPANLASHRRW--HKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYL 372 (500)
T ss_pred eecCCcccccccCchhhhhhhcc--cCCchhhhhcCCCChhhhhhhhhhhhhccccCCcccCceeecHHhhhhhHHHHHH
Confidence 38999999999999999999987 621 11 1 599999999999999
Q ss_pred hhhh
Q 025404 60 REHL 63 (253)
Q Consensus 60 ~~H~ 63 (253)
+.|+
T Consensus 373 rKHq 376 (500)
T KOG3993|consen 373 RKHQ 376 (500)
T ss_pred HHhH
Confidence 9996
No 73
>KOG3242 consensus Oligoribonuclease (3'->5' exoribonuclease) [RNA processing and modification]
Probab=98.01 E-value=1.4e-06 Score=65.12 Aligned_cols=107 Identities=21% Similarity=0.282 Sum_probs=74.2
Q ss_pred CCceeeeecccccCC--CCCcccccceeeeecCCCCe---EEeeeccCCC----Ccccceeee---ccCCHHhhcCCCCH
Q 025404 134 GPKAVAMDCEMVGGG--SNGTLDLCARVCLVDEDENV---IFHTYVQPQL----PVTNYRYEV---TGLTEEDIKNAMPL 201 (253)
Q Consensus 134 ~~~~~~~dcE~~g~~--~~~~~~ll~~v~iv~~~~~~---~~~~~v~P~~----~i~~~~~~~---~Git~~~l~~~~~~ 201 (253)
..+++.+||||||.. .+.++++ ...|.|.+.+. -++..++-+. ...+|..+. +|+|..-++...++
T Consensus 25 ~q~lVWiD~EMTGLdvekd~i~Ei--acIITD~dL~~~~egpd~vI~~~~evld~MneWc~ehhg~SGLt~kv~~S~~tl 102 (208)
T KOG3242|consen 25 KQPLVWIDCEMTGLDVEKDRIIEI--ACIITDGDLNPVAEGPDLVIHQPKEVLDKMNEWCIEHHGNSGLTEKVLASKITL 102 (208)
T ss_pred cCceEEEeeeccccccccceeEEE--EEEEecCCccccccCccchhcCCHHHHHHHHHHHHHhccchhHHHHHHHhhccH
Confidence 456799999999965 5555554 23344444444 3444554333 334555544 47998888999999
Q ss_pred HHHHHHHHHHHhcCCCCCcccccCCCCeEEEeechhhhhhhhcCCCCCC
Q 025404 202 KEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNYPDH 250 (253)
Q Consensus 202 ~~v~~~l~~~~~~~~~~~~~~~~~~~~~~lv~h~~~~D~~~l~~~~~~~ 250 (253)
++|..++.+|+.. ..+ .+..+|.|+++..|..||.-++|+.
T Consensus 103 ~~aEnevl~yikk----~ip----~~~~~laGNSV~~DrlFl~k~mPk~ 143 (208)
T KOG3242|consen 103 ADAENEVLEYIKK----HIP----KGKCPLAGNSVYMDRLFLKKYMPKL 143 (208)
T ss_pred HHHHHHHHHHHHH----hCC----CCCCCccCcchhhHHHHHHHHhHHH
Confidence 9999999999931 111 2456999999999999999888764
No 74
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=97.90 E-value=5.5e-06 Score=42.70 Aligned_cols=22 Identities=23% Similarity=0.298 Sum_probs=17.8
Q ss_pred HHHHHHHHccCCCCCC---ccccCc
Q 025404 93 SLIKHKEACSLSAPVP---FEKTLS 114 (253)
Q Consensus 93 ~l~~H~~~h~~~~~~~---C~~~f~ 114 (253)
+|.+|+++|++++||+ |+++|.
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEES
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeC
Confidence 5889999999999997 665554
No 75
>cd05160 DEDDy_DNA_polB_exo DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. The 3'-5' exonuclease domain of family-B DNA polymerases. This domain has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The exonuclease domain of family B polymerase also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members include Escherichia coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative
Probab=97.77 E-value=6.7e-05 Score=59.30 Aligned_cols=90 Identities=16% Similarity=0.184 Sum_probs=56.4
Q ss_pred eeeecccccCCC--C-CcccccceeeeecC-CCCeE-EeeeccCCCCcccceeeeccCCHHhhcCCCCHHHHHHHHHHHH
Q 025404 138 VAMDCEMVGGGS--N-GTLDLCARVCLVDE-DENVI-FHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEIL 212 (253)
Q Consensus 138 ~~~dcE~~g~~~--~-~~~~ll~~v~iv~~-~~~~~-~~~~v~P~~~i~~~~~~~~Git~~~l~~~~~~~~v~~~l~~~~ 212 (253)
.++|.|++|... . ..-++ ..++++.. +|... +.....+...... ||+...+...++..+++..+.+++
T Consensus 2 ~~~DIEt~~~~~~p~~~~d~I-i~I~~~~~~~g~~~~~~~~~~~~~~~~~------~i~~~~v~~~~~E~~lL~~f~~~i 74 (199)
T cd05160 2 LSFDIETTPPVGGPEPDRDPI-ICITYADSFDGVKVVFLLKTSTVGDDIE------FIDGIEVEYFADEKELLKRFFDII 74 (199)
T ss_pred ccEEEeecCCCCCcCCCCCCE-EEEEEEEeeCCceeeEEEeecccCCcCC------CCCCceEEEeCCHHHHHHHHHHHH
Confidence 579999998621 1 11222 44444433 45442 2222222111111 888888999999999999999999
Q ss_pred hcCCCCCcccccCCCCeEEEeech-hhhhhhhcC
Q 025404 213 NNGESTGRLMLDDGKARLLVGHGL-EHDLDSLRM 245 (253)
Q Consensus 213 ~~~~~~~~~~~~~~~~~~lv~h~~-~~D~~~l~~ 245 (253)
.. .+ -.+|||||+ .||+.+|.-
T Consensus 75 ~~--------~d---pdiivg~N~~~FD~~~L~~ 97 (199)
T cd05160 75 RE--------YD---PDILTGYNIDDFDLPYLLK 97 (199)
T ss_pred Hh--------cC---CCEEEEeccCCCcHHHHHH
Confidence 31 00 149999999 899999864
No 76
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=97.74 E-value=1.4e-05 Score=39.81 Aligned_cols=22 Identities=41% Similarity=0.689 Sum_probs=19.9
Q ss_pred ccccccccccCCHHHHHHhhhh
Q 025404 15 HKCVACYKQFKRKDHLIEHMKI 36 (253)
Q Consensus 15 ~~C~~C~k~f~~~~~l~~H~~~ 36 (253)
|.|+.|++.|..+..|..|++.
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 6899999999999999999886
No 77
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=97.71 E-value=2.3e-05 Score=39.06 Aligned_cols=21 Identities=33% Similarity=0.640 Sum_probs=18.6
Q ss_pred ccccccccCChHHHHHHHHHc
Q 025404 81 CNLCMNIFDSPSSLIKHKEAC 101 (253)
Q Consensus 81 C~~C~k~f~~~~~l~~H~~~h 101 (253)
|+.|++.|.+.+.|..|++.|
T Consensus 3 C~~C~~~f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 3 CPICGKSFSSKSNLKRHMRRH 23 (23)
T ss_dssp ETTTTEEESSHHHHHHHHHHH
T ss_pred CCCCCCccCCHHHHHHHHhHC
Confidence 888999999999999999875
No 78
>COG1949 Orn Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification]
Probab=97.71 E-value=2.5e-05 Score=58.08 Aligned_cols=106 Identities=17% Similarity=0.245 Sum_probs=74.0
Q ss_pred CCceeeeecccccCC--CCCcccccceeeeecCCCCeEEee---ecc-CC---CCcccceeeec---cCCHHhhcCCCCH
Q 025404 134 GPKAVAMDCEMVGGG--SNGTLDLCARVCLVDEDENVIFHT---YVQ-PQ---LPVTNYRYEVT---GLTEEDIKNAMPL 201 (253)
Q Consensus 134 ~~~~~~~dcE~~g~~--~~~~~~ll~~v~iv~~~~~~~~~~---~v~-P~---~~i~~~~~~~~---Git~~~l~~~~~~ 201 (253)
..+.+.+||||||.. .+.++++ ...|.|.+.+++-.- .|. |. ....+|+++.+ |++..-.+...+.
T Consensus 5 ~~nLiWIDlEMTGLd~~~drIIEi--A~iVTD~~Lnilaegp~~~Ihq~~e~L~~Mdew~~~~H~~sGL~~rV~~S~~t~ 82 (184)
T COG1949 5 KNNLIWIDLEMTGLDPERDRIIEI--ATIVTDANLNILAEGPVIAIHQSDEQLAKMDEWNTETHGRSGLTERVKASTVTE 82 (184)
T ss_pred CCceEEEeeeeccCCcCcceEEEE--EEEEecCcccccccCceEEEeCCHHHHHHHHHHHHHccccccHHHHHHHhhccH
Confidence 456799999999976 4455554 334445555553221 111 21 23456766665 6887777888999
Q ss_pred HHHHHHHHHHHhcCCCCCcccccCCCCeEEEeechhhhhhhhcCCCCC
Q 025404 202 KEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNYPD 249 (253)
Q Consensus 202 ~~v~~~l~~~~~~~~~~~~~~~~~~~~~~lv~h~~~~D~~~l~~~~~~ 249 (253)
.+|..++++||. .|-+. .+ .++-|+++..|-+||--.+|+
T Consensus 83 ~~aE~~~l~flk----kwvp~-~~---spicGNSI~qDRrFl~r~MP~ 122 (184)
T COG1949 83 AEAEAQTLDFLK----KWVPK-GV---SPICGNSIAQDRRFLFRYMPK 122 (184)
T ss_pred HHHHHHHHHHHH----HhCCC-CC---CCCccchhhHHHHHHHHHhhh
Confidence 999999999993 45555 33 499999999999999888776
No 79
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.38 E-value=0.00012 Score=37.92 Aligned_cols=23 Identities=30% Similarity=0.504 Sum_probs=21.6
Q ss_pred cccccccccccCCHHHHHHhhhh
Q 025404 14 RHKCVACYKQFKRKDHLIEHMKI 36 (253)
Q Consensus 14 ~~~C~~C~k~f~~~~~l~~H~~~ 36 (253)
||+|..|++.|.....|..|++.
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~ 23 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRS 23 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCT
T ss_pred CCCCCccCCccCChhHHHHHhHH
Confidence 68999999999999999999988
No 80
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=97.36 E-value=0.0002 Score=44.00 Aligned_cols=46 Identities=26% Similarity=0.481 Sum_probs=28.1
Q ss_pred cccccccccccCCHHHHHHhhhhcCCCCCc-c-ccccccccccCHHHHhhhh
Q 025404 14 RHKCVACYKQFKRKDHLIEHMKISYHSVHQ-P-KCAVCQKLSKSFESLREHL 63 (253)
Q Consensus 14 ~~~C~~C~k~f~~~~~l~~H~~~~~H~~~~-~-~C~~C~~~f~~~~~l~~H~ 63 (253)
.|.|+.|++ ..+...|..|.... |..+. . .|++|...+. .+|..|+
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~-H~~~~~~v~CPiC~~~~~--~~l~~Hl 49 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDE-HRSESKNVVCPICSSRVT--DNLIRHL 49 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhH-CcCCCCCccCCCchhhhh--hHHHHHH
Confidence 478888888 45567788887663 65432 2 6666655433 2454444
No 81
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.34 E-value=0.00014 Score=36.33 Aligned_cols=22 Identities=36% Similarity=0.765 Sum_probs=18.3
Q ss_pred ccccccccccCCHHHHHHhhhh
Q 025404 15 HKCVACYKQFKRKDHLIEHMKI 36 (253)
Q Consensus 15 ~~C~~C~k~f~~~~~l~~H~~~ 36 (253)
|.|+.|++.|.+...|..|++.
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~ 22 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRT 22 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHh
Confidence 6899999999999999999987
No 82
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.23 E-value=0.00022 Score=35.55 Aligned_cols=22 Identities=32% Similarity=0.581 Sum_probs=17.7
Q ss_pred ccccccccCChHHHHHHHHHcc
Q 025404 81 CNLCMNIFDSPSSLIKHKEACS 102 (253)
Q Consensus 81 C~~C~k~f~~~~~l~~H~~~h~ 102 (253)
|+.|++.|.+...|+.|+++|+
T Consensus 3 C~~C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 3 CPICGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp -SSTS-EESSHHHHHHHHHHHS
T ss_pred CcCCCCcCCcHHHHHHHHHhhC
Confidence 7889999999999999998874
No 83
>PHA00732 hypothetical protein
Probab=97.20 E-value=0.00029 Score=46.78 Aligned_cols=34 Identities=18% Similarity=0.218 Sum_probs=15.4
Q ss_pred ccccccccCChHHHHHHHHH-ccCCCCCCccccCc
Q 025404 81 CNLCMNIFDSPSSLIKHKEA-CSLSAPVPFEKTLS 114 (253)
Q Consensus 81 C~~C~k~f~~~~~l~~H~~~-h~~~~~~~C~~~f~ 114 (253)
|..||+.|.+.+.|+.|++. |.+...-.|+++|.
T Consensus 4 C~~Cgk~F~s~s~Lk~H~r~~H~~~~C~~CgKsF~ 38 (79)
T PHA00732 4 CPICGFTTVTLFALKQHARRNHTLTKCPVCNKSYR 38 (79)
T ss_pred CCCCCCccCCHHHHHHHhhcccCCCccCCCCCEeC
Confidence 44455555555555555542 33322222444444
No 84
>KOG0542 consensus Predicted exonuclease [Replication, recombination and repair]
Probab=97.19 E-value=0.00021 Score=57.00 Aligned_cols=77 Identities=21% Similarity=0.360 Sum_probs=58.2
Q ss_pred eeeeecccccCC------CCCcccccceeeeec-CCCCe--EEeeeccCCC--CcccceeeeccCCHHhhcCCCCHHHHH
Q 025404 137 AVAMDCEMVGGG------SNGTLDLCARVCLVD-EDENV--IFHTYVQPQL--PVTNYRYEVTGLTEEDIKNAMPLKEVK 205 (253)
Q Consensus 137 ~~~~dcE~~g~~------~~~~~~ll~~v~iv~-~~~~~--~~~~~v~P~~--~i~~~~~~~~Git~~~l~~~~~~~~v~ 205 (253)
++++|.|.|-.. ...++++ ..|.+.+ +.+.+ .|+.||+|.. .+.+|.+.++||.++.|+.|++|.+|+
T Consensus 58 LliiDFEaTC~e~~~~~~~~EIIEf-P~V~l~~~~~~~Ie~eF~qYVrP~~np~LS~fC~~lTgI~Q~tVD~a~~f~~vl 136 (280)
T KOG0542|consen 58 LLILDFEATCEEGNKPHYVQEIIEF-PAVLLDNTETSIIEDEFHQYVRPVENPRLSDFCTSLTGIQQETVDEAPTFPQVL 136 (280)
T ss_pred EEEEeeeeeccccCCCCcchheeec-ceeEeeccchhhHHHHHHhhcCcccCchHHHHHHHhhCchHhhhccCCCHHHHH
Confidence 478888877321 2344455 4443322 34444 6899999985 478999999999999999999999999
Q ss_pred HHHHHHHhc
Q 025404 206 DKILEILNN 214 (253)
Q Consensus 206 ~~l~~~~~~ 214 (253)
+++..+|.+
T Consensus 137 ~~f~~Wlr~ 145 (280)
T KOG0542|consen 137 SEFDSWLRK 145 (280)
T ss_pred HHHHHHHHH
Confidence 999999954
No 85
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.08 E-value=0.00017 Score=59.25 Aligned_cols=28 Identities=32% Similarity=0.523 Sum_probs=23.2
Q ss_pred CCccccc--ccccccCCHHHHHHhhhhcCCC
Q 025404 12 TARHKCV--ACYKQFKRKDHLIEHMKISYHS 40 (253)
Q Consensus 12 ~k~~~C~--~C~k~f~~~~~l~~H~~~~~H~ 40 (253)
+|||+|+ .|.|+|+..-.|+-|+. |+|-
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~l-hGH~ 376 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHML-HGHQ 376 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhh-cccc
Confidence 5999995 59999999999999986 3453
No 86
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.70 E-value=0.0014 Score=33.06 Aligned_cols=24 Identities=46% Similarity=0.789 Sum_probs=21.2
Q ss_pred ccccccccccCCHHHHHHhhhhcCCC
Q 025404 15 HKCVACYKQFKRKDHLIEHMKISYHS 40 (253)
Q Consensus 15 ~~C~~C~k~f~~~~~l~~H~~~~~H~ 40 (253)
|.|+.|++.|.....|..|++. |.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~--H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRT--HX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHH--hc
Confidence 6799999999999999999987 64
No 87
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=96.70 E-value=0.0012 Score=45.68 Aligned_cols=74 Identities=26% Similarity=0.429 Sum_probs=19.7
Q ss_pred cccccccccCCHHHHHHhhhhcCCCCCccccccccccccCHHHHhhhhCCCCCCCcCCcccccccccccccccCChHHHH
Q 025404 16 KCVACYKQFKRKDHLIEHMKISYHSVHQPKCAVCQKLSKSFESLREHLTGPLSKAHCSGIFSDRGCNLCMNIFDSPSSLI 95 (253)
Q Consensus 16 ~C~~C~k~f~~~~~l~~H~~~~~H~~~~~~C~~C~~~f~~~~~l~~H~~~~~~C~~C~~~f~~~~C~~C~k~f~~~~~l~ 95 (253)
+|..|+..|.....|..|+... |.-..+.. ..+.....+..++... ......|..|++.|.+...|.
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~-H~~~~~~~----~~l~~~~~~~~~~~~~--------~~~~~~C~~C~~~f~s~~~l~ 67 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKK-HGFDIPDQ----KYLVDPNRLLNYLRKK--------VKESFRCPYCNKTFRSREALQ 67 (100)
T ss_dssp -------------------------------------------------------------SSEEBSSSS-EESSHHHHH
T ss_pred Cccccccccccccccccccccc-cccccccc----cccccccccccccccc--------cCCCCCCCccCCCCcCHHHHH
Confidence 4888999999999999998652 43222211 1111222222222100 000124888999999999999
Q ss_pred HHHHHcc
Q 025404 96 KHKEACS 102 (253)
Q Consensus 96 ~H~~~h~ 102 (253)
.||+.+.
T Consensus 68 ~Hm~~~~ 74 (100)
T PF12756_consen 68 EHMRSKH 74 (100)
T ss_dssp HHHHHTT
T ss_pred HHHcCcc
Confidence 9999764
No 88
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=96.66 E-value=0.00083 Score=34.69 Aligned_cols=22 Identities=36% Similarity=0.638 Sum_probs=18.0
Q ss_pred ccccccccCChHHHHHHHHHcc
Q 025404 81 CNLCMNIFDSPSSLIKHKEACS 102 (253)
Q Consensus 81 C~~C~k~f~~~~~l~~H~~~h~ 102 (253)
|..|++.|.+...|..|++.|.
T Consensus 4 C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 4 CDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp ETTTTEEESSHHHHHHHHCTTT
T ss_pred CCccCCccCChhHHHHHhHHhc
Confidence 7778888888888888887764
No 89
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=96.62 E-value=0.0016 Score=38.46 Aligned_cols=26 Identities=23% Similarity=0.566 Sum_probs=18.2
Q ss_pred ccccccccCChHHHHHHHHHccCCCC
Q 025404 81 CNLCMNIFDSPSSLIKHKEACSLSAP 106 (253)
Q Consensus 81 C~~C~k~f~~~~~l~~H~~~h~~~~~ 106 (253)
|++|+..+.+..+|++|+.++++.||
T Consensus 27 CP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 27 CPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp -TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred CCcchhhccchhhHHHHHHHHhcccC
Confidence 77778888888888888888877776
No 90
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.57 E-value=0.002 Score=32.40 Aligned_cols=22 Identities=32% Similarity=0.608 Sum_probs=19.3
Q ss_pred ccccccccCChHHHHHHHHHcc
Q 025404 81 CNLCMNIFDSPSSLIKHKEACS 102 (253)
Q Consensus 81 C~~C~k~f~~~~~l~~H~~~h~ 102 (253)
|..|+++|.+.+.|..|++.|.
T Consensus 3 C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 3 CPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCcchhCCHHHHHHHHHHhc
Confidence 7889999999999999998774
No 91
>cd06125 DnaQ_like_exo DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily. The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy
Probab=96.37 E-value=0.0045 Score=42.81 Aligned_cols=21 Identities=33% Similarity=0.452 Sum_probs=17.3
Q ss_pred eEEEeechhhhhhhhcCCCCC
Q 025404 229 RLLVGHGLEHDLDSLRMNYPD 249 (253)
Q Consensus 229 ~~lv~h~~~~D~~~l~~~~~~ 249 (253)
.++||||+.||+.||+-...+
T Consensus 45 ~v~V~hn~~fD~~fL~~~~~~ 65 (96)
T cd06125 45 AILVGHNGSFDLPFLNNRCAE 65 (96)
T ss_pred CEEEEeCcHHhHHHHHHHHHH
Confidence 599999999999998765433
No 92
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=96.36 E-value=0.0032 Score=37.28 Aligned_cols=26 Identities=23% Similarity=0.475 Sum_probs=12.6
Q ss_pred CCCcccccccccccCCHHHHHHhhhh
Q 025404 11 STARHKCVACYKQFKRKDHLIEHMKI 36 (253)
Q Consensus 11 ~~k~~~C~~C~k~f~~~~~l~~H~~~ 36 (253)
.+.|..|+.|+..+.+..+|.+|+.+
T Consensus 21 S~~PatCP~C~a~~~~srnLrRHle~ 46 (54)
T PF09237_consen 21 SEQPATCPICGAVIRQSRNLRRHLEI 46 (54)
T ss_dssp TS--EE-TTT--EESSHHHHHHHHHH
T ss_pred cCCCCCCCcchhhccchhhHHHHHHH
Confidence 34556666666666666666666655
No 93
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=96.25 E-value=0.0067 Score=37.10 Aligned_cols=44 Identities=30% Similarity=0.480 Sum_probs=30.2
Q ss_pred ccccccccccCHHHHhhhh-------CCCCCCCcCCcccccccccccccccCChHHHHHHHHHccC
Q 025404 45 KCAVCQKLSKSFESLREHL-------TGPLSKAHCSGIFSDRGCNLCMNIFDSPSSLIKHKEACSL 103 (253)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~-------~~~~~C~~C~~~f~~~~C~~C~k~f~~~~~l~~H~~~h~~ 103 (253)
.|+.|++. .+...|..|. .+.+. |+.|...+. .+|..|+..+++
T Consensus 4 ~CP~C~~~-~~~~~L~~H~~~~H~~~~~~v~------------CPiC~~~~~--~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 4 TCPYCGKG-FSESSLVEHCEDEHRSESKNVV------------CPICSSRVT--DNLIRHLNSQHR 54 (54)
T ss_pred CCCCCCCc-cCHHHHHHHHHhHCcCCCCCcc------------CCCchhhhh--hHHHHHHHHhcC
Confidence 79999994 5567899997 12344 555555444 489999987653
No 94
>PF01612 DNA_pol_A_exo1: 3'-5' exonuclease; InterPro: IPR002562 This domain is responsible for the 3'-5' exonuclease proofreading activity of Escherichia coli DNA polymerase I (polI) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli polI it is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D) [].; GO: 0003676 nucleic acid binding, 0008408 3'-5' exonuclease activity, 0006139 nucleobase-containing compound metabolic process, 0005622 intracellular; PDB: 2HBK_A 2HBJ_A 2HBM_A 2HBL_A 2FC0_A 2FBY_A 2FBX_A 2FBT_A 2FBV_A 1YT3_A ....
Probab=96.01 E-value=0.029 Score=42.88 Aligned_cols=30 Identities=30% Similarity=0.418 Sum_probs=25.3
Q ss_pred HHHHHHHHHhcCCCCCcccccCCCCeEEEeechhhhhhhhcC
Q 025404 204 VKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRM 245 (253)
Q Consensus 204 v~~~l~~~~~~~~~~~~~~~~~~~~~~lv~h~~~~D~~~l~~ 245 (253)
+...|.+++. +.+.+.||||+.||+.+|.-
T Consensus 65 ~~~~l~~ll~------------~~~i~kv~~n~~~D~~~L~~ 94 (176)
T PF01612_consen 65 ILDALKELLE------------DPNIIKVGHNAKFDLKWLYR 94 (176)
T ss_dssp HHHHHHHHHT------------TTTSEEEESSHHHHHHHHHH
T ss_pred hHHHHHHHHh------------CCCccEEEEEEechHHHHHH
Confidence 7888889993 25679999999999999875
No 95
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.01 E-value=0.0037 Score=31.51 Aligned_cols=22 Identities=27% Similarity=0.640 Sum_probs=18.7
Q ss_pred ccccccccccCCHHHHHHhhhh
Q 025404 15 HKCVACYKQFKRKDHLIEHMKI 36 (253)
Q Consensus 15 ~~C~~C~k~f~~~~~l~~H~~~ 36 (253)
|.|+.|++.|.....|..|++.
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTT
T ss_pred CCCCCCCCCcCCHHHHHHHHCc
Confidence 5788899999998888888875
No 96
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=95.54 E-value=0.0074 Score=31.11 Aligned_cols=22 Identities=41% Similarity=0.694 Sum_probs=17.9
Q ss_pred ccccccccccCCHHHHHHhhhh
Q 025404 15 HKCVACYKQFKRKDHLIEHMKI 36 (253)
Q Consensus 15 ~~C~~C~k~f~~~~~l~~H~~~ 36 (253)
|.|..|++.|.+...|..|+++
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTS
T ss_pred CCcccCCCCcCCHHHHHHHHcc
Confidence 6788888888888888888765
No 97
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=95.51 E-value=0.007 Score=41.79 Aligned_cols=20 Identities=40% Similarity=0.753 Sum_probs=17.9
Q ss_pred cccccccccccCHHHHhhhh
Q 025404 44 PKCAVCQKLSKSFESLREHL 63 (253)
Q Consensus 44 ~~C~~C~~~f~~~~~l~~H~ 63 (253)
..|..|++.|.+...|..|+
T Consensus 51 ~~C~~C~~~f~s~~~l~~Hm 70 (100)
T PF12756_consen 51 FRCPYCNKTFRSREALQEHM 70 (100)
T ss_dssp EEBSSSS-EESSHHHHHHHH
T ss_pred CCCCccCCCCcCHHHHHHHH
Confidence 48999999999999999999
No 98
>PRK04860 hypothetical protein; Provisional
Probab=95.44 E-value=0.0045 Score=46.93 Aligned_cols=39 Identities=13% Similarity=0.254 Sum_probs=32.1
Q ss_pred CcccccccccccCCHHHHHHhhhhcCCCCCcc-ccccccccccCHH
Q 025404 13 ARHKCVACYKQFKRKDHLIEHMKISYHSVHQP-KCAVCQKLSKSFE 57 (253)
Q Consensus 13 k~~~C~~C~k~f~~~~~l~~H~~~~~H~~~~~-~C~~C~~~f~~~~ 57 (253)
-+|.|. |++ ....+.+|.++ |+++++ .|..|++.|....
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri--~~g~~~YrC~~C~~~l~~~~ 157 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRV--VRGEAVYRCRRCGETLVFKG 157 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHH--hcCCccEECCCCCceeEEec
Confidence 469997 987 56778899999 999888 9999998887543
No 99
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=95.14 E-value=0.01 Score=29.86 Aligned_cols=21 Identities=33% Similarity=0.680 Sum_probs=16.0
Q ss_pred ccccccccCChHHHHHHHHHc
Q 025404 81 CNLCMNIFDSPSSLIKHKEAC 101 (253)
Q Consensus 81 C~~C~k~f~~~~~l~~H~~~h 101 (253)
|..|++.|.+...|+.|++.+
T Consensus 3 C~~C~~~f~s~~~~~~H~~s~ 23 (25)
T PF12874_consen 3 CDICNKSFSSENSLRQHLRSK 23 (25)
T ss_dssp ETTTTEEESSHHHHHHHHTTH
T ss_pred CCCCCCCcCCHHHHHHHHCcC
Confidence 777888888888888887643
No 100
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=94.66 E-value=0.013 Score=48.51 Aligned_cols=56 Identities=29% Similarity=0.556 Sum_probs=28.4
Q ss_pred Ccc-cccc--ccccccCHHHHhhhh-CC-------CCCCCcCCccc----ccccccccccccCChHHHHHH
Q 025404 42 HQP-KCAV--CQKLSKSFESLREHL-TG-------PLSKAHCSGIF----SDRGCNLCMNIFDSPSSLIKH 97 (253)
Q Consensus 42 ~~~-~C~~--C~~~f~~~~~l~~H~-~~-------~~~C~~C~~~f----~~~~C~~C~k~f~~~~~l~~H 97 (253)
++| +|++ |+|.+.....|+-|+ .+ +-+-+.--..| +.+.|+.|+|.|+....|+-|
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYH 417 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYH 417 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceec
Confidence 355 6655 666666666666665 11 11122222233 223356666666655555555
No 101
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=94.52 E-value=0.026 Score=28.06 Aligned_cols=22 Identities=23% Similarity=0.330 Sum_probs=16.6
Q ss_pred ccccccccCChHHHHHHHHHccC
Q 025404 81 CNLCMNIFDSPSSLIKHKEACSL 103 (253)
Q Consensus 81 C~~C~k~f~~~~~l~~H~~~h~~ 103 (253)
|+.|+.... ...|..|++.|++
T Consensus 3 C~~C~y~t~-~~~l~~H~~~~H~ 24 (24)
T PF13909_consen 3 CPHCSYSTS-KSNLKRHLKRHHP 24 (24)
T ss_dssp -SSSS-EES-HHHHHHHHHHHHS
T ss_pred CCCCCCcCC-HHHHHHHHHhhCc
Confidence 788888887 8899999988753
No 102
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=94.51 E-value=0.032 Score=28.18 Aligned_cols=20 Identities=40% Similarity=0.982 Sum_probs=13.4
Q ss_pred ccccccccCChHHHHHHHHHc
Q 025404 81 CNLCMNIFDSPSSLIKHKEAC 101 (253)
Q Consensus 81 C~~C~k~f~~~~~l~~H~~~h 101 (253)
|+.||+.| ..+.|..|+.+.
T Consensus 5 C~~CgR~F-~~~~l~~H~~~C 24 (25)
T PF13913_consen 5 CPICGRKF-NPDRLEKHEKIC 24 (25)
T ss_pred CCCCCCEE-CHHHHHHHHHhc
Confidence 66777777 466777776553
No 103
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=94.45 E-value=0.021 Score=28.41 Aligned_cols=21 Identities=33% Similarity=0.513 Sum_probs=16.9
Q ss_pred ccccccccccCCHHHHHHhhhh
Q 025404 15 HKCVACYKQFKRKDHLIEHMKI 36 (253)
Q Consensus 15 ~~C~~C~k~f~~~~~l~~H~~~ 36 (253)
|+|+.|+.... ...|..|++.
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~ 21 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKR 21 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHh
Confidence 68999998887 8899999987
No 104
>COG2925 SbcB Exonuclease I [DNA replication, recombination, and repair]
Probab=93.84 E-value=0.34 Score=41.54 Aligned_cols=98 Identities=17% Similarity=0.214 Sum_probs=70.0
Q ss_pred CCceeeeecccccCC--CCCcccccceeeeecCCCCe---EEeeeccCCCCc--ccceeeeccCCHHhhc-CCCCHHHHH
Q 025404 134 GPKAVAMDCEMVGGG--SNGTLDLCARVCLVDEDENV---IFHTYVQPQLPV--TNYRYEVTGLTEEDIK-NAMPLKEVK 205 (253)
Q Consensus 134 ~~~~~~~dcE~~g~~--~~~~~~ll~~v~iv~~~~~~---~~~~~v~P~~~i--~~~~~~~~Git~~~l~-~~~~~~~v~ 205 (253)
...+..+|-|+-|.. .++..++ +.|.. |.+-++ -...|++|.... .+..+=++||||.... ++.+..+..
T Consensus 8 ~~tF~~yDYETfG~~Pa~DRPaQF-AgiRT-D~~~NiIgeP~~fyCkpsdDyLP~P~a~LITGITPQ~~~~~G~~E~~F~ 85 (475)
T COG2925 8 QPTFLFYDYETFGVHPALDRPAQF-AGIRT-DIEFNIIGEPIVFYCKPADDYLPQPGAVLITGITPQEAREKGINEAAFA 85 (475)
T ss_pred CCcEEEEehhhcCCCcccccchhh-heeec-cccccccCCCeEEEecCccccCCCCCceeeecCCHHHHHhcCCChHHHH
Confidence 345789999999965 5566666 55543 222233 344577777542 2468889999999875 568899999
Q ss_pred HHHHHHHhcCCCCCcccccCCCCeEEEee-chhhhhhhhcC
Q 025404 206 DKILEILNNGESTGRLMLDDGKARLLVGH-GLEHDLDSLRM 245 (253)
Q Consensus 206 ~~l~~~~~~~~~~~~~~~~~~~~~~lv~h-~~~~D~~~l~~ 245 (253)
..|...++. .++.+||+ |+.||=.|-+-
T Consensus 86 ~~I~~~ls~------------P~Tcv~GYNniRFDDEvtRy 114 (475)
T COG2925 86 ARIHAELTQ------------PNTCVLGYNNIRFDDEVTRY 114 (475)
T ss_pred HHHHHHhCC------------CCeeeecccccccchHHHHH
Confidence 999988843 67799995 59999887664
No 105
>cd05780 DNA_polB_Kod1_like_exo DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of archaeal family-B DNA polymerases with similarity to Pyrococcus kodakaraensis Kod1, including polymerases from Desulfurococcus (D. Tok Pol) and Thermococcus gorgonarius (Tgo Pol). Kod1, D. Tok Pol, and Tgo Pol are thermostable enzymes that exhibit both polymerase and 3'-5' exonuclease activities. They are family-B DNA polymerases. Their amino termini harbor a DEDDy-type DnaQ-like 3'-5' exonuclease domain that contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members of this subfamily show
Probab=93.75 E-value=0.24 Score=38.94 Aligned_cols=39 Identities=15% Similarity=0.274 Sum_probs=28.7
Q ss_pred hcCCCCHHHHHHHHHHHHhcCCCCCcccccCCCCeEEEeech-hhhhhhhc
Q 025404 195 IKNAMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGL-EHDLDSLR 244 (253)
Q Consensus 195 l~~~~~~~~v~~~l~~~~~~~~~~~~~~~~~~~~~~lv~h~~-~~D~~~l~ 244 (253)
+....+-.++..++.+++..-+ -.+|||||. .||+.+|.
T Consensus 50 v~~~~~E~~lL~~F~~~i~~~d-----------pdiivgyN~~~FD~pyL~ 89 (195)
T cd05780 50 VEVVKTEKEMIKRFIEIVKEKD-----------PDVIYTYNGDNFDFPYLK 89 (195)
T ss_pred EEEeCCHHHHHHHHHHHHHHcC-----------CCEEEecCCCCCcHHHHH
Confidence 3445677899999999993100 249999995 59999885
No 106
>cd05785 DNA_polB_like2_exo Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Probab=93.67 E-value=0.26 Score=39.22 Aligned_cols=36 Identities=25% Similarity=0.508 Sum_probs=28.8
Q ss_pred CCCHHHHHHHHHHHHhcCCCCCcccccCCCCeEEEeech-hhhhhhhc
Q 025404 198 AMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGL-EHDLDSLR 244 (253)
Q Consensus 198 ~~~~~~v~~~l~~~~~~~~~~~~~~~~~~~~~~lv~h~~-~~D~~~l~ 244 (253)
..+..++...+.+++.+-+ -.||||||+ .||+.+|.
T Consensus 55 ~~~E~~lL~~f~~~i~~~d-----------Pdii~g~N~~~FD~pyl~ 91 (207)
T cd05785 55 DAAEKELLEELVAIIRERD-----------PDVIEGHNIFRFDLPYLR 91 (207)
T ss_pred CCCHHHHHHHHHHHHHHhC-----------CCEEeccCCcccCHHHHH
Confidence 5789999999999994211 149999998 99999975
No 107
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=93.28 E-value=0.069 Score=26.94 Aligned_cols=21 Identities=38% Similarity=0.694 Sum_probs=15.7
Q ss_pred ccccccccccCCHHHHHHhhhh
Q 025404 15 HKCVACYKQFKRKDHLIEHMKI 36 (253)
Q Consensus 15 ~~C~~C~k~f~~~~~l~~H~~~ 36 (253)
.+|+.|++.| ....|..|+.+
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 4688888888 45678888754
No 108
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=93.08 E-value=0.036 Score=48.60 Aligned_cols=113 Identities=24% Similarity=0.339 Sum_probs=79.9
Q ss_pred CcccccccccccCCHHHHHHhhh--hcCCCCC--cc-ccc--cccccccCHHHHhhhh-----CCCCCC--CcCCccccc
Q 025404 13 ARHKCVACYKQFKRKDHLIEHMK--ISYHSVH--QP-KCA--VCQKLSKSFESLREHL-----TGPLSK--AHCSGIFSD 78 (253)
Q Consensus 13 k~~~C~~C~k~f~~~~~l~~H~~--~~~H~~~--~~-~C~--~C~~~f~~~~~l~~H~-----~~~~~C--~~C~~~f~~ 78 (253)
.++.|..|...|+....|..|.+ . |+++ ++ .|. .|++.|.+...+..|. ..++.+ ..|.+.+..
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~--h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 365 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVN--HSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSP 365 (467)
T ss_pred cCCCCccccCCccccccccccccccc--cccccCCceeeeccCCCccccccccccCCcccccCCCccccccccCcccccc
Confidence 58999999999999999999999 7 9999 88 999 7999999999999997 222222 223222221
Q ss_pred cc-----------------------ccccccccCChHHHHHHHHHccCCCCCC-----ccccCccchhhhhhccccc
Q 025404 79 RG-----------------------CNLCMNIFDSPSSLIKHKEACSLSAPVP-----FEKTLSNAESQKKISGAID 127 (253)
Q Consensus 79 ~~-----------------------C~~C~k~f~~~~~l~~H~~~h~~~~~~~-----C~~~f~~~~~l~~h~~~~~ 127 (253)
.. -..|-..+.....+..|...|....++. |...+.....+..|.+.+.
T Consensus 366 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 442 (467)
T COG5048 366 LLNNEPPQSLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHIITHLSFRPYNCKNPPCSKSFNRHYNLIPHKKIHT 442 (467)
T ss_pred ccCCCCccchhhccCccCCccccccccchhhhhccccccccccccccccCCcCCCCCcchhhccCcccccccccccc
Confidence 10 2336667777777777776666554332 7777777777777775443
No 109
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=93.04 E-value=0.057 Score=27.53 Aligned_cols=22 Identities=18% Similarity=0.427 Sum_probs=15.0
Q ss_pred CCCcCCcccccc--cccccccccC
Q 025404 68 SKAHCSGIFSDR--GCNLCMNIFD 89 (253)
Q Consensus 68 ~C~~C~~~f~~~--~C~~C~k~f~ 89 (253)
.|+.|++..... .|+.||..|.
T Consensus 2 ~CP~C~~~V~~~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 2 TCPECGAEVPESAKFCPHCGYDFE 25 (26)
T ss_pred cCCCCcCCchhhcCcCCCCCCCCc
Confidence 477777766543 3888888775
No 110
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=92.92 E-value=0.079 Score=28.87 Aligned_cols=23 Identities=22% Similarity=0.355 Sum_probs=20.0
Q ss_pred cccccccccccCCHHHHHHhhhh
Q 025404 14 RHKCVACYKQFKRKDHLIEHMKI 36 (253)
Q Consensus 14 ~~~C~~C~k~f~~~~~l~~H~~~ 36 (253)
+|.|+.|++.|.....+..|++.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 58899999999998889888865
No 111
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=92.80 E-value=0.079 Score=27.15 Aligned_cols=19 Identities=32% Similarity=0.679 Sum_probs=13.4
Q ss_pred ccccccccccCHHHHhhhh
Q 025404 45 KCAVCQKLSKSFESLREHL 63 (253)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~ 63 (253)
.|..|++.|.+...|..|+
T Consensus 3 ~C~~C~k~f~~~~~~~~H~ 21 (27)
T PF12171_consen 3 YCDACDKYFSSENQLKQHM 21 (27)
T ss_dssp BBTTTTBBBSSHHHHHCCT
T ss_pred CcccCCCCcCCHHHHHHHH
Confidence 4677777777777777775
No 112
>cd05781 DNA_polB_B3_exo DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of archaeal proteins with similarity to Sulfurisphaera ohwakuensis DNA polymerase B3. B3 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B3 exhibits both polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Archaeal proteins that are involved in DNA replicatio
Probab=90.68 E-value=1.4 Score=34.48 Aligned_cols=37 Identities=11% Similarity=0.180 Sum_probs=28.2
Q ss_pred CCCHHHHHHHHHHHHhcCCCCCcccccCCCCeEEEeec-hhhhhhhhcC
Q 025404 198 AMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHG-LEHDLDSLRM 245 (253)
Q Consensus 198 ~~~~~~v~~~l~~~~~~~~~~~~~~~~~~~~~~lv~h~-~~~D~~~l~~ 245 (253)
..+..++...+.+++..- .-.+|+|+| ..||+.+|.-
T Consensus 45 ~~~E~~lL~~F~~~i~~~-----------dPd~i~gyN~~~FDlpyl~~ 82 (188)
T cd05781 45 GLDDRKIIREFVKYVKEY-----------DPDIIVGYNSNAFDWPYLVE 82 (188)
T ss_pred CCCHHHHHHHHHHHHHHc-----------CCCEEEecCCCcCcHHHHHH
Confidence 478899999999999421 113999999 6699999753
No 113
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.43 E-value=0.39 Score=44.41 Aligned_cols=72 Identities=24% Similarity=0.253 Sum_probs=34.9
Q ss_pred CCHHHHHHhhhhcCCCCCc-------c-ccccccccccCHHHHhhhh-CCCCCCCcCCccccc-ccccccccccCChHHH
Q 025404 25 KRKDHLIEHMKISYHSVHQ-------P-KCAVCQKLSKSFESLREHL-TGPLSKAHCSGIFSD-RGCNLCMNIFDSPSSL 94 (253)
Q Consensus 25 ~~~~~l~~H~~~~~H~~~~-------~-~C~~C~~~f~~~~~l~~H~-~~~~~C~~C~~~f~~-~~C~~C~k~f~~~~~l 94 (253)
.....|+.|+.. .|..-. . .+..+.+.| +...|..|+ .+.. +++.+.. .-|..|...|.....|
T Consensus 125 ~s~~~Lk~H~~~-~H~~~~c~lC~~~~kif~~e~k~Y-t~~el~~h~~~gd~----d~~s~rGhp~C~~C~~~fld~~el 198 (669)
T KOG2231|consen 125 KSVENLKNHMRD-QHKLHLCSLCLQNLKIFINERKLY-TRAELNLHLMFGDP----DDESCRGHPLCKFCHERFLDDDEL 198 (669)
T ss_pred hHHHHHHHHHHH-hhhhhccccccccceeeeeeeehe-hHHHHHHHHhcCCC----ccccccCCccchhhhhhhccHHHH
Confidence 366778888843 143221 1 223333333 445566666 2211 2223322 2366666666666666
Q ss_pred HHHHHHcc
Q 025404 95 IKHKEACS 102 (253)
Q Consensus 95 ~~H~~~h~ 102 (253)
.+|++.++
T Consensus 199 ~rH~~~~h 206 (669)
T KOG2231|consen 199 YRHLRFDH 206 (669)
T ss_pred HHhhccce
Confidence 66665443
No 114
>cd06139 DNA_polA_I_Ecoli_like_exo DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial family-A DNA polymerases. Escherichia coli-like Polymerase I (Pol I), a subgroup of family-A DNA polymerases, contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase domain. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The 3'-5' exonuclease domain of DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. E. coli DNA Pol I is involved in genome replication but is not the main replicating enzyme. It is also implicated in DNA repair.
Probab=90.22 E-value=0.37 Score=37.43 Aligned_cols=37 Identities=27% Similarity=0.400 Sum_probs=29.7
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCCcccccCCCCeEEEeechhhhhhhhcC
Q 025404 197 NAMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRM 245 (253)
Q Consensus 197 ~~~~~~~v~~~l~~~~~~~~~~~~~~~~~~~~~~lv~h~~~~D~~~l~~ 245 (253)
+++++.++...|..++.+ .+.++||||+.||+.+|+.
T Consensus 48 ~~~~~~~~~~~l~~~l~~------------~~~~~v~hn~k~d~~~l~~ 84 (193)
T cd06139 48 EQLPREEVLAALKPLLED------------PSIKKVGQNLKFDLHVLAN 84 (193)
T ss_pred cCCCHHHHHHHHHHHHhC------------CCCcEEeeccHHHHHHHHH
Confidence 456788999999999931 3348999999999999963
No 115
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=89.04 E-value=0.19 Score=36.34 Aligned_cols=25 Identities=32% Similarity=0.708 Sum_probs=16.8
Q ss_pred CCCCCcCCccccccc------ccccc-cccCC
Q 025404 66 PLSKAHCSGIFSDRG------CNLCM-NIFDS 90 (253)
Q Consensus 66 ~~~C~~C~~~f~~~~------C~~C~-k~f~~ 90 (253)
|+.|..||+.|..-+ |+.|| +.|.+
T Consensus 1 PH~Ct~Cg~~f~dgs~eil~GCP~CGg~kF~y 32 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGSKEILSGCPECGGNKFQY 32 (131)
T ss_pred CcccCcCCCCcCCCcHHHHccCcccCCcceEE
Confidence 456777777776543 88887 56654
No 116
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=88.88 E-value=0.21 Score=30.18 Aligned_cols=28 Identities=21% Similarity=0.509 Sum_probs=23.3
Q ss_pred CCCCCcccccccccccCCHHHHHHhhhh
Q 025404 9 KRSTARHKCVACYKQFKRKDHLIEHMKI 36 (253)
Q Consensus 9 ~~~~k~~~C~~C~k~f~~~~~l~~H~~~ 36 (253)
..||--+.|+.|+..|.....+.+|+.-
T Consensus 12 RDGE~~lrCPRC~~~FR~~K~Y~RHVNK 39 (65)
T COG4049 12 RDGEEFLRCPRCGMVFRRRKDYIRHVNK 39 (65)
T ss_pred cCCceeeeCCchhHHHHHhHHHHHHhhH
Confidence 4578888999999999988888888864
No 117
>cd05784 DNA_polB_II_exo DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial family-B DNA polymerases. The 3'-5' exonuclease domain of Escherichia coli DNA polymerase II (Pol II) and similar bacterial proteins. Pol II is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain has a fundamental role in the proofreading activity of polII. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Pol II is involved in a variety of cellular activities, such as the repair of DNA damaged
Probab=88.54 E-value=1.6 Score=34.25 Aligned_cols=36 Identities=17% Similarity=0.265 Sum_probs=26.9
Q ss_pred CCCHHHHHHHHHHHHhcCCCCCcccccCCCCeEEEeec-hhhhhhhhc
Q 025404 198 AMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHG-LEHDLDSLR 244 (253)
Q Consensus 198 ~~~~~~v~~~l~~~~~~~~~~~~~~~~~~~~~~lv~h~-~~~D~~~l~ 244 (253)
-.+-.++...+.+++.+- +- .||+||| ..||+.+|.
T Consensus 48 ~~~E~~lL~~f~~~i~~~--------dP---Dvi~g~N~~~FD~~yl~ 84 (193)
T cd05784 48 FADEKSLLLALIAWFAQY--------DP---DIIIGWNVINFDLRLLQ 84 (193)
T ss_pred ECCHHHHHHHHHHHHHhh--------CC---CEEEECCCcCcCHHHHH
Confidence 468888999999999421 11 3999999 567999874
No 118
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=88.14 E-value=0.23 Score=39.74 Aligned_cols=13 Identities=38% Similarity=0.667 Sum_probs=9.6
Q ss_pred ccccccccccCHH
Q 025404 45 KCAVCQKLSKSFE 57 (253)
Q Consensus 45 ~C~~C~~~f~~~~ 57 (253)
.|++|++.|.++.
T Consensus 7 ~CPvC~~~F~~~~ 19 (214)
T PF09986_consen 7 TCPVCGKEFKTKK 19 (214)
T ss_pred ECCCCCCeeeeeE
Confidence 6888888887664
No 119
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=88.01 E-value=0.3 Score=34.45 Aligned_cols=10 Identities=20% Similarity=0.468 Sum_probs=5.7
Q ss_pred cccccccccc
Q 025404 45 KCAVCQKLSK 54 (253)
Q Consensus 45 ~C~~C~~~f~ 54 (253)
.|+.||++|-
T Consensus 11 ~Cp~CG~kFY 20 (108)
T PF09538_consen 11 TCPSCGAKFY 20 (108)
T ss_pred cCCCCcchhc
Confidence 5666665553
No 120
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=87.94 E-value=0.32 Score=26.33 Aligned_cols=19 Identities=32% Similarity=0.597 Sum_probs=15.9
Q ss_pred ccccccccCChHHHHHHHH
Q 025404 81 CNLCMNIFDSPSSLIKHKE 99 (253)
Q Consensus 81 C~~C~k~f~~~~~l~~H~~ 99 (253)
|..|++.|.+...+..|+.
T Consensus 6 C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 6 CKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred ccccCCccCCHHHHHHHHC
Confidence 7888888888888888874
No 121
>PRK04860 hypothetical protein; Provisional
Probab=87.31 E-value=0.36 Score=36.63 Aligned_cols=28 Identities=14% Similarity=0.330 Sum_probs=23.2
Q ss_pred cccccccccCChHHHHHHHHHccCCCCCCccc
Q 025404 80 GCNLCMNIFDSPSSLIKHKEACSLSAPVPFEK 111 (253)
Q Consensus 80 ~C~~C~k~f~~~~~l~~H~~~h~~~~~~~C~~ 111 (253)
.|. |++ ....+++|.++|+++++|.|++
T Consensus 121 ~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~ 148 (160)
T PRK04860 121 RCK-CQE---HQLTVRRHNRVVRGEAVYRCRR 148 (160)
T ss_pred EcC-CCC---eeCHHHHHHHHhcCCccEECCC
Confidence 476 887 6778899999999999998554
No 122
>PF03104 DNA_pol_B_exo1: DNA polymerase family B, exonuclease domain Several related DNA polymerases were too dissimilar to be included.; InterPro: IPR006133 DNA is the biological information that instructs cells how to exist in an ordered fashion: accurate replication is thus one of the most important events in the life cycle of a cell. This function is performed by DNA- directed DNA-polymerases 2.7.7.7 from EC) by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA, using a complementary DNA chain as a template. Small RNA molecules are generally used as primers for chain elongation, although terminal proteins may also be used for the de novo synthesis of a DNA chain. Even though there are 2 different methods of priming, these are mediated by 2 very similar polymerases classes, A and B, with similar methods of chain elongation. A number of DNA polymerases have been grouped under the designation of DNA polymerase family B. Six regions of similarity (numbered from I to VI) are found in all or a subset of the B family polymerases. The most conserved region (I) includes a conserved tetrapeptide with two aspartate residues. Its function is not yet known. However, it has been suggested that it may be involved in binding a magnesium ion. All sequences in the B family contain a characteristic DTDS motif, and possess many functional domains, including a 5'-3' elongation domain, a 3'-5' exonuclease domain [], a DNA binding domain, and binding domains for both dNTP's and pyrophosphate []. This domain has 3' to 5' exonuclease activity and adopts a ribonuclease H type fold [].; GO: 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 1QHT_A 4AHC_A 3A2F_A 2JGU_A 4AIL_C 1NOY_A 1NOZ_B 3IAY_A 1WNS_A 3K5O_A ....
Probab=87.25 E-value=1.8 Score=36.65 Aligned_cols=41 Identities=22% Similarity=0.369 Sum_probs=29.4
Q ss_pred HhhcCCCCHHHHHHHHHHHHhcCCCCCcccccCCCCeEEEeechh-hhhhhhc
Q 025404 193 EDIKNAMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLE-HDLDSLR 244 (253)
Q Consensus 193 ~~l~~~~~~~~v~~~l~~~~~~~~~~~~~~~~~~~~~~lv~h~~~-~D~~~l~ 244 (253)
..+....+..++...+.+++.. .+-| ||+|||+. ||+.+|.
T Consensus 214 ~~v~~~~~E~~lL~~f~~~i~~--------~dPD---ii~GyN~~~fD~~yl~ 255 (325)
T PF03104_consen 214 VEVIYFDSEKELLEAFLDIIQE--------YDPD---IITGYNIDGFDLPYLI 255 (325)
T ss_dssp TEEEEESSHHHHHHHHHHHHHH--------HS-S---EEEESSTTTTHHHHHH
T ss_pred cEEEEECCHHHHHHHHHHHHHh--------cCCc---EEEEecccCCCHHHHH
Confidence 3344457888999999999842 2223 99999965 9999874
No 123
>PF13482 RNase_H_2: RNase_H superfamily; PDB: 1TKD_A 1TK5_A 2AJQ_F 1T8E_A 1T7P_A 1SKR_A 1X9W_A 1TK8_A 1TK0_A 1SL2_A ....
Probab=87.03 E-value=1 Score=34.06 Aligned_cols=21 Identities=19% Similarity=0.151 Sum_probs=15.1
Q ss_pred CCeEEEeec-hhhhhhhhcCCC
Q 025404 227 KARLLVGHG-LEHDLDSLRMNY 247 (253)
Q Consensus 227 ~~~~lv~h~-~~~D~~~l~~~~ 247 (253)
+...+|+|| ..||+.+|+-..
T Consensus 56 ~~~~iv~yng~~FD~p~L~~~~ 77 (164)
T PF13482_consen 56 EADNIVTYNGKNFDIPFLKRRA 77 (164)
T ss_dssp TT--EEESSTTTTHHHHHHHHH
T ss_pred cCCeEEEEeCcccCHHHHHHHH
Confidence 556899988 799999997543
No 124
>COG5018 KapD Inhibitor of the KinA pathway to sporulation, predicted exonuclease [General function prediction only]
Probab=86.79 E-value=0.21 Score=37.83 Aligned_cols=45 Identities=24% Similarity=0.397 Sum_probs=41.0
Q ss_pred EEeeeccCCC--CcccceeeeccCCHHhhcCCCCHHHHHHHHHHHHh
Q 025404 169 IFHTYVQPQL--PVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEILN 213 (253)
Q Consensus 169 ~~~~~v~P~~--~i~~~~~~~~Git~~~l~~~~~~~~v~~~l~~~~~ 213 (253)
.|++||+|.. .++++...++||++..|+.||-|..|++++..+|+
T Consensus 45 ~F~syVRP~~~P~Lt~~Ckslt~I~Q~~VD~apifs~v~E~f~r~L~ 91 (210)
T COG5018 45 TFSSYVRPKKFPKLTKRCKSLTKITQKQVDEAPIFSMVFEDFIRKLN 91 (210)
T ss_pred HHHHhcCcccCchHHHHHHHhhhhhhhhccccchHHHHHHHHHHHHH
Confidence 6889999984 37899999999999999999999999999999994
No 125
>cd06146 mut-7_like_exo DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins. The mut-7 subfamily is composed of Caenorhabditis elegans mut-7 and similar proteins found in plants and metazoans. Mut-7 is implicated in posttranscriptional gene silencing. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs, termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis.
Probab=86.55 E-value=4.8 Score=31.53 Aligned_cols=35 Identities=23% Similarity=0.538 Sum_probs=25.7
Q ss_pred HHHHHHHHHHHhcCCCCCcccccCCCCeEEEeechhhhhhhhcCCCC
Q 025404 202 KEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNYP 248 (253)
Q Consensus 202 ~~v~~~l~~~~~~~~~~~~~~~~~~~~~~lv~h~~~~D~~~l~~~~~ 248 (253)
+.+.+.|..++.| .+.+.|||++.+|+.+|.-.++
T Consensus 68 ~~~~~~L~~ll~d------------~~i~KVg~~~~~D~~~L~~~~~ 102 (193)
T cd06146 68 EDWDRLLKRLFED------------PDVLKLGFGFKQDLKALSASYP 102 (193)
T ss_pred HHHHHHHHHHhCC------------CCeeEEEechHHHHHHHHHhcC
Confidence 3445567888842 4557899999999999986543
No 126
>PRK05755 DNA polymerase I; Provisional
Probab=86.33 E-value=2 Score=41.89 Aligned_cols=31 Identities=32% Similarity=0.366 Sum_probs=25.0
Q ss_pred HHHHHHHHHHhcCCCCCcccccCCCCeEEEeechhhhhhhhcC
Q 025404 203 EVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRM 245 (253)
Q Consensus 203 ~v~~~l~~~~~~~~~~~~~~~~~~~~~~lv~h~~~~D~~~l~~ 245 (253)
++++.|.+++.+ ...++|+||+.||+.+|.-
T Consensus 357 ~~l~~l~~~L~d------------~~v~kV~HNakfDl~~L~~ 387 (880)
T PRK05755 357 EVLAALKPLLED------------PAIKKVGQNLKYDLHVLAR 387 (880)
T ss_pred HHHHHHHHHHhC------------CCCcEEEeccHhHHHHHHh
Confidence 678889999932 3456899999999999874
No 127
>cd05779 DNA_polB_epsilon_exo DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon. DNA polymerase epsilon is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and delta are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase epsilon plays a role in elongating the leading strand during DNA replication. It is also involved in DNA repair. The catalytic subunit contains both polymerase and 3'-5' exonuclease activities. The N-terminal exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. DNA polymerase epsilon also carries a unique
Probab=85.87 E-value=3.7 Score=32.58 Aligned_cols=37 Identities=11% Similarity=0.050 Sum_probs=27.8
Q ss_pred CCCHHHHHHHHHHHHhcCCCCCcccccCCCCeEEEeec-hhhhhhhhcC
Q 025404 198 AMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHG-LEHDLDSLRM 245 (253)
Q Consensus 198 ~~~~~~v~~~l~~~~~~~~~~~~~~~~~~~~~~lv~h~-~~~D~~~l~~ 245 (253)
-.+-.++..++.+++.+- . -.+++|+| ..||+.+|.-
T Consensus 70 ~~~E~~lL~~f~~~i~~~------~-----Pd~i~gyN~~~FD~pyl~~ 107 (204)
T cd05779 70 EPDEKALLQRFFEHIREV------K-----PHIIVTYNGDFFDWPFVEA 107 (204)
T ss_pred CCCHHHHHHHHHHHHHHh------C-----CCEEEecCccccCHHHHHH
Confidence 468889999999999420 0 13999988 7899999853
No 128
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=85.52 E-value=0.47 Score=36.99 Aligned_cols=88 Identities=18% Similarity=0.354 Sum_probs=58.6
Q ss_pred CCCccccc--ccccccCCHHHHHHhhhhcCCCCCccccccccccccCHHHHhhhh------------CC---CCCCCcCC
Q 025404 11 STARHKCV--ACYKQFKRKDHLIEHMKISYHSVHQPKCAVCQKLSKSFESLREHL------------TG---PLSKAHCS 73 (253)
Q Consensus 11 ~~k~~~C~--~C~k~f~~~~~l~~H~~~~~H~~~~~~C~~C~~~f~~~~~l~~H~------------~~---~~~C~~C~ 73 (253)
..+.|.|+ .|...|.....+..|..+ -....|..|.+.|++..-|..|+ ++ =|+|.
T Consensus 76 ~~~~~~cqvagc~~~~d~lD~~E~hY~~----~h~~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~Cl--- 148 (253)
T KOG4173|consen 76 RVPAFACQVAGCCQVFDALDDYEHHYHT----LHGNSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCL--- 148 (253)
T ss_pred ccccccccccchHHHHhhhhhHHHhhhh----cccchhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHH---
Confidence 44568885 477888877777766643 22238999999999999999998 11 13442
Q ss_pred cccccccccccccccCChHHHHHHH-HHccCCCCCCcccc
Q 025404 74 GIFSDRGCNLCMNIFDSPSSLIKHK-EACSLSAPVPFEKT 112 (253)
Q Consensus 74 ~~f~~~~C~~C~k~f~~~~~l~~H~-~~h~~~~~~~C~~~ 112 (253)
-+.|+..|...-.-..|+ ++|.----|...+.
T Consensus 149 -------vEgCt~KFkT~r~RkdH~I~~Hk~Pa~frFdk~ 181 (253)
T KOG4173|consen 149 -------VEGCTEKFKTSRDRKDHMIRMHKYPADFRFDKP 181 (253)
T ss_pred -------HHhhhhhhhhhhhhhhHHHHhccCCcceeecCc
Confidence 355888888887777886 45643333334444
No 129
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=85.34 E-value=0.52 Score=46.57 Aligned_cols=115 Identities=24% Similarity=0.286 Sum_probs=73.4
Q ss_pred CCCcccccccccccCCHHHHHHhhhhcCCC------------------------CCcc-ccccccccccCHHHHhhhh--
Q 025404 11 STARHKCVACYKQFKRKDHLIEHMKISYHS------------------------VHQP-KCAVCQKLSKSFESLREHL-- 63 (253)
Q Consensus 11 ~~k~~~C~~C~k~f~~~~~l~~H~~~~~H~------------------------~~~~-~C~~C~~~f~~~~~l~~H~-- 63 (253)
..|.|+|+.|+..|.....|..|||.. |. +.++ .|..|...++.+.+|..|+
T Consensus 462 ~~kt~~cpkc~~~yk~a~~L~vhmRsk-hp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~LsihlqS 540 (1406)
T KOG1146|consen 462 FFKTLKCPKCNWHYKLAQTLGVHMRSK-HPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIHLQS 540 (1406)
T ss_pred ccccccCCccchhhhhHHHhhhccccc-ccccchhHhHhccccccccccccccCCCCcccceeeeeeeecchHHHHHHHH
Confidence 458899999999999999999999974 31 1245 8899999999999998887
Q ss_pred -----C--------C------CCC-CCcC--------------CcccccccccccccccCChHHHHHHHHHc-cCCCCCC
Q 025404 64 -----T--------G------PLS-KAHC--------------SGIFSDRGCNLCMNIFDSPSSLIKHKEAC-SLSAPVP 108 (253)
Q Consensus 64 -----~--------~------~~~-C~~C--------------~~~f~~~~C~~C~k~f~~~~~l~~H~~~h-~~~~~~~ 108 (253)
+ + +.. |..| .+.....+|..|+..-.-.-+|+.||..- +-..|--
T Consensus 541 ~~h~~~lee~~~~~g~~v~~~~~~v~s~~P~~ag~~~~ags~~pktkP~~~C~vc~yetniarnlrihmtss~~s~~p~~ 620 (1406)
T KOG1146|consen 541 DLHRNELEEAEENAGEQVRLLPASVTSAVPEEAGLGPSAGSSGPKTKPSWRCEVCSYETNIARNLRIHMTASPSSSPPSL 620 (1406)
T ss_pred HhhHHHHHHHHhccccchhhhhhhhcccCcccccCCCCCCCCCCCCCCCcchhhhcchhhhhhccccccccCCCCCChHH
Confidence 0 0 011 2111 22223334999988877777888887532 2222222
Q ss_pred ---ccccCccchhhhhhcccc
Q 025404 109 ---FEKTLSNAESQKKISGAI 126 (253)
Q Consensus 109 ---C~~~f~~~~~l~~h~~~~ 126 (253)
|.-.+.....+..+...+
T Consensus 621 ~Lq~~it~~l~~~~~~~~~lp 641 (1406)
T KOG1146|consen 621 VLQQNITSSLASLLGGQGRLP 641 (1406)
T ss_pred HhhhcchhhccccccCcCCCC
Confidence 444444444555554433
No 130
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=85.23 E-value=0.33 Score=38.95 Aligned_cols=60 Identities=13% Similarity=0.287 Sum_probs=30.9
Q ss_pred CCCCCCcccccccccccCCHHHHHHhhhhcCCCCCcc--ccccccccccCHHHHhhhhCCCCCCCcCCccccc
Q 025404 8 PKRSTARHKCVACYKQFKRKDHLIEHMKISYHSVHQP--KCAVCQKLSKSFESLREHLTGPLSKAHCSGIFSD 78 (253)
Q Consensus 8 ~~~~~k~~~C~~C~k~f~~~~~l~~H~~~~~H~~~~~--~C~~C~~~f~~~~~l~~H~~~~~~C~~C~~~f~~ 78 (253)
-++.++.|-|..|+..+=. + ....+. .|..|.+.|--...=+.--...|.|+.|+..|..
T Consensus 106 ip~~drqFaC~~Cd~~WwR--------r---vp~rKeVSRCr~C~~rYDPVP~dkmwG~aef~C~~C~h~F~G 167 (278)
T PF15135_consen 106 IPSVDRQFACSSCDHMWWR--------R---VPQRKEVSRCRKCRKRYDPVPCDKMWGIAEFHCPKCRHNFRG 167 (278)
T ss_pred ccccceeeeccccchHHHh--------c---cCcccccccccccccccCCCccccccceeeeecccccccchh
Confidence 3456677778777643211 1 222233 6777776664433111111445666666666654
No 131
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=84.22 E-value=0.38 Score=38.41 Aligned_cols=42 Identities=33% Similarity=0.555 Sum_probs=34.1
Q ss_pred cccccccccCCHHHHHHhhhhcCCCCCcc-ccccccccccCHHHHhhhh
Q 025404 16 KCVACYKQFKRKDHLIEHMKISYHSVHQP-KCAVCQKLSKSFESLREHL 63 (253)
Q Consensus 16 ~C~~C~k~f~~~~~l~~H~~~~~H~~~~~-~C~~C~~~f~~~~~l~~H~ 63 (253)
.|-.|++.|.+..-|..|++. +. +|.+|-|.+.+.-.|..|-
T Consensus 12 wcwycnrefddekiliqhqka------khfkchichkkl~sgpglsihc 54 (341)
T KOG2893|consen 12 WCWYCNREFDDEKILIQHQKA------KHFKCHICHKKLFSGPGLSIHC 54 (341)
T ss_pred eeeecccccchhhhhhhhhhh------ccceeeeehhhhccCCCceeeh
Confidence 688999999999888888876 44 8999988887777777763
No 132
>cd05776 DNA_polB_alpha_exo inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha. DNA polymerase alpha is a family-B DNA polymerase with a catalytic subunit that contains a DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (delta and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase alpha is almost exclusively required for the initiation of DNA replication and the priming of Okazaki fragments during elongation. It associates with DNA primase and is the only enzyme able to start DNA synthesis de novo. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are
Probab=84.03 E-value=1.3 Score=35.90 Aligned_cols=39 Identities=31% Similarity=0.435 Sum_probs=29.0
Q ss_pred hcCCCCHHHHHHHHHHHHhcCCCCCcccccCCCCeEEEeech-hhhhhhhc
Q 025404 195 IKNAMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGL-EHDLDSLR 244 (253)
Q Consensus 195 l~~~~~~~~v~~~l~~~~~~~~~~~~~~~~~~~~~~lv~h~~-~~D~~~l~ 244 (253)
+....+..+....+.+++.+ -|-| ||||||+ .||+.+|-
T Consensus 76 v~~~~~E~~LL~~f~~~i~~--------~DPD---iivG~Ni~~fdl~~L~ 115 (234)
T cd05776 76 VRIFENERALLNFFLAKLQK--------IDPD---VLVGHDLEGFDLDVLL 115 (234)
T ss_pred EEEeCCHHHHHHHHHHHHhh--------cCCC---EEEeeccCCCCHHHHH
Confidence 34456788899999999842 2223 9999998 89999873
No 133
>cd05783 DNA_polB_B1_exo DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal proteins. B1 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B1displays thermostable polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family-B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Family-B DNA polymerases from thermophilic archaea are uniq
Probab=84.02 E-value=11 Score=29.87 Aligned_cols=36 Identities=17% Similarity=0.125 Sum_probs=28.3
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCCcccccCCCCeEEEeec-hhhhhhhhcC
Q 025404 197 NAMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHG-LEHDLDSLRM 245 (253)
Q Consensus 197 ~~~~~~~v~~~l~~~~~~~~~~~~~~~~~~~~~~lv~h~-~~~D~~~l~~ 245 (253)
.-.+-.++..++.+++. .-.+|||+| ..||+.+|.-
T Consensus 69 ~~~~E~~lL~~F~~~i~-------------~~~~iig~N~~~FDlpyl~~ 105 (204)
T cd05783 69 FFDSEKELIREAFKIIS-------------EYPIVLTFNGDNFDLPYLYN 105 (204)
T ss_pred ecCCHHHHHHHHHHHHh-------------cCCEEEEeCCCCcCHHHHHH
Confidence 34688999999999994 224999988 7899999853
No 134
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=82.15 E-value=1.3 Score=41.18 Aligned_cols=29 Identities=21% Similarity=0.311 Sum_probs=19.8
Q ss_pred ccccccccccCHHHHhhhh-CCCCCCCcCC
Q 025404 45 KCAVCQKLSKSFESLREHL-TGPLSKAHCS 73 (253)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~-~~~~~C~~C~ 73 (253)
.|..|...|.....|.+|+ ...|.|..|.
T Consensus 184 ~C~~C~~~fld~~el~rH~~~~h~~chfC~ 213 (669)
T KOG2231|consen 184 LCKFCHERFLDDDELYRHLRFDHEFCHFCD 213 (669)
T ss_pred cchhhhhhhccHHHHHHhhccceeheeecC
Confidence 6777777777777777777 4455666664
No 135
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=80.73 E-value=0.74 Score=31.61 Aligned_cols=25 Identities=36% Similarity=0.741 Sum_probs=15.0
Q ss_pred CCCCCcCCcccccc------cccccc-cccCC
Q 025404 66 PLSKAHCSGIFSDR------GCNLCM-NIFDS 90 (253)
Q Consensus 66 ~~~C~~C~~~f~~~------~C~~C~-k~f~~ 90 (253)
|+.|..||..|..- .|+.|| +.|.+
T Consensus 2 pH~CtrCG~vf~~g~~~il~GCp~CG~nkF~y 33 (112)
T COG3364 2 PHQCTRCGEVFDDGSEEILSGCPKCGCNKFLY 33 (112)
T ss_pred CceecccccccccccHHHHccCccccchheEe
Confidence 45666666666552 377777 45554
No 136
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=80.16 E-value=3.2 Score=35.67 Aligned_cols=46 Identities=15% Similarity=0.060 Sum_probs=37.5
Q ss_pred ccccccccCChHHHHHHHHHccCC----CCC----------------------Ccc---ccCccchhhhhhcccc
Q 025404 81 CNLCMNIFDSPSSLIKHKEACSLS----APV----------------------PFE---KTLSNAESQKKISGAI 126 (253)
Q Consensus 81 C~~C~k~f~~~~~l~~H~~~h~~~----~~~----------------------~C~---~~f~~~~~l~~h~~~~ 126 (253)
|-.|++.|.+...-..||..++|= +.| -|. +.|+.....+.|+...
T Consensus 169 CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~K 243 (390)
T KOG2785|consen 169 CLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRDK 243 (390)
T ss_pred eeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhhc
Confidence 999999999999999999988863 222 188 8899999999999643
No 137
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=79.63 E-value=0.71 Score=25.67 Aligned_cols=13 Identities=23% Similarity=0.626 Sum_probs=7.1
Q ss_pred ccccccccccCCH
Q 025404 15 HKCVACYKQFKRK 27 (253)
Q Consensus 15 ~~C~~C~k~f~~~ 27 (253)
+.|+.|+..|.-.
T Consensus 3 ~~CP~C~~~~~v~ 15 (38)
T TIGR02098 3 IQCPNCKTSFRVV 15 (38)
T ss_pred EECCCCCCEEEeC
Confidence 3566666655443
No 138
>cd06141 WRN_exo DEDDy 3'-5' exonuclease domain of WRN and similar proteins. WRN is a unique RecQ DNA helicase exhibiting an exonuclease activity. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Mutations in the WRN gene cause Werner syndrome, an autosomal recessive disorder associated with premature aging and increased susceptibility to cancer and type II diabetes. WRN interacts with key proteins involved in DNA replication, recombination, and repair. It is believed to maintain genomic stability and life span by participating in DNA processes. WRN is stimulated by Ku70/80, an important regulator of genomic stability.
Probab=79.52 E-value=6.6 Score=29.78 Aligned_cols=28 Identities=25% Similarity=0.405 Sum_probs=21.4
Q ss_pred HHHHHHHhcCCCCCcccccCCCCeEEEeechhhhhhhhcC
Q 025404 206 DKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRM 245 (253)
Q Consensus 206 ~~l~~~~~~~~~~~~~~~~~~~~~~lv~h~~~~D~~~l~~ 245 (253)
+.|.+++.+ .+.+.|||++.+|+.+|.-
T Consensus 63 ~~l~~ll~~------------~~i~kv~~~~k~D~~~L~~ 90 (170)
T cd06141 63 PSLKQLLED------------PSILKVGVGIKGDARKLAR 90 (170)
T ss_pred HHHHHHhcC------------CCeeEEEeeeHHHHHHHHh
Confidence 467778832 4557899999999999863
No 139
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=79.35 E-value=0.98 Score=31.85 Aligned_cols=25 Identities=24% Similarity=0.424 Sum_probs=17.8
Q ss_pred CCCCcCCcccccc-----cccccccccCCh
Q 025404 67 LSKAHCSGIFSDR-----GCNLCMNIFDSP 91 (253)
Q Consensus 67 ~~C~~C~~~f~~~-----~C~~C~k~f~~~ 91 (253)
..|+.||+.|.-. .|+.||..|.-.
T Consensus 10 R~Cp~CG~kFYDLnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCGAKFYDLNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCcchhccCCCCCccCCCCCCccCcc
Confidence 4588888888643 288888877754
No 140
>cd06148 Egl_like_exo DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins. The Egalitarian (Egl) protein subfamily is composed of Drosophila Egl and similar proteins. Egl is a component of an mRNA-binding complex which is required for oocyte specification. Egl contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation of this subfamily throughout eukaryotes suggests that its members may be part of ancient RNA processing complexes that are likely to participate in the regulated processing of specific mRNAs. Some members of this subfamily do not have a completely conserved YX(3)D pattern at the ExoIII motif.
Probab=79.25 E-value=6.2 Score=30.99 Aligned_cols=27 Identities=33% Similarity=0.389 Sum_probs=20.0
Q ss_pred HHHHHHHHhcCCCCCcccccCCCCeEEEeechhhhhhhh
Q 025404 205 KDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSL 243 (253)
Q Consensus 205 ~~~l~~~~~~~~~~~~~~~~~~~~~~lv~h~~~~D~~~l 243 (253)
.+.|.+++.+ .+.+.|||++.+|+.+|
T Consensus 54 ~~~L~~iLe~------------~~i~Kv~h~~k~D~~~L 80 (197)
T cd06148 54 INGLKDILES------------KKILKVIHDCRRDSDAL 80 (197)
T ss_pred HHHHHHHhcC------------CCccEEEEechhHHHHH
Confidence 3556677732 44567999999999998
No 141
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=78.81 E-value=1.3 Score=31.91 Aligned_cols=11 Identities=9% Similarity=0.015 Sum_probs=6.2
Q ss_pred ccccccccCCh
Q 025404 81 CNLCMNIFDSP 91 (253)
Q Consensus 81 C~~C~k~f~~~ 91 (253)
|+.||..|.-.
T Consensus 29 cP~cg~~~~~~ 39 (129)
T TIGR02300 29 SPYTGEQFPPE 39 (129)
T ss_pred CCCcCCccCcc
Confidence 56666665543
No 142
>cd05778 DNA_polB_zeta_exo inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta. DNA polymerase zeta is a family-B DNA polymerase which is distantly related to DNA polymerase delta. It plays a major role in translesion replication and the production of either spontaneous or induced mutations. In addition, DNA polymerase zeta also appears to be involved in somatic hypermutability in B lymphocytes, an important element for the production of high affinity antibodies in response to an antigen. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The DnaQ-like 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are crucial for metal binding and catalysis.
Probab=77.99 E-value=7.7 Score=31.35 Aligned_cols=40 Identities=13% Similarity=0.271 Sum_probs=29.2
Q ss_pred HhhcCCCCHHHHHHHHHHHHhcCCCCCcccccCCCCeEEEeech-hhhhhhh
Q 025404 193 EDIKNAMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGL-EHDLDSL 243 (253)
Q Consensus 193 ~~l~~~~~~~~v~~~l~~~~~~~~~~~~~~~~~~~~~~lv~h~~-~~D~~~l 243 (253)
..+....+..++..++.+++.. -|-| ||+|||+ .||+.+|
T Consensus 73 ~~v~~~~~E~~LL~~f~~~i~~--------~DPD---ii~GyNi~~fd~~YL 113 (231)
T cd05778 73 IPVEVVESELELFEELIDLVRR--------FDPD---ILSGYEIQRSSWGYL 113 (231)
T ss_pred CeEEEeCCHHHHHHHHHHHHHH--------hCCC---EEEEeccccCcHHHH
Confidence 3444557888999999999842 2223 9999997 6898876
No 143
>cd00007 35EXOc 3'-5' exonuclease. The 35EXOc domain is responsible for the 3'-5' exonuclease proofreading activity of prokaryotic DNA polymerase I (pol I) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli pol I. 35EXOc is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D).
Probab=77.96 E-value=2.6 Score=30.96 Aligned_cols=32 Identities=28% Similarity=0.355 Sum_probs=24.9
Q ss_pred HHHHHHHHHHHhcCCCCCcccccCCCCeEEEeechhhhhhhhcC
Q 025404 202 KEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRM 245 (253)
Q Consensus 202 ~~v~~~l~~~~~~~~~~~~~~~~~~~~~~lv~h~~~~D~~~l~~ 245 (253)
..+.+.+.+++.+ .+..+||||+.+|+.+|.-
T Consensus 40 ~~~~~~l~~~l~~------------~~~~~v~~~~k~d~~~L~~ 71 (155)
T cd00007 40 EEDLEALKELLED------------EDITKVGHDAKFDLVVLAR 71 (155)
T ss_pred HHHHHHHHHHHcC------------CCCcEEeccHHHHHHHHHH
Confidence 6677778888832 3456999999999999853
No 144
>cd05777 DNA_polB_delta_exo DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase delta. DNA polymerase delta is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase delta is the enzyme responsible for both elongation and maturation of Okazaki fragments on the lagging strand. It is also implicated in mismatch repair (MMR) and base excision repair (BER). The catalytic subunit displays both polymerase and 3'-5' exonuclease activities. The exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic
Probab=77.93 E-value=24 Score=28.39 Aligned_cols=38 Identities=13% Similarity=0.069 Sum_probs=27.8
Q ss_pred cCCCCHHHHHHHHHHHHhcCCCCCcccccCCCCeEEEeec-hhhhhhhhc
Q 025404 196 KNAMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHG-LEHDLDSLR 244 (253)
Q Consensus 196 ~~~~~~~~v~~~l~~~~~~~~~~~~~~~~~~~~~~lv~h~-~~~D~~~l~ 244 (253)
....+..++...+.+++.. ..| .||+||| -.||+.+|.
T Consensus 66 ~~~~~E~eLL~~f~~~i~~------~DP-----Dii~GyN~~~FDl~yL~ 104 (230)
T cd05777 66 FSFETEEELLLAWRDFVQE------VDP-----DIITGYNICNFDLPYLL 104 (230)
T ss_pred EEECCHHHHHHHHHHHHHh------cCC-----CEEEEecCCCCCHHHHH
Confidence 3346889999999999932 111 3999999 557999863
No 145
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=77.59 E-value=1 Score=36.00 Aligned_cols=34 Identities=18% Similarity=0.303 Sum_probs=28.6
Q ss_pred ccccccccccccCHHHHhhhh-CCCCCCCcCCccc
Q 025404 43 QPKCAVCQKLSKSFESLREHL-TGPLSKAHCSGIF 76 (253)
Q Consensus 43 ~~~C~~C~~~f~~~~~l~~H~-~~~~~C~~C~~~f 76 (253)
++=|..|++.|-..--|.+|+ .+.|+|.+|-|..
T Consensus 10 kpwcwycnrefddekiliqhqkakhfkchichkkl 44 (341)
T KOG2893|consen 10 KPWCWYCNREFDDEKILIQHQKAKHFKCHICHKKL 44 (341)
T ss_pred Cceeeecccccchhhhhhhhhhhccceeeeehhhh
Confidence 347999999999999999999 8899988776543
No 146
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=77.43 E-value=1.3 Score=32.50 Aligned_cols=23 Identities=26% Similarity=0.452 Sum_probs=15.5
Q ss_pred ccccccccCChHHHHHHHHHccCCCC
Q 025404 81 CNLCMNIFDSPSSLIKHKEACSLSAP 106 (253)
Q Consensus 81 C~~C~k~f~~~~~l~~H~~~h~~~~~ 106 (253)
|-+||+.|+. |++|++.|+|-.|
T Consensus 75 clecGk~~k~---LkrHL~~~~gltp 97 (132)
T PF05443_consen 75 CLECGKKFKT---LKRHLRTHHGLTP 97 (132)
T ss_dssp -TBT--EESB---HHHHHHHTT-S-H
T ss_pred EccCCcccch---HHHHHHHccCCCH
Confidence 8999999985 6899999988655
No 147
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=76.74 E-value=0.51 Score=37.74 Aligned_cols=19 Identities=32% Similarity=0.560 Sum_probs=15.6
Q ss_pred CCcccccccccccCCHHHH
Q 025404 12 TARHKCVACYKQFKRKDHL 30 (253)
Q Consensus 12 ~k~~~C~~C~k~f~~~~~l 30 (253)
+|...|+.|++.|..+...
T Consensus 3 ~k~~~CPvC~~~F~~~~vr 21 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVR 21 (214)
T ss_pred CCceECCCCCCeeeeeEEE
Confidence 5778999999999987543
No 148
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=76.10 E-value=1.6 Score=21.39 Aligned_cols=18 Identities=22% Similarity=0.567 Sum_probs=8.8
Q ss_pred CCcCCccccccc--cccccc
Q 025404 69 KAHCSGIFSDRG--CNLCMN 86 (253)
Q Consensus 69 C~~C~~~f~~~~--C~~C~k 86 (253)
|+.||+.....+ |+.||.
T Consensus 2 Cp~CG~~~~~~~~fC~~CG~ 21 (23)
T PF13240_consen 2 CPNCGAEIEDDAKFCPNCGT 21 (23)
T ss_pred CcccCCCCCCcCcchhhhCC
Confidence 445554444322 666664
No 149
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=75.68 E-value=2.2 Score=25.36 Aligned_cols=22 Identities=23% Similarity=0.483 Sum_probs=13.4
Q ss_pred ccccccccCC-----hHHHHHHHH-Hcc
Q 025404 81 CNLCMNIFDS-----PSSLIKHKE-ACS 102 (253)
Q Consensus 81 C~~C~k~f~~-----~~~l~~H~~-~h~ 102 (253)
|..|++.+.. .++|.+|++ .|.
T Consensus 21 C~~C~~~l~~~~~~gTs~L~rHl~~~h~ 48 (50)
T smart00614 21 CKYCGKKLSRSSKGGTSNLRRHLRRKHP 48 (50)
T ss_pred ecCCCCEeeeCCCCCcHHHHHHHHhHCc
Confidence 5555555543 468888887 453
No 150
>PF14353 CpXC: CpXC protein
Probab=75.61 E-value=1.4 Score=32.07 Aligned_cols=14 Identities=29% Similarity=0.479 Sum_probs=8.2
Q ss_pred CCHHHHHHHHHHHH
Q 025404 199 MPLKEVKDKILEIL 212 (253)
Q Consensus 199 ~~~~~v~~~l~~~~ 212 (253)
.++.+..+++.-+-
T Consensus 103 ~~~~~l~EKI~i~e 116 (128)
T PF14353_consen 103 IDYNELREKILIFE 116 (128)
T ss_pred CCHHHHHHHHHHHH
Confidence 45666666665554
No 151
>PHA00626 hypothetical protein
Probab=75.28 E-value=0.98 Score=27.38 Aligned_cols=11 Identities=9% Similarity=-0.088 Sum_probs=4.6
Q ss_pred CCCCCcCCccc
Q 025404 66 PLSKAHCSGIF 76 (253)
Q Consensus 66 ~~~C~~C~~~f 76 (253)
.|.|+.||..|
T Consensus 23 rYkCkdCGY~f 33 (59)
T PHA00626 23 DYVCCDCGYND 33 (59)
T ss_pred ceEcCCCCCee
Confidence 34444444333
No 152
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=74.91 E-value=3.1 Score=31.09 Aligned_cols=33 Identities=21% Similarity=0.454 Sum_probs=22.1
Q ss_pred ccccccccccCHHHHhh-hhCCCCCCCcCCcccc
Q 025404 45 KCAVCQKLSKSFESLRE-HLTGPLSKAHCSGIFS 77 (253)
Q Consensus 45 ~C~~C~~~f~~~~~l~~-H~~~~~~C~~C~~~f~ 77 (253)
.|+.|+..|.....+.. ..++.|.|+.||....
T Consensus 101 ~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~l~ 134 (147)
T smart00531 101 KCPNCQSKYTFLEANQLLDMDGTFTCPRCGEELE 134 (147)
T ss_pred ECcCCCCEeeHHHHHHhcCCCCcEECCCCCCEEE
Confidence 88889888886655433 2355577877776553
No 153
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=74.90 E-value=3 Score=29.49 Aligned_cols=21 Identities=19% Similarity=0.298 Sum_probs=14.9
Q ss_pred CCcccccccccccCCHHHHHH
Q 025404 12 TARHKCVACYKQFKRKDHLIE 32 (253)
Q Consensus 12 ~k~~~C~~C~k~f~~~~~l~~ 32 (253)
+-|-.|+.|+-+.....+|.+
T Consensus 13 ~LP~~CpiCgLtLVss~HLAR 33 (112)
T TIGR00622 13 ELPVECPICGLTLILSTHLAR 33 (112)
T ss_pred CCCCcCCcCCCEEeccchHHH
Confidence 456778888877777777765
No 154
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=74.82 E-value=1.2 Score=26.99 Aligned_cols=24 Identities=13% Similarity=0.319 Sum_probs=13.9
Q ss_pred CCCcc-ccccccccccCHHHHhhhh
Q 025404 40 SVHQP-KCAVCQKLSKSFESLREHL 63 (253)
Q Consensus 40 ~~~~~-~C~~C~~~f~~~~~l~~H~ 63 (253)
-|+.. .|+.||..|...-+..+|.
T Consensus 13 DGE~~lrCPRC~~~FR~~K~Y~RHV 37 (65)
T COG4049 13 DGEEFLRCPRCGMVFRRRKDYIRHV 37 (65)
T ss_pred CCceeeeCCchhHHHHHhHHHHHHh
Confidence 34555 6666666666665555555
No 155
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=74.78 E-value=1 Score=26.31 Aligned_cols=22 Identities=18% Similarity=0.294 Sum_probs=10.6
Q ss_pred CCCCcCCcccccc------ccccccccc
Q 025404 67 LSKAHCSGIFSDR------GCNLCMNIF 88 (253)
Q Consensus 67 ~~C~~C~~~f~~~------~C~~C~k~f 88 (253)
|.|+.||..|... .|+.||..+
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~~ 31 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCPYCGYRI 31 (46)
T ss_pred EECCCCCCEEEECCCCCceECCCCCCeE
Confidence 4455555544321 266666433
No 156
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=74.18 E-value=1.6 Score=24.21 Aligned_cols=12 Identities=25% Similarity=0.777 Sum_probs=7.3
Q ss_pred cccccccccCCH
Q 025404 16 KCVACYKQFKRK 27 (253)
Q Consensus 16 ~C~~C~k~f~~~ 27 (253)
.|+.|+..|.-.
T Consensus 4 ~CP~C~~~f~v~ 15 (37)
T PF13719_consen 4 TCPNCQTRFRVP 15 (37)
T ss_pred ECCCCCceEEcC
Confidence 466666666544
No 157
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=73.72 E-value=2.1 Score=28.64 Aligned_cols=28 Identities=18% Similarity=0.313 Sum_probs=17.1
Q ss_pred CCCCCCCcCCcccccc------cccccccccCCh
Q 025404 64 TGPLSKAHCSGIFSDR------GCNLCMNIFDSP 91 (253)
Q Consensus 64 ~~~~~C~~C~~~f~~~------~C~~C~k~f~~~ 91 (253)
...|.|+.|++.-... .|..||..|.--
T Consensus 33 ~~~~~Cp~C~~~~VkR~a~GIW~C~kCg~~fAGg 66 (89)
T COG1997 33 RAKHVCPFCGRTTVKRIATGIWKCRKCGAKFAGG 66 (89)
T ss_pred hcCCcCCCCCCcceeeeccCeEEcCCCCCeeccc
Confidence 3466777777663322 277788777653
No 158
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=73.60 E-value=3.9 Score=34.71 Aligned_cols=102 Identities=23% Similarity=0.290 Sum_probs=57.5
Q ss_pred cccc--ccccccCCHHHHHHhhhhcCCCCCcccccccc---cc------ccCHHHHhhhhCCCCCCCcCCccccc-cccc
Q 025404 15 HKCV--ACYKQFKRKDHLIEHMKISYHSVHQPKCAVCQ---KL------SKSFESLREHLTGPLSKAHCSGIFSD-RGCN 82 (253)
Q Consensus 15 ~~C~--~C~k~f~~~~~l~~H~~~~~H~~~~~~C~~C~---~~------f~~~~~l~~H~~~~~~C~~C~~~f~~-~~C~ 82 (253)
|.|+ .|.........|+.|.+.. |. +..|.+|- +. ..++..|..|.++--+ +..|+- ..|.
T Consensus 152 F~CP~skc~~~C~~~k~lk~H~K~~-H~--~~~C~~C~~nKk~F~~E~~lF~~~~Lr~H~~~G~~----e~GFKGHP~C~ 224 (493)
T COG5236 152 FKCPKSKCHRRCGSLKELKKHYKAQ-HG--FVLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLE----EEGFKGHPLCI 224 (493)
T ss_pred hcCCchhhhhhhhhHHHHHHHHHhh-cC--cEEhHhhhcCcccCccceeeeecccccccccCCcc----ccCcCCCchhh
Confidence 6774 3665555567788887762 22 11344432 22 2344556666521110 112321 2388
Q ss_pred ccccccCChHHHHHHHHHccCCCCCCcccc-------Cccchhhhhhcc
Q 025404 83 LCMNIFDSPSSLIKHKEACSLSAPVPFEKT-------LSNAESQKKISG 124 (253)
Q Consensus 83 ~C~k~f~~~~~l~~H~~~h~~~~~~~C~~~-------f~~~~~l~~h~~ 124 (253)
.|...|.+...|..|+|.-+ |+.+-|++. |.+..+|..|-+
T Consensus 225 FC~~~FYdDDEL~~HcR~~H-E~ChICD~v~p~~~QYFK~Y~~Le~HF~ 272 (493)
T COG5236 225 FCKIYFYDDDELRRHCRLRH-EACHICDMVGPIRYQYFKSYEDLEAHFR 272 (493)
T ss_pred hccceecChHHHHHHHHhhh-hhhhhhhccCccchhhhhCHHHHHHHhh
Confidence 88888888899999987543 455555543 666667777753
No 159
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=73.46 E-value=1.5 Score=24.14 Aligned_cols=13 Identities=23% Similarity=0.756 Sum_probs=7.2
Q ss_pred cccccccccCCHH
Q 025404 16 KCVACYKQFKRKD 28 (253)
Q Consensus 16 ~C~~C~k~f~~~~ 28 (253)
.|+.|+..|.-..
T Consensus 4 ~Cp~C~~~y~i~d 16 (36)
T PF13717_consen 4 TCPNCQAKYEIDD 16 (36)
T ss_pred ECCCCCCEEeCCH
Confidence 4666666655443
No 160
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=72.70 E-value=1.3 Score=24.93 Aligned_cols=10 Identities=20% Similarity=0.650 Sum_probs=5.4
Q ss_pred cccccccccc
Q 025404 45 KCAVCQKLSK 54 (253)
Q Consensus 45 ~C~~C~~~f~ 54 (253)
.|..||..|.
T Consensus 7 ~C~~Cg~~fe 16 (41)
T smart00834 7 RCEDCGHTFE 16 (41)
T ss_pred EcCCCCCEEE
Confidence 4555555554
No 161
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=71.45 E-value=1.2 Score=33.51 Aligned_cols=16 Identities=31% Similarity=0.576 Sum_probs=12.6
Q ss_pred CCCCHHHHHHHHHHHH
Q 025404 197 NAMPLKEVKDKILEIL 212 (253)
Q Consensus 197 ~~~~~~~v~~~l~~~~ 212 (253)
+.++.+++++-+.+.|
T Consensus 101 ~~IsveEIqDiVE~~L 116 (154)
T PRK00464 101 REVPSKEIGELVMEEL 116 (154)
T ss_pred CCCCHHHHHHHHHHHH
Confidence 3578888888888877
No 162
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=71.17 E-value=1.6 Score=41.32 Aligned_cols=42 Identities=24% Similarity=0.386 Sum_probs=21.0
Q ss_pred ccccccccccCH---HHHhhhh-CCCCCCCcCCcccc-ccccccccc
Q 025404 45 KCAVCQKLSKSF---ESLREHL-TGPLSKAHCSGIFS-DRGCNLCMN 86 (253)
Q Consensus 45 ~C~~C~~~f~~~---~~l~~H~-~~~~~C~~C~~~f~-~~~C~~C~k 86 (253)
.|..||..+.-. ..|..|+ ++...|..||..-. ...|+.||.
T Consensus 437 ~C~~Cg~v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs 483 (730)
T COG1198 437 LCRDCGYIAECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGS 483 (730)
T ss_pred ecccCCCcccCCCCCcceEEecCCCeeEeCCCCCCCCCCCCCCCCCC
Confidence 566666555322 3344454 44555666665522 223666653
No 163
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=71.16 E-value=2.2 Score=42.52 Aligned_cols=84 Identities=19% Similarity=0.283 Sum_probs=58.0
Q ss_pred cccccccccCCHHHHHHhhhhcCCCCCcc-ccccccccccCHHHHhhhh-CC-CC----CC----CcC----Cccc----
Q 025404 16 KCVACYKQFKRKDHLIEHMKISYHSVHQP-KCAVCQKLSKSFESLREHL-TG-PL----SK----AHC----SGIF---- 76 (253)
Q Consensus 16 ~C~~C~k~f~~~~~l~~H~~~~~H~~~~~-~C~~C~~~f~~~~~l~~H~-~~-~~----~C----~~C----~~~f---- 76 (253)
.|..|+..+.....+..|+... |+-.+- +|+.|+..|+....|..|+ ++ +. -| ..| +.+|
T Consensus 438 e~~~~e~~~~s~r~~~~~t~~L-~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~ 516 (1406)
T KOG1146|consen 438 ELTKAEPLLESKRSLEGQTVVL-HSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPG 516 (1406)
T ss_pred cccchhhhhhhhcccccceeee-ecccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCC
Confidence 4556777777777777777653 666566 9999999999999999998 21 10 01 000 1111
Q ss_pred ccccccccccccCChHHHHHHHHH
Q 025404 77 SDRGCNLCMNIFDSPSSLIKHKEA 100 (253)
Q Consensus 77 ~~~~C~~C~k~f~~~~~l~~H~~~ 100 (253)
....|..|..++..+.+|.+|+..
T Consensus 517 ~p~~C~~C~~stttng~LsihlqS 540 (1406)
T KOG1146|consen 517 KPYPCRACNYSTTTNGNLSIHLQS 540 (1406)
T ss_pred CcccceeeeeeeecchHHHHHHHH
Confidence 122399999999999999999864
No 164
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=70.42 E-value=1.4 Score=25.23 Aligned_cols=12 Identities=17% Similarity=0.556 Sum_probs=6.7
Q ss_pred ccccccccccCH
Q 025404 45 KCAVCQKLSKSF 56 (253)
Q Consensus 45 ~C~~C~~~f~~~ 56 (253)
.|..||..|...
T Consensus 7 ~C~~Cg~~fe~~ 18 (42)
T PF09723_consen 7 RCEECGHEFEVL 18 (42)
T ss_pred EeCCCCCEEEEE
Confidence 466666555544
No 165
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=70.25 E-value=7.1 Score=27.39 Aligned_cols=22 Identities=23% Similarity=0.108 Sum_probs=20.2
Q ss_pred cccccccCChHHHHHHHHHccC
Q 025404 82 NLCMNIFDSPSSLIKHKEACSL 103 (253)
Q Consensus 82 ~~C~k~f~~~~~l~~H~~~h~~ 103 (253)
..|+..+.+...+++|++.++|
T Consensus 88 ~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 88 PHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CCCCcEeccHHHHHHHHHHhcC
Confidence 8999999999999999998765
No 166
>PF15269 zf-C2H2_7: Zinc-finger
Probab=70.10 E-value=4.7 Score=23.24 Aligned_cols=23 Identities=39% Similarity=0.710 Sum_probs=20.2
Q ss_pred cccccccccccCCHHHHHHhhhh
Q 025404 14 RHKCVACYKQFKRKDHLIEHMKI 36 (253)
Q Consensus 14 ~~~C~~C~k~f~~~~~l~~H~~~ 36 (253)
.|+|=+|..+...+++|-.||+.
T Consensus 20 ~ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 20 KYKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred cceeecCCcccchHHHHHHHHHH
Confidence 37899999998999999999986
No 167
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=69.93 E-value=3.2 Score=20.93 Aligned_cols=20 Identities=15% Similarity=0.237 Sum_probs=10.6
Q ss_pred CCCcCCcccccc--cccccccc
Q 025404 68 SKAHCSGIFSDR--GCNLCMNI 87 (253)
Q Consensus 68 ~C~~C~~~f~~~--~C~~C~k~ 87 (253)
.|+.||+..... .|+.||..
T Consensus 4 ~Cp~Cg~~~~~~~~fC~~CG~~ 25 (26)
T PF13248_consen 4 FCPNCGAEIDPDAKFCPNCGAK 25 (26)
T ss_pred CCcccCCcCCcccccChhhCCC
Confidence 466666643222 27777753
No 168
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=68.94 E-value=4.4 Score=38.01 Aligned_cols=36 Identities=14% Similarity=0.215 Sum_probs=26.4
Q ss_pred ccccccccccCHHHHhhhhCCCCCCCcCCcccccc--cccccccccCCh
Q 025404 45 KCAVCQKLSKSFESLREHLTGPLSKAHCSGIFSDR--GCNLCMNIFDSP 91 (253)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~~~~~~C~~C~~~f~~~--~C~~C~k~f~~~ 91 (253)
.|..||..+.. ..|+.||...... .|+.||......
T Consensus 17 FC~~CG~~l~~-----------~~Cp~CG~~~~~~~~fC~~CG~~~~~~ 54 (645)
T PRK14559 17 FCQKCGTSLTH-----------KPCPQCGTEVPVDEAHCPNCGAETGTI 54 (645)
T ss_pred cccccCCCCCC-----------CcCCCCCCCCCcccccccccCCcccch
Confidence 68999887742 2599999886644 399999876654
No 169
>PF10108 DNA_pol_B_exo2: Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; InterPro: IPR019288 This entry represents various prokaryotic 3'-5' exonucleases and hypothetical proteins.
Probab=68.78 E-value=6.4 Score=31.30 Aligned_cols=34 Identities=21% Similarity=0.233 Sum_probs=27.3
Q ss_pred CHHHHHHHHHHHHhcCCCCCcccccCCCCeEEEeec-hhhhhhhhcC
Q 025404 200 PLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHG-LEHDLDSLRM 245 (253)
Q Consensus 200 ~~~~v~~~l~~~~~~~~~~~~~~~~~~~~~~lv~h~-~~~D~~~l~~ 245 (253)
+..++.+.+.+++.+ ..-.||+|| .+||+.||..
T Consensus 36 ~E~~lL~~F~~~~~~------------~~p~LVs~NG~~FDlP~L~~ 70 (209)
T PF10108_consen 36 DEKELLQDFFDLVEK------------YNPQLVSFNGRGFDLPVLCR 70 (209)
T ss_pred CHHHHHHHHHHHHHh------------CCCeEEecCCccCCHHHHHH
Confidence 488899999999932 233799998 8999999865
No 170
>PRK04023 DNA polymerase II large subunit; Validated
Probab=68.72 E-value=3.4 Score=40.21 Aligned_cols=28 Identities=29% Similarity=0.571 Sum_probs=16.2
Q ss_pred CCCeEEeeeccCCCCcccceeeeccCCHHhh
Q 025404 165 DENVIFHTYVQPQLPVTNYRYEVTGLTEEDI 195 (253)
Q Consensus 165 ~~~~~~~~~v~P~~~i~~~~~~~~Git~~~l 195 (253)
+|.+.||. .+.|++.+.-+..|+|.+.|
T Consensus 735 DGTiR~D~---tD~PlTHfrp~Eigvsvekl 762 (1121)
T PRK04023 735 DGTVRYDM---TDLPLTHFRPREIGVSVEKL 762 (1121)
T ss_pred CcceeccC---cCCCcccccHHHcCCCHHHH
Confidence 56655554 33456666666666666655
No 171
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=68.60 E-value=2.3 Score=22.86 Aligned_cols=9 Identities=33% Similarity=0.844 Sum_probs=4.3
Q ss_pred ccccccccc
Q 025404 45 KCAVCQKLS 53 (253)
Q Consensus 45 ~C~~C~~~f 53 (253)
.|..||..+
T Consensus 3 ~C~~CGy~y 11 (33)
T cd00350 3 VCPVCGYIY 11 (33)
T ss_pred ECCCCCCEE
Confidence 355555443
No 172
>cd05782 DNA_polB_like1_exo Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Probab=68.52 E-value=6.2 Score=31.34 Aligned_cols=35 Identities=23% Similarity=0.351 Sum_probs=27.1
Q ss_pred CCHHHHHHHHHHHHhcCCCCCcccccCCCCeEEEeec-hhhhhhhhcC
Q 025404 199 MPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHG-LEHDLDSLRM 245 (253)
Q Consensus 199 ~~~~~v~~~l~~~~~~~~~~~~~~~~~~~~~~lv~h~-~~~D~~~l~~ 245 (253)
.+-.++..++.+++.+ ..-+||||| ..||+.+|..
T Consensus 76 ~~E~elL~~F~~~i~~------------~~p~lv~yNg~~FDlP~L~~ 111 (208)
T cd05782 76 ADEKELLEDFFQLIEK------------KNPRLVSFNGRGFDLPVLHL 111 (208)
T ss_pred CCHHHHHHHHHHHHHH------------hCCEEEecCCCcCCHHHHHH
Confidence 3458899999999942 134899988 4999999975
No 173
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=68.51 E-value=1.3 Score=41.24 Aligned_cols=55 Identities=22% Similarity=0.376 Sum_probs=33.4
Q ss_pred cccccccccCCHHHHHHhhhhcCCCCCcc--ccccccccccCHHHHhhhhCCCCCCCcCCc
Q 025404 16 KCVACYKQFKRKDHLIEHMKISYHSVHQP--KCAVCQKLSKSFESLREHLTGPLSKAHCSG 74 (253)
Q Consensus 16 ~C~~C~k~f~~~~~l~~H~~~~~H~~~~~--~C~~C~~~f~~~~~l~~H~~~~~~C~~C~~ 74 (253)
.|..||-.|+-...|---+ . +|.... .|+.|.+.+....+-+-| ..|..|+.||-
T Consensus 125 ~CT~CGPRfTIi~alPYDR-~--nTsM~~F~lC~~C~~EY~dP~nRRfH-AQp~aCp~CGP 181 (750)
T COG0068 125 NCTNCGPRFTIIEALPYDR-E--NTSMADFPLCPFCDKEYKDPLNRRFH-AQPIACPKCGP 181 (750)
T ss_pred ccCCCCcceeeeccCCCCc-c--cCccccCcCCHHHHHHhcCccccccc-cccccCcccCC
Confidence 5777777777655443222 2 333222 788887777777666666 55667777765
No 174
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=67.72 E-value=3.6 Score=23.63 Aligned_cols=19 Identities=26% Similarity=0.644 Sum_probs=10.5
Q ss_pred ccccccccCC----hHHHHHHHH
Q 025404 81 CNLCMNIFDS----PSSLIKHKE 99 (253)
Q Consensus 81 C~~C~k~f~~----~~~l~~H~~ 99 (253)
|..|++.+.. .+.|..|++
T Consensus 19 C~~C~~~~~~~~~~ts~l~~HL~ 41 (45)
T PF02892_consen 19 CKYCGKVIKYSSGGTSNLKRHLK 41 (45)
T ss_dssp ETTTTEE-----SSTHHHHHHHH
T ss_pred eCCCCeEEeeCCCcHHHHHHhhh
Confidence 6666665554 467777773
No 175
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=67.13 E-value=3.4 Score=29.84 Aligned_cols=30 Identities=10% Similarity=0.100 Sum_probs=17.4
Q ss_pred ccccccccccccCHHHHhhhhCCCCCCCcCCccccc
Q 025404 43 QPKCAVCQKLSKSFESLREHLTGPLSKAHCSGIFSD 78 (253)
Q Consensus 43 ~~~C~~C~~~f~~~~~l~~H~~~~~~C~~C~~~f~~ 78 (253)
|..|+.||++|--. . ..|..|+.||..|..
T Consensus 9 Kr~Cp~cg~kFYDL---n---k~p~vcP~cg~~~~~ 38 (129)
T TIGR02300 9 KRICPNTGSKFYDL---N---RRPAVSPYTGEQFPP 38 (129)
T ss_pred cccCCCcCcccccc---C---CCCccCCCcCCccCc
Confidence 33677777766432 1 346667777766643
No 176
>PHA02528 43 DNA polymerase; Provisional
Probab=65.45 E-value=29 Score=34.04 Aligned_cols=36 Identities=8% Similarity=0.039 Sum_probs=27.0
Q ss_pred CCCHHHHHHHHHHHHhcCCCCCcccccCCCCeEEEeec-hhhhhhhhc
Q 025404 198 AMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHG-LEHDLDSLR 244 (253)
Q Consensus 198 ~~~~~~v~~~l~~~~~~~~~~~~~~~~~~~~~~lv~h~-~~~D~~~l~ 244 (253)
-.+-.++...+.+++.. -+- .||+|+| ..||+.+|.
T Consensus 175 ~~sE~eLL~~F~~~i~~--------~DP---DII~GyNi~~FDlpYL~ 211 (881)
T PHA02528 175 FDTEREMLLEYINFWEE--------NTP---VIFTGWNVELFDVPYII 211 (881)
T ss_pred cCCHHHHHHHHHHHHHH--------hCC---cEEEecCCccCCHHHHH
Confidence 46788999999999831 112 3999999 678999874
No 177
>PRK14873 primosome assembly protein PriA; Provisional
Probab=64.41 E-value=2.4 Score=39.97 Aligned_cols=43 Identities=21% Similarity=0.329 Sum_probs=27.4
Q ss_pred ccccccccccCH---HHHhhhh-CCCCCCCcCCcccccccccccccc
Q 025404 45 KCAVCQKLSKSF---ESLREHL-TGPLSKAHCSGIFSDRGCNLCMNI 87 (253)
Q Consensus 45 ~C~~C~~~f~~~---~~l~~H~-~~~~~C~~C~~~f~~~~C~~C~k~ 87 (253)
.|..||..+.-. ..|..|. .+...|..||.......|+.||..
T Consensus 385 ~C~~Cg~~~~C~~C~~~L~~h~~~~~l~Ch~CG~~~~p~~Cp~Cgs~ 431 (665)
T PRK14873 385 ACARCRTPARCRHCTGPLGLPSAGGTPRCRWCGRAAPDWRCPRCGSD 431 (665)
T ss_pred EhhhCcCeeECCCCCCceeEecCCCeeECCCCcCCCcCccCCCCcCC
Confidence 677676655432 3455565 445668888876656668888754
No 178
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=64.32 E-value=2.7 Score=24.33 Aligned_cols=11 Identities=9% Similarity=0.051 Sum_probs=4.8
Q ss_pred CCCCcCCcccc
Q 025404 67 LSKAHCSGIFS 77 (253)
Q Consensus 67 ~~C~~C~~~f~ 77 (253)
|.|..||..|.
T Consensus 3 Y~C~~Cg~~~~ 13 (44)
T smart00659 3 YICGECGRENE 13 (44)
T ss_pred EECCCCCCEee
Confidence 34444444443
No 179
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=64.30 E-value=3.8 Score=29.83 Aligned_cols=23 Identities=26% Similarity=0.218 Sum_probs=19.5
Q ss_pred ccccccccCChHHHHHHHHHccCCCC
Q 025404 81 CNLCMNIFDSPSSLIKHKEACSLSAP 106 (253)
Q Consensus 81 C~~C~k~f~~~~~l~~H~~~h~~~~~ 106 (253)
|-++||.|+ +|++|+.+|.+=-|
T Consensus 79 cLEDGkkfK---SLKRHL~t~~gmTP 101 (148)
T COG4957 79 CLEDGKKFK---SLKRHLTTHYGLTP 101 (148)
T ss_pred EeccCcchH---HHHHHHhcccCCCH
Confidence 899999998 58999999987544
No 180
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=64.00 E-value=2.4 Score=25.30 Aligned_cols=11 Identities=18% Similarity=0.643 Sum_probs=6.2
Q ss_pred ccccccccccC
Q 025404 45 KCAVCQKLSKS 55 (253)
Q Consensus 45 ~C~~C~~~f~~ 55 (253)
.|..||..|..
T Consensus 7 ~C~~Cg~~fe~ 17 (52)
T TIGR02605 7 RCTACGHRFEV 17 (52)
T ss_pred EeCCCCCEeEE
Confidence 46666655553
No 181
>cd06129 RNaseD_like DEDDy 3'-5' exonuclease domain of RNase D, WRN, and similar proteins. The RNase D-like group is composed of RNase D, WRN, and similar proteins. They contain a DEDDy-type, DnaQ-like, 3'-5' exonuclease domain that contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase D is involved in the 3'-end processing of tRNA precursors. RNase D-like proteins in eukaryotes include yeast Rrp6p, human PM/Scl-100 and Drosophila melanogaster egalitarian (Egl) protein. WRN is a unique DNA helicase possessing exonuclease activity. Mutation in the WRN gene is implicated in Werner syndrome, a disease associated with premature aging and increased predisposition to cancer. Yeast Rrp6p and the human Polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100) are exosome-
Probab=63.95 E-value=45 Score=25.00 Aligned_cols=19 Identities=32% Similarity=0.261 Sum_probs=15.5
Q ss_pred CCeEEEeechhhhhhhhcC
Q 025404 227 KARLLVGHGLEHDLDSLRM 245 (253)
Q Consensus 227 ~~~~lv~h~~~~D~~~l~~ 245 (253)
.+.+.|||++..|+..|.-
T Consensus 66 ~~i~Kvg~~~k~D~~~L~~ 84 (161)
T cd06129 66 PSIVKALHGIEGDLWKLLR 84 (161)
T ss_pred CCEEEEEeccHHHHHHHHH
Confidence 4557899999999999853
No 182
>PRK14873 primosome assembly protein PriA; Provisional
Probab=62.70 E-value=2.7 Score=39.56 Aligned_cols=54 Identities=15% Similarity=0.374 Sum_probs=34.1
Q ss_pred CCCCCCcc-cccccccccCCHHHHHHhhhhcCCCCCcc-ccccccccccCHHHHhhhhCCCCCCCcCCcc
Q 025404 8 PKRSTARH-KCVACYKQFKRKDHLIEHMKISYHSVHQP-KCAVCQKLSKSFESLREHLTGPLSKAHCSGI 75 (253)
Q Consensus 8 ~~~~~k~~-~C~~C~k~f~~~~~l~~H~~~~~H~~~~~-~C~~C~~~f~~~~~l~~H~~~~~~C~~C~~~ 75 (253)
+.+|.-|+ .|..||..+.... -...+.. |..... .|..||.. ..++.|+.||..
T Consensus 376 nRrGyap~l~C~~Cg~~~~C~~-C~~~L~~--h~~~~~l~Ch~CG~~-----------~~p~~Cp~Cgs~ 431 (665)
T PRK14873 376 PRRGYVPSLACARCRTPARCRH-CTGPLGL--PSAGGTPRCRWCGRA-----------APDWRCPRCGSD 431 (665)
T ss_pred cCCCCCCeeEhhhCcCeeECCC-CCCceeE--ecCCCeeECCCCcCC-----------CcCccCCCCcCC
Confidence 45566665 8888887776531 1122344 544444 89999853 136789999875
No 183
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=62.61 E-value=6.4 Score=24.30 Aligned_cols=7 Identities=29% Similarity=0.985 Sum_probs=3.5
Q ss_pred ccccccc
Q 025404 45 KCAVCQK 51 (253)
Q Consensus 45 ~C~~C~~ 51 (253)
.|+.||.
T Consensus 29 ~CPnCGe 35 (61)
T COG2888 29 PCPNCGE 35 (61)
T ss_pred eCCCCCc
Confidence 4555553
No 184
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 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 [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=61.79 E-value=2.5 Score=28.58 Aligned_cols=26 Identities=19% Similarity=0.428 Sum_probs=14.7
Q ss_pred CCCCCCcCCcccccc------cccccccccCC
Q 025404 65 GPLSKAHCSGIFSDR------GCNLCMNIFDS 90 (253)
Q Consensus 65 ~~~~C~~C~~~f~~~------~C~~C~k~f~~ 90 (253)
..|.|+.|++.-... .|..|++.|..
T Consensus 34 ~ky~Cp~Cgk~~vkR~a~GIW~C~~C~~~~AG 65 (90)
T PF01780_consen 34 AKYTCPFCGKTSVKRVATGIWKCKKCGKKFAG 65 (90)
T ss_dssp S-BEESSSSSSEEEEEETTEEEETTTTEEEE-
T ss_pred CCCcCCCCCCceeEEeeeEEeecCCCCCEEeC
Confidence 456677776655332 27777776653
No 185
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=61.13 E-value=2.4 Score=25.13 Aligned_cols=9 Identities=44% Similarity=0.907 Sum_probs=4.4
Q ss_pred ccccccccc
Q 025404 45 KCAVCQKLS 53 (253)
Q Consensus 45 ~C~~C~~~f 53 (253)
.|-.||+.|
T Consensus 8 ~C~~Cg~~~ 16 (49)
T COG1996 8 KCARCGREV 16 (49)
T ss_pred EhhhcCCee
Confidence 444555444
No 186
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=61.13 E-value=9.5 Score=28.90 Aligned_cols=33 Identities=9% Similarity=0.078 Sum_probs=23.0
Q ss_pred CCcc-ccccccccccCHHHHhhhhCCCCCCCcCCcccc
Q 025404 41 VHQP-KCAVCQKLSKSFESLREHLTGPLSKAHCSGIFS 77 (253)
Q Consensus 41 ~~~~-~C~~C~~~f~~~~~l~~H~~~~~~C~~C~~~f~ 77 (253)
+... .|+.|+..|+....+. ..|.|+.||....
T Consensus 106 ~~~~Y~Cp~c~~r~tf~eA~~----~~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 106 NNMFFICPNMCVRFTFNEAME----LNFTCPRCGAMLD 139 (158)
T ss_pred CCCeEECCCCCcEeeHHHHHH----cCCcCCCCCCEee
Confidence 3444 8888988888877664 3688877776543
No 187
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional
Probab=60.12 E-value=24 Score=35.40 Aligned_cols=39 Identities=23% Similarity=0.216 Sum_probs=28.2
Q ss_pred hcCCCCHHHHHHHHHHHHhcCCCCCcccccCCCCeEEEeech-hhhhhhhc
Q 025404 195 IKNAMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGL-EHDLDSLR 244 (253)
Q Consensus 195 l~~~~~~~~v~~~l~~~~~~~~~~~~~~~~~~~~~~lv~h~~-~~D~~~l~ 244 (253)
+..-.+..++...+.+++.. -|- .||+|||+ .||+.+|-
T Consensus 324 V~~f~sE~eLL~~f~~~I~~--------~DP---DII~GYNi~~FDlpYL~ 363 (1054)
T PTZ00166 324 VLSFETEKELLLAWAEFVIA--------VDP---DFLTGYNIINFDLPYLL 363 (1054)
T ss_pred EEEeCCHHHHHHHHHHHHHh--------cCC---CEEEecCCcCCcHHHHH
Confidence 33446888999999998831 122 39999996 59998863
No 188
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=60.07 E-value=5.1 Score=27.13 Aligned_cols=26 Identities=15% Similarity=0.289 Sum_probs=13.6
Q ss_pred CCCCCCcCCcccccc------cccccccccCC
Q 025404 65 GPLSKAHCSGIFSDR------GCNLCMNIFDS 90 (253)
Q Consensus 65 ~~~~C~~C~~~f~~~------~C~~C~k~f~~ 90 (253)
..|.|+.|++.-... .|..|++.|..
T Consensus 35 a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~AG 66 (90)
T PTZ00255 35 AKYFCPFCGKHAVKRQAVGIWRCKGCKKTVAG 66 (90)
T ss_pred CCccCCCCCCCceeeeeeEEEEcCCCCCEEeC
Confidence 355666665433221 26666666654
No 189
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=59.81 E-value=4.9 Score=27.26 Aligned_cols=26 Identities=19% Similarity=0.364 Sum_probs=14.5
Q ss_pred CCCCCCcCCcccccc------cccccccccCC
Q 025404 65 GPLSKAHCSGIFSDR------GCNLCMNIFDS 90 (253)
Q Consensus 65 ~~~~C~~C~~~f~~~------~C~~C~k~f~~ 90 (253)
..|.|+.|++.-... .|..|++.|..
T Consensus 34 a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~AG 65 (91)
T TIGR00280 34 AKYVCPFCGKKTVKRGSTGIWTCRKCGAKFAG 65 (91)
T ss_pred cCccCCCCCCCceEEEeeEEEEcCCCCCEEeC
Confidence 456666666543222 27777776654
No 190
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=59.35 E-value=4 Score=21.86 Aligned_cols=8 Identities=25% Similarity=0.684 Sum_probs=3.4
Q ss_pred cccccccc
Q 025404 46 CAVCQKLS 53 (253)
Q Consensus 46 C~~C~~~f 53 (253)
|..||..+
T Consensus 3 C~~Cg~~~ 10 (32)
T PF03604_consen 3 CGECGAEV 10 (32)
T ss_dssp ESSSSSSE
T ss_pred CCcCCCee
Confidence 44444443
No 191
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=59.13 E-value=11 Score=32.06 Aligned_cols=18 Identities=17% Similarity=0.276 Sum_probs=11.8
Q ss_pred cccCChHHHHHHHHHccC
Q 025404 86 NIFDSPSSLIKHKEACSL 103 (253)
Q Consensus 86 k~f~~~~~l~~H~~~h~~ 103 (253)
..|.+...|..|+..-++
T Consensus 289 ~vf~~~~el~~h~~~~h~ 306 (493)
T COG5236 289 YVFPYHTELLEHLTRFHK 306 (493)
T ss_pred EEeccHHHHHHHHHHHhh
Confidence 367777778888754443
No 192
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=58.74 E-value=5.2 Score=32.44 Aligned_cols=45 Identities=22% Similarity=0.373 Sum_probs=34.4
Q ss_pred ccccccccccCCHHHHHHhhhhcCCCCCccccccccccccCHHHHhhhh
Q 025404 15 HKCVACYKQFKRKDHLIEHMKISYHSVHQPKCAVCQKLSKSFESLREHL 63 (253)
Q Consensus 15 ~~C~~C~k~f~~~~~l~~H~~~~~H~~~~~~C~~C~~~f~~~~~l~~H~ 63 (253)
|.|..||....- ..+..|+-. -.+..+.|--|++.|-. .+...|.
T Consensus 4 FtCnvCgEsvKK-p~vekH~sr--Crn~~fSCIDC~k~F~~-~sYknH~ 48 (276)
T KOG2186|consen 4 FTCNVCGESVKK-PQVEKHMSR--CRNAYFSCIDCGKTFER-VSYKNHT 48 (276)
T ss_pred Eehhhhhhhccc-cchHHHHHh--ccCCeeEEeeccccccc-chhhhhh
Confidence 789999987664 467778876 66655599999999988 5677775
No 193
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=58.14 E-value=3.1 Score=39.22 Aligned_cols=71 Identities=13% Similarity=0.129 Sum_probs=39.7
Q ss_pred ccccccccccCHHHHhhhhCCCCCCCcCCcccccccccccccccCChHHHHHHHHHcc-C--CCCC-CccccCccchhhh
Q 025404 45 KCAVCQKLSKSFESLREHLTGPLSKAHCSGIFSDRGCNLCMNIFDSPSSLIKHKEACS-L--SAPV-PFEKTLSNAESQK 120 (253)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~~~~~~C~~C~~~f~~~~C~~C~k~f~~~~~l~~H~~~h~-~--~~~~-~C~~~f~~~~~l~ 120 (253)
.|..|++.|.....+. ..+.+.|..||..| |..|.......+.-+. ...- . ..|+ .|+..|.....+.
T Consensus 462 tC~~C~kkFfSlsK~L--~~RKHHCRkCGrVF----C~~CSSnRs~yp~aKL--pKPgsseE~ppRRVCD~CYdq~EnLl 533 (1374)
T PTZ00303 462 SCPSCGRAFISLSRPL--GTRAHHCRSCGIRL----CVFCITKRAHYSFAKL--AKPGSSDEAEERLVCDTCYKEYETVS 533 (1374)
T ss_pred cccCcCCccccccccc--ccccccccCCcccc----CccccCCcccCccccc--CCCCCcccccccchhHHHHHHHHhHH
Confidence 5999999997642100 13456799999888 7778765554322211 1110 0 1133 3777776666665
Q ss_pred hhc
Q 025404 121 KIS 123 (253)
Q Consensus 121 ~h~ 123 (253)
+|.
T Consensus 534 Qm~ 536 (1374)
T PTZ00303 534 QLH 536 (1374)
T ss_pred hhH
Confidence 554
No 194
>KOG3657 consensus Mitochondrial DNA polymerase gamma, catalytic subunit [Replication, recombination and repair]
Probab=58.08 E-value=5.7 Score=37.85 Aligned_cols=19 Identities=42% Similarity=0.805 Sum_probs=15.6
Q ss_pred CCCeEEEeechhhhhhhhc
Q 025404 226 GKARLLVGHGLEHDLDSLR 244 (253)
Q Consensus 226 ~~~~~lv~h~~~~D~~~l~ 244 (253)
.++.++|||||.||-.-++
T Consensus 239 ~ke~liVGHNVsfDRaRir 257 (1075)
T KOG3657|consen 239 GKEQLIVGHNVSFDRARIR 257 (1075)
T ss_pred CCCceEEeccccchHHHHH
Confidence 3678999999999976554
No 195
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=57.81 E-value=8.4 Score=19.45 Aligned_cols=19 Identities=16% Similarity=0.746 Sum_probs=13.0
Q ss_pred cccccccccCCHHHHHHhhh
Q 025404 16 KCVACYKQFKRKDHLIEHMK 35 (253)
Q Consensus 16 ~C~~C~k~f~~~~~l~~H~~ 35 (253)
.|+.|++.+ ....+..|..
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 578888877 4466666764
No 196
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=57.78 E-value=3.5 Score=30.29 Aligned_cols=30 Identities=30% Similarity=0.367 Sum_probs=23.5
Q ss_pred CCcCCcccccccccccccccCChHHHHHHHH
Q 025404 69 KAHCSGIFSDRGCNLCMNIFDSPSSLIKHKE 99 (253)
Q Consensus 69 C~~C~~~f~~~~C~~C~k~f~~~~~l~~H~~ 99 (253)
|.+|| -++.++|.-||..+-+..-|..|..
T Consensus 121 CaVCG-~~S~ysC~~CG~kyCsv~C~~~Hne 150 (156)
T KOG3362|consen 121 CAVCG-YDSKYSCVNCGTKYCSVRCLKTHNE 150 (156)
T ss_pred hhhcC-CCchhHHHhcCCceeechhhhhccc
Confidence 88888 6666779999988888877777653
No 197
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=57.57 E-value=4.1 Score=38.68 Aligned_cols=53 Identities=19% Similarity=0.276 Sum_probs=31.1
Q ss_pred CCCCc-ccccccccccCCHHHHHHhhhhcCCCCCcc-ccccccccccCHHHHhhhhCCCCCCCcCCcc
Q 025404 10 RSTAR-HKCVACYKQFKRKDHLIEHMKISYHSVHQP-KCAVCQKLSKSFESLREHLTGPLSKAHCSGI 75 (253)
Q Consensus 10 ~~~k~-~~C~~C~k~f~~~~~l~~H~~~~~H~~~~~-~C~~C~~~f~~~~~l~~H~~~~~~C~~C~~~ 75 (253)
+|.-| ..|..||..+..... ..-+.. |..... .|..||.. ...|..|+.||..
T Consensus 430 RGys~~l~C~~Cg~v~~Cp~C-d~~lt~--H~~~~~L~CH~Cg~~----------~~~p~~Cp~Cgs~ 484 (730)
T COG1198 430 RGYAPLLLCRDCGYIAECPNC-DSPLTL--HKATGQLRCHYCGYQ----------EPIPQSCPECGSE 484 (730)
T ss_pred CCccceeecccCCCcccCCCC-CcceEE--ecCCCeeEeCCCCCC----------CCCCCCCCCCCCC
Confidence 34433 367777776654311 111233 444455 99999844 1457889999977
No 198
>PRK05762 DNA polymerase II; Reviewed
Probab=57.18 E-value=40 Score=32.66 Aligned_cols=39 Identities=18% Similarity=0.318 Sum_probs=29.3
Q ss_pred hcCCCCHHHHHHHHHHHHhcCCCCCcccccCCCCeEEEeec-hhhhhhhhc
Q 025404 195 IKNAMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHG-LEHDLDSLR 244 (253)
Q Consensus 195 l~~~~~~~~v~~~l~~~~~~~~~~~~~~~~~~~~~~lv~h~-~~~D~~~l~ 244 (253)
+....+-.++...+.+++.. -+- .|||||| ..||+.+|.
T Consensus 197 v~~~~sE~~LL~~F~~~i~~--------~DP---DIIvGyNi~~FDlpyL~ 236 (786)
T PRK05762 197 LEYVADEKALLEKFNAWFAE--------HDP---DVIIGWNVVQFDLRLLQ 236 (786)
T ss_pred EEEcCCHHHHHHHHHHHHHh--------cCC---CEEEEeCCCCCcHHHHH
Confidence 44557889999999999932 111 3999999 569999874
No 199
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=57.10 E-value=4.2 Score=37.06 Aligned_cols=43 Identities=23% Similarity=0.298 Sum_probs=28.8
Q ss_pred ccccccccccCH---HHHhhhh-CCCCCCCcCCcccc-cccccccccc
Q 025404 45 KCAVCQKLSKSF---ESLREHL-TGPLSKAHCSGIFS-DRGCNLCMNI 87 (253)
Q Consensus 45 ~C~~C~~~f~~~---~~l~~H~-~~~~~C~~C~~~f~-~~~C~~C~k~ 87 (253)
.|..||....-. ..|..|. .+...|..||.... ...|+.||..
T Consensus 215 ~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 215 LCRSCGYILCCPNCDVSLTYHKKEGKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred EhhhCcCccCCCCCCCceEEecCCCeEEcCCCcCcCCCCCCCCCCCCC
Confidence 566666655432 4566665 55667999998876 4469999863
No 200
>smart00486 POLBc DNA polymerase type-B family. DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), DNA polymerases in archaea, DNA polymerase II in e. coli, mitochondrial DNA polymerases and and virus DNA polymerases
Probab=57.06 E-value=22 Score=31.61 Aligned_cols=35 Identities=26% Similarity=0.442 Sum_probs=25.9
Q ss_pred CCHHHHHHHHHHHHhcCCCCCcccccCCCCeEEEeechh-hhhhhhc
Q 025404 199 MPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLE-HDLDSLR 244 (253)
Q Consensus 199 ~~~~~v~~~l~~~~~~~~~~~~~~~~~~~~~~lv~h~~~-~D~~~l~ 244 (253)
.+..+....+.+++.. .+ ..+++|||.. ||+.+|.
T Consensus 67 ~~E~~lL~~f~~~i~~--------~d---pdii~g~N~~~FD~~~i~ 102 (471)
T smart00486 67 NNEKELLKAFLEFIKK--------YD---PDIIYGHNISNFDLPYII 102 (471)
T ss_pred CCHHHHHHHHHHHHHH--------hC---CCEEEeecCCCCCHHHHH
Confidence 3777888888888831 11 1499999985 9999875
No 201
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=56.71 E-value=5.8 Score=24.10 Aligned_cols=7 Identities=29% Similarity=0.757 Sum_probs=3.4
Q ss_pred ccccccc
Q 025404 81 CNLCMNI 87 (253)
Q Consensus 81 C~~C~k~ 87 (253)
|+.||..
T Consensus 25 Cp~CGae 31 (54)
T TIGR01206 25 CDECGAE 31 (54)
T ss_pred CCCCCCE
Confidence 5555543
No 202
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=56.53 E-value=6 Score=24.00 Aligned_cols=22 Identities=23% Similarity=0.459 Sum_probs=11.3
Q ss_pred CCCcCCcccccc----cccccccccC
Q 025404 68 SKAHCSGIFSDR----GCNLCMNIFD 89 (253)
Q Consensus 68 ~C~~C~~~f~~~----~C~~C~k~f~ 89 (253)
.|..|++.|... .|+.||..+-
T Consensus 7 ~C~~Cg~~~~~~dDiVvCp~CgapyH 32 (54)
T PF14446_consen 7 KCPVCGKKFKDGDDIVVCPECGAPYH 32 (54)
T ss_pred cChhhCCcccCCCCEEECCCCCCccc
Confidence 355566655432 2666665443
No 203
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=56.51 E-value=3.8 Score=34.25 Aligned_cols=21 Identities=29% Similarity=0.604 Sum_probs=12.3
Q ss_pred ccccccccCChHHHHHHHHHc
Q 025404 81 CNLCMNIFDSPSSLIKHKEAC 101 (253)
Q Consensus 81 C~~C~k~f~~~~~l~~H~~~h 101 (253)
|+.|...|-.....-.|...|
T Consensus 391 Ce~CK~~FC~dCdvfiHe~Lh 411 (421)
T COG5151 391 CELCKSTFCSDCDVFIHETLH 411 (421)
T ss_pred chhhhhhhhhhhHHHHHHHHh
Confidence 555555555555555676655
No 204
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=56.25 E-value=6.1 Score=26.76 Aligned_cols=26 Identities=19% Similarity=0.300 Sum_probs=15.2
Q ss_pred CCCCCCcCCcccccc------cccccccccCC
Q 025404 65 GPLSKAHCSGIFSDR------GCNLCMNIFDS 90 (253)
Q Consensus 65 ~~~~C~~C~~~f~~~------~C~~C~k~f~~ 90 (253)
..|.|+.|++.-... .|..|++.|..
T Consensus 35 a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~AG 66 (90)
T PRK03976 35 AKHVCPVCGRPKVKRVGTGIWECRKCGAKFAG 66 (90)
T ss_pred cCccCCCCCCCceEEEEEEEEEcCCCCCEEeC
Confidence 456677775543322 27777777664
No 205
>PRK12496 hypothetical protein; Provisional
Probab=56.22 E-value=4.6 Score=30.81 Aligned_cols=24 Identities=13% Similarity=0.369 Sum_probs=17.8
Q ss_pred CCCCCcCCccccc----ccccccccccC
Q 025404 66 PLSKAHCSGIFSD----RGCNLCMNIFD 89 (253)
Q Consensus 66 ~~~C~~C~~~f~~----~~C~~C~k~f~ 89 (253)
.|.|..|++.|.. ..|+.||..-.
T Consensus 127 ~~~C~gC~~~~~~~~~~~~C~~CG~~~~ 154 (164)
T PRK12496 127 RKVCKGCKKKYPEDYPDDVCEICGSPVK 154 (164)
T ss_pred eEECCCCCccccCCCCCCcCCCCCChhh
Confidence 3679999999953 23999996544
No 206
>PHA02570 dexA exonuclease; Provisional
Probab=55.42 E-value=26 Score=28.07 Aligned_cols=39 Identities=21% Similarity=0.112 Sum_probs=28.3
Q ss_pred CCCHHHHHHHHHHHHhc-CCCCCcccccCCCCeEEEeechhhhhhhhc
Q 025404 198 AMPLKEVKDKILEILNN-GESTGRLMLDDGKARLLVGHGLEHDLDSLR 244 (253)
Q Consensus 198 ~~~~~~v~~~l~~~~~~-~~~~~~~~~~~~~~~~lv~h~~~~D~~~l~ 244 (253)
..++.++..++.++|.- +.+ .....+=|.+.+||..+|+
T Consensus 85 ~~~l~~al~~F~~fi~~~~~~--------~~~~~vWgnG~sFD~~IL~ 124 (220)
T PHA02570 85 DVSTYEGHKKFFEYLEANGVD--------PWKSQGWCRGNSFDFPILV 124 (220)
T ss_pred cccHHHHHHHHHHHHHHcCCC--------ccceeEecCCCccCHHHHH
Confidence 36799999999999941 111 1224577899999999994
No 207
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=54.98 E-value=15 Score=28.52 Aligned_cols=29 Identities=14% Similarity=0.264 Sum_probs=21.3
Q ss_pred ccccccccccCHHHHhhhhCCCCCCCcCCcccc
Q 025404 45 KCAVCQKLSKSFESLREHLTGPLSKAHCSGIFS 77 (253)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~~~~~~C~~C~~~f~ 77 (253)
.|+.|+..|+....+ +..|.|+.||....
T Consensus 119 ~Cp~C~~rytf~eA~----~~~F~Cp~Cg~~L~ 147 (178)
T PRK06266 119 FCPNCHIRFTFDEAM----EYGFRCPQCGEMLE 147 (178)
T ss_pred ECCCCCcEEeHHHHh----hcCCcCCCCCCCCe
Confidence 888898888877665 34688877776654
No 208
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]
Probab=54.65 E-value=17 Score=29.61 Aligned_cols=17 Identities=18% Similarity=0.180 Sum_probs=13.8
Q ss_pred CCCceeeeecccccCCC
Q 025404 133 RGPKAVAMDCEMVGGGS 149 (253)
Q Consensus 133 ~~~~~~~~dcE~~g~~~ 149 (253)
...++..+|.||+|.+.
T Consensus 96 ~~e~~~FFDiETTGL~~ 112 (278)
T COG3359 96 EAEDVAFFDIETTGLDR 112 (278)
T ss_pred cccceEEEeeeccccCC
Confidence 35668999999999864
No 209
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=54.14 E-value=5.8 Score=30.25 Aligned_cols=19 Identities=16% Similarity=0.349 Sum_probs=12.5
Q ss_pred CCCCcCCcccccc---cccccc
Q 025404 67 LSKAHCSGIFSDR---GCNLCM 85 (253)
Q Consensus 67 ~~C~~C~~~f~~~---~C~~C~ 85 (253)
|.|++||.++... .|+.||
T Consensus 135 ~vC~vCGy~~~ge~P~~CPiCg 156 (166)
T COG1592 135 WVCPVCGYTHEGEAPEVCPICG 156 (166)
T ss_pred EEcCCCCCcccCCCCCcCCCCC
Confidence 6677777766542 377777
No 210
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=54.03 E-value=5.2 Score=36.46 Aligned_cols=47 Identities=15% Similarity=0.277 Sum_probs=29.1
Q ss_pred cccccccccCCHHHHHHhhhhcCCCCCcc-ccccccccccCHHHHhhhhCCCCCCCcCCcc
Q 025404 16 KCVACYKQFKRKDHLIEHMKISYHSVHQP-KCAVCQKLSKSFESLREHLTGPLSKAHCSGI 75 (253)
Q Consensus 16 ~C~~C~k~f~~~~~l~~H~~~~~H~~~~~-~C~~C~~~f~~~~~l~~H~~~~~~C~~C~~~ 75 (253)
.|..||....... -...+.. |..... .|..||... .-|..|+.|+..
T Consensus 215 ~C~~Cg~~~~C~~-C~~~l~~--h~~~~~l~Ch~Cg~~~----------~~~~~Cp~C~s~ 262 (505)
T TIGR00595 215 LCRSCGYILCCPN-CDVSLTY--HKKEGKLRCHYCGYQE----------PIPKTCPQCGSE 262 (505)
T ss_pred EhhhCcCccCCCC-CCCceEE--ecCCCeEEcCCCcCcC----------CCCCCCCCCCCC
Confidence 6777777665431 1223444 554455 899998554 336789999864
No 211
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=52.83 E-value=2.4 Score=27.20 Aligned_cols=35 Identities=20% Similarity=0.438 Sum_probs=15.6
Q ss_pred ccccccccccCHHHHhhhhCCCCCCCcCCccccccc-cccccc
Q 025404 45 KCAVCQKLSKSFESLREHLTGPLSKAHCSGIFSDRG-CNLCMN 86 (253)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~~~~~~C~~C~~~f~~~~-C~~C~k 86 (253)
.|+.|........ +.|.|..|++.|.... |+.|+.
T Consensus 3 ~CP~C~~~L~~~~-------~~~~C~~C~~~~~~~a~CPdC~~ 38 (70)
T PF07191_consen 3 TCPKCQQELEWQG-------GHYHCEACQKDYKKEAFCPDCGQ 38 (70)
T ss_dssp B-SSS-SBEEEET-------TEEEETTT--EEEEEEE-TTT-S
T ss_pred cCCCCCCccEEeC-------CEEECccccccceecccCCCccc
Confidence 3555654433322 3566777777666543 666653
No 212
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=51.72 E-value=7.3 Score=21.45 Aligned_cols=10 Identities=20% Similarity=0.707 Sum_probs=6.0
Q ss_pred cccccccccC
Q 025404 16 KCVACYKQFK 25 (253)
Q Consensus 16 ~C~~C~k~f~ 25 (253)
.|+.||+.|.
T Consensus 3 ~C~~Cg~~Yh 12 (36)
T PF05191_consen 3 ICPKCGRIYH 12 (36)
T ss_dssp EETTTTEEEE
T ss_pred CcCCCCCccc
Confidence 4666666654
No 213
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=48.89 E-value=4.9 Score=37.69 Aligned_cols=16 Identities=19% Similarity=0.358 Sum_probs=9.6
Q ss_pred ccccccccCChHHHHH
Q 025404 81 CNLCMNIFDSPSSLIK 96 (253)
Q Consensus 81 C~~C~k~f~~~~~l~~ 96 (253)
||.|+.+|.....++.
T Consensus 681 CP~Cn~aFganDv~~I 696 (698)
T KOG0978|consen 681 CPKCNAAFGANDVHRI 696 (698)
T ss_pred CCCCCCCCCccccccc
Confidence 6666666665554443
No 214
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=46.82 E-value=15 Score=26.24 Aligned_cols=26 Identities=23% Similarity=0.512 Sum_probs=20.0
Q ss_pred CCCcccccccccccCCHHHHHHhhhh
Q 025404 11 STARHKCVACYKQFKRKDHLIEHMKI 36 (253)
Q Consensus 11 ~~k~~~C~~C~k~f~~~~~l~~H~~~ 36 (253)
|-..|-|-.|.+-|.+...|..|.++
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHhc
Confidence 44447888888888888888888765
No 215
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=46.79 E-value=9.4 Score=35.85 Aligned_cols=36 Identities=17% Similarity=0.351 Sum_probs=21.8
Q ss_pred ccccccccccCHHHHhhhhCCCCCCCcCCcccccccccccccccC
Q 025404 45 KCAVCQKLSKSFESLREHLTGPLSKAHCSGIFSDRGCNLCMNIFD 89 (253)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~~~~~~C~~C~~~f~~~~C~~C~k~f~ 89 (253)
.|+.||..-.. +..-|+.||..+....|+.||....
T Consensus 3 ~Cp~Cg~~n~~---------~akFC~~CG~~l~~~~Cp~CG~~~~ 38 (645)
T PRK14559 3 ICPQCQFENPN---------NNRFCQKCGTSLTHKPCPQCGTEVP 38 (645)
T ss_pred cCCCCCCcCCC---------CCccccccCCCCCCCcCCCCCCCCC
Confidence 47777644322 1223777777776666777776643
No 216
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=46.42 E-value=13 Score=25.10 Aligned_cols=11 Identities=18% Similarity=0.513 Sum_probs=7.1
Q ss_pred ccccccccccC
Q 025404 45 KCAVCQKLSKS 55 (253)
Q Consensus 45 ~C~~C~~~f~~ 55 (253)
.|..||..|..
T Consensus 60 ~CkkCGfef~~ 70 (97)
T COG3357 60 RCKKCGFEFRD 70 (97)
T ss_pred hhcccCccccc
Confidence 66666666654
No 217
>COG1773 Rubredoxin [Energy production and conversion]
Probab=45.94 E-value=8.9 Score=23.36 Aligned_cols=10 Identities=30% Similarity=0.916 Sum_probs=5.9
Q ss_pred cccccccccc
Q 025404 45 KCAVCQKLSK 54 (253)
Q Consensus 45 ~C~~C~~~f~ 54 (253)
+|..||..|.
T Consensus 5 ~C~~CG~vYd 14 (55)
T COG1773 5 RCSVCGYVYD 14 (55)
T ss_pred EecCCceEec
Confidence 5666665553
No 218
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=44.70 E-value=18 Score=30.78 Aligned_cols=72 Identities=21% Similarity=0.325 Sum_probs=0.0
Q ss_pred HHHHHHhhhhcCCCCCcc--cccccccccc-CHHHHhhhh--------CCCCCCCcCCccccccc-------cccccccc
Q 025404 27 KDHLIEHMKISYHSVHQP--KCAVCQKLSK-SFESLREHL--------TGPLSKAHCSGIFSDRG-------CNLCMNIF 88 (253)
Q Consensus 27 ~~~l~~H~~~~~H~~~~~--~C~~C~~~f~-~~~~l~~H~--------~~~~~C~~C~~~f~~~~-------C~~C~k~f 88 (253)
+..|.+|++- ..+... +|-.|...+. ..+....|+ -.|-.=-.|..-.-.-. |-.|.|.|
T Consensus 128 ~eaLeqqQ~E--redt~fslqClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~r~~CLyCekif 205 (423)
T KOG2482|consen 128 KEALEQQQKE--REDTIFSLQCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLERLRCLYCEKIF 205 (423)
T ss_pred HHHHHHHHHH--hcCCeeeeEEEEecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHhhheeeeecccc
Q ss_pred CChHHHHHHHHH
Q 025404 89 DSPSSLIKHKEA 100 (253)
Q Consensus 89 ~~~~~l~~H~~~ 100 (253)
..+..|+.|||.
T Consensus 206 rdkntLkeHMrk 217 (423)
T KOG2482|consen 206 RDKNTLKEHMRK 217 (423)
T ss_pred CCcHHHHHHHHh
No 219
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=44.68 E-value=13 Score=26.04 Aligned_cols=10 Identities=10% Similarity=-0.403 Sum_probs=5.8
Q ss_pred cccccccccc
Q 025404 45 KCAVCQKLSK 54 (253)
Q Consensus 45 ~C~~C~~~f~ 54 (253)
.|+.||+.|-
T Consensus 11 idPetg~KFY 20 (129)
T COG4530 11 IDPETGKKFY 20 (129)
T ss_pred cCccccchhh
Confidence 4666666653
No 220
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=44.51 E-value=8 Score=36.28 Aligned_cols=25 Identities=32% Similarity=0.416 Sum_probs=20.1
Q ss_pred CCcccccccccccCCHHHHHHhhhh
Q 025404 12 TARHKCVACYKQFKRKDHLIEHMKI 36 (253)
Q Consensus 12 ~k~~~C~~C~k~f~~~~~l~~H~~~ 36 (253)
+.-|.|..|+|.|....+++.||++
T Consensus 790 ~giFpCreC~kvF~KiKSrNAHMK~ 814 (907)
T KOG4167|consen 790 TGIFPCRECGKVFFKIKSRNAHMKT 814 (907)
T ss_pred CceeehHHHHHHHHHHhhhhHHHHH
Confidence 3448888888888888888888888
No 221
>PRK05580 primosome assembly protein PriA; Validated
Probab=44.47 E-value=9.5 Score=36.17 Aligned_cols=43 Identities=23% Similarity=0.350 Sum_probs=26.9
Q ss_pred ccccccccccC---HHHHhhhh-CCCCCCCcCCcccc-cccccccccc
Q 025404 45 KCAVCQKLSKS---FESLREHL-TGPLSKAHCSGIFS-DRGCNLCMNI 87 (253)
Q Consensus 45 ~C~~C~~~f~~---~~~l~~H~-~~~~~C~~C~~~f~-~~~C~~C~k~ 87 (253)
.|..||....- ...|..|. .+...|..||.... ...|+.||..
T Consensus 383 ~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 383 LCRDCGWVAECPHCDASLTLHRFQRRLRCHHCGYQEPIPKACPECGST 430 (679)
T ss_pred EhhhCcCccCCCCCCCceeEECCCCeEECCCCcCCCCCCCCCCCCcCC
Confidence 56666655432 23455565 45567888888765 4469999764
No 222
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=44.17 E-value=26 Score=26.01 Aligned_cols=28 Identities=25% Similarity=0.425 Sum_probs=21.4
Q ss_pred HHHHHHHHhcCCCCCcccccCCCCeEEEeechhhhhhhhc
Q 025404 205 KDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLR 244 (253)
Q Consensus 205 ~~~l~~~~~~~~~~~~~~~~~~~~~~lv~h~~~~D~~~l~ 244 (253)
...|.+++.+ .+...||||+.+|+.+|+
T Consensus 64 ~~~l~~~l~~------------~~~~kv~~d~k~~~~~L~ 91 (172)
T smart00474 64 LEILKDLLED------------ETITKVGHNAKFDLHVLA 91 (172)
T ss_pred HHHHHHHhcC------------CCceEEEechHHHHHHHH
Confidence 4557777832 445799999999999985
No 223
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=44.08 E-value=11 Score=23.91 Aligned_cols=30 Identities=23% Similarity=0.629 Sum_probs=14.1
Q ss_pred ccccccccccCHHHHhhhhCCCCCCCcCCcccccccccccc
Q 025404 45 KCAVCQKLSKSFESLREHLTGPLSKAHCSGIFSDRGCNLCM 85 (253)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~~~~~~C~~C~~~f~~~~C~~C~ 85 (253)
.|..|++.|... .+.+.|..||..| |..|.
T Consensus 11 ~C~~C~~~F~~~-------~rrhhCr~CG~~v----C~~Cs 40 (69)
T PF01363_consen 11 NCMICGKKFSLF-------RRRHHCRNCGRVV----CSSCS 40 (69)
T ss_dssp B-TTT--B-BSS-------S-EEE-TTT--EE----ECCCS
T ss_pred cCcCcCCcCCCc-------eeeEccCCCCCEE----CCchh
Confidence 788888888432 3345688888777 65565
No 224
>PRK05580 primosome assembly protein PriA; Validated
Probab=43.96 E-value=8.8 Score=36.41 Aligned_cols=8 Identities=13% Similarity=0.385 Sum_probs=3.4
Q ss_pred CCCCcCCc
Q 025404 67 LSKAHCSG 74 (253)
Q Consensus 67 ~~C~~C~~ 74 (253)
..|+.|+.
T Consensus 422 ~~Cp~Cg~ 429 (679)
T PRK05580 422 KACPECGS 429 (679)
T ss_pred CCCCCCcC
Confidence 34444443
No 225
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=43.92 E-value=9.1 Score=20.10 Aligned_cols=20 Identities=15% Similarity=0.321 Sum_probs=9.5
Q ss_pred CCcCCcccccccccccccccC
Q 025404 69 KAHCSGIFSDRGCNLCMNIFD 89 (253)
Q Consensus 69 C~~C~~~f~~~~C~~C~k~f~ 89 (253)
|.+|+. +....|+.|+..+-
T Consensus 5 C~vC~~-~~kY~Cp~C~~~~C 24 (30)
T PF04438_consen 5 CSVCGN-PAKYRCPRCGARYC 24 (30)
T ss_dssp ETSSSS-EESEE-TTT--EES
T ss_pred CccCcC-CCEEECCCcCCcee
Confidence 555666 55555666665543
No 226
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=43.89 E-value=13 Score=22.17 Aligned_cols=10 Identities=20% Similarity=0.833 Sum_probs=5.9
Q ss_pred cccccccccc
Q 025404 45 KCAVCQKLSK 54 (253)
Q Consensus 45 ~C~~C~~~f~ 54 (253)
.|..||..+.
T Consensus 3 ~C~~CgyiYd 12 (50)
T cd00730 3 ECRICGYIYD 12 (50)
T ss_pred CCCCCCeEEC
Confidence 4666666554
No 227
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=43.42 E-value=3.9 Score=26.55 Aligned_cols=31 Identities=23% Similarity=0.546 Sum_probs=18.4
Q ss_pred ccccccccccCCHHHHHHhhhhcCCCCCcc-cccccccccc
Q 025404 15 HKCVACYKQFKRKDHLIEHMKISYHSVHQP-KCAVCQKLSK 54 (253)
Q Consensus 15 ~~C~~C~k~f~~~~~l~~H~~~~~H~~~~~-~C~~C~~~f~ 54 (253)
|+|..|+..| .+.+||.. ... .|+.|+..+.
T Consensus 13 Y~c~~cg~~~----dvvq~~~d-----dplt~ce~c~a~~k 44 (82)
T COG2331 13 YECTECGNRF----DVVQAMTD-----DPLTTCEECGARLK 44 (82)
T ss_pred EeecccchHH----HHHHhccc-----CccccChhhChHHH
Confidence 7888888754 33334432 223 7888876543
No 228
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=42.56 E-value=24 Score=29.91 Aligned_cols=7 Identities=29% Similarity=0.880 Sum_probs=4.3
Q ss_pred ccccccc
Q 025404 80 GCNLCMN 86 (253)
Q Consensus 80 ~C~~C~k 86 (253)
.|+.||.
T Consensus 228 ~C~~Cg~ 234 (309)
T PRK03564 228 KCSNCEQ 234 (309)
T ss_pred cCCCCCC
Confidence 3666764
No 229
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=41.82 E-value=18 Score=31.83 Aligned_cols=34 Identities=32% Similarity=0.544 Sum_probs=26.2
Q ss_pred ccccccccccCHHHHhhhh--CCCCCCCcCCccccc
Q 025404 45 KCAVCQKLSKSFESLREHL--TGPLSKAHCSGIFSD 78 (253)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~--~~~~~C~~C~~~f~~ 78 (253)
.|+.|++.|.....++--- ++.|.|..|+.-..-
T Consensus 130 ~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~gelve 165 (436)
T KOG2593|consen 130 VCPNCQKKYTSLEALQLLDNETGEFHCENCGGELVE 165 (436)
T ss_pred cCCccccchhhhHHHHhhcccCceEEEecCCCchhc
Confidence 8999999998876654433 678999999876653
No 230
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=41.22 E-value=7 Score=32.78 Aligned_cols=9 Identities=33% Similarity=0.689 Sum_probs=2.8
Q ss_pred ccccccccc
Q 025404 14 RHKCVACYK 22 (253)
Q Consensus 14 ~~~C~~C~k 22 (253)
.-.|+.||.
T Consensus 172 ~g~CPvCGs 180 (290)
T PF04216_consen 172 RGYCPVCGS 180 (290)
T ss_dssp -SS-TTT--
T ss_pred CCcCCCCCC
Confidence 345666654
No 231
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=41.05 E-value=15 Score=22.13 Aligned_cols=31 Identities=26% Similarity=0.525 Sum_probs=18.8
Q ss_pred ccccccccccCHHHHhhhhCCCCCCCcCCccccccccccccc
Q 025404 45 KCAVCQKLSKSFESLREHLTGPLSKAHCSGIFSDRGCNLCMN 86 (253)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~~~~~~C~~C~~~f~~~~C~~C~k 86 (253)
.|..|++.|... .+.+.|..||+.| |..|-.
T Consensus 4 ~C~~C~~~F~~~-------~rk~~Cr~Cg~~~----C~~C~~ 34 (57)
T cd00065 4 SCMGCGKPFTLT-------RRRHHCRNCGRIF----CSKCSS 34 (57)
T ss_pred cCcccCccccCC-------ccccccCcCcCCc----ChHHcC
Confidence 467777777652 3445677777766 444543
No 232
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=40.92 E-value=18 Score=26.89 Aligned_cols=18 Identities=22% Similarity=0.353 Sum_probs=14.0
Q ss_pred ccccccccCChHHHHHHH
Q 025404 81 CNLCMNIFDSPSSLIKHK 98 (253)
Q Consensus 81 C~~C~k~f~~~~~l~~H~ 98 (253)
|+.||+.|-.-+++++-.
T Consensus 127 C~~C~kiyW~GsH~~~~~ 144 (147)
T PF01927_consen 127 CPGCGKIYWEGSHWRRME 144 (147)
T ss_pred CCCCCCEecccccHHHHH
Confidence 999999998877765543
No 233
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=40.69 E-value=31 Score=19.49 Aligned_cols=24 Identities=21% Similarity=0.436 Sum_probs=13.4
Q ss_pred ccccccccccCC--hHHHHHHHHHcc
Q 025404 79 RGCNLCMNIFDS--PSSLIKHKEACS 102 (253)
Q Consensus 79 ~~C~~C~k~f~~--~~~l~~H~~~h~ 102 (253)
..|+.||-.|.. ...-..|.+-|.
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHHh
Confidence 346666655544 444556666653
No 234
>PF12773 DZR: Double zinc ribbon
Probab=40.59 E-value=22 Score=20.74 Aligned_cols=35 Identities=14% Similarity=0.237 Sum_probs=17.2
Q ss_pred ccccccccccCHHHHhhhhCCCCCCCcCCccccccc--ccccc
Q 025404 45 KCAVCQKLSKSFESLREHLTGPLSKAHCSGIFSDRG--CNLCM 85 (253)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~~~~~~C~~C~~~f~~~~--C~~C~ 85 (253)
.|..||..+.. -......|+.|+....... |..||
T Consensus 14 fC~~CG~~l~~------~~~~~~~C~~Cg~~~~~~~~fC~~CG 50 (50)
T PF12773_consen 14 FCPHCGTPLPP------PDQSKKICPNCGAENPPNAKFCPNCG 50 (50)
T ss_pred CChhhcCChhh------ccCCCCCCcCCcCCCcCCcCccCccc
Confidence 56667666550 0022345666666543221 55554
No 235
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=40.54 E-value=26 Score=19.69 Aligned_cols=16 Identities=31% Similarity=0.540 Sum_probs=11.2
Q ss_pred ccccccccCChHHHHH
Q 025404 81 CNLCMNIFDSPSSLIK 96 (253)
Q Consensus 81 C~~C~k~f~~~~~l~~ 96 (253)
|+.|+-.+-....|.+
T Consensus 22 C~~C~G~W~d~~el~~ 37 (41)
T PF13453_consen 22 CPSCGGIWFDAGELEK 37 (41)
T ss_pred CCCCCeEEccHHHHHH
Confidence 7778777777766653
No 236
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=39.87 E-value=6.1 Score=32.20 Aligned_cols=9 Identities=11% Similarity=0.386 Sum_probs=4.5
Q ss_pred CCCCCcCCc
Q 025404 66 PLSKAHCSG 74 (253)
Q Consensus 66 ~~~C~~C~~ 74 (253)
.|+|.-|++
T Consensus 171 ~~KC~SCNr 179 (314)
T PF06524_consen 171 TFKCQSCNR 179 (314)
T ss_pred ccccccccc
Confidence 455555543
No 237
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=39.74 E-value=7.8 Score=36.35 Aligned_cols=34 Identities=18% Similarity=0.347 Sum_probs=16.7
Q ss_pred ccccccccccCHHHHhhhh----CCCCC-CCcCCccccc
Q 025404 45 KCAVCQKLSKSFESLREHL----TGPLS-KAHCSGIFSD 78 (253)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~----~~~~~-C~~C~~~f~~ 78 (253)
.|..||-.|+-.-.|---. -..|+ |+.|.+.+..
T Consensus 125 ~CT~CGPRfTIi~alPYDR~nTsM~~F~lC~~C~~EY~d 163 (750)
T COG0068 125 NCTNCGPRFTIIEALPYDRENTSMADFPLCPFCDKEYKD 163 (750)
T ss_pred ccCCCCcceeeeccCCCCcccCccccCcCCHHHHHHhcC
Confidence 6667776666544332222 12333 5666555543
No 238
>COG0417 PolB DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair]
Probab=39.29 E-value=1.2e+02 Score=29.56 Aligned_cols=40 Identities=15% Similarity=0.286 Sum_probs=30.4
Q ss_pred hcCCCCHHHHHHHHHHHHhcCCCCCcccccCCCCeEEEeechh-hhhhhhcC
Q 025404 195 IKNAMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLE-HDLDSLRM 245 (253)
Q Consensus 195 l~~~~~~~~v~~~l~~~~~~~~~~~~~~~~~~~~~~lv~h~~~-~D~~~l~~ 245 (253)
+....+-.+++..+..++... .-.|+||+|.. ||+.+|.-
T Consensus 205 v~~~~~e~e~l~~~~~~i~~~-----------dPdVIvgyn~~~fd~pyl~~ 245 (792)
T COG0417 205 VEVVISEAELLERFVELIREY-----------DPDVIVGYNGDNFDWPYLAE 245 (792)
T ss_pred eEEecCHHHHHHHHHHHHHhc-----------CCCEEEeccCCcCChHHHHH
Confidence 455668889999999888421 23499999987 99998864
No 239
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=39.08 E-value=14 Score=20.05 Aligned_cols=12 Identities=33% Similarity=0.484 Sum_probs=5.3
Q ss_pred ccccccccccCH
Q 025404 45 KCAVCQKLSKSF 56 (253)
Q Consensus 45 ~C~~C~~~f~~~ 56 (253)
.|..|++.|...
T Consensus 5 ~C~eC~~~f~dS 16 (34)
T PF01286_consen 5 KCDECGKPFMDS 16 (34)
T ss_dssp E-TTT--EES-S
T ss_pred hHhHhCCHHHHH
Confidence 677777777553
No 240
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=37.99 E-value=14 Score=20.71 Aligned_cols=14 Identities=29% Similarity=0.522 Sum_probs=11.6
Q ss_pred cccccccccccCCH
Q 025404 14 RHKCVACYKQFKRK 27 (253)
Q Consensus 14 ~~~C~~C~k~f~~~ 27 (253)
||+|..|++.|-..
T Consensus 12 ~f~C~~C~~~FC~~ 25 (39)
T smart00154 12 GFKCRHCGNLFCGE 25 (39)
T ss_pred CeECCccCCccccc
Confidence 88999999888654
No 241
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=37.70 E-value=18 Score=31.92 Aligned_cols=23 Identities=17% Similarity=0.418 Sum_probs=12.3
Q ss_pred CCcCCcccccc-----cccccccccCCh
Q 025404 69 KAHCSGIFSDR-----GCNLCMNIFDSP 91 (253)
Q Consensus 69 C~~C~~~f~~~-----~C~~C~k~f~~~ 91 (253)
|+.||.+..+. .|+.||..+...
T Consensus 353 Cp~Cg~~m~S~G~~g~rC~kCg~~~~~~ 380 (421)
T COG1571 353 CPRCGGRMKSAGRNGFRCKKCGTRARET 380 (421)
T ss_pred CCccCCchhhcCCCCcccccccccCCcc
Confidence 55555444433 266676666654
No 242
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=37.45 E-value=12 Score=27.48 Aligned_cols=11 Identities=27% Similarity=0.458 Sum_probs=5.6
Q ss_pred ccccccccccC
Q 025404 45 KCAVCQKLSKS 55 (253)
Q Consensus 45 ~C~~C~~~f~~ 55 (253)
.|..||..|..
T Consensus 72 ~C~~CG~~~~~ 82 (135)
T PRK03824 72 KCRNCGNEWSL 82 (135)
T ss_pred ECCCCCCEEec
Confidence 55555555443
No 243
>PF03337 Pox_F12L: Poxvirus F12L protein; InterPro: IPR005005 The vaccinia virus F12L gene encodes a 65 kDa protein that is expressed late during infection and is important for plaque formation, EEV production and virulence. The F12L protein is located on intracellular enveloped virus (IEV) particles, but is absent from immature virions, intracellular mature virus and cell-associated enveloped virus. F12L shows co-localization with endosomal compartments and microtubules and appears to play a role in the the transport of IEV particles to the cell surface on microtubules [].; GO: 0016032 viral reproduction
Probab=37.03 E-value=45 Score=31.23 Aligned_cols=71 Identities=18% Similarity=0.241 Sum_probs=49.6
Q ss_pred EEeeeccCCCCcccceeeeccCCHHhhcCCC-CHHHHHHHHHH-HHhcCCCCCcccccCCCCeEEEe-echhhhhhhhcC
Q 025404 169 IFHTYVQPQLPVTNYRYEVTGLTEEDIKNAM-PLKEVKDKILE-ILNNGESTGRLMLDDGKARLLVG-HGLEHDLDSLRM 245 (253)
Q Consensus 169 ~~~~~v~P~~~i~~~~~~~~Git~~~l~~~~-~~~~v~~~l~~-~~~~~~~~~~~~~~~~~~~~lv~-h~~~~D~~~l~~ 245 (253)
.+...+-|..|.+-.++...|.+.-+..... -+.+..+.|.+ ++.| ..--+||| |+--||+..|+.
T Consensus 225 ~v~a~it~~gp~iymIstyPG~~F~nf~s~~~li~~FL~Wl~e~~~~n-----------~~ti~LvGy~ss~FD~pLLra 293 (651)
T PF03337_consen 225 SVNAIITPNGPSIYMISTYPGKCFINFDSNKALISDFLKWLRECIMKN-----------IRTIILVGYFSSFFDFPLLRA 293 (651)
T ss_pred EEEEEecCCCceeEEEEecCCceEEeCCCchHHHHHHHHHHHHHHhcc-----------CceEEEeehhhhhhccHHHHh
Confidence 4566666777777677777777765555544 56666666766 3311 12458999 888999999999
Q ss_pred CCCCC
Q 025404 246 NYPDH 250 (253)
Q Consensus 246 ~~~~~ 250 (253)
.||++
T Consensus 294 ~wp~~ 298 (651)
T PF03337_consen 294 YWPKN 298 (651)
T ss_pred hcccC
Confidence 99987
No 244
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=36.60 E-value=19 Score=17.87 Aligned_cols=11 Identities=18% Similarity=0.386 Sum_probs=8.5
Q ss_pred CCccccccccc
Q 025404 12 TARHKCVACYK 22 (253)
Q Consensus 12 ~k~~~C~~C~k 22 (253)
--+|.|+.||+
T Consensus 14 ~v~f~CPnCG~ 24 (24)
T PF07754_consen 14 AVPFPCPNCGF 24 (24)
T ss_pred CceEeCCCCCC
Confidence 45789999984
No 245
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=36.58 E-value=12 Score=36.00 Aligned_cols=28 Identities=14% Similarity=0.133 Sum_probs=0.0
Q ss_pred CCCCCCCcCCcccccccccccccccCCh
Q 025404 64 TGPLSKAHCSGIFSDRGCNLCMNIFDSP 91 (253)
Q Consensus 64 ~~~~~C~~C~~~f~~~~C~~C~k~f~~~ 91 (253)
+..|.|+.|+.......|+.|+......
T Consensus 678 ~~~~~Cp~C~~~~~~~~C~~C~~~~~~~ 705 (900)
T PF03833_consen 678 EPVYVCPDCGIEVEEDECPKCGRETTSY 705 (900)
T ss_dssp ----------------------------
T ss_pred ccceeccccccccCccccccccccCccc
Confidence 3457788888888777888888765543
No 246
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=36.04 E-value=10 Score=22.33 Aligned_cols=11 Identities=27% Similarity=0.785 Sum_probs=6.5
Q ss_pred ccccccccccC
Q 025404 45 KCAVCQKLSKS 55 (253)
Q Consensus 45 ~C~~C~~~f~~ 55 (253)
.|..||..+.-
T Consensus 3 ~C~~CgyvYd~ 13 (47)
T PF00301_consen 3 QCPVCGYVYDP 13 (47)
T ss_dssp EETTTSBEEET
T ss_pred CCCCCCEEEcC
Confidence 46667665543
No 247
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=35.93 E-value=16 Score=30.46 Aligned_cols=45 Identities=13% Similarity=0.072 Sum_probs=32.9
Q ss_pred CCCCCCcCCcccccccccccccccCChHHHHHHHHHccCCCCCCcccc
Q 025404 65 GPLSKAHCSGIFSDRGCNLCMNIFDSPSSLIKHKEACSLSAPVPFEKT 112 (253)
Q Consensus 65 ~~~~C~~C~~~f~~~~C~~C~k~f~~~~~l~~H~~~h~~~~~~~C~~~ 112 (253)
-||.|.+|.+.|....-..|+..|-....|..++ .+++.|.|++.
T Consensus 240 ~Pf~c~icr~~f~~pVvt~c~h~fc~~ca~~~~q---k~~~c~vC~~~ 284 (313)
T KOG1813|consen 240 LPFKCFICRKYFYRPVVTKCGHYFCEVCALKPYQ---KGEKCYVCSQQ 284 (313)
T ss_pred CCccccccccccccchhhcCCceeehhhhccccc---cCCcceecccc
Confidence 3788999999998887777888888777776543 24566667765
No 248
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=35.65 E-value=21 Score=33.74 Aligned_cols=13 Identities=15% Similarity=0.368 Sum_probs=6.6
Q ss_pred CCCCCCcCCcccc
Q 025404 65 GPLSKAHCSGIFS 77 (253)
Q Consensus 65 ~~~~C~~C~~~f~ 77 (253)
+.-.||.|+.+|+
T Consensus 677 RqRKCP~Cn~aFg 689 (698)
T KOG0978|consen 677 RQRKCPKCNAAFG 689 (698)
T ss_pred hcCCCCCCCCCCC
Confidence 3444555555554
No 249
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=35.26 E-value=17 Score=29.59 Aligned_cols=45 Identities=24% Similarity=0.501 Sum_probs=27.6
Q ss_pred ccccccccccCHHHHhhhhCCCCCCCcCCcccccccccccccccCChHHHHHHHH
Q 025404 45 KCAVCQKLSKSFESLREHLTGPLSKAHCSGIFSDRGCNLCMNIFDSPSSLIKHKE 99 (253)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~~~~~~C~~C~~~f~~~~C~~C~k~f~~~~~l~~H~~ 99 (253)
.|..||.+..-+ .+.+|+ +.|+. ..| +|-.|++.|.+ ..++.|..
T Consensus 5 tCnvCgEsvKKp-~vekH~---srCrn--~~f---SCIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 5 TCNVCGESVKKP-QVEKHM---SRCRN--AYF---SCIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred ehhhhhhhcccc-chHHHH---HhccC--Cee---EEeeccccccc-chhhhhhh
Confidence 688888776543 355565 22332 222 37888888887 55667753
No 251
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=34.90 E-value=38 Score=28.97 Aligned_cols=38 Identities=16% Similarity=0.292 Sum_probs=27.4
Q ss_pred CCcccccccccccCCHHHHHHhhhhcCCCCCcc--cccccc
Q 025404 12 TARHKCVACYKQFKRKDHLIEHMKISYHSVHQP--KCAVCQ 50 (253)
Q Consensus 12 ~k~~~C~~C~k~f~~~~~l~~H~~~~~H~~~~~--~C~~C~ 50 (253)
+.-|.|+.|++.=.+...|..|+..+ |....+ .|+.|+
T Consensus 77 ~qSftCPyC~~~Gfte~~f~~Hv~s~-Hpda~~~~icp~c~ 116 (381)
T KOG1280|consen 77 PQSFTCPYCGIMGFTERQFGTHVLSQ-HPEASTSVICPLCA 116 (381)
T ss_pred cccccCCcccccccchhHHHHHhhhc-CcccCcceeeeccc
Confidence 34688888888767777888887654 765555 677775
No 252
>PF06821 Ser_hydrolase: Serine hydrolase; InterPro: IPR010662 This family contains a number of hypothetical bacterial proteins of unknown function, which may be cytosolic. The Crystal Structure Of The Yden Gene Product Swiss:P96671 from B. Subtilis has been solved. The structure shows an alpha-beta hydrolase fold suggesting an enzymatic function for these proteins [].; GO: 0016787 hydrolase activity; PDB: 3BDV_B 2QS9_A 1UXO_A.
Probab=34.75 E-value=42 Score=25.68 Aligned_cols=31 Identities=19% Similarity=0.275 Sum_probs=20.7
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCCcccccCCCCeEEEeechh
Q 025404 197 NAMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLE 237 (253)
Q Consensus 197 ~~~~~~~v~~~l~~~~~~~~~~~~~~~~~~~~~~lv~h~~~ 237 (253)
+.|.+++=...|.+.|.. .++.++||||++.
T Consensus 35 ~~P~~~~W~~~l~~~i~~----------~~~~~ilVaHSLG 65 (171)
T PF06821_consen 35 DNPDLDEWVQALDQAIDA----------IDEPTILVAHSLG 65 (171)
T ss_dssp TS--HHHHHHHHHHCCHC-----------TTTEEEEEETHH
T ss_pred CCCCHHHHHHHHHHHHhh----------cCCCeEEEEeCHH
Confidence 567788777778777732 1266899999964
No 253
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=34.22 E-value=20 Score=21.73 Aligned_cols=38 Identities=21% Similarity=0.537 Sum_probs=15.7
Q ss_pred cccccc--cccccCCHHHHHHhhhhcCCCCCcc-cccc----cccccc
Q 025404 14 RHKCVA--CYKQFKRKDHLIEHMKISYHSVHQP-KCAV----CQKLSK 54 (253)
Q Consensus 14 ~~~C~~--C~k~f~~~~~l~~H~~~~~H~~~~~-~C~~----C~~~f~ 54 (253)
+..|+. |...+.. ..|..|... --...+ .|.. |+..+.
T Consensus 9 ~v~C~~~cc~~~i~r-~~l~~H~~~--~C~~~~v~C~~~~~GC~~~~~ 53 (60)
T PF02176_consen 9 PVPCPNGCCNEMIPR-KELDDHLEN--ECPKRPVPCPYSPYGCKERVP 53 (60)
T ss_dssp EEE-TT--S-BEEEC-CCHHHHHHT--TSTTSEEE-SS----S--EEE
T ss_pred EeeCCCCCcccceeH-HHHHHHHHc--cCCCCcEECCCCCCCCCCccc
Confidence 445555 4343432 456666654 333444 5555 555443
No 254
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=34.18 E-value=10 Score=28.38 Aligned_cols=14 Identities=29% Similarity=0.427 Sum_probs=7.8
Q ss_pred CCCCcc-----cccccccc
Q 025404 39 HSVHQP-----KCAVCQKL 52 (253)
Q Consensus 39 H~~~~~-----~C~~C~~~ 52 (253)
|+|+.+ .|..||..
T Consensus 103 ~sGE~~g~G~l~C~~Cg~~ 121 (146)
T PF07295_consen 103 HSGEVVGPGTLVCENCGHE 121 (146)
T ss_pred ecCcEecCceEecccCCCE
Confidence 555543 56666643
No 255
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=33.86 E-value=26 Score=30.39 Aligned_cols=51 Identities=29% Similarity=0.632 Sum_probs=44.2
Q ss_pred CCCcccccccccccCCHHHHHHhhhhcCCCCCcc-cccc--ccccccCHHHHhhhh
Q 025404 11 STARHKCVACYKQFKRKDHLIEHMKISYHSVHQP-KCAV--CQKLSKSFESLREHL 63 (253)
Q Consensus 11 ~~k~~~C~~C~k~f~~~~~l~~H~~~~~H~~~~~-~C~~--C~~~f~~~~~l~~H~ 63 (253)
..+++.|+.|...|.....+..|.+. |+++++ .|.. |...|.....+..|.
T Consensus 30 ~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 83 (467)
T COG5048 30 APRPDSCPNCTDSFSRLEHLTRHIRS--HTGEKPSQCSYSGCDKSFSRPLELSRHL 83 (467)
T ss_pred CCchhhcccccccccccchhhhhccc--ccccCCccccccccccccCCcchhhhhc
Confidence 45778999999999999999999999 999999 8865 777888888887775
No 256
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=33.61 E-value=29 Score=26.40 Aligned_cols=18 Identities=22% Similarity=0.340 Sum_probs=14.0
Q ss_pred ccccccccCChHHHHHHH
Q 025404 81 CNLCMNIFDSPSSLIKHK 98 (253)
Q Consensus 81 C~~C~k~f~~~~~l~~H~ 98 (253)
|+.||+.|---++++.-.
T Consensus 133 C~~CgkiYW~GsHw~~m~ 150 (165)
T COG1656 133 CPKCGKIYWKGSHWRRMV 150 (165)
T ss_pred CCCCcccccCchHHHHHH
Confidence 889999998887776443
No 257
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=33.41 E-value=24 Score=35.59 Aligned_cols=28 Identities=32% Similarity=0.590 Sum_probs=15.6
Q ss_pred CCCeEEeeeccCCCCcccceeeeccCCHHhh
Q 025404 165 DENVIFHTYVQPQLPVTNYRYEVTGLTEEDI 195 (253)
Q Consensus 165 ~~~~~~~~~v~P~~~i~~~~~~~~Git~~~l 195 (253)
+|.+.||. .+.|++.+.-+..|+|.+.|
T Consensus 782 DGTiR~D~---td~PlThfrp~Eigvs~ekl 809 (1337)
T PRK14714 782 DGTVRYDM---TDLPVTHFRPREIGVSVEKL 809 (1337)
T ss_pred CCceeccC---cCCccccccHHHcCCCHHHH
Confidence 55555544 33455566666666666655
No 258
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=33.31 E-value=19 Score=28.11 Aligned_cols=45 Identities=16% Similarity=0.047 Sum_probs=31.7
Q ss_pred CCCCCCcCCcccccccccccccccCChHHHHHHHHHccCCCCCCcccc
Q 025404 65 GPLSKAHCSGIFSDRGCNLCMNIFDSPSSLIKHKEACSLSAPVPFEKT 112 (253)
Q Consensus 65 ~~~~C~~C~~~f~~~~C~~C~k~f~~~~~l~~H~~~h~~~~~~~C~~~ 112 (253)
-||.|..|-+.|....-..||..|-.....+. .-.|...+.|++.
T Consensus 195 IPF~C~iCKkdy~spvvt~CGH~FC~~Cai~~---y~kg~~C~~Cgk~ 239 (259)
T COG5152 195 IPFLCGICKKDYESPVVTECGHSFCSLCAIRK---YQKGDECGVCGKA 239 (259)
T ss_pred CceeehhchhhccchhhhhcchhHHHHHHHHH---hccCCcceecchh
Confidence 37889999999988877888888886665442 2344555556654
No 259
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=33.30 E-value=13 Score=26.33 Aligned_cols=11 Identities=18% Similarity=0.540 Sum_probs=4.6
Q ss_pred ccccccccccC
Q 025404 45 KCAVCQKLSKS 55 (253)
Q Consensus 45 ~C~~C~~~f~~ 55 (253)
.|..||..|.-
T Consensus 72 ~C~~Cg~~~~~ 82 (113)
T PF01155_consen 72 RCRDCGHEFEP 82 (113)
T ss_dssp EETTTS-EEEC
T ss_pred ECCCCCCEEec
Confidence 44445444433
No 260
>PHA02524 43A DNA polymerase subunit A; Provisional
Probab=33.24 E-value=39 Score=30.76 Aligned_cols=35 Identities=9% Similarity=0.080 Sum_probs=26.5
Q ss_pred CCCHHHHHHHHHHHHhcCCCCCcccccCCCCeEEEeec-hhhhhhhh
Q 025404 198 AMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHG-LEHDLDSL 243 (253)
Q Consensus 198 ~~~~~~v~~~l~~~~~~~~~~~~~~~~~~~~~~lv~h~-~~~D~~~l 243 (253)
-.+-.++..++.+++.. -+- .||+|+| ..||+.+|
T Consensus 177 f~sE~eLL~~F~~~i~~--------~DP---DIItGYNi~nFDlPYL 212 (498)
T PHA02524 177 FEDEVDLLLNYIQLWKA--------NTP---DLVFGWNSEGFDIPYI 212 (498)
T ss_pred eCCHHHHHHHHHHHHHH--------hCC---CEEEeCCCcccCHHHH
Confidence 36788999999999932 111 3999998 67999876
No 261
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=33.13 E-value=12 Score=35.17 Aligned_cols=23 Identities=22% Similarity=0.307 Sum_probs=20.5
Q ss_pred ccccccccCChHHHHHHHHHccC
Q 025404 81 CNLCMNIFDSPSSLIKHKEACSL 103 (253)
Q Consensus 81 C~~C~k~f~~~~~l~~H~~~h~~ 103 (253)
|..|+|.|-...++..||++|.-
T Consensus 795 CreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 795 CRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred hHHHHHHHHHHhhhhHHHHHHHH
Confidence 88999999999999999999953
No 262
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=32.87 E-value=19 Score=25.52 Aligned_cols=10 Identities=20% Similarity=0.228 Sum_probs=4.6
Q ss_pred CCCcCCcccc
Q 025404 68 SKAHCSGIFS 77 (253)
Q Consensus 68 ~C~~C~~~f~ 77 (253)
.|..|+..|.
T Consensus 72 ~C~~Cg~~~~ 81 (113)
T PRK12380 72 WCWDCSQVVE 81 (113)
T ss_pred EcccCCCEEe
Confidence 3455554443
No 263
>PF04857 CAF1: CAF1 family ribonuclease; InterPro: IPR006941 CAF1 is an RNase of the DEDD superfamily, and a subunit of the Ccr4-Not complex that mediates 3' to 5' mRNA deadenylation. The major pathways of mRNA turnover in eukaryotes initiate with shortening of the poly(A) tail. CAF1 P39008 from SWISSPROT encodes a critical component of the major cytoplasmic deadenylase in yeast. Caf1p is required for normal mRNA deadenylation in vivo and localises to the cytoplasm. Caf1p copurifies with a Ccr4p-dependent poly(A)-specific exonuclease activity. Some members of this family contain a single-stranded nucleic acid binding domain, R3H.; GO: 0005634 nucleus; PDB: 3D45_B 1UG8_A 2D5R_A 2A1S_C 2A1R_A 2FC6_A 1UOC_A 3G10_A 2P51_A 3G0Z_A.
Probab=32.74 E-value=29 Score=28.62 Aligned_cols=18 Identities=33% Similarity=0.337 Sum_probs=14.7
Q ss_pred CCCeEEEeechhhhhhhh
Q 025404 226 GKARLLVGHGLEHDLDSL 243 (253)
Q Consensus 226 ~~~~~lv~h~~~~D~~~l 243 (253)
+...+|||||.-.|+-+|
T Consensus 147 ~~~~p~Vghn~~~Dl~~l 164 (262)
T PF04857_consen 147 SSKKPIVGHNGLYDLMYL 164 (262)
T ss_dssp CC-SEEEESSTHHHHHHH
T ss_pred ccCCcEEEeChHhHHHHH
Confidence 356899999999999875
No 264
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=32.72 E-value=26 Score=30.65 Aligned_cols=25 Identities=12% Similarity=0.162 Sum_probs=17.7
Q ss_pred CCCCcCCcccccc--cccccccccCCh
Q 025404 67 LSKAHCSGIFSDR--GCNLCMNIFDSP 91 (253)
Q Consensus 67 ~~C~~C~~~f~~~--~C~~C~k~f~~~ 91 (253)
|.|..||.....+ +|+.|+.+-+-.
T Consensus 1 ~~c~~cg~~~~~~~g~cp~c~~w~~~~ 27 (372)
T cd01121 1 YVCSECGYVSPKWLGKCPECGEWNTLV 27 (372)
T ss_pred CCCCCCCCCCCCccEECcCCCCceeee
Confidence 6788888877765 388888654433
No 265
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=32.52 E-value=20 Score=28.08 Aligned_cols=63 Identities=14% Similarity=0.267 Sum_probs=29.1
Q ss_pred eeeccCCCCcccceeeeccCCHHh---hcCCC----------CHHHHHHHHHHHHhcCCCCCccccc-CCCCeEEEee
Q 025404 171 HTYVQPQLPVTNYRYEVTGLTEED---IKNAM----------PLKEVKDKILEILNNGESTGRLMLD-DGKARLLVGH 234 (253)
Q Consensus 171 ~~~v~P~~~i~~~~~~~~Git~~~---l~~~~----------~~~~v~~~l~~~~~~~~~~~~~~~~-~~~~~~lv~h 234 (253)
..-+.|..--..+.+.+=|+-..- |..+. ...++...+.+.+ +|...+|+--. ..++..++++
T Consensus 95 g~~iePG~~s~G~ITtIEGvL~rv~e~l~~a~~~~~~dE~~~k~~e~~~~i~~~i-eg~~~fTlIieDp~G~S~I~~~ 171 (201)
T COG1779 95 GLEIEPGPASEGFITTIEGVLERVYEVLETAIKLAEDDESKKKAEELLKRIDEAI-EGKRKFTLIIEDPLGNSAIISE 171 (201)
T ss_pred ceEeccccccCceEehHHHHHHHHHHHHHHHHhcccchHHHHHHHHHHHHHHHHh-ccCccEEEEEECCCCCceeecc
Confidence 334455544445777777754322 22221 2345566666666 44444443322 2233444443
No 266
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=32.02 E-value=29 Score=30.59 Aligned_cols=39 Identities=18% Similarity=0.359 Sum_probs=25.8
Q ss_pred CCCCcccccccccccCCHHHHHHhhhhcCCC-CCccccccccccc
Q 025404 10 RSTARHKCVACYKQFKRKDHLIEHMKISYHS-VHQPKCAVCQKLS 53 (253)
Q Consensus 10 ~~~k~~~C~~C~k~f~~~~~l~~H~~~~~H~-~~~~~C~~C~~~f 53 (253)
+.-.-|.|+.|.+.|+....+. .. -. ...+.|..|+-..
T Consensus 124 t~~~~Y~Cp~C~kkyt~Lea~~---L~--~~~~~~F~C~~C~gel 163 (436)
T KOG2593|consen 124 TNVAGYVCPNCQKKYTSLEALQ---LL--DNETGEFHCENCGGEL 163 (436)
T ss_pred cccccccCCccccchhhhHHHH---hh--cccCceEEEecCCCch
Confidence 3456799999999998766553 22 11 2234899997543
No 267
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=31.75 E-value=29 Score=25.91 Aligned_cols=10 Identities=30% Similarity=0.763 Sum_probs=5.7
Q ss_pred ccccccccCC
Q 025404 81 CNLCMNIFDS 90 (253)
Q Consensus 81 C~~C~k~f~~ 90 (253)
|..||+.|+.
T Consensus 31 C~~C~~RFTT 40 (147)
T TIGR00244 31 CLECHERFTT 40 (147)
T ss_pred CCccCCccce
Confidence 5555555554
No 268
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=31.33 E-value=31 Score=25.83 Aligned_cols=11 Identities=27% Similarity=0.513 Sum_probs=6.9
Q ss_pred ccccccccCCh
Q 025404 81 CNLCMNIFDSP 91 (253)
Q Consensus 81 C~~C~k~f~~~ 91 (253)
|+.||+.|+..
T Consensus 31 C~~C~~RFTTf 41 (156)
T COG1327 31 CLECGERFTTF 41 (156)
T ss_pred ccccccccchh
Confidence 66666666653
No 269
>COG4640 Predicted membrane protein [Function unknown]
Probab=30.86 E-value=33 Score=29.98 Aligned_cols=28 Identities=25% Similarity=0.413 Sum_probs=16.4
Q ss_pred CCcCCcccc--cccccccccccCChHHHHH
Q 025404 69 KAHCSGIFS--DRGCNLCMNIFDSPSSLIK 96 (253)
Q Consensus 69 C~~C~~~f~--~~~C~~C~k~f~~~~~l~~ 96 (253)
|+-||..-. ...|.+||..|...+.+-+
T Consensus 4 C~kcG~qk~Ed~~qC~qCG~~~t~~~sqan 33 (465)
T COG4640 4 CPKCGSQKAEDDVQCTQCGHKFTSRQSQAN 33 (465)
T ss_pred ccccccccccccccccccCCcCCchhhhhh
Confidence 666662221 2237888888877666544
No 270
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=30.75 E-value=51 Score=32.45 Aligned_cols=34 Identities=21% Similarity=0.152 Sum_probs=26.1
Q ss_pred CHHHHHHHHHHHHhcCCCCCcccccCCCCeEEEeechhhhhhhhcC
Q 025404 200 PLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRM 245 (253)
Q Consensus 200 ~~~~v~~~l~~~~~~~~~~~~~~~~~~~~~~lv~h~~~~D~~~l~~ 245 (253)
+...+...|..++.+ .+...||||+.||+.+|.-
T Consensus 362 ~~~~~~~~l~~~l~~------------~~~~~v~~n~K~d~~~l~~ 395 (887)
T TIGR00593 362 LTILTDDKFARWLLN------------EQIKKIGHDAKFLMHLLKR 395 (887)
T ss_pred hhHHHHHHHHHHHhC------------CCCcEEEeeHHHHHHHHHh
Confidence 456677778888832 4456899999999999963
No 271
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=30.58 E-value=16 Score=28.07 Aligned_cols=22 Identities=27% Similarity=0.525 Sum_probs=15.5
Q ss_pred CCCCCcCCcccc--cccccccccc
Q 025404 66 PLSKAHCSGIFS--DRGCNLCMNI 87 (253)
Q Consensus 66 ~~~C~~C~~~f~--~~~C~~C~k~ 87 (253)
.+.|..|.+.|. ..-|+.||.-
T Consensus 139 ~~rC~GC~~~f~~~~~~Cp~CG~~ 162 (177)
T COG1439 139 RLRCHGCKRIFPEPKDFCPICGSP 162 (177)
T ss_pred eEEEecCceecCCCCCcCCCCCCc
Confidence 356888888888 3348888854
No 272
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=30.27 E-value=22 Score=20.20 Aligned_cols=6 Identities=33% Similarity=0.700 Sum_probs=2.4
Q ss_pred cccccc
Q 025404 81 CNLCMN 86 (253)
Q Consensus 81 C~~C~k 86 (253)
|..||.
T Consensus 22 C~~CG~ 27 (43)
T PF08271_consen 22 CPNCGL 27 (43)
T ss_dssp ETTT-B
T ss_pred CCCCCC
Confidence 555543
No 273
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=29.89 E-value=33 Score=27.41 Aligned_cols=26 Identities=23% Similarity=0.469 Sum_probs=19.9
Q ss_pred CCCcccccccccccCCHHHHHHhhhh
Q 025404 11 STARHKCVACYKQFKRKDHLIEHMKI 36 (253)
Q Consensus 11 ~~k~~~C~~C~k~f~~~~~l~~H~~~ 36 (253)
.+..|.|..|+|.|.-..-+..|+..
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~n 99 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIFN 99 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHHH
T ss_pred cCCEECCCCCCcccCChHHHHHHHhh
Confidence 34569999999999999999999865
No 274
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=29.62 E-value=30 Score=24.29 Aligned_cols=10 Identities=20% Similarity=0.823 Sum_probs=5.7
Q ss_pred ccccccccCC
Q 025404 81 CNLCMNIFDS 90 (253)
Q Consensus 81 C~~C~k~f~~ 90 (253)
|+.|+..+..
T Consensus 22 CpeC~~EW~~ 31 (109)
T TIGR00686 22 CPSCLYEWNE 31 (109)
T ss_pred Cccccccccc
Confidence 6666655543
No 275
>cd06142 RNaseD_exo DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins. Ribonuclease (RNase) D is a bacterial enzyme involved in the maturation of small stable RNAs and the 3' maturation of tRNA. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. In vivo, RNase D only becomes essential upon removal of other ribonucleases. Eukaryotic RNase D homologs include yeast Rrp6p, human PM/Scl-100, and the Drosophila melanogaster egalitarian protein.
Probab=29.58 E-value=53 Score=24.69 Aligned_cols=29 Identities=24% Similarity=0.284 Sum_probs=21.7
Q ss_pred HHHHHHHHHhcCCCCCcccccCCCCeEEEeechhhhhhhhc
Q 025404 204 VKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLR 244 (253)
Q Consensus 204 v~~~l~~~~~~~~~~~~~~~~~~~~~~lv~h~~~~D~~~l~ 244 (253)
+.+.|..++.+ .+...||||+.+|+.+|.
T Consensus 52 ~~~~l~~ll~~------------~~i~kv~~d~K~~~~~L~ 80 (178)
T cd06142 52 DLSPLKELLAD------------PNIVKVFHAAREDLELLK 80 (178)
T ss_pred cHHHHHHHHcC------------CCceEEEeccHHHHHHHH
Confidence 44556777832 456799999999999984
No 276
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=29.57 E-value=21 Score=21.20 Aligned_cols=15 Identities=20% Similarity=0.401 Sum_probs=10.2
Q ss_pred CCcccccccccccCC
Q 025404 12 TARHKCVACYKQFKR 26 (253)
Q Consensus 12 ~k~~~C~~C~k~f~~ 26 (253)
++++.|..||..|.-
T Consensus 2 Dk~l~C~dCg~~Fvf 16 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVF 16 (49)
T ss_pred CeeEEcccCCCeEEE
Confidence 466777777776653
No 277
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=29.34 E-value=27 Score=29.61 Aligned_cols=20 Identities=25% Similarity=0.498 Sum_probs=11.0
Q ss_pred CCCCcCCccccc--cccccccc
Q 025404 67 LSKAHCSGIFSD--RGCNLCMN 86 (253)
Q Consensus 67 ~~C~~C~~~f~~--~~C~~C~k 86 (253)
..|..|+-.+.. ..|+.||.
T Consensus 211 L~CslC~teW~~~R~~C~~Cg~ 232 (305)
T TIGR01562 211 LSCSLCATEWHYVRVKCSHCEE 232 (305)
T ss_pred EEcCCCCCcccccCccCCCCCC
Confidence 345555544432 24778875
No 278
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=29.03 E-value=18 Score=20.65 Aligned_cols=15 Identities=40% Similarity=0.580 Sum_probs=9.1
Q ss_pred CcccccccccccCCH
Q 025404 13 ARHKCVACYKQFKRK 27 (253)
Q Consensus 13 k~~~C~~C~k~f~~~ 27 (253)
-|+.|+.|++.|=..
T Consensus 12 ~~~~C~~C~~~FC~~ 26 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLK 26 (43)
T ss_dssp SHEE-TTTS-EE-TT
T ss_pred CCeECCCCCcccCcc
Confidence 478888888888654
No 279
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=28.86 E-value=24 Score=31.16 Aligned_cols=24 Identities=13% Similarity=0.196 Sum_probs=17.3
Q ss_pred CCCCCcCCccccccc--ccccccccC
Q 025404 66 PLSKAHCSGIFSDRG--CNLCMNIFD 89 (253)
Q Consensus 66 ~~~C~~C~~~f~~~~--C~~C~k~f~ 89 (253)
.|.|..||..+..+. |+.||.+-+
T Consensus 7 ~f~C~~CG~~s~KW~GkCp~Cg~Wns 32 (456)
T COG1066 7 AFVCQECGYVSPKWLGKCPACGAWNT 32 (456)
T ss_pred EEEcccCCCCCccccccCCCCCCccc
Confidence 477888888777663 888985433
No 280
>PRK11823 DNA repair protein RadA; Provisional
Probab=28.45 E-value=25 Score=31.50 Aligned_cols=25 Identities=12% Similarity=0.141 Sum_probs=15.3
Q ss_pred CCCCCcCCcccccc--cccccccccCC
Q 025404 66 PLSKAHCSGIFSDR--GCNLCMNIFDS 90 (253)
Q Consensus 66 ~~~C~~C~~~f~~~--~C~~C~k~f~~ 90 (253)
.|.|..||..+... .|+.|+.+=+-
T Consensus 7 ~y~C~~Cg~~~~~~~g~Cp~C~~w~t~ 33 (446)
T PRK11823 7 AYVCQECGAESPKWLGRCPECGAWNTL 33 (446)
T ss_pred eEECCcCCCCCcccCeeCcCCCCccce
Confidence 36677777666654 37777755443
No 281
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=28.28 E-value=27 Score=25.55 Aligned_cols=15 Identities=20% Similarity=0.569 Sum_probs=9.0
Q ss_pred CCcc-ccccccccccC
Q 025404 41 VHQP-KCAVCQKLSKS 55 (253)
Q Consensus 41 ~~~~-~C~~C~~~f~~ 55 (253)
+.+. +|++|......
T Consensus 77 d~~lYeCnIC~etS~e 92 (140)
T PF05290_consen 77 DPKLYECNICKETSAE 92 (140)
T ss_pred CCCceeccCcccccch
Confidence 3444 78888765544
No 282
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=28.22 E-value=38 Score=20.76 Aligned_cols=21 Identities=14% Similarity=0.241 Sum_probs=12.2
Q ss_pred CCcCCcccccccccccccccC
Q 025404 69 KAHCSGIFSDRGCNLCMNIFD 89 (253)
Q Consensus 69 C~~C~~~f~~~~C~~C~k~f~ 89 (253)
|+.||.-.-...|+.||....
T Consensus 8 C~~CgvYTLk~~CP~CG~~t~ 28 (56)
T PRK13130 8 CPKCGVYTLKEICPVCGGKTK 28 (56)
T ss_pred CCCCCCEEccccCcCCCCCCC
Confidence 556655555555777775543
No 283
>PRK10829 ribonuclease D; Provisional
Probab=28.02 E-value=66 Score=28.17 Aligned_cols=27 Identities=15% Similarity=0.132 Sum_probs=20.7
Q ss_pred HHHHHHHhcCCCCCcccccCCCCeEEEeechhhhhhhhc
Q 025404 206 DKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLR 244 (253)
Q Consensus 206 ~~l~~~~~~~~~~~~~~~~~~~~~~lv~h~~~~D~~~l~ 244 (253)
..|.+++.| .+.+-|+|++.+|+.+|.
T Consensus 64 ~~L~~ll~~------------~~ivKV~H~~~~Dl~~l~ 90 (373)
T PRK10829 64 SPFKALLRD------------PQVTKFLHAGSEDLEVFL 90 (373)
T ss_pred HHHHHHHcC------------CCeEEEEeChHhHHHHHH
Confidence 457788843 455669999999999983
No 284
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=27.63 E-value=44 Score=23.30 Aligned_cols=23 Identities=17% Similarity=0.332 Sum_probs=20.8
Q ss_pred cccc----cccccccCCHHHHHHhhhh
Q 025404 14 RHKC----VACYKQFKRKDHLIEHMKI 36 (253)
Q Consensus 14 ~~~C----~~C~k~f~~~~~l~~H~~~ 36 (253)
-|.| ..|+..+.+...+..|.+.
T Consensus 80 G~~C~~~~~~C~y~~~~~~~m~~H~~~ 106 (109)
T PF12013_consen 80 GYRCQCDPPHCGYITRSKKTMRKHWRK 106 (109)
T ss_pred CeeeecCCCCCCcEeccHHHHHHHHHH
Confidence 3899 9999999999999999987
No 285
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=27.56 E-value=27 Score=24.91 Aligned_cols=9 Identities=22% Similarity=0.766 Sum_probs=3.9
Q ss_pred ccccccccc
Q 025404 45 KCAVCQKLS 53 (253)
Q Consensus 45 ~C~~C~~~f 53 (253)
.|..||..|
T Consensus 73 ~C~~Cg~~~ 81 (117)
T PRK00564 73 ECKDCSHVF 81 (117)
T ss_pred EhhhCCCcc
Confidence 444444333
No 286
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=27.55 E-value=19 Score=30.99 Aligned_cols=13 Identities=15% Similarity=0.350 Sum_probs=4.6
Q ss_pred ccccccccccCHH
Q 025404 45 KCAVCQKLSKSFE 57 (253)
Q Consensus 45 ~C~~C~~~f~~~~ 57 (253)
.|..|.+.....+
T Consensus 254 ~C~~C~yt~~~~~ 266 (344)
T PF09332_consen 254 TCKQCKYTAFKPS 266 (344)
T ss_dssp EETTT--EESS--
T ss_pred EcCCCCCcccCcc
Confidence 4555655444433
No 287
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=27.33 E-value=28 Score=31.32 Aligned_cols=26 Identities=15% Similarity=0.259 Sum_probs=17.1
Q ss_pred CCCCCcCCcccccc--cccccccccCCh
Q 025404 66 PLSKAHCSGIFSDR--GCNLCMNIFDSP 91 (253)
Q Consensus 66 ~~~C~~C~~~f~~~--~C~~C~k~f~~~ 91 (253)
.|.|..||..+... +|+.|+.+=+-.
T Consensus 7 ~y~C~~Cg~~~~~~~g~Cp~C~~w~t~~ 34 (454)
T TIGR00416 7 KFVCQHCGADSPKWQGKCPACHAWNTIT 34 (454)
T ss_pred eEECCcCCCCCccccEECcCCCCccccc
Confidence 36777777777655 388887654443
No 288
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=27.09 E-value=19 Score=22.26 Aligned_cols=8 Identities=25% Similarity=0.874 Sum_probs=4.5
Q ss_pred cccccccc
Q 025404 45 KCAVCQKL 52 (253)
Q Consensus 45 ~C~~C~~~ 52 (253)
.|+.||..
T Consensus 27 ~CPnCG~~ 34 (59)
T PRK14890 27 LCPNCGEV 34 (59)
T ss_pred eCCCCCCe
Confidence 56666543
No 289
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=26.82 E-value=28 Score=25.78 Aligned_cols=17 Identities=18% Similarity=0.542 Sum_probs=8.0
Q ss_pred CCcCCccccccc--ccccc
Q 025404 69 KAHCSGIFSDRG--CNLCM 85 (253)
Q Consensus 69 C~~C~~~f~~~~--C~~C~ 85 (253)
|..||+.|-..+ |+.|+
T Consensus 32 C~~CG~v~~PPr~~Cp~C~ 50 (140)
T COG1545 32 CKKCGRVYFPPRAYCPKCG 50 (140)
T ss_pred cCCCCeEEcCCcccCCCCC
Confidence 444444443322 55555
No 290
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=26.54 E-value=19 Score=19.71 Aligned_cols=10 Identities=30% Similarity=0.464 Sum_probs=3.5
Q ss_pred cccccccccC
Q 025404 46 CAVCQKLSKS 55 (253)
Q Consensus 46 C~~C~~~f~~ 55 (253)
|+.|.+.+..
T Consensus 2 C~~C~~Ey~~ 11 (35)
T PF07503_consen 2 CDDCLKEYFD 11 (35)
T ss_dssp -HHHHHHHCS
T ss_pred CHHHHHHHcC
Confidence 3444443333
No 291
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=26.48 E-value=28 Score=27.85 Aligned_cols=25 Identities=28% Similarity=0.472 Sum_probs=17.9
Q ss_pred cccccccccCChHHHHHHHHHccCC
Q 025404 80 GCNLCMNIFDSPSSLIKHKEACSLS 104 (253)
Q Consensus 80 ~C~~C~k~f~~~~~l~~H~~~h~~~ 104 (253)
.|..|+|.|......+.|+..-|.+
T Consensus 79 ~C~lc~KlFkg~eFV~KHI~nKH~e 103 (214)
T PF04959_consen 79 RCPLCGKLFKGPEFVRKHIFNKHPE 103 (214)
T ss_dssp EE-SSS-EESSHHHHHHHHHHH-HH
T ss_pred CCCCCCcccCChHHHHHHHhhcCHH
Confidence 3888999999999999998754443
No 292
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=26.46 E-value=38 Score=30.24 Aligned_cols=19 Identities=32% Similarity=0.697 Sum_probs=15.9
Q ss_pred ccccccccCChHHHHHHHH
Q 025404 81 CNLCMNIFDSPSSLIKHKE 99 (253)
Q Consensus 81 C~~C~k~f~~~~~l~~H~~ 99 (253)
|..|+|+|.+--.|.+|..
T Consensus 295 C~vCnKsFKseKq~kNHEn 313 (508)
T KOG0717|consen 295 CVVCNKSFKSEKQLKNHEN 313 (508)
T ss_pred EeeccccccchHHHHhhHH
Confidence 8888889988888888864
No 293
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.21 E-value=24 Score=25.35 Aligned_cols=55 Identities=16% Similarity=0.266 Sum_probs=28.8
Q ss_pred HHHHHhhhhcCCCCCcc--ccccccccccCHHHHhhhh--CCCCCCCcCCcccccccccccccccCChH
Q 025404 28 DHLIEHMKISYHSVHQP--KCAVCQKLSKSFESLREHL--TGPLSKAHCSGIFSDRGCNLCMNIFDSPS 92 (253)
Q Consensus 28 ~~l~~H~~~~~H~~~~~--~C~~C~~~f~~~~~l~~H~--~~~~~C~~C~~~f~~~~C~~C~k~f~~~~ 92 (253)
..|..---. +.|+.. +|+.|..+.+-......-. -+.|.-+ .-|..||+.|.+..
T Consensus 24 pel~eafcs--kcgeati~qcp~csasirgd~~vegvlglg~dye~p--------sfchncgs~fpwte 82 (160)
T COG4306 24 PELMEAFCS--KCGEATITQCPICSASIRGDYYVEGVLGLGGDYEPP--------SFCHNCGSRFPWTE 82 (160)
T ss_pred HHHHHHHHh--hhchHHHhcCCccCCcccccceeeeeeccCCCCCCc--------chhhcCCCCCCcHH
Confidence 445444445 666554 8999976665443221111 2233321 12777888887753
No 294
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=25.80 E-value=29 Score=23.03 Aligned_cols=9 Identities=22% Similarity=0.874 Sum_probs=4.1
Q ss_pred ccccccccC
Q 025404 81 CNLCMNIFD 89 (253)
Q Consensus 81 C~~C~k~f~ 89 (253)
|..|.+.|.
T Consensus 57 C~~C~kv~a 65 (92)
T KOG0402|consen 57 CGSCKKVVA 65 (92)
T ss_pred cCCccceec
Confidence 444544443
No 295
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=25.70 E-value=60 Score=27.40 Aligned_cols=32 Identities=22% Similarity=0.285 Sum_probs=18.7
Q ss_pred ccccccccccCHHHHhhhh---CCCCCCCcCCccc
Q 025404 45 KCAVCQKLSKSFESLREHL---TGPLSKAHCSGIF 76 (253)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~---~~~~~C~~C~~~f 76 (253)
.|-.|...|+-...-..-. .+.|.|+.|...|
T Consensus 364 ~Cf~CQ~~fp~~~~~~~~~~~ss~rY~Ce~CK~~F 398 (421)
T COG5151 364 HCFVCQGPFPKPPVSPFDESTSSGRYQCELCKSTF 398 (421)
T ss_pred cceeccCCCCCCCCCcccccccccceechhhhhhh
Confidence 4777777776543211111 4567777777777
No 296
>cd06140 DNA_polA_I_Bacillus_like_exo inactive DEDDy 3'-5' exonuclease domain of Bacillus stearothermophilus DNA polymerase I and similar family-A DNA polymerases. Bacillus stearothermophilus-like Polymerase I (Pol I), a subgroup of the family-A DNA polymerases, contains an inactive DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase region. The exonuclease-like domain of these proteins possess the same fold as the Klenow fragment (KF) of Escherichia coli Pol I, but does not contain the four critical metal-binding residues necessary for activity. The function of this domain is unknown. It might act as a spacer between the polymerase and the 5'-3' exonuclease domains. Some members of this subgroup, such as those from Bacillus sphaericus and Thermus aquaticus, are thermostable DNA polymerases.
Probab=25.66 E-value=66 Score=24.31 Aligned_cols=29 Identities=21% Similarity=0.223 Sum_probs=21.9
Q ss_pred HHHHHHHHHhcCCCCCcccccCCCCeEEEeechhhhhhhhc
Q 025404 204 VKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLR 244 (253)
Q Consensus 204 v~~~l~~~~~~~~~~~~~~~~~~~~~~lv~h~~~~D~~~l~ 244 (253)
+...+.+++.+ .+...|+||+.+|+.+|.
T Consensus 44 ~~~~l~~~l~~------------~~~~ki~~d~K~~~~~l~ 72 (178)
T cd06140 44 DLAALKEWLED------------EKIPKVGHDAKRAYVALK 72 (178)
T ss_pred HHHHHHHHHhC------------CCCceeccchhHHHHHHH
Confidence 45567777832 445789999999999984
No 297
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=25.65 E-value=26 Score=21.76 Aligned_cols=24 Identities=13% Similarity=0.313 Sum_probs=14.1
Q ss_pred CCCCcCCccccccc--c-cccccccCC
Q 025404 67 LSKAHCSGIFSDRG--C-NLCMNIFDS 90 (253)
Q Consensus 67 ~~C~~C~~~f~~~~--C-~~C~k~f~~ 90 (253)
..|..||+.-.... | +.|++.+..
T Consensus 4 kHC~~CG~~Ip~~~~fCS~~C~~~~~k 30 (59)
T PF09889_consen 4 KHCPVCGKPIPPDESFCSPKCREEYRK 30 (59)
T ss_pred CcCCcCCCcCCcchhhhCHHHHHHHHH
Confidence 34777776665443 6 467665553
No 298
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=25.56 E-value=46 Score=25.71 Aligned_cols=20 Identities=30% Similarity=0.607 Sum_probs=12.6
Q ss_pred CCCCCCcccccccccccCCH
Q 025404 8 PKRSTARHKCVACYKQFKRK 27 (253)
Q Consensus 8 ~~~~~k~~~C~~C~k~f~~~ 27 (253)
|...+..|+|+.|=-.|..+
T Consensus 125 ~~~~~~~~~CPiCl~~~sek 144 (187)
T KOG0320|consen 125 PLRKEGTYKCPICLDSVSEK 144 (187)
T ss_pred ccccccccCCCceecchhhc
Confidence 34445568888886665543
No 299
>PF11238 DUF3039: Protein of unknown function (DUF3039); InterPro: IPR021400 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=25.53 E-value=21 Score=21.91 Aligned_cols=8 Identities=38% Similarity=1.161 Sum_probs=4.6
Q ss_pred cccccccc
Q 025404 81 CNLCMNIF 88 (253)
Q Consensus 81 C~~C~k~f 88 (253)
|+.|.+.|
T Consensus 47 CP~Ck~iy 54 (58)
T PF11238_consen 47 CPECKEIY 54 (58)
T ss_pred CcCHHHHH
Confidence 66665554
No 300
>PF12083 DUF3560: Domain of unknown function (DUF3560); InterPro: IPR021944 This presumed domain is functionally uncharacterised. This domain is found in bacteria. This domain is about 120 amino acids in length. This domain has a conserved GHHSE sequence motif.
Probab=25.46 E-value=52 Score=23.90 Aligned_cols=27 Identities=26% Similarity=0.239 Sum_probs=17.3
Q ss_pred CCHHHHHHHHHHHHhcCCCCCcccccCCCCeEEEeechh
Q 025404 199 MPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLE 237 (253)
Q Consensus 199 ~~~~~v~~~l~~~~~~~~~~~~~~~~~~~~~~lv~h~~~ 237 (253)
..+.+....+.+.|. + +|| |||||.-+
T Consensus 26 ~~~~~~a~~~~~~ip-----~-GQP------IlVGHHSE 52 (126)
T PF12083_consen 26 EAAYEAANRMAEAIP-----F-GQP------ILVGHHSE 52 (126)
T ss_pred HHHHHHHHHHHhccC-----C-CCC------eeccccch
Confidence 345566777777772 2 333 99998644
No 301
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=25.04 E-value=36 Score=20.27 Aligned_cols=7 Identities=29% Similarity=0.814 Sum_probs=4.0
Q ss_pred ccccccc
Q 025404 45 KCAVCQK 51 (253)
Q Consensus 45 ~C~~C~~ 51 (253)
.|+.||.
T Consensus 22 fCP~Cg~ 28 (50)
T PRK00432 22 FCPRCGS 28 (50)
T ss_pred cCcCCCc
Confidence 5666653
No 302
>PRK05978 hypothetical protein; Provisional
Probab=24.87 E-value=43 Score=25.11 Aligned_cols=31 Identities=19% Similarity=0.289 Sum_probs=13.9
Q ss_pred ccccccccccCHHHHhhhhCCCCCCCcCCcccccc
Q 025404 45 KCAVCQKLSKSFESLREHLTGPLSKAHCSGIFSDR 79 (253)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~~~~~~C~~C~~~f~~~ 79 (253)
+|+.||+.=-....|+.+ -.|+.||..|...
T Consensus 35 rCP~CG~G~LF~g~Lkv~----~~C~~CG~~~~~~ 65 (148)
T PRK05978 35 RCPACGEGKLFRAFLKPV----DHCAACGEDFTHH 65 (148)
T ss_pred cCCCCCCCcccccccccC----CCccccCCccccC
Confidence 677776533222333222 2355555544433
No 303
>PRK00420 hypothetical protein; Validated
Probab=24.65 E-value=42 Score=23.84 Aligned_cols=9 Identities=33% Similarity=0.733 Sum_probs=4.5
Q ss_pred ccccccccc
Q 025404 45 KCAVCQKLS 53 (253)
Q Consensus 45 ~C~~C~~~f 53 (253)
.|+.||..+
T Consensus 25 ~CP~Cg~pL 33 (112)
T PRK00420 25 HCPVCGLPL 33 (112)
T ss_pred CCCCCCCcc
Confidence 455555433
No 304
>PRK10220 hypothetical protein; Provisional
Probab=24.22 E-value=45 Score=23.42 Aligned_cols=9 Identities=22% Similarity=0.848 Sum_probs=4.7
Q ss_pred ccccccccC
Q 025404 81 CNLCMNIFD 89 (253)
Q Consensus 81 C~~C~k~f~ 89 (253)
|+.|+.-+.
T Consensus 23 CpeC~hEW~ 31 (111)
T PRK10220 23 CPECAHEWN 31 (111)
T ss_pred CCcccCcCC
Confidence 555554444
No 305
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=23.82 E-value=92 Score=27.13 Aligned_cols=21 Identities=24% Similarity=0.431 Sum_probs=17.2
Q ss_pred ccccc---cccCChHHHHHHHHHc
Q 025404 81 CNLCM---NIFDSPSSLIKHKEAC 101 (253)
Q Consensus 81 C~~C~---k~f~~~~~l~~H~~~h 101 (253)
|-.|+ +.|.+....+.||+.-
T Consensus 220 CL~CN~~~~~f~sleavr~HM~~K 243 (390)
T KOG2785|consen 220 CLFCNELGRPFSSLEAVRAHMRDK 243 (390)
T ss_pred EEEeccccCcccccHHHHHHHhhc
Confidence 55666 9999999999999753
No 306
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=23.30 E-value=42 Score=18.42 Aligned_cols=7 Identities=43% Similarity=1.122 Sum_probs=3.2
Q ss_pred ccccccc
Q 025404 46 CAVCQKL 52 (253)
Q Consensus 46 C~~C~~~ 52 (253)
|.+|+..
T Consensus 11 C~~C~~~ 17 (36)
T PF11781_consen 11 CPVCGSR 17 (36)
T ss_pred CCCCCCe
Confidence 4444433
No 307
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=23.23 E-value=47 Score=19.42 Aligned_cols=6 Identities=33% Similarity=1.187 Sum_probs=2.8
Q ss_pred cccccc
Q 025404 46 CAVCQK 51 (253)
Q Consensus 46 C~~C~~ 51 (253)
|+.||.
T Consensus 3 Cp~Cg~ 8 (52)
T smart00661 3 CPKCGN 8 (52)
T ss_pred CCCCCC
Confidence 444543
No 308
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=23.20 E-value=40 Score=24.32 Aligned_cols=10 Identities=20% Similarity=0.471 Sum_probs=6.2
Q ss_pred ccccccccccC
Q 025404 45 KCAVCQKLSKS 55 (253)
Q Consensus 45 ~C~~C~~~f~~ 55 (253)
.| .||..|..
T Consensus 72 ~C-~Cg~~~~~ 81 (124)
T PRK00762 72 EC-ECGYEGVV 81 (124)
T ss_pred Ee-eCcCcccc
Confidence 67 77766544
No 309
>PF15616 TerY-C: TerY-C metal binding domain
Probab=22.98 E-value=39 Score=24.69 Aligned_cols=22 Identities=23% Similarity=0.498 Sum_probs=15.7
Q ss_pred CCCcCCcccccccccccccccCC
Q 025404 68 SKAHCSGIFSDRGCNLCMNIFDS 90 (253)
Q Consensus 68 ~C~~C~~~f~~~~C~~C~k~f~~ 90 (253)
-|+.||..+....| .|||.|-.
T Consensus 79 gCP~CGn~~~fa~C-~CGkl~Ci 100 (131)
T PF15616_consen 79 GCPHCGNQYAFAVC-GCGKLFCI 100 (131)
T ss_pred CCCCCcChhcEEEe-cCCCEEEe
Confidence 48888887776667 58877763
No 310
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=22.97 E-value=35 Score=19.01 Aligned_cols=7 Identities=29% Similarity=0.643 Sum_probs=3.2
Q ss_pred ccccccc
Q 025404 81 CNLCMNI 87 (253)
Q Consensus 81 C~~C~k~ 87 (253)
|..||+.
T Consensus 31 C~~C~~~ 37 (39)
T PF01096_consen 31 CCNCGHR 37 (39)
T ss_dssp ESSSTEE
T ss_pred eCCCCCe
Confidence 4445443
No 311
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=22.95 E-value=50 Score=18.87 Aligned_cols=18 Identities=17% Similarity=0.492 Sum_probs=14.0
Q ss_pred ccccccccccCCHHHHHH
Q 025404 15 HKCVACYKQFKRKDHLIE 32 (253)
Q Consensus 15 ~~C~~C~k~f~~~~~l~~ 32 (253)
-.|..|++.|+.......
T Consensus 9 K~C~~C~rpf~WRKKW~~ 26 (42)
T PF10013_consen 9 KICPVCGRPFTWRKKWAR 26 (42)
T ss_pred CcCcccCCcchHHHHHHH
Confidence 369999999998776653
No 312
>PRK07218 replication factor A; Provisional
Probab=22.90 E-value=42 Score=29.89 Aligned_cols=21 Identities=10% Similarity=0.260 Sum_probs=14.8
Q ss_pred CCCCcCCcccccccccccccc
Q 025404 67 LSKAHCSGIFSDRGCNLCMNI 87 (253)
Q Consensus 67 ~~C~~C~~~f~~~~C~~C~k~ 87 (253)
..|+.|++......|+.||+.
T Consensus 298 ~rCP~C~r~v~~~~C~~hG~v 318 (423)
T PRK07218 298 ERCPECGRVIQKGQCRSHGAV 318 (423)
T ss_pred ecCcCccccccCCcCCCCCCc
Confidence 357788877776667777744
No 313
>TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF. A previously described regulatory effect of HypF mutatation is attributable to loss of activity of a regulatory hydrogenase. A zinc finger-like region CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported the regulatory hypothesis. However, more recent work (PUBMED:11375153) shows the direct effect is on the activity of expressed hydrogenases with nickel/iron centers, rather than on expression.
Probab=22.87 E-value=15 Score=34.97 Aligned_cols=13 Identities=31% Similarity=0.299 Sum_probs=8.4
Q ss_pred CHHHHHHHHHHHH
Q 025404 200 PLKEVKDKILEIL 212 (253)
Q Consensus 200 ~~~~v~~~l~~~~ 212 (253)
+.+++.++|...+
T Consensus 301 ~~~e~~~~l~~~~ 313 (711)
T TIGR00143 301 DNAEILDKLQGIA 313 (711)
T ss_pred CHHHHHHHhcCCc
Confidence 4667777766555
No 314
>COG3545 Predicted esterase of the alpha/beta hydrolase fold [General function prediction only]
Probab=22.33 E-value=1.7e+02 Score=22.74 Aligned_cols=30 Identities=23% Similarity=0.258 Sum_probs=21.2
Q ss_pred CCCHHHHHHHHHHHHhcCCCCCcccccCCCCeEEEeechh
Q 025404 198 AMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLE 237 (253)
Q Consensus 198 ~~~~~~v~~~l~~~~~~~~~~~~~~~~~~~~~~lv~h~~~ 237 (253)
.|.+++=..+|.+.++-. .+..|||||++.
T Consensus 40 ~P~~~dWi~~l~~~v~a~----------~~~~vlVAHSLG 69 (181)
T COG3545 40 APVLDDWIARLEKEVNAA----------EGPVVLVAHSLG 69 (181)
T ss_pred CCCHHHHHHHHHHHHhcc----------CCCeEEEEeccc
Confidence 577888888888777311 144899999975
No 315
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=22.22 E-value=39 Score=26.70 Aligned_cols=47 Identities=21% Similarity=0.419 Sum_probs=37.7
Q ss_pred cccccccccCCHHHHHHhhhhcCC---------CCCcc-cc--ccccccccCHHHHhhhh
Q 025404 16 KCVACYKQFKRKDHLIEHMKISYH---------SVHQP-KC--AVCQKLSKSFESLREHL 63 (253)
Q Consensus 16 ~C~~C~k~f~~~~~l~~H~~~~~H---------~~~~~-~C--~~C~~~f~~~~~l~~H~ 63 (253)
.|..|.+.|.+...|..|+..- | .|... .| +.|+..|.+.-.-+.|+
T Consensus 108 sCs~C~r~~Pt~hLLd~HI~E~-HDs~Fqa~veRG~dMy~ClvEgCt~KFkT~r~RkdH~ 166 (253)
T KOG4173|consen 108 SCSFCKRAFPTGHLLDAHILEW-HDSLFQALVERGQDMYQCLVEGCTEKFKTSRDRKDHM 166 (253)
T ss_pred hhHHHHHhCCchhhhhHHHHHH-HHHHHHHHHHcCccHHHHHHHhhhhhhhhhhhhhhHH
Confidence 8999999999999998887531 3 23333 88 45999999999999998
No 316
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=22.11 E-value=36 Score=22.58 Aligned_cols=10 Identities=30% Similarity=1.002 Sum_probs=5.8
Q ss_pred ccccccccCC
Q 025404 81 CNLCMNIFDS 90 (253)
Q Consensus 81 C~~C~k~f~~ 90 (253)
|..||..|..
T Consensus 49 C~~Cg~~~~~ 58 (81)
T PF05129_consen 49 CRVCGESFQT 58 (81)
T ss_dssp ESSS--EEEE
T ss_pred ecCCCCeEEE
Confidence 8888777754
No 317
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=21.94 E-value=39 Score=17.75 Aligned_cols=11 Identities=27% Similarity=0.634 Sum_probs=2.4
Q ss_pred ccccccccccC
Q 025404 45 KCAVCQKLSKS 55 (253)
Q Consensus 45 ~C~~C~~~f~~ 55 (253)
+|+.|+..+..
T Consensus 4 ~Cp~C~se~~y 14 (30)
T PF08274_consen 4 KCPLCGSEYTY 14 (30)
T ss_dssp --TTT-----E
T ss_pred CCCCCCCccee
Confidence 56666655544
No 318
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=21.84 E-value=40 Score=23.37 Aligned_cols=9 Identities=22% Similarity=0.508 Sum_probs=4.9
Q ss_pred ccccccccC
Q 025404 81 CNLCMNIFD 89 (253)
Q Consensus 81 C~~C~k~f~ 89 (253)
|..||..+.
T Consensus 45 C~~CG~y~~ 53 (99)
T PRK14892 45 CGNCGLYTE 53 (99)
T ss_pred CCCCCCccC
Confidence 666664444
No 319
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=21.82 E-value=44 Score=29.56 Aligned_cols=29 Identities=21% Similarity=0.348 Sum_probs=13.5
Q ss_pred cccccccccccCHHHHhhhhCCCCCCCcCCccccc
Q 025404 44 PKCAVCQKLSKSFESLREHLTGPLSKAHCSGIFSD 78 (253)
Q Consensus 44 ~~C~~C~~~f~~~~~l~~H~~~~~~C~~C~~~f~~ 78 (253)
|.|+.||.+..+.. .+-|.|+.||..+..
T Consensus 351 p~Cp~Cg~~m~S~G------~~g~rC~kCg~~~~~ 379 (421)
T COG1571 351 PVCPRCGGRMKSAG------RNGFRCKKCGTRARE 379 (421)
T ss_pred CCCCccCCchhhcC------CCCcccccccccCCc
Confidence 35555554443332 114555555555543
No 320
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=21.78 E-value=37 Score=18.41 Aligned_cols=6 Identities=33% Similarity=0.794 Sum_probs=2.8
Q ss_pred cccccc
Q 025404 81 CNLCMN 86 (253)
Q Consensus 81 C~~C~k 86 (253)
|+.||.
T Consensus 25 C~~Cg~ 30 (34)
T PF14803_consen 25 CPACGF 30 (34)
T ss_dssp ETTTTE
T ss_pred CCCCCC
Confidence 444543
No 321
>KOG4317 consensus Predicted Zn-finger protein [Function unknown]
Probab=21.67 E-value=23 Score=29.86 Aligned_cols=26 Identities=15% Similarity=0.575 Sum_probs=15.7
Q ss_pred ccccccccccCHHHHhhhhCCCCCCCcCCcccccccc
Q 025404 45 KCAVCQKLSKSFESLREHLTGPLSKAHCSGIFSDRGC 81 (253)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~~~~~~C~~C~~~f~~~~C 81 (253)
.|..|+.-| ..|.|+.|+-.+-+..|
T Consensus 9 ~C~ic~vq~-----------~~YtCPRCn~~YCsl~C 34 (383)
T KOG4317|consen 9 ACGICGVQK-----------REYTCPRCNLLYCSLKC 34 (383)
T ss_pred ecccccccc-----------ccccCCCCCccceeeee
Confidence 566666544 23777777766655544
No 322
>KOG3276 consensus Uncharacterized conserved protein, contains YggU domain [Function unknown]
Probab=21.04 E-value=1.7e+02 Score=20.83 Aligned_cols=47 Identities=19% Similarity=0.225 Sum_probs=34.9
Q ss_pred cCCCCeEEeeeccCCCCcccceeeeccCCHHhhc----CCCCHHHHHHHHHHHHh
Q 025404 163 DEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIK----NAMPLKEVKDKILEILN 213 (253)
Q Consensus 163 ~~~~~~~~~~~v~P~~~i~~~~~~~~Git~~~l~----~~~~~~~v~~~l~~~~~ 213 (253)
+..|.+......+|.. -...+++|+.+++. ..|.-.|+..+|.+|+.
T Consensus 30 d~~g~V~i~Ihakpga----K~s~It~v~~e~V~V~IaApp~eGeANaeLl~yls 80 (125)
T KOG3276|consen 30 DTGGLVQIAIHAKPGA----KQSAITDVGDEAVGVAIAAPPREGEANAELLEYLS 80 (125)
T ss_pred cCCCeEEEEEEecCCc----cccceeeccccccceEEecCCccchhhHHHHHHHH
Confidence 4567777788888854 45678888888874 33677889999999884
No 323
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=20.47 E-value=98 Score=26.41 Aligned_cols=58 Identities=21% Similarity=0.399 Sum_probs=37.3
Q ss_pred ccccccccccCHHHHhhhh-----CCCC------------CCCcCCcccc---cccccccccccCChHHHHHHHHHcc
Q 025404 45 KCAVCQKLSKSFESLREHL-----TGPL------------SKAHCSGIFS---DRGCNLCMNIFDSPSSLIKHKEACS 102 (253)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~-----~~~~------------~C~~C~~~f~---~~~C~~C~k~f~~~~~l~~H~~~h~ 102 (253)
.|+.|+-......+|.+-. -++| -|-.|+.... ...|+.|...|-....--.|...|.
T Consensus 292 eCpiC~ltLVss~hLARSyhhL~PL~~F~Eip~~~~~~~~~Cf~C~~~~~~~~~y~C~~Ck~~FCldCDv~iHesLh~ 369 (378)
T KOG2807|consen 292 ECPICSLTLVSSPHLARSYHHLFPLKPFVEIPETEYNGSRFCFACQGELLSSGRYRCESCKNVFCLDCDVFIHESLHN 369 (378)
T ss_pred cCCccceeEecchHHHHHHHhhcCCcchhhccccccCCCcceeeeccccCCCCcEEchhccceeeccchHHHHhhhhc
Confidence 7888888877777776542 1111 2666632222 2248889888888877777876663
No 324
>cd09018 DEDDy_polA_RNaseD_like_exo DEDDy 3'-5' exonuclease domain of family-A DNA polymerases, RNase D, WRN, and similar proteins. DEDDy exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. They contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDy exonucleases are classified as such because of the presence of a specific YX(3)D pattern at ExoIII. The four conserved acidic residues serve as ligands for the two metal ions required for catalysis. This family of DEDDy exonucleases includes the proofreading domains of family A DNA polymerases, as well as RNases such as RNase D and yeast Rrp6p. The Egalitarian (Egl) and Bacillus-like DNA Polymerase I subfamilies do not possess a completely conserved YX(3)D pattern at the ExoIII motif. In addition, the Bacillus-like DNA polymerase I subfamily has inactive 3'-5' exonucle
Probab=20.36 E-value=1.1e+02 Score=22.13 Aligned_cols=18 Identities=33% Similarity=0.359 Sum_probs=15.1
Q ss_pred CCeEEEeechhhhhhhhc
Q 025404 227 KARLLVGHGLEHDLDSLR 244 (253)
Q Consensus 227 ~~~~lv~h~~~~D~~~l~ 244 (253)
.+...||||+.+|+.+|.
T Consensus 52 ~~~~kv~~d~K~~~~~L~ 69 (150)
T cd09018 52 EKALKVGQNLKYDRGILL 69 (150)
T ss_pred CCCceeeecHHHHHHHHH
Confidence 456789999999999984
No 325
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=20.13 E-value=55 Score=29.29 Aligned_cols=22 Identities=36% Similarity=0.655 Sum_probs=19.7
Q ss_pred ccccccccccCCHHHHHHhhhh
Q 025404 15 HKCVACYKQFKRKDHLIEHMKI 36 (253)
Q Consensus 15 ~~C~~C~k~f~~~~~l~~H~~~ 36 (253)
+-|..|+|+|.+...|..|..+
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 8899999999999999998764
Done!