Query 022922
Match_columns 290
No_of_seqs 170 out of 1284
Neff 6.7
Searched_HMMs 46136
Date Fri Mar 29 07:07:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022922.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022922hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0266 Nei Formamidopyrimidin 100.0 1.7E-77 3.6E-82 545.1 26.0 256 1-271 1-270 (273)
2 PRK13945 formamidopyrimidine-D 100.0 3.4E-75 7.5E-80 539.0 27.8 257 1-271 1-279 (282)
3 PRK01103 formamidopyrimidine/5 100.0 3.8E-74 8.3E-79 530.2 28.4 256 1-271 1-270 (274)
4 TIGR00577 fpg formamidopyrimid 100.0 9.3E-74 2E-78 527.0 27.5 255 2-271 1-270 (272)
5 PRK14811 formamidopyrimidine-D 100.0 2.6E-73 5.6E-78 523.1 26.8 244 1-271 1-260 (269)
6 PRK14810 formamidopyrimidine-D 100.0 3E-71 6.4E-76 510.3 28.4 253 1-271 1-269 (272)
7 PRK10445 endonuclease VIII; Pr 100.0 3E-70 6.5E-75 501.4 27.8 248 1-271 1-260 (263)
8 cd08972 PF_Nei_N N-terminal do 100.0 1.1E-34 2.3E-39 242.0 16.6 134 1-134 1-137 (137)
9 cd08976 BaFpgNei_N_4 Uncharact 100.0 1.8E-33 3.9E-38 228.5 15.7 117 2-133 1-117 (117)
10 cd08966 EcFpg-like_N N-termina 100.0 2.8E-32 6E-37 222.2 16.4 120 2-135 1-120 (120)
11 PF01149 Fapy_DNA_glyco: Forma 100.0 9.4E-33 2E-37 223.8 13.3 116 2-132 1-116 (116)
12 cd08967 MeNeil1_N N-terminal d 100.0 5.5E-31 1.2E-35 217.6 14.8 113 1-134 1-130 (131)
13 cd08773 FpgNei_N N-terminal do 100.0 7.6E-31 1.6E-35 212.8 15.0 116 2-132 1-116 (117)
14 cd08973 BaFpgNei_N_1 Uncharact 100.0 1.7E-30 3.7E-35 212.7 15.6 115 1-130 1-116 (122)
15 PF06831 H2TH: Formamidopyrimi 100.0 2E-31 4.3E-36 208.0 7.5 83 146-228 1-84 (92)
16 cd08975 BaFpgNei_N_3 Uncharact 100.0 1.2E-28 2.5E-33 200.5 14.9 112 3-131 2-115 (117)
17 cd08971 AcNei2_N N-terminal do 100.0 5.5E-28 1.2E-32 195.7 15.6 111 1-135 1-112 (114)
18 cd08974 BaFpgNei_N_2 Uncharact 99.9 4.7E-27 1E-31 185.4 13.6 96 1-124 1-96 (98)
19 cd08965 EcNei-like_N N-termina 99.9 2.5E-26 5.5E-31 186.3 15.9 113 2-136 1-113 (115)
20 cd08970 AcNei1_N N-terminal do 99.9 3.1E-26 6.6E-31 184.4 14.7 109 1-133 1-109 (110)
21 cd08968 MeNeil2_N N-terminal d 99.9 1.7E-22 3.8E-27 165.0 14.1 111 1-125 1-121 (126)
22 cd08969 MeNeil3_N N-terminal d 99.7 5E-16 1.1E-20 128.6 10.9 118 1-135 1-128 (140)
23 PF05833 FbpA: Fibronectin-bin 98.1 2.5E-05 5.3E-10 76.9 11.8 76 146-225 165-241 (455)
24 COG1293 Predicted RNA-binding 96.9 0.0092 2E-07 60.8 11.7 72 149-225 168-239 (564)
25 PRK05179 rpsM 30S ribosomal pr 96.9 0.00077 1.7E-08 55.3 3.1 51 168-221 12-62 (122)
26 PRK04184 DNA topoisomerase VI 96.8 0.0069 1.5E-07 61.2 9.2 74 145-222 233-307 (535)
27 PF00416 Ribosomal_S13: Riboso 96.6 0.0037 8E-08 50.0 5.0 52 167-221 9-60 (107)
28 COG0099 RpsM Ribosomal protein 96.6 0.0018 3.8E-08 52.6 2.8 49 169-220 13-61 (121)
29 PF06827 zf-FPG_IleRS: Zinc fi 96.5 0.0017 3.7E-08 39.9 1.7 23 249-271 1-26 (30)
30 TIGR01052 top6b DNA topoisomer 96.1 0.024 5.3E-07 56.7 8.7 73 145-221 224-300 (488)
31 PTZ00134 40S ribosomal protein 95.8 0.0079 1.7E-07 51.3 3.2 52 167-221 24-75 (154)
32 CHL00137 rps13 ribosomal prote 95.8 0.0095 2.1E-07 48.9 3.5 50 168-220 12-61 (122)
33 TIGR03631 bact_S13 30S ribosom 95.4 0.016 3.5E-07 46.9 3.3 50 168-220 10-59 (113)
34 TIGR03629 arch_S13P archaeal r 95.1 0.022 4.7E-07 48.1 3.5 51 168-221 16-66 (144)
35 PRK04053 rps13p 30S ribosomal 95.1 0.022 4.9E-07 48.3 3.5 52 167-221 19-70 (149)
36 PF03119 DNA_ligase_ZBD: NAD-d 93.9 0.037 8E-07 33.6 1.6 22 251-272 1-23 (28)
37 COG1389 DNA topoisomerase VI, 91.1 0.45 9.8E-06 47.2 5.9 98 119-222 207-311 (538)
38 PF06677 Auto_anti-p27: Sjogre 90.5 0.18 3.9E-06 33.4 1.7 24 248-271 16-39 (41)
39 COG1645 Uncharacterized Zn-fin 89.7 0.14 3.1E-06 42.3 1.0 22 250-272 29-50 (131)
40 KOG3311 Ribosomal protein S18 89.4 0.26 5.7E-06 41.7 2.3 55 167-224 22-76 (152)
41 PRK00420 hypothetical protein; 89.3 0.22 4.7E-06 40.3 1.7 24 249-272 23-46 (112)
42 TIGR03847 conserved hypothetic 80.0 1.9 4.1E-05 37.4 3.3 49 197-270 126-174 (177)
43 PRK09710 lar restriction allev 78.4 1.7 3.6E-05 31.6 2.0 22 250-276 7-28 (64)
44 TIGR00275 flavoprotein, HI0933 78.1 3.1 6.7E-05 40.4 4.5 63 153-220 263-330 (400)
45 PF07191 zinc-ribbons_6: zinc- 74.5 1.9 4.1E-05 31.9 1.5 23 251-273 32-57 (70)
46 TIGR00755 ksgA dimethyladenosi 73.8 3.7 8.1E-05 37.2 3.6 51 163-218 202-252 (253)
47 PF11290 DUF3090: Protein of u 73.3 4.4 9.6E-05 35.1 3.7 52 193-269 120-171 (171)
48 PF13240 zinc_ribbon_2: zinc-r 71.4 1.5 3.2E-05 25.3 0.2 9 252-260 2-10 (23)
49 PF11781 RRN7: RNA polymerase 71.2 2.8 6.2E-05 26.9 1.6 23 250-272 9-32 (36)
50 smart00778 Prim_Zn_Ribbon Zinc 70.4 2.8 6.1E-05 27.1 1.4 23 249-271 3-30 (37)
51 COG0030 KsgA Dimethyladenosine 68.6 5.4 0.00012 36.9 3.4 52 163-222 206-257 (259)
52 PF08273 Prim_Zn_Ribbon: Zinc- 67.7 2.2 4.8E-05 28.1 0.5 21 250-270 4-30 (40)
53 PRK00274 ksgA 16S ribosomal RN 67.0 7.5 0.00016 35.7 4.1 55 162-220 215-269 (272)
54 COG2331 Uncharacterized protei 65.2 3 6.6E-05 31.3 0.9 34 250-283 34-69 (82)
55 PF00398 RrnaAD: Ribosomal RNA 64.7 7.4 0.00016 35.5 3.5 52 163-220 209-261 (262)
56 COG4049 Uncharacterized protei 62.4 3.7 8E-05 29.1 0.8 19 242-260 7-28 (65)
57 COG1439 Predicted nucleic acid 61.5 7.5 0.00016 33.9 2.7 18 244-261 148-165 (177)
58 PRK10246 exonuclease subunit S 60.4 3.9 8.4E-05 44.9 1.0 9 207-215 213-221 (1047)
59 PF13248 zf-ribbon_3: zinc-rib 59.7 4 8.8E-05 24.0 0.6 18 251-271 4-21 (26)
60 PF10892 DUF2688: Protein of u 57.8 1.9 4.1E-05 30.5 -1.2 16 250-265 11-26 (60)
61 PF03486 HI0933_like: HI0933-l 56.8 4.9 0.00011 39.5 0.9 63 153-220 270-338 (409)
62 COG2081 Predicted flavoprotein 56.2 16 0.00034 36.0 4.2 62 153-220 268-331 (408)
63 PF09297 zf-NADH-PPase: NADH p 55.8 6.3 0.00014 24.2 1.0 14 249-262 3-16 (32)
64 PF01396 zf-C4_Topoisom: Topoi 55.6 8 0.00017 25.1 1.5 19 250-268 2-21 (39)
65 PRK12495 hypothetical protein; 51.2 6.9 0.00015 35.3 0.9 27 250-277 43-69 (226)
66 COG3024 Uncharacterized protei 49.6 6.9 0.00015 28.4 0.5 23 248-270 6-30 (65)
67 PF13453 zf-TFIIB: Transcripti 49.3 22 0.00048 23.0 2.9 35 251-286 1-39 (41)
68 PF08271 TF_Zn_Ribbon: TFIIB z 48.6 15 0.00032 24.1 1.9 21 251-271 2-24 (43)
69 COG1998 RPS31 Ribosomal protei 48.0 7.6 0.00017 26.8 0.5 17 246-262 16-32 (51)
70 PF12760 Zn_Tnp_IS1595: Transp 47.5 22 0.00048 23.6 2.7 12 247-258 16-27 (46)
71 COG4643 Uncharacterized protei 46.8 11 0.00023 36.2 1.4 31 249-280 32-67 (366)
72 PRK14351 ligA NAD-dependent DN 45.2 13 0.00028 39.2 1.9 22 250-272 424-445 (689)
73 PRK12496 hypothetical protein; 42.3 11 0.00023 32.4 0.7 15 247-261 141-155 (164)
74 TIGR00375 conserved hypothetic 41.7 23 0.00049 34.6 2.9 10 250-260 260-269 (374)
75 smart00834 CxxC_CXXC_SSSS Puta 41.7 13 0.00028 23.6 0.8 15 248-262 25-39 (41)
76 PF02294 7kD_DNA_binding: 7kD 40.7 41 0.00088 23.5 3.2 32 48-85 15-46 (62)
77 smart00532 LIGANc Ligase N fam 40.7 18 0.00038 36.1 2.0 23 250-272 400-423 (441)
78 PTZ00338 dimethyladenosine tra 40.5 40 0.00087 31.6 4.3 57 163-220 210-287 (294)
79 PRK00398 rpoP DNA-directed RNA 39.3 16 0.00035 24.2 1.0 16 250-265 22-37 (46)
80 PRK14896 ksgA 16S ribosomal RN 39.2 58 0.0013 29.5 5.0 59 161-221 197-256 (258)
81 COG1996 RPC10 DNA-directed RNA 38.0 17 0.00037 25.0 1.0 19 249-267 24-42 (49)
82 PF08063 PADR1: PADR1 (NUC008) 37.8 24 0.00051 24.8 1.7 21 250-270 15-35 (55)
83 PRK14350 ligA NAD-dependent DN 37.6 21 0.00045 37.5 2.0 21 251-272 400-420 (669)
84 COG1571 Predicted DNA-binding 37.3 13 0.00027 36.8 0.4 26 245-270 346-371 (421)
85 TIGR03655 anti_R_Lar restricti 37.1 15 0.00033 25.2 0.7 11 250-260 2-12 (53)
86 COG3809 Uncharacterized protei 37.0 34 0.00074 26.0 2.6 36 251-288 3-43 (88)
87 PF14768 RPA_interact_C: Repli 36.8 34 0.00074 25.8 2.6 36 251-287 1-39 (82)
88 PF13005 zf-IS66: zinc-finger 36.7 21 0.00046 23.5 1.3 17 249-265 2-18 (47)
89 COG0272 Lig NAD-dependent DNA 36.1 21 0.00046 37.2 1.8 22 252-273 407-429 (667)
90 PF11197 DUF2835: Protein of u 35.5 87 0.0019 23.0 4.5 48 38-85 7-56 (68)
91 PRK07956 ligA NAD-dependent DN 34.5 24 0.00051 37.0 1.9 21 252-272 407-428 (665)
92 PF07282 OrfB_Zn_ribbon: Putat 34.2 25 0.00055 25.1 1.5 29 249-277 28-57 (69)
93 TIGR00575 dnlj DNA ligase, NAD 33.4 27 0.00058 36.6 2.0 22 251-272 394-416 (652)
94 PF07754 DUF1610: Domain of un 32.9 23 0.0005 20.7 0.8 17 252-268 1-17 (24)
95 PF09723 Zn-ribbon_8: Zinc rib 32.2 29 0.00063 22.7 1.4 15 248-262 25-40 (42)
96 PF02318 FYVE_2: FYVE-type zin 31.4 23 0.00049 28.5 0.9 22 250-271 55-76 (118)
97 PRK00418 DNA gyrase inhibitor; 31.2 21 0.00045 25.8 0.6 22 250-271 7-30 (62)
98 PF09889 DUF2116: Uncharacteri 30.7 22 0.00047 25.5 0.6 18 250-270 4-21 (59)
99 PF12773 DZR: Double zinc ribb 28.8 22 0.00048 23.7 0.4 9 252-260 15-23 (50)
100 PF06170 DUF983: Protein of un 28.4 25 0.00054 27.0 0.6 20 239-262 2-21 (86)
101 COG2995 PqiA Uncharacterized p 28.3 24 0.00052 34.6 0.6 15 250-264 39-53 (418)
102 PHA02998 RNA polymerase subuni 28.1 67 0.0015 28.2 3.3 24 235-258 128-152 (195)
103 PF10609 ParA: ParA/MinD ATPas 27.6 23 0.00051 26.9 0.4 17 249-265 65-81 (81)
104 PF14803 Nudix_N_2: Nudix N-te 27.6 57 0.0012 20.6 2.1 21 251-271 2-27 (34)
105 PF14354 Lar_restr_allev: Rest 26.8 46 0.001 23.1 1.8 11 250-260 4-14 (61)
106 COG2176 PolC DNA polymerase II 26.8 30 0.00066 38.5 1.1 35 244-280 934-968 (1444)
107 PF11248 DUF3046: Protein of u 26.7 48 0.001 24.1 1.8 43 158-201 4-47 (63)
108 PRK08665 ribonucleotide-diphos 26.1 29 0.00063 36.9 0.8 22 249-271 724-745 (752)
109 TIGR00409 proS_fam_II prolyl-t 25.6 30 0.00065 35.5 0.8 15 246-260 390-404 (568)
110 PF08646 Rep_fac-A_C: Replicat 25.5 45 0.00098 27.5 1.7 20 252-271 21-42 (146)
111 PF10825 DUF2752: Protein of u 25.2 32 0.0007 23.7 0.7 12 247-258 7-18 (52)
112 PRK12286 rpmF 50S ribosomal pr 24.8 33 0.00071 24.3 0.6 20 250-273 28-48 (57)
113 cd00350 rubredoxin_like Rubred 24.5 38 0.00081 20.9 0.8 11 248-258 16-26 (33)
114 PF06462 Hyd_WA: Propeller; I 24.0 33 0.00071 21.2 0.5 16 191-206 11-26 (32)
115 PF11023 DUF2614: Protein of u 23.7 25 0.00055 28.4 -0.1 14 252-265 72-85 (114)
116 PF09151 DUF1936: Domain of un 23.7 39 0.00084 21.1 0.7 10 251-260 3-12 (36)
117 COG1675 TFA1 Transcription ini 23.3 60 0.0013 28.3 2.1 29 154-182 32-63 (176)
118 PF03884 DUF329: Domain of unk 23.1 30 0.00065 24.6 0.2 20 251-270 4-25 (57)
119 cd00729 rubredoxin_SM Rubredox 23.0 38 0.00081 21.2 0.6 10 249-258 18-27 (34)
120 PRK12267 methionyl-tRNA synthe 22.8 1.2E+02 0.0027 31.4 4.7 21 249-269 143-163 (648)
121 PRK00432 30S ribosomal protein 22.8 47 0.001 22.8 1.1 25 247-271 18-42 (50)
122 TIGR02098 MJ0042_CXXC MJ0042 f 22.7 40 0.00087 21.1 0.7 10 251-260 27-36 (38)
123 TIGR00373 conserved hypothetic 22.6 45 0.00097 28.3 1.2 28 155-182 29-59 (158)
124 COG1885 Uncharacterized protei 21.8 36 0.00078 27.2 0.4 11 250-260 50-60 (115)
125 TIGR03826 YvyF flagellar opero 21.7 36 0.00079 28.4 0.5 14 248-261 80-93 (137)
126 PF04423 Rad50_zn_hook: Rad50 21.4 37 0.0008 23.3 0.4 11 250-260 21-31 (54)
127 PRK02935 hypothetical protein; 21.4 34 0.00073 27.4 0.2 16 251-266 72-87 (110)
128 PF03811 Zn_Tnp_IS1: InsA N-te 21.1 49 0.0011 21.1 0.9 16 251-266 7-24 (36)
129 TIGR02605 CxxC_CxxC_SSSS putat 21.0 62 0.0013 21.7 1.4 14 250-263 27-41 (52)
130 PF09862 DUF2089: Protein of u 20.9 48 0.001 26.8 1.0 11 252-262 1-11 (113)
131 KOG2712 Transcriptional coacti 20.6 1.1E+02 0.0024 24.5 3.0 29 197-225 73-101 (108)
132 cd04476 RPA1_DBD_C RPA1_DBD_C: 20.6 53 0.0012 27.6 1.3 20 252-271 37-56 (166)
133 PF01258 zf-dskA_traR: Prokary 20.6 30 0.00066 21.7 -0.2 20 252-271 6-29 (36)
134 cd08975 BaFpgNei_N_3 Uncharact 20.5 1.2E+02 0.0025 24.4 3.2 70 12-82 42-115 (117)
No 1
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=100.00 E-value=1.7e-77 Score=545.12 Aligned_cols=256 Identities=30% Similarity=0.442 Sum_probs=235.1
Q ss_pred CCChHHHHHHHHHHHHHcCCCeEEEEEecCCCceeccCChhhHHhhhcCCEEEEEEeeeeEEEEEeCCCCceEEecCceE
Q 022922 1 MPELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKNLWLRLDSPPFPSFQFGMTG 80 (290)
Q Consensus 1 MPELPEVe~~~~~L~~~~~Gk~I~~v~~~~~~~~~~~~~~~~f~~~L~G~~i~~v~RrGK~L~~~l~~~~~L~~HLgMtG 80 (290)
||||||||++++.|++.+.|++|++|++. .|++.++.+ ++|...|.|++|++|.||||||+++|+++.+|++||||+|
T Consensus 1 MPELPEVetv~rgL~~~~~G~~I~~v~~~-~p~l~~~~~-~~~~~~L~G~~I~~v~rRgKyLl~~l~g~~~Li~HLgM~G 78 (273)
T COG0266 1 MPELPEVETVRRGLEPHLVGKTITRVEVR-RPRLRWPDS-EEFAERLTGQRITSVERRGKYLLIELSGDLTLISHLGMSG 78 (273)
T ss_pred CCCCcHHHHHHHhhHHHhCCCEEEEEEec-CCceeccCC-HHHHhhcCCcEEeeEecccceEEEEcCCCcEEEEecCcce
Confidence 99999999999999999999999999997 577776554 7999999999999999999999999976669999999999
Q ss_pred EEEEeecceeccccccccCCCCCCCCeeEEEEEEcCC-ceEEEecCCcccEEEEecCCC-CCCCcccCCCCCCCCCCCHH
Q 022922 81 AIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDG-LELSFTDKRRFAKVRLLNDPT-SVPPISELGPDALLEPMTVD 158 (290)
Q Consensus 81 ~l~~~~~~~~~y~~~~~~~~~~~p~k~~~l~l~l~~g-~~L~f~D~R~fG~i~l~~~~~-~~~~l~~LGpDpL~~~f~~~ 158 (290)
+|++.+. +.+..+|+|+.|+|+|| ..|+|+|+|+||.|++++..+ ..+.+++||||||+++||++
T Consensus 79 ~~~~~~~-------------~~~~~kH~hv~~~~~~g~~~l~y~D~R~FG~~~~~~~~~~~~~~l~~LGpePl~~~f~~~ 145 (273)
T COG0266 79 SLRLEAR-------------GEPDEKHDHVDFVLSDGKDVLRYNDPRRFGTMLLIEDLEEVHPVLAKLGPEPLSDDFDPE 145 (273)
T ss_pred EEEEecC-------------CCCCCcceEEEEEEcCCceEEEEecCCcCcEEEEecccccccHHHHhcCCCCCccccCHH
Confidence 9999753 23467999999999999 599999999999999998654 67789999999999999999
Q ss_pred HHHHHHcCCCCchHHHhhcccccccCCchhhhhhhhcccccccCcCCCCCHHHHHHHHHHHHHHHHH-Hhc-cccc----
Q 022922 159 EFTDSLSKKKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVREA-LGV-SLQF---- 232 (290)
Q Consensus 159 ~f~~~l~~~~~~IK~~LLDQ~~iaGIGNiyadEiLf~A~IhP~~~~~~Ls~~e~~~L~~~i~~vL~~-i~~-~~~~---- 232 (290)
++++++++++++||++||||++|||||||||||+||+|||||.+++++||.++++.|+++|+.||.. |+. ++++
T Consensus 146 ~l~~~l~~~~~~IK~~LLDQ~vvaGvGNIYa~E~Lf~agI~P~~~a~~l~~~~~~~l~~~i~~vl~~ai~~gGtt~r~~~ 225 (273)
T COG0266 146 YLAEKLAKKKRRIKTALLDQKVVAGVGNIYADEILFRAGIHPARPAGDLSLAQLALLHEAIKDVLADAIERGGTTLRDFV 225 (273)
T ss_pred HHHHHHhcCccchHHHhhcCCceecccHHHHHHHHHHcCCCcccCccccCHHHHHHHHHHHHHHHHHHHHhCCCccccee
Confidence 9999999999999999999999999999999999999999999999999999999999999999999 999 3332
Q ss_pred ---cccccCccceeecCCCCCCccccccceeee---ccceeeecc
Q 022922 233 ---YKCYFAKPYVHKKHRENKICRLFKVRLKLM---LTAAAFLLN 271 (290)
Q Consensus 233 ---~~~~~~~~~~~vy~R~g~~C~~Cg~~i~~~---~~~~~~~~~ 271 (290)
++.+.|+.+++||+|+|+||++||++|.++ ||+|+||-+
T Consensus 226 ~~~g~~G~fq~~l~VYgR~GepC~~CGt~I~k~~~~gR~t~~CP~ 270 (273)
T COG0266 226 NADGKPGYFQQELKVYGRAGEPCRRCGTPIEKIKLGGRSTFYCPV 270 (273)
T ss_pred ccCCCCCccceeEEEecCCCCCCCccCCEeEEEEEcCCcCEeCCC
Confidence 335679999999999999999999998865 999999975
No 2
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=100.00 E-value=3.4e-75 Score=539.03 Aligned_cols=257 Identities=28% Similarity=0.372 Sum_probs=228.9
Q ss_pred CCChHHHHHHHHHHHHHcCCCeEEEEEecCCCceec-cCChhhHHhhhcCCEEEEEEeeeeEEEEEeCC-----CCceEE
Q 022922 1 MPELPEVEAARRAIEEHCIGKKIVKSIIADDNKVID-GVSASDFEASVLGKAILSAHRKGKNLWLRLDS-----PPFPSF 74 (290)
Q Consensus 1 MPELPEVe~~~~~L~~~~~Gk~I~~v~~~~~~~~~~-~~~~~~f~~~L~G~~i~~v~RrGK~L~~~l~~-----~~~L~~ 74 (290)
||||||||++++.|++.+.|++|++|++. .++++. +.++++|.+.|.|++|++|+|+||||++.|++ +.+|++
T Consensus 1 MPELPEVe~~~~~L~~~~~g~~I~~v~~~-~~~~~~~~~~~~~~~~~L~G~~i~~v~rrGK~l~~~l~~~~~~~~~~L~~ 79 (282)
T PRK13945 1 MPELPEVETVRRGLEQLLLNFIIKGVEVL-LERTIASPGGVEEFIKGLKGSLIGQWQRRGKYLLASLKKEGSENAGWLGV 79 (282)
T ss_pred CCCcchHHHHHHHHHHHhCCCEEEEEEEe-cCCeecCCCChHHHHHhhcCCEEeeEEEeeeEEEEECCCCccCCCCEEEE
Confidence 99999999999999999999999999997 455443 22467899999999999999999999999986 358999
Q ss_pred ecCceEEEEEeecceeccccccccCCCCCCCCeeEEEEEEcCCceEEEecCCcccEEEEecCC----CCCCCcccCCCCC
Q 022922 75 QFGMTGAIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELSFTDKRRFAKVRLLNDP----TSVPPISELGPDA 150 (290)
Q Consensus 75 HLgMtG~l~~~~~~~~~y~~~~~~~~~~~p~k~~~l~l~l~~g~~L~f~D~R~fG~i~l~~~~----~~~~~l~~LGpDp 150 (290)
||||||+|++... +.+|++|.|++|.|+|+..|+|+|+|+||++++++.. .....+++|||||
T Consensus 80 HLgMtG~~~~~~~-------------~~~~~~~~~l~l~~~~~~~L~f~d~R~fG~~~l~~~~~~~~~~~~~l~~LGpDp 146 (282)
T PRK13945 80 HLRMTGQFLWVEQ-------------STPPCKHTRVRLFFEKNQELRFVDIRSFGQMWWVPPGVSPESIITGLQKLGPEP 146 (282)
T ss_pred ECCeeEEEEEecC-------------CCCCCCcEEEEEEeCCCCEEEEEeCCCCceEEEEcCcccccccchHHHhcCCCc
Confidence 9999999998642 2356789999999999989999999999999998742 2234589999999
Q ss_pred CCCCCCHHHHHHHHcCCCCchHHHhhcccccccCCchhhhhhhhcccccccCcCCCCCHHHHHHHHHHHHHHHHH-Hhc-
Q 022922 151 LLEPMTVDEFTDSLSKKKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVREA-LGV- 228 (290)
Q Consensus 151 L~~~f~~~~f~~~l~~~~~~IK~~LLDQ~~iaGIGNiyadEiLf~A~IhP~~~~~~Ls~~e~~~L~~~i~~vL~~-i~~- 228 (290)
|+++||.++|.+++++++++||++||||++||||||||||||||+|||||.+++++||++|+++|+++|++||+. |+.
T Consensus 147 L~~~~~~~~~~~~l~~~~~~IK~~LLDQ~~vaGIGNiya~EiLf~A~IhP~~~~~~Ls~~~~~~L~~~i~~vl~~ai~~g 226 (282)
T PRK13945 147 FSPEFSVEYLKKKLKKRTRSIKTALLDQSIVAGIGNIYADESLFKAGIHPTTPAGQLKKKQLERLREAIIEVLKTSIGAG 226 (282)
T ss_pred CCCCCCHHHHHHHHhcCCccHHHHhhcCCeEeccchhHHHHHHHHcCCCccCccccCCHHHHHHHHHHHHHHHHHHHHcC
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999999 998
Q ss_pred cccc-------cccccCccceeecCCCCCCccccccceeee---ccceeeecc
Q 022922 229 SLQF-------YKCYFAKPYVHKKHRENKICRLFKVRLKLM---LTAAAFLLN 271 (290)
Q Consensus 229 ~~~~-------~~~~~~~~~~~vy~R~g~~C~~Cg~~i~~~---~~~~~~~~~ 271 (290)
++++ +..+.|+.+++||+|+|+|||+||++|.+. ||+|+||-+
T Consensus 227 g~~~~~~~~~~g~~g~~~~~~~Vy~R~g~pC~~Cg~~I~~~~~~gR~t~~CP~ 279 (282)
T PRK13945 227 GTTFSDFRDLEGVNGNYGGQAWVYRRTGKPCRKCGTPIERIKLAGRSTHWCPN 279 (282)
T ss_pred CCccccccccCCCCCcccceEEEeCCCcCCCCcCCCeeEEEEECCCccEECCC
Confidence 3332 234467888999999999999999998855 999999964
No 3
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=100.00 E-value=3.8e-74 Score=530.18 Aligned_cols=256 Identities=33% Similarity=0.469 Sum_probs=230.5
Q ss_pred CCChHHHHHHHHHHHHHcCCCeEEEEEecCCCceeccCChhhHHhhhcCCEEEEEEeeeeEEEEEeCCCCceEEecCceE
Q 022922 1 MPELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKNLWLRLDSPPFPSFQFGMTG 80 (290)
Q Consensus 1 MPELPEVe~~~~~L~~~~~Gk~I~~v~~~~~~~~~~~~~~~~f~~~L~G~~i~~v~RrGK~L~~~l~~~~~L~~HLgMtG 80 (290)
||||||||++++.|++.+.|++|++|++. .+++... ++++|.+.|.|++|++|+|+||||+|+|+++.+|++||||||
T Consensus 1 MPELPEve~v~~~L~~~l~G~~I~~v~~~-~~~~~~~-~~~~~~~~L~G~~i~~v~r~GK~L~~~l~~~~~L~~HLgM~G 78 (274)
T PRK01103 1 MPELPEVETVRRGLEPHLVGKTITRVEVR-RPKLRWP-VPEDFAERLSGQTILAVGRRGKYLLLDLDDGGTLISHLGMSG 78 (274)
T ss_pred CCchhHHHHHHHHHHHHcCCCEEEEEEEc-CCccccC-ChHHHHhhcCCCEEEEEEeeeeEEEEEeCCCCEEEEeCCcEE
Confidence 99999999999999999999999999997 4555543 478899999999999999999999999997679999999999
Q ss_pred EEEEeecceeccccccccCCCCCCCCeeEEEEEEcCCceEEEecCCcccEEEEecC--CCCCCCcccCCCCCCCCCCCHH
Q 022922 81 AIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELSFTDKRRFAKVRLLND--PTSVPPISELGPDALLEPMTVD 158 (290)
Q Consensus 81 ~l~~~~~~~~~y~~~~~~~~~~~p~k~~~l~l~l~~g~~L~f~D~R~fG~i~l~~~--~~~~~~l~~LGpDpL~~~f~~~ 158 (290)
+|++... +.++++|.|++|.|+||..|.|+|+|+||++++++. ....+.+++||||||+++|+.+
T Consensus 79 ~~~~~~~-------------~~~~~~~~~~~l~l~~~~~l~f~D~R~fg~~~l~~~~~~~~~~~~~~LGpdpl~~~~~~~ 145 (274)
T PRK01103 79 SLRLLPE-------------DTPPEKHDHVDFVLDDGTVLRYNDPRRFGAMLLTPKGDLEAHPLLAHLGPEPLSDAFDGE 145 (274)
T ss_pred EEEEeCC-------------CCCCCceEEEEEEECCCCEEEEEcCCcCCEEEEEeCCccccchhHHhcCCCCCCccCCHH
Confidence 9998642 225568999999999998999999999999999963 2345568999999999999999
Q ss_pred HHHHHHcCCCCchHHHhhcccccccCCchhhhhhhhcccccccCcCCCCCHHHHHHHHHHHHHHHHH-Hhc-cccc----
Q 022922 159 EFTDSLSKKKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVREA-LGV-SLQF---- 232 (290)
Q Consensus 159 ~f~~~l~~~~~~IK~~LLDQ~~iaGIGNiyadEiLf~A~IhP~~~~~~Ls~~e~~~L~~~i~~vL~~-i~~-~~~~---- 232 (290)
+|.+++++++++||++||||++||||||||||||||+|||||.+++++||++|+++|++++++||+. |+. ++++
T Consensus 146 ~~~~~l~~~~~~Ik~~LLDQ~~iaGiGNiya~EiLf~a~I~P~~~~~~Ls~~~~~~L~~~~~~vl~~ai~~gg~t~~~~~ 225 (274)
T PRK01103 146 YLAAKLRKKKTAIKPALLDQTVVVGVGNIYADEALFRAGIHPERPAGSLSRAEAERLVDAIKAVLAEAIEQGGTTLRDYV 225 (274)
T ss_pred HHHHHHhcCCccHHHHhhcCCeEecccHhHHHHHHHHcCCCccCccccCCHHHHHHHHHHHHHHHHHHHHcCCCcccccc
Confidence 9999999999999999999999999999999999999999999999999999999999999999999 998 3332
Q ss_pred ---cccccCccceeecCCCCCCccccccceeee---ccceeeecc
Q 022922 233 ---YKCYFAKPYVHKKHRENKICRLFKVRLKLM---LTAAAFLLN 271 (290)
Q Consensus 233 ---~~~~~~~~~~~vy~R~g~~C~~Cg~~i~~~---~~~~~~~~~ 271 (290)
+..+.|+.+++||+|+|+|||+||++|.++ ||+|+||-+
T Consensus 226 ~~~g~~g~~~~~l~Vy~R~g~pC~~Cg~~I~~~~~~gR~t~~CP~ 270 (274)
T PRK01103 226 NADGKPGYFQQSLQVYGREGEPCRRCGTPIEKIKQGGRSTFFCPR 270 (274)
T ss_pred ccCCCCCCccceeEEcCCCCCCCCCCCCeeEEEEECCCCcEECcC
Confidence 334568889999999999999999999855 899999964
No 4
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=100.00 E-value=9.3e-74 Score=527.03 Aligned_cols=255 Identities=34% Similarity=0.497 Sum_probs=227.8
Q ss_pred CChHHHHHHHHHHHHHcCCCeEEEEEecCCCceec-cCChhhHHhhhcCCEEEEEEeeeeEEEEEeCCCCceEEecCceE
Q 022922 2 PELPEVEAARRAIEEHCIGKKIVKSIIADDNKVID-GVSASDFEASVLGKAILSAHRKGKNLWLRLDSPPFPSFQFGMTG 80 (290)
Q Consensus 2 PELPEVe~~~~~L~~~~~Gk~I~~v~~~~~~~~~~-~~~~~~f~~~L~G~~i~~v~RrGK~L~~~l~~~~~L~~HLgMtG 80 (290)
|||||||++++.|++.+.|++|++|++.. ++++. ..++++|.+.|.|++|++|+|+||||+|+|+++ +|++||||||
T Consensus 1 PELPEVe~~~~~L~~~~~G~~I~~v~~~~-~~~~~~~~~~~~~~~~L~G~~i~~v~r~GK~L~~~l~~~-~l~~HLgM~G 78 (272)
T TIGR00577 1 PELPEVETVRRGLEPLVLGKTIKSVEVVL-RNPVLRPAGPEDLQKRLLGQTILSIQRRGKYLLFELDDG-ALVSHLRMEG 78 (272)
T ss_pred CCCccHHHHHHHHHHHcCCCEEEEEEEeC-CceeecCCChHHHHHHhcCCeeeeEEEeeeEEEEECCCC-EEEEECceEE
Confidence 99999999999999999999999999974 45443 235678999999999999999999999999977 9999999999
Q ss_pred EEEEeecceeccccccccCCCCCCCCeeEEEEEEcCCceEEEecCCcccEEEEecCCC--CCCCcccCCCCCCCCCCCHH
Q 022922 81 AIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELSFTDKRRFAKVRLLNDPT--SVPPISELGPDALLEPMTVD 158 (290)
Q Consensus 81 ~l~~~~~~~~~y~~~~~~~~~~~p~k~~~l~l~l~~g~~L~f~D~R~fG~i~l~~~~~--~~~~l~~LGpDpL~~~f~~~ 158 (290)
+|++... +.++++|.|++|.|+|+..|+|+|+|+||++++++..+ ..+.+++||||||+++||.+
T Consensus 79 ~~~~~~~-------------~~~~~~~~~~~l~~~~~~~l~~~D~R~fg~~~l~~~~~~~~~~~l~~LGpDpl~~~~~~~ 145 (272)
T TIGR00577 79 KYRLEAV-------------PDAPEKHDHVDFLFDDGTELRYHDPRRFGTWLLFDRGQVENVPLLAKLGPEPLSEDFTAE 145 (272)
T ss_pred EEEEecC-------------CCCCCCcEEEEEEECCCCEEEEEcCCcCCEEEEEeCcccccchHHHhcCCCCCCCcCCHH
Confidence 9998642 22446899999999999899999999999999997422 23468999999999999999
Q ss_pred HHHHHHcCCCCchHHHhhcccccccCCchhhhhhhhcccccccCcCCCCCHHHHHHHHHHHHHHHHH-Hhc-cccc----
Q 022922 159 EFTDSLSKKKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVREA-LGV-SLQF---- 232 (290)
Q Consensus 159 ~f~~~l~~~~~~IK~~LLDQ~~iaGIGNiyadEiLf~A~IhP~~~~~~Ls~~e~~~L~~~i~~vL~~-i~~-~~~~---- 232 (290)
+|.+++++++++||++||||++||||||||||||||+|||||.+++++||++|+++|+++|++||+. |+. ++++
T Consensus 146 ~~~~~l~~~~~~Ik~~LlDQ~vvaGIGNiyadEiLf~a~I~P~~~~~~Ls~~~~~~L~~~i~~vL~~ai~~gg~~~~~~~ 225 (272)
T TIGR00577 146 YLFEKLAKSKRKIKTALLDQRLVAGIGNIYADEVLFRAGIHPERLANSLSKEECELLHRAIKEVLRKAIEMGGTTIRDYS 225 (272)
T ss_pred HHHHHHhcCCCcHHHHHhcCCeEecccHHHHHHHHHHcCCCcchhhccCCHHHHHHHHHHHHHHHHHHHHcCCCcccccc
Confidence 9999999999999999999999999999999999999999999999999999999999999999999 998 3332
Q ss_pred ---cccccCccceeecCCCCCCccccccceeee---ccceeeecc
Q 022922 233 ---YKCYFAKPYVHKKHRENKICRLFKVRLKLM---LTAAAFLLN 271 (290)
Q Consensus 233 ---~~~~~~~~~~~vy~R~g~~C~~Cg~~i~~~---~~~~~~~~~ 271 (290)
+..+.|+.+++||+|+|+|||+||++|.+. ||+|+||-+
T Consensus 226 ~~~g~~g~~~~~~~Vy~r~g~pC~~Cg~~I~~~~~~gR~t~~CP~ 270 (272)
T TIGR00577 226 NSDGHNGYFQQELQVYGRKGEPCRRCGTPIEKIKVGGRGTHFCPQ 270 (272)
T ss_pred ccCCCCCcccceeEEeCCCCCCCCCCCCeeEEEEECCCCCEECCC
Confidence 223457888999999999999999999855 999999964
No 5
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=100.00 E-value=2.6e-73 Score=523.13 Aligned_cols=244 Identities=30% Similarity=0.434 Sum_probs=219.0
Q ss_pred CCChHHHHHHHHHHHHHcCCCeEEEEEecCCCceeccCChhhHHhhhcCCEEEEEEeeeeEEEEEeCCCCceEEecCceE
Q 022922 1 MPELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKNLWLRLDSPPFPSFQFGMTG 80 (290)
Q Consensus 1 MPELPEVe~~~~~L~~~~~Gk~I~~v~~~~~~~~~~~~~~~~f~~~L~G~~i~~v~RrGK~L~~~l~~~~~L~~HLgMtG 80 (290)
||||||||++++.|++.+.|++|++|++.. ++++ .|.+.|.|++|++|+|+||||+|+|+++.+|++||||||
T Consensus 1 MPELPEVe~~~~~L~~~~~G~~I~~v~~~~-~~~~------~~~~~l~G~~i~~v~rrGK~L~~~l~~~~~L~~HLgMtG 73 (269)
T PRK14811 1 MPELPEVETTRRKLEPLLLGQTIQQVVHDD-PARY------RNTELAEGRRVLGLSRRGKYLLLHLPHDLELIVHLGMTG 73 (269)
T ss_pred CCcchHHHHHHHHHHHHhCCCEEEEEEeCC-ccee------chHHhCCCCEEEEEEEEeeEEEEEcCCCCEEEEeCCceE
Confidence 999999999999999999999999999873 4443 467789999999999999999999997679999999999
Q ss_pred EEEEeecceeccccccccCCCCCCCCeeEEEEEEcCCceEEEecCCcccEEEEecCC--CCCCCcccCCCCCCCCCCCHH
Q 022922 81 AIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELSFTDKRRFAKVRLLNDP--TSVPPISELGPDALLEPMTVD 158 (290)
Q Consensus 81 ~l~~~~~~~~~y~~~~~~~~~~~p~k~~~l~l~l~~g~~L~f~D~R~fG~i~l~~~~--~~~~~l~~LGpDpL~~~f~~~ 158 (290)
+|++. |++|.|++|.|+ +..|+|+|+|+||++++++.. .....+++||||||+++|+.+
T Consensus 74 ~~~~~------------------~~~~~~l~l~~~-~~~l~~~D~R~fg~~~l~~~~~~~~~~~l~~LGpDpL~~~~~~~ 134 (269)
T PRK14811 74 GFRLE------------------PGPHTRVTLELP-GRTLYFTDPRRFGKWWVVRAGDYREIPLLARMGPEPLSDDFTEP 134 (269)
T ss_pred EEEEE------------------CCCeEEEEEEeC-CCEEEEEeCCCCCEEEEEeCcccccchHHhhcCCCCCCCcCCHH
Confidence 99974 236999999998 668999999999999999632 223558999999999999999
Q ss_pred HHHHHHcCCCCchHHHhhcccccccCCchhhhhhhhcccccccCcCCCCCHHHHHHHHHHHHHHHHH-Hhc-ccccc---
Q 022922 159 EFTDSLSKKKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVREA-LGV-SLQFY--- 233 (290)
Q Consensus 159 ~f~~~l~~~~~~IK~~LLDQ~~iaGIGNiyadEiLf~A~IhP~~~~~~Ls~~e~~~L~~~i~~vL~~-i~~-~~~~~--- 233 (290)
+|.++++ ++++||++||||++||||||||||||||+|||||.+++++||++|+++|+++|++||+. |+. ++++.
T Consensus 135 ~~~~~l~-~~~~Ik~~LlDQ~~iaGIGNiyadEiLf~A~I~P~~~~~~Ls~~~~~~L~~~i~~vl~~ai~~gg~~~~~~~ 213 (269)
T PRK14811 135 EFVRALA-TARPVKPWLLSQKPVAGVGNIYADESLWRARIHPARPATSLKAPEARRLYRAIREVMAEAVEAGGSTLSDGS 213 (269)
T ss_pred HHHHHHh-cCCcHHHHHhcCceeecccHHHHHHHHHHcCCCccCCcccCCHHHHHHHHHHHHHHHHHHHHcCCccccCcc
Confidence 9999999 89999999999999999999999999999999999999999999999999999999999 999 33332
Q ss_pred ------ccccCccceeecCCCCCCccccccceeee---ccceeeecc
Q 022922 234 ------KCYFAKPYVHKKHRENKICRLFKVRLKLM---LTAAAFLLN 271 (290)
Q Consensus 234 ------~~~~~~~~~~vy~R~g~~C~~Cg~~i~~~---~~~~~~~~~ 271 (290)
..+.|+.+++||+|+|+|||+||++|.+. ||+|+||-+
T Consensus 214 ~~~~~g~~g~~~~~~~Vy~R~g~pC~~Cg~~I~~~~~~gR~ty~Cp~ 260 (269)
T PRK14811 214 YRQPDGEPGGFQFQHAVYGREGQPCPRCGTPIEKIVVGGRGTHFCPQ 260 (269)
T ss_pred cccCCCCcccccceEEecCCCcCCCCcCCCeeEEEEECCCCcEECCC
Confidence 23467888999999999999999998855 899999975
No 6
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=100.00 E-value=3e-71 Score=510.30 Aligned_cols=253 Identities=27% Similarity=0.418 Sum_probs=225.7
Q ss_pred CCChHHHHHHHHHHHHHcCCCeEEEEEecCCCceeccCChhhHHhhhcCCEEEEEEeeeeEEEEEeCCCC----ceEEec
Q 022922 1 MPELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKNLWLRLDSPP----FPSFQF 76 (290)
Q Consensus 1 MPELPEVe~~~~~L~~~~~Gk~I~~v~~~~~~~~~~~~~~~~f~~~L~G~~i~~v~RrGK~L~~~l~~~~----~L~~HL 76 (290)
||||||||++++.|++.+.|++|++|++. .+++++..++++|.+.|.|++|++|.|+||||+++|+++. +|++||
T Consensus 1 MPELPEVe~~~~~L~~~~~G~~I~~v~~~-~~~~~~~~~~~~~~~~l~G~~i~~v~rrGK~L~~~l~~~~~~~~~L~~HL 79 (272)
T PRK14810 1 MPELPEVETVARGLAPRAAGRRIATAEFR-NLRIPRKGDPDLMAARLAGRKILSVKRVGKHIVADLEGPGEPRGQWIIHL 79 (272)
T ss_pred CCchHHHHHHHHHHHHHhCCCEEEEEEEC-CCCccccCChHHHHHhcCCCEEEEEEEEeeEEEEECCCCCCccCeEEEeC
Confidence 99999999999999999999999999997 4566554456789999999999999999999999999764 899999
Q ss_pred CceEEEEEeecceeccccccccCCCCCCCCeeEEEEEEcCCceEEEecCCcccEEEEecCCCCCCCcccCCCCCCCCCCC
Q 022922 77 GMTGAIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELSFTDKRRFAKVRLLNDPTSVPPISELGPDALLEPMT 156 (290)
Q Consensus 77 gMtG~l~~~~~~~~~y~~~~~~~~~~~p~k~~~l~l~l~~g~~L~f~D~R~fG~i~l~~~~~~~~~l~~LGpDpL~~~f~ 156 (290)
||||+|++.+. +.++++|.|++|.|++|..|.|+|+|+||+++++++. ...+++||||||+ +|
T Consensus 80 gMtG~~~~~~~-------------~~~~~~~~~~~l~l~~~~~l~f~d~R~fg~~~l~~~~--~~~~~~LGpdpl~--~~ 142 (272)
T PRK14810 80 GMTGKLLLGGP-------------DTPSPKHTHAVLTLSSGKELRFVDSRQFGCIEYSEAF--PKRFARPGPEPLE--IS 142 (272)
T ss_pred ceeEEEEEecC-------------CCCCCCcEEEEEEeCCCCEEEEEecccCCEEEEeccc--cchhhhCCCCCCC--CC
Confidence 99999998642 2244689999999999888999999999999988632 3357999999997 89
Q ss_pred HHHHHHHHcCCCCchHHHhhcccccccCCchhhhhhhhcccccccCcCCCCCHHHHHHHHHHHHHHHHH-Hhc-cccc--
Q 022922 157 VDEFTDSLSKKKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVREA-LGV-SLQF-- 232 (290)
Q Consensus 157 ~~~f~~~l~~~~~~IK~~LLDQ~~iaGIGNiyadEiLf~A~IhP~~~~~~Ls~~e~~~L~~~i~~vL~~-i~~-~~~~-- 232 (290)
.++|.+++++++++||.+||||++||||||||||||||+|||||.+++++||++|+++|+++|++||+. |+. ++++
T Consensus 143 ~~~~~~~~~~~~~~ik~~Lldq~viaGiGNiya~EiLf~a~i~P~~~~~~l~~~~~~~l~~a~~~vl~~ai~~gg~~~~~ 222 (272)
T PRK14810 143 FEDFAALFRGRKTRIKSALLNQTLLRGVGNIYADEALFRAGIRPQRLASSLSRERLRKLHDAIGEVLREAIELGGSSVSD 222 (272)
T ss_pred HHHHHHHHhcCCccHHHHhhcCceeccccHhHHHHHHHHcCCCCCCCcccCCHHHHHHHHHHHHHHHHHHHHcCCCcccc
Confidence 999999999999999999999999999999999999999999999999999999999999999999999 998 3322
Q ss_pred -----cccccCccceeecCCCCCCccccccceeee---ccceeeecc
Q 022922 233 -----YKCYFAKPYVHKKHRENKICRLFKVRLKLM---LTAAAFLLN 271 (290)
Q Consensus 233 -----~~~~~~~~~~~vy~R~g~~C~~Cg~~i~~~---~~~~~~~~~ 271 (290)
+..+.|+.+++||+|+|+|||+||++|.++ ||+|+||-+
T Consensus 223 ~~~~~g~~g~~~~~~~Vy~R~g~pCprCG~~I~~~~~~gR~t~~CP~ 269 (272)
T PRK14810 223 YVDAEGRSGFFQLSHRVYQRTGEPCLNCKTPIRRVVVAGRSSHYCPH 269 (272)
T ss_pred ccCCCCCCCcchhhEeecCCCCCcCCCCCCeeEEEEECCCccEECcC
Confidence 234467888999999999999999998855 999999964
No 7
>PRK10445 endonuclease VIII; Provisional
Probab=100.00 E-value=3e-70 Score=501.42 Aligned_cols=248 Identities=19% Similarity=0.278 Sum_probs=217.2
Q ss_pred CCChHHHHHHHHHHHHHcCCCeEEEEEecCCCceeccCChhhHHhhhcCCEEEEEEeeeeEEEEEeCCCCceEEecCceE
Q 022922 1 MPELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKNLWLRLDSPPFPSFQFGMTG 80 (290)
Q Consensus 1 MPELPEVe~~~~~L~~~~~Gk~I~~v~~~~~~~~~~~~~~~~f~~~L~G~~i~~v~RrGK~L~~~l~~~~~L~~HLgMtG 80 (290)
||||||||++++.|++.+.|++|++|++.. ++ ..+|.+.|.|++|++|+|+||||+|+|+++.+|++||||||
T Consensus 1 MPELPEVe~~~~~L~~~~~g~~I~~v~~~~-~~------~~~~~~~l~g~~i~~v~rrGK~l~~~l~~~~~L~~HLgM~G 73 (263)
T PRK10445 1 MPEGPEIRRAADNLEAAIKGKPLTDVWFAF-PQ------LKPYESQLIGQRVTHIETRGKALLTHFSNGLTLYSHNQLYG 73 (263)
T ss_pred CCCchHHHHHHHHHHHHhCCCEEEEEEeCC-CC------hHHHHhhCCCCEEeEEEEEeEEEEEEcCCCCEEEEeCCcee
Confidence 999999999999999999999999999873 33 25788899999999999999999999997779999999999
Q ss_pred EEEEeecceeccccccccCCCCCCCCeeEEEEEEcCCceEEEecCCcccEEEEecC--CCCCCCcccCCCCCCCCCCCHH
Q 022922 81 AIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELSFTDKRRFAKVRLLND--PTSVPPISELGPDALLEPMTVD 158 (290)
Q Consensus 81 ~l~~~~~~~~~y~~~~~~~~~~~p~k~~~l~l~l~~g~~L~f~D~R~fG~i~l~~~--~~~~~~l~~LGpDpL~~~f~~~ 158 (290)
+|++..+. ...++.+|.|++|.|+|+..|.|+|+ ++++++. ....+.+++||||||+++||++
T Consensus 74 ~~~~~~~~-----------~~~~~~~~~~l~l~~~~~~~l~~~d~----~~~l~~~~~~~~~~~l~~lGpDpL~~~~~~~ 138 (263)
T PRK10445 74 VWRVVDTG-----------EEPQTTRVLRVRLQTADKTILLYSAS----DIEMLTPEQLTTHPFLQRVGPDVLDPNLTPE 138 (263)
T ss_pred EEEEeCCC-----------CCCCCCCcEEEEEEcCCCcEEEEECC----EEEEEeCccccccchHHhcCCCCCCCcCCHH
Confidence 99986431 11135689999999999989999994 7888863 2234457999999999999999
Q ss_pred HHHHHHcCC---CCchHHHhhcccccccCCchhhhhhhhcccccccCcCCCCCHHHHHHHHHHHHHHHHH-Hhc-cccc-
Q 022922 159 EFTDSLSKK---KITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVREA-LGV-SLQF- 232 (290)
Q Consensus 159 ~f~~~l~~~---~~~IK~~LLDQ~~iaGIGNiyadEiLf~A~IhP~~~~~~Ls~~e~~~L~~~i~~vL~~-i~~-~~~~- 232 (290)
+|.++++++ +++||++||||++||||||||||||||+|||||.+++++||++|+++|+++|++||+. |+. +++.
T Consensus 139 ~~~~~l~~~~~~~~~IK~~LLDQ~~vaGIGNiyadEiLf~A~I~P~~~~~~Ls~~~~~~L~~~i~~vl~~ai~~gg~~~~ 218 (263)
T PRK10445 139 QVKERLLSPRFRNRQFSGLLLDQAFLAGLGNYLRVEILWQAGLTPQHKAKDLNEAQLDALAHALLDIPRLSYATRGQVDE 218 (263)
T ss_pred HHHHHHhcCccccccHHHHHhcCCccccccHHHHHHHHHHcCCCcCCCcccCCHHHHHHHHHHHHHHHHHHHHcCCCCCC
Confidence 999999987 9999999999999999999999999999999999999999999999999999999999 998 3332
Q ss_pred -cccccCccceeecCCCCCCccccccceeee---ccceeeecc
Q 022922 233 -YKCYFAKPYVHKKHRENKICRLFKVRLKLM---LTAAAFLLN 271 (290)
Q Consensus 233 -~~~~~~~~~~~vy~R~g~~C~~Cg~~i~~~---~~~~~~~~~ 271 (290)
+..+.+ .+++||+|+|+|||+||++|.++ ||+|+||-+
T Consensus 219 ~~~~g~~-~~~~Vy~r~g~~Cp~Cg~~I~~~~~~gR~t~~CP~ 260 (263)
T PRK10445 219 NKHHGAL-FRFKVFHRDGEACERCGGIIEKTTLSSRPFYWCPG 260 (263)
T ss_pred CCCCCCc-ceEEEeCCCCCCCCCCCCEeEEEEECCCCcEECCC
Confidence 233445 46899999999999999998855 999999965
No 8
>cd08972 PF_Nei_N N-terminal domain of the plant and fungal Nei and related proteins. This family contains the N-terminal domain of plant and Fungi Nei and related proteins. It belongs to the FpgNei_N, [N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII)] domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. The plant and fungal FpgNei glycosylases prefer the
Probab=100.00 E-value=1.1e-34 Score=242.00 Aligned_cols=134 Identities=55% Similarity=0.989 Sum_probs=110.3
Q ss_pred CCChHHHHHHHHHHHHHcCCCeEEEEEecCCCceeccCChhhHHhhhcCCEEEEEEeeeeEEEEEeCC-CCceEEecCce
Q 022922 1 MPELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKNLWLRLDS-PPFPSFQFGMT 79 (290)
Q Consensus 1 MPELPEVe~~~~~L~~~~~Gk~I~~v~~~~~~~~~~~~~~~~f~~~L~G~~i~~v~RrGK~L~~~l~~-~~~L~~HLgMt 79 (290)
||||||||++++.|++.+.|++|++|++..+++++....+.+|.+.|.|++|++|.|+||||+|.|++ +.+|++|||||
T Consensus 1 MPELPEVe~v~~~L~~~l~G~~I~~v~~~~~~~~~~~~~~~~~~~~L~G~~i~~v~RrGKyL~~~l~~~~~~L~~HLgMt 80 (137)
T cd08972 1 MPELPEVERARRLLEEHCLGKKITKVDAQDDDKVFGGVTPGAFQKALLGRTITSAHRKGKYFWLTLDGDAPVPVMHFGMT 80 (137)
T ss_pred CCchHHHHHHHHHHHHHhCCCEEEEEEEcCCcceecCCChHHHHhhCCCCEEEeEeccccEEEEEcCCCCCEEEEEcccc
Confidence 99999999999999999999999999997556666544577899999999999999999999999997 56999999999
Q ss_pred EEEEEeecceeccc--cccccCCCCCCCCeeEEEEEEcCCceEEEecCCcccEEEEe
Q 022922 80 GAIYIKGVAVTQYK--RSAVKDTDEWPSKYSKFFVELDDGLELSFTDKRRFAKVRLL 134 (290)
Q Consensus 80 G~l~~~~~~~~~y~--~~~~~~~~~~p~k~~~l~l~l~~g~~L~f~D~R~fG~i~l~ 134 (290)
|+|.+.+++...|. .......+.+|+||+|+.|.|+||..|+|+|+|+||+++++
T Consensus 81 G~l~~~~~~~~~~~~~~~~~~~~~~~~~kh~~~~l~l~~g~~L~f~D~RrFG~~~l~ 137 (137)
T cd08972 81 GAISIKGVKTIYYKMLRPPKEEDQTWPPRFYKFVLTLEDGTELAFTDPRRLGRVRLV 137 (137)
T ss_pred eEEEEecCccceeeccccccccCCCCCCceEEEEEEeCCCCEEEEeCCCccceEecC
Confidence 99999754222221 11111112346789999999999999999999999999863
No 9
>cd08976 BaFpgNei_N_4 Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases. This family is an uncharacterized bacterial subgroup of the FpgNei_N domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. This N-terminal proline is conserved in this family. Escherichia coli Fpg prefers 8
Probab=100.00 E-value=1.8e-33 Score=228.54 Aligned_cols=117 Identities=32% Similarity=0.608 Sum_probs=104.6
Q ss_pred CChHHHHHHHHHHHHHcCCCeEEEEEecCCCceeccCChhhHHhhhcCCEEEEEEeeeeEEEEEeCCCCceEEecCceEE
Q 022922 2 PELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKNLWLRLDSPPFPSFQFGMTGA 81 (290)
Q Consensus 2 PELPEVe~~~~~L~~~~~Gk~I~~v~~~~~~~~~~~~~~~~f~~~L~G~~i~~v~RrGK~L~~~l~~~~~L~~HLgMtG~ 81 (290)
|||||||++++.|++.++|++|.+|++. .++++.. ++++|.+.|.|++|.+|+|+||||+++|+++.+|++||||||+
T Consensus 1 PELPEVe~~~~~l~~~~~g~~I~~v~~~-~~~~~~~-~~~~~~~~L~G~~i~~v~RrGK~L~~~l~~~~~L~~HLgMtG~ 78 (117)
T cd08976 1 PELPEVEVQKQYLERTSLHRKIVEVEVG-DDKILGE-PKATLREVLEGRTFTETHRIGKYLFLKTKEGGWLVMHFGMTGK 78 (117)
T ss_pred CCCcchHHHHHHHHHHhCCCEEEEEEEC-CCCEecc-CHHHHHhhcCCCEEEEEEEeeeEEEEEcCCCCEEEEEcceEEE
Confidence 9999999999999999999999999997 4565542 2678999999999999999999999999976799999999999
Q ss_pred EEEeecceeccccccccCCCCCCCCeeEEEEEEcCCceEEEecCCcccEEEE
Q 022922 82 IYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELSFTDKRRFAKVRL 133 (290)
Q Consensus 82 l~~~~~~~~~y~~~~~~~~~~~p~k~~~l~l~l~~g~~L~f~D~R~fG~i~l 133 (290)
|.+.++ +.+|++|.|++|.|+||..|+|+|+|+||++++
T Consensus 79 ~~~~~~-------------~~~~~kh~~~~l~l~~g~~l~~~D~R~fg~~~~ 117 (117)
T cd08976 79 LDYYPD-------------DEDPPKHARLLLHFEDGFRLAFECPRKFGRVRL 117 (117)
T ss_pred EEEECC-------------CCCCCCEEEEEEEECCCCEEEEeCCCccceeEC
Confidence 998642 235678999999999998999999999999874
No 10
>cd08966 EcFpg-like_N N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases. This family contains the N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases. It belongs to the FpgNei_N, [N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII)] domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. Es
Probab=100.00 E-value=2.8e-32 Score=222.23 Aligned_cols=120 Identities=36% Similarity=0.600 Sum_probs=107.3
Q ss_pred CChHHHHHHHHHHHHHcCCCeEEEEEecCCCceeccCChhhHHhhhcCCEEEEEEeeeeEEEEEeCCCCceEEecCceEE
Q 022922 2 PELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKNLWLRLDSPPFPSFQFGMTGA 81 (290)
Q Consensus 2 PELPEVe~~~~~L~~~~~Gk~I~~v~~~~~~~~~~~~~~~~f~~~L~G~~i~~v~RrGK~L~~~l~~~~~L~~HLgMtG~ 81 (290)
|||||||++++.|++.++|++|.+|++.+ ++.....++++|.+.|.|++|++|.|+||||+|.|+++.+|++||||||+
T Consensus 1 PELPEve~~~~~l~~~l~G~~I~~v~~~~-~~~~~~~~~~~~~~~l~G~~i~~v~r~GK~l~~~l~~~~~l~~HlgMtG~ 79 (120)
T cd08966 1 PELPEVETVRRGLAPHLVGRRIEDVEVRR-PKLRRPPDPEEFAERLVGRRITGVERRGKYLLFELDDGLVLVIHLGMTGR 79 (120)
T ss_pred CCCccHHHHHHHHHHHhCCCEEEEEEECC-CCeeccCChHHHHhhCCCCEEEEEEeeeEEEEEEcCCCCEEEEECCceeE
Confidence 99999999999999999999999999975 44544446788999999999999999999999999987899999999999
Q ss_pred EEEeecceeccccccccCCCCCCCCeeEEEEEEcCCceEEEecCCcccEEEEec
Q 022922 82 IYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELSFTDKRRFAKVRLLN 135 (290)
Q Consensus 82 l~~~~~~~~~y~~~~~~~~~~~p~k~~~l~l~l~~g~~L~f~D~R~fG~i~l~~ 135 (290)
|++.+. +.++++|.|+.|.|+||..|+|+|+|+||++++++
T Consensus 80 ~~~~~~-------------~~~~~~~~~l~l~~~~g~~l~f~D~R~fG~~~~~~ 120 (120)
T cd08966 80 LLVVPP-------------DEPPEKHDHVIFELDDGRELRFNDPRRFGTLLLVP 120 (120)
T ss_pred EEEeCC-------------CCCCCCcEEEEEEeCCCCEEEEEcCCCCcEEEEeC
Confidence 998642 23567899999999999999999999999999863
No 11
>PF01149 Fapy_DNA_glyco: Formamidopyrimidine-DNA glycosylase N-terminal domain; InterPro: IPR012319 This entry represents the catalytic domain of DNA glycosylase/AP lyase enzymes, which are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Most damage to bases in DNA is repaired by the base excision repair pathway []. These enzymes are primarily from bacteria, and have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC). Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines [, ]. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above (3.2.2 from EC, 4.2.99.18 from EC), but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine []. These protein contains three structural domains: an N-terminal catalytic core domain, a central helix-two turn-helix (H2TH) module and a C-terminal zinc finger []. The N-terminal catalytic domain and the C-terminal zinc finger straddle the DNA with the long axis of the protein oriented roughly orthogonal to the helical axis of the DNA. Residues that contact DNA are located in the catalytic domain and in a beta-hairpin loop formed by the zinc finger [].; GO: 0003684 damaged DNA binding, 0003906 DNA-(apurinic or apyrimidinic site) lyase activity, 0008270 zinc ion binding, 0016799 hydrolase activity, hydrolyzing N-glycosyl compounds, 0006284 base-excision repair; PDB: 1K82_C 3GQ3_A 3JR5_A 3SAT_A 3GPX_A 2F5Q_A 3SBJ_A 3U6S_A 3SAU_A 3SAR_A ....
Probab=100.00 E-value=9.4e-33 Score=223.80 Aligned_cols=116 Identities=34% Similarity=0.667 Sum_probs=100.8
Q ss_pred CChHHHHHHHHHHHHHcCCCeEEEEEecCCCceeccCChhhHHhhhcCCEEEEEEeeeeEEEEEeCCCCceEEecCceEE
Q 022922 2 PELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKNLWLRLDSPPFPSFQFGMTGA 81 (290)
Q Consensus 2 PELPEVe~~~~~L~~~~~Gk~I~~v~~~~~~~~~~~~~~~~f~~~L~G~~i~~v~RrGK~L~~~l~~~~~L~~HLgMtG~ 81 (290)
|||||||++++.|++.++|++|.+|++. ++++++++++++|.+.|.|++|++|+|+||||+|.|+++.+|++||||||+
T Consensus 1 PElPEVe~~~~~L~~~~~g~~I~~v~~~-~~~~~~~~~~~~~~~~l~g~~i~~v~rrGK~L~~~l~~~~~l~~HlgMtG~ 79 (116)
T PF01149_consen 1 PELPEVETVRRGLRPALVGKRIESVEVR-RPKILRNPEPEEFRKALQGRKITDVERRGKYLFFHLDGGLVLVVHLGMTGR 79 (116)
T ss_dssp --HHHHHHHHHHHHHHHTTCEEEEEEES-SGGGCCSSCCHHHHHHHTTEEEEEEEEETTEEEEEETTTEEEEEE-TTTEE
T ss_pred CCcHHHHHHHHHHHHHhCCCEEEEEEEc-CCccccCCCchHHHhhccceEEEEEEecccEEEEEeCCCCEEEEeeCCcEE
Confidence 9999999999999999999999999998 567777777777999999999999999999999999988899999999999
Q ss_pred EEEeecceeccccccccCCCCCCCCeeEEEEEEcCCceEEEecCCcccEEE
Q 022922 82 IYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELSFTDKRRFAKVR 132 (290)
Q Consensus 82 l~~~~~~~~~y~~~~~~~~~~~p~k~~~l~l~l~~g~~L~f~D~R~fG~i~ 132 (290)
|.+.. ..++++|+|++|.|+||..|+|+|+|+||+++
T Consensus 80 ~~~~~--------------~~~~~~~~~~~l~~~~g~~L~f~D~R~fg~~r 116 (116)
T PF01149_consen 80 LRLDP--------------PDWPPKHTRLRLRFEDGSRLRFVDPRRFGRVR 116 (116)
T ss_dssp EEEST--------------TCG-STTEEEEEEETSSEEEEEEETTS--EE-
T ss_pred EEecC--------------CCCCCCeEEEEEEECCCCEEEEEcCCCCCCCC
Confidence 99832 34678999999999999999999999999985
No 12
>cd08967 MeNeil1_N N-terminal domain of metazoan Nei-like glycosylase 1 (NEIL1). This family contains the N-terminal domain of metazoan NEIL1. It belongs to the FpgNei_N, [N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII)] domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. NEIL1 recognizes the oxidized pyrimidines 2,6-diamino-4-hydroxy-5-formamidopyrimidi
Probab=99.97 E-value=5.5e-31 Score=217.64 Aligned_cols=113 Identities=27% Similarity=0.336 Sum_probs=95.9
Q ss_pred CCChHHHHHHHHHHHHHcCCCeEEEEEecCCCceeccC-ChhhHHhhhcCCEEEEEEeeeeEEEEEeCCC----------
Q 022922 1 MPELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGV-SASDFEASVLGKAILSAHRKGKNLWLRLDSP---------- 69 (290)
Q Consensus 1 MPELPEVe~~~~~L~~~~~Gk~I~~v~~~~~~~~~~~~-~~~~f~~~L~G~~i~~v~RrGK~L~~~l~~~---------- 69 (290)
||||||||++++.|+++++|++|++|++.+ + +..++ .+..|.+ ++|+ +.||||||++.|+++
T Consensus 1 MPELPEVe~vr~~L~~~~~g~~I~~v~v~~-~-~~~~~~~~~~~~~----~~i~-~~RrGKyL~l~l~~~~~~~~~~~~~ 73 (131)
T cd08967 1 MPEGPELHLASLFVNKMCKGLIFTGAVEKS-S-VSKNPEVPFACKA----YTIS-AESRGKELRLILSPLPAANGKKECK 73 (131)
T ss_pred CCCcHHHHHHHHHHHHhcCCCEEEEEEEec-c-cccCCCCCcchhc----EEEE-EEeeeeEEEEEccCCcccccccccc
Confidence 999999999999999999999999999984 4 44332 3444444 8899 999999999999886
Q ss_pred ---C-ceEEecCceEEEEEeecceeccccccccCCCCCCCCeeEEEEEEcCC--ceEEEecCCcccEEEEe
Q 022922 70 ---P-FPSFQFGMTGAIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDG--LELSFTDKRRFAKVRLL 134 (290)
Q Consensus 70 ---~-~L~~HLgMtG~l~~~~~~~~~y~~~~~~~~~~~p~k~~~l~l~l~~g--~~L~f~D~R~fG~i~l~ 134 (290)
. +|++||||||++++.++ ++++||+|++|.|+|| ..|+|+|+|+||++++-
T Consensus 74 ~~~~~~Lv~HLgMtG~l~~~~~--------------~~~~kh~~l~~~~~dg~g~~L~f~D~RrFG~~~l~ 130 (131)
T cd08967 74 SQEEMRIVFRFGMSGSFQFTPV--------------DEIPKHAHLRFYTKEEPKRVLSFVDIRRFGTWQVG 130 (131)
T ss_pred ccCCCEEEEecCceeEEEEecC--------------CCCCCcEEEEEEeCCCCCCEEEEECCCceeEEEeC
Confidence 2 89999999999998632 1356899999999985 78999999999999863
No 13
>cd08773 FpgNei_N N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. These enzymes initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycolsylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. The FpgNei DNA glycosylases represent one of the two structural superfamilies of DNA glycosylases that recognize oxidized bases (the other is the HTH-GPD superfamily exemplified by Escherichia coli Nth). Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. One e
Probab=99.97 E-value=7.6e-31 Score=212.83 Aligned_cols=116 Identities=34% Similarity=0.608 Sum_probs=102.8
Q ss_pred CChHHHHHHHHHHHHHcCCCeEEEEEecCCCceeccCChhhHHhhhcCCEEEEEEeeeeEEEEEeCCCCceEEecCceEE
Q 022922 2 PELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKNLWLRLDSPPFPSFQFGMTGA 81 (290)
Q Consensus 2 PELPEVe~~~~~L~~~~~Gk~I~~v~~~~~~~~~~~~~~~~f~~~L~G~~i~~v~RrGK~L~~~l~~~~~L~~HLgMtG~ 81 (290)
|||||||++++.|++.++|++|++|++.+. .+..+ .+++|.+.|.|++|++|+|+||||++.|+++.+|++||||||+
T Consensus 1 PElPEVe~~~~~l~~~~~G~~I~~v~~~~~-~~~~~-~~~~~~~~l~G~~i~~v~r~GK~l~~~l~~~~~l~~HlgMtG~ 78 (117)
T cd08773 1 PELPEVELLRRKLRRALKGKRVTRVEVSDP-RRLFT-PAAELAAALIGRRVRGAERRGKYLLLELSGGPWLVIHLGMTGR 78 (117)
T ss_pred CCCccHHHHHHHHHHHhCCCEEEEEEECCC-ceecC-ChHHHHHHcCCCEEeeEEEeeeEEEEEcCCCCEEEEECCceEE
Confidence 999999999999999999999999999754 44432 3678999999999999999999999999977799999999999
Q ss_pred EEEeecceeccccccccCCCCCCCCeeEEEEEEcCCceEEEecCCcccEEE
Q 022922 82 IYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELSFTDKRRFAKVR 132 (290)
Q Consensus 82 l~~~~~~~~~y~~~~~~~~~~~p~k~~~l~l~l~~g~~L~f~D~R~fG~i~ 132 (290)
|++.+. +.++++|.|++|.|+|+..|+|+|+|+||+++
T Consensus 79 ~~~~~~-------------~~~~~~~~~~~~~~~~~~~l~f~d~R~fG~~~ 116 (117)
T cd08773 79 LRVCPE-------------GEPPPKHDRLVLRLANGSQLRFTDPRKFGRVE 116 (117)
T ss_pred EEEeCC-------------CCCCCCeEEEEEEECCCCEEEEECCCcccccc
Confidence 998642 23456899999999999899999999999985
No 14
>cd08973 BaFpgNei_N_1 Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases. This family is an uncharacterized bacterial subgroup of the FpgNei_N domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. This N-terminal proline is conserved in this family. Escherichia coli Fpg prefers 8
Probab=99.97 E-value=1.7e-30 Score=212.68 Aligned_cols=115 Identities=23% Similarity=0.371 Sum_probs=100.1
Q ss_pred CCChHHHHHHHHHHHHHcCCCeEEEEEecCCCceeccCChhhHHhhhcCCEEEEEEeeeeEEEEEeCCCCceEEecCceE
Q 022922 1 MPELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKNLWLRLDSPPFPSFQFGMTG 80 (290)
Q Consensus 1 MPELPEVe~~~~~L~~~~~Gk~I~~v~~~~~~~~~~~~~~~~f~~~L~G~~i~~v~RrGK~L~~~l~~~~~L~~HLgMtG 80 (290)
||||||||++++.|++.+.|++|.+|++.. +++.. ++++|.+.|.|++|++|.|+||||+|+|+++.+|++||||||
T Consensus 1 MPELPEve~~~~~L~~~l~Gk~I~~v~~~~-~~~~~--~~~~~~~~L~G~~i~~v~RrGK~l~~~~~~~~~L~~HLgMtG 77 (122)
T cd08973 1 MPELPEVEVYAENLERRLTGKTITRVELAS-KSLLV--TPDPPLEALEGRTVTGVRRHGKRLDFEFDNGLHLVLHLMLAG 77 (122)
T ss_pred CCChHHHHHHHHHHHHhcCCCEEEEEEEcC-ccccC--ChhHHHhhCCCCEEeEEEEEeeEEEEEcCCCCEEEEeCCCeE
Confidence 999999999999999999999999999974 44432 477899999999999999999999999997679999999999
Q ss_pred EEEEeecceeccccccccCCCCCCCCeeEEEEEEcC-CceEEEecCCcccE
Q 022922 81 AIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDD-GLELSFTDKRRFAK 130 (290)
Q Consensus 81 ~l~~~~~~~~~y~~~~~~~~~~~p~k~~~l~l~l~~-g~~L~f~D~R~fG~ 130 (290)
+|++.+. +..++++|+|++|.|+| |..|.|+|+|.--.
T Consensus 78 ~l~~~~~------------~~~~~~~~~~v~l~~~~~g~~L~~~D~r~~~~ 116 (122)
T cd08973 78 WLYWTEA------------GALLPGKKGPIALRFEDYGGGLDLTEAGTKKR 116 (122)
T ss_pred EEEEeCC------------CCCCCCCcEEEEEEEcCCCCEEEEECCCcccc
Confidence 9998643 11255689999999999 88999999986533
No 15
>PF06831 H2TH: Formamidopyrimidine-DNA glycosylase H2TH domain; InterPro: IPR015886 This entry represents a helix-2turn-helix DNA-binding domain found in DNA glycosylase/AP lyase enzymes, which are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Most damage to bases in DNA is repaired by the base excision repair pathway []. These enzymes are primarily from bacteria, and have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC). Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines [, ]. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above (3.2.2 from EC, 4.2.99.18 from EC), but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine []. These protein contains three structural domains: an N-terminal catalytic core domain, a central helix-two turn-helix (H2TH) module and a C-terminal zinc finger []. The N-terminal catalytic domain and the C-terminal zinc finger straddle the DNA with the long axis of the protein oriented roughly orthogonal to the helical axis of the DNA. Residues that contact DNA are located in the catalytic domain and in a beta-hairpin loop formed by the zinc finger []. This entry represents the central domain containing the DNA-binding helix-two turn-helix domain [].; GO: 0003684 damaged DNA binding, 0003906 DNA-(apurinic or apyrimidinic site) lyase activity, 0008270 zinc ion binding, 0016799 hydrolase activity, hydrolyzing N-glycosyl compounds, 0006289 nucleotide-excision repair; PDB: 3GQ3_A 3JR5_A 3SAT_A 3GPX_A 2F5Q_A 3SBJ_A 3U6S_A 3SAU_A 3SAR_A 2F5P_A ....
Probab=99.97 E-value=2e-31 Score=208.00 Aligned_cols=83 Identities=47% Similarity=0.684 Sum_probs=76.0
Q ss_pred CCCCCCCCCCCHHHHHHHHcCCCCchHHHhhcccccccCCchhhhhhhhcccccccCcCCCCCHHHHHHHHHHHHHHHHH
Q 022922 146 LGPDALLEPMTVDEFTDSLSKKKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVREA 225 (290)
Q Consensus 146 LGpDpL~~~f~~~~f~~~l~~~~~~IK~~LLDQ~~iaGIGNiyadEiLf~A~IhP~~~~~~Ls~~e~~~L~~~i~~vL~~ 225 (290)
||||||+++|+.++|.+++++++++||.+||||++||||||||+|||||+|||||.+++++||++++++|++++++||+.
T Consensus 1 LGpD~l~~~~~~~~~~~~l~~~~~~ik~~LlDQ~~iaGiGNiy~~EiLf~a~i~P~~~~~~L~~~~~~~l~~~~~~vl~~ 80 (92)
T PF06831_consen 1 LGPDPLSDEFDAEYFAERLRKRRRPIKAALLDQSVIAGIGNIYADEILFRAGIHPERPASSLSEEELRRLHEAIKRVLRE 80 (92)
T ss_dssp S--BTTSTTS-HHHHHHHHHTCCSBHHHHHHCTTTSTT--HHHHHHHHHHTTB-TTSBGGGSHHHHHHHHHHHHHHHHHH
T ss_pred CCCCCCCCcCCHHHHHHHHhcCcchHHHHHhCCCccccCcHHHHHHHHHHcCCCccCccccCCHHHHHHHHHHHHHHHHH
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred -Hhc
Q 022922 226 -LGV 228 (290)
Q Consensus 226 -i~~ 228 (290)
|+.
T Consensus 81 ai~~ 84 (92)
T PF06831_consen 81 AIEV 84 (92)
T ss_dssp HHHT
T ss_pred HHHc
Confidence 987
No 16
>cd08975 BaFpgNei_N_3 Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases. This family is an uncharacterized bacterial subgroup of the FpgNei_N domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. One exception is mouse Nei-like glycosylase 3 (Neil3) which forms a Schiff base int
Probab=99.96 E-value=1.2e-28 Score=200.49 Aligned_cols=112 Identities=23% Similarity=0.288 Sum_probs=99.0
Q ss_pred ChHHHHHHHHHHHHHcCCCeEEEEEecCCC--ceeccCChhhHHhhhcCCEEEEEEeeeeEEEEEeCCCCceEEecCceE
Q 022922 3 ELPEVEAARRAIEEHCIGKKIVKSIIADDN--KVIDGVSASDFEASVLGKAILSAHRKGKNLWLRLDSPPFPSFQFGMTG 80 (290)
Q Consensus 3 ELPEVe~~~~~L~~~~~Gk~I~~v~~~~~~--~~~~~~~~~~f~~~L~G~~i~~v~RrGK~L~~~l~~~~~L~~HLgMtG 80 (290)
||||||++++.|++.++|++|.+|++.++. .+++++++++|.+.|.|++|++++||||||+|.|+++ +|++||||||
T Consensus 2 ELPEVEtv~r~L~~~l~G~~I~~v~v~~~~~~~~~~~~~~~~~~~~L~G~~i~~v~RrGKyl~~~l~~~-~Li~HLgMtG 80 (117)
T cd08975 2 ELPESATLSKQLNETLKGKRITDVFPATSPHKFTWYNGDPNEYDELLVGKRITSAEGFGGFVEIIFEDK-RLLFNDGVNV 80 (117)
T ss_pred CchhHHHHHHHHHHHcCCCEEeEEEECCCcccceeccCChHHHHHhCCCCEEEeEeeEeeEEEEEeCCC-EEEEECceEE
Confidence 999999999999999999999999998542 4444445789999999999999999999999999975 9999999999
Q ss_pred EEEEeecceeccccccccCCCCCCCCeeEEEEEEcCCceEEEecCCcccEE
Q 022922 81 AIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELSFTDKRRFAKV 131 (290)
Q Consensus 81 ~l~~~~~~~~~y~~~~~~~~~~~p~k~~~l~l~l~~g~~L~f~D~R~fG~i 131 (290)
+|.+. +.+|++|+|++|.|+||..|+|+ +++||.+
T Consensus 81 ~l~~~---------------~~~~~kh~~l~l~~~dg~~L~f~-~~~~~~~ 115 (117)
T cd08975 81 RYYYG---------------GEKIPKKYQLLIEFDDDSFLVFT-VAMYGGI 115 (117)
T ss_pred EEEeC---------------CCCCCCeEEEEEEECCCCEEEEE-EEEEeee
Confidence 99973 12456899999999999899999 9999986
No 17
>cd08971 AcNei2_N N-terminal domain of the actinomycetal Nei2 and related DNA glycosylases. This family contains the N-terminal domain of the actinomycetal Nei2 and related DNA glycosylases. It belongs to the FpgNei_N, [N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII)] domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. This family contains mostly actinom
Probab=99.96 E-value=5.5e-28 Score=195.72 Aligned_cols=111 Identities=18% Similarity=0.272 Sum_probs=95.6
Q ss_pred CCChHHHHHHHHHHHHHcCCCeEEEEEecCCCceeccCChhhHHhhhcCCEEEEEEeeeeEEEEEeCCCCceEEecCceE
Q 022922 1 MPELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKNLWLRLDSPPFPSFQFGMTG 80 (290)
Q Consensus 1 MPELPEVe~~~~~L~~~~~Gk~I~~v~~~~~~~~~~~~~~~~f~~~L~G~~i~~v~RrGK~L~~~l~~~~~L~~HLgMtG 80 (290)
||||||||++++.|++.+.|++|.+|++.+ +++ +.+.|.|++|++++|+||||++.|+++.+|++||||||
T Consensus 1 MPELPEVe~v~~~L~~~~~G~~I~~v~~~~-~~~--------~~~~l~G~~i~~v~R~GK~L~~~l~~~~~l~vHLgMtG 71 (114)
T cd08971 1 MPEGDTVHRAARRLRRALAGRVLTRADLRV-PRL--------ATADLAGRTVEEVVARGKHLLIRFDGGLTLHTHLRMDG 71 (114)
T ss_pred CCCcHHHHHHHHHHHHHhCCCEEEEEEecC-chh--------hhhhcCCCEEEEEEEeeeEEEEEcCCCCEEEEeCCCcc
Confidence 999999999999999999999999999863 332 35689999999999999999999987779999999999
Q ss_pred EEEEeecceeccccccccCCC-CCCCCeeEEEEEEcCCceEEEecCCcccEEEEec
Q 022922 81 AIYIKGVAVTQYKRSAVKDTD-EWPSKYSKFFVELDDGLELSFTDKRRFAKVRLLN 135 (290)
Q Consensus 81 ~l~~~~~~~~~y~~~~~~~~~-~~p~k~~~l~l~l~~g~~L~f~D~R~fG~i~l~~ 135 (290)
+|++.++. .. .+|++|.|++|.|+||..|.|+| +.|++++
T Consensus 72 ~~~~~~~~-----------~~~~~~~k~~~~~l~~~~g~~l~f~~----~~~~~~~ 112 (114)
T cd08971 72 SWHVYRPG-----------ERWRRPAHQARAVLATADWTAVGFRL----GVLELVP 112 (114)
T ss_pred EEEEecCC-----------CCCCCCCCeEEEEEEcCCCeEEEEEc----ceEEEEe
Confidence 99986431 01 13568999999999999999999 4788875
No 18
>cd08974 BaFpgNei_N_2 Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases. This family is an uncharacterized bacterial subgroup of the FpgNei_N domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. This N-terminal proline is conserved in this family. Escherichia coli Fpg prefers 8
Probab=99.95 E-value=4.7e-27 Score=185.42 Aligned_cols=96 Identities=19% Similarity=0.250 Sum_probs=83.8
Q ss_pred CCChHHHHHHHHHHHHHcCCCeEEEEEecCCCceeccCChhhHHhhhcCCEEEEEEeeeeEEEEEeCCCCceEEecCceE
Q 022922 1 MPELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKNLWLRLDSPPFPSFQFGMTG 80 (290)
Q Consensus 1 MPELPEVe~~~~~L~~~~~Gk~I~~v~~~~~~~~~~~~~~~~f~~~L~G~~i~~v~RrGK~L~~~l~~~~~L~~HLgMtG 80 (290)
||||||||++++.|++ +.|++|++++.. ++ .+.+.|.|++|++|+||||||++.|++ .+|++||||||
T Consensus 1 MPELPEVe~~~~~L~~-~~g~~I~~v~~~--~~--------~~~~~l~G~~i~~v~RrGK~L~~~l~~-~~L~~HLgMtG 68 (98)
T cd08974 1 MPEGPSIVILREAAAA-FKGQTVIRASGN--AK--------IDKDRLAGQKVLAIRSWGKHFLLEFED-FTVRIHLLLFG 68 (98)
T ss_pred CCccHHHHHHHHHHHH-hCCCEEEEEEEc--cc--------chhhhcCCCEEEEEEEEccEEEEEECC-CEEEEeCCCee
Confidence 9999999999999998 999999999853 22 135689999999999999999999986 49999999999
Q ss_pred EEEEeecceeccccccccCCCCCCCCeeEEEEEEcCCceEEEec
Q 022922 81 AIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELSFTD 124 (290)
Q Consensus 81 ~l~~~~~~~~~y~~~~~~~~~~~p~k~~~l~l~l~~g~~L~f~D 124 (290)
+|++.+ +|++|+|++|.|+||..+.|+|
T Consensus 69 ~l~~~~----------------~~~~~~~~~l~~~~g~~~~~~~ 96 (98)
T cd08974 69 SYRINE----------------RKDAPPRLSLGFDNGELNFYTC 96 (98)
T ss_pred EEEEeC----------------CCCCcEEEEEEeCCCcEEEEec
Confidence 999852 2568999999999998777776
No 19
>cd08965 EcNei-like_N N-terminal domain of Escherichia coli Nei/endonuclease VIII and related DNA glycosylases. This family contains the N-terminal domain of proteobacteria Nei and related DNA glycosylases. It includes Escherichia coli Nei, and belongs to the FpgNei_N, [N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII)] domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff bas
Probab=99.94 E-value=2.5e-26 Score=186.25 Aligned_cols=113 Identities=17% Similarity=0.227 Sum_probs=96.8
Q ss_pred CChHHHHHHHHHHHHHcCCCeEEEEEecCCCceeccCChhhHHhhhcCCEEEEEEeeeeEEEEEeCCCCceEEecCceEE
Q 022922 2 PELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKNLWLRLDSPPFPSFQFGMTGA 81 (290)
Q Consensus 2 PELPEVe~~~~~L~~~~~Gk~I~~v~~~~~~~~~~~~~~~~f~~~L~G~~i~~v~RrGK~L~~~l~~~~~L~~HLgMtG~ 81 (290)
|||||||++++.|++.+.|++|.+|++.+ ++ ..+|.+.|.|++|++|+|+||||+++|+++.+|++||||||+
T Consensus 1 PELPEVe~~~~~L~~~~~g~~I~~v~~~~-~~------~~~~~~~l~G~~i~~v~RrGK~L~~~l~~~~~l~~HLgMtG~ 73 (115)
T cd08965 1 PEGPEIRRAADRIEAAIKGRPLEEVWFAF-PH------LKEYEAQLKGQNVTRVETRGKALLTHFDNGLSIYSHNQLYGV 73 (115)
T ss_pred CCchhHHHHHHHHHHHhCCCEEEEEEEcC-CC------hhHHHhhCCCCEEeEEEEeeeEEEEEeCCCCEEEEeCCceEE
Confidence 99999999999999999999999999873 32 357888999999999999999999999877799999999999
Q ss_pred EEEeecceeccccccccCCCCCCCCeeEEEEEEcCCceEEEecCCcccEEEEecC
Q 022922 82 IYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELSFTDKRRFAKVRLLND 136 (290)
Q Consensus 82 l~~~~~~~~~y~~~~~~~~~~~p~k~~~l~l~l~~g~~L~f~D~R~fG~i~l~~~ 136 (290)
|++..+. ...+|++|++++|.++||..+.|.+ +.++++++
T Consensus 74 ~~~~~~~-----------~~~~~~~~~rl~l~~~~g~~l~~~~----~~~~l~~~ 113 (115)
T cd08965 74 WRVRKRG-----------NYPKTNRQLRVALHTAKKSALLYSA----SDIDVLPT 113 (115)
T ss_pred EEEeCCC-----------CCCCCCCeEEEEEEcCCceEEeeCC----CEEEEecC
Confidence 9986421 0125678999999999998888887 47888763
No 20
>cd08970 AcNei1_N N-terminal domain of the actinomycetal Nei1 and related DNA glycosylases. This family contains the N-terminal domain of the actinomycetal Nei1 and related DNA glycosylases. It belongs to the FpgNei_N, [N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII)] domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. This family contains mostly actinom
Probab=99.94 E-value=3.1e-26 Score=184.37 Aligned_cols=109 Identities=19% Similarity=0.263 Sum_probs=89.9
Q ss_pred CCChHHHHHHHHHHHHHcCCCeEEEEEecCCCceeccCChhhHHhhhcCCEEEEEEeeeeEEEEEeCCCCceEEecCceE
Q 022922 1 MPELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKNLWLRLDSPPFPSFQFGMTG 80 (290)
Q Consensus 1 MPELPEVe~~~~~L~~~~~Gk~I~~v~~~~~~~~~~~~~~~~f~~~L~G~~i~~v~RrGK~L~~~l~~~~~L~~HLgMtG 80 (290)
||||||||++++.|++.+.|++| ++. .+++. +++|.+.|.|++|++|+||||||+++|+++.+|++||||||
T Consensus 1 MPELPEVe~v~~~L~~~l~G~~I---~v~-~~~~~----~~~~~~~l~G~~i~~v~RrGK~Ll~~l~~~~~L~~HLgMtG 72 (110)
T cd08970 1 MPEGHVIHRLARDLNAAFAGQPV---RVS-SPQGR----FADGAALLDGRVLADAEAHGKHLFLGFEGDRILHVHLGLYG 72 (110)
T ss_pred CCCcHHHHHHHHHHHHHhCCCEE---EEc-CCccc----chhHHhhCCCCEEEEEEEeeeEEEEEeCCCCEEEEeCCCee
Confidence 99999999999999999999999 343 23432 34788899999999999999999999987669999999999
Q ss_pred EEEEeecceeccccccccCCCCCCCCeeEEEEEEcCCceEEEecCCcccEEEE
Q 022922 81 AIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELSFTDKRRFAKVRL 133 (290)
Q Consensus 81 ~l~~~~~~~~~y~~~~~~~~~~~p~k~~~l~l~l~~g~~L~f~D~R~fG~i~l 133 (290)
+|++..+ + ++++|+|++|.|++... . .|+|+.+-+++
T Consensus 73 ~~~~~~~-------------~-~~~~h~~~~l~l~~~~~-~-~~~~~~~~~~~ 109 (110)
T cd08970 73 KFRFGGD-------------P-PPPPRGQVRLRLVGDTH-A-ADLRGPTVCEL 109 (110)
T ss_pred EEEEecC-------------C-CCCceEEEEEEECCCCc-E-EcCCCCceEEe
Confidence 9998642 1 34689999999977644 4 56777776665
No 21
>cd08968 MeNeil2_N N-terminal domain of metazoan Nei-like glycosylase 2 (NEIL2). This family contains the N-terminal domain of the metazoan protein Neil2. It belongs to the FpgNei_N, [N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII)] domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. NEIL2 repairs 5-hydroxyuracil (5-OHU) and other oxidized derivatives of
Probab=99.89 E-value=1.7e-22 Score=164.98 Aligned_cols=111 Identities=21% Similarity=0.404 Sum_probs=91.4
Q ss_pred CCChHHHHHHHHHHHHHcCCCeEEEEEecCCCceeccCChhhHHhhhcCCEEEEEEeeeeEEEEEeCC----------CC
Q 022922 1 MPELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKNLWLRLDS----------PP 70 (290)
Q Consensus 1 MPELPEVe~~~~~L~~~~~Gk~I~~v~~~~~~~~~~~~~~~~f~~~L~G~~i~~v~RrGK~L~~~l~~----------~~ 70 (290)
|||+|+|+++++.++ .+.|++|+.++.. .+ ....+.|.|+++++++++||+||+.|++ +.
T Consensus 1 MPEG~sIhrla~~~~-~f~G~~v~~~s~~-~~--------~~~a~~L~G~~l~~a~a~GKHL~l~F~~~~~~~~~~~~~~ 70 (126)
T cd08968 1 MPEGPSVRKFHHLVS-PFVGQRVVKVGGS-SK--------KINPNDLQGLRLQDSQVHGKNLFLHFDLDEEMGPDRDAGR 70 (126)
T ss_pred CCCcHHHHHHHHHHH-HhCCCEEEEcCCC-CC--------cchhhhcCCcEEEEEEEeccEEEEEecCcccccccccCCc
Confidence 999999999998887 7899999888543 11 1235679999999999999999999975 35
Q ss_pred ceEEecCceEEEEEeecceeccccccccCCCCCCCCeeEEEEEEcCCceEEEecC
Q 022922 71 FPSFQFGMTGAIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELSFTDK 125 (290)
Q Consensus 71 ~L~~HLgMtG~l~~~~~~~~~y~~~~~~~~~~~p~k~~~l~l~l~~g~~L~f~D~ 125 (290)
+|++||||+|+|++++.. +.+++.++++||+++.++.|+|+||..|.|+|+
T Consensus 71 ~lhvHLGM~Gs~~~~~~~----~~~~~~~~~~~~~~~~~l~l~f~~~~~l~F~~~ 121 (126)
T cd08968 71 WLRFHFGLFGSVRANEFS----RAKKANKRGDWKDPNPRLVLHFESGGFLVFYNC 121 (126)
T ss_pred eEEEeCCCEEEEEEcccc----cCcccccccCCCCCCCeEEEEeCCCcEEEEEcc
Confidence 899999999999998642 113344566799999999999999988999994
No 22
>cd08969 MeNeil3_N N-terminal domain of metazoan Nei-like glycosylase 3 (NEIL3). This family contains the N-terminal domain of the Metazoan Neil3. It belongs to the FpgNei_N, [N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII)] domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. In contrast, mouse NEIL3 (MmuNEIL3) forms a Schiff base intermediate via its N-
Probab=99.67 E-value=5e-16 Score=128.61 Aligned_cols=118 Identities=19% Similarity=0.258 Sum_probs=86.9
Q ss_pred CCChHHHHHHHHHHHH-HcCCCeEEEEEecCCCcee----ccC-----ChhhHHhhhcCCEEEEEEeeeeEEEEEeCCCC
Q 022922 1 MPELPEVEAARRAIEE-HCIGKKIVKSIIADDNKVI----DGV-----SASDFEASVLGKAILSAHRKGKNLWLRLDSPP 70 (290)
Q Consensus 1 MPELPEVe~~~~~L~~-~~~Gk~I~~v~~~~~~~~~----~~~-----~~~~f~~~L~G~~i~~v~RrGK~L~~~l~~~~ 70 (290)
|-|+|....-.+.+.. ...|+++..++.......- .+. +...|.+.|.|++|++++|+||||++.|+++
T Consensus 1 mvegpgc~lngek~~~~v~~~q~v~~~~g~~~~~~~~~~~~~~~~~~~~~~~f~~~L~G~~I~~v~RrGK~Lll~f~~~- 79 (140)
T cd08969 1 MVEGPGCTLNGEKIRARVEKGQRVVHVRGSAPSSPSGAASRNGAGSKDERSHVLDSLTGQVYTGVETLGKELFMYFGDK- 79 (140)
T ss_pred CccCCccccccHHHHHHhhccceeeeecccCCcCCCcccccccccccchhhHHHHhcCCCEEEEEEecccEEEEEcCCC-
Confidence 8899998777777764 3578999877654211111 010 1146899999999999999999999999875
Q ss_pred ceEEecCceEEEEEeecceeccccccccCCCCCCCCeeEEEEEEcCCceEEEecCCcccEEEEec
Q 022922 71 FPSFQFGMTGAIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELSFTDKRRFAKVRLLN 135 (290)
Q Consensus 71 ~L~~HLgMtG~l~~~~~~~~~y~~~~~~~~~~~p~k~~~l~l~l~~g~~L~f~D~R~fG~i~l~~ 135 (290)
+|++||||||+|++.++. ....+.++.++.+.|+++ .|+|+|+ .+.+-+
T Consensus 80 ~L~vHLGMtGsl~i~~~~-----------kk~~~~~~p~l~l~~~~~-~I~F~d~----sV~~r~ 128 (140)
T cd08969 80 ALRIHFGMNGSMRINPLE-----------SKDRSGASPVLEVQLTKD-LICFFDS----TVEIRN 128 (140)
T ss_pred EEEEecCeeeEEEEeccc-----------ccccCCCCCeEEEEcCCC-EEEEEec----ceEEeh
Confidence 999999999999997531 112345688999999887 5999994 455543
No 23
>PF05833 FbpA: Fibronectin-binding protein A N-terminus (FbpA); InterPro: IPR008616 This family consists of the N-terminal region of the prokaryotic fibronectin-binding protein, the C-terminal region is IPR008532 from INTERPRO. Fibronectin binding is considered to be an important virulence factor in streptococcal infections. Fibronectin is a dimeric glycoprotein that is present in a soluble form in plasma and extracellular fluids; it is also present in a fibrillar form on cell surfaces. Both the soluble and cellular forms of fibronectin may be incorporated into the extracellular tissue matrix. While fibronectin has critical roles in eukaryotic cellular processes, such as adhesion, migration and differentiation, it is also a substrate for the attachment of bacteria. The binding of pathogenic Streptococcus pyogenes and Staphylococcus aureus to epithelial cells via fibronectin facilitates their internalisation and systemic spread within the host [].; PDB: 3DOA_A 2ZBK_F 2HKJ_A 1Z5B_A 1Z5C_B 1MX0_F 1Z5A_A 1MU5_A 1Z59_A.
Probab=98.12 E-value=2.5e-05 Score=76.95 Aligned_cols=76 Identities=30% Similarity=0.412 Sum_probs=58.7
Q ss_pred CCCCCCCCCCCH-HHHHHHHcCCCCchHHHhhcccccccCCchhhhhhhhcccccccCcCCCCCHHHHHHHHHHHHHHHH
Q 022922 146 LGPDALLEPMTV-DEFTDSLSKKKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVRE 224 (290)
Q Consensus 146 LGpDpL~~~f~~-~~f~~~l~~~~~~IK~~LLDQ~~iaGIGNiyadEiLf~A~IhP~~~~~~Ls~~e~~~L~~~i~~vL~ 224 (290)
-+.+|++ ++. +.|.+.+......+..+|+.+ +.|+|..++.|++++|+|+|..++.+++++++.+|+++++.++.
T Consensus 165 ~~~~p~~--~~~~~~~~~~l~~~~~~l~~~L~~~--~~G~~~~la~ei~~ra~i~~~~~~~~~~~~~~~~l~~~~~~l~~ 240 (455)
T PF05833_consen 165 DKLDPLD--LEEFEEFIELLKKKEKTLVKALSKN--FQGFGPELAEEILYRAGIDKNKKVEELSDEEIEKLFEAIRELLN 240 (455)
T ss_dssp --B-CCC----H-HHHHHHHHCCG-BHHHHHHHH--CTT--HHHHHHHHCCCTS-TTSBGGG--HHHHCHHHHHHHHHHH
T ss_pred cCCCccc--chhHHHHHHhhccCcccHHHHHHHH--HHHhHHHHHHHHHHHhCCCCccccccchhhhHHHHHHHHHHhhh
Confidence 3677773 555 678888877778899998875 89999999999999999999999999999999999999999999
Q ss_pred H
Q 022922 225 A 225 (290)
Q Consensus 225 ~ 225 (290)
.
T Consensus 241 ~ 241 (455)
T PF05833_consen 241 E 241 (455)
T ss_dssp H
T ss_pred h
Confidence 8
No 24
>COG1293 Predicted RNA-binding protein homologous to eukaryotic snRNP [Transcription]
Probab=96.92 E-value=0.0092 Score=60.83 Aligned_cols=72 Identities=18% Similarity=0.264 Sum_probs=56.2
Q ss_pred CCCCCCCCHHHHHHHHcCCCCchHHHhhcccccccCCchhhhhhhhcccccccCcCCCCCHHHHHHHHHHHHHHHHH
Q 022922 149 DALLEPMTVDEFTDSLSKKKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVREA 225 (290)
Q Consensus 149 DpL~~~f~~~~f~~~l~~~~~~IK~~LLDQ~~iaGIGNiyadEiLf~A~IhP~~~~~~Ls~~e~~~L~~~i~~vL~~ 225 (290)
+|++ .+.+.|.........-++.+ ++.+.|+|-.|++|+||+||+.+..++.+++++++..+..++...+..
T Consensus 168 ~p~~--~~~~~~~~~~~~~~~~~~~~---~~~~~g~~~~~a~el~~rag~~~~~~~~~~~~~~~~~v~~~~~~~~~~ 239 (564)
T COG1293 168 NPYE--QSEEDFKELQLNSGADIVRL---LARFLGLGGLLAEELLSRAGLDKKVPAKDLFEEEIKKVREALEELLNP 239 (564)
T ss_pred Chhh--cChHHHHHHHhccchHHHHH---HHHhcCCCHHHHHHHHHhcCCCcCCchhhhhHHHHHHHHHHHHhhhhc
Confidence 7775 44455665554442333333 467899999999999999999999999999999999999999888764
No 25
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=96.91 E-value=0.00077 Score=55.29 Aligned_cols=51 Identities=29% Similarity=0.374 Sum_probs=45.4
Q ss_pred CCchHHHhhcccccccCCchhhhhhhhcccccccCcCCCCCHHHHHHHHHHHHH
Q 022922 168 KITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKE 221 (290)
Q Consensus 168 ~~~IK~~LLDQ~~iaGIGNiyadEiLf~A~IhP~~~~~~Ls~~e~~~L~~~i~~ 221 (290)
+.+|.-+| +-|-|||.-.|..|+-.+||||..++++||++|+++|-+.+..
T Consensus 12 ~k~v~~aL---~~I~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi~~l~~~i~~ 62 (122)
T PRK05179 12 NKRVVIAL---TYIYGIGRTRAKEILAAAGIDPDTRVKDLTDEELDKIREEIDK 62 (122)
T ss_pred CcEEEeee---cccccccHHHHHHHHHHhCcCcccccccCCHHHHHHHHHHHHh
Confidence 55666666 4588999999999999999999999999999999999998874
No 26
>PRK04184 DNA topoisomerase VI subunit B; Validated
Probab=96.76 E-value=0.0069 Score=61.19 Aligned_cols=74 Identities=24% Similarity=0.406 Sum_probs=65.5
Q ss_pred cCCCCCCCCCCCHHHHHHHHcC-CCCchHHHhhcccccccCCchhhhhhhhcccccccCcCCCCCHHHHHHHHHHHHHH
Q 022922 145 ELGPDALLEPMTVDEFTDSLSK-KKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEV 222 (290)
Q Consensus 145 ~LGpDpL~~~f~~~~f~~~l~~-~~~~IK~~LLDQ~~iaGIGNiyadEiLf~A~IhP~~~~~~Ls~~e~~~L~~~i~~v 222 (290)
..-|-|.. .+.+.+.+.++. ++++++.+|. +-++.||+--|+|++-.+|++|..+..+|+.+|+++|+++++.+
T Consensus 233 e~kpHP~g--v~~~~l~~m~~~t~~~~l~~fL~--~~f~~v~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~~ 307 (535)
T PRK04184 233 EIKPHPHG--VDLGTLKRMAARTKRRTLKEFLV--EEFSRVGDKTADEILEKAGLDPNKKPKELTREELERLVEAFKKY 307 (535)
T ss_pred cCCCCCCc--cCHHHHHHHHHhcccCCHHHHHH--HhhcccCHHHHHHHHHHcCCCCCCChhhCCHHHHHHHHHHHHhc
Confidence 45577764 788899999874 4689999994 67999999999999999999999999999999999999999976
No 27
>PF00416 Ribosomal_S13: Ribosomal protein S13/S18; InterPro: IPR001892 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S13 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S13 is known to be involved in binding fMet-tRNA and, hence, in the initiation of translation. It is a basic protein of 115 to 177 amino-acid residues that contains thee helices and a beta-hairpin in the core of the protein, forming a helix-two turns-helix (H2TH) motif, and a non-globular C-terminal extension. This family of ribosomal proteins is present in prokaryotes, eukaryotes and archaea [, ].; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3BBN_M 2QBB_M 3I1M_M 3OFP_M 3OFX_M 3OFO_M 1VS5_M 3OAQ_M 2QAL_M 3J18_M ....
Probab=96.62 E-value=0.0037 Score=50.01 Aligned_cols=52 Identities=29% Similarity=0.296 Sum_probs=46.1
Q ss_pred CCCchHHHhhcccccccCCchhhhhhhhcccccccCcCCCCCHHHHHHHHHHHHH
Q 022922 167 KKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKE 221 (290)
Q Consensus 167 ~~~~IK~~LLDQ~~iaGIGNiyadEiLf~A~IhP~~~~~~Ls~~e~~~L~~~i~~ 221 (290)
.+.+|.-+|. -|-|||+..|..|+-.+||||..++++||++|+.+|-+.+..
T Consensus 9 ~~k~i~~aLt---~IyGIG~~~A~~Ic~~lgi~~~~~~~~Ls~~~i~~l~~~i~~ 60 (107)
T PF00416_consen 9 GNKPIYIALT---KIYGIGRRKAKQICKKLGINPNKKVGDLSDEQIDKLRKIIEK 60 (107)
T ss_dssp TSSBHHHHHT---TSTTBCHHHHHHHHHHTTS-SSSBTTTSTHHHHHHHHHHHHT
T ss_pred CCcchHhHHh---hhhccCHHHHHHHHHHcCCChhhhcccCCHHHHHHHHHHHHH
Confidence 3667888884 789999999999999999999999999999999999988776
No 28
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=96.56 E-value=0.0018 Score=52.64 Aligned_cols=49 Identities=31% Similarity=0.384 Sum_probs=42.6
Q ss_pred CchHHHhhcccccccCCchhhhhhhhcccccccCcCCCCCHHHHHHHHHHHH
Q 022922 169 ITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIK 220 (290)
Q Consensus 169 ~~IK~~LLDQ~~iaGIGNiyadEiLf~A~IhP~~~~~~Ls~~e~~~L~~~i~ 220 (290)
..+.-+|. .|-|||--+|.||+-.+||+|..++++||++|+.+|-+.+.
T Consensus 13 K~v~iALt---~IyGIG~~~a~~I~~~~gi~~~~r~~eLteeei~~ir~~i~ 61 (121)
T COG0099 13 KRVVIALT---YIYGIGRRRAKEICKKAGIDPDKRVGELTEEEIERLRDAIQ 61 (121)
T ss_pred ceEeehhh---hhccccHHHHHHHHHHcCCCHhHhhccCCHHHHHHHHHHHH
Confidence 33444443 38899999999999999999999999999999999999888
No 29
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=96.47 E-value=0.0017 Score=39.89 Aligned_cols=23 Identities=4% Similarity=-0.063 Sum_probs=15.4
Q ss_pred CCCccccccceeee---ccceeeecc
Q 022922 249 NKICRLFKVRLKLM---LTAAAFLLN 271 (290)
Q Consensus 249 g~~C~~Cg~~i~~~---~~~~~~~~~ 271 (290)
|++|+||+..|..+ +|+++||..
T Consensus 1 G~~C~rC~~~~~~~~~~~r~~~~C~r 26 (30)
T PF06827_consen 1 GEKCPRCWNYIEDIGINGRSTYLCPR 26 (30)
T ss_dssp TSB-TTT--BBEEEEETTEEEEE-TT
T ss_pred CCcCccCCCcceEeEecCCCCeECcC
Confidence 68999999887744 889999963
No 30
>TIGR01052 top6b DNA topoisomerase VI, B subunit. This model describes DNA topoisomerase VI, an archaeal type II DNA topoisomerase (DNA gyrase).
Probab=96.13 E-value=0.024 Score=56.66 Aligned_cols=73 Identities=22% Similarity=0.307 Sum_probs=64.4
Q ss_pred cCCCCCCCCCCCHHHHHHHHcCC-CCchHHHhhcccccccCCchhhhhhhhccccc---ccCcCCCCCHHHHHHHHHHHH
Q 022922 145 ELGPDALLEPMTVDEFTDSLSKK-KITIKALLLDQSYISGIGNWVADEVLYQAKIH---PLQTAVSLSKESCATLLKCIK 220 (290)
Q Consensus 145 ~LGpDpL~~~f~~~~f~~~l~~~-~~~IK~~LLDQ~~iaGIGNiyadEiLf~A~Ih---P~~~~~~Ls~~e~~~L~~~i~ 220 (290)
..-|-|.. .+.+.+...++.. ++++..+|. +-++.||+-.|+|++..||+. |..+..+|+.+|+++|+++++
T Consensus 224 e~kpHP~g--v~~~~l~~m~~~t~~~~l~~fL~--~~f~~v~~~~a~~~~~~~g~~~~~~~~~~~~l~~~~~~~l~~~~~ 299 (488)
T TIGR01052 224 EMKPHPHG--VTIDDLKSMARSTRASTLRSFLV--SEFSRIGEKKIKELLEKYGIDVDPLDKKPKELTWDEAEKIVNAFK 299 (488)
T ss_pred cCCCCCCc--cCHHHHHHHHHhcCcccHHHHHH--HhhcccCHHHHHHHHHHhCCCccccCCChhhCCHHHHHHHHHHHH
Confidence 45577764 6888999988754 589999995 679999999999999999999 999999999999999999999
Q ss_pred H
Q 022922 221 E 221 (290)
Q Consensus 221 ~ 221 (290)
+
T Consensus 300 ~ 300 (488)
T TIGR01052 300 E 300 (488)
T ss_pred h
Confidence 7
No 31
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=95.83 E-value=0.0079 Score=51.25 Aligned_cols=52 Identities=27% Similarity=0.263 Sum_probs=47.5
Q ss_pred CCCchHHHhhcccccccCCchhhhhhhhcccccccCcCCCCCHHHHHHHHHHHHH
Q 022922 167 KKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKE 221 (290)
Q Consensus 167 ~~~~IK~~LLDQ~~iaGIGNiyadEiLf~A~IhP~~~~~~Ls~~e~~~L~~~i~~ 221 (290)
.+.+|.-+| +-|-|||.-.|..||-.+||||..++++||++|+.+|-+.|..
T Consensus 24 ~~K~v~~aL---t~I~GIG~~~A~~I~~~lgi~~~~~~~~Lt~~qi~~l~~~i~~ 75 (154)
T PTZ00134 24 GKRKVPYAL---TAIKGIGRRFAYLVCKKAGIDVTKRAGELTAEEIEKIVEIIAN 75 (154)
T ss_pred CCCEEEEee---cccccccHHHHHHHHHHcCcCcCCCcccCCHHHHHHHHHHHhc
Confidence 467888888 4599999999999999999999999999999999999998875
No 32
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=95.81 E-value=0.0095 Score=48.88 Aligned_cols=50 Identities=34% Similarity=0.426 Sum_probs=44.3
Q ss_pred CCchHHHhhcccccccCCchhhhhhhhcccccccCcCCCCCHHHHHHHHHHHH
Q 022922 168 KITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIK 220 (290)
Q Consensus 168 ~~~IK~~LLDQ~~iaGIGNiyadEiLf~A~IhP~~~~~~Ls~~e~~~L~~~i~ 220 (290)
+.+|.-+| +-|-|||--.|..|+-.+||||..++++||++|+++|.+.+.
T Consensus 12 ~k~v~~aL---t~i~GIG~~~A~~ic~~lgi~~~~~~~~Lt~~qi~~l~~~i~ 61 (122)
T CHL00137 12 NKRIEYAL---TYIYGIGLTSAKEILEKANIDPDIRTKDLTDEQISALREIIE 61 (122)
T ss_pred CCEeeeee---cccccccHHHHHHHHHHcCcCcCcCcccCCHHHHHHHHHHHH
Confidence 45566666 448899999999999999999999999999999999999885
No 33
>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=95.36 E-value=0.016 Score=46.91 Aligned_cols=50 Identities=28% Similarity=0.403 Sum_probs=44.5
Q ss_pred CCchHHHhhcccccccCCchhhhhhhhcccccccCcCCCCCHHHHHHHHHHHH
Q 022922 168 KITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIK 220 (290)
Q Consensus 168 ~~~IK~~LLDQ~~iaGIGNiyadEiLf~A~IhP~~~~~~Ls~~e~~~L~~~i~ 220 (290)
+.+|.-+| +-|-|||.-.|..|+-.+||||..++++||++|+++|-+.+.
T Consensus 10 ~k~v~~aL---~~i~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi~~l~~~l~ 59 (113)
T TIGR03631 10 NKRVEIAL---TYIYGIGRTRARKILEKAGIDPDKRVKDLTEEELNAIREEIE 59 (113)
T ss_pred CCEEeeee---eeeecccHHHHHHHHHHhCcCcccccccCCHHHHHHHHHHHH
Confidence 55666666 448999999999999999999999999999999999999885
No 34
>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=95.14 E-value=0.022 Score=48.10 Aligned_cols=51 Identities=20% Similarity=0.264 Sum_probs=45.5
Q ss_pred CCchHHHhhcccccccCCchhhhhhhhcccccccCcCCCCCHHHHHHHHHHHHH
Q 022922 168 KITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKE 221 (290)
Q Consensus 168 ~~~IK~~LLDQ~~iaGIGNiyadEiLf~A~IhP~~~~~~Ls~~e~~~L~~~i~~ 221 (290)
+.+|.-+| .-|-|||--.|..|+-++||||..++++||++|+.+|-+.|..
T Consensus 16 ~k~v~~aL---t~I~GIG~~~a~~I~~~lgi~~~~~~~~Lt~~qi~~l~~~i~~ 66 (144)
T TIGR03629 16 NKPVEYAL---TGIKGIGRRFARAIARKLGVDPNAKLGYLDDEEIEKLEEAVEN 66 (144)
T ss_pred CCEEEEee---cceeccCHHHHHHHHHHcCcCCCCCcccCCHHHHHHHHHHHHh
Confidence 55666666 3489999999999999999999999999999999999998876
No 35
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=95.10 E-value=0.022 Score=48.25 Aligned_cols=52 Identities=19% Similarity=0.258 Sum_probs=46.9
Q ss_pred CCCchHHHhhcccccccCCchhhhhhhhcccccccCcCCCCCHHHHHHHHHHHHH
Q 022922 167 KKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKE 221 (290)
Q Consensus 167 ~~~~IK~~LLDQ~~iaGIGNiyadEiLf~A~IhP~~~~~~Ls~~e~~~L~~~i~~ 221 (290)
.+.+|.-+| +.|-|||.-.|..||-.+||||..++++||++|+.+|-+.|..
T Consensus 19 ~~k~i~~aL---t~IyGIG~~~a~~Ic~~lgi~~~~~~~~Lt~~qi~~l~~~i~~ 70 (149)
T PRK04053 19 GTKPVEYAL---TGIKGIGRRTARAIARKLGLDPNAKLGYLSDEEIEKIEEALED 70 (149)
T ss_pred CCCEEeeec---cccccccHHHHHHHHHHcCcCCCCccCcCCHHHHHHHHHHHHh
Confidence 467888888 4599999999999999999999999999999999999988853
No 36
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=93.92 E-value=0.037 Score=33.62 Aligned_cols=22 Identities=14% Similarity=-0.007 Sum_probs=13.7
Q ss_pred Cccccccceeee-ccceeeecce
Q 022922 251 ICRLFKVRLKLM-LTAAAFLLNG 272 (290)
Q Consensus 251 ~C~~Cg~~i~~~-~~~~~~~~~~ 272 (290)
.||.||+++.+. +...+||.|+
T Consensus 1 ~CP~C~s~l~~~~~ev~~~C~N~ 23 (28)
T PF03119_consen 1 TCPVCGSKLVREEGEVDIRCPNP 23 (28)
T ss_dssp B-TTT--BEEE-CCTTCEEE--C
T ss_pred CcCCCCCEeEcCCCCEeEECCCC
Confidence 399999997754 8889999997
No 37
>COG1389 DNA topoisomerase VI, subunit B [DNA replication, recombination, and repair]
Probab=91.14 E-value=0.45 Score=47.16 Aligned_cols=98 Identities=21% Similarity=0.347 Sum_probs=73.4
Q ss_pred eEEEecCCcccEEEEecCC--CCCCCcccCCCCCCCCCCCHHHHHHHHcC-CCCchHHHhhcccccccCCchhhhhhhhc
Q 022922 119 ELSFTDKRRFAKVRLLNDP--TSVPPISELGPDALLEPMTVDEFTDSLSK-KKITIKALLLDQSYISGIGNWVADEVLYQ 195 (290)
Q Consensus 119 ~L~f~D~R~fG~i~l~~~~--~~~~~l~~LGpDpL~~~f~~~~f~~~l~~-~~~~IK~~LLDQ~~iaGIGNiyadEiLf~ 195 (290)
.+.|.|| -|.+++.+-. ...++=..+-|-|-. .+.+.+...++. +++.++.+|+ +-+.-||---++|+|=.
T Consensus 207 ~I~l~dP--dG~~~vf~r~t~~lP~pP~E~kPHP~g--vd~~~L~~M~~~T~~~tv~~fL~--sef~rig~~ta~e~~e~ 280 (538)
T COG1389 207 RIVLKDP--DGNLVVFPRSTDKLPKPPKEIKPHPHG--VDLDTLKKMAHRTRRSTVREFLV--SEFSRIGEKTADELLEY 280 (538)
T ss_pred EEEEECC--CCcEEEeccchhhCCCCccccCCCCcc--ccHHHHHHHHHHhhhhhHHHHHH--HHHHHhhhhhHHHHHHH
Confidence 3455555 2445554311 112233455677764 788899988875 5789999996 67888999999999999
Q ss_pred ccccccCcCCCCC----HHHHHHHHHHHHHH
Q 022922 196 AKIHPLQTAVSLS----KESCATLLKCIKEV 222 (290)
Q Consensus 196 A~IhP~~~~~~Ls----~~e~~~L~~~i~~v 222 (290)
+|.+|......|+ .+|+++|+++++++
T Consensus 281 ~g~~~~~~p~~L~~~~~~eea~~lv~a~~~~ 311 (538)
T COG1389 281 AGFDPDKKPRELTKKKTREEAEKLVEAFKKM 311 (538)
T ss_pred hcCCcccCHHHhhcccCHHHHHHHHHHHHhC
Confidence 9999999999999 99999999998854
No 38
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=90.48 E-value=0.18 Score=33.44 Aligned_cols=24 Identities=8% Similarity=0.045 Sum_probs=20.1
Q ss_pred CCCCccccccceeeeccceeeecc
Q 022922 248 ENKICRLFKVRLKLMLTAAAFLLN 271 (290)
Q Consensus 248 ~g~~C~~Cg~~i~~~~~~~~~~~~ 271 (290)
-++.||.||+|+-+--+|..||.+
T Consensus 16 L~~~Cp~C~~PL~~~k~g~~~Cv~ 39 (41)
T PF06677_consen 16 LDEHCPDCGTPLMRDKDGKIYCVS 39 (41)
T ss_pred hcCccCCCCCeeEEecCCCEECCC
Confidence 357899999999887788899964
No 39
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=89.73 E-value=0.14 Score=42.34 Aligned_cols=22 Identities=18% Similarity=0.043 Sum_probs=19.0
Q ss_pred CCccccccceeeeccceeeecce
Q 022922 250 KICRLFKVRLKLMLTAAAFLLNG 272 (290)
Q Consensus 250 ~~C~~Cg~~i~~~~~~~~~~~~~ 272 (290)
..||.||+|+-. =+|++||-+-
T Consensus 29 ~hCp~Cg~PLF~-KdG~v~CPvC 50 (131)
T COG1645 29 KHCPKCGTPLFR-KDGEVFCPVC 50 (131)
T ss_pred hhCcccCCccee-eCCeEECCCC
Confidence 569999999888 8999999863
No 40
>KOG3311 consensus Ribosomal protein S18 [Translation, ribosomal structure and biogenesis]
Probab=89.39 E-value=0.26 Score=41.66 Aligned_cols=55 Identities=25% Similarity=0.332 Sum_probs=47.7
Q ss_pred CCCchHHHhhcccccccCCchhhhhhhhcccccccCcCCCCCHHHHHHHHHHHHHHHH
Q 022922 167 KKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVRE 224 (290)
Q Consensus 167 ~~~~IK~~LLDQ~~iaGIGNiyadEiLf~A~IhP~~~~~~Ls~~e~~~L~~~i~~vL~ 224 (290)
-+..|.-+|+- |.|||--||.+++=.+++++...+++|+++|+.++.+.+..--+
T Consensus 22 g~~~V~fAl~~---i~Gig~~~A~~ic~K~~~~~~~r~gelt~~qi~~i~~i~~d~~~ 76 (152)
T KOG3311|consen 22 GKRKVTFALTS---IKGIGRRYAEIVCKKADLDLTKRAGELTEEQILRILQILNDPRQ 76 (152)
T ss_pred CCceeEEEEEE---EeeechhhhhhhhhhcCcchhhhhccccHHHHHHHHHHhcCHHH
Confidence 35677777765 99999999999999999999999999999999999998874333
No 41
>PRK00420 hypothetical protein; Validated
Probab=89.27 E-value=0.22 Score=40.29 Aligned_cols=24 Identities=13% Similarity=0.074 Sum_probs=20.9
Q ss_pred CCCccccccceeeeccceeeecce
Q 022922 249 NKICRLFKVRLKLMLTAAAFLLNG 272 (290)
Q Consensus 249 g~~C~~Cg~~i~~~~~~~~~~~~~ 272 (290)
+..||.||+++-..-+|..||.+=
T Consensus 23 ~~~CP~Cg~pLf~lk~g~~~Cp~C 46 (112)
T PRK00420 23 SKHCPVCGLPLFELKDGEVVCPVH 46 (112)
T ss_pred cCCCCCCCCcceecCCCceECCCC
Confidence 478999999999888999999863
No 42
>TIGR03847 conserved hypothetical protein. The conserved hypothetical protein described here occurs as part of the trio of uncharacterized proteins common in the Actinobacteria.
Probab=80.02 E-value=1.9 Score=37.39 Aligned_cols=49 Identities=16% Similarity=0.141 Sum_probs=38.4
Q ss_pred cccccCcCCCCCHHHHHHHHHHHHHHHHHHhccccccccccCccceeecCCCCCCccccccceeeeccceeeec
Q 022922 197 KIHPLQTAVSLSKESCATLLKCIKEVREALGVSLQFYKCYFAKPYVHKKHRENKICRLFKVRLKLMLTAAAFLL 270 (290)
Q Consensus 197 ~IhP~~~~~~Ls~~e~~~L~~~i~~vL~~i~~~~~~~~~~~~~~~~~vy~R~g~~C~~Cg~~i~~~~~~~~~~~ 270 (290)
--.|..---.||.++.+.+.+.+++|.. -|| .+||.||.||. -.-|+|-
T Consensus 126 ~~~p~~lrv~lt~~~ARafa~Ra~~VVa--------------------AGR--P~CPlCg~Pld---P~GH~Cp 174 (177)
T TIGR03847 126 EDGPDALRVRLTPGQARAFAKRARRVVA--------------------AGR--PPCPLCGRPID---PDGHICP 174 (177)
T ss_pred ccCCceEEEEcCHHHHHHHHHHHHHHHh--------------------CCC--CCCCCCCCCCC---CCCccCC
Confidence 3456666677999999999999998876 366 78999999994 4468884
No 43
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=78.41 E-value=1.7 Score=31.62 Aligned_cols=22 Identities=18% Similarity=0.363 Sum_probs=15.6
Q ss_pred CCccccccceeeeccceeeecceeEEe
Q 022922 250 KICRLFKVRLKLMLTAAAFLLNGYFIF 276 (290)
Q Consensus 250 ~~C~~Cg~~i~~~~~~~~~~~~~~~~~ 276 (290)
+|||-||.....+.. .+|||.|
T Consensus 7 KPCPFCG~~~~~v~~-----~~g~~~v 28 (64)
T PRK09710 7 KPCPFCGCPSVTVKA-----ISGYYRA 28 (64)
T ss_pred cCCCCCCCceeEEEe-----cCceEEE
Confidence 899999988776643 2556544
No 44
>TIGR00275 flavoprotein, HI0933 family. The model when searched with a partial length search brings in proteins with a dinucleotide-binding motif (Rossman fold) over the initial 40 residues of the model, including oxidoreductases and dehydrogenases. Partially characterized members include an FAD-binding protein from Bacillus cereus and flavoprotein HI0933 from Haemophilus influenzae.
Probab=78.13 E-value=3.1 Score=40.38 Aligned_cols=63 Identities=27% Similarity=0.335 Sum_probs=47.2
Q ss_pred CCCCHHHHHHHHc-----CCCCchHHHhhcccccccCCchhhhhhhhcccccccCcCCCCCHHHHHHHHHHHH
Q 022922 153 EPMTVDEFTDSLS-----KKKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIK 220 (290)
Q Consensus 153 ~~f~~~~f~~~l~-----~~~~~IK~~LLDQ~~iaGIGNiyadEiLf~A~IhP~~~~~~Ls~~e~~~L~~~i~ 220 (290)
++++.+++.+.+. .+++.++.+|- --+=+=+++.+|-.++|+|.+++++||++++++|.+.++
T Consensus 263 p~~~~~~~~~~~~~~~~~~~~~~~~~~l~-----~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~lk 330 (400)
T TIGR00275 263 PDLSEEELEQRLKRLRKSNPKKTVKNILK-----GLLPKRLAELLLEQLGIDPDLPAAQLSKKEIKKLVQLLK 330 (400)
T ss_pred CCCCHHHHHHHHHHHHHHChhhhHHHHhh-----hhhhHHHHHHHHHHcCCCCCCChHHCCHHHHHHHHHHHh
Confidence 3456666666553 34678887763 112344678889999999999999999999999998887
No 45
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=74.48 E-value=1.9 Score=31.94 Aligned_cols=23 Identities=13% Similarity=0.095 Sum_probs=15.5
Q ss_pred Cccccccceeee---ccceeeeccee
Q 022922 251 ICRLFKVRLKLM---LTAAAFLLNGY 273 (290)
Q Consensus 251 ~C~~Cg~~i~~~---~~~~~~~~~~~ 273 (290)
.||.|+.++.+. |-..+||-+|-
T Consensus 32 ~CPdC~~~Le~LkACGAvdYFC~~c~ 57 (70)
T PF07191_consen 32 FCPDCGQPLEVLKACGAVDYFCNHCH 57 (70)
T ss_dssp E-TTT-SB-EEEEETTEEEEE-TTTT
T ss_pred cCCCcccHHHHHHHhcccceeeccCC
Confidence 399999998855 78889999874
No 46
>TIGR00755 ksgA dimethyladenosine transferase. Alternate name: S-adenosylmethionine--6-N',N'-adenosyl (rRNA) dimethyltransferase
Probab=73.82 E-value=3.7 Score=37.17 Aligned_cols=51 Identities=25% Similarity=0.295 Sum_probs=40.4
Q ss_pred HHcCCCCchHHHhhcccccccCCchhhhhhhhcccccccCcCCCCCHHHHHHHHHH
Q 022922 163 SLSKKKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKC 218 (290)
Q Consensus 163 ~l~~~~~~IK~~LLDQ~~iaGIGNiyadEiLf~A~IhP~~~~~~Ls~~e~~~L~~~ 218 (290)
.+..++++|+..|- +.++| -...++|-.++|.|..++.+||.+|+.+|+++
T Consensus 202 ~F~~rrk~l~~~l~--~~~~~---~~~~~~l~~~~i~~~~r~~~l~~~~~~~l~~~ 252 (253)
T TIGR00755 202 AFSQRRKTLRNNLK--QLLKA---SKLEEVLEQLGLDPTARAEQLSPEDFLRLANL 252 (253)
T ss_pred HHccchHHHHHHHh--hhcch---hHHHHHHHHCCcCCCCCcccCCHHHHHHHHHh
Confidence 35778999999883 23333 14567888899999999999999999999875
No 47
>PF11290 DUF3090: Protein of unknown function (DUF3090); InterPro: IPR021441 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=73.35 E-value=4.4 Score=35.09 Aligned_cols=52 Identities=19% Similarity=0.179 Sum_probs=37.8
Q ss_pred hhcccccccCcCCCCCHHHHHHHHHHHHHHHHHHhccccccccccCccceeecCCCCCCccccccceeeeccceeee
Q 022922 193 LYQAKIHPLQTAVSLSKESCATLLKCIKEVREALGVSLQFYKCYFAKPYVHKKHRENKICRLFKVRLKLMLTAAAFL 269 (290)
Q Consensus 193 Lf~A~IhP~~~~~~Ls~~e~~~L~~~i~~vL~~i~~~~~~~~~~~~~~~~~vy~R~g~~C~~Cg~~i~~~~~~~~~~ 269 (290)
+...--.|..---.||..+.+.+.+.+.+|.. -|| .+||.||.||.- .-|+|
T Consensus 120 ~~~~~~~~~~lrv~lt~~~ARafa~ra~~VVa--------------------AGR--P~CPlCg~PlDP---~GH~C 171 (171)
T PF11290_consen 120 LDDDEEGPDALRVRLTPGQARAFARRAREVVA--------------------AGR--PPCPLCGEPLDP---EGHIC 171 (171)
T ss_pred ccCCcCCCCeEEEEcCHHHHHHHHHHHHHHHh--------------------CCC--CCCCCCCCCCCC---CCCcC
Confidence 33344455555666899999999999987765 366 789999999653 44666
No 48
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=71.39 E-value=1.5 Score=25.34 Aligned_cols=9 Identities=11% Similarity=0.379 Sum_probs=5.5
Q ss_pred cccccccee
Q 022922 252 CRLFKVRLK 260 (290)
Q Consensus 252 C~~Cg~~i~ 260 (290)
||.||..|.
T Consensus 2 Cp~CG~~~~ 10 (23)
T PF13240_consen 2 CPNCGAEIE 10 (23)
T ss_pred CcccCCCCC
Confidence 666666654
No 49
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=71.23 E-value=2.8 Score=26.86 Aligned_cols=23 Identities=13% Similarity=0.083 Sum_probs=19.4
Q ss_pred CCccccccceeeeccceeee-cce
Q 022922 250 KICRLFKVRLKLMLTAAAFL-LNG 272 (290)
Q Consensus 250 ~~C~~Cg~~i~~~~~~~~~~-~~~ 272 (290)
.+|+.||...-....|.+|| --|
T Consensus 9 ~~C~~C~~~~~~~~dG~~yC~~cG 32 (36)
T PF11781_consen 9 EPCPVCGSRWFYSDDGFYYCDRCG 32 (36)
T ss_pred CcCCCCCCeEeEccCCEEEhhhCc
Confidence 56999999977889999999 544
No 50
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=70.42 E-value=2.8 Score=27.15 Aligned_cols=23 Identities=9% Similarity=-0.093 Sum_probs=17.1
Q ss_pred CCCccccccc--ee---eeccceeeecc
Q 022922 249 NKICRLFKVR--LK---LMLTAAAFLLN 271 (290)
Q Consensus 249 g~~C~~Cg~~--i~---~~~~~~~~~~~ 271 (290)
..|||.||.. .. +-++|+.||..
T Consensus 3 ~~pCP~CGG~DrFr~~d~~g~G~~~C~~ 30 (37)
T smart00778 3 HGPCPNCGGSDRFRFDDKDGRGTWFCSV 30 (37)
T ss_pred ccCCCCCCCccccccccCCCCcCEEeCC
Confidence 4799999974 43 34779999863
No 51
>COG0030 KsgA Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis]
Probab=68.63 E-value=5.4 Score=36.88 Aligned_cols=52 Identities=29% Similarity=0.313 Sum_probs=43.3
Q ss_pred HHcCCCCchHHHhhcccccccCCchhhhhhhhcccccccCcCCCCCHHHHHHHHHHHHHH
Q 022922 163 SLSKKKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEV 222 (290)
Q Consensus 163 ~l~~~~~~IK~~LLDQ~~iaGIGNiyadEiLf~A~IhP~~~~~~Ls~~e~~~L~~~i~~v 222 (290)
.+..|++.+.+.|-+=.- ..|+|=+++|+|.+++.+||.+|+.+|+++++..
T Consensus 206 ~F~~RRKtl~n~l~~~~~--------~~~~l~~~~i~~~~R~e~ls~~~f~~L~~~l~~~ 257 (259)
T COG0030 206 AFSQRRKTLRNNLKNLFG--------LEEVLEAAGIDPNARAENLSPEDFLKLANALKGF 257 (259)
T ss_pred HHhhhhHHHHHHHHhhhh--------HHHHHHhcCCCcccChhhCCHHHHHHHHHHHhhh
Confidence 456788888888754321 6899999999999999999999999999988754
No 52
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=67.71 E-value=2.2 Score=28.09 Aligned_cols=21 Identities=5% Similarity=-0.045 Sum_probs=10.1
Q ss_pred CCccccccc--ee----eeccceeeec
Q 022922 250 KICRLFKVR--LK----LMLTAAAFLL 270 (290)
Q Consensus 250 ~~C~~Cg~~--i~----~~~~~~~~~~ 270 (290)
.|||.||.. .. +.++|+.||-
T Consensus 4 ~pCP~CGG~DrFri~~d~~~~G~~~C~ 30 (40)
T PF08273_consen 4 GPCPICGGKDRFRIFDDKDGRGTWICR 30 (40)
T ss_dssp E--TTTT-TTTEEEETT----S-EEET
T ss_pred CCCCCCcCccccccCcCcccCCCEECC
Confidence 689999965 33 3477999994
No 53
>PRK00274 ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed
Probab=66.96 E-value=7.5 Score=35.75 Aligned_cols=55 Identities=24% Similarity=0.336 Sum_probs=41.0
Q ss_pred HHHcCCCCchHHHhhcccccccCCchhhhhhhhcccccccCcCCCCCHHHHHHHHHHHH
Q 022922 162 DSLSKKKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIK 220 (290)
Q Consensus 162 ~~l~~~~~~IK~~LLDQ~~iaGIGNiyadEiLf~A~IhP~~~~~~Ls~~e~~~L~~~i~ 220 (290)
..+..++++|+..|-. ++ +..+ -..++|=.+||+|..++.+|+.+|+.+|++.+.
T Consensus 215 ~~F~~rrk~l~~~l~~--~~-~~~~-~~~~~l~~~~~~~~~r~~~l~~~~~~~L~~~~~ 269 (272)
T PRK00274 215 AAFAQRRKTLRNNLKN--LF-GSKE-KLEEALEAAGIDPNRRAETLSVEEFVRLANALA 269 (272)
T ss_pred HHHhchHHHHHHHHHh--hc-cchH-HHHHHHHHCCCCcCCCceeCCHHHHHHHHHHHH
Confidence 3456788999998832 11 1011 135778899999999999999999999998765
No 54
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=65.19 E-value=3 Score=31.33 Aligned_cols=34 Identities=29% Similarity=0.486 Sum_probs=26.2
Q ss_pred CCccccccceeeecc--ceeeecceeEEeechhhHH
Q 022922 250 KICRLFKVRLKLMLT--AAAFLLNGYFIFDGAKSLE 283 (290)
Q Consensus 250 ~~C~~Cg~~i~~~~~--~~~~~~~~~~~~~~~~~~~ 283 (290)
..|+.||+++++..+ |-.|=-.|+++-|.-||=+
T Consensus 34 t~ce~c~a~~kk~l~~vgi~fKGSGfYvtDsRksg~ 69 (82)
T COG2331 34 TTCEECGARLKKLLNAVGIVFKGSGFYVTDSRKSGK 69 (82)
T ss_pred ccChhhChHHHHhhccceEEEecceEEEecccccCC
Confidence 459999999997744 5566678899999877643
No 55
>PF00398 RrnaAD: Ribosomal RNA adenine dimethylase; InterPro: IPR001737 This family of proteins include rRNA adenine dimethylases (e.g. KsgA) and the Erythromycin resistance methylases (Erm). The bacterial enzyme KsgA catalyses the transfer of a total of four methyl groups from S-adenosyl-l-methionine (S-AdoMet) to two adjacent adenosine bases in 16S rRNA. This enzyme and the resulting modified adenosine bases appear to be conserved in all species of eubacteria, eukaryotes, and archaea, and in eukaryotic organelles. Bacterial resistance to the aminoglycoside antibiotic kasugamycin involves inactivation of KsgA and resulting loss of the dimethylations, with modest consequences to the overall fitness of the organism. In contrast, the yeast ortholog, Dim1, is essential. In Saccharomyces cerevisiae (Baker's yeast), and presumably in other eukaryotes, the enzyme performs a vital role in pre-rRNA processing in addition to its methylating activity. The best conserved region in these enzymes is located in the N-terminal section and corresponds to a region that is probably involved in S-adenosyl methionine (SAM) binding domain. The crystal structure of KsgA from Escherichia coli has been solved to a resolution of 2.1A. It bears a strong similarity to the crystal structure of ErmC' from Bacillus stearothermophilus and a lesser similarity to the yeast mitochondrial transcription factor, sc-mtTFB []. The Erm family of RNA methyltransferases, which methylate a single adenosine base in 23S rRNA confer resistance to the MLS-B group of antibiotics. Despite their sequence similarity, the two enzyme families have strikingly different levels of regulation that remain to be elucidated. Other orthologs, of this family include the yeast and Homo sapiens (Human) mitochondrial transcription factors (MTF1 and h-mtTFB respectively), which are nuclear encoded []. Human-mtTFB is able to stimulate transcription in vitro independently of its S-adenosylmethionine binding and rRNA methyltransferase activity [].; GO: 0000179 rRNA (adenine-N6,N6-)-dimethyltransferase activity, 0008649 rRNA methyltransferase activity, 0000154 rRNA modification; PDB: 3FTF_A 3R9X_B 3FTE_A 3FTC_A 3FTD_A 3GRY_A 3FYC_A 3GRU_A 3FYD_A 3GRV_A ....
Probab=64.70 E-value=7.4 Score=35.53 Aligned_cols=52 Identities=27% Similarity=0.295 Sum_probs=39.9
Q ss_pred HHcCCCCchHHHhhcccccccCCchh-hhhhhhcccccccCcCCCCCHHHHHHHHHHHH
Q 022922 163 SLSKKKITIKALLLDQSYISGIGNWV-ADEVLYQAKIHPLQTAVSLSKESCATLLKCIK 220 (290)
Q Consensus 163 ~l~~~~~~IK~~LLDQ~~iaGIGNiy-adEiLf~A~IhP~~~~~~Ls~~e~~~L~~~i~ 220 (290)
.+..++.+++..|-- +++-- .++++-.+||+|..++.+||.+++.+|++.+.
T Consensus 209 ~F~~rrk~l~~~L~~------~~~~~~~~~~~~~~~i~~~~r~~~ls~~~~~~l~~~l~ 261 (262)
T PF00398_consen 209 LFSQRRKTLRNSLKS------LFPGEQLEELLEKAGIDPNARAEELSPEQFLKLFKYLN 261 (262)
T ss_dssp HHTTTTSBHHHHTTC------THHHHHHHHHHHHCTHTTTTCGGCHHHHHHHHHHHHHH
T ss_pred HHhCcchHHHHHHhh------hcCHHHHHHhhhhcCCCCCCCcccCCHHHHHHHHHHhh
Confidence 346788999988652 22222 35555569999999999999999999999875
No 56
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=62.37 E-value=3.7 Score=29.13 Aligned_cols=19 Identities=11% Similarity=0.391 Sum_probs=14.2
Q ss_pred eeecCCCCCC---cccccccee
Q 022922 242 VHKKHRENKI---CRLFKVRLK 260 (290)
Q Consensus 242 ~~vy~R~g~~---C~~Cg~~i~ 260 (290)
..|-.|+|+. |||||.-..
T Consensus 7 ~Kv~~RDGE~~lrCPRC~~~FR 28 (65)
T COG4049 7 IKVRDRDGEEFLRCPRCGMVFR 28 (65)
T ss_pred eEeeccCCceeeeCCchhHHHH
Confidence 4566788876 999997654
No 57
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=61.47 E-value=7.5 Score=33.92 Aligned_cols=18 Identities=17% Similarity=0.193 Sum_probs=14.3
Q ss_pred ecCCCCCCccccccceee
Q 022922 244 KKHRENKICRLFKVRLKL 261 (290)
Q Consensus 244 vy~R~g~~C~~Cg~~i~~ 261 (290)
+|.-++..||.||+++++
T Consensus 148 ~f~~~~~~Cp~CG~~~~~ 165 (177)
T COG1439 148 IFPEPKDFCPICGSPLKR 165 (177)
T ss_pred ecCCCCCcCCCCCCceEE
Confidence 556677889999999764
No 58
>PRK10246 exonuclease subunit SbcC; Provisional
Probab=60.37 E-value=3.9 Score=44.92 Aligned_cols=9 Identities=33% Similarity=0.519 Sum_probs=3.8
Q ss_pred CCHHHHHHH
Q 022922 207 LSKESCATL 215 (290)
Q Consensus 207 Ls~~e~~~L 215 (290)
+|+++...+
T Consensus 213 ls~e~~~~l 221 (1047)
T PRK10246 213 LTPEQVQSL 221 (1047)
T ss_pred CCHHHHHHH
Confidence 344444333
No 59
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=59.73 E-value=4 Score=24.00 Aligned_cols=18 Identities=22% Similarity=0.276 Sum_probs=10.2
Q ss_pred Cccccccceeeeccceeeecc
Q 022922 251 ICRLFKVRLKLMLTAAAFLLN 271 (290)
Q Consensus 251 ~C~~Cg~~i~~~~~~~~~~~~ 271 (290)
.||.||+.+ ..++.||-+
T Consensus 4 ~Cp~Cg~~~---~~~~~fC~~ 21 (26)
T PF13248_consen 4 FCPNCGAEI---DPDAKFCPN 21 (26)
T ss_pred CCcccCCcC---CcccccChh
Confidence 477777743 344556643
No 60
>PF10892 DUF2688: Protein of unknown function (DUF2688); InterPro: IPR024392 Members of this protein family are annotated as KleB, and may play a role in the regulation of transcription in plasmids.
Probab=57.77 E-value=1.9 Score=30.46 Aligned_cols=16 Identities=13% Similarity=0.283 Sum_probs=12.6
Q ss_pred CCccccccceeeeccc
Q 022922 250 KICRLFKVRLKLMLTA 265 (290)
Q Consensus 250 ~~C~~Cg~~i~~~~~~ 265 (290)
.+|.|||++|.+.-++
T Consensus 11 t~CrRCGk~i~tl~~S 26 (60)
T PF10892_consen 11 TPCRRCGKSIRTLSRS 26 (60)
T ss_pred ehhhhhCccHHHHHHH
Confidence 5699999999876543
No 61
>PF03486 HI0933_like: HI0933-like protein; InterPro: IPR004792 This is a family of conserved hypothetical proteins that may include proteins with a dinucleotide-binding motif (Rossman fold), including oxidoreductases and dehydrogenases.; PDB: 2I0Z_A 3V76_A 2GQF_A.
Probab=56.79 E-value=4.9 Score=39.49 Aligned_cols=63 Identities=25% Similarity=0.308 Sum_probs=47.3
Q ss_pred CCCCHHHHHHHHc-----CCCCchHHHhhcccccccCCchhhhhhhhcccc-cccCcCCCCCHHHHHHHHHHHH
Q 022922 153 EPMTVDEFTDSLS-----KKKITIKALLLDQSYISGIGNWVADEVLYQAKI-HPLQTAVSLSKESCATLLKCIK 220 (290)
Q Consensus 153 ~~f~~~~f~~~l~-----~~~~~IK~~LLDQ~~iaGIGNiyadEiLf~A~I-hP~~~~~~Ls~~e~~~L~~~i~ 220 (290)
++++.+.+.+.|. .+++.++.+|-.- +=+=++..+|-+++| +|.++++++|++++++|.+.++
T Consensus 270 p~~~~e~l~~~l~~~~~~~~~~~~~~~l~~~-----lp~rl~~~ll~~~~i~~~~~~~~~l~~~~~~~L~~~lk 338 (409)
T PF03486_consen 270 PDLSEEELEELLQERKEKNPKRTLKNFLKGL-----LPKRLALALLKRAGIKDPDKKVSELSKKERNRLANLLK 338 (409)
T ss_dssp TTS-HHHHHHHHHHHHHHTTTSBHHHHHTTT-----S-HHHHHHHHHHTTS-STTSBGGGS-HHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHHHHhhHHHHHHHHH-----hHHHHHHHHHHHcCCCccccchhhcCHHHHHHHHHHHH
Confidence 4577777776664 3578888887421 345577889999999 9999999999999999988887
No 62
>COG2081 Predicted flavoproteins [General function prediction only]
Probab=56.20 E-value=16 Score=35.99 Aligned_cols=62 Identities=23% Similarity=0.268 Sum_probs=49.7
Q ss_pred CCCCHHHHHHHHcC--CCCchHHHhhcccccccCCchhhhhhhhcccccccCcCCCCCHHHHHHHHHHHH
Q 022922 153 EPMTVDEFTDSLSK--KKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIK 220 (290)
Q Consensus 153 ~~f~~~~f~~~l~~--~~~~IK~~LLDQ~~iaGIGNiyadEiLf~A~IhP~~~~~~Ls~~e~~~L~~~i~ 220 (290)
++.+.+.+.+.+.+ +++++|++|-..- +-=++.=+|=+++| |..+..++|+.+.++|.++|+
T Consensus 268 P~~~~~~l~~~l~~~~~~kslkn~L~~~l-----p~rlv~~~l~~~~i-~~~~~~~ls~~~~~~l~~~ik 331 (408)
T COG2081 268 PDVDAEELLRELRRANPKKSLKNALAKLL-----PKRLVEFLLERAGI-PDEPLAQLSPKELAQLAAALK 331 (408)
T ss_pred CCCCHHHHHHHHHhhChhhHHHHHHHHHh-----hhHHHHHHHHhccC-CCcchhhcCHHHHHHHHHHHh
Confidence 56788888887754 4899999986542 34455566779999 999999999999999999988
No 63
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=55.79 E-value=6.3 Score=24.24 Aligned_cols=14 Identities=14% Similarity=0.226 Sum_probs=7.9
Q ss_pred CCCccccccceeee
Q 022922 249 NKICRLFKVRLKLM 262 (290)
Q Consensus 249 g~~C~~Cg~~i~~~ 262 (290)
.+-|++||++....
T Consensus 3 ~rfC~~CG~~t~~~ 16 (32)
T PF09297_consen 3 HRFCGRCGAPTKPA 16 (32)
T ss_dssp TSB-TTT--BEEE-
T ss_pred CcccCcCCccccCC
Confidence 46799999998866
No 64
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=55.64 E-value=8 Score=25.08 Aligned_cols=19 Identities=16% Similarity=0.043 Sum_probs=12.9
Q ss_pred CCcccccccee-eeccceee
Q 022922 250 KICRLFKVRLK-LMLTAAAF 268 (290)
Q Consensus 250 ~~C~~Cg~~i~-~~~~~~~~ 268 (290)
+.||.||..+. +.++...|
T Consensus 2 ~~CP~Cg~~lv~r~~k~g~F 21 (39)
T PF01396_consen 2 EKCPKCGGPLVLRRGKKGKF 21 (39)
T ss_pred cCCCCCCceeEEEECCCCCE
Confidence 67999997754 55554443
No 65
>PRK12495 hypothetical protein; Provisional
Probab=51.23 E-value=6.9 Score=35.27 Aligned_cols=27 Identities=7% Similarity=-0.105 Sum_probs=21.6
Q ss_pred CCccccccceeeeccceeeecceeEEee
Q 022922 250 KICRLFKVRLKLMLTAAAFLLNGYFIFD 277 (290)
Q Consensus 250 ~~C~~Cg~~i~~~~~~~~~~~~~~~~~~ 277 (290)
..|+.||.||-.. .|..||.+---+++
T Consensus 43 ~hC~~CG~PIpa~-pG~~~Cp~CQ~~~~ 69 (226)
T PRK12495 43 AHCDECGDPIFRH-DGQEFCPTCQQPVT 69 (226)
T ss_pred hhcccccCcccCC-CCeeECCCCCCccc
Confidence 5699999999965 99999987655544
No 66
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=49.56 E-value=6.9 Score=28.43 Aligned_cols=23 Identities=9% Similarity=-0.087 Sum_probs=16.0
Q ss_pred CCCCccccccceeeecccee--eec
Q 022922 248 ENKICRLFKVRLKLMLTAAA--FLL 270 (290)
Q Consensus 248 ~g~~C~~Cg~~i~~~~~~~~--~~~ 270 (290)
.--+||.||+++.-.-.+++ ||.
T Consensus 6 ~~v~CP~Cgkpv~w~~~s~frPFCS 30 (65)
T COG3024 6 ITVPCPTCGKPVVWGEESPFRPFCS 30 (65)
T ss_pred ccccCCCCCCcccccccCCcCcchh
Confidence 34689999999886544443 554
No 67
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=49.27 E-value=22 Score=23.01 Aligned_cols=35 Identities=29% Similarity=0.325 Sum_probs=21.2
Q ss_pred Cccccccceeee---ccceeeecc-eeEEeechhhHHHHH
Q 022922 251 ICRLFKVRLKLM---LTAAAFLLN-GYFIFDGAKSLEKLM 286 (290)
Q Consensus 251 ~C~~Cg~~i~~~---~~~~~~~~~-~~~~~~~~~~~~~~~ 286 (290)
.||+|++.+... +-....|-+ |-..|| +..++++.
T Consensus 1 ~CP~C~~~l~~~~~~~~~id~C~~C~G~W~d-~~el~~~~ 39 (41)
T PF13453_consen 1 KCPRCGTELEPVRLGDVEIDVCPSCGGIWFD-AGELEKLL 39 (41)
T ss_pred CcCCCCcccceEEECCEEEEECCCCCeEEcc-HHHHHHHH
Confidence 399999876643 334556776 334444 45566654
No 68
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=48.59 E-value=15 Score=24.12 Aligned_cols=21 Identities=10% Similarity=-0.149 Sum_probs=14.2
Q ss_pred Ccccccccee--eeccceeeecc
Q 022922 251 ICRLFKVRLK--LMLTAAAFLLN 271 (290)
Q Consensus 251 ~C~~Cg~~i~--~~~~~~~~~~~ 271 (290)
.||.||..-. -..+|...|.+
T Consensus 2 ~Cp~Cg~~~~~~D~~~g~~vC~~ 24 (43)
T PF08271_consen 2 KCPNCGSKEIVFDPERGELVCPN 24 (43)
T ss_dssp SBTTTSSSEEEEETTTTEEEETT
T ss_pred CCcCCcCCceEEcCCCCeEECCC
Confidence 4888887642 33678888876
No 69
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=47.99 E-value=7.6 Score=26.81 Aligned_cols=17 Identities=18% Similarity=0.360 Sum_probs=12.3
Q ss_pred CCCCCCccccccceeee
Q 022922 246 HRENKICRLFKVRLKLM 262 (290)
Q Consensus 246 ~R~g~~C~~Cg~~i~~~ 262 (290)
-|..+.|||||..+-++
T Consensus 16 ~rk~~~CPrCG~gvfmA 32 (51)
T COG1998 16 KRKNRFCPRCGPGVFMA 32 (51)
T ss_pred EEccccCCCCCCcchhh
Confidence 36778899999655443
No 70
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=47.51 E-value=22 Score=23.62 Aligned_cols=12 Identities=8% Similarity=0.213 Sum_probs=9.5
Q ss_pred CCCCCccccccc
Q 022922 247 RENKICRLFKVR 258 (290)
Q Consensus 247 R~g~~C~~Cg~~ 258 (290)
.+|-.||+||..
T Consensus 16 ~~g~~CP~Cg~~ 27 (46)
T PF12760_consen 16 PDGFVCPHCGST 27 (46)
T ss_pred CCCCCCCCCCCe
Confidence 466779999975
No 71
>COG4643 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=46.76 E-value=11 Score=36.21 Aligned_cols=31 Identities=13% Similarity=-0.067 Sum_probs=21.4
Q ss_pred CCCcccccccee-----eeccceeeecceeEEeechh
Q 022922 249 NKICRLFKVRLK-----LMLTAAAFLLNGYFIFDGAK 280 (290)
Q Consensus 249 g~~C~~Cg~~i~-----~~~~~~~~~~~~~~~~~~~~ 280 (290)
++|||-||.+=+ .-||||-||.-+- --||-+
T Consensus 32 ~~~cpvcg~k~RFr~dD~kGrGtw~c~y~~-~GDGl~ 67 (366)
T COG4643 32 GHPCPVCGGKDRFRFDDRKGRGTWFCNYCG-HGDGLP 67 (366)
T ss_pred CCCCCccCCccccccCCccCCccEEEEeec-cCCCcc
Confidence 459999997643 4589999997543 235544
No 72
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=45.16 E-value=13 Score=39.18 Aligned_cols=22 Identities=18% Similarity=0.286 Sum_probs=17.7
Q ss_pred CCccccccceeeeccceeeecce
Q 022922 250 KICRLFKVRLKLMLTAAAFLLNG 272 (290)
Q Consensus 250 ~~C~~Cg~~i~~~~~~~~~~~~~ 272 (290)
..||.||+++.+ +....||.|+
T Consensus 424 ~~CP~C~~~l~~-~~~~~~C~n~ 445 (689)
T PRK14351 424 DTCPVCDSAVER-DGPLAFCTGG 445 (689)
T ss_pred CCCCCCCCEeee-CCceEEcCCC
Confidence 349999999877 5567889985
No 73
>PRK12496 hypothetical protein; Provisional
Probab=42.30 E-value=11 Score=32.38 Aligned_cols=15 Identities=13% Similarity=0.383 Sum_probs=11.7
Q ss_pred CCCCCccccccceee
Q 022922 247 RENKICRLFKVRLKL 261 (290)
Q Consensus 247 R~g~~C~~Cg~~i~~ 261 (290)
.+++.||.||.++++
T Consensus 141 ~~~~~C~~CG~~~~r 155 (164)
T PRK12496 141 YPDDVCEICGSPVKR 155 (164)
T ss_pred CCCCcCCCCCChhhh
Confidence 355779999999874
No 74
>TIGR00375 conserved hypothetical protein TIGR00375. The member of this family from Methanococcus jannaschii, MJ0043, is considerably longer and appears to contain an intein N-terminal to the region of homology.
Probab=41.72 E-value=23 Score=34.59 Aligned_cols=10 Identities=30% Similarity=0.431 Sum_probs=6.9
Q ss_pred CCcccccccee
Q 022922 250 KICRLFKVRLK 260 (290)
Q Consensus 250 ~~C~~Cg~~i~ 260 (290)
..|| ||.+|+
T Consensus 260 ~~Cp-CG~~i~ 269 (374)
T TIGR00375 260 ANCP-CGGRIK 269 (374)
T ss_pred CCCC-CCCcce
Confidence 4488 887755
No 75
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=41.70 E-value=13 Score=23.62 Aligned_cols=15 Identities=7% Similarity=0.067 Sum_probs=10.8
Q ss_pred CCCCccccccceeee
Q 022922 248 ENKICRLFKVRLKLM 262 (290)
Q Consensus 248 ~g~~C~~Cg~~i~~~ 262 (290)
+-..||.||+.+++.
T Consensus 25 ~~~~CP~Cg~~~~r~ 39 (41)
T smart00834 25 PLATCPECGGDVRRL 39 (41)
T ss_pred CCCCCCCCCCcceec
Confidence 345699999977653
No 76
>PF02294 7kD_DNA_binding: 7kD DNA-binding domain; InterPro: IPR003212 This family contains members of the hyperthermophilic archaebacterium 7kDa DNA-binding/endoribonuclease P2 family. There are five 7kDa DNA-binding proteins, 7a-7e, found as monomers in the cell. Protein 7e shows the tightest DNA-binding ability.; GO: 0003677 DNA binding, 0004521 endoribonuclease activity; PDB: 1SSO_A 2CVR_A 1B4O_A 2XIW_B 1WTV_A 1WTQ_A 1BF4_A 1WVL_B 1WTR_A 1WTP_B ....
Probab=40.75 E-value=41 Score=23.48 Aligned_cols=32 Identities=25% Similarity=0.172 Sum_probs=25.3
Q ss_pred cCCEEEEEEeeeeEEEEEeCCCCceEEecCceEEEEEe
Q 022922 48 LGKAILSAHRKGKNLWLRLDSPPFPSFQFGMTGAIYIK 85 (290)
Q Consensus 48 ~G~~i~~v~RrGK~L~~~l~~~~~L~~HLgMtG~l~~~ 85 (290)
.=.+|..|+|.||.+-|..|++. |-||+=-+.
T Consensus 15 diskikkvwrvgkmvsftyddgn------gktgrgavs 46 (62)
T PF02294_consen 15 DISKIKKVWRVGKMVSFTYDDGN------GKTGRGAVS 46 (62)
T ss_dssp EGGGEEEEEECSSEEEEEEECSS------SSEEEEEEE
T ss_pred cHHHHHHHHhhcceEEEEEecCC------Ccccccccc
Confidence 34579999999999999998853 677775554
No 77
>smart00532 LIGANc Ligase N family.
Probab=40.69 E-value=18 Score=36.05 Aligned_cols=23 Identities=13% Similarity=-0.117 Sum_probs=17.7
Q ss_pred CCccccccceeee-ccceeeecce
Q 022922 250 KICRLFKVRLKLM-LTAAAFLLNG 272 (290)
Q Consensus 250 ~~C~~Cg~~i~~~-~~~~~~~~~~ 272 (290)
+.||.||+++... +....||.|+
T Consensus 400 ~~CP~C~s~l~~~~~~~~~~C~n~ 423 (441)
T smart00532 400 THCPSCGSELVREEGEVDIRCPNP 423 (441)
T ss_pred CCCCCCCCEeEecCCceEEEeCCC
Confidence 3399999998765 4456789987
No 78
>PTZ00338 dimethyladenosine transferase-like protein; Provisional
Probab=40.48 E-value=40 Score=31.57 Aligned_cols=57 Identities=21% Similarity=0.247 Sum_probs=40.6
Q ss_pred HHcCCCCchHHHhhcccc----------cccCCc-----------hhhhhhhhcccccccCcCCCCCHHHHHHHHHHHH
Q 022922 163 SLSKKKITIKALLLDQSY----------ISGIGN-----------WVADEVLYQAKIHPLQTAVSLSKESCATLLKCIK 220 (290)
Q Consensus 163 ~l~~~~~~IK~~LLDQ~~----------iaGIGN-----------iyadEiLf~A~IhP~~~~~~Ls~~e~~~L~~~i~ 220 (290)
.+..|++.+++.|-...+ +.|++| --..++|=.++|. .+++.+||-+|+.+|.+++.
T Consensus 210 ~F~~rrK~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~~R~e~l~~~~f~~L~~~~~ 287 (294)
T PTZ00338 210 CFSRKNKTLSAIFKTKSVLQTLEHNYKSWCTMINKKVPVSLEPFKEFIAEILEDSGMF-EKRSVKLDIDDFLKLLLAFN 287 (294)
T ss_pred HHhhccHHHHHHhCcchhHHHHHhhhhhhhccccccccchhhhHHHHHHHHHHHcCCc-ccChhhCCHHHHHHHHHHHH
Confidence 456788999988866432 122121 1123678889985 79999999999999998886
No 79
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=39.32 E-value=16 Score=24.24 Aligned_cols=16 Identities=13% Similarity=0.144 Sum_probs=10.8
Q ss_pred CCccccccceeeeccc
Q 022922 250 KICRLFKVRLKLMLTA 265 (290)
Q Consensus 250 ~~C~~Cg~~i~~~~~~ 265 (290)
..||.||.++....|+
T Consensus 22 ~~Cp~CG~~~~~~~~~ 37 (46)
T PRK00398 22 VRCPYCGYRILFKERP 37 (46)
T ss_pred eECCCCCCeEEEccCC
Confidence 4588888877655443
No 80
>PRK14896 ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Provisional
Probab=39.15 E-value=58 Score=29.53 Aligned_cols=59 Identities=20% Similarity=0.202 Sum_probs=38.3
Q ss_pred HHHHcCCCCchHHHhhcccccccCCchhhhhhhhcc-cccccCcCCCCCHHHHHHHHHHHHH
Q 022922 161 TDSLSKKKITIKALLLDQSYISGIGNWVADEVLYQA-KIHPLQTAVSLSKESCATLLKCIKE 221 (290)
Q Consensus 161 ~~~l~~~~~~IK~~LLDQ~~iaGIGNiyadEiLf~A-~IhP~~~~~~Ls~~e~~~L~~~i~~ 221 (290)
...+..++++++..|-.--...+.|.+ ++++-.+ ++.|..++.+||.+|+.+|++.+..
T Consensus 197 ~~~F~~rrk~l~~~l~~~~~~~~~~~~--~~~~~~~~~~~~~~R~e~L~~~~~~~l~~~~~~ 256 (258)
T PRK14896 197 KALFQHRRKTLRNALKNSAHISGKEDI--KAVVEALPEELLNKRVFQLSPEEIAELANLLYE 256 (258)
T ss_pred HHHHccccHHHHHHHhhhccccchhHH--HHHHHHcCCCCcCCCCccCCHHHHHHHHHHHHh
Confidence 334677899999998431100122211 2334444 3557999999999999999988764
No 81
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=37.97 E-value=17 Score=25.01 Aligned_cols=19 Identities=11% Similarity=0.114 Sum_probs=14.2
Q ss_pred CCCccccccceeeecccee
Q 022922 249 NKICRLFKVRLKLMLTAAA 267 (290)
Q Consensus 249 g~~C~~Cg~~i~~~~~~~~ 267 (290)
+-.||.||.+|..-.|.+.
T Consensus 24 ~irCp~Cg~rIl~K~R~~~ 42 (49)
T COG1996 24 GIRCPYCGSRILVKERPKV 42 (49)
T ss_pred ceeCCCCCcEEEEeccCCc
Confidence 3459999999887766553
No 82
>PF08063 PADR1: PADR1 (NUC008) domain; InterPro: IPR012982 This domain is found in poly(ADP-ribose)-synthetases []. The function of this domain is unknown.; GO: 0003950 NAD+ ADP-ribosyltransferase activity, 0005634 nucleus; PDB: 2JVN_A 4DQY_E 2RIQ_A.
Probab=37.81 E-value=24 Score=24.78 Aligned_cols=21 Identities=10% Similarity=-0.135 Sum_probs=11.9
Q ss_pred CCccccccceeeeccceeeec
Q 022922 250 KICRLFKVRLKLMLTAAAFLL 270 (290)
Q Consensus 250 ~~C~~Cg~~i~~~~~~~~~~~ 270 (290)
++||.|+..-.......++|.
T Consensus 15 ~~Cp~C~~~~l~~~~~~Y~C~ 35 (55)
T PF08063_consen 15 EPCPKCKGGQLYFDGSGYKCT 35 (55)
T ss_dssp ---SSSSE-EEEEETTEEEEE
T ss_pred CCCCCCCCCeEEecCCccEeC
Confidence 689999985444444488885
No 83
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=37.55 E-value=21 Score=37.52 Aligned_cols=21 Identities=29% Similarity=0.244 Sum_probs=17.3
Q ss_pred Cccccccceeeeccceeeecce
Q 022922 251 ICRLFKVRLKLMLTAAAFLLNG 272 (290)
Q Consensus 251 ~C~~Cg~~i~~~~~~~~~~~~~ 272 (290)
.||.||+++.+ +....||.|.
T Consensus 400 ~CP~C~s~l~~-~~~~~~C~n~ 420 (669)
T PRK14350 400 NCPSCKTALIK-EGAHLFCVNN 420 (669)
T ss_pred CCCCCCCEeee-CCEEEEECCC
Confidence 49999999877 4578899986
No 84
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=37.32 E-value=13 Score=36.79 Aligned_cols=26 Identities=19% Similarity=0.066 Sum_probs=21.0
Q ss_pred cCCCCCCccccccceeeeccceeeec
Q 022922 245 KHRENKICRLFKVRLKLMLTAAAFLL 270 (290)
Q Consensus 245 y~R~g~~C~~Cg~~i~~~~~~~~~~~ 270 (290)
|-+.+-.||+||+..+..||+-.=|-
T Consensus 346 ~~~~~p~Cp~Cg~~m~S~G~~g~rC~ 371 (421)
T COG1571 346 YERVNPVCPRCGGRMKSAGRNGFRCK 371 (421)
T ss_pred eEEcCCCCCccCCchhhcCCCCcccc
Confidence 56777789999999999999844455
No 85
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=37.08 E-value=15 Score=25.23 Aligned_cols=11 Identities=18% Similarity=0.054 Sum_probs=8.9
Q ss_pred CCcccccccee
Q 022922 250 KICRLFKVRLK 260 (290)
Q Consensus 250 ~~C~~Cg~~i~ 260 (290)
+|||-||+.-.
T Consensus 2 kPCPfCGg~~~ 12 (53)
T TIGR03655 2 KPCPFCGGADV 12 (53)
T ss_pred CCCCCCCCcce
Confidence 69999997644
No 86
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.05 E-value=34 Score=25.98 Aligned_cols=36 Identities=25% Similarity=0.539 Sum_probs=19.8
Q ss_pred Cccccccceeeeccc---eeeecc--eeEEeechhhHHHHHhh
Q 022922 251 ICRLFKVRLKLMLTA---AAFLLN--GYFIFDGAKSLEKLMVR 288 (290)
Q Consensus 251 ~C~~Cg~~i~~~~~~---~~~~~~--~~~~~~~~~~~~~~~~~ 288 (290)
-||.|+.-+++..|. --||-. |-+ .|+ -.|+|||.|
T Consensus 3 lCP~C~v~l~~~~rs~vEiD~CPrCrGVW-LDr-GELdKli~r 43 (88)
T COG3809 3 LCPICGVELVMSVRSGVEIDYCPRCRGVW-LDR-GELDKLIER 43 (88)
T ss_pred ccCcCCceeeeeeecCceeeeCCccccEe-ecc-hhHHHHHHH
Confidence 477777766655443 335543 222 333 357888754
No 87
>PF14768 RPA_interact_C: Replication protein A interacting C-terminal
Probab=36.80 E-value=34 Score=25.77 Aligned_cols=36 Identities=17% Similarity=0.118 Sum_probs=29.6
Q ss_pred CccccccceeeeccceeeecceeEEeech---hhHHHHHh
Q 022922 251 ICRLFKVRLKLMLTAAAFLLNGYFIFDGA---KSLEKLMV 287 (290)
Q Consensus 251 ~C~~Cg~~i~~~~~~~~~~~~~~~~~~~~---~~~~~~~~ 287 (290)
.||.|...-.+...+..+|.-| +-++.+ .++++|-.
T Consensus 1 iCPVC~~~~L~~~~~~i~C~Cg-l~l~~~~~~~tl~~l~~ 39 (82)
T PF14768_consen 1 ICPVCQKGNLRENSNVISCSCG-LRLNTQQDELTLEELRQ 39 (82)
T ss_pred CCCccCCCcccccCCeEECCCc-cEEecCCCCCCHHHHHH
Confidence 4999998877778999999999 888887 67777643
No 88
>PF13005 zf-IS66: zinc-finger binding domain of transposase IS66 ; InterPro: IPR024474 This entry represents a predicted helix-turn-helix domain from insertion element IS66 transposases [].
Probab=36.67 E-value=21 Score=23.47 Aligned_cols=17 Identities=18% Similarity=0.104 Sum_probs=13.8
Q ss_pred CCCccccccceeeeccc
Q 022922 249 NKICRLFKVRLKLMLTA 265 (290)
Q Consensus 249 g~~C~~Cg~~i~~~~~~ 265 (290)
...||.||+.+..+|..
T Consensus 2 ~~~C~~Cg~~l~~ig~~ 18 (47)
T PF13005_consen 2 PRACPDCGGELKEIGEE 18 (47)
T ss_pred CCcCCCCCceeeECCce
Confidence 35699999999987765
No 89
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=36.09 E-value=21 Score=37.22 Aligned_cols=22 Identities=18% Similarity=0.113 Sum_probs=19.6
Q ss_pred ccccccceee-eccceeeeccee
Q 022922 252 CRLFKVRLKL-MLTAAAFLLNGY 273 (290)
Q Consensus 252 C~~Cg~~i~~-~~~~~~~~~~~~ 273 (290)
||.||+.+.+ .+-...||.||.
T Consensus 407 CP~C~s~l~r~~~e~~~rC~n~~ 429 (667)
T COG0272 407 CPVCGSELVREEGEVVIRCTNGL 429 (667)
T ss_pred CCCCCCeeEeccCceeEecCCCC
Confidence 9999999886 688999999974
No 90
>PF11197 DUF2835: Protein of unknown function (DUF2835); InterPro: IPR021363 This is a bacterial family of uncharacterised proteins. One member of this family (A4VM42 from SWISSPROT) is annotated as the A subunit of Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV).
Probab=35.53 E-value=87 Score=22.98 Aligned_cols=48 Identities=15% Similarity=0.175 Sum_probs=36.9
Q ss_pred CChhhHHhhhcCC--EEEEEEeeeeEEEEEeCCCCceEEecCceEEEEEe
Q 022922 38 VSASDFEASVLGK--AILSAHRKGKNLWLRLDSPPFPSFQFGMTGAIYIK 85 (290)
Q Consensus 38 ~~~~~f~~~L~G~--~i~~v~RrGK~L~~~l~~~~~L~~HLgMtG~l~~~ 85 (290)
.+.++|..--.|. +|.-+.+-|+-|.|....=...+.|.|..|++.+.
T Consensus 7 is~~~~l~~Y~G~a~~V~v~s~~Gr~v~~Pa~~lRpFvt~~Gv~G~F~l~ 56 (68)
T PF11197_consen 7 ISYQEFLAYYQGAASKVVVRSDDGRRVQFPARHLRPFVTHDGVHGRFRLE 56 (68)
T ss_pred cCHHHHHHhccccccEEEEEecCCcEEEEeHHHCcceecCCCceEEEEEE
Confidence 4667887777774 77778888999999765434578899999998875
No 91
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=34.47 E-value=24 Score=37.03 Aligned_cols=21 Identities=24% Similarity=0.148 Sum_probs=17.1
Q ss_pred ccccccceee-eccceeeecce
Q 022922 252 CRLFKVRLKL-MLTAAAFLLNG 272 (290)
Q Consensus 252 C~~Cg~~i~~-~~~~~~~~~~~ 272 (290)
||.||+++.+ .+....||.|+
T Consensus 407 CP~Cgs~l~~~~~~~~~~C~n~ 428 (665)
T PRK07956 407 CPVCGSELVRVEGEAVLRCTNG 428 (665)
T ss_pred CCCCCCEeEecCCCeEEECCCC
Confidence 9999999875 45567889986
No 92
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=34.21 E-value=25 Score=25.06 Aligned_cols=29 Identities=21% Similarity=0.046 Sum_probs=21.4
Q ss_pred CCCccccccceee-eccceeeecceeEEee
Q 022922 249 NKICRLFKVRLKL-MLTAAAFLLNGYFIFD 277 (290)
Q Consensus 249 g~~C~~Cg~~i~~-~~~~~~~~~~~~~~~~ 277 (290)
-+.||.||..... .....+.|.+--+.+|
T Consensus 28 Sq~C~~CG~~~~~~~~~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 28 SQTCPRCGHRNKKRRSGRVFTCPNCGFEMD 57 (69)
T ss_pred ccCccCcccccccccccceEEcCCCCCEEC
Confidence 3679999999887 6777888985333454
No 93
>TIGR00575 dnlj DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.
Probab=33.44 E-value=27 Score=36.57 Aligned_cols=22 Identities=18% Similarity=-0.052 Sum_probs=17.2
Q ss_pred Cccccccceeee-ccceeeecce
Q 022922 251 ICRLFKVRLKLM-LTAAAFLLNG 272 (290)
Q Consensus 251 ~C~~Cg~~i~~~-~~~~~~~~~~ 272 (290)
.||.||+++.+. +....||.|.
T Consensus 394 ~CP~C~s~l~~~~~~~~~~C~n~ 416 (652)
T TIGR00575 394 HCPSCGSPLVKIEEEAVIRCPNL 416 (652)
T ss_pred CCCCCCCEeEecCCcEEEEECCC
Confidence 399999998764 5567789984
No 94
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=32.93 E-value=23 Score=20.75 Aligned_cols=17 Identities=18% Similarity=0.194 Sum_probs=13.3
Q ss_pred ccccccceeeeccceee
Q 022922 252 CRLFKVRLKLMLTAAAF 268 (290)
Q Consensus 252 C~~Cg~~i~~~~~~~~~ 268 (290)
|-+||..|.-..+++.|
T Consensus 1 C~sC~~~i~~r~~~v~f 17 (24)
T PF07754_consen 1 CTSCGRPIAPREQAVPF 17 (24)
T ss_pred CccCCCcccCcccCceE
Confidence 77888888877777776
No 95
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=32.21 E-value=29 Score=22.69 Aligned_cols=15 Identities=7% Similarity=0.151 Sum_probs=10.9
Q ss_pred CCCCcccccc-ceeee
Q 022922 248 ENKICRLFKV-RLKLM 262 (290)
Q Consensus 248 ~g~~C~~Cg~-~i~~~ 262 (290)
+...||.||+ .++++
T Consensus 25 ~~~~CP~Cg~~~~~r~ 40 (42)
T PF09723_consen 25 DPVPCPECGSTEVRRV 40 (42)
T ss_pred CCCcCCCCCCCceEEe
Confidence 4567999998 66553
No 96
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=31.40 E-value=23 Score=28.50 Aligned_cols=22 Identities=5% Similarity=0.226 Sum_probs=14.8
Q ss_pred CCccccccceeeeccceeeecc
Q 022922 250 KICRLFKVRLKLMLTAAAFLLN 271 (290)
Q Consensus 250 ~~C~~Cg~~i~~~~~~~~~~~~ 271 (290)
..|.+|+.++...++..+-|.+
T Consensus 55 ~~C~~C~~~fg~l~~~~~~C~~ 76 (118)
T PF02318_consen 55 RHCARCGKPFGFLFNRGRVCVD 76 (118)
T ss_dssp SB-TTTS-BCSCTSTTCEEETT
T ss_pred cchhhhCCcccccCCCCCcCCc
Confidence 5799999998877665566654
No 97
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=31.22 E-value=21 Score=25.82 Aligned_cols=22 Identities=9% Similarity=-0.038 Sum_probs=13.9
Q ss_pred CCccccccceeeecc--ceeeecc
Q 022922 250 KICRLFKVRLKLMLT--AAAFLLN 271 (290)
Q Consensus 250 ~~C~~Cg~~i~~~~~--~~~~~~~ 271 (290)
-+||.||.++.-... ---||..
T Consensus 7 v~CP~C~k~~~w~~~~~~rPFCS~ 30 (62)
T PRK00418 7 VNCPTCGKPVEWGEISPFRPFCSK 30 (62)
T ss_pred ccCCCCCCcccccCCCCcCCcccH
Confidence 469999998763322 2247753
No 98
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=30.67 E-value=22 Score=25.47 Aligned_cols=18 Identities=17% Similarity=0.242 Sum_probs=14.1
Q ss_pred CCccccccceeeeccceeeec
Q 022922 250 KICRLFKVRLKLMLTAAAFLL 270 (290)
Q Consensus 250 ~~C~~Cg~~i~~~~~~~~~~~ 270 (290)
+.|+.||.+|.. ...||.
T Consensus 4 kHC~~CG~~Ip~---~~~fCS 21 (59)
T PF09889_consen 4 KHCPVCGKPIPP---DESFCS 21 (59)
T ss_pred CcCCcCCCcCCc---chhhhC
Confidence 579999999884 467774
No 99
>PF12773 DZR: Double zinc ribbon
Probab=28.84 E-value=22 Score=23.71 Aligned_cols=9 Identities=22% Similarity=0.346 Sum_probs=4.2
Q ss_pred cccccccee
Q 022922 252 CRLFKVRLK 260 (290)
Q Consensus 252 C~~Cg~~i~ 260 (290)
|+.||+++.
T Consensus 15 C~~CG~~l~ 23 (50)
T PF12773_consen 15 CPHCGTPLP 23 (50)
T ss_pred ChhhcCChh
Confidence 444444444
No 100
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=28.40 E-value=25 Score=26.97 Aligned_cols=20 Identities=10% Similarity=0.202 Sum_probs=13.4
Q ss_pred ccceeecCCCCCCccccccceeee
Q 022922 239 KPYVHKKHRENKICRLFKVRLKLM 262 (290)
Q Consensus 239 ~~~~~vy~R~g~~C~~Cg~~i~~~ 262 (290)
+.++++. +.|+.||......
T Consensus 2 ~g~Lk~~----~~C~~CG~d~~~~ 21 (86)
T PF06170_consen 2 RGYLKVA----PRCPHCGLDYSHA 21 (86)
T ss_pred CccccCC----CcccccCCccccC
Confidence 3445553 4599999887744
No 101
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=28.27 E-value=24 Score=34.61 Aligned_cols=15 Identities=13% Similarity=-0.060 Sum_probs=12.1
Q ss_pred CCccccccceeeecc
Q 022922 250 KICRLFKVRLKLMLT 264 (290)
Q Consensus 250 ~~C~~Cg~~i~~~~~ 264 (290)
-.|||||+.|...++
T Consensus 39 A~CPRC~~~l~~~~~ 53 (418)
T COG2995 39 AYCPRCGHTLTRGGD 53 (418)
T ss_pred ccCCCCCCccccCCC
Confidence 459999999987654
No 102
>PHA02998 RNA polymerase subunit; Provisional
Probab=28.12 E-value=67 Score=28.19 Aligned_cols=24 Identities=17% Similarity=0.074 Sum_probs=19.2
Q ss_pred cccCccceeecCC-CCCCccccccc
Q 022922 235 CYFAKPYVHKKHR-ENKICRLFKVR 258 (290)
Q Consensus 235 ~~~~~~~~~vy~R-~g~~C~~Cg~~ 258 (290)
++.|..++.|..+ ...+||+||.+
T Consensus 128 d~~y~~yfnvlpkkt~v~CPkCg~~ 152 (195)
T PHA02998 128 DVDYDDYFNVLDEKYNTPCPNCKSK 152 (195)
T ss_pred cccchhheeccCcccCCCCCCCCCC
Confidence 4567788888888 77889999954
No 103
>PF10609 ParA: ParA/MinD ATPase like; InterPro: IPR019591 This entry represents ATPases involved in plasmid partitioning []. It also contains cytosolic Fe-S cluster assembling factors, NBP35 and CFD1 which are required for biogenesis and export of both ribosomal subunits probably through assembling the ISCs in RLI1, a protein which performs rRNA processing and ribosome export [, , ].; PDB: 2PH1_A 3KB1_B.
Probab=27.63 E-value=23 Score=26.89 Aligned_cols=17 Identities=12% Similarity=0.184 Sum_probs=10.7
Q ss_pred CCCccccccceeeeccc
Q 022922 249 NKICRLFKVRLKLMLTA 265 (290)
Q Consensus 249 g~~C~~Cg~~i~~~~~~ 265 (290)
+-.||.||..+...|+|
T Consensus 65 ~~~Cp~Cg~~~~iFg~G 81 (81)
T PF10609_consen 65 YFVCPHCGERIYIFGKG 81 (81)
T ss_dssp EEE-TTT--EEETTTTT
T ss_pred ccCCCCCCCeecCCCCC
Confidence 34599999999888765
No 104
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=27.59 E-value=57 Score=20.58 Aligned_cols=21 Identities=10% Similarity=-0.073 Sum_probs=10.3
Q ss_pred Cccccccceeee-----ccceeeecc
Q 022922 251 ICRLFKVRLKLM-----LTAAAFLLN 271 (290)
Q Consensus 251 ~C~~Cg~~i~~~-----~~~~~~~~~ 271 (290)
-||.||+++... .|--++|.+
T Consensus 2 fC~~CG~~l~~~ip~gd~r~R~vC~~ 27 (34)
T PF14803_consen 2 FCPQCGGPLERRIPEGDDRERLVCPA 27 (34)
T ss_dssp B-TTT--B-EEE--TT-SS-EEEETT
T ss_pred ccccccChhhhhcCCCCCccceECCC
Confidence 499999987743 455566654
No 105
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=26.80 E-value=46 Score=23.06 Aligned_cols=11 Identities=18% Similarity=0.123 Sum_probs=8.6
Q ss_pred CCcccccccee
Q 022922 250 KICRLFKVRLK 260 (290)
Q Consensus 250 ~~C~~Cg~~i~ 260 (290)
+|||-||.+..
T Consensus 4 kPCPFCG~~~~ 14 (61)
T PF14354_consen 4 KPCPFCGSADV 14 (61)
T ss_pred cCCCCCCCcce
Confidence 78999986644
No 106
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=26.80 E-value=30 Score=38.54 Aligned_cols=35 Identities=23% Similarity=0.189 Sum_probs=24.4
Q ss_pred ecCCCCCCccccccceeeeccceeeecceeEEeechh
Q 022922 244 KKHRENKICRLFKVRLKLMLTAAAFLLNGYFIFDGAK 280 (290)
Q Consensus 244 vy~R~g~~C~~Cg~~i~~~~~~~~~~~~~~~~~~~~~ 280 (290)
.|+=..+.||.||+|+++-|..--|=. +.=|+|.|
T Consensus 934 GfDLpdK~CPkCg~pl~kDG~dIPFET--FlGF~GDK 968 (1444)
T COG2176 934 GFDLPDKDCPKCGTPLKKDGHDIPFET--FLGFKGDK 968 (1444)
T ss_pred CCCCCCCCCCcCCCccccCCCCCChhh--hcCCCCCC
Confidence 466778899999999998888755532 22355544
No 107
>PF11248 DUF3046: Protein of unknown function (DUF3046); InterPro: IPR021408 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=26.69 E-value=48 Score=24.06 Aligned_cols=43 Identities=23% Similarity=0.311 Sum_probs=33.3
Q ss_pred HHHHHHHcCC-CCchHHHhhcccccccCCchhhhhhhhccccccc
Q 022922 158 DEFTDSLSKK-KITIKALLLDQSYISGIGNWVADEVLYQAKIHPL 201 (290)
Q Consensus 158 ~~f~~~l~~~-~~~IK~~LLDQ~~iaGIGNiyadEiLf~A~IhP~ 201 (290)
.+|.+++..- -..-...|.+..+++++|+--++|+| .+|++|.
T Consensus 4 teFw~~~~~~FG~~~~~~la~dhvL~~LGgrT~~eAL-~~G~dpr 47 (63)
T PF11248_consen 4 TEFWQLMEEEFGPAYGRSLARDHVLSELGGRTAAEAL-EAGVDPR 47 (63)
T ss_pred HHHHHHHHHHhCchhHHHHHHhcchhhcCCcCHHHHH-HcCCCHH
Confidence 4677777543 34556788999999999999999988 6788874
No 108
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=26.07 E-value=29 Score=36.92 Aligned_cols=22 Identities=9% Similarity=-0.026 Sum_probs=15.4
Q ss_pred CCCccccccceeeeccceeeecc
Q 022922 249 NKICRLFKVRLKLMLTAAAFLLN 271 (290)
Q Consensus 249 g~~C~~Cg~~i~~~~~~~~~~~~ 271 (290)
+..||.||.++...+ |-..|.+
T Consensus 724 ~~~Cp~Cg~~l~~~~-GC~~C~~ 745 (752)
T PRK08665 724 RGACPECGSILEHEE-GCVVCHS 745 (752)
T ss_pred CCCCCCCCcccEECC-CCCcCCC
Confidence 357999997655444 7777765
No 109
>TIGR00409 proS_fam_II prolyl-tRNA synthetase, family II. Prolyl-tRNA synthetase is a class II tRNA synthetase and is recognized by pfam model tRNA-synt_2b, which recognizes tRNA synthetases for Gly, His, Ser, and Pro. The prolyl-tRNA synthetases are divided into two widely divergent groups. This group includes enzymes from Escherichia coli, Bacillus subtilis, Aquifex aeolicus, the spirochete Treponema pallidum, Synechocystis PCC6803, and one of the two prolyL-tRNA synthetases of Saccharomyces cerevisiae. The other group includes the Pro-specific domain of a human multifunctional tRNA ligase and the prolyl-tRNA synthetases from the Archaea, the Mycoplasmas, and the spirochete Borrelia burgdorferi.
Probab=25.57 E-value=30 Score=35.54 Aligned_cols=15 Identities=20% Similarity=-0.046 Sum_probs=12.8
Q ss_pred CCCCCCcccccccee
Q 022922 246 HRENKICRLFKVRLK 260 (290)
Q Consensus 246 ~R~g~~C~~Cg~~i~ 260 (290)
-++|.+||.||+++.
T Consensus 390 ~~eGd~cp~c~~~l~ 404 (568)
T TIGR00409 390 VKEGDPSPDGQGTLK 404 (568)
T ss_pred hhccCCCCCCCCccc
Confidence 378999999998775
No 110
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=25.45 E-value=45 Score=27.45 Aligned_cols=20 Identities=5% Similarity=-0.086 Sum_probs=15.1
Q ss_pred cc--ccccceeeeccceeeecc
Q 022922 252 CR--LFKVRLKLMLTAAAFLLN 271 (290)
Q Consensus 252 C~--~Cg~~i~~~~~~~~~~~~ 271 (290)
|| .|+.++...+.|+++|-+
T Consensus 21 C~~~~C~kKv~~~~~~~y~C~~ 42 (146)
T PF08646_consen 21 CPNEKCNKKVTENGDGSYRCEK 42 (146)
T ss_dssp -TSTTTS-B-EEETTTEEEETT
T ss_pred CCCccCCCEeecCCCcEEECCC
Confidence 99 999998888889999965
No 111
>PF10825 DUF2752: Protein of unknown function (DUF2752); InterPro: IPR021215 This family is conserved in bacteria. Many members are annotated as being putative membrane proteins.
Probab=25.19 E-value=32 Score=23.67 Aligned_cols=12 Identities=8% Similarity=-0.022 Sum_probs=9.3
Q ss_pred CCCCCccccccc
Q 022922 247 RENKICRLFKVR 258 (290)
Q Consensus 247 R~g~~C~~Cg~~ 258 (290)
-.|-+||.||..
T Consensus 7 ltG~~CPgCG~t 18 (52)
T PF10825_consen 7 LTGIPCPGCGMT 18 (52)
T ss_pred hhCCCCCCCcHH
Confidence 357899999953
No 112
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=24.85 E-value=33 Score=24.29 Aligned_cols=20 Identities=15% Similarity=0.039 Sum_probs=12.8
Q ss_pred CCccccccceeeeccceeeecc-ee
Q 022922 250 KICRLFKVRLKLMLTAAAFLLN-GY 273 (290)
Q Consensus 250 ~~C~~Cg~~i~~~~~~~~~~~~-~~ 273 (290)
..||.||..... -+-|.+ ||
T Consensus 28 ~~C~~CG~~~~~----H~vC~~CG~ 48 (57)
T PRK12286 28 VECPNCGEPKLP----HRVCPSCGY 48 (57)
T ss_pred eECCCCCCccCC----eEECCCCCc
Confidence 449999987653 455654 54
No 113
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=24.55 E-value=38 Score=20.94 Aligned_cols=11 Identities=9% Similarity=0.256 Sum_probs=8.7
Q ss_pred CCCCccccccc
Q 022922 248 ENKICRLFKVR 258 (290)
Q Consensus 248 ~g~~C~~Cg~~ 258 (290)
+...||.||++
T Consensus 16 ~~~~CP~Cg~~ 26 (33)
T cd00350 16 APWVCPVCGAP 26 (33)
T ss_pred CCCcCcCCCCc
Confidence 46679999975
No 114
>PF06462 Hyd_WA: Propeller; InterPro: IPR006624 Tectonins I and II are two dominant proteins in the nuclei and nuclear matrix from plasmodia of Physarum polycephalum (Slime mold) which encode 217 and 353 amino acids, respectively. Tectonin I is homologous to the C-terminal two-thirds of tectonin II. Both proteins contain six tandem repeats that are each 33-37 amino acids in length and define a new consensus sequence. Homologous repeats are found in L-6, a bacterial lipopolysaccharide-binding lectin from horseshoe crab hemocytes. The repetitive sequences of the tectonins and L-6 are reminiscent of the WD repeats of the beta-subunit of G proteins, suggesting that they form beta-propeller domains. The tectonins may be lectins that function as part of a transmembrane signalling complex during phagocytosis [].
Probab=23.99 E-value=33 Score=21.17 Aligned_cols=16 Identities=19% Similarity=0.376 Sum_probs=13.3
Q ss_pred hhhhcccccccCcCCC
Q 022922 191 EVLYQAKIHPLQTAVS 206 (290)
Q Consensus 191 EiLf~A~IhP~~~~~~ 206 (290)
.++||.||+|..|.++
T Consensus 11 ~v~~R~Gis~~~P~G~ 26 (32)
T PF06462_consen 11 SVYFRTGISPSNPEGT 26 (32)
T ss_pred CEEEECcCCCCCCCCC
Confidence 4669999999998775
No 115
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=23.71 E-value=25 Score=28.42 Aligned_cols=14 Identities=14% Similarity=0.204 Sum_probs=12.4
Q ss_pred ccccccceeeeccc
Q 022922 252 CRLFKVRLKLMLTA 265 (290)
Q Consensus 252 C~~Cg~~i~~~~~~ 265 (290)
||.|+..++..||.
T Consensus 72 CP~C~K~TKmLGr~ 85 (114)
T PF11023_consen 72 CPNCGKQTKMLGRV 85 (114)
T ss_pred CCCCCChHhhhchh
Confidence 99999999888775
No 116
>PF09151 DUF1936: Domain of unknown function (DUF1936); InterPro: IPR015234 This domain is found in a set of hypothetical archaeal proteins. Its exact function has not, as yet, been defined. ; PDB: 2QH1_B 1PVM_B.
Probab=23.70 E-value=39 Score=21.08 Aligned_cols=10 Identities=20% Similarity=0.385 Sum_probs=6.9
Q ss_pred Ccccccccee
Q 022922 251 ICRLFKVRLK 260 (290)
Q Consensus 251 ~C~~Cg~~i~ 260 (290)
-||.||..+.
T Consensus 3 lcpkcgvgvl 12 (36)
T PF09151_consen 3 LCPKCGVGVL 12 (36)
T ss_dssp B-TTTSSSBE
T ss_pred cCCccCceEE
Confidence 4999997754
No 117
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=23.33 E-value=60 Score=28.34 Aligned_cols=29 Identities=31% Similarity=0.348 Sum_probs=20.5
Q ss_pred CCCHHHHHHHHcCCC---CchHHHhhcccccc
Q 022922 154 PMTVDEFTDSLSKKK---ITIKALLLDQSYIS 182 (290)
Q Consensus 154 ~f~~~~f~~~l~~~~---~~IK~~LLDQ~~ia 182 (290)
.+|-+.+.+.+.-+. +.|=.+|.|+.+|+
T Consensus 32 e~tDeela~~l~i~~~~vrriL~~L~e~~li~ 63 (176)
T COG1675 32 ELTDEELAELLGIKKNEVRRILYALYEDGLIS 63 (176)
T ss_pred CcChHHHHHHhCccHHHHHHHHHHHHhCCceE
Confidence 477788888876543 55666778888776
No 118
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=23.06 E-value=30 Score=24.56 Aligned_cols=20 Identities=10% Similarity=0.104 Sum_probs=9.6
Q ss_pred Cccccccceee-eccce-eeec
Q 022922 251 ICRLFKVRLKL-MLTAA-AFLL 270 (290)
Q Consensus 251 ~C~~Cg~~i~~-~~~~~-~~~~ 270 (290)
+||.||.++.. ..+.. -||.
T Consensus 4 ~CP~C~k~~~~~~~n~~rPFCS 25 (57)
T PF03884_consen 4 KCPICGKPVEWSPENPFRPFCS 25 (57)
T ss_dssp E-TTT--EEE-SSSSS--SSSS
T ss_pred cCCCCCCeecccCCCCcCCccc
Confidence 59999999876 33332 3674
No 119
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=23.03 E-value=38 Score=21.24 Aligned_cols=10 Identities=10% Similarity=0.298 Sum_probs=8.0
Q ss_pred CCCccccccc
Q 022922 249 NKICRLFKVR 258 (290)
Q Consensus 249 g~~C~~Cg~~ 258 (290)
-+.||.||++
T Consensus 18 p~~CP~Cg~~ 27 (34)
T cd00729 18 PEKCPICGAP 27 (34)
T ss_pred CCcCcCCCCc
Confidence 4579999985
No 120
>PRK12267 methionyl-tRNA synthetase; Reviewed
Probab=22.80 E-value=1.2e+02 Score=31.43 Aligned_cols=21 Identities=14% Similarity=0.233 Sum_probs=14.8
Q ss_pred CCCccccccceeeeccceeee
Q 022922 249 NKICRLFKVRLKLMLTAAAFL 269 (290)
Q Consensus 249 g~~C~~Cg~~i~~~~~~~~~~ 269 (290)
+..|++||+++...-..-.|-
T Consensus 143 ~~~c~~cg~~~e~~~~~~~f~ 163 (648)
T PRK12267 143 GGKCPDCGREVELVKEESYFF 163 (648)
T ss_pred CCcCCCCCCcCeEEecceEEE
Confidence 356999999987665555443
No 121
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=22.77 E-value=47 Score=22.75 Aligned_cols=25 Identities=16% Similarity=0.041 Sum_probs=15.2
Q ss_pred CCCCCccccccceeeeccceeeecc
Q 022922 247 RENKICRLFKVRLKLMLTAAAFLLN 271 (290)
Q Consensus 247 R~g~~C~~Cg~~i~~~~~~~~~~~~ 271 (290)
+..+-||+||..+.....+...|-.
T Consensus 18 ~~~~fCP~Cg~~~m~~~~~r~~C~~ 42 (50)
T PRK00432 18 RKNKFCPRCGSGFMAEHLDRWHCGK 42 (50)
T ss_pred EccCcCcCCCcchheccCCcEECCC
Confidence 3457899999853333345556653
No 122
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=22.67 E-value=40 Score=21.13 Aligned_cols=10 Identities=10% Similarity=-0.087 Sum_probs=8.3
Q ss_pred Ccccccccee
Q 022922 251 ICRLFKVRLK 260 (290)
Q Consensus 251 ~C~~Cg~~i~ 260 (290)
.||+||+.+.
T Consensus 27 ~C~~C~~~~~ 36 (38)
T TIGR02098 27 RCGKCGHVWY 36 (38)
T ss_pred ECCCCCCEEE
Confidence 4999998875
No 123
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=22.56 E-value=45 Score=28.34 Aligned_cols=28 Identities=21% Similarity=0.116 Sum_probs=17.7
Q ss_pred CCHHHHHHHHcCCC---CchHHHhhcccccc
Q 022922 155 MTVDEFTDSLSKKK---ITIKALLLDQSYIS 182 (290)
Q Consensus 155 f~~~~f~~~l~~~~---~~IK~~LLDQ~~ia 182 (290)
.+.+.+...+.=+. +.+-..|.+..+++
T Consensus 29 ~tdEeLa~~Lgi~~~~VRk~L~~L~e~~Lv~ 59 (158)
T TIGR00373 29 FTDEEISLELGIKLNEVRKALYALYDAGLAD 59 (158)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCce
Confidence 56778888775443 34455567777664
No 124
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=21.75 E-value=36 Score=27.19 Aligned_cols=11 Identities=9% Similarity=0.163 Sum_probs=9.7
Q ss_pred CCcccccccee
Q 022922 250 KICRLFKVRLK 260 (290)
Q Consensus 250 ~~C~~Cg~~i~ 260 (290)
..||.||.++.
T Consensus 50 t~CP~Cg~~~e 60 (115)
T COG1885 50 TSCPKCGEPFE 60 (115)
T ss_pred ccCCCCCCccc
Confidence 56999999987
No 125
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=21.73 E-value=36 Score=28.44 Aligned_cols=14 Identities=7% Similarity=0.078 Sum_probs=11.4
Q ss_pred CCCCccccccceee
Q 022922 248 ENKICRLFKVRLKL 261 (290)
Q Consensus 248 ~g~~C~~Cg~~i~~ 261 (290)
-+-||.+||++|+.
T Consensus 80 l~~~CE~CG~~I~~ 93 (137)
T TIGR03826 80 LGYPCERCGTSIRE 93 (137)
T ss_pred CcCcccccCCcCCC
Confidence 45789999999863
No 126
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=21.41 E-value=37 Score=23.26 Aligned_cols=11 Identities=27% Similarity=0.368 Sum_probs=5.7
Q ss_pred CCcccccccee
Q 022922 250 KICRLFKVRLK 260 (290)
Q Consensus 250 ~~C~~Cg~~i~ 260 (290)
..||-||.++.
T Consensus 21 ~~CPlC~r~l~ 31 (54)
T PF04423_consen 21 GCCPLCGRPLD 31 (54)
T ss_dssp EE-TTT--EE-
T ss_pred CcCCCCCCCCC
Confidence 37999999875
No 127
>PRK02935 hypothetical protein; Provisional
Probab=21.41 E-value=34 Score=27.40 Aligned_cols=16 Identities=19% Similarity=0.272 Sum_probs=13.4
Q ss_pred Cccccccceeeeccce
Q 022922 251 ICRLFKVRLKLMLTAA 266 (290)
Q Consensus 251 ~C~~Cg~~i~~~~~~~ 266 (290)
.||.|+.++++.||.-
T Consensus 72 ~CP~C~K~TKmLGrvD 87 (110)
T PRK02935 72 ICPSCEKPTKMLGRVD 87 (110)
T ss_pred ECCCCCchhhhcccee
Confidence 4999999999888753
No 128
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=21.06 E-value=49 Score=21.15 Aligned_cols=16 Identities=13% Similarity=0.075 Sum_probs=11.6
Q ss_pred Cccccccc--eeeeccce
Q 022922 251 ICRLFKVR--LKLMLTAA 266 (290)
Q Consensus 251 ~C~~Cg~~--i~~~~~~~ 266 (290)
.||+|+.. +.+.|.+.
T Consensus 7 ~CP~C~s~~~v~k~G~~~ 24 (36)
T PF03811_consen 7 HCPRCQSTEGVKKNGKSP 24 (36)
T ss_pred eCCCCCCCCcceeCCCCC
Confidence 49999844 67777654
No 129
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=20.99 E-value=62 Score=21.70 Aligned_cols=14 Identities=21% Similarity=0.373 Sum_probs=10.1
Q ss_pred CCcccccc-ceeeec
Q 022922 250 KICRLFKV-RLKLML 263 (290)
Q Consensus 250 ~~C~~Cg~-~i~~~~ 263 (290)
..||.||. .++++-
T Consensus 27 ~~CP~Cg~~~~~r~~ 41 (52)
T TIGR02605 27 ATCPECGGEKLRRLL 41 (52)
T ss_pred CCCCCCCCCceeEEe
Confidence 45999997 675553
No 130
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=20.85 E-value=48 Score=26.84 Aligned_cols=11 Identities=18% Similarity=0.338 Sum_probs=8.9
Q ss_pred ccccccceeee
Q 022922 252 CRLFKVRLKLM 262 (290)
Q Consensus 252 C~~Cg~~i~~~ 262 (290)
||.||.++..+
T Consensus 1 CPvCg~~l~vt 11 (113)
T PF09862_consen 1 CPVCGGELVVT 11 (113)
T ss_pred CCCCCCceEEE
Confidence 89999887755
No 131
>KOG2712 consensus Transcriptional coactivator [Transcription]
Probab=20.63 E-value=1.1e+02 Score=24.51 Aligned_cols=29 Identities=34% Similarity=0.455 Sum_probs=23.5
Q ss_pred cccccCcCCCCCHHHHHHHHHHHHHHHHH
Q 022922 197 KIHPLQTAVSLSKESCATLLKCIKEVREA 225 (290)
Q Consensus 197 ~IhP~~~~~~Ls~~e~~~L~~~i~~vL~~ 225 (290)
.+-|.+++=+||.+||..|-+.+..|=+.
T Consensus 73 ~mlPgkKGISLs~~qW~~Lk~~~~eId~A 101 (108)
T KOG2712|consen 73 KMLPGKKGISLSLEQWSKLKEHIEEIDKA 101 (108)
T ss_pred ccccCccccccCHHHHHHHHHHHHHHHHH
Confidence 35678888899999999999988776543
No 132
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=20.63 E-value=53 Score=27.62 Aligned_cols=20 Identities=5% Similarity=-0.150 Sum_probs=14.6
Q ss_pred ccccccceeeeccceeeecc
Q 022922 252 CRLFKVRLKLMLTAAAFLLN 271 (290)
Q Consensus 252 C~~Cg~~i~~~~~~~~~~~~ 271 (290)
||.|..++...+.++.+|.+
T Consensus 37 C~~C~kkv~~~~~~~~~C~~ 56 (166)
T cd04476 37 CPGCNKKVVEEGNGTYRCEK 56 (166)
T ss_pred ccccCcccEeCCCCcEECCC
Confidence 88888877766557777764
No 133
>PF01258 zf-dskA_traR: Prokaryotic dksA/traR C4-type zinc finger; InterPro: IPR000962 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents domains identified in zinc finger-containing members of the DksA/TraR family. DksA is a critical component of the rRNA transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. In delta-dksA mutants, rRNA promoters are unresponsive to changes in amino acid availability, growth rate, or growth phase. In vitro, DksA binds to RNAP, reduces open complex lifetime, inhibits rRNA promoter activity, and amplifies effects of ppGpp and the initiating NTP on rRNA transcription [, ]. The dksA gene product suppresses the temperature-sensitive growth and filamentation of a dnaK deletion mutant of Escherichia coli. Gene knockout [] and deletion [] experiments have shown the gene to be non-essential, mutations causing a mild sensitivity to UV light, but not affecting DNA recombination []. In Pseudomonas aeruginosa, dksA is a novel regulator involved in the post-transcriptional control of extracellular virulence factor production []. The proteins contain a C-terminal region thought to fold into a 4-cysteine zinc finger. Other proteins found to contain a similar zinc finger domain include: the traR gene products encoded on the E. coli F and R100 plasmids [, ] the traR gene products encoded on Salmonella spp. plasmids pED208 and pSLT the dnaK suppressor hypothetical proteins from bacteria and bacteriophage FHL4, LIM proteins from Homo sapiens (Human) and Mus musculus (Mouse) [] More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2GVI_A 2KQ9_A 2KGO_A 1TJL_I.
Probab=20.61 E-value=30 Score=21.68 Aligned_cols=20 Identities=10% Similarity=0.253 Sum_probs=13.7
Q ss_pred cccccccee----eeccceeeecc
Q 022922 252 CRLFKVRLK----LMLTAAAFLLN 271 (290)
Q Consensus 252 C~~Cg~~i~----~~~~~~~~~~~ 271 (290)
|-.||.+|- ++-.++.+|..
T Consensus 6 C~~CGe~I~~~Rl~~~p~~~~C~~ 29 (36)
T PF01258_consen 6 CEDCGEPIPEERLVAVPGATLCVE 29 (36)
T ss_dssp -TTTSSBEEHHHHHHCTTECS-HH
T ss_pred ccccCChHHHHHHHhCCCcEECHH
Confidence 999999987 33567777764
No 134
>cd08975 BaFpgNei_N_3 Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases. This family is an uncharacterized bacterial subgroup of the FpgNei_N domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. One exception is mouse Nei-like glycosylase 3 (Neil3) which forms a Schiff base int
Probab=20.48 E-value=1.2e+02 Score=24.36 Aligned_cols=70 Identities=20% Similarity=0.204 Sum_probs=37.4
Q ss_pred HHHHHHcCCCeEEEEEecCCCceeccCChhhH--HhhhcCCEEEEEE--eeeeEEEEEeCCCCceEEecCceEEE
Q 022922 12 RAIEEHCIGKKIVKSIIADDNKVIDGVSASDF--EASVLGKAILSAH--RKGKNLWLRLDSPPFPSFQFGMTGAI 82 (290)
Q Consensus 12 ~~L~~~~~Gk~I~~v~~~~~~~~~~~~~~~~f--~~~L~G~~i~~v~--RrGK~L~~~l~~~~~L~~HLgMtG~l 82 (290)
..+.+.+.|++|.+|.-. ...++-..+..-+ .-..+|+-...-. ..=-++.++|+++..|.++..|.|.+
T Consensus 42 ~~~~~~L~G~~i~~v~Rr-GKyl~~~l~~~~Li~HLgMtG~l~~~~~~~~kh~~l~l~~~dg~~L~f~~~~~~~~ 115 (117)
T cd08975 42 NEYDELLVGKRITSAEGF-GGFVEIIFEDKRLLFNDGVNVRYYYGGEKIPKKYQLLIEFDDDSFLVFTVAMYGGI 115 (117)
T ss_pred HHHHHhCCCCEEEeEeeE-eeEEEEEeCCCEEEEECceEEEEEeCCCCCCCeEEEEEEECCCCEEEEEEEEEeee
Confidence 457778999999999865 4434322221000 0112233211100 11123556777776788888888865
Done!