Query 002607
Match_columns 901
No_of_seqs 265 out of 1381
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 03:26:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/002607.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/002607hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF15628 RRM_DME: RRM in Demet 100.0 2.5E-70 5.4E-75 497.0 7.8 103 784-886 1-103 (103)
2 COG2231 Uncharacterized protei 100.0 1.3E-31 2.9E-36 271.5 9.2 142 405-556 34-214 (215)
3 PRK10702 endonuclease III; Pro 99.9 2.8E-28 6E-33 249.3 9.4 143 405-556 33-207 (211)
4 COG0177 Nth Predicted EndoIII- 99.9 6.9E-28 1.5E-32 246.8 9.5 143 406-557 34-208 (211)
5 PRK10880 adenine DNA glycosyla 99.9 1.3E-25 2.8E-30 244.8 10.0 157 404-573 33-226 (350)
6 TIGR01084 mutY A/G-specific ad 99.9 1E-24 2.2E-29 231.0 10.3 156 405-573 30-222 (275)
7 PRK13913 3-methyladenine DNA g 99.9 9.2E-24 2E-28 217.6 8.5 133 404-538 33-216 (218)
8 TIGR01083 nth endonuclease III 99.9 2.6E-22 5.6E-27 201.3 8.2 130 405-543 30-191 (191)
9 PRK13910 DNA glycosylase MutY; 99.9 1.1E-21 2.5E-26 209.3 10.5 138 412-560 3-174 (289)
10 KOG1921 Endonuclease III [Repl 99.8 2.9E-21 6.3E-26 200.5 5.6 142 406-555 83-260 (286)
11 COG1194 MutY A/G-specific DNA 99.7 2.2E-18 4.7E-23 187.0 8.3 154 407-573 40-231 (342)
12 TIGR03252 uncharacterized HhH- 99.6 2.4E-15 5.1E-20 151.5 5.2 87 405-498 22-129 (177)
13 smart00478 ENDO3c endonuclease 99.5 4.3E-14 9.3E-19 135.3 9.4 116 410-534 1-149 (149)
14 PRK01229 N-glycosylase/DNA lya 99.5 2.7E-14 5.8E-19 147.1 7.7 118 403-535 39-187 (208)
15 cd00056 ENDO3c endonuclease II 99.4 8.3E-13 1.8E-17 127.4 8.2 117 407-532 6-158 (158)
16 KOG2457 A/G-specific adenine D 99.3 6.9E-13 1.5E-17 145.2 4.7 142 406-557 130-310 (555)
17 PF15629 Perm-CXXC: Permuted s 99.2 5.4E-12 1.2E-16 95.1 0.9 32 750-781 1-32 (32)
18 PF00730 HhH-GPD: HhH-GPD supe 98.9 3.2E-09 7E-14 96.6 6.9 85 407-512 2-86 (108)
19 TIGR00588 ogg 8-oxoguanine DNA 98.4 2.7E-07 5.8E-12 100.4 6.5 103 406-513 124-261 (310)
20 PRK10308 3-methyl-adenine DNA 97.2 0.0004 8.7E-09 75.2 5.0 68 438-509 154-245 (283)
21 COG0122 AlkA 3-methyladenine D 96.9 0.0015 3.2E-08 71.1 6.0 98 408-510 112-237 (285)
22 PF10576 EndIII_4Fe-2S: Iron-s 96.4 0.0011 2.3E-08 44.6 0.7 17 536-552 1-17 (17)
23 KOG2875 8-oxoguanine DNA glyco 96.4 0.004 8.7E-08 67.9 5.3 72 435-510 157-256 (323)
24 smart00525 FES FES domain. iro 95.5 0.0058 1.3E-07 44.1 1.1 22 535-556 1-22 (26)
25 COG1059 Thermostable 8-oxoguan 92.5 0.23 5E-06 52.2 5.7 113 408-535 46-189 (210)
26 KOG1918 3-methyladenine DNA gl 63.0 7.2 0.00016 42.3 3.4 85 407-498 81-179 (254)
27 cd04370 BAH BAH, or Bromo Adja 54.8 20 0.00043 32.8 4.5 64 804-878 59-122 (123)
28 PRK10353 3-methyl-adenine DNA 51.6 37 0.0008 35.9 6.3 63 415-484 45-112 (187)
29 PF00633 HHH: Helix-hairpin-he 49.9 3.4 7.3E-05 31.5 -1.1 14 485-498 12-25 (30)
30 PF03352 Adenine_glyco: Methyl 42.8 39 0.00085 35.4 4.9 47 438-484 56-107 (179)
31 COG2818 Tag 3-methyladenine DN 35.4 1E+02 0.0023 32.8 6.6 46 439-484 63-113 (188)
32 COG1555 ComEA DNA uptake prote 34.7 27 0.00058 35.4 2.2 45 445-496 91-139 (149)
33 TIGR00426 competence protein C 34.0 21 0.00046 30.9 1.2 48 445-498 10-61 (69)
34 PRK02515 psbU photosystem II c 29.8 37 0.00081 34.3 2.2 44 444-498 54-101 (132)
35 TIGR00624 tag DNA-3-methyladen 29.1 1.4E+02 0.003 31.5 6.3 58 415-479 44-103 (179)
36 PF08876 DUF1836: Domain of un 28.5 43 0.00092 32.4 2.3 57 646-702 3-59 (105)
37 smart00439 BAH Bromo adjacent 27.9 61 0.0013 29.8 3.2 64 804-878 56-119 (120)
38 PF14520 HHH_5: Helix-hairpin- 27.8 71 0.0015 27.0 3.3 36 437-475 24-59 (60)
39 PRK13482 DNA integrity scannin 25.9 26 0.00055 40.3 0.4 71 417-497 244-332 (352)
40 PRK13844 recombination protein 24.9 63 0.0014 34.6 3.0 48 486-547 17-64 (200)
41 TIGR00615 recR recombination p 24.1 66 0.0014 34.3 3.0 48 486-547 13-60 (195)
42 PF15414 DUF4621: Protein of u 22.9 27 0.00059 37.5 -0.1 28 619-646 195-222 (329)
43 PRK00076 recR recombination pr 21.8 79 0.0017 33.7 3.0 41 486-535 13-53 (196)
44 PRK01172 ski2-like helicase; P 20.7 1.5E+02 0.0033 36.1 5.5 44 435-481 629-672 (674)
No 1
>PF15628 RRM_DME: RRM in Demeter
Probab=100.00 E-value=2.5e-70 Score=497.02 Aligned_cols=103 Identities=82% Similarity=1.488 Sum_probs=102.1
Q ss_pred eeEeeeccccccCCccCCccceeeeeeeeccCCCCCCcccchhhhccCCceeEEecCChhhhcccCCHHHHHHhhhccce
Q 002607 784 GTILIPCRTAMRGSFPLNGTYFQVNEVFADHDSSLKPINVPREWLWNLPRRTVYFGTSIPSIFKGLTTEGIQHCFWRGYV 863 (901)
Q Consensus 784 gTiLiPCRTAmrG~FPLNGTYFQvNEVFaDh~SS~~Pi~vpr~~iw~L~rr~vyfGtSv~sIfkglt~~~Iq~cF~~G~v 863 (901)
|||||||||||||+|||||||||||||||||+||+|||+|||+|||+|+||+|||||||+|||||||++|||+|||+|||
T Consensus 1 gtiLiPCrtAmrg~FPLnGTYFQ~nEVFaD~~Ss~~Pi~vpr~~iw~L~rr~vYfGtsv~SIfrGls~~eIq~cF~~G~V 80 (103)
T PF15628_consen 1 GTILIPCRTAMRGSFPLNGTYFQVNEVFADHESSRNPIDVPRELIWNLPRRIVYFGTSVSSIFRGLSREEIQQCFWKGFV 80 (103)
T ss_pred CceEeeehhhhCCccccCceEEEEEEEEeccccccCCeeccHHHhhcCCceEEEecCcHHHHhcccCHHHHHHHHhcCcE
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EeecccccccCCcccccccccCc
Q 002607 864 CVRGFDQKSRAPRPLMARLHFPA 886 (901)
Q Consensus 864 CVR~fdr~tr~PrpL~~rlH~~~ 886 (901)
|||||||+||+||||++|||+++
T Consensus 81 CVR~FDr~Tr~PrpL~~rLH~~~ 103 (103)
T PF15628_consen 81 CVRGFDRKTRAPRPLCARLHFPA 103 (103)
T ss_pred EEeecccccCCCcchhhhccCCC
Confidence 99999999999999999999985
No 2
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=99.97 E-value=1.3e-31 Score=271.53 Aligned_cols=142 Identities=22% Similarity=0.449 Sum_probs=127.2
Q ss_pred ccCccccccCChHHHHHHHHhcCCCCCCCCCcCCCCCHHHHHcCCHHHHHHHHhhcCchHHHHHHHHHHHHHHHHHcCCc
Q 002607 405 RVSKEKQNDFDWDSLRRQVEANGGKKERPEHTKDSLDWEAVRCADVNKIANTIKERGMNNMLAGRIKDFLNRLVRDHGSV 484 (901)
Q Consensus 405 ~~gaiLtQNTsW~NVeKAL~N~Lkk~er~~~~agl~dpEaLa~Ad~EELeeLIRPaGFYnqKArRIKa~A~~Ive~~Ggi 484 (901)
=.||||||||+|+||++|++| |+ .++.+++++|..++.++|+++|||+||||+||+|||+++.+|...+.++
T Consensus 34 iigAILtQNT~WknvekAlen-Lk-------~~~~~~l~~I~~~~~~~L~elIrpsGFYnqKa~rLk~l~k~l~~~~~~~ 105 (215)
T COG2231 34 IIGAILTQNTSWKNVEKALEN-LK-------NEGILNLKKILKLDEEELAELIRPSGFYNQKAKRLKALSKNLAKFFINL 105 (215)
T ss_pred HHHHHHhccccHHHHHHHHHH-HH-------HcccCCHHHHhcCCHHHHHHHHhccchHHHHHHHHHHHHHHHHHHhhhh
Confidence 469999999999999999999 97 4689999999999999999999999999999999999999999887664
Q ss_pred ----------cccccCCCCccccC----C-------cc------------------hHHHHHHHhhhhccCCHHHHHHHH
Q 002607 485 ----------DLEWLRDVPPDKAK----Y-------PV------------------LESIQKYLWPRLCKLDQRTLYELH 525 (901)
Q Consensus 485 ----------DLe~LrGIGpETAd----Y-------PV------------------yd~VqR~Le~~L~~Ld~e~~~EFH 525 (901)
.|+.++|||.|||| | +| |++|++.|++.++. +..+|++||
T Consensus 106 ~~~~~~~~R~~LL~iKGIG~ETaDsILlYa~~rp~FVvD~Yt~R~l~rlg~i~~k~ydeik~~fe~~l~~-~~~lyqe~H 184 (215)
T COG2231 106 ESFKSEVLREELLSIKGIGKETADSILLYALDRPVFVVDKYTRRLLSRLGGIEEKKYDEIKELFEENLPE-NLRLYQEFH 184 (215)
T ss_pred hccchHHHHHHHHccCCcchhhHHHHHHHHhcCcccchhHHHHHHHHHhcccccccHHHHHHHHHhcchh-HHHHHHHHH
Confidence 47888999999999 2 22 67889999988775 567899999
Q ss_pred HHHHHHhhhhcccCCCCCCCCCCcccchhhh
Q 002607 526 YQMITFGKVFCTKSKPNCNACPMRGECRHFA 556 (901)
Q Consensus 526 aLIVefGK~iCtkrkPkC~~CPLrd~C~yy~ 556 (901)
++||.|||.+|++ +|.|+.|||+..|.++.
T Consensus 185 AlIv~~~K~f~~k-~~~~~~cpL~~~~~~~~ 214 (215)
T COG2231 185 ALIVEHAKHFCKK-KPLCEKCPLKEKCKKYR 214 (215)
T ss_pred HHHHHHHHHHccC-CcCCCCchHHHHHhhcc
Confidence 9999999999975 69999999999998864
No 3
>PRK10702 endonuclease III; Provisional
Probab=99.95 E-value=2.8e-28 Score=249.32 Aligned_cols=143 Identities=20% Similarity=0.164 Sum_probs=126.9
Q ss_pred ccCccccccCChHHHHHHHHhcCCCCCCCCCcCCCCCHHHHHcCCHHHHHHHHhhcCchHHHHHHHHHHHHHHHHHcCC-
Q 002607 405 RVSKEKQNDFDWDSLRRQVEANGGKKERPEHTKDSLDWEAVRCADVNKIANTIKERGMNNMLAGRIKDFLNRLVRDHGS- 483 (901)
Q Consensus 405 ~~gaiLtQNTsW~NVeKAL~N~Lkk~er~~~~agl~dpEaLa~Ad~EELeeLIRPaGFYnqKArRIKa~A~~Ive~~Gg- 483 (901)
=++.||.|||+|.+|.+++.+ |. ...++|++|++|+.++|+++||++|||++||++|++++++|.++||+
T Consensus 33 lvs~iLsq~t~~~~v~~~~~~-L~--------~~~pt~e~l~~a~~~~l~~~i~~~G~y~~kA~~l~~~a~~i~~~~~~~ 103 (211)
T PRK10702 33 LIAVLLSAQATDVSVNKATAK-LY--------PVANTPAAMLELGVEGVKTYIKTIGLYNSKAENVIKTCRILLEQHNGE 103 (211)
T ss_pred HHHHHHHhhcCHHHHHHHHHH-HH--------HHcCCHHHHHCCCHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHcCCC
Confidence 467899999999999999999 85 24799999999999999999999999999999999999999998877
Q ss_pred c-----cccccCCCCccccC-----------CcchHHHHHHHhhh---------------hccCCHHHHHHHHHHHHHHh
Q 002607 484 V-----DLEWLRDVPPDKAK-----------YPVLESIQKYLWPR---------------LCKLDQRTLYELHYQMITFG 532 (901)
Q Consensus 484 i-----DLe~LrGIGpETAd-----------YPVyd~VqR~Le~~---------------L~~Ld~e~~~EFHaLIVefG 532 (901)
+ .|..|+|||++||+ ||||+||+|.+... ...+|.+.+.+||.+||+||
T Consensus 104 ~p~~~~~Ll~lpGVG~ktA~~ill~a~~~~~~~VDt~v~Rv~~r~g~~~~~~~~~~~~~l~~~lp~~~~~~~~~~li~~G 183 (211)
T PRK10702 104 VPEDRAALEALPGVGRKTANVVLNTAFGWPTIAVDTHIFRVCNRTQFAPGKNVEQVEEKLLKVVPAEFKVDCHHWLILHG 183 (211)
T ss_pred CCchHHHHhcCCcccHHHHHHHHHHHcCCCcccccchHHHHHHHhCCCCCCCHHHHHHHHHHhCCchHHHHHHHHHHHHh
Confidence 3 68999999999999 58999999865321 12356778889999999999
Q ss_pred hhhcccCCCCCCCCCCcccchhhh
Q 002607 533 KVFCTKSKPNCNACPMRGECRHFA 556 (901)
Q Consensus 533 K~iCtkrkPkC~~CPLrd~C~yy~ 556 (901)
|.+|++++|+|+.|||++.|+|+.
T Consensus 184 r~~C~~~~P~C~~Cpl~~~C~~~~ 207 (211)
T PRK10702 184 RYTCIARKPRCGSCIIEDLCEYKE 207 (211)
T ss_pred HHHcCCCCCCCCCCcChhhcCccc
Confidence 999999999999999999999764
No 4
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=99.95 E-value=6.9e-28 Score=246.79 Aligned_cols=143 Identities=22% Similarity=0.274 Sum_probs=128.4
Q ss_pred cCccccccCChHHHHHHHHhcCCCCCCCCCcCCCCCHHHHHcCCHHHHHHHHhhcCchHHHHHHHHHHHHHHHHHcCC-c
Q 002607 406 VSKEKQNDFDWDSLRRQVEANGGKKERPEHTKDSLDWEAVRCADVNKIANTIKERGMNNMLAGRIKDFLNRLVRDHGS-V 484 (901)
Q Consensus 406 ~gaiLtQNTsW~NVeKAL~N~Lkk~er~~~~agl~dpEaLa~Ad~EELeeLIRPaGFYnqKArRIKa~A~~Ive~~Gg-i 484 (901)
+..||.|+|+.+.|.+|..+ |.+ -..+|++|++|++++|+++|+++|||++||++|+++++.|+++||| +
T Consensus 34 va~iLSaqttD~~vn~at~~-Lf~--------~~~t~e~l~~a~~~~l~~~I~~iGlyr~KAk~I~~~~~~l~e~~~g~v 104 (211)
T COG0177 34 VAVILSAQTTDEVVNKATPA-LFK--------RYPTPEDLLNADEEELEELIKSIGLYRNKAKNIKELARILLEKFGGEV 104 (211)
T ss_pred HHHHHhccCchHHHHHHHHH-HHH--------HcCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHcCCCC
Confidence 45689999999999999999 862 3679999999999999999999999999999999999999999988 3
Q ss_pred -----cccccCCCCccccC-----------CcchHHHHHHH--------------hh-hhccCCHHHHHHHHHHHHHHhh
Q 002607 485 -----DLEWLRDVPPDKAK-----------YPVLESIQKYL--------------WP-RLCKLDQRTLYELHYQMITFGK 533 (901)
Q Consensus 485 -----DLe~LrGIGpETAd-----------YPVyd~VqR~L--------------e~-~L~~Ld~e~~~EFHaLIVefGK 533 (901)
+|..|+|||++||+ +|||+||.|.- +. ....+|.+.|..+|.+||.||+
T Consensus 105 P~~~~eL~~LPGVGrKTAnvVL~~a~g~p~i~VDTHV~Rvs~R~gl~~~~~p~~ve~~L~~~iP~~~~~~~h~~lI~~GR 184 (211)
T COG0177 105 PDTREELLSLPGVGRKTANVVLSFAFGIPAIAVDTHVHRVSNRLGLVPGKTPEEVEEALMKLIPKELWTDLHHWLILHGR 184 (211)
T ss_pred CchHHHHHhCCCcchHHHHHHHHhhcCCCcccccchHHHHHHHhCCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHhhh
Confidence 69999999999999 48999998852 11 2234689999999999999999
Q ss_pred hhcccCCCCCCCCCCcccchhhhh
Q 002607 534 VFCTKSKPNCNACPMRGECRHFAS 557 (901)
Q Consensus 534 ~iCtkrkPkC~~CPLrd~C~yy~s 557 (901)
.+|++++|+|+.|||+++|+++..
T Consensus 185 ~iC~ar~P~C~~C~l~~~C~~~~~ 208 (211)
T COG0177 185 YICKARKPRCEECPLADLCPSAGK 208 (211)
T ss_pred hhccCCCCCcCcccchhhCchhcc
Confidence 999999999999999999999864
No 5
>PRK10880 adenine DNA glycosylase; Provisional
Probab=99.92 E-value=1.3e-25 Score=244.76 Aligned_cols=157 Identities=17% Similarity=0.231 Sum_probs=134.4
Q ss_pred cccCccccccCChHHHHHHHHhcCCCCCCCCCcCCCCCHHHHHcCCHHHHHHHHhhcCchHHHHHHHHHHHHHHHHHcCC
Q 002607 404 TRVSKEKQNDFDWDSLRRQVEANGGKKERPEHTKDSLDWEAVRCADVNKIANTIKERGMNNMLAGRIKDFLNRLVRDHGS 483 (901)
Q Consensus 404 ~~~gaiLtQNTsW~NVeKAL~N~Lkk~er~~~~agl~dpEaLa~Ad~EELeeLIRPaGFYnqKArRIKa~A~~Ive~~Gg 483 (901)
-=++.||.|+|.|++|.+++.+ +. ..++|+++|++|+.++|.++|+++|||+ ||++|+++|+.|+++|+|
T Consensus 33 ilVseILlQQT~v~~v~~~~~r-l~--------~~fPt~~~La~a~~eel~~~~~glGyy~-RAr~L~~~A~~i~~~~~g 102 (350)
T PRK10880 33 VWLSEVMLQQTQVATVIPYFER-FM--------ARFPTVTDLANAPLDEVLHLWTGLGYYA-RARNLHKAAQQVATLHGG 102 (350)
T ss_pred HHHHHHHHhhccHHHHHHHHHH-HH--------HHCcCHHHHHCcCHHHHHHHHHcCChHH-HHHHHHHHHHHHHHHhCC
Confidence 3457799999999999999988 75 2589999999999999999999999997 999999999999999876
Q ss_pred -c-----cccccCCCCccccC------C-----cchHHHHHHHhhh---------------h-----ccCCHHHHHHHHH
Q 002607 484 -V-----DLEWLRDVPPDKAK------Y-----PVLESIQKYLWPR---------------L-----CKLDQRTLYELHY 526 (901)
Q Consensus 484 -i-----DLe~LrGIGpETAd------Y-----PVyd~VqR~Le~~---------------L-----~~Ld~e~~~EFHa 526 (901)
+ .|..|+|||++||+ | +||.||+|.+... + ..++.+.+.+||+
T Consensus 103 ~~p~~~~~L~~LpGIG~~TA~aIl~~af~~~~~iVD~nV~RV~~Rl~~i~~~~~~~~~~~~l~~~~~~l~p~~~~~~~nq 182 (350)
T PRK10880 103 EFPETFEEVAALPGVGRSTAGAILSLSLGKHFPILDGNVKRVLARCYAVSGWPGKKEVENRLWQLSEQVTPAVGVERFNQ 182 (350)
T ss_pred CchhhHHHHhcCCCccHHHHHHHHHHHCCCCeecccHHHHHHHHHHhcccCCCChHHHHHHHHHHHHHhCChhHHHHHHH
Confidence 3 68999999999999 2 3689988764321 1 1246678999999
Q ss_pred HHHHHhhhhcccCCCCCCCCCCcccchhhhhccccccccCCCccccc
Q 002607 527 QMITFGKVFCTKSKPNCNACPMRGECRHFASAFASSRLALPGPEEKA 573 (901)
Q Consensus 527 LIVefGK~iCtkrkPkC~~CPLrd~C~yy~s~~as~rl~lP~~e~k~ 573 (901)
+||+||+.+|++++|+|..|||++.|.+|+.+.. ..+|++..|.
T Consensus 183 alm~lGa~vC~p~~P~C~~Cpl~~~C~~~~~~~~---~~~P~k~~k~ 226 (350)
T PRK10880 183 AMMDLGAMVCTRSKPKCELCPLQNGCIAYANHSW---ALYPGKKPKQ 226 (350)
T ss_pred HHHHhhHHhccCCCCCCCCCccHhhhHHHHcCCH---hhCCCCCCCC
Confidence 9999999999999999999999999999998753 6788876654
No 6
>TIGR01084 mutY A/G-specific adenine glycosylase. This equivalog model identifies mutY members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=99.91 E-value=1e-24 Score=231.02 Aligned_cols=156 Identities=17% Similarity=0.216 Sum_probs=132.7
Q ss_pred ccCccccccCChHHHHHHHHhcCCCCCCCCCcCCCCCHHHHHcCCHHHHHHHHhhcCchHHHHHHHHHHHHHHHHHcCC-
Q 002607 405 RVSKEKQNDFDWDSLRRQVEANGGKKERPEHTKDSLDWEAVRCADVNKIANTIKERGMNNMLAGRIKDFLNRLVRDHGS- 483 (901)
Q Consensus 405 ~~gaiLtQNTsW~NVeKAL~N~Lkk~er~~~~agl~dpEaLa~Ad~EELeeLIRPaGFYnqKArRIKa~A~~Ive~~Gg- 483 (901)
=+..|+.|+|+|++|.+++.+ +. ..++|+++|++|+.++|.++|+++|||+ ||++|+++|+.|.++|||
T Consensus 30 lvseIL~QQT~v~~v~~~~~r-l~--------~~fpt~~~La~a~~eeL~~~~~~lG~y~-RAr~L~~~A~~i~~~~~g~ 99 (275)
T TIGR01084 30 WLSEVMLQQTQVATVIPYFER-FL--------ERFPTVQALANAPQDEVLKLWEGLGYYA-RARNLHKAAQEVVEEFGGE 99 (275)
T ss_pred HHHHHHHhhccHHHHHHHHHH-HH--------HhCCCHHHHHCcCHHHHHHHHHHCCcHH-HHHHHHHHHHHHHHHcCCC
Confidence 356799999999999999988 75 2489999999999999999999999995 999999999999999877
Q ss_pred c-----cccccCCCCccccC-----------CcchHHHHHHHhhh-------------------h-ccCCHHHHHHHHHH
Q 002607 484 V-----DLEWLRDVPPDKAK-----------YPVLESIQKYLWPR-------------------L-CKLDQRTLYELHYQ 527 (901)
Q Consensus 484 i-----DLe~LrGIGpETAd-----------YPVyd~VqR~Le~~-------------------L-~~Ld~e~~~EFHaL 527 (901)
+ .|..|+|||++||+ ++||.+|+|.+... + ..+|.+.+.+||++
T Consensus 100 ~p~~~~~L~~LpGIG~~TA~~Il~~a~~~~~~~vD~~v~RVl~Rl~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~~~n~a 179 (275)
T TIGR01084 100 FPQDFEDLAALPGVGRYTAGAILSFALNKPYPILDGNVKRVLSRLFAVEGWPGKKKVENRLWTLAESLLPKADPEAFNQA 179 (275)
T ss_pred CcHHHHHHHhCCCCCHHHHHHHHHHHCCCCCCcchHhHHHHHHHHccCcCCCCHHHHHHHHHHHHHHHCChhhHHHHHHH
Confidence 3 68999999999999 25788888754221 1 12466788999999
Q ss_pred HHHHhhhhcccCCCCCCCCCCcccchhhhhccccccccCCCccccc
Q 002607 528 MITFGKVFCTKSKPNCNACPMRGECRHFASAFASSRLALPGPEEKA 573 (901)
Q Consensus 528 IVefGK~iCtkrkPkC~~CPLrd~C~yy~s~~as~rl~lP~~e~k~ 573 (901)
||+||+.+|++++|+|..|||++.|.++..+.. ..+|.+..|.
T Consensus 180 lm~lG~~vC~~~~P~C~~Cpl~~~C~~~~~~~~---~~~p~~~~~~ 222 (275)
T TIGR01084 180 LMDLGAMICTRKKPKCDLCPLQDFCLAYQQGTW---EEYPVKKPKA 222 (275)
T ss_pred HHHHhHHHcCCCCCCCCCCCChhhCHHHHcCCH---hhcCCCCCCC
Confidence 999999999999999999999999999987643 6788876554
No 7
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=99.89 E-value=9.2e-24 Score=217.59 Aligned_cols=133 Identities=14% Similarity=0.173 Sum_probs=106.2
Q ss_pred cccCccccccCChHHHHHHHHhcCCCCCCCCCcCCCCCHHHHHcCCHHHHHHHHhhcCchHHHHHHHHHHHHHHHHHcCC
Q 002607 404 TRVSKEKQNDFDWDSLRRQVEANGGKKERPEHTKDSLDWEAVRCADVNKIANTIKERGMNNMLAGRIKDFLNRLVRDHGS 483 (901)
Q Consensus 404 ~~~gaiLtQNTsW~NVeKAL~N~Lkk~er~~~~agl~dpEaLa~Ad~EELeeLIRPaGFYnqKArRIKa~A~~Ive~~Gg 483 (901)
.=+|+||+|||+|+||++|+.+ |++.- ....-..++|++|++++.++|+++|||+|||++||++|+++|++|.+++|+
T Consensus 33 vLV~aILsQqT~~~~v~~a~~~-L~~~~-~~~~~~~~t~e~L~~a~~eeL~~~Irp~Gf~~~KA~~Lk~la~~i~~~~g~ 110 (218)
T PRK13913 33 ALLGAVLTQNTKFEAVEKSLEN-LKNAF-ILENDDEINLKKIAYIEFSKLAECVRPSGFYNQKAKRLIDLSENILKDFGS 110 (218)
T ss_pred HHHHHHHHhhhhHHHHHHHHHH-HHHhc-ccccccCCCHHHHHcCCHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHcCC
Confidence 3478999999999999999999 86110 000002359999999999999999999999999999999999999999987
Q ss_pred c----------cccccCCCCccccC-----------CcchHHHHHH-----------------Hhhhh-----------c
Q 002607 484 V----------DLEWLRDVPPDKAK-----------YPVLESIQKY-----------------LWPRL-----------C 514 (901)
Q Consensus 484 i----------DLe~LrGIGpETAd-----------YPVyd~VqR~-----------------Le~~L-----------~ 514 (901)
+ .|..|+|||++||+ |+||++++|. |+..+ +
T Consensus 111 ~~~~~~~~~re~Ll~l~GIG~kTAd~iLlya~~rp~fvVDty~~Rv~~RlG~~~~~y~~~~~~~~~~l~~~~~~~~~~~~ 190 (218)
T PRK13913 111 FENFKQEVTREWLLDQKGIGKESADAILCYVCAKEVMVVDKYSYLFLKKLGIEIEDYDELQHFFEKGVQENLNSALALYE 190 (218)
T ss_pred chhccCchHHHHHHcCCCccHHHHHHHHHHHcCCCccccchhHHHHHHHcCCCCCCHHHHHHHHHHhhhhhhhhhhcccc
Confidence 4 37889999999999 4677776664 33322 0
Q ss_pred cC--CHHHHHHHHHHHHHHhhhhccc
Q 002607 515 KL--DQRTLYELHYQMITFGKVFCTK 538 (901)
Q Consensus 515 ~L--d~e~~~EFHaLIVefGK~iCtk 538 (901)
.. ..++|++||++||+|||.+|.-
T Consensus 191 ~~~~~~~~~~~~Halive~~k~~~~~ 216 (218)
T PRK13913 191 NTISLAQLYARFHGKIVEFSKQKLEL 216 (218)
T ss_pred ccchHHHHHHHHHHHHHHHHHHhhhc
Confidence 10 1268999999999999999964
No 8
>TIGR01083 nth endonuclease III. This equivalog model identifes nth members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=99.86 E-value=2.6e-22 Score=201.28 Aligned_cols=130 Identities=21% Similarity=0.171 Sum_probs=113.4
Q ss_pred ccCccccccCChHHHHHHHHhcCCCCCCCCCcCCCCCHHHHHcCCHHHHHHHHhhcCchHHHHHHHHHHHHHHHHHcCC-
Q 002607 405 RVSKEKQNDFDWDSLRRQVEANGGKKERPEHTKDSLDWEAVRCADVNKIANTIKERGMNNMLAGRIKDFLNRLVRDHGS- 483 (901)
Q Consensus 405 ~~gaiLtQNTsW~NVeKAL~N~Lkk~er~~~~agl~dpEaLa~Ad~EELeeLIRPaGFYnqKArRIKa~A~~Ive~~Gg- 483 (901)
=+++||.|||+|+++.+++.+ |. ...+||++|++++.++|+++||++|||++||++|++++++|.+++++
T Consensus 30 Li~~ILsqqt~~~~~~~~~~~-l~--------~~~pt~~~l~~~~~~~L~~~ir~~G~~~~Ka~~i~~~a~~i~~~~~~~ 100 (191)
T TIGR01083 30 LVATILSAQATDKSVNKATKK-LF--------EVYPTPQALAQAGLEELEEYIKSIGLYRNKAKNIIALCRILVERYGGE 100 (191)
T ss_pred HHHHHHHhhCcHHHHHHHHHH-HH--------HHCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHcCCC
Confidence 356899999999999999998 75 25789999999999999999999999999999999999999988876
Q ss_pred c-----cccccCCCCccccC-----------CcchHHHHHHHhh--------------hh-ccCCHHHHHHHHHHHHHHh
Q 002607 484 V-----DLEWLRDVPPDKAK-----------YPVLESIQKYLWP--------------RL-CKLDQRTLYELHYQMITFG 532 (901)
Q Consensus 484 i-----DLe~LrGIGpETAd-----------YPVyd~VqR~Le~--------------~L-~~Ld~e~~~EFHaLIVefG 532 (901)
+ .|..|+|||++||+ ||||+||+|.+.. .+ ..++...|.+||++||+||
T Consensus 101 ~~~~~~~L~~l~GIG~ktA~~ill~~~~~~~~~vD~~v~Ri~~r~g~~~~~~~~~~~~~l~~~~p~~~~~~~h~~li~~G 180 (191)
T TIGR01083 101 VPEDREELVKLPGVGRKTANVVLNVAFGIPAIAVDTHVFRVSNRLGLSKGKDPDKVEEELLKLIPREFWTKLHHWLILHG 180 (191)
T ss_pred CchHHHHHHhCCCCcHHHHHHHHHHHcCCCccccchhHHHHHHHcCCCCCCCHHHHHHHHHHHCCchhHHHHHHHHHHHh
Confidence 2 57899999999999 4789999886522 11 1245677999999999999
Q ss_pred hhhcccCCCCC
Q 002607 533 KVFCTKSKPNC 543 (901)
Q Consensus 533 K~iCtkrkPkC 543 (901)
|.+|++++|+|
T Consensus 181 ~~~C~~~~P~C 191 (191)
T TIGR01083 181 RYTCKARKPLC 191 (191)
T ss_pred HHhcCCCCCCC
Confidence 99999999999
No 9
>PRK13910 DNA glycosylase MutY; Provisional
Probab=99.85 E-value=1.1e-21 Score=209.34 Aligned_cols=138 Identities=17% Similarity=0.223 Sum_probs=114.9
Q ss_pred ccCChHHHH-HHHHhcCCCCCCCCCcCCCCCHHHHHcCCHHHHHHHHhhcCchHHHHHHHHHHHHHHHHHcCC-c-----
Q 002607 412 NDFDWDSLR-RQVEANGGKKERPEHTKDSLDWEAVRCADVNKIANTIKERGMNNMLAGRIKDFLNRLVRDHGS-V----- 484 (901)
Q Consensus 412 QNTsW~NVe-KAL~N~Lkk~er~~~~agl~dpEaLa~Ad~EELeeLIRPaGFYnqKArRIKa~A~~Ive~~Gg-i----- 484 (901)
|+|.=+.|. +.+.+ +. .-++||++|++|++++|+++|+++|||+ ||++|+++|++|.++|+| +
T Consensus 3 QQT~v~~v~~~yy~r-f~--------~~fPt~e~La~a~~~el~~~~~glGyy~-RAr~L~~~A~~i~~~~~g~~P~~~~ 72 (289)
T PRK13910 3 QQTQINTVVERFYSP-FL--------EAFPTLKDLANAPLEEVLLLWRGLGYYS-RAKNLKKSAEICVKEHHSQLPNDYQ 72 (289)
T ss_pred CCCcHHHhHHHHHHH-HH--------HHCCCHHHHHCCCHHHHHHHHHcCCcHH-HHHHHHHHHHHHHHHhCCCCChhHH
Confidence 677767775 45555 43 2589999999999999999999999996 999999999999998866 3
Q ss_pred cccccCCCCccccC-----------CcchHHHHHHHhhhh----------------ccCCHHHHHHHHHHHHHHhhhhcc
Q 002607 485 DLEWLRDVPPDKAK-----------YPVLESIQKYLWPRL----------------CKLDQRTLYELHYQMITFGKVFCT 537 (901)
Q Consensus 485 DLe~LrGIGpETAd-----------YPVyd~VqR~Le~~L----------------~~Ld~e~~~EFHaLIVefGK~iCt 537 (901)
.|..|+|||++||+ ++||.+|+|.+...+ ..++...+.+||++||+||+.+|+
T Consensus 73 ~L~~LpGIG~kTA~aIl~~af~~~~~~VD~nV~RVl~Rl~g~~~~~~~~~l~~~~~~~l~~~~~~~~nqaLm~~Ga~iC~ 152 (289)
T PRK13910 73 SLLKLPGIGAYTANAILCFGFREKSACVDANIKRVLLRLFGLDPNIHAKDLQIKANDFLNLNESFNHNQALIDLGALICS 152 (289)
T ss_pred HHHhCCCCCHHHHHHHHHHHCCCCcCcccHHHHHHHHHHhcCCCCccHHHHHHHHHHhCCccchHHHHHHHHHHhHHHcC
Confidence 68999999999999 378999998763311 113445678899999999999999
Q ss_pred cCCCCCCCCCCcccchhhhhccc
Q 002607 538 KSKPNCNACPMRGECRHFASAFA 560 (901)
Q Consensus 538 krkPkC~~CPLrd~C~yy~s~~a 560 (901)
+ +|+|..|||++.|.++..+..
T Consensus 153 ~-~P~C~~CPl~~~C~~~~~~~~ 174 (289)
T PRK13910 153 P-KPKCAICPLNPYCLGKNNPEK 174 (289)
T ss_pred C-CCCCCCCcChhhhhhhhcCCc
Confidence 8 799999999999999987654
No 10
>KOG1921 consensus Endonuclease III [Replication, recombination and repair]
Probab=99.83 E-value=2.9e-21 Score=200.54 Aligned_cols=142 Identities=22% Similarity=0.280 Sum_probs=125.5
Q ss_pred cCccccccCChHHHHHHHHhcCCCCCCCCCcCCCCCHHHHHcCCHHHHHHHHhhcCchHHHHHHHHHHHHHHHHHcCC-c
Q 002607 406 VSKEKQNDFDWDSLRRQVEANGGKKERPEHTKDSLDWEAVRCADVNKIANTIKERGMNNMLAGRIKDFLNRLVRDHGS-V 484 (901)
Q Consensus 406 ~gaiLtQNTsW~NVeKAL~N~Lkk~er~~~~agl~dpEaLa~Ad~EELeeLIRPaGFYnqKArRIKa~A~~Ive~~Gg-i 484 (901)
+|.+|.-+|...-...|+.| |+ ..+.+++++|+++++..|.++|+|+|||++||++||..|+++.++|+| +
T Consensus 83 v~lmLSSQTKDevt~~Am~r-L~-------~~~gLT~e~v~~~de~~l~~LI~~VgFy~rKA~ylkkta~IL~d~f~gDI 154 (286)
T KOG1921|consen 83 VGLMLSSQTKDEVTAAAMLR-LK-------EYGGLTLEAVLKIDEPTLNELIYPVGFYTRKAKYLKKTAKILQDKFDGDI 154 (286)
T ss_pred HHHHHhcchHHHHHHHHHHH-HH-------HhcCCCHHHHhccChHhHHhhhhhccchHHHHHHHHHHHHHHHHHhCCCC
Confidence 68889989998888888888 87 347899999999999999999999999999999999999999999866 4
Q ss_pred -----cccccCCCCccccC------------CcchHHHHHHH----hh------------hhcc-CCHHHHHHHHHHHHH
Q 002607 485 -----DLEWLRDVPPDKAK------------YPVLESIQKYL----WP------------RLCK-LDQRTLYELHYQMIT 530 (901)
Q Consensus 485 -----DLe~LrGIGpETAd------------YPVyd~VqR~L----e~------------~L~~-Ld~e~~~EFHaLIVe 530 (901)
||..|+|||++.|. +.||+||+|+. |- .|.. +|..+|.++|.+||.
T Consensus 155 P~~v~dLlsLPGVGPKMa~L~m~~AWn~i~GI~VDtHVHRi~nrlgWv~~ktkspE~TR~aLq~wLPk~lW~eIN~lLVG 234 (286)
T KOG1921|consen 155 PDTVEDLLSLPGVGPKMAHLTMQVAWNKIVGICVDTHVHRICNRLGWVDTKTKSPEQTRVALQQWLPKSLWVEINHLLVG 234 (286)
T ss_pred chhHHHHhcCCCCchHHHHHHHHHHhccceeEEeehHHHHHHHHhcccccccCCHHHHHHHHHHhCcHHHHhhhhceeec
Confidence 89999999999998 36899999853 10 1222 588999999999999
Q ss_pred HhhhhcccCCCCCCCCCC-cccchhh
Q 002607 531 FGKVFCTKSKPNCNACPM-RGECRHF 555 (901)
Q Consensus 531 fGK~iCtkrkPkC~~CPL-rd~C~yy 555 (901)
||+.+|++++|+|+.|-+ ++.|+..
T Consensus 235 FGQ~iC~p~~prC~~C~~~~~~Cpss 260 (286)
T KOG1921|consen 235 FGQTICTPRRPRCGLCLLSRDLCPSS 260 (286)
T ss_pred ccceeeecCCCCccccccCcccCchh
Confidence 999999999999999999 7999963
No 11
>COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair]
Probab=99.74 E-value=2.2e-18 Score=187.04 Aligned_cols=154 Identities=21% Similarity=0.332 Sum_probs=123.9
Q ss_pred CccccccCChHHHHHHHHhcCCCCCCCCCcCCCCCHHHHHcCCHHHHHHHHhhcCchHHHHHHHHHHHHHHHHHcCCc--
Q 002607 407 SKEKQNDFDWDSLRRQVEANGGKKERPEHTKDSLDWEAVRCADVNKIANTIKERGMNNMLAGRIKDFLNRLVRDHGSV-- 484 (901)
Q Consensus 407 gaiLtQNTsW~NVeKAL~N~Lkk~er~~~~agl~dpEaLa~Ad~EELeeLIRPaGFYnqKArRIKa~A~~Ive~~Ggi-- 484 (901)
-.|.-|+|.=+.|..-+.+ -. .-++++++|++|+.++|..+|.+.|||. ||++|+..++.|+++|||.
T Consensus 40 SEiMLQQT~v~~Vi~yy~~-fl--------~rfPti~~LA~A~~~evl~~W~gLGYys-RArnL~~~A~~v~~~~~G~~P 109 (342)
T COG1194 40 SEIMLQQTQVATVIPYYER-FL--------ERFPTIKALAAAPEDEVLKAWEGLGYYS-RARNLHKAAQEVVERHGGEFP 109 (342)
T ss_pred HHHHhhhccHhhhhhhHHH-HH--------HhCCCHHHHhcCCHHHHHHHHHhcChHH-HHHHHHHHHHHHHHHcCCCCC
Confidence 3466688888888886665 32 2589999999999999999999999885 9999999999999999984
Q ss_pred ----cccccCCCCccccC----------Cc-chHHHHHH-------------------Hhhhhcc-CC-HHHHHHHHHHH
Q 002607 485 ----DLEWLRDVPPDKAK----------YP-VLESIQKY-------------------LWPRLCK-LD-QRTLYELHYQM 528 (901)
Q Consensus 485 ----DLe~LrGIGpETAd----------YP-Vyd~VqR~-------------------Le~~L~~-Ld-~e~~~EFHaLI 528 (901)
+|..|+|||++||. +| ||.+|.|+ +|..+.. ++ .....+|+++|
T Consensus 110 ~~~~~l~~LpGiG~yTa~Ail~~a~~~~~~~lDgNV~RVl~R~f~i~~~~~~~~~~~~~~~~~~~ll~p~~~~~~fnqam 189 (342)
T COG1194 110 DDEEELAALPGVGPYTAGAILSFAFNQPEPVLDGNVKRVLSRLFAISGDIGKPKTKKELWELAEQLLTPDRRPGDFNQAM 189 (342)
T ss_pred CCHHHHHhCCCCcHHHHHHHHHHHhCCCCceeecchheeehhhhcccccccccchhHHHHHHHHHhcCCCCChHHHHHHH
Confidence 68889999999999 24 36666553 3322221 22 23378999999
Q ss_pred HHHhhhhcccCCCCCCCCCCcccchhhhhccccccccCCCccccc
Q 002607 529 ITFGKVFCTKSKPNCNACPMRGECRHFASAFASSRLALPGPEEKA 573 (901)
Q Consensus 529 VefGK~iCtkrkPkC~~CPLrd~C~yy~s~~as~rl~lP~~e~k~ 573 (901)
|++|..+|++++|+|..|||++.|..|..+.. ..+|++..|.
T Consensus 190 mdlGA~ICt~~~P~C~~CPl~~~c~a~~~g~~---~~~P~k~~k~ 231 (342)
T COG1194 190 MDLGATICTAKKPKCSLCPLRDNCAAYRNGTP---EKYPVKKPKK 231 (342)
T ss_pred HHhhhHhhcCCCCCCCcCcchHHHHHHHcCCc---ccCCCcCccc
Confidence 99999999999999999999999999998764 5678766553
No 12
>TIGR03252 uncharacterized HhH-GPD family protein. This model describes a small, well-conserved bacterial protein family. Its sequence largely consists of a domain, HhH-GPD, found in a variety of related base excision DNA repair enzymes (see pfam00730).
Probab=99.56 E-value=2.4e-15 Score=151.46 Aligned_cols=87 Identities=17% Similarity=0.124 Sum_probs=77.7
Q ss_pred ccCccccccCChHHHHHHHHhcCCCCCCCCCcCCCCCHHHHHcCCHHHHHHHHhhc----CchHHHHHHHHHHHHHHHHH
Q 002607 405 RVSKEKQNDFDWDSLRRQVEANGGKKERPEHTKDSLDWEAVRCADVNKIANTIKER----GMNNMLAGRIKDFLNRLVRD 480 (901)
Q Consensus 405 ~~gaiLtQNTsW~NVeKAL~N~Lkk~er~~~~agl~dpEaLa~Ad~EELeeLIRPa----GFYnqKArRIKa~A~~Ive~ 480 (901)
=+|.||+|||+|+||.+|+.+ |++ ..+.+||++|++++.++|+++|++. |||++||++|++++++|.++
T Consensus 22 LVa~ILSQqTtd~nv~kA~~~-L~~------~~g~~tp~~La~a~~eeL~~lI~~~pal~Gfy~~KAk~Lk~~a~~iie~ 94 (177)
T TIGR03252 22 LTGMLLDQQVPMERAFAGPHK-IAR------RMGSLDAEDIAKYDPQAFVALFSERPAVHRFPGSMAKRVQALAQYVVDT 94 (177)
T ss_pred HHHHHHhccCcHHHHHHHHHH-HHH------HhCCCCHHHHHcCCHHHHHHHHhcCccccCchHHHHHHHHHHHHHHHHH
Confidence 468899999999999999999 852 3466899999999999999999865 99999999999999999988
Q ss_pred cCC-c----------------cccccCCCCccccC
Q 002607 481 HGS-V----------------DLEWLRDVPPDKAK 498 (901)
Q Consensus 481 ~Gg-i----------------DLe~LrGIGpETAd 498 (901)
|+| + .|..|+|||++||+
T Consensus 95 y~G~v~~L~~~~~p~t~~lre~Ll~LpGVG~KTAn 129 (177)
T TIGR03252 95 YDGDATAVWTEGDPDGKELLRRLKALPGFGKQKAK 129 (177)
T ss_pred hCCChhhhhcccCCCcHHHHHHHHcCCCCCHHHHH
Confidence 866 2 37889999999999
No 13
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=99.51 E-value=4.3e-14 Score=135.25 Aligned_cols=116 Identities=21% Similarity=0.205 Sum_probs=97.7
Q ss_pred ccccCChHHHHHHHHhcCCCCCCCCCcCCCCCHHHHHcCCHHHHHHHHhhcCchHHHHHHHHHHHHHHHHHcCC-c----
Q 002607 410 KQNDFDWDSLRRQVEANGGKKERPEHTKDSLDWEAVRCADVNKIANTIKERGMNNMLAGRIKDFLNRLVRDHGS-V---- 484 (901)
Q Consensus 410 LtQNTsW~NVeKAL~N~Lkk~er~~~~agl~dpEaLa~Ad~EELeeLIRPaGFYnqKArRIKa~A~~Ive~~Gg-i---- 484 (901)
|.|||+|+++.+++.+ |. ..+++|++|++++.++|.++|+++||+++||++|+++++.|.+.+++ +
T Consensus 1 l~qq~~~~~a~~~~~~-l~--------~~~~~~~~l~~~~~~eL~~~l~~~g~~~~ka~~i~~~a~~~~~~~~~~~~~~~ 71 (149)
T smart00478 1 LSQQTSDEAVNKATER-LF--------EKFPTPEDLAAADEEELEELIRPLGFYRRKAKYLIELARILVEEYGGEVPDDR 71 (149)
T ss_pred CCCcccHHHHHHHHHH-HH--------HHCCCHHHHHCCCHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHCCCccHHH
Confidence 5799999999999998 85 13679999999999999999999999999999999999999988755 2
Q ss_pred -cccccCCCCccccC-----------CcchHHHHHHHhhh---------------h-ccCCHHHHHHHHHHHHHHhhh
Q 002607 485 -DLEWLRDVPPDKAK-----------YPVLESIQKYLWPR---------------L-CKLDQRTLYELHYQMITFGKV 534 (901)
Q Consensus 485 -DLe~LrGIGpETAd-----------YPVyd~VqR~Le~~---------------L-~~Ld~e~~~EFHaLIVefGK~ 534 (901)
.|..|+|||++||+ +|||.+|.|.+... + ..++...|..||++++.||+.
T Consensus 72 ~~L~~l~GIG~~tA~~~l~~~~~~~~~~~D~~v~r~~~rl~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~l~~g~~ 149 (149)
T smart00478 72 EELLKLPGVGRKTANAVLSFALGKPFIPVDTHVLRIAKRLGLVDKKSTPEEVEKLLEKLLPKEDWRELNLLLIDFGRT 149 (149)
T ss_pred HHHHcCCCCcHHHHHHHHHHHCCCCCCccchHHHHHHHHhCCCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHcCC
Confidence 57889999999999 37898888754221 0 124567799999999999973
No 14
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=99.50 E-value=2.7e-14 Score=147.07 Aligned_cols=118 Identities=13% Similarity=0.023 Sum_probs=92.9
Q ss_pred ccccCccccccCChHHHHHHHHhcCCCCCCCCCcCCCCCHHHHHcCCHHHHHHHHhhcC--chHHHHHHHHHHHHH---H
Q 002607 403 STRVSKEKQNDFDWDSLRRQVEANGGKKERPEHTKDSLDWEAVRCADVNKIANTIKERG--MNNMLAGRIKDFLNR---L 477 (901)
Q Consensus 403 ~~~~gaiLtQNTsW~NVeKAL~N~Lkk~er~~~~agl~dpEaLa~Ad~EELeeLIRPaG--FYnqKArRIKa~A~~---I 477 (901)
..=++.||+|||+|.|+.+|+.+ |+ ++.+ +++.++|+++|||+| ||++||++|++++++ +
T Consensus 39 ~~Lv~~ILsqnT~~~~v~~a~~~-L~-------------~~~l-~~~~eeL~~~Ir~~Gygf~~~KAk~I~~~~~~~~~l 103 (208)
T PRK01229 39 SELSFCILTANSSAEGGIKAQKE-IG-------------DGFL-YLSEEELEEKLKEVGHRFYNKRAEYIVEARKLYGKL 103 (208)
T ss_pred HHHHHHHhcCcCcHHHHHHHHHh-cC-------------HHHc-CCCHHHHHHHHHHhhcccHHHHHHHHHHHHHHHHHH
Confidence 34468899999999999999999 74 2345 899999999999995 999999999999998 5
Q ss_pred HHHc--CC-c-----ccc-ccCCCCccccC-----------CcchHHHHHHHhhh--hc----cCCHHHHHHHHHHHHHH
Q 002607 478 VRDH--GS-V-----DLE-WLRDVPPDKAK-----------YPVLESIQKYLWPR--LC----KLDQRTLYELHYQMITF 531 (901)
Q Consensus 478 ve~~--Gg-i-----DLe-~LrGIGpETAd-----------YPVyd~VqR~Le~~--L~----~Ld~e~~~EFHaLIVef 531 (901)
.+.+ ++ . .|. .|+|||++||+ |+||+|+.|++... .. .++...|.+....|.++
T Consensus 104 ~~~~~~~~~~~~~R~~Ll~~lpGIG~KTAd~vL~~~~~~~~~iVDtHv~Ri~~RlG~~~~~~~~lt~~~y~~~E~~l~~~ 183 (208)
T PRK01229 104 KEIIKADKDQFEAREFLVKNIKGIGYKEASHFLRNVGYEDLAILDRHILRFLKRYGLIEEIPKTLSKKRYLEIEEILREI 183 (208)
T ss_pred HHHHhccCCchHHHHHHHHcCCCCcHHHHHHHHHHccCCCeeeeeHHHHHHHHHhCCCcccccccCcCCHHHHHHHHHHH
Confidence 5454 22 2 577 99999999999 36899999987542 11 12346788888888877
Q ss_pred hhhh
Q 002607 532 GKVF 535 (901)
Q Consensus 532 GK~i 535 (901)
.+.+
T Consensus 184 ~~~~ 187 (208)
T PRK01229 184 AEEL 187 (208)
T ss_pred HHHc
Confidence 6643
No 15
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=99.38 E-value=8.3e-13 Score=127.38 Aligned_cols=117 Identities=19% Similarity=0.173 Sum_probs=96.8
Q ss_pred CccccccCChHHHHHHHHhcCCCCCCCCCcCCCCCHHHHHcCCHHHHHHHHhhcCchHHHHHHHHHHHHHHHHHcCCc--
Q 002607 407 SKEKQNDFDWDSLRRQVEANGGKKERPEHTKDSLDWEAVRCADVNKIANTIKERGMNNMLAGRIKDFLNRLVRDHGSV-- 484 (901)
Q Consensus 407 gaiLtQNTsW~NVeKAL~N~Lkk~er~~~~agl~dpEaLa~Ad~EELeeLIRPaGFYnqKArRIKa~A~~Ive~~Ggi-- 484 (901)
.+|+.|+|+|+++.+++.+ |.. .-.+||++|+.++.++|+++|.+.| |+.||++|+++++.+.+.+++.
T Consensus 6 ~~il~q~~s~~~a~~~~~~-l~~-------~~gpt~~~l~~~~~~~l~~~~~~~G-~~~kA~~i~~~a~~~~~~~~~~~~ 76 (158)
T cd00056 6 SEILSQQTTDKAVNKAYER-LFE-------RYGPTPEALAAADEEELRELIRSLG-YRRKAKYLKELARAIVEGFGGLVL 76 (158)
T ss_pred HHHHHhcccHHHHHHHHHH-HHH-------HhCCCHHHHHCCCHHHHHHHHHhcC-hHHHHHHHHHHHHHHHHHcCCccC
Confidence 5689999999999999999 861 1129999999999999999999999 8999999999999999988764
Q ss_pred -------cccccCCCCccccC-----------CcchHHHHHHHhhhh----------------ccCCHHHHHHHHHHHHH
Q 002607 485 -------DLEWLRDVPPDKAK-----------YPVLESIQKYLWPRL----------------CKLDQRTLYELHYQMIT 530 (901)
Q Consensus 485 -------DLe~LrGIGpETAd-----------YPVyd~VqR~Le~~L----------------~~Ld~e~~~EFHaLIVe 530 (901)
.|..|+|||++||+ ||+|.+++|.+.... ..++...+..+|++|++
T Consensus 77 ~~~~~~~~L~~l~GIG~~tA~~~l~~~~~~~~~pvD~~v~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ 156 (158)
T cd00056 77 DDPDAREELLALPGVGRKTANVVLLFALGPDAFPVDTHVRRVLKRLGLIPKKKTPEELEELLEELLPKPYWGEANQALMD 156 (158)
T ss_pred CCcccHHHHHcCCCCCHHHHHHHHHHHCCCCCCccchhHHHHHHHhCCCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHH
Confidence 35788999999999 588999988753321 11234566788999988
Q ss_pred Hh
Q 002607 531 FG 532 (901)
Q Consensus 531 fG 532 (901)
||
T Consensus 157 ~g 158 (158)
T cd00056 157 LG 158 (158)
T ss_pred cC
Confidence 86
No 16
>KOG2457 consensus A/G-specific adenine DNA glycosylase [Replication, recombination and repair]
Probab=99.33 E-value=6.9e-13 Score=145.25 Aligned_cols=142 Identities=18% Similarity=0.278 Sum_probs=117.3
Q ss_pred cCccccccCChHHHHHHHHhcCCCCCCCCCcCCCCCHHHHHcCCH-HHHHHHHhhcCchHHHHHHHHHHHHHHHHHcCC-
Q 002607 406 VSKEKQNDFDWDSLRRQVEANGGKKERPEHTKDSLDWEAVRCADV-NKIANTIKERGMNNMLAGRIKDFLNRLVRDHGS- 483 (901)
Q Consensus 406 ~gaiLtQNTsW~NVeKAL~N~Lkk~er~~~~agl~dpEaLa~Ad~-EELeeLIRPaGFYnqKArRIKa~A~~Ive~~Gg- 483 (901)
|..|.-|+|.=..|.+-+.. |+...+++.+|+.|+. +++-++|.+.|||+ ++|||++-++.+++.++|
T Consensus 130 VSEiMLQQTrV~TV~~YYt~---------WMqkwPTl~dla~Asl~~eVn~lWaGlGyY~-R~rrL~ega~~vv~~~~ge 199 (555)
T KOG2457|consen 130 VSEIMLQQTRVQTVMKYYTR---------WMQKWPTLYDLAQASLEKEVNELWAGLGYYR-RARRLLEGAKMVVAGTEGE 199 (555)
T ss_pred HHHHHHHHHHHHHHHHHHHH---------HHHhCchHHHHHHHHHHHHHHHHHhhhhHHH-HHHHHHHHHHHHHHhCCCC
Confidence 34466688888888887766 3456899999999999 89999999999996 999999999999999887
Q ss_pred c-----cccc-cCCCCccccC------C-----cchHHHHHHH-------------------hhhh-ccCCHHHHHHHHH
Q 002607 484 V-----DLEW-LRDVPPDKAK------Y-----PVLESIQKYL-------------------WPRL-CKLDQRTLYELHY 526 (901)
Q Consensus 484 i-----DLe~-LrGIGpETAd------Y-----PVyd~VqR~L-------------------e~~L-~~Ld~e~~~EFHa 526 (901)
+ .|.. ++|||+|||. | -||.+|-|++ |... ..+|+....+|++
T Consensus 200 ~Prta~~l~kgvpGVG~YTAGAiaSIAf~q~tGiVDGNVirvlsRalAIhsDcSkgk~~q~~wkLA~qLVDP~RPGDFNQ 279 (555)
T KOG2457|consen 200 FPRTASSLMKGVPGVGQYTAGAIASIAFNQVTGIVDGNVIRVLSRALAIHSDCSKGKFFQSSWKLAAQLVDPSRPGDFNQ 279 (555)
T ss_pred CCChHHHHHhhCCCCCccchhhhhhhhhcCcccccccchHHHhHHhHhhcCCcchhhHHHHHHHHHHHhcCCCCCCcHHH
Confidence 5 4544 8999999999 3 3566665543 3321 2357777889999
Q ss_pred HHHHHhhhhcccCCCCCCCCCCcccchhhhh
Q 002607 527 QMITFGKVFCTKSKPNCNACPMRGECRHFAS 557 (901)
Q Consensus 527 LIVefGK~iCtkrkPkC~~CPLrd~C~yy~s 557 (901)
++|++|...||+.+|.|..||+...|+.|..
T Consensus 280 alMELGAt~CTpq~P~CS~CPvss~CrA~q~ 310 (555)
T KOG2457|consen 280 ALMELGATLCTPQKPSCSSCPVSSQCRAFQL 310 (555)
T ss_pred HHHHhcCeeccCCCCCcCCCCcHHHHHHHhH
Confidence 9999999999999999999999999999884
No 17
>PF15629 Perm-CXXC: Permuted single zf-CXXC unit
Probab=99.18 E-value=5.4e-12 Score=95.13 Aligned_cols=32 Identities=69% Similarity=1.284 Sum_probs=30.9
Q ss_pred CccccccccccCccCCCcccccCccccccceE
Q 002607 750 PESRCSSQEHGKMCDEKTCFSCNSVRESEFQI 781 (901)
Q Consensus 750 p~~~c~s~e~~~lc~~~~c~~c~~~~e~~~~~ 781 (901)
|+++|+||++|+||+++|||+||||||+++|+
T Consensus 1 Pe~~C~sqe~gkLC~~~tCfsCNsiREa~sQ~ 32 (32)
T PF15629_consen 1 PERRCNSQESGKLCDEETCFSCNSIREANSQT 32 (32)
T ss_pred CcccccccccccccCCccccccccHhHHhccC
Confidence 89999999999999999999999999999985
No 18
>PF00730 HhH-GPD: HhH-GPD superfamily base excision DNA repair protein This entry corresponds to Endonuclease III This entry corresponds to Alkylbase DNA glycosidase; InterPro: IPR003265 Endonuclease III (4.2.99.18 from EC) is a DNA repair enzyme which removes a number of damaged pyrimidines from DNA via its glycosylase activity and also cleaves the phosphodiester backbone at apurinic / apyrimidinic sites via a beta-elimination mechanism [, ]. The structurally related DNA glycosylase MutY recognises and excises the mutational intermediate 8-oxoguanine-adenine mispair []. The 3-D structures of Escherichia coli endonuclease III [] and catalytic domain of MutY [] have been determined. The structures contain two all-alpha domains: a sequence-continuous, six-helix domain (residues 22-132) and a Greek-key, four-helix domain formed by one N-terminal and three C-terminal helices (residues 1-21 and 133-211) together with the [Fe4S4] cluster. The cluster is bound entirely within the C-terminal loop by four cysteine residues with a ligation pattern Cys-(Xaa)6-Cys-(Xaa)2-Cys-(Xaa)5-Cys which is distinct from all other known Fe4S4 proteins. This structural motif is referred to as a [Fe4S4] cluster loop (FCL) []. Two DNA-binding motifs have been proposed, one at either end of the interdomain groove: the helix-hairpin-helix (HhH) and FCL motifs (see IPR003651 from INTERPRO). The primary role of the iron-sulphur cluster appears to involve positioning conserved basic residues for interaction with the DNA phosphate backbone by forming the loop of the FCL motif [, ]. The HhH-GPD domain gets its name from its hallmark helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate. This domain is found in a diverse range of structurally related DNA repair proteins that include: endonuclease III, 4.2.99.18 from EC and DNA glycosylase MutY, an A/G-specific adenine glycosylase. Both of these enzymes have a C-terminal iron-sulphur cluster loop (FCL). The methyl-CPG binding protein (MBD4) also contain a related domain that is a thymine DNA glycosylase. The family also includes DNA-3-methyladenine glycosylase II 3.2.2.21 from EC, 8-oxoguanine DNA glycosylases and other members of the AlkA family.; GO: 0006284 base-excision repair; PDB: 3F0Z_A 3I0X_A 3F10_A 3I0W_A 3S6I_D 3N5N_Y 1PU7_A 1PU8_B 1PU6_B 1NGN_A ....
Probab=98.89 E-value=3.2e-09 Score=96.62 Aligned_cols=85 Identities=14% Similarity=0.039 Sum_probs=71.3
Q ss_pred CccccccCChHHHHHHHHhcCCCCCCCCCcCCCCCHHHHHcCCHHHHHHHHhhcCchHHHHHHHHHHHHHHHHHcCCccc
Q 002607 407 SKEKQNDFDWDSLRRQVEANGGKKERPEHTKDSLDWEAVRCADVNKIANTIKERGMNNMLAGRIKDFLNRLVRDHGSVDL 486 (901)
Q Consensus 407 gaiLtQNTsW~NVeKAL~N~Lkk~er~~~~agl~dpEaLa~Ad~EELeeLIRPaGFYnqKArRIKa~A~~Ive~~GgiDL 486 (901)
.+||.|+|+|+++.+.+.+ |. + ..|++||++|+.++.++|.++|+++||++.||++|+++++.+.
T Consensus 2 ~~Il~qq~s~~~a~~~~~~-l~--~----~~g~pt~~~l~~~~~~el~~~i~~~G~~~~ka~~i~~~a~~~~-------- 66 (108)
T PF00730_consen 2 RAILSQQTSIKAARKIYRR-LF--E----RYGFPTPEALAEASEEELRELIRPLGFSRRKAKYIIELARAIL-------- 66 (108)
T ss_dssp HHHHCTTS-HHHHHHHHHH-HH--H----HHSCSSHHHHHCSHHHHHHHHHTTSTSHHHHHHHHHHHHHHHH--------
T ss_pred eeeecCcCcHHHHHHHHHH-HH--H----HhcCCCHHHHHhCCHHHHHHHhhccCCCHHHHHHHHHHHHHhh--------
Confidence 5799999999999999999 86 1 3468999999999999999999999999999999999999998
Q ss_pred cccCCCCccccCCcchHHHHHHHhhh
Q 002607 487 EWLRDVPPDKAKYPVLESIQKYLWPR 512 (901)
Q Consensus 487 e~LrGIGpETAdYPVyd~VqR~Le~~ 512 (901)
|....-+|+|.+++|.+...
T Consensus 67 ------~~~d~~~~~D~~v~r~~~r~ 86 (108)
T PF00730_consen 67 ------GRPDPFPPVDTHVRRVLQRL 86 (108)
T ss_dssp ------C-SSSS-TTSHHHHHHHHHH
T ss_pred ------hcccceecCcHHHHHHHHHH
Confidence 33223368899999987654
No 19
>TIGR00588 ogg 8-oxoguanine DNA-glycosylase (ogg). All proteins in this family for which functions are known are 8-oxo-guanaine DNA glycosylases that function in base excision repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is distantly realted to the Nth-MutY superfamily.
Probab=98.44 E-value=2.7e-07 Score=100.37 Aligned_cols=103 Identities=17% Similarity=0.138 Sum_probs=78.4
Q ss_pred cCccccccCChHHHHHHHHhcCCCCC--CC-----CCcCCCCCHHHHHcCCHHHHHHHHhhcCchHHHHHHHHHHHHHHH
Q 002607 406 VSKEKQNDFDWDSLRRQVEANGGKKE--RP-----EHTKDSLDWEAVRCADVNKIANTIKERGMNNMLAGRIKDFLNRLV 478 (901)
Q Consensus 406 ~gaiLtQNTsW~NVeKAL~N~Lkk~e--r~-----~~~agl~dpEaLa~Ad~EELeeLIRPaGFYnqKArRIKa~A~~Iv 478 (901)
+.+|+.||+++..+.+.+.+ |...- .. .....+|++++|+.++. ++.||++||. .||++|+++|+.+.
T Consensus 124 v~~IlsQq~si~~a~~~~~r-L~~~~G~~~~~~~g~~~~~FPtp~~La~~~~---e~~Lr~~G~g-~Ra~~I~~~A~~i~ 198 (310)
T TIGR00588 124 ISFICSSNNNIARITRMVER-LCQAFGPRLITLDGVTYHGFPSLHALTGPEA---EAHLRKLGLG-YRARYIRETARALL 198 (310)
T ss_pred HHHHHhCCCCHHHHHHHHHH-HHHHhCCCcccCCCcccccCCCHHHHhCCCh---HHHHHHcCCH-HHHHHHHHHHHHHH
Confidence 56799999999999999887 74100 00 00124789999998654 4578889993 47999999999999
Q ss_pred HHcCCc----------------cccccCCCCccccC------------CcchHHHHHHHhhhh
Q 002607 479 RDHGSV----------------DLEWLRDVPPDKAK------------YPVLESIQKYLWPRL 513 (901)
Q Consensus 479 e~~Ggi----------------DLe~LrGIGpETAd------------YPVyd~VqR~Le~~L 513 (901)
+.+++. .|..|+|||++||+ ||||.+|+|.+...+
T Consensus 199 ~~~~~~~~l~~l~~~~~~~~~~~L~~l~GIG~~tAd~vll~~l~~~d~~PvD~~v~r~~~r~y 261 (310)
T TIGR00588 199 EEQGGRAWLQQIRGASYEDAREALCELPGVGPKVADCICLMGLDKPQAVPVDVHVWRIANRDY 261 (310)
T ss_pred hccCCchhHHhhccCChHHHHHHHHhCCCccHHHHHHHHHHhCCCCCceeecHHHHHHHHHHh
Confidence 877542 35778999999999 489999999876643
No 20
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=97.18 E-value=0.0004 Score=75.21 Aligned_cols=68 Identities=16% Similarity=0.079 Sum_probs=54.6
Q ss_pred CCCCHHHHHcCCHHHHHHHHhhcCchHHHHHHHHHHHHHHHHHcCCc-----------cccccCCCCccccC--------
Q 002607 438 DSLDWEAVRCADVNKIANTIKERGMNNMLAGRIKDFLNRLVRDHGSV-----------DLEWLRDVPPDKAK-------- 498 (901)
Q Consensus 438 gl~dpEaLa~Ad~EELeeLIRPaGFYnqKArRIKa~A~~Ive~~Ggi-----------DLe~LrGIGpETAd-------- 498 (901)
-++++++|++++.++|. .+||+++||++|+++++.+.+..-.+ .|..|+|||+.||+
T Consensus 154 ~FPtpe~La~~~~~eL~----~~Gl~~~Ra~~L~~lA~~i~~g~l~l~~~~~~~~~~~~L~~LpGIGpwTA~~vllr~lg 229 (283)
T PRK10308 154 CFPTPERLAAADPQALK----ALGMPLKRAEALIHLANAALEGTLPLTIPGDVEQAMKTLQTFPGIGRWTANYFALRGWQ 229 (283)
T ss_pred CCCCHHHHHcCCHHHHH----HCCCCHHHHHHHHHHHHHHHcCCCCccccCCHHHHHHHHhcCCCcCHHHHHHHHHHhCC
Confidence 46899999999999875 58999999999999999988621111 47889999999999
Q ss_pred ----C-cchHHHHHHH
Q 002607 499 ----Y-PVLESIQKYL 509 (901)
Q Consensus 499 ----Y-PVyd~VqR~L 509 (901)
| ++|..|++.+
T Consensus 230 ~~D~fp~~D~~l~~~~ 245 (283)
T PRK10308 230 AKDVFLPDDYLIKQRF 245 (283)
T ss_pred CCCCCCcccHHHHHhc
Confidence 4 3467777655
No 21
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=96.89 E-value=0.0015 Score=71.15 Aligned_cols=98 Identities=12% Similarity=0.046 Sum_probs=68.2
Q ss_pred ccccccCChHHHHHHHHhcCCCCC--CCCCcCCCCCHHHHHcCCHHHHHHHHhhcCchHHHHHHHHHHHHHHHHHcCCc-
Q 002607 408 KEKQNDFDWDSLRRQVEANGGKKE--RPEHTKDSLDWEAVRCADVNKIANTIKERGMNNMLAGRIKDFLNRLVRDHGSV- 484 (901)
Q Consensus 408 aiLtQNTsW~NVeKAL~N~Lkk~e--r~~~~agl~dpEaLa~Ad~EELeeLIRPaGFYnqKArRIKa~A~~Ive~~Ggi- 484 (901)
+|+-|+.+=+...+...+ |...- .......++++++|+.++.+.|. ..|+...||++|+.+|+.+.+..-++
T Consensus 112 aI~~QqvS~~~A~~i~~r-l~~~~g~~~~~~~~fptpe~l~~~~~~~l~----~~g~s~~Ka~yi~~~A~~~~~g~~~~~ 186 (285)
T COG0122 112 AILSQQVSVAAAAKIWAR-LVSLYGNALEIYHSFPTPEQLAAADEEALR----RCGLSGRKAEYIISLARAAAEGELDLS 186 (285)
T ss_pred HHHHhHhhHHHHHHHHHH-HHHHhCCccccccCCCCHHHHHhcCHHHHH----HhCCcHHHHHHHHHHHHHHHcCCccHH
Confidence 577787776666665555 43100 00011238999999999998776 78999999999999999988652121
Q ss_pred ------------cccccCCCCccccC------------Ccc-hHHHHHHHh
Q 002607 485 ------------DLEWLRDVPPDKAK------------YPV-LESIQKYLW 510 (901)
Q Consensus 485 ------------DLe~LrGIGpETAd------------YPV-yd~VqR~Le 510 (901)
.|..|+|||+.||+ ||+ |..|++.+.
T Consensus 187 ~l~~~~~e~a~e~L~~i~GIG~WTAe~~llf~lgr~dvfP~~D~~lr~~~~ 237 (285)
T COG0122 187 ELKPLSDEEAIEELTALKGIGPWTAEMFLLFGLGRPDVFPADDLGLRRAIK 237 (285)
T ss_pred HhccCCHHHHHHHHHcCCCcCHHHHHHHHHHcCCCCCCCChHHHHHHHHHH
Confidence 36778999999999 575 445665543
No 22
>PF10576 EndIII_4Fe-2S: Iron-sulfur binding domain of endonuclease III; InterPro: IPR003651 Endonuclease III (4.2.99.18 from EC) is a DNA repair enzyme which removes a number of damaged pyrimidines from DNA via its glycosylase activity and also cleaves the phosphodiester backbone at apurinic / apyrimidinic sites via a beta-elimination mechanism [, ]. The structurally related DNA glycosylase MutY recognises and excises the mutational intermediate 8-oxoguanine-adenine mispair []. The 3-D structures of Escherichia coli endonuclease III [] and catalytic domain of MutY [] have been determined. The structures contain two all-alpha domains: a sequence-continuous, six-helix domain (residues 22-132) and a Greek-key, four-helix domain formed by one N-terminal and three C-terminal helices (residues 1-21 and 133-211) together with the [Fe4S4] cluster. The cluster is bound entirely within the C-terminal loop by four cysteine residues with a ligation pattern Cys-(Xaa)6-Cys-(Xaa)2-Cys-(Xaa)5-Cys which is distinct from all other known Fe4S4 proteins. This structural motif is referred to as a [Fe4S4] cluster loop (FCL) []. Two DNA-binding motifs have been proposed, one at either end of the interdomain groove: the helix-hairpin-helix (HhH) and FCL motifs. The primary role of the iron-sulphur cluster appears to involve positioning conserved basic residues for interaction with the DNA phosphate backbone by forming the loop of the FCL motif [, ]. The iron-sulphur cluster loop (FCL) is also found in DNA-(apurinic or apyrimidinic site) lyase, a subfamily of endonuclease III. The enzyme has both apurinic and apyrimidinic endonuclease activity and a DNA N-glycosylase activity. It cuts damaged DNA at cytosines, thymines and guanines, and acts on the damaged strand 5' of the damaged site. The enzyme binds a 4Fe-4S cluster which is not important for the catalytic activity, but is probably involved in the alignment of the enzyme along the DNA strand.; GO: 0004519 endonuclease activity, 0051539 4 iron, 4 sulfur cluster binding; PDB: 1VRL_A 1RRQ_A 3G0Q_A 3FSQ_A 1RRS_A 3FSP_A 2ABK_A 1KG7_A 1KG2_A 1MUN_A ....
Probab=96.45 E-value=0.0011 Score=44.57 Aligned_cols=17 Identities=47% Similarity=1.323 Sum_probs=11.5
Q ss_pred cccCCCCCCCCCCcccc
Q 002607 536 CTKSKPNCNACPMRGEC 552 (901)
Q Consensus 536 CtkrkPkC~~CPLrd~C 552 (901)
|++++|+|+.|||+++|
T Consensus 1 Ctar~P~C~~Cpl~~~C 17 (17)
T PF10576_consen 1 CTARKPKCEECPLADYC 17 (17)
T ss_dssp S-SSS--GGG-TTGGG-
T ss_pred CcCCCCccccCCCcccC
Confidence 89999999999999988
No 23
>KOG2875 consensus 8-oxoguanine DNA glycosylase [Replication, recombination and repair]
Probab=96.43 E-value=0.004 Score=67.88 Aligned_cols=72 Identities=19% Similarity=0.176 Sum_probs=61.7
Q ss_pred CcCCCCCHHHHHcCCHHHHHHHHhhcCchHHHHHHHHHHHHHHHHHcCCc----------------cccccCCCCccccC
Q 002607 435 HTKDSLDWEAVRCADVNKIANTIKERGMNNMLAGRIKDFLNRLVRDHGSV----------------DLEWLRDVPPDKAK 498 (901)
Q Consensus 435 ~~agl~dpEaLa~Ad~EELeeLIRPaGFYnqKArRIKa~A~~Ive~~Ggi----------------DLe~LrGIGpETAd 498 (901)
+..++|++++|.. .++++-+|.+||-- +||+|-+.++.|+++.|+. .|-.|+|||++.||
T Consensus 157 ~~h~FPsl~~L~g---~~~Ea~LR~~gfGY-RAkYI~~ta~~l~~~~g~~~wLqsl~~~~yeear~~L~~lpGVG~KVAD 232 (323)
T KOG2875|consen 157 DYHGFPSLQALAG---PEVEAELRKLGFGY-RAKYISATARALQEKQGGLAWLQSLRKSSYEEAREALCSLPGVGPKVAD 232 (323)
T ss_pred ccccCccHHHhcC---cHhHHHHHHcCcch-hHHHHHHHHHHHHHhcccchHHHHHhcccHHHHHHHHhcCCCCcchHhh
Confidence 5668889998886 78999999999975 8999999999999999983 25667899999999
Q ss_pred ------------CcchHHHHHHHh
Q 002607 499 ------------YPVLESIQKYLW 510 (901)
Q Consensus 499 ------------YPVyd~VqR~Le 510 (901)
-|||.||.|...
T Consensus 233 CI~Lm~l~~~~~VPVDvHi~ria~ 256 (323)
T KOG2875|consen 233 CICLMSLDKLSAVPVDVHIWRIAQ 256 (323)
T ss_pred hhhhhhcCCCCcccchhhHHHHhh
Confidence 289999988654
No 24
>smart00525 FES FES domain. iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3)
Probab=95.55 E-value=0.0058 Score=44.14 Aligned_cols=22 Identities=36% Similarity=1.141 Sum_probs=19.9
Q ss_pred hcccCCCCCCCCCCcccchhhh
Q 002607 535 FCTKSKPNCNACPMRGECRHFA 556 (901)
Q Consensus 535 iCtkrkPkC~~CPLrd~C~yy~ 556 (901)
+|++++|+|..|||+.+|++|.
T Consensus 1 vC~ar~P~C~~Cpl~~~C~~~~ 22 (26)
T smart00525 1 ICTARKPRCDECPLKDLCPAYX 22 (26)
T ss_pred CccCCCCCCCCCcCHHHhhhhh
Confidence 6999999999999999998754
No 25
>COG1059 Thermostable 8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=92.47 E-value=0.23 Score=52.15 Aligned_cols=113 Identities=12% Similarity=0.106 Sum_probs=78.6
Q ss_pred ccccccCChHHHHHHHHhcCCCCCCCCCcCCCCCHHHHHcCCHHHHHHHHhhc--CchHHHHHHHHHHHHHHH------H
Q 002607 408 KEKQNDFDWDSLRRQVEANGGKKERPEHTKDSLDWEAVRCADVNKIANTIKER--GMNNMLAGRIKDFLNRLV------R 479 (901)
Q Consensus 408 aiLtQNTsW~NVeKAL~N~Lkk~er~~~~agl~dpEaLa~Ad~EELeeLIRPa--GFYnqKArRIKa~A~~Iv------e 479 (901)
-|||-|++-.+.-++... |+ +.+..++.+||++.++.. -|||+||++|.+.-..+. +
T Consensus 46 CILTANsSA~~~~~~q~~-lG--------------~gfly~~~eEL~e~Lk~~g~Rf~n~raeyIVeaR~~~~~lk~~v~ 110 (210)
T COG1059 46 CILTANSSATMGLRAQNE-LG--------------DGFLYLSEEELREKLKEVGYRFYNVRAEYIVEAREKFDDLKIIVK 110 (210)
T ss_pred HhccccchHHHHHHHHHH-hc--------------cccccCCHHHHHHHHHHhcchhcccchHHHHHHHHHHHHHHHHHh
Confidence 378999998888888887 64 255667999999999998 689999999988544432 1
Q ss_pred Hc--CCcc----ccccCCCCccccC-C---------c-chHHHHHHHhhh-----hc-cCCHHHHHHHHHHHHHHhhhh
Q 002607 480 DH--GSVD----LEWLRDVPPDKAK-Y---------P-VLESIQKYLWPR-----LC-KLDQRTLYELHYQMITFGKVF 535 (901)
Q Consensus 480 ~~--GgiD----Le~LrGIGpETAd-Y---------P-Vyd~VqR~Le~~-----L~-~Ld~e~~~EFHaLIVefGK~i 535 (901)
.. ..+. ++.++|||-+.|. | + +|.||-|++... .+ .++...|-++--.|.+.++.+
T Consensus 111 ~~~~~~vaRE~Lv~nikGiGyKEASHFLRNVG~~D~AIlDrHIlr~l~r~g~i~e~~kt~t~K~YLe~E~ilr~iae~~ 189 (210)
T COG1059 111 ADENEKVARELLVENIKGIGYKEASHFLRNVGFEDLAILDRHILRWLVRYGLIDENPKTLTRKLYLEIEEILRSIAEEV 189 (210)
T ss_pred cCcchHHHHHHHHHHcccccHHHHHHHHHhcChhHHHHHHHHHHHHHHHhcccccCcccccHHHHHHHHHHHHHHHHHh
Confidence 00 1111 2467799999999 2 2 488998887652 22 345666777666666655543
No 26
>KOG1918 consensus 3-methyladenine DNA glycosidase [Replication, recombination and repair]
Probab=62.98 E-value=7.2 Score=42.31 Aligned_cols=85 Identities=6% Similarity=-0.008 Sum_probs=56.6
Q ss_pred CccccccCChHHHHHHHHhcCCCCCCCCCcCCCCCHHHHHcCCHHHHHHHHhhcCchHHHHHHHHHHHHHHHHHc-C---
Q 002607 407 SKEKQNDFDWDSLRRQVEANGGKKERPEHTKDSLDWEAVRCADVNKIANTIKERGMNNMLAGRIKDFLNRLVRDH-G--- 482 (901)
Q Consensus 407 gaiLtQNTsW~NVeKAL~N~Lkk~er~~~~agl~dpEaLa~Ad~EELeeLIRPaGFYnqKArRIKa~A~~Ive~~-G--- 482 (901)
-+||.|+-+-+... ++.||.. .--.+...+++++.+..++.++| |.+||-.+||.+|+.+|......+ .
T Consensus 81 raIlsQQLs~kAan-sI~~Rfv--sl~~g~~~~~~pe~i~~~~~~~l----rkcG~S~rK~~yLh~lA~~~~ng~I~s~~ 153 (254)
T KOG1918|consen 81 RAILSQQLSGKAAN-SIYNRFV--SLCGGAEKFPTPEFIDPLDCEEL----RKCGFSKRKASYLHSLAEAYTNGYIPSKS 153 (254)
T ss_pred HHHHHHHHHHHHHH-HHHHHHH--HHhCCCcCCCCchhcCcCCHHHH----HHhCcchhhHHHHHHHHHHHhcCCCCchH
Confidence 45777766554332 2222121 00011245799999999998875 568999999999999999877643 1
Q ss_pred Cc----------cccccCCCCccccC
Q 002607 483 SV----------DLEWLRDVPPDKAK 498 (901)
Q Consensus 483 gi----------DLe~LrGIGpETAd 498 (901)
++ -|..++|||+-|+.
T Consensus 154 ~i~~mseEeL~~~LT~VKGIg~Wtv~ 179 (254)
T KOG1918|consen 154 GIEKMSEEELIERLTNVKGIGRWTVE 179 (254)
T ss_pred HHhhcCHHHHHHHHHhccCccceeee
Confidence 11 14556799999999
No 27
>cd04370 BAH BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in mammalian DNA methyltransferases and the MTA1 subunits of histone deacetylase complexes. A BAH domain is also found in Yeast Sir3p and in the origin receptor complex protein 1 (Orc1p), where it was found to interact with the N-terminal lobe of the silence information regulator 1 protein (Sir1p), confirming the initial hypothesis that BAH plays a role in protein-protein interactions.
Probab=54.85 E-value=20 Score=32.77 Aligned_cols=64 Identities=13% Similarity=0.250 Sum_probs=44.3
Q ss_pred ceeeeeeeeccCCCCCCcccchhhhccCCceeEEecCChhhhcccCCHHHHHHhhhccceEeecccccccCCccc
Q 002607 804 YFQVNEVFADHDSSLKPINVPREWLWNLPRRTVYFGTSIPSIFKGLTTEGIQHCFWRGYVCVRGFDQKSRAPRPL 878 (901)
Q Consensus 804 YFQvNEVFaDh~SS~~Pi~vpr~~iw~L~rr~vyfGtSv~sIfkglt~~~Iq~cF~~G~vCVR~fdr~tr~PrpL 878 (901)
+|.-||||+=.....+||. .| +.++.|.+-...-.... ....-...-|+|=++||+.++.-|+|
T Consensus 59 ~~~~~Elf~s~~~~~i~v~----~I--~gkc~V~~~~~~~~~~~-----~~~~~~~~~f~~r~~yd~~~~~fk~~ 122 (123)
T cd04370 59 FALRRELFLSDHLDEIPVE----SI--IGKCKVLFVSEFEGLKQ-----RPNKIDTDDFFCRLAYDPTTKEFKAL 122 (123)
T ss_pred ccccceeEEecCccccCHH----Hh--ccccEEEechHhhcccc-----ccccCCCCeEEEEEEECcCcceEEeC
Confidence 7999999998877776664 33 34778887765443321 00111456899999999998887765
No 28
>PRK10353 3-methyl-adenine DNA glycosylase I; Provisional
Probab=51.57 E-value=37 Score=35.89 Aligned_cols=63 Identities=10% Similarity=0.107 Sum_probs=42.2
Q ss_pred ChHHHHHHHHhcCCCCCCCCCcCCCCCHHHHHcCCHHHHHHHHhhcCchHHHHH--HHHHHHHHH---HHHcCCc
Q 002607 415 DWDSLRRQVEANGGKKERPEHTKDSLDWEAVRCADVNKIANTIKERGMNNMLAG--RIKDFLNRL---VRDHGSV 484 (901)
Q Consensus 415 sW~NVeKAL~N~Lkk~er~~~~agl~dpEaLa~Ad~EELeeLIRPaGFYnqKAr--RIKa~A~~I---ve~~Ggi 484 (901)
+|..|.+--.+ ++ + .-+.+|++.|+..++++|+.++.-.|.-|.++| .+.+=|+.+ .+++|++
T Consensus 45 SW~tIL~Kre~-fr--~----aF~~Fd~~~VA~~~e~die~Ll~d~~IIRnr~KI~Avi~NA~~~l~i~~e~gSf 112 (187)
T PRK10353 45 SWITVLKKREN-YR--A----CFHQFDPVKVAAMQEEDVERLVQDAGIIRHRGKIQAIIGNARAYLQMEQNGEPF 112 (187)
T ss_pred cHHHHHHHHHH-HH--H----HHcCCCHHHHhCCCHHHHHHHhcCchhHHhHHHHHHHHHHHHHHHHHHHhcCCH
Confidence 56666555544 43 1 335589999999999999999999999665443 444434443 3456665
No 29
>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=49.88 E-value=3.4 Score=31.50 Aligned_cols=14 Identities=29% Similarity=0.413 Sum_probs=11.6
Q ss_pred cccccCCCCccccC
Q 002607 485 DLEWLRDVPPDKAK 498 (901)
Q Consensus 485 DLe~LrGIGpETAd 498 (901)
+|..|+|||++||.
T Consensus 12 eL~~lpGIG~~tA~ 25 (30)
T PF00633_consen 12 ELMKLPGIGPKTAN 25 (30)
T ss_dssp HHHTSTT-SHHHHH
T ss_pred HHHhCCCcCHHHHH
Confidence 68899999999985
No 30
>PF03352 Adenine_glyco: Methyladenine glycosylase; InterPro: IPR005019 This family of methyladenine glycosylases includes DNA-3-methyladenine glycosylase I (3.2.2.20 from EC) which acts as a base excision repair enzyme by severing the glycosylic bond of numerous damaged bases. The enzyme is constitutively expressed and is specific for the alkylated 3-methyladenine DNA.; GO: 0008725 DNA-3-methyladenine glycosylase I activity, 0006284 base-excision repair; PDB: 2OFI_A 2OFK_A 2JG6_A 4AIA_E 4AI5_C 4AI4_A 1LMZ_A 1P7M_A 1NKU_A.
Probab=42.85 E-value=39 Score=35.45 Aligned_cols=47 Identities=19% Similarity=0.281 Sum_probs=32.8
Q ss_pred CCCCHHHHHcCCHHHHHHHHhhcCc--hHHHHHHHHHHHHHHH---HHcCCc
Q 002607 438 DSLDWEAVRCADVNKIANTIKERGM--NNMLAGRIKDFLNRLV---RDHGSV 484 (901)
Q Consensus 438 gl~dpEaLa~Ad~EELeeLIRPaGF--YnqKArRIKa~A~~Iv---e~~Ggi 484 (901)
..+|++.|+.+++++|++++.--|. .+.|-+.+..=|+.++ ++||++
T Consensus 56 ~~Fd~~~vA~~~e~~ie~l~~d~~iIRnr~KI~Avi~NA~~~l~i~~e~gsF 107 (179)
T PF03352_consen 56 AGFDPEKVAKMDEEDIERLMQDPGIIRNRRKIRAVINNARAILKIQEEFGSF 107 (179)
T ss_dssp GGGHHHHHHT--HHHHHHHTTSTTSS--HHHHHHHHHHHHHHHHHHHTTS-H
T ss_pred HCCCHHHHHcCCHHHHHHHhcCcchhhhHHHHHHHHHHHHHHHHHHHhcCCH
Confidence 3479999999999999999999999 5556666655555554 466765
No 31
>COG2818 Tag 3-methyladenine DNA glycosylase [DNA replication, recombination, and repair]
Probab=35.36 E-value=1e+02 Score=32.84 Aligned_cols=46 Identities=15% Similarity=0.182 Sum_probs=34.4
Q ss_pred CCCHHHHHcCCHHHHHHHHhhcCchHHHHHH--HHHHHHH---HHHHcCCc
Q 002607 439 SLDWEAVRCADVNKIANTIKERGMNNMLAGR--IKDFLNR---LVRDHGSV 484 (901)
Q Consensus 439 l~dpEaLa~Ad~EELeeLIRPaGFYnqKArR--IKa~A~~---Ive~~Ggi 484 (901)
.+|++.|+.++.++++.++.-.|--|.|.|. +.+=|+. |.++||++
T Consensus 63 ~Fd~~kVA~~~~~dverLl~d~gIIR~r~KI~A~i~NA~~~l~l~~e~Gsf 113 (188)
T COG2818 63 GFDPEKVAAMTEEDVERLLADAGIIRNRGKIKATINNARAVLELQKEFGSF 113 (188)
T ss_pred cCCHHHHHcCCHHHHHHHHhCcchhhhHHHHHHHHHHHHHHHHHHHHcCCH
Confidence 4799999999999999999999998866543 2222333 34567876
No 32
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=34.67 E-value=27 Score=35.38 Aligned_cols=45 Identities=20% Similarity=0.374 Sum_probs=32.8
Q ss_pred HHcCCHHHHHHHHhhcCchHHHHHHHHHHHHHHHHHcCCc----cccccCCCCccc
Q 002607 445 VRCADVNKIANTIKERGMNNMLAGRIKDFLNRLVRDHGSV----DLEWLRDVPPDK 496 (901)
Q Consensus 445 La~Ad~EELeeLIRPaGFYnqKArRIKa~A~~Ive~~Ggi----DLe~LrGIGpET 496 (901)
|-.|+.++| +.+...|-+ ||+.|.+ ..+.+|.| ||...+|||+.+
T Consensus 91 iNtAs~eeL-~~lpgIG~~--kA~aIi~----yRe~~G~f~sv~dL~~v~GiG~~~ 139 (149)
T COG1555 91 INTASAEEL-QALPGIGPK--KAQAIID----YREENGPFKSVDDLAKVKGIGPKT 139 (149)
T ss_pred ccccCHHHH-HHCCCCCHH--HHHHHHH----HHHHcCCCCcHHHHHhccCCCHHH
Confidence 556788888 778778876 6777665 24556655 788888999865
No 33
>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region. Members of the subfamily recognized by this model include competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model.
Probab=33.96 E-value=21 Score=30.90 Aligned_cols=48 Identities=15% Similarity=0.252 Sum_probs=31.4
Q ss_pred HHcCCHHHHHHHHhhcCchHHHHHHHHHHHHHHHHHcCCc----cccccCCCCccccC
Q 002607 445 VRCADVNKIANTIKERGMNNMLAGRIKDFLNRLVRDHGSV----DLEWLRDVPPDKAK 498 (901)
Q Consensus 445 La~Ad~EELeeLIRPaGFYnqKArRIKa~A~~Ive~~Ggi----DLe~LrGIGpETAd 498 (901)
|-.|+.++|..+|...|.. +|++|.+ + ...+|++ +|..++|||.++|+
T Consensus 10 vNta~~~~L~~~ipgig~~--~a~~Il~---~-R~~~g~~~s~~dL~~v~gi~~~~~~ 61 (69)
T TIGR00426 10 INTATAEELQRAMNGVGLK--KAEAIVS---Y-REEYGPFKTVEDLKQVPGIGNSLVE 61 (69)
T ss_pred CcCCCHHHHHhHCCCCCHH--HHHHHHH---H-HHHcCCcCCHHHHHcCCCCCHHHHH
Confidence 4457888888888777774 4444433 2 1225554 67778899998876
No 34
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=29.78 E-value=37 Score=34.25 Aligned_cols=44 Identities=20% Similarity=0.272 Sum_probs=32.5
Q ss_pred HHHcCCHHHHHHHHhhcCchHHHHHHHHHHHHHHHHHcCCc----cccccCCCCccccC
Q 002607 444 AVRCADVNKIANTIKERGMNNMLAGRIKDFLNRLVRDHGSV----DLEWLRDVPPDKAK 498 (901)
Q Consensus 444 aLa~Ad~EELeeLIRPaGFYnqKArRIKa~A~~Ive~~Ggi----DLe~LrGIGpETAd 498 (901)
+|-.|+.++++. --|+|-.||++|. .+|.+ ||..++|||+.+..
T Consensus 54 diN~A~~~el~~---lpGigP~~A~~IV--------~nGpf~sveDL~~V~GIgekqk~ 101 (132)
T PRK02515 54 DLNNSSVRAFRQ---FPGMYPTLAGKIV--------KNAPYDSVEDVLNLPGLSERQKE 101 (132)
T ss_pred cCCccCHHHHHH---CCCCCHHHHHHHH--------HCCCCCCHHHHHcCCCCCHHHHH
Confidence 455667766655 4799999999887 25555 88999999986544
No 35
>TIGR00624 tag DNA-3-methyladenine glycosylase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=29.14 E-value=1.4e+02 Score=31.54 Aligned_cols=58 Identities=10% Similarity=0.091 Sum_probs=39.9
Q ss_pred ChHHHHHHHHhcCCCCCCCCCcCCCCCHHHHHcCCHHHHHHHHhhcCchHHHHHH--HHHHHHHHHH
Q 002607 415 DWDSLRRQVEANGGKKERPEHTKDSLDWEAVRCADVNKIANTIKERGMNNMLAGR--IKDFLNRLVR 479 (901)
Q Consensus 415 sW~NVeKAL~N~Lkk~er~~~~agl~dpEaLa~Ad~EELeeLIRPaGFYnqKArR--IKa~A~~Ive 479 (901)
+|..|.+--.+ ++ + .-..+|++.|+..++++|++++.-.|.-|.|+|- +.+=|+.+++
T Consensus 44 SW~tIL~Kr~~-fr--~----aF~~Fd~~~VA~~~e~~ie~L~~d~~IIRnr~KI~Avi~NA~~~l~ 103 (179)
T TIGR00624 44 SWITVLRKREN-YR--R----AFSGFDIVKVARMTDADVERLLQDDGIIRNRGKIEATIANARAALQ 103 (179)
T ss_pred CHHHHHHhHHH-HH--H----HHcCCCHHHHhCCCHHHHHHHhcCccchhhHHHHHHHHHHHHHHHH
Confidence 56666555544 33 1 2355899999999999999999999998866543 3333455443
No 36
>PF08876 DUF1836: Domain of unknown function (DUF1836); InterPro: IPR014975 This group of proteins are functionally uncharacterised.
Probab=28.48 E-value=43 Score=32.37 Aligned_cols=57 Identities=26% Similarity=0.359 Sum_probs=39.2
Q ss_pred CCCCcccccchhhhhHhHHHHHHhccccccCcchhhhhhcCcCccccCCCCCCcccc
Q 002607 646 PEEIPTIKLNMKEFTQTLQNYMQENLELQEGDMSKALVALTAGAASIPAPKLKNVSR 702 (901)
Q Consensus 646 ~~eip~i~ln~e~~~~~l~~~~~~n~~~~~~~~skaLval~p~aasip~pklKnvsR 702 (901)
-+|+|+|.|-|++...=+.+++.......+..+.++||-==-....|+.|.-|..+|
T Consensus 3 ~~elP~i~LYmdQvi~~~n~~l~~~~~~~~~~lT~tMInNYvK~~li~~P~kKkYsr 59 (105)
T PF08876_consen 3 WEELPDIDLYMDQVITYINQYLKPLKRDDEKILTKTMINNYVKRGLIPPPIKKKYSR 59 (105)
T ss_pred HHHcCCCcchHHHHHHHHHHHhhhccccccccCCHHHHHHHHhcccCCCcccCccCH
Confidence 378999999999998666666653322223566777765333456789998888886
No 37
>smart00439 BAH Bromo adjacent homology domain.
Probab=27.95 E-value=61 Score=29.81 Aligned_cols=64 Identities=23% Similarity=0.292 Sum_probs=45.2
Q ss_pred ceeeeeeeeccCCCCCCcccchhhhccCCceeEEecCChhhhcccCCHHHHHHhhhccceEeecccccccCCccc
Q 002607 804 YFQVNEVFADHDSSLKPINVPREWLWNLPRRTVYFGTSIPSIFKGLTTEGIQHCFWRGYVCVRGFDQKSRAPRPL 878 (901)
Q Consensus 804 YFQvNEVFaDh~SS~~Pi~vpr~~iw~L~rr~vyfGtSv~sIfkglt~~~Iq~cF~~G~vCVR~fdr~tr~PrpL 878 (901)
+|.-||||+-.... +||-+.|+. ++.|++.+....+.- ++. .-...-|+|=++||..++...+|
T Consensus 56 ~~~~~Elf~s~~~~----~i~~~~I~~--kc~V~~~~~~~~~~~----~~~-~~~~~~f~cr~~yd~~~~~f~~~ 119 (120)
T smart00439 56 LFDKNEVFLSDEYD----TVPLSDIIG--KCNVLSKSDYPGLRP----EGK-IGEPDVFFCESLYDPEKGAFKKL 119 (120)
T ss_pred cCCCcceEEEccCc----cCChHHeee--EEEEEEcchhccccc----ccC-CCCCCeEEEEEEEccccCcccCC
Confidence 46789999887653 667777776 899998876644321 111 01347899999999999887765
No 38
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=27.80 E-value=71 Score=27.04 Aligned_cols=36 Identities=22% Similarity=0.259 Sum_probs=28.6
Q ss_pred CCCCCHHHHHcCCHHHHHHHHhhcCchHHHHHHHHHHHH
Q 002607 437 KDSLDWEAVRCADVNKIANTIKERGMNNMLAGRIKDFLN 475 (901)
Q Consensus 437 agl~dpEaLa~Ad~EELeeLIRPaGFYnqKArRIKa~A~ 475 (901)
.|+.++++|+.++.++|.+ | -|+-..+|++|.+-++
T Consensus 24 ~G~~t~~~l~~a~~~~L~~-i--~Gig~~~a~~i~~~~~ 59 (60)
T PF14520_consen 24 AGIKTLEDLANADPEELAE-I--PGIGEKTAEKIIEAAR 59 (60)
T ss_dssp TTCSSHHHHHTSHHHHHHT-S--TTSSHHHHHHHHHHHH
T ss_pred cCCCcHHHHHcCCHHHHhc-C--CCCCHHHHHHHHHHHh
Confidence 4788999999998888776 3 5677788999887664
No 39
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=25.93 E-value=26 Score=40.31 Aligned_cols=71 Identities=20% Similarity=0.368 Sum_probs=0.0
Q ss_pred HHHHHHHHhcCCCCCCCCCcCCCCCHHHHHcC-----CHHHHHHHHhhcCchHHHHHHH----HHHHHHHHHHcCCc---
Q 002607 417 DSLRRQVEANGGKKERPEHTKDSLDWEAVRCA-----DVNKIANTIKERGMNNMLAGRI----KDFLNRLVRDHGSV--- 484 (901)
Q Consensus 417 ~NVeKAL~N~Lkk~er~~~~agl~dpEaLa~A-----d~EELeeLIRPaGFYnqKArRI----Ka~A~~Ive~~Ggi--- 484 (901)
+.+.+.+.. |. ..+++|+..|+.+ ..+.+...|.|.|| +--..| +.+++.|+++||++
T Consensus 244 ~~~~~~l~~-l~-------~~~lld~~~ia~~lGy~~~~~~ld~~v~prGy--RiLs~IPrl~k~iAk~Ll~~FGSL~~I 313 (352)
T PRK13482 244 EEILEELQE-LS-------SEELLDLSAIARLLGYPGGSEALDTPVSPRGY--RLLSKIPRLPSAVIENLVEHFGSLQGL 313 (352)
T ss_pred HHHHHHHHh-CC-------HHHhcCHHHHHHHhCCCCCCcccccccCCcHH--HHHhcCCCCCHHHHHHHHHHcCCHHHH
Q ss_pred ------cccccCCCCcccc
Q 002607 485 ------DLEWLRDVPPDKA 497 (901)
Q Consensus 485 ------DLe~LrGIGpETA 497 (901)
+|..++|||+..|
T Consensus 314 l~As~eeL~~VeGIGe~rA 332 (352)
T PRK13482 314 LAASIEDLDEVEGIGEVRA 332 (352)
T ss_pred HcCCHHHHhhCCCcCHHHH
No 40
>PRK13844 recombination protein RecR; Provisional
Probab=24.94 E-value=63 Score=34.63 Aligned_cols=48 Identities=13% Similarity=0.151 Sum_probs=33.1
Q ss_pred ccccCCCCccccCCcchHHHHHHHhhhhccCCHHHHHHHHHHHHHHhhhhcccCCCCCCCCC
Q 002607 486 LEWLRDVPPDKAKYPVLESIQKYLWPRLCKLDQRTLYELHYQMITFGKVFCTKSKPNCNACP 547 (901)
Q Consensus 486 Le~LrGIGpETAdYPVyd~VqR~Le~~L~~Ld~e~~~EFHaLIVefGK~iCtkrkPkC~~CP 547 (901)
|..|||||+++|. |+....|. .+.....+|-..|.+.-+.+. .|..|-
T Consensus 17 l~~LPGIG~KsA~--------Rla~~lL~-~~~~~~~~la~~i~~~~~~i~-----~C~~C~ 64 (200)
T PRK13844 17 LRKLPTIGKKSSQ--------RLALYLLD-KSPETAIAIANSLLDATANIK-----KCVYCQ 64 (200)
T ss_pred HHHCCCCCHHHHH--------HHHHHHHc-CCHHHHHHHHHHHHHHHHhCC-----cCCCCC
Confidence 5689999999997 44333332 467777788888888777664 366664
No 41
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=24.10 E-value=66 Score=34.32 Aligned_cols=48 Identities=19% Similarity=0.354 Sum_probs=32.6
Q ss_pred ccccCCCCccccCCcchHHHHHHHhhhhccCCHHHHHHHHHHHHHHhhhhcccCCCCCCCCC
Q 002607 486 LEWLRDVPPDKAKYPVLESIQKYLWPRLCKLDQRTLYELHYQMITFGKVFCTKSKPNCNACP 547 (901)
Q Consensus 486 Le~LrGIGpETAdYPVyd~VqR~Le~~L~~Ld~e~~~EFHaLIVefGK~iCtkrkPkC~~CP 547 (901)
|..|||||+++|. |+....|. .+.+....|-..|.+.-..+. .|..|-
T Consensus 13 l~~LPGIG~KsA~--------RlA~~ll~-~~~~~~~~la~ai~~~~~~i~-----~C~~C~ 60 (195)
T TIGR00615 13 LKKLPGIGPKSAQ--------RLAFHLLK-RDPSEVLRLAQALLEAKENLR-----TCSVCG 60 (195)
T ss_pred HHHCCCCCHHHHH--------HHHHHHHc-CCHHHHHHHHHHHHHHHHcCC-----cCCCCC
Confidence 5689999999997 44333332 366777777778877776664 366664
No 42
>PF15414 DUF4621: Protein of unknown function (DUF4621)
Probab=22.86 E-value=27 Score=37.46 Aligned_cols=28 Identities=50% Similarity=0.618 Sum_probs=25.4
Q ss_pred cccCCCCChhhhccccccCcccccCCCC
Q 002607 619 IIEEPATPEPERVQVSENDIEDTFCEDP 646 (901)
Q Consensus 619 IiE~P~SPe~e~~e~~e~diEd~~~eD~ 646 (901)
-+|.|-+|.||...++-+.|||.|+||+
T Consensus 195 avelpltpapefsavsveriedafdedf 222 (329)
T PF15414_consen 195 AVELPLTPAPEFSAVSVERIEDAFDEDF 222 (329)
T ss_pred heeccCCCCcccceeehhhhhhhhhhhh
Confidence 5899999999998888899999999875
No 43
>PRK00076 recR recombination protein RecR; Reviewed
Probab=21.78 E-value=79 Score=33.74 Aligned_cols=41 Identities=17% Similarity=0.214 Sum_probs=27.8
Q ss_pred ccccCCCCccccCCcchHHHHHHHhhhhccCCHHHHHHHHHHHHHHhhhh
Q 002607 486 LEWLRDVPPDKAKYPVLESIQKYLWPRLCKLDQRTLYELHYQMITFGKVF 535 (901)
Q Consensus 486 Le~LrGIGpETAdYPVyd~VqR~Le~~L~~Ld~e~~~EFHaLIVefGK~i 535 (901)
|..|||||+++|. |+....|. .+......|-..|.+.-+.+
T Consensus 13 l~~LPGIG~KsA~--------Rla~~ll~-~~~~~~~~la~~i~~~~~~i 53 (196)
T PRK00076 13 LRKLPGIGPKSAQ--------RLAFHLLQ-RDREDVLRLAQALEEAKEKI 53 (196)
T ss_pred HHHCCCCCHHHHH--------HHHHHHHc-CCHHHHHHHHHHHHHHHHcC
Confidence 5689999999997 44333332 36666777777777766654
No 44
>PRK01172 ski2-like helicase; Provisional
Probab=20.67 E-value=1.5e+02 Score=36.09 Aligned_cols=44 Identities=11% Similarity=0.101 Sum_probs=38.5
Q ss_pred CcCCCCCHHHHHcCCHHHHHHHHhhcCchHHHHHHHHHHHHHHHHHc
Q 002607 435 HTKDSLDWEAVRCADVNKIANTIKERGMNNMLAGRIKDFLNRLVRDH 481 (901)
Q Consensus 435 ~~agl~dpEaLa~Ad~EELeeLIRPaGFYnqKArRIKa~A~~Ive~~ 481 (901)
..+|.-++++|+.++++++.+++ |+...+|+.|.+-++.+++-|
T Consensus 629 ~~~g~~~~~di~~~~~~~~~~i~---~~~~~~~~~i~~~~~~~~~~~ 672 (674)
T PRK01172 629 YDAGFKTVDDIARSSPERIKKIY---GFSDTLANAIVNRAMKISSMY 672 (674)
T ss_pred HHcCCCCHHHHHhCCHHHHHHHh---ccCHHHHHHHHHHHHHHHHHh
Confidence 35688899999999999998874 899999999999999988765
Done!