Query 002448
Match_columns 921
No_of_seqs 409 out of 1962
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 00:11:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/002448.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/002448hhsearch_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 5.2E-58 1.1E-62 417.0 6.8 85 833-917 1-85 (103)
2 COG0177 Nth Predicted EndoIII- 100.0 9.1E-53 2E-57 432.4 20.2 209 344-609 1-209 (211)
3 PRK10702 endonuclease III; Pro 100.0 1.5E-43 3.3E-48 365.3 20.2 208 344-608 1-208 (211)
4 TIGR01083 nth endonuclease III 100.0 3.7E-36 8E-41 304.9 19.1 190 348-594 2-191 (191)
5 TIGR01084 mutY A/G-specific ad 100.0 5.8E-36 1.3E-40 319.8 17.7 197 378-624 22-222 (275)
6 PRK10880 adenine DNA glycosyla 100.0 9.2E-36 2E-40 327.2 18.6 202 378-625 26-227 (350)
7 COG2231 Uncharacterized protei 100.0 3.1E-33 6.7E-38 284.7 18.7 209 347-607 6-214 (215)
8 PRK13913 3-methyladenine DNA g 100.0 7.3E-33 1.6E-37 287.4 18.6 189 379-589 27-216 (218)
9 KOG1921 Endonuclease III [Repl 100.0 2.4E-33 5.2E-38 290.5 13.6 181 381-606 77-260 (286)
10 PRK13910 DNA glycosylase MutY; 100.0 9.1E-32 2E-36 289.3 18.5 150 431-609 22-172 (289)
11 COG1194 MutY A/G-specific DNA 100.0 1.4E-27 3E-32 259.8 18.8 196 378-623 30-230 (342)
12 smart00478 ENDO3c endonuclease 99.9 8.7E-25 1.9E-29 211.7 16.3 147 404-585 3-149 (149)
13 cd00056 ENDO3c endonuclease II 99.9 2.5E-24 5.3E-29 210.2 14.8 158 383-583 1-158 (158)
14 PRK01229 N-glycosylase/DNA lya 99.9 1.2E-23 2.6E-28 217.4 15.3 138 379-551 34-185 (208)
15 TIGR03252 uncharacterized HhH- 99.8 5.5E-20 1.2E-24 185.9 10.5 112 380-510 16-134 (177)
16 KOG2457 A/G-specific adenine D 99.8 4.4E-20 9.4E-25 201.2 9.5 217 348-608 89-310 (555)
17 TIGR00588 ogg 8-oxoguanine DNA 99.8 1.7E-19 3.6E-24 196.4 13.9 141 381-532 118-263 (310)
18 COG0122 AlkA 3-methyladenine D 99.7 9.8E-18 2.1E-22 181.0 13.8 167 380-562 103-271 (285)
19 PRK10308 3-methyl-adenine DNA 99.6 4.4E-15 9.6E-20 160.3 13.9 150 380-551 111-262 (283)
20 KOG2875 8-oxoguanine DNA glyco 99.5 3.3E-14 7E-19 151.3 8.1 138 382-530 117-258 (323)
21 PF00730 HhH-GPD: HhH-GPD supe 99.5 1.5E-13 3.3E-18 126.6 9.2 107 387-551 1-107 (108)
22 KOG1918 3-methyladenine DNA gl 99.5 1.1E-13 2.4E-18 143.2 7.9 168 374-562 67-238 (254)
23 PF15629 Perm-CXXC: Permuted s 99.1 1.5E-11 3.4E-16 92.2 0.8 32 799-830 1-32 (32)
24 COG1059 Thermostable 8-oxoguan 98.5 2.8E-07 6E-12 94.7 6.7 123 382-536 39-166 (210)
25 PF00633 HHH: Helix-hairpin-he 97.6 1.6E-05 3.6E-10 59.7 0.8 26 483-510 5-30 (30)
26 PF10576 EndIII_4Fe-2S: Iron-s 96.8 0.00044 9.6E-09 46.1 0.7 17 587-603 1-17 (17)
27 PF09674 DUF2400: Protein of u 96.7 0.0014 3E-08 70.2 3.9 89 456-584 142-230 (232)
28 TIGR02757 conserved hypothetic 96.2 0.0043 9.2E-08 66.5 4.0 86 458-584 142-227 (229)
29 smart00525 FES FES domain. iro 95.8 0.0043 9.3E-08 44.8 1.3 22 586-607 1-22 (26)
30 smart00278 HhH1 Helix-hairpin- 91.4 0.13 2.9E-06 37.2 1.9 20 492-511 2-21 (26)
31 PF12826 HHH_2: Helix-hairpin- 90.6 0.3 6.6E-06 42.4 3.7 40 465-510 15-54 (64)
32 PF14716 HHH_8: Helix-hairpin- 85.9 3 6.6E-05 36.5 6.9 58 443-510 9-66 (68)
33 PF09171 DUF1886: Domain of un 84.9 2.6 5.5E-05 46.2 7.2 133 443-589 77-232 (246)
34 PRK13901 ruvA Holliday junctio 84.4 2.1 4.6E-05 45.3 6.2 65 429-514 60-130 (196)
35 PF14520 HHH_5: Helix-hairpin- 83.7 3.1 6.7E-05 35.4 5.8 30 477-510 28-57 (60)
36 TIGR00426 competence protein C 83.6 2.1 4.6E-05 37.3 4.9 57 437-510 10-66 (69)
37 PRK02515 psbU photosystem II c 82.5 1.9 4.1E-05 43.2 4.6 53 436-510 54-106 (132)
38 PRK00076 recR recombination pr 79.8 1.6 3.5E-05 46.3 3.3 27 487-513 7-33 (196)
39 PRK13844 recombination protein 79.5 1.7 3.6E-05 46.3 3.3 28 486-513 10-37 (200)
40 TIGR00615 recR recombination p 79.3 1.7 3.7E-05 46.0 3.3 28 486-513 6-33 (195)
41 PRK00116 ruvA Holliday junctio 77.7 3.7 8E-05 43.0 5.2 21 490-510 107-127 (192)
42 PRK10353 3-methyl-adenine DNA 76.8 2.2 4.7E-05 45.0 3.2 47 429-475 60-111 (187)
43 PRK00024 hypothetical protein; 76.3 4.6 9.9E-05 43.4 5.5 61 439-508 23-83 (224)
44 COG0353 RecR Recombinational D 75.8 2.4 5.2E-05 45.0 3.2 27 487-513 8-34 (198)
45 PRK14606 ruvA Holliday junctio 75.8 6.1 0.00013 41.5 6.2 65 429-514 61-131 (188)
46 PRK14601 ruvA Holliday junctio 75.6 6.3 0.00014 41.4 6.2 69 429-514 61-131 (183)
47 TIGR00608 radc DNA repair prot 74.8 5.5 0.00012 42.8 5.7 61 439-508 13-77 (218)
48 PF14520 HHH_5: Helix-hairpin- 74.5 2.8 6E-05 35.7 2.7 27 489-515 3-29 (60)
49 COG0632 RuvA Holliday junction 73.1 2.5 5.4E-05 45.0 2.5 67 430-511 62-128 (201)
50 PF03352 Adenine_glyco: Methyl 71.8 10 0.00022 39.9 6.6 48 429-476 55-107 (179)
51 PRK14602 ruvA Holliday junctio 71.5 4.5 9.7E-05 42.9 4.0 24 490-513 108-131 (203)
52 COG1555 ComEA DNA uptake prote 71.3 6.3 0.00014 40.0 4.8 56 437-510 91-146 (149)
53 PRK14603 ruvA Holliday junctio 71.1 8 0.00017 40.9 5.7 22 490-511 106-127 (197)
54 PRK14604 ruvA Holliday junctio 70.9 8.1 0.00018 40.9 5.7 69 429-514 61-131 (195)
55 PF12836 HHH_3: Helix-hairpin- 70.8 4.9 0.00011 34.9 3.5 52 439-508 10-61 (65)
56 PF14229 DUF4332: Domain of un 70.6 40 0.00087 33.0 10.0 59 430-513 15-75 (122)
57 PRK14605 ruvA Holliday junctio 70.4 9.2 0.0002 40.3 6.0 64 429-509 61-126 (194)
58 TIGR00575 dnlj DNA ligase, NAD 70.0 19 0.00041 44.6 9.3 62 432-509 455-516 (652)
59 PRK14973 DNA topoisomerase I; 69.8 6.7 0.00015 50.2 5.7 97 429-533 821-919 (936)
60 PRK14600 ruvA Holliday junctio 69.2 7.5 0.00016 40.8 5.0 67 429-513 61-129 (186)
61 TIGR00084 ruvA Holliday juncti 68.4 4.9 0.00011 42.2 3.5 65 429-510 60-126 (191)
62 TIGR00624 tag DNA-3-methyladen 67.2 6 0.00013 41.5 3.8 43 429-471 59-103 (179)
63 TIGR01259 comE comEA protein. 65.2 8.8 0.00019 37.5 4.3 59 434-510 59-117 (120)
64 PF14490 HHH_4: Helix-hairpin- 64.6 11 0.00023 35.1 4.5 57 441-509 7-64 (94)
65 PRK00116 ruvA Holliday junctio 63.9 6.5 0.00014 41.1 3.4 42 490-532 72-116 (192)
66 PRK07956 ligA NAD-dependent DN 61.4 19 0.00041 44.7 7.1 33 432-467 468-500 (665)
67 PF02371 Transposase_20: Trans 61.4 5.9 0.00013 36.2 2.2 42 491-535 2-43 (87)
68 PF12836 HHH_3: Helix-hairpin- 59.9 8.2 0.00018 33.5 2.7 21 490-510 13-33 (65)
69 PF11731 Cdd1: Pathogenicity l 58.7 9.5 0.0002 36.3 3.1 27 489-515 10-36 (93)
70 COG1555 ComEA DNA uptake prote 56.4 8.5 0.00018 39.1 2.6 22 490-511 96-117 (149)
71 PRK14351 ligA NAD-dependent DN 56.1 44 0.00096 41.8 9.0 59 432-508 485-545 (689)
72 TIGR00084 ruvA Holliday juncti 55.3 9.3 0.0002 40.2 2.7 22 488-509 69-90 (191)
73 TIGR01259 comE comEA protein. 54.3 11 0.00023 36.9 2.8 21 490-510 67-87 (120)
74 COG2003 RadC DNA repair protei 53.7 25 0.00054 38.3 5.6 89 439-548 23-115 (224)
75 PF05559 DUF763: Protein of un 53.4 32 0.00069 39.3 6.6 24 485-510 265-288 (319)
76 PRK14350 ligA NAD-dependent DN 53.1 18 0.0004 44.8 5.1 21 490-510 540-560 (669)
77 PRK07945 hypothetical protein; 53.1 21 0.00045 40.5 5.2 61 443-510 8-68 (335)
78 COG2818 Tag 3-methyladenine DN 52.4 52 0.0011 35.1 7.5 48 429-476 61-113 (188)
79 PRK08609 hypothetical protein; 52.3 39 0.00084 41.1 7.6 49 452-507 54-104 (570)
80 PRK14605 ruvA Holliday junctio 52.3 11 0.00025 39.6 2.8 23 488-510 70-92 (194)
81 smart00483 POLXc DNA polymeras 50.2 35 0.00076 38.8 6.4 57 443-510 11-67 (334)
82 smart00483 POLXc DNA polymeras 49.7 25 0.00054 39.9 5.2 50 453-507 55-105 (334)
83 PRK08097 ligB NAD-dependent DN 49.2 75 0.0016 39.0 9.3 70 432-510 448-539 (562)
84 KOG2841 Structure-specific end 48.9 53 0.0011 36.3 7.1 95 342-469 156-250 (254)
85 PF11798 IMS_HHH: IMS family H 48.0 12 0.00027 28.6 1.7 15 493-507 13-27 (32)
86 COG0272 Lig NAD-dependent DNA 45.0 33 0.00071 42.6 5.5 58 443-510 505-562 (667)
87 PRK13482 DNA integrity scannin 45.0 26 0.00057 40.4 4.4 59 443-507 275-335 (352)
88 cd00141 NT_POLXc Nucleotidyltr 41.4 48 0.001 37.2 5.7 16 490-505 84-99 (307)
89 smart00279 HhH2 Helix-hairpin- 40.8 19 0.00041 28.5 1.7 16 494-509 19-34 (36)
90 cd00141 NT_POLXc Nucleotidyltr 40.7 36 0.00078 38.2 4.6 57 443-510 8-64 (307)
91 TIGR00426 competence protein C 39.6 27 0.00059 30.4 2.8 21 490-510 15-36 (69)
92 PRK14973 DNA topoisomerase I; 38.3 2.3E+02 0.005 37.0 11.6 76 429-512 763-856 (936)
93 PRK13901 ruvA Holliday junctio 35.4 29 0.00063 37.0 2.7 22 488-509 69-90 (196)
94 PRK14600 ruvA Holliday junctio 35.2 29 0.00062 36.6 2.6 23 488-510 70-92 (186)
95 PRK14601 ruvA Holliday junctio 34.2 31 0.00067 36.3 2.6 22 488-509 70-91 (183)
96 PRK14606 ruvA Holliday junctio 33.8 32 0.00069 36.3 2.7 22 488-509 70-91 (188)
97 COG1796 POL4 DNA polymerase IV 33.5 68 0.0015 36.8 5.3 60 443-510 13-72 (326)
98 PF03118 RNA_pol_A_CTD: Bacter 33.3 47 0.001 29.4 3.3 48 449-508 14-61 (66)
99 PRK14603 ruvA Holliday junctio 33.2 32 0.0007 36.5 2.6 22 488-509 69-90 (197)
100 PRK00254 ski2-like helicase; P 33.1 81 0.0017 39.3 6.4 41 492-532 646-686 (720)
101 cd00080 HhH2_motif Helix-hairp 32.7 21 0.00046 32.1 1.0 19 492-510 23-41 (75)
102 PRK14602 ruvA Holliday junctio 32.4 35 0.00076 36.4 2.7 23 488-510 71-93 (203)
103 PF10391 DNA_pol_lambd_f: Fing 32.3 39 0.00084 28.8 2.5 19 491-509 2-20 (52)
104 PRK14604 ruvA Holliday junctio 31.7 35 0.00076 36.2 2.6 23 488-510 70-92 (195)
105 PRK02515 psbU photosystem II c 30.6 38 0.00082 34.3 2.4 20 490-509 60-79 (132)
106 PRK13280 N-glycosylase/DNA lya 29.6 1.9E+02 0.004 32.6 7.7 134 443-586 87-242 (269)
107 PRK07758 hypothetical protein; 29.2 69 0.0015 30.8 3.8 28 477-508 57-84 (95)
108 COG0632 RuvA Holliday junction 27.6 45 0.00098 35.7 2.6 23 488-510 70-92 (201)
109 PF00416 Ribosomal_S13: Riboso 26.4 59 0.0013 31.2 2.9 23 488-510 12-34 (107)
110 PF11372 DUF3173: Domain of un 26.2 1.6E+02 0.0035 26.1 5.2 44 452-496 12-57 (59)
111 PRK14670 uvrC excinuclease ABC 25.8 64 0.0014 39.6 3.7 37 468-510 529-565 (574)
112 PF13592 HTH_33: Winged helix- 25.3 94 0.002 26.6 3.6 36 500-535 3-39 (60)
113 PRK08609 hypothetical protein; 25.0 1.1E+02 0.0025 37.3 5.6 57 443-510 11-67 (570)
114 PRK12766 50S ribosomal protein 24.5 1.2E+02 0.0025 33.5 5.0 30 477-510 26-55 (232)
115 COG1491 Predicted RNA-binding 23.5 88 0.0019 33.5 3.7 26 490-515 129-154 (202)
116 COG4277 Predicted DNA-binding 23.1 55 0.0012 37.5 2.2 21 490-510 329-349 (404)
117 PRK14469 ribosomal RNA large s 22.0 1.4E+02 0.003 34.0 5.3 55 437-496 4-58 (343)
118 COG1948 MUS81 ERCC4-type nucle 21.9 1.1E+02 0.0023 34.2 4.2 20 348-367 86-105 (254)
119 KOG0400 40S ribosomal protein 21.6 1E+02 0.0023 31.3 3.6 65 479-546 24-92 (151)
120 COG2019 AdkA Archaeal adenylat 21.1 2.9E+02 0.0062 29.7 6.8 42 493-534 9-51 (189)
121 PRK01172 ski2-like helicase; P 20.9 2.1E+02 0.0046 35.3 6.8 42 429-473 631-672 (674)
122 PRK13890 conjugal transfer pro 20.2 3.7E+02 0.0079 26.4 7.0 94 409-533 8-101 (120)
123 TIGR01448 recD_rel helicase, p 20.1 4.3E+02 0.0093 33.4 9.3 56 442-509 143-199 (720)
No 1
>PF15628 RRM_DME: RRM in Demeter
Probab=100.00 E-value=5.2e-58 Score=417.01 Aligned_cols=85 Identities=80% Similarity=1.327 Sum_probs=83.7
Q ss_pred eeEeeeccccccCCccCCCcceeeceeeecccCCCCCccccchhhccCCceeEEeccChhhhccCCCHHHHHHHhhcCce
Q 002448 833 GTLLIPCRTAMRGSFPLNGTYFQVNEVFADHDSSLNPIDVPREWLWNLPRRMVYFGTSVSSIFKGLSTEGIQFCFWKGKN 912 (921)
Q Consensus 833 gTiLiPCRtAmrg~FPLnGTYFQvNEVFaDh~Ss~~Pi~vpr~~iw~L~rr~vyfGtsv~sI~kg~s~~~iq~cf~~g~v 912 (921)
|||||||||||||+|||||||||||||||||+||+|||+|||+|||+|+||+|||||||+|||||||++|||+|||+|||
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 Eeecc
Q 002448 913 YEIPV 917 (921)
Q Consensus 913 Cv~~~ 917 (921)
|||--
T Consensus 81 CVR~F 85 (103)
T PF15628_consen 81 CVRGF 85 (103)
T ss_pred EEeec
Confidence 99953
No 2
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=100.00 E-value=9.1e-53 Score=432.42 Aligned_cols=209 Identities=27% Similarity=0.402 Sum_probs=196.3
Q ss_pred CcHHHHHHHHHhHhhhcCCCccccCCCCchhhhhcccccccchhhhhhcccccccccccccccChHHHHHHHHhccCccc
Q 002448 344 MLAEKTRNLGDDISVANKLSDNKLIEPNSVEQVLSAHKVYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQE 423 (921)
Q Consensus 344 ~~~~~~~~i~~rl~~~~~~p~~~l~~~~~~~~~~~~~~~~~lLia~iLsaq~~d~~vnk~qnT~W~nL~kaL~n~~Lk~e 423 (921)
|.++++.+|++||...||.|..++.|. ++|++|||+|||||+||+.+|++ | .+|++.
T Consensus 1 ~~~~~~~~i~~~l~~~~p~~~~~l~~~----------~pf~lLva~iLSaqttD~~vn~a--t--~~Lf~~--------- 57 (211)
T COG0177 1 LNKKKALEILDRLRELYPEPKTELDFK----------DPFELLVAVILSAQTTDEVVNKA--T--PALFKR--------- 57 (211)
T ss_pred CcHhhHHHHHHHHHHHCCCCCCccCcC----------CcHHHHHHHHHhccCchHHHHHH--H--HHHHHH---------
Confidence 467889999999999999999998777 89999999999999999999976 5 788765
Q ss_pred cccCcCCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHcCCCccHhh
Q 002448 424 RSRDRMDSLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKS 503 (921)
Q Consensus 424 rl~~~~~~pTpEaLa~A~~EELeelIR~iGfyr~KAk~Ik~lA~~Lve~~GGlDLe~L~~vP~deaReeLLsLPGVG~KT 503 (921)
++||++|++|++++|+++|+++|||++||++|+++|++|+++||| ++|.+ +++|++|||||+||
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 679999999999999999999999999999999999999999999 89988 99999999999999
Q ss_pred HHHHHHHhcCCceeecchHHHHHHHHhCCCCCCCCHHHHHHHHHHhcCchHHHHHhhhhhhhcCChhhHHHHHHHHHHHh
Q 002448 504 VECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQPLPESLQLHLLELYPVLESIQKYLWPRLCKLDQRTLYELHYQLITFG 583 (921)
Q Consensus 504 Ad~ILlfafgrpvfpVDTHV~RVl~RLGlv~~~~tpeeve~~L~~llP~~e~Iqk~LW~rl~~ld~e~~~e~H~lLI~fG 583 (921)
|++||+++||+|+|+|||||+||++|+||++ .++|+++++.|++++| +. .+..+|++||.||
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------KE-----------LWTDLHHWLILHG 183 (211)
T ss_pred HHHHHHhhcCCCcccccchHHHHHHHhCCCC-CCCHHHHHHHHHHHCC------HH-----------HHHHHHHHHHHhh
Confidence 9999999999999999999999999999999 4899999999999999 33 4468999999999
Q ss_pred HhhcccCCCCCCCCCCchhchhhhhh
Q 002448 584 KVFCTKSKPNCNACPMRGECRHFASA 609 (921)
Q Consensus 584 R~IC~arkP~C~~CPLrdlC~y~~~~ 609 (921)
|++|++|+|+|+.|||+++|+++.+.
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=1.5e-43 Score=365.32 Aligned_cols=208 Identities=21% Similarity=0.261 Sum_probs=183.7
Q ss_pred CcHHHHHHHHHhHhhhcCCCccccCCCCchhhhhcccccccchhhhhhcccccccccccccccChHHHHHHHHhccCccc
Q 002448 344 MLAEKTRNLGDDISVANKLSDNKLIEPNSVEQVLSAHKVYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQE 423 (921)
Q Consensus 344 ~~~~~~~~i~~rl~~~~~~p~~~l~~~~~~~~~~~~~~~~~lLia~iLsaq~~d~~vnk~qnT~W~nL~kaL~n~~Lk~e 423 (921)
|+.++..+|+++|.+.||.+...+.+. ++|+.||+.|||+|+++..++++ +.+|+.
T Consensus 1 ~~~~~~~~i~~~l~~~~~~~~~~~~~~----------~p~e~lvs~iLsq~t~~~~v~~~----~~~L~~---------- 56 (211)
T PRK10702 1 MNKAKRLEILTRLRDNNPHPTTELNFS----------SPFELLIAVLLSAQATDVSVNKA----TAKLYP---------- 56 (211)
T ss_pred CCHHHHHHHHHHHHHHCCCCCCCCCCC----------ChHHHHHHHHHHhhcCHHHHHHH----HHHHHH----------
Confidence 345678999999999999876554443 78999999999999999887754 244442
Q ss_pred cccCcCCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHcCCCccHhh
Q 002448 424 RSRDRMDSLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKS 503 (921)
Q Consensus 424 rl~~~~~~pTpEaLa~A~~EELeelIR~iGfyr~KAk~Ik~lA~~Lve~~GGlDLe~L~~vP~deaReeLLsLPGVG~KT 503 (921)
.++||++|++|+.++|+++|+++|||++||++|+++|++++++||| .+|.+ +++|++|||||+||
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 2889999999999999999999999999999999999999999988 67766 99999999999999
Q ss_pred HHHHHHHhcCCceeecchHHHHHHHHhCCCCCCCCHHHHHHHHHHhcCchHHHHHhhhhhhhcCChhhHHHHHHHHHHHh
Q 002448 504 VECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQPLPESLQLHLLELYPVLESIQKYLWPRLCKLDQRTLYELHYQLITFG 583 (921)
Q Consensus 504 Ad~ILlfafgrpvfpVDTHV~RVl~RLGlv~~~~tpeeve~~L~~llP~~e~Iqk~LW~rl~~ld~e~~~e~H~lLI~fG 583 (921)
|++||+|+||+++||||+||.||+.|+||.+. .+++++++.+++.+|. . .+.++|++||+||
T Consensus 122 A~~ill~a~~~~~~~VDt~v~Rv~~r~g~~~~-~~~~~~~~~l~~~lp~------~-----------~~~~~~~~li~~G 183 (211)
T PRK10702 122 ANVVLNTAFGWPTIAVDTHIFRVCNRTQFAPG-KNVEQVEEKLLKVVPA------E-----------FKVDCHHWLILHG 183 (211)
T ss_pred HHHHHHHHcCCCcccccchHHHHHHHhCCCCC-CCHHHHHHHHHHhCCc------h-----------HHHHHHHHHHHHh
Confidence 99999999999999999999999999999875 6899999999998883 2 2357999999999
Q ss_pred HhhcccCCCCCCCCCCchhchhhhh
Q 002448 584 KVFCTKSKPNCNACPMRGECRHFAS 608 (921)
Q Consensus 584 R~IC~arkP~C~~CPLrdlC~y~~~ 608 (921)
|.+|++++|+|+.|||++.|+|+.+
T Consensus 184 r~~C~~~~P~C~~Cpl~~~C~~~~~ 208 (211)
T PRK10702 184 RYTCIARKPRCGSCIIEDLCEYKEK 208 (211)
T ss_pred HHHcCCCCCCCCCCcChhhcCcccc
Confidence 9999999999999999999997654
No 4
>TIGR01083 nth endonuclease III. This equivalog model identifes nth members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=100.00 E-value=3.7e-36 Score=304.88 Aligned_cols=190 Identities=25% Similarity=0.328 Sum_probs=165.4
Q ss_pred HHHHHHHhHhhhcCCCccccCCCCchhhhhcccccccchhhhhhcccccccccccccccChHHHHHHHHhccCccccccC
Q 002448 348 KTRNLGDDISVANKLSDNKLIEPNSVEQVLSAHKVYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQERSRD 427 (921)
Q Consensus 348 ~~~~i~~rl~~~~~~p~~~l~~~~~~~~~~~~~~~~~lLia~iLsaq~~d~~vnk~qnT~W~nL~kaL~n~~Lk~erl~~ 427 (921)
+..+|+++|.+.||.+...+.+ .++|+.||+.||++|++++.+.++ |.+|+.
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 4678999999999977643322 378999999999999888777632 344432
Q ss_pred cCCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHcCCCccHhhHHHH
Q 002448 428 RMDSLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECV 507 (921)
Q Consensus 428 ~~~~pTpEaLa~A~~EELeelIR~iGfyr~KAk~Ik~lA~~Lve~~GGlDLe~L~~vP~deaReeLLsLPGVG~KTAd~I 507 (921)
.++||++|++++.++|+++|+++||+++||++|+++|+.+.+++++ .+|.. +++|++|||||+|||++|
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 45544 899999999999999999
Q ss_pred HHHhcCCceeecchHHHHHHHHhCCCCCCCCHHHHHHHHHHhcCchHHHHHhhhhhhhcCChhhHHHHHHHHHHHhHhhc
Q 002448 508 RLLTLHHLAFPVDTNVGRIAVRLGWVPLQPLPESLQLHLLELYPVLESIQKYLWPRLCKLDQRTLYELHYQLITFGKVFC 587 (921)
Q Consensus 508 LlfafgrpvfpVDTHV~RVl~RLGlv~~~~tpeeve~~L~~llP~~e~Iqk~LW~rl~~ld~e~~~e~H~lLI~fGR~IC 587 (921)
|+|+||+++||||+||.||+.|+||... .+++++++.++.++|. ..+.+||.+||+|||.+|
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 235789999999999999
Q ss_pred ccCCCCC
Q 002448 588 TKSKPNC 594 (921)
Q Consensus 588 ~arkP~C 594 (921)
++++|+|
T Consensus 185 ~~~~P~C 191 (191)
T TIGR01083 185 KARKPLC 191 (191)
T ss_pred CCCCCCC
Confidence 9999999
No 5
>TIGR01084 mutY A/G-specific adenine glycosylase. This equivalog model identifies mutY members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=100.00 E-value=5.8e-36 Score=319.83 Aligned_cols=197 Identities=21% Similarity=0.299 Sum_probs=167.6
Q ss_pred cccccccchhhhhhcccccccccccccccChHHHHHHHHhccCccccccCcCCCCCHHHHHcCCHHHHHHHHHhcCCcHH
Q 002448 378 SAHKVYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQERSRDRMDSLDYEALRCANVKEISEAIKERGMNNM 457 (921)
Q Consensus 378 ~~~~~~~lLia~iLsaq~~d~~vnk~qnT~W~nL~kaL~n~~Lk~erl~~~~~~pTpEaLa~A~~EELeelIR~iGfyr~ 457 (921)
...++|+.||+.||++|++++.+.. .|.++.+. ++||++|+++++++|.++|+++||| +
T Consensus 22 ~~~dpy~vlvseIL~QQT~v~~v~~----~~~rl~~~----------------fpt~~~La~a~~eeL~~~~~~lG~y-~ 80 (275)
T TIGR01084 22 QNKTPYRVWLSEVMLQQTQVATVIP----YFERFLER----------------FPTVQALANAPQDEVLKLWEGLGYY-A 80 (275)
T ss_pred CCCCHHHHHHHHHHHhhccHHHHHH----HHHHHHHh----------------CCCHHHHHCcCHHHHHHHHHHCCcH-H
Confidence 4458899999999999998877763 34555422 8999999999999999999999999 5
Q ss_pred HHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHcCCCccHhhHHHHHHHhcCCceeecchHHHHHHHHhCCCCCCC
Q 002448 458 LAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQP 537 (921)
Q Consensus 458 KAk~Ik~lA~~Lve~~GGlDLe~L~~vP~deaReeLLsLPGVG~KTAd~ILlfafgrpvfpVDTHV~RVl~RLGlv~~~~ 537 (921)
||++|+++|+.|.++||| .+|.+ +++|++|||||+|||++||+|+||+++++||+||.||+.|++......
T Consensus 81 RAr~L~~~A~~i~~~~~g-------~~p~~--~~~L~~LpGIG~~TA~~Il~~a~~~~~~~vD~~v~RVl~Rl~~~~~~~ 151 (275)
T TIGR01084 81 RARNLHKAAQEVVEEFGG-------EFPQD--FEDLAALPGVGRYTAGAILSFALNKPYPILDGNVKRVLSRLFAVEGWP 151 (275)
T ss_pred HHHHHHHHHHHHHHHcCC-------CCcHH--HHHHHhCCCCCHHHHHHHHHHHCCCCCCcchHhHHHHHHHHccCcCCC
Confidence 999999999999999998 67866 999999999999999999999999999999999999999997665545
Q ss_pred CHHHHHHHH----HHhcCchHHHHHhhhhhhhcCChhhHHHHHHHHHHHhHhhcccCCCCCCCCCCchhchhhhhhcccc
Q 002448 538 LPESLQLHL----LELYPVLESIQKYLWPRLCKLDQRTLYELHYQLITFGKVFCTKSKPNCNACPMRGECRHFASAFASA 613 (921)
Q Consensus 538 tpeeve~~L----~~llP~~e~Iqk~LW~rl~~ld~e~~~e~H~lLI~fGR~IC~arkP~C~~CPLrdlC~y~~~~~asa 613 (921)
++.++++.+ ++++| ...+.+||++||+||+.+|++++|+|+.|||++.|.++..+ .
T Consensus 152 ~~~~~~~~l~~~~~~~lp-----------------~~~~~~~n~alm~lG~~vC~~~~P~C~~Cpl~~~C~~~~~~---~ 211 (275)
T TIGR01084 152 GKKKVENRLWTLAESLLP-----------------KADPEAFNQALMDLGAMICTRKKPKCDLCPLQDFCLAYQQG---T 211 (275)
T ss_pred CHHHHHHHHHHHHHHHCC-----------------hhhHHHHHHHHHHHhHHHcCCCCCCCCCCCChhhCHHHHcC---C
Confidence 666666653 34443 34678999999999999999999999999999999998875 4
Q ss_pred cccCCCCCccc
Q 002448 614 RLALPGPEEKS 624 (921)
Q Consensus 614 r~alP~~~~~~ 624 (921)
...+|.+.++.
T Consensus 212 ~~~~p~~~~~~ 222 (275)
T TIGR01084 212 WEEYPVKKPKA 222 (275)
T ss_pred HhhcCCCCCCC
Confidence 56688776544
No 6
>PRK10880 adenine DNA glycosylase; Provisional
Probab=100.00 E-value=9.2e-36 Score=327.25 Aligned_cols=202 Identities=19% Similarity=0.272 Sum_probs=167.7
Q ss_pred cccccccchhhhhhcccccccccccccccChHHHHHHHHhccCccccccCcCCCCCHHHHHcCCHHHHHHHHHhcCCcHH
Q 002448 378 SAHKVYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQERSRDRMDSLDYEALRCANVKEISEAIKERGMNNM 457 (921)
Q Consensus 378 ~~~~~~~lLia~iLsaq~~d~~vnk~qnT~W~nL~kaL~n~~Lk~erl~~~~~~pTpEaLa~A~~EELeelIR~iGfyr~ 457 (921)
...++|..+|+.||++|++++.|... |.++.+. +||+++|++|++++|.++|+++|||+
T Consensus 26 ~~~dpy~ilVseILlQQT~v~~v~~~----~~rl~~~----------------fPt~~~La~a~~eel~~~~~glGyy~- 84 (350)
T PRK10880 26 IDKTPYKVWLSEVMLQQTQVATVIPY----FERFMAR----------------FPTVTDLANAPLDEVLHLWTGLGYYA- 84 (350)
T ss_pred CCCCHHHHHHHHHHHhhccHHHHHHH----HHHHHHH----------------CcCHHHHHCcCHHHHHHHHHcCChHH-
Confidence 34588999999999999998877742 4555432 89999999999999999999999996
Q ss_pred HHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHcCCCccHhhHHHHHHHhcCCceeecchHHHHHHHHhCCCCCCC
Q 002448 458 LAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQP 537 (921)
Q Consensus 458 KAk~Ik~lA~~Lve~~GGlDLe~L~~vP~deaReeLLsLPGVG~KTAd~ILlfafgrpvfpVDTHV~RVl~RLGlv~~~~ 537 (921)
||++|+++|+.++++||| .+|.+ +++|++|||||+|||++||+|+||+++++||+||+||+.|++.+....
T Consensus 85 RAr~L~~~A~~i~~~~~g-------~~p~~--~~~L~~LpGIG~~TA~aIl~~af~~~~~iVD~nV~RV~~Rl~~i~~~~ 155 (350)
T PRK10880 85 RARNLHKAAQQVATLHGG-------EFPET--FEEVAALPGVGRSTAGAILSLSLGKHFPILDGNVKRVLARCYAVSGWP 155 (350)
T ss_pred HHHHHHHHHHHHHHHhCC-------Cchhh--HHHHhcCCCccHHHHHHHHHHHCCCCeecccHHHHHHHHHHhcccCCC
Confidence 999999999999999998 67766 999999999999999999999999999999999999999985544334
Q ss_pred CHHHHHHHHHHhcCchHHHHHhhhhhhhcCChhhHHHHHHHHHHHhHhhcccCCCCCCCCCCchhchhhhhhcccccccC
Q 002448 538 LPESLQLHLLELYPVLESIQKYLWPRLCKLDQRTLYELHYQLITFGKVFCTKSKPNCNACPMRGECRHFASAFASARLAL 617 (921)
Q Consensus 538 tpeeve~~L~~llP~~e~Iqk~LW~rl~~ld~e~~~e~H~lLI~fGR~IC~arkP~C~~CPLrdlC~y~~~~~asar~al 617 (921)
.+.++++.+.++.. . .++...+.+||++||+||+.+|++++|+|..|||++.|+++... ....+
T Consensus 156 ~~~~~~~~l~~~~~-------~------l~p~~~~~~~nqalm~lGa~vC~p~~P~C~~Cpl~~~C~~~~~~---~~~~~ 219 (350)
T PRK10880 156 GKKEVENRLWQLSE-------Q------VTPAVGVERFNQAMMDLGAMVCTRSKPKCELCPLQNGCIAYANH---SWALY 219 (350)
T ss_pred ChHHHHHHHHHHHH-------H------hCChhHHHHHHHHHHHhhHHhccCCCCCCCCCccHhhhHHHHcC---CHhhC
Confidence 56666655433211 0 12235678999999999999999999999999999999998875 44668
Q ss_pred CCCCcccc
Q 002448 618 PGPEEKSI 625 (921)
Q Consensus 618 P~~~~~~~ 625 (921)
|.+.++..
T Consensus 220 P~k~~k~~ 227 (350)
T PRK10880 220 PGKKPKQT 227 (350)
T ss_pred CCCCCCCC
Confidence 87765543
No 7
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=100.00 E-value=3.1e-33 Score=284.66 Aligned_cols=209 Identities=23% Similarity=0.396 Sum_probs=174.7
Q ss_pred HHHHHHHHhHhhhcCCCccccCCCCchhhhhcccccccchhhhhhcccccccccccccccChHHHHHHHHhccCcccccc
Q 002448 347 EKTRNLGDDISVANKLSDNKLIEPNSVEQVLSAHKVYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQERSR 426 (921)
Q Consensus 347 ~~~~~i~~rl~~~~~~p~~~l~~~~~~~~~~~~~~~~~lLia~iLsaq~~d~~vnk~qnT~W~nL~kaL~n~~Lk~erl~ 426 (921)
.....|++-|-..|+... +-..++.++.++.+| .+|||+|++|.++|+| |+.+
T Consensus 6 ~~~~~iy~~L~~~yg~q~-----------WWp~~~~~EiiigAI-----------LtQNT~WknvekAlen--Lk~~--- 58 (215)
T COG2231 6 ENITKIYKELLRLYGDQG-----------WWPADNKDEIIIGAI-----------LTQNTSWKNVEKALEN--LKNE--- 58 (215)
T ss_pred HHHHHHHHHHHHHcCCcc-----------CCCCCCchhHHHHHH-----------HhccccHHHHHHHHHH--HHHc---
Confidence 345677777777777544 112234445666555 4689999999999987 8865
Q ss_pred CcCCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHcCCCccHhhHHH
Q 002448 427 DRMDSLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVEC 506 (921)
Q Consensus 427 ~~~~~pTpEaLa~A~~EELeelIR~iGfyr~KAk~Ik~lA~~Lve~~GGlDLe~L~~vP~deaReeLLsLPGVG~KTAd~ 506 (921)
+..++++|..++.++|+++||++|||++||+||+++...+++.+.++ + .+-+..+|++|++++|||.+|||+
T Consensus 59 ---~~~~l~~I~~~~~~~L~elIrpsGFYnqKa~rLk~l~k~l~~~~~~~--~---~~~~~~~R~~LL~iKGIG~ETaDs 130 (215)
T COG2231 59 ---GILNLKKILKLDEEELAELIRPSGFYNQKAKRLKALSKNLAKFFINL--E---SFKSEVLREELLSIKGIGKETADS 130 (215)
T ss_pred ---ccCCHHHHhcCCHHHHHHHHhccchHHHHHHHHHHHHHHHHHHhhhh--h---ccchHHHHHHHHccCCcchhhHHH
Confidence 67789999999999999999999999999999999999999877653 3 333444799999999999999999
Q ss_pred HHHHhcCCceeecchHHHHHHHHhCCCCCCCCHHHHHHHHHHhcCchHHHHHhhhhhhhcCChhhHHHHHHHHHHHhHhh
Q 002448 507 VRLLTLHHLAFPVDTNVGRIAVRLGWVPLQPLPESLQLHLLELYPVLESIQKYLWPRLCKLDQRTLYELHYQLITFGKVF 586 (921)
Q Consensus 507 ILlfafgrpvfpVDTHV~RVl~RLGlv~~~~tpeeve~~L~~llP~~e~Iqk~LW~rl~~ld~e~~~e~H~lLI~fGR~I 586 (921)
||+|||++|+|+||.|.+|++.|+|.+.. ++|+++++.+++-+|. +...+++||++|+.|||.+
T Consensus 131 ILlYa~~rp~FVvD~Yt~R~l~rlg~i~~-k~ydeik~~fe~~l~~---------------~~~lyqe~HAlIv~~~K~f 194 (215)
T COG2231 131 ILLYALDRPVFVVDKYTRRLLSRLGGIEE-KKYDEIKELFEENLPE---------------NLRLYQEFHALIVEHAKHF 194 (215)
T ss_pred HHHHHhcCcccchhHHHHHHHHHhccccc-ccHHHHHHHHHhcchh---------------HHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999886 4899999999887773 2245789999999999999
Q ss_pred cccCCCCCCCCCCchhchhhh
Q 002448 587 CTKSKPNCNACPMRGECRHFA 607 (921)
Q Consensus 587 C~arkP~C~~CPLrdlC~y~~ 607 (921)
|+. +|.|+.|||...|.++.
T Consensus 195 ~~k-~~~~~~cpL~~~~~~~~ 214 (215)
T COG2231 195 CKK-KPLCEKCPLKEKCKKYR 214 (215)
T ss_pred ccC-CcCCCCchHHHHHhhcc
Confidence 985 69999999999998753
No 8
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=100.00 E-value=7.3e-33 Score=287.37 Aligned_cols=189 Identities=16% Similarity=0.225 Sum_probs=148.5
Q ss_pred ccccccchhhhhhcccccccccccccccChHHHHHHHHhccCccccccCcCCCCCHHHHHcCCHHHHHHHHHhcCCcHHH
Q 002448 379 AHKVYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQERSRDRMDSLDYEALRCANVKEISEAIKERGMNNML 458 (921)
Q Consensus 379 ~~~~~~lLia~iLsaq~~d~~vnk~qnT~W~nL~kaL~n~~Lk~erl~~~~~~pTpEaLa~A~~EELeelIR~iGfyr~K 458 (921)
..++|+.||++||++| |.|+++.+++.+ |++..+.+...++||++|++++.++|+++||++|||++|
T Consensus 27 ~~~~fevLV~aILsQq-----------T~~~~v~~a~~~--L~~~~~~~~~~~~t~e~L~~a~~eeL~~~Irp~Gf~~~K 93 (218)
T PRK13913 27 NALKFEALLGAVLTQN-----------TKFEAVEKSLEN--LKNAFILENDDEINLKKIAYIEFSKLAECVRPSGFYNQK 93 (218)
T ss_pred CcCHHHHHHHHHHHhh-----------hhHHHHHHHHHH--HHHhcccccccCCCHHHHHcCCHHHHHHHHHhcCCHHHH
Confidence 3578999999999987 667777777755 443211112246799999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHcCCCccHhhHHHHHHHhcCCceeecchHHHHHHHHhCCCCCCCC
Q 002448 459 AERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQPL 538 (921)
Q Consensus 459 Ak~Ik~lA~~Lve~~GGlDLe~L~~vP~deaReeLLsLPGVG~KTAd~ILlfafgrpvfpVDTHV~RVl~RLGlv~~~~t 538 (921)
|++|+++|+++.++||++ +.+ ...++|++|++|||||+|||++||+|+||+|+|+||+|++||+.|+||.. .+
T Consensus 94 A~~Lk~la~~i~~~~g~~--~~~---~~~~~re~Ll~l~GIG~kTAd~iLlya~~rp~fvVDty~~Rv~~RlG~~~--~~ 166 (218)
T PRK13913 94 AKRLIDLSENILKDFGSF--ENF---KQEVTREWLLDQKGIGKESADAILCYVCAKEVMVVDKYSYLFLKKLGIEI--ED 166 (218)
T ss_pred HHHHHHHHHHHHHHcCCc--hhc---cCchHHHHHHcCCCccHHHHHHHHHHHcCCCccccchhHHHHHHHcCCCC--CC
Confidence 999999999999988863 333 22356999999999999999999999999999999999999999999975 57
Q ss_pred HHHHHHHHHHhcCc-hHHHHHhhhhhhhcCChhhHHHHHHHHHHHhHhhccc
Q 002448 539 PESLQLHLLELYPV-LESIQKYLWPRLCKLDQRTLYELHYQLITFGKVFCTK 589 (921)
Q Consensus 539 peeve~~L~~llP~-~e~Iqk~LW~rl~~ld~e~~~e~H~lLI~fGR~IC~a 589 (921)
|++++..++..++. ...+.. ..+.. ..+...+.+||.+||+|||..|.-
T Consensus 167 y~~~~~~~~~~l~~~~~~~~~-~~~~~-~~~~~~~~~~Halive~~k~~~~~ 216 (218)
T PRK13913 167 YDELQHFFEKGVQENLNSALA-LYENT-ISLAQLYARFHGKIVEFSKQKLEL 216 (218)
T ss_pred HHHHHHHHHHhhhhhhhhhhc-ccccc-chHHHHHHHHHHHHHHHHHHhhhc
Confidence 99999998886642 000000 00000 002257899999999999999964
No 9
>KOG1921 consensus Endonuclease III [Replication, recombination and repair]
Probab=100.00 E-value=2.4e-33 Score=290.52 Aligned_cols=181 Identities=27% Similarity=0.446 Sum_probs=162.1
Q ss_pred ccccchhhhhhcccccccccccccccChHHHHHHHHhccCccccccCcCCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHH
Q 002448 381 KVYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQERSRDRMDSLDYEALRCANVKEISEAIKERGMNNMLAE 460 (921)
Q Consensus 381 ~~~~lLia~iLsaq~~d~~vnk~qnT~W~nL~kaL~n~~Lk~erl~~~~~~pTpEaLa~A~~EELeelIR~iGfyr~KAk 460 (921)
-.|+-||+.|||+|++|..... ++.+ |++ .+.+|+++|+++++..|.++|.+.|||++||+
T Consensus 77 ~RfqvLv~lmLSSQTKDevt~~-----------Am~r--L~~------~~gLT~e~v~~~de~~l~~LI~~VgFy~rKA~ 137 (286)
T KOG1921|consen 77 RRFQVLVGLMLSSQTKDEVTAA-----------AMLR--LKE------YGGLTLEAVLKIDEPTLNELIYPVGFYTRKAK 137 (286)
T ss_pred HhHHHHHHHHHhcchHHHHHHH-----------HHHH--HHH------hcCCCHHHHhccChHhHHhhhhhccchHHHHH
Confidence 4599999999999999965442 2221 332 24789999999999999999999999999999
Q ss_pred HHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHcCCCccHhhHHHHHHHhcCCc-eeecchHHHHHHHHhCCCCCC-CC
Q 002448 461 RMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLLTLHHL-AFPVDTNVGRIAVRLGWVPLQ-PL 538 (921)
Q Consensus 461 ~Ik~lA~~Lve~~GGlDLe~L~~vP~deaReeLLsLPGVG~KTAd~ILlfafgrp-vfpVDTHV~RVl~RLGlv~~~-~t 538 (921)
||+.+|+++.++|+| ++|++ .++|++|||||+|.|..+|..|+|+- .|.||+||+||++||||++.+ ++
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 99999999999999999999999986 899999999999999999853 35
Q ss_pred HHHHHHHHHHhcCchHHHHHhhhhhhhcCChhhHHHHHHHHHHHhHhhcccCCCCCCCCCC-chhchhh
Q 002448 539 PESLQLHLLELYPVLESIQKYLWPRLCKLDQRTLYELHYQLITFGKVFCTKSKPNCNACPM-RGECRHF 606 (921)
Q Consensus 539 peeve~~L~~llP~~e~Iqk~LW~rl~~ld~e~~~e~H~lLI~fGR~IC~arkP~C~~CPL-rdlC~y~ 606 (921)
|++++.+|+.|+| +.+| .+++++||.||+.||++++|+|+.|.+ +++|+..
T Consensus 209 pE~TR~aLq~wLP------k~lW-----------~eIN~lLVGFGQ~iC~p~~prC~~C~~~~~~Cpss 260 (286)
T KOG1921|consen 209 PEQTRVALQQWLP------KSLW-----------VEINHLLVGFGQTICTPRRPRCGLCLLSRDLCPSS 260 (286)
T ss_pred HHHHHHHHHHhCc------HHHH-----------hhhhceeecccceeeecCCCCccccccCcccCchh
Confidence 9999999999999 5666 589999999999999999999999999 6999963
No 10
>PRK13910 DNA glycosylase MutY; Provisional
Probab=99.98 E-value=9.1e-32 Score=289.31 Aligned_cols=150 Identities=24% Similarity=0.403 Sum_probs=132.8
Q ss_pred CCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHcCCCccHhhHHHHHHH
Q 002448 431 SLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLL 510 (921)
Q Consensus 431 ~pTpEaLa~A~~EELeelIR~iGfyr~KAk~Ik~lA~~Lve~~GGlDLe~L~~vP~deaReeLLsLPGVG~KTAd~ILlf 510 (921)
+||+++|++|++++|.++|+++|||+ ||++|+++|+.++++|+| .+|.+ +++|++|||||+|||++||+|
T Consensus 22 fPt~e~La~a~~~el~~~~~glGyy~-RAr~L~~~A~~i~~~~~g-------~~P~~--~~~L~~LpGIG~kTA~aIl~~ 91 (289)
T PRK13910 22 FPTLKDLANAPLEEVLLLWRGLGYYS-RAKNLKKSAEICVKEHHS-------QLPND--YQSLLKLPGIGAYTANAILCF 91 (289)
T ss_pred CCCHHHHHCCCHHHHHHHHHcCCcHH-HHHHHHHHHHHHHHHhCC-------CCChh--HHHHHhCCCCCHHHHHHHHHH
Confidence 89999999999999999999999995 999999999999999988 78887 999999999999999999999
Q ss_pred hcCCceeecchHHHHHHHHh-CCCCCCCCHHHHHHHHHHhcCchHHHHHhhhhhhhcCChhhHHHHHHHHHHHhHhhccc
Q 002448 511 TLHHLAFPVDTNVGRIAVRL-GWVPLQPLPESLQLHLLELYPVLESIQKYLWPRLCKLDQRTLYELHYQLITFGKVFCTK 589 (921)
Q Consensus 511 afgrpvfpVDTHV~RVl~RL-Glv~~~~tpeeve~~L~~llP~~e~Iqk~LW~rl~~ld~e~~~e~H~lLI~fGR~IC~a 589 (921)
+||+++++||+||+||+.|+ |+... ..+.+++.....++| ...+.++|++||+||+.+|++
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 455554444334444 245678999999999999999
Q ss_pred CCCCCCCCCCchhchhhhhh
Q 002448 590 SKPNCNACPMRGECRHFASA 609 (921)
Q Consensus 590 rkP~C~~CPLrdlC~y~~~~ 609 (921)
+|+|..|||++.|.++...
T Consensus 154 -~P~C~~CPl~~~C~~~~~~ 172 (289)
T PRK13910 154 -KPKCAICPLNPYCLGKNNP 172 (289)
T ss_pred -CCCCCCCcChhhhhhhhcC
Confidence 7999999999999998875
No 11
>COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair]
Probab=99.95 E-value=1.4e-27 Score=259.82 Aligned_cols=196 Identities=20% Similarity=0.293 Sum_probs=160.1
Q ss_pred cccccccchhhhhhcccccccccccccccChHHHHHHHHhccCccccccCcCCCCCHHHHHcCCHHHHHHHHHhcCCcHH
Q 002448 378 SAHKVYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQERSRDRMDSLDYEALRCANVKEISEAIKERGMNNM 457 (921)
Q Consensus 378 ~~~~~~~lLia~iLsaq~~d~~vnk~qnT~W~nL~kaL~n~~Lk~erl~~~~~~pTpEaLa~A~~EELeelIR~iGfyr~ 457 (921)
...++|..+|+.++..||+-++|.. --.+-++ .+||+++||+|+.++|..+|.++||| +
T Consensus 30 ~~~~PY~VwvSEiMLQQT~v~~Vi~-------yy~~fl~-------------rfPti~~LA~A~~~evl~~W~gLGYy-s 88 (342)
T COG1194 30 ETKDPYRVWVSEIMLQQTQVATVIP-------YYERFLE-------------RFPTIKALAAAPEDEVLKAWEGLGYY-S 88 (342)
T ss_pred CCCCcceehhHHHHhhhccHhhhhh-------hHHHHHH-------------hCCCHHHHhcCCHHHHHHHHHhcChH-H
Confidence 4446899999999999999877762 2233333 29999999999999999999999987 7
Q ss_pred HHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHcCCCccHhhHHHHHHHhcCCceeecchHHHHHHHHhCCCCCCC
Q 002448 458 LAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQP 537 (921)
Q Consensus 458 KAk~Ik~lA~~Lve~~GGlDLe~L~~vP~deaReeLLsLPGVG~KTAd~ILlfafgrpvfpVDTHV~RVl~RLGlv~~~~ 537 (921)
||++|+++|+.++++||| .+|.+ .+.|.+|||||++||.+||.++|+++..+||+||.||+.|+.-+....
T Consensus 89 RArnL~~~A~~v~~~~~G-------~~P~~--~~~l~~LpGiG~yTa~Ail~~a~~~~~~~lDgNV~RVl~R~f~i~~~~ 159 (342)
T COG1194 89 RARNLHKAAQEVVERHGG-------EFPDD--EEELAALPGVGPYTAGAILSFAFNQPEPVLDGNVKRVLSRLFAISGDI 159 (342)
T ss_pred HHHHHHHHHHHHHHHcCC-------CCCCC--HHHHHhCCCCcHHHHHHHHHHHhCCCCceeecchheeehhhhcccccc
Confidence 999999999999999999 89999 899999999999999999999999999999999999999995544322
Q ss_pred ----CHHHHHHHHHHhcCchHHHHHhhhhhhhcCChhh-HHHHHHHHHHHhHhhcccCCCCCCCCCCchhchhhhhhccc
Q 002448 538 ----LPESLQLHLLELYPVLESIQKYLWPRLCKLDQRT-LYELHYQLITFGKVFCTKSKPNCNACPMRGECRHFASAFAS 612 (921)
Q Consensus 538 ----tpeeve~~L~~llP~~e~Iqk~LW~rl~~ld~e~-~~e~H~lLI~fGR~IC~arkP~C~~CPLrdlC~y~~~~~as 612 (921)
+..+++..++.+ +++.. +.+|+++||++|+.||++++|+|..|||++.|..+..+.
T Consensus 160 ~~~~~~~~~~~~~~~l-----------------l~p~~~~~~fnqammdlGA~ICt~~~P~C~~CPl~~~c~a~~~g~-- 220 (342)
T COG1194 160 GKPKTKKELWELAEQL-----------------LTPDRRPGDFNQAMMDLGATICTAKKPKCSLCPLRDNCAAYRNGT-- 220 (342)
T ss_pred cccchhHHHHHHHHHh-----------------cCCCCChHHHHHHHHHhhhHhhcCCCCCCCcCcchHHHHHHHcCC--
Confidence 122233333331 12222 789999999999999999999999999999999988762
Q ss_pred ccccCCCCCcc
Q 002448 613 ARLALPGPEEK 623 (921)
Q Consensus 613 ar~alP~~~~~ 623 (921)
-..+|.+..+
T Consensus 221 -~~~~P~k~~k 230 (342)
T COG1194 221 -PEKYPVKKPK 230 (342)
T ss_pred -cccCCCcCcc
Confidence 2356665543
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=8.7e-25 Score=211.74 Aligned_cols=147 Identities=32% Similarity=0.426 Sum_probs=128.7
Q ss_pred cccChHHHHHHHHhccCccccccCcCCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhc
Q 002448 404 NAIDWESLRKEVQRNSGKQERSRDRMDSLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRD 483 (921)
Q Consensus 404 qnT~W~nL~kaL~n~~Lk~erl~~~~~~pTpEaLa~A~~EELeelIR~iGfyr~KAk~Ik~lA~~Lve~~GGlDLe~L~~ 483 (921)
|+|.|.++.+++.+ +.. .++||++|++++.++|.++|+++||+++||++|+++++.+.+.+++ .
T Consensus 3 qq~~~~~a~~~~~~--l~~-------~~~~~~~l~~~~~~eL~~~l~~~g~~~~ka~~i~~~a~~~~~~~~~-------~ 66 (149)
T smart00478 3 QQTSDEAVNKATER--LFE-------KFPTPEDLAAADEEELEELIRPLGFYRRKAKYLIELARILVEEYGG-------E 66 (149)
T ss_pred CcccHHHHHHHHHH--HHH-------HCCCHHHHHCCCHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHCC-------C
Confidence 56777777777654 443 2789999999999999999999999999999999999999998876 4
Q ss_pred CCchHHHHHHHcCCCccHhhHHHHHHHhcCCceeecchHHHHHHHHhCCCCCCCCHHHHHHHHHHhcCchHHHHHhhhhh
Q 002448 484 VPPDKAKDYLLSIRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQPLPESLQLHLLELYPVLESIQKYLWPR 563 (921)
Q Consensus 484 vP~deaReeLLsLPGVG~KTAd~ILlfafgrpvfpVDTHV~RVl~RLGlv~~~~tpeeve~~L~~llP~~e~Iqk~LW~r 563 (921)
+|. .+++|++|||||+|||++||+|+|++++++||+||.|++.|+|+++..+++++++++++.++|.
T Consensus 67 ~~~--~~~~L~~l~GIG~~tA~~~l~~~~~~~~~~~D~~v~r~~~rl~~~~~~~~~~~~~~~~~~~~p~----------- 133 (149)
T smart00478 67 VPD--DREELLKLPGVGRKTANAVLSFALGKPFIPVDTHVLRIAKRLGLVDKKSTPEEVEKLLEKLLPK----------- 133 (149)
T ss_pred ccH--HHHHHHcCCCCcHHHHHHHHHHHCCCCCCccchHHHHHHHHhCCCCCCCCHHHHHHHHHHHCCH-----------
Confidence 553 5899999999999999999999999999999999999999999998767899999999998882
Q ss_pred hhcCChhhHHHHHHHHHHHhHh
Q 002448 564 LCKLDQRTLYELHYQLITFGKV 585 (921)
Q Consensus 564 l~~ld~e~~~e~H~lLI~fGR~ 585 (921)
..++.+|.+++.||+.
T Consensus 134 ------~~~~~~~~~~l~~g~~ 149 (149)
T smart00478 134 ------EDWRELNLLLIDFGRT 149 (149)
T ss_pred ------HHHHHHHHHHHHHcCC
Confidence 2457899999999973
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=2.5e-24 Score=210.20 Aligned_cols=158 Identities=30% Similarity=0.426 Sum_probs=135.2
Q ss_pred ccchhhhhhcccccccccccccccChHHHHHHHHhccCccccccCcCCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHH
Q 002448 383 YDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQERSRDRMDSLDYEALRCANVKEISEAIKERGMNNMLAERM 462 (921)
Q Consensus 383 ~~lLia~iLsaq~~d~~vnk~qnT~W~nL~kaL~n~~Lk~erl~~~~~~pTpEaLa~A~~EELeelIR~iGfyr~KAk~I 462 (921)
|+.|++.||++|++.+.+.+ .|.+|.+.+ .+||++|+.++.++|++++.+.| +++||++|
T Consensus 1 ~e~Li~~il~q~~s~~~a~~----~~~~l~~~~---------------gpt~~~l~~~~~~~l~~~~~~~G-~~~kA~~i 60 (158)
T cd00056 1 FEVLVSEILSQQTTDKAVNK----AYERLFERY---------------GPTPEALAAADEEELRELIRSLG-YRRKAKYL 60 (158)
T ss_pred CHHHHHHHHHhcccHHHHHH----HHHHHHHHh---------------CCCHHHHHCCCHHHHHHHHHhcC-hHHHHHHH
Confidence 67889999999998876653 345554331 18999999999999999999999 88999999
Q ss_pred HHHHHHHHHhhCCCChhhhhcCCchHHHHHHHcCCCccHhhHHHHHHHhcCCceeecchHHHHHHHHhCCCCCCCCHHHH
Q 002448 463 KDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQPLPESL 542 (921)
Q Consensus 463 k~lA~~Lve~~GGlDLe~L~~vP~deaReeLLsLPGVG~KTAd~ILlfafgrpvfpVDTHV~RVl~RLGlv~~~~tpeev 542 (921)
+++|+.+.+.+++.+. +.++++++|++|||||+|||++||+|+||.++||||+|+.|++.|+|+.+..++++++
T Consensus 61 ~~~a~~~~~~~~~~~~------~~~~~~~~L~~l~GIG~~tA~~~l~~~~~~~~~pvD~~v~r~~~~~~~~~~~~~~~~~ 134 (158)
T cd00056 61 KELARAIVEGFGGLVL------DDPDAREELLALPGVGRKTANVVLLFALGPDAFPVDTHVRRVLKRLGLIPKKKTPEEL 134 (158)
T ss_pred HHHHHHHHHHcCCccC------CCcccHHHHHcCCCCCHHHHHHHHHHHCCCCCCccchhHHHHHHHhCCCCCCCCHHHH
Confidence 9999999998877432 6677899999999999999999999999988999999999999999997666789999
Q ss_pred HHHHHHhcCchHHHHHhhhhhhhcCChhhHHHHHHHHHHHh
Q 002448 543 QLHLLELYPVLESIQKYLWPRLCKLDQRTLYELHYQLITFG 583 (921)
Q Consensus 543 e~~L~~llP~~e~Iqk~LW~rl~~ld~e~~~e~H~lLI~fG 583 (921)
+..+..+.|. .....+|+.||.||
T Consensus 135 ~~~~~~~~~~-----------------~~~~~~~~~l~~~g 158 (158)
T cd00056 135 EELLEELLPK-----------------PYWGEANQALMDLG 158 (158)
T ss_pred HHHHHHHCCH-----------------HHHHHHHHHHHHcC
Confidence 9998888751 23467999999987
No 14
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=99.90 E-value=1.2e-23 Score=217.37 Aligned_cols=138 Identities=19% Similarity=0.142 Sum_probs=111.8
Q ss_pred ccccccchhhhhhcccccccccccccccChHHHHHHHHhccCccccccCcCCCCCHHHHHcCCHHHHHHHHHhcC--CcH
Q 002448 379 AHKVYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQERSRDRMDSLDYEALRCANVKEISEAIKERG--MNN 456 (921)
Q Consensus 379 ~~~~~~lLia~iLsaq~~d~~vnk~qnT~W~nL~kaL~n~~Lk~erl~~~~~~pTpEaLa~A~~EELeelIR~iG--fyr 456 (921)
..++|++|+++|||+|+++. ++.+++.+ | .++.+ .++.++|+++||++| ||+
T Consensus 34 ~~~~f~~Lv~~ILsqnT~~~-----------~v~~a~~~--L------------~~~~l-~~~~eeL~~~Ir~~Gygf~~ 87 (208)
T PRK01229 34 EEDLFSELSFCILTANSSAE-----------GGIKAQKE--I------------GDGFL-YLSEEELEEKLKEVGHRFYN 87 (208)
T ss_pred cCChHHHHHHHHhcCcCcHH-----------HHHHHHHh--c------------CHHHc-CCCHHHHHHHHHHhhcccHH
Confidence 35889999999999866554 44555433 2 34556 899999999999995 999
Q ss_pred HHHHHHHHHHHH---HHHhh--CCCChhhhhcCCchHHHHHHH-cCCCccHhhHHHHHHHhcCCceeecchHHHHHHHHh
Q 002448 457 MLAERMKDFLNR---LVREH--GSIDLEWLRDVPPDKAKDYLL-SIRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRL 530 (921)
Q Consensus 457 ~KAk~Ik~lA~~---Lve~~--GGlDLe~L~~vP~deaReeLL-sLPGVG~KTAd~ILlfafgrpvfpVDTHV~RVl~RL 530 (921)
+||++|++++++ +.+.+ ++ .+ .++|++|+ +|||||+|||++||++.+.+|+|+||+||.|+++|+
T Consensus 88 ~KAk~I~~~~~~~~~l~~~~~~~~-------~~--~~~R~~Ll~~lpGIG~KTAd~vL~~~~~~~~~iVDtHv~Ri~~Rl 158 (208)
T PRK01229 88 KRAEYIVEARKLYGKLKEIIKADK-------DQ--FEAREFLVKNIKGIGYKEASHFLRNVGYEDLAILDRHILRFLKRY 158 (208)
T ss_pred HHHHHHHHHHHHHHHHHHHHhccC-------Cc--hHHHHHHHHcCCCCcHHHHHHHHHHccCCCeeeeeHHHHHHHHHh
Confidence 999999999987 43333 22 33 45699999 999999999999997665599999999999999999
Q ss_pred CCCCCC------CCHHHHHHHHHHhcC
Q 002448 531 GWVPLQ------PLPESLQLHLLELYP 551 (921)
Q Consensus 531 Glv~~~------~tpeeve~~L~~llP 551 (921)
|+++.. .+|.+++..|.++.+
T Consensus 159 G~~~~~~~~lt~~~y~~~E~~l~~~~~ 185 (208)
T PRK01229 159 GLIEEIPKTLSKKRYLEIEEILREIAE 185 (208)
T ss_pred CCCcccccccCcCCHHHHHHHHHHHHH
Confidence 998752 579999999887654
No 15
>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=99.81 E-value=5.5e-20 Score=185.86 Aligned_cols=112 Identities=13% Similarity=0.120 Sum_probs=96.5
Q ss_pred cccccchhhhhhcccccccccccccccChHHHHHHHHhccCccccccCcCCCCCHHHHHcCCHHHHHHHHHhc----CCc
Q 002448 380 HKVYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQERSRDRMDSLDYEALRCANVKEISEAIKER----GMN 455 (921)
Q Consensus 380 ~~~~~lLia~iLsaq~~d~~vnk~qnT~W~nL~kaL~n~~Lk~erl~~~~~~pTpEaLa~A~~EELeelIR~i----Gfy 455 (921)
.++|++||++|||+|++|+.++++ +.+|++.+ +.+||++|++++.++|+++|++. |||
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 478999999999999998888754 35565442 35799999999999999999876 999
Q ss_pred HHHHHHHHHHHHHHHHhhCCCChhhhhc---CCchHHHHHHHcCCCccHhhHHHHHHH
Q 002448 456 NMLAERMKDFLNRLVREHGSIDLEWLRD---VPPDKAKDYLLSIRGLGLKSVECVRLL 510 (921)
Q Consensus 456 r~KAk~Ik~lA~~Lve~~GGlDLe~L~~---vP~deaReeLLsLPGVG~KTAd~ILlf 510 (921)
++||++|+++|++|+++|+| +++.|.. .+..++|++|++|||||+|||++||++
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 344577999999999999999999986
No 16
>KOG2457 consensus A/G-specific adenine DNA glycosylase [Replication, recombination and repair]
Probab=99.81 E-value=4.4e-20 Score=201.24 Aligned_cols=217 Identities=19% Similarity=0.250 Sum_probs=164.6
Q ss_pred HHHHHHHhHhhhcCCCccccCCCCch-hhhhc-ccccccchhhhhhcccccccccccccccChHHHHHHHHhccCccccc
Q 002448 348 KTRNLGDDISVANKLSDNKLIEPNSV-EQVLS-AHKVYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQERS 425 (921)
Q Consensus 348 ~~~~i~~rl~~~~~~p~~~l~~~~~~-~~~~~-~~~~~~lLia~iLsaq~~d~~vnk~qnT~W~nL~kaL~n~~Lk~erl 425 (921)
+...+..-|-..|..-+..|+..+.. +--.+ -.-.|+-+|+-|.-.|++-.+|.+- -.+-++
T Consensus 89 Ev~~fR~sLl~wYD~~KRdLPWR~r~sEde~DwerRaYeVwVSEiMLQQTrV~TV~~Y-------Yt~WMq--------- 152 (555)
T KOG2457|consen 89 EVQKFRMSLLDWYDVNKRDLPWRNRRSEDEKDWERRAYEVWVSEIMLQQTRVQTVMKY-------YTRWMQ--------- 152 (555)
T ss_pred HHHHHHHHHHHHhhhhcccCccccCCccchhhHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHH---------
Confidence 34444445555666555556655441 10000 1134777888888888876655421 112222
Q ss_pred cCcCCCCCHHHHHcCCH-HHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHc-CCCccHhh
Q 002448 426 RDRMDSLDYEALRCANV-KEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLS-IRGLGLKS 503 (921)
Q Consensus 426 ~~~~~~pTpEaLa~A~~-EELeelIR~iGfyr~KAk~Ik~lA~~Lve~~GGlDLe~L~~vP~deaReeLLs-LPGVG~KT 503 (921)
.+||..+++.|+. +++.++|.++||| +|+++|++-|+.+++.++| .+|.. -+.|.+ +||||+||
T Consensus 153 ----kwPTl~dla~Asl~~eVn~lWaGlGyY-~R~rrL~ega~~vv~~~~g-------e~Prt--a~~l~kgvpGVG~YT 218 (555)
T KOG2457|consen 153 ----KWPTLYDLAQASLEKEVNELWAGLGYY-RRARRLLEGAKMVVAGTEG-------EFPRT--ASSLMKGVPGVGQYT 218 (555)
T ss_pred ----hCchHHHHHHHHHHHHHHHHHhhhhHH-HHHHHHHHHHHHHHHhCCC-------CCCCh--HHHHHhhCCCCCccc
Confidence 3899999999999 8999999999999 6999999999999999998 89988 567776 99999999
Q ss_pred HHHHHHHhcCCceeecchHHHHHHHHhCCCCCCCCHHHHHHHHHHhcCchHHHHHhhhhhh-hcCChhhHHHHHHHHHHH
Q 002448 504 VECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQPLPESLQLHLLELYPVLESIQKYLWPRL-CKLDQRTLYELHYQLITF 582 (921)
Q Consensus 504 Ad~ILlfafgrpvfpVDTHV~RVl~RLGlv~~~~tpeeve~~L~~llP~~e~Iqk~LW~rl-~~ld~e~~~e~H~lLI~f 582 (921)
|.+|+.+||+++.=+||.||.||+.|.--+..+.+..++-. .+|... -..|+..+++|+++||++
T Consensus 219 AGAiaSIAf~q~tGiVDGNVirvlsRalAIhsDcSkgk~~q--------------~~wkLA~qLVDP~RPGDFNQalMEL 284 (555)
T KOG2457|consen 219 AGAIASIAFNQVTGIVDGNVIRVLSRALAIHSDCSKGKFFQ--------------SSWKLAAQLVDPSRPGDFNQALMEL 284 (555)
T ss_pred hhhhhhhhhcCcccccccchHHHhHHhHhhcCCcchhhHHH--------------HHHHHHHHhcCCCCCCcHHHHHHHh
Confidence 99999999999999999999999999744443333333222 345432 246788999999999999
Q ss_pred hHhhcccCCCCCCCCCCchhchhhhh
Q 002448 583 GKVFCTKSKPNCNACPMRGECRHFAS 608 (921)
Q Consensus 583 GR~IC~arkP~C~~CPLrdlC~y~~~ 608 (921)
|..+|++.+|.|..||+...|+.|.-
T Consensus 285 GAt~CTpq~P~CS~CPvss~CrA~q~ 310 (555)
T KOG2457|consen 285 GATLCTPQKPSCSSCPVSSQCRAFQL 310 (555)
T ss_pred cCeeccCCCCCcCCCCcHHHHHHHhH
Confidence 99999999999999999999998874
No 17
>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=99.81 E-value=1.7e-19 Score=196.43 Aligned_cols=141 Identities=23% Similarity=0.289 Sum_probs=114.0
Q ss_pred ccccchhhhhhcccccccccccccccChHHHHHHHHhccCcccc--ccCcCCCCCHHHHHcCCHHHHHHHHHhcCCcHHH
Q 002448 381 KVYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQER--SRDRMDSLDYEALRCANVKEISEAIKERGMNNML 458 (921)
Q Consensus 381 ~~~~lLia~iLsaq~~d~~vnk~qnT~W~nL~kaL~n~~Lk~er--l~~~~~~pTpEaLa~A~~EELeelIR~iGfyr~K 458 (921)
++|+.||+.|+|+|.+.+.+. +.+.+|.+.+ |-.... ......+|||++|++++.+ +.||.+||. .|
T Consensus 118 d~fE~lv~~IlsQq~si~~a~----~~~~rL~~~~---G~~~~~~~g~~~~~FPtp~~La~~~~e---~~Lr~~G~g-~R 186 (310)
T TIGR00588 118 DPFECLISFICSSNNNIARIT----RMVERLCQAF---GPRLITLDGVTYHGFPSLHALTGPEAE---AHLRKLGLG-YR 186 (310)
T ss_pred CHHHHHHHHHHhCCCCHHHHH----HHHHHHHHHh---CCCcccCCCcccccCCCHHHHhCCChH---HHHHHcCCH-HH
Confidence 679999999999999987766 3456665442 211000 0012358999999997654 357889994 58
Q ss_pred HHHHHHHHHHHHHhhCCC-ChhhhhcCCchHHHHHHHcCCCccHhhHHHHHHHhcCCc-eeecchHHHHHHHHh-CC
Q 002448 459 AERMKDFLNRLVREHGSI-DLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLLTLHHL-AFPVDTNVGRIAVRL-GW 532 (921)
Q Consensus 459 Ak~Ik~lA~~Lve~~GGl-DLe~L~~vP~deaReeLLsLPGVG~KTAd~ILlfafgrp-vfpVDTHV~RVl~RL-Gl 532 (921)
|++|+++|+.+.+.+++. +++.|..++.++++++|++|||||+|||+|||+|+||++ +||||+||+|++.|+ |+
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 678888899999999999999999999999999999998 899999999999998 55
No 18
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=99.74 E-value=9.8e-18 Score=180.96 Aligned_cols=167 Identities=19% Similarity=0.241 Sum_probs=131.0
Q ss_pred cccccchhhhhhcccccccccccccccChHHHHHHHHhccCccccccCcCCCCCHHHHHcCCHHHHHHHHHhcCCcHHHH
Q 002448 380 HKVYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQERSRDRMDSLDYEALRCANVKEISEAIKERGMNNMLA 459 (921)
Q Consensus 380 ~~~~~lLia~iLsaq~~d~~vnk~qnT~W~nL~kaL~n~~Lk~erl~~~~~~pTpEaLa~A~~EELeelIR~iGfyr~KA 459 (921)
.++|+-||..|+++|-..+... +.|.+|...+-+ . +.....+|||++|++++++.|. .+|+...||
T Consensus 103 ~d~fe~lv~aI~~QqvS~~~A~----~i~~rl~~~~g~---~---~~~~~~fptpe~l~~~~~~~l~----~~g~s~~Ka 168 (285)
T COG0122 103 PDPFEALVRAILSQQVSVAAAA----KIWARLVSLYGN---A---LEIYHSFPTPEQLAAADEEALR----RCGLSGRKA 168 (285)
T ss_pred CCHHHHHHHHHHHhHhhHHHHH----HHHHHHHHHhCC---c---cccccCCCCHHHHHhcCHHHHH----HhCCcHHHH
Confidence 5889999999999999887666 668888876422 1 1123358999999999999875 599999999
Q ss_pred HHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHcCCCccHhhHHHHHHHhcCCc-eee-cchHHHHHHHHhCCCCCCC
Q 002448 460 ERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLLTLHHL-AFP-VDTNVGRIAVRLGWVPLQP 537 (921)
Q Consensus 460 k~Ik~lA~~Lve~~GGlDLe~L~~vP~deaReeLLsLPGVG~KTAd~ILlfafgrp-vfp-VDTHV~RVl~RLGlv~~~~ 537 (921)
+||+.+|+.+.+ |.+|+..+..++.++++++|.+|+|||+|||+|||+|++|++ +|| .|.+++|.+.+++..+...
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 899 5777888888887333333
Q ss_pred CHHHHHHHHHHhcCchHHHHHhhhh
Q 002448 538 LPESLQLHLLELYPVLESIQKYLWP 562 (921)
Q Consensus 538 tpeeve~~L~~llP~~e~Iqk~LW~ 562 (921)
+...++...+.+-|.....+.++|.
T Consensus 247 ~~~~~~~~~e~w~p~rs~A~~yLw~ 271 (285)
T COG0122 247 TEKEVRELAERWGPYRSYAALYLWR 271 (285)
T ss_pred hHHHHHHHHhcccCHHHHHHHHHHH
Confidence 3333555555555532233456665
No 19
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=99.61 E-value=4.4e-15 Score=160.28 Aligned_cols=150 Identities=15% Similarity=0.097 Sum_probs=114.1
Q ss_pred cccccchhhhhhcccccccccccccccChHHHHHHHHhccCccccccCcCCCCCHHHHHcCCHHHHHHHHHhcCCcHHHH
Q 002448 380 HKVYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQERSRDRMDSLDYEALRCANVKEISEAIKERGMNNMLA 459 (921)
Q Consensus 380 ~~~~~lLia~iLsaq~~d~~vnk~qnT~W~nL~kaL~n~~Lk~erl~~~~~~pTpEaLa~A~~EELeelIR~iGfyr~KA 459 (921)
-++|+.|+..|+++|.+-+... +.+.++...+ |-+-........+|||++|++++.++|+ .+||+++||
T Consensus 111 ~d~fE~lv~aIigQqisv~~a~----~~~~rlv~~~---G~~l~~~~~~~~FPtpe~La~~~~~eL~----~~Gl~~~Ra 179 (283)
T PRK10308 111 VDAFEQGVRAILGQLVSVAMAA----KLTAKVAQLY---GERLDDFPEYVCFPTPERLAAADPQALK----ALGMPLKRA 179 (283)
T ss_pred CCHHHHHHHHHHHhHHHHHHHH----HHHHHHHHHh---CccccCCCCccCCCCHHHHHcCCHHHHH----HCCCCHHHH
Confidence 3779999999999998765554 3345554442 2211000112458999999999999875 589999999
Q ss_pred HHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHcCCCccHhhHHHHHHHhcCCc-ee-ecchHHHHHHHHhCCCCCCC
Q 002448 460 ERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLLTLHHL-AF-PVDTNVGRIAVRLGWVPLQP 537 (921)
Q Consensus 460 k~Ik~lA~~Lve~~GGlDLe~L~~vP~deaReeLLsLPGVG~KTAd~ILlfafgrp-vf-pVDTHV~RVl~RLGlv~~~~ 537 (921)
++|+++|+.+.+ |.++++... +.+++++.|++|||||+|||++|++++||++ +| ++|.+++|.+ + ..
T Consensus 180 ~~L~~lA~~i~~--g~l~l~~~~--~~~~~~~~L~~LpGIGpwTA~~vllr~lg~~D~fp~~D~~l~~~~---~----~~ 248 (283)
T PRK10308 180 EALIHLANAALE--GTLPLTIPG--DVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFLPDDYLIKQRF---P----GM 248 (283)
T ss_pred HHHHHHHHHHHc--CCCCccccC--CHHHHHHHHhcCCCcCHHHHHHHHHHhCCCCCCCCcccHHHHHhc---c----cC
Confidence 999999999987 666665433 4577899999999999999999999999997 77 7899998744 1 24
Q ss_pred CHHHHHHHHHHhcC
Q 002448 538 LPESLQLHLLELYP 551 (921)
Q Consensus 538 tpeeve~~L~~llP 551 (921)
++.+++...+.+-|
T Consensus 249 ~~~~~~~~a~~w~P 262 (283)
T PRK10308 249 TPAQIRRYAERWKP 262 (283)
T ss_pred CHHHHHHHHHhcCC
Confidence 67788888777776
No 20
>KOG2875 consensus 8-oxoguanine DNA glycosylase [Replication, recombination and repair]
Probab=99.50 E-value=3.3e-14 Score=151.26 Aligned_cols=138 Identities=23% Similarity=0.280 Sum_probs=104.8
Q ss_pred cccchhhhhhcccccccccccccccChHHHHHHHHhccCccc--cccCcCCCCCHHHHHcCCHHHHHHHHHhcCCcHHHH
Q 002448 382 VYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQE--RSRDRMDSLDYEALRCANVKEISEAIKERGMNNMLA 459 (921)
Q Consensus 382 ~~~lLia~iLsaq~~d~~vnk~qnT~W~nL~kaL~n~~Lk~e--rl~~~~~~pTpEaLa~A~~EELeelIR~iGfyr~KA 459 (921)
+++-|++-|-|...-.+.. | .-+..-..++|.+-- ...+..++|+.++|+. .++++-+|.+||- .||
T Consensus 117 P~E~lfSFiCSSNNNIaRI-----T--~Mve~fc~~fG~~i~~~dg~~~h~FPsl~~L~g---~~~Ea~LR~~gfG-YRA 185 (323)
T KOG2875|consen 117 PIECLFSFICSSNNNIARI-----T--GMVERFCQAFGPRIIQLDGVDYHGFPSLQALAG---PEVEAELRKLGFG-YRA 185 (323)
T ss_pred cHHHHHHHHhcCCCcHHHH-----H--HHHHHHHHhhCcceEeecCcccccCccHHHhcC---cHhHHHHHHcCcc-hhH
Confidence 3555555555544333222 2 334445555554321 1223457899999987 6888889999996 799
Q ss_pred HHHHHHHHHHHHhhCCC-ChhhhhcCCchHHHHHHHcCCCccHhhHHHHHHHhcCCc-eeecchHHHHHHHHh
Q 002448 460 ERMKDFLNRLVREHGSI-DLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLLTLHHL-AFPVDTNVGRIAVRL 530 (921)
Q Consensus 460 k~Ik~lA~~Lve~~GGl-DLe~L~~vP~deaReeLLsLPGVG~KTAd~ILlfafgrp-vfpVDTHV~RVl~RL 530 (921)
|||.+.|+.|.++.|+. -|-.|++++.+++|+.|..|||||+|+||||+++++|+. ++|||+||.|++.-.
T Consensus 186 kYI~~ta~~l~~~~g~~~wLqsl~~~~yeear~~L~~lpGVG~KVADCI~Lm~l~~~~~VPVDvHi~ria~~y 258 (323)
T KOG2875|consen 186 KYISATARALQEKQGGLAWLQSLRKSSYEEAREALCSLPGVGPKVADCICLMSLDKLSAVPVDVHIWRIAQDY 258 (323)
T ss_pred HHHHHHHHHHHHhcccchHHHHHhcccHHHHHHHHhcCCCCcchHhhhhhhhhcCCCCcccchhhHHHHhhcc
Confidence 99999999999999882 234556889999999999999999999999999999987 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=99.47 E-value=1.5e-13 Score=126.58 Aligned_cols=107 Identities=25% Similarity=0.279 Sum_probs=87.1
Q ss_pred hhhhhcccccccccccccccChHHHHHHHHhccCccccccCcCCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHH
Q 002448 387 NPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQERSRDRMDSLDYEALRCANVKEISEAIKERGMNNMLAERMKDFL 466 (921)
Q Consensus 387 ia~iLsaq~~d~~vnk~qnT~W~nL~kaL~n~~Lk~erl~~~~~~pTpEaLa~A~~EELeelIR~iGfyr~KAk~Ik~lA 466 (921)
|+.||++|++...+.+ .|.+|.+. .|+|||++|+++++++|+++|+++||+++||++|+++|
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 5678888888876663 34555544 25899999999999999999999999999999999999
Q ss_pred HHHHHhhCCCChhhhhcCCchHHHHHHHcCCCccHhhHHHHHHHhcCCceeecchHHHHHHHHhCCCCCCCCHHHHHHHH
Q 002448 467 NRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQPLPESLQLHL 546 (921)
Q Consensus 467 ~~Lve~~GGlDLe~L~~vP~deaReeLLsLPGVG~KTAd~ILlfafgrpvfpVDTHV~RVl~RLGlv~~~~tpeeve~~L 546 (921)
+.+. ++..++++||+|+.|++.|+|+.+.+++++++++.+
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 122358999999999999999998777999999988
Q ss_pred HHhcC
Q 002448 547 LELYP 551 (921)
Q Consensus 547 ~~llP 551 (921)
++++|
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=99.45 E-value=1.1e-13 Score=143.22 Aligned_cols=168 Identities=15% Similarity=0.225 Sum_probs=130.5
Q ss_pred hhhhcccccccchhhhhhcccccccccccccccChHHHHHHHHhccCccccccCcCCCCCHHHHHcCCHHHHHHHHHhcC
Q 002448 374 EQVLSAHKVYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQERSRDRMDSLDYEALRCANVKEISEAIKERG 453 (921)
Q Consensus 374 ~~~~~~~~~~~lLia~iLsaq~~d~~vnk~qnT~W~nL~kaL~n~~Lk~erl~~~~~~pTpEaLa~A~~EELeelIR~iG 453 (921)
..++.+..||..|+.+|||.|-.++..|-. ..+ +..+.+.+ ..+++|+.+..++.++| +.+|
T Consensus 67 ~~~~~~q~Pf~~LiraIlsQQLs~kAansI----~~R-fvsl~~g~---------~~~~~pe~i~~~~~~~l----rkcG 128 (254)
T KOG1918|consen 67 LTFKETQTPFERLIRAILSQQLSGKAANSI----YNR-FVSLCGGA---------EKFPTPEFIDPLDCEEL----RKCG 128 (254)
T ss_pred CCcccccCcHHHHHHHHHHHHHHHHHHHHH----HHH-HHHHhCCC---------cCCCCchhcCcCCHHHH----HHhC
Confidence 456677889999999999999988776633 333 34444311 24899999999999996 4599
Q ss_pred CcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHcCCCccHhhHHHHHHHhcCCc-eeecchHHH-HHHHHh-
Q 002448 454 MNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLLTLHHL-AFPVDTNVG-RIAVRL- 530 (921)
Q Consensus 454 fyr~KAk~Ik~lA~~Lve~~GGlDLe~L~~vP~deaReeLLsLPGVG~KTAd~ILlfafgrp-vfpVDTHV~-RVl~RL- 530 (921)
|+.+|+.||+.+|+...+.| =...+.+.+++.+++.+.|..++|||+||+.++|.|+++|+ +||+|.-.. |-+..|
T Consensus 129 ~S~rK~~yLh~lA~~~~ng~-I~s~~~i~~mseEeL~~~LT~VKGIg~Wtv~MflIfsL~R~DVmp~dDlgir~g~k~l~ 207 (254)
T KOG1918|consen 129 FSKRKASYLHSLAEAYTNGY-IPSKSGIEKMSEEELIERLTNVKGIGRWTVEMFLIFSLHRPDVMPADDLGIRNGVKKLL 207 (254)
T ss_pred cchhhHHHHHHHHHHHhcCC-CCchHHHhhcCHHHHHHHHHhccCccceeeeeeeeeccCCCcccCchhhhHHHHHHHHh
Confidence 99999999999999998743 13566778999999999999999999999999999999998 999976544 444444
Q ss_pred CCCCCCCCHHHHHHHHHHhcCchHHH-HHhhhh
Q 002448 531 GWVPLQPLPESLQLHLLELYPVLESI-QKYLWP 562 (921)
Q Consensus 531 Glv~~~~tpeeve~~L~~llP~~e~I-qk~LW~ 562 (921)
|+-+. +.+.+++++-+.+-| ++.+ ..|+|.
T Consensus 208 gl~~~-p~~~evekl~e~~kp-yRtvaawYlWk 238 (254)
T KOG1918|consen 208 GLKPL-PLPKEVEKLCEKCKP-YRTVAAWYLWK 238 (254)
T ss_pred CCCCC-CchHHHHHHhhhccc-hHHHHHHHHHh
Confidence 66543 678889888776666 4544 356665
No 23
>PF15629 Perm-CXXC: Permuted single zf-CXXC unit
Probab=99.11 E-value=1.5e-11 Score=92.19 Aligned_cols=32 Identities=81% Similarity=1.405 Sum_probs=30.9
Q ss_pred chhhhccccccCccCcCcccccccccccccce
Q 002448 799 PESRCRSKESGKLCDEKTCFSCNSMRETNSQT 830 (921)
Q Consensus 799 p~~~c~~~~~~~~c~~~~~~~c~~~~e~~~~~ 830 (921)
|+++|++|++|+||+++|||+||||||+++|+
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=98.46 E-value=2.8e-07 Score=94.68 Aligned_cols=123 Identities=20% Similarity=0.265 Sum_probs=90.7
Q ss_pred cccchhhhhhcccccccccccccccChHHHHHHHHhccCccccccCcCCCCCHHHHHcCCHHHHHHHHHhcC--CcHHHH
Q 002448 382 VYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQERSRDRMDSLDYEALRCANVKEISEAIKERG--MNNMLA 459 (921)
Q Consensus 382 ~~~lLia~iLsaq~~d~~vnk~qnT~W~nL~kaL~n~~Lk~erl~~~~~~pTpEaLa~A~~EELeelIR~iG--fyr~KA 459 (921)
-|.+|.=.||-|+++....-++|+ . +. +.+..++.+||++.++.+| ||+.||
T Consensus 39 lf~ELsFCILTANsSA~~~~~~q~--------~-----lG-------------~gfly~~~eEL~e~Lk~~g~Rf~n~ra 92 (210)
T COG1059 39 LFKELSFCILTANSSATMGLRAQN--------E-----LG-------------DGFLYLSEEELREKLKEVGYRFYNVRA 92 (210)
T ss_pred HHHHHHHHhccccchHHHHHHHHH--------H-----hc-------------cccccCCHHHHHHHHHHhcchhcccch
Confidence 377888888888876644432211 1 11 3456678999999999996 799999
Q ss_pred HHHHHHHHHHHHhhCCCChhhhhcCCchH--HHHHHH-cCCCccHhhHHHHHHHhcCCceeecchHHHHHHHHhCCCCCC
Q 002448 460 ERMKDFLNRLVREHGSIDLEWLRDVPPDK--AKDYLL-SIRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQ 536 (921)
Q Consensus 460 k~Ik~lA~~Lve~~GGlDLe~L~~vP~de--aReeLL-sLPGVG~KTAd~ILlfafgrpvfpVDTHV~RVl~RLGlv~~~ 536 (921)
+||...-+.+. ++..+-+.+..+ +|+.|. .++|||.|-|..+|...--....++|.||.|.+.|.|++...
T Consensus 93 eyIVeaR~~~~------~lk~~v~~~~~~~vaRE~Lv~nikGiGyKEASHFLRNVG~~D~AIlDrHIlr~l~r~g~i~e~ 166 (210)
T COG1059 93 EYIVEAREKFD------DLKIIVKADENEKVARELLVENIKGIGYKEASHFLRNVGFEDLAILDRHILRWLVRYGLIDEN 166 (210)
T ss_pred HHHHHHHHHHH------HHHHHHhcCcchHHHHHHHHHHcccccHHHHHHHHHhcChhHHHHHHHHHHHHHHHhcccccC
Confidence 99998555442 344444444333 899999 899999999999995543366778999999999999998643
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=97.63 E-value=1.6e-05 Score=59.70 Aligned_cols=26 Identities=19% Similarity=0.448 Sum_probs=21.8
Q ss_pred cCCchHHHHHHHcCCCccHhhHHHHHHH
Q 002448 483 DVPPDKAKDYLLSIRGLGLKSVECVRLL 510 (921)
Q Consensus 483 ~vP~deaReeLLsLPGVG~KTAd~ILlf 510 (921)
.+|.+ +++|++|||||+|||++|+.|
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=96.79 E-value=0.00044 Score=46.08 Aligned_cols=17 Identities=47% Similarity=1.323 Sum_probs=11.6
Q ss_pred cccCCCCCCCCCCchhc
Q 002448 587 CTKSKPNCNACPMRGEC 603 (921)
Q Consensus 587 C~arkP~C~~CPLrdlC 603 (921)
|++|+|+|+.|||++.|
T Consensus 1 Ctar~P~C~~Cpl~~~C 17 (17)
T PF10576_consen 1 CTARKPKCEECPLADYC 17 (17)
T ss_dssp S-SSS--GGG-TTGGG-
T ss_pred CcCCCCccccCCCcccC
Confidence 89999999999999988
No 27
>PF09674 DUF2400: Protein of unknown function (DUF2400); InterPro: IPR014127 Members of this uncharacterised protein family are found sporadically, so far only among spirochetes, epsilon and delta proteobacteria, and Bacteroides. The function is unknown and its gene neighbourhoods show little conservation.
Probab=96.68 E-value=0.0014 Score=70.20 Aligned_cols=89 Identities=24% Similarity=0.386 Sum_probs=61.0
Q ss_pred HHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHcCCCccHhhHHHHHHHhcCCceeecchHHHHHHHHhCCCCC
Q 002448 456 NMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPL 535 (921)
Q Consensus 456 r~KAk~Ik~lA~~Lve~~GGlDLe~L~~vP~deaReeLLsLPGVG~KTAd~ILlfafgrpvfpVDTHV~RVl~RLGlv~~ 535 (921)
+.=+|+|--+++|++++..++|+.-+..+++.++ .+|+||||.||+.+||+...
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 3457999999999998766799998888887743 68999999999999999876
Q ss_pred CCCHHHHHHHHHHhcCchHHHHHhhhhhhhcCChhhHHHHHHHHHHHhH
Q 002448 536 QPLPESLQLHLLELYPVLESIQKYLWPRLCKLDQRTLYELHYQLITFGK 584 (921)
Q Consensus 536 ~~tpeeve~~L~~llP~~e~Iqk~LW~rl~~ld~e~~~e~H~lLI~fGR 584 (921)
+..--++...+-+. +..+++.++-.+..+|-.+|.
T Consensus 196 k~~d~k~A~elT~~--------------lr~~~p~DPvKYDFAL~~~Gi 230 (232)
T PF09674_consen 196 KSADWKAARELTEA--------------LREFDPDDPVKYDFALFRLGI 230 (232)
T ss_pred CCccHHHHHHHHHH--------------HHhcCCCCCcchhhhcccCCc
Confidence 42211211111111 113455666677777766663
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=96.20 E-value=0.0043 Score=66.47 Aligned_cols=86 Identities=23% Similarity=0.405 Sum_probs=58.4
Q ss_pred HHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHcCCCccHhhHHHHHHHhcCCceeecchHHHHHHHHhCCCCCCC
Q 002448 458 LAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQP 537 (921)
Q Consensus 458 KAk~Ik~lA~~Lve~~GGlDLe~L~~vP~deaReeLLsLPGVG~KTAd~ILlfafgrpvfpVDTHV~RVl~RLGlv~~~~ 537 (921)
-+|+|--+++|++++ +++|+.-+..+++.++ ++|+||||.||+.+||+...+.
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 4489988888877633 6999999999999999987532
Q ss_pred CHHHHHHHHHHhcCchHHHHHhhhhhhhcCChhhHHHHHHHHHHHhH
Q 002448 538 LPESLQLHLLELYPVLESIQKYLWPRLCKLDQRTLYELHYQLITFGK 584 (921)
Q Consensus 538 tpeeve~~L~~llP~~e~Iqk~LW~rl~~ld~e~~~e~H~lLI~fGR 584 (921)
.--++...+-+ .+.++++.++-.+..+|-.+|.
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 1223556677777777766663
No 29
>smart00525 FES FES domain. iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3)
Probab=95.82 E-value=0.0043 Score=44.85 Aligned_cols=22 Identities=36% Similarity=1.141 Sum_probs=19.9
Q ss_pred hcccCCCCCCCCCCchhchhhh
Q 002448 586 FCTKSKPNCNACPMRGECRHFA 607 (921)
Q Consensus 586 IC~arkP~C~~CPLrdlC~y~~ 607 (921)
+|++++|+|+.|||++.|+++.
T Consensus 1 vC~ar~P~C~~Cpl~~~C~~~~ 22 (26)
T smart00525 1 ICTARKPRCDECPLKDLCPAYX 22 (26)
T ss_pred CccCCCCCCCCCcCHHHhhhhh
Confidence 6999999999999999998744
No 30
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=91.43 E-value=0.13 Score=37.22 Aligned_cols=20 Identities=30% Similarity=0.338 Sum_probs=17.7
Q ss_pred HHHcCCCccHhhHHHHHHHh
Q 002448 492 YLLSIRGLGLKSVECVRLLT 511 (921)
Q Consensus 492 eLLsLPGVG~KTAd~ILlfa 511 (921)
.|.++||||+|+|+.|+.+.
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=90.57 E-value=0.3 Score=42.42 Aligned_cols=40 Identities=28% Similarity=0.351 Sum_probs=28.2
Q ss_pred HHHHHHHhhCCCChhhhhcCCchHHHHHHHcCCCccHhhHHHHHHH
Q 002448 465 FLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLL 510 (921)
Q Consensus 465 lA~~Lve~~GGlDLe~L~~vP~deaReeLLsLPGVG~KTAd~ILlf 510 (921)
.|+.|.+.|+. ++.|...+ .++|.+++|||+++|+.|..|
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 35666677774 67776543 668999999999999999876
No 32
>PF14716 HHH_8: Helix-hairpin-helix domain; PDB: 2W9M_A 1HUZ_A 1HUO_A 2BPG_B 2BPF_A 1DK3_A 1BPE_A 1BNO_A 1BNP_A 1DK2_A ....
Probab=85.94 E-value=3 Score=36.50 Aligned_cols=58 Identities=12% Similarity=0.188 Sum_probs=38.5
Q ss_pred HHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHcCCCccHhhHHHHHHH
Q 002448 443 KEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLL 510 (921)
Q Consensus 443 EELeelIR~iGfyr~KAk~Ik~lA~~Lve~~GGlDLe~L~~vP~deaReeLLsLPGVG~KTAd~ILlf 510 (921)
+++.++..-.|=...|++.-.+.+..|.. ++. |-+...+.|.+|||||.++|..|--|
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 45566666665445688888888877765 332 22222225999999999999988543
No 33
>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=84.89 E-value=2.6 Score=46.20 Aligned_cols=133 Identities=16% Similarity=0.132 Sum_probs=74.7
Q ss_pred HHHHHHHHhc----CCcHHHHHHHHHHHHHHHHhhCCCChhhhhc--CCchHHHHHHHcCCCcc--HhhH-------HHH
Q 002448 443 KEISEAIKER----GMNNMLAERMKDFLNRLVREHGSIDLEWLRD--VPPDKAKDYLLSIRGLG--LKSV-------ECV 507 (921)
Q Consensus 443 EELeelIR~i----Gfyr~KAk~Ik~lA~~Lve~~GGlDLe~L~~--vP~deaReeLLsLPGVG--~KTA-------d~I 507 (921)
+++.+.+... -+.++|.++|.+++..+.. +.+..+.. -.-.++++.|..+=|-. .||. ...
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 4555555543 2567899999998776543 22222211 22345566777654443 3333 333
Q ss_pred HHHhcCC--c-----eeecchHHHHHHHHhCCCCCCCCHHHHHHHHHHhcCchHHHHHhhhhhhhcCChhhHHHHHHHHH
Q 002448 508 RLLTLHH--L-----AFPVDTNVGRIAVRLGWVPLQPLPESLQLHLLELYPVLESIQKYLWPRLCKLDQRTLYELHYQLI 580 (921)
Q Consensus 508 Llfafgr--p-----vfpVDTHV~RVl~RLGlv~~~~tpeeve~~L~~llP~~e~Iqk~LW~rl~~ld~e~~~e~H~lLI 580 (921)
...+||. + -+|||.||.++..++|++.. .++ ... . .+......|..++....-.+.+++..||
T Consensus 153 ~r~~~g~~~~~p~~IpIPvD~Rva~~T~~sGi~~~--~~~---~~~--~---~~~~v~~~W~~Va~~sgIpplhLDs~lW 222 (246)
T PF09171_consen 153 CRIAFGEFRPYPEEIPIPVDYRVAKLTKRSGIIEC--ERE---EMM--R---TREEVQKAWREVAKESGIPPLHLDSLLW 222 (246)
T ss_dssp HHHHCTS-----TTS-----HHHHHHHHCTTS-SS---HH---HHH--C---TCCHHHHHHHHHHHHHT--HHHHHHHHH
T ss_pred HHHhcCCCCCCcccCCCCccHHHHHHHHHhccccc--cHH---hhh--c---cHHHHHHHHHHHHhhcCCCchhhhhHHH
Confidence 3445564 2 58999999999999999764 222 111 1 1233456798877666677899999999
Q ss_pred -HHhHhhccc
Q 002448 581 -TFGKVFCTK 589 (921)
Q Consensus 581 -~fGR~IC~a 589 (921)
.+|+.....
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 34
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=84.41 E-value=2.1 Score=45.33 Aligned_cols=65 Identities=20% Similarity=0.247 Sum_probs=43.6
Q ss_pred CCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHH------HHHHHHHHhhCCCChhhhhcCCchHHHHHHHcCCCccHh
Q 002448 429 MDSLDYEALRCANVKEISEAIKERGMNNMLAERMK------DFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLK 502 (921)
Q Consensus 429 ~~~pTpEaLa~A~~EELeelIR~iGfyr~KAk~Ik------~lA~~Lve~~GGlDLe~L~~vP~deaReeLLsLPGVG~K 502 (921)
+||.|.+.. +-.+.+|.-.|.-...|-.|. +++++|.. + | .+.|.++||||+|
T Consensus 60 YGF~t~~Er-----~lF~~LisVsGIGPK~ALaILs~~~~~el~~aI~~--~------------D--~~~L~~vpGIGkK 118 (196)
T PRK13901 60 FGFLNSSER-----EVFEELIGVDGIGPRAALRVLSGIKYNEFRDAIDR--E------------D--IELISKVKGIGNK 118 (196)
T ss_pred eCCCCHHHH-----HHHHHHhCcCCcCHHHHHHHHcCCCHHHHHHHHHh--C------------C--HHHHhhCCCCCHH
Confidence 567776653 334556666777777776666 44555543 2 2 5689999999999
Q ss_pred hHHHHHHHhcCC
Q 002448 503 SVECVRLLTLHH 514 (921)
Q Consensus 503 TAd~ILlfafgr 514 (921)
||+-|.+---++
T Consensus 119 tAeRIIlELkdK 130 (196)
T PRK13901 119 MAGKIFLKLRGK 130 (196)
T ss_pred HHHHHHHHHHHh
Confidence 999887654443
No 35
>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=83.70 E-value=3.1 Score=35.42 Aligned_cols=30 Identities=30% Similarity=0.317 Sum_probs=23.1
Q ss_pred ChhhhhcCCchHHHHHHHcCCCccHhhHHHHHHH
Q 002448 477 DLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLL 510 (921)
Q Consensus 477 DLe~L~~vP~deaReeLLsLPGVG~KTAd~ILlf 510 (921)
+++.|...+ .+.|.+++|||+++|+-|...
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 566666653 457999999999999988654
No 36
>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region. Members of the subfamily recognized by this model include competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model.
Probab=83.60 E-value=2.1 Score=37.28 Aligned_cols=57 Identities=23% Similarity=0.325 Sum_probs=36.8
Q ss_pred HHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHcCCCccHhhHHHHHHH
Q 002448 437 LRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLL 510 (921)
Q Consensus 437 La~A~~EELeelIR~iGfyr~KAk~Ik~lA~~Lve~~GGlDLe~L~~vP~deaReeLLsLPGVG~KTAd~ILlf 510 (921)
|-.|+.++|..++..+|. .+|+.|.+.- ..+|++ .+ .++|..++|||.++|+-|+.+
T Consensus 10 vNta~~~~L~~~ipgig~--~~a~~Il~~R----~~~g~~---------~s--~~dL~~v~gi~~~~~~~i~~~ 66 (69)
T TIGR00426 10 INTATAEELQRAMNGVGL--KKAEAIVSYR----EEYGPF---------KT--VEDLKQVPGIGNSLVEKNLAV 66 (69)
T ss_pred CcCCCHHHHHhHCCCCCH--HHHHHHHHHH----HHcCCc---------CC--HHHHHcCCCCCHHHHHHHHhh
Confidence 334677777776554554 4555554321 124543 13 678999999999999998866
No 37
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=82.54 E-value=1.9 Score=43.18 Aligned_cols=53 Identities=19% Similarity=0.277 Sum_probs=38.9
Q ss_pred HHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHcCCCccHhhHHHHHHH
Q 002448 436 ALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLL 510 (921)
Q Consensus 436 aLa~A~~EELeelIR~iGfyr~KAk~Ik~lA~~Lve~~GGlDLe~L~~vP~deaReeLLsLPGVG~KTAd~ILlf 510 (921)
+|-.|+.+++.. --|++..+|+.|. .+|.+ .+ .++|+.+||||+++...+--+
T Consensus 54 diN~A~~~el~~---lpGigP~~A~~IV--------~nGpf---------~s--veDL~~V~GIgekqk~~l~k~ 106 (132)
T PRK02515 54 DLNNSSVRAFRQ---FPGMYPTLAGKIV--------KNAPY---------DS--VEDVLNLPGLSERQKELLEAN 106 (132)
T ss_pred cCCccCHHHHHH---CCCCCHHHHHHHH--------HCCCC---------CC--HHHHHcCCCCCHHHHHHHHHh
Confidence 556777777765 3788889998887 25653 12 678999999999988776543
No 38
>PRK00076 recR recombination protein RecR; Reviewed
Probab=79.79 E-value=1.6 Score=46.26 Aligned_cols=27 Identities=26% Similarity=0.381 Sum_probs=21.9
Q ss_pred hHHHHHHHcCCCccHhhHHHHHHHhcC
Q 002448 487 DKAKDYLLSIRGLGLKSVECVRLLTLH 513 (921)
Q Consensus 487 deaReeLLsLPGVG~KTAd~ILlfafg 513 (921)
+++.+.|.+|||||+|||.-+..+-+.
T Consensus 7 ~~Li~~l~~LPGIG~KsA~Rla~~ll~ 33 (196)
T PRK00076 7 EKLIEALRKLPGIGPKSAQRLAFHLLQ 33 (196)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHHHc
Confidence 567889999999999999776666554
No 39
>PRK13844 recombination protein RecR; Provisional
Probab=79.48 E-value=1.7 Score=46.27 Aligned_cols=28 Identities=21% Similarity=0.222 Sum_probs=22.5
Q ss_pred chHHHHHHHcCCCccHhhHHHHHHHhcC
Q 002448 486 PDKAKDYLLSIRGLGLKSVECVRLLTLH 513 (921)
Q Consensus 486 ~deaReeLLsLPGVG~KTAd~ILlfafg 513 (921)
-+++.+.|.+|||||+|||.-+..+-+.
T Consensus 10 ~~~LI~~l~~LPGIG~KsA~Rla~~lL~ 37 (200)
T PRK13844 10 ISAVIESLRKLPTIGKKSSQRLALYLLD 37 (200)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHHHc
Confidence 3577889999999999999776666554
No 40
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=79.35 E-value=1.7 Score=46.02 Aligned_cols=28 Identities=25% Similarity=0.309 Sum_probs=22.2
Q ss_pred chHHHHHHHcCCCccHhhHHHHHHHhcC
Q 002448 486 PDKAKDYLLSIRGLGLKSVECVRLLTLH 513 (921)
Q Consensus 486 ~deaReeLLsLPGVG~KTAd~ILlfafg 513 (921)
-+++.+.|.+|||||+|||.-+..+-+.
T Consensus 6 ~~~Li~~l~~LPGIG~KsA~RlA~~ll~ 33 (195)
T TIGR00615 6 ISKLIESLKKLPGIGPKSAQRLAFHLLK 33 (195)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHHHc
Confidence 3567889999999999999766655443
No 41
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=77.72 E-value=3.7 Score=42.97 Aligned_cols=21 Identities=29% Similarity=0.382 Sum_probs=18.4
Q ss_pred HHHHHcCCCccHhhHHHHHHH
Q 002448 490 KDYLLSIRGLGLKSVECVRLL 510 (921)
Q Consensus 490 ReeLLsLPGVG~KTAd~ILlf 510 (921)
.+.|.++||||+|+|+.|+..
T Consensus 107 ~~~L~~v~Gig~k~A~~I~~~ 127 (192)
T PRK00116 107 VKALTKVPGIGKKTAERIVLE 127 (192)
T ss_pred HHHHHhCCCCCHHHHHHHHHH
Confidence 557999999999999999865
No 42
>PRK10353 3-methyl-adenine DNA glycosylase I; Provisional
Probab=76.80 E-value=2.2 Score=44.97 Aligned_cols=47 Identities=4% Similarity=0.116 Sum_probs=35.2
Q ss_pred CCCCCHHHHHcCCHHHHHHHHHhcCCcH--HHHHHHHHHHHHHH---HhhCC
Q 002448 429 MDSLDYEALRCANVKEISEAIKERGMNN--MLAERMKDFLNRLV---REHGS 475 (921)
Q Consensus 429 ~~~pTpEaLa~A~~EELeelIR~iGfyr--~KAk~Ik~lA~~Lv---e~~GG 475 (921)
...++|+.+|..++++|++++..-|.-| .|.+.++.=|+.+. +++|+
T Consensus 60 F~~Fd~~~VA~~~e~die~Ll~d~~IIRnr~KI~Avi~NA~~~l~i~~e~gS 111 (187)
T PRK10353 60 FHQFDPVKVAAMQEEDVERLVQDAGIIRHRGKIQAIIGNARAYLQMEQNGEP 111 (187)
T ss_pred HcCCCHHHHhCCCHHHHHHHhcCchhHHhHHHHHHHHHHHHHHHHHHHhcCC
Confidence 4678999999999999999999999854 45456666455554 34554
No 43
>PRK00024 hypothetical protein; Reviewed
Probab=76.32 E-value=4.6 Score=43.40 Aligned_cols=61 Identities=23% Similarity=0.349 Sum_probs=44.1
Q ss_pred cCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHcCCCccHhhHHHHH
Q 002448 439 CANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVR 508 (921)
Q Consensus 439 ~A~~EELeelIR~iGfyr~KAk~Ik~lA~~Lve~~GGlDLe~L~~vP~deaReeLLsLPGVG~KTAd~IL 508 (921)
.++..||-++|=..|..+ +-.+.+|+.++++||+ +..+...+. ++|.+++|||+..|-.++
T Consensus 23 ~Lsd~ELLa~lL~~g~~~---~~~~~LA~~LL~~fgs--L~~l~~as~----~eL~~i~GIG~akA~~L~ 83 (224)
T PRK00024 23 ALSDAELLAILLRTGTKG---KSVLDLARELLQRFGS--LRGLLDASL----EELQSIKGIGPAKAAQLK 83 (224)
T ss_pred cCCHHHHHHHHHcCCCCC---CCHHHHHHHHHHHcCC--HHHHHhCCH----HHHhhccCccHHHHHHHH
Confidence 445667777665566543 4556788999988875 677776664 479999999999886554
No 44
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=75.84 E-value=2.4 Score=45.01 Aligned_cols=27 Identities=30% Similarity=0.395 Sum_probs=21.3
Q ss_pred hHHHHHHHcCCCccHhhHHHHHHHhcC
Q 002448 487 DKAKDYLLSIRGLGLKSVECVRLLTLH 513 (921)
Q Consensus 487 deaReeLLsLPGVG~KTAd~ILlfafg 513 (921)
+++.+.|.+|||||+|+|.-+..+.+.
T Consensus 8 ~~LI~~l~kLPGvG~KsA~R~AfhLL~ 34 (198)
T COG0353 8 EKLIDALKKLPGVGPKSAQRLAFHLLQ 34 (198)
T ss_pred HHHHHHHhhCCCCChhHHHHHHHHHHc
Confidence 467889999999999999766555443
No 45
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=75.81 E-value=6.1 Score=41.52 Aligned_cols=65 Identities=11% Similarity=0.075 Sum_probs=39.0
Q ss_pred CCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHH------HHHHHHHhhCCCChhhhhcCCchHHHHHHHcCCCccHh
Q 002448 429 MDSLDYEALRCANVKEISEAIKERGMNNMLAERMKD------FLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLK 502 (921)
Q Consensus 429 ~~~pTpEaLa~A~~EELeelIR~iGfyr~KAk~Ik~------lA~~Lve~~GGlDLe~L~~vP~deaReeLLsLPGVG~K 502 (921)
+||.|.++. +-.+.+|.-.|.-.+.|-.|.. ++++|.. .| .+.|.++||||+|
T Consensus 61 yGF~~~~Er-----~lF~~Li~V~GIGpK~AL~iLs~~~~~el~~aI~~--------------~D--~~~L~~vpGIGkK 119 (188)
T PRK14606 61 YGFSNERKK-----ELFLSLTKVSRLGPKTALKIISNEDAETLVTMIAS--------------QD--VEGLSKLPGISKK 119 (188)
T ss_pred eCCCCHHHH-----HHHHHHhccCCccHHHHHHHHcCCCHHHHHHHHHh--------------CC--HHHHhhCCCCCHH
Confidence 466666542 2334455556666656655442 2333332 12 5689999999999
Q ss_pred hHHHHHHHhcCC
Q 002448 503 SVECVRLLTLHH 514 (921)
Q Consensus 503 TAd~ILlfafgr 514 (921)
||+-|.+---++
T Consensus 120 tAerIilELkdK 131 (188)
T PRK14606 120 TAERIVMELKDE 131 (188)
T ss_pred HHHHHHHHHHHh
Confidence 999887644333
No 46
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=75.62 E-value=6.3 Score=41.38 Aligned_cols=69 Identities=19% Similarity=0.170 Sum_probs=40.2
Q ss_pred CCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcC--CchHHHHHHHcCCCccHhhHHH
Q 002448 429 MDSLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDV--PPDKAKDYLLSIRGLGLKSVEC 506 (921)
Q Consensus 429 ~~~pTpEaLa~A~~EELeelIR~iGfyr~KAk~Ik~lA~~Lve~~GGlDLe~L~~v--P~deaReeLLsLPGVG~KTAd~ 506 (921)
+||.|.++- +-.+.+|+-.|.-...|-.|... ++.+.|... ..| .+.|.++||||+|||+-
T Consensus 61 yGF~~~~Er-----~lF~~Li~VsGIGpK~Al~ILs~----------~~~~el~~aI~~~D--~~~L~~vpGIGkKtAeR 123 (183)
T PRK14601 61 YGFLDKDEQ-----KMFEMLLKVNGIGANTAMAVCSS----------LDVNSFYKALSLGD--ESVLKKVPGIGPKSAKR 123 (183)
T ss_pred eCCCCHHHH-----HHHHHHhccCCccHHHHHHHHcC----------CCHHHHHHHHHhCC--HHHHhhCCCCCHHHHHH
Confidence 566666652 33445555566665555444421 122222111 123 67899999999999998
Q ss_pred HHHHhcCC
Q 002448 507 VRLLTLHH 514 (921)
Q Consensus 507 ILlfafgr 514 (921)
|++---++
T Consensus 124 IilELkdK 131 (183)
T PRK14601 124 IIAELSDA 131 (183)
T ss_pred HHHHHHHH
Confidence 88654444
No 47
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=74.84 E-value=5.5 Score=42.77 Aligned_cols=61 Identities=23% Similarity=0.305 Sum_probs=44.4
Q ss_pred cCCHHHHHHHHHhcCCcHHHHH-HHHHHHHHHHHhh---CCCChhhhhcCCchHHHHHHHcCCCccHhhHHHHH
Q 002448 439 CANVKEISEAIKERGMNNMLAE-RMKDFLNRLVREH---GSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVR 508 (921)
Q Consensus 439 ~A~~EELeelIR~iGfyr~KAk-~Ik~lA~~Lve~~---GGlDLe~L~~vP~deaReeLLsLPGVG~KTAd~IL 508 (921)
.++..||-++|=..|..+ + ..+.+|+.|+++| |+ |..|...+. ++|.+++|||+..|-.++
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 445667777665566653 3 5678899999888 64 777777764 479999999997776554
No 48
>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=74.46 E-value=2.8 Score=35.69 Aligned_cols=27 Identities=37% Similarity=0.391 Sum_probs=22.3
Q ss_pred HHHHHHcCCCccHhhHHHHHHHhcCCc
Q 002448 489 AKDYLLSIRGLGLKSVECVRLLTLHHL 515 (921)
Q Consensus 489 aReeLLsLPGVG~KTAd~ILlfafgrp 515 (921)
+.+.|+++||||+++|..+...+++-.
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 49
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=73.10 E-value=2.5 Score=45.01 Aligned_cols=67 Identities=24% Similarity=0.213 Sum_probs=38.3
Q ss_pred CCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHcCCCccHhhHHHHHH
Q 002448 430 DSLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRL 509 (921)
Q Consensus 430 ~~pTpEaLa~A~~EELeelIR~iGfyr~KAk~Ik~lA~~Lve~~GGlDLe~L~~vP~deaReeLLsLPGVG~KTAd~ILl 509 (921)
||.|.+. -+=...+|+-.|.-.+-|-.|.. .+|++.|...=..+-.+.|.++||||.|||+-|++
T Consensus 62 GF~~~~E-----R~lF~~LisVnGIGpK~ALaiLs----------~~~~~~l~~aI~~~d~~~L~k~PGIGkKtAerivl 126 (201)
T COG0632 62 GFLTEEE-----RELFRLLISVNGIGPKLALAILS----------NLDPEELAQAIANEDVKALSKIPGIGKKTAERIVL 126 (201)
T ss_pred CCCCHHH-----HHHHHHHHccCCccHHHHHHHHc----------CCCHHHHHHHHHhcChHhhhcCCCCCHHHHHHHHH
Confidence 4555443 23345566666766433333222 23444443221222267899999999999998876
Q ss_pred Hh
Q 002448 510 LT 511 (921)
Q Consensus 510 fa 511 (921)
--
T Consensus 127 eL 128 (201)
T COG0632 127 EL 128 (201)
T ss_pred HH
Confidence 43
No 50
>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=71.84 E-value=10 Score=39.85 Aligned_cols=48 Identities=17% Similarity=0.303 Sum_probs=33.9
Q ss_pred CCCCCHHHHHcCCHHHHHHHHHhcCC--cHHHHHHHHHHHHHHH---HhhCCC
Q 002448 429 MDSLDYEALRCANVKEISEAIKERGM--NNMLAERMKDFLNRLV---REHGSI 476 (921)
Q Consensus 429 ~~~pTpEaLa~A~~EELeelIR~iGf--yr~KAk~Ik~lA~~Lv---e~~GGl 476 (921)
...++|+.++..++++|++++..-|. .+.|.+.++.=|+.++ ++||++
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 5566666766666655 355553
No 51
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=71.53 E-value=4.5 Score=42.93 Aligned_cols=24 Identities=21% Similarity=0.221 Sum_probs=19.7
Q ss_pred HHHHHcCCCccHhhHHHHHHHhcC
Q 002448 490 KDYLLSIRGLGLKSVECVRLLTLH 513 (921)
Q Consensus 490 ReeLLsLPGVG~KTAd~ILlfafg 513 (921)
.+.|.++||||+|||+-|++---+
T Consensus 108 ~~~L~~ipGIGkKtAerIilELkd 131 (203)
T PRK14602 108 VAALTRVSGIGKKTAQHIFLELKY 131 (203)
T ss_pred HHHHhcCCCcCHHHHHHHHHHHHH
Confidence 678999999999999988764333
No 52
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=71.28 E-value=6.3 Score=40.02 Aligned_cols=56 Identities=25% Similarity=0.412 Sum_probs=38.0
Q ss_pred HHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHcCCCccHhhHHHHHHH
Q 002448 437 LRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLL 510 (921)
Q Consensus 437 La~A~~EELeelIR~iGfyr~KAk~Ik~lA~~Lve~~GGlDLe~L~~vP~deaReeLLsLPGVG~KTAd~ILlf 510 (921)
|-.|+.++| +.|.++| ..||+.|++ ..+++|.| .+ .+.|..++|||++|.+-+.-+
T Consensus 91 iNtAs~eeL-~~lpgIG--~~kA~aIi~----yRe~~G~f---------~s--v~dL~~v~GiG~~~~ekl~~~ 146 (149)
T COG1555 91 INTASAEEL-QALPGIG--PKKAQAIID----YREENGPF---------KS--VDDLAKVKGIGPKTLEKLKDY 146 (149)
T ss_pred ccccCHHHH-HHCCCCC--HHHHHHHHH----HHHHcCCC---------Cc--HHHHHhccCCCHHHHHHHHhh
Confidence 345677777 5555566 458877775 44556653 12 678999999999998876543
No 53
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=71.09 E-value=8 Score=40.91 Aligned_cols=22 Identities=32% Similarity=0.321 Sum_probs=18.8
Q ss_pred HHHHHcCCCccHhhHHHHHHHh
Q 002448 490 KDYLLSIRGLGLKSVECVRLLT 511 (921)
Q Consensus 490 ReeLLsLPGVG~KTAd~ILlfa 511 (921)
.+.|.++||||+|||+-|.+--
T Consensus 106 ~~~L~kvpGIGkKtAerIilEL 127 (197)
T PRK14603 106 ARLLTSASGVGKKLAERIALEL 127 (197)
T ss_pred HHHHhhCCCCCHHHHHHHHHHH
Confidence 6789999999999999887543
No 54
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=70.93 E-value=8.1 Score=40.87 Aligned_cols=69 Identities=16% Similarity=0.019 Sum_probs=39.2
Q ss_pred CCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcC--CchHHHHHHHcCCCccHhhHHH
Q 002448 429 MDSLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDV--PPDKAKDYLLSIRGLGLKSVEC 506 (921)
Q Consensus 429 ~~~pTpEaLa~A~~EELeelIR~iGfyr~KAk~Ik~lA~~Lve~~GGlDLe~L~~v--P~deaReeLLsLPGVG~KTAd~ 506 (921)
+||.|.++. +-...+|.-.|.-.+.|-.|... ++.+.|... ..| .+.|.++||||+|||+-
T Consensus 61 yGF~~~~Er-----~lF~~Li~V~GIGpK~Al~iLs~----------~~~~el~~aI~~~D--~~~L~kvpGIGkKtAer 123 (195)
T PRK14604 61 YGFSTPAQR-----QLFELLIGVSGVGPKAALNLLSS----------GTPDELQLAIAGGD--VARLARVPGIGKKTAER 123 (195)
T ss_pred eCCCCHHHH-----HHHHHHhCcCCcCHHHHHHHHcC----------CCHHHHHHHHHhCC--HHHHhhCCCCCHHHHHH
Confidence 466665542 33444555566666666555431 112222111 122 67899999999999998
Q ss_pred HHHHhcCC
Q 002448 507 VRLLTLHH 514 (921)
Q Consensus 507 ILlfafgr 514 (921)
|++---++
T Consensus 124 IilELk~K 131 (195)
T PRK14604 124 IVLELKGK 131 (195)
T ss_pred HHHHHHHH
Confidence 87644443
No 55
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=70.81 E-value=4.9 Score=34.89 Aligned_cols=52 Identities=19% Similarity=0.381 Sum_probs=29.9
Q ss_pred cCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHcCCCccHhhHHHHH
Q 002448 439 CANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVR 508 (921)
Q Consensus 439 ~A~~EELeelIR~iGfyr~KAk~Ik~lA~~Lve~~GGlDLe~L~~vP~deaReeLLsLPGVG~KTAd~IL 508 (921)
.|+.++|..+ -|+....|+.|.+. .+.+|++ .+ .++|..++|||+++.+-+.
T Consensus 10 ~as~~eL~~l---pgi~~~~A~~Iv~~----R~~~G~f---------~s--~~dL~~v~gi~~~~~~~l~ 61 (65)
T PF12836_consen 10 TASAEELQAL---PGIGPKQAKAIVEY----REKNGPF---------KS--LEDLKEVPGIGPKTYEKLK 61 (65)
T ss_dssp TS-HHHHHTS---TT--HHHHHHHHHH----HHHH-S----------SS--GGGGGGSTT--HHHHHHHC
T ss_pred cCCHHHHHHc---CCCCHHHHHHHHHH----HHhCcCC---------CC--HHHHhhCCCCCHHHHHHHH
Confidence 4566665441 38888888888763 3344653 11 5579999999999987663
No 56
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=70.60 E-value=40 Score=33.04 Aligned_cols=59 Identities=15% Similarity=0.206 Sum_probs=39.7
Q ss_pred CCCCHHHHHcCCHHHHHH--HHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHcCCCccHhhHHHH
Q 002448 430 DSLDYEALRCANVKEISE--AIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECV 507 (921)
Q Consensus 430 ~~pTpEaLa~A~~EELee--lIR~iGfyr~KAk~Ik~lA~~Lve~~GGlDLe~L~~vP~deaReeLLsLPGVG~KTAd~I 507 (921)
|..|+++|+.++...+.. +.+..|.. +++|.+.. .+..|..++|||+..|..+
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 556899999888877766 55555555 23332211 1557889999999999877
Q ss_pred HHHhcC
Q 002448 508 RLLTLH 513 (921)
Q Consensus 508 Llfafg 513 (921)
+--++.
T Consensus 70 ~~AGv~ 75 (122)
T PF14229_consen 70 EHAGVD 75 (122)
T ss_pred HHhCcC
Confidence 665554
No 57
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=70.37 E-value=9.2 Score=40.32 Aligned_cols=64 Identities=22% Similarity=0.280 Sum_probs=37.8
Q ss_pred CCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhh-hcC-CchHHHHHHHcCCCccHhhHHH
Q 002448 429 MDSLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWL-RDV-PPDKAKDYLLSIRGLGLKSVEC 506 (921)
Q Consensus 429 ~~~pTpEaLa~A~~EELeelIR~iGfyr~KAk~Ik~lA~~Lve~~GGlDLe~L-~~v-P~deaReeLLsLPGVG~KTAd~ 506 (921)
+||.+.+.- +-.+.+|+--|.-...|..|... ++.+.| ..+ ..| .+.|.++||||+|||+-
T Consensus 61 yGF~~~~Er-----~lF~~Li~V~GIGpK~Al~ILs~----------~~~~~l~~aI~~~D--~~~L~~vpGIGkKtAer 123 (194)
T PRK14605 61 FGFATTEEL-----SLFETLIDVSGIGPKLGLAMLSA----------MNAEALASAIISGN--AELLSTIPGIGKKTASR 123 (194)
T ss_pred eCCCCHHHH-----HHHHHHhCCCCCCHHHHHHHHHh----------CCHHHHHHHHHhCC--HHHHHhCCCCCHHHHHH
Confidence 466666542 33445555567766666555542 112221 111 123 56799999999999998
Q ss_pred HHH
Q 002448 507 VRL 509 (921)
Q Consensus 507 ILl 509 (921)
|.+
T Consensus 124 Iil 126 (194)
T PRK14605 124 IVL 126 (194)
T ss_pred HHH
Confidence 664
No 58
>TIGR00575 dnlj DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.
Probab=69.97 E-value=19 Score=44.56 Aligned_cols=62 Identities=15% Similarity=0.213 Sum_probs=36.5
Q ss_pred CCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHcCCCccHhhHHHHHH
Q 002448 432 LDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRL 509 (921)
Q Consensus 432 pTpEaLa~A~~EELeelIR~iGfyr~KAk~Ik~lA~~Lve~~GGlDLe~L~~vP~deaReeLLsLPGVG~KTAd~ILl 509 (921)
-++.+|..+..++|.++ -||-..+|.+|++..+.-.. .+-.+. =..+.|||||+++|..++.
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------------KPLARL-LFALGIRHVGEVTAKNLAK 516 (652)
T ss_pred CCHHHHHhcCHHHHhhc---cCccHHHHHHHHHHHHHhcc------------CcHHHH-HhhccCCCcCHHHHHHHHH
Confidence 38889999988877653 47777777777665543321 111111 1233566667766665543
No 59
>PRK14973 DNA topoisomerase I; Provisional
Probab=69.85 E-value=6.7 Score=50.22 Aligned_cols=97 Identities=16% Similarity=0.128 Sum_probs=63.2
Q ss_pred CCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHH-HHHHhhCCCChhhhhcCCchHHHHHHHcCCCccHhhHHHH
Q 002448 429 MDSLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLN-RLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECV 507 (921)
Q Consensus 429 ~~~pTpEaLa~A~~EELeelIR~iGfyr~KAk~Ik~lA~-~Lve~~GGlDLe~L~~vP~deaReeLLsLPGVG~KTAd~I 507 (921)
.|+-++++++.|++++|.. .-|+.--.+..+...+. .++.. +.+.+.+-..+..+.+|++++|||++|++-.
T Consensus 821 ~G~~~~~d~~~a~p~~La~---~~g~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~el~~vkg~ge~t~~~l 893 (936)
T PRK14973 821 AGFDTPEDFCSVHPAYLAL---KTGISPETICRHAKLVCEKLGRP----VPEKISKAAFERGRAELLSVPGLGETTLEKL 893 (936)
T ss_pred hcCCCHHHHHhcCHHHHhc---CCCCChhhHHHHHHHHHHHhcCC----CchhhhhhhhcccchhhhhccCCCHHHHHHH
Confidence 4678999999999999876 38998766666655554 44431 2223323333344666999999999999654
Q ss_pred HHHhcCCc-eeecchHHHHHHHHhCCC
Q 002448 508 RLLTLHHL-AFPVDTNVGRIAVRLGWV 533 (921)
Q Consensus 508 Llfafgrp-vfpVDTHV~RVl~RLGlv 533 (921)
-.-+.-.+ .+..+ -..|++.+.|+.
T Consensus 894 ~~ag~~~~e~l~~~-d~~~la~~~~i~ 919 (936)
T PRK14973 894 YLAGVYDGDLLVSA-DPKKLAKVTGID 919 (936)
T ss_pred HHcCCCCHHHhccC-CHHHHhhhcCCC
Confidence 44333333 33333 677888777763
No 60
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=69.25 E-value=7.5 Score=40.84 Aligned_cols=67 Identities=21% Similarity=0.177 Sum_probs=37.9
Q ss_pred CCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhc-C-CchHHHHHHHcCCCccHhhHHH
Q 002448 429 MDSLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRD-V-PPDKAKDYLLSIRGLGLKSVEC 506 (921)
Q Consensus 429 ~~~pTpEaLa~A~~EELeelIR~iGfyr~KAk~Ik~lA~~Lve~~GGlDLe~L~~-v-P~deaReeLLsLPGVG~KTAd~ 506 (921)
+||.|.++. +-.+.+|+-.|.-...|-.|... ++.+.|.. + ..| .+.| ++||||+|||+-
T Consensus 61 yGF~~~~Er-----~lF~~LisV~GIGpK~Al~iLs~----------~~~~~l~~aI~~~D--~~~L-~vpGIGkKtAer 122 (186)
T PRK14600 61 YGFLNREEQ-----DCLRMLVKVSGVNYKTAMSILSK----------LTPEQLFSAIVNED--KAAL-KVNGIGEKLINR 122 (186)
T ss_pred eCCCCHHHH-----HHHHHHhCcCCcCHHHHHHHHcc----------CCHHHHHHHHHcCC--Hhhe-ECCCCcHHHHHH
Confidence 466666652 33445555567666566555432 11221211 1 112 4678 999999999998
Q ss_pred HHHHhcC
Q 002448 507 VRLLTLH 513 (921)
Q Consensus 507 ILlfafg 513 (921)
|++---+
T Consensus 123 IilELk~ 129 (186)
T PRK14600 123 IITELQY 129 (186)
T ss_pred HHHHHHH
Confidence 8864333
No 61
>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=68.43 E-value=4.9 Score=42.21 Aligned_cols=65 Identities=23% Similarity=0.204 Sum_probs=40.4
Q ss_pred CCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhc-CC-chHHHHHHHcCCCccHhhHHH
Q 002448 429 MDSLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRD-VP-PDKAKDYLLSIRGLGLKSVEC 506 (921)
Q Consensus 429 ~~~pTpEaLa~A~~EELeelIR~iGfyr~KAk~Ik~lA~~Lve~~GGlDLe~L~~-vP-~deaReeLLsLPGVG~KTAd~ 506 (921)
+||.|.++- +-...+|+--|.-..+|..|... ++.+.|.. +- .| .+.|.++||||+|||+-
T Consensus 60 yGF~~~~Er-----~lF~~L~~V~GIGpK~Al~iL~~----------~~~~el~~aI~~~d--~~~L~~ipGiGkKtAer 122 (191)
T TIGR00084 60 FGFNTLEER-----ELFKELIKVNGVGPKLALAILSN----------MSPEEFVYAIETEE--VKALVKIPGVGKKTAER 122 (191)
T ss_pred eCCCCHHHH-----HHHHHHhCCCCCCHHHHHHHHhc----------CCHHHHHHHHHhCC--HHHHHhCCCCCHHHHHH
Confidence 567776652 34455666678877777666332 22222221 11 12 46799999999999999
Q ss_pred HHHH
Q 002448 507 VRLL 510 (921)
Q Consensus 507 ILlf 510 (921)
|++-
T Consensus 123 Iile 126 (191)
T TIGR00084 123 LLLE 126 (191)
T ss_pred HHHH
Confidence 9843
No 62
>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=67.15 E-value=6 Score=41.50 Aligned_cols=43 Identities=7% Similarity=0.109 Sum_probs=33.8
Q ss_pred CCCCCHHHHHcCCHHHHHHHHHhcCCcHHHH--HHHHHHHHHHHH
Q 002448 429 MDSLDYEALRCANVKEISEAIKERGMNNMLA--ERMKDFLNRLVR 471 (921)
Q Consensus 429 ~~~pTpEaLa~A~~EELeelIR~iGfyr~KA--k~Ik~lA~~Lve 471 (921)
...++|+.++..++++|++++..-|.-|.|+ +.++.=|+.+.+
T Consensus 59 F~~Fd~~~VA~~~e~~ie~L~~d~~IIRnr~KI~Avi~NA~~~l~ 103 (179)
T TIGR00624 59 FSGFDIVKVARMTDADVERLLQDDGIIRNRGKIEATIANARAALQ 103 (179)
T ss_pred HcCCCHHHHhCCCHHHHHHHhcCccchhhHHHHHHHHHHHHHHHH
Confidence 4678999999999999999999999866654 445555666654
No 63
>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=65.17 E-value=8.8 Score=37.48 Aligned_cols=59 Identities=22% Similarity=0.401 Sum_probs=38.9
Q ss_pred HHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHcCCCccHhhHHHHHHH
Q 002448 434 YEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLL 510 (921)
Q Consensus 434 pEaLa~A~~EELeelIR~iGfyr~KAk~Ik~lA~~Lve~~GGlDLe~L~~vP~deaReeLLsLPGVG~KTAd~ILlf 510 (921)
+-+|-.|+.++|.. | -|....+|+.|++.-. .+|.+ .+ .++|..++|||+|+++-|.-|
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 33455667777755 2 4555567877765332 24542 22 678999999999999988755
No 64
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=64.58 E-value=11 Score=35.11 Aligned_cols=57 Identities=26% Similarity=0.533 Sum_probs=35.4
Q ss_pred CHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHc-CCCccHhhHHHHHH
Q 002448 441 NVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLS-IRGLGLKSVECVRL 509 (921)
Q Consensus 441 ~~EELeelIR~iGfyr~KAk~Ik~lA~~Lve~~GGlDLe~L~~vP~deaReeLLs-LPGVG~KTAd~ILl 509 (921)
...++...+...|+....|..| .+.||.-.++.|++=|.. |+. ++|||-++||-|..
T Consensus 7 ~~~~~~~~L~~~gl~~~~a~kl-------~~~yg~~ai~~l~~nPY~-----L~~~i~gi~F~~aD~iA~ 64 (94)
T PF14490_consen 7 GLRELMAFLQEYGLSPKLAMKL-------YKKYGDDAIEILKENPYR-----LIEDIDGIGFKTADKIAL 64 (94)
T ss_dssp --HHHHHHHHHTT--HHHHHHH-------HHHH-TTHHHHHHH-STC-----CCB-SSSSBHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCCHHHHHHH-------HHHHhHHHHHHHHHChHH-----HHHHccCCCHHHHHHHHH
Confidence 3467777888899987555444 445666455556655654 555 89999999988744
No 65
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=63.94 E-value=6.5 Score=41.14 Aligned_cols=42 Identities=19% Similarity=0.168 Sum_probs=25.8
Q ss_pred HHHHHcCCCccHhhHHHHHHHhcCCcee---ecchHHHHHHHHhCC
Q 002448 490 KDYLLSIRGLGLKSVECVRLLTLHHLAF---PVDTNVGRIAVRLGW 532 (921)
Q Consensus 490 ReeLLsLPGVG~KTAd~ILlfafgrpvf---pVDTHV~RVl~RLGl 532 (921)
...|+.+||||+|||..||.. ||-..+ +.+....++..--|+
T Consensus 72 f~~L~~i~GIGpk~A~~il~~-fg~~~l~~~i~~~d~~~L~~v~Gi 116 (192)
T PRK00116 72 FRLLISVSGVGPKLALAILSG-LSPEELVQAIANGDVKALTKVPGI 116 (192)
T ss_pred HHHHhcCCCCCHHHHHHHHHh-CCHHHHHHHHHhCCHHHHHhCCCC
Confidence 457889999999999988643 443222 334444454332254
No 66
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=61.43 E-value=19 Score=44.66 Aligned_cols=33 Identities=15% Similarity=0.174 Sum_probs=22.1
Q ss_pred CCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHH
Q 002448 432 LDYEALRCANVKEISEAIKERGMNNMLAERMKDFLN 467 (921)
Q Consensus 432 pTpEaLa~A~~EELeelIR~iGfyr~KAk~Ik~lA~ 467 (921)
-++.+|.++..++|..+ -||-..+|.+|++..+
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 48888888887776543 3777667766655443
No 67
>PF02371 Transposase_20: Transposase IS116/IS110/IS902 family; InterPro: IPR003346 Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This family includes transposases for IS116, IS110 and IS902. It is often found with the transposase IS111A/IS1328/IS1533 family (see IPR002525 from INTERPRO) [, ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=61.36 E-value=5.9 Score=36.16 Aligned_cols=42 Identities=21% Similarity=0.239 Sum_probs=29.9
Q ss_pred HHHHcCCCccHhhHHHHHHHhcCCceeecchHHHHHHHHhCCCCC
Q 002448 491 DYLLSIRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPL 535 (921)
Q Consensus 491 eeLLsLPGVG~KTAd~ILlfafgrpvfpVDTHV~RVl~RLGlv~~ 535 (921)
+.|+++||||+-||..++....+...|. +...+..-+|+.|.
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 3588999999999999998774333554 33445555688774
No 68
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=59.88 E-value=8.2 Score=33.53 Aligned_cols=21 Identities=19% Similarity=0.354 Sum_probs=17.2
Q ss_pred HHHHHcCCCccHhhHHHHHHH
Q 002448 490 KDYLLSIRGLGLKSVECVRLL 510 (921)
Q Consensus 490 ReeLLsLPGVG~KTAd~ILlf 510 (921)
.++|.++||||++.|..|+.|
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 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=58.72 E-value=9.5 Score=36.28 Aligned_cols=27 Identities=26% Similarity=0.322 Sum_probs=21.9
Q ss_pred HHHHHHcCCCccHhhHHHHHHHhcCCc
Q 002448 489 AKDYLLSIRGLGLKSVECVRLLTLHHL 515 (921)
Q Consensus 489 aReeLLsLPGVG~KTAd~ILlfafgrp 515 (921)
....|..|||||+.+|.-+...++..+
T Consensus 10 ~~~~L~~iP~IG~a~a~DL~~LGi~s~ 36 (93)
T PF11731_consen 10 GLSDLTDIPNIGKATAEDLRLLGIRSP 36 (93)
T ss_pred HHHHHhcCCCccHHHHHHHHHcCCCCH
Confidence 456899999999999988877766654
No 70
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=56.41 E-value=8.5 Score=39.08 Aligned_cols=22 Identities=18% Similarity=0.317 Sum_probs=19.4
Q ss_pred HHHHHcCCCccHhhHHHHHHHh
Q 002448 490 KDYLLSIRGLGLKSVECVRLLT 511 (921)
Q Consensus 490 ReeLLsLPGVG~KTAd~ILlfa 511 (921)
-++|..|||||+|.|..|..|-
T Consensus 96 ~eeL~~lpgIG~~kA~aIi~yR 117 (149)
T COG1555 96 AEELQALPGIGPKKAQAIIDYR 117 (149)
T ss_pred HHHHHHCCCCCHHHHHHHHHHH
Confidence 5678999999999999998773
No 71
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=56.11 E-value=44 Score=41.76 Aligned_cols=59 Identities=20% Similarity=0.268 Sum_probs=34.3
Q ss_pred CCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHH--cCCCccHhhHHHHH
Q 002448 432 LDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLL--SIRGLGLKSVECVR 508 (921)
Q Consensus 432 pTpEaLa~A~~EELeelIR~iGfyr~KAk~Ik~lA~~Lve~~GGlDLe~L~~vP~deaReeLL--sLPGVG~KTAd~IL 508 (921)
-++.+|..+..++|..+ -||...+|.+|.+-.+.-. .+|-. ..|. .|||||.++|..++
T Consensus 485 ~~~~Dl~~L~~~~L~~l---~g~g~Ksa~~Ll~~Ie~sk------------~~~l~---r~l~ALgIpgIG~~~ak~L~ 545 (689)
T PRK14351 485 ESLADLYDLTVADLAEL---EGWGETSAENLLAELEASR------------EPPLA---DFLVALGIPEVGPTTARNLA 545 (689)
T ss_pred CCHHHHHHcCHHHHhcC---cCcchhHHHHHHHHHHHHc------------cCCHH---HHHHHcCCCCcCHHHHHHHH
Confidence 37888888887775543 4777777776655433221 12222 2232 36777777776655
No 72
>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=55.32 E-value=9.3 Score=40.21 Aligned_cols=22 Identities=18% Similarity=0.232 Sum_probs=18.8
Q ss_pred HHHHHHHcCCCccHhhHHHHHH
Q 002448 488 KAKDYLLSIRGLGLKSVECVRL 509 (921)
Q Consensus 488 eaReeLLsLPGVG~KTAd~ILl 509 (921)
++...|++++|||||+|-.||.
T Consensus 69 ~lF~~L~~V~GIGpK~Al~iL~ 90 (191)
T TIGR00084 69 ELFKELIKVNGVGPKLALAILS 90 (191)
T ss_pred HHHHHHhCCCCCCHHHHHHHHh
Confidence 4567899999999999988865
No 73
>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=54.33 E-value=11 Score=36.93 Aligned_cols=21 Identities=14% Similarity=0.262 Sum_probs=19.2
Q ss_pred HHHHHcCCCccHhhHHHHHHH
Q 002448 490 KDYLLSIRGLGLKSVECVRLL 510 (921)
Q Consensus 490 ReeLLsLPGVG~KTAd~ILlf 510 (921)
.+.|.+|||||+++|..|+.+
T Consensus 67 ~~eL~~lpGIG~~~A~~Ii~~ 87 (120)
T TIGR01259 67 LEELQALPGIGPAKAKAIIEY 87 (120)
T ss_pred HHHHhcCCCCCHHHHHHHHHH
Confidence 678999999999999999877
No 74
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=53.68 E-value=25 Score=38.30 Aligned_cols=89 Identities=26% Similarity=0.336 Sum_probs=57.5
Q ss_pred cCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHcCCCccHhhHHHHH-HHhcCCcee
Q 002448 439 CANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVR-LLTLHHLAF 517 (921)
Q Consensus 439 ~A~~EELeelIR~iGfyr~KAk~Ik~lA~~Lve~~GGlDLe~L~~vP~deaReeLLsLPGVG~KTAd~IL-lfafgrpvf 517 (921)
.++..||-+++=..|-. -+..+.+|+.+..+||+ |..|...+ .++|.+++|||.--|--+. +.-+
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 44556777777666753 56778899999999987 66776665 5589999999976553332 2222
Q ss_pred ecchHHHHHHHHh---CCCCCCCCHHHHHHHHHH
Q 002448 518 PVDTNVGRIAVRL---GWVPLQPLPESLQLHLLE 548 (921)
Q Consensus 518 pVDTHV~RVl~RL---Glv~~~~tpeeve~~L~~ 548 (921)
..|++.+. |.+- .+|+++.+.+..
T Consensus 89 -----~~R~~~~~~~~~~~i--~sp~~~~~~l~~ 115 (224)
T COG2003 89 -----GKRILAERLREGVVI--TSPEAVAEYLRA 115 (224)
T ss_pred -----HHHHHHHHhccCCcc--CCHHHHHHHHHH
Confidence 33444432 2222 467777776654
No 75
>PF05559 DUF763: Protein of unknown function (DUF763); InterPro: IPR008482 This family consists of several uncharacterised bacterial and archaeal proteins of unknown function.
Probab=53.39 E-value=32 Score=39.25 Aligned_cols=24 Identities=33% Similarity=0.639 Sum_probs=20.3
Q ss_pred CchHHHHHHHcCCCccHhhHHHHHHH
Q 002448 485 PPDKAKDYLLSIRGLGLKSVECVRLL 510 (921)
Q Consensus 485 P~deaReeLLsLPGVG~KTAd~ILlf 510 (921)
|.+ .++|+.++|||++|..++.+.
T Consensus 265 p~~--feeLL~~~GvGp~TlRALaLv 288 (319)
T PF05559_consen 265 PSD--FEELLLIKGVGPSTLRALALV 288 (319)
T ss_pred ccC--HHHHHhcCCCCHHHHHHHHHH
Confidence 455 889999999999999887664
No 76
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=53.07 E-value=18 Score=44.82 Aligned_cols=21 Identities=29% Similarity=0.286 Sum_probs=18.8
Q ss_pred HHHHHcCCCccHhhHHHHHHH
Q 002448 490 KDYLLSIRGLGLKSVECVRLL 510 (921)
Q Consensus 490 ReeLLsLPGVG~KTAd~ILlf 510 (921)
.++|++++|||+++|..|..|
T Consensus 540 ~e~l~~i~giG~~~a~si~~f 560 (669)
T PRK14350 540 LSKLLKIKGIGEKIALNIIEA 560 (669)
T ss_pred HHHHhhCCCccHHHHHHHHHH
Confidence 567999999999999999877
No 77
>PRK07945 hypothetical protein; Provisional
Probab=53.05 E-value=21 Score=40.54 Aligned_cols=61 Identities=10% Similarity=0.103 Sum_probs=39.0
Q ss_pred HHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHcCCCccHhhHHHHHHH
Q 002448 443 KEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLL 510 (921)
Q Consensus 443 EELeelIR~iGfyr~KAk~Ik~lA~~Lve~~GGlDLe~L~~vP~deaReeLLsLPGVG~KTAd~ILlf 510 (921)
++++.++.-.|=..-|.+.-+++|+.|.. .+. + .+..+.. ...|.+|||||.-||..|.-+
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 45666666667555677778888887764 221 2 1222211 116889999999999988755
No 78
>COG2818 Tag 3-methyladenine DNA glycosylase [DNA replication, recombination, and repair]
Probab=52.40 E-value=52 Score=35.05 Aligned_cols=48 Identities=13% Similarity=0.262 Sum_probs=35.3
Q ss_pred CCCCCHHHHHcCCHHHHHHHHHhcCCcHHHH--HHHHHHHHHHH---HhhCCC
Q 002448 429 MDSLDYEALRCANVKEISEAIKERGMNNMLA--ERMKDFLNRLV---REHGSI 476 (921)
Q Consensus 429 ~~~pTpEaLa~A~~EELeelIR~iGfyr~KA--k~Ik~lA~~Lv---e~~GGl 476 (921)
...++|+.+|..+.++++.++...|.-|.|. +.++.=|+.+. ++||++
T Consensus 61 F~~Fd~~kVA~~~~~dverLl~d~gIIR~r~KI~A~i~NA~~~l~l~~e~Gsf 113 (188)
T COG2818 61 FHGFDPEKVAAMTEEDVERLLADAGIIRNRGKIKATINNARAVLELQKEFGSF 113 (188)
T ss_pred HhcCCHHHHHcCCHHHHHHHHhCcchhhhHHHHHHHHHHHHHHHHHHHHcCCH
Confidence 3468999999999999999999999866554 44444444443 456764
No 79
>PRK08609 hypothetical protein; Provisional
Probab=52.30 E-value=39 Score=41.15 Aligned_cols=49 Identities=29% Similarity=0.443 Sum_probs=29.6
Q ss_pred cCCcHHHHHHHHHHHHHHHHhhCCC-Chhhhh-cCCchHHHHHHHcCCCccHhhHHHH
Q 002448 452 RGMNNMLAERMKDFLNRLVREHGSI-DLEWLR-DVPPDKAKDYLLSIRGLGLKSVECV 507 (921)
Q Consensus 452 iGfyr~KAk~Ik~lA~~Lve~~GGl-DLe~L~-~vP~deaReeLLsLPGVG~KTAd~I 507 (921)
-|.-..-|+.|.++.+ .|.+ -|+.|+ ++|.. ..+|+++||||+|||..+
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 3554555666665443 2332 234454 45544 557999999999999554
No 80
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=52.28 E-value=11 Score=39.63 Aligned_cols=23 Identities=17% Similarity=0.174 Sum_probs=19.9
Q ss_pred HHHHHHHcCCCccHhhHHHHHHH
Q 002448 488 KAKDYLLSIRGLGLKSVECVRLL 510 (921)
Q Consensus 488 eaReeLLsLPGVG~KTAd~ILlf 510 (921)
++.+.|++++|||+|+|-.||..
T Consensus 70 ~lF~~Li~V~GIGpK~Al~ILs~ 92 (194)
T PRK14605 70 SLFETLIDVSGIGPKLGLAMLSA 92 (194)
T ss_pred HHHHHHhCCCCCCHHHHHHHHHh
Confidence 45678999999999999999874
No 81
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=50.20 E-value=35 Score=38.77 Aligned_cols=57 Identities=14% Similarity=0.119 Sum_probs=36.5
Q ss_pred HHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHcCCCccHhhHHHHHHH
Q 002448 443 KEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLL 510 (921)
Q Consensus 443 EELeelIR~iGfyr~KAk~Ik~lA~~Lve~~GGlDLe~L~~vP~deaReeLLsLPGVG~KTAd~ILlf 510 (921)
+++++++.-.|=...|+++..++++.|.. ++. ++ +. .+.|.+|||||.++|+.|--+
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 34555555456544577777777777754 332 22 22 247899999999999988743
No 82
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=49.74 E-value=25 Score=39.94 Aligned_cols=50 Identities=12% Similarity=0.259 Sum_probs=30.1
Q ss_pred CCcHHHHHHHHHHHHHHHHhhCCCC-hhhhhcCCchHHHHHHHcCCCccHhhHHHH
Q 002448 453 GMNNMLAERMKDFLNRLVREHGSID-LEWLRDVPPDKAKDYLLSIRGLGLKSVECV 507 (921)
Q Consensus 453 Gfyr~KAk~Ik~lA~~Lve~~GGlD-Le~L~~vP~deaReeLLsLPGVG~KTAd~I 507 (921)
|.-..-|+.|.++.+ .|.+. +..+..-+.-....+|+++||||+|||..+
T Consensus 55 gIG~~ia~kI~Eil~-----tG~~~~~~e~l~~~~p~~l~~l~~i~GiGpk~a~~l 105 (334)
T smart00483 55 GIGDKIKKKIEEIIE-----TGKSSKVLEILNDEVYKSLKLFTNVFGVGPKTAAKW 105 (334)
T ss_pred CccHHHHHHHHHHHH-----hCcHHHHHHHhcCcHHHHHHHHHccCCcCHHHHHHH
Confidence 554556666665543 35544 222222222344889999999999999655
No 83
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=49.17 E-value=75 Score=38.95 Aligned_cols=70 Identities=10% Similarity=0.113 Sum_probs=44.2
Q ss_pred CCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHH----------------------hhCCCChhhhhcCCchHH
Q 002448 432 LDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVR----------------------EHGSIDLEWLRDVPPDKA 489 (921)
Q Consensus 432 pTpEaLa~A~~EELeelIR~iGfyr~KAk~Ik~lA~~Lve----------------------~~GGlDLe~L~~vP~dea 489 (921)
-++.+|..+..++|.++ -||-..++++|.+..+.-.. .|+ +++.|....
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 37888888887766543 47777777777554331110 111 344444322
Q ss_pred HHHHHcCCCccHhhHHHHHHH
Q 002448 490 KDYLLSIRGLGLKSVECVRLL 510 (921)
Q Consensus 490 ReeLLsLPGVG~KTAd~ILlf 510 (921)
.+.|.+++|||+++|+.|..|
T Consensus 519 ~e~l~~i~gIG~~~a~si~~~ 539 (562)
T PRK08097 519 EQQWQQLPGIGEGRARQLIAF 539 (562)
T ss_pred HHHHhcCCCchHHHHHHHHHH
Confidence 457889999999999988776
No 84
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair]
Probab=48.90 E-value=53 Score=36.29 Aligned_cols=95 Identities=13% Similarity=0.082 Sum_probs=64.5
Q ss_pred CcCcHHHHHHHHHhHhhhcCCCccccCCCCchhhhhcccccccchhhhhhcccccccccccccccChHHHHHHHHhccCc
Q 002448 342 GSMLAEKTRNLGDDISVANKLSDNKLIEPNSVEQVLSAHKVYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGK 421 (921)
Q Consensus 342 ~~~~~~~~~~i~~rl~~~~~~p~~~l~~~~~~~~~~~~~~~~~lLia~iLsaq~~d~~vnk~qnT~W~nL~kaL~n~~Lk 421 (921)
+.-+.|++..+.+-+.+.-..|.+.+- ...+. .+.+.++..=++..+|||.+.. . .|.
T Consensus 156 lA~s~EeaaryIE~~k~~ek~p~dli~------~~~~~-----d~ls~~~~~Lt~i~~VnKtda~---~---LL~----- 213 (254)
T KOG2841|consen 156 LAWSMEEAARYIETYKEYEKKPIDLIM------ERKDR-----DLLSSLLGFLTTIPGVNKTDAQ---L---LLQ----- 213 (254)
T ss_pred eeccHHHHHHHHHHHHHhhcCCchhhh------hcccc-----cHHHHHHHHHHhCCCCCcccHH---H---HHH-----
Confidence 446778888888888777555443211 11111 2244667777788889985222 2 222
Q ss_pred cccccCcCCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHH
Q 002448 422 QERSRDRMDSLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRL 469 (921)
Q Consensus 422 ~erl~~~~~~pTpEaLa~A~~EELeelIR~iGfyr~KAk~Ik~lA~~L 469 (921)
.+.+.+.|..|+.++|+.+ -|+-.+||++|+++....
T Consensus 214 --------~FgsLq~~~~AS~~ele~~---~G~G~~kak~l~~~l~~p 250 (254)
T KOG2841|consen 214 --------KFGSLQQISNASEGELEQC---PGLGPAKAKRLHKFLHQP 250 (254)
T ss_pred --------hcccHHHHHhcCHhHHHhC---cCcCHHHHHHHHHHHhcc
Confidence 3889999999999999874 788899999999887643
No 85
>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=48.04 E-value=12 Score=28.62 Aligned_cols=15 Identities=20% Similarity=0.424 Sum_probs=11.1
Q ss_pred HHcCCCccHhhHHHH
Q 002448 493 LLSIRGLGLKSVECV 507 (921)
Q Consensus 493 LLsLPGVG~KTAd~I 507 (921)
+.+++|||++|+.-+
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 86
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=45.04 E-value=33 Score=42.58 Aligned_cols=58 Identities=21% Similarity=0.300 Sum_probs=37.5
Q ss_pred HHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHcCCCccHhhHHHHHHH
Q 002448 443 KEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLL 510 (921)
Q Consensus 443 EELeelIR~iGfyr~KAk~Ik~lA~~Lve~~GGlDLe~L~~vP~deaReeLLsLPGVG~KTAd~ILlf 510 (921)
-.|..+|-.+|....-... |+.|...|+. ++.|...+ .++|.+++|||.+.|..|..|
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 3455556666665444433 3333444443 66776655 458899999999999998776
No 87
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=44.96 E-value=26 Score=40.44 Aligned_cols=59 Identities=20% Similarity=0.340 Sum_probs=39.5
Q ss_pred HHHHHHHHhcCCcH-HHHHHH-HHHHHHHHHhhCCCChhhhhcCCchHHHHHHHcCCCccHhhHHHH
Q 002448 443 KEISEAIKERGMNN-MLAERM-KDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECV 507 (921)
Q Consensus 443 EELeelIR~iGfyr-~KAk~I-k~lA~~Lve~~GGlDLe~L~~vP~deaReeLLsLPGVG~KTAd~I 507 (921)
+.+...+.+.||.- .|..+| +.+|+.|+++||+ |..+...+ .++|.+++|||++.|..|
T Consensus 275 ~~ld~~v~prGyRiLs~IPrl~k~iAk~Ll~~FGS--L~~Il~As----~eeL~~VeGIGe~rA~~I 335 (352)
T PRK13482 275 EALDTPVSPRGYRLLSKIPRLPSAVIENLVEHFGS--LQGLLAAS----IEDLDEVEGIGEVRARAI 335 (352)
T ss_pred cccccccCCcHHHHHhcCCCCCHHHHHHHHHHcCC--HHHHHcCC----HHHHhhCCCcCHHHHHHH
Confidence 34555556666521 011222 5678999999985 66666555 558999999999999764
No 88
>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=41.44 E-value=48 Score=37.21 Aligned_cols=16 Identities=31% Similarity=0.455 Sum_probs=8.4
Q ss_pred HHHHHcCCCccHhhHH
Q 002448 490 KDYLLSIRGLGLKSVE 505 (921)
Q Consensus 490 ReeLLsLPGVG~KTAd 505 (921)
..+|++++|||+|||.
T Consensus 84 l~~l~~i~GiGpk~a~ 99 (307)
T cd00141 84 LLLLLRVPGVGPKTAR 99 (307)
T ss_pred HHHHHcCCCCCHHHHH
Confidence 4455555555555553
No 89
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=40.81 E-value=19 Score=28.49 Aligned_cols=16 Identities=19% Similarity=0.297 Sum_probs=12.9
Q ss_pred HcCCCccHhhHHHHHH
Q 002448 494 LSIRGLGLKSVECVRL 509 (921)
Q Consensus 494 LsLPGVG~KTAd~ILl 509 (921)
-.+||||+|||--+|.
T Consensus 19 ~Gv~giG~ktA~~ll~ 34 (36)
T smart00279 19 PGVKGIGPKTALKLLR 34 (36)
T ss_pred CCCCcccHHHHHHHHH
Confidence 4689999999977653
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=40.70 E-value=36 Score=38.21 Aligned_cols=57 Identities=14% Similarity=0.166 Sum_probs=36.0
Q ss_pred HHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHcCCCccHhhHHHHHHH
Q 002448 443 KEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLL 510 (921)
Q Consensus 443 EELeelIR~iGfyr~KAk~Ik~lA~~Lve~~GGlDLe~L~~vP~deaReeLLsLPGVG~KTAd~ILlf 510 (921)
++|+.++.-.|=..-|++.-+.+|..|.. .+. + .+. .+++.+|||||+++|+.|--+
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 34555555554333466666777777764 232 1 222 346799999999999998754
No 91
>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=39.63 E-value=27 Score=30.40 Aligned_cols=21 Identities=29% Similarity=0.479 Sum_probs=18.3
Q ss_pred HHHHHc-CCCccHhhHHHHHHH
Q 002448 490 KDYLLS-IRGLGLKSVECVRLL 510 (921)
Q Consensus 490 ReeLLs-LPGVG~KTAd~ILlf 510 (921)
.+.|.. +||||.++|..|+.+
T Consensus 15 ~~~L~~~ipgig~~~a~~Il~~ 36 (69)
T TIGR00426 15 AEELQRAMNGVGLKKAEAIVSY 36 (69)
T ss_pred HHHHHhHCCCCCHHHHHHHHHH
Confidence 457888 999999999999876
No 92
>PRK14973 DNA topoisomerase I; Provisional
Probab=38.32 E-value=2.3e+02 Score=36.96 Aligned_cols=76 Identities=21% Similarity=0.220 Sum_probs=53.0
Q ss_pred CCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHH-----Hh------------hCCC-ChhhhhcCCchHHH
Q 002448 429 MDSLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLV-----RE------------HGSI-DLEWLRDVPPDKAK 490 (921)
Q Consensus 429 ~~~pTpEaLa~A~~EELeelIR~iGfyr~KAk~Ik~lA~~Lv-----e~------------~GGl-DLe~L~~vP~deaR 490 (921)
.|..+..+|+.|++..| +..|++..+++.+++.|+-++ +. -+|| +++.+....+
T Consensus 763 ~~~~~~~~~~~~~~~~~----~~~~~sE~~~~~~~~~a~~~~~~~~~~~~gv~~~~~~~~~~~G~~~~~d~~~a~p---- 834 (936)
T PRK14973 763 SGINDIAALARADPADL----KKAGLSEAEAASLLAEAKSLCNISRLKEIGVPAVSLKKYQEAGFDTPEDFCSVHP---- 834 (936)
T ss_pred cCcchHHHHhhCCHHHH----HHcCCCHHHHHHHHHHHHHHHHHHhhcccCCCHHHHHHHHHhcCCCHHHHHhcCH----
Confidence 35679999999999886 459999999999999884332 11 0223 4444544443
Q ss_pred HHHHcCCCccHhhHHHHHHHhc
Q 002448 491 DYLLSIRGLGLKSVECVRLLTL 512 (921)
Q Consensus 491 eeLLsLPGVG~KTAd~ILlfaf 512 (921)
++|..++||++-|+......+.
T Consensus 835 ~~La~~~g~~~~~~~~~~~~~~ 856 (936)
T PRK14973 835 AYLALKTGISPETICRHAKLVC 856 (936)
T ss_pred HHHhcCCCCChhhHHHHHHHHH
Confidence 4899999999988876544433
No 93
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=35.35 E-value=29 Score=37.02 Aligned_cols=22 Identities=18% Similarity=0.300 Sum_probs=19.0
Q ss_pred HHHHHHHcCCCccHhhHHHHHH
Q 002448 488 KAKDYLLSIRGLGLKSVECVRL 509 (921)
Q Consensus 488 eaReeLLsLPGVG~KTAd~ILl 509 (921)
++.+.|+++.|||||+|=.||.
T Consensus 69 ~lF~~LisVsGIGPK~ALaILs 90 (196)
T PRK13901 69 EVFEELIGVDGIGPRAALRVLS 90 (196)
T ss_pred HHHHHHhCcCCcCHHHHHHHHc
Confidence 4567899999999999988885
No 94
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=35.16 E-value=29 Score=36.62 Aligned_cols=23 Identities=13% Similarity=0.228 Sum_probs=19.4
Q ss_pred HHHHHHHcCCCccHhhHHHHHHH
Q 002448 488 KAKDYLLSIRGLGLKSVECVRLL 510 (921)
Q Consensus 488 eaReeLLsLPGVG~KTAd~ILlf 510 (921)
++.+.|+++.|||||+|=.||..
T Consensus 70 ~lF~~LisV~GIGpK~Al~iLs~ 92 (186)
T PRK14600 70 DCLRMLVKVSGVNYKTAMSILSK 92 (186)
T ss_pred HHHHHHhCcCCcCHHHHHHHHcc
Confidence 45677999999999999988873
No 95
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=34.22 E-value=31 Score=36.35 Aligned_cols=22 Identities=27% Similarity=0.425 Sum_probs=19.0
Q ss_pred HHHHHHHcCCCccHhhHHHHHH
Q 002448 488 KAKDYLLSIRGLGLKSVECVRL 509 (921)
Q Consensus 488 eaReeLLsLPGVG~KTAd~ILl 509 (921)
++.+.|+++.|||||+|=.||.
T Consensus 70 ~lF~~Li~VsGIGpK~Al~ILs 91 (183)
T PRK14601 70 KMFEMLLKVNGIGANTAMAVCS 91 (183)
T ss_pred HHHHHHhccCCccHHHHHHHHc
Confidence 4567899999999999988885
No 96
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=33.83 E-value=32 Score=36.32 Aligned_cols=22 Identities=18% Similarity=0.027 Sum_probs=19.0
Q ss_pred HHHHHHHcCCCccHhhHHHHHH
Q 002448 488 KAKDYLLSIRGLGLKSVECVRL 509 (921)
Q Consensus 488 eaReeLLsLPGVG~KTAd~ILl 509 (921)
++.+.|+++.|||||+|=.||.
T Consensus 70 ~lF~~Li~V~GIGpK~AL~iLs 91 (188)
T PRK14606 70 ELFLSLTKVSRLGPKTALKIIS 91 (188)
T ss_pred HHHHHHhccCCccHHHHHHHHc
Confidence 4577899999999999988874
No 97
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=33.46 E-value=68 Score=36.80 Aligned_cols=60 Identities=18% Similarity=0.250 Sum_probs=36.5
Q ss_pred HHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHcCCCccHhhHHHHHHH
Q 002448 443 KEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLL 510 (921)
Q Consensus 443 EELeelIR~iGfyr~KAk~Ik~lA~~Lve~~GGlDLe~L~~vP~deaReeLLsLPGVG~KTAd~ILlf 510 (921)
++++.++--.|=..-|++.-+.+|+.|-.. ..|++.+.+ +..|..|||||+.||+.|--|
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 355555555554434666666667666542 223333322 224889999999999998765
No 98
>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=33.27 E-value=47 Score=29.36 Aligned_cols=48 Identities=27% Similarity=0.369 Sum_probs=29.6
Q ss_pred HHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHcCCCccHhhHHHHH
Q 002448 449 IKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVR 508 (921)
Q Consensus 449 IR~iGfyr~KAk~Ik~lA~~Lve~~GGlDLe~L~~vP~deaReeLLsLPGVG~KTAd~IL 508 (921)
|..+|++ .||.+. +. +.|=-.+..|..++ .+.|++++|+|+++.+-|.
T Consensus 14 I~~L~LS-~Ra~n~------L~-~~~I~tv~dL~~~s----~~~L~~i~n~G~ksl~EI~ 61 (66)
T PF03118_consen 14 IEDLGLS-VRAYNC------LK-RAGIHTVGDLVKYS----EEDLLKIKNFGKKSLEEIK 61 (66)
T ss_dssp GGGSTSB-HHHHHH------HH-CTT--BHHHHHCS-----HHHHHTSTTSHHHHHHHHH
T ss_pred HHHhCCC-HHHHHH------HH-HhCCcCHHHHHhCC----HHHHHhCCCCCHhHHHHHH
Confidence 3447887 344322 22 12323566776765 4589999999999998764
No 99
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=33.17 E-value=32 Score=36.46 Aligned_cols=22 Identities=23% Similarity=0.301 Sum_probs=19.1
Q ss_pred HHHHHHHcCCCccHhhHHHHHH
Q 002448 488 KAKDYLLSIRGLGLKSVECVRL 509 (921)
Q Consensus 488 eaReeLLsLPGVG~KTAd~ILl 509 (921)
++.+.|+++.|||||+|=.||.
T Consensus 69 ~lF~~L~~V~GIGpK~AL~iLs 90 (197)
T PRK14603 69 ELFELLLGVSGVGPKLALALLS 90 (197)
T ss_pred HHHHHHhCcCCcCHHHHHHHHc
Confidence 4567799999999999988886
No 100
>PRK00254 ski2-like helicase; Provisional
Probab=33.11 E-value=81 Score=39.25 Aligned_cols=41 Identities=12% Similarity=0.101 Sum_probs=23.3
Q ss_pred HHHcCCCccHhhHHHHHHHhcCCceeecchHHHHHHHHhCC
Q 002448 492 YLLSIRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGW 532 (921)
Q Consensus 492 eLLsLPGVG~KTAd~ILlfafgrpvfpVDTHV~RVl~RLGl 532 (921)
.|..|||||+++|...+..+|+-..=..+.....+..-.|+
T Consensus 646 ~L~~ipgig~~~~~~l~~~g~~s~~~i~~a~~~el~~~~gi 686 (720)
T PRK00254 646 ELMRLPMIGRKRARALYNAGFRSIEDIVNAKPSELLKVEGI 686 (720)
T ss_pred hhhcCCCCCHHHHHHHHHccCCCHHHHHhCCHHHHhcCCCC
Confidence 46677888888777777776665432233333333333244
No 101
>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=32.70 E-value=21 Score=32.06 Aligned_cols=19 Identities=16% Similarity=0.165 Sum_probs=15.2
Q ss_pred HHHcCCCccHhhHHHHHHH
Q 002448 492 YLLSIRGLGLKSVECVRLL 510 (921)
Q Consensus 492 eLLsLPGVG~KTAd~ILlf 510 (921)
.+-.+||||+|||.-++.-
T Consensus 23 ~i~gv~giG~k~A~~ll~~ 41 (75)
T cd00080 23 NIPGVPGIGPKTALKLLKE 41 (75)
T ss_pred cCCCCCcccHHHHHHHHHH
Confidence 5667999999999877643
No 102
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=32.37 E-value=35 Score=36.36 Aligned_cols=23 Identities=22% Similarity=0.183 Sum_probs=19.5
Q ss_pred HHHHHHHcCCCccHhhHHHHHHH
Q 002448 488 KAKDYLLSIRGLGLKSVECVRLL 510 (921)
Q Consensus 488 eaReeLLsLPGVG~KTAd~ILlf 510 (921)
++.+.|+++.|||||+|=.||..
T Consensus 71 ~lF~~Li~V~GIGpK~Al~iLs~ 93 (203)
T PRK14602 71 QTFIVLISISKVGAKTALAILSQ 93 (203)
T ss_pred HHHHHHhCCCCcCHHHHHHHHhh
Confidence 45677899999999999888864
No 103
>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=32.34 E-value=39 Score=28.83 Aligned_cols=19 Identities=21% Similarity=0.239 Sum_probs=13.3
Q ss_pred HHHHcCCCccHhhHHHHHH
Q 002448 491 DYLLSIRGLGLKSVECVRL 509 (921)
Q Consensus 491 eeLLsLPGVG~KTAd~ILl 509 (921)
+.|..+.|||+.||.-...
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 4688999999999966543
No 104
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=31.67 E-value=35 Score=36.19 Aligned_cols=23 Identities=17% Similarity=0.258 Sum_probs=19.6
Q ss_pred HHHHHHHcCCCccHhhHHHHHHH
Q 002448 488 KAKDYLLSIRGLGLKSVECVRLL 510 (921)
Q Consensus 488 eaReeLLsLPGVG~KTAd~ILlf 510 (921)
++...|+++.|||||+|=.||..
T Consensus 70 ~lF~~Li~V~GIGpK~Al~iLs~ 92 (195)
T PRK14604 70 QLFELLIGVSGVGPKAALNLLSS 92 (195)
T ss_pred HHHHHHhCcCCcCHHHHHHHHcC
Confidence 45678999999999999888873
No 105
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=30.63 E-value=38 Score=34.26 Aligned_cols=20 Identities=5% Similarity=-0.122 Sum_probs=17.3
Q ss_pred HHHHHcCCCccHhhHHHHHH
Q 002448 490 KDYLLSIRGLGLKSVECVRL 509 (921)
Q Consensus 490 ReeLLsLPGVG~KTAd~ILl 509 (921)
.++|.+|||||+..|..|..
T Consensus 60 ~~el~~lpGigP~~A~~IV~ 79 (132)
T PRK02515 60 VRAFRQFPGMYPTLAGKIVK 79 (132)
T ss_pred HHHHHHCCCCCHHHHHHHHH
Confidence 45689999999999999873
No 106
>PRK13280 N-glycosylase/DNA lyase; Provisional
Probab=29.63 E-value=1.9e+02 Score=32.63 Aligned_cols=134 Identities=14% Similarity=0.107 Sum_probs=75.3
Q ss_pred HHHHHHHHhc----CCcHHHHHHHHHHHHHHHHhhCCCChhhhhc--CCchHHHHHHHcCCCc--cHhh-------HHHH
Q 002448 443 KEISEAIKER----GMNNMLAERMKDFLNRLVREHGSIDLEWLRD--VPPDKAKDYLLSIRGL--GLKS-------VECV 507 (921)
Q Consensus 443 EELeelIR~i----Gfyr~KAk~Ik~lA~~Lve~~GGlDLe~L~~--vP~deaReeLLsLPGV--G~KT-------Ad~I 507 (921)
+++...+... -+..+|-++|.+++..+-+ +.+.++.. ..-+++++.|..+=|- -.|| +...
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 3455556554 2345788888888765432 22222221 2234556666665444 2333 3333
Q ss_pred HHHhcCC--c-----eeecchHHHHHHHHhCCCCCCCCHHHHHHHHHHhcCchHHHHHhhhhhhhcCChhhHHHHHHHHH
Q 002448 508 RLLTLHH--L-----AFPVDTNVGRIAVRLGWVPLQPLPESLQLHLLELYPVLESIQKYLWPRLCKLDQRTLYELHYQLI 580 (921)
Q Consensus 508 Llfafgr--p-----vfpVDTHV~RVl~RLGlv~~~~tpeeve~~L~~llP~~e~Iqk~LW~rl~~ld~e~~~e~H~lLI 580 (921)
...+++. | -||||.-|..+....|++.+..........+.. ......|..++..+.--+.+++..||
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 3333433 2 488999999999999999863221111122111 11235788876666566678888888
Q ss_pred HHhHhh
Q 002448 581 TFGKVF 586 (921)
Q Consensus 581 ~fGR~I 586 (921)
..|+..
T Consensus 237 ~~~g~~ 242 (269)
T PRK13280 237 LVLGAL 242 (269)
T ss_pred hhcCCc
Confidence 887654
No 107
>PRK07758 hypothetical protein; Provisional
Probab=29.16 E-value=69 Score=30.84 Aligned_cols=28 Identities=25% Similarity=0.412 Sum_probs=21.7
Q ss_pred ChhhhhcCCchHHHHHHHcCCCccHhhHHHHH
Q 002448 477 DLEWLRDVPPDKAKDYLLSIRGLGLKSVECVR 508 (921)
Q Consensus 477 DLe~L~~vP~deaReeLLsLPGVG~KTAd~IL 508 (921)
.++.|..++ .++|++|+|+|+|+.+-|.
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 455665655 5589999999999998764
No 108
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=27.62 E-value=45 Score=35.74 Aligned_cols=23 Identities=22% Similarity=0.251 Sum_probs=19.6
Q ss_pred HHHHHHHcCCCccHhhHHHHHHH
Q 002448 488 KAKDYLLSIRGLGLKSVECVRLL 510 (921)
Q Consensus 488 eaReeLLsLPGVG~KTAd~ILlf 510 (921)
++...|+++-|||+|+|=+||..
T Consensus 70 ~lF~~LisVnGIGpK~ALaiLs~ 92 (201)
T COG0632 70 ELFRLLISVNGIGPKLALAILSN 92 (201)
T ss_pred HHHHHHHccCCccHHHHHHHHcC
Confidence 45678999999999999888765
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=26.44 E-value=59 Score=31.16 Aligned_cols=23 Identities=17% Similarity=0.114 Sum_probs=18.7
Q ss_pred HHHHHHHcCCCccHhhHHHHHHH
Q 002448 488 KAKDYLLSIRGLGLKSVECVRLL 510 (921)
Q Consensus 488 eaReeLLsLPGVG~KTAd~ILlf 510 (921)
.+.-.|.++.|||+.+|..|+..
T Consensus 12 ~i~~aLt~IyGIG~~~A~~Ic~~ 34 (107)
T PF00416_consen 12 PIYIALTKIYGIGRRKAKQICKK 34 (107)
T ss_dssp BHHHHHTTSTTBCHHHHHHHHHH
T ss_pred chHhHHhhhhccCHHHHHHHHHH
Confidence 35778999999999999877543
No 110
>PF11372 DUF3173: Domain of unknown function (DUF3173); InterPro: IPR021512 This family of proteins with unknown function appears to be restricted to Firmicutes.
Probab=26.23 E-value=1.6e+02 Score=26.15 Aligned_cols=44 Identities=23% Similarity=0.293 Sum_probs=29.9
Q ss_pred cCCcHHHHHHHHHHHHHHHHhhC--CCChhhhhcCCchHHHHHHHcC
Q 002448 452 RGMNNMLAERMKDFLNRLVREHG--SIDLEWLRDVPPDKAKDYLLSI 496 (921)
Q Consensus 452 iGfyr~KAk~Ik~lA~~Lve~~G--GlDLe~L~~vP~deaReeLLsL 496 (921)
+||....|+.|+.-|+.+.-+.| -++=..|..+|.. +.++|+.+
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 69999999999998888764322 1233456667765 56667644
No 111
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=25.83 E-value=64 Score=39.62 Aligned_cols=37 Identities=8% Similarity=0.200 Sum_probs=25.6
Q ss_pred HHHHhhCCCChhhhhcCCchHHHHHHHcCCCccHhhHHHHHHH
Q 002448 468 RLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLL 510 (921)
Q Consensus 468 ~Lve~~GGlDLe~L~~vP~deaReeLLsLPGVG~KTAd~ILlf 510 (921)
.|.+.||+ ++.++..+ .++|.++||||.++|..|..+
T Consensus 529 ~LL~~Fgs--~~~I~~As----~eeL~~v~gi~~~~A~~I~~~ 565 (574)
T PRK14670 529 KILKSLGT--YKDILLLN----EDEIAEKMKINIKMAKKIKKF 565 (574)
T ss_pred HHHHHhCC--HHHHHhCC----HHHHHhCCCCCHHHHHHHHHH
Confidence 34455665 56666544 457888888888888888655
No 112
>PF13592 HTH_33: Winged helix-turn helix
Probab=25.26 E-value=94 Score=26.65 Aligned_cols=36 Identities=17% Similarity=0.134 Sum_probs=22.5
Q ss_pred cHhhHHHHHHHhcCCc-eeecchHHHHHHHHhCCCCC
Q 002448 500 GLKSVECVRLLTLHHL-AFPVDTNVGRIAVRLGWVPL 535 (921)
Q Consensus 500 G~KTAd~ILlfafgrp-vfpVDTHV~RVl~RLGlv~~ 535 (921)
|.||+..|..+.-..- +-.-..+|.|++.|+||...
T Consensus 3 ~~wt~~~i~~~I~~~fgv~ys~~~v~~lL~r~G~s~~ 39 (60)
T PF13592_consen 3 GRWTLKEIAAYIEEEFGVKYSPSGVYRLLKRLGFSYQ 39 (60)
T ss_pred CcccHHHHHHHHHHHHCCEEcHHHHHHHHHHcCCccc
Confidence 4556655554433222 11256899999999999754
No 113
>PRK08609 hypothetical protein; Provisional
Probab=25.02 E-value=1.1e+02 Score=37.25 Aligned_cols=57 Identities=16% Similarity=0.283 Sum_probs=36.6
Q ss_pred HHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHcCCCccHhhHHHHHHH
Q 002448 443 KEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLL 510 (921)
Q Consensus 443 EELeelIR~iGfyr~KAk~Ik~lA~~Lve~~GGlDLe~L~~vP~deaReeLLsLPGVG~KTAd~ILlf 510 (921)
++++.++.-.|=..-|++.-+++|+.|... .. ++. . ...|.+|||||..+|..|--+
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 455566555564335676677777777642 21 211 1 246899999999999988744
No 114
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=24.51 E-value=1.2e+02 Score=33.51 Aligned_cols=30 Identities=17% Similarity=0.229 Sum_probs=23.8
Q ss_pred ChhhhhcCCchHHHHHHHcCCCccHhhHHHHHHH
Q 002448 477 DLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLL 510 (921)
Q Consensus 477 DLe~L~~vP~deaReeLLsLPGVG~KTAd~ILlf 510 (921)
+++.|...+ .++|.+++|||.++|..|..+
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 115
>COG1491 Predicted RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=23.54 E-value=88 Score=33.52 Aligned_cols=26 Identities=15% Similarity=0.078 Sum_probs=20.3
Q ss_pred HHHHHcCCCccHhhHHHHHHHhcCCc
Q 002448 490 KDYLLSIRGLGLKSVECVRLLTLHHL 515 (921)
Q Consensus 490 ReeLLsLPGVG~KTAd~ILlfafgrp 515 (921)
.-.|.-|||||.|++..||---=.+|
T Consensus 129 LH~LELLpGiGkK~m~~ILeERkkkp 154 (202)
T COG1491 129 LHQLELLPGIGKKTMWAILEERKKKP 154 (202)
T ss_pred HHHHHhcccccHHHHHHHHHHHhcCC
Confidence 55788899999999999987543343
No 116
>COG4277 Predicted DNA-binding protein with the Helix-hairpin-helix motif [General function prediction only]
Probab=23.05 E-value=55 Score=37.47 Aligned_cols=21 Identities=29% Similarity=0.474 Sum_probs=18.4
Q ss_pred HHHHHcCCCccHhhHHHHHHH
Q 002448 490 KDYLLSIRGLGLKSVECVRLL 510 (921)
Q Consensus 490 ReeLLsLPGVG~KTAd~ILlf 510 (921)
+++|+.+||||.|+|.-|+..
T Consensus 329 ~~~llRVPGiG~ksa~rIv~~ 349 (404)
T COG4277 329 YKELLRVPGIGVKSARRIVMT 349 (404)
T ss_pred HHHhcccCCCChHHHHHHHHH
Confidence 679999999999999887653
No 117
>PRK14469 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=22.02 E-value=1.4e+02 Score=34.01 Aligned_cols=55 Identities=13% Similarity=0.270 Sum_probs=42.6
Q ss_pred HHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHHcC
Q 002448 437 LRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSI 496 (921)
Q Consensus 437 La~A~~EELeelIR~iGfyr~KAk~Ik~lA~~Lve~~GGlDLe~L~~vP~deaReeLLsL 496 (921)
|..++.++|++++...|+...+|+.|. +|+-.+ +..|.+.+.++|.+ +|+.|.+.
T Consensus 4 ~~~~~~~~~~~~~~~~g~~~~r~~qi~---~~~~~~-~~~~~~~~~~~~~~-~r~~l~~~ 58 (343)
T PRK14469 4 ILDLSYEELVSEITELGLEKYRADQIL---DWIYKK-KVFNFDEMTNLSKD-HRALLSEH 58 (343)
T ss_pred cccCCHHHHHHHHHHcCCCchHHHHHH---HHHHhc-CCCCHHHhccccHH-HHHHHhhc
Confidence 667889999999999999877787765 466664 34588889899876 67777653
No 118
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=21.87 E-value=1.1e+02 Score=34.18 Aligned_cols=20 Identities=0% Similarity=-0.125 Sum_probs=13.7
Q ss_pred HHHHHHHhHhhhcCCCcccc
Q 002448 348 KTRNLGDDISVANKLSDNKL 367 (921)
Q Consensus 348 ~~~~i~~rl~~~~~~p~~~l 367 (921)
+..+=..||+..|+.|.--+
T Consensus 86 RlfeQ~~rL~~~y~rpvliV 105 (254)
T COG1948 86 RLFEQAKRLKKSYERPVLIV 105 (254)
T ss_pred hHHHHHHHHHhcCCccEEEE
Confidence 44555578888898887433
No 119
>KOG0400 consensus 40S ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=21.60 E-value=1e+02 Score=31.33 Aligned_cols=65 Identities=22% Similarity=0.414 Sum_probs=47.0
Q ss_pred hhhhcCCchHHHHHHHcC--CCccHhhHHHHHHHhcC--CceeecchHHHHHHHHhCCCCCCCCHHHHHHHH
Q 002448 479 EWLRDVPPDKAKDYLLSI--RGLGLKSVECVRLLTLH--HLAFPVDTNVGRIAVRLGWVPLQPLPESLQLHL 546 (921)
Q Consensus 479 e~L~~vP~deaReeLLsL--PGVG~KTAd~ILlfafg--rpvfpVDTHV~RVl~RLGlv~~~~tpeeve~~L 546 (921)
.||. +..|++.+.+.++ +|+-+--..++|.-+.| +-.++...-+.|++.+-|++|. -|+.+...+
T Consensus 24 tWlK-~~~ddvkeqI~K~akKGltpsqIGviLRDshGi~q~r~v~G~kI~Rilk~~Gl~Pe--iPeDLy~li 92 (151)
T KOG0400|consen 24 TWLK-LTADDVKEQIYKLAKKGLTPSQIGVILRDSHGIGQVRFVTGNKILRILKSNGLAPE--IPEDLYHLI 92 (151)
T ss_pred HHHh-cCHHHHHHHHHHHHHcCCChhHceeeeecccCcchhheechhHHHHHHHHcCCCCC--CcHHHHHHH
Confidence 3443 4455677777765 88888888888865555 4578889999999999999984 566555443
No 120
>COG2019 AdkA Archaeal adenylate kinase [Nucleotide transport and metabolism]
Probab=21.05 E-value=2.9e+02 Score=29.67 Aligned_cols=42 Identities=24% Similarity=0.282 Sum_probs=32.4
Q ss_pred HHcCCCccHhhHHHHHHHhc-CCceeecchHHHHHHHHhCCCC
Q 002448 493 LLSIRGLGLKSVECVRLLTL-HHLAFPVDTNVGRIAVRLGWVP 534 (921)
Q Consensus 493 LLsLPGVG~KTAd~ILlfaf-grpvfpVDTHV~RVl~RLGlv~ 534 (921)
+..+||||.-|.=-++.-.+ +...+---+.+.+++.+.|++.
T Consensus 9 itGVpGvGKTTVl~~~~~~l~~~~ivNyG~~Mle~A~k~glve 51 (189)
T COG2019 9 ITGVPGVGKTTVLKIALKELVKHKIVNYGDLMLEIAKKKGLVE 51 (189)
T ss_pred EEcCCCCChHHHHHHHHHHHhhceeeeHhHHHHHHHHHhCCcc
Confidence 45789999999865554444 5566667888999999999985
No 121
>PRK01172 ski2-like helicase; Provisional
Probab=20.86 E-value=2.1e+02 Score=35.30 Aligned_cols=42 Identities=10% Similarity=0.115 Sum_probs=36.5
Q ss_pred CCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhh
Q 002448 429 MDSLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREH 473 (921)
Q Consensus 429 ~~~pTpEaLa~A~~EELeelIR~iGfyr~KAk~Ik~lA~~Lve~~ 473 (921)
.|.-|+.+|++++.+++.++ .|+...+|+.|++-|+.+++-|
T Consensus 631 ~g~~~~~di~~~~~~~~~~i---~~~~~~~~~~i~~~~~~~~~~~ 672 (674)
T PRK01172 631 AGFKTVDDIARSSPERIKKI---YGFSDTLANAIVNRAMKISSMY 672 (674)
T ss_pred cCCCCHHHHHhCCHHHHHHH---hccCHHHHHHHHHHHHHHHHHh
Confidence 56779999999999999876 5899999999999999888643
No 122
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=20.22 E-value=3.7e+02 Score=26.36 Aligned_cols=94 Identities=12% Similarity=0.083 Sum_probs=55.2
Q ss_pred HHHHHHHHhccCccccccCcCCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchH
Q 002448 409 ESLRKEVQRNSGKQERSRDRMDSLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDK 488 (921)
Q Consensus 409 ~nL~kaL~n~~Lk~erl~~~~~~pTpEaLa~A~~EELeelIR~iGfyr~KAk~Ik~lA~~Lve~~GGlDLe~L~~vP~de 488 (921)
.++.+.+..+|+..+ .....+..+...|..+.++..- -....|.++|+.+ ++++++|.....++
T Consensus 8 ~~l~~ll~~~Glsq~---------eLA~~~Gis~~~is~iE~g~~~--ps~~~l~kIa~aL-----~v~~~~L~~~~~~~ 71 (120)
T PRK13890 8 TNVLRLLDERHMTKK---------ELSERSGVSISFLSDLTTGKAN--PSLKVMEAIADAL-----ETPLPLLLESTDLD 71 (120)
T ss_pred HHHHHHHHHcCCCHH---------HHHHHHCcCHHHHHHHHcCCCC--CCHHHHHHHHHHH-----CCCHHHHhccCccC
Confidence 345555555444432 4555566688888777665542 3567777877766 36667665443332
Q ss_pred HHHHHHcCCCccHhhHHHHHHHhcCCceeecchHHHHHHHHhCCC
Q 002448 489 AKDYLLSIRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWV 533 (921)
Q Consensus 489 aReeLLsLPGVG~KTAd~ILlfafgrpvfpVDTHV~RVl~RLGlv 533 (921)
++.|..|.|.-. .-.|...+.|++.+|.-.
T Consensus 72 -~~~l~~la~~~~--------------~~~~~~~~~~lld~L~~~ 101 (120)
T PRK13890 72 -KEALDALAGGKA--------------PRSLPPGFERVAAVLPEH 101 (120)
T ss_pred -HHHHHHHcCCCC--------------CCCCChHHHHHHHHcCCc
Confidence 555555555311 224556789999988543
No 123
>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=20.09 E-value=4.3e+02 Score=33.41 Aligned_cols=56 Identities=16% Similarity=0.268 Sum_probs=39.0
Q ss_pred HHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCChhhhhcCCchHHHHHHH-cCCCccHhhHHHHHH
Q 002448 442 VKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLL-SIRGLGLKSVECVRL 509 (921)
Q Consensus 442 ~EELeelIR~iGfyr~KAk~Ik~lA~~Lve~~GGlDLe~L~~vP~deaReeLL-sLPGVG~KTAd~ILl 509 (921)
..++...+...|+....|..|.+ .||.-.++.|++=|.. |+ .++|||-++||.|..
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 56788888999999766665554 3444344555555543 44 589999999998754
Done!