Query 015345
Match_columns 408
No_of_seqs 150 out of 1167
Neff 5.7
Searched_HMMs 46136
Date Fri Mar 29 05:26:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/015345.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/015345hhsearch_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 4.3E-79 9.3E-84 591.1 28.3 260 1-277 1-273 (273)
2 PRK13945 formamidopyrimidine-D 100.0 1.5E-77 3.3E-82 588.0 30.4 261 1-277 1-282 (282)
3 PRK01103 formamidopyrimidine/5 100.0 6.5E-77 1.4E-81 581.3 30.5 261 1-278 1-274 (274)
4 TIGR00577 fpg formamidopyrimid 100.0 4.1E-76 8.9E-81 575.2 29.9 258 2-276 1-272 (272)
5 PRK14811 formamidopyrimidine-D 100.0 4.6E-76 1E-80 574.1 29.3 251 1-280 1-266 (269)
6 PRK14810 formamidopyrimidine-D 100.0 5.8E-74 1.3E-78 560.1 30.6 257 1-277 1-272 (272)
7 PRK10445 endonuclease VIII; Pr 100.0 3.6E-73 7.8E-78 552.1 30.0 251 1-277 1-263 (263)
8 cd08972 PF_Nei_N N-terminal do 100.0 1.2E-32 2.6E-37 244.2 15.9 134 1-134 1-137 (137)
9 cd08976 BaFpgNei_N_4 Uncharact 100.0 2.2E-31 4.8E-36 229.3 15.1 117 2-133 1-117 (117)
10 PF01149 Fapy_DNA_glyco: Forma 100.0 5.7E-31 1.2E-35 226.2 13.5 116 2-132 1-116 (116)
11 cd08966 EcFpg-like_N N-termina 100.0 1.6E-30 3.5E-35 224.4 15.8 120 2-135 1-120 (120)
12 PF06831 H2TH: Formamidopyrimi 100.0 2.2E-31 4.8E-36 221.1 8.5 90 146-235 1-90 (92)
13 cd08967 MeNeil1_N N-terminal d 100.0 3.4E-29 7.3E-34 220.5 14.2 113 1-134 1-130 (131)
14 cd08773 FpgNei_N N-terminal do 100.0 3.8E-29 8.2E-34 215.0 14.2 117 2-133 1-117 (117)
15 cd08973 BaFpgNei_N_1 Uncharact 100.0 1.3E-28 2.8E-33 214.0 14.9 114 1-129 1-115 (122)
16 cd08975 BaFpgNei_N_3 Uncharact 99.9 5.8E-27 1.2E-31 202.7 14.7 113 3-132 2-116 (117)
17 cd08971 AcNei2_N N-terminal do 99.9 4.1E-26 9E-31 196.4 14.8 112 1-135 1-112 (114)
18 cd08974 BaFpgNei_N_2 Uncharact 99.9 2.3E-25 5E-30 187.1 13.0 97 1-125 1-97 (98)
19 cd08965 EcNei-like_N N-termina 99.9 1.4E-24 3.1E-29 187.2 15.2 113 2-136 1-113 (115)
20 cd08970 AcNei1_N N-terminal do 99.9 1.4E-24 3.1E-29 185.9 14.0 109 1-133 1-109 (110)
21 cd08968 MeNeil2_N N-terminal d 99.9 1.3E-21 2.8E-26 170.6 13.5 111 1-125 1-121 (126)
22 cd08969 MeNeil3_N N-terminal d 99.6 4.8E-15 1E-19 131.2 10.4 112 1-125 1-122 (140)
23 PF06827 zf-FPG_IleRS: Zinc fi 98.6 5.2E-08 1.1E-12 64.7 3.4 29 247-277 1-29 (30)
24 PF05833 FbpA: Fibronectin-bin 98.1 2.1E-05 4.6E-10 82.0 11.9 196 6-228 4-244 (455)
25 COG1293 Predicted RNA-binding 97.0 0.0096 2.1E-07 64.6 13.0 71 149-224 168-238 (564)
26 PRK04184 DNA topoisomerase VI 96.2 0.03 6.4E-07 60.4 10.3 75 144-222 232-307 (535)
27 PF00416 Ribosomal_S13: Riboso 95.9 0.015 3.3E-07 49.6 5.5 52 167-221 9-60 (107)
28 COG0099 RpsM Ribosomal protein 95.8 0.0084 1.8E-07 52.3 3.3 41 180-220 21-61 (121)
29 PRK05179 rpsM 30S ribosomal pr 95.5 0.016 3.5E-07 50.9 4.0 51 168-221 12-62 (122)
30 TIGR01052 top6b DNA topoisomer 95.3 0.1 2.3E-06 55.7 9.9 74 145-222 224-301 (488)
31 PTZ00134 40S ribosomal protein 95.0 0.027 5.9E-07 51.4 4.0 52 167-221 24-75 (154)
32 CHL00137 rps13 ribosomal prote 95.0 0.032 6.9E-07 49.1 4.2 50 168-220 12-61 (122)
33 TIGR03631 bact_S13 30S ribosom 94.4 0.047 1E-06 47.3 3.8 50 168-220 10-59 (113)
34 PRK04053 rps13p 30S ribosomal 94.1 0.059 1.3E-06 49.0 4.0 52 167-221 19-70 (149)
35 TIGR03629 arch_S13P archaeal r 94.0 0.069 1.5E-06 48.2 4.2 51 168-221 16-66 (144)
36 PF13453 zf-TFIIB: Transcripti 89.7 0.37 8E-06 34.0 3.0 27 250-278 2-28 (41)
37 PRK00420 hypothetical protein; 88.4 0.36 7.8E-06 41.9 2.5 27 248-279 24-50 (112)
38 COG1389 DNA topoisomerase VI, 87.9 1.4 3.1E-05 46.7 7.0 76 143-222 231-311 (538)
39 COG1645 Uncharacterized Zn-fin 86.2 0.48 1E-05 42.2 2.1 25 248-278 29-53 (131)
40 PF06677 Auto_anti-p27: Sjogre 85.1 0.9 2E-05 32.5 2.7 25 247-276 17-41 (41)
41 KOG3311 Ribosomal protein S18 84.4 0.75 1.6E-05 41.8 2.5 50 168-220 23-72 (152)
42 PF14803 Nudix_N_2: Nudix N-te 84.1 0.96 2.1E-05 31.1 2.4 26 250-277 3-30 (34)
43 KOG0066 eIF2-interacting prote 83.2 1.3 2.8E-05 47.2 4.0 62 309-371 48-110 (807)
44 PHA00626 hypothetical protein 79.1 1.9 4.2E-05 33.0 2.6 44 249-294 2-53 (59)
45 smart00661 RPOL9 RNA polymeras 76.5 1.7 3.7E-05 31.6 1.7 28 250-279 3-30 (52)
46 PRK12495 hypothetical protein; 75.4 1.6 3.5E-05 42.0 1.7 25 249-279 44-68 (226)
47 COG1096 Predicted RNA-binding 70.1 3.3 7.1E-05 39.1 2.3 30 239-278 145-174 (188)
48 TIGR00275 flavoprotein, HI0933 69.4 8.3 0.00018 39.8 5.4 64 153-221 263-331 (400)
49 COG3809 Uncharacterized protei 67.8 5 0.00011 32.9 2.6 28 249-278 3-30 (88)
50 PF07282 OrfB_Zn_ribbon: Putat 65.1 6.1 0.00013 30.5 2.6 28 247-278 28-55 (69)
51 PRK09710 lar restriction allev 64.2 7.9 0.00017 30.4 3.0 45 248-294 7-54 (64)
52 TIGR00755 ksgA dimethyladenosi 62.6 10 0.00022 36.5 4.3 58 157-219 195-253 (253)
53 PF08273 Prim_Zn_Ribbon: Zinc- 62.2 6 0.00013 28.2 1.9 28 248-277 4-34 (40)
54 PF14205 Cys_rich_KTR: Cystein 57.9 5.5 0.00012 30.3 1.2 28 250-279 7-38 (55)
55 PF07191 zinc-ribbons_6: zinc- 57.8 12 0.00026 29.9 3.1 28 250-279 33-60 (70)
56 KOG2846 Predicted membrane pro 57.7 17 0.00038 37.1 5.0 36 245-282 218-255 (328)
57 TIGR03655 anti_R_Lar restricti 57.5 8.2 0.00018 28.7 2.0 30 248-279 2-36 (53)
58 COG0030 KsgA Dimethyladenosine 56.4 14 0.00031 36.6 4.1 52 163-222 206-257 (259)
59 PF03119 DNA_ligase_ZBD: NAD-d 56.1 8.4 0.00018 25.2 1.6 21 250-274 2-22 (28)
60 COG0675 Transposase and inacti 55.4 31 0.00068 33.5 6.4 80 170-278 249-331 (364)
61 smart00778 Prim_Zn_Ribbon Zinc 55.3 9.2 0.0002 26.8 1.9 29 247-277 3-33 (37)
62 PF08394 Arc_trans_TRASH: Arch 54.7 8.3 0.00018 27.1 1.5 25 254-278 3-32 (37)
63 PRK00274 ksgA 16S ribosomal RN 54.5 18 0.0004 35.4 4.6 59 158-220 210-269 (272)
64 PRK12860 transcriptional activ 54.2 8.9 0.00019 36.3 2.2 30 248-279 135-164 (189)
65 PF04945 YHS: YHS domain; Int 52.7 14 0.0003 26.6 2.5 25 253-277 4-34 (47)
66 PF12760 Zn_Tnp_IS1595: Transp 52.6 20 0.00044 25.7 3.4 28 247-277 18-45 (46)
67 PRK12722 transcriptional activ 51.2 10 0.00022 35.8 2.0 30 248-279 135-164 (187)
68 PF08271 TF_Zn_Ribbon: TFIIB z 50.5 18 0.00039 25.6 2.8 26 250-278 3-28 (43)
69 PRK00398 rpoP DNA-directed RNA 49.9 11 0.00024 27.1 1.6 25 250-278 6-30 (46)
70 TIGR03826 YvyF flagellar opero 49.1 8.8 0.00019 34.5 1.2 52 211-278 51-103 (137)
71 PRK10664 transcriptional regul 47.8 86 0.0019 25.8 6.9 67 205-274 14-82 (90)
72 PF00398 RrnaAD: Ribosomal RNA 47.6 23 0.0005 34.5 4.0 57 158-220 203-261 (262)
73 COG2824 PhnA Uncharacterized Z 47.6 13 0.00029 32.0 2.0 75 248-337 4-79 (112)
74 PF03486 HI0933_like: HI0933-l 46.9 11 0.00024 39.5 1.7 64 153-221 270-339 (409)
75 PF06044 DRP: Dam-replacing fa 45.8 12 0.00026 36.7 1.7 29 249-279 33-63 (254)
76 PF07191 zinc-ribbons_6: zinc- 45.5 14 0.0003 29.6 1.6 24 249-278 3-26 (70)
77 COG2081 Predicted flavoprotein 45.4 34 0.00074 36.0 5.0 63 153-221 268-332 (408)
78 cd04476 RPA1_DBD_C RPA1_DBD_C: 44.5 11 0.00024 34.0 1.2 25 249-278 36-60 (166)
79 COG3350 Uncharacterized conser 43.4 21 0.00046 27.1 2.3 22 253-274 6-33 (53)
80 PF08646 Rep_fac-A_C: Replicat 43.3 17 0.00037 32.1 2.1 26 250-278 21-46 (146)
81 PF05280 FlhC: Flagellar trans 43.2 8.5 0.00018 35.9 0.2 30 249-280 136-165 (175)
82 TIGR00988 hip integration host 43.0 1.2E+02 0.0026 24.7 7.0 66 205-274 15-83 (94)
83 PRK10753 transcriptional regul 42.8 1.2E+02 0.0027 24.8 7.1 67 205-274 14-82 (90)
84 PF13248 zf-ribbon_3: zinc-rib 42.6 8.2 0.00018 24.6 0.0 21 249-277 4-24 (26)
85 PF07754 DUF1610: Domain of un 42.6 17 0.00037 23.2 1.4 21 254-276 3-23 (24)
86 TIGR02098 MJ0042_CXXC MJ0042 f 41.2 19 0.00041 24.5 1.6 28 249-278 4-34 (38)
87 PF02591 DUF164: Putative zinc 41.0 6 0.00013 29.6 -1.0 30 247-278 22-55 (56)
88 COG2995 PqiA Uncharacterized p 40.8 13 0.00029 38.8 1.2 28 249-278 20-47 (418)
89 KOG3064 RNA-binding nuclear pr 40.4 18 0.0004 35.9 2.0 26 311-336 253-278 (303)
90 COG0776 HimA Bacterial nucleoi 39.8 82 0.0018 26.5 5.6 53 207-260 17-71 (94)
91 PRK12366 replication factor A; 39.4 17 0.00037 40.4 1.8 24 249-278 534-557 (637)
92 cd01675 RNR_III Class III ribo 38.7 16 0.00035 39.8 1.5 93 171-278 426-541 (555)
93 COG3024 Uncharacterized protei 38.2 10 0.00023 29.8 -0.0 31 247-279 7-37 (65)
94 PF09538 FYDLN_acid: Protein o 38.1 38 0.00082 29.2 3.4 30 247-281 9-38 (108)
95 PRK10220 hypothetical protein; 37.5 35 0.00076 29.6 3.0 66 249-330 5-71 (111)
96 PRK00199 ihfB integration host 37.0 1.1E+02 0.0023 25.1 5.9 54 205-259 15-70 (94)
97 KOG2923 Uncharacterized conser 37.0 22 0.00047 28.1 1.5 28 248-278 23-53 (67)
98 PF09862 DUF2089: Protein of u 36.5 33 0.00072 29.9 2.8 20 253-278 2-21 (113)
99 TIGR00987 himA integration hos 35.6 1.6E+02 0.0036 24.1 6.8 66 205-274 15-83 (96)
100 COG5216 Uncharacterized conser 35.2 35 0.00075 26.6 2.4 28 248-278 23-53 (67)
101 PRK14973 DNA topoisomerase I; 34.5 27 0.00059 40.6 2.5 30 248-279 636-667 (936)
102 PF11197 DUF2835: Protein of u 34.0 70 0.0015 25.4 4.0 49 37-85 6-56 (68)
103 PF13240 zinc_ribbon_2: zinc-r 33.8 15 0.00033 22.9 0.2 18 254-277 4-21 (23)
104 PTZ00338 dimethyladenosine tra 31.9 79 0.0017 31.6 5.1 57 163-220 210-287 (294)
105 PF10571 UPF0547: Uncharacteri 31.7 32 0.00069 22.2 1.5 23 249-279 2-24 (26)
106 PF13005 zf-IS66: zinc-finger 31.7 44 0.00095 23.7 2.4 11 266-276 37-47 (47)
107 PF01927 Mut7-C: Mut7-C RNAse 30.6 35 0.00075 30.5 2.1 32 249-282 93-139 (147)
108 PF10263 SprT-like: SprT-like 30.3 36 0.00077 30.1 2.1 27 249-277 125-151 (157)
109 COG2888 Predicted Zn-ribbon RN 29.6 22 0.00048 27.6 0.5 26 249-276 29-57 (61)
110 PRK14896 ksgA 16S ribosomal RN 29.3 1.3E+02 0.0028 29.1 6.0 62 158-221 193-256 (258)
111 cd08975 BaFpgNei_N_3 Uncharact 26.6 65 0.0014 27.8 3.0 71 11-83 41-116 (117)
112 PRK14892 putative transcriptio 26.3 65 0.0014 27.4 2.8 31 249-281 23-54 (99)
113 KOG0066 eIF2-interacting prote 26.0 75 0.0016 34.4 3.8 17 305-321 92-112 (807)
114 PF12773 DZR: Double zinc ribb 25.8 30 0.00064 24.9 0.6 27 248-279 13-39 (50)
115 COG4643 Uncharacterized protei 25.0 25 0.00055 36.1 0.2 32 247-280 32-65 (366)
116 COG4871 Uncharacterized protei 24.5 1.2E+02 0.0025 28.4 4.3 48 208-257 91-144 (193)
117 TIGR02487 NrdD anaerobic ribon 24.4 45 0.00098 36.7 2.0 93 170-277 432-546 (579)
118 PF13408 Zn_ribbon_recom: Reco 23.9 88 0.0019 22.6 2.9 27 250-278 8-35 (58)
119 PRK09521 exosome complex RNA-b 23.9 69 0.0015 29.7 2.9 31 240-279 146-176 (189)
120 PRK10144 formate-dependent nit 23.6 25 0.00053 31.3 -0.2 19 271-289 42-60 (126)
121 TIGR01206 lysW lysine biosynth 23.4 51 0.0011 25.0 1.5 28 249-278 4-31 (54)
122 PRK13195 pyrrolidone-carboxyla 23.2 2.8E+02 0.006 26.9 6.9 82 142-230 106-209 (222)
123 PF09723 Zn-ribbon_8: Zinc rib 23.0 73 0.0016 22.5 2.2 26 250-277 8-34 (42)
124 KOG2906 RNA polymerase III sub 23.0 71 0.0015 27.3 2.4 30 250-281 4-33 (105)
125 TIGR00686 phnA alkylphosphonat 22.8 74 0.0016 27.6 2.5 66 249-330 4-70 (109)
126 PF14354 Lar_restr_allev: Rest 22.6 1.1E+02 0.0023 22.8 3.2 28 248-277 4-37 (61)
127 PHA02942 putative transposase; 22.6 52 0.0011 34.3 1.9 27 247-278 325-351 (383)
128 smart00659 RPOLCX RNA polymera 22.4 62 0.0013 23.4 1.7 24 250-278 5-28 (44)
129 PRK00241 nudC NADH pyrophospha 22.0 68 0.0015 31.5 2.5 28 247-278 99-126 (256)
130 TIGR00310 ZPR1_znf ZPR1 zinc f 22.0 79 0.0017 30.0 2.8 12 268-279 29-40 (192)
131 PF11248 DUF3046: Protein of u 21.6 79 0.0017 24.8 2.3 44 158-202 4-48 (63)
132 PRK00285 ihfA integration host 20.8 4.6E+02 0.01 21.5 7.0 67 205-274 16-84 (99)
133 PF13719 zinc_ribbon_5: zinc-r 20.7 70 0.0015 22.0 1.6 26 250-278 5-34 (37)
134 smart00531 TFIIE Transcription 20.7 31 0.00068 30.9 -0.2 28 249-278 101-132 (147)
135 PF02294 7kD_DNA_binding: 7kD 20.6 91 0.002 23.7 2.3 30 49-84 16-45 (62)
136 PF14353 CpXC: CpXC protein 20.2 91 0.002 26.9 2.7 11 269-279 38-48 (128)
137 smart00834 CxxC_CXXC_SSSS Puta 20.2 91 0.002 21.1 2.2 27 249-277 7-34 (41)
No 1
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=100.00 E-value=4.3e-79 Score=591.08 Aligned_cols=260 Identities=35% Similarity=0.533 Sum_probs=244.2
Q ss_pred CCChhHHHHHHHHHHHhcCCCEEEEEEeccCCceeccCChhhHHHhhcCCeEeeeeeeeeEEEEEeCCCCcceeeeceee
Q 015345 1 MPELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKNLWLRLDSPPFPSFQFGMTG 80 (408)
Q Consensus 1 MPELPEVe~~~~~L~~~l~Gk~I~~V~v~~~~~v~~~~~~~~f~~~L~G~~I~~V~RrGK~L~~~l~~~~~L~vHLGMtG 80 (408)
||||||||++++.|+++++|++|.+|++. .|++.++.+ ++|...|.|++|.+|.||||||||+|.++.+|++||||+|
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 99999999999999999999999999996 577776544 8999999999999999999999999966679999999999
Q ss_pred eEEEecccchhcccccccCCCCCCCCccEEEEEEcCC-ceEEEeecCcccEEEEcCCCC-CCCcccccCCCCCCCCCCHH
Q 015345 81 AIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDG-LELSFTDKRRFAKVRLLNDPT-SVPPISELGPDALLEPMTVD 158 (408)
Q Consensus 81 ~l~i~~~~~~~y~~~~~~~~~~~p~kh~~l~l~~~dg-~~L~f~D~RrfG~i~l~~~~~-~~~~l~~LGPDpL~~~f~~e 158 (408)
+|++... +.+..+|+|+.|+|+|| ..|+|+|+|+||.|++++..+ .++.+++||||||+++|+.+
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 9999642 33467999999999999 599999999999999998765 67789999999999999999
Q ss_pred HHHHHHcCCCchhHHHHhCCCccccCchhhhhhHhhhcccCccCcCCCCCHHHHHHHHHHHHHHHHHHHHcCCCC-----
Q 015345 159 EFTDSLSKKKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVIEKALEVGADS----- 233 (408)
Q Consensus 159 ~f~~~l~k~k~~IK~lLLDQ~iiAGIGNiYadEILF~AgIhP~~~~~~Ls~~e~~~L~~ai~~VL~~Ai~~gg~s----- 233 (408)
++...+++++++||++||||++||||||||||||||+|||||.+++++|+.+++..|+++|+.||..||+.||++
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 999999999999999999999999999999999999999999999999999999999999999999999999987
Q ss_pred ------CCCCCceEEEccCCCCCCCCCCCCceEEEEECCceeEEcCCCCC
Q 015345 234 ------SQFPSNWIFHSREKKPGKAFVDGKKIDFITAGGRTTAYVPELQK 277 (408)
Q Consensus 234 ------~~f~~~~~vy~R~g~pC~~~~CG~~I~~~~vgGRtT~~CP~CQ~ 277 (408)
+.|+..+.||+|+|+||+ +||++|.+++++||+|||||+||+
T Consensus 226 ~~~g~~G~fq~~l~VYgR~GepC~--~CGt~I~k~~~~gR~t~~CP~CQ~ 273 (273)
T COG0266 226 NADGKPGYFQQELKVYGRAGEPCR--RCGTPIEKIKLGGRSTFYCPVCQK 273 (273)
T ss_pred ccCCCCCccceeEEEecCCCCCCC--ccCCEeEEEEEcCCcCEeCCCCCC
Confidence 468999999999999999 999999999999999999999996
No 2
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=100.00 E-value=1.5e-77 Score=588.01 Aligned_cols=261 Identities=30% Similarity=0.441 Sum_probs=237.1
Q ss_pred CCChhHHHHHHHHHHHhcCCCEEEEEEeccCCceec-cCChhhHHHhhcCCeEeeeeeeeeEEEEEeCC-----CCccee
Q 015345 1 MPELPEVEAARRAIEEHCIGKKIVKSIIADDNKVID-GVSASDFEASVLGKAILSAHRKGKNLWLRLDS-----PPFPSF 74 (408)
Q Consensus 1 MPELPEVe~~~~~L~~~l~Gk~I~~V~v~~~~~v~~-~~~~~~f~~~L~G~~I~~V~RrGK~L~~~l~~-----~~~L~v 74 (408)
||||||||++++.|++.++|++|+.|++.. ++++. ...+.+|.+.|.|++|++|+|+||||||.|++ +.+|++
T Consensus 1 MPELPEVe~~~~~L~~~~~g~~I~~v~~~~-~~~~~~~~~~~~~~~~L~G~~i~~v~rrGK~l~~~l~~~~~~~~~~L~~ 79 (282)
T PRK13945 1 MPELPEVETVRRGLEQLLLNFIIKGVEVLL-ERTIASPGGVEEFIKGLKGSLIGQWQRRGKYLLASLKKEGSENAGWLGV 79 (282)
T ss_pred CCCcchHHHHHHHHHHHhCCCEEEEEEEec-CCeecCCCChHHHHHhhcCCEEeeEEEeeeEEEEECCCCccCCCCEEEE
Confidence 999999999999999999999999999974 55432 22577899999999999999999999999986 358999
Q ss_pred eeceeeeEEEecccchhcccccccCCCCCCCCccEEEEEEcCCceEEEeecCcccEEEEcCCC----CCCCcccccCCCC
Q 015345 75 QFGMTGAIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELSFTDKRRFAKVRLLNDP----TSVPPISELGPDA 150 (408)
Q Consensus 75 HLGMtG~l~i~~~~~~~y~~~~~~~~~~~p~kh~~l~l~~~dg~~L~f~D~RrfG~i~l~~~~----~~~~~l~~LGPDp 150 (408)
||||||+|++.. .+.+|.+|.|++|.|+|+..|+|+|+|+||++++++.. .....+.+|||||
T Consensus 80 HLgMtG~~~~~~-------------~~~~~~~~~~l~l~~~~~~~L~f~d~R~fG~~~l~~~~~~~~~~~~~l~~LGpDp 146 (282)
T PRK13945 80 HLRMTGQFLWVE-------------QSTPPCKHTRVRLFFEKNQELRFVDIRSFGQMWWVPPGVSPESIITGLQKLGPEP 146 (282)
T ss_pred ECCeeEEEEEec-------------CCCCCCCcEEEEEEeCCCCEEEEEeCCCCceEEEEcCcccccccchHHHhcCCCc
Confidence 999999999853 22356789999999999999999999999999998742 2234589999999
Q ss_pred CCCCCCHHHHHHHHcCCCchhHHHHhCCCccccCchhhhhhHhhhcccCccCcCCCCCHHHHHHHHHHHHHHHHHHHHcC
Q 015345 151 LLEPMTVDEFTDSLSKKKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVIEKALEVG 230 (408)
Q Consensus 151 L~~~f~~e~f~~~l~k~k~~IK~lLLDQ~iiAGIGNiYadEILF~AgIhP~~~~~~Ls~~e~~~L~~ai~~VL~~Ai~~g 230 (408)
|+++|+.++|.++|++++++||++||||++||||||||||||||+|||||.+++++||++++++|+++|+.||+.||+.|
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 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCC-----------CCCCCceEEEccCCCCCCCCCCCCceEEEEECCceeEEcCCCCC
Q 015345 231 ADS-----------SQFPSNWIFHSREKKPGKAFVDGKKIDFITAGGRTTAYVPELQK 277 (408)
Q Consensus 231 g~s-----------~~f~~~~~vy~R~g~pC~~~~CG~~I~~~~vgGRtT~~CP~CQ~ 277 (408)
|++ +.|+..+.||+|.|+||+ +||++|.++++|||+|||||.||+
T Consensus 227 g~~~~~~~~~~g~~g~~~~~~~Vy~R~g~pC~--~Cg~~I~~~~~~gR~t~~CP~CQ~ 282 (282)
T PRK13945 227 GTTFSDFRDLEGVNGNYGGQAWVYRRTGKPCR--KCGTPIERIKLAGRSTHWCPNCQK 282 (282)
T ss_pred CCccccccccCCCCCcccceEEEeCCCcCCCC--cCCCeeEEEEECCCccEECCCCcC
Confidence 975 246667789999999999 999999999999999999999996
No 3
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=100.00 E-value=6.5e-77 Score=581.30 Aligned_cols=261 Identities=36% Similarity=0.552 Sum_probs=239.9
Q ss_pred CCChhHHHHHHHHHHHhcCCCEEEEEEeccCCceeccCChhhHHHhhcCCeEeeeeeeeeEEEEEeCCCCcceeeeceee
Q 015345 1 MPELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKNLWLRLDSPPFPSFQFGMTG 80 (408)
Q Consensus 1 MPELPEVe~~~~~L~~~l~Gk~I~~V~v~~~~~v~~~~~~~~f~~~L~G~~I~~V~RrGK~L~~~l~~~~~L~vHLGMtG 80 (408)
||||||||++++.|++.++|++|+.|++.. ++++.. .+.+|.+.|.|++|++|.|+||||||+|+++.+|++||||+|
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 MPELPEVETVRRGLEPHLVGKTITRVEVRR-PKLRWP-VPEDFAERLSGQTILAVGRRGKYLLLDLDDGGTLISHLGMSG 78 (274)
T ss_pred CCchhHHHHHHHHHHHHcCCCEEEEEEEcC-CccccC-ChHHHHhhcCCCEEEEEEeeeeEEEEEeCCCCEEEEeCCcEE
Confidence 999999999999999999999999999874 555433 478899999999999999999999999997779999999999
Q ss_pred eEEEecccchhcccccccCCCCCCCCccEEEEEEcCCceEEEeecCcccEEEEcCCC--CCCCcccccCCCCCCCCCCHH
Q 015345 81 AIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELSFTDKRRFAKVRLLNDP--TSVPPISELGPDALLEPMTVD 158 (408)
Q Consensus 81 ~l~i~~~~~~~y~~~~~~~~~~~p~kh~~l~l~~~dg~~L~f~D~RrfG~i~l~~~~--~~~~~l~~LGPDpL~~~f~~e 158 (408)
+|++.. .+.++++|.|++|.|+|+..|.|+|+|+||++++++.. ...+.+..||||||+++|+.+
T Consensus 79 ~~~~~~-------------~~~~~~~~~~~~l~l~~~~~l~f~D~R~fg~~~l~~~~~~~~~~~~~~LGpdpl~~~~~~~ 145 (274)
T PRK01103 79 SLRLLP-------------EDTPPEKHDHVDFVLDDGTVLRYNDPRRFGAMLLTPKGDLEAHPLLAHLGPEPLSDAFDGE 145 (274)
T ss_pred EEEEeC-------------CCCCCCceEEEEEEECCCCEEEEEcCCcCCEEEEEeCCccccchhHHhcCCCCCCccCCHH
Confidence 999853 12356789999999999999999999999999999742 345668999999999999999
Q ss_pred HHHHHHcCCCchhHHHHhCCCccccCchhhhhhHhhhcccCccCcCCCCCHHHHHHHHHHHHHHHHHHHHcCCCC-----
Q 015345 159 EFTDSLSKKKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVIEKALEVGADS----- 233 (408)
Q Consensus 159 ~f~~~l~k~k~~IK~lLLDQ~iiAGIGNiYadEILF~AgIhP~~~~~~Ls~~e~~~L~~ai~~VL~~Ai~~gg~s----- 233 (408)
+|.++|++++++||++||||++||||||||||||||+|||||.+++++||++++++|+++|++||+.||+.||++
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 999999999999999999999999999999999999999999999999999999999999999999999999865
Q ss_pred ------CCCCCceEEEccCCCCCCCCCCCCceEEEEECCceeEEcCCCCCC
Q 015345 234 ------SQFPSNWIFHSREKKPGKAFVDGKKIDFITAGGRTTAYVPELQKL 278 (408)
Q Consensus 234 ------~~f~~~~~vy~R~g~pC~~~~CG~~I~~~~vgGRtT~~CP~CQ~~ 278 (408)
+.|+..|.||+|.|+||+ +||++|.++++|||+|||||.||+.
T Consensus 226 ~~~g~~g~~~~~l~Vy~R~g~pC~--~Cg~~I~~~~~~gR~t~~CP~CQ~~ 274 (274)
T PRK01103 226 NADGKPGYFQQSLQVYGREGEPCR--RCGTPIEKIKQGGRSTFFCPRCQKR 274 (274)
T ss_pred ccCCCCCCccceeEEcCCCCCCCC--CCCCeeEEEEECCCCcEECcCCCCc
Confidence 357888999999999999 9999999999999999999999974
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=4.1e-76 Score=575.24 Aligned_cols=258 Identities=38% Similarity=0.582 Sum_probs=236.2
Q ss_pred CChhHHHHHHHHHHHhcCCCEEEEEEeccCCceecc-CChhhHHHhhcCCeEeeeeeeeeEEEEEeCCCCcceeeeceee
Q 015345 2 PELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDG-VSASDFEASVLGKAILSAHRKGKNLWLRLDSPPFPSFQFGMTG 80 (408)
Q Consensus 2 PELPEVe~~~~~L~~~l~Gk~I~~V~v~~~~~v~~~-~~~~~f~~~L~G~~I~~V~RrGK~L~~~l~~~~~L~vHLGMtG 80 (408)
|||||||++++.|++.++|++|+.|++.. ++++.. .++.+|.+.|.|++|++|.|+||||||+|+++ +|++||||+|
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 454432 35788999999999999999999999999877 9999999999
Q ss_pred eEEEecccchhcccccccCCCCCCCCccEEEEEEcCCceEEEeecCcccEEEEcCCCC--CCCcccccCCCCCCCCCCHH
Q 015345 81 AIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELSFTDKRRFAKVRLLNDPT--SVPPISELGPDALLEPMTVD 158 (408)
Q Consensus 81 ~l~i~~~~~~~y~~~~~~~~~~~p~kh~~l~l~~~dg~~L~f~D~RrfG~i~l~~~~~--~~~~l~~LGPDpL~~~f~~e 158 (408)
+|++.. .++++++|.|++|.|+|+..|+|+|+|+||++++++..+ ....+.+||||||+++|+.+
T Consensus 79 ~~~~~~-------------~~~~~~~~~~~~l~~~~~~~l~~~D~R~fg~~~l~~~~~~~~~~~l~~LGpDpl~~~~~~~ 145 (272)
T TIGR00577 79 KYRLEA-------------VPDAPEKHDHVDFLFDDGTELRYHDPRRFGTWLLFDRGQVENVPLLAKLGPEPLSEDFTAE 145 (272)
T ss_pred EEEEec-------------CCCCCCCcEEEEEEECCCCEEEEEcCCcCCEEEEEeCcccccchHHHhcCCCCCCCcCCHH
Confidence 999853 223446899999999999999999999999999997533 34568999999999999999
Q ss_pred HHHHHHcCCCchhHHHHhCCCccccCchhhhhhHhhhcccCccCcCCCCCHHHHHHHHHHHHHHHHHHHHcCCCC-----
Q 015345 159 EFTDSLSKKKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVIEKALEVGADS----- 233 (408)
Q Consensus 159 ~f~~~l~k~k~~IK~lLLDQ~iiAGIGNiYadEILF~AgIhP~~~~~~Ls~~e~~~L~~ai~~VL~~Ai~~gg~s----- 233 (408)
+|.++|++++++||++||||++||||||||||||||+|||||.+++++||++++++||++|++||+.||+.||++
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 999999999999999999999999999999999999999999999999999999999999999999999999976
Q ss_pred ------CCCCCceEEEccCCCCCCCCCCCCceEEEEECCceeEEcCCCC
Q 015345 234 ------SQFPSNWIFHSREKKPGKAFVDGKKIDFITAGGRTTAYVPELQ 276 (408)
Q Consensus 234 ------~~f~~~~~vy~R~g~pC~~~~CG~~I~~~~vgGRtT~~CP~CQ 276 (408)
+.|+..+.||+|.|+||+ +||++|.++++|||+|||||.||
T Consensus 226 ~~~g~~g~~~~~~~Vy~r~g~pC~--~Cg~~I~~~~~~gR~t~~CP~CQ 272 (272)
T TIGR00577 226 NSDGHNGYFQQELQVYGRKGEPCR--RCGTPIEKIKVGGRGTHFCPQCQ 272 (272)
T ss_pred ccCCCCCcccceeEEeCCCCCCCC--CCCCeeEEEEECCCCCEECCCCC
Confidence 246778899999999999 99999999999999999999999
No 5
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=100.00 E-value=4.6e-76 Score=574.09 Aligned_cols=251 Identities=34% Similarity=0.538 Sum_probs=230.2
Q ss_pred CCChhHHHHHHHHHHHhcCCCEEEEEEeccCCceeccCChhhHHHhhcCCeEeeeeeeeeEEEEEeCCCCcceeeeceee
Q 015345 1 MPELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKNLWLRLDSPPFPSFQFGMTG 80 (408)
Q Consensus 1 MPELPEVe~~~~~L~~~l~Gk~I~~V~v~~~~~v~~~~~~~~f~~~L~G~~I~~V~RrGK~L~~~l~~~~~L~vHLGMtG 80 (408)
||||||||++++.|++.++|++|+.|++.. +.++ .|.+.|.|++|++|+|+||||+|+|+++.+|++||||||
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 999999999999999999999999999864 4343 477789999999999999999999998779999999999
Q ss_pred eEEEecccchhcccccccCCCCCCCCccEEEEEEcCCceEEEeecCcccEEEEcCCC--CCCCcccccCCCCCCCCCCHH
Q 015345 81 AIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELSFTDKRRFAKVRLLNDP--TSVPPISELGPDALLEPMTVD 158 (408)
Q Consensus 81 ~l~i~~~~~~~y~~~~~~~~~~~p~kh~~l~l~~~dg~~L~f~D~RrfG~i~l~~~~--~~~~~l~~LGPDpL~~~f~~e 158 (408)
+|++. +++|.|++|.|+ +..|+|+|+|+||+++|++.. .....+.+||||||+++|+.+
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 246999999998 668999999999999999742 234568999999999999999
Q ss_pred HHHHHHcCCCchhHHHHhCCCccccCchhhhhhHhhhcccCccCcCCCCCHHHHHHHHHHHHHHHHHHHHcCCCCC----
Q 015345 159 EFTDSLSKKKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVIEKALEVGADSS---- 234 (408)
Q Consensus 159 ~f~~~l~k~k~~IK~lLLDQ~iiAGIGNiYadEILF~AgIhP~~~~~~Ls~~e~~~L~~ai~~VL~~Ai~~gg~s~---- 234 (408)
+|.++++ ++++||++||||++||||||||||||||+|||||.+++++||++|+++||++|+.||+.||+.||++.
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 89999999999999999999999999999999999999999999999999999999999999999652
Q ss_pred ---------CCCCceEEEccCCCCCCCCCCCCceEEEEECCceeEEcCCCCCCCc
Q 015345 235 ---------QFPSNWIFHSREKKPGKAFVDGKKIDFITAGGRTTAYVPELQKLNG 280 (408)
Q Consensus 235 ---------~f~~~~~vy~R~g~pC~~~~CG~~I~~~~vgGRtT~~CP~CQ~~~~ 280 (408)
.|+..+.||+|.|+||+ +||++|.++++|||+|||||.||++++
T Consensus 214 ~~~~~g~~g~~~~~~~Vy~R~g~pC~--~Cg~~I~~~~~~gR~ty~Cp~CQ~~~~ 266 (269)
T PRK14811 214 YRQPDGEPGGFQFQHAVYGREGQPCP--RCGTPIEKIVVGGRGTHFCPQCQPLRP 266 (269)
T ss_pred cccCCCCcccccceEEecCCCcCCCC--cCCCeeEEEEECCCCcEECCCCcCCCC
Confidence 45667889999999999 999999999999999999999999865
No 6
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=100.00 E-value=5.8e-74 Score=560.14 Aligned_cols=257 Identities=31% Similarity=0.481 Sum_probs=234.4
Q ss_pred CCChhHHHHHHHHHHHhcCCCEEEEEEeccCCceeccCChhhHHHhhcCCeEeeeeeeeeEEEEEeCCCC----cceeee
Q 015345 1 MPELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKNLWLRLDSPP----FPSFQF 76 (408)
Q Consensus 1 MPELPEVe~~~~~L~~~l~Gk~I~~V~v~~~~~v~~~~~~~~f~~~L~G~~I~~V~RrGK~L~~~l~~~~----~L~vHL 76 (408)
||||||||++++.|++.++|++|+.|++.+ ++++....+.+|.+.|.|++|++|.|+||||||+|+++. +|++||
T Consensus 1 MPELPEVe~~~~~L~~~~~G~~I~~v~~~~-~~~~~~~~~~~~~~~l~G~~i~~v~rrGK~L~~~l~~~~~~~~~L~~HL 79 (272)
T PRK14810 1 MPELPEVETVARGLAPRAAGRRIATAEFRN-LRIPRKGDPDLMAARLAGRKILSVKRVGKHIVADLEGPGEPRGQWIIHL 79 (272)
T ss_pred CCchHHHHHHHHHHHHHhCCCEEEEEEECC-CCccccCChHHHHHhcCCCEEEEEEEEeeEEEEECCCCCCccCeEEEeC
Confidence 999999999999999999999999999974 555544457789999999999999999999999998764 899999
Q ss_pred ceeeeEEEecccchhcccccccCCCCCCCCccEEEEEEcCCceEEEeecCcccEEEEcCCCCCCCcccccCCCCCCCCCC
Q 015345 77 GMTGAIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELSFTDKRRFAKVRLLNDPTSVPPISELGPDALLEPMT 156 (408)
Q Consensus 77 GMtG~l~i~~~~~~~y~~~~~~~~~~~p~kh~~l~l~~~dg~~L~f~D~RrfG~i~l~~~~~~~~~l~~LGPDpL~~~f~ 156 (408)
||||+|++... +.++++|.|++|+|++|..|.|+|+|+||++++++.. ...+.+||||||+ ++
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 99999998531 2244589999999999889999999999999998632 3448999999997 89
Q ss_pred HHHHHHHHcCCCchhHHHHhCCCccccCchhhhhhHhhhcccCccCcCCCCCHHHHHHHHHHHHHHHHHHHHcCCCC---
Q 015345 157 VDEFTDSLSKKKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVIEKALEVGADS--- 233 (408)
Q Consensus 157 ~e~f~~~l~k~k~~IK~lLLDQ~iiAGIGNiYadEILF~AgIhP~~~~~~Ls~~e~~~L~~ai~~VL~~Ai~~gg~s--- 233 (408)
.++|.+++.+++++||.+||||++||||||||||||||+|||||.+++++||++++++|+++|+.||+.||+.||++
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 99999999999999999999999999999999999999999999999999999999999999999999999999974
Q ss_pred --------CCCCCceEEEccCCCCCCCCCCCCceEEEEECCceeEEcCCCCC
Q 015345 234 --------SQFPSNWIFHSREKKPGKAFVDGKKIDFITAGGRTTAYVPELQK 277 (408)
Q Consensus 234 --------~~f~~~~~vy~R~g~pC~~~~CG~~I~~~~vgGRtT~~CP~CQ~ 277 (408)
+.|+..+.||+|.|+||+ +||++|.++.+|||+|||||.||+
T Consensus 223 ~~~~~g~~g~~~~~~~Vy~R~g~pCp--rCG~~I~~~~~~gR~t~~CP~CQ~ 272 (272)
T PRK14810 223 YVDAEGRSGFFQLSHRVYQRTGEPCL--NCKTPIRRVVVAGRSSHYCPHCQK 272 (272)
T ss_pred ccCCCCCCCcchhhEeecCCCCCcCC--CCCCeeEEEEECCCccEECcCCcC
Confidence 357778899999999999 999999999999999999999996
No 7
>PRK10445 endonuclease VIII; Provisional
Probab=100.00 E-value=3.6e-73 Score=552.13 Aligned_cols=251 Identities=20% Similarity=0.329 Sum_probs=226.3
Q ss_pred CCChhHHHHHHHHHHHhcCCCEEEEEEeccCCceeccCChhhHHHhhcCCeEeeeeeeeeEEEEEeCCCCcceeeeceee
Q 015345 1 MPELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKNLWLRLDSPPFPSFQFGMTG 80 (408)
Q Consensus 1 MPELPEVe~~~~~L~~~l~Gk~I~~V~v~~~~~v~~~~~~~~f~~~L~G~~I~~V~RrGK~L~~~l~~~~~L~vHLGMtG 80 (408)
||||||||++++.|++.++|++|+.|++.. +. ..+|.+.|.|++|++|+||||||||+|+++.+|++||||||
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 999999999999999999999999999863 32 35788999999999999999999999998789999999999
Q ss_pred eEEEecccchhcccccccCCC-CCCCCccEEEEEEcCCceEEEeecCcccEEEEcCCC--CCCCcccccCCCCCCCCCCH
Q 015345 81 AIYIKGVAVTQYKRSAVKDTD-EWPSKYSKFFVELDDGLELSFTDKRRFAKVRLLNDP--TSVPPISELGPDALLEPMTV 157 (408)
Q Consensus 81 ~l~i~~~~~~~y~~~~~~~~~-~~p~kh~~l~l~~~dg~~L~f~D~RrfG~i~l~~~~--~~~~~l~~LGPDpL~~~f~~ 157 (408)
+|++... .. .++.+|.|++|.|+|+..|.|+|+ ++++++.. .....+..||||||+++|+.
T Consensus 74 ~~~~~~~------------~~~~~~~~~~~l~l~~~~~~~l~~~d~----~~~l~~~~~~~~~~~l~~lGpDpL~~~~~~ 137 (263)
T PRK10445 74 VWRVVDT------------GEEPQTTRVLRVRLQTADKTILLYSAS----DIEMLTPEQLTTHPFLQRVGPDVLDPNLTP 137 (263)
T ss_pred EEEEeCC------------CCCCCCCCcEEEEEEcCCCcEEEEECC----EEEEEeCccccccchHHhcCCCCCCCcCCH
Confidence 9988532 11 124689999999999989999995 68887642 23456899999999999999
Q ss_pred HHHHHHHcCC---CchhHHHHhCCCccccCchhhhhhHhhhcccCccCcCCCCCHHHHHHHHHHHHHHHHHHHHcCCCC-
Q 015345 158 DEFTDSLSKK---KITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVIEKALEVGADS- 233 (408)
Q Consensus 158 e~f~~~l~k~---k~~IK~lLLDQ~iiAGIGNiYadEILF~AgIhP~~~~~~Ls~~e~~~L~~ai~~VL~~Ai~~gg~s- 233 (408)
++|.++|+++ +++||++||||++||||||||||||||+|||||.+++++||++++++||++|+.||+.||+.||++
T Consensus 138 ~~~~~~l~~~~~~~~~IK~~LLDQ~~vaGIGNiyadEiLf~A~I~P~~~~~~Ls~~~~~~L~~~i~~vl~~ai~~gg~~~ 217 (263)
T PRK10445 138 EQVKERLLSPRFRNRQFSGLLLDQAFLAGLGNYLRVEILWQAGLTPQHKAKDLNEAQLDALAHALLDIPRLSYATRGQVD 217 (263)
T ss_pred HHHHHHHhcCccccccHHHHHhcCCccccccHHHHHHHHHHcCCCcCCCcccCCHHHHHHHHHHHHHHHHHHHHcCCCCC
Confidence 9999999887 899999999999999999999999999999999999999999999999999999999999999976
Q ss_pred -----CCCCCceEEEccCCCCCCCCCCCCceEEEEECCceeEEcCCCCC
Q 015345 234 -----SQFPSNWIFHSREKKPGKAFVDGKKIDFITAGGRTTAYVPELQK 277 (408)
Q Consensus 234 -----~~f~~~~~vy~R~g~pC~~~~CG~~I~~~~vgGRtT~~CP~CQ~ 277 (408)
+.| ..+.||+|.|++|+ +||++|.++++|||+|||||+||+
T Consensus 218 ~~~~~g~~-~~~~Vy~r~g~~Cp--~Cg~~I~~~~~~gR~t~~CP~CQ~ 263 (263)
T PRK10445 218 ENKHHGAL-FRFKVFHRDGEACE--RCGGIIEKTTLSSRPFYWCPGCQK 263 (263)
T ss_pred CCCCCCCc-ceEEEeCCCCCCCC--CCCCEeEEEEECCCCcEECCCCcC
Confidence 234 46789999999999 999999999999999999999996
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=1.2e-32 Score=244.23 Aligned_cols=134 Identities=55% Similarity=0.989 Sum_probs=110.4
Q ss_pred CCChhHHHHHHHHHHHhcCCCEEEEEEeccCCceeccCChhhHHHhhcCCeEeeeeeeeeEEEEEeCC-CCcceeeecee
Q 015345 1 MPELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKNLWLRLDS-PPFPSFQFGMT 79 (408)
Q Consensus 1 MPELPEVe~~~~~L~~~l~Gk~I~~V~v~~~~~v~~~~~~~~f~~~L~G~~I~~V~RrGK~L~~~l~~-~~~L~vHLGMt 79 (408)
||||||||++++.|++.++|++|.+|++..++.++....+.+|.+.|.|++|++|.|+||||||.|++ +.+|++|||||
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 99999999999999999999999999997566666544578899999999999999999999999987 67999999999
Q ss_pred eeEEEecccchhcc--cccccCCCCCCCCccEEEEEEcCCceEEEeecCcccEEEEc
Q 015345 80 GAIYIKGVAVTQYK--RSAVKDTDEWPSKYSKFFVELDDGLELSFTDKRRFAKVRLL 134 (408)
Q Consensus 80 G~l~i~~~~~~~y~--~~~~~~~~~~p~kh~~l~l~~~dg~~L~f~D~RrfG~i~l~ 134 (408)
|+|++......+|. .........+|++|+|++|.|+||..|+|+|+|+||+++|+
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 99998643222221 00001112346789999999999999999999999999863
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=99.97 E-value=2.2e-31 Score=229.31 Aligned_cols=117 Identities=32% Similarity=0.616 Sum_probs=104.5
Q ss_pred CChhHHHHHHHHHHHhcCCCEEEEEEeccCCceeccCChhhHHHhhcCCeEeeeeeeeeEEEEEeCCCCcceeeeceeee
Q 015345 2 PELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKNLWLRLDSPPFPSFQFGMTGA 81 (408)
Q Consensus 2 PELPEVe~~~~~L~~~l~Gk~I~~V~v~~~~~v~~~~~~~~f~~~L~G~~I~~V~RrGK~L~~~l~~~~~L~vHLGMtG~ 81 (408)
|||||||++++.|++.++|++|.+|++.+ ++++.. .+.+|.+.|.|++|.+|.|+||||+|+|+++.+|++||||||+
T Consensus 1 PELPEVe~~~~~l~~~~~g~~I~~v~~~~-~~~~~~-~~~~~~~~L~G~~i~~v~RrGK~L~~~l~~~~~L~~HLgMtG~ 78 (117)
T cd08976 1 PELPEVEVQKQYLERTSLHRKIVEVEVGD-DKILGE-PKATLREVLEGRTFTETHRIGKYLFLKTKEGGWLVMHFGMTGK 78 (117)
T ss_pred CCCcchHHHHHHHHHHhCCCEEEEEEECC-CCEecc-CHHHHHhhcCCCEEEEEEEeeeEEEEEcCCCCEEEEEcceEEE
Confidence 99999999999999999999999999974 565542 3778999999999999999999999999877799999999999
Q ss_pred EEEecccchhcccccccCCCCCCCCccEEEEEEcCCceEEEeecCcccEEEE
Q 015345 82 IYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELSFTDKRRFAKVRL 133 (408)
Q Consensus 82 l~i~~~~~~~y~~~~~~~~~~~p~kh~~l~l~~~dg~~L~f~D~RrfG~i~l 133 (408)
|.+.. .+.+|++|.|++|.|+||..|+|+|+|+||+++|
T Consensus 79 ~~~~~-------------~~~~~~kh~~~~l~l~~g~~l~~~D~R~fg~~~~ 117 (117)
T cd08976 79 LDYYP-------------DDEDPPKHARLLLHFEDGFRLAFECPRKFGRVRL 117 (117)
T ss_pred EEEEC-------------CCCCCCCEEEEEEEECCCCEEEEeCCCccceeEC
Confidence 98853 2235678999999999999999999999999875
No 10
>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=99.97 E-value=5.7e-31 Score=226.16 Aligned_cols=116 Identities=34% Similarity=0.672 Sum_probs=101.0
Q ss_pred CChhHHHHHHHHHHHhcCCCEEEEEEeccCCceeccCChhhHHHhhcCCeEeeeeeeeeEEEEEeCCCCcceeeeceeee
Q 015345 2 PELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKNLWLRLDSPPFPSFQFGMTGA 81 (408)
Q Consensus 2 PELPEVe~~~~~L~~~l~Gk~I~~V~v~~~~~v~~~~~~~~f~~~L~G~~I~~V~RrGK~L~~~l~~~~~L~vHLGMtG~ 81 (408)
|||||||++++.|++.++|++|.+|++. ++++++.+.+..|.+.|.|++|++|+|+||||||.|+++.+|++||||||+
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 9999999999999999999999999997 467777777777999999999999999999999999999999999999999
Q ss_pred EEEecccchhcccccccCCCCCCCCccEEEEEEcCCceEEEeecCcccEEE
Q 015345 82 IYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELSFTDKRRFAKVR 132 (408)
Q Consensus 82 l~i~~~~~~~y~~~~~~~~~~~p~kh~~l~l~~~dg~~L~f~D~RrfG~i~ 132 (408)
|++. ..+++++|+|++|.|+||..|+|+|+|+||+|+
T Consensus 80 ~~~~--------------~~~~~~~~~~~~l~~~~g~~L~f~D~R~fg~~r 116 (116)
T PF01149_consen 80 LRLD--------------PPDWPPKHTRLRLRFEDGSRLRFVDPRRFGRVR 116 (116)
T ss_dssp EEES--------------TTCG-STTEEEEEEETSSEEEEEEETTS--EE-
T ss_pred EEec--------------CCCCCCCeEEEEEEECCCCEEEEEcCCCCCCCC
Confidence 9982 334678999999999999999999999999986
No 11
>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=99.97 E-value=1.6e-30 Score=224.41 Aligned_cols=120 Identities=36% Similarity=0.605 Sum_probs=107.4
Q ss_pred CChhHHHHHHHHHHHhcCCCEEEEEEeccCCceeccCChhhHHHhhcCCeEeeeeeeeeEEEEEeCCCCcceeeeceeee
Q 015345 2 PELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKNLWLRLDSPPFPSFQFGMTGA 81 (408)
Q Consensus 2 PELPEVe~~~~~L~~~l~Gk~I~~V~v~~~~~v~~~~~~~~f~~~L~G~~I~~V~RrGK~L~~~l~~~~~L~vHLGMtG~ 81 (408)
|||||||++++.|++.++|++|..|++.++ .++..+++.+|.+.|.|++|++|.|+||||||.|+++.+|++||||||+
T Consensus 1 PELPEve~~~~~l~~~l~G~~I~~v~~~~~-~~~~~~~~~~~~~~l~G~~i~~v~r~GK~l~~~l~~~~~l~~HlgMtG~ 79 (120)
T cd08966 1 PELPEVETVRRGLAPHLVGRRIEDVEVRRP-KLRRPPDPEEFAERLVGRRITGVERRGKYLLFELDDGLVLVIHLGMTGR 79 (120)
T ss_pred CCCccHHHHHHHHHHHhCCCEEEEEEECCC-CeeccCChHHHHhhCCCCEEEEEEeeeEEEEEEcCCCCEEEEECCceeE
Confidence 999999999999999999999999999754 4544456888999999999999999999999999988899999999999
Q ss_pred EEEecccchhcccccccCCCCCCCCccEEEEEEcCCceEEEeecCcccEEEEcC
Q 015345 82 IYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELSFTDKRRFAKVRLLN 135 (408)
Q Consensus 82 l~i~~~~~~~y~~~~~~~~~~~p~kh~~l~l~~~dg~~L~f~D~RrfG~i~l~~ 135 (408)
|++.. ...++++|++++|+|+||..|+|+|+|+||++++++
T Consensus 80 ~~~~~-------------~~~~~~~~~~l~l~~~~g~~l~f~D~R~fG~~~~~~ 120 (120)
T cd08966 80 LLVVP-------------PDEPPEKHDHVIFELDDGRELRFNDPRRFGTLLLVP 120 (120)
T ss_pred EEEeC-------------CCCCCCCcEEEEEEeCCCCEEEEEcCCCCcEEEEeC
Confidence 98853 223567899999999999999999999999999863
No 12
>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=2.2e-31 Score=221.07 Aligned_cols=90 Identities=47% Similarity=0.710 Sum_probs=80.0
Q ss_pred cCCCCCCCCCCHHHHHHHHcCCCchhHHHHhCCCccccCchhhhhhHhhhcccCccCcCCCCCHHHHHHHHHHHHHHHHH
Q 015345 146 LGPDALLEPMTVDEFTDSLSKKKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVIEK 225 (408)
Q Consensus 146 LGPDpL~~~f~~e~f~~~l~k~k~~IK~lLLDQ~iiAGIGNiYadEILF~AgIhP~~~~~~Ls~~e~~~L~~ai~~VL~~ 225 (408)
||||||++.|+.++|.+++.+++++||.+||||++||||||||+|||||+|||||.+++++|+++++.+|+++|+.||+.
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 HHHcCCCCCC
Q 015345 226 ALEVGADSSQ 235 (408)
Q Consensus 226 Ai~~gg~s~~ 235 (408)
||+.||++..
T Consensus 81 ai~~gg~t~~ 90 (92)
T PF06831_consen 81 AIEVGGTTIR 90 (92)
T ss_dssp HHHTT-B-SS
T ss_pred HHHcCCCccc
Confidence 9999998754
No 13
>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=99.96 E-value=3.4e-29 Score=220.47 Aligned_cols=113 Identities=27% Similarity=0.336 Sum_probs=95.8
Q ss_pred CCChhHHHHHHHHHHHhcCCCEEEEEEeccCCceeccC-ChhhHHHhhcCCeEeeeeeeeeEEEEEeCCC----------
Q 015345 1 MPELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGV-SASDFEASVLGKAILSAHRKGKNLWLRLDSP---------- 69 (408)
Q Consensus 1 MPELPEVe~~~~~L~~~l~Gk~I~~V~v~~~~~v~~~~-~~~~f~~~L~G~~I~~V~RrGK~L~~~l~~~---------- 69 (408)
||||||||++++.|+++++|++|+.|++.+ + +..++ .+..|.+ ++|. +.||||||||.|+++
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 999999999999999999999999999975 4 44332 3444544 8899 999999999999887
Q ss_pred ---C-cceeeeceeeeEEEecccchhcccccccCCCCCCCCccEEEEEEcCC--ceEEEeecCcccEEEEc
Q 015345 70 ---P-FPSFQFGMTGAIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDG--LELSFTDKRRFAKVRLL 134 (408)
Q Consensus 70 ---~-~L~vHLGMtG~l~i~~~~~~~y~~~~~~~~~~~p~kh~~l~l~~~dg--~~L~f~D~RrfG~i~l~ 134 (408)
. +|++||||||+|++... +++++|+|++|.|+|| ..|+|+|+|+||+++|-
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 89999999999998531 1356899999999985 78999999999999863
No 14
>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=99.96 E-value=3.8e-29 Score=215.00 Aligned_cols=117 Identities=34% Similarity=0.620 Sum_probs=103.0
Q ss_pred CChhHHHHHHHHHHHhcCCCEEEEEEeccCCceeccCChhhHHHhhcCCeEeeeeeeeeEEEEEeCCCCcceeeeceeee
Q 015345 2 PELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKNLWLRLDSPPFPSFQFGMTGA 81 (408)
Q Consensus 2 PELPEVe~~~~~L~~~l~Gk~I~~V~v~~~~~v~~~~~~~~f~~~L~G~~I~~V~RrGK~L~~~l~~~~~L~vHLGMtG~ 81 (408)
|||||||++++.|++.++|++|++|++.+. .++.+ .+.+|.+.|.|++|++|+|+||||+|.|+++.+|++||||||+
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 44332 3678999999999999999999999999977899999999999
Q ss_pred EEEecccchhcccccccCCCCCCCCccEEEEEEcCCceEEEeecCcccEEEE
Q 015345 82 IYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELSFTDKRRFAKVRL 133 (408)
Q Consensus 82 l~i~~~~~~~y~~~~~~~~~~~p~kh~~l~l~~~dg~~L~f~D~RrfG~i~l 133 (408)
|++.. .+.++++|.|++|.|+|+..|+|+|+|+||++++
T Consensus 79 ~~~~~-------------~~~~~~~~~~~~~~~~~~~~l~f~d~R~fG~~~~ 117 (117)
T cd08773 79 LRVCP-------------EGEPPPKHDRLVLRLANGSQLRFTDPRKFGRVEL 117 (117)
T ss_pred EEEeC-------------CCCCCCCeEEEEEEECCCCEEEEECCCccccccC
Confidence 99853 2234568999999999999999999999999863
No 15
>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=99.96 E-value=1.3e-28 Score=214.02 Aligned_cols=114 Identities=25% Similarity=0.385 Sum_probs=99.6
Q ss_pred CCChhHHHHHHHHHHHhcCCCEEEEEEeccCCceeccCChhhHHHhhcCCeEeeeeeeeeEEEEEeCCCCcceeeeceee
Q 015345 1 MPELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKNLWLRLDSPPFPSFQFGMTG 80 (408)
Q Consensus 1 MPELPEVe~~~~~L~~~l~Gk~I~~V~v~~~~~v~~~~~~~~f~~~L~G~~I~~V~RrGK~L~~~l~~~~~L~vHLGMtG 80 (408)
||||||||++++.|++.++|++|..|++.. +.+. .++.+|.+.|.|++|++|.|+||||||+|+++.+|++||||||
T Consensus 1 MPELPEve~~~~~L~~~l~Gk~I~~v~~~~-~~~~--~~~~~~~~~L~G~~i~~v~RrGK~l~~~~~~~~~L~~HLgMtG 77 (122)
T cd08973 1 MPELPEVEVYAENLERRLTGKTITRVELAS-KSLL--VTPDPPLEALEGRTVTGVRRHGKRLDFEFDNGLHLVLHLMLAG 77 (122)
T ss_pred CCChHHHHHHHHHHHHhcCCCEEEEEEEcC-cccc--CChhHHHhhCCCCEEeEEEEEeeEEEEEcCCCCEEEEeCCCeE
Confidence 999999999999999999999999999974 4443 2478899999999999999999999999987779999999999
Q ss_pred eEEEecccchhcccccccCCCCCCCCccEEEEEEcC-CceEEEeecCccc
Q 015345 81 AIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDD-GLELSFTDKRRFA 129 (408)
Q Consensus 81 ~l~i~~~~~~~y~~~~~~~~~~~p~kh~~l~l~~~d-g~~L~f~D~RrfG 129 (408)
+|++... ...++++|.|++|.|+| |..|.|+|+|.--
T Consensus 78 ~l~~~~~------------~~~~~~~~~~v~l~~~~~g~~L~~~D~r~~~ 115 (122)
T cd08973 78 WLYWTEA------------GALLPGKKGPIALRFEDYGGGLDLTEAGTKK 115 (122)
T ss_pred EEEEeCC------------CCCCCCCcEEEEEEEcCCCCEEEEECCCccc
Confidence 9998532 11256799999999999 9999999998543
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=99.95 E-value=5.8e-27 Score=202.67 Aligned_cols=113 Identities=24% Similarity=0.303 Sum_probs=99.3
Q ss_pred ChhHHHHHHHHHHHhcCCCEEEEEEeccCC--ceeccCChhhHHHhhcCCeEeeeeeeeeEEEEEeCCCCcceeeeceee
Q 015345 3 ELPEVEAARRAIEEHCIGKKIVKSIIADDN--KVIDGVSASDFEASVLGKAILSAHRKGKNLWLRLDSPPFPSFQFGMTG 80 (408)
Q Consensus 3 ELPEVe~~~~~L~~~l~Gk~I~~V~v~~~~--~v~~~~~~~~f~~~L~G~~I~~V~RrGK~L~~~l~~~~~L~vHLGMtG 80 (408)
||||||++++.|++.++|++|.+|++.++. .++..+++.+|.+.|.|++|++|+||||||+|.|+++ +|++||||||
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 999999999999999999999999997543 4444446789999999999999999999999999875 9999999999
Q ss_pred eEEEecccchhcccccccCCCCCCCCccEEEEEEcCCceEEEeecCcccEEE
Q 015345 81 AIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELSFTDKRRFAKVR 132 (408)
Q Consensus 81 ~l~i~~~~~~~y~~~~~~~~~~~p~kh~~l~l~~~dg~~L~f~D~RrfG~i~ 132 (408)
+|++.. .++++|+|++|+|+||..|+|+ +++||.+-
T Consensus 81 ~l~~~~---------------~~~~kh~~l~l~~~dg~~L~f~-~~~~~~~~ 116 (117)
T cd08975 81 RYYYGG---------------EKIPKKYQLLIEFDDDSFLVFT-VAMYGGIA 116 (117)
T ss_pred EEEeCC---------------CCCCCeEEEEEEECCCCEEEEE-EEEEeeee
Confidence 999731 2456899999999999999999 89999763
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=99.94 E-value=4.1e-26 Score=196.40 Aligned_cols=112 Identities=18% Similarity=0.258 Sum_probs=95.2
Q ss_pred CCChhHHHHHHHHHHHhcCCCEEEEEEeccCCceeccCChhhHHHhhcCCeEeeeeeeeeEEEEEeCCCCcceeeeceee
Q 015345 1 MPELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKNLWLRLDSPPFPSFQFGMTG 80 (408)
Q Consensus 1 MPELPEVe~~~~~L~~~l~Gk~I~~V~v~~~~~v~~~~~~~~f~~~L~G~~I~~V~RrGK~L~~~l~~~~~L~vHLGMtG 80 (408)
||||||||++++.|++.++|++|..|++.+ +++ +.+.|.|++|.+|.|+||||+|.|+++.+|++||||||
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 36689999999999999999999987779999999999
Q ss_pred eEEEecccchhcccccccCCCCCCCCccEEEEEEcCCceEEEeecCcccEEEEcC
Q 015345 81 AIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELSFTDKRRFAKVRLLN 135 (408)
Q Consensus 81 ~l~i~~~~~~~y~~~~~~~~~~~p~kh~~l~l~~~dg~~L~f~D~RrfG~i~l~~ 135 (408)
+|++.... ....+|.+|.|++|.|+||..|.|+|+ .|++++
T Consensus 72 ~~~~~~~~----------~~~~~~~k~~~~~l~~~~g~~l~f~~~----~~~~~~ 112 (114)
T cd08971 72 SWHVYRPG----------ERWRRPAHQARAVLATADWTAVGFRLG----VLELVP 112 (114)
T ss_pred EEEEecCC----------CCCCCCCCeEEEEEEcCCCeEEEEEcc----eEEEEe
Confidence 99985321 000235689999999999999999984 677765
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=99.93 E-value=2.3e-25 Score=187.06 Aligned_cols=97 Identities=19% Similarity=0.271 Sum_probs=84.4
Q ss_pred CCChhHHHHHHHHHHHhcCCCEEEEEEeccCCceeccCChhhHHHhhcCCeEeeeeeeeeEEEEEeCCCCcceeeeceee
Q 015345 1 MPELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKNLWLRLDSPPFPSFQFGMTG 80 (408)
Q Consensus 1 MPELPEVe~~~~~L~~~l~Gk~I~~V~v~~~~~v~~~~~~~~f~~~L~G~~I~~V~RrGK~L~~~l~~~~~L~vHLGMtG 80 (408)
||||||||++++.|++ ++|++|..|++. ++. +.+.|.|++|++|+||||||||.|++ .+|++||||||
T Consensus 1 MPELPEVe~~~~~L~~-~~g~~I~~v~~~--~~~--------~~~~l~G~~i~~v~RrGK~L~~~l~~-~~L~~HLgMtG 68 (98)
T cd08974 1 MPEGPSIVILREAAAA-FKGQTVIRASGN--AKI--------DKDRLAGQKVLAIRSWGKHFLLEFED-FTVRIHLLLFG 68 (98)
T ss_pred CCccHHHHHHHHHHHH-hCCCEEEEEEEc--ccc--------hhhhcCCCEEEEEEEEccEEEEEECC-CEEEEeCCCee
Confidence 9999999999999998 999999999953 221 36789999999999999999999985 49999999999
Q ss_pred eEEEecccchhcccccccCCCCCCCCccEEEEEEcCCceEEEeec
Q 015345 81 AIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELSFTDK 125 (408)
Q Consensus 81 ~l~i~~~~~~~y~~~~~~~~~~~p~kh~~l~l~~~dg~~L~f~D~ 125 (408)
+|++.. ++++|.|++|.|+||..+.|+|.
T Consensus 69 ~l~~~~----------------~~~~~~~~~l~~~~g~~~~~~~~ 97 (98)
T cd08974 69 SYRINE----------------RKDAPPRLSLGFDNGELNFYTCS 97 (98)
T ss_pred EEEEeC----------------CCCCcEEEEEEeCCCcEEEEecC
Confidence 999852 25689999999999987777763
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=99.92 E-value=1.4e-24 Score=187.17 Aligned_cols=113 Identities=17% Similarity=0.225 Sum_probs=96.3
Q ss_pred CChhHHHHHHHHHHHhcCCCEEEEEEeccCCceeccCChhhHHHhhcCCeEeeeeeeeeEEEEEeCCCCcceeeeceeee
Q 015345 2 PELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKNLWLRLDSPPFPSFQFGMTGA 81 (408)
Q Consensus 2 PELPEVe~~~~~L~~~l~Gk~I~~V~v~~~~~v~~~~~~~~f~~~L~G~~I~~V~RrGK~L~~~l~~~~~L~vHLGMtG~ 81 (408)
|||||||++++.|++.++|++|..|++.. ++ +.+|.+.|.|++|++|+|+||||+|+|+++.+|++||||||+
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 99999999999999999999999999864 32 357888999999999999999999999887799999999999
Q ss_pred EEEecccchhcccccccCCCCCCCCccEEEEEEcCCceEEEeecCcccEEEEcCC
Q 015345 82 IYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELSFTDKRRFAKVRLLND 136 (408)
Q Consensus 82 l~i~~~~~~~y~~~~~~~~~~~p~kh~~l~l~~~dg~~L~f~D~RrfG~i~l~~~ 136 (408)
|++.... ...+|.+|++++|.|+||..|.|.++ .+++++.
T Consensus 74 ~~~~~~~-----------~~~~~~~~~rl~l~~~~g~~l~~~~~----~~~l~~~ 113 (115)
T cd08965 74 WRVRKRG-----------NYPKTNRQLRVALHTAKKSALLYSAS----DIDVLPT 113 (115)
T ss_pred EEEeCCC-----------CCCCCCCeEEEEEEcCCceEEeeCCC----EEEEecC
Confidence 9985321 11256789999999999988888774 6787763
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=99.92 E-value=1.4e-24 Score=185.90 Aligned_cols=109 Identities=19% Similarity=0.253 Sum_probs=89.5
Q ss_pred CCChhHHHHHHHHHHHhcCCCEEEEEEeccCCceeccCChhhHHHhhcCCeEeeeeeeeeEEEEEeCCCCcceeeeceee
Q 015345 1 MPELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKNLWLRLDSPPFPSFQFGMTG 80 (408)
Q Consensus 1 MPELPEVe~~~~~L~~~l~Gk~I~~V~v~~~~~v~~~~~~~~f~~~L~G~~I~~V~RrGK~L~~~l~~~~~L~vHLGMtG 80 (408)
||||||||++++.|++.++|++| ++.+ +.++ +.+|.+.|.|++|++|.||||||+|.|+++.+|++||||||
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---RVSS-PQGR----FADGAALLDGRVLADAEAHGKHLFLGFEGDRILHVHLGLYG 72 (110)
T ss_pred CCCcHHHHHHHHHHHHHhCCCEE---EEcC-Cccc----chhHHhhCCCCEEEEEEEeeeEEEEEeCCCCEEEEeCCCee
Confidence 99999999999999999999999 3432 3432 45788999999999999999999999987679999999999
Q ss_pred eEEEecccchhcccccccCCCCCCCCccEEEEEEcCCceEEEeecCcccEEEE
Q 015345 81 AIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELSFTDKRRFAKVRL 133 (408)
Q Consensus 81 ~l~i~~~~~~~y~~~~~~~~~~~p~kh~~l~l~~~dg~~L~f~D~RrfG~i~l 133 (408)
+|++... . ++++|+|++|.|++... -.|+|..+-+.|
T Consensus 73 ~~~~~~~-------------~-~~~~h~~~~l~l~~~~~--~~~~~~~~~~~~ 109 (110)
T cd08970 73 KFRFGGD-------------P-PPPPRGQVRLRLVGDTH--AADLRGPTVCEL 109 (110)
T ss_pred EEEEecC-------------C-CCCceEEEEEEECCCCc--EEcCCCCceEEe
Confidence 9998531 1 35689999999976543 367777776665
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=99.87 E-value=1.3e-21 Score=170.64 Aligned_cols=111 Identities=21% Similarity=0.404 Sum_probs=91.8
Q ss_pred CCChhHHHHHHHHHHHhcCCCEEEEEEeccCCceeccCChhhHHHhhcCCeEeeeeeeeeEEEEEeCC----------CC
Q 015345 1 MPELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKNLWLRLDS----------PP 70 (408)
Q Consensus 1 MPELPEVe~~~~~L~~~l~Gk~I~~V~v~~~~~v~~~~~~~~f~~~L~G~~I~~V~RrGK~L~~~l~~----------~~ 70 (408)
|||+|+|+++++.++ .+.|++|+.++... + ....+.|.|++|++++++|||||+.|++ +.
T Consensus 1 MPEG~sIhrla~~~~-~f~G~~v~~~s~~~-~--------~~~a~~L~G~~l~~a~a~GKHL~l~F~~~~~~~~~~~~~~ 70 (126)
T cd08968 1 MPEGPSVRKFHHLVS-PFVGQRVVKVGGSS-K--------KINPNDLQGLRLQDSQVHGKNLFLHFDLDEEMGPDRDAGR 70 (126)
T ss_pred CCCcHHHHHHHHHHH-HhCCCEEEEcCCCC-C--------cchhhhcCCcEEEEEEEeccEEEEEecCcccccccccCCc
Confidence 999999999998887 68999999886431 1 1235679999999999999999999975 35
Q ss_pred cceeeeceeeeEEEecccchhcccccccCCCCCCCCccEEEEEEcCCceEEEeec
Q 015345 71 FPSFQFGMTGAIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELSFTDK 125 (408)
Q Consensus 71 ~L~vHLGMtG~l~i~~~~~~~y~~~~~~~~~~~p~kh~~l~l~~~dg~~L~f~D~ 125 (408)
+|++||||+|+|++++.. +....+..++||.++.+|+|+|++|..|+|+|+
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 899999999999997632 112335567799999999999999999999996
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=99.60 E-value=4.8e-15 Score=131.23 Aligned_cols=112 Identities=19% Similarity=0.247 Sum_probs=84.6
Q ss_pred CCChhHHHHHHHHHHH-hcCCCEEEEEEeccCCcee----ccC-----ChhhHHHhhcCCeEeeeeeeeeEEEEEeCCCC
Q 015345 1 MPELPEVEAARRAIEE-HCIGKKIVKSIIADDNKVI----DGV-----SASDFEASVLGKAILSAHRKGKNLWLRLDSPP 70 (408)
Q Consensus 1 MPELPEVe~~~~~L~~-~l~Gk~I~~V~v~~~~~v~----~~~-----~~~~f~~~L~G~~I~~V~RrGK~L~~~l~~~~ 70 (408)
|-|+|-..+-.+.|.. ...|+++..++......-- .+. +-..|.+.|.|++|++|+|+||||||+|+++
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 8899998887777764 4579999987764321110 010 1256999999999999999999999999875
Q ss_pred cceeeeceeeeEEEecccchhcccccccCCCCCCCCccEEEEEEcCCceEEEeec
Q 015345 71 FPSFQFGMTGAIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELSFTDK 125 (408)
Q Consensus 71 ~L~vHLGMtG~l~i~~~~~~~y~~~~~~~~~~~p~kh~~l~l~~~dg~~L~f~D~ 125 (408)
+|++||||+|+|++..+. ....+.++.+|.+.|+++ .|+|+|+
T Consensus 80 ~L~vHLGMtGsl~i~~~~-----------kk~~~~~~p~l~l~~~~~-~I~F~d~ 122 (140)
T cd08969 80 ALRIHFGMNGSMRINPLE-----------SKDRSGASPVLEVQLTKD-LICFFDS 122 (140)
T ss_pred EEEEecCeeeEEEEeccc-----------ccccCCCCCeEEEEcCCC-EEEEEec
Confidence 899999999999986321 112345678999999876 5999996
No 23
>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=98.57 E-value=5.2e-08 Score=64.73 Aligned_cols=29 Identities=28% Similarity=0.193 Sum_probs=23.6
Q ss_pred CCCCCCCCCCCceEEEEECCceeEEcCCCCC
Q 015345 247 KKPGKAFVDGKKIDFITAGGRTTAYVPELQK 277 (408)
Q Consensus 247 g~pC~~~~CG~~I~~~~vgGRtT~~CP~CQ~ 277 (408)
|++|+ +|++.|..+.+++|++||||.||+
T Consensus 1 G~~C~--rC~~~~~~~~~~~r~~~~C~rCq~ 29 (30)
T PF06827_consen 1 GEKCP--RCWNYIEDIGINGRSTYLCPRCQK 29 (30)
T ss_dssp TSB-T--TT--BBEEEEETTEEEEE-TTTCC
T ss_pred CCcCc--cCCCcceEeEecCCCCeECcCCcC
Confidence 57888 999999999999999999999997
No 24
>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=2.1e-05 Score=82.03 Aligned_cols=196 Identities=23% Similarity=0.310 Sum_probs=104.1
Q ss_pred HHHHHHHHHHHhcCCCEEEEEEeccC------------------------Cceec------c-CChhhH----HHhhcCC
Q 015345 6 EVEAARRAIEEHCIGKKIVKSIIADD------------------------NKVID------G-VSASDF----EASVLGK 50 (408)
Q Consensus 6 EVe~~~~~L~~~l~Gk~I~~V~v~~~------------------------~~v~~------~-~~~~~f----~~~L~G~ 50 (408)
.|..++.-|+..+.|.+|..|.-.+. +.+.- . ..|..| ...|.|.
T Consensus 4 ~l~a~~~El~~~l~g~~i~~i~q~~~~~~~l~~~~~~~~~~L~i~~~~~~~ri~lt~~~~~~~~~~~~f~~~Lrk~l~g~ 83 (455)
T PF05833_consen 4 DLRALVKELKKKLEGGRIDKIYQPDKRELLLKFRKPGGNHWLLISAHPSGPRIHLTEKPRENPKEPSPFCMLLRKHLRGA 83 (455)
T ss_dssp HHHHHHHHHGG-GTT-EEEEEEEEETTEEEEEEEETTEEEEEEEE--TTT-EEEEE-----------HHHHHHHHHHTT-
T ss_pred HHHHHHHHHHHhhcCCEEEEEEcCCCCEEEEEEEeCCCcEEEEEEEcCCCceeEecCCCCCCCCCCchHHHHHHHHhCCC
Confidence 57888999999999999998862221 11100 0 012334 3678899
Q ss_pred eEeeeeeeeeEEEEEeCCCCcceeeecee------eeEEEecccchhcccccccCCCCCCCCccEEEEEEcCCceEEEee
Q 015345 51 AILSAHRKGKNLWLRLDSPPFPSFQFGMT------GAIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELSFTD 124 (408)
Q Consensus 51 ~I~~V~RrGK~L~~~l~~~~~L~vHLGMt------G~l~i~~~~~~~y~~~~~~~~~~~p~kh~~l~l~~~dg~~L~f~D 124 (408)
+|++|.-.| .++++.+||+-. ..+++.- +.-++|.-++|.=+++..|.-.=
T Consensus 84 ~i~~i~q~~--------~dRii~~~~~~~~~~~~~~~~~Li~---------------El~g~~~NiiL~d~~~~Il~a~~ 140 (455)
T PF05833_consen 84 RIVSIEQLG--------FDRIIEIEFESGDELGDDEKYRLII---------------ELMGRHSNIILTDEDGKILDALR 140 (455)
T ss_dssp EEEEEEEST--------TSSEEEEEEEEE-TTS-EEEEEEEE---------------E--GGG-EEEEEETT-BEEEESS
T ss_pred EEEEEEEcC--------CcEEEEEEeeccCcCCCceeEEEEE---------------EEcCCcccEEEEcCCCeEEeehh
Confidence 999998653 234555555433 1111100 01133444444323443322211
Q ss_pred cCccc--EEEEc-CCCCCCCcccccCCCCCCCCCCH-HHHHHHHcCCCchhHHHHhCCCccccCchhhhhhHhhhcccCc
Q 015345 125 KRRFA--KVRLL-NDPTSVPPISELGPDALLEPMTV-DEFTDSLSKKKITIKALLLDQSYISGIGNWVADEVLYQAKIHP 200 (408)
Q Consensus 125 ~RrfG--~i~l~-~~~~~~~~l~~LGPDpL~~~f~~-e~f~~~l~k~k~~IK~lLLDQ~iiAGIGNiYadEILF~AgIhP 200 (408)
.+.+. +.+.+ .+....++-..-+.+|++ ++. +.|...|......|..+|+.. +.|+|..++.|+|++|+|.|
T Consensus 141 ~~~~~~~~~R~i~~G~~Y~~Pp~~~~~~p~~--~~~~~~~~~~l~~~~~~l~~~L~~~--~~G~~~~la~ei~~ra~i~~ 216 (455)
T PF05833_consen 141 RVSFSQSRDREILPGEPYIPPPPQDKLDPLD--LEEFEEFIELLKKKEKTLVKALSKN--FQGFGPELAEEILYRAGIDK 216 (455)
T ss_dssp -B---------BSTTSB---------B-CCC----H-HHHHHHHHCCG-BHHHHHHHH--CTT--HHHHHHHHCCCTS-T
T ss_pred hcCcccccceeeccCccccccccccCCCccc--chhHHHHHHhhccCcccHHHHHHHH--HHHhHHHHHHHHHHHhCCCC
Confidence 11111 11222 222222222334677773 554 678888877678888888875 89999999999999999999
Q ss_pred cCcCCCCCHHHHHHHHHHHHHHHHHHHH
Q 015345 201 LQTAVSLSKESCATLLKCIKEVIEKALE 228 (408)
Q Consensus 201 ~~~~~~Ls~~e~~~L~~ai~~VL~~Ai~ 228 (408)
..++..|+++++..|+.++..++.....
T Consensus 217 ~~~~~~~~~~~~~~l~~~~~~l~~~l~~ 244 (455)
T PF05833_consen 217 NKKVEELSDEEIEKLFEAIRELLNELEE 244 (455)
T ss_dssp TSBGGG--HHHHCHHHHHHHHHHHHHT-
T ss_pred ccccccchhhhHHHHHHHHHHhhhhccc
Confidence 9999999999999999999999988773
No 25
>COG1293 Predicted RNA-binding protein homologous to eukaryotic snRNP [Transcription]
Probab=96.96 E-value=0.0096 Score=64.59 Aligned_cols=71 Identities=18% Similarity=0.290 Sum_probs=53.9
Q ss_pred CCCCCCCCHHHHHHHHcCCCchhHHHHhCCCccccCchhhhhhHhhhcccCccCcCCCCCHHHHHHHHHHHHHHHH
Q 015345 149 DALLEPMTVDEFTDSLSKKKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVIE 224 (408)
Q Consensus 149 DpL~~~f~~e~f~~~l~k~k~~IK~lLLDQ~iiAGIGNiYadEILF~AgIhP~~~~~~Ls~~e~~~L~~ai~~VL~ 224 (408)
+|+. ++.+.|...+.....-++.+ ++.+.|+|-.|++|+||+||+.+..++.+++.+++..+..++..++.
T Consensus 168 ~p~~--~~~~~~~~~~~~~~~~~~~~---~~~~~g~~~~~a~el~~rag~~~~~~~~~~~~~~~~~v~~~~~~~~~ 238 (564)
T COG1293 168 NPYE--QSEEDFKELQLNSGADIVRL---LARFLGLGGLLAEELLSRAGLDKKVPAKDLFEEEIKKVREALEELLN 238 (564)
T ss_pred Chhh--cChHHHHHHHhccchHHHHH---HHHhcCCCHHHHHHHHHhcCCCcCCchhhhhHHHHHHHHHHHHhhhh
Confidence 6765 44445555554442222332 46789999999999999999999999999999999999998877643
No 26
>PRK04184 DNA topoisomerase VI subunit B; Validated
Probab=96.17 E-value=0.03 Score=60.40 Aligned_cols=75 Identities=24% Similarity=0.401 Sum_probs=65.2
Q ss_pred cccCCCCCCCCCCHHHHHHHHcC-CCchhHHHHhCCCccccCchhhhhhHhhhcccCccCcCCCCCHHHHHHHHHHHHHH
Q 015345 144 SELGPDALLEPMTVDEFTDSLSK-KKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEV 222 (408)
Q Consensus 144 ~~LGPDpL~~~f~~e~f~~~l~k-~k~~IK~lLLDQ~iiAGIGNiYadEILF~AgIhP~~~~~~Ls~~e~~~L~~ai~~V 222 (408)
...=|-|.. ++++.+..++.. ...++..+|. .-|+.||+-.|+|+|..+|++|..+..+|+.+|+.+|+++++.+
T Consensus 232 ~e~kpHP~g--v~~~~l~~m~~~t~~~~l~~fL~--~~f~~v~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~~ 307 (535)
T PRK04184 232 KEIKPHPHG--VDLGTLKRMAARTKRRTLKEFLV--EEFSRVGDKTADEILEKAGLDPNKKPKELTREELERLVEAFKKY 307 (535)
T ss_pred ccCCCCCCc--cCHHHHHHHHHhcccCCHHHHHH--HhhcccCHHHHHHHHHHcCCCCCCChhhCCHHHHHHHHHHHHhc
Confidence 344566664 788889888874 5689999995 57999999999999999999999999999999999999999986
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=95.93 E-value=0.015 Score=49.64 Aligned_cols=52 Identities=29% Similarity=0.296 Sum_probs=45.3
Q ss_pred CCchhHHHHhCCCccccCchhhhhhHhhhcccCccCcCCCCCHHHHHHHHHHHHH
Q 015345 167 KKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKE 221 (408)
Q Consensus 167 ~k~~IK~lLLDQ~iiAGIGNiYadEILF~AgIhP~~~~~~Ls~~e~~~L~~ai~~ 221 (408)
.+.+|.-+|. -|-|||+..|..||..+||+|...+++|+++|+..|...|..
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 3567777774 789999999999999999999999999999999999887765
No 28
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=95.80 E-value=0.0084 Score=52.33 Aligned_cols=41 Identities=34% Similarity=0.460 Sum_probs=39.0
Q ss_pred ccccCchhhhhhHhhhcccCccCcCCCCCHHHHHHHHHHHH
Q 015345 180 YISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIK 220 (408)
Q Consensus 180 iiAGIGNiYadEILF~AgIhP~~~~~~Ls~~e~~~L~~ai~ 220 (408)
.|-|||--+|.|||..+||+|...+..||++|+..|-+.|.
T Consensus 21 ~IyGIG~~~a~~I~~~~gi~~~~r~~eLteeei~~ir~~i~ 61 (121)
T COG0099 21 YIYGIGRRRAKEICKKAGIDPDKRVGELTEEEIERLRDAIQ 61 (121)
T ss_pred hhccccHHHHHHHHHHcCCCHhHhhccCCHHHHHHHHHHHH
Confidence 38899999999999999999999999999999999988887
No 29
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=95.49 E-value=0.016 Score=50.88 Aligned_cols=51 Identities=29% Similarity=0.374 Sum_probs=44.5
Q ss_pred CchhHHHHhCCCccccCchhhhhhHhhhcccCccCcCCCCCHHHHHHHHHHHHH
Q 015345 168 KITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKE 221 (408)
Q Consensus 168 k~~IK~lLLDQ~iiAGIGNiYadEILF~AgIhP~~~~~~Ls~~e~~~L~~ai~~ 221 (408)
+.+|.-+| ..|-|||...|..||..+||||...+++|+++|+..|-..|..
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 45555566 4588999999999999999999999999999999999888864
No 30
>TIGR01052 top6b DNA topoisomerase VI, B subunit. This model describes DNA topoisomerase VI, an archaeal type II DNA topoisomerase (DNA gyrase).
Probab=95.27 E-value=0.1 Score=55.72 Aligned_cols=74 Identities=22% Similarity=0.322 Sum_probs=63.9
Q ss_pred ccCCCCCCCCCCHHHHHHHHcC-CCchhHHHHhCCCccccCchhhhhhHhhhcccC---ccCcCCCCCHHHHHHHHHHHH
Q 015345 145 ELGPDALLEPMTVDEFTDSLSK-KKITIKALLLDQSYISGIGNWVADEVLYQAKIH---PLQTAVSLSKESCATLLKCIK 220 (408)
Q Consensus 145 ~LGPDpL~~~f~~e~f~~~l~k-~k~~IK~lLLDQ~iiAGIGNiYadEILF~AgIh---P~~~~~~Ls~~e~~~L~~ai~ 220 (408)
..=|-|.. ++++.+..+++. +..++..+|. +-|+.||.-.|+||+..||+. |.....+|+.+|+.+|+++++
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 44566654 788889888875 4589999995 579999999999999999999 999999999999999999998
Q ss_pred HH
Q 015345 221 EV 222 (408)
Q Consensus 221 ~V 222 (408)
.+
T Consensus 300 ~~ 301 (488)
T TIGR01052 300 EM 301 (488)
T ss_pred hc
Confidence 73
No 31
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=94.97 E-value=0.027 Score=51.36 Aligned_cols=52 Identities=27% Similarity=0.263 Sum_probs=46.6
Q ss_pred CCchhHHHHhCCCccccCchhhhhhHhhhcccCccCcCCCCCHHHHHHHHHHHHH
Q 015345 167 KKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKE 221 (408)
Q Consensus 167 ~k~~IK~lLLDQ~iiAGIGNiYadEILF~AgIhP~~~~~~Ls~~e~~~L~~ai~~ 221 (408)
.+.+|.-+| ..|-|||.-.|..||-.+||||...+++||++|+..|-..|..
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 467777777 4599999999999999999999999999999999998888864
No 32
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=94.97 E-value=0.032 Score=49.05 Aligned_cols=50 Identities=34% Similarity=0.426 Sum_probs=43.5
Q ss_pred CchhHHHHhCCCccccCchhhhhhHhhhcccCccCcCCCCCHHHHHHHHHHHH
Q 015345 168 KITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIK 220 (408)
Q Consensus 168 k~~IK~lLLDQ~iiAGIGNiYadEILF~AgIhP~~~~~~Ls~~e~~~L~~ai~ 220 (408)
+.+|.-+| ..|-|||--+|..||..+||||...+++|+++|+..|...|.
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 44555555 448899999999999999999999999999999999988885
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=94.35 E-value=0.047 Score=47.33 Aligned_cols=50 Identities=28% Similarity=0.403 Sum_probs=43.8
Q ss_pred CchhHHHHhCCCccccCchhhhhhHhhhcccCccCcCCCCCHHHHHHHHHHHH
Q 015345 168 KITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIK 220 (408)
Q Consensus 168 k~~IK~lLLDQ~iiAGIGNiYadEILF~AgIhP~~~~~~Ls~~e~~~L~~ai~ 220 (408)
+.+|.-+| .-|-|||.-+|..||-.+||||...+.+|+++|+..|...|.
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 45555566 348999999999999999999999999999999999988875
No 34
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=94.10 E-value=0.059 Score=48.95 Aligned_cols=52 Identities=19% Similarity=0.258 Sum_probs=46.1
Q ss_pred CCchhHHHHhCCCccccCchhhhhhHhhhcccCccCcCCCCCHHHHHHHHHHHHH
Q 015345 167 KKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKE 221 (408)
Q Consensus 167 ~k~~IK~lLLDQ~iiAGIGNiYadEILF~AgIhP~~~~~~Ls~~e~~~L~~ai~~ 221 (408)
.+.+|.-+| ..|-|||.-+|..||-.+||||...+++||++++..|-..|..
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 467777777 4499999999999999999999999999999999998888753
No 35
>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=94.00 E-value=0.069 Score=48.24 Aligned_cols=51 Identities=20% Similarity=0.264 Sum_probs=44.2
Q ss_pred CchhHHHHhCCCccccCchhhhhhHhhhcccCccCcCCCCCHHHHHHHHHHHHH
Q 015345 168 KITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKE 221 (408)
Q Consensus 168 k~~IK~lLLDQ~iiAGIGNiYadEILF~AgIhP~~~~~~Ls~~e~~~L~~ai~~ 221 (408)
+.+|.-+| ..|-|||--+|..||-.+||||...+++||++|+..|-..|..
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 45555566 3489999999999999999999999999999999998888765
No 36
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=89.74 E-value=0.37 Score=34.04 Aligned_cols=27 Identities=11% Similarity=0.164 Sum_probs=24.8
Q ss_pred CCCCCCCCceEEEEECCceeEEcCCCCCC
Q 015345 250 GKAFVDGKKIDFITAGGRTTAYVPELQKL 278 (408)
Q Consensus 250 C~~~~CG~~I~~~~vgGRtT~~CP~CQ~~ 278 (408)
|| +|++.+....+++-..++||.|+-+
T Consensus 2 CP--~C~~~l~~~~~~~~~id~C~~C~G~ 28 (41)
T PF13453_consen 2 CP--RCGTELEPVRLGDVEIDVCPSCGGI 28 (41)
T ss_pred cC--CCCcccceEEECCEEEEECCCCCeE
Confidence 66 9999999999999999999999985
No 37
>PRK00420 hypothetical protein; Validated
Probab=88.35 E-value=0.36 Score=41.91 Aligned_cols=27 Identities=19% Similarity=0.062 Sum_probs=21.6
Q ss_pred CCCCCCCCCCceEEEEECCceeEEcCCCCCCC
Q 015345 248 KPGKAFVDGKKIDFITAGGRTTAYVPELQKLN 279 (408)
Q Consensus 248 ~pC~~~~CG~~I~~~~vgGRtT~~CP~CQ~~~ 279 (408)
..|| .||+++.+.. -+..|||.|+...
T Consensus 24 ~~CP--~Cg~pLf~lk---~g~~~Cp~Cg~~~ 50 (112)
T PRK00420 24 KHCP--VCGLPLFELK---DGEVVCPVHGKVY 50 (112)
T ss_pred CCCC--CCCCcceecC---CCceECCCCCCee
Confidence 6788 9999988763 3478999999964
No 38
>COG1389 DNA topoisomerase VI, subunit B [DNA replication, recombination, and repair]
Probab=87.91 E-value=1.4 Score=46.74 Aligned_cols=76 Identities=25% Similarity=0.397 Sum_probs=64.6
Q ss_pred ccccCCCCCCCCCCHHHHHHHHcC-CCchhHHHHhCCCccccCchhhhhhHhhhcccCccCcCCCCC----HHHHHHHHH
Q 015345 143 ISELGPDALLEPMTVDEFTDSLSK-KKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLS----KESCATLLK 217 (408)
Q Consensus 143 l~~LGPDpL~~~f~~e~f~~~l~k-~k~~IK~lLLDQ~iiAGIGNiYadEILF~AgIhP~~~~~~Ls----~~e~~~L~~ 217 (408)
-.++=|-|.. ++.+.+...+.. ++..++.+|+ +-|.-||---++|+|=.+|.+|......|+ .+|++.|++
T Consensus 231 P~E~kPHP~g--vd~~~L~~M~~~T~~~tv~~fL~--sef~rig~~ta~e~~e~~g~~~~~~p~~L~~~~~~eea~~lv~ 306 (538)
T COG1389 231 PKEIKPHPHG--VDLDTLKKMAHRTRRSTVREFLV--SEFSRIGEKTADELLEYAGFDPDKKPRELTKKKTREEAEKLVE 306 (538)
T ss_pred ccccCCCCcc--ccHHHHHHHHHHhhhhhHHHHHH--HHHHHhhhhhHHHHHHHhcCCcccCHHHhhcccCHHHHHHHHH
Confidence 3455566664 788899888864 5789999997 678999999999999999999999999999 999999999
Q ss_pred HHHHH
Q 015345 218 CIKEV 222 (408)
Q Consensus 218 ai~~V 222 (408)
+++.+
T Consensus 307 a~~~~ 311 (538)
T COG1389 307 AFKKM 311 (538)
T ss_pred HHHhC
Confidence 99864
No 39
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=86.20 E-value=0.48 Score=42.21 Aligned_cols=25 Identities=12% Similarity=-0.033 Sum_probs=19.6
Q ss_pred CCCCCCCCCCceEEEEECCceeEEcCCCCCC
Q 015345 248 KPGKAFVDGKKIDFITAGGRTTAYVPELQKL 278 (408)
Q Consensus 248 ~pC~~~~CG~~I~~~~vgGRtT~~CP~CQ~~ 278 (408)
..|| .||+|+-+ -=.+.|||.|+..
T Consensus 29 ~hCp--~Cg~PLF~----KdG~v~CPvC~~~ 53 (131)
T COG1645 29 KHCP--KCGTPLFR----KDGEVFCPVCGYR 53 (131)
T ss_pred hhCc--ccCCccee----eCCeEECCCCCce
Confidence 3588 99999887 2347899999964
No 40
>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=85.08 E-value=0.9 Score=32.55 Aligned_cols=25 Identities=12% Similarity=0.011 Sum_probs=19.2
Q ss_pred CCCCCCCCCCCceEEEEECCceeEEcCCCC
Q 015345 247 KKPGKAFVDGKKIDFITAGGRTTAYVPELQ 276 (408)
Q Consensus 247 g~pC~~~~CG~~I~~~~vgGRtT~~CP~CQ 276 (408)
+..|+ .||.|+.+.. .| ..|||.|+
T Consensus 17 ~~~Cp--~C~~PL~~~k-~g--~~~Cv~C~ 41 (41)
T PF06677_consen 17 DEHCP--DCGTPLMRDK-DG--KIYCVSCG 41 (41)
T ss_pred cCccC--CCCCeeEEec-CC--CEECCCCC
Confidence 46788 9999988743 44 36999996
No 41
>KOG3311 consensus Ribosomal protein S18 [Translation, ribosomal structure and biogenesis]
Probab=84.37 E-value=0.75 Score=41.82 Aligned_cols=50 Identities=26% Similarity=0.323 Sum_probs=44.8
Q ss_pred CchhHHHHhCCCccccCchhhhhhHhhhcccCccCcCCCCCHHHHHHHHHHHH
Q 015345 168 KITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIK 220 (408)
Q Consensus 168 k~~IK~lLLDQ~iiAGIGNiYadEILF~AgIhP~~~~~~Ls~~e~~~L~~ai~ 220 (408)
+..|.-+|+- |.|||=-||.+||=.++|++.-.+..|+++|+..+...+.
T Consensus 23 ~~~V~fAl~~---i~Gig~~~A~~ic~K~~~~~~~r~gelt~~qi~~i~~i~~ 72 (152)
T KOG3311|consen 23 KRKVTFALTS---IKGIGRRYAEIVCKKADLDLTKRAGELTEEQILRILQILN 72 (152)
T ss_pred CceeEEEEEE---EeeechhhhhhhhhhcCcchhhhhccccHHHHHHHHHHhc
Confidence 5666666665 9999999999999999999999999999999999888776
No 42
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=84.12 E-value=0.96 Score=31.11 Aligned_cols=26 Identities=12% Similarity=0.019 Sum_probs=16.1
Q ss_pred CCCCCCCCceEEEEE--CCceeEEcCCCCC
Q 015345 250 GKAFVDGKKIDFITA--GGRTTAYVPELQK 277 (408)
Q Consensus 250 C~~~~CG~~I~~~~v--gGRtT~~CP~CQ~ 277 (408)
|+ .||+++..... .+|.-++||.|.-
T Consensus 3 C~--~CG~~l~~~ip~gd~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 3 CP--QCGGPLERRIPEGDDRERLVCPACGF 30 (34)
T ss_dssp -T--TT--B-EEE--TT-SS-EEEETTTTE
T ss_pred cc--cccChhhhhcCCCCCccceECCCCCC
Confidence 66 99999998888 6899999999974
No 43
>KOG0066 consensus eIF2-interacting protein ABC50 (ABC superfamily) [Translation, ribosomal structure and biogenesis]
Probab=83.22 E-value=1.3 Score=47.19 Aligned_cols=62 Identities=24% Similarity=0.268 Sum_probs=36.9
Q ss_pred CCCCCCchhhhhhhhccccccccCCCCCCCCccccCCCCCCCCCCC-CCCCCCCCCCCCCCCcc
Q 015345 309 GDESESDGEEIAENVKSKKRQKLGGQVKQPSPRKRKSKESDTEDDD-GGNDDDGGGSDDNAEEA 371 (408)
Q Consensus 309 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~ 371 (408)
.+-.++|.|+|...+.+++++--.+++++-+|++|++ .|.+++|. .++-++..-.+.+.++.
T Consensus 48 ~nr~~~d~e~i~~~~q~kqq~~~kkq~kk~kkgkr~~-d~~de~e~~e~~~~~~~l~~~~~de~ 110 (807)
T KOG0066|consen 48 RNRDNEDLESIASSNQSKQQTAGKKQAKKGKKGKRNN-DWSDEDEKPEKSLPANDLDDEDDDEA 110 (807)
T ss_pred ccccchhHHHHhhhhhHHHHHHHHHHhhhcccccccC-CCCccccchhhcCcccccCCCCchhh
Confidence 3345677789999988887776666666766666655 44444443 33444444444444443
No 44
>PHA00626 hypothetical protein
Probab=79.11 E-value=1.9 Score=32.99 Aligned_cols=44 Identities=14% Similarity=0.039 Sum_probs=29.2
Q ss_pred CCCCCCCCC-ceEEE-EECC-ceeEEcCCCCCCC-----ccchhhhhCCCCCcC
Q 015345 249 PGKAFVDGK-KIDFI-TAGG-RTTAYVPELQKLN-----GVQAAKAVGKPRKQA 294 (408)
Q Consensus 249 pC~~~~CG~-~I~~~-~vgG-RtT~~CP~CQ~~~-----~~~~~~~~~~~~~~~ 294 (408)
.|| .||. .|.+- .+-+ |..|-||.|+-.. |..-+.|++.+||-+
T Consensus 2 ~CP--~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft~~~~~~~~~~~~~~~~~~~ 53 (59)
T PHA00626 2 SCP--KCGSGNIAKEKTMRGWSDDYVCCDCGYNDSKDAFGERGKNEFVRINKER 53 (59)
T ss_pred CCC--CCCCceeeeeceecccCcceEcCCCCCeechhhhhhccccceEEechhh
Confidence 366 9999 46653 4444 9999999999863 333445556666655
No 45
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=76.52 E-value=1.7 Score=31.63 Aligned_cols=28 Identities=4% Similarity=-0.202 Sum_probs=21.5
Q ss_pred CCCCCCCCceEEEEECCceeEEcCCCCCCC
Q 015345 250 GKAFVDGKKIDFITAGGRTTAYVPELQKLN 279 (408)
Q Consensus 250 C~~~~CG~~I~~~~vgGRtT~~CP~CQ~~~ 279 (408)
|| .||..+......++..|.||.|.-..
T Consensus 3 Cp--~Cg~~l~~~~~~~~~~~vC~~Cg~~~ 30 (52)
T smart00661 3 CP--KCGNMLIPKEGKEKRRFVCRKCGYEE 30 (52)
T ss_pred CC--CCCCccccccCCCCCEEECCcCCCeE
Confidence 66 99997765555556799999999754
No 46
>PRK12495 hypothetical protein; Provisional
Probab=75.42 E-value=1.6 Score=42.02 Aligned_cols=25 Identities=16% Similarity=0.033 Sum_probs=20.3
Q ss_pred CCCCCCCCCceEEEEECCceeEEcCCCCCCC
Q 015345 249 PGKAFVDGKKIDFITAGGRTTAYVPELQKLN 279 (408)
Q Consensus 249 pC~~~~CG~~I~~~~vgGRtT~~CP~CQ~~~ 279 (408)
.|+ .||.+|-.+ -...|||.||.+.
T Consensus 44 hC~--~CG~PIpa~----pG~~~Cp~CQ~~~ 68 (226)
T PRK12495 44 HCD--ECGDPIFRH----DGQEFCPTCQQPV 68 (226)
T ss_pred hcc--cccCcccCC----CCeeECCCCCCcc
Confidence 477 999999832 5678999999974
No 47
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=70.14 E-value=3.3 Score=39.07 Aligned_cols=30 Identities=7% Similarity=-0.128 Sum_probs=24.3
Q ss_pred ceEEEccCCCCCCCCCCCCceEEEEECCceeEEcCCCCCC
Q 015345 239 NWIFHSREKKPGKAFVDGKKIDFITAGGRTTAYVPELQKL 278 (408)
Q Consensus 239 ~~~vy~R~g~pC~~~~CG~~I~~~~vgGRtT~~CP~CQ~~ 278 (408)
.-.+|.+ |. +|++.+.+ ...+.+||+||..
T Consensus 145 lGVI~A~----Cs--rC~~~L~~----~~~~l~Cp~Cg~t 174 (188)
T COG1096 145 LGVIYAR----CS--RCRAPLVK----KGNMLKCPNCGNT 174 (188)
T ss_pred ceEEEEE----cc--CCCcceEE----cCcEEECCCCCCE
Confidence 3477765 76 99999887 6678999999985
No 48
>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=69.41 E-value=8.3 Score=39.83 Aligned_cols=64 Identities=27% Similarity=0.335 Sum_probs=47.8
Q ss_pred CCCCHHHHHHHHc-----CCCchhHHHHhCCCccccCchhhhhhHhhhcccCccCcCCCCCHHHHHHHHHHHHH
Q 015345 153 EPMTVDEFTDSLS-----KKKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKE 221 (408)
Q Consensus 153 ~~f~~e~f~~~l~-----k~k~~IK~lLLDQ~iiAGIGNiYadEILF~AgIhP~~~~~~Ls~~e~~~L~~ai~~ 221 (408)
++++.+++.+.|. .+++.++.+|- --+=+=+++.+|-.++|+|..++++|+++++.+|.+.++.
T Consensus 263 p~~~~~~~~~~~~~~~~~~~~~~~~~~l~-----~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~lk~ 331 (400)
T TIGR00275 263 PDLSEEELEQRLKRLRKSNPKKTVKNILK-----GLLPKRLAELLLEQLGIDPDLPAAQLSKKEIKKLVQLLKN 331 (400)
T ss_pred CCCCHHHHHHHHHHHHHHChhhhHHHHhh-----hhhhHHHHHHHHHHcCCCCCCChHHCCHHHHHHHHHHHhC
Confidence 4466666655443 24677887763 1233446789999999999999999999999999998874
No 49
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=67.80 E-value=5 Score=32.86 Aligned_cols=28 Identities=14% Similarity=0.248 Sum_probs=25.2
Q ss_pred CCCCCCCCCceEEEEECCceeEEcCCCCCC
Q 015345 249 PGKAFVDGKKIDFITAGGRTTAYVPELQKL 278 (408)
Q Consensus 249 pC~~~~CG~~I~~~~vgGRtT~~CP~CQ~~ 278 (408)
-|| .|+..+......|=-.-|||.|--.
T Consensus 3 lCP--~C~v~l~~~~rs~vEiD~CPrCrGV 30 (88)
T COG3809 3 LCP--ICGVELVMSVRSGVEIDYCPRCRGV 30 (88)
T ss_pred ccC--cCCceeeeeeecCceeeeCCccccE
Confidence 466 9999999999999999999999984
No 50
>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=65.10 E-value=6.1 Score=30.46 Aligned_cols=28 Identities=7% Similarity=-0.098 Sum_probs=22.2
Q ss_pred CCCCCCCCCCCceEEEEECCceeEEcCCCCCC
Q 015345 247 KKPGKAFVDGKKIDFITAGGRTTAYVPELQKL 278 (408)
Q Consensus 247 g~pC~~~~CG~~I~~~~vgGRtT~~CP~CQ~~ 278 (408)
-+.|+ .||..... -.....|.||.|...
T Consensus 28 Sq~C~--~CG~~~~~--~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 28 SQTCP--RCGHRNKK--RRSGRVFTCPNCGFE 55 (69)
T ss_pred ccCcc--Cccccccc--ccccceEEcCCCCCE
Confidence 46787 99999887 345559999999885
No 51
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=64.25 E-value=7.9 Score=30.44 Aligned_cols=45 Identities=18% Similarity=0.062 Sum_probs=29.0
Q ss_pred CCCCCCCCCCceEEEEECCce-eEEcCCCCCCC--ccchhhhhCCCCCcC
Q 015345 248 KPGKAFVDGKKIDFITAGGRT-TAYVPELQKLN--GVQAAKAVGKPRKQA 294 (408)
Q Consensus 248 ~pC~~~~CG~~I~~~~vgGRt-T~~CP~CQ~~~--~~~~~~~~~~~~~~~ 294 (408)
+||| -||..+..++.-+.- .+.|..||-.- ....+..+..=|+++
T Consensus 7 KPCP--FCG~~~~~v~~~~g~~~v~C~~CgA~~~~~~te~~Aie~WN~Ra 54 (64)
T PRK09710 7 KPCP--FCGCPSVTVKAISGYYRAKCNGCESRTGYGGSEKEALERWNKRT 54 (64)
T ss_pred cCCC--CCCCceeEEEecCceEEEEcCCCCcCcccccCHHHHHHHHHhhh
Confidence 6888 999988877654333 36799999963 223344444455555
No 52
>TIGR00755 ksgA dimethyladenosine transferase. Alternate name: S-adenosylmethionine--6-N',N'-adenosyl (rRNA) dimethyltransferase
Probab=62.65 E-value=10 Score=36.54 Aligned_cols=58 Identities=22% Similarity=0.305 Sum_probs=43.5
Q ss_pred HHHHHH-HHcCCCchhHHHHhCCCccccCchhhhhhHhhhcccCccCcCCCCCHHHHHHHHHHH
Q 015345 157 VDEFTD-SLSKKKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCI 219 (408)
Q Consensus 157 ~e~f~~-~l~k~k~~IK~lLLDQ~iiAGIGNiYadEILF~AgIhP~~~~~~Ls~~e~~~L~~ai 219 (408)
.+.|.+ .+..++++|+..|- .++.| -...++|-.++|.|..++.+||.+++.+|++++
T Consensus 195 ~~~~~~~~F~~rrk~l~~~l~--~~~~~---~~~~~~l~~~~i~~~~r~~~l~~~~~~~l~~~~ 253 (253)
T TIGR00755 195 FEKLLKAAFSQRRKTLRNNLK--QLLKA---SKLEEVLEQLGLDPTARAEQLSPEDFLRLANLL 253 (253)
T ss_pred HHHHHHHHHccchHHHHHHHh--hhcch---hHHHHHHHHCCcCCCCCcccCCHHHHHHHHHhC
Confidence 344544 46778899999883 23333 245678889999999999999999999998753
No 53
>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=62.23 E-value=6 Score=28.20 Aligned_cols=28 Identities=25% Similarity=0.213 Sum_probs=15.2
Q ss_pred CCCCCCCCCCceEEEE---ECCceeEEcCCCCC
Q 015345 248 KPGKAFVDGKKIDFIT---AGGRTTAYVPELQK 277 (408)
Q Consensus 248 ~pC~~~~CG~~I~~~~---vgGRtT~~CP~CQ~ 277 (408)
.||| .||..=.+.. ..++.+|||-.||.
T Consensus 4 ~pCP--~CGG~DrFri~~d~~~~G~~~C~~C~~ 34 (40)
T PF08273_consen 4 GPCP--ICGGKDRFRIFDDKDGRGTWICRQCGG 34 (40)
T ss_dssp E--T--TTT-TTTEEEETT----S-EEETTTTB
T ss_pred CCCC--CCcCccccccCcCcccCCCEECCCCCC
Confidence 4777 9988655442 24789999999975
No 54
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=57.85 E-value=5.5 Score=30.32 Aligned_cols=28 Identities=21% Similarity=0.166 Sum_probs=21.6
Q ss_pred CCCCCCCC----ceEEEEECCceeEEcCCCCCCC
Q 015345 250 GKAFVDGK----KIDFITAGGRTTAYVPELQKLN 279 (408)
Q Consensus 250 C~~~~CG~----~I~~~~vgGRtT~~CP~CQ~~~ 279 (408)
|| .||. .|..-++.-.=-.|||.|-...
T Consensus 7 CP--~CgnKTR~kir~DT~LkNfPlyCpKCK~Et 38 (55)
T PF14205_consen 7 CP--ICGNKTRLKIREDTVLKNFPLYCPKCKQET 38 (55)
T ss_pred CC--CCCCccceeeecCceeccccccCCCCCceE
Confidence 76 9984 4555577788889999998864
No 55
>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=57.79 E-value=12 Score=29.92 Aligned_cols=28 Identities=14% Similarity=0.191 Sum_probs=21.0
Q ss_pred CCCCCCCCceEEEEECCceeEEcCCCCCCC
Q 015345 250 GKAFVDGKKIDFITAGGRTTAYVPELQKLN 279 (408)
Q Consensus 250 C~~~~CG~~I~~~~vgGRtT~~CP~CQ~~~ 279 (408)
|| .||.+++....=|=..|||-+|-.|.
T Consensus 33 CP--dC~~~Le~LkACGAvdYFC~~c~gLi 60 (70)
T PF07191_consen 33 CP--DCGQPLEVLKACGAVDYFCNHCHGLI 60 (70)
T ss_dssp -T--TT-SB-EEEEETTEEEEE-TTTT-EE
T ss_pred CC--CcccHHHHHHHhcccceeeccCCcee
Confidence 66 99999999999999999999998874
No 56
>KOG2846 consensus Predicted membrane protein [Function unknown]
Probab=57.70 E-value=17 Score=37.07 Aligned_cols=36 Identities=14% Similarity=-0.062 Sum_probs=22.7
Q ss_pred cCCCCCCCCCCCCc--eEEEEECCceeEEcCCCCCCCccc
Q 015345 245 REKKPGKAFVDGKK--IDFITAGGRTTAYVPELQKLNGVQ 282 (408)
Q Consensus 245 R~g~pC~~~~CG~~--I~~~~vgGRtT~~CP~CQ~~~~~~ 282 (408)
|..-.|+ .|.+. +.+-.---=.+|+||.|--+.++.
T Consensus 218 ryALIC~--~C~~HNGla~~ee~~yi~F~C~~Cn~LN~~~ 255 (328)
T KOG2846|consen 218 RYALICS--QCHHHNGLARKEEYEYITFRCPHCNALNPAK 255 (328)
T ss_pred hhhhcch--hhccccCcCChhhcCceEEECccccccCCCc
Confidence 4456787 77532 222233456799999999986543
No 57
>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=57.50 E-value=8.2 Score=28.67 Aligned_cols=30 Identities=10% Similarity=-0.064 Sum_probs=21.0
Q ss_pred CCCCCCCCCCceEEEE-----ECCceeEEcCCCCCCC
Q 015345 248 KPGKAFVDGKKIDFIT-----AGGRTTAYVPELQKLN 279 (408)
Q Consensus 248 ~pC~~~~CG~~I~~~~-----vgGRtT~~CP~CQ~~~ 279 (408)
+||| -||..-..+. .+++..|.|+.|+...
T Consensus 2 kPCP--fCGg~~~~~~~~~~~~~~~~~~~C~~Cga~~ 36 (53)
T TIGR03655 2 KPCP--FCGGADVYLRRGFDPLDLSHYFECSTCGASG 36 (53)
T ss_pred CCCC--CCCCcceeeEeccCCCCCEEEEECCCCCCCc
Confidence 5788 9998766443 2355555699999864
No 58
>COG0030 KsgA Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis]
Probab=56.37 E-value=14 Score=36.55 Aligned_cols=52 Identities=29% Similarity=0.313 Sum_probs=43.0
Q ss_pred HHcCCCchhHHHHhCCCccccCchhhhhhHhhhcccCccCcCCCCCHHHHHHHHHHHHHH
Q 015345 163 SLSKKKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEV 222 (408)
Q Consensus 163 ~l~k~k~~IK~lLLDQ~iiAGIGNiYadEILF~AgIhP~~~~~~Ls~~e~~~L~~ai~~V 222 (408)
.+..+++.+...|-+=.- ..|+|=+++|+|..++.+|+.+++.+|++++...
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 456788888887753221 6899999999999999999999999999988754
No 59
>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=56.08 E-value=8.4 Score=25.23 Aligned_cols=21 Identities=24% Similarity=0.218 Sum_probs=12.3
Q ss_pred CCCCCCCCceEEEEECCceeEEcCC
Q 015345 250 GKAFVDGKKIDFITAGGRTTAYVPE 274 (408)
Q Consensus 250 C~~~~CG~~I~~~~vgGRtT~~CP~ 274 (408)
|| .||++|.+. .+...+||++
T Consensus 2 CP--~C~s~l~~~--~~ev~~~C~N 22 (28)
T PF03119_consen 2 CP--VCGSKLVRE--EGEVDIRCPN 22 (28)
T ss_dssp -T--TT--BEEE---CCTTCEEE--
T ss_pred cC--CCCCEeEcC--CCCEeEECCC
Confidence 55 999999844 6777999985
No 60
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=55.40 E-value=31 Score=33.48 Aligned_cols=80 Identities=14% Similarity=0.101 Sum_probs=50.0
Q ss_pred hhHHHHhCCCccccCchhhhhhHhhhcccCccCcCCCCCHHHHHHHHHHHHHHHHHHHHcCCCCCCCCCceEEEcc---C
Q 015345 170 TIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVIEKALEVGADSSQFPSNWIFHSR---E 246 (408)
Q Consensus 170 ~IK~lLLDQ~iiAGIGNiYadEILF~AgIhP~~~~~~Ls~~e~~~L~~ai~~VL~~Ai~~gg~s~~f~~~~~vy~R---~ 246 (408)
-+-..|.+....-|+++|..-.+.- ...|+..-+..|...|.+..+ . ||.. +++.+ .
T Consensus 249 k~~~~~v~~~~~~~~~~~~~~~~~~---------~~~i~~~~~~~~~~~l~yka~---~-~~~~-------v~~~~~~~t 308 (364)
T COG0675 249 KLAKKLVELADLVGVETLVVEDLVK---------RRSISDWAFGELRRQLEYKAE---W-GGIV-------VKVVPPYYT 308 (364)
T ss_pred HHHHHHHhhcceEeeeeeehhhhhh---------cccHhhhhHHHHHHHHHHHHH---h-CCeE-------EEECCCCCC
Confidence 3444566666667777776544433 666777777777776665433 3 4432 33333 2
Q ss_pred CCCCCCCCCCCceEEEEECCceeEEcCCCCCC
Q 015345 247 KKPGKAFVDGKKIDFITAGGRTTAYVPELQKL 278 (408)
Q Consensus 247 g~pC~~~~CG~~I~~~~vgGRtT~~CP~CQ~~ 278 (408)
-+.|+ .||. -....|.||.|...
T Consensus 309 S~~C~--~cg~-------~~~r~~~C~~cg~~ 331 (364)
T COG0675 309 SKTCP--CCGH-------LSGRLFKCPRCGFV 331 (364)
T ss_pred ccccc--ccCC-------ccceeEECCCCCCe
Confidence 35677 8998 23678999999984
No 61
>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=55.33 E-value=9.2 Score=26.81 Aligned_cols=29 Identities=21% Similarity=0.155 Sum_probs=20.5
Q ss_pred CCCCCCCCCCCceE--EEEECCceeEEcCCCCC
Q 015345 247 KKPGKAFVDGKKID--FITAGGRTTAYVPELQK 277 (408)
Q Consensus 247 g~pC~~~~CG~~I~--~~~vgGRtT~~CP~CQ~ 277 (408)
..||| .||..=. .....++.++||-.|-.
T Consensus 3 ~~pCP--~CGG~DrFr~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 3 HGPCP--NCGGSDRFRFDDKDGRGTWFCSVCGA 33 (37)
T ss_pred ccCCC--CCCCccccccccCCCCcCEEeCCCCC
Confidence 35787 9988533 23345889999999953
No 62
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=54.67 E-value=8.3 Score=27.11 Aligned_cols=25 Identities=16% Similarity=0.301 Sum_probs=18.2
Q ss_pred CCCCceE----EEEECCceeEEc-CCCCCC
Q 015345 254 VDGKKID----FITAGGRTTAYV-PELQKL 278 (408)
Q Consensus 254 ~CG~~I~----~~~vgGRtT~~C-P~CQ~~ 278 (408)
-||.+|. ..++++|.-||| |.|...
T Consensus 3 ~CG~~I~~eP~~~k~~~~~y~fCC~tC~~~ 32 (37)
T PF08394_consen 3 YCGGEITGEPIVVKIGNKVYYFCCPTCLSQ 32 (37)
T ss_pred ccCCcccCCEEEEEECCeEEEEECHHHHHH
Confidence 4666555 346799999998 888764
No 63
>PRK00274 ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed
Probab=54.54 E-value=18 Score=35.39 Aligned_cols=59 Identities=22% Similarity=0.274 Sum_probs=42.8
Q ss_pred HHHHH-HHcCCCchhHHHHhCCCccccCchhhhhhHhhhcccCccCcCCCCCHHHHHHHHHHHH
Q 015345 158 DEFTD-SLSKKKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIK 220 (408)
Q Consensus 158 e~f~~-~l~k~k~~IK~lLLDQ~iiAGIGNiYadEILF~AgIhP~~~~~~Ls~~e~~~L~~ai~ 220 (408)
+.|.+ .+..++.+|+..|-. + .+..+ -..++|=.+||+|..++.+|+.+++.+|++.+.
T Consensus 210 ~~~~~~~F~~rrk~l~~~l~~--~-~~~~~-~~~~~l~~~~~~~~~r~~~l~~~~~~~L~~~~~ 269 (272)
T PRK00274 210 FRVVKAAFAQRRKTLRNNLKN--L-FGSKE-KLEEALEAAGIDPNRRAETLSVEEFVRLANALA 269 (272)
T ss_pred HHHHHHHHhchHHHHHHHHHh--h-ccchH-HHHHHHHHCCCCcCCCceeCCHHHHHHHHHHHH
Confidence 34433 456788999988832 1 11111 236788999999999999999999999998864
No 64
>PRK12860 transcriptional activator FlhC; Provisional
Probab=54.22 E-value=8.9 Score=36.31 Aligned_cols=30 Identities=13% Similarity=-0.187 Sum_probs=22.1
Q ss_pred CCCCCCCCCCceEEEEECCceeEEcCCCCCCC
Q 015345 248 KPGKAFVDGKKIDFITAGGRTTAYVPELQKLN 279 (408)
Q Consensus 248 ~pC~~~~CG~~I~~~~vgGRtT~~CP~CQ~~~ 279 (408)
.+|. .||+.-..-..--+..|.||-||+..
T Consensus 135 ~~C~--~Cgg~fv~~~~e~~~~f~CplC~~ps 164 (189)
T PRK12860 135 ARCC--RCGGKFVTHAHDLRHNFVCGLCQPPS 164 (189)
T ss_pred ccCC--CCCCCeeccccccCCCCcCCCCCCcc
Confidence 4687 89988554444567899999999754
No 65
>PF04945 YHS: YHS domain; InterPro: IPR007029 This short presumed domain is about 50 amino acid residues long. It often contains two cysteines that may be functionally important. This domain is found in copper transporting ATPases, some phenol hydroxylases and in a set of uncharacterised membrane proteins including Q9CNI0 from SWISSPROT. This domain is named after three of the most conserved amino acids it contains. The domain may be metal binding, possibly copper ions. This domain is duplicated in some copper transporting ATPases.; PDB: 3U52_B 2INN_A 2INP_B 1T0Q_A 2RDB_A 1T0R_A 2IND_A 1T0S_A 2INC_A 3DHI_A ....
Probab=52.69 E-value=14 Score=26.60 Aligned_cols=25 Identities=24% Similarity=0.256 Sum_probs=17.6
Q ss_pred CCCCCce-----EEEEECCceeEEcC-CCCC
Q 015345 253 FVDGKKI-----DFITAGGRTTAYVP-ELQK 277 (408)
Q Consensus 253 ~~CG~~I-----~~~~vgGRtT~~CP-~CQ~ 277 (408)
|+||..| ......||+=|||. .|+.
T Consensus 4 Pvcg~~v~~~~~~~~~y~G~~Y~FCS~~C~~ 34 (47)
T PF04945_consen 4 PVCGMKVPGNAAYSVEYNGRTYYFCSEGCKE 34 (47)
T ss_dssp -GGG-BE-----EEEEETTEEEEESSHHHHH
T ss_pred CCCCCEEccCccEEEEECCEEEEEcCHHHHH
Confidence 4999999 25578899999995 3443
No 66
>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=52.59 E-value=20 Score=25.71 Aligned_cols=28 Identities=11% Similarity=-0.105 Sum_probs=22.5
Q ss_pred CCCCCCCCCCCceEEEEECCceeEEcCCCCC
Q 015345 247 KKPGKAFVDGKKIDFITAGGRTTAYVPELQK 277 (408)
Q Consensus 247 g~pC~~~~CG~~I~~~~vgGRtT~~CP~CQ~ 277 (408)
|-.|| .||.. ....+.+|..|-|-.|-.
T Consensus 18 g~~CP--~Cg~~-~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 18 GFVCP--HCGST-KHYRLKTRGRYRCKACRK 45 (46)
T ss_pred CCCCC--CCCCe-eeEEeCCCCeEECCCCCC
Confidence 44577 99998 666778899999999964
No 67
>PRK12722 transcriptional activator FlhC; Provisional
Probab=51.16 E-value=10 Score=35.84 Aligned_cols=30 Identities=7% Similarity=-0.175 Sum_probs=22.0
Q ss_pred CCCCCCCCCCceEEEEECCceeEEcCCCCCCC
Q 015345 248 KPGKAFVDGKKIDFITAGGRTTAYVPELQKLN 279 (408)
Q Consensus 248 ~pC~~~~CG~~I~~~~vgGRtT~~CP~CQ~~~ 279 (408)
.+|. .||+.-..-...-...|.||-||+..
T Consensus 135 ~~C~--~Cgg~fv~~~~e~~~~f~CplC~~ps 164 (187)
T PRK12722 135 SSCN--CCGGHFVTHAHDPVGSFVCGLCQPPS 164 (187)
T ss_pred ccCC--CCCCCeeccccccCCCCcCCCCCCcc
Confidence 4687 89988553333457799999999954
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=50.49 E-value=18 Score=25.59 Aligned_cols=26 Identities=15% Similarity=0.070 Sum_probs=19.6
Q ss_pred CCCCCCCCceEEEEECCceeEEcCCCCCC
Q 015345 250 GKAFVDGKKIDFITAGGRTTAYVPELQKL 278 (408)
Q Consensus 250 C~~~~CG~~I~~~~vgGRtT~~CP~CQ~~ 278 (408)
|| .||..- .+.=..+..+.|+.|-..
T Consensus 3 Cp--~Cg~~~-~~~D~~~g~~vC~~CG~V 28 (43)
T PF08271_consen 3 CP--NCGSKE-IVFDPERGELVCPNCGLV 28 (43)
T ss_dssp BT--TTSSSE-EEEETTTTEEEETTT-BB
T ss_pred Cc--CCcCCc-eEEcCCCCeEECCCCCCE
Confidence 66 999975 344478999999999654
No 69
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=49.94 E-value=11 Score=27.07 Aligned_cols=25 Identities=16% Similarity=0.122 Sum_probs=18.6
Q ss_pred CCCCCCCCceEEEEECCceeEEcCCCCCC
Q 015345 250 GKAFVDGKKIDFITAGGRTTAYVPELQKL 278 (408)
Q Consensus 250 C~~~~CG~~I~~~~vgGRtT~~CP~CQ~~ 278 (408)
|+ .||..+...... +..-||.|...
T Consensus 6 C~--~CG~~~~~~~~~--~~~~Cp~CG~~ 30 (46)
T PRK00398 6 CA--RCGREVELDEYG--TGVRCPYCGYR 30 (46)
T ss_pred CC--CCCCEEEECCCC--CceECCCCCCe
Confidence 66 999987755322 28999999874
No 70
>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=49.11 E-value=8.8 Score=34.48 Aligned_cols=52 Identities=15% Similarity=0.065 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHHHHHHHHcCCCC-CCCCCceEEEccCCCCCCCCCCCCceEEEEECCceeEEcCCCCCC
Q 015345 211 SCATLLKCIKEVIEKALEVGADS-SQFPSNWIFHSREKKPGKAFVDGKKIDFITAGGRTTAYVPELQKL 278 (408)
Q Consensus 211 e~~~L~~ai~~VL~~Ai~~gg~s-~~f~~~~~vy~R~g~pC~~~~CG~~I~~~~vgGRtT~~CP~CQ~~ 278 (408)
++..--..-...+...|+.|.-. ..|+. -+-||. +||++|..- -||+.|+..
T Consensus 51 eV~e~tgVs~~~I~~~IreGRL~~~~~~n-------l~~~CE--~CG~~I~~G-------r~C~~C~~~ 103 (137)
T TIGR03826 51 EIVEETGVSEKLILKFIREGRLQLKHFPN-------LGYPCE--RCGTSIREG-------RLCDSCAGE 103 (137)
T ss_pred HHHHHHCcCHHHHHHHHHcCCeeccCCCC-------CcCccc--ccCCcCCCC-------CccHHHHHH
Confidence 33333333444555556555432 11221 235898 999998732 699999995
No 71
>PRK10664 transcriptional regulator HU subunit beta; Provisional
Probab=47.78 E-value=86 Score=25.77 Aligned_cols=67 Identities=21% Similarity=0.396 Sum_probs=47.8
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHcCCCC--CCCCCceEEEccCCCCCCCCCCCCceEEEEECCceeEEcCC
Q 015345 205 VSLSKESCATLLKCIKEVIEKALEVGADS--SQFPSNWIFHSREKKPGKAFVDGKKIDFITAGGRTTAYVPE 274 (408)
Q Consensus 205 ~~Ls~~e~~~L~~ai~~VL~~Ai~~gg~s--~~f~~~~~vy~R~g~pC~~~~CG~~I~~~~vgGRtT~~CP~ 274 (408)
..||..++..+++++-.++..++..|+.- ..|+. |.+..|....+..|.-|.+|.. -+.+...|.|.
T Consensus 14 ~~~s~~~~~~~v~~~~~~i~~~L~~~~~v~l~gfG~-F~v~~r~aR~grNP~Tge~i~i--~a~~~v~Fk~s 82 (90)
T PRK10664 14 ADISKAAAGRALDAIIASVTESLKEGDDVALVGFGT-FAVKERAARTGRNPQTGKEITI--AAAKVPSFRAG 82 (90)
T ss_pred hCCCHHHHHHHHHHHHHHHHHHHhCCCEEEECCcEE-EEEEEeCCccccCCCCCCEEEE--cCcccEEEEEC
Confidence 35899999999999999999999998854 23443 3445566666766788887652 25566666553
No 72
>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=47.58 E-value=23 Score=34.47 Aligned_cols=57 Identities=26% Similarity=0.308 Sum_probs=41.8
Q ss_pred HHHHH-HHcCCCchhHHHHhCCCccccCchhh-hhhHhhhcccCccCcCCCCCHHHHHHHHHHHH
Q 015345 158 DEFTD-SLSKKKITIKALLLDQSYISGIGNWV-ADEVLYQAKIHPLQTAVSLSKESCATLLKCIK 220 (408)
Q Consensus 158 e~f~~-~l~k~k~~IK~lLLDQ~iiAGIGNiY-adEILF~AgIhP~~~~~~Ls~~e~~~L~~ai~ 220 (408)
++|.+ .+..++.+|+..|-- +++.- .++++..+||+|..++..|+.+++.+|++.+.
T Consensus 203 ~~~~~~~F~~rrk~l~~~L~~------~~~~~~~~~~~~~~~i~~~~r~~~ls~~~~~~l~~~l~ 261 (262)
T PF00398_consen 203 EYFVRQLFSQRRKTLRNSLKS------LFPGEQLEELLEKAGIDPNARAEELSPEQFLKLFKYLN 261 (262)
T ss_dssp HHHHHHHHTTTTSBHHHHTTC------THHHHHHHHHHHHCTHTTTTCGGCHHHHHHHHHHHHHH
T ss_pred HHHHHHHHhCcchHHHHHHhh------hcCHHHHHHhhhhcCCCCCCCcccCCHHHHHHHHHHhh
Confidence 34433 456788899887652 33222 35556669999999999999999999998875
No 73
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=47.57 E-value=13 Score=32.02 Aligned_cols=75 Identities=15% Similarity=0.032 Sum_probs=44.0
Q ss_pred CCCCCCCCCCceEEEEECCceeEEcCCCCCCCccchhhhhCCCCCcCCCCCCCCCcc-cCCCCCCCCCchhhhhhhhccc
Q 015345 248 KPGKAFVDGKKIDFITAGGRTTAYVPELQKLNGVQAAKAVGKPRKQAPKGEDSKDDD-KYNSGDESESDGEEIAENVKSK 326 (408)
Q Consensus 248 ~pC~~~~CG~~I~~~~vgGRtT~~CP~CQ~~~~~~~~~~~~~~~~~~~~~~~~k~~~-~~~~~~~~~~~~~~~~~~~~~~ 326 (408)
.+|| .|++.-. +--...|+||.|-..-...+..+.. ...... .+..-.+.|.|+..+.+--|.|
T Consensus 4 p~cp--~c~sEyt---Yed~~~~~cpec~~ew~~~~~~~~~----------~~~~~v~DsnGn~L~dGDsV~lIKDLkVK 68 (112)
T COG2824 4 PPCP--KCNSEYT---YEDGGQLICPECAHEWNENEAAEEA----------DEALIVKDSNGNLLADGDSVTLIKDLKVK 68 (112)
T ss_pred CCCC--ccCCceE---EecCceEeCchhccccccccccccc----------cCceEEEcCCCcEeccCCeEEEEEeeeec
Confidence 4677 8987744 3344499999999864321111111 111112 3334447888888888888888
Q ss_pred cccccCCCCCC
Q 015345 327 KRQKLGGQVKQ 337 (408)
Q Consensus 327 ~~~~~~~~~~~ 337 (408)
++-..=+++.+
T Consensus 69 Gss~~lK~GTk 79 (112)
T COG2824 69 GSSKVLKQGTK 79 (112)
T ss_pred CCcceeecccE
Confidence 87655444443
No 74
>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=46.85 E-value=11 Score=39.51 Aligned_cols=64 Identities=25% Similarity=0.291 Sum_probs=47.3
Q ss_pred CCCCHHHHHHHHc-----CCCchhHHHHhCCCccccCchhhhhhHhhhccc-CccCcCCCCCHHHHHHHHHHHHH
Q 015345 153 EPMTVDEFTDSLS-----KKKITIKALLLDQSYISGIGNWVADEVLYQAKI-HPLQTAVSLSKESCATLLKCIKE 221 (408)
Q Consensus 153 ~~f~~e~f~~~l~-----k~k~~IK~lLLDQ~iiAGIGNiYadEILF~AgI-hP~~~~~~Ls~~e~~~L~~ai~~ 221 (408)
++++.+.+.+.|. ..++.|+.+|.. -+=+=++..+|-+++| .|.+++++|+.+++.+|.+.++.
T Consensus 270 p~~~~e~l~~~l~~~~~~~~~~~~~~~l~~-----~lp~rl~~~ll~~~~i~~~~~~~~~l~~~~~~~L~~~lk~ 339 (409)
T PF03486_consen 270 PDLSEEELEELLQERKEKNPKRTLKNFLKG-----LLPKRLALALLKRAGIKDPDKKVSELSKKERNRLANLLKR 339 (409)
T ss_dssp TTS-HHHHHHHHHHHHHHTTTSBHHHHHTT-----TS-HHHHHHHHHHTTS-STTSBGGGS-HHHHHHHHHHHHC
T ss_pred CCCCHHHHHHHHHHHHHHHHhhHHHHHHHH-----HhHHHHHHHHHHHcCCCccccchhhcCHHHHHHHHHHHHh
Confidence 4577666666553 356788888642 2445678899999999 99999999999999999988873
No 75
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=45.84 E-value=12 Score=36.75 Aligned_cols=29 Identities=14% Similarity=0.102 Sum_probs=11.2
Q ss_pred CCCCCCCCCc-eEEEEECCc-eeEEcCCCCCCC
Q 015345 249 PGKAFVDGKK-IDFITAGGR-TTAYVPELQKLN 279 (408)
Q Consensus 249 pC~~~~CG~~-I~~~~vgGR-tT~~CP~CQ~~~ 279 (408)
-|| .||.. |....-+.. .-||||.|+-..
T Consensus 33 yCP--~Cg~~~L~~f~NN~PVaDF~C~~C~eey 63 (254)
T PF06044_consen 33 YCP--NCGSKPLSKFENNRPVADFYCPNCNEEY 63 (254)
T ss_dssp --T--TT--SS-EE--------EEE-TTT--EE
T ss_pred cCC--CCCChhHhhccCCCccceeECCCCchHH
Confidence 477 99998 766643333 249999999864
No 76
>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=45.49 E-value=14 Score=29.64 Aligned_cols=24 Identities=8% Similarity=-0.074 Sum_probs=13.7
Q ss_pred CCCCCCCCCceEEEEECCceeEEcCCCCCC
Q 015345 249 PGKAFVDGKKIDFITAGGRTTAYVPELQKL 278 (408)
Q Consensus 249 pC~~~~CG~~I~~~~vgGRtT~~CP~CQ~~ 278 (408)
.|| .|+.++.... ..|+|..||..
T Consensus 3 ~CP--~C~~~L~~~~----~~~~C~~C~~~ 26 (70)
T PF07191_consen 3 TCP--KCQQELEWQG----GHYHCEACQKD 26 (70)
T ss_dssp B-S--SS-SBEEEET----TEEEETTT--E
T ss_pred cCC--CCCCccEEeC----CEEECcccccc
Confidence 366 8999977553 56777777763
No 77
>COG2081 Predicted flavoproteins [General function prediction only]
Probab=45.42 E-value=34 Score=36.03 Aligned_cols=63 Identities=22% Similarity=0.289 Sum_probs=50.4
Q ss_pred CCCCHHHHHHHHcC--CCchhHHHHhCCCccccCchhhhhhHhhhcccCccCcCCCCCHHHHHHHHHHHHH
Q 015345 153 EPMTVDEFTDSLSK--KKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKE 221 (408)
Q Consensus 153 ~~f~~e~f~~~l~k--~k~~IK~lLLDQ~iiAGIGNiYadEILF~AgIhP~~~~~~Ls~~e~~~L~~ai~~ 221 (408)
++.+.+.+.+.+.+ ++++||.+|-.. ++-=++.=+|=+++| |.....+||..+++.|.+.|+.
T Consensus 268 P~~~~~~l~~~l~~~~~~kslkn~L~~~-----lp~rlv~~~l~~~~i-~~~~~~~ls~~~~~~l~~~ik~ 332 (408)
T COG2081 268 PDVDAEELLRELRRANPKKSLKNALAKL-----LPKRLVEFLLERAGI-PDEPLAQLSPKELAQLAAALKA 332 (408)
T ss_pred CCCCHHHHHHHHHhhChhhHHHHHHHHH-----hhhHHHHHHHHhccC-CCcchhhcCHHHHHHHHHHHhc
Confidence 56788888777654 488999988543 344456667789999 9999999999999999999974
No 78
>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=44.47 E-value=11 Score=34.00 Aligned_cols=25 Identities=20% Similarity=-0.039 Sum_probs=18.9
Q ss_pred CCCCCCCCCceEEEEECCceeEEcCCCCCC
Q 015345 249 PGKAFVDGKKIDFITAGGRTTAYVPELQKL 278 (408)
Q Consensus 249 pC~~~~CG~~I~~~~vgGRtT~~CP~CQ~~ 278 (408)
.|+ .|+..+... +=++|+|+.|+..
T Consensus 36 aC~--~C~kkv~~~---~~~~~~C~~C~~~ 60 (166)
T cd04476 36 ACP--GCNKKVVEE---GNGTYRCEKCNKS 60 (166)
T ss_pred ccc--ccCcccEeC---CCCcEECCCCCCc
Confidence 577 899886532 2289999999985
No 79
>COG3350 Uncharacterized conserved protein [Function unknown]
Probab=43.36 E-value=21 Score=27.07 Aligned_cols=22 Identities=36% Similarity=0.459 Sum_probs=18.8
Q ss_pred CCCCCceE------EEEECCceeEEcCC
Q 015345 253 FVDGKKID------FITAGGRTTAYVPE 274 (408)
Q Consensus 253 ~~CG~~I~------~~~vgGRtT~~CP~ 274 (408)
|+||..|. +..++|-+=|||..
T Consensus 6 PVcgm~v~~~~a~~k~~Y~GktYYFcse 33 (53)
T COG3350 6 PVCGMKVDNENAEYKSSYGGKTYYFCSE 33 (53)
T ss_pred CCcCccccccccceeEEeCCEEEEEeCH
Confidence 59999988 56889999999974
No 80
>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=43.35 E-value=17 Score=32.15 Aligned_cols=26 Identities=15% Similarity=-0.049 Sum_probs=16.8
Q ss_pred CCCCCCCCceEEEEECCceeEEcCCCCCC
Q 015345 250 GKAFVDGKKIDFITAGGRTTAYVPELQKL 278 (408)
Q Consensus 250 C~~~~CG~~I~~~~vgGRtT~~CP~CQ~~ 278 (408)
|+...|+..+... +-++|+|+.|+..
T Consensus 21 C~~~~C~kKv~~~---~~~~y~C~~C~~~ 46 (146)
T PF08646_consen 21 CPNEKCNKKVTEN---GDGSYRCEKCNKT 46 (146)
T ss_dssp -TSTTTS-B-EEE---TTTEEEETTTTEE
T ss_pred CCCccCCCEeecC---CCcEEECCCCCCc
Confidence 5433799876644 4477999999985
No 81
>PF05280 FlhC: Flagellar transcriptional activator (FlhC); InterPro: IPR007944 This family consists of several bacterial flagellar transcriptional activator (FlhC) proteins. FlhC combines with FlhD to form a regulatory complex in Escherichia coli, this complex has been shown to be a global regulator involved in many cellular processes as well as a flagellar transcriptional activator [].; GO: 0003677 DNA binding, 0030092 regulation of flagellum assembly, 0045893 positive regulation of transcription, DNA-dependent; PDB: 2AVU_E.
Probab=43.21 E-value=8.5 Score=35.91 Aligned_cols=30 Identities=17% Similarity=0.064 Sum_probs=10.0
Q ss_pred CCCCCCCCCceEEEEECCceeEEcCCCCCCCc
Q 015345 249 PGKAFVDGKKIDFITAGGRTTAYVPELQKLNG 280 (408)
Q Consensus 249 pC~~~~CG~~I~~~~vgGRtT~~CP~CQ~~~~ 280 (408)
+|. .||+.-......-+..|.||-||+...
T Consensus 136 ~C~--~C~~~fv~~~~~~~~~~~Cp~C~~psR 165 (175)
T PF05280_consen 136 PCR--RCGGHFVTHAHDPRHSFVCPFCQPPSR 165 (175)
T ss_dssp E-T--TT--EEEEESS--SS----TT------
T ss_pred CCC--CCCCCeECcCCCCCcCcCCCCCCCccc
Confidence 577 899875533333388999999998643
No 82
>TIGR00988 hip integration host factor, beta subunit. This protein forms a site-specific DNA-binding heterodimer with the homologous integration host factor alpha subunit. It is closely related to the DNA-binding protein HU.
Probab=42.96 E-value=1.2e+02 Score=24.67 Aligned_cols=66 Identities=21% Similarity=0.324 Sum_probs=44.7
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHcCCCC--CCCCCceEEEccCCCCCCCCCCCCceEEEEECCcee-EEcCC
Q 015345 205 VSLSKESCATLLKCIKEVIEKALEVGADS--SQFPSNWIFHSREKKPGKAFVDGKKIDFITAGGRTT-AYVPE 274 (408)
Q Consensus 205 ~~Ls~~e~~~L~~ai~~VL~~Ai~~gg~s--~~f~~~~~vy~R~g~pC~~~~CG~~I~~~~vgGRtT-~~CP~ 274 (408)
..||..++..+++++-.+|..++..|+.- ..|+.-+ +..|....+..|.-|.+| .+.++.. .|.|.
T Consensus 15 ~~~s~~~v~~vv~~~~~~i~~~L~~g~~V~l~gfG~F~-~~~r~~r~~~np~tge~i---~I~~~~~~~F~ps 83 (94)
T TIGR00988 15 SHLPAKDVEDAVKTMLEHMASALAQGDRIEIRGFGSFS-LHYRAPRTGRNPKTGDSV---ELDGKYVPHFKPG 83 (94)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHcCCeEEEcCcEEEE-EEEeCCccccCCCCCCEE---EEcCcccEEEecC
Confidence 35899999999999999999999998854 3454433 333544444444566654 3445544 77765
No 83
>PRK10753 transcriptional regulator HU subunit alpha; Provisional
Probab=42.85 E-value=1.2e+02 Score=24.78 Aligned_cols=67 Identities=24% Similarity=0.377 Sum_probs=46.8
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHcCCCC--CCCCCceEEEccCCCCCCCCCCCCceEEEEECCceeEEcCC
Q 015345 205 VSLSKESCATLLKCIKEVIEKALEVGADS--SQFPSNWIFHSREKKPGKAFVDGKKIDFITAGGRTTAYVPE 274 (408)
Q Consensus 205 ~~Ls~~e~~~L~~ai~~VL~~Ai~~gg~s--~~f~~~~~vy~R~g~pC~~~~CG~~I~~~~vgGRtT~~CP~ 274 (408)
..||..++..+++++-.+|.+++..|+.- ..|+. |.+..|.......|.-|.+|. .-+.+..+|.|.
T Consensus 14 ~~~s~~~~~~~v~~~~~~i~~~L~~g~~V~i~gfG~-F~v~~r~~R~grNP~Tge~i~--i~a~~~v~Fk~s 82 (90)
T PRK10753 14 AELSKTQAKAALESTLAAITESLKEGDAVQLVGFGT-FKVNHRAERTGRNPQTGKEIK--IAAANVPAFVSG 82 (90)
T ss_pred hCCCHHHHHHHHHHHHHHHHHHHHcCCeEEEcCCEE-EEEeeeCCccccCCCCCCEEE--EcCCccEEEecC
Confidence 35899999999999999999999998854 34543 334445555555567787764 235566666664
No 84
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=42.61 E-value=8.2 Score=24.59 Aligned_cols=21 Identities=19% Similarity=0.229 Sum_probs=15.0
Q ss_pred CCCCCCCCCceEEEEECCceeEEcCCCCC
Q 015345 249 PGKAFVDGKKIDFITAGGRTTAYVPELQK 277 (408)
Q Consensus 249 pC~~~~CG~~I~~~~vgGRtT~~CP~CQ~ 277 (408)
.|+ .||..|. -..-|||.|-.
T Consensus 4 ~Cp--~Cg~~~~------~~~~fC~~CG~ 24 (26)
T PF13248_consen 4 FCP--NCGAEID------PDAKFCPNCGA 24 (26)
T ss_pred CCc--ccCCcCC------cccccChhhCC
Confidence 576 8998654 34679999864
No 85
>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=42.59 E-value=17 Score=23.18 Aligned_cols=21 Identities=14% Similarity=0.018 Sum_probs=13.6
Q ss_pred CCCCceEEEEECCceeEEcCCCC
Q 015345 254 VDGKKIDFITAGGRTTAYVPELQ 276 (408)
Q Consensus 254 ~CG~~I~~~~vgGRtT~~CP~CQ 276 (408)
.||..|.-.. .-..|.||+|-
T Consensus 3 sC~~~i~~r~--~~v~f~CPnCG 23 (24)
T PF07754_consen 3 SCGRPIAPRE--QAVPFPCPNCG 23 (24)
T ss_pred cCCCcccCcc--cCceEeCCCCC
Confidence 7887665221 23589999994
No 86
>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=41.16 E-value=19 Score=24.54 Aligned_cols=28 Identities=4% Similarity=-0.040 Sum_probs=18.1
Q ss_pred CCCCCCCCCceEEE--EEC-CceeEEcCCCCCC
Q 015345 249 PGKAFVDGKKIDFI--TAG-GRTTAYVPELQKL 278 (408)
Q Consensus 249 pC~~~~CG~~I~~~--~vg-GRtT~~CP~CQ~~ 278 (408)
.|| .||+.+.-- .++ ......||+|+..
T Consensus 4 ~CP--~C~~~~~v~~~~~~~~~~~v~C~~C~~~ 34 (38)
T TIGR02098 4 QCP--NCKTSFRVVDSQLGANGGKVRCGKCGHV 34 (38)
T ss_pred ECC--CCCCEEEeCHHHcCCCCCEEECCCCCCE
Confidence 366 999875533 221 2237899999975
No 87
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=40.99 E-value=6 Score=29.63 Aligned_cols=30 Identities=7% Similarity=0.049 Sum_probs=21.5
Q ss_pred CCCCCCCCCCCceEEEEE----CCceeEEcCCCCCC
Q 015345 247 KKPGKAFVDGKKIDFITA----GGRTTAYVPELQKL 278 (408)
Q Consensus 247 g~pC~~~~CG~~I~~~~v----gGRtT~~CP~CQ~~ 278 (408)
+..|. -|+..|....+ .+....+||+|+++
T Consensus 22 ~~~C~--gC~~~l~~~~~~~i~~~~~i~~Cp~CgRi 55 (56)
T PF02591_consen 22 GGTCS--GCHMELPPQELNEIRKGDEIVFCPNCGRI 55 (56)
T ss_pred CCccC--CCCEEcCHHHHHHHHcCCCeEECcCCCcc
Confidence 34677 79887764432 35789999999974
No 88
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=40.80 E-value=13 Score=38.83 Aligned_cols=28 Identities=11% Similarity=0.052 Sum_probs=24.8
Q ss_pred CCCCCCCCCceEEEEECCceeEEcCCCCCC
Q 015345 249 PGKAFVDGKKIDFITAGGRTTAYVPELQKL 278 (408)
Q Consensus 249 pC~~~~CG~~I~~~~vgGRtT~~CP~CQ~~ 278 (408)
.|+ .|+-.+.--.+.+-.+.|||+|+..
T Consensus 20 ~C~--eCd~~~~~P~l~~~q~A~CPRC~~~ 47 (418)
T COG2995 20 LCP--ECDMLVSLPRLDSGQSAYCPRCGHT 47 (418)
T ss_pred cCC--CCCceeccccCCCCCcccCCCCCCc
Confidence 466 9999988889999999999999985
No 89
>KOG3064 consensus RNA-binding nuclear protein (MAK16) containing a distinct C4 Zn-finger [RNA processing and modification]
Probab=40.39 E-value=18 Score=35.85 Aligned_cols=26 Identities=35% Similarity=0.314 Sum_probs=10.1
Q ss_pred CCCCchhhhhhhhccccccccCCCCC
Q 015345 311 ESESDGEEIAENVKSKKRQKLGGQVK 336 (408)
Q Consensus 311 ~~~~~~~~~~~~~~~~~~~~~~~~~~ 336 (408)
+||+|++|..+...++++.+-+++++
T Consensus 253 esd~de~Ee~K~~~k~kk~~~~~k~k 278 (303)
T KOG3064|consen 253 ESDSDEIEENKKESKKKKGKKAAKGK 278 (303)
T ss_pred CCchhhHHHhhhhhhhcccCCCcccc
Confidence 33444444433333333333333333
No 90
>COG0776 HimA Bacterial nucleoid DNA-binding protein [DNA replication, recombination, and repair]
Probab=39.80 E-value=82 Score=26.55 Aligned_cols=53 Identities=25% Similarity=0.390 Sum_probs=42.9
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHcCCCCC--CCCCceEEEccCCCCCCCCCCCCceE
Q 015345 207 LSKESCATLLKCIKEVIEKALEVGADSS--QFPSNWIFHSREKKPGKAFVDGKKID 260 (408)
Q Consensus 207 Ls~~e~~~L~~ai~~VL~~Ai~~gg~s~--~f~~~~~vy~R~g~pC~~~~CG~~I~ 260 (408)
|+..+++.+++++-..|..|+..|.... .| ..|.+..|...+...|.-|..|.
T Consensus 17 l~k~~a~~~v~~~~~~i~~aL~~G~~V~l~gF-G~F~v~~R~aR~GRNPkTGe~i~ 71 (94)
T COG0776 17 LSKKDAEEAVDAFLEEITEALAKGERVELRGF-GTFEVRERAARTGRNPKTGEEIK 71 (94)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHcCCeEEEeee-eeeEeeccCCCCCCCCCCCCeEe
Confidence 8999999999999999999999987652 34 35677788777777777887765
No 91
>PRK12366 replication factor A; Reviewed
Probab=39.40 E-value=17 Score=40.36 Aligned_cols=24 Identities=4% Similarity=-0.164 Sum_probs=18.7
Q ss_pred CCCCCCCCCceEEEEECCceeEEcCCCCCC
Q 015345 249 PGKAFVDGKKIDFITAGGRTTAYVPELQKL 278 (408)
Q Consensus 249 pC~~~~CG~~I~~~~vgGRtT~~CP~CQ~~ 278 (408)
.|| .|...+. .+...|+||.|+..
T Consensus 534 aCp--~CnkKv~----~~~g~~~C~~c~~~ 557 (637)
T PRK12366 534 LCP--NCRKRVE----EVDGEYICEFCGEV 557 (637)
T ss_pred ccc--ccCeEeE----cCCCcEECCCCCCC
Confidence 477 8987764 35689999999985
No 92
>cd01675 RNR_III Class III ribonucleotide reductase. Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit w
Probab=38.75 E-value=16 Score=39.81 Aligned_cols=93 Identities=15% Similarity=0.159 Sum_probs=60.1
Q ss_pred hHHHHhCCC----ccccCc--hhhh--------------hhHhhhcccCccCcCCCCCHHHHHHH---HHHHHHHHHHHH
Q 015345 171 IKALLLDQS----YISGIG--NWVA--------------DEVLYQAKIHPLQTAVSLSKESCATL---LKCIKEVIEKAL 227 (408)
Q Consensus 171 IK~lLLDQ~----iiAGIG--NiYa--------------dEILF~AgIhP~~~~~~Ls~~e~~~L---~~ai~~VL~~Ai 227 (408)
-+-+.+|-. ++.|+- ++|- +=|-+.+..||...++.++--++... .+++..+++.|.
T Consensus 426 ~rfa~~D~~~~g~i~~g~~d~~yyTNS~hipv~~~~~~~eki~~e~~f~~~~~GG~i~hv~l~e~~~n~~al~~lv~~a~ 505 (555)
T cd01675 426 YRFAKKDRKKYGDIIPGVTDKPYYTNSFHVPVYEDIDPFEKIDIEAKLHPLTTGGHILHIELGEAKPNPEALEALVKKAA 505 (555)
T ss_pred HHHHHHHHHHcCccCCCCCCCCCCCCCEEeeCCCCCCHHHHHHhhcccccccCCceEEEEECCCCCCCHHHHHHHHHHHH
Confidence 444567775 666664 2333 45678999999999887765544444 467777888887
Q ss_pred HcCCCCCCCCCceEEEccCCCCCCCCCCCCceEEEEECCceeEEcCCCCCC
Q 015345 228 EVGADSSQFPSNWIFHSREKKPGKAFVDGKKIDFITAGGRTTAYVPELQKL 278 (408)
Q Consensus 228 ~~gg~s~~f~~~~~vy~R~g~pC~~~~CG~~I~~~~vgGRtT~~CP~CQ~~ 278 (408)
+.| -..+-++...- .|. .||.... +..+-||.|...
T Consensus 506 ~~~------~~y~~~~~p~~-~C~--~CG~~~~------~~~~~CP~CGs~ 541 (555)
T cd01675 506 KRG------VIYFGINTPID-ICN--DCGYIGE------GEGFKCPKCGSE 541 (555)
T ss_pred HcC------CceEEEecCCc-cCC--CCCCCCc------CCCCCCcCCCCc
Confidence 754 12334454444 677 8996432 445899999853
No 93
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=38.15 E-value=10 Score=29.78 Aligned_cols=31 Identities=10% Similarity=0.035 Sum_probs=25.2
Q ss_pred CCCCCCCCCCCceEEEEECCceeEEcCCCCCCC
Q 015345 247 KKPGKAFVDGKKIDFITAGGRTTAYVPELQKLN 279 (408)
Q Consensus 247 g~pC~~~~CG~~I~~~~vgGRtT~~CP~CQ~~~ 279 (408)
.-+|| .||+++......-=--|-|.+||-+.
T Consensus 7 ~v~CP--~Cgkpv~w~~~s~frPFCSkRCklID 37 (65)
T COG3024 7 TVPCP--TCGKPVVWGEESPFRPFCSKRCKLID 37 (65)
T ss_pred cccCC--CCCCcccccccCCcCcchhHhhhhcc
Confidence 45788 99999998877777778889999863
No 94
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=38.15 E-value=38 Score=29.23 Aligned_cols=30 Identities=13% Similarity=0.018 Sum_probs=21.3
Q ss_pred CCCCCCCCCCCceEEEEECCceeEEcCCCCCCCcc
Q 015345 247 KKPGKAFVDGKKIDFITAGGRTTAYVPELQKLNGV 281 (408)
Q Consensus 247 g~pC~~~~CG~~I~~~~vgGRtT~~CP~CQ~~~~~ 281 (408)
++.|+ .||+. ..=-+|.-..||.|......
T Consensus 9 KR~Cp--~CG~k---FYDLnk~PivCP~CG~~~~~ 38 (108)
T PF09538_consen 9 KRTCP--SCGAK---FYDLNKDPIVCPKCGTEFPP 38 (108)
T ss_pred cccCC--CCcch---hccCCCCCccCCCCCCccCc
Confidence 46787 99976 22346677889999997543
No 95
>PRK10220 hypothetical protein; Provisional
Probab=37.50 E-value=35 Score=29.61 Aligned_cols=66 Identities=14% Similarity=0.028 Sum_probs=41.0
Q ss_pred CCCCCCCCCceEEEEECCceeEEcCCCCCCCccchhhhhCCCCCcCCCCCCCCCcccCCCCC-CCCCchhhhhhhhcccc
Q 015345 249 PGKAFVDGKKIDFITAGGRTTAYVPELQKLNGVQAAKAVGKPRKQAPKGEDSKDDDKYNSGD-ESESDGEEIAENVKSKK 327 (408)
Q Consensus 249 pC~~~~CG~~I~~~~vgGRtT~~CP~CQ~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~-~~~~~~~~~~~~~~~~~ 327 (408)
+|| .|+.. .++.-...|.||.|...-...+.++.+ . ....+-.+|. +.|.|..-..+.-|.|+
T Consensus 5 ~CP--~C~se---ytY~d~~~~vCpeC~hEW~~~~~~~~~--~---------~~~vkDsnG~~L~dGDsV~viKDLkVKG 68 (111)
T PRK10220 5 HCP--KCNSE---YTYEDNGMYICPECAHEWNDAEPAQES--D---------ELIVKDANGNLLADGDSVTIVKDLKVKG 68 (111)
T ss_pred cCC--CCCCc---ceEcCCCeEECCcccCcCCcccccccc--C---------CceEEcCCCCCccCCCEEEEEeeccccc
Confidence 566 99876 456677789999999964332111100 0 0113444554 78888888888878877
Q ss_pred ccc
Q 015345 328 RQK 330 (408)
Q Consensus 328 ~~~ 330 (408)
+-.
T Consensus 69 ss~ 71 (111)
T PRK10220 69 SSS 71 (111)
T ss_pred ccc
Confidence 543
No 96
>PRK00199 ihfB integration host factor subunit beta; Reviewed
Probab=37.05 E-value=1.1e+02 Score=25.08 Aligned_cols=54 Identities=28% Similarity=0.313 Sum_probs=37.5
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHcCCCC--CCCCCceEEEccCCCCCCCCCCCCce
Q 015345 205 VSLSKESCATLLKCIKEVIEKALEVGADS--SQFPSNWIFHSREKKPGKAFVDGKKI 259 (408)
Q Consensus 205 ~~Ls~~e~~~L~~ai~~VL~~Ai~~gg~s--~~f~~~~~vy~R~g~pC~~~~CG~~I 259 (408)
..||..++..+++++..+|..++..|+.- ..|+.-. +..|....+..|.-|..|
T Consensus 15 ~~~s~~~~~~vv~~~~~~i~~~L~~g~~V~l~gfG~F~-~~~r~~r~~~np~Tge~i 70 (94)
T PRK00199 15 PHLSAKDVENAVKEILEEMSDALARGDRIEIRGFGSFS-LHYRPPRVGRNPKTGEKV 70 (94)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHcCCeEEEcCCEEEE-EEEecCeeccCcCCCCEE
Confidence 46999999999999999999999999864 3454333 333444444444555554
No 97
>KOG2923 consensus Uncharacterized conserved protein [Function unknown]
Probab=37.05 E-value=22 Score=28.07 Aligned_cols=28 Identities=18% Similarity=0.307 Sum_probs=20.6
Q ss_pred CCCCCCCCCCceEEE---EECCceeEEcCCCCCC
Q 015345 248 KPGKAFVDGKKIDFI---TAGGRTTAYVPELQKL 278 (408)
Q Consensus 248 ~pC~~~~CG~~I~~~---~vgGRtT~~CP~CQ~~ 278 (408)
-||| ||...... ...|+...-||.|-=.
T Consensus 23 yPCp---CGDrf~It~edL~~ge~Va~CpsCSL~ 53 (67)
T KOG2923|consen 23 YPCP---CGDRFQITLEDLENGEDVARCPSCSLI 53 (67)
T ss_pred cCCC---CCCeeeecHHHHhCCCeeecCCCceEE
Confidence 4886 99874422 3469999999999653
No 98
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=36.53 E-value=33 Score=29.90 Aligned_cols=20 Identities=15% Similarity=0.029 Sum_probs=15.7
Q ss_pred CCCCCceEEEEECCceeEEcCCCCCC
Q 015345 253 FVDGKKIDFITAGGRTTAYVPELQKL 278 (408)
Q Consensus 253 ~~CG~~I~~~~vgGRtT~~CP~CQ~~ 278 (408)
|+||.++.-. -+.||+|...
T Consensus 2 PvCg~~l~vt------~l~C~~C~t~ 21 (113)
T PF09862_consen 2 PVCGGELVVT------RLKCPSCGTE 21 (113)
T ss_pred CCCCCceEEE------EEEcCCCCCE
Confidence 3999987754 3689999984
No 99
>TIGR00987 himA integration host factor, alpha subunit. This protein forms a site-specific DNA-binding heterodimer with the integration host factor beta subunit. It is closely related to the DNA-binding protein HU.
Probab=35.59 E-value=1.6e+02 Score=24.13 Aligned_cols=66 Identities=27% Similarity=0.434 Sum_probs=43.9
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHcCCCC--CCCCCceEEEccCCCCCCCCCCCCceEEEEECC-ceeEEcCC
Q 015345 205 VSLSKESCATLLKCIKEVIEKALEVGADS--SQFPSNWIFHSREKKPGKAFVDGKKIDFITAGG-RTTAYVPE 274 (408)
Q Consensus 205 ~~Ls~~e~~~L~~ai~~VL~~Ai~~gg~s--~~f~~~~~vy~R~g~pC~~~~CG~~I~~~~vgG-RtT~~CP~ 274 (408)
..+|..+++.+++++..+|.+++..|+.- ..|+.-. +..|....+..|.-|..|. +.. +...|.|.
T Consensus 15 ~~~s~~~v~~vv~~~~~~i~~~L~~g~~V~l~gfG~F~-~~~r~~r~~~np~t~e~~~---i~~~~~v~Fkps 83 (96)
T TIGR00987 15 LGLSKREAKELVELFFEEIRRALENGEQVKLSGFGNFD-LRDKNQRPGRNPKTGEEIP---ITARRVVTFRPG 83 (96)
T ss_pred hCcCHHHHHHHHHHHHHHHHHHHHcCCeEEecCCEEEE-EEEEcCccCcCCCCCCEEE---EeCCccEEEeeC
Confidence 35899999999999999999999998754 3454333 3334333444446676654 444 44477764
No 100
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=35.17 E-value=35 Score=26.57 Aligned_cols=28 Identities=18% Similarity=0.307 Sum_probs=21.1
Q ss_pred CCCCCCCCCCceEEE---EECCceeEEcCCCCCC
Q 015345 248 KPGKAFVDGKKIDFI---TAGGRTTAYVPELQKL 278 (408)
Q Consensus 248 ~pC~~~~CG~~I~~~---~vgGRtT~~CP~CQ~~ 278 (408)
-||| ||...... ...|-...-||.|--+
T Consensus 23 yPCP---CGDRFeIsLeDl~~GE~VArCPSCSLi 53 (67)
T COG5216 23 YPCP---CGDRFEISLEDLRNGEVVARCPSCSLI 53 (67)
T ss_pred ecCC---CCCEeEEEHHHhhCCceEEEcCCceEE
Confidence 3897 99876533 3468899999999754
No 101
>PRK14973 DNA topoisomerase I; Provisional
Probab=34.50 E-value=27 Score=40.60 Aligned_cols=30 Identities=10% Similarity=0.077 Sum_probs=21.5
Q ss_pred CCCCCCCCCCceEEE-EECCceeEE-cCCCCCCC
Q 015345 248 KPGKAFVDGKKIDFI-TAGGRTTAY-VPELQKLN 279 (408)
Q Consensus 248 ~pC~~~~CG~~I~~~-~vgGRtT~~-CP~CQ~~~ 279 (408)
..|+ .||.++.++ ..|-+.-|+ ||.|.-..
T Consensus 636 ~~Cp--~CG~p~~~~~r~Gr~g~fl~CP~C~~~~ 667 (936)
T PRK14973 636 EVCP--IHHLNHVRLIRKGARPWDIGCPLCSHIE 667 (936)
T ss_pred CCCC--CCCCCceEEeecCCCcccccCccccchh
Confidence 4577 999985544 555556677 99998853
No 102
>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=34.00 E-value=70 Score=25.41 Aligned_cols=49 Identities=14% Similarity=0.175 Sum_probs=37.9
Q ss_pred cCChhhHHHhhcCC--eEeeeeeeeeEEEEEeCCCCcceeeeceeeeEEEe
Q 015345 37 GVSASDFEASVLGK--AILSAHRKGKNLWLRLDSPPFPSFQFGMTGAIYIK 85 (408)
Q Consensus 37 ~~~~~~f~~~L~G~--~I~~V~RrGK~L~~~l~~~~~L~vHLGMtG~l~i~ 85 (408)
+.+.++|..-..|. +|.-+.+-|.-|+|....=.-.+.|.|..|+|.+.
T Consensus 6 ~is~~~~l~~Y~G~a~~V~v~s~~Gr~v~~Pa~~lRpFvt~~Gv~G~F~l~ 56 (68)
T PF11197_consen 6 NISYQEFLAYYQGAASKVVVRSDDGRRVQFPARHLRPFVTHDGVHGRFRLE 56 (68)
T ss_pred EcCHHHHHHhccccccEEEEEecCCcEEEEeHHHCcceecCCCceEEEEEE
Confidence 35678888888885 78888899999999765434457899999998774
No 103
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=33.81 E-value=15 Score=22.92 Aligned_cols=18 Identities=17% Similarity=0.290 Sum_probs=12.2
Q ss_pred CCCCceEEEEECCceeEEcCCCCC
Q 015345 254 VDGKKIDFITAGGRTTAYVPELQK 277 (408)
Q Consensus 254 ~CG~~I~~~~vgGRtT~~CP~CQ~ 277 (408)
.||..|.. ..-|||.|-.
T Consensus 4 ~CG~~~~~------~~~fC~~CG~ 21 (23)
T PF13240_consen 4 NCGAEIED------DAKFCPNCGT 21 (23)
T ss_pred ccCCCCCC------cCcchhhhCC
Confidence 88888752 3457888853
No 104
>PTZ00338 dimethyladenosine transferase-like protein; Provisional
Probab=31.87 E-value=79 Score=31.64 Aligned_cols=57 Identities=21% Similarity=0.247 Sum_probs=40.8
Q ss_pred HHcCCCchhHHHHhCCCc----------cccCch-----------hhhhhHhhhcccCccCcCCCCCHHHHHHHHHHHH
Q 015345 163 SLSKKKITIKALLLDQSY----------ISGIGN-----------WVADEVLYQAKIHPLQTAVSLSKESCATLLKCIK 220 (408)
Q Consensus 163 ~l~k~k~~IK~lLLDQ~i----------iAGIGN-----------iYadEILF~AgIhP~~~~~~Ls~~e~~~L~~ai~ 220 (408)
.+..+++.|...|-...+ +.+++| --..++|=.+||. ..++.+|+-+++.+|++++.
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 356788999988866432 222121 1123678899985 79999999999999998876
No 105
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=31.74 E-value=32 Score=22.19 Aligned_cols=23 Identities=9% Similarity=0.085 Sum_probs=16.1
Q ss_pred CCCCCCCCCceEEEEECCceeEEcCCCCCCC
Q 015345 249 PGKAFVDGKKIDFITAGGRTTAYVPELQKLN 279 (408)
Q Consensus 249 pC~~~~CG~~I~~~~vgGRtT~~CP~CQ~~~ 279 (408)
.|| .|+..|- -++-+||.|.-..
T Consensus 2 ~CP--~C~~~V~------~~~~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCP--ECGAEVP------ESAKFCPHCGYDF 24 (26)
T ss_pred cCC--CCcCCch------hhcCcCCCCCCCC
Confidence 466 8998874 3456899997643
No 106
>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=31.70 E-value=44 Score=23.68 Aligned_cols=11 Identities=18% Similarity=-0.031 Sum_probs=8.7
Q ss_pred CceeEEcCCCC
Q 015345 266 GRTTAYVPELQ 276 (408)
Q Consensus 266 GRtT~~CP~CQ 276 (408)
-|-.|+||.|+
T Consensus 37 ~~~~y~C~~C~ 47 (47)
T PF13005_consen 37 VRHKYACPCCG 47 (47)
T ss_pred EeceEECCCCC
Confidence 47788898885
No 107
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=30.65 E-value=35 Score=30.54 Aligned_cols=32 Identities=9% Similarity=-0.014 Sum_probs=22.4
Q ss_pred CCCCCCCCCceEEEEEC-------------CceeEEcCCCCCC--Cccc
Q 015345 249 PGKAFVDGKKIDFITAG-------------GRTTAYVPELQKL--NGVQ 282 (408)
Q Consensus 249 pC~~~~CG~~I~~~~vg-------------GRtT~~CP~CQ~~--~~~~ 282 (408)
-|+ .|++++..+.-. ...-|.||.|++. .|.+
T Consensus 93 RC~--~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW~GsH 139 (147)
T PF01927_consen 93 RCP--KCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIYWEGSH 139 (147)
T ss_pred ccC--CCCcEeeechhhccccccCccccccCCeEEECCCCCCEeccccc
Confidence 477 999988755221 3458899999995 4544
No 108
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=30.33 E-value=36 Score=30.07 Aligned_cols=27 Identities=7% Similarity=-0.102 Sum_probs=21.9
Q ss_pred CCCCCCCCCceEEEEECCceeEEcCCCCC
Q 015345 249 PGKAFVDGKKIDFITAGGRTTAYVPELQK 277 (408)
Q Consensus 249 pC~~~~CG~~I~~~~vgGRtT~~CP~CQ~ 277 (408)
.|+ .||..+.+.....+..|.|+.|..
T Consensus 125 ~C~--~C~~~~~r~~~~~~~~~~C~~C~~ 151 (157)
T PF10263_consen 125 RCP--SCGREYKRHRRSKRKRYRCGRCGG 151 (157)
T ss_pred EcC--CCCCEeeeecccchhhEECCCCCC
Confidence 376 899888866555888999999985
No 109
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=29.63 E-value=22 Score=27.62 Aligned_cols=26 Identities=15% Similarity=-0.008 Sum_probs=13.1
Q ss_pred CCCCCCCCCc-eEEEEE--CCceeEEcCCCC
Q 015345 249 PGKAFVDGKK-IDFITA--GGRTTAYVPELQ 276 (408)
Q Consensus 249 pC~~~~CG~~-I~~~~v--gGRtT~~CP~CQ 276 (408)
+|| .||.. |-+-.- -.-.+|-||+|-
T Consensus 29 ~CP--nCGe~~I~Rc~~CRk~g~~Y~Cp~CG 57 (61)
T COG2888 29 PCP--NCGEVEIYRCAKCRKLGNPYRCPKCG 57 (61)
T ss_pred eCC--CCCceeeehhhhHHHcCCceECCCcC
Confidence 566 77733 322110 023567777774
No 110
>PRK14896 ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Provisional
Probab=29.30 E-value=1.3e+02 Score=29.14 Aligned_cols=62 Identities=23% Similarity=0.269 Sum_probs=39.5
Q ss_pred HHHH-HHHcCCCchhHHHHhCCCccccCchhhhhhHhhhc-ccCccCcCCCCCHHHHHHHHHHHHH
Q 015345 158 DEFT-DSLSKKKITIKALLLDQSYISGIGNWVADEVLYQA-KIHPLQTAVSLSKESCATLLKCIKE 221 (408)
Q Consensus 158 e~f~-~~l~k~k~~IK~lLLDQ~iiAGIGNiYadEILF~A-gIhP~~~~~~Ls~~e~~~L~~ai~~ 221 (408)
+.|. ..+..++.+|+..|-.--...+.|.+ +++|-.+ .+.|..++.+||.+++.+|++.+..
T Consensus 193 ~~~~~~~F~~rrk~l~~~l~~~~~~~~~~~~--~~~~~~~~~~~~~~R~e~L~~~~~~~l~~~~~~ 256 (258)
T PRK14896 193 DDFVKALFQHRRKTLRNALKNSAHISGKEDI--KAVVEALPEELLNKRVFQLSPEEIAELANLLYE 256 (258)
T ss_pred HHHHHHHHccccHHHHHHHhhhccccchhHH--HHHHHHcCCCCcCCCCccCCHHHHHHHHHHHHh
Confidence 3443 34677889999988431101122222 2334444 3557999999999999999988754
No 111
>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=26.55 E-value=65 Score=27.78 Aligned_cols=71 Identities=20% Similarity=0.146 Sum_probs=37.6
Q ss_pred HHHHHHhcCCCEEEEEEeccCCceeccCChhhHH---HhhcCCeEeeee--eeeeEEEEEeCCCCcceeeeceeeeEE
Q 015345 11 RRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFE---ASVLGKAILSAH--RKGKNLWLRLDSPPFPSFQFGMTGAIY 83 (408)
Q Consensus 11 ~~~L~~~l~Gk~I~~V~v~~~~~v~~~~~~~~f~---~~L~G~~I~~V~--RrGK~L~~~l~~~~~L~vHLGMtG~l~ 83 (408)
...+...+.|++|.+|.-. ...++-..+.. +. =..+|+-...-. ..=-++.|.|++|..|+++..|+|.+.
T Consensus 41 ~~~~~~~L~G~~i~~v~Rr-GKyl~~~l~~~-~Li~HLgMtG~l~~~~~~~~kh~~l~l~~~dg~~L~f~~~~~~~~~ 116 (117)
T cd08975 41 PNEYDELLVGKRITSAEGF-GGFVEIIFEDK-RLLFNDGVNVRYYYGGEKIPKKYQLLIEFDDDSFLVFTVAMYGGIA 116 (117)
T ss_pred hHHHHHhCCCCEEEeEeeE-eeEEEEEeCCC-EEEEECceEEEEEeCCCCCCCeEEEEEEECCCCEEEEEEEEEeeee
Confidence 3457778999999998754 22232222210 00 012333221100 112245577777777888888888763
No 112
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=26.30 E-value=65 Score=27.42 Aligned_cols=31 Identities=6% Similarity=-0.185 Sum_probs=22.3
Q ss_pred CCCCCCCCCceEEEEEC-CceeEEcCCCCCCCcc
Q 015345 249 PGKAFVDGKKIDFITAG-GRTTAYVPELQKLNGV 281 (408)
Q Consensus 249 pC~~~~CG~~I~~~~vg-GRtT~~CP~CQ~~~~~ 281 (408)
.|| .||.....+.+. |+....||+|.--.+-
T Consensus 23 ~CP--~Cge~~v~v~~~k~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 23 ECP--RCGKVSISVKIKKNIAIITCGNCGLYTEF 54 (99)
T ss_pred ECC--CCCCeEeeeecCCCcceEECCCCCCccCE
Confidence 577 999765544333 8899999999985433
No 113
>KOG0066 consensus eIF2-interacting protein ABC50 (ABC superfamily) [Translation, ribosomal structure and biogenesis]
Probab=25.99 E-value=75 Score=34.41 Aligned_cols=17 Identities=24% Similarity=0.237 Sum_probs=8.7
Q ss_pred cCCCCC----CCCCchhhhhh
Q 015345 305 KYNSGD----ESESDGEEIAE 321 (408)
Q Consensus 305 ~~~~~~----~~~~~~~~~~~ 321 (408)
++|... .+|+|+||..+
T Consensus 92 ~~e~~~~~~~l~~~~~de~~~ 112 (807)
T KOG0066|consen 92 KPEKSLPANDLDDEDDDEAAK 112 (807)
T ss_pred chhhcCcccccCCCCchhhhc
Confidence 555443 55666655443
No 114
>PF12773 DZR: Double zinc ribbon
Probab=25.81 E-value=30 Score=24.88 Aligned_cols=27 Identities=15% Similarity=0.091 Sum_probs=19.2
Q ss_pred CCCCCCCCCCceEEEEECCceeEEcCCCCCCC
Q 015345 248 KPGKAFVDGKKIDFITAGGRTTAYVPELQKLN 279 (408)
Q Consensus 248 ~pC~~~~CG~~I~~~~vgGRtT~~CP~CQ~~~ 279 (408)
.-|+ .||+++. .....+.+||.|-...
T Consensus 13 ~fC~--~CG~~l~---~~~~~~~~C~~Cg~~~ 39 (50)
T PF12773_consen 13 KFCP--HCGTPLP---PPDQSKKICPNCGAEN 39 (50)
T ss_pred cCCh--hhcCChh---hccCCCCCCcCCcCCC
Confidence 3466 7888877 4466778888887753
No 115
>COG4643 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.99 E-value=25 Score=36.15 Aligned_cols=32 Identities=28% Similarity=0.265 Sum_probs=22.8
Q ss_pred CCCCCCCCCCCceEEE--EECCceeEEcCCCCCCCc
Q 015345 247 KKPGKAFVDGKKIDFI--TAGGRTTAYVPELQKLNG 280 (408)
Q Consensus 247 g~pC~~~~CG~~I~~~--~vgGRtT~~CP~CQ~~~~ 280 (408)
+.||| +||..=++. ---||.|+||--|-...|
T Consensus 32 ~~~cp--vcg~k~RFr~dD~kGrGtw~c~y~~~GDG 65 (366)
T COG4643 32 GHPCP--VCGGKDRFRFDDRKGRGTWFCNYCGHGDG 65 (366)
T ss_pred CCCCC--ccCCccccccCCccCCccEEEEeeccCCC
Confidence 34888 999764433 334899999999985433
No 116
>COG4871 Uncharacterized protein conserved in archaea [Function unknown]
Probab=24.45 E-value=1.2e+02 Score=28.41 Aligned_cols=48 Identities=15% Similarity=0.183 Sum_probs=34.6
Q ss_pred CHHHHHHHHHHHHHHHHHHHHcCCCCCCCCC-----ceEEEcc-CCCCCCCCCCCC
Q 015345 208 SKESCATLLKCIKEVIEKALEVGADSSQFPS-----NWIFHSR-EKKPGKAFVDGK 257 (408)
Q Consensus 208 s~~e~~~L~~ai~~VL~~Ai~~gg~s~~f~~-----~~~vy~R-~g~pC~~~~CG~ 257 (408)
.++|...+...+..++++|++.||......+ .+-||.- -+..|. .||.
T Consensus 91 dedEAkeilgel~d~ineA~~kg~d~s~prek~rV~p~dVykyLP~tNCg--~CGE 144 (193)
T COG4871 91 DEDEAKEILGELMDIINEAIAKGGDASDPREKVRVGPMDVYKYLPQTNCG--KCGE 144 (193)
T ss_pred CHHHHHHHHHHHHHHHHHHHHccCCCCCchhhcccChHHHHHhCCCCccc--cchh
Confidence 5789999999999999999999986543221 2233321 467888 8886
No 117
>TIGR02487 NrdD anaerobic ribonucleoside-triphosphate reductase. This model represents the oxygen-sensitive (anaerobic, class III) ribonucleotide reductase. The mechanism of the enzyme involves a glycine-centered radical, a C-terminal zinc binding site, and a set of conserved active site cysteines and asparagines. This enzyme requires an activating component, NrdG, a radical-SAM domain containing enzyme (TIGR02491). Together the two form an alpha-2/beta-2 heterodimer.
Probab=24.44 E-value=45 Score=36.66 Aligned_cols=93 Identities=15% Similarity=0.195 Sum_probs=59.1
Q ss_pred hhHHHHhCCCc---cccCc--hhhh--------------hhHhhhcccCccCcCCCCCHHHHHHH---HHHHHHHHHHHH
Q 015345 170 TIKALLLDQSY---ISGIG--NWVA--------------DEVLYQAKIHPLQTAVSLSKESCATL---LKCIKEVIEKAL 227 (408)
Q Consensus 170 ~IK~lLLDQ~i---iAGIG--NiYa--------------dEILF~AgIhP~~~~~~Ls~~e~~~L---~~ai~~VL~~Ai 227 (408)
.-+-+.||... |+||. .+|. +=|=+.+..||...++.++--++... .+++..|++.|.
T Consensus 432 ~~rfa~~D~~~fg~i~gv~d~~yYTNS~hipv~~~~~~~eki~~e~~f~~~~~GG~i~~v~l~e~~~n~eal~~lv~~a~ 511 (579)
T TIGR02487 432 CGRFAKKDREEFGEIPGVTDKPYYTNSFHVPVYEDVNLGEKIDIEAPFHPLTNGGHITYIELDEAIPDPEALKDITKKAM 511 (579)
T ss_pred HHHHHHHHHHHcCCCCCCCCCCcCCCCEeeCCCCCCCHHHHHHhhcchhcccCCceEEEEEcCCCCCCHHHHHHHHHHHH
Confidence 35556888873 56776 2553 34556788999888887765544433 478888888888
Q ss_pred HcCCCCCCCCCceEEEccCCCCCCCCCCCCceEEEEECCceeEEcCCCCC
Q 015345 228 EVGADSSQFPSNWIFHSREKKPGKAFVDGKKIDFITAGGRTTAYVPELQK 277 (408)
Q Consensus 228 ~~gg~s~~f~~~~~vy~R~g~pC~~~~CG~~I~~~~vgGRtT~~CP~CQ~ 277 (408)
+.| .+ .|-+. ..=..|. .||. .|.+..+.||.|..
T Consensus 512 ~~~--i~----Y~~~n-~~~~~C~--~CG~------~g~~~~~~CP~Cgs 546 (579)
T TIGR02487 512 KNG--IG----YFGIN-PPVDVCE--DCGY------TGEGLNDKCPKCGS 546 (579)
T ss_pred hcC--Cc----eEEec-cCCccCC--CCCC------CCCCCCCcCcCCCC
Confidence 764 11 22222 3335677 8985 25554588999984
No 118
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=23.95 E-value=88 Score=22.63 Aligned_cols=27 Identities=11% Similarity=-0.037 Sum_probs=20.9
Q ss_pred CCCCCCCCceEEEEE-CCceeEEcCCCCCC
Q 015345 250 GKAFVDGKKIDFITA-GGRTTAYVPELQKL 278 (408)
Q Consensus 250 C~~~~CG~~I~~~~v-gGRtT~~CP~CQ~~ 278 (408)
|+ .||.++..... +++.-|+|..++..
T Consensus 8 C~--~CG~~m~~~~~~~~~~yy~C~~~~~~ 35 (58)
T PF13408_consen 8 CG--HCGSKMTRRKRKGKYRYYRCSNRRRK 35 (58)
T ss_pred cc--cCCcEeEEEECCCCceEEEcCCCcCC
Confidence 66 89999776544 56788999998864
No 119
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=23.89 E-value=69 Score=29.74 Aligned_cols=31 Identities=6% Similarity=-0.010 Sum_probs=23.3
Q ss_pred eEEEccCCCCCCCCCCCCceEEEEECCceeEEcCCCCCCC
Q 015345 240 WIFHSREKKPGKAFVDGKKIDFITAGGRTTAYVPELQKLN 279 (408)
Q Consensus 240 ~~vy~R~g~pC~~~~CG~~I~~~~vgGRtT~~CP~CQ~~~ 279 (408)
-.++.+ |+ .||.++.. .++++.+||.|-...
T Consensus 146 Gvv~a~----~~--~~g~~~~~---~~~~~~~c~~~~~~e 176 (189)
T PRK09521 146 GVIYAM----CS--RCRTPLVK---KGENELKCPNCGNIE 176 (189)
T ss_pred eEEEEE----cc--ccCCceEE---CCCCEEECCCCCCEE
Confidence 356644 66 89999853 667899999998763
No 120
>PRK10144 formate-dependent nitrite reductase complex subunit NrfF; Provisional
Probab=23.58 E-value=25 Score=31.28 Aligned_cols=19 Identities=21% Similarity=0.242 Sum_probs=11.5
Q ss_pred EcCCCCCCCccchhhhhCC
Q 015345 271 YVPELQKLNGVQAAKAVGK 289 (408)
Q Consensus 271 ~CP~CQ~~~~~~~~~~~~~ 289 (408)
-||.||..+-+.+.++++.
T Consensus 42 RC~vCqnqsiadSna~iA~ 60 (126)
T PRK10144 42 RCPQCQNQNLLESNAPVAV 60 (126)
T ss_pred CCCCCCCCChhhcCCHHHH
Confidence 4888888754444444443
No 121
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=23.36 E-value=51 Score=25.01 Aligned_cols=28 Identities=11% Similarity=-0.069 Sum_probs=18.9
Q ss_pred CCCCCCCCCceEEEEECCceeEEcCCCCCC
Q 015345 249 PGKAFVDGKKIDFITAGGRTTAYVPELQKL 278 (408)
Q Consensus 249 pC~~~~CG~~I~~~~vgGRtT~~CP~CQ~~ 278 (408)
.|| .||..|.--..----..-||.|...
T Consensus 4 ~CP--~CG~~iev~~~~~GeiV~Cp~CGae 31 (54)
T TIGR01206 4 ECP--DCGAEIELENPELGELVICDECGAE 31 (54)
T ss_pred CCC--CCCCEEecCCCccCCEEeCCCCCCE
Confidence 477 9999887432111347799999874
No 122
>PRK13195 pyrrolidone-carboxylate peptidase; Provisional
Probab=23.24 E-value=2.8e+02 Score=26.93 Aligned_cols=82 Identities=22% Similarity=0.332 Sum_probs=46.4
Q ss_pred cccccCCCCCCCCCCHHHHHHHHcCCCchhHHHHhCCCccccCchhhhhhHhhhcc--------------cC----ccCc
Q 015345 142 PISELGPDALLEPMTVDEFTDSLSKKKITIKALLLDQSYISGIGNWVADEVLYQAK--------------IH----PLQT 203 (408)
Q Consensus 142 ~l~~LGPDpL~~~f~~e~f~~~l~k~k~~IK~lLLDQ~iiAGIGNiYadEILF~Ag--------------Ih----P~~~ 203 (408)
++..-||+.+...+..+.+.+.|+...-+. .+--=-|.+..|-++|.+- || |...
T Consensus 106 ~I~~~gp~ay~stLpv~~iv~~l~~~gipa-------~vS~~AGtYvCN~v~Y~sL~~~~~~~~~~~agFIHVP~~p~q~ 178 (222)
T PRK13195 106 PTDPAGPVAYHATVPVRAMVLAMRKAGVPA-------DVSDAAGTFVCNHLMYGVLHHLAQKGLPVRAGWIHLPCLPSVA 178 (222)
T ss_pred cccCCCcceeecCCCHHHHHHHHHhcCCCc-------eEecCCCcceehHHHHHHHHHHhhcCCCceEEEEEcCCCHHHh
Confidence 344559999988888888888887543221 1111236666666666441 11 2221
Q ss_pred C-C---CCCHHHHHHHHHHHHHHHHHHHHcC
Q 015345 204 A-V---SLSKESCATLLKCIKEVIEKALEVG 230 (408)
Q Consensus 204 ~-~---~Ls~~e~~~L~~ai~~VL~~Ai~~g 230 (408)
+ . ....-.++.+.++++..++.++...
T Consensus 179 ~~~~~~~~psm~l~~~~~av~~~i~~~~~~~ 209 (222)
T PRK13195 179 ALDHNLGVPSMSVQTAVAGVTAGIEAAIRQS 209 (222)
T ss_pred hhcCCCCCCCCcHHHHHHHHHHHHHHHHccc
Confidence 1 0 1233345677777777777777543
No 123
>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=23.02 E-value=73 Score=22.49 Aligned_cols=26 Identities=12% Similarity=0.194 Sum_probs=18.9
Q ss_pred CCCCCCCCceEEE-EECCceeEEcCCCCC
Q 015345 250 GKAFVDGKKIDFI-TAGGRTTAYVPELQK 277 (408)
Q Consensus 250 C~~~~CG~~I~~~-~vgGRtT~~CP~CQ~ 277 (408)
|. .||...... .++.-.+.-||.|..
T Consensus 8 C~--~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 8 CE--ECGHEFEVLQSISEDDPVPCPECGS 34 (42)
T ss_pred eC--CCCCEEEEEEEcCCCCCCcCCCCCC
Confidence 66 899876644 444457889999987
No 124
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=22.98 E-value=71 Score=27.33 Aligned_cols=30 Identities=3% Similarity=-0.136 Sum_probs=23.0
Q ss_pred CCCCCCCCceEEEEECCceeEEcCCCCCCCcc
Q 015345 250 GKAFVDGKKIDFITAGGRTTAYVPELQKLNGV 281 (408)
Q Consensus 250 C~~~~CG~~I~~~~vgGRtT~~CP~CQ~~~~~ 281 (408)
|| .||..+.-..-+.+..|.|+.|--+..+
T Consensus 4 CP--~Cgn~Live~g~~~~rf~C~tCpY~~~I 33 (105)
T KOG2906|consen 4 CP--TCGNMLIVESGESCNRFSCRTCPYVFPI 33 (105)
T ss_pred cC--CCCCEEEEecCCeEeeEEcCCCCceeeE
Confidence 66 8998776555445699999999987655
No 125
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=22.82 E-value=74 Score=27.61 Aligned_cols=66 Identities=12% Similarity=0.012 Sum_probs=39.9
Q ss_pred CCCCCCCCCceEEEEECCceeEEcCCCCCCCccchhhhhCCCCCcCCCCCCCCCcccCCCCC-CCCCchhhhhhhhcccc
Q 015345 249 PGKAFVDGKKIDFITAGGRTTAYVPELQKLNGVQAAKAVGKPRKQAPKGEDSKDDDKYNSGD-ESESDGEEIAENVKSKK 327 (408)
Q Consensus 249 pC~~~~CG~~I~~~~vgGRtT~~CP~CQ~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~-~~~~~~~~~~~~~~~~~ 327 (408)
+|| .|+..-. +--...|.||.|...-...+..+ . . .....+-.+|. +.|.|..-..+-=|.|+
T Consensus 4 ~CP--~C~seyt---Y~dg~~~iCpeC~~EW~~~~~~~-------~--~--~~~~~kDsnG~~L~dGDsV~liKDLkVKG 67 (109)
T TIGR00686 4 PCP--KCNSEYT---YHDGTQLICPSCLYEWNENEVND-------D--D--DELIVKDCNGNLLANGDSVILIKDLKVKG 67 (109)
T ss_pred cCC--cCCCcce---EecCCeeECcccccccccccccc-------c--c--CCceEEcCCCCCccCCCEEEEEeeccccC
Confidence 566 9997644 45566899999998532221000 0 0 00113444554 78888888888878877
Q ss_pred ccc
Q 015345 328 RQK 330 (408)
Q Consensus 328 ~~~ 330 (408)
+-.
T Consensus 68 ss~ 70 (109)
T TIGR00686 68 SSL 70 (109)
T ss_pred ccc
Confidence 543
No 126
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=22.60 E-value=1.1e+02 Score=22.85 Aligned_cols=28 Identities=18% Similarity=0.089 Sum_probs=19.3
Q ss_pred CCCCCCCCCCceEEEEEC-Cc-----eeEEcCCCCC
Q 015345 248 KPGKAFVDGKKIDFITAG-GR-----TTAYVPELQK 277 (408)
Q Consensus 248 ~pC~~~~CG~~I~~~~vg-GR-----tT~~CP~CQ~ 277 (408)
+||| -||.....+... +. ...+|..|.-
T Consensus 4 kPCP--FCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 4 KPCP--FCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred cCCC--CCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 5888 899876655443 22 4567999976
No 127
>PHA02942 putative transposase; Provisional
Probab=22.56 E-value=52 Score=34.28 Aligned_cols=27 Identities=15% Similarity=-0.020 Sum_probs=19.9
Q ss_pred CCCCCCCCCCCceEEEEECCceeEEcCCCCCC
Q 015345 247 KKPGKAFVDGKKIDFITAGGRTTAYVPELQKL 278 (408)
Q Consensus 247 g~pC~~~~CG~~I~~~~vgGRtT~~CP~CQ~~ 278 (408)
-+.|+ .||.... ..++| .|-||.|.-.
T Consensus 325 Sq~Cs--~CG~~~~--~l~~r-~f~C~~CG~~ 351 (383)
T PHA02942 325 SVSCP--KCGHKMV--EIAHR-YFHCPSCGYE 351 (383)
T ss_pred CccCC--CCCCccC--cCCCC-EEECCCCCCE
Confidence 35687 8998654 33555 7999999984
No 128
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=22.38 E-value=62 Score=23.38 Aligned_cols=24 Identities=8% Similarity=-0.006 Sum_probs=18.7
Q ss_pred CCCCCCCCceEEEEECCceeEEcCCCCCC
Q 015345 250 GKAFVDGKKIDFITAGGRTTAYVPELQKL 278 (408)
Q Consensus 250 C~~~~CG~~I~~~~vgGRtT~~CP~CQ~~ 278 (408)
|. .||..+.. -.+.+..||.|.-.
T Consensus 5 C~--~Cg~~~~~---~~~~~irC~~CG~r 28 (44)
T smart00659 5 CG--ECGRENEI---KSKDVVRCRECGYR 28 (44)
T ss_pred CC--CCCCEeec---CCCCceECCCCCce
Confidence 66 89987663 36788999999874
No 129
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=22.03 E-value=68 Score=31.49 Aligned_cols=28 Identities=7% Similarity=-0.026 Sum_probs=20.9
Q ss_pred CCCCCCCCCCCceEEEEECCceeEEcCCCCCC
Q 015345 247 KKPGKAFVDGKKIDFITAGGRTTAYVPELQKL 278 (408)
Q Consensus 247 g~pC~~~~CG~~I~~~~vgGRtT~~CP~CQ~~ 278 (408)
.+-|+ .||+++... .+.....||.|+..
T Consensus 99 ~~fC~--~CG~~~~~~--~~~~~~~C~~c~~~ 126 (256)
T PRK00241 99 HRFCG--YCGHPMHPS--KTEWAMLCPHCRER 126 (256)
T ss_pred Ccccc--ccCCCCeec--CCceeEECCCCCCE
Confidence 45688 999997643 34556889999984
No 130
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=21.95 E-value=79 Score=29.96 Aligned_cols=12 Identities=8% Similarity=-0.056 Sum_probs=10.1
Q ss_pred eeEEcCCCCCCC
Q 015345 268 TTAYVPELQKLN 279 (408)
Q Consensus 268 tT~~CP~CQ~~~ 279 (408)
++|.||+|--..
T Consensus 29 ~sf~C~~CGyr~ 40 (192)
T TIGR00310 29 TSTICEHCGYRS 40 (192)
T ss_pred EEEECCCCCCcc
Confidence 689999998864
No 131
>PF11248 DUF3046: Protein of unknown function (DUF3046); InterPro: IPR021408 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=21.62 E-value=79 Score=24.83 Aligned_cols=44 Identities=23% Similarity=0.311 Sum_probs=34.1
Q ss_pred HHHHHHHcCC-CchhHHHHhCCCccccCchhhhhhHhhhcccCccC
Q 015345 158 DEFTDSLSKK-KITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQ 202 (408)
Q Consensus 158 e~f~~~l~k~-k~~IK~lLLDQ~iiAGIGNiYadEILF~AgIhP~~ 202 (408)
.+|.+++..- -..-...|++..+++++|+--++|+| .+|++|..
T Consensus 4 teFw~~~~~~FG~~~~~~la~dhvL~~LGgrT~~eAL-~~G~dpr~ 48 (63)
T PF11248_consen 4 TEFWQLMEEEFGPAYGRSLARDHVLSELGGRTAAEAL-EAGVDPRD 48 (63)
T ss_pred HHHHHHHHHHhCchhHHHHHHhcchhhcCCcCHHHHH-HcCCCHHH
Confidence 4677766542 34557788999999999999999987 68888864
No 132
>PRK00285 ihfA integration host factor subunit alpha; Reviewed
Probab=20.78 E-value=4.6e+02 Score=21.47 Aligned_cols=67 Identities=30% Similarity=0.509 Sum_probs=42.6
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHcCCCC--CCCCCceEEEccCCCCCCCCCCCCceEEEEECCceeEEcCC
Q 015345 205 VSLSKESCATLLKCIKEVIEKALEVGADS--SQFPSNWIFHSREKKPGKAFVDGKKIDFITAGGRTTAYVPE 274 (408)
Q Consensus 205 ~~Ls~~e~~~L~~ai~~VL~~Ai~~gg~s--~~f~~~~~vy~R~g~pC~~~~CG~~I~~~~vgGRtT~~CP~ 274 (408)
..||..++..+++++..+|.+++..|+.- ..|+ .|.+..|....+..|.-|..+.. -+.+...|.|.
T Consensus 16 ~~~s~~~v~~vl~~~~~~i~~~L~~g~~V~l~gfG-~F~~~~~~~r~~~np~t~e~~~i--~~~~~v~Fkps 84 (99)
T PRK00285 16 VGLSKREAKELVELFFEEIRDALENGEQVKLSGFG-NFQLRDKNQRPGRNPKTGEEIPI--SARRVVTFRPS 84 (99)
T ss_pred hCcCHHHHHHHHHHHHHHHHHHHHcCCeEEEcCCE-EEEEEEECCccccCCCCCCEEEE--cCcccEEEeeC
Confidence 45899999999999999999999999764 3343 23333343344444455655431 13333466554
No 133
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=20.68 E-value=70 Score=22.03 Aligned_cols=26 Identities=15% Similarity=0.215 Sum_probs=16.2
Q ss_pred CCCCCCCCceE----EEEECCceeEEcCCCCCC
Q 015345 250 GKAFVDGKKID----FITAGGRTTAYVPELQKL 278 (408)
Q Consensus 250 C~~~~CG~~I~----~~~vgGRtT~~CP~CQ~~ 278 (408)
|| .|++... ++..+| ...-||+|+..
T Consensus 5 CP--~C~~~f~v~~~~l~~~~-~~vrC~~C~~~ 34 (37)
T PF13719_consen 5 CP--NCQTRFRVPDDKLPAGG-RKVRCPKCGHV 34 (37)
T ss_pred CC--CCCceEEcCHHHcccCC-cEEECCCCCcE
Confidence 55 8887644 223334 47888888864
No 134
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=20.66 E-value=31 Score=30.86 Aligned_cols=28 Identities=18% Similarity=0.032 Sum_probs=18.3
Q ss_pred CCCCCCCCCceEEEEE----CCceeEEcCCCCCC
Q 015345 249 PGKAFVDGKKIDFITA----GGRTTAYVPELQKL 278 (408)
Q Consensus 249 pC~~~~CG~~I~~~~v----gGRtT~~CP~CQ~~ 278 (408)
.|| .||........ .--..|.||.|...
T Consensus 101 ~Cp--~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~ 132 (147)
T smart00531 101 KCP--NCQSKYTFLEANQLLDMDGTFTCPRCGEE 132 (147)
T ss_pred ECc--CCCCEeeHHHHHHhcCCCCcEECCCCCCE
Confidence 377 99987764321 11223999999985
No 135
>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=20.58 E-value=91 Score=23.66 Aligned_cols=30 Identities=27% Similarity=0.226 Sum_probs=23.1
Q ss_pred CCeEeeeeeeeeEEEEEeCCCCcceeeeceeeeEEE
Q 015345 49 GKAILSAHRKGKNLWLRLDSPPFPSFQFGMTGAIYI 84 (408)
Q Consensus 49 G~~I~~V~RrGK~L~~~l~~~~~L~vHLGMtG~l~i 84 (408)
=.+|..|+|.||.+-|..++|. |-||+=-+
T Consensus 16 iskikkvwrvgkmvsftyddgn------gktgrgav 45 (62)
T PF02294_consen 16 ISKIKKVWRVGKMVSFTYDDGN------GKTGRGAV 45 (62)
T ss_dssp GGGEEEEEECSSEEEEEEECSS------SSEEEEEE
T ss_pred HHHHHHHHhhcceEEEEEecCC------Cccccccc
Confidence 3579999999999999998752 45666544
No 136
>PF14353 CpXC: CpXC protein
Probab=20.20 E-value=91 Score=26.90 Aligned_cols=11 Identities=9% Similarity=-0.058 Sum_probs=9.1
Q ss_pred eEEcCCCCCCC
Q 015345 269 TAYVPELQKLN 279 (408)
Q Consensus 269 T~~CP~CQ~~~ 279 (408)
+|-||+|+...
T Consensus 38 ~~~CP~Cg~~~ 48 (128)
T PF14353_consen 38 SFTCPSCGHKF 48 (128)
T ss_pred EEECCCCCCce
Confidence 78899999853
No 137
>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=20.15 E-value=91 Score=21.11 Aligned_cols=27 Identities=15% Similarity=0.160 Sum_probs=17.9
Q ss_pred CCCCCCCCCceEEEEE-CCceeEEcCCCCC
Q 015345 249 PGKAFVDGKKIDFITA-GGRTTAYVPELQK 277 (408)
Q Consensus 249 pC~~~~CG~~I~~~~v-gGRtT~~CP~CQ~ 277 (408)
.|+ .||.......- +.....-||.|..
T Consensus 7 ~C~--~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 7 RCE--DCGHTFEVLQKISDDPLATCPECGG 34 (41)
T ss_pred EcC--CCCCEEEEEEecCCCCCCCCCCCCC
Confidence 366 89987764432 2245667999987
Done!