Query 002141
Match_columns 960
No_of_seqs 356 out of 1878
Neff 3.9
Searched_HMMs 46136
Date Thu Mar 28 17:26:32 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/002141.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/002141hhsearch_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 3.2E-70 7E-75 499.0 7.9 103 843-945 1-103 (103)
2 COG0177 Nth Predicted EndoIII- 100.0 4.9E-38 1.1E-42 323.8 17.5 178 413-617 27-209 (211)
3 PRK10702 endonuclease III; Pro 100.0 2.1E-37 4.4E-42 319.4 17.8 174 407-616 35-208 (211)
4 COG2231 Uncharacterized protei 100.0 2.1E-35 4.5E-40 301.2 15.6 180 406-615 35-214 (215)
5 TIGR01084 mutY A/G-specific ad 100.0 8.5E-34 1.8E-38 302.8 19.0 186 408-632 33-222 (275)
6 PRK10880 adenine DNA glycosyla 100.0 8.7E-34 1.9E-38 311.3 18.1 190 408-632 37-226 (350)
7 PRK13913 3-methyladenine DNA g 100.0 3.2E-32 6.9E-37 282.5 15.4 180 406-597 35-216 (218)
8 TIGR01083 nth endonuclease III 100.0 9.7E-32 2.1E-36 272.0 17.2 159 408-602 33-191 (191)
9 KOG1921 Endonuclease III [Repl 100.0 2E-32 4.3E-37 284.6 11.3 180 410-615 73-261 (286)
10 PRK13910 DNA glycosylase MutY; 100.0 2.3E-31 5E-36 285.9 18.0 151 438-617 21-172 (289)
11 COG1194 MutY A/G-specific DNA 99.9 2E-26 4.3E-31 251.0 15.7 192 415-633 34-232 (342)
12 smart00478 ENDO3c endonuclease 99.9 9.1E-25 2E-29 210.8 16.3 148 411-593 2-149 (149)
13 cd00056 ENDO3c endonuclease II 99.9 6.9E-23 1.5E-27 199.3 15.4 151 409-591 8-158 (158)
14 PRK01229 N-glycosylase/DNA lya 99.9 1.2E-21 2.7E-26 202.6 13.9 132 406-559 42-185 (208)
15 KOG2457 A/G-specific adenine D 99.8 1.2E-19 2.6E-24 198.3 9.7 156 438-617 153-311 (555)
16 TIGR00588 ogg 8-oxoguanine DNA 99.8 4.2E-18 9E-23 185.2 14.5 147 409-559 127-290 (310)
17 TIGR03252 uncharacterized HhH- 99.7 6.3E-17 1.4E-21 164.1 10.0 105 407-519 24-135 (177)
18 COG0122 AlkA 3-methyladenine D 99.6 2.5E-15 5.4E-20 162.3 12.6 153 407-571 118-272 (285)
19 PRK10308 3-methyl-adenine DNA 99.5 2E-13 4.3E-18 147.4 12.6 117 438-570 154-273 (283)
20 KOG2875 8-oxoguanine DNA glyco 99.4 3.7E-13 8.1E-18 143.7 7.7 97 438-538 160-258 (323)
21 PF00730 HhH-GPD: HhH-GPD supe 99.4 1.3E-12 2.8E-17 120.1 8.9 104 409-559 4-107 (108)
22 KOG1918 3-methyladenine DNA gl 99.2 3.4E-11 7.4E-16 125.5 8.2 126 438-570 109-238 (254)
23 PF15629 Perm-CXXC: Permuted s 99.2 7.6E-12 1.7E-16 94.7 1.5 32 809-840 1-32 (32)
24 COG1059 Thermostable 8-oxoguan 98.3 5E-06 1.1E-10 86.0 10.8 114 410-544 48-166 (210)
25 PF00633 HHH: Helix-hairpin-he 97.4 0.0001 2.2E-09 55.9 2.2 25 492-518 6-30 (30)
26 PF10576 EndIII_4Fe-2S: Iron-s 96.4 0.0011 2.4E-08 44.7 0.7 17 595-611 1-17 (17)
27 PF09674 DUF2400: Protein of u 96.3 0.0035 7.6E-08 67.3 3.8 88 465-592 143-230 (232)
28 TIGR02757 conserved hypothetic 95.8 0.0077 1.7E-07 64.7 3.8 85 466-592 142-227 (229)
29 smart00525 FES FES domain. iro 95.5 0.0064 1.4E-07 44.2 1.4 23 594-616 1-23 (26)
30 PF12826 HHH_2: Helix-hairpin- 91.2 0.31 6.6E-06 42.5 4.3 39 474-518 16-54 (64)
31 smart00278 HhH1 Helix-hairpin- 90.4 0.2 4.3E-06 36.5 2.0 20 500-519 2-21 (26)
32 PF14716 HHH_8: Helix-hairpin- 87.5 2.4 5.1E-05 37.3 7.1 58 451-518 9-66 (68)
33 PRK10353 3-methyl-adenine DNA 86.6 0.33 7.1E-06 51.1 1.5 63 414-483 44-111 (187)
34 PF14520 HHH_5: Helix-hairpin- 86.0 2.8 6.1E-05 35.8 6.6 52 455-518 6-57 (60)
35 PRK13901 ruvA Holliday junctio 82.8 2.9 6.4E-05 44.4 6.4 62 437-519 60-127 (196)
36 TIGR00426 competence protein C 81.0 3.4 7.4E-05 36.1 5.2 58 444-518 9-66 (69)
37 TIGR00624 tag DNA-3-methyladen 78.8 1.3 2.8E-05 46.5 2.2 59 414-479 43-103 (179)
38 TIGR00608 radc DNA repair prot 78.0 4 8.7E-05 43.9 5.7 62 447-517 13-78 (218)
39 PRK00024 hypothetical protein; 77.0 4.1 9E-05 43.8 5.4 63 446-517 22-84 (224)
40 PRK00076 recR recombination pr 76.5 2.5 5.3E-05 45.1 3.5 28 494-521 6-33 (196)
41 PRK13844 recombination protein 76.4 2.5 5.4E-05 45.2 3.5 28 494-521 10-37 (200)
42 TIGR00615 recR recombination p 76.2 2.5 5.5E-05 44.9 3.5 28 494-521 6-33 (195)
43 PF03352 Adenine_glyco: Methyl 75.7 3.3 7.1E-05 43.5 4.1 63 414-483 39-106 (179)
44 PF09171 DUF1886: Domain of un 75.6 7.4 0.00016 42.9 6.9 133 451-597 77-232 (246)
45 PRK02515 psbU photosystem II c 74.7 3.7 8E-05 41.4 4.0 52 444-517 54-105 (132)
46 PRK14606 ruvA Holliday junctio 73.0 8.5 0.00018 40.6 6.4 21 498-518 107-127 (188)
47 PRK14601 ruvA Holliday junctio 72.7 8.7 0.00019 40.5 6.4 25 498-522 107-131 (183)
48 PRK00116 ruvA Holliday junctio 72.7 5.7 0.00012 41.6 5.1 21 498-518 107-127 (192)
49 COG0353 RecR Recombinational D 71.0 3.8 8.2E-05 43.7 3.3 28 494-521 7-34 (198)
50 PRK14603 ruvA Holliday junctio 69.3 10 0.00022 40.3 5.9 21 498-518 106-126 (197)
51 PRK14604 ruvA Holliday junctio 68.4 11 0.00023 40.1 5.9 21 498-518 107-127 (195)
52 PRK14602 ruvA Holliday junctio 68.3 12 0.00027 39.8 6.4 21 498-518 108-128 (203)
53 PRK14605 ruvA Holliday junctio 68.3 12 0.00026 39.6 6.3 64 437-517 61-126 (194)
54 PF14520 HHH_5: Helix-hairpin- 68.1 5.1 0.00011 34.2 2.9 26 497-522 3-28 (60)
55 COG1555 ComEA DNA uptake prote 67.3 8.4 0.00018 39.2 4.8 55 445-517 91-145 (149)
56 COG2003 RadC DNA repair protei 65.9 11 0.00025 41.0 5.6 90 446-556 22-115 (224)
57 TIGR00084 ruvA Holliday juncti 65.4 6.5 0.00014 41.4 3.7 65 437-518 60-126 (191)
58 COG0632 RuvA Holliday junction 65.0 6.6 0.00014 42.0 3.7 56 453-519 72-128 (201)
59 TIGR00575 dnlj DNA ligase, NAD 64.4 19 0.00042 44.5 7.9 61 440-516 455-515 (652)
60 PRK14600 ruvA Holliday junctio 64.2 11 0.00023 39.8 5.0 60 437-518 61-126 (186)
61 PRK07956 ligA NAD-dependent DN 62.0 36 0.00077 42.4 9.5 33 440-475 468-500 (665)
62 PF11731 Cdd1: Pathogenicity l 59.4 8.7 0.00019 36.7 3.0 27 497-523 10-36 (93)
63 smart00483 POLXc DNA polymeras 58.9 16 0.00035 41.4 5.5 51 460-515 54-105 (334)
64 PRK07945 hypothetical protein; 57.4 20 0.00044 40.6 6.0 61 451-518 8-68 (335)
65 smart00483 POLXc DNA polymeras 57.4 27 0.00059 39.7 7.0 57 451-518 11-67 (334)
66 PF12836 HHH_3: Helix-hairpin- 56.1 11 0.00024 32.9 2.9 21 498-518 13-33 (65)
67 PF14229 DUF4332: Domain of un 55.6 28 0.0006 34.2 5.9 77 437-538 14-92 (122)
68 PF02371 Transposase_20: Trans 55.2 8.8 0.00019 35.2 2.2 42 499-543 2-43 (87)
69 COG1555 ComEA DNA uptake prote 54.7 10 0.00022 38.7 2.7 22 498-519 96-117 (149)
70 PF14490 HHH_4: Helix-hairpin- 53.6 17 0.00036 34.0 3.8 57 449-517 7-64 (94)
71 cd04370 BAH BAH, or Bromo Adja 52.9 20 0.00043 33.2 4.2 64 863-937 59-122 (123)
72 cd00141 NT_POLXc Nucleotidyltr 52.8 20 0.00043 40.3 4.9 50 460-516 51-102 (307)
73 PRK14973 DNA topoisomerase I; 52.1 19 0.00041 46.4 5.2 98 437-541 821-919 (936)
74 PRK00116 ruvA Holliday junctio 51.5 12 0.00026 39.3 2.8 20 498-517 72-91 (192)
75 PRK14350 ligA NAD-dependent DN 51.2 18 0.0004 44.9 4.7 21 498-518 540-560 (669)
76 TIGR01259 comE comEA protein. 51.0 13 0.00028 36.4 2.8 21 498-518 67-87 (120)
77 TIGR00084 ruvA Holliday juncti 50.7 12 0.00027 39.4 2.8 23 495-517 68-90 (191)
78 PF12836 HHH_3: Helix-hairpin- 50.0 24 0.00051 30.8 4.0 54 445-516 8-61 (65)
79 COG0272 Lig NAD-dependent DNA 49.3 28 0.00061 43.2 5.8 56 453-518 507-562 (667)
80 TIGR01259 comE comEA protein. 48.3 26 0.00056 34.4 4.4 59 442-518 59-117 (120)
81 PRK14605 ruvA Holliday junctio 46.9 15 0.00033 38.8 2.7 23 495-517 69-91 (194)
82 PRK13482 DNA integrity scannin 46.6 28 0.0006 40.4 4.9 59 451-515 275-335 (352)
83 COG2818 Tag 3-methyladenine DN 46.0 19 0.0004 38.5 3.2 64 414-484 45-113 (188)
84 cd00141 NT_POLXc Nucleotidyltr 44.2 42 0.00091 37.7 5.8 57 451-518 8-64 (307)
85 PRK14351 ligA NAD-dependent DN 42.9 28 0.0006 43.5 4.5 29 441-472 486-514 (689)
86 PRK08097 ligB NAD-dependent DN 42.5 76 0.0016 39.0 7.9 69 441-518 449-539 (562)
87 PRK08609 hypothetical protein; 40.7 40 0.00087 41.1 5.3 49 460-515 54-104 (570)
88 PF03118 RNA_pol_A_CTD: Bacter 40.0 40 0.00086 30.0 3.9 28 485-516 34-61 (66)
89 PF11798 IMS_HHH: IMS family H 39.1 16 0.00036 28.2 1.2 15 501-515 13-27 (32)
90 PF10391 DNA_pol_lambd_f: Fing 38.6 28 0.00061 29.9 2.6 21 499-519 2-22 (52)
91 PF05559 DUF763: Protein of un 38.6 68 0.0015 36.9 6.3 21 498-518 268-288 (319)
92 PRK07758 hypothetical protein; 37.4 51 0.0011 31.9 4.3 28 485-516 57-84 (95)
93 TIGR00426 competence protein C 36.9 34 0.00073 29.9 2.9 21 498-518 15-36 (69)
94 PRK00254 ski2-like helicase; P 35.8 74 0.0016 39.6 6.6 43 468-523 627-669 (720)
95 smart00279 HhH2 Helix-hairpin- 35.3 25 0.00053 28.1 1.6 15 502-516 19-33 (36)
96 COG1796 POL4 DNA polymerase IV 34.5 68 0.0015 36.9 5.5 60 451-518 13-72 (326)
97 PRK14600 ruvA Holliday junctio 32.1 35 0.00076 36.1 2.6 22 496-517 70-91 (186)
98 PRK13901 ruvA Holliday junctio 32.1 36 0.00078 36.5 2.8 23 495-517 68-90 (196)
99 PRK12766 50S ribosomal protein 31.4 85 0.0018 34.7 5.4 47 460-518 9-55 (232)
100 PRK02515 psbU photosystem II c 30.9 39 0.00085 34.4 2.6 20 498-517 60-79 (132)
101 PRK14606 ruvA Holliday junctio 30.8 39 0.00085 35.7 2.7 25 493-517 67-91 (188)
102 PRK14601 ruvA Holliday junctio 30.7 39 0.00084 35.7 2.7 23 495-517 69-91 (183)
103 PRK14603 ruvA Holliday junctio 30.1 40 0.00086 35.9 2.7 24 494-517 67-90 (197)
104 PRK08609 hypothetical protein; 30.1 88 0.0019 38.3 5.9 57 451-518 11-67 (570)
105 cd00080 HhH2_motif Helix-hairp 29.0 24 0.00051 31.9 0.7 18 500-517 23-40 (75)
106 PRK14604 ruvA Holliday junctio 28.6 43 0.00094 35.6 2.6 23 495-517 69-91 (195)
107 PRK14602 ruvA Holliday junctio 28.6 44 0.00095 35.7 2.7 23 495-517 70-92 (203)
108 smart00439 BAH Bromo adjacent 28.5 57 0.0012 30.3 3.2 64 863-937 56-119 (120)
109 KOG0028 Ca2+-binding protein ( 25.6 1.4E+02 0.0031 31.6 5.6 87 446-540 48-137 (172)
110 COG0632 RuvA Holliday junction 23.8 60 0.0013 35.0 2.7 24 495-518 69-92 (201)
111 PF00416 Ribosomal_S13: Riboso 23.0 75 0.0016 30.6 2.9 22 496-517 12-33 (107)
112 COG4277 Predicted DNA-binding 22.0 57 0.0012 37.6 2.1 21 498-518 329-349 (404)
113 PF08876 DUF1836: Domain of un 21.9 63 0.0014 31.5 2.2 57 705-761 3-59 (105)
114 PF15414 DUF4621: Protein of u 21.2 31 0.00066 37.3 -0.1 28 678-705 195-222 (329)
115 COG1948 MUS81 ERCC4-type nucle 20.6 1.4E+02 0.0031 33.4 4.8 32 498-529 181-213 (254)
No 1
>PF15628 RRM_DME: RRM in Demeter
Probab=100.00 E-value=3.2e-70 Score=498.99 Aligned_cols=103 Identities=82% Similarity=1.488 Sum_probs=102.1
Q ss_pred eeEEeeccccccCCccCCccceeeeeeeeccCCCCCCcccchhhhccCCceeEEecCChhhhcccCCHHHHHHHhhccce
Q 002141 843 GTILIPCRTAMRGSFPLNGTYFQVNEVFADHDSSLKPINVPREWLWNLPRRTVYFGTSIPSIFKGLTTEGIQHCFWRGYV 922 (960)
Q Consensus 843 gTiLiPCRTAmrG~FPLNGTYFQvNEVFaDh~SS~~PI~vpr~~iw~L~rr~vyfGtSv~sIfkglt~~~Iq~cF~~G~v 922 (960)
|||||||||||||+|||||||||||||||||+||+|||+|||+|||+|+||+|||||||+|||||||++|||+|||+|||
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 002141 923 CVRGFDQKSRAPRPLMARLHFPA 945 (960)
Q Consensus 923 CVR~Fdr~tr~PrpL~~rlh~~~ 945 (960)
|||||||+||+||||++|||+++
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
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=100.00 E-value=4.9e-38 Score=323.82 Aligned_cols=178 Identities=30% Similarity=0.490 Sum_probs=157.8
Q ss_pred CCcHHHHHHHHHHcCCCCCCCCCC-----CCCCCHHHHHcCCHHHHHHHHhhcCChHHHHHHHHHHHHHHHHhcCCCCch
Q 002141 413 DFDWDSLRRQVEANGGKKERPEHT-----KDSLDWEAVRCADVNKIANTIKERGMNNMLAGRIKDFLNRLVRDHGSVDLE 487 (960)
Q Consensus 413 nT~W~nL~kaL~nL~~k~er~~~~-----~g~~TpEaLA~As~eELeeLIRp~Gfyn~KAkrIk~lA~~Ive~yGgiDLe 487 (960)
.+.++-|...+.+.++.++++-.+ ....||++|++|++++|+++|+++|||++||++|+++|+.|+++|||
T Consensus 27 ~~pf~lLva~iLSaqttD~~vn~at~~Lf~~~~t~e~l~~a~~~~l~~~I~~iGlyr~KAk~I~~~~~~l~e~~~g---- 102 (211)
T COG0177 27 KDPFELLVAVILSAQTTDEVVNKATPALFKRYPTPEDLLNADEEELEELIKSIGLYRNKAKNIKELARILLEKFGG---- 102 (211)
T ss_pred CCcHHHHHHHHHhccCchHHHHHHHHHHHHHcCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHcCC----
Confidence 455666666666666544432221 12469999999999999999999999999999999999999999999
Q ss_pred hhhcCChHHHHHHHHhCCCccHHHHHHHHHHhcCCeeeecchHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCchHHHHHh
Q 002141 488 WLRDVPPDKAKEYLLSFRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQPLPESLQLHLLELYPVLESIQKY 567 (960)
Q Consensus 488 ~Lr~vP~deareeLLsLpGIGpKTAd~ILLfafgrpvfpVDThV~RIl~RLG~V~~~~tpEklek~LeellP~~e~Iqk~ 567 (960)
.+|.+ +++|++|||||+|||++||.++||+|+|+|||||.||.+|+||++ ..+|+++++.|++++| +.
T Consensus 103 ---~vP~~--~~eL~~LPGVGrKTAnvVL~~a~g~p~i~VDTHV~Rvs~R~gl~~-~~~p~~ve~~L~~~iP------~~ 170 (211)
T COG0177 103 ---EVPDT--REELLSLPGVGRKTANVVLSFAFGIPAIAVDTHVHRVSNRLGLVP-GKTPEEVEEALMKLIP------KE 170 (211)
T ss_pred ---CCCch--HHHHHhCCCcchHHHHHHHHhhcCCCcccccchHHHHHHHhCCCC-CCCHHHHHHHHHHHCC------HH
Confidence 89988 999999999999999999999999999999999999999999998 6899999999999999 56
Q ss_pred hhhhhhcCChhhHHHHHHHHHHHhHhhcccCCCCCCCCCCchhchhhhhc
Q 002141 568 LWPRLCKLDQRTLYELHYQMITFGKVFCTKSKPNCNACPMRGECRHFASA 617 (960)
Q Consensus 568 LW~rL~klD~e~l~EfH~lLVefGK~ICt~rkP~Cd~CPLr~~C~yyas~ 617 (960)
+| ..+|.+||.|||.+|++++|+|+.|||++.|+++...
T Consensus 171 ~~-----------~~~h~~lI~~GR~iC~ar~P~C~~C~l~~~C~~~~~~ 209 (211)
T COG0177 171 LW-----------TDLHHWLILHGRYICKARKPRCEECPLADLCPSAGKT 209 (211)
T ss_pred HH-----------HHHHHHHHHhhhhhccCCCCCcCcccchhhCchhccc
Confidence 66 4899999999999999999999999999999998764
No 3
>PRK10702 endonuclease III; Provisional
Probab=100.00 E-value=2.1e-37 Score=319.37 Aligned_cols=174 Identities=21% Similarity=0.264 Sum_probs=158.1
Q ss_pred ccccccCCcHHHHHHHHHHcCCCCCCCCCCCCCCCHHHHHcCCHHHHHHHHhhcCChHHHHHHHHHHHHHHHHhcCCCCc
Q 002141 407 SKEKQNDFDWDSLRRQVEANGGKKERPEHTKDSLDWEAVRCADVNKIANTIKERGMNNMLAGRIKDFLNRLVRDHGSVDL 486 (960)
Q Consensus 407 ~~~~~QnT~W~nL~kaL~nL~~k~er~~~~~g~~TpEaLA~As~eELeeLIRp~Gfyn~KAkrIk~lA~~Ive~yGgiDL 486 (960)
.....|||+|.++.+++.+|.. ..++|++|++|+.++|+++|+++|||++||++|+++|+++.++||+
T Consensus 35 s~iLsq~t~~~~v~~~~~~L~~---------~~pt~e~l~~a~~~~l~~~i~~~G~y~~kA~~l~~~a~~i~~~~~~--- 102 (211)
T PRK10702 35 AVLLSAQATDVSVNKATAKLYP---------VANTPAAMLELGVEGVKTYIKTIGLYNSKAENVIKTCRILLEQHNG--- 102 (211)
T ss_pred HHHHHhhcCHHHHHHHHHHHHH---------HcCCHHHHHCCCHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHcCC---
Confidence 3467899999999999999862 4689999999999999999999999999999999999999998887
Q ss_pred hhhhcCChHHHHHHHHhCCCccHHHHHHHHHHhcCCeeeecchHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCchHHHHH
Q 002141 487 EWLRDVPPDKAKEYLLSFRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQPLPESLQLHLLELYPVLESIQK 566 (960)
Q Consensus 487 e~Lr~vP~deareeLLsLpGIGpKTAd~ILLfafgrpvfpVDThV~RIl~RLG~V~~~~tpEklek~LeellP~~e~Iqk 566 (960)
.+|.+ +++|++|||||+|||++||+|+||+++||||+||+||+.|+||... .+|+++++.+++.+| +
T Consensus 103 ----~~p~~--~~~Ll~lpGVG~ktA~~ill~a~~~~~~~VDt~v~Rv~~r~g~~~~-~~~~~~~~~l~~~lp------~ 169 (211)
T PRK10702 103 ----EVPED--RAALEALPGVGRKTANVVLNTAFGWPTIAVDTHIFRVCNRTQFAPG-KNVEQVEEKLLKVVP------A 169 (211)
T ss_pred ----CCCch--HHHHhcCCcccHHHHHHHHHHHcCCCcccccchHHHHHHHhCCCCC-CCHHHHHHHHHHhCC------c
Confidence 57765 9999999999999999999999999999999999999999999874 689999999998888 3
Q ss_pred hhhhhhhcCChhhHHHHHHHHHHHhHhhcccCCCCCCCCCCchhchhhhh
Q 002141 567 YLWPRLCKLDQRTLYELHYQMITFGKVFCTKSKPNCNACPMRGECRHFAS 616 (960)
Q Consensus 567 ~LW~rL~klD~e~l~EfH~lLVefGK~ICt~rkP~Cd~CPLr~~C~yyas 616 (960)
..| .++|.+||+|||.+|++++|+|+.|||++.|+++.+
T Consensus 170 ~~~-----------~~~~~~li~~Gr~~C~~~~P~C~~Cpl~~~C~~~~~ 208 (211)
T PRK10702 170 EFK-----------VDCHHWLILHGRYTCIARKPRCGSCIIEDLCEYKEK 208 (211)
T ss_pred hHH-----------HHHHHHHHHHhHHHcCCCCCCCCCCcChhhcCcccc
Confidence 344 479999999999999999999999999999997643
No 4
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=100.00 E-value=2.1e-35 Score=301.19 Aligned_cols=180 Identities=23% Similarity=0.447 Sum_probs=160.4
Q ss_pred cccccccCCcHHHHHHHHHHcCCCCCCCCCCCCCCCHHHHHcCCHHHHHHHHhhcCChHHHHHHHHHHHHHHHHhcCCCC
Q 002141 406 VSKEKQNDFDWDSLRRQVEANGGKKERPEHTKDSLDWEAVRCADVNKIANTIKERGMNNMLAGRIKDFLNRLVRDHGSVD 485 (960)
Q Consensus 406 ~~~~~~QnT~W~nL~kaL~nL~~k~er~~~~~g~~TpEaLA~As~eELeeLIRp~Gfyn~KAkrIk~lA~~Ive~yGgiD 485 (960)
.+..++|||+|+||++||.||+. .+.++++.|..++.++|+++|||+|||++||+||+++..++.+.|.++
T Consensus 35 igAILtQNT~WknvekAlenLk~--------~~~~~l~~I~~~~~~~L~elIrpsGFYnqKa~rLk~l~k~l~~~~~~~- 105 (215)
T COG2231 35 IGAILTQNTSWKNVEKALENLKN--------EGILNLKKILKLDEEELAELIRPSGFYNQKAKRLKALSKNLAKFFINL- 105 (215)
T ss_pred HHHHHhccccHHHHHHHHHHHHH--------cccCCHHHHhcCCHHHHHHHHhccchHHHHHHHHHHHHHHHHHHhhhh-
Confidence 45678999999999999999984 578899999999999999999999999999999999999999876653
Q ss_pred chhhhcCChHHHHHHHHhCCCccHHHHHHHHHHhcCCeeeecchHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCchHHHH
Q 002141 486 LEWLRDVPPDKAKEYLLSFRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQPLPESLQLHLLELYPVLESIQ 565 (960)
Q Consensus 486 Le~Lr~vP~deareeLLsLpGIGpKTAd~ILLfafgrpvfpVDThV~RIl~RLG~V~~~~tpEklek~LeellP~~e~Iq 565 (960)
..+-...+|++|++++|||++|||+||+|+|++|+|+||.|++|++.|+|.+..+ +|+++++.+++-+|.
T Consensus 106 ----~~~~~~~~R~~LL~iKGIG~ETaDsILlYa~~rp~FVvD~Yt~R~l~rlg~i~~k-~ydeik~~fe~~l~~----- 175 (215)
T COG2231 106 ----ESFKSEVLREELLSIKGIGKETADSILLYALDRPVFVVDKYTRRLLSRLGGIEEK-KYDEIKELFEENLPE----- 175 (215)
T ss_pred ----hccchHHHHHHHHccCCcchhhHHHHHHHHhcCcccchhHHHHHHHHHhcccccc-cHHHHHHHHHhcchh-----
Confidence 2444444799999999999999999999999999999999999999999998864 899999999887772
Q ss_pred HhhhhhhhcCChhhHHHHHHHHHHHhHhhcccCCCCCCCCCCchhchhhh
Q 002141 566 KYLWPRLCKLDQRTLYELHYQMITFGKVFCTKSKPNCNACPMRGECRHFA 615 (960)
Q Consensus 566 k~LW~rL~klD~e~l~EfH~lLVefGK~ICt~rkP~Cd~CPLr~~C~yya 615 (960)
+...+++||++|+.|||.+|+. +|.|+.|||...|.++.
T Consensus 176 ----------~~~lyqe~HAlIv~~~K~f~~k-~~~~~~cpL~~~~~~~~ 214 (215)
T COG2231 176 ----------NLRLYQEFHALIVEHAKHFCKK-KPLCEKCPLKEKCKKYR 214 (215)
T ss_pred ----------HHHHHHHHHHHHHHHHHHHccC-CcCCCCchHHHHHhhcc
Confidence 2345789999999999999986 69999999999998864
No 5
>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=100.00 E-value=8.5e-34 Score=302.77 Aligned_cols=186 Identities=20% Similarity=0.281 Sum_probs=160.2
Q ss_pred cccccCCcHHHHHHHHHHcCCCCCCCCCCCCCCCHHHHHcCCHHHHHHHHhhcCChHHHHHHHHHHHHHHHHhcCCCCch
Q 002141 408 KEKQNDFDWDSLRRQVEANGGKKERPEHTKDSLDWEAVRCADVNKIANTIKERGMNNMLAGRIKDFLNRLVRDHGSVDLE 487 (960)
Q Consensus 408 ~~~~QnT~W~nL~kaL~nL~~k~er~~~~~g~~TpEaLA~As~eELeeLIRp~Gfyn~KAkrIk~lA~~Ive~yGgiDLe 487 (960)
....|+|.|+++.....++.. .++||++|++++.++|.++|+++||| +||++|+++|+.|.++||+
T Consensus 33 eIL~QQT~v~~v~~~~~rl~~---------~fpt~~~La~a~~eeL~~~~~~lG~y-~RAr~L~~~A~~i~~~~~g---- 98 (275)
T TIGR01084 33 EVMLQQTQVATVIPYFERFLE---------RFPTVQALANAPQDEVLKLWEGLGYY-ARARNLHKAAQEVVEEFGG---- 98 (275)
T ss_pred HHHHhhccHHHHHHHHHHHHH---------hCCCHHHHHCcCHHHHHHHHHHCCcH-HHHHHHHHHHHHHHHHcCC----
Confidence 356788999999988877752 46999999999999999999999999 5999999999999999988
Q ss_pred hhhcCChHHHHHHHHhCCCccHHHHHHHHHHhcCCeeeecchHHHHHHHHhcCCCCCCCHHHHHHHH----HHhCCchHH
Q 002141 488 WLRDVPPDKAKEYLLSFRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQPLPESLQLHL----LELYPVLES 563 (960)
Q Consensus 488 ~Lr~vP~deareeLLsLpGIGpKTAd~ILLfafgrpvfpVDThV~RIl~RLG~V~~~~tpEklek~L----eellP~~e~ 563 (960)
.+|.+ +++|++|||||+|||++||+|+||+++++||+||+||+.|++......++.++++.+ ++++|
T Consensus 99 ---~~p~~--~~~L~~LpGIG~~TA~~Il~~a~~~~~~~vD~~v~RVl~Rl~~~~~~~~~~~~~~~l~~~~~~~lp---- 169 (275)
T TIGR01084 99 ---EFPQD--FEDLAALPGVGRYTAGAILSFALNKPYPILDGNVKRVLSRLFAVEGWPGKKKVENRLWTLAESLLP---- 169 (275)
T ss_pred ---CCcHH--HHHHHhCCCCCHHHHHHHHHHHCCCCCCcchHhHHHHHHHHccCcCCCCHHHHHHHHHHHHHHHCC----
Confidence 57766 899999999999999999999999999999999999999997665545566665553 33333
Q ss_pred HHHhhhhhhhcCChhhHHHHHHHHHHHhHhhcccCCCCCCCCCCchhchhhhhccccccccCCCccccc
Q 002141 564 IQKYLWPRLCKLDQRTLYELHYQMITFGKVFCTKSKPNCNACPMRGECRHFASAFASSRLALPGPEEKA 632 (960)
Q Consensus 564 Iqk~LW~rL~klD~e~l~EfH~lLVefGK~ICt~rkP~Cd~CPLr~~C~yyas~~as~r~~lP~~e~k~ 632 (960)
...+.+||++||+||+.+|++++|+|+.|||++.|.+|..+ ....+|.+++|+
T Consensus 170 -------------~~~~~~~n~alm~lG~~vC~~~~P~C~~Cpl~~~C~~~~~~---~~~~~p~~~~~~ 222 (275)
T TIGR01084 170 -------------KADPEAFNQALMDLGAMICTRKKPKCDLCPLQDFCLAYQQG---TWEEYPVKKPKA 222 (275)
T ss_pred -------------hhhHHHHHHHHHHHhHHHcCCCCCCCCCCCChhhCHHHHcC---CHhhcCCCCCCC
Confidence 44567999999999999999999999999999999999987 566788877654
No 6
>PRK10880 adenine DNA glycosylase; Provisional
Probab=100.00 E-value=8.7e-34 Score=311.28 Aligned_cols=190 Identities=19% Similarity=0.265 Sum_probs=160.2
Q ss_pred cccccCCcHHHHHHHHHHcCCCCCCCCCCCCCCCHHHHHcCCHHHHHHHHhhcCChHHHHHHHHHHHHHHHHhcCCCCch
Q 002141 408 KEKQNDFDWDSLRRQVEANGGKKERPEHTKDSLDWEAVRCADVNKIANTIKERGMNNMLAGRIKDFLNRLVRDHGSVDLE 487 (960)
Q Consensus 408 ~~~~QnT~W~nL~kaL~nL~~k~er~~~~~g~~TpEaLA~As~eELeeLIRp~Gfyn~KAkrIk~lA~~Ive~yGgiDLe 487 (960)
....|+|.|++|.....++.. .++|+++|++|+.++|.++|+++|||+ ||++|+++|+.|.++|+|
T Consensus 37 eILlQQT~v~~v~~~~~rl~~---------~fPt~~~La~a~~eel~~~~~glGyy~-RAr~L~~~A~~i~~~~~g---- 102 (350)
T PRK10880 37 EVMLQQTQVATVIPYFERFMA---------RFPTVTDLANAPLDEVLHLWTGLGYYA-RARNLHKAAQQVATLHGG---- 102 (350)
T ss_pred HHHHhhccHHHHHHHHHHHHH---------HCcCHHHHHCcCHHHHHHHHHcCChHH-HHHHHHHHHHHHHHHhCC----
Confidence 356799999999999888752 468999999999999999999999996 999999999999999988
Q ss_pred hhhcCChHHHHHHHHhCCCccHHHHHHHHHHhcCCeeeecchHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCchHHHHHh
Q 002141 488 WLRDVPPDKAKEYLLSFRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQPLPESLQLHLLELYPVLESIQKY 567 (960)
Q Consensus 488 ~Lr~vP~deareeLLsLpGIGpKTAd~ILLfafgrpvfpVDThV~RIl~RLG~V~~~~tpEklek~LeellP~~e~Iqk~ 567 (960)
.+|.+ +++|++|||||+|||++||+|+||+++++||+||+||+.|++.+....++.++++.+.++.. .
T Consensus 103 ---~~p~~--~~~L~~LpGIG~~TA~aIl~~af~~~~~iVD~nV~RV~~Rl~~i~~~~~~~~~~~~l~~~~~-------~ 170 (350)
T PRK10880 103 ---EFPET--FEEVAALPGVGRSTAGAILSLSLGKHFPILDGNVKRVLARCYAVSGWPGKKEVENRLWQLSE-------Q 170 (350)
T ss_pred ---Cchhh--HHHHhcCCCccHHHHHHHHHHHCCCCeecccHHHHHHHHHHhcccCCCChHHHHHHHHHHHH-------H
Confidence 56755 89999999999999999999999999999999999999998544433455555554432211 0
Q ss_pred hhhhhhcCChhhHHHHHHHHHHHhHhhcccCCCCCCCCCCchhchhhhhccccccccCCCccccc
Q 002141 568 LWPRLCKLDQRTLYELHYQMITFGKVFCTKSKPNCNACPMRGECRHFASAFASSRLALPGPEEKA 632 (960)
Q Consensus 568 LW~rL~klD~e~l~EfH~lLVefGK~ICt~rkP~Cd~CPLr~~C~yyas~~as~r~~lP~~e~k~ 632 (960)
.++...+++||++||+||+.+|++++|+|..|||++.|.+|+.+ ....+|.++.|+
T Consensus 171 ------l~p~~~~~~~nqalm~lGa~vC~p~~P~C~~Cpl~~~C~~~~~~---~~~~~P~k~~k~ 226 (350)
T PRK10880 171 ------VTPAVGVERFNQAMMDLGAMVCTRSKPKCELCPLQNGCIAYANH---SWALYPGKKPKQ 226 (350)
T ss_pred ------hCChhHHHHHHHHHHHhhHHhccCCCCCCCCCccHhhhHHHHcC---CHhhCCCCCCCC
Confidence 12345678999999999999999999999999999999999987 566788887654
No 7
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=99.98 E-value=3.2e-32 Score=282.46 Aligned_cols=180 Identities=17% Similarity=0.229 Sum_probs=143.0
Q ss_pred cccccccCCcHHHHHHHHHHcCCCCCCCC-CCCCCCCHHHHHcCCHHHHHHHHhhcCChHHHHHHHHHHHHHHHHhcCCC
Q 002141 406 VSKEKQNDFDWDSLRRQVEANGGKKERPE-HTKDSLDWEAVRCADVNKIANTIKERGMNNMLAGRIKDFLNRLVRDHGSV 484 (960)
Q Consensus 406 ~~~~~~QnT~W~nL~kaL~nL~~k~er~~-~~~g~~TpEaLA~As~eELeeLIRp~Gfyn~KAkrIk~lA~~Ive~yGgi 484 (960)
++....|||.|++|++++.+|+. +.. +....++|++|++++.++|+++||++|||++||++|+++|+++.++||++
T Consensus 35 V~aILsQqT~~~~v~~a~~~L~~---~~~~~~~~~~t~e~L~~a~~eeL~~~Irp~Gf~~~KA~~Lk~la~~i~~~~g~~ 111 (218)
T PRK13913 35 LGAVLTQNTKFEAVEKSLENLKN---AFILENDDEINLKKIAYIEFSKLAECVRPSGFYNQKAKRLIDLSENILKDFGSF 111 (218)
T ss_pred HHHHHHhhhhHHHHHHHHHHHHH---hcccccccCCCHHHHHcCCHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHcCCc
Confidence 45678999999999999999862 100 00123599999999999999999999999999999999999999988763
Q ss_pred CchhhhcCChHHHHHHHHhCCCccHHHHHHHHHHhcCCeeeecchHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCc-hHH
Q 002141 485 DLEWLRDVPPDKAKEYLLSFRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQPLPESLQLHLLELYPV-LES 563 (960)
Q Consensus 485 DLe~Lr~vP~deareeLLsLpGIGpKTAd~ILLfafgrpvfpVDThV~RIl~RLG~V~~~~tpEklek~LeellP~-~e~ 563 (960)
+.+ ...++|++|++|||||+|||++||+|+|++|+|+||+|++||+.|+||.. .+|++++..++..++. +..
T Consensus 112 --~~~---~~~~~re~Ll~l~GIG~kTAd~iLlya~~rp~fvVDty~~Rv~~RlG~~~--~~y~~~~~~~~~~l~~~~~~ 184 (218)
T PRK13913 112 --ENF---KQEVTREWLLDQKGIGKESADAILCYVCAKEVMVVDKYSYLFLKKLGIEI--EDYDELQHFFEKGVQENLNS 184 (218)
T ss_pred --hhc---cCchHHHHHHcCCCccHHHHHHHHHHHcCCCccccchhHHHHHHHcCCCC--CCHHHHHHHHHHhhhhhhhh
Confidence 333 22356999999999999999999999999999999999999999999975 4799999999887641 111
Q ss_pred HHHhhhhhhhcCChhhHHHHHHHHHHHhHhhccc
Q 002141 564 IQKYLWPRLCKLDQRTLYELHYQMITFGKVFCTK 597 (960)
Q Consensus 564 Iqk~LW~rL~klD~e~l~EfH~lLVefGK~ICt~ 597 (960)
+... .+... .+...+++||++||+|||.+|.-
T Consensus 185 ~~~~-~~~~~-~~~~~~~~~Halive~~k~~~~~ 216 (218)
T PRK13913 185 ALAL-YENTI-SLAQLYARFHGKIVEFSKQKLEL 216 (218)
T ss_pred hhcc-ccccc-hHHHHHHHHHHHHHHHHHHhhhc
Confidence 1100 00000 02367899999999999999963
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=99.98 E-value=9.7e-32 Score=271.96 Aligned_cols=159 Identities=26% Similarity=0.311 Sum_probs=143.4
Q ss_pred cccccCCcHHHHHHHHHHcCCCCCCCCCCCCCCCHHHHHcCCHHHHHHHHhhcCChHHHHHHHHHHHHHHHHhcCCCCch
Q 002141 408 KEKQNDFDWDSLRRQVEANGGKKERPEHTKDSLDWEAVRCADVNKIANTIKERGMNNMLAGRIKDFLNRLVRDHGSVDLE 487 (960)
Q Consensus 408 ~~~~QnT~W~nL~kaL~nL~~k~er~~~~~g~~TpEaLA~As~eELeeLIRp~Gfyn~KAkrIk~lA~~Ive~yGgiDLe 487 (960)
....|+|+|.++.+++.+|.. ..+||++|++++.++|+++|+++||+++||++|+++|+++.+++++
T Consensus 33 ~ILsqqt~~~~~~~~~~~l~~---------~~pt~~~l~~~~~~~L~~~ir~~G~~~~Ka~~i~~~a~~i~~~~~~---- 99 (191)
T TIGR01083 33 TILSAQATDKSVNKATKKLFE---------VYPTPQALAQAGLEELEEYIKSIGLYRNKAKNIIALCRILVERYGG---- 99 (191)
T ss_pred HHHHhhCcHHHHHHHHHHHHH---------HCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHcCC----
Confidence 456799999999999888752 4689999999999999999999999999999999999999998876
Q ss_pred hhhcCChHHHHHHHHhCCCccHHHHHHHHHHhcCCeeeecchHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCchHHHHHh
Q 002141 488 WLRDVPPDKAKEYLLSFRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQPLPESLQLHLLELYPVLESIQKY 567 (960)
Q Consensus 488 ~Lr~vP~deareeLLsLpGIGpKTAd~ILLfafgrpvfpVDThV~RIl~RLG~V~~~~tpEklek~LeellP~~e~Iqk~ 567 (960)
.+|. ++++|++|||||+|||++||+|+||+++||||+||+||+.|+||... .+|+++++.++.++| ..
T Consensus 100 ---~~~~--~~~~L~~l~GIG~ktA~~ill~~~~~~~~~vD~~v~Ri~~r~g~~~~-~~~~~~~~~l~~~~p------~~ 167 (191)
T TIGR01083 100 ---EVPE--DREELVKLPGVGRKTANVVLNVAFGIPAIAVDTHVFRVSNRLGLSKG-KDPDKVEEELLKLIP------RE 167 (191)
T ss_pred ---CCch--HHHHHHhCCCCcHHHHHHHHHHHcCCCccccchhHHHHHHHcCCCCC-CCHHHHHHHHHHHCC------ch
Confidence 4554 48999999999999999999999999999999999999999999864 579999999999888 22
Q ss_pred hhhhhhcCChhhHHHHHHHHHHHhHhhcccCCCCC
Q 002141 568 LWPRLCKLDQRTLYELHYQMITFGKVFCTKSKPNC 602 (960)
Q Consensus 568 LW~rL~klD~e~l~EfH~lLVefGK~ICt~rkP~C 602 (960)
.+.+||.+||+|||.+|++++|+|
T Consensus 168 -----------~~~~~h~~li~~G~~~C~~~~P~C 191 (191)
T TIGR01083 168 -----------FWTKLHHWLILHGRYTCKARKPLC 191 (191)
T ss_pred -----------hHHHHHHHHHHHhHHhcCCCCCCC
Confidence 246899999999999999999999
No 9
>KOG1921 consensus Endonuclease III [Replication, recombination and repair]
Probab=99.97 E-value=2e-32 Score=284.57 Aligned_cols=180 Identities=28% Similarity=0.437 Sum_probs=164.9
Q ss_pred cccCCcHHHHHHHHHHcCCCCCCCCCCC------CCCCHHHHHcCCHHHHHHHHhhcCChHHHHHHHHHHHHHHHHhcCC
Q 002141 410 KQNDFDWDSLRRQVEANGGKKERPEHTK------DSLDWEAVRCADVNKIANTIKERGMNNMLAGRIKDFLNRLVRDHGS 483 (960)
Q Consensus 410 ~~QnT~W~nL~kaL~nL~~k~er~~~~~------g~~TpEaLA~As~eELeeLIRp~Gfyn~KAkrIk~lA~~Ive~yGg 483 (960)
...+.+++.|...|.+.|+|++++..+| +.+++++|+++++..|.++|+++|||++||+||+..|+.+.++|+|
T Consensus 73 ~pk~~RfqvLv~lmLSSQTKDevt~~Am~rL~~~~gLT~e~v~~~de~~l~~LI~~VgFy~rKA~ylkkta~IL~d~f~g 152 (286)
T KOG1921|consen 73 DPKERRFQVLVGLMLSSQTKDEVTAAAMLRLKEYGGLTLEAVLKIDEPTLNELIYPVGFYTRKAKYLKKTAKILQDKFDG 152 (286)
T ss_pred ChhhHhHHHHHHHHHhcchHHHHHHHHHHHHHHhcCCCHHHHhccChHhHHhhhhhccchHHHHHHHHHHHHHHHHHhCC
Confidence 3457788999999999999888766543 5699999999999999999999999999999999999999999999
Q ss_pred CCchhhhcCChHHHHHHHHhCCCccHHHHHHHHHHhcCCe-eeecchHHHHHHHHhcCCCCC-CCHHHHHHHHHHhCCch
Q 002141 484 VDLEWLRDVPPDKAKEYLLSFRGLGLKSVECVRLLTLHHL-AFPVDTNVGRIAVRLGWVPLQ-PLPESLQLHLLELYPVL 561 (960)
Q Consensus 484 iDLe~Lr~vP~deareeLLsLpGIGpKTAd~ILLfafgrp-vfpVDThV~RIl~RLG~V~~~-~tpEklek~LeellP~~ 561 (960)
++|++ .++|++|||||||+|..+|..|||.- .|.||+||+||++||||+... .+||+++..|+.|+|
T Consensus 153 -------DIP~~--v~dLlsLPGVGPKMa~L~m~~AWn~i~GI~VDtHVHRi~nrlgWv~~ktkspE~TR~aLq~wLP-- 221 (286)
T KOG1921|consen 153 -------DIPDT--VEDLLSLPGVGPKMAHLTMQVAWNKIVGICVDTHVHRICNRLGWVDTKTKSPEQTRVALQQWLP-- 221 (286)
T ss_pred -------CCchh--HHHHhcCCCCchHHHHHHHHHHhccceeEEeehHHHHHHHHhcccccccCCHHHHHHHHHHhCc--
Confidence 89998 89999999999999999999999985 899999999999999999853 459999999999999
Q ss_pred HHHHHhhhhhhhcCChhhHHHHHHHHHHHhHhhcccCCCCCCCCCC-chhchhhh
Q 002141 562 ESIQKYLWPRLCKLDQRTLYELHYQMITFGKVFCTKSKPNCNACPM-RGECRHFA 615 (960)
Q Consensus 562 e~Iqk~LW~rL~klD~e~l~EfH~lLVefGK~ICt~rkP~Cd~CPL-r~~C~yya 615 (960)
+.+| .++|.+||.||+.||++++|+|+.|.+ ++.|++.-
T Consensus 222 ----k~lW-----------~eIN~lLVGFGQ~iC~p~~prC~~C~~~~~~Cpss~ 261 (286)
T KOG1921|consen 222 ----KSLW-----------VEINHLLVGFGQTICTPRRPRCGLCLLSRDLCPSSF 261 (286)
T ss_pred ----HHHH-----------hhhhceeecccceeeecCCCCccccccCcccCchhh
Confidence 7788 589999999999999999999999999 79999744
No 10
>PRK13910 DNA glycosylase MutY; Provisional
Probab=99.97 E-value=2.3e-31 Score=285.88 Aligned_cols=151 Identities=21% Similarity=0.387 Sum_probs=132.5
Q ss_pred CCCCHHHHHcCCHHHHHHHHhhcCChHHHHHHHHHHHHHHHHhcCCCCchhhhcCChHHHHHHHHhCCCccHHHHHHHHH
Q 002141 438 DSLDWEAVRCADVNKIANTIKERGMNNMLAGRIKDFLNRLVRDHGSVDLEWLRDVPPDKAKEYLLSFRGLGLKSVECVRL 517 (960)
Q Consensus 438 g~~TpEaLA~As~eELeeLIRp~Gfyn~KAkrIk~lA~~Ive~yGgiDLe~Lr~vP~deareeLLsLpGIGpKTAd~ILL 517 (960)
.++|+++|++|++++|.++|+++|||+ ||++|+++|++|.++|+| .+|.+ +++|++|||||+|||++||+
T Consensus 21 ~fPt~e~La~a~~~el~~~~~glGyy~-RAr~L~~~A~~i~~~~~g-------~~P~~--~~~L~~LpGIG~kTA~aIl~ 90 (289)
T PRK13910 21 AFPTLKDLANAPLEEVLLLWRGLGYYS-RAKNLKKSAEICVKEHHS-------QLPND--YQSLLKLPGIGAYTANAILC 90 (289)
T ss_pred HCCCHHHHHCCCHHHHHHHHHcCCcHH-HHHHHHHHHHHHHHHhCC-------CCChh--HHHHHhCCCCCHHHHHHHHH
Confidence 358999999999999999999999995 999999999999999888 68876 89999999999999999999
Q ss_pred HhcCCeeeecchHHHHHHHHh-cCCCCCCCHHHHHHHHHHhCCchHHHHHhhhhhhhcCChhhHHHHHHHHHHHhHhhcc
Q 002141 518 LTLHHLAFPVDTNVGRIAVRL-GWVPLQPLPESLQLHLLELYPVLESIQKYLWPRLCKLDQRTLYELHYQMITFGKVFCT 596 (960)
Q Consensus 518 fafgrpvfpVDThV~RIl~RL-G~V~~~~tpEklek~LeellP~~e~Iqk~LW~rL~klD~e~l~EfH~lLVefGK~ICt 596 (960)
|+||+++++||+||+||+.|+ |+.. ...+.+++...++++| ...++.||++||+||+.+|+
T Consensus 91 ~af~~~~~~VD~nV~RVl~Rl~g~~~-~~~~~~l~~~~~~~l~-----------------~~~~~~~nqaLm~~Ga~iC~ 152 (289)
T PRK13910 91 FGFREKSACVDANIKRVLLRLFGLDP-NIHAKDLQIKANDFLN-----------------LNESFNHNQALIDLGALICS 152 (289)
T ss_pred HHCCCCcCcccHHHHHHHHHHhcCCC-CccHHHHHHHHHHhCC-----------------ccchHHHHHHHHHHhHHHcC
Confidence 999999999999999999997 7754 3445544443334444 23457899999999999999
Q ss_pred cCCCCCCCCCCchhchhhhhc
Q 002141 597 KSKPNCNACPMRGECRHFASA 617 (960)
Q Consensus 597 ~rkP~Cd~CPLr~~C~yyas~ 617 (960)
+ +|+|..|||++.|.++..+
T Consensus 153 ~-~P~C~~CPl~~~C~~~~~~ 172 (289)
T PRK13910 153 P-KPKCAICPLNPYCLGKNNP 172 (289)
T ss_pred C-CCCCCCCcChhhhhhhhcC
Confidence 9 7999999999999999887
No 11
>COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair]
Probab=99.94 E-value=2e-26 Score=250.96 Aligned_cols=192 Identities=18% Similarity=0.288 Sum_probs=154.1
Q ss_pred cHHHHHHHHHHcCCCCCCCCCC-----CCCCCHHHHHcCCHHHHHHHHhhcCChHHHHHHHHHHHHHHHHhcCCCCchhh
Q 002141 415 DWDSLRRQVEANGGKKERPEHT-----KDSLDWEAVRCADVNKIANTIKERGMNNMLAGRIKDFLNRLVRDHGSVDLEWL 489 (960)
Q Consensus 415 ~W~nL~kaL~nL~~k~er~~~~-----~g~~TpEaLA~As~eELeeLIRp~Gfyn~KAkrIk~lA~~Ive~yGgiDLe~L 489 (960)
.|.-+..+++-.++..+++.+. ..+||+++||+|+.++|..+|.++||| .||++|+.+|+.++++|||
T Consensus 34 PY~VwvSEiMLQQT~v~~Vi~yy~~fl~rfPti~~LA~A~~~evl~~W~gLGYy-sRArnL~~~A~~v~~~~~G------ 106 (342)
T COG1194 34 PYRVWVSEIMLQQTQVATVIPYYERFLERFPTIKALAAAPEDEVLKAWEGLGYY-SRARNLHKAAQEVVERHGG------ 106 (342)
T ss_pred cceehhHHHHhhhccHhhhhhhHHHHHHhCCCHHHHhcCCHHHHHHHHHhcChH-HHHHHHHHHHHHHHHHcCC------
Confidence 7777777777777654443332 246899999999999999999999988 5999999999999999999
Q ss_pred hcCChHHHHHHHHhCCCccHHHHHHHHHHhcCCeeeecchHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCchHHHHHhhh
Q 002141 490 RDVPPDKAKEYLLSFRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQPLPESLQLHLLELYPVLESIQKYLW 569 (960)
Q Consensus 490 r~vP~deareeLLsLpGIGpKTAd~ILLfafgrpvfpVDThV~RIl~RLG~V~~~~tpEklek~LeellP~~e~Iqk~LW 569 (960)
.+|++ .+.|.+|||||+|||.+||+|+|+++..+||+||.||+.|+.-+.......+.++ .+|
T Consensus 107 -~~P~~--~~~l~~LpGiG~yTa~Ail~~a~~~~~~~lDgNV~RVl~R~f~i~~~~~~~~~~~--------------~~~ 169 (342)
T COG1194 107 -EFPDD--EEELAALPGVGPYTAGAILSFAFNQPEPVLDGNVKRVLSRLFAISGDIGKPKTKK--------------ELW 169 (342)
T ss_pred -CCCCC--HHHHHhCCCCcHHHHHHHHHHHhCCCCceeecchheeehhhhcccccccccchhH--------------HHH
Confidence 79999 7899999999999999999999999999999999999999954442221111111 222
Q ss_pred hhhhc-CChhh-HHHHHHHHHHHhHhhcccCCCCCCCCCCchhchhhhhccccccccCCCcccccc
Q 002141 570 PRLCK-LDQRT-LYELHYQMITFGKVFCTKSKPNCNACPMRGECRHFASAFASSRLALPGPEEKAI 633 (960)
Q Consensus 570 ~rL~k-lD~e~-l~EfH~lLVefGK~ICt~rkP~Cd~CPLr~~C~yyas~~as~r~~lP~~e~k~~ 633 (960)
..+.. +++.. +.+|+++||++|+.||++++|+|..|||+..|..|..+ ....+|++..|+.
T Consensus 170 ~~~~~ll~p~~~~~~fnqammdlGA~ICt~~~P~C~~CPl~~~c~a~~~g---~~~~~P~k~~k~~ 232 (342)
T COG1194 170 ELAEQLLTPDRRPGDFNQAMMDLGATICTAKKPKCSLCPLRDNCAAYRNG---TPEKYPVKKPKKK 232 (342)
T ss_pred HHHHHhcCCCCChHHHHHHHHHhhhHhhcCCCCCCCcCcchHHHHHHHcC---CcccCCCcCcccc
Confidence 22211 22233 78999999999999999999999999999999999988 5557888766643
No 12
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=99.92 E-value=9.1e-25 Score=210.84 Aligned_cols=148 Identities=29% Similarity=0.385 Sum_probs=132.8
Q ss_pred ccCCcHHHHHHHHHHcCCCCCCCCCCCCCCCHHHHHcCCHHHHHHHHhhcCChHHHHHHHHHHHHHHHHhcCCCCchhhh
Q 002141 411 QNDFDWDSLRRQVEANGGKKERPEHTKDSLDWEAVRCADVNKIANTIKERGMNNMLAGRIKDFLNRLVRDHGSVDLEWLR 490 (960)
Q Consensus 411 ~QnT~W~nL~kaL~nL~~k~er~~~~~g~~TpEaLA~As~eELeeLIRp~Gfyn~KAkrIk~lA~~Ive~yGgiDLe~Lr 490 (960)
.|+|+|.++.+++.++.. ..++|++|++++.++|.++|+++||+++||++|+++++.+.+.+++
T Consensus 2 ~qq~~~~~a~~~~~~l~~---------~~~~~~~l~~~~~~eL~~~l~~~g~~~~ka~~i~~~a~~~~~~~~~------- 65 (149)
T smart00478 2 SQQTSDEAVNKATERLFE---------KFPTPEDLAAADEEELEELIRPLGFYRRKAKYLIELARILVEEYGG------- 65 (149)
T ss_pred CCcccHHHHHHHHHHHHH---------HCCCHHHHHCCCHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHCC-------
Confidence 589999999999998862 3569999999999999999999999999999999999999988776
Q ss_pred cCChHHHHHHHHhCCCccHHHHHHHHHHhcCCeeeecchHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCchHHHHHhhhh
Q 002141 491 DVPPDKAKEYLLSFRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQPLPESLQLHLLELYPVLESIQKYLWP 570 (960)
Q Consensus 491 ~vP~deareeLLsLpGIGpKTAd~ILLfafgrpvfpVDThV~RIl~RLG~V~~~~tpEklek~LeellP~~e~Iqk~LW~ 570 (960)
.++ +.+++|++|||||+|||++||+|+|++++++||+||.|++.|+|+++...+|++++++++.++| ..
T Consensus 66 ~~~--~~~~~L~~l~GIG~~tA~~~l~~~~~~~~~~~D~~v~r~~~rl~~~~~~~~~~~~~~~~~~~~p------~~--- 134 (149)
T smart00478 66 EVP--DDREELLKLPGVGRKTANAVLSFALGKPFIPVDTHVLRIAKRLGLVDKKSTPEEVEKLLEKLLP------KE--- 134 (149)
T ss_pred Ccc--HHHHHHHcCCCCcHHHHHHHHHHHCCCCCCccchHHHHHHHHhCCCCCCCCHHHHHHHHHHHCC------HH---
Confidence 345 3589999999999999999999999999999999999999999999877789999999999988 22
Q ss_pred hhhcCChhhHHHHHHHHHHHhHh
Q 002141 571 RLCKLDQRTLYELHYQMITFGKV 593 (960)
Q Consensus 571 rL~klD~e~l~EfH~lLVefGK~ 593 (960)
.++.||++++.||+.
T Consensus 135 --------~~~~~~~~~l~~g~~ 149 (149)
T smart00478 135 --------DWRELNLLLIDFGRT 149 (149)
T ss_pred --------HHHHHHHHHHHHcCC
Confidence 346899999999973
No 13
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=99.89 E-value=6.9e-23 Score=199.26 Aligned_cols=151 Identities=30% Similarity=0.376 Sum_probs=132.0
Q ss_pred ccccCCcHHHHHHHHHHcCCCCCCCCCCCCCCCHHHHHcCCHHHHHHHHhhcCChHHHHHHHHHHHHHHHHhcCCCCchh
Q 002141 409 EKQNDFDWDSLRRQVEANGGKKERPEHTKDSLDWEAVRCADVNKIANTIKERGMNNMLAGRIKDFLNRLVRDHGSVDLEW 488 (960)
Q Consensus 409 ~~~QnT~W~nL~kaL~nL~~k~er~~~~~g~~TpEaLA~As~eELeeLIRp~Gfyn~KAkrIk~lA~~Ive~yGgiDLe~ 488 (960)
...|++.|+++.+.+.++.. + .+ +||++|+.++.++|.+++.+.| +++||++|+++++.+.+.+++...
T Consensus 8 il~q~~s~~~a~~~~~~l~~---~----~g-pt~~~l~~~~~~~l~~~~~~~G-~~~kA~~i~~~a~~~~~~~~~~~~-- 76 (158)
T cd00056 8 ILSQQTTDKAVNKAYERLFE---R----YG-PTPEALAAADEEELRELIRSLG-YRRKAKYLKELARAIVEGFGGLVL-- 76 (158)
T ss_pred HHHhcccHHHHHHHHHHHHH---H----hC-CCHHHHHCCCHHHHHHHHHhcC-hHHHHHHHHHHHHHHHHHcCCccC--
Confidence 45699999999999998863 1 12 8999999999999999999999 789999999999999998876432
Q ss_pred hhcCChHHHHHHHHhCCCccHHHHHHHHHHhcCCeeeecchHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCchHHHHHhh
Q 002141 489 LRDVPPDKAKEYLLSFRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQPLPESLQLHLLELYPVLESIQKYL 568 (960)
Q Consensus 489 Lr~vP~deareeLLsLpGIGpKTAd~ILLfafgrpvfpVDThV~RIl~RLG~V~~~~tpEklek~LeellP~~e~Iqk~L 568 (960)
+.++++++|++|||||+|||++||+|+++.++||||+|++|++.|+|++....++++++..++.+.| .
T Consensus 77 ----~~~~~~~~L~~l~GIG~~tA~~~l~~~~~~~~~pvD~~v~r~~~~~~~~~~~~~~~~~~~~~~~~~~------~-- 144 (158)
T cd00056 77 ----DDPDAREELLALPGVGRKTANVVLLFALGPDAFPVDTHVRRVLKRLGLIPKKKTPEELEELLEELLP------K-- 144 (158)
T ss_pred ----CCcccHHHHHcCCCCCHHHHHHHHHHHCCCCCCccchhHHHHHHHhCCCCCCCCHHHHHHHHHHHCC------H--
Confidence 6677899999999999999999999999988999999999999999997667889999999888875 1
Q ss_pred hhhhhcCChhhHHHHHHHHHHHh
Q 002141 569 WPRLCKLDQRTLYELHYQMITFG 591 (960)
Q Consensus 569 W~rL~klD~e~l~EfH~lLVefG 591 (960)
.....+|+.|+.||
T Consensus 145 ---------~~~~~~~~~l~~~g 158 (158)
T cd00056 145 ---------PYWGEANQALMDLG 158 (158)
T ss_pred ---------HHHHHHHHHHHHcC
Confidence 12357999999987
No 14
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=99.86 E-value=1.2e-21 Score=202.55 Aligned_cols=132 Identities=15% Similarity=0.060 Sum_probs=109.2
Q ss_pred cccccccCCcHHHHHHHHHHcCCCCCCCCCCCCCCCHHHHHcCCHHHHHHHHhhcC--ChHHHHHHHHHHHHHH---HHh
Q 002141 406 VSKEKQNDFDWDSLRRQVEANGGKKERPEHTKDSLDWEAVRCADVNKIANTIKERG--MNNMLAGRIKDFLNRL---VRD 480 (960)
Q Consensus 406 ~~~~~~QnT~W~nL~kaL~nL~~k~er~~~~~g~~TpEaLA~As~eELeeLIRp~G--fyn~KAkrIk~lA~~I---ve~ 480 (960)
+.-.+.|||.|.++.+++.+|+ ++.+ .++.++|+++||++| ||++||++|+++++++ .+.
T Consensus 42 v~~ILsqnT~~~~v~~a~~~L~--------------~~~l-~~~~eeL~~~Ir~~Gygf~~~KAk~I~~~~~~~~~l~~~ 106 (208)
T PRK01229 42 SFCILTANSSAEGGIKAQKEIG--------------DGFL-YLSEEELEEKLKEVGHRFYNKRAEYIVEARKLYGKLKEI 106 (208)
T ss_pred HHHHhcCcCcHHHHHHHHHhcC--------------HHHc-CCCHHHHHHHHHHhhcccHHHHHHHHHHHHHHHHHHHHH
Confidence 3457899999999999998874 3445 899999999999995 9999999999999984 333
Q ss_pred cCCCCchhhhcCChHHHHHHHH-hCCCccHHHHHHHHHHhcCCeeeecchHHHHHHHHhcCCCC------CCCHHHHHHH
Q 002141 481 HGSVDLEWLRDVPPDKAKEYLL-SFRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPL------QPLPESLQLH 553 (960)
Q Consensus 481 yGgiDLe~Lr~vP~deareeLL-sLpGIGpKTAd~ILLfafgrpvfpVDThV~RIl~RLG~V~~------~~tpEklek~ 553 (960)
+. ...+..++|++|+ +|||||+|||++||++.+.+|+|+||+||+|++.|+||++. ..+|.+++..
T Consensus 107 ~~-------~~~~~~~~R~~Ll~~lpGIG~KTAd~vL~~~~~~~~~iVDtHv~Ri~~RlG~~~~~~~~lt~~~y~~~E~~ 179 (208)
T PRK01229 107 IK-------ADKDQFEAREFLVKNIKGIGYKEASHFLRNVGYEDLAILDRHILRFLKRYGLIEEIPKTLSKKRYLEIEEI 179 (208)
T ss_pred Hh-------ccCCchHHHHHHHHcCCCCcHHHHHHHHHHccCCCeeeeeHHHHHHHHHhCCCcccccccCcCCHHHHHHH
Confidence 20 0223346699999 99999999999999876669999999999999999999875 2679999988
Q ss_pred HHHhCC
Q 002141 554 LLELYP 559 (960)
Q Consensus 554 LeellP 559 (960)
|.++.+
T Consensus 180 l~~~~~ 185 (208)
T PRK01229 180 LREIAE 185 (208)
T ss_pred HHHHHH
Confidence 877644
No 15
>KOG2457 consensus A/G-specific adenine DNA glycosylase [Replication, recombination and repair]
Probab=99.79 E-value=1.2e-19 Score=198.32 Aligned_cols=156 Identities=18% Similarity=0.310 Sum_probs=133.6
Q ss_pred CCCCHHHHHcCCH-HHHHHHHhhcCChHHHHHHHHHHHHHHHHhcCCCCchhhhcCChHHHHHHHHh-CCCccHHHHHHH
Q 002141 438 DSLDWEAVRCADV-NKIANTIKERGMNNMLAGRIKDFLNRLVRDHGSVDLEWLRDVPPDKAKEYLLS-FRGLGLKSVECV 515 (960)
Q Consensus 438 g~~TpEaLA~As~-eELeeLIRp~Gfyn~KAkrIk~lA~~Ive~yGgiDLe~Lr~vP~deareeLLs-LpGIGpKTAd~I 515 (960)
..+|+.+|+.|+. +++.++|.++|||+ |+++|++.|+.+++.++| .+|.. -+.|.+ +||||+|||.+|
T Consensus 153 kwPTl~dla~Asl~~eVn~lWaGlGyY~-R~rrL~ega~~vv~~~~g-------e~Prt--a~~l~kgvpGVG~YTAGAi 222 (555)
T KOG2457|consen 153 KWPTLYDLAQASLEKEVNELWAGLGYYR-RARRLLEGAKMVVAGTEG-------EFPRT--ASSLMKGVPGVGQYTAGAI 222 (555)
T ss_pred hCchHHHHHHHHHHHHHHHHHhhhhHHH-HHHHHHHHHHHHHHhCCC-------CCCCh--HHHHHhhCCCCCccchhhh
Confidence 5799999999999 89999999999995 999999999999999888 78877 456666 999999999999
Q ss_pred HHHhcCCeeeecchHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCchHHHHHhhhhhhh-cCChhhHHHHHHHHHHHhHhh
Q 002141 516 RLLTLHHLAFPVDTNVGRIAVRLGWVPLQPLPESLQLHLLELYPVLESIQKYLWPRLC-KLDQRTLYELHYQMITFGKVF 594 (960)
Q Consensus 516 LLfafgrpvfpVDThV~RIl~RLG~V~~~~tpEklek~LeellP~~e~Iqk~LW~rL~-klD~e~l~EfH~lLVefGK~I 594 (960)
+..||+++.=+||.||.|++.|.--+..+.+..++- ..+|..+. .+|+..+++||+++|++|+..
T Consensus 223 aSIAf~q~tGiVDGNVirvlsRalAIhsDcSkgk~~--------------q~~wkLA~qLVDP~RPGDFNQalMELGAt~ 288 (555)
T KOG2457|consen 223 ASIAFNQVTGIVDGNVIRVLSRALAIHSDCSKGKFF--------------QSSWKLAAQLVDPSRPGDFNQALMELGATL 288 (555)
T ss_pred hhhhhcCcccccccchHHHhHHhHhhcCCcchhhHH--------------HHHHHHHHHhcCCCCCCcHHHHHHHhcCee
Confidence 999999999999999999999974444333322222 34566542 358999999999999999999
Q ss_pred cccCCCCCCCCCCchhchhhhhc
Q 002141 595 CTKSKPNCNACPMRGECRHFASA 617 (960)
Q Consensus 595 Ct~rkP~Cd~CPLr~~C~yyas~ 617 (960)
|++.+|.|..||+...|+.|...
T Consensus 289 CTpq~P~CS~CPvss~CrA~q~~ 311 (555)
T KOG2457|consen 289 CTPQKPSCSSCPVSSQCRAFQLS 311 (555)
T ss_pred ccCCCCCcCCCCcHHHHHHHhHh
Confidence 99999999999999999999843
No 16
>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=99.76 E-value=4.2e-18 Score=185.18 Aligned_cols=147 Identities=22% Similarity=0.297 Sum_probs=109.8
Q ss_pred ccccCCcHHHHHHHHHHcCC----CCCCCCC--CCCCCCHHHHHcCCHHHHHHHHhhcCChHHHHHHHHHHHHHHHHhcC
Q 002141 409 EKQNDFDWDSLRRQVEANGG----KKERPEH--TKDSLDWEAVRCADVNKIANTIKERGMNNMLAGRIKDFLNRLVRDHG 482 (960)
Q Consensus 409 ~~~QnT~W~nL~kaL~nL~~----k~er~~~--~~g~~TpEaLA~As~eELeeLIRp~Gfyn~KAkrIk~lA~~Ive~yG 482 (960)
..-||+++.+..+.+.+|.. +...... ...+|+|++|+.++.++ .||.+||. .||++|+++|+.+.+.++
T Consensus 127 IlsQq~si~~a~~~~~rL~~~~G~~~~~~~g~~~~~FPtp~~La~~~~e~---~Lr~~G~g-~Ra~~I~~~A~~i~~~~~ 202 (310)
T TIGR00588 127 ICSSNNNIARITRMVERLCQAFGPRLITLDGVTYHGFPSLHALTGPEAEA---HLRKLGLG-YRARYIRETARALLEEQG 202 (310)
T ss_pred HHhCCCCHHHHHHHHHHHHHHhCCCcccCCCcccccCCCHHHHhCCChHH---HHHHcCCH-HHHHHHHHHHHHHHhccC
Confidence 44577777777666665521 0000000 12478999999976543 47889994 589999999999999876
Q ss_pred CC-CchhhhcCChHHHHHHHHhCCCccHHHHHHHHHHhcCCe-eeecchHHHHHHHHh-cCCC--------CCCCHHHHH
Q 002141 483 SV-DLEWLRDVPPDKAKEYLLSFRGLGLKSVECVRLLTLHHL-AFPVDTNVGRIAVRL-GWVP--------LQPLPESLQ 551 (960)
Q Consensus 483 gi-DLe~Lr~vP~deareeLLsLpGIGpKTAd~ILLfafgrp-vfpVDThV~RIl~RL-G~V~--------~~~tpEkle 551 (960)
+. +++.|..++.++++++|++|||||+|||+|||+|+|+++ +||||+||+|++.|+ |+.+ .+.++++++
T Consensus 203 ~~~~l~~l~~~~~~~~~~~L~~l~GIG~~tAd~vll~~l~~~d~~PvD~~v~r~~~r~y~~~~~~~~~~~~~~~~~~~i~ 282 (310)
T TIGR00588 203 GRAWLQQIRGASYEDAREALCELPGVGPKVADCICLMGLDKPQAVPVDVHVWRIANRDYPWHPKTSRAKGPSPFARKELG 282 (310)
T ss_pred CchhHHhhccCChHHHHHHHHhCCCccHHHHHHHHHHhCCCCCceeecHHHHHHHHHHhcccccccccccCChhHHHHHH
Confidence 64 677888999999999999999999999999999999997 899999999999998 6532 123455555
Q ss_pred HHHHHhCC
Q 002141 552 LHLLELYP 559 (960)
Q Consensus 552 k~LeellP 559 (960)
....+.+.
T Consensus 283 ~~~~~~~g 290 (310)
T TIGR00588 283 NFFRSLWG 290 (310)
T ss_pred HHHHHHhc
Confidence 55554444
No 17
>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=99.69 E-value=6.3e-17 Score=164.06 Aligned_cols=105 Identities=14% Similarity=0.101 Sum_probs=92.1
Q ss_pred ccccccCCcHHHHHHHHHHcCCCCCCCCCCCCCCCHHHHHcCCHHHHHHHHhhc----CChHHHHHHHHHHHHHHHHhcC
Q 002141 407 SKEKQNDFDWDSLRRQVEANGGKKERPEHTKDSLDWEAVRCADVNKIANTIKER----GMNNMLAGRIKDFLNRLVRDHG 482 (960)
Q Consensus 407 ~~~~~QnT~W~nL~kaL~nL~~k~er~~~~~g~~TpEaLA~As~eELeeLIRp~----Gfyn~KAkrIk~lA~~Ive~yG 482 (960)
+..+.|||.|+++.+++.+|.. ..+.+||++|++++.++|+++|++. |||++||++|++++++|+++|+
T Consensus 24 a~ILSQqTtd~nv~kA~~~L~~-------~~g~~tp~~La~a~~eeL~~lI~~~pal~Gfy~~KAk~Lk~~a~~iie~y~ 96 (177)
T TIGR03252 24 GMLLDQQVPMERAFAGPHKIAR-------RMGSLDAEDIAKYDPQAFVALFSERPAVHRFPGSMAKRVQALAQYVVDTYD 96 (177)
T ss_pred HHHHhccCcHHHHHHHHHHHHH-------HhCCCCHHHHHcCCHHHHHHHHhcCccccCchHHHHHHHHHHHHHHHHHhC
Confidence 4568999999999999999842 1356899999999999999999866 9999999999999999999999
Q ss_pred CCCchhhhc---CChHHHHHHHHhCCCccHHHHHHHHHHh
Q 002141 483 SVDLEWLRD---VPPDKAKEYLLSFRGLGLKSVECVRLLT 519 (960)
Q Consensus 483 giDLe~Lr~---vP~deareeLLsLpGIGpKTAd~ILLfa 519 (960)
| +++.|.. .+..+++++|++|||||+|||++||.+.
T Consensus 97 G-~v~~L~~~~~p~t~~lre~Ll~LpGVG~KTAnvVL~~l 135 (177)
T TIGR03252 97 G-DATAVWTEGDPDGKELLRRLKALPGFGKQKAKIFLALL 135 (177)
T ss_pred C-ChhhhhcccCCCcHHHHHHHHcCCCCCHHHHHHHHHHH
Confidence 8 7777765 4456789999999999999999999853
No 18
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=99.62 E-value=2.5e-15 Score=162.26 Aligned_cols=153 Identities=21% Similarity=0.244 Sum_probs=112.8
Q ss_pred ccccccCCcHHHHHHHHHHcCCCCCCCCCCCCCCCHHHHHcCCHHHHHHHHhhcCChHHHHHHHHHHHHHHHHhcCCCCc
Q 002141 407 SKEKQNDFDWDSLRRQVEANGGKKERPEHTKDSLDWEAVRCADVNKIANTIKERGMNNMLAGRIKDFLNRLVRDHGSVDL 486 (960)
Q Consensus 407 ~~~~~QnT~W~nL~kaL~nL~~k~er~~~~~g~~TpEaLA~As~eELeeLIRp~Gfyn~KAkrIk~lA~~Ive~yGgiDL 486 (960)
.+.+.-++.|.+|....-+.. + ....+|+|+.|+.++.+.+ +.+|+...||+||+.+|+.+.+ |.+|+
T Consensus 118 vS~~~A~~i~~rl~~~~g~~~---~---~~~~fptpe~l~~~~~~~l----~~~g~s~~Ka~yi~~~A~~~~~--g~~~~ 185 (285)
T COG0122 118 VSVAAAAKIWARLVSLYGNAL---E---IYHSFPTPEQLAAADEEAL----RRCGLSGRKAEYIISLARAAAE--GELDL 185 (285)
T ss_pred hhHHHHHHHHHHHHHHhCCcc---c---cccCCCCHHHHHhcCHHHH----HHhCCcHHHHHHHHHHHHHHHc--CCccH
Confidence 334444556666665532111 1 1224799999999999886 5789999999999999999986 55789
Q ss_pred hhhhcCChHHHHHHHHhCCCccHHHHHHHHHHhcCCe-eee-cchHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCchHHH
Q 002141 487 EWLRDVPPDKAKEYLLSFRGLGLKSVECVRLLTLHHL-AFP-VDTNVGRIAVRLGWVPLQPLPESLQLHLLELYPVLESI 564 (960)
Q Consensus 487 e~Lr~vP~deareeLLsLpGIGpKTAd~ILLfafgrp-vfp-VDThV~RIl~RLG~V~~~~tpEklek~LeellP~~e~I 564 (960)
..+..++.++++++|++|+|||+|||+|||+|++|++ +|| .|.+++|.+.+++..+...+...+....+.+-|.-...
T Consensus 186 ~~l~~~~~e~a~e~L~~i~GIG~WTAe~~llf~lgr~dvfP~~D~~lr~~~~~~~~~~~~~~~~~~~~~~e~w~p~rs~A 265 (285)
T COG0122 186 SELKPLSDEEAIEELTALKGIGPWTAEMFLLFGLGRPDVFPADDLGLRRAIKKLYRLPTRPTEKEVRELAERWGPYRSYA 265 (285)
T ss_pred HHhccCCHHHHHHHHHcCCCcCHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhcCCCCchHHHHHHHHhcccCHHHHH
Confidence 9999999999999999999999999999999999987 888 56777777888863333333333455556666633333
Q ss_pred HHhhhhh
Q 002141 565 QKYLWPR 571 (960)
Q Consensus 565 qk~LW~r 571 (960)
+-|||..
T Consensus 266 ~~yLw~~ 272 (285)
T COG0122 266 ALYLWRY 272 (285)
T ss_pred HHHHHHh
Confidence 5577764
No 19
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=99.48 E-value=2e-13 Score=147.37 Aligned_cols=117 Identities=20% Similarity=0.183 Sum_probs=93.9
Q ss_pred CCCCHHHHHcCCHHHHHHHHhhcCChHHHHHHHHHHHHHHHHhcCCCCchhhhcCChHHHHHHHHhCCCccHHHHHHHHH
Q 002141 438 DSLDWEAVRCADVNKIANTIKERGMNNMLAGRIKDFLNRLVRDHGSVDLEWLRDVPPDKAKEYLLSFRGLGLKSVECVRL 517 (960)
Q Consensus 438 g~~TpEaLA~As~eELeeLIRp~Gfyn~KAkrIk~lA~~Ive~yGgiDLe~Lr~vP~deareeLLsLpGIGpKTAd~ILL 517 (960)
.+++|++|++++.++| +.+||+++||++|+++|+.+.+ |.++++... +.+++++.|++|||||+|||+||++
T Consensus 154 ~FPtpe~La~~~~~eL----~~~Gl~~~Ra~~L~~lA~~i~~--g~l~l~~~~--~~~~~~~~L~~LpGIGpwTA~~vll 225 (283)
T PRK10308 154 CFPTPERLAAADPQAL----KALGMPLKRAEALIHLANAALE--GTLPLTIPG--DVEQAMKTLQTFPGIGRWTANYFAL 225 (283)
T ss_pred CCCCHHHHHcCCHHHH----HHCCCCHHHHHHHHHHHHHHHc--CCCCccccC--CHHHHHHHHhcCCCcCHHHHHHHHH
Confidence 4689999999999986 5789999999999999999986 666665433 4577899999999999999999999
Q ss_pred HhcCCe-ee-ecchHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCchHHH-HHhhhh
Q 002141 518 LTLHHL-AF-PVDTNVGRIAVRLGWVPLQPLPESLQLHLLELYPVLESI-QKYLWP 570 (960)
Q Consensus 518 fafgrp-vf-pVDThV~RIl~RLG~V~~~~tpEklek~LeellP~~e~I-qk~LW~ 570 (960)
|+||++ +| +.|.+++|.+ + ..++++++...+.+-| ++.+ .-++|.
T Consensus 226 r~lg~~D~fp~~D~~l~~~~---~----~~~~~~~~~~a~~w~P-~rsya~~~LW~ 273 (283)
T PRK10308 226 RGWQAKDVFLPDDYLIKQRF---P----GMTPAQIRRYAERWKP-WRSYALLHIWY 273 (283)
T ss_pred HhCCCCCCCCcccHHHHHhc---c----cCCHHHHHHHHHhcCC-HHHHHHHHHHH
Confidence 999997 77 7899998854 2 2367788888877777 3332 335664
No 20
>KOG2875 consensus 8-oxoguanine DNA glycosylase [Replication, recombination and repair]
Probab=99.40 E-value=3.7e-13 Score=143.72 Aligned_cols=97 Identities=28% Similarity=0.410 Sum_probs=86.3
Q ss_pred CCCCHHHHHcCCHHHHHHHHhhcCChHHHHHHHHHHHHHHHHhcCCC-CchhhhcCChHHHHHHHHhCCCccHHHHHHHH
Q 002141 438 DSLDWEAVRCADVNKIANTIKERGMNNMLAGRIKDFLNRLVRDHGSV-DLEWLRDVPPDKAKEYLLSFRGLGLKSVECVR 516 (960)
Q Consensus 438 g~~TpEaLA~As~eELeeLIRp~Gfyn~KAkrIk~lA~~Ive~yGgi-DLe~Lr~vP~deareeLLsLpGIGpKTAd~IL 516 (960)
++|+.++|+. .++++-+|.+||. .|||||-+.|+.|.+++|+. .|..|++++.+++++.|+.|||||+|+||||+
T Consensus 160 ~FPsl~~L~g---~~~Ea~LR~~gfG-YRAkYI~~ta~~l~~~~g~~~wLqsl~~~~yeear~~L~~lpGVG~KVADCI~ 235 (323)
T KOG2875|consen 160 GFPSLQALAG---PEVEAELRKLGFG-YRAKYISATARALQEKQGGLAWLQSLRKSSYEEAREALCSLPGVGPKVADCIC 235 (323)
T ss_pred cCccHHHhcC---cHhHHHHHHcCcc-hhHHHHHHHHHHHHHhcccchHHHHHhcccHHHHHHHHhcCCCCcchHhhhhh
Confidence 5789999887 6778889999997 59999999999999999882 34556788999999999999999999999999
Q ss_pred HHhcCCe-eeecchHHHHHHHHh
Q 002141 517 LLTLHHL-AFPVDTNVGRIAVRL 538 (960)
Q Consensus 517 Lfafgrp-vfpVDThV~RIl~RL 538 (960)
++++++. ++|||+||.||+.-.
T Consensus 236 Lm~l~~~~~VPVDvHi~ria~~y 258 (323)
T KOG2875|consen 236 LMSLDKLSAVPVDVHIWRIAQDY 258 (323)
T ss_pred hhhcCCCCcccchhhHHHHhhcc
Confidence 9999986 899999999999833
No 21
>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=99.38 E-value=1.3e-12 Score=120.10 Aligned_cols=104 Identities=22% Similarity=0.196 Sum_probs=88.7
Q ss_pred ccccCCcHHHHHHHHHHcCCCCCCCCCCCCCCCHHHHHcCCHHHHHHHHhhcCChHHHHHHHHHHHHHHHHhcCCCCchh
Q 002141 409 EKQNDFDWDSLRRQVEANGGKKERPEHTKDSLDWEAVRCADVNKIANTIKERGMNNMLAGRIKDFLNRLVRDHGSVDLEW 488 (960)
Q Consensus 409 ~~~QnT~W~nL~kaL~nL~~k~er~~~~~g~~TpEaLA~As~eELeeLIRp~Gfyn~KAkrIk~lA~~Ive~yGgiDLe~ 488 (960)
...|++.|+.+.+.+.+|.. ..|++||++|+.++.++|.++|+++||+++||++|+++|+.+.
T Consensus 4 Il~qq~s~~~a~~~~~~l~~-------~~g~pt~~~l~~~~~~el~~~i~~~G~~~~ka~~i~~~a~~~~---------- 66 (108)
T PF00730_consen 4 ILSQQTSIKAARKIYRRLFE-------RYGFPTPEALAEASEEELRELIRPLGFSRRKAKYIIELARAIL---------- 66 (108)
T ss_dssp HHCTTS-HHHHHHHHHHHHH-------HHSCSSHHHHHCSHHHHHHHHHTTSTSHHHHHHHHHHHHHHHH----------
T ss_pred eecCcCcHHHHHHHHHHHHH-------HhcCCCHHHHHhCCHHHHHHHhhccCCCHHHHHHHHHHHHHhh----------
Confidence 45799999999999988862 2468999999999999999999999999999999999999987
Q ss_pred hhcCChHHHHHHHHhCCCccHHHHHHHHHHhcCCeeeecchHHHHHHHHhcCCCCCCCHHHHHHHHHHhCC
Q 002141 489 LRDVPPDKAKEYLLSFRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQPLPESLQLHLLELYP 559 (960)
Q Consensus 489 Lr~vP~deareeLLsLpGIGpKTAd~ILLfafgrpvfpVDThV~RIl~RLG~V~~~~tpEklek~LeellP 559 (960)
++..+++++|+|++|++.|+|+++.+.+++++++.+++++|
T Consensus 67 ------------------------------~~~d~~~~~D~~v~r~~~r~~~~~~~~~~~~~~~~~~e~~~ 107 (108)
T PF00730_consen 67 ------------------------------GRPDPFPPVDTHVRRVLQRLGGIPEKKTKEETEKKLEELWP 107 (108)
T ss_dssp ------------------------------C-SSSS-TTSHHHHHHHHHHTSSSSSTTHHHHHHHHHHHGT
T ss_pred ------------------------------hcccceecCcHHHHHHHHHHcCCCCCCCHHHHHHHHHhhCc
Confidence 22235899999999999999999877899999998877655
No 22
>KOG1918 consensus 3-methyladenine DNA glycosidase [Replication, recombination and repair]
Probab=99.19 E-value=3.4e-11 Score=125.48 Aligned_cols=126 Identities=20% Similarity=0.310 Sum_probs=102.2
Q ss_pred CCCCHHHHHcCCHHHHHHHHhhcCChHHHHHHHHHHHHHHHHhcCCCCchhhhcCChHHHHHHHHhCCCccHHHHHHHHH
Q 002141 438 DSLDWEAVRCADVNKIANTIKERGMNNMLAGRIKDFLNRLVRDHGSVDLEWLRDVPPDKAKEYLLSFRGLGLKSVECVRL 517 (960)
Q Consensus 438 g~~TpEaLA~As~eELeeLIRp~Gfyn~KAkrIk~lA~~Ive~yGgiDLe~Lr~vP~deareeLLsLpGIGpKTAd~ILL 517 (960)
.+++|+.+..++.++| |.+||+.+|+.||+.+|.+..+.| -...+...+++.+++.+.|..++|||+|||.|+|+
T Consensus 109 ~~~~pe~i~~~~~~~l----rkcG~S~rK~~yLh~lA~~~~ng~-I~s~~~i~~mseEeL~~~LT~VKGIg~Wtv~MflI 183 (254)
T KOG1918|consen 109 KFPTPEFIDPLDCEEL----RKCGFSKRKASYLHSLAEAYTNGY-IPSKSGIEKMSEEELIERLTNVKGIGRWTVEMFLI 183 (254)
T ss_pred CCCCchhcCcCCHHHH----HHhCcchhhHHHHHHHHHHHhcCC-CCchHHHhhcCHHHHHHHHHhccCccceeeeeeee
Confidence 4689999999999985 788999999999999999998643 12566777999999999999999999999999999
Q ss_pred HhcCCe-eeecchHHHH-HHHHh-cCCCCCCCHHHHHHHHHHhCCchHHHHH-hhhh
Q 002141 518 LTLHHL-AFPVDTNVGR-IAVRL-GWVPLQPLPESLQLHLLELYPVLESIQK-YLWP 570 (960)
Q Consensus 518 fafgrp-vfpVDThV~R-Il~RL-G~V~~~~tpEklek~LeellP~~e~Iqk-~LW~ 570 (960)
|+++|+ |||+|.-..| -+..| |+-+ -+.+.+++++.+.+-| |+.+.. |+|.
T Consensus 184 fsL~R~DVmp~dDlgir~g~k~l~gl~~-~p~~~evekl~e~~kp-yRtvaawYlWk 238 (254)
T KOG1918|consen 184 FSLHRPDVMPADDLGIRNGVKKLLGLKP-LPLPKEVEKLCEKCKP-YRTVAAWYLWK 238 (254)
T ss_pred eccCCCcccCchhhhHHHHHHHHhCCCC-CCchHHHHHHhhhccc-hHHHHHHHHHh
Confidence 999998 8999765555 44444 5543 3677888888877766 555533 6675
No 23
>PF15629 Perm-CXXC: Permuted single zf-CXXC unit
Probab=99.17 E-value=7.6e-12 Score=94.68 Aligned_cols=32 Identities=69% Similarity=1.284 Sum_probs=30.9
Q ss_pred CCCccCcccccCccCCccccccCchhhcccce
Q 002141 809 PESRCSSQEHGKMCDEKTCFSCNSVRESEFQI 840 (960)
Q Consensus 809 p~~~c~s~~~~~~c~~~~~~~c~s~~e~~~~~ 840 (960)
|+++|+||++||||+++|||+||||||+++|+
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 24
>COG1059 Thermostable 8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=98.27 E-value=5e-06 Score=85.99 Aligned_cols=114 Identities=18% Similarity=0.198 Sum_probs=84.9
Q ss_pred cccCCcHHHHHHHHHHcCCCCCCCCCCCCCCCHHHHHcCCHHHHHHHHhhcC--ChHHHHHHHHHHHHHHHHhcCCCCch
Q 002141 410 KQNDFDWDSLRRQVEANGGKKERPEHTKDSLDWEAVRCADVNKIANTIKERG--MNNMLAGRIKDFLNRLVRDHGSVDLE 487 (960)
Q Consensus 410 ~~QnT~W~nL~kaL~nL~~k~er~~~~~g~~TpEaLA~As~eELeeLIRp~G--fyn~KAkrIk~lA~~Ive~yGgiDLe 487 (960)
.+.|+.-..--++...++ +.+.-++.+||++.++.+| ||++||+||..+-+.+. ++.
T Consensus 48 LTANsSA~~~~~~q~~lG---------------~gfly~~~eEL~e~Lk~~g~Rf~n~raeyIVeaR~~~~------~lk 106 (210)
T COG1059 48 LTANSSATMGLRAQNELG---------------DGFLYLSEEELREKLKEVGYRFYNVRAEYIVEAREKFD------DLK 106 (210)
T ss_pred ccccchHHHHHHHHHHhc---------------cccccCCHHHHHHHHHHhcchhcccchHHHHHHHHHHH------HHH
Confidence 344555555555555554 2356679999999999996 68999999998544442 244
Q ss_pred hhhcCChHH--HHHHHH-hCCCccHHHHHHHHHHhcCCeeeecchHHHHHHHHhcCCCCC
Q 002141 488 WLRDVPPDK--AKEYLL-SFRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQ 544 (960)
Q Consensus 488 ~Lr~vP~de--areeLL-sLpGIGpKTAd~ILLfafgrpvfpVDThV~RIl~RLG~V~~~ 544 (960)
.+-+.+..+ +|++|+ .++|||-|-|..+|-..--..+.++|.|+.|.+.|.|++...
T Consensus 107 ~~v~~~~~~~vaRE~Lv~nikGiGyKEASHFLRNVG~~D~AIlDrHIlr~l~r~g~i~e~ 166 (210)
T COG1059 107 IIVKADENEKVARELLVENIKGIGYKEASHFLRNVGFEDLAILDRHILRWLVRYGLIDEN 166 (210)
T ss_pred HHHhcCcchHHHHHHHHHHcccccHHHHHHHHHhcChhHHHHHHHHHHHHHHHhcccccC
Confidence 444444333 899999 999999999999996644467889999999999999998643
No 25
>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=97.39 E-value=0.0001 Score=55.91 Aligned_cols=25 Identities=24% Similarity=0.521 Sum_probs=21.1
Q ss_pred CChHHHHHHHHhCCCccHHHHHHHHHH
Q 002141 492 VPPDKAKEYLLSFRGLGLKSVECVRLL 518 (960)
Q Consensus 492 vP~deareeLLsLpGIGpKTAd~ILLf 518 (960)
+|.+ +++|++|||||+|||++|+.|
T Consensus 6 ~pas--~eeL~~lpGIG~~tA~~I~~~ 30 (30)
T PF00633_consen 6 IPAS--IEELMKLPGIGPKTANAILSF 30 (30)
T ss_dssp HTSS--HHHHHTSTT-SHHHHHHHHHH
T ss_pred CCCC--HHHHHhCCCcCHHHHHHHHhC
Confidence 4555 899999999999999999976
No 26
>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=96.43 E-value=0.0011 Score=44.69 Aligned_cols=17 Identities=47% Similarity=1.323 Sum_probs=11.6
Q ss_pred cccCCCCCCCCCCchhc
Q 002141 595 CTKSKPNCNACPMRGEC 611 (960)
Q Consensus 595 Ct~rkP~Cd~CPLr~~C 611 (960)
|++++|+|+.|||+++|
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 27
>PF09674 DUF2400: Protein of unknown function (DUF2400); InterPro: IPR014127 Members of this uncharacterised protein family are found sporadically, so far only among spirochetes, epsilon and delta proteobacteria, and Bacteroides. The function is unknown and its gene neighbourhoods show little conservation.
Probab=96.27 E-value=0.0035 Score=67.33 Aligned_cols=88 Identities=24% Similarity=0.377 Sum_probs=60.5
Q ss_pred HHHHHHHHHHHHHHHhcCCCCchhhhcCChHHHHHHHHhCCCccHHHHHHHHHHhcCCeeeecchHHHHHHHHhcCCCCC
Q 002141 465 MLAGRIKDFLNRLVRDHGSVDLEWLRDVPPDKAKEYLLSFRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQ 544 (960)
Q Consensus 465 ~KAkrIk~lA~~Ive~yGgiDLe~Lr~vP~deareeLLsLpGIGpKTAd~ILLfafgrpvfpVDThV~RIl~RLG~V~~~ 544 (960)
.-+|+|-.+++|++.+..++|+.-...++..++ ++|+||||.||+.+||+...+
T Consensus 143 SacKR~~MFLRWMVR~d~~VD~GlW~~i~ps~L--------------------------iiPLDtHv~~var~LGL~~rk 196 (232)
T PF09674_consen 143 SACKRLNMFLRWMVRKDSPVDFGLWSSIDPSDL--------------------------IIPLDTHVFRVARKLGLLKRK 196 (232)
T ss_pred cHHHHHHHHHHhhccCCCCCCCcCCCCCCHHHc--------------------------cccchHhHHHHHHHcCCccCC
Confidence 457999999999998755688887777887643 689999999999999998754
Q ss_pred CCHHHHHHHHHHhCCchHHHHHhhhhhhhcCChhhHHHHHHHHHHHhH
Q 002141 545 PLPESLQLHLLELYPVLESIQKYLWPRLCKLDQRTLYELHYQMITFGK 592 (960)
Q Consensus 545 ~tpEklek~LeellP~~e~Iqk~LW~rL~klD~e~l~EfH~lLVefGK 592 (960)
..--++...+-+ .+.++++.++-.+..+|-.+|.
T Consensus 197 ~~d~k~A~elT~--------------~lr~~~p~DPvKYDFAL~~~Gi 230 (232)
T PF09674_consen 197 SADWKAARELTE--------------ALREFDPDDPVKYDFALFRLGI 230 (232)
T ss_pred CccHHHHHHHHH--------------HHHhcCCCCCcchhhhcccCCc
Confidence 221122212111 1223566667777777776664
No 28
>TIGR02757 conserved hypothetical protein TIGR02757. Members of this uncharacterized protein family are found sporadically, so far only among spirochetes, epsilon and delta proteobacteria, and Bacteroides. The function is unknown and its gene neighborhoods show little conservation.
Probab=95.81 E-value=0.0077 Score=64.68 Aligned_cols=85 Identities=24% Similarity=0.401 Sum_probs=58.9
Q ss_pred HHHHHHHHHHHHHHhcCCCCchhhhcCChHHHHHHHHhCCCccHHHHHHHHHHhcCCeeeecchHHHHHHHHhcCCCCCC
Q 002141 466 LAGRIKDFLNRLVRDHGSVDLEWLRDVPPDKAKEYLLSFRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQP 545 (960)
Q Consensus 466 KAkrIk~lA~~Ive~yGgiDLe~Lr~vP~deareeLLsLpGIGpKTAd~ILLfafgrpvfpVDThV~RIl~RLG~V~~~~ 545 (960)
-+|+|-.+++|++.+ .++|+.-...++..+ -++|+||||.||+.+||+...+
T Consensus 142 a~KR~nMFLRWMVR~-d~VD~GlW~~i~ps~--------------------------LiiPLDtH~~rvar~LgL~~Rk- 193 (229)
T TIGR02757 142 PLKRLNMFLRWMIRK-DEVDLGIWESFKPSD--------------------------LILPLDTHVFRIAKKLKLLKRK- 193 (229)
T ss_pred hHHHHHHHHHhhccC-CCCCCcCCCCCCHHH--------------------------ceeechHhHHHHHHHhCCcccC-
Confidence 359999999999985 448887777777663 2689999999999999998753
Q ss_pred CHH-HHHHHHHHhCCchHHHHHhhhhhhhcCChhhHHHHHHHHHHHhH
Q 002141 546 LPE-SLQLHLLELYPVLESIQKYLWPRLCKLDQRTLYELHYQMITFGK 592 (960)
Q Consensus 546 tpE-klek~LeellP~~e~Iqk~LW~rL~klD~e~l~EfH~lLVefGK 592 (960)
+++ ++...+- ..+.++++.++-.+..+|-.+|.
T Consensus 194 ~~d~kaa~ElT--------------~~Lr~~dp~DPvKYDFAL~~lGi 227 (229)
T TIGR02757 194 SYDLKAAIEIT--------------EALRELNPEDPIKYDFALFRLGQ 227 (229)
T ss_pred chhHHHHHHHH--------------HHHHhcCCCCCcchhhhcccCCc
Confidence 321 1111111 12234567777777777777764
No 29
>smart00525 FES FES domain. iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3)
Probab=95.54 E-value=0.0064 Score=44.22 Aligned_cols=23 Identities=35% Similarity=1.100 Sum_probs=20.4
Q ss_pred hcccCCCCCCCCCCchhchhhhh
Q 002141 594 FCTKSKPNCNACPMRGECRHFAS 616 (960)
Q Consensus 594 ICt~rkP~Cd~CPLr~~C~yyas 616 (960)
+|++++|+|+.|||+..|.+|..
T Consensus 1 vC~ar~P~C~~Cpl~~~C~~~~~ 23 (26)
T smart00525 1 ICTARKPRCDECPLKDLCPAYXX 23 (26)
T ss_pred CccCCCCCCCCCcCHHHhhhhhc
Confidence 69999999999999999997543
No 30
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=91.16 E-value=0.31 Score=42.54 Aligned_cols=39 Identities=26% Similarity=0.347 Sum_probs=27.8
Q ss_pred HHHHHHhcCCCCchhhhcCChHHHHHHHHhCCCccHHHHHHHHHH
Q 002141 474 LNRLVRDHGSVDLEWLRDVPPDKAKEYLLSFRGLGLKSVECVRLL 518 (960)
Q Consensus 474 A~~Ive~yGgiDLe~Lr~vP~deareeLLsLpGIGpKTAd~ILLf 518 (960)
|+.+.+.|+ +++.|...+ .++|.+++|||+++|..|..|
T Consensus 16 ak~L~~~f~--sl~~l~~a~----~e~L~~i~gIG~~~A~si~~f 54 (64)
T PF12826_consen 16 AKLLAKHFG--SLEALMNAS----VEELSAIPGIGPKIAQSIYEF 54 (64)
T ss_dssp HHHHHHCCS--CHHHHCC------HHHHCTSTT--HHHHHHHHHH
T ss_pred HHHHHHHcC--CHHHHHHcC----HHHHhccCCcCHHHHHHHHHH
Confidence 556667777 477777665 568999999999999999766
No 31
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=90.35 E-value=0.2 Score=36.55 Aligned_cols=20 Identities=30% Similarity=0.288 Sum_probs=17.7
Q ss_pred HHHhCCCccHHHHHHHHHHh
Q 002141 500 YLLSFRGLGLKSVECVRLLT 519 (960)
Q Consensus 500 eLLsLpGIGpKTAd~ILLfa 519 (960)
.|++++|||+|+|+.|+.+.
T Consensus 2 ~L~~i~GiG~k~A~~il~~~ 21 (26)
T smart00278 2 ELLKVPGIGPKTAEKILEAX 21 (26)
T ss_pred hhhhCCCCCHHHHHHHHHhc
Confidence 58899999999999998754
No 32
>PF14716 HHH_8: Helix-hairpin-helix domain; PDB: 2W9M_A 1HUZ_A 1HUO_A 2BPG_B 2BPF_A 1DK3_A 1BPE_A 1BNO_A 1BNP_A 1DK2_A ....
Probab=87.48 E-value=2.4 Score=37.32 Aligned_cols=58 Identities=14% Similarity=0.166 Sum_probs=40.0
Q ss_pred HHHHHHHhhcCChHHHHHHHHHHHHHHHHhcCCCCchhhhcCChHHHHHHHHhCCCccHHHHHHHHHH
Q 002141 451 NKIANTIKERGMNNMLAGRIKDFLNRLVRDHGSVDLEWLRDVPPDKAKEYLLSFRGLGLKSVECVRLL 518 (960)
Q Consensus 451 eELeeLIRp~Gfyn~KAkrIk~lA~~Ive~yGgiDLe~Lr~vP~deareeLLsLpGIGpKTAd~ILLf 518 (960)
+++.++..-.|=...|++..+.++..|.. ++. +-....+.|.+|||||.++|..|--|
T Consensus 9 ~~la~~~~~~~~~~~r~~aY~~Aa~~i~~-l~~---------~i~~~~~~~~~l~gIG~~ia~kI~E~ 66 (68)
T PF14716_consen 9 EELADLYELQGGDPFRARAYRRAAAAIKA-LPY---------PITSGEEDLKKLPGIGKSIAKKIDEI 66 (68)
T ss_dssp HHHHHHHHHTSTSHHHHHHHHHHHHHHHH-SSS----------HHSHHHHHCTSTTTTHHHHHHHHHH
T ss_pred HHHHHHHHHhhCCcHHHHHHHHHHHHHHh-CCH---------hHhhHHHHHhhCCCCCHHHHHHHHHH
Confidence 45666666665455788888898888876 332 22222225999999999999988543
No 33
>PRK10353 3-methyl-adenine DNA glycosylase I; Provisional
Probab=86.58 E-value=0.33 Score=51.12 Aligned_cols=63 Identities=10% Similarity=0.136 Sum_probs=44.3
Q ss_pred CcHHHHHHHHHHcCCCCCCCCCCCCCCCHHHHHcCCHHHHHHHHhhcCCh--HHHHHHHHHHHHHHH---HhcCC
Q 002141 414 FDWDSLRRQVEANGGKKERPEHTKDSLDWEAVRCADVNKIANTIKERGMN--NMLAGRIKDFLNRLV---RDHGS 483 (960)
Q Consensus 414 T~W~nL~kaL~nL~~k~er~~~~~g~~TpEaLA~As~eELeeLIRp~Gfy--n~KAkrIk~lA~~Iv---e~yGg 483 (960)
-.|..+.+--.+. ..+...++++.||..++++|+.++...|.- +.|.+.+..=|+.+. +++|+
T Consensus 44 LSW~tIL~Kre~f-------r~aF~~Fd~~~VA~~~e~die~Ll~d~~IIRnr~KI~Avi~NA~~~l~i~~e~gS 111 (187)
T PRK10353 44 LSWITVLKKRENY-------RACFHQFDPVKVAAMQEEDVERLVQDAGIIRHRGKIQAIIGNARAYLQMEQNGEP 111 (187)
T ss_pred ccHHHHHHHHHHH-------HHHHcCCCHHHHhCCCHHHHHHHhcCchhHHhHHHHHHHHHHHHHHHHHHHhcCC
Confidence 3677776543333 235678999999999999999999999994 456666666455544 34554
No 34
>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=86.00 E-value=2.8 Score=35.78 Aligned_cols=52 Identities=23% Similarity=0.263 Sum_probs=34.0
Q ss_pred HHHhhcCChHHHHHHHHHHHHHHHHhcCCCCchhhhcCChHHHHHHHHhCCCccHHHHHHHHHH
Q 002141 455 NTIKERGMNNMLAGRIKDFLNRLVRDHGSVDLEWLRDVPPDKAKEYLLSFRGLGLKSVECVRLL 518 (960)
Q Consensus 455 eLIRp~Gfyn~KAkrIk~lA~~Ive~yGgiDLe~Lr~vP~deareeLLsLpGIGpKTAd~ILLf 518 (960)
++..--|.....|+.| .+. |-.+++.|...+ .+.|.+++|||+++|+-|...
T Consensus 6 ~L~~I~Gig~~~a~~L-------~~~-G~~t~~~l~~a~----~~~L~~i~Gig~~~a~~i~~~ 57 (60)
T PF14520_consen 6 DLLSIPGIGPKRAEKL-------YEA-GIKTLEDLANAD----PEELAEIPGIGEKTAEKIIEA 57 (60)
T ss_dssp HHHTSTTCHHHHHHHH-------HHT-TCSSHHHHHTSH----HHHHHTSTTSSHHHHHHHHHH
T ss_pred hhccCCCCCHHHHHHH-------Hhc-CCCcHHHHHcCC----HHHHhcCCCCCHHHHHHHHHH
Confidence 3444456666555444 332 333567777665 458999999999999988654
No 35
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=82.77 E-value=2.9 Score=44.45 Aligned_cols=62 Identities=19% Similarity=0.192 Sum_probs=42.0
Q ss_pred CCCCCHHHHHcCCHHHHHHHHhhcCChHHHHHHHH------HHHHHHHHhcCCCCchhhhcCChHHHHHHHHhCCCccHH
Q 002141 437 KDSLDWEAVRCADVNKIANTIKERGMNNMLAGRIK------DFLNRLVRDHGSVDLEWLRDVPPDKAKEYLLSFRGLGLK 510 (960)
Q Consensus 437 ~g~~TpEaLA~As~eELeeLIRp~Gfyn~KAkrIk------~lA~~Ive~yGgiDLe~Lr~vP~deareeLLsLpGIGpK 510 (960)
.|+.+.+.. +-...+|.-.|...+.|-.|. +++++|.. ++ .+.|.++||||+|
T Consensus 60 YGF~t~~Er-----~lF~~LisVsGIGPK~ALaILs~~~~~el~~aI~~--~D--------------~~~L~~vpGIGkK 118 (196)
T PRK13901 60 FGFLNSSER-----EVFEELIGVDGIGPRAALRVLSGIKYNEFRDAIDR--ED--------------IELISKVKGIGNK 118 (196)
T ss_pred eCCCCHHHH-----HHHHHHhCcCCcCHHHHHHHHcCCCHHHHHHHHHh--CC--------------HHHHhhCCCCCHH
Confidence 466666553 334556666777777777766 45555543 22 5789999999999
Q ss_pred HHHHHHHHh
Q 002141 511 SVECVRLLT 519 (960)
Q Consensus 511 TAd~ILLfa 519 (960)
||+-|++--
T Consensus 119 tAeRIIlEL 127 (196)
T PRK13901 119 MAGKIFLKL 127 (196)
T ss_pred HHHHHHHHH
Confidence 999887543
No 36
>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=80.98 E-value=3.4 Score=36.08 Aligned_cols=58 Identities=19% Similarity=0.255 Sum_probs=37.3
Q ss_pred HHHcCCHHHHHHHHhhcCChHHHHHHHHHHHHHHHHhcCCCCchhhhcCChHHHHHHHHhCCCccHHHHHHHHHH
Q 002141 444 AVRCADVNKIANTIKERGMNNMLAGRIKDFLNRLVRDHGSVDLEWLRDVPPDKAKEYLLSFRGLGLKSVECVRLL 518 (960)
Q Consensus 444 aLA~As~eELeeLIRp~Gfyn~KAkrIk~lA~~Ive~yGgiDLe~Lr~vP~deareeLLsLpGIGpKTAd~ILLf 518 (960)
.|-.|+.++|..++..+|. .+|+.|... . ..+|++. + .++|..++|||.++|+-|+.|
T Consensus 9 nvNta~~~~L~~~ipgig~--~~a~~Il~~---R-~~~g~~~---------s--~~dL~~v~gi~~~~~~~i~~~ 66 (69)
T TIGR00426 9 NINTATAEELQRAMNGVGL--KKAEAIVSY---R-EEYGPFK---------T--VEDLKQVPGIGNSLVEKNLAV 66 (69)
T ss_pred ECcCCCHHHHHhHCCCCCH--HHHHHHHHH---H-HHcCCcC---------C--HHHHHcCCCCCHHHHHHHHhh
Confidence 3445777888776555554 455444332 1 1245431 2 578999999999999998876
No 37
>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=78.81 E-value=1.3 Score=46.52 Aligned_cols=59 Identities=10% Similarity=0.112 Sum_probs=42.3
Q ss_pred CcHHHHHHHHHHcCCCCCCCCCCCCCCCHHHHHcCCHHHHHHHHhhcCChH--HHHHHHHHHHHHHHH
Q 002141 414 FDWDSLRRQVEANGGKKERPEHTKDSLDWEAVRCADVNKIANTIKERGMNN--MLAGRIKDFLNRLVR 479 (960)
Q Consensus 414 T~W~nL~kaL~nL~~k~er~~~~~g~~TpEaLA~As~eELeeLIRp~Gfyn--~KAkrIk~lA~~Ive 479 (960)
-.|..+.+--.+ ...+...++++.++..++++|+.++..-|.-+ .|.+.+..=|+.+.+
T Consensus 43 LSW~tIL~Kr~~-------fr~aF~~Fd~~~VA~~~e~~ie~L~~d~~IIRnr~KI~Avi~NA~~~l~ 103 (179)
T TIGR00624 43 LSWITVLRKREN-------YRRAFSGFDIVKVARMTDADVERLLQDDGIIRNRGKIEATIANARAALQ 103 (179)
T ss_pred CCHHHHHHhHHH-------HHHHHcCCCHHHHhCCCHHHHHHHhcCccchhhHHHHHHHHHHHHHHHH
Confidence 367777654333 23356889999999999999999999999865 444445555566554
No 38
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=77.99 E-value=4 Score=43.87 Aligned_cols=62 Identities=23% Similarity=0.308 Sum_probs=45.8
Q ss_pred cCCHHHHHHHHhhcCChHHHHH-HHHHHHHHHHHhc---CCCCchhhhcCChHHHHHHHHhCCCccHHHHHHHHH
Q 002141 447 CADVNKIANTIKERGMNNMLAG-RIKDFLNRLVRDH---GSVDLEWLRDVPPDKAKEYLLSFRGLGLKSVECVRL 517 (960)
Q Consensus 447 ~As~eELeeLIRp~Gfyn~KAk-rIk~lA~~Ive~y---GgiDLe~Lr~vP~deareeLLsLpGIGpKTAd~ILL 517 (960)
.++..||.++|=..|..+ + -.+.+|+.+.+.| | +|..+...+. ++|.+++|||+..|..++.
T Consensus 13 ~Lsd~ELLailL~~g~~~---~~~~~~lA~~ll~~f~~~g--~l~~l~~a~~----~eL~~i~GiG~aka~~l~a 78 (218)
T TIGR00608 13 ALSDYELLAIILRTGTPK---GLDVLSLSKRLLDVFGRQD--SLGHLLSAPP----EELSSVPGIGEAKAIQLKA 78 (218)
T ss_pred cCCHHHHHHHHHhCCCCC---CCCHHHHHHHHHHHhcccC--CHHHHHhCCH----HHHHhCcCCcHHHHHHHHH
Confidence 456677777766667643 3 5668899999888 6 4788888874 5899999999977766653
No 39
>PRK00024 hypothetical protein; Reviewed
Probab=76.98 E-value=4.1 Score=43.80 Aligned_cols=63 Identities=21% Similarity=0.299 Sum_probs=45.6
Q ss_pred HcCCHHHHHHHHhhcCChHHHHHHHHHHHHHHHHhcCCCCchhhhcCChHHHHHHHHhCCCccHHHHHHHHH
Q 002141 446 RCADVNKIANTIKERGMNNMLAGRIKDFLNRLVRDHGSVDLEWLRDVPPDKAKEYLLSFRGLGLKSVECVRL 517 (960)
Q Consensus 446 A~As~eELeeLIRp~Gfyn~KAkrIk~lA~~Ive~yGgiDLe~Lr~vP~deareeLLsLpGIGpKTAd~ILL 517 (960)
..++..||.++|=..|..+ +-.+.+|+.+.++||+ |..+...+. ++|.+++|||+..|..++.
T Consensus 22 ~~Lsd~ELLa~lL~~g~~~---~~~~~LA~~LL~~fgs--L~~l~~as~----~eL~~i~GIG~akA~~L~a 84 (224)
T PRK00024 22 AALSDAELLAILLRTGTKG---KSVLDLARELLQRFGS--LRGLLDASL----EELQSIKGIGPAKAAQLKA 84 (224)
T ss_pred ccCCHHHHHHHHHcCCCCC---CCHHHHHHHHHHHcCC--HHHHHhCCH----HHHhhccCccHHHHHHHHH
Confidence 3456667777665666644 4456778899988875 677777774 5899999999998866643
No 40
>PRK00076 recR recombination protein RecR; Reviewed
Probab=76.45 E-value=2.5 Score=45.05 Aligned_cols=28 Identities=29% Similarity=0.338 Sum_probs=22.2
Q ss_pred hHHHHHHHHhCCCccHHHHHHHHHHhcC
Q 002141 494 PDKAKEYLLSFRGLGLKSVECVRLLTLH 521 (960)
Q Consensus 494 ~deareeLLsLpGIGpKTAd~ILLfafg 521 (960)
-+++.+.|.+|||||+|||.=+.++-+.
T Consensus 6 ~~~Li~~l~~LPGIG~KsA~Rla~~ll~ 33 (196)
T PRK00076 6 IEKLIEALRKLPGIGPKSAQRLAFHLLQ 33 (196)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHHHc
Confidence 3578899999999999999766555443
No 41
>PRK13844 recombination protein RecR; Provisional
Probab=76.36 E-value=2.5 Score=45.16 Aligned_cols=28 Identities=25% Similarity=0.223 Sum_probs=22.5
Q ss_pred hHHHHHHHHhCCCccHHHHHHHHHHhcC
Q 002141 494 PDKAKEYLLSFRGLGLKSVECVRLLTLH 521 (960)
Q Consensus 494 ~deareeLLsLpGIGpKTAd~ILLfafg 521 (960)
-+++.+.|.+|||||+|+|.=+.++-+.
T Consensus 10 ~~~LI~~l~~LPGIG~KsA~Rla~~lL~ 37 (200)
T PRK13844 10 ISAVIESLRKLPTIGKKSSQRLALYLLD 37 (200)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHHHc
Confidence 4678999999999999999766655543
No 42
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=76.24 E-value=2.5 Score=44.93 Aligned_cols=28 Identities=29% Similarity=0.310 Sum_probs=22.2
Q ss_pred hHHHHHHHHhCCCccHHHHHHHHHHhcC
Q 002141 494 PDKAKEYLLSFRGLGLKSVECVRLLTLH 521 (960)
Q Consensus 494 ~deareeLLsLpGIGpKTAd~ILLfafg 521 (960)
-+++.+.|.+|||||+|||.=+.++-+.
T Consensus 6 ~~~Li~~l~~LPGIG~KsA~RlA~~ll~ 33 (195)
T TIGR00615 6 ISKLIESLKKLPGIGPKSAQRLAFHLLK 33 (195)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHHHc
Confidence 4578999999999999999766555443
No 43
>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=75.69 E-value=3.3 Score=43.53 Aligned_cols=63 Identities=19% Similarity=0.341 Sum_probs=41.7
Q ss_pred CcHHHHHHHHHHcCCCCCCCCCCCCCCCHHHHHcCCHHHHHHHHhhcCC--hHHHHHHHHHHHHHHHH---hcCC
Q 002141 414 FDWDSLRRQVEANGGKKERPEHTKDSLDWEAVRCADVNKIANTIKERGM--NNMLAGRIKDFLNRLVR---DHGS 483 (960)
Q Consensus 414 T~W~nL~kaL~nL~~k~er~~~~~g~~TpEaLA~As~eELeeLIRp~Gf--yn~KAkrIk~lA~~Ive---~yGg 483 (960)
-+|..+.+--..+ ..+...++++.|+..++++|++++..-|. +++|.+.+..=|+.+.+ +||+
T Consensus 39 LsW~~Il~Kr~~~-------r~aF~~Fd~~~vA~~~e~~ie~l~~d~~iIRnr~KI~Avi~NA~~~l~i~~e~gs 106 (179)
T PF03352_consen 39 LSWSTILKKREAF-------REAFAGFDPEKVAKMDEEDIERLMQDPGIIRNRRKIRAVINNARAILKIQEEFGS 106 (179)
T ss_dssp S-HHHHHHTHHHH-------HHHTGGGHHHHHHT--HHHHHHHTTSTTSS--HHHHHHHHHHHHHHHHHHHTTS-
T ss_pred CCHHHHHHHHHHH-------HHHHHCCCHHHHHcCCHHHHHHHhcCcchhhhHHHHHHHHHHHHHHHHHHHhcCC
Confidence 4677766532222 22467799999999999999999999998 56777777766666543 4554
No 44
>PF09171 DUF1886: Domain of unknown function (DUF1886); InterPro: IPR015254 This entry represents a set of known and suspected archaeal N-glycosylase/DNA lyases. These DNA repair enzymes are part of the base excision repair (BER) pathway; they protect from oxidative damage by removing the major product of DNA oxidation, 8-oxoguanine (GO), from single- and double-stranded DNA substrates [].Cleavage of the N-glycosidic bond between the aberrant base and the sugar-phosphate backbone generates an apurinic (AP) site. Subsequently, the phosphodiester bond 3' from the AP site is cleaved by an elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate. The protein contains two alpha-helical subdomains, with the 8-oxoguanine binding site located in a cleft at their interface. A helix-hairpin-helix (HhH) structural motif and a Gly/Pro-rich sequence followed by a conserved Asp (HhH-GPD motif) are present [].; GO: 0003906 DNA-(apurinic or apyrimidinic site) lyase activity, 0016799 hydrolase activity, hydrolyzing N-glycosyl compounds; PDB: 1XQP_A 1XQO_A 1XG7_A.
Probab=75.56 E-value=7.4 Score=42.89 Aligned_cols=133 Identities=14% Similarity=0.110 Sum_probs=74.1
Q ss_pred HHHHHHHhhc----CChHHHHHHHHHHHHHHHHhcCCCCchhhhc--CChHHHHHHHHhCCCcc--H-------HHHHHH
Q 002141 451 NKIANTIKER----GMNNMLAGRIKDFLNRLVRDHGSVDLEWLRD--VPPDKAKEYLLSFRGLG--L-------KSVECV 515 (960)
Q Consensus 451 eELeeLIRp~----Gfyn~KAkrIk~lA~~Ive~yGgiDLe~Lr~--vP~deareeLLsLpGIG--p-------KTAd~I 515 (960)
+++...|... -+.++|.++|+.++..+.. +.+..... -.-..+++.|..+=|-. . |++...
T Consensus 77 ~~~~~FL~~s~~n~r~~~~KikRl~k~~~~~~~----l~l~~~~~~y~~l~~l~~~La~~L~~~~~~KTiVFAvKM~~Ya 152 (246)
T PF09171_consen 77 EAFIEFLSNSKYNRRLLEQKIKRLRKFCPFLEN----LSLQDNPLYYEDLEELWRELAKILNSKPESKTIVFAVKMFGYA 152 (246)
T ss_dssp HHHHHHCCC-TTS-TTHHHHHHHHHHHCCHHHT----T-HHHHHHHHCTHHHHHHHHHHHHTS-TTSHHHHHHHHHHHHH
T ss_pred HHHHHHHhhCcchHHHHHHHHHHHHHHHHHHHH----hhhhhhhhhhhhHHHHHHHHHHHhCCCCccchhhHHHHHHHHH
Confidence 4455556543 3456899999998776542 12222221 23345567777765544 2 334444
Q ss_pred HHHhcCC--e-----eeecchHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCchHHHHHhhhhhhhcCChhhHHHHHHHHH
Q 002141 516 RLLTLHH--L-----AFPVDTNVGRIAVRLGWVPLQPLPESLQLHLLELYPVLESIQKYLWPRLCKLDQRTLYELHYQMI 588 (960)
Q Consensus 516 LLfafgr--p-----vfpVDThV~RIl~RLG~V~~~~tpEklek~LeellP~~e~Iqk~LW~rL~klD~e~l~EfH~lLV 588 (960)
+..+||. + -+|||.++.++..++|++.. .++. +. .. +......|..+++...-.+-+++..||
T Consensus 153 ~r~~~g~~~~~p~~IpIPvD~Rva~~T~~sGi~~~--~~~~----~~-~~---~~~v~~~W~~Va~~sgIpplhLDs~lW 222 (246)
T PF09171_consen 153 CRIAFGEFRPYPEEIPIPVDYRVAKLTKRSGIIEC--EREE----MM-RT---REEVQKAWREVAKESGIPPLHLDSLLW 222 (246)
T ss_dssp HHHHCTS-----TTS-----HHHHHHHHCTTS-SS---HHH----HH-CT---CCHHHHHHHHHHHHHT--HHHHHHHHH
T ss_pred HHHhcCCCCCCcccCCCCccHHHHHHHHHhccccc--cHHh----hh-cc---HHHHHHHHHHHHhhcCCCchhhhhHHH
Confidence 4445565 2 58999999999999999763 2221 11 11 122346788776655566789999999
Q ss_pred -HHhHhhccc
Q 002141 589 -TFGKVFCTK 597 (960)
Q Consensus 589 -efGK~ICt~ 597 (960)
-+|+..+..
T Consensus 223 ~l~G~~~~~~ 232 (246)
T PF09171_consen 223 PLLGRARDVK 232 (246)
T ss_dssp HHHCCHHCCT
T ss_pred Hhcccchhhh
Confidence 999987654
No 45
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=74.72 E-value=3.7 Score=41.41 Aligned_cols=52 Identities=23% Similarity=0.308 Sum_probs=34.4
Q ss_pred HHHcCCHHHHHHHHhhcCChHHHHHHHHHHHHHHHHhcCCCCchhhhcCChHHHHHHHHhCCCccHHHHHHHHH
Q 002141 444 AVRCADVNKIANTIKERGMNNMLAGRIKDFLNRLVRDHGSVDLEWLRDVPPDKAKEYLLSFRGLGLKSVECVRL 517 (960)
Q Consensus 444 aLA~As~eELeeLIRp~Gfyn~KAkrIk~lA~~Ive~yGgiDLe~Lr~vP~deareeLLsLpGIGpKTAd~ILL 517 (960)
+|-.|+.+++.. --|++..+|+.|. + +|.| -. .++|+++||||+++.+.+--
T Consensus 54 diN~A~~~el~~---lpGigP~~A~~IV-------~-nGpf-------~s----veDL~~V~GIgekqk~~l~k 105 (132)
T PRK02515 54 DLNNSSVRAFRQ---FPGMYPTLAGKIV-------K-NAPY-------DS----VEDVLNLPGLSERQKELLEA 105 (132)
T ss_pred cCCccCHHHHHH---CCCCCHHHHHHHH-------H-CCCC-------CC----HHHHHcCCCCCHHHHHHHHH
Confidence 355666666644 3688888887776 2 4543 11 56889999999887766543
No 46
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=73.02 E-value=8.5 Score=40.60 Aligned_cols=21 Identities=24% Similarity=0.256 Sum_probs=18.4
Q ss_pred HHHHHhCCCccHHHHHHHHHH
Q 002141 498 KEYLLSFRGLGLKSVECVRLL 518 (960)
Q Consensus 498 reeLLsLpGIGpKTAd~ILLf 518 (960)
.+.|.++||||+|||+-|.+-
T Consensus 107 ~~~L~~vpGIGkKtAerIilE 127 (188)
T PRK14606 107 VEGLSKLPGISKKTAERIVME 127 (188)
T ss_pred HHHHhhCCCCCHHHHHHHHHH
Confidence 578999999999999988744
No 47
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=72.75 E-value=8.7 Score=40.46 Aligned_cols=25 Identities=20% Similarity=0.170 Sum_probs=20.0
Q ss_pred HHHHHhCCCccHHHHHHHHHHhcCC
Q 002141 498 KEYLLSFRGLGLKSVECVRLLTLHH 522 (960)
Q Consensus 498 reeLLsLpGIGpKTAd~ILLfafgr 522 (960)
.+.|.++||||+|||+-|++---++
T Consensus 107 ~~~L~~vpGIGkKtAeRIilELkdK 131 (183)
T PRK14601 107 ESVLKKVPGIGPKSAKRIIAELSDA 131 (183)
T ss_pred HHHHhhCCCCCHHHHHHHHHHHHHH
Confidence 6789999999999999887543333
No 48
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=72.73 E-value=5.7 Score=41.61 Aligned_cols=21 Identities=29% Similarity=0.346 Sum_probs=18.3
Q ss_pred HHHHHhCCCccHHHHHHHHHH
Q 002141 498 KEYLLSFRGLGLKSVECVRLL 518 (960)
Q Consensus 498 reeLLsLpGIGpKTAd~ILLf 518 (960)
.+.|.++||||+|+|+.|+..
T Consensus 107 ~~~L~~v~Gig~k~A~~I~~~ 127 (192)
T PRK00116 107 VKALTKVPGIGKKTAERIVLE 127 (192)
T ss_pred HHHHHhCCCCCHHHHHHHHHH
Confidence 468999999999999999854
No 49
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=71.05 E-value=3.8 Score=43.74 Aligned_cols=28 Identities=25% Similarity=0.317 Sum_probs=21.6
Q ss_pred hHHHHHHHHhCCCccHHHHHHHHHHhcC
Q 002141 494 PDKAKEYLLSFRGLGLKSVECVRLLTLH 521 (960)
Q Consensus 494 ~deareeLLsLpGIGpKTAd~ILLfafg 521 (960)
-+++++.|.+|||||+|+|.=+..+-+.
T Consensus 7 i~~LI~~l~kLPGvG~KsA~R~AfhLL~ 34 (198)
T COG0353 7 IEKLIDALKKLPGVGPKSAQRLAFHLLQ 34 (198)
T ss_pred HHHHHHHHhhCCCCChhHHHHHHHHHHc
Confidence 3568999999999999999655544443
No 50
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=69.26 E-value=10 Score=40.32 Aligned_cols=21 Identities=33% Similarity=0.344 Sum_probs=18.2
Q ss_pred HHHHHhCCCccHHHHHHHHHH
Q 002141 498 KEYLLSFRGLGLKSVECVRLL 518 (960)
Q Consensus 498 reeLLsLpGIGpKTAd~ILLf 518 (960)
.+.|.++||||+|||+-|++-
T Consensus 106 ~~~L~kvpGIGkKtAerIilE 126 (197)
T PRK14603 106 ARLLTSASGVGKKLAERIALE 126 (197)
T ss_pred HHHHhhCCCCCHHHHHHHHHH
Confidence 678999999999999988743
No 51
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=68.37 E-value=11 Score=40.11 Aligned_cols=21 Identities=29% Similarity=0.330 Sum_probs=18.4
Q ss_pred HHHHHhCCCccHHHHHHHHHH
Q 002141 498 KEYLLSFRGLGLKSVECVRLL 518 (960)
Q Consensus 498 reeLLsLpGIGpKTAd~ILLf 518 (960)
.+.|.++||||+|||+-|++-
T Consensus 107 ~~~L~kvpGIGkKtAerIilE 127 (195)
T PRK14604 107 VARLARVPGIGKKTAERIVLE 127 (195)
T ss_pred HHHHhhCCCCCHHHHHHHHHH
Confidence 678999999999999988754
No 52
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=68.33 E-value=12 Score=39.76 Aligned_cols=21 Identities=24% Similarity=0.298 Sum_probs=18.4
Q ss_pred HHHHHhCCCccHHHHHHHHHH
Q 002141 498 KEYLLSFRGLGLKSVECVRLL 518 (960)
Q Consensus 498 reeLLsLpGIGpKTAd~ILLf 518 (960)
.+.|.++||||+|||+-|++-
T Consensus 108 ~~~L~~ipGIGkKtAerIilE 128 (203)
T PRK14602 108 VAALTRVSGIGKKTAQHIFLE 128 (203)
T ss_pred HHHHhcCCCcCHHHHHHHHHH
Confidence 578999999999999988744
No 53
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=68.31 E-value=12 Score=39.60 Aligned_cols=64 Identities=19% Similarity=0.196 Sum_probs=37.2
Q ss_pred CCCCCHHHHHcCCHHHHHHHHhhcCChHHHHHHHHHHHHHHHHhcCCCCchhh-hcC-ChHHHHHHHHhCCCccHHHHHH
Q 002141 437 KDSLDWEAVRCADVNKIANTIKERGMNNMLAGRIKDFLNRLVRDHGSVDLEWL-RDV-PPDKAKEYLLSFRGLGLKSVEC 514 (960)
Q Consensus 437 ~g~~TpEaLA~As~eELeeLIRp~Gfyn~KAkrIk~lA~~Ive~yGgiDLe~L-r~v-P~deareeLLsLpGIGpKTAd~ 514 (960)
.|+.+.+.- +-...+|.-.|...+.|..|... + +.+.| ..+ ..| .+.|.++||||+|||+-
T Consensus 61 yGF~~~~Er-----~lF~~Li~V~GIGpK~Al~ILs~-------~---~~~~l~~aI~~~D--~~~L~~vpGIGkKtAer 123 (194)
T PRK14605 61 FGFATTEEL-----SLFETLIDVSGIGPKLGLAMLSA-------M---NAEALASAIISGN--AELLSTIPGIGKKTASR 123 (194)
T ss_pred eCCCCHHHH-----HHHHHHhCCCCCCHHHHHHHHHh-------C---CHHHHHHHHHhCC--HHHHHhCCCCCHHHHHH
Confidence 355555542 23445566667776666555542 1 12221 112 222 56899999999999998
Q ss_pred HHH
Q 002141 515 VRL 517 (960)
Q Consensus 515 ILL 517 (960)
|++
T Consensus 124 Iil 126 (194)
T PRK14605 124 IVL 126 (194)
T ss_pred HHH
Confidence 653
No 54
>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=68.06 E-value=5.1 Score=34.23 Aligned_cols=26 Identities=27% Similarity=0.291 Sum_probs=21.7
Q ss_pred HHHHHHhCCCccHHHHHHHHHHhcCC
Q 002141 497 AKEYLLSFRGLGLKSVECVRLLTLHH 522 (960)
Q Consensus 497 areeLLsLpGIGpKTAd~ILLfafgr 522 (960)
+...|++++|||+++|..+.-.+++-
T Consensus 3 ~~~~L~~I~Gig~~~a~~L~~~G~~t 28 (60)
T PF14520_consen 3 VFDDLLSIPGIGPKRAEKLYEAGIKT 28 (60)
T ss_dssp HHHHHHTSTTCHHHHHHHHHHTTCSS
T ss_pred HHHhhccCCCCCHHHHHHHHhcCCCc
Confidence 46789999999999998887776654
No 55
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=67.32 E-value=8.4 Score=39.22 Aligned_cols=55 Identities=20% Similarity=0.321 Sum_probs=37.6
Q ss_pred HHcCCHHHHHHHHhhcCChHHHHHHHHHHHHHHHHhcCCCCchhhhcCChHHHHHHHHhCCCccHHHHHHHHH
Q 002141 445 VRCADVNKIANTIKERGMNNMLAGRIKDFLNRLVRDHGSVDLEWLRDVPPDKAKEYLLSFRGLGLKSVECVRL 517 (960)
Q Consensus 445 LA~As~eELeeLIRp~Gfyn~KAkrIk~lA~~Ive~yGgiDLe~Lr~vP~deareeLLsLpGIGpKTAd~ILL 517 (960)
|-.|+.++| +.|..+|- .||+.|.+ ..+.+|.| .. .+.|..++|||+++.+-+.-
T Consensus 91 iNtAs~eeL-~~lpgIG~--~kA~aIi~----yRe~~G~f-------~s----v~dL~~v~GiG~~~~ekl~~ 145 (149)
T COG1555 91 INTASAEEL-QALPGIGP--KKAQAIID----YREENGPF-------KS----VDDLAKVKGIGPKTLEKLKD 145 (149)
T ss_pred ccccCHHHH-HHCCCCCH--HHHHHHHH----HHHHcCCC-------Cc----HHHHHhccCCCHHHHHHHHh
Confidence 456777887 55555665 58877766 34556653 12 56899999999999876543
No 56
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=65.88 E-value=11 Score=40.98 Aligned_cols=90 Identities=23% Similarity=0.295 Sum_probs=59.4
Q ss_pred HcCCHHHHHHHHhhcCChHHHHHHHHHHHHHHHHhcCCCCchhhhcCChHHHHHHHHhCCCccHHHHHHHH-HHhcCCee
Q 002141 446 RCADVNKIANTIKERGMNNMLAGRIKDFLNRLVRDHGSVDLEWLRDVPPDKAKEYLLSFRGLGLKSVECVR-LLTLHHLA 524 (960)
Q Consensus 446 A~As~eELeeLIRp~Gfyn~KAkrIk~lA~~Ive~yGgiDLe~Lr~vP~deareeLLsLpGIGpKTAd~IL-Lfafgrpv 524 (960)
..++..||.+++=..|- |-+-.+.+|+.+.++||+ |..|...+ .++|.+++|||+.-|--+. +.-+
T Consensus 22 ~~Lsd~ELLailLrtG~---~~~~~~~la~~lL~~fg~--L~~l~~a~----~~el~~v~GiG~aka~~l~a~~El---- 88 (224)
T COG2003 22 EALSDAELLAILLRTGT---KGESVLDLAKELLQEFGS--LAELLKAS----VEELSSVKGIGLAKAIQIKAAIEL---- 88 (224)
T ss_pred hhcchHHHHHHHHhcCC---CCCCHHHHHHHHHHHccc--HHHHHhCC----HHHHhhCCCccHHHHHHHHHHHHH----
Confidence 34556778788777776 446677899999999987 67787777 5689999999976554333 3333
Q ss_pred eecchHHHHHHHHh---cCCCCCCCHHHHHHHHHH
Q 002141 525 FPVDTNVGRIAVRL---GWVPLQPLPESLQLHLLE 556 (960)
Q Consensus 525 fpVDThV~RIl~RL---G~V~~~~tpEklek~Lee 556 (960)
.+|++.+- |.+- .+|+.+...+..
T Consensus 89 ------~~R~~~~~~~~~~~i--~sp~~~~~~l~~ 115 (224)
T COG2003 89 ------GKRILAERLREGVVI--TSPEAVAEYLRA 115 (224)
T ss_pred ------HHHHHHHHhccCCcc--CCHHHHHHHHHH
Confidence 34554443 2222 466776666543
No 57
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=65.36 E-value=6.5 Score=41.40 Aligned_cols=65 Identities=22% Similarity=0.157 Sum_probs=40.0
Q ss_pred CCCCCHHHHHcCCHHHHHHHHhhcCChHHHHHHHHHHHHHHHHhcCCCCchhhh-cCC-hHHHHHHHHhCCCccHHHHHH
Q 002141 437 KDSLDWEAVRCADVNKIANTIKERGMNNMLAGRIKDFLNRLVRDHGSVDLEWLR-DVP-PDKAKEYLLSFRGLGLKSVEC 514 (960)
Q Consensus 437 ~g~~TpEaLA~As~eELeeLIRp~Gfyn~KAkrIk~lA~~Ive~yGgiDLe~Lr-~vP-~deareeLLsLpGIGpKTAd~ 514 (960)
.|+.|.+.- +-...+|+--|...++|..|... ++.+.|. .+- .| ...|.++||||+|||+-
T Consensus 60 yGF~~~~Er-----~lF~~L~~V~GIGpK~Al~iL~~----------~~~~el~~aI~~~d--~~~L~~ipGiGkKtAer 122 (191)
T TIGR00084 60 FGFNTLEER-----ELFKELIKVNGVGPKLALAILSN----------MSPEEFVYAIETEE--VKALVKIPGVGKKTAER 122 (191)
T ss_pred eCCCCHHHH-----HHHHHHhCCCCCCHHHHHHHHhc----------CCHHHHHHHHHhCC--HHHHHhCCCCCHHHHHH
Confidence 466665542 33456677778887777766332 1222222 111 12 46799999999999999
Q ss_pred HHHH
Q 002141 515 VRLL 518 (960)
Q Consensus 515 ILLf 518 (960)
|++-
T Consensus 123 Iile 126 (191)
T TIGR00084 123 LLLE 126 (191)
T ss_pred HHHH
Confidence 8843
No 58
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=65.02 E-value=6.6 Score=42.02 Aligned_cols=56 Identities=25% Similarity=0.249 Sum_probs=33.3
Q ss_pred HHHHHhhcCChHHHHHHHHHHHHHHHHhcCCCCchhhhcC-ChHHHHHHHHhCCCccHHHHHHHHHHh
Q 002141 453 IANTIKERGMNNMLAGRIKDFLNRLVRDHGSVDLEWLRDV-PPDKAKEYLLSFRGLGLKSVECVRLLT 519 (960)
Q Consensus 453 LeeLIRp~Gfyn~KAkrIk~lA~~Ive~yGgiDLe~Lr~v-P~deareeLLsLpGIGpKTAd~ILLfa 519 (960)
...+|+-.|...+-|-.|.. .+|++.|... ...+ ...|.++||||+|||+-|++--
T Consensus 72 F~~LisVnGIGpK~ALaiLs----------~~~~~~l~~aI~~~d-~~~L~k~PGIGkKtAerivleL 128 (201)
T COG0632 72 FRLLISVNGIGPKLALAILS----------NLDPEELAQAIANED-VKALSKIPGIGKKTAERIVLEL 128 (201)
T ss_pred HHHHHccCCccHHHHHHHHc----------CCCHHHHHHHHHhcC-hHhhhcCCCCCHHHHHHHHHHH
Confidence 45566667776644433322 2233333321 1111 6799999999999999877543
No 59
>TIGR00575 dnlj DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.
Probab=64.41 E-value=19 Score=44.47 Aligned_cols=61 Identities=10% Similarity=0.158 Sum_probs=35.5
Q ss_pred CCHHHHHcCCHHHHHHHHhhcCChHHHHHHHHHHHHHHHHhcCCCCchhhhcCChHHHHHHHHhCCCccHHHHHHHH
Q 002141 440 LDWEAVRCADVNKIANTIKERGMNNMLAGRIKDFLNRLVRDHGSVDLEWLRDVPPDKAKEYLLSFRGLGLKSVECVR 516 (960)
Q Consensus 440 ~TpEaLA~As~eELeeLIRp~Gfyn~KAkrIk~lA~~Ive~yGgiDLe~Lr~vP~deareeLLsLpGIGpKTAd~IL 516 (960)
-++.+|..+..++|..+ -||...+|..|.+..+.-.. .+-+++ =..+.|||||+++|..++
T Consensus 455 ~~~~Dl~~L~~~~L~~L---~GfG~Ksa~nIl~~Ie~sk~------------~~l~r~-L~aLgIpgVG~~~ak~L~ 515 (652)
T TIGR00575 455 RSVADLYALKKEDLLEL---EGFGEKSAQNLLNAIEKSKE------------KPLARL-LFALGIRHVGEVTAKNLA 515 (652)
T ss_pred CCHHHHHhcCHHHHhhc---cCccHHHHHHHHHHHHHhcc------------CcHHHH-HhhccCCCcCHHHHHHHH
Confidence 37888888887776543 47777777777665543221 121221 234456677776666554
No 60
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=64.21 E-value=11 Score=39.84 Aligned_cols=60 Identities=23% Similarity=0.258 Sum_probs=36.0
Q ss_pred CCCCCHHHHHcCCHHHHHHHHhhcCChHHHHHHHHH------HHHHHHHhcCCCCchhhhcCChHHHHHHHHhCCCccHH
Q 002141 437 KDSLDWEAVRCADVNKIANTIKERGMNNMLAGRIKD------FLNRLVRDHGSVDLEWLRDVPPDKAKEYLLSFRGLGLK 510 (960)
Q Consensus 437 ~g~~TpEaLA~As~eELeeLIRp~Gfyn~KAkrIk~------lA~~Ive~yGgiDLe~Lr~vP~deareeLLsLpGIGpK 510 (960)
.|+.|.+.. +-...+|.-.|...+.|-.|.. +.+.|.. + | .+.| ++||||+|
T Consensus 61 yGF~~~~Er-----~lF~~LisV~GIGpK~Al~iLs~~~~~~l~~aI~~--~------------D--~~~L-~vpGIGkK 118 (186)
T PRK14600 61 YGFLNREEQ-----DCLRMLVKVSGVNYKTAMSILSKLTPEQLFSAIVN--E------------D--KAAL-KVNGIGEK 118 (186)
T ss_pred eCCCCHHHH-----HHHHHHhCcCCcCHHHHHHHHccCCHHHHHHHHHc--C------------C--Hhhe-ECCCCcHH
Confidence 366655542 3344555666776666655544 2222322 1 2 4678 99999999
Q ss_pred HHHHHHHH
Q 002141 511 SVECVRLL 518 (960)
Q Consensus 511 TAd~ILLf 518 (960)
||+-|++-
T Consensus 119 tAerIilE 126 (186)
T PRK14600 119 LINRIITE 126 (186)
T ss_pred HHHHHHHH
Confidence 99988754
No 61
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=61.96 E-value=36 Score=42.39 Aligned_cols=33 Identities=12% Similarity=0.095 Sum_probs=20.5
Q ss_pred CCHHHHHcCCHHHHHHHHhhcCChHHHHHHHHHHHH
Q 002141 440 LDWEAVRCADVNKIANTIKERGMNNMLAGRIKDFLN 475 (960)
Q Consensus 440 ~TpEaLA~As~eELeeLIRp~Gfyn~KAkrIk~lA~ 475 (960)
-++.+|..+..++|..+ -||...+|..|.+..+
T Consensus 468 ~~i~DL~~L~~~~L~~l---~gfG~Ksa~~ll~~Ie 500 (665)
T PRK07956 468 HDPADLFKLTAEDLLGL---EGFGEKSAQNLLDAIE 500 (665)
T ss_pred CCHHHHHhcCHHHHhcC---cCcchHHHHHHHHHHH
Confidence 47777777777665433 3777666666654433
No 62
>PF11731 Cdd1: Pathogenicity locus; InterPro: IPR021725 Cdd1 is expressed as part of the pathogenicity locus operon in several different orders of bacteria []. Many members of the family are annotated as being putative mitomycin resistance proteins but this could not be confirmed.
Probab=59.40 E-value=8.7 Score=36.73 Aligned_cols=27 Identities=22% Similarity=0.282 Sum_probs=21.8
Q ss_pred HHHHHHhCCCccHHHHHHHHHHhcCCe
Q 002141 497 AKEYLLSFRGLGLKSVECVRLLTLHHL 523 (960)
Q Consensus 497 areeLLsLpGIGpKTAd~ILLfafgrp 523 (960)
....|..|||||+.+|.-+...++..+
T Consensus 10 ~~~~L~~iP~IG~a~a~DL~~LGi~s~ 36 (93)
T PF11731_consen 10 GLSDLTDIPNIGKATAEDLRLLGIRSP 36 (93)
T ss_pred HHHHHhcCCCccHHHHHHHHHcCCCCH
Confidence 467899999999999988877666543
No 63
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=58.90 E-value=16 Score=41.45 Aligned_cols=51 Identities=14% Similarity=0.233 Sum_probs=32.1
Q ss_pred cCChHHHHHHHHHHHHHHHHhcCCCC-chhhhcCChHHHHHHHHhCCCccHHHHHHH
Q 002141 460 RGMNNMLAGRIKDFLNRLVRDHGSVD-LEWLRDVPPDKAKEYLLSFRGLGLKSVECV 515 (960)
Q Consensus 460 ~Gfyn~KAkrIk~lA~~Ive~yGgiD-Le~Lr~vP~deareeLLsLpGIGpKTAd~I 515 (960)
-|....-|+.|.++.+ .|.+. +.....-+...+..+|++++|||++||..+
T Consensus 54 pgIG~~ia~kI~Eil~-----tG~~~~~~e~l~~~~p~~l~~l~~i~GiGpk~a~~l 105 (334)
T smart00483 54 PGIGDKIKKKIEEIIE-----TGKSSKVLEILNDEVYKSLKLFTNVFGVGPKTAAKW 105 (334)
T ss_pred CCccHHHHHHHHHHHH-----hCcHHHHHHHhcCcHHHHHHHHHccCCcCHHHHHHH
Confidence 4555556666666543 25544 222223333456889999999999998554
No 64
>PRK07945 hypothetical protein; Provisional
Probab=57.42 E-value=20 Score=40.62 Aligned_cols=61 Identities=11% Similarity=0.093 Sum_probs=42.2
Q ss_pred HHHHHHHhhcCChHHHHHHHHHHHHHHHHhcCCCCchhhhcCChHHHHHHHHhCCCccHHHHHHHHHH
Q 002141 451 NKIANTIKERGMNNMLAGRIKDFLNRLVRDHGSVDLEWLRDVPPDKAKEYLLSFRGLGLKSVECVRLL 518 (960)
Q Consensus 451 eELeeLIRp~Gfyn~KAkrIk~lA~~Ive~yGgiDLe~Lr~vP~deareeLLsLpGIGpKTAd~ILLf 518 (960)
++++.++.-.|=..-|++..+++|+.|.. .+. + .+..+.. ...|.+|||||.-||..|.-+
T Consensus 8 ~~~a~lle~~~~n~frv~ayr~aa~~~~~-~~~-~--~~~~~~~---~g~l~~~~giG~~~a~~i~e~ 68 (335)
T PRK07945 8 RRIAFLLERARADTYRVRAFRRAADVVEA-LDA-A--ERARRAR---AGSLTSLPGIGPKTAKVIAQA 68 (335)
T ss_pred HHHHHHHHHcCCChhhHHHHHHHHHHHHh-cCh-h--HHHHHHh---cCCcccCCCcCHHHHHHHHHH
Confidence 56777777778766788999999988864 221 1 1222211 116999999999999988765
No 65
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=57.35 E-value=27 Score=39.69 Aligned_cols=57 Identities=14% Similarity=0.098 Sum_probs=39.4
Q ss_pred HHHHHHHhhcCChHHHHHHHHHHHHHHHHhcCCCCchhhhcCChHHHHHHHHhCCCccHHHHHHHHHH
Q 002141 451 NKIANTIKERGMNNMLAGRIKDFLNRLVRDHGSVDLEWLRDVPPDKAKEYLLSFRGLGLKSVECVRLL 518 (960)
Q Consensus 451 eELeeLIRp~Gfyn~KAkrIk~lA~~Ive~yGgiDLe~Lr~vP~deareeLLsLpGIGpKTAd~ILLf 518 (960)
++|++++.-.|=...|+++.+.++..|.. ++. + +. . .+.|.+|||||+.+|+-|--+
T Consensus 11 ~~la~l~el~gen~~k~~ay~~Aa~~i~~-l~~-~------i~--~-~~~l~~lpgIG~~ia~kI~Ei 67 (334)
T smart00483 11 EILAENYEVFGENKRKCSYFRKAASVLKS-LPF-P------IN--S-MKDLKGLPGIGDKIKKKIEEI 67 (334)
T ss_pred HHHHHHHHHhcccHHHHHHHHHHHHHHHh-CCC-C------CC--C-HHHHhcCCCccHHHHHHHHHH
Confidence 45566666567666688888888887764 332 2 22 1 247899999999999988744
No 66
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=56.08 E-value=11 Score=32.87 Aligned_cols=21 Identities=24% Similarity=0.355 Sum_probs=17.2
Q ss_pred HHHHHhCCCccHHHHHHHHHH
Q 002141 498 KEYLLSFRGLGLKSVECVRLL 518 (960)
Q Consensus 498 reeLLsLpGIGpKTAd~ILLf 518 (960)
.++|.++||||++.|..|+.|
T Consensus 13 ~~eL~~lpgi~~~~A~~Iv~~ 33 (65)
T PF12836_consen 13 AEELQALPGIGPKQAKAIVEY 33 (65)
T ss_dssp HHHHHTSTT--HHHHHHHHHH
T ss_pred HHHHHHcCCCCHHHHHHHHHH
Confidence 578999999999999999876
No 67
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=55.63 E-value=28 Score=34.25 Aligned_cols=77 Identities=12% Similarity=0.146 Sum_probs=47.8
Q ss_pred CCCCCHHHHHcCCHHHHHH--HHhhcCChHHHHHHHHHHHHHHHHhcCCCCchhhhcCChHHHHHHHHhCCCccHHHHHH
Q 002141 437 KDSLDWEAVRCADVNKIAN--TIKERGMNNMLAGRIKDFLNRLVRDHGSVDLEWLRDVPPDKAKEYLLSFRGLGLKSVEC 514 (960)
Q Consensus 437 ~g~~TpEaLA~As~eELee--LIRp~Gfyn~KAkrIk~lA~~Ive~yGgiDLe~Lr~vP~deareeLLsLpGIGpKTAd~ 514 (960)
.|.-|+++|+.+....+.. +....|... ++|..+ . .+..|..++|||+..|..
T Consensus 14 ~GI~t~~~Ll~~~~~~~~r~~La~~~~i~~---~~l~~w---~-------------------~~AdL~ri~gi~~~~a~L 68 (122)
T PF14229_consen 14 AGIKTTGDLLEAGDTPLGRKALAKKLGISE---RNLLKW---V-------------------NQADLMRIPGIGPQYAEL 68 (122)
T ss_pred cCCCcHHHHHHcCCCHHHHHHHHHhcCCCH---HHHHHH---H-------------------hHHHhhhcCCCCHHHHHH
Confidence 4778999999988877766 666666653 222221 1 145788999999999987
Q ss_pred HHHHhcCCeeeecchHHHHHHHHh
Q 002141 515 VRLLTLHHLAFPVDTNVGRIAVRL 538 (960)
Q Consensus 515 ILLfafgrpvfpVDThV~RIl~RL 538 (960)
++--++.-..=....+..++..++
T Consensus 69 L~~AGv~Tv~~LA~~~p~~L~~~l 92 (122)
T PF14229_consen 69 LEHAGVDTVEELAQRNPQNLHQKL 92 (122)
T ss_pred HHHhCcCcHHHHHhCCHHHHHHHH
Confidence 766555433222334444444444
No 68
>PF02371 Transposase_20: Transposase IS116/IS110/IS902 family; InterPro: IPR003346 Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This family includes transposases for IS116, IS110 and IS902. It is often found with the transposase IS111A/IS1328/IS1533 family (see IPR002525 from INTERPRO) [, ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=55.22 E-value=8.8 Score=35.15 Aligned_cols=42 Identities=21% Similarity=0.222 Sum_probs=30.6
Q ss_pred HHHHhCCCccHHHHHHHHHHhcCCeeeecchHHHHHHHHhcCCCC
Q 002141 499 EYLLSFRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPL 543 (960)
Q Consensus 499 eeLLsLpGIGpKTAd~ILLfafgrpvfpVDThV~RIl~RLG~V~~ 543 (960)
+.|+++||||+-||..++....+...|. +...+...+|+.+.
T Consensus 2 ~~l~sipGig~~~a~~llaeigd~~rF~---~~~~l~~~~Gl~P~ 43 (87)
T PF02371_consen 2 ELLTSIPGIGPITAATLLAEIGDISRFK---SAKQLASYAGLAPR 43 (87)
T ss_pred chhcCCCCccHHHHHHHHHHHcCchhcc---cchhhhhccccccc
Confidence 4689999999999999998774433454 44455666788764
No 69
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=54.65 E-value=10 Score=38.70 Aligned_cols=22 Identities=23% Similarity=0.318 Sum_probs=19.6
Q ss_pred HHHHHhCCCccHHHHHHHHHHh
Q 002141 498 KEYLLSFRGLGLKSVECVRLLT 519 (960)
Q Consensus 498 reeLLsLpGIGpKTAd~ILLfa 519 (960)
-++|..|||||++.|.+|..|-
T Consensus 96 ~eeL~~lpgIG~~kA~aIi~yR 117 (149)
T COG1555 96 AEELQALPGIGPKKAQAIIDYR 117 (149)
T ss_pred HHHHHHCCCCCHHHHHHHHHHH
Confidence 5688999999999999998873
No 70
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=53.61 E-value=17 Score=33.96 Aligned_cols=57 Identities=23% Similarity=0.482 Sum_probs=35.7
Q ss_pred CHHHHHHHHhhcCChHHHHHHHHHHHHHHHHhcCCCCchhhhcCChHHHHHHHHh-CCCccHHHHHHHHH
Q 002141 449 DVNKIANTIKERGMNNMLAGRIKDFLNRLVRDHGSVDLEWLRDVPPDKAKEYLLS-FRGLGLKSVECVRL 517 (960)
Q Consensus 449 s~eELeeLIRp~Gfyn~KAkrIk~lA~~Ive~yGgiDLe~Lr~vP~deareeLLs-LpGIGpKTAd~ILL 517 (960)
...++...|...|+....|.+| .+.||.-.++.|++=|.. |+. ++|||-++||-|..
T Consensus 7 ~~~~~~~~L~~~gl~~~~a~kl-------~~~yg~~ai~~l~~nPY~-----L~~~i~gi~F~~aD~iA~ 64 (94)
T PF14490_consen 7 GLRELMAFLQEYGLSPKLAMKL-------YKKYGDDAIEILKENPYR-----LIEDIDGIGFKTADKIAL 64 (94)
T ss_dssp --HHHHHHHHHTT--HHHHHHH-------HHHH-TTHHHHHHH-STC-----CCB-SSSSBHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCCHHHHHHH-------HHHHhHHHHHHHHHChHH-----HHHHccCCCHHHHHHHHH
Confidence 3466777889999987555444 445666555666666643 555 89999999988744
No 71
>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=52.91 E-value=20 Score=33.19 Aligned_cols=64 Identities=13% Similarity=0.250 Sum_probs=44.5
Q ss_pred ceeeeeeeeccCCCCCCcccchhhhccCCceeEEecCChhhhcccCCHHHHHHHhhccceEeecccccccCCccc
Q 002141 863 YFQVNEVFADHDSSLKPINVPREWLWNLPRRTVYFGTSIPSIFKGLTTEGIQHCFWRGYVCVRGFDQKSRAPRPL 937 (960)
Q Consensus 863 YFQvNEVFaDh~SS~~PI~vpr~~iw~L~rr~vyfGtSv~sIfkglt~~~Iq~cF~~G~vCVR~Fdr~tr~PrpL 937 (960)
+|.-||||+-.....+||. .| +.++.|.+-...-.... ....-...-|+|=++||+.++.-|+|
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 7999999998887777765 33 34778887665443321 01112457899999999998887765
No 72
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this
Probab=52.77 E-value=20 Score=40.26 Aligned_cols=50 Identities=32% Similarity=0.537 Sum_probs=32.0
Q ss_pred cCChHHHHHHHHHHHHHHHHhcCCC-Cchhhhc-CChHHHHHHHHhCCCccHHHHHHHH
Q 002141 460 RGMNNMLAGRIKDFLNRLVRDHGSV-DLEWLRD-VPPDKAKEYLLSFRGLGLKSVECVR 516 (960)
Q Consensus 460 ~Gfyn~KAkrIk~lA~~Ive~yGgi-DLe~Lr~-vP~deareeLLsLpGIGpKTAd~IL 516 (960)
-|....-|..|.++.+. |.+ .++.|+. .| ....+|++++|||++||..+.
T Consensus 51 pgiG~~ia~kI~E~~~t-----G~~~~le~l~~~~~--~~l~~l~~i~GiGpk~a~~l~ 102 (307)
T cd00141 51 PGIGKKIAEKIEEILET-----GKLRKLEELREDVP--PGLLLLLRVPGVGPKTARKLY 102 (307)
T ss_pred CCccHHHHHHHHHHHHc-----CCHHHHHHHhccch--HHHHHHHcCCCCCHHHHHHHH
Confidence 35656677777776432 332 2344443 33 347899999999999996654
No 73
>PRK14973 DNA topoisomerase I; Provisional
Probab=52.07 E-value=19 Score=46.38 Aligned_cols=98 Identities=18% Similarity=0.126 Sum_probs=62.2
Q ss_pred CCCCCHHHHHcCCHHHHHHHHhhcCChHHHHHHHHHHHH-HHHHhcCCCCchhhhcCChHHHHHHHHhCCCccHHHHHHH
Q 002141 437 KDSLDWEAVRCADVNKIANTIKERGMNNMLAGRIKDFLN-RLVRDHGSVDLEWLRDVPPDKAKEYLLSFRGLGLKSVECV 515 (960)
Q Consensus 437 ~g~~TpEaLA~As~eELeeLIRp~Gfyn~KAkrIk~lA~-~Ive~yGgiDLe~Lr~vP~deareeLLsLpGIGpKTAd~I 515 (960)
.|+-++++++.|+.++|+.+ -|+..-.+..+...+. .+..- +-+.+.....+..+.+|++++|||++|++-.
T Consensus 821 ~G~~~~~d~~~a~p~~La~~---~g~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~el~~vkg~ge~t~~~l 893 (936)
T PRK14973 821 AGFDTPEDFCSVHPAYLALK---TGISPETICRHAKLVCEKLGRP----VPEKISKAAFERGRAELLSVPGLGETTLEKL 893 (936)
T ss_pred hcCCCHHHHHhcCHHHHhcC---CCCChhhHHHHHHHHHHHhcCC----CchhhhhhhhcccchhhhhccCCCHHHHHHH
Confidence 46779999999999998554 6998777777765555 44321 1222222222333566999999999999665
Q ss_pred HHHhcCCeeeecchHHHHHHHHhcCC
Q 002141 516 RLLTLHHLAFPVDTNVGRIAVRLGWV 541 (960)
Q Consensus 516 LLfafgrpvfpVDThV~RIl~RLG~V 541 (960)
-.-+.-.+.-.+-.-..|++.+-|+.
T Consensus 894 ~~ag~~~~e~l~~~d~~~la~~~~i~ 919 (936)
T PRK14973 894 YLAGVYDGDLLVSADPKKLAKVTGID 919 (936)
T ss_pred HHcCCCCHHHhccCCHHHHhhhcCCC
Confidence 54444443222222567777777764
No 74
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=51.47 E-value=12 Score=39.32 Aligned_cols=20 Identities=25% Similarity=0.275 Sum_probs=17.1
Q ss_pred HHHHHhCCCccHHHHHHHHH
Q 002141 498 KEYLLSFRGLGLKSVECVRL 517 (960)
Q Consensus 498 reeLLsLpGIGpKTAd~ILL 517 (960)
...|+.+||||+|||..||-
T Consensus 72 f~~L~~i~GIGpk~A~~il~ 91 (192)
T PRK00116 72 FRLLISVSGVGPKLALAILS 91 (192)
T ss_pred HHHHhcCCCCCHHHHHHHHH
Confidence 45789999999999988863
No 75
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=51.19 E-value=18 Score=44.91 Aligned_cols=21 Identities=24% Similarity=0.234 Sum_probs=18.4
Q ss_pred HHHHHhCCCccHHHHHHHHHH
Q 002141 498 KEYLLSFRGLGLKSVECVRLL 518 (960)
Q Consensus 498 reeLLsLpGIGpKTAd~ILLf 518 (960)
.++|++++|||+++|..|..|
T Consensus 540 ~e~l~~i~giG~~~a~si~~f 560 (669)
T PRK14350 540 LSKLLKIKGIGEKIALNIIEA 560 (669)
T ss_pred HHHHhhCCCccHHHHHHHHHH
Confidence 467999999999999999877
No 76
>TIGR01259 comE comEA protein. This model describes the ComEA protein in bacteria. The com E locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. Lesions in the loci has been variously described for the appearance of competence-related pheonotypes and impairment of competence, suggesting their intimate functional role in bacterial transformation.
Probab=50.98 E-value=13 Score=36.41 Aligned_cols=21 Identities=19% Similarity=0.264 Sum_probs=19.2
Q ss_pred HHHHHhCCCccHHHHHHHHHH
Q 002141 498 KEYLLSFRGLGLKSVECVRLL 518 (960)
Q Consensus 498 reeLLsLpGIGpKTAd~ILLf 518 (960)
.++|..|||||++.|..|+.|
T Consensus 67 ~~eL~~lpGIG~~~A~~Ii~~ 87 (120)
T TIGR01259 67 LEELQALPGIGPAKAKAIIEY 87 (120)
T ss_pred HHHHhcCCCCCHHHHHHHHHH
Confidence 568999999999999999877
No 77
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=50.68 E-value=12 Score=39.36 Aligned_cols=23 Identities=17% Similarity=0.185 Sum_probs=19.4
Q ss_pred HHHHHHHHhCCCccHHHHHHHHH
Q 002141 495 DKAKEYLLSFRGLGLKSVECVRL 517 (960)
Q Consensus 495 deareeLLsLpGIGpKTAd~ILL 517 (960)
.++-..|++++|||||+|-.||.
T Consensus 68 r~lF~~L~~V~GIGpK~Al~iL~ 90 (191)
T TIGR00084 68 RELFKELIKVNGVGPKLALAILS 90 (191)
T ss_pred HHHHHHHhCCCCCCHHHHHHHHh
Confidence 35678899999999999988854
No 78
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=50.04 E-value=24 Score=30.82 Aligned_cols=54 Identities=20% Similarity=0.319 Sum_probs=30.4
Q ss_pred HHcCCHHHHHHHHhhcCChHHHHHHHHHHHHHHHHhcCCCCchhhhcCChHHHHHHHHhCCCccHHHHHHHH
Q 002141 445 VRCADVNKIANTIKERGMNNMLAGRIKDFLNRLVRDHGSVDLEWLRDVPPDKAKEYLLSFRGLGLKSVECVR 516 (960)
Q Consensus 445 LA~As~eELeeLIRp~Gfyn~KAkrIk~lA~~Ive~yGgiDLe~Lr~vP~deareeLLsLpGIGpKTAd~IL 516 (960)
|-.|+.++|.. --|+....|+.|.+. .+.+|+| .. .++|..++|||+++.+-+.
T Consensus 8 iN~as~~eL~~---lpgi~~~~A~~Iv~~----R~~~G~f-------~s----~~dL~~v~gi~~~~~~~l~ 61 (65)
T PF12836_consen 8 INTASAEELQA---LPGIGPKQAKAIVEY----REKNGPF-------KS----LEDLKEVPGIGPKTYEKLK 61 (65)
T ss_dssp TTTS-HHHHHT---STT--HHHHHHHHHH----HHHH-S--------SS----GGGGGGSTT--HHHHHHHC
T ss_pred CccCCHHHHHH---cCCCCHHHHHHHHHH----HHhCcCC-------CC----HHHHhhCCCCCHHHHHHHH
Confidence 34566666532 238888888888763 3334553 12 4589999999999987663
No 79
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=49.31 E-value=28 Score=43.24 Aligned_cols=56 Identities=25% Similarity=0.306 Sum_probs=35.0
Q ss_pred HHHHHhhcCChHHHHHHHHHHHHHHHHhcCCCCchhhhcCChHHHHHHHHhCCCccHHHHHHHHHH
Q 002141 453 IANTIKERGMNNMLAGRIKDFLNRLVRDHGSVDLEWLRDVPPDKAKEYLLSFRGLGLKSVECVRLL 518 (960)
Q Consensus 453 LeeLIRp~Gfyn~KAkrIk~lA~~Ive~yGgiDLe~Lr~vP~deareeLLsLpGIGpKTAd~ILLf 518 (960)
|..+|-.+|....-...-+. +...|+ +++.|...+ .++|.+++|||.+.|..|.-|
T Consensus 507 l~r~l~aLGIr~VG~~~Ak~----La~~f~--sl~~l~~a~----~e~l~~i~giG~~vA~si~~f 562 (667)
T COG0272 507 LARFLYALGIRHVGETTAKS----LARHFG--TLEALLAAS----EEELASIPGIGEVVARSIIEF 562 (667)
T ss_pred HHHHHHHcCCchhhHHHHHH----HHHHhh--hHHHHHhcC----HHHHhhccchhHHHHHHHHHH
Confidence 34444455554433333333 333444 367777777 458999999999999988765
No 80
>TIGR01259 comE comEA protein. This model describes the ComEA protein in bacteria. The com E locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. Lesions in the loci has been variously described for the appearance of competence-related pheonotypes and impairment of competence, suggesting their intimate functional role in bacterial transformation.
Probab=48.28 E-value=26 Score=34.42 Aligned_cols=59 Identities=19% Similarity=0.300 Sum_probs=38.6
Q ss_pred HHHHHcCCHHHHHHHHhhcCChHHHHHHHHHHHHHHHHhcCCCCchhhhcCChHHHHHHHHhCCCccHHHHHHHHHH
Q 002141 442 WEAVRCADVNKIANTIKERGMNNMLAGRIKDFLNRLVRDHGSVDLEWLRDVPPDKAKEYLLSFRGLGLKSVECVRLL 518 (960)
Q Consensus 442 pEaLA~As~eELeeLIRp~Gfyn~KAkrIk~lA~~Ive~yGgiDLe~Lr~vP~deareeLLsLpGIGpKTAd~ILLf 518 (960)
+-.|-.|+.++|..+ -|....+|+.|.+.-. .+|.| -+ .++|..++|||+++++-|.-|
T Consensus 59 ~iniNtA~~~eL~~l---pGIG~~~A~~Ii~~R~----~~g~f-------~s----~eeL~~V~GIg~k~~~~i~~~ 117 (120)
T TIGR01259 59 AVNINAASLEELQAL---PGIGPAKAKAIIEYRE----ENGAF-------KS----VDDLTKVSGIGEKSLEKLKDY 117 (120)
T ss_pred CEeCCcCCHHHHhcC---CCCCHHHHHHHHHHHH----hcCCc-------CC----HHHHHcCCCCCHHHHHHHHhc
Confidence 345666777777543 3555567777665322 23442 11 578999999999999988755
No 81
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=46.94 E-value=15 Score=38.84 Aligned_cols=23 Identities=22% Similarity=0.104 Sum_probs=20.3
Q ss_pred HHHHHHHHhCCCccHHHHHHHHH
Q 002141 495 DKAKEYLLSFRGLGLKSVECVRL 517 (960)
Q Consensus 495 deareeLLsLpGIGpKTAd~ILL 517 (960)
.++-+.|++++|||||+|-.||.
T Consensus 69 r~lF~~Li~V~GIGpK~Al~ILs 91 (194)
T PRK14605 69 LSLFETLIDVSGIGPKLGLAMLS 91 (194)
T ss_pred HHHHHHHhCCCCCCHHHHHHHHH
Confidence 35678899999999999999987
No 82
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=46.57 E-value=28 Score=40.36 Aligned_cols=59 Identities=20% Similarity=0.246 Sum_probs=41.0
Q ss_pred HHHHHHHhhcCChH-HHHH-HHHHHHHHHHHhcCCCCchhhhcCChHHHHHHHHhCCCccHHHHHHH
Q 002141 451 NKIANTIKERGMNN-MLAG-RIKDFLNRLVRDHGSVDLEWLRDVPPDKAKEYLLSFRGLGLKSVECV 515 (960)
Q Consensus 451 eELeeLIRp~Gfyn-~KAk-rIk~lA~~Ive~yGgiDLe~Lr~vP~deareeLLsLpGIGpKTAd~I 515 (960)
+.+...+.|.||.- .+.. .=+.+|+.++++||+ |..+...+ .++|.+++|||++.|..|
T Consensus 275 ~~ld~~v~prGyRiLs~IPrl~k~iAk~Ll~~FGS--L~~Il~As----~eeL~~VeGIGe~rA~~I 335 (352)
T PRK13482 275 EALDTPVSPRGYRLLSKIPRLPSAVIENLVEHFGS--LQGLLAAS----IEDLDEVEGIGEVRARAI 335 (352)
T ss_pred cccccccCCcHHHHHhcCCCCCHHHHHHHHHHcCC--HHHHHcCC----HHHHhhCCCcCHHHHHHH
Confidence 44556677777731 1111 114678899999985 67776666 458999999999999774
No 83
>COG2818 Tag 3-methyladenine DNA glycosylase [DNA replication, recombination, and repair]
Probab=45.97 E-value=19 Score=38.48 Aligned_cols=64 Identities=13% Similarity=0.212 Sum_probs=44.4
Q ss_pred CcHHHHHHHHHHcCCCCCCCCCCCCCCCHHHHHcCCHHHHHHHHhhcCChH--HHHHHHHHHHHHH---HHhcCCC
Q 002141 414 FDWDSLRRQVEANGGKKERPEHTKDSLDWEAVRCADVNKIANTIKERGMNN--MLAGRIKDFLNRL---VRDHGSV 484 (960)
Q Consensus 414 T~W~nL~kaL~nL~~k~er~~~~~g~~TpEaLA~As~eELeeLIRp~Gfyn--~KAkrIk~lA~~I---ve~yGgi 484 (960)
-.|..|.+- ++.+..+...++|+.||..+.++|+.++...|.-+ .|.+.+..=|+.+ .+.||+|
T Consensus 45 LSW~tVL~K-------Re~freaF~~Fd~~kVA~~~~~dverLl~d~gIIR~r~KI~A~i~NA~~~l~l~~e~Gsf 113 (188)
T COG2818 45 LSWLTVLKK-------REAFREAFHGFDPEKVAAMTEEDVERLLADAGIIRNRGKIKATINNARAVLELQKEFGSF 113 (188)
T ss_pred chHHHHHHh-------HHHHHHHHhcCCHHHHHcCCHHHHHHHHhCcchhhhHHHHHHHHHHHHHHHHHHHHcCCH
Confidence 467777653 33344456779999999999999999999999965 4555555545544 3456653
No 84
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this
Probab=44.19 E-value=42 Score=37.73 Aligned_cols=57 Identities=16% Similarity=0.159 Sum_probs=38.4
Q ss_pred HHHHHHHhhcCChHHHHHHHHHHHHHHHHhcCCCCchhhhcCChHHHHHHHHhCCCccHHHHHHHHHH
Q 002141 451 NKIANTIKERGMNNMLAGRIKDFLNRLVRDHGSVDLEWLRDVPPDKAKEYLLSFRGLGLKSVECVRLL 518 (960)
Q Consensus 451 eELeeLIRp~Gfyn~KAkrIk~lA~~Ive~yGgiDLe~Lr~vP~deareeLLsLpGIGpKTAd~ILLf 518 (960)
++|+.++.-.|=..-|++..+.+|..|.. .+. + +. . .+++.+|||||+++|+.|--+
T Consensus 8 ~~ia~~~e~~~~~~~r~~aY~~Aa~~l~~-l~~-~------i~--~-~~~~~~ipgiG~~ia~kI~E~ 64 (307)
T cd00141 8 EELADLLELLGGNPFRVRAYRKAARALES-LPE-P------IE--S-LEEAKKLPGIGKKIAEKIEEI 64 (307)
T ss_pred HHHHHHHHhccCCcchHHHHHHHHHHHHh-CCc-c------cC--C-HHHhcCCCCccHHHHHHHHHH
Confidence 45556665555444578888888888765 232 1 21 1 346799999999999998755
No 85
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=42.93 E-value=28 Score=43.52 Aligned_cols=29 Identities=14% Similarity=0.122 Sum_probs=17.3
Q ss_pred CHHHHHcCCHHHHHHHHhhcCChHHHHHHHHH
Q 002141 441 DWEAVRCADVNKIANTIKERGMNNMLAGRIKD 472 (960)
Q Consensus 441 TpEaLA~As~eELeeLIRp~Gfyn~KAkrIk~ 472 (960)
++.+|..+..++|..+ -||...+|..|.+
T Consensus 486 ~~~Dl~~L~~~~L~~l---~g~g~Ksa~~Ll~ 514 (689)
T PRK14351 486 SLADLYDLTVADLAEL---EGWGETSAENLLA 514 (689)
T ss_pred CHHHHHHcCHHHHhcC---cCcchhHHHHHHH
Confidence 6777777776654333 4666666655443
No 86
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=42.50 E-value=76 Score=39.00 Aligned_cols=69 Identities=14% Similarity=0.118 Sum_probs=42.0
Q ss_pred CHHHHHcCCHHHHHHHHhhcCChHHHHHHHHHHHHHHH---------------------H-hcCCCCchhhhcCChHHHH
Q 002141 441 DWEAVRCADVNKIANTIKERGMNNMLAGRIKDFLNRLV---------------------R-DHGSVDLEWLRDVPPDKAK 498 (960)
Q Consensus 441 TpEaLA~As~eELeeLIRp~Gfyn~KAkrIk~lA~~Iv---------------------e-~yGgiDLe~Lr~vP~dear 498 (960)
++.+|..+..++|..+ -||...+|+.|.+..+.-. + .|+ +++.|.... .
T Consensus 449 ~~~Diy~L~~~~l~~l---~gfgeks~~nll~aIe~sk~~~l~r~l~aLGI~~vG~~~ak~~~~--~i~~l~~a~----~ 519 (562)
T PRK08097 449 HLFSWLALTPEQLANT---PGIGKARAEQLWHQFNLARQQPFSRWLKALGIPLPQAALNALDDR--SWQQLLSRS----E 519 (562)
T ss_pred CHHHHhcCCHHHHhcC---cCccHHHHHHHHHHHHHHcCCCHHHHHHHcCCccHHHHHHHHhcC--CHHHHHcCC----H
Confidence 6677777776655333 4776666666654432111 0 121 345554433 3
Q ss_pred HHHHhCCCccHHHHHHHHHH
Q 002141 499 EYLLSFRGLGLKSVECVRLL 518 (960)
Q Consensus 499 eeLLsLpGIGpKTAd~ILLf 518 (960)
+.|.+++|||+++|+.|..|
T Consensus 520 e~l~~i~gIG~~~a~si~~~ 539 (562)
T PRK08097 520 QQWQQLPGIGEGRARQLIAF 539 (562)
T ss_pred HHHhcCCCchHHHHHHHHHH
Confidence 57999999999999998876
No 87
>PRK08609 hypothetical protein; Provisional
Probab=40.66 E-value=40 Score=41.07 Aligned_cols=49 Identities=29% Similarity=0.432 Sum_probs=30.6
Q ss_pred cCChHHHHHHHHHHHHHHHHhcCCC-Cchhhh-cCChHHHHHHHHhCCCccHHHHHHH
Q 002141 460 RGMNNMLAGRIKDFLNRLVRDHGSV-DLEWLR-DVPPDKAKEYLLSFRGLGLKSVECV 515 (960)
Q Consensus 460 ~Gfyn~KAkrIk~lA~~Ive~yGgi-DLe~Lr-~vP~deareeLLsLpGIGpKTAd~I 515 (960)
-|....-|+.|.++++. |.+ -|+.|+ ++|.. ..+|+++|||||+||..+
T Consensus 54 pgIG~~ia~kI~Eil~t-----G~~~~le~l~~~~p~~--~~~l~~i~GiGpk~a~~l 104 (570)
T PRK08609 54 KGIGKGTAEVIQEYRET-----GESSVLQELKKEVPEG--LLPLLKLPGLGGKKIAKL 104 (570)
T ss_pred CCcCHHHHHHHHHHHHh-----CChHHHHHHHhhCcHH--HHHHhcCCCCCHHHHHHH
Confidence 45555566666665432 332 244554 44543 558999999999998544
No 88
>PF03118 RNA_pol_A_CTD: Bacterial RNA polymerase, alpha chain C terminal domain; InterPro: IPR011260 The core of the bacterial RNA polymerase (RNAP) consists of four subunits, two alpha, a beta and a beta', which are conserved from bacteria to mammals. The alpha subunit (RpoA) initiates RNAP assembly by dimerising to form a platform on which the beta subunits can interact. The alpha subunit consists of a N-terminal domain (NTD) and a C-terminal domain (CTD), connected by a short linker. The NTD is essential for RNAP assembly, while the CTD is necessary for transcription regulation, interacting with transcription factors and promoter upstream elements. In Escherichia coli, the catabolite activator protein (CAP or CRP) was shown to exert its effect through its interactions with the CTD, where CAP binding to CTD promotes RNAP binding to promoter DNA, thereby stimulating transcription initiation at class I CAP-dependent promoters. At class II CAP-dependent promoters, the interaction of CAP with CTD is one of multiple interactions involved in activation []. The CTD has a compact structure of four helices and two long arms enclosing its hydrophobic core, making its folding topology distinct from most other binding proteins. The upstream promoter element-binding site is formed from helices 1 and 4 [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3N97_B 1XS9_D 3K4G_A 3N4M_B 1COO_A 1LB2_E 3IYD_A 1Z3E_B 3GFK_B 3IHQ_B ....
Probab=39.96 E-value=40 Score=30.00 Aligned_cols=28 Identities=29% Similarity=0.361 Sum_probs=22.2
Q ss_pred CchhhhcCChHHHHHHHHhCCCccHHHHHHHH
Q 002141 485 DLEWLRDVPPDKAKEYLLSFRGLGLKSVECVR 516 (960)
Q Consensus 485 DLe~Lr~vP~deareeLLsLpGIGpKTAd~IL 516 (960)
.+..|..++. +.|++++|+|+++.+-|.
T Consensus 34 tv~dL~~~s~----~~L~~i~n~G~ksl~EI~ 61 (66)
T PF03118_consen 34 TVGDLVKYSE----EDLLKIKNFGKKSLEEIK 61 (66)
T ss_dssp BHHHHHCS-H----HHHHTSTTSHHHHHHHHH
T ss_pred CHHHHHhCCH----HHHHhCCCCCHhHHHHHH
Confidence 6677777874 589999999999998764
No 89
>PF11798 IMS_HHH: IMS family HHH motif; InterPro: IPR024728 This helix-hairpin-helix motif is found in proteins belonging to the type-Y family of DNA polymerases []. This type of polymerases are thought to be involved in UV protection and mutation [, ]. ; PDB: 3PZP_B 2OH2_B 2W7O_B 3IN5_B 1T94_A 2W7P_B 2W8K_A 2AGQ_A 1RYR_A 3RAX_A ....
Probab=39.12 E-value=16 Score=28.19 Aligned_cols=15 Identities=27% Similarity=0.556 Sum_probs=11.0
Q ss_pred HHhCCCccHHHHHHH
Q 002141 501 LLSFRGLGLKSVECV 515 (960)
Q Consensus 501 LLsLpGIGpKTAd~I 515 (960)
+..++|||++|+.-+
T Consensus 13 i~~~~GIG~kt~~kL 27 (32)
T PF11798_consen 13 IRKFWGIGKKTAKKL 27 (32)
T ss_dssp GGGSTTS-HHHHHHH
T ss_pred HHhhCCccHHHHHHH
Confidence 457899999999753
No 90
>PF10391 DNA_pol_lambd_f: Fingers domain of DNA polymerase lambda; InterPro: IPR018944 DNA polymerases catalyse the addition of dNMPs onto the 3-prime ends of DNA chains. There is a general polymerase fold consisting of three subdomains that have been likened to the fingers, palm, and thumb of a right hand. This entry represents the central three-helical region of DNA polymerase lambda referred to as the F and G helices of the fingers domain. Contacts with DNA involve this conserved helix-hairpin-helix motif in the fingers region which interacts with the primer strand. This motif is common to several DNA binding proteins and confers a sequence-independent interaction with the DNA backbone []. ; GO: 0016779 nucleotidyltransferase activity; PDB: 1KDH_A 1KEJ_A 1JMS_A 2IHM_A 3OGU_A 1MQ2_A 2P66_A 7ICI_A 1ZQN_A 1ZQK_A ....
Probab=38.64 E-value=28 Score=29.87 Aligned_cols=21 Identities=14% Similarity=0.129 Sum_probs=14.7
Q ss_pred HHHHhCCCccHHHHHHHHHHh
Q 002141 499 EYLLSFRGLGLKSVECVRLLT 519 (960)
Q Consensus 499 eeLLsLpGIGpKTAd~ILLfa 519 (960)
+.|..+.|||+.||.-....+
T Consensus 2 ~~f~~I~GVG~~tA~~w~~~G 22 (52)
T PF10391_consen 2 KLFTGIWGVGPKTARKWYAKG 22 (52)
T ss_dssp HHHHTSTT--HHHHHHHHHTT
T ss_pred cchhhcccccHHHHHHHHHhC
Confidence 578999999999997665433
No 91
>PF05559 DUF763: Protein of unknown function (DUF763); InterPro: IPR008482 This family consists of several uncharacterised bacterial and archaeal proteins of unknown function.
Probab=38.62 E-value=68 Score=36.86 Aligned_cols=21 Identities=29% Similarity=0.496 Sum_probs=18.4
Q ss_pred HHHHHhCCCccHHHHHHHHHH
Q 002141 498 KEYLLSFRGLGLKSVECVRLL 518 (960)
Q Consensus 498 reeLLsLpGIGpKTAd~ILLf 518 (960)
.++|+.++|||++|..++.+.
T Consensus 268 feeLL~~~GvGp~TlRALaLv 288 (319)
T PF05559_consen 268 FEELLLIKGVGPSTLRALALV 288 (319)
T ss_pred HHHHHhcCCCCHHHHHHHHHH
Confidence 789999999999999877654
No 92
>PRK07758 hypothetical protein; Provisional
Probab=37.37 E-value=51 Score=31.93 Aligned_cols=28 Identities=25% Similarity=0.411 Sum_probs=21.9
Q ss_pred CchhhhcCChHHHHHHHHhCCCccHHHHHHHH
Q 002141 485 DLEWLRDVPPDKAKEYLLSFRGLGLKSVECVR 516 (960)
Q Consensus 485 DLe~Lr~vP~deareeLLsLpGIGpKTAd~IL 516 (960)
.++.|..++ .++|++|+|+|+++.+-|.
T Consensus 57 TL~dLv~~t----e~ELl~iknlGkKSL~EIk 84 (95)
T PRK07758 57 TVEELSKYS----EKEILKLHGMGPASLPKLR 84 (95)
T ss_pred cHHHHHcCC----HHHHHHccCCCHHHHHHHH
Confidence 455666666 4589999999999987764
No 93
>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=36.90 E-value=34 Score=29.94 Aligned_cols=21 Identities=33% Similarity=0.479 Sum_probs=18.3
Q ss_pred HHHHHh-CCCccHHHHHHHHHH
Q 002141 498 KEYLLS-FRGLGLKSVECVRLL 518 (960)
Q Consensus 498 reeLLs-LpGIGpKTAd~ILLf 518 (960)
.+.|.. +||||.++|..|+.+
T Consensus 15 ~~~L~~~ipgig~~~a~~Il~~ 36 (69)
T TIGR00426 15 AEELQRAMNGVGLKKAEAIVSY 36 (69)
T ss_pred HHHHHhHCCCCCHHHHHHHHHH
Confidence 457888 999999999999876
No 94
>PRK00254 ski2-like helicase; Provisional
Probab=35.83 E-value=74 Score=39.55 Aligned_cols=43 Identities=14% Similarity=0.186 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHHhcCCCCchhhhcCChHHHHHHHHhCCCccHHHHHHHHHHhcCCe
Q 002141 468 GRIKDFLNRLVRDHGSVDLEWLRDVPPDKAKEYLLSFRGLGLKSVECVRLLTLHHL 523 (960)
Q Consensus 468 krIk~lA~~Ive~yGgiDLe~Lr~vP~deareeLLsLpGIGpKTAd~ILLfafgrp 523 (960)
..|..+.++|.. | ++.+ --.|.+|||||++.|..++-.+|+-.
T Consensus 627 ~~l~~l~~rl~~--g---------~~~~--~~~L~~ipgig~~~~~~l~~~g~~s~ 669 (720)
T PRK00254 627 DYLETLHLRVKH--G---------VREE--LLELMRLPMIGRKRARALYNAGFRSI 669 (720)
T ss_pred HHHHHHHHHHHc--C---------CCHH--HhhhhcCCCCCHHHHHHHHHccCCCH
Confidence 345566666653 2 3433 23566777777777777666666544
No 95
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=35.34 E-value=25 Score=28.06 Aligned_cols=15 Identities=20% Similarity=0.299 Sum_probs=12.4
Q ss_pred HhCCCccHHHHHHHH
Q 002141 502 LSFRGLGLKSVECVR 516 (960)
Q Consensus 502 LsLpGIGpKTAd~IL 516 (960)
-.+||||+|||--+|
T Consensus 19 ~Gv~giG~ktA~~ll 33 (36)
T smart00279 19 PGVKGIGPKTALKLL 33 (36)
T ss_pred CCCCcccHHHHHHHH
Confidence 468999999997665
No 96
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=34.50 E-value=68 Score=36.95 Aligned_cols=60 Identities=20% Similarity=0.245 Sum_probs=39.4
Q ss_pred HHHHHHHhhcCChHHHHHHHHHHHHHHHHhcCCCCchhhhcCChHHHHHHHHhCCCccHHHHHHHHHH
Q 002141 451 NKIANTIKERGMNNMLAGRIKDFLNRLVRDHGSVDLEWLRDVPPDKAKEYLLSFRGLGLKSVECVRLL 518 (960)
Q Consensus 451 eELeeLIRp~Gfyn~KAkrIk~lA~~Ive~yGgiDLe~Lr~vP~deareeLLsLpGIGpKTAd~ILLf 518 (960)
++++..+.-.|=..-|++.-+.+|+.|... ..|++.+.. +..|+.|||||+.+|+.|--|
T Consensus 13 e~iA~~me~~Gen~fk~~aYr~Aa~sle~~--~e~~~ei~e------~~~~t~l~gIGk~ia~~I~e~ 72 (326)
T COG1796 13 ERIADYMELEGENPFKIRAYRKAAQSLENL--TEDLEEIEE------RGRLTELPGIGKGIAEKISEY 72 (326)
T ss_pred HHHHHHHHhcCCCccchHHHHHHHHhhhhc--ccchHHHHh------hcccCCCCCccHHHHHHHHHH
Confidence 455566655665545777777878877642 222222221 224899999999999999876
No 97
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=32.15 E-value=35 Score=36.10 Aligned_cols=22 Identities=14% Similarity=0.235 Sum_probs=19.4
Q ss_pred HHHHHHHhCCCccHHHHHHHHH
Q 002141 496 KAKEYLLSFRGLGLKSVECVRL 517 (960)
Q Consensus 496 eareeLLsLpGIGpKTAd~ILL 517 (960)
++-+.|+++.|||||+|=.||.
T Consensus 70 ~lF~~LisV~GIGpK~Al~iLs 91 (186)
T PRK14600 70 DCLRMLVKVSGVNYKTAMSILS 91 (186)
T ss_pred HHHHHHhCcCCcCHHHHHHHHc
Confidence 4677899999999999988886
No 98
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=32.08 E-value=36 Score=36.47 Aligned_cols=23 Identities=22% Similarity=0.252 Sum_probs=19.7
Q ss_pred HHHHHHHHhCCCccHHHHHHHHH
Q 002141 495 DKAKEYLLSFRGLGLKSVECVRL 517 (960)
Q Consensus 495 deareeLLsLpGIGpKTAd~ILL 517 (960)
.++-+.|+++.|||||+|=.||.
T Consensus 68 r~lF~~LisVsGIGPK~ALaILs 90 (196)
T PRK13901 68 REVFEELIGVDGIGPRAALRVLS 90 (196)
T ss_pred HHHHHHHhCcCCcCHHHHHHHHc
Confidence 35678899999999999988884
No 99
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=31.44 E-value=85 Score=34.70 Aligned_cols=47 Identities=15% Similarity=0.195 Sum_probs=32.0
Q ss_pred cCChHHHHHHHHHHHHHHHHhcCCCCchhhhcCChHHHHHHHHhCCCccHHHHHHHHHH
Q 002141 460 RGMNNMLAGRIKDFLNRLVRDHGSVDLEWLRDVPPDKAKEYLLSFRGLGLKSVECVRLL 518 (960)
Q Consensus 460 ~Gfyn~KAkrIk~lA~~Ive~yGgiDLe~Lr~vP~deareeLLsLpGIGpKTAd~ILLf 518 (960)
-|....+++.|.+. .|+ +++.+...+ .++|.+++|||.++|..|..+
T Consensus 9 pGIG~krakkLl~~------GF~--Sve~Ik~AS----~eEL~~V~GIg~k~AekI~e~ 55 (232)
T PRK12766 9 SGVGPSKAEALREA------GFE--SVEDVRAAD----QSELAEVDGIGNALAARIKAD 55 (232)
T ss_pred CCcCHHHHHHHHHc------CCC--CHHHHHhCC----HHHHHHccCCCHHHHHHHHHH
Confidence 45555565555331 033 456666666 568999999999999999876
No 100
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=30.94 E-value=39 Score=34.36 Aligned_cols=20 Identities=10% Similarity=-0.011 Sum_probs=17.5
Q ss_pred HHHHHhCCCccHHHHHHHHH
Q 002141 498 KEYLLSFRGLGLKSVECVRL 517 (960)
Q Consensus 498 reeLLsLpGIGpKTAd~ILL 517 (960)
.++|.+||||||..|..|..
T Consensus 60 ~~el~~lpGigP~~A~~IV~ 79 (132)
T PRK02515 60 VRAFRQFPGMYPTLAGKIVK 79 (132)
T ss_pred HHHHHHCCCCCHHHHHHHHH
Confidence 45789999999999999984
No 101
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=30.76 E-value=39 Score=35.75 Aligned_cols=25 Identities=16% Similarity=-0.013 Sum_probs=20.5
Q ss_pred ChHHHHHHHHhCCCccHHHHHHHHH
Q 002141 493 PPDKAKEYLLSFRGLGLKSVECVRL 517 (960)
Q Consensus 493 P~deareeLLsLpGIGpKTAd~ILL 517 (960)
...++-+.|+++.|||||+|=.||.
T Consensus 67 ~Er~lF~~Li~V~GIGpK~AL~iLs 91 (188)
T PRK14606 67 RKKELFLSLTKVSRLGPKTALKIIS 91 (188)
T ss_pred HHHHHHHHHhccCCccHHHHHHHHc
Confidence 3345678899999999999988874
No 102
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=30.73 E-value=39 Score=35.73 Aligned_cols=23 Identities=30% Similarity=0.390 Sum_probs=19.7
Q ss_pred HHHHHHHHhCCCccHHHHHHHHH
Q 002141 495 DKAKEYLLSFRGLGLKSVECVRL 517 (960)
Q Consensus 495 deareeLLsLpGIGpKTAd~ILL 517 (960)
.++-+.|+++.|||||+|=.||.
T Consensus 69 r~lF~~Li~VsGIGpK~Al~ILs 91 (183)
T PRK14601 69 QKMFEMLLKVNGIGANTAMAVCS 91 (183)
T ss_pred HHHHHHHhccCCccHHHHHHHHc
Confidence 35678899999999999988875
No 103
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=30.13 E-value=40 Score=35.90 Aligned_cols=24 Identities=25% Similarity=0.198 Sum_probs=20.3
Q ss_pred hHHHHHHHHhCCCccHHHHHHHHH
Q 002141 494 PDKAKEYLLSFRGLGLKSVECVRL 517 (960)
Q Consensus 494 ~deareeLLsLpGIGpKTAd~ILL 517 (960)
..++-+.|+++.|||||+|=.||.
T Consensus 67 Er~lF~~L~~V~GIGpK~AL~iLs 90 (197)
T PRK14603 67 SLELFELLLGVSGVGPKLALALLS 90 (197)
T ss_pred HHHHHHHHhCcCCcCHHHHHHHHc
Confidence 345677899999999999988886
No 104
>PRK08609 hypothetical protein; Provisional
Probab=30.09 E-value=88 Score=38.26 Aligned_cols=57 Identities=18% Similarity=0.288 Sum_probs=39.8
Q ss_pred HHHHHHHhhcCChHHHHHHHHHHHHHHHHhcCCCCchhhhcCChHHHHHHHHhCCCccHHHHHHHHHH
Q 002141 451 NKIANTIKERGMNNMLAGRIKDFLNRLVRDHGSVDLEWLRDVPPDKAKEYLLSFRGLGLKSVECVRLL 518 (960)
Q Consensus 451 eELeeLIRp~Gfyn~KAkrIk~lA~~Ive~yGgiDLe~Lr~vP~deareeLLsLpGIGpKTAd~ILLf 518 (960)
++++.++.-.|=..-|++..+.+|+.|... .. ++. . ...|.+|||||..+|+.|--+
T Consensus 11 ~~~A~~le~~g~n~fr~~aYr~Aa~~i~~l-~~-~i~--------~-~~~l~~ipgIG~~ia~kI~Ei 67 (570)
T PRK08609 11 ETIATYMELKGENPFKISAFRKAAQALELD-ER-SLS--------E-IDDFTKLKGIGKGTAEVIQEY 67 (570)
T ss_pred HHHHHHHHhcCCCcHHHHHHHHHHHHHHhC-ch-hhh--------h-hhhhccCCCcCHHHHHHHHHH
Confidence 466666766675445888888888887653 22 211 1 247899999999999988755
No 105
>cd00080 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) motif. HhH2 domains are found in Rad2 family of prokaryotic and eukaryotic replication and repair nucleases, i.e., DNA polymerase I, Taq DNA polymerase, DNA repair protein Rad2 endonuclease, flap endonuclease, exonuclease I and IX, 5'-3' exonuclease and also bacteriophage Rnase H. These nucleases degrade RNA-DNA or DNA-DNA duplexes, or both and play essential roles in DNA duplication, repair, and recombination.
Probab=29.02 E-value=24 Score=31.89 Aligned_cols=18 Identities=17% Similarity=0.171 Sum_probs=14.7
Q ss_pred HHHhCCCccHHHHHHHHH
Q 002141 500 YLLSFRGLGLKSVECVRL 517 (960)
Q Consensus 500 eLLsLpGIGpKTAd~ILL 517 (960)
.+-.+||||+|||.-++.
T Consensus 23 ~i~gv~giG~k~A~~ll~ 40 (75)
T cd00080 23 NIPGVPGIGPKTALKLLK 40 (75)
T ss_pred cCCCCCcccHHHHHHHHH
Confidence 566899999999977664
No 106
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=28.59 E-value=43 Score=35.62 Aligned_cols=23 Identities=22% Similarity=0.254 Sum_probs=19.9
Q ss_pred HHHHHHHHhCCCccHHHHHHHHH
Q 002141 495 DKAKEYLLSFRGLGLKSVECVRL 517 (960)
Q Consensus 495 deareeLLsLpGIGpKTAd~ILL 517 (960)
.++-..|+++.|||||+|=.||.
T Consensus 69 r~lF~~Li~V~GIGpK~Al~iLs 91 (195)
T PRK14604 69 RQLFELLIGVSGVGPKAALNLLS 91 (195)
T ss_pred HHHHHHHhCcCCcCHHHHHHHHc
Confidence 35677899999999999988886
No 107
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=28.57 E-value=44 Score=35.73 Aligned_cols=23 Identities=17% Similarity=0.174 Sum_probs=19.8
Q ss_pred HHHHHHHHhCCCccHHHHHHHHH
Q 002141 495 DKAKEYLLSFRGLGLKSVECVRL 517 (960)
Q Consensus 495 deareeLLsLpGIGpKTAd~ILL 517 (960)
.++-+.|+++.|||||+|=.||.
T Consensus 70 r~lF~~Li~V~GIGpK~Al~iLs 92 (203)
T PRK14602 70 RQTFIVLISISKVGAKTALAILS 92 (203)
T ss_pred HHHHHHHhCCCCcCHHHHHHHHh
Confidence 35677899999999999988886
No 108
>smart00439 BAH Bromo adjacent homology domain.
Probab=28.52 E-value=57 Score=30.35 Aligned_cols=64 Identities=23% Similarity=0.292 Sum_probs=45.1
Q ss_pred ceeeeeeeeccCCCCCCcccchhhhccCCceeEEecCChhhhcccCCHHHHHHHhhccceEeecccccccCCccc
Q 002141 863 YFQVNEVFADHDSSLKPINVPREWLWNLPRRTVYFGTSIPSIFKGLTTEGIQHCFWRGYVCVRGFDQKSRAPRPL 937 (960)
Q Consensus 863 YFQvNEVFaDh~SS~~PI~vpr~~iw~L~rr~vyfGtSv~sIfkglt~~~Iq~cF~~G~vCVR~Fdr~tr~PrpL 937 (960)
+|.-||||+-.... .||-+.|+. ++.|++.+......- ++. .-...-|+|=++||+.++...+|
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 46689999887653 666677776 889998876644221 111 01347899999999999887766
No 109
>KOG0028 consensus Ca2+-binding protein (centrin/caltractin), EF-Hand superfamily protein [Cytoskeleton; Cell cycle control, cell division, chromosome partitioning]
Probab=25.56 E-value=1.4e+02 Score=31.64 Aligned_cols=87 Identities=17% Similarity=0.149 Sum_probs=51.6
Q ss_pred HcCCHHHHHHHHhhcCChHHHHHHHHHHHHHHHHhcCCCCchhhhcCChHHHHHHHHhCCCccH---HHHHHHHHHhcCC
Q 002141 446 RCADVNKIANTIKERGMNNMLAGRIKDFLNRLVRDHGSVDLEWLRDVPPDKAKEYLLSFRGLGL---KSVECVRLLTLHH 522 (960)
Q Consensus 446 A~As~eELeeLIRp~Gfyn~KAkrIk~lA~~Ive~yGgiDLe~Lr~vP~deareeLLsLpGIGp---KTAd~ILLfafgr 522 (960)
-.++.++|.-+++..||...|...++-++..=.+.-|-++++.+. .-....-|.+. ..-.++.+|-+..
T Consensus 48 g~iD~~EL~vAmralGFE~~k~ei~kll~d~dk~~~g~i~fe~f~--------~~mt~k~~e~dt~eEi~~afrl~D~D~ 119 (172)
T KOG0028|consen 48 GKIDVEELKVAMRALGFEPKKEEILKLLADVDKEGSGKITFEDFR--------RVMTVKLGERDTKEEIKKAFRLFDDDK 119 (172)
T ss_pred CcccHHHHHHHHHHcCCCcchHHHHHHHHhhhhccCceechHHHH--------HHHHHHHhccCcHHHHHHHHHcccccC
Confidence 356778888889999999878776666655433323444444333 33233333333 1122344444445
Q ss_pred eeeecchHHHHHHHHhcC
Q 002141 523 LAFPVDTNVGRIAVRLGW 540 (960)
Q Consensus 523 pvfpVDThV~RIl~RLG~ 540 (960)
..-+-=.+..||+.+||=
T Consensus 120 ~Gkis~~~lkrvakeLge 137 (172)
T KOG0028|consen 120 TGKISQRNLKRVAKELGE 137 (172)
T ss_pred CCCcCHHHHHHHHHHhCc
Confidence 555555789999999985
No 110
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=23.76 E-value=60 Score=34.95 Aligned_cols=24 Identities=21% Similarity=0.205 Sum_probs=20.0
Q ss_pred HHHHHHHHhCCCccHHHHHHHHHH
Q 002141 495 DKAKEYLLSFRGLGLKSVECVRLL 518 (960)
Q Consensus 495 deareeLLsLpGIGpKTAd~ILLf 518 (960)
.++-..|+++-|||||+|=+||..
T Consensus 69 R~lF~~LisVnGIGpK~ALaiLs~ 92 (201)
T COG0632 69 RELFRLLISVNGIGPKLALAILSN 92 (201)
T ss_pred HHHHHHHHccCCccHHHHHHHHcC
Confidence 356778999999999999888754
No 111
>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=23.03 E-value=75 Score=30.59 Aligned_cols=22 Identities=14% Similarity=0.122 Sum_probs=18.2
Q ss_pred HHHHHHHhCCCccHHHHHHHHH
Q 002141 496 KAKEYLLSFRGLGLKSVECVRL 517 (960)
Q Consensus 496 eareeLLsLpGIGpKTAd~ILL 517 (960)
.+.-.|.++.|||+.+|..|+.
T Consensus 12 ~i~~aLt~IyGIG~~~A~~Ic~ 33 (107)
T PF00416_consen 12 PIYIALTKIYGIGRRKAKQICK 33 (107)
T ss_dssp BHHHHHTTSTTBCHHHHHHHHH
T ss_pred chHhHHhhhhccCHHHHHHHHH
Confidence 3677899999999999976653
No 112
>COG4277 Predicted DNA-binding protein with the Helix-hairpin-helix motif [General function prediction only]
Probab=21.96 E-value=57 Score=37.55 Aligned_cols=21 Identities=29% Similarity=0.438 Sum_probs=18.4
Q ss_pred HHHHHhCCCccHHHHHHHHHH
Q 002141 498 KEYLLSFRGLGLKSVECVRLL 518 (960)
Q Consensus 498 reeLLsLpGIGpKTAd~ILLf 518 (960)
.++|+.+||||.|+|.-|++.
T Consensus 329 ~~~llRVPGiG~ksa~rIv~~ 349 (404)
T COG4277 329 YKELLRVPGIGVKSARRIVMT 349 (404)
T ss_pred HHHhcccCCCChHHHHHHHHH
Confidence 789999999999999887653
No 113
>PF08876 DUF1836: Domain of unknown function (DUF1836); InterPro: IPR014975 This group of proteins are functionally uncharacterised.
Probab=21.86 E-value=63 Score=31.48 Aligned_cols=57 Identities=26% Similarity=0.359 Sum_probs=37.2
Q ss_pred CCCCCccccchhhhhHhHHHHHHhccccccCccchhhhccCcCccccCCCCCCcccc
Q 002141 705 PEEIPTIKLNMKEFTQTLQNYMQENLELQEGDMSKALVALTAGAASIPAPKLKNVSR 761 (960)
Q Consensus 705 ~~~ip~i~l~~e~~~~~l~~~~~~n~~~~~~~~sk~lv~l~~~aasip~pklKnv~R 761 (960)
-+|||+|.|-|+....=+.+++.......+..++++||-==-....|+.|.-|..+|
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 368999999999988666666543222122456666654222346788888788775
No 114
>PF15414 DUF4621: Protein of unknown function (DUF4621)
Probab=21.25 E-value=31 Score=37.27 Aligned_cols=28 Identities=50% Similarity=0.618 Sum_probs=25.3
Q ss_pred cccCCCCChhhhcccccCCcccccCCCC
Q 002141 678 IIEEPATPEPERVQVSENDIEDTFCEDP 705 (960)
Q Consensus 678 IiE~P~sPe~e~~~~~e~died~~~ed~ 705 (960)
-+|.|-+|.||...++-+.|||+|+||.
T Consensus 195 avelpltpapefsavsveriedafdedf 222 (329)
T PF15414_consen 195 AVELPLTPAPEFSAVSVERIEDAFDEDF 222 (329)
T ss_pred heeccCCCCcccceeehhhhhhhhhhhh
Confidence 5899999999998888899999998875
No 115
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=20.59 E-value=1.4e+02 Score=33.37 Aligned_cols=32 Identities=19% Similarity=-0.002 Sum_probs=19.1
Q ss_pred HHHHHhCCCccHHHHHHHHHHhcCC-eeeecch
Q 002141 498 KEYLLSFRGLGLKSVECVRLLTLHH-LAFPVDT 529 (960)
Q Consensus 498 reeLLsLpGIGpKTAd~ILLfafgr-pvfpVDT 529 (960)
...|.+|||||.+.|.-+|..-... .++-++.
T Consensus 181 ~~il~s~pgig~~~a~~ll~~fgS~~~~~tas~ 213 (254)
T COG1948 181 LYILESIPGIGPKLAERLLKKFGSVEDVLTASE 213 (254)
T ss_pred HHHHHcCCCccHHHHHHHHHHhcCHHHHhhcCH
Confidence 4567777888888887766443332 2444444
Done!