Query 001299
Match_columns 1105
No_of_seqs 325 out of 1946
Neff 4.0
Searched_HMMs 46136
Date Thu Mar 28 21:09:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001299.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001299hhsearch_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 4.6E-69 1E-73 497.5 8.3 103 989-1091 1-103 (103)
2 COG0177 Nth Predicted EndoIII- 100.0 2.8E-40 6.1E-45 345.3 16.8 183 551-766 27-209 (211)
3 PRK10702 endonuclease III; Pro 100.0 1.7E-38 3.7E-43 332.5 16.5 181 552-765 28-208 (211)
4 TIGR01084 mutY A/G-specific ad 100.0 1.3E-34 2.8E-39 313.8 18.7 191 552-778 25-219 (275)
5 PRK10880 adenine DNA glycosyla 100.0 1.7E-34 3.7E-39 321.6 17.8 187 552-767 29-215 (350)
6 TIGR01083 nth endonuclease III 100.0 3.7E-33 7.9E-38 287.0 16.2 167 552-751 25-191 (191)
7 PRK13910 DNA glycosylase MutY; 100.0 2.1E-32 4.6E-37 298.3 18.6 172 562-768 1-174 (289)
8 COG2231 Uncharacterized protei 100.0 8.4E-32 1.8E-36 278.5 16.0 182 556-764 33-214 (215)
9 PRK13913 3-methyladenine DNA g 100.0 7E-31 1.5E-35 276.6 16.4 184 552-746 29-216 (218)
10 KOG1921 Endonuclease III [Repl 100.0 6.1E-30 1.3E-34 269.3 13.0 180 553-763 78-260 (286)
11 COG1194 MutY A/G-specific DNA 100.0 4.1E-28 8.8E-33 267.8 16.1 184 553-768 34-221 (342)
12 smart00478 ENDO3c endonuclease 99.9 1.7E-25 3.7E-30 219.7 17.2 148 562-741 1-148 (149)
13 cd00056 ENDO3c endonuclease II 99.9 9.2E-25 2E-29 216.1 15.4 155 556-740 3-158 (158)
14 PRK01229 N-glycosylase/DNA lya 99.9 3E-22 6.5E-27 210.2 12.9 140 550-708 34-185 (208)
15 KOG2457 A/G-specific adenine D 99.8 3.4E-21 7.4E-26 212.7 9.1 184 553-766 125-311 (555)
16 TIGR00588 ogg 8-oxoguanine DNA 99.8 3.1E-20 6.6E-25 205.0 14.8 134 553-690 119-264 (310)
17 COG0122 AlkA 3-methyladenine D 99.8 2.9E-19 6.2E-24 195.5 13.5 161 553-719 105-271 (285)
18 TIGR03252 uncharacterized HhH- 99.7 6.5E-18 1.4E-22 173.7 10.7 112 552-668 17-135 (177)
19 PRK10308 3-methyl-adenine DNA 99.7 6.2E-17 1.3E-21 177.0 13.2 152 553-719 113-273 (283)
20 KOG1918 3-methyladenine DNA gl 99.6 2.1E-16 4.5E-21 165.7 8.0 162 552-719 74-238 (254)
21 PF00730 HhH-GPD: HhH-GPD supe 99.6 2.7E-15 5.9E-20 140.1 8.9 107 558-708 1-107 (108)
22 KOG2875 8-oxoguanine DNA glyco 99.6 6E-15 1.3E-19 159.2 10.7 127 557-687 121-258 (323)
23 COG1059 Thermostable 8-oxoguan 98.9 5.5E-09 1.2E-13 108.7 9.9 122 554-693 40-166 (210)
24 PF15629 Perm-CXXC: Permuted s 98.9 6.7E-10 1.5E-14 85.4 1.3 31 956-986 1-32 (32)
25 PF00633 HHH: Helix-hairpin-he 97.1 0.00035 7.5E-09 53.8 2.4 25 641-667 6-30 (30)
26 PF10576 EndIII_4Fe-2S: Iron-s 96.4 0.0013 2.7E-08 45.1 0.8 17 744-760 1-17 (17)
27 PF09674 DUF2400: Protein of u 95.6 0.0094 2E-07 65.1 3.5 54 614-693 143-196 (232)
28 smart00525 FES FES domain. iro 95.4 0.0071 1.5E-07 44.7 1.3 23 743-765 1-23 (26)
29 TIGR02757 conserved hypothetic 94.7 0.025 5.4E-07 61.8 3.4 50 616-692 143-192 (229)
30 smart00278 HhH1 Helix-hairpin- 88.0 0.37 8E-06 35.8 2.0 20 649-668 2-21 (26)
31 PF12826 HHH_2: Helix-hairpin- 87.9 0.64 1.4E-05 41.3 3.9 40 622-667 15-54 (64)
32 PRK13901 ruvA Holliday junctio 87.2 1.9 4.1E-05 46.6 7.6 65 585-670 59-129 (196)
33 PF03352 Adenine_glyco: Methyl 82.1 3 6.6E-05 44.5 6.3 72 557-632 30-106 (179)
34 PF14716 HHH_8: Helix-hairpin- 81.6 6.9 0.00015 35.0 7.5 58 600-667 9-66 (68)
35 TIGR00426 competence protein C 81.1 3.1 6.8E-05 37.0 5.1 57 594-667 10-66 (69)
36 PRK10353 3-methyl-adenine DNA 80.9 10 0.00023 40.9 9.7 68 557-628 35-104 (187)
37 PF14520 HHH_5: Helix-hairpin- 80.7 4.2 9.2E-05 35.3 5.6 49 607-667 9-57 (60)
38 PRK14601 ruvA Holliday junctio 80.5 5.5 0.00012 42.6 7.5 70 585-671 60-131 (183)
39 PRK14606 ruvA Holliday junctio 80.1 5.9 0.00013 42.5 7.6 63 585-668 60-128 (188)
40 TIGR00624 tag DNA-3-methyladen 78.1 16 0.00035 39.2 10.0 68 557-628 34-103 (179)
41 TIGR00608 radc DNA repair prot 77.5 3.9 8.5E-05 44.7 5.5 61 596-665 13-77 (218)
42 PRK00024 hypothetical protein; 76.9 3.9 8.5E-05 44.7 5.3 62 595-665 22-83 (224)
43 PRK14602 ruvA Holliday junctio 75.8 8.3 0.00018 41.7 7.3 66 585-667 61-128 (203)
44 COG0632 RuvA Holliday junction 75.7 4 8.6E-05 44.4 4.9 69 586-669 61-129 (201)
45 PRK14605 ruvA Holliday junctio 75.0 9.1 0.0002 41.1 7.3 65 585-666 60-126 (194)
46 PF09171 DUF1886: Domain of un 74.5 9.7 0.00021 42.7 7.5 133 600-746 77-232 (246)
47 PRK14604 ruvA Holliday junctio 73.9 9.4 0.0002 41.2 7.1 63 585-668 60-128 (195)
48 PRK14603 ruvA Holliday junctio 73.5 9.6 0.00021 41.2 7.1 21 647-667 106-126 (197)
49 PRK00076 recR recombination pr 73.4 3.2 7E-05 44.9 3.5 29 643-671 6-34 (196)
50 PRK14600 ruvA Holliday junctio 73.4 8.1 0.00017 41.4 6.4 62 585-668 60-127 (186)
51 PRK02515 psbU photosystem II c 73.1 5.2 0.00011 41.0 4.6 53 593-667 54-106 (132)
52 TIGR00615 recR recombination p 72.8 3.4 7.4E-05 44.7 3.5 29 643-671 6-34 (195)
53 PRK13844 recombination protein 72.8 3.4 7.4E-05 44.9 3.5 29 643-671 10-38 (200)
54 TIGR00084 ruvA Holliday juncti 69.4 6.6 0.00014 42.1 4.7 66 585-667 59-126 (191)
55 COG0353 RecR Recombinational D 67.8 4.8 0.0001 43.7 3.3 29 643-671 7-35 (198)
56 PF14490 HHH_4: Helix-hairpin- 64.2 11 0.00025 35.6 4.7 57 598-666 7-64 (94)
57 COG2818 Tag 3-methyladenine DN 64.2 30 0.00065 37.5 8.3 65 565-633 44-113 (188)
58 TIGR00575 dnlj DNA ligase, NAD 63.9 19 0.00041 45.3 7.8 32 590-624 456-487 (652)
59 COG2003 RadC DNA repair protei 63.1 13 0.00028 41.2 5.5 60 596-664 23-82 (224)
60 PRK00116 ruvA Holliday junctio 63.0 12 0.00026 39.9 5.2 21 647-667 107-127 (192)
61 COG1555 ComEA DNA uptake prote 61.8 14 0.00029 38.4 5.1 55 594-666 91-145 (149)
62 PRK07956 ligA NAD-dependent DN 61.5 27 0.00058 44.2 8.5 20 648-667 543-562 (665)
63 PRK14973 DNA topoisomerase I; 60.3 15 0.00034 47.9 6.4 98 586-690 821-919 (936)
64 PF12836 HHH_3: Helix-hairpin- 57.1 19 0.0004 32.1 4.5 52 595-664 9-60 (65)
65 TIGR01259 comE comEA protein. 56.6 23 0.0005 35.3 5.6 57 593-667 61-117 (120)
66 PF11731 Cdd1: Pathogenicity l 56.1 10 0.00022 36.9 2.8 28 645-672 9-36 (93)
67 PF02371 Transposase_20: Trans 52.6 11 0.00023 35.2 2.4 42 648-692 2-43 (87)
68 smart00483 POLXc DNA polymeras 52.3 20 0.00043 41.5 4.9 51 610-665 55-106 (334)
69 cd04370 BAH BAH, or Bromo Adja 49.8 24 0.00051 33.3 4.3 64 1009-1083 59-122 (123)
70 PRK14351 ligA NAD-dependent DN 49.1 66 0.0014 41.0 9.1 29 590-621 486-514 (689)
71 PRK07945 hypothetical protein; 48.6 27 0.00058 40.4 5.3 61 600-667 8-68 (335)
72 PF14229 DUF4332: Domain of un 44.9 2.5E+02 0.0054 28.2 10.7 60 586-670 14-75 (122)
73 smart00483 POLXc DNA polymeras 44.9 59 0.0013 37.7 7.2 57 600-667 11-67 (334)
74 PF14520 HHH_5: Helix-hairpin- 44.7 42 0.00091 29.2 4.7 35 587-624 25-59 (60)
75 TIGR00084 ruvA Holliday juncti 44.3 18 0.00039 38.8 2.9 22 645-666 69-90 (191)
76 PRK00116 ruvA Holliday junctio 43.3 19 0.00042 38.5 2.8 20 647-666 72-91 (192)
77 cd00141 NT_POLXc Nucleotidyltr 42.5 30 0.00065 39.5 4.4 50 610-665 52-102 (307)
78 PRK14350 ligA NAD-dependent DN 41.1 42 0.00091 42.6 5.7 22 647-668 540-561 (669)
79 PRK14605 ruvA Holliday junctio 41.1 21 0.00046 38.4 2.8 23 645-667 70-92 (194)
80 PF03118 RNA_pol_A_CTD: Bacter 41.0 34 0.00073 31.0 3.6 28 634-665 34-61 (66)
81 PF12836 HHH_3: Helix-hairpin- 40.9 26 0.00055 31.2 2.8 21 647-667 13-33 (65)
82 PRK14973 DNA topoisomerase I; 40.4 2.7E+02 0.006 37.0 12.8 75 587-669 764-856 (936)
83 TIGR01259 comE comEA protein. 38.7 27 0.00058 34.9 2.9 22 647-668 67-88 (120)
84 PF03568 Peptidase_C50: Peptid 38.7 30 0.00065 40.7 3.7 36 172-213 62-98 (383)
85 PF05559 DUF763: Protein of un 38.5 78 0.0017 37.0 6.8 25 642-668 265-289 (319)
86 PF11798 IMS_HHH: IMS family H 38.2 24 0.00051 27.8 1.9 15 650-664 13-27 (32)
87 COG1555 ComEA DNA uptake prote 37.8 26 0.00056 36.4 2.7 27 641-668 91-117 (149)
88 PRK13482 DNA integrity scannin 36.9 44 0.00096 39.4 4.6 39 620-664 297-335 (352)
89 COG0272 Lig NAD-dependent DNA 36.8 57 0.0012 41.4 5.8 36 626-667 527-562 (667)
90 cd00141 NT_POLXc Nucleotidyltr 34.6 87 0.0019 35.9 6.5 56 601-667 9-64 (307)
91 PF10391 DNA_pol_lambd_f: Fing 34.6 31 0.00068 30.1 2.3 20 648-667 2-21 (52)
92 PRK08097 ligB NAD-dependent DN 32.0 1.3E+02 0.0028 37.7 7.7 69 590-667 449-539 (562)
93 COG1796 POL4 DNA polymerase IV 29.6 90 0.002 36.6 5.5 60 600-667 13-72 (326)
94 smart00279 HhH2 Helix-hairpin- 29.5 36 0.00078 27.6 1.7 16 650-665 18-33 (36)
95 TIGR01083 nth endonuclease III 29.4 26 0.00056 37.1 1.2 55 191-245 2-56 (191)
96 TIGR01448 recD_rel helicase, p 28.6 3.1E+02 0.0066 35.3 10.4 57 599-667 143-200 (720)
97 PRK13901 ruvA Holliday junctio 27.6 49 0.0011 36.1 2.8 22 645-666 69-90 (196)
98 PRK14600 ruvA Holliday junctio 27.4 48 0.001 35.7 2.7 22 645-666 70-91 (186)
99 PRK14601 ruvA Holliday junctio 26.7 51 0.0011 35.5 2.8 22 645-666 70-91 (183)
100 cd00080 HhH2_motif Helix-hairp 26.3 33 0.00071 31.6 1.1 20 648-667 22-41 (75)
101 PRK14606 ruvA Holliday junctio 26.2 53 0.0011 35.4 2.8 23 644-666 69-91 (188)
102 PRK14603 ruvA Holliday junctio 26.0 53 0.0011 35.6 2.8 22 645-666 69-90 (197)
103 TIGR00426 competence protein C 25.4 67 0.0015 28.6 2.9 21 647-667 15-36 (69)
104 PRK14604 ruvA Holliday junctio 24.8 56 0.0012 35.4 2.7 22 645-666 70-91 (195)
105 PRK00254 ski2-like helicase; P 24.2 1.5E+02 0.0032 37.7 6.5 23 649-671 646-668 (720)
106 PRK14602 ruvA Holliday junctio 24.2 60 0.0013 35.3 2.8 23 645-667 71-93 (203)
107 PRK07758 hypothetical protein; 24.0 1E+02 0.0023 30.4 4.0 28 634-665 57-84 (95)
108 PF00416 Ribosomal_S13: Riboso 22.6 78 0.0017 31.0 3.0 23 645-667 12-34 (107)
109 PRK08609 hypothetical protein; 22.6 1.7E+02 0.0036 36.6 6.4 57 600-667 11-67 (570)
110 KOG0028 Ca2+-binding protein ( 21.4 2.4E+02 0.0051 30.6 6.3 98 597-705 50-150 (172)
111 PRK02515 psbU photosystem II c 21.4 73 0.0016 33.0 2.6 20 647-666 60-79 (132)
112 COG0632 RuvA Holliday junction 20.8 75 0.0016 34.8 2.7 23 645-667 70-92 (201)
No 1
>PF15628 RRM_DME: RRM in Demeter
Probab=100.00 E-value=4.6e-69 Score=497.45 Aligned_cols=103 Identities=67% Similarity=1.197 Sum_probs=102.1
Q ss_pred eeEEeecccccCCCCCCCccceeeeeeeeccCCCCCCcccchhhhhcccceeEEecCchhhhhcccCHHHHHHHHhhcce
Q 001299 989 GTILIPCRTANRGRFPLNGTYFQVNEVFADHETSHHPINVPRHTIANLRREIVCFGSSATTLFNALDMRQIQEYFWRGFV 1068 (1105)
Q Consensus 989 gTiLiPCRTAmrG~FPLNGTYFQvNEVFaDh~SS~~PI~Vpr~~iw~L~rr~VYfGtSv~sIfkglt~~~Iq~cF~~G~v 1068 (1105)
|||||||||||||+|||||||||||||||||+||+|||+|||+|||+|+||+|||||||+|||||||++|||+|||+|||
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 001299 1069 CVRGFDRRYRCPRPLVNRLHCSP 1091 (1105)
Q Consensus 1069 CVR~fdr~tr~PrpL~~rlh~~~ 1091 (1105)
|||||||+||+||||++|||+++
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=2.8e-40 Score=345.26 Aligned_cols=183 Identities=30% Similarity=0.431 Sum_probs=172.0
Q ss_pred CcccccceeceecccccHHHHHHHHHHhhhhccCCCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHh
Q 001299 551 TKKTTPKKNSDNTVQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELH 630 (1105)
Q Consensus 551 ~k~~~~~vgaILsQQTsw~~V~ka~~rL~er~~~~~~fpTpEaLA~Ad~EELeelIR~lGf~n~KAk~Ik~lA~~Ive~~ 630 (1105)
..+...+|..||+||+.-+.+.++..+|.+ .++||++|+.|++++|+++|+.+|||++||++|+++++.|+++|
T Consensus 27 ~~pf~lLva~iLSaqttD~~vn~at~~Lf~------~~~t~e~l~~a~~~~l~~~I~~iGlyr~KAk~I~~~~~~l~e~~ 100 (211)
T COG0177 27 KDPFELLVAVILSAQTTDEVVNKATPALFK------RYPTPEDLLNADEEELEELIKSIGLYRNKAKNIKELARILLEKF 100 (211)
T ss_pred CCcHHHHHHHHHhccCchHHHHHHHHHHHH------HcCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHc
Confidence 357777899999999999999999999964 57799999999999999999999999999999999999999999
Q ss_pred CCCChhhhhCCCchHHHHHHhcCCCCcHHHHHHHHHHhcCCeeeecchHHHHHHHHhCCCCCCCChHHHHHHHHhhCCch
Q 001299 631 GSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPLQPLPGDLHIHLLKEYPVM 710 (1105)
Q Consensus 631 GglDLE~Lr~vP~deaReeLLsLpGIG~KTAd~ILLfalgrpvfPVDThV~RIl~RLG~Vp~k~tpeeiE~~Leel~P~~ 710 (1105)
|| .+|.+ +++|++|||||+|||++||.++||.|+|+|||||.||.+|+||++ ..+|++++..|++++|
T Consensus 101 ~g-------~vP~~--~~eL~~LPGVGrKTAnvVL~~a~g~p~i~VDTHV~Rvs~R~gl~~-~~~p~~ve~~L~~~iP-- 168 (211)
T COG0177 101 GG-------EVPDT--REELLSLPGVGRKTANVVLSFAFGIPAIAVDTHVHRVSNRLGLVP-GKTPEEVEEALMKLIP-- 168 (211)
T ss_pred CC-------CCCch--HHHHHhCCCcchHHHHHHHHhhcCCCcccccchHHHHHHHhCCCC-CCCHHHHHHHHHHHCC--
Confidence 99 79988 999999999999999999999999999999999999999999998 5799999999999998
Q ss_pred hhhhhhhhhhcccCChhhHHHHHHHHHHHhHHhccCCCCCCCCCCCccchhhHhhh
Q 001299 711 DKIQMYLWPRLCYLDQKTLYELHYQMITFGKIFCKKRSPNCGACPLRGECKHFASA 766 (1105)
Q Consensus 711 e~Iqk~lW~rL~~ld~e~l~eLH~lLIdfGR~ICtarkP~Cd~CPLr~~C~yyas~ 766 (1105)
+++|. .+|.+||.|||.+|++++|+|+.||+++.|+++...
T Consensus 169 ----~~~~~-----------~~h~~lI~~GR~iC~ar~P~C~~C~l~~~C~~~~~~ 209 (211)
T COG0177 169 ----KELWT-----------DLHHWLILHGRYICKARKPRCEECPLADLCPSAGKT 209 (211)
T ss_pred ----HHHHH-----------HHHHHHHHhhhhhccCCCCCcCcccchhhCchhccc
Confidence 55564 999999999999999999999999999999998653
No 3
>PRK10702 endonuclease III; Provisional
Probab=100.00 E-value=1.7e-38 Score=332.53 Aligned_cols=181 Identities=20% Similarity=0.212 Sum_probs=165.3
Q ss_pred cccccceeceecccccHHHHHHHHHHhhhhccCCCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhC
Q 001299 552 KKTTPKKNSDNTVQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHG 631 (1105)
Q Consensus 552 k~~~~~vgaILsQQTsw~~V~ka~~rL~er~~~~~~fpTpEaLA~Ad~EELeelIR~lGf~n~KAk~Ik~lA~~Ive~~G 631 (1105)
.+...+|++||+|||+|.++.+++.+|.. .+|+|++|++|+.++|+++|+++|||++||++|+++|+.+.++||
T Consensus 28 ~p~e~lvs~iLsq~t~~~~v~~~~~~L~~------~~pt~e~l~~a~~~~l~~~i~~~G~y~~kA~~l~~~a~~i~~~~~ 101 (211)
T PRK10702 28 SPFELLIAVLLSAQATDVSVNKATAKLYP------VANTPAAMLELGVEGVKTYIKTIGLYNSKAENVIKTCRILLEQHN 101 (211)
T ss_pred ChHHHHHHHHHHhhcCHHHHHHHHHHHHH------HcCCHHHHHCCCHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHcC
Confidence 35667899999999999999999999963 589999999999999999999999999999999999999999888
Q ss_pred CCChhhhhCCCchHHHHHHhcCCCCcHHHHHHHHHHhcCCeeeecchHHHHHHHHhCCCCCCCChHHHHHHHHhhCCchh
Q 001299 632 SIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPLQPLPGDLHIHLLKEYPVMD 711 (1105)
Q Consensus 632 glDLE~Lr~vP~deaReeLLsLpGIG~KTAd~ILLfalgrpvfPVDThV~RIl~RLG~Vp~k~tpeeiE~~Leel~P~~e 711 (1105)
+ .+|.+ +++|++|||||+|||++||+|+||+++||||+||.||+.|+||.+. .++++++..+++.+|
T Consensus 102 ~-------~~p~~--~~~Ll~lpGVG~ktA~~ill~a~~~~~~~VDt~v~Rv~~r~g~~~~-~~~~~~~~~l~~~lp--- 168 (211)
T PRK10702 102 G-------EVPED--RAALEALPGVGRKTANVVLNTAFGWPTIAVDTHIFRVCNRTQFAPG-KNVEQVEEKLLKVVP--- 168 (211)
T ss_pred C-------CCCch--HHHHhcCCcccHHHHHHHHHHHcCCCcccccchHHHHHHHhCCCCC-CCHHHHHHHHHHhCC---
Confidence 7 56766 9999999999999999999999999999999999999999999864 578999999998887
Q ss_pred hhhhhhhhhcccCChhhHHHHHHHHHHHhHHhccCCCCCCCCCCCccchhhHhh
Q 001299 712 KIQMYLWPRLCYLDQKTLYELHYQMITFGKIFCKKRSPNCGACPLRGECKHFAS 765 (1105)
Q Consensus 712 ~Iqk~lW~rL~~ld~e~l~eLH~lLIdfGR~ICtarkP~Cd~CPLr~~C~yyas 765 (1105)
+..| .++|.+||+||+.+|++++|+|+.|||++.|+|+.+
T Consensus 169 ---~~~~-----------~~~~~~li~~Gr~~C~~~~P~C~~Cpl~~~C~~~~~ 208 (211)
T PRK10702 169 ---AEFK-----------VDCHHWLILHGRYTCIARKPRCGSCIIEDLCEYKEK 208 (211)
T ss_pred ---chHH-----------HHHHHHHHHHhHHHcCCCCCCCCCCcChhhcCcccc
Confidence 3334 389999999999999999999999999999997643
No 4
>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=1.3e-34 Score=313.83 Aligned_cols=191 Identities=19% Similarity=0.217 Sum_probs=165.1
Q ss_pred cccccceeceecccccHHHHHHHHHHhhhhccCCCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhC
Q 001299 552 KKTTPKKNSDNTVQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHG 631 (1105)
Q Consensus 552 k~~~~~vgaILsQQTsw~~V~ka~~rL~er~~~~~~fpTpEaLA~Ad~EELeelIR~lGf~n~KAk~Ik~lA~~Ive~~G 631 (1105)
.+-..++++||+|||++++|.+++.+|.+ .|||+++|+++++++|.++|+++|||+ ||++|+++|+.|.++||
T Consensus 25 dpy~vlvseIL~QQT~v~~v~~~~~rl~~------~fpt~~~La~a~~eeL~~~~~~lG~y~-RAr~L~~~A~~i~~~~~ 97 (275)
T TIGR01084 25 TPYRVWLSEVMLQQTQVATVIPYFERFLE------RFPTVQALANAPQDEVLKLWEGLGYYA-RARNLHKAAQEVVEEFG 97 (275)
T ss_pred CHHHHHHHHHHHhhccHHHHHHHHHHHHH------hCCCHHHHHCcCHHHHHHHHHHCCcHH-HHHHHHHHHHHHHHHcC
Confidence 35667899999999999999999999974 589999999999999999999999995 99999999999999998
Q ss_pred CCChhhhhCCCchHHHHHHhcCCCCcHHHHHHHHHHhcCCeeeecchHHHHHHHHhCCCCCCCChHHHHHHH----HhhC
Q 001299 632 SIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPLQPLPGDLHIHL----LKEY 707 (1105)
Q Consensus 632 glDLE~Lr~vP~deaReeLLsLpGIG~KTAd~ILLfalgrpvfPVDThV~RIl~RLG~Vp~k~tpeeiE~~L----eel~ 707 (1105)
+ .+|.+ +++|++|||||+|||+|||+|+||+++++||+||.||+.|++......++.++++.+ ++++
T Consensus 98 g-------~~p~~--~~~L~~LpGIG~~TA~~Il~~a~~~~~~~vD~~v~RVl~Rl~~~~~~~~~~~~~~~l~~~~~~~l 168 (275)
T TIGR01084 98 G-------EFPQD--FEDLAALPGVGRYTAGAILSFALNKPYPILDGNVKRVLSRLFAVEGWPGKKKVENRLWTLAESLL 168 (275)
T ss_pred C-------CCcHH--HHHHHhCCCCCHHHHHHHHHHHCCCCCCcchHhHHHHHHHHccCcCCCCHHHHHHHHHHHHHHHC
Confidence 7 47766 899999999999999999999999999999999999999997665545566666653 4443
Q ss_pred CchhhhhhhhhhhcccCChhhHHHHHHHHHHHhHHhccCCCCCCCCCCCccchhhHhhhhccccccCCCCC
Q 001299 708 PVMDKIQMYLWPRLCYLDQKTLYELHYQMITFGKIFCKKRSPNCGACPLRGECKHFASAVASARFALPGPS 778 (1105)
Q Consensus 708 P~~e~Iqk~lW~rL~~ld~e~l~eLH~lLIdfGR~ICtarkP~Cd~CPLr~~C~yyas~~asar~alp~p~ 778 (1105)
| ...++.||++||+||+.+|++++|+|+.|||+..|.+|..+.. ..+|.+.
T Consensus 169 p-----------------~~~~~~~n~alm~lG~~vC~~~~P~C~~Cpl~~~C~~~~~~~~---~~~p~~~ 219 (275)
T TIGR01084 169 P-----------------KADPEAFNQALMDLGAMICTRKKPKCDLCPLQDFCLAYQQGTW---EEYPVKK 219 (275)
T ss_pred C-----------------hhhHHHHHHHHHHHhHHHcCCCCCCCCCCCChhhCHHHHcCCH---hhcCCCC
Confidence 3 3456799999999999999999999999999999999987632 3455443
No 5
>PRK10880 adenine DNA glycosylase; Provisional
Probab=100.00 E-value=1.7e-34 Score=321.62 Aligned_cols=187 Identities=18% Similarity=0.195 Sum_probs=161.4
Q ss_pred cccccceeceecccccHHHHHHHHHHhhhhccCCCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhC
Q 001299 552 KKTTPKKNSDNTVQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHG 631 (1105)
Q Consensus 552 k~~~~~vgaILsQQTsw~~V~ka~~rL~er~~~~~~fpTpEaLA~Ad~EELeelIR~lGf~n~KAk~Ik~lA~~Ive~~G 631 (1105)
.+-...|++||+|||+|++|.+++.+|.+ .|||+++|++|++++|.++|+++|||+ ||++|+++|+.|+++||
T Consensus 29 dpy~ilVseILlQQT~v~~v~~~~~rl~~------~fPt~~~La~a~~eel~~~~~glGyy~-RAr~L~~~A~~i~~~~~ 101 (350)
T PRK10880 29 TPYKVWLSEVMLQQTQVATVIPYFERFMA------RFPTVTDLANAPLDEVLHLWTGLGYYA-RARNLHKAAQQVATLHG 101 (350)
T ss_pred CHHHHHHHHHHHhhccHHHHHHHHHHHHH------HCcCHHHHHCcCHHHHHHHHHcCChHH-HHHHHHHHHHHHHHHhC
Confidence 35667889999999999999999999974 589999999999999999999999997 99999999999999998
Q ss_pred CCChhhhhCCCchHHHHHHhcCCCCcHHHHHHHHHHhcCCeeeecchHHHHHHHHhCCCCCCCChHHHHHHHHhhCCchh
Q 001299 632 SIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPLQPLPGDLHIHLLKEYPVMD 711 (1105)
Q Consensus 632 glDLE~Lr~vP~deaReeLLsLpGIG~KTAd~ILLfalgrpvfPVDThV~RIl~RLG~Vp~k~tpeeiE~~Leel~P~~e 711 (1105)
| .+|.+ +++|++|||||+|||+|||+|+||+++++||+||.||+.|++.+...+.+.++++.+.++..
T Consensus 102 g-------~~p~~--~~~L~~LpGIG~~TA~aIl~~af~~~~~iVD~nV~RV~~Rl~~i~~~~~~~~~~~~l~~~~~--- 169 (350)
T PRK10880 102 G-------EFPET--FEEVAALPGVGRSTAGAILSLSLGKHFPILDGNVKRVLARCYAVSGWPGKKEVENRLWQLSE--- 169 (350)
T ss_pred C-------Cchhh--HHHHhcCCCccHHHHHHHHHHHCCCCeecccHHHHHHHHHHhcccCCCChHHHHHHHHHHHH---
Confidence 7 46765 89999999999999999999999999999999999999998554433455566655543321
Q ss_pred hhhhhhhhhcccCChhhHHHHHHHHHHHhHHhccCCCCCCCCCCCccchhhHhhhh
Q 001299 712 KIQMYLWPRLCYLDQKTLYELHYQMITFGKIFCKKRSPNCGACPLRGECKHFASAV 767 (1105)
Q Consensus 712 ~Iqk~lW~rL~~ld~e~l~eLH~lLIdfGR~ICtarkP~Cd~CPLr~~C~yyas~~ 767 (1105)
. .++.+.+++||++||+||+.+|++++|+|..|||+..|.+|+.+.
T Consensus 170 ----~------l~p~~~~~~~nqalm~lGa~vC~p~~P~C~~Cpl~~~C~~~~~~~ 215 (350)
T PRK10880 170 ----Q------VTPAVGVERFNQAMMDLGAMVCTRSKPKCELCPLQNGCIAYANHS 215 (350)
T ss_pred ----H------hCChhHHHHHHHHHHHhhHHhccCCCCCCCCCccHhhhHHHHcCC
Confidence 0 123456789999999999999999999999999999999998763
No 6
>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=100.00 E-value=3.7e-33 Score=286.98 Aligned_cols=167 Identities=26% Similarity=0.249 Sum_probs=151.6
Q ss_pred cccccceeceecccccHHHHHHHHHHhhhhccCCCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhC
Q 001299 552 KKTTPKKNSDNTVQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHG 631 (1105)
Q Consensus 552 k~~~~~vgaILsQQTsw~~V~ka~~rL~er~~~~~~fpTpEaLA~Ad~EELeelIR~lGf~n~KAk~Ik~lA~~Ive~~G 631 (1105)
.+...++++||+|||+|+++.+++.+|.. .+|||++|+.++.++|+++|+++||+++||++|+++|+.+.++++
T Consensus 25 dpf~~Li~~ILsqqt~~~~~~~~~~~l~~------~~pt~~~l~~~~~~~L~~~ir~~G~~~~Ka~~i~~~a~~i~~~~~ 98 (191)
T TIGR01083 25 NPFELLVATILSAQATDKSVNKATKKLFE------VYPTPQALAQAGLEELEEYIKSIGLYRNKAKNIIALCRILVERYG 98 (191)
T ss_pred CHHHHHHHHHHHhhCcHHHHHHHHHHHHH------HCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHcC
Confidence 35667899999999999999999999964 589999999999999999999999999999999999999999887
Q ss_pred CCChhhhhCCCchHHHHHHhcCCCCcHHHHHHHHHHhcCCeeeecchHHHHHHHHhCCCCCCCChHHHHHHHHhhCCchh
Q 001299 632 SIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPLQPLPGDLHIHLLKEYPVMD 711 (1105)
Q Consensus 632 glDLE~Lr~vP~deaReeLLsLpGIG~KTAd~ILLfalgrpvfPVDThV~RIl~RLG~Vp~k~tpeeiE~~Leel~P~~e 711 (1105)
+ .+|. +++.|++|||||+|||+|||+|+|++++||||+||.|++.|+||... .++++++..++.++|.
T Consensus 99 ~-------~~~~--~~~~L~~l~GIG~ktA~~ill~~~~~~~~~vD~~v~Ri~~r~g~~~~-~~~~~~~~~l~~~~p~-- 166 (191)
T TIGR01083 99 G-------EVPE--DREELVKLPGVGRKTANVVLNVAFGIPAIAVDTHVFRVSNRLGLSKG-KDPDKVEEELLKLIPR-- 166 (191)
T ss_pred C-------CCch--HHHHHHhCCCCcHHHHHHHHHHHcCCCccccchhHHHHHHHcCCCCC-CCHHHHHHHHHHHCCc--
Confidence 6 3454 48999999999999999999999999999999999999999999864 5789999999988872
Q ss_pred hhhhhhhhhcccCChhhHHHHHHHHHHHhHHhccCCCCCC
Q 001299 712 KIQMYLWPRLCYLDQKTLYELHYQMITFGKIFCKKRSPNC 751 (1105)
Q Consensus 712 ~Iqk~lW~rL~~ld~e~l~eLH~lLIdfGR~ICtarkP~C 751 (1105)
. .+.+||.+||+||+.+|++++|+|
T Consensus 167 ----~-----------~~~~~h~~li~~G~~~C~~~~P~C 191 (191)
T TIGR01083 167 ----E-----------FWTKLHHWLILHGRYTCKARKPLC 191 (191)
T ss_pred ----h-----------hHHHHHHHHHHHhHHhcCCCCCCC
Confidence 2 245999999999999999999999
No 7
>PRK13910 DNA glycosylase MutY; Provisional
Probab=100.00 E-value=2.1e-32 Score=298.29 Aligned_cols=172 Identities=22% Similarity=0.313 Sum_probs=149.2
Q ss_pred ecccccHHHHHH-HHHHhhhhccCCCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhC
Q 001299 562 NTVQQDWDLLRR-IYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRN 640 (1105)
Q Consensus 562 LsQQTsw~~V~k-a~~rL~er~~~~~~fpTpEaLA~Ad~EELeelIR~lGf~n~KAk~Ik~lA~~Ive~~GglDLE~Lr~ 640 (1105)
+.|||..++|.. .|.+|.+ .|||+++|++|++++|+++|+++|||+ ||++|+++|+.|.++|+| .
T Consensus 1 mlQQT~v~~v~~~yy~rf~~------~fPt~e~La~a~~~el~~~~~glGyy~-RAr~L~~~A~~i~~~~~g-------~ 66 (289)
T PRK13910 1 MSQQTQINTVVERFYSPFLE------AFPTLKDLANAPLEEVLLLWRGLGYYS-RAKNLKKSAEICVKEHHS-------Q 66 (289)
T ss_pred CCCCCcHHHhHHHHHHHHHH------HCCCHHHHHCCCHHHHHHHHHcCCcHH-HHHHHHHHHHHHHHHhCC-------C
Confidence 469999999975 9999964 699999999999999999999999996 999999999999999887 5
Q ss_pred CCchHHHHHHhcCCCCcHHHHHHHHHHhcCCeeeecchHHHHHHHHh-CCCCCCCChHHHHHHHHhhCCchhhhhhhhhh
Q 001299 641 VPPDKVKEYLLDIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRL-GWVPLQPLPGDLHIHLLKEYPVMDKIQMYLWP 719 (1105)
Q Consensus 641 vP~deaReeLLsLpGIG~KTAd~ILLfalgrpvfPVDThV~RIl~RL-G~Vp~k~tpeeiE~~Leel~P~~e~Iqk~lW~ 719 (1105)
+|.+ +++|++|||||+|||++||+|+||+++++||+||.||+.|+ |+... ..+.+++...++++|
T Consensus 67 ~P~~--~~~L~~LpGIG~kTA~aIl~~af~~~~~~VD~nV~RVl~Rl~g~~~~-~~~~~l~~~~~~~l~----------- 132 (289)
T PRK13910 67 LPND--YQSLLKLPGIGAYTANAILCFGFREKSACVDANIKRVLLRLFGLDPN-IHAKDLQIKANDFLN----------- 132 (289)
T ss_pred CChh--HHHHHhCCCCCHHHHHHHHHHHCCCCcCcccHHHHHHHHHHhcCCCC-ccHHHHHHHHHHhCC-----------
Confidence 7877 89999999999999999999999999999999999999997 77542 344444433334443
Q ss_pred hcccCChhhHHHHHHHHHHHhHHhccCCCCCCCCCCCccchhhHhhhhc
Q 001299 720 RLCYLDQKTLYELHYQMITFGKIFCKKRSPNCGACPLRGECKHFASAVA 768 (1105)
Q Consensus 720 rL~~ld~e~l~eLH~lLIdfGR~ICtarkP~Cd~CPLr~~C~yyas~~a 768 (1105)
...++.+|++||+||+.+|++ +|+|..|||++.|.+|..+..
T Consensus 133 ------~~~~~~~nqaLm~~Ga~iC~~-~P~C~~CPl~~~C~~~~~~~~ 174 (289)
T PRK13910 133 ------LNESFNHNQALIDLGALICSP-KPKCAICPLNPYCLGKNNPEK 174 (289)
T ss_pred ------ccchHHHHHHHHHHhHHHcCC-CCCCCCCcChhhhhhhhcCCc
Confidence 235679999999999999999 799999999999999987643
No 8
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=99.97 E-value=8.4e-32 Score=278.45 Aligned_cols=182 Identities=24% Similarity=0.427 Sum_probs=161.5
Q ss_pred cceeceecccccHHHHHHHHHHhhhhccCCCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCCh
Q 001299 556 PKKNSDNTVQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDL 635 (1105)
Q Consensus 556 ~~vgaILsQQTsw~~V~ka~~rL~er~~~~~~fpTpEaLA~Ad~EELeelIR~lGf~n~KAk~Ik~lA~~Ive~~GglDL 635 (1105)
.++||||+|+|+|++|.+++++|+. .+-.++++|..++.++|+++||+.|||++||+||+++...++..|.++
T Consensus 33 iiigAILtQNT~WknvekAlenLk~-----~~~~~l~~I~~~~~~~L~elIrpsGFYnqKa~rLk~l~k~l~~~~~~~-- 105 (215)
T COG2231 33 IIIGAILTQNTSWKNVEKALENLKN-----EGILNLKKILKLDEEELAELIRPSGFYNQKAKRLKALSKNLAKFFINL-- 105 (215)
T ss_pred HHHHHHHhccccHHHHHHHHHHHHH-----cccCCHHHHhcCCHHHHHHHHhccchHHHHHHHHHHHHHHHHHHhhhh--
Confidence 5789999999999999999999975 566789999999999999999999999999999999999998876553
Q ss_pred hhhhCCCchHHHHHHhcCCCCcHHHHHHHHHHhcCCeeeecchHHHHHHHHhCCCCCCCChHHHHHHHHhhCCchhhhhh
Q 001299 636 EWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPLQPLPGDLHIHLLKEYPVMDKIQM 715 (1105)
Q Consensus 636 E~Lr~vP~deaReeLLsLpGIG~KTAd~ILLfalgrpvfPVDThV~RIl~RLG~Vp~k~tpeeiE~~Leel~P~~e~Iqk 715 (1105)
+ .+-...+|++|++|+|||..|||.||+|+|++|+|+||.+.+|++.|+|.+..+ ++++++...++-+|.
T Consensus 106 ~---~~~~~~~R~~LL~iKGIG~ETaDsILlYa~~rp~FVvD~Yt~R~l~rlg~i~~k-~ydeik~~fe~~l~~------ 175 (215)
T COG2231 106 E---SFKSEVLREELLSIKGIGKETADSILLYALDRPVFVVDKYTRRLLSRLGGIEEK-KYDEIKELFEENLPE------ 175 (215)
T ss_pred h---ccchHHHHHHHHccCCcchhhHHHHHHHHhcCcccchhHHHHHHHHHhcccccc-cHHHHHHHHHhcchh------
Confidence 2 344445799999999999999999999999999999999999999999998764 899999888877761
Q ss_pred hhhhhcccCChhhHHHHHHHHHHHhHHhccCCCCCCCCCCCccchhhHh
Q 001299 716 YLWPRLCYLDQKTLYELHYQMITFGKIFCKKRSPNCGACPLRGECKHFA 764 (1105)
Q Consensus 716 ~lW~rL~~ld~e~l~eLH~lLIdfGR~ICtarkP~Cd~CPLr~~C~yya 764 (1105)
+...+.+||.+|+.|||.+|++ +|.|+.|||+..|.++.
T Consensus 176 ---------~~~lyqe~HAlIv~~~K~f~~k-~~~~~~cpL~~~~~~~~ 214 (215)
T COG2231 176 ---------NLRLYQEFHALIVEHAKHFCKK-KPLCEKCPLKEKCKKYR 214 (215)
T ss_pred ---------HHHHHHHHHHHHHHHHHHHccC-CcCCCCchHHHHHhhcc
Confidence 2235779999999999999987 59999999999998764
No 9
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=99.97 E-value=7e-31 Score=276.63 Aligned_cols=184 Identities=15% Similarity=0.166 Sum_probs=149.8
Q ss_pred cccccceeceecccccHHHHHHHHHHhhhhcc-CCCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHh
Q 001299 552 KKTTPKKNSDNTVQQDWDLLRRIYSTGEERSH-DKMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELH 630 (1105)
Q Consensus 552 k~~~~~vgaILsQQTsw~~V~ka~~rL~er~~-~~~~fpTpEaLA~Ad~EELeelIR~lGf~n~KAk~Ik~lA~~Ive~~ 630 (1105)
.+...++++||+|||+|+++.+++.+|..++. +..++++|++|++++.++|+++||++||+++||++|+++|+.+.+++
T Consensus 29 ~~fevLV~aILsQqT~~~~v~~a~~~L~~~~~~~~~~~~t~e~L~~a~~eeL~~~Irp~Gf~~~KA~~Lk~la~~i~~~~ 108 (218)
T PRK13913 29 LKFEALLGAVLTQNTKFEAVEKSLENLKNAFILENDDEINLKKIAYIEFSKLAECVRPSGFYNQKAKRLIDLSENILKDF 108 (218)
T ss_pred CHHHHHHHHHHHhhhhHHHHHHHHHHHHHhcccccccCCCHHHHHcCCHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHc
Confidence 35667899999999999999999999965321 01246799999999999999999999999999999999999999988
Q ss_pred CCCChhhhhCCCchHHHHHHhcCCCCcHHHHHHHHHHhcCCeeeecchHHHHHHHHhCCCCCCCChHHHHHHHHhhCCch
Q 001299 631 GSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPLQPLPGDLHIHLLKEYPVM 710 (1105)
Q Consensus 631 GglDLE~Lr~vP~deaReeLLsLpGIG~KTAd~ILLfalgrpvfPVDThV~RIl~RLG~Vp~k~tpeeiE~~Leel~P~~ 710 (1105)
|++ +.+ ...++|++|++|||||+|||++||+|+|++|+|+||+|++||+.|+||.. .+|++++..++..++
T Consensus 109 g~~--~~~---~~~~~re~Ll~l~GIG~kTAd~iLlya~~rp~fvVDty~~Rv~~RlG~~~--~~y~~~~~~~~~~l~-- 179 (218)
T PRK13913 109 GSF--ENF---KQEVTREWLLDQKGIGKESADAILCYVCAKEVMVVDKYSYLFLKKLGIEI--EDYDELQHFFEKGVQ-- 179 (218)
T ss_pred CCc--hhc---cCchHHHHHHcCCCccHHHHHHHHHHHcCCCccccchhHHHHHHHcCCCC--CCHHHHHHHHHHhhh--
Confidence 763 322 23356999999999999999999999999999999999999999999975 479999998888663
Q ss_pred hhhhhhhhhhcccC---ChhhHHHHHHHHHHHhHHhccC
Q 001299 711 DKIQMYLWPRLCYL---DQKTLYELHYQMITFGKIFCKK 746 (1105)
Q Consensus 711 e~Iqk~lW~rL~~l---d~e~l~eLH~lLIdfGR~ICta 746 (1105)
+.+.+ +... -+. ....+.+||.+|++||+..|.-
T Consensus 180 ~~~~~-~~~~-~~~~~~~~~~~~~~Halive~~k~~~~~ 216 (218)
T PRK13913 180 ENLNS-ALAL-YENTISLAQLYARFHGKIVEFSKQKLEL 216 (218)
T ss_pred hhhhh-hhcc-ccccchHHHHHHHHHHHHHHHHHHhhhc
Confidence 11110 0000 001 2357899999999999999964
No 10
>KOG1921 consensus Endonuclease III [Replication, recombination and repair]
Probab=99.96 E-value=6.1e-30 Score=269.34 Aligned_cols=180 Identities=26% Similarity=0.386 Sum_probs=166.8
Q ss_pred ccccceeceecccccHHHHHHHHHHhhhhccCCCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCC
Q 001299 553 KTTPKKNSDNTVQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGS 632 (1105)
Q Consensus 553 ~~~~~vgaILsQQTsw~~V~ka~~rL~er~~~~~~fpTpEaLA~Ad~EELeelIR~lGf~n~KAk~Ik~lA~~Ive~~Gg 632 (1105)
...++++.+|+-||.-+....++.||++ .+.+|+++|+++++..|.++|.++|||++||+||+..|+.+.++|+|
T Consensus 78 RfqvLv~lmLSSQTKDevt~~Am~rL~~-----~~gLT~e~v~~~de~~l~~LI~~VgFy~rKA~ylkkta~IL~d~f~g 152 (286)
T KOG1921|consen 78 RFQVLVGLMLSSQTKDEVTAAAMLRLKE-----YGGLTLEAVLKIDEPTLNELIYPVGFYTRKAKYLKKTAKILQDKFDG 152 (286)
T ss_pred hHHHHHHHHHhcchHHHHHHHHHHHHHH-----hcCCCHHHHhccChHhHHhhhhhccchHHHHHHHHHHHHHHHHHhCC
Confidence 4455789999999999999999999976 35799999999999999999999999999999999999999999998
Q ss_pred CChhhhhCCCchHHHHHHhcCCCCcHHHHHHHHHHhcCC-eeeecchHHHHHHHHhCCCCCC-CChHHHHHHHHhhCCch
Q 001299 633 IDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQH-IAFPVDVNVGRIAVRLGWVPLQ-PLPGDLHIHLLKEYPVM 710 (1105)
Q Consensus 633 lDLE~Lr~vP~deaReeLLsLpGIG~KTAd~ILLfalgr-pvfPVDThV~RIl~RLG~Vp~k-~tpeeiE~~Leel~P~~ 710 (1105)
++|++ .+.|++|||||+|.|..+|..|+|. ..+.||+||+||.+||||++.+ .+||+++..|+.++|
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 79999 8999999999999999999999998 5899999999999999999854 359999999999998
Q ss_pred hhhhhhhhhhcccCChhhHHHHHHHHHHHhHHhccCCCCCCCCCCC-ccchhhH
Q 001299 711 DKIQMYLWPRLCYLDQKTLYELHYQMITFGKIFCKKRSPNCGACPL-RGECKHF 763 (1105)
Q Consensus 711 e~Iqk~lW~rL~~ld~e~l~eLH~lLIdfGR~ICtarkP~Cd~CPL-r~~C~yy 763 (1105)
+.+|. ++|.+|+.||+.||++++|+|+.|-+ ++.|+..
T Consensus 222 ----k~lW~-----------eIN~lLVGFGQ~iC~p~~prC~~C~~~~~~Cpss 260 (286)
T KOG1921|consen 222 ----KSLWV-----------EINHLLVGFGQTICTPRRPRCGLCLLSRDLCPSS 260 (286)
T ss_pred ----HHHHh-----------hhhceeecccceeeecCCCCccccccCcccCchh
Confidence 67775 99999999999999999999999999 7999963
No 11
>COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair]
Probab=99.95 E-value=4.1e-28 Score=267.77 Aligned_cols=184 Identities=20% Similarity=0.266 Sum_probs=158.5
Q ss_pred ccccceeceecccccHHHHHHHHHHhhhhccCCCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCC
Q 001299 553 KTTPKKNSDNTVQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGS 632 (1105)
Q Consensus 553 ~~~~~vgaILsQQTsw~~V~ka~~rL~er~~~~~~fpTpEaLA~Ad~EELeelIR~lGf~n~KAk~Ik~lA~~Ive~~Gg 632 (1105)
+=++.|..|+.|||..+.|...|.++.+ .|||+++||+|+.+||..+|.++|||. ||++|+.+|+.++++|||
T Consensus 34 PY~VwvSEiMLQQT~v~~Vi~yy~~fl~------rfPti~~LA~A~~~evl~~W~gLGYys-RArnL~~~A~~v~~~~~G 106 (342)
T COG1194 34 PYRVWVSEIMLQQTQVATVIPYYERFLE------RFPTIKALAAAPEDEVLKAWEGLGYYS-RARNLHKAAQEVVERHGG 106 (342)
T ss_pred cceehhHHHHhhhccHhhhhhhHHHHHH------hCCCHHHHhcCCHHHHHHHHHhcChHH-HHHHHHHHHHHHHHHcCC
Confidence 6667889999999999999999999974 699999999999999999999999776 999999999999999999
Q ss_pred CChhhhhCCCchHHHHHHhcCCCCcHHHHHHHHHHhcCCeeeecchHHHHHHHHhCCCCCCC----ChHHHHHHHHhhCC
Q 001299 633 IDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPLQP----LPGDLHIHLLKEYP 708 (1105)
Q Consensus 633 lDLE~Lr~vP~deaReeLLsLpGIG~KTAd~ILLfalgrpvfPVDThV~RIl~RLG~Vp~k~----tpeeiE~~Leel~P 708 (1105)
.+|++ .+.|.+|||||++||.+||.|+|+++...||+||.||+.|+.-+.... +...+...++.++.
T Consensus 107 -------~~P~~--~~~l~~LpGiG~yTa~Ail~~a~~~~~~~lDgNV~RVl~R~f~i~~~~~~~~~~~~~~~~~~~ll~ 177 (342)
T COG1194 107 -------EFPDD--EEELAALPGVGPYTAGAILSFAFNQPEPVLDGNVKRVLSRLFAISGDIGKPKTKKELWELAEQLLT 177 (342)
T ss_pred -------CCCCC--HHHHHhCCCCcHHHHHHHHHHHhCCCCceeecchheeehhhhcccccccccchhHHHHHHHHHhcC
Confidence 69999 789999999999999999999999999999999999999995443221 12233333333221
Q ss_pred chhhhhhhhhhhcccCChhhHHHHHHHHHHHhHHhccCCCCCCCCCCCccchhhHhhhhc
Q 001299 709 VMDKIQMYLWPRLCYLDQKTLYELHYQMITFGKIFCKKRSPNCGACPLRGECKHFASAVA 768 (1105)
Q Consensus 709 ~~e~Iqk~lW~rL~~ld~e~l~eLH~lLIdfGR~ICtarkP~Cd~CPLr~~C~yyas~~a 768 (1105)
....+.+|+++||++|+.||++++|+|..|||+..|..|..+.-
T Consensus 178 ----------------p~~~~~~fnqammdlGA~ICt~~~P~C~~CPl~~~c~a~~~g~~ 221 (342)
T COG1194 178 ----------------PDRRPGDFNQAMMDLGATICTAKKPKCSLCPLRDNCAAYRNGTP 221 (342)
T ss_pred ----------------CCCChHHHHHHHHHhhhHhhcCCCCCCCcCcchHHHHHHHcCCc
Confidence 12237899999999999999999999999999999999988753
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=99.93 E-value=1.7e-25 Score=219.70 Aligned_cols=148 Identities=30% Similarity=0.345 Sum_probs=134.2
Q ss_pred ecccccHHHHHHHHHHhhhhccCCCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhCC
Q 001299 562 NTVQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNV 641 (1105)
Q Consensus 562 LsQQTsw~~V~ka~~rL~er~~~~~~fpTpEaLA~Ad~EELeelIR~lGf~n~KAk~Ik~lA~~Ive~~GglDLE~Lr~v 641 (1105)
|+||++++++.+++.+|.+ .|++|++|+.++.++|.++|+++||+++||++|+++++.+.+.+++ .+
T Consensus 1 l~qq~~~~~a~~~~~~l~~------~~~~~~~l~~~~~~eL~~~l~~~g~~~~ka~~i~~~a~~~~~~~~~-------~~ 67 (149)
T smart00478 1 LSQQTSDEAVNKATERLFE------KFPTPEDLAAADEEELEELIRPLGFYRRKAKYLIELARILVEEYGG-------EV 67 (149)
T ss_pred CCCcccHHHHHHHHHHHHH------HCCCHHHHHCCCHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHCC-------Cc
Confidence 5899999999999999974 4789999999999999999999999999999999999999988765 24
Q ss_pred CchHHHHHHhcCCCCcHHHHHHHHHHhcCCeeeecchHHHHHHHHhCCCCCCCChHHHHHHHHhhCCchhhhhhhhhhhc
Q 001299 642 PPDKVKEYLLDIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPLQPLPGDLHIHLLKEYPVMDKIQMYLWPRL 721 (1105)
Q Consensus 642 P~deaReeLLsLpGIG~KTAd~ILLfalgrpvfPVDThV~RIl~RLG~Vp~k~tpeeiE~~Leel~P~~e~Iqk~lW~rL 721 (1105)
| +.+++|++|||||+|||+|||+|+|+++++|||+|+.|++.|+|+++..+++++++.+++.++| ..
T Consensus 68 ~--~~~~~L~~l~GIG~~tA~~~l~~~~~~~~~~~D~~v~r~~~rl~~~~~~~~~~~~~~~~~~~~p------~~----- 134 (149)
T smart00478 68 P--DDREELLKLPGVGRKTANAVLSFALGKPFIPVDTHVLRIAKRLGLVDKKSTPEEVEKLLEKLLP------KE----- 134 (149)
T ss_pred c--HHHHHHHcCCCCcHHHHHHHHHHHCCCCCCccchHHHHHHHHhCCCCCCCCHHHHHHHHHHHCC------HH-----
Confidence 4 3489999999999999999999999999999999999999999999877789999999999887 12
Q ss_pred ccCChhhHHHHHHHHHHHhH
Q 001299 722 CYLDQKTLYELHYQMITFGK 741 (1105)
Q Consensus 722 ~~ld~e~l~eLH~lLIdfGR 741 (1105)
.++.||.+++.||+
T Consensus 135 ------~~~~~~~~~l~~g~ 148 (149)
T smart00478 135 ------DWRELNLLLIDFGR 148 (149)
T ss_pred ------HHHHHHHHHHHHcC
Confidence 34589999999997
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=99.92 E-value=9.2e-25 Score=216.11 Aligned_cols=155 Identities=28% Similarity=0.347 Sum_probs=137.5
Q ss_pred cceeceecccccHHHHHHHHHHhhhhccCCCCC-CCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCC
Q 001299 556 PKKNSDNTVQQDWDLLRRIYSTGEERSHDKMDS-VDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSID 634 (1105)
Q Consensus 556 ~~vgaILsQQTsw~~V~ka~~rL~er~~~~~~f-pTpEaLA~Ad~EELeelIR~lGf~n~KAk~Ik~lA~~Ive~~GglD 634 (1105)
.++++||.||++++++.+++.+|.+ .+ |||++|+.++.++|++++.++| ++.||++|+++++.+.+.+++..
T Consensus 3 ~Li~~il~q~~s~~~a~~~~~~l~~------~~gpt~~~l~~~~~~~l~~~~~~~G-~~~kA~~i~~~a~~~~~~~~~~~ 75 (158)
T cd00056 3 VLVSEILSQQTTDKAVNKAYERLFE------RYGPTPEALAAADEEELRELIRSLG-YRRKAKYLKELARAIVEGFGGLV 75 (158)
T ss_pred HHHHHHHHhcccHHHHHHHHHHHHH------HhCCCHHHHHCCCHHHHHHHHHhcC-hHHHHHHHHHHHHHHHHHcCCcc
Confidence 4678999999999999999999964 23 9999999999999999999999 78899999999999999877632
Q ss_pred hhhhhCCCchHHHHHHhcCCCCcHHHHHHHHHHhcCCeeeecchHHHHHHHHhCCCCCCCChHHHHHHHHhhCCchhhhh
Q 001299 635 LEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPLQPLPGDLHIHLLKEYPVMDKIQ 714 (1105)
Q Consensus 635 LE~Lr~vP~deaReeLLsLpGIG~KTAd~ILLfalgrpvfPVDThV~RIl~RLG~Vp~k~tpeeiE~~Leel~P~~e~Iq 714 (1105)
. +.+++++.|++|||||+|||+|||+|+++.++||||+|+.|++.|+|+++..+++++++.+++.+.|
T Consensus 76 ~------~~~~~~~~L~~l~GIG~~tA~~~l~~~~~~~~~pvD~~v~r~~~~~~~~~~~~~~~~~~~~~~~~~~------ 143 (158)
T cd00056 76 L------DDPDAREELLALPGVGRKTANVVLLFALGPDAFPVDTHVRRVLKRLGLIPKKKTPEELEELLEELLP------ 143 (158)
T ss_pred C------CCcccHHHHHcCCCCCHHHHHHHHHHHCCCCCCccchhHHHHHHHhCCCCCCCCHHHHHHHHHHHCC------
Confidence 2 6677899999999999999999999999988999999999999999997667889999999888875
Q ss_pred hhhhhhcccCChhhHHHHHHHHHHHh
Q 001299 715 MYLWPRLCYLDQKTLYELHYQMITFG 740 (1105)
Q Consensus 715 k~lW~rL~~ld~e~l~eLH~lLIdfG 740 (1105)
......+|+.|++||
T Consensus 144 -----------~~~~~~~~~~l~~~g 158 (158)
T cd00056 144 -----------KPYWGEANQALMDLG 158 (158)
T ss_pred -----------HHHHHHHHHHHHHcC
Confidence 112358999999987
No 14
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=99.87 E-value=3e-22 Score=210.23 Aligned_cols=140 Identities=16% Similarity=0.026 Sum_probs=117.7
Q ss_pred cCcccccceeceecccccHHHHHHHHHHhhhhccCCCCCCCHHHHHcCCHHHHHHHHHhcC--ChHHHHHHHHHHHHHH-
Q 001299 550 RTKKTTPKKNSDNTVQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERG--QQNIIAGRIKEFLNRL- 626 (1105)
Q Consensus 550 ~~k~~~~~vgaILsQQTsw~~V~ka~~rL~er~~~~~~fpTpEaLA~Ad~EELeelIR~lG--f~n~KAk~Ik~lA~~I- 626 (1105)
...+...++.+||+|||+|.++.+++.+|. ++.+ .++.++|+++||++| |+++||++|+++++.+
T Consensus 34 ~~~~f~~Lv~~ILsqnT~~~~v~~a~~~L~-----------~~~l-~~~~eeL~~~Ir~~Gygf~~~KAk~I~~~~~~~~ 101 (208)
T PRK01229 34 EEDLFSELSFCILTANSSAEGGIKAQKEIG-----------DGFL-YLSEEELEEKLKEVGHRFYNKRAEYIVEARKLYG 101 (208)
T ss_pred cCChHHHHHHHHhcCcCcHHHHHHHHHhcC-----------HHHc-CCCHHHHHHHHHHhhcccHHHHHHHHHHHHHHHH
Confidence 345777899999999999999999999995 2445 899999999999995 9999999999999874
Q ss_pred --HHHhCCCChhhhhCCCchHHHHHHh-cCCCCcHHHHHHHHHHhcCCeeeecchHHHHHHHHhCCCCC------CCChH
Q 001299 627 --VELHGSIDLEWLRNVPPDKVKEYLL-DIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPL------QPLPG 697 (1105)
Q Consensus 627 --ve~~GglDLE~Lr~vP~deaReeLL-sLpGIG~KTAd~ILLfalgrpvfPVDThV~RIl~RLG~Vp~------k~tpe 697 (1105)
.+.+. ...+..++|++|+ +|||||+|||++||++.+.+|+|+||+||.|++.|+|+++. ..+|.
T Consensus 102 ~l~~~~~-------~~~~~~~~R~~Ll~~lpGIG~KTAd~vL~~~~~~~~~iVDtHv~Ri~~RlG~~~~~~~~lt~~~y~ 174 (208)
T PRK01229 102 KLKEIIK-------ADKDQFEAREFLVKNIKGIGYKEASHFLRNVGYEDLAILDRHILRFLKRYGLIEEIPKTLSKKRYL 174 (208)
T ss_pred HHHHHHh-------ccCCchHHHHHHHHcCCCCcHHHHHHHHHHccCCCeeeeeHHHHHHHHHhCCCcccccccCcCCHH
Confidence 33320 1223456699999 99999999999999766559999999999999999999875 25799
Q ss_pred HHHHHHHhhCC
Q 001299 698 DLHIHLLKEYP 708 (1105)
Q Consensus 698 eiE~~Leel~P 708 (1105)
+++..|+++.+
T Consensus 175 ~~E~~l~~~~~ 185 (208)
T PRK01229 175 EIEEILREIAE 185 (208)
T ss_pred HHHHHHHHHHH
Confidence 99999887764
No 15
>KOG2457 consensus A/G-specific adenine DNA glycosylase [Replication, recombination and repair]
Probab=99.84 E-value=3.4e-21 Score=212.73 Aligned_cols=184 Identities=16% Similarity=0.237 Sum_probs=156.0
Q ss_pred ccccceeceecccccHHHHHHHHHHhhhhccCCCCCCCHHHHHcCCH-HHHHHHHHhcCChHHHHHHHHHHHHHHHHHhC
Q 001299 553 KTTPKKNSDNTVQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADE-SEIADAIKERGQQNIIAGRIKEFLNRLVELHG 631 (1105)
Q Consensus 553 ~~~~~vgaILsQQTsw~~V~ka~~rL~er~~~~~~fpTpEaLA~Ad~-EELeelIR~lGf~n~KAk~Ik~lA~~Ive~~G 631 (1105)
+-.+.|..|+.|||....|.+.|.+..+ ..||..+|+.|+. +++..+|.++|||+ |+++|++-|+.+++.++
T Consensus 125 aYeVwVSEiMLQQTrV~TV~~YYt~WMq------kwPTl~dla~Asl~~eVn~lWaGlGyY~-R~rrL~ega~~vv~~~~ 197 (555)
T KOG2457|consen 125 AYEVWVSEIMLQQTRVQTVMKYYTRWMQ------KWPTLYDLAQASLEKEVNELWAGLGYYR-RARRLLEGAKMVVAGTE 197 (555)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH------hCchHHHHHHHHHHHHHHHHHhhhhHHH-HHHHHHHHHHHHHHhCC
Confidence 3345679999999999999999999964 6899999999998 89999999999998 99999999999999988
Q ss_pred CCChhhhhCCCchHHHHHHhc-CCCCcHHHHHHHHHHhcCCeeeecchHHHHHHHHhCCCCCCCChHHHHHHHHhhCCch
Q 001299 632 SIDLEWLRNVPPDKVKEYLLD-IEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPLQPLPGDLHIHLLKEYPVM 710 (1105)
Q Consensus 632 glDLE~Lr~vP~deaReeLLs-LpGIG~KTAd~ILLfalgrpvfPVDThV~RIl~RLG~Vp~k~tpeeiE~~Leel~P~~ 710 (1105)
| .+|.. -+.|.+ |||||+|||.+|+.++|+.+.=+||.||.|++.|.--+...++....-..
T Consensus 198 g-------e~Prt--a~~l~kgvpGVG~YTAGAiaSIAf~q~tGiVDGNVirvlsRalAIhsDcSkgk~~q~-------- 260 (555)
T KOG2457|consen 198 G-------EFPRT--ASSLMKGVPGVGQYTAGAIASIAFNQVTGIVDGNVIRVLSRALAIHSDCSKGKFFQS-------- 260 (555)
T ss_pred C-------CCCCh--HHHHHhhCCCCCccchhhhhhhhhcCcccccccchHHHhHHhHhhcCCcchhhHHHH--------
Confidence 8 68877 466776 99999999999999999999999999999999987443333333332222
Q ss_pred hhhhhhhhhhc-ccCChhhHHHHHHHHHHHhHHhccCCCCCCCCCCCccchhhHhhh
Q 001299 711 DKIQMYLWPRL-CYLDQKTLYELHYQMITFGKIFCKKRSPNCGACPLRGECKHFASA 766 (1105)
Q Consensus 711 e~Iqk~lW~rL-~~ld~e~l~eLH~lLIdfGR~ICtarkP~Cd~CPLr~~C~yyas~ 766 (1105)
+|... ..+|+.++++||+++|++|+..||+.+|.|..||+...|+.|...
T Consensus 261 ------~wkLA~qLVDP~RPGDFNQalMELGAt~CTpq~P~CS~CPvss~CrA~q~~ 311 (555)
T KOG2457|consen 261 ------SWKLAAQLVDPSRPGDFNQALMELGATLCTPQKPSCSSCPVSSQCRAFQLS 311 (555)
T ss_pred ------HHHHHHHhcCCCCCCcHHHHHHHhcCeeccCCCCCcCCCCcHHHHHHHhHh
Confidence 34322 246888899999999999999999999999999999999998843
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=99.83 E-value=3.1e-20 Score=204.98 Aligned_cols=134 Identities=22% Similarity=0.261 Sum_probs=115.3
Q ss_pred ccccceeceecccccHHHHHHHHHHhhhh-ccC--------CCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHH
Q 001299 553 KTTPKKNSDNTVQQDWDLLRRIYSTGEER-SHD--------KMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFL 623 (1105)
Q Consensus 553 ~~~~~vgaILsQQTsw~~V~ka~~rL~er-~~~--------~~~fpTpEaLA~Ad~EELeelIR~lGf~n~KAk~Ik~lA 623 (1105)
+...++.+|++||+++.++.+++++|.++ |.. ...||+|++|+.++.++ .||.+||.. ||++|+++|
T Consensus 119 ~fE~lv~~IlsQq~si~~a~~~~~rL~~~~G~~~~~~~g~~~~~FPtp~~La~~~~e~---~Lr~~G~g~-Ra~~I~~~A 194 (310)
T TIGR00588 119 PFECLISFICSSNNNIARITRMVERLCQAFGPRLITLDGVTYHGFPSLHALTGPEAEA---HLRKLGLGY-RARYIRETA 194 (310)
T ss_pred HHHHHHHHHHhCCCCHHHHHHHHHHHHHHhCCCcccCCCcccccCCCHHHHhCCChHH---HHHHcCCHH-HHHHHHHHH
Confidence 44568899999999999999999999543 321 23589999999976553 478899954 899999999
Q ss_pred HHHHHHhCCC-ChhhhhCCCchHHHHHHhcCCCCcHHHHHHHHHHhcCCe-eeecchHHHHHHHHh-CCC
Q 001299 624 NRLVELHGSI-DLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHI-AFPVDVNVGRIAVRL-GWV 690 (1105)
Q Consensus 624 ~~Ive~~Ggl-DLE~Lr~vP~deaReeLLsLpGIG~KTAd~ILLfalgrp-vfPVDThV~RIl~RL-G~V 690 (1105)
+.+.+.+++. +++.|+.++.++++++|++|||||+|||+|||+|+|+++ +||||+||+|++.|+ |+.
T Consensus 195 ~~i~~~~~~~~~l~~l~~~~~~~~~~~L~~l~GIG~~tAd~vll~~l~~~d~~PvD~~v~r~~~r~y~~~ 264 (310)
T TIGR00588 195 RALLEEQGGRAWLQQIRGASYEDAREALCELPGVGPKVADCICLMGLDKPQAVPVDVHVWRIANRDYPWH 264 (310)
T ss_pred HHHHhccCCchhHHhhccCChHHHHHHHHhCCCccHHHHHHHHHHhCCCCCceeecHHHHHHHHHHhccc
Confidence 9999977665 688889999999999999999999999999999999997 899999999999998 553
No 17
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=99.80 E-value=2.9e-19 Score=195.51 Aligned_cols=161 Identities=20% Similarity=0.235 Sum_probs=134.5
Q ss_pred ccccceeceecccccHHHHHHHHHHhhhh-ccC---CCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHH
Q 001299 553 KTTPKKNSDNTVQQDWDLLRRIYSTGEER-SHD---KMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVE 628 (1105)
Q Consensus 553 ~~~~~vgaILsQQTsw~~V~ka~~rL~er-~~~---~~~fpTpEaLA~Ad~EELeelIR~lGf~n~KAk~Ik~lA~~Ive 628 (1105)
+...++.+|++||.|.+.+.+++++|.+. +.. ...||+|++|+.++++.| +.+|++..||+||+++|+++.+
T Consensus 105 ~fe~lv~aI~~QqvS~~~A~~i~~rl~~~~g~~~~~~~~fptpe~l~~~~~~~l----~~~g~s~~Ka~yi~~~A~~~~~ 180 (285)
T COG0122 105 PFEALVRAILSQQVSVAAAAKIWARLVSLYGNALEIYHSFPTPEQLAAADEEAL----RRCGLSGRKAEYIISLARAAAE 180 (285)
T ss_pred HHHHHHHHHHHhHhhHHHHHHHHHHHHHHhCCccccccCCCCHHHHHhcCHHHH----HHhCCcHHHHHHHHHHHHHHHc
Confidence 44558899999999999999999999653 211 123899999999999986 6789999999999999999998
Q ss_pred HhCCCChhhhhCCCchHHHHHHhcCCCCcHHHHHHHHHHhcCCe-eeec-chHHHHHHHHhCCCCCCCChHHHHHHHHhh
Q 001299 629 LHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHI-AFPV-DVNVGRIAVRLGWVPLQPLPGDLHIHLLKE 706 (1105)
Q Consensus 629 ~~GglDLE~Lr~vP~deaReeLLsLpGIG~KTAd~ILLfalgrp-vfPV-DThV~RIl~RLG~Vp~k~tpeeiE~~Leel 706 (1105)
|.+|++.+..++.++++++|++|+|||+|||+|+|+|++|++ +||+ |.+++|.+.+++..+..++...+....+.+
T Consensus 181 --g~~~~~~l~~~~~e~a~e~L~~i~GIG~WTAe~~llf~lgr~dvfP~~D~~lr~~~~~~~~~~~~~~~~~~~~~~e~w 258 (285)
T COG0122 181 --GELDLSELKPLSDEEAIEELTALKGIGPWTAEMFLLFGLGRPDVFPADDLGLRRAIKKLYRLPTRPTEKEVRELAERW 258 (285)
T ss_pred --CCccHHHhccCCHHHHHHHHHcCCCcCHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhcCCCCchHHHHHHHHhcc
Confidence 668999999999999999999999999999999999999985 9995 677888888887444444444567777888
Q ss_pred CCchhhhhhhhhh
Q 001299 707 YPVMDKIQMYLWP 719 (1105)
Q Consensus 707 ~P~~e~Iqk~lW~ 719 (1105)
-|+..-.+.|+|.
T Consensus 259 ~p~rs~A~~yLw~ 271 (285)
T COG0122 259 GPYRSYAALYLWR 271 (285)
T ss_pred cCHHHHHHHHHHH
Confidence 8866666777775
No 18
>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=99.74 E-value=6.5e-18 Score=173.66 Aligned_cols=112 Identities=15% Similarity=0.069 Sum_probs=99.0
Q ss_pred cccccceeceecccccHHHHHHHHHHhhhhccCCCCCCCHHHHHcCCHHHHHHHHHhc----CChHHHHHHHHHHHHHHH
Q 001299 552 KKTTPKKNSDNTVQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKER----GQQNIIAGRIKEFLNRLV 627 (1105)
Q Consensus 552 k~~~~~vgaILsQQTsw~~V~ka~~rL~er~~~~~~fpTpEaLA~Ad~EELeelIR~l----Gf~n~KAk~Ik~lA~~Iv 627 (1105)
.+...++++||+|||+|+++.+++.+|..+ .+.+||++|++++.++|+++|++. |||++||++|+++++.|+
T Consensus 17 ~pFelLVa~ILSQqTtd~nv~kA~~~L~~~----~g~~tp~~La~a~~eeL~~lI~~~pal~Gfy~~KAk~Lk~~a~~ii 92 (177)
T TIGR03252 17 DPFALLTGMLLDQQVPMERAFAGPHKIARR----MGSLDAEDIAKYDPQAFVALFSERPAVHRFPGSMAKRVQALAQYVV 92 (177)
T ss_pred ChHHHHHHHHHhccCcHHHHHHHHHHHHHH----hCCCCHHHHHcCCHHHHHHHHhcCccccCchHHHHHHHHHHHHHHH
Confidence 467789999999999999999999999431 345899999999999999999876 999999999999999999
Q ss_pred HHhCCCChhhhhC---CCchHHHHHHhcCCCCcHHHHHHHHHHh
Q 001299 628 ELHGSIDLEWLRN---VPPDKVKEYLLDIEGLGLKSVECVRLLS 668 (1105)
Q Consensus 628 e~~GglDLE~Lr~---vP~deaReeLLsLpGIG~KTAd~ILLfa 668 (1105)
++|+| +++.|.. .+..+++++|++|||||+|||++||.+.
T Consensus 93 e~y~G-~v~~L~~~~~p~t~~lre~Ll~LpGVG~KTAnvVL~~l 135 (177)
T TIGR03252 93 DTYDG-DATAVWTEGDPDGKELLRRLKALPGFGKQKAKIFLALL 135 (177)
T ss_pred HHhCC-ChhhhhcccCCCcHHHHHHHHcCCCCCHHHHHHHHHHH
Confidence 99987 7777766 3455789999999999999999999863
No 19
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=99.70 E-value=6.2e-17 Score=177.04 Aligned_cols=152 Identities=14% Similarity=0.083 Sum_probs=122.8
Q ss_pred ccccceeceecccccHHHHHHHHHHhhhh-ccC------CCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHH
Q 001299 553 KTTPKKNSDNTVQQDWDLLRRIYSTGEER-SHD------KMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNR 625 (1105)
Q Consensus 553 ~~~~~vgaILsQQTsw~~V~ka~~rL~er-~~~------~~~fpTpEaLA~Ad~EELeelIR~lGf~n~KAk~Ik~lA~~ 625 (1105)
+...++.+|++||.+...+.++..++.++ ++. ...||+|++|++++.++| +.+||+++||++|+++|+.
T Consensus 113 ~fE~lv~aIigQqisv~~a~~~~~rlv~~~G~~l~~~~~~~~FPtpe~La~~~~~eL----~~~Gl~~~Ra~~L~~lA~~ 188 (283)
T PRK10308 113 AFEQGVRAILGQLVSVAMAAKLTAKVAQLYGERLDDFPEYVCFPTPERLAAADPQAL----KALGMPLKRAEALIHLANA 188 (283)
T ss_pred HHHHHHHHHHHhHHHHHHHHHHHHHHHHHhCccccCCCCccCCCCHHHHHcCCHHHH----HHCCCCHHHHHHHHHHHHH
Confidence 44457899999999999999999999544 432 246899999999999986 6789999999999999999
Q ss_pred HHHHhCCCChhhhhCCCchHHHHHHhcCCCCcHHHHHHHHHHhcCCe-ee-ecchHHHHHHHHhCCCCCCCChHHHHHHH
Q 001299 626 LVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHI-AF-PVDVNVGRIAVRLGWVPLQPLPGDLHIHL 703 (1105)
Q Consensus 626 Ive~~GglDLE~Lr~vP~deaReeLLsLpGIG~KTAd~ILLfalgrp-vf-PVDThV~RIl~RLG~Vp~k~tpeeiE~~L 703 (1105)
+.+ |.++++.+. +.+++++.|++|||||+|||+||++|+||++ +| +.|.+++|.+ + ..++++++...
T Consensus 189 i~~--g~l~l~~~~--~~~~~~~~L~~LpGIGpwTA~~vllr~lg~~D~fp~~D~~l~~~~---~----~~~~~~~~~~a 257 (283)
T PRK10308 189 ALE--GTLPLTIPG--DVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFLPDDYLIKQRF---P----GMTPAQIRRYA 257 (283)
T ss_pred HHc--CCCCccccC--CHHHHHHHHhcCCCcCHHHHHHHHHHhCCCCCCCCcccHHHHHhc---c----cCCHHHHHHHH
Confidence 988 677766543 4578899999999999999999999999996 77 6799999854 1 23677888888
Q ss_pred HhhCCchhhhhhhhhh
Q 001299 704 LKEYPVMDKIQMYLWP 719 (1105)
Q Consensus 704 eel~P~~e~Iqk~lW~ 719 (1105)
+.+-|+..-...++|.
T Consensus 258 ~~w~P~rsya~~~LW~ 273 (283)
T PRK10308 258 ERWKPWRSYALLHIWY 273 (283)
T ss_pred HhcCCHHHHHHHHHHH
Confidence 8888844444455554
No 20
>KOG1918 consensus 3-methyladenine DNA glycosidase [Replication, recombination and repair]
Probab=99.65 E-value=2.1e-16 Score=165.68 Aligned_cols=162 Identities=18% Similarity=0.168 Sum_probs=137.4
Q ss_pred cccccceeceecccccHHHHHHHHHHhhhhccCCCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhC
Q 001299 552 KKTTPKKNSDNTVQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHG 631 (1105)
Q Consensus 552 k~~~~~vgaILsQQTsw~~V~ka~~rL~er~~~~~~fpTpEaLA~Ad~EELeelIR~lGf~n~KAk~Ik~lA~~Ive~~G 631 (1105)
.|.-.++++|+.||.+-+++..+++||...-.....||+|+.+..++.++| |.|||+.+||.||+.+|.+..+.+
T Consensus 74 ~Pf~~LiraIlsQQLs~kAansI~~Rfvsl~~g~~~~~~pe~i~~~~~~~l----rkcG~S~rK~~yLh~lA~~~~ng~- 148 (254)
T KOG1918|consen 74 TPFERLIRAILSQQLSGKAANSIYNRFVSLCGGAEKFPTPEFIDPLDCEEL----RKCGFSKRKASYLHSLAEAYTNGY- 148 (254)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCCCchhcCcCCHHHH----HHhCcchhhHHHHHHHHHHHhcCC-
Confidence 356668899999999999999999999543222367999999999999986 788999999999999999998843
Q ss_pred CCChhhhhCCCchHHHHHHhcCCCCcHHHHHHHHHHhcCCe-eeecchH-HHHHHHHh-CCCCCCCChHHHHHHHHhhCC
Q 001299 632 SIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHI-AFPVDVN-VGRIAVRL-GWVPLQPLPGDLHIHLLKEYP 708 (1105)
Q Consensus 632 glDLE~Lr~vP~deaReeLLsLpGIG~KTAd~ILLfalgrp-vfPVDTh-V~RIl~RL-G~Vp~k~tpeeiE~~Leel~P 708 (1105)
=...+.+.+++.+++.+.|+.++|||+|||.|+|.|+++|+ ++|+|.- |++-+..| |+-+ .+.+.+++++.+.+.|
T Consensus 149 I~s~~~i~~mseEeL~~~LT~VKGIg~Wtv~MflIfsL~R~DVmp~dDlgir~g~k~l~gl~~-~p~~~evekl~e~~kp 227 (254)
T KOG1918|consen 149 IPSKSGIEKMSEEELIERLTNVKGIGRWTVEMFLIFSLHRPDVMPADDLGIRNGVKKLLGLKP-LPLPKEVEKLCEKCKP 227 (254)
T ss_pred CCchHHHhhcCHHHHHHHHHhccCccceeeeeeeeeccCCCcccCchhhhHHHHHHHHhCCCC-CCchHHHHHHhhhccc
Confidence 23677888999999999999999999999999999999996 8999655 66666666 6543 4788999999999999
Q ss_pred chhhhhhhhhh
Q 001299 709 VMDKIQMYLWP 719 (1105)
Q Consensus 709 ~~e~Iqk~lW~ 719 (1105)
+.....+|+|.
T Consensus 228 yRtvaawYlWk 238 (254)
T KOG1918|consen 228 YRTVAAWYLWK 238 (254)
T ss_pred hHHHHHHHHHh
Confidence 88778889996
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=99.59 E-value=2.7e-15 Score=140.14 Aligned_cols=107 Identities=25% Similarity=0.241 Sum_probs=92.1
Q ss_pred eeceecccccHHHHHHHHHHhhhhccCCCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhh
Q 001299 558 KNSDNTVQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEW 637 (1105)
Q Consensus 558 vgaILsQQTsw~~V~ka~~rL~er~~~~~~fpTpEaLA~Ad~EELeelIR~lGf~n~KAk~Ik~lA~~Ive~~GglDLE~ 637 (1105)
|++||+||++++++.+++.+|.++ ++||||++|+.+++++|.++|+++||++.||++|+++|+.+.
T Consensus 1 V~~Il~qq~s~~~a~~~~~~l~~~----~g~pt~~~l~~~~~~el~~~i~~~G~~~~ka~~i~~~a~~~~---------- 66 (108)
T PF00730_consen 1 VRAILSQQTSIKAARKIYRRLFER----YGFPTPEALAEASEEELRELIRPLGFSRRKAKYIIELARAIL---------- 66 (108)
T ss_dssp HHHHHCTTS-HHHHHHHHHHHHHH----HSCSSHHHHHCSHHHHHHHHHTTSTSHHHHHHHHHHHHHHHH----------
T ss_pred CeeeecCcCcHHHHHHHHHHHHHH----hcCCCHHHHHhCCHHHHHHHhhccCCCHHHHHHHHHHHHHhh----------
Confidence 468999999999999999999652 459999999999999999999999999999999999999887
Q ss_pred hhCCCchHHHHHHhcCCCCcHHHHHHHHHHhcCCeeeecchHHHHHHHHhCCCCCCCChHHHHHHHHhhCC
Q 001299 638 LRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPLQPLPGDLHIHLLKEYP 708 (1105)
Q Consensus 638 Lr~vP~deaReeLLsLpGIG~KTAd~ILLfalgrpvfPVDThV~RIl~RLG~Vp~k~tpeeiE~~Leel~P 708 (1105)
+...+++|+|+|+.|++.|+|+++.+++++++++.+++.+|
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 12225899999999999999999877789999988876654
No 22
>KOG2875 consensus 8-oxoguanine DNA glycosylase [Replication, recombination and repair]
Probab=99.58 E-value=6e-15 Score=159.18 Aligned_cols=127 Identities=23% Similarity=0.261 Sum_probs=110.8
Q ss_pred ceeceecccccHHHHHHHHHHhhh-h--------ccCCCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHH
Q 001299 557 KKNSDNTVQQDWDLLRRIYSTGEE-R--------SHDKMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLV 627 (1105)
Q Consensus 557 ~vgaILsQQTsw~~V~ka~~rL~e-r--------~~~~~~fpTpEaLA~Ad~EELeelIR~lGf~n~KAk~Ik~lA~~Iv 627 (1105)
+...|+++|.+..++-++.++|.. . +.+..+||+.++|+. .++++-||.+||.. ||+||...|++|.
T Consensus 121 lfSFiCSSNNNIaRIT~Mve~fc~~fG~~i~~~dg~~~h~FPsl~~L~g---~~~Ea~LR~~gfGY-RAkYI~~ta~~l~ 196 (323)
T KOG2875|consen 121 LFSFICSSNNNIARITGMVERFCQAFGPRIIQLDGVDYHGFPSLQALAG---PEVEAELRKLGFGY-RAKYISATARALQ 196 (323)
T ss_pred HHHHHhcCCCcHHHHHHHHHHHHHhhCcceEeecCcccccCccHHHhcC---cHhHHHHHHcCcch-hHHHHHHHHHHHH
Confidence 668899999999999999997732 2 233458999999986 67778889999988 9999999999999
Q ss_pred HHhCCC-ChhhhhCCCchHHHHHHhcCCCCcHHHHHHHHHHhcCCe-eeecchHHHHHHHHh
Q 001299 628 ELHGSI-DLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHI-AFPVDVNVGRIAVRL 687 (1105)
Q Consensus 628 e~~Ggl-DLE~Lr~vP~deaReeLLsLpGIG~KTAd~ILLfalgrp-vfPVDThV~RIl~RL 687 (1105)
++.|++ .|..|++++.+++++.|+.|||||+|+||||++++++.. ++|||+||.||+.-+
T Consensus 197 ~~~g~~~wLqsl~~~~yeear~~L~~lpGVG~KVADCI~Lm~l~~~~~VPVDvHi~ria~~y 258 (323)
T KOG2875|consen 197 EKQGGLAWLQSLRKSSYEEAREALCSLPGVGPKVADCICLMSLDKLSAVPVDVHIWRIAQDY 258 (323)
T ss_pred HhcccchHHHHHhcccHHHHHHHHhcCCCCcchHhhhhhhhhcCCCCcccchhhHHHHhhcc
Confidence 999883 466677889999999999999999999999999999985 999999999999944
No 23
>COG1059 Thermostable 8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=98.90 E-value=5.5e-09 Score=108.68 Aligned_cols=122 Identities=20% Similarity=0.154 Sum_probs=98.9
Q ss_pred cccceeceecccccHHHHHHHHHHhhhhccCCCCCCCHHHHHcCCHHHHHHHHHhcC--ChHHHHHHHHHHHHHHHHHhC
Q 001299 554 TTPKKNSDNTVQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERG--QQNIIAGRIKEFLNRLVELHG 631 (1105)
Q Consensus 554 ~~~~vgaILsQQTsw~~V~ka~~rL~er~~~~~~fpTpEaLA~Ad~EELeelIR~lG--f~n~KAk~Ik~lA~~Ive~~G 631 (1105)
.+.+.=.||+.|++...+.++...+. +.+..++.+||++.|+.+| |+++||+||..+-+.+.
T Consensus 40 f~ELsFCILTANsSA~~~~~~q~~lG------------~gfly~~~eEL~e~Lk~~g~Rf~n~raeyIVeaR~~~~---- 103 (210)
T COG1059 40 FKELSFCILTANSSATMGLRAQNELG------------DGFLYLSEEELREKLKEVGYRFYNVRAEYIVEAREKFD---- 103 (210)
T ss_pred HHHHHHHhccccchHHHHHHHHHHhc------------cccccCCHHHHHHHHHHhcchhcccchHHHHHHHHHHH----
Confidence 34466689999999999999999886 3356679999999999996 89999999999765543
Q ss_pred CCChhhhhCCCchH--HHHHHh-cCCCCcHHHHHHHHHHhcCCeeeecchHHHHHHHHhCCCCCC
Q 001299 632 SIDLEWLRNVPPDK--VKEYLL-DIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPLQ 693 (1105)
Q Consensus 632 glDLE~Lr~vP~de--aReeLL-sLpGIG~KTAd~ILLfalgrpvfPVDThV~RIl~RLG~Vp~k 693 (1105)
++..+-..+..+ +|++|+ .++|||.|-|.++|....-..+.++|.|+.|.+.|+|.+...
T Consensus 104 --~lk~~v~~~~~~~vaRE~Lv~nikGiGyKEASHFLRNVG~~D~AIlDrHIlr~l~r~g~i~e~ 166 (210)
T COG1059 104 --DLKIIVKADENEKVARELLVENIKGIGYKEASHFLRNVGFEDLAILDRHILRWLVRYGLIDEN 166 (210)
T ss_pred --HHHHHHhcCcchHHHHHHHHHHcccccHHHHHHHHHhcChhHHHHHHHHHHHHHHHhcccccC
Confidence 233343444333 899999 999999999999998866578889999999999999998643
No 24
>PF15629 Perm-CXXC: Permuted single zf-CXXC unit
Probab=98.86 E-value=6.7e-10 Score=85.38 Aligned_cols=31 Identities=55% Similarity=1.114 Sum_probs=29.9
Q ss_pred CCcccCCcCC-CCcCcccccccccccccccce
Q 001299 956 PQYRCNSKDS-KLCNSEICYSCNSVCERNAGI 986 (1105)
Q Consensus 956 p~~~c~s~~~-~lc~~~~~~~c~~~~e~~~~~ 986 (1105)
|+++|+|+++ +||+++|||+||||||+++|+
T Consensus 1 Pe~~C~sqe~gkLC~~~tCfsCNsiREa~sQ~ 32 (32)
T PF15629_consen 1 PERRCNSQESGKLCDEETCFSCNSIREANSQT 32 (32)
T ss_pred CcccccccccccccCCccccccccHhHHhccC
Confidence 7999999999 999999999999999999986
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=97.09 E-value=0.00035 Score=53.85 Aligned_cols=25 Identities=24% Similarity=0.542 Sum_probs=21.0
Q ss_pred CCchHHHHHHhcCCCCcHHHHHHHHHH
Q 001299 641 VPPDKVKEYLLDIEGLGLKSVECVRLL 667 (1105)
Q Consensus 641 vP~deaReeLLsLpGIG~KTAd~ILLf 667 (1105)
+|.+ +++|++|||||+|||+.|+.|
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 4556 789999999999999999876
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=96.39 E-value=0.0013 Score=45.07 Aligned_cols=17 Identities=47% Similarity=1.302 Sum_probs=11.6
Q ss_pred ccCCCCCCCCCCCccch
Q 001299 744 CKKRSPNCGACPLRGEC 760 (1105)
Q Consensus 744 CtarkP~Cd~CPLr~~C 760 (1105)
|++++|+|+.|||++.|
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=95.60 E-value=0.0094 Score=65.12 Aligned_cols=54 Identities=24% Similarity=0.462 Sum_probs=45.0
Q ss_pred HHHHHHHHHHHHHHHHhCCCChhhhhCCCchHHHHHHhcCCCCcHHHHHHHHHHhcCCeeeecchHHHHHHHHhCCCCCC
Q 001299 614 IIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPLQ 693 (1105)
Q Consensus 614 ~KAk~Ik~lA~~Ive~~GglDLE~Lr~vP~deaReeLLsLpGIG~KTAd~ILLfalgrpvfPVDThV~RIl~RLG~Vp~k 693 (1105)
.-+|+|.-+++|++.+..++|+.-+..+++.++ ++|+||||.|++.+||+...+
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 356899999999998755688887777887754 689999999999999998653
No 28
>smart00525 FES FES domain. iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3)
Probab=95.42 E-value=0.0071 Score=44.72 Aligned_cols=23 Identities=35% Similarity=1.083 Sum_probs=20.4
Q ss_pred hccCCCCCCCCCCCccchhhHhh
Q 001299 743 FCKKRSPNCGACPLRGECKHFAS 765 (1105)
Q Consensus 743 ICtarkP~Cd~CPLr~~C~yyas 765 (1105)
+|++++|+|+.|||+..|++|..
T Consensus 1 vC~ar~P~C~~Cpl~~~C~~~~~ 23 (26)
T smart00525 1 ICTARKPRCDECPLKDLCPAYXX 23 (26)
T ss_pred CccCCCCCCCCCcCHHHhhhhhc
Confidence 69999999999999999997543
No 29
>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=94.67 E-value=0.025 Score=61.83 Aligned_cols=50 Identities=26% Similarity=0.440 Sum_probs=41.7
Q ss_pred HHHHHHHHHHHHHHhCCCChhhhhCCCchHHHHHHhcCCCCcHHHHHHHHHHhcCCeeeecchHHHHHHHHhCCCCC
Q 001299 616 AGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPL 692 (1105)
Q Consensus 616 Ak~Ik~lA~~Ive~~GglDLE~Lr~vP~deaReeLLsLpGIG~KTAd~ILLfalgrpvfPVDThV~RIl~RLG~Vp~ 692 (1105)
+|+|--+++|++++ ..+||.-+..+++.++ ++|+||||.||+.+||+...
T Consensus 143 ~KR~nMFLRWMVR~-d~VD~GlW~~i~ps~L--------------------------iiPLDtH~~rvar~LgL~~R 192 (229)
T TIGR02757 143 LKRLNMFLRWMIRK-DEVDLGIWESFKPSDL--------------------------ILPLDTHVFRIAKKLKLLKR 192 (229)
T ss_pred HHHHHHHHHhhccC-CCCCCcCCCCCCHHHc--------------------------eeechHhHHHHHHHhCCccc
Confidence 48899999999985 4488887777877743 78999999999999999864
No 30
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=88.04 E-value=0.37 Score=35.77 Aligned_cols=20 Identities=30% Similarity=0.421 Sum_probs=17.5
Q ss_pred HHhcCCCCcHHHHHHHHHHh
Q 001299 649 YLLDIEGLGLKSVECVRLLS 668 (1105)
Q Consensus 649 eLLsLpGIG~KTAd~ILLfa 668 (1105)
.|++++|||+|+|+.++.+.
T Consensus 2 ~L~~i~GiG~k~A~~il~~~ 21 (26)
T smart00278 2 ELLKVPGIGPKTAEKILEAX 21 (26)
T ss_pred hhhhCCCCCHHHHHHHHHhc
Confidence 58899999999999998653
No 31
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=87.91 E-value=0.64 Score=41.25 Aligned_cols=40 Identities=30% Similarity=0.318 Sum_probs=28.1
Q ss_pred HHHHHHHHhCCCChhhhhCCCchHHHHHHhcCCCCcHHHHHHHHHH
Q 001299 622 FLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLL 667 (1105)
Q Consensus 622 lA~~Ive~~GglDLE~Lr~vP~deaReeLLsLpGIG~KTAd~ILLf 667 (1105)
.|+.+.+.|| +++.|...+ .++|.+++|||+++|+.|..|
T Consensus 15 ~ak~L~~~f~--sl~~l~~a~----~e~L~~i~gIG~~~A~si~~f 54 (64)
T PF12826_consen 15 TAKLLAKHFG--SLEALMNAS----VEELSAIPGIGPKIAQSIYEF 54 (64)
T ss_dssp HHHHHHHCCS--CHHHHCC------HHHHCTSTT--HHHHHHHHHH
T ss_pred HHHHHHHHcC--CHHHHHHcC----HHHHhccCCcCHHHHHHHHHH
Confidence 3566667776 477777654 458999999999999999776
No 32
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=87.24 E-value=1.9 Score=46.57 Aligned_cols=65 Identities=18% Similarity=0.153 Sum_probs=43.7
Q ss_pred CCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHH------HHHHHHHHHhCCCChhhhhCCCchHHHHHHhcCCCCcH
Q 001299 585 KMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIK------EFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGL 658 (1105)
Q Consensus 585 ~~~fpTpEaLA~Ad~EELeelIR~lGf~n~KAk~Ik------~lA~~Ive~~GglDLE~Lr~vP~deaReeLLsLpGIG~ 658 (1105)
.++|.+.++. +-.+.+|.--|...+.|-.|. +++++|.. + | .+.|.++||||+
T Consensus 59 LYGF~t~~Er-----~lF~~LisVsGIGPK~ALaILs~~~~~el~~aI~~--~------------D--~~~L~~vpGIGk 117 (196)
T PRK13901 59 LFGFLNSSER-----EVFEELIGVDGIGPRAALRVLSGIKYNEFRDAIDR--E------------D--IELISKVKGIGN 117 (196)
T ss_pred eeCCCCHHHH-----HHHHHHhCcCCcCHHHHHHHHcCCCHHHHHHHHHh--C------------C--HHHHhhCCCCCH
Confidence 5688887763 334455666677776776665 34444443 2 2 578999999999
Q ss_pred HHHHHHHHHhcC
Q 001299 659 KSVECVRLLSLQ 670 (1105)
Q Consensus 659 KTAd~ILLfalg 670 (1105)
|||+-|++---+
T Consensus 118 KtAeRIIlELkd 129 (196)
T PRK13901 118 KMAGKIFLKLRG 129 (196)
T ss_pred HHHHHHHHHHHH
Confidence 999988754333
No 33
>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=82.09 E-value=3 Score=44.49 Aligned_cols=72 Identities=15% Similarity=0.157 Sum_probs=49.4
Q ss_pred ceeceecccccHHHHHHHHHHhhhhccCCCCCCCHHHHHcCCHHHHHHHHHhcCC--hHHHHHHHHHHHHHHHH---HhC
Q 001299 557 KKNSDNTVQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERGQ--QNIIAGRIKEFLNRLVE---LHG 631 (1105)
Q Consensus 557 ~vgaILsQQTsw~~V~ka~~rL~er~~~~~~fpTpEaLA~Ad~EELeelIR~lGf--~n~KAk~Ik~lA~~Ive---~~G 631 (1105)
++-.++---.+|..+.+-...+++ ....++++.|+..++++|++++..-|+ +++|.+.+..=|+.+.+ +||
T Consensus 30 L~Le~fQaGLsW~~Il~Kr~~~r~----aF~~Fd~~~vA~~~e~~ie~l~~d~~iIRnr~KI~Avi~NA~~~l~i~~e~g 105 (179)
T PF03352_consen 30 LTLEGFQAGLSWSTILKKREAFRE----AFAGFDPEKVAKMDEEDIERLMQDPGIIRNRRKIRAVINNARAILKIQEEFG 105 (179)
T ss_dssp HHHHHHTTTS-HHHHHHTHHHHHH----HTGGGHHHHHHT--HHHHHHHTTSTTSS--HHHHHHHHHHHHHHHHHHHTTS
T ss_pred HHHHHHHhhCCHHHHHHHHHHHHH----HHHCCCHHHHHcCCHHHHHHHhcCcchhhhHHHHHHHHHHHHHHHHHHHhcC
Confidence 333344444579999887777753 345689999999999999999999887 55777888887777654 455
Q ss_pred C
Q 001299 632 S 632 (1105)
Q Consensus 632 g 632 (1105)
+
T Consensus 106 s 106 (179)
T PF03352_consen 106 S 106 (179)
T ss_dssp -
T ss_pred C
Confidence 4
No 34
>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=81.62 E-value=6.9 Score=35.03 Aligned_cols=58 Identities=17% Similarity=0.188 Sum_probs=37.5
Q ss_pred HHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhCCCchHHHHHHhcCCCCcHHHHHHHHHH
Q 001299 600 SEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLL 667 (1105)
Q Consensus 600 EELeelIR~lGf~n~KAk~Ik~lA~~Ive~~GglDLE~Lr~vP~deaReeLLsLpGIG~KTAd~ILLf 667 (1105)
+++.++..-.|-..-|++....++..|.. ++. |-....+.|.+|||||.++|..|.-|
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 44555555554344588888888888766 221 22332225999999999999988544
No 35
>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=81.07 E-value=3.1 Score=37.00 Aligned_cols=57 Identities=25% Similarity=0.255 Sum_probs=36.2
Q ss_pred HHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhCCCchHHHHHHhcCCCCcHHHHHHHHHH
Q 001299 594 VRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLL 667 (1105)
Q Consensus 594 LA~Ad~EELeelIR~lGf~n~KAk~Ik~lA~~Ive~~GglDLE~Lr~vP~deaReeLLsLpGIG~KTAd~ILLf 667 (1105)
|=.|+.++|..++..+|. .+|+.|.+.- ..+|++ .+ .++|..++|||.++|+-|+.+
T Consensus 10 vNta~~~~L~~~ipgig~--~~a~~Il~~R----~~~g~~---------~s--~~dL~~v~gi~~~~~~~i~~~ 66 (69)
T TIGR00426 10 INTATAEELQRAMNGVGL--KKAEAIVSYR----EEYGPF---------KT--VEDLKQVPGIGNSLVEKNLAV 66 (69)
T ss_pred CcCCCHHHHHhHCCCCCH--HHHHHHHHHH----HHcCCc---------CC--HHHHHcCCCCCHHHHHHHHhh
Confidence 444677777665555554 4554443322 124543 12 578999999999999998765
No 36
>PRK10353 3-methyl-adenine DNA glycosylase I; Provisional
Probab=80.86 E-value=10 Score=40.86 Aligned_cols=68 Identities=9% Similarity=0.027 Sum_probs=50.4
Q ss_pred ceeceecccccHHHHHHHHHHhhhhccCCCCCCCHHHHHcCCHHHHHHHHHhcCChH--HHHHHHHHHHHHHHH
Q 001299 557 KKNSDNTVQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERGQQN--IIAGRIKEFLNRLVE 628 (1105)
Q Consensus 557 ~vgaILsQQTsw~~V~ka~~rL~er~~~~~~fpTpEaLA~Ad~EELeelIR~lGf~n--~KAk~Ik~lA~~Ive 628 (1105)
++-.++---.+|..+.+-...+++ ....++++.||..++++|++++..-|+-+ .|.+.+++=|+.+.+
T Consensus 35 L~Le~~QAGLSW~tIL~Kre~fr~----aF~~Fd~~~VA~~~e~die~Ll~d~~IIRnr~KI~Avi~NA~~~l~ 104 (187)
T PRK10353 35 ICLEGQQAGLSWITVLKKRENYRA----CFHQFDPVKVAAMQEEDVERLVQDAGIIRHRGKIQAIIGNARAYLQ 104 (187)
T ss_pred HHHHHhcccccHHHHHHHHHHHHH----HHcCCCHHHHhCCCHHHHHHHhcCchhHHhHHHHHHHHHHHHHHHH
Confidence 333333344589999988887764 35678999999999999999999999744 566677776666554
No 37
>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=80.66 E-value=4.2 Score=35.33 Aligned_cols=49 Identities=33% Similarity=0.327 Sum_probs=31.8
Q ss_pred HhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhCCCchHHHHHHhcCCCCcHHHHHHHHHH
Q 001299 607 KERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLL 667 (1105)
Q Consensus 607 R~lGf~n~KAk~Ik~lA~~Ive~~GglDLE~Lr~vP~deaReeLLsLpGIG~KTAd~ILLf 667 (1105)
.--|.....|+.| .+. |--+++.|...+. +.|.+++|||+++|+-+...
T Consensus 9 ~I~Gig~~~a~~L-------~~~-G~~t~~~l~~a~~----~~L~~i~Gig~~~a~~i~~~ 57 (60)
T PF14520_consen 9 SIPGIGPKRAEKL-------YEA-GIKTLEDLANADP----EELAEIPGIGEKTAEKIIEA 57 (60)
T ss_dssp TSTTCHHHHHHHH-------HHT-TCSSHHHHHTSHH----HHHHTSTTSSHHHHHHHHHH
T ss_pred cCCCCCHHHHHHH-------Hhc-CCCcHHHHHcCCH----HHHhcCCCCCHHHHHHHHHH
Confidence 3346655444433 332 3336777776643 57999999999999988643
No 38
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=80.55 E-value=5.5 Score=42.64 Aligned_cols=70 Identities=16% Similarity=0.089 Sum_probs=40.2
Q ss_pred CCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhC--CCchHHHHHHhcCCCCcHHHHH
Q 001299 585 KMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRN--VPPDKVKEYLLDIEGLGLKSVE 662 (1105)
Q Consensus 585 ~~~fpTpEaLA~Ad~EELeelIR~lGf~n~KAk~Ik~lA~~Ive~~GglDLE~Lr~--vP~deaReeLLsLpGIG~KTAd 662 (1105)
.++|.+.++- +-.+.+|.--|...+.|-.|... ++.+.|.. ...| .+.|.++||||+|||+
T Consensus 60 LyGF~~~~Er-----~lF~~Li~VsGIGpK~Al~ILs~----------~~~~el~~aI~~~D--~~~L~~vpGIGkKtAe 122 (183)
T PRK14601 60 LYGFLDKDEQ-----KMFEMLLKVNGIGANTAMAVCSS----------LDVNSFYKALSLGD--ESVLKKVPGIGPKSAK 122 (183)
T ss_pred eeCCCCHHHH-----HHHHHHhccCCccHHHHHHHHcC----------CCHHHHHHHHHhCC--HHHHhhCCCCCHHHHH
Confidence 4677777753 23344555566666555444321 11221111 1122 5789999999999999
Q ss_pred HHHHHhcCC
Q 001299 663 CVRLLSLQH 671 (1105)
Q Consensus 663 ~ILLfalgr 671 (1105)
-|++---++
T Consensus 123 RIilELkdK 131 (183)
T PRK14601 123 RIIAELSDA 131 (183)
T ss_pred HHHHHHHHH
Confidence 887553333
No 39
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=80.12 E-value=5.9 Score=42.48 Aligned_cols=63 Identities=14% Similarity=0.047 Sum_probs=39.1
Q ss_pred CCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHH------HHHHHHHHhCCCChhhhhCCCchHHHHHHhcCCCCcH
Q 001299 585 KMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKE------FLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGL 658 (1105)
Q Consensus 585 ~~~fpTpEaLA~Ad~EELeelIR~lGf~n~KAk~Ik~------lA~~Ive~~GglDLE~Lr~vP~deaReeLLsLpGIG~ 658 (1105)
.++|.+.++. +-.+.+|.--|...+.|-.|.. ++++|.. .| .+.|.++||||+
T Consensus 60 LyGF~~~~Er-----~lF~~Li~V~GIGpK~AL~iLs~~~~~el~~aI~~--------------~D--~~~L~~vpGIGk 118 (188)
T PRK14606 60 LYGFSNERKK-----ELFLSLTKVSRLGPKTALKIISNEDAETLVTMIAS--------------QD--VEGLSKLPGISK 118 (188)
T ss_pred eeCCCCHHHH-----HHHHHHhccCCccHHHHHHHHcCCCHHHHHHHHHh--------------CC--HHHHhhCCCCCH
Confidence 5677777753 2234445556666655554442 2333332 22 578999999999
Q ss_pred HHHHHHHHHh
Q 001299 659 KSVECVRLLS 668 (1105)
Q Consensus 659 KTAd~ILLfa 668 (1105)
|||+-|.+--
T Consensus 119 KtAerIilEL 128 (188)
T PRK14606 119 KTAERIVMEL 128 (188)
T ss_pred HHHHHHHHHH
Confidence 9999887543
No 40
>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=78.13 E-value=16 Score=39.20 Aligned_cols=68 Identities=7% Similarity=0.032 Sum_probs=50.5
Q ss_pred ceeceecccccHHHHHHHHHHhhhhccCCCCCCCHHHHHcCCHHHHHHHHHhcCChHHH--HHHHHHHHHHHHH
Q 001299 557 KKNSDNTVQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERGQQNII--AGRIKEFLNRLVE 628 (1105)
Q Consensus 557 ~vgaILsQQTsw~~V~ka~~rL~er~~~~~~fpTpEaLA~Ad~EELeelIR~lGf~n~K--Ak~Ik~lA~~Ive 628 (1105)
++-.++---.+|..+.+-...+++ ....++++.+|..++++|++++..-|+-+.| .+.++.=|+.+.+
T Consensus 34 L~Le~fQAGLSW~tIL~Kr~~fr~----aF~~Fd~~~VA~~~e~~ie~L~~d~~IIRnr~KI~Avi~NA~~~l~ 103 (179)
T TIGR00624 34 MSLEGFQAGLSWITVLRKRENYRR----AFSGFDIVKVARMTDADVERLLQDDGIIRNRGKIEATIANARAALQ 103 (179)
T ss_pred HHHHHHhCcCCHHHHHHhHHHHHH----HHcCCCHHHHhCCCHHHHHHHhcCccchhhHHHHHHHHHHHHHHHH
Confidence 333344444589999988887754 3567899999999999999999998876644 4556666676665
No 41
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=77.46 E-value=3.9 Score=44.71 Aligned_cols=61 Identities=23% Similarity=0.423 Sum_probs=44.8
Q ss_pred cCCHHHHHHHHHhcCChHHHHH-HHHHHHHHHHHHh---CCCChhhhhCCCchHHHHHHhcCCCCcHHHHHHHH
Q 001299 596 CADESEIADAIKERGQQNIIAG-RIKEFLNRLVELH---GSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVR 665 (1105)
Q Consensus 596 ~Ad~EELeelIR~lGf~n~KAk-~Ik~lA~~Ive~~---GglDLE~Lr~vP~deaReeLLsLpGIG~KTAd~IL 665 (1105)
.++..||.++|=..|..+ + -.+.+|+.+.++| |+ |..|...+.+ +|.+++|||+..|..++
T Consensus 13 ~Lsd~ELLailL~~g~~~---~~~~~~lA~~ll~~f~~~g~--l~~l~~a~~~----eL~~i~GiG~aka~~l~ 77 (218)
T TIGR00608 13 ALSDYELLAIILRTGTPK---GLDVLSLSKRLLDVFGRQDS--LGHLLSAPPE----ELSSVPGIGEAKAIQLK 77 (218)
T ss_pred cCCHHHHHHHHHhCCCCC---CCCHHHHHHHHHHHhcccCC--HHHHHhCCHH----HHHhCcCCcHHHHHHHH
Confidence 446677777766667644 3 5668899999888 64 7777777655 79999999997766554
No 42
>PRK00024 hypothetical protein; Reviewed
Probab=76.87 E-value=3.9 Score=44.73 Aligned_cols=62 Identities=18% Similarity=0.328 Sum_probs=45.0
Q ss_pred HcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhCCCchHHHHHHhcCCCCcHHHHHHHH
Q 001299 595 RCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVR 665 (1105)
Q Consensus 595 A~Ad~EELeelIR~lGf~n~KAk~Ik~lA~~Ive~~GglDLE~Lr~vP~deaReeLLsLpGIG~KTAd~IL 665 (1105)
..++..||.++|=..|..+ +-.+.+|+.+.++||+ |..+...+.+ +|.+++|||+..|..++
T Consensus 22 ~~Lsd~ELLa~lL~~g~~~---~~~~~LA~~LL~~fgs--L~~l~~as~~----eL~~i~GIG~akA~~L~ 83 (224)
T PRK00024 22 AALSDAELLAILLRTGTKG---KSVLDLARELLQRFGS--LRGLLDASLE----ELQSIKGIGPAKAAQLK 83 (224)
T ss_pred ccCCHHHHHHHHHcCCCCC---CCHHHHHHHHHHHcCC--HHHHHhCCHH----HHhhccCccHHHHHHHH
Confidence 3446677777765666644 4456789999988875 6777776654 79999999999886554
No 43
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=75.82 E-value=8.3 Score=41.74 Aligned_cols=66 Identities=18% Similarity=0.155 Sum_probs=38.6
Q ss_pred CCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhC--CCchHHHHHHhcCCCCcHHHHH
Q 001299 585 KMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRN--VPPDKVKEYLLDIEGLGLKSVE 662 (1105)
Q Consensus 585 ~~~fpTpEaLA~Ad~EELeelIR~lGf~n~KAk~Ik~lA~~Ive~~GglDLE~Lr~--vP~deaReeLLsLpGIG~KTAd 662 (1105)
.++|.+.++. +-.+.+|.--|...+.|-.|... ++.+.|.. ...| .+.|.++||||+|||+
T Consensus 61 LyGF~~~~Er-----~lF~~Li~V~GIGpK~Al~iLs~----------~~~~~l~~aI~~~D--~~~L~~ipGIGkKtAe 123 (203)
T PRK14602 61 LFGFATWDER-----QTFIVLISISKVGAKTALAILSQ----------FRPDDLRRLVAEED--VAALTRVSGIGKKTAQ 123 (203)
T ss_pred eeCCCCHHHH-----HHHHHHhCCCCcCHHHHHHHHhh----------CCHHHHHHHHHhCC--HHHHhcCCCcCHHHHH
Confidence 4677777653 22334455566666555544442 11111111 1123 5789999999999999
Q ss_pred HHHHH
Q 001299 663 CVRLL 667 (1105)
Q Consensus 663 ~ILLf 667 (1105)
-|++-
T Consensus 124 rIilE 128 (203)
T PRK14602 124 HIFLE 128 (203)
T ss_pred HHHHH
Confidence 88754
No 44
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=75.72 E-value=4 Score=44.36 Aligned_cols=69 Identities=20% Similarity=0.140 Sum_probs=38.8
Q ss_pred CCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhCCCchHHHHHHhcCCCCcHHHHHHHH
Q 001299 586 MDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVR 665 (1105)
Q Consensus 586 ~~fpTpEaLA~Ad~EELeelIR~lGf~n~KAk~Ik~lA~~Ive~~GglDLE~Lr~vP~deaReeLLsLpGIG~KTAd~IL 665 (1105)
++|.+.++ .+=...+|+--|...+-|-. |+. .+|++.|...=..+=.+.|.++||||+|||+-++
T Consensus 61 yGF~~~~E-----R~lF~~LisVnGIGpK~ALa-------iLs---~~~~~~l~~aI~~~d~~~L~k~PGIGkKtAeriv 125 (201)
T COG0632 61 YGFLTEEE-----RELFRLLISVNGIGPKLALA-------ILS---NLDPEELAQAIANEDVKALSKIPGIGKKTAERIV 125 (201)
T ss_pred cCCCCHHH-----HHHHHHHHccCCccHHHHHH-------HHc---CCCHHHHHHHHHhcChHhhhcCCCCCHHHHHHHH
Confidence 46666554 22334556666666633333 332 2334433321111116799999999999999887
Q ss_pred HHhc
Q 001299 666 LLSL 669 (1105)
Q Consensus 666 Lfal 669 (1105)
+---
T Consensus 126 leLk 129 (201)
T COG0632 126 LELK 129 (201)
T ss_pred HHHh
Confidence 6533
No 45
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=75.05 E-value=9.1 Score=41.14 Aligned_cols=65 Identities=20% Similarity=0.183 Sum_probs=38.9
Q ss_pred CCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhh-hCC-CchHHHHHHhcCCCCcHHHHH
Q 001299 585 KMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWL-RNV-PPDKVKEYLLDIEGLGLKSVE 662 (1105)
Q Consensus 585 ~~~fpTpEaLA~Ad~EELeelIR~lGf~n~KAk~Ik~lA~~Ive~~GglDLE~L-r~v-P~deaReeLLsLpGIG~KTAd 662 (1105)
.++|.+.++- +-.+.+|.--|...+.|..|... + +.+.| ..+ ..| .+.|.++||||+|||+
T Consensus 60 LyGF~~~~Er-----~lF~~Li~V~GIGpK~Al~ILs~-------~---~~~~l~~aI~~~D--~~~L~~vpGIGkKtAe 122 (194)
T PRK14605 60 LFGFATTEEL-----SLFETLIDVSGIGPKLGLAMLSA-------M---NAEALASAIISGN--AELLSTIPGIGKKTAS 122 (194)
T ss_pred eeCCCCHHHH-----HHHHHHhCCCCCCHHHHHHHHHh-------C---CHHHHHHHHHhCC--HHHHHhCCCCCHHHHH
Confidence 5688877753 23344555567777555554442 1 12221 111 223 5689999999999999
Q ss_pred HHHH
Q 001299 663 CVRL 666 (1105)
Q Consensus 663 ~ILL 666 (1105)
-|++
T Consensus 123 rIil 126 (194)
T PRK14605 123 RIVL 126 (194)
T ss_pred HHHH
Confidence 9653
No 46
>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=74.46 E-value=9.7 Score=42.66 Aligned_cols=133 Identities=13% Similarity=0.119 Sum_probs=72.8
Q ss_pred HHHHHHHHhc----CChHHHHHHHHHHHHHHHHHhCCCChhhhhC--CCchHHHHHHhcCCCCc--HH-------HHHHH
Q 001299 600 SEIADAIKER----GQQNIIAGRIKEFLNRLVELHGSIDLEWLRN--VPPDKVKEYLLDIEGLG--LK-------SVECV 664 (1105)
Q Consensus 600 EELeelIR~l----Gf~n~KAk~Ik~lA~~Ive~~GglDLE~Lr~--vP~deaReeLLsLpGIG--~K-------TAd~I 664 (1105)
+++...|... -+.++|.++|..+...+.. +.+..+.. -.-..+++.|..+=|-. .| ++...
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 3444455432 2556888888888765533 22222211 22345566666554433 23 33444
Q ss_pred HHHhcCC--e-----eeecchHHHHHHHHhCCCCCCCChHHHHHHHHhhCCchhhhhhhhhhhcccCChhhHHHHHHHHH
Q 001299 665 RLLSLQH--I-----AFPVDVNVGRIAVRLGWVPLQPLPGDLHIHLLKEYPVMDKIQMYLWPRLCYLDQKTLYELHYQMI 737 (1105)
Q Consensus 665 LLfalgr--p-----vfPVDThV~RIl~RLG~Vp~k~tpeeiE~~Leel~P~~e~Iqk~lW~rL~~ld~e~l~eLH~lLI 737 (1105)
+..++|. + -+|||.||.++..++|++.. .++. .+ .. .+.+ ...|..++..+.-.+..++..||
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--REEV-QKAWREVAKESGIPPLHLDSLLW 222 (246)
T ss_dssp HHHHCTS-----TTS-----HHHHHHHHCTTS-SS---HHH---HH--CT--CCHH-HHHHHHHHHHHT--HHHHHHHHH
T ss_pred HHHhcCCCCCCcccCCCCccHHHHHHHHHhccccc--cHHh---hh--cc--HHHH-HHHHHHHHhhcCCCchhhhhHHH
Confidence 4445564 2 58999999999999999753 2221 11 12 1233 45798877767777889999999
Q ss_pred -HHhHHhccC
Q 001299 738 -TFGKIFCKK 746 (1105)
Q Consensus 738 -dfGR~ICta 746 (1105)
-+|+..+..
T Consensus 223 ~l~G~~~~~~ 232 (246)
T PF09171_consen 223 PLLGRARDVK 232 (246)
T ss_dssp HHHCCHHCCT
T ss_pred Hhcccchhhh
Confidence 999988765
No 47
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=73.91 E-value=9.4 Score=41.19 Aligned_cols=63 Identities=16% Similarity=0.025 Sum_probs=38.7
Q ss_pred CCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHH------HHHHHHHHhCCCChhhhhCCCchHHHHHHhcCCCCcH
Q 001299 585 KMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKE------FLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGL 658 (1105)
Q Consensus 585 ~~~fpTpEaLA~Ad~EELeelIR~lGf~n~KAk~Ik~------lA~~Ive~~GglDLE~Lr~vP~deaReeLLsLpGIG~ 658 (1105)
.++|.|.++. +-...+|.--|...+.|-.|.. ++.+|.+ .| .+.|.++||||+
T Consensus 60 LyGF~~~~Er-----~lF~~Li~V~GIGpK~Al~iLs~~~~~el~~aI~~--------------~D--~~~L~kvpGIGk 118 (195)
T PRK14604 60 LYGFSTPAQR-----QLFELLIGVSGVGPKAALNLLSSGTPDELQLAIAG--------------GD--VARLARVPGIGK 118 (195)
T ss_pred eeCCCCHHHH-----HHHHHHhCcCCcCHHHHHHHHcCCCHHHHHHHHHh--------------CC--HHHHhhCCCCCH
Confidence 4677777653 2234445555666655554443 2222222 22 578999999999
Q ss_pred HHHHHHHHHh
Q 001299 659 KSVECVRLLS 668 (1105)
Q Consensus 659 KTAd~ILLfa 668 (1105)
|||+-|++--
T Consensus 119 KtAerIilEL 128 (195)
T PRK14604 119 KTAERIVLEL 128 (195)
T ss_pred HHHHHHHHHH
Confidence 9999887543
No 48
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=73.54 E-value=9.6 Score=41.15 Aligned_cols=21 Identities=29% Similarity=0.347 Sum_probs=18.4
Q ss_pred HHHHhcCCCCcHHHHHHHHHH
Q 001299 647 KEYLLDIEGLGLKSVECVRLL 667 (1105)
Q Consensus 647 ReeLLsLpGIG~KTAd~ILLf 667 (1105)
.+.|.++||||+|||+-|++-
T Consensus 106 ~~~L~kvpGIGkKtAerIilE 126 (197)
T PRK14603 106 ARLLTSASGVGKKLAERIALE 126 (197)
T ss_pred HHHHhhCCCCCHHHHHHHHHH
Confidence 578999999999999988744
No 49
>PRK00076 recR recombination protein RecR; Reviewed
Probab=73.39 E-value=3.2 Score=44.92 Aligned_cols=29 Identities=31% Similarity=0.394 Sum_probs=23.7
Q ss_pred chHHHHHHhcCCCCcHHHHHHHHHHhcCC
Q 001299 643 PDKVKEYLLDIEGLGLKSVECVRLLSLQH 671 (1105)
Q Consensus 643 ~deaReeLLsLpGIG~KTAd~ILLfalgr 671 (1105)
-+++.+.|.+|||||+|||.-+.++-+.+
T Consensus 6 ~~~Li~~l~~LPGIG~KsA~Rla~~ll~~ 34 (196)
T PRK00076 6 IEKLIEALRKLPGIGPKSAQRLAFHLLQR 34 (196)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHHHcC
Confidence 45778999999999999998777765543
No 50
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=73.39 E-value=8.1 Score=41.42 Aligned_cols=62 Identities=19% Similarity=0.175 Sum_probs=37.4
Q ss_pred CCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHH------HHHHHHHhCCCChhhhhCCCchHHHHHHhcCCCCcH
Q 001299 585 KMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEF------LNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGL 658 (1105)
Q Consensus 585 ~~~fpTpEaLA~Ad~EELeelIR~lGf~n~KAk~Ik~l------A~~Ive~~GglDLE~Lr~vP~deaReeLLsLpGIG~ 658 (1105)
.++|.|.++. +-.+.+|.--|...+.|-.|... .++|.+ .| .+.| ++||||+
T Consensus 60 LyGF~~~~Er-----~lF~~LisV~GIGpK~Al~iLs~~~~~~l~~aI~~--------------~D--~~~L-~vpGIGk 117 (186)
T PRK14600 60 LYGFLNREEQ-----DCLRMLVKVSGVNYKTAMSILSKLTPEQLFSAIVN--------------ED--KAAL-KVNGIGE 117 (186)
T ss_pred eeCCCCHHHH-----HHHHHHhCcCCcCHHHHHHHHccCCHHHHHHHHHc--------------CC--Hhhe-ECCCCcH
Confidence 4677777653 23344555566666555544432 222222 22 4678 9999999
Q ss_pred HHHHHHHHHh
Q 001299 659 KSVECVRLLS 668 (1105)
Q Consensus 659 KTAd~ILLfa 668 (1105)
|||+-|++--
T Consensus 118 KtAerIilEL 127 (186)
T PRK14600 118 KLINRIITEL 127 (186)
T ss_pred HHHHHHHHHH
Confidence 9999987543
No 51
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=73.07 E-value=5.2 Score=41.01 Aligned_cols=53 Identities=17% Similarity=0.211 Sum_probs=34.9
Q ss_pred HHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhCCCchHHHHHHhcCCCCcHHHHHHHHHH
Q 001299 593 AVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLL 667 (1105)
Q Consensus 593 aLA~Ad~EELeelIR~lGf~n~KAk~Ik~lA~~Ive~~GglDLE~Lr~vP~deaReeLLsLpGIG~KTAd~ILLf 667 (1105)
+|-.|+.+++.. --|++..+|+.|. .+|.+ .. .+.|++++|||+++.+.+--+
T Consensus 54 diN~A~~~el~~---lpGigP~~A~~IV--------~nGpf---------~s--veDL~~V~GIgekqk~~l~k~ 106 (132)
T PRK02515 54 DLNNSSVRAFRQ---FPGMYPTLAGKIV--------KNAPY---------DS--VEDVLNLPGLSERQKELLEAN 106 (132)
T ss_pred cCCccCHHHHHH---CCCCCHHHHHHHH--------HCCCC---------CC--HHHHHcCCCCCHHHHHHHHHh
Confidence 455667777644 3677787777766 24553 12 578899999998877665433
No 52
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=72.84 E-value=3.4 Score=44.70 Aligned_cols=29 Identities=28% Similarity=0.360 Sum_probs=23.6
Q ss_pred chHHHHHHhcCCCCcHHHHHHHHHHhcCC
Q 001299 643 PDKVKEYLLDIEGLGLKSVECVRLLSLQH 671 (1105)
Q Consensus 643 ~deaReeLLsLpGIG~KTAd~ILLfalgr 671 (1105)
-+++.+.|.+|||||+|||.-+.++-+..
T Consensus 6 ~~~Li~~l~~LPGIG~KsA~RlA~~ll~~ 34 (195)
T TIGR00615 6 ISKLIESLKKLPGIGPKSAQRLAFHLLKR 34 (195)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHHHcC
Confidence 46778999999999999998776665543
No 53
>PRK13844 recombination protein RecR; Provisional
Probab=72.76 E-value=3.4 Score=44.88 Aligned_cols=29 Identities=28% Similarity=0.275 Sum_probs=23.8
Q ss_pred chHHHHHHhcCCCCcHHHHHHHHHHhcCC
Q 001299 643 PDKVKEYLLDIEGLGLKSVECVRLLSLQH 671 (1105)
Q Consensus 643 ~deaReeLLsLpGIG~KTAd~ILLfalgr 671 (1105)
-+++.+.|.+|||||+|+|.-+.++-+..
T Consensus 10 ~~~LI~~l~~LPGIG~KsA~Rla~~lL~~ 38 (200)
T PRK13844 10 ISAVIESLRKLPTIGKKSSQRLALYLLDK 38 (200)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHHHcC
Confidence 46788999999999999998877765543
No 54
>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=69.42 E-value=6.6 Score=42.08 Aligned_cols=66 Identities=21% Similarity=0.160 Sum_probs=41.6
Q ss_pred CCCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhC-CC-chHHHHHHhcCCCCcHHHHH
Q 001299 585 KMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRN-VP-PDKVKEYLLDIEGLGLKSVE 662 (1105)
Q Consensus 585 ~~~fpTpEaLA~Ad~EELeelIR~lGf~n~KAk~Ik~lA~~Ive~~GglDLE~Lr~-vP-~deaReeLLsLpGIG~KTAd 662 (1105)
.++|.|.++- +-...+|+--|...++|..|... ++.+.|.. +- .| .+.|.++||||+|||+
T Consensus 59 LyGF~~~~Er-----~lF~~L~~V~GIGpK~Al~iL~~----------~~~~el~~aI~~~d--~~~L~~ipGiGkKtAe 121 (191)
T TIGR00084 59 LFGFNTLEER-----ELFKELIKVNGVGPKLALAILSN----------MSPEEFVYAIETEE--VKALVKIPGVGKKTAE 121 (191)
T ss_pred eeCCCCHHHH-----HHHHHHhCCCCCCHHHHHHHHhc----------CCHHHHHHHHHhCC--HHHHHhCCCCCHHHHH
Confidence 5688887763 33455666678878777666332 22222221 11 12 4679999999999999
Q ss_pred HHHHH
Q 001299 663 CVRLL 667 (1105)
Q Consensus 663 ~ILLf 667 (1105)
-|++-
T Consensus 122 rIile 126 (191)
T TIGR00084 122 RLLLE 126 (191)
T ss_pred HHHHH
Confidence 99843
No 55
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=67.84 E-value=4.8 Score=43.69 Aligned_cols=29 Identities=28% Similarity=0.374 Sum_probs=23.4
Q ss_pred chHHHHHHhcCCCCcHHHHHHHHHHhcCC
Q 001299 643 PDKVKEYLLDIEGLGLKSVECVRLLSLQH 671 (1105)
Q Consensus 643 ~deaReeLLsLpGIG~KTAd~ILLfalgr 671 (1105)
-+.+++.|..|||||+|+|.-+..+-+.+
T Consensus 7 i~~LI~~l~kLPGvG~KsA~R~AfhLL~~ 35 (198)
T COG0353 7 IEKLIDALKKLPGVGPKSAQRLAFHLLQR 35 (198)
T ss_pred HHHHHHHHhhCCCCChhHHHHHHHHHHcc
Confidence 45778999999999999998776665543
No 56
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=64.24 E-value=11 Score=35.64 Aligned_cols=57 Identities=25% Similarity=0.428 Sum_probs=36.6
Q ss_pred CHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhCCCchHHHHHHhc-CCCCcHHHHHHHHH
Q 001299 598 DESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLD-IEGLGLKSVECVRL 666 (1105)
Q Consensus 598 d~EELeelIR~lGf~n~KAk~Ik~lA~~Ive~~GglDLE~Lr~vP~deaReeLLs-LpGIG~KTAd~ILL 666 (1105)
...++...|...|+.... +..|.+.||.-.++.|++=|.. |+. +.|||-++||-|.+
T Consensus 7 ~~~~~~~~L~~~gl~~~~-------a~kl~~~yg~~ai~~l~~nPY~-----L~~~i~gi~F~~aD~iA~ 64 (94)
T PF14490_consen 7 GLRELMAFLQEYGLSPKL-------AMKLYKKYGDDAIEILKENPYR-----LIEDIDGIGFKTADKIAL 64 (94)
T ss_dssp --HHHHHHHHHTT--HHH-------HHHHHHHH-TTHHHHHHH-STC-----CCB-SSSSBHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCCHHH-------HHHHHHHHhHHHHHHHHHChHH-----HHHHccCCCHHHHHHHHH
Confidence 345667778899998744 4455556776566667666664 555 99999999988744
No 57
>COG2818 Tag 3-methyladenine DNA glycosylase [DNA replication, recombination, and repair]
Probab=64.17 E-value=30 Score=37.54 Aligned_cols=65 Identities=14% Similarity=0.135 Sum_probs=48.3
Q ss_pred cccHHHHHHHHHHhhhhccCCCCCCCHHHHHcCCHHHHHHHHHhcCChHH--HHHHHHHHHHHHH---HHhCCC
Q 001299 565 QQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERGQQNI--IAGRIKEFLNRLV---ELHGSI 633 (1105)
Q Consensus 565 QTsw~~V~ka~~rL~er~~~~~~fpTpEaLA~Ad~EELeelIR~lGf~n~--KAk~Ik~lA~~Iv---e~~Ggl 633 (1105)
-.+|..+.+-.+++++ ....++|+.||..++++++.++...|.-+. |.+.++.-|+++. ++||++
T Consensus 44 GLSW~tVL~KRe~fre----aF~~Fd~~kVA~~~~~dverLl~d~gIIR~r~KI~A~i~NA~~~l~l~~e~Gsf 113 (188)
T COG2818 44 GLSWLTVLKKREAFRE----AFHGFDPEKVAAMTEEDVERLLADAGIIRNRGKIKATINNARAVLELQKEFGSF 113 (188)
T ss_pred cchHHHHHHhHHHHHH----HHhcCCHHHHHcCCHHHHHHHHhCcchhhhHHHHHHHHHHHHHHHHHHHHcCCH
Confidence 3479999988888864 234689999999999999999999997664 4455555555544 456663
No 58
>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=63.92 E-value=19 Score=45.34 Aligned_cols=32 Identities=6% Similarity=0.103 Sum_probs=19.6
Q ss_pred CHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHH
Q 001299 590 DWEAVRCADESEIADAIKERGQQNIIAGRIKEFLN 624 (1105)
Q Consensus 590 TpEaLA~Ad~EELeelIR~lGf~n~KAk~Ik~lA~ 624 (1105)
++++|..+..++|.++ -||....|..|.+..+
T Consensus 456 ~~~Dl~~L~~~~L~~L---~GfG~Ksa~nIl~~Ie 487 (652)
T TIGR00575 456 SVADLYALKKEDLLEL---EGFGEKSAQNLLNAIE 487 (652)
T ss_pred CHHHHHhcCHHHHhhc---cCccHHHHHHHHHHHH
Confidence 6777777777766433 3666666665555443
No 59
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=63.10 E-value=13 Score=41.23 Aligned_cols=60 Identities=20% Similarity=0.324 Sum_probs=44.6
Q ss_pred cCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhCCCchHHHHHHhcCCCCcHHHHHHH
Q 001299 596 CADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECV 664 (1105)
Q Consensus 596 ~Ad~EELeelIR~lGf~n~KAk~Ik~lA~~Ive~~GglDLE~Lr~vP~deaReeLLsLpGIG~KTAd~I 664 (1105)
.++..||.+++=..|- |-+-...+|+.+..+||+ |..|...+. ++|.+++|||+--|--+
T Consensus 23 ~Lsd~ELLailLrtG~---~~~~~~~la~~lL~~fg~--L~~l~~a~~----~el~~v~GiG~aka~~l 82 (224)
T COG2003 23 ALSDAELLAILLRTGT---KGESVLDLAKELLQEFGS--LAELLKASV----EELSSVKGIGLAKAIQI 82 (224)
T ss_pred hcchHHHHHHHHhcCC---CCCCHHHHHHHHHHHccc--HHHHHhCCH----HHHhhCCCccHHHHHHH
Confidence 3466788888777776 446677999999999987 667766654 58999999996554433
No 60
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=63.04 E-value=12 Score=39.93 Aligned_cols=21 Identities=29% Similarity=0.406 Sum_probs=18.4
Q ss_pred HHHHhcCCCCcHHHHHHHHHH
Q 001299 647 KEYLLDIEGLGLKSVECVRLL 667 (1105)
Q Consensus 647 ReeLLsLpGIG~KTAd~ILLf 667 (1105)
.+.|.++||||+|+|+.|+..
T Consensus 107 ~~~L~~v~Gig~k~A~~I~~~ 127 (192)
T PRK00116 107 VKALTKVPGIGKKTAERIVLE 127 (192)
T ss_pred HHHHHhCCCCCHHHHHHHHHH
Confidence 458999999999999999855
No 61
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=61.75 E-value=14 Score=38.41 Aligned_cols=55 Identities=24% Similarity=0.375 Sum_probs=37.0
Q ss_pred HHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhCCCchHHHHHHhcCCCCcHHHHHHHHH
Q 001299 594 VRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRL 666 (1105)
Q Consensus 594 LA~Ad~EELeelIR~lGf~n~KAk~Ik~lA~~Ive~~GglDLE~Lr~vP~deaReeLLsLpGIG~KTAd~ILL 666 (1105)
|=.|+.++| ..|.++| ..||+.|.+.. +++|.| .+ .+.|...+|||+++.+-+.-
T Consensus 91 iNtAs~eeL-~~lpgIG--~~kA~aIi~yR----e~~G~f---------~s--v~dL~~v~GiG~~~~ekl~~ 145 (149)
T COG1555 91 INTASAEEL-QALPGIG--PKKAQAIIDYR----EENGPF---------KS--VDDLAKVKGIGPKTLEKLKD 145 (149)
T ss_pred ccccCHHHH-HHCCCCC--HHHHHHHHHHH----HHcCCC---------Cc--HHHHHhccCCCHHHHHHHHh
Confidence 455677777 5555555 45787776643 456653 12 56899999999999876643
No 62
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=61.54 E-value=27 Score=44.17 Aligned_cols=20 Identities=25% Similarity=0.365 Sum_probs=13.6
Q ss_pred HHHhcCCCCcHHHHHHHHHH
Q 001299 648 EYLLDIEGLGLKSVECVRLL 667 (1105)
Q Consensus 648 eeLLsLpGIG~KTAd~ILLf 667 (1105)
++|.+++|||+++|..|..|
T Consensus 543 eeL~~i~GIG~~~A~sI~~f 562 (665)
T PRK07956 543 EELAAVEGVGEVVAQSIVEF 562 (665)
T ss_pred HHHhccCCcCHHHHHHHHHH
Confidence 45677777777777777555
No 63
>PRK14973 DNA topoisomerase I; Provisional
Probab=60.31 E-value=15 Score=47.89 Aligned_cols=98 Identities=16% Similarity=0.099 Sum_probs=60.9
Q ss_pred CCCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHH-HHHHHhCCCChhhhhCCCchHHHHHHhcCCCCcHHHHHHH
Q 001299 586 MDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLN-RLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECV 664 (1105)
Q Consensus 586 ~~fpTpEaLA~Ad~EELeelIR~lGf~n~KAk~Ik~lA~-~Ive~~GglDLE~Lr~vP~deaReeLLsLpGIG~KTAd~I 664 (1105)
.||-++++++.|++++|.. --|+..-.+..+...+. .+.. -+-+.......+..+.+|++++|||++|++-.
T Consensus 821 ~G~~~~~d~~~a~p~~La~---~~g~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~el~~vkg~ge~t~~~l 893 (936)
T PRK14973 821 AGFDTPEDFCSVHPAYLAL---KTGISPETICRHAKLVCEKLGR----PVPEKISKAAFERGRAELLSVPGLGETTLEKL 893 (936)
T ss_pred hcCCCHHHHHhcCHHHHhc---CCCCChhhHHHHHHHHHHHhcC----CCchhhhhhhhcccchhhhhccCCCHHHHHHH
Confidence 4788999999999999854 47888766666655554 4333 12222222333334666999999999999665
Q ss_pred HHHhcCCeeeecchHHHHHHHHhCCC
Q 001299 665 RLLSLQHIAFPVDVNVGRIAVRLGWV 690 (1105)
Q Consensus 665 LLfalgrpvfPVDThV~RIl~RLG~V 690 (1105)
-.-+.-.+.-.+-.-..|++.+-|+.
T Consensus 894 ~~ag~~~~e~l~~~d~~~la~~~~i~ 919 (936)
T PRK14973 894 YLAGVYDGDLLVSADPKKLAKVTGID 919 (936)
T ss_pred HHcCCCCHHHhccCCHHHHhhhcCCC
Confidence 44444333222222566666666664
No 64
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=57.12 E-value=19 Score=32.07 Aligned_cols=52 Identities=27% Similarity=0.321 Sum_probs=29.5
Q ss_pred HcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhCCCchHHHHHHhcCCCCcHHHHHHH
Q 001299 595 RCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECV 664 (1105)
Q Consensus 595 A~Ad~EELeelIR~lGf~n~KAk~Ik~lA~~Ive~~GglDLE~Lr~vP~deaReeLLsLpGIG~KTAd~I 664 (1105)
-.|+.++|.. --|+....|+.|.+.- +.+|++ .+ .++|..++|||+++.+-+
T Consensus 9 N~as~~eL~~---lpgi~~~~A~~Iv~~R----~~~G~f---------~s--~~dL~~v~gi~~~~~~~l 60 (65)
T PF12836_consen 9 NTASAEELQA---LPGIGPKQAKAIVEYR----EKNGPF---------KS--LEDLKEVPGIGPKTYEKL 60 (65)
T ss_dssp TTS-HHHHHT---STT--HHHHHHHHHHH----HHH-S----------SS--GGGGGGSTT--HHHHHHH
T ss_pred ccCCHHHHHH---cCCCCHHHHHHHHHHH----HhCcCC---------CC--HHHHhhCCCCCHHHHHHH
Confidence 3456666532 2388888888887754 334653 11 457999999999998765
No 65
>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=56.62 E-value=23 Score=35.33 Aligned_cols=57 Identities=23% Similarity=0.300 Sum_probs=37.2
Q ss_pred HHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhCCCchHHHHHHhcCCCCcHHHHHHHHHH
Q 001299 593 AVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLL 667 (1105)
Q Consensus 593 aLA~Ad~EELeelIR~lGf~n~KAk~Ik~lA~~Ive~~GglDLE~Lr~vP~deaReeLLsLpGIG~KTAd~ILLf 667 (1105)
+|-.|+.++|..+ -|....+|+.|.+.-. .+|.+ .+ .++|..++|||+++++-+.-|
T Consensus 61 niNtA~~~eL~~l---pGIG~~~A~~Ii~~R~----~~g~f---------~s--~eeL~~V~GIg~k~~~~i~~~ 117 (120)
T TIGR01259 61 NINAASLEELQAL---PGIGPAKAKAIIEYRE----ENGAF---------KS--VDDLTKVSGIGEKSLEKLKDY 117 (120)
T ss_pred eCCcCCHHHHhcC---CCCCHHHHHHHHHHHH----hcCCc---------CC--HHHHHcCCCCCHHHHHHHHhc
Confidence 4555667776432 4555667776665432 23542 12 578999999999999988654
No 66
>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=56.10 E-value=10 Score=36.91 Aligned_cols=28 Identities=29% Similarity=0.337 Sum_probs=22.4
Q ss_pred HHHHHHhcCCCCcHHHHHHHHHHhcCCe
Q 001299 645 KVKEYLLDIEGLGLKSVECVRLLSLQHI 672 (1105)
Q Consensus 645 eaReeLLsLpGIG~KTAd~ILLfalgrp 672 (1105)
.....|+.|||||+.+|..+..+++..+
T Consensus 9 ~~~~~L~~iP~IG~a~a~DL~~LGi~s~ 36 (93)
T PF11731_consen 9 AGLSDLTDIPNIGKATAEDLRLLGIRSP 36 (93)
T ss_pred HHHHHHhcCCCccHHHHHHHHHcCCCCH
Confidence 3467899999999999998877666543
No 67
>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=52.56 E-value=11 Score=35.24 Aligned_cols=42 Identities=21% Similarity=0.218 Sum_probs=29.7
Q ss_pred HHHhcCCCCcHHHHHHHHHHhcCCeeeecchHHHHHHHHhCCCCC
Q 001299 648 EYLLDIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPL 692 (1105)
Q Consensus 648 eeLLsLpGIG~KTAd~ILLfalgrpvfPVDThV~RIl~RLG~Vp~ 692 (1105)
+.|++|||||+-||..++....+...|+= ...+..-+|+.|.
T Consensus 2 ~~l~sipGig~~~a~~llaeigd~~rF~~---~~~l~~~~Gl~P~ 43 (87)
T PF02371_consen 2 ELLTSIPGIGPITAATLLAEIGDISRFKS---AKQLASYAGLAPR 43 (87)
T ss_pred chhcCCCCccHHHHHHHHHHHcCchhccc---chhhhhccccccc
Confidence 36889999999999999888744445543 3444455688763
No 68
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=52.33 E-value=20 Score=41.49 Aligned_cols=51 Identities=20% Similarity=0.214 Sum_probs=31.9
Q ss_pred CChHHHHHHHHHHHHHHHHHhCCCC-hhhhhCCCchHHHHHHhcCCCCcHHHHHHHH
Q 001299 610 GQQNIIAGRIKEFLNRLVELHGSID-LEWLRNVPPDKVKEYLLDIEGLGLKSVECVR 665 (1105)
Q Consensus 610 Gf~n~KAk~Ik~lA~~Ive~~GglD-LE~Lr~vP~deaReeLLsLpGIG~KTAd~IL 665 (1105)
|....-|+.|.++++ .|.+. +..+..-+.-.+..+|++|+|||+|+|..+-
T Consensus 55 gIG~~ia~kI~Eil~-----tG~~~~~~e~l~~~~p~~l~~l~~i~GiGpk~a~~l~ 106 (334)
T smart00483 55 GIGDKIKKKIEEIIE-----TGKSSKVLEILNDEVYKSLKLFTNVFGVGPKTAAKWY 106 (334)
T ss_pred CccHHHHHHHHHHHH-----hCcHHHHHHHhcCcHHHHHHHHHccCCcCHHHHHHHH
Confidence 555555666655542 36554 3323233444568899999999999996653
No 69
>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=49.82 E-value=24 Score=33.35 Aligned_cols=64 Identities=17% Similarity=0.216 Sum_probs=44.6
Q ss_pred ceeeeeeeeccCCCCCCcccchhhhhcccceeEEecCchhhhhcccCHHHHHHHHhhcceeeeccccccCCCccc
Q 001299 1009 YFQVNEVFADHETSHHPINVPRHTIANLRREIVCFGSSATTLFNALDMRQIQEYFWRGFVCVRGFDRRYRCPRPL 1083 (1105)
Q Consensus 1009 YFQvNEVFaDh~SS~~PI~Vpr~~iw~L~rr~VYfGtSv~sIfkglt~~~Iq~cF~~G~vCVR~fdr~tr~PrpL 1083 (1105)
+|.-||||+=.....+||. .=+.++.|.+-........ ....-...-|+|=++||+.++.-|+|
T Consensus 59 ~~~~~Elf~s~~~~~i~v~------~I~gkc~V~~~~~~~~~~~-----~~~~~~~~~f~~r~~yd~~~~~fk~~ 122 (123)
T cd04370 59 FALRRELFLSDHLDEIPVE------SIIGKCKVLFVSEFEGLKQ-----RPNKIDTDDFFCRLAYDPTTKEFKAL 122 (123)
T ss_pred ccccceeEEecCccccCHH------HhccccEEEechHhhcccc-----ccccCCCCeEEEEEEECcCcceEEeC
Confidence 7999999998888877775 3355777777664433321 00112457899999999998877765
No 70
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=49.14 E-value=66 Score=41.03 Aligned_cols=29 Identities=10% Similarity=0.095 Sum_probs=18.0
Q ss_pred CHHHHHcCCHHHHHHHHHhcCChHHHHHHHHH
Q 001299 590 DWEAVRCADESEIADAIKERGQQNIIAGRIKE 621 (1105)
Q Consensus 590 TpEaLA~Ad~EELeelIR~lGf~n~KAk~Ik~ 621 (1105)
++.+|..+..++|..+ -||...+|..|.+
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 6778888887765332 3666666655443
No 71
>PRK07945 hypothetical protein; Provisional
Probab=48.65 E-value=27 Score=40.40 Aligned_cols=61 Identities=11% Similarity=0.110 Sum_probs=38.9
Q ss_pred HHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhCCCchHHHHHHhcCCCCcHHHHHHHHHH
Q 001299 600 SEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLL 667 (1105)
Q Consensus 600 EELeelIR~lGf~n~KAk~Ik~lA~~Ive~~GglDLE~Lr~vP~deaReeLLsLpGIG~KTAd~ILLf 667 (1105)
++++.+|.-.|=..=|++..+++|+.|.. ++-+.+..+.. ...|.+|||||.-+|..|.-+
T Consensus 8 ~~~a~lle~~~~n~frv~ayr~aa~~~~~----~~~~~~~~~~~---~g~l~~~~giG~~~a~~i~e~ 68 (335)
T PRK07945 8 RRIAFLLERARADTYRVRAFRRAADVVEA----LDAAERARRAR---AGSLTSLPGIGPKTAKVIAQA 68 (335)
T ss_pred HHHHHHHHHcCCChhhHHHHHHHHHHHHh----cChhHHHHHHh---cCCcccCCCcCHHHHHHHHHH
Confidence 45556666666544488888888887755 21111211111 116899999999999988655
No 72
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=44.85 E-value=2.5e+02 Score=28.24 Aligned_cols=60 Identities=15% Similarity=0.127 Sum_probs=38.5
Q ss_pred CCCCCHHHHHcCCHHHHHH--HHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhCCCchHHHHHHhcCCCCcHHHHHH
Q 001299 586 MDSVDWEAVRCADESEIAD--AIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVEC 663 (1105)
Q Consensus 586 ~~fpTpEaLA~Ad~EELee--lIR~lGf~n~KAk~Ik~lA~~Ive~~GglDLE~Lr~vP~deaReeLLsLpGIG~KTAd~ 663 (1105)
.+--|+++|+.++...+.. +....|... ..+.++ ..+..|..++|||+..|..
T Consensus 14 ~GI~t~~~Ll~~~~~~~~r~~La~~~~i~~----------------------~~l~~w---~~~AdL~ri~gi~~~~a~L 68 (122)
T PF14229_consen 14 AGIKTTGDLLEAGDTPLGRKALAKKLGISE----------------------RNLLKW---VNQADLMRIPGIGPQYAEL 68 (122)
T ss_pred cCCCcHHHHHHcCCCHHHHHHHHHhcCCCH----------------------HHHHHH---HhHHHhhhcCCCCHHHHHH
Confidence 3556888888887776655 444455432 222221 1156788999999999987
Q ss_pred HHHHhcC
Q 001299 664 VRLLSLQ 670 (1105)
Q Consensus 664 ILLfalg 670 (1105)
++--++.
T Consensus 69 L~~AGv~ 75 (122)
T PF14229_consen 69 LEHAGVD 75 (122)
T ss_pred HHHhCcC
Confidence 7666654
No 73
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=44.85 E-value=59 Score=37.71 Aligned_cols=57 Identities=14% Similarity=0.162 Sum_probs=37.2
Q ss_pred HHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhCCCchHHHHHHhcCCCCcHHHHHHHHHH
Q 001299 600 SEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLL 667 (1105)
Q Consensus 600 EELeelIR~lGf~n~KAk~Ik~lA~~Ive~~GglDLE~Lr~vP~deaReeLLsLpGIG~KTAd~ILLf 667 (1105)
+++++++.-.|-...|+.+..++|..|.. ++ . |.+. .+.|.+|||||.++|+.|--+
T Consensus 11 ~~la~l~el~gen~~k~~ay~~Aa~~i~~-l~-~--------~i~~-~~~l~~lpgIG~~ia~kI~Ei 67 (334)
T smart00483 11 EILAENYEVFGENKRKCSYFRKAASVLKS-LP-F--------PINS-MKDLKGLPGIGDKIKKKIEEI 67 (334)
T ss_pred HHHHHHHHHhcccHHHHHHHHHHHHHHHh-CC-C--------CCCC-HHHHhcCCCccHHHHHHHHHH
Confidence 34444555456555577777777777755 22 1 2222 247899999999999998744
No 74
>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=44.67 E-value=42 Score=29.20 Aligned_cols=35 Identities=26% Similarity=0.210 Sum_probs=28.6
Q ss_pred CCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHH
Q 001299 587 DSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLN 624 (1105)
Q Consensus 587 ~fpTpEaLA~Ad~EELeelIR~lGf~n~KAk~Ik~lA~ 624 (1105)
++.|+++|+.++.++|.+ --|+...+|+.|++.++
T Consensus 25 G~~t~~~l~~a~~~~L~~---i~Gig~~~a~~i~~~~~ 59 (60)
T PF14520_consen 25 GIKTLEDLANADPEELAE---IPGIGEKTAEKIIEAAR 59 (60)
T ss_dssp TCSSHHHHHTSHHHHHHT---STTSSHHHHHHHHHHHH
T ss_pred CCCcHHHHHcCCHHHHhc---CCCCCHHHHHHHHHHHh
Confidence 677999999999998754 36788889998887765
No 75
>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=44.29 E-value=18 Score=38.84 Aligned_cols=22 Identities=18% Similarity=0.303 Sum_probs=18.7
Q ss_pred HHHHHHhcCCCCcHHHHHHHHH
Q 001299 645 KVKEYLLDIEGLGLKSVECVRL 666 (1105)
Q Consensus 645 eaReeLLsLpGIG~KTAd~ILL 666 (1105)
++...|++++|||||+|-.||.
T Consensus 69 ~lF~~L~~V~GIGpK~Al~iL~ 90 (191)
T TIGR00084 69 ELFKELIKVNGVGPKLALAILS 90 (191)
T ss_pred HHHHHHhCCCCCCHHHHHHHHh
Confidence 5677899999999999988843
No 76
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=43.25 E-value=19 Score=38.47 Aligned_cols=20 Identities=20% Similarity=0.303 Sum_probs=16.9
Q ss_pred HHHHhcCCCCcHHHHHHHHH
Q 001299 647 KEYLLDIEGLGLKSVECVRL 666 (1105)
Q Consensus 647 ReeLLsLpGIG~KTAd~ILL 666 (1105)
...|+.++|||+|+|..+|.
T Consensus 72 f~~L~~i~GIGpk~A~~il~ 91 (192)
T PRK00116 72 FRLLISVSGVGPKLALAILS 91 (192)
T ss_pred HHHHhcCCCCCHHHHHHHHH
Confidence 45788999999999988853
No 77
>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=42.48 E-value=30 Score=39.54 Aligned_cols=50 Identities=32% Similarity=0.396 Sum_probs=31.7
Q ss_pred CChHHHHHHHHHHHHHHHHHhCCC-ChhhhhCCCchHHHHHHhcCCCCcHHHHHHHH
Q 001299 610 GQQNIIAGRIKEFLNRLVELHGSI-DLEWLRNVPPDKVKEYLLDIEGLGLKSVECVR 665 (1105)
Q Consensus 610 Gf~n~KAk~Ik~lA~~Ive~~Ggl-DLE~Lr~vP~deaReeLLsLpGIG~KTAd~IL 665 (1105)
|....-|..|.++.+ .|.+ .|+.|+.- .-....+|++|+|||+++|..+.
T Consensus 52 giG~~ia~kI~E~~~-----tG~~~~le~l~~~-~~~~l~~l~~i~GiGpk~a~~l~ 102 (307)
T cd00141 52 GIGKKIAEKIEEILE-----TGKLRKLEELRED-VPPGLLLLLRVPGVGPKTARKLY 102 (307)
T ss_pred CccHHHHHHHHHHHH-----cCCHHHHHHHhcc-chHHHHHHHcCCCCCHHHHHHHH
Confidence 555556666666643 1443 24444432 23347899999999999997665
No 78
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=41.09 E-value=42 Score=42.58 Aligned_cols=22 Identities=27% Similarity=0.209 Sum_probs=19.2
Q ss_pred HHHHhcCCCCcHHHHHHHHHHh
Q 001299 647 KEYLLDIEGLGLKSVECVRLLS 668 (1105)
Q Consensus 647 ReeLLsLpGIG~KTAd~ILLfa 668 (1105)
.+.|++|+|||+++|..|..|-
T Consensus 540 ~e~l~~i~giG~~~a~si~~ff 561 (669)
T PRK14350 540 LSKLLKIKGIGEKIALNIIEAF 561 (669)
T ss_pred HHHHhhCCCccHHHHHHHHHHH
Confidence 4679999999999999998773
No 79
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=41.08 E-value=21 Score=38.40 Aligned_cols=23 Identities=26% Similarity=0.297 Sum_probs=19.9
Q ss_pred HHHHHHhcCCCCcHHHHHHHHHH
Q 001299 645 KVKEYLLDIEGLGLKSVECVRLL 667 (1105)
Q Consensus 645 eaReeLLsLpGIG~KTAd~ILLf 667 (1105)
++...|++++|||+|+|-.||..
T Consensus 70 ~lF~~Li~V~GIGpK~Al~ILs~ 92 (194)
T PRK14605 70 SLFETLIDVSGIGPKLGLAMLSA 92 (194)
T ss_pred HHHHHHhCCCCCCHHHHHHHHHh
Confidence 56778999999999999999873
No 80
>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=41.01 E-value=34 Score=30.98 Aligned_cols=28 Identities=32% Similarity=0.387 Sum_probs=21.6
Q ss_pred ChhhhhCCCchHHHHHHhcCCCCcHHHHHHHH
Q 001299 634 DLEWLRNVPPDKVKEYLLDIEGLGLKSVECVR 665 (1105)
Q Consensus 634 DLE~Lr~vP~deaReeLLsLpGIG~KTAd~IL 665 (1105)
.+..|..++. +.|++++|+|+++++-|.
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 5667777754 489999999999988764
No 81
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=40.91 E-value=26 Score=31.19 Aligned_cols=21 Identities=24% Similarity=0.352 Sum_probs=17.0
Q ss_pred HHHHhcCCCCcHHHHHHHHHH
Q 001299 647 KEYLLDIEGLGLKSVECVRLL 667 (1105)
Q Consensus 647 ReeLLsLpGIG~KTAd~ILLf 667 (1105)
.++|.++||||++.|..|+.+
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 568999999999999999876
No 82
>PRK14973 DNA topoisomerase I; Provisional
Probab=40.38 E-value=2.7e+02 Score=36.99 Aligned_cols=75 Identities=20% Similarity=0.168 Sum_probs=54.0
Q ss_pred CCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHH---------------Hh--CCC-ChhhhhCCCchHHHH
Q 001299 587 DSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVE---------------LH--GSI-DLEWLRNVPPDKVKE 648 (1105)
Q Consensus 587 ~fpTpEaLA~Ad~EELeelIR~lGf~n~KAk~Ik~lA~~Ive---------------~~--Ggl-DLE~Lr~vP~deaRe 648 (1105)
+..+.++|+.|++..| +..|++..+++.+.+.|+-+.. .+ +|| +++.+....+ +
T Consensus 764 ~~~~~~~~~~~~~~~~----~~~~~sE~~~~~~~~~a~~~~~~~~~~~~gv~~~~~~~~~~~G~~~~~d~~~a~p----~ 835 (936)
T PRK14973 764 GINDIAALARADPADL----KKAGLSEAEAASLLAEAKSLCNISRLKEIGVPAVSLKKYQEAGFDTPEDFCSVHP----A 835 (936)
T ss_pred CcchHHHHhhCCHHHH----HHcCCCHHHHHHHHHHHHHHHHHHhhcccCCCHHHHHHHHHhcCCCHHHHHhcCH----H
Confidence 5568999999999886 7789999999999998843221 10 233 4555555554 4
Q ss_pred HHhcCCCCcHHHHHHHHHHhc
Q 001299 649 YLLDIEGLGLKSVECVRLLSL 669 (1105)
Q Consensus 649 eLLsLpGIG~KTAd~ILLfal 669 (1105)
+|..++||++-|+......+.
T Consensus 836 ~La~~~g~~~~~~~~~~~~~~ 856 (936)
T PRK14973 836 YLALKTGISPETICRHAKLVC 856 (936)
T ss_pred HHhcCCCCChhhHHHHHHHHH
Confidence 899999999988876654444
No 83
>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=38.75 E-value=27 Score=34.90 Aligned_cols=22 Identities=18% Similarity=0.246 Sum_probs=19.4
Q ss_pred HHHHhcCCCCcHHHHHHHHHHh
Q 001299 647 KEYLLDIEGLGLKSVECVRLLS 668 (1105)
Q Consensus 647 ReeLLsLpGIG~KTAd~ILLfa 668 (1105)
.+.|.+|||||++.|..|+.+-
T Consensus 67 ~~eL~~lpGIG~~~A~~Ii~~R 88 (120)
T TIGR01259 67 LEELQALPGIGPAKAKAIIEYR 88 (120)
T ss_pred HHHHhcCCCCCHHHHHHHHHHH
Confidence 5689999999999999998773
No 84
>PF03568 Peptidase_C50: Peptidase family C50; InterPro: IPR005314 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to MEROPS peptidase family C50 (separase family, clan CD). The active site residues for members of this family and family C14 occur in the same order in the sequence: H,C. The separases are caspase-like proteases, which plays a central role in the chromosome segregation. In yeast they cleave the rad21 subunit of the cohesin complex at the onset of anaphase. During most of the cell cycle, separase is inactivated by the securin/cut2 protein, which probably covers its active site. ; GO: 0008233 peptidase activity, 0006508 proteolysis, 0005634 nucleus
Probab=38.72 E-value=30 Score=40.65 Aligned_cols=36 Identities=36% Similarity=0.924 Sum_probs=30.6
Q ss_pred CCchhhHHHHHHHHHHHhhhHHHHHHHHHh-hhcCcccccCCC
Q 001299 172 TSNEDMEKWWQKEREVFEGRIQSFTARMHL-ILGDRRFKPWKG 213 (1105)
Q Consensus 172 g~D~~k~kwWeeeR~vF~gr~dsFiarmhl-vqGDRRFSpWKG 213 (1105)
.+.++|.+||+ +|+-...|...++..|-- ..| +|||
T Consensus 62 ~t~~~kk~WW~-~R~~LD~rL~~LL~~iE~~wLG-----~wkg 98 (383)
T PF03568_consen 62 KTKEDKKKWWK-ERKALDSRLKDLLENIENSWLG-----GWKG 98 (383)
T ss_pred CCHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHH-----HHhh
Confidence 37789999997 588899999999999987 554 8997
No 85
>PF05559 DUF763: Protein of unknown function (DUF763); InterPro: IPR008482 This family consists of several uncharacterised bacterial and archaeal proteins of unknown function.
Probab=38.54 E-value=78 Score=37.01 Aligned_cols=25 Identities=36% Similarity=0.595 Sum_probs=20.8
Q ss_pred CchHHHHHHhcCCCCcHHHHHHHHHHh
Q 001299 642 PPDKVKEYLLDIEGLGLKSVECVRLLS 668 (1105)
Q Consensus 642 P~deaReeLLsLpGIG~KTAd~ILLfa 668 (1105)
|.+ .++|+.++|||++|..++.+.+
T Consensus 265 p~~--feeLL~~~GvGp~TlRALaLva 289 (319)
T PF05559_consen 265 PSD--FEELLLIKGVGPSTLRALALVA 289 (319)
T ss_pred ccC--HHHHHhcCCCCHHHHHHHHHHH
Confidence 455 7899999999999998887664
No 86
>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=38.23 E-value=24 Score=27.82 Aligned_cols=15 Identities=20% Similarity=0.373 Sum_probs=11.1
Q ss_pred HhcCCCCcHHHHHHH
Q 001299 650 LLDIEGLGLKSVECV 664 (1105)
Q Consensus 650 LLsLpGIG~KTAd~I 664 (1105)
+..++|||++|+.-+
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 347899999999764
No 87
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=37.78 E-value=26 Score=36.42 Aligned_cols=27 Identities=19% Similarity=0.283 Sum_probs=21.3
Q ss_pred CCchHHHHHHhcCCCCcHHHHHHHHHHh
Q 001299 641 VPPDKVKEYLLDIEGLGLKSVECVRLLS 668 (1105)
Q Consensus 641 vP~deaReeLLsLpGIG~KTAd~ILLfa 668 (1105)
++... .++|..|||||++.|..|.-+-
T Consensus 91 iNtAs-~eeL~~lpgIG~~kA~aIi~yR 117 (149)
T COG1555 91 INTAS-AEELQALPGIGPKKAQAIIDYR 117 (149)
T ss_pred ccccC-HHHHHHCCCCCHHHHHHHHHHH
Confidence 44433 4678999999999999998774
No 88
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=36.86 E-value=44 Score=39.42 Aligned_cols=39 Identities=31% Similarity=0.417 Sum_probs=30.7
Q ss_pred HHHHHHHHHHhCCCChhhhhCCCchHHHHHHhcCCCCcHHHHHHH
Q 001299 620 KEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECV 664 (1105)
Q Consensus 620 k~lA~~Ive~~GglDLE~Lr~vP~deaReeLLsLpGIG~KTAd~I 664 (1105)
+.+|+.++++||+ |..+...+. ++|..++|||++.|..|
T Consensus 297 k~iAk~Ll~~FGS--L~~Il~As~----eeL~~VeGIGe~rA~~I 335 (352)
T PRK13482 297 SAVIENLVEHFGS--LQGLLAASI----EDLDEVEGIGEVRARAI 335 (352)
T ss_pred HHHHHHHHHHcCC--HHHHHcCCH----HHHhhCCCcCHHHHHHH
Confidence 3578889999985 666666554 47999999999999874
No 89
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=36.79 E-value=57 Score=41.37 Aligned_cols=36 Identities=25% Similarity=0.315 Sum_probs=26.3
Q ss_pred HHHHhCCCChhhhhCCCchHHHHHHhcCCCCcHHHHHHHHHH
Q 001299 626 LVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLL 667 (1105)
Q Consensus 626 Ive~~GglDLE~Lr~vP~deaReeLLsLpGIG~KTAd~ILLf 667 (1105)
+...|+. ++.|...+.+ .|.+|+|||.+.|..|.-|
T Consensus 527 La~~f~s--l~~l~~a~~e----~l~~i~giG~~vA~si~~f 562 (667)
T COG0272 527 LARHFGT--LEALLAASEE----ELASIPGIGEVVARSIIEF 562 (667)
T ss_pred HHHHhhh--HHHHHhcCHH----HHhhccchhHHHHHHHHHH
Confidence 3344443 6677666544 7889999999999999776
No 90
>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=34.62 E-value=87 Score=35.92 Aligned_cols=56 Identities=20% Similarity=0.216 Sum_probs=35.5
Q ss_pred HHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhCCCchHHHHHHhcCCCCcHHHHHHHHHH
Q 001299 601 EIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLL 667 (1105)
Q Consensus 601 ELeelIR~lGf~n~KAk~Ik~lA~~Ive~~GglDLE~Lr~vP~deaReeLLsLpGIG~KTAd~ILLf 667 (1105)
+|+.++.-.|=..-|++..+.+|..|.. +. .|.+. .+++.+|||||+++|+.|--+
T Consensus 9 ~ia~~~e~~~~~~~r~~aY~~Aa~~l~~-l~---------~~i~~-~~~~~~ipgiG~~ia~kI~E~ 64 (307)
T cd00141 9 ELADLLELLGGNPFRVRAYRKAARALES-LP---------EPIES-LEEAKKLPGIGKKIAEKIEEI 64 (307)
T ss_pred HHHHHHHhccCCcchHHHHHHHHHHHHh-CC---------cccCC-HHHhcCCCCccHHHHHHHHHH
Confidence 4444444444223377777777777765 22 12222 346799999999999999765
No 91
>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=34.57 E-value=31 Score=30.09 Aligned_cols=20 Identities=20% Similarity=0.154 Sum_probs=14.6
Q ss_pred HHHhcCCCCcHHHHHHHHHH
Q 001299 648 EYLLDIEGLGLKSVECVRLL 667 (1105)
Q Consensus 648 eeLLsLpGIG~KTAd~ILLf 667 (1105)
+.|++|.|||+.||.-....
T Consensus 2 ~~f~~I~GVG~~tA~~w~~~ 21 (52)
T PF10391_consen 2 KLFTGIWGVGPKTARKWYAK 21 (52)
T ss_dssp HHHHTSTT--HHHHHHHHHT
T ss_pred cchhhcccccHHHHHHHHHh
Confidence 57899999999999876543
No 92
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=31.96 E-value=1.3e+02 Score=37.69 Aligned_cols=69 Identities=10% Similarity=0.047 Sum_probs=42.2
Q ss_pred CHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHH---------------------HH-HhCCCChhhhhCCCchHHH
Q 001299 590 DWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRL---------------------VE-LHGSIDLEWLRNVPPDKVK 647 (1105)
Q Consensus 590 TpEaLA~Ad~EELeelIR~lGf~n~KAk~Ik~lA~~I---------------------ve-~~GglDLE~Lr~vP~deaR 647 (1105)
++.+|..++.++|..+ -||...+|..|.+..+.- .. .|+ +++.|.... .
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 6677777776665332 366666666554443221 00 121 355555432 3
Q ss_pred HHHhcCCCCcHHHHHHHHHH
Q 001299 648 EYLLDIEGLGLKSVECVRLL 667 (1105)
Q Consensus 648 eeLLsLpGIG~KTAd~ILLf 667 (1105)
+.|.+|+|||+++|+.|..|
T Consensus 520 e~l~~i~gIG~~~a~si~~~ 539 (562)
T PRK08097 520 QQWQQLPGIGEGRARQLIAF 539 (562)
T ss_pred HHHhcCCCchHHHHHHHHHH
Confidence 57999999999999999877
No 93
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=29.61 E-value=90 Score=36.56 Aligned_cols=60 Identities=22% Similarity=0.298 Sum_probs=36.7
Q ss_pred HHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhCCCchHHHHHHhcCCCCcHHHHHHHHHH
Q 001299 600 SEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLL 667 (1105)
Q Consensus 600 EELeelIR~lGf~n~KAk~Ik~lA~~Ive~~GglDLE~Lr~vP~deaReeLLsLpGIG~KTAd~ILLf 667 (1105)
+++...+.-.|=..-|++.-+.+|+.|... ..|++.+.. +..|+.|||||+.+|+.|.-|
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 344444544554434777777777777552 223322221 224899999999999999766
No 94
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=29.55 E-value=36 Score=27.61 Aligned_cols=16 Identities=19% Similarity=0.364 Sum_probs=13.0
Q ss_pred HhcCCCCcHHHHHHHH
Q 001299 650 LLDIEGLGLKSVECVR 665 (1105)
Q Consensus 650 LLsLpGIG~KTAd~IL 665 (1105)
+-.+||||+|||--++
T Consensus 18 i~Gv~giG~ktA~~ll 33 (36)
T smart00279 18 IPGVKGIGPKTALKLL 33 (36)
T ss_pred CCCCCcccHHHHHHHH
Confidence 3578999999997665
No 95
>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=29.41 E-value=26 Score=37.14 Aligned_cols=55 Identities=15% Similarity=0.139 Sum_probs=42.0
Q ss_pred hHHHHHHHHHhhhcCcccccCCCccccceeeeeeeccccccchhhHHhhhhhccC
Q 001299 191 RIQSFTARMHLILGDRRFKPWKGSVVDSVVGVYLTQNVSDNLSSSAYMSLAARFP 245 (1105)
Q Consensus 191 r~dsFiarmhlvqGDRRFSpWKGSVvDSVVGVFLTQNVSDhLSSsAFMsLAA~FP 245 (1105)
+++....+|----|+.+-.-|...-...+|+..|+||.++.-...||-.|.++||
T Consensus 2 ~~~~i~~~l~~~~~~~~~~~~~~dpf~~Li~~ILsqqt~~~~~~~~~~~l~~~~p 56 (191)
T TIGR01083 2 KAQEILERLRKNYPHPTTELDYNNPFELLVATILSAQATDKSVNKATKKLFEVYP 56 (191)
T ss_pred hHHHHHHHHHHHCCCCCcccCCCCHHHHHHHHHHHhhCcHHHHHHHHHHHHHHCC
Confidence 3444555555555655434455677899999999999999999999999999998
No 96
>TIGR01448 recD_rel helicase, putative, RecD/TraA family. This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.
Probab=28.63 E-value=3.1e+02 Score=35.31 Aligned_cols=57 Identities=18% Similarity=0.278 Sum_probs=35.2
Q ss_pred HHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhCCCchHHHHHHh-cCCCCcHHHHHHHHHH
Q 001299 599 ESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLL-DIEGLGLKSVECVRLL 667 (1105)
Q Consensus 599 ~EELeelIR~lGf~n~KAk~Ik~lA~~Ive~~GglDLE~Lr~vP~deaReeLL-sLpGIG~KTAd~ILLf 667 (1105)
..++...|...|+....|. .|.+.||.-.++.|+.=|.. |+ .++|||-++||.|...
T Consensus 143 ~~~~~~~L~~~gi~~~~a~-------ki~~~yg~~~~~~i~~nPY~-----L~~~i~gigF~~aD~iA~~ 200 (720)
T TIGR01448 143 ERRLLAGLQGLGIGIKLAQ-------RIYKFYQADTLDRVEKDPYL-----LAEDVKGIGFLTADQLAQA 200 (720)
T ss_pred HHHHHHHHHHcCCCHHHHH-------HHHHHHhHHHHHHHHhCchh-----hhhhcCCCCHHHHHHHHHH
Confidence 4455555666666664443 34444555445556655553 44 6999999999998643
No 97
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=27.62 E-value=49 Score=36.13 Aligned_cols=22 Identities=27% Similarity=0.404 Sum_probs=19.0
Q ss_pred HHHHHHhcCCCCcHHHHHHHHH
Q 001299 645 KVKEYLLDIEGLGLKSVECVRL 666 (1105)
Q Consensus 645 eaReeLLsLpGIG~KTAd~ILL 666 (1105)
++.+.|+++.|||||+|=.||.
T Consensus 69 ~lF~~LisVsGIGPK~ALaILs 90 (196)
T PRK13901 69 EVFEELIGVDGIGPRAALRVLS 90 (196)
T ss_pred HHHHHHhCcCCcCHHHHHHHHc
Confidence 5677899999999999988874
No 98
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=27.38 E-value=48 Score=35.72 Aligned_cols=22 Identities=14% Similarity=0.285 Sum_probs=19.1
Q ss_pred HHHHHHhcCCCCcHHHHHHHHH
Q 001299 645 KVKEYLLDIEGLGLKSVECVRL 666 (1105)
Q Consensus 645 eaReeLLsLpGIG~KTAd~ILL 666 (1105)
++.+.|+++.|||||+|=.||.
T Consensus 70 ~lF~~LisV~GIGpK~Al~iLs 91 (186)
T PRK14600 70 DCLRMLVKVSGVNYKTAMSILS 91 (186)
T ss_pred HHHHHHhCcCCcCHHHHHHHHc
Confidence 4577899999999999988876
No 99
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=26.67 E-value=51 Score=35.48 Aligned_cols=22 Identities=32% Similarity=0.489 Sum_probs=18.9
Q ss_pred HHHHHHhcCCCCcHHHHHHHHH
Q 001299 645 KVKEYLLDIEGLGLKSVECVRL 666 (1105)
Q Consensus 645 eaReeLLsLpGIG~KTAd~ILL 666 (1105)
++.+.|+++.|||||+|=.||.
T Consensus 70 ~lF~~Li~VsGIGpK~Al~ILs 91 (183)
T PRK14601 70 KMFEMLLKVNGIGANTAMAVCS 91 (183)
T ss_pred HHHHHHhccCCccHHHHHHHHc
Confidence 5677899999999999988774
No 100
>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=26.29 E-value=33 Score=31.56 Aligned_cols=20 Identities=15% Similarity=0.204 Sum_probs=15.9
Q ss_pred HHHhcCCCCcHHHHHHHHHH
Q 001299 648 EYLLDIEGLGLKSVECVRLL 667 (1105)
Q Consensus 648 eeLLsLpGIG~KTAd~ILLf 667 (1105)
+.+-.+||||+|||.-++.-
T Consensus 22 D~i~gv~giG~k~A~~ll~~ 41 (75)
T cd00080 22 DNIPGVPGIGPKTALKLLKE 41 (75)
T ss_pred ccCCCCCcccHHHHHHHHHH
Confidence 36778999999999877643
No 101
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=26.25 E-value=53 Score=35.42 Aligned_cols=23 Identities=17% Similarity=0.105 Sum_probs=19.3
Q ss_pred hHHHHHHhcCCCCcHHHHHHHHH
Q 001299 644 DKVKEYLLDIEGLGLKSVECVRL 666 (1105)
Q Consensus 644 deaReeLLsLpGIG~KTAd~ILL 666 (1105)
.++...|+++.|||||+|=.||.
T Consensus 69 r~lF~~Li~V~GIGpK~AL~iLs 91 (188)
T PRK14606 69 KELFLSLTKVSRLGPKTALKIIS 91 (188)
T ss_pred HHHHHHHhccCCccHHHHHHHHc
Confidence 35677899999999999988873
No 102
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=26.01 E-value=53 Score=35.63 Aligned_cols=22 Identities=27% Similarity=0.362 Sum_probs=19.0
Q ss_pred HHHHHHhcCCCCcHHHHHHHHH
Q 001299 645 KVKEYLLDIEGLGLKSVECVRL 666 (1105)
Q Consensus 645 eaReeLLsLpGIG~KTAd~ILL 666 (1105)
++...|+++.|||||+|=.||.
T Consensus 69 ~lF~~L~~V~GIGpK~AL~iLs 90 (197)
T PRK14603 69 ELFELLLGVSGVGPKLALALLS 90 (197)
T ss_pred HHHHHHhCcCCcCHHHHHHHHc
Confidence 4567899999999999988876
No 103
>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=25.44 E-value=67 Score=28.61 Aligned_cols=21 Identities=33% Similarity=0.501 Sum_probs=18.0
Q ss_pred HHHHhc-CCCCcHHHHHHHHHH
Q 001299 647 KEYLLD-IEGLGLKSVECVRLL 667 (1105)
Q Consensus 647 ReeLLs-LpGIG~KTAd~ILLf 667 (1105)
.+.|.. +||||.++|..|+.+
T Consensus 15 ~~~L~~~ipgig~~~a~~Il~~ 36 (69)
T TIGR00426 15 AEELQRAMNGVGLKKAEAIVSY 36 (69)
T ss_pred HHHHHhHCCCCCHHHHHHHHHH
Confidence 457888 999999999999876
No 104
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=24.81 E-value=56 Score=35.39 Aligned_cols=22 Identities=23% Similarity=0.362 Sum_probs=19.2
Q ss_pred HHHHHHhcCCCCcHHHHHHHHH
Q 001299 645 KVKEYLLDIEGLGLKSVECVRL 666 (1105)
Q Consensus 645 eaReeLLsLpGIG~KTAd~ILL 666 (1105)
++...|+++.|||||+|=.||.
T Consensus 70 ~lF~~Li~V~GIGpK~Al~iLs 91 (195)
T PRK14604 70 QLFELLIGVSGVGPKAALNLLS 91 (195)
T ss_pred HHHHHHhCcCCcCHHHHHHHHc
Confidence 5677899999999999988876
No 105
>PRK00254 ski2-like helicase; Provisional
Probab=24.21 E-value=1.5e+02 Score=37.73 Aligned_cols=23 Identities=13% Similarity=0.195 Sum_probs=14.3
Q ss_pred HHhcCCCCcHHHHHHHHHHhcCC
Q 001299 649 YLLDIEGLGLKSVECVRLLSLQH 671 (1105)
Q Consensus 649 eLLsLpGIG~KTAd~ILLfalgr 671 (1105)
.|.+|||||++.|..++..+|+-
T Consensus 646 ~L~~ipgig~~~~~~l~~~g~~s 668 (720)
T PRK00254 646 ELMRLPMIGRKRARALYNAGFRS 668 (720)
T ss_pred hhhcCCCCCHHHHHHHHHccCCC
Confidence 45566777777666665555553
No 106
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=24.20 E-value=60 Score=35.35 Aligned_cols=23 Identities=17% Similarity=0.171 Sum_probs=19.5
Q ss_pred HHHHHHhcCCCCcHHHHHHHHHH
Q 001299 645 KVKEYLLDIEGLGLKSVECVRLL 667 (1105)
Q Consensus 645 eaReeLLsLpGIG~KTAd~ILLf 667 (1105)
++...|+++.|||||+|=.||..
T Consensus 71 ~lF~~Li~V~GIGpK~Al~iLs~ 93 (203)
T PRK14602 71 QTFIVLISISKVGAKTALAILSQ 93 (203)
T ss_pred HHHHHHhCCCCcCHHHHHHHHhh
Confidence 45778999999999999888763
No 107
>PRK07758 hypothetical protein; Provisional
Probab=24.00 E-value=1e+02 Score=30.37 Aligned_cols=28 Identities=25% Similarity=0.406 Sum_probs=21.1
Q ss_pred ChhhhhCCCchHHHHHHhcCCCCcHHHHHHHH
Q 001299 634 DLEWLRNVPPDKVKEYLLDIEGLGLKSVECVR 665 (1105)
Q Consensus 634 DLE~Lr~vP~deaReeLLsLpGIG~KTAd~IL 665 (1105)
.++.|..++. ++|++|+|+|+|+.+-|.
T Consensus 57 TL~dLv~~te----~ELl~iknlGkKSL~EIk 84 (95)
T PRK07758 57 TVEELSKYSE----KEILKLHGMGPASLPKLR 84 (95)
T ss_pred cHHHHHcCCH----HHHHHccCCCHHHHHHHH
Confidence 4555655654 489999999999987764
No 108
>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=22.65 E-value=78 Score=31.03 Aligned_cols=23 Identities=17% Similarity=0.179 Sum_probs=19.1
Q ss_pred HHHHHHhcCCCCcHHHHHHHHHH
Q 001299 645 KVKEYLLDIEGLGLKSVECVRLL 667 (1105)
Q Consensus 645 eaReeLLsLpGIG~KTAd~ILLf 667 (1105)
.+.-.|.+|+|||+.+|..|+..
T Consensus 12 ~i~~aLt~IyGIG~~~A~~Ic~~ 34 (107)
T PF00416_consen 12 PIYIALTKIYGIGRRKAKQICKK 34 (107)
T ss_dssp BHHHHHTTSTTBCHHHHHHHHHH
T ss_pred chHhHHhhhhccCHHHHHHHHHH
Confidence 45778999999999999877644
No 109
>PRK08609 hypothetical protein; Provisional
Probab=22.61 E-value=1.7e+02 Score=36.58 Aligned_cols=57 Identities=12% Similarity=0.179 Sum_probs=33.8
Q ss_pred HHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhCCCchHHHHHHhcCCCCcHHHHHHHHHH
Q 001299 600 SEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLL 667 (1105)
Q Consensus 600 EELeelIR~lGf~n~KAk~Ik~lA~~Ive~~GglDLE~Lr~vP~deaReeLLsLpGIG~KTAd~ILLf 667 (1105)
++++.++.-.|=..-|++..+++|+.|... . .+ ... ...|.+|||||..+|+.|--+
T Consensus 11 ~~~A~~le~~g~n~fr~~aYr~Aa~~i~~l-~-~~--------i~~-~~~l~~ipgIG~~ia~kI~Ei 67 (570)
T PRK08609 11 ETIATYMELKGENPFKISAFRKAAQALELD-E-RS--------LSE-IDDFTKLKGIGKGTAEVIQEY 67 (570)
T ss_pred HHHHHHHHhcCCCcHHHHHHHHHHHHHHhC-c-hh--------hhh-hhhhccCCCcCHHHHHHHHHH
Confidence 344455555553333666677777766552 1 11 111 246788999999988888655
No 110
>KOG0028 consensus Ca2+-binding protein (centrin/caltractin), EF-Hand superfamily protein [Cytoskeleton; Cell cycle control, cell division, chromosome partitioning]
Probab=21.45 E-value=2.4e+02 Score=30.56 Aligned_cols=98 Identities=17% Similarity=0.070 Sum_probs=51.4
Q ss_pred CCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHhCCCChhhhhCCCchHHHHHHhcCCCCcHHHHHHHHHHh---cCCee
Q 001299 597 ADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLS---LQHIA 673 (1105)
Q Consensus 597 Ad~EELeelIR~lGf~n~KAk~Ik~lA~~Ive~~GglDLE~Lr~vP~deaReeLLsLpGIG~KTAd~ILLfa---lgrpv 673 (1105)
++.++|.-+++.+||...|.+..+-++..=.+.-|-++++.+ +.-.+..=|.+.---+.--+|- +....
T Consensus 50 iD~~EL~vAmralGFE~~k~ei~kll~d~dk~~~g~i~fe~f--------~~~mt~k~~e~dt~eEi~~afrl~D~D~~G 121 (172)
T KOG0028|consen 50 IDVEELKVAMRALGFEPKKEEILKLLADVDKEGSGKITFEDF--------RRVMTVKLGERDTKEEIKKAFRLFDDDKTG 121 (172)
T ss_pred ccHHHHHHHHHHcCCCcchHHHHHHHHhhhhccCceechHHH--------HHHHHHHHhccCcHHHHHHHHHcccccCCC
Confidence 466777777899999987766555444332222243444433 3333333344431122222333 33334
Q ss_pred eecchHHHHHHHHhCCCCCCCChHHHHHHHHh
Q 001299 674 FPVDVNVGRIAVRLGWVPLQPLPGDLHIHLLK 705 (1105)
Q Consensus 674 fPVDThV~RIl~RLG~Vp~k~tpeeiE~~Lee 705 (1105)
-+-=.++.||+.+||=. .+-++++..+++
T Consensus 122 kis~~~lkrvakeLgen---ltD~El~eMIeE 150 (172)
T KOG0028|consen 122 KISQRNLKRVAKELGEN---LTDEELMEMIEE 150 (172)
T ss_pred CcCHHHHHHHHHHhCcc---ccHHHHHHHHHH
Confidence 44457899999999853 233444444433
No 111
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=21.42 E-value=73 Score=33.04 Aligned_cols=20 Identities=5% Similarity=-0.092 Sum_probs=17.4
Q ss_pred HHHHhcCCCCcHHHHHHHHH
Q 001299 647 KEYLLDIEGLGLKSVECVRL 666 (1105)
Q Consensus 647 ReeLLsLpGIG~KTAd~ILL 666 (1105)
.++|.+|||||+..|..|..
T Consensus 60 ~~el~~lpGigP~~A~~IV~ 79 (132)
T PRK02515 60 VRAFRQFPGMYPTLAGKIVK 79 (132)
T ss_pred HHHHHHCCCCCHHHHHHHHH
Confidence 45688999999999999984
No 112
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=20.79 E-value=75 Score=34.83 Aligned_cols=23 Identities=17% Similarity=0.288 Sum_probs=19.3
Q ss_pred HHHHHHhcCCCCcHHHHHHHHHH
Q 001299 645 KVKEYLLDIEGLGLKSVECVRLL 667 (1105)
Q Consensus 645 eaReeLLsLpGIG~KTAd~ILLf 667 (1105)
++...|+++.|||+|+|=.||..
T Consensus 70 ~lF~~LisVnGIGpK~ALaiLs~ 92 (201)
T COG0632 70 ELFRLLISVNGIGPKLALAILSN 92 (201)
T ss_pred HHHHHHHccCCccHHHHHHHHcC
Confidence 56778999999999999777654
Done!