Query gi|254780553|ref|YP_003064966.1| Holliday junction DNA helicase RuvA [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 207
No_of_seqs 117 out of 1856
Neff 6.5
Searched_HMMs 39220
Date Sun May 29 22:32:27 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780553.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK00116 ruvA Holliday junctio 100.0 0 0 412.1 23.9 196 1-206 1-196 (198)
2 COG0632 RuvA Holliday junction 100.0 0 0 405.8 20.9 201 1-206 1-201 (201)
3 PRK13901 ruvA Holliday junctio 100.0 0 0 402.7 22.5 191 1-207 1-196 (196)
4 TIGR00084 ruvA Holliday juncti 100.0 0 0 364.6 17.8 203 1-205 1-215 (217)
5 pfam01330 RuvA_N RuvA N termin 99.7 4.1E-16 1E-20 128.1 8.3 61 1-62 1-61 (61)
6 pfam07499 RuvA_C RuvA, C-termi 98.5 2.5E-07 6.3E-12 69.6 6.4 46 159-206 2-47 (47)
7 PRK13766 Hef nuclease; Provisi 98.1 3.3E-06 8.3E-11 62.1 4.4 63 63-129 697-759 (764)
8 TIGR01448 recD_rel helicase, R 97.6 0.00023 6E-09 49.7 7.1 128 33-189 43-181 (769)
9 PRK00558 uvrC excinuclease ABC 97.2 0.00027 7E-09 49.2 3.2 53 74-129 555-607 (609)
10 PRK08609 hypothetical protein; 97.0 0.00035 8.8E-09 48.6 1.9 52 72-126 87-141 (570)
11 TIGR00615 recR recombination p 96.9 0.00058 1.5E-08 47.1 2.4 22 107-128 11-32 (205)
12 COG1948 MUS81 ERCC4-type nucle 96.8 0.0015 3.9E-08 44.3 3.9 63 63-129 173-235 (254)
13 PRK00076 recR recombination pr 96.7 0.0011 2.8E-08 45.2 2.6 23 107-129 10-32 (197)
14 PRK13844 recombination protein 96.7 0.0012 3E-08 45.1 2.6 24 107-130 14-37 (200)
15 smart00483 POLXc DNA polymeras 96.1 0.0065 1.6E-07 40.1 3.8 55 73-128 48-108 (334)
16 COG0353 RecR Recombinational D 96.1 0.0039 1E-07 41.5 2.5 23 107-129 11-33 (198)
17 TIGR01259 comE comEA protein; 95.9 0.0014 3.5E-08 44.6 -0.4 50 70-124 69-118 (124)
18 PRK08609 hypothetical protein; 95.9 0.0047 1.2E-07 41.0 2.2 57 73-129 48-109 (570)
19 cd00141 NT_POLXc Nucleotidyltr 95.6 0.0062 1.6E-07 40.2 1.9 54 73-128 45-104 (307)
20 TIGR00426 TIGR00426 competence 95.5 0.0073 1.8E-07 39.8 1.8 49 73-126 17-66 (70)
21 PRK07945 hypothetical protein; 95.2 0.05 1.3E-06 34.2 5.4 87 84-173 28-126 (335)
22 COG1555 ComEA DNA uptake prote 94.8 0.026 6.7E-07 36.0 3.0 27 102-128 91-117 (149)
23 PRK07456 consensus 94.8 0.032 8.3E-07 35.4 3.4 143 25-175 136-306 (975)
24 TIGR00593 pola DNA polymerase 94.7 0.044 1.1E-06 34.5 4.1 107 23-130 124-251 (1005)
25 PTZ00217 flap endonuclease-1; 94.7 0.26 6.7E-06 29.4 7.9 102 84-187 212-333 (394)
26 smart00475 53EXOc 5'-3' exonuc 94.6 0.075 1.9E-06 33.0 5.0 36 94-129 170-207 (259)
27 pfam00633 HHH Helix-hairpin-he 94.6 0.019 5E-07 36.9 2.0 25 101-125 4-28 (30)
28 PRK05755 DNA polymerase I; Pro 94.4 0.078 2E-06 32.9 4.7 135 25-175 127-279 (889)
29 PRK06887 consensus 94.2 0.13 3.2E-06 31.5 5.4 134 25-174 129-286 (954)
30 KOG2534 consensus 94.1 0.043 1.1E-06 34.6 2.8 55 73-127 56-116 (353)
31 PRK08835 consensus 94.1 0.1 2.6E-06 32.1 4.8 135 25-175 129-287 (931)
32 PRK07300 consensus 94.0 0.12 3E-06 31.7 4.9 136 22-175 130-289 (880)
33 TIGR02236 recomb_radA DNA repa 93.9 0.063 1.6E-06 33.5 3.4 54 75-130 2-55 (333)
34 PRK08786 consensus 93.8 0.13 3.4E-06 31.3 5.0 76 24-102 122-213 (927)
35 PRK07997 consensus 93.8 0.14 3.6E-06 31.2 5.0 75 25-102 129-218 (928)
36 TIGR00575 dnlj DNA ligase, NAD 93.8 0.072 1.8E-06 33.1 3.5 137 18-176 454-613 (706)
37 COG1796 POL4 DNA polymerase IV 93.8 0.36 9.1E-06 28.5 7.0 51 72-125 92-145 (326)
38 PRK07898 consensus 93.7 0.13 3.3E-06 31.4 4.8 131 25-175 139-294 (902)
39 PRK08076 consensus 93.7 0.1 2.7E-06 32.0 4.2 133 25-175 125-281 (877)
40 COG1796 POL4 DNA polymerase IV 93.7 0.085 2.2E-06 32.6 3.8 67 63-129 41-114 (326)
41 PRK03980 flap endonuclease-1; 93.5 0.71 1.8E-05 26.5 8.4 100 87-188 169-283 (295)
42 PRK08928 consensus 93.4 0.21 5.3E-06 30.1 5.3 135 25-175 127-279 (861)
43 COG0258 Exo 5'-3' exonuclease 93.3 0.24 6.1E-06 29.6 5.5 21 78-98 203-223 (310)
44 PRK09482 xni exonuclease IX; P 93.0 0.078 2E-06 32.9 2.7 38 93-130 165-204 (256)
45 TIGR03674 fen_arch flap struct 92.9 0.18 4.6E-06 30.4 4.4 93 93-187 221-326 (338)
46 KOG2841 consensus 92.7 0.24 6E-06 29.7 4.7 57 71-130 193-249 (254)
47 TIGR01083 nth endonuclease III 92.3 0.056 1.4E-06 33.9 1.2 24 103-126 102-125 (192)
48 COG0258 Exo 5'-3' exonuclease 92.3 0.095 2.4E-06 32.3 2.3 93 25-129 117-219 (310)
49 COG0272 Lig NAD-dependent DNA 92.3 0.41 1E-05 28.1 5.6 73 54-129 478-564 (667)
50 PRK07556 consensus 92.1 0.24 6.1E-06 29.6 4.1 78 24-102 134-224 (977)
51 cd00080 HhH2_motif Helix-hairp 92.0 0.15 3.8E-06 31.0 3.0 39 92-130 4-44 (75)
52 PRK05797 consensus 91.9 0.4 1E-05 28.2 5.2 136 24-175 124-282 (869)
53 PRK05929 consensus 91.9 0.12 2.9E-06 31.7 2.4 77 24-103 124-216 (870)
54 PRK07456 consensus 91.9 0.32 8.2E-06 28.8 4.6 37 94-130 189-227 (975)
55 PRK10880 adenine DNA glycosyla 91.8 0.11 2.9E-06 31.8 2.2 59 72-132 108-171 (350)
56 PRK07956 ligA NAD-dependent DN 91.6 0.19 4.9E-06 30.3 3.3 72 54-129 478-564 (668)
57 COG1555 ComEA DNA uptake prote 91.6 0.12 2.9E-06 31.8 2.1 58 59-125 87-144 (149)
58 PRK10702 endonuclease III; Pro 91.2 0.081 2.1E-06 32.8 1.0 26 103-128 104-129 (211)
59 COG0322 UvrC Nuclease subunit 91.1 0.17 4.3E-06 30.7 2.5 54 68-125 524-578 (581)
60 PRK08097 ligB NAD-dependent DN 90.9 0.7 1.8E-05 26.5 5.5 53 74-130 427-482 (563)
61 smart00278 HhH1 Helix-hairpin- 90.8 0.1 2.6E-06 32.1 1.2 21 109-129 2-22 (26)
62 PRK10702 endonuclease III; Pro 90.7 0.14 3.5E-06 31.2 1.8 56 72-129 108-164 (211)
63 pfam01367 5_3_exonuc 5'-3' exo 90.7 0.13 3.4E-06 31.4 1.6 18 77-94 22-39 (100)
64 PRK05797 consensus 90.5 0.13 3.4E-06 31.4 1.6 76 40-130 123-210 (869)
65 pfam00730 HhH-GPD HhH-GPD supe 90.5 0.56 1.4E-05 27.2 4.8 63 59-127 23-100 (144)
66 COG4277 Predicted DNA-binding 90.3 0.17 4.4E-06 30.6 2.0 70 56-129 282-351 (404)
67 cd00080 HhH2_motif Helix-hairp 90.2 0.33 8.4E-06 28.7 3.4 42 61-103 3-53 (75)
68 smart00475 53EXOc 5'-3' exonuc 90.2 0.24 6.1E-06 29.7 2.6 74 28-104 128-218 (259)
69 TIGR02903 spore_lon_C ATP-depe 90.1 0.16 4.1E-06 30.8 1.7 50 84-133 140-204 (616)
70 PRK08434 consensus 90.0 0.17 4.3E-06 30.7 1.8 75 25-102 124-214 (887)
71 PRK07300 consensus 89.9 0.17 4.2E-06 30.7 1.6 38 93-130 179-218 (880)
72 PRK07625 consensus 89.8 0.17 4.4E-06 30.6 1.7 75 24-101 127-216 (922)
73 TIGR01084 mutY A/G-specific ad 89.8 0.37 9.4E-06 28.4 3.3 60 72-133 117-181 (297)
74 PRK07997 consensus 89.6 0.2 5.2E-06 30.1 1.9 77 40-130 127-210 (928)
75 PRK08928 consensus 89.5 0.18 4.6E-06 30.5 1.6 75 40-130 125-208 (861)
76 PRK07556 consensus 89.5 0.19 4.9E-06 30.3 1.7 77 40-130 133-216 (977)
77 PRK05929 consensus 89.4 0.19 4.8E-06 30.3 1.6 74 40-129 123-206 (870)
78 PRK08786 consensus 89.3 0.21 5.2E-06 30.1 1.7 74 40-129 121-204 (927)
79 PRK07898 consensus 89.1 0.21 5.4E-06 30.0 1.7 75 40-130 137-224 (902)
80 PRK08434 consensus 89.1 0.21 5.4E-06 30.0 1.7 75 40-130 122-206 (887)
81 COG0177 Nth Predicted EndoIII- 89.0 0.2 5.2E-06 30.1 1.5 27 104-130 105-131 (211)
82 PRK06887 consensus 89.0 0.24 6.1E-06 29.7 1.9 76 40-129 127-209 (954)
83 PRK08835 consensus 88.8 0.25 6.4E-06 29.5 1.9 77 40-130 127-210 (931)
84 PHA00439 exonuclease 88.7 0.24 6E-06 29.7 1.7 82 97-180 176-262 (288)
85 cd00056 ENDO3c endonuclease II 88.6 0.27 6.8E-06 29.3 1.9 23 105-127 80-102 (158)
86 cd00008 53EXOc 5'-3' exonuclea 88.4 0.3 7.6E-06 29.0 2.0 36 93-128 166-203 (240)
87 TIGR00593 pola DNA polymerase 88.1 0.26 6.7E-06 29.4 1.6 87 34-130 117-214 (1005)
88 PRK12766 50S ribosomal protein 87.7 0.58 1.5E-05 27.1 3.2 59 70-130 7-65 (238)
89 PRK08076 consensus 87.7 0.29 7.5E-06 29.0 1.7 38 93-130 171-210 (877)
90 KOG2875 consensus 87.6 0.4 1E-05 28.2 2.3 90 85-190 108-201 (323)
91 pfam02371 Transposase_20 Trans 87.5 0.35 8.9E-06 28.5 2.0 23 108-130 2-24 (87)
92 pfam01367 5_3_exonuc 5'-3' exo 87.4 0.36 9.2E-06 28.5 2.0 37 94-130 2-40 (100)
93 COG2003 RadC DNA repair protei 87.4 2.3 6E-05 23.0 6.1 127 61-206 19-166 (224)
94 pfam00633 HHH Helix-hairpin-he 87.4 0.27 6.9E-06 29.3 1.3 21 71-91 9-29 (30)
95 PRK07625 consensus 87.3 0.34 8.6E-06 28.7 1.8 77 40-130 126-209 (922)
96 smart00478 ENDO3c endonuclease 87.2 0.44 1.1E-05 27.9 2.3 51 78-130 39-94 (149)
97 PRK05755 DNA polymerase I; Pro 87.1 0.33 8.4E-06 28.7 1.6 77 40-130 125-208 (889)
98 TIGR02236 recomb_radA DNA repa 86.5 0.31 8E-06 28.9 1.3 16 110-125 2-17 (333)
99 PRK09482 xni exonuclease IX; P 86.4 0.43 1.1E-05 28.0 1.9 86 25-124 123-223 (256)
100 smart00483 POLXc DNA polymeras 86.2 0.35 9E-06 28.5 1.4 49 71-124 87-138 (334)
101 cd00141 NT_POLXc Nucleotidyltr 86.1 1.1 2.8E-05 25.3 3.8 29 73-102 85-116 (307)
102 cd00128 XPG Xeroderma pigmento 86.0 0.77 2E-05 26.3 3.1 42 87-130 203-245 (316)
103 cd00008 53EXOc 5'-3' exonuclea 85.9 0.54 1.4E-05 27.3 2.2 73 28-103 129-214 (240)
104 pfam10391 DNA_pol_lambd_f Fing 85.8 0.42 1.1E-05 28.0 1.6 19 108-126 2-20 (52)
105 smart00279 HhH2 Helix-hairpin- 85.7 0.48 1.2E-05 27.7 1.8 25 103-127 10-35 (36)
106 PRK03103 DNA polymerase IV; Re 85.3 0.73 1.9E-05 26.4 2.7 29 93-124 170-198 (410)
107 PRK07956 ligA NAD-dependent DN 85.3 0.95 2.4E-05 25.7 3.2 52 74-129 446-500 (668)
108 PRK00024 radC DNA repair prote 84.9 1.4 3.5E-05 24.5 3.9 71 59-133 17-93 (224)
109 TIGR03674 fen_arch flap struct 84.8 1.1 2.8E-05 25.2 3.4 43 60-103 218-267 (338)
110 cd00128 XPG Xeroderma pigmento 84.3 0.55 1.4E-05 27.3 1.6 46 58-104 203-255 (316)
111 COG0122 AlkA 3-methyladenine D 84.1 0.69 1.7E-05 26.6 2.1 20 107-126 197-216 (285)
112 PRK13910 DNA glycosylase MutY; 84.1 0.47 1.2E-05 27.7 1.2 23 104-126 69-91 (290)
113 cd01702 Pol_eta Pol eta is mem 83.6 3.9 1E-04 21.6 8.8 30 93-125 170-199 (358)
114 PRK01216 DNA polymerase IV; Va 83.6 1 2.5E-05 25.5 2.7 29 93-124 166-194 (351)
115 PRK13913 3-methyladenine DNA g 83.0 0.43 1.1E-05 27.9 0.7 24 107-130 120-143 (218)
116 smart00279 HhH2 Helix-hairpin- 82.1 0.43 1.1E-05 28.0 0.4 17 76-92 19-35 (36)
117 smart00478 ENDO3c endonuclease 82.0 0.32 8.1E-06 28.8 -0.3 57 71-128 70-127 (149)
118 PRK03980 flap endonuclease-1; 81.8 0.6 1.5E-05 27.0 1.0 45 59-104 170-221 (295)
119 PRK02794 DNA polymerase IV; Pr 81.1 1.5 3.8E-05 24.3 2.8 51 75-130 211-261 (417)
120 TIGR01259 comE comEA protein; 80.6 0.82 2.1E-05 26.1 1.4 18 109-126 73-90 (124)
121 smart00278 HhH1 Helix-hairpin- 80.4 0.41 1E-05 28.1 -0.2 21 74-94 2-22 (26)
122 PRK02406 DNA polymerase IV; Va 80.3 1.8 4.6E-05 23.8 3.1 53 69-124 132-196 (355)
123 PRK00116 ruvA Holliday junctio 80.2 1.1 2.8E-05 25.2 1.9 21 108-128 73-93 (198)
124 TIGR02902 spore_lonB ATP-depen 80.1 1 2.7E-05 25.4 1.8 20 113-132 94-113 (532)
125 pfam11731 Cdd1 Pathogenicity l 79.6 0.99 2.5E-05 25.5 1.5 23 103-125 7-29 (92)
126 pfam04919 DUF655 Protein of un 79.5 1.3 3.3E-05 24.8 2.1 22 109-130 117-138 (181)
127 cd00056 ENDO3c endonuclease II 79.4 0.92 2.3E-05 25.7 1.3 24 69-92 79-102 (158)
128 pfam11798 IMS_HHH IMS family H 79.4 0.91 2.3E-05 25.8 1.3 16 109-124 13-28 (33)
129 cd03586 Pol_IV_kappa Pol_IV_ka 79.1 1.9 4.9E-05 23.6 2.9 43 79-124 136-188 (337)
130 cd01703 Pol_iota Pol iota is m 79.1 1 2.5E-05 25.5 1.4 16 109-124 211-226 (394)
131 PRK03858 DNA polymerase IV; Va 78.0 2.4 6.1E-05 23.0 3.1 42 80-124 138-189 (398)
132 pfam07223 DUF1421 Protein of u 78.0 2.5 6.4E-05 22.9 3.2 41 154-195 316-356 (359)
133 TIGR03629 arch_S13P archaeal r 77.2 5.6 0.00014 20.5 4.8 22 108-129 21-42 (144)
134 TIGR03631 bact_S13 30S ribosom 77.2 1.5 3.9E-05 24.3 1.9 22 108-129 15-36 (113)
135 PRK05179 rpsM 30S ribosomal pr 75.8 1.8 4.6E-05 23.8 2.0 22 108-129 17-38 (122)
136 CHL00137 rps13 ribosomal prote 75.8 1.6 4.2E-05 24.1 1.8 22 108-129 17-38 (122)
137 COG0539 RpsA Ribosomal protein 74.6 7.4 0.00019 19.7 8.5 51 5-56 25-80 (541)
138 COG1491 Predicted RNA-binding 74.4 2.3 5.8E-05 23.1 2.2 23 109-131 131-153 (202)
139 cd00194 UBA Ubiquitin Associat 73.7 4.4 0.00011 21.2 3.5 24 161-184 2-25 (38)
140 cd01701 Pol_zeta Pol_zeta, a m 73.6 1.7 4.2E-05 24.0 1.3 42 80-124 189-240 (405)
141 pfam00416 Ribosomal_S13 Riboso 73.3 1.8 4.5E-05 23.9 1.4 22 108-129 15-36 (106)
142 smart00165 UBA Ubiquitin assoc 73.0 4.7 0.00012 21.1 3.5 24 161-184 2-25 (37)
143 TIGR00608 radc DNA repair prot 72.5 3.9 9.8E-05 21.6 3.0 128 61-204 9-161 (223)
144 PRK06676 rpsA 30S ribosomal pr 71.8 8.6 0.00022 19.3 8.9 56 4-59 20-83 (390)
145 TIGR00588 ogg 8-oxoguanine DNA 70.4 2.7 6.9E-05 22.6 1.8 77 56-145 114-194 (379)
146 KOG1921 consensus 70.4 2.2 5.6E-05 23.2 1.4 16 107-122 158-173 (286)
147 PRK06531 yajC preprotein trans 70.2 5.7 0.00015 20.5 3.4 36 1-38 45-82 (120)
148 PRK04053 rps13p 30S ribosomal 70.1 2.5 6.4E-05 22.8 1.6 22 108-129 25-46 (149)
149 PRK06299 rpsA 30S ribosomal pr 70.0 9.4 0.00024 19.0 9.2 56 4-60 23-83 (556)
150 PRK03352 DNA polymerase IV; Va 69.2 2.4 6.2E-05 22.9 1.4 58 64-124 124-193 (345)
151 COG1031 Uncharacterized Fe-S o 68.0 3.1 8E-05 22.2 1.7 21 107-127 515-535 (560)
152 PTZ00134 40S ribosomal protein 67.8 2.4 6.1E-05 23.0 1.1 36 94-129 7-51 (154)
153 pfam05559 DUF763 Protein of un 67.5 2.4 6.2E-05 22.9 1.1 16 106-121 267-282 (319)
154 pfam10440 WIYLD WIYLD domain. 67.3 9.5 0.00024 19.0 4.1 31 160-190 11-41 (65)
155 pfam09374 PG_binding_3 Predict 67.1 5 0.00013 20.8 2.6 33 81-114 21-53 (67)
156 PRK10308 3-methyl-adenine DNA 66.1 7.6 0.00019 19.6 3.4 76 86-179 104-181 (283)
157 KOG1918 consensus 66.1 1.6 4.1E-05 24.1 -0.0 14 94-107 75-88 (254)
158 COG0099 RpsM Ribosomal protein 64.3 4.4 0.00011 21.2 1.9 22 108-129 17-38 (121)
159 TIGR00882 2A0105 oligosacchari 64.2 7.5 0.00019 19.7 3.1 38 53-90 249-291 (397)
160 PRK03348 DNA polymerase IV; Pr 63.9 3.8 9.8E-05 21.6 1.5 42 80-124 144-195 (456)
161 pfam10842 DUF2642 Protein of u 63.0 13 0.00033 18.1 4.2 28 3-30 31-58 (66)
162 COG1862 YajC Preprotein transl 62.7 13 0.00033 18.1 4.5 42 2-44 53-94 (97)
163 KOG2518 consensus 62.6 8.7 0.00022 19.2 3.2 73 48-129 163-246 (556)
164 PRK12269 bifunctional cytidyla 62.3 13 0.00034 18.0 5.4 58 4-67 324-381 (863)
165 PRK13806 rpsA 30S ribosomal pr 62.0 13 0.00034 18.0 7.8 55 4-60 36-95 (489)
166 pfam02699 YajC Preprotein tran 61.2 14 0.00035 17.9 4.9 33 2-35 47-79 (83)
167 PRK04301 radA DNA repair and r 59.8 7.3 0.00019 19.7 2.4 56 74-131 8-63 (318)
168 PRK01810 DNA polymerase IV; Va 58.6 15 0.00039 17.6 4.0 50 76-130 182-231 (410)
169 cd00424 Pol_Y Y-family of DNA 57.8 5.3 0.00014 20.7 1.4 51 76-130 176-226 (341)
170 pfam00627 UBA UBA/TS-N domain. 57.4 14 0.00036 17.8 3.5 23 161-183 3-25 (37)
171 PRK03609 umuC DNA polymerase V 56.2 5 0.00013 20.9 1.0 51 75-130 181-231 (422)
172 COG2231 Uncharacterized protei 54.1 6.4 0.00016 20.1 1.3 26 106-131 113-138 (215)
173 pfam12482 DUF3701 Phage integr 53.7 13 0.00033 18.1 2.8 37 94-130 36-72 (96)
174 PRK10917 ATP-dependent DNA hel 53.0 7.8 0.0002 19.6 1.6 48 3-51 61-118 (677)
175 PRK02515 psbU photosystem II c 52.6 8.7 0.00022 19.2 1.8 25 102-126 67-91 (144)
176 pfam08587 UBA_2 Ubiquitin asso 52.6 19 0.00048 17.0 4.7 23 161-183 3-26 (46)
177 KOG2519 consensus 52.2 19 0.00049 17.0 5.9 96 77-188 233-330 (449)
178 TIGR02168 SMC_prok_B chromosom 52.2 2.5 6.3E-05 22.9 -1.1 121 66-189 511-631 (1191)
179 pfam11372 DUF3173 Protein of u 52.1 13 0.00032 18.2 2.5 20 165-184 7-26 (59)
180 cd05687 S1_RPS1_repeat_ec1_hs1 51.0 20 0.00051 16.8 7.6 53 4-57 3-63 (70)
181 PRK07220 DNA topoisomerase I; 49.3 9.2 0.00023 19.1 1.5 24 162-185 282-305 (740)
182 PRK06645 DNA polymerase III su 48.7 16 0.00041 17.4 2.7 50 59-108 180-233 (507)
183 COG1936 Predicted nucleotide k 44.7 6.9 0.00018 19.9 0.3 28 109-136 4-31 (180)
184 TIGR03252 uncharacterized HhH- 44.6 20 0.00052 16.8 2.6 20 162-181 112-132 (177)
185 cd01017 AdcA Metal binding pro 44.6 16 0.00041 17.5 2.1 13 18-30 55-67 (282)
186 PRK12402 replication factor C 44.5 17 0.00044 17.3 2.2 116 59-189 177-300 (337)
187 COG1194 MutY A/G-specific DNA 44.4 2.8 7.2E-05 22.5 -1.8 52 73-126 76-131 (342)
188 PRK12278 50S ribosomal protein 44.3 11 0.00027 18.6 1.2 20 105-124 150-169 (216)
189 PRK00087 4-hydroxy-3-methylbut 43.1 26 0.00067 16.0 8.9 52 5-57 308-367 (670)
190 COG2183 Tex Transcriptional ac 42.0 14 0.00035 17.9 1.4 23 104-126 505-527 (780)
191 pfam06514 PsbU Photosystem II 41.8 16 0.00041 17.4 1.8 25 102-126 59-83 (135)
192 PRK07899 rpsA 30S ribosomal pr 41.6 28 0.00071 15.9 8.8 52 5-57 39-98 (484)
193 TIGR01931 cysJ sulfite reducta 41.6 28 0.00071 15.9 4.5 41 13-54 426-473 (628)
194 cd01700 Pol_V Pol V was discov 41.4 28 0.00071 15.9 6.2 15 191-205 311-325 (344)
195 pfam03352 Adenine_glyco Methyl 41.2 28 0.00072 15.8 5.0 114 60-174 15-151 (179)
196 COG3743 Uncharacterized conser 40.9 13 0.00034 18.0 1.2 17 108-124 67-83 (133)
197 TIGR00538 hemN oxygen-independ 40.6 29 0.00073 15.8 5.2 72 117-205 119-199 (462)
198 PTZ00205 DNA polymerase kappa; 40.2 14 0.00037 17.8 1.3 43 79-124 270-325 (571)
199 pfam03459 TOBE TOBE domain. Th 39.9 29 0.00075 15.7 6.9 47 3-50 5-55 (61)
200 PRK07400 30S ribosomal protein 39.6 30 0.00076 15.7 9.8 72 4-76 34-113 (314)
201 pfam08823 PG_binding_2 Putativ 39.6 14 0.00035 17.9 1.1 24 154-177 12-35 (74)
202 LOAD_Hrd consensus 38.6 20 0.00052 16.8 1.9 55 67-125 3-64 (77)
203 KOG2457 consensus 38.3 10 0.00026 18.8 0.3 45 76-121 209-253 (555)
204 pfam03118 RNA_pol_A_CTD Bacter 37.3 29 0.00074 15.8 2.5 41 87-128 20-60 (62)
205 PRK00440 rfc replication facto 35.8 28 0.0007 15.9 2.2 46 59-104 153-202 (318)
206 PRK05563 DNA polymerase III su 34.4 36 0.00091 15.1 2.8 20 59-78 171-190 (541)
207 PHA00542 putative Cro-like pro 34.1 36 0.00092 15.1 2.8 21 160-180 20-40 (82)
208 PRK10409 hydrogenase isoenzyme 33.9 36 0.00093 15.1 4.6 53 1-53 1-56 (90)
209 TIGR00750 lao LAO/AO transport 32.3 29 0.00075 15.7 1.8 54 73-131 8-65 (333)
210 TIGR02606 antidote_CC2985 puta 31.8 28 0.00072 15.8 1.7 14 192-205 24-37 (77)
211 PRK03839 putative kinase; Prov 30.9 25 0.00064 16.2 1.3 18 162-179 92-109 (180)
212 PRK04040 adenylate kinase; Pro 30.6 29 0.00075 15.7 1.6 20 109-128 6-25 (189)
213 cd04455 S1_NusA S1_NusA: N-uti 30.0 42 0.0011 14.7 5.5 49 4-56 6-58 (67)
214 PRK12311 rpsB 30S ribosomal pr 29.9 28 0.0007 15.9 1.4 20 105-124 266-285 (332)
215 PTZ00296 choline kinase; Provi 29.7 43 0.0011 14.6 3.3 63 58-124 141-209 (439)
216 COG0507 RecD ATP-dependent exo 29.6 31 0.00079 15.6 1.6 52 76-129 83-134 (696)
217 TIGR01703 hybrid_clust hydroxy 29.3 43 0.0011 14.6 3.9 35 168-202 174-210 (567)
218 COG1415 Uncharacterized conser 29.2 26 0.00065 16.1 1.1 76 93-168 261-341 (373)
219 COG0298 HypC Hydrogenase matur 28.8 44 0.0011 14.5 5.6 52 1-54 1-54 (82)
220 pfam00834 Ribul_P_3_epim Ribul 28.3 45 0.0011 14.5 4.4 105 13-118 25-142 (201)
221 TIGR02624 rhamnu_1P_ald rhamnu 28.1 25 0.00064 16.2 0.9 10 115-124 192-201 (273)
222 cd01018 ZntC Metal binding pro 27.6 41 0.0011 14.7 1.9 11 18-28 54-64 (266)
223 TIGR02142 modC_ABC molybdate A 27.2 15 0.00037 17.8 -0.4 43 42-86 81-126 (361)
224 PRK05585 yajC preprotein trans 26.0 49 0.0013 14.2 4.8 35 2-38 63-98 (107)
225 TIGR02194 GlrX_NrdH Glutaredox 26.0 30 0.00076 15.7 1.0 19 158-176 32-50 (72)
226 TIGR00601 rad23 UV excision re 25.7 50 0.0013 14.2 3.0 23 162-184 194-219 (453)
227 TIGR01166 cbiO cobalt ABC tran 25.5 35 0.00091 15.2 1.3 85 101-188 14-115 (190)
228 COG0389 DinP Nucleotidyltransf 24.8 40 0.001 14.8 1.5 17 109-125 177-193 (354)
229 PRK04195 replication factor C 24.7 37 0.00095 15.0 1.3 44 159-206 242-286 (403)
230 COG3880 Modulator of heat shoc 24.6 52 0.0013 14.1 2.6 65 72-137 84-150 (176)
231 PRK13866 plasmid partitioning 23.7 54 0.0014 13.9 3.2 96 26-124 118-228 (336)
232 smart00316 S1 Ribosomal protei 23.7 54 0.0014 13.9 8.4 53 4-57 5-65 (72)
233 PRK13482 DNA integrity scannin 22.9 56 0.0014 13.8 3.9 16 110-125 289-304 (352)
234 KOG3111 consensus 22.8 46 0.0012 14.4 1.5 130 10-139 27-174 (224)
235 COG1245 Predicted ATPase, RNas 22.3 4.8 0.00012 21.0 -3.7 88 43-136 74-185 (591)
236 PRK08451 DNA polymerase III su 22.3 58 0.0015 13.8 2.4 52 81-132 230-289 (523)
237 pfam00570 HRDC HRDC domain. Th 21.9 59 0.0015 13.7 2.8 26 103-128 39-64 (68)
238 TIGR03454 partition_RepB plasm 21.8 59 0.0015 13.7 4.1 102 24-128 114-230 (325)
239 TIGR02538 type_IV_pilB type IV 21.4 54 0.0014 14.0 1.6 52 61-117 308-372 (577)
240 COG3722 MtlR Transcriptional r 21.3 51 0.0013 14.1 1.4 23 61-83 107-129 (174)
241 TIGR00302 TIGR00302 phosphorib 21.2 61 0.0015 13.6 1.8 15 162-176 20-34 (80)
242 cd00644 HMG-CoA_reductase_clas 20.9 12 0.00031 18.3 -1.8 44 83-126 199-242 (417)
243 pfam02961 BAF Barrier to autoi 20.8 42 0.0011 14.7 0.9 19 108-126 19-37 (89)
244 COG5207 UBP14 Isopeptidase T [ 20.6 62 0.0016 13.5 3.6 21 163-183 624-644 (749)
No 1
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=100.00 E-value=0 Score=412.10 Aligned_cols=196 Identities=37% Similarity=0.567 Sum_probs=179.8
Q ss_pred CCCEEEEEEEEEECCEEEEEECCEEEEEECCHHHHHHCCCCCCEEEEEEEEEECCCCEEEEEEECHHHHHHHHHHHHHHH
Q ss_conf 93258999999609979998588323897086889850247984999999997388418999706779999999850100
Q gi|254780553|r 1 MIGKIKGNIEGLYEDYVLIDVQGVCYIIYCPIRTLSCLGKIGDFCTLFVETHMRQDQIRLFGFLSDLDRQWFMLLQSVQG 80 (207)
Q Consensus 1 MI~~i~G~i~~~~~~~ivi~v~GvGY~i~vs~~~~~~l~~~g~~v~l~~~~~vrEd~~~LyGF~~~~Er~~F~~Li~V~G 80 (207)
||+||+|+|.++.+++++|+||||||+|++|.+++..+++.|++++||||++||||+++||||.+++||++|++|++|+|
T Consensus 1 MI~~i~G~i~~~~~~~iil~v~GvGY~v~v~~~~~~~l~~~g~~~~l~~~~~vrEd~~~LyGF~~~~Er~~F~~Li~V~G 80 (198)
T PRK00116 1 MIGYLRGILTEKGPDYVVIEVNGVGYEVQVPMRTLYELPEVGEEVKLYTHLVVREDAQLLYGFLTKEERELFRLLISVSG 80 (198)
T ss_pred CCCEEEEEEEEEECCEEEEEECCEEEEEEECHHHHHHCCCCCCEEEEEEEEEEECCCCEEEEECCHHHHHHHHHHHCCCC
T ss_conf 94479999999619989999799889999168999862468983999999998068875784088899999999856688
Q ss_pred CCCHHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHH
Q ss_conf 05101124431578999999985156687510457116799999999742221101133443233333445555653158
Q gi|254780553|r 81 VGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMTELKGKAISLSSVVQQDMSCVNKEQAHICSMPSFA 160 (207)
Q Consensus 81 IGpK~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~K~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 160 (207)
||||+||+|||++++++|++||.++|.+.|+++||||+|||+||++|||||+.++........ .......+..
T Consensus 81 IGpK~AL~ILs~~~~~~l~~aI~~~D~~~L~~vpGIG~KtA~rIi~ELk~K~~~~~~~~~~~~-------~~~~~~~~~~ 153 (198)
T PRK00116 81 VGPKLALAILSGLSPEELAQAIANGDIKALTKVPGVGKKTAERIVLELKDKLAALADAGAAAA-------AAASAANDAL 153 (198)
T ss_pred CCHHHHHHHHCCCCHHHHHHHHHHCCHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCC-------CCCCCCCCHH
T ss_conf 578999988702999999999985899997068897889999999999988874212455454-------5667775259
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHC
Q ss_conf 9999999967999899999999998516888898999999999745
Q gi|254780553|r 161 INAISALVNLGYGQDQATTAVVSVLKKEKNIADDSQIIRLALRAIS 206 (207)
Q Consensus 161 ~d~~~AL~~LGy~~~ea~~ai~~i~~~~~~~~~~eelIk~aLk~Ls 206 (207)
.|+++||.+|||++++|++|++.+..+ ..++|++||.|||+||
T Consensus 154 ~d~~~AL~~LGy~~~ea~~ai~~i~~~---~~~~eelIk~aLk~Ls 196 (198)
T PRK00116 154 EEAVSALVALGYKPKEAQKAVAAILKE---GASVEELIREALKLLS 196 (198)
T ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHCC---CCCHHHHHHHHHHHHC
T ss_conf 999999998599999999999986436---9999999999999972
No 2
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=100.00 E-value=0 Score=405.76 Aligned_cols=201 Identities=36% Similarity=0.544 Sum_probs=179.1
Q ss_pred CCCEEEEEEEEEECCEEEEEECCEEEEEECCHHHHHHCCCCCCEEEEEEEEEECCCCEEEEEEECHHHHHHHHHHHHHHH
Q ss_conf 93258999999609979998588323897086889850247984999999997388418999706779999999850100
Q gi|254780553|r 1 MIGKIKGNIEGLYEDYVLIDVQGVCYIIYCPIRTLSCLGKIGDFCTLFVETHMRQDQIRLFGFLSDLDRQWFMLLQSVQG 80 (207)
Q Consensus 1 MI~~i~G~i~~~~~~~ivi~v~GvGY~i~vs~~~~~~l~~~g~~v~l~~~~~vrEd~~~LyGF~~~~Er~~F~~Li~V~G 80 (207)
||+||+|+|.++.++++|+|||||||+|+||.+++.++++.|+.+.+|||++||||++.||||.|.+||+||+.|++|||
T Consensus 1 Mi~~l~G~v~~~~~~~ivie~~GVGY~i~~~~~~~~~l~~~g~~~~l~t~~~vREd~~~LyGF~~~~ER~lF~~LisVnG 80 (201)
T COG0632 1 MIGYLRGKVTEKNPDYIVIEVNGVGYEINVPMRTLAELPEVGEEVKLFTHLVVREDAHLLYGFLTEEERELFRLLISVNG 80 (201)
T ss_pred CCCEEEEEEEEECCCEEEEEECCEEEEEECCHHHHHHCCCCCCEEEEEEEEEEHHHHHHHCCCCCHHHHHHHHHHHCCCC
T ss_conf 96516899999659989999578789997682888634469974999999752202788708998899999999871188
Q ss_pred CCCHHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHH
Q ss_conf 05101124431578999999985156687510457116799999999742221101133443233333445555653158
Q gi|254780553|r 81 VGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMTELKGKAISLSSVVQQDMSCVNKEQAHICSMPSFA 160 (207)
Q Consensus 81 IGpK~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~K~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 160 (207)
||||+||+|||++++++|++||.++|+++|+++||||||||+||++|||||+..+............ .. ... ....
T Consensus 81 IGpK~ALaiLs~~~~~~l~~aI~~~d~~~L~k~PGIGkKtAerivleLk~K~~~~~~~~~~~~~~~~--~~-~~~-~~~~ 156 (201)
T COG0632 81 IGPKLALAILSNLDPEELAQAIANEDVKALSKIPGIGKKTAERIVLELKGKLAAFLKGDGGSPAEDL--SL-DES-SPAL 156 (201)
T ss_pred CCHHHHHHHHCCCCHHHHHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCC--CC-CCC-CHHH
T ss_conf 0589999998489999999999832867644189877889999999976056411321135532345--65-655-1235
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHC
Q ss_conf 9999999967999899999999998516888898999999999745
Q gi|254780553|r 161 INAISALVNLGYGQDQATTAVVSVLKKEKNIADDSQIIRLALRAIS 206 (207)
Q Consensus 161 ~d~~~AL~~LGy~~~ea~~ai~~i~~~~~~~~~~eelIk~aLk~Ls 206 (207)
+++++||++|||+++|+++|+..+..+ ++..+++++||.|||+++
T Consensus 157 ~~~v~AL~~LGy~~~e~~~av~~v~~~-~~~~~~~~~Ik~aLk~~~ 201 (201)
T COG0632 157 EEAVEALVALGYKEKEIKKAVKKVLKE-NPDADVEELIKEALKLLL 201 (201)
T ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHC-CCCCCHHHHHHHHHHHCC
T ss_conf 689999998499999999999998733-788889999999998609
No 3
>PRK13901 ruvA Holliday junction DNA helicase motor protein; Provisional
Probab=100.00 E-value=0 Score=402.67 Aligned_cols=191 Identities=25% Similarity=0.393 Sum_probs=173.6
Q ss_pred CCCEEEEEEEEEECCEEEEEECCEEEEEECCHHHHHHCCCCCCEEEEEEEEEECCCCEEEEEEECHHHHHHHHHHHHHHH
Q ss_conf 93258999999609979998588323897086889850247984999999997388418999706779999999850100
Q gi|254780553|r 1 MIGKIKGNIEGLYEDYVLIDVQGVCYIIYCPIRTLSCLGKIGDFCTLFVETHMRQDQIRLFGFLSDLDRQWFMLLQSVQG 80 (207)
Q Consensus 1 MI~~i~G~i~~~~~~~ivi~v~GvGY~i~vs~~~~~~l~~~g~~v~l~~~~~vrEd~~~LyGF~~~~Er~~F~~Li~V~G 80 (207)
||+||+|++.++.++++||+||||||+|++|.++++.+ +.|++++||||++||||+++||||.+.+||++|++|++|+|
T Consensus 1 MI~~l~G~i~~~~~~~vvl~v~GvGY~V~vs~~~~~~l-~~~~~v~l~t~~~vrEd~~~LyGF~~~~Er~~F~~LisVsG 79 (196)
T PRK13901 1 MINKIYGKIIEKKESSIVIMATPFEFELLVSSFCLAEL-RLLEDVEILTYLHTREDELKLFGFLNSSEREVFEELIGVDG 79 (196)
T ss_pred CCCEEEEEEEEECCCEEEEEECCEEEEEEECHHHHHHC-CCCCEEEEEEEEEEEECCCEEECCCCHHHHHHHHHHHCCCC
T ss_conf 95479999999629979999348799999678999765-89980899999999516771336598899999999876588
Q ss_pred CCCHHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHH
Q ss_conf 05101124431578999999985156687510457116799999999742221101133443233333445555653158
Q gi|254780553|r 81 VGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMTELKGKAISLSSVVQQDMSCVNKEQAHICSMPSFA 160 (207)
Q Consensus 81 IGpK~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~K~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 160 (207)
||||+||+|||+++|+++++||.++|.+.|+++||||+|||+|||+|||||+.+..... ......
T Consensus 80 IGpk~Al~iLs~~~~~~l~~aI~~~D~~~L~~vpGIG~KtA~rIi~ELk~Kl~~~~~~~---------------~~~~~~ 144 (196)
T PRK13901 80 IGPRAALRVLSGIKYNEFRDAIDREDIELISKVKGIGNKMAGKIFLKLRGKLVKNDELE---------------SSLFKF 144 (196)
T ss_pred CCHHHHHHHHCCCCHHHHHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCC---------------CCCCCH
T ss_conf 26899999975799999999999289999831999589999999999976531566556---------------553448
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHCCC-----CCCHHHHHHHHHHHHCC
Q ss_conf 999999996799989999999999851688-----88989999999997459
Q gi|254780553|r 161 INAISALVNLGYGQDQATTAVVSVLKKEKN-----IADDSQIIRLALRAISC 207 (207)
Q Consensus 161 ~d~~~AL~~LGy~~~ea~~ai~~i~~~~~~-----~~~~eelIk~aLk~Ls~ 207 (207)
.|+.+||.+|||++++|++|++++.+.++. ..+.|++||+|||+||-
T Consensus 145 ~e~~~AL~~LGy~~~~a~~al~~i~~~~~~~~~~~~~~~e~likeaLK~Ls~ 196 (196)
T PRK13901 145 KELEQSIVNMGFDRKLVNSAIKEIMLLDEFLNLKDSEQEQFLFKEVLKRLSN 196 (196)
T ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCC
T ss_conf 9999999984999899999999998508456778504289999999998539
No 4
>TIGR00084 ruvA Holliday junction DNA helicase RuvA; InterPro: IPR000085 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure . In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB.; GO: 0003678 DNA helicase activity, 0006281 DNA repair, 0006310 DNA recombination.
Probab=100.00 E-value=0 Score=364.65 Aligned_cols=203 Identities=29% Similarity=0.420 Sum_probs=178.1
Q ss_pred CCCEEEEEEEEEEC-----CEEEEEECCEEEEEECCHHHHHHCCCCC-CEEEEEEEEEECCCC----EEEEEEECHHHHH
Q ss_conf 93258999999609-----9799985883238970868898502479-849999999973884----1899970677999
Q gi|254780553|r 1 MIGKIKGNIEGLYE-----DYVLIDVQGVCYIIYCPIRTLSCLGKIG-DFCTLFVETHMRQDQ----IRLFGFLSDLDRQ 70 (207)
Q Consensus 1 MI~~i~G~i~~~~~-----~~ivi~v~GvGY~i~vs~~~~~~l~~~g-~~v~l~~~~~vrEd~----~~LyGF~~~~Er~ 70 (207)
||.+|+|+|.++.+ .+++|++|||||++++|.++...++..| ++.++|||+++|||+ +.||||.+.+||+
T Consensus 1 mI~~l~G~v~~v~~niqnr~~i~~e~~gv~Y~~~v~~~~~~~~~~~gP~~~~~Ft~~~~RedaNQi~~~LfGF~~~~Er~ 80 (217)
T TIGR00084 1 MIGFLQGKVIEVSKNIQNRREIILEVNGVGYELQVPMTCAYELNLEGPQKAQLFTHLVVREDANQILHLLFGFNTLEERE 80 (217)
T ss_pred CCCEEEEEEEEECCCCCCCCEEEEEEEEEEEEEECCCHHHHHCCCCCCCCCEEEEEEEEECCHHHHHHHHHCCCCHHHHH
T ss_conf 97514568888446522461788873128999878721432047871486346787777604678999973479877899
Q ss_pred HHHHHHHHHHCCCHHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHH-HHHHHHHHHCCCCCCCCCCCCCCC
Q ss_conf 9999850100051011244315789999999851566875104571167999999-997422211011334432333334
Q gi|254780553|r 71 WFMLLQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIM-TELKGKAISLSSVVQQDMSCVNKE 149 (207)
Q Consensus 71 ~F~~Li~V~GIGpK~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi-~ELk~K~~~~~~~~~~~~~~~~~~ 149 (207)
||+.||+|||||||+||+|||+++++++..||.++|++.|+++||||||+|+||+ +||+||+.................
T Consensus 81 lF~~Li~~nGvGpk~ALaiL~~~~~~~~~~ai~~~~~~~L~k~pGvGKK~A~~l~~leL~gk~~~~~~~~~~~~~~~~~~ 160 (217)
T TIGR00084 81 LFKELIKVNGVGPKLALAILSNMSPEEFVQAIETEEVKALVKIPGVGKKTAERLLALELKGKLKGVKNLEMFTNLANHLE 160 (217)
T ss_pred HHHHHHHCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCC
T ss_conf 99998514880289999986678875898888641044420458857378999987775454405521124554335335
Q ss_pred CCCCCCCCCHH-HHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH
Q ss_conf 45555653158-999999996799989999999999851688889899999999974
Q gi|254780553|r 150 QAHICSMPSFA-INAISALVNLGYGQDQATTAVVSVLKKEKNIADDSQIIRLALRAI 205 (207)
Q Consensus 150 ~~~~~~~~~~~-~d~~~AL~~LGy~~~ea~~ai~~i~~~~~~~~~~eelIk~aLk~L 205 (207)
........... +|+.+||.+|||+++||.+++..+. .+++.+.++.+++|||.+
T Consensus 161 ~~~~~~~~~~~y~E~~~aL~sLGY~~~Ei~~~l~~~~--~~~~~~~~~~~~eal~~l 215 (217)
T TIGR00084 161 TDEKLTAEAARYDELFEALVSLGYKPQEIQKALKKIK--EKPDLAIEQDIKEALKQL 215 (217)
T ss_pred CCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHC--CCCCCCHHHHHHHHHHHH
T ss_conf 5410121021188999999972988889999998640--467885446799999997
No 5
>pfam01330 RuvA_N RuvA N terminal domain. The N terminal domain of RuvA has an OB-fold structure. This domain forms the RuvA tetramer contacts.
Probab=99.66 E-value=4.1e-16 Score=128.08 Aligned_cols=61 Identities=34% Similarity=0.624 Sum_probs=58.8
Q ss_pred CCCEEEEEEEEEECCEEEEEECCEEEEEECCHHHHHHCCCCCCEEEEEEEEEECCCCEEEEE
Q ss_conf 93258999999609979998588323897086889850247984999999997388418999
Q gi|254780553|r 1 MIGKIKGNIEGLYEDYVLIDVQGVCYIIYCPIRTLSCLGKIGDFCTLFVETHMRQDQIRLFG 62 (207)
Q Consensus 1 MI~~i~G~i~~~~~~~ivi~v~GvGY~i~vs~~~~~~l~~~g~~v~l~~~~~vrEd~~~LyG 62 (207)
||+||+|++.++++++++||||||||+|++|.+++++++. ++++++|||++||||+++|||
T Consensus 1 MI~~l~G~i~~~~~~~ivi~~~GvGY~v~is~~~~~~l~~-~~~v~l~t~~~vRED~~~LyG 61 (61)
T pfam01330 1 MIAYLRGKVTEVGPDYIVVEVNGVGYEINVSARTLAELPE-GGEVKLFTHLIVREDALLLYG 61 (61)
T ss_pred CEEEEEEEEEEECCCEEEEEECCEEEEEEECHHHHHHCCC-CCEEEEEEEEEEEECCHHCCC
T ss_conf 9119999999972999999967879999988899976799-988999999999016221079
No 6
>pfam07499 RuvA_C RuvA, C-terminal domain. Homologous recombination is a crucial process in all living organisms. In bacteria, this process the RuvA, RuvB, and RuvC proteins are involved. More specifically the proteins process the Holliday junction DNA. RuvA is comprised of three distinct domains. The domain represents the C-terminal domain and plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB. Within the Holliday junction, the C-terminal domain makes no interaction with DNA.
Probab=98.53 E-value=2.5e-07 Score=69.57 Aligned_cols=46 Identities=39% Similarity=0.499 Sum_probs=40.4
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHC
Q ss_conf 589999999967999899999999998516888898999999999745
Q gi|254780553|r 159 FAINAISALVNLGYGQDQATTAVVSVLKKEKNIADDSQIIRLALRAIS 206 (207)
Q Consensus 159 ~~~d~~~AL~~LGy~~~ea~~ai~~i~~~~~~~~~~eelIk~aLk~Ls 206 (207)
..+|+++||++|||++.+|.+++..+.. .+..+++++||.|||+||
T Consensus 2 ~~~da~~AL~~LGy~~~ea~~av~~v~~--~~~~~~e~~Ir~ALk~L~ 47 (47)
T pfam07499 2 ALEEAVSALLALGYKEKEAEKAVAKVLE--DPGASVEELIRAALKLLS 47 (47)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHC--CCCCCHHHHHHHHHHHHC
T ss_conf 5889999999939989999999999764--899999999999998719
No 7
>PRK13766 Hef nuclease; Provisional
Probab=98.12 E-value=3.3e-06 Score=62.08 Aligned_cols=63 Identities=21% Similarity=0.359 Sum_probs=52.9
Q ss_pred EECHHHHHHHHHHHHHHHCCCHHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHH
Q ss_conf 7067799999998501000510112443157899999998515668751045711679999999974
Q gi|254780553|r 63 FLSDLDRQWFMLLQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMTELK 129 (207)
Q Consensus 63 F~~~~Er~~F~~Li~V~GIGpK~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk 129 (207)
..+..|+..| .|-++.||||+.|-.+|..+.. ++.|.+-+..-|++|+|||+|+|++|--=|.
T Consensus 697 ~~~~~e~q~~-~l~~~pgvg~~~a~~ll~~fgs---i~~i~~a~~~eL~~v~giG~~~A~~i~~~~~ 759 (764)
T PRK13766 697 AMTLKEQQEY-IVSSLPDVGPVLARNLLDHFGS---VENVMTASEEELKAVEGIGEKTAKKIREVVT 759 (764)
T ss_pred CCCHHHHHHH-HHHHCCCCCHHHHHHHHHHCCC---HHHHHCCCHHHHHHCCCCCHHHHHHHHHHHC
T ss_conf 6877899999-9983899999999999997199---9999659999995474969999999999852
No 8
>TIGR01448 recD_rel helicase, RecD/TraA family; InterPro: IPR006345 These sequences represent a family similar to RecD, the exodeoxyribonuclease V alpha chain of IPR006344 from INTERPRO. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD. .
Probab=97.64 E-value=0.00023 Score=49.71 Aligned_cols=128 Identities=16% Similarity=0.199 Sum_probs=88.2
Q ss_pred HHHHHCCCCCCEEEEEEEEEECCCCEEEEEEECHHH---------HHH--HHHHHHHHHCCCHHHHHHHCCCCHHHHHHH
Q ss_conf 889850247984999999997388418999706779---------999--999850100051011244315789999999
Q gi|254780553|r 33 RTLSCLGKIGDFCTLFVETHMRQDQIRLFGFLSDLD---------RQW--FMLLQSVQGVGARVAMGVLSRITATELVES 101 (207)
Q Consensus 33 ~~~~~l~~~g~~v~l~~~~~vrEd~~~LyGF~~~~E---------r~~--F~~Li~V~GIGpK~AL~iLs~l~~~~l~~a 101 (207)
++++.+ .+|+.++++.+....-..=.=|=|.+.+. .-+ |..=-.|.|||+|+|=.|..++.-+.| -
T Consensus 43 s~l~~~-~~G~~~~f~Gq~~~h~~yG~q~~~~~~~~~amP~~~~~~gi~~Yl~S~~~KGvGk~~Aq~Iv~TfGe~~~--~ 119 (769)
T TIGR01448 43 SVLAAL-AEGDSYTFEGQWEEHAKYGKQFKAERMEKEAMPAPTSKEGIVAYLSSSSIKGVGKKLAQRIVETFGEAAI--D 119 (769)
T ss_pred CCCCCC-CCCCEEEEEEEEEECCCCCEEEEEEEEHHHHCCCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHH--H
T ss_conf 546753-0166156889888875445152335201430788650678765552254167205778999998769999--8
Q ss_pred HHCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHH
Q ss_conf 85156687510457116799999999742221101133443233333445555653158999999996799989999999
Q gi|254780553|r 102 IILQNSKVIAQIPGISMKIASRIMTELKGKAISLSSVVQQDMSCVNKEQAHICSMPSFAINAISALVNLGYGQDQATTAV 181 (207)
Q Consensus 102 I~~~D~~~L~~vpGIGkKtA~rIi~ELk~K~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~AL~~LGy~~~ea~~ai 181 (207)
...+|...|.+|+||++|+-++|+-.|+..- -...++.-|..|||..+.+.++.
T Consensus 120 ~l~~~P~kL~~V~G~s~~~~~~~~~~~~~~~--------------------------~~~~~l~~L~~lG~~~~l~~~~~ 173 (769)
T TIGR01448 120 VLDDDPEKLLEVSGISKANLEKIVSQLSKQK--------------------------DERKLLLKLQQLGIGIKLALRIY 173 (769)
T ss_pred HHHCCCHHEEEECCCCHHHHHHHHHHHHHHH--------------------------HHHHHHHHHHHCCCCHHHHHHHH
T ss_conf 8740860103307756677899999999755--------------------------89999999985387678999999
Q ss_pred HHHHHHCC
Q ss_conf 99985168
Q gi|254780553|r 182 VSVLKKEK 189 (207)
Q Consensus 182 ~~i~~~~~ 189 (207)
+.....+|
T Consensus 174 k~y~eadP 181 (769)
T TIGR01448 174 KFYREADP 181 (769)
T ss_pred HHHCCCCC
T ss_conf 98403587
No 9
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=97.22 E-value=0.00027 Score=49.25 Aligned_cols=53 Identities=26% Similarity=0.504 Sum_probs=45.8
Q ss_pred HHHHHHHCCCHHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHH
Q ss_conf 98501000510112443157899999998515668751045711679999999974
Q gi|254780553|r 74 LLQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMTELK 129 (207)
Q Consensus 74 ~Li~V~GIGpK~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk 129 (207)
.|-+|.|||||..-.+|..+.. ++.|.+....-|.++||||+++|++|--.|.
T Consensus 555 ~Ld~I~GIG~kr~~~Ll~~Fgs---~~~i~~As~eeL~~v~Gi~~~~A~~I~~~l~ 607 (609)
T PRK00558 555 RLDDIPGIGPKRRKALLKHFGS---LKAIKEASVEELAKVPGISKKLAEKIYEALH 607 (609)
T ss_pred CCCCCCCCCHHHHHHHHHHCCC---HHHHHHCCHHHHHHCCCCCHHHHHHHHHHHH
T ss_conf 1647899799999999997079---9999738999996489989999999999970
No 10
>PRK08609 hypothetical protein; Provisional
Probab=96.99 E-value=0.00035 Score=48.57 Aligned_cols=52 Identities=15% Similarity=0.323 Sum_probs=38.5
Q ss_pred HHHHHHHHHCCCHHHHHHHCC---CCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHH
Q ss_conf 999850100051011244315---7899999998515668751045711679999999
Q gi|254780553|r 72 FMLLQSVQGVGARVAMGVLSR---ITATELVESIILQNSKVIAQIPGISMKIASRIMT 126 (207)
Q Consensus 72 F~~Li~V~GIGpK~AL~iLs~---l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ 126 (207)
+..|..|.|||||.|-.+-.. -+.++|.+|..++. +.++||+|.||.++|+-
T Consensus 87 l~eLl~IpGlGPKka~~L~~eLGI~sleeL~~A~~~gr---i~~L~GfG~Ktee~IL~ 141 (570)
T PRK08609 87 LLPLLKLPGLGGKKIAKLYKELGVVDKESLKEACENGK---VQALAGFGKKTEEKILE 141 (570)
T ss_pred HHHHHCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHCC---HHHHHHHHHHHHHHHHH
T ss_conf 99997789877899999999829999999999987384---87654342689999999
No 11
>TIGR00615 recR recombination protein RecR; InterPro: IPR000093 The bacterial protein recR seems to play a role in a recombinational process of DNA repair . It may act with recF and recO. RecR is a protein of about 200 amino acid residues. This protein contains a putative C4-type zinc finger in the N-terminal section.; GO: 0006281 DNA repair, 0006310 DNA recombination.
Probab=96.89 E-value=0.00058 Score=47.10 Aligned_cols=22 Identities=32% Similarity=0.520 Sum_probs=20.3
Q ss_pred HHHHHHCCCCCHHHHHHHHHHH
Q ss_conf 6875104571167999999997
Q gi|254780553|r 107 SKVIAQIPGISMKIASRIMTEL 128 (207)
Q Consensus 107 ~~~L~~vpGIGkKtA~rIi~EL 128 (207)
+..|.++||||+|+|+||.++|
T Consensus 11 ie~L~kLPgiG~KsA~RlAf~L 32 (205)
T TIGR00615 11 IESLKKLPGIGPKSAQRLAFHL 32 (205)
T ss_pred HHHHHHCCCCCHHHHHHHHHHH
T ss_conf 9986407898714789999986
No 12
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=96.80 E-value=0.0015 Score=44.26 Aligned_cols=63 Identities=24% Similarity=0.423 Sum_probs=47.2
Q ss_pred EECHHHHHHHHHHHHHHHCCCHHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHH
Q ss_conf 7067799999998501000510112443157899999998515668751045711679999999974
Q gi|254780553|r 63 FLSDLDRQWFMLLQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMTELK 129 (207)
Q Consensus 63 F~~~~Er~~F~~Li~V~GIGpK~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk 129 (207)
=.+..|+..+ .|.+++||||+.|-.+|..+.. +..+.+.....|.++.|||.|.|.+|--=|.
T Consensus 173 ~~t~~e~q~~-il~s~pgig~~~a~~ll~~fgS---~~~~~tas~~eL~~v~gig~k~A~~I~~~~~ 235 (254)
T COG1948 173 AKTLKELQLY-ILESIPGIGPKLAERLLKKFGS---VEDVLTASEEELMKVKGIGEKKAREIYRFLR 235 (254)
T ss_pred CCCHHHHHHH-HHHCCCCCCHHHHHHHHHHHCC---HHHHHHCCHHHHHHHCCCCHHHHHHHHHHHH
T ss_conf 2455789999-9970899648999999998568---8877655999997744846889999999983
No 13
>PRK00076 recR recombination protein RecR; Reviewed
Probab=96.70 E-value=0.0011 Score=45.18 Aligned_cols=23 Identities=30% Similarity=0.481 Sum_probs=20.1
Q ss_pred HHHHHHCCCCCHHHHHHHHHHHH
Q ss_conf 68751045711679999999974
Q gi|254780553|r 107 SKVIAQIPGISMKIASRIMTELK 129 (207)
Q Consensus 107 ~~~L~~vpGIGkKtA~rIi~ELk 129 (207)
+..|+++||||+|||+||.+.|=
T Consensus 10 I~~l~kLPGIG~KsA~Rla~~LL 32 (197)
T PRK00076 10 IEALRKLPGIGPKSAQRLAFHLL 32 (197)
T ss_pred HHHHHHCCCCCHHHHHHHHHHHH
T ss_conf 99998789998899999999998
No 14
>PRK13844 recombination protein RecR; Provisional
Probab=96.68 E-value=0.0012 Score=45.08 Aligned_cols=24 Identities=21% Similarity=0.306 Sum_probs=20.6
Q ss_pred HHHHHHCCCCCHHHHHHHHHHHHH
Q ss_conf 687510457116799999999742
Q gi|254780553|r 107 SKVIAQIPGISMKIASRIMTELKG 130 (207)
Q Consensus 107 ~~~L~~vpGIGkKtA~rIi~ELk~ 130 (207)
+..|+++||||+|||+|+.+.|=.
T Consensus 14 I~~l~kLPGIG~KsA~Rla~~Ll~ 37 (200)
T PRK13844 14 IESLRKLPTIGKKSSQRLALYLLD 37 (200)
T ss_pred HHHHHHCCCCCHHHHHHHHHHHHC
T ss_conf 999816899878899999999864
No 15
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=96.15 E-value=0.0065 Score=40.10 Aligned_cols=55 Identities=15% Similarity=0.255 Sum_probs=39.4
Q ss_pred HHHHHHHHCCCHHHHHHH---CCCCHHHHHHHHHC---CCHHHHHHCCCCCHHHHHHHHHHH
Q ss_conf 998501000510112443---15789999999851---566875104571167999999997
Q gi|254780553|r 73 MLLQSVQGVGARVAMGVL---SRITATELVESIIL---QNSKVIAQIPGISMKIASRIMTEL 128 (207)
Q Consensus 73 ~~Li~V~GIGpK~AL~iL---s~l~~~~l~~aI~~---~D~~~L~~vpGIGkKtA~rIi~EL 128 (207)
..|..++|||+++|=.|- .+-...++-+.-.+ .....|++|||||+|||.++. ++
T Consensus 48 ~~l~~ipGIG~~ia~kI~Eil~TG~~~~~e~~~~~~~~~~l~el~~I~GvGpk~a~~l~-~~ 108 (334)
T smart00483 48 KDLKGLPGIGDKIKKKIEEIIETGKSSKVLEILNDEVYKSLKLFTNVFGVGPKTAAKWY-RK 108 (334)
T ss_pred HHHCCCCCCCHHHHHHHHHHHHCCCCHHHHHHHCCCCCHHHHHHHCCCCCCHHHHHHHH-HC
T ss_conf 99727999878999999999984994899998728651689998538887789999999-84
No 16
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=96.08 E-value=0.0039 Score=41.53 Aligned_cols=23 Identities=26% Similarity=0.460 Sum_probs=20.1
Q ss_pred HHHHHHCCCCCHHHHHHHHHHHH
Q ss_conf 68751045711679999999974
Q gi|254780553|r 107 SKVIAQIPGISMKIASRIMTELK 129 (207)
Q Consensus 107 ~~~L~~vpGIGkKtA~rIi~ELk 129 (207)
+..|.++||||+|+|+|+.+.|=
T Consensus 11 I~~l~kLPGvG~KsA~R~AfhLL 33 (198)
T COG0353 11 IDALKKLPGVGPKSAQRLAFHLL 33 (198)
T ss_pred HHHHHHCCCCCHHHHHHHHHHHH
T ss_conf 99997689988327999999997
No 17
>TIGR01259 comE comEA protein; InterPro: IPR004787 The comE locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. comEA and comEC are required for transformability, whereas the products of comEB and of the overlapping comER, which is transcribed in the reverse direction, are dispensable . ComEA has been shown to be an integral membrane protein, as predicted from hydropathy analysis, with its C-terminal domain outside the cytoplasmic membrane. This C-terminal domain possesses a sequence with similarity to those of several proteins known to be involved in nucleic acid transactions including UvrC and a human protein that binds to the replication origin of the Human herpesvirus 4 (Epstein-Barr virus) ..
Probab=95.95 E-value=0.0014 Score=44.57 Aligned_cols=50 Identities=16% Similarity=0.287 Sum_probs=37.1
Q ss_pred HHHHHHHHHHHCCCHHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHH
Q ss_conf 9999985010005101124431578999999985156687510457116799999
Q gi|254780553|r 70 QWFMLLQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRI 124 (207)
Q Consensus 70 ~~F~~Li~V~GIGpK~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rI 124 (207)
---+.|..|+||||+.|=+|.+. --+ -=.-.-+.-|++|.|||+|+-++|
T Consensus 69 As~~EL~~l~GiGP~kA~aIi~Y-Re~----nG~F~SvddL~kVsGIG~k~~eKL 118 (124)
T TIGR01259 69 ASLEELQALPGIGPAKAKAIIEY-REE----NGAFKSVDDLTKVSGIGEKSLEKL 118 (124)
T ss_pred HHHHHHHHCCCCCCHHHHHHHHH-HHH----CCCCCCHHHHHCCCCCCHHHHHHH
T ss_conf 78999863699981337999999-985----699777555003578854668742
No 18
>PRK08609 hypothetical protein; Provisional
Probab=95.91 E-value=0.0047 Score=41.05 Aligned_cols=57 Identities=18% Similarity=0.219 Sum_probs=40.5
Q ss_pred HHHHHHHHCCCHHHHHHHC---CCCHHHHHHHHH--CCCHHHHHHCCCCCHHHHHHHHHHHH
Q ss_conf 9985010005101124431---578999999985--15668751045711679999999974
Q gi|254780553|r 73 MLLQSVQGVGARVAMGVLS---RITATELVESII--LQNSKVIAQIPGISMKIASRIMTELK 129 (207)
Q Consensus 73 ~~Li~V~GIGpK~AL~iLs---~l~~~~l~~aI~--~~D~~~L~~vpGIGkKtA~rIi~ELk 129 (207)
..|.+++|||..+|-.|-- |-....+-+.-. -.....|.+|||||+|+|.++.-||.
T Consensus 48 ~~L~~ipGIGk~Ia~KI~Eil~TG~l~~le~L~~~~P~gl~eLl~IpGlGPKka~~L~~eLG 109 (570)
T PRK08609 48 EDFTKIKGIGKGTAEVIQEYRETGESSVLQELQKEVPEGLLPLLKLPGLGGKKIAKLYKELG 109 (570)
T ss_pred HHHHCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHCCHHHHHHHCCCCCCHHHHHHHHHHHC
T ss_conf 87745999549999999999972990899999854877799997789877899999999829
No 19
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this
Probab=95.63 E-value=0.0062 Score=40.22 Aligned_cols=54 Identities=20% Similarity=0.343 Sum_probs=37.5
Q ss_pred HHHHHHHHCCCHHHHHHH---CCCCHHHHHHHHHCC---CHHHHHHCCCCCHHHHHHHHHHH
Q ss_conf 998501000510112443---157899999998515---66875104571167999999997
Q gi|254780553|r 73 MLLQSVQGVGARVAMGVL---SRITATELVESIILQ---NSKVIAQIPGISMKIASRIMTEL 128 (207)
Q Consensus 73 ~~Li~V~GIGpK~AL~iL---s~l~~~~l~~aI~~~---D~~~L~~vpGIGkKtA~rIi~EL 128 (207)
..+.+++|||+++|=.|- .+-...++-+ +.++ ....|.++||||+|+|.++. ++
T Consensus 45 ~~~~~lpGIG~~ia~kI~Eil~tG~~~~le~-l~~~~p~~l~~l~~I~GiGpk~a~~l~-~~ 104 (307)
T cd00141 45 EEAKKLPGIGKKIAEKIEEILETGKLRKLEE-LREDVPPGLLLLLRVPGVGPKTARKLY-EL 104 (307)
T ss_pred HHHCCCCCCCHHHHHHHHHHHHHCCHHHHHH-HHCCCCHHHHHHHCCCCCCHHHHHHHH-HC
T ss_conf 9871799964899999999999798089999-866563789999647887889999999-82
No 20
>TIGR00426 TIGR00426 competence protein ComEA helix-hairpin-helix repeat region; InterPro: IPR004509 This domain is found in competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This domain represents a region of two tandem copies of a helix-hairpin-helix domain, each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to this domain..
Probab=95.46 E-value=0.0073 Score=39.77 Aligned_cols=49 Identities=20% Similarity=0.293 Sum_probs=35.5
Q ss_pred HHHHH-HHHCCCHHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHH
Q ss_conf 99850-1000510112443157899999998515668751045711679999999
Q gi|254780553|r 73 MLLQS-VQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMT 126 (207)
Q Consensus 73 ~~Li~-V~GIGpK~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ 126 (207)
+.|.. ++|||||.|=+|.+ +-=+ .=.-.++.-|++|||||+++-||+--
T Consensus 17 eElq~~~~GvG~kKAeAIv~-YREe----~G~F~t~Edl~~V~GiG~~~~Ek~~~ 66 (70)
T TIGR00426 17 EELQKALSGVGAKKAEAIVA-YREE----YGRFKTVEDLKKVSGIGEKLLEKNKA 66 (70)
T ss_pred HHHHHHHCCCCHHHHHHHHH-HHHC----CCCCCCHHHHHHCCCCCHHHHHHHHH
T ss_conf 88887642887237899988-7532----77957622232147876245555644
No 21
>PRK07945 hypothetical protein; Provisional
Probab=95.22 E-value=0.05 Score=34.16 Aligned_cols=87 Identities=16% Similarity=0.139 Sum_probs=55.0
Q ss_pred HHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC---------C---CC
Q ss_conf 01124431578999999985156687510457116799999999742221101133443233333---------4---45
Q gi|254780553|r 84 RVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMTELKGKAISLSSVVQQDMSCVNK---------E---QA 151 (207)
Q Consensus 84 K~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~K~~~~~~~~~~~~~~~~~---------~---~~ 151 (207)
+.|-.++..++++++.+-...+ .|+.+||||+|||+-|.--+.+.++.............+. + .+
T Consensus 28 r~aa~~~~~~~~~~~~~~~~~~---~~~~l~gig~~ta~vi~~a~~g~~p~~l~~l~~~~~~~~g~~l~~~LRGDLH~HT 104 (335)
T PRK07945 28 RNAADVVEALDEAERARHGRAG---SWQSLPGIGPKTAKVIAQAWAGRVPDYLAELRAAAEDLGGGELRAALRGDLHLHS 104 (335)
T ss_pred HHHHHHHHHCCHHHHHHHHHCC---CCEECCCCCHHHHHHHHHHHCCCCCHHHHHHHHHCCCCCHHHHHHHHHHCCCCCC
T ss_conf 9999999837999999987449---8112788780589999999658982899999974469864899998630653378
Q ss_pred CCCCCCCHHHHHHHHHHHCCCC
Q ss_conf 5556531589999999967999
Q gi|254780553|r 152 HICSMPSFAINAISALVNLGYG 173 (207)
Q Consensus 152 ~~~~~~~~~~d~~~AL~~LGy~ 173 (207)
.-+......+|...|-..|||.
T Consensus 105 ~wSDG~~sieeMa~aA~~lGye 126 (335)
T PRK07945 105 DWSDGGSPIEEMMATAAALGHE 126 (335)
T ss_pred CCCCCCCHHHHHHHHHHHCCCE
T ss_conf 8457978699999999983982
No 22
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=94.79 E-value=0.026 Score=36.02 Aligned_cols=27 Identities=26% Similarity=0.336 Sum_probs=17.6
Q ss_pred HHCCCHHHHHHCCCCCHHHHHHHHHHH
Q ss_conf 851566875104571167999999997
Q gi|254780553|r 102 IILQNSKVIAQIPGISMKIASRIMTEL 128 (207)
Q Consensus 102 I~~~D~~~L~~vpGIGkKtA~rIi~EL 128 (207)
|.+.|..-|..+||||+|.|++|+-.-
T Consensus 91 iNtAs~eeL~~lpgIG~~kA~aIi~yR 117 (149)
T COG1555 91 INTASAEELQALPGIGPKKAQAIIDYR 117 (149)
T ss_pred CCCCCHHHHHHCCCCCHHHHHHHHHHH
T ss_conf 661089999886798999999999999
No 23
>PRK07456 consensus
Probab=94.77 E-value=0.032 Score=35.42 Aligned_cols=143 Identities=10% Similarity=0.029 Sum_probs=65.8
Q ss_pred EEEEECCHHHHHHCCCCCCEEEEEEEE-E---E-CCCC---------EEEEEEECHHHHHHHHHHH--------HHHHCC
Q ss_conf 238970868898502479849999999-9---7-3884---------1899970677999999985--------010005
Q gi|254780553|r 25 CYIIYCPIRTLSCLGKIGDFCTLFVET-H---M-RQDQ---------IRLFGFLSDLDRQWFMLLQ--------SVQGVG 82 (207)
Q Consensus 25 GY~i~vs~~~~~~l~~~g~~v~l~~~~-~---v-rEd~---------~~LyGF~~~~Er~~F~~Li--------~V~GIG 82 (207)
||+|++-...-+.+.=+++++.+++.. . . +-.. ..=||+.-.+=.+ |.-|+ +|.|||
T Consensus 136 g~~v~IvSgDKDl~QLV~d~~~v~vl~~~~~p~~~~~~~~~~d~~~V~ek~GV~P~qiiD-~lAL~GDsSDNIPGVpGIG 214 (975)
T PRK07456 136 GWRVRILSGDRDLFQLVDDERDIAVLYMGGGPYAKSGGPTLINEAGVKEKLGVAPEQVVD-LKALTGDSSDNIPGVKGVG 214 (975)
T ss_pred CCEEEEECCCCCHHHHCCCCCCEEEEECCCCCCCCCCCCEEECHHHHHHHHCCCHHHHHH-HHHHCCCCCCCCCCCCCCC
T ss_conf 990899788824886087876669982168754466776562699999986959899899-9997288656889999855
Q ss_pred CHHHHHHHCCC-CHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHH-----HHHHHHHCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 10112443157-8999999985156687510457116799999999-----74222110113344323333344555565
Q gi|254780553|r 83 ARVAMGVLSRI-TATELVESIILQNSKVIAQIPGISMKIASRIMTE-----LKGKAISLSSVVQQDMSCVNKEQAHICSM 156 (207)
Q Consensus 83 pK~AL~iLs~l-~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~E-----Lk~K~~~~~~~~~~~~~~~~~~~~~~~~~ 156 (207)
||+|..+|+.+ +.+.+++.+.+=..+.- +-.-|..|..++|.-. |.-++..+....+-+.. ......
T Consensus 215 ~KTA~kLL~eyGsLE~Iyen~d~i~~~k~-~~~~IKgkl~e~L~~~~d~A~LSkeLvTI~~Dvpl~~~------~dl~~~ 287 (975)
T PRK07456 215 PKTAINLLKENGDLDGIYKALDEIEGEKA-YRGAIKGALKKKLKNDKDNAYLSRFLAEILVDVPLPLD------ESLELT 287 (975)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHHCCCCC-CCCCCCHHHHHHHHHHHHHHHHHHHHHHEEECCCCCCC------HHHCCC
T ss_conf 99999999984999999982876200111-11234448899999979999988997650017988865------554268
Q ss_pred CCHHHHHHHHHHHCCCCHH
Q ss_conf 3158999999996799989
Q gi|254780553|r 157 PSFAINAISALVNLGYGQD 175 (207)
Q Consensus 157 ~~~~~d~~~AL~~LGy~~~ 175 (207)
+...+.+..-+..|+|+.-
T Consensus 288 ~~d~~~L~~lf~elEF~sL 306 (975)
T PRK07456 288 GFDQELLSPLLEKLELNSL 306 (975)
T ss_pred CCCHHHHHHHHHHHCCHHH
T ss_conf 9999999999999554789
No 24
>TIGR00593 pola DNA polymerase I; InterPro: IPR002298 DNA carries 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 cell life cycle. This function is mediated by DNA-directed DNA polymerases, which add nucleotide triphosphate (dNTP) residues to the 5'-end of the growing DNA chain, using a complementary DNA as template. Small RNA molecules are generally used as primers for chain elongation, although terminal proteins may also be used. DNA-dependent DNA polymerases have been grouped into families, denoted A, B and X, on the basis of sequence similarities , . Members of family A, which includes bacterial and bacteriophage polymerases, share significant similarity to Escherichia coli polymerase I; hence family A is also known as the pol I family. The bacterial polymerases also contain an exonuclease activity, which is coded for in the N-terminal portion. Three motifs, A, B and C , are seen to be conserved across all DNA polymerases, with motifs A and C also seen in RNA polymerases. They are centred on invariant residues, and their structural significance was implied from the Klenow (E. coli) structure. Motif A contains a strictly-conserved aspartate at the junction of a beta-strand and an alpha-helix; motif B contains an alpha-helix with positive charges; and motif C has a doublet of negative charges, located in a beta-turn-beta secondary structure .; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication.
Probab=94.75 E-value=0.044 Score=34.53 Aligned_cols=107 Identities=13% Similarity=0.218 Sum_probs=68.3
Q ss_pred CEEEEEECCHHHHHHCCCCCC-EEEEEEEEE------EC----CCCEEEEEEECHHHHHHHHHHH--------HHHHCCC
Q ss_conf 832389708688985024798-499999999------73----8841899970677999999985--------0100051
Q gi|254780553|r 23 GVCYIIYCPIRTLSCLGKIGD-FCTLFVETH------MR----QDQIRLFGFLSDLDRQWFMLLQ--------SVQGVGA 83 (207)
Q Consensus 23 GvGY~i~vs~~~~~~l~~~g~-~v~l~~~~~------vr----Ed~~~LyGF~~~~Er~~F~~Li--------~V~GIGp 83 (207)
.-||+|.|=....+.+.=..+ +|+++.-.. +. |+=..=||=.-.+=.+++ -|+ +|+||||
T Consensus 124 ~~G~~V~I~sgDrD~lQLvs~e~V~V~~~~~~~g~~~~~~~t~e~V~eKyGv~P~Q~~D~~-AL~GD~SDNiPGV~GIGe 202 (1005)
T TIGR00593 124 KEGYEVRIISGDRDLLQLVSDENVKVLIPERKKGKTEFTEITPEYVVEKYGVTPSQLVDLK-ALVGDSSDNIPGVKGIGE 202 (1005)
T ss_pred HCCCEEEEEECCCCCCCCCCCCCEEEEECCCCCCCCCCEECCHHHHHHHCCCCHHHHHHHH-HCCCCCCCCCCCCCCCCC
T ss_conf 4685489983784621121786148864354567543101177898754186745788762-046888878599897376
Q ss_pred HHHHHHHCCC-CHHHHHHHHHCCCHHHHHHCCCCCH-HHHHHHHHHHHH
Q ss_conf 0112443157-8999999985156687510457116-799999999742
Q gi|254780553|r 84 RVAMGVLSRI-TATELVESIILQNSKVIAQIPGISM-KIASRIMTELKG 130 (207)
Q Consensus 84 K~AL~iLs~l-~~~~l~~aI~~~D~~~L~~vpGIGk-KtA~rIi~ELk~ 130 (207)
|+|..+|..+ |.+.+.++-.-...-.+..+..|-+ |.-+++.-+.-+
T Consensus 203 KTA~kLL~~fgsLe~iy~~~ylkealr~~~~~~~k~~~~~~~L~~~~e~ 251 (1005)
T TIGR00593 203 KTAAKLLQEFGSLENIYENTYLKEALRLDNLDQIKSEKLREKLIAHKED 251 (1005)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf 5689999872108999988778888747758622865788999987753
No 25
>PTZ00217 flap endonuclease-1; Provisional
Probab=94.68 E-value=0.26 Score=29.35 Aligned_cols=102 Identities=13% Similarity=0.150 Sum_probs=53.5
Q ss_pred HHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCC-------CC------------CC
Q ss_conf 011244315789999999851566875104571167999999997422211011334-------43------------23
Q gi|254780553|r 84 RVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMTELKGKAISLSSVVQ-------QD------------MS 144 (207)
Q Consensus 84 K~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~K~~~~~~~~~-------~~------------~~ 144 (207)
...|.-|. ++.++|+..-.----.....+||||+|+|=++|-+.+. +.++..... .+ ..
T Consensus 212 ~~il~~l~-lt~eqfidlcIL~GcDY~~~I~GIGpk~A~klIk~~~s-ie~il~~~~~~k~~~p~~~~~~~~r~~Fl~P~ 289 (394)
T PTZ00217 212 DKVLKGLG-LSMDQFIDLCILCGCDYCDTIEGIGPKTAYELIKKYGS-IEEILEHLDGTKYPVPENFPYKEARELFLNPK 289 (394)
T ss_pred HHHHHHCC-CCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHCC-HHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCC
T ss_conf 99887749-99999999999818644689987488999999999599-99999874124677998799799999962998
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHH-CCCCHHHHHHHHHHHHHH
Q ss_conf 3333445555653158999999996-799989999999999851
Q gi|254780553|r 145 CVNKEQAHICSMPSFAINAISALVN-LGYGQDQATTAVVSVLKK 187 (207)
Q Consensus 145 ~~~~~~~~~~~~~~~~~d~~~AL~~-LGy~~~ea~~ai~~i~~~ 187 (207)
....+.....-.....+.++.-|+. -||++..+++++.++.+.
T Consensus 290 V~~~~~~~l~w~~pd~e~l~~fL~~e~~Fse~Rv~~~~~~l~k~ 333 (394)
T PTZ00217 290 VTPAEEIDIKWSEPDIEGLKKFLVEEKNFNEERVEKGIERLRKA 333 (394)
T ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHH
T ss_conf 88976676508999989999997646697989999999999987
No 26
>smart00475 53EXOc 5'-3' exonuclease.
Probab=94.64 E-value=0.075 Score=32.98 Aligned_cols=36 Identities=25% Similarity=0.536 Sum_probs=19.8
Q ss_pred CHHHHH--HHHHCCCHHHHHHCCCCCHHHHHHHHHHHH
Q ss_conf 899999--998515668751045711679999999974
Q gi|254780553|r 94 TATELV--ESIILQNSKVIAQIPGISMKIASRIMTELK 129 (207)
Q Consensus 94 ~~~~l~--~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk 129 (207)
+|++++ .|+.-.-..-+..|||||+|||.+++-+..
T Consensus 170 ~P~q~~d~~aL~GD~sDnIpGV~GIG~KtA~kLL~~yg 207 (259)
T smart00475 170 TPEQIIDYKALMGDSSDNIPGVPGIGEKTAAKLLKEFG 207 (259)
T ss_pred CHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHCC
T ss_conf 98998637640464535899999847899999999839
No 27
>pfam00633 HHH Helix-hairpin-helix motif. The helix-hairpin-helix DNA-binding motif is found to be duplicated in the central domain of RuvA. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain.
Probab=94.62 E-value=0.019 Score=36.91 Aligned_cols=25 Identities=24% Similarity=0.476 Sum_probs=20.1
Q ss_pred HHHCCCHHHHHHCCCCCHHHHHHHH
Q ss_conf 9851566875104571167999999
Q gi|254780553|r 101 SIILQNSKVIAQIPGISMKIASRIM 125 (207)
Q Consensus 101 aI~~~D~~~L~~vpGIGkKtA~rIi 125 (207)
.+...+...|.++||||+|||++|+
T Consensus 4 ~~~~as~eeL~~lpGVG~~tA~~I~ 28 (30)
T pfam00633 4 GLIPASREELLALPGVGPKTAEAIL 28 (30)
T ss_pred CCCCCCHHHHHHCCCCCHHHHHHHH
T ss_conf 4352359999728897768899885
No 28
>PRK05755 DNA polymerase I; Provisional
Probab=94.43 E-value=0.078 Score=32.91 Aligned_cols=135 Identities=19% Similarity=0.224 Sum_probs=66.7
Q ss_pred EEEEECCHHHHHHCCCCCCEEEEEEEEEEC----CCCEEEEEEECHHHHHHHHHHH--------HHHHCCCHHHHHHHCC
Q ss_conf 238970868898502479849999999973----8841899970677999999985--------0100051011244315
Q gi|254780553|r 25 CYIIYCPIRTLSCLGKIGDFCTLFVETHMR----QDQIRLFGFLSDLDRQWFMLLQ--------SVQGVGARVAMGVLSR 92 (207)
Q Consensus 25 GY~i~vs~~~~~~l~~~g~~v~l~~~~~vr----Ed~~~LyGF~~~~Er~~F~~Li--------~V~GIGpK~AL~iLs~ 92 (207)
||+|++-...-+.+.=+++++++|-...-+ +.-..-||+.-.+=.+ |.-|. +|.|||||+|..+|..
T Consensus 127 ~~~v~i~s~DkD~~QLv~~~v~~~~~~k~~~~~~~~v~ek~Gv~P~q~~D-~~aL~GD~sDNIPGVpGIG~KtA~kLl~~ 205 (889)
T PRK05755 127 GFEVLIVTGDKDLLQLVDDNVTVLNTMKNERIDPEGVIEKYGVTPEQIID-FLALMGDSSDNIPGVPGVGEKTAAKLLKE 205 (889)
T ss_pred CCEEEEEECCCCHHHHCCCCEEEEECCCCCEECHHHHHHHHCCCHHHHHH-HHHHCCCCCCCCCCCCCCCHHHHHHHHHH
T ss_conf 99599980898785618898699989999285899999997969899999-99980886457899886269999999986
Q ss_pred CC-HHHHHHHHHCCCHHHHHHCCCCCHHHHHHHH-----HHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHH
Q ss_conf 78-9999999851566875104571167999999-----99742221101133443233333445555653158999999
Q gi|254780553|r 93 IT-ATELVESIILQNSKVIAQIPGISMKIASRIM-----TELKGKAISLSSVVQQDMSCVNKEQAHICSMPSFAINAISA 166 (207)
Q Consensus 93 l~-~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi-----~ELk~K~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~A 166 (207)
++ .+.+...+. +++ |+|..+++. ..|.-++..+....+-+.. .......+...+.+..-
T Consensus 206 ygsle~i~~~~d--------~i~--g~k~~~~l~~~~e~a~ls~~L~ti~~dvpl~~~-----le~l~~~~~d~~~l~~l 270 (889)
T PRK05755 206 FGSLEGLYENLD--------EIK--GKKLKEKLRENKEQAFLSRKLATIKTDVPLDVD-----LEDLELKPPDREKLIAL 270 (889)
T ss_pred CCCHHHHHHHHH--------HCC--CHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC-----HHHHCCCCCCHHHHHHH
T ss_conf 786899999898--------523--256788898469999999998565228989999-----99922589999999999
Q ss_pred HHHCCCCHH
Q ss_conf 996799989
Q gi|254780553|r 167 LVNLGYGQD 175 (207)
Q Consensus 167 L~~LGy~~~ 175 (207)
+..|+|+.-
T Consensus 271 f~elEFksL 279 (889)
T PRK05755 271 LKKLEFKSL 279 (889)
T ss_pred HHHHCCHHH
T ss_conf 998285999
No 29
>PRK06887 consensus
Probab=94.19 E-value=0.13 Score=31.49 Aligned_cols=134 Identities=17% Similarity=0.297 Sum_probs=58.9
Q ss_pred EEEEECC--HHHHHHCCCCCCEEEEEEEEEE----CCCCEEEEEEECHHHHHHHHHHH--------HHHHCCCHHHHHHH
Q ss_conf 2389708--6889850247984999999997----38841899970677999999985--------01000510112443
Q gi|254780553|r 25 CYIIYCP--IRTLSCLGKIGDFCTLFVETHM----RQDQIRLFGFLSDLDRQWFMLLQ--------SVQGVGARVAMGVL 90 (207)
Q Consensus 25 GY~i~vs--~~~~~~l~~~g~~v~l~~~~~v----rEd~~~LyGF~~~~Er~~F~~Li--------~V~GIGpK~AL~iL 90 (207)
|++|++- .+.+.+| ++++|.+|-...- .+.-..=||+.-.+=.+ |.-|. +|.|||||+|..+|
T Consensus 129 g~~v~IvS~DKDl~QL--V~~~v~i~~~~~~~~~d~~~V~ek~GV~P~qiiD-~lAL~GDsSDNIPGVpGIG~KTA~kLL 205 (954)
T PRK06887 129 GKKVLISTGDKDMAQL--VDDNIMLINTMNNSLLDREGVIEKYGIPPELIID-YLALMGDSSDNIPGVAGVGEKTALGLL 205 (954)
T ss_pred CCEEEEECCCCCCHHH--CCCCEEEEECCCCEEECHHHHHHHHCCCHHHHHH-HHHHCCCCCCCCCCCCCEEHHHHHHHH
T ss_conf 9929997588770121--6798799989898275799998987979899999-999718852477887854169999999
Q ss_pred CCC-CHHHHHHHHHCCCHHHHHHCCCCC----HHHHHHHHH-----HHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHH
Q ss_conf 157-899999998515668751045711----679999999-----9742221101133443233333445555653158
Q gi|254780553|r 91 SRI-TATELVESIILQNSKVIAQIPGIS----MKIASRIMT-----ELKGKAISLSSVVQQDMSCVNKEQAHICSMPSFA 160 (207)
Q Consensus 91 s~l-~~~~l~~aI~~~D~~~L~~vpGIG----kKtA~rIi~-----ELk~K~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 160 (207)
..+ +.+.+++.+. +++|.- +|..+++.- -|.-++..+....+-+.. ...........
T Consensus 206 ~eyGsLe~Iy~nld--------~i~~~~~rg~~Kl~e~L~~~~e~a~LSk~LvtI~~Dvpl~~~-----~~~l~~~~~d~ 272 (954)
T PRK06887 206 QGIGSMAEIYANLD--------KVAELPIRGAKKLGEKLLAEKANADLSYLLATIKTDVELDVT-----PEQLLLGESNK 272 (954)
T ss_pred HHHCCHHHHHHHHH--------HHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC-----HHHHCCCCCCH
T ss_conf 99577999998698--------732554200578999999989989999986014557888899-----89944489999
Q ss_pred HHHHHHHHHCCCCH
Q ss_conf 99999999679998
Q gi|254780553|r 161 INAISALVNLGYGQ 174 (207)
Q Consensus 161 ~d~~~AL~~LGy~~ 174 (207)
+.+..-+..|+|+.
T Consensus 273 ~~L~~~f~elEFks 286 (954)
T PRK06887 273 DELIEYFARYEFKR 286 (954)
T ss_pred HHHHHHHHHHCCHH
T ss_conf 99999999834858
No 30
>KOG2534 consensus
Probab=94.10 E-value=0.043 Score=34.64 Aligned_cols=55 Identities=24% Similarity=0.300 Sum_probs=40.0
Q ss_pred HHHHHHHHCCCHHHHHH---HCCCCHHHHHHHH---HCCCHHHHHHCCCCCHHHHHHHHHH
Q ss_conf 99850100051011244---3157899999998---5156687510457116799999999
Q gi|254780553|r 73 MLLQSVQGVGARVAMGV---LSRITATELVESI---ILQNSKVIAQIPGISMKIASRIMTE 127 (207)
Q Consensus 73 ~~Li~V~GIGpK~AL~i---Ls~l~~~~l~~aI---~~~D~~~L~~vpGIGkKtA~rIi~E 127 (207)
+.+.+..|||||.|=.| |++-...++-+.. ...-.+.|+++-|||.|||+|-..+
T Consensus 56 ~ea~~lP~iG~kia~ki~EiletG~l~ele~v~~de~~~~lklFtnifGvG~ktA~~Wy~~ 116 (353)
T KOG2534 56 EEAEKLPGIGPKIAEKIQEILETGVLRELEAVRNDERSQSLKLFTNIFGVGLKTAEKWYRE 116 (353)
T ss_pred HHHCCCCCCCHHHHHHHHHHHHCCCCHHHHHHHCCHHHHHHHHHHHHHCCCHHHHHHHHHH
T ss_conf 8855799977779999999997087366787754506789999998725577899999995
No 31
>PRK08835 consensus
Probab=94.07 E-value=0.1 Score=32.06 Aligned_cols=135 Identities=16% Similarity=0.236 Sum_probs=62.7
Q ss_pred EEEEECC--HHHHHHCCCCCCEEEEEEEE---EEC-CCCEEEEEEECHHHHHHHHHHH--------HHHHCCCHHHHHHH
Q ss_conf 2389708--68898502479849999999---973-8841899970677999999985--------01000510112443
Q gi|254780553|r 25 CYIIYCP--IRTLSCLGKIGDFCTLFVET---HMR-QDQIRLFGFLSDLDRQWFMLLQ--------SVQGVGARVAMGVL 90 (207)
Q Consensus 25 GY~i~vs--~~~~~~l~~~g~~v~l~~~~---~vr-Ed~~~LyGF~~~~Er~~F~~Li--------~V~GIGpK~AL~iL 90 (207)
||+|++- .+.+.+| ++++|++|-.. .+- +.-..-||+.-.+=.+ |.-|. +|.|||||+|..+|
T Consensus 129 g~~v~IvS~DKDl~QL--V~~~v~v~~~~~~~~~d~~~V~ek~GV~P~qviD-~lAL~GDsSDNIPGVpGIG~KTA~kLL 205 (931)
T PRK08835 129 GMPVLISTGDKDMAQL--VDDNITLINTMTNVVMDREGVVEKFGIPPELIID-YLALMGDKVDNIPGVPGVGDKTATALL 205 (931)
T ss_pred CCEEEEEECCCCHHHH--CCCCEEEEECCCCEEECHHHHHHHHCCCHHHHHH-HHHHCCCCCCCCCCCCCCCHHHHHHHH
T ss_conf 9939998289976341--7898599988898687899999987969899899-999718864688999974588899999
Q ss_pred CCC-CHHHHHHHHHCCCHHHHHHCCCCCHH---HHHHHHHHHHH------HHHHCCCCCCCCCCCCCCCCCCCCCCCCHH
Q ss_conf 157-89999999851566875104571167---99999999742------221101133443233333445555653158
Q gi|254780553|r 91 SRI-TATELVESIILQNSKVIAQIPGISMK---IASRIMTELKG------KAISLSSVVQQDMSCVNKEQAHICSMPSFA 160 (207)
Q Consensus 91 s~l-~~~~l~~aI~~~D~~~L~~vpGIGkK---tA~rIi~ELk~------K~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 160 (207)
..+ +.+.+...+ -.++|.|.| ..+.-+.+=++ ++..+....+-+. ............
T Consensus 206 ~eyGsLE~Iy~nl--------d~Ik~~~~rg~kk~~ekL~e~~e~A~LSk~LaTI~~Dvpl~~-----~le~l~~~~pd~ 272 (931)
T PRK08835 206 QGIGGLDALYDNL--------DDIAALGFRGSKTMAKKLVDNKDNAYLSYELATIKLDVELEE-----TPESLLKQEPNK 272 (931)
T ss_pred HHHCCHHHHHHHH--------HHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC-----CHHHHHCCCCCH
T ss_conf 9848699999769--------861444331056899999987999999898742033556788-----989973079999
Q ss_pred HHHHHHHHHCCCCHH
Q ss_conf 999999996799989
Q gi|254780553|r 161 INAISALVNLGYGQD 175 (207)
Q Consensus 161 ~d~~~AL~~LGy~~~ 175 (207)
+.+..-+..|+|+.-
T Consensus 273 ~~L~~~f~eleFksl 287 (931)
T PRK08835 273 DELIKLYGQLTFKSW 287 (931)
T ss_pred HHHHHHHHHHHCHHH
T ss_conf 999999999747899
No 32
>PRK07300 consensus
Probab=93.97 E-value=0.12 Score=31.73 Aligned_cols=136 Identities=10% Similarity=0.113 Sum_probs=66.7
Q ss_pred CCEEEEEECCHHHHHHCCCCCCEEEEEEEEEECC-CCE---------EEEEEECHHHHHHHHHHH--------HHHHCCC
Q ss_conf 8832389708688985024798499999999738-841---------899970677999999985--------0100051
Q gi|254780553|r 22 QGVCYIIYCPIRTLSCLGKIGDFCTLFVETHMRQ-DQI---------RLFGFLSDLDRQWFMLLQ--------SVQGVGA 83 (207)
Q Consensus 22 ~GvGY~i~vs~~~~~~l~~~g~~v~l~~~~~vrE-d~~---------~LyGF~~~~Er~~F~~Li--------~V~GIGp 83 (207)
.|.+|+|++-...-+.+.=+++++.++.. .+. ... .=||+.-.+=.++ .-|. +|.||||
T Consensus 130 ~~~~~~v~Ivs~DkD~~QLV~~~v~v~~~--~~~~~~~~~~~~~~v~ek~GV~P~qiiD~-lAL~GDsSDNIPGVpGIG~ 206 (880)
T PRK07300 130 TEVPFDVTIVSGDKDLIQLTDENTVVEIS--KKGVAEFEEFTPAYLMEKMGLTPNQFIDL-KALMGDKSDNIPGVTKIGE 206 (880)
T ss_pred CCCCCEEEEECCCCCCCCCCCCCEEEEEC--CCCCCCCEECCHHHHHHHHCCCHHHHHHH-HHHCCCCCCCCCCCCCCCH
T ss_conf 49997189974898616107698589746--89974121058999999978898999999-9980886246778898536
Q ss_pred HHHHHHHCCC-CHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHH-----HHHHHHHCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 0112443157-8999999985156687510457116799999999-----742221101133443233333445555653
Q gi|254780553|r 84 RVAMGVLSRI-TATELVESIILQNSKVIAQIPGISMKIASRIMTE-----LKGKAISLSSVVQQDMSCVNKEQAHICSMP 157 (207)
Q Consensus 84 K~AL~iLs~l-~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~E-----Lk~K~~~~~~~~~~~~~~~~~~~~~~~~~~ 157 (207)
|+|..+|+.+ +.+.++..+. .++ |+|.-++|.-. |.-++..+....+-+. .........
T Consensus 207 KTA~kLL~eyGsLE~I~~n~d--------~Ik--~~K~re~L~~~ke~a~lSk~LvTI~~Dvpl~~-----~ledl~~~~ 271 (880)
T PRK07300 207 KTGLKLLHEFGSLEGIYENID--------GMK--ASKMKENLINDKEQAFLSKTLATINTASPITI-----GLDDIVYKG 271 (880)
T ss_pred HHHHHHHHHCCCHHHHHHHHH--------HHC--CHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCC-----CHHHHCCCC
T ss_conf 999999997786999998575--------313--25688999863888888865201020798999-----989955589
Q ss_pred CHHHHHHHHHHHCCCCHH
Q ss_conf 158999999996799989
Q gi|254780553|r 158 SFAINAISALVNLGYGQD 175 (207)
Q Consensus 158 ~~~~d~~~AL~~LGy~~~ 175 (207)
...+.+..-+..|||+.-
T Consensus 272 ~d~~~L~~~f~elEFksL 289 (880)
T PRK07300 272 PDVASLSQFYDEMGFVQL 289 (880)
T ss_pred CCHHHHHHHHHHHCHHHH
T ss_conf 999999999998664999
No 33
>TIGR02236 recomb_radA DNA repair and recombination protein RadA; InterPro: IPR011938 This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA, eukaryotic RAD51 (IPR011941 from INTERPRO), and archaeal RadB (IPR011939 from INTERPRO). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein .; GO: 0003684 damaged DNA binding, 0005524 ATP binding, 0008094 DNA-dependent ATPase activity, 0006281 DNA repair, 0006310 DNA recombination.
Probab=93.91 E-value=0.063 Score=33.53 Aligned_cols=54 Identities=24% Similarity=0.393 Sum_probs=43.8
Q ss_pred HHHHHHCCCHHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHH
Q ss_conf 85010005101124431578999999985156687510457116799999999742
Q gi|254780553|r 75 LQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMTELKG 130 (207)
Q Consensus 75 Li~V~GIGpK~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~ 130 (207)
|-...||||+||=.+-.. .... .++|+.-..+-|+.+-|||.++|++||--=+.
T Consensus 2 ledLPGVGp~TA~KL~Ea-Gy~t-~~~iA~A~~~EL~~~~gI~E~~A~kiI~AAR~ 55 (333)
T TIGR02236 2 LEDLPGVGPATAEKLREA-GYDT-LEAIAVASPKELSEIAGIGEGTAAKIIQAARK 55 (333)
T ss_pred CCCCCCCCHHHHHHHHHH-HHHH-HHHHHCCCHHHHHHHCCCCHHHHHHHHHHHHH
T ss_conf 665789757688998861-0788-99984458579532037877789999999999
No 34
>PRK08786 consensus
Probab=93.84 E-value=0.13 Score=31.32 Aligned_cols=76 Identities=16% Similarity=0.159 Sum_probs=41.6
Q ss_pred EEEEEECC--HHHHHHCCCCCCEEEEEEEEE-EC---C-CCEEEEEEECHHHHHHHHHHH--------HHHHCCCHHHHH
Q ss_conf 32389708--688985024798499999999-73---8-841899970677999999985--------010005101124
Q gi|254780553|r 24 VCYIIYCP--IRTLSCLGKIGDFCTLFVETH-MR---Q-DQIRLFGFLSDLDRQWFMLLQ--------SVQGVGARVAMG 88 (207)
Q Consensus 24 vGY~i~vs--~~~~~~l~~~g~~v~l~~~~~-vr---E-d~~~LyGF~~~~Er~~F~~Li--------~V~GIGpK~AL~ 88 (207)
-||+|.+- .+.+.+| ++++|++|-... .+ + .-..=||+.-.+=.+ |.-|+ +|.|||||+|..
T Consensus 122 ~g~~v~IvSgDKD~~QL--V~~~v~i~~~~kg~~~~~~~~V~eK~GV~P~qviD-~lAL~GDsSDNIPGVpGIG~KTA~k 198 (927)
T PRK08786 122 DGLAVTISTGDKDFAQL--VRPGVELVNTMSGSRMDSDAAVIAKFGVRPDQIVD-LLALMGDTVDNVPGVEKCGPKTAAK 198 (927)
T ss_pred CCCEEEEECCCCCHHHH--CCCCEEEEECCCCCEECCHHHHHHHHCCCHHHHHH-HHHHCCCCCCCCCCCCCCCHHHHHH
T ss_conf 89919998289875241--78985999889997765789999996969899999-9998087646789999856899999
Q ss_pred HHCCCC-HHHHHHHH
Q ss_conf 431578-99999998
Q gi|254780553|r 89 VLSRIT-ATELVESI 102 (207)
Q Consensus 89 iLs~l~-~~~l~~aI 102 (207)
+|..++ .+.+++.+
T Consensus 199 LL~eyGsLE~I~~n~ 213 (927)
T PRK08786 199 WLAEYDSLDGVIANA 213 (927)
T ss_pred HHHHCCCHHHHHHHH
T ss_conf 999757699999998
No 35
>PRK07997 consensus
Probab=93.83 E-value=0.14 Score=31.19 Aligned_cols=75 Identities=19% Similarity=0.266 Sum_probs=41.1
Q ss_pred EEEEEC--CHHHHHHCCCCCCEEEEEEEEE---E-CCCCEEEEEEECHHHHHHHHHHH--------HHHHCCCHHHHHHH
Q ss_conf 238970--8688985024798499999999---7-38841899970677999999985--------01000510112443
Q gi|254780553|r 25 CYIIYC--PIRTLSCLGKIGDFCTLFVETH---M-RQDQIRLFGFLSDLDRQWFMLLQ--------SVQGVGARVAMGVL 90 (207)
Q Consensus 25 GY~i~v--s~~~~~~l~~~g~~v~l~~~~~---v-rEd~~~LyGF~~~~Er~~F~~Li--------~V~GIGpK~AL~iL 90 (207)
|++|++ +.+.+.+| ++++|++|=... + .++-..-||+.-.+=.+ |.-|. +|.|||||+|..+|
T Consensus 129 g~~v~IvSgDKDl~QL--V~~~v~v~~~~~~~~~~~~~V~ek~GV~P~qv~D-~laL~GDsSDNIPGVpGIG~KTA~kLL 205 (928)
T PRK07997 129 GRPVLISTGDKDMAQL--VTPNITLINTMTNTILGPEEVVNKYGVPPELIID-FLALMGDSSDNIPGVPGVGEKTAQALL 205 (928)
T ss_pred CCEEEEECCCCCHHHH--CCCCEEEEECCCCEEECHHHHHHHHCCCHHHHHH-HHHHCCCCCCCCCCCCCCCHHHHHHHH
T ss_conf 9959998389876553--7898599988898487799999987979898899-999728865688999975489999999
Q ss_pred CCC-CHHHHHHHH
Q ss_conf 157-899999998
Q gi|254780553|r 91 SRI-TATELVESI 102 (207)
Q Consensus 91 s~l-~~~~l~~aI 102 (207)
+.+ +.+.++..+
T Consensus 206 ~eyGsLE~I~~n~ 218 (928)
T PRK07997 206 QGLGGLDTLYAEP 218 (928)
T ss_pred HHHCCHHHHHHHH
T ss_conf 9827799999809
No 36
>TIGR00575 dnlj DNA ligase, NAD-dependent; InterPro: IPR001679 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalyzing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase: one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC). This family is predominantly composed of NAD-dependent bacterial DNA ligases. They are proteins of about 75 to 85 Kd whose sequence is well conserved , . They also show similarity to yicF, an Escherichia coli hypothetical protein of 63 Kd.; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair.
Probab=93.79 E-value=0.072 Score=33.13 Aligned_cols=137 Identities=16% Similarity=0.206 Sum_probs=88.0
Q ss_pred EEEECCEEEEEECCHHHHHHCCCCCCEEEEEEEEEECCCCEEEEE-EECHHHHHH-----------HHHH---HHHHHCC
Q ss_conf 998588323897086889850247984999999997388418999-706779999-----------9998---5010005
Q gi|254780553|r 18 LIDVQGVCYIIYCPIRTLSCLGKIGDFCTLFVETHMRQDQIRLFG-FLSDLDRQW-----------FMLL---QSVQGVG 82 (207)
Q Consensus 18 vi~v~GvGY~i~vs~~~~~~l~~~g~~v~l~~~~~vrEd~~~LyG-F~~~~Er~~-----------F~~L---i~V~GIG 82 (207)
-+|..|+|.++-.. .++. .-+.+..-||.-..-.||-+.|=| |.+..-+.+ |..| +++.+||
T Consensus 454 AmdI~GLG~~~I~~--LfE~-~Lv~~~~DLY~L~~k~~~Ll~le~~~g~~sa~nLl~aIe~sK~~pl~RlL~aLGIr~VG 530 (706)
T TIGR00575 454 AMDIDGLGEKVIEQ--LFEE-KLVRSVADLYALKEKLEDLLELEGKFGEKSAQNLLSAIEKSKKKPLARLLFALGIRHVG 530 (706)
T ss_pred CCCCCCCCHHHHHH--HHHC-CCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHH
T ss_conf 03322223899999--9872-66678566657788999987064035568899999999985210489999862860357
Q ss_pred CHHHHHHHCCC-CHHHHHHHHHC-------CCHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCC
Q ss_conf 10112443157-89999999851-------56687510457116799999999742221101133443233333445555
Q gi|254780553|r 83 ARVAMGVLSRI-TATELVESIIL-------QNSKVIAQIPGISMKIASRIMTELKGKAISLSSVVQQDMSCVNKEQAHIC 154 (207)
Q Consensus 83 pK~AL~iLs~l-~~~~l~~aI~~-------~D~~~L~~vpGIGkKtA~rIi~ELk~K~~~~~~~~~~~~~~~~~~~~~~~ 154 (207)
..+|-.+-..+ +.+.|.+|-.. =|.+.|.+++|||+++|+.|+--+.+--. . .-
T Consensus 531 ~~~A~~La~~f~tl~~L~~A~~e~~~~~~~f~~s~L~~~~g~G~~vA~~~~~~F~~~~~---------~---------~~ 592 (706)
T TIGR00575 531 EVTAKLLAKHFGTLDKLKAASLETLESIYQFDRSELLSVEGVGPKVAESIVNFFHDPNN---------L---------SL 592 (706)
T ss_pred HHHHHHHHHHCCCHHHHHHCCHHHHHHHHHHCCHHHHHCCCCHHHHHHHHHHHHHCCCC---------C---------CC
T ss_conf 99999999855886899850821677887516055641014027899999998712000---------1---------35
Q ss_pred CCCCHHHHHHHHHHHCCCCHHH
Q ss_conf 6531589999999967999899
Q gi|254780553|r 155 SMPSFAINAISALVNLGYGQDQ 176 (207)
Q Consensus 155 ~~~~~~~d~~~AL~~LGy~~~e 176 (207)
.+--..+.+..|..+|..-..
T Consensus 593 -qPYRta~~~~~L~~~gv~~~~ 613 (706)
T TIGR00575 593 -QPYRTAELIEKLEELGVNMES 613 (706)
T ss_pred -CHHHHHHHHHHHHHHHCCCHH
T ss_conf -604689999999883163101
No 37
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=93.76 E-value=0.36 Score=28.50 Aligned_cols=51 Identities=24% Similarity=0.307 Sum_probs=21.3
Q ss_pred HHHHHHHHHCCCHHHH---HHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHH
Q ss_conf 9998501000510112---44315789999999851566875104571167999999
Q gi|254780553|r 72 FMLLQSVQGVGARVAM---GVLSRITATELVESIILQNSKVIAQIPGISMKIASRIM 125 (207)
Q Consensus 72 F~~Li~V~GIGpK~AL---~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi 125 (207)
|..|..|.|.|||.=- ..|.--+.++|..|..++. +..++|.|+|.|+.|.
T Consensus 92 l~~Ll~v~GlGpkKi~~Ly~elgi~~~e~l~~a~~~~~---~~~l~GfG~kse~~il 145 (326)
T COG1796 92 LEPLLKVPGLGPKKIVSLYKELGIKDLEELQEALENGK---IRGLRGFGKKSEAKIL 145 (326)
T ss_pred HHHHHHCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHCC---CCCCCCCCCHHHHHHH
T ss_conf 58786077989288999999978664999999998477---0326785602199999
No 38
>PRK07898 consensus
Probab=93.74 E-value=0.13 Score=31.38 Aligned_cols=131 Identities=16% Similarity=0.180 Sum_probs=64.7
Q ss_pred EEEEECCH--HHHHHCCCCCCEEEEEE-EEEEC-------CCCEEEEEEECHHHHHHHHHHH--------HHHHCCCHHH
Q ss_conf 23897086--88985024798499999-99973-------8841899970677999999985--------0100051011
Q gi|254780553|r 25 CYIIYCPI--RTLSCLGKIGDFCTLFV-ETHMR-------QDQIRLFGFLSDLDRQWFMLLQ--------SVQGVGARVA 86 (207)
Q Consensus 25 GY~i~vs~--~~~~~l~~~g~~v~l~~-~~~vr-------Ed~~~LyGF~~~~Er~~F~~Li--------~V~GIGpK~A 86 (207)
||+|++-. +.+.+| +++++++|- .-.++ |+-..-||+.-.+=.+ |.-|. +|.|||||+|
T Consensus 139 g~~v~IvSgDKDl~QL--V~d~v~vl~~~kg~~~~~~~d~~~V~ek~GV~P~qviD-~lAL~GDsSDNIPGVpGIG~KTA 215 (902)
T PRK07898 139 GYRVLVVTGDRDALQL--VSDDVTVLYPRKGVSDLTRFTPEAVEEKYGLTPAQYPD-FAALRGDPSDNLPGIPGVGEKTA 215 (902)
T ss_pred CCEEEEECCCCCHHHH--CCCCEEEEECCCCCCCCEECCHHHHHHHHCCCHHHHHH-HHHHCCCCCCCCCCCCCCCHHHH
T ss_conf 9969997689977551--78987999778998635442899999986979899999-99981886457999998447889
Q ss_pred HHHHCCC-CHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHH------HHHHCCCCCCCCCCCCCCCCCCCCCCCCH
Q ss_conf 2443157-8999999985156687510457116799999999742------22110113344323333344555565315
Q gi|254780553|r 87 MGVLSRI-TATELVESIILQNSKVIAQIPGISMKIASRIMTELKG------KAISLSSVVQQDMSCVNKEQAHICSMPSF 159 (207)
Q Consensus 87 L~iLs~l-~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~------K~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 159 (207)
..+|..+ +.+.+..-+. .++| |..+++ .+=++ ++..+....+-+. +.......+..
T Consensus 216 ~kLL~eyGsLE~I~~n~d--------~Ikg---K~~e~L-~~~~d~a~LSk~LvTI~~Dvpl~~-----~le~l~~~~~d 278 (902)
T PRK07898 216 AKWIAQYGSLDGLVDHAD--------EIKG---KVGDAL-RANLESVVRNRELTELVRDVPLPV-----TPDDLRLQPWD 278 (902)
T ss_pred HHHHHHCCCHHHHHHHHH--------HHHH---HHHHHH-HHHHHHHHHHHHHHHHHHCCCCCC-----CHHHHCCCCCC
T ss_conf 999997677899999987--------5215---778899-965999999899868875488887-----88871248999
Q ss_pred HHHHHHHHHHCCCCHH
Q ss_conf 8999999996799989
Q gi|254780553|r 160 AINAISALVNLGYGQD 175 (207)
Q Consensus 160 ~~d~~~AL~~LGy~~~ 175 (207)
.+.+..-+..|+|+.-
T Consensus 279 ~~~L~~lf~eLEF~sL 294 (902)
T PRK07898 279 RDAVHRLFDDLEFRVL 294 (902)
T ss_pred HHHHHHHHHHHCCHHH
T ss_conf 9999999998466789
No 39
>PRK08076 consensus
Probab=93.73 E-value=0.1 Score=32.05 Aligned_cols=133 Identities=16% Similarity=0.207 Sum_probs=62.7
Q ss_pred EEEEEC--CHHHHHHCCCCCCEEEEEEEE-EECC-------CCEEEEEEECHHHHHHHHHHH--------HHHHCCCHHH
Q ss_conf 238970--868898502479849999999-9738-------841899970677999999985--------0100051011
Q gi|254780553|r 25 CYIIYC--PIRTLSCLGKIGDFCTLFVET-HMRQ-------DQIRLFGFLSDLDRQWFMLLQ--------SVQGVGARVA 86 (207)
Q Consensus 25 GY~i~v--s~~~~~~l~~~g~~v~l~~~~-~vrE-------d~~~LyGF~~~~Er~~F~~Li--------~V~GIGpK~A 86 (207)
|++|.+ +.+.+.+| +++++++|.-. .+.+ .-..=||+.-.+=.+ |.-|. +|.|||||+|
T Consensus 125 ~~~v~i~s~DkD~~QL--v~~~v~v~~~~k~~~~~~~~~~~~v~ek~Gv~P~q~~D-~~aL~GDssDNIPGVpGiG~KtA 201 (877)
T PRK08076 125 GFEVKVISGDKDLLQL--VSDNTTVCITKKGITDVEEYTPEALFEKYGLTPKQIID-MKGLMGDSSDNIPGVPGVGEKTA 201 (877)
T ss_pred CCCEEEECCCCCHHHH--CCCCEEEEECCCCCCCCEECCHHHHHHHHCCCHHHHHH-HHHHCCCCCCCCCCCCCCCHHHH
T ss_conf 9909998289876252--74986999758998644105899999997969899999-99971876467999998637999
Q ss_pred HHHHCCCC-HHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHH-----HHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHH
Q ss_conf 24431578-99999998515668751045711679999999-----9742221101133443233333445555653158
Q gi|254780553|r 87 MGVLSRIT-ATELVESIILQNSKVIAQIPGISMKIASRIMT-----ELKGKAISLSSVVQQDMSCVNKEQAHICSMPSFA 160 (207)
Q Consensus 87 L~iLs~l~-~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~-----ELk~K~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 160 (207)
..+|+.++ .+.++..+.+ ++ |+|..+++.- -|.-++..+....+-+.. ...........
T Consensus 202 ~~ll~~~gsle~i~~~~~~--------ik--g~k~re~L~e~~e~A~LSkeLaTI~~Dvpl~~~-----l~~l~~~~~d~ 266 (877)
T PRK08076 202 IKLLKQFGTVEEVLESIDE--------VS--GKKLKEKLEENKEQALMSKELATIITDAPIEVT-----VDDLEYKGYEA 266 (877)
T ss_pred HHHHHHCCCHHHHHHHHHH--------CC--CHHHHHHHHHCHHHHHHHHHHHHHHCCCCCCCC-----HHHCCCCCCCH
T ss_conf 9999966866889987773--------26--446788988489999999999885318989999-----88817579999
Q ss_pred HHHHHHHHHCCCCHH
Q ss_conf 999999996799989
Q gi|254780553|r 161 INAISALVNLGYGQD 175 (207)
Q Consensus 161 ~d~~~AL~~LGy~~~ 175 (207)
+++..-+..|||+.-
T Consensus 267 ~~L~~lf~eLEFksL 281 (877)
T PRK08076 267 EDVIPLFKELGFTSL 281 (877)
T ss_pred HHHHHHHHHCCHHHH
T ss_conf 999999998060999
No 40
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=93.72 E-value=0.085 Score=32.65 Aligned_cols=67 Identities=16% Similarity=0.201 Sum_probs=48.1
Q ss_pred EECHHHHHHHHH--HHHHHHCCCHHHHHHHCCCCHHHHHHHHH-----CCCHHHHHHCCCCCHHHHHHHHHHHH
Q ss_conf 706779999999--85010005101124431578999999985-----15668751045711679999999974
Q gi|254780553|r 63 FLSDLDRQWFML--LQSVQGVGARVAMGVLSRITATELVESII-----LQNSKVIAQIPGISMKIASRIMTELK 129 (207)
Q Consensus 63 F~~~~Er~~F~~--Li~V~GIGpK~AL~iLs~l~~~~l~~aI~-----~~D~~~L~~vpGIGkKtA~rIi~ELk 129 (207)
+.+++=.+++.. +.+++|||+.+|-.|---++..++..... -.|..-|.++||.|+|+-.++--||.
T Consensus 41 ~~~e~~~ei~e~~~~t~l~gIGk~ia~~I~e~l~tG~~~~le~lk~~~P~gl~~Ll~v~GlGpkKi~~Ly~elg 114 (326)
T COG1796 41 NLTEDLEEIEERGRLTELPGIGKGIAEKISEYLDTGEVKKLEALKKEVPEGLEPLLKVPGLGPKKIVSLYKELG 114 (326)
T ss_pred HCCCCHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHCCCCHHHHHHCCCCCCHHHHHHHHHHC
T ss_conf 31354688973301477887568899999999972860789999885795558786077989288999999978
No 41
>PRK03980 flap endonuclease-1; Provisional
Probab=93.55 E-value=0.71 Score=26.50 Aligned_cols=100 Identities=18% Similarity=0.207 Sum_probs=51.6
Q ss_pred HHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCC-----------CCC---CCCC
Q ss_conf 24431578999999985156687510457116799999999742221101133443233-----------333---4455
Q gi|254780553|r 87 MGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMTELKGKAISLSSVVQQDMSC-----------VNK---EQAH 152 (207)
Q Consensus 87 L~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~K~~~~~~~~~~~~~~-----------~~~---~~~~ 152 (207)
|.-|. ++.++|+..-.----.....+||||+|||=++|-+.++ +.++.......... .++ +...
T Consensus 169 l~~l~-lt~eqfidlcIL~GcDY~~gI~gIGpk~Alklikk~~~-ie~il~~~~~~~~~~~~~~e~r~lF~~p~v~~~~~ 246 (295)
T PRK03980 169 LKELG-ITREQLIDIAILVGTDYNPGVKGIGPKTALKLIKKHGD-LEKVLEAVGEGIDEPVDPEEIREFFLNPPVTDDYE 246 (295)
T ss_pred HHHCC-CCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHCC-HHHHHHHCCCCCCCCCCHHHHHHHHCCCCCCCCCC
T ss_conf 98839-99999999998458889999998429999999999699-99999863767788999799999847999888788
Q ss_pred CCCCCCHHHHHHHHHHH-CCCCHHHHHHHHHHHHHHC
Q ss_conf 55653158999999996-7999899999999998516
Q gi|254780553|r 153 ICSMPSFAINAISALVN-LGYGQDQATTAVVSVLKKE 188 (207)
Q Consensus 153 ~~~~~~~~~d~~~AL~~-LGy~~~ea~~ai~~i~~~~ 188 (207)
..-.....+.+..=|+. -||++..+++++.++.+..
T Consensus 247 l~~~~pd~e~l~~fL~~e~~fse~RV~~~i~kl~k~~ 283 (295)
T PRK03980 247 LKWKKPDKEGIIEFLVEEHDFSEDRVEKALERLKKAL 283 (295)
T ss_pred CCCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHH
T ss_conf 7879999899999987642989999999999999874
No 42
>PRK08928 consensus
Probab=93.39 E-value=0.21 Score=30.06 Aligned_cols=135 Identities=17% Similarity=0.182 Sum_probs=62.7
Q ss_pred EEEEECCHHHHHHCCCCCCEEEEEEEEEE---C-CCCEEEEEEECHHHHHHHHHHH--------HHHHCCCHHHHHHHCC
Q ss_conf 23897086889850247984999999997---3-8841899970677999999985--------0100051011244315
Q gi|254780553|r 25 CYIIYCPIRTLSCLGKIGDFCTLFVETHM---R-QDQIRLFGFLSDLDRQWFMLLQ--------SVQGVGARVAMGVLSR 92 (207)
Q Consensus 25 GY~i~vs~~~~~~l~~~g~~v~l~~~~~v---r-Ed~~~LyGF~~~~Er~~F~~Li--------~V~GIGpK~AL~iLs~ 92 (207)
|++|++-...-+.+.=++++|++|-...- - ++-..=||+.-.+=.+ |.-|. +|.|||||+|..+|+.
T Consensus 127 g~~v~IvSgDKDl~QLV~~~v~v~~~~k~~~~~~~~V~ek~GV~P~qiiD-~laL~GDsSDNIPGVpGIG~KTA~kLL~e 205 (861)
T PRK08928 127 GDEVVIISSDKDLLQLMNENIKIYDPIKNKYITEDDVVEKFGVTSDKLLD-VMALTGDRSDNIPGVPSIGPKTAAKLITQ 205 (861)
T ss_pred CCEEEEECCCCCHHHHCCCCEEEEECCCCCCCCHHHHHHHHCCCHHHHHH-HHHHCCCCCCCCCCCCCCCHHHHHHHHHH
T ss_conf 99099984899750318898599988888176899999997979899999-99980876468899988562899999996
Q ss_pred C-CHHHHHHHHHCCCHHHHHHCCCCCHHHHHHH-----HHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHH
Q ss_conf 7-8999999985156687510457116799999-----999742221101133443233333445555653158999999
Q gi|254780553|r 93 I-TATELVESIILQNSKVIAQIPGISMKIASRI-----MTELKGKAISLSSVVQQDMSCVNKEQAHICSMPSFAINAISA 166 (207)
Q Consensus 93 l-~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rI-----i~ELk~K~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~A 166 (207)
+ +.+.+...+. +++ |+|.-+.+ ..-|.-++..+....+-+.. ...........+.+..-
T Consensus 206 yGsLE~Iy~n~d--------~Ik--~~K~re~L~e~ke~a~lSkeLvTI~~Dvpl~~~-----l~~l~~~~~d~~~L~~l 270 (861)
T PRK08928 206 FGSLENILNSLD--------QIS--SNKQRETLQNSREQALISRQLIGLCSNVDLDFD-----LNKLEWSPPNSEKLTGF 270 (861)
T ss_pred CCCHHHHHHHHH--------HCC--CHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC-----HHHHCCCCCCHHHHHHH
T ss_conf 797999999886--------113--024678888558889998998643547887646-----78734489999999999
Q ss_pred HHHCCCCHH
Q ss_conf 996799989
Q gi|254780553|r 167 LVNLGYGQD 175 (207)
Q Consensus 167 L~~LGy~~~ 175 (207)
+..|+|+.-
T Consensus 271 f~elEF~sL 279 (861)
T PRK08928 271 LKKYEFKSL 279 (861)
T ss_pred HHHHCCHHH
T ss_conf 998267899
No 43
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=93.28 E-value=0.24 Score=29.62 Aligned_cols=21 Identities=29% Similarity=0.507 Sum_probs=11.7
Q ss_pred HHHCCCHHHHHHHCCCCHHHH
Q ss_conf 100051011244315789999
Q gi|254780553|r 78 VQGVGARVAMGVLSRITATEL 98 (207)
Q Consensus 78 V~GIGpK~AL~iLs~l~~~~l 98 (207)
|.|||||+|+.+|..++.-+.
T Consensus 203 V~GIG~ktA~~Ll~~~gs~e~ 223 (310)
T COG0258 203 VKGIGPKTALKLLQEYGSLEG 223 (310)
T ss_pred CCCCCHHHHHHHHHHHCCHHH
T ss_conf 998389999999998385999
No 44
>PRK09482 xni exonuclease IX; Provisional
Probab=93.03 E-value=0.078 Score=32.91 Aligned_cols=38 Identities=18% Similarity=0.361 Sum_probs=23.3
Q ss_pred CCHHHHHH--HHHCCCHHHHHHCCCCCHHHHHHHHHHHHH
Q ss_conf 78999999--985156687510457116799999999742
Q gi|254780553|r 93 ITATELVE--SIILQNSKVIAQIPGISMKIASRIMTELKG 130 (207)
Q Consensus 93 l~~~~l~~--aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~ 130 (207)
..|+++.. |+.-.-..-+-.|||||+|||.+++-+...
T Consensus 165 v~P~q~~d~~aL~GD~SDNIPGV~GIG~KtA~~LL~~fgs 204 (256)
T PRK09482 165 VEPQQLPDYWGLAGISSSKIPGVAGIGPKSAAELLNQFRS 204 (256)
T ss_pred CCHHHHHHEEEEECCCCCCCCCCCCCCHHHHHHHHHHHCC
T ss_conf 2873532302474654368999998588899999998550
No 45
>TIGR03674 fen_arch flap structure-specific endonuclease. Endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA
Probab=92.89 E-value=0.18 Score=30.44 Aligned_cols=93 Identities=16% Similarity=0.209 Sum_probs=45.7
Q ss_pred CCHHHHHHH-HHCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCC--------CCCC---CCCCCCCCCCHH
Q ss_conf 789999999-8515668751045711679999999974222110113344323--------3333---445555653158
Q gi|254780553|r 93 ITATELVES-IILQNSKVIAQIPGISMKIASRIMTELKGKAISLSSVVQQDMS--------CVNK---EQAHICSMPSFA 160 (207)
Q Consensus 93 l~~~~l~~a-I~~~D~~~L~~vpGIGkKtA~rIi~ELk~K~~~~~~~~~~~~~--------~~~~---~~~~~~~~~~~~ 160 (207)
++.++|+.. |..| -.....+||||+|||=++|-+.++ +.++......... ..++ +.....-.....
T Consensus 221 lt~eqfidlcIL~G-cDY~~gI~GIG~k~A~klIkk~~~-ie~i~~~~~~~~~~~~~~r~lF~~p~v~d~~~~~~~~pd~ 298 (338)
T TIGR03674 221 ITREQLIDIAILVG-TDYNEGVKGIGPKTALKLIKEHGD-LEKVLKARGEDIENYDEIREFFLNPPVTDDYELKWRKPDK 298 (338)
T ss_pred CCHHHHHHHHHHHC-CCCCCCCCCCCHHHHHHHHHHHCC-HHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCH
T ss_conf 99999999999708-756789998568999999998599-9999986568877899999984899989877776799998
Q ss_pred HHHHHHHHH-CCCCHHHHHHHHHHHHHH
Q ss_conf 999999996-799989999999999851
Q gi|254780553|r 161 INAISALVN-LGYGQDQATTAVVSVLKK 187 (207)
Q Consensus 161 ~d~~~AL~~-LGy~~~ea~~ai~~i~~~ 187 (207)
+.++.=|+. .||++..+++++.++.+.
T Consensus 299 e~l~~fL~~e~~fse~RV~~~i~kl~k~ 326 (338)
T TIGR03674 299 EGIIEFLCDEHDFSEDRVERALERLEAA 326 (338)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHHHHH
T ss_conf 9999995535597999999999999976
No 46
>KOG2841 consensus
Probab=92.65 E-value=0.24 Score=29.67 Aligned_cols=57 Identities=21% Similarity=0.282 Sum_probs=37.8
Q ss_pred HHHHHHHHHHCCCHHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHH
Q ss_conf 999985010005101124431578999999985156687510457116799999999742
Q gi|254780553|r 71 WFMLLQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMTELKG 130 (207)
Q Consensus 71 ~F~~Li~V~GIGpK~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~ 130 (207)
+-.-|.++.||+---|..+|++++. .+.|.+.-...|.++||+|+..|+||.--|..
T Consensus 193 ~~~~Lt~i~~VnKtda~~LL~~Fgs---Lq~~~~AS~~ele~~~G~G~~kak~l~~~l~~ 249 (254)
T KOG2841 193 LLGFLTTIPGVNKTDAQLLLQKFGS---LQQISNASEGELEQCPGLGPAKAKRLHKFLHQ 249 (254)
T ss_pred HHHHHHHCCCCCCCCHHHHHHHCCC---HHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHC
T ss_conf 9999881789770018999885535---99987417767986757378999999999845
No 47
>TIGR01083 nth endonuclease III; InterPro: IPR005759 The spectrum of DNA damage caused by reactive oxygen species includes a wide variety of modifications of purine and pyrimidine bases. Among these modified bases, 7,8-dihydro-8-oxoguanine (8-oxoG) is an important mutagenic lesion. Base excision repair is a critical mechanism for preventing mutations by removing the oxidative lesion from the DNA. Escherichia coli Nth protein (endonuclease III) has an 8-oxoG DNA glycosylase/AP lyase activity which removes 8-oxoG preferentially from 8-oxoG/G mispairs. Human hNTH1 protein, a homolog of E. coli Nth protein, has similar DNA glycosylase/AP lyase activity that removes 8-oxoG from 8-oxoG/G mispairs . ; GO: 0003906 DNA-(apurinic or apyrimidinic site) lyase activity, 0006284 base-excision repair, 0005622 intracellular.
Probab=92.34 E-value=0.056 Score=33.87 Aligned_cols=24 Identities=17% Similarity=0.519 Sum_probs=19.3
Q ss_pred HCCCHHHHHHCCCCCHHHHHHHHH
Q ss_conf 515668751045711679999999
Q gi|254780553|r 103 ILQNSKVIAQIPGISMKIASRIMT 126 (207)
Q Consensus 103 ~~~D~~~L~~vpGIGkKtA~rIi~ 126 (207)
.=+|...|-++||||.|||.=++.
T Consensus 102 VP~~~~eL~~LPGVGRKTANVVL~ 125 (192)
T TIGR01083 102 VPEDREELVKLPGVGRKTANVVLN 125 (192)
T ss_pred CCCCHHHHHCCCCCCCHHHHHHHH
T ss_conf 775537661789987114562433
No 48
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=92.31 E-value=0.095 Score=32.30 Aligned_cols=93 Identities=18% Similarity=0.236 Sum_probs=50.7
Q ss_pred EEEEECCHHHHHHCC-CCCCEEEEEEE-----EEECCCCEEEEEEECHHHH-HHHHHHHHHH-HCCCHHHHHHHCCCCHH
Q ss_conf 238970868898502-47984999999-----9973884189997067799-9999985010-00510112443157899
Q gi|254780553|r 25 CYIIYCPIRTLSCLG-KIGDFCTLFVE-----THMRQDQIRLFGFLSDLDR-QWFMLLQSVQ-GVGARVAMGVLSRITAT 96 (207)
Q Consensus 25 GY~i~vs~~~~~~l~-~~g~~v~l~~~-----~~vrEd~~~LyGF~~~~Er-~~F~~Li~V~-GIGpK~AL~iLs~l~~~ 96 (207)
||++--+..+.+... +.|..+.+++. +.+.+.....+++.....+ --...+...- |+.|.
T Consensus 117 G~eadd~i~t~A~~a~~~g~~~~I~S~DkD~lql~~~~~~~~~~~~~~~~~~~~~~~~~e~~~g~~p~------------ 184 (310)
T COG0258 117 GIEADDPIETLAQKAYKKGDVVLIISGDKDLLQLVSPNVLVINGKKGEPEKFLDLEEVEEKFKGLTPE------------ 184 (310)
T ss_pred CCCCCCCCCHHHHHHHHCCCCEEEEECCCCEEEECCCCEEEEECCCCCCCCCCCHHHHHHHHCCCCHH------------
T ss_conf 96831444089999886499579997896700114896178625778852348999999985699989------------
Q ss_pred HHHHH-HHCCC-HHHHHHCCCCCHHHHHHHHHHHH
Q ss_conf 99999-85156-68751045711679999999974
Q gi|254780553|r 97 ELVES-IILQN-SKVIAQIPGISMKIASRIMTELK 129 (207)
Q Consensus 97 ~l~~a-I~~~D-~~~L~~vpGIGkKtA~rIi~ELk 129 (207)
+++.. +..|| ..-.-.|||||+|||-+++-+..
T Consensus 185 qliD~~~L~Gd~sDnipGV~GIG~ktA~~Ll~~~g 219 (310)
T COG0258 185 QLIDLKALVGDSSDNIPGVKGIGPKTALKLLQEYG 219 (310)
T ss_pred HHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHC
T ss_conf 98899998296535789999838999999999838
No 49
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=92.31 E-value=0.41 Score=28.10 Aligned_cols=73 Identities=21% Similarity=0.361 Sum_probs=51.4
Q ss_pred CCCCEEEEEEECHHHHHHH--------------HHHHHHHHCCCHHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHH
Q ss_conf 3884189997067799999--------------99850100051011244315789999999851566875104571167
Q gi|254780553|r 54 RQDQIRLFGFLSDLDRQWF--------------MLLQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMK 119 (207)
Q Consensus 54 rEd~~~LyGF~~~~Er~~F--------------~~Li~V~GIGpK~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkK 119 (207)
.||-..|=||....-+.++ ..=+++..||+++|-.+-..+.. .+++.......|..+||||.+
T Consensus 478 ~~~l~~l~~~~~ks~~nLl~aIe~sK~~~l~r~l~aLGIr~VG~~~Ak~La~~f~s---l~~l~~a~~e~l~~i~giG~~ 554 (667)
T COG0272 478 EEDLLSLEGFGEKSAENLLNAIEKSKKQPLARFLYALGIRHVGETTAKSLARHFGT---LEALLAASEEELASIPGIGEV 554 (667)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHHHHHHHHH---HHHHHHCCHHHHHHCCCHHHH
T ss_conf 98884162244657999999999860498999999879711408999999987602---999984299999506661289
Q ss_pred HHHHHHHHHH
Q ss_conf 9999999974
Q gi|254780553|r 120 IASRIMTELK 129 (207)
Q Consensus 120 tA~rIi~ELk 129 (207)
.|+.|+--+.
T Consensus 555 vA~si~~ff~ 564 (667)
T COG0272 555 VARSIIEFFA 564 (667)
T ss_pred HHHHHHHHHC
T ss_conf 9999999972
No 50
>PRK07556 consensus
Probab=92.06 E-value=0.24 Score=29.64 Aligned_cols=78 Identities=13% Similarity=0.183 Sum_probs=41.0
Q ss_pred EEEEEECCHHHHHHCCCCCCEEEEEEEEE---EC-CCCEEEEEEECHHHHHHHHHHH--------HHHHCCCHHHHHHHC
Q ss_conf 32389708688985024798499999999---73-8841899970677999999985--------010005101124431
Q gi|254780553|r 24 VCYIIYCPIRTLSCLGKIGDFCTLFVETH---MR-QDQIRLFGFLSDLDRQWFMLLQ--------SVQGVGARVAMGVLS 91 (207)
Q Consensus 24 vGY~i~vs~~~~~~l~~~g~~v~l~~~~~---vr-Ed~~~LyGF~~~~Er~~F~~Li--------~V~GIGpK~AL~iLs 91 (207)
-|++|++-...-+.+.=++++|++|-... +- ++-..=||+.-.+=.+ |.-|+ +|.|||||+|..+|+
T Consensus 134 ~g~~v~IvSgDKDl~QLV~d~V~i~~~~k~~~~d~~~V~eK~GV~P~qv~D-~lAL~GDsSDNIPGVpGIG~KTA~kLL~ 212 (977)
T PRK07556 134 AGGDVTIISSDKDLMQLVGDGVSMYDPMKDKRIGIPEVIEKFGVPPEKVVD-VQALAGDSVDNVPGIPGIGIKTAAQLIN 212 (977)
T ss_pred CCCCEEEECCCCCHHHHCCCCEEEEECCCCCEECHHHHHHHHCCCHHHHHH-HHHHCCCCCCCCCCCCCCCHHHHHHHHH
T ss_conf 799299981898675627798699978898481799999986969899999-9997187646789899854899999999
Q ss_pred CCC-HHHHHHHH
Q ss_conf 578-99999998
Q gi|254780553|r 92 RIT-ATELVESI 102 (207)
Q Consensus 92 ~l~-~~~l~~aI 102 (207)
.++ .+.+++.+
T Consensus 213 eyGsLE~Iy~n~ 224 (977)
T PRK07556 213 EYGDLDTLLARA 224 (977)
T ss_pred HCCCHHHHHHHH
T ss_conf 757899999988
No 51
>cd00080 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) motif. HhH2 domains are found in Rad2 family of prokaryotic and eukaryotic replication and repair nucleases, i.e., DNA polymerase I, Taq DNA polymerase, DNA repair protein Rad2 endonuclease, flap endonuclease, exonuclease I and IX, 5'-3' exonuclease and also bacteriophage Rnase H. These nucleases degrade RNA-DNA or DNA-DNA duplexes, or both and play essential roles in DNA duplication, repair, and recombination.
Probab=91.99 E-value=0.15 Score=31.01 Aligned_cols=39 Identities=26% Similarity=0.474 Sum_probs=24.7
Q ss_pred CCCHHHHHHHHH-CCC-HHHHHHCCCCCHHHHHHHHHHHHH
Q ss_conf 578999999985-156-687510457116799999999742
Q gi|254780553|r 92 RITATELVESII-LQN-SKVIAQIPGISMKIASRIMTELKG 130 (207)
Q Consensus 92 ~l~~~~l~~aI~-~~D-~~~L~~vpGIGkKtA~rIi~ELk~ 130 (207)
.++|++++.... .+| ..-+..|||||+|||.+++-+..+
T Consensus 4 g~~p~q~~d~~~L~GD~sDnipGV~GIG~ktA~~ll~~~~~ 44 (75)
T cd00080 4 GLTPEQFIDLAILVGDKSDNIPGVPGIGPKTALKLLKEYGS 44 (75)
T ss_pred CCCHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCCC
T ss_conf 97999999999991965458877586379999999999099
No 52
>PRK05797 consensus
Probab=91.94 E-value=0.4 Score=28.17 Aligned_cols=136 Identities=13% Similarity=0.139 Sum_probs=61.7
Q ss_pred EEEEEECCHHHHHHCCCCCCEEEEEEEEE-ECC-------CCEEEEEEECHHHHHHHHHHH--------HHHHCCCHHHH
Q ss_conf 32389708688985024798499999999-738-------841899970677999999985--------01000510112
Q gi|254780553|r 24 VCYIIYCPIRTLSCLGKIGDFCTLFVETH-MRQ-------DQIRLFGFLSDLDRQWFMLLQ--------SVQGVGARVAM 87 (207)
Q Consensus 24 vGY~i~vs~~~~~~l~~~g~~v~l~~~~~-vrE-------d~~~LyGF~~~~Er~~F~~Li--------~V~GIGpK~AL 87 (207)
-||+|.+-...-+.+.=+++++++|.-.. +.+ .-..=||+.-.+=.+ |.-|. +|.|||||+|.
T Consensus 124 ~g~~v~i~s~DkD~~QLv~~~v~v~~~~k~~~~~~~~~~~~v~ek~Gv~P~q~~D-~~aL~GD~sDNIPGVpGIG~KTA~ 202 (869)
T PRK05797 124 KGIEVYIVTGDKDALQLASDNVKVVITKKGITEKEIYDKNKMVEEYGVTPTQFID-VKGLMGDKSDNIPGVPGIGEKTAF 202 (869)
T ss_pred CCCCEEEEECCCCCCCCCCCCEEEEECCCCCCCCEEECHHHHHHHHCCCHHHHHH-HHHHCCCCCCCCCCCCCCCHHHHH
T ss_conf 8995899807986001087998999888999745563799989997789999999-999808864578999987818999
Q ss_pred HHHCCCC-HHHHHHHHHCCCHHHHHHCCCCCHHHHHHHH-----HHHHHHHHHCCCCCCCCCCCCCCCCCCCCC-CCCHH
Q ss_conf 4431578-9999999851566875104571167999999-----997422211011334432333334455556-53158
Q gi|254780553|r 88 GVLSRIT-ATELVESIILQNSKVIAQIPGISMKIASRIM-----TELKGKAISLSSVVQQDMSCVNKEQAHICS-MPSFA 160 (207)
Q Consensus 88 ~iLs~l~-~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi-----~ELk~K~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~ 160 (207)
.+|+.++ .+.+...+. +++ |||..++|. .-|.-++..+....+-+.. ...... .+...
T Consensus 203 kLL~eyGsLE~I~~n~d--------eIk--gkk~~e~L~e~~d~a~LSkeLvTI~~Dvpl~~~-----le~l~~~~~~d~ 267 (869)
T PRK05797 203 KLIKEYGSIENVLENID--------NIK--GKKLKENLEENREQAIFSKKLATIMRNVPIEID-----LEEIKSKEEYDI 267 (869)
T ss_pred HHHHHCCCHHHHHHHHH--------HCC--CHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC-----HHHHCCCCCCCH
T ss_conf 99986787889998788--------505--388999999548888998777741117988999-----899514788999
Q ss_pred HHHHHHHHHCCCCHH
Q ss_conf 999999996799989
Q gi|254780553|r 161 INAISALVNLGYGQD 175 (207)
Q Consensus 161 ~d~~~AL~~LGy~~~ 175 (207)
+.+..-+..|+|+.-
T Consensus 268 ~~L~~~f~elEFksL 282 (869)
T PRK05797 268 EKLRELFEKLEFKSL 282 (869)
T ss_pred HHHHHHHHHHCCHHH
T ss_conf 999999998265999
No 53
>PRK05929 consensus
Probab=91.92 E-value=0.12 Score=31.75 Aligned_cols=77 Identities=16% Similarity=0.236 Sum_probs=45.7
Q ss_pred EEEEEECCHHHHHHCCCCCCEEEEEEEEEECCC-------CEEEEEEECHHHHHHHHHHH--------HHHHCCCHHHHH
Q ss_conf 323897086889850247984999999997388-------41899970677999999985--------010005101124
Q gi|254780553|r 24 VCYIIYCPIRTLSCLGKIGDFCTLFVETHMRQD-------QIRLFGFLSDLDRQWFMLLQ--------SVQGVGARVAMG 88 (207)
Q Consensus 24 vGY~i~vs~~~~~~l~~~g~~v~l~~~~~vrEd-------~~~LyGF~~~~Er~~F~~Li--------~V~GIGpK~AL~ 88 (207)
-||+|++-...-+.+.=+.++|++|-.. ++. -..=||+.-.+=.+ |.-|. +|.|||||+|..
T Consensus 124 ~g~~v~IvTgDKD~~QLv~~~v~v~~~~--k~~~~~d~~~V~ek~Gv~P~qi~D-~laL~GDsSDNIPGVpGIG~KTA~k 200 (870)
T PRK05929 124 EGYEVCICTADKDLLQLVNSHVVAWNPW--KDQEVIGYNEVIEQYGVPPGQIAD-YLALVGDSSDNIPGVSGCGPKKAAA 200 (870)
T ss_pred CCCEEEEECCCCCHHHHCCCCEEEEECC--CCCCCCCHHHHHHHHCCCHHHHHH-HHHHCCCCCCCCCCCCCCCHHHHHH
T ss_conf 7992999848997624177987999768--888126799999997969899999-9997287646899999760999999
Q ss_pred HHCCC-CHHHHHHHHH
Q ss_conf 43157-8999999985
Q gi|254780553|r 89 VLSRI-TATELVESII 103 (207)
Q Consensus 89 iLs~l-~~~~l~~aI~ 103 (207)
+|+.+ +.+.+++.+.
T Consensus 201 LL~~ygsLE~Iy~n~d 216 (870)
T PRK05929 201 LLKEFQSVEGLLENLD 216 (870)
T ss_pred HHHHCCCHHHHHHHHH
T ss_conf 9986787779999998
No 54
>PRK07456 consensus
Probab=91.91 E-value=0.32 Score=28.80 Aligned_cols=37 Identities=19% Similarity=0.278 Sum_probs=24.2
Q ss_pred CHHHHHHH--HHCCCHHHHHHCCCCCHHHHHHHHHHHHH
Q ss_conf 89999999--85156687510457116799999999742
Q gi|254780553|r 94 TATELVES--IILQNSKVIAQIPGISMKIASRIMTELKG 130 (207)
Q Consensus 94 ~~~~l~~a--I~~~D~~~L~~vpGIGkKtA~rIi~ELk~ 130 (207)
+|++++.. +.-.-..=+-.|||||+|||.+++-+..+
T Consensus 189 ~P~qiiD~lAL~GDsSDNIPGVpGIG~KTA~kLL~eyGs 227 (975)
T PRK07456 189 APEQVVDLKALTGDSSDNIPGVKGVGPKTAINLLKENGD 227 (975)
T ss_pred CHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCC
T ss_conf 989989999972886568899998559999999998499
No 55
>PRK10880 adenine DNA glycosylase; Provisional
Probab=91.83 E-value=0.11 Score=31.83 Aligned_cols=59 Identities=22% Similarity=0.273 Sum_probs=40.5
Q ss_pred HHHHHHHHHCCCHHHHHHHCCCCHHHHHHHHHCCCH-HHHHHCCCC----CHHHHHHHHHHHHHHH
Q ss_conf 999850100051011244315789999999851566-875104571----1679999999974222
Q gi|254780553|r 72 FMLLQSVQGVGARVAMGVLSRITATELVESIILQNS-KVIAQIPGI----SMKIASRIMTELKGKA 132 (207)
Q Consensus 72 F~~Li~V~GIGpK~AL~iLs~l~~~~l~~aI~~~D~-~~L~~vpGI----GkKtA~rIi~ELk~K~ 132 (207)
++.|++..|||+-+|=+|+| +..++= .+|..+|+ ..|+++-|| ++|..++-+.++.+++
T Consensus 108 ~~~L~~LPGIG~yTA~AI~s-iaf~~~-~~ivDgNV~RVlsR~~~i~~~~~~~~~~~~l~~~a~~~ 171 (350)
T PRK10880 108 FEEVAALPGVGRSTAGAILS-LSLGKH-FPILDGNVKRVLARCYAVSGWPGKKEVENKLWSLSEQV 171 (350)
T ss_pred HHHHHHCCCCCHHHHHHHHH-HHCCCC-CCCCCCCCHHHHHHHHCCCCCCCCHHHHHHHHHHHHHH
T ss_conf 99986266887279999999-976995-35766440328888750336887559999999999973
No 56
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=91.63 E-value=0.19 Score=30.29 Aligned_cols=72 Identities=17% Similarity=0.283 Sum_probs=50.5
Q ss_pred CCCCEEEEEEECHHHHHHHHHH--------------HHHHHCCCHHHHHHHCCCC-HHHHHHHHHCCCHHHHHHCCCCCH
Q ss_conf 3884189997067799999998--------------5010005101124431578-999999985156687510457116
Q gi|254780553|r 54 RQDQIRLFGFLSDLDRQWFMLL--------------QSVQGVGARVAMGVLSRIT-ATELVESIILQNSKVIAQIPGISM 118 (207)
Q Consensus 54 rEd~~~LyGF~~~~Er~~F~~L--------------i~V~GIGpK~AL~iLs~l~-~~~l~~aI~~~D~~~L~~vpGIGk 118 (207)
.||-..|-||....-..++..+ +++.+||.++|-.+...+. .++ +.+.+...|..++|||+
T Consensus 478 ~~~L~~l~gfgeKsa~nLl~aIe~SK~~~l~r~L~ALGI~~VG~~~Ak~La~~f~sl~~----l~~as~e~L~~I~giG~ 553 (668)
T PRK07956 478 EEDLLQLEGFGEKSAQNLLDAIEKSKETPLARFLYALGIRHVGEKAAKALARHFGSLEA----LEAASEEELAAVEGIGE 553 (668)
T ss_pred HHHHHCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHCCCCCCCHHHHHHHHHHHCCHHH----HHHCCHHHHHCCCCCCH
T ss_conf 54540212355669999999999854775888998627864129999999999668999----97089999857688449
Q ss_pred HHHHHHHHHHH
Q ss_conf 79999999974
Q gi|254780553|r 119 KIASRIMTELK 129 (207)
Q Consensus 119 KtA~rIi~ELk 129 (207)
++|+.|+-=+.
T Consensus 554 ~~A~si~~ff~ 564 (668)
T PRK07956 554 EVAQSIVEFFA 564 (668)
T ss_pred HHHHHHHHHHC
T ss_conf 99999999970
No 57
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=91.55 E-value=0.12 Score=31.75 Aligned_cols=58 Identities=16% Similarity=0.257 Sum_probs=39.5
Q ss_pred EEEEEECHHHHHHHHHHHHHHHCCCHHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHH
Q ss_conf 8999706779999999850100051011244315789999999851566875104571167999999
Q gi|254780553|r 59 RLFGFLSDLDRQWFMLLQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIM 125 (207)
Q Consensus 59 ~LyGF~~~~Er~~F~~Li~V~GIGpK~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi 125 (207)
....-.+...- .|..++|||||.|=+|...-.-. -.-.++.-|.+++|||+|+=+|+-
T Consensus 87 ~~vNiNtAs~e----eL~~lpgIG~~kA~aIi~yRe~~-----G~f~sv~dL~~v~GiG~~~~ekl~ 144 (149)
T COG1555 87 KKVNINTASAE----ELQALPGIGPKKAQAIIDYREEN-----GPFKSVDDLAKVKGIGPKTLEKLK 144 (149)
T ss_pred CCCCCCCCCHH----HHHHCCCCCHHHHHHHHHHHHHC-----CCCCCHHHHCCCCCCCHHHHHHHH
T ss_conf 41366610899----99886798999999999999973-----997657887107777899999877
No 58
>PRK10702 endonuclease III; Provisional
Probab=91.21 E-value=0.081 Score=32.77 Aligned_cols=26 Identities=15% Similarity=0.445 Sum_probs=20.8
Q ss_pred HCCCHHHHHHCCCCCHHHHHHHHHHH
Q ss_conf 51566875104571167999999997
Q gi|254780553|r 103 ILQNSKVIAQIPGISMKIASRIMTEL 128 (207)
Q Consensus 103 ~~~D~~~L~~vpGIGkKtA~rIi~EL 128 (207)
.-.|...|.++||||+|||.-|..--
T Consensus 104 vP~~~~~L~~LpGIG~kTA~aIl~~a 129 (211)
T PRK10702 104 VPEDRAALEALPGVGRKTANVVLNTA 129 (211)
T ss_pred CHHHHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 76669999987663588999999998
No 59
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=91.07 E-value=0.17 Score=30.67 Aligned_cols=54 Identities=22% Similarity=0.439 Sum_probs=35.2
Q ss_pred HHHHHH-HHHHHHHCCCHHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHH
Q ss_conf 999999-9850100051011244315789999999851566875104571167999999
Q gi|254780553|r 68 DRQWFM-LLQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIM 125 (207)
Q Consensus 68 Er~~F~-~Li~V~GIGpK~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi 125 (207)
.+.+|. .|-.|.|||||..=++|..+.. ...|.+-.+.-|.++ ||+++.|++|-
T Consensus 524 ~k~~~~s~Ld~I~GiG~~r~~~LL~~Fgs---~~~i~~As~eel~~v-gi~~~~a~~i~ 578 (581)
T COG0322 524 SKAMLQSSLDDIPGIGPKRRKALLKHFGS---LKGIKSASVEELAKV-GISKKLAEKIY 578 (581)
T ss_pred HHHHHCCCCCCCCCCCHHHHHHHHHHHHC---HHHHHHCCHHHHHHC-CCCHHHHHHHH
T ss_conf 66640270004888688999999998317---888885599999874-99999999998
No 60
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=90.92 E-value=0.7 Score=26.55 Aligned_cols=53 Identities=13% Similarity=0.152 Sum_probs=39.3
Q ss_pred HHHHHHHCCCHHHHHHHCCC---CHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHH
Q ss_conf 98501000510112443157---8999999985156687510457116799999999742
Q gi|254780553|r 74 LLQSVQGVGARVAMGVLSRI---TATELVESIILQNSKVIAQIPGISMKIASRIMTELKG 130 (207)
Q Consensus 74 ~Li~V~GIGpK~AL~iLs~l---~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~ 130 (207)
.=+.+.|+|+|+.-.+...- ++.+|..- +..-|.+++|.|+|.|++++-....
T Consensus 427 ~amdI~GLGek~i~~L~~~gli~~~~Dly~L----~~~~L~~l~g~geKsa~nLl~aIe~ 482 (563)
T PRK08097 427 QGLGLDGIGEGTWRALHQTGRFEHLFSWLAL----TPEQLANTPGIGKARAAQLWHQFNL 482 (563)
T ss_pred CCCCCCCCCHHHHHHHHHCCCCCCHHHHHHC----CHHHHHCCCCHHHHHHHHHHHHHHH
T ss_conf 4158567699999999975888997997508----9999855898578999999999999
No 61
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=90.84 E-value=0.1 Score=32.08 Aligned_cols=21 Identities=29% Similarity=0.557 Sum_probs=15.8
Q ss_pred HHHHCCCCCHHHHHHHHHHHH
Q ss_conf 751045711679999999974
Q gi|254780553|r 109 VIAQIPGISMKIASRIMTELK 129 (207)
Q Consensus 109 ~L~~vpGIGkKtA~rIi~ELk 129 (207)
.|.++||||+|+|++|+-...
T Consensus 2 ~L~~v~GIG~k~A~~ll~~~~ 22 (26)
T smart00278 2 ELLKVPGIGPKTAEKILEAXX 22 (26)
T ss_pred CCCCCCCCCCHHHHHHHHHHH
T ss_conf 210179988115999999762
No 62
>PRK10702 endonuclease III; Provisional
Probab=90.71 E-value=0.14 Score=31.24 Aligned_cols=56 Identities=16% Similarity=0.053 Sum_probs=33.9
Q ss_pred HHHHHHHHHCCCHHHHHHHCCCCHHHHHHHHHCCCHHHH-HHCCCCCHHHHHHHHHHHH
Q ss_conf 999850100051011244315789999999851566875-1045711679999999974
Q gi|254780553|r 72 FMLLQSVQGVGARVAMGVLSRITATELVESIILQNSKVI-AQIPGISMKIASRIMTELK 129 (207)
Q Consensus 72 F~~Li~V~GIGpK~AL~iLs~l~~~~l~~aI~~~D~~~L-~~vpGIGkKtA~rIi~ELk 129 (207)
++.|+++.|||||+|=+||+ +..+.=. .+...++..+ +++..+..+..+++--+|.
T Consensus 108 ~~~L~~LpGIG~kTA~aIl~-~a~~~~~-~~VDtnV~RV~~Rlg~~~~~~~~~~~~~l~ 164 (211)
T PRK10702 108 RAALEALPGVGRKTANVVLN-TAFGWPT-IAVDTHIFRVCNRTQFAPGKNVEQVEEKLL 164 (211)
T ss_pred HHHHHHHHCCCHHHHHHHHH-HHCCCCC-CCCCCCHHHHHHHHCCCCCCCHHHHHHHHH
T ss_conf 99999876635889999999-9849986-525735999999976577899999999999
No 63
>pfam01367 5_3_exonuc 5'-3' exonuclease, C-terminal SAM fold.
Probab=90.66 E-value=0.13 Score=31.38 Aligned_cols=18 Identities=28% Similarity=0.514 Sum_probs=10.5
Q ss_pred HHHHCCCHHHHHHHCCCC
Q ss_conf 010005101124431578
Q gi|254780553|r 77 SVQGVGARVAMGVLSRIT 94 (207)
Q Consensus 77 ~V~GIGpK~AL~iLs~l~ 94 (207)
+|.|||||+|..+|+.+.
T Consensus 22 Gv~GiG~KtA~~Ll~~~g 39 (100)
T pfam01367 22 GVPGIGEKTAAKLLKEYG 39 (100)
T ss_pred CCCCCCCHHHHHHHHHCC
T ss_conf 999988168999999819
No 64
>PRK05797 consensus
Probab=90.54 E-value=0.13 Score=31.36 Aligned_cols=76 Identities=16% Similarity=0.162 Sum_probs=41.5
Q ss_pred CCCCEEEEEEE-----EEECCCCEEEE-EEE------CHHHHHHHHHHHHHHHCCCHHHHHHHCCCCHHHHHHHHHCCCH
Q ss_conf 47984999999-----99738841899-970------6779999999850100051011244315789999999851566
Q gi|254780553|r 40 KIGDFCTLFVE-----THMRQDQIRLF-GFL------SDLDRQWFMLLQSVQGVGARVAMGVLSRITATELVESIILQNS 107 (207)
Q Consensus 40 ~~g~~v~l~~~-----~~vrEd~~~Ly-GF~------~~~Er~~F~~Li~V~GIGpK~AL~iLs~l~~~~l~~aI~~~D~ 107 (207)
+.|-+|.+.+. +.|.++ .++| .-. -..+..+++.. ||.|..=.-.+ |+.-.-.
T Consensus 123 ~~g~~v~i~s~DkD~~QLv~~~-v~v~~~~k~~~~~~~~~~~~v~ek~----Gv~P~q~~D~~----------aL~GD~s 187 (869)
T PRK05797 123 EKGIEVYIVTGDKDALQLASDN-VKVVITKKGITEKEIYDKNKMVEEY----GVTPTQFIDVK----------GLMGDKS 187 (869)
T ss_pred HCCCCEEEEECCCCCCCCCCCC-EEEEECCCCCCCCEEECHHHHHHHH----CCCHHHHHHHH----------HHCCCCC
T ss_conf 7899589980798600108799-8999888999745563799989997----78999999999----------9808864
Q ss_pred HHHHHCCCCCHHHHHHHHHHHHH
Q ss_conf 87510457116799999999742
Q gi|254780553|r 108 KVIAQIPGISMKIASRIMTELKG 130 (207)
Q Consensus 108 ~~L~~vpGIGkKtA~rIi~ELk~ 130 (207)
.-+-.|||||+|||.+++-+..+
T Consensus 188 DNIPGVpGIG~KTA~kLL~eyGs 210 (869)
T PRK05797 188 DNIPGVPGIGEKTAFKLIKEYGS 210 (869)
T ss_pred CCCCCCCCCCHHHHHHHHHHCCC
T ss_conf 57899998781899999986787
No 65
>pfam00730 HhH-GPD HhH-GPD superfamily base excision DNA repair protein. This family contains a diverse range of structurally related DNA repair proteins. The superfamily is called the HhH-GPD family after its hallmark Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate. This includes endonuclease III, EC:4.2.99.18 and MutY an A/G-specific adenine glycosylase, both have a C terminal 4Fe-4S cluster. The family also includes 8-oxoguanine DNA glycosylases. The methyl-CPG binding protein MBD4 also contains a related domain that is a thymine DNA glycosylase. The family also includes DNA-3-methyladenine glycosylase II EC:3.2.2.21 and other members of the AlkA family.
Probab=90.54 E-value=0.56 Score=27.17 Aligned_cols=63 Identities=17% Similarity=0.211 Sum_probs=32.8
Q ss_pred EEEEEECHHH-----HHHHHHHHHHHHCCCHHHHHHHCCCCHHHHHHHHHC----------CCHHHHHHCCCCCHHHHHH
Q ss_conf 8999706779-----999999850100051011244315789999999851----------5668751045711679999
Q gi|254780553|r 59 RLFGFLSDLD-----RQWFMLLQSVQGVGARVAMGVLSRITATELVESIIL----------QNSKVIAQIPGISMKIASR 123 (207)
Q Consensus 59 ~LyGF~~~~E-----r~~F~~Li~V~GIGpK~AL~iLs~l~~~~l~~aI~~----------~D~~~L~~vpGIGkKtA~r 123 (207)
..|||.|.+. -+-++.++.--|..-+.|-.|.. +.+++.+ .+...|+++||||++||+-
T Consensus 23 ~~~~~pt~~~l~~~~~~~l~~~i~~~G~~~~Ka~~I~~------~a~~~~~~~~~~~~~~~~~~~~L~~l~GIG~~ta~~ 96 (144)
T pfam00730 23 ERYGFPTPEDLAEADEEELRELIKGLGFYRRKAKYIKE------LARILVEGYLGLVPLDLEELEALLALPGVGRWTAEA 96 (144)
T ss_pred HHHCCCCHHHHHCCCHHHHHHHHHCCCCHHHHHHHHHH------HHHHHHHHCCCCCCCCHHHHHHHHCCCCCCHHHHHH
T ss_conf 98289899999859999999998708976999999999------998889862897886115699986088976999999
Q ss_pred HHHH
Q ss_conf 9999
Q gi|254780553|r 124 IMTE 127 (207)
Q Consensus 124 Ii~E 127 (207)
+..-
T Consensus 97 ~l~~ 100 (144)
T pfam00730 97 VLLF 100 (144)
T ss_pred HHHH
T ss_conf 9999
No 66
>COG4277 Predicted DNA-binding protein with the Helix-hairpin-helix motif [General function prediction only]
Probab=90.31 E-value=0.17 Score=30.56 Aligned_cols=70 Identities=19% Similarity=0.178 Sum_probs=45.2
Q ss_pred CCEEEEEEECHHHHHHHHHHHHHHHCCCHHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHH
Q ss_conf 84189997067799999998501000510112443157899999998515668751045711679999999974
Q gi|254780553|r 56 DQIRLFGFLSDLDRQWFMLLQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMTELK 129 (207)
Q Consensus 56 d~~~LyGF~~~~Er~~F~~Li~V~GIGpK~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk 129 (207)
.-...|||.-.+-+.-=.. .-=.-+-||+|-++=. ++ -|---+...+.+.|-+|||||.|+|.||+..=+
T Consensus 282 wLlrfYgF~~~Ei~~~g~~-~ld~~lDPK~~wAl~~-~d--~FPVdvn~A~~~~llRVPGiG~ksa~rIv~~Rr 351 (404)
T COG4277 282 WLLRFYGFSADEILASGGD-FLDPDLDPKTAWALKH-MD--RFPVDVNKAPYKELLRVPGIGVKSARRIVMTRR 351 (404)
T ss_pred HHHHHHCCCHHHHHHCCCC-CCCCCCCHHHHHHHHC-CC--CCCCCCCCCCHHHHCCCCCCCHHHHHHHHHHHH
T ss_conf 8999708887888744897-5578878345777733-55--365133456777821168877378899988742
No 67
>cd00080 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) motif. HhH2 domains are found in Rad2 family of prokaryotic and eukaryotic replication and repair nucleases, i.e., DNA polymerase I, Taq DNA polymerase, DNA repair protein Rad2 endonuclease, flap endonuclease, exonuclease I and IX, 5'-3' exonuclease and also bacteriophage Rnase H. These nucleases degrade RNA-DNA or DNA-DNA duplexes, or both and play essential roles in DNA duplication, repair, and recombination.
Probab=90.25 E-value=0.33 Score=28.72 Aligned_cols=42 Identities=21% Similarity=0.368 Sum_probs=28.2
Q ss_pred EEEECHHHHHHHHHHHH--------HHHCCCHHHHHHHCCCC-HHHHHHHHH
Q ss_conf 99706779999999850--------10005101124431578-999999985
Q gi|254780553|r 61 FGFLSDLDRQWFMLLQS--------VQGVGARVAMGVLSRIT-ATELVESII 103 (207)
Q Consensus 61 yGF~~~~Er~~F~~Li~--------V~GIGpK~AL~iLs~l~-~~~l~~aI~ 103 (207)
||+ +.++---|..|.. |.|||||+|+.+++.++ .+.+...+.
T Consensus 3 ~g~-~p~q~~d~~~L~GD~sDnipGV~GIG~ktA~~ll~~~~~l~~i~~~~~ 53 (75)
T cd00080 3 LGL-TPEQFIDLAILVGDKSDNIPGVPGIGPKTALKLLKEYGSLENLLENLD 53 (75)
T ss_pred CCC-CHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCCCHHHHHHHHH
T ss_conf 897-999999999991965458877586379999999999099999998387
No 68
>smart00475 53EXOc 5'-3' exonuclease.
Probab=90.19 E-value=0.24 Score=29.67 Aligned_cols=74 Identities=18% Similarity=0.263 Sum_probs=41.4
Q ss_pred EECCHHHHHHCCCCCCEEEEEEEEEECCCCEEEEEEECHHHH--------HHHHHHH--------HHHHCCCHHHHHHHC
Q ss_conf 970868898502479849999999973884189997067799--------9999985--------010005101124431
Q gi|254780553|r 28 IYCPIRTLSCLGKIGDFCTLFVETHMRQDQIRLFGFLSDLDR--------QWFMLLQ--------SVQGVGARVAMGVLS 91 (207)
Q Consensus 28 i~vs~~~~~~l~~~g~~v~l~~~~~vrEd~~~LyGF~~~~Er--------~~F~~Li--------~V~GIGpK~AL~iLs 91 (207)
|.-+.+.+.+| ..+.+.+|.... +.....+|+.....|+ --|..|. +|.|||||+|..+|.
T Consensus 128 IvS~DkDl~QL--v~~~v~v~~~~~-~~~~~~~~~~~~v~e~~gv~P~q~~d~~aL~GD~sDnIpGV~GIG~KtA~kLL~ 204 (259)
T smart00475 128 IVSGDKDLLQL--VSDKVSVLDPTK-GIKEFELYTPENVIEKYGLTPEQIIDYKALMGDSSDNIPGVPGIGEKTAAKLLK 204 (259)
T ss_pred EECCCCCHHHH--CCCCEEEEECCC-CCCCCEEECHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHH
T ss_conf 95088378884--888719998158-996567965999998848998998637640464535899999847899999999
Q ss_pred CC-CHHHHHHHHHC
Q ss_conf 57-89999999851
Q gi|254780553|r 92 RI-TATELVESIIL 104 (207)
Q Consensus 92 ~l-~~~~l~~aI~~ 104 (207)
.+ +.+.+.+.+..
T Consensus 205 ~ygsle~i~~~~d~ 218 (259)
T smart00475 205 EFGSLENILENLDK 218 (259)
T ss_pred HCCCHHHHHHHHHH
T ss_conf 83999999983985
No 69
>TIGR02903 spore_lon_C ATP-dependent protease, Lon family; InterPro: IPR014252 This entry shows some relation to the widely distributed ATP-dependent protease La, also called Lon or LonA (IPR004815 from INTERPRO), but is more closely related to LonB (IPR014251 from INTERPRO), a LonA paralog found only in endospore-forming bacteria. Proteins in this entry are unassigned peptidases belonging to the MEROPS peptidase family S16 (lon protease family, clan SJ). They are restricted to a subset of endospore-forming species, and probably participate in the program of endospore formation. We propose the designation LonC..
Probab=90.07 E-value=0.16 Score=30.77 Aligned_cols=50 Identities=20% Similarity=0.314 Sum_probs=30.4
Q ss_pred HHHHHHHCCCCHHHHHHHHHCCC--HHHHHHC-------------CCCCHHHHHHHHHHHHHHHH
Q ss_conf 01124431578999999985156--6875104-------------57116799999999742221
Q gi|254780553|r 84 RVAMGVLSRITATELVESIILQN--SKVIAQI-------------PGISMKIASRIMTELKGKAI 133 (207)
Q Consensus 84 K~AL~iLs~l~~~~l~~aI~~~D--~~~L~~v-------------pGIGkKtA~rIi~ELk~K~~ 133 (207)
|++-++.|-|-|++|-+.+=++- .+.|+|+ |||||.||.||++|=--|+.
T Consensus 140 kl~~s~~slLRP~~f~EiVGQerAI~aLlaK~aSPfPQHiiLYGPPGVGKTTaARl~LEe~K~~~ 204 (616)
T TIGR02903 140 KLAKSIQSLLRPRAFSEIVGQERAIKALLAKLASPFPQHIILYGPPGVGKTTAARLALEEAKKLK 204 (616)
T ss_pred HHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCEEEECCCCCCHHHHHHHHHHHCCCCC
T ss_conf 89999998628766764333468999999763188866078557338847899999876213687
No 70
>PRK08434 consensus
Probab=90.03 E-value=0.17 Score=30.66 Aligned_cols=75 Identities=19% Similarity=0.296 Sum_probs=40.3
Q ss_pred EEEEEC--CHHHHHHCCCCCC-EEEEEEEEEEC---C-CCEEEEEEECHHHHHHHHHHH--------HHHHCCCHHHHHH
Q ss_conf 238970--8688985024798-49999999973---8-841899970677999999985--------0100051011244
Q gi|254780553|r 25 CYIIYC--PIRTLSCLGKIGD-FCTLFVETHMR---Q-DQIRLFGFLSDLDRQWFMLLQ--------SVQGVGARVAMGV 89 (207)
Q Consensus 25 GY~i~v--s~~~~~~l~~~g~-~v~l~~~~~vr---E-d~~~LyGF~~~~Er~~F~~Li--------~V~GIGpK~AL~i 89 (207)
||+|++ +.+.+.+| +.+ .+.+|.....+ + +-..=||+.-.+=.++ .-|. +|.|||||+|..+
T Consensus 124 g~~v~IvSgDKDl~QL--V~d~~v~l~~~~k~~~~d~~~V~eK~GV~P~qv~D~-lAL~GDsSDNIPGVpGIG~KTA~kL 200 (887)
T PRK08434 124 DIFVRIVSHDKDLYQL--IDDGKVSIYDPIKKNEIDEAACLEKYGVKPKQIRDF-LALCGDSADNIPGVKGIGAKGAKKL 200 (887)
T ss_pred CCEEEEECCCCCHHHH--CCCCEEEEEECCCCEEECHHHHHHHHCCCHHHHHHH-HHHCCCCCCCCCCCCCCCHHHHHHH
T ss_conf 9939998089877761--839808999789986877999999979698999999-9981886457899998568999999
Q ss_pred HCCC-CHHHHHHHH
Q ss_conf 3157-899999998
Q gi|254780553|r 90 LSRI-TATELVESI 102 (207)
Q Consensus 90 Ls~l-~~~~l~~aI 102 (207)
|+.+ +.+.+.+.+
T Consensus 201 L~eyGsLE~I~~n~ 214 (887)
T PRK08434 201 LDEFGSLEGIYENL 214 (887)
T ss_pred HHHCCCHHHHHHHH
T ss_conf 99828889999988
No 71
>PRK07300 consensus
Probab=89.94 E-value=0.17 Score=30.72 Aligned_cols=38 Identities=16% Similarity=0.365 Sum_probs=25.6
Q ss_pred CCHHHHHH--HHHCCCHHHHHHCCCCCHHHHHHHHHHHHH
Q ss_conf 78999999--985156687510457116799999999742
Q gi|254780553|r 93 ITATELVE--SIILQNSKVIAQIPGISMKIASRIMTELKG 130 (207)
Q Consensus 93 l~~~~l~~--aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~ 130 (207)
.+|++++. |+.-.-..=+-.|||||+|||.+++-|..+
T Consensus 179 V~P~qiiD~lAL~GDsSDNIPGVpGIG~KTA~kLL~eyGs 218 (880)
T PRK07300 179 LTPNQFIDLKALMGDKSDNIPGVTKIGEKTGLKLLHEFGS 218 (880)
T ss_pred CCHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCC
T ss_conf 8989999999980886246778898536999999997786
No 72
>PRK07625 consensus
Probab=89.84 E-value=0.17 Score=30.57 Aligned_cols=75 Identities=20% Similarity=0.257 Sum_probs=38.7
Q ss_pred EEEEEECC--HHHHHHCCCCCCEEEEEEEEE---ECCCC-EEEEEEECHHHHHHHHHHH--------HHHHCCCHHHHHH
Q ss_conf 32389708--688985024798499999999---73884-1899970677999999985--------0100051011244
Q gi|254780553|r 24 VCYIIYCP--IRTLSCLGKIGDFCTLFVETH---MRQDQ-IRLFGFLSDLDRQWFMLLQ--------SVQGVGARVAMGV 89 (207)
Q Consensus 24 vGY~i~vs--~~~~~~l~~~g~~v~l~~~~~---vrEd~-~~LyGF~~~~Er~~F~~Li--------~V~GIGpK~AL~i 89 (207)
-||+|++- .+.+.+| +++++++|-... +-++. ..=||+.-.+=.+ |.-|+ +|.|||||+|..+
T Consensus 127 ~g~~v~IvSgDKDl~QL--V~~~v~i~~~~k~~~~d~~~V~ek~GV~P~qviD-~lAL~GDsSDNIPGVpGIG~KTA~kL 203 (922)
T PRK07625 127 HGMNVIVSTGDKDLAQL--VTDRVTLVNTMTNEVLDRDGVLAKFGVPPERIVD-YLSLIGDTVDNVPGVEKCGPKTAVKW 203 (922)
T ss_pred CCCEEEEECCCCCHHHH--CCCCEEEEECCCCCCCCHHHHHHHHCCCHHHHHH-HHHHCCCCCCCCCCCCCCCHHHHHHH
T ss_conf 88939998189868661--8998699978899270899999987979899999-99971976357899998567989999
Q ss_pred HCCCC-HHHHHHH
Q ss_conf 31578-9999999
Q gi|254780553|r 90 LSRIT-ATELVES 101 (207)
Q Consensus 90 Ls~l~-~~~l~~a 101 (207)
|+.++ .+.++..
T Consensus 204 L~eyGsLE~I~~n 216 (922)
T PRK07625 204 LTQYGSLDGVVEH 216 (922)
T ss_pred HHHCCCHHHHHHH
T ss_conf 9974789999998
No 73
>TIGR01084 mutY A/G-specific adenine glycosylase; InterPro: IPR005760 The DNA repair enzyme MutY plays an important role in the prevention of DNA mutations resulting from the presence of the oxidatively damaged lesion 7,8-dihydro-8-oxo-2'-deoxyguanosine (8-OxoG). 8-OxoG can mispair with 2'-deoxycytidine 5'-triphosphate or with 2'-deoxyadenosine triphosphate during DNA replication, forming C*8-oxoG and A*8-oxoG mispairs. Human MutY is responsible for recognition and removal of the inappropriately inserted adenine in an A=8-oxoG mispair. If unrepaired, the A=8-oxoG mispairs can result in deleterious C:G to A:T transversions. Multiple forms of mammalian MutY are formed by alternative splicing and locate to the nucleus or mitochondrion, where they have been shown to interact with several other proteins involved in the repair of DNA damage . The HhH-GPD domain within the protein binds the phosphate backbone of the substrate. This family represents bacterial MutY and a limited number of murine homologs. In rat, the Escherichia coli MutY DNA glycosylase homolog (MYH) is induced in response to mitochondrial DNA damage . ; GO: 0019104 DNA N-glycosylase activity, 0006284 base-excision repair, 0005622 intracellular.
Probab=89.80 E-value=0.37 Score=28.38 Aligned_cols=60 Identities=23% Similarity=0.224 Sum_probs=49.4
Q ss_pred HHHHHHHHHCCCHHHHHHHCCCCHHHHHHHHHCCCHHH----HHHCCC-CCHHHHHHHHHHHHHHHH
Q ss_conf 99985010005101124431578999999985156687----510457-116799999999742221
Q gi|254780553|r 72 FMLLQSVQGVGARVAMGVLSRITATELVESIILQNSKV----IAQIPG-ISMKIASRIMTELKGKAI 133 (207)
Q Consensus 72 F~~Li~V~GIGpK~AL~iLs~l~~~~l~~aI~~~D~~~----L~~vpG-IGkKtA~rIi~ELk~K~~ 133 (207)
|+.|-+.+||||=||=|||| +..+ =..+|.+||++. +-.+.| +++|.-++.+.++-+.+.
T Consensus 117 ~~~~~~L~GVG~yTAgAils-~a~~-~~~p~~DGNV~RVLsR~fA~~~~~~~k~~e~~l~~~~~~ll 181 (297)
T TIGR01084 117 LEDLKALPGVGRYTAGAILS-FAYN-KPVPILDGNVKRVLSRLFAVEGWPGKKKVENRLWELAESLL 181 (297)
T ss_pred HHHHHHCCCCCHHHHHHHHH-HHHC-CCCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHC
T ss_conf 79785178976217999999-8726-87620154078899999862489887348899999999858
No 74
>PRK07997 consensus
Probab=89.56 E-value=0.2 Score=30.10 Aligned_cols=77 Identities=17% Similarity=0.326 Sum_probs=40.5
Q ss_pred CCCCEEEEEEE-----EEECCCCEEEEEEECHHHHHHHHHHHHHHHCCCHHHHHHHCCCCHHHHHHH--HHCCCHHHHHH
Q ss_conf 47984999999-----997388418999706779999999850100051011244315789999999--85156687510
Q gi|254780553|r 40 KIGDFCTLFVE-----THMRQDQIRLFGFLSDLDRQWFMLLQSVQGVGARVAMGVLSRITATELVES--IILQNSKVIAQ 112 (207)
Q Consensus 40 ~~g~~v~l~~~-----~~vrEd~~~LyGF~~~~Er~~F~~Li~V~GIGpK~AL~iLs~l~~~~l~~a--I~~~D~~~L~~ 112 (207)
+.|.+|.+.|- +-|.+ ...+|.-.+. .. ++|..=..=. ..+|++++.. +.-.-..=+-.
T Consensus 127 ~~g~~v~IvSgDKDl~QLV~~-~v~v~~~~~~-------~~-----~~~~~V~ek~-GV~P~qv~D~laL~GDsSDNIPG 192 (928)
T PRK07997 127 KAGRPVLISTGDKDMAQLVTP-NITLINTMTN-------TI-----LGPEEVVNKY-GVPPELIIDFLALMGDSSDNIPG 192 (928)
T ss_pred HCCCEEEEECCCCCHHHHCCC-CEEEEECCCC-------EE-----ECHHHHHHHH-CCCHHHHHHHHHHCCCCCCCCCC
T ss_conf 679959998389876553789-8599988898-------48-----7799999987-97989889999972886568899
Q ss_pred CCCCCHHHHHHHHHHHHH
Q ss_conf 457116799999999742
Q gi|254780553|r 113 IPGISMKIASRIMTELKG 130 (207)
Q Consensus 113 vpGIGkKtA~rIi~ELk~ 130 (207)
|||||+|||.+++-+..+
T Consensus 193 VpGIG~KTA~kLL~eyGs 210 (928)
T PRK07997 193 VPGVGEKTAQALLQGLGG 210 (928)
T ss_pred CCCCCHHHHHHHHHHHCC
T ss_conf 997548999999998277
No 75
>PRK08928 consensus
Probab=89.54 E-value=0.18 Score=30.48 Aligned_cols=75 Identities=17% Similarity=0.261 Sum_probs=42.7
Q ss_pred CCCCEEEEEEE-----EEECCCCEEEEEEEC--HHHHHHHHHHHHHHHCCCHHHHHHHCCCCHHHHHHH--HHCCCHHHH
Q ss_conf 47984999999-----997388418999706--779999999850100051011244315789999999--851566875
Q gi|254780553|r 40 KIGDFCTLFVE-----THMRQDQIRLFGFLS--DLDRQWFMLLQSVQGVGARVAMGVLSRITATELVES--IILQNSKVI 110 (207)
Q Consensus 40 ~~g~~v~l~~~-----~~vrEd~~~LyGF~~--~~Er~~F~~Li~V~GIGpK~AL~iLs~l~~~~l~~a--I~~~D~~~L 110 (207)
+.|.+|.+.+. +-|.|+-..++-... ..|.++++.. | .+|++++.. +.-.-..=+
T Consensus 125 ~~g~~v~IvSgDKDl~QLV~~~v~v~~~~k~~~~~~~~V~ek~----G------------V~P~qiiD~laL~GDsSDNI 188 (861)
T PRK08928 125 SLGDEVVIISSDKDLLQLMNENIKIYDPIKNKYITEDDVVEKF----G------------VTSDKLLDVMALTGDRSDNI 188 (861)
T ss_pred HCCCEEEEECCCCCHHHHCCCCEEEEECCCCCCCCHHHHHHHH----C------------CCHHHHHHHHHHCCCCCCCC
T ss_conf 7799099984899750318898599988888176899999997----9------------79899999999808764688
Q ss_pred HHCCCCCHHHHHHHHHHHHH
Q ss_conf 10457116799999999742
Q gi|254780553|r 111 AQIPGISMKIASRIMTELKG 130 (207)
Q Consensus 111 ~~vpGIGkKtA~rIi~ELk~ 130 (207)
-.|||||+|||.+++-+..+
T Consensus 189 PGVpGIG~KTA~kLL~eyGs 208 (861)
T PRK08928 189 PGVPSIGPKTAAKLITQFGS 208 (861)
T ss_pred CCCCCCCHHHHHHHHHHCCC
T ss_conf 99988562899999996797
No 76
>PRK07556 consensus
Probab=89.49 E-value=0.19 Score=30.27 Aligned_cols=77 Identities=14% Similarity=0.195 Sum_probs=43.1
Q ss_pred CCCCEEEEEEE-----EEECCCCEEEEEEECHHHHHHHHHHHHHHHCCCHHHHHHHCCCCHHHHHHH--HHCCCHHHHHH
Q ss_conf 47984999999-----997388418999706779999999850100051011244315789999999--85156687510
Q gi|254780553|r 40 KIGDFCTLFVE-----THMRQDQIRLFGFLSDLDRQWFMLLQSVQGVGARVAMGVLSRITATELVES--IILQNSKVIAQ 112 (207)
Q Consensus 40 ~~g~~v~l~~~-----~~vrEd~~~LyGF~~~~Er~~F~~Li~V~GIGpK~AL~iLs~l~~~~l~~a--I~~~D~~~L~~ 112 (207)
+.|-+|.+.+. +-|.|+-..++++.+. .+...+|= .=. ..+|++++.. +.-.-..=+-.
T Consensus 133 ~~g~~v~IvSgDKDl~QLV~d~V~i~~~~k~~--------~~d~~~V~-----eK~-GV~P~qv~D~lAL~GDsSDNIPG 198 (977)
T PRK07556 133 EAGGDVTIISSDKDLMQLVGDGVSMYDPMKDK--------RIGIPEVI-----EKF-GVPPEKVVDVQALAGDSVDNVPG 198 (977)
T ss_pred HCCCCEEEECCCCCHHHHCCCCEEEEECCCCC--------EECHHHHH-----HHH-CCCHHHHHHHHHHCCCCCCCCCC
T ss_conf 77992999818986756277986999788984--------81799999-----986-96989999999971876467898
Q ss_pred CCCCCHHHHHHHHHHHHH
Q ss_conf 457116799999999742
Q gi|254780553|r 113 IPGISMKIASRIMTELKG 130 (207)
Q Consensus 113 vpGIGkKtA~rIi~ELk~ 130 (207)
|||||+|||.+++-+..+
T Consensus 199 VpGIG~KTA~kLL~eyGs 216 (977)
T PRK07556 199 IPGIGIKTAAQLINEYGD 216 (977)
T ss_pred CCCCCHHHHHHHHHHCCC
T ss_conf 998548999999997578
No 77
>PRK05929 consensus
Probab=89.44 E-value=0.19 Score=30.32 Aligned_cols=74 Identities=12% Similarity=0.149 Sum_probs=40.4
Q ss_pred CCCCEEEEEEE-----EEECCCCEEEEEEECH---HHHHHHHHHHHHHHCCCHHHHHHHCCCCHHHHHHH--HHCCCHHH
Q ss_conf 47984999999-----9973884189997067---79999999850100051011244315789999999--85156687
Q gi|254780553|r 40 KIGDFCTLFVE-----THMRQDQIRLFGFLSD---LDRQWFMLLQSVQGVGARVAMGVLSRITATELVES--IILQNSKV 109 (207)
Q Consensus 40 ~~g~~v~l~~~-----~~vrEd~~~LyGF~~~---~Er~~F~~Li~V~GIGpK~AL~iLs~l~~~~l~~a--I~~~D~~~ 109 (207)
+.|-+|.+.|. +.|.++-..++-+.+. ++.++++.. || +|++++.. ..-.-..=
T Consensus 123 ~~g~~v~IvTgDKD~~QLv~~~v~v~~~~k~~~~~d~~~V~ek~----Gv------------~P~qi~D~laL~GDsSDN 186 (870)
T PRK05929 123 AEGYEVCICTADKDLLQLVNSHVVAWNPWKDQEVIGYNEVIEQY----GV------------PPGQIADYLALVGDSSDN 186 (870)
T ss_pred HCCCEEEEECCCCCHHHHCCCCEEEEECCCCCCCCCHHHHHHHH----CC------------CHHHHHHHHHHCCCCCCC
T ss_conf 77992999848997624177987999768888126799999997----96------------989999999972876468
Q ss_pred HHHCCCCCHHHHHHHHHHHH
Q ss_conf 51045711679999999974
Q gi|254780553|r 110 IAQIPGISMKIASRIMTELK 129 (207)
Q Consensus 110 L~~vpGIGkKtA~rIi~ELk 129 (207)
+-.|||||+|||.+++-+..
T Consensus 187 IPGVpGIG~KTA~kLL~~yg 206 (870)
T PRK05929 187 IPGVSGCGPKKAAALLKEFQ 206 (870)
T ss_pred CCCCCCCCHHHHHHHHHHCC
T ss_conf 99999760999999998678
No 78
>PRK08786 consensus
Probab=89.26 E-value=0.21 Score=30.08 Aligned_cols=74 Identities=15% Similarity=0.155 Sum_probs=39.3
Q ss_pred CCCCEEEEEE-----EEEECCCCEEEEEEEC---HHHHHHHHHHHHHHHCCCHHHHHHHCCCCHHHHHH--HHHCCCHHH
Q ss_conf 4798499999-----9997388418999706---77999999985010005101124431578999999--985156687
Q gi|254780553|r 40 KIGDFCTLFV-----ETHMRQDQIRLFGFLS---DLDRQWFMLLQSVQGVGARVAMGVLSRITATELVE--SIILQNSKV 109 (207)
Q Consensus 40 ~~g~~v~l~~-----~~~vrEd~~~LyGF~~---~~Er~~F~~Li~V~GIGpK~AL~iLs~l~~~~l~~--aI~~~D~~~ 109 (207)
..|-+|.+.+ .+-|.++-..++.+.. ..+.++++.. ||. |++++. |+.-.-..=
T Consensus 121 ~~g~~v~IvSgDKD~~QLV~~~v~i~~~~kg~~~~~~~~V~eK~----GV~------------P~qviD~lAL~GDsSDN 184 (927)
T PRK08786 121 ADGLAVTISTGDKDFAQLVRPGVELVNTMSGSRMDSDAAVIAKF----GVR------------PDQIVDLLALMGDTVDN 184 (927)
T ss_pred HCCCEEEEECCCCCHHHHCCCCEEEEECCCCCEECCHHHHHHHH----CCC------------HHHHHHHHHHCCCCCCC
T ss_conf 78991999828987524178985999889997765789999996----969------------89999999980876467
Q ss_pred HHHCCCCCHHHHHHHHHHHH
Q ss_conf 51045711679999999974
Q gi|254780553|r 110 IAQIPGISMKIASRIMTELK 129 (207)
Q Consensus 110 L~~vpGIGkKtA~rIi~ELk 129 (207)
+-.|||||+|||.+++-+..
T Consensus 185 IPGVpGIG~KTA~kLL~eyG 204 (927)
T PRK08786 185 VPGVEKCGPKTAAKWLAEYD 204 (927)
T ss_pred CCCCCCCCHHHHHHHHHHCC
T ss_conf 89999856899999999757
No 79
>PRK07898 consensus
Probab=89.07 E-value=0.21 Score=30.01 Aligned_cols=75 Identities=15% Similarity=0.166 Sum_probs=40.9
Q ss_pred CCCCEEEEEEE-----EEECCCCEEEE---EEEC---HHHHHHHHHHHHHHHCCCHHHHHHHCCCCHHHHHH--HHHCCC
Q ss_conf 47984999999-----99738841899---9706---77999999985010005101124431578999999--985156
Q gi|254780553|r 40 KIGDFCTLFVE-----THMRQDQIRLF---GFLS---DLDRQWFMLLQSVQGVGARVAMGVLSRITATELVE--SIILQN 106 (207)
Q Consensus 40 ~~g~~v~l~~~-----~~vrEd~~~Ly---GF~~---~~Er~~F~~Li~V~GIGpK~AL~iLs~l~~~~l~~--aI~~~D 106 (207)
+.|-+|.+.+. +-|.|+-..+| |+.+ ..+.++++.. ||. |++++. |+.-.-
T Consensus 137 ~~g~~v~IvSgDKDl~QLV~d~v~vl~~~kg~~~~~~~d~~~V~ek~----GV~------------P~qviD~lAL~GDs 200 (902)
T PRK07898 137 AEGYRVLVVTGDRDALQLVSDDVTVLYPRKGVSDLTRFTPEAVEEKY----GLT------------PAQYPDFAALRGDP 200 (902)
T ss_pred HCCCEEEEECCCCCHHHHCCCCEEEEECCCCCCCCEECCHHHHHHHH----CCC------------HHHHHHHHHHCCCC
T ss_conf 77996999768997755178987999778998635442899999986----979------------89999999981886
Q ss_pred HHHHHHCCCCCHHHHHHHHHHHHH
Q ss_conf 687510457116799999999742
Q gi|254780553|r 107 SKVIAQIPGISMKIASRIMTELKG 130 (207)
Q Consensus 107 ~~~L~~vpGIGkKtA~rIi~ELk~ 130 (207)
..=.-.|||||+|||.+++-|..+
T Consensus 201 SDNIPGVpGIG~KTA~kLL~eyGs 224 (902)
T PRK07898 201 SDNLPGIPGVGEKTAAKWIAQYGS 224 (902)
T ss_pred CCCCCCCCCCCHHHHHHHHHHCCC
T ss_conf 457999998447889999997677
No 80
>PRK08434 consensus
Probab=89.06 E-value=0.21 Score=29.98 Aligned_cols=75 Identities=12% Similarity=0.213 Sum_probs=42.9
Q ss_pred CCCCEEEEEE-----EEEECCCCEEEEEEE---CHHHHHHHHHHHHHHHCCCHHHHHHHCCCCHHHHHHH--HHCCCHHH
Q ss_conf 4798499999-----999738841899970---6779999999850100051011244315789999999--85156687
Q gi|254780553|r 40 KIGDFCTLFV-----ETHMRQDQIRLFGFL---SDLDRQWFMLLQSVQGVGARVAMGVLSRITATELVES--IILQNSKV 109 (207)
Q Consensus 40 ~~g~~v~l~~-----~~~vrEd~~~LyGF~---~~~Er~~F~~Li~V~GIGpK~AL~iLs~l~~~~l~~a--I~~~D~~~ 109 (207)
+.|-+|.+.+ .+-|.++...+|.-. ..++..+++.. || +|++++.. +.-.-..=
T Consensus 122 ~~g~~v~IvSgDKDl~QLV~d~~v~l~~~~k~~~~d~~~V~eK~----GV------------~P~qv~D~lAL~GDsSDN 185 (887)
T PRK08434 122 EQDIFVRIVSHDKDLYQLIDDGKVSIYDPIKKNEIDEAACLEKY----GV------------KPKQIRDFLALCGDSADN 185 (887)
T ss_pred HCCCEEEEECCCCCHHHHCCCCEEEEEECCCCEEECHHHHHHHH----CC------------CHHHHHHHHHHCCCCCCC
T ss_conf 78993999808987776183980899978998687799999997----96------------989999999981886457
Q ss_pred HHHCCCCCHHHHHHHHHHHHH
Q ss_conf 510457116799999999742
Q gi|254780553|r 110 IAQIPGISMKIASRIMTELKG 130 (207)
Q Consensus 110 L~~vpGIGkKtA~rIi~ELk~ 130 (207)
+-.|||||+|||.+++-+..+
T Consensus 186 IPGVpGIG~KTA~kLL~eyGs 206 (887)
T PRK08434 186 IPGVKGIGAKGAKKLLDEFGS 206 (887)
T ss_pred CCCCCCCCHHHHHHHHHHCCC
T ss_conf 899998568999999998288
No 81
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=88.98 E-value=0.2 Score=30.11 Aligned_cols=27 Identities=19% Similarity=0.351 Sum_probs=20.7
Q ss_pred CCCHHHHHHCCCCCHHHHHHHHHHHHH
Q ss_conf 156687510457116799999999742
Q gi|254780553|r 104 LQNSKVIAQIPGISMKIASRIMTELKG 130 (207)
Q Consensus 104 ~~D~~~L~~vpGIGkKtA~rIi~ELk~ 130 (207)
-+|...|.++||||+|||.=.+..--+
T Consensus 105 P~~~~eL~~LPGVGrKTAnvVL~~a~g 131 (211)
T COG0177 105 PDTREELLSLPGVGRKTANVVLSFAFG 131 (211)
T ss_pred CCHHHHHHHCCCCCHHHHHHHHHHHCC
T ss_conf 815999974899665778989986559
No 82
>PRK06887 consensus
Probab=88.97 E-value=0.24 Score=29.67 Aligned_cols=76 Identities=17% Similarity=0.268 Sum_probs=41.5
Q ss_pred CCCCEEEEEEE-----EEECCCCEEEEEEECHHHHHHHHHHHHHHHCCCHHHHHHHCCCCHHHHHHH--HHCCCHHHHHH
Q ss_conf 47984999999-----997388418999706779999999850100051011244315789999999--85156687510
Q gi|254780553|r 40 KIGDFCTLFVE-----THMRQDQIRLFGFLSDLDRQWFMLLQSVQGVGARVAMGVLSRITATELVES--IILQNSKVIAQ 112 (207)
Q Consensus 40 ~~g~~v~l~~~-----~~vrEd~~~LyGF~~~~Er~~F~~Li~V~GIGpK~AL~iLs~l~~~~l~~a--I~~~D~~~L~~ 112 (207)
+.|.+|.+.+. +-| .|...+|..... .++...+|=-| . ..+|++++.. +.-.-..=+-.
T Consensus 127 ~~g~~v~IvS~DKDl~QLV-~~~v~i~~~~~~-------~~~d~~~V~ek-----~-GV~P~qiiD~lAL~GDsSDNIPG 192 (954)
T PRK06887 127 SAGKKVLISTGDKDMAQLV-DDNIMLINTMNN-------SLLDREGVIEK-----Y-GIPPELIIDYLALMGDSSDNIPG 192 (954)
T ss_pred HCCCEEEEECCCCCCHHHC-CCCEEEEECCCC-------EEECHHHHHHH-----H-CCCHHHHHHHHHHCCCCCCCCCC
T ss_conf 7899299975887701216-798799989898-------27579999898-----7-97989999999971885247788
Q ss_pred CCCCCHHHHHHHHHHHH
Q ss_conf 45711679999999974
Q gi|254780553|r 113 IPGISMKIASRIMTELK 129 (207)
Q Consensus 113 vpGIGkKtA~rIi~ELk 129 (207)
|||||+|||.+++-+..
T Consensus 193 VpGIG~KTA~kLL~eyG 209 (954)
T PRK06887 193 VAGVGEKTALGLLQGIG 209 (954)
T ss_pred CCCEEHHHHHHHHHHHC
T ss_conf 78541699999999957
No 83
>PRK08835 consensus
Probab=88.76 E-value=0.25 Score=29.50 Aligned_cols=77 Identities=10% Similarity=0.185 Sum_probs=40.6
Q ss_pred CCCCEEEEEE-----EEEECCCCEEEEEEECHHHHHHHHHHHHHHHCCCHHHHHHHCCCCHHHHHHH--HHCCCHHHHHH
Q ss_conf 4798499999-----9997388418999706779999999850100051011244315789999999--85156687510
Q gi|254780553|r 40 KIGDFCTLFV-----ETHMRQDQIRLFGFLSDLDRQWFMLLQSVQGVGARVAMGVLSRITATELVES--IILQNSKVIAQ 112 (207)
Q Consensus 40 ~~g~~v~l~~-----~~~vrEd~~~LyGF~~~~Er~~F~~Li~V~GIGpK~AL~iLs~l~~~~l~~a--I~~~D~~~L~~ 112 (207)
+.|-+|.+.| .+-|.|+-..++...+. . ++|+.=..-. ..+|++++.. +.-.-..=+-.
T Consensus 127 ~~g~~v~IvS~DKDl~QLV~~~v~v~~~~~~~--------~-----~d~~~V~ek~-GV~P~qviD~lAL~GDsSDNIPG 192 (931)
T PRK08835 127 QAGMPVLISTGDKDMAQLVDDNITLINTMTNV--------V-----MDREGVVEKF-GIPPELIIDYLALMGDKVDNIPG 192 (931)
T ss_pred HCCCEEEEEECCCCHHHHCCCCEEEEECCCCE--------E-----ECHHHHHHHH-CCCHHHHHHHHHHCCCCCCCCCC
T ss_conf 77993999828997634178985999888986--------8-----7899999987-96989989999971886468899
Q ss_pred CCCCCHHHHHHHHHHHHH
Q ss_conf 457116799999999742
Q gi|254780553|r 113 IPGISMKIASRIMTELKG 130 (207)
Q Consensus 113 vpGIGkKtA~rIi~ELk~ 130 (207)
|||||+|||.+++-+..+
T Consensus 193 VpGIG~KTA~kLL~eyGs 210 (931)
T PRK08835 193 VPGVGDKTATALLQGIGG 210 (931)
T ss_pred CCCCCHHHHHHHHHHHCC
T ss_conf 997458889999998486
No 84
>PHA00439 exonuclease
Probab=88.70 E-value=0.24 Score=29.67 Aligned_cols=82 Identities=12% Similarity=0.082 Sum_probs=42.8
Q ss_pred HHHHHHHCCCHHHHHHCCCCCHHHHHHHHHH-----HHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCC
Q ss_conf 9999985156687510457116799999999-----74222110113344323333344555565315899999999679
Q gi|254780553|r 97 ELVESIILQNSKVIAQIPGISMKIASRIMTE-----LKGKAISLSSVVQQDMSCVNKEQAHICSMPSFAINAISALVNLG 171 (207)
Q Consensus 97 ~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~E-----Lk~K~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~AL~~LG 171 (207)
-+++++.-.-..-...+||||+|||++|+-+ --.+..+ +......+...-.........+.=+-+++|-.-=|
T Consensus 176 ~~~QtL~GD~tDgy~GvpGiG~ktA~klL~~~~~~~~~~~~~k--~g~~kg~t~~~w~k~~~~~~~~~W~~vv~~y~k~g 253 (288)
T PHA00439 176 HLFQTIKGDSTDGYSGIPGWGPDTAEAFLNNPYIFEQVEKVLK--SGKNKGQTVTKWVKRAPGDEETLWDCIVSLGAKAG 253 (288)
T ss_pred HHHHHHCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCHHCC--CCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCC
T ss_conf 8888624747689789988488999998637442221000002--34445543110012466542028999999999859
Q ss_pred CCHHHHHHH
Q ss_conf 998999999
Q gi|254780553|r 172 YGQDQATTA 180 (207)
Q Consensus 172 y~~~ea~~a 180 (207)
+++.+|-.-
T Consensus 254 ~te~dAl~q 262 (288)
T PHA00439 254 MTEEDIIKQ 262 (288)
T ss_pred CCHHHHHHH
T ss_conf 999999999
No 85
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=88.58 E-value=0.27 Score=29.32 Aligned_cols=23 Identities=17% Similarity=0.356 Sum_probs=18.7
Q ss_pred CCHHHHHHCCCCCHHHHHHHHHH
Q ss_conf 56687510457116799999999
Q gi|254780553|r 105 QNSKVIAQIPGISMKIASRIMTE 127 (207)
Q Consensus 105 ~D~~~L~~vpGIGkKtA~rIi~E 127 (207)
.....|+++||||+|||.=++.-
T Consensus 80 ~~~~~L~~l~GIG~~TA~~vl~~ 102 (158)
T cd00056 80 DAREELLALPGVGRKTANVVLLF 102 (158)
T ss_pred HHHHHHHCCCCCCHHHHHHHHHH
T ss_conf 89999875898289999999999
No 86
>cd00008 53EXOc 5'-3' exonuclease; T5 type 5'-3' exonuclease domains may co-occur with DNA polymerase I (Pol I) domains, or be part of Pol I containing complexes. They digest dsDNA and ssDNA, releasing mono-,di- and tri-nucleotides, as well as oligonucleotides, and have also been reported to possess RNase H activity. Also called 5' nuclease family, involved in structure-specific cleavage of flaps formed by Pol I activity (similar to mammalian flap endonuclease I, FEN-1). A single nucleic acid strand may be threaded through the 5' nuclease enzyme before cleavage occurs. The domain binds two divalent metal ions which are necessary for activity.
Probab=88.36 E-value=0.3 Score=29.00 Aligned_cols=36 Identities=25% Similarity=0.577 Sum_probs=23.8
Q ss_pred CCHHHHHH--HHHCCCHHHHHHCCCCCHHHHHHHHHHH
Q ss_conf 78999999--9851566875104571167999999997
Q gi|254780553|r 93 ITATELVE--SIILQNSKVIAQIPGISMKIASRIMTEL 128 (207)
Q Consensus 93 l~~~~l~~--aI~~~D~~~L~~vpGIGkKtA~rIi~EL 128 (207)
.+|+++.. ++.-....-+..|||||+|||.+++-+.
T Consensus 166 v~p~q~~d~~aL~GD~sDnIpGV~GiG~KtA~kLl~~~ 203 (240)
T cd00008 166 VTPAQIIDYKALMGDSSDNIPGVPGIGEKTAAKLLKEY 203 (240)
T ss_pred CCHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHH
T ss_conf 89999987699728764688999985789999999980
No 87
>TIGR00593 pola DNA polymerase I; InterPro: IPR002298 DNA carries 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 cell life cycle. This function is mediated by DNA-directed DNA polymerases, which add nucleotide triphosphate (dNTP) residues to the 5'-end of the growing DNA chain, using a complementary DNA as template. Small RNA molecules are generally used as primers for chain elongation, although terminal proteins may also be used. DNA-dependent DNA polymerases have been grouped into families, denoted A, B and X, on the basis of sequence similarities , . Members of family A, which includes bacterial and bacteriophage polymerases, share significant similarity to Escherichia coli polymerase I; hence family A is also known as the pol I family. The bacterial polymerases also contain an exonuclease activity, which is coded for in the N-terminal portion. Three motifs, A, B and C , are seen to be conserved across all DNA polymerases, with motifs A and C also seen in RNA polymerases. They are centred on invariant residues, and their structural significance was implied from the Klenow (E. coli) structure. Motif A contains a strictly-conserved aspartate at the junction of a beta-strand and an alpha-helix; motif B contains an alpha-helix with positive charges; and motif C has a doublet of negative charges, located in a beta-turn-beta secondary structure .; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication.
Probab=88.12 E-value=0.26 Score=29.37 Aligned_cols=87 Identities=18% Similarity=0.192 Sum_probs=55.2
Q ss_pred HHHHC-CCCCCEEEEEE-----EEEECC-CCEEEEE--EECHHHHHHHHHHHHHHHCCCHHHHHHHCCCCHHHHHH--HH
Q ss_conf 89850-24798499999-----999738-8418999--70677999999985010005101124431578999999--98
Q gi|254780553|r 34 TLSCL-GKIGDFCTLFV-----ETHMRQ-DQIRLFG--FLSDLDRQWFMLLQSVQGVGARVAMGVLSRITATELVE--SI 102 (207)
Q Consensus 34 ~~~~l-~~~g~~v~l~~-----~~~vrE-d~~~LyG--F~~~~Er~~F~~Li~V~GIGpK~AL~iLs~l~~~~l~~--aI 102 (207)
|+++- .+.|-+|.+.| .+-|.+ +-..++. |....+-+.| +...|=-|- +..|+++.. |+
T Consensus 117 TLA~~a~~~G~~V~I~sgDrD~lQLvs~e~V~V~~~~~~~g~~~~~~~----t~e~V~eKy------Gv~P~Q~~D~~AL 186 (1005)
T TIGR00593 117 TLAKQAEKEGYEVRIISGDRDLLQLVSDENVKVLIPERKKGKTEFTEI----TPEYVVEKY------GVTPSQLVDLKAL 186 (1005)
T ss_pred HHHHHHHHCCCEEEEEECCCCCCCCCCCCCEEEEECCCCCCCCCCEEC----CHHHHHHHC------CCCHHHHHHHHHC
T ss_conf 988877546854899837846211217861488643545675431011----778987541------8674578876204
Q ss_pred HCCCHHHHHHCCCCCHHHHHHHHHHHHH
Q ss_conf 5156687510457116799999999742
Q gi|254780553|r 103 ILQNSKVIAQIPGISMKIASRIMTELKG 130 (207)
Q Consensus 103 ~~~D~~~L~~vpGIGkKtA~rIi~ELk~ 130 (207)
.-.--.=+-.|||||+|||.+++-|...
T Consensus 187 ~GD~SDNiPGV~GIGeKTA~kLL~~fgs 214 (1005)
T TIGR00593 187 VGDSSDNIPGVKGIGEKTAAKLLQEFGS 214 (1005)
T ss_pred CCCCCCCCCCCCCCCCHHHHHHHHHHHH
T ss_conf 6888878599897376568999987210
No 88
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=87.71 E-value=0.58 Score=27.10 Aligned_cols=59 Identities=24% Similarity=0.354 Sum_probs=45.8
Q ss_pred HHHHHHHHHHHCCCHHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHH
Q ss_conf 9999985010005101124431578999999985156687510457116799999999742
Q gi|254780553|r 70 QWFMLLQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMTELKG 130 (207)
Q Consensus 70 ~~F~~Li~V~GIGpK~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~ 130 (207)
+-+..|..+|||||-.|=++-. ...+ -+.-+...|.+.|..+.|||.-.|.||-.+.-+
T Consensus 7 ~~~~~l~disgvg~~~a~~l~~-ag~e-~~~d~~~a~q~~l~~~~gignalaarikadvg~ 65 (238)
T PRK12766 7 DEYEELTDISGVGPSKAESLRE-AGFE-SVEDVRAADQSELADVDGIGNALAARIKADVGG 65 (238)
T ss_pred CCHHHHHCCCCCCHHHHHHHHH-CCCC-HHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCC
T ss_conf 4767764123668003678887-0401-289897642776642013138999987414565
No 89
>PRK08076 consensus
Probab=87.69 E-value=0.29 Score=29.04 Aligned_cols=38 Identities=18% Similarity=0.482 Sum_probs=25.0
Q ss_pred CCHHHHHH--HHHCCCHHHHHHCCCCCHHHHHHHHHHHHH
Q ss_conf 78999999--985156687510457116799999999742
Q gi|254780553|r 93 ITATELVE--SIILQNSKVIAQIPGISMKIASRIMTELKG 130 (207)
Q Consensus 93 l~~~~l~~--aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~ 130 (207)
.+|++++. |+.-.-..-+-.|||||+|||.+++-+...
T Consensus 171 v~P~q~~D~~aL~GDssDNIPGVpGiG~KtA~~ll~~~gs 210 (877)
T PRK08076 171 LTPKQIIDMKGLMGDSSDNIPGVPGVGEKTAIKLLKQFGT 210 (877)
T ss_pred CCHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCC
T ss_conf 6989999999971876467999998637999999996686
No 90
>KOG2875 consensus
Probab=87.61 E-value=0.4 Score=28.15 Aligned_cols=90 Identities=14% Similarity=0.166 Sum_probs=51.6
Q ss_pred HHHHHHCCCCHHHHHHHHH--CCCHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHH
Q ss_conf 1124431578999999985--15668751045711679999999974222110113344323333344555565315899
Q gi|254780553|r 85 VAMGVLSRITATELVESII--LQNSKVIAQIPGISMKIASRIMTELKGKAISLSSVVQQDMSCVNKEQAHICSMPSFAIN 162 (207)
Q Consensus 85 ~AL~iLs~l~~~~l~~aI~--~~D~~~L~~vpGIGkKtA~rIi~ELk~K~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d 162 (207)
-.+.+|+.-+.+-|..-|. |||++.++ |+-+|.+-.+--++..++.......+..+.-.. .+
T Consensus 108 qgvRlLrQdP~E~lfSFiCSSNNNIaRIT-------~Mve~fc~~fG~~i~~~dg~~~h~FPsl~~L~g---------~~ 171 (323)
T KOG2875 108 QGVRLLRQDPIECLFSFICSSNNNIARIT-------GMVERFCQAFGPRIIQLDGVDYHGFPSLQALAG---------PE 171 (323)
T ss_pred HHHHHHHCCCHHHHHHHHHCCCCCHHHHH-------HHHHHHHHHHCCCEEEECCCCCCCCCCHHHHCC---------HH
T ss_conf 66578751719788988725787599999-------999999986175037555712036854777647---------47
Q ss_pred HHHHHHH--CCCCHHHHHHHHHHHHHHCCC
Q ss_conf 9999996--799989999999999851688
Q gi|254780553|r 163 AISALVN--LGYGQDQATTAVVSVLKKEKN 190 (207)
Q Consensus 163 ~~~AL~~--LGy~~~ea~~ai~~i~~~~~~ 190 (207)
+..-|.. +||.-+-+..++..+..+.+.
T Consensus 172 ~Ea~LR~~gfGYRAkYI~~ta~~l~~~~g~ 201 (323)
T KOG2875 172 VEAELRKLGFGYRAKYISATARALQEKQGG 201 (323)
T ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHCCC
T ss_conf 699999817644689999999999972350
No 91
>pfam02371 Transposase_20 Transposase IS116/IS110/IS902 family. Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This family includes transposases for IS116, IS110 and IS902. This region is often found with pfam01548. The exact function of this region is uncertain. This family contains a HHH motif suggesting a DNA-binding function.
Probab=87.51 E-value=0.35 Score=28.55 Aligned_cols=23 Identities=26% Similarity=0.534 Sum_probs=20.7
Q ss_pred HHHHHCCCCCHHHHHHHHHHHHH
Q ss_conf 87510457116799999999742
Q gi|254780553|r 108 KVIAQIPGISMKIASRIMTELKG 130 (207)
Q Consensus 108 ~~L~~vpGIGkKtA~rIi~ELk~ 130 (207)
..|.++||||..||.+|+.|+-|
T Consensus 2 ~~L~sipGiG~~~a~~l~aeigd 24 (87)
T pfam02371 2 ELLLSIPGIGPITAAALLAEIGD 24 (87)
T ss_pred CHHHCCCCCCHHHHHHHHHHHCC
T ss_conf 23426999529999999999298
No 92
>pfam01367 5_3_exonuc 5'-3' exonuclease, C-terminal SAM fold.
Probab=87.44 E-value=0.36 Score=28.46 Aligned_cols=37 Identities=24% Similarity=0.526 Sum_probs=24.6
Q ss_pred CHHHHHH--HHHCCCHHHHHHCCCCCHHHHHHHHHHHHH
Q ss_conf 8999999--985156687510457116799999999742
Q gi|254780553|r 94 TATELVE--SIILQNSKVIAQIPGISMKIASRIMTELKG 130 (207)
Q Consensus 94 ~~~~l~~--aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~ 130 (207)
.|+++.. |+.-.-..-+-.|||||+|||.+++-+..+
T Consensus 2 ~P~q~~d~~aL~GD~sDnIPGv~GiG~KtA~~Ll~~~gs 40 (100)
T pfam01367 2 TPEQIIDYKALVGDSSDNIPGVPGIGEKTAAKLLKEYGS 40 (100)
T ss_pred CHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHCCC
T ss_conf 889999999992976458899999881689999998198
No 93
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=87.40 E-value=2.3 Score=23.05 Aligned_cols=127 Identities=13% Similarity=0.159 Sum_probs=72.4
Q ss_pred EEEECHHHHHHHHHHHHHHHCCCHHHH----HHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHH--HHHHHHHHHH
Q ss_conf 997067799999998501000510112----4431578999999985156687510457116799999--9997422211
Q gi|254780553|r 61 FGFLSDLDRQWFMLLQSVQGVGARVAM----GVLSRITATELVESIILQNSKVIAQIPGISMKIASRI--MTELKGKAIS 134 (207)
Q Consensus 61 yGF~~~~Er~~F~~Li~V~GIGpK~AL----~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rI--i~ELk~K~~~ 134 (207)
||=....+-|+-..|+. .|+.-+.++ .+|+.++. .......+...|+++||||+-.|-++ ++||.-++.+
T Consensus 19 ~G~~~Lsd~ELLailLr-tG~~~~~~~~la~~lL~~fg~---L~~l~~a~~~el~~v~GiG~aka~~l~a~~El~~R~~~ 94 (224)
T COG2003 19 LGAEALSDAELLAILLR-TGTKGESVLDLAKELLQEFGS---LAELLKASVEELSSVKGIGLAKAIQIKAAIELGKRILA 94 (224)
T ss_pred HCHHHCCHHHHHHHHHH-CCCCCCCHHHHHHHHHHHCCC---HHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf 28453466899999996-289998789999999997325---88887379999951788338899999999999999999
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHH-HCCCCHHHHHHHHHHHHHHCC--------------CCCCHHHHHH
Q ss_conf 0113344323333344555565315899999999-679998999999999985168--------------8889899999
Q gi|254780553|r 135 LSSVVQQDMSCVNKEQAHICSMPSFAINAISALV-NLGYGQDQATTAVVSVLKKEK--------------NIADDSQIIR 199 (207)
Q Consensus 135 ~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~AL~-~LGy~~~ea~~ai~~i~~~~~--------------~~~~~eelIk 199 (207)
....... . -..-+++...|. .||+.++|...++-- ..++. ...-.-|++|
T Consensus 95 ~~~~~~~-------------~-i~sp~~~~~~l~~~l~~~~~E~f~vL~L-d~qnrlI~~e~lf~GTi~~s~V~PREI~k 159 (224)
T COG2003 95 ERLREGV-------------V-ITSPEAVAEYLRAELGGEEREHFVVLYL-DSQNRLIATETLFIGTLNVSEVHPREIFK 159 (224)
T ss_pred HHHCCCC-------------C-CCCHHHHHHHHHHHHHHHHHHHHHHHHH-CCCCCEEEEEEEEEEECCCCEECHHHHHH
T ss_conf 8750577-------------5-4899999999999861348899999995-47684331003775201450433799999
Q ss_pred HHHHHHC
Q ss_conf 9999745
Q gi|254780553|r 200 LALRAIS 206 (207)
Q Consensus 200 ~aLk~Ls 206 (207)
.||+.-+
T Consensus 160 ~Al~~nA 166 (224)
T COG2003 160 EALKYNA 166 (224)
T ss_pred HHHHHCC
T ss_conf 9998221
No 94
>pfam00633 HHH Helix-hairpin-helix motif. The helix-hairpin-helix DNA-binding motif is found to be duplicated in the central domain of RuvA. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain.
Probab=87.37 E-value=0.27 Score=29.30 Aligned_cols=21 Identities=33% Similarity=0.376 Sum_probs=18.6
Q ss_pred HHHHHHHHHHCCCHHHHHHHC
Q ss_conf 999985010005101124431
Q gi|254780553|r 71 WFMLLQSVQGVGARVAMGVLS 91 (207)
Q Consensus 71 ~F~~Li~V~GIGpK~AL~iLs 91 (207)
-++.|.++.|||||+|=+|++
T Consensus 9 s~eeL~~lpGVG~~tA~~I~~ 29 (30)
T pfam00633 9 SREELLALPGVGPKTAEAILS 29 (30)
T ss_pred CHHHHHHCCCCCHHHHHHHHC
T ss_conf 599997288977688998853
No 95
>PRK07625 consensus
Probab=87.29 E-value=0.34 Score=28.67 Aligned_cols=77 Identities=12% Similarity=0.111 Sum_probs=40.7
Q ss_pred CCCCEEEEEE-----EEEECCCCEEEEEEECHHHHHHHHHHHHHHHCCCHHHHHHHCCCCHHHHHHH--HHCCCHHHHHH
Q ss_conf 4798499999-----9997388418999706779999999850100051011244315789999999--85156687510
Q gi|254780553|r 40 KIGDFCTLFV-----ETHMRQDQIRLFGFLSDLDRQWFMLLQSVQGVGARVAMGVLSRITATELVES--IILQNSKVIAQ 112 (207)
Q Consensus 40 ~~g~~v~l~~-----~~~vrEd~~~LyGF~~~~Er~~F~~Li~V~GIGpK~AL~iLs~l~~~~l~~a--I~~~D~~~L~~ 112 (207)
+.|-+|.+.| .+-|.++-..++.+.. ..+...+|=-| . ..+|++++.. +.-.-..=+-.
T Consensus 126 ~~g~~v~IvSgDKDl~QLV~~~v~i~~~~k~--------~~~d~~~V~ek-----~-GV~P~qviD~lAL~GDsSDNIPG 191 (922)
T PRK07625 126 QHGMNVIVSTGDKDLAQLVTDRVTLVNTMTN--------EVLDRDGVLAK-----F-GVPPERIVDYLSLIGDTVDNVPG 191 (922)
T ss_pred HCCCEEEEECCCCCHHHHCCCCEEEEECCCC--------CCCCHHHHHHH-----H-CCCHHHHHHHHHHCCCCCCCCCC
T ss_conf 7889399981898686618998699978899--------27089999998-----7-97989999999971976357899
Q ss_pred CCCCCHHHHHHHHHHHHH
Q ss_conf 457116799999999742
Q gi|254780553|r 113 IPGISMKIASRIMTELKG 130 (207)
Q Consensus 113 vpGIGkKtA~rIi~ELk~ 130 (207)
|||||+|||.+++-+..+
T Consensus 192 VpGIG~KTA~kLL~eyGs 209 (922)
T PRK07625 192 VEKCGPKTAVKWLTQYGS 209 (922)
T ss_pred CCCCCHHHHHHHHHHCCC
T ss_conf 998567989999997478
No 96
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=87.15 E-value=0.44 Score=27.88 Aligned_cols=51 Identities=22% Similarity=0.363 Sum_probs=30.6
Q ss_pred HHHCC--CHHHHHHHCCCCHHHHHH---HHHCCCHHHHHHCCCCCHHHHHHHHHHHHH
Q ss_conf 10005--101124431578999999---985156687510457116799999999742
Q gi|254780553|r 78 VQGVG--ARVAMGVLSRITATELVE---SIILQNSKVIAQIPGISMKIASRIMTELKG 130 (207)
Q Consensus 78 V~GIG--pK~AL~iLs~l~~~~l~~---aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~ 130 (207)
+.++| .+.|-.|.+.. ..+.+ .-.-.+...|.++||||+|||.-+..---+
T Consensus 39 i~~~g~~~~ka~~i~~~a--~~i~~~~~~~~p~~~~~L~~lpGVG~~tA~~vl~~~~~ 94 (149)
T smart00478 39 IRPLGFYRRKAKYLIELA--RILVEEYGGEVPDDREELLKLPGVGRKTANAVLSFALG 94 (149)
T ss_pred HHHCCCHHHHHHHHHHHH--HHHHHHCCCCCCCHHHHHHCCCCCCHHHHHHHHHHHCC
T ss_conf 998688999999999999--99998665558855999875898659999999999879
No 97
>PRK05755 DNA polymerase I; Provisional
Probab=87.09 E-value=0.33 Score=28.72 Aligned_cols=77 Identities=13% Similarity=0.231 Sum_probs=40.4
Q ss_pred CCCCEEEEEEE-----EEECCCCEEEEEEECHHHHHHHHHHHHHHHCCCHHHHHHHCCCCHHHHHH--HHHCCCHHHHHH
Q ss_conf 47984999999-----99738841899970677999999985010005101124431578999999--985156687510
Q gi|254780553|r 40 KIGDFCTLFVE-----THMRQDQIRLFGFLSDLDRQWFMLLQSVQGVGARVAMGVLSRITATELVE--SIILQNSKVIAQ 112 (207)
Q Consensus 40 ~~g~~v~l~~~-----~~vrEd~~~LyGF~~~~Er~~F~~Li~V~GIGpK~AL~iLs~l~~~~l~~--aI~~~D~~~L~~ 112 (207)
+.|-+|.+.+. +-|.++-..++-+.. .. ++|..=..-. ..+|++++. |+.-.-..-+-.
T Consensus 125 ~~~~~v~i~s~DkD~~QLv~~~v~~~~~~k~--------~~-----~~~~~v~ek~-Gv~P~q~~D~~aL~GD~sDNIPG 190 (889)
T PRK05755 125 AAGFEVLIVTGDKDLLQLVDDNVTVLNTMKN--------ER-----IDPEGVIEKY-GVTPEQIIDFLALMGDSSDNIPG 190 (889)
T ss_pred HCCCEEEEEECCCCHHHHCCCCEEEEECCCC--------CE-----ECHHHHHHHH-CCCHHHHHHHHHHCCCCCCCCCC
T ss_conf 7799599980898785618898699989999--------28-----5899999997-96989999999980886457899
Q ss_pred CCCCCHHHHHHHHHHHHH
Q ss_conf 457116799999999742
Q gi|254780553|r 113 IPGISMKIASRIMTELKG 130 (207)
Q Consensus 113 vpGIGkKtA~rIi~ELk~ 130 (207)
|||||+|||.+++-+..+
T Consensus 191 VpGIG~KtA~kLl~~ygs 208 (889)
T PRK05755 191 VPGVGEKTAAKLLKEFGS 208 (889)
T ss_pred CCCCCHHHHHHHHHHCCC
T ss_conf 886269999999986786
No 98
>TIGR02236 recomb_radA DNA repair and recombination protein RadA; InterPro: IPR011938 This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA, eukaryotic RAD51 (IPR011941 from INTERPRO), and archaeal RadB (IPR011939 from INTERPRO). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein .; GO: 0003684 damaged DNA binding, 0005524 ATP binding, 0008094 DNA-dependent ATPase activity, 0006281 DNA repair, 0006310 DNA recombination.
Probab=86.52 E-value=0.31 Score=28.87 Aligned_cols=16 Identities=19% Similarity=0.567 Sum_probs=13.7
Q ss_pred HHHCCCCCHHHHHHHH
Q ss_conf 5104571167999999
Q gi|254780553|r 110 IAQIPGISMKIASRIM 125 (207)
Q Consensus 110 L~~vpGIGkKtA~rIi 125 (207)
|.-+||||++||+|+-
T Consensus 2 ledLPGVGp~TA~KL~ 17 (333)
T TIGR02236 2 LEDLPGVGPATAEKLR 17 (333)
T ss_pred CCCCCCCCHHHHHHHH
T ss_conf 6657897576889988
No 99
>PRK09482 xni exonuclease IX; Provisional
Probab=86.39 E-value=0.43 Score=27.97 Aligned_cols=86 Identities=15% Similarity=0.102 Sum_probs=49.2
Q ss_pred EEEE--ECCHHHHHHCCCCCCEEEEEEEEEEC----CCCEEEEEEECHHHHHHHHHHH--------HHHHCCCHHHHHHH
Q ss_conf 2389--70868898502479849999999973----8841899970677999999985--------01000510112443
Q gi|254780553|r 25 CYII--YCPIRTLSCLGKIGDFCTLFVETHMR----QDQIRLFGFLSDLDRQWFMLLQ--------SVQGVGARVAMGVL 90 (207)
Q Consensus 25 GY~i--~vs~~~~~~l~~~g~~v~l~~~~~vr----Ed~~~LyGF~~~~Er~~F~~Li--------~V~GIGpK~AL~iL 90 (207)
||+| ..+.+.+.+| +.+++++|-+..-+ ++-..-||+.- ++---|.-|. +|.|||||+|..+|
T Consensus 123 ~~~v~IvS~DkDl~QL--v~~~v~v~~~~~~~~~~~~~v~ek~Gv~P-~q~~d~~aL~GD~SDNIPGV~GIG~KtA~~LL 199 (256)
T PRK09482 123 GHQATIVSTDKGYCQL--LSPTIQIRDYFQKRWLDIPFIEQEFGVEP-QQLPDYWGLAGISSSKIPGVAGIGPKSAAELL 199 (256)
T ss_pred CCEEEEEECCCCHHHH--CCCCEEEEECCCCCCCCHHHHHHHCCCCH-HHHHHEEEEECCCCCCCCCCCCCCHHHHHHHH
T ss_conf 9969999668889996--75984999786771317999878528287-35323024746543689999985888999999
Q ss_pred CCCC-HHHHHHHHHCCCHHHHHHCCCCCHHHHHHH
Q ss_conf 1578-999999985156687510457116799999
Q gi|254780553|r 91 SRIT-ATELVESIILQNSKVIAQIPGISMKIASRI 124 (207)
Q Consensus 91 s~l~-~~~l~~aI~~~D~~~L~~vpGIGkKtA~rI 124 (207)
+.++ .+.+.+.+.+ |++|..+++
T Consensus 200 ~~fgsle~i~~n~d~-----------i~~k~~~~l 223 (256)
T PRK09482 200 NQFRSLEGIYESLDA-----------LPEKWRKKL 223 (256)
T ss_pred HHHCCHHHHHHHHHH-----------CCHHHHHHH
T ss_conf 985509999983775-----------568999999
No 100
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=86.23 E-value=0.35 Score=28.52 Aligned_cols=49 Identities=20% Similarity=0.203 Sum_probs=31.4
Q ss_pred HHHHHHHHHHCCCHHHHHHHCCCCH---HHHHHHHHCCCHHHHHHCCCCCHHHHHHH
Q ss_conf 9999850100051011244315789---99999985156687510457116799999
Q gi|254780553|r 71 WFMLLQSVQGVGARVAMGVLSRITA---TELVESIILQNSKVIAQIPGISMKIASRI 124 (207)
Q Consensus 71 ~F~~Li~V~GIGpK~AL~iLs~l~~---~~l~~aI~~~D~~~L~~vpGIGkKtA~rI 124 (207)
-...|.+|.|||||+|-.+-. ... ++|..+- + ..|+..+++|-|.-+.+
T Consensus 87 ~l~el~~I~GvGpk~a~~l~~-~Gi~tl~dL~~a~---~-~~l~~~q~~Glk~~ed~ 138 (334)
T smart00483 87 SLKLFTNVFGVGPKTAAKWYR-KGIRTLEELKKNK---E-LKLTKQQKAGLKYYEDI 138 (334)
T ss_pred HHHHHHCCCCCCHHHHHHHHH-CCCCCHHHHHHHH---H-HHHHHHHHHHHHHHHHH
T ss_conf 899985388877899999998-4988799999878---8-76788988769999999
No 101
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this
Probab=86.10 E-value=1.1 Score=25.27 Aligned_cols=29 Identities=31% Similarity=0.502 Sum_probs=19.0
Q ss_pred HHHHHHHHCCCHHHHHHHCCC---CHHHHHHHH
Q ss_conf 998501000510112443157---899999998
Q gi|254780553|r 73 MLLQSVQGVGARVAMGVLSRI---TATELVESI 102 (207)
Q Consensus 73 ~~Li~V~GIGpK~AL~iLs~l---~~~~l~~aI 102 (207)
..|.+|.|||||+|-.+.. + +.++|..+.
T Consensus 85 ~~l~~I~GiGpk~a~~l~~-~Gi~sl~dL~~a~ 116 (307)
T cd00141 85 LLLLRVPGVGPKTARKLYE-LGIRTLEDLRKAA 116 (307)
T ss_pred HHHHCCCCCCHHHHHHHHH-CCCCCHHHHHHHH
T ss_conf 9996478878899999998-2999799999750
No 102
>cd00128 XPG Xeroderma pigmentosum G N- and I-regions (XPGN, XPGI); contains the HhH2 motif; domain in nucleases. XPG is a eukaryotic enzyme that functions in nucleotide-excision repair and transcription-coupled repair of oxidative DNA damage. Functionally/structurally related to FEN-1; divalent metal ion-dependent exo- and endonuclease, and bacterial and bacteriophage 5'3' exonucleases.
Probab=86.05 E-value=0.77 Score=26.27 Aligned_cols=42 Identities=24% Similarity=0.427 Sum_probs=28.2
Q ss_pred HHHHCCCCHHHHHH-HHHCCCHHHHHHCCCCCHHHHHHHHHHHHH
Q ss_conf 24431578999999-985156687510457116799999999742
Q gi|254780553|r 87 MGVLSRITATELVE-SIILQNSKVIAQIPGISMKIASRIMTELKG 130 (207)
Q Consensus 87 L~iLs~l~~~~l~~-aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~ 130 (207)
+.-| .++.++|+. +|..| ......+||||+|||-++|-+.+.
T Consensus 203 ~~~l-~l~~~~~id~~iL~G-~Dy~~gi~giG~k~A~kli~~~~~ 245 (316)
T cd00128 203 LKEL-GLTREKLIDLAILLG-CDYTEGIPGIGPVTALKLIKKYGD 245 (316)
T ss_pred HHHC-CCCHHHHHHHHHHHC-CCCCCCCCCCCHHHHHHHHHHHCC
T ss_conf 8773-999999999999729-887899997359999999999199
No 103
>cd00008 53EXOc 5'-3' exonuclease; T5 type 5'-3' exonuclease domains may co-occur with DNA polymerase I (Pol I) domains, or be part of Pol I containing complexes. They digest dsDNA and ssDNA, releasing mono-,di- and tri-nucleotides, as well as oligonucleotides, and have also been reported to possess RNase H activity. Also called 5' nuclease family, involved in structure-specific cleavage of flaps formed by Pol I activity (similar to mammalian flap endonuclease I, FEN-1). A single nucleic acid strand may be threaded through the 5' nuclease enzyme before cleavage occurs. The domain binds two divalent metal ions which are necessary for activity.
Probab=85.93 E-value=0.54 Score=27.27 Aligned_cols=73 Identities=18% Similarity=0.261 Sum_probs=41.0
Q ss_pred EECCHHHHHHCCCCCCEEEEEEEEEECC----CCEEEEEEECHHHHHHHHHHH--------HHHHCCCHHHHHHHCCC-C
Q ss_conf 9708688985024798499999999738----841899970677999999985--------01000510112443157-8
Q gi|254780553|r 28 IYCPIRTLSCLGKIGDFCTLFVETHMRQ----DQIRLFGFLSDLDRQWFMLLQ--------SVQGVGARVAMGVLSRI-T 94 (207)
Q Consensus 28 i~vs~~~~~~l~~~g~~v~l~~~~~vrE----d~~~LyGF~~~~Er~~F~~Li--------~V~GIGpK~AL~iLs~l-~ 94 (207)
|.-+.+.+..| ..+++.+|....-++ +-..-||+ +.++--.|..|. +|.|||||+|..+|..+ +
T Consensus 129 IvS~DkD~~QL--v~~~v~~~~~~~~~~~~~~~v~~~~gv-~p~q~~d~~aL~GD~sDnIpGV~GiG~KtA~kLl~~~gs 205 (240)
T cd00008 129 IVSGDKDLLQL--VSDNVKVVSPMKKKLVTEENVIEKYGV-TPAQIIDYKALMGDSSDNIPGVPGIGEKTAAKLLKEYGS 205 (240)
T ss_pred EECCCCCHHHH--HHHHHCCCCCCCCCCCCHHHHHHHCCC-CHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHCC
T ss_conf 96288068887--243300135555765788999996098-999998769972876468899998578999999998099
Q ss_pred HHHHHHHHH
Q ss_conf 999999985
Q gi|254780553|r 95 ATELVESII 103 (207)
Q Consensus 95 ~~~l~~aI~ 103 (207)
.+.+.+.+.
T Consensus 206 le~i~~~~~ 214 (240)
T cd00008 206 LEGILENLD 214 (240)
T ss_pred HHHHHHHHH
T ss_conf 999998298
No 104
>pfam10391 DNA_pol_lambd_f Fingers domain of DNA polymerase lambda. DNA polymerases catalyse the addition of dNMPs onto the 3-prime ends of DNA chains. There is a general polymerase fold consisting of three subdomains that have been likened to the fingers, palm, and thumb of a right hand. DNA_pol_lambd_f is the central three-helical region of DNA polymerase lambda referred to as the F and G helices of the fingers domain. Contacts with DNA involve this conserved helix-hairpin-helix motif in the fingers region which interacts with the primer strand. This motif is common to several DNA binding proteins and confers a sequence-independent interaction with the DNA backbone.
Probab=85.79 E-value=0.42 Score=28.03 Aligned_cols=19 Identities=26% Similarity=0.340 Sum_probs=15.6
Q ss_pred HHHHHCCCCCHHHHHHHHH
Q ss_conf 8751045711679999999
Q gi|254780553|r 108 KVIAQIPGISMKIASRIMT 126 (207)
Q Consensus 108 ~~L~~vpGIGkKtA~rIi~ 126 (207)
+.|++|.|||+++|++.+-
T Consensus 2 ~~f~~I~GvGp~~A~~~~~ 20 (52)
T pfam10391 2 KLFTNIWGVGPKTARKWYR 20 (52)
T ss_pred HHHHHCCCCCHHHHHHHHH
T ss_conf 0366354406999999999
No 105
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=85.65 E-value=0.48 Score=27.66 Aligned_cols=25 Identities=24% Similarity=0.402 Sum_probs=16.9
Q ss_pred HCCCHHH-HHHCCCCCHHHHHHHHHH
Q ss_conf 5156687-510457116799999999
Q gi|254780553|r 103 ILQNSKV-IAQIPGISMKIASRIMTE 127 (207)
Q Consensus 103 ~~~D~~~-L~~vpGIGkKtA~rIi~E 127 (207)
..+|.+- ...|||||+|||.+++-|
T Consensus 10 L~GD~sDnipGV~GIG~ktA~~ll~~ 35 (36)
T smart00279 10 LVGDYSDNIPGVKGIGPKTALKLLRE 35 (36)
T ss_pred HCCCCCCCCCCCCCCCHHHHHHHHHH
T ss_conf 81876468899997478999999985
No 106
>PRK03103 DNA polymerase IV; Reviewed
Probab=85.33 E-value=0.73 Score=26.40 Aligned_cols=29 Identities=7% Similarity=0.198 Sum_probs=15.7
Q ss_pred CCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHH
Q ss_conf 78999999985156687510457116799999
Q gi|254780553|r 93 ITATELVESIILQNSKVIAQIPGISMKIASRI 124 (207)
Q Consensus 93 l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rI 124 (207)
++++++...+..= -+..+||||+++++|+
T Consensus 170 ~~~~~~~~~l~~l---pv~~iwGIG~~~~~kL 198 (410)
T PRK03103 170 LRKDSMDLDLWPL---PIGKLFGVGRRMEHHL 198 (410)
T ss_pred ECHHHHHHHHHCC---CHHHCCCCCHHHHHHH
T ss_conf 8789999987258---8133068788999999
No 107
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=85.27 E-value=0.95 Score=25.66 Aligned_cols=52 Identities=15% Similarity=0.343 Sum_probs=30.2
Q ss_pred HHHHHHHCCCHHHHHHHCCC---CHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHH
Q ss_conf 98501000510112443157---899999998515668751045711679999999974
Q gi|254780553|r 74 LLQSVQGVGARVAMGVLSRI---TATELVESIILQNSKVIAQIPGISMKIASRIMTELK 129 (207)
Q Consensus 74 ~Li~V~GIGpK~AL~iLs~l---~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk 129 (207)
.-+++.|+|+++.-.+...- ++.+|... ...-|.+++|.|.|.|++|+-.+.
T Consensus 446 ~amdI~GlG~~~i~~L~~~g~i~~~~Diy~L----~~~~L~~l~gfgeKsa~nLl~aIe 500 (668)
T PRK07956 446 NAMDIDGLGEKIIEQLFEKGLIHTPADLFKL----TEEDLLQLEGFGEKSAQNLLDAIE 500 (668)
T ss_pred CCCCCCCCCHHHHHHHHHCCCCCCHHHHHCC----CHHHHHCCCCHHHHHHHHHHHHHH
T ss_conf 5316466599999999876876658999728----854540212355669999999999
No 108
>PRK00024 radC DNA repair protein RadC; Reviewed
Probab=84.90 E-value=1.4 Score=24.55 Aligned_cols=71 Identities=17% Similarity=0.232 Sum_probs=52.9
Q ss_pred EEEEEECHHHHHHHHHHHHHHHCCCH----HHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHH--HHHHHHHH
Q ss_conf 89997067799999998501000510----1124431578999999985156687510457116799999--99974222
Q gi|254780553|r 59 RLFGFLSDLDRQWFMLLQSVQGVGAR----VAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRI--MTELKGKA 132 (207)
Q Consensus 59 ~LyGF~~~~Er~~F~~Li~V~GIGpK----~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rI--i~ELk~K~ 132 (207)
.-+|..+..+.|+...|+... +.-+ .|=.+|+.++- ...+.+-+...|.++||||+..|-+| +.||-.++
T Consensus 17 l~~G~~~LsD~ELLallL~~g-~~~~d~~~lA~~ll~~~g~---l~~l~~a~~~eL~~i~GiG~~kA~~l~a~~El~rR~ 92 (224)
T PRK00024 17 LRRGAAALSDAELLAILLRTG-TKGKSVLDLARELLERFGS---LRGLLDASLEELQEIKGIGPAKAAQLKAALELARRI 92 (224)
T ss_pred HHHCCCCCCHHHHHHHHHHCC-CCCCCHHHHHHHHHHHCCC---HHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf 860932077799999998469-9999989999999998599---999987088988447898899999999999999999
Q ss_pred H
Q ss_conf 1
Q gi|254780553|r 133 I 133 (207)
Q Consensus 133 ~ 133 (207)
.
T Consensus 93 ~ 93 (224)
T PRK00024 93 L 93 (224)
T ss_pred H
T ss_conf 7
No 109
>TIGR03674 fen_arch flap structure-specific endonuclease. Endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA
Probab=84.80 E-value=1.1 Score=25.23 Aligned_cols=43 Identities=14% Similarity=0.257 Sum_probs=27.5
Q ss_pred EEEEECHHHHHHHHHHH------HHHHCCCHHHHHHHCCC-CHHHHHHHHH
Q ss_conf 99970677999999985------01000510112443157-8999999985
Q gi|254780553|r 60 LFGFLSDLDRQWFMLLQ------SVQGVGARVAMGVLSRI-TATELVESII 103 (207)
Q Consensus 60 LyGF~~~~Er~~F~~Li------~V~GIGpK~AL~iLs~l-~~~~l~~aI~ 103 (207)
-.|| ++++---|..|. +|.|||||+|+.++..+ +.+.+.+.+.
T Consensus 218 ~l~l-t~eqfidlcIL~GcDY~~gI~GIG~k~A~klIkk~~~ie~i~~~~~ 267 (338)
T TIGR03674 218 ELGI-TREQLIDIAILVGTDYNEGVKGIGPKTALKLIKEHGDLEKVLKARG 267 (338)
T ss_pred HCCC-CHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHCCHHHHHHHCC
T ss_conf 7389-9999999999708756789998568999999998599999998656
No 110
>cd00128 XPG Xeroderma pigmentosum G N- and I-regions (XPGN, XPGI); contains the HhH2 motif; domain in nucleases. XPG is a eukaryotic enzyme that functions in nucleotide-excision repair and transcription-coupled repair of oxidative DNA damage. Functionally/structurally related to FEN-1; divalent metal ion-dependent exo- and endonuclease, and bacterial and bacteriophage 5'3' exonucleases.
Probab=84.29 E-value=0.55 Score=27.26 Aligned_cols=46 Identities=13% Similarity=0.280 Sum_probs=31.7
Q ss_pred EEEEEEECHHHHHHHHHHH------HHHHCCCHHHHHHHCCCC-HHHHHHHHHC
Q ss_conf 1899970677999999985------010005101124431578-9999999851
Q gi|254780553|r 58 IRLFGFLSDLDRQWFMLLQ------SVQGVGARVAMGVLSRIT-ATELVESIIL 104 (207)
Q Consensus 58 ~~LyGF~~~~Er~~F~~Li------~V~GIGpK~AL~iLs~l~-~~~l~~aI~~ 104 (207)
..-+|| ++++---|..|. +|+|||||+|+.++..+. .+.+...+..
T Consensus 203 ~~~l~l-~~~~~id~~iL~G~Dy~~gi~giG~k~A~kli~~~~~~e~~~~~l~~ 255 (316)
T cd00128 203 LKELGL-TREKLIDLAILLGCDYTEGIPGIGPVTALKLIKKYGDIEKDIERLKK 255 (316)
T ss_pred HHHCCC-CHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHCCHHHHHHHHHH
T ss_conf 877399-99999999997298878999973599999999991999999999983
No 111
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=84.14 E-value=0.69 Score=26.59 Aligned_cols=20 Identities=15% Similarity=0.182 Sum_probs=14.1
Q ss_pred HHHHHHCCCCCHHHHHHHHH
Q ss_conf 68751045711679999999
Q gi|254780553|r 107 SKVIAQIPGISMKIASRIMT 126 (207)
Q Consensus 107 ~~~L~~vpGIGkKtA~rIi~ 126 (207)
...|++++|||++||+=+++
T Consensus 197 ~e~L~~i~GIG~WTAe~~ll 216 (285)
T COG0122 197 IEELTALKGIGPWTAEMFLL 216 (285)
T ss_pred HHHHHCCCCCCHHHHHHHHH
T ss_conf 99987378867999999999
No 112
>PRK13910 DNA glycosylase MutY; Provisional
Probab=84.14 E-value=0.47 Score=27.71 Aligned_cols=23 Identities=22% Similarity=0.426 Sum_probs=12.2
Q ss_pred CCCHHHHHHCCCCCHHHHHHHHH
Q ss_conf 15668751045711679999999
Q gi|254780553|r 104 LQNSKVIAQIPGISMKIASRIMT 126 (207)
Q Consensus 104 ~~D~~~L~~vpGIGkKtA~rIi~ 126 (207)
=.|...|.++||||+-||.-|..
T Consensus 69 P~~~~~L~~LPGIG~yTA~AI~s 91 (290)
T PRK13910 69 PNDYQSLLKLPGIGAYTANAILC 91 (290)
T ss_pred CCHHHHHHHCCCCCCHHHHHHHH
T ss_conf 85299997588998269999999
No 113
>cd01702 Pol_eta Pol eta is member of the DNA polimerase Y-family. Unlike other Y-family members, Pol eta can efficiently and accurately replicate DNA past UV-induced cis-syn cyclobutane thymine-thumine (T-T) lesions. It synthesizes AA opposite a TT dimer. Pol eta is able to replicate through a variety of other distorting DNA lesion as well.
Probab=83.63 E-value=3.9 Score=21.55 Aligned_cols=30 Identities=17% Similarity=0.296 Sum_probs=18.3
Q ss_pred CCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHH
Q ss_conf 789999999851566875104571167999999
Q gi|254780553|r 93 ITATELVESIILQNSKVIAQIPGISMKIASRIM 125 (207)
Q Consensus 93 l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi 125 (207)
+.++++...+..-+ +.++||||+|+++|+.
T Consensus 170 i~~~~~~~~l~~lp---I~~i~GvG~k~~~~L~ 199 (358)
T cd01702 170 LRNDAVASFLSSLP---ITKIRGLGGKLGESII 199 (358)
T ss_pred ECHHHHHHHHHCCC---CCEECCCCHHHHHHHH
T ss_conf 78899999985599---7662786789999999
No 114
>PRK01216 DNA polymerase IV; Validated
Probab=83.61 E-value=1 Score=25.51 Aligned_cols=29 Identities=28% Similarity=0.491 Sum_probs=17.6
Q ss_pred CCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHH
Q ss_conf 78999999985156687510457116799999
Q gi|254780553|r 93 ITATELVESIILQNSKVIAQIPGISMKIASRI 124 (207)
Q Consensus 93 l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rI 124 (207)
++++++..-+..-+ +.++||||+||++|+
T Consensus 166 v~~~~~~~fl~~lp---v~~i~GIG~~t~~~L 194 (351)
T PRK01216 166 ISPEEVKEFLNNLD---IDDVPGIGKVLSERL 194 (351)
T ss_pred ECHHHHHHHHHCCC---CCEECCCCHHHHHHH
T ss_conf 88368999876099---438548579999999
No 115
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=83.00 E-value=0.43 Score=27.95 Aligned_cols=24 Identities=17% Similarity=0.180 Sum_probs=19.8
Q ss_pred HHHHHHCCCCCHHHHHHHHHHHHH
Q ss_conf 687510457116799999999742
Q gi|254780553|r 107 SKVIAQIPGISMKIASRIMTELKG 130 (207)
Q Consensus 107 ~~~L~~vpGIGkKtA~rIi~ELk~ 130 (207)
-..|-+++|||+.||.-|++---+
T Consensus 120 Re~LL~lkGIG~ETADsILlYa~~ 143 (218)
T PRK13913 120 REWLLDQKGIGKESADAILCYVCA 143 (218)
T ss_pred HHHHHCCCCCCHHHHHHHHHHHCC
T ss_conf 999974898663339999999749
No 116
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=82.09 E-value=0.43 Score=27.95 Aligned_cols=17 Identities=29% Similarity=0.677 Sum_probs=14.9
Q ss_pred HHHHHCCCHHHHHHHCC
Q ss_conf 50100051011244315
Q gi|254780553|r 76 QSVQGVGARVAMGVLSR 92 (207)
Q Consensus 76 i~V~GIGpK~AL~iLs~ 92 (207)
-+|.|||||+|+.+|+.
T Consensus 19 pGV~GIG~ktA~~ll~~ 35 (36)
T smart00279 19 PGVKGIGPKTALKLLRE 35 (36)
T ss_pred CCCCCCCHHHHHHHHHH
T ss_conf 99997478999999985
No 117
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=81.96 E-value=0.32 Score=28.81 Aligned_cols=57 Identities=18% Similarity=0.130 Sum_probs=31.8
Q ss_pred HHHHHHHHHHCCCHHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHH-HHHHHHHHH
Q ss_conf 9999850100051011244315789999999851566875104571167-999999997
Q gi|254780553|r 71 WFMLLQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMK-IASRIMTEL 128 (207)
Q Consensus 71 ~F~~Li~V~GIGpK~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkK-tA~rIi~EL 128 (207)
-.+.|++++|||||+|=.+|+ +..+.-.-+|..+=...+.++.++..+ +.+++--.+
T Consensus 70 ~~~~L~~lpGVG~~tA~~vl~-~~~~~~~~~vD~~v~Rv~~R~~~~~~~~~~~~~~~~l 127 (149)
T smart00478 70 DREELLKLPGVGRKTANAVLS-FALGKPFIPVDTHVLRIAKRLGLVDKKSTPEEVEKLL 127 (149)
T ss_pred HHHHHHCCCCCCHHHHHHHHH-HHCCCCCCCCCCCHHHHHHHHCCCCCCCCHHHHHHHH
T ss_conf 599987589865999999999-9879983513413999999984788889899999999
No 118
>PRK03980 flap endonuclease-1; Provisional
Probab=81.84 E-value=0.6 Score=26.98 Aligned_cols=45 Identities=16% Similarity=0.320 Sum_probs=30.7
Q ss_pred EEEEEECHHHHHHHHHHH------HHHHCCCHHHHHHHCCC-CHHHHHHHHHC
Q ss_conf 899970677999999985------01000510112443157-89999999851
Q gi|254780553|r 59 RLFGFLSDLDRQWFMLLQ------SVQGVGARVAMGVLSRI-TATELVESIIL 104 (207)
Q Consensus 59 ~LyGF~~~~Er~~F~~Li------~V~GIGpK~AL~iLs~l-~~~~l~~aI~~ 104 (207)
.-.|| ++++---|..|. +|+|||||+|+.++... +.+.+...+..
T Consensus 170 ~~l~l-t~eqfidlcIL~GcDY~~gI~gIGpk~Alklikk~~~ie~il~~~~~ 221 (295)
T PRK03980 170 KELGI-TREQLIDIAILVGTDYNPGVKGIGPKTALKLIKKHGDLEKVLEAVGE 221 (295)
T ss_pred HHCCC-CHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHCCHHHHHHHCCC
T ss_conf 88399-99999999984588899999984299999999996999999986376
No 119
>PRK02794 DNA polymerase IV; Provisional
Probab=81.06 E-value=1.5 Score=24.35 Aligned_cols=51 Identities=14% Similarity=0.183 Sum_probs=27.9
Q ss_pred HHHHHHCCCHHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHH
Q ss_conf 85010005101124431578999999985156687510457116799999999742
Q gi|254780553|r 75 LQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMTELKG 130 (207)
Q Consensus 75 Li~V~GIGpK~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~ 130 (207)
+-.|-|||++++-.+- .+....+.+ +.+-|...|.+.-| +.++++.-+++|
T Consensus 211 v~diwGIG~rt~~kL~-~~GI~Ti~D-L~~~~~~~L~~~fG---~~g~~l~~~a~G 261 (417)
T PRK02794 211 VGFIWGVGPATAARLA-ADGIRTIGD-LQRADEADLMRRFG---SMGRRLWRLARG 261 (417)
T ss_pred HHHHCCCCHHHHHHHH-HCCCCCHHH-HHCCCHHHHHHHHC---HHHHHHHHHHCC
T ss_conf 4551684689999999-849909999-86599989778719---789999999659
No 120
>TIGR01259 comE comEA protein; InterPro: IPR004787 The comE locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. comEA and comEC are required for transformability, whereas the products of comEB and of the overlapping comER, which is transcribed in the reverse direction, are dispensable . ComEA has been shown to be an integral membrane protein, as predicted from hydropathy analysis, with its C-terminal domain outside the cytoplasmic membrane. This C-terminal domain possesses a sequence with similarity to those of several proteins known to be involved in nucleic acid transactions including UvrC and a human protein that binds to the replication origin of the Human herpesvirus 4 (Epstein-Barr virus) ..
Probab=80.55 E-value=0.82 Score=26.07 Aligned_cols=18 Identities=28% Similarity=0.469 Sum_probs=13.4
Q ss_pred HHHHCCCCCHHHHHHHHH
Q ss_conf 751045711679999999
Q gi|254780553|r 109 VIAQIPGISMKIASRIMT 126 (207)
Q Consensus 109 ~L~~vpGIGkKtA~rIi~ 126 (207)
-|..+|||||+-|+-||-
T Consensus 73 EL~~l~GiGP~kA~aIi~ 90 (124)
T TIGR01259 73 ELQALPGIGPAKAKAIIE 90 (124)
T ss_pred HHHHCCCCCCHHHHHHHH
T ss_conf 986369998133799999
No 121
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=80.38 E-value=0.41 Score=28.11 Aligned_cols=21 Identities=29% Similarity=0.448 Sum_probs=17.9
Q ss_pred HHHHHHHCCCHHHHHHHCCCC
Q ss_conf 985010005101124431578
Q gi|254780553|r 74 LLQSVQGVGARVAMGVLSRIT 94 (207)
Q Consensus 74 ~Li~V~GIGpK~AL~iLs~l~ 94 (207)
.|.+|+|||||+|-++++...
T Consensus 2 ~L~~v~GIG~k~A~~ll~~~~ 22 (26)
T smart00278 2 ELLKVPGIGPKTAEKILEAXX 22 (26)
T ss_pred CCCCCCCCCCHHHHHHHHHHH
T ss_conf 210179988115999999762
No 122
>PRK02406 DNA polymerase IV; Validated
Probab=80.34 E-value=1.8 Score=23.79 Aligned_cols=53 Identities=21% Similarity=0.353 Sum_probs=27.9
Q ss_pred HHHHHHHH-HH-HHCCCHHHHHHHCC----------CCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHH
Q ss_conf 99999985-01-00051011244315----------78999999985156687510457116799999
Q gi|254780553|r 69 RQWFMLLQ-SV-QGVGARVAMGVLSR----------ITATELVESIILQNSKVIAQIPGISMKIASRI 124 (207)
Q Consensus 69 r~~F~~Li-~V-~GIGpK~AL~iLs~----------l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rI 124 (207)
+++++.+- .+ =||||-.-||=+.+ .+++++...+..=. +..+||||++|++|+
T Consensus 132 ~~I~~~~gl~~SiGIa~nk~lAK~As~~~KP~G~~vv~~~~~~~~L~~lp---v~~l~GIG~~~~~~L 196 (355)
T PRK02406 132 RDIWNELGLTASAGVAPNKFLAKIASDWNKPNGQFVITPEEVPAFVATLP---VEKIPGVGKVTAEKL 196 (355)
T ss_pred HHHHHHHCCCEEEECCCCHHHHHHHHHHCCCCCCEEECHHHHHHHHHHCC---CCCCCCCCHHHHHHH
T ss_conf 99999879966870256799999988623987663656789999996188---740588588999999
No 123
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=80.21 E-value=1.1 Score=25.23 Aligned_cols=21 Identities=24% Similarity=0.558 Sum_probs=16.1
Q ss_pred HHHHHCCCCCHHHHHHHHHHH
Q ss_conf 875104571167999999997
Q gi|254780553|r 108 KVIAQIPGISMKIASRIMTEL 128 (207)
Q Consensus 108 ~~L~~vpGIGkKtA~rIi~EL 128 (207)
..|.+|+|||+|+|-+|+..+
T Consensus 73 ~~Li~V~GIGpK~AL~ILs~~ 93 (198)
T PRK00116 73 RLLISVSGVGPKLALAILSGL 93 (198)
T ss_pred HHHHCCCCCCHHHHHHHHCCC
T ss_conf 998566885789999887029
No 124
>TIGR02902 spore_lonB ATP-dependent protease LonB; InterPro: IPR014251 This entry represents LonB, a paralog of the ATP-dependent protease La (LonA, IPR004815 from INTERPRO). LonB proteins are unassigned peptidases belonging to the MEROPS peptidase family S16 (lon protease family, clan SJ) and are found strictly, and almost universally, in endospore-forming bacteria. This protease was shown, in Bacillus subtilis, to be expressed specifically in the forespore during sporulation, under control of sigmaF . The lonB gene, despite being located immediately upstream of lonA, was shown to be monocistronic. LonB appears to be involved in the post-translation control of sigmaH, but lonB mutation did not produce an obvious sporulation defect under the conditions tested . Note that additional paralogs of LonA and LonB occur in the Clostridium lineage and these are excluded from this entry. .
Probab=80.11 E-value=1 Score=25.36 Aligned_cols=20 Identities=30% Similarity=0.443 Sum_probs=16.8
Q ss_pred CCCCCHHHHHHHHHHHHHHH
Q ss_conf 45711679999999974222
Q gi|254780553|r 113 IPGISMKIASRIMTELKGKA 132 (207)
Q Consensus 113 vpGIGkKtA~rIi~ELk~K~ 132 (207)
=|||||..|.|+++|---|-
T Consensus 94 PPGVGKTAAARLVLeeAKk~ 113 (532)
T TIGR02902 94 PPGVGKTAAARLVLEEAKKN 113 (532)
T ss_pred CCCCCHHHHHHHHHHHHHCC
T ss_conf 86961789999999986508
No 125
>pfam11731 Cdd1 Pathogenicity locus. Cdd1 is expressed as part of the pathogenicity locus operon in several different orders of bacteria. Many members of the family are annotated as being putative mitomycin resistance proteins but this could not be confirmed.
Probab=79.57 E-value=0.99 Score=25.54 Aligned_cols=23 Identities=17% Similarity=0.198 Sum_probs=19.0
Q ss_pred HCCCHHHHHHCCCCCHHHHHHHH
Q ss_conf 51566875104571167999999
Q gi|254780553|r 103 ILQNSKVIAQIPGISMKIASRIM 125 (207)
Q Consensus 103 ~~~D~~~L~~vpGIGkKtA~rIi 125 (207)
..+..+.|+.+||||+++|+-+.
T Consensus 7 ~~~~l~~L~~lPnIG~a~a~DL~ 29 (92)
T pfam11731 7 DRSALKELTDLPNIGKATAKDLR 29 (92)
T ss_pred CHHHHHHHHCCCCCCHHHHHHHH
T ss_conf 88999987418974699999999
No 126
>pfam04919 DUF655 Protein of unknown function, DUF655. This family includes several uncharacterized archaeal proteins.
Probab=79.49 E-value=1.3 Score=24.79 Aligned_cols=22 Identities=32% Similarity=0.471 Sum_probs=17.7
Q ss_pred HHHHCCCCCHHHHHHHHHHHHH
Q ss_conf 7510457116799999999742
Q gi|254780553|r 109 VIAQIPGISMKIASRIMTELKG 130 (207)
Q Consensus 109 ~L~~vpGIGkKtA~rIi~ELk~ 130 (207)
+|.-+||||||++..|+-|=+.
T Consensus 117 ~leLLPGIGkK~~~~ileeR~~ 138 (181)
T pfam04919 117 QLELLPGIGKKMMWAILEERKK 138 (181)
T ss_pred HHHHCCCCCHHHHHHHHHHHCC
T ss_conf 8875334038999999999655
No 127
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=79.44 E-value=0.92 Score=25.75 Aligned_cols=24 Identities=29% Similarity=0.158 Sum_probs=17.5
Q ss_pred HHHHHHHHHHHHCCCHHHHHHHCC
Q ss_conf 999999850100051011244315
Q gi|254780553|r 69 RQWFMLLQSVQGVGARVAMGVLSR 92 (207)
Q Consensus 69 r~~F~~Li~V~GIGpK~AL~iLs~ 92 (207)
-+..+.|+++.|||||+|=.+|..
T Consensus 79 ~~~~~~L~~l~GIG~~TA~~vl~~ 102 (158)
T cd00056 79 PDAREELLALPGVGRKTANVVLLF 102 (158)
T ss_pred HHHHHHHHCCCCCCHHHHHHHHHH
T ss_conf 889999875898289999999999
No 128
>pfam11798 IMS_HHH IMS family HHH motif. These proteins are involved in UV protection, eg.
Probab=79.36 E-value=0.91 Score=25.77 Aligned_cols=16 Identities=44% Similarity=0.758 Sum_probs=13.7
Q ss_pred HHHHCCCCCHHHHHHH
Q ss_conf 7510457116799999
Q gi|254780553|r 109 VIAQIPGISMKIASRI 124 (207)
Q Consensus 109 ~L~~vpGIGkKtA~rI 124 (207)
-++++||||+|+++++
T Consensus 13 pi~~i~GIG~~~~~~L 28 (33)
T pfam11798 13 PISKIPGIGRKTAEKL 28 (33)
T ss_pred CCCCCCCCCHHHHHHH
T ss_conf 6221688666789999
No 129
>cd03586 Pol_IV_kappa Pol_IV_kappa, a member of the Y-family of DNA polymerases. Pol_Y's can transverse replication-blocking DNA lesions, such as cyclobutane pyrimidine dimers resulting from UV damage, at the cost of an elevated error rate. The Y-family has no 3'-5' exonuclease activity. In addition to possessing a topology akin to a right hand, with "thumb", "fingers" and "palm" motifs, like polymerases from the A-, B-, C- and X-families, the Y-family has a unique "little finger" motif. Expression of Y-family polymerases is often induced by DNA damage. These polymerases are phylogenetically unrelated to classical DNA polymerases. Originally called the DinB family, they belong to the recently described Y-family of DNA polymerases. Pol IV is mostly found in bacteria and archaea. Although the structure of Pol IV is similar to that of Pol eta, it shows markedly differenct efficiencies and fidelities in bypassing various DNA lesions. All Pol IV-like polymerases studied to date are able to b
Probab=79.06 E-value=1.9 Score=23.61 Aligned_cols=43 Identities=14% Similarity=0.220 Sum_probs=27.6
Q ss_pred HHCCCHHHHHHHCC----------CCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHH
Q ss_conf 00051011244315----------78999999985156687510457116799999
Q gi|254780553|r 79 QGVGARVAMGVLSR----------ITATELVESIILQNSKVIAQIPGISMKIASRI 124 (207)
Q Consensus 79 ~GIGpK~AL~iLs~----------l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rI 124 (207)
=||||..-||=+.+ ++++++...+..-+ +..+||||+++++|+
T Consensus 136 iGIa~nk~lAKiAs~~~KP~G~~~i~~~~~~~~L~~lp---v~~l~GIG~~~~~~L 188 (337)
T cd03586 136 VGIAPNKFLAKIASDLNKPNGLTVIPPEKVWAFLAPLP---VRKIWGIGKVTAEKL 188 (337)
T ss_pred EEEECCHHHHHHHHHHHCCCCCEEECHHHHHHHHCCCC---CHHCCCCCHHHHHHH
T ss_conf 99957399999998761007967608899999861276---302078468999999
No 130
>cd01703 Pol_iota Pol iota is member of the DNA polymerase Y-family, and has also been called Rad30 homolog B. Unlike classic DNA polymerases,Y-family polymerases are induced by DNA damage. They can transverse normal replication-blocking DNA lesions. Unlike Pol eta, Pol iota is unable to replicate through a cis-syn T-T dimer. In human Pol iota, the base-pairing mode in the active site at the replicative end mat bee Hoogsteen instead of Watson-Click. Human Pol iota can incorporate the correct nucleotide opposite a purine much more efficiently than opposite a pyrimidine. Pol iota prefers to insert Guanosine instead of Adenosine opposite Thymidine.
Probab=79.05 E-value=1 Score=25.51 Aligned_cols=16 Identities=38% Similarity=0.744 Sum_probs=12.6
Q ss_pred HHHHCCCCCHHHHHHH
Q ss_conf 7510457116799999
Q gi|254780553|r 109 VIAQIPGISMKIASRI 124 (207)
Q Consensus 109 ~L~~vpGIGkKtA~rI 124 (207)
-+.++||||+|||+++
T Consensus 211 ~i~ki~GIG~kt~~~L 226 (394)
T cd01703 211 SLRKIPGIGYKTAKKL 226 (394)
T ss_pred CHHHHCCCCHHHHHHH
T ss_conf 8055278179999999
No 131
>PRK03858 DNA polymerase IV; Validated
Probab=78.04 E-value=2.4 Score=22.99 Aligned_cols=42 Identities=7% Similarity=0.165 Sum_probs=24.2
Q ss_pred HCCCHHHHHHHC----------CCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHH
Q ss_conf 005101124431----------578999999985156687510457116799999
Q gi|254780553|r 80 GVGARVAMGVLS----------RITATELVESIILQNSKVIAQIPGISMKIASRI 124 (207)
Q Consensus 80 GIGpK~AL~iLs----------~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rI 124 (207)
||||-.-|+=+. .+++++....+..= -+..+||||+++++|+
T Consensus 138 GIa~nk~LAKiAs~~aKp~G~~~i~~~~~~~~L~~l---pv~~iwGIG~~~~~~L 189 (398)
T PRK03858 138 GIARTKFLAKVASQVAKPDGLLLVPPDRELAFLHPL---PVRRLWGVGAVTAAKL 189 (398)
T ss_pred EECCCHHHHHHHHHHHCCCCCEECCHHHHHHHHHHC---CCCCCCCCCHHHHHHH
T ss_conf 866428999998986065772415888999998646---6012158687999999
No 132
>pfam07223 DUF1421 Protein of unknown function (DUF1421). This family represents a conserved region approximately 350 residues long within a number of plant proteins of unknown function.
Probab=78.00 E-value=2.5 Score=22.86 Aligned_cols=41 Identities=12% Similarity=0.184 Sum_probs=30.4
Q ss_pred CCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCHH
Q ss_conf 565315899999999679998999999999985168888989
Q gi|254780553|r 154 CSMPSFAINAISALVNLGYGQDQATTAVVSVLKKEKNIADDS 195 (207)
Q Consensus 154 ~~~~~~~~d~~~AL~~LGy~~~ea~~ai~~i~~~~~~~~~~e 195 (207)
...+--++|+++-+.++||.++.++.+|.++ .++....|+.
T Consensus 316 s~nr~P~ddvieKva~MGF~rDqVratvrrl-tEnGQ~VDlN 356 (359)
T pfam07223 316 SGNRVPIDDVVEKVATMGFPRDQVRATVRRL-TENGQPVDLN 356 (359)
T ss_pred CCCCCCHHHHHHHHHHCCCCHHHHHHHHHHH-HHCCCCCCCC
T ss_conf 6677744788988775387388999999998-6578633210
No 133
>TIGR03629 arch_S13P archaeal ribosomal protein S13P. This model describes exclusively the archaeal ribosomal protein S13P. It excludes the homologous eukaryotic 40S ribosomal protein S18 and bacterial 30S ribosomal protein S13.
Probab=77.25 E-value=5.6 Score=20.52 Aligned_cols=22 Identities=27% Similarity=0.389 Sum_probs=19.2
Q ss_pred HHHHHCCCCCHHHHHHHHHHHH
Q ss_conf 8751045711679999999974
Q gi|254780553|r 108 KVIAQIPGISMKIASRIMTELK 129 (207)
Q Consensus 108 ~~L~~vpGIGkKtA~rIi~ELk 129 (207)
-+|+.+.|||+++|.+||-.+.
T Consensus 21 ~aLt~I~GIG~~~A~~Ic~~~g 42 (144)
T TIGR03629 21 YALTGIKGIGRRFARAIARKLG 42 (144)
T ss_pred EEEEEECCCCHHHHHHHHHHHC
T ss_conf 8722123728999999999909
No 134
>TIGR03631 bact_S13 30S ribosomal protein S13. This model describes bacterial ribosomal protein S13, to the exclusion of the homologous archaeal S13P and eukaryotic ribosomal protein S18. This model identifies some (but not all) instances of chloroplast and mitochondrial S13, which is of bacterial type.
Probab=77.23 E-value=1.5 Score=24.30 Aligned_cols=22 Identities=23% Similarity=0.276 Sum_probs=18.2
Q ss_pred HHHHHCCCCCHHHHHHHHHHHH
Q ss_conf 8751045711679999999974
Q gi|254780553|r 108 KVIAQIPGISMKIASRIMTELK 129 (207)
Q Consensus 108 ~~L~~vpGIGkKtA~rIi~ELk 129 (207)
-+|+++.|||+++|.+||-.|.
T Consensus 15 ~ALt~I~GIG~~~A~~Ic~~lg 36 (113)
T TIGR03631 15 IALTYIYGIGRTRARKILEKAG 36 (113)
T ss_pred HHHHCEECCCHHHHHHHHHHCC
T ss_conf 0652002758999999999929
No 135
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=75.84 E-value=1.8 Score=23.81 Aligned_cols=22 Identities=23% Similarity=0.238 Sum_probs=16.9
Q ss_pred HHHHHCCCCCHHHHHHHHHHHH
Q ss_conf 8751045711679999999974
Q gi|254780553|r 108 KVIAQIPGISMKIASRIMTELK 129 (207)
Q Consensus 108 ~~L~~vpGIGkKtA~rIi~ELk 129 (207)
-+|+.+.|||+++|.+||-.|.
T Consensus 17 ~ALt~I~GIG~~~A~~Ic~~lg 38 (122)
T PRK05179 17 IALTYIYGIGRTRAKEILAAAG 38 (122)
T ss_pred HHHHHHCCCCHHHHHHHHHHCC
T ss_conf 4773002758999999999829
No 136
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=75.83 E-value=1.6 Score=24.06 Aligned_cols=22 Identities=23% Similarity=0.386 Sum_probs=18.9
Q ss_pred HHHHHCCCCCHHHHHHHHHHHH
Q ss_conf 8751045711679999999974
Q gi|254780553|r 108 KVIAQIPGISMKIASRIMTELK 129 (207)
Q Consensus 108 ~~L~~vpGIGkKtA~rIi~ELk 129 (207)
-+|+++.|||+++|.+||-.|.
T Consensus 17 ~aLt~I~GIG~~~A~~Ic~~lg 38 (122)
T CHL00137 17 IALTYIYGIGLTSAKKILEKAN 38 (122)
T ss_pred EHHHHHCCCCHHHHHHHHHHCC
T ss_conf 3111000618999999999849
No 137
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=74.61 E-value=7.4 Score=19.71 Aligned_cols=51 Identities=25% Similarity=0.267 Sum_probs=23.6
Q ss_pred EEEEEEEEECCEEEEEECCEEEEEECCHHHHHHCCCC-----CCEEEEEEEEEECCC
Q ss_conf 8999999609979998588323897086889850247-----984999999997388
Q gi|254780553|r 5 IKGNIEGLYEDYVLIDVQGVCYIIYCPIRTLSCLGKI-----GDFCTLFVETHMRQD 56 (207)
Q Consensus 5 i~G~i~~~~~~~ivi~v~GvGY~i~vs~~~~~~l~~~-----g~~v~l~~~~~vrEd 56 (207)
++|+++.+.++.+++|+++ .-+-.+|.+-+...+.. |+.+.+++.....++
T Consensus 25 V~G~Vv~i~~~~v~Vdig~-Kseg~ip~~E~~~~~~~~~~~~gd~v~v~v~~~e~~~ 80 (541)
T COG0539 25 VKGTVVSIEKDGVLVDIGG-KSEGVIPISEFSNEPVEDVVQVGDEVEVLVLRVEDGE 80 (541)
T ss_pred EEEEEEEEECCEEEEEECC-CCCCEEEHHHCCCCCCCCEECCCCEEEEEEEEEECCC
T ss_conf 9999999938849998367-6155768898056665513158988999999983688
No 138
>COG1491 Predicted RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=74.41 E-value=2.3 Score=23.14 Aligned_cols=23 Identities=35% Similarity=0.452 Sum_probs=19.1
Q ss_pred HHHHCCCCCHHHHHHHHHHHHHH
Q ss_conf 75104571167999999997422
Q gi|254780553|r 109 VIAQIPGISMKIASRIMTELKGK 131 (207)
Q Consensus 109 ~L~~vpGIGkKtA~rIi~ELk~K 131 (207)
.|.-+||||||+...|+-|=+-|
T Consensus 131 ~LELLpGiGkK~m~~IleERkkk 153 (202)
T COG1491 131 QLELLPGIGKKTMWAILEERKKK 153 (202)
T ss_pred HHHHCCCCCHHHHHHHHHHHHCC
T ss_conf 88753120499999999987428
No 139
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=73.69 E-value=4.4 Score=21.20 Aligned_cols=24 Identities=17% Similarity=0.469 Sum_probs=20.4
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf 999999996799989999999999
Q gi|254780553|r 161 INAISALVNLGYGQDQATTAVVSV 184 (207)
Q Consensus 161 ~d~~~AL~~LGy~~~ea~~ai~~i 184 (207)
++.++-|.++||++.++.+|+..-
T Consensus 2 ~~~v~~L~~MGF~~~~~~~AL~~~ 25 (38)
T cd00194 2 EEKLEQLLEMGFSREEARKALRAT 25 (38)
T ss_pred HHHHHHHHHCCCCHHHHHHHHHHH
T ss_conf 898999998599999999999985
No 140
>cd01701 Pol_zeta Pol_zeta, a member of the Y-family of DNA polymerases. Y-family polymerases can transverse normal replication-blocking DNA lesions, such as cyclobutane pyrimidine dimers resulting from UV damage, at higher error rate. The Y-family has no 3'-5' exonuclease activity. Pol zeta has also been named Rev1; this subfamily is mainly present in eukaryotes.
Probab=73.64 E-value=1.7 Score=24.04 Aligned_cols=42 Identities=14% Similarity=0.418 Sum_probs=23.1
Q ss_pred HCCCHHHHHHHC----------CCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHH
Q ss_conf 005101124431----------578999999985156687510457116799999
Q gi|254780553|r 80 GVGARVAMGVLS----------RITATELVESIILQNSKVIAQIPGISMKIASRI 124 (207)
Q Consensus 80 GIGpK~AL~iLs----------~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rI 124 (207)
||||-.-||=+. .++++++...+..-. +.++||||+||++|+
T Consensus 189 GIa~nK~lAKiAs~~~KP~G~~~i~~~~~~~~L~~lp---v~~i~GIG~~t~~kL 240 (405)
T cd01701 189 GIGPNILLARLATRKAKPNGQYYLSPEKVEEFLDTLP---VKDLPGVGSSTKEKL 240 (405)
T ss_pred CCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCC---CCCCCCCCHHHHHHH
T ss_conf 4376499999988736998732368789999998552---111587178999999
No 141
>pfam00416 Ribosomal_S13 Ribosomal protein S13/S18. This family includes ribosomal protein S13 from prokaryotes and S18 from eukaryotes.
Probab=73.30 E-value=1.8 Score=23.85 Aligned_cols=22 Identities=23% Similarity=0.359 Sum_probs=19.2
Q ss_pred HHHHHCCCCCHHHHHHHHHHHH
Q ss_conf 8751045711679999999974
Q gi|254780553|r 108 KVIAQIPGISMKIASRIMTELK 129 (207)
Q Consensus 108 ~~L~~vpGIGkKtA~rIi~ELk 129 (207)
-+|+++.|||+++|.+||-.|.
T Consensus 15 ~ALt~I~GIG~~~A~~Ic~~lg 36 (106)
T pfam00416 15 IALTYIKGIGRRKANQILKKAG 36 (106)
T ss_pred EEECCCCCCCHHHHHHHHHHCC
T ss_conf 4411210528999999999919
No 142
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=72.96 E-value=4.7 Score=21.05 Aligned_cols=24 Identities=21% Similarity=0.476 Sum_probs=20.3
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf 999999996799989999999999
Q gi|254780553|r 161 INAISALVNLGYGQDQATTAVVSV 184 (207)
Q Consensus 161 ~d~~~AL~~LGy~~~ea~~ai~~i 184 (207)
++.++-|.++||++.++.+|+..-
T Consensus 2 ee~i~~L~~MGF~~~~~~~AL~~~ 25 (37)
T smart00165 2 EEKIDQLLEMGFSREEALKALRAA 25 (37)
T ss_pred HHHHHHHHHCCCCHHHHHHHHHHH
T ss_conf 788999998599999999999981
No 143
>TIGR00608 radc DNA repair protein RadC; InterPro: IPR001405 RadC is a DNA repair protein found in many bacteria. They share a region of similarity at the C-terminus that contains two perfectly conserved histidine residues.; GO: 0006281 DNA repair.
Probab=72.54 E-value=3.9 Score=21.60 Aligned_cols=128 Identities=18% Similarity=0.255 Sum_probs=74.0
Q ss_pred EEEECHHHHHHHHHHHHHHHCCCH------HHHHHHCCCCHHHH--HHHHHCCCHHHHHHCCCCCHHHHHHH--HHHHHH
Q ss_conf 997067799999998501000510------11244315789999--99985156687510457116799999--999742
Q gi|254780553|r 61 FGFLSDLDRQWFMLLQSVQGVGAR------VAMGVLSRITATEL--VESIILQNSKVIAQIPGISMKIASRI--MTELKG 130 (207)
Q Consensus 61 yGF~~~~Er~~F~~Li~V~GIGpK------~AL~iLs~l~~~~l--~~aI~~~D~~~L~~vpGIGkKtA~rI--i~ELk~ 130 (207)
||=.+..+-|+-..++. +|.+-+ +|=.+|..++++++ ...+.+-+...|++|||||.-.|.+| ++||..
T Consensus 9 ~Ga~~L~d~ELLAi~L~-tG~~k~k~dVl~Lsk~lL~~fG~~~~d~l~~L~~~~~~~L~~v~GiG~ak~~qlka~~El~~ 87 (223)
T TIGR00608 9 FGAEALSDYELLAILLR-TGTKKGKADVLSLSKELLKQFGQEELDSLDLLLSAEPEELSSVPGIGLAKAIQLKAIVELAK 87 (223)
T ss_pred CCHHCCCCHHHHHHHHH-CCCCCCCCCHHHHHHHHHHHHCHHCCCCHHHHHCCCHHHHHCCCCCHHHHHHHHHHHHHHHH
T ss_conf 16300564679999984-38999766626789999987070001300143215857850468850889999999999986
Q ss_pred HHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHH-HHCCCCHHHHHHHHHHHHHHCC----------CC----CCHH
Q ss_conf 2211011334432333334455556531589999999-9679998999999999985168----------88----8989
Q gi|254780553|r 131 KAISLSSVVQQDMSCVNKEQAHICSMPSFAINAISAL-VNLGYGQDQATTAVVSVLKKEK----------NI----ADDS 195 (207)
Q Consensus 131 K~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~AL-~~LGy~~~ea~~ai~~i~~~~~----------~~----~~~e 195 (207)
++.+..... .....+. +++...| ..|-|.++|...++- ...++- .. --.-
T Consensus 88 R~~~~~~~~-------------~~~i~sP-e~~~~~l~~~l~~~~~E~F~vlf-LD~~nrli~~~~~~~Gt~~~v~v~PR 152 (223)
T TIGR00608 88 RYAKSRMLE-------------RPVIRSP-EAAAEFLSTDLAHEEREHFMVLF-LDLKNRLIAKEVVFIGTVNHVLVHPR 152 (223)
T ss_pred HHHCCCCCC-------------CCCCCCH-HHHHHHHHHHHCCCCCEEEEEEE-ECCCCCEECCEEEEEEEEEEEEECCC
T ss_conf 775244214-------------6664898-99999999863347642678887-16854101002456541242236650
Q ss_pred HHHHHHHHH
Q ss_conf 999999997
Q gi|254780553|r 196 QIIRLALRA 204 (207)
Q Consensus 196 elIk~aLk~ 204 (207)
|++|+|+|.
T Consensus 153 Ei~keA~k~ 161 (223)
T TIGR00608 153 EIIKEALKL 161 (223)
T ss_pred HHHHHHHHH
T ss_conf 787788761
No 144
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=71.78 E-value=8.6 Score=19.27 Aligned_cols=56 Identities=20% Similarity=0.229 Sum_probs=38.8
Q ss_pred EEEEEEEEEECCEEEEEECCEEEEEECCHHHHHHC--------CCCCCEEEEEEEEEECCCCEE
Q ss_conf 58999999609979998588323897086889850--------247984999999997388418
Q gi|254780553|r 4 KIKGNIEGLYEDYVLIDVQGVCYIIYCPIRTLSCL--------GKIGDFCTLFVETHMRQDQIR 59 (207)
Q Consensus 4 ~i~G~i~~~~~~~ivi~v~GvGY~i~vs~~~~~~l--------~~~g~~v~l~~~~~vrEd~~~ 59 (207)
-+.|+|..+.++++.++..|-+-+=++|...++.- .+.|+.++.++--.-.++...
T Consensus 20 iV~G~V~~I~~~~v~Vdi~G~k~eG~I~~~E~s~~~~~~~~~~~kvGd~V~~~Vl~~~~~~~~l 83 (390)
T PRK06676 20 VVTGEVLKVEDKQVFVNIEGYKVEGVIPISELSNDHIEDINDVVKVGDTLEVYVLKVEDGEGNY 83 (390)
T ss_pred EEEEEEEEEECCEEEEEECCCEEEEEEEHHHHCCCCCCCHHHCCCCCCEEEEEEEEEECCCCEE
T ss_conf 8999999998998999933863589999999456643584024699899999999998899739
No 145
>TIGR00588 ogg 8-oxoguanine DNA-glycosylase (ogg); InterPro: IPR004577 All proteins in this family for which functions are known are 8-oxo-guanaine DNA glycosylases that function in base excision repair. The enzyme incises DNA at 8-oxoG residues, and excises 7,8-dihydro-8-oxoguanine from damaged DNA. It has beta-lyase activity that nicks DNA 3' to the lesion.; GO: 0008534 oxidized purine base lesion DNA N-glycosylase activity, 0006281 DNA repair, 0005634 nucleus.
Probab=70.40 E-value=2.7 Score=22.62 Aligned_cols=77 Identities=19% Similarity=0.283 Sum_probs=43.6
Q ss_pred CCEEEEEE-ECHHHHHHHHHHHHHHHCCCHHHHHHHCC-CCHHHHHHHHHCCC--HHHHHHCCCCCHHHHHHHHHHHHHH
Q ss_conf 84189997-06779999999850100051011244315-78999999985156--6875104571167999999997422
Q gi|254780553|r 56 DQIRLFGF-LSDLDRQWFMLLQSVQGVGARVAMGVLSR-ITATELVESIILQN--SKVIAQIPGISMKIASRIMTELKGK 131 (207)
Q Consensus 56 d~~~LyGF-~~~~Er~~F~~Li~V~GIGpK~AL~iLs~-l~~~~l~~aI~~~D--~~~L~~vpGIGkKtA~rIi~ELk~K 131 (207)
+-..||-| =-..++.|=+.+.+-+|| .+|.. =+.|-++-.|.+.| +...| ++-++|+-.--.+
T Consensus 114 ~l~~ly~~vW~~~D~~f~~~~~~~qG~------Rll~qkdP~EcliSfIcSsNnni~RiT-------rm~e~lc~~fG~~ 180 (379)
T TIGR00588 114 SLEQLYTHVWISVDKHFQKVAQKFQGV------RLLRQKDPFECLISFICSSNNNIARIT-------RMVERLCQAFGPR 180 (379)
T ss_pred CHHHHHHHCCCCCHHHHHHHHHHHCCE------EEECCCCCHHHHHHHHHHHCCCHHHHH-------HHHHHHHHHHCCH
T ss_conf 288874021611116899875551363------521027871566778875046521254-------3389999862203
Q ss_pred HHHCCCCCCCCCCC
Q ss_conf 21101133443233
Q gi|254780553|r 132 AISLSSVVQQDMSC 145 (207)
Q Consensus 132 ~~~~~~~~~~~~~~ 145 (207)
+..++...-...+.
T Consensus 181 ~~~~dgvtyH~FP~ 194 (379)
T TIGR00588 181 LITLDGVTYHGFPS 194 (379)
T ss_pred HHHHCCEEECCCCC
T ss_conf 21224621147987
No 146
>KOG1921 consensus
Probab=70.39 E-value=2.2 Score=23.22 Aligned_cols=16 Identities=25% Similarity=0.524 Sum_probs=9.7
Q ss_pred HHHHHHCCCCCHHHHH
Q ss_conf 6875104571167999
Q gi|254780553|r 107 SKVIAQIPGISMKIAS 122 (207)
Q Consensus 107 ~~~L~~vpGIGkKtA~ 122 (207)
++-|.++||||+|+|-
T Consensus 158 v~dLlsLPGVGPKMa~ 173 (286)
T KOG1921 158 VEDLLSLPGVGPKMAH 173 (286)
T ss_pred HHHHHCCCCCCHHHHH
T ss_conf 9988558997659999
No 147
>PRK06531 yajC preprotein translocase subunit YajC; Validated
Probab=70.23 E-value=5.7 Score=20.47 Aligned_cols=36 Identities=19% Similarity=0.426 Sum_probs=26.1
Q ss_pred CCCEEEEEEEEEECC--EEEEEECCEEEEEECCHHHHHHC
Q ss_conf 932589999996099--79998588323897086889850
Q gi|254780553|r 1 MIGKIKGNIEGLYED--YVLIDVQGVCYIIYCPIRTLSCL 38 (207)
Q Consensus 1 MI~~i~G~i~~~~~~--~ivi~v~GvGY~i~vs~~~~~~l 38 (207)
.|+.|.|+|.++.++ .++|||.|+-..+.-+ .....
T Consensus 45 TiGGl~G~V~~Vd~e~~tV~Ld~~Gv~l~f~r~--AI~~V 82 (120)
T PRK06531 45 TIGGLFGTVDEVDTEAKKIVLDVDGVYLTFELS--AIKRV 82 (120)
T ss_pred ECCCCEEEEEEEECCCCEEEEEECCEEEEEEHH--HHHHH
T ss_conf 789828999999278988999828979999867--76522
No 148
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=70.09 E-value=2.5 Score=22.84 Aligned_cols=22 Identities=27% Similarity=0.365 Sum_probs=19.3
Q ss_pred HHHHHCCCCCHHHHHHHHHHHH
Q ss_conf 8751045711679999999974
Q gi|254780553|r 108 KVIAQIPGISMKIASRIMTELK 129 (207)
Q Consensus 108 ~~L~~vpGIGkKtA~rIi~ELk 129 (207)
-+|+.+-|||+++|.+||-.|.
T Consensus 25 ~ALt~IyGIG~~~A~~Ic~~lg 46 (149)
T PRK04053 25 YALTGIKGIGRRTARAIARKLG 46 (149)
T ss_pred EECCCCCCCCHHHHHHHHHHHC
T ss_conf 4411114848999999999918
No 149
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=70.01 E-value=9.4 Score=19.02 Aligned_cols=56 Identities=23% Similarity=0.298 Sum_probs=35.6
Q ss_pred EEEEEEEEEECCEEEEEECCEEEEEECCHHHHHH-----CCCCCCEEEEEEEEEECCCCEEE
Q ss_conf 5899999960997999858832389708688985-----02479849999999973884189
Q gi|254780553|r 4 KIKGNIEGLYEDYVLIDVQGVCYIIYCPIRTLSC-----LGKIGDFCTLFVETHMRQDQIRL 60 (207)
Q Consensus 4 ~i~G~i~~~~~~~ivi~v~GvGY~i~vs~~~~~~-----l~~~g~~v~l~~~~~vrEd~~~L 60 (207)
-++|+|..+.++++.+|+| --.+-.+|.+-+.. ..+.|+++.+|+.-.-.+++...
T Consensus 23 iV~G~Vv~i~~~~v~VdiG-~K~eG~I~~~E~~~~~~~~~~~vGd~i~v~v~~~~d~~G~i~ 83 (556)
T PRK06299 23 IVKGTVVAIDKDYVLVDVG-LKSEGRIPLEEFKNDQGELEVKVGDEVEVYLERIEDGFGETV 83 (556)
T ss_pred EEEEEEEEEECCEEEEEEC-CCCEEEEEHHHHCCCCCCCCCCCCCEEEEEEEEEECCCCEEE
T ss_conf 8999999997999999968-883578799993477677467999999999999878897499
No 150
>PRK03352 DNA polymerase IV; Validated
Probab=69.18 E-value=2.4 Score=22.92 Aligned_cols=58 Identities=10% Similarity=0.151 Sum_probs=31.8
Q ss_pred ECHHHHHHHHHH--HHHHHCCCHHHHHHHC----------CCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHH
Q ss_conf 067799999998--5010005101124431----------578999999985156687510457116799999
Q gi|254780553|r 64 LSDLDRQWFMLL--QSVQGVGARVAMGVLS----------RITATELVESIILQNSKVIAQIPGISMKIASRI 124 (207)
Q Consensus 64 ~~~~Er~~F~~L--i~V~GIGpK~AL~iLs----------~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rI 124 (207)
...-.+++|+.+ .-==||||-.-|+=+. .+++++....+..- -+.++||||++|++|+
T Consensus 124 a~~ir~~I~~~tgl~~SiGIa~nk~LAKiAs~~~KP~G~~~i~~~~~~~~l~~l---pv~~i~GIG~~~~~kL 193 (345)
T PRK03352 124 AEEIRAVVLEETGLSCSVGISDNKQRAKIATGFAKPAGVFRLTDANWMAVMGDR---PVDALWGVGPKTAKKL 193 (345)
T ss_pred HHHHHHHHHHHHCCCCEECCHHHHHHHHHHHHHHHCCCEEECCHHHHHHHHHCC---CCHHCCCCCHHHHHHH
T ss_conf 999999999987898243040799999999876104874744888999998527---8211278289999999
No 151
>COG1031 Uncharacterized Fe-S oxidoreductase [Energy production and conversion]
Probab=67.97 E-value=3.1 Score=22.20 Aligned_cols=21 Identities=38% Similarity=0.668 Sum_probs=12.9
Q ss_pred HHHHHHCCCCCHHHHHHHHHH
Q ss_conf 687510457116799999999
Q gi|254780553|r 107 SKVIAQIPGISMKIASRIMTE 127 (207)
Q Consensus 107 ~~~L~~vpGIGkKtA~rIi~E 127 (207)
.+.|..+||||+|+|.+|+.+
T Consensus 515 ~~vl~~ipgig~~~~~~I~~~ 535 (560)
T COG1031 515 KDVLRAIPGIGKKTLRKILAE 535 (560)
T ss_pred HHHHHHCCCCHHHHHHHHHHC
T ss_conf 889986656116667778743
No 152
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=67.75 E-value=2.4 Score=22.96 Aligned_cols=36 Identities=14% Similarity=0.306 Sum_probs=27.4
Q ss_pred CHHHHHHHHHCCCHH---------HHHHCCCCCHHHHHHHHHHHH
Q ss_conf 899999998515668---------751045711679999999974
Q gi|254780553|r 94 TATELVESIILQNSK---------VIAQIPGISMKIASRIMTELK 129 (207)
Q Consensus 94 ~~~~l~~aI~~~D~~---------~L~~vpGIGkKtA~rIi~ELk 129 (207)
++++|...|.--|+. +|+.+.|||.++|..||-.+.
T Consensus 7 ~~~~f~~ivRI~gtdi~g~K~v~~aLt~I~GIG~~~A~~Ic~~~g 51 (154)
T PTZ00134 7 DSDQFQHILRILNTNVDGREKVTIALTAIKGIGRRFATVVCKQAG 51 (154)
T ss_pred CHHHHHHHHHHCCCCCCCCCEEEEEEEEECCCCHHHHHHHHHHCC
T ss_conf 778833515403875899958899853220648999999999809
No 153
>pfam05559 DUF763 Protein of unknown function (DUF763). This family consists of several uncharacterized bacterial and archaeal proteins of unknown function.
Probab=67.49 E-value=2.4 Score=22.94 Aligned_cols=16 Identities=6% Similarity=0.146 Sum_probs=6.9
Q ss_pred CHHHHHHCCCCCHHHH
Q ss_conf 6687510457116799
Q gi|254780553|r 106 NSKVIAQIPGISMKIA 121 (207)
Q Consensus 106 D~~~L~~vpGIGkKtA 121 (207)
|-.-|-.+||||++|.
T Consensus 267 dfeeLLl~~GvGp~Tl 282 (319)
T pfam05559 267 DFEELLLLKGVGPSTL 282 (319)
T ss_pred CHHHHHHCCCCCHHHH
T ss_conf 6999971479888999
No 154
>pfam10440 WIYLD WIYLD domain. This presumed domain has been predicted to contain three alpha helices. The domain was named the WIYLD domain based on the pattern of most conserved residues. The domain appears to be specific to plant SET-domain proteins.
Probab=67.32 E-value=9.5 Score=18.98 Aligned_cols=31 Identities=13% Similarity=0.104 Sum_probs=25.8
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHCCC
Q ss_conf 8999999996799989999999999851688
Q gi|254780553|r 160 AINAISALVNLGYGQDQATTAVVSVLKKEKN 190 (207)
Q Consensus 160 ~~d~~~AL~~LGy~~~ea~~ai~~i~~~~~~ 190 (207)
..-|++|+..|||++..++.+++++++-...
T Consensus 11 idaA~dam~~~G~~~~~v~~vlk~LL~~yg~ 41 (65)
T pfam10440 11 IDAAIDRMREFGIPDAVIRPVLKELLELYGG 41 (65)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHCC
T ss_conf 9999999998299879999999999999678
No 155
>pfam09374 PG_binding_3 Predicted Peptidoglycan domain. This family contains a potential peptidoglycan binding domain.
Probab=67.09 E-value=5 Score=20.83 Aligned_cols=33 Identities=9% Similarity=0.381 Sum_probs=25.9
Q ss_pred CCCHHHHHHHCCCCHHHHHHHHHCCCHHHHHHCC
Q ss_conf 0510112443157899999998515668751045
Q gi|254780553|r 81 VGARVAMGVLSRITATELVESIILQNSKVIAQIP 114 (207)
Q Consensus 81 IGpK~AL~iLs~l~~~~l~~aI~~~D~~~L~~vp 114 (207)
|||++ |+.++..+|++++.++...-...+.+++
T Consensus 21 IGp~T-l~Av~~~d~~~l~~~~~~~R~~fy~~L~ 53 (67)
T pfam09374 21 IGPKT-LAALASMGENDLIKALNAARIRFYLRLA 53 (67)
T ss_pred CCHHH-HHHHHHCCHHHHHHHHHHHHHHHHHHCC
T ss_conf 28999-9999967999999999999999998367
No 156
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=66.14 E-value=7.6 Score=19.63 Aligned_cols=76 Identities=16% Similarity=0.164 Sum_probs=33.3
Q ss_pred HHHHHCCCCH-HHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHH-H
Q ss_conf 1244315789-9999998515668751045711679999999974222110113344323333344555565315899-9
Q gi|254780553|r 86 AMGVLSRITA-TELVESIILQNSKVIAQIPGISMKIASRIMTELKGKAISLSSVVQQDMSCVNKEQAHICSMPSFAIN-A 163 (207)
Q Consensus 86 AL~iLs~l~~-~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~K~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d-~ 163 (207)
.|.+-...++ +..++||.-+.++.=. ..+.+.|++-.+-..+.+.. ... ....+....+ -
T Consensus 104 GlRvPg~~d~fE~~vrAIlGQQvSv~a-----A~tl~~Rlv~~~G~~~~~~~------------~~~-~FPtp~~la~~~ 165 (283)
T PRK10308 104 GLRLPGSVDAFEQGVRAILGQLVSVAM-----AAKLTAKVAQLYGERLDDFP------------DYV-CFPTPQRLAAAD 165 (283)
T ss_pred CCCCCCCCCHHHHHHHHHHHCCCCHHH-----HHHHHHHHHHHHCCCCCCCC------------CCE-ECCCHHHHHCCC
T ss_conf 977888798899999999714021999-----99999999999489578898------------853-479989985389
Q ss_pred HHHHHHCCCCHHHHHH
Q ss_conf 9999967999899999
Q gi|254780553|r 164 ISALVNLGYGQDQATT 179 (207)
Q Consensus 164 ~~AL~~LGy~~~ea~~ 179 (207)
.+.|..||++...++.
T Consensus 166 ~~~L~~lg~p~~ra~t 181 (283)
T PRK10308 166 PQALKALGMPLKRAEA 181 (283)
T ss_pred HHHHHHCCCCHHHHHH
T ss_conf 7566455896689999
No 157
>KOG1918 consensus
Probab=66.11 E-value=1.6 Score=24.11 Aligned_cols=14 Identities=21% Similarity=0.304 Sum_probs=7.4
Q ss_pred CHHHHHHHHHCCCH
Q ss_conf 89999999851566
Q gi|254780553|r 94 TATELVESIILQNS 107 (207)
Q Consensus 94 ~~~~l~~aI~~~D~ 107 (207)
+...|+++|.++..
T Consensus 75 Pf~~LiraIlsQQL 88 (254)
T KOG1918 75 PFERLIRAILSQQL 88 (254)
T ss_pred CHHHHHHHHHHHHH
T ss_conf 09999999999999
No 158
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=64.26 E-value=4.4 Score=21.22 Aligned_cols=22 Identities=23% Similarity=0.232 Sum_probs=19.2
Q ss_pred HHHHHCCCCCHHHHHHHHHHHH
Q ss_conf 8751045711679999999974
Q gi|254780553|r 108 KVIAQIPGISMKIASRIMTELK 129 (207)
Q Consensus 108 ~~L~~vpGIGkKtA~rIi~ELk 129 (207)
-+|+.+.|||+.+|+.||-++.
T Consensus 17 iALt~IyGIG~~~a~~I~~~~g 38 (121)
T COG0099 17 IALTYIYGIGRRRAKEICKKAG 38 (121)
T ss_pred EHHHHHCCCCHHHHHHHHHHCC
T ss_conf 5046303536999999999919
No 159
>TIGR00882 2A0105 oligosaccharide:H+ symporter; InterPro: IPR000576 In bacteria there are a number of families of transport proteins, including symporters and antiporters, that mediate the intake of a variety of sugars with the concomitant uptake of hydrogen ions (proton symporters) . The lacY family of Escherichia coli and Klebsiella pneumoniae are proton/beta-galactoside symporters, which, like most sugar transporters, are integral membrane proteins with 12 predicted transmembrane (TM) regions. Also similar to the lacY family are the rafinose (rafB) and sucrose (cscB) permeases from E. coli .; GO: 0005403 hydrogen:sugar symporter activity, 0006810 transport, 0016020 membrane.
Probab=64.17 E-value=7.5 Score=19.67 Aligned_cols=38 Identities=21% Similarity=0.378 Sum_probs=28.7
Q ss_pred ECCCCEEEEEEECHHHHH-----HHHHHHHHHHCCCHHHHHHH
Q ss_conf 738841899970677999-----99998501000510112443
Q gi|254780553|r 53 MRQDQIRLFGFLSDLDRQ-----WFMLLQSVQGVGARVAMGVL 90 (207)
Q Consensus 53 vrEd~~~LyGF~~~~Er~-----~F~~Li~V~GIGpK~AL~iL 90 (207)
-.|.+.++|||.|....- ||-.=.=||.||||-||=|=
T Consensus 249 ~~~~Gtr~fGy~tt~ge~lnA~iMf~~P~iiNRiG~KNaLLia 291 (397)
T TIGR00882 249 TPQQGTRVFGYVTTAGELLNALIMFCAPLIINRIGAKNALLIA 291 (397)
T ss_pred CCCCCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCHHHHHHHH
T ss_conf 7677627665301288999999998703776166715899999
No 160
>PRK03348 DNA polymerase IV; Provisional
Probab=63.89 E-value=3.8 Score=21.60 Aligned_cols=42 Identities=14% Similarity=0.218 Sum_probs=24.0
Q ss_pred HCCCHHHHHHHC----------CCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHH
Q ss_conf 005101124431----------578999999985156687510457116799999
Q gi|254780553|r 80 GVGARVAMGVLS----------RITATELVESIILQNSKVIAQIPGISMKIASRI 124 (207)
Q Consensus 80 GIGpK~AL~iLs----------~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rI 124 (207)
||||-.-|+=+. .+++++....+..= -+.++||||+||++|+
T Consensus 144 GIa~nK~LAKiAS~~aKP~G~~vi~p~~~~~~L~~l---PV~~lwGIG~~t~~kL 195 (456)
T PRK03348 144 GAGSGKQIAKIASGLAKPDGIRVVPPGEERELLAPL---PVRRLWGIGPVAEEKL 195 (456)
T ss_pred EECHHHHHHHHHHHHCCCCCEEEECHHHHHHHHHHC---CHHHCCCCCHHHHHHH
T ss_conf 874159999999872489837996888999998756---5743387759999999
No 161
>pfam10842 DUF2642 Protein of unknown function (DUF2642). This family of proteins with unknown function appear to be restricted to Bacillus spp.
Probab=62.99 E-value=13 Score=18.13 Aligned_cols=28 Identities=18% Similarity=0.471 Sum_probs=24.4
Q ss_pred CEEEEEEEEEECCEEEEEECCEEEEEEC
Q ss_conf 2589999996099799985883238970
Q gi|254780553|r 3 GKIKGNIEGLYEDYVLIDVQGVCYIIYC 30 (207)
Q Consensus 3 ~~i~G~i~~~~~~~ivi~v~GvGY~i~v 30 (207)
++++|++.++.+|.++++.++--|-|.+
T Consensus 31 gsvrG~L~dVkPDHivle~~~~~f~IRi 58 (66)
T pfam10842 31 GSVRGRLRDVKPDHLVIEAGDAVFYIRI 58 (66)
T ss_pred CCEEEEEEEECCCEEEEECCCCEEEEEE
T ss_conf 5168789610798899971892799999
No 162
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=62.73 E-value=13 Score=18.10 Aligned_cols=42 Identities=24% Similarity=0.287 Sum_probs=32.0
Q ss_pred CCEEEEEEEEEECCEEEEEECCEEEEEECCHHHHHHCCCCCCE
Q ss_conf 3258999999609979998588323897086889850247984
Q gi|254780553|r 2 IGKIKGNIEGLYEDYVLIDVQGVCYIIYCPIRTLSCLGKIGDF 44 (207)
Q Consensus 2 I~~i~G~i~~~~~~~ivi~v~GvGY~i~vs~~~~~~l~~~g~~ 44 (207)
++-|.|+|.++.++.+.|++| -|-++.+..+.....-+.++.
T Consensus 53 ~gGi~G~V~~v~d~~v~I~l~-~~~~i~~~k~aI~~v~~~~~~ 94 (97)
T COG1862 53 IGGIVGTVTKVGDDTVEIELG-DGTKIKFEKEAIATVLEKGDL 94 (97)
T ss_pred CCCEEEEEEEEECCCEEEEEC-CCEEEEEEHHHHHHHCCCCCC
T ss_conf 587399999970681899978-986999987998865056664
No 163
>KOG2518 consensus
Probab=62.63 E-value=8.7 Score=19.24 Aligned_cols=73 Identities=18% Similarity=0.397 Sum_probs=44.1
Q ss_pred EEEEEECCCCE-EEEEEE----------CHHHHHHHHHHHHHHHCCCHHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCC
Q ss_conf 99999738841-899970----------6779999999850100051011244315789999999851566875104571
Q gi|254780553|r 48 FVETHMRQDQI-RLFGFL----------SDLDRQWFMLLQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGI 116 (207)
Q Consensus 48 ~~~~~vrEd~~-~LyGF~----------~~~Er~~F~~Li~V~GIGpK~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGI 116 (207)
++.-++.||+- ..||-. .-.|-+ |..|-...+. . ..++-+.|.+...-.--..|.++|||
T Consensus 163 ~i~~IITEDSDLl~fGc~~vifK~d~~G~~le~~-~~~l~~~~~l------~--~~~~~ekfr~mciLSGCDYl~slpGv 233 (556)
T KOG2518 163 IVDAIITEDSDLLVFGCKKVIFKMDSFGNGLEIN-RSKLPECKPL------G--DKFTEEKFRRMCILSGCDYLSSLPGV 233 (556)
T ss_pred CCEEEEECCCCCCCCCCHHHEEECCCCCCCCCCC-HHHHHHCCCC------C--CCCCHHHHHHHHHHCCCCCCCCCCCC
T ss_conf 6427982365565668524322014788850322-7652221265------4--44579999999984277311247652
Q ss_pred CHHHHHHHHHHHH
Q ss_conf 1679999999974
Q gi|254780553|r 117 SMKIASRIMTELK 129 (207)
Q Consensus 117 GkKtA~rIi~ELk 129 (207)
|-+||-|++.--+
T Consensus 234 Gl~tA~k~l~k~~ 246 (556)
T KOG2518 234 GLATAHKLLSKYN 246 (556)
T ss_pred CHHHHHHHHHHCC
T ss_conf 2999999998537
No 164
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=62.26 E-value=13 Score=18.04 Aligned_cols=58 Identities=21% Similarity=0.185 Sum_probs=38.8
Q ss_pred EEEEEEEEEECCEEEEEECCEEEEEECCHHHHHHCCCCCCEEEEEEEEEECCCCEEEEEEECHH
Q ss_conf 5899999960997999858832389708688985024798499999999738841899970677
Q gi|254780553|r 4 KIKGNIEGLYEDYVLIDVQGVCYIIYCPIRTLSCLGKIGDFCTLFVETHMRQDQIRLFGFLSDL 67 (207)
Q Consensus 4 ~i~G~i~~~~~~~ivi~v~GvGY~i~vs~~~~~~l~~~g~~v~l~~~~~vrEd~~~LyGF~~~~ 67 (207)
-++|++..+..+++++|+|.- -|=.+|..-+..-++.|+.|.+|+.-. ||. +|=++++
T Consensus 324 vi~g~Vv~i~~d~V~vdvG~K-sEg~ip~~eF~~~~~vGD~v~V~ie~~--e~~---~~~LSr~ 381 (863)
T PRK12269 324 VRMGTVVQVNAGTVFVDIGGK-SEGRVPVEEFEAPPKAGDGVRVYVERV--TPY---GPELSKT 381 (863)
T ss_pred EEEEEEEEEECCEEEEECCCC-CCCCCCHHHCCCCCCCCCEEEEEEEEE--CCC---CCEECHH
T ss_conf 589999999589799964774-455326999277889999999999997--088---9756189
No 165
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=62.05 E-value=13 Score=18.02 Aligned_cols=55 Identities=27% Similarity=0.273 Sum_probs=39.0
Q ss_pred EEEEEEEEEECCEEEEEECCEEEEEECCHHHHHHC-----CCCCCEEEEEEEEEECCCCEEE
Q ss_conf 58999999609979998588323897086889850-----2479849999999973884189
Q gi|254780553|r 4 KIKGNIEGLYEDYVLIDVQGVCYIIYCPIRTLSCL-----GKIGDFCTLFVETHMRQDQIRL 60 (207)
Q Consensus 4 ~i~G~i~~~~~~~ivi~v~GvGY~i~vs~~~~~~l-----~~~g~~v~l~~~~~vrEd~~~L 60 (207)
-++|+|..+.++++++|+|+ --+-++|.+-+... .+.|+++.+|+ ...++....|
T Consensus 36 iV~G~Vv~I~~d~v~VDiG~-KsEG~Ip~~E~~d~~~~~~~kvGD~Iev~V-~~~~dgei~L 95 (489)
T PRK13806 36 RIKAAIVAIGEDSVFVATGS-KVDGVIDRRELEDAEGNLPYAVGDRLDLYV-VAVNGGEIRL 95 (489)
T ss_pred EEEEEEEEEECCEEEEEECC-CEEEEEEHHHHCCCCCCCCCCCCCEEEEEE-EEECCCCEEE
T ss_conf 89999999979989999689-828995899925755775658998999999-9964981899
No 166
>pfam02699 YajC Preprotein translocase subunit. See.
Probab=61.23 E-value=14 Score=17.92 Aligned_cols=33 Identities=21% Similarity=0.374 Sum_probs=25.1
Q ss_pred CCEEEEEEEEEECCEEEEEECCEEEEEECCHHHH
Q ss_conf 3258999999609979998588323897086889
Q gi|254780553|r 2 IGKIKGNIEGLYEDYVLIDVQGVCYIIYCPIRTL 35 (207)
Q Consensus 2 I~~i~G~i~~~~~~~ivi~v~GvGY~i~vs~~~~ 35 (207)
++-|.|++.++.++++.++++. |-++.+..+..
T Consensus 47 ~gGi~G~V~~i~~~~v~lei~~-gv~i~v~r~aI 79 (83)
T pfam02699 47 IGGIHGKIVKVDDDTVVLEIAD-GVKVKVDKSAI 79 (83)
T ss_pred CCCEEEEEEEEECCEEEEEECC-CCEEEEEHHHH
T ss_conf 9971999999979999999889-93999996986
No 167
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=59.81 E-value=7.3 Score=19.74 Aligned_cols=56 Identities=25% Similarity=0.370 Sum_probs=42.9
Q ss_pred HHHHHHHCCCHHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHH
Q ss_conf 9850100051011244315789999999851566875104571167999999997422
Q gi|254780553|r 74 LLQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMTELKGK 131 (207)
Q Consensus 74 ~Li~V~GIGpK~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~K 131 (207)
.|-...||||..+=.+-+ -....+ ..+..-+.+-|.++.||+...|++|+-..+.-
T Consensus 8 ~l~~lpGv~~~~~~kL~~-aG~~tv-~~l~~~~~~~L~~~~gis~~~a~ki~~~a~~~ 63 (318)
T PRK04301 8 DLEDLPGVGPATAEKLRE-AGYDTV-EAIAVASPKELSEIAGISESTAAKIIEAAREA 63 (318)
T ss_pred CCCCCCCCCHHHHHHHHH-CCCCCH-HHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_conf 745589989999999998-699549-99874899999985099999999999999985
No 168
>PRK01810 DNA polymerase IV; Validated
Probab=58.57 E-value=15 Score=17.63 Aligned_cols=50 Identities=14% Similarity=0.323 Sum_probs=23.3
Q ss_pred HHHHHCCCHHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHH
Q ss_conf 5010005101124431578999999985156687510457116799999999742
Q gi|254780553|r 76 QSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMTELKG 130 (207)
Q Consensus 76 i~V~GIGpK~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~ 130 (207)
-.|.|||++++-.+ ..+....+.+ +++-|...|.+.-| +.++|+..+++|
T Consensus 182 ~~iwGIG~~~~~~L-~~~GI~Ti~d-l~~~~~~~l~~~fG---~~g~~l~~~~~G 231 (410)
T PRK01810 182 EEMHGIGEKTAEKL-KDIHIHTIGD-LAKADEHILRAKLG---INGPRLQRRANG 231 (410)
T ss_pred CCCCCCCHHHHHHH-HHCCCCCHHH-HHHCCHHHHHHHHH---HHHHHHHHHHCC
T ss_conf 12058677899999-9869968999-87499999998765---499999999719
No 169
>cd00424 Pol_Y Y-family of DNA polymerases. Pol_Y's can transverse replication-blocking DNA lesions, such as cyclobutane pyrimidine dimers resulting from UV damage, at the cost of an elevated error rate. The Y-family has no 3'-5' exonuclease activity. In addition to possessing a topology akin to a right hand, with "thumb", "fingers" and "palm" motifs, like polymerases from the A-, B-, C- and X-families, the Y-family has a unique "little finger" motif. Expression of Y-family polymerases is often induced by DNA damage. These polymerases are phylogenetically unrelated to classical DNA polymerases.
Probab=57.76 E-value=5.3 Score=20.66 Aligned_cols=51 Identities=20% Similarity=0.403 Sum_probs=21.7
Q ss_pred HHHHHCCCHHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHH
Q ss_conf 5010005101124431578999999985156687510457116799999999742
Q gi|254780553|r 76 QSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMTELKG 130 (207)
Q Consensus 76 i~V~GIGpK~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~ 130 (207)
-.+.|||++++-.+- .+....+.+.........+. -.|.+.++++.-+++|
T Consensus 176 ~~l~GIG~~~~~~L~-~~gi~ti~dl~~~~~~~l~~---~~~~~~g~~l~~~~~G 226 (341)
T cd00424 176 SDIPGIGSVTASRLE-ALGIIRKCDLLALQPDQLLA---SLGGKLGERLWSALRG 226 (341)
T ss_pred HHHCCCCHHHHHHHH-HCCCCCHHHHHHCCHHHHHH---HHCCHHHHHHHHHHCC
T ss_conf 887487889999999-84993599987189999999---9768899999999659
No 170
>pfam00627 UBA UBA/TS-N domain. This small domain is composed of three alpha helices. This family includes the previously defined UBA and TS-N domains. The UBA-domain (ubiquitin associated domain) is a novel sequence motif found in several proteins having connections to ubiquitin and the ubiquitination pathway. The structure of the UBA domain consists of a compact three helix bundle. This domain is found at the N terminus of EF-TS hence the name TS-N. The structure of EF-TS is known and this domain is implicated in its interaction with EF-TU. The domain has been found in non EF-TS proteins such as alpha-NAC and MJ0280.
Probab=57.36 E-value=14 Score=17.81 Aligned_cols=23 Identities=22% Similarity=0.443 Sum_probs=19.5
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf 99999999679998999999999
Q gi|254780553|r 161 INAISALVNLGYGQDQATTAVVS 183 (207)
Q Consensus 161 ~d~~~AL~~LGy~~~ea~~ai~~ 183 (207)
.+.+..|..+||++.++.+|+..
T Consensus 3 ~~~i~~L~~mGf~~~~~~~AL~~ 25 (37)
T pfam00627 3 EELIKQLREMGFSREEAKKALRA 25 (37)
T ss_pred HHHHHHHHHCCCCHHHHHHHHHH
T ss_conf 89999999909999999999998
No 171
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=56.24 E-value=5 Score=20.85 Aligned_cols=51 Identities=20% Similarity=0.367 Sum_probs=28.6
Q ss_pred HHHHHHCCCHHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHH
Q ss_conf 85010005101124431578999999985156687510457116799999999742
Q gi|254780553|r 75 LQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMTELKG 130 (207)
Q Consensus 75 Li~V~GIGpK~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~ 130 (207)
+-.+-|||++++-.+ +.+....+.+. ++-|...|.+.-|+ ..+|+..||.|
T Consensus 181 v~~lwGIG~~~~~kL-~~~GI~Ti~dL-a~~~~~~l~k~fgv---~g~r~~~~l~G 231 (422)
T PRK03609 181 VEEVWGVGRRISKKL-NAMGIKTALDL-ADTDIRFIRKHFNV---VLERTVRELRG 231 (422)
T ss_pred HHHHHHHHHHHHHHH-HHCCCCHHHHH-HHCCHHHHHHHHHH---HHHHHHHHHCC
T ss_conf 889861139999999-98788108998-72998999988889---99999999679
No 172
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=54.11 E-value=6.4 Score=20.14 Aligned_cols=26 Identities=19% Similarity=0.213 Sum_probs=21.3
Q ss_pred CHHHHHHCCCCCHHHHHHHHHHHHHH
Q ss_conf 66875104571167999999997422
Q gi|254780553|r 106 NSKVIAQIPGISMKIASRIMTELKGK 131 (207)
Q Consensus 106 D~~~L~~vpGIGkKtA~rIi~ELk~K 131 (207)
..+.|.++.|||+-||.-|.+-.=+|
T Consensus 113 ~R~~LL~iKGIG~ETaDsILlYa~~r 138 (215)
T COG2231 113 LREELLSIKGIGKETADSILLYALDR 138 (215)
T ss_pred HHHHHHCCCCCCHHHHHHHHHHHHCC
T ss_conf 99998726886622399999998048
No 173
>pfam12482 DUF3701 Phage integrase protein. This domain family is found in bacteria, and is approximately 100 amino acids in length. The family is found in association with pfam00589.
Probab=53.74 E-value=13 Score=18.08 Aligned_cols=37 Identities=24% Similarity=0.266 Sum_probs=30.0
Q ss_pred CHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHH
Q ss_conf 8999999985156687510457116799999999742
Q gi|254780553|r 94 TATELVESIILQNSKVIAQIPGISMKIASRIMTELKG 130 (207)
Q Consensus 94 ~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~ 130 (207)
+..+|...|..---..-..|||+|...|.||--=|..
T Consensus 36 TLa~L~~~i~~rg~~Wwr~vp~lG~~~Ar~Iea~la~ 72 (96)
T pfam12482 36 TLADLTVRINRRGRRWWRAVPGLGAAGARRIEAFLAA 72 (96)
T ss_pred HHHHHHHHHHHCCCCHHHCCCCCCHHHHHHHHHHHHH
T ss_conf 3999999997226502441876106879999999998
No 174
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=53.02 E-value=7.8 Score=19.56 Aligned_cols=48 Identities=17% Similarity=0.234 Sum_probs=22.4
Q ss_pred CEEEEEEEEEECC-------EEEEEE-CCEEEEEECC-HHHH-HHCCCCCCEEEEEEEE
Q ss_conf 2589999996099-------799985-8832389708-6889-8502479849999999
Q gi|254780553|r 3 GKIKGNIEGLYED-------YVLIDV-QGVCYIIYCP-IRTL-SCLGKIGDFCTLFVET 51 (207)
Q Consensus 3 ~~i~G~i~~~~~~-------~ivi~v-~GvGY~i~vs-~~~~-~~l~~~g~~v~l~~~~ 51 (207)
..+.|+|.+.... .+.+.. .|.--.++-. ...+ ..+ ..|+.+.+|=-.
T Consensus 61 vtI~g~V~~~~~~~~~r~~l~v~v~D~tG~I~lvfFn~~pyl~k~l-~~G~~v~VsGKV 118 (677)
T PRK10917 61 VTVEGTVLSAEVYFGPRRRLRVTLSDGTGVLTLVFFNNQPYLKKQL-KVGKRVAVYGKV 118 (677)
T ss_pred EEEEEEEEEEECCCCCCCEEEEEEEECCEEEEEEEECCCHHHHHHC-CCCCEEEEEEEE
T ss_conf 9999999998437789724999999898799999989847899638-999989999999
No 175
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=52.64 E-value=8.7 Score=19.23 Aligned_cols=25 Identities=20% Similarity=0.408 Sum_probs=21.4
Q ss_pred HHCCCHHHHHHCCCCCHHHHHHHHH
Q ss_conf 8515668751045711679999999
Q gi|254780553|r 102 IILQNSKVIAQIPGISMKIASRIMT 126 (207)
Q Consensus 102 I~~~D~~~L~~vpGIGkKtA~rIi~ 126 (207)
+.+.++..+.+.||..+..|.+|+.
T Consensus 67 lNNa~vr~f~q~pGmYPtlA~kIv~ 91 (144)
T PRK02515 67 LNNSSVRAFRQFPGMYPTLAGKIVK 91 (144)
T ss_pred CCCHHHHHHHHCCCCCHHHHHHHHH
T ss_conf 5627499998688846799999984
No 176
>pfam08587 UBA_2 Ubiquitin associated domain (UBA). This is a UBA (ubiquitin associated) domain. Ubiquitin is involved in intracellular proteolysis.
Probab=52.55 E-value=19 Score=16.99 Aligned_cols=23 Identities=35% Similarity=0.562 Sum_probs=18.9
Q ss_pred HHHHHHHHH-CCCCHHHHHHHHHH
Q ss_conf 999999996-79998999999999
Q gi|254780553|r 161 INAISALVN-LGYGQDQATTAVVS 183 (207)
Q Consensus 161 ~d~~~AL~~-LGy~~~ea~~ai~~ 183 (207)
++++.+|.. +||.+.++..|+..
T Consensus 3 d~vv~~Ls~TMGYdkdeI~eal~s 26 (46)
T pfam08587 3 ENVVSKLSKTMGYDKDEIVEALES 26 (46)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHC
T ss_conf 799999999808879999999982
No 177
>KOG2519 consensus
Probab=52.24 E-value=19 Score=16.95 Aligned_cols=96 Identities=13% Similarity=0.147 Sum_probs=55.2
Q ss_pred HHHHCCCHHHHHHHCCCCHHHHHHHHH-CCCHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 010005101124431578999999985-1566875104571167999999997422211011334432333334455556
Q gi|254780553|r 77 SVQGVGARVAMGVLSRITATELVESII-LQNSKVIAQIPGISMKIASRIMTELKGKAISLSSVVQQDMSCVNKEQAHICS 155 (207)
Q Consensus 77 ~V~GIGpK~AL~iLs~l~~~~l~~aI~-~~D~~~L~~vpGIGkKtA~rIi~ELk~K~~~~~~~~~~~~~~~~~~~~~~~~ 155 (207)
+|-||||+.|+.++.+.. .+-+... +.|.+.+.-=+---+|-|.++.++-.- ...... ....-
T Consensus 233 ~I~Gig~~~al~lir~~~--~i~~ile~~~~~~~~~ip~~w~~~~~r~~f~~p~~---------~~~~~~-----~~i~w 296 (449)
T KOG2519 233 TIRGIGPKKALKLIRQHG--DIENILEINSDLKEYPIPEDWSYKLARKLFLEPEF---------PNPESI-----LDLKW 296 (449)
T ss_pred CCCCCCHHHHHHHHHHHC--CHHHHHHHCCCHHHCCCCCCCCHHHHHHHHCCCCC---------CCCCCE-----EECCC
T ss_conf 125637387999999756--78777511241332289977567778887548444---------884300-----34136
Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHHHHHHHC
Q ss_conf 5315899999999-67999899999999998516
Q gi|254780553|r 156 MPSFAINAISALV-NLGYGQDQATTAVVSVLKKE 188 (207)
Q Consensus 156 ~~~~~~d~~~AL~-~LGy~~~ea~~ai~~i~~~~ 188 (207)
.....+..+.-|. ..+|...-.++++.++.+.-
T Consensus 297 ~~pd~~~li~fl~~~~~f~~~rv~~~~~kl~~~~ 330 (449)
T KOG2519 297 KTPDTEGLIQFLVGEKQFNEERVRKGIRKLKSSL 330 (449)
T ss_pred CCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf 7897688899997664259788750067776552
No 178
>TIGR02168 SMC_prok_B chromosome segregation protein SMC; InterPro: IPR011890 The SMC (structural maintenance of chromosomes) family of proteins, exist in virtually all organisms including both bacteria and archaea. The SMC proteins are essential for successful chromosome transmission during replication and segregation of the genome in all organisms and form three types of heterodimer (SMC1SMC3, SMC2SMC4, SMC5SMC6), which are core components of large multiprotein complexes. The best known complexes are cohesin, which is responsible for sister-chromatid cohesion, and condensin, which is required for full chromosome condensation in mitosis. SMCs are generally present as single proteins in bacteria, and as at least six distinct proteins in eukaryotes. The proteins range in size from approximately 110 to 170 kDa, and share a five-domain structure, with globular N- and C-terminal (IPR003395 from INTERPRO) domains separated by a long (circa 100 nm or 900 residues) coiled coil segment in the centre of which is a globular ''hinge'' domain, characterised by a set of four highly conserved glycine residues that are typical of flexible regions in a protein. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif (XXXXD, where X is any hydrophobic residue), and a LSGG motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases . All SMC proteins appear to form dimers, either forming homodimers with themselves, as in the case of prokaryotic SMC proteins, or heterodimers between different but related SMC proteins. The dimers are arranged in an antiparallel alignment. This orientation brings the N- and C-terminal globular domains (from either different or identical protamers) together, which unites an ATP binding site (Walker A motif) within the N-terminal domain with a Walker B motif (DA box) within the C-terminal domain, to form a potentially functional ATPase. Protein interaction and microscopy data suggest that SMC dimers form a ring-like structure which might embrace DNA molecules. Non-SMC subunits associate with the SMC amino- and carboxy-terminal domains. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. SMCs share not only sequence similarity but also structural similarity with ABC proteins. SMC proteins function together with other proteins in a range of chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, recombination, DNA repair and epigenetic silencing of gene expression . The smc gene is often associated with scpB (IPR005234 from INTERPRO) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle , , .; GO: 0005515 protein binding, 0005524 ATP binding, 0005694 chromosome.
Probab=52.19 E-value=2.5 Score=22.90 Aligned_cols=121 Identities=8% Similarity=-0.015 Sum_probs=47.4
Q ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCC
Q ss_conf 77999999985010005101124431578999999985156687510457116799999999742221101133443233
Q gi|254780553|r 66 DLDRQWFMLLQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMTELKGKAISLSSVVQQDMSC 145 (207)
Q Consensus 66 ~~Er~~F~~Li~V~GIGpK~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~K~~~~~~~~~~~~~~ 145 (207)
..-+.+|..-...+||.|.++=.| + .++ ..-.||..-=-..|..+=--+...|.+.|--|+..-.--....+.+...
T Consensus 511 ~gv~~~~~~~~~~~G~~g~l~~~i-~-v~~-~ye~A~e~aLg~~l~~~vv~~~~~a~~a~~~L~~~~~Gr~~fl~l~~~~ 587 (1191)
T TIGR02168 511 EGVKALLKNASGLAGIVGVLSELI-E-VDE-GYEAAIEAALGGRLQAVVVENLNAAKKAIAFLKQNELGRVTFLPLDVIK 587 (1191)
T ss_pred HHHHHHHHHHHCCCCCCHHHHHHH-C-CCH-HHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEECCCCC
T ss_conf 899999986632787300357652-1-548-8999999997860020014897999999973110258827763025567
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCC
Q ss_conf 33344555565315899999999679998999999999985168
Q gi|254780553|r 146 VNKEQAHICSMPSFAINAISALVNLGYGQDQATTAVVSVLKKEK 189 (207)
Q Consensus 146 ~~~~~~~~~~~~~~~~d~~~AL~~LGy~~~ea~~ai~~i~~~~~ 189 (207)
.................++..+..|=+-+..++.++..++...-
T Consensus 588 ~~~~~~~~~~~~~~~~Gf~g~~~~lv~~~~~~~~~~~~lL~~~~ 631 (1191)
T TIGR02168 588 GAEIQGNDREVLKSIEGFLGVAKDLVKFDPKLRKALSYLLGGVL 631 (1191)
T ss_pred CCCCCCCCHHHHCCCCHHHHHHHHHHCCCHHHHHHHHHHHCCEE
T ss_conf 76677762454237750678876664060667899998558728
No 179
>pfam11372 DUF3173 Protein of unknown function (DUF3173). This family of proteins with unknown function appears to be restricted to Firmicutes.
Probab=52.08 E-value=13 Score=18.18 Aligned_cols=20 Identities=20% Similarity=0.423 Sum_probs=15.1
Q ss_pred HHHHHCCCCHHHHHHHHHHH
Q ss_conf 99996799989999999999
Q gi|254780553|r 165 SALVNLGYGQDQATTAVVSV 184 (207)
Q Consensus 165 ~AL~~LGy~~~ea~~ai~~i 184 (207)
.-|+.|||++.+|+..+.++
T Consensus 7 ~dLi~lGf~~~~A~~IIrqA 26 (59)
T pfam11372 7 KDLIKLGFKPHTARDIIRQA 26 (59)
T ss_pred HHHHHHCCCHHHHHHHHHHH
T ss_conf 99999579887999999999
No 180
>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=51.03 E-value=20 Score=16.83 Aligned_cols=53 Identities=25% Similarity=0.286 Sum_probs=37.1
Q ss_pred EEEEEEEEEECCEEEEEECCEEEEEECCHHHHHH--------CCCCCCEEEEEEEEEECCCC
Q ss_conf 5899999960997999858832389708688985--------02479849999999973884
Q gi|254780553|r 4 KIKGNIEGLYEDYVLIDVQGVCYIIYCPIRTLSC--------LGKIGDFCTLFVETHMRQDQ 57 (207)
Q Consensus 4 ~i~G~i~~~~~~~ivi~v~GvGY~i~vs~~~~~~--------l~~~g~~v~l~~~~~vrEd~ 57 (207)
-++|++..+.++.+.++.+ -+-+=++|.+-++. .-+.|+++..++--.-.++.
T Consensus 3 iV~G~V~~i~~~gv~Vdig-~k~eG~ip~~E~s~~~~~~~~~~~~vGd~i~~~V~~~d~~~g 63 (70)
T cd05687 3 IVKGTVVSVDDDEVLVDIG-YKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEG 63 (70)
T ss_pred EEEEEEEEEECCEEEEEEC-CCCCEEEEHHHHCCCCCCCHHHCCCCCCEEEEEEEEEECCCC
T ss_conf 8999999997886999968-985026899994533238974712699999999999999999
No 181
>PRK07220 DNA topoisomerase I; Validated
Probab=49.27 E-value=9.2 Score=19.08 Aligned_cols=24 Identities=25% Similarity=0.328 Sum_probs=15.5
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHH
Q ss_conf 999999967999899999999998
Q gi|254780553|r 162 NAISALVNLGYGQDQATTAVVSVL 185 (207)
Q Consensus 162 d~~~AL~~LGy~~~ea~~ai~~i~ 185 (207)
.+..+--.|||+.++.-+....+.
T Consensus 282 ~Lq~~Asklg~Sa~~Tm~iAQ~LY 305 (740)
T PRK07220 282 GFISAASSIGFSPANAMRIAESLY 305 (740)
T ss_pred HHHHHHHHCCCCHHHHHHHHHHHH
T ss_conf 999999876997999999999874
No 182
>PRK06645 DNA polymerase III subunits gamma and tau; Validated
Probab=48.69 E-value=16 Score=17.43 Aligned_cols=50 Identities=8% Similarity=0.113 Sum_probs=27.8
Q ss_pred EEEEEECHHHHHHHHHHHHHHHC----CCHHHHHHHCCCCHHHHHHHHHCCCHH
Q ss_conf 89997067799999998501000----510112443157899999998515668
Q gi|254780553|r 59 RLFGFLSDLDRQWFMLLQSVQGV----GARVAMGVLSRITATELVESIILQNSK 108 (207)
Q Consensus 59 ~LyGF~~~~Er~~F~~Li~V~GI----GpK~AL~iLs~l~~~~l~~aI~~~D~~ 108 (207)
.-|-|..-.+.+++..|..|.-- =..-||.++...+-..+..|+.-=|-.
T Consensus 180 q~f~~~~i~~~~i~~~l~~i~~~E~~~~~~~al~~ia~~a~Gs~RDalslldqa 233 (507)
T PRK06645 180 QRYDLRRLSFEEIFKLLEYITKQENLKADIEALRIIAYKSEGSARDAVSILDQA 233 (507)
T ss_pred EEEEEECCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHH
T ss_conf 278754599799999999999976877778999999985599867899999999
No 183
>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]
Probab=44.68 E-value=6.9 Score=19.89 Aligned_cols=28 Identities=29% Similarity=0.502 Sum_probs=21.7
Q ss_pred HHHHCCCCCHHHHHHHHHHHHHHHHHCC
Q ss_conf 7510457116799999999742221101
Q gi|254780553|r 109 VIAQIPGISMKIASRIMTELKGKAISLS 136 (207)
Q Consensus 109 ~L~~vpGIGkKtA~rIi~ELk~K~~~~~ 136 (207)
.++.-||+||-|+-+.+-+|..+...+.
T Consensus 4 ~ITGTPGvGKTT~~~~L~~lg~~~i~l~ 31 (180)
T COG1936 4 AITGTPGVGKTTVCKLLRELGYKVIELN 31 (180)
T ss_pred EEECCCCCCHHHHHHHHHHHCCCEEEHH
T ss_conf 9937999866879999998298466199
No 184
>TIGR03252 uncharacterized HhH-GPD family protein. This model describes a small, well-conserved bacterial protein family. Its sequence largely consists of a domain, HhH-GPD, found in a variety of related base excision DNA repair enzymes (see pfam00730).
Probab=44.65 E-value=20 Score=16.77 Aligned_cols=20 Identities=25% Similarity=0.522 Sum_probs=8.1
Q ss_pred HHHHHHHHC-CCCHHHHHHHH
Q ss_conf 999999967-99989999999
Q gi|254780553|r 162 NAISALVNL-GYGQDQATTAV 181 (207)
Q Consensus 162 d~~~AL~~L-Gy~~~ea~~ai 181 (207)
|+..-|..| ||.++.|+--+
T Consensus 112 ell~Rl~~LPGFG~qKA~IFl 132 (177)
T TIGR03252 112 ELLRRLKALPGFGKQKAKIFL 132 (177)
T ss_pred HHHHHHHHCCCCCHHHHHHHH
T ss_conf 999999867996199999999
No 185
>cd01017 AdcA Metal binding protein AcdA. These proteins have been shown to function in the ABC uptake of Zn2+ and Mn2+ and in competence for genetic transformation and adhesion. The AcdA proteins belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. They are comprised of two globular subdomains connected by a long alpha helix and they bind their ligand in the cleft between these domains. In addition, many of these proteins have a low complexity region containing metal binding histidine-rich motif (repetitive HDH sequence).
Probab=44.57 E-value=16 Score=17.47 Aligned_cols=13 Identities=8% Similarity=0.181 Sum_probs=7.1
Q ss_pred EEEECCEEEEEEC
Q ss_conf 9985883238970
Q gi|254780553|r 18 LIDVQGVCYIIYC 30 (207)
Q Consensus 18 vi~v~GvGY~i~v 30 (207)
++-++|.||+-.+
T Consensus 55 li~~nG~~lE~~l 67 (282)
T cd01017 55 VFVYNGLGMETWA 67 (282)
T ss_pred EEEEECCCCHHHH
T ss_conf 9999187836899
No 186
>PRK12402 replication factor C small subunit 2; Reviewed
Probab=44.51 E-value=17 Score=17.27 Aligned_cols=116 Identities=14% Similarity=0.151 Sum_probs=52.5
Q ss_pred EEEEEECHHHHHHHHHHHHHH---HCC-CHHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 899970677999999985010---005-1011244315789999999851566875104571167999999997422211
Q gi|254780553|r 59 RLFGFLSDLDRQWFMLLQSVQ---GVG-ARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMTELKGKAIS 134 (207)
Q Consensus 59 ~LyGF~~~~Er~~F~~Li~V~---GIG-pK~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~K~~~ 134 (207)
..|=|....+.+++..|..|- |+- +.-||..+...+-..+.+||..=... .-+-|+.+.+..+.++-+....
T Consensus 177 ~~i~F~~~s~~~i~~~L~~I~~~E~i~~~~~~l~~ia~~s~GdlR~ain~Lq~~----~~~~~~~~~~~~~~~~~~~~~~ 252 (337)
T PRK12402 177 LPLFFRPVPDDEIRSVLESIAAAEGVEISDDGLDLIAYYAEGDLRKAILTLQLA----AEAEGEVTTEAALEELSDTGTD 252 (337)
T ss_pred EEEECCCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHH----HHHCCCCCCHHHHHHHHCCCCH
T ss_conf 454358989999999999999984999899999999998699899999999999----8727997718899998778979
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHH----HHCCCCHHHHHHHHHHHHHHCC
Q ss_conf 011334432333334455556531589999999----9679998999999999985168
Q gi|254780553|r 135 LSSVVQQDMSCVNKEQAHICSMPSFAINAISAL----VNLGYGQDQATTAVVSVLKKEK 189 (207)
Q Consensus 135 ~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~AL----~~LGy~~~ea~~ai~~i~~~~~ 189 (207)
..... . ... ..+....++...+ ..-||+..++-+.+...+.+..
T Consensus 253 --~~i~~----~----~~~-~~~~~~~~~~~~~~~l~~~~g~~~~~il~~l~~~~~~~~ 300 (337)
T PRK12402 253 --ETVEE----A----LDA-AEAGDFTDARSLLDDLLIDEGLSGREVLRELLEVARRGY 300 (337)
T ss_pred --HHHHH----H----HHH-HHCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHC
T ss_conf --99999----9----999-984899999999999887559999999999999998747
No 187
>COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair]
Probab=44.45 E-value=2.8 Score=22.49 Aligned_cols=52 Identities=25% Similarity=0.398 Sum_probs=32.3
Q ss_pred HHHHHHHHCC-CHHHHHHHCCCCHHHHHHH---HHCCCHHHHHHCCCCCHHHHHHHHH
Q ss_conf 9985010005-1011244315789999999---8515668751045711679999999
Q gi|254780553|r 73 MLLQSVQGVG-ARVAMGVLSRITATELVES---IILQNSKVIAQIPGISMKIASRIMT 126 (207)
Q Consensus 73 ~~Li~V~GIG-pK~AL~iLs~l~~~~l~~a---I~~~D~~~L~~vpGIGkKtA~rIi~ 126 (207)
+.|.--.|.| +.-|..+-. .+.++.+- +.-.|...|.++||||.=||.-|..
T Consensus 76 evl~~W~gLGYysRArnL~~--~A~~v~~~~~G~~P~~~~~l~~LpGiG~yTa~Ail~ 131 (342)
T COG1194 76 EVLKAWEGLGYYSRARNLHK--AAQEVVERHGGEFPDDEEELAALPGVGPYTAGAILS 131 (342)
T ss_pred HHHHHHHHCCHHHHHHHHHH--HHHHHHHHCCCCCCCCHHHHHHCCCCCHHHHHHHHH
T ss_conf 99999871673789999999--999999981997999999998678973889999999
No 188
>PRK12278 50S ribosomal protein L21/unknown domain fusion protein; Provisional
Probab=44.28 E-value=11 Score=18.64 Aligned_cols=20 Identities=15% Similarity=0.429 Sum_probs=15.8
Q ss_pred CCHHHHHHCCCCCHHHHHHH
Q ss_conf 56687510457116799999
Q gi|254780553|r 105 QNSKVIAQIPGISMKIASRI 124 (207)
Q Consensus 105 ~D~~~L~~vpGIGkKtA~rI 124 (207)
+-..-|+++.|||++.++++
T Consensus 150 g~aDDLk~I~GIGP~~e~~L 169 (216)
T PRK12278 150 GEADDLTKITGVGPALAKKL 169 (216)
T ss_pred CCCCCCCEECCCCHHHHHHH
T ss_conf 89965436026588999999
No 189
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=43.12 E-value=26 Score=16.04 Aligned_cols=52 Identities=27% Similarity=0.309 Sum_probs=29.9
Q ss_pred EEEEEEEEECCEEEEEECCEEEEEECCHHHHHH--------CCCCCCEEEEEEEEEECCCC
Q ss_conf 899999960997999858832389708688985--------02479849999999973884
Q gi|254780553|r 5 IKGNIEGLYEDYVLIDVQGVCYIIYCPIRTLSC--------LGKIGDFCTLFVETHMRQDQ 57 (207)
Q Consensus 5 i~G~i~~~~~~~ivi~v~GvGY~i~vs~~~~~~--------l~~~g~~v~l~~~~~vrEd~ 57 (207)
++|++..+.++.+++|+ |.-.+=++|.+-+.. .-+.|+++.+|+.-.-.+++
T Consensus 308 V~G~Vv~v~~~~v~VDi-G~KseG~Ip~~E~~~~~~~~~~~~~kvGDei~v~V~k~ed~~G 367 (670)
T PRK00087 308 VKGTVVSVNENEVFVDV-GYKSEGVIPLEELTKDEDSSLKESVKVGDEIEVKVLKLENEDG 367 (670)
T ss_pred EEEEEEEEECCEEEEEE-CCCCCEEEEHHHHCCCCCCCCCCCCCCCCEEEEEEEEEECCCC
T ss_conf 99999999389899983-6784368889993667677733457999989999999868998
No 190
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=42.03 E-value=14 Score=17.95 Aligned_cols=23 Identities=13% Similarity=0.420 Sum_probs=15.4
Q ss_pred CCCHHHHHHCCCCCHHHHHHHHH
Q ss_conf 15668751045711679999999
Q gi|254780553|r 104 LQNSKVIAQIPGISMKIASRIMT 126 (207)
Q Consensus 104 ~~D~~~L~~vpGIGkKtA~rIi~ 126 (207)
+-+.+.|+.|.|+||..|+.|+-
T Consensus 505 tAsa~lL~~VsGL~kt~A~nIv~ 527 (780)
T COG2183 505 TASASLLSYVSGLNKTLAKNIVA 527 (780)
T ss_pred CCCHHHHHHHHHHCHHHHHHHHH
T ss_conf 27899998774025667899999
No 191
>pfam06514 PsbU Photosystem II 12 kDa extrinsic protein (PsbU). This family consists of several photosystem II 12 kDa extrinsic protein (PsbU) proteins from cyanobacteria and algae. PsbU is an extrinsic protein of the photosystem II complex of cyanobacteria and red algae. PsbU is known to stabilize the oxygen-evolving machinery of the photosystem II complex against heat-induced inactivation.
Probab=41.81 E-value=16 Score=17.43 Aligned_cols=25 Identities=24% Similarity=0.465 Sum_probs=21.3
Q ss_pred HHCCCHHHHHHCCCCCHHHHHHHHH
Q ss_conf 8515668751045711679999999
Q gi|254780553|r 102 IILQNSKVIAQIPGISMKIASRIMT 126 (207)
Q Consensus 102 I~~~D~~~L~~vpGIGkKtA~rIi~ 126 (207)
+.+.++..+.+.||..+..|.+|+.
T Consensus 59 lNNanvr~f~q~pGmYPtlA~kIv~ 83 (135)
T pfam06514 59 LNNANVRAFRQLPGMYPTLAGKIVK 83 (135)
T ss_pred CCCHHHHHHHHCCCCCHHHHHHHHH
T ss_conf 4647499998688846789999973
No 192
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=41.59 E-value=28 Score=15.88 Aligned_cols=52 Identities=25% Similarity=0.257 Sum_probs=25.1
Q ss_pred EEEEEEEEECCEEEEEECCEEEEEECCHHHHH--------HCCCCCCEEEEEEEEEECCCC
Q ss_conf 89999996099799985883238970868898--------502479849999999973884
Q gi|254780553|r 5 IKGNIEGLYEDYVLIDVQGVCYIIYCPIRTLS--------CLGKIGDFCTLFVETHMRQDQ 57 (207)
Q Consensus 5 i~G~i~~~~~~~ivi~v~GvGY~i~vs~~~~~--------~l~~~g~~v~l~~~~~vrEd~ 57 (207)
++|+|..+.++.+++|+|. -.+=.+|.+-+. ...+.|+++.+|+--.-.++.
T Consensus 39 V~GtVv~I~~d~VlVDIG~-KsEGiIP~~E~s~~~d~d~~e~vkvGDeIeV~Vi~~ed~eG 98 (484)
T PRK07899 39 VEGTVVKVDRDEVLLDIGY-KTEGVIPSRELSIKHDVDPNEVVSVGDEVEALVLTKEDKEG 98 (484)
T ss_pred EEEEEEEEECCEEEEEECC-CEEEEEEHHHHCCCCCCCCCCCCCCCCEEEEEEEEEECCCC
T ss_conf 9999999978989998268-70478799994667577845457899999999998737887
No 193
>TIGR01931 cysJ sulfite reductase [NADPH] flavoprotein, alpha-component; InterPro: IPR010199 This entry describes an NADPH-dependent sulphite reductase flavoprotein subunit. Most members of the proteins of this entry are found in Cys biosynthesis gene clusters. The closest homologues are designated as subunits nitrate reductase.; GO: 0004783 sulfite reductase (NADPH) activity, 0000103 sulfate assimilation, 0019344 cysteine biosynthetic process.
Probab=41.56 E-value=28 Score=15.88 Aligned_cols=41 Identities=24% Similarity=0.184 Sum_probs=31.8
Q ss_pred ECCEEEEEECCEEEEEE-------CCHHHHHHCCCCCCEEEEEEEEEEC
Q ss_conf 09979998588323897-------0868898502479849999999973
Q gi|254780553|r 13 YEDYVLIDVQGVCYIIY-------CPIRTLSCLGKIGDFCTLFVETHMR 54 (207)
Q Consensus 13 ~~~~ivi~v~GvGY~i~-------vs~~~~~~l~~~g~~v~l~~~~~vr 54 (207)
-+|.|+|-|+-|-|++. +|..+...+ +.|+.|.+||+..-+
T Consensus 426 v~dEVHlTVg~V~y~~~G~~r~GgaS~fLA~rl-~~gd~v~vyve~N~n 473 (628)
T TIGR01931 426 VDDEVHLTVGVVRYEAEGRARLGGASGFLAERL-EEGDTVKVYVERNDN 473 (628)
T ss_pred CCCEEEEEEEEEEEEECCEEEECCCHHHHHHHC-CCCCEEEEEEEECCC
T ss_conf 688068876688982056477441057788650-889767788751778
No 194
>cd01700 Pol_V Pol V was discovered in Escherichia coli as Umuc and UmuD proteins induced by UV. This branch of DNA polymerases is mostly found in bacteria. Pol V enables DNA replication to bypass covalently linked cys-sin T-T photo-dimers and 6-4 T-T or T-C photoproducts, which would otherwise stall the DNA replication fork.
Probab=41.43 E-value=28 Score=15.87 Aligned_cols=15 Identities=40% Similarity=0.678 Sum_probs=10.3
Q ss_pred CCCHHHHHHHHHHHH
Q ss_conf 889899999999974
Q gi|254780553|r 191 IADDSQIIRLALRAI 205 (207)
Q Consensus 191 ~~~~eelIk~aLk~L 205 (207)
..+++++.+.|++.|
T Consensus 311 T~~~~~I~~~a~~Ll 325 (344)
T cd01700 311 TSDTRDLIKAALRAL 325 (344)
T ss_pred CCCHHHHHHHHHHHH
T ss_conf 889999999999999
No 195
>pfam03352 Adenine_glyco Methyladenine glycosylase. The DNA-3-methyladenine glycosylase I is constitutively expressed and is specific for the alkylated 3-methyladenine DNA.
Probab=41.22 E-value=28 Score=15.84 Aligned_cols=114 Identities=18% Similarity=0.191 Sum_probs=60.3
Q ss_pred EEEEECHHHHHHHHHHHH-H--HHCCCHHHHH-------HHCCCCHHHHHHHHHCCCHHHHHHCCCCCH---H-H----H
Q ss_conf 999706779999999850-1--0005101124-------431578999999985156687510457116---7-9----9
Q gi|254780553|r 60 LFGFLSDLDRQWFMLLQS-V--QGVGARVAMG-------VLSRITATELVESIILQNSKVIAQIPGISM---K-I----A 121 (207)
Q Consensus 60 LyGF~~~~Er~~F~~Li~-V--~GIGpK~AL~-------iLs~l~~~~l~~aI~~~D~~~L~~vpGIGk---K-t----A 121 (207)
=+|+...+++.+|++|.= + .|.-=.+-|. ....++|+.+ ..-...|+..|..=|||=+ | . =
T Consensus 15 EWG~P~~dd~~LFE~L~LE~~QaGLSW~tIL~KR~~fr~aF~~Fd~~~V-A~~~e~~ie~Ll~d~~IIRnr~KI~Avi~N 93 (179)
T pfam03352 15 EWGVPVHDDRKLFELLCLEGFQAGLSWITILKKREAFREAFAGFDPEKV-AAFTEADVERLLADPGIIRNRLKIEATINN 93 (179)
T ss_pred CCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCHHHH-HCCCHHHHHHHHCCHHHHHHHHHHHHHHHH
T ss_conf 6898488879999999998973647899999879999999828999999-648999999985267878768999999999
Q ss_pred HHHHHHHHHHHHHCCCCCCC---CCCCCC--CCCCCCCCCCCHHHHHHHHHHHCCCCH
Q ss_conf 99999974222110113344---323333--344555565315899999999679998
Q gi|254780553|r 122 SRIMTELKGKAISLSSVVQQ---DMSCVN--KEQAHICSMPSFAINAISALVNLGYGQ 174 (207)
Q Consensus 122 ~rIi~ELk~K~~~~~~~~~~---~~~~~~--~~~~~~~~~~~~~~d~~~AL~~LGy~~ 174 (207)
.|.+++++....+|....=. ..+..+ ......+..++.....-..|+..||+=
T Consensus 94 A~~~l~i~~e~gSF~~ylW~fv~~~pi~~~~~~~~~ip~~t~~S~~isk~LKkrGFkF 151 (179)
T pfam03352 94 ARAILKLQEEFGSFSAYLWSFVDGKPIVNRWKSLAEVPAKTPLSDAISKDLKKRGFKF 151 (179)
T ss_pred HHHHHHHHHHCCCHHHHHHHHCCCCCCCCCCCCHHHCCCCCHHHHHHHHHHHHCCCEE
T ss_conf 9999999983799999998737998776885786556588987899999998787946
No 196
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=40.93 E-value=13 Score=18.01 Aligned_cols=17 Identities=24% Similarity=0.440 Sum_probs=13.4
Q ss_pred HHHHHCCCCCHHHHHHH
Q ss_conf 87510457116799999
Q gi|254780553|r 108 KVIAQIPGISMKIASRI 124 (207)
Q Consensus 108 ~~L~~vpGIGkKtA~rI 124 (207)
.-|+.+.|||+|.++++
T Consensus 67 DDLt~I~GIGPk~e~~L 83 (133)
T COG3743 67 DDLTRISGIGPKLEKVL 83 (133)
T ss_pred CCCHHHCCCCHHHHHHH
T ss_conf 54211004378899899
No 197
>TIGR00538 hemN oxygen-independent coproporphyrinogen III oxidase; InterPro: IPR004558 This family represents HemN, the oxygen-independent coproporphyrinogen III oxidase that replaces HemF function under anaerobic conditions. HemN catalyses the anaerobic transformation of coproporhyrinogen-III into protoporphyrinogen-IX during porphyrin biosynthesis. Several species, including Escherichia coli, Helicobacter pylori, and Aquifex aeolicus, have both a member of this family and a member of another, closely related family for which there is no evidence of coproporphyrinogen III oxidase activity, IPR004559 from INTERPRO. Members of this family have a perfectly conserved motif PYRT[SC]YP in a region N-terminal to the region of homology with the related uncharacterised protein.; GO: 0004109 coproporphyrinogen oxidase activity, 0006779 porphyrin biosynthetic process, 0005737 cytoplasm.
Probab=40.61 E-value=29 Score=15.78 Aligned_cols=72 Identities=15% Similarity=0.193 Sum_probs=45.7
Q ss_pred CHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCHH---------HHHHHHHHHHHH
Q ss_conf 16799999999742221101133443233333445555653158999999996799989---------999999999851
Q gi|254780553|r 117 SMKIASRIMTELKGKAISLSSVVQQDMSCVNKEQAHICSMPSFAINAISALVNLGYGQD---------QATTAVVSVLKK 187 (207)
Q Consensus 117 GkKtA~rIi~ELk~K~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~AL~~LGy~~~---------ea~~ai~~i~~~ 187 (207)
.+-=+++|.-++++.+.+|....+- +.+ ..-..+..|.+.||...||.+- ++++||.++
T Consensus 119 ~~~Q~~~l~~~i~~~F~nf~~daEi---SiE------idPR~~~~e~~~~L~~~GFNRlS~GvQDfd~~VQ~avnR~--- 186 (462)
T TIGR00538 119 SPEQIEELMKEIREAFPNFSEDAEI---SIE------IDPRYLTKEVIKALRDEGFNRLSFGVQDFDKEVQQAVNRI--- 186 (462)
T ss_pred CHHHHHHHHHHHHHHHHHHCCCCEE---EEE------ECCCCCCHHHHHHHHHCCCCEEECCEECCCHHHHHHHCCC---
T ss_conf 8899999999999873201158447---765------2374137889999997589664235210785554443134---
Q ss_pred CCCCCCHHHHHHHHHHHH
Q ss_conf 688889899999999974
Q gi|254780553|r 188 EKNIADDSQIIRLALRAI 205 (207)
Q Consensus 188 ~~~~~~~eelIk~aLk~L 205 (207)
. .+|+|++.++++
T Consensus 187 Q-----P~e~i~~~~~~~ 199 (462)
T TIGR00538 187 Q-----PEEMIFELMEKA 199 (462)
T ss_pred C-----CHHHHHHHHHHH
T ss_conf 8-----689999999999
No 198
>PTZ00205 DNA polymerase kappa; Provisional
Probab=40.16 E-value=14 Score=17.78 Aligned_cols=43 Identities=14% Similarity=0.305 Sum_probs=24.5
Q ss_pred HHCCCHHHHHHHCC-------------CCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHH
Q ss_conf 00051011244315-------------78999999985156687510457116799999
Q gi|254780553|r 79 QGVGARVAMGVLSR-------------ITATELVESIILQNSKVIAQIPGISMKIASRI 124 (207)
Q Consensus 79 ~GIGpK~AL~iLs~-------------l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rI 124 (207)
-||+|-.-|+=+.+ .+++++..-+.. --+.+|||||+=|++++
T Consensus 270 AGIApNK~LAKIASd~nKPNGQfvl~~~~r~~V~~F~~~---LPvRKIpGIGkVte~~L 325 (571)
T PTZ00205 270 AGIGPTAALAKIASNINKPNGQHDLNLHTRGDVMTYVRD---LGLRSVPGVGKVTEALL 325 (571)
T ss_pred ECCHHHHHHHHHHHCCCCCCCCEEECCCCHHHHHHHHHH---CCCCCCCCCCHHHHHHH
T ss_conf 554048999998762379898545458998999999983---89766897568889999
No 199
>pfam03459 TOBE TOBE domain. The TOBE domain (Transport-associated OB) always occurs as a dimer as the C-terminal strand of each domain is supplied by the partner. Probably involved in the recognition of small ligands such as molybdenum and sulfate. Found in ABC transporters immediately after the ATPase domain.
Probab=39.87 E-value=29 Score=15.71 Aligned_cols=47 Identities=17% Similarity=0.113 Sum_probs=37.5
Q ss_pred CEEEEEEEEEECC----EEEEEECCEEEEEECCHHHHHHCCCCCCEEEEEEE
Q ss_conf 2589999996099----79998588323897086889850247984999999
Q gi|254780553|r 3 GKIKGNIEGLYED----YVLIDVQGVCYIIYCPIRTLSCLGKIGDFCTLFVE 50 (207)
Q Consensus 3 ~~i~G~i~~~~~~----~ivi~v~GvGY~i~vs~~~~~~l~~~g~~v~l~~~ 50 (207)
..+.|++..+.+. .+.++++|-.....++......| +.|+++.+.+-
T Consensus 5 N~l~g~V~~ie~~g~~~~V~v~~~~~~l~a~it~~s~~~L-~~G~~V~~~ik 55 (61)
T pfam03459 5 NQLPGTVDVVEPLGSETEVRVDLGGGELTARITRRSAEEL-APGDEVYAGIK 55 (61)
T ss_pred CEEEEEEEEEEECCCEEEEEEEECCCEEEEEECHHHHHHC-CCCCEEEEEEE
T ss_conf 3887999999989976999999799389999848899655-99988999998
No 200
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=39.63 E-value=30 Score=15.68 Aligned_cols=72 Identities=14% Similarity=0.159 Sum_probs=47.2
Q ss_pred EEEEEEEEEECCEEEEEECCEEEEEECCHHHHH--------HCCCCCCEEEEEEEEEECCCCEEEEEEECHHHHHHHHHH
Q ss_conf 589999996099799985883238970868898--------502479849999999973884189997067799999998
Q gi|254780553|r 4 KIKGNIEGLYEDYVLIDVQGVCYIIYCPIRTLS--------CLGKIGDFCTLFVETHMRQDQIRLFGFLSDLDRQWFMLL 75 (207)
Q Consensus 4 ~i~G~i~~~~~~~ivi~v~GvGY~i~vs~~~~~--------~l~~~g~~v~l~~~~~vrEd~~~LyGF~~~~Er~~F~~L 75 (207)
-++|+|..+.++.+.+|+|+ .-+-++|.+-++ .+-+.|+.+.+++.-.-.++...+....-.+-..-+..|
T Consensus 34 iVeG~V~~I~~~~v~VdiG~-k~eG~i~~~E~s~~~~~~~~e~~~vGd~iev~V~~~~~~~g~i~LS~k~~~~~~~w~~l 112 (314)
T PRK07400 34 IVNGTVFSLEPKGALIDIGA-KTAAFMPLQEMSINRVEGPSEVLQPGETREFFILSEENEDGQLTLSIRRIEYMRAWERV 112 (314)
T ss_pred EEEEEEEEEECCEEEEEECC-CEEEEEEHHHHCCCCCCCCCCCCCCCCEEEEEEEEEECCCCCEEEEECHHHHHHHHHHH
T ss_conf 89999999979989999779-80799999993666568943013589769999999856889689986043212069999
Q ss_pred H
Q ss_conf 5
Q gi|254780553|r 76 Q 76 (207)
Q Consensus 76 i 76 (207)
.
T Consensus 113 ~ 113 (314)
T PRK07400 113 R 113 (314)
T ss_pred H
T ss_conf 9
No 201
>pfam08823 PG_binding_2 Putative peptidoglycan binding domain. This family may be a peptidoglycan binding domain.
Probab=39.58 E-value=14 Score=17.93 Aligned_cols=24 Identities=29% Similarity=0.307 Sum_probs=16.9
Q ss_pred CCCCCHHHHHHHHHHHCCCCHHHH
Q ss_conf 565315899999999679998999
Q gi|254780553|r 154 CSMPSFAINAISALVNLGYGQDQA 177 (207)
Q Consensus 154 ~~~~~~~~d~~~AL~~LGy~~~ea 177 (207)
....+...++.++|..|||-+.++
T Consensus 12 ~l~~dv~~ev~~~L~rLGyy~g~~ 35 (74)
T pfam08823 12 VLTGDVAEEVQAALSRLGYYKGEA 35 (74)
T ss_pred CCHHHHHHHHHHHHHHCCCCCCCC
T ss_conf 312899999999999838534887
No 202
>LOAD_Hrd consensus
Probab=38.57 E-value=20 Score=16.77 Aligned_cols=55 Identities=15% Similarity=0.216 Sum_probs=32.3
Q ss_pred HHHHHHHHHHHH-------HHCCCHHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHH
Q ss_conf 799999998501-------00051011244315789999999851566875104571167999999
Q gi|254780553|r 67 LDRQWFMLLQSV-------QGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIM 125 (207)
Q Consensus 67 ~Er~~F~~Li~V-------~GIGpK~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi 125 (207)
.+..+|..|... .|+= +-.|++.-...+++.. .-.+...|.+++|||++.++|-=
T Consensus 3 ~~~~l~~~L~~~R~~~A~~~~~p---~~~I~~~~~L~~ia~~-~P~t~~eL~~I~Gig~~k~~~yG 64 (77)
T LOAD_Hrd 3 EQARLLERLRELRKEIAKERGVS---PYSIFSDATLKEMAAL-LPTTVSELLAIDGVGEAKVEKYG 64 (77)
T ss_pred HHHHHHHHHHHHHHHHHHHCCCC---CEEEECHHHHHHHHHH-CCCCHHHHCCCCCCCHHHHHHHH
T ss_conf 17999999999999998756989---6445899999999997-89999998289996999999999
No 203
>KOG2457 consensus
Probab=38.28 E-value=10 Score=18.82 Aligned_cols=45 Identities=20% Similarity=0.226 Sum_probs=27.3
Q ss_pred HHHHHCCCHHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHH
Q ss_conf 5010005101124431578999999985156687510457116799
Q gi|254780553|r 76 QSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIA 121 (207)
Q Consensus 76 i~V~GIGpK~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA 121 (207)
..|.||||-+|=+|+| +-.++.--.+.-|=+..|+++--||.--.
T Consensus 209 kgvpGVG~YTAGAiaS-IAf~q~tGiVDGNVirvlsRalAIhsDcS 253 (555)
T KOG2457 209 KGVPGVGQYTAGAIAS-IAFNQVTGIVDGNVIRVLSRALAIHSDCS 253 (555)
T ss_pred HHCCCCCCCCHHHHHH-HHHCCCCCCCCCCHHHHHHHHHHHCCCCC
T ss_conf 5188877423104554-23047643204615777677676137743
No 204
>pfam03118 RNA_pol_A_CTD Bacterial RNA polymerase, alpha chain C terminal domain. The alpha subunit of RNA polymerase consists of two independently folded domains, referred to as amino-terminal and carboxyl terminal domains. The amino terminal domain is involved in the interaction with the other subunits of the RNA polymerase. The carboxyl-terminal domain interacts with the DNA and activators. The amino acid sequence of the alpha subunit is conserved in prokaryotic and chloroplast RNA polymerases. There are three regions of particularly strong conservation, two in the amino-terminal and one in the carboxyl- terminal.
Probab=37.25 E-value=29 Score=15.77 Aligned_cols=41 Identities=15% Similarity=0.161 Sum_probs=22.7
Q ss_pred HHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHH
Q ss_conf 244315789999999851566875104571167999999997
Q gi|254780553|r 87 MGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMTEL 128 (207)
Q Consensus 87 L~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~EL 128 (207)
...|.......+-+-+.- ...-|.++|++|+|+-+.|.--|
T Consensus 20 ~N~Lk~~~I~tv~dL~~~-s~~dLl~i~N~G~kSl~EI~~~L 60 (62)
T pfam03118 20 YNCLKRAGINTVGDLLSK-SEEDLLKIKNFGKKSLEEIKEKL 60 (62)
T ss_pred HHHHHHCCCCCHHHHHHC-CHHHHHHCCCCCHHHHHHHHHHH
T ss_conf 999989499679999858-99999748898685799999998
No 205
>PRK00440 rfc replication factor C small subunit; Reviewed
Probab=35.82 E-value=28 Score=15.89 Aligned_cols=46 Identities=11% Similarity=0.131 Sum_probs=24.4
Q ss_pred EEEEEECHHHHHHHHHHHHHHH---CC-CHHHHHHHCCCCHHHHHHHHHC
Q ss_conf 8999706779999999850100---05-1011244315789999999851
Q gi|254780553|r 59 RLFGFLSDLDRQWFMLLQSVQG---VG-ARVAMGVLSRITATELVESIIL 104 (207)
Q Consensus 59 ~LyGF~~~~Er~~F~~Li~V~G---IG-pK~AL~iLs~l~~~~l~~aI~~ 104 (207)
..|=|....+.+++..|..|.- +- +.-|+..+...+-.++..||..
T Consensus 153 ~~i~f~~~~~~~i~~~L~~I~~~E~i~~~~~~l~~i~~~s~gdlR~ain~ 202 (318)
T PRK00440 153 AVFRFSPLPKEAVIERLRYIAKNEGLEITDDALEAIYYVSEGDMRKAINA 202 (318)
T ss_pred EEEECCCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCCHHHHHHH
T ss_conf 01115789999999999999998599989999999998649989999999
No 206
>PRK05563 DNA polymerase III subunits gamma and tau; Validated
Probab=34.42 E-value=36 Score=15.15 Aligned_cols=20 Identities=20% Similarity=0.272 Sum_probs=15.9
Q ss_pred EEEEEECHHHHHHHHHHHHH
Q ss_conf 89997067799999998501
Q gi|254780553|r 59 RLFGFLSDLDRQWFMLLQSV 78 (207)
Q Consensus 59 ~LyGF~~~~Er~~F~~Li~V 78 (207)
.-|-|.--...+++..|..|
T Consensus 171 q~f~f~~i~~~~i~~~L~~I 190 (541)
T PRK05563 171 QRFDFKRIKVKDIFKRLRKI 190 (541)
T ss_pred EEEEEEECCHHHHHHHHHHH
T ss_conf 35775438999999999999
No 207
>PHA00542 putative Cro-like protein
Probab=34.05 E-value=36 Score=15.11 Aligned_cols=21 Identities=29% Similarity=0.468 Sum_probs=17.6
Q ss_pred HHHHHHHHHHCCCCHHHHHHH
Q ss_conf 899999999679998999999
Q gi|254780553|r 160 AINAISALVNLGYGQDQATTA 180 (207)
Q Consensus 160 ~~d~~~AL~~LGy~~~ea~~a 180 (207)
-.|.+.||...||.+.++...
T Consensus 20 P~E~V~aLi~~G~tQ~qI~~~ 40 (82)
T PHA00542 20 PDELVCALIRAGWSQEQIADA 40 (82)
T ss_pred HHHHHHHHHHCCCCHHHHHHH
T ss_conf 899999999822569999986
No 208
>PRK10409 hydrogenase isoenzymes formation protein; Provisional
Probab=33.95 E-value=36 Score=15.10 Aligned_cols=53 Identities=17% Similarity=0.200 Sum_probs=38.2
Q ss_pred CCCEEEEEEEEEECCEEEEEECCEEEEEECCHHHHH---HCCCCCCEEEEEEEEEE
Q ss_conf 932589999996099799985883238970868898---50247984999999997
Q gi|254780553|r 1 MIGKIKGNIEGLYEDYVLIDVQGVCYIIYCPIRTLS---CLGKIGDFCTLFVETHM 53 (207)
Q Consensus 1 MI~~i~G~i~~~~~~~ivi~v~GvGY~i~vs~~~~~---~l~~~g~~v~l~~~~~v 53 (207)
|==.+-|+|.++..+...+|++|+--+|.+..-.-. .-++.|+.|.+|+=+-+
T Consensus 1 MCLaIPg~Iv~I~~~~A~Vd~~Gv~r~V~l~lv~~~~~~~~~~vGDyVLVHvGfAi 56 (90)
T PRK10409 1 MCIGVPGQIRTIDGNQAKVDVCGIQRDVDLTLVGSCDENGQPRVGQWVLVHVGFAM 56 (90)
T ss_pred CCCCCCEEEEEECCCEEEEEECCCEEEEEEEEEECCCCCCCCCCCCEEEEECCEEH
T ss_conf 95045438999859889999578079998765404567775688989999705001
No 209
>TIGR00750 lao LAO/AO transport system ATPase; InterPro: IPR005129 Bacterial periplasmic transport systems require the function of a specific substrate-binding protein, located in the periplasm, and several cytoplasmic membrane transport components. In Escherichia coli K-12, the arginine-ornithine transport system requires an arginine-ornithine-binding protein and the lysine-arginine-ornithine (LAO) transport system includes a LAO-binding protein. Both periplasmic proteins can be phosphorylated by a single kinase, ArgK resulting in reduced levels of transport activity of the periplasmic transport systems that include each of the binding proteins. The ArgK protein acts as an ATPase enzyme and as a kinase..
Probab=32.29 E-value=29 Score=15.73 Aligned_cols=54 Identities=19% Similarity=0.255 Sum_probs=31.5
Q ss_pred HHHHHHHHCCCH---HHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHH-HHHHHHHHHH
Q ss_conf 998501000510---1124431578999999985156687510457116799-9999997422
Q gi|254780553|r 73 MLLQSVQGVGAR---VAMGVLSRITATELVESIILQNSKVIAQIPGISMKIA-SRIMTELKGK 131 (207)
Q Consensus 73 ~~Li~V~GIGpK---~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA-~rIi~ELk~K 131 (207)
+.+.=|.-=.|+ .|-.||..+.|. -=+--.--+|-+||+||=|+ +|++-+|..+
T Consensus 8 raiTLVEn~~p~H~~~a~~ll~~i~p~-----~GnA~~vG~TG~PGaGKSTl~~~l~~~lrRr 65 (333)
T TIGR00750 8 RAITLVENEEPEHRELAKELLERILPK-----TGNAHVVGITGVPGAGKSTLVEKLIMELRRR 65 (333)
T ss_pred HHHHHHCCCCCHHHHHHHHHHHHHHHH-----CCCCEEEEEECCCCCCHHHHHHHHHHHHHHC
T ss_conf 787443487970479999999986243-----2790787664688885777999998999765
No 210
>TIGR02606 antidote_CC2985 putative addiction module antidote protein, CC2985 family; InterPro: IPR005360 Proteins in this entry are almost always found adjacent to a plasmid stabilisation protein (IPR007712 from INTERPRO), which is the killing partner of an addiction module for plasmid stabilisation. Proteins in this entry, therefore, are putative addiction module antidote proteins. Some are encoded on plasmids or in prophage regions, but others appear to be chromosomal. A genome may contain several identical copies, for example four are found in Magnetococcus sp. MC-1. This entry is named after one member, CC2985 of Caulobacter crescentus CB15..
Probab=31.84 E-value=28 Score=15.82 Aligned_cols=14 Identities=36% Similarity=0.643 Sum_probs=10.3
Q ss_pred CCHHHHHHHHHHHH
Q ss_conf 89899999999974
Q gi|254780553|r 192 ADDSQIIRLALRAI 205 (207)
Q Consensus 192 ~~~eelIk~aLk~L 205 (207)
.+..|+||.|||.|
T Consensus 24 gsaSEVvR~aLRlL 37 (77)
T TIGR02606 24 GSASEVVRAALRLL 37 (77)
T ss_pred CCHHHHHHHHHHHH
T ss_conf 98636999999861
No 211
>PRK03839 putative kinase; Provisional
Probab=30.91 E-value=25 Score=16.16 Aligned_cols=18 Identities=17% Similarity=0.230 Sum_probs=12.3
Q ss_pred HHHHHHHHCCCCHHHHHH
Q ss_conf 999999967999899999
Q gi|254780553|r 162 NAISALVNLGYGQDQATT 179 (207)
Q Consensus 162 d~~~AL~~LGy~~~ea~~ 179 (207)
.+..-|..=||+++-++.
T Consensus 92 iL~~RL~~RgYs~~KI~E 109 (180)
T PRK03839 92 LIAERLKERGYSKKKIGE 109 (180)
T ss_pred HHHHHHHHCCCCHHHHHH
T ss_conf 999999976999899999
No 212
>PRK04040 adenylate kinase; Provisional
Probab=30.64 E-value=29 Score=15.72 Aligned_cols=20 Identities=20% Similarity=0.346 Sum_probs=11.7
Q ss_pred HHHHCCCCCHHHHHHHHHHH
Q ss_conf 75104571167999999997
Q gi|254780553|r 109 VIAQIPGISMKIASRIMTEL 128 (207)
Q Consensus 109 ~L~~vpGIGkKtA~rIi~EL 128 (207)
.++.+||+||-|--+.+.+.
T Consensus 6 vvtGiPGvGKTTv~~~~~~~ 25 (189)
T PRK04040 6 VVTGVPGVGKTTVLNKALEK 25 (189)
T ss_pred EEECCCCCCHHHHHHHHHHH
T ss_conf 99758988789999999997
No 213
>cd04455 S1_NusA S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three RNA binding domains (RBD's). The RBD's include one S1 domain and two KH domains that form an RNA binding surface. DNA transcription by RNA polymerase (RNAP) includes three phases - initiation, elongation, and termination. During initiation, sigma factors bind RNAP and target RNAP to specific promoters. During elongation, N-utilization substances (NusA, B, E, and G) replace sigma factors and regulate pausing, termination, and antitermination. NusA is cold-shock-inducible.
Probab=30.01 E-value=42 Score=14.68 Aligned_cols=49 Identities=14% Similarity=0.214 Sum_probs=37.7
Q ss_pred EEEEEEEEEECCEEEEEECCEEEEEECCHHHHHHCC----CCCCEEEEEEEEEECCC
Q ss_conf 589999996099799985883238970868898502----47984999999997388
Q gi|254780553|r 4 KIKGNIEGLYEDYVLIDVQGVCYIIYCPIRTLSCLG----KIGDFCTLFVETHMRQD 56 (207)
Q Consensus 4 ~i~G~i~~~~~~~ivi~v~GvGY~i~vs~~~~~~l~----~~g~~v~l~~~~~vrEd 56 (207)
-++|++...+...+++|.++ -+-.+|.+- .+| +.|+.++.|+.-.-++.
T Consensus 6 iv~G~V~r~~~~~v~vdlg~--~eailp~~e--qip~E~~~~Gdrik~~i~~V~~~~ 58 (67)
T cd04455 6 IVTGIVKRVDRGNVIVDLGK--VEAILPKKE--QIPGESYRPGDRIKAYVLEVRKTS 58 (67)
T ss_pred EEEEEEEEEECCCEEEEECC--CEEECCHHH--CCCCCCCCCCCEEEEEEEEEEECC
T ss_conf 89999999808979999899--489737899--578866399998999999987469
No 214
>PRK12311 rpsB 30S ribosomal protein S2; Provisional
Probab=29.86 E-value=28 Score=15.90 Aligned_cols=20 Identities=15% Similarity=0.353 Sum_probs=13.1
Q ss_pred CCHHHHHHCCCCCHHHHHHH
Q ss_conf 56687510457116799999
Q gi|254780553|r 105 QNSKVIAQIPGISMKIASRI 124 (207)
Q Consensus 105 ~D~~~L~~vpGIGkKtA~rI 124 (207)
+-..-|++++|||||.++++
T Consensus 266 g~~ddl~ki~gvgp~~~~~l 285 (332)
T PRK12311 266 GAPDDLKKLTGVSGAIEKKL 285 (332)
T ss_pred CCCCHHHHHCCCCHHHHHHH
T ss_conf 98425777157678899985
No 215
>PTZ00296 choline kinase; Provisional
Probab=29.74 E-value=43 Score=14.64 Aligned_cols=63 Identities=11% Similarity=0.111 Sum_probs=36.6
Q ss_pred EEEEE------EECHHHHHHHHHHHHHHHCCCHHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHH
Q ss_conf 18999------70677999999985010005101124431578999999985156687510457116799999
Q gi|254780553|r 58 IRLFG------FLSDLDRQWFMLLQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRI 124 (207)
Q Consensus 58 ~~LyG------F~~~~Er~~F~~Li~V~GIGpK~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rI 124 (207)
..+|| |--..|...|+ +++=.|+|||+ +++-..--.+|++.+. .=+..-| +-|-|-.+.|+|+
T Consensus 141 vRIYG~~td~fiDR~~E~~vF~-lLSe~glGPKL-yG~FpnGRIEEFI~gr-tLtt~dL-rdP~IS~~IA~kL 209 (439)
T PTZ00296 141 FRIYGKDVDALYNPISEFEVYK-TMSKYKIAPLL-LNTFDGGRIEEWLYGD-PLRIDDL-KNKSILIGIANVL 209 (439)
T ss_pred EEECCCCCCEEECHHHHHHHHH-HHHHCCCCCEE-EEECCCCEEEEEECCC-CCCHHHC-CCHHHHHHHHHHH
T ss_conf 9973699554767289999999-99867999807-9983895678740784-2796785-6988999999999
No 216
>COG0507 RecD ATP-dependent exoDNAse (exonuclease V), alpha subunit - helicase superfamily I member [DNA replication, recombination, and repair]
Probab=29.60 E-value=31 Score=15.58 Aligned_cols=52 Identities=21% Similarity=0.323 Sum_probs=37.7
Q ss_pred HHHHHCCCHHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHH
Q ss_conf 501000510112443157899999998515668751045711679999999974
Q gi|254780553|r 76 QSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMTELK 129 (207)
Q Consensus 76 i~V~GIGpK~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk 129 (207)
-...|+|++.+-.+.+.+. +... -+...+...+..++|+|+|.++.+...+.
T Consensus 83 ~~~~G~~~~~~~~i~~~~~-~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 134 (696)
T COG0507 83 DLFKGKGKLTAEKIVATFG-DGTL-DIIASTPSLLLEVSGIGKKKAWAIKSQLS 134 (696)
T ss_pred HHCCCCCHHHHHHHHHHCC-CCCH-HHHHCCCHHHHHCCCCCCHHHHHHHHHHH
T ss_conf 7608962210888875313-4430-02330734444303522001677765543
No 217
>TIGR01703 hybrid_clust hydroxylamine reductase; InterPro: IPR010048 Hybrid cluster proteins (HCP, or Prismane) have been identified in bacteria, archaea and eukaryotic protozoa. No specific function has yet been assigned to these proteins, but it may involve oxidoreductase enzymatic activity. These proteins contain one 4Fe-4S cluster, and one hybrid 4Fe-2O-2S cluster, the latter being similar to the Ni-Fe-S cluster found in carbon monoxide dehydrogenase enzymes (IPR010047 from INTERPRO) , . This subfamily is heterogeneous with respect to the presence or absence of a region of about 100 amino acids not far from the N terminus of the protein. Members have been described as monomeric. ; GO: 0016661 oxidoreductase activity acting on other nitrogenous compounds as donors, 0051536 iron-sulfur cluster binding, 0006118 electron transport, 0005737 cytoplasm.
Probab=29.27 E-value=43 Score=14.59 Aligned_cols=35 Identities=26% Similarity=0.293 Sum_probs=29.2
Q ss_pred HHCCCCHHHHHHHHHHHHHHCCCC--CCHHHHHHHHH
Q ss_conf 967999899999999998516888--89899999999
Q gi|254780553|r 168 VNLGYGQDQATTAVVSVLKKEKNI--ADDSQIIRLAL 202 (207)
Q Consensus 168 ~~LGy~~~ea~~ai~~i~~~~~~~--~~~eelIk~aL 202 (207)
..|||+..|+...+.+++...... .|.+++|-+||
T Consensus 174 ~~Lgy~d~eI~~f~~~~La~~~~~~n~D~~~li~l~L 210 (567)
T TIGR01703 174 RVLGYDDEEIYAFLEEALAALLTNVNRDLDELIDLAL 210 (567)
T ss_pred HHHCCCCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHH
T ss_conf 9808888468999999998307874667789999975
No 218
>COG1415 Uncharacterized conserved protein [Function unknown]
Probab=29.18 E-value=26 Score=16.11 Aligned_cols=76 Identities=13% Similarity=0.052 Sum_probs=35.7
Q ss_pred CCHHHHHHHH--HCCCHHHHHHCCCCCHHHHHHH--HHHHHHHHH-HCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHH
Q ss_conf 7899999998--5156687510457116799999--999742221-1011334432333334455556531589999999
Q gi|254780553|r 93 ITATELVESI--ILQNSKVIAQIPGISMKIASRI--MTELKGKAI-SLSSVVQQDMSCVNKEQAHICSMPSFAINAISAL 167 (207)
Q Consensus 93 l~~~~l~~aI--~~~D~~~L~~vpGIGkKtA~rI--i~ELk~K~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~AL 167 (207)
+++..+..+- .-.|-+.|--+||||++|..-+ +.|+=.... ++..-..-.....+++...........++++..|
T Consensus 261 i~~~~l~~~ye~~p~Df~elLl~~GiGpstvRALalVAEvIyg~~~s~rDP~~yafA~GGKDgvP~pV~~~~yde~I~~l 340 (373)
T COG1415 261 LNWRRLRRLYELNPDDFEELLLVPGIGPSTVRALALVAEVIYGEPPSFRDPVKYAFAVGGKDGVPFPVNRKTYDELIEFL 340 (373)
T ss_pred CCHHHHHHHHHCCCCCHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHCCCCCCCCCCCHHHHHHHHHHH
T ss_conf 76999976644683249998740687889999999999998089988677046433305878998775530299999999
Q ss_pred H
Q ss_conf 9
Q gi|254780553|r 168 V 168 (207)
Q Consensus 168 ~ 168 (207)
.
T Consensus 341 ~ 341 (373)
T COG1415 341 E 341 (373)
T ss_pred H
T ss_conf 9
No 219
>COG0298 HypC Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=28.78 E-value=44 Score=14.54 Aligned_cols=52 Identities=25% Similarity=0.309 Sum_probs=38.8
Q ss_pred CCCEEEEEEEEEECC--EEEEEECCEEEEEECCHHHHHHCCCCCCEEEEEEEEEEC
Q ss_conf 932589999996099--799985883238970868898502479849999999973
Q gi|254780553|r 1 MIGKIKGNIEGLYED--YVLIDVQGVCYIIYCPIRTLSCLGKIGDFCTLFVETHMR 54 (207)
Q Consensus 1 MI~~i~G~i~~~~~~--~ivi~v~GvGY~i~vs~~~~~~l~~~g~~v~l~~~~~vr 54 (207)
|==.+-|++.++.++ ..++|++||--+|++..-.- . .+.|+.|.+|+-+.+.
T Consensus 1 MClaiPgqI~~I~~~~~~A~Vd~gGvkreV~l~Lv~~-~-v~~GdyVLVHvGfAi~ 54 (82)
T COG0298 1 MCLAIPGQIVEIDDNNHLAIVDVGGVKREVNLDLVGE-E-VKVGDYVLVHVGFAMS 54 (82)
T ss_pred CCCCCCCEEEEEECCCCEEEEEECCEEEEEEEEEECC-C-CCCCCEEEEEEEEEEE
T ss_conf 9326672789980788558998656768987533047-5-3347789999508876
No 220
>pfam00834 Ribul_P_3_epim Ribulose-phosphate 3 epimerase family. This enzyme catalyses the conversion of D-ribulose 5-phosphate into D-xylulose 5-phosphate.
Probab=28.30 E-value=45 Score=14.48 Aligned_cols=105 Identities=11% Similarity=0.060 Sum_probs=71.1
Q ss_pred ECCEEEEEE--CCEEEEEECCHHHHHHCCCCCCEEEEEEEEEECCC----------CEEEEEEECHHHHHHHHHHHHHHH
Q ss_conf 099799985--88323897086889850247984999999997388----------418999706779999999850100
Q gi|254780553|r 13 YEDYVLIDV--QGVCYIIYCPIRTLSCLGKIGDFCTLFVETHMRQD----------QIRLFGFLSDLDRQWFMLLQSVQG 80 (207)
Q Consensus 13 ~~~~ivi~v--~GvGY~i~vs~~~~~~l~~~g~~v~l~~~~~vrEd----------~~~LyGF~~~~Er~~F~~Li~V~G 80 (207)
+-+++.+|+ |-+-=.+.........+. ....+.+-+|+-|.+- ...++-|.-.......+.+-.+..
T Consensus 25 g~d~iHiDimDG~FVpn~t~g~~~i~~ir-~~t~~~~DvHLMv~~P~~~i~~~~~~g~d~i~~H~E~~~~~~~~i~~ik~ 103 (201)
T pfam00834 25 GADWLHVDVMDGHFVPNLTIGPLVVEALR-PLTELPLDVHLMVEEPDRIIPDFAEAGADIISFHAEASDHPHRTIQLIKE 103 (201)
T ss_pred CCCEEEEECCCCCCCCCCCCCHHHHHHHH-HCCCCCEEEEEEEECHHHHHHHHHHCCCCEEEECHHHHHCHHHHHHHHHH
T ss_conf 99989982767972775555877999998-63899638999983776639999873998899754441379999999986
Q ss_pred CCCHHHHHHHCCCCHHHHHHHHHCCCHH-HHHHCCCCCH
Q ss_conf 0510112443157899999998515668-7510457116
Q gi|254780553|r 81 VGARVAMGVLSRITATELVESIILQNSK-VIAQIPGISM 118 (207)
Q Consensus 81 IGpK~AL~iLs~l~~~~l~~aI~~~D~~-~L~~vpGIGk 118 (207)
-|-|..|++--.-+.+.+...+..=|.- .++--||.|-
T Consensus 104 ~g~k~GlAlnP~T~~~~l~~~l~~iD~VLvMtV~PGf~G 142 (201)
T pfam00834 104 AGAKAGLVLNPATPLDAIEYLLDDLDLVLLMSVNPGFGG 142 (201)
T ss_pred CCCEEEEEECCCCCCHHHHHHHHHCCEEEEEEECCCCCC
T ss_conf 497268885699860288876742798999886689887
No 221
>TIGR02624 rhamnu_1P_ald rhamnulose-1-phosphate aldolase; InterPro: IPR013447 Proteins in this entry match the enzyme RhaD, rhamnulose-1-phosphate aldolase (4.1.2.19 from EC).; GO: 0008994 rhamnulose-1-phosphate aldolase activity.
Probab=28.10 E-value=25 Score=16.19 Aligned_cols=10 Identities=20% Similarity=0.282 Sum_probs=5.9
Q ss_pred CCCHHHHHHH
Q ss_conf 7116799999
Q gi|254780553|r 115 GISMKIASRI 124 (207)
Q Consensus 115 GIGkKtA~rI 124 (207)
+||++||+++
T Consensus 192 EIG~~TAekM 201 (273)
T TIGR02624 192 EIGEATAEKM 201 (273)
T ss_pred HHHHHHHHHH
T ss_conf 5678999987
No 222
>cd01018 ZntC Metal binding protein ZntC. These proteins are predicted to function as initial receptors in ABC transport of metal ions. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. They are comprised of two globular subdomains connected by a long alpha helix and bind their specific ligands in the cleft between these domains. In addition, many of these proteins possess a metal-binding histidine-rich motif (repetitive HDH sequence).
Probab=27.61 E-value=41 Score=14.73 Aligned_cols=11 Identities=18% Similarity=0.033 Sum_probs=5.9
Q ss_pred EEEECCEEEEE
Q ss_conf 99858832389
Q gi|254780553|r 18 LIDVQGVCYII 28 (207)
Q Consensus 18 vi~v~GvGY~i 28 (207)
++-++|.||+.
T Consensus 54 lvv~~G~~lE~ 64 (266)
T cd01018 54 LYFRIGLGFEE 64 (266)
T ss_pred EEEEECCCHHH
T ss_conf 99995873458
No 223
>TIGR02142 modC_ABC molybdate ABC transporter, ATP-binding protein; InterPro: IPR011868 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain . The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , . The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , . Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). This entry represents the ATP-binding cassette (ABC) protein of the three subunit molybdate ABC transporter. The three proteins of this complex are homologous to proteins of the sulphate ABC transporter. Molybdenum may be used in nitrogenases of nitrogen-fixing bacteria and in molybdopterin cofactors. In some cases, molybdate may be transported by a sulphate transporter rather than by a specific molybdate transporter.; GO: 0005524 ATP binding, 0015098 molybdate ion transmembrane transporter activity, 0015689 molybdate ion transport, 0009276 1-2nm peptidoglycan-based cell wall.
Probab=27.15 E-value=15 Score=17.75 Aligned_cols=43 Identities=14% Similarity=0.185 Sum_probs=33.4
Q ss_pred CCEEEEEEEEEECCCCEEEEEEECHHHHH---HHHHHHHHHHCCCHHH
Q ss_conf 98499999999738841899970677999---9999850100051011
Q gi|254780553|r 42 GDFCTLFVETHMRQDQIRLFGFLSDLDRQ---WFMLLQSVQGVGARVA 86 (207)
Q Consensus 42 g~~v~l~~~~~vrEd~~~LyGF~~~~Er~---~F~~Li~V~GIGpK~A 86 (207)
=|+.+||.|+.||+|= .||.....=.+ =|..++.+=||||=+-
T Consensus 81 FQeA~LFPHl~Vr~NL--~YG~~~~~~~~r~i~~~~v~~lLgi~hLL~ 126 (361)
T TIGR02142 81 FQEARLFPHLSVRGNL--RYGMKRARPKERRISFERVIELLGIEHLLE 126 (361)
T ss_pred EECCEECCCHHHHHHH--HCCCCCCCHHHCCCCHHHHHHHHCCCCCCC
T ss_conf 8535507852334551--257210574121378899998746751121
No 224
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=25.99 E-value=49 Score=14.22 Aligned_cols=35 Identities=23% Similarity=0.431 Sum_probs=25.9
Q ss_pred CCEEEEEEEEEECCEEEEEEC-CEEEEEECCHHHHHHC
Q ss_conf 325899999960997999858-8323897086889850
Q gi|254780553|r 2 IGKIKGNIEGLYEDYVLIDVQ-GVCYIIYCPIRTLSCL 38 (207)
Q Consensus 2 I~~i~G~i~~~~~~~ivi~v~-GvGY~i~vs~~~~~~l 38 (207)
++-|.|+|.++.+++++++++ |+ ++.+..+.....
T Consensus 63 ~gGi~G~I~~v~d~~v~leia~gv--~i~~~r~aI~~V 98 (107)
T PRK05585 63 NGGIIGKVTKVSEDFVIIELNDDT--EIKIQKSAIAAV 98 (107)
T ss_pred CCCCEEEEEEEECCEEEEEECCCC--EEEEEHHHHHHH
T ss_conf 998589999997998999988995--899995896643
No 225
>TIGR02194 GlrX_NrdH Glutaredoxin-like protein NrdH; InterPro: IPR011909 Glutaredoxins , , , also known as thioltransferases (disulphide reductases, are small proteins of approximately one hundred amino-acid residues which utilise glutathione and NADPH as cofactors. Oxidized glutathione is regenerated by glutathione reductase. Together these components compose the glutathione system . Glutaredoxin functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. Like thioredoxin, which functions in a similar way, glutaredoxin possesses an active centre disulphide bond . It exists in either a reduced or an oxidized form where the two cysteine residues are linked in an intramolecular disulphide bond. Glutaredoxin has been sequenced in a variety of species. On the basis of extensive sequence similarity, it has been proposed that Vaccinia virus protein O2L is most probably a glutaredoxin. Finally, it must be noted that Bacteriophage T4 thioredoxin seems also to be evolutionary related. In position 5 of the pattern T4 thioredoxin has Val instead of Pro. NrdH-redoxin is a representative of a class of small redox proteins that contain a conserved CXXC motif and are characterised by a glutaredoxin-like amino acid sequence and thioredoxin-like activity profile. Unlike other the glutaredoxins to which it is most closely related, NrdH aparrently does not interact with glutathione/glutathione reductase, but rather with thioredoxin reductase to catalyze the reduction of ribonucleotide reductase .; GO: 0006118 electron transport, 0045454 cell redox homeostasis.
Probab=25.99 E-value=30 Score=15.68 Aligned_cols=19 Identities=21% Similarity=0.223 Sum_probs=14.5
Q ss_pred CHHHHHHHHHHHCCCCHHH
Q ss_conf 1589999999967999899
Q gi|254780553|r 158 SFAINAISALVNLGYGQDQ 176 (207)
Q Consensus 158 ~~~~d~~~AL~~LGy~~~e 176 (207)
+...|+++-|++|||....
T Consensus 32 d~~pea~d~vk~lGF~~~P 50 (72)
T TIGR02194 32 DEQPEAVDYVKALGFRQVP 50 (72)
T ss_pred CCCHHHHHHHHHCCCEECC
T ss_conf 8884378999874863076
No 226
>TIGR00601 rad23 UV excision repair protein Rad23; InterPro: IPR004806 All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. Rad23 contains a ubiquitin-like domain that interacts with catalytically active proteasomes and two ubiquitin (Ub)-associated (UBA) sequences that bind Ub. Rad23 interacts with ubiquitinated cellular proteins through the synergistic action of its UBA domains. In humans, Rad23 complexes with the XPC protein.; GO: 0006289 nucleotide-excision repair, 0005634 nucleus.
Probab=25.71 E-value=50 Score=14.18 Aligned_cols=23 Identities=17% Similarity=0.530 Sum_probs=10.1
Q ss_pred HHHHHHHHCC---CCHHHHHHHHHHH
Q ss_conf 9999999679---9989999999999
Q gi|254780553|r 162 NAISALVNLG---YGQDQATTAVVSV 184 (207)
Q Consensus 162 d~~~AL~~LG---y~~~ea~~ai~~i 184 (207)
..+.-.+.+| |.+.++.+|++..
T Consensus 194 ~~~~~Im~MGGGmYeRe~V~rALRAa 219 (453)
T TIGR00601 194 ETIEEIMEMGGGMYEREEVERALRAA 219 (453)
T ss_pred HHHHHHHHCCCCCCHHHHHHHHHHHH
T ss_conf 89999986278835088999999740
No 227
>TIGR01166 cbiO cobalt ABC transporter, ATP-binding protein; InterPro: IPR005876 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain . The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , . The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , . Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). This entry represents the ATP binding subunit of the multisubunit cobalt transporter in bacteria and its equivalents in archaea. This superfamily includes two groups, one which catalyses the uptake of small molecules, including ions from the external milieu and the other group which is engaged in the efflux of small molecular weight compounds and ions from within the cell. Energy derived from the hydrolysis of ATP drives both the process of uptake and efflux.; GO: 0006824 cobalt ion transport, 0009276 1-2nm peptidoglycan-based cell wall.
Probab=25.53 E-value=35 Score=15.17 Aligned_cols=85 Identities=13% Similarity=0.092 Sum_probs=46.8
Q ss_pred HHHCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCC--CCC---------------CCCCCCCCCCCHHHHH
Q ss_conf 98515668751045711679999999974222110113344323--333---------------3445555653158999
Q gi|254780553|r 101 SIILQNSKVIAQIPGISMKIASRIMTELKGKAISLSSVVQQDMS--CVN---------------KEQAHICSMPSFAINA 163 (207)
Q Consensus 101 aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~K~~~~~~~~~~~~~--~~~---------------~~~~~~~~~~~~~~d~ 163 (207)
++..+...+|--..|=||-| ++..|.|-+..-.....-+-. ... -+..++--.+++.+|+
T Consensus 14 ~~~~G~~~aLlG~NGaGKsT---Ll~~LnG~LrP~~G~v~~dG~~l~YsrkgL~~~R~~V~~VfQdPDDQlF~a~V~~DV 90 (190)
T TIGR01166 14 AVERGEVLALLGANGAGKST---LLLHLNGLLRPQSGKVLLDGEPLDYSRKGLLEVRQRVGLVFQDPDDQLFAADVDQDV 90 (190)
T ss_pred EECCCCEEEEECCCCCCHHH---HHHHHCCCCCCCCCEEEECCEECCCCCHHHHHHCCEEEEEEECHHHHCCCCCCCCCC
T ss_conf 22057168987289985789---988743677797555876785403572446752503003762634420267622100
Q ss_pred HHHHHHCCCCHHHHHHHHHHHHHHC
Q ss_conf 9999967999899999999998516
Q gi|254780553|r 164 ISALVNLGYGQDQATTAVVSVLKKE 188 (207)
Q Consensus 164 ~~AL~~LGy~~~ea~~ai~~i~~~~ 188 (207)
-=.+.|||-++.|+++.|.+++...
T Consensus 91 aFGPlNLGL~e~Ev~~RV~eAL~~v 115 (190)
T TIGR01166 91 AFGPLNLGLSEAEVERRVREALTAV 115 (190)
T ss_pred CCCCCCCCCCHHHHHHHHHHHHHHC
T ss_conf 3354567337157678789999860
No 228
>COG0389 DinP Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]
Probab=24.79 E-value=40 Score=14.82 Aligned_cols=17 Identities=12% Similarity=0.210 Sum_probs=12.4
Q ss_pred HHHHCCCCCHHHHHHHH
Q ss_conf 75104571167999999
Q gi|254780553|r 109 VIAQIPGISMKIASRIM 125 (207)
Q Consensus 109 ~L~~vpGIGkKtA~rIi 125 (207)
-+..++|||+.|++++-
T Consensus 177 pv~~~~GvG~~~~~~l~ 193 (354)
T COG0389 177 PVLEFWGVGKVTAEKLR 193 (354)
T ss_pred CHHHHCCCCHHHHHHHH
T ss_conf 56772684589999999
No 229
>PRK04195 replication factor C large subunit; Provisional
Probab=24.69 E-value=37 Score=15.04 Aligned_cols=44 Identities=16% Similarity=0.068 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCC-CCHHHHHHHHHHHHC
Q ss_conf 589999999967999899999999998516888-898999999999745
Q gi|254780553|r 159 FAINAISALVNLGYGQDQATTAVVSVLKKEKNI-ADDSQIIRLALRAIS 206 (207)
Q Consensus 159 ~~~d~~~AL~~LGy~~~ea~~ai~~i~~~~~~~-~~~eelIk~aLk~Ls 206 (207)
...++..++.++-.++.+.-..+.+ +.+.. .+.++ +..|...||
T Consensus 242 ~~~~a~~~~~~~d~dpd~~~~wi~e---Nip~~y~~~~~-~~~a~~~ls 286 (403)
T PRK04195 242 NYDQALEASYDVDEDPDDLIQWIDE---NIPKEYKDPED-LARAYEALS 286 (403)
T ss_pred CHHHHHHHHHCCCCCHHHHHHHHHH---CCCCCCCCHHH-HHHHHHHHH
T ss_conf 8999999885247998999999996---28644799999-999999998
No 230
>COG3880 Modulator of heat shock repressor CtsR, McsA [Signal transduction mechanisms]
Probab=24.64 E-value=52 Score=14.05 Aligned_cols=65 Identities=14% Similarity=0.175 Sum_probs=44.5
Q ss_pred HHHHHHHHHCCCHHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCC-CCHHHHHHH-HHHHHHHHHHCCC
Q ss_conf 99985010005101124431578999999985156687510457-116799999-9997422211011
Q gi|254780553|r 72 FMLLQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPG-ISMKIASRI-MTELKGKAISLSS 137 (207)
Q Consensus 72 F~~Li~V~GIGpK~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpG-IGkKtA~rI-i~ELk~K~~~~~~ 137 (207)
|+.++.+.-.|-----+--.. ....++.-+..+...-.-++|+ +|++++-|. |..|++.+.++..
T Consensus 84 fk~f~~~g~fGCaeCY~tf~~-~i~pi~~rvq~g~~~H~GK~P~~~~~~i~~~~~I~~L~e~Lq~~i~ 150 (176)
T COG3880 84 FKEFIQSGLFGCAECYKTFES-QISPIITRVQGGYVEHVGKVPKRIGRKINPKRKIIALKEALQDLIE 150 (176)
T ss_pred HHHHHHHCCCCHHHHHHHHHH-HHHHHHHHHHCCCEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf 999998343240888998888-7537888862785336575752102332388999999999999998
No 231
>PRK13866 plasmid partitioning protein RepB; Provisional
Probab=23.69 E-value=54 Score=13.93 Aligned_cols=96 Identities=19% Similarity=0.152 Sum_probs=61.4
Q ss_pred EEEECCHHHHHHCCCCCCEEEEEEEEE---------ECCCCEEEEEEECHHHHHHHHHHHHHHHCCCHHHHHHHCCCCHH
Q ss_conf 389708688985024798499999999---------73884189997067799999998501000510112443157899
Q gi|254780553|r 26 YIIYCPIRTLSCLGKIGDFCTLFVETH---------MRQDQIRLFGFLSDLDRQWFMLLQSVQGVGARVAMGVLSRITAT 96 (207)
Q Consensus 26 Y~i~vs~~~~~~l~~~g~~v~l~~~~~---------vrEd~~~LyGF~~~~Er~~F~~Li~V~GIGpK~AL~iLs~l~~~ 96 (207)
|+|---.+-+....+.|..|+=++-.. -.||... -=+++.||-+|-.-+.-.|....+-+..|+. +-.
T Consensus 118 yqi~yG~RRl~A~~~Lg~~VkA~Vr~L~D~~~v~aQG~EN~~R--~dLSfIErAlFA~~l~~~g~~r~~i~~aL~~-dk~ 194 (336)
T PRK13866 118 YQIVYGRRRLRAAVNLRREVSAIVRNLTDRELVVAQGRENLDR--ADLSFIEKALFALRLEDAGFDRATIIAALST-DKA 194 (336)
T ss_pred EEEEHHHHHHHHHHHHCCCHHHHHHCCCCHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHHCCCCHHHHHHHHCC-CHH
T ss_conf 6630548999999980996332211488099999876453312--3430999999999999769988899999678-888
Q ss_pred HHH------HHHHCCCHHHHHHCCCCCHHHHHHH
Q ss_conf 999------9985156687510457116799999
Q gi|254780553|r 97 ELV------ESIILQNSKVIAQIPGISMKIASRI 124 (207)
Q Consensus 97 ~l~------~aI~~~D~~~L~~vpGIGkKtA~rI 124 (207)
.+. .+|-..=+.++-..||||..-=..+
T Consensus 195 ~lS~m~~v~~~iP~~~i~aIG~Ap~iGR~rW~~L 228 (336)
T PRK13866 195 DLSRYITVARGIPLNLATQIGPASKAGRSRWVAL 228 (336)
T ss_pred HHHHHHHHHHHCCHHHHHHHCCCCCCCCHHHHHH
T ss_conf 9999999999789999997478886770789999
No 232
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=23.65 E-value=54 Score=13.93 Aligned_cols=53 Identities=19% Similarity=0.142 Sum_probs=40.4
Q ss_pred EEEEEEEEEECCEEEEEECCEEEEEECCHHHHHHC--------CCCCCEEEEEEEEEECCCC
Q ss_conf 58999999609979998588323897086889850--------2479849999999973884
Q gi|254780553|r 4 KIKGNIEGLYEDYVLIDVQGVCYIIYCPIRTLSCL--------GKIGDFCTLFVETHMRQDQ 57 (207)
Q Consensus 4 ~i~G~i~~~~~~~ivi~v~GvGY~i~vs~~~~~~l--------~~~g~~v~l~~~~~vrEd~ 57 (207)
.+.|+|..+.+..+.++.++ |..-++|.+.++.- -+.|+.+...+.-.-.++.
T Consensus 5 iv~g~V~~v~~~g~~v~i~~-~~~g~l~~~~l~~~~~~~~~~~~~~G~~v~~~V~~~~~~~~ 65 (72)
T smart00316 5 VVEGTVTEITPFGAFVDLGN-GVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKG 65 (72)
T ss_pred EEEEEEEEEECCEEEEEECC-CCEEEEEHHHCCCCCCCCHHHEECCCCEEEEEEEEEECCCC
T ss_conf 99999999978739999769-98999980750555547846836389899999999999999
No 233
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=22.93 E-value=56 Score=13.84 Aligned_cols=16 Identities=19% Similarity=0.540 Sum_probs=5.1
Q ss_pred HHHCCCCCHHHHHHHH
Q ss_conf 5104571167999999
Q gi|254780553|r 110 IAQIPGISMKIASRIM 125 (207)
Q Consensus 110 L~~vpGIGkKtA~rIi 125 (207)
|.++|.+-++.+++++
T Consensus 289 L~kiprlp~~vie~lV 304 (352)
T PRK13482 289 LAKIPRLPSAVIENLV 304 (352)
T ss_pred HCCCCCCCHHHHHHHH
T ss_conf 6059999999999999
No 234
>KOG3111 consensus
Probab=22.83 E-value=46 Score=14.40 Aligned_cols=130 Identities=15% Similarity=0.121 Sum_probs=83.0
Q ss_pred EEEECCEEEEEE--CCEEEEEECCHHHHHHCC-CCCCEEEEEEEEEECCC----------CEEEEEEECHHHHHHHHHHH
Q ss_conf 996099799985--883238970868898502-47984999999997388----------41899970677999999985
Q gi|254780553|r 10 EGLYEDYVLIDV--QGVCYIIYCPIRTLSCLG-KIGDFCTLFVETHMRQD----------QIRLFGFLSDLDRQWFMLLQ 76 (207)
Q Consensus 10 ~~~~~~~ivi~v--~GvGY~i~vs~~~~~~l~-~~g~~v~l~~~~~vrEd----------~~~LyGF~~~~Er~~F~~Li 76 (207)
..-+-+++.+|| +-+-=.+..-......|. ..+.+-.+-+|+-|.+. .-++|-|....-.++-+..-
T Consensus 27 ~~~GadwlHlDVMDg~FVpNiT~G~pvV~slr~~~~~~~ffD~HmMV~~Peq~v~~~a~agas~~tfH~E~~q~~~~lv~ 106 (224)
T KOG3111 27 LDAGADWLHLDVMDGHFVPNITFGPPVVESLRKHTGADPFFDVHMMVENPEQWVDQMAKAGASLFTFHYEATQKPAELVE 106 (224)
T ss_pred HHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHCCCCCCCEEEEEEECCHHHHHHHHHHCCCCEEEEEEEECCCHHHHHH
T ss_conf 97498758786014710477433618899998525888523678764698887679986477569998643257899999
Q ss_pred HHHHCCCHHHHHHHCCCCHHHHHHHHHCCCHHH-HHHCCCCCHHHH-HHH---HHHHHHHHHHCCCCC
Q ss_conf 010005101124431578999999985156687-510457116799-999---999742221101133
Q gi|254780553|r 77 SVQGVGARVAMGVLSRITATELVESIILQNSKV-IAQIPGISMKIA-SRI---MTELKGKAISLSSVV 139 (207)
Q Consensus 77 ~V~GIGpK~AL~iLs~l~~~~l~~aI~~~D~~~-L~~vpGIGkKtA-~rI---i~ELk~K~~~~~~~~ 139 (207)
.+.--|-|.++++=-..+.+.+......-|... .+-=||.|-..= +-+ +-+|+.|..++....
T Consensus 107 ~ir~~gmk~G~alkPgT~Ve~~~~~~~~~D~vLvMtVePGFGGQkFme~mm~KV~~lR~kyp~l~ieV 174 (224)
T KOG3111 107 KIREKGMKVGLALKPGTPVEDLEPLAEHVDMVLVMTVEPGFGGQKFMEDMMPKVEWLREKYPNLDIEV 174 (224)
T ss_pred HHHHCCCEEEEEECCCCCHHHHHHHHHHCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHCCCCEEEE
T ss_conf 99974975668748999589999764102579999854897504578999899999998689843885
No 235
>COG1245 Predicted ATPase, RNase L inhibitor (RLI) homolog [General function prediction only]
Probab=22.29 E-value=4.8 Score=20.98 Aligned_cols=88 Identities=14% Similarity=0.142 Sum_probs=58.1
Q ss_pred CEEEEEEEEEECCCCEEEEEEECHHHHHHHHHHHHHHHCCCHHHHHHHCCC------------CHHHHHH----------
Q ss_conf 849999999973884189997067799999998501000510112443157------------8999999----------
Q gi|254780553|r 43 DFCTLFVETHMRQDQIRLFGFLSDLDRQWFMLLQSVQGVGARVAMGVLSRI------------TATELVE---------- 100 (207)
Q Consensus 43 ~~v~l~~~~~vrEd~~~LyGF~~~~Er~~F~~Li~V~GIGpK~AL~iLs~l------------~~~~l~~---------- 100 (207)
++..=-+.|-...|+..|||......-.+- -+++-||||--+|+.|||.- +|++++.
T Consensus 74 ~eLe~e~vHRYg~NgFkL~~LP~pr~G~V~-GilG~NGiGKsTalkILaGel~PNLG~~~~pp~wdeVi~~FrGtELq~Y 152 (591)
T COG1245 74 EELEEEVVHRYGVNGFKLYRLPTPRPGKVV-GILGPNGIGKSTALKILAGELKPNLGRYEDPPSWDEVIKRFRGTELQNY 152 (591)
T ss_pred HHHCCCCEEECCCCCEEEECCCCCCCCCEE-EEECCCCCCHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHH
T ss_conf 464344304405774378457878888479-9876897657889999747607788888899898999998612589999
Q ss_pred --HHHCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHHCC
Q ss_conf --985156687510457116799999999742221101
Q gi|254780553|r 101 --SIILQNSKVIAQIPGISMKIASRIMTELKGKAISLS 136 (207)
Q Consensus 101 --aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~K~~~~~ 136 (207)
.+.+++++...|...| +.|=--+|+|+..+.
T Consensus 153 F~~l~~g~~r~v~K~QYV-----d~iPk~~KG~v~elL 185 (591)
T COG1245 153 FKKLYEGELRAVHKPQYV-----DLIPKVVKGKVGELL 185 (591)
T ss_pred HHHHHCCCCCEECCHHHH-----HHHHHHHCCHHHHHH
T ss_conf 999873881134251889-----887788535199999
No 236
>PRK08451 DNA polymerase III subunits gamma and tau; Validated
Probab=22.29 E-value=58 Score=13.75 Aligned_cols=52 Identities=12% Similarity=0.240 Sum_probs=27.9
Q ss_pred CCCHHHHHHHCCCCHH---HHHHHHHCCCHHH-HHHCCCCCHHHHHHHHHHH----HHHH
Q ss_conf 0510112443157899---9999985156687-5104571167999999997----4222
Q gi|254780553|r 81 VGARVAMGVLSRITAT---ELVESIILQNSKV-IAQIPGISMKIASRIMTEL----KGKA 132 (207)
Q Consensus 81 IGpK~AL~iLs~l~~~---~l~~aI~~~D~~~-L~~vpGIGkKtA~rIi~EL----k~K~ 132 (207)
|-......+|...+++ ++.++|.++|... +..+..+-.+-+++++-|| |+++
T Consensus 230 i~~~~v~~~lG~~d~~~~~~l~~~i~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 289 (523)
T PRK08451 230 ITESKVADMLGLLDPSKIEDFFQAILNKDKEKLFELLAELEDYEAEMVLDEMLLFLKEKL 289 (523)
T ss_pred CCHHHHHHHHCCCCHHHHHHHHHHHHHCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 779999998588899999999999994589999999999853189999999999999997
No 237
>pfam00570 HRDC HRDC domain. The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic acid binding. Mutations in the HRDC domain cause human disease. It is interesting to note that the RecQ helicase in Deinococcus radiodurans has three tandem HRDC domains.
Probab=21.90 E-value=59 Score=13.70 Aligned_cols=26 Identities=19% Similarity=0.367 Sum_probs=20.3
Q ss_pred HCCCHHHHHHCCCCCHHHHHHHHHHH
Q ss_conf 51566875104571167999999997
Q gi|254780553|r 103 ILQNSKVIAQIPGISMKIASRIMTEL 128 (207)
Q Consensus 103 ~~~D~~~L~~vpGIGkKtA~rIi~EL 128 (207)
.-.+...|.+++|+|++.++|---++
T Consensus 39 ~P~s~~~L~~i~g~~~~~~~~~G~~i 64 (68)
T pfam00570 39 LPRTLEELLRIPGVGPRKLERYGEEI 64 (68)
T ss_pred CCCCHHHHHCCCCCCHHHHHHHHHHH
T ss_conf 84999998089999999999999999
No 238
>TIGR03454 partition_RepB plasmid partitioning protein RepB. Members of this family are the RepB protein involved in replicon partitioning. RepB is found, in general, as part of a repABC operon in plasmids and small chromosomes, separate from the main chromosome, in various bacteria. This model describes a rather narrow clade of proteins; it should be noted that additional homologs scoring below the trusted cutoff have very similar functions, although they may be named differently.
Probab=21.82 E-value=59 Score=13.69 Aligned_cols=102 Identities=23% Similarity=0.209 Sum_probs=69.0
Q ss_pred EEEEEECCHHHHHHCCCCCCEEEEEEEEE---------ECCCCEEEEEEECHHHHHHHHHHHHHHHCCCHHHHHHHCCCC
Q ss_conf 32389708688985024798499999999---------738841899970677999999985010005101124431578
Q gi|254780553|r 24 VCYIIYCPIRTLSCLGKIGDFCTLFVETH---------MRQDQIRLFGFLSDLDRQWFMLLQSVQGVGARVAMGVLSRIT 94 (207)
Q Consensus 24 vGY~i~vs~~~~~~l~~~g~~v~l~~~~~---------vrEd~~~LyGF~~~~Er~~F~~Li~V~GIGpK~AL~iLs~l~ 94 (207)
=.|+|-.-.+-+..+...|-.|.-++-.. ..||... -=+|+.||-+|-.-+.-.|.+.++-++.|+ .+
T Consensus 114 gry~iv~G~RR~~A~~~lg~~v~A~vr~l~D~~~v~aqg~EN~~R--~dLSfIErA~fA~~l~~~g~~r~~I~~aL~-vd 190 (325)
T TIGR03454 114 GRYQVAYGHRRLRAARDLGIPVKAVVRELSDEELVIAQGQENSAR--RDLSFIERALFAQRLEDRGFDRDTIMAALS-VD 190 (325)
T ss_pred CCEEEEECHHHHHHHHHCCCCCEEEECCCCCHHHHHHHHHHHHHC--CCCCHHHHHHHHHHHHHCCCCHHHHHHHHC-CC
T ss_conf 847885108999999982997203345799299999988764521--467799999999999984999999999988-89
Q ss_pred HHHHHHHHHC------CCHHHHHHCCCCCHHHHHHHHHHH
Q ss_conf 9999999851------566875104571167999999997
Q gi|254780553|r 95 ATELVESIIL------QNSKVIAQIPGISMKIASRIMTEL 128 (207)
Q Consensus 95 ~~~l~~aI~~------~D~~~L~~vpGIGkKtA~rIi~EL 128 (207)
-..+.+.+.- .=+.++-..||||..-=..+.--|
T Consensus 191 ks~lSrml~Va~~iP~elI~aIGpAp~iGR~RW~~La~~l 230 (325)
T TIGR03454 191 KTELSRMISVARRIPEELIEAIGPAPGIGRPRWMELAKLL 230 (325)
T ss_pred HHHHHHHHHHHHHCCHHHHHHHCCCCCCCCHHHHHHHHHH
T ss_conf 9999999999997899999973798734733799999998
No 239
>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB; InterPro: IPR013374 This model describes a protein involved in type IV pilus biogenesis designated PilB in Pseudomonas aeruginosa but PilF in Neisseria gonorrhoeae; the more common usage, reflected here, is PilB. This protein is an ATPase involved in protein export for pilin assembly, and is closely related to GspE (IPR013369 from INTERPRO) of type II secretion systems (also referred to as the main terminal branch of the general secretion pathway). Note that type IV pilus systems are often divided into type IV-A and IV-B, with the latter group including bundle-forming pilus, mannose-sensitive hemagglutinin, etc. Members of this family are found in type IV-A systems.; GO: 0005524 ATP binding, 0008565 protein transporter activity, 0009297 pilus biogenesis.
Probab=21.38 E-value=54 Score=13.96 Aligned_cols=52 Identities=23% Similarity=0.450 Sum_probs=26.2
Q ss_pred EEEECHHHHHHHHHHHHHHHC----CCH---------HHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCC
Q ss_conf 997067799999998501000----510---------112443157899999998515668751045711
Q gi|254780553|r 61 FGFLSDLDRQWFMLLQSVQGV----GAR---------VAMGVLSRITATELVESIILQNSKVIAQIPGIS 117 (207)
Q Consensus 61 yGF~~~~Er~~F~~Li~V~GI----GpK---------~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIG 117 (207)
=||-..+-..|-+-|-+=+|. ||- +||+|||+-+.+ .=..+|..-+ .+|||.
T Consensus 308 LGFeP~Qk~~fL~Ai~kPqGMvLVTGPTGSGKTVSLYTaLniLN~~~~N----ISTAEDPVEI-NLpGIN 372 (577)
T TIGR02538 308 LGFEPDQKALFLEAIHKPQGMVLVTGPTGSGKTVSLYTALNILNTEEVN----ISTAEDPVEI-NLPGIN 372 (577)
T ss_pred HCCCHHHHHHHHHHHHCCCCCEEEECCCCCCHHHHHHHHHCCCCCCCCC----CCCCCCCEEE-EECCCC
T ss_conf 0688889999999970799728862665984168787631125776745----0114477246-407715
No 240
>COG3722 MtlR Transcriptional regulator [Transcription]
Probab=21.26 E-value=51 Score=14.10 Aligned_cols=23 Identities=26% Similarity=0.287 Sum_probs=10.4
Q ss_pred EEEECHHHHHHHHHHHHHHHCCC
Q ss_conf 99706779999999850100051
Q gi|254780553|r 61 FGFLSDLDRQWFMLLQSVQGVGA 83 (207)
Q Consensus 61 yGF~~~~Er~~F~~Li~V~GIGp 83 (207)
|||.+..-.+.|..|-.|+.++|
T Consensus 107 y~FtDd~ildpf~~lscvn~~~~ 129 (174)
T COG3722 107 YGFTDDEILDPFGELSCVNSLPP 129 (174)
T ss_pred CCCCCHHHHHHHHHHHHCCCCCC
T ss_conf 47665898868887552045797
No 241
>TIGR00302 TIGR00302 phosphoribosylformylglycinamidine synthase, purS protein; InterPro: IPR003850 Phosphoribosylformylglycinamidine(FGAM) synthetase, 6.3.5.3 from EC, catalyses the fourth step in the de novo purine biosynthetic pathway . 5-phosphoribosylformylglycinamide (FGAR) + glutamine + ATP = FGAM + glutamate + ADP + Pi In eukaryotes and many bacterial systems (including Escherichia coli and Salmonella typhimurium), the FGAM synthetase is encoded by the large form of PurL (lgPurL), which contains an N-terminal ATPase domain and a C-terminal glutamine-binding domain. In archaeal and other bacterial systems, however, FGAM synthetase is encoded by separate genes, making it a multisubunit (rather than multidomain) enzyme. The protein is composed of the small form of PurL (smPurL), which is homologus to the ATPase domain of lgPurL, PurQ which is homologous to the glutamine-binding domain of of lgPurL, and PurS, whose function is not known. This entry represents the PurS subunit of the multisubunit FGAM synthetase. Recent studies showed that disruption of the purS gene in B. subtilis resulted in a purine auxotrophic phenotype, due to defective FGAM synthetase activity. Therefore, the PurS protein appears to be required for the function of the PurL and PurQ subunits of the FGAM synthetase, but the molecular mechanism for the functional role of PurS is currently not known. For additional information please see , . ; GO: 0016879 ligase activity forming carbon-nitrogen bonds.
Probab=21.21 E-value=61 Score=13.61 Aligned_cols=15 Identities=33% Similarity=0.406 Sum_probs=12.0
Q ss_pred HHHHHHHHCCCCHHH
Q ss_conf 999999967999899
Q gi|254780553|r 162 NAISALVNLGYGQDQ 176 (207)
Q Consensus 162 d~~~AL~~LGy~~~e 176 (207)
-+..||..|||++-+
T Consensus 20 a~~~AL~~LGy~~V~ 34 (80)
T TIGR00302 20 AVQRALRLLGYNEVK 34 (80)
T ss_pred HHHHHHHHCCCCCCC
T ss_conf 899998633778730
No 242
>cd00644 HMG-CoA_reductase_classII Class II hydroxymethylglutaryl-coenzyme A (HMG-CoA) reductase (HMGR). Hydroxymethylglutaryl-coenzyme A (HMG-CoA) reductase (HMGR), class II, prokaryotic enzyme is a homodimer. Class II enzymes are found primarily in prokaryotes and Archaeoglobus fulgidus and are soluble as they lack the membrane region. Enzymes catalyze the synthesis of coenzyme A and mevalonate in isoprenoid synthesis. Bacteria, such as Pseudomonas mevalonii, which rely solely on mevalonate for their carbon source, catalyze the reverse reaction, using an NAD-dependent HMGR to deacetylate mevalonate into 3-hydroxy-3-methylglutaryl-CoA. Human and bacterial HMGR differ in their active site architecture.
Probab=20.86 E-value=12 Score=18.29 Aligned_cols=44 Identities=18% Similarity=0.266 Sum_probs=39.3
Q ss_pred CHHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHH
Q ss_conf 10112443157899999998515668751045711679999999
Q gi|254780553|r 83 ARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMT 126 (207)
Q Consensus 83 pK~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ 126 (207)
.+.-|+|||.+.++.+..|-..-+.+.|..-...|+..|+||+.
T Consensus 199 ~~~~~~IlSN~~~~~~v~A~~~i~~~~l~~~~~~g~~va~~i~~ 242 (417)
T cd00644 199 GEVLLRILSNYATERLVRAKVSIPVEALGTKGGSGEEVAKKIAL 242 (417)
T ss_pred CCEEEEEECCCCCCCEEEEEEEECHHHHCCCCCCHHHHHHHHHH
T ss_conf 85699974346777757899997299955457767999999999
No 243
>pfam02961 BAF Barrier to autointegration factor. The BAF protein has a SAM-domain-like bundle of orthogonally packed alpha-hairpins - one classic and one pseudo helix-hairpin-helix motif. The protein is involved in the prevention of retroviral DNA integration.
Probab=20.80 E-value=42 Score=14.66 Aligned_cols=19 Identities=21% Similarity=0.431 Sum_probs=14.4
Q ss_pred HHHHHCCCCCHHHHHHHHH
Q ss_conf 8751045711679999999
Q gi|254780553|r 108 KVIAQIPGISMKIASRIMT 126 (207)
Q Consensus 108 ~~L~~vpGIGkKtA~rIi~ 126 (207)
+..+.+||||+..++|+.-
T Consensus 19 K~V~~l~GIG~~lg~~L~~ 37 (89)
T pfam02961 19 KPVTALAGIGEVLGGRLED 37 (89)
T ss_pred CCCCCCCCCCHHHHHHHHH
T ss_conf 8745057862899889998
No 244
>COG5207 UBP14 Isopeptidase T [Posttranslational modification, protein turnover, chaperones]
Probab=20.63 E-value=62 Score=13.53 Aligned_cols=21 Identities=14% Similarity=0.279 Sum_probs=10.7
Q ss_pred HHHHHHHCCCCHHHHHHHHHH
Q ss_conf 999999679998999999999
Q gi|254780553|r 163 AISALVNLGYGQDQATTAVVS 183 (207)
Q Consensus 163 ~~~AL~~LGy~~~ea~~ai~~ 183 (207)
-+..|...||.+..+++++..
T Consensus 624 ~~~Slle~Gln~n~~Rkal~~ 644 (749)
T COG5207 624 KARSLLENGLNPNLCRKALMD 644 (749)
T ss_pred HHHHHHHCCCCHHHHHHHHHH
T ss_conf 899999738987888889987
Done!