Query 024924
Match_columns 260
No_of_seqs 113 out of 1053
Neff 7.2
Searched_HMMs 46136
Date Fri Mar 29 08:31:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024924.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024924hhsearch_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 2.8E-73 6.2E-78 502.6 25.6 243 1-259 1-256 (273)
2 PRK13945 formamidopyrimidine-D 100.0 8.7E-71 1.9E-75 496.0 27.7 244 1-259 1-265 (282)
3 PRK01103 formamidopyrimidine/5 100.0 3.8E-70 8.3E-75 490.2 28.1 243 1-259 1-256 (274)
4 TIGR00577 fpg formamidopyrimid 100.0 1.2E-69 2.7E-74 486.3 27.5 242 2-259 1-256 (272)
5 PRK14811 formamidopyrimidine-D 100.0 5.5E-69 1.2E-73 481.1 26.5 231 1-259 1-246 (269)
6 PRK14810 formamidopyrimidine-D 100.0 2.6E-67 5.6E-72 471.1 27.8 240 1-259 1-255 (272)
7 PRK10445 endonuclease VIII; Pr 100.0 1.2E-66 2.6E-71 464.8 27.6 235 1-259 1-246 (263)
8 cd08972 PF_Nei_N N-terminal do 100.0 2.4E-33 5.3E-38 227.3 16.0 133 1-133 1-136 (137)
9 PF06831 H2TH: Formamidopyrimi 100.0 7.7E-34 1.7E-38 215.3 9.0 90 146-235 1-90 (92)
10 cd08976 BaFpgNei_N_4 Uncharact 100.0 2.4E-32 5.3E-37 216.0 15.3 117 2-133 1-117 (117)
11 PF01149 Fapy_DNA_glyco: Forma 100.0 4.2E-32 9E-37 214.2 13.2 116 2-132 1-116 (116)
12 cd08966 EcFpg-like_N N-termina 100.0 1.5E-31 3.3E-36 212.2 16.1 119 2-134 1-119 (120)
13 cd08773 FpgNei_N N-terminal do 100.0 5E-30 1.1E-34 202.6 14.7 116 2-132 1-116 (117)
14 cd08973 BaFpgNei_N_1 Uncharact 100.0 8.1E-30 1.8E-34 203.0 15.4 115 1-130 1-116 (122)
15 cd08967 MeNeil1_N N-terminal d 100.0 1.4E-29 3E-34 203.3 14.6 112 1-133 1-129 (131)
16 cd08975 BaFpgNei_N_3 Uncharact 100.0 8.3E-28 1.8E-32 190.0 14.3 113 3-132 2-116 (117)
17 cd08971 AcNei2_N N-terminal do 100.0 1.6E-27 3.4E-32 187.7 15.1 111 1-135 1-112 (114)
18 cd08974 BaFpgNei_N_2 Uncharact 99.9 9.7E-27 2.1E-31 178.4 13.2 96 1-124 1-96 (98)
19 cd08965 EcNei-like_N N-termina 99.9 4.8E-26 1E-30 179.5 15.5 113 2-136 1-113 (115)
20 cd08970 AcNei1_N N-terminal do 99.9 9.6E-26 2.1E-30 176.4 14.2 109 1-133 1-109 (110)
21 cd08968 MeNeil2_N N-terminal d 99.9 5.8E-23 1.2E-27 162.8 13.7 111 1-125 1-121 (126)
22 cd08969 MeNeil3_N N-terminal d 99.7 2.2E-16 4.8E-21 126.8 10.8 112 1-125 1-122 (140)
23 PF05833 FbpA: Fibronectin-bin 98.2 4.3E-05 9.4E-10 73.3 14.4 79 146-228 165-244 (455)
24 COG0099 RpsM Ribosomal protein 97.1 0.00069 1.5E-08 53.2 4.0 40 181-220 22-61 (121)
25 PF00416 Ribosomal_S13: Riboso 97.0 0.0021 4.5E-08 49.9 6.1 52 167-221 9-60 (107)
26 PRK04184 DNA topoisomerase VI 97.0 0.0048 1E-07 60.5 10.0 75 144-222 232-307 (535)
27 COG1293 Predicted RNA-binding 96.8 0.031 6.7E-07 55.5 13.9 73 149-226 168-240 (564)
28 PRK05179 rpsM 30S ribosomal pr 96.7 0.0024 5.2E-08 50.8 4.4 51 168-221 12-62 (122)
29 CHL00137 rps13 ribosomal prote 96.5 0.0044 9.6E-08 49.3 4.7 50 168-220 12-61 (122)
30 TIGR01052 top6b DNA topoisomer 96.5 0.018 3.8E-07 56.0 9.7 74 145-222 224-301 (488)
31 PTZ00134 40S ribosomal protein 96.5 0.0041 8.9E-08 51.4 4.4 52 167-221 24-75 (154)
32 TIGR03631 bact_S13 30S ribosom 96.2 0.0078 1.7E-07 47.3 4.4 50 168-220 10-59 (113)
33 TIGR03629 arch_S13P archaeal r 96.0 0.011 2.3E-07 48.4 4.6 52 167-221 15-66 (144)
34 PRK04053 rps13p 30S ribosomal 96.0 0.01 2.2E-07 48.8 4.4 51 167-220 19-69 (149)
35 COG1389 DNA topoisomerase VI, 93.8 0.21 4.6E-06 48.0 7.3 97 120-222 208-311 (538)
36 KOG3311 Ribosomal protein S18 91.8 0.15 3.2E-06 41.8 2.7 50 168-220 23-72 (152)
37 TIGR00275 flavoprotein, HI0933 81.6 3.5 7.6E-05 38.9 6.0 63 154-221 264-331 (400)
38 TIGR00755 ksgA dimethyladenosi 73.4 6.1 0.00013 34.8 4.8 55 159-218 197-252 (253)
39 COG0030 KsgA Dimethyladenosine 70.8 7 0.00015 35.1 4.5 52 163-222 206-257 (259)
40 COG2081 Predicted flavoprotein 67.7 11 0.00024 35.9 5.4 63 153-221 268-332 (408)
41 PF00398 RrnaAD: Ribosomal RNA 66.3 12 0.00026 33.2 5.2 51 164-220 210-261 (262)
42 PRK00274 ksgA 16S ribosomal RN 62.7 15 0.00033 32.8 5.1 54 163-220 216-269 (272)
43 PF03486 HI0933_like: HI0933-l 62.6 6.4 0.00014 37.6 2.8 64 153-221 270-339 (409)
44 PF10892 DUF2688: Protein of u 52.0 3.4 7.3E-05 28.2 -0.7 11 250-260 12-22 (60)
45 COG0776 HimA Bacterial nucleoi 51.5 43 0.00092 25.4 5.1 51 207-259 17-71 (94)
46 PTZ00338 dimethyladenosine tra 48.3 41 0.00088 30.6 5.5 57 164-221 211-288 (294)
47 PRK10664 transcriptional regul 47.6 58 0.0013 24.1 5.3 53 205-259 14-70 (90)
48 PRK00199 ihfB integration host 42.6 71 0.0015 23.6 5.2 52 205-258 15-70 (94)
49 PF10815 ComZ: ComZ; InterPro 37.9 1E+02 0.0022 20.9 4.7 36 189-231 17-52 (56)
50 PRK10753 transcriptional regul 37.8 92 0.002 23.0 5.1 52 205-258 14-69 (90)
51 PRK14896 ksgA 16S ribosomal RN 37.3 97 0.0021 27.3 6.0 57 163-221 199-256 (258)
52 PF06827 zf-FPG_IleRS: Zinc fi 36.4 15 0.00032 21.3 0.5 12 247-259 1-12 (30)
53 TIGR00987 himA integration hos 36.1 1E+02 0.0022 22.9 5.1 40 205-245 15-56 (96)
54 COG4871 Uncharacterized protei 35.7 48 0.001 27.8 3.4 48 208-256 91-144 (193)
55 PF02294 7kD_DNA_binding: 7kD 31.0 66 0.0014 21.6 2.9 31 49-85 16-46 (62)
56 TIGR03826 YvyF flagellar opero 30.4 82 0.0018 25.5 4.0 45 208-260 48-93 (137)
57 PRK13195 pyrrolidone-carboxyla 28.1 3.1E+02 0.0067 24.0 7.5 26 142-167 106-131 (222)
58 PF11197 DUF2835: Protein of u 26.9 1.2E+02 0.0027 21.5 3.9 48 38-85 7-56 (68)
59 TIGR00988 hip integration host 26.8 1.9E+02 0.0041 21.2 5.2 52 205-258 15-70 (94)
60 PRK00222 methionine sulfoxide 26.8 55 0.0012 26.7 2.4 49 207-258 5-53 (142)
61 COG3743 Uncharacterized conser 26.1 53 0.0012 26.5 2.1 40 177-217 68-107 (133)
62 PRK10874 cysteine sulfinate de 24.5 1.1E+02 0.0024 28.4 4.4 18 208-225 381-398 (401)
63 PF11248 DUF3046: Protein of u 22.6 36 0.00078 23.9 0.5 44 158-202 4-48 (63)
64 PF10474 DUF2451: Protein of u 22.3 78 0.0017 27.9 2.7 69 155-230 67-140 (234)
65 PF00633 HHH: Helix-hairpin-he 22.0 60 0.0013 19.0 1.3 14 180-193 15-28 (30)
66 PF00216 Bac_DNA_binding: Bact 21.7 1.5E+02 0.0032 21.3 3.7 28 206-233 15-42 (90)
67 TIGR00357 methionine-R-sulfoxi 21.7 83 0.0018 25.4 2.5 48 208-258 3-50 (134)
68 PRK00285 ihfA integration host 21.5 1.5E+02 0.0032 22.0 3.8 29 205-233 16-44 (99)
69 smart00411 BHL bacterial (prok 20.9 1.6E+02 0.0035 21.1 3.8 29 205-233 14-42 (90)
No 1
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=100.00 E-value=2.8e-73 Score=502.57 Aligned_cols=243 Identities=34% Similarity=0.496 Sum_probs=227.0
Q ss_pred CCChhHHHHHHHHHHhhcCCceEEEEEecCCCccccCCChhhHHHHhcCCeEEeEEEeeeEEEEecCCCCccEEeecceE
Q 024924 1 MPELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKNLWLRLDSPPFPSFQFGMTG 80 (260)
Q Consensus 1 MPElPEVe~~~~~L~~~~~G~~I~~v~~~~~~~~~~~~~~~~~~~~L~G~~i~~v~r~GK~l~~~~~~~~~L~~HlgMtG 80 (260)
||||||||++++.|++.++|++|.+|++. .+++.++.+ ++|...|.|++|.+|.||||||+++|+++.+|++||||+|
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 99999999999999999999999999998 466666554 7899999999999999999999999977779999999999
Q ss_pred EEEEeeccccccccccccCCCCCCCCceEEEEEEcCC-ceEEEecCCcceEEEEecCCC-CCCCccCCCCCCCCCCCCHH
Q 024924 81 AIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDG-LELSFTDKRRFAKVRLLNDPT-SVPPISELGPDALLEPMTVD 158 (260)
Q Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~p~k~~~l~l~l~~~-~~l~f~d~R~fg~~~l~~~~~-~~~~l~~lGpDpl~~~~~~~ 158 (260)
+|++... +.+..+|+|+.|+|+|| ..|.|+|+|+||.+++++..+ .++.+++||||||+++||++
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 9999653 22356899999999999 599999999999999998665 77789999999999999999
Q ss_pred HHHHHHcCCCcchhHHhhcCcccccchhHHHHHHHhhcCCCcccccCCCCHHHHHHHHHHHHHHHHHHHHcCCCC-----
Q 024924 159 EFTDSLSKKKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVIQSAVEVDADC----- 233 (260)
Q Consensus 159 ~~~~~l~~~~~~Ik~~LlDQ~~iaGiGNiya~EiLf~a~IhP~~~~~~Ls~~e~~~L~~~i~~vL~~ai~~gg~~----- 233 (260)
++.+++++++++||.+||||++||||||||+||+||+|||||.+++++|+.+++..|+++|+.||..||+.|||+
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 999999999999999999999999999999999999999999999999999999999999999999999999986
Q ss_pred ------CCCCcccEEeeeCCCCCCCcCCcccC
Q 024924 234 ------SRFPLEWLFHFRWGKKPGKVNGKIFM 259 (260)
Q Consensus 234 ------~~~~~~~lv~~R~~~~~~~~~~~~~~ 259 (260)
|.|+..+.||+|.|+ ||.+||++|+
T Consensus 226 ~~~g~~G~fq~~l~VYgR~Ge-pC~~CGt~I~ 256 (273)
T COG0266 226 NADGKPGYFQQELKVYGRAGE-PCRRCGTPIE 256 (273)
T ss_pred ccCCCCCccceeEEEecCCCC-CCCccCCEeE
Confidence 688999999999997 9999999996
No 2
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=100.00 E-value=8.7e-71 Score=496.05 Aligned_cols=244 Identities=28% Similarity=0.404 Sum_probs=219.5
Q ss_pred CCChhHHHHHHHHHHhhcCCceEEEEEecCCCcccc-CCChhhHHHHhcCCeEEeEEEeeeEEEEecCC-----CCccEE
Q 024924 1 MPELPEVEAARRAIEEHCIGKKIVKSIIADDNKVID-GVSASDFEASVLGKAILSAHRKGKNLWLRLDS-----PPFPSF 74 (260)
Q Consensus 1 MPElPEVe~~~~~L~~~~~G~~I~~v~~~~~~~~~~-~~~~~~~~~~L~G~~i~~v~r~GK~l~~~~~~-----~~~L~~ 74 (260)
||||||||++++.|++.+.|++|++|++.. ++++. +..+++|.+.|.|++|.+|+|+||||+++|++ +.+|++
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 54432 22467899999999999999999999999986 358999
Q ss_pred eecceEEEEEeeccccccccccccCCCCCCCCceEEEEEEcCCceEEEecCCcceEEEEecCC----CCCCCccCCCCCC
Q 024924 75 QFGMTGAIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELSFTDKRRFAKVRLLNDP----TSVPPISELGPDA 150 (260)
Q Consensus 75 HlgMtG~~~~~~~~~~~~~~~~~~~~~~~p~k~~~l~l~l~~~~~l~f~d~R~fg~~~l~~~~----~~~~~l~~lGpDp 150 (260)
||||||+|++... +.+|.+|.+++|.|+|+..|+|+|+|+||++++++.. .....+.+|||||
T Consensus 80 HLgMtG~~~~~~~-------------~~~~~~~~~l~l~~~~~~~L~f~d~R~fG~~~l~~~~~~~~~~~~~l~~LGpDp 146 (282)
T PRK13945 80 HLRMTGQFLWVEQ-------------STPPCKHTRVRLFFEKNQELRFVDIRSFGQMWWVPPGVSPESIITGLQKLGPEP 146 (282)
T ss_pred ECCeeEEEEEecC-------------CCCCCCcEEEEEEeCCCCEEEEEeCCCCceEEEEcCcccccccchHHHhcCCCc
Confidence 9999999998532 2245689999999999999999999999999998742 2234589999999
Q ss_pred CCCCCCHHHHHHHHcCCCcchhHHhhcCcccccchhHHHHHHHhhcCCCcccccCCCCHHHHHHHHHHHHHHHHHHHHcC
Q 024924 151 LLEPMTVDEFTDSLSKKKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVIQSAVEVD 230 (260)
Q Consensus 151 l~~~~~~~~~~~~l~~~~~~Ik~~LlDQ~~iaGiGNiya~EiLf~a~IhP~~~~~~Ls~~e~~~L~~~i~~vL~~ai~~g 230 (260)
|+++||.++|.+++++++++||++||||++||||||||+|||||+|||||.+++++||++|+++|+++|++||+.||+.|
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-----------CCCCcccEEeeeCCCCCCCcCCcccC
Q 024924 231 ADC-----------SRFPLEWLFHFRWGKKPGKVNGKIFM 259 (260)
Q Consensus 231 g~~-----------~~~~~~~lv~~R~~~~~~~~~~~~~~ 259 (260)
|++ +.|+..++||+|.|+ ||.+||++|.
T Consensus 227 g~~~~~~~~~~g~~g~~~~~~~Vy~R~g~-pC~~Cg~~I~ 265 (282)
T PRK13945 227 GTTFSDFRDLEGVNGNYGGQAWVYRRTGK-PCRKCGTPIE 265 (282)
T ss_pred CCccccccccCCCCCcccceEEEeCCCcC-CCCcCCCeeE
Confidence 975 356777899999997 9999999985
No 3
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=100.00 E-value=3.8e-70 Score=490.24 Aligned_cols=243 Identities=35% Similarity=0.506 Sum_probs=221.3
Q ss_pred CCChhHHHHHHHHHHhhcCCceEEEEEecCCCccccCCChhhHHHHhcCCeEEeEEEeeeEEEEecCCCCccEEeecceE
Q 024924 1 MPELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKNLWLRLDSPPFPSFQFGMTG 80 (260)
Q Consensus 1 MPElPEVe~~~~~L~~~~~G~~I~~v~~~~~~~~~~~~~~~~~~~~L~G~~i~~v~r~GK~l~~~~~~~~~L~~HlgMtG 80 (260)
||||||||++++.|++.+.|++|++|++.. +++... ++++|.+.|.|++|++|+|+||||+|+|+++.+|++||||+|
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 554433 478899999999999999999999999997679999999999
Q ss_pred EEEEeeccccccccccccCCCCCCCCceEEEEEEcCCceEEEecCCcceEEEEecCC--CCCCCccCCCCCCCCCCCCHH
Q 024924 81 AIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELSFTDKRRFAKVRLLNDP--TSVPPISELGPDALLEPMTVD 158 (260)
Q Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~p~k~~~l~l~l~~~~~l~f~d~R~fg~~~l~~~~--~~~~~l~~lGpDpl~~~~~~~ 158 (260)
+|++... +.++++|.+++|.|+|+..|.|.|+|+||++++++.. ...+.+.+||||||+++|+.+
T Consensus 79 ~~~~~~~-------------~~~~~~~~~~~l~l~~~~~l~f~D~R~fg~~~l~~~~~~~~~~~~~~LGpdpl~~~~~~~ 145 (274)
T PRK01103 79 SLRLLPE-------------DTPPEKHDHVDFVLDDGTVLRYNDPRRFGAMLLTPKGDLEAHPLLAHLGPEPLSDAFDGE 145 (274)
T ss_pred EEEEeCC-------------CCCCCceEEEEEEECCCCEEEEEcCCcCCEEEEEeCCccccchhHHhcCCCCCCccCCHH
Confidence 9998532 1255689999999999989999999999999999742 335568999999999999999
Q ss_pred HHHHHHcCCCcchhHHhhcCcccccchhHHHHHHHhhcCCCcccccCCCCHHHHHHHHHHHHHHHHHHHHcCCCC-----
Q 024924 159 EFTDSLSKKKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVIQSAVEVDADC----- 233 (260)
Q Consensus 159 ~~~~~l~~~~~~Ik~~LlDQ~~iaGiGNiya~EiLf~a~IhP~~~~~~Ls~~e~~~L~~~i~~vL~~ai~~gg~~----- 233 (260)
+|.+++++++++||.+||||+++|||||||||||||+|||||++++++||++|+.+|++++++||+.|++.||++
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 999999989999999999999999999999999999999999999999999999999999999999999999865
Q ss_pred ------CCCCcccEEeeeCCCCCCCcCCcccC
Q 024924 234 ------SRFPLEWLFHFRWGKKPGKVNGKIFM 259 (260)
Q Consensus 234 ------~~~~~~~lv~~R~~~~~~~~~~~~~~ 259 (260)
+.|+..|+||+|.|+ ||.+||++|.
T Consensus 226 ~~~g~~g~~~~~l~Vy~R~g~-pC~~Cg~~I~ 256 (274)
T PRK01103 226 NADGKPGYFQQSLQVYGREGE-PCRRCGTPIE 256 (274)
T ss_pred ccCCCCCCccceeEEcCCCCC-CCCCCCCeeE
Confidence 467889999999997 9999999985
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=1.2e-69 Score=486.27 Aligned_cols=242 Identities=37% Similarity=0.548 Sum_probs=218.9
Q ss_pred CChhHHHHHHHHHHhhcCCceEEEEEecCCCcccc-CCChhhHHHHhcCCeEEeEEEeeeEEEEecCCCCccEEeecceE
Q 024924 2 PELPEVEAARRAIEEHCIGKKIVKSIIADDNKVID-GVSASDFEASVLGKAILSAHRKGKNLWLRLDSPPFPSFQFGMTG 80 (260)
Q Consensus 2 PElPEVe~~~~~L~~~~~G~~I~~v~~~~~~~~~~-~~~~~~~~~~L~G~~i~~v~r~GK~l~~~~~~~~~L~~HlgMtG 80 (260)
|||||||++++.|++.+.|++|++|++.. ++++. ..++++|.+.|.|++|++|+|+||||+|+|+++ +|++||||+|
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 99999999999999999999999999874 44432 234678999999999999999999999999976 9999999999
Q ss_pred EEEEeeccccccccccccCCCCCCCCceEEEEEEcCCceEEEecCCcceEEEEecCCC--CCCCccCCCCCCCCCCCCHH
Q 024924 81 AIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELSFTDKRRFAKVRLLNDPT--SVPPISELGPDALLEPMTVD 158 (260)
Q Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~p~k~~~l~l~l~~~~~l~f~d~R~fg~~~l~~~~~--~~~~l~~lGpDpl~~~~~~~ 158 (260)
+|++... +.++++|.+++|.|+|+..|.|+|+|+||++++++..+ ....+.+||||||+++||.+
T Consensus 79 ~~~~~~~-------------~~~~~~~~~~~l~~~~~~~l~~~D~R~fg~~~l~~~~~~~~~~~l~~LGpDpl~~~~~~~ 145 (272)
T TIGR00577 79 KYRLEAV-------------PDAPEKHDHVDFLFDDGTELRYHDPRRFGTWLLFDRGQVENVPLLAKLGPEPLSEDFTAE 145 (272)
T ss_pred EEEEecC-------------CCCCCCcEEEEEEECCCCEEEEEcCCcCCEEEEEeCcccccchHHHhcCCCCCCCcCCHH
Confidence 9998532 12446899999999999899999999999999997433 23468999999999999999
Q ss_pred HHHHHHcCCCcchhHHhhcCcccccchhHHHHHHHhhcCCCcccccCCCCHHHHHHHHHHHHHHHHHHHHcCCCC-----
Q 024924 159 EFTDSLSKKKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVIQSAVEVDADC----- 233 (260)
Q Consensus 159 ~~~~~l~~~~~~Ik~~LlDQ~~iaGiGNiya~EiLf~a~IhP~~~~~~Ls~~e~~~L~~~i~~vL~~ai~~gg~~----- 233 (260)
+|.+++++++++||++||||++||||||||+|||||+|||||.+++++||++|+++|+++|++||+.||+.||++
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 999999999999999999999999999999999999999999999999999999999999999999999999965
Q ss_pred ------CCCCcccEEeeeCCCCCCCcCCcccC
Q 024924 234 ------SRFPLEWLFHFRWGKKPGKVNGKIFM 259 (260)
Q Consensus 234 ------~~~~~~~lv~~R~~~~~~~~~~~~~~ 259 (260)
+.|+..++||+|.|+ ||.+||++|.
T Consensus 226 ~~~g~~g~~~~~~~Vy~r~g~-pC~~Cg~~I~ 256 (272)
T TIGR00577 226 NSDGHNGYFQQELQVYGRKGE-PCRRCGTPIE 256 (272)
T ss_pred ccCCCCCcccceeEEeCCCCC-CCCCCCCeeE
Confidence 356788999999997 9999999985
No 5
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=100.00 E-value=5.5e-69 Score=481.11 Aligned_cols=231 Identities=33% Similarity=0.511 Sum_probs=210.0
Q ss_pred CCChhHHHHHHHHHHhhcCCceEEEEEecCCCccccCCChhhHHHHhcCCeEEeEEEeeeEEEEecCCCCccEEeecceE
Q 024924 1 MPELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKNLWLRLDSPPFPSFQFGMTG 80 (260)
Q Consensus 1 MPElPEVe~~~~~L~~~~~G~~I~~v~~~~~~~~~~~~~~~~~~~~L~G~~i~~v~r~GK~l~~~~~~~~~L~~HlgMtG 80 (260)
||||||||++++.|++.+.|++|++|++.. ++++ +|.+.|.|++|++|+|+||||+|+|+++.+|++||||+|
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 999999999999999999999999999874 4433 366789999999999999999999997779999999999
Q ss_pred EEEEeeccccccccccccCCCCCCCCceEEEEEEcCCceEEEecCCcceEEEEecCC--CCCCCccCCCCCCCCCCCCHH
Q 024924 81 AIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELSFTDKRRFAKVRLLNDP--TSVPPISELGPDALLEPMTVD 158 (260)
Q Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~p~k~~~l~l~l~~~~~l~f~d~R~fg~~~l~~~~--~~~~~l~~lGpDpl~~~~~~~ 158 (260)
+|++. |++|.+++|.|+ +..|.|+|+|+||++++++.. .....+.+||||||+++||.+
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 99973 236899999998 668999999999999999742 224568999999999999999
Q ss_pred HHHHHHcCCCcchhHHhhcCcccccchhHHHHHHHhhcCCCcccccCCCCHHHHHHHHHHHHHHHHHHHHcCCCC-----
Q 024924 159 EFTDSLSKKKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVIQSAVEVDADC----- 233 (260)
Q Consensus 159 ~~~~~l~~~~~~Ik~~LlDQ~~iaGiGNiya~EiLf~a~IhP~~~~~~Ls~~e~~~L~~~i~~vL~~ai~~gg~~----- 233 (260)
+|.++++ ++++||++||||++||||||||||||||+|||||.+++++||++|+++|+++|++||+.||+.||++
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 8999999999999999999999999999999999999999999999999999999999999999964
Q ss_pred --------CCCCcccEEeeeCCCCCCCcCCcccC
Q 024924 234 --------SRFPLEWLFHFRWGKKPGKVNGKIFM 259 (260)
Q Consensus 234 --------~~~~~~~lv~~R~~~~~~~~~~~~~~ 259 (260)
+.|+..++||+|.|+ ||.+||++|.
T Consensus 214 ~~~~~g~~g~~~~~~~Vy~R~g~-pC~~Cg~~I~ 246 (269)
T PRK14811 214 YRQPDGEPGGFQFQHAVYGREGQ-PCPRCGTPIE 246 (269)
T ss_pred cccCCCCcccccceEEecCCCcC-CCCcCCCeeE
Confidence 355777899999997 9999999985
No 6
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=100.00 E-value=2.6e-67 Score=471.14 Aligned_cols=240 Identities=30% Similarity=0.459 Sum_probs=216.8
Q ss_pred CCChhHHHHHHHHHHhhcCCceEEEEEecCCCccccCCChhhHHHHhcCCeEEeEEEeeeEEEEecCCCC----ccEEee
Q 024924 1 MPELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKNLWLRLDSPP----FPSFQF 76 (260)
Q Consensus 1 MPElPEVe~~~~~L~~~~~G~~I~~v~~~~~~~~~~~~~~~~~~~~L~G~~i~~v~r~GK~l~~~~~~~~----~L~~Hl 76 (260)
||||||||++++.|++.+.|++|++|++.. +++++...+++|.+.|.|++|++|.|+||||+++|+++. +|++||
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 999999999999999999999999999874 555543356788999999999999999999999999754 899999
Q ss_pred cceEEEEEeeccccccccccccCCCCCCCCceEEEEEEcCCceEEEecCCcceEEEEecCCCCCCCccCCCCCCCCCCCC
Q 024924 77 GMTGAIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELSFTDKRRFAKVRLLNDPTSVPPISELGPDALLEPMT 156 (260)
Q Consensus 77 gMtG~~~~~~~~~~~~~~~~~~~~~~~p~k~~~l~l~l~~~~~l~f~d~R~fg~~~l~~~~~~~~~l~~lGpDpl~~~~~ 156 (260)
||+|+|++... +.++++|.+++|.|+||..|.|+|+|+||+++++++ ....+.+||||||+ +|
T Consensus 80 gMtG~~~~~~~-------------~~~~~~~~~~~l~l~~~~~l~f~d~R~fg~~~l~~~--~~~~~~~LGpdpl~--~~ 142 (272)
T PRK14810 80 GMTGKLLLGGP-------------DTPSPKHTHAVLTLSSGKELRFVDSRQFGCIEYSEA--FPKRFARPGPEPLE--IS 142 (272)
T ss_pred ceeEEEEEecC-------------CCCCCCcEEEEEEeCCCCEEEEEecccCCEEEEecc--ccchhhhCCCCCCC--CC
Confidence 99999998532 123458999999999988899999999999998863 23458999999996 89
Q ss_pred HHHHHHHHcCCCcchhHHhhcCcccccchhHHHHHHHhhcCCCcccccCCCCHHHHHHHHHHHHHHHHHHHHcCCCC---
Q 024924 157 VDEFTDSLSKKKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVIQSAVEVDADC--- 233 (260)
Q Consensus 157 ~~~~~~~l~~~~~~Ik~~LlDQ~~iaGiGNiya~EiLf~a~IhP~~~~~~Ls~~e~~~L~~~i~~vL~~ai~~gg~~--- 233 (260)
.++|.+++++++++||.+||||++|||||||||+||||+|||||++++++||++|+.+|+++|++||+.|++.||++
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 --------CCCCcccEEeeeCCCCCCCcCCcccC
Q 024924 234 --------SRFPLEWLFHFRWGKKPGKVNGKIFM 259 (260)
Q Consensus 234 --------~~~~~~~lv~~R~~~~~~~~~~~~~~ 259 (260)
+.|+..++||+|.|+ ||.+||++|.
T Consensus 223 ~~~~~g~~g~~~~~~~Vy~R~g~-pCprCG~~I~ 255 (272)
T PRK14810 223 YVDAEGRSGFFQLSHRVYQRTGE-PCLNCKTPIR 255 (272)
T ss_pred ccCCCCCCCcchhhEeecCCCCC-cCCCCCCeeE
Confidence 467788999999997 9999999986
No 7
>PRK10445 endonuclease VIII; Provisional
Probab=100.00 E-value=1.2e-66 Score=464.75 Aligned_cols=235 Identities=20% Similarity=0.342 Sum_probs=208.9
Q ss_pred CCChhHHHHHHHHHHhhcCCceEEEEEecCCCccccCCChhhHHHHhcCCeEEeEEEeeeEEEEecCCCCccEEeecceE
Q 024924 1 MPELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKNLWLRLDSPPFPSFQFGMTG 80 (260)
Q Consensus 1 MPElPEVe~~~~~L~~~~~G~~I~~v~~~~~~~~~~~~~~~~~~~~L~G~~i~~v~r~GK~l~~~~~~~~~L~~HlgMtG 80 (260)
||||||||++++.|++.+.|++|.+|++.. ++ .++|.+.|.|++|++|+|+||||+|+|+++.+|++||||+|
T Consensus 1 MPELPEVe~~~~~L~~~~~g~~I~~v~~~~-~~------~~~~~~~l~g~~i~~v~rrGK~l~~~l~~~~~L~~HLgM~G 73 (263)
T PRK10445 1 MPEGPEIRRAADNLEAAIKGKPLTDVWFAF-PQ------LKPYESQLIGQRVTHIETRGKALLTHFSNGLTLYSHNQLYG 73 (263)
T ss_pred CCCchHHHHHHHHHHHHhCCCEEEEEEeCC-CC------hHHHHhhCCCCEEeEEEEEeEEEEEEcCCCCEEEEeCCcee
Confidence 999999999999999999999999999873 33 25688899999999999999999999997779999999999
Q ss_pred EEEEeeccccccccccccCCCCCCCCceEEEEEEcCCceEEEecCCcceEEEEecCC--CCCCCccCCCCCCCCCCCCHH
Q 024924 81 AIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELSFTDKRRFAKVRLLNDP--TSVPPISELGPDALLEPMTVD 158 (260)
Q Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~p~k~~~l~l~l~~~~~l~f~d~R~fg~~~l~~~~--~~~~~l~~lGpDpl~~~~~~~ 158 (260)
+|++.... ..+++.+|.+++|.|+|+..|.|.|+ ++++++.. +....+.+||||||+++||++
T Consensus 74 ~~~~~~~~-----------~~~~~~~~~~l~l~~~~~~~l~~~d~----~~~l~~~~~~~~~~~l~~lGpDpL~~~~~~~ 138 (263)
T PRK10445 74 VWRVVDTG-----------EEPQTTRVLRVRLQTADKTILLYSAS----DIEMLTPEQLTTHPFLQRVGPDVLDPNLTPE 138 (263)
T ss_pred EEEEeCCC-----------CCCCCCCcEEEEEEcCCCcEEEEECC----EEEEEeCccccccchHHhcCCCCCCCcCCHH
Confidence 99885321 11134689999999999989999994 78887632 234457999999999999999
Q ss_pred HHHHHHcCC---CcchhHHhhcCcccccchhHHHHHHHhhcCCCcccccCCCCHHHHHHHHHHHHHHHHHHHHcCCCC--
Q 024924 159 EFTDSLSKK---KITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVIQSAVEVDADC-- 233 (260)
Q Consensus 159 ~~~~~l~~~---~~~Ik~~LlDQ~~iaGiGNiya~EiLf~a~IhP~~~~~~Ls~~e~~~L~~~i~~vL~~ai~~gg~~-- 233 (260)
+|.++++++ +++||++||||++||||||||||||||+|||||.+++++||++|+.+|+++|++||+.||+.||++
T Consensus 139 ~~~~~l~~~~~~~~~IK~~LLDQ~~vaGIGNiyadEiLf~A~I~P~~~~~~Ls~~~~~~L~~~i~~vl~~ai~~gg~~~~ 218 (263)
T PRK10445 139 QVKERLLSPRFRNRQFSGLLLDQAFLAGLGNYLRVEILWQAGLTPQHKAKDLNEAQLDALAHALLDIPRLSYATRGQVDE 218 (263)
T ss_pred HHHHHHhcCccccccHHHHHhcCCccccccHHHHHHHHHHcCCCcCCCcccCCHHHHHHHHHHHHHHHHHHHHcCCCCCC
Confidence 999999887 899999999999999999999999999999999999999999999999999999999999999976
Q ss_pred ----CCCCcccEEeeeCCCCCCCcCCcccC
Q 024924 234 ----SRFPLEWLFHFRWGKKPGKVNGKIFM 259 (260)
Q Consensus 234 ----~~~~~~~lv~~R~~~~~~~~~~~~~~ 259 (260)
|.| ..++||+|.|+ +|.+||++|.
T Consensus 219 ~~~~g~~-~~~~Vy~r~g~-~Cp~Cg~~I~ 246 (263)
T PRK10445 219 NKHHGAL-FRFKVFHRDGE-ACERCGGIIE 246 (263)
T ss_pred CCCCCCc-ceEEEeCCCCC-CCCCCCCEeE
Confidence 344 57899999997 9999999986
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=2.4e-33 Score=227.34 Aligned_cols=133 Identities=56% Similarity=0.992 Sum_probs=108.6
Q ss_pred CCChhHHHHHHHHHHhhcCCceEEEEEecCCCccccCCChhhHHHHhcCCeEEeEEEeeeEEEEecCC-CCccEEeecce
Q 024924 1 MPELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKNLWLRLDS-PPFPSFQFGMT 79 (260)
Q Consensus 1 MPElPEVe~~~~~L~~~~~G~~I~~v~~~~~~~~~~~~~~~~~~~~L~G~~i~~v~r~GK~l~~~~~~-~~~L~~HlgMt 79 (260)
||||||||++++.|++.+.|++|.+|++..++.++....+.+|.+.|.|++|++|.|+||||+|+|++ +.+|++|||||
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 99999999999999999999999999987445566544577899999999999999999999999987 66999999999
Q ss_pred EEEEEeeccccccc--cccccCCCCCCCCceEEEEEEcCCceEEEecCCcceEEEE
Q 024924 80 GAIYIKGVAVTQYK--RSAVKDTDEWPSKYSKFFVELDDGLELSFTDKRRFAKVRL 133 (260)
Q Consensus 80 G~~~~~~~~~~~~~--~~~~~~~~~~p~k~~~l~l~l~~~~~l~f~d~R~fg~~~l 133 (260)
|+|.+.+.....|. ........++|+||.|+.|.|+||..|.|+|+|+||++++
T Consensus 81 G~l~~~~~~~~~~~~~~~~~~~~~~~~~kh~~~~l~l~~g~~L~f~D~RrFG~~~l 136 (137)
T cd08972 81 GAISIKGVKTIYYKMLRPPKEEDQTWPPRFYKFVLTLEDGTELAFTDPRRLGRVRL 136 (137)
T ss_pred eEEEEecCccceeeccccccccCCCCCCceEEEEEEeCCCCEEEEeCCCccceEec
Confidence 99998643211110 0000111234668999999999999999999999999986
No 9
>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=100.00 E-value=7.7e-34 Score=215.31 Aligned_cols=90 Identities=47% Similarity=0.692 Sum_probs=80.0
Q ss_pred CCCCCCCCCCCHHHHHHHHcCCCcchhHHhhcCcccccchhHHHHHHHhhcCCCcccccCCCCHHHHHHHHHHHHHHHHH
Q 024924 146 LGPDALLEPMTVDEFTDSLSKKKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVIQS 225 (260)
Q Consensus 146 lGpDpl~~~~~~~~~~~~l~~~~~~Ik~~LlDQ~~iaGiGNiya~EiLf~a~IhP~~~~~~Ls~~e~~~L~~~i~~vL~~ 225 (260)
||||||+++|+.++|.+++++++++||.+||||++||||||||+|||||+|||||.+++++||++++.+|++++++||+.
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 024924 226 AVEVDADCSR 235 (260)
Q Consensus 226 ai~~gg~~~~ 235 (260)
||+.||++-.
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 9999998753
No 10
>cd08976 BaFpgNei_N_4 Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases. This family is an uncharacterized bacterial subgroup of the FpgNei_N domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. This N-terminal proline is conserved in this family. Escherichia coli Fpg prefers 8
Probab=100.00 E-value=2.4e-32 Score=215.99 Aligned_cols=117 Identities=32% Similarity=0.602 Sum_probs=103.7
Q ss_pred CChhHHHHHHHHHHhhcCCceEEEEEecCCCccccCCChhhHHHHhcCCeEEeEEEeeeEEEEecCCCCccEEeecceEE
Q 024924 2 PELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKNLWLRLDSPPFPSFQFGMTGA 81 (260)
Q Consensus 2 PElPEVe~~~~~L~~~~~G~~I~~v~~~~~~~~~~~~~~~~~~~~L~G~~i~~v~r~GK~l~~~~~~~~~L~~HlgMtG~ 81 (260)
|||||||++++.|++.++|++|.+|++.+ ++++... +++|.+.|.|++|.+|+|+||||+++|+++.+|++||||||+
T Consensus 1 PELPEVe~~~~~l~~~~~g~~I~~v~~~~-~~~~~~~-~~~~~~~L~G~~i~~v~RrGK~L~~~l~~~~~L~~HLgMtG~ 78 (117)
T cd08976 1 PELPEVEVQKQYLERTSLHRKIVEVEVGD-DKILGEP-KATLREVLEGRTFTETHRIGKYLFLKTKEGGWLVMHFGMTGK 78 (117)
T ss_pred CCCcchHHHHHHHHHHhCCCEEEEEEECC-CCEeccC-HHHHHhhcCCCEEEEEEEeeeEEEEEcCCCCEEEEEcceEEE
Confidence 99999999999999999999999999984 5555422 678999999999999999999999999976799999999999
Q ss_pred EEEeeccccccccccccCCCCCCCCceEEEEEEcCCceEEEecCCcceEEEE
Q 024924 82 IYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELSFTDKRRFAKVRL 133 (260)
Q Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~p~k~~~l~l~l~~~~~l~f~d~R~fg~~~l 133 (260)
|.+... +.+|++|.|++|.|+||..|.|+|+|+||++++
T Consensus 79 ~~~~~~-------------~~~~~kh~~~~l~l~~g~~l~~~D~R~fg~~~~ 117 (117)
T cd08976 79 LDYYPD-------------DEDPPKHARLLLHFEDGFRLAFECPRKFGRVRL 117 (117)
T ss_pred EEEECC-------------CCCCCCEEEEEEEECCCCEEEEeCCCccceeEC
Confidence 988532 235668999999999998999999999999874
No 11
>PF01149 Fapy_DNA_glyco: Formamidopyrimidine-DNA glycosylase N-terminal domain; InterPro: IPR012319 This entry represents the catalytic domain of DNA glycosylase/AP lyase enzymes, which are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Most damage to bases in DNA is repaired by the base excision repair pathway []. These enzymes are primarily from bacteria, and have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC). Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines [, ]. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above (3.2.2 from EC, 4.2.99.18 from EC), but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine []. These protein contains three structural domains: an N-terminal catalytic core domain, a central helix-two turn-helix (H2TH) module and a C-terminal zinc finger []. The N-terminal catalytic domain and the C-terminal zinc finger straddle the DNA with the long axis of the protein oriented roughly orthogonal to the helical axis of the DNA. Residues that contact DNA are located in the catalytic domain and in a beta-hairpin loop formed by the zinc finger [].; GO: 0003684 damaged DNA binding, 0003906 DNA-(apurinic or apyrimidinic site) lyase activity, 0008270 zinc ion binding, 0016799 hydrolase activity, hydrolyzing N-glycosyl compounds, 0006284 base-excision repair; PDB: 1K82_C 3GQ3_A 3JR5_A 3SAT_A 3GPX_A 2F5Q_A 3SBJ_A 3U6S_A 3SAU_A 3SAR_A ....
Probab=99.98 E-value=4.2e-32 Score=214.24 Aligned_cols=116 Identities=34% Similarity=0.667 Sum_probs=100.3
Q ss_pred CChhHHHHHHHHHHhhcCCceEEEEEecCCCccccCCChhhHHHHhcCCeEEeEEEeeeEEEEecCCCCccEEeecceEE
Q 024924 2 PELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKNLWLRLDSPPFPSFQFGMTGA 81 (260)
Q Consensus 2 PElPEVe~~~~~L~~~~~G~~I~~v~~~~~~~~~~~~~~~~~~~~L~G~~i~~v~r~GK~l~~~~~~~~~L~~HlgMtG~ 81 (260)
|||||||++++.|++.++|++|.+|++. .+++++++++++|.+.|.|++|++++|+||||+|+|+++.+|++||||||+
T Consensus 1 PElPEVe~~~~~L~~~~~g~~I~~v~~~-~~~~~~~~~~~~~~~~l~g~~i~~v~rrGK~L~~~l~~~~~l~~HlgMtG~ 79 (116)
T PF01149_consen 1 PELPEVETVRRGLRPALVGKRIESVEVR-RPKILRNPEPEEFRKALQGRKITDVERRGKYLFFHLDGGLVLVVHLGMTGR 79 (116)
T ss_dssp --HHHHHHHHHHHHHHHTTCEEEEEEES-SGGGCCSSCCHHHHHHHTTEEEEEEEEETTEEEEEETTTEEEEEE-TTTEE
T ss_pred CCcHHHHHHHHHHHHHhCCCEEEEEEEc-CCccccCCCchHHHhhccceEEEEEEecccEEEEEeCCCCEEEEeeCCcEE
Confidence 9999999999999999999999999998 567777777777999999999999999999999999988999999999999
Q ss_pred EEEeeccccccccccccCCCCCCCCceEEEEEEcCCceEEEecCCcceEEE
Q 024924 82 IYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELSFTDKRRFAKVR 132 (260)
Q Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~p~k~~~l~l~l~~~~~l~f~d~R~fg~~~ 132 (260)
|.+.. ..++++|++++|.|+||..|.|+|+|+||+++
T Consensus 80 ~~~~~--------------~~~~~~~~~~~l~~~~g~~L~f~D~R~fg~~r 116 (116)
T PF01149_consen 80 LRLDP--------------PDWPPKHTRLRLRFEDGSRLRFVDPRRFGRVR 116 (116)
T ss_dssp EEEST--------------TCG-STTEEEEEEETSSEEEEEEETTS--EE-
T ss_pred EEecC--------------CCCCCCeEEEEEEECCCCEEEEEcCCCCCCCC
Confidence 99821 34677899999999999999999999999985
No 12
>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=99.98 E-value=1.5e-31 Score=212.15 Aligned_cols=119 Identities=36% Similarity=0.608 Sum_probs=106.1
Q ss_pred CChhHHHHHHHHHHhhcCCceEEEEEecCCCccccCCChhhHHHHhcCCeEEeEEEeeeEEEEecCCCCccEEeecceEE
Q 024924 2 PELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKNLWLRLDSPPFPSFQFGMTGA 81 (260)
Q Consensus 2 PElPEVe~~~~~L~~~~~G~~I~~v~~~~~~~~~~~~~~~~~~~~L~G~~i~~v~r~GK~l~~~~~~~~~L~~HlgMtG~ 81 (260)
|||||||++++.|++.++|++|.+|++.+. ....+.++++|.+.|.|++|.+|.|+||||+|+|+++.+|++||||||+
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 999999999999999999999999998754 4444446788999999999999999999999999987899999999999
Q ss_pred EEEeeccccccccccccCCCCCCCCceEEEEEEcCCceEEEecCCcceEEEEe
Q 024924 82 IYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELSFTDKRRFAKVRLL 134 (260)
Q Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~p~k~~~l~l~l~~~~~l~f~d~R~fg~~~l~ 134 (260)
|.+.+. ..++++|.+++|.|+||..|.|+|+|+||+++++
T Consensus 80 ~~~~~~-------------~~~~~~~~~l~l~~~~g~~l~f~D~R~fG~~~~~ 119 (120)
T cd08966 80 LLVVPP-------------DEPPEKHDHVIFELDDGRELRFNDPRRFGTLLLV 119 (120)
T ss_pred EEEeCC-------------CCCCCCcEEEEEEeCCCCEEEEEcCCCCcEEEEe
Confidence 988532 2355689999999999999999999999999976
No 13
>cd08773 FpgNei_N N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. These enzymes initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycolsylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. The FpgNei DNA glycosylases represent one of the two structural superfamilies of DNA glycosylases that recognize oxidized bases (the other is the HTH-GPD superfamily exemplified by Escherichia coli Nth). Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. One e
Probab=99.97 E-value=5e-30 Score=202.57 Aligned_cols=116 Identities=34% Similarity=0.608 Sum_probs=101.8
Q ss_pred CChhHHHHHHHHHHhhcCCceEEEEEecCCCccccCCChhhHHHHhcCCeEEeEEEeeeEEEEecCCCCccEEeecceEE
Q 024924 2 PELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKNLWLRLDSPPFPSFQFGMTGA 81 (260)
Q Consensus 2 PElPEVe~~~~~L~~~~~G~~I~~v~~~~~~~~~~~~~~~~~~~~L~G~~i~~v~r~GK~l~~~~~~~~~L~~HlgMtG~ 81 (260)
|||||||++++.|++.+.|++|++|++.+. ....+ .+++|.+.|.|++|.+++|+||||+++|+++.+|++||||||+
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 999999999999999999999999999753 33322 2678999999999999999999999999977799999999999
Q ss_pred EEEeeccccccccccccCCCCCCCCceEEEEEEcCCceEEEecCCcceEEE
Q 024924 82 IYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELSFTDKRRFAKVR 132 (260)
Q Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~p~k~~~l~l~l~~~~~l~f~d~R~fg~~~ 132 (260)
|++.+. +.++++|.+++|.|+|+..|.|+|+|+||+++
T Consensus 79 ~~~~~~-------------~~~~~~~~~~~~~~~~~~~l~f~d~R~fG~~~ 116 (117)
T cd08773 79 LRVCPE-------------GEPPPKHDRLVLRLANGSQLRFTDPRKFGRVE 116 (117)
T ss_pred EEEeCC-------------CCCCCCeEEEEEEECCCCEEEEECCCcccccc
Confidence 998542 22456899999999999899999999999975
No 14
>cd08973 BaFpgNei_N_1 Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases. This family is an uncharacterized bacterial subgroup of the FpgNei_N domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. This N-terminal proline is conserved in this family. Escherichia coli Fpg prefers 8
Probab=99.97 E-value=8.1e-30 Score=203.04 Aligned_cols=115 Identities=23% Similarity=0.375 Sum_probs=99.4
Q ss_pred CCChhHHHHHHHHHHhhcCCceEEEEEecCCCccccCCChhhHHHHhcCCeEEeEEEeeeEEEEecCCCCccEEeecceE
Q 024924 1 MPELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKNLWLRLDSPPFPSFQFGMTG 80 (260)
Q Consensus 1 MPElPEVe~~~~~L~~~~~G~~I~~v~~~~~~~~~~~~~~~~~~~~L~G~~i~~v~r~GK~l~~~~~~~~~L~~HlgMtG 80 (260)
||||||||++++.|++.+.|++|.+|++.. +.... ++++|.+.|.|++|++|.|+||||+|+|+++.+|++||||||
T Consensus 1 MPELPEve~~~~~L~~~l~Gk~I~~v~~~~-~~~~~--~~~~~~~~L~G~~i~~v~RrGK~l~~~~~~~~~L~~HLgMtG 77 (122)
T cd08973 1 MPELPEVEVYAENLERRLTGKTITRVELAS-KSLLV--TPDPPLEALEGRTVTGVRRHGKRLDFEFDNGLHLVLHLMLAG 77 (122)
T ss_pred CCChHHHHHHHHHHHHhcCCCEEEEEEEcC-ccccC--ChhHHHhhCCCCEEeEEEEEeeEEEEEcCCCCEEEEeCCCeE
Confidence 999999999999999999999999999874 44432 478899999999999999999999999997679999999999
Q ss_pred EEEEeeccccccccccccCCCCCCCCceEEEEEEcC-CceEEEecCCcceE
Q 024924 81 AIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDD-GLELSFTDKRRFAK 130 (260)
Q Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~p~k~~~l~l~l~~-~~~l~f~d~R~fg~ 130 (260)
+|++...+ ..++++|.|++|.|+| |..|.|+|+|.--.
T Consensus 78 ~l~~~~~~------------~~~~~~~~~v~l~~~~~g~~L~~~D~r~~~~ 116 (122)
T cd08973 78 WLYWTEAG------------ALLPGKKGPIALRFEDYGGGLDLTEAGTKKR 116 (122)
T ss_pred EEEEeCCC------------CCCCCCcEEEEEEEcCCCCEEEEECCCcccc
Confidence 99985421 1245689999999999 88999999986543
No 15
>cd08967 MeNeil1_N N-terminal domain of metazoan Nei-like glycosylase 1 (NEIL1). This family contains the N-terminal domain of metazoan NEIL1. It belongs to the FpgNei_N, [N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII)] domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. NEIL1 recognizes the oxidized pyrimidines 2,6-diamino-4-hydroxy-5-formamidopyrimidi
Probab=99.97 E-value=1.4e-29 Score=203.34 Aligned_cols=112 Identities=28% Similarity=0.352 Sum_probs=94.7
Q ss_pred CCChhHHHHHHHHHHhhcCCceEEEEEecCCCccccCC-ChhhHHHHhcCCeEEeEEEeeeEEEEecCCC----------
Q 024924 1 MPELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGV-SASDFEASVLGKAILSAHRKGKNLWLRLDSP---------- 69 (260)
Q Consensus 1 MPElPEVe~~~~~L~~~~~G~~I~~v~~~~~~~~~~~~-~~~~~~~~L~G~~i~~v~r~GK~l~~~~~~~---------- 69 (260)
||||||||++++.|+++++|++|.+|++.+ + +..++ .+.+|.+ ++|. ++|+||||++.|+++
T Consensus 1 MPELPEVe~vr~~L~~~~~g~~I~~v~v~~-~-~~~~~~~~~~~~~----~~i~-~~RrGKyL~l~l~~~~~~~~~~~~~ 73 (131)
T cd08967 1 MPEGPELHLASLFVNKMCKGLIFTGAVEKS-S-VSKNPEVPFACKA----YTIS-AESRGKELRLILSPLPAANGKKECK 73 (131)
T ss_pred CCCcHHHHHHHHHHHHhcCCCEEEEEEEec-c-cccCCCCCcchhc----EEEE-EEeeeeEEEEEccCCcccccccccc
Confidence 999999999999999999999999999984 4 44332 3444443 8899 999999999999876
Q ss_pred ---C-ccEEeecceEEEEEeeccccccccccccCCCCCCCCceEEEEEEcCC--ceEEEecCCcceEEEE
Q 024924 70 ---P-FPSFQFGMTGAIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDG--LELSFTDKRRFAKVRL 133 (260)
Q Consensus 70 ---~-~L~~HlgMtG~~~~~~~~~~~~~~~~~~~~~~~p~k~~~l~l~l~~~--~~l~f~d~R~fg~~~l 133 (260)
. +|++||||||++++... ..++||.|++|.|+|| ..|.|+|+|+||++++
T Consensus 74 ~~~~~~Lv~HLgMtG~l~~~~~--------------~~~~kh~~l~~~~~dg~g~~L~f~D~RrFG~~~l 129 (131)
T cd08967 74 SQEEMRIVFRFGMSGSFQFTPV--------------DEIPKHAHLRFYTKEEPKRVLSFVDIRRFGTWQV 129 (131)
T ss_pred ccCCCEEEEecCceeEEEEecC--------------CCCCCcEEEEEEeCCCCCCEEEEECCCceeEEEe
Confidence 2 89999999999998532 1346899999999985 7899999999999985
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=8.3e-28 Score=190.04 Aligned_cols=113 Identities=23% Similarity=0.284 Sum_probs=98.5
Q ss_pred ChhHHHHHHHHHHhhcCCceEEEEEecCCC--ccccCCChhhHHHHhcCCeEEeEEEeeeEEEEecCCCCccEEeecceE
Q 024924 3 ELPEVEAARRAIEEHCIGKKIVKSIIADDN--KVIDGVSASDFEASVLGKAILSAHRKGKNLWLRLDSPPFPSFQFGMTG 80 (260)
Q Consensus 3 ElPEVe~~~~~L~~~~~G~~I~~v~~~~~~--~~~~~~~~~~~~~~L~G~~i~~v~r~GK~l~~~~~~~~~L~~HlgMtG 80 (260)
||||||++++.|++.+.|++|.+|++.++. .+++++++++|.+.|.|++|++++|+||||+|.|+++ +|++||||||
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 999999999999999999999999998532 3334445788999999999999999999999999975 9999999999
Q ss_pred EEEEeeccccccccccccCCCCCCCCceEEEEEEcCCceEEEecCCcceEEE
Q 024924 81 AIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELSFTDKRRFAKVR 132 (260)
Q Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~p~k~~~l~l~l~~~~~l~f~d~R~fg~~~ 132 (260)
+|++. +.+|++|.+++|.|+||..|.|+ +++||.+.
T Consensus 81 ~l~~~---------------~~~~~kh~~l~l~~~dg~~L~f~-~~~~~~~~ 116 (117)
T cd08975 81 RYYYG---------------GEKIPKKYQLLIEFDDDSFLVFT-VAMYGGIA 116 (117)
T ss_pred EEEeC---------------CCCCCCeEEEEEEECCCCEEEEE-EEEEeeee
Confidence 99872 12456899999999999899999 99999763
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=99.95 E-value=1.6e-27 Score=187.67 Aligned_cols=111 Identities=18% Similarity=0.267 Sum_probs=95.1
Q ss_pred CCChhHHHHHHHHHHhhcCCceEEEEEecCCCccccCCChhhHHHHhcCCeEEeEEEeeeEEEEecCCCCccEEeecceE
Q 024924 1 MPELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKNLWLRLDSPPFPSFQFGMTG 80 (260)
Q Consensus 1 MPElPEVe~~~~~L~~~~~G~~I~~v~~~~~~~~~~~~~~~~~~~~L~G~~i~~v~r~GK~l~~~~~~~~~L~~HlgMtG 80 (260)
||||||||++++.|++.+.|++|.++++.. +.+ +.+.|.|++|.+++|+||||++.|+++.+|++||||||
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 999999999999999999999999999873 332 25679999999999999999999987779999999999
Q ss_pred EEEEeeccccccccccccCCC-CCCCCceEEEEEEcCCceEEEecCCcceEEEEec
Q 024924 81 AIYIKGVAVTQYKRSAVKDTD-EWPSKYSKFFVELDDGLELSFTDKRRFAKVRLLN 135 (260)
Q Consensus 81 ~~~~~~~~~~~~~~~~~~~~~-~~p~k~~~l~l~l~~~~~l~f~d~R~fg~~~l~~ 135 (260)
+|++.... .. ++|.+|.+++|.|+||..|.|+|. .|++++
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 99985421 11 235689999999999999999984 777775
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=99.94 E-value=9.7e-27 Score=178.44 Aligned_cols=96 Identities=19% Similarity=0.274 Sum_probs=83.3
Q ss_pred CCChhHHHHHHHHHHhhcCCceEEEEEecCCCccccCCChhhHHHHhcCCeEEeEEEeeeEEEEecCCCCccEEeecceE
Q 024924 1 MPELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKNLWLRLDSPPFPSFQFGMTG 80 (260)
Q Consensus 1 MPElPEVe~~~~~L~~~~~G~~I~~v~~~~~~~~~~~~~~~~~~~~L~G~~i~~v~r~GK~l~~~~~~~~~L~~HlgMtG 80 (260)
||||||||++++.|++ +.|++|.+++.. ++. +.+.|.|++|++|+|+||||+++|++ .+|++||||||
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 999999999954 221 25689999999999999999999986 49999999999
Q ss_pred EEEEeeccccccccccccCCCCCCCCceEEEEEEcCCceEEEec
Q 024924 81 AIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELSFTD 124 (260)
Q Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~p~k~~~l~l~l~~~~~l~f~d 124 (260)
+|++.+ .|++|.|++|.|+||..+.|+|
T Consensus 69 ~l~~~~----------------~~~~~~~~~l~~~~g~~~~~~~ 96 (98)
T cd08974 69 SYRINE----------------RKDAPPRLSLGFDNGELNFYTC 96 (98)
T ss_pred EEEEeC----------------CCCCcEEEEEEeCCCcEEEEec
Confidence 999842 2558999999999997777766
No 19
>cd08965 EcNei-like_N N-terminal domain of Escherichia coli Nei/endonuclease VIII and related DNA glycosylases. This family contains the N-terminal domain of proteobacteria Nei and related DNA glycosylases. It includes Escherichia coli Nei, and belongs to the FpgNei_N, [N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII)] domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff bas
Probab=99.94 E-value=4.8e-26 Score=179.51 Aligned_cols=113 Identities=17% Similarity=0.227 Sum_probs=96.1
Q ss_pred CChhHHHHHHHHHHhhcCCceEEEEEecCCCccccCCChhhHHHHhcCCeEEeEEEeeeEEEEecCCCCccEEeecceEE
Q 024924 2 PELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKNLWLRLDSPPFPSFQFGMTGA 81 (260)
Q Consensus 2 PElPEVe~~~~~L~~~~~G~~I~~v~~~~~~~~~~~~~~~~~~~~L~G~~i~~v~r~GK~l~~~~~~~~~L~~HlgMtG~ 81 (260)
|||||||++++.|++.+.|++|.++++.+ ++ ..+|.+.|.|++|.+|+|+||||+++|+++.+|++||||||+
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 99999999999999999999999999874 32 256788999999999999999999999877799999999999
Q ss_pred EEEeeccccccccccccCCCCCCCCceEEEEEEcCCceEEEecCCcceEEEEecC
Q 024924 82 IYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELSFTDKRRFAKVRLLND 136 (260)
Q Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~p~k~~~l~l~l~~~~~l~f~d~R~fg~~~l~~~ 136 (260)
|++..+. ...+|.+|++++|.++||..+.|.+ +.|+++++
T Consensus 74 ~~~~~~~-----------~~~~~~~~~rl~l~~~~g~~l~~~~----~~~~l~~~ 113 (115)
T cd08965 74 WRVRKRG-----------NYPKTNRQLRVALHTAKKSALLYSA----SDIDVLPT 113 (115)
T ss_pred EEEeCCC-----------CCCCCCCeEEEEEEcCCceEEeeCC----CEEEEecC
Confidence 9985321 1125668999999999998888776 47888864
No 20
>cd08970 AcNei1_N N-terminal domain of the actinomycetal Nei1 and related DNA glycosylases. This family contains the N-terminal domain of the actinomycetal Nei1 and related DNA glycosylases. It belongs to the FpgNei_N, [N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII)] domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. This family contains mostly actinom
Probab=99.94 E-value=9.6e-26 Score=176.36 Aligned_cols=109 Identities=19% Similarity=0.263 Sum_probs=88.8
Q ss_pred CCChhHHHHHHHHHHhhcCCceEEEEEecCCCccccCCChhhHHHHhcCCeEEeEEEeeeEEEEecCCCCccEEeecceE
Q 024924 1 MPELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKNLWLRLDSPPFPSFQFGMTG 80 (260)
Q Consensus 1 MPElPEVe~~~~~L~~~~~G~~I~~v~~~~~~~~~~~~~~~~~~~~L~G~~i~~v~r~GK~l~~~~~~~~~L~~HlgMtG 80 (260)
||||||||++++.|++.+.|++| ++.. +.+. +++|.+.|.|++|++|+|+||||+++|+++.+|++||||||
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 3332 3332 35788899999999999999999999987669999999999
Q ss_pred EEEEeeccccccccccccCCCCCCCCceEEEEEEcCCceEEEecCCcceEEEE
Q 024924 81 AIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELSFTDKRRFAKVRL 133 (260)
Q Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~p~k~~~l~l~l~~~~~l~f~d~R~fg~~~l 133 (260)
+|++... . ++++|.+++|.|++... . .|+|..+.+.+
T Consensus 73 ~~~~~~~-------------~-~~~~h~~~~l~l~~~~~-~-~~~~~~~~~~~ 109 (110)
T cd08970 73 KFRFGGD-------------P-PPPPRGQVRLRLVGDTH-A-ADLRGPTVCEL 109 (110)
T ss_pred EEEEecC-------------C-CCCceEEEEEEECCCCc-E-EcCCCCceEEe
Confidence 9998532 1 34589999999977644 4 56777676665
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=99.90 E-value=5.8e-23 Score=162.78 Aligned_cols=111 Identities=22% Similarity=0.400 Sum_probs=90.8
Q ss_pred CCChhHHHHHHHHHHhhcCCceEEEEEecCCCccccCCChhhHHHHhcCCeEEeEEEeeeEEEEecCC----------CC
Q 024924 1 MPELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKNLWLRLDS----------PP 70 (260)
Q Consensus 1 MPElPEVe~~~~~L~~~~~G~~I~~v~~~~~~~~~~~~~~~~~~~~L~G~~i~~v~r~GK~l~~~~~~----------~~ 70 (260)
|||+|+|+++++.++ .+.|++|..++... +. ...+.|.|+++++++++||+|+++|++ +.
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-KK--------INPNDLQGLRLQDSQVHGKNLFLHFDLDEEMGPDRDAGR 70 (126)
T ss_pred CCCcHHHHHHHHHHH-HhCCCEEEEcCCCC-Cc--------chhhhcCCcEEEEEEEeccEEEEEecCcccccccccCCc
Confidence 999999999998887 78999999887541 11 124579999999999999999999975 35
Q ss_pred ccEEeecceEEEEEeeccccccccccccCCCCCCCCceEEEEEEcCCceEEEecC
Q 024924 71 FPSFQFGMTGAIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELSFTDK 125 (260)
Q Consensus 71 ~L~~HlgMtG~~~~~~~~~~~~~~~~~~~~~~~p~k~~~l~l~l~~~~~l~f~d~ 125 (260)
+|++||||+|+|++++.. + ..++..+..||+++.+|+|.|+||..|+|+|+
T Consensus 71 ~lhvHLGM~Gs~~~~~~~---~-~~~~~~~~~~~~~~~~l~l~f~~~~~l~F~~~ 121 (126)
T cd08968 71 WLRFHFGLFGSVRANEFS---R-AKKANKRGDWKDPNPRLVLHFESGGFLVFYNC 121 (126)
T ss_pred eEEEeCCCEEEEEEcccc---c-CcccccccCCCCCCCeEEEEeCCCcEEEEEcc
Confidence 899999999999997642 1 12234445688899999999999989999985
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=99.69 E-value=2.2e-16 Score=126.77 Aligned_cols=112 Identities=19% Similarity=0.255 Sum_probs=85.0
Q ss_pred CCChhHHHHHHHHHHhh-cCCceEEEEEecCCCccc----cCC-----ChhhHHHHhcCCeEEeEEEeeeEEEEecCCCC
Q 024924 1 MPELPEVEAARRAIEEH-CIGKKIVKSIIADDNKVI----DGV-----SASDFEASVLGKAILSAHRKGKNLWLRLDSPP 70 (260)
Q Consensus 1 MPElPEVe~~~~~L~~~-~~G~~I~~v~~~~~~~~~----~~~-----~~~~~~~~L~G~~i~~v~r~GK~l~~~~~~~~ 70 (260)
|-|+|-...-.+.+... ..|+++..+........- .+. +...|.+.|.|++|++++|+||||+++|+++
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 88999998888888753 479999877754321111 010 1256889999999999999999999999875
Q ss_pred ccEEeecceEEEEEeeccccccccccccCCCCCCCCceEEEEEEcCCceEEEecC
Q 024924 71 FPSFQFGMTGAIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELSFTDK 125 (260)
Q Consensus 71 ~L~~HlgMtG~~~~~~~~~~~~~~~~~~~~~~~p~k~~~l~l~l~~~~~l~f~d~ 125 (260)
+|++||||+|+|++..+. ....+.+++++.+.|+++ .|+|+|+
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 899999999999996431 011345688999999887 5999996
No 23
>PF05833 FbpA: Fibronectin-binding protein A N-terminus (FbpA); InterPro: IPR008616 This family consists of the N-terminal region of the prokaryotic fibronectin-binding protein, the C-terminal region is IPR008532 from INTERPRO. Fibronectin binding is considered to be an important virulence factor in streptococcal infections. Fibronectin is a dimeric glycoprotein that is present in a soluble form in plasma and extracellular fluids; it is also present in a fibrillar form on cell surfaces. Both the soluble and cellular forms of fibronectin may be incorporated into the extracellular tissue matrix. While fibronectin has critical roles in eukaryotic cellular processes, such as adhesion, migration and differentiation, it is also a substrate for the attachment of bacteria. The binding of pathogenic Streptococcus pyogenes and Staphylococcus aureus to epithelial cells via fibronectin facilitates their internalisation and systemic spread within the host [].; PDB: 3DOA_A 2ZBK_F 2HKJ_A 1Z5B_A 1Z5C_B 1MX0_F 1Z5A_A 1MU5_A 1Z59_A.
Probab=98.17 E-value=4.3e-05 Score=73.28 Aligned_cols=79 Identities=30% Similarity=0.433 Sum_probs=59.4
Q ss_pred CCCCCCCCCCCH-HHHHHHHcCCCcchhHHhhcCcccccchhHHHHHHHhhcCCCcccccCCCCHHHHHHHHHHHHHHHH
Q 024924 146 LGPDALLEPMTV-DEFTDSLSKKKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVIQ 224 (260)
Q Consensus 146 lGpDpl~~~~~~-~~~~~~l~~~~~~Ik~~LlDQ~~iaGiGNiya~EiLf~a~IhP~~~~~~Ls~~e~~~L~~~i~~vL~ 224 (260)
-+.||+ .++. +.|...+......+..+|+++ +.|+|..++.|++++|||+|..++..++++++.+|+++++.++.
T Consensus 165 ~~~~p~--~~~~~~~~~~~l~~~~~~l~~~L~~~--~~G~~~~la~ei~~ra~i~~~~~~~~~~~~~~~~l~~~~~~l~~ 240 (455)
T PF05833_consen 165 DKLDPL--DLEEFEEFIELLKKKEKTLVKALSKN--FQGFGPELAEEILYRAGIDKNKKVEELSDEEIEKLFEAIRELLN 240 (455)
T ss_dssp --B-CC--C--H-HHHHHHHHCCG-BHHHHHHHH--CTT--HHHHHHHHCCCTS-TTSBGGG--HHHHCHHHHHHHHHHH
T ss_pred cCCCcc--cchhHHHHHHhhccCcccHHHHHHHH--HHHhHHHHHHHHHHHhCCCCccccccchhhhHHHHHHHHHHhhh
Confidence 366777 3444 678888877778888888865 89999999999999999999999999999999999999999999
Q ss_pred HHHH
Q 024924 225 SAVE 228 (260)
Q Consensus 225 ~ai~ 228 (260)
....
T Consensus 241 ~l~~ 244 (455)
T PF05833_consen 241 ELEE 244 (455)
T ss_dssp HHT-
T ss_pred hccc
Confidence 8873
No 24
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=97.07 E-value=0.00069 Score=53.25 Aligned_cols=40 Identities=33% Similarity=0.406 Sum_probs=38.8
Q ss_pred cccchhHHHHHHHhhcCCCcccccCCCCHHHHHHHHHHHH
Q 024924 181 ISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIK 220 (260)
Q Consensus 181 iaGiGNiya~EiLf~a~IhP~~~~~~Ls~~e~~~L~~~i~ 220 (260)
|-|||--+|.|||-.+||+|..++++||++|+.+|-+.+.
T Consensus 22 IyGIG~~~a~~I~~~~gi~~~~r~~eLteeei~~ir~~i~ 61 (121)
T COG0099 22 IYGIGRRRAKEICKKAGIDPDKRVGELTEEEIERLRDAIQ 61 (121)
T ss_pred hccccHHHHHHHHHHcCCCHhHhhccCCHHHHHHHHHHHH
Confidence 8899999999999999999999999999999999998887
No 25
>PF00416 Ribosomal_S13: Ribosomal protein S13/S18; InterPro: IPR001892 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S13 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S13 is known to be involved in binding fMet-tRNA and, hence, in the initiation of translation. It is a basic protein of 115 to 177 amino-acid residues that contains thee helices and a beta-hairpin in the core of the protein, forming a helix-two turns-helix (H2TH) motif, and a non-globular C-terminal extension. This family of ribosomal proteins is present in prokaryotes, eukaryotes and archaea [, ].; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3BBN_M 2QBB_M 3I1M_M 3OFP_M 3OFX_M 3OFO_M 1VS5_M 3OAQ_M 2QAL_M 3J18_M ....
Probab=96.99 E-value=0.0021 Score=49.92 Aligned_cols=52 Identities=29% Similarity=0.296 Sum_probs=45.4
Q ss_pred CCcchhHHhhcCcccccchhHHHHHHHhhcCCCcccccCCCCHHHHHHHHHHHHH
Q 024924 167 KKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKE 221 (260)
Q Consensus 167 ~~~~Ik~~LlDQ~~iaGiGNiya~EiLf~a~IhP~~~~~~Ls~~e~~~L~~~i~~ 221 (260)
.+.+|.-+|. -|-|||+..|..||-.+||||..++++||++|+.+|-+.+..
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 26
>PRK04184 DNA topoisomerase VI subunit B; Validated
Probab=96.99 E-value=0.0048 Score=60.52 Aligned_cols=75 Identities=24% Similarity=0.413 Sum_probs=65.6
Q ss_pred cCCCCCCCCCCCCHHHHHHHHcC-CCcchhHHhhcCcccccchhHHHHHHHhhcCCCcccccCCCCHHHHHHHHHHHHHH
Q 024924 144 SELGPDALLEPMTVDEFTDSLSK-KKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEV 222 (260)
Q Consensus 144 ~~lGpDpl~~~~~~~~~~~~l~~-~~~~Ik~~LlDQ~~iaGiGNiya~EiLf~a~IhP~~~~~~Ls~~e~~~L~~~i~~v 222 (260)
...-|-|. .++.+.+.+.++. ++.++.++|. +-|+.||+-.|+|++-.+|++|..+..+|+++|+.+|+++++.+
T Consensus 232 ~e~kpHP~--gv~~~~l~~m~~~t~~~~l~~fL~--~~f~~v~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~~ 307 (535)
T PRK04184 232 KEIKPHPH--GVDLGTLKRMAARTKRRTLKEFLV--EEFSRVGDKTADEILEKAGLDPNKKPKELTREELERLVEAFKKY 307 (535)
T ss_pred ccCCCCCC--ccCHHHHHHHHHhcccCCHHHHHH--HhhcccCHHHHHHHHHHcCCCCCCChhhCCHHHHHHHHHHHHhc
Confidence 34556666 4688899998874 5689999995 67999999999999999999999999999999999999999975
No 27
>COG1293 Predicted RNA-binding protein homologous to eukaryotic snRNP [Transcription]
Probab=96.79 E-value=0.031 Score=55.48 Aligned_cols=73 Identities=16% Similarity=0.241 Sum_probs=55.0
Q ss_pred CCCCCCCCHHHHHHHHcCCCcchhHHhhcCcccccchhHHHHHHHhhcCCCcccccCCCCHHHHHHHHHHHHHHHHHH
Q 024924 149 DALLEPMTVDEFTDSLSKKKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVIQSA 226 (260)
Q Consensus 149 Dpl~~~~~~~~~~~~l~~~~~~Ik~~LlDQ~~iaGiGNiya~EiLf~a~IhP~~~~~~Ls~~e~~~L~~~i~~vL~~a 226 (260)
+|+. .+.+.|.......-.-++. =++.+.|+|-.|++|+||+||+++..++.+++++++..+..++...+...
T Consensus 168 ~p~~--~~~~~~~~~~~~~~~~~~~---~~~~~~g~~~~~a~el~~rag~~~~~~~~~~~~~~~~~v~~~~~~~~~~~ 240 (564)
T COG1293 168 NPYE--QSEEDFKELQLNSGADIVR---LLARFLGLGGLLAEELLSRAGLDKKVPAKDLFEEEIKKVREALEELLNPL 240 (564)
T ss_pred Chhh--cChHHHHHHHhccchHHHH---HHHHhcCCCHHHHHHHHHhcCCCcCCchhhhhHHHHHHHHHHHHhhhhcc
Confidence 6664 3444455554443222222 24678999999999999999999999999999999999999998876544
No 28
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=96.71 E-value=0.0024 Score=50.82 Aligned_cols=51 Identities=29% Similarity=0.374 Sum_probs=45.0
Q ss_pred CcchhHHhhcCcccccchhHHHHHHHhhcCCCcccccCCCCHHHHHHHHHHHHH
Q 024924 168 KITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKE 221 (260)
Q Consensus 168 ~~~Ik~~LlDQ~~iaGiGNiya~EiLf~a~IhP~~~~~~Ls~~e~~~L~~~i~~ 221 (260)
+.+|.-+| +-|-|||.-.|..||-.+||||..++++||++|+..|-+.+..
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 45666666 4588999999999999999999999999999999999988864
No 29
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=96.49 E-value=0.0044 Score=49.30 Aligned_cols=50 Identities=34% Similarity=0.426 Sum_probs=43.9
Q ss_pred CcchhHHhhcCcccccchhHHHHHHHhhcCCCcccccCCCCHHHHHHHHHHHH
Q 024924 168 KITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIK 220 (260)
Q Consensus 168 ~~~Ik~~LlDQ~~iaGiGNiya~EiLf~a~IhP~~~~~~Ls~~e~~~L~~~i~ 220 (260)
+.+|.-+| +-|-|||--+|..||-.+||||..++++||++|+.+|.+.+.
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 45555566 448899999999999999999999999999999999998885
No 30
>TIGR01052 top6b DNA topoisomerase VI, B subunit. This model describes DNA topoisomerase VI, an archaeal type II DNA topoisomerase (DNA gyrase).
Probab=96.49 E-value=0.018 Score=56.03 Aligned_cols=74 Identities=22% Similarity=0.334 Sum_probs=64.2
Q ss_pred CCCCCCCCCCCCHHHHHHHHcC-CCcchhHHhhcCcccccchhHHHHHHHhhcCCC---cccccCCCCHHHHHHHHHHHH
Q 024924 145 ELGPDALLEPMTVDEFTDSLSK-KKITIKALLLDQSYISGIGNWVADEVLYQAKIH---PLQTAVSLSKESCATLLKCIK 220 (260)
Q Consensus 145 ~lGpDpl~~~~~~~~~~~~l~~-~~~~Ik~~LlDQ~~iaGiGNiya~EiLf~a~Ih---P~~~~~~Ls~~e~~~L~~~i~ 220 (260)
..-|-|. ..+.+.+...++. +.+++.++|. +-|+.||.-.|+|++..+|+. |..+..+|+++|+.+|+++++
T Consensus 224 e~kpHP~--gv~~~~l~~m~~~t~~~~l~~fL~--~~f~~v~~~~a~~~~~~~g~~~~~~~~~~~~l~~~~~~~l~~~~~ 299 (488)
T TIGR01052 224 EMKPHPH--GVTIDDLKSMARSTRASTLRSFLV--SEFSRIGEKKIKELLEKYGIDVDPLDKKPKELTWDEAEKIVNAFK 299 (488)
T ss_pred cCCCCCC--ccCHHHHHHHHHhcCcccHHHHHH--HhhcccCHHHHHHHHHHhCCCccccCCChhhCCHHHHHHHHHHHH
Confidence 4456666 4688899988875 4689999995 579999999999999999999 999999999999999999999
Q ss_pred HH
Q 024924 221 EV 222 (260)
Q Consensus 221 ~v 222 (260)
.+
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=96.46 E-value=0.0041 Score=51.39 Aligned_cols=52 Identities=27% Similarity=0.263 Sum_probs=46.8
Q ss_pred CCcchhHHhhcCcccccchhHHHHHHHhhcCCCcccccCCCCHHHHHHHHHHHHH
Q 024924 167 KKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKE 221 (260)
Q Consensus 167 ~~~~Ik~~LlDQ~~iaGiGNiya~EiLf~a~IhP~~~~~~Ls~~e~~~L~~~i~~ 221 (260)
.+.+|.-+| +-|-|||.-.|..||-.+||||..++++||++|+.+|-+.+..
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 477888888 4599999999999999999999999999999999999888863
No 32
>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=96.19 E-value=0.0078 Score=47.27 Aligned_cols=50 Identities=28% Similarity=0.403 Sum_probs=44.2
Q ss_pred CcchhHHhhcCcccccchhHHHHHHHhhcCCCcccccCCCCHHHHHHHHHHHH
Q 024924 168 KITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIK 220 (260)
Q Consensus 168 ~~~Ik~~LlDQ~~iaGiGNiya~EiLf~a~IhP~~~~~~Ls~~e~~~L~~~i~ 220 (260)
+.+|.-+| +-|-|||.-.|..||-.+||||...+++|+++|+..|-+.+.
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 45666666 448999999999999999999999999999999999998875
No 33
>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=96.01 E-value=0.011 Score=48.43 Aligned_cols=52 Identities=19% Similarity=0.252 Sum_probs=45.0
Q ss_pred CCcchhHHhhcCcccccchhHHHHHHHhhcCCCcccccCCCCHHHHHHHHHHHHH
Q 024924 167 KKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKE 221 (260)
Q Consensus 167 ~~~~Ik~~LlDQ~~iaGiGNiya~EiLf~a~IhP~~~~~~Ls~~e~~~L~~~i~~ 221 (260)
.+.+|.-+| +-|-|||--.|..||-.+||||..++++||++|+..|-+.+..
T Consensus 15 ~~k~v~~aL---t~I~GIG~~~a~~I~~~lgi~~~~~~~~Lt~~qi~~l~~~i~~ 66 (144)
T TIGR03629 15 GNKPVEYAL---TGIKGIGRRFARAIARKLGVDPNAKLGYLDDEEIEKLEEAVEN 66 (144)
T ss_pred CCCEEEEee---cceeccCHHHHHHHHHHcCcCCCCCcccCCHHHHHHHHHHHHh
Confidence 355666666 3489999999999999999999999999999999999888764
No 34
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=95.98 E-value=0.01 Score=48.80 Aligned_cols=51 Identities=20% Similarity=0.246 Sum_probs=45.9
Q ss_pred CCcchhHHhhcCcccccchhHHHHHHHhhcCCCcccccCCCCHHHHHHHHHHHH
Q 024924 167 KKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIK 220 (260)
Q Consensus 167 ~~~~Ik~~LlDQ~~iaGiGNiya~EiLf~a~IhP~~~~~~Ls~~e~~~L~~~i~ 220 (260)
.+.+|.-+| +-|-|||.-.|..||-.+||||..++++||++|+.+|-+.|.
T Consensus 19 ~~k~i~~aL---t~IyGIG~~~a~~Ic~~lgi~~~~~~~~Lt~~qi~~l~~~i~ 69 (149)
T PRK04053 19 GTKPVEYAL---TGIKGIGRRTARAIARKLGLDPNAKLGYLSDEEIEKIEEALE 69 (149)
T ss_pred CCCEEeeec---cccccccHHHHHHHHHHcCcCCCCccCcCCHHHHHHHHHHHH
Confidence 467788888 459999999999999999999999999999999999888775
No 35
>COG1389 DNA topoisomerase VI, subunit B [DNA replication, recombination, and repair]
Probab=93.84 E-value=0.21 Score=47.99 Aligned_cols=97 Identities=22% Similarity=0.358 Sum_probs=73.4
Q ss_pred EEEecCCcceEEEEecCC--CCCCCccCCCCCCCCCCCCHHHHHHHHcC-CCcchhHHhhcCcccccchhHHHHHHHhhc
Q 024924 120 LSFTDKRRFAKVRLLNDP--TSVPPISELGPDALLEPMTVDEFTDSLSK-KKITIKALLLDQSYISGIGNWVADEVLYQA 196 (260)
Q Consensus 120 l~f~d~R~fg~~~l~~~~--~~~~~l~~lGpDpl~~~~~~~~~~~~l~~-~~~~Ik~~LlDQ~~iaGiGNiya~EiLf~a 196 (260)
+.|.|| -|.+++.+-. ...++=..+-|-|- ..+.+.+...++. ++.+++.+|+ +-++-||---++|+|=.+
T Consensus 208 I~l~dP--dG~~~vf~r~t~~lP~pP~E~kPHP~--gvd~~~L~~M~~~T~~~tv~~fL~--sef~rig~~ta~e~~e~~ 281 (538)
T COG1389 208 IVLKDP--DGNLVVFPRSTDKLPKPPKEIKPHPH--GVDLDTLKKMAHRTRRSTVREFLV--SEFSRIGEKTADELLEYA 281 (538)
T ss_pred EEEECC--CCcEEEeccchhhCCCCccccCCCCc--cccHHHHHHHHHHhhhhhHHHHHH--HHHHHhhhhhHHHHHHHh
Confidence 445555 3444444311 12223345566676 4788899888864 5789999997 678899999999999999
Q ss_pred CCCcccccCCCC----HHHHHHHHHHHHHH
Q 024924 197 KIHPLQTAVSLS----KESCATLLKCIKEV 222 (260)
Q Consensus 197 ~IhP~~~~~~Ls----~~e~~~L~~~i~~v 222 (260)
|.+|......|+ .+|..+|+++++.+
T Consensus 282 g~~~~~~p~~L~~~~~~eea~~lv~a~~~~ 311 (538)
T COG1389 282 GFDPDKKPRELTKKKTREEAEKLVEAFKKM 311 (538)
T ss_pred cCCcccCHHHhhcccCHHHHHHHHHHHHhC
Confidence 999999999999 99999999999864
No 36
>KOG3311 consensus Ribosomal protein S18 [Translation, ribosomal structure and biogenesis]
Probab=91.79 E-value=0.15 Score=41.83 Aligned_cols=50 Identities=26% Similarity=0.323 Sum_probs=44.9
Q ss_pred CcchhHHhhcCcccccchhHHHHHHHhhcCCCcccccCCCCHHHHHHHHHHHH
Q 024924 168 KITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIK 220 (260)
Q Consensus 168 ~~~Ik~~LlDQ~~iaGiGNiya~EiLf~a~IhP~~~~~~Ls~~e~~~L~~~i~ 220 (260)
+..|.-+|.- |.|||--||.++|=.+++++...+..|+++|+.++.+.+.
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 5666666664 9999999999999999999999999999999999998776
No 37
>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=81.59 E-value=3.5 Score=38.92 Aligned_cols=63 Identities=27% Similarity=0.343 Sum_probs=47.7
Q ss_pred CCCHHHHHHHHc-----CCCcchhHHhhcCcccccchhHHHHHHHhhcCCCcccccCCCCHHHHHHHHHHHHH
Q 024924 154 PMTVDEFTDSLS-----KKKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKE 221 (260)
Q Consensus 154 ~~~~~~~~~~l~-----~~~~~Ik~~LlDQ~~iaGiGNiya~EiLf~a~IhP~~~~~~Ls~~e~~~L~~~i~~ 221 (260)
+++.+.+.+.+. .+++.++.+|- --+=+=+++.+|-.++|+|.+++++||++++.+|.+.++.
T Consensus 264 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~-----~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~lk~ 331 (400)
T TIGR00275 264 DLSEEELEQRLKRLRKSNPKKTVKNILK-----GLLPKRLAELLLEQLGIDPDLPAAQLSKKEIKKLVQLLKN 331 (400)
T ss_pred CCCHHHHHHHHHHHHHHChhhhHHHHhh-----hhhhHHHHHHHHHHcCCCCCCChHHCCHHHHHHHHHHHhC
Confidence 456666555443 34677887764 2234557889999999999999999999999999999885
No 38
>TIGR00755 ksgA dimethyladenosine transferase. Alternate name: S-adenosylmethionine--6-N',N'-adenosyl (rRNA) dimethyltransferase
Probab=73.37 E-value=6.1 Score=34.77 Aligned_cols=55 Identities=24% Similarity=0.288 Sum_probs=42.1
Q ss_pred HHHHH-HcCCCcchhHHhhcCcccccchhHHHHHHHhhcCCCcccccCCCCHHHHHHHHHH
Q 024924 159 EFTDS-LSKKKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKC 218 (260)
Q Consensus 159 ~~~~~-l~~~~~~Ik~~LlDQ~~iaGiGNiya~EiLf~a~IhP~~~~~~Ls~~e~~~L~~~ 218 (260)
.|.+. +..++++|+..|- +.++| -...++|-.++|.|..++.+||.+|+.+|+++
T Consensus 197 ~~~~~~F~~rrk~l~~~l~--~~~~~---~~~~~~l~~~~i~~~~r~~~l~~~~~~~l~~~ 252 (253)
T TIGR00755 197 KLLKAAFSQRRKTLRNNLK--QLLKA---SKLEEVLEQLGLDPTARAEQLSPEDFLRLANL 252 (253)
T ss_pred HHHHHHHccchHHHHHHHh--hhcch---hHHHHHHHHCCcCCCCCcccCCHHHHHHHHHh
Confidence 44443 5678999999883 23333 24567888999999999999999999999875
No 39
>COG0030 KsgA Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis]
Probab=70.80 E-value=7 Score=35.08 Aligned_cols=52 Identities=29% Similarity=0.313 Sum_probs=43.0
Q ss_pred HHcCCCcchhHHhhcCcccccchhHHHHHHHhhcCCCcccccCCCCHHHHHHHHHHHHHH
Q 024924 163 SLSKKKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEV 222 (260)
Q Consensus 163 ~l~~~~~~Ik~~LlDQ~~iaGiGNiya~EiLf~a~IhP~~~~~~Ls~~e~~~L~~~i~~v 222 (260)
.+..+|+.++..|-+=.- ..|+|=+++|+|.+++.+||.+|+.+|+++++..
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 345688888888754321 6899999999999999999999999999988753
No 40
>COG2081 Predicted flavoproteins [General function prediction only]
Probab=67.72 E-value=11 Score=35.88 Aligned_cols=63 Identities=22% Similarity=0.264 Sum_probs=51.3
Q ss_pred CCCCHHHHHHHHcC--CCcchhHHhhcCcccccchhHHHHHHHhhcCCCcccccCCCCHHHHHHHHHHHHH
Q 024924 153 EPMTVDEFTDSLSK--KKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKE 221 (260)
Q Consensus 153 ~~~~~~~~~~~l~~--~~~~Ik~~LlDQ~~iaGiGNiya~EiLf~a~IhP~~~~~~Ls~~e~~~L~~~i~~ 221 (260)
++.+.+.+.+.+.+ +++++|.+|-..- +-=++.=+|=+++| |.....++|+++.++|.+.++.
T Consensus 268 P~~~~~~l~~~l~~~~~~kslkn~L~~~l-----p~rlv~~~l~~~~i-~~~~~~~ls~~~~~~l~~~ik~ 332 (408)
T COG2081 268 PDVDAEELLRELRRANPKKSLKNALAKLL-----PKRLVEFLLERAGI-PDEPLAQLSPKELAQLAAALKA 332 (408)
T ss_pred CCCCHHHHHHHHHhhChhhHHHHHHHHHh-----hhHHHHHHHHhccC-CCcchhhcCHHHHHHHHHHHhc
Confidence 56788888887754 5889999986543 44566667779999 9999999999999999999985
No 41
>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=66.29 E-value=12 Score=33.17 Aligned_cols=51 Identities=27% Similarity=0.317 Sum_probs=39.7
Q ss_pred HcCCCcchhHHhhcCcccccchhH-HHHHHHhhcCCCcccccCCCCHHHHHHHHHHHH
Q 024924 164 LSKKKITIKALLLDQSYISGIGNW-VADEVLYQAKIHPLQTAVSLSKESCATLLKCIK 220 (260)
Q Consensus 164 l~~~~~~Ik~~LlDQ~~iaGiGNi-ya~EiLf~a~IhP~~~~~~Ls~~e~~~L~~~i~ 220 (260)
+..++++++..|-- +++- -.++++..+||+|..++..||.+++.+|+..+.
T Consensus 210 F~~rrk~l~~~L~~------~~~~~~~~~~~~~~~i~~~~r~~~ls~~~~~~l~~~l~ 261 (262)
T PF00398_consen 210 FSQRRKTLRNSLKS------LFPGEQLEELLEKAGIDPNARAEELSPEQFLKLFKYLN 261 (262)
T ss_dssp HTTTTSBHHHHTTC------THHHHHHHHHHHHCTHTTTTCGGCHHHHHHHHHHHHHH
T ss_pred HhCcchHHHHHHhh------hcCHHHHHHhhhhcCCCCCCCcccCCHHHHHHHHHHhh
Confidence 45788999988652 2322 235566669999999999999999999998875
No 42
>PRK00274 ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed
Probab=62.69 E-value=15 Score=32.78 Aligned_cols=54 Identities=24% Similarity=0.344 Sum_probs=40.4
Q ss_pred HHcCCCcchhHHhhcCcccccchhHHHHHHHhhcCCCcccccCCCCHHHHHHHHHHHH
Q 024924 163 SLSKKKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIK 220 (260)
Q Consensus 163 ~l~~~~~~Ik~~LlDQ~~iaGiGNiya~EiLf~a~IhP~~~~~~Ls~~e~~~L~~~i~ 220 (260)
.+..++++|+..|-. ++ +..+ -..++|=.+||+|..++.+|+.+|+.+|+..+.
T Consensus 216 ~F~~rrk~l~~~l~~--~~-~~~~-~~~~~l~~~~~~~~~r~~~l~~~~~~~L~~~~~ 269 (272)
T PRK00274 216 AFAQRRKTLRNNLKN--LF-GSKE-KLEEALEAAGIDPNRRAETLSVEEFVRLANALA 269 (272)
T ss_pred HHhchHHHHHHHHHh--hc-cchH-HHHHHHHHCCCCcCCCceeCCHHHHHHHHHHHH
Confidence 346788999988832 11 1011 235778899999999999999999999998765
No 43
>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=62.64 E-value=6.4 Score=37.61 Aligned_cols=64 Identities=25% Similarity=0.306 Sum_probs=48.1
Q ss_pred CCCCHHHHHHHHc-----CCCcchhHHhhcCcccccchhHHHHHHHhhcCC-CcccccCCCCHHHHHHHHHHHHH
Q 024924 153 EPMTVDEFTDSLS-----KKKITIKALLLDQSYISGIGNWVADEVLYQAKI-HPLQTAVSLSKESCATLLKCIKE 221 (260)
Q Consensus 153 ~~~~~~~~~~~l~-----~~~~~Ik~~LlDQ~~iaGiGNiya~EiLf~a~I-hP~~~~~~Ls~~e~~~L~~~i~~ 221 (260)
++++.+.+.+.|. .++++++.+|-.- +=+=++..+|-+++| +|.+++++++++++.+|.+.+++
T Consensus 270 p~~~~e~l~~~l~~~~~~~~~~~~~~~l~~~-----lp~rl~~~ll~~~~i~~~~~~~~~l~~~~~~~L~~~lk~ 339 (409)
T PF03486_consen 270 PDLSEEELEELLQERKEKNPKRTLKNFLKGL-----LPKRLALALLKRAGIKDPDKKVSELSKKERNRLANLLKR 339 (409)
T ss_dssp TTS-HHHHHHHHHHHHHHTTTSBHHHHHTTT-----S-HHHHHHHHHHTTS-STTSBGGGS-HHHHHHHHHHHHC
T ss_pred CCCCHHHHHHHHHHHHHHHHhhHHHHHHHHH-----hHHHHHHHHHHHcCCCccccchhhcCHHHHHHHHHHHHh
Confidence 4567666666553 3577888887532 456688899999999 99999999999999999998873
No 44
>PF10892 DUF2688: Protein of unknown function (DUF2688); InterPro: IPR024392 Members of this protein family are annotated as KleB, and may play a role in the regulation of transcription in plasmids.
Probab=51.99 E-value=3.4 Score=28.22 Aligned_cols=11 Identities=36% Similarity=0.435 Sum_probs=9.3
Q ss_pred CCCcCCcccCC
Q 024924 250 PGKVNGKIFMT 260 (260)
Q Consensus 250 ~~~~~~~~~~~ 260 (260)
+|+|||++|.|
T Consensus 12 ~CrRCGk~i~t 22 (60)
T PF10892_consen 12 PCRRCGKSIRT 22 (60)
T ss_pred hhhhhCccHHH
Confidence 79999999854
No 45
>COG0776 HimA Bacterial nucleoid DNA-binding protein [DNA replication, recombination, and repair]
Probab=51.50 E-value=43 Score=25.36 Aligned_cols=51 Identities=20% Similarity=0.242 Sum_probs=40.1
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHcCCCCC--CCCcccEEeeeCCCCCCC--cCCcccC
Q 024924 207 LSKESCATLLKCIKEVIQSAVEVDADCS--RFPLEWLFHFRWGKKPGK--VNGKIFM 259 (260)
Q Consensus 207 Ls~~e~~~L~~~i~~vL~~ai~~gg~~~--~~~~~~lv~~R~~~~~~~--~~~~~~~ 259 (260)
|+..++..+++++-..+..|+..|.+.. .| -.|-|..|... +++ .+|+.|.
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-GTFEVRERAAR-TGRNPKTGEEIK 71 (94)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHcCCeEEEeee-eeeEeeccCCC-CCCCCCCCCeEe
Confidence 8999999999999999999999998652 33 45788888654 554 6777653
No 46
>PTZ00338 dimethyladenosine transferase-like protein; Provisional
Probab=48.26 E-value=41 Score=30.62 Aligned_cols=57 Identities=21% Similarity=0.260 Sum_probs=40.6
Q ss_pred HcCCCcchhHHhhcCcc-------cc---cchh-----------HHHHHHHhhcCCCcccccCCCCHHHHHHHHHHHHH
Q 024924 164 LSKKKITIKALLLDQSY-------IS---GIGN-----------WVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKE 221 (260)
Q Consensus 164 l~~~~~~Ik~~LlDQ~~-------ia---GiGN-----------iya~EiLf~a~IhP~~~~~~Ls~~e~~~L~~~i~~ 221 (260)
+..+|++++..|-...+ +. +++| --..++|=.+||. .+++.+||-+|+.+|..++..
T Consensus 211 F~~rrK~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~~R~e~l~~~~f~~L~~~~~~ 288 (294)
T PTZ00338 211 FSRKNKTLSAIFKTKSVLQTLEHNYKSWCTMINKKVPVSLEPFKEFIAEILEDSGMF-EKRSVKLDIDDFLKLLLAFNK 288 (294)
T ss_pred HhhccHHHHHHhCcchhHHHHHhhhhhhhccccccccchhhhHHHHHHHHHHHcCCc-ccChhhCCHHHHHHHHHHHHH
Confidence 45688999988866432 11 1111 1123678899986 799999999999999988763
No 47
>PRK10664 transcriptional regulator HU subunit beta; Provisional
Probab=47.58 E-value=58 Score=24.12 Aligned_cols=53 Identities=19% Similarity=0.287 Sum_probs=38.5
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHcCCCC--CCCCcccEEeeeCCCCCCC--cCCcccC
Q 024924 205 VSLSKESCATLLKCIKEVIQSAVEVDADC--SRFPLEWLFHFRWGKKPGK--VNGKIFM 259 (260)
Q Consensus 205 ~~Ls~~e~~~L~~~i~~vL~~ai~~gg~~--~~~~~~~lv~~R~~~~~~~--~~~~~~~ 259 (260)
..+|..++..+++++.+++.+++..|+.- ..| -.|-+..|... .++ ++|++|.
T Consensus 14 ~~~s~~~~~~~v~~~~~~i~~~L~~~~~v~l~gf-G~F~v~~r~aR-~grNP~Tge~i~ 70 (90)
T PRK10664 14 ADISKAAAGRALDAIIASVTESLKEGDDVALVGF-GTFAVKERAAR-TGRNPQTGKEIT 70 (90)
T ss_pred hCCCHHHHHHHHHHHHHHHHHHHhCCCEEEECCc-EEEEEEEeCCc-cccCCCCCCEEE
Confidence 35899999999999999999999999854 233 34555566543 443 6777653
No 48
>PRK00199 ihfB integration host factor subunit beta; Reviewed
Probab=42.62 E-value=71 Score=23.58 Aligned_cols=52 Identities=21% Similarity=0.297 Sum_probs=36.2
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHcCCCC--CCCCcccEEeeeCCCCCCC--cCCccc
Q 024924 205 VSLSKESCATLLKCIKEVIQSAVEVDADC--SRFPLEWLFHFRWGKKPGK--VNGKIF 258 (260)
Q Consensus 205 ~~Ls~~e~~~L~~~i~~vL~~ai~~gg~~--~~~~~~~lv~~R~~~~~~~--~~~~~~ 258 (260)
..+|..++..+++++-+++.+++..|++- ..|. .|-+..|..+ .+. ++|+.|
T Consensus 15 ~~~s~~~~~~vv~~~~~~i~~~L~~g~~V~l~gfG-~F~~~~r~~r-~~~np~Tge~i 70 (94)
T PRK00199 15 PHLSAKDVENAVKEILEEMSDALARGDRIEIRGFG-SFSLHYRPPR-VGRNPKTGEKV 70 (94)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHcCCeEEEcCCE-EEEEEEecCe-eccCcCCCCEE
Confidence 46999999999999999999999999865 3342 3444444332 332 456655
No 49
>PF10815 ComZ: ComZ; InterPro: IPR024558 ComZ, which contains a leucine zipper motif, negatively regulates transcription of the ComG operon [].
Probab=37.87 E-value=1e+02 Score=20.88 Aligned_cols=36 Identities=31% Similarity=0.367 Sum_probs=29.7
Q ss_pred HHHHHhhcCCCcccccCCCCHHHHHHHHHHHHHHHHHHHHcCC
Q 024924 189 ADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVIQSAVEVDA 231 (260)
Q Consensus 189 a~EiLf~a~IhP~~~~~~Ls~~e~~~L~~~i~~vL~~ai~~gg 231 (260)
+.|.|=.+|| .||-+.+.-+.+-+-.|+.+|++.|-
T Consensus 17 ak~~L~k~GI-------eLsme~~qP~m~L~~~VM~eAYElG~ 52 (56)
T PF10815_consen 17 AKEELDKKGI-------ELSMEMLQPLMQLLTKVMNEAYELGK 52 (56)
T ss_pred HHHHHHHcCc-------cCCHHHHHHHHHHHHHHHHHHHHhhh
Confidence 3455555555 59999999999999999999999884
No 50
>PRK10753 transcriptional regulator HU subunit alpha; Provisional
Probab=37.82 E-value=92 Score=22.96 Aligned_cols=52 Identities=19% Similarity=0.262 Sum_probs=36.6
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHcCCCC--CCCCcccEEeeeCCCCCCC--cCCccc
Q 024924 205 VSLSKESCATLLKCIKEVIQSAVEVDADC--SRFPLEWLFHFRWGKKPGK--VNGKIF 258 (260)
Q Consensus 205 ~~Ls~~e~~~L~~~i~~vL~~ai~~gg~~--~~~~~~~lv~~R~~~~~~~--~~~~~~ 258 (260)
..+|..++..+++++-+++.+++..|+.- ..| -.|-+..|... ... .+|++|
T Consensus 14 ~~~s~~~~~~~v~~~~~~i~~~L~~g~~V~i~gf-G~F~v~~r~~R-~grNP~Tge~i 69 (90)
T PRK10753 14 AELSKTQAKAALESTLAAITESLKEGDAVQLVGF-GTFKVNHRAER-TGRNPQTGKEI 69 (90)
T ss_pred hCCCHHHHHHHHHHHHHHHHHHHHcCCeEEEcCC-EEEEEeeeCCc-cccCCCCCCEE
Confidence 35899999999999999999999999864 233 33444555432 332 566654
No 51
>PRK14896 ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Provisional
Probab=37.33 E-value=97 Score=27.29 Aligned_cols=57 Identities=21% Similarity=0.210 Sum_probs=37.7
Q ss_pred HHcCCCcchhHHhhcCcccccchhHHHHHHHhhc-CCCcccccCCCCHHHHHHHHHHHHH
Q 024924 163 SLSKKKITIKALLLDQSYISGIGNWVADEVLYQA-KIHPLQTAVSLSKESCATLLKCIKE 221 (260)
Q Consensus 163 ~l~~~~~~Ik~~LlDQ~~iaGiGNiya~EiLf~a-~IhP~~~~~~Ls~~e~~~L~~~i~~ 221 (260)
.+..++++++..|-.--...+.|.+ ++++-.+ ++.|..++.+||.+|+.+|++.+..
T Consensus 199 ~F~~rrk~l~~~l~~~~~~~~~~~~--~~~~~~~~~~~~~~R~e~L~~~~~~~l~~~~~~ 256 (258)
T PRK14896 199 LFQHRRKTLRNALKNSAHISGKEDI--KAVVEALPEELLNKRVFQLSPEEIAELANLLYE 256 (258)
T ss_pred HHccccHHHHHHHhhhccccchhHH--HHHHHHcCCCCcCCCCccCCHHHHHHHHHHHHh
Confidence 3567899999999531101122222 2334444 4557999999999999999987764
No 52
>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=36.38 E-value=15 Score=21.31 Aligned_cols=12 Identities=8% Similarity=-0.111 Sum_probs=6.8
Q ss_pred CCCCCCcCCcccC
Q 024924 247 GKKPGKVNGKIFM 259 (260)
Q Consensus 247 ~~~~~~~~~~~~~ 259 (260)
|+ +|.+||..|.
T Consensus 1 G~-~C~rC~~~~~ 12 (30)
T PF06827_consen 1 GE-KCPRCWNYIE 12 (30)
T ss_dssp TS-B-TTT--BBE
T ss_pred CC-cCccCCCcce
Confidence 44 8999999874
No 53
>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=36.07 E-value=1e+02 Score=22.87 Aligned_cols=40 Identities=25% Similarity=0.277 Sum_probs=30.7
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHcCCCC--CCCCcccEEeee
Q 024924 205 VSLSKESCATLLKCIKEVIQSAVEVDADC--SRFPLEWLFHFR 245 (260)
Q Consensus 205 ~~Ls~~e~~~L~~~i~~vL~~ai~~gg~~--~~~~~~~lv~~R 245 (260)
..+|..++..+++++..+|.+++..|++- +.|.. |-+..|
T Consensus 15 ~~~s~~~v~~vv~~~~~~i~~~L~~g~~V~l~gfG~-F~~~~r 56 (96)
T TIGR00987 15 LGLSKREAKELVELFFEEIRRALENGEQVKLSGFGN-FDLRDK 56 (96)
T ss_pred hCcCHHHHHHHHHHHHHHHHHHHHcCCeEEecCCEE-EEEEEE
Confidence 45899999999999999999999999864 34433 344443
No 54
>COG4871 Uncharacterized protein conserved in archaea [Function unknown]
Probab=35.69 E-value=48 Score=27.76 Aligned_cols=48 Identities=13% Similarity=0.027 Sum_probs=33.0
Q ss_pred CHHHHHHHHHHHHHHHHHHHHcCCCCCCCC-----cccEEeee-CCCCCCCcCCc
Q 024924 208 SKESCATLLKCIKEVIQSAVEVDADCSRFP-----LEWLFHFR-WGKKPGKVNGK 256 (260)
Q Consensus 208 s~~e~~~L~~~i~~vL~~ai~~gg~~~~~~-----~~~lv~~R-~~~~~~~~~~~ 256 (260)
+++|...+...+++.+++|++.||.....- .-+=||.= .+. -|..||+
T Consensus 91 dedEAkeilgel~d~ineA~~kg~d~s~prek~rV~p~dVykyLP~t-NCg~CGE 144 (193)
T COG4871 91 DEDEAKEILGELMDIINEAIAKGGDASDPREKVRVGPMDVYKYLPQT-NCGKCGE 144 (193)
T ss_pred CHHHHHHHHHHHHHHHHHHHHccCCCCCchhhcccChHHHHHhCCCC-ccccchh
Confidence 688999999999999999999998543221 11223332 243 6778875
No 55
>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=30.96 E-value=66 Score=21.63 Aligned_cols=31 Identities=26% Similarity=0.220 Sum_probs=24.4
Q ss_pred CCeEEeEEEeeeEEEEecCCCCccEEeecceEEEEEe
Q 024924 49 GKAILSAHRKGKNLWLRLDSPPFPSFQFGMTGAIYIK 85 (260)
Q Consensus 49 G~~i~~v~r~GK~l~~~~~~~~~L~~HlgMtG~~~~~ 85 (260)
=.+|..|+|.||.+-|..+++. |-||+=-+.
T Consensus 16 iskikkvwrvgkmvsftyddgn------gktgrgavs 46 (62)
T PF02294_consen 16 ISKIKKVWRVGKMVSFTYDDGN------GKTGRGAVS 46 (62)
T ss_dssp GGGEEEEEECSSEEEEEEECSS------SSEEEEEEE
T ss_pred HHHHHHHHhhcceEEEEEecCC------Ccccccccc
Confidence 3579999999999999998753 677775553
No 56
>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=30.42 E-value=82 Score=25.51 Aligned_cols=45 Identities=13% Similarity=0.109 Sum_probs=24.9
Q ss_pred CHHHHHHHHHHHHHHHHHHHHcCCCC-CCCCcccEEeeeCCCCCCCcCCcccCC
Q 024924 208 SKESCATLLKCIKEVIQSAVEVDADC-SRFPLEWLFHFRWGKKPGKVNGKIFMT 260 (260)
Q Consensus 208 s~~e~~~L~~~i~~vL~~ai~~gg~~-~~~~~~~lv~~R~~~~~~~~~~~~~~~ 260 (260)
|-.|+..-...-...+...|+.|.-. ..++. -+- ||.+||++|.+
T Consensus 48 ti~eV~e~tgVs~~~I~~~IreGRL~~~~~~n-------l~~-~CE~CG~~I~~ 93 (137)
T TIGR03826 48 TVSEIVEETGVSEKLILKFIREGRLQLKHFPN-------LGY-PCERCGTSIRE 93 (137)
T ss_pred CHHHHHHHHCcCHHHHHHHHHcCCeeccCCCC-------CcC-cccccCCcCCC
Confidence 33344444444445555666666522 22221 245 99999999964
No 57
>PRK13195 pyrrolidone-carboxylate peptidase; Provisional
Probab=28.06 E-value=3.1e+02 Score=23.99 Aligned_cols=26 Identities=23% Similarity=0.342 Sum_probs=20.3
Q ss_pred CccCCCCCCCCCCCCHHHHHHHHcCC
Q 024924 142 PISELGPDALLEPMTVDEFTDSLSKK 167 (260)
Q Consensus 142 ~l~~lGpDpl~~~~~~~~~~~~l~~~ 167 (260)
.+..-||+.+-..+..+.+.+.+++.
T Consensus 106 ~I~~~gp~ay~stLpv~~iv~~l~~~ 131 (222)
T PRK13195 106 PTDPAGPVAYHATVPVRAMVLAMRKA 131 (222)
T ss_pred cccCCCcceeecCCCHHHHHHHHHhc
Confidence 45556999988888888888888753
No 58
>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=26.91 E-value=1.2e+02 Score=21.46 Aligned_cols=48 Identities=15% Similarity=0.175 Sum_probs=35.3
Q ss_pred CChhhHHHHhcCC--eEEeEEEeeeEEEEecCCCCccEEeecceEEEEEe
Q 024924 38 VSASDFEASVLGK--AILSAHRKGKNLWLRLDSPPFPSFQFGMTGAIYIK 85 (260)
Q Consensus 38 ~~~~~~~~~L~G~--~i~~v~r~GK~l~~~~~~~~~L~~HlgMtG~~~~~ 85 (260)
.+.++|..--.|. .+.-..+-|+-+.|....=.-.+.|.|..|++.+.
T Consensus 7 is~~~~l~~Y~G~a~~V~v~s~~Gr~v~~Pa~~lRpFvt~~Gv~G~F~l~ 56 (68)
T PF11197_consen 7 ISYQEFLAYYQGAASKVVVRSDDGRRVQFPARHLRPFVTHDGVHGRFRLE 56 (68)
T ss_pred cCHHHHHHhccccccEEEEEecCCcEEEEeHHHCcceecCCCceEEEEEE
Confidence 4567787777775 67777778999999654323467899999998874
No 59
>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=26.84 E-value=1.9e+02 Score=21.16 Aligned_cols=52 Identities=19% Similarity=0.323 Sum_probs=36.1
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHcCCCC--CCCCcccEEeeeCCCCCCC--cCCccc
Q 024924 205 VSLSKESCATLLKCIKEVIQSAVEVDADC--SRFPLEWLFHFRWGKKPGK--VNGKIF 258 (260)
Q Consensus 205 ~~Ls~~e~~~L~~~i~~vL~~ai~~gg~~--~~~~~~~lv~~R~~~~~~~--~~~~~~ 258 (260)
..+|..++..+++++-+.|.+++..|++- +.|. .|.+..|..+ .+. .+|+++
T Consensus 15 ~~~s~~~v~~vv~~~~~~i~~~L~~g~~V~l~gfG-~F~~~~r~~r-~~~np~tge~i 70 (94)
T TIGR00988 15 SHLPAKDVEDAVKTMLEHMASALAQGDRIEIRGFG-SFSLHYRAPR-TGRNPKTGDSV 70 (94)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHcCCeEEEcCcE-EEEEEEeCCc-cccCCCCCCEE
Confidence 45899999999999999999999999864 3443 3444445422 332 455554
No 60
>PRK00222 methionine sulfoxide reductase B; Provisional
Probab=26.78 E-value=55 Score=26.72 Aligned_cols=49 Identities=20% Similarity=0.055 Sum_probs=33.6
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHcCCCCCCCCcccEEeeeCCCCCCCcCCccc
Q 024924 207 LSKESCATLLKCIKEVIQSAVEVDADCSRFPLEWLFHFRWGKKPGKVNGKIF 258 (260)
Q Consensus 207 Ls~~e~~~L~~~i~~vL~~ai~~gg~~~~~~~~~lv~~R~~~~~~~~~~~~~ 258 (260)
.+++|+++++...+. .-++..||-..|-..++-+.+.|.=.|..||.++
T Consensus 5 ~~~~ew~~~Lt~~qy---~V~r~~gTE~pftg~~~~~~~~G~Y~C~~Cg~pL 53 (142)
T PRK00222 5 KSKEEWKKQLTPEQY---RVTQEHGTERPFTGEYLDNKEKGIYVCIVCGEPL 53 (142)
T ss_pred CCHHHHHhhCCHHHH---HHHHhcCCCCCCCCCCCCCCCCeEEEecCCCchh
Confidence 478888888776653 2234456666665556666677877889999886
No 61
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=26.06 E-value=53 Score=26.46 Aligned_cols=40 Identities=25% Similarity=0.308 Sum_probs=34.5
Q ss_pred cCcccccchhHHHHHHHhhcCCCcccccCCCCHHHHHHHHH
Q 024924 177 DQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLK 217 (260)
Q Consensus 177 DQ~~iaGiGNiya~EiLf~a~IhP~~~~~~Ls~~e~~~L~~ 217 (260)
|=+.|+|||-.|.. .|...||-=+.++...|.+++..+=+
T Consensus 68 DLt~I~GIGPk~e~-~Ln~~GI~tfaQIAAwt~~di~~id~ 107 (133)
T COG3743 68 DLTRISGIGPKLEK-VLNELGIFTFAQIAAWTRADIAWIDD 107 (133)
T ss_pred cchhhcccCHHHHH-HHHHcCCccHHHHHhcCHHHHHHHHh
Confidence 44799999999964 79999999999999999999887644
No 62
>PRK10874 cysteine sulfinate desulfinase; Provisional
Probab=24.55 E-value=1.1e+02 Score=28.35 Aligned_cols=18 Identities=6% Similarity=0.327 Sum_probs=16.3
Q ss_pred CHHHHHHHHHHHHHHHHH
Q 024924 208 SKESCATLLKCIKEVIQS 225 (260)
Q Consensus 208 s~~e~~~L~~~i~~vL~~ 225 (260)
|++|+++++++++.+++.
T Consensus 381 t~edid~ll~al~~~~~~ 398 (401)
T PRK10874 381 TQSDVDALVNAVDRALEL 398 (401)
T ss_pred CHHHHHHHHHHHHHHHHH
Confidence 999999999999998764
No 63
>PF11248 DUF3046: Protein of unknown function (DUF3046); InterPro: IPR021408 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=22.61 E-value=36 Score=23.87 Aligned_cols=44 Identities=23% Similarity=0.311 Sum_probs=33.4
Q ss_pred HHHHHHHcCC-CcchhHHhhcCcccccchhHHHHHHHhhcCCCccc
Q 024924 158 DEFTDSLSKK-KITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQ 202 (260)
Q Consensus 158 ~~~~~~l~~~-~~~Ik~~LlDQ~~iaGiGNiya~EiLf~a~IhP~~ 202 (260)
..|.+++..- -..-...|.+..+++++|+--++|+| .+|++|..
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 4566766542 34456788899999999999999987 68888864
No 64
>PF10474 DUF2451: Protein of unknown function C-terminus (DUF2451); InterPro: IPR019514 This protein is found in eukaryotes but its function is not known. The N-terminal domain of some members is PF10475 from PFAM (DUF2450).
Probab=22.31 E-value=78 Score=27.86 Aligned_cols=69 Identities=10% Similarity=0.220 Sum_probs=47.2
Q ss_pred CCHHHHHHHHcCCCcchhHHhhcCcccccchhHHHHHHH-----hhcCCCcccccCCCCHHHHHHHHHHHHHHHHHHHHc
Q 024924 155 MTVDEFTDSLSKKKITIKALLLDQSYISGIGNWVADEVL-----YQAKIHPLQTAVSLSKESCATLLKCIKEVIQSAVEV 229 (260)
Q Consensus 155 ~~~~~~~~~l~~~~~~Ik~~LlDQ~~iaGiGNiya~EiL-----f~a~IhP~~~~~~Ls~~e~~~L~~~i~~vL~~ai~~ 229 (260)
++.+.+...+.+-+=.||.+ +.|+ |-|+|.++ |..++.=-.....++++-...||+.+..++..+.=.
T Consensus 67 l~~~~i~~~Ia~vKWdvkev-~~qh------s~YVd~l~~~~~~f~~rL~~i~~~~~i~~~~~~~lw~~~i~~~~~~Lve 139 (234)
T PF10474_consen 67 LDLEQILNSIANVKWDVKEV-MSQH------SSYVDQLVQEFQQFSERLDEISKQGPIPPEVQNVLWDRLIFFAFETLVE 139 (234)
T ss_pred cCHHHHHHHHHHcCCCCCCC-CCcc------CHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 34556677776666777777 6665 77888776 444443333456788888888888888888777655
Q ss_pred C
Q 024924 230 D 230 (260)
Q Consensus 230 g 230 (260)
|
T Consensus 140 g 140 (234)
T PF10474_consen 140 G 140 (234)
T ss_pred H
Confidence 5
No 65
>PF00633 HHH: Helix-hairpin-helix motif; InterPro: IPR000445 The HhH motif is an around 20 amino acids domain present in prokaryotic and eukaryotic non-sequence-specific DNA binding proteins [, , ]. The HhH motif is similar to, but distinct from, the HtH motif. Both of these motifs have two helices connected by a short turn. In the HtH motif the second helix binds to DNA with the helix in the major groove. This allows the contact between specific base and residues throughout the protein. In the HhH motif the second helix does not protrude from the surface of the protein and therefore cannot lie in the major groove of the DNA. Crystallographic studies suggest that the interaction of the HhH domain with DNA is mediated by amino acids located in the strongly conserved loop (L-P-G-V) and at the N-terminal end of the second helix []. This interaction could involve the formation of hydrogen bonds between protein backbone nitrogens and DNA phosphate groups []. The structural difference between the HtH and HhH domains is reflected at the functional level: whereas the HtH domain, found primarily in gene regulatory proteins, binds DNA in a sequence specific manner, the HhH domain is rather found in proteins involved in enzymatic activities and binds DNA with no sequence specificity []. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain [].; GO: 0003677 DNA binding; PDB: 3C1Z_A 3C23_A 3C1Y_A 3C21_A 1Z00_A 2A1J_B 1KEA_A 1VRL_A 1RRQ_A 3G0Q_A ....
Probab=22.01 E-value=60 Score=19.04 Aligned_cols=14 Identities=36% Similarity=0.610 Sum_probs=11.0
Q ss_pred ccccchhHHHHHHH
Q 024924 180 YISGIGNWVADEVL 193 (260)
Q Consensus 180 ~iaGiGNiya~EiL 193 (260)
-++|||..-|+.|+
T Consensus 15 ~lpGIG~~tA~~I~ 28 (30)
T PF00633_consen 15 KLPGIGPKTANAIL 28 (30)
T ss_dssp TSTT-SHHHHHHHH
T ss_pred hCCCcCHHHHHHHH
Confidence 47899999998886
No 66
>PF00216 Bac_DNA_binding: Bacterial DNA-binding protein; InterPro: IPR000119 Bacteria synthesise a set of small, usually basic proteins of about 90 residues that bind DNA and are known as histone-like proteins [, ]. Examples include the HU protein in Escherichia coli is a dimer of closely related alpha and beta chains and in other bacteria can be a dimer of identical chains. HU-type proteins have been found in a variety of eubacteria, cyanobacteria and archaebacteria, and are also encoded in the chloroplast genome of some algae []. The integration host factor (IHF), a dimer of closely related chains which seem to function in genetic recombination as well as in translational and transcriptional control [] is found in enterobacteria and viral proteins include the African Swine fever virus protein A104R (or LMW5-AR) []. The exact function of these proteins is not yet clear but they are capable of wrapping DNA and stabilising it from denaturation under extreme environmental conditions. The structure is known for one of these proteins []. The protein exists as a dimer and two "beta-arms" function as the non-specific binding site for bacterial DNA. ; GO: 0003677 DNA binding; PDB: 3C4I_B 2O97_A 1MUL_A 1P78_A 1P51_C 1P71_B 2HT0_A 1OWG_A 2IIF_A 1OUZ_A ....
Probab=21.69 E-value=1.5e+02 Score=21.25 Aligned_cols=28 Identities=25% Similarity=0.410 Sum_probs=25.1
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHcCCCC
Q 024924 206 SLSKESCATLLKCIKEVIQSAVEVDADC 233 (260)
Q Consensus 206 ~Ls~~e~~~L~~~i~~vL~~ai~~gg~~ 233 (260)
.+|..++..+++++.+++.+++..|++-
T Consensus 15 ~~s~~~v~~vl~~~~~~i~~~L~~g~~V 42 (90)
T PF00216_consen 15 GLSKKDVEAVLDALFDVIKEALKEGESV 42 (90)
T ss_dssp TSSHHHHHHHHHHHHHHHHHHHHTT-EE
T ss_pred CCCHHHHHHHHHHHHHHHHHHHhcCCeE
Confidence 4899999999999999999999999864
No 67
>TIGR00357 methionine-R-sulfoxide reductase. This model describes a domain found in PilB, a protein important for pilin expression, N-terminal to a domain coextensive to with the known peptide methionine sulfoxide reductase (MsrA), a protein repair enzyme, of E. coli. Among the early completed genomes, this module is found if and only if MsrA is also found, whether N-terminal to MsrA (as for Helicobacter pylori), C-terminal (as for Treponema pallidum), or in a separate polypeptide. Although the function of this region is not clear, an auxiliary function to MsrA is suggested.
Probab=21.67 E-value=83 Score=25.43 Aligned_cols=48 Identities=15% Similarity=0.046 Sum_probs=29.6
Q ss_pred CHHHHHHHHHHHHHHHHHHHHcCCCCCCCCcccEEeeeCCCCCCCcCCccc
Q 024924 208 SKESCATLLKCIKEVIQSAVEVDADCSRFPLEWLFHFRWGKKPGKVNGKIF 258 (260)
Q Consensus 208 s~~e~~~L~~~i~~vL~~ai~~gg~~~~~~~~~lv~~R~~~~~~~~~~~~~ 258 (260)
+++|+++.+...+. .-.+..|+-..|...++-+.+.|.=.|..||.++
T Consensus 3 ~~~ewr~~Lt~~qy---~V~r~~gTE~pftg~y~~~~~~G~Y~C~~Cg~pL 50 (134)
T TIGR00357 3 SDEELKKKLTPLQY---EVTQNAGTEPPFTNEYWDNKEEGIYVDITCGEPL 50 (134)
T ss_pred CHHHHHHhCCHHHH---HHHHHhCCCCCCCCCCCCCCCCeEEEccCCCCcc
Confidence 56666665554443 1123346655665556666677776789999886
No 68
>PRK00285 ihfA integration host factor subunit alpha; Reviewed
Probab=21.48 E-value=1.5e+02 Score=22.01 Aligned_cols=29 Identities=31% Similarity=0.361 Sum_probs=26.5
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHcCCCC
Q 024924 205 VSLSKESCATLLKCIKEVIQSAVEVDADC 233 (260)
Q Consensus 205 ~~Ls~~e~~~L~~~i~~vL~~ai~~gg~~ 233 (260)
..+|..++...++++.+++.+++..|+.-
T Consensus 16 ~~~s~~~v~~vl~~~~~~i~~~L~~g~~V 44 (99)
T PRK00285 16 VGLSKREAKELVELFFEEIRDALENGEQV 44 (99)
T ss_pred hCcCHHHHHHHHHHHHHHHHHHHHcCCeE
Confidence 46899999999999999999999999864
No 69
>smart00411 BHL bacterial (prokaryotic) histone like domain.
Probab=20.88 E-value=1.6e+02 Score=21.12 Aligned_cols=29 Identities=21% Similarity=0.323 Sum_probs=26.1
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHcCCCC
Q 024924 205 VSLSKESCATLLKCIKEVIQSAVEVDADC 233 (260)
Q Consensus 205 ~~Ls~~e~~~L~~~i~~vL~~ai~~gg~~ 233 (260)
..++..++..+++++..++.+++..|+.-
T Consensus 14 ~~~~~~~v~~vl~~l~~~i~~~L~~g~~V 42 (90)
T smart00411 14 AGLSKKDAKAAVDAFLEIITEALKKGEKV 42 (90)
T ss_pred hCCCHHHHHHHHHHHHHHHHHHHhCCCeE
Confidence 45889999999999999999999999854
Done!