Query 002245
Match_columns 947
No_of_seqs 402 out of 1928
Neff 4.2
Searched_HMMs 46136
Date Thu Mar 28 19:46:29 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/002245.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/002245hhsearch_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 4.9E-70 1.1E-74 496.8 7.5 103 833-935 1-103 (103)
2 COG0177 Nth Predicted EndoIII- 100.0 6.6E-53 1.4E-57 434.4 20.5 209 344-609 1-209 (211)
3 PRK10702 endonuclease III; Pro 100.0 1E-43 2.2E-48 367.4 20.6 208 344-608 1-208 (211)
4 TIGR01084 mutY A/G-specific ad 100.0 1.1E-36 2.5E-41 325.9 18.2 199 377-625 21-223 (275)
5 TIGR01083 nth endonuclease III 100.0 2.9E-36 6.3E-41 306.2 19.0 190 348-594 2-191 (191)
6 PRK10880 adenine DNA glycosyla 100.0 1.5E-36 3.2E-41 334.1 17.5 203 377-625 25-227 (350)
7 KOG1921 Endonuclease III [Repl 100.0 1.7E-34 3.7E-39 299.7 13.9 182 381-607 77-261 (286)
8 PRK13910 DNA glycosylase MutY; 100.0 1.2E-32 2.7E-37 296.5 18.3 150 431-609 22-172 (289)
9 PRK13913 3-methyladenine DNA g 100.0 9.7E-32 2.1E-36 279.6 18.8 188 380-589 28-216 (218)
10 COG2231 Uncharacterized protei 100.0 7.2E-31 1.6E-35 268.1 19.0 208 348-607 7-214 (215)
11 COG1194 MutY A/G-specific DNA 100.0 1.1E-28 2.3E-33 269.0 18.9 200 377-625 29-232 (342)
12 smart00478 ENDO3c endonuclease 99.9 1.2E-24 2.5E-29 211.2 16.2 129 431-585 21-149 (149)
13 cd00056 ENDO3c endonuclease II 99.9 1.2E-24 2.6E-29 212.7 15.0 157 383-583 1-158 (158)
14 PRK01229 N-glycosylase/DNA lya 99.9 8.1E-24 1.8E-28 219.2 12.5 137 380-551 35-185 (208)
15 TIGR00588 ogg 8-oxoguanine DNA 99.8 3.1E-20 6.7E-25 202.5 15.7 141 381-532 118-263 (310)
16 KOG2457 A/G-specific adenine D 99.8 1.4E-20 3.1E-25 205.4 10.0 215 348-608 89-310 (555)
17 TIGR03252 uncharacterized HhH- 99.8 1E-19 2.2E-24 184.3 10.6 112 380-510 16-134 (177)
18 COG0122 AlkA 3-methyladenine D 99.8 2.3E-18 4.9E-23 186.2 14.3 167 380-562 103-271 (285)
19 PRK10308 3-methyl-adenine DNA 99.7 5.6E-16 1.2E-20 167.5 17.6 160 381-562 112-273 (283)
20 KOG2875 8-oxoguanine DNA glyco 99.6 1.1E-15 2.4E-20 162.7 9.6 139 381-530 116-258 (323)
21 PF00730 HhH-GPD: HhH-GPD supe 99.5 7.7E-14 1.7E-18 128.8 9.6 107 387-551 1-107 (108)
22 KOG1918 3-methyladenine DNA gl 99.5 4.3E-14 9.4E-19 146.6 8.5 167 375-562 68-238 (254)
23 PF15629 Perm-CXXC: Permuted s 99.1 1.9E-11 4.1E-16 92.1 0.8 32 799-830 1-32 (32)
24 COG1059 Thermostable 8-oxoguan 98.4 3.8E-07 8.3E-12 93.9 7.1 124 381-536 38-166 (210)
25 PF00633 HHH: Helix-hairpin-he 97.6 1.6E-05 3.5E-10 59.9 0.9 26 483-510 5-30 (30)
26 PF10576 EndIII_4Fe-2S: Iron-s 96.8 0.00041 8.9E-09 46.4 0.8 17 587-603 1-17 (17)
27 PF09674 DUF2400: Protein of u 96.6 0.0017 3.7E-08 69.7 3.7 55 456-536 142-196 (232)
28 TIGR02757 conserved hypothetic 96.0 0.0056 1.2E-07 65.7 3.9 86 458-584 142-227 (229)
29 smart00525 FES FES domain. iro 96.0 0.0035 7.5E-08 45.5 1.4 22 586-607 1-22 (26)
30 smart00278 HhH1 Helix-hairpin- 91.1 0.15 3.3E-06 37.0 2.0 20 492-511 2-21 (26)
31 PF12826 HHH_2: Helix-hairpin- 90.6 0.29 6.4E-06 42.6 3.6 40 465-510 15-54 (64)
32 PRK13901 ruvA Holliday junctio 88.0 1.7 3.7E-05 46.2 7.7 66 428-514 59-130 (196)
33 PF14716 HHH_8: Helix-hairpin- 86.8 2.7 5.8E-05 36.9 7.1 58 443-510 9-66 (68)
34 TIGR00426 competence protein C 84.7 1.3 2.8E-05 38.8 4.0 58 436-510 9-66 (69)
35 PF09171 DUF1886: Domain of un 84.7 2.8 6E-05 46.1 7.3 133 443-589 77-232 (246)
36 PF14520 HHH_5: Helix-hairpin- 83.6 3.4 7.3E-05 35.3 6.0 30 477-510 28-57 (60)
37 PRK02515 psbU photosystem II c 83.1 1.8 3.8E-05 43.5 4.6 53 436-510 54-106 (132)
38 PRK14601 ruvA Holliday junctio 81.4 5.2 0.00011 42.1 7.6 70 428-514 60-131 (183)
39 PRK14606 ruvA Holliday junctio 80.8 5.6 0.00012 41.9 7.6 66 428-514 60-131 (188)
40 PRK00076 recR recombination pr 80.1 1.6 3.5E-05 46.4 3.4 27 487-513 7-33 (196)
41 PF03352 Adenine_glyco: Methyl 79.8 4.2 9.1E-05 42.8 6.3 48 429-476 55-107 (179)
42 PRK13844 recombination protein 79.8 1.7 3.6E-05 46.4 3.4 28 486-513 10-37 (200)
43 TIGR00615 recR recombination p 79.7 1.7 3.7E-05 46.2 3.5 28 486-513 6-33 (195)
44 PRK00024 hypothetical protein; 78.9 3.5 7.7E-05 44.4 5.6 61 439-508 23-83 (224)
45 PRK10353 3-methyl-adenine DNA 77.6 2.4 5.1E-05 44.9 3.7 49 428-476 59-112 (187)
46 TIGR00608 radc DNA repair prot 77.5 4.3 9.4E-05 43.7 5.8 61 439-508 13-77 (218)
47 PRK14602 ruvA Holliday junctio 77.4 7.3 0.00016 41.5 7.3 70 428-514 61-132 (203)
48 PRK14605 ruvA Holliday junctio 76.8 8.2 0.00018 40.8 7.4 66 428-510 60-127 (194)
49 PRK00116 ruvA Holliday junctio 76.6 4.2 9.2E-05 42.6 5.3 22 490-511 107-128 (192)
50 COG0353 RecR Recombinational D 76.3 2.3 5.1E-05 45.2 3.3 27 487-513 8-34 (198)
51 PRK14604 ruvA Holliday junctio 76.1 8 0.00017 41.0 7.2 70 428-514 60-131 (195)
52 PRK14600 ruvA Holliday junctio 75.7 6.5 0.00014 41.4 6.3 69 428-514 60-130 (186)
53 PF14520 HHH_5: Helix-hairpin- 75.2 2.6 5.7E-05 35.9 2.8 27 489-515 3-29 (60)
54 PRK14603 ruvA Holliday junctio 74.4 9.3 0.0002 40.6 7.1 25 490-514 106-130 (197)
55 COG1555 ComEA DNA uptake prote 72.4 5.2 0.00011 40.7 4.6 56 437-510 91-146 (149)
56 COG0632 RuvA Holliday junction 71.9 2.8 6E-05 44.8 2.6 70 429-513 61-130 (201)
57 TIGR00624 tag DNA-3-methyladen 71.6 4.4 9.5E-05 42.6 3.9 44 428-471 58-103 (179)
58 TIGR00084 ruvA Holliday juncti 71.3 6.2 0.00013 41.6 4.9 68 428-512 59-128 (191)
59 PF12836 HHH_3: Helix-hairpin- 70.2 3.9 8.4E-05 35.7 2.7 53 438-508 9-61 (65)
60 TIGR00575 dnlj DNA ligase, NAD 69.9 19 0.00041 44.7 9.4 62 432-509 455-516 (652)
61 PRK07956 ligA NAD-dependent DN 69.6 16 0.00036 45.3 8.8 33 432-467 468-500 (665)
62 PRK14350 ligA NAD-dependent DN 68.2 22 0.00047 44.3 9.4 21 490-510 540-560 (669)
63 PF14229 DUF4332: Domain of un 67.6 19 0.00041 35.4 7.1 60 430-514 15-76 (122)
64 PRK00116 ruvA Holliday junctio 66.6 5 0.00011 42.1 3.1 24 490-514 72-95 (192)
65 PRK14973 DNA topoisomerase I; 66.6 8.3 0.00018 49.5 5.6 97 429-533 821-919 (936)
66 TIGR01259 comE comEA protein. 65.8 8.5 0.00018 37.7 4.3 59 434-510 59-117 (120)
67 PF14490 HHH_4: Helix-hairpin- 65.1 9.9 0.00022 35.4 4.4 57 441-509 7-64 (94)
68 PF02371 Transposase_20: Trans 61.0 6 0.00013 36.2 2.2 42 491-535 2-43 (87)
69 PF11731 Cdd1: Pathogenicity l 60.6 8.1 0.00018 36.8 3.0 26 489-514 10-35 (93)
70 cd04370 BAH BAH, or Bromo Adja 58.8 17 0.00036 33.8 4.8 64 853-927 59-122 (123)
71 COG2003 RadC DNA repair protei 58.3 19 0.00041 39.3 5.7 89 439-548 23-115 (224)
72 PF12836 HHH_3: Helix-hairpin- 57.8 9.6 0.00021 33.2 2.8 21 490-510 13-33 (65)
73 PRK14351 ligA NAD-dependent DN 57.4 41 0.00088 42.2 9.0 60 432-509 485-546 (689)
74 KOG2841 Structure-specific end 56.8 33 0.00071 37.9 7.1 94 342-468 156-249 (254)
75 COG1555 ComEA DNA uptake prote 55.8 9.1 0.0002 39.0 2.7 22 490-511 96-117 (149)
76 TIGR00084 ruvA Holliday juncti 55.6 9.2 0.0002 40.4 2.7 22 488-509 69-90 (191)
77 PRK08609 hypothetical protein; 54.8 33 0.00073 41.8 7.6 49 452-507 54-104 (570)
78 PF05559 DUF763: Protein of un 54.8 30 0.00065 39.6 6.7 24 485-510 265-288 (319)
79 PRK14605 ruvA Holliday junctio 53.5 11 0.00023 40.0 2.8 23 488-510 70-92 (194)
80 PRK07945 hypothetical protein; 53.0 21 0.00045 40.6 5.2 61 443-510 8-68 (335)
81 smart00483 POLXc DNA polymeras 52.7 19 0.00042 40.9 4.9 51 453-508 55-106 (334)
82 TIGR01259 comE comEA protein. 52.7 12 0.00025 36.8 2.8 21 490-510 67-87 (120)
83 COG2818 Tag 3-methyladenine DN 52.2 26 0.00056 37.4 5.4 49 428-476 60-113 (188)
84 PRK08097 ligB NAD-dependent DN 50.6 69 0.0015 39.4 9.3 70 432-510 448-539 (562)
85 smart00483 POLXc DNA polymeras 50.4 37 0.00081 38.7 6.7 57 443-510 11-67 (334)
86 PF11798 IMS_HHH: IMS family H 49.4 11 0.00025 28.9 1.7 15 493-507 13-27 (32)
87 COG0272 Lig NAD-dependent DNA 48.9 25 0.00055 43.6 5.3 58 443-510 505-562 (667)
88 PRK13482 DNA integrity scannin 43.5 32 0.0007 39.8 4.8 58 444-507 276-335 (352)
89 cd00141 NT_POLXc Nucleotidyltr 43.2 43 0.00094 37.7 5.7 18 490-507 84-101 (307)
90 cd00141 NT_POLXc Nucleotidyltr 42.4 34 0.00074 38.5 4.8 57 443-510 8-64 (307)
91 smart00279 HhH2 Helix-hairpin- 40.7 19 0.00041 28.6 1.8 17 493-509 18-34 (36)
92 TIGR00426 competence protein C 38.4 30 0.00065 30.2 2.8 21 490-510 15-36 (69)
93 PF10391 DNA_pol_lambd_f: Fing 37.2 30 0.00065 29.6 2.5 19 491-509 2-20 (52)
94 PRK13901 ruvA Holliday junctio 36.8 27 0.00058 37.4 2.7 23 488-510 69-91 (196)
95 PRK14600 ruvA Holliday junctio 36.7 26 0.00057 37.0 2.6 23 488-510 70-92 (186)
96 COG1796 POL4 DNA polymerase IV 36.5 56 0.0012 37.5 5.2 60 443-510 13-72 (326)
97 PRK14606 ruvA Holliday junctio 35.7 28 0.00062 36.8 2.7 22 488-509 70-91 (188)
98 PRK14601 ruvA Holliday junctio 35.7 28 0.00061 36.7 2.7 23 488-510 70-92 (183)
99 PRK14973 DNA topoisomerase I; 34.8 4.2E+02 0.0091 34.8 13.1 76 429-512 763-856 (936)
100 PRK14603 ruvA Holliday junctio 34.8 30 0.00064 36.9 2.6 23 488-510 69-91 (197)
101 PRK14602 ruvA Holliday junctio 34.4 31 0.00067 36.9 2.7 23 488-510 71-93 (203)
102 cd00080 HhH2_motif Helix-hairp 33.3 20 0.00044 32.3 1.0 19 492-510 23-41 (75)
103 PRK14604 ruvA Holliday junctio 33.2 32 0.00069 36.6 2.6 23 488-510 70-92 (195)
104 PRK00254 ski2-like helicase; P 33.0 81 0.0018 39.3 6.4 24 492-515 646-669 (720)
105 PF11372 DUF3173: Domain of un 32.4 1.1E+02 0.0023 27.4 5.2 44 452-496 12-57 (59)
106 PRK02515 psbU photosystem II c 31.7 37 0.00079 34.5 2.5 20 490-509 60-79 (132)
107 PF03118 RNA_pol_A_CTD: Bacter 31.0 57 0.0012 29.0 3.4 47 450-508 15-61 (66)
108 COG0632 RuvA Holliday junction 29.6 38 0.00082 36.4 2.4 23 488-510 70-92 (201)
109 PF00416 Ribosomal_S13: Riboso 29.6 47 0.001 31.9 2.9 22 489-510 13-34 (107)
110 smart00439 BAH Bromo adjacent 28.6 59 0.0013 30.3 3.3 64 853-927 56-119 (120)
111 PRK07758 hypothetical protein; 27.4 80 0.0017 30.5 3.9 28 477-508 57-84 (95)
112 PRK08609 hypothetical protein; 26.4 1.1E+02 0.0024 37.6 5.8 57 443-510 11-67 (570)
113 PRK13280 N-glycosylase/DNA lya 25.1 2.5E+02 0.0053 31.8 7.7 134 443-586 87-242 (269)
114 PRK01172 ski2-like helicase; P 25.0 1.6E+02 0.0034 36.5 6.8 64 407-473 607-672 (674)
115 PRK12766 50S ribosomal protein 24.8 1.2E+02 0.0026 33.5 5.1 30 477-510 26-55 (232)
116 PF13592 HTH_33: Winged helix- 23.8 1E+02 0.0023 26.5 3.7 37 500-536 3-40 (60)
117 PRK14670 uvrC excinuclease ABC 22.5 73 0.0016 39.2 3.3 36 469-510 530-565 (574)
118 TIGR01448 recD_rel helicase, p 22.2 3.7E+02 0.0079 34.1 9.3 57 442-509 143-199 (720)
119 COG4277 Predicted DNA-binding 21.2 62 0.0014 37.1 2.2 21 490-510 329-349 (404)
120 PF00730 HhH-GPD: HhH-GPD supe 20.9 1.6E+02 0.0035 27.3 4.6 54 457-511 9-62 (108)
121 TIGR01954 nusA_Cterm_rpt trans 20.8 1.9E+02 0.0041 23.3 4.4 36 430-468 13-48 (50)
122 PRK14469 ribosomal RNA large s 20.4 1.6E+02 0.0035 33.7 5.3 54 437-495 4-57 (343)
123 KOG0400 40S ribosomal protein 20.3 1.1E+02 0.0025 31.2 3.6 66 479-547 24-93 (151)
No 1
>PF15628 RRM_DME: RRM in Demeter
Probab=100.00 E-value=4.9e-70 Score=496.81 Aligned_cols=103 Identities=87% Similarity=1.516 Sum_probs=102.1
Q ss_pred eeEeeeccccccCCccCCCccceeceeeeccCCCCCCcccchhhhccCCceEEEeccChhhhcccCCHHHHHHhhhccce
Q 002245 833 GTLLIPCRTAMRGSFPLNGTYFQVNEVFADHDSSLNPIDVPREWLWNLPRRMVYFGTSVSSIFKGLSTEGIQFCFWKGFV 912 (947)
Q Consensus 833 gTiLiPCRtAmrg~FPLnGTYFQvNEVFaDh~Ss~~Pi~vpr~~iw~L~rr~vyfGtsv~sI~kg~s~~~iq~cf~~g~v 912 (947)
|||||||||||||+|||||||||||||||||+||+|||+|||+|||+|+||+|||||||+|||||||++|||+|||+|||
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 002245 913 CVRGFDQKSRAPRPLMARLHFPA 935 (947)
Q Consensus 913 CvR~fdr~tr~P~pl~~~lh~~~ 935 (947)
|||||||+||+||||++|||+++
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=6.6e-53 Score=434.42 Aligned_cols=209 Identities=28% Similarity=0.436 Sum_probs=196.1
Q ss_pred CcHHHHHHHHHhhhhhcCCCccccCCCCchhhhhcccccccchhhhhhcccccccccccccccChHHHHHHHHhccCccc
Q 002245 344 MLAEKTRNLGDDISVANKLSDNKLIEPNSVEQVLSAHKVYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQE 423 (947)
Q Consensus 344 ~~~~~~~~i~~rl~~~~~~p~~~l~~~~~~~~~~~~~~~~~lLia~iLSaq~~d~~vnk~qnT~W~~L~k~l~~~glk~e 423 (947)
|.++++.+|++||...||.|..++.| .++|++||++|||||+||+.+|++ | .+|++.
T Consensus 1 ~~~~~~~~i~~~l~~~~p~~~~~l~~----------~~pf~lLva~iLSaqttD~~vn~a--t--~~Lf~~--------- 57 (211)
T COG0177 1 LNKKKALEILDRLRELYPEPKTELDF----------KDPFELLVAVILSAQTTDEVVNKA--T--PALFKR--------- 57 (211)
T ss_pred CcHhhHHHHHHHHHHHCCCCCCccCc----------CCcHHHHHHHHHhccCchHHHHHH--H--HHHHHH---------
Confidence 46788999999999999999999876 378999999999999999999976 5 888765
Q ss_pred cccCcCCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHhCCCCcHhH
Q 002245 424 RSRDRMDSLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKS 503 (947)
Q Consensus 424 r~~~~~~~pTpeaLa~A~~eELeelIR~lGfyn~KAk~Ik~lA~~Lve~yGgiDLe~L~~vP~deareeLlsLPGVG~KT 503 (947)
++||++|++|++++|+++|+++|||++||++|+++|++|+++||| ++|.+ +++|++|||||+||
T Consensus 58 -------~~t~e~l~~a~~~~l~~~I~~iGlyr~KAk~I~~~~~~l~e~~~g-------~vP~~--~~eL~~LPGVGrKT 121 (211)
T COG0177 58 -------YPTPEDLLNADEEELEELIKSIGLYRNKAKNIKELARILLEKFGG-------EVPDT--REELLSLPGVGRKT 121 (211)
T ss_pred -------cCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHcCC-------CCCch--HHHHHhCCCcchHH
Confidence 779999999999999999999999999999999999999999999 89998 99999999999999
Q ss_pred HHHHHHHhcCCceeecchHHHHHHHHhCCCCCCCCHHHHHHHHHHhcCchHHHHHhhhhhhhcCChhhHHHHHHHHHHHh
Q 002245 504 VECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQPLPESLQLHLLELYPVLESIQKYLWPRLCKLDQRTLYELHYQLITFG 583 (947)
Q Consensus 504 Ad~ILlfafgrpafPVDTHV~RVl~RLGlv~~k~tpeevEk~Le~llP~~e~Iqk~LW~rlc~ld~~~~~e~H~~LI~fG 583 (947)
|++||+++||+|+|+|||||+||++|+||++ .++|+++|+.|++++| +++| .++|++||.||
T Consensus 122 AnvVL~~a~g~p~i~VDTHV~Rvs~R~gl~~-~~~p~~ve~~L~~~iP------~~~~-----------~~~h~~lI~~G 183 (211)
T COG0177 122 ANVVLSFAFGIPAIAVDTHVHRVSNRLGLVP-GKTPEEVEEALMKLIP------KELW-----------TDLHHWLILHG 183 (211)
T ss_pred HHHHHHhhcCCCcccccchHHHHHHHhCCCC-CCCHHHHHHHHHHHCC------HHHH-----------HHHHHHHHHhh
Confidence 9999999999999999999999999999999 5899999999999999 3444 68999999999
Q ss_pred HhhcccCCCCCCCCCChhhchhhhhh
Q 002245 584 KVFCTKSKPNCNACPMRGECRHFASA 609 (947)
Q Consensus 584 R~ICtarkPkC~~CPLrdlC~yy~k~ 609 (947)
|++|+||+|+|+.|||+++|+|+.+.
T Consensus 184 R~iC~ar~P~C~~C~l~~~C~~~~~~ 209 (211)
T COG0177 184 RYICKARKPRCEECPLADLCPSAGKT 209 (211)
T ss_pred hhhccCCCCCcCcccchhhCchhccc
Confidence 99999999999999999999998763
No 3
>PRK10702 endonuclease III; Provisional
Probab=100.00 E-value=1e-43 Score=367.35 Aligned_cols=208 Identities=21% Similarity=0.265 Sum_probs=184.6
Q ss_pred CcHHHHHHHHHhhhhhcCCCccccCCCCchhhhhcccccccchhhhhhcccccccccccccccChHHHHHHHHhccCccc
Q 002245 344 MLAEKTRNLGDDISVANKLSDNKLIEPNSVEQVLSAHKVYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQE 423 (947)
Q Consensus 344 ~~~~~~~~i~~rl~~~~~~p~~~l~~~~~~~~~~~~~~~~~lLia~iLSaq~~d~~vnk~qnT~W~~L~k~l~~~glk~e 423 (947)
|+.++..+|+++|.+.||.+...+.+ .++|+.||++|||+|+++..++++ +.+|+.
T Consensus 1 ~~~~~~~~i~~~l~~~~~~~~~~~~~----------~~p~e~lvs~iLsq~t~~~~v~~~----~~~L~~---------- 56 (211)
T PRK10702 1 MNKAKRLEILTRLRDNNPHPTTELNF----------SSPFELLIAVLLSAQATDVSVNKA----TAKLYP---------- 56 (211)
T ss_pred CCHHHHHHHHHHHHHHCCCCCCCCCC----------CChHHHHHHHHHHhhcCHHHHHHH----HHHHHH----------
Confidence 34567899999999999987655443 378999999999999999988754 355542
Q ss_pred cccCcCCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHhCCCCcHhH
Q 002245 424 RSRDRMDSLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKS 503 (947)
Q Consensus 424 r~~~~~~~pTpeaLa~A~~eELeelIR~lGfyn~KAk~Ik~lA~~Lve~yGgiDLe~L~~vP~deareeLlsLPGVG~KT 503 (947)
.++||++|++++.++|+++|+++|||++||++|+++|+.++++|+| .+|.+ +++|++|||||+||
T Consensus 57 ------~~pt~e~l~~a~~~~l~~~i~~~G~y~~kA~~l~~~a~~i~~~~~~-------~~p~~--~~~Ll~lpGVG~kt 121 (211)
T PRK10702 57 ------VANTPAAMLELGVEGVKTYIKTIGLYNSKAENVIKTCRILLEQHNG-------EVPED--RAALEALPGVGRKT 121 (211)
T ss_pred ------HcCCHHHHHCCCHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHcCC-------CCCch--HHHHhcCCcccHHH
Confidence 2899999999999999999999999999999999999999999988 67876 99999999999999
Q ss_pred HHHHHHHhcCCceeecchHHHHHHHHhCCCCCCCCHHHHHHHHHHhcCchHHHHHhhhhhhhcCChhhHHHHHHHHHHHh
Q 002245 504 VECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQPLPESLQLHLLELYPVLESIQKYLWPRLCKLDQRTLYELHYQLITFG 583 (947)
Q Consensus 504 Ad~ILlfafgrpafPVDTHV~RVl~RLGlv~~k~tpeevEk~Le~llP~~e~Iqk~LW~rlc~ld~~~~~e~H~~LI~fG 583 (947)
|++||+|+||+++|||||||.||+.|+||.+. .+++++++.+++.+|. ..| .++|++||+||
T Consensus 122 A~~ill~a~~~~~~~VDt~v~Rv~~r~g~~~~-~~~~~~~~~l~~~lp~------~~~-----------~~~~~~li~~G 183 (211)
T PRK10702 122 ANVVLNTAFGWPTIAVDTHIFRVCNRTQFAPG-KNVEQVEEKLLKVVPA------EFK-----------VDCHHWLILHG 183 (211)
T ss_pred HHHHHHHHcCCCcccccchHHHHHHHhCCCCC-CCHHHHHHHHHHhCCc------hHH-----------HHHHHHHHHHh
Confidence 99999999999999999999999999999875 6899999999998883 333 47999999999
Q ss_pred HhhcccCCCCCCCCCChhhchhhhh
Q 002245 584 KVFCTKSKPNCNACPMRGECRHFAS 608 (947)
Q Consensus 584 R~ICtarkPkC~~CPLrdlC~yy~k 608 (947)
|.+|++++|+|+.|||++.|+|+.+
T Consensus 184 r~~C~~~~P~C~~Cpl~~~C~~~~~ 208 (211)
T PRK10702 184 RYTCIARKPRCGSCIIEDLCEYKEK 208 (211)
T ss_pred HHHcCCCCCCCCCCcChhhcCcccc
Confidence 9999999999999999999998654
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=1.1e-36 Score=325.89 Aligned_cols=199 Identities=21% Similarity=0.291 Sum_probs=169.4
Q ss_pred hcccccccchhhhhhcccccccccccccccChHHHHHHHHhccCccccccCcCCCCCHHHHHcCCHHHHHHHHHhcCCcH
Q 002245 377 LSAHKVYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQERSRDRMDSLDYEALRCANVKEISEAIKERGMNN 456 (947)
Q Consensus 377 ~~~~~~~~lLia~iLSaq~~d~~vnk~qnT~W~~L~k~l~~~glk~er~~~~~~~pTpeaLa~A~~eELeelIR~lGfyn 456 (947)
....++|+.||+.||++|++++.+.. .|.++.+. +|||++|+++++++|.++|+++|||
T Consensus 21 r~~~dpy~vlvseIL~QQT~v~~v~~----~~~rl~~~----------------fpt~~~La~a~~eeL~~~~~~lG~y- 79 (275)
T TIGR01084 21 RQNKTPYRVWLSEVMLQQTQVATVIP----YFERFLER----------------FPTVQALANAPQDEVLKLWEGLGYY- 79 (275)
T ss_pred CCCCCHHHHHHHHHHHhhccHHHHHH----HHHHHHHh----------------CCCHHHHHCcCHHHHHHHHHHCCcH-
Confidence 44568899999999999999888763 34555422 8999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHhCCCCcHhHHHHHHHHhcCCceeecchHHHHHHHHhCCCCCC
Q 002245 457 MLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQ 536 (947)
Q Consensus 457 ~KAk~Ik~lA~~Lve~yGgiDLe~L~~vP~deareeLlsLPGVG~KTAd~ILlfafgrpafPVDTHV~RVl~RLGlv~~k 536 (947)
+||++|+++|+.|.++|+| .+|.+ +++|++|||||+|||++||+|+||+++++||+||.||+.|++.....
T Consensus 80 ~RAr~L~~~A~~i~~~~~g-------~~p~~--~~~L~~LpGIG~~TA~~Il~~a~~~~~~~vD~~v~RVl~Rl~~~~~~ 150 (275)
T TIGR01084 80 ARARNLHKAAQEVVEEFGG-------EFPQD--FEDLAALPGVGRYTAGAILSFALNKPYPILDGNVKRVLSRLFAVEGW 150 (275)
T ss_pred HHHHHHHHHHHHHHHHcCC-------CCcHH--HHHHHhCCCCCHHHHHHHHHHHCCCCCCcchHhHHHHHHHHccCcCC
Confidence 6999999999999999998 67876 99999999999999999999999999999999999999999766554
Q ss_pred CCHHHHHHHH----HHhcCchHHHHHhhhhhhhcCChhhHHHHHHHHHHHhHhhcccCCCCCCCCCChhhchhhhhhccc
Q 002245 537 PLPESLQLHL----LELYPVLESIQKYLWPRLCKLDQRTLYELHYQLITFGKVFCTKSKPNCNACPMRGECRHFASAFAS 612 (947)
Q Consensus 537 ~tpeevEk~L----e~llP~~e~Iqk~LW~rlc~ld~~~~~e~H~~LI~fGR~ICtarkPkC~~CPLrdlC~yy~k~~a~ 612 (947)
.++.++++.+ ++++| ...+.+||++||+||+.+|++++|+|+.|||++.|.++...
T Consensus 151 ~~~~~~~~~l~~~~~~~lp-----------------~~~~~~~n~alm~lG~~vC~~~~P~C~~Cpl~~~C~~~~~~--- 210 (275)
T TIGR01084 151 PGKKKVENRLWTLAESLLP-----------------KADPEAFNQALMDLGAMICTRKKPKCDLCPLQDFCLAYQQG--- 210 (275)
T ss_pred CCHHHHHHHHHHHHHHHCC-----------------hhhHHHHHHHHHHHhHHHcCCCCCCCCCCCChhhCHHHHcC---
Confidence 5666666653 44444 34568999999999999999999999999999999998864
Q ss_pred cccccCCCCcccc
Q 002245 613 ARLALPGPEEKSI 625 (947)
Q Consensus 613 ar~alP~p~~k~~ 625 (947)
....+|.+..|..
T Consensus 211 ~~~~~p~~~~~~~ 223 (275)
T TIGR01084 211 TWEEYPVKKPKAA 223 (275)
T ss_pred CHhhcCCCCCCCC
Confidence 4566888776543
No 5
>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=2.9e-36 Score=306.24 Aligned_cols=190 Identities=25% Similarity=0.328 Sum_probs=166.4
Q ss_pred HHHHHHHhhhhhcCCCccccCCCCchhhhhcccccccchhhhhhcccccccccccccccChHHHHHHHHhccCccccccC
Q 002245 348 KTRNLGDDISVANKLSDNKLIEPNSVEQVLSAHKVYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQERSRD 427 (947)
Q Consensus 348 ~~~~i~~rl~~~~~~p~~~l~~~~~~~~~~~~~~~~~lLia~iLSaq~~d~~vnk~qnT~W~~L~k~l~~~glk~er~~~ 427 (947)
+..+|+++|.+.||.+...+.+ .++|+.||+.|||+|+++..+.++ |.+|+.
T Consensus 2 ~~~~i~~~l~~~~~~~~~~~~~----------~dpf~~Li~~ILsqqt~~~~~~~~----~~~l~~-------------- 53 (191)
T TIGR01083 2 KAQEILERLRKNYPHPTTELDY----------NNPFELLVATILSAQATDKSVNKA----TKKLFE-------------- 53 (191)
T ss_pred hHHHHHHHHHHHCCCCCcccCC----------CCHHHHHHHHHHHhhCcHHHHHHH----HHHHHH--------------
Confidence 4578999999999987643322 367999999999999998888643 355542
Q ss_pred cCCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHhCCCCcHhHHHHH
Q 002245 428 RMDSLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECV 507 (947)
Q Consensus 428 ~~~~pTpeaLa~A~~eELeelIR~lGfyn~KAk~Ik~lA~~Lve~yGgiDLe~L~~vP~deareeLlsLPGVG~KTAd~I 507 (947)
.++||++|++++.++|+++|+++||+++||++|+++|+.+.++|++ .+|.. ++.|++|||||+|||++|
T Consensus 54 --~~pt~~~l~~~~~~~L~~~ir~~G~~~~Ka~~i~~~a~~i~~~~~~-------~~~~~--~~~L~~l~GIG~ktA~~i 122 (191)
T TIGR01083 54 --VYPTPQALAQAGLEELEEYIKSIGLYRNKAKNIIALCRILVERYGG-------EVPED--REELVKLPGVGRKTANVV 122 (191)
T ss_pred --HCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHcCC-------CCchH--HHHHHhCCCCcHHHHHHH
Confidence 2789999999999999999999999999999999999999998887 45644 899999999999999999
Q ss_pred HHHhcCCceeecchHHHHHHHHhCCCCCCCCHHHHHHHHHHhcCchHHHHHhhhhhhhcCChhhHHHHHHHHHHHhHhhc
Q 002245 508 RLLTLHHLAFPVDTNVGRIAVRLGWVPLQPLPESLQLHLLELYPVLESIQKYLWPRLCKLDQRTLYELHYQLITFGKVFC 587 (947)
Q Consensus 508 LlfafgrpafPVDTHV~RVl~RLGlv~~k~tpeevEk~Le~llP~~e~Iqk~LW~rlc~ld~~~~~e~H~~LI~fGR~IC 587 (947)
|+|+||+++||||+||.||+.|+||... ++++++++.++.++|. ..+.+||.+||+|||.+|
T Consensus 123 ll~~~~~~~~~vD~~v~Ri~~r~g~~~~-~~~~~~~~~l~~~~p~-----------------~~~~~~h~~li~~G~~~C 184 (191)
T TIGR01083 123 LNVAFGIPAIAVDTHVFRVSNRLGLSKG-KDPDKVEEELLKLIPR-----------------EFWTKLHHWLILHGRYTC 184 (191)
T ss_pred HHHHcCCCccccchhHHHHHHHcCCCCC-CCHHHHHHHHHHHCCc-----------------hhHHHHHHHHHHHhHHhc
Confidence 9999999999999999999999999865 6899999999998883 234689999999999999
Q ss_pred ccCCCCC
Q 002245 588 TKSKPNC 594 (947)
Q Consensus 588 tarkPkC 594 (947)
++++|+|
T Consensus 185 ~~~~P~C 191 (191)
T TIGR01083 185 KARKPLC 191 (191)
T ss_pred CCCCCCC
Confidence 9999999
No 6
>PRK10880 adenine DNA glycosylase; Provisional
Probab=100.00 E-value=1.5e-36 Score=334.12 Aligned_cols=203 Identities=19% Similarity=0.274 Sum_probs=169.2
Q ss_pred hcccccccchhhhhhcccccccccccccccChHHHHHHHHhccCccccccCcCCCCCHHHHHcCCHHHHHHHHHhcCCcH
Q 002245 377 LSAHKVYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQERSRDRMDSLDYEALRCANVKEISEAIKERGMNN 456 (947)
Q Consensus 377 ~~~~~~~~lLia~iLSaq~~d~~vnk~qnT~W~~L~k~l~~~glk~er~~~~~~~pTpeaLa~A~~eELeelIR~lGfyn 456 (947)
....++|..||+.||++|++++.+... |.++.+. +||+++|++|++++|.++|+++|||+
T Consensus 25 r~~~dpy~ilVseILlQQT~v~~v~~~----~~rl~~~----------------fPt~~~La~a~~eel~~~~~glGyy~ 84 (350)
T PRK10880 25 QIDKTPYKVWLSEVMLQQTQVATVIPY----FERFMAR----------------FPTVTDLANAPLDEVLHLWTGLGYYA 84 (350)
T ss_pred CCCCCHHHHHHHHHHHhhccHHHHHHH----HHHHHHH----------------CcCHHHHHCcCHHHHHHHHHcCChHH
Confidence 344588999999999999999888743 4555432 89999999999999999999999995
Q ss_pred HHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHhCCCCcHhHHHHHHHHhcCCceeecchHHHHHHHHhCCCCCC
Q 002245 457 MLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQ 536 (947)
Q Consensus 457 ~KAk~Ik~lA~~Lve~yGgiDLe~L~~vP~deareeLlsLPGVG~KTAd~ILlfafgrpafPVDTHV~RVl~RLGlv~~k 536 (947)
||++|+++|+.|+++|+| .+|.+ +++|++|||||+|||++||+|+||+++++||+||+||+.|++.+...
T Consensus 85 -RAr~L~~~A~~i~~~~~g-------~~p~~--~~~L~~LpGIG~~TA~aIl~~af~~~~~iVD~nV~RV~~Rl~~i~~~ 154 (350)
T PRK10880 85 -RARNLHKAAQQVATLHGG-------EFPET--FEEVAALPGVGRSTAGAILSLSLGKHFPILDGNVKRVLARCYAVSGW 154 (350)
T ss_pred -HHHHHHHHHHHHHHHhCC-------Cchhh--HHHHhcCCCccHHHHHHHHHHHCCCCeecccHHHHHHHHHHhcccCC
Confidence 999999999999999998 67866 99999999999999999999999999999999999999998554433
Q ss_pred CCHHHHHHHHHHhcCchHHHHHhhhhhhhcCChhhHHHHHHHHHHHhHhhcccCCCCCCCCCChhhchhhhhhccccccc
Q 002245 537 PLPESLQLHLLELYPVLESIQKYLWPRLCKLDQRTLYELHYQLITFGKVFCTKSKPNCNACPMRGECRHFASAFASARLA 616 (947)
Q Consensus 537 ~tpeevEk~Le~llP~~e~Iqk~LW~rlc~ld~~~~~e~H~~LI~fGR~ICtarkPkC~~CPLrdlC~yy~k~~a~ar~a 616 (947)
..+.++++.+.++.. .+ ++...+.+||++||+||+.+|++++|+|..|||++.|++|... ....
T Consensus 155 ~~~~~~~~~l~~~~~-------~l------~p~~~~~~~nqalm~lGa~vC~p~~P~C~~Cpl~~~C~~~~~~---~~~~ 218 (350)
T PRK10880 155 PGKKEVENRLWQLSE-------QV------TPAVGVERFNQAMMDLGAMVCTRSKPKCELCPLQNGCIAYANH---SWAL 218 (350)
T ss_pred CChHHHHHHHHHHHH-------Hh------CChhHHHHHHHHHHHhhHHhccCCCCCCCCCccHhhhHHHHcC---CHhh
Confidence 456666665543221 11 2235678999999999999999999999999999999999864 4466
Q ss_pred cCCCCcccc
Q 002245 617 LPGPEEKSI 625 (947)
Q Consensus 617 lP~p~~k~~ 625 (947)
+|++..|..
T Consensus 219 ~P~k~~k~~ 227 (350)
T PRK10880 219 YPGKKPKQT 227 (350)
T ss_pred CCCCCCCCC
Confidence 888776554
No 7
>KOG1921 consensus Endonuclease III [Replication, recombination and repair]
Probab=100.00 E-value=1.7e-34 Score=299.71 Aligned_cols=182 Identities=26% Similarity=0.441 Sum_probs=163.3
Q ss_pred ccccchhhhhhcccccccccccccccChHHHHHHHHhccCccccccCcCCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHH
Q 002245 381 KVYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQERSRDRMDSLDYEALRCANVKEISEAIKERGMNNMLAE 460 (947)
Q Consensus 381 ~~~~lLia~iLSaq~~d~~vnk~qnT~W~~L~k~l~~~glk~er~~~~~~~pTpeaLa~A~~eELeelIR~lGfyn~KAk 460 (947)
-.|+.|++.|||+|++|..... ++.+. ++ ++.+|+++|+++++..|.++|.++|||++||+
T Consensus 77 ~RfqvLv~lmLSSQTKDevt~~-------Am~rL------~~------~~gLT~e~v~~~de~~l~~LI~~VgFy~rKA~ 137 (286)
T KOG1921|consen 77 RRFQVLVGLMLSSQTKDEVTAA-------AMLRL------KE------YGGLTLEAVLKIDEPTLNELIYPVGFYTRKAK 137 (286)
T ss_pred HhHHHHHHHHHhcchHHHHHHH-------HHHHH------HH------hcCCCHHHHhccChHhHHhhhhhccchHHHHH
Confidence 3599999999999999976542 22222 21 24689999999999999999999999999999
Q ss_pred HHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHhCCCCcHhHHHHHHHHhcCCc-eeecchHHHHHHHHhCCCCCC-CC
Q 002245 461 RMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLLTLHHL-AFPVDTNVGRIAVRLGWVPLQ-PL 538 (947)
Q Consensus 461 ~Ik~lA~~Lve~yGgiDLe~L~~vP~deareeLlsLPGVG~KTAd~ILlfafgrp-afPVDTHV~RVl~RLGlv~~k-~t 538 (947)
||+.+|+++.++|+| ++|++ .+.|++|||||||+|..+|..|+|+- .|.|||||+||++||||++.+ ++
T Consensus 138 ylkkta~IL~d~f~g-------DIP~~--v~dLlsLPGVGPKMa~L~m~~AWn~i~GI~VDtHVHRi~nrlgWv~~ktks 208 (286)
T KOG1921|consen 138 YLKKTAKILQDKFDG-------DIPDT--VEDLLSLPGVGPKMAHLTMQVAWNKIVGICVDTHVHRICNRLGWVDTKTKS 208 (286)
T ss_pred HHHHHHHHHHHHhCC-------CCchh--HHHHhcCCCCchHHHHHHHHHHhccceeEEeehHHHHHHHHhcccccccCC
Confidence 999999999999999 89999 99999999999999999999999985 999999999999999999853 35
Q ss_pred HHHHHHHHHHhcCchHHHHHhhhhhhhcCChhhHHHHHHHHHHHhHhhcccCCCCCCCCCC-hhhchhhh
Q 002245 539 PESLQLHLLELYPVLESIQKYLWPRLCKLDQRTLYELHYQLITFGKVFCTKSKPNCNACPM-RGECRHFA 607 (947)
Q Consensus 539 peevEk~Le~llP~~e~Iqk~LW~rlc~ld~~~~~e~H~~LI~fGR~ICtarkPkC~~CPL-rdlC~yy~ 607 (947)
|++++..|+.|+| +.+| .++|++||.||+.||++++|+|+.|.+ ++.|++..
T Consensus 209 pE~TR~aLq~wLP------k~lW-----------~eIN~lLVGFGQ~iC~p~~prC~~C~~~~~~Cpss~ 261 (286)
T KOG1921|consen 209 PEQTRVALQQWLP------KSLW-----------VEINHLLVGFGQTICTPRRPRCGLCLLSRDLCPSSF 261 (286)
T ss_pred HHHHHHHHHHhCc------HHHH-----------hhhhceeecccceeeecCCCCccccccCcccCchhh
Confidence 9999999999999 5777 589999999999999999999999999 69999743
No 8
>PRK13910 DNA glycosylase MutY; Provisional
Probab=100.00 E-value=1.2e-32 Score=296.55 Aligned_cols=150 Identities=24% Similarity=0.398 Sum_probs=132.6
Q ss_pred CCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHhCCCCcHhHHHHHHHH
Q 002245 431 SLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLL 510 (947)
Q Consensus 431 ~pTpeaLa~A~~eELeelIR~lGfyn~KAk~Ik~lA~~Lve~yGgiDLe~L~~vP~deareeLlsLPGVG~KTAd~ILlf 510 (947)
|||+++|++|++++|.++|+++||| +||++|+++|+.|.++|+| .+|.+ +++|++|||||+|||++||+|
T Consensus 22 fPt~e~La~a~~~el~~~~~glGyy-~RAr~L~~~A~~i~~~~~g-------~~P~~--~~~L~~LpGIG~kTA~aIl~~ 91 (289)
T PRK13910 22 FPTLKDLANAPLEEVLLLWRGLGYY-SRAKNLKKSAEICVKEHHS-------QLPND--YQSLLKLPGIGAYTANAILCF 91 (289)
T ss_pred CCCHHHHHCCCHHHHHHHHHcCCcH-HHHHHHHHHHHHHHHHhCC-------CCChh--HHHHHhCCCCCHHHHHHHHHH
Confidence 9999999999999999999999999 5999999999999999988 78887 999999999999999999999
Q ss_pred hcCCceeecchHHHHHHHHh-CCCCCCCCHHHHHHHHHHhcCchHHHHHhhhhhhhcCChhhHHHHHHHHHHHhHhhccc
Q 002245 511 TLHHLAFPVDTNVGRIAVRL-GWVPLQPLPESLQLHLLELYPVLESIQKYLWPRLCKLDQRTLYELHYQLITFGKVFCTK 589 (947)
Q Consensus 511 afgrpafPVDTHV~RVl~RL-Glv~~k~tpeevEk~Le~llP~~e~Iqk~LW~rlc~ld~~~~~e~H~~LI~fGR~ICta 589 (947)
+||+++++||+||.||+.|+ |+... ....+++....+++| ...+.++|++||+||+.+|++
T Consensus 92 af~~~~~~VD~nV~RVl~Rl~g~~~~-~~~~~l~~~~~~~l~-----------------~~~~~~~nqaLm~~Ga~iC~~ 153 (289)
T PRK13910 92 GFREKSACVDANIKRVLLRLFGLDPN-IHAKDLQIKANDFLN-----------------LNESFNHNQALIDLGALICSP 153 (289)
T ss_pred HCCCCcCcccHHHHHHHHHHhcCCCC-ccHHHHHHHHHHhCC-----------------ccchHHHHHHHHHHhHHHcCC
Confidence 99999999999999999997 77543 445444443334444 245678999999999999999
Q ss_pred CCCCCCCCCChhhchhhhhh
Q 002245 590 SKPNCNACPMRGECRHFASA 609 (947)
Q Consensus 590 rkPkC~~CPLrdlC~yy~k~ 609 (947)
+|+|..|||++.|.++...
T Consensus 154 -~P~C~~CPl~~~C~~~~~~ 172 (289)
T PRK13910 154 -KPKCAICPLNPYCLGKNNP 172 (289)
T ss_pred -CCCCCCCcChhhhhhhhcC
Confidence 7999999999999998764
No 9
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=99.98 E-value=9.7e-32 Score=279.60 Aligned_cols=188 Identities=16% Similarity=0.234 Sum_probs=144.4
Q ss_pred cccccchhhhhhcccccccccccccccChHHHHHHHHhccCccccccCcCCCCCHHHHHcCCHHHHHHHHHhcCCcHHHH
Q 002245 380 HKVYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQERSRDRMDSLDYEALRCANVKEISEAIKERGMNNMLA 459 (947)
Q Consensus 380 ~~~~~lLia~iLSaq~~d~~vnk~qnT~W~~L~k~l~~~glk~er~~~~~~~pTpeaLa~A~~eELeelIR~lGfyn~KA 459 (947)
.++|+.||++||++|+ .|+++.+++.+ +++....+...++||++|++++.++|+++||++|||++||
T Consensus 28 ~~~fevLV~aILsQqT-----------~~~~v~~a~~~--L~~~~~~~~~~~~t~e~L~~a~~eeL~~~Irp~Gf~~~KA 94 (218)
T PRK13913 28 ALKFEALLGAVLTQNT-----------KFEAVEKSLEN--LKNAFILENDDEINLKKIAYIEFSKLAECVRPSGFYNQKA 94 (218)
T ss_pred cCHHHHHHHHHHHhhh-----------hHHHHHHHHHH--HHHhcccccccCCCHHHHHcCCHHHHHHHHHhcCCHHHHH
Confidence 4789999999999984 45555555543 3221110111367999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHhCCCCcHhHHHHHHHHhcCCceeecchHHHHHHHHhCCCCCCCCH
Q 002245 460 ERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQPLP 539 (947)
Q Consensus 460 k~Ik~lA~~Lve~yGgiDLe~L~~vP~deareeLlsLPGVG~KTAd~ILlfafgrpafPVDTHV~RVl~RLGlv~~k~tp 539 (947)
++|+++|+++.++||++ +.+. ..++|++|++|||||+|||++||+|+||+|+|+||+|++||+.|+||.. .+|
T Consensus 95 ~~Lk~la~~i~~~~g~~--~~~~---~~~~re~Ll~l~GIG~kTAd~iLlya~~rp~fvVDty~~Rv~~RlG~~~--~~y 167 (218)
T PRK13913 95 KRLIDLSENILKDFGSF--ENFK---QEVTREWLLDQKGIGKESADAILCYVCAKEVMVVDKYSYLFLKKLGIEI--EDY 167 (218)
T ss_pred HHHHHHHHHHHHHcCCc--hhcc---CchHHHHHHcCCCccHHHHHHHHHHHcCCCccccchhHHHHHHHcCCCC--CCH
Confidence 99999999999998773 3332 2346999999999999999999999999999999999999999999975 479
Q ss_pred HHHHHHHHHhcCc-hHHHHHhhhhhhhcCChhhHHHHHHHHHHHhHhhccc
Q 002245 540 ESLQLHLLELYPV-LESIQKYLWPRLCKLDQRTLYELHYQLITFGKVFCTK 589 (947)
Q Consensus 540 eevEk~Le~llP~-~e~Iqk~LW~rlc~ld~~~~~e~H~~LI~fGR~ICta 589 (947)
++++..++..++. ...+.. ..+.. ..+...+.+||.+|++||+..|.-
T Consensus 168 ~~~~~~~~~~l~~~~~~~~~-~~~~~-~~~~~~~~~~Halive~~k~~~~~ 216 (218)
T PRK13913 168 DELQHFFEKGVQENLNSALA-LYENT-ISLAQLYARFHGKIVEFSKQKLEL 216 (218)
T ss_pred HHHHHHHHHhhhhhhhhhhc-ccccc-chHHHHHHHHHHHHHHHHHHhhhc
Confidence 9999998886642 000000 00000 001256899999999999999964
No 10
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=99.97 E-value=7.2e-31 Score=268.09 Aligned_cols=208 Identities=23% Similarity=0.388 Sum_probs=172.6
Q ss_pred HHHHHHHhhhhhcCCCccccCCCCchhhhhcccccccchhhhhhcccccccccccccccChHHHHHHHHhccCccccccC
Q 002245 348 KTRNLGDDISVANKLSDNKLIEPNSVEQVLSAHKVYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQERSRD 427 (947)
Q Consensus 348 ~~~~i~~rl~~~~~~p~~~l~~~~~~~~~~~~~~~~~lLia~iLSaq~~d~~vnk~qnT~W~~L~k~l~~~glk~er~~~ 427 (947)
....|+.-|-..|+... =. -.++.++.+|.+|| +|||.|++|.+++.+ ++.+
T Consensus 7 ~~~~iy~~L~~~yg~q~---WW--------p~~~~~EiiigAIL-----------tQNT~WknvekAlen--Lk~~---- 58 (215)
T COG2231 7 NITKIYKELLRLYGDQG---WW--------PADNKDEIIIGAIL-----------TQNTSWKNVEKALEN--LKNE---- 58 (215)
T ss_pred HHHHHHHHHHHHcCCcc---CC--------CCCCchhHHHHHHH-----------hccccHHHHHHHHHH--HHHc----
Confidence 34566666666676544 11 11244566666665 578999999999987 7754
Q ss_pred cCCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHhCCCCcHhHHHHH
Q 002245 428 RMDSLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECV 507 (947)
Q Consensus 428 ~~~~pTpeaLa~A~~eELeelIR~lGfyn~KAk~Ik~lA~~Lve~yGgiDLe~L~~vP~deareeLlsLPGVG~KTAd~I 507 (947)
+..++++|..++.++|+++||+.||||+||+||+++.+.+++.|.++ + .+-+..+|++|++++|||..|||+|
T Consensus 59 --~~~~l~~I~~~~~~~L~elIrpsGFYnqKa~rLk~l~k~l~~~~~~~--~---~~~~~~~R~~LL~iKGIG~ETaDsI 131 (215)
T COG2231 59 --GILNLKKILKLDEEELAELIRPSGFYNQKAKRLKALSKNLAKFFINL--E---SFKSEVLREELLSIKGIGKETADSI 131 (215)
T ss_pred --ccCCHHHHhcCCHHHHHHHHhccchHHHHHHHHHHHHHHHHHHhhhh--h---ccchHHHHHHHHccCCcchhhHHHH
Confidence 56789999999999999999999999999999999999999877653 2 3333447999999999999999999
Q ss_pred HHHhcCCceeecchHHHHHHHHhCCCCCCCCHHHHHHHHHHhcCchHHHHHhhhhhhhcCChhhHHHHHHHHHHHhHhhc
Q 002245 508 RLLTLHHLAFPVDTNVGRIAVRLGWVPLQPLPESLQLHLLELYPVLESIQKYLWPRLCKLDQRTLYELHYQLITFGKVFC 587 (947)
Q Consensus 508 LlfafgrpafPVDTHV~RVl~RLGlv~~k~tpeevEk~Le~llP~~e~Iqk~LW~rlc~ld~~~~~e~H~~LI~fGR~IC 587 (947)
|+|||++|+|+||.+.+|++.|+|.+.. ++++++++.+++-+|. +...+.+||.+|+.|||.+|
T Consensus 132 LlYa~~rp~FVvD~Yt~R~l~rlg~i~~-k~ydeik~~fe~~l~~---------------~~~lyqe~HAlIv~~~K~f~ 195 (215)
T COG2231 132 LLYALDRPVFVVDKYTRRLLSRLGGIEE-KKYDEIKELFEENLPE---------------NLRLYQEFHALIVEHAKHFC 195 (215)
T ss_pred HHHHhcCcccchhHHHHHHHHHhccccc-ccHHHHHHHHHhcchh---------------HHHHHHHHHHHHHHHHHHHc
Confidence 9999999999999999999999999886 4899999999987773 12357899999999999999
Q ss_pred ccCCCCCCCCCChhhchhhh
Q 002245 588 TKSKPNCNACPMRGECRHFA 607 (947)
Q Consensus 588 tarkPkC~~CPLrdlC~yy~ 607 (947)
+. +|.|+.|||...|.++.
T Consensus 196 ~k-~~~~~~cpL~~~~~~~~ 214 (215)
T COG2231 196 KK-KPLCEKCPLKEKCKKYR 214 (215)
T ss_pred cC-CcCCCCchHHHHHhhcc
Confidence 85 69999999999998763
No 11
>COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair]
Probab=99.96 E-value=1.1e-28 Score=269.03 Aligned_cols=200 Identities=20% Similarity=0.296 Sum_probs=163.0
Q ss_pred hcccccccchhhhhhcccccccccccccccChHHHHHHHHhccCccccccCcCCCCCHHHHHcCCHHHHHHHHHhcCCcH
Q 002245 377 LSAHKVYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQERSRDRMDSLDYEALRCANVKEISEAIKERGMNN 456 (947)
Q Consensus 377 ~~~~~~~~lLia~iLSaq~~d~~vnk~qnT~W~~L~k~l~~~glk~er~~~~~~~pTpeaLa~A~~eELeelIR~lGfyn 456 (947)
+...++|..+++.++.+|++-++|. .-..+.+++ +||+++||+|+++||..+|.++|||
T Consensus 29 R~~~~PY~VwvSEiMLQQT~v~~Vi-------~yy~~fl~r-------------fPti~~LA~A~~~evl~~W~gLGYy- 87 (342)
T COG1194 29 RETKDPYRVWVSEIMLQQTQVATVI-------PYYERFLER-------------FPTIKALAAAPEDEVLKAWEGLGYY- 87 (342)
T ss_pred CCCCCcceehhHHHHhhhccHhhhh-------hhHHHHHHh-------------CCCHHHHhcCCHHHHHHHHHhcChH-
Confidence 4455689999999999999988775 223344432 9999999999999999999999987
Q ss_pred HHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHhCCCCcHhHHHHHHHHhcCCceeecchHHHHHHHHhCCCCCC
Q 002245 457 MLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQ 536 (947)
Q Consensus 457 ~KAk~Ik~lA~~Lve~yGgiDLe~L~~vP~deareeLlsLPGVG~KTAd~ILlfafgrpafPVDTHV~RVl~RLGlv~~k 536 (947)
+||++|+++|+.++++||| .+|++ .+.|.+|||||++||.+||.++|+++..+||+||.||+.|+.-+...
T Consensus 88 sRArnL~~~A~~v~~~~~G-------~~P~~--~~~l~~LpGiG~yTa~Ail~~a~~~~~~~lDgNV~RVl~R~f~i~~~ 158 (342)
T COG1194 88 SRARNLHKAAQEVVERHGG-------EFPDD--EEELAALPGVGPYTAGAILSFAFNQPEPVLDGNVKRVLSRLFAISGD 158 (342)
T ss_pred HHHHHHHHHHHHHHHHcCC-------CCCCC--HHHHHhCCCCcHHHHHHHHHHHhCCCCceeecchheeehhhhccccc
Confidence 8999999999999999999 89999 88999999999999999999999999999999999999999444432
Q ss_pred C----CHHHHHHHHHHhcCchHHHHHhhhhhhhcCChhhHHHHHHHHHHHhHhhcccCCCCCCCCCChhhchhhhhhccc
Q 002245 537 P----LPESLQLHLLELYPVLESIQKYLWPRLCKLDQRTLYELHYQLITFGKVFCTKSKPNCNACPMRGECRHFASAFAS 612 (947)
Q Consensus 537 ~----tpeevEk~Le~llP~~e~Iqk~LW~rlc~ld~~~~~e~H~~LI~fGR~ICtarkPkC~~CPLrdlC~yy~k~~a~ 612 (947)
. +..+++..++.++. ......+|+++||++|+.||++++|+|..|||++.|..|...
T Consensus 159 ~~~~~~~~~~~~~~~~ll~----------------p~~~~~~fnqammdlGA~ICt~~~P~C~~CPl~~~c~a~~~g--- 219 (342)
T COG1194 159 IGKPKTKKELWELAEQLLT----------------PDRRPGDFNQAMMDLGATICTAKKPKCSLCPLRDNCAAYRNG--- 219 (342)
T ss_pred ccccchhHHHHHHHHHhcC----------------CCCChHHHHHHHHHhhhHhhcCCCCCCCcCcchHHHHHHHcC---
Confidence 2 22233333333111 112278999999999999999999999999999999988875
Q ss_pred cccccCCCCcccc
Q 002245 613 ARLALPGPEEKSI 625 (947)
Q Consensus 613 ar~alP~p~~k~~ 625 (947)
....+|++..|..
T Consensus 220 ~~~~~P~k~~k~~ 232 (342)
T COG1194 220 TPEKYPVKKPKKK 232 (342)
T ss_pred CcccCCCcCcccc
Confidence 3345776665443
No 12
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=99.92 E-value=1.2e-24 Score=211.25 Aligned_cols=129 Identities=34% Similarity=0.469 Sum_probs=117.7
Q ss_pred CCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHhCCCCcHhHHHHHHHH
Q 002245 431 SLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLL 510 (947)
Q Consensus 431 ~pTpeaLa~A~~eELeelIR~lGfyn~KAk~Ik~lA~~Lve~yGgiDLe~L~~vP~deareeLlsLPGVG~KTAd~ILlf 510 (947)
++||++|++++.++|.++|+++||+++||++|+++|+.+.+.+++ .+|. .++.|++|||||+|||++||+|
T Consensus 21 ~~~~~~l~~~~~~eL~~~l~~~g~~~~ka~~i~~~a~~~~~~~~~-------~~~~--~~~~L~~l~GIG~~tA~~~l~~ 91 (149)
T smart00478 21 FPTPEDLAAADEEELEELIRPLGFYRRKAKYLIELARILVEEYGG-------EVPD--DREELLKLPGVGRKTANAVLSF 91 (149)
T ss_pred CCCHHHHHCCCHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHCC-------CccH--HHHHHHcCCCCcHHHHHHHHHH
Confidence 789999999999999999999999999999999999999998877 4553 4899999999999999999999
Q ss_pred hcCCceeecchHHHHHHHHhCCCCCCCCHHHHHHHHHHhcCchHHHHHhhhhhhhcCChhhHHHHHHHHHHHhHh
Q 002245 511 TLHHLAFPVDTNVGRIAVRLGWVPLQPLPESLQLHLLELYPVLESIQKYLWPRLCKLDQRTLYELHYQLITFGKV 585 (947)
Q Consensus 511 afgrpafPVDTHV~RVl~RLGlv~~k~tpeevEk~Le~llP~~e~Iqk~LW~rlc~ld~~~~~e~H~~LI~fGR~ 585 (947)
+|+++++|||+||.|++.|+|+++..+++++++++++.++|. ..++.+|.++++||+.
T Consensus 92 ~~~~~~~~~D~~v~r~~~rl~~~~~~~~~~~~~~~~~~~~p~-----------------~~~~~~~~~~l~~g~~ 149 (149)
T smart00478 92 ALGKPFIPVDTHVLRIAKRLGLVDKKSTPEEVEKLLEKLLPK-----------------EDWRELNLLLIDFGRT 149 (149)
T ss_pred HCCCCCCccchHHHHHHHHhCCCCCCCCHHHHHHHHHHHCCH-----------------HHHHHHHHHHHHHcCC
Confidence 999999999999999999999998767899999999998882 2356899999999973
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=1.2e-24 Score=212.75 Aligned_cols=157 Identities=31% Similarity=0.426 Sum_probs=136.2
Q ss_pred ccchhhhhhcccccccccccccccChHHHHHHHHhccCccccccCcCCC-CCHHHHHcCCHHHHHHHHHhcCCcHHHHHH
Q 002245 383 YDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQERSRDRMDS-LDYEALRCANVKEISEAIKERGMNNMLAER 461 (947)
Q Consensus 383 ~~lLia~iLSaq~~d~~vnk~qnT~W~~L~k~l~~~glk~er~~~~~~~-pTpeaLa~A~~eELeelIR~lGfyn~KAk~ 461 (947)
|+.|++.||++|++.+.+.+ .|.+|.+. + |||++|+.++.++|++++.+.| ++.||++
T Consensus 1 ~e~Li~~il~q~~s~~~a~~----~~~~l~~~----------------~gpt~~~l~~~~~~~l~~~~~~~G-~~~kA~~ 59 (158)
T cd00056 1 FEVLVSEILSQQTTDKAVNK----AYERLFER----------------YGPTPEALAAADEEELRELIRSLG-YRRKAKY 59 (158)
T ss_pred CHHHHHHHHHhcccHHHHHH----HHHHHHHH----------------hCCCHHHHHCCCHHHHHHHHHhcC-hHHHHHH
Confidence 67899999999999987763 34555433 3 8999999999999999999999 8899999
Q ss_pred HHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHhCCCCcHhHHHHHHHHhcCCceeecchHHHHHHHHhCCCCCCCCHHH
Q 002245 462 MKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQPLPES 541 (947)
Q Consensus 462 Ik~lA~~Lve~yGgiDLe~L~~vP~deareeLlsLPGVG~KTAd~ILlfafgrpafPVDTHV~RVl~RLGlv~~k~tpee 541 (947)
|+++|+.+.+++++.+. +.+++++.|++|||||+|||++||+|+||.++||||+||.|++.|+|+.+..+++++
T Consensus 60 i~~~a~~~~~~~~~~~~------~~~~~~~~L~~l~GIG~~tA~~~l~~~~~~~~~pvD~~v~r~~~~~~~~~~~~~~~~ 133 (158)
T cd00056 60 LKELARAIVEGFGGLVL------DDPDAREELLALPGVGRKTANVVLLFALGPDAFPVDTHVRRVLKRLGLIPKKKTPEE 133 (158)
T ss_pred HHHHHHHHHHHcCCccC------CCcccHHHHHcCCCCCHHHHHHHHHHHCCCCCCccchhHHHHHHHhCCCCCCCCHHH
Confidence 99999999998877432 667789999999999999999999999998899999999999999999766678999
Q ss_pred HHHHHHHhcCchHHHHHhhhhhhhcCChhhHHHHHHHHHHHh
Q 002245 542 LQLHLLELYPVLESIQKYLWPRLCKLDQRTLYELHYQLITFG 583 (947)
Q Consensus 542 vEk~Le~llP~~e~Iqk~LW~rlc~ld~~~~~e~H~~LI~fG 583 (947)
+++.++.+.|. .....+|+.|+.||
T Consensus 134 ~~~~~~~~~~~-----------------~~~~~~~~~l~~~g 158 (158)
T cd00056 134 LEELLEELLPK-----------------PYWGEANQALMDLG 158 (158)
T ss_pred HHHHHHHHCCH-----------------HHHHHHHHHHHHcC
Confidence 99998888761 23467999999987
No 14
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=99.90 E-value=8.1e-24 Score=219.17 Aligned_cols=137 Identities=20% Similarity=0.187 Sum_probs=112.1
Q ss_pred cccccchhhhhhcccccccccccccccChHHHHHHHHhccCccccccCcCCCCCHHHHHcCCHHHHHHHHHhcC--CcHH
Q 002245 380 HKVYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQERSRDRMDSLDYEALRCANVKEISEAIKERG--MNNM 457 (947)
Q Consensus 380 ~~~~~lLia~iLSaq~~d~~vnk~qnT~W~~L~k~l~~~glk~er~~~~~~~pTpeaLa~A~~eELeelIR~lG--fyn~ 457 (947)
.++|++|+++|||+|+++..++++ +.+ +.++.+ +++.++|+++||++| ||++
T Consensus 35 ~~~f~~Lv~~ILsqnT~~~~v~~a-----------~~~--------------L~~~~l-~~~~eeL~~~Ir~~Gygf~~~ 88 (208)
T PRK01229 35 EDLFSELSFCILTANSSAEGGIKA-----------QKE--------------IGDGFL-YLSEEELEEKLKEVGHRFYNK 88 (208)
T ss_pred CChHHHHHHHHhcCcCcHHHHHHH-----------HHh--------------cCHHHc-CCCHHHHHHHHHHhhcccHHH
Confidence 478999999999998777666543 221 134556 899999999999995 9999
Q ss_pred HHHHHHHHHHH---HHHhh--CCCChhhhhcCCchHHHHHHH-hCCCCcHhHHHHHHHHhcCCceeecchHHHHHHHHhC
Q 002245 458 LAERMKDFLNR---LVREH--GSIDLEWLRDVPPDKAKDYLL-SIRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLG 531 (947)
Q Consensus 458 KAk~Ik~lA~~---Lve~y--GgiDLe~L~~vP~deareeLl-sLPGVG~KTAd~ILlfafgrpafPVDTHV~RVl~RLG 531 (947)
||++|++++++ +.+.+ ++ ++| ++|++|+ +|||||+|||++||++.+.+|+|+||+||.|+++|+|
T Consensus 89 KAk~I~~~~~~~~~l~~~~~~~~-------~~~--~~R~~Ll~~lpGIG~KTAd~vL~~~~~~~~~iVDtHv~Ri~~RlG 159 (208)
T PRK01229 89 RAEYIVEARKLYGKLKEIIKADK-------DQF--EAREFLVKNIKGIGYKEASHFLRNVGYEDLAILDRHILRFLKRYG 159 (208)
T ss_pred HHHHHHHHHHHHHHHHHHHhccC-------Cch--HHHHHHHHcCCCCcHHHHHHHHHHccCCCeeeeeHHHHHHHHHhC
Confidence 99999999987 44333 22 344 5699999 9999999999999976555999999999999999999
Q ss_pred CCCCC------CCHHHHHHHHHHhcC
Q 002245 532 WVPLQ------PLPESLQLHLLELYP 551 (947)
Q Consensus 532 lv~~k------~tpeevEk~Le~llP 551 (947)
+++.. .+|.+++..|+++.+
T Consensus 160 ~~~~~~~~lt~~~y~~~E~~l~~~~~ 185 (208)
T PRK01229 160 LIEEIPKTLSKKRYLEIEEILREIAE 185 (208)
T ss_pred CCcccccccCcCCHHHHHHHHHHHHH
Confidence 98852 579999999887755
No 15
>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=202.51 Aligned_cols=141 Identities=23% Similarity=0.294 Sum_probs=114.8
Q ss_pred ccccchhhhhhcccccccccccccccChHHHHHHHHhccCcccc--ccCcCCCCCHHHHHcCCHHHHHHHHHhcCCcHHH
Q 002245 381 KVYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQER--SRDRMDSLDYEALRCANVKEISEAIKERGMNNML 458 (947)
Q Consensus 381 ~~~~lLia~iLSaq~~d~~vnk~qnT~W~~L~k~l~~~glk~er--~~~~~~~pTpeaLa~A~~eELeelIR~lGfyn~K 458 (947)
++|+.||+.|+|+|.+.+.+.+ .+.+|.+. +|-+-.. ....+.||||++|++++.++ .||.+||. .|
T Consensus 118 d~fE~lv~~IlsQq~si~~a~~----~~~rL~~~---~G~~~~~~~g~~~~~FPtp~~La~~~~e~---~Lr~~G~g-~R 186 (310)
T TIGR00588 118 DPFECLISFICSSNNNIARITR----MVERLCQA---FGPRLITLDGVTYHGFPSLHALTGPEAEA---HLRKLGLG-YR 186 (310)
T ss_pred CHHHHHHHHHHhCCCCHHHHHH----HHHHHHHH---hCCCcccCCCcccccCCCHHHHhCCChHH---HHHHcCCH-HH
Confidence 6799999999999999988763 34555443 3421110 11134699999999976543 46789994 58
Q ss_pred HHHHHHHHHHHHHhhCCC-ChhhhhcCCchHHHHHHHhCCCCcHhHHHHHHHHhcCCc-eeecchHHHHHHHHh-CC
Q 002245 459 AERMKDFLNRLVREHGSI-DLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLLTLHHL-AFPVDTNVGRIAVRL-GW 532 (947)
Q Consensus 459 Ak~Ik~lA~~Lve~yGgi-DLe~L~~vP~deareeLlsLPGVG~KTAd~ILlfafgrp-afPVDTHV~RVl~RL-Gl 532 (947)
|++|+++|+.+.+.+++. +++.|..++.++++++|++|||||+|||+|||+|+||++ +||||+||+|++.|+ |+
T Consensus 187 a~~I~~~A~~i~~~~~~~~~l~~l~~~~~~~~~~~L~~l~GIG~~tAd~vll~~l~~~d~~PvD~~v~r~~~r~y~~ 263 (310)
T TIGR00588 187 ARYIRETARALLEEQGGRAWLQQIRGASYEDAREALCELPGVGPKVADCICLMGLDKPQAVPVDVHVWRIANRDYPW 263 (310)
T ss_pred HHHHHHHHHHHHhccCCchhHHhhccCChHHHHHHHHhCCCccHHHHHHHHHHhCCCCCceeecHHHHHHHHHHhcc
Confidence 999999999999987665 678888999999999999999999999999999999998 899999999999998 55
No 16
>KOG2457 consensus A/G-specific adenine DNA glycosylase [Replication, recombination and repair]
Probab=99.82 E-value=1.4e-20 Score=205.40 Aligned_cols=215 Identities=19% Similarity=0.247 Sum_probs=163.7
Q ss_pred HHHHHHHhhhhhcCCCccccCCCCch----hhhhcccccccchhhhhhcccccccccccccccChHHHHHHHHhccCccc
Q 002245 348 KTRNLGDDISVANKLSDNKLIEPNSV----EQVLSAHKVYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQE 423 (947)
Q Consensus 348 ~~~~i~~rl~~~~~~p~~~l~~~~~~----~~~~~~~~~~~lLia~iLSaq~~d~~vnk~qnT~W~~L~k~l~~~glk~e 423 (947)
+...+..-|...|..-+..|+.-+.. .-+.. -.|+-+|+-|.-+|++-.+|.+- ..+-++
T Consensus 89 Ev~~fR~sLl~wYD~~KRdLPWR~r~sEde~Dwer--RaYeVwVSEiMLQQTrV~TV~~Y-------Yt~WMq------- 152 (555)
T KOG2457|consen 89 EVQKFRMSLLDWYDVNKRDLPWRNRRSEDEKDWER--RAYEVWVSEIMLQQTRVQTVMKY-------YTRWMQ------- 152 (555)
T ss_pred HHHHHHHHHHHHhhhhcccCccccCCccchhhHHH--HHHHHHHHHHHHHHHHHHHHHHH-------HHHHHH-------
Confidence 33444444455555444445443321 11111 34788899888888887666431 122222
Q ss_pred cccCcCCCCCHHHHHcCCH-HHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHh-CCCCcH
Q 002245 424 RSRDRMDSLDYEALRCANV-KEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLS-IRGLGL 501 (947)
Q Consensus 424 r~~~~~~~pTpeaLa~A~~-eELeelIR~lGfyn~KAk~Ik~lA~~Lve~yGgiDLe~L~~vP~deareeLls-LPGVG~ 501 (947)
..||..+|+.|+. +++.++|.++||| +|+++|++.|+.+++.++| .+|.. -+.|.+ +||||+
T Consensus 153 ------kwPTl~dla~Asl~~eVn~lWaGlGyY-~R~rrL~ega~~vv~~~~g-------e~Prt--a~~l~kgvpGVG~ 216 (555)
T KOG2457|consen 153 ------KWPTLYDLAQASLEKEVNELWAGLGYY-RRARRLLEGAKMVVAGTEG-------EFPRT--ASSLMKGVPGVGQ 216 (555)
T ss_pred ------hCchHHHHHHHHHHHHHHHHHhhhhHH-HHHHHHHHHHHHHHHhCCC-------CCCCh--HHHHHhhCCCCCc
Confidence 3899999999999 8999999999999 7999999999999999999 89988 567777 999999
Q ss_pred hHHHHHHHHhcCCceeecchHHHHHHHHhCCCCCCCCHHHHHHHHHHhcCchHHHHHhhhhhh-hcCChhhHHHHHHHHH
Q 002245 502 KSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQPLPESLQLHLLELYPVLESIQKYLWPRL-CKLDQRTLYELHYQLI 580 (947)
Q Consensus 502 KTAd~ILlfafgrpafPVDTHV~RVl~RLGlv~~k~tpeevEk~Le~llP~~e~Iqk~LW~rl-c~ld~~~~~e~H~~LI 580 (947)
|||.+|+.+||+++.=+||.||.||+.|.--+....+..++-.. +|... ...|+..+.+||++||
T Consensus 217 YTAGAiaSIAf~q~tGiVDGNVirvlsRalAIhsDcSkgk~~q~--------------~wkLA~qLVDP~RPGDFNQalM 282 (555)
T KOG2457|consen 217 YTAGAIASIAFNQVTGIVDGNVIRVLSRALAIHSDCSKGKFFQS--------------SWKLAAQLVDPSRPGDFNQALM 282 (555)
T ss_pred cchhhhhhhhhcCcccccccchHHHhHHhHhhcCCcchhhHHHH--------------HHHHHHHhcCCCCCCcHHHHHH
Confidence 99999999999999999999999999997444433333333332 34432 2467888999999999
Q ss_pred HHhHhhcccCCCCCCCCCChhhchhhhh
Q 002245 581 TFGKVFCTKSKPNCNACPMRGECRHFAS 608 (947)
Q Consensus 581 ~fGR~ICtarkPkC~~CPLrdlC~yy~k 608 (947)
++|..+||+.+|.|..||+...|+.|.-
T Consensus 283 ELGAt~CTpq~P~CS~CPvss~CrA~q~ 310 (555)
T KOG2457|consen 283 ELGATLCTPQKPSCSSCPVSSQCRAFQL 310 (555)
T ss_pred HhcCeeccCCCCCcCCCCcHHHHHHHhH
Confidence 9999999999999999999999998873
No 17
>TIGR03252 uncharacterized HhH-GPD family protein. This model describes a small, well-conserved bacterial protein family. Its sequence largely consists of a domain, HhH-GPD, found in a variety of related base excision DNA repair enzymes (see pfam00730).
Probab=99.80 E-value=1e-19 Score=184.34 Aligned_cols=112 Identities=13% Similarity=0.141 Sum_probs=97.3
Q ss_pred cccccchhhhhhcccccccccccccccChHHHHHHHHhccCccccccCcCCCCCHHHHHcCCHHHHHHHHHhc----CCc
Q 002245 380 HKVYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQERSRDRMDSLDYEALRCANVKEISEAIKER----GMN 455 (947)
Q Consensus 380 ~~~~~lLia~iLSaq~~d~~vnk~qnT~W~~L~k~l~~~glk~er~~~~~~~pTpeaLa~A~~eELeelIR~l----Gfy 455 (947)
.++|++||++|||+|++|..++++ +.+|++.+ +.+||++|++++.++|+++|++. |||
T Consensus 16 ~~pFelLVa~ILSQqTtd~nv~kA----~~~L~~~~--------------g~~tp~~La~a~~eeL~~lI~~~pal~Gfy 77 (177)
T TIGR03252 16 SDPFALLTGMLLDQQVPMERAFAG----PHKIARRM--------------GSLDAEDIAKYDPQAFVALFSERPAVHRFP 77 (177)
T ss_pred CChHHHHHHHHHhccCcHHHHHHH----HHHHHHHh--------------CCCCHHHHHcCCHHHHHHHHhcCccccCch
Confidence 378999999999999999988864 36665442 34799999999999999999876 999
Q ss_pred HHHHHHHHHHHHHHHHhhCCCChhhhhc--CC-chHHHHHHHhCCCCcHhHHHHHHHH
Q 002245 456 NMLAERMKDFLNRLVREHGSIDLEWLRD--VP-PDKAKDYLLSIRGLGLKSVECVRLL 510 (947)
Q Consensus 456 n~KAk~Ik~lA~~Lve~yGgiDLe~L~~--vP-~deareeLlsLPGVG~KTAd~ILlf 510 (947)
++||++|+++|++|+++|+| +++.|.. +| ..+++++|++|||||+|||++||++
T Consensus 78 ~~KAk~Lk~~a~~iie~y~G-~v~~L~~~~~p~t~~lre~Ll~LpGVG~KTAnvVL~~ 134 (177)
T TIGR03252 78 GSMAKRVQALAQYVVDTYDG-DATAVWTEGDPDGKELLRRLKALPGFGKQKAKIFLAL 134 (177)
T ss_pred HHHHHHHHHHHHHHHHHhCC-ChhhhhcccCCCcHHHHHHHHcCCCCCHHHHHHHHHH
Confidence 99999999999999999998 7777765 24 4567999999999999999999986
No 18
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=99.77 E-value=2.3e-18 Score=186.20 Aligned_cols=167 Identities=19% Similarity=0.244 Sum_probs=134.5
Q ss_pred cccccchhhhhhcccccccccccccccChHHHHHHHHhccCccccccCcCCCCCHHHHHcCCHHHHHHHHHhcCCcHHHH
Q 002245 380 HKVYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQERSRDRMDSLDYEALRCANVKEISEAIKERGMNNMLA 459 (947)
Q Consensus 380 ~~~~~lLia~iLSaq~~d~~vnk~qnT~W~~L~k~l~~~glk~er~~~~~~~pTpeaLa~A~~eELeelIR~lGfyn~KA 459 (947)
.++|+-||..|+|+|.+.+... +.|.+|...+ |-. ....+.||||++|+.++++.|. .+|+...||
T Consensus 103 ~d~fe~lv~aI~~QqvS~~~A~----~i~~rl~~~~---g~~---~~~~~~fptpe~l~~~~~~~l~----~~g~s~~Ka 168 (285)
T COG0122 103 PDPFEALVRAILSQQVSVAAAA----KIWARLVSLY---GNA---LEIYHSFPTPEQLAAADEEALR----RCGLSGRKA 168 (285)
T ss_pred CCHHHHHHHHHHHhHhhHHHHH----HHHHHHHHHh---CCc---cccccCCCCHHHHHhcCHHHHH----HhCCcHHHH
Confidence 4789999999999999988776 5688887664 211 1134569999999999999975 589999999
Q ss_pred HHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHhCCCCcHhHHHHHHHHhcCCc-eee-cchHHHHHHHHhCCCCCCC
Q 002245 460 ERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLLTLHHL-AFP-VDTNVGRIAVRLGWVPLQP 537 (947)
Q Consensus 460 k~Ik~lA~~Lve~yGgiDLe~L~~vP~deareeLlsLPGVG~KTAd~ILlfafgrp-afP-VDTHV~RVl~RLGlv~~k~ 537 (947)
+||+.+|+++.+ |.+|+..|..++.+++++.|++|+|||+|||+|||+|++|++ +|| .|.+++|.+.+++..+...
T Consensus 169 ~yi~~~A~~~~~--g~~~~~~l~~~~~e~a~e~L~~i~GIG~WTAe~~llf~lgr~dvfP~~D~~lr~~~~~~~~~~~~~ 246 (285)
T COG0122 169 EYIISLARAAAE--GELDLSELKPLSDEEAIEELTALKGIGPWTAEMFLLFGLGRPDVFPADDLGLRRAIKKLYRLPTRP 246 (285)
T ss_pred HHHHHHHHHHHc--CCccHHHhccCCHHHHHHHHHcCCCcCHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhcCCCCc
Confidence 999999999997 557999999999999999999999999999999999999987 999 5788888888887333333
Q ss_pred CHHHHHHHHHHhcCchHHHHHhhhh
Q 002245 538 LPESLQLHLLELYPVLESIQKYLWP 562 (947)
Q Consensus 538 tpeevEk~Le~llP~~e~Iqk~LW~ 562 (947)
+...++...+.+-|.-...+.+||.
T Consensus 247 ~~~~~~~~~e~w~p~rs~A~~yLw~ 271 (285)
T COG0122 247 TEKEVRELAERWGPYRSYAALYLWR 271 (285)
T ss_pred hHHHHHHHHhcccCHHHHHHHHHHH
Confidence 4444566666676643345566665
No 19
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=99.69 E-value=5.6e-16 Score=167.52 Aligned_cols=160 Identities=15% Similarity=0.100 Sum_probs=120.6
Q ss_pred ccccchhhhhhcccccccccccccccChHHHHHHHHhccCccccccCcCCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHH
Q 002245 381 KVYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQERSRDRMDSLDYEALRCANVKEISEAIKERGMNNMLAE 460 (947)
Q Consensus 381 ~~~~lLia~iLSaq~~d~~vnk~qnT~W~~L~k~l~~~glk~er~~~~~~~pTpeaLa~A~~eELeelIR~lGfyn~KAk 460 (947)
++|+.|+..|+++|.+-+... +.+.+|. ..+|-+-........||||++|++++.++|+ .+||+++||+
T Consensus 112 d~fE~lv~aIigQqisv~~a~----~~~~rlv---~~~G~~l~~~~~~~~FPtpe~La~~~~~eL~----~~Gl~~~Ra~ 180 (283)
T PRK10308 112 DAFEQGVRAILGQLVSVAMAA----KLTAKVA---QLYGERLDDFPEYVCFPTPERLAAADPQALK----ALGMPLKRAE 180 (283)
T ss_pred CHHHHHHHHHHHhHHHHHHHH----HHHHHHH---HHhCccccCCCCccCCCCHHHHHcCCHHHHH----HCCCCHHHHH
Confidence 679999999999998876665 2234443 3334321101123568999999999999975 5899999999
Q ss_pred HHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHhCCCCcHhHHHHHHHHhcCCc-ee-ecchHHHHHHHHhCCCCCCCC
Q 002245 461 RMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLLTLHHL-AF-PVDTNVGRIAVRLGWVPLQPL 538 (947)
Q Consensus 461 ~Ik~lA~~Lve~yGgiDLe~L~~vP~deareeLlsLPGVG~KTAd~ILlfafgrp-af-PVDTHV~RVl~RLGlv~~k~t 538 (947)
+|+++|+.+.+ |.++++.+. +.+++++.|++|||||+|||++|++++||++ +| ++|.+++|.+ + ..+
T Consensus 181 ~L~~lA~~i~~--g~l~l~~~~--~~~~~~~~L~~LpGIGpwTA~~vllr~lg~~D~fp~~D~~l~~~~---~----~~~ 249 (283)
T PRK10308 181 ALIHLANAALE--GTLPLTIPG--DVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFLPDDYLIKQRF---P----GMT 249 (283)
T ss_pred HHHHHHHHHHc--CCCCccccC--CHHHHHHHHhcCCCcCHHHHHHHHHHhCCCCCCCCcccHHHHHhc---c----cCC
Confidence 99999999997 666665443 4567899999999999999999999999997 77 6899999844 1 246
Q ss_pred HHHHHHHHHHhcCchHHHHHhhhh
Q 002245 539 PESLQLHLLELYPVLESIQKYLWP 562 (947)
Q Consensus 539 peevEk~Le~llP~~e~Iqk~LW~ 562 (947)
++++++..+.+-|.-....-+||.
T Consensus 250 ~~~~~~~a~~w~P~rsya~~~LW~ 273 (283)
T PRK10308 250 PAQIRRYAERWKPWRSYALLHIWY 273 (283)
T ss_pred HHHHHHHHHhcCCHHHHHHHHHHH
Confidence 788888888887743233345554
No 20
>KOG2875 consensus 8-oxoguanine DNA glycosylase [Replication, recombination and repair]
Probab=99.62 E-value=1.1e-15 Score=162.72 Aligned_cols=139 Identities=23% Similarity=0.279 Sum_probs=117.1
Q ss_pred ccccchhhhhhcccccccccccccccChHHHHHHHHhccCccccc--cCcCCCCCHHHHHcCCHHHHHHHHHhcCCcHHH
Q 002245 381 KVYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQERS--RDRMDSLDYEALRCANVKEISEAIKERGMNNML 458 (947)
Q Consensus 381 ~~~~lLia~iLSaq~~d~~vnk~qnT~W~~L~k~l~~~glk~er~--~~~~~~pTpeaLa~A~~eELeelIR~lGfyn~K 458 (947)
.+++-|++.|-|.....+.+. .-+...++++|.+-..+ -+..+||+.++|+. .++++-+|.+||. .|
T Consensus 116 dP~E~lfSFiCSSNNNIaRIT-------~Mve~fc~~fG~~i~~~dg~~~h~FPsl~~L~g---~~~Ea~LR~~gfG-YR 184 (323)
T KOG2875|consen 116 DPIECLFSFICSSNNNIARIT-------GMVERFCQAFGPRIIQLDGVDYHGFPSLQALAG---PEVEAELRKLGFG-YR 184 (323)
T ss_pred CcHHHHHHHHhcCCCcHHHHH-------HHHHHHHHhhCcceEeecCcccccCccHHHhcC---cHhHHHHHHcCcc-hh
Confidence 568899999999988887774 45677888888653222 24568999999987 7788888999997 79
Q ss_pred HHHHHHHHHHHHHhhCCC-ChhhhhcCCchHHHHHHHhCCCCcHhHHHHHHHHhcCCc-eeecchHHHHHHHHh
Q 002245 459 AERMKDFLNRLVREHGSI-DLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLLTLHHL-AFPVDTNVGRIAVRL 530 (947)
Q Consensus 459 Ak~Ik~lA~~Lve~yGgi-DLe~L~~vP~deareeLlsLPGVG~KTAd~ILlfafgrp-afPVDTHV~RVl~RL 530 (947)
||||.+.|+.|.+++|+. .|..|++++.+++|+.|..|||||+|+||||+++++|+. ++|||+||.||+.-.
T Consensus 185 AkYI~~ta~~l~~~~g~~~wLqsl~~~~yeear~~L~~lpGVG~KVADCI~Lm~l~~~~~VPVDvHi~ria~~y 258 (323)
T KOG2875|consen 185 AKYISATARALQEKQGGLAWLQSLRKSSYEEAREALCSLPGVGPKVADCICLMSLDKLSAVPVDVHIWRIAQDY 258 (323)
T ss_pred HHHHHHHHHHHHHhcccchHHHHHhcccHHHHHHHHhcCCCCcchHhhhhhhhhcCCCCcccchhhHHHHhhcc
Confidence 999999999999999882 233456889999999999999999999999999999997 999999999999943
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=99.50 E-value=7.7e-14 Score=128.79 Aligned_cols=107 Identities=25% Similarity=0.279 Sum_probs=88.6
Q ss_pred hhhhhcccccccccccccccChHHHHHHHHhccCccccccCcCCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHH
Q 002245 387 NPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQERSRDRMDSLDYEALRCANVKEISEAIKERGMNNMLAERMKDFL 466 (947)
Q Consensus 387 ia~iLSaq~~d~~vnk~qnT~W~~L~k~l~~~glk~er~~~~~~~pTpeaLa~A~~eELeelIR~lGfyn~KAk~Ik~lA 466 (947)
|+.||++|++...+.+ .|.+|.+. +++|||++|+++++++|+++|+++||++.||++|+++|
T Consensus 1 V~~Il~qq~s~~~a~~----~~~~l~~~--------------~g~pt~~~l~~~~~~el~~~i~~~G~~~~ka~~i~~~a 62 (108)
T PF00730_consen 1 VRAILSQQTSIKAARK----IYRRLFER--------------YGFPTPEALAEASEEELRELIRPLGFSRRKAKYIIELA 62 (108)
T ss_dssp HHHHHCTTS-HHHHHH----HHHHHHHH--------------HSCSSHHHHHCSHHHHHHHHHTTSTSHHHHHHHHHHHH
T ss_pred CeeeecCcCcHHHHHH----HHHHHHHH--------------hcCCCHHHHHhCCHHHHHHHhhccCCCHHHHHHHHHHH
Confidence 5789999999988764 35556544 24899999999999999999999999999999999999
Q ss_pred HHHHHhhCCCChhhhhcCCchHHHHHHHhCCCCcHhHHHHHHHHhcCCceeecchHHHHHHHHhCCCCCCCCHHHHHHHH
Q 002245 467 NRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQPLPESLQLHL 546 (947)
Q Consensus 467 ~~Lve~yGgiDLe~L~~vP~deareeLlsLPGVG~KTAd~ILlfafgrpafPVDTHV~RVl~RLGlv~~k~tpeevEk~L 546 (947)
+.+. ++..++++||+|+.|++.|+|+.+.+++++++++.+
T Consensus 63 ~~~~----------------------------------------~~~d~~~~~D~~v~r~~~r~~~~~~~~~~~~~~~~~ 102 (108)
T PF00730_consen 63 RAIL----------------------------------------GRPDPFPPVDTHVRRVLQRLGGIPEKKTKEETEKKL 102 (108)
T ss_dssp HHHH----------------------------------------C-SSSS-TTSHHHHHHHHHHTSSSSSTTHHHHHHHH
T ss_pred HHhh----------------------------------------hcccceecCcHHHHHHHHHHcCCCCCCCHHHHHHHH
Confidence 9987 122258999999999999999998777999999988
Q ss_pred HHhcC
Q 002245 547 LELYP 551 (947)
Q Consensus 547 e~llP 551 (947)
++++|
T Consensus 103 ~e~~~ 107 (108)
T PF00730_consen 103 EELWP 107 (108)
T ss_dssp HHHGT
T ss_pred HhhCc
Confidence 77654
No 22
>KOG1918 consensus 3-methyladenine DNA glycosidase [Replication, recombination and repair]
Probab=99.49 E-value=4.3e-14 Score=146.57 Aligned_cols=167 Identities=16% Similarity=0.271 Sum_probs=129.9
Q ss_pred hhhcccccccchhhhhhcccccccccccccccChHHHHHHHHhccCccccccCcCCCCCHHHHHcCCHHHHHHHHHhcCC
Q 002245 375 QVLSAHKVYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQERSRDRMDSLDYEALRCANVKEISEAIKERGM 454 (947)
Q Consensus 375 ~~~~~~~~~~lLia~iLSaq~~d~~vnk~qnT~W~~L~k~l~~~glk~er~~~~~~~pTpeaLa~A~~eELeelIR~lGf 454 (947)
.++....+|..||.+|||+|-.++..|-+ ..++. .+.+ - ...+++|+.+..++.++|++ +||
T Consensus 68 ~~~~~q~Pf~~LiraIlsQQLs~kAansI----~~Rfv-sl~~--g-------~~~~~~pe~i~~~~~~~lrk----cG~ 129 (254)
T KOG1918|consen 68 TFKETQTPFERLIRAILSQQLSGKAANSI----YNRFV-SLCG--G-------AEKFPTPEFIDPLDCEELRK----CGF 129 (254)
T ss_pred CcccccCcHHHHHHHHHHHHHHHHHHHHH----HHHHH-HHhC--C-------CcCCCCchhcCcCCHHHHHH----hCc
Confidence 34556688999999999999988877643 33332 3332 1 13489999999999999755 999
Q ss_pred cHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHhCCCCcHhHHHHHHHHhcCCc-eeecch-HHHHHHHHh-C
Q 002245 455 NNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLLTLHHL-AFPVDT-NVGRIAVRL-G 531 (947)
Q Consensus 455 yn~KAk~Ik~lA~~Lve~yGgiDLe~L~~vP~deareeLlsLPGVG~KTAd~ILlfafgrp-afPVDT-HV~RVl~RL-G 531 (947)
+.+|+.||+.+|++..+.| =...+.+.+++.+++.+.|..++|||+|||.++|+|+++|+ +||+|. -|+|=+..| |
T Consensus 130 S~rK~~yLh~lA~~~~ng~-I~s~~~i~~mseEeL~~~LT~VKGIg~Wtv~MflIfsL~R~DVmp~dDlgir~g~k~l~g 208 (254)
T KOG1918|consen 130 SKRKASYLHSLAEAYTNGY-IPSKSGIEKMSEEELIERLTNVKGIGRWTVEMFLIFSLHRPDVMPADDLGIRNGVKKLLG 208 (254)
T ss_pred chhhHHHHHHHHHHHhcCC-CCchHHHhhcCHHHHHHHHHhccCccceeeeeeeeeccCCCcccCchhhhHHHHHHHHhC
Confidence 9999999999999998744 23566778999999999999999999999999999999998 999965 455555544 6
Q ss_pred CCCCCCCHHHHHHHHHHhcCchHHHH-Hhhhh
Q 002245 532 WVPLQPLPESLQLHLLELYPVLESIQ-KYLWP 562 (947)
Q Consensus 532 lv~~k~tpeevEk~Le~llP~~e~Iq-k~LW~ 562 (947)
+-+. +.+.++++..+.+-| ++.+. .|+|+
T Consensus 209 l~~~-p~~~evekl~e~~kp-yRtvaawYlWk 238 (254)
T KOG1918|consen 209 LKPL-PLPKEVEKLCEKCKP-YRTVAAWYLWK 238 (254)
T ss_pred CCCC-CchHHHHHHhhhccc-hHHHHHHHHHh
Confidence 6543 678899988877766 55444 56675
No 23
>PF15629 Perm-CXXC: Permuted single zf-CXXC unit
Probab=99.10 E-value=1.9e-11 Score=92.08 Aligned_cols=32 Identities=81% Similarity=1.405 Sum_probs=30.9
Q ss_pred chhhhccccccCccCcCcccccccccccccce
Q 002245 799 PESRCRSKESGKLCDEKTCFSCNSMRETNSQT 830 (947)
Q Consensus 799 p~~~c~~~~~~~~c~~~~~~~c~~~~e~~~~~ 830 (947)
|+++|++|++|+||+++|||+||||||+++|+
T Consensus 1 Pe~~C~sqe~gkLC~~~tCfsCNsiREa~sQ~ 32 (32)
T PF15629_consen 1 PERRCNSQESGKLCDEETCFSCNSIREANSQT 32 (32)
T ss_pred CcccccccccccccCCccccccccHhHHhccC
Confidence 89999999999999999999999999999985
No 24
>COG1059 Thermostable 8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=98.43 E-value=3.8e-07 Score=93.93 Aligned_cols=124 Identities=20% Similarity=0.259 Sum_probs=91.4
Q ss_pred ccccchhhhhhcccccccccccccccChHHHHHHHHhccCccccccCcCCCCCHHHHHcCCHHHHHHHHHhcC--CcHHH
Q 002245 381 KVYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQERSRDRMDSLDYEALRCANVKEISEAIKERG--MNNML 458 (947)
Q Consensus 381 ~~~~lLia~iLSaq~~d~~vnk~qnT~W~~L~k~l~~~glk~er~~~~~~~pTpeaLa~A~~eELeelIR~lG--fyn~K 458 (947)
.-|..|.=.||-|+.+....-++ .. . +. +.+..++.+||++.++.+| ||+.|
T Consensus 38 ~lf~ELsFCILTANsSA~~~~~~-------q~-~-----lG-------------~gfly~~~eEL~e~Lk~~g~Rf~n~r 91 (210)
T COG1059 38 DLFKELSFCILTANSSATMGLRA-------QN-E-----LG-------------DGFLYLSEEELREKLKEVGYRFYNVR 91 (210)
T ss_pred HHHHHHHHHhccccchHHHHHHH-------HH-H-----hc-------------cccccCCHHHHHHHHHHhcchhcccc
Confidence 34778888899888776544332 11 1 11 3456779999999999995 79999
Q ss_pred HHHHHHHHHHHHHhhCCCChhhhhcCCchH--HHHHHH-hCCCCcHhHHHHHHHHhcCCceeecchHHHHHHHHhCCCCC
Q 002245 459 AERMKDFLNRLVREHGSIDLEWLRDVPPDK--AKDYLL-SIRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPL 535 (947)
Q Consensus 459 Ak~Ik~lA~~Lve~yGgiDLe~L~~vP~de--areeLl-sLPGVG~KTAd~ILlfafgrpafPVDTHV~RVl~RLGlv~~ 535 (947)
|+||..+-+.+. ++..+-+.+..+ +|+.|. .++|||.|-|..+|...--....++|.||.|.+.|.|++..
T Consensus 92 aeyIVeaR~~~~------~lk~~v~~~~~~~vaRE~Lv~nikGiGyKEASHFLRNVG~~D~AIlDrHIlr~l~r~g~i~e 165 (210)
T COG1059 92 AEYIVEAREKFD------DLKIIVKADENEKVARELLVENIKGIGYKEASHFLRNVGFEDLAILDRHILRWLVRYGLIDE 165 (210)
T ss_pred hHHHHHHHHHHH------HHHHHHhcCcchHHHHHHHHHHcccccHHHHHHHHHhcChhHHHHHHHHHHHHHHHhccccc
Confidence 999998655542 345454455433 899999 89999999999998553335567789999999999999875
Q ss_pred C
Q 002245 536 Q 536 (947)
Q Consensus 536 k 536 (947)
.
T Consensus 166 ~ 166 (210)
T COG1059 166 N 166 (210)
T ss_pred C
Confidence 3
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=97.64 E-value=1.6e-05 Score=59.94 Aligned_cols=26 Identities=19% Similarity=0.448 Sum_probs=21.9
Q ss_pred cCCchHHHHHHHhCCCCcHhHHHHHHHH
Q 002245 483 DVPPDKAKDYLLSIRGLGLKSVECVRLL 510 (947)
Q Consensus 483 ~vP~deareeLlsLPGVG~KTAd~ILlf 510 (947)
.+|.+ +++|++|||||+|||++|+.|
T Consensus 5 ~~pas--~eeL~~lpGIG~~tA~~I~~~ 30 (30)
T PF00633_consen 5 LIPAS--IEELMKLPGIGPKTANAILSF 30 (30)
T ss_dssp HHTSS--HHHHHTSTT-SHHHHHHHHHH
T ss_pred cCCCC--HHHHHhCCCcCHHHHHHHHhC
Confidence 35666 899999999999999999976
No 26
>PF10576 EndIII_4Fe-2S: Iron-sulfur binding domain of endonuclease III; InterPro: IPR003651 Endonuclease III (4.2.99.18 from EC) is a DNA repair enzyme which removes a number of damaged pyrimidines from DNA via its glycosylase activity and also cleaves the phosphodiester backbone at apurinic / apyrimidinic sites via a beta-elimination mechanism [, ]. The structurally related DNA glycosylase MutY recognises and excises the mutational intermediate 8-oxoguanine-adenine mispair []. The 3-D structures of Escherichia coli endonuclease III [] and catalytic domain of MutY [] have been determined. The structures contain two all-alpha domains: a sequence-continuous, six-helix domain (residues 22-132) and a Greek-key, four-helix domain formed by one N-terminal and three C-terminal helices (residues 1-21 and 133-211) together with the [Fe4S4] cluster. The cluster is bound entirely within the C-terminal loop by four cysteine residues with a ligation pattern Cys-(Xaa)6-Cys-(Xaa)2-Cys-(Xaa)5-Cys which is distinct from all other known Fe4S4 proteins. This structural motif is referred to as a [Fe4S4] cluster loop (FCL) []. Two DNA-binding motifs have been proposed, one at either end of the interdomain groove: the helix-hairpin-helix (HhH) and FCL motifs. The primary role of the iron-sulphur cluster appears to involve positioning conserved basic residues for interaction with the DNA phosphate backbone by forming the loop of the FCL motif [, ]. The iron-sulphur cluster loop (FCL) is also found in DNA-(apurinic or apyrimidinic site) lyase, a subfamily of endonuclease III. The enzyme has both apurinic and apyrimidinic endonuclease activity and a DNA N-glycosylase activity. It cuts damaged DNA at cytosines, thymines and guanines, and acts on the damaged strand 5' of the damaged site. The enzyme binds a 4Fe-4S cluster which is not important for the catalytic activity, but is probably involved in the alignment of the enzyme along the DNA strand.; GO: 0004519 endonuclease activity, 0051539 4 iron, 4 sulfur cluster binding; PDB: 1VRL_A 1RRQ_A 3G0Q_A 3FSQ_A 1RRS_A 3FSP_A 2ABK_A 1KG7_A 1KG2_A 1MUN_A ....
Probab=96.84 E-value=0.00041 Score=46.41 Aligned_cols=17 Identities=47% Similarity=1.323 Sum_probs=11.6
Q ss_pred cccCCCCCCCCCChhhc
Q 002245 587 CTKSKPNCNACPMRGEC 603 (947)
Q Consensus 587 CtarkPkC~~CPLrdlC 603 (947)
|++|+|+|+.|||+++|
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 89999999999999998
No 27
>PF09674 DUF2400: Protein of unknown function (DUF2400); InterPro: IPR014127 Members of this uncharacterised protein family are found sporadically, so far only among spirochetes, epsilon and delta proteobacteria, and Bacteroides. The function is unknown and its gene neighbourhoods show little conservation.
Probab=96.58 E-value=0.0017 Score=69.72 Aligned_cols=55 Identities=27% Similarity=0.504 Sum_probs=46.4
Q ss_pred HHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHhCCCCcHhHHHHHHHHhcCCceeecchHHHHHHHHhCCCCC
Q 002245 456 NMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPL 535 (947)
Q Consensus 456 n~KAk~Ik~lA~~Lve~yGgiDLe~L~~vP~deareeLlsLPGVG~KTAd~ILlfafgrpafPVDTHV~RVl~RLGlv~~ 535 (947)
+.=+|+|.-+++|++.+-.++|+.-+..+++.++ .+|+||||.||+.+||++..
T Consensus 142 ~SacKR~~MFLRWMVR~d~~VD~GlW~~i~ps~L--------------------------iiPLDtHv~~var~LGL~~r 195 (232)
T PF09674_consen 142 GSACKRLNMFLRWMVRKDSPVDFGLWSSIDPSDL--------------------------IIPLDTHVFRVARKLGLLKR 195 (232)
T ss_pred CcHHHHHHHHHHhhccCCCCCCCcCCCCCCHHHc--------------------------cccchHhHHHHHHHcCCccC
Confidence 3457999999999998766699988888887743 69999999999999999875
Q ss_pred C
Q 002245 536 Q 536 (947)
Q Consensus 536 k 536 (947)
+
T Consensus 196 k 196 (232)
T PF09674_consen 196 K 196 (232)
T ss_pred C
Confidence 4
No 28
>TIGR02757 conserved hypothetical protein TIGR02757. Members of this uncharacterized protein family are found sporadically, so far only among spirochetes, epsilon and delta proteobacteria, and Bacteroides. The function is unknown and its gene neighborhoods show little conservation.
Probab=96.02 E-value=0.0056 Score=65.75 Aligned_cols=86 Identities=23% Similarity=0.405 Sum_probs=57.7
Q ss_pred HHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHhCCCCcHhHHHHHHHHhcCCceeecchHHHHHHHHhCCCCCCC
Q 002245 458 LAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQP 537 (947)
Q Consensus 458 KAk~Ik~lA~~Lve~yGgiDLe~L~~vP~deareeLlsLPGVG~KTAd~ILlfafgrpafPVDTHV~RVl~RLGlv~~k~ 537 (947)
=+|+|--+++|++++ +++|+.-+..+++.++ ++|+||||.||+.+|||...+.
T Consensus 142 a~KR~nMFLRWMVR~-d~VD~GlW~~i~ps~L--------------------------iiPLDtH~~rvar~LgL~~Rk~ 194 (229)
T TIGR02757 142 PLKRLNMFLRWMIRK-DEVDLGIWESFKPSDL--------------------------ILPLDTHVFRIAKKLKLLKRKS 194 (229)
T ss_pred hHHHHHHHHHhhccC-CCCCCcCCCCCCHHHc--------------------------eeechHhHHHHHHHhCCcccCc
Confidence 358999999999985 4489888878877643 7999999999999999987532
Q ss_pred CHHHHHHHHHHhcCchHHHHHhhhhhhhcCChhhHHHHHHHHHHHhH
Q 002245 538 LPESLQLHLLELYPVLESIQKYLWPRLCKLDQRTLYELHYQLITFGK 584 (947)
Q Consensus 538 tpeevEk~Le~llP~~e~Iqk~LW~rlc~ld~~~~~e~H~~LI~fGR 584 (947)
.--++...+-+ .+..+++.++..+..+|-.+|.
T Consensus 195 ~d~kaa~ElT~--------------~Lr~~dp~DPvKYDFAL~~lGi 227 (229)
T TIGR02757 195 YDLKAAIEITE--------------ALRELNPEDPIKYDFALFRLGQ 227 (229)
T ss_pred hhHHHHHHHHH--------------HHHhcCCCCCcchhhhcccCCc
Confidence 11111111111 1223455666667777766663
No 29
>smart00525 FES FES domain. iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3)
Probab=95.96 E-value=0.0035 Score=45.48 Aligned_cols=22 Identities=36% Similarity=1.141 Sum_probs=20.1
Q ss_pred hcccCCCCCCCCCChhhchhhh
Q 002245 586 FCTKSKPNCNACPMRGECRHFA 607 (947)
Q Consensus 586 ICtarkPkC~~CPLrdlC~yy~ 607 (947)
+|++++|+|+.|||+..|++|.
T Consensus 1 vC~ar~P~C~~Cpl~~~C~~~~ 22 (26)
T smart00525 1 ICTARKPRCDECPLKDLCPAYX 22 (26)
T ss_pred CccCCCCCCCCCcCHHHhhhhh
Confidence 6999999999999999999754
No 30
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=91.11 E-value=0.15 Score=37.05 Aligned_cols=20 Identities=30% Similarity=0.338 Sum_probs=17.6
Q ss_pred HHHhCCCCcHhHHHHHHHHh
Q 002245 492 YLLSIRGLGLKSVECVRLLT 511 (947)
Q Consensus 492 eLlsLPGVG~KTAd~ILlfa 511 (947)
.|.++||||+|+|+.|+.+.
T Consensus 2 ~L~~i~GiG~k~A~~il~~~ 21 (26)
T smart00278 2 ELLKVPGIGPKTAEKILEAX 21 (26)
T ss_pred hhhhCCCCCHHHHHHHHHhc
Confidence 58899999999999998754
No 31
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=90.59 E-value=0.29 Score=42.64 Aligned_cols=40 Identities=28% Similarity=0.351 Sum_probs=28.4
Q ss_pred HHHHHHHhhCCCChhhhhcCCchHHHHHHHhCCCCcHhHHHHHHHH
Q 002245 465 FLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLL 510 (947)
Q Consensus 465 lA~~Lve~yGgiDLe~L~~vP~deareeLlsLPGVG~KTAd~ILlf 510 (947)
.|+.|.+.|+. ++.|...+ .++|.+++|||+++|+.|..|
T Consensus 15 ~ak~L~~~f~s--l~~l~~a~----~e~L~~i~gIG~~~A~si~~f 54 (64)
T PF12826_consen 15 TAKLLAKHFGS--LEALMNAS----VEELSAIPGIGPKIAQSIYEF 54 (64)
T ss_dssp HHHHHHHCCSC--HHHHCC------HHHHCTSTT--HHHHHHHHHH
T ss_pred HHHHHHHHcCC--HHHHHHcC----HHHHhccCCcCHHHHHHHHHH
Confidence 45667777774 67776543 668999999999999999876
No 32
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=88.01 E-value=1.7 Score=46.21 Aligned_cols=66 Identities=20% Similarity=0.233 Sum_probs=44.5
Q ss_pred cCCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHH------HHHHHHHHhhCCCChhhhhcCCchHHHHHHHhCCCCcH
Q 002245 428 RMDSLDYEALRCANVKEISEAIKERGMNNMLAERMK------DFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGL 501 (947)
Q Consensus 428 ~~~~pTpeaLa~A~~eELeelIR~lGfyn~KAk~Ik------~lA~~Lve~yGgiDLe~L~~vP~deareeLlsLPGVG~ 501 (947)
-++|.|.++. +-.+.+|.--|.--..|-.|. +++++|.. + | .+.|.++||||+
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 4678887764 334555555677766776666 44555543 1 2 568999999999
Q ss_pred hHHHHHHHHhcCC
Q 002245 502 KSVECVRLLTLHH 514 (947)
Q Consensus 502 KTAd~ILlfafgr 514 (947)
|||+-|.+---++
T Consensus 118 KtAeRIIlELkdK 130 (196)
T PRK13901 118 KMAGKIFLKLRGK 130 (196)
T ss_pred HHHHHHHHHHHHh
Confidence 9999888654444
No 33
>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=86.80 E-value=2.7 Score=36.95 Aligned_cols=58 Identities=12% Similarity=0.188 Sum_probs=38.9
Q ss_pred HHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHhCCCCcHhHHHHHHHH
Q 002245 443 KEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLL 510 (947)
Q Consensus 443 eELeelIR~lGfyn~KAk~Ik~lA~~Lve~yGgiDLe~L~~vP~deareeLlsLPGVG~KTAd~ILlf 510 (947)
++|.++..-.|=...|++.-..++..|.. ++. |-....+.|.+|||||.++|..|--|
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 45566666665445688888888888775 332 22222225999999999999988644
No 34
>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=84.70 E-value=1.3 Score=38.77 Aligned_cols=58 Identities=22% Similarity=0.318 Sum_probs=37.6
Q ss_pred HHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHhCCCCcHhHHHHHHHH
Q 002245 436 ALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLL 510 (947)
Q Consensus 436 aLa~A~~eELeelIR~lGfyn~KAk~Ik~lA~~Lve~yGgiDLe~L~~vP~deareeLlsLPGVG~KTAd~ILlf 510 (947)
+|-.|+.++|..++.++|. .+|+.|++.- ..+|++ .+ .++|..++|||.++|+-|+.+
T Consensus 9 nvNta~~~~L~~~ipgig~--~~a~~Il~~R----~~~g~~---------~s--~~dL~~v~gi~~~~~~~i~~~ 66 (69)
T TIGR00426 9 NINTATAEELQRAMNGVGL--KKAEAIVSYR----EEYGPF---------KT--VEDLKQVPGIGNSLVEKNLAV 66 (69)
T ss_pred ECcCCCHHHHHhHCCCCCH--HHHHHHHHHH----HHcCCc---------CC--HHHHHcCCCCCHHHHHHHHhh
Confidence 3445777888776555554 4555554321 124543 12 678999999999999998865
No 35
>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=84.65 E-value=2.8 Score=46.09 Aligned_cols=133 Identities=16% Similarity=0.124 Sum_probs=75.0
Q ss_pred HHHHHHHHhc----CCcHHHHHHHHHHHHHHHHhhCCCChhhhhc--CCchHHHHHHHhCCCCc--Hh-------HHHHH
Q 002245 443 KEISEAIKER----GMNNMLAERMKDFLNRLVREHGSIDLEWLRD--VPPDKAKDYLLSIRGLG--LK-------SVECV 507 (947)
Q Consensus 443 eELeelIR~l----Gfyn~KAk~Ik~lA~~Lve~yGgiDLe~L~~--vP~deareeLlsLPGVG--~K-------TAd~I 507 (947)
+++...+... -+.++|.++|.+++..+.. +.+..+.. -.-..+++.|..+=|-. .| ++...
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 4555555542 3567899999988776543 21221111 12234566666654443 23 34445
Q ss_pred HHHhcCC--c-----eeecchHHHHHHHHhCCCCCCCCHHHHHHHHHHhcCchHHHHHhhhhhhhcCChhhHHHHHHHHH
Q 002245 508 RLLTLHH--L-----AFPVDTNVGRIAVRLGWVPLQPLPESLQLHLLELYPVLESIQKYLWPRLCKLDQRTLYELHYQLI 580 (947)
Q Consensus 508 Llfafgr--p-----afPVDTHV~RVl~RLGlv~~k~tpeevEk~Le~llP~~e~Iqk~LW~rlc~ld~~~~~e~H~~LI 580 (947)
+..+||. + -||||.||.++..++|++.. .++. . . . .+......|..++....-.+.+++..||
T Consensus 153 ~r~~~g~~~~~p~~IpIPvD~Rva~~T~~sGi~~~--~~~~---~-~-~---~~~~v~~~W~~Va~~sgIpplhLDs~lW 222 (246)
T PF09171_consen 153 CRIAFGEFRPYPEEIPIPVDYRVAKLTKRSGIIEC--EREE---M-M-R---TREEVQKAWREVAKESGIPPLHLDSLLW 222 (246)
T ss_dssp HHHHCTS-----TTS-----HHHHHHHHCTTS-SS---HHH---H-H-C---TCCHHHHHHHHHHHHHT--HHHHHHHHH
T ss_pred HHHhcCCCCCCcccCCCCccHHHHHHHHHhccccc--cHHh---h-h-c---cHHHHHHHHHHHHhhcCCCchhhhhHHH
Confidence 5556564 2 68999999999999999764 2221 1 1 1 1223346798887767777899999999
Q ss_pred -HHhHhhccc
Q 002245 581 -TFGKVFCTK 589 (947)
Q Consensus 581 -~fGR~ICta 589 (947)
.+|+.....
T Consensus 223 ~l~G~~~~~~ 232 (246)
T PF09171_consen 223 PLLGRARDVK 232 (246)
T ss_dssp HHHCCHHCCT
T ss_pred Hhcccchhhh
Confidence 999988754
No 36
>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=83.59 E-value=3.4 Score=35.28 Aligned_cols=30 Identities=30% Similarity=0.317 Sum_probs=23.1
Q ss_pred ChhhhhcCCchHHHHHHHhCCCCcHhHHHHHHHH
Q 002245 477 DLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLL 510 (947)
Q Consensus 477 DLe~L~~vP~deareeLlsLPGVG~KTAd~ILlf 510 (947)
+++.|...+ .+.|.+++|||+++|+-|...
T Consensus 28 t~~~l~~a~----~~~L~~i~Gig~~~a~~i~~~ 57 (60)
T PF14520_consen 28 TLEDLANAD----PEELAEIPGIGEKTAEKIIEA 57 (60)
T ss_dssp SHHHHHTSH----HHHHHTSTTSSHHHHHHHHHH
T ss_pred cHHHHHcCC----HHHHhcCCCCCHHHHHHHHHH
Confidence 566676653 457999999999999988654
No 37
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=83.11 E-value=1.8 Score=43.53 Aligned_cols=53 Identities=19% Similarity=0.287 Sum_probs=38.9
Q ss_pred HHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHhCCCCcHhHHHHHHHH
Q 002245 436 ALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLL 510 (947)
Q Consensus 436 aLa~A~~eELeelIR~lGfyn~KAk~Ik~lA~~Lve~yGgiDLe~L~~vP~deareeLlsLPGVG~KTAd~ILlf 510 (947)
+|-.|+.+++..+ -|++-.+|+.|. ++|.+ .+ .++|+.+||||+++...+--+
T Consensus 54 diN~A~~~el~~l---pGigP~~A~~IV--------~nGpf---------~s--veDL~~V~GIgekqk~~l~k~ 106 (132)
T PRK02515 54 DLNNSSVRAFRQF---PGMYPTLAGKIV--------KNAPY---------DS--VEDVLNLPGLSERQKELLEAN 106 (132)
T ss_pred cCCccCHHHHHHC---CCCCHHHHHHHH--------HCCCC---------CC--HHHHHcCCCCCHHHHHHHHHh
Confidence 5667788887663 688888998887 25653 12 678999999999988776543
No 38
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=81.36 E-value=5.2 Score=42.10 Aligned_cols=70 Identities=20% Similarity=0.181 Sum_probs=41.2
Q ss_pred cCCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcC--CchHHHHHHHhCCCCcHhHHH
Q 002245 428 RMDSLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDV--PPDKAKDYLLSIRGLGLKSVE 505 (947)
Q Consensus 428 ~~~~pTpeaLa~A~~eELeelIR~lGfyn~KAk~Ik~lA~~Lve~yGgiDLe~L~~v--P~deareeLlsLPGVG~KTAd 505 (947)
-++|.|.++. +-.+.+|+--|.--..|-.|.. .++.+.|... ..| .+.|.++||||+|||+
T Consensus 60 LyGF~~~~Er-----~lF~~Li~VsGIGpK~Al~ILs----------~~~~~el~~aI~~~D--~~~L~~vpGIGkKtAe 122 (183)
T PRK14601 60 LYGFLDKDEQ-----KMFEMLLKVNGIGANTAMAVCS----------SLDVNSFYKALSLGD--ESVLKKVPGIGPKSAK 122 (183)
T ss_pred eeCCCCHHHH-----HHHHHHhccCCccHHHHHHHHc----------CCCHHHHHHHHHhCC--HHHHhhCCCCCHHHHH
Confidence 3677777663 3344455555666555544442 1222222211 123 6789999999999999
Q ss_pred HHHHHhcCC
Q 002245 506 CVRLLTLHH 514 (947)
Q Consensus 506 ~ILlfafgr 514 (947)
-|++---++
T Consensus 123 RIilELkdK 131 (183)
T PRK14601 123 RIIAELSDA 131 (183)
T ss_pred HHHHHHHHH
Confidence 888655554
No 39
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=80.77 E-value=5.6 Score=41.93 Aligned_cols=66 Identities=11% Similarity=0.062 Sum_probs=40.0
Q ss_pred cCCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHH------HHHHHHHhhCCCChhhhhcCCchHHHHHHHhCCCCcH
Q 002245 428 RMDSLDYEALRCANVKEISEAIKERGMNNMLAERMKD------FLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGL 501 (947)
Q Consensus 428 ~~~~pTpeaLa~A~~eELeelIR~lGfyn~KAk~Ik~------lA~~Lve~yGgiDLe~L~~vP~deareeLlsLPGVG~ 501 (947)
-++|.|.++. +-.+.+|.--|.--+.|-.|.. ++++|.. .| .+.|.++||||+
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 3677777653 3334444445666555555442 2333332 22 568999999999
Q ss_pred hHHHHHHHHhcCC
Q 002245 502 KSVECVRLLTLHH 514 (947)
Q Consensus 502 KTAd~ILlfafgr 514 (947)
|||+-|.+---++
T Consensus 119 KtAerIilELkdK 131 (188)
T PRK14606 119 KTAERIVMELKDE 131 (188)
T ss_pred HHHHHHHHHHHHh
Confidence 9999888654443
No 40
>PRK00076 recR recombination protein RecR; Reviewed
Probab=80.06 E-value=1.6 Score=46.39 Aligned_cols=27 Identities=26% Similarity=0.381 Sum_probs=21.9
Q ss_pred hHHHHHHHhCCCCcHhHHHHHHHHhcC
Q 002245 487 DKAKDYLLSIRGLGLKSVECVRLLTLH 513 (947)
Q Consensus 487 deareeLlsLPGVG~KTAd~ILlfafg 513 (947)
+++.+.|.+|||||+|||.-+..+.+.
T Consensus 7 ~~Li~~l~~LPGIG~KsA~Rla~~ll~ 33 (196)
T PRK00076 7 EKLIEALRKLPGIGPKSAQRLAFHLLQ 33 (196)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHHHc
Confidence 567889999999999999776665444
No 41
>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=79.81 E-value=4.2 Score=42.76 Aligned_cols=48 Identities=17% Similarity=0.319 Sum_probs=34.8
Q ss_pred CCCCCHHHHHcCCHHHHHHHHHhcCC--cHHHHHHHHHHHHHHHH---hhCCC
Q 002245 429 MDSLDYEALRCANVKEISEAIKERGM--NNMLAERMKDFLNRLVR---EHGSI 476 (947)
Q Consensus 429 ~~~pTpeaLa~A~~eELeelIR~lGf--yn~KAk~Ik~lA~~Lve---~yGgi 476 (947)
+..++|+.|+..++++|++++..-|+ .+.|.+.++.=|+.+++ +||++
T Consensus 55 F~~Fd~~~vA~~~e~~ie~l~~d~~iIRnr~KI~Avi~NA~~~l~i~~e~gsF 107 (179)
T PF03352_consen 55 FAGFDPEKVAKMDEEDIERLMQDPGIIRNRRKIRAVINNARAILKIQEEFGSF 107 (179)
T ss_dssp TGGGHHHHHHT--HHHHHHHTTSTTSS--HHHHHHHHHHHHHHHHHHHTTS-H
T ss_pred HHCCCHHHHHcCCHHHHHHHhcCcchhhhHHHHHHHHHHHHHHHHHHHhcCCH
Confidence 45789999999999999999999998 56677777776766653 55653
No 42
>PRK13844 recombination protein RecR; Provisional
Probab=79.78 E-value=1.7 Score=46.40 Aligned_cols=28 Identities=21% Similarity=0.222 Sum_probs=22.4
Q ss_pred chHHHHHHHhCCCCcHhHHHHHHHHhcC
Q 002245 486 PDKAKDYLLSIRGLGLKSVECVRLLTLH 513 (947)
Q Consensus 486 ~deareeLlsLPGVG~KTAd~ILlfafg 513 (947)
-+++.+.|.+|||||+|||.-+..+.+.
T Consensus 10 ~~~LI~~l~~LPGIG~KsA~Rla~~lL~ 37 (200)
T PRK13844 10 ISAVIESLRKLPTIGKKSSQRLALYLLD 37 (200)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHHHc
Confidence 3567889999999999999776666544
No 43
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=79.66 E-value=1.7 Score=46.17 Aligned_cols=28 Identities=25% Similarity=0.309 Sum_probs=22.1
Q ss_pred chHHHHHHHhCCCCcHhHHHHHHHHhcC
Q 002245 486 PDKAKDYLLSIRGLGLKSVECVRLLTLH 513 (947)
Q Consensus 486 ~deareeLlsLPGVG~KTAd~ILlfafg 513 (947)
-+++.+.|.+|||||+|||.-+..+.+.
T Consensus 6 ~~~Li~~l~~LPGIG~KsA~RlA~~ll~ 33 (195)
T TIGR00615 6 ISKLIESLKKLPGIGPKSAQRLAFHLLK 33 (195)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHHHc
Confidence 3567889999999999999766655444
No 44
>PRK00024 hypothetical protein; Reviewed
Probab=78.89 E-value=3.5 Score=44.37 Aligned_cols=61 Identities=23% Similarity=0.351 Sum_probs=44.5
Q ss_pred cCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHhCCCCcHhHHHHHH
Q 002245 439 CANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVR 508 (947)
Q Consensus 439 ~A~~eELeelIR~lGfyn~KAk~Ik~lA~~Lve~yGgiDLe~L~~vP~deareeLlsLPGVG~KTAd~IL 508 (947)
.++..||.++|=..|.. -+-.+.+|+.|.++||+ +..|...+ .++|.+++|||+..|..++
T Consensus 23 ~Lsd~ELLa~lL~~g~~---~~~~~~LA~~LL~~fgs--L~~l~~as----~~eL~~i~GIG~akA~~L~ 83 (224)
T PRK00024 23 ALSDAELLAILLRTGTK---GKSVLDLARELLQRFGS--LRGLLDAS----LEELQSIKGIGPAKAAQLK 83 (224)
T ss_pred cCCHHHHHHHHHcCCCC---CCCHHHHHHHHHHHcCC--HHHHHhCC----HHHHhhccCccHHHHHHHH
Confidence 44667777776556655 34566789999988875 67776665 4479999999999886654
No 45
>PRK10353 3-methyl-adenine DNA glycosylase I; Provisional
Probab=77.57 E-value=2.4 Score=44.87 Aligned_cols=49 Identities=4% Similarity=0.103 Sum_probs=36.6
Q ss_pred cCCCCCHHHHHcCCHHHHHHHHHhcCCcH--HHHHHHHHHHHHHH---HhhCCC
Q 002245 428 RMDSLDYEALRCANVKEISEAIKERGMNN--MLAERMKDFLNRLV---REHGSI 476 (947)
Q Consensus 428 ~~~~pTpeaLa~A~~eELeelIR~lGfyn--~KAk~Ik~lA~~Lv---e~yGgi 476 (947)
+++.++|+.++..++++|+.++..-|+-+ .|.+.++.=|+.++ +++|++
T Consensus 59 aF~~Fd~~~VA~~~e~die~Ll~d~~IIRnr~KI~Avi~NA~~~l~i~~e~gSf 112 (187)
T PRK10353 59 CFHQFDPVKVAAMQEEDVERLVQDAGIIRHRGKIQAIIGNARAYLQMEQNGEPF 112 (187)
T ss_pred HHcCCCHHHHhCCCHHHHHHHhcCchhHHhHHHHHHHHHHHHHHHHHHHhcCCH
Confidence 35678999999999999999999999854 45556766555554 345543
No 46
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=77.54 E-value=4.3 Score=43.67 Aligned_cols=61 Identities=23% Similarity=0.305 Sum_probs=44.7
Q ss_pred cCCHHHHHHHHHhcCCcHHHHH-HHHHHHHHHHHhh---CCCChhhhhcCCchHHHHHHHhCCCCcHhHHHHHH
Q 002245 439 CANVKEISEAIKERGMNNMLAE-RMKDFLNRLVREH---GSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVR 508 (947)
Q Consensus 439 ~A~~eELeelIR~lGfyn~KAk-~Ik~lA~~Lve~y---GgiDLe~L~~vP~deareeLlsLPGVG~KTAd~IL 508 (947)
.++..||.++|=..|..+ + ..+.+|+.|+++| |+ |..|...+. ++|.+++|||+..|..++
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--LGHLLSAPP----EELSSVPGIGEAKAIQLK 77 (218)
T ss_pred cCCHHHHHHHHHhCCCCC---CCCHHHHHHHHHHHhcccCC--HHHHHhCCH----HHHHhCcCCcHHHHHHHH
Confidence 446677777775666653 3 6678899999888 54 777777664 479999999997776554
No 47
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=77.42 E-value=7.3 Score=41.50 Aligned_cols=70 Identities=14% Similarity=0.090 Sum_probs=40.0
Q ss_pred cCCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhc--CCchHHHHHHHhCCCCcHhHHH
Q 002245 428 RMDSLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRD--VPPDKAKDYLLSIRGLGLKSVE 505 (947)
Q Consensus 428 ~~~~pTpeaLa~A~~eELeelIR~lGfyn~KAk~Ik~lA~~Lve~yGgiDLe~L~~--vP~deareeLlsLPGVG~KTAd 505 (947)
-++|.|.++. +-.+.+|.--|.--..|-.|... ++.+.|.. ...| .+.|.++||||+|||+
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 3567776653 33344444456665556555442 11222211 1123 5689999999999999
Q ss_pred HHHHHhcCC
Q 002245 506 CVRLLTLHH 514 (947)
Q Consensus 506 ~ILlfafgr 514 (947)
-|++---++
T Consensus 124 rIilELkdK 132 (203)
T PRK14602 124 HIFLELKYK 132 (203)
T ss_pred HHHHHHHHh
Confidence 888644443
No 48
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=76.81 E-value=8.2 Score=40.82 Aligned_cols=66 Identities=21% Similarity=0.244 Sum_probs=39.3
Q ss_pred cCCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhh-cC-CchHHHHHHHhCCCCcHhHHH
Q 002245 428 RMDSLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLR-DV-PPDKAKDYLLSIRGLGLKSVE 505 (947)
Q Consensus 428 ~~~~pTpeaLa~A~~eELeelIR~lGfyn~KAk~Ik~lA~~Lve~yGgiDLe~L~-~v-P~deareeLlsLPGVG~KTAd 505 (947)
-++|.+.++- +-.+.+|.--|.....|..|... ++.+.|. .+ ..| .+.|.++||||+|||+
T Consensus 60 LyGF~~~~Er-----~lF~~Li~V~GIGpK~Al~ILs~----------~~~~~l~~aI~~~D--~~~L~~vpGIGkKtAe 122 (194)
T PRK14605 60 LFGFATTEEL-----SLFETLIDVSGIGPKLGLAMLSA----------MNAEALASAIISGN--AELLSTIPGIGKKTAS 122 (194)
T ss_pred eeCCCCHHHH-----HHHHHHhCCCCCCHHHHHHHHHh----------CCHHHHHHHHHhCC--HHHHHhCCCCCHHHHH
Confidence 3677777653 33444555567766666555542 1222221 11 223 5679999999999999
Q ss_pred HHHHH
Q 002245 506 CVRLL 510 (947)
Q Consensus 506 ~ILlf 510 (947)
-|++-
T Consensus 123 rIilE 127 (194)
T PRK14605 123 RIVLE 127 (194)
T ss_pred HHHHH
Confidence 86643
No 49
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=76.64 E-value=4.2 Score=42.64 Aligned_cols=22 Identities=27% Similarity=0.345 Sum_probs=18.8
Q ss_pred HHHHHhCCCCcHhHHHHHHHHh
Q 002245 490 KDYLLSIRGLGLKSVECVRLLT 511 (947)
Q Consensus 490 reeLlsLPGVG~KTAd~ILlfa 511 (947)
.+.|.++||||+|+|+.|+..-
T Consensus 107 ~~~L~~v~Gig~k~A~~I~~~l 128 (192)
T PRK00116 107 VKALTKVPGIGKKTAERIVLEL 128 (192)
T ss_pred HHHHHhCCCCCHHHHHHHHHHH
Confidence 4579999999999999998653
No 50
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=76.33 E-value=2.3 Score=45.23 Aligned_cols=27 Identities=30% Similarity=0.395 Sum_probs=21.3
Q ss_pred hHHHHHHHhCCCCcHhHHHHHHHHhcC
Q 002245 487 DKAKDYLLSIRGLGLKSVECVRLLTLH 513 (947)
Q Consensus 487 deareeLlsLPGVG~KTAd~ILlfafg 513 (947)
+++++.|.+|||||+|+|.-+..+.+.
T Consensus 8 ~~LI~~l~kLPGvG~KsA~R~AfhLL~ 34 (198)
T COG0353 8 EKLIDALKKLPGVGPKSAQRLAFHLLQ 34 (198)
T ss_pred HHHHHHHhhCCCCChhHHHHHHHHHHc
Confidence 467889999999999999766555444
No 51
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=76.10 E-value=8 Score=41.02 Aligned_cols=70 Identities=16% Similarity=0.009 Sum_probs=40.3
Q ss_pred cCCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcC--CchHHHHHHHhCCCCcHhHHH
Q 002245 428 RMDSLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDV--PPDKAKDYLLSIRGLGLKSVE 505 (947)
Q Consensus 428 ~~~~pTpeaLa~A~~eELeelIR~lGfyn~KAk~Ik~lA~~Lve~yGgiDLe~L~~v--P~deareeLlsLPGVG~KTAd 505 (947)
-++|.|.++. +-...+|.--|.--+.|-.|... ++.+.|... ..| .+.|.++||||+|||+
T Consensus 60 LyGF~~~~Er-----~lF~~Li~V~GIGpK~Al~iLs~----------~~~~el~~aI~~~D--~~~L~kvpGIGkKtAe 122 (195)
T PRK14604 60 LYGFSTPAQR-----QLFELLIGVSGVGPKAALNLLSS----------GTPDELQLAIAGGD--VARLARVPGIGKKTAE 122 (195)
T ss_pred eeCCCCHHHH-----HHHHHHhCcCCcCHHHHHHHHcC----------CCHHHHHHHHHhCC--HHHHhhCCCCCHHHHH
Confidence 3567776653 33344454456665556555431 122222111 123 5689999999999999
Q ss_pred HHHHHhcCC
Q 002245 506 CVRLLTLHH 514 (947)
Q Consensus 506 ~ILlfafgr 514 (947)
-|++---++
T Consensus 123 rIilELk~K 131 (195)
T PRK14604 123 RIVLELKGK 131 (195)
T ss_pred HHHHHHHHH
Confidence 888654444
No 52
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=75.69 E-value=6.5 Score=41.44 Aligned_cols=69 Identities=20% Similarity=0.150 Sum_probs=39.5
Q ss_pred cCCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcC--CchHHHHHHHhCCCCcHhHHH
Q 002245 428 RMDSLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDV--PPDKAKDYLLSIRGLGLKSVE 505 (947)
Q Consensus 428 ~~~~pTpeaLa~A~~eELeelIR~lGfyn~KAk~Ik~lA~~Lve~yGgiDLe~L~~v--P~deareeLlsLPGVG~KTAd 505 (947)
-++|.|.++. +-.+.+|+--|.--..|-.|... ++.+.|... ..| .+.| ++||||+|||+
T Consensus 60 LyGF~~~~Er-----~lF~~LisV~GIGpK~Al~iLs~----------~~~~~l~~aI~~~D--~~~L-~vpGIGkKtAe 121 (186)
T PRK14600 60 LYGFLNREEQ-----DCLRMLVKVSGVNYKTAMSILSK----------LTPEQLFSAIVNED--KAAL-KVNGIGEKLIN 121 (186)
T ss_pred eeCCCCHHHH-----HHHHHHhCcCCcCHHHHHHHHcc----------CCHHHHHHHHHcCC--Hhhe-ECCCCcHHHHH
Confidence 3677777663 33444555556665556555432 122222111 122 4678 99999999999
Q ss_pred HHHHHhcCC
Q 002245 506 CVRLLTLHH 514 (947)
Q Consensus 506 ~ILlfafgr 514 (947)
-|++---++
T Consensus 122 rIilELk~K 130 (186)
T PRK14600 122 RIITELQYK 130 (186)
T ss_pred HHHHHHHHH
Confidence 988654443
No 53
>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=75.17 E-value=2.6 Score=35.94 Aligned_cols=27 Identities=37% Similarity=0.391 Sum_probs=22.5
Q ss_pred HHHHHHhCCCCcHhHHHHHHHHhcCCc
Q 002245 489 AKDYLLSIRGLGLKSVECVRLLTLHHL 515 (947)
Q Consensus 489 areeLlsLPGVG~KTAd~ILlfafgrp 515 (947)
+.+.|.++||||+++|..+...+++-.
T Consensus 3 ~~~~L~~I~Gig~~~a~~L~~~G~~t~ 29 (60)
T PF14520_consen 3 VFDDLLSIPGIGPKRAEKLYEAGIKTL 29 (60)
T ss_dssp HHHHHHTSTTCHHHHHHHHHHTTCSSH
T ss_pred HHHhhccCCCCCHHHHHHHHhcCCCcH
Confidence 467899999999999998887766643
No 54
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=74.41 E-value=9.3 Score=40.57 Aligned_cols=25 Identities=28% Similarity=0.244 Sum_probs=20.0
Q ss_pred HHHHHhCCCCcHhHHHHHHHHhcCC
Q 002245 490 KDYLLSIRGLGLKSVECVRLLTLHH 514 (947)
Q Consensus 490 reeLlsLPGVG~KTAd~ILlfafgr 514 (947)
.+.|.++||||+|||+-|++---++
T Consensus 106 ~~~L~kvpGIGkKtAerIilELkdK 130 (197)
T PRK14603 106 ARLLTSASGVGKKLAERIALELKGK 130 (197)
T ss_pred HHHHhhCCCCCHHHHHHHHHHHHHH
Confidence 5689999999999999887543333
No 55
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=72.42 E-value=5.2 Score=40.70 Aligned_cols=56 Identities=25% Similarity=0.403 Sum_probs=38.6
Q ss_pred HHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHhCCCCcHhHHHHHHHH
Q 002245 437 LRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLL 510 (947)
Q Consensus 437 La~A~~eELeelIR~lGfyn~KAk~Ik~lA~~Lve~yGgiDLe~L~~vP~deareeLlsLPGVG~KTAd~ILlf 510 (947)
|-.|+.++| +.|.++|- .||+.|++ ..+++|.| .+ .+.|...+|||++|.+-+..+
T Consensus 91 iNtAs~eeL-~~lpgIG~--~kA~aIi~----yRe~~G~f---------~s--v~dL~~v~GiG~~~~ekl~~~ 146 (149)
T COG1555 91 INTASAEEL-QALPGIGP--KKAQAIID----YREENGPF---------KS--VDDLAKVKGIGPKTLEKLKDY 146 (149)
T ss_pred ccccCHHHH-HHCCCCCH--HHHHHHHH----HHHHcCCC---------Cc--HHHHHhccCCCHHHHHHHHhh
Confidence 446778888 55665665 58877764 34556653 12 678999999999998876543
No 56
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=71.86 E-value=2.8 Score=44.79 Aligned_cols=70 Identities=23% Similarity=0.202 Sum_probs=39.7
Q ss_pred CCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHhCCCCcHhHHHHHH
Q 002245 429 MDSLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVR 508 (947)
Q Consensus 429 ~~~pTpeaLa~A~~eELeelIR~lGfyn~KAk~Ik~lA~~Lve~yGgiDLe~L~~vP~deareeLlsLPGVG~KTAd~IL 508 (947)
++|.|.++- +=...+|+--|.--+-|- .|+. .+|++.|...=..+=.+.|.++||||.|||+-|+
T Consensus 61 yGF~~~~ER-----~lF~~LisVnGIGpK~AL-------aiLs---~~~~~~l~~aI~~~d~~~L~k~PGIGkKtAeriv 125 (201)
T COG0632 61 YGFLTEEER-----ELFRLLISVNGIGPKLAL-------AILS---NLDPEELAQAIANEDVKALSKIPGIGKKTAERIV 125 (201)
T ss_pred cCCCCHHHH-----HHHHHHHccCCccHHHHH-------HHHc---CCCHHHHHHHHHhcChHhhhcCCCCCHHHHHHHH
Confidence 456665542 334555665666643332 2332 2445544322111116789999999999999887
Q ss_pred HHhcC
Q 002245 509 LLTLH 513 (947)
Q Consensus 509 lfafg 513 (947)
+---|
T Consensus 126 leLk~ 130 (201)
T COG0632 126 LELKG 130 (201)
T ss_pred HHHhh
Confidence 74433
No 57
>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=71.64 E-value=4.4 Score=42.64 Aligned_cols=44 Identities=7% Similarity=0.102 Sum_probs=34.8
Q ss_pred cCCCCCHHHHHcCCHHHHHHHHHhcCCcHHHH--HHHHHHHHHHHH
Q 002245 428 RMDSLDYEALRCANVKEISEAIKERGMNNMLA--ERMKDFLNRLVR 471 (947)
Q Consensus 428 ~~~~pTpeaLa~A~~eELeelIR~lGfyn~KA--k~Ik~lA~~Lve 471 (947)
++..++|+.++..++++|+.++..-|.-+.|+ +.++.=|+.+.+
T Consensus 58 aF~~Fd~~~VA~~~e~~ie~L~~d~~IIRnr~KI~Avi~NA~~~l~ 103 (179)
T TIGR00624 58 AFSGFDIVKVARMTDADVERLLQDDGIIRNRGKIEATIANARAALQ 103 (179)
T ss_pred HHcCCCHHHHhCCCHHHHHHHhcCccchhhHHHHHHHHHHHHHHHH
Confidence 35678999999999999999999999866554 446666666664
No 58
>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=71.26 E-value=6.2 Score=41.61 Aligned_cols=68 Identities=22% Similarity=0.171 Sum_probs=42.2
Q ss_pred cCCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhc-C-CchHHHHHHHhCCCCcHhHHH
Q 002245 428 RMDSLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRD-V-PPDKAKDYLLSIRGLGLKSVE 505 (947)
Q Consensus 428 ~~~~pTpeaLa~A~~eELeelIR~lGfyn~KAk~Ik~lA~~Lve~yGgiDLe~L~~-v-P~deareeLlsLPGVG~KTAd 505 (947)
-++|.|.++. +-...+|+--|.-..+|..|... ++.+.|.. + ..| .+.|.++||||+|||+
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 4677777763 34555666668877777666332 22322221 1 122 4579999999999999
Q ss_pred HHHHHhc
Q 002245 506 CVRLLTL 512 (947)
Q Consensus 506 ~ILlfaf 512 (947)
-|++---
T Consensus 122 rIileLk 128 (191)
T TIGR00084 122 RLLLELK 128 (191)
T ss_pred HHHHHHH
Confidence 9985433
No 59
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=70.24 E-value=3.9 Score=35.66 Aligned_cols=53 Identities=19% Similarity=0.376 Sum_probs=30.4
Q ss_pred HcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHhCCCCcHhHHHHHH
Q 002245 438 RCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVR 508 (947)
Q Consensus 438 a~A~~eELeelIR~lGfyn~KAk~Ik~lA~~Lve~yGgiDLe~L~~vP~deareeLlsLPGVG~KTAd~IL 508 (947)
-.|+.++|..+ -|+....|+.|.+. .+.+|+| .+ .++|..++|||+++.+-+.
T Consensus 9 N~as~~eL~~l---pgi~~~~A~~Iv~~----R~~~G~f---------~s--~~dL~~v~gi~~~~~~~l~ 61 (65)
T PF12836_consen 9 NTASAEELQAL---PGIGPKQAKAIVEY----REKNGPF---------KS--LEDLKEVPGIGPKTYEKLK 61 (65)
T ss_dssp TTS-HHHHHTS---TT--HHHHHHHHHH----HHHH-S----------SS--GGGGGGSTT--HHHHHHHC
T ss_pred ccCCHHHHHHc---CCCCHHHHHHHHHH----HHhCcCC---------CC--HHHHhhCCCCCHHHHHHHH
Confidence 35666776542 38887888888753 3344664 11 5579999999999987663
No 60
>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=69.93 E-value=19 Score=44.66 Aligned_cols=62 Identities=15% Similarity=0.223 Sum_probs=36.6
Q ss_pred CCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHhCCCCcHhHHHHHHH
Q 002245 432 LDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRL 509 (947)
Q Consensus 432 pTpeaLa~A~~eELeelIR~lGfyn~KAk~Ik~lA~~Lve~yGgiDLe~L~~vP~deareeLlsLPGVG~KTAd~ILl 509 (947)
-++.+|..+..++|.++ -||...+|.+|++..+.-.. .+-++.. ..+.|||||+++|..++.
T Consensus 455 ~~~~Dl~~L~~~~L~~L---~GfG~Ksa~nIl~~Ie~sk~------------~~l~r~L-~aLgIpgVG~~~ak~L~~ 516 (652)
T TIGR00575 455 RSVADLYALKKEDLLEL---EGFGEKSAQNLLNAIEKSKE------------KPLARLL-FALGIRHVGEVTAKNLAK 516 (652)
T ss_pred CCHHHHHhcCHHHHhhc---cCccHHHHHHHHHHHHHhcc------------CcHHHHH-hhccCCCcCHHHHHHHHH
Confidence 38888988888887653 47777777777765553321 1111111 233566777766665543
No 61
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=69.59 E-value=16 Score=45.28 Aligned_cols=33 Identities=15% Similarity=0.174 Sum_probs=22.4
Q ss_pred CCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHH
Q 002245 432 LDYEALRCANVKEISEAIKERGMNNMLAERMKDFLN 467 (947)
Q Consensus 432 pTpeaLa~A~~eELeelIR~lGfyn~KAk~Ik~lA~ 467 (947)
-++.+|..+..++|..+ -||...++.+|++..+
T Consensus 468 ~~i~DL~~L~~~~L~~l---~gfG~Ksa~~ll~~Ie 500 (665)
T PRK07956 468 HDPADLFKLTAEDLLGL---EGFGEKSAQNLLDAIE 500 (665)
T ss_pred CCHHHHHhcCHHHHhcC---cCcchHHHHHHHHHHH
Confidence 48888888887776553 3777667776655444
No 62
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=68.21 E-value=22 Score=44.35 Aligned_cols=21 Identities=29% Similarity=0.286 Sum_probs=15.8
Q ss_pred HHHHHhCCCCcHhHHHHHHHH
Q 002245 490 KDYLLSIRGLGLKSVECVRLL 510 (947)
Q Consensus 490 reeLlsLPGVG~KTAd~ILlf 510 (947)
.++|++++|||+++|..|..|
T Consensus 540 ~e~l~~i~giG~~~a~si~~f 560 (669)
T PRK14350 540 LSKLLKIKGIGEKIALNIIEA 560 (669)
T ss_pred HHHHhhCCCccHHHHHHHHHH
Confidence 456778888888888877766
No 63
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=67.65 E-value=19 Score=35.39 Aligned_cols=60 Identities=15% Similarity=0.201 Sum_probs=39.6
Q ss_pred CCCCHHHHHcCCHHHHHH--HHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHhCCCCcHhHHHHH
Q 002245 430 DSLDYEALRCANVKEISE--AIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECV 507 (947)
Q Consensus 430 ~~pTpeaLa~A~~eELee--lIR~lGfyn~KAk~Ik~lA~~Lve~yGgiDLe~L~~vP~deareeLlsLPGVG~KTAd~I 507 (947)
+-.|+++|+.++.+.+.. +.+..|.. +++|++.. .+..|..++|||+..|..+
T Consensus 15 GI~t~~~Ll~~~~~~~~r~~La~~~~i~---~~~l~~w~----------------------~~AdL~ri~gi~~~~a~LL 69 (122)
T PF14229_consen 15 GIKTTGDLLEAGDTPLGRKALAKKLGIS---ERNLLKWV----------------------NQADLMRIPGIGPQYAELL 69 (122)
T ss_pred CCCcHHHHHHcCCCHHHHHHHHHhcCCC---HHHHHHHH----------------------hHHHhhhcCCCCHHHHHHH
Confidence 345888888888777765 55555554 22332211 1556889999999999887
Q ss_pred HHHhcCC
Q 002245 508 RLLTLHH 514 (947)
Q Consensus 508 Llfafgr 514 (947)
+.-++.-
T Consensus 70 ~~AGv~T 76 (122)
T PF14229_consen 70 EHAGVDT 76 (122)
T ss_pred HHhCcCc
Confidence 7666553
No 64
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=66.60 E-value=5 Score=42.13 Aligned_cols=24 Identities=25% Similarity=0.238 Sum_probs=18.7
Q ss_pred HHHHHhCCCCcHhHHHHHHHHhcCC
Q 002245 490 KDYLLSIRGLGLKSVECVRLLTLHH 514 (947)
Q Consensus 490 reeLlsLPGVG~KTAd~ILlfafgr 514 (947)
...|+.+||||+|||..||.. ||-
T Consensus 72 f~~L~~i~GIGpk~A~~il~~-fg~ 95 (192)
T PRK00116 72 FRLLISVSGVGPKLALAILSG-LSP 95 (192)
T ss_pred HHHHhcCCCCCHHHHHHHHHh-CCH
Confidence 457889999999999988643 443
No 65
>PRK14973 DNA topoisomerase I; Provisional
Probab=66.58 E-value=8.3 Score=49.55 Aligned_cols=97 Identities=16% Similarity=0.115 Sum_probs=63.0
Q ss_pred CCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHH-HHHHhhCCCChhhhhcCCchHHHHHHHhCCCCcHhHHHHH
Q 002245 429 MDSLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLN-RLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECV 507 (947)
Q Consensus 429 ~~~pTpeaLa~A~~eELeelIR~lGfyn~KAk~Ik~lA~-~Lve~yGgiDLe~L~~vP~deareeLlsLPGVG~KTAd~I 507 (947)
.||-++++++.|+.++|..+ -|+.--.+..+...+. .+.. -|.+.+..-..+..+.+|++++|||++|++-.
T Consensus 821 ~G~~~~~d~~~a~p~~La~~---~g~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~el~~vkg~ge~t~~~l 893 (936)
T PRK14973 821 AGFDTPEDFCSVHPAYLALK---TGISPETICRHAKLVCEKLGR----PVPEKISKAAFERGRAELLSVPGLGETTLEKL 893 (936)
T ss_pred hcCCCHHHHHhcCHHHHhcC---CCCChhhHHHHHHHHHHHhcC----CCchhhhhhhhcccchhhhhccCCCHHHHHHH
Confidence 46789999999999999764 7998666666655444 4443 12233323333334566999999999999655
Q ss_pred HHHhcCCc-eeecchHHHHHHHHhCCC
Q 002245 508 RLLTLHHL-AFPVDTNVGRIAVRLGWV 533 (947)
Q Consensus 508 Llfafgrp-afPVDTHV~RVl~RLGlv 533 (947)
-.-+.-.+ .+..+ -..|++.+.|+-
T Consensus 894 ~~ag~~~~e~l~~~-d~~~la~~~~i~ 919 (936)
T PRK14973 894 YLAGVYDGDLLVSA-DPKKLAKVTGID 919 (936)
T ss_pred HHcCCCCHHHhccC-CHHHHhhhcCCC
Confidence 44444343 33333 567777777763
No 66
>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=65.76 E-value=8.5 Score=37.71 Aligned_cols=59 Identities=22% Similarity=0.401 Sum_probs=39.4
Q ss_pred HHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHhCCCCcHhHHHHHHHH
Q 002245 434 YEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLL 510 (947)
Q Consensus 434 peaLa~A~~eELeelIR~lGfyn~KAk~Ik~lA~~Lve~yGgiDLe~L~~vP~deareeLlsLPGVG~KTAd~ILlf 510 (947)
+-+|-.|+.++|.. | -|....+|+.|++.-. .+|.+ .+ .++|..++|||+|+++-|.-+
T Consensus 59 ~iniNtA~~~eL~~-l--pGIG~~~A~~Ii~~R~----~~g~f---------~s--~eeL~~V~GIg~k~~~~i~~~ 117 (120)
T TIGR01259 59 AVNINAASLEELQA-L--PGIGPAKAKAIIEYRE----ENGAF---------KS--VDDLTKVSGIGEKSLEKLKDY 117 (120)
T ss_pred CEeCCcCCHHHHhc-C--CCCCHHHHHHHHHHHH----hcCCc---------CC--HHHHHcCCCCCHHHHHHHHhc
Confidence 34566677777765 3 3555567877765332 24442 12 678999999999999988655
No 67
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=65.07 E-value=9.9 Score=35.42 Aligned_cols=57 Identities=28% Similarity=0.540 Sum_probs=36.2
Q ss_pred CHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHh-CCCCcHhHHHHHHH
Q 002245 441 NVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLS-IRGLGLKSVECVRL 509 (947)
Q Consensus 441 ~~eELeelIR~lGfyn~KAk~Ik~lA~~Lve~yGgiDLe~L~~vP~deareeLls-LPGVG~KTAd~ILl 509 (947)
...++...+...|+....|. +|.+.||.-.++.|++-|.. |+. ++|||-++||-|..
T Consensus 7 ~~~~~~~~L~~~gl~~~~a~-------kl~~~yg~~ai~~l~~nPY~-----L~~~i~gi~F~~aD~iA~ 64 (94)
T PF14490_consen 7 GLRELMAFLQEYGLSPKLAM-------KLYKKYGDDAIEILKENPYR-----LIEDIDGIGFKTADKIAL 64 (94)
T ss_dssp --HHHHHHHHHTT--HHHHH-------HHHHHH-TTHHHHHHH-STC-----CCB-SSSSBHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCCHHHHH-------HHHHHHhHHHHHHHHHChHH-----HHHHccCCCHHHHHHHHH
Confidence 34677778888999865554 44455676556667766765 555 89999999988743
No 68
>PF02371 Transposase_20: Transposase IS116/IS110/IS902 family; InterPro: IPR003346 Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This family includes transposases for IS116, IS110 and IS902. It is often found with the transposase IS111A/IS1328/IS1533 family (see IPR002525 from INTERPRO) [, ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=60.96 E-value=6 Score=36.23 Aligned_cols=42 Identities=21% Similarity=0.239 Sum_probs=30.0
Q ss_pred HHHHhCCCCcHhHHHHHHHHhcCCceeecchHHHHHHHHhCCCCC
Q 002245 491 DYLLSIRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPL 535 (947)
Q Consensus 491 eeLlsLPGVG~KTAd~ILlfafgrpafPVDTHV~RVl~RLGlv~~ 535 (947)
+.|+++||||+-||..++....+...|. +...+..-+|+.+.
T Consensus 2 ~~l~sipGig~~~a~~llaeigd~~rF~---~~~~l~~~~Gl~P~ 43 (87)
T PF02371_consen 2 ELLTSIPGIGPITAATLLAEIGDISRFK---SAKQLASYAGLAPR 43 (87)
T ss_pred chhcCCCCccHHHHHHHHHHHcCchhcc---cchhhhhccccccc
Confidence 3589999999999999998874433554 33445555688774
No 69
>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=60.58 E-value=8.1 Score=36.85 Aligned_cols=26 Identities=27% Similarity=0.364 Sum_probs=20.5
Q ss_pred HHHHHHhCCCCcHhHHHHHHHHhcCC
Q 002245 489 AKDYLLSIRGLGLKSVECVRLLTLHH 514 (947)
Q Consensus 489 areeLlsLPGVG~KTAd~ILlfafgr 514 (947)
....|..|||||+.+|.-+..+++..
T Consensus 10 ~~~~L~~iP~IG~a~a~DL~~LGi~s 35 (93)
T PF11731_consen 10 GLSDLTDIPNIGKATAEDLRLLGIRS 35 (93)
T ss_pred HHHHHhcCCCccHHHHHHHHHcCCCC
Confidence 46689999999999998776655544
No 70
>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=58.79 E-value=17 Score=33.82 Aligned_cols=64 Identities=14% Similarity=0.240 Sum_probs=44.6
Q ss_pred cceeceeeeccCCCCCCcccchhhhccCCceEEEeccChhhhcccCCHHHHHHhhhccceEeecccccccCCccc
Q 002245 853 YFQVNEVFADHDSSLNPIDVPREWLWNLPRRMVYFGTSVSSIFKGLSTEGIQFCFWKGFVCVRGFDQKSRAPRPL 927 (947)
Q Consensus 853 YFQvNEVFaDh~Ss~~Pi~vpr~~iw~L~rr~vyfGtsv~sI~kg~s~~~iq~cf~~g~vCvR~fdr~tr~P~pl 927 (947)
+|..||||+=.....+||. .| +.++.|.+-...-.... ....-...-|+|=++||+.++.-|+|
T Consensus 59 ~~~~~Elf~s~~~~~i~v~----~I--~gkc~V~~~~~~~~~~~-----~~~~~~~~~f~~r~~yd~~~~~fk~~ 122 (123)
T cd04370 59 FALRRELFLSDHLDEIPVE----SI--IGKCKVLFVSEFEGLKQ-----RPNKIDTDDFFCRLAYDPTTKEFKAL 122 (123)
T ss_pred ccccceeEEecCccccCHH----Hh--ccccEEEechHhhcccc-----ccccCCCCeEEEEEEECcCcceEEeC
Confidence 7999999998888777765 33 34778887665443321 00112456899999999998877765
No 71
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=58.27 E-value=19 Score=39.28 Aligned_cols=89 Identities=26% Similarity=0.336 Sum_probs=57.8
Q ss_pred cCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHhCCCCcHhHHHHHH-HHhcCCcee
Q 002245 439 CANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVR-LLTLHHLAF 517 (947)
Q Consensus 439 ~A~~eELeelIR~lGfyn~KAk~Ik~lA~~Lve~yGgiDLe~L~~vP~deareeLlsLPGVG~KTAd~IL-lfafgrpaf 517 (947)
.++..||.+++=..|-. -+..+.+|+.|..+||+ |..|...+ .++|.+++|||.--|--+. +.-+
T Consensus 23 ~Lsd~ELLailLrtG~~---~~~~~~la~~lL~~fg~--L~~l~~a~----~~el~~v~GiG~aka~~l~a~~El----- 88 (224)
T COG2003 23 ALSDAELLAILLRTGTK---GESVLDLAKELLQEFGS--LAELLKAS----VEELSSVKGIGLAKAIQIKAAIEL----- 88 (224)
T ss_pred hcchHHHHHHHHhcCCC---CCCHHHHHHHHHHHccc--HHHHHhCC----HHHHhhCCCccHHHHHHHHHHHHH-----
Confidence 34557777777666764 55778999999999987 56666655 5589999999976554332 2222
Q ss_pred ecchHHHHHHHHh---CCCCCCCCHHHHHHHHHH
Q 002245 518 PVDTNVGRIAVRL---GWVPLQPLPESLQLHLLE 548 (947)
Q Consensus 518 PVDTHV~RVl~RL---Glv~~k~tpeevEk~Le~ 548 (947)
..|++.+- +.+- .+|+.+.+.+..
T Consensus 89 -----~~R~~~~~~~~~~~i--~sp~~~~~~l~~ 115 (224)
T COG2003 89 -----GKRILAERLREGVVI--TSPEAVAEYLRA 115 (224)
T ss_pred -----HHHHHHHHhccCCcc--CCHHHHHHHHHH
Confidence 23444432 2222 467777776654
No 72
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=57.83 E-value=9.6 Score=33.22 Aligned_cols=21 Identities=19% Similarity=0.354 Sum_probs=17.2
Q ss_pred HHHHHhCCCCcHhHHHHHHHH
Q 002245 490 KDYLLSIRGLGLKSVECVRLL 510 (947)
Q Consensus 490 reeLlsLPGVG~KTAd~ILlf 510 (947)
.++|.+|||||++.|..|+.+
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 678999999999999999876
No 73
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=57.42 E-value=41 Score=42.18 Aligned_cols=60 Identities=22% Similarity=0.263 Sum_probs=34.9
Q ss_pred CCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHH--HhCCCCcHhHHHHHHH
Q 002245 432 LDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYL--LSIRGLGLKSVECVRL 509 (947)
Q Consensus 432 pTpeaLa~A~~eELeelIR~lGfyn~KAk~Ik~lA~~Lve~yGgiDLe~L~~vP~deareeL--lsLPGVG~KTAd~ILl 509 (947)
-++.+|..+..++|..+ -||...+|.+|++..+.-. ++|-. ..| +.|||||.++|..++.
T Consensus 485 ~~~~Dl~~L~~~~L~~l---~g~g~Ksa~~Ll~~Ie~sk------------~~~l~---r~l~ALgIpgIG~~~ak~L~~ 546 (689)
T PRK14351 485 ESLADLYDLTVADLAEL---EGWGETSAENLLAELEASR------------EPPLA---DFLVALGIPEVGPTTARNLAR 546 (689)
T ss_pred CCHHHHHHcCHHHHhcC---cCcchhHHHHHHHHHHHHc------------cCCHH---HHHHHcCCCCcCHHHHHHHHH
Confidence 37888888888776543 4777677776655433211 12222 222 2367777777776553
No 74
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair]
Probab=56.78 E-value=33 Score=37.92 Aligned_cols=94 Identities=15% Similarity=0.123 Sum_probs=64.1
Q ss_pred CCCcHHHHHHHHHhhhhhcCCCccccCCCCchhhhhcccccccchhhhhhcccccccccccccccChHHHHHHHHhccCc
Q 002245 342 GSMLAEKTRNLGDDISVANKLSDNKLIEPNSVEQVLSAHKVYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGK 421 (947)
Q Consensus 342 ~~~~~~~~~~i~~rl~~~~~~p~~~l~~~~~~~~~~~~~~~~~lLia~iLSaq~~d~~vnk~qnT~W~~L~k~l~~~glk 421 (947)
..-+-|++..+.+-+.+.-..|.+..-. ... ..+.+.++..=++..+|||.++. .| +.
T Consensus 156 lA~s~EeaaryIE~~k~~ek~p~dli~~------~~~-----~d~ls~~~~~Lt~i~~VnKtda~---~L---L~----- 213 (254)
T KOG2841|consen 156 LAWSMEEAARYIETYKEYEKKPIDLIME------RKD-----RDLLSSLLGFLTTIPGVNKTDAQ---LL---LQ----- 213 (254)
T ss_pred eeccHHHHHHHHHHHHHhhcCCchhhhh------ccc-----ccHHHHHHHHHHhCCCCCcccHH---HH---HH-----
Confidence 4456788888888877774444422111 111 12344677777888889985222 22 22
Q ss_pred cccccCcCCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHH
Q 002245 422 QERSRDRMDSLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNR 468 (947)
Q Consensus 422 ~er~~~~~~~pTpeaLa~A~~eELeelIR~lGfyn~KAk~Ik~lA~~ 468 (947)
.|.+.+.|..|+.+||+.+ -|+..+||++|+++...
T Consensus 214 --------~FgsLq~~~~AS~~ele~~---~G~G~~kak~l~~~l~~ 249 (254)
T KOG2841|consen 214 --------KFGSLQQISNASEGELEQC---PGLGPAKAKRLHKFLHQ 249 (254)
T ss_pred --------hcccHHHHHhcCHhHHHhC---cCcCHHHHHHHHHHHhc
Confidence 3889999999999999875 78888999999987754
No 75
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=55.80 E-value=9.1 Score=38.99 Aligned_cols=22 Identities=18% Similarity=0.317 Sum_probs=19.3
Q ss_pred HHHHHhCCCCcHhHHHHHHHHh
Q 002245 490 KDYLLSIRGLGLKSVECVRLLT 511 (947)
Q Consensus 490 reeLlsLPGVG~KTAd~ILlfa 511 (947)
-++|..|||||+|.|..|..+-
T Consensus 96 ~eeL~~lpgIG~~kA~aIi~yR 117 (149)
T COG1555 96 AEELQALPGIGPKKAQAIIDYR 117 (149)
T ss_pred HHHHHHCCCCCHHHHHHHHHHH
Confidence 5678999999999999998773
No 76
>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=55.59 E-value=9.2 Score=40.36 Aligned_cols=22 Identities=18% Similarity=0.232 Sum_probs=18.9
Q ss_pred HHHHHHHhCCCCcHhHHHHHHH
Q 002245 488 KAKDYLLSIRGLGLKSVECVRL 509 (947)
Q Consensus 488 eareeLlsLPGVG~KTAd~ILl 509 (947)
++...|++++|||||+|-.||.
T Consensus 69 ~lF~~L~~V~GIGpK~Al~iL~ 90 (191)
T TIGR00084 69 ELFKELIKVNGVGPKLALAILS 90 (191)
T ss_pred HHHHHHhCCCCCCHHHHHHHHh
Confidence 4677899999999999988865
No 77
>PRK08609 hypothetical protein; Provisional
Probab=54.83 E-value=33 Score=41.81 Aligned_cols=49 Identities=29% Similarity=0.443 Sum_probs=30.0
Q ss_pred cCCcHHHHHHHHHHHHHHHHhhCCC-Chhhhh-cCCchHHHHHHHhCCCCcHhHHHHH
Q 002245 452 RGMNNMLAERMKDFLNRLVREHGSI-DLEWLR-DVPPDKAKDYLLSIRGLGLKSVECV 507 (947)
Q Consensus 452 lGfyn~KAk~Ik~lA~~Lve~yGgi-DLe~L~-~vP~deareeLlsLPGVG~KTAd~I 507 (947)
-|....-|+.|.++.+ -|.+ -|+.|+ ++|.. ..+|+++||||+|||..+
T Consensus 54 pgIG~~ia~kI~Eil~-----tG~~~~le~l~~~~p~~--~~~l~~i~GiGpk~a~~l 104 (570)
T PRK08609 54 KGIGKGTAEVIQEYRE-----TGESSVLQELKKEVPEG--LLPLLKLPGLGGKKIAKL 104 (570)
T ss_pred CCcCHHHHHHHHHHHH-----hCChHHHHHHHhhCcHH--HHHHhcCCCCCHHHHHHH
Confidence 3555555666655443 1332 244554 45544 558999999999999554
No 78
>PF05559 DUF763: Protein of unknown function (DUF763); InterPro: IPR008482 This family consists of several uncharacterised bacterial and archaeal proteins of unknown function.
Probab=54.80 E-value=30 Score=39.58 Aligned_cols=24 Identities=33% Similarity=0.639 Sum_probs=20.3
Q ss_pred CchHHHHHHHhCCCCcHhHHHHHHHH
Q 002245 485 PPDKAKDYLLSIRGLGLKSVECVRLL 510 (947)
Q Consensus 485 P~deareeLlsLPGVG~KTAd~ILlf 510 (947)
|.+ .++|+.++|||++|..++.+.
T Consensus 265 p~~--feeLL~~~GvGp~TlRALaLv 288 (319)
T PF05559_consen 265 PSD--FEELLLIKGVGPSTLRALALV 288 (319)
T ss_pred ccC--HHHHHhcCCCCHHHHHHHHHH
Confidence 556 889999999999999886654
No 79
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=53.54 E-value=11 Score=39.98 Aligned_cols=23 Identities=17% Similarity=0.174 Sum_probs=20.0
Q ss_pred HHHHHHHhCCCCcHhHHHHHHHH
Q 002245 488 KAKDYLLSIRGLGLKSVECVRLL 510 (947)
Q Consensus 488 eareeLlsLPGVG~KTAd~ILlf 510 (947)
++.+.|++++|||+|+|-.||..
T Consensus 70 ~lF~~Li~V~GIGpK~Al~ILs~ 92 (194)
T PRK14605 70 SLFETLIDVSGIGPKLGLAMLSA 92 (194)
T ss_pred HHHHHHhCCCCCCHHHHHHHHHh
Confidence 45778999999999999999874
No 80
>PRK07945 hypothetical protein; Provisional
Probab=53.00 E-value=21 Score=40.65 Aligned_cols=61 Identities=10% Similarity=0.103 Sum_probs=39.8
Q ss_pred HHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHhCCCCcHhHHHHHHHH
Q 002245 443 KEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLL 510 (947)
Q Consensus 443 eELeelIR~lGfyn~KAk~Ik~lA~~Lve~yGgiDLe~L~~vP~deareeLlsLPGVG~KTAd~ILlf 510 (947)
++++.++.-.|=..-|++..+++|+.|.. .+. + .+..+.. ...|.+|||||.-||..|.-+
T Consensus 8 ~~~a~lle~~~~n~frv~ayr~aa~~~~~-~~~-~--~~~~~~~---~g~l~~~~giG~~~a~~i~e~ 68 (335)
T PRK07945 8 RRIAFLLERARADTYRVRAFRRAADVVEA-LDA-A--ERARRAR---AGSLTSLPGIGPKTAKVIAQA 68 (335)
T ss_pred HHHHHHHHHcCCChhhHHHHHHHHHHHHh-cCh-h--HHHHHHh---cCCcccCCCcCHHHHHHHHHH
Confidence 45666666677655678888888888764 221 2 1211111 116889999999999988765
No 81
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=52.74 E-value=19 Score=40.91 Aligned_cols=51 Identities=12% Similarity=0.242 Sum_probs=30.7
Q ss_pred CCcHHHHHHHHHHHHHHHHhhCCCC-hhhhhcCCchHHHHHHHhCCCCcHhHHHHHH
Q 002245 453 GMNNMLAERMKDFLNRLVREHGSID-LEWLRDVPPDKAKDYLLSIRGLGLKSVECVR 508 (947)
Q Consensus 453 Gfyn~KAk~Ik~lA~~Lve~yGgiD-Le~L~~vP~deareeLlsLPGVG~KTAd~IL 508 (947)
|....-|+.|.++.+ .|.+. +..+..-+...+..+|+++||||+|||..+-
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 555555666665543 25544 2222222233458899999999999996553
No 82
>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=52.74 E-value=12 Score=36.76 Aligned_cols=21 Identities=14% Similarity=0.262 Sum_probs=19.2
Q ss_pred HHHHHhCCCCcHhHHHHHHHH
Q 002245 490 KDYLLSIRGLGLKSVECVRLL 510 (947)
Q Consensus 490 reeLlsLPGVG~KTAd~ILlf 510 (947)
.+.|.+|||||+++|..|+.+
T Consensus 67 ~~eL~~lpGIG~~~A~~Ii~~ 87 (120)
T TIGR01259 67 LEELQALPGIGPAKAKAIIEY 87 (120)
T ss_pred HHHHhcCCCCCHHHHHHHHHH
Confidence 678999999999999999877
No 83
>COG2818 Tag 3-methyladenine DNA glycosylase [DNA replication, recombination, and repair]
Probab=52.24 E-value=26 Score=37.35 Aligned_cols=49 Identities=12% Similarity=0.253 Sum_probs=36.3
Q ss_pred cCCCCCHHHHHcCCHHHHHHHHHhcCCcHHHH--HHHHHHHHHHH---HhhCCC
Q 002245 428 RMDSLDYEALRCANVKEISEAIKERGMNNMLA--ERMKDFLNRLV---REHGSI 476 (947)
Q Consensus 428 ~~~~pTpeaLa~A~~eELeelIR~lGfyn~KA--k~Ik~lA~~Lv---e~yGgi 476 (947)
+...++|+.|+..+.++|+.++.-.|.-|.|. +.++.=|+.++ ++||++
T Consensus 60 aF~~Fd~~kVA~~~~~dverLl~d~gIIR~r~KI~A~i~NA~~~l~l~~e~Gsf 113 (188)
T COG2818 60 AFHGFDPEKVAAMTEEDVERLLADAGIIRNRGKIKATINNARAVLELQKEFGSF 113 (188)
T ss_pred HHhcCCHHHHHcCCHHHHHHHHhCcchhhhHHHHHHHHHHHHHHHHHHHHcCCH
Confidence 34578999999999999999999999865544 45555555544 456764
No 84
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=50.61 E-value=69 Score=39.36 Aligned_cols=70 Identities=10% Similarity=0.103 Sum_probs=44.6
Q ss_pred CCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHH---------------------H-hhCCCChhhhhcCCchHH
Q 002245 432 LDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLV---------------------R-EHGSIDLEWLRDVPPDKA 489 (947)
Q Consensus 432 pTpeaLa~A~~eELeelIR~lGfyn~KAk~Ik~lA~~Lv---------------------e-~yGgiDLe~L~~vP~dea 489 (947)
-++.+|..+..++|.++ -||...++++|.+..+.-. + .|+ +++.|....
T Consensus 448 ~~~~Diy~L~~~~l~~l---~gfgeks~~nll~aIe~sk~~~l~r~l~aLGI~~vG~~~ak~~~~--~i~~l~~a~---- 518 (562)
T PRK08097 448 EHLFSWLALTPEQLANT---PGIGKARAEQLWHQFNLARQQPFSRWLKALGIPLPQAALNALDDR--SWQQLLSRS---- 518 (562)
T ss_pred CCHHHHhcCCHHHHhcC---cCccHHHHHHHHHHHHHHcCCCHHHHHHHcCCccHHHHHHHHhcC--CHHHHHcCC----
Confidence 37888888887776553 4777777777765433211 0 121 344444322
Q ss_pred HHHHHhCCCCcHhHHHHHHHH
Q 002245 490 KDYLLSIRGLGLKSVECVRLL 510 (947)
Q Consensus 490 reeLlsLPGVG~KTAd~ILlf 510 (947)
.+.|.+++|||+++|+.|..|
T Consensus 519 ~e~l~~i~gIG~~~a~si~~~ 539 (562)
T PRK08097 519 EQQWQQLPGIGEGRARQLIAF 539 (562)
T ss_pred HHHHhcCCCchHHHHHHHHHH
Confidence 457889999999999988877
No 85
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=50.41 E-value=37 Score=38.67 Aligned_cols=57 Identities=14% Similarity=0.119 Sum_probs=37.3
Q ss_pred HHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHhCCCCcHhHHHHHHHH
Q 002245 443 KEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLL 510 (947)
Q Consensus 443 eELeelIR~lGfyn~KAk~Ik~lA~~Lve~yGgiDLe~L~~vP~deareeLlsLPGVG~KTAd~ILlf 510 (947)
++|++++.-.|=...|+++..++|..|.. ++. ++ +. .+.|.+|||||.++|+.|--+
T Consensus 11 ~~la~l~el~gen~~k~~ay~~Aa~~i~~-l~~-~i--------~~-~~~l~~lpgIG~~ia~kI~Ei 67 (334)
T smart00483 11 EILAENYEVFGENKRKCSYFRKAASVLKS-LPF-PI--------NS-MKDLKGLPGIGDKIKKKIEEI 67 (334)
T ss_pred HHHHHHHHHhcccHHHHHHHHHHHHHHHh-CCC-CC--------CC-HHHHhcCCCccHHHHHHHHHH
Confidence 44555555456555577777777777764 332 22 22 247899999999999988744
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=49.42 E-value=11 Score=28.94 Aligned_cols=15 Identities=20% Similarity=0.424 Sum_probs=11.1
Q ss_pred HHhCCCCcHhHHHHH
Q 002245 493 LLSIRGLGLKSVECV 507 (947)
Q Consensus 493 LlsLPGVG~KTAd~I 507 (947)
+.+++|||++|+.-+
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 446899999999764
No 87
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=48.90 E-value=25 Score=43.64 Aligned_cols=58 Identities=21% Similarity=0.300 Sum_probs=37.0
Q ss_pred HHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHhCCCCcHhHHHHHHHH
Q 002245 443 KEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLL 510 (947)
Q Consensus 443 eELeelIR~lGfyn~KAk~Ik~lA~~Lve~yGgiDLe~L~~vP~deareeLlsLPGVG~KTAd~ILlf 510 (947)
-.|..+|-.+|....-.+. |+.|...|+. ++.|...+ .++|.+++|||.+.|..|..|
T Consensus 505 ~~l~r~l~aLGIr~VG~~~----Ak~La~~f~s--l~~l~~a~----~e~l~~i~giG~~vA~si~~f 562 (667)
T COG0272 505 QPLARFLYALGIRHVGETT----AKSLARHFGT--LEALLAAS----EEELASIPGIGEVVARSIIEF 562 (667)
T ss_pred CCHHHHHHHcCCchhhHHH----HHHHHHHhhh--HHHHHhcC----HHHHhhccchhHHHHHHHHHH
Confidence 3444556666665443333 3334444443 66676655 457899999999999998776
No 88
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=43.47 E-value=32 Score=39.82 Aligned_cols=58 Identities=21% Similarity=0.339 Sum_probs=38.3
Q ss_pred HHHHHHHhcCCcH-HHHHHH-HHHHHHHHHhhCCCChhhhhcCCchHHHHHHHhCCCCcHhHHHHH
Q 002245 444 EISEAIKERGMNN-MLAERM-KDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECV 507 (947)
Q Consensus 444 ELeelIR~lGfyn-~KAk~I-k~lA~~Lve~yGgiDLe~L~~vP~deareeLlsLPGVG~KTAd~I 507 (947)
.+...+.|.||.- .|..+| +.+|+.|+++||+ |..+...+ .++|.+++|||++.|..|
T Consensus 276 ~ld~~v~prGyRiLs~IPrl~k~iAk~Ll~~FGS--L~~Il~As----~eeL~~VeGIGe~rA~~I 335 (352)
T PRK13482 276 ALDTPVSPRGYRLLSKIPRLPSAVIENLVEHFGS--LQGLLAAS----IEDLDEVEGIGEVRARAI 335 (352)
T ss_pred ccccccCCcHHHHHhcCCCCCHHHHHHHHHHcCC--HHHHHcCC----HHHHhhCCCcCHHHHHHH
Confidence 3444455555521 011222 5788999999985 56665544 558999999999999764
No 89
>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=43.17 E-value=43 Score=37.67 Aligned_cols=18 Identities=28% Similarity=0.386 Sum_probs=10.3
Q ss_pred HHHHHhCCCCcHhHHHHH
Q 002245 490 KDYLLSIRGLGLKSVECV 507 (947)
Q Consensus 490 reeLlsLPGVG~KTAd~I 507 (947)
..+|++++|||+|||..+
T Consensus 84 l~~l~~i~GiGpk~a~~l 101 (307)
T cd00141 84 LLLLLRVPGVGPKTARKL 101 (307)
T ss_pred HHHHHcCCCCCHHHHHHH
Confidence 555566666666665443
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=42.36 E-value=34 Score=38.48 Aligned_cols=57 Identities=14% Similarity=0.166 Sum_probs=36.8
Q ss_pred HHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHhCCCCcHhHHHHHHHH
Q 002245 443 KEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLL 510 (947)
Q Consensus 443 eELeelIR~lGfyn~KAk~Ik~lA~~Lve~yGgiDLe~L~~vP~deareeLlsLPGVG~KTAd~ILlf 510 (947)
++|+.++.-.|=..-|++....+|..|.. .+. + -+. .+++.+|||||.++|+.|--+
T Consensus 8 ~~ia~~~e~~~~~~~r~~aY~~Aa~~l~~-l~~-~--------i~~-~~~~~~ipgiG~~ia~kI~E~ 64 (307)
T cd00141 8 EELADLLELLGGNPFRVRAYRKAARALES-LPE-P--------IES-LEEAKKLPGIGKKIAEKIEEI 64 (307)
T ss_pred HHHHHHHHhccCCcchHHHHHHHHHHHHh-CCc-c--------cCC-HHHhcCCCCccHHHHHHHHHH
Confidence 45555555554333467777777777764 222 1 222 346799999999999998754
No 91
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=40.73 E-value=19 Score=28.59 Aligned_cols=17 Identities=18% Similarity=0.335 Sum_probs=13.3
Q ss_pred HHhCCCCcHhHHHHHHH
Q 002245 493 LLSIRGLGLKSVECVRL 509 (947)
Q Consensus 493 LlsLPGVG~KTAd~ILl 509 (947)
+-.+||||+|||--+|.
T Consensus 18 i~Gv~giG~ktA~~ll~ 34 (36)
T smart00279 18 IPGVKGIGPKTALKLLR 34 (36)
T ss_pred CCCCCcccHHHHHHHHH
Confidence 34689999999987653
No 92
>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=38.35 E-value=30 Score=30.23 Aligned_cols=21 Identities=29% Similarity=0.479 Sum_probs=18.3
Q ss_pred HHHHHh-CCCCcHhHHHHHHHH
Q 002245 490 KDYLLS-IRGLGLKSVECVRLL 510 (947)
Q Consensus 490 reeLls-LPGVG~KTAd~ILlf 510 (947)
.+.|.. +||||.++|..|+.+
T Consensus 15 ~~~L~~~ipgig~~~a~~Il~~ 36 (69)
T TIGR00426 15 AEELQRAMNGVGLKKAEAIVSY 36 (69)
T ss_pred HHHHHhHCCCCCHHHHHHHHHH
Confidence 457888 999999999999876
No 93
>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=37.19 E-value=30 Score=29.62 Aligned_cols=19 Identities=21% Similarity=0.239 Sum_probs=13.6
Q ss_pred HHHHhCCCCcHhHHHHHHH
Q 002245 491 DYLLSIRGLGLKSVECVRL 509 (947)
Q Consensus 491 eeLlsLPGVG~KTAd~ILl 509 (947)
+.|..+.|||+.||.-...
T Consensus 2 ~~f~~I~GVG~~tA~~w~~ 20 (52)
T PF10391_consen 2 KLFTGIWGVGPKTARKWYA 20 (52)
T ss_dssp HHHHTSTT--HHHHHHHHH
T ss_pred cchhhcccccHHHHHHHHH
Confidence 4688999999999976544
No 94
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=36.77 E-value=27 Score=37.39 Aligned_cols=23 Identities=17% Similarity=0.224 Sum_probs=19.5
Q ss_pred HHHHHHHhCCCCcHhHHHHHHHH
Q 002245 488 KAKDYLLSIRGLGLKSVECVRLL 510 (947)
Q Consensus 488 eareeLlsLPGVG~KTAd~ILlf 510 (947)
++.+.|+++.|||||+|=.||..
T Consensus 69 ~lF~~LisVsGIGPK~ALaILs~ 91 (196)
T PRK13901 69 EVFEELIGVDGIGPRAALRVLSG 91 (196)
T ss_pred HHHHHHhCcCCcCHHHHHHHHcC
Confidence 45778999999999999888853
No 95
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=36.70 E-value=26 Score=37.02 Aligned_cols=23 Identities=13% Similarity=0.228 Sum_probs=19.6
Q ss_pred HHHHHHHhCCCCcHhHHHHHHHH
Q 002245 488 KAKDYLLSIRGLGLKSVECVRLL 510 (947)
Q Consensus 488 eareeLlsLPGVG~KTAd~ILlf 510 (947)
++.+.|+++.|||||+|=.||..
T Consensus 70 ~lF~~LisV~GIGpK~Al~iLs~ 92 (186)
T PRK14600 70 DCLRMLVKVSGVNYKTAMSILSK 92 (186)
T ss_pred HHHHHHhCcCCcCHHHHHHHHcc
Confidence 35678999999999999998873
No 96
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=36.52 E-value=56 Score=37.55 Aligned_cols=60 Identities=18% Similarity=0.250 Sum_probs=37.4
Q ss_pred HHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHhCCCCcHhHHHHHHHH
Q 002245 443 KEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLL 510 (947)
Q Consensus 443 eELeelIR~lGfyn~KAk~Ik~lA~~Lve~yGgiDLe~L~~vP~deareeLlsLPGVG~KTAd~ILlf 510 (947)
++++.++.-.|=..-|++.-+.+|+.|... ..|++.+.+ +..|+.|||||+.||+.|.-|
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 455555555565445666666777777542 223333322 224889999999999998765
No 97
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=35.74 E-value=28 Score=36.78 Aligned_cols=22 Identities=18% Similarity=0.027 Sum_probs=19.1
Q ss_pred HHHHHHHhCCCCcHhHHHHHHH
Q 002245 488 KAKDYLLSIRGLGLKSVECVRL 509 (947)
Q Consensus 488 eareeLlsLPGVG~KTAd~ILl 509 (947)
++.+.|+++.|||||+|=.||.
T Consensus 70 ~lF~~Li~V~GIGpK~AL~iLs 91 (188)
T PRK14606 70 ELFLSLTKVSRLGPKTALKIIS 91 (188)
T ss_pred HHHHHHhccCCccHHHHHHHHc
Confidence 4677899999999999988885
No 98
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=35.70 E-value=28 Score=36.73 Aligned_cols=23 Identities=26% Similarity=0.377 Sum_probs=19.5
Q ss_pred HHHHHHHhCCCCcHhHHHHHHHH
Q 002245 488 KAKDYLLSIRGLGLKSVECVRLL 510 (947)
Q Consensus 488 eareeLlsLPGVG~KTAd~ILlf 510 (947)
++.+.|+++.|||||+|=.||..
T Consensus 70 ~lF~~Li~VsGIGpK~Al~ILs~ 92 (183)
T PRK14601 70 KMFEMLLKVNGIGANTAMAVCSS 92 (183)
T ss_pred HHHHHHhccCCccHHHHHHHHcC
Confidence 45778999999999999888853
No 99
>PRK14973 DNA topoisomerase I; Provisional
Probab=34.81 E-value=4.2e+02 Score=34.80 Aligned_cols=76 Identities=20% Similarity=0.196 Sum_probs=52.2
Q ss_pred CCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHH-----h------------hCCC-ChhhhhcCCchHHH
Q 002245 429 MDSLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVR-----E------------HGSI-DLEWLRDVPPDKAK 490 (947)
Q Consensus 429 ~~~pTpeaLa~A~~eELeelIR~lGfyn~KAk~Ik~lA~~Lve-----~------------yGgi-DLe~L~~vP~dear 490 (947)
.+..+..+|+.|++..|. ..|++..+++.+++.|+-+.. . -+|| +++.+....+
T Consensus 763 ~~~~~~~~~~~~~~~~~~----~~~~sE~~~~~~~~~a~~~~~~~~~~~~gv~~~~~~~~~~~G~~~~~d~~~a~p---- 834 (936)
T PRK14973 763 SGINDIAALARADPADLK----KAGLSEAEAASLLAEAKSLCNISRLKEIGVPAVSLKKYQEAGFDTPEDFCSVHP---- 834 (936)
T ss_pred cCcchHHHHhhCCHHHHH----HcCCCHHHHHHHHHHHHHHHHHHhhcccCCCHHHHHHHHHhcCCCHHHHHhcCH----
Confidence 356789999999998875 489999999999998843321 1 0222 3444444443
Q ss_pred HHHHhCCCCcHhHHHHHHHHhc
Q 002245 491 DYLLSIRGLGLKSVECVRLLTL 512 (947)
Q Consensus 491 eeLlsLPGVG~KTAd~ILlfaf 512 (947)
++|..++||++-|+......+.
T Consensus 835 ~~La~~~g~~~~~~~~~~~~~~ 856 (936)
T PRK14973 835 AYLALKTGISPETICRHAKLVC 856 (936)
T ss_pred HHHhcCCCCChhhHHHHHHHHH
Confidence 4799999999888876544333
No 100
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=34.76 E-value=30 Score=36.87 Aligned_cols=23 Identities=22% Similarity=0.271 Sum_probs=19.6
Q ss_pred HHHHHHHhCCCCcHhHHHHHHHH
Q 002245 488 KAKDYLLSIRGLGLKSVECVRLL 510 (947)
Q Consensus 488 eareeLlsLPGVG~KTAd~ILlf 510 (947)
++.+.|+++.|||||+|=.||..
T Consensus 69 ~lF~~L~~V~GIGpK~AL~iLs~ 91 (197)
T PRK14603 69 ELFELLLGVSGVGPKLALALLSA 91 (197)
T ss_pred HHHHHHhCcCCcCHHHHHHHHcC
Confidence 45778999999999999988873
No 101
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=34.42 E-value=31 Score=36.87 Aligned_cols=23 Identities=22% Similarity=0.183 Sum_probs=19.7
Q ss_pred HHHHHHHhCCCCcHhHHHHHHHH
Q 002245 488 KAKDYLLSIRGLGLKSVECVRLL 510 (947)
Q Consensus 488 eareeLlsLPGVG~KTAd~ILlf 510 (947)
++.+.|+++.|||||+|=.||..
T Consensus 71 ~lF~~Li~V~GIGpK~Al~iLs~ 93 (203)
T PRK14602 71 QTFIVLISISKVGAKTALAILSQ 93 (203)
T ss_pred HHHHHHhCCCCcCHHHHHHHHhh
Confidence 45778999999999999888874
No 102
>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=33.30 E-value=20 Score=32.32 Aligned_cols=19 Identities=16% Similarity=0.165 Sum_probs=15.3
Q ss_pred HHHhCCCCcHhHHHHHHHH
Q 002245 492 YLLSIRGLGLKSVECVRLL 510 (947)
Q Consensus 492 eLlsLPGVG~KTAd~ILlf 510 (947)
.+-.+||||+|||.-++.-
T Consensus 23 ~i~gv~giG~k~A~~ll~~ 41 (75)
T cd00080 23 NIPGVPGIGPKTALKLLKE 41 (75)
T ss_pred cCCCCCcccHHHHHHHHHH
Confidence 5667999999999877644
No 103
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=33.21 E-value=32 Score=36.60 Aligned_cols=23 Identities=17% Similarity=0.258 Sum_probs=19.8
Q ss_pred HHHHHHHhCCCCcHhHHHHHHHH
Q 002245 488 KAKDYLLSIRGLGLKSVECVRLL 510 (947)
Q Consensus 488 eareeLlsLPGVG~KTAd~ILlf 510 (947)
++...|+++.|||||+|=.||..
T Consensus 70 ~lF~~Li~V~GIGpK~Al~iLs~ 92 (195)
T PRK14604 70 QLFELLIGVSGVGPKAALNLLSS 92 (195)
T ss_pred HHHHHHhCcCCcCHHHHHHHHcC
Confidence 45778999999999999988874
No 104
>PRK00254 ski2-like helicase; Provisional
Probab=33.02 E-value=81 Score=39.34 Aligned_cols=24 Identities=13% Similarity=0.188 Sum_probs=17.2
Q ss_pred HHHhCCCCcHhHHHHHHHHhcCCc
Q 002245 492 YLLSIRGLGLKSVECVRLLTLHHL 515 (947)
Q Consensus 492 eLlsLPGVG~KTAd~ILlfafgrp 515 (947)
.|..|||||+++|..++..+|+-.
T Consensus 646 ~L~~ipgig~~~~~~l~~~g~~s~ 669 (720)
T PRK00254 646 ELMRLPMIGRKRARALYNAGFRSI 669 (720)
T ss_pred hhhcCCCCCHHHHHHHHHccCCCH
Confidence 466777777777777777666654
No 105
>PF11372 DUF3173: Domain of unknown function (DUF3173); InterPro: IPR021512 This family of proteins with unknown function appears to be restricted to Firmicutes.
Probab=32.42 E-value=1.1e+02 Score=27.37 Aligned_cols=44 Identities=20% Similarity=0.246 Sum_probs=30.0
Q ss_pred cCCcHHHHHHHHHHHHHHHHhh--CCCChhhhhcCCchHHHHHHHhC
Q 002245 452 RGMNNMLAERMKDFLNRLVREH--GSIDLEWLRDVPPDKAKDYLLSI 496 (947)
Q Consensus 452 lGfyn~KAk~Ik~lA~~Lve~y--GgiDLe~L~~vP~deareeLlsL 496 (947)
+||....|+.|+.-|+.+.-+. .-++=.+|..+|.. +.++|+.+
T Consensus 12 lGf~~~tA~~IIrqAK~~lV~~G~~~Y~nkRlg~VP~~-~VEeiLG~ 57 (59)
T PF11372_consen 12 LGFSESTARDIIRQAKALLVQKGFSFYNNKRLGRVPAS-AVEEILGI 57 (59)
T ss_pred cCCCHHHHHHHHHHHHHHHHHcCCCcccCCccCcccHH-HHHHHHCC
Confidence 7999999999999888877442 22233466677765 55666643
No 106
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=31.68 E-value=37 Score=34.48 Aligned_cols=20 Identities=5% Similarity=-0.122 Sum_probs=17.4
Q ss_pred HHHHHhCCCCcHhHHHHHHH
Q 002245 490 KDYLLSIRGLGLKSVECVRL 509 (947)
Q Consensus 490 reeLlsLPGVG~KTAd~ILl 509 (947)
.++|.+||||||..|..|..
T Consensus 60 ~~el~~lpGigP~~A~~IV~ 79 (132)
T PRK02515 60 VRAFRQFPGMYPTLAGKIVK 79 (132)
T ss_pred HHHHHHCCCCCHHHHHHHHH
Confidence 45689999999999999983
No 107
>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=31.05 E-value=57 Score=28.98 Aligned_cols=47 Identities=23% Similarity=0.321 Sum_probs=29.1
Q ss_pred HhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHhCCCCcHhHHHHHH
Q 002245 450 KERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVR 508 (947)
Q Consensus 450 R~lGfyn~KAk~Ik~lA~~Lve~yGgiDLe~L~~vP~deareeLlsLPGVG~KTAd~IL 508 (947)
..+|++ .||.+... +.|=-.+..|..++ .+.|++++|+|+++.+-|.
T Consensus 15 ~~L~LS-~Ra~n~L~-------~~~I~tv~dL~~~s----~~~L~~i~n~G~ksl~EI~ 61 (66)
T PF03118_consen 15 EDLGLS-VRAYNCLK-------RAGIHTVGDLVKYS----EEDLLKIKNFGKKSLEEIK 61 (66)
T ss_dssp GGSTSB-HHHHHHHH-------CTT--BHHHHHCS-----HHHHHTSTTSHHHHHHHHH
T ss_pred HHhCCC-HHHHHHHH-------HhCCcCHHHHHhCC----HHHHHhCCCCCHhHHHHHH
Confidence 347888 44433221 12322566676665 4589999999999998764
No 108
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=29.62 E-value=38 Score=36.44 Aligned_cols=23 Identities=22% Similarity=0.251 Sum_probs=19.6
Q ss_pred HHHHHHHhCCCCcHhHHHHHHHH
Q 002245 488 KAKDYLLSIRGLGLKSVECVRLL 510 (947)
Q Consensus 488 eareeLlsLPGVG~KTAd~ILlf 510 (947)
++...|+++-|||+|+|=.||..
T Consensus 70 ~lF~~LisVnGIGpK~ALaiLs~ 92 (201)
T COG0632 70 ELFRLLISVNGIGPKLALAILSN 92 (201)
T ss_pred HHHHHHHccCCccHHHHHHHHcC
Confidence 45678999999999999888865
No 109
>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=29.61 E-value=47 Score=31.93 Aligned_cols=22 Identities=18% Similarity=0.128 Sum_probs=18.4
Q ss_pred HHHHHHhCCCCcHhHHHHHHHH
Q 002245 489 AKDYLLSIRGLGLKSVECVRLL 510 (947)
Q Consensus 489 areeLlsLPGVG~KTAd~ILlf 510 (947)
+.-.|.++.|||+++|..|+..
T Consensus 13 i~~aLt~IyGIG~~~A~~Ic~~ 34 (107)
T PF00416_consen 13 IYIALTKIYGIGRRKAKQICKK 34 (107)
T ss_dssp HHHHHTTSTTBCHHHHHHHHHH
T ss_pred hHhHHhhhhccCHHHHHHHHHH
Confidence 6778999999999999877543
No 110
>smart00439 BAH Bromo adjacent homology domain.
Probab=28.60 E-value=59 Score=30.33 Aligned_cols=64 Identities=23% Similarity=0.266 Sum_probs=45.2
Q ss_pred cceeceeeeccCCCCCCcccchhhhccCCceEEEeccChhhhcccCCHHHHHHhhhccceEeecccccccCCccc
Q 002245 853 YFQVNEVFADHDSSLNPIDVPREWLWNLPRRMVYFGTSVSSIFKGLSTEGIQFCFWKGFVCVRGFDQKSRAPRPL 927 (947)
Q Consensus 853 YFQvNEVFaDh~Ss~~Pi~vpr~~iw~L~rr~vyfGtsv~sI~kg~s~~~iq~cf~~g~vCvR~fdr~tr~P~pl 927 (947)
+|.-||||+-.... +||-+.|+. ++.|++.+....+.- ++. .-...-|+|=++||..++...+|
T Consensus 56 ~~~~~Elf~s~~~~----~i~~~~I~~--kc~V~~~~~~~~~~~----~~~-~~~~~~f~cr~~yd~~~~~f~~~ 119 (120)
T smart00439 56 LFDKNEVFLSDEYD----TVPLSDIIG--KCNVLSKSDYPGLRP----EGK-IGEPDVFFCESLYDPEKGAFKKL 119 (120)
T ss_pred cCCCcceEEEccCc----cCChHHeee--EEEEEEcchhccccc----ccC-CCCCCeEEEEEEEccccCcccCC
Confidence 46789999887764 666677776 899998876644321 111 01347899999999999887765
No 111
>PRK07758 hypothetical protein; Provisional
Probab=27.45 E-value=80 Score=30.54 Aligned_cols=28 Identities=25% Similarity=0.412 Sum_probs=21.4
Q ss_pred ChhhhhcCCchHHHHHHHhCCCCcHhHHHHHH
Q 002245 477 DLEWLRDVPPDKAKDYLLSIRGLGLKSVECVR 508 (947)
Q Consensus 477 DLe~L~~vP~deareeLlsLPGVG~KTAd~IL 508 (947)
.++.|..++ .++|++|+|+|+|+.+-|.
T Consensus 57 TL~dLv~~t----e~ELl~iknlGkKSL~EIk 84 (95)
T PRK07758 57 TVEELSKYS----EKEILKLHGMGPASLPKLR 84 (95)
T ss_pred cHHHHHcCC----HHHHHHccCCCHHHHHHHH
Confidence 455665555 4589999999999998764
No 112
>PRK08609 hypothetical protein; Provisional
Probab=26.41 E-value=1.1e+02 Score=37.55 Aligned_cols=57 Identities=16% Similarity=0.283 Sum_probs=37.4
Q ss_pred HHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHhCCCCcHhHHHHHHHH
Q 002245 443 KEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLL 510 (947)
Q Consensus 443 eELeelIR~lGfyn~KAk~Ik~lA~~Lve~yGgiDLe~L~~vP~deareeLlsLPGVG~KTAd~ILlf 510 (947)
++++.++.-.|=..-|++.-.++|+.|... .. ++. . ...|.+|||||..+|..|--+
T Consensus 11 ~~~A~~le~~g~n~fr~~aYr~Aa~~i~~l-~~-~i~--------~-~~~l~~ipgIG~~ia~kI~Ei 67 (570)
T PRK08609 11 ETIATYMELKGENPFKISAFRKAAQALELD-ER-SLS--------E-IDDFTKLKGIGKGTAEVIQEY 67 (570)
T ss_pred HHHHHHHHhcCCCcHHHHHHHHHHHHHHhC-ch-hhh--------h-hhhhccCCCcCHHHHHHHHHH
Confidence 455666655664345777777878777642 21 221 1 246899999999999988754
No 113
>PRK13280 N-glycosylase/DNA lyase; Provisional
Probab=25.13 E-value=2.5e+02 Score=31.79 Aligned_cols=134 Identities=14% Similarity=0.099 Sum_probs=74.9
Q ss_pred HHHHHHHHhc----CCcHHHHHHHHHHHHHHHHhhCCCChhhhhc--CCchHHHHHHHhCCCCc--H-------hHHHHH
Q 002245 443 KEISEAIKER----GMNNMLAERMKDFLNRLVREHGSIDLEWLRD--VPPDKAKDYLLSIRGLG--L-------KSVECV 507 (947)
Q Consensus 443 eELeelIR~l----Gfyn~KAk~Ik~lA~~Lve~yGgiDLe~L~~--vP~deareeLlsLPGVG--~-------KTAd~I 507 (947)
+++...+... -+..+|-++|..++..+.+ +.+..+.. ..-+++++.|..+=|-- . |++...
T Consensus 87 ~~~~~Fl~~s~~nrrl~e~KikRi~r~~~fl~~----L~l~~~~~~y~~l~~l~~~La~~L~s~~~~KTiVFAvKM~~Ya 162 (269)
T PRK13280 87 EAYIEFLKNSKGNRRLLEQKIKRIEKVEPFLES----LTLLDLPLYYEDLEELLEQLAKILGAKKESKTVVFAVKMFGYA 162 (269)
T ss_pred HHHHHHHhcCchhHHHHHHHHHHHHHHHHHhhh----hccchhhhhHhhHHHHHHHHHHHhCCCCCcceeeeHHHHHHHH
Confidence 3455555554 2345788888888765433 22222211 12244566666544432 2 334444
Q ss_pred HHHhcCC--c-----eeecchHHHHHHHHhCCCCCCCCHHHHHHHHHHhcCchHHHHHhhhhhhhcCChhhHHHHHHHHH
Q 002245 508 RLLTLHH--L-----AFPVDTNVGRIAVRLGWVPLQPLPESLQLHLLELYPVLESIQKYLWPRLCKLDQRTLYELHYQLI 580 (947)
Q Consensus 508 Llfafgr--p-----afPVDTHV~RVl~RLGlv~~k~tpeevEk~Le~llP~~e~Iqk~LW~rlc~ld~~~~~e~H~~LI 580 (947)
...+++. | -||||.-|..+....|++.+..........+.. ......|..++..+.--+..+...||
T Consensus 163 ~r~~~~~~~p~p~~IpIPvD~Ria~~T~~sglv~~~~~~~~~~~~~~~------e~~~~~W~~Var~sgIPplhLDSilW 236 (269)
T PRK13280 163 CRAAFGEFRPYPMEIPIPVDYRIAKLTKCSGLVEGPPEEAMRRYKLTQ------EEPIEFWNKVARESGIPPLHIDSILW 236 (269)
T ss_pred HHHhccccCCCCcCCCCcccHHHHHHHHHhccccCcchhhhhhhhhhh------hHHHHHHHHHHHhcCCCceeehhhhh
Confidence 4444443 2 488999999999999999863221111112111 11235688776666666677888888
Q ss_pred HHhHhh
Q 002245 581 TFGKVF 586 (947)
Q Consensus 581 ~fGR~I 586 (947)
..|+..
T Consensus 237 ~~~g~~ 242 (269)
T PRK13280 237 LVLGAL 242 (269)
T ss_pred hhcCCc
Confidence 877654
No 114
>PRK01172 ski2-like helicase; Provisional
Probab=24.99 E-value=1.6e+02 Score=36.51 Aligned_cols=64 Identities=14% Similarity=0.072 Sum_probs=45.4
Q ss_pred ChHHHHHHHHhccCcccccc--CcCCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhh
Q 002245 407 DWESLRKEVQRNSGKQERSR--DRMDSLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREH 473 (947)
Q Consensus 407 ~W~~L~k~l~~~glk~er~~--~~~~~pTpeaLa~A~~eELeelIR~lGfyn~KAk~Ik~lA~~Lve~y 473 (947)
.|+.+-..++--|+.+.+.. ...++-|+.+|++++.+++.++ .|+...+|+.|++-|+.+++-|
T Consensus 607 v~~~~~~L~~ip~~~~~~a~~l~~~g~~~~~di~~~~~~~~~~i---~~~~~~~~~~i~~~~~~~~~~~ 672 (674)
T PRK01172 607 IREDLIDLVLIPKVGRVRARRLYDAGFKTVDDIARSSPERIKKI---YGFSDTLANAIVNRAMKISSMY 672 (674)
T ss_pred CCHHHHhhcCCCCCCHHHHHHHHHcCCCCHHHHHhCCHHHHHHH---hccCHHHHHHHHHHHHHHHHHh
Confidence 45555444433333332222 2356779999999999999876 6899999999999999998754
No 115
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=24.77 E-value=1.2e+02 Score=33.54 Aligned_cols=30 Identities=17% Similarity=0.229 Sum_probs=23.8
Q ss_pred ChhhhhcCCchHHHHHHHhCCCCcHhHHHHHHHH
Q 002245 477 DLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLL 510 (947)
Q Consensus 477 DLe~L~~vP~deareeLlsLPGVG~KTAd~ILlf 510 (947)
+++.|..-+ .++|.+++|||.++|..|..+
T Consensus 26 Sve~Ik~AS----~eEL~~V~GIg~k~AekI~e~ 55 (232)
T PRK12766 26 SVEDVRAAD----QSELAEVDGIGNALAARIKAD 55 (232)
T ss_pred CHHHHHhCC----HHHHHHccCCCHHHHHHHHHH
Confidence 456665544 568999999999999999877
No 116
>PF13592 HTH_33: Winged helix-turn helix
Probab=23.78 E-value=1e+02 Score=26.45 Aligned_cols=37 Identities=16% Similarity=0.200 Sum_probs=23.0
Q ss_pred cHhHHHHHHHHhcCCceee-cchHHHHHHHHhCCCCCC
Q 002245 500 GLKSVECVRLLTLHHLAFP-VDTNVGRIAVRLGWVPLQ 536 (947)
Q Consensus 500 G~KTAd~ILlfafgrpafP-VDTHV~RVl~RLGlv~~k 536 (947)
|.||+.-|..+.-..-.+- -..+|.|++.|+|+...+
T Consensus 3 ~~wt~~~i~~~I~~~fgv~ys~~~v~~lL~r~G~s~~k 40 (60)
T PF13592_consen 3 GRWTLKEIAAYIEEEFGVKYSPSGVYRLLKRLGFSYQK 40 (60)
T ss_pred CcccHHHHHHHHHHHHCCEEcHHHHHHHHHHcCCcccc
Confidence 4556655554433332222 468999999999997643
No 117
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=22.49 E-value=73 Score=39.24 Aligned_cols=36 Identities=8% Similarity=0.181 Sum_probs=24.9
Q ss_pred HHHhhCCCChhhhhcCCchHHHHHHHhCCCCcHhHHHHHHHH
Q 002245 469 LVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLL 510 (947)
Q Consensus 469 Lve~yGgiDLe~L~~vP~deareeLlsLPGVG~KTAd~ILlf 510 (947)
|.+.||+ ++.|+.-+ .++|.++||||.++|..|..+
T Consensus 530 LL~~Fgs--~~~I~~As----~eeL~~v~gi~~~~A~~I~~~ 565 (574)
T PRK14670 530 ILKSLGT--YKDILLLN----EDEIAEKMKINIKMAKKIKKF 565 (574)
T ss_pred HHHHhCC--HHHHHhCC----HHHHHhCCCCCHHHHHHHHHH
Confidence 4455665 45665544 457888888888888888665
No 118
>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=22.16 E-value=3.7e+02 Score=34.10 Aligned_cols=57 Identities=14% Similarity=0.224 Sum_probs=39.7
Q ss_pred HHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHhCCCCcHhHHHHHHH
Q 002245 442 VKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRL 509 (947)
Q Consensus 442 ~eELeelIR~lGfyn~KAk~Ik~lA~~Lve~yGgiDLe~L~~vP~deareeLlsLPGVG~KTAd~ILl 509 (947)
..++...+...|+....|..|.+ .||.-.++.|++-|.. .+..++|||-++||-|..
T Consensus 143 ~~~~~~~L~~~gi~~~~a~ki~~-------~yg~~~~~~i~~nPY~----L~~~i~gigF~~aD~iA~ 199 (720)
T TIGR01448 143 ERRLLAGLQGLGIGIKLAQRIYK-------FYQADTLDRVEKDPYL----LAEDVKGIGFLTADQLAQ 199 (720)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHH-------HHhHHHHHHHHhCchh----hhhhcCCCCHHHHHHHHH
Confidence 56788888999999766655544 3555445566666654 233699999999998754
No 119
>COG4277 Predicted DNA-binding protein with the Helix-hairpin-helix motif [General function prediction only]
Probab=21.20 E-value=62 Score=37.15 Aligned_cols=21 Identities=29% Similarity=0.474 Sum_probs=18.5
Q ss_pred HHHHHhCCCCcHhHHHHHHHH
Q 002245 490 KDYLLSIRGLGLKSVECVRLL 510 (947)
Q Consensus 490 reeLlsLPGVG~KTAd~ILlf 510 (947)
+++|+.+||||.|+|.-|+..
T Consensus 329 ~~~llRVPGiG~ksa~rIv~~ 349 (404)
T COG4277 329 YKELLRVPGIGVKSARRIVMT 349 (404)
T ss_pred HHHhcccCCCChHHHHHHHHH
Confidence 678999999999999887753
No 120
>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=20.88 E-value=1.6e+02 Score=27.28 Aligned_cols=54 Identities=15% Similarity=0.191 Sum_probs=40.2
Q ss_pred HHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHhCCCCcHhHHHHHHHHh
Q 002245 457 MLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLLT 511 (947)
Q Consensus 457 ~KAk~Ik~lA~~Lve~yGgiDLe~L~~vP~deareeLlsLPGVG~KTAd~ILlfa 511 (947)
...+....+...|.+.||..+.+.|...+.++++ .++.--|++..=|..|..++
T Consensus 9 ~s~~~a~~~~~~l~~~~g~pt~~~l~~~~~~el~-~~i~~~G~~~~ka~~i~~~a 62 (108)
T PF00730_consen 9 TSIKAARKIYRRLFERYGFPTPEALAEASEEELR-ELIRPLGFSRRKAKYIIELA 62 (108)
T ss_dssp S-HHHHHHHHHHHHHHHSCSSHHHHHCSHHHHHH-HHHTTSTSHHHHHHHHHHHH
T ss_pred CcHHHHHHHHHHHHHHhcCCCHHHHHhCCHHHHH-HHhhccCCCHHHHHHHHHHH
Confidence 4667777888899999987799999998877655 44444788877777776654
No 121
>TIGR01954 nusA_Cterm_rpt transcription termination factor NusA, C-terminal duplication. NusA is a bacterial transcription termination factor. It is named for its interaction with phage lambda protein N, as part of the N utilization substance. Some members of the NusA family have a long C-terminal extension. This model represents an acidic 50-residue region found in two copies toward the C-terminus of most Proteobacterial NusA proteins, spaced about 26 residues apart. Analogous C-terminal extensions in some other bacterial lineages lack apparent homology but appear similarly acidic.
Probab=20.77 E-value=1.9e+02 Score=23.27 Aligned_cols=36 Identities=14% Similarity=0.179 Sum_probs=30.0
Q ss_pred CCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHH
Q 002245 430 DSLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNR 468 (947)
Q Consensus 430 ~~pTpeaLa~A~~eELeelIR~lGfyn~KAk~Ik~lA~~ 468 (947)
++-+.++|+.++.++|... .|+...++..|+..++.
T Consensus 13 G~~s~e~la~~~~~eL~~i---~g~~~e~a~~ii~~a~~ 48 (50)
T TIGR01954 13 GFTTVEDLAYVPIDELLSI---EGFDEETAKELINRARN 48 (50)
T ss_pred CCCCHHHHHccCHHHHhcC---CCCCHHHHHHHHHHHHH
Confidence 5679999999999999773 68888888888877763
No 122
>PRK14469 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=20.39 E-value=1.6e+02 Score=33.65 Aligned_cols=54 Identities=13% Similarity=0.289 Sum_probs=42.0
Q ss_pred HHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHh
Q 002245 437 LRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLS 495 (947)
Q Consensus 437 La~A~~eELeelIR~lGfyn~KAk~Ik~lA~~Lve~yGgiDLe~L~~vP~deareeLls 495 (947)
|..++.++|++++...|+...+|+.|. +++..+ +..|++.+.++|.+ .|+.|..
T Consensus 4 ~~~~~~~~~~~~~~~~g~~~~r~~qi~---~~~~~~-~~~~~~~~~~~~~~-~r~~l~~ 57 (343)
T PRK14469 4 ILDLSYEELVSEITELGLEKYRADQIL---DWIYKK-KVFNFDEMTNLSKD-HRALLSE 57 (343)
T ss_pred cccCCHHHHHHHHHHcCCCchHHHHHH---HHHHhc-CCCCHHHhccccHH-HHHHHhh
Confidence 567889999999999999877777665 577664 44689999999876 6776665
No 123
>KOG0400 consensus 40S ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=20.29 E-value=1.1e+02 Score=31.20 Aligned_cols=66 Identities=21% Similarity=0.380 Sum_probs=47.5
Q ss_pred hhhhcCCchHHHHHHHhC--CCCcHhHHHHHHHHhcCC--ceeecchHHHHHHHHhCCCCCCCCHHHHHHHHH
Q 002245 479 EWLRDVPPDKAKDYLLSI--RGLGLKSVECVRLLTLHH--LAFPVDTNVGRIAVRLGWVPLQPLPESLQLHLL 547 (947)
Q Consensus 479 e~L~~vP~deareeLlsL--PGVG~KTAd~ILlfafgr--pafPVDTHV~RVl~RLGlv~~k~tpeevEk~Le 547 (947)
.||. +..|++.+.+.++ +|+-+--..++|.-+.|. -.++...-+.||+.+-|++|. -|+.++..+.
T Consensus 24 tWlK-~~~ddvkeqI~K~akKGltpsqIGviLRDshGi~q~r~v~G~kI~Rilk~~Gl~Pe--iPeDLy~lik 93 (151)
T KOG0400|consen 24 TWLK-LTADDVKEQIYKLAKKGLTPSQIGVILRDSHGIGQVRFVTGNKILRILKSNGLAPE--IPEDLYHLIK 93 (151)
T ss_pred HHHh-cCHHHHHHHHHHHHHcCCChhHceeeeecccCcchhheechhHHHHHHHHcCCCCC--CcHHHHHHHH
Confidence 4553 4455677777765 888888888888766554 478888999999999999984 5666554433
Done!