Query 024455
Match_columns 267
No_of_seqs 398 out of 3159
Neff 9.4
Searched_HMMs 46136
Date Fri Mar 29 04:44:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024455.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024455hhsearch_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 3.7E-35 7.9E-40 235.1 7.8 218 16-263 2-219 (280)
2 cd06143 PAN2_exo DEDDh 3'-5' e 99.9 5.8E-27 1.3E-31 180.9 8.8 113 138-263 1-137 (174)
3 cd06149 ISG20 DEDDh 3'-5' exon 99.9 2.2E-25 4.8E-30 173.1 10.0 110 138-261 1-110 (157)
4 cd06145 REX1_like DEDDh 3'-5' 99.9 3.3E-24 7.1E-29 165.4 9.3 106 138-261 1-107 (150)
5 cd06144 REX4_like DEDDh 3'-5' 99.9 2.3E-23 5E-28 161.3 10.0 111 138-262 1-111 (152)
6 KOG2248 3'-5' exonuclease [Rep 99.9 2.2E-22 4.8E-27 173.8 8.3 116 131-264 212-328 (380)
7 cd06137 DEDDh_RNase DEDDh 3'-5 99.9 4.2E-22 9E-27 155.6 6.8 107 138-262 1-116 (161)
8 KOG2462 C2H2-type Zn-finger pr 99.9 1.9E-22 4.1E-27 163.0 4.3 115 8-124 124-264 (279)
9 PRK07247 DNA polymerase III su 99.8 2.3E-18 4.9E-23 137.9 8.2 97 135-245 5-102 (195)
10 TIGR01406 dnaQ_proteo DNA poly 99.7 2.4E-18 5.2E-23 141.2 5.9 107 137-257 2-122 (225)
11 PRK05711 DNA polymerase III su 99.7 2.6E-18 5.7E-23 141.7 5.9 108 136-257 5-126 (240)
12 KOG2462 C2H2-type Zn-finger pr 99.7 7.6E-19 1.7E-23 142.2 1.7 99 45-151 132-255 (279)
13 PRK05601 DNA polymerase III su 99.7 1.3E-17 2.8E-22 142.7 7.0 98 132-245 43-142 (377)
14 cd06130 DNA_pol_III_epsilon_li 99.7 2.2E-17 4.8E-22 128.4 7.7 108 137-259 1-115 (156)
15 PRK09146 DNA polymerase III su 99.7 2E-17 4.3E-22 136.7 7.8 114 131-258 43-166 (239)
16 PRK06310 DNA polymerase III su 99.7 1.6E-17 3.5E-22 138.4 6.9 112 135-259 7-128 (250)
17 PRK07740 hypothetical protein; 99.7 5E-17 1.1E-21 135.0 7.0 113 133-259 57-179 (244)
18 TIGR00573 dnaq exonuclease, DN 99.7 9E-17 2E-21 131.5 7.8 100 133-246 5-105 (217)
19 PRK06807 DNA polymerase III su 99.7 9.9E-17 2.1E-21 137.4 8.0 111 134-258 7-125 (313)
20 cd06131 DNA_pol_III_epsilon_Ec 99.7 8.6E-17 1.9E-21 126.6 6.2 108 137-258 1-121 (167)
21 COG2176 PolC DNA polymerase II 99.7 7.3E-17 1.6E-21 152.1 5.9 120 132-265 418-550 (1444)
22 PRK06195 DNA polymerase III su 99.7 2.9E-16 6.3E-21 135.0 8.7 107 136-257 2-116 (309)
23 PRK07983 exodeoxyribonuclease 99.7 2.2E-16 4.7E-21 128.7 7.4 101 137-258 2-102 (219)
24 KOG1074 Transcriptional repres 99.7 9.9E-17 2.1E-21 146.3 5.7 67 11-79 602-681 (958)
25 PRK07246 bifunctional ATP-depe 99.6 2.6E-16 5.6E-21 150.8 8.1 110 134-257 6-121 (820)
26 PRK09145 DNA polymerase III su 99.6 5.6E-16 1.2E-20 125.6 7.6 112 133-258 27-148 (202)
27 PRK06309 DNA polymerase III su 99.6 5.8E-16 1.2E-20 128.0 7.6 108 136-259 3-119 (232)
28 PRK08517 DNA polymerase III su 99.6 8.3E-16 1.8E-20 128.2 8.1 100 131-245 64-164 (257)
29 PRK06063 DNA polymerase III su 99.6 2E-15 4.4E-20 129.6 9.3 109 134-258 14-131 (313)
30 KOG1074 Transcriptional repres 99.6 3.7E-16 8E-21 142.7 4.7 78 81-162 608-691 (958)
31 smart00479 EXOIII exonuclease 99.6 6.3E-16 1.4E-20 121.7 5.3 109 137-259 2-120 (169)
32 PRK07883 hypothetical protein; 99.6 1.6E-15 3.6E-20 139.5 8.2 112 133-258 13-132 (557)
33 PRK07942 DNA polymerase III su 99.6 1.8E-15 3.8E-20 124.9 7.0 116 134-258 5-131 (232)
34 PRK08074 bifunctional ATP-depe 99.6 2.1E-15 4.6E-20 146.7 8.3 109 135-257 3-120 (928)
35 PRK06722 exonuclease; Provisio 99.6 2.5E-15 5.5E-20 126.0 7.5 97 135-245 5-107 (281)
36 cd06136 TREX1_2 DEDDh 3'-5' ex 99.6 2.2E-15 4.8E-20 119.5 6.5 113 137-259 1-138 (177)
37 PRK05168 ribonuclease T; Provi 99.6 6.4E-15 1.4E-19 119.9 6.6 121 134-259 16-155 (211)
38 PRK07748 sporulation inhibitor 99.6 7.4E-15 1.6E-19 119.4 7.0 108 136-257 5-130 (207)
39 cd06134 RNaseT DEDDh 3'-5' exo 99.5 4.8E-15 1E-19 118.7 4.4 119 136-259 6-143 (189)
40 TIGR01407 dinG_rel DnaQ family 99.5 1.4E-14 3E-19 140.3 8.5 107 137-257 2-116 (850)
41 TIGR01298 RNaseT ribonuclease 99.5 1.2E-14 2.7E-19 117.3 6.8 121 134-259 7-146 (200)
42 TIGR01405 polC_Gram_pos DNA po 99.5 6.6E-15 1.4E-19 144.5 5.9 113 133-259 188-308 (1213)
43 COG0847 DnaQ DNA polymerase II 99.5 2.4E-14 5.2E-19 119.5 7.8 97 135-245 13-112 (243)
44 PRK05359 oligoribonuclease; Pr 99.5 1.1E-14 2.5E-19 115.5 4.4 116 135-258 3-134 (181)
45 cd06127 DEDDh DEDDh 3'-5' exon 99.5 2.5E-14 5.4E-19 110.9 6.2 108 138-259 1-117 (159)
46 KOG3608 Zn finger proteins [Ge 99.5 1.7E-14 3.7E-19 120.3 3.7 110 15-126 178-315 (467)
47 cd06138 ExoI_N N-terminal DEDD 99.5 5E-14 1.1E-18 112.4 5.4 95 139-245 2-102 (183)
48 PF00929 RNase_T: Exonuclease; 99.5 2E-14 4.3E-19 111.8 2.4 94 138-244 1-99 (164)
49 cd06135 Orn DEDDh 3'-5' exonuc 99.4 1.8E-13 4E-18 108.1 4.2 111 138-256 2-128 (173)
50 PRK09182 DNA polymerase III su 99.4 6E-13 1.3E-17 113.1 6.3 98 134-247 36-140 (294)
51 KOG3623 Homeobox transcription 99.4 1.5E-13 3.4E-18 123.9 2.5 107 14-124 210-330 (1007)
52 KOG3576 Ovo and related transc 99.3 3.2E-13 7E-18 104.7 1.8 67 10-78 113-185 (267)
53 cd06133 ERI-1_3'hExo_like DEDD 99.3 2.6E-12 5.6E-17 101.8 6.7 109 137-259 1-131 (176)
54 PRK00448 polC DNA polymerase I 99.3 5.9E-12 1.3E-16 125.5 7.3 110 134-257 418-535 (1437)
55 PTZ00315 2'-phosphotransferase 99.3 1E-11 2.2E-16 112.6 7.6 105 135-243 56-169 (582)
56 KOG3608 Zn finger proteins [Ge 99.2 8.1E-12 1.8E-16 104.5 4.6 114 14-130 237-379 (467)
57 KOG3623 Homeobox transcription 99.2 7.3E-12 1.6E-16 113.3 3.3 81 4-98 884-970 (1007)
58 PRK11779 sbcB exonuclease I; P 99.2 6E-11 1.3E-15 106.7 8.1 99 135-245 6-111 (476)
59 KOG3576 Ovo and related transc 99.2 3.6E-12 7.8E-17 98.9 -0.8 97 45-148 119-221 (267)
60 KOG1275 PAB-dependent poly(A) 99.1 3.4E-11 7.4E-16 111.5 4.2 119 132-263 907-1049(1118)
61 PHA02768 hypothetical protein; 98.9 3.9E-10 8.5E-15 69.7 1.7 43 14-60 5-48 (55)
62 KOG3242 Oligoribonuclease (3'- 98.8 6.6E-10 1.4E-14 84.4 0.8 120 134-262 25-161 (208)
63 PHA00733 hypothetical protein 98.8 2.8E-09 6.1E-14 79.4 4.0 81 11-103 37-124 (128)
64 PHA02768 hypothetical protein; 98.7 8.4E-09 1.8E-13 63.8 2.2 42 80-121 7-49 (55)
65 PHA00733 hypothetical protein 98.5 9.9E-08 2.1E-12 71.1 4.5 57 9-69 68-126 (128)
66 PLN03086 PRLI-interacting fact 98.5 2.7E-07 5.8E-12 84.1 6.1 95 11-126 450-563 (567)
67 COG1949 Orn Oligoribonuclease 98.3 1.7E-07 3.8E-12 70.7 0.8 120 134-262 5-141 (184)
68 PHA00616 hypothetical protein 98.3 4.2E-07 9E-12 53.5 1.5 33 80-112 3-35 (44)
69 PHA00616 hypothetical protein 98.2 6.1E-07 1.3E-11 52.8 1.8 34 14-49 1-35 (44)
70 PHA00732 hypothetical protein 98.2 8.2E-07 1.8E-11 60.1 2.4 44 14-63 1-44 (79)
71 KOG3993 Transcription factor ( 98.2 3.2E-07 6.8E-12 79.1 0.4 87 14-103 267-381 (500)
72 KOG3993 Transcription factor ( 98.2 1E-06 2.2E-11 76.0 3.2 48 14-63 295-376 (500)
73 PF13465 zf-H2C2_2: Zinc-finge 98.2 5.5E-07 1.2E-11 47.5 1.0 25 29-55 1-26 (26)
74 PLN03086 PRLI-interacting fact 98.2 4.5E-06 9.8E-11 76.3 6.9 116 14-149 407-551 (567)
75 cd05160 DEDDy_DNA_polB_exo DED 98.0 1.2E-05 2.7E-10 64.8 5.9 89 138-244 2-96 (199)
76 PF00096 zf-C2H2: Zinc finger, 97.8 1E-05 2.3E-10 41.2 1.5 22 15-36 1-22 (23)
77 PF13465 zf-H2C2_2: Zinc-finge 97.8 1.4E-05 3E-10 42.1 1.5 22 93-114 1-25 (26)
78 PF00096 zf-C2H2: Zinc finger, 97.8 1.7E-05 3.7E-10 40.4 1.8 21 81-101 3-23 (23)
79 PF13894 zf-C2H2_4: C2H2-type 97.4 0.00011 2.5E-09 37.4 2.2 22 15-36 1-22 (24)
80 PF05605 zf-Di19: Drought indu 97.4 0.00023 4.9E-09 44.6 3.7 46 14-63 2-49 (54)
81 PF13894 zf-C2H2_4: C2H2-type 97.4 0.00012 2.6E-09 37.3 1.8 22 81-102 3-24 (24)
82 PF13912 zf-C2H2_6: C2H2-type 97.4 0.00013 2.7E-09 38.7 1.9 23 14-36 1-23 (27)
83 PHA00732 hypothetical protein 97.3 0.00017 3.8E-09 48.8 2.5 19 45-63 3-21 (79)
84 KOG0542 Predicted exonuclease 97.3 0.00025 5.4E-09 57.8 3.4 77 138-214 59-145 (280)
85 cd06125 DnaQ_like_exo DnaQ-lik 97.1 0.001 2.2E-08 47.1 4.5 30 229-258 45-83 (96)
86 PF09237 GAGA: GAGA factor; I 97.0 0.00056 1.2E-08 41.3 2.1 26 81-106 27-52 (54)
87 PF12756 zf-C2H2_2: C2H2 type 96.9 0.00062 1.3E-08 48.1 1.9 73 16-101 1-73 (100)
88 COG5189 SFP1 Putative transcri 96.8 0.00038 8.3E-09 58.3 0.9 29 11-40 346-376 (423)
89 PF13912 zf-C2H2_6: C2H2-type 96.8 0.00058 1.3E-08 36.0 1.2 22 81-102 4-25 (27)
90 smart00355 ZnF_C2H2 zinc finge 96.8 0.0012 2.5E-08 34.0 2.4 24 15-40 1-24 (26)
91 PF05605 zf-Di19: Drought indu 96.7 0.0022 4.7E-08 40.1 3.3 51 45-103 4-54 (54)
92 smart00355 ZnF_C2H2 zinc finge 96.6 0.0016 3.5E-08 33.5 2.1 22 81-102 3-24 (26)
93 PF09237 GAGA: GAGA factor; I 96.6 0.0023 5E-08 38.7 2.5 27 10-36 20-46 (54)
94 PF12874 zf-met: Zinc-finger o 96.3 0.002 4.3E-08 33.2 1.1 22 15-36 1-22 (25)
95 PF01612 DNA_pol_A_exo1: 3'-5' 96.2 0.022 4.8E-07 44.4 7.0 85 136-256 21-107 (176)
96 PF12756 zf-C2H2_2: C2H2 type 95.8 0.0041 8.8E-08 43.9 1.1 20 44-63 51-70 (100)
97 PRK04860 hypothetical protein; 95.7 0.0053 1.1E-07 47.5 1.4 38 13-56 118-156 (160)
98 PF12874 zf-met: Zinc-finger o 95.4 0.0083 1.8E-07 30.8 1.1 21 81-101 3-23 (25)
99 PF12171 zf-C2H2_jaz: Zinc-fin 95.2 0.0059 1.3E-07 32.2 0.2 22 15-36 2-23 (27)
100 PF13909 zf-H2C2_5: C2H2-type 95.0 0.017 3.6E-07 29.4 1.6 22 81-103 3-24 (24)
101 PF13913 zf-C2HC_2: zinc-finge 94.9 0.02 4.2E-07 29.6 1.7 19 81-100 5-23 (25)
102 cd05780 DNA_polB_Kod1_like_exo 94.8 0.11 2.5E-06 41.6 6.6 83 136-244 4-89 (195)
103 COG2925 SbcB Exonuclease I [DN 94.5 0.16 3.5E-06 44.3 7.2 100 134-245 8-114 (475)
104 cd05785 DNA_polB_like2_exo Unc 94.5 0.12 2.6E-06 41.9 6.2 36 198-244 55-91 (207)
105 PF13909 zf-H2C2_5: C2H2-type 94.4 0.022 4.7E-07 29.0 1.1 21 15-36 1-21 (24)
106 COG5189 SFP1 Putative transcri 94.4 0.016 3.5E-07 48.9 0.9 57 42-98 347-418 (423)
107 PF12171 zf-C2H2_jaz: Zinc-fin 94.3 0.01 2.2E-07 31.3 -0.3 19 81-99 4-22 (27)
108 cd06146 mut-7_like_exo DEDDy 3 94.1 0.17 3.8E-06 40.5 6.4 45 203-259 69-121 (193)
109 PF13913 zf-C2HC_2: zinc-finge 94.1 0.043 9.4E-07 28.3 1.9 21 15-36 3-23 (25)
110 cd06139 DNA_polA_I_Ecoli_like_ 94.1 0.041 8.9E-07 43.7 2.7 51 197-259 48-100 (193)
111 KOG2231 Predicted E3 ubiquitin 93.4 0.11 2.3E-06 48.9 4.4 74 23-102 123-206 (669)
112 PF10571 UPF0547: Uncharacteri 93.3 0.048 1E-06 28.4 1.2 22 68-89 2-25 (26)
113 smart00451 ZnF_U1 U1-like zinc 93.3 0.066 1.4E-06 29.8 1.9 23 14-36 3-25 (35)
114 COG5018 KapD Inhibitor of the 93.1 0.0095 2.1E-07 45.8 -2.4 77 138-214 7-92 (210)
115 cd05781 DNA_polB_B3_exo DEDDy 93.0 0.5 1.1E-05 37.7 7.2 75 136-244 4-81 (188)
116 COG5048 FOG: Zn-finger [Genera 92.8 0.037 8E-07 49.5 0.4 112 13-126 288-441 (467)
117 cd05784 DNA_polB_II_exo DEDDy 92.5 0.45 9.7E-06 38.2 6.3 38 196-244 46-84 (193)
118 PF03104 DNA_pol_B_exo1: DNA p 92.2 0.36 7.7E-06 41.7 5.9 91 133-244 155-255 (325)
119 KOG2893 Zn finger protein [Gen 92.1 0.052 1.1E-06 44.0 0.5 31 43-73 10-41 (341)
120 PRK05755 DNA polymerase I; Pro 90.7 0.5 1.1E-05 46.9 5.8 45 203-259 357-403 (880)
121 cd06141 WRN_exo DEDDy 3'-5' ex 90.5 0.68 1.5E-05 36.0 5.3 45 206-262 63-109 (170)
122 cd05779 DNA_polB_epsilon_exo D 90.3 1.2 2.6E-05 36.1 6.7 36 198-244 70-106 (204)
123 cd05783 DNA_polB_B1_exo DEDDy 90.3 2.1 4.6E-05 34.6 8.2 35 197-244 69-104 (204)
124 KOG4173 Alpha-SNAP protein [In 89.5 0.27 5.8E-06 39.1 2.2 98 1-112 66-181 (253)
125 COG4049 Uncharacterized protei 89.3 0.17 3.6E-06 31.2 0.7 28 9-36 12-39 (65)
126 cd05777 DNA_polB_delta_exo DED 89.0 2 4.3E-05 35.4 7.3 38 196-244 66-104 (230)
127 PF09538 FYDLN_acid: Protein o 89.0 0.24 5.1E-06 35.7 1.5 11 81-91 29-39 (108)
128 PF09986 DUF2225: Uncharacteri 88.4 0.23 5E-06 40.5 1.3 13 45-57 7-19 (214)
129 smart00451 ZnF_U1 U1-like zinc 88.3 0.29 6.4E-06 27.1 1.3 19 81-99 6-24 (35)
130 cd05776 DNA_polB_alpha_exo ina 87.9 0.5 1.1E-05 39.1 3.0 38 195-243 76-114 (234)
131 PRK04860 hypothetical protein; 87.4 0.38 8.3E-06 37.3 1.9 28 80-111 121-148 (160)
132 cd05778 DNA_polB_zeta_exo inac 86.8 1.9 4.2E-05 35.5 5.9 41 193-244 73-114 (231)
133 PF09845 DUF2072: Zn-ribbon co 86.1 0.39 8.4E-06 35.5 1.2 22 66-87 1-28 (131)
134 KOG2231 Predicted E3 ubiquitin 85.9 0.65 1.4E-05 43.8 2.9 29 45-73 184-213 (669)
135 KOG2785 C2H2-type Zn-finger pr 85.3 2.4 5.3E-05 37.1 5.8 47 81-127 169-244 (390)
136 PF09538 FYDLN_acid: Protein o 85.2 0.45 9.7E-06 34.2 1.2 28 45-78 11-38 (108)
137 PF13482 RNase_H_2: RNase_H su 83.2 1.7 3.6E-05 33.5 3.8 21 227-247 56-77 (164)
138 cd06148 Egl_like_exo DEDDy 3'- 82.7 3.3 7.2E-05 33.2 5.4 41 206-258 55-97 (197)
139 cd00007 35EXOc 3'-5' exonuclea 82.4 1.2 2.5E-05 33.6 2.6 45 202-259 40-87 (155)
140 TIGR02098 MJ0042_CXXC MJ0042 f 82.3 0.4 8.7E-06 27.3 -0.0 14 15-28 3-16 (38)
141 PTZ00166 DNA polymerase delta 82.0 3 6.4E-05 42.3 5.8 38 195-243 324-362 (1054)
142 PHA02528 43 DNA polymerase; Pr 81.0 6.8 0.00015 38.9 7.7 101 133-244 104-211 (881)
143 KOG3657 Mitochondrial DNA poly 79.9 1.2 2.6E-05 42.9 2.1 31 226-256 239-273 (1075)
144 smart00614 ZnF_BED BED zinc fi 79.9 1.3 2.9E-05 26.9 1.7 23 80-102 20-48 (50)
145 TIGR02300 FYDLN_acid conserved 79.9 1.1 2.3E-05 33.0 1.4 24 68-91 11-39 (129)
146 PF09986 DUF2225: Uncharacteri 79.8 0.26 5.7E-06 40.2 -2.0 22 12-33 3-24 (214)
147 cd05782 DNA_polB_like1_exo Unc 79.7 2 4.4E-05 34.8 3.2 34 199-244 76-110 (208)
148 PF10108 DNA_pol_B_exo2: Predi 79.4 2 4.4E-05 34.8 3.0 33 200-244 36-69 (209)
149 COG4049 Uncharacterized protei 78.6 0.96 2.1E-05 27.9 0.7 23 41-63 14-37 (65)
150 PRK00398 rpoP DNA-directed RNA 78.5 0.81 1.8E-05 27.3 0.4 23 66-88 3-31 (46)
151 PHA02570 dexA exonuclease; Pro 78.2 6.7 0.00015 31.9 5.6 99 138-244 4-124 (220)
152 PF13717 zinc_ribbon_4: zinc-r 78.1 0.81 1.7E-05 25.8 0.3 13 16-28 4-16 (36)
153 PHA00626 hypothetical protein 78.1 0.66 1.4E-05 28.7 -0.1 12 66-77 23-34 (59)
154 COG5236 Uncharacterized conser 77.9 2.1 4.6E-05 36.9 2.8 102 15-124 152-272 (493)
155 PF05443 ROS_MUCR: ROS/MUCR tr 77.8 1.3 2.8E-05 33.1 1.4 24 81-107 75-98 (132)
156 PF14353 CpXC: CpXC protein 77.8 1.2 2.6E-05 33.1 1.2 14 81-94 41-54 (128)
157 TIGR02300 FYDLN_acid conserved 77.4 1.4 3E-05 32.4 1.4 27 45-77 11-37 (129)
158 KOG2893 Zn finger protein [Gen 77.4 0.84 1.8E-05 37.2 0.3 42 16-63 12-54 (341)
159 smart00834 CxxC_CXXC_SSSS Puta 77.2 0.98 2.1E-05 25.9 0.5 6 81-86 29-34 (41)
160 PRK10829 ribonuclease D; Provi 76.9 5.7 0.00012 35.3 5.4 44 206-261 64-109 (373)
161 COG3364 Zn-ribbon containing p 76.5 1.2 2.6E-05 31.2 0.8 21 66-86 2-28 (112)
162 PF13719 zinc_ribbon_5: zinc-r 76.1 0.98 2.1E-05 25.6 0.3 13 16-28 4-16 (37)
163 PTZ00303 phosphatidylinositol 75.9 0.26 5.7E-06 46.8 -3.3 71 45-123 462-536 (1374)
164 PF09723 Zn-ribbon_8: Zinc rib 75.9 1 2.2E-05 26.4 0.3 9 45-53 7-15 (42)
165 cd00729 rubredoxin_SM Rubredox 75.8 1.3 2.7E-05 24.7 0.7 20 67-86 3-26 (34)
166 PF15269 zf-C2H2_7: Zinc-finge 75.2 3.4 7.4E-05 24.3 2.3 23 14-36 20-42 (54)
167 PF13240 zinc_ribbon_2: zinc-r 75.1 1.6 3.5E-05 21.9 0.9 19 69-87 2-22 (23)
168 PF15135 UPF0515: Uncharacteri 74.9 1.4 3E-05 36.2 1.0 58 11-79 109-168 (278)
169 cd00350 rubredoxin_like Rubred 74.8 1.5 3.2E-05 24.2 0.7 18 68-85 3-24 (33)
170 smart00531 TFIIE Transcription 74.5 2.8 6E-05 32.0 2.5 33 45-77 101-134 (147)
171 PRK00464 nrdR transcriptional 74.3 0.85 1.8E-05 35.1 -0.4 15 198-212 102-116 (154)
172 smart00659 RPOLCX RNA polymera 73.7 1.5 3.2E-05 26.0 0.6 20 67-86 3-27 (44)
173 TIGR00622 ssl1 transcription f 73.3 3.6 7.8E-05 29.7 2.6 22 12-33 13-34 (112)
174 KOG1146 Homeobox protein [Gene 72.5 1.4 3E-05 44.6 0.5 79 15-104 1261-1354(1406)
175 PF02892 zf-BED: BED zinc fing 72.4 2.4 5.1E-05 24.9 1.3 21 80-100 18-42 (45)
176 COG1997 RPL43A Ribosomal prote 72.4 2.3 4.9E-05 29.0 1.3 28 64-91 33-66 (89)
177 PRK04023 DNA polymerase II lar 72.2 2.2 4.8E-05 42.2 1.7 29 165-196 735-763 (1121)
178 cd06129 RNaseD_like DEDDy 3'-5 71.8 19 0.00042 27.6 6.7 33 227-259 66-100 (161)
179 TIGR02605 CxxC_CxxC_SSSS putat 71.5 1.6 3.5E-05 26.7 0.4 10 45-54 7-16 (52)
180 KOG2186 Cell growth-regulating 71.5 1.9 4.1E-05 35.5 1.0 46 14-63 3-48 (276)
181 KOG1146 Homeobox protein [Gene 71.4 2.6 5.5E-05 42.8 2.0 83 17-100 439-540 (1406)
182 PRK14714 DNA polymerase II lar 71.2 3.1 6.7E-05 42.2 2.5 23 66-88 692-719 (1337)
183 PRK05762 DNA polymerase II; Re 70.8 13 0.00027 36.7 6.6 39 195-244 197-236 (786)
184 smart00531 TFIIE Transcription 68.7 3.6 7.8E-05 31.4 1.9 40 10-54 95-134 (147)
185 PF03604 DNA_RNApol_7kD: DNA d 68.1 2.5 5.4E-05 23.2 0.7 19 68-86 2-25 (32)
186 PF13248 zf-ribbon_3: zinc-rib 67.5 3.5 7.6E-05 21.2 1.1 20 68-87 4-25 (26)
187 COG1996 RPC10 DNA-directed RNA 67.3 1.7 3.8E-05 26.3 -0.1 20 67-86 7-32 (49)
188 smart00486 POLBc DNA polymeras 67.3 12 0.00027 33.8 5.5 35 199-244 67-102 (471)
189 COG2888 Predicted Zn-ribbon RN 67.2 4.5 9.7E-05 25.5 1.7 29 45-73 29-57 (61)
190 smart00474 35EXOc 3'-5' exonuc 65.4 5.6 0.00012 30.3 2.5 41 205-259 64-107 (172)
191 COG1198 PriA Primosomal protei 65.0 2.2 4.8E-05 41.2 0.1 31 45-75 437-471 (730)
192 PF14446 Prok-RING_1: Prokaryo 64.6 3.5 7.5E-05 25.6 0.9 22 68-89 7-32 (54)
193 PRK14559 putative protein seri 63.1 6.5 0.00014 37.6 2.8 36 45-91 17-54 (645)
194 smart00734 ZnF_Rad18 Rad18-lik 62.0 7 0.00015 20.2 1.7 19 16-35 3-21 (26)
195 COG1592 Rubrerythrin [Energy p 61.9 3.5 7.6E-05 32.1 0.7 20 66-85 134-156 (166)
196 PF01780 Ribosomal_L37ae: Ribo 61.8 2.7 5.9E-05 29.0 0.1 27 64-90 33-65 (90)
197 TIGR01206 lysW lysine biosynth 61.7 4.6 0.0001 25.1 1.1 8 81-88 25-32 (54)
198 COG3359 Predicted exonuclease 60.6 13 0.00028 30.9 3.7 19 133-151 96-114 (278)
199 PF07191 zinc-ribbons_6: zinc- 60.3 1.2 2.7E-05 29.1 -1.7 35 45-86 3-38 (70)
200 COG0068 HypF Hydrogenase matur 60.2 2.2 4.9E-05 40.5 -0.7 54 17-74 126-181 (750)
201 PRK12496 hypothetical protein; 60.0 3.7 8E-05 32.0 0.5 24 66-89 127-154 (164)
202 COG2331 Uncharacterized protei 58.8 5.7 0.00012 26.3 1.2 31 14-53 12-43 (82)
203 TIGR00373 conserved hypothetic 58.5 11 0.00023 29.2 2.9 28 45-76 111-138 (158)
204 COG4957 Predicted transcriptio 58.3 5.3 0.00011 29.7 1.1 23 81-106 79-101 (148)
205 PRK14873 primosome assembly pr 58.1 2.8 6.1E-05 40.2 -0.4 43 45-87 385-431 (665)
206 COG5236 Uncharacterized conser 57.7 15 0.00032 31.9 3.8 16 87-102 290-305 (493)
207 KOG4167 Predicted DNA-binding 57.2 3.7 8.1E-05 39.1 0.2 25 12-36 790-814 (907)
208 TIGR00280 L37a ribosomal prote 56.8 6 0.00013 27.4 1.1 26 65-90 34-65 (91)
209 PTZ00255 60S ribosomal protein 56.7 6.3 0.00014 27.3 1.2 26 65-90 35-66 (90)
210 PF04857 CAF1: CAF1 family rib 55.9 4.9 0.00011 33.8 0.7 33 227-261 148-199 (262)
211 cd06142 RNaseD_exo DEDDy 3'-5' 55.7 11 0.00023 29.2 2.5 42 204-257 52-95 (178)
212 PRK03976 rpl37ae 50S ribosomal 53.7 7.2 0.00016 27.0 1.1 26 65-90 35-66 (90)
213 KOG1280 Uncharacterized conser 53.4 11 0.00025 32.6 2.4 38 12-50 77-116 (381)
214 PHA02524 43A DNA polymerase su 52.6 11 0.00024 34.8 2.5 35 199-244 178-213 (498)
215 KOG3362 Predicted BBOX Zn-fing 51.8 5 0.00011 30.1 0.1 30 69-99 121-150 (156)
216 COG1773 Rubredoxin [Energy pro 51.5 7 0.00015 24.3 0.7 10 45-54 5-14 (55)
217 PRK09678 DNA-binding transcrip 51.5 3.7 8E-05 27.2 -0.6 6 46-51 4-9 (72)
218 PF05191 ADK_lid: Adenylate ki 51.0 5.8 0.00013 22.3 0.2 8 46-53 4-11 (36)
219 TIGR00595 priA primosomal prot 50.8 5 0.00011 37.3 -0.1 43 45-87 215-262 (505)
220 PF13878 zf-C2H2_3: zinc-finge 50.1 18 0.00039 20.9 2.3 28 75-102 10-39 (41)
221 PF12013 DUF3505: Protein of u 50.0 12 0.00026 26.8 1.8 22 82-103 88-109 (109)
222 cd00730 rubredoxin Rubredoxin; 49.7 9.8 0.00021 23.2 1.1 10 45-54 3-12 (50)
223 PF01927 Mut7-C: Mut7-C RNAse 49.3 12 0.00027 28.4 1.9 19 80-98 126-144 (147)
224 COG4530 Uncharacterized protei 48.9 7.6 0.00017 27.7 0.6 8 81-88 29-36 (129)
225 PRK14559 putative protein seri 48.4 7.9 0.00017 37.1 0.8 36 45-89 3-38 (645)
226 PF07754 DUF1610: Domain of un 48.3 7.4 0.00016 19.8 0.3 11 12-22 14-24 (24)
227 KOG0978 E3 ubiquitin ligase in 47.1 6 0.00013 37.8 -0.2 17 80-96 680-696 (698)
228 PRK06266 transcription initiat 47.0 19 0.00042 28.4 2.7 29 45-77 119-147 (178)
229 PF01363 FYVE: FYVE zinc finge 46.3 9.5 0.00021 24.6 0.8 25 45-76 11-35 (69)
230 COG1571 Predicted DNA-binding 46.2 11 0.00023 34.0 1.2 23 69-91 353-380 (421)
231 KOG2593 Transcription initiati 46.1 16 0.00034 32.8 2.3 34 45-78 130-165 (436)
232 PF07295 DUF1451: Protein of u 44.5 6.8 0.00015 29.9 -0.2 7 81-87 133-139 (146)
233 cd00065 FYVE FYVE domain; Zinc 43.6 12 0.00027 22.9 1.0 25 45-76 4-28 (57)
234 PF00301 Rubredoxin: Rubredoxi 43.4 8.2 0.00018 23.2 0.1 11 45-55 3-13 (47)
235 PF06524 NOA36: NOA36 protein; 41.8 7 0.00015 32.5 -0.5 11 11-21 139-149 (314)
236 PF04438 zf-HIT: HIT zinc fing 40.9 12 0.00027 20.0 0.5 21 68-89 4-24 (30)
237 KOG3408 U1-like Zn-finger-cont 40.5 27 0.00059 25.5 2.4 26 11-36 54-79 (129)
238 KOG2186 Cell growth-regulating 40.4 8.7 0.00019 31.8 -0.2 33 45-78 5-41 (276)
239 PF01155 HypA: Hydrogenase exp 40.3 10 0.00022 27.5 0.2 21 67-87 71-95 (113)
240 PF13453 zf-TFIIB: Transcripti 40.2 24 0.00053 20.2 1.8 16 81-96 22-37 (41)
241 PRK12380 hydrogenase nickel in 39.9 14 0.0003 26.8 0.8 19 67-85 71-93 (113)
242 COG4888 Uncharacterized Zn rib 39.0 2.5 5.3E-05 29.7 -3.0 13 12-24 20-32 (104)
243 COG3357 Predicted transcriptio 39.0 15 0.00033 25.3 0.9 12 67-78 59-70 (97)
244 PF02176 zf-TRAF: TRAF-type zi 38.8 13 0.00027 23.2 0.4 39 13-54 8-53 (60)
245 PF12773 DZR: Double zinc ribb 38.6 22 0.00047 21.2 1.5 35 45-85 14-50 (50)
246 PRK14890 putative Zn-ribbon RN 38.6 16 0.00034 23.1 0.8 8 45-52 27-34 (59)
247 TIGR00100 hypA hydrogenase nic 38.1 15 0.00034 26.6 0.9 20 67-86 71-94 (115)
248 PRK05580 primosome assembly pr 38.0 10 0.00022 36.7 -0.2 43 45-87 383-430 (679)
249 PF06821 Ser_hydrolase: Serine 38.0 26 0.00056 27.4 2.2 31 197-237 35-65 (171)
250 PF04959 ARS2: Arsenite-resist 37.5 24 0.00051 28.8 1.9 29 11-40 74-102 (214)
251 PRK03564 formate dehydrogenase 37.4 26 0.00057 30.3 2.3 20 67-86 213-234 (309)
252 TIGR00593 pola DNA polymerase 37.2 27 0.00059 34.9 2.6 46 200-257 362-409 (887)
253 KOG2593 Transcription initiati 37.1 23 0.00049 31.9 1.8 39 9-52 123-162 (436)
254 smart00064 FYVE Protein presen 36.7 18 0.0004 23.2 1.0 25 45-76 12-36 (68)
255 COG0417 PolB DNA polymerase el 36.3 1.2E+02 0.0027 30.0 7.0 39 195-244 205-244 (792)
256 PF03833 PolC_DP2: DNA polymer 36.3 12 0.00026 36.6 0.0 27 65-91 679-705 (900)
257 COG1327 Predicted transcriptio 36.3 22 0.00047 27.1 1.4 12 81-92 31-42 (156)
258 PF10013 DUF2256: Uncharacteri 35.8 27 0.00059 20.3 1.4 16 45-60 10-25 (42)
259 COG1656 Uncharacterized conser 35.8 34 0.00073 26.6 2.4 19 81-99 133-151 (165)
260 PF11288 DUF3089: Protein of u 35.6 54 0.0012 26.6 3.7 32 199-238 75-106 (207)
261 KOG2482 Predicted C2H2-type Zn 35.6 25 0.00054 30.6 1.8 20 16-35 30-51 (423)
262 COG1779 C4-type Zn-finger prot 35.5 17 0.00038 29.0 0.8 20 172-191 96-115 (201)
263 TIGR01388 rnd ribonuclease D. 35.4 27 0.00059 31.0 2.2 31 227-258 69-102 (367)
264 PF12013 DUF3505: Protein of u 35.3 30 0.00066 24.6 2.0 22 15-36 81-106 (109)
265 PRK13130 H/ACA RNA-protein com 35.2 25 0.00055 22.0 1.4 22 68-89 7-28 (56)
266 KOG0320 Predicted E3 ubiquitin 34.9 25 0.00054 27.6 1.6 19 10-28 127-145 (187)
267 TIGR00686 phnA alkylphosphonat 34.8 22 0.00048 25.4 1.2 23 69-91 5-32 (109)
268 TIGR00595 priA primosomal prot 34.8 11 0.00024 35.0 -0.4 47 16-75 215-262 (505)
269 KOG4167 Predicted DNA-binding 34.6 10 0.00023 36.2 -0.6 23 81-103 795-817 (907)
270 PF04959 ARS2: Arsenite-resist 34.6 13 0.00028 30.3 -0.0 26 80-105 79-104 (214)
271 KOG0969 DNA polymerase delta, 34.6 42 0.00092 32.7 3.3 61 188-259 325-402 (1066)
272 TIGR00244 transcriptional regu 34.4 23 0.00051 26.9 1.3 12 81-92 31-42 (147)
273 COG3677 Transposase and inacti 33.9 21 0.00045 26.6 1.0 18 10-27 49-66 (129)
274 PRK00420 hypothetical protein; 33.8 23 0.0005 25.6 1.2 22 68-89 25-51 (112)
275 COG1439 Predicted nucleic acid 33.6 14 0.00031 29.0 0.1 22 66-87 139-162 (177)
276 PF09332 Mcm10: Mcm10 replicat 33.2 15 0.00032 32.3 0.1 12 45-56 254-265 (344)
277 COG1198 PriA Primosomal protei 33.2 21 0.00046 34.7 1.2 44 16-75 437-484 (730)
278 cd01121 Sms Sms (bacterial rad 33.1 24 0.00052 31.4 1.4 23 67-89 1-25 (372)
279 TIGR00143 hypF [NiFe] hydrogen 32.9 5.9 0.00013 38.4 -2.6 13 200-212 301-313 (711)
280 PRK00564 hypA hydrogenase nick 32.7 20 0.00042 26.2 0.7 10 68-77 73-82 (117)
281 TIGR01562 FdhE formate dehydro 32.7 21 0.00046 30.8 1.0 41 45-86 186-232 (305)
282 cd06140 DNA_polA_I_Bacillus_li 32.5 33 0.00072 26.5 2.0 41 204-257 44-87 (178)
283 KOG0402 60S ribosomal protein 32.4 20 0.00043 24.3 0.6 7 45-51 38-44 (92)
284 COG0068 HypF Hydrogenase matur 31.9 9.7 0.00021 36.4 -1.3 35 45-79 125-164 (750)
285 COG3545 Predicted esterase of 31.8 76 0.0016 25.1 3.8 30 198-237 40-69 (181)
286 PRK03681 hypA hydrogenase nick 31.7 22 0.00047 25.8 0.8 20 67-86 71-95 (114)
287 PF08274 PhnA_Zn_Ribbon: PhnA 31.6 21 0.00046 19.2 0.5 10 45-54 4-13 (30)
288 smart00154 ZnF_AN1 AN1-like Zi 31.5 21 0.00045 20.4 0.5 14 14-27 12-25 (39)
289 PF04606 Ogr_Delta: Ogr/Delta- 31.0 6.3 0.00014 23.6 -1.8 10 46-55 2-11 (47)
290 COG5048 FOG: Zn-finger [Genera 30.6 28 0.00061 30.7 1.5 51 11-63 30-83 (467)
291 COG1545 Predicted nucleic-acid 30.6 23 0.00051 26.7 0.8 18 69-86 32-51 (140)
292 PF08271 TF_Zn_Ribbon: TFIIB z 30.5 25 0.00053 20.4 0.7 7 81-87 22-28 (43)
293 PRK11823 DNA repair protein Ra 30.2 23 0.00049 32.4 0.8 23 66-88 7-31 (446)
294 KOG2807 RNA polymerase II tran 30.0 47 0.001 28.8 2.5 58 44-101 290-368 (378)
295 KOG2482 Predicted C2H2-type Zn 29.7 43 0.00093 29.2 2.3 89 14-102 195-303 (423)
296 COG5151 SSL1 RNA polymerase II 29.6 17 0.00038 31.1 -0.1 21 81-101 391-411 (421)
297 KOG0978 E3 ubiquitin ligase in 29.5 26 0.00056 33.7 1.0 12 66-77 678-689 (698)
298 KOG2907 RNA polymerase I trans 29.3 41 0.00088 24.3 1.8 8 15-22 75-82 (116)
299 TIGR00416 sms DNA repair prote 29.3 24 0.00052 32.3 0.8 24 66-89 7-32 (454)
300 PF01286 XPA_N: XPA protein N- 29.1 26 0.00056 19.5 0.6 11 45-55 5-15 (34)
301 PRK10220 hypothetical protein; 28.8 34 0.00074 24.5 1.3 22 69-90 6-32 (111)
302 PF14803 Nudix_N_2: Nudix N-te 28.8 26 0.00055 19.4 0.5 6 81-86 25-30 (34)
303 PF11781 RRN7: RNA polymerase 28.5 31 0.00068 19.3 0.9 7 69-75 11-17 (36)
304 PRK05978 hypothetical protein; 28.2 33 0.00071 26.2 1.2 9 81-89 55-63 (148)
305 COG4640 Predicted membrane pro 28.1 37 0.0008 30.2 1.7 28 69-96 4-33 (465)
306 PF12907 zf-met2: Zinc-binding 27.9 45 0.00097 19.3 1.5 29 15-44 2-33 (40)
307 KOG0731 AAA+-type ATPase conta 27.8 32 0.0007 33.6 1.4 47 187-233 305-351 (774)
308 PRK00432 30S ribosomal protein 27.6 31 0.00067 21.0 0.8 26 45-76 22-47 (50)
309 PLN02965 Probable pheophorbida 27.6 87 0.0019 25.6 3.9 32 198-237 51-82 (255)
310 PF14447 Prok-RING_4: Prokaryo 27.4 30 0.00065 21.5 0.7 12 79-90 40-51 (55)
311 PF07503 zf-HYPF: HypF finger; 27.4 22 0.00047 19.9 0.1 13 46-58 2-14 (35)
312 PF07975 C1_4: TFIIH C1-like d 26.8 16 0.00034 22.4 -0.6 24 13-36 20-43 (51)
313 COG1066 Sms Predicted ATP-depe 26.6 27 0.00059 31.5 0.6 62 186-261 176-243 (456)
314 smart00661 RPOL9 RNA polymeras 26.6 34 0.00073 20.5 0.9 6 46-51 3-8 (52)
315 PRK14892 putative transcriptio 26.5 29 0.00062 24.6 0.6 11 80-90 44-54 (99)
316 PF12096 DUF3572: Protein of u 26.5 55 0.0012 22.6 2.0 28 186-213 29-56 (88)
317 COG5152 Uncharacterized conser 26.5 27 0.00059 27.8 0.5 44 66-112 196-239 (259)
318 cd09018 DEDDy_polA_RNaseD_like 26.4 46 0.001 24.6 1.8 31 227-258 52-85 (150)
319 COG1645 Uncharacterized Zn-fin 26.4 31 0.00067 25.7 0.8 23 67-89 29-55 (131)
320 KOG4173 Alpha-SNAP protein [In 26.4 31 0.00067 27.8 0.8 47 16-63 108-166 (253)
321 smart00290 ZnF_UBP Ubiquitin C 26.4 45 0.00097 19.8 1.4 33 69-102 2-34 (50)
322 smart00878 Biotin_carb_C Bioti 25.6 2.5E+02 0.0055 20.0 5.7 54 168-244 31-88 (107)
323 TIGR00515 accD acetyl-CoA carb 25.6 27 0.00059 29.8 0.4 10 45-54 28-37 (285)
324 CHL00174 accD acetyl-CoA carbo 25.3 28 0.00061 29.9 0.4 11 81-91 60-70 (296)
325 KOG4317 Predicted Zn-finger pr 25.0 20 0.00044 30.7 -0.4 15 67-81 20-34 (383)
326 PF01428 zf-AN1: AN1-like Zinc 25.0 24 0.00052 20.5 -0.0 15 13-27 12-26 (43)
327 COG1571 Predicted DNA-binding 24.4 39 0.00085 30.4 1.2 31 43-79 350-380 (421)
328 COG1326 Uncharacterized archae 24.3 48 0.001 26.4 1.5 14 179-192 153-166 (201)
329 KOG2785 C2H2-type Zn-finger pr 24.2 79 0.0017 28.0 2.9 74 13-100 165-242 (390)
330 PRK07218 replication factor A; 24.2 37 0.00081 30.8 1.0 48 184-244 346-400 (423)
331 TIGR00354 polC DNA polymerase, 24.0 86 0.0019 31.5 3.4 108 67-196 626-738 (1095)
332 PF03337 Pox_F12L: Poxvirus F1 23.8 75 0.0016 30.4 2.9 70 170-250 226-298 (651)
333 PF05290 Baculo_IE-1: Baculovi 23.3 39 0.00085 25.2 0.8 11 45-55 82-92 (140)
334 TIGR00143 hypF [NiFe] hydrogen 23.3 17 0.00036 35.4 -1.4 12 45-56 92-103 (711)
335 COG1655 Uncharacterized protei 23.2 30 0.00066 28.3 0.3 13 45-57 21-33 (267)
336 PRK11032 hypothetical protein; 23.0 25 0.00055 27.2 -0.2 7 81-87 145-151 (160)
337 KOG0717 Molecular chaperone (D 22.9 46 0.001 30.3 1.3 19 81-99 295-313 (508)
338 PF13451 zf-trcl: Probable zin 22.8 36 0.00077 20.7 0.5 39 12-51 2-41 (49)
339 KOG1280 Uncharacterized conser 22.7 54 0.0012 28.7 1.6 41 64-107 68-108 (381)
340 PRK08351 DNA-directed RNA poly 22.6 40 0.00087 21.5 0.7 19 68-86 5-23 (61)
341 PF05129 Elf1: Transcription e 22.5 37 0.00081 23.0 0.5 11 81-91 49-59 (81)
342 PRK05654 acetyl-CoA carboxylas 22.5 32 0.00069 29.6 0.2 10 45-54 29-38 (292)
343 PLN02211 methyl indole-3-aceta 22.1 1.3E+02 0.0028 25.2 3.9 31 199-237 67-97 (273)
344 KOG2906 RNA polymerase III sub 22.1 16 0.00035 25.5 -1.3 9 45-53 23-31 (105)
345 PF08792 A2L_zn_ribbon: A2L zi 22.0 47 0.001 18.2 0.8 8 81-88 24-31 (33)
346 PF07819 PGAP1: PGAP1-like pro 21.8 81 0.0017 25.8 2.5 46 185-237 49-95 (225)
347 PF08790 zf-LYAR: LYAR-type C2 21.8 16 0.00034 19.4 -1.1 11 15-25 1-11 (28)
348 COG3809 Uncharacterized protei 21.8 82 0.0018 21.1 2.0 34 68-101 3-44 (88)
349 PF13017 Maelstrom: piRNA path 21.6 84 0.0018 25.5 2.6 49 166-214 24-80 (213)
350 KOG1813 Predicted E3 ubiquitin 21.5 40 0.00087 28.7 0.6 44 66-112 241-284 (313)
351 COG5112 UFD2 U1-like Zn-finger 21.4 59 0.0013 23.1 1.4 30 7-36 48-77 (126)
352 PRK06393 rpoE DNA-directed RNA 21.4 46 0.001 21.4 0.8 20 68-87 7-26 (64)
353 PRK00762 hypA hydrogenase nick 21.4 41 0.0009 24.8 0.6 9 45-54 72-80 (124)
354 COG5151 SSL1 RNA polymerase II 21.2 88 0.0019 27.0 2.6 12 65-76 387-398 (421)
355 PF11238 DUF3039: Protein of u 21.2 28 0.00062 21.8 -0.2 8 81-88 47-54 (58)
356 TIGR03826 YvyF flagellar opero 20.8 32 0.00068 25.9 -0.1 14 135-148 77-90 (137)
357 PRK14138 NAD-dependent deacety 20.5 74 0.0016 26.4 2.1 16 45-60 121-136 (244)
358 PF04780 DUF629: Protein of un 20.5 70 0.0015 29.4 2.0 26 79-104 58-84 (466)
359 KOG2636 Splicing factor 3a, su 20.2 61 0.0013 29.4 1.5 23 13-35 400-423 (497)
360 PF01096 TFIIS_C: Transcriptio 20.2 49 0.0011 18.8 0.6 11 14-24 28-38 (39)
No 1
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=100.00 E-value=3.7e-35 Score=235.07 Aligned_cols=218 Identities=42% Similarity=0.743 Sum_probs=169.1
Q ss_pred ccccCccccCChHHHHHHHhHhcCCCCCCCcccchhhcCCHHHHHhhcCCCCCCCcCCcccccccccccccccCChhhHH
Q 024455 16 KCVACYKQFKRKDHLIEHMKISYHSVHQPKCAVCQKLSKSFESLREHLTGPLSKAHCSGIFSDRGCNLCMNIFDSPSSLI 95 (267)
Q Consensus 16 ~C~~C~k~f~~~~~l~~H~~~~~H~~~~~~C~~C~~~f~~~~~l~~H~~~~~~C~~C~k~f~~~~C~~C~~~F~~~~~L~ 95 (267)
.|..|.+.|.-...+-.|+ +..|....+.|..|.+.-.....+..++-.+.+- .|...|++..|..|.-.-.......
T Consensus 2 ~~~~~~~~~~~~~~~~~~~-v~~~~~~~~~~~~~k~~~~~~~~~~e~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~ 79 (280)
T KOG2249|consen 2 KASSCAQQFNKKEHLPNHK-VSRHKLHERKCGKCKKVARSFESNEEGLIAPLPK-EGKNIFSQRGNRFKATIKASPGKRR 79 (280)
T ss_pred CccHHHHHhCccccCcccc-chhhccCcchhhhHHHhccCcccccccccCCCCc-ccCccccchhhHHHhhHhhcCCcch
Confidence 3667778888888887887 2115544448889988888888788887555554 7777888877776654433333333
Q ss_pred HHHHHhcCCCCccccccCcchhhhhhhccccccccccCCCceeeeeccccCCcCCCCccceeeEEEecCCCCeeEecccC
Q 024455 96 KHKEACSLSAPVPFEKTLSNAESQKKISGAIDEKRTCRGPKAVAMDCEMVGGGSNGTLDLCARVCLVDEDENVIFHTYVQ 175 (267)
Q Consensus 96 ~H~~~h~~~~~~~C~~~f~~~~~l~~H~~~~~~~r~~~~~~~~~~dcE~~g~~~~~~~~~i~~v~vvd~~~~~~~~~~v~ 175 (267)
.|+-.+.+. |..+ ..+.. ..+.....+++++||||+|.+..++.+++||++|||..|+++||+||+
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 333222221 1100 00000 011222236899999999999999999999999999999999999999
Q ss_pred CCCCccccccccccCCHHhhccCCCHHHHHHHHHHHHhcCCCCCcccccCCCceEEEeccchhhhccccccCCCCceecc
Q 024455 176 PQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNYPDHMLRDT 255 (267)
Q Consensus 176 P~~~i~~~~~~~~GIt~~~l~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~Dl~~l~~~~~~~~~~dt 255 (267)
|..+|+||+|+++||+++++.+|++|+.|+.+++++| .|+|||||.+++||.+|.+.||+.+|+||
T Consensus 146 P~~~VtDyRT~vSGIrpehm~~A~pf~~aQ~ev~klL--------------~gRIlVGHaLhnDl~~L~l~hp~s~iRDT 211 (280)
T KOG2249|consen 146 PTEPVTDYRTRVSGIRPEHMRDAMPFKVAQKEVLKLL--------------KGRILVGHALHNDLQALKLEHPRSMIRDT 211 (280)
T ss_pred CCcccccceeeecccCHHHhccCccHHHHHHHHHHHH--------------hCCEEeccccccHHHHHhhhCchhhhccc
Confidence 9999999999999999999999999999999999999 88999999999999999999999999999
Q ss_pred cccccccc
Q 024455 256 AKYRPLMK 263 (267)
Q Consensus 256 ~~~~~~~~ 263 (267)
|.++||.+
T Consensus 212 s~~~pl~k 219 (280)
T KOG2249|consen 212 SKYPPLMK 219 (280)
T ss_pred ccCchHHH
Confidence 99999987
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=99.94 E-value=5.8e-27 Score=180.89 Aligned_cols=113 Identities=27% Similarity=0.393 Sum_probs=100.1
Q ss_pred eeeeccccCCcC-------CCCc-------cceeeEEEec----CCCCeeEecccCCCCCccccccccccCCHHhhccCC
Q 024455 138 VAMDCEMVGGGS-------NGTL-------DLCARVCLVD----EDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAM 199 (267)
Q Consensus 138 ~~~dcE~~g~~~-------~~~~-------~~i~~v~vvd----~~~~~~~~~~v~P~~~i~~~~~~~~GIt~~~l~~~~ 199 (267)
+++|||+.|.+. .++. .++|||++|| ..|.+++|.+|+|..+|.+|+|++||||+++|++++
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 367888887764 3443 3689999999 689999999999999999999999999999999874
Q ss_pred ------CHHHHHHHHHHHHhcCCCCCcccccCCCceEEEeccchhhhccccccCCCCceecccccccccc
Q 024455 200 ------PLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNYPDHMLRDTAKYRPLMK 263 (267)
Q Consensus 200 ------~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~Dl~~l~~~~~~~~~~dt~~~~~~~~ 263 (267)
++++|.++|+++|. .|+|||||++++||++|++.||+..+||||.||+++.
T Consensus 81 ~~~~~~t~~~v~~~l~~li~-------------~~tILVGHsL~nDL~aL~l~hp~~~viDTa~l~~~~~ 137 (174)
T cd06143 81 SSKNLTTLKSAYLKLRLLVD-------------LGCIFVGHGLAKDFRVINIQVPKEQVIDTVELFHLPG 137 (174)
T ss_pred cccccCCHHHHHHHHHHHcC-------------CCCEEEeccchhHHHHhcCcCCCcceEEcHHhccCCC
Confidence 69999999999993 6899999999999999999999999999999987764
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=99.92 E-value=2.2e-25 Score=173.14 Aligned_cols=110 Identities=38% Similarity=0.712 Sum_probs=101.8
Q ss_pred eeeeccccCCcCCCCccceeeEEEecCCCCeeEecccCCCCCccccccccccCCHHhhccCCCHHHHHHHHHHHHhcCCC
Q 024455 138 VAMDCEMVGGGSNGTLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEILNNGES 217 (267)
Q Consensus 138 ~~~dcE~~g~~~~~~~~~i~~v~vvd~~~~~~~~~~v~P~~~i~~~~~~~~GIt~~~l~~~~~~~~v~~~~~~~~~~~~~ 217 (267)
+++||||+|.+..++..+++++.+++.++..+++++|+|..+|+++++++||||+++|+++|++++|+.+|++|+
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 VAIDCEMVGTGPGGRESELARCSIVNYHGDVLYDKYIRPEGPVTDYRTRWSGIRRQHLVNATPFAVAQKEILKIL----- 75 (157)
T ss_pred CEEEeEeccccCCCCeEEEEEEEEEeCCCCEEEEEeECCCCccCccceECCCCCHHHHhcCCCHHHHHHHHHHHc-----
Confidence 479999999987666778899999998899999999999999999999999999999999999999999999999
Q ss_pred CCcccccCCCceEEEeccchhhhccccccCCCCceecccccccc
Q 024455 218 TGRLMLDDGKARLLVGHGLEHDLDSLRMNYPDHMLRDTAKYRPL 261 (267)
Q Consensus 218 ~~~~~~~~~~~~~lvgh~~~~Dl~~l~~~~~~~~~~dt~~~~~~ 261 (267)
+|+||||||+.||++||++.++...++||+.+..+
T Consensus 76 ---------~~~vlV~Hn~~~D~~~l~~~~~~~~~~Dt~~l~~~ 110 (157)
T cd06149 76 ---------KGKVVVGHAIHNDFKALKYFHPKHMTRDTSTIPLL 110 (157)
T ss_pred ---------CCCEEEEeCcHHHHHHhcccCCCcCEEECcccccc
Confidence 78999999999999999999998889999876544
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=99.91 E-value=3.3e-24 Score=165.42 Aligned_cols=106 Identities=35% Similarity=0.582 Sum_probs=95.9
Q ss_pred eeeeccccCCcCCCCccceeeEEEecCCCCeeEecccCCCCCccccccccccCCHHhhccCC-CHHHHHHHHHHHHhcCC
Q 024455 138 VAMDCEMVGGGSNGTLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAM-PLKEVKDKILEILNNGE 216 (267)
Q Consensus 138 ~~~dcE~~g~~~~~~~~~i~~v~vvd~~~~~~~~~~v~P~~~i~~~~~~~~GIt~~~l~~~~-~~~~v~~~~~~~~~~~~ 216 (267)
+++||||+|.+.+ ++++++.+++.++..+|+++|+|..+|+++++++||||+++|+++| ++++|+.++++|++
T Consensus 1 ~~iD~E~~g~~~g---~ei~~i~~v~~~~~~~f~~lv~P~~~i~~~~t~itGIt~~~l~~a~~~~~~v~~~~~~fl~--- 74 (150)
T cd06145 1 FALDCEMCYTTDG---LELTRVTVVDENGKVVLDELVKPDGEIVDYNTRFSGITEEMLENVTTTLEDVQKKLLSLIS--- 74 (150)
T ss_pred CEEeeeeeeecCC---CEEEEEEEEeCCCCEEEEEeECCCCccchhccCcCCCCHHHhccCCCCHHHHHHHHHHHhC---
Confidence 4789999998653 6779999999999999999999999999999999999999999995 99999999999992
Q ss_pred CCCcccccCCCceEEEeccchhhhccccccCCCCceecccccccc
Q 024455 217 STGRLMLDDGKARLLVGHGLEHDLDSLRMNYPDHMLRDTAKYRPL 261 (267)
Q Consensus 217 ~~~~~~~~~~~~~~lvgh~~~~Dl~~l~~~~~~~~~~dt~~~~~~ 261 (267)
.+.+|||||+.||+.||+..++ ++|||+.+++.
T Consensus 75 ----------~~~vlVgHn~~fD~~fL~~~~~--~~iDT~~l~r~ 107 (150)
T cd06145 75 ----------PDTILVGHSLENDLKALKLIHP--RVIDTAILFPH 107 (150)
T ss_pred ----------CCCEEEEcChHHHHHHhhccCC--CEEEcHHhccc
Confidence 3789999999999999999887 68999987654
No 5
>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=99.90 E-value=2.3e-23 Score=161.26 Aligned_cols=111 Identities=50% Similarity=0.908 Sum_probs=101.9
Q ss_pred eeeeccccCCcCCCCccceeeEEEecCCCCeeEecccCCCCCccccccccccCCHHhhccCCCHHHHHHHHHHHHhcCCC
Q 024455 138 VAMDCEMVGGGSNGTLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEILNNGES 217 (267)
Q Consensus 138 ~~~dcE~~g~~~~~~~~~i~~v~vvd~~~~~~~~~~v~P~~~i~~~~~~~~GIt~~~l~~~~~~~~v~~~~~~~~~~~~~ 217 (267)
+++||||+|.....+.++++.+.+++..+...++++|+|..+++++++.+||||+++++++|++++++.+|++|+
T Consensus 1 v~lD~EttGl~~~~~~~~i~~v~~v~~~~~~~~~~~v~P~~~i~~~~~~ihGIt~~~v~~a~~~~~~~~~l~~~l----- 75 (152)
T cd06144 1 VALDCEMVGVGPDGSESALARVSIVNEDGNVVYDTYVKPQEPVTDYRTAVSGIRPEHLKDAPDFEEVQKKVAELL----- 75 (152)
T ss_pred CEEEEEeecccCCCCEEEEEEEEEEeCCCCEEEEEEECCCCCCCcccccCCCCCHHHHcCCCCHHHHHHHHHHHh-----
Confidence 478999999876556788899999998899899999999999999999999999999999999999999999999
Q ss_pred CCcccccCCCceEEEeccchhhhccccccCCCCceeccccccccc
Q 024455 218 TGRLMLDDGKARLLVGHGLEHDLDSLRMNYPDHMLRDTAKYRPLM 262 (267)
Q Consensus 218 ~~~~~~~~~~~~~lvgh~~~~Dl~~l~~~~~~~~~~dt~~~~~~~ 262 (267)
++.+|||||+.||+.||++..|+..++||..+..++
T Consensus 76 ---------~~~vlVgHn~~fD~~~L~~~~~~~~~~dt~~l~~~~ 111 (152)
T cd06144 76 ---------KGRILVGHALKNDLKVLKLDHPKKLIRDTSKYKPLR 111 (152)
T ss_pred ---------CCCEEEEcCcHHHHHHhcCcCCCccEEEeEEeeccc
Confidence 678999999999999999999998999998766554
No 6
>KOG2248 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=99.87 E-value=2.2e-22 Score=173.78 Aligned_cols=116 Identities=38% Similarity=0.649 Sum_probs=105.2
Q ss_pred ccCCCceeeeeccccCCcCCCCccceeeEEEecCCCCeeEecccCCCCCccccccccccCCHHhhccC-CCHHHHHHHHH
Q 024455 131 TCRGPKAVAMDCEMVGGGSNGTLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNA-MPLKEVKDKIL 209 (267)
Q Consensus 131 ~~~~~~~~~~dcE~~g~~~~~~~~~i~~v~vvd~~~~~~~~~~v~P~~~i~~~~~~~~GIt~~~l~~~-~~~~~v~~~~~ 209 (267)
.....+++++|||||....+ .+++||.+||.++.+++|.+|+|..+|.+|+++++|||.++++++ .++++|..+|.
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---LELTRVTAVDRDGKVILDTFVKPNKPVVDYNTRYSGITEEDLENSTITLEDVQKELL 288 (380)
T ss_pred CCCCCCeEEEEeeeeeeccc---eeeEEeeeeeccCcEEeEEeecCCCcccccccccccccHHHHhcCccCHHHHHHHHH
Confidence 45567789999999998543 567999999999999999999999999999999999999999876 69999999999
Q ss_pred HHHhcCCCCCcccccCCCceEEEeccchhhhccccccCCCCceeccccccccccc
Q 024455 210 EILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNYPDHMLRDTAKYRPLMKT 264 (267)
Q Consensus 210 ~~~~~~~~~~~~~~~~~~~~~lvgh~~~~Dl~~l~~~~~~~~~~dt~~~~~~~~~ 264 (267)
.+++ .++|||||++++||++|++.|| .+||||.+|++...
T Consensus 289 ~~~~-------------~~TILVGHSLenDL~aLKl~H~--~ViDTa~lf~~~~g 328 (380)
T KOG2248|consen 289 ELIS-------------KNTILVGHSLENDLKALKLDHP--SVIDTAVLFKHPTG 328 (380)
T ss_pred hhcC-------------cCcEEEeechhhHHHHHhhhCC--ceeeeeEEEecCCC
Confidence 9994 8899999999999999999999 78999988877654
No 7
>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=99.86 E-value=4.2e-22 Score=155.63 Aligned_cols=107 Identities=31% Similarity=0.520 Sum_probs=89.4
Q ss_pred eeeeccccCCcC-CCCccceeeEEEecCCCCeeEecccCCCCCccccccccccCCHHhhccCCC-------HHHHHHHHH
Q 024455 138 VAMDCEMVGGGS-NGTLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMP-------LKEVKDKIL 209 (267)
Q Consensus 138 ~~~dcE~~g~~~-~~~~~~i~~v~vvd~~~~~~~~~~v~P~~~i~~~~~~~~GIt~~~l~~~~~-------~~~v~~~~~ 209 (267)
+++||||+|.+. .+++.+++.|.+. ++.++++.+|+|..+|+++++++||||+++|+++|+ +++++++|+
T Consensus 1 v~lD~EttGl~~~~d~ii~Ig~V~v~--~g~i~~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~~~~~~~~~~~~~~~ 78 (161)
T cd06137 1 VALDCEMVGLADGDSEVVRISAVDVL--TGEVLIDSLVRPSVRVTDWRTRFSGVTPADLEEAAKAGKTIFGWEAARAALW 78 (161)
T ss_pred CEEEeeeeeEcCCCCEEEEEEEEEcC--CCeEEEeccccCCCCCCccceeccCCCHHHHhhhhhcCCccccHHHHHHHHH
Confidence 479999999875 3344444555443 566779999999999999999999999999999875 459999999
Q ss_pred HHHhcCCCCCcccccCCCc-eEEEeccchhhhccccccCCCCceeccccccccc
Q 024455 210 EILNNGESTGRLMLDDGKA-RLLVGHGLEHDLDSLRMNYPDHMLRDTAKYRPLM 262 (267)
Q Consensus 210 ~~~~~~~~~~~~~~~~~~~-~~lvgh~~~~Dl~~l~~~~~~~~~~dt~~~~~~~ 262 (267)
+|+ ++ .||||||+.||++||+..++ .+|||..+++..
T Consensus 79 ~~i--------------~~~~vlVgHn~~fD~~fL~~~~~--~~iDT~~l~~~~ 116 (161)
T cd06137 79 KFI--------------DPDTILVGHSLQNDLDALRMIHT--RVVDTAILTREA 116 (161)
T ss_pred Hhc--------------CCCcEEEeccHHHHHHHHhCcCC--CeeEehhhhhhc
Confidence 999 55 89999999999999999877 789999887643
No 8
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.86 E-value=1.9e-22 Score=163.01 Aligned_cols=115 Identities=25% Similarity=0.390 Sum_probs=95.3
Q ss_pred CCCCCCccccccCccccCChHHHHHHHhHhcCCC--CCC--CcccchhhcCCHHHHHhhc---CCCCCCCcCCcccccc-
Q 024455 8 PKRSTARHKCVACYKQFKRKDHLIEHMKISYHSV--HQP--KCAVCQKLSKSFESLREHL---TGPLSKAHCSGIFSDR- 79 (267)
Q Consensus 8 ~~~~~k~~~C~~C~k~f~~~~~l~~H~~~~~H~~--~~~--~C~~C~~~f~~~~~l~~H~---~~~~~C~~C~k~f~~~- 79 (267)
++...-.|+|+.|||.+.+.++|.+|+++ |-. ++. .|+.|||.|.+...|+.|+ +-++.|.+|||.|++.
T Consensus 124 ~~~~~~r~~c~eCgk~ysT~snLsrHkQ~--H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaFSRPW 201 (279)
T KOG2462|consen 124 SAAKHPRYKCPECGKSYSTSSNLSRHKQT--HRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHTLPCECGICGKAFSRPW 201 (279)
T ss_pred ccccCCceeccccccccccccccchhhcc--cccccccccccCCCCCceeeehHHHhhHhhccCCCcccccccccccchH
Confidence 34456679999999999999999999999 743 333 9999999999999999999 4477788888888864
Q ss_pred ---------------cccccccccCChhhHHHHHHHhcCCCCcc---ccccCcchhhhhhhcc
Q 024455 80 ---------------GCNLCMNIFDSPSSLIKHKEACSLSAPVP---FEKTLSNAESQKKISG 124 (267)
Q Consensus 80 ---------------~C~~C~~~F~~~~~L~~H~~~h~~~~~~~---C~~~f~~~~~l~~H~~ 124 (267)
+|+.|+|.|..++||+.||++|.+.|+|+ |+++|+..+.|.+|.+
T Consensus 202 LLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~E 264 (279)
T KOG2462|consen 202 LLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHSE 264 (279)
T ss_pred HhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhhh
Confidence 28888888888888888888888888886 7788888888888874
No 9
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=99.75 E-value=2.3e-18 Score=137.90 Aligned_cols=97 Identities=24% Similarity=0.298 Sum_probs=88.9
Q ss_pred CceeeeeccccCCcCCCCccceeeEEEecCCCCeeEecccCCCCCccccccccccCCHHhhccCCCHHHHHHHHHHHHhc
Q 024455 135 PKAVAMDCEMVGGGSNGTLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEILNN 214 (267)
Q Consensus 135 ~~~~~~dcE~~g~~~~~~~~~i~~v~vvd~~~~~~~~~~v~P~~~i~~~~~~~~GIt~~~l~~~~~~~~v~~~~~~~~~~ 214 (267)
..++++|+||+|.....++++|+.|.+.++.....++.+|+|..+++.+.+.+||||+++|+++|++.+|+++|.+|+
T Consensus 5 ~~~vvlD~EtTGl~~~~eIIeIgaV~v~~g~~~~~f~~lv~P~~~i~~~~~~lhGIt~~~v~~ap~~~evl~~f~~f~-- 82 (195)
T PRK07247 5 ETYIAFDLEFNTVNGVSHIIQVSAVKYDDHKEVDSFDSYVYTDVPLQSFINGLTGITADKIADAPKVEEVLAAFKEFV-- 82 (195)
T ss_pred CeEEEEEeeCCCCCCCCeEEEEEEEEEECCEEEEEEEEEECCCCCCCccceecCCCCHHHHhCCCCHHHHHHHHHHHH--
Confidence 467999999999876678899999999877666789999999999999999999999999999999999999999999
Q ss_pred CCCCCcccccCCCceEEEeccch-hhhccccc
Q 024455 215 GESTGRLMLDDGKARLLVGHGLE-HDLDSLRM 245 (267)
Q Consensus 215 ~~~~~~~~~~~~~~~~lvgh~~~-~Dl~~l~~ 245 (267)
++.+|||||+. ||+.||+.
T Consensus 83 ------------~~~~lVaHNa~~fD~~fL~~ 102 (195)
T PRK07247 83 ------------GELPLIGYNAQKSDLPILAE 102 (195)
T ss_pred ------------CCCeEEEEeCcHhHHHHHHH
Confidence 77899999997 89999964
No 10
>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=99.74 E-value=2.4e-18 Score=141.18 Aligned_cols=107 Identities=24% Similarity=0.296 Sum_probs=92.1
Q ss_pred eeeeeccccCCcCC--CCccceeeEEEecCCC-CeeEecccCCCCCccccccccccCCHHhhccCCCHHHHHHHHHHHHh
Q 024455 137 AVAMDCEMVGGGSN--GTLDLCARVCLVDEDE-NVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEILN 213 (267)
Q Consensus 137 ~~~~dcE~~g~~~~--~~~~~i~~v~vvd~~~-~~~~~~~v~P~~~i~~~~~~~~GIt~~~l~~~~~~~~v~~~~~~~~~ 213 (267)
++++|+||+|.... .++++++.|.+.+... ...|+.+|+|..++++..+++||||+++|+++|+|++|+.+|.+|+
T Consensus 2 ~vvlD~ETTGl~p~~~d~IIEIgav~~~~~~~~~~~f~~~i~P~~~i~~~a~~vhGIt~e~l~~~p~f~ev~~~f~~fi- 80 (225)
T TIGR01406 2 QIILDTETTGLDPKGGHRIVEIGAVELVNRMLTGDNFHVYVNPERDMPAEAAKVHGITDEFLADKPKFKEIADEFLDFI- 80 (225)
T ss_pred EEEEEeeCCCcCCCCCCeEEEEEEEEEECCcEecceEEEEECcCCCCCHHHHhccCCCHHHHhCCCCHHHHHHHHHHHh-
Confidence 58899999998754 5789999999887542 2479999999999999999999999999999999999999999999
Q ss_pred cCCCCCcccccCCCceEEEeccchhhhccccccC-------C----CCceecccc
Q 024455 214 NGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNY-------P----DHMLRDTAK 257 (267)
Q Consensus 214 ~~~~~~~~~~~~~~~~~lvgh~~~~Dl~~l~~~~-------~----~~~~~dt~~ 257 (267)
++.+|||||+.||+.||+... + ...++||..
T Consensus 81 -------------~~~~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~ 122 (225)
T TIGR01406 81 -------------GGSELVIHNAAFDVGFLNYELERLGPTIKKIGEFCRVIDTLA 122 (225)
T ss_pred -------------CCCEEEEEecHHHHHHHHHHHHHhCCCCcccccCCCEEEHHH
Confidence 778999999999999996421 2 147889864
No 11
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=99.73 E-value=2.6e-18 Score=141.65 Aligned_cols=108 Identities=22% Similarity=0.355 Sum_probs=93.1
Q ss_pred ceeeeeccccCCcC--CCCccceeeEEEecCCC-CeeEecccCCCCCccccccccccCCHHhhccCCCHHHHHHHHHHHH
Q 024455 136 KAVAMDCEMVGGGS--NGTLDLCARVCLVDEDE-NVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEIL 212 (267)
Q Consensus 136 ~~~~~dcE~~g~~~--~~~~~~i~~v~vvd~~~-~~~~~~~v~P~~~i~~~~~~~~GIt~~~l~~~~~~~~v~~~~~~~~ 212 (267)
.++++|+|++|... .+++++|+.|.+.+... ...|+.+|+|..+|++...++||||+++|+++|+|++|+++|++|+
T Consensus 5 r~vvlDtETTGldp~~~drIIEIGaV~v~~~~~~~~~f~~~i~P~~~i~~~a~~VHGIT~e~l~~~p~f~ev~~~f~~fi 84 (240)
T PRK05711 5 RQIVLDTETTGLNQREGHRIIEIGAVELINRRLTGRNFHVYIKPDRLVDPEALAVHGITDEFLADKPTFAEVADEFLDFI 84 (240)
T ss_pred eEEEEEeeCCCcCCCCCCeEEEEEEEEEECCEEeccEEEEEECcCCcCCHHHhhhcCCCHHHHcCCCCHHHHHHHHHHHh
Confidence 57899999999875 46889999999987643 2468999999999999999999999999999999999999999999
Q ss_pred hcCCCCCcccccCCCceEEEeccchhhhcccccc-------CCC----Cceecccc
Q 024455 213 NNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMN-------YPD----HMLRDTAK 257 (267)
Q Consensus 213 ~~~~~~~~~~~~~~~~~~lvgh~~~~Dl~~l~~~-------~~~----~~~~dt~~ 257 (267)
++.+|||||+.||+.||+.. .|+ ..++||..
T Consensus 85 --------------~~~~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~ 126 (240)
T PRK05711 85 --------------RGAELIIHNAPFDIGFMDYEFALLGRDIPKTNTFCKVTDTLA 126 (240)
T ss_pred --------------CCCEEEEEccHHhHHHHHHHHHHhCCCCCcccccCceeeHHH
Confidence 77899999999999999643 231 35788863
No 12
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.73 E-value=7.6e-19 Score=142.23 Aligned_cols=99 Identities=18% Similarity=0.322 Sum_probs=88.9
Q ss_pred CcccchhhcCCHHHHHhhc--------CCCCCCCcCCccccccc--------------ccccccccCChhhHHHHHHHhc
Q 024455 45 KCAVCQKLSKSFESLREHL--------TGPLSKAHCSGIFSDRG--------------CNLCMNIFDSPSSLIKHKEACS 102 (267)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~--------~~~~~C~~C~k~f~~~~--------------C~~C~~~F~~~~~L~~H~~~h~ 102 (267)
+|..||+.+++.++|.+|. .+-+.|+.|+|.+.+.. |.+|||.|.+..-|+.|+|+|+
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 9999999999999999998 45688999999999863 9999999999999999999999
Q ss_pred CCCCcc---ccccCcchhhhhhhccccccccccCCCceeeeeccccCCcCCC
Q 024455 103 LSAPVP---FEKTLSNAESQKKISGAIDEKRTCRGPKAVAMDCEMVGGGSNG 151 (267)
Q Consensus 103 ~~~~~~---C~~~f~~~~~l~~H~~~~~~~r~~~~~~~~~~dcE~~g~~~~~ 151 (267)
|||||. |+++|..+++|+.|+..+.+. .-+.|..|++.|..
T Consensus 212 GEKPF~C~hC~kAFADRSNLRAHmQTHS~~--------K~~qC~~C~KsFsl 255 (279)
T KOG2462|consen 212 GEKPFSCPHCGKAFADRSNLRAHMQTHSDV--------KKHQCPRCGKSFAL 255 (279)
T ss_pred CCCCccCCcccchhcchHHHHHHHHhhcCC--------ccccCcchhhHHHH
Confidence 999997 999999999999999877643 45789999987543
No 13
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=99.71 E-value=1.3e-17 Score=142.69 Aligned_cols=98 Identities=17% Similarity=0.242 Sum_probs=85.0
Q ss_pred cCCCceeeeeccccCCcC-CCCccceeeEEEe-cCCCCeeEecccCCCCCccccccccccCCHHhhccCCCHHHHHHHHH
Q 024455 132 CRGPKAVAMDCEMVGGGS-NGTLDLCARVCLV-DEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKIL 209 (267)
Q Consensus 132 ~~~~~~~~~dcE~~g~~~-~~~~~~i~~v~vv-d~~~~~~~~~~v~P~~~i~~~~~~~~GIt~~~l~~~~~~~~v~~~~~ 209 (267)
.....++++|+|++|.+. .+++++|+.|.+. ++.....|+++|+|..++.. ..+||||+++|+++|+|.+|+.+|.
T Consensus 43 ~~~~~fVvlDiETTGLdp~~drIIeIgAV~i~~~g~ive~f~tLVnP~~~~~p--~~LHGIT~e~La~AP~f~eVl~el~ 120 (377)
T PRK05601 43 IEAAPFVAVSIQTSGIHPSTSRLITIDAVTLTADGEEVEHFHAVLNPGEDPGP--FHLHGLSAEEFAQGKRFSQILKPLD 120 (377)
T ss_pred CCCCCEEEEEEECCCCCCCCCeEEEEEEEEEEcCCEEEEEEEEEECcCCCCCC--ccccCCCHHHHhcCCCHHHHHHHHH
Confidence 344579999999999975 4678888999988 55556789999999876554 4799999999999999999999999
Q ss_pred HHHhcCCCCCcccccCCCceEEEeccchhhhccccc
Q 024455 210 EILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRM 245 (267)
Q Consensus 210 ~~~~~~~~~~~~~~~~~~~~~lvgh~~~~Dl~~l~~ 245 (267)
+|| +|.+|||||+.||+.||..
T Consensus 121 ~fL--------------~g~vLVaHNA~FD~~FL~~ 142 (377)
T PRK05601 121 RLI--------------DGRTLILHNAPRTWGFIVS 142 (377)
T ss_pred HHh--------------CCCEEEEECcHHHHHHHHH
Confidence 999 8899999999999999965
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=99.71 E-value=2.2e-17 Score=128.40 Aligned_cols=108 Identities=24% Similarity=0.282 Sum_probs=93.4
Q ss_pred eeeeeccccCCcCCCCccceeeEEEecCCCCeeEecccCCCCCccccccccccCCHHhhccCCCHHHHHHHHHHHHhcCC
Q 024455 137 AVAMDCEMVGGGSNGTLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEILNNGE 216 (267)
Q Consensus 137 ~~~~dcE~~g~~~~~~~~~i~~v~vvd~~~~~~~~~~v~P~~~i~~~~~~~~GIt~~~l~~~~~~~~v~~~~~~~~~~~~ 216 (267)
++++|+|++|.. .+++.+++.+.+.++.....++.+++|..++++..+++||||++++++++++++|+++|.+++
T Consensus 1 ~v~~D~Ettg~~-~~~ii~ig~v~~~~~~~~~~~~~~i~p~~~~~~~~~~i~GIt~e~l~~~~~~~~v~~~l~~~l---- 75 (156)
T cd06130 1 FVAIDFETANAD-RASACSIGLVKVRDGQIVDTFYTLIRPPTRFDPFNIAIHGITPEDVADAPTFPEVWPEIKPFL---- 75 (156)
T ss_pred CEEEEEeCCCCC-CCceEEEEEEEEECCEEEEEEEEEeCcCCCCChhhccccCcCHHHHhcCCCHHHHHHHHHHHh----
Confidence 478999999865 567888888888766555668899999999999999999999999999999999999999999
Q ss_pred CCCcccccCCCceEEEeccchhhhcccc-------ccCCCCceecccccc
Q 024455 217 STGRLMLDDGKARLLVGHGLEHDLDSLR-------MNYPDHMLRDTAKYR 259 (267)
Q Consensus 217 ~~~~~~~~~~~~~~lvgh~~~~Dl~~l~-------~~~~~~~~~dt~~~~ 259 (267)
++.+|||||+.||+.||+ +..+...+|||..+.
T Consensus 76 ----------~~~~lv~hn~~fD~~~l~~~~~~~g~~~~~~~~idt~~~~ 115 (156)
T cd06130 76 ----------GGSLVVAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLA 115 (156)
T ss_pred ----------CCCEEEEeChHHhHHHHHHHHHHcCCCCCCCCEEEHHHHH
Confidence 668999999999999995 456677889997443
No 15
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=99.71 E-value=2e-17 Score=136.70 Aligned_cols=114 Identities=21% Similarity=0.226 Sum_probs=97.0
Q ss_pred ccCCCceeeeeccccCCcC-CCCccceeeEEEecCCC--CeeEecccCCCCCccccccccccCCHHhhccCCCHHHHHHH
Q 024455 131 TCRGPKAVAMDCEMVGGGS-NGTLDLCARVCLVDEDE--NVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDK 207 (267)
Q Consensus 131 ~~~~~~~~~~dcE~~g~~~-~~~~~~i~~v~vvd~~~--~~~~~~~v~P~~~i~~~~~~~~GIt~~~l~~~~~~~~v~~~ 207 (267)
......++++|+|++|.+. .++++++|.|.+.++.. ...++.+|+|..+|+...+.+||||+++++++|++++|+.+
T Consensus 43 ~~~~~~~vviD~ETTGl~p~~d~IieIg~v~v~~~~i~~~~~~~~li~P~~~i~~~~~~IhGIt~e~l~~ap~~~evl~~ 122 (239)
T PRK09146 43 PLSEVPFVALDFETTGLDAEQDAIVSIGLVPFTLQRIRCRQARHWVVKPRRPLEEESVVIHGITHSELQDAPDLERILDE 122 (239)
T ss_pred CcccCCEEEEEeECCCCCCCCCcEEEEEEEEEECCeEeecceEEEEECCCCCCChhhhhhcCCCHHHHhCCCCHHHHHHH
Confidence 4445678999999999874 56788999998876543 35688999999999999999999999999999999999999
Q ss_pred HHHHHhcCCCCCcccccCCCceEEEeccchhhhcccccc-------CCCCceeccccc
Q 024455 208 ILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMN-------YPDHMLRDTAKY 258 (267)
Q Consensus 208 ~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~Dl~~l~~~-------~~~~~~~dt~~~ 258 (267)
|.+++ ++.+|||||+.||+.||+-. .+...+|||..+
T Consensus 123 l~~~~--------------~~~~lVaHna~FD~~fL~~~l~~~~~~~~~~~~iDTl~L 166 (239)
T PRK09146 123 LLEAL--------------AGKVVVVHYRRIERDFLDQALRNRIGEGIEFPVIDTMEI 166 (239)
T ss_pred HHHHh--------------CCCEEEEECHHHHHHHHHHHHHHhcCCCCCCceechHHH
Confidence 99999 77899999999999999643 234578999865
No 16
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=99.71 E-value=1.6e-17 Score=138.43 Aligned_cols=112 Identities=17% Similarity=0.257 Sum_probs=94.6
Q ss_pred CceeeeeccccCCcC-CCCccceeeEEEecCCCCeeEecccCCCCCccccccccccCCHHhhccCCCHHHHHHHHHHHHh
Q 024455 135 PKAVAMDCEMVGGGS-NGTLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEILN 213 (267)
Q Consensus 135 ~~~~~~dcE~~g~~~-~~~~~~i~~v~vvd~~~~~~~~~~v~P~~~i~~~~~~~~GIt~~~l~~~~~~~~v~~~~~~~~~ 213 (267)
..++++|+|++|... .+++++++.|.+..+.....++.+|+|..+|+...+.+||||+++|+++|++.+|+.+|.+|++
T Consensus 7 ~~~v~~D~ETTGl~~~~d~IIEIa~v~v~~~~~~~~~~~li~P~~~I~~~a~~ihgIt~e~v~~~p~~~ev~~~~~~fl~ 86 (250)
T PRK06310 7 TEFVCLDCETTGLDVKKDRIIEFAAIRFTFDEVIDSVEFLINPERVVSAESQRIHHISDAMLRDKPKIAEVFPQIKGFFK 86 (250)
T ss_pred CcEEEEEEeCCCCCCCCCeEEEEEEEEEECCeEEEEEEEEECcCCCCCHhhhhccCcCHHHHhCCCCHHHHHHHHHHHhC
Confidence 468999999999863 4678898999887655556789999999999999999999999999999999999999999992
Q ss_pred cCCCCCcccccCCCceEEEeccchhhhccccccCC---------CCceecccccc
Q 024455 214 NGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNYP---------DHMLRDTAKYR 259 (267)
Q Consensus 214 ~~~~~~~~~~~~~~~~~lvgh~~~~Dl~~l~~~~~---------~~~~~dt~~~~ 259 (267)
++.+|||||+.||+.||+..++ ...+|||..+.
T Consensus 87 -------------~~~~lvghn~~FD~~~L~~~~~r~g~~~~~~~~~~iDtl~la 128 (250)
T PRK06310 87 -------------EGDYIVGHSVGFDLQVLSQESERIGETFLSKHYYIIDTLRLA 128 (250)
T ss_pred -------------CCCEEEEECHHHHHHHHHHHHHHcCCCccccCCcEEehHHHH
Confidence 3379999999999999964331 25789987543
No 17
>PRK07740 hypothetical protein; Provisional
Probab=99.68 E-value=5e-17 Score=134.97 Aligned_cols=113 Identities=28% Similarity=0.315 Sum_probs=95.4
Q ss_pred CCCceeeeeccccCCcCC--CCccceeeEEEecCCC-CeeEecccCCCCCccccccccccCCHHhhccCCCHHHHHHHHH
Q 024455 133 RGPKAVAMDCEMVGGGSN--GTLDLCARVCLVDEDE-NVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKIL 209 (267)
Q Consensus 133 ~~~~~~~~dcE~~g~~~~--~~~~~i~~v~vvd~~~-~~~~~~~v~P~~~i~~~~~~~~GIt~~~l~~~~~~~~v~~~~~ 209 (267)
...+++++|+|++|.... +++++++.|.+.++.. ...|+.+|+|..++++...++||||+++|++++++.+|+.+|.
T Consensus 57 ~~~~~vv~D~ETTGl~p~~~deIIeIgaV~~~~~~i~~~~f~~lv~P~~~i~~~~~~ltGIt~e~l~~ap~~~evl~~f~ 136 (244)
T PRK07740 57 TDLPFVVFDLETTGFSPQQGDEILSIGAVKTKGGEVETDTFYSLVKPKRPIPEHILELTGITAEDVAFAPPLAEVLHRFY 136 (244)
T ss_pred cCCCEEEEEEeCCCCCCCCCCeEEEEEEEEEECCEEEEEEEEEEeCcCCCCChhheeccCCCHHHHhCCCCHHHHHHHHH
Confidence 455789999999998753 5788999999876554 4568889999999999999999999999999999999999999
Q ss_pred HHHhcCCCCCcccccCCCceEEEeccchhhhccccccC-------CCCceecccccc
Q 024455 210 EILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNY-------PDHMLRDTAKYR 259 (267)
Q Consensus 210 ~~~~~~~~~~~~~~~~~~~~~lvgh~~~~Dl~~l~~~~-------~~~~~~dt~~~~ 259 (267)
+|+ ++.+|||||+.||+.||+-.. ....+|||..+.
T Consensus 137 ~fi--------------~~~~lVahna~fD~~fL~~~~~~~~~~~~~~~~iDt~~l~ 179 (244)
T PRK07740 137 AFI--------------GAGVLVAHHAGHDKAFLRHALWRTYRQPFTHRLIDTMFLT 179 (244)
T ss_pred HHh--------------CCCEEEEeCHHHHHHHHHHHHHHhcCCCcCCCeechHHHH
Confidence 999 778999999999999995321 134788988554
No 18
>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=99.68 E-value=9e-17 Score=131.54 Aligned_cols=100 Identities=20% Similarity=0.302 Sum_probs=88.3
Q ss_pred CCCceeeeeccccCCcCCCCccceeeEEEecCCC-CeeEecccCCCCCccccccccccCCHHhhccCCCHHHHHHHHHHH
Q 024455 133 RGPKAVAMDCEMVGGGSNGTLDLCARVCLVDEDE-NVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEI 211 (267)
Q Consensus 133 ~~~~~~~~dcE~~g~~~~~~~~~i~~v~vvd~~~-~~~~~~~v~P~~~i~~~~~~~~GIt~~~l~~~~~~~~v~~~~~~~ 211 (267)
....++++|+||+|......++++|.+.+.++.. ...|+.+++|..++++....+||||+++|+++|++++|+++|.+|
T Consensus 5 ~~~~fvv~D~ETTGl~~~~~IIeIgav~v~~~~~~~~~f~~li~P~~~i~~~a~~ihGIt~e~l~~~p~~~ev~~~~~~~ 84 (217)
T TIGR00573 5 VLDTETTGDNETTGLYAGHDIIEIGAVEIINRRITGNKFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDFADY 84 (217)
T ss_pred EecCEEEEEecCCCCCCCCCEEEEEEEEEECCCEeeeEEEEEECcCCCCCHHHHhhcCCCHHHHcCCCCHHHHHHHHHHH
Confidence 3456899999999988655589999999876642 357899999999999999999999999999999999999999999
Q ss_pred HhcCCCCCcccccCCCceEEEeccchhhhcccccc
Q 024455 212 LNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMN 246 (267)
Q Consensus 212 ~~~~~~~~~~~~~~~~~~~lvgh~~~~Dl~~l~~~ 246 (267)
+ ++.+|||||+.||+.||+-.
T Consensus 85 ~--------------~~~~lVaHNa~FD~~fL~~~ 105 (217)
T TIGR00573 85 I--------------RGAELVIHNASFDVGFLNYE 105 (217)
T ss_pred h--------------CCCEEEEeccHHHHHHHHHH
Confidence 9 67899999999999999743
No 19
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=99.68 E-value=9.9e-17 Score=137.35 Aligned_cols=111 Identities=24% Similarity=0.325 Sum_probs=96.3
Q ss_pred CCceeeeeccccCCcC-CCCccceeeEEEecCCCCeeEecccCCCCCccccccccccCCHHhhccCCCHHHHHHHHHHHH
Q 024455 134 GPKAVAMDCEMVGGGS-NGTLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEIL 212 (267)
Q Consensus 134 ~~~~~~~dcE~~g~~~-~~~~~~i~~v~vvd~~~~~~~~~~v~P~~~i~~~~~~~~GIt~~~l~~~~~~~~v~~~~~~~~ 212 (267)
...++++|+|++|... .+++++++++.+.++.....++.+|+|..++++..+++||||+++|++++++++|+.+|++|+
T Consensus 7 ~~~~Vv~DlETTGl~p~~~eIIEIgaV~v~~g~i~~~f~~lVkP~~~I~~~a~~ihGIT~e~l~~~~~~~evl~~f~~fl 86 (313)
T PRK06807 7 PLDYVVIDFETTGFNPYNDKIIQVAAVKYRNHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFLAFL 86 (313)
T ss_pred CCCEEEEEEECCCCCCCCCeEEEEEEEEEECCEEEEEEEEEECcCCCCCHhhhccCCCCHHHHhCCCCHHHHHHHHHHHH
Confidence 4468999999999875 368899999998766555568999999999999999999999999999999999999999999
Q ss_pred hcCCCCCcccccCCCceEEEeccchhhhccccc-------cCCCCceeccccc
Q 024455 213 NNGESTGRLMLDDGKARLLVGHGLEHDLDSLRM-------NYPDHMLRDTAKY 258 (267)
Q Consensus 213 ~~~~~~~~~~~~~~~~~~lvgh~~~~Dl~~l~~-------~~~~~~~~dt~~~ 258 (267)
++.+|||||+.||+.||+- ..|...+|||..+
T Consensus 87 --------------~~~~lVaHNa~FD~~fL~~~~~~~gl~~~~~~~iDtl~l 125 (313)
T PRK06807 87 --------------HTNVIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFL 125 (313)
T ss_pred --------------cCCeEEEEcHHHHHHHHHHHHHHcCCCCCCCCEeeHHHH
Confidence 6789999999999999952 3566788998754
No 20
>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=99.67 E-value=8.6e-17 Score=126.56 Aligned_cols=108 Identities=21% Similarity=0.332 Sum_probs=90.5
Q ss_pred eeeeeccccCCcC--CCCccceeeEEEecCCC-CeeEecccCCCCCccccccccccCCHHhhccCCCHHHHHHHHHHHHh
Q 024455 137 AVAMDCEMVGGGS--NGTLDLCARVCLVDEDE-NVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEILN 213 (267)
Q Consensus 137 ~~~~dcE~~g~~~--~~~~~~i~~v~vvd~~~-~~~~~~~v~P~~~i~~~~~~~~GIt~~~l~~~~~~~~v~~~~~~~~~ 213 (267)
++++|+|++|... ..++.+++.+.+.++.. ...++.+++|..++++..+++||||++++++++++++|+++|.+|+
T Consensus 1 ~v~~D~ETTGl~~~~~~~iieig~v~v~~~~~~~~~~~~~v~P~~~i~~~~~~ihGIt~e~l~~~~~~~~v~~~l~~~l- 79 (167)
T cd06131 1 QIVLDTETTGLDPREGHRIIEIGCVELINRRLTGNTFHVYINPERDIPEEAFKVHGITDEFLADKPKFAEIADEFLDFI- 79 (167)
T ss_pred CEEEEeeCCCCCCCCCCeEEEEEEEEEECCcEeccEEEEEECCCCCCCHHHHHHhCCCHHHHhcCCCHHHHHHHHHHHH-
Confidence 4789999999875 35788889998776542 2368899999999999999999999999999999999999999999
Q ss_pred cCCCCCcccccCCCceEEEeccchhhhccccccC----------CCCceeccccc
Q 024455 214 NGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNY----------PDHMLRDTAKY 258 (267)
Q Consensus 214 ~~~~~~~~~~~~~~~~~lvgh~~~~Dl~~l~~~~----------~~~~~~dt~~~ 258 (267)
++.+|||||+.||+.||+-.. ....++||..+
T Consensus 80 -------------~~~~lv~hn~~fD~~~l~~~~~~~~~~~~~~~~~~~idt~~~ 121 (167)
T cd06131 80 -------------RGAELVIHNASFDVGFLNAELSLLGLGKKIIDFCRVIDTLAL 121 (167)
T ss_pred -------------CCCeEEEeChHHhHHHHHHHHHHhCCCcccccCCCceEhHHH
Confidence 667999999999999996432 22467898643
No 21
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=99.66 E-value=7.3e-17 Score=152.10 Aligned_cols=120 Identities=24% Similarity=0.302 Sum_probs=104.0
Q ss_pred cCCCceeeeeccccCCcCC-CCccceeeEEEecCCCCeeEecccCCCCCccccccccccCCHHhhccCCCHHHHHHHHHH
Q 024455 132 CRGPKAVAMDCEMVGGGSN-GTLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILE 210 (267)
Q Consensus 132 ~~~~~~~~~dcE~~g~~~~-~~~~~i~~v~vvd~~~~~~~~~~v~P~~~i~~~~~~~~GIt~~~l~~~~~~~~v~~~~~~ 210 (267)
-....++++|.|++|.+.. +.++++|++.+.+++....++.+++|..|++...+++||||+++|++++++++|+.++.+
T Consensus 418 l~datyVVfDiETTGLs~~~d~iIE~aAvKikng~iId~f~~Fi~P~~pl~~~~telTgITdeml~~a~~i~~vL~kf~~ 497 (1444)
T COG2176 418 LDDATYVVFDIETTGLSPVYDEIIEIAAVKIKNGRIIDKFQFFIKPGRPLSATITELTGITDEMLENAPEIEEVLEKFRE 497 (1444)
T ss_pred cccccEEEEEeecCCcCcccchhhhheeeeeeCCcchHHHHHhcCCCCcCchhhhhccccCHHHHcCCccHHHHHHHHHH
Confidence 3445689999999999844 678999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhcCCCCCcccccCCCceEEEeccchhhhccccccCC-------CCceeccc-----ccccccccc
Q 024455 211 ILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNYP-------DHMLRDTA-----KYRPLMKTN 265 (267)
Q Consensus 211 ~~~~~~~~~~~~~~~~~~~~lvgh~~~~Dl~~l~~~~~-------~~~~~dt~-----~~~~~~~~~ 265 (267)
|+ +|+||||||+.||+.||+..+. ...+|||- .+|.|.++.
T Consensus 498 ~~--------------~d~IlVAHNasFD~gFl~~~~~k~~~~~~~~pvIDTL~lar~L~P~~ksh~ 550 (1444)
T COG2176 498 FI--------------GDSILVAHNASFDMGFLNTNYEKYGLEPLTNPVIDTLELARALNPEFKSHR 550 (1444)
T ss_pred Hh--------------cCcEEEeccCccchhHHHHHHHHhCCccccCchhhHHHHHHHhChhhhhcc
Confidence 99 8999999999999999975432 33578886 445555443
No 22
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=99.66 E-value=2.9e-16 Score=135.00 Aligned_cols=107 Identities=18% Similarity=0.256 Sum_probs=92.4
Q ss_pred ceeeeeccccCCcCCCCccceeeEEEecCCCCeeEecccCCCC-CccccccccccCCHHhhccCCCHHHHHHHHHHHHhc
Q 024455 136 KAVAMDCEMVGGGSNGTLDLCARVCLVDEDENVIFHTYVQPQL-PVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEILNN 214 (267)
Q Consensus 136 ~~~~~dcE~~g~~~~~~~~~i~~v~vvd~~~~~~~~~~v~P~~-~i~~~~~~~~GIt~~~l~~~~~~~~v~~~~~~~~~~ 214 (267)
.++++|+|++|. ..+++++++.+.+.++.....++++|+|.. .+++..+.+||||+++|+++|+|.+|+++|.+|+
T Consensus 2 ~~vviD~ETTg~-~~d~IieIgav~v~~g~i~~~f~~lv~P~~~~~~~~~~~IhGIT~e~v~~ap~f~ev~~~~~~fl-- 78 (309)
T PRK06195 2 NFVAIDFETANE-KRNSPCSIGIVVVKDGEIVEKVHYLIKPKEMRFMPINIGIHGIRPHMVEDELEFDKIWEKIKHYF-- 78 (309)
T ss_pred cEEEEEEeCCCC-CCCceEEEEEEEEECCEEEEEEEEEECCCCCCCChhheeccCcCHHHHhCCCCHHHHHHHHHHHh--
Confidence 478999999986 456788999999987766677999999984 5777889999999999999999999999999999
Q ss_pred CCCCCcccccCCCceEEEeccchhhhccccc-------cCCCCceecccc
Q 024455 215 GESTGRLMLDDGKARLLVGHGLEHDLDSLRM-------NYPDHMLRDTAK 257 (267)
Q Consensus 215 ~~~~~~~~~~~~~~~~lvgh~~~~Dl~~l~~-------~~~~~~~~dt~~ 257 (267)
++.+|||||+.||+.||+. ..|...++||..
T Consensus 79 ------------~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~idT~~ 116 (309)
T PRK06195 79 ------------NNNLVIAHNASFDISVLRKTLELYNIPMPSFEYICTMK 116 (309)
T ss_pred ------------CCCEEEEECcHHHHHHHHHHHHHhCCCCCCCCEEEHHH
Confidence 7789999999999999953 346668899963
No 23
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=99.66 E-value=2.2e-16 Score=128.72 Aligned_cols=101 Identities=19% Similarity=0.160 Sum_probs=86.9
Q ss_pred eeeeeccccCCcCCCCccceeeEEEecCCCCeeEecccCCCCCccccccccccCCHHhhccCCCHHHHHHHHHHHHhcCC
Q 024455 137 AVAMDCEMVGGGSNGTLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEILNNGE 216 (267)
Q Consensus 137 ~~~~dcE~~g~~~~~~~~~i~~v~vvd~~~~~~~~~~v~P~~~i~~~~~~~~GIt~~~l~~~~~~~~v~~~~~~~~~~~~ 216 (267)
++++|+|++|.. ..+++++.+.+.++.....++++++|..+|+...+.+||||+++++++|++++|+.+ |+
T Consensus 2 ~~vlD~ETTGl~--~~IieIg~v~v~~~~i~~~~~~lv~P~~~i~~~~~~ihgIt~e~v~~ap~~~ev~~~---~~---- 72 (219)
T PRK07983 2 LRVIDTETCGLQ--GGIVEIASVDVIDGKIVNPMSHLVRPDRPISPQAMAIHRITEAMVADKPWIEDVIPH---YY---- 72 (219)
T ss_pred eEEEEEECCCCC--CCCEEEEEEEEECCEEEEEEEEEECcCCCCCHHHhhcCCCCHHHHcCCCCHHHHHHH---Hc----
Confidence 478999999975 458899999998776666799999999999999999999999999999999998776 56
Q ss_pred CCCcccccCCCceEEEeccchhhhccccccCCCCceeccccc
Q 024455 217 STGRLMLDDGKARLLVGHGLEHDLDSLRMNYPDHMLRDTAKY 258 (267)
Q Consensus 217 ~~~~~~~~~~~~~~lvgh~~~~Dl~~l~~~~~~~~~~dt~~~ 258 (267)
++.+|||||+.||+.||... ....|||-.+
T Consensus 73 ----------~~~~lVaHNa~FD~~~L~~~--~~~~idTl~l 102 (219)
T PRK07983 73 ----------GSEWYVAHNASFDRRVLPEM--PGEWICTMKL 102 (219)
T ss_pred ----------CCCEEEEeCcHhhHHHHhCc--CCCcEeHHHH
Confidence 66799999999999999753 3478898754
No 24
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.65 E-value=9.9e-17 Score=146.33 Aligned_cols=67 Identities=22% Similarity=0.528 Sum_probs=59.7
Q ss_pred CCCccccccCccccCChHHHHHHHhHhcCCCCCC-CcccchhhcCCHHHHHhhc---------CCCCCCC---cCCcccc
Q 024455 11 STARHKCVACYKQFKRKDHLIEHMKISYHSVHQP-KCAVCQKLSKSFESLREHL---------TGPLSKA---HCSGIFS 77 (267)
Q Consensus 11 ~~k~~~C~~C~k~f~~~~~l~~H~~~~~H~~~~~-~C~~C~~~f~~~~~l~~H~---------~~~~~C~---~C~k~f~ 77 (267)
.--|-.|-+|-+....++.|+.|.|+ |+|++| +|.+||+.|.++.+|+.|+ ..++.|+ +|-+.|.
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 34467899999999999999999999 999999 9999999999999999999 3467788 8888888
Q ss_pred cc
Q 024455 78 DR 79 (267)
Q Consensus 78 ~~ 79 (267)
..
T Consensus 680 n~ 681 (958)
T KOG1074|consen 680 NA 681 (958)
T ss_pred cc
Confidence 64
No 25
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.65 E-value=2.6e-16 Score=150.78 Aligned_cols=110 Identities=22% Similarity=0.317 Sum_probs=95.9
Q ss_pred CCceeeeeccccCCcCCCCccceeeEEEecCCCCeeEecccCCCCCccccccccccCCHHhhccCCCHHHHHHHHHHHHh
Q 024455 134 GPKAVAMDCEMVGGGSNGTLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEILN 213 (267)
Q Consensus 134 ~~~~~~~dcE~~g~~~~~~~~~i~~v~vvd~~~~~~~~~~v~P~~~i~~~~~~~~GIt~~~l~~~~~~~~v~~~~~~~~~ 213 (267)
...++++|+|++|.+..++++++|.|.+.++.....|+++|+|..+|++.++.+||||+++|+++|++++|+.+|.+++
T Consensus 6 ~~~~vvvD~ETTGl~~~d~IIeIgaV~v~~g~i~~~f~~lv~P~~~i~~~~~~ltGIt~e~l~~ap~~~ev~~~~~~~l- 84 (820)
T PRK07246 6 LRKYAVVDLEATGAGPNASIIQVGIVIIEGGEIIDSYTTDVNPHEPLDEHIKHLTGITDQQLAQAPDFSQVARHIYDLI- 84 (820)
T ss_pred CCCEEEEEEecCCcCCCCeEEEEEEEEEECCEEEEEEEEEeCcCCCCCHhHhhcCCCCHHHHhcCCCHHHHHHHHHHHh-
Confidence 3468999999999976778999999999877666779999999999999999999999999999999999999999999
Q ss_pred cCCCCCcccccCCCceEEEeccchhhhcccccc-----C-CCCceecccc
Q 024455 214 NGESTGRLMLDDGKARLLVGHGLEHDLDSLRMN-----Y-PDHMLRDTAK 257 (267)
Q Consensus 214 ~~~~~~~~~~~~~~~~~lvgh~~~~Dl~~l~~~-----~-~~~~~~dt~~ 257 (267)
++.++||||+.||+.||+-. + .....|||..
T Consensus 85 -------------~~~~lVaHN~~FD~~fL~~~~~~~g~~~~~~~iDT~~ 121 (820)
T PRK07246 85 -------------EDCIFVAHNVKFDANLLAEALFLEGYELRTPRVDTVE 121 (820)
T ss_pred -------------CCCEEEEECcHHHHHHHHHHHHHcCCCCCCCceeHHH
Confidence 77999999999999999632 1 1235678763
No 26
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=99.63 E-value=5.6e-16 Score=125.59 Aligned_cols=112 Identities=21% Similarity=0.255 Sum_probs=93.0
Q ss_pred CCCceeeeeccccCCcC-CCCccceeeEEEecCCCC--eeEecccCCCCCccccccccccCCHHhhccCCCHHHHHHHHH
Q 024455 133 RGPKAVAMDCEMVGGGS-NGTLDLCARVCLVDEDEN--VIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKIL 209 (267)
Q Consensus 133 ~~~~~~~~dcE~~g~~~-~~~~~~i~~v~vvd~~~~--~~~~~~v~P~~~i~~~~~~~~GIt~~~l~~~~~~~~v~~~~~ 209 (267)
....++++|+||+|... .+++++++.|.+.++... ..++.+|+|..++++..+++||||++++++++++++|+++|.
T Consensus 27 ~~~~~vviD~ETTGl~~~~d~IieIgaV~~~~~~~~~~~~f~~~i~p~~~i~~~~~~ihGIt~~~l~~~~~~~~vl~~~~ 106 (202)
T PRK09145 27 PPDEWVALDCETTGLDPRRAEIVSIAAVKIRGNRILTSERLELLVRPPQSLSAESIKIHRLRHQDLEDGLSEEEALRQLL 106 (202)
T ss_pred CCCCEEEEEeECCCCCCCCCceEEEEEEEEECCEEeecCceEEEECCCCCCCHhHhhhcCcCHHHHhcCCCHHHHHHHHH
Confidence 34578999999999874 467888898888765322 358899999999999999999999999999999999999999
Q ss_pred HHHhcCCCCCcccccCCCceEEEeccchhhhccccccC-------CCCceeccccc
Q 024455 210 EILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNY-------PDHMLRDTAKY 258 (267)
Q Consensus 210 ~~~~~~~~~~~~~~~~~~~~~lvgh~~~~Dl~~l~~~~-------~~~~~~dt~~~ 258 (267)
+|+ ++.+|||||+.||+.||+... ....++|++.+
T Consensus 107 ~~i--------------~~~~lv~hn~~fD~~fL~~~~~~~~~~~~~~~~id~~~l 148 (202)
T PRK09145 107 AFI--------------GNRPLVGYYLEFDVAMLNRYVRPLLGIPLPNPLIEVSAL 148 (202)
T ss_pred HHH--------------cCCeEEEeCHHHHHHHHHHHHHHhcCCCCCCCeeeHHHH
Confidence 999 778999999999999996321 12357888643
No 27
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=99.63 E-value=5.8e-16 Score=127.96 Aligned_cols=108 Identities=22% Similarity=0.335 Sum_probs=89.8
Q ss_pred ceeeeeccccCCcC-CCCccceeeEEEecCCCCeeEecccCCCCCccccccccccCCHHhhccCCCHHHHHHHHHHHHhc
Q 024455 136 KAVAMDCEMVGGGS-NGTLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEILNN 214 (267)
Q Consensus 136 ~~~~~dcE~~g~~~-~~~~~~i~~v~vvd~~~~~~~~~~v~P~~~i~~~~~~~~GIt~~~l~~~~~~~~v~~~~~~~~~~ 214 (267)
.++++|+||+|... .+++++++. ++......++.+++|..+|+...+.+||||+++++++|++.+|+++|.+|++
T Consensus 3 ~~vv~D~ETTGl~~~~d~IIeig~---v~~~~~~~f~~lv~P~~~I~~~a~~IhGIt~e~v~~~p~f~ev~~~~~~fi~- 78 (232)
T PRK06309 3 ALIFYDTETTGTQIDKDRIIEIAA---YNGVTSESFQTLVNPEIPIPAEASKIHGITTDEVADAPKFPEAYQKFIEFCG- 78 (232)
T ss_pred cEEEEEeeCCCCCCCCCEEEEEEE---EcCccccEEEEEeCCCCCCChhHHhhcCCCHHHHhCCCCHHHHHHHHHHHHc-
Confidence 47899999999873 356666665 4556667899999999999999999999999999999999999999999993
Q ss_pred CCCCCcccccCCCceEEEeccc-hhhhcccccc-------CCCCceecccccc
Q 024455 215 GESTGRLMLDDGKARLLVGHGL-EHDLDSLRMN-------YPDHMLRDTAKYR 259 (267)
Q Consensus 215 ~~~~~~~~~~~~~~~~lvgh~~-~~Dl~~l~~~-------~~~~~~~dt~~~~ 259 (267)
++.+|||||+ .||+.||+-. .+...+|||..++
T Consensus 79 ------------~~~~lVaHN~~~FD~~~L~~e~~r~g~~~~~~~~iDt~~l~ 119 (232)
T PRK06309 79 ------------TDNILVAHNNDAFDFPLLRKECRRHGLEPPTLRTIDSLKWA 119 (232)
T ss_pred ------------CCCEEEEeCCHHHHHHHHHHHHHHcCCCCCCCcEEeHHHHH
Confidence 3569999995 8999999643 3456889997544
No 28
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=99.63 E-value=8.3e-16 Score=128.21 Aligned_cols=100 Identities=24% Similarity=0.317 Sum_probs=88.0
Q ss_pred ccCCCceeeeeccccCCcCC-CCccceeeEEEecCCCCeeEecccCCCCCccccccccccCCHHhhccCCCHHHHHHHHH
Q 024455 131 TCRGPKAVAMDCEMVGGGSN-GTLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKIL 209 (267)
Q Consensus 131 ~~~~~~~~~~dcE~~g~~~~-~~~~~i~~v~vvd~~~~~~~~~~v~P~~~i~~~~~~~~GIt~~~l~~~~~~~~v~~~~~ 209 (267)
......++++|+|++|.... ++++++|+|.+.++.....|+.+|+|. +++...+++||||+++++++|++++|+.+|.
T Consensus 64 ~~~~~~~vv~DiETTG~~~~~~~IIEIGAv~v~~g~i~~~f~~~v~p~-~ip~~~~~itGIt~e~l~~ap~~~evl~~f~ 142 (257)
T PRK08517 64 PIKDQVFCFVDIETNGSKPKKHQIIEIGAVKVKNGEIIDRFESFVKAK-EVPEYITELTGITYEDLENAPSLKEVLEEFR 142 (257)
T ss_pred CCCCCCEEEEEEeCCCCCCCCCeEEEEEEEEEECCEEEEEEEEEECCC-CCChhhhhhcCcCHHHHcCCCCHHHHHHHHH
Confidence 34556789999999998754 478999999998765556789999996 8999999999999999999999999999999
Q ss_pred HHHhcCCCCCcccccCCCceEEEeccchhhhccccc
Q 024455 210 EILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRM 245 (267)
Q Consensus 210 ~~~~~~~~~~~~~~~~~~~~~lvgh~~~~Dl~~l~~ 245 (267)
+|+ ++.++||||+.||+.||+.
T Consensus 143 ~fl--------------~~~v~VaHNa~FD~~fL~~ 164 (257)
T PRK08517 143 LFL--------------GDSVFVAHNVNFDYNFISR 164 (257)
T ss_pred HHH--------------CCCeEEEECHHHHHHHHHH
Confidence 999 6789999999999999963
No 29
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=99.61 E-value=2e-15 Score=129.59 Aligned_cols=109 Identities=21% Similarity=0.240 Sum_probs=89.4
Q ss_pred CCceeeeeccccCCcCC-CCccceeeEEEe-cCCCCeeEecccCCCCCccccccccccCCHHhhccCCCHHHHHHHHHHH
Q 024455 134 GPKAVAMDCEMVGGGSN-GTLDLCARVCLV-DEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEI 211 (267)
Q Consensus 134 ~~~~~~~dcE~~g~~~~-~~~~~i~~v~vv-d~~~~~~~~~~v~P~~~i~~~~~~~~GIt~~~l~~~~~~~~v~~~~~~~ 211 (267)
...++++|+|++|.... +++++++.+.+. ++.....+..+++|.. +...+.+||||+++|+++|+|++++++|.+|
T Consensus 14 ~~~fvvlD~ETTGl~p~~d~IIeIgav~v~~~g~i~~~~~~lv~P~~--~~~~~~IhGIt~e~l~~ap~f~ev~~~l~~~ 91 (313)
T PRK06063 14 PRGWAVVDVETSGFRPGQARIISLAVLGLDADGNVEQSVVTLLNPGV--DPGPTHVHGLTAEMLEGQPQFADIAGEVAEL 91 (313)
T ss_pred CCCEEEEEEECCCCCCCCCEEEEEEEEEEECCceeeeEEEEEECcCC--CCCCeecCCCCHHHHhCCCCHHHHHHHHHHH
Confidence 45689999999998754 678888888886 4444557899999975 3467899999999999999999999999999
Q ss_pred HhcCCCCCcccccCCCceEEEeccchhhhcccccc-------CCCCceeccccc
Q 024455 212 LNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMN-------YPDHMLRDTAKY 258 (267)
Q Consensus 212 ~~~~~~~~~~~~~~~~~~~lvgh~~~~Dl~~l~~~-------~~~~~~~dt~~~ 258 (267)
+ ++.+|||||+.||+.||+-. .|...++||-.+
T Consensus 92 l--------------~~~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~ldTl~l 131 (313)
T PRK06063 92 L--------------RGRTLVAHNVAFDYSFLAAEAERAGAELPVDQVMCTVEL 131 (313)
T ss_pred c--------------CCCEEEEeCHHHHHHHHHHHHHHcCCCCCCCCEEehHHH
Confidence 9 77899999999999999643 343456787643
No 30
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.61 E-value=3.7e-16 Score=142.66 Aligned_cols=78 Identities=15% Similarity=0.324 Sum_probs=63.2
Q ss_pred ccccccccCChhhHHHHHHHhcCCCCcc---ccccCcchhhhhhhccccccccccCCCceeeeecc---ccCCcCCCCcc
Q 024455 81 CNLCMNIFDSPSSLIKHKEACSLSAPVP---FEKTLSNAESQKKISGAIDEKRTCRGPKAVAMDCE---MVGGGSNGTLD 154 (267)
Q Consensus 81 C~~C~~~F~~~~~L~~H~~~h~~~~~~~---C~~~f~~~~~l~~H~~~~~~~r~~~~~~~~~~dcE---~~g~~~~~~~~ 154 (267)
|=+|-+..+-++.|+.|.|+|+||+||+ |++.|..+.+|+.|+..|..+- ..+ +.+.|. .|-..+...+.
T Consensus 608 CiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p---~~R-~q~ScP~~~ic~~kftn~V~ 683 (958)
T KOG1074|consen 608 CIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKP---PAR-VQFSCPSTFICQKKFTNAVT 683 (958)
T ss_pred eeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCc---ccc-ccccCCchhhhccccccccc
Confidence 9999999999999999999999999998 9999999999999997664321 111 567787 77666666666
Q ss_pred ceeeEEEe
Q 024455 155 LCARVCLV 162 (267)
Q Consensus 155 ~i~~v~vv 162 (267)
+--+|++.
T Consensus 684 lpQhIriH 691 (958)
T KOG1074|consen 684 LPQHIRIH 691 (958)
T ss_pred ccceEEee
Confidence 65666663
No 31
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=99.61 E-value=6.3e-16 Score=121.66 Aligned_cols=109 Identities=33% Similarity=0.514 Sum_probs=91.6
Q ss_pred eeeeeccccCCcCC-CCccceeeEEEecCCCCeeEecccCCCCCccccccccccCCHHhhccCCCHHHHHHHHHHHHhcC
Q 024455 137 AVAMDCEMVGGGSN-GTLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEILNNG 215 (267)
Q Consensus 137 ~~~~dcE~~g~~~~-~~~~~i~~v~vvd~~~~~~~~~~v~P~~~i~~~~~~~~GIt~~~l~~~~~~~~v~~~~~~~~~~~ 215 (267)
++++|+|++|.... .++.+++.+.+.++.....|+.+|+|..+++++.++++|||++++++++++++|.++|.+++
T Consensus 2 ~v~~D~Ettg~~~~~~~Iieig~v~~~~~~~~~~f~~~v~p~~~i~~~~~~~~Git~~~l~~~~~~~~~~~~~~~~l--- 78 (169)
T smart00479 2 LVVIDCETTGLDPGKDEIIEIAAVDVDGGRIIVVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFL--- 78 (169)
T ss_pred EEEEEeeCCCCCCCCCeEEEEEEEEEECCEeEEEEEEEECCCCCCCHHHHHHhCCCHHHHhCCCCHHHHHHHHHHHh---
Confidence 58899999998765 67888888887766545679999999999999999999999999999999999999999999
Q ss_pred CCCCcccccCCCceEEEeccc-hhhhccccccCCC--------Cceecccccc
Q 024455 216 ESTGRLMLDDGKARLLVGHGL-EHDLDSLRMNYPD--------HMLRDTAKYR 259 (267)
Q Consensus 216 ~~~~~~~~~~~~~~~lvgh~~-~~Dl~~l~~~~~~--------~~~~dt~~~~ 259 (267)
++.++||||. .||+.||+..+.+ ..+|||..+.
T Consensus 79 -----------~~~~~v~~n~~~fD~~~L~~~~~~~~~~~~~~~~~iD~~~~~ 120 (169)
T smart00479 79 -----------KGKILVAGNALNFDLRFLKLEHPRLGIKDPPKNPVIDTLKLA 120 (169)
T ss_pred -----------cCCEEEEeCCHHHhHHHHHHHHHHhCCCCCcCCCeeEHHHHH
Confidence 5677888887 9999999764432 2368887544
No 32
>PRK07883 hypothetical protein; Validated
Probab=99.60 E-value=1.6e-15 Score=139.47 Aligned_cols=112 Identities=26% Similarity=0.363 Sum_probs=97.3
Q ss_pred CCCceeeeeccccCCcCC-CCccceeeEEEecCCCCeeEecccCCCCCccccccccccCCHHhhccCCCHHHHHHHHHHH
Q 024455 133 RGPKAVAMDCEMVGGGSN-GTLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEI 211 (267)
Q Consensus 133 ~~~~~~~~dcE~~g~~~~-~~~~~i~~v~vvd~~~~~~~~~~v~P~~~i~~~~~~~~GIt~~~l~~~~~~~~v~~~~~~~ 211 (267)
....++++|+|++|.+.. .++.+++.|.+.++.....|+.+|+|..++++..+.+||||+++|++++++++|+.+|.+|
T Consensus 13 ~~~~~Vv~D~ETTGl~p~~~~IIEIgaV~v~~g~iv~~f~~lV~P~~~i~~~~~~itGIt~e~l~~ap~~~evl~~f~~f 92 (557)
T PRK07883 13 RDVTFVVVDLETTGGSPAGDAITEIGAVKVRGGEVLGEFATLVNPGRPIPPFITVLTGITTAMVAGAPPIEEVLPAFLEF 92 (557)
T ss_pred cCCCEEEEEEecCCCCCCCCeEEEEEEEEEECCEEEEEEEEEECCCCCCChhHHhhcCCCHHHHhCCCCHHHHHHHHHHH
Confidence 345789999999998754 6889999999976655566899999999999999999999999999999999999999999
Q ss_pred HhcCCCCCcccccCCCceEEEeccchhhhccccc-------cCCCCceeccccc
Q 024455 212 LNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRM-------NYPDHMLRDTAKY 258 (267)
Q Consensus 212 ~~~~~~~~~~~~~~~~~~~lvgh~~~~Dl~~l~~-------~~~~~~~~dt~~~ 258 (267)
+ ++.+|||||+.||+.||+. .+|...++||..+
T Consensus 93 l--------------~~~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~iDTl~l 132 (557)
T PRK07883 93 A--------------RGAVLVAHNAPFDIGFLRAAAARCGYPWPGPPVLCTVRL 132 (557)
T ss_pred h--------------cCCEEEEeCcHHHHHHHHHHHHHcCCCCCCCCcEecHHH
Confidence 9 6789999999999999963 4455678999643
No 33
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=99.60 E-value=1.8e-15 Score=124.93 Aligned_cols=116 Identities=18% Similarity=0.128 Sum_probs=89.6
Q ss_pred CCceeeeeccccCCcC-CCCccceeeEEEec-CCCCeeEecccCCCCCccccccccccCCHHhhcc-CCCHHHHHHHHHH
Q 024455 134 GPKAVAMDCEMVGGGS-NGTLDLCARVCLVD-EDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKN-AMPLKEVKDKILE 210 (267)
Q Consensus 134 ~~~~~~~dcE~~g~~~-~~~~~~i~~v~vvd-~~~~~~~~~~v~P~~~i~~~~~~~~GIt~~~l~~-~~~~~~v~~~~~~ 210 (267)
...++++|+|++|.+. .+++++++.+.+.+ +.....++.+++|..+|++..+.+||||++++.+ ++++++|+.+|.+
T Consensus 5 ~~~~vv~D~ETTGl~p~~d~Iieig~v~v~~~g~~~~~~~~lv~P~~~i~~~a~~IhGIt~e~l~~~g~~~~~vl~e~~~ 84 (232)
T PRK07942 5 PGPLAAFDLETTGVDPETARIVTAALVVVDADGEVVESREWLADPGVEIPEEASAVHGITTEYARAHGRPAAEVLAEIAD 84 (232)
T ss_pred cCcEEEEEeccCCCCCCCCeeEEEEEEEEeCCCccccceEEEECCCCCCCHHHHHHhCCCHHHHHhhCCCHHHHHHHHHH
Confidence 3467999999999874 45677878777763 4444568889999999999999999999999976 6888899999988
Q ss_pred HHhcCCCCCcccccCCCceEEEeccchhhhccccccCC--------CCceeccccc
Q 024455 211 ILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNYP--------DHMLRDTAKY 258 (267)
Q Consensus 211 ~~~~~~~~~~~~~~~~~~~~lvgh~~~~Dl~~l~~~~~--------~~~~~dt~~~ 258 (267)
+|..... ++.+|||||+.||+.||+-... ...++||-.+
T Consensus 85 ~l~~~~~---------~~~~lVahNa~FD~~fL~~~~~r~~~~~~~~~~~iDt~~l 131 (232)
T PRK07942 85 ALREAWA---------RGVPVVVFNAPYDLTVLDRELRRHGLPSLVPGPVIDPYVI 131 (232)
T ss_pred HHHHHhh---------cCCEEEEeCcHhhHHHHHHHHHHcCCCCccCCcEeeHHHH
Confidence 8731111 4679999999999999964332 2356787644
No 34
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.59 E-value=2.1e-15 Score=146.74 Aligned_cols=109 Identities=27% Similarity=0.393 Sum_probs=95.4
Q ss_pred CceeeeeccccCCcC--CCCccceeeEEEecCCCCeeEecccCCCCCccccccccccCCHHhhccCCCHHHHHHHHHHHH
Q 024455 135 PKAVAMDCEMVGGGS--NGTLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEIL 212 (267)
Q Consensus 135 ~~~~~~dcE~~g~~~--~~~~~~i~~v~vvd~~~~~~~~~~v~P~~~i~~~~~~~~GIt~~~l~~~~~~~~v~~~~~~~~ 212 (267)
..++++|+|++|... .+++++++.+.+.++.....|+.+|+|..+|+++++++||||+++|+++|++++|+.+|.+|+
T Consensus 3 ~~~vvvD~ETTG~~p~~~d~IIeigav~v~~~~i~~~f~~~v~P~~~i~~~~~~ltGIt~~~l~~ap~f~ev~~~l~~~l 82 (928)
T PRK08074 3 KRFVVVDLETTGNSPKKGDKIIQIAAVVVEDGEILERFSSFVNPERPIPPFITELTGISEEMVKQAPLFEDVAPEIVELL 82 (928)
T ss_pred CCEEEEEEeCCCCCCCCCCcEEEEEEEEEECCEEEEEEEEEECcCCCCCHHHhhcCCCCHHHHhcCCCHHHHHHHHHHHh
Confidence 357999999999863 357999999999877666679999999999999999999999999999999999999999999
Q ss_pred hcCCCCCcccccCCCceEEEeccchhhhccccc-------cCCCCceecccc
Q 024455 213 NNGESTGRLMLDDGKARLLVGHGLEHDLDSLRM-------NYPDHMLRDTAK 257 (267)
Q Consensus 213 ~~~~~~~~~~~~~~~~~~lvgh~~~~Dl~~l~~-------~~~~~~~~dt~~ 257 (267)
+|.++||||+.||+.||+- ..+...+|||..
T Consensus 83 --------------~~~~~VaHN~~FD~~fL~~~~~~~g~~~~~~~~iDt~~ 120 (928)
T PRK08074 83 --------------EGAYFVAHNVHFDLNFLNEELERAGYTEIHCPKLDTVE 120 (928)
T ss_pred --------------CCCeEEEEChHHHHHHHHHHHHHcCCCCCCCCeeeHHH
Confidence 7899999999999999963 223457889863
No 35
>PRK06722 exonuclease; Provisional
Probab=99.59 E-value=2.5e-15 Score=125.97 Aligned_cols=97 Identities=14% Similarity=0.117 Sum_probs=84.0
Q ss_pred CceeeeeccccCCcC----CCCccceeeEEEecCCC--CeeEecccCCCCCccccccccccCCHHhhccCCCHHHHHHHH
Q 024455 135 PKAVAMDCEMVGGGS----NGTLDLCARVCLVDEDE--NVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKI 208 (267)
Q Consensus 135 ~~~~~~dcE~~g~~~----~~~~~~i~~v~vvd~~~--~~~~~~~v~P~~~i~~~~~~~~GIt~~~l~~~~~~~~v~~~~ 208 (267)
..++++|.|+++... .++++++|.|.+.++.+ ...|+++|+|..+|+++.+.+||||+++|+++|++++|+.+|
T Consensus 5 ~~~vViD~ETT~~p~~~~~~deIIEIGAVkV~~g~i~Ivd~F~sLV~P~~~I~~~i~~LTGIT~emV~~AP~f~eVl~ef 84 (281)
T PRK06722 5 THFIVFDIERNFRPYKSEDPSEIVDIGAVKIEASTMKVIGEFSELVKPGARLTRHTTKLTGITKKDLIGVEKFPQIIEKF 84 (281)
T ss_pred CEEEEEEeeCCCCCCCCCCCCeEEEEEEEEEECCceeEEeeEEEEECCCCcCCHhHhhhcCCCHHHHcCCCCHHHHHHHH
Confidence 457899999986432 26789999999988743 455999999999999999999999999999999999999999
Q ss_pred HHHHhcCCCCCcccccCCCceEEEeccchhhhccccc
Q 024455 209 LEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRM 245 (267)
Q Consensus 209 ~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~Dl~~l~~ 245 (267)
.+|+ ++.++|+||+.||++||..
T Consensus 85 ~~fi--------------g~~~lvahna~FD~~FL~~ 107 (281)
T PRK06722 85 IQFI--------------GEDSIFVTWGKEDYRFLSH 107 (281)
T ss_pred HHHH--------------CCCcEEEEEeHHHHHHHHH
Confidence 9999 5567777788999999965
No 36
>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=99.59 E-value=2.2e-15 Score=119.47 Aligned_cols=113 Identities=20% Similarity=0.211 Sum_probs=86.7
Q ss_pred eeeeeccccCCc--CCCCccceeeEEEecCCC-------------CeeEecccCCCCCccccccccccCCHHhhccCCCH
Q 024455 137 AVAMDCEMVGGG--SNGTLDLCARVCLVDEDE-------------NVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPL 201 (267)
Q Consensus 137 ~~~~dcE~~g~~--~~~~~~~i~~v~vvd~~~-------------~~~~~~~v~P~~~i~~~~~~~~GIt~~~l~~~~~~ 201 (267)
++++|+|++|.. ..+++++++.+.+.++.. ...++++++|..+|++..+.+||||++++.+++++
T Consensus 1 ~vv~D~ETTGl~~~~~d~Iiei~av~v~~~~~~~~~~~~~~~~~~~~~~~~lv~P~~~I~~~a~~IhGIt~e~l~~~~~~ 80 (177)
T cd06136 1 FVFLDLETTGLPKHNRPEITELCLVAVHRDHLLNTSRDKPALPRVLDKLSLCFNPGRAISPGASEITGLSNDLLEHKAPF 80 (177)
T ss_pred CeEEeeecCCCCCCCCCceEEEEEEEEecccccccccccccccceeeeeeEEeCCCCcCChhHHHHhCcCHHHHhcCCCc
Confidence 478999999997 457889999999876531 23578999999999999999999999999999887
Q ss_pred HH-HHHHHHHHHhcCCCCCcccccCCCceEEEeccc-hhhhccccccC-------C-CCceecccccc
Q 024455 202 KE-VKDKILEILNNGESTGRLMLDDGKARLLVGHGL-EHDLDSLRMNY-------P-DHMLRDTAKYR 259 (267)
Q Consensus 202 ~~-v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~-~~Dl~~l~~~~-------~-~~~~~dt~~~~ 259 (267)
++ +.+.|.+|+... +++.+|||||+ .||+.||+-.. + ....+||..+.
T Consensus 81 ~~~~~~~l~~f~~~~----------~~~~~lVaHNa~~FD~~fL~~~~~r~~~~~~~~~~~iDtl~l~ 138 (177)
T cd06136 81 DSDTANLIKLFLRRQ----------PKPICLVAHNGNRFDFPILRSELERLGTKLPDDILCVDSLPAF 138 (177)
T ss_pred cHHHHHHHHHHHHhc----------CCCCEEEEcCCcccCHHHHHHHHHHcCCCCCCCCEEEEeHHHH
Confidence 64 667777777320 03469999998 89999995432 2 23457876443
No 37
>PRK05168 ribonuclease T; Provisional
Probab=99.55 E-value=6.4e-15 Score=119.93 Aligned_cols=121 Identities=22% Similarity=0.264 Sum_probs=90.3
Q ss_pred CCceeeeeccccCCcC-CCCccceeeEEEecC-CC----CeeEecccCC--CCCccccccccccCCHHh-hccCCCHHHH
Q 024455 134 GPKAVAMDCEMVGGGS-NGTLDLCARVCLVDE-DE----NVIFHTYVQP--QLPVTNYRYEVTGLTEED-IKNAMPLKEV 204 (267)
Q Consensus 134 ~~~~~~~dcE~~g~~~-~~~~~~i~~v~vvd~-~~----~~~~~~~v~P--~~~i~~~~~~~~GIt~~~-l~~~~~~~~v 204 (267)
...++++|.|++|.+. .+++++++.|.+... ++ ...|+.+|+| ..+|+...+.+||||+++ +.++++++++
T Consensus 16 ~~~~vv~D~ETTGl~~~~d~IieIgaV~v~~d~~g~i~~~~~f~~lv~P~~~~~i~~~~~~ihGIt~e~~~~~~~~~~~~ 95 (211)
T PRK05168 16 GFLPVVIDVETAGFNAKTDALLEIAAVTLKMDEQGWLYPDETLHFHVEPFEGANLEPEALAFNGIDPDNPLRGAVSEKEA 95 (211)
T ss_pred CCceEEEEeeCCCCCCCCCEEEEEeEEEEEecCCCcEeccceEEEEECCCCCCCCCHHHHhhcCCCchhhhhcCCChHHH
Confidence 4456899999999874 467889999998732 22 3578999999 468999999999999986 7888999999
Q ss_pred HHHHHHHHhcCCCCCcccccCCCceEEEeccchhhhccccccC----------CCCceecccccc
Q 024455 205 KDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNY----------PDHMLRDTAKYR 259 (267)
Q Consensus 205 ~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~Dl~~l~~~~----------~~~~~~dt~~~~ 259 (267)
+.++++++..... .. ...+.+|||||+.||+.||+... +...++||..+.
T Consensus 96 l~~~~~~l~~~~~----~~-~~~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~iDt~~la 155 (211)
T PRK05168 96 LHEIFKMVRKGIK----AS-GCNRAILVAHNAHFDLSFLMAAAERAGLKRNPFHPFSTFDTATLS 155 (211)
T ss_pred HHHHHHHHHHHHH----hc-ccCCceEEEeccHHhHHHHHHHHHHhCCCCCCCCCCcEeeHHHHH
Confidence 9888888731000 00 00257999999999999996432 234578987554
No 38
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=99.55 E-value=7.4e-15 Score=119.42 Aligned_cols=108 Identities=20% Similarity=0.260 Sum_probs=87.1
Q ss_pred ceeeeeccccCCcC-------CCCccceeeEEEecCCCCeeEecccCCCC--CccccccccccCCHHhhccCCCHHHHHH
Q 024455 136 KAVAMDCEMVGGGS-------NGTLDLCARVCLVDEDENVIFHTYVQPQL--PVTNYRYEVTGLTEEDIKNAMPLKEVKD 206 (267)
Q Consensus 136 ~~~~~dcE~~g~~~-------~~~~~~i~~v~vvd~~~~~~~~~~v~P~~--~i~~~~~~~~GIt~~~l~~~~~~~~v~~ 206 (267)
.++++|+|++|... ..+++++++|.+.++.....|+++|+|.. +++++.+++||||+++|+++|++++|++
T Consensus 5 ~~vvlD~EtTg~~~~~~~~~~~~eIIeIGaV~v~~~~i~~~f~~lV~P~~~~~i~~~~~~ltGIt~~~l~~ap~~~evl~ 84 (207)
T PRK07748 5 QFLFLDFEFTMPQHKKKPKGFFPEIIEVGLVSVVGCEVEDTFSSYVKPKTFPSLTERCKSFLGITQEDVDKGISFEELVE 84 (207)
T ss_pred eEEEEEeecCCcCCCCCCCCCCCceEEEeEEEEecCcChhhhcceECCCccCccChhhhhhcCcCHHHHccCCCHHHHHH
Confidence 57999999998532 35789999999987766677999999986 6899999999999999999999999999
Q ss_pred HHHHHHhcCCCCCcccccCCCc-eEEEeccchhhhccccc-------cCCC-Cceecccc
Q 024455 207 KILEILNNGESTGRLMLDDGKA-RLLVGHGLEHDLDSLRM-------NYPD-HMLRDTAK 257 (267)
Q Consensus 207 ~~~~~~~~~~~~~~~~~~~~~~-~~lvgh~~~~Dl~~l~~-------~~~~-~~~~dt~~ 257 (267)
+|.+|+ ++ .++|+|+..||+.||+. ..|- ..++|++.
T Consensus 85 ~f~~~~--------------~~~~~~iv~~~~fD~~fL~~~~~~~~~~~~~~~~~~dl~~ 130 (207)
T PRK07748 85 KLAEYD--------------KRCKPTIVTWGNMDMKVLKHNCEKAGVPFPFKGQCRDLSL 130 (207)
T ss_pred HHHHHh--------------CcCCeEEEEECHHHHHHHHHHHHHcCCCCcccccceeHHH
Confidence 999999 44 34444557999999953 2232 25667764
No 39
>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=99.54 E-value=4.8e-15 Score=118.74 Aligned_cols=119 Identities=23% Similarity=0.232 Sum_probs=85.6
Q ss_pred ceeeeeccccCCcC-CCCccceeeEEEecC-CC----CeeEecccCC--CCCccccccccccCCHHh-hccCCCHHHHHH
Q 024455 136 KAVAMDCEMVGGGS-NGTLDLCARVCLVDE-DE----NVIFHTYVQP--QLPVTNYRYEVTGLTEED-IKNAMPLKEVKD 206 (267)
Q Consensus 136 ~~~~~dcE~~g~~~-~~~~~~i~~v~vvd~-~~----~~~~~~~v~P--~~~i~~~~~~~~GIt~~~-l~~~~~~~~v~~ 206 (267)
..+++|+||+|.+. .+++++++.|.+.+. ++ ...|+++++| ..+|+....++||||+++ +..++..++++.
T Consensus 6 ~~vv~D~ETTGl~~~~d~Iieigav~v~~~~~~~i~~~~~f~~lv~P~~~~~i~~~~~~ihGIt~~~~~~~~~~~~~~~~ 85 (189)
T cd06134 6 LPVVVDVETGGFNPQTDALLEIAAVTLEMDEQGNLYPDETFHFHILPFEGANLDPAALEFNGIDPFHPFRFAVDEKEALK 85 (189)
T ss_pred eeEEEEecCCCCCCCCCeEEEEEEEEEEECCCCceeccceEEEEEcCCCCCCCCHHHHhhcCCCchhhhccccchHHHHH
Confidence 45899999999874 467899999999853 22 3578999999 578999999999999987 566676666666
Q ss_pred HHHHHHhcCCCCCcccccCCCceEEEeccchhhhcccccc----------CCCCceecccccc
Q 024455 207 KILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMN----------YPDHMLRDTAKYR 259 (267)
Q Consensus 207 ~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~Dl~~l~~~----------~~~~~~~dt~~~~ 259 (267)
++++++.+.- . ....++.+|||||+.||+.||+.. ++...++||..+.
T Consensus 86 ~~~~~l~~~~----~-~~~~~~~~lVaHna~FD~~fL~~~~~~~~~~~~~~~~~~~lDt~~la 143 (189)
T cd06134 86 EIFKPIRKAL----K-AQGCTRAILVGHNAHFDLGFLNAAVARCKIKRNPFHPFSTFDTATLA 143 (189)
T ss_pred HHHHHHHHHH----h-hcccCCCeEEEecchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHH
Confidence 6666552100 0 000035799999999999999642 2234578987654
No 40
>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=99.54 E-value=1.4e-14 Score=140.29 Aligned_cols=107 Identities=23% Similarity=0.316 Sum_probs=93.2
Q ss_pred eeeeeccccCCcC-CCCccceeeEEEecCCCCeeEecccCCCCCccccccccccCCHHhhccCCCHHHHHHHHHHHHhcC
Q 024455 137 AVAMDCEMVGGGS-NGTLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEILNNG 215 (267)
Q Consensus 137 ~~~~dcE~~g~~~-~~~~~~i~~v~vvd~~~~~~~~~~v~P~~~i~~~~~~~~GIt~~~l~~~~~~~~v~~~~~~~~~~~ 215 (267)
++++|+||+|... .++++++|.|.+.++.....|+++|+|..+|++..+.+||||+++++++|++++|+.+|.+++
T Consensus 2 ~vvvD~ETTG~~~~~~~IIeig~v~v~~~~i~~~f~~~v~P~~~i~~~~~~ltGIt~e~l~~ap~~~ev~~~l~~~l--- 78 (850)
T TIGR01407 2 YAVVDLETTGTQLSFDKIIQIGIVVVEDGEIVDTFHTDVNPNEPIPPFIQELTGISDNMLQQAPYFSQVAQEIYDLL--- 78 (850)
T ss_pred EEEEEEECCCCCCCCCeEEEEEEEEEECCEEEEEEEEEeCCCCCCChhhhhhcCcCHHHHhCCCCHHHHHHHHHHHh---
Confidence 6899999999873 478899999998776656679999999999999999999999999999999999999999999
Q ss_pred CCCCcccccCCCceEEEeccchhhhcccccc-------CCCCceecccc
Q 024455 216 ESTGRLMLDDGKARLLVGHGLEHDLDSLRMN-------YPDHMLRDTAK 257 (267)
Q Consensus 216 ~~~~~~~~~~~~~~~lvgh~~~~Dl~~l~~~-------~~~~~~~dt~~ 257 (267)
++.++||||+.||+.||+-. .....++||..
T Consensus 79 -----------~~~~~VahN~~fD~~fL~~~~~~~g~~~~~~~~iDt~~ 116 (850)
T TIGR01407 79 -----------EDGIFVAHNVHFDLNFLAKALKDCGYEPLPKPRIDTVE 116 (850)
T ss_pred -----------CCCEEEEeCcHHHHHHHHHHHHHcCCCCCCCCeEeHHH
Confidence 77899999999999999642 12446788763
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=99.54 E-value=1.2e-14 Score=117.28 Aligned_cols=121 Identities=22% Similarity=0.244 Sum_probs=88.7
Q ss_pred CCceeeeeccccCCcC-CCCccceeeEEEecC-CCC----eeEecccCCC--CCccccccccccCCHH-hhccCCCHHHH
Q 024455 134 GPKAVAMDCEMVGGGS-NGTLDLCARVCLVDE-DEN----VIFHTYVQPQ--LPVTNYRYEVTGLTEE-DIKNAMPLKEV 204 (267)
Q Consensus 134 ~~~~~~~dcE~~g~~~-~~~~~~i~~v~vvd~-~~~----~~~~~~v~P~--~~i~~~~~~~~GIt~~-~l~~~~~~~~v 204 (267)
...++++|+||+|.+. .++++++|.|.+... .+. ..++.+++|. .+|+.....+||||++ ++.++++.+++
T Consensus 7 ~~~~vv~D~ETTGl~~~~d~IieIgav~v~~~~~g~i~~~~~f~~~v~p~p~~~i~~~a~~ihGIt~~~~~~~~~~~~~~ 86 (200)
T TIGR01298 7 GYLPVVVDVETGGFNAKTDALLEIAAITLKMDEQGWLFPDTTLHFHVEPFEGANIQPEALEFTGIDLDHPLRGAVSEYEA 86 (200)
T ss_pred CCeeEEEEeeCCCCCCCCCeEEEEEEEEEEEcCCCcEeecceeEEEEcCCCCCCCCHHHHHccCCChhhhhhcCcchHHH
Confidence 3456899999999885 457889999998732 333 3488999974 7899999999999976 68899998888
Q ss_pred HHHHHHHHhcCCCCCcccccCCCceEEEeccchhhhccccccC----------CCCceecccccc
Q 024455 205 KDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNY----------PDHMLRDTAKYR 259 (267)
Q Consensus 205 ~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~Dl~~l~~~~----------~~~~~~dt~~~~ 259 (267)
+.++++++.... .+...++.+|||||+.||+.||+... +...++||..+.
T Consensus 87 ~~~~~~~l~~~~-----~~~~~~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~lDTl~la 146 (200)
T TIGR01298 87 LHEIFKVVRKAM-----KASGCQRAILVGHNANFDLGFLNAAVERTSLKRNPFHPFSTFDTATLA 146 (200)
T ss_pred HHHHHHHHHHHH-----HhcccCCCEEEEECchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHH
Confidence 888888762100 00000357999999999999996421 234578998655
No 42
>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=99.53 E-value=6.6e-15 Score=144.49 Aligned_cols=113 Identities=24% Similarity=0.360 Sum_probs=97.4
Q ss_pred CCCceeeeeccccCCcC-CCCccceeeEEEecCCCCeeEecccCCCCCccccccccccCCHHhhccCCCHHHHHHHHHHH
Q 024455 133 RGPKAVAMDCEMVGGGS-NGTLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEI 211 (267)
Q Consensus 133 ~~~~~~~~dcE~~g~~~-~~~~~~i~~v~vvd~~~~~~~~~~v~P~~~i~~~~~~~~GIt~~~l~~~~~~~~v~~~~~~~ 211 (267)
....++++|+|++|.+. .++++++++|.+.++.....|+.+|+|..+|++..+++||||+++|++++++++|+++|++|
T Consensus 188 ~~~~~VVfDiETTGL~~~~d~IIEIGAVkv~~g~iid~f~~~V~P~~~I~~~~~~ltGIT~e~L~~ap~~~evl~~f~~f 267 (1213)
T TIGR01405 188 DDATYVVFDIETTGLSPQYDEIIEFGAVKVKNGRIIDKFQFFIKPHEPLSAFVTELTGITQDMLENAPEIEEVLEKFKEF 267 (1213)
T ss_pred cCCcEEEEEeEecCCCCCCCeEEEEEEEEEECCeEEEEEEEEECCCCCCCHHHHHHhCCCHHHHhCCCCHHHHHHHHHHH
Confidence 34578999999999874 46789999999988766667999999999999999999999999999999999999999999
Q ss_pred HhcCCCCCcccccCCCceEEEeccchhhhccccccC-------CCCceecccccc
Q 024455 212 LNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNY-------PDHMLRDTAKYR 259 (267)
Q Consensus 212 ~~~~~~~~~~~~~~~~~~~lvgh~~~~Dl~~l~~~~-------~~~~~~dt~~~~ 259 (267)
+ ++.+|||||+.||+.||+-.+ ....+|||..+.
T Consensus 268 l--------------~~~iLVaHNa~FD~~fL~~~~~r~g~~~~~~~~IDTl~la 308 (1213)
T TIGR01405 268 F--------------KDSILVAHNASFDIGFLNTNFEKVGLEPLENPVIDTLELA 308 (1213)
T ss_pred h--------------CCCeEEEEChHHHHHHHHHHHHHcCCCccCCCEeEHHHHH
Confidence 9 778999999999999996432 224678887433
No 43
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=99.53 E-value=2.4e-14 Score=119.47 Aligned_cols=97 Identities=29% Similarity=0.428 Sum_probs=89.1
Q ss_pred CceeeeeccccCCcC-CCCccceeeEEEecCCCCee-EecccCCCCCccccccccccCCHHhhccCCCHHHHHHHHHHHH
Q 024455 135 PKAVAMDCEMVGGGS-NGTLDLCARVCLVDEDENVI-FHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEIL 212 (267)
Q Consensus 135 ~~~~~~dcE~~g~~~-~~~~~~i~~v~vvd~~~~~~-~~~~v~P~~~i~~~~~~~~GIt~~~l~~~~~~~~v~~~~~~~~ 212 (267)
..++++|+|++|... .+++++++.|.+.++..... ++.+++|..+|++...+++|||.+++.++|.+.++.+++.+++
T Consensus 13 ~~~vv~D~ETtg~~~~~~~iieIgav~~~~~~i~~~~~~~~v~P~~~i~~~~~~i~git~e~l~~~p~~~~v~~~~~~~i 92 (243)
T COG0847 13 TRFVVIDLETTGLNPKKDRIIEIGAVTLEDGRIVERSFHTLVNPERPIPPEIFKIHGITDEMLADAPKFAEVLPEFLDFI 92 (243)
T ss_pred CcEEEEecccCCCCCCCCceEEEEeEEEECCeeecceeEEEECCCCCCChhhhhhcCCCHHHHhcCCCHHHHHHHHHHHH
Confidence 457999999999985 78999999999998866544 9999999989999999999999999999999999999999999
Q ss_pred hcCCCCCcccccCCCc-eEEEeccchhhhccccc
Q 024455 213 NNGESTGRLMLDDGKA-RLLVGHGLEHDLDSLRM 245 (267)
Q Consensus 213 ~~~~~~~~~~~~~~~~-~~lvgh~~~~Dl~~l~~ 245 (267)
.+ .++||||+.||+.||+.
T Consensus 93 --------------~~~~~~Vahna~fD~~fl~~ 112 (243)
T COG0847 93 --------------GGLRLLVAHNAAFDVGFLRV 112 (243)
T ss_pred --------------CCCCeEEEEchhhcHHHHHH
Confidence 56 89999999999999964
No 44
>PRK05359 oligoribonuclease; Provisional
Probab=99.51 E-value=1.1e-14 Score=115.46 Aligned_cols=116 Identities=14% Similarity=0.060 Sum_probs=86.6
Q ss_pred CceeeeeccccCCcC-CCCccceeeEEEecCC--CCeeEecccCCCCC----ccccccccc---cCCHHhhccCCCHHHH
Q 024455 135 PKAVAMDCEMVGGGS-NGTLDLCARVCLVDED--ENVIFHTYVQPQLP----VTNYRYEVT---GLTEEDIKNAMPLKEV 204 (267)
Q Consensus 135 ~~~~~~dcE~~g~~~-~~~~~~i~~v~vvd~~--~~~~~~~~v~P~~~----i~~~~~~~~---GIt~~~l~~~~~~~~v 204 (267)
..++++|+||+|.+. .+++.++|.|.+.++. ....++.+++|... ++.+...+| |||++++++++++++|
T Consensus 3 ~~~vvlD~ETTGLdp~~d~IieIgaV~~~~~~~~~~~~~~~~i~~~~~~l~~~~~~~~~ih~~tGIt~~~l~~~~~~~e~ 82 (181)
T PRK05359 3 DNLIWIDLEMTGLDPERDRIIEIATIVTDADLNILAEGPVIAIHQSDEALAAMDEWNTRTHTRSGLIDRVRASTVSEAEA 82 (181)
T ss_pred CcEEEEEeecCCCCCCCCeEEEEEEEEEcCCceEcccceEEEECCCHHHhhccChHHHHhcccccCcHHHHhcCCCHHHH
Confidence 458999999999874 4678888888664332 22348888998754 466777776 8999999999999999
Q ss_pred HHHHHHHHhcCCCCCcccccCCCceEEEeccchhhhccccccC------CCCceeccccc
Q 024455 205 KDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNY------PDHMLRDTAKY 258 (267)
Q Consensus 205 ~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~Dl~~l~~~~------~~~~~~dt~~~ 258 (267)
+.+|++|+++ +.+ ..+.+|||||+.||+.||+... ....++|++.+
T Consensus 83 ~~~~l~fl~~----~~~----~~~~~l~g~~v~FD~~FL~~~~~~~~~~l~~~~~Dv~tl 134 (181)
T PRK05359 83 EAQTLEFLKQ----WVP----AGKSPLCGNSIGQDRRFLARYMPELEAYFHYRNLDVSTL 134 (181)
T ss_pred HHHHHHHHHH----hcC----CCCCceeecchhhCHHHHHHHHHHhcccCCCcccchhHH
Confidence 9999999942 000 1356899999999999997643 23456675433
No 45
>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=99.51 E-value=2.5e-14 Score=110.88 Aligned_cols=108 Identities=27% Similarity=0.324 Sum_probs=92.2
Q ss_pred eeeeccccCCcC-CCCccceeeEEEecC-CCCeeEecccCCCCCccccccccccCCHHhhccCCCHHHHHHHHHHHHhcC
Q 024455 138 VAMDCEMVGGGS-NGTLDLCARVCLVDE-DENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEILNNG 215 (267)
Q Consensus 138 ~~~dcE~~g~~~-~~~~~~i~~v~vvd~-~~~~~~~~~v~P~~~i~~~~~~~~GIt~~~l~~~~~~~~v~~~~~~~~~~~ 215 (267)
+.+|+|++|... ..++.+++.+.+.+. .....++.+++|..++.+..+.++||+++++++++++.++..+|.+++
T Consensus 1 v~~D~Ettg~~~~~~~iiei~~v~~~~~~~~~~~~~~~i~p~~~~~~~~~~~~gi~~~~~~~~~~~~~~~~~~~~~l--- 77 (159)
T cd06127 1 VVFDTETTGLDPKKDRIIEIGAVKVDGGIEIVERFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFL--- 77 (159)
T ss_pred CeEEeeCCCcCCCCCeEEEEEEEEEECCcChhhhhheeeCcCCcCCHhheeccCCCHHHHhcCCCHHHHHHHHHHHH---
Confidence 468999999875 677888888887655 455678999999999999999999999999999999999999999999
Q ss_pred CCCCcccccCCCceEEEeccchhhhcccccc-------CCCCceecccccc
Q 024455 216 ESTGRLMLDDGKARLLVGHGLEHDLDSLRMN-------YPDHMLRDTAKYR 259 (267)
Q Consensus 216 ~~~~~~~~~~~~~~~lvgh~~~~Dl~~l~~~-------~~~~~~~dt~~~~ 259 (267)
.+.++||||+.||+.||+.. .+...++||..+.
T Consensus 78 -----------~~~~~v~~n~~fD~~~l~~~~~~~~~~~~~~~~iDt~~~~ 117 (159)
T cd06127 78 -----------GGRVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLA 117 (159)
T ss_pred -----------CCCEEEEeCcHhhHHHHHHHHHHhCCCCCCCCeeEHHHHH
Confidence 55899999999999999754 3466889998543
No 46
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=99.48 E-value=1.7e-14 Score=120.26 Aligned_cols=110 Identities=27% Similarity=0.419 Sum_probs=98.1
Q ss_pred ccc--ccCccccCChHHHHHHHhHhcCCCCCC-CcccchhhcCCHHHHHhhc-------CCCCCCCcCCccccccc----
Q 024455 15 HKC--VACYKQFKRKDHLIEHMKISYHSVHQP-KCAVCQKLSKSFESLREHL-------TGPLSKAHCSGIFSDRG---- 80 (267)
Q Consensus 15 ~~C--~~C~k~f~~~~~l~~H~~~~~H~~~~~-~C~~C~~~f~~~~~l~~H~-------~~~~~C~~C~k~f~~~~---- 80 (267)
+.| ..|-+.|..++.|.+|.++ |++++. .|+.||..|+++..|-.|. +.+|.|..|.|.|...+
T Consensus 178 ~~C~W~~Ct~~~~~k~~LreH~r~--Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~ 255 (467)
T KOG3608|consen 178 TMCNWAMCTKHMGNKYRLREHIRT--HSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKS 255 (467)
T ss_pred eeccchhhhhhhccHHHHHHHHHh--cCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHH
Confidence 666 7899999999999999999 999999 9999999999999999997 56899999999999874
Q ss_pred ----------ccccccccCChhhHHHHHH-HhcCCCCcc---ccccCcchhhhhhhcccc
Q 024455 81 ----------CNLCMNIFDSPSSLIKHKE-ACSLSAPVP---FEKTLSNAESQKKISGAI 126 (267)
Q Consensus 81 ----------C~~C~~~F~~~~~L~~H~~-~h~~~~~~~---C~~~f~~~~~l~~H~~~~ 126 (267)
|+.|..+-...+.|.+|++ .|...|||+ |++.+.+.+.|.+|...+
T Consensus 256 Hv~rHvn~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~H 315 (467)
T KOG3608|consen 256 HVVRHVNCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVH 315 (467)
T ss_pred HHHHhhhcccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhc
Confidence 9999999999999999987 577888987 778888888888888644
No 47
>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=99.47 E-value=5e-14 Score=112.36 Aligned_cols=95 Identities=20% Similarity=0.217 Sum_probs=78.3
Q ss_pred eeeccccCCcC-CCCccceeeEEEecC-CCCeeEecccCCCC--CccccccccccCCHHhhcc-CCCHHHHHHHHHHHHh
Q 024455 139 AMDCEMVGGGS-NGTLDLCARVCLVDE-DENVIFHTYVQPQL--PVTNYRYEVTGLTEEDIKN-AMPLKEVKDKILEILN 213 (267)
Q Consensus 139 ~~dcE~~g~~~-~~~~~~i~~v~vvd~-~~~~~~~~~v~P~~--~i~~~~~~~~GIt~~~l~~-~~~~~~v~~~~~~~~~ 213 (267)
.+|+||+|.+. .+++++++.|.+.++ .....++.+++|.. +++.....+||||+++|.+ ++++.+++++|.+|+.
T Consensus 2 ~~D~ETTGl~~~~d~Iieig~v~v~~~~~~~~~~~~~v~p~~~~~~~~~a~~ihGIt~e~l~~~~~~~~~~l~~~~~~~~ 81 (183)
T cd06138 2 FYDYETFGLNPSFDQILQFAAIRTDENFNEIEPFNIFCRLPPDVLPSPEALIVTGITPQQLLKEGLSEYEFIAKIHRLFN 81 (183)
T ss_pred EEEeecCCCCCCCCceEEEEEEEECCCCCCccceeEEEeCCCCCCCCHHHHHHhCCCHHHHHhcCCCHHHHHHHHHHHHc
Confidence 68999999874 457888888877654 33356889999874 5677789999999999999 8999999999999994
Q ss_pred cCCCCCcccccCCCceEEEecc-chhhhccccc
Q 024455 214 NGESTGRLMLDDGKARLLVGHG-LEHDLDSLRM 245 (267)
Q Consensus 214 ~~~~~~~~~~~~~~~~~lvgh~-~~~Dl~~l~~ 245 (267)
+ .+.+||||| +.||+.||+.
T Consensus 82 ~------------~~~~lVahn~~~FD~~fL~~ 102 (183)
T cd06138 82 T------------PGTCIVGYNNIRFDDEFLRF 102 (183)
T ss_pred c------------CCCcEEeeCchhhHHHHHHH
Confidence 2 356999997 8999999964
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=99.46 E-value=2e-14 Score=111.83 Aligned_cols=94 Identities=30% Similarity=0.501 Sum_probs=85.7
Q ss_pred eeeeccccCCcC-CCCccceeeEEEecCC--CCeeEecccCCCCC--ccccccccccCCHHhhccCCCHHHHHHHHHHHH
Q 024455 138 VAMDCEMVGGGS-NGTLDLCARVCLVDED--ENVIFHTYVQPQLP--VTNYRYEVTGLTEEDIKNAMPLKEVKDKILEIL 212 (267)
Q Consensus 138 ~~~dcE~~g~~~-~~~~~~i~~v~vvd~~--~~~~~~~~v~P~~~--i~~~~~~~~GIt~~~l~~~~~~~~v~~~~~~~~ 212 (267)
+++|+|++|... ...+.+++.+.+.+.. ....++.+|+|..+ ++++.+++||||.++|++++++.++.+++.+++
T Consensus 1 v~~D~Ettg~~~~~~~iieig~v~~~~~~~~~~~~~~~~i~p~~~~~i~~~~~~~~gIt~~~l~~~~~~~~~~~~~~~~~ 80 (164)
T PF00929_consen 1 VVFDTETTGLDPRQDEIIEIGAVKVDDDENEEVESFNSLIRPEEPPKISPWATKVHGITQEDLEDAPSFEEALDEFEEFL 80 (164)
T ss_dssp EEEEEEESSSTTTTCTEEEEEEEEEETTTTEEEEEEEEEBEHSSHCSSEHHHHHHHHHCHHHHHCHCEHHHHHHHHHHHH
T ss_pred cEEEeEcCCCCCCCCeEEEEEEEEeeCCccccceeeeecccccccccCCHHHeeecCCcccccccCCcHHHHHHhhhhhh
Confidence 478999999986 6789999999999887 56779999999988 999999999999999999999999999999999
Q ss_pred hcCCCCCcccccCCCceEEEeccchhhhcccc
Q 024455 213 NNGESTGRLMLDDGKARLLVGHGLEHDLDSLR 244 (267)
Q Consensus 213 ~~~~~~~~~~~~~~~~~~lvgh~~~~Dl~~l~ 244 (267)
. ++.++||||+.||..+|.
T Consensus 81 ~-------------~~~~~v~~n~~fd~~~l~ 99 (164)
T PF00929_consen 81 K-------------KNDILVGHNASFDIGFLR 99 (164)
T ss_dssp H-------------HHTEEEETTCCHEEESSH
T ss_pred h-------------cccccccccccchhhHHH
Confidence 4 367999999999999985
No 49
>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=99.40 E-value=1.8e-13 Score=108.08 Aligned_cols=111 Identities=19% Similarity=0.178 Sum_probs=83.5
Q ss_pred eeeeccccCCcC-CCCccceeeEEEecCCC--CeeEecccCCCCCcc----cccccc---ccCCHHhhccCCCHHHHHHH
Q 024455 138 VAMDCEMVGGGS-NGTLDLCARVCLVDEDE--NVIFHTYVQPQLPVT----NYRYEV---TGLTEEDIKNAMPLKEVKDK 207 (267)
Q Consensus 138 ~~~dcE~~g~~~-~~~~~~i~~v~vvd~~~--~~~~~~~v~P~~~i~----~~~~~~---~GIt~~~l~~~~~~~~v~~~ 207 (267)
+++|+||+|.+. .++++++|.|.+.+..+ ...|+.+++|..+++ .+...+ +||+++++++++++.+|+.+
T Consensus 2 v~iD~ETTGl~p~~d~IieIgaV~~~~~~~~i~~~f~~~i~p~~~~~~~~~~~~~~ih~~tgIt~~~l~~~~~~~~vl~~ 81 (173)
T cd06135 2 VWIDLEMTGLDPEKDRILEIACIITDGDLNIIAEGPELVIHQPDEVLDGMDEWCTEMHTKSGLTERVRASTVTLAQAEAE 81 (173)
T ss_pred EEEEEecCCCCCCCCeeEEEEEEEEeCCCceecCceeEEECCCHHHhhhccHHHHHcccccccHHHHHhCCCCHHHHHHH
Confidence 689999999984 57789999997755432 356899999987654 344555 59999999999999999999
Q ss_pred HHHHHhcCCCCCcccccCCCceEEEeccchhhhccccccCC------CCceeccc
Q 024455 208 ILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNYP------DHMLRDTA 256 (267)
Q Consensus 208 ~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~Dl~~l~~~~~------~~~~~dt~ 256 (267)
|.+|+.+.- ...+.+|||||+.||+.||+...+ ....+||.
T Consensus 82 ~~~f~~~~~--------~~~~~~lvgh~~~FD~~fL~~~~~~~~~~~~~~~~D~~ 128 (173)
T cd06135 82 LLEFIKKYV--------PKGKSPLAGNSVHQDRRFLDKYMPELEEYLHYRILDVS 128 (173)
T ss_pred HHHHHHHhc--------CCCCCceeecchhhCHHHHHHHHHHHhccCCcchhhHH
Confidence 999994200 002369999999999999975432 22457773
No 50
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=99.38 E-value=6e-13 Score=113.06 Aligned_cols=98 Identities=19% Similarity=0.176 Sum_probs=78.7
Q ss_pred CCceeeeeccccCCcC-CCCccceeeEEEecC-CC-----CeeEecccCCCCCccccccccccCCHHhhccCCCHHHHHH
Q 024455 134 GPKAVAMDCEMVGGGS-NGTLDLCARVCLVDE-DE-----NVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKD 206 (267)
Q Consensus 134 ~~~~~~~dcE~~g~~~-~~~~~~i~~v~vvd~-~~-----~~~~~~~v~P~~~i~~~~~~~~GIt~~~l~~~~~~~~v~~ 206 (267)
...++++|+||+|.+. .+++++||.|.+... .+ ...++.+++|..+|+...+.+||||++++++++... +
T Consensus 36 ~~~~vvlD~ETTGLd~~~d~IIEIg~V~v~~~~~g~i~~v~~~~~~lv~P~~~I~~~~t~IhGIt~e~v~~~~~~~---~ 112 (294)
T PRK09182 36 VRLGVILDTETTGLDPRKDEIIEIGMVAFEYDDDGRIGDVLDTFGGLQQPSRPIPPEITRLTGITDEMVAGQTIDP---A 112 (294)
T ss_pred CCeEEEEEeeCCCCCCCCCeEEEEEEEEEEecCCCceeeeeeEEEEEeCCCCCCCHHHHHhcCCCHHHHhcCCCcH---H
Confidence 3457899999999974 467899999988732 22 345888999999999999999999999999987653 3
Q ss_pred HHHHHHhcCCCCCcccccCCCceEEEeccchhhhccccccC
Q 024455 207 KILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNY 247 (267)
Q Consensus 207 ~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~Dl~~l~~~~ 247 (267)
.|.+|+. .+.+|||||+.||+.||+...
T Consensus 113 ~l~~fl~-------------~~~vlVAHNA~FD~~fL~~~~ 140 (294)
T PRK09182 113 AVDALIA-------------PADLIIAHNAGFDRPFLERFS 140 (294)
T ss_pred HHHHHhc-------------CCCEEEEeCHHHHHHHHHHHH
Confidence 4677783 335999999999999997543
No 51
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.38 E-value=1.5e-13 Score=123.94 Aligned_cols=107 Identities=24% Similarity=0.382 Sum_probs=90.9
Q ss_pred ccccccCccccCChHHHHHHHhHhcCCCCCC--CcccchhhcCCHHHHHhhcCCC---------CCCCcCCccccccccc
Q 024455 14 RHKCVACYKQFKRKDHLIEHMKISYHSVHQP--KCAVCQKLSKSFESLREHLTGP---------LSKAHCSGIFSDRGCN 82 (267)
Q Consensus 14 ~~~C~~C~k~f~~~~~l~~H~~~~~H~~~~~--~C~~C~~~f~~~~~l~~H~~~~---------~~C~~C~k~f~~~~C~ 82 (267)
...|+.|.+.+.+-..|+.|++.+ |....+ .|..|.+.|+.+..|.+|+.-. ..=..|.+.|+ |.
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 467999999999999999999874 665444 9999999999999999999222 22245555555 99
Q ss_pred ccccccCChhhHHHHHHHhcCCCCcc---ccccCcchhhhhhhcc
Q 024455 83 LCMNIFDSPSSLIKHKEACSLSAPVP---FEKTLSNAESQKKISG 124 (267)
Q Consensus 83 ~C~~~F~~~~~L~~H~~~h~~~~~~~---C~~~f~~~~~l~~H~~ 124 (267)
+|||.|..+-.|+.|+|+|+|||||+ |.+.|+...+...|+.
T Consensus 286 ECgKAFKfKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHmS 330 (1007)
T KOG3623|consen 286 ECGKAFKFKHHLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHMS 330 (1007)
T ss_pred ccchhhhhHHHHHhhheeecCCCCcCCcccccccccCCccccccc
Confidence 99999999999999999999999998 8899999999999984
No 52
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.34 E-value=3.2e-13 Score=104.65 Aligned_cols=67 Identities=25% Similarity=0.439 Sum_probs=57.9
Q ss_pred CCCCccccccCccccCChHHHHHHHhHhcCCCCCC-CcccchhhcCCHHHHHhhc-----CCCCCCCcCCccccc
Q 024455 10 RSTARHKCVACYKQFKRKDHLIEHMKISYHSVHQP-KCAVCQKLSKSFESLREHL-----TGPLSKAHCSGIFSD 78 (267)
Q Consensus 10 ~~~k~~~C~~C~k~f~~~~~l~~H~~~~~H~~~~~-~C~~C~~~f~~~~~l~~H~-----~~~~~C~~C~k~f~~ 78 (267)
++.-.|.|.+|+|.|.-...|.+|++- |+..+. .|..|||.|...-.|++|+ .+||+|..|+|.|.+
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 456689999999999999999999999 998777 9999999999999999999 468887666555554
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=99.33 E-value=2.6e-12 Score=101.77 Aligned_cols=109 Identities=25% Similarity=0.232 Sum_probs=86.3
Q ss_pred eeeeeccccCCcCC------CCccceeeEEEecCCC--CeeEecccCCCC--CccccccccccCCHHhhccCCCHHHHHH
Q 024455 137 AVAMDCEMVGGGSN------GTLDLCARVCLVDEDE--NVIFHTYVQPQL--PVTNYRYEVTGLTEEDIKNAMPLKEVKD 206 (267)
Q Consensus 137 ~~~~dcE~~g~~~~------~~~~~i~~v~vvd~~~--~~~~~~~v~P~~--~i~~~~~~~~GIt~~~l~~~~~~~~v~~ 206 (267)
++++|+|++|.... .++++++.+.+.+... ...|+.+|+|.. +++++.++++|||++++++++++++|++
T Consensus 1 ~vv~D~Ettg~~~~~~~~~~~~IieIgav~v~~~~~~~~~~f~~~i~P~~~~~i~~~~~~i~gIt~e~l~~~~~~~~vl~ 80 (176)
T cd06133 1 YLVIDFEATCWEGNSKPDYPNEIIEIGAVLVDVKTKEIIDTFSSYVKPVINPKLSDFCTELTGITQEDVDNAPSFPEVLK 80 (176)
T ss_pred CEEEEeeccccCCCCCCCCCcceEEEEEEEEEcCCCeEEeeeeeeECCCcCCchhHHHHHhcCcCHHHHhcCCCHHHHHH
Confidence 47899999998753 6788888888876554 457999999997 8999999999999999999999999999
Q ss_pred HHHHHHhcCCCCCcccccCCCce--EEEeccchhhhcccccc----------CCCCceecccccc
Q 024455 207 KILEILNNGESTGRLMLDDGKAR--LLVGHGLEHDLDSLRMN----------YPDHMLRDTAKYR 259 (267)
Q Consensus 207 ~~~~~~~~~~~~~~~~~~~~~~~--~lvgh~~~~Dl~~l~~~----------~~~~~~~dt~~~~ 259 (267)
+|.+|+ ++. .+++|+..||+.+|.-. ......+|++.++
T Consensus 81 ~~~~~l--------------~~~~~~~~v~~~~~d~~~l~~~~~~~~~~~~~~~~~~~~D~~~~~ 131 (176)
T cd06133 81 EFLEWL--------------GKNGKYAFVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEF 131 (176)
T ss_pred HHHHHH--------------HhCCCeEEEeecHhhHHHHHHHHHHhcCCCCcccccceEEHHHHH
Confidence 999999 444 45555569998876421 1233677887544
No 54
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=99.28 E-value=5.9e-12 Score=125.50 Aligned_cols=110 Identities=22% Similarity=0.327 Sum_probs=94.9
Q ss_pred CCceeeeeccccCCcC-CCCccceeeEEEecCCCCeeEecccCCCCCccccccccccCCHHhhccCCCHHHHHHHHHHHH
Q 024455 134 GPKAVAMDCEMVGGGS-NGTLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEIL 212 (267)
Q Consensus 134 ~~~~~~~dcE~~g~~~-~~~~~~i~~v~vvd~~~~~~~~~~v~P~~~i~~~~~~~~GIt~~~l~~~~~~~~v~~~~~~~~ 212 (267)
...++++|+|++|... ..++++++.+.+.++.....|+.+|+|..+++...+++||||++++.+++++.+|+++|.+|+
T Consensus 418 ~~~~VVfDLETTGL~~~~deIIEIgAV~V~~G~iie~F~~~V~P~~~I~~~~~~LTGIT~e~L~~aps~~EaL~~f~~fi 497 (1437)
T PRK00448 418 DATYVVFDVETTGLSAVYDEIIEIGAVKIKNGEIIDKFEFFIKPGHPLSAFTTELTGITDDMVKDAPSIEEVLPKFKEFC 497 (1437)
T ss_pred cCcEEEEEhhhcCCCCchhhhheeeeEEEeCCeEeeeEEEEECCCCCCCHHHHHHhCCCHHHHcCCCCHHHHHHHHHHHh
Confidence 3468999999999874 356888899988877666789999999999999999999999999999999999999999999
Q ss_pred hcCCCCCcccccCCCceEEEeccchhhhcccc-------ccCCCCceecccc
Q 024455 213 NNGESTGRLMLDDGKARLLVGHGLEHDLDSLR-------MNYPDHMLRDTAK 257 (267)
Q Consensus 213 ~~~~~~~~~~~~~~~~~~lvgh~~~~Dl~~l~-------~~~~~~~~~dt~~ 257 (267)
+|.+|||||+.||+.||+ +..+...++||-.
T Consensus 498 --------------gg~vLVAHNa~FD~~fL~~~l~rlgl~~l~~~~IDTLe 535 (1437)
T PRK00448 498 --------------GDSILVAHNASFDVGFINTNYEKLGLEKIKNPVIDTLE 535 (1437)
T ss_pred --------------CCCEEEEeCccccHHHHHHHHHHcCCccccccceeHHH
Confidence 789999999999999984 3234556788753
No 55
>PTZ00315 2'-phosphotransferase; Provisional
Probab=99.27 E-value=1e-11 Score=112.63 Aligned_cols=105 Identities=21% Similarity=0.210 Sum_probs=83.2
Q ss_pred CceeeeeccccCCcC----CCCccceeeEEEe--cCCCCeeEecccCCCC--CccccccccccCCHHhhccCCCHHHHHH
Q 024455 135 PKAVAMDCEMVGGGS----NGTLDLCARVCLV--DEDENVIFHTYVQPQL--PVTNYRYEVTGLTEEDIKNAMPLKEVKD 206 (267)
Q Consensus 135 ~~~~~~dcE~~g~~~----~~~~~~i~~v~vv--d~~~~~~~~~~v~P~~--~i~~~~~~~~GIt~~~l~~~~~~~~v~~ 206 (267)
..++++|.|++|... ..++++++.|.+. ++.....|+.||+|.. +++.+.+++||||+++|+++|+|++|+.
T Consensus 56 d~~IV~DlETTgl~~~~~~~dEIIEIGaV~Vd~~ng~Ii~~F~~yVkP~~~p~Ls~fct~LTGITqe~V~~Ap~F~eVl~ 135 (582)
T PTZ00315 56 DAYVVLDFEATCEADRRIEDAEVIEFPMVLVDARTATPVAEFQRYVRPVKNPVLSRFCTELTGITQSMVSRADPFPVVYC 135 (582)
T ss_pred CeEEEEEEecCCCCCCCCCCCceEEEEEEEEEccCCEEEEEEEEEECCCCCCCCChhHhhhcCcCHHHHhcCCCHHHHHH
Confidence 467899999999753 3678899999985 3344567999999986 6999999999999999999999999999
Q ss_pred HHHHHHhcCCCCCcccccCCCceEEEeccchhhhc-cc
Q 024455 207 KILEILNNGESTGRLMLDDGKARLLVGHGLEHDLD-SL 243 (267)
Q Consensus 207 ~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~Dl~-~l 243 (267)
+|.+||.+..- . .. .+.+.++|+||..||+. ||
T Consensus 136 ef~~fL~~~~~-~--e~-~~~~~~~vah~g~fDl~~fL 169 (582)
T PTZ00315 136 EALQFLAEAGL-G--DA-PPLRSYCVVTCGDWDLKTML 169 (582)
T ss_pred HHHHHHhcccc-c--cc-cccCceEEEeccHHHHHHHH
Confidence 99999954210 0 00 01235899999999995 77
No 56
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=99.23 E-value=8.1e-12 Score=104.48 Aligned_cols=114 Identities=18% Similarity=0.327 Sum_probs=60.6
Q ss_pred ccccccCccccCChHHHHHHHhHhcCCCCCCCcccchhhcCCHHHHHhhc------CCCCCCCcCCccccccc-------
Q 024455 14 RHKCVACYKQFKRKDHLIEHMKISYHSVHQPKCAVCQKLSKSFESLREHL------TGPLSKAHCSGIFSDRG------- 80 (267)
Q Consensus 14 ~~~C~~C~k~f~~~~~l~~H~~~~~H~~~~~~C~~C~~~f~~~~~l~~H~------~~~~~C~~C~k~f~~~~------- 80 (267)
+|.|..|.|.|.+...|..|+.. |-.- .+|+.|.......++|..|+ .+||+|+.|++.|...+
T Consensus 237 ~fqC~~C~KrFaTeklL~~Hv~r--Hvn~-ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~ 313 (467)
T KOG3608|consen 237 SFQCAQCFKRFATEKLLKSHVVR--HVNC-YKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQ 313 (467)
T ss_pred chHHHHHHHHHhHHHHHHHHHHH--hhhc-ccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHH
Confidence 45555555555555555555554 3321 15555555555555555555 34566666666555432
Q ss_pred --------ccc--cccccCChhhHHHHHHHhc-CCC--Ccc---ccccCcchhhhhhhcccccccc
Q 024455 81 --------CNL--CMNIFDSPSSLIKHKEACS-LSA--PVP---FEKTLSNAESQKKISGAIDEKR 130 (267)
Q Consensus 81 --------C~~--C~~~F~~~~~L~~H~~~h~-~~~--~~~---C~~~f~~~~~l~~H~~~~~~~r 130 (267)
|+. |..+|.....+++|++.++ |.. +|. |++.|.+-.+|..|....++-+
T Consensus 314 ~HS~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np~~Y~CH~Cdr~ft~G~~L~~HL~kkH~f~ 379 (467)
T KOG3608|consen 314 VHSKTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNPILYACHCCDRFFTSGKSLSAHLMKKHGFR 379 (467)
T ss_pred hccccceecCCCCCcHHHHHHHHHHHHHHHhccCCCCCceeeecchhhhccchhHHHHHHHhhccc
Confidence 555 6666666666666655544 332 222 5666666666666654444433
No 57
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.20 E-value=7.3e-12 Score=113.32 Aligned_cols=81 Identities=28% Similarity=0.522 Sum_probs=59.6
Q ss_pred CCCCCCCCCCccccccCccccCChHHHHHHHhHhcCCCCCC-CcccchhhcCCHHHHHhhc-----CCCCCCCcCCcccc
Q 024455 4 EAELPKRSTARHKCVACYKQFKRKDHLIEHMKISYHSVHQP-KCAVCQKLSKSFESLREHL-----TGPLSKAHCSGIFS 77 (267)
Q Consensus 4 ~~~~~~~~~k~~~C~~C~k~f~~~~~l~~H~~~~~H~~~~~-~C~~C~~~f~~~~~l~~H~-----~~~~~C~~C~k~f~ 77 (267)
++.+-++.+.+|.|++|.|.|...++|.+|.-- |+|.+| +|.+|.|.|..+..|..|+ ++||+|
T Consensus 884 ~tk~~kte~gmyaCDqCDK~FqKqSSLaRHKYE--HsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQC-------- 953 (1007)
T KOG3623|consen 884 ETKHAKTEDGMYACDQCDKAFQKQSSLARHKYE--HSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQC-------- 953 (1007)
T ss_pred ccccccCccccchHHHHHHHHHhhHHHHHhhhh--hcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchh--------
Confidence 344556778889999999999999999999988 999888 8888887777777777776 445543
Q ss_pred cccccccccccCChhhHHHHH
Q 024455 78 DRGCNLCMNIFDSPSSLIKHK 98 (267)
Q Consensus 78 ~~~C~~C~~~F~~~~~L~~H~ 98 (267)
+.|+|.|+....+.+||
T Consensus 954 ----dKClKRFSHSGSYSQHM 970 (1007)
T KOG3623|consen 954 ----DKCLKRFSHSGSYSQHM 970 (1007)
T ss_pred ----hhhhhhcccccchHhhh
Confidence 34555555555566665
No 58
>PRK11779 sbcB exonuclease I; Provisional
Probab=99.18 E-value=6e-11 Score=106.72 Aligned_cols=99 Identities=16% Similarity=0.178 Sum_probs=79.7
Q ss_pred CceeeeeccccCCc-CCCCccceeeEEEecCC--CCeeEecccCCCCC--ccccccccccCCHHhhccC-CCHHHHHHHH
Q 024455 135 PKAVAMDCEMVGGG-SNGTLDLCARVCLVDED--ENVIFHTYVQPQLP--VTNYRYEVTGLTEEDIKNA-MPLKEVKDKI 208 (267)
Q Consensus 135 ~~~~~~dcE~~g~~-~~~~~~~i~~v~vvd~~--~~~~~~~~v~P~~~--i~~~~~~~~GIt~~~l~~~-~~~~~v~~~~ 208 (267)
..++++|+||+|.+ ..++++++|.|.+.++. ....+..+++|..+ +.+..+.+||||++++.+. .+..++.++|
T Consensus 6 ~~fvv~D~ETTGLdP~~DrIIeiAaVrvd~~~~~i~e~~~~~~~P~~~~lp~p~a~~IhGIT~e~l~~~g~~e~e~~~~i 85 (476)
T PRK11779 6 PTFLWHDYETFGANPALDRPAQFAGIRTDADLNIIGEPLVFYCKPADDYLPSPEAVLITGITPQEALEKGLPEAEFAARI 85 (476)
T ss_pred CcEEEEEEECCCCCCCCCeeEEEEEEEEeCCCceecceeEEEEcCCcCcCCCHHHHHHhCCCHHHHHhcCCCHHHHHHHH
Confidence 45799999999998 45678899999887653 22458899999853 4566899999999999664 5799999999
Q ss_pred HHHHhcCCCCCcccccCCCceEEEecc-chhhhccccc
Q 024455 209 LEILNNGESTGRLMLDDGKARLLVGHG-LEHDLDSLRM 245 (267)
Q Consensus 209 ~~~~~~~~~~~~~~~~~~~~~~lvgh~-~~~Dl~~l~~ 245 (267)
.++++. .|+++|||| +.||+.||+.
T Consensus 86 ~~~l~~------------~~~~lVGhNni~FD~eflr~ 111 (476)
T PRK11779 86 HAEFSQ------------PGTCILGYNNIRFDDEVTRY 111 (476)
T ss_pred HHHHhc------------CCCEEEEeCchhhcHHHHHH
Confidence 999942 368999997 7999999864
No 59
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.16 E-value=3.6e-12 Score=98.91 Aligned_cols=97 Identities=21% Similarity=0.270 Sum_probs=74.2
Q ss_pred CcccchhhcCCHHHHHhhcCCCCCCCcCCcccccccccccccccCChhhHHHHHHHhcCCCCcc---ccccCcchhhhhh
Q 024455 45 KCAVCQKLSKSFESLREHLTGPLSKAHCSGIFSDRGCNLCMNIFDSPSSLIKHKEACSLSAPVP---FEKTLSNAESQKK 121 (267)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~~~~~~C~~C~k~f~~~~C~~C~~~F~~~~~L~~H~~~h~~~~~~~---C~~~f~~~~~l~~ 121 (267)
.|.+|||.|.....|.+|+. | -...+..-|..|||.|...-.|++|+|+|+|.+||+ |+++|.+..+|..
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 89999999998888888872 2 111111227789999999999999999999999998 8999999999999
Q ss_pred hcccccccc---ccCCCceeeeeccccCCc
Q 024455 122 ISGAIDEKR---TCRGPKAVAMDCEMVGGG 148 (267)
Q Consensus 122 H~~~~~~~r---~~~~~~~~~~dcE~~g~~ 148 (267)
|....++.. .....+...+-||.||..
T Consensus 192 hl~kvhgv~~~yaykerr~kl~vcedcg~t 221 (267)
T KOG3576|consen 192 HLKKVHGVQHQYAYKERRAKLYVCEDCGYT 221 (267)
T ss_pred HHHHHcCchHHHHHHHhhhheeeecccCCC
Confidence 987655432 223334456778999864
No 60
>KOG1275 consensus PAB-dependent poly(A) ribonuclease, subunit PAN2 [Replication, recombination and repair]
Probab=99.13 E-value=3.4e-11 Score=111.54 Aligned_cols=119 Identities=23% Similarity=0.345 Sum_probs=95.2
Q ss_pred cCCCceeeeeccccCCc-------CC-------CCccceeeEEEecCC----CCeeEecccCCCCCccccccccccCCHH
Q 024455 132 CRGPKAVAMDCEMVGGG-------SN-------GTLDLCARVCLVDED----ENVIFHTYVQPQLPVTNYRYEVTGLTEE 193 (267)
Q Consensus 132 ~~~~~~~~~dcE~~g~~-------~~-------~~~~~i~~v~vvd~~----~~~~~~~~v~P~~~i~~~~~~~~GIt~~ 193 (267)
...+..+++|-|+.... .+ .....+||++++.+. |....|.+|-.+..|.||.|+++||-+.
T Consensus 907 Pk~g~LVgiDAEFVtLq~Ee~Eir~DG~~stIkP~~msvARiScvRGeGp~eGiPFiDDYv~T~d~VvDYLTqySGI~PG 986 (1118)
T KOG1275|consen 907 PKSGDLVGIDAEFVTLQTEELEIRSDGKTSTIKPSRMSVARISCVRGEGPNEGIPFIDDYVSTDDKVVDYLTQYSGIKPG 986 (1118)
T ss_pred CCCCceeeeehhheecchHHhccccCCceeEeccccceeEEEEEEcccCCCCCCccccceecchhHHHHHHHHhcCCCcc
Confidence 34456677777666432 11 122357999999886 4455788898889999999999999999
Q ss_pred hhccCC------CHHHHHHHHHHHHhcCCCCCcccccCCCceEEEeccchhhhccccccCCCCceecccccccccc
Q 024455 194 DIKNAM------PLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNYPDHMLRDTAKYRPLMK 263 (267)
Q Consensus 194 ~l~~~~------~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~Dl~~l~~~~~~~~~~dt~~~~~~~~ 263 (267)
||+... +++-+..+|+-++. .|.++|||++++|+++|++..|+.+||||+.|+-+..
T Consensus 987 DLDp~~S~K~Lt~lK~~Y~Kl~~Li~-------------~GviFVGHGL~nDFrvINi~Vp~~QiiDTv~lf~~~s 1049 (1118)
T KOG1275|consen 987 DLDPTTSEKRLTTLKVLYLKLRLLIQ-------------RGVIFVGHGLQNDFRVINIHVPEEQIIDTVTLFRLGS 1049 (1118)
T ss_pred ccCCccCcceehhHHHHHHHHHHHHH-------------cCcEEEcccccccceEEEEecChhhheeeeEEEeccc
Confidence 998653 57788888888884 8999999999999999999999999999999887654
No 61
>PHA02768 hypothetical protein; Provisional
Probab=98.93 E-value=3.9e-10 Score=69.65 Aligned_cols=43 Identities=19% Similarity=0.453 Sum_probs=38.7
Q ss_pred ccccccCccccCChHHHHHHHhHhcCCCCCC-CcccchhhcCCHHHHH
Q 024455 14 RHKCVACYKQFKRKDHLIEHMKISYHSVHQP-KCAVCQKLSKSFESLR 60 (267)
Q Consensus 14 ~~~C~~C~k~f~~~~~l~~H~~~~~H~~~~~-~C~~C~~~f~~~~~l~ 60 (267)
-|+|+.||+.|.+.++|..||++ |+ ++ +|..|++.|.+.+.|.
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 48999999999999999999999 88 45 9999999999887664
No 62
>KOG3242 consensus Oligoribonuclease (3'->5' exoribonuclease) [RNA processing and modification]
Probab=98.85 E-value=6.6e-10 Score=84.37 Aligned_cols=120 Identities=21% Similarity=0.243 Sum_probs=85.8
Q ss_pred CCceeeeeccccCCcCC-CCccceeeEEEecCCCCee---EecccCCCCCcccccccc-------ccCCHHhhccCCCHH
Q 024455 134 GPKAVAMDCEMVGGGSN-GTLDLCARVCLVDEDENVI---FHTYVQPQLPVTNYRYEV-------TGLTEEDIKNAMPLK 202 (267)
Q Consensus 134 ~~~~~~~dcE~~g~~~~-~~~~~i~~v~vvd~~~~~~---~~~~v~P~~~i~~~~~~~-------~GIt~~~l~~~~~~~ 202 (267)
..+++.+||||+|..-. +++.+ .+..+.|++...+ ++..|+-+.++.+....| +|+|..-+.+..+++
T Consensus 25 ~q~lVWiD~EMTGLdvekd~i~E-iacIITD~dL~~~~egpd~vI~~~~evld~MneWc~ehhg~SGLt~kv~~S~~tl~ 103 (208)
T KOG3242|consen 25 KQPLVWIDCEMTGLDVEKDRIIE-IACIITDGDLNPVAEGPDLVIHQPKEVLDKMNEWCIEHHGNSGLTEKVLASKITLA 103 (208)
T ss_pred cCceEEEeeeccccccccceeEE-EEEEEecCCccccccCccchhcCCHHHHHHHHHHHHHhccchhHHHHHHHhhccHH
Confidence 34679999999999844 44544 4555667765443 566676554444433333 579999999999999
Q ss_pred HHHHHHHHHHhcCCCCCcccccCCCceEEEeccchhhhccccccCC------CCceeccccccccc
Q 024455 203 EVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNYP------DHMLRDTAKYRPLM 262 (267)
Q Consensus 203 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~Dl~~l~~~~~------~~~~~dt~~~~~~~ 262 (267)
+|..++++||.. +++ + +..+|.|+++..|..||..++| .++|||.+.+..+-
T Consensus 104 ~aEnevl~yikk----~ip-~---~~~~laGNSV~~DrlFl~k~mPk~~~~lhyrivDVStIkeL~ 161 (208)
T KOG3242|consen 104 DAENEVLEYIKK----HIP-K---GKCPLAGNSVYMDRLFLKKYMPKLIKHLHYRIVDVSTIKELA 161 (208)
T ss_pred HHHHHHHHHHHH----hCC-C---CCCCccCcchhhHHHHHHHHhHHHHHhcceeeeeHHHHHHHH
Confidence 999999999942 222 2 4569999999999999986655 56788888665444
No 63
>PHA00733 hypothetical protein
Probab=98.84 E-value=2.8e-09 Score=79.41 Aligned_cols=81 Identities=19% Similarity=0.199 Sum_probs=61.4
Q ss_pred CCCccccccCccccCChHHHHHH--HhHh-cCCCCCC-CcccchhhcCCHHHHHhhcC---CCCCCCcCCcccccccccc
Q 024455 11 STARHKCVACYKQFKRKDHLIEH--MKIS-YHSVHQP-KCAVCQKLSKSFESLREHLT---GPLSKAHCSGIFSDRGCNL 83 (267)
Q Consensus 11 ~~k~~~C~~C~k~f~~~~~l~~H--~~~~-~H~~~~~-~C~~C~~~f~~~~~l~~H~~---~~~~C~~C~k~f~~~~C~~ 83 (267)
..|++.|.+|.+.|.....|..| ++.+ .+.+.+| .|+.||+.|.+.++|..|+. .+| .|+.
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 57789999999988887777666 2110 0233566 99999999999999999983 222 4778
Q ss_pred cccccCChhhHHHHHHHhcC
Q 024455 84 CMNIFDSPSSLIKHKEACSL 103 (267)
Q Consensus 84 C~~~F~~~~~L~~H~~~h~~ 103 (267)
|++.|.....|..|++..|+
T Consensus 105 CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 105 CGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred CCCccCCHHHHHHHHHHhcC
Confidence 88899999999999887664
No 64
>PHA02768 hypothetical protein; Provisional
Probab=98.70 E-value=8.4e-09 Score=63.79 Aligned_cols=42 Identities=14% Similarity=0.200 Sum_probs=34.5
Q ss_pred cccccccccCChhhHHHHHHHhc-CCCCccccccCcchhhhhh
Q 024455 80 GCNLCMNIFDSPSSLIKHKEACS-LSAPVPFEKTLSNAESQKK 121 (267)
Q Consensus 80 ~C~~C~~~F~~~~~L~~H~~~h~-~~~~~~C~~~f~~~~~l~~ 121 (267)
.|+.||+.|...++|..|+++|+ +.++..|++.|...+.|..
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 48999999999999999999998 5555569998887776543
No 65
>PHA00733 hypothetical protein
Probab=98.54 E-value=9.9e-08 Score=71.11 Aligned_cols=57 Identities=19% Similarity=0.371 Sum_probs=48.7
Q ss_pred CCCCCccccccCccccCChHHHHHHHhHhcCCCCCC-CcccchhhcCCHHHHHhhc-CCCCCC
Q 024455 9 KRSTARHKCVACYKQFKRKDHLIEHMKISYHSVHQP-KCAVCQKLSKSFESLREHL-TGPLSK 69 (267)
Q Consensus 9 ~~~~k~~~C~~C~k~f~~~~~l~~H~~~~~H~~~~~-~C~~C~~~f~~~~~l~~H~-~~~~~C 69 (267)
..+++||.|+.|++.|.+...|..|++. |. .+ .|+.|++.|.....|..|+ .+.-.|
T Consensus 68 ~~~~kPy~C~~Cgk~Fss~s~L~~H~r~--h~--~~~~C~~CgK~F~~~~sL~~H~~~~h~~~ 126 (128)
T PHA00733 68 SKAVSPYVCPLCLMPFSSSVSLKQHIRY--TE--HSKVCPVCGKEFRNTDSTLDHVCKKHNIC 126 (128)
T ss_pred cCCCCCccCCCCCCcCCCHHHHHHHHhc--CC--cCccCCCCCCccCCHHHHHHHHHHhcCcc
Confidence 3468899999999999999999999998 73 34 9999999999999999998 443334
No 66
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.46 E-value=2.7e-07 Score=84.15 Aligned_cols=95 Identities=18% Similarity=0.417 Sum_probs=63.7
Q ss_pred CCCccccccCccccCChHHHHHHHhHhcCCCCCC-CcccchhhcCCHHHHHhhc-----CCCCCCCcCCccccccccccc
Q 024455 11 STARHKCVACYKQFKRKDHLIEHMKISYHSVHQP-KCAVCQKLSKSFESLREHL-----TGPLSKAHCSGIFSDRGCNLC 84 (267)
Q Consensus 11 ~~k~~~C~~C~k~f~~~~~l~~H~~~~~H~~~~~-~C~~C~~~f~~~~~l~~H~-----~~~~~C~~C~k~f~~~~C~~C 84 (267)
-++.+.|+.|++.|. ...|..|+++ |. .+ .|+ ||+.+ .+..|..|+ .+++.| +.|
T Consensus 450 l~~H~~C~~Cgk~f~-~s~LekH~~~--~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C------------~fC 510 (567)
T PLN03086 450 AKNHVHCEKCGQAFQ-QGEMEKHMKV--FH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITC------------RFC 510 (567)
T ss_pred cccCccCCCCCCccc-hHHHHHHHHh--cC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeC------------CCC
Confidence 456788999999885 6778999988 53 55 898 99755 668898887 344444 445
Q ss_pred ccccC----------ChhhHHHHHHHhcCCCCcc---ccccCcchhhhhhhcccc
Q 024455 85 MNIFD----------SPSSLIKHKEACSLSAPVP---FEKTLSNAESQKKISGAI 126 (267)
Q Consensus 85 ~~~F~----------~~~~L~~H~~~h~~~~~~~---C~~~f~~~~~l~~H~~~~ 126 (267)
++.|. ..+.|..|+.++ |.+++. |++.+.. ..+..|+...
T Consensus 511 ~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt~~C~~Cgk~Vrl-rdm~~H~~~~ 563 (567)
T PLN03086 511 GDMVQAGGSAMDVRDRLRGMSEHESIC-GSRTAPCDSCGRSVML-KEMDIHQIAV 563 (567)
T ss_pred CCccccCccccchhhhhhhHHHHHHhc-CCcceEccccCCeeee-hhHHHHHHHh
Confidence 55553 245788888886 777776 4444333 3455565433
No 67
>COG1949 Orn Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification]
Probab=98.30 E-value=1.7e-07 Score=70.72 Aligned_cols=120 Identities=17% Similarity=0.206 Sum_probs=82.8
Q ss_pred CCceeeeeccccCCcCCC-CccceeeEEEecCCCCeeEec---ccC-CC---CCcccccccc---ccCCHHhhccCCCHH
Q 024455 134 GPKAVAMDCEMVGGGSNG-TLDLCARVCLVDEDENVIFHT---YVQ-PQ---LPVTNYRYEV---TGLTEEDIKNAMPLK 202 (267)
Q Consensus 134 ~~~~~~~dcE~~g~~~~~-~~~~i~~v~vvd~~~~~~~~~---~v~-P~---~~i~~~~~~~---~GIt~~~l~~~~~~~ 202 (267)
..+.+.+||||+|..... ++++ .+..|.|.+.+++-+. .|. |. ....+|.++. +|++....++..+.+
T Consensus 5 ~~nLiWIDlEMTGLd~~~drIIE-iA~iVTD~~Lnilaegp~~~Ihq~~e~L~~Mdew~~~~H~~sGL~~rV~~S~~t~~ 83 (184)
T COG1949 5 KNNLIWIDLEMTGLDPERDRIIE-IATIVTDANLNILAEGPVIAIHQSDEQLAKMDEWNTETHGRSGLTERVKASTVTEA 83 (184)
T ss_pred CCceEEEeeeeccCCcCcceEEE-EEEEEecCcccccccCceEEEeCCHHHHHHHHHHHHHccccccHHHHHHHhhccHH
Confidence 346789999999998554 4555 3444556655544322 222 21 2345666665 468888888889999
Q ss_pred HHHHHHHHHHhcCCCCCcccccCCCceEEEeccchhhhccccccCC------CCceeccccccccc
Q 024455 203 EVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNYP------DHMLRDTAKYRPLM 262 (267)
Q Consensus 203 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~Dl~~l~~~~~------~~~~~dt~~~~~~~ 262 (267)
+|..++++||.+ |.+. +-+++.|+++..|.+||-..+| .++++|.+.++.+-
T Consensus 84 ~aE~~~l~flkk----wvp~----~~spicGNSI~qDRrFl~r~MP~Le~yfHYR~lDVSTlKELa 141 (184)
T COG1949 84 EAEAQTLDFLKK----WVPK----GVSPICGNSIAQDRRFLFRYMPKLEAYFHYRYLDVSTLKELA 141 (184)
T ss_pred HHHHHHHHHHHH----hCCC----CCCCCccchhhHHHHHHHHHhhhHHHHhhhHhhhHHHHHHHH
Confidence 999999999942 4433 3359999999999999976555 45777877666554
No 68
>PHA00616 hypothetical protein
Probab=98.26 E-value=4.2e-07 Score=53.53 Aligned_cols=33 Identities=21% Similarity=0.341 Sum_probs=29.8
Q ss_pred cccccccccCChhhHHHHHHHhcCCCCcccccc
Q 024455 80 GCNLCMNIFDSPSSLIKHKEACSLSAPVPFEKT 112 (267)
Q Consensus 80 ~C~~C~~~F~~~~~L~~H~~~h~~~~~~~C~~~ 112 (267)
.|+.||+.|.++++|..|++.||+++++.|+.-
T Consensus 3 qC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~~ 35 (44)
T PHA00616 3 QCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEYF 35 (44)
T ss_pred ccchhhHHHhhHHHHHHHHHHhcCCCccceeEE
Confidence 388899999999999999999999999987654
No 69
>PHA00616 hypothetical protein
Probab=98.23 E-value=6.1e-07 Score=52.81 Aligned_cols=34 Identities=21% Similarity=0.390 Sum_probs=30.8
Q ss_pred ccccccCccccCChHHHHHHHhHhcCCCCCC-Ccccc
Q 024455 14 RHKCVACYKQFKRKDHLIEHMKISYHSVHQP-KCAVC 49 (267)
Q Consensus 14 ~~~C~~C~k~f~~~~~l~~H~~~~~H~~~~~-~C~~C 49 (267)
||+|+.||+.|..++.|.+|++. |+++++ .|+.-
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 69999999999999999999999 888888 87754
No 70
>PHA00732 hypothetical protein
Probab=98.21 E-value=8.2e-07 Score=60.15 Aligned_cols=44 Identities=30% Similarity=0.519 Sum_probs=35.6
Q ss_pred ccccccCccccCChHHHHHHHhHhcCCCCCCCcccchhhcCCHHHHHhhc
Q 024455 14 RHKCVACYKQFKRKDHLIEHMKISYHSVHQPKCAVCQKLSKSFESLREHL 63 (267)
Q Consensus 14 ~~~C~~C~k~f~~~~~l~~H~~~~~H~~~~~~C~~C~~~f~~~~~l~~H~ 63 (267)
||.|+.|++.|.+...|..|++.+ |.+. .|+.||+.|. +|..|.
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 688999999999999999999841 5532 7889998887 477777
No 71
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=98.21 E-value=3.2e-07 Score=79.07 Aligned_cols=87 Identities=21% Similarity=0.339 Sum_probs=64.3
Q ss_pred ccccccCccccCChHHHHHHH--hHhcCCCCCCCcccchhhcCCHHHHHhhcCCCCCCCcCCccc---------------
Q 024455 14 RHKCVACYKQFKRKDHLIEHM--KISYHSVHQPKCAVCQKLSKSFESLREHLTGPLSKAHCSGIF--------------- 76 (267)
Q Consensus 14 ~~~C~~C~k~f~~~~~l~~H~--~~~~H~~~~~~C~~C~~~f~~~~~l~~H~~~~~~C~~C~k~f--------------- 76 (267)
-|.|..|...|...-.|.+|. +++ |. .++|++|+|.|.-..||..|.....+-..-+++-
T Consensus 267 dyiCqLCK~kYeD~F~LAQHrC~RIV-~v--EYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ 343 (500)
T KOG3993|consen 267 DYICQLCKEKYEDAFALAQHRCPRIV-HV--EYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQ 343 (500)
T ss_pred HHHHHHHHHhhhhHHHHhhccCCeeE-Ee--eecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhh
Confidence 488999999999999999997 442 22 2399999999999999999983222211111000
Q ss_pred --------cc---ccccccccccCChhhHHHHHHHhcC
Q 024455 77 --------SD---RGCNLCMNIFDSPSSLIKHKEACSL 103 (267)
Q Consensus 77 --------~~---~~C~~C~~~F~~~~~L~~H~~~h~~ 103 (267)
++ ..|.+|+|.|.+...|+.|+.+|+.
T Consensus 344 ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~ 381 (500)
T KOG3993|consen 344 EAERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQR 381 (500)
T ss_pred hccccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhc
Confidence 00 1299999999999999999999874
No 72
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=98.20 E-value=1e-06 Score=76.04 Aligned_cols=48 Identities=29% Similarity=0.544 Sum_probs=41.8
Q ss_pred ccccccCccccCChHHHHHHHhHhcCCC--------CCC--------------------------CcccchhhcCCHHHH
Q 024455 14 RHKCVACYKQFKRKDHLIEHMKISYHSV--------HQP--------------------------KCAVCQKLSKSFESL 59 (267)
Q Consensus 14 ~~~C~~C~k~f~~~~~l~~H~~~~~H~~--------~~~--------------------------~C~~C~~~f~~~~~l 59 (267)
.|+|+.|+|.|+...+|..|.|. |.. ..| .|.+|+|.|.+...|
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 49999999999999999999999 731 111 599999999999999
Q ss_pred Hhhc
Q 024455 60 REHL 63 (267)
Q Consensus 60 ~~H~ 63 (267)
+.|+
T Consensus 373 rKHq 376 (500)
T KOG3993|consen 373 RKHQ 376 (500)
T ss_pred HHhH
Confidence 9996
No 73
>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=98.20 E-value=5.5e-07 Score=47.48 Aligned_cols=25 Identities=36% Similarity=0.707 Sum_probs=22.4
Q ss_pred HHHHHHhHhcCCCCCC-CcccchhhcCC
Q 024455 29 HLIEHMKISYHSVHQP-KCAVCQKLSKS 55 (267)
Q Consensus 29 ~l~~H~~~~~H~~~~~-~C~~C~~~f~~ 55 (267)
+|.+|+++ |++++| .|+.|++.|.+
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 99999999864
No 74
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.16 E-value=4.5e-06 Score=76.29 Aligned_cols=116 Identities=12% Similarity=0.307 Sum_probs=78.3
Q ss_pred ccccccCccccCChHHHHHHHhHhcCCCCCC-Cccc--chhhcCCHHHHHhhcCCCCCCCcCCcccccc-----------
Q 024455 14 RHKCVACYKQFKRKDHLIEHMKISYHSVHQP-KCAV--CQKLSKSFESLREHLTGPLSKAHCSGIFSDR----------- 79 (267)
Q Consensus 14 ~~~C~~C~k~f~~~~~l~~H~~~~~H~~~~~-~C~~--C~~~f~~~~~l~~H~~~~~~C~~C~k~f~~~----------- 79 (267)
.-.|+.|.+... ...|..|... -. ... .|+. ||..|. +..+.. ++.|+.|++.|...
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-SRSIALHEAY--CS-RHNVVCPHDGCGIVLR-VEEAKN----HVHCEKCGQAFQQGEMEKHMKVFHE 477 (567)
T ss_pred eEECCCCCCccc-hhHHHHHHhh--CC-CcceeCCcccccceee-cccccc----CccCCCCCCccchHHHHHHHHhcCC
Confidence 447999987654 4567788753 33 333 7874 888883 333333 46788888887532
Q ss_pred --cccccccccCChhhHHHHHHHhcCCCCcc---ccccCc----------chhhhhhhccccccccccCCCceeeeeccc
Q 024455 80 --GCNLCMNIFDSPSSLIKHKEACSLSAPVP---FEKTLS----------NAESQKKISGAIDEKRTCRGPKAVAMDCEM 144 (267)
Q Consensus 80 --~C~~C~~~F~~~~~L~~H~~~h~~~~~~~---C~~~f~----------~~~~l~~H~~~~~~~r~~~~~~~~~~dcE~ 144 (267)
.|+ ||+.+ .+..|..|+++|.+++++. |++.+. ..+.|..|..... ...+.|..
T Consensus 478 pv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~CG---------~rt~~C~~ 546 (567)
T PLN03086 478 PLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESICG---------SRTAPCDS 546 (567)
T ss_pred CccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhcC---------CcceEccc
Confidence 388 99755 6789999999999999998 555553 1346788874321 24578899
Q ss_pred cCCcC
Q 024455 145 VGGGS 149 (267)
Q Consensus 145 ~g~~~ 149 (267)
||...
T Consensus 547 Cgk~V 551 (567)
T PLN03086 547 CGRSV 551 (567)
T ss_pred cCCee
Confidence 98753
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=98.00 E-value=1.2e-05 Score=64.84 Aligned_cols=89 Identities=15% Similarity=0.122 Sum_probs=56.5
Q ss_pred eeeeccccCCc-----CCCCccceeeEEEecCCCCeeEecccCCCCCccccccccccCCHHhhccCCCHHHHHHHHHHHH
Q 024455 138 VAMDCEMVGGG-----SNGTLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEIL 212 (267)
Q Consensus 138 ~~~dcE~~g~~-----~~~~~~~i~~v~vvd~~~~~~~~~~v~P~~~i~~~~~~~~GIt~~~l~~~~~~~~v~~~~~~~~ 212 (267)
.++|.|++|.. ..+++.+|+.+...++.. ..+.....+..... .||+..++...++..+++..+++++
T Consensus 2 ~~~DIEt~~~~~~p~~~~d~Ii~I~~~~~~~g~~-~~~~~~~~~~~~~~------~~i~~~~v~~~~~E~~lL~~f~~~i 74 (199)
T cd05160 2 LSFDIETTPPVGGPEPDRDPIICITYADSFDGVK-VVFLLKTSTVGDDI------EFIDGIEVEYFADEKELLKRFFDII 74 (199)
T ss_pred ccEEEeecCCCCCcCCCCCCEEEEEEEEeeCCce-eeEEEeecccCCcC------CCCCCceEEEeCCHHHHHHHHHHHH
Confidence 57899999862 234444444433322222 12222222211111 1888889999999999999999999
Q ss_pred hcCCCCCcccccCCCceEEEeccc-hhhhcccc
Q 024455 213 NNGESTGRLMLDDGKARLLVGHGL-EHDLDSLR 244 (267)
Q Consensus 213 ~~~~~~~~~~~~~~~~~~lvgh~~-~~Dl~~l~ 244 (267)
.+ .+| .+|||||+ .||+.+|.
T Consensus 75 ~~------~dp-----diivg~N~~~FD~~~L~ 96 (199)
T cd05160 75 RE------YDP-----DILTGYNIDDFDLPYLL 96 (199)
T ss_pred Hh------cCC-----CEEEEeccCCCcHHHHH
Confidence 42 111 39999999 89999994
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=97.81 E-value=1e-05 Score=41.18 Aligned_cols=22 Identities=41% Similarity=0.689 Sum_probs=20.4
Q ss_pred cccccCccccCChHHHHHHHhH
Q 024455 15 HKCVACYKQFKRKDHLIEHMKI 36 (267)
Q Consensus 15 ~~C~~C~k~f~~~~~l~~H~~~ 36 (267)
|.|+.|++.|.++..|..|++.
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 7899999999999999999987
No 77
>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=97.76 E-value=1.4e-05 Score=42.06 Aligned_cols=22 Identities=23% Similarity=0.298 Sum_probs=17.4
Q ss_pred hHHHHHHHhcCCCCcc---ccccCc
Q 024455 93 SLIKHKEACSLSAPVP---FEKTLS 114 (267)
Q Consensus 93 ~L~~H~~~h~~~~~~~---C~~~f~ 114 (267)
+|.+|+++|++++||+ |++.|.
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 555553
No 78
>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=97.75 E-value=1.7e-05 Score=40.37 Aligned_cols=21 Identities=33% Similarity=0.640 Sum_probs=19.0
Q ss_pred ccccccccCChhhHHHHHHHh
Q 024455 81 CNLCMNIFDSPSSLIKHKEAC 101 (267)
Q Consensus 81 C~~C~~~F~~~~~L~~H~~~h 101 (267)
|+.|++.|.+++.|..|++.|
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 889999999999999999875
No 79
>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=97.43 E-value=0.00011 Score=37.40 Aligned_cols=22 Identities=36% Similarity=0.765 Sum_probs=18.7
Q ss_pred cccccCccccCChHHHHHHHhH
Q 024455 15 HKCVACYKQFKRKDHLIEHMKI 36 (267)
Q Consensus 15 ~~C~~C~k~f~~~~~l~~H~~~ 36 (267)
|.|+.|++.|.+...|..|+++
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 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=97.40 E-value=0.00023 Score=44.64 Aligned_cols=46 Identities=26% Similarity=0.481 Sum_probs=29.1
Q ss_pred ccccccCccccCChHHHHHHHhHhcCCCCC-C-CcccchhhcCCHHHHHhhc
Q 024455 14 RHKCVACYKQFKRKDHLIEHMKISYHSVHQ-P-KCAVCQKLSKSFESLREHL 63 (267)
Q Consensus 14 ~~~C~~C~k~f~~~~~l~~H~~~~~H~~~~-~-~C~~C~~~f~~~~~l~~H~ 63 (267)
.|.|+.|++ ..+...|..|.... |..+. . .|++|...+. .+|..|+
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 66543 2 6777765433 2555554
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=97.36 E-value=0.00012 Score=37.31 Aligned_cols=22 Identities=32% Similarity=0.581 Sum_probs=18.1
Q ss_pred ccccccccCChhhHHHHHHHhc
Q 024455 81 CNLCMNIFDSPSSLIKHKEACS 102 (267)
Q Consensus 81 C~~C~~~F~~~~~L~~H~~~h~ 102 (267)
|+.|++.|.+...|+.|+++|+
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 8889999999999999998875
No 82
>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=97.36 E-value=0.00013 Score=38.68 Aligned_cols=23 Identities=30% Similarity=0.504 Sum_probs=21.8
Q ss_pred ccccccCccccCChHHHHHHHhH
Q 024455 14 RHKCVACYKQFKRKDHLIEHMKI 36 (267)
Q Consensus 14 ~~~C~~C~k~f~~~~~l~~H~~~ 36 (267)
||+|+.|++.|.+...|..|++.
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 83
>PHA00732 hypothetical protein
Probab=97.31 E-value=0.00017 Score=48.81 Aligned_cols=19 Identities=26% Similarity=0.662 Sum_probs=10.9
Q ss_pred CcccchhhcCCHHHHHhhc
Q 024455 45 KCAVCQKLSKSFESLREHL 63 (267)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~ 63 (267)
.|..||+.|.+.++|+.|+
T Consensus 3 ~C~~Cgk~F~s~s~Lk~H~ 21 (79)
T PHA00732 3 KCPICGFTTVTLFALKQHA 21 (79)
T ss_pred cCCCCCCccCCHHHHHHHh
Confidence 4555555555555555555
No 84
>KOG0542 consensus Predicted exonuclease [Replication, recombination and repair]
Probab=97.27 E-value=0.00025 Score=57.77 Aligned_cols=77 Identities=19% Similarity=0.269 Sum_probs=60.3
Q ss_pred eeeeccccCC-----cCCCCccceeeEEEecCC---CCeeEecccCCCC--CccccccccccCCHHhhccCCCHHHHHHH
Q 024455 138 VAMDCEMVGG-----GSNGTLDLCARVCLVDED---ENVIFHTYVQPQL--PVTNYRYEVTGLTEEDIKNAMPLKEVKDK 207 (267)
Q Consensus 138 ~~~dcE~~g~-----~~~~~~~~i~~v~vvd~~---~~~~~~~~v~P~~--~i~~~~~~~~GIt~~~l~~~~~~~~v~~~ 207 (267)
.++|.|.+-. .+..+++++..|.+.+-+ ....|+.||+|.. .+.++.+.+|||..+.++.|++|++|+++
T Consensus 59 liiDFEaTC~e~~~~~~~~EIIEfP~V~l~~~~~~~Ie~eF~qYVrP~~np~LS~fC~~lTgI~Q~tVD~a~~f~~vl~~ 138 (280)
T KOG0542|consen 59 LILDFEATCEEGNKPHYVQEIIEFPAVLLDNTETSIIEDEFHQYVRPVENPRLSDFCTSLTGIQQETVDEAPTFPQVLSE 138 (280)
T ss_pred EEEeeeeeccccCCCCcchheeecceeEeeccchhhHHHHHHhhcCcccCchHHHHHHHhhCchHhhhccCCCHHHHHHH
Confidence 5677766532 355677777777555442 2236999999983 58999999999999999999999999999
Q ss_pred HHHHHhc
Q 024455 208 ILEILNN 214 (267)
Q Consensus 208 ~~~~~~~ 214 (267)
+..+|.+
T Consensus 139 f~~Wlr~ 145 (280)
T KOG0542|consen 139 FDSWLRK 145 (280)
T ss_pred HHHHHHH
Confidence 9999964
No 85
>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=97.06 E-value=0.001 Score=47.06 Aligned_cols=30 Identities=33% Similarity=0.325 Sum_probs=21.8
Q ss_pred eEEEeccchhhhccccccCC---------CCceeccccc
Q 024455 229 RLLVGHGLEHDLDSLRMNYP---------DHMLRDTAKY 258 (267)
Q Consensus 229 ~~lvgh~~~~Dl~~l~~~~~---------~~~~~dt~~~ 258 (267)
.++||||+.||+.||+.... ...++||..+
T Consensus 45 ~v~V~hn~~fD~~fL~~~~~~~~~~~p~~~~~~lDT~~l 83 (96)
T cd06125 45 AILVGHNGSFDLPFLNNRCAELGLKYPLLAGSWIDTIKL 83 (96)
T ss_pred CEEEEeCcHHhHHHHHHHHHHcCCCCCCcCCcEEEehHH
Confidence 69999999999999964321 2356777543
No 86
>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=96.98 E-value=0.00056 Score=41.28 Aligned_cols=26 Identities=23% Similarity=0.566 Sum_probs=19.1
Q ss_pred ccccccccCChhhHHHHHHHhcCCCC
Q 024455 81 CNLCMNIFDSPSSLIKHKEACSLSAP 106 (267)
Q Consensus 81 C~~C~~~F~~~~~L~~H~~~h~~~~~ 106 (267)
|++|+..+.+..+|++|+..+|+.||
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 88888888889999999988888776
No 87
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=96.85 E-value=0.00062 Score=48.13 Aligned_cols=73 Identities=27% Similarity=0.443 Sum_probs=19.5
Q ss_pred ccccCccccCChHHHHHHHhHhcCCCCCCCcccchhhcCCHHHHHhhcCCCCCCCcCCcccccccccccccccCChhhHH
Q 024455 16 KCVACYKQFKRKDHLIEHMKISYHSVHQPKCAVCQKLSKSFESLREHLTGPLSKAHCSGIFSDRGCNLCMNIFDSPSSLI 95 (267)
Q Consensus 16 ~C~~C~k~f~~~~~l~~H~~~~~H~~~~~~C~~C~~~f~~~~~l~~H~~~~~~C~~C~k~f~~~~C~~C~~~F~~~~~L~ 95 (267)
+|..|+..|.....|..|+... |.-..+ ....+.....+..+.... ......|..|++.|.+...|.
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~-H~~~~~----~~~~l~~~~~~~~~~~~~--------~~~~~~C~~C~~~f~s~~~l~ 67 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKK-HGFDIP----DQKYLVDPNRLLNYLRKK--------VKESFRCPYCNKTFRSREALQ 67 (100)
T ss_dssp -------------------------------------------------------------SSEEBSSSS-EESSHHHHH
T ss_pred Cccccccccccccccccccccc-cccccc----cccccccccccccccccc--------cCCCCCCCccCCCCcCHHHHH
Confidence 5888999999999999998763 443222 111111222222222100 000124888999999999999
Q ss_pred HHHHHh
Q 024455 96 KHKEAC 101 (267)
Q Consensus 96 ~H~~~h 101 (267)
.|++.+
T Consensus 68 ~Hm~~~ 73 (100)
T PF12756_consen 68 EHMRSK 73 (100)
T ss_dssp HHHHHT
T ss_pred HHHcCc
Confidence 999975
No 88
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=96.85 E-value=0.00038 Score=58.33 Aligned_cols=29 Identities=31% Similarity=0.488 Sum_probs=23.8
Q ss_pred CCCccccc--cCccccCChHHHHHHHhHhcCC
Q 024455 11 STARHKCV--ACYKQFKRKDHLIEHMKISYHS 40 (267)
Q Consensus 11 ~~k~~~C~--~C~k~f~~~~~l~~H~~~~~H~ 40 (267)
++|||+|+ .|.|+|+....|+-|+.- .|.
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lh-GH~ 376 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLH-GHQ 376 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhc-ccc
Confidence 46999995 599999999999999864 353
No 89
>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=96.81 E-value=0.00058 Score=36.04 Aligned_cols=22 Identities=36% Similarity=0.638 Sum_probs=19.2
Q ss_pred ccccccccCChhhHHHHHHHhc
Q 024455 81 CNLCMNIFDSPSSLIKHKEACS 102 (267)
Q Consensus 81 C~~C~~~F~~~~~L~~H~~~h~ 102 (267)
|..|++.|.+...|..|++.|.
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 7888999999999999998775
No 90
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.81 E-value=0.0012 Score=34.04 Aligned_cols=24 Identities=46% Similarity=0.789 Sum_probs=21.4
Q ss_pred cccccCccccCChHHHHHHHhHhcCC
Q 024455 15 HKCVACYKQFKRKDHLIEHMKISYHS 40 (267)
Q Consensus 15 ~~C~~C~k~f~~~~~l~~H~~~~~H~ 40 (267)
|.|+.|++.|.....|..|++. |.
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 65
No 91
>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=96.70 E-value=0.0022 Score=40.14 Aligned_cols=51 Identities=27% Similarity=0.414 Sum_probs=31.9
Q ss_pred CcccchhhcCCHHHHHhhcCCCCCCCcCCcccccccccccccccCChhhHHHHHHHhcC
Q 024455 45 KCAVCQKLSKSFESLREHLTGPLSKAHCSGIFSDRGCNLCMNIFDSPSSLIKHKEACSL 103 (267)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~~~~~~C~~C~k~f~~~~C~~C~~~F~~~~~L~~H~~~h~~ 103 (267)
.|+.|++ ..+...|..|....+.-+ ++ ...|++|...+. .+|..|+..+++
T Consensus 4 ~CP~C~~-~~~~~~L~~H~~~~H~~~--~~---~v~CPiC~~~~~--~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 4 TCPYCGK-GFSESSLVEHCEDEHRSE--SK---NVVCPICSSRVT--DNLIRHLNSQHR 54 (54)
T ss_pred CCCCCCC-ccCHHHHHHHHHhHCcCC--CC---CccCCCchhhhh--hHHHHHHHHhcC
Confidence 7999999 456788999982111100 00 112666766544 499999987763
No 92
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.64 E-value=0.0016 Score=33.50 Aligned_cols=22 Identities=32% Similarity=0.608 Sum_probs=19.2
Q ss_pred ccccccccCChhhHHHHHHHhc
Q 024455 81 CNLCMNIFDSPSSLIKHKEACS 102 (267)
Q Consensus 81 C~~C~~~F~~~~~L~~H~~~h~ 102 (267)
|+.|++.|...+.|..|++.|.
T Consensus 3 C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 3 CPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCcchhCCHHHHHHHHHHhc
Confidence 7889999999999999998774
No 93
>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=96.55 E-value=0.0023 Score=38.65 Aligned_cols=27 Identities=22% Similarity=0.476 Sum_probs=16.4
Q ss_pred CCCCccccccCccccCChHHHHHHHhH
Q 024455 10 RSTARHKCVACYKQFKRKDHLIEHMKI 36 (267)
Q Consensus 10 ~~~k~~~C~~C~k~f~~~~~l~~H~~~ 36 (267)
..+.|..|++|+..+.+..+|++|+.+
T Consensus 20 ~S~~PatCP~C~a~~~~srnLrRHle~ 46 (54)
T PF09237_consen 20 QSEQPATCPICGAVIRQSRNLRRHLEI 46 (54)
T ss_dssp TTS--EE-TTT--EESSHHHHHHHHHH
T ss_pred ccCCCCCCCcchhhccchhhHHHHHHH
Confidence 356677788888878888888888766
No 94
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.30 E-value=0.002 Score=33.24 Aligned_cols=22 Identities=27% Similarity=0.640 Sum_probs=19.7
Q ss_pred cccccCccccCChHHHHHHHhH
Q 024455 15 HKCVACYKQFKRKDHLIEHMKI 36 (267)
Q Consensus 15 ~~C~~C~k~f~~~~~l~~H~~~ 36 (267)
|.|+.|++.|.+...|..|++.
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 6799999999999999999876
No 95
>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=96.16 E-value=0.022 Score=44.42 Aligned_cols=85 Identities=22% Similarity=0.203 Sum_probs=51.6
Q ss_pred ceeeeeccccCCcCCCCccceeeEEEecCCCCeeEecccCCCCCccccccccccCCHHhhccCCCHHHHHHHHHHHHhcC
Q 024455 136 KAVAMDCEMVGGGSNGTLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEILNNG 215 (267)
Q Consensus 136 ~~~~~dcE~~g~~~~~~~~~i~~v~vvd~~~~~~~~~~v~P~~~i~~~~~~~~GIt~~~l~~~~~~~~v~~~~~~~~~~~ 215 (267)
..+++|+|+.+.........++.+.+....+..+++..-.... . +.+.|.+++.+
T Consensus 21 ~~~a~D~E~~~~~~~~~~~~~~~iq~~~~~~~~i~~~~~~~~~----~--------------------~~~~l~~ll~~- 75 (176)
T PF01612_consen 21 KVLAFDTETTGLDPYSYNPKIALIQLATGEGCYIIDPIDLGDN----W--------------------ILDALKELLED- 75 (176)
T ss_dssp SEEEEEEEEETSTSTTSSEEEEEEEEEESCEEEEECGTTSTTT----T--------------------HHHHHHHHHTT-
T ss_pred CeEEEEEEECCCCccccCCeEEEEEEecCCCceeeeecccccc----c--------------------hHHHHHHHHhC-
Confidence 4799999999976533343445555554422222221111100 0 67788888854
Q ss_pred CCCCcccccCCCceEEEeccchhhhccccc--cCCCCceeccc
Q 024455 216 ESTGRLMLDDGKARLLVGHGLEHDLDSLRM--NYPDHMLRDTA 256 (267)
Q Consensus 216 ~~~~~~~~~~~~~~~lvgh~~~~Dl~~l~~--~~~~~~~~dt~ 256 (267)
.+.+.||||+.||+.+|.- ..+-..++||.
T Consensus 76 -----------~~i~kv~~n~~~D~~~L~~~~~i~~~~~~D~~ 107 (176)
T PF01612_consen 76 -----------PNIIKVGHNAKFDLKWLYRSFGIDLKNVFDTM 107 (176)
T ss_dssp -----------TTSEEEESSHHHHHHHHHHHHTS--SSEEEHH
T ss_pred -----------CCccEEEEEEechHHHHHHHhccccCCccchh
Confidence 5679999999999999965 22223667884
No 96
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=95.78 E-value=0.0041 Score=43.86 Aligned_cols=20 Identities=40% Similarity=0.753 Sum_probs=17.8
Q ss_pred CCcccchhhcCCHHHHHhhc
Q 024455 44 PKCAVCQKLSKSFESLREHL 63 (267)
Q Consensus 44 ~~C~~C~~~f~~~~~l~~H~ 63 (267)
..|..|++.|.+...|..|+
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 38999999999999999999
No 97
>PRK04860 hypothetical protein; Provisional
Probab=95.67 E-value=0.0053 Score=47.51 Aligned_cols=38 Identities=13% Similarity=0.267 Sum_probs=32.5
Q ss_pred CccccccCccccCChHHHHHHHhHhcCCCCCC-CcccchhhcCCH
Q 024455 13 ARHKCVACYKQFKRKDHLIEHMKISYHSVHQP-KCAVCQKLSKSF 56 (267)
Q Consensus 13 k~~~C~~C~k~f~~~~~l~~H~~~~~H~~~~~-~C~~C~~~f~~~ 56 (267)
-+|.|. |++ ....+.+|.++ |+++++ .|..|++.|...
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri--~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRV--VRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHH--hcCCccEECCCCCceeEEe
Confidence 369998 987 67889999999 999988 999999988653
No 98
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=95.38 E-value=0.0083 Score=30.83 Aligned_cols=21 Identities=33% Similarity=0.680 Sum_probs=17.2
Q ss_pred ccccccccCChhhHHHHHHHh
Q 024455 81 CNLCMNIFDSPSSLIKHKEAC 101 (267)
Q Consensus 81 C~~C~~~F~~~~~L~~H~~~h 101 (267)
|..|++.|.+...|+.|++.+
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 788888888888888888654
No 99
>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=95.21 E-value=0.0059 Score=32.15 Aligned_cols=22 Identities=41% Similarity=0.694 Sum_probs=17.3
Q ss_pred cccccCccccCChHHHHHHHhH
Q 024455 15 HKCVACYKQFKRKDHLIEHMKI 36 (267)
Q Consensus 15 ~~C~~C~k~f~~~~~l~~H~~~ 36 (267)
|.|..|++.|.+...+..|+++
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 6788888888888888877764
No 100
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=94.98 E-value=0.017 Score=29.37 Aligned_cols=22 Identities=23% Similarity=0.330 Sum_probs=16.9
Q ss_pred ccccccccCChhhHHHHHHHhcC
Q 024455 81 CNLCMNIFDSPSSLIKHKEACSL 103 (267)
Q Consensus 81 C~~C~~~F~~~~~L~~H~~~h~~ 103 (267)
|+.|+.... .+.|..|++.|++
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 8899999998764
No 101
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=94.92 E-value=0.02 Score=29.60 Aligned_cols=19 Identities=37% Similarity=0.833 Sum_probs=13.4
Q ss_pred ccccccccCChhhHHHHHHH
Q 024455 81 CNLCMNIFDSPSSLIKHKEA 100 (267)
Q Consensus 81 C~~C~~~F~~~~~L~~H~~~ 100 (267)
|+.||+.| ....|..|+.+
T Consensus 5 C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 5 CPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CCCCCCEE-CHHHHHHHHHh
Confidence 67777777 56677777654
No 102
>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=94.75 E-value=0.11 Score=41.63 Aligned_cols=83 Identities=17% Similarity=0.204 Sum_probs=49.4
Q ss_pred ceeeeeccccCCc-C-CCCccceeeEEEecCCCCeeEecccCCCCCccccccccccCCHHhhccCCCHHHHHHHHHHHHh
Q 024455 136 KAVAMDCEMVGGG-S-NGTLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEILN 213 (267)
Q Consensus 136 ~~~~~dcE~~g~~-~-~~~~~~i~~v~vvd~~~~~~~~~~v~P~~~i~~~~~~~~GIt~~~l~~~~~~~~v~~~~~~~~~ 213 (267)
++.++|.|+.+.. + ......+..+++....+..++.. ++ +....+..-.+-.+++..+++++.
T Consensus 4 ~i~~fDIEt~~~~g~p~~~~d~Ii~Is~~~~~~~~~~~~--~~-------------~~~~~v~~~~~E~~lL~~F~~~i~ 68 (195)
T cd05780 4 KILSFDIEVLNHEGEPNPEKDPIIMISFADEGGNKVITW--KK-------------FDLPFVEVVKTEKEMIKRFIEIVK 68 (195)
T ss_pred eEEEEEEEecCCCCCCCCCCCcEEEEEEecCCCceEEEe--cC-------------CCCCeEEEeCCHHHHHHHHHHHHH
Confidence 4678999998432 1 23334455555555444322211 11 001134445677899999999994
Q ss_pred cCCCCCcccccCCCceEEEeccc-hhhhcccc
Q 024455 214 NGESTGRLMLDDGKARLLVGHGL-EHDLDSLR 244 (267)
Q Consensus 214 ~~~~~~~~~~~~~~~~~lvgh~~-~~Dl~~l~ 244 (267)
+ .+ -.+|||||. .||+.+|.
T Consensus 69 ~------~d-----pdiivgyN~~~FD~pyL~ 89 (195)
T cd05780 69 E------KD-----PDVIYTYNGDNFDFPYLK 89 (195)
T ss_pred H------cC-----CCEEEecCCCCCcHHHHH
Confidence 2 11 149999998 58999994
No 103
>COG2925 SbcB Exonuclease I [DNA replication, recombination, and repair]
Probab=94.54 E-value=0.16 Score=44.30 Aligned_cols=100 Identities=15% Similarity=0.135 Sum_probs=70.2
Q ss_pred CCceeeeeccccCCcC-CCCccceeeEEEe-cCC-CCeeEecccCCCCCc--cccccccccCCHHhhc-cCCCHHHHHHH
Q 024455 134 GPKAVAMDCEMVGGGS-NGTLDLCARVCLV-DED-ENVIFHTYVQPQLPV--TNYRYEVTGLTEEDIK-NAMPLKEVKDK 207 (267)
Q Consensus 134 ~~~~~~~dcE~~g~~~-~~~~~~i~~v~vv-d~~-~~~~~~~~v~P~~~i--~~~~~~~~GIt~~~l~-~~~~~~~v~~~ 207 (267)
...+..+|-|+-|... .++..+.|.|+-- +.+ ..+-..-+++|.... .+..+=|||||+.... ++.+..+..+.
T Consensus 8 ~~tF~~yDYETfG~~Pa~DRPaQFAgiRTD~~~NiIgeP~~fyCkpsdDyLP~P~a~LITGITPQ~~~~~G~~E~~F~~~ 87 (475)
T COG2925 8 QPTFLFYDYETFGVHPALDRPAQFAGIRTDIEFNIIGEPIVFYCKPADDYLPQPGAVLITGITPQEAREKGINEAAFAAR 87 (475)
T ss_pred CCcEEEEehhhcCCCcccccchhhheeeccccccccCCCeEEEecCccccCCCCCceeeecCCHHHHHhcCCChHHHHHH
Confidence 3457889999999873 3556666666653 222 122244567776432 2346889999999985 56899999999
Q ss_pred HHHHHhcCCCCCcccccCCCceEEEec-cchhhhccccc
Q 024455 208 ILEILNNGESTGRLMLDDGKARLLVGH-GLEHDLDSLRM 245 (267)
Q Consensus 208 ~~~~~~~~~~~~~~~~~~~~~~~lvgh-~~~~Dl~~l~~ 245 (267)
|...+.. .++.+||+ |+.||=.|-+.
T Consensus 88 I~~~ls~------------P~Tcv~GYNniRFDDEvtRy 114 (475)
T COG2925 88 IHAELTQ------------PNTCVLGYNNIRFDDEVTRY 114 (475)
T ss_pred HHHHhCC------------CCeeeecccccccchHHHHH
Confidence 9998864 67899995 57999888764
No 104
>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=94.49 E-value=0.12 Score=41.91 Aligned_cols=36 Identities=25% Similarity=0.421 Sum_probs=29.2
Q ss_pred CCCHHHHHHHHHHHHhcCCCCCcccccCCCceEEEeccc-hhhhcccc
Q 024455 198 AMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGL-EHDLDSLR 244 (267)
Q Consensus 198 ~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~-~~Dl~~l~ 244 (267)
..+.++++..+.+++.+ .+| .||||||+ .||+.+|.
T Consensus 55 ~~~E~~lL~~f~~~i~~------~dP-----dii~g~N~~~FD~pyl~ 91 (207)
T cd05785 55 DAAEKELLEELVAIIRE------RDP-----DVIEGHNIFRFDLPYLR 91 (207)
T ss_pred CCCHHHHHHHHHHHHHH------hCC-----CEEeccCCcccCHHHHH
Confidence 57899999999999952 111 49999999 89999983
No 105
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=94.41 E-value=0.022 Score=28.96 Aligned_cols=21 Identities=33% Similarity=0.513 Sum_probs=17.1
Q ss_pred cccccCccccCChHHHHHHHhH
Q 024455 15 HKCVACYKQFKRKDHLIEHMKI 36 (267)
Q Consensus 15 ~~C~~C~k~f~~~~~l~~H~~~ 36 (267)
|+|+.|+.... +..|..|++.
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 78999998887 8899999987
No 106
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=94.40 E-value=0.016 Score=48.86 Aligned_cols=57 Identities=30% Similarity=0.574 Sum_probs=38.2
Q ss_pred CCC-Cccc--chhhcCCHHHHHhhc-CC-------CCCCCcCCcccc----cccccccccccCChhhHHHHH
Q 024455 42 HQP-KCAV--CQKLSKSFESLREHL-TG-------PLSKAHCSGIFS----DRGCNLCMNIFDSPSSLIKHK 98 (267)
Q Consensus 42 ~~~-~C~~--C~~~f~~~~~l~~H~-~~-------~~~C~~C~k~f~----~~~C~~C~~~F~~~~~L~~H~ 98 (267)
++| +|++ |.|.+.....|+.|+ .| +-+-++--..|+ -..|+.|+|.|.....|+-|.
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr 418 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHR 418 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceecc
Confidence 477 8887 999999998899888 11 222233333342 224888888888888887774
No 107
>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=94.30 E-value=0.01 Score=31.25 Aligned_cols=19 Identities=32% Similarity=0.712 Sum_probs=13.4
Q ss_pred ccccccccCChhhHHHHHH
Q 024455 81 CNLCMNIFDSPSSLIKHKE 99 (267)
Q Consensus 81 C~~C~~~F~~~~~L~~H~~ 99 (267)
|..|++.|.+...|..|++
T Consensus 4 C~~C~k~f~~~~~~~~H~~ 22 (27)
T PF12171_consen 4 CDACDKYFSSENQLKQHMK 22 (27)
T ss_dssp BTTTTBBBSSHHHHHCCTT
T ss_pred cccCCCCcCCHHHHHHHHc
Confidence 6677777777777777764
No 108
>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=94.15 E-value=0.17 Score=40.50 Aligned_cols=45 Identities=20% Similarity=0.423 Sum_probs=31.9
Q ss_pred HHHHHHHHHHhcCCCCCcccccCCCceEEEeccchhhhccccccCCC--------Cceecccccc
Q 024455 203 EVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNYPD--------HMLRDTAKYR 259 (267)
Q Consensus 203 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~Dl~~l~~~~~~--------~~~~dt~~~~ 259 (267)
.+.+.|.+++.+ .+.+-|||++.+|+.+|.-.++. ..++||+.+.
T Consensus 69 ~~~~~L~~ll~d------------~~i~KVg~~~~~D~~~L~~~~~~~~~~~~~~~~v~Dl~~~a 121 (193)
T cd06146 69 DWDRLLKRLFED------------PDVLKLGFGFKQDLKALSASYPALKCMFERVQNVLDLQNLA 121 (193)
T ss_pred HHHHHHHHHhCC------------CCeeEEEechHHHHHHHHHhcCccccccccCCceEEHHHHH
Confidence 344567788843 44577999999999999754432 4788997543
No 109
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=94.15 E-value=0.043 Score=28.28 Aligned_cols=21 Identities=38% Similarity=0.694 Sum_probs=16.2
Q ss_pred cccccCccccCChHHHHHHHhH
Q 024455 15 HKCVACYKQFKRKDHLIEHMKI 36 (267)
Q Consensus 15 ~~C~~C~k~f~~~~~l~~H~~~ 36 (267)
.+|+.||+.| ....|..|+..
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 4788999998 56778888754
No 110
>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=94.11 E-value=0.041 Score=43.71 Aligned_cols=51 Identities=24% Similarity=0.215 Sum_probs=37.5
Q ss_pred cCCCHHHHHHHHHHHHhcCCCCCcccccCCCceEEEeccchhhhccccccC--CCCceecccccc
Q 024455 197 NAMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNY--PDHMLRDTAKYR 259 (267)
Q Consensus 197 ~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~Dl~~l~~~~--~~~~~~dt~~~~ 259 (267)
++++++++.+.|.+++.+ .+..+||||+.||+.+|+... ....++||..+.
T Consensus 48 ~~~~~~~~~~~l~~~l~~------------~~~~~v~hn~k~d~~~l~~~gi~~~~~~~Dt~l~a 100 (193)
T cd06139 48 EQLPREEVLAALKPLLED------------PSIKKVGQNLKFDLHVLANHGIELRGPAFDTMLAS 100 (193)
T ss_pred cCCCHHHHHHHHHHHHhC------------CCCcEEeeccHHHHHHHHHCCCCCCCCcccHHHHH
Confidence 456788999999999943 335899999999999996432 123568887543
No 111
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.42 E-value=0.11 Score=48.94 Aligned_cols=74 Identities=24% Similarity=0.291 Sum_probs=39.4
Q ss_pred ccCChHHHHHHHhHhcCCCCCC--------CcccchhhcCCHHHHHhhc-CCCCCCCcCCccccc-ccccccccccCChh
Q 024455 23 QFKRKDHLIEHMKISYHSVHQP--------KCAVCQKLSKSFESLREHL-TGPLSKAHCSGIFSD-RGCNLCMNIFDSPS 92 (267)
Q Consensus 23 ~f~~~~~l~~H~~~~~H~~~~~--------~C~~C~~~f~~~~~l~~H~-~~~~~C~~C~k~f~~-~~C~~C~~~F~~~~ 92 (267)
.|.....|+.|+... |..-.- .+..+.+.| +...|+.|+ .+.. +++.|.. .-|..|...|-...
T Consensus 123 ~~~s~~~Lk~H~~~~-H~~~~c~lC~~~~kif~~e~k~Y-t~~el~~h~~~gd~----d~~s~rGhp~C~~C~~~fld~~ 196 (669)
T KOG2231|consen 123 EFKSVENLKNHMRDQ-HKLHLCSLCLQNLKIFINERKLY-TRAELNLHLMFGDP----DDESCRGHPLCKFCHERFLDDD 196 (669)
T ss_pred chhHHHHHHHHHHHh-hhhhccccccccceeeeeeeehe-hHHHHHHHHhcCCC----ccccccCCccchhhhhhhccHH
Confidence 344778899998541 543221 222233333 456677777 2211 3333333 34666666666666
Q ss_pred hHHHHHHHhc
Q 024455 93 SLIKHKEACS 102 (267)
Q Consensus 93 ~L~~H~~~h~ 102 (267)
.|.+|++.++
T Consensus 197 el~rH~~~~h 206 (669)
T KOG2231|consen 197 ELYRHLRFDH 206 (669)
T ss_pred HHHHhhccce
Confidence 6666666543
No 112
>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=93.32 E-value=0.048 Score=28.41 Aligned_cols=22 Identities=18% Similarity=0.427 Sum_probs=15.6
Q ss_pred CCCcCCcccccc--cccccccccC
Q 024455 68 SKAHCSGIFSDR--GCNLCMNIFD 89 (267)
Q Consensus 68 ~C~~C~k~f~~~--~C~~C~~~F~ 89 (267)
.|+.|++..... .|+.||..|.
T Consensus 2 ~CP~C~~~V~~~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 2 TCPECGAEVPESAKFCPHCGYDFE 25 (26)
T ss_pred cCCCCcCCchhhcCcCCCCCCCCc
Confidence 477777776543 4888888875
No 113
>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=93.27 E-value=0.066 Score=29.79 Aligned_cols=23 Identities=22% Similarity=0.355 Sum_probs=20.4
Q ss_pred ccccccCccccCChHHHHHHHhH
Q 024455 14 RHKCVACYKQFKRKDHLIEHMKI 36 (267)
Q Consensus 14 ~~~C~~C~k~f~~~~~l~~H~~~ 36 (267)
+|.|+.|++.|.....+..|++.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 68899999999999999999865
No 114
>COG5018 KapD Inhibitor of the KinA pathway to sporulation, predicted exonuclease [General function prediction only]
Probab=93.12 E-value=0.0095 Score=45.76 Aligned_cols=77 Identities=18% Similarity=0.209 Sum_probs=55.1
Q ss_pred eeeecccc-----CCcCCCCccceeeE--EEecCCCCeeEecccCCCC--CccccccccccCCHHhhccCCCHHHHHHHH
Q 024455 138 VAMDCEMV-----GGGSNGTLDLCARV--CLVDEDENVIFHTYVQPQL--PVTNYRYEVTGLTEEDIKNAMPLKEVKDKI 208 (267)
Q Consensus 138 ~~~dcE~~-----g~~~~~~~~~i~~v--~vvd~~~~~~~~~~v~P~~--~i~~~~~~~~GIt~~~l~~~~~~~~v~~~~ 208 (267)
..+|.|.+ +....-.+++|.+. ..+|......|+++|+|.. .++++...++||+...++.||-|..|.+++
T Consensus 7 LIID~EaT~~eG~~~~~e~eiiei~a~lv~~id~~vvd~F~syVRP~~~P~Lt~~Ckslt~I~Q~~VD~apifs~v~E~f 86 (210)
T COG5018 7 LIIDFEATMPEGKYSPQEFEIIEIEAGLVKSIDDEVVDTFSSYVRPKKFPKLTKRCKSLTKITQKQVDEAPIFSMVFEDF 86 (210)
T ss_pred EEEEeeeeccCCCCCchhceeeeehhhHHHHhhHHHHHHHHHhcCcccCchHHHHHHHhhhhhhhhccccchHHHHHHHH
Confidence 45566554 22233344443322 2234445566899999983 488889999999999999999999999999
Q ss_pred HHHHhc
Q 024455 209 LEILNN 214 (267)
Q Consensus 209 ~~~~~~ 214 (267)
..+|..
T Consensus 87 ~r~L~~ 92 (210)
T COG5018 87 IRKLNE 92 (210)
T ss_pred HHHHHh
Confidence 999953
No 115
>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=93.01 E-value=0.5 Score=37.70 Aligned_cols=75 Identities=17% Similarity=0.219 Sum_probs=46.9
Q ss_pred ceeeeeccccCCc-C-CCCccceeeEEEecCCCCeeEecccCCCCCccccccccccCCHHhhccCCCHHHHHHHHHHHHh
Q 024455 136 KAVAMDCEMVGGG-S-NGTLDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKEVKDKILEILN 213 (267)
Q Consensus 136 ~~~~~dcE~~g~~-~-~~~~~~i~~v~vvd~~~~~~~~~~v~P~~~i~~~~~~~~GIt~~~l~~~~~~~~v~~~~~~~~~ 213 (267)
+..++|.|+.+.. + ......|..|++...++...+-. .+..+-++++..+.+++.
T Consensus 4 ~~l~fDIEt~~~~gfp~~~~d~Ii~Is~~~~~g~~~~~~-----------------------~~~~~E~~lL~~F~~~i~ 60 (188)
T cd05781 4 KTLAFDIEVYSKYGTPNPRRDPIIVISLATSNGDVEFIL-----------------------AEGLDDRKIIREFVKYVK 60 (188)
T ss_pred eEEEEEEEecCCCCCCCCCCCCEEEEEEEeCCCCEEEEE-----------------------ecCCCHHHHHHHHHHHHH
Confidence 4578999997432 1 23334455555554433311100 124788999999999995
Q ss_pred cCCCCCcccccCCCceEEEeccc-hhhhcccc
Q 024455 214 NGESTGRLMLDDGKARLLVGHGL-EHDLDSLR 244 (267)
Q Consensus 214 ~~~~~~~~~~~~~~~~~lvgh~~-~~Dl~~l~ 244 (267)
. .+| .+|+|+|. .||+.+|.
T Consensus 61 ~------~dP-----d~i~gyN~~~FDlpyl~ 81 (188)
T cd05781 61 E------YDP-----DIIVGYNSNAFDWPYLV 81 (188)
T ss_pred H------cCC-----CEEEecCCCcCcHHHHH
Confidence 2 111 48999997 59999984
No 116
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=92.76 E-value=0.037 Score=49.48 Aligned_cols=112 Identities=24% Similarity=0.342 Sum_probs=80.2
Q ss_pred CccccccCccccCChHHHHHHHh--HhcCCCC--CC-Ccc--cchhhcCCHHHHHhhc-----CCCCCC--CcCCccccc
Q 024455 13 ARHKCVACYKQFKRKDHLIEHMK--ISYHSVH--QP-KCA--VCQKLSKSFESLREHL-----TGPLSK--AHCSGIFSD 78 (267)
Q Consensus 13 k~~~C~~C~k~f~~~~~l~~H~~--~~~H~~~--~~-~C~--~C~~~f~~~~~l~~H~-----~~~~~C--~~C~k~f~~ 78 (267)
.++.|..|...|.....|..|.+ . |+++ ++ .|+ .|++.|.+...+..|. ..++.+ ..|.+.+..
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~--h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 365 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVN--HSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSP 365 (467)
T ss_pred cCCCCccccCCccccccccccccccc--cccccCCceeeeccCCCccccccccccCCcccccCCCccccccccCcccccc
Confidence 57999999999999999999999 8 9999 88 999 7999999999999997 122332 333333332
Q ss_pred cc-----------------------ccccccccCChhhHHHHHHHhcCCCCcc-----ccccCcchhhhhhhcccc
Q 024455 79 RG-----------------------CNLCMNIFDSPSSLIKHKEACSLSAPVP-----FEKTLSNAESQKKISGAI 126 (267)
Q Consensus 79 ~~-----------------------C~~C~~~F~~~~~L~~H~~~h~~~~~~~-----C~~~f~~~~~l~~H~~~~ 126 (267)
.. =..|-..+.....+..|...|-...++. |...+.....+..|.+.+
T Consensus 366 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 441 (467)
T COG5048 366 LLNNEPPQSLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHIITHLSFRPYNCKNPPCSKSFNRHYNLIPHKKIH 441 (467)
T ss_pred ccCCCCccchhhccCccCCccccccccchhhhhccccccccccccccccCCcCCCCCcchhhccCccccccccccc
Confidence 21 2346667777777777777776544332 666777777777776544
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=92.47 E-value=0.45 Score=38.18 Aligned_cols=38 Identities=13% Similarity=0.175 Sum_probs=28.8
Q ss_pred ccCCCHHHHHHHHHHHHhcCCCCCcccccCCCceEEEeccc-hhhhcccc
Q 024455 196 KNAMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGL-EHDLDSLR 244 (267)
Q Consensus 196 ~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~-~~Dl~~l~ 244 (267)
.--.+-.+++..+.+++.+ .+| .||+|||+ .||+.+|.
T Consensus 46 ~~~~~E~~lL~~f~~~i~~------~dP-----Dvi~g~N~~~FD~~yl~ 84 (193)
T cd05784 46 EWFADEKSLLLALIAWFAQ------YDP-----DIIIGWNVINFDLRLLQ 84 (193)
T ss_pred EEECCHHHHHHHHHHHHHh------hCC-----CEEEECCCcCcCHHHHH
Confidence 3346888999999999943 111 39999998 58999993
No 118
>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=92.20 E-value=0.36 Score=41.73 Aligned_cols=91 Identities=14% Similarity=0.134 Sum_probs=53.7
Q ss_pred CCCceeeeeccccCCcC---CCCccceeeEEEe-cC-----CCCeeEecccCCCCCccccccccccCCHHhhccCCCHHH
Q 024455 133 RGPKAVAMDCEMVGGGS---NGTLDLCARVCLV-DE-----DENVIFHTYVQPQLPVTNYRYEVTGLTEEDIKNAMPLKE 203 (267)
Q Consensus 133 ~~~~~~~~dcE~~g~~~---~~~~~~i~~v~vv-d~-----~~~~~~~~~v~P~~~i~~~~~~~~GIt~~~l~~~~~~~~ 203 (267)
..-.+.++|.|+..... .....++..|+++ .. ......-.+... ..+.+ ...+....+..+
T Consensus 155 p~l~i~s~DIe~~~~~~~~P~~~~d~I~~Is~~~~~~~~~~~~~~~~~~~~~~-~~~~~---------~~~v~~~~~E~~ 224 (325)
T PF03104_consen 155 PPLRILSFDIETYSNDGKFPDPEKDEIIMISYVVYRNGSSEPYRRKVFTLGSC-DSIED---------NVEVIYFDSEKE 224 (325)
T ss_dssp GGSEEEEEEEEECSSSSSS-TTTTSEEEEEEEEEEETTEEETTEEEEEECSCS-CCTTC---------TTEEEEESSHHH
T ss_pred cccceeEEEEEEccccCCCCCCCCCeEEEEEEEEEeccccCCCceEEEEecCC-CCCCC---------CcEEEEECCHHH
Confidence 45567899999987652 3344555566642 11 122222222222 11111 334444578899
Q ss_pred HHHHHHHHHhcCCCCCcccccCCCceEEEeccch-hhhcccc
Q 024455 204 VKDKILEILNNGESTGRLMLDDGKARLLVGHGLE-HDLDSLR 244 (267)
Q Consensus 204 v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~-~Dl~~l~ 244 (267)
++..++++|. ..+| .||+|||+. |||.+|.
T Consensus 225 lL~~f~~~i~------~~dP-----Dii~GyN~~~fD~~yl~ 255 (325)
T PF03104_consen 225 LLEAFLDIIQ------EYDP-----DIITGYNIDGFDLPYLI 255 (325)
T ss_dssp HHHHHHHHHH------HHS------SEEEESSTTTTHHHHHH
T ss_pred HHHHHHHHHH------hcCC-----cEEEEecccCCCHHHHH
Confidence 9999999994 2333 299999995 8999993
No 119
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=92.09 E-value=0.052 Score=44.00 Aligned_cols=31 Identities=19% Similarity=0.344 Sum_probs=21.3
Q ss_pred CCCcccchhhcCCHHHHHhhc-CCCCCCCcCC
Q 024455 43 QPKCAVCQKLSKSFESLREHL-TGPLSKAHCS 73 (267)
Q Consensus 43 ~~~C~~C~~~f~~~~~l~~H~-~~~~~C~~C~ 73 (267)
++-|.+|++.|....-|.+|+ .+.|+|-+|-
T Consensus 10 kpwcwycnrefddekiliqhqkakhfkchich 41 (341)
T KOG2893|consen 10 KPWCWYCNREFDDEKILIQHQKAKHFKCHICH 41 (341)
T ss_pred Cceeeecccccchhhhhhhhhhhccceeeeeh
Confidence 447777777777777777777 5666654443
No 120
>PRK05755 DNA polymerase I; Provisional
Probab=90.71 E-value=0.5 Score=46.93 Aligned_cols=45 Identities=27% Similarity=0.182 Sum_probs=32.5
Q ss_pred HHHHHHHHHHhcCCCCCcccccCCCceEEEeccchhhhccccccCC--CCceecccccc
Q 024455 203 EVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNYP--DHMLRDTAKYR 259 (267)
Q Consensus 203 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~Dl~~l~~~~~--~~~~~dt~~~~ 259 (267)
++++.|.+++.+ ...++||||+.||+.+|..... ...++||-+..
T Consensus 357 ~~l~~l~~~L~d------------~~v~kV~HNakfDl~~L~~~gi~~~~~~~DT~iAa 403 (880)
T PRK05755 357 EVLAALKPLLED------------PAIKKVGQNLKYDLHVLARYGIELRGIAFDTMLAS 403 (880)
T ss_pred HHHHHHHHHHhC------------CCCcEEEeccHhHHHHHHhCCCCcCCCcccHHHHH
Confidence 678889999953 3456899999999999963211 23578887543
No 121
>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=90.45 E-value=0.68 Score=36.01 Aligned_cols=45 Identities=18% Similarity=0.275 Sum_probs=30.2
Q ss_pred HHHHHHHhcCCCCCcccccCCCceEEEeccchhhhccccccCC--CCceeccccccccc
Q 024455 206 DKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNYP--DHMLRDTAKYRPLM 262 (267)
Q Consensus 206 ~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~Dl~~l~~~~~--~~~~~dt~~~~~~~ 262 (267)
+.|.+++.+ .+.+.|||++.+|+.+|...++ -..++||.....+.
T Consensus 63 ~~l~~ll~~------------~~i~kv~~~~k~D~~~L~~~~g~~~~~~~Dl~~aa~ll 109 (170)
T cd06141 63 PSLKQLLED------------PSILKVGVGIKGDARKLARDFGIEVRGVVDLSHLAKRV 109 (170)
T ss_pred HHHHHHhcC------------CCeeEEEeeeHHHHHHHHhHcCCCCCCeeeHHHHHHHh
Confidence 467778843 4567899999999999963222 12458888655443
No 122
>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=90.33 E-value=1.2 Score=36.09 Aligned_cols=36 Identities=11% Similarity=0.077 Sum_probs=28.3
Q ss_pred CCCHHHHHHHHHHHHhcCCCCCcccccCCCceEEEeccc-hhhhcccc
Q 024455 198 AMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGL-EHDLDSLR 244 (267)
Q Consensus 198 ~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~-~~Dl~~l~ 244 (267)
-.+-.+++.++.+++.+ .+| .+|+|+|. .||+.+|.
T Consensus 70 ~~~E~~lL~~f~~~i~~------~~P-----d~i~gyN~~~FD~pyl~ 106 (204)
T cd05779 70 EPDEKALLQRFFEHIRE------VKP-----HIIVTYNGDFFDWPFVE 106 (204)
T ss_pred CCCHHHHHHHHHHHHHH------hCC-----CEEEecCccccCHHHHH
Confidence 46889999999999942 111 39999997 69999994
No 123
>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=90.28 E-value=2.1 Score=34.60 Aligned_cols=35 Identities=17% Similarity=0.144 Sum_probs=28.5
Q ss_pred cCCCHHHHHHHHHHHHhcCCCCCcccccCCCceEEEeccc-hhhhcccc
Q 024455 197 NAMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGL-EHDLDSLR 244 (267)
Q Consensus 197 ~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~-~~Dl~~l~ 244 (267)
.-.+-++++..+.+++.+ - .+|||+|. .||+.+|.
T Consensus 69 ~~~~E~~lL~~F~~~i~~------------~-~~iig~N~~~FDlpyl~ 104 (204)
T cd05783 69 FFDSEKELIREAFKIISE------------Y-PIVLTFNGDNFDLPYLY 104 (204)
T ss_pred ecCCHHHHHHHHHHHHhc------------C-CEEEEeCCCCcCHHHHH
Confidence 346889999999999953 2 48999997 69999984
No 124
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=89.48 E-value=0.27 Score=39.07 Aligned_cols=98 Identities=20% Similarity=0.336 Sum_probs=64.9
Q ss_pred CCCCCCCCCCCCCcccccc--CccccCChHHHHHHHhHhcCCCCCCCcccchhhcCCHHHHHhhcC-------------C
Q 024455 1 MDTEAELPKRSTARHKCVA--CYKQFKRKDHLIEHMKISYHSVHQPKCAVCQKLSKSFESLREHLT-------------G 65 (267)
Q Consensus 1 ~~~~~~~~~~~~k~~~C~~--C~k~f~~~~~l~~H~~~~~H~~~~~~C~~C~~~f~~~~~l~~H~~-------------~ 65 (267)
||.-+++-+-..+.+.|.+ |.+.|..-.....|..+. |+. .|..|.+.|.+..-|..|+. |
T Consensus 66 ~d~~d~~~~~~~~~~~cqvagc~~~~d~lD~~E~hY~~~-h~~---sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG 141 (253)
T KOG4173|consen 66 MDVADVPEKPRVPAFACQVAGCCQVFDALDDYEHHYHTL-HGN---SCSFCKRAFPTGHLLDAHILEWHDSLFQALVERG 141 (253)
T ss_pred eeccccccccccccccccccchHHHHhhhhhHHHhhhhc-ccc---hhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcC
Confidence 3444444444566788855 667777777676776441 333 79999999999999999981 1
Q ss_pred --CCCCCcCCcccccccccccccccCChhhHHHHH-HHhcCCCCcccccc
Q 024455 66 --PLSKAHCSGIFSDRGCNLCMNIFDSPSSLIKHK-EACSLSAPVPFEKT 112 (267)
Q Consensus 66 --~~~C~~C~k~f~~~~C~~C~~~F~~~~~L~~H~-~~h~~~~~~~C~~~ 112 (267)
-|.| --+.|+..|.....-..|+ ++|.-...|...+.
T Consensus 142 ~dMy~C----------lvEgCt~KFkT~r~RkdH~I~~Hk~Pa~frFdk~ 181 (253)
T KOG4173|consen 142 QDMYQC----------LVEGCTEKFKTSRDRKDHMIRMHKYPADFRFDKP 181 (253)
T ss_pred ccHHHH----------HHHhhhhhhhhhhhhhhHHHHhccCCcceeecCc
Confidence 1334 1356888999888888886 46644444444444
No 125
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=89.29 E-value=0.17 Score=31.24 Aligned_cols=28 Identities=21% Similarity=0.509 Sum_probs=23.1
Q ss_pred CCCCCccccccCccccCChHHHHHHHhH
Q 024455 9 KRSTARHKCVACYKQFKRKDHLIEHMKI 36 (267)
Q Consensus 9 ~~~~k~~~C~~C~k~f~~~~~l~~H~~~ 36 (267)
+-||-.+.|+.|+..|....++.+|...
T Consensus 12 RDGE~~lrCPRC~~~FR~~K~Y~RHVNK 39 (65)
T COG4049 12 RDGEEFLRCPRCGMVFRRRKDYIRHVNK 39 (65)
T ss_pred cCCceeeeCCchhHHHHHhHHHHHHhhH
Confidence 4578888899999999888888888755
No 126
>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=89.02 E-value=2 Score=35.38 Aligned_cols=38 Identities=13% Similarity=0.107 Sum_probs=29.0
Q ss_pred ccCCCHHHHHHHHHHHHhcCCCCCcccccCCCceEEEeccc-hhhhcccc
Q 024455 196 KNAMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGL-EHDLDSLR 244 (267)
Q Consensus 196 ~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~-~~Dl~~l~ 244 (267)
..-.+..+++..+.+++.. .+| .||+|||+ .|||.+|.
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 3346889999999999942 222 39999998 57999983
No 127
>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=88.97 E-value=0.24 Score=35.68 Aligned_cols=11 Identities=27% Similarity=0.621 Sum_probs=6.6
Q ss_pred ccccccccCCh
Q 024455 81 CNLCMNIFDSP 91 (267)
Q Consensus 81 C~~C~~~F~~~ 91 (267)
|+.||..|.-.
T Consensus 29 CP~CG~~~~~~ 39 (108)
T PF09538_consen 29 CPKCGTEFPPE 39 (108)
T ss_pred CCCCCCccCcc
Confidence 66666666543
No 128
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=88.44 E-value=0.23 Score=40.52 Aligned_cols=13 Identities=38% Similarity=0.667 Sum_probs=9.2
Q ss_pred CcccchhhcCCHH
Q 024455 45 KCAVCQKLSKSFE 57 (267)
Q Consensus 45 ~C~~C~~~f~~~~ 57 (267)
.|++|++.|..+.
T Consensus 7 ~CPvC~~~F~~~~ 19 (214)
T PF09986_consen 7 TCPVCGKEFKTKK 19 (214)
T ss_pred ECCCCCCeeeeeE
Confidence 6777777777654
No 129
>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=88.32 E-value=0.29 Score=27.07 Aligned_cols=19 Identities=32% Similarity=0.597 Sum_probs=16.2
Q ss_pred ccccccccCChhhHHHHHH
Q 024455 81 CNLCMNIFDSPSSLIKHKE 99 (267)
Q Consensus 81 C~~C~~~F~~~~~L~~H~~ 99 (267)
|+.|++.|.+...+..|++
T Consensus 6 C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 6 CKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred ccccCCccCCHHHHHHHHC
Confidence 8888889988888888874
No 130
>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=87.91 E-value=0.5 Score=39.09 Aligned_cols=38 Identities=29% Similarity=0.381 Sum_probs=29.7
Q ss_pred hccCCCHHHHHHHHHHHHhcCCCCCcccccCCCceEEEeccc-hhhhccc
Q 024455 195 IKNAMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGL-EHDLDSL 243 (267)
Q Consensus 195 l~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~-~~Dl~~l 243 (267)
+.--.+..+++..+.+++.+ .+| .||||||+ .|||.+|
T Consensus 76 v~~~~~E~~LL~~f~~~i~~------~DP-----DiivG~Ni~~fdl~~L 114 (234)
T cd05776 76 VRIFENERALLNFFLAKLQK------IDP-----DVLVGHDLEGFDLDVL 114 (234)
T ss_pred EEEeCCHHHHHHHHHHHHhh------cCC-----CEEEeeccCCCCHHHH
Confidence 44456888999999999942 333 29999999 7999998
No 131
>PRK04860 hypothetical protein; Provisional
Probab=87.44 E-value=0.38 Score=37.26 Aligned_cols=28 Identities=14% Similarity=0.330 Sum_probs=23.6
Q ss_pred cccccccccCChhhHHHHHHHhcCCCCccccc
Q 024455 80 GCNLCMNIFDSPSSLIKHKEACSLSAPVPFEK 111 (267)
Q Consensus 80 ~C~~C~~~F~~~~~L~~H~~~h~~~~~~~C~~ 111 (267)
.|. |++ ....+++|.++|+++++|.|++
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 487 887 6788999999999999998654
No 132
>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=86.78 E-value=1.9 Score=35.53 Aligned_cols=41 Identities=10% Similarity=0.166 Sum_probs=31.0
Q ss_pred HhhccCCCHHHHHHHHHHHHhcCCCCCcccccCCCceEEEeccc-hhhhcccc
Q 024455 193 EDIKNAMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGL-EHDLDSLR 244 (267)
Q Consensus 193 ~~l~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~-~~Dl~~l~ 244 (267)
..+.--.+..+++..+.+++.. .+| .||+|||+ .||+.+|.
T Consensus 73 ~~v~~~~~E~~LL~~f~~~i~~------~DP-----Dii~GyNi~~fd~~YL~ 114 (231)
T cd05778 73 IPVEVVESELELFEELIDLVRR------FDP-----DILSGYEIQRSSWGYLI 114 (231)
T ss_pred CeEEEeCCHHHHHHHHHHHHHH------hCC-----CEEEEeccccCcHHHHH
Confidence 3455567889999999999942 222 39999999 58999983
No 133
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=86.07 E-value=0.39 Score=35.50 Aligned_cols=22 Identities=27% Similarity=0.652 Sum_probs=16.7
Q ss_pred CCCCCcCCccccccc------ccccccc
Q 024455 66 PLSKAHCSGIFSDRG------CNLCMNI 87 (267)
Q Consensus 66 ~~~C~~C~k~f~~~~------C~~C~~~ 87 (267)
|++|..||+.|...+ |+.||..
T Consensus 1 PH~Ct~Cg~~f~dgs~eil~GCP~CGg~ 28 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGSKEILSGCPECGGN 28 (131)
T ss_pred CcccCcCCCCcCCCcHHHHccCcccCCc
Confidence 577888888888753 9999743
No 134
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.91 E-value=0.65 Score=43.85 Aligned_cols=29 Identities=21% Similarity=0.311 Sum_probs=18.7
Q ss_pred CcccchhhcCCHHHHHhhc-CCCCCCCcCC
Q 024455 45 KCAVCQKLSKSFESLREHL-TGPLSKAHCS 73 (267)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~-~~~~~C~~C~ 73 (267)
.|..|...|-....|.+|+ ...|.|..|.
T Consensus 184 ~C~~C~~~fld~~el~rH~~~~h~~chfC~ 213 (669)
T KOG2231|consen 184 LCKFCHERFLDDDELYRHLRFDHEFCHFCD 213 (669)
T ss_pred cchhhhhhhccHHHHHHhhccceeheeecC
Confidence 6777777777777777776 3445565554
No 135
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=85.25 E-value=2.4 Score=37.08 Aligned_cols=47 Identities=15% Similarity=0.047 Sum_probs=37.8
Q ss_pred ccccccccCChhhHHHHHHHhcCCC----Cc----------------------ccc---ccCcchhhhhhhccccc
Q 024455 81 CNLCMNIFDSPSSLIKHKEACSLSA----PV----------------------PFE---KTLSNAESQKKISGAID 127 (267)
Q Consensus 81 C~~C~~~F~~~~~L~~H~~~h~~~~----~~----------------------~C~---~~f~~~~~l~~H~~~~~ 127 (267)
|-.|++.|.+-..-..||..+||-. .| -|. +.|+.-...+.||....
T Consensus 169 CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~K~ 244 (390)
T KOG2785|consen 169 CLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRDKG 244 (390)
T ss_pred eeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhhcc
Confidence 9999999999999999999888632 22 077 88999999999996543
No 136
>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=85.19 E-value=0.45 Score=34.24 Aligned_cols=28 Identities=21% Similarity=0.493 Sum_probs=13.5
Q ss_pred CcccchhhcCCHHHHHhhcCCCCCCCcCCccccc
Q 024455 45 KCAVCQKLSKSFESLREHLTGPLSKAHCSGIFSD 78 (267)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~~~~~~C~~C~k~f~~ 78 (267)
.|+.||+.|-. |+ ..|..|+.||..|.-
T Consensus 11 ~Cp~CG~kFYD---Ln---k~PivCP~CG~~~~~ 38 (108)
T PF09538_consen 11 TCPSCGAKFYD---LN---KDPIVCPKCGTEFPP 38 (108)
T ss_pred cCCCCcchhcc---CC---CCCccCCCCCCccCc
Confidence 55555555533 11 234445555555543
No 137
>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=83.19 E-value=1.7 Score=33.47 Aligned_cols=21 Identities=19% Similarity=0.151 Sum_probs=14.7
Q ss_pred CceEEEecc-chhhhccccccC
Q 024455 227 KARLLVGHG-LEHDLDSLRMNY 247 (267)
Q Consensus 227 ~~~~lvgh~-~~~Dl~~l~~~~ 247 (267)
....+|+|| ..||+.+|+-..
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 446899988 589999997433
No 138
>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=82.71 E-value=3.3 Score=33.19 Aligned_cols=41 Identities=27% Similarity=0.224 Sum_probs=26.6
Q ss_pred HHHHHHHhcCCCCCcccccCCCceEEEeccchhhhcccc--ccCCCCceeccccc
Q 024455 206 DKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLR--MNYPDHMLRDTAKY 258 (267)
Q Consensus 206 ~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~Dl~~l~--~~~~~~~~~dt~~~ 258 (267)
..|.+++.+ .+.+-|||++.+|+.+|. ....-..++||.+.
T Consensus 55 ~~L~~iLe~------------~~i~Kv~h~~k~D~~~L~~~~gi~~~~~fDt~iA 97 (197)
T cd06148 55 NGLKDILES------------KKILKVIHDCRRDSDALYHQYGIKLNNVFDTQVA 97 (197)
T ss_pred HHHHHHhcC------------CCccEEEEechhHHHHHHHhcCccccceeeHHHH
Confidence 456667743 345679999999999983 11111255898754
No 139
>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=82.43 E-value=1.2 Score=33.55 Aligned_cols=45 Identities=27% Similarity=0.307 Sum_probs=32.0
Q ss_pred HHHHHHHHHHHhcCCCCCcccccCCCceEEEeccchhhhcccccc---CCCCceecccccc
Q 024455 202 KEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMN---YPDHMLRDTAKYR 259 (267)
Q Consensus 202 ~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~Dl~~l~~~---~~~~~~~dt~~~~ 259 (267)
.++.+.|.+++.+ .+..+||||+.+|+.+|.-. .+ ..++||....
T Consensus 40 ~~~~~~l~~~l~~------------~~~~~v~~~~k~d~~~L~~~~~~~~-~~~~D~~~~a 87 (155)
T cd00007 40 EEDLEALKELLED------------EDITKVGHDAKFDLVVLARDGIELP-GNIFDTMLAA 87 (155)
T ss_pred HHHHHHHHHHHcC------------CCCcEEeccHHHHHHHHHHCCCCCC-CCcccHHHHH
Confidence 5677778899953 34579999999999999532 22 2467887443
No 140
>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=82.35 E-value=0.4 Score=27.26 Aligned_cols=14 Identities=29% Similarity=0.693 Sum_probs=7.0
Q ss_pred cccccCccccCChH
Q 024455 15 HKCVACYKQFKRKD 28 (267)
Q Consensus 15 ~~C~~C~k~f~~~~ 28 (267)
+.|+.|+..|.-..
T Consensus 3 ~~CP~C~~~~~v~~ 16 (38)
T TIGR02098 3 IQCPNCKTSFRVVD 16 (38)
T ss_pred EECCCCCCEEEeCH
Confidence 34555555544443
No 141
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional
Probab=82.05 E-value=3 Score=42.34 Aligned_cols=38 Identities=21% Similarity=0.157 Sum_probs=29.2
Q ss_pred hccCCCHHHHHHHHHHHHhcCCCCCcccccCCCceEEEeccc-hhhhccc
Q 024455 195 IKNAMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGL-EHDLDSL 243 (267)
Q Consensus 195 l~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~-~~Dl~~l 243 (267)
+..-.+..+++..+.+++. ..+| .||+|||+ .|||.+|
T Consensus 324 V~~f~sE~eLL~~f~~~I~------~~DP-----DII~GYNi~~FDlpYL 362 (1054)
T PTZ00166 324 VLSFETEKELLLAWAEFVI------AVDP-----DFLTGYNIINFDLPYL 362 (1054)
T ss_pred EEEeCCHHHHHHHHHHHHH------hcCC-----CEEEecCCcCCcHHHH
Confidence 3445688999999999993 2223 39999998 5899998
No 142
>PHA02528 43 DNA polymerase; Provisional
Probab=80.99 E-value=6.8 Score=38.93 Aligned_cols=101 Identities=9% Similarity=-0.028 Sum_probs=52.8
Q ss_pred CCCceeeeeccccCCc-CC-CC--ccceeeEEEecCCCCeeEecccCCCCCccccccccc--cCCHHhhccCCCHHHHHH
Q 024455 133 RGPKAVAMDCEMVGGG-SN-GT--LDLCARVCLVDEDENVIFHTYVQPQLPVTNYRYEVT--GLTEEDIKNAMPLKEVKD 206 (267)
Q Consensus 133 ~~~~~~~~dcE~~g~~-~~-~~--~~~i~~v~vvd~~~~~~~~~~v~P~~~i~~~~~~~~--GIt~~~l~~~~~~~~v~~ 206 (267)
..-+++++|+|+.... +. .. ...|..|.+.+.......-..+....+......... -....++..-.+-.+++.
T Consensus 104 p~lrv~s~DIE~~~~~gfP~p~~~~d~IisIsl~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~sE~eLL~ 183 (881)
T PHA02528 104 SKIRIANLDIEVTAEDGFPDPEEAKYEIDAITHYDSIDDRFYVFDLGSVEEWDAKGDEVPQEILDKVVYMPFDTEREMLL 183 (881)
T ss_pred CCccEEEEEEEECCCCCCCCcccCCCcEEEEEEecCCCCEEEEEEecCcccccccCCcccccccCCeeEEEcCCHHHHHH
Confidence 3556789999996522 11 11 334566777666655422222210000000000000 000011112468889999
Q ss_pred HHHHHHhcCCCCCcccccCCCceEEEeccc-hhhhcccc
Q 024455 207 KILEILNNGESTGRLMLDDGKARLLVGHGL-EHDLDSLR 244 (267)
Q Consensus 207 ~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~-~~Dl~~l~ 244 (267)
.+.+++.. .+| .||+|||+ .|||.+|.
T Consensus 184 ~F~~~i~~------~DP-----DII~GyNi~~FDlpYL~ 211 (881)
T PHA02528 184 EYINFWEE------NTP-----VIFTGWNVELFDVPYII 211 (881)
T ss_pred HHHHHHHH------hCC-----cEEEecCCccCCHHHHH
Confidence 99999932 222 39999997 68999983
No 143
>KOG3657 consensus Mitochondrial DNA polymerase gamma, catalytic subunit [Replication, recombination and repair]
Probab=79.89 E-value=1.2 Score=42.92 Aligned_cols=31 Identities=35% Similarity=0.554 Sum_probs=24.1
Q ss_pred CCceEEEeccchhhhcccc----ccCCCCceeccc
Q 024455 226 GKARLLVGHGLEHDLDSLR----MNYPDHMLRDTA 256 (267)
Q Consensus 226 ~~~~~lvgh~~~~Dl~~l~----~~~~~~~~~dt~ 256 (267)
+.+.++||||+.||..-++ |.-.+....||-
T Consensus 239 ~ke~liVGHNVsfDRaRirEeY~i~~Sk~rFlDTM 273 (1075)
T KOG3657|consen 239 GKEQLIVGHNVSFDRARIREEYNINGSKIRFLDTM 273 (1075)
T ss_pred CCCceEEeccccchHHHHHHHHhccccceeeeech
Confidence 4788999999999998875 444566677775
No 144
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=79.89 E-value=1.3 Score=26.86 Aligned_cols=23 Identities=22% Similarity=0.450 Sum_probs=15.5
Q ss_pred cccccccccCCh-----hhHHHHHH-Hhc
Q 024455 80 GCNLCMNIFDSP-----SSLIKHKE-ACS 102 (267)
Q Consensus 80 ~C~~C~~~F~~~-----~~L~~H~~-~h~ 102 (267)
.|..|++.++.. ++|.+|++ .|.
T Consensus 20 ~C~~C~~~l~~~~~~gTs~L~rHl~~~h~ 48 (50)
T smart00614 20 KCKYCGKKLSRSSKGGTSNLRRHLRRKHP 48 (50)
T ss_pred EecCCCCEeeeCCCCCcHHHHHHHHhHCc
Confidence 366777666554 68888887 553
No 145
>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=79.88 E-value=1.1 Score=32.98 Aligned_cols=24 Identities=13% Similarity=0.051 Sum_probs=13.3
Q ss_pred CCCcCCccccccc-----ccccccccCCh
Q 024455 68 SKAHCSGIFSDRG-----CNLCMNIFDSP 91 (267)
Q Consensus 68 ~C~~C~k~f~~~~-----C~~C~~~F~~~ 91 (267)
.|+.||+.|.... |+.||..|.-.
T Consensus 11 ~Cp~cg~kFYDLnk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 11 ICPNTGSKFYDLNRRPAVSPYTGEQFPPE 39 (129)
T ss_pred cCCCcCccccccCCCCccCCCcCCccCcc
Confidence 3555555554432 77777776544
No 146
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=79.77 E-value=0.26 Score=40.16 Aligned_cols=22 Identities=27% Similarity=0.454 Sum_probs=17.2
Q ss_pred CCccccccCccccCChHHHHHH
Q 024455 12 TARHKCVACYKQFKRKDHLIEH 33 (267)
Q Consensus 12 ~k~~~C~~C~k~f~~~~~l~~H 33 (267)
+|...|++|++.|.++......
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~ 24 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGK 24 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCC
Confidence 5788999999999987754333
No 147
>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=79.68 E-value=2 Score=34.83 Aligned_cols=34 Identities=24% Similarity=0.312 Sum_probs=27.1
Q ss_pred CCHHHHHHHHHHHHhcCCCCCcccccCCCceEEEeccc-hhhhcccc
Q 024455 199 MPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGL-EHDLDSLR 244 (267)
Q Consensus 199 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~-~~Dl~~l~ 244 (267)
.+-+++++.+++++.+ .+.+|||||. .||+.+|.
T Consensus 76 ~~E~elL~~F~~~i~~------------~~p~lv~yNg~~FDlP~L~ 110 (208)
T cd05782 76 ADEKELLEDFFQLIEK------------KNPRLVSFNGRGFDLPVLH 110 (208)
T ss_pred CCHHHHHHHHHHHHHH------------hCCEEEecCCCcCCHHHHH
Confidence 3458899999999953 1348999998 79999995
No 148
>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=79.44 E-value=2 Score=34.79 Aligned_cols=33 Identities=21% Similarity=0.235 Sum_probs=26.9
Q ss_pred CHHHHHHHHHHHHhcCCCCCcccccCCCceEEEeccc-hhhhcccc
Q 024455 200 PLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGL-EHDLDSLR 244 (267)
Q Consensus 200 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~-~~Dl~~l~ 244 (267)
+.+++++.+++++.+ ..-.|||||. .||+.||.
T Consensus 36 ~E~~lL~~F~~~~~~------------~~p~LVs~NG~~FDlP~L~ 69 (209)
T PF10108_consen 36 DEKELLQDFFDLVEK------------YNPQLVSFNGRGFDLPVLC 69 (209)
T ss_pred CHHHHHHHHHHHHHh------------CCCeEEecCCccCCHHHHH
Confidence 478999999999953 2347999995 79999994
No 149
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=78.56 E-value=0.96 Score=27.94 Aligned_cols=23 Identities=13% Similarity=0.326 Sum_probs=15.0
Q ss_pred CCCC-CcccchhhcCCHHHHHhhc
Q 024455 41 VHQP-KCAVCQKLSKSFESLREHL 63 (267)
Q Consensus 41 ~~~~-~C~~C~~~f~~~~~l~~H~ 63 (267)
|+.. .|+.||..|....+..+|.
T Consensus 14 GE~~lrCPRC~~~FR~~K~Y~RHV 37 (65)
T COG4049 14 GEEFLRCPRCGMVFRRRKDYIRHV 37 (65)
T ss_pred CceeeeCCchhHHHHHhHHHHHHh
Confidence 4444 6777777777666666666
No 150
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=78.49 E-value=0.81 Score=27.30 Aligned_cols=23 Identities=17% Similarity=0.274 Sum_probs=13.8
Q ss_pred CCCCCcCCcccccc------ccccccccc
Q 024455 66 PLSKAHCSGIFSDR------GCNLCMNIF 88 (267)
Q Consensus 66 ~~~C~~C~k~f~~~------~C~~C~~~F 88 (267)
.|.|+.||..|... .|+.||..+
T Consensus 3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG~~~ 31 (46)
T PRK00398 3 EYKCARCGREVELDEYGTGVRCPYCGYRI 31 (46)
T ss_pred EEECCCCCCEEEECCCCCceECCCCCCeE
Confidence 45677777666432 377777544
No 151
>PHA02570 dexA exonuclease; Provisional
Probab=78.23 E-value=6.7 Score=31.93 Aligned_cols=99 Identities=17% Similarity=0.125 Sum_probs=60.6
Q ss_pred eeeeccccCCcCCCCccceeeEEEecCC-CCeeEecccCCCC------------Ccc--ccccccccCCHHh---hc---
Q 024455 138 VAMDCEMVGGGSNGTLDLCARVCLVDED-ENVIFHTYVQPQL------------PVT--NYRYEVTGLTEED---IK--- 196 (267)
Q Consensus 138 ~~~dcE~~g~~~~~~~~~i~~v~vvd~~-~~~~~~~~v~P~~------------~i~--~~~~~~~GIt~~~---l~--- 196 (267)
+.+|.|+-|......+..|++|.+.... ....|..+|.... .+. +-+.+|-.-++|- |.
T Consensus 4 lMIDlETmG~~p~AaIisIgAV~Fdp~~~~g~tF~elV~~~~~~k~d~~sq~g~~~~d~~TI~WW~kQS~EAR~~L~~s~ 83 (220)
T PHA02570 4 FIIDFETFGNTPDGAVIDLAVIAFEHDPHNPPTFEELVSRGRRIKFDLKSQKGKRLFDKSTIEWWKNQSPEARKNLKPSD 83 (220)
T ss_pred EEEEeeccCCCCCceEEEEEEEEecCCCCccccHHHHhhcccccccchhhccCCCccCchHHHHHHhCCHHHHHhccCCC
Confidence 5789999999988888888888776432 2233454443211 011 1122232333222 11
Q ss_pred cCCCHHHHHHHHHHHHhc-CCCCCcccccCCCceEEEeccchhhhcccc
Q 024455 197 NAMPLKEVKDKILEILNN-GESTGRLMLDDGKARLLVGHGLEHDLDSLR 244 (267)
Q Consensus 197 ~~~~~~~v~~~~~~~~~~-~~~~~~~~~~~~~~~~lvgh~~~~Dl~~l~ 244 (267)
+..++.+++.+|.+||.. +.+ .....+=|.+..||+.+|+
T Consensus 84 ~~~~l~~al~~F~~fi~~~~~~--------~~~~~vWgnG~sFD~~IL~ 124 (220)
T PHA02570 84 EDVSTYEGHKKFFEYLEANGVD--------PWKSQGWCRGNSFDFPILV 124 (220)
T ss_pred ccccHHHHHHHHHHHHHHcCCC--------ccceeEecCCCccCHHHHH
Confidence 235799999999999952 111 0224678999999999995
No 152
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=78.13 E-value=0.81 Score=25.82 Aligned_cols=13 Identities=23% Similarity=0.756 Sum_probs=6.4
Q ss_pred ccccCccccCChH
Q 024455 16 KCVACYKQFKRKD 28 (267)
Q Consensus 16 ~C~~C~k~f~~~~ 28 (267)
.|+.|+..|.-..
T Consensus 4 ~Cp~C~~~y~i~d 16 (36)
T PF13717_consen 4 TCPNCQAKYEIDD 16 (36)
T ss_pred ECCCCCCEEeCCH
Confidence 4555555554443
No 153
>PHA00626 hypothetical protein
Probab=78.13 E-value=0.66 Score=28.71 Aligned_cols=12 Identities=17% Similarity=-0.020 Sum_probs=5.1
Q ss_pred CCCCCcCCcccc
Q 024455 66 PLSKAHCSGIFS 77 (267)
Q Consensus 66 ~~~C~~C~k~f~ 77 (267)
.|.|..||..|+
T Consensus 23 rYkCkdCGY~ft 34 (59)
T PHA00626 23 DYVCCDCGYNDS 34 (59)
T ss_pred ceEcCCCCCeec
Confidence 344444444433
No 154
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=77.88 E-value=2.1 Score=36.92 Aligned_cols=102 Identities=23% Similarity=0.297 Sum_probs=53.6
Q ss_pred cccc--cCccccCChHHHHHHHhHhcCCCCCCCcccch---hhc------CCHHHHHhhcCCCCCCCcCCccccc-cccc
Q 024455 15 HKCV--ACYKQFKRKDHLIEHMKISYHSVHQPKCAVCQ---KLS------KSFESLREHLTGPLSKAHCSGIFSD-RGCN 82 (267)
Q Consensus 15 ~~C~--~C~k~f~~~~~l~~H~~~~~H~~~~~~C~~C~---~~f------~~~~~l~~H~~~~~~C~~C~k~f~~-~~C~ 82 (267)
|.|+ .|......-..|+.|.+.. |.. ..|.+|- +.| .++..|+.|.++-.. +..|+- ..|.
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-HGF--VLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLE----EEGFKGHPLCI 224 (493)
T ss_pred hcCCchhhhhhhhhHHHHHHHHHhh-cCc--EEhHhhhcCcccCccceeeeecccccccccCCcc----ccCcCCCchhh
Confidence 4553 3555544456677777662 221 1444442 222 234556666521110 001221 1388
Q ss_pred ccccccCChhhHHHHHHHhcCCCCcccccc-------Ccchhhhhhhcc
Q 024455 83 LCMNIFDSPSSLIKHKEACSLSAPVPFEKT-------LSNAESQKKISG 124 (267)
Q Consensus 83 ~C~~~F~~~~~L~~H~~~h~~~~~~~C~~~-------f~~~~~l~~H~~ 124 (267)
.|...|.....|..|+|..| |+.+-|++. |.+..+|..|-+
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 88888888888888887543 556655543 455556666653
No 155
>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=77.80 E-value=1.3 Score=33.06 Aligned_cols=24 Identities=25% Similarity=0.407 Sum_probs=15.7
Q ss_pred ccccccccCChhhHHHHHHHhcCCCCc
Q 024455 81 CNLCMNIFDSPSSLIKHKEACSLSAPV 107 (267)
Q Consensus 81 C~~C~~~F~~~~~L~~H~~~h~~~~~~ 107 (267)
|-+||+.|. .|.+|++.|+|-.|-
T Consensus 75 clecGk~~k---~LkrHL~~~~gltp~ 98 (132)
T PF05443_consen 75 CLECGKKFK---TLKRHLRTHHGLTPE 98 (132)
T ss_dssp -TBT--EES---BHHHHHHHTT-S-HH
T ss_pred EccCCcccc---hHHHHHHHccCCCHH
Confidence 889999987 469999999887653
No 156
>PF14353 CpXC: CpXC protein
Probab=77.78 E-value=1.2 Score=33.08 Aligned_cols=14 Identities=29% Similarity=0.529 Sum_probs=9.0
Q ss_pred ccccccccCChhhH
Q 024455 81 CNLCMNIFDSPSSL 94 (267)
Q Consensus 81 C~~C~~~F~~~~~L 94 (267)
|+.||..|.-...+
T Consensus 41 CP~Cg~~~~~~~p~ 54 (128)
T PF14353_consen 41 CPSCGHKFRLEYPL 54 (128)
T ss_pred CCCCCCceecCCCE
Confidence 77887777654433
No 157
>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=77.40 E-value=1.4 Score=32.42 Aligned_cols=27 Identities=15% Similarity=0.137 Sum_probs=13.9
Q ss_pred CcccchhhcCCHHHHHhhcCCCCCCCcCCcccc
Q 024455 45 KCAVCQKLSKSFESLREHLTGPLSKAHCSGIFS 77 (267)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~~~~~~C~~C~k~f~ 77 (267)
.|+.||+.|-. |+ +.|..|+.||..|.
T Consensus 11 ~Cp~cg~kFYD---Ln---k~p~vcP~cg~~~~ 37 (129)
T TIGR02300 11 ICPNTGSKFYD---LN---RRPAVSPYTGEQFP 37 (129)
T ss_pred cCCCcCccccc---cC---CCCccCCCcCCccC
Confidence 56666665533 11 23555666665554
No 158
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=77.37 E-value=0.84 Score=37.21 Aligned_cols=42 Identities=33% Similarity=0.555 Sum_probs=35.6
Q ss_pred ccccCccccCChHHHHHHHhHhcCCCCCC-CcccchhhcCCHHHHHhhc
Q 024455 16 KCVACYKQFKRKDHLIEHMKISYHSVHQP-KCAVCQKLSKSFESLREHL 63 (267)
Q Consensus 16 ~C~~C~k~f~~~~~l~~H~~~~~H~~~~~-~C~~C~~~f~~~~~l~~H~ 63 (267)
.|=.|++.|....-|..|++. +. +|.+|-|...+-..|..|-
T Consensus 12 wcwycnrefddekiliqhqka------khfkchichkkl~sgpglsihc 54 (341)
T KOG2893|consen 12 WCWYCNREFDDEKILIQHQKA------KHFKCHICHKKLFSGPGLSIHC 54 (341)
T ss_pred eeeecccccchhhhhhhhhhh------ccceeeeehhhhccCCCceeeh
Confidence 588999999999999999887 34 9999999888877777774
No 159
>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=77.22 E-value=0.98 Score=25.94 Aligned_cols=6 Identities=33% Similarity=0.899 Sum_probs=3.3
Q ss_pred cccccc
Q 024455 81 CNLCMN 86 (267)
Q Consensus 81 C~~C~~ 86 (267)
|+.||.
T Consensus 29 CP~Cg~ 34 (41)
T smart00834 29 CPECGG 34 (41)
T ss_pred CCCCCC
Confidence 555554
No 160
>PRK10829 ribonuclease D; Provisional
Probab=76.93 E-value=5.7 Score=35.32 Aligned_cols=44 Identities=16% Similarity=0.073 Sum_probs=30.4
Q ss_pred HHHHHHHhcCCCCCcccccCCCceEEEeccchhhhcccccc--CCCCceecccccccc
Q 024455 206 DKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMN--YPDHMLRDTAKYRPL 261 (267)
Q Consensus 206 ~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~Dl~~l~~~--~~~~~~~dt~~~~~~ 261 (267)
+.|.+++.| .+.+-|+|++.+|+.+|... ..-..++||.+...+
T Consensus 64 ~~L~~ll~~------------~~ivKV~H~~~~Dl~~l~~~~g~~p~~~fDTqiaa~~ 109 (373)
T PRK10829 64 SPFKALLRD------------PQVTKFLHAGSEDLEVFLNAFGELPQPLIDTQILAAF 109 (373)
T ss_pred HHHHHHHcC------------CCeEEEEeChHhHHHHHHHHcCCCcCCeeeHHHHHHH
Confidence 457788854 44566999999999998332 222478999865543
No 161
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=76.45 E-value=1.2 Score=31.23 Aligned_cols=21 Identities=33% Similarity=0.809 Sum_probs=14.3
Q ss_pred CCCCCcCCcccccc------ccccccc
Q 024455 66 PLSKAHCSGIFSDR------GCNLCMN 86 (267)
Q Consensus 66 ~~~C~~C~k~f~~~------~C~~C~~ 86 (267)
|+.|..||..|..- +|+.||.
T Consensus 2 pH~CtrCG~vf~~g~~~il~GCp~CG~ 28 (112)
T COG3364 2 PHQCTRCGEVFDDGSEEILSGCPKCGC 28 (112)
T ss_pred CceecccccccccccHHHHccCccccc
Confidence 46677777777763 3888874
No 162
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=76.06 E-value=0.98 Score=25.61 Aligned_cols=13 Identities=31% Similarity=0.838 Sum_probs=6.2
Q ss_pred ccccCccccCChH
Q 024455 16 KCVACYKQFKRKD 28 (267)
Q Consensus 16 ~C~~C~k~f~~~~ 28 (267)
.|+.|+..|.-..
T Consensus 4 ~CP~C~~~f~v~~ 16 (37)
T PF13719_consen 4 TCPNCQTRFRVPD 16 (37)
T ss_pred ECCCCCceEEcCH
Confidence 3555555544433
No 163
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=75.92 E-value=0.26 Score=46.81 Aligned_cols=71 Identities=13% Similarity=0.129 Sum_probs=38.5
Q ss_pred CcccchhhcCCHHHHHhhcCCCCCCCcCCcccccccccccccccCChhhHHHHHHHhcC---CCCc-cccccCcchhhhh
Q 024455 45 KCAVCQKLSKSFESLREHLTGPLSKAHCSGIFSDRGCNLCMNIFDSPSSLIKHKEACSL---SAPV-PFEKTLSNAESQK 120 (267)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~~~~~~C~~C~k~f~~~~C~~C~~~F~~~~~L~~H~~~h~~---~~~~-~C~~~f~~~~~l~ 120 (267)
.|..|++.|.....+. ..+.+.|..||..| |..|...+...+.-+. ..... ..++ .|+..|.....+.
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 6999999997642100 13456798898875 6677655544322211 11100 0122 3777776666666
Q ss_pred hhc
Q 024455 121 KIS 123 (267)
Q Consensus 121 ~H~ 123 (267)
+|.
T Consensus 534 Qm~ 536 (1374)
T PTZ00303 534 QLH 536 (1374)
T ss_pred hhH
Confidence 665
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=75.89 E-value=1 Score=26.36 Aligned_cols=9 Identities=22% Similarity=0.659 Sum_probs=3.9
Q ss_pred Ccccchhhc
Q 024455 45 KCAVCQKLS 53 (267)
Q Consensus 45 ~C~~C~~~f 53 (267)
.|..||..|
T Consensus 7 ~C~~Cg~~f 15 (42)
T PF09723_consen 7 RCEECGHEF 15 (42)
T ss_pred EeCCCCCEE
Confidence 344444444
No 165
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, 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), 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=75.84 E-value=1.3 Score=24.65 Aligned_cols=20 Identities=20% Similarity=0.439 Sum_probs=10.7
Q ss_pred CCCCcCCcccccc----ccccccc
Q 024455 67 LSKAHCSGIFSDR----GCNLCMN 86 (267)
Q Consensus 67 ~~C~~C~k~f~~~----~C~~C~~ 86 (267)
|.|..||..+... .|+.||.
T Consensus 3 ~~C~~CG~i~~g~~~p~~CP~Cg~ 26 (34)
T cd00729 3 WVCPVCGYIHEGEEAPEKCPICGA 26 (34)
T ss_pred EECCCCCCEeECCcCCCcCcCCCC
Confidence 4556666554432 3666654
No 166
>PF15269 zf-C2H2_7: Zinc-finger
Probab=75.22 E-value=3.4 Score=24.29 Aligned_cols=23 Identities=39% Similarity=0.710 Sum_probs=20.4
Q ss_pred ccccccCccccCChHHHHHHHhH
Q 024455 14 RHKCVACYKQFKRKDHLIEHMKI 36 (267)
Q Consensus 14 ~~~C~~C~k~f~~~~~l~~H~~~ 36 (267)
.|+|=+|..+...+++|-.||+-
T Consensus 20 ~ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 20 KYKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred cceeecCCcccchHHHHHHHHHH
Confidence 37899999999999999999976
No 167
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=75.11 E-value=1.6 Score=21.87 Aligned_cols=19 Identities=21% Similarity=0.492 Sum_probs=9.1
Q ss_pred CCcCCccccccc--ccccccc
Q 024455 69 KAHCSGIFSDRG--CNLCMNI 87 (267)
Q Consensus 69 C~~C~k~f~~~~--C~~C~~~ 87 (267)
|+.||....... |+.||..
T Consensus 2 Cp~CG~~~~~~~~fC~~CG~~ 22 (23)
T PF13240_consen 2 CPNCGAEIEDDAKFCPNCGTP 22 (23)
T ss_pred CcccCCCCCCcCcchhhhCCc
Confidence 445555443322 6666643
No 168
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=74.94 E-value=1.4 Score=36.19 Aligned_cols=58 Identities=12% Similarity=0.271 Sum_probs=29.1
Q ss_pred CCCccccccCccccCChHHHHHHHhHhcCCCCCC--CcccchhhcCCHHHHHhhcCCCCCCCcCCcccccc
Q 024455 11 STARHKCVACYKQFKRKDHLIEHMKISYHSVHQP--KCAVCQKLSKSFESLREHLTGPLSKAHCSGIFSDR 79 (267)
Q Consensus 11 ~~k~~~C~~C~k~f~~~~~l~~H~~~~~H~~~~~--~C~~C~~~f~~~~~l~~H~~~~~~C~~C~k~f~~~ 79 (267)
..+.|.|..|...+ .+. ....++ .|..|.+.|.-...=+.--..+|.|+.|+..|...
T Consensus 109 ~drqFaC~~Cd~~W---------wRr--vp~rKeVSRCr~C~~rYDPVP~dkmwG~aef~C~~C~h~F~G~ 168 (278)
T PF15135_consen 109 VDRQFACSSCDHMW---------WRR--VPQRKEVSRCRKCRKRYDPVPCDKMWGIAEFHCPKCRHNFRGF 168 (278)
T ss_pred cceeeeccccchHH---------Hhc--cCcccccccccccccccCCCccccccceeeeecccccccchhh
Confidence 45667777775321 122 222333 77777776654331111114466676666666643
No 169
>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=74.84 E-value=1.5 Score=24.16 Aligned_cols=18 Identities=22% Similarity=0.549 Sum_probs=8.2
Q ss_pred CCCcCCcccccc----cccccc
Q 024455 68 SKAHCSGIFSDR----GCNLCM 85 (267)
Q Consensus 68 ~C~~C~k~f~~~----~C~~C~ 85 (267)
.|..||..+... .|+.||
T Consensus 3 ~C~~CGy~y~~~~~~~~CP~Cg 24 (33)
T cd00350 3 VCPVCGYIYDGEEAPWVCPVCG 24 (33)
T ss_pred ECCCCCCEECCCcCCCcCcCCC
Confidence 444554443332 255554
No 170
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=74.45 E-value=2.8 Score=31.99 Aligned_cols=33 Identities=21% Similarity=0.454 Sum_probs=21.3
Q ss_pred CcccchhhcCCHHHHHh-hcCCCCCCCcCCcccc
Q 024455 45 KCAVCQKLSKSFESLRE-HLTGPLSKAHCSGIFS 77 (267)
Q Consensus 45 ~C~~C~~~f~~~~~l~~-H~~~~~~C~~C~k~f~ 77 (267)
.|+.|+..|.....+.. +..+.|.|+.||....
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 88888888876554433 3355577777766543
No 171
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=74.31 E-value=0.85 Score=35.08 Aligned_cols=15 Identities=33% Similarity=0.607 Sum_probs=11.2
Q ss_pred CCCHHHHHHHHHHHH
Q 024455 198 AMPLKEVKDKILEIL 212 (267)
Q Consensus 198 ~~~~~~v~~~~~~~~ 212 (267)
.++.+++...+.+.|
T Consensus 102 ~IsveEIqDiVE~~L 116 (154)
T PRK00464 102 EVPSKEIGELVMEEL 116 (154)
T ss_pred CCCHHHHHHHHHHHH
Confidence 467777777777777
No 172
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=73.66 E-value=1.5 Score=26.01 Aligned_cols=20 Identities=15% Similarity=0.277 Sum_probs=11.2
Q ss_pred CCCCcCCccccccc-----cccccc
Q 024455 67 LSKAHCSGIFSDRG-----CNLCMN 86 (267)
Q Consensus 67 ~~C~~C~k~f~~~~-----C~~C~~ 86 (267)
|.|..||..|.... |+.||.
T Consensus 3 Y~C~~Cg~~~~~~~~~~irC~~CG~ 27 (44)
T smart00659 3 YICGECGRENEIKSKDVVRCRECGY 27 (44)
T ss_pred EECCCCCCEeecCCCCceECCCCCc
Confidence 45666666555442 666664
No 173
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=73.29 E-value=3.6 Score=29.70 Aligned_cols=22 Identities=18% Similarity=0.282 Sum_probs=14.1
Q ss_pred CCccccccCccccCChHHHHHH
Q 024455 12 TARHKCVACYKQFKRKDHLIEH 33 (267)
Q Consensus 12 ~k~~~C~~C~k~f~~~~~l~~H 33 (267)
+-|-.|+.||-+.....+|.+.
T Consensus 13 ~LP~~CpiCgLtLVss~HLARS 34 (112)
T TIGR00622 13 ELPVECPICGLTLILSTHLARS 34 (112)
T ss_pred CCCCcCCcCCCEEeccchHHHh
Confidence 4456677777776666666553
No 174
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=72.51 E-value=1.4 Score=44.58 Aligned_cols=79 Identities=15% Similarity=0.280 Sum_probs=55.8
Q ss_pred cccccCccccCChHHHHHHHhHhcCCCCCC-CcccchhhcCCHHHHHhhcC-----------C--CCC-CCcCCcccccc
Q 024455 15 HKCVACYKQFKRKDHLIEHMKISYHSVHQP-KCAVCQKLSKSFESLREHLT-----------G--PLS-KAHCSGIFSDR 79 (267)
Q Consensus 15 ~~C~~C~k~f~~~~~l~~H~~~~~H~~~~~-~C~~C~~~f~~~~~l~~H~~-----------~--~~~-C~~C~k~f~~~ 79 (267)
+.|..|.+.|.-...+. |+-. ..+ .|..|...|.....|..|.. . ++. -..|..
T Consensus 1261 ~~c~~~~~~~~~~~~~~-~l~~-----~~~~~~~~~~~~~~~~~~l~~~~~k~~~~~~~~~~~~~~~l~~~d~~~----- 1329 (1406)
T KOG1146|consen 1261 GECGAVDELLTPSFGIS-TLDV-----THRYLCRQCKMAFDGEAPLTAHQRKFCFAGRGSGGSMPPPLRVPDCTY----- 1329 (1406)
T ss_pred chhhhccccccCcccee-eccc-----chhHHHHHHHhhhcchhHHHHHHHHHHhccCccccCCCCcccCccccc-----
Confidence 67999998888777766 5533 223 89999999999999998870 0 010 111211
Q ss_pred cccccccccCChhhHHHHHHHhcCC
Q 024455 80 GCNLCMNIFDSPSSLIKHKEACSLS 104 (267)
Q Consensus 80 ~C~~C~~~F~~~~~L~~H~~~h~~~ 104 (267)
.|..|...|+....|+.||+.-.++
T Consensus 1330 ~c~~c~~~~~~~~alqihm~~~~~~ 1354 (1406)
T KOG1146|consen 1330 HCLACEVLLSGREALQIHMRSSAHR 1354 (1406)
T ss_pred cchHHHhhcchhHHHHHHHHHhhhc
Confidence 2899999999999999999864433
No 175
>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=72.42 E-value=2.4 Score=24.93 Aligned_cols=21 Identities=24% Similarity=0.559 Sum_probs=12.7
Q ss_pred cccccccccCC----hhhHHHHHHH
Q 024455 80 GCNLCMNIFDS----PSSLIKHKEA 100 (267)
Q Consensus 80 ~C~~C~~~F~~----~~~L~~H~~~ 100 (267)
.|..|++.+.. .++|.+|++.
T Consensus 18 ~C~~C~~~~~~~~~~ts~l~~HL~~ 42 (45)
T PF02892_consen 18 KCKYCGKVIKYSSGGTSNLKRHLKK 42 (45)
T ss_dssp EETTTTEE-----SSTHHHHHHHHH
T ss_pred EeCCCCeEEeeCCCcHHHHHHhhhh
Confidence 37777777765 3788888843
No 176
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=72.39 E-value=2.3 Score=29.04 Aligned_cols=28 Identities=18% Similarity=0.313 Sum_probs=17.4
Q ss_pred CCCCCCCcCCcccccc------cccccccccCCh
Q 024455 64 TGPLSKAHCSGIFSDR------GCNLCMNIFDSP 91 (267)
Q Consensus 64 ~~~~~C~~C~k~f~~~------~C~~C~~~F~~~ 91 (267)
...|.|+.|++.-... .|..||..|.--
T Consensus 33 ~~~~~Cp~C~~~~VkR~a~GIW~C~kCg~~fAGg 66 (89)
T COG1997 33 RAKHVCPFCGRTTVKRIATGIWKCRKCGAKFAGG 66 (89)
T ss_pred hcCCcCCCCCCcceeeeccCeEEcCCCCCeeccc
Confidence 4467777777762221 288888877653
No 177
>PRK04023 DNA polymerase II large subunit; Validated
Probab=72.18 E-value=2.2 Score=42.17 Aligned_cols=29 Identities=28% Similarity=0.582 Sum_probs=16.7
Q ss_pred CCCeeEecccCCCCCccccccccccCCHHhhc
Q 024455 165 DENVIFHTYVQPQLPVTNYRYEVTGLTEEDIK 196 (267)
Q Consensus 165 ~~~~~~~~~v~P~~~i~~~~~~~~GIt~~~l~ 196 (267)
+|.+.||. .+.|++.++-+..|+|.+.|.
T Consensus 735 DGTiR~D~---tD~PlTHfrp~Eigvsveklr 763 (1121)
T PRK04023 735 DGTVRYDM---TDLPLTHFRPREIGVSVEKLR 763 (1121)
T ss_pred CcceeccC---cCCCcccccHHHcCCCHHHHH
Confidence 34444443 244566666666777766664
No 178
>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=71.83 E-value=19 Score=27.59 Aligned_cols=33 Identities=27% Similarity=0.211 Sum_probs=22.4
Q ss_pred CceEEEeccchhhhccccccC--CCCceecccccc
Q 024455 227 KARLLVGHGLEHDLDSLRMNY--PDHMLRDTAKYR 259 (267)
Q Consensus 227 ~~~~lvgh~~~~Dl~~l~~~~--~~~~~~dt~~~~ 259 (267)
.+.+.|||++..|+..|...+ .-..++||....
T Consensus 66 ~~i~Kvg~~~k~D~~~L~~~~gi~~~~~~D~~~aa 100 (161)
T cd06129 66 PSIVKALHGIEGDLWKLLRDFGEKLQRLFDTTIAA 100 (161)
T ss_pred CCEEEEEeccHHHHHHHHHHcCCCcccHhHHHHHH
Confidence 445789999999999985321 112458887544
No 179
>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=71.51 E-value=1.6 Score=26.66 Aligned_cols=10 Identities=20% Similarity=0.740 Sum_probs=4.4
Q ss_pred CcccchhhcC
Q 024455 45 KCAVCQKLSK 54 (267)
Q Consensus 45 ~C~~C~~~f~ 54 (267)
.|..||..|.
T Consensus 7 ~C~~Cg~~fe 16 (52)
T TIGR02605 7 RCTACGHRFE 16 (52)
T ss_pred EeCCCCCEeE
Confidence 3444444443
No 180
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=71.46 E-value=1.9 Score=35.54 Aligned_cols=46 Identities=22% Similarity=0.342 Sum_probs=36.0
Q ss_pred ccccccCccccCChHHHHHHHhHhcCCCCCCCcccchhhcCCHHHHHhhc
Q 024455 14 RHKCVACYKQFKRKDHLIEHMKISYHSVHQPKCAVCQKLSKSFESLREHL 63 (267)
Q Consensus 14 ~~~C~~C~k~f~~~~~l~~H~~~~~H~~~~~~C~~C~~~f~~~~~l~~H~ 63 (267)
-|.|..||.+..- ..+..|+.. -.+....|-.||+.|-. .+...|.
T Consensus 3 ~FtCnvCgEsvKK-p~vekH~sr--Crn~~fSCIDC~k~F~~-~sYknH~ 48 (276)
T KOG2186|consen 3 FFTCNVCGESVKK-PQVEKHMSR--CRNAYFSCIDCGKTFER-VSYKNHT 48 (276)
T ss_pred EEehhhhhhhccc-cchHHHHHh--ccCCeeEEeeccccccc-chhhhhh
Confidence 3789999987664 557779877 66655599999999988 6677786
No 181
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=71.45 E-value=2.6 Score=42.81 Aligned_cols=83 Identities=20% Similarity=0.296 Sum_probs=44.4
Q ss_pred cccCccccCChHHHHHHHhHhcCCCCCC-CcccchhhcCCHHHHHhhcCC--CCC----C----CcC----Ccccc----
Q 024455 17 CVACYKQFKRKDHLIEHMKISYHSVHQP-KCAVCQKLSKSFESLREHLTG--PLS----K----AHC----SGIFS---- 77 (267)
Q Consensus 17 C~~C~k~f~~~~~l~~H~~~~~H~~~~~-~C~~C~~~f~~~~~l~~H~~~--~~~----C----~~C----~k~f~---- 77 (267)
|..|+..+.++..+.-|+... |+-.+. .|+.|+..|.....|..|+.. +.. | ..| +.+|.
T Consensus 439 ~~~~e~~~~s~r~~~~~t~~L-~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~ 517 (1406)
T KOG1146|consen 439 LTKAEPLLESKRSLEGQTVVL-HSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGK 517 (1406)
T ss_pred ccchhhhhhhhcccccceeee-ecccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCC
Confidence 344444455555555554432 444444 666666666666666666611 000 0 000 00011
Q ss_pred cccccccccccCChhhHHHHHHH
Q 024455 78 DRGCNLCMNIFDSPSSLIKHKEA 100 (267)
Q Consensus 78 ~~~C~~C~~~F~~~~~L~~H~~~ 100 (267)
-..|..|...+..+.+|.+|+..
T Consensus 518 p~~C~~C~~stttng~LsihlqS 540 (1406)
T KOG1146|consen 518 PYPCRACNYSTTTNGNLSIHLQS 540 (1406)
T ss_pred cccceeeeeeeecchHHHHHHHH
Confidence 11288888899999999999864
No 182
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=71.18 E-value=3.1 Score=42.22 Aligned_cols=23 Identities=13% Similarity=0.255 Sum_probs=14.4
Q ss_pred CCCCCcCCcccccc-----ccccccccc
Q 024455 66 PLSKAHCSGIFSDR-----GCNLCMNIF 88 (267)
Q Consensus 66 ~~~C~~C~k~f~~~-----~C~~C~~~F 88 (267)
.|.|+.||...... .|+.||...
T Consensus 692 vy~CPsCGaev~~des~a~~CP~CGtpl 719 (1337)
T PRK14714 692 VYVCPDCGAEVPPDESGRVECPRCDVEL 719 (1337)
T ss_pred ceeCccCCCccCCCccccccCCCCCCcc
Confidence 45677777765443 577777443
No 183
>PRK05762 DNA polymerase II; Reviewed
Probab=70.83 E-value=13 Score=36.74 Aligned_cols=39 Identities=15% Similarity=0.239 Sum_probs=30.3
Q ss_pred hccCCCHHHHHHHHHHHHhcCCCCCcccccCCCceEEEeccc-hhhhcccc
Q 024455 195 IKNAMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGL-EHDLDSLR 244 (267)
Q Consensus 195 l~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~-~~Dl~~l~ 244 (267)
+..-++-.+++..+.+++.. .+| .||||||+ .|||.+|.
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 45567899999999999942 222 39999997 58999993
No 184
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=68.67 E-value=3.6 Score=31.37 Aligned_cols=40 Identities=15% Similarity=0.246 Sum_probs=26.1
Q ss_pred CCCCccccccCccccCChHHHHHHHhHhcCCCCCCCcccchhhcC
Q 024455 10 RSTARHKCVACYKQFKRKDHLIEHMKISYHSVHQPKCAVCQKLSK 54 (267)
Q Consensus 10 ~~~k~~~C~~C~k~f~~~~~l~~H~~~~~H~~~~~~C~~C~~~f~ 54 (267)
++..-|.|+.|+..|.....+.. . +......|+.||....
T Consensus 95 ~~~~~Y~Cp~C~~~y~~~ea~~~---~--d~~~~f~Cp~Cg~~l~ 134 (147)
T smart00531 95 TNNAYYKCPNCQSKYTFLEANQL---L--DMDGTFTCPRCGEELE 134 (147)
T ss_pred cCCcEEECcCCCCEeeHHHHHHh---c--CCCCcEECCCCCCEEE
Confidence 34568999999999985443221 1 2222249999998653
No 185
>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=68.10 E-value=2.5 Score=23.15 Aligned_cols=19 Identities=16% Similarity=0.370 Sum_probs=7.9
Q ss_pred CCCcCCcccccc-----ccccccc
Q 024455 68 SKAHCSGIFSDR-----GCNLCMN 86 (267)
Q Consensus 68 ~C~~C~k~f~~~-----~C~~C~~ 86 (267)
.|..||..+... .|+.||.
T Consensus 2 ~C~~Cg~~~~~~~~~~irC~~CG~ 25 (32)
T PF03604_consen 2 ICGECGAEVELKPGDPIRCPECGH 25 (32)
T ss_dssp BESSSSSSE-BSTSSTSSBSSSS-
T ss_pred CCCcCCCeeEcCCCCcEECCcCCC
Confidence 344455444432 2555553
No 186
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=67.52 E-value=3.5 Score=21.24 Aligned_cols=20 Identities=15% Similarity=0.237 Sum_probs=10.4
Q ss_pred CCCcCCcccccc--cccccccc
Q 024455 68 SKAHCSGIFSDR--GCNLCMNI 87 (267)
Q Consensus 68 ~C~~C~k~f~~~--~C~~C~~~ 87 (267)
.|+.||+.-... .|+.||..
T Consensus 4 ~Cp~Cg~~~~~~~~fC~~CG~~ 25 (26)
T PF13248_consen 4 FCPNCGAEIDPDAKFCPNCGAK 25 (26)
T ss_pred CCcccCCcCCcccccChhhCCC
Confidence 466666632221 27777653
No 187
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=67.31 E-value=1.7 Score=26.29 Aligned_cols=20 Identities=20% Similarity=0.385 Sum_probs=10.5
Q ss_pred CCCCcCCcccccc------ccccccc
Q 024455 67 LSKAHCSGIFSDR------GCNLCMN 86 (267)
Q Consensus 67 ~~C~~C~k~f~~~------~C~~C~~ 86 (267)
|.|..||+.|... .|+.||.
T Consensus 7 Y~C~~Cg~~~~~~~~~~~irCp~Cg~ 32 (49)
T COG1996 7 YKCARCGREVELDQETRGIRCPYCGS 32 (49)
T ss_pred EEhhhcCCeeehhhccCceeCCCCCc
Confidence 4555566555422 2666653
No 188
>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=67.27 E-value=12 Score=33.82 Aligned_cols=35 Identities=23% Similarity=0.344 Sum_probs=26.9
Q ss_pred CCHHHHHHHHHHHHhcCCCCCcccccCCCceEEEeccch-hhhcccc
Q 024455 199 MPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLE-HDLDSLR 244 (267)
Q Consensus 199 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~-~Dl~~l~ 244 (267)
.+..+++..+.+++.. .+| .+++|||.. ||+.+|.
T Consensus 67 ~~E~~lL~~f~~~i~~------~dp-----dii~g~N~~~FD~~~i~ 102 (471)
T smart00486 67 NNEKELLKAFLEFIKK------YDP-----DIIYGHNISNFDLPYII 102 (471)
T ss_pred CCHHHHHHHHHHHHHH------hCC-----CEEEeecCCCCCHHHHH
Confidence 4778899999999842 111 499999995 8999984
No 189
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=67.24 E-value=4.5 Score=25.47 Aligned_cols=29 Identities=17% Similarity=0.358 Sum_probs=11.9
Q ss_pred CcccchhhcCCHHHHHhhcCCCCCCCcCC
Q 024455 45 KCAVCQKLSKSFESLREHLTGPLSKAHCS 73 (267)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~~~~~~C~~C~ 73 (267)
.|+.||..--.+..--+-+..+|.|+.||
T Consensus 29 ~CPnCGe~~I~Rc~~CRk~g~~Y~Cp~CG 57 (61)
T COG2888 29 PCPNCGEVEIYRCAKCRKLGNPYRCPKCG 57 (61)
T ss_pred eCCCCCceeeehhhhHHHcCCceECCCcC
Confidence 55555543333322222223445554444
No 190
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=65.40 E-value=5.6 Score=30.33 Aligned_cols=41 Identities=22% Similarity=0.306 Sum_probs=28.1
Q ss_pred HHHHHHHHhcCCCCCcccccCCCceEEEeccchhhhcccc---ccCCCCceecccccc
Q 024455 205 KDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLR---MNYPDHMLRDTAKYR 259 (267)
Q Consensus 205 ~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~Dl~~l~---~~~~~~~~~dt~~~~ 259 (267)
...|.+++.+ .+...||||+.+|+.+|+ +..+ .++||....
T Consensus 64 ~~~l~~~l~~------------~~~~kv~~d~k~~~~~L~~~gi~~~--~~~D~~laa 107 (172)
T smart00474 64 LEILKDLLED------------ETITKVGHNAKFDLHVLARFGIELE--NIFDTMLAA 107 (172)
T ss_pred HHHHHHHhcC------------CCceEEEechHHHHHHHHHCCCccc--chhHHHHHH
Confidence 4556777843 456799999999999994 3333 237887443
No 191
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=64.98 E-value=2.2 Score=41.19 Aligned_cols=31 Identities=26% Similarity=0.368 Sum_probs=14.5
Q ss_pred CcccchhhcCCH---HHHHhhc-CCCCCCCcCCcc
Q 024455 45 KCAVCQKLSKSF---ESLREHL-TGPLSKAHCSGI 75 (267)
Q Consensus 45 ~C~~C~~~f~~~---~~l~~H~-~~~~~C~~C~k~ 75 (267)
.|..||..+.-. ..|..|+ ++...|..||..
T Consensus 437 ~C~~Cg~v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~ 471 (730)
T COG1198 437 LCRDCGYIAECPNCDSPLTLHKATGQLRCHYCGYQ 471 (730)
T ss_pred ecccCCCcccCCCCCcceEEecCCCeeEeCCCCCC
Confidence 666666554321 2333444 334445555444
No 192
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=64.56 E-value=3.5 Score=25.55 Aligned_cols=22 Identities=23% Similarity=0.459 Sum_probs=13.4
Q ss_pred CCCcCCcccccc----cccccccccC
Q 024455 68 SKAHCSGIFSDR----GCNLCMNIFD 89 (267)
Q Consensus 68 ~C~~C~k~f~~~----~C~~C~~~F~ 89 (267)
.|..||+.|... .|+.||..+.
T Consensus 7 ~C~~Cg~~~~~~dDiVvCp~CgapyH 32 (54)
T PF14446_consen 7 KCPVCGKKFKDGDDIVVCPECGAPYH 32 (54)
T ss_pred cChhhCCcccCCCCEEECCCCCCccc
Confidence 466777777533 2777776554
No 193
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=63.10 E-value=6.5 Score=37.62 Aligned_cols=36 Identities=14% Similarity=0.215 Sum_probs=26.7
Q ss_pred CcccchhhcCCHHHHHhhcCCCCCCCcCCcccccc--cccccccccCCh
Q 024455 45 KCAVCQKLSKSFESLREHLTGPLSKAHCSGIFSDR--GCNLCMNIFDSP 91 (267)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~~~~~~C~~C~k~f~~~--~C~~C~~~F~~~ 91 (267)
-|..||..+.. ..|+.||...... .|+.||......
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 69999887642 3599999885543 499999887654
No 194
>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=61.99 E-value=7 Score=20.17 Aligned_cols=19 Identities=16% Similarity=0.746 Sum_probs=12.6
Q ss_pred ccccCccccCChHHHHHHHh
Q 024455 16 KCVACYKQFKRKDHLIEHMK 35 (267)
Q Consensus 16 ~C~~C~k~f~~~~~l~~H~~ 35 (267)
.|++|++.+ ....+..|..
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 577887776 4456666654
No 195
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=61.93 E-value=3.5 Score=32.07 Aligned_cols=20 Identities=15% Similarity=0.302 Sum_probs=14.7
Q ss_pred CCCCCcCCcccccc---cccccc
Q 024455 66 PLSKAHCSGIFSDR---GCNLCM 85 (267)
Q Consensus 66 ~~~C~~C~k~f~~~---~C~~C~ 85 (267)
-|.|++||.++... .||+||
T Consensus 134 ~~vC~vCGy~~~ge~P~~CPiCg 156 (166)
T COG1592 134 VWVCPVCGYTHEGEAPEVCPICG 156 (166)
T ss_pred EEEcCCCCCcccCCCCCcCCCCC
Confidence 37788888877763 388887
No 196
>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=61.81 E-value=2.7 Score=29.01 Aligned_cols=27 Identities=19% Similarity=0.409 Sum_probs=17.0
Q ss_pred CCCCCCCcCCcccccc------cccccccccCC
Q 024455 64 TGPLSKAHCSGIFSDR------GCNLCMNIFDS 90 (267)
Q Consensus 64 ~~~~~C~~C~k~f~~~------~C~~C~~~F~~ 90 (267)
...|.|+.|++.-... .|..|++.|.-
T Consensus 33 ~~ky~Cp~Cgk~~vkR~a~GIW~C~~C~~~~AG 65 (90)
T PF01780_consen 33 HAKYTCPFCGKTSVKRVATGIWKCKKCGKKFAG 65 (90)
T ss_dssp HS-BEESSSSSSEEEEEETTEEEETTTTEEEE-
T ss_pred hCCCcCCCCCCceeEEeeeEEeecCCCCCEEeC
Confidence 3467788887765432 38888887764
No 197
>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=61.73 E-value=4.6 Score=25.07 Aligned_cols=8 Identities=25% Similarity=0.746 Sum_probs=4.3
Q ss_pred cccccccc
Q 024455 81 CNLCMNIF 88 (267)
Q Consensus 81 C~~C~~~F 88 (267)
|+.||..|
T Consensus 25 Cp~CGael 32 (54)
T TIGR01206 25 CDECGAEL 32 (54)
T ss_pred CCCCCCEE
Confidence 55665444
No 198
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]
Probab=60.61 E-value=13 Score=30.92 Aligned_cols=19 Identities=21% Similarity=0.272 Sum_probs=14.5
Q ss_pred CCCceeeeeccccCCcCCC
Q 024455 133 RGPKAVAMDCEMVGGGSNG 151 (267)
Q Consensus 133 ~~~~~~~~dcE~~g~~~~~ 151 (267)
...++..+|.|++|.+..+
T Consensus 96 ~~e~~~FFDiETTGL~~ag 114 (278)
T COG3359 96 EAEDVAFFDIETTGLDRAG 114 (278)
T ss_pred cccceEEEeeeccccCCCC
Confidence 3456789999999987533
No 199
>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=60.35 E-value=1.2 Score=29.09 Aligned_cols=35 Identities=20% Similarity=0.435 Sum_probs=18.0
Q ss_pred CcccchhhcCCHHHHHhhcCCCCCCCcCCccccccc-cccccc
Q 024455 45 KCAVCQKLSKSFESLREHLTGPLSKAHCSGIFSDRG-CNLCMN 86 (267)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~~~~~~C~~C~k~f~~~~-C~~C~~ 86 (267)
.|+.|.....+. .+.|.|..|++.|.... |+.|+.
T Consensus 3 ~CP~C~~~L~~~-------~~~~~C~~C~~~~~~~a~CPdC~~ 38 (70)
T PF07191_consen 3 TCPKCQQELEWQ-------GGHYHCEACQKDYKKEAFCPDCGQ 38 (70)
T ss_dssp B-SSS-SBEEEE-------TTEEEETTT--EEEEEEE-TTT-S
T ss_pred cCCCCCCccEEe-------CCEEECccccccceecccCCCccc
Confidence 466666543322 24677888888877654 787764
No 200
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=60.22 E-value=2.2 Score=40.49 Aligned_cols=54 Identities=22% Similarity=0.405 Sum_probs=26.3
Q ss_pred cccCccccCChHHHHHHHhHhcCCCCCC--CcccchhhcCCHHHHHhhcCCCCCCCcCCc
Q 024455 17 CVACYKQFKRKDHLIEHMKISYHSVHQP--KCAVCQKLSKSFESLREHLTGPLSKAHCSG 74 (267)
Q Consensus 17 C~~C~k~f~~~~~l~~H~~~~~H~~~~~--~C~~C~~~f~~~~~l~~H~~~~~~C~~C~k 74 (267)
|..||-.|+--..|--- |- +|.... .|+.|.+.|....+-+-| ..+..|+.||-
T Consensus 126 CT~CGPRfTIi~alPYD-R~--nTsM~~F~lC~~C~~EY~dP~nRRfH-AQp~aCp~CGP 181 (750)
T COG0068 126 CTNCGPRFTIIEALPYD-RE--NTSMADFPLCPFCDKEYKDPLNRRFH-AQPIACPKCGP 181 (750)
T ss_pred cCCCCcceeeeccCCCC-cc--cCccccCcCCHHHHHHhcCccccccc-cccccCcccCC
Confidence 56666555554443221 11 222222 666666666655555444 34455555554
No 201
>PRK12496 hypothetical protein; Provisional
Probab=60.00 E-value=3.7 Score=31.98 Aligned_cols=24 Identities=13% Similarity=0.369 Sum_probs=18.1
Q ss_pred CCCCCcCCccccc----ccccccccccC
Q 024455 66 PLSKAHCSGIFSD----RGCNLCMNIFD 89 (267)
Q Consensus 66 ~~~C~~C~k~f~~----~~C~~C~~~F~ 89 (267)
.|.|..|++.|.. ..|+.||..-.
T Consensus 127 ~~~C~gC~~~~~~~~~~~~C~~CG~~~~ 154 (164)
T PRK12496 127 RKVCKGCKKKYPEDYPDDVCEICGSPVK 154 (164)
T ss_pred eEECCCCCccccCCCCCCcCCCCCChhh
Confidence 3679999999953 23999996543
No 202
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=58.78 E-value=5.7 Score=26.33 Aligned_cols=31 Identities=19% Similarity=0.509 Sum_probs=18.9
Q ss_pred ccccccCccccCChHHHHHHHhHhcCCCCCC-Ccccchhhc
Q 024455 14 RHKCVACYKQFKRKDHLIEHMKISYHSVHQP-KCAVCQKLS 53 (267)
Q Consensus 14 ~~~C~~C~k~f~~~~~l~~H~~~~~H~~~~~-~C~~C~~~f 53 (267)
.|+|..|+..| .+..||.- ... .|+.||..+
T Consensus 12 ~Y~c~~cg~~~----dvvq~~~d-----dplt~ce~c~a~~ 43 (82)
T COG2331 12 SYECTECGNRF----DVVQAMTD-----DPLTTCEECGARL 43 (82)
T ss_pred EEeecccchHH----HHHHhccc-----CccccChhhChHH
Confidence 48888888653 34444432 222 888888654
No 203
>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=58.45 E-value=11 Score=29.17 Aligned_cols=28 Identities=11% Similarity=0.154 Sum_probs=18.2
Q ss_pred CcccchhhcCCHHHHHhhcCCCCCCCcCCccc
Q 024455 45 KCAVCQKLSKSFESLREHLTGPLSKAHCSGIF 76 (267)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~~~~~~C~~C~k~f 76 (267)
.|+.|+..|+....+. ..|.|+.||...
T Consensus 111 ~Cp~c~~r~tf~eA~~----~~F~Cp~Cg~~L 138 (158)
T TIGR00373 111 ICPNMCVRFTFNEAME----LNFTCPRCGAML 138 (158)
T ss_pred ECCCCCcEeeHHHHHH----cCCcCCCCCCEe
Confidence 7777777777666553 357776666543
No 204
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=58.30 E-value=5.3 Score=29.66 Aligned_cols=23 Identities=26% Similarity=0.218 Sum_probs=19.4
Q ss_pred ccccccccCChhhHHHHHHHhcCCCC
Q 024455 81 CNLCMNIFDSPSSLIKHKEACSLSAP 106 (267)
Q Consensus 81 C~~C~~~F~~~~~L~~H~~~h~~~~~ 106 (267)
|-++||.|. .|++|+.+|.+=-|
T Consensus 79 cLEDGkkfK---SLKRHL~t~~gmTP 101 (148)
T COG4957 79 CLEDGKKFK---SLKRHLTTHYGLTP 101 (148)
T ss_pred EeccCcchH---HHHHHHhcccCCCH
Confidence 888999996 68999999987654
No 205
>PRK14873 primosome assembly protein PriA; Provisional
Probab=58.11 E-value=2.8 Score=40.22 Aligned_cols=43 Identities=21% Similarity=0.329 Sum_probs=25.9
Q ss_pred CcccchhhcCCH---HHHHhhc-CCCCCCCcCCcccccccccccccc
Q 024455 45 KCAVCQKLSKSF---ESLREHL-TGPLSKAHCSGIFSDRGCNLCMNI 87 (267)
Q Consensus 45 ~C~~C~~~f~~~---~~l~~H~-~~~~~C~~C~k~f~~~~C~~C~~~ 87 (267)
.|..||..+.-. ..|..|. .+...|..||..-....|+.||..
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 677776655432 3455555 345567777776555567777754
No 206
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=57.71 E-value=15 Score=31.93 Aligned_cols=16 Identities=19% Similarity=0.382 Sum_probs=10.7
Q ss_pred ccCChhhHHHHHHHhc
Q 024455 87 IFDSPSSLIKHKEACS 102 (267)
Q Consensus 87 ~F~~~~~L~~H~~~h~ 102 (267)
.|.....|..|+..-|
T Consensus 290 vf~~~~el~~h~~~~h 305 (493)
T COG5236 290 VFPYHTELLEHLTRFH 305 (493)
T ss_pred EeccHHHHHHHHHHHh
Confidence 5777777888865444
No 207
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=57.17 E-value=3.7 Score=39.06 Aligned_cols=25 Identities=32% Similarity=0.416 Sum_probs=19.3
Q ss_pred CCccccccCccccCChHHHHHHHhH
Q 024455 12 TARHKCVACYKQFKRKDHLIEHMKI 36 (267)
Q Consensus 12 ~k~~~C~~C~k~f~~~~~l~~H~~~ 36 (267)
.--|.|..|+|.|....++..||++
T Consensus 790 ~giFpCreC~kvF~KiKSrNAHMK~ 814 (907)
T KOG4167|consen 790 TGIFPCRECGKVFFKIKSRNAHMKT 814 (907)
T ss_pred CceeehHHHHHHHHHHhhhhHHHHH
Confidence 3457888888888887888888887
No 208
>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=56.77 E-value=6 Score=27.39 Aligned_cols=26 Identities=15% Similarity=0.284 Sum_probs=14.6
Q ss_pred CCCCCCcCCccccc------ccccccccccCC
Q 024455 65 GPLSKAHCSGIFSD------RGCNLCMNIFDS 90 (267)
Q Consensus 65 ~~~~C~~C~k~f~~------~~C~~C~~~F~~ 90 (267)
..|.|+.|++.-.. +.|..|++.|.-
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 35666666654222 137777776654
No 209
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=56.72 E-value=6.3 Score=27.25 Aligned_cols=26 Identities=15% Similarity=0.289 Sum_probs=13.5
Q ss_pred CCCCCCcCCcccccc------cccccccccCC
Q 024455 65 GPLSKAHCSGIFSDR------GCNLCMNIFDS 90 (267)
Q Consensus 65 ~~~~C~~C~k~f~~~------~C~~C~~~F~~ 90 (267)
..|.|+.|++.-... .|..|++.|.-
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 355666665442211 26666666654
No 210
>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=55.90 E-value=4.9 Score=33.82 Aligned_cols=33 Identities=30% Similarity=0.306 Sum_probs=24.8
Q ss_pred CceEEEeccchhhhccc-------------------cccCCCCceecccccccc
Q 024455 227 KARLLVGHGLEHDLDSL-------------------RMNYPDHMLRDTAKYRPL 261 (267)
Q Consensus 227 ~~~~lvgh~~~~Dl~~l-------------------~~~~~~~~~~dt~~~~~~ 261 (267)
...+|||||.-+||-+| +..+| .|+||-.+...
T Consensus 148 ~~~p~Vghn~~~Dl~~l~~~f~~~LP~t~~eF~~~~~~~FP--~i~DtK~la~~ 199 (262)
T PF04857_consen 148 SKKPIVGHNGLYDLMYLYKKFIGPLPETLEEFKELLRELFP--RIYDTKYLAEE 199 (262)
T ss_dssp C-SEEEESSTHHHHHHHHHHHTTS--SSHHHHHHHHHHHSS--SEEEHHHHHTS
T ss_pred cCCcEEEeChHhHHHHHHHHhcCCCCCCHHHHHHHHHHHCc--ccccHHHHHHh
Confidence 45799999999999887 22468 58899866553
No 211
>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=55.70 E-value=11 Score=29.22 Aligned_cols=42 Identities=24% Similarity=0.209 Sum_probs=27.7
Q ss_pred HHHHHHHHHhcCCCCCcccccCCCceEEEeccchhhhcccccc--CCCCceecccc
Q 024455 204 VKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMN--YPDHMLRDTAK 257 (267)
Q Consensus 204 v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~Dl~~l~~~--~~~~~~~dt~~ 257 (267)
+...|.+++.+ .+...||||+.+|+.+|... .....+.||..
T Consensus 52 ~~~~l~~ll~~------------~~i~kv~~d~K~~~~~L~~~~gi~~~~~~D~~l 95 (178)
T cd06142 52 DLSPLKELLAD------------PNIVKVFHAAREDLELLKRDFGILPQNLFDTQI 95 (178)
T ss_pred cHHHHHHHHcC------------CCceEEEeccHHHHHHHHHHcCCCCCCcccHHH
Confidence 34456677743 45689999999999998422 11235578873
No 212
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=53.71 E-value=7.2 Score=26.96 Aligned_cols=26 Identities=19% Similarity=0.300 Sum_probs=15.3
Q ss_pred CCCCCCcCCcccccc------cccccccccCC
Q 024455 65 GPLSKAHCSGIFSDR------GCNLCMNIFDS 90 (267)
Q Consensus 65 ~~~~C~~C~k~f~~~------~C~~C~~~F~~ 90 (267)
..|.|+.|++.-... .|..|++.|.-
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 456677776543221 37777777754
No 213
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=53.42 E-value=11 Score=32.61 Aligned_cols=38 Identities=16% Similarity=0.292 Sum_probs=27.5
Q ss_pred CCccccccCccccCChHHHHHHHhHhcCCCCCC--Ccccch
Q 024455 12 TARHKCVACYKQFKRKDHLIEHMKISYHSVHQP--KCAVCQ 50 (267)
Q Consensus 12 ~k~~~C~~C~k~f~~~~~l~~H~~~~~H~~~~~--~C~~C~ 50 (267)
+..|.|+.|++.=.+...|..|...+ |....+ .|+.|+
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 44788888888777778888887664 665545 777775
No 214
>PHA02524 43A DNA polymerase subunit A; Provisional
Probab=52.58 E-value=11 Score=34.76 Aligned_cols=35 Identities=9% Similarity=0.065 Sum_probs=27.5
Q ss_pred CCHHHHHHHHHHHHhcCCCCCcccccCCCceEEEeccc-hhhhcccc
Q 024455 199 MPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGL-EHDLDSLR 244 (267)
Q Consensus 199 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~-~~Dl~~l~ 244 (267)
.+-.+++.++.+++.+ .+| .||+|+|+ .|||..|.
T Consensus 178 ~sE~eLL~~F~~~i~~------~DP-----DIItGYNi~nFDlPYL~ 213 (498)
T PHA02524 178 EDEVDLLLNYIQLWKA------NTP-----DLVFGWNSEGFDIPYII 213 (498)
T ss_pred CCHHHHHHHHHHHHHH------hCC-----CEEEeCCCcccCHHHHH
Confidence 5788999999999942 222 39999998 68999983
No 215
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=51.84 E-value=5 Score=30.14 Aligned_cols=30 Identities=30% Similarity=0.367 Sum_probs=23.6
Q ss_pred CCcCCcccccccccccccccCChhhHHHHHH
Q 024455 69 KAHCSGIFSDRGCNLCMNIFDSPSSLIKHKE 99 (267)
Q Consensus 69 C~~C~k~f~~~~C~~C~~~F~~~~~L~~H~~ 99 (267)
|.+|| -++-.+|.-||..+-+..-|..|..
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 88998 4555679999999988888877753
No 216
>COG1773 Rubredoxin [Energy production and conversion]
Probab=51.49 E-value=7 Score=24.30 Aligned_cols=10 Identities=30% Similarity=0.916 Sum_probs=5.8
Q ss_pred CcccchhhcC
Q 024455 45 KCAVCQKLSK 54 (267)
Q Consensus 45 ~C~~C~~~f~ 54 (267)
+|..||..|.
T Consensus 5 ~C~~CG~vYd 14 (55)
T COG1773 5 RCSVCGYVYD 14 (55)
T ss_pred EecCCceEec
Confidence 5666665553
No 217
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=51.47 E-value=3.7 Score=27.17 Aligned_cols=6 Identities=50% Similarity=1.575 Sum_probs=2.7
Q ss_pred cccchh
Q 024455 46 CAVCQK 51 (267)
Q Consensus 46 C~~C~~ 51 (267)
|+.||.
T Consensus 4 CP~Cg~ 9 (72)
T PRK09678 4 CPLCQH 9 (72)
T ss_pred CCCCCC
Confidence 444443
No 218
>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=51.03 E-value=5.8 Score=22.33 Aligned_cols=8 Identities=25% Similarity=1.007 Sum_probs=3.8
Q ss_pred cccchhhc
Q 024455 46 CAVCQKLS 53 (267)
Q Consensus 46 C~~C~~~f 53 (267)
|+.||+.|
T Consensus 4 C~~Cg~~Y 11 (36)
T PF05191_consen 4 CPKCGRIY 11 (36)
T ss_dssp ETTTTEEE
T ss_pred cCCCCCcc
Confidence 44455444
No 219
>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=50.77 E-value=5 Score=37.29 Aligned_cols=43 Identities=23% Similarity=0.292 Sum_probs=27.5
Q ss_pred CcccchhhcCC---HHHHHhhc-CCCCCCCcCCcccc-cccccccccc
Q 024455 45 KCAVCQKLSKS---FESLREHL-TGPLSKAHCSGIFS-DRGCNLCMNI 87 (267)
Q Consensus 45 ~C~~C~~~f~~---~~~l~~H~-~~~~~C~~C~k~f~-~~~C~~C~~~ 87 (267)
.|..||....- ...|..|. .+...|..||.... ...|+.||..
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 56666655433 23466666 45667888888766 3469999864
No 220
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=50.09 E-value=18 Score=20.92 Aligned_cols=28 Identities=18% Similarity=0.328 Sum_probs=16.7
Q ss_pred ccccccccccccccCCh--hhHHHHHHHhc
Q 024455 75 IFSDRGCNLCMNIFDSP--SSLIKHKEACS 102 (267)
Q Consensus 75 ~f~~~~C~~C~~~F~~~--~~L~~H~~~h~ 102 (267)
.|....|+.||..|... ..-..|.+-|.
T Consensus 10 ~~~~~~C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 10 SFGATTCPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred ccCCcCCCCCCCEECCCCHHHHHHHHHHHh
Confidence 34444577787777653 44566666663
No 221
>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=49.98 E-value=12 Score=26.79 Aligned_cols=22 Identities=23% Similarity=0.108 Sum_probs=20.3
Q ss_pred cccccccCChhhHHHHHHHhcC
Q 024455 82 NLCMNIFDSPSSLIKHKEACSL 103 (267)
Q Consensus 82 ~~C~~~F~~~~~L~~H~~~h~~ 103 (267)
..|+..+.+...+++|.+.+||
T Consensus 88 ~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 88 PHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CCCCcEeccHHHHHHHHHHhcC
Confidence 8999999999999999998875
No 222
>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=49.69 E-value=9.8 Score=23.19 Aligned_cols=10 Identities=20% Similarity=0.833 Sum_probs=5.9
Q ss_pred CcccchhhcC
Q 024455 45 KCAVCQKLSK 54 (267)
Q Consensus 45 ~C~~C~~~f~ 54 (267)
+|..||..+.
T Consensus 3 ~C~~CgyiYd 12 (50)
T cd00730 3 ECRICGYIYD 12 (50)
T ss_pred CCCCCCeEEC
Confidence 4666666554
No 223
>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=49.33 E-value=12 Score=28.37 Aligned_cols=19 Identities=21% Similarity=0.317 Sum_probs=14.6
Q ss_pred cccccccccCChhhHHHHH
Q 024455 80 GCNLCMNIFDSPSSLIKHK 98 (267)
Q Consensus 80 ~C~~C~~~F~~~~~L~~H~ 98 (267)
.|+.||+.|..-++.++-.
T Consensus 126 ~C~~C~kiyW~GsH~~~~~ 144 (147)
T PF01927_consen 126 RCPGCGKIYWEGSHWRRME 144 (147)
T ss_pred ECCCCCCEecccccHHHHH
Confidence 3999999998877766543
No 224
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=48.90 E-value=7.6 Score=27.70 Aligned_cols=8 Identities=0% Similarity=-0.027 Sum_probs=4.7
Q ss_pred cccccccc
Q 024455 81 CNLCMNIF 88 (267)
Q Consensus 81 C~~C~~~F 88 (267)
|+.||++|
T Consensus 29 sPytG~s~ 36 (129)
T COG4530 29 SPYTGKSY 36 (129)
T ss_pred cCcccccc
Confidence 55566666
No 225
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=48.36 E-value=7.9 Score=37.06 Aligned_cols=36 Identities=17% Similarity=0.348 Sum_probs=23.7
Q ss_pred CcccchhhcCCHHHHHhhcCCCCCCCcCCcccccccccccccccC
Q 024455 45 KCAVCQKLSKSFESLREHLTGPLSKAHCSGIFSDRGCNLCMNIFD 89 (267)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~~~~~~C~~C~k~f~~~~C~~C~~~F~ 89 (267)
.|+.||..-. .+..-|..||..+....|+.||....
T Consensus 3 ~Cp~Cg~~n~---------~~akFC~~CG~~l~~~~Cp~CG~~~~ 38 (645)
T PRK14559 3 ICPQCQFENP---------NNNRFCQKCGTSLTHKPCPQCGTEVP 38 (645)
T ss_pred cCCCCCCcCC---------CCCccccccCCCCCCCcCCCCCCCCC
Confidence 5778875422 22234888888887777888887643
No 226
>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=48.29 E-value=7.4 Score=19.77 Aligned_cols=11 Identities=18% Similarity=0.386 Sum_probs=9.0
Q ss_pred CCccccccCcc
Q 024455 12 TARHKCVACYK 22 (267)
Q Consensus 12 ~k~~~C~~C~k 22 (267)
--+|.|+.||+
T Consensus 14 ~v~f~CPnCG~ 24 (24)
T PF07754_consen 14 AVPFPCPNCGF 24 (24)
T ss_pred CceEeCCCCCC
Confidence 45799999984
No 227
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=47.14 E-value=6 Score=37.84 Aligned_cols=17 Identities=18% Similarity=0.315 Sum_probs=10.6
Q ss_pred cccccccccCChhhHHH
Q 024455 80 GCNLCMNIFDSPSSLIK 96 (267)
Q Consensus 80 ~C~~C~~~F~~~~~L~~ 96 (267)
.||.|+..|....-++.
T Consensus 680 KCP~Cn~aFganDv~~I 696 (698)
T KOG0978|consen 680 KCPKCNAAFGANDVHRI 696 (698)
T ss_pred CCCCCCCCCCccccccc
Confidence 37777777776554443
No 228
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=46.96 E-value=19 Score=28.40 Aligned_cols=29 Identities=14% Similarity=0.264 Sum_probs=17.7
Q ss_pred CcccchhhcCCHHHHHhhcCCCCCCCcCCcccc
Q 024455 45 KCAVCQKLSKSFESLREHLTGPLSKAHCSGIFS 77 (267)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~~~~~~C~~C~k~f~ 77 (267)
.|+.|+..|+....+ ...|.|+.||....
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 777777777665544 23566666665443
No 229
>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=46.28 E-value=9.5 Score=24.63 Aligned_cols=25 Identities=16% Similarity=0.417 Sum_probs=8.8
Q ss_pred CcccchhhcCCHHHHHhhcCCCCCCCcCCccc
Q 024455 45 KCAVCQKLSKSFESLREHLTGPLSKAHCSGIF 76 (267)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~~~~~~C~~C~k~f 76 (267)
.|..|++.|.. ..+.+.|..||..|
T Consensus 11 ~C~~C~~~F~~-------~~rrhhCr~CG~~v 35 (69)
T PF01363_consen 11 NCMICGKKFSL-------FRRRHHCRNCGRVV 35 (69)
T ss_dssp B-TTT--B-BS-------SS-EEE-TTT--EE
T ss_pred cCcCcCCcCCC-------ceeeEccCCCCCEE
Confidence 67777777732 13334566666544
No 230
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=46.20 E-value=11 Score=33.96 Aligned_cols=23 Identities=22% Similarity=0.528 Sum_probs=12.3
Q ss_pred CCcCCccccccc-----ccccccccCCh
Q 024455 69 KAHCSGIFSDRG-----CNLCMNIFDSP 91 (267)
Q Consensus 69 C~~C~k~f~~~~-----C~~C~~~F~~~ 91 (267)
|+.||.+..+.+ |+.||..+...
T Consensus 353 Cp~Cg~~m~S~G~~g~rC~kCg~~~~~~ 380 (421)
T COG1571 353 CPRCGGRMKSAGRNGFRCKKCGTRARET 380 (421)
T ss_pred CCccCCchhhcCCCCcccccccccCCcc
Confidence 555555444432 66666666544
No 231
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=46.14 E-value=16 Score=32.81 Aligned_cols=34 Identities=32% Similarity=0.544 Sum_probs=26.6
Q ss_pred CcccchhhcCCHHHHHhhc--CCCCCCCcCCccccc
Q 024455 45 KCAVCQKLSKSFESLREHL--TGPLSKAHCSGIFSD 78 (267)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~--~~~~~C~~C~k~f~~ 78 (267)
.|+.|++.|.....++.-- ++.|.|..|+....-
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 9999999998876665443 688999999876554
No 232
>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=44.46 E-value=6.8 Score=29.85 Aligned_cols=7 Identities=29% Similarity=0.814 Sum_probs=4.1
Q ss_pred ccccccc
Q 024455 81 CNLCMNI 87 (267)
Q Consensus 81 C~~C~~~ 87 (267)
|+.||..
T Consensus 133 Cp~C~~~ 139 (146)
T PF07295_consen 133 CPKCGHT 139 (146)
T ss_pred CCCCCCC
Confidence 6666544
No 233
>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=43.61 E-value=12 Score=22.93 Aligned_cols=25 Identities=24% Similarity=0.380 Sum_probs=12.3
Q ss_pred CcccchhhcCCHHHHHhhcCCCCCCCcCCccc
Q 024455 45 KCAVCQKLSKSFESLREHLTGPLSKAHCSGIF 76 (267)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~~~~~~C~~C~k~f 76 (267)
.|..|++.|.. ..+.+.|..||+.|
T Consensus 4 ~C~~C~~~F~~-------~~rk~~Cr~Cg~~~ 28 (57)
T cd00065 4 SCMGCGKPFTL-------TRRRHHCRNCGRIF 28 (57)
T ss_pred cCcccCccccC-------CccccccCcCcCCc
Confidence 45566666654 12334455555543
No 234
>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=43.38 E-value=8.2 Score=23.19 Aligned_cols=11 Identities=27% Similarity=0.785 Sum_probs=5.6
Q ss_pred CcccchhhcCC
Q 024455 45 KCAVCQKLSKS 55 (267)
Q Consensus 45 ~C~~C~~~f~~ 55 (267)
+|..||..+.-
T Consensus 3 ~C~~CgyvYd~ 13 (47)
T PF00301_consen 3 QCPVCGYVYDP 13 (47)
T ss_dssp EETTTSBEEET
T ss_pred CCCCCCEEEcC
Confidence 35555555433
No 235
>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=41.76 E-value=7 Score=32.51 Aligned_cols=11 Identities=27% Similarity=0.495 Sum_probs=5.2
Q ss_pred CCCccccccCc
Q 024455 11 STARHKCVACY 21 (267)
Q Consensus 11 ~~k~~~C~~C~ 21 (267)
|-+.|+|..|.
T Consensus 139 GGrif~CsfC~ 149 (314)
T PF06524_consen 139 GGRIFKCSFCD 149 (314)
T ss_pred CCeEEEeecCC
Confidence 34445555544
No 236
>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=40.91 E-value=12 Score=20.03 Aligned_cols=21 Identities=14% Similarity=0.273 Sum_probs=10.9
Q ss_pred CCCcCCcccccccccccccccC
Q 024455 68 SKAHCSGIFSDRGCNLCMNIFD 89 (267)
Q Consensus 68 ~C~~C~k~f~~~~C~~C~~~F~ 89 (267)
.|.+|+. +....|+.|+..+=
T Consensus 4 ~C~vC~~-~~kY~Cp~C~~~~C 24 (30)
T PF04438_consen 4 LCSVCGN-PAKYRCPRCGARYC 24 (30)
T ss_dssp EETSSSS-EESEE-TTT--EES
T ss_pred CCccCcC-CCEEECCCcCCcee
Confidence 3666766 55556777766543
No 237
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=40.53 E-value=27 Score=25.51 Aligned_cols=26 Identities=23% Similarity=0.512 Sum_probs=20.6
Q ss_pred CCCccccccCccccCChHHHHHHHhH
Q 024455 11 STARHKCVACYKQFKRKDHLIEHMKI 36 (267)
Q Consensus 11 ~~k~~~C~~C~k~f~~~~~l~~H~~~ 36 (267)
|-..|-|-.|.+-|.+...|..|.++
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHhc
Confidence 66668888888888888888888765
No 238
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=40.38 E-value=8.7 Score=31.83 Aligned_cols=33 Identities=24% Similarity=0.517 Sum_probs=20.4
Q ss_pred CcccchhhcCCHHHHHhhc----CCCCCCCcCCccccc
Q 024455 45 KCAVCQKLSKSFESLREHL----TGPLSKAHCSGIFSD 78 (267)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~----~~~~~C~~C~k~f~~ 78 (267)
.|..||.... +..+.+|+ ...|.|-.|+++|..
T Consensus 5 tCnvCgEsvK-Kp~vekH~srCrn~~fSCIDC~k~F~~ 41 (276)
T KOG2186|consen 5 TCNVCGESVK-KPQVEKHMSRCRNAYFSCIDCGKTFER 41 (276)
T ss_pred ehhhhhhhcc-ccchHHHHHhccCCeeEEeeccccccc
Confidence 7999998765 45577787 223445555444443
No 239
>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=40.34 E-value=10 Score=27.47 Aligned_cols=21 Identities=19% Similarity=0.393 Sum_probs=10.3
Q ss_pred CCCCcCCcccccc----cccccccc
Q 024455 67 LSKAHCSGIFSDR----GCNLCMNI 87 (267)
Q Consensus 67 ~~C~~C~k~f~~~----~C~~C~~~ 87 (267)
..|..||+.|... .||.||..
T Consensus 71 ~~C~~Cg~~~~~~~~~~~CP~Cgs~ 95 (113)
T PF01155_consen 71 ARCRDCGHEFEPDEFDFSCPRCGSP 95 (113)
T ss_dssp EEETTTS-EEECHHCCHH-SSSSSS
T ss_pred EECCCCCCEEecCCCCCCCcCCcCC
Confidence 3466666666543 26666643
No 240
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=40.22 E-value=24 Score=20.20 Aligned_cols=16 Identities=31% Similarity=0.540 Sum_probs=10.9
Q ss_pred ccccccccCChhhHHH
Q 024455 81 CNLCMNIFDSPSSLIK 96 (267)
Q Consensus 81 C~~C~~~F~~~~~L~~ 96 (267)
|+.|+-.|-....|.+
T Consensus 22 C~~C~G~W~d~~el~~ 37 (41)
T PF13453_consen 22 CPSCGGIWFDAGELEK 37 (41)
T ss_pred CCCCCeEEccHHHHHH
Confidence 7777777776666653
No 241
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=39.90 E-value=14 Score=26.83 Aligned_cols=19 Identities=21% Similarity=0.357 Sum_probs=11.1
Q ss_pred CCCCcCCcccccc----cccccc
Q 024455 67 LSKAHCSGIFSDR----GCNLCM 85 (267)
Q Consensus 67 ~~C~~C~k~f~~~----~C~~C~ 85 (267)
..|..|+..|... .||.||
T Consensus 71 ~~C~~Cg~~~~~~~~~~~CP~Cg 93 (113)
T PRK12380 71 AWCWDCSQVVEIHQHDAQCPHCH 93 (113)
T ss_pred EEcccCCCEEecCCcCccCcCCC
Confidence 4466666666542 277776
No 242
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=38.99 E-value=2.5 Score=29.67 Aligned_cols=13 Identities=15% Similarity=0.388 Sum_probs=8.6
Q ss_pred CCccccccCcccc
Q 024455 12 TARHKCVACYKQF 24 (267)
Q Consensus 12 ~k~~~C~~C~k~f 24 (267)
++.|.|+.|+..-
T Consensus 20 ~k~FtCp~Cghe~ 32 (104)
T COG4888 20 PKTFTCPRCGHEK 32 (104)
T ss_pred CceEecCccCCee
Confidence 4567777777643
No 243
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=38.96 E-value=15 Score=25.29 Aligned_cols=12 Identities=25% Similarity=0.321 Sum_probs=5.5
Q ss_pred CCCCcCCccccc
Q 024455 67 LSKAHCSGIFSD 78 (267)
Q Consensus 67 ~~C~~C~k~f~~ 78 (267)
=.|..||..|..
T Consensus 59 a~CkkCGfef~~ 70 (97)
T COG3357 59 ARCKKCGFEFRD 70 (97)
T ss_pred hhhcccCccccc
Confidence 334444444444
No 244
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=38.79 E-value=13 Score=23.18 Aligned_cols=39 Identities=18% Similarity=0.502 Sum_probs=18.2
Q ss_pred Ccccccc--CccccCChHHHHHHHhHhcCCCCCC-Cccc----chhhcC
Q 024455 13 ARHKCVA--CYKQFKRKDHLIEHMKISYHSVHQP-KCAV----CQKLSK 54 (267)
Q Consensus 13 k~~~C~~--C~k~f~~~~~l~~H~~~~~H~~~~~-~C~~----C~~~f~ 54 (267)
.+-.|+. |...+. +..|..|... .-..++ .|.. |+..+.
T Consensus 8 ~~v~C~~~cc~~~i~-r~~l~~H~~~--~C~~~~v~C~~~~~GC~~~~~ 53 (60)
T PF02176_consen 8 RPVPCPNGCCNEMIP-RKELDDHLEN--ECPKRPVPCPYSPYGCKERVP 53 (60)
T ss_dssp SEEE-TT--S-BEEE-CCCHHHHHHT--TSTTSEEE-SS----S--EEE
T ss_pred CEeeCCCCCccccee-HHHHHHHHHc--cCCCCcEECCCCCCCCCCccc
Confidence 3456665 444344 4467777765 334444 6666 665543
No 245
>PF12773 DZR: Double zinc ribbon
Probab=38.64 E-value=22 Score=21.25 Aligned_cols=35 Identities=14% Similarity=0.174 Sum_probs=16.7
Q ss_pred CcccchhhcCCHHHHHhhcCCCCCCCcCCcccccc--cccccc
Q 024455 45 KCAVCQKLSKSFESLREHLTGPLSKAHCSGIFSDR--GCNLCM 85 (267)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~~~~~~C~~C~k~f~~~--~C~~C~ 85 (267)
.|+.||..+. .-......|+.|+...... .|+.||
T Consensus 14 fC~~CG~~l~------~~~~~~~~C~~Cg~~~~~~~~fC~~CG 50 (50)
T PF12773_consen 14 FCPHCGTPLP------PPDQSKKICPNCGAENPPNAKFCPNCG 50 (50)
T ss_pred CChhhcCChh------hccCCCCCCcCCcCCCcCCcCccCccc
Confidence 5666666554 0002234566666653322 155554
No 246
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=38.58 E-value=16 Score=23.07 Aligned_cols=8 Identities=25% Similarity=0.874 Sum_probs=4.4
Q ss_pred Ccccchhh
Q 024455 45 KCAVCQKL 52 (267)
Q Consensus 45 ~C~~C~~~ 52 (267)
.|+.||+.
T Consensus 27 ~CPnCG~~ 34 (59)
T PRK14890 27 LCPNCGEV 34 (59)
T ss_pred eCCCCCCe
Confidence 55556543
No 247
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=38.15 E-value=15 Score=26.63 Aligned_cols=20 Identities=25% Similarity=0.444 Sum_probs=10.7
Q ss_pred CCCCcCCcccccc----ccccccc
Q 024455 67 LSKAHCSGIFSDR----GCNLCMN 86 (267)
Q Consensus 67 ~~C~~C~k~f~~~----~C~~C~~ 86 (267)
..|..|+..|... .||.||.
T Consensus 71 ~~C~~Cg~~~~~~~~~~~CP~Cgs 94 (115)
T TIGR00100 71 CECEDCSEEVSPEIDLYRCPKCHG 94 (115)
T ss_pred EEcccCCCEEecCCcCccCcCCcC
Confidence 4466666555442 2666653
No 248
>PRK05580 primosome assembly protein PriA; Validated
Probab=38.02 E-value=10 Score=36.70 Aligned_cols=43 Identities=23% Similarity=0.350 Sum_probs=28.5
Q ss_pred CcccchhhcCC---HHHHHhhc-CCCCCCCcCCcccc-cccccccccc
Q 024455 45 KCAVCQKLSKS---FESLREHL-TGPLSKAHCSGIFS-DRGCNLCMNI 87 (267)
Q Consensus 45 ~C~~C~~~f~~---~~~l~~H~-~~~~~C~~C~k~f~-~~~C~~C~~~ 87 (267)
.|..||....- ...|..|. .+...|..||.... ...|+.||..
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 67777765532 23556665 45567999998765 3469999765
No 249
>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=38.01 E-value=26 Score=27.38 Aligned_cols=31 Identities=19% Similarity=0.275 Sum_probs=19.7
Q ss_pred cCCCHHHHHHHHHHHHhcCCCCCcccccCCCceEEEeccch
Q 024455 197 NAMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLE 237 (267)
Q Consensus 197 ~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~ 237 (267)
+.|.+++=.+.|.+.|.. .++++|||||++.
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 567777777777777631 1256899999964
No 250
>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=37.54 E-value=24 Score=28.81 Aligned_cols=29 Identities=24% Similarity=0.495 Sum_probs=21.6
Q ss_pred CCCccccccCccccCChHHHHHHHhHhcCC
Q 024455 11 STARHKCVACYKQFKRKDHLIEHMKISYHS 40 (267)
Q Consensus 11 ~~k~~~C~~C~k~f~~~~~l~~H~~~~~H~ 40 (267)
.+..|.|..|+|.|.-..-...|+..- |.
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~nK-H~ 102 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIFNK-HP 102 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHHHH--H
T ss_pred cCCEECCCCCCcccCChHHHHHHHhhc-CH
Confidence 456799999999999999999998762 54
No 251
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=37.41 E-value=26 Score=30.26 Aligned_cols=20 Identities=20% Similarity=0.464 Sum_probs=12.8
Q ss_pred CCCCcCCcccc--ccccccccc
Q 024455 67 LSKAHCSGIFS--DRGCNLCMN 86 (267)
Q Consensus 67 ~~C~~C~k~f~--~~~C~~C~~ 86 (267)
..|..|+..+. +.+|+.||.
T Consensus 213 L~CslC~teW~~~R~~C~~Cg~ 234 (309)
T PRK03564 213 LHCNLCESEWHVVRVKCSNCEQ 234 (309)
T ss_pred EEcCCCCCcccccCccCCCCCC
Confidence 44777766544 335888886
No 252
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=37.20 E-value=27 Score=34.94 Aligned_cols=46 Identities=20% Similarity=0.105 Sum_probs=31.3
Q ss_pred CHHHHHHHHHHHHhcCCCCCcccccCCCceEEEeccchhhhccccccC--CCCceecccc
Q 024455 200 PLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNY--PDHMLRDTAK 257 (267)
Q Consensus 200 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~Dl~~l~~~~--~~~~~~dt~~ 257 (267)
+...+.+.|.+++.+ .+...||||+.||+.+|.... ....+.||.+
T Consensus 362 ~~~~~~~~l~~~l~~------------~~~~~v~~n~K~d~~~l~~~gi~~~~~~~Dt~l 409 (887)
T TIGR00593 362 LTILTDDKFARWLLN------------EQIKKIGHDAKFLMHLLKREGIELGGVIFDTML 409 (887)
T ss_pred hhHHHHHHHHHHHhC------------CCCcEEEeeHHHHHHHHHhCCCCCCCcchhHHH
Confidence 455677778888853 445689999999999995321 1124567764
No 253
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=37.07 E-value=23 Score=31.86 Aligned_cols=39 Identities=18% Similarity=0.382 Sum_probs=26.0
Q ss_pred CCCCCccccccCccccCChHHHHHHHhHhcCCCC-CCCcccchhh
Q 024455 9 KRSTARHKCVACYKQFKRKDHLIEHMKISYHSVH-QPKCAVCQKL 52 (267)
Q Consensus 9 ~~~~k~~~C~~C~k~f~~~~~l~~H~~~~~H~~~-~~~C~~C~~~ 52 (267)
.+...-|.|+.|.++|+.-..+ +.. -... .+.|..|+.-
T Consensus 123 ~t~~~~Y~Cp~C~kkyt~Lea~---~L~--~~~~~~F~C~~C~ge 162 (436)
T KOG2593|consen 123 DTNVAGYVCPNCQKKYTSLEAL---QLL--DNETGEFHCENCGGE 162 (436)
T ss_pred ccccccccCCccccchhhhHHH---Hhh--cccCceEEEecCCCc
Confidence 3566789999999998865544 333 2222 2389999754
No 254
>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 COG0417 PolB DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair]
Probab=36.34 E-value=1.2e+02 Score=30.01 Aligned_cols=39 Identities=15% Similarity=0.344 Sum_probs=30.6
Q ss_pred hccCCCHHHHHHHHHHHHhcCCCCCcccccCCCceEEEeccch-hhhcccc
Q 024455 195 IKNAMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLE-HDLDSLR 244 (267)
Q Consensus 195 l~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~-~Dl~~l~ 244 (267)
+....+-.+++..+.+++.. . .-.|+||+|.. ||+.+|.
T Consensus 205 v~~~~~e~e~l~~~~~~i~~------~-----dPdVIvgyn~~~fd~pyl~ 244 (792)
T COG0417 205 VEVVISEAELLERFVELIRE------Y-----DPDVIVGYNGDNFDWPYLA 244 (792)
T ss_pred eEEecCHHHHHHHHHHHHHh------c-----CCCEEEeccCCcCChHHHH
Confidence 55567888999999999842 1 22499999997 9999994
No 256
>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=36.27 E-value=12 Score=36.62 Aligned_cols=27 Identities=15% Similarity=0.139 Sum_probs=0.0
Q ss_pred CCCCCCcCCcccccccccccccccCCh
Q 024455 65 GPLSKAHCSGIFSDRGCNLCMNIFDSP 91 (267)
Q Consensus 65 ~~~~C~~C~k~f~~~~C~~C~~~F~~~ 91 (267)
..|.|+.|+.......|+.|+......
T Consensus 679 ~~~~Cp~C~~~~~~~~C~~C~~~~~~~ 705 (900)
T PF03833_consen 679 PVYVCPDCGIEVEEDECPKCGRETTSY 705 (900)
T ss_dssp ---------------------------
T ss_pred cceeccccccccCccccccccccCccc
Confidence 356788888888777888888765543
No 257
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=36.26 E-value=22 Score=27.14 Aligned_cols=12 Identities=25% Similarity=0.476 Sum_probs=8.5
Q ss_pred ccccccccCChh
Q 024455 81 CNLCMNIFDSPS 92 (267)
Q Consensus 81 C~~C~~~F~~~~ 92 (267)
|+.||+.|.+..
T Consensus 31 C~~C~~RFTTfE 42 (156)
T COG1327 31 CLECGERFTTFE 42 (156)
T ss_pred ccccccccchhh
Confidence 777777777643
No 258
>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=35.80 E-value=27 Score=20.34 Aligned_cols=16 Identities=19% Similarity=0.310 Sum_probs=9.2
Q ss_pred CcccchhhcCCHHHHH
Q 024455 45 KCAVCQKLSKSFESLR 60 (267)
Q Consensus 45 ~C~~C~~~f~~~~~l~ 60 (267)
.|..||+.|.......
T Consensus 10 ~C~~C~rpf~WRKKW~ 25 (42)
T PF10013_consen 10 ICPVCGRPFTWRKKWA 25 (42)
T ss_pred cCcccCCcchHHHHHH
Confidence 5666666666554443
No 259
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=35.79 E-value=34 Score=26.56 Aligned_cols=19 Identities=26% Similarity=0.385 Sum_probs=14.8
Q ss_pred ccccccccCChhhHHHHHH
Q 024455 81 CNLCMNIFDSPSSLIKHKE 99 (267)
Q Consensus 81 C~~C~~~F~~~~~L~~H~~ 99 (267)
|+.||+.|..-++++.-.+
T Consensus 133 C~~CgkiYW~GsHw~~m~~ 151 (165)
T COG1656 133 CPKCGKIYWKGSHWRRMVE 151 (165)
T ss_pred CCCCcccccCchHHHHHHH
Confidence 8999999988887765443
No 260
>PF11288 DUF3089: Protein of unknown function (DUF3089); InterPro: IPR021440 This family of proteins has no known function.
Probab=35.59 E-value=54 Score=26.59 Aligned_cols=32 Identities=22% Similarity=0.354 Sum_probs=24.4
Q ss_pred CCHHHHHHHHHHHHhcCCCCCcccccCCCceEEEeccchh
Q 024455 199 MPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEH 238 (267)
Q Consensus 199 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~ 238 (267)
....+|...+..||.+.+. |..-||+||+-.-
T Consensus 75 ~ay~DV~~AF~~yL~~~n~--------GRPfILaGHSQGs 106 (207)
T PF11288_consen 75 LAYSDVRAAFDYYLANYNN--------GRPFILAGHSQGS 106 (207)
T ss_pred hhHHHHHHHHHHHHHhcCC--------CCCEEEEEeChHH
Confidence 5688999999999975322 3567999999643
No 261
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=35.57 E-value=25 Score=30.61 Aligned_cols=20 Identities=25% Similarity=0.587 Sum_probs=11.9
Q ss_pred ccccCccccCCh--HHHHHHHh
Q 024455 16 KCVACYKQFKRK--DHLIEHMK 35 (267)
Q Consensus 16 ~C~~C~k~f~~~--~~l~~H~~ 35 (267)
+|-.|.+.|.-. ..+..|+.
T Consensus 30 ~C~~C~e~f~~peq~~~l~Hl~ 51 (423)
T KOG2482|consen 30 KCLKCDEVFIFPEQKDCLAHLM 51 (423)
T ss_pred eeeehhhcccCcchHHHHHHHH
Confidence 488888776433 33556653
No 262
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=35.53 E-value=17 Score=28.98 Aligned_cols=20 Identities=10% Similarity=0.260 Sum_probs=11.8
Q ss_pred cccCCCCCccccccccccCC
Q 024455 172 TYVQPQLPVTNYRYEVTGLT 191 (267)
Q Consensus 172 ~~v~P~~~i~~~~~~~~GIt 191 (267)
.-+.|..--..+.+.+=|+-
T Consensus 96 ~~iePG~~s~G~ITtIEGvL 115 (201)
T COG1779 96 LEIEPGPASEGFITTIEGVL 115 (201)
T ss_pred eEeccccccCceEehHHHHH
Confidence 33556555556777777754
No 263
>TIGR01388 rnd ribonuclease D. This model describes ribonuclease D, a 3'-exonuclease shown to act on tRNA both in vitro and when overexpressed in vivo. Trusted members of this family are restricted to the Proteobacteria; Aquifex, Mycobacterial, and eukaryotic homologs are not full-length homologs. Ribonuclease D is not essential in E. coli and is deleterious when overexpressed. Its precise biological role is still unknown.
Probab=35.40 E-value=27 Score=30.98 Aligned_cols=31 Identities=26% Similarity=0.256 Sum_probs=22.5
Q ss_pred CceEEEeccchhhhccccc---cCCCCceeccccc
Q 024455 227 KARLLVGHGLEHDLDSLRM---NYPDHMLRDTAKY 258 (267)
Q Consensus 227 ~~~~lvgh~~~~Dl~~l~~---~~~~~~~~dt~~~ 258 (267)
.+.+.|+|++.+|+.+|.- ..| ..++||.+.
T Consensus 69 ~~i~KV~h~~k~Dl~~L~~~~~~~~-~~~fDtqlA 102 (367)
T TIGR01388 69 ESVVKVLHAASEDLEVFLNLFGELP-QPLFDTQIA 102 (367)
T ss_pred CCceEEEeecHHHHHHHHHHhCCCC-CCcccHHHH
Confidence 4457899999999999853 344 356898753
No 264
>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=35.26 E-value=30 Score=24.64 Aligned_cols=22 Identities=18% Similarity=0.362 Sum_probs=20.5
Q ss_pred ccc----ccCccccCChHHHHHHHhH
Q 024455 15 HKC----VACYKQFKRKDHLIEHMKI 36 (267)
Q Consensus 15 ~~C----~~C~k~f~~~~~l~~H~~~ 36 (267)
|.| ..|+....+...|..|.+.
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~ 106 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRK 106 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHH
Confidence 889 9999999999999999987
No 265
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=35.25 E-value=25 Score=21.96 Aligned_cols=22 Identities=14% Similarity=0.232 Sum_probs=15.4
Q ss_pred CCCcCCcccccccccccccccC
Q 024455 68 SKAHCSGIFSDRGCNLCMNIFD 89 (267)
Q Consensus 68 ~C~~C~k~f~~~~C~~C~~~F~ 89 (267)
.|+.||.-.....|+.||....
T Consensus 7 ~C~~CgvYTLk~~CP~CG~~t~ 28 (56)
T PRK13130 7 KCPKCGVYTLKEICPVCGGKTK 28 (56)
T ss_pred ECCCCCCEEccccCcCCCCCCC
Confidence 4777777666666888886543
No 266
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=34.93 E-value=25 Score=27.64 Aligned_cols=19 Identities=26% Similarity=0.492 Sum_probs=12.3
Q ss_pred CCCCccccccCccccCChH
Q 024455 10 RSTARHKCVACYKQFKRKD 28 (267)
Q Consensus 10 ~~~k~~~C~~C~k~f~~~~ 28 (267)
..+..|+|++|--.|..+.
T Consensus 127 ~~~~~~~CPiCl~~~sek~ 145 (187)
T KOG0320|consen 127 RKEGTYKCPICLDSVSEKV 145 (187)
T ss_pred ccccccCCCceecchhhcc
Confidence 3455688888876655443
No 267
>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=34.82 E-value=22 Score=25.41 Aligned_cols=23 Identities=13% Similarity=0.530 Sum_probs=12.9
Q ss_pred CCcCCccccccc-----ccccccccCCh
Q 024455 69 KAHCSGIFSDRG-----CNLCMNIFDSP 91 (267)
Q Consensus 69 C~~C~k~f~~~~-----C~~C~~~F~~~ 91 (267)
|+.|+..|.... |++|+..+...
T Consensus 5 CP~C~seytY~dg~~~iCpeC~~EW~~~ 32 (109)
T TIGR00686 5 CPKCNSEYTYHDGTQLICPSCLYEWNEN 32 (109)
T ss_pred CCcCCCcceEecCCeeECcccccccccc
Confidence 555555544432 77777666543
No 268
>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=34.77 E-value=11 Score=34.98 Aligned_cols=47 Identities=15% Similarity=0.278 Sum_probs=27.5
Q ss_pred ccccCccccCChHHHHHHHhHhcCCCCCC-CcccchhhcCCHHHHHhhcCCCCCCCcCCcc
Q 024455 16 KCVACYKQFKRKDHLIEHMKISYHSVHQP-KCAVCQKLSKSFESLREHLTGPLSKAHCSGI 75 (267)
Q Consensus 16 ~C~~C~k~f~~~~~l~~H~~~~~H~~~~~-~C~~C~~~f~~~~~l~~H~~~~~~C~~C~k~ 75 (267)
.|..||.......- ...+.. |..... .|..||... .-+..|+.|+..
T Consensus 215 ~C~~Cg~~~~C~~C-~~~l~~--h~~~~~l~Ch~Cg~~~----------~~~~~Cp~C~s~ 262 (505)
T TIGR00595 215 LCRSCGYILCCPNC-DVSLTY--HKKEGKLRCHYCGYQE----------PIPKTCPQCGSE 262 (505)
T ss_pred EhhhCcCccCCCCC-CCceEE--ecCCCeEEcCCCcCcC----------CCCCCCCCCCCC
Confidence 56666655443221 122333 554455 999999654 336789999874
No 269
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=34.65 E-value=10 Score=36.20 Aligned_cols=23 Identities=22% Similarity=0.307 Sum_probs=20.4
Q ss_pred ccccccccCChhhHHHHHHHhcC
Q 024455 81 CNLCMNIFDSPSSLIKHKEACSL 103 (267)
Q Consensus 81 C~~C~~~F~~~~~L~~H~~~h~~ 103 (267)
|.+|+|.|-.-..+..||++|..
T Consensus 795 CreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 795 CRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred hHHHHHHHHHHhhhhHHHHHHHH
Confidence 88999999988999999999953
No 270
>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=34.64 E-value=13 Score=30.30 Aligned_cols=26 Identities=27% Similarity=0.448 Sum_probs=19.2
Q ss_pred cccccccccCChhhHHHHHHHhcCCC
Q 024455 80 GCNLCMNIFDSPSSLIKHKEACSLSA 105 (267)
Q Consensus 80 ~C~~C~~~F~~~~~L~~H~~~h~~~~ 105 (267)
.|..|+|.|......++|+..-|.++
T Consensus 79 ~C~lc~KlFkg~eFV~KHI~nKH~e~ 104 (214)
T PF04959_consen 79 RCPLCGKLFKGPEFVRKHIFNKHPEK 104 (214)
T ss_dssp EE-SSS-EESSHHHHHHHHHHH-HHH
T ss_pred CCCCCCcccCChHHHHHHHhhcCHHH
Confidence 49999999999999999987655553
No 271
>KOG0969 consensus DNA polymerase delta, catalytic subunit [Replication, recombination and repair]
Probab=34.56 E-value=42 Score=32.71 Aligned_cols=61 Identities=13% Similarity=0.279 Sum_probs=37.7
Q ss_pred ccCCHHhhccCCCHHHHHHHHHHHHhcCCCCCcccccCCCceEEEeccc-hhhhccc----------------cccCCCC
Q 024455 188 TGLTEEDIKNAMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGL-EHDLDSL----------------RMNYPDH 250 (267)
Q Consensus 188 ~GIt~~~l~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~-~~Dl~~l----------------~~~~~~~ 250 (267)
.||.-.++-.-.+-+++++.-.+|+.. -+| .||+|+|+ .||+.-| ++...++
T Consensus 325 apI~G~~V~~~~~e~elL~~W~~fire------vDP-----DvI~GYNi~nFDiPYll~RA~~L~Ie~Fp~LGRikn~~s 393 (1066)
T KOG0969|consen 325 APIVGSNVHSYETEKELLESWRKFIRE------VDP-----DVIIGYNICNFDIPYLLNRAKTLGIENFPYLGRIKNSRS 393 (1066)
T ss_pred CCCCCceeEEeccHHHHHHHHHHHHHh------cCC-----CeEecccccccccceecChHhhcCcccccccceecccce
Confidence 344444444445667777777777731 112 39999998 6798766 2233466
Q ss_pred ceecccccc
Q 024455 251 MLRDTAKYR 259 (267)
Q Consensus 251 ~~~dt~~~~ 259 (267)
.|.||++-.
T Consensus 394 ~irDttfSS 402 (1066)
T KOG0969|consen 394 VIRDSTFSS 402 (1066)
T ss_pred eeeccccch
Confidence 777887543
No 272
>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=34.41 E-value=23 Score=26.89 Aligned_cols=12 Identities=25% Similarity=0.537 Sum_probs=8.4
Q ss_pred ccccccccCChh
Q 024455 81 CNLCMNIFDSPS 92 (267)
Q Consensus 81 C~~C~~~F~~~~ 92 (267)
|..||+.|.+..
T Consensus 31 C~~C~~RFTTyE 42 (147)
T TIGR00244 31 CLECHERFTTFE 42 (147)
T ss_pred CCccCCccceee
Confidence 777777777654
No 273
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=33.85 E-value=21 Score=26.59 Aligned_cols=18 Identities=33% Similarity=0.650 Sum_probs=11.3
Q ss_pred CCCCccccccCccccCCh
Q 024455 10 RSTARHKCVACYKQFKRK 27 (267)
Q Consensus 10 ~~~k~~~C~~C~k~f~~~ 27 (267)
.|...|+|..|+++|...
T Consensus 49 ~~~qRyrC~~C~~tf~~~ 66 (129)
T COG3677 49 RGHQRYKCKSCGSTFTVE 66 (129)
T ss_pred ccccccccCCcCcceeee
Confidence 345567777777766543
No 274
>PRK00420 hypothetical protein; Validated
Probab=33.85 E-value=23 Score=25.63 Aligned_cols=22 Identities=9% Similarity=0.218 Sum_probs=11.3
Q ss_pred CCCcCCccccc-c----cccccccccC
Q 024455 68 SKAHCSGIFSD-R----GCNLCMNIFD 89 (267)
Q Consensus 68 ~C~~C~k~f~~-~----~C~~C~~~F~ 89 (267)
.|+.||..+.. . .|+.||....
T Consensus 25 ~CP~Cg~pLf~lk~g~~~Cp~Cg~~~~ 51 (112)
T PRK00420 25 HCPVCGLPLFELKDGEVVCPVHGKVYI 51 (112)
T ss_pred CCCCCCCcceecCCCceECCCCCCeee
Confidence 45555554433 1 2777766443
No 275
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=33.58 E-value=14 Score=28.97 Aligned_cols=22 Identities=27% Similarity=0.525 Sum_probs=16.7
Q ss_pred CCCCCcCCcccc--cccccccccc
Q 024455 66 PLSKAHCSGIFS--DRGCNLCMNI 87 (267)
Q Consensus 66 ~~~C~~C~k~f~--~~~C~~C~~~ 87 (267)
.+.|..|.+.|. ...|+.||..
T Consensus 139 ~~rC~GC~~~f~~~~~~Cp~CG~~ 162 (177)
T COG1439 139 RLRCHGCKRIFPEPKDFCPICGSP 162 (177)
T ss_pred eEEEecCceecCCCCCcCCCCCCc
Confidence 456999999998 3349999864
No 276
>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=33.19 E-value=15 Score=32.27 Aligned_cols=12 Identities=17% Similarity=0.373 Sum_probs=4.6
Q ss_pred CcccchhhcCCH
Q 024455 45 KCAVCQKLSKSF 56 (267)
Q Consensus 45 ~C~~C~~~f~~~ 56 (267)
.|..|.+.....
T Consensus 254 ~C~~C~yt~~~~ 265 (344)
T PF09332_consen 254 TCKQCKYTAFKP 265 (344)
T ss_dssp EETTT--EESS-
T ss_pred EcCCCCCcccCc
Confidence 455555544443
No 277
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=33.19 E-value=21 Score=34.67 Aligned_cols=44 Identities=20% Similarity=0.320 Sum_probs=25.7
Q ss_pred ccccCccccCCh---HHHHHHHhHhcCCCCCC-CcccchhhcCCHHHHHhhcCCCCCCCcCCcc
Q 024455 16 KCVACYKQFKRK---DHLIEHMKISYHSVHQP-KCAVCQKLSKSFESLREHLTGPLSKAHCSGI 75 (267)
Q Consensus 16 ~C~~C~k~f~~~---~~l~~H~~~~~H~~~~~-~C~~C~~~f~~~~~l~~H~~~~~~C~~C~k~ 75 (267)
.|..||..+..+ ..|.. |..... .|..||..- ..|..|+.||..
T Consensus 437 ~C~~Cg~v~~Cp~Cd~~lt~------H~~~~~L~CH~Cg~~~----------~~p~~Cp~Cgs~ 484 (730)
T COG1198 437 LCRDCGYIAECPNCDSPLTL------HKATGQLRCHYCGYQE----------PIPQSCPECGSE 484 (730)
T ss_pred ecccCCCcccCCCCCcceEE------ecCCCeeEeCCCCCCC----------CCCCCCCCCCCC
Confidence 366666554432 22333 444455 999999542 447778877755
No 278
>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=33.06 E-value=24 Score=31.42 Aligned_cols=23 Identities=13% Similarity=0.232 Sum_probs=17.5
Q ss_pred CCCCcCCcccccc--cccccccccC
Q 024455 67 LSKAHCSGIFSDR--GCNLCMNIFD 89 (267)
Q Consensus 67 ~~C~~C~k~f~~~--~C~~C~~~F~ 89 (267)
|.|..||.....+ +|+.|+..=+
T Consensus 1 ~~c~~cg~~~~~~~g~cp~c~~w~~ 25 (372)
T cd01121 1 YVCSECGYVSPKWLGKCPECGEWNT 25 (372)
T ss_pred CCCCCCCCCCCCccEECcCCCCcee
Confidence 6788999888876 4999986533
No 279
>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=32.93 E-value=5.9 Score=38.41 Aligned_cols=13 Identities=31% Similarity=0.299 Sum_probs=7.6
Q ss_pred CHHHHHHHHHHHH
Q 024455 200 PLKEVKDKILEIL 212 (267)
Q Consensus 200 ~~~~v~~~~~~~~ 212 (267)
+.+++.++|...+
T Consensus 301 ~~~e~~~~l~~~~ 313 (711)
T TIGR00143 301 DNAEILDKLQGIA 313 (711)
T ss_pred CHHHHHHHhcCCc
Confidence 3566666665554
No 280
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=32.72 E-value=20 Score=26.20 Aligned_cols=10 Identities=30% Similarity=0.664 Sum_probs=4.6
Q ss_pred CCCcCCcccc
Q 024455 68 SKAHCSGIFS 77 (267)
Q Consensus 68 ~C~~C~k~f~ 77 (267)
.|..||..|.
T Consensus 73 ~C~~Cg~~~~ 82 (117)
T PRK00564 73 ECKDCSHVFK 82 (117)
T ss_pred EhhhCCCccc
Confidence 3444544443
No 281
>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=32.71 E-value=21 Score=30.77 Aligned_cols=41 Identities=20% Similarity=0.373 Sum_probs=21.7
Q ss_pred CcccchhhcCCHHHHHh---hc-CCCCCCCcCCccccc--cccccccc
Q 024455 45 KCAVCQKLSKSFESLRE---HL-TGPLSKAHCSGIFSD--RGCNLCMN 86 (267)
Q Consensus 45 ~C~~C~~~f~~~~~l~~---H~-~~~~~C~~C~k~f~~--~~C~~C~~ 86 (267)
.|++||..= ..+.+.. .. .+...|..|+..+.. .+|+.||.
T Consensus 186 ~CPvCGs~P-~~s~~~~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~ 232 (305)
T TIGR01562 186 LCPACGSPP-VASMVRQGGKETGLRYLSCSLCATEWHYVRVKCSHCEE 232 (305)
T ss_pred cCCCCCChh-hhhhhcccCCCCCceEEEcCCCCCcccccCccCCCCCC
Confidence 788887431 1122221 11 223457777765443 35888886
No 282
>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=32.49 E-value=33 Score=26.50 Aligned_cols=41 Identities=20% Similarity=0.202 Sum_probs=27.6
Q ss_pred HHHHHHHHHhcCCCCCcccccCCCceEEEeccchhhhcccc---ccCCCCceecccc
Q 024455 204 VKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLR---MNYPDHMLRDTAK 257 (267)
Q Consensus 204 v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~Dl~~l~---~~~~~~~~~dt~~ 257 (267)
+.+.+.+++.+ .+...|+||+.+|+.+|. +..+. .+.||.+
T Consensus 44 ~~~~l~~~l~~------------~~~~ki~~d~K~~~~~l~~~gi~~~~-~~fDt~l 87 (178)
T cd06140 44 DLAALKEWLED------------EKIPKVGHDAKRAYVALKRHGIELAG-VAFDTML 87 (178)
T ss_pred HHHHHHHHHhC------------CCCceeccchhHHHHHHHHCCCcCCC-cchhHHH
Confidence 44557777843 446799999999999994 33332 3467764
No 283
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=32.35 E-value=20 Score=24.26 Aligned_cols=7 Identities=43% Similarity=1.260 Sum_probs=3.7
Q ss_pred Ccccchh
Q 024455 45 KCAVCQK 51 (267)
Q Consensus 45 ~C~~C~~ 51 (267)
.|+.||+
T Consensus 38 ~CsfCGK 44 (92)
T KOG0402|consen 38 TCSFCGK 44 (92)
T ss_pred hhhhcch
Confidence 5555554
No 284
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=31.93 E-value=9.7 Score=36.44 Aligned_cols=35 Identities=17% Similarity=0.329 Sum_probs=18.6
Q ss_pred CcccchhhcCCHHHHHhhc----CCCCC-CCcCCcccccc
Q 024455 45 KCAVCQKLSKSFESLREHL----TGPLS-KAHCSGIFSDR 79 (267)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~----~~~~~-C~~C~k~f~~~ 79 (267)
.|..||-.|+--..|-.-. ...|+ |+.|.+.+...
T Consensus 125 ~CT~CGPRfTIi~alPYDR~nTsM~~F~lC~~C~~EY~dP 164 (750)
T COG0068 125 NCTNCGPRFTIIEALPYDRENTSMADFPLCPFCDKEYKDP 164 (750)
T ss_pred ccCCCCcceeeeccCCCCcccCccccCcCCHHHHHHhcCc
Confidence 6777776666544442222 23444 66666655554
No 285
>COG3545 Predicted esterase of the alpha/beta hydrolase fold [General function prediction only]
Probab=31.81 E-value=76 Score=25.08 Aligned_cols=30 Identities=23% Similarity=0.269 Sum_probs=19.7
Q ss_pred CCCHHHHHHHHHHHHhcCCCCCcccccCCCceEEEeccch
Q 024455 198 AMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLE 237 (267)
Q Consensus 198 ~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~ 237 (267)
+|.+++=..+|.+.+.-. . +.+|||||++.
T Consensus 40 ~P~~~dWi~~l~~~v~a~-~---------~~~vlVAHSLG 69 (181)
T COG3545 40 APVLDDWIARLEKEVNAA-E---------GPVVLVAHSLG 69 (181)
T ss_pred CCCHHHHHHHHHHHHhcc-C---------CCeEEEEeccc
Confidence 466777666676666321 1 45899999964
No 286
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=31.71 E-value=22 Score=25.81 Aligned_cols=20 Identities=15% Similarity=0.270 Sum_probs=10.9
Q ss_pred CCCCcCCcccccc-----ccccccc
Q 024455 67 LSKAHCSGIFSDR-----GCNLCMN 86 (267)
Q Consensus 67 ~~C~~C~k~f~~~-----~C~~C~~ 86 (267)
..|..|+..|... .||.||.
T Consensus 71 ~~C~~Cg~~~~~~~~~~~~CP~Cgs 95 (114)
T PRK03681 71 CWCETCQQYVTLLTQRVRRCPQCHG 95 (114)
T ss_pred EEcccCCCeeecCCccCCcCcCcCC
Confidence 4466666655432 2666663
No 287
>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=31.64 E-value=21 Score=19.16 Aligned_cols=10 Identities=30% Similarity=0.760 Sum_probs=1.8
Q ss_pred CcccchhhcC
Q 024455 45 KCAVCQKLSK 54 (267)
Q Consensus 45 ~C~~C~~~f~ 54 (267)
+|+.|+..+.
T Consensus 4 ~Cp~C~se~~ 13 (30)
T PF08274_consen 4 KCPLCGSEYT 13 (30)
T ss_dssp --TTT-----
T ss_pred CCCCCCCcce
Confidence 4555554443
No 288
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=31.52 E-value=21 Score=20.43 Aligned_cols=14 Identities=29% Similarity=0.522 Sum_probs=11.4
Q ss_pred ccccccCccccCCh
Q 024455 14 RHKCVACYKQFKRK 27 (267)
Q Consensus 14 ~~~C~~C~k~f~~~ 27 (267)
||+|..|++.|-.+
T Consensus 12 ~f~C~~C~~~FC~~ 25 (39)
T smart00154 12 GFKCRHCGNLFCGE 25 (39)
T ss_pred CeECCccCCccccc
Confidence 78899999888654
No 289
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=31.00 E-value=6.3 Score=23.56 Aligned_cols=10 Identities=20% Similarity=0.677 Sum_probs=5.0
Q ss_pred cccchhhcCC
Q 024455 46 CAVCQKLSKS 55 (267)
Q Consensus 46 C~~C~~~f~~ 55 (267)
|+.||....-
T Consensus 2 CP~Cg~~a~i 11 (47)
T PF04606_consen 2 CPHCGSKARI 11 (47)
T ss_pred cCCCCCeeEE
Confidence 5556554433
No 290
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=30.61 E-value=28 Score=30.72 Aligned_cols=51 Identities=29% Similarity=0.632 Sum_probs=43.9
Q ss_pred CCCccccccCccccCChHHHHHHHhHhcCCCCCC-Cccc--chhhcCCHHHHHhhc
Q 024455 11 STARHKCVACYKQFKRKDHLIEHMKISYHSVHQP-KCAV--CQKLSKSFESLREHL 63 (267)
Q Consensus 11 ~~k~~~C~~C~k~f~~~~~l~~H~~~~~H~~~~~-~C~~--C~~~f~~~~~l~~H~ 63 (267)
..+++.|+.|...|........|.+. |+++++ .|.. |...|.....+.+|.
T Consensus 30 ~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 83 (467)
T COG5048 30 APRPDSCPNCTDSFSRLEHLTRHIRS--HTGEKPSQCSYSGCDKSFSRPLELSRHL 83 (467)
T ss_pred CCchhhcccccccccccchhhhhccc--ccccCCccccccccccccCCcchhhhhc
Confidence 45678999999999999999999999 999998 8876 677788777777776
No 291
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=30.59 E-value=23 Score=26.71 Aligned_cols=18 Identities=17% Similarity=0.528 Sum_probs=9.3
Q ss_pred CCcCCccccccc--cccccc
Q 024455 69 KAHCSGIFSDRG--CNLCMN 86 (267)
Q Consensus 69 C~~C~k~f~~~~--C~~C~~ 86 (267)
|..||+.|--.. |+.|+.
T Consensus 32 C~~CG~v~~PPr~~Cp~C~~ 51 (140)
T COG1545 32 CKKCGRVYFPPRAYCPKCGS 51 (140)
T ss_pred cCCCCeEEcCCcccCCCCCC
Confidence 555555544332 666654
No 292
>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=30.54 E-value=25 Score=20.42 Aligned_cols=7 Identities=29% Similarity=0.747 Sum_probs=3.0
Q ss_pred ccccccc
Q 024455 81 CNLCMNI 87 (267)
Q Consensus 81 C~~C~~~ 87 (267)
|..||..
T Consensus 22 C~~CG~V 28 (43)
T PF08271_consen 22 CPNCGLV 28 (43)
T ss_dssp ETTT-BB
T ss_pred CCCCCCE
Confidence 5555543
No 293
>PRK11823 DNA repair protein RadA; Provisional
Probab=30.19 E-value=23 Score=32.43 Aligned_cols=23 Identities=13% Similarity=0.183 Sum_probs=16.2
Q ss_pred CCCCCcCCcccccc--ccccccccc
Q 024455 66 PLSKAHCSGIFSDR--GCNLCMNIF 88 (267)
Q Consensus 66 ~~~C~~C~k~f~~~--~C~~C~~~F 88 (267)
.|.|..||..+..+ .|+.|+..=
T Consensus 7 ~y~C~~Cg~~~~~~~g~Cp~C~~w~ 31 (446)
T PRK11823 7 AYVCQECGAESPKWLGRCPECGAWN 31 (446)
T ss_pred eEECCcCCCCCcccCeeCcCCCCcc
Confidence 47788888777765 388887543
No 294
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=30.04 E-value=47 Score=28.79 Aligned_cols=58 Identities=22% Similarity=0.440 Sum_probs=38.7
Q ss_pred C-CcccchhhcCCHHHHHhhc-----------------CCCCCCCcCCcccccc---cccccccccCChhhHHHHHHHh
Q 024455 44 P-KCAVCQKLSKSFESLREHL-----------------TGPLSKAHCSGIFSDR---GCNLCMNIFDSPSSLIKHKEAC 101 (267)
Q Consensus 44 ~-~C~~C~~~f~~~~~l~~H~-----------------~~~~~C~~C~k~f~~~---~C~~C~~~F~~~~~L~~H~~~h 101 (267)
| .|+.|+-..-...+|.+-. .+.-.|-.|+...... .|+.|...|-....--.|...|
T Consensus 290 P~eCpiC~ltLVss~hLARSyhhL~PL~~F~Eip~~~~~~~~~Cf~C~~~~~~~~~y~C~~Ck~~FCldCDv~iHesLh 368 (378)
T KOG2807|consen 290 PIECPICSLTLVSSPHLARSYHHLFPLKPFVEIPETEYNGSRFCFACQGELLSSGRYRCESCKNVFCLDCDVFIHESLH 368 (378)
T ss_pred CccCCccceeEecchHHHHHHHhhcCCcchhhccccccCCCcceeeeccccCCCCcEEchhccceeeccchHHHHhhhh
Confidence 5 8888988887777775543 1122277773333322 3899999998888877787666
No 295
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=29.69 E-value=43 Score=29.19 Aligned_cols=89 Identities=24% Similarity=0.337 Sum_probs=46.2
Q ss_pred ccccccCccccCChHHHHHHHhHhcCCCCCCCcccchhhcC------CHHHHHhhcC---------CCC---CCC--cCC
Q 024455 14 RHKCVACYKQFKRKDHLIEHMKISYHSVHQPKCAVCQKLSK------SFESLREHLT---------GPL---SKA--HCS 73 (267)
Q Consensus 14 ~~~C~~C~k~f~~~~~l~~H~~~~~H~~~~~~C~~C~~~f~------~~~~l~~H~~---------~~~---~C~--~C~ 73 (267)
.+.|-.|.+.|..+..|+.||+...|..-.|+-.+-.+.|- .++-..+|.. ++. -|+ .=+
T Consensus 195 r~~CLyCekifrdkntLkeHMrkK~HrrinPknreYDkfyiINY~ev~ks~t~~~~e~dret~~d~~E~D~~wsDw~ed~ 274 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRKKRHRRINPKNREYDKFYIINYLEVGKSWTIVHSEDDRETNEDINETDDTWSDWNEDD 274 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHhccCcccCCCccccceEEEEeHhhcCCccchhhhhhhhhhhccccccccchhhhhcCC
Confidence 46788888888888888888876445444442222222111 1111111110 000 000 000
Q ss_pred cccccccccccccccCChhhHHHHHHHhc
Q 024455 74 GIFSDRGCNLCMNIFDSPSSLIKHKEACS 102 (267)
Q Consensus 74 k~f~~~~C~~C~~~F~~~~~L~~H~~~h~ 102 (267)
..-.+..|-.|.+..-+...|..||++-|
T Consensus 275 a~a~~v~CLfC~~~~en~~~l~eHmk~vH 303 (423)
T KOG2482|consen 275 AEALSVVCLFCTNFYENPVFLFEHMKIVH 303 (423)
T ss_pred CCccceEEEeeccchhhHHHHHHHHHHHH
Confidence 00001139999998888999999998644
No 296
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=29.60 E-value=17 Score=31.06 Aligned_cols=21 Identities=29% Similarity=0.604 Sum_probs=14.4
Q ss_pred ccccccccCChhhHHHHHHHh
Q 024455 81 CNLCMNIFDSPSSLIKHKEAC 101 (267)
Q Consensus 81 C~~C~~~F~~~~~L~~H~~~h 101 (267)
|+.|...|-.....-.|...|
T Consensus 391 Ce~CK~~FC~dCdvfiHe~Lh 411 (421)
T COG5151 391 CELCKSTFCSDCDVFIHETLH 411 (421)
T ss_pred chhhhhhhhhhhHHHHHHHHh
Confidence 666766776666666777666
No 297
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=29.50 E-value=26 Score=33.73 Aligned_cols=12 Identities=17% Similarity=0.426 Sum_probs=5.4
Q ss_pred CCCCCcCCcccc
Q 024455 66 PLSKAHCSGIFS 77 (267)
Q Consensus 66 ~~~C~~C~k~f~ 77 (267)
..+||.|+..|.
T Consensus 678 qRKCP~Cn~aFg 689 (698)
T KOG0978|consen 678 QRKCPKCNAAFG 689 (698)
T ss_pred cCCCCCCCCCCC
Confidence 334444444444
No 298
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=29.31 E-value=41 Score=24.26 Aligned_cols=8 Identities=50% Similarity=1.107 Sum_probs=4.4
Q ss_pred cccccCcc
Q 024455 15 HKCVACYK 22 (267)
Q Consensus 15 ~~C~~C~k 22 (267)
.+|+.||.
T Consensus 75 ~kCpkCgh 82 (116)
T KOG2907|consen 75 HKCPKCGH 82 (116)
T ss_pred ccCcccCC
Confidence 45555553
No 299
>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=29.31 E-value=24 Score=32.33 Aligned_cols=24 Identities=17% Similarity=0.304 Sum_probs=17.6
Q ss_pred CCCCCcCCcccccc--cccccccccC
Q 024455 66 PLSKAHCSGIFSDR--GCNLCMNIFD 89 (267)
Q Consensus 66 ~~~C~~C~k~f~~~--~C~~C~~~F~ 89 (267)
.|.|..||..+..+ +|+.|+..=+
T Consensus 7 ~y~C~~Cg~~~~~~~g~Cp~C~~w~t 32 (454)
T TIGR00416 7 KFVCQHCGADSPKWQGKCPACHAWNT 32 (454)
T ss_pred eEECCcCCCCCccccEECcCCCCccc
Confidence 47788888887776 4888875543
No 300
>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=29.13 E-value=26 Score=19.47 Aligned_cols=11 Identities=36% Similarity=0.612 Sum_probs=4.9
Q ss_pred CcccchhhcCC
Q 024455 45 KCAVCQKLSKS 55 (267)
Q Consensus 45 ~C~~C~~~f~~ 55 (267)
.|.+||+.|..
T Consensus 5 ~C~eC~~~f~d 15 (34)
T PF01286_consen 5 KCDECGKPFMD 15 (34)
T ss_dssp E-TTT--EES-
T ss_pred hHhHhCCHHHH
Confidence 67777777754
No 301
>PRK10220 hypothetical protein; Provisional
Probab=28.83 E-value=34 Score=24.51 Aligned_cols=22 Identities=14% Similarity=0.545 Sum_probs=11.3
Q ss_pred CCcCCccccccc-----ccccccccCC
Q 024455 69 KAHCSGIFSDRG-----CNLCMNIFDS 90 (267)
Q Consensus 69 C~~C~k~f~~~~-----C~~C~~~F~~ 90 (267)
|+.|+..|.... |++|+.-+..
T Consensus 6 CP~C~seytY~d~~~~vCpeC~hEW~~ 32 (111)
T PRK10220 6 CPKCNSEYTYEDNGMYICPECAHEWND 32 (111)
T ss_pred CCCCCCcceEcCCCeEECCcccCcCCc
Confidence 555544444332 6667665543
No 302
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=28.78 E-value=26 Score=19.44 Aligned_cols=6 Identities=33% Similarity=0.794 Sum_probs=2.9
Q ss_pred cccccc
Q 024455 81 CNLCMN 86 (267)
Q Consensus 81 C~~C~~ 86 (267)
|+.||.
T Consensus 25 C~~Cg~ 30 (34)
T PF14803_consen 25 CPACGF 30 (34)
T ss_dssp ETTTTE
T ss_pred CCCCCC
Confidence 445544
No 303
>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=28.51 E-value=31 Score=19.33 Aligned_cols=7 Identities=14% Similarity=0.259 Sum_probs=3.3
Q ss_pred CCcCCcc
Q 024455 69 KAHCSGI 75 (267)
Q Consensus 69 C~~C~k~ 75 (267)
|.+|+..
T Consensus 11 C~~C~~~ 17 (36)
T PF11781_consen 11 CPVCGSR 17 (36)
T ss_pred CCCCCCe
Confidence 4444444
No 304
>PRK05978 hypothetical protein; Provisional
Probab=28.16 E-value=33 Score=26.20 Aligned_cols=9 Identities=33% Similarity=0.818 Sum_probs=4.8
Q ss_pred ccccccccC
Q 024455 81 CNLCMNIFD 89 (267)
Q Consensus 81 C~~C~~~F~ 89 (267)
|+.||..|.
T Consensus 55 C~~CG~~~~ 63 (148)
T PRK05978 55 CAACGEDFT 63 (148)
T ss_pred ccccCCccc
Confidence 555555543
No 305
>COG4640 Predicted membrane protein [Function unknown]
Probab=28.11 E-value=37 Score=30.21 Aligned_cols=28 Identities=25% Similarity=0.413 Sum_probs=16.5
Q ss_pred CCcCCcccc--cccccccccccCChhhHHH
Q 024455 69 KAHCSGIFS--DRGCNLCMNIFDSPSSLIK 96 (267)
Q Consensus 69 C~~C~k~f~--~~~C~~C~~~F~~~~~L~~ 96 (267)
|+.||+.=. ...|+.||..|...+.+.+
T Consensus 4 C~kcG~qk~Ed~~qC~qCG~~~t~~~sqan 33 (465)
T COG4640 4 CPKCGSQKAEDDVQCTQCGHKFTSRQSQAN 33 (465)
T ss_pred ccccccccccccccccccCCcCCchhhhhh
Confidence 666663211 1237888888877766554
No 306
>PF12907 zf-met2: Zinc-binding
Probab=27.87 E-value=45 Score=19.28 Aligned_cols=29 Identities=24% Similarity=0.402 Sum_probs=17.7
Q ss_pred cccccCccccC---ChHHHHHHHhHhcCCCCCC
Q 024455 15 HKCVACYKQFK---RKDHLIEHMKISYHSVHQP 44 (267)
Q Consensus 15 ~~C~~C~k~f~---~~~~l~~H~~~~~H~~~~~ 44 (267)
+.|.+|-.+|. ....|..|...- |....+
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enK-HpK~~~ 33 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENK-HPKNTF 33 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHcc-CCCCCH
Confidence 56888886553 445688886542 665433
No 307
>KOG0731 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]
Probab=27.80 E-value=32 Score=33.56 Aligned_cols=47 Identities=30% Similarity=0.269 Sum_probs=33.2
Q ss_pred cccCCHHhhccCCCHHHHHHHHHHHHhcCCCCCcccccCCCceEEEe
Q 024455 187 VTGLTEEDIKNAMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVG 233 (267)
Q Consensus 187 ~~GIt~~~l~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvg 233 (267)
-+||+..|+++.-..++-+.+|.+||.|-+.-...-...++|.+|+|
T Consensus 305 ~t~V~FkDVAG~deAK~El~E~V~fLKNP~~Y~~lGAKiPkGvLL~G 351 (774)
T KOG0731|consen 305 NTGVKFKDVAGVDEAKEELMEFVKFLKNPEQYQELGAKIPKGVLLVG 351 (774)
T ss_pred CCCCccccccCcHHHHHHHHHHHHHhcCHHHHHHcCCcCcCceEEEC
Confidence 35688888888877788888999999774443334444557777776
No 308
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=27.63 E-value=31 Score=20.97 Aligned_cols=26 Identities=19% Similarity=0.263 Sum_probs=13.5
Q ss_pred CcccchhhcCCHHHHHhhcCCCCCCCcCCccc
Q 024455 45 KCAVCQKLSKSFESLREHLTGPLSKAHCSGIF 76 (267)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~~~~~~C~~C~k~f 76 (267)
.|+.||..| |..| .+.+.|..||.++
T Consensus 22 fCP~Cg~~~-----m~~~-~~r~~C~~Cgyt~ 47 (50)
T PRK00432 22 FCPRCGSGF-----MAEH-LDRWHCGKCGYTE 47 (50)
T ss_pred cCcCCCcch-----hecc-CCcEECCCcCCEE
Confidence 677776422 3333 2455666666543
No 309
>PLN02965 Probable pheophorbidase
Probab=27.60 E-value=87 Score=25.64 Aligned_cols=32 Identities=16% Similarity=0.320 Sum_probs=21.3
Q ss_pred CCCHHHHHHHHHHHHhcCCCCCcccccCCCceEEEeccch
Q 024455 198 AMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLE 237 (267)
Q Consensus 198 ~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~ 237 (267)
..++++..+.|.++|+.-. .++..+||||+..
T Consensus 51 ~~~~~~~a~dl~~~l~~l~--------~~~~~~lvGhSmG 82 (255)
T PLN02965 51 VSSSDQYNRPLFALLSDLP--------PDHKVILVGHSIG 82 (255)
T ss_pred cCCHHHHHHHHHHHHHhcC--------CCCCEEEEecCcc
Confidence 3468888888888884210 0135799999964
No 310
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=27.41 E-value=30 Score=21.51 Aligned_cols=12 Identities=33% Similarity=0.897 Sum_probs=9.0
Q ss_pred ccccccccccCC
Q 024455 79 RGCNLCMNIFDS 90 (267)
Q Consensus 79 ~~C~~C~~~F~~ 90 (267)
.+|+.|++.|..
T Consensus 40 ngCPfC~~~~~~ 51 (55)
T PF14447_consen 40 NGCPFCGTPFEF 51 (55)
T ss_pred cCCCCCCCcccC
Confidence 359999988864
No 311
>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=27.37 E-value=22 Score=19.88 Aligned_cols=13 Identities=23% Similarity=0.289 Sum_probs=5.6
Q ss_pred cccchhhcCCHHH
Q 024455 46 CAVCQKLSKSFES 58 (267)
Q Consensus 46 C~~C~~~f~~~~~ 58 (267)
|+.|.+-+....+
T Consensus 2 C~~C~~Ey~~p~~ 14 (35)
T PF07503_consen 2 CDDCLKEYFDPSN 14 (35)
T ss_dssp -HHHHHHHCSTTS
T ss_pred CHHHHHHHcCCCC
Confidence 4555554444443
No 312
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=26.84 E-value=16 Score=22.41 Aligned_cols=24 Identities=21% Similarity=0.466 Sum_probs=11.3
Q ss_pred CccccccCccccCChHHHHHHHhH
Q 024455 13 ARHKCVACYKQFKRKDHLIEHMKI 36 (267)
Q Consensus 13 k~~~C~~C~k~f~~~~~l~~H~~~ 36 (267)
..|.|+.|.+.|-..-.+-.|...
T Consensus 20 ~~y~C~~C~~~FC~dCD~fiHE~L 43 (51)
T PF07975_consen 20 SRYRCPKCKNHFCIDCDVFIHETL 43 (51)
T ss_dssp EEE--TTTT--B-HHHHHTTTTTS
T ss_pred CeEECCCCCCccccCcChhhhccc
Confidence 457777777666665555555544
No 313
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=26.59 E-value=27 Score=31.48 Aligned_cols=62 Identities=23% Similarity=0.311 Sum_probs=36.4
Q ss_pred ccccCCHHhhccCCC----HHHHHHHHHHHHhcCCCCCcccccCCCceEEEeccchhhhccccccCCCC--ceecccccc
Q 024455 186 EVTGLTEEDIKNAMP----LKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSLRMNYPDH--MLRDTAKYR 259 (267)
Q Consensus 186 ~~~GIt~~~l~~~~~----~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~Dl~~l~~~~~~~--~~~dt~~~~ 259 (267)
.|-.+..+++..+|- ..++..+|.++... . +.-.+||||=-. |= .|.-||+ -+|||..||
T Consensus 176 SIQT~~s~~~~SapGsVsQVRe~t~~L~~~AK~-~---------~i~~fiVGHVTK-eG---~IAGPrvLEHmVDtVlyF 241 (456)
T COG1066 176 SIQTLYSEEITSAPGSVSQVREVAAELMRLAKT-K---------NIAIFIVGHVTK-EG---AIAGPRVLEHMVDTVLYF 241 (456)
T ss_pred ccceeecccccCCCCcHHHHHHHHHHHHHHHHH-c---------CCeEEEEEEEcc-cc---cccCchheeeeeeEEEEE
Confidence 344566777888873 55666677777632 1 134688898422 11 1444554 467888777
Q ss_pred cc
Q 024455 260 PL 261 (267)
Q Consensus 260 ~~ 261 (267)
.-
T Consensus 242 EG 243 (456)
T COG1066 242 EG 243 (456)
T ss_pred ec
Confidence 54
No 314
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=26.55 E-value=34 Score=20.50 Aligned_cols=6 Identities=33% Similarity=1.187 Sum_probs=3.1
Q ss_pred cccchh
Q 024455 46 CAVCQK 51 (267)
Q Consensus 46 C~~C~~ 51 (267)
|+.||.
T Consensus 3 Cp~Cg~ 8 (52)
T smart00661 3 CPKCGN 8 (52)
T ss_pred CCCCCC
Confidence 555554
No 315
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=26.52 E-value=29 Score=24.56 Aligned_cols=11 Identities=18% Similarity=0.298 Sum_probs=6.1
Q ss_pred cccccccccCC
Q 024455 80 GCNLCMNIFDS 90 (267)
Q Consensus 80 ~C~~C~~~F~~ 90 (267)
.|+.||..|..
T Consensus 44 ~C~~CG~y~~~ 54 (99)
T PRK14892 44 TCGNCGLYTEF 54 (99)
T ss_pred ECCCCCCccCE
Confidence 36666655443
No 316
>PF12096 DUF3572: Protein of unknown function (DUF3572); InterPro: IPR021955 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 100 amino acids in length.
Probab=26.50 E-value=55 Score=22.56 Aligned_cols=28 Identities=25% Similarity=0.395 Sum_probs=25.0
Q ss_pred ccccCCHHhhccCCCHHHHHHHHHHHHh
Q 024455 186 EVTGLTEEDIKNAMPLKEVKDKILEILN 213 (267)
Q Consensus 186 ~~~GIt~~~l~~~~~~~~v~~~~~~~~~ 213 (267)
..||+++++|..+..-++.+..+++||-
T Consensus 29 a~TG~~p~~LR~~a~dp~FL~~VLdFl~ 56 (88)
T PF12096_consen 29 ALTGLSPDDLRAAAGDPAFLAAVLDFLL 56 (88)
T ss_pred HHhCCCHHHHHHHccChHHHHHHHHHHH
Confidence 5699999999999888899999999984
No 317
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=26.45 E-value=27 Score=27.85 Aligned_cols=44 Identities=16% Similarity=0.082 Sum_probs=30.0
Q ss_pred CCCCCcCCcccccccccccccccCChhhHHHHHHHhcCCCCcccccc
Q 024455 66 PLSKAHCSGIFSDRGCNLCMNIFDSPSSLIKHKEACSLSAPVPFEKT 112 (267)
Q Consensus 66 ~~~C~~C~k~f~~~~C~~C~~~F~~~~~L~~H~~~h~~~~~~~C~~~ 112 (267)
||.|..|-+.|.+.--..||..|-.....+. ...+.+.+.|++.
T Consensus 196 PF~C~iCKkdy~spvvt~CGH~FC~~Cai~~---y~kg~~C~~Cgk~ 239 (259)
T COG5152 196 PFLCGICKKDYESPVVTECGHSFCSLCAIRK---YQKGDECGVCGKA 239 (259)
T ss_pred ceeehhchhhccchhhhhcchhHHHHHHHHH---hccCCcceecchh
Confidence 7889999999998877788888866554432 2334455556644
No 318
>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=26.43 E-value=46 Score=24.59 Aligned_cols=31 Identities=26% Similarity=0.169 Sum_probs=21.0
Q ss_pred CceEEEeccchhhhccccc---cCCCCceeccccc
Q 024455 227 KARLLVGHGLEHDLDSLRM---NYPDHMLRDTAKY 258 (267)
Q Consensus 227 ~~~~lvgh~~~~Dl~~l~~---~~~~~~~~dt~~~ 258 (267)
.+...||||+..|+.+|.. ..+ ..+.||.+.
T Consensus 52 ~~~~kv~~d~K~~~~~L~~~~~~~~-~~~~D~~la 85 (150)
T cd09018 52 EKALKVGQNLKYDRGILLNYFIELR-GIAFDTMLE 85 (150)
T ss_pred CCCceeeecHHHHHHHHHHcCCccC-CcchhHHHH
Confidence 4467899999999999842 222 234677643
No 319
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=26.41 E-value=31 Score=25.70 Aligned_cols=23 Identities=13% Similarity=0.150 Sum_probs=12.0
Q ss_pred CCCCcCCcccccc----cccccccccC
Q 024455 67 LSKAHCSGIFSDR----GCNLCMNIFD 89 (267)
Q Consensus 67 ~~C~~C~k~f~~~----~C~~C~~~F~ 89 (267)
+.|+.||--.-.+ .|+.|++.+.
T Consensus 29 ~hCp~Cg~PLF~KdG~v~CPvC~~~~~ 55 (131)
T COG1645 29 KHCPKCGTPLFRKDGEVFCPVCGYREV 55 (131)
T ss_pred hhCcccCCcceeeCCeEECCCCCceEE
Confidence 3466665543222 2777775443
No 320
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=26.37 E-value=31 Score=27.78 Aligned_cols=47 Identities=23% Similarity=0.431 Sum_probs=37.9
Q ss_pred ccccCccccCChHHHHHHHhHhcCC--------CCCC--Ccc--cchhhcCCHHHHHhhc
Q 024455 16 KCVACYKQFKRKDHLIEHMKISYHS--------VHQP--KCA--VCQKLSKSFESLREHL 63 (267)
Q Consensus 16 ~C~~C~k~f~~~~~l~~H~~~~~H~--------~~~~--~C~--~C~~~f~~~~~l~~H~ 63 (267)
.|..|.+.|.+...|..|+... |. ...+ .|- .|+..|.+...-+.|+
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 7999999999999999998542 42 1133 774 4999999999999998
No 321
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=26.37 E-value=45 Score=19.76 Aligned_cols=33 Identities=18% Similarity=0.084 Sum_probs=18.0
Q ss_pred CCcCCcccccccccccccccCChhhHHHHHHHhc
Q 024455 69 KAHCSGIFSDRGCNLCMNIFDSPSSLIKHKEACS 102 (267)
Q Consensus 69 C~~C~k~f~~~~C~~C~~~F~~~~~L~~H~~~h~ 102 (267)
|..|+..-..+.|-.|+..+...... .|...|.
T Consensus 2 C~~C~~~~~l~~CL~C~~~~c~~~~~-~h~~~H~ 34 (50)
T smart00290 2 CSVCGTIENLWLCLTCGQVGCGRYQL-GHALEHF 34 (50)
T ss_pred cccCCCcCCeEEecCCCCcccCCCCC-cHHHHHh
Confidence 55666544444577777666544321 3565664
No 322
>smart00878 Biotin_carb_C Biotin carboxylase C-terminal domain. Biotin carboxylase is a component of the acetyl-CoA carboxylase multi-component enzyme which catalyses the first committed step in fatty acid synthesis in animals, plants and bacteria. Most of the active site residues reported in reference are in this C-terminal domain.
Probab=25.61 E-value=2.5e+02 Score=19.98 Aligned_cols=54 Identities=19% Similarity=0.199 Sum_probs=35.9
Q ss_pred eeEecccCCCCCccccccccccCCHHhh----ccCCCHHHHHHHHHHHHhcCCCCCcccccCCCceEEEeccchhhhccc
Q 024455 168 VIFHTYVQPQLPVTNYRYEVTGLTEEDI----KNAMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLEHDLDSL 243 (267)
Q Consensus 168 ~~~~~~v~P~~~i~~~~~~~~GIt~~~l----~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~~Dl~~l 243 (267)
+.+|+.+.+...|+.+ -+.+| .-+++.+++++.+...| .+..|.| +.-.+.||
T Consensus 31 vR~Dt~~~~G~~v~~~-------yDsmlAKliv~g~~R~~A~~rl~~aL--------------~e~~i~G--v~TN~~~l 87 (107)
T smart00878 31 VRVDSGVYEGYEVPPY-------YDSMIAKLIVHGETREEAIARLRRAL--------------DEFRIEG--VKTNIPFL 87 (107)
T ss_pred EEEEccCcCCCCcCcc-------hhhhceEEEEEcCCHHHHHHHHHHHH--------------HhCEEEC--ccCCHHHH
Confidence 5677777766555433 22333 23678999999999999 6778888 44444444
Q ss_pred c
Q 024455 244 R 244 (267)
Q Consensus 244 ~ 244 (267)
.
T Consensus 88 ~ 88 (107)
T smart00878 88 R 88 (107)
T ss_pred H
Confidence 3
No 323
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=25.59 E-value=27 Score=29.84 Aligned_cols=10 Identities=30% Similarity=0.763 Sum_probs=6.9
Q ss_pred CcccchhhcC
Q 024455 45 KCAVCQKLSK 54 (267)
Q Consensus 45 ~C~~C~~~f~ 54 (267)
+|+.|+....
T Consensus 28 ~c~~c~~~~~ 37 (285)
T TIGR00515 28 KCPKCGQVLY 37 (285)
T ss_pred ECCCCcchhh
Confidence 7888876553
No 324
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=25.28 E-value=28 Score=29.88 Aligned_cols=11 Identities=18% Similarity=0.507 Sum_probs=6.2
Q ss_pred ccccccccCCh
Q 024455 81 CNLCMNIFDSP 91 (267)
Q Consensus 81 C~~C~~~F~~~ 91 (267)
|+.|+..|.-.
T Consensus 60 cp~c~~h~rlt 70 (296)
T CHL00174 60 CEQCGYHLKMS 70 (296)
T ss_pred CCCCCCCcCCC
Confidence 55666655543
No 325
>KOG4317 consensus Predicted Zn-finger protein [Function unknown]
Probab=24.96 E-value=20 Score=30.69 Aligned_cols=15 Identities=13% Similarity=0.541 Sum_probs=8.6
Q ss_pred CCCCcCCcccccccc
Q 024455 67 LSKAHCSGIFSDRGC 81 (267)
Q Consensus 67 ~~C~~C~k~f~~~~C 81 (267)
|.|+.|+-.+-+-.|
T Consensus 20 YtCPRCn~~YCsl~C 34 (383)
T KOG4317|consen 20 YTCPRCNLLYCSLKC 34 (383)
T ss_pred ccCCCCCccceeeee
Confidence 666666655554443
No 326
>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=24.95 E-value=24 Score=20.54 Aligned_cols=15 Identities=40% Similarity=0.580 Sum_probs=9.2
Q ss_pred CccccccCccccCCh
Q 024455 13 ARHKCVACYKQFKRK 27 (267)
Q Consensus 13 k~~~C~~C~k~f~~~ 27 (267)
-|+.|+.|++.|-.+
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 578898898887653
No 327
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=24.43 E-value=39 Score=30.44 Aligned_cols=31 Identities=19% Similarity=0.332 Sum_probs=16.4
Q ss_pred CCCcccchhhcCCHHHHHhhcCCCCCCCcCCcccccc
Q 024455 43 QPKCAVCQKLSKSFESLREHLTGPLSKAHCSGIFSDR 79 (267)
Q Consensus 43 ~~~C~~C~~~f~~~~~l~~H~~~~~~C~~C~k~f~~~ 79 (267)
+|.|+.||....+.. .+-|.|+.||+.+...
T Consensus 350 ~p~Cp~Cg~~m~S~G------~~g~rC~kCg~~~~~~ 380 (421)
T COG1571 350 NPVCPRCGGRMKSAG------RNGFRCKKCGTRARET 380 (421)
T ss_pred CCCCCccCCchhhcC------CCCcccccccccCCcc
Confidence 346666665443322 1256666666666543
No 328
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=24.34 E-value=48 Score=26.43 Aligned_cols=14 Identities=29% Similarity=0.601 Sum_probs=6.9
Q ss_pred CccccccccccCCH
Q 024455 179 PVTNYRYEVTGLTE 192 (267)
Q Consensus 179 ~i~~~~~~~~GIt~ 192 (267)
++.++..++.+|..
T Consensus 153 ~vg~~~Frv~~IK~ 166 (201)
T COG1326 153 EVGGYRFRVEKIKT 166 (201)
T ss_pred EECCEEEEEEEEEe
Confidence 34445555555543
No 329
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=24.22 E-value=79 Score=28.04 Aligned_cols=74 Identities=20% Similarity=0.213 Sum_probs=39.6
Q ss_pred CccccccCccccCChHHHHHHHhHhcCCCCCCCcccchhhcCCHHHHHhhc----CCCCCCCcCCccccccccccccccc
Q 024455 13 ARHKCVACYKQFKRKDHLIEHMKISYHSVHQPKCAVCQKLSKSFESLREHL----TGPLSKAHCSGIFSDRGCNLCMNIF 88 (267)
Q Consensus 13 k~~~C~~C~k~f~~~~~l~~H~~~~~H~~~~~~C~~C~~~f~~~~~l~~H~----~~~~~C~~C~k~f~~~~C~~C~~~F 88 (267)
-|-.|-.|++.+.+-..-..||..+ |.--.|.=+. ......|-..+ ...|.|-. |+.=++.|
T Consensus 165 ~Pt~CLfC~~~~k~~e~~~~HM~~~-HgffIPdreY----L~D~~GLl~YLgeKV~~~~~CL~---------CN~~~~~f 230 (390)
T KOG2785|consen 165 IPTDCLFCDKKSKSLEENLKHMFKE-HGFFIPDREY----LTDEKGLLKYLGEKVGIGFICLF---------CNELGRPF 230 (390)
T ss_pred CCcceeecCCCcccHHHHHHHHhhc-cCCcCCchHh----hhchhHHHHHHHHHhccCceEEE---------eccccCcc
Confidence 3466777777777777777777662 3322221111 11222232222 22333321 33333899
Q ss_pred CChhhHHHHHHH
Q 024455 89 DSPSSLIKHKEA 100 (267)
Q Consensus 89 ~~~~~L~~H~~~ 100 (267)
.+....+.||+.
T Consensus 231 ~sleavr~HM~~ 242 (390)
T KOG2785|consen 231 SSLEAVRAHMRD 242 (390)
T ss_pred cccHHHHHHHhh
Confidence 999999999864
No 330
>PRK07218 replication factor A; Provisional
Probab=24.19 E-value=37 Score=30.78 Aligned_cols=48 Identities=31% Similarity=0.270 Sum_probs=28.0
Q ss_pred ccccccCCHHhhcc----CCCHHHHHHHHHHHHhcCCCCCcccccCCCceEEEeccc---hhhhcccc
Q 024455 184 RYEVTGLTEEDIKN----AMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGL---EHDLDSLR 244 (267)
Q Consensus 184 ~~~~~GIt~~~l~~----~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~---~~Dl~~l~ 244 (267)
.-.+.|++.+++.. +.....++.+|.+.|- |..-.+-| |+ .|++.|+-
T Consensus 346 ~e~l~G~~~e~a~~~~~~~~d~~~v~~~i~~~ll------------G~~~~v~G-~~~~~~~g~~~~a 400 (423)
T PRK07218 346 TEIVYGGTLEDAEELAREAMDKDVVAEDIRERLV------------GREYRVRG-NLSVDEYGANLVA 400 (423)
T ss_pred hHhHhCCCHHHHHHHHHhhhcchhhHHHHHHhhc------------CcEEEEEe-ccccccCCcEEEE
Confidence 45788888886543 3445556677766441 14456677 45 35555553
No 331
>TIGR00354 polC DNA polymerase, archaeal type II, large subunit. This model represents the large subunit, DP2, of a two subunit novel Archaeal replicative DNA polymerase first characterized for Pyrococcus furiosus. Structure of DP2 appears to be organized 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.
Probab=24.04 E-value=86 Score=31.48 Aligned_cols=108 Identities=12% Similarity=0.089 Sum_probs=0.0
Q ss_pred CCCCcCCcccccccccccccccCChhhHHHHHHHhcCCCCccccccCcchhhhhhhccccccccccCCCceeeeeccccC
Q 024455 67 LSKAHCSGIFSDRGCNLCMNIFDSPSSLIKHKEACSLSAPVPFEKTLSNAESQKKISGAIDEKRTCRGPKAVAMDCEMVG 146 (267)
Q Consensus 67 ~~C~~C~k~f~~~~C~~C~~~F~~~~~L~~H~~~h~~~~~~~C~~~f~~~~~l~~H~~~~~~~r~~~~~~~~~~dcE~~g 146 (267)
+.|+.||.--....|+.||.. -+..+.|.+.......+..-...........-..+.. ++.
T Consensus 626 RKCPkCG~yTlk~rCP~CG~~---------------Te~~~pc~~~i~l~~~~~~A~~~lg~~~~~~~KGVkg----l~S 686 (1095)
T TIGR00354 626 RKCPQCGKESFWLKCPVCGEL---------------TEQLYYGKRKVDLRELYEEAIANLGEYKFDTIKGVKG----MTS 686 (1095)
T ss_pred EECCCCCcccccccCCCCCCc---------------cccccceeEEecHHHHHHHHHHHhCCCCcccccccee----ccc
Q ss_pred CcCCCCccceeeEEEecC-----CCCeeEecccCCCCCccccccccccCCHHhhc
Q 024455 147 GGSNGTLDLCARVCLVDE-----DENVIFHTYVQPQLPVTNYRYEVTGLTEEDIK 196 (267)
Q Consensus 147 ~~~~~~~~~i~~v~vvd~-----~~~~~~~~~v~P~~~i~~~~~~~~GIt~~~l~ 196 (267)
.....+..+-+.++..++ +|.+.||.- +.|++.++-+..|+|.+.|.
T Consensus 687 ~~k~pEPlEKGILRAk~~v~vFKDGTiRfD~t---D~PlTHfrp~Eigvsveklr 738 (1095)
T TIGR00354 687 KTKIPEPLEKGILRAKNGVYVFKDGTARFDAT---DLPITHFKPAEIGVSVEKLR 738 (1095)
T ss_pred CCCCCcchHhhhhhhhcCeeEecCCceeccCc---CCCcccccHHHcCCCHHHHH
No 332
>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=23.81 E-value=75 Score=30.42 Aligned_cols=70 Identities=19% Similarity=0.253 Sum_probs=39.1
Q ss_pred EecccCCCCCccccccccccCCHHhhccCC-CHHHHHHHHHH-HHhcCCCCCcccccCCCceEEEe-ccchhhhcccccc
Q 024455 170 FHTYVQPQLPVTNYRYEVTGLTEEDIKNAM-PLKEVKDKILE-ILNNGESTGRLMLDDGKARLLVG-HGLEHDLDSLRMN 246 (267)
Q Consensus 170 ~~~~v~P~~~i~~~~~~~~GIt~~~l~~~~-~~~~v~~~~~~-~~~~~~~~~~~~~~~~~~~~lvg-h~~~~Dl~~l~~~ 246 (267)
++..+.|..+.+-.++...|.+.-+..... -+.+.+..|.+ +..|. .-.+||| |+-=||+..|+-.
T Consensus 226 v~a~it~~gp~iymIstyPG~~F~nf~s~~~li~~FL~Wl~e~~~~n~-----------~ti~LvGy~ss~FD~pLLra~ 294 (651)
T PF03337_consen 226 VNAIITPNGPSIYMISTYPGKCFINFDSNKALISDFLKWLRECIMKNI-----------RTIILVGYFSSFFDFPLLRAY 294 (651)
T ss_pred EEEEecCCCceeEEEEecCCceEEeCCCchHHHHHHHHHHHHHHhccC-----------ceEEEeehhhhhhccHHHHhh
Confidence 445555655655555555666543333332 33444444444 22221 3468999 6667899999877
Q ss_pred CCCC
Q 024455 247 YPDH 250 (267)
Q Consensus 247 ~~~~ 250 (267)
+|+.
T Consensus 295 wp~~ 298 (651)
T PF03337_consen 295 WPKN 298 (651)
T ss_pred cccC
Confidence 7643
No 333
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=23.32 E-value=39 Score=25.20 Aligned_cols=11 Identities=27% Similarity=0.921 Sum_probs=7.6
Q ss_pred CcccchhhcCC
Q 024455 45 KCAVCQKLSKS 55 (267)
Q Consensus 45 ~C~~C~~~f~~ 55 (267)
+|.+|...+..
T Consensus 82 eCnIC~etS~e 92 (140)
T PF05290_consen 82 ECNICKETSAE 92 (140)
T ss_pred eccCcccccch
Confidence 88888766544
No 334
>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=23.26 E-value=17 Score=35.39 Aligned_cols=12 Identities=17% Similarity=0.401 Sum_probs=6.2
Q ss_pred CcccchhhcCCH
Q 024455 45 KCAVCQKLSKSF 56 (267)
Q Consensus 45 ~C~~C~~~f~~~ 56 (267)
.|..||-.|+-.
T Consensus 92 nCt~CGPr~~i~ 103 (711)
T TIGR00143 92 SCTHCGPRFTII 103 (711)
T ss_pred cccCCCCCeEEe
Confidence 555555555443
No 335
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.16 E-value=30 Score=28.35 Aligned_cols=13 Identities=38% Similarity=0.687 Sum_probs=8.7
Q ss_pred CcccchhhcCCHH
Q 024455 45 KCAVCQKLSKSFE 57 (267)
Q Consensus 45 ~C~~C~~~f~~~~ 57 (267)
.|++|+-.|....
T Consensus 21 eCPvC~tkFkkee 33 (267)
T COG1655 21 ECPVCNTKFKKEE 33 (267)
T ss_pred ccCcccchhhhhh
Confidence 7777777775543
No 336
>PRK11032 hypothetical protein; Provisional
Probab=23.00 E-value=25 Score=27.20 Aligned_cols=7 Identities=29% Similarity=0.662 Sum_probs=4.3
Q ss_pred ccccccc
Q 024455 81 CNLCMNI 87 (267)
Q Consensus 81 C~~C~~~ 87 (267)
|+.||..
T Consensus 145 Cp~C~~~ 151 (160)
T PRK11032 145 CPKCGHD 151 (160)
T ss_pred CCCCCCC
Confidence 6666654
No 337
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=22.91 E-value=46 Score=30.32 Aligned_cols=19 Identities=32% Similarity=0.697 Sum_probs=16.7
Q ss_pred ccccccccCChhhHHHHHH
Q 024455 81 CNLCMNIFDSPSSLIKHKE 99 (267)
Q Consensus 81 C~~C~~~F~~~~~L~~H~~ 99 (267)
|..|+|+|.+.-.|.+|..
T Consensus 295 C~vCnKsFKseKq~kNHEn 313 (508)
T KOG0717|consen 295 CVVCNKSFKSEKQLKNHEN 313 (508)
T ss_pred EeeccccccchHHHHhhHH
Confidence 8999999999999999864
No 338
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=22.84 E-value=36 Score=20.66 Aligned_cols=39 Identities=15% Similarity=0.352 Sum_probs=19.9
Q ss_pred CCccccccCccccCChHHHHHHHhHhcCCCCCC-Ccccchh
Q 024455 12 TARHKCVACYKQFKRKDHLIEHMKISYHSVHQP-KCAVCQK 51 (267)
Q Consensus 12 ~k~~~C~~C~k~f~~~~~l~~H~~~~~H~~~~~-~C~~C~~ 51 (267)
++.+.|..||..|.....=+.....- --...| .|..|-+
T Consensus 2 Dk~l~C~dCg~~FvfTa~EQ~fy~eK-gf~n~p~RC~~CR~ 41 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVFTAGEQKFYAEK-GFDNEPKRCPSCRQ 41 (49)
T ss_pred CeeEEcccCCCeEEEehhHHHHHHhc-CCcCCCccCHHHHH
Confidence 46677888887766544433322210 111234 6776643
No 339
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=22.65 E-value=54 Score=28.66 Aligned_cols=41 Identities=15% Similarity=0.074 Sum_probs=28.9
Q ss_pred CCCCCCCcCCcccccccccccccccCChhhHHHHHHHhcCCCCc
Q 024455 64 TGPLSKAHCSGIFSDRGCNLCMNIFDSPSSLIKHKEACSLSAPV 107 (267)
Q Consensus 64 ~~~~~C~~C~k~f~~~~C~~C~~~F~~~~~L~~H~~~h~~~~~~ 107 (267)
.|.+.|..+...|. |+.|++.=.+...|..|...-|.+.++
T Consensus 68 ~Ge~i~~y~~qSft---CPyC~~~Gfte~~f~~Hv~s~Hpda~~ 108 (381)
T KOG1280|consen 68 GGEPISHYDPQSFT---CPYCGIMGFTERQFGTHVLSQHPEAST 108 (381)
T ss_pred cCcccccccccccc---CCcccccccchhHHHHHhhhcCcccCc
Confidence 45555555665454 899998888888888998766666554
No 340
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=22.60 E-value=40 Score=21.48 Aligned_cols=19 Identities=26% Similarity=0.649 Sum_probs=13.7
Q ss_pred CCCcCCccccccccccccc
Q 024455 68 SKAHCSGIFSDRGCNLCMN 86 (267)
Q Consensus 68 ~C~~C~k~f~~~~C~~C~~ 86 (267)
.|..|........|+.||.
T Consensus 5 AC~~C~~i~~~~~CP~Cgs 23 (61)
T PRK08351 5 ACRHCHYITTEDRCPVCGS 23 (61)
T ss_pred hhhhCCcccCCCcCCCCcC
Confidence 5777777766666888875
No 341
>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=22.46 E-value=37 Score=22.96 Aligned_cols=11 Identities=27% Similarity=0.893 Sum_probs=6.2
Q ss_pred ccccccccCCh
Q 024455 81 CNLCMNIFDSP 91 (267)
Q Consensus 81 C~~C~~~F~~~ 91 (267)
|..||..|...
T Consensus 49 C~~Cg~~~~~~ 59 (81)
T PF05129_consen 49 CRVCGESFQTK 59 (81)
T ss_dssp ESSS--EEEEE
T ss_pred ecCCCCeEEEc
Confidence 88888777543
No 342
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=22.46 E-value=32 Score=29.56 Aligned_cols=10 Identities=30% Similarity=0.786 Sum_probs=7.0
Q ss_pred CcccchhhcC
Q 024455 45 KCAVCQKLSK 54 (267)
Q Consensus 45 ~C~~C~~~f~ 54 (267)
+|+.|+...-
T Consensus 29 ~c~~c~~~~~ 38 (292)
T PRK05654 29 KCPSCGQVLY 38 (292)
T ss_pred ECCCccchhh
Confidence 7888876553
No 343
>PLN02211 methyl indole-3-acetate methyltransferase
Probab=22.13 E-value=1.3e+02 Score=25.19 Aligned_cols=31 Identities=19% Similarity=0.415 Sum_probs=21.5
Q ss_pred CCHHHHHHHHHHHHhcCCCCCcccccCCCceEEEeccch
Q 024455 199 MPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLE 237 (267)
Q Consensus 199 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~ 237 (267)
.++++..+.+.++|.... .++..+||||+..
T Consensus 67 ~~~~~~~~~l~~~i~~l~--------~~~~v~lvGhS~G 97 (273)
T PLN02211 67 TTFDEYNKPLIDFLSSLP--------ENEKVILVGHSAG 97 (273)
T ss_pred CCHHHHHHHHHHHHHhcC--------CCCCEEEEEECch
Confidence 578888888888884210 0145799999954
No 344
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=22.08 E-value=16 Score=25.54 Aligned_cols=9 Identities=22% Similarity=0.711 Sum_probs=3.8
Q ss_pred Ccccchhhc
Q 024455 45 KCAVCQKLS 53 (267)
Q Consensus 45 ~C~~C~~~f 53 (267)
.|..|++.|
T Consensus 23 ~C~tCpY~~ 31 (105)
T KOG2906|consen 23 SCRTCPYVF 31 (105)
T ss_pred EcCCCCcee
Confidence 344444443
No 345
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=22.02 E-value=47 Score=18.20 Aligned_cols=8 Identities=38% Similarity=1.032 Sum_probs=5.1
Q ss_pred cccccccc
Q 024455 81 CNLCMNIF 88 (267)
Q Consensus 81 C~~C~~~F 88 (267)
|..||..|
T Consensus 24 C~~Cg~~~ 31 (33)
T PF08792_consen 24 CIFCGSSF 31 (33)
T ss_pred cccCCcEe
Confidence 66666655
No 346
>PF07819 PGAP1: PGAP1-like protein; InterPro: IPR012908 The sequences found in this family are similar to PGAP1 (Q765A7 from SWISSPROT). This is an endoplasmic reticulum membrane protein with a catalytic serine-containing motif that is conserved in a number of lipases. PGAP1 functions as a GPI inositol-deacylase; this deacylation is important for the efficient transport of GPI-anchored proteins from the endoplasmic reticulum to the Golgi body [].; GO: 0016788 hydrolase activity, acting on ester bonds, 0006505 GPI anchor metabolic process, 0006886 intracellular protein transport, 0031227 intrinsic to endoplasmic reticulum membrane
Probab=21.84 E-value=81 Score=25.80 Aligned_cols=46 Identities=24% Similarity=0.350 Sum_probs=25.5
Q ss_pred cccccCCHHhh-ccCCCHHHHHHHHHHHHhcCCCCCcccccCCCceEEEeccch
Q 024455 185 YEVTGLTEEDI-KNAMPLKEVKDKILEILNNGESTGRLMLDDGKARLLVGHGLE 237 (267)
Q Consensus 185 ~~~~GIt~~~l-~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~lvgh~~~ 237 (267)
..+++.....+ .++..+.++.+.|++.... ....+...+||||+..
T Consensus 49 ~~~s~~~g~~l~~q~~~~~~~i~~i~~~~~~-------~~~~~~~vilVgHSmG 95 (225)
T PF07819_consen 49 EELSAFHGRTLQRQAEFLAEAIKYILELYKS-------NRPPPRSVILVGHSMG 95 (225)
T ss_pred ccccccccccHHHHHHHHHHHHHHHHHhhhh-------ccCCCCceEEEEEchh
Confidence 33333333333 3345667777777777621 1122266899999953
No 347
>PF08790 zf-LYAR: LYAR-type C2HC zinc finger ; InterPro: IPR014898 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 C2HC zinc finger domain is found in LYAR proteins such as Q08288 from SWISSPROT, which are involved in cell growth regulation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1WJV_A.
Probab=21.77 E-value=16 Score=19.35 Aligned_cols=11 Identities=36% Similarity=1.074 Sum_probs=7.0
Q ss_pred cccccCccccC
Q 024455 15 HKCVACYKQFK 25 (267)
Q Consensus 15 ~~C~~C~k~f~ 25 (267)
|.|-.|++.|.
T Consensus 1 ~sCiDC~~~F~ 11 (28)
T PF08790_consen 1 FSCIDCSKDFD 11 (28)
T ss_dssp EEETTTTEEEE
T ss_pred CeeecCCCCcC
Confidence 45667777773
No 348
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.75 E-value=82 Score=21.13 Aligned_cols=34 Identities=18% Similarity=0.175 Sum_probs=25.1
Q ss_pred CCCcCCccccccc--------ccccccccCChhhHHHHHHHh
Q 024455 68 SKAHCSGIFSDRG--------CNLCMNIFDSPSSLIKHKEAC 101 (267)
Q Consensus 68 ~C~~C~k~f~~~~--------C~~C~~~F~~~~~L~~H~~~h 101 (267)
.|+.|+-...... |+.|+-..-....|.+-+..-
T Consensus 3 lCP~C~v~l~~~~rs~vEiD~CPrCrGVWLDrGELdKli~r~ 44 (88)
T COG3809 3 LCPICGVELVMSVRSGVEIDYCPRCRGVWLDRGELDKLIERS 44 (88)
T ss_pred ccCcCCceeeeeeecCceeeeCCccccEeecchhHHHHHHHh
Confidence 4777776665542 999999999999988776443
No 349
>PF13017 Maelstrom: piRNA pathway germ-plasm component
Probab=21.64 E-value=84 Score=25.53 Aligned_cols=49 Identities=20% Similarity=0.250 Sum_probs=35.1
Q ss_pred CCeeEecccCCCCCccccc-------cccccCCHHhhccC-CCHHHHHHHHHHHHhc
Q 024455 166 ENVIFHTYVQPQLPVTNYR-------YEVTGLTEEDIKNA-MPLKEVKDKILEILNN 214 (267)
Q Consensus 166 ~~~~~~~~v~P~~~i~~~~-------~~~~GIt~~~l~~~-~~~~~v~~~~~~~~~~ 214 (267)
....++++|+|......+. ...|+|..+..+.+ ..+..+..+|.+||..
T Consensus 24 I~~~~H~~I~Pg~~p~G~~~~a~~hs~~tH~ip~~~~~~~~~d~~~l~~~l~~fl~~ 80 (213)
T PF13017_consen 24 IIDSFHTFINPGQIPLGYRYDAQHHSDETHQIPIPPNALGESDYSELYNELLNFLKP 80 (213)
T ss_pred cchhhhcccCCCCCCcHHHHHHHHhhhhhcCCCCCCcccccCCHHHHHHHHHHHhhh
Confidence 5567999999986544443 34466766655555 4799999999999953
No 350
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=21.51 E-value=40 Score=28.75 Aligned_cols=44 Identities=14% Similarity=0.115 Sum_probs=30.9
Q ss_pred CCCCCcCCcccccccccccccccCChhhHHHHHHHhcCCCCcccccc
Q 024455 66 PLSKAHCSGIFSDRGCNLCMNIFDSPSSLIKHKEACSLSAPVPFEKT 112 (267)
Q Consensus 66 ~~~C~~C~k~f~~~~C~~C~~~F~~~~~L~~H~~~h~~~~~~~C~~~ 112 (267)
||.|..|.+.|...-=..|+..|-....|..+++ +++.|.|++.
T Consensus 241 Pf~c~icr~~f~~pVvt~c~h~fc~~ca~~~~qk---~~~c~vC~~~ 284 (313)
T KOG1813|consen 241 PFKCFICRKYFYRPVVTKCGHYFCEVCALKPYQK---GEKCYVCSQQ 284 (313)
T ss_pred CccccccccccccchhhcCCceeehhhhcccccc---CCcceecccc
Confidence 7889999999988876677777777666655432 3556667654
No 351
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=21.43 E-value=59 Score=23.14 Aligned_cols=30 Identities=27% Similarity=0.480 Sum_probs=22.0
Q ss_pred CCCCCCCccccccCccccCChHHHHHHHhH
Q 024455 7 LPKRSTARHKCVACYKQFKRKDHLIEHMKI 36 (267)
Q Consensus 7 ~~~~~~k~~~C~~C~k~f~~~~~l~~H~~~ 36 (267)
|-..|-..|-|-.|.+-|.+...|..|.+.
T Consensus 48 p~lPGlGqhYCieCaryf~t~~aL~~Hkkg 77 (126)
T COG5112 48 PELPGLGQHYCIECARYFITEKALMEHKKG 77 (126)
T ss_pred CCCCCCceeeeehhHHHHHHHHHHHHHhcc
Confidence 333466667888888888888888888754
No 352
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=21.37 E-value=46 Score=21.42 Aligned_cols=20 Identities=10% Similarity=0.360 Sum_probs=14.4
Q ss_pred CCCcCCcccccccccccccc
Q 024455 68 SKAHCSGIFSDRGCNLCMNI 87 (267)
Q Consensus 68 ~C~~C~k~f~~~~C~~C~~~ 87 (267)
.|..|........|+.||-.
T Consensus 7 AC~~C~~i~~~~~Cp~Cgs~ 26 (64)
T PRK06393 7 ACKKCKRLTPEKTCPVHGDE 26 (64)
T ss_pred hHhhCCcccCCCcCCCCCCC
Confidence 47777777666678888865
No 353
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=21.35 E-value=41 Score=24.77 Aligned_cols=9 Identities=22% Similarity=0.560 Sum_probs=4.4
Q ss_pred CcccchhhcC
Q 024455 45 KCAVCQKLSK 54 (267)
Q Consensus 45 ~C~~C~~~f~ 54 (267)
.| .||..|.
T Consensus 72 ~C-~Cg~~~~ 80 (124)
T PRK00762 72 EC-ECGYEGV 80 (124)
T ss_pred Ee-eCcCccc
Confidence 55 5554443
No 354
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=21.22 E-value=88 Score=26.96 Aligned_cols=12 Identities=25% Similarity=0.545 Sum_probs=5.9
Q ss_pred CCCCCCcCCccc
Q 024455 65 GPLSKAHCSGIF 76 (267)
Q Consensus 65 ~~~~C~~C~k~f 76 (267)
+.|.|+.|...|
T Consensus 387 ~rY~Ce~CK~~F 398 (421)
T COG5151 387 GRYQCELCKSTF 398 (421)
T ss_pred cceechhhhhhh
Confidence 345555554444
No 355
>PF11238 DUF3039: Protein of unknown function (DUF3039); InterPro: IPR021400 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=21.21 E-value=28 Score=21.82 Aligned_cols=8 Identities=38% Similarity=1.161 Sum_probs=4.2
Q ss_pred cccccccc
Q 024455 81 CNLCMNIF 88 (267)
Q Consensus 81 C~~C~~~F 88 (267)
|+.|.+.|
T Consensus 47 CP~Ck~iy 54 (58)
T PF11238_consen 47 CPECKEIY 54 (58)
T ss_pred CcCHHHHH
Confidence 55555444
No 356
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=20.79 E-value=32 Score=25.94 Aligned_cols=14 Identities=21% Similarity=0.382 Sum_probs=9.9
Q ss_pred CceeeeeccccCCc
Q 024455 135 PKAVAMDCEMVGGG 148 (267)
Q Consensus 135 ~~~~~~dcE~~g~~ 148 (267)
.+...+.||.||..
T Consensus 77 ~~nl~~~CE~CG~~ 90 (137)
T TIGR03826 77 FPNLGYPCERCGTS 90 (137)
T ss_pred CCCCcCcccccCCc
Confidence 34567888888864
No 357
>PRK14138 NAD-dependent deacetylase; Provisional
Probab=20.54 E-value=74 Score=26.43 Aligned_cols=16 Identities=19% Similarity=0.360 Sum_probs=11.3
Q ss_pred CcccchhhcCCHHHHH
Q 024455 45 KCAVCQKLSKSFESLR 60 (267)
Q Consensus 45 ~C~~C~~~f~~~~~l~ 60 (267)
.|..|++.|.....+.
T Consensus 121 ~C~~C~~~~~~~~~~~ 136 (244)
T PRK14138 121 YCVRCGKRYTVEDVIE 136 (244)
T ss_pred EECCCCCcccHHHHHH
Confidence 8988998877654443
No 358
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=20.46 E-value=70 Score=29.39 Aligned_cols=26 Identities=23% Similarity=0.382 Sum_probs=20.7
Q ss_pred ccccccccccCChhhHHHHHH-HhcCC
Q 024455 79 RGCNLCMNIFDSPSSLIKHKE-ACSLS 104 (267)
Q Consensus 79 ~~C~~C~~~F~~~~~L~~H~~-~h~~~ 104 (267)
+.|+.|.+.|.....+..|+. .|-+.
T Consensus 58 WiCp~CskkF~d~~~~~~H~~~eH~~~ 84 (466)
T PF04780_consen 58 WICPRCSKKFSDAESCLSHMEQEHPAG 84 (466)
T ss_pred eeCCcccceeCCHHHHHHHHHHhhhhh
Confidence 348889999999999999987 45443
No 359
>KOG2636 consensus Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=20.17 E-value=61 Score=29.36 Aligned_cols=23 Identities=17% Similarity=0.401 Sum_probs=18.3
Q ss_pred CccccccCc-cccCChHHHHHHHh
Q 024455 13 ARHKCVACY-KQFKRKDHLIEHMK 35 (267)
Q Consensus 13 k~~~C~~C~-k~f~~~~~l~~H~~ 35 (267)
..|.|++|| +++.-+..+.+|-.
T Consensus 400 ~ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 400 IEYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred cccceeeccCccccCcHHHHHHhH
Confidence 458899999 78888888888863
No 360
>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=20.16 E-value=49 Score=18.82 Aligned_cols=11 Identities=18% Similarity=0.525 Sum_probs=8.1
Q ss_pred ccccccCcccc
Q 024455 14 RHKCVACYKQF 24 (267)
Q Consensus 14 ~~~C~~C~k~f 24 (267)
-|.|..|+..|
T Consensus 28 fy~C~~C~~~w 38 (39)
T PF01096_consen 28 FYVCCNCGHRW 38 (39)
T ss_dssp EEEESSSTEEE
T ss_pred EEEeCCCCCee
Confidence 47888888765
Done!