Query 002604
Match_columns 901
No_of_seqs 415 out of 1971
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 03:22:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/002604.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/002604hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0177 Nth Predicted EndoIII- 100.0 4.2E-53 9.1E-58 434.1 20.6 209 344-609 1-209 (211)
2 PF15628 RRM_DME: RRM in Demet 100.0 1E-47 2.3E-52 349.0 3.8 69 833-901 1-69 (103)
3 PRK10702 endonuclease III; Pro 100.0 5.6E-44 1.2E-48 367.9 20.6 208 344-608 1-208 (211)
4 TIGR01083 nth endonuclease III 100.0 1.6E-36 3.5E-41 307.0 19.5 190 348-594 2-191 (191)
5 TIGR01084 mutY A/G-specific ad 100.0 8.2E-37 1.8E-41 325.8 18.3 199 376-624 20-222 (275)
6 PRK10880 adenine DNA glycosyla 100.0 1E-36 2.2E-41 334.3 17.6 202 377-624 25-226 (350)
7 KOG1921 Endonuclease III [Repl 100.0 8.2E-34 1.8E-38 293.4 13.9 183 380-607 76-261 (286)
8 PRK13913 3-methyladenine DNA g 100.0 6.5E-33 1.4E-37 287.3 19.1 189 379-589 27-216 (218)
9 PRK13910 DNA glycosylase MutY; 100.0 1.2E-32 2.6E-37 295.6 18.8 150 431-609 22-172 (289)
10 COG2231 Uncharacterized protei 100.0 2.8E-32 6.1E-37 277.2 19.3 209 347-607 6-214 (215)
11 COG1194 MutY A/G-specific DNA 100.0 1.1E-28 2.5E-33 267.8 17.2 200 376-624 28-231 (342)
12 smart00478 ENDO3c endonuclease 99.9 1.1E-24 2.3E-29 210.8 16.3 129 431-585 21-149 (149)
13 cd00056 ENDO3c endonuclease II 99.9 9.6E-25 2.1E-29 212.7 15.2 158 383-583 1-158 (158)
14 PRK01229 N-glycosylase/DNA lya 99.9 3E-24 6.5E-29 221.5 11.8 137 380-551 35-185 (208)
15 TIGR00588 ogg 8-oxoguanine DNA 99.8 4E-20 8.7E-25 200.9 15.6 142 381-533 118-264 (310)
16 KOG2457 A/G-specific adenine D 99.8 7.7E-21 1.7E-25 206.7 9.9 184 381-608 124-310 (555)
17 TIGR03252 uncharacterized HhH- 99.8 4.6E-20 9.9E-25 186.1 10.9 112 380-510 16-134 (177)
18 COG0122 AlkA 3-methyladenine D 99.7 7E-18 1.5E-22 181.8 13.3 167 380-562 103-271 (285)
19 PRK10308 3-methyl-adenine DNA 99.7 1.3E-15 2.8E-20 164.1 17.4 151 380-552 111-263 (283)
20 KOG2875 8-oxoguanine DNA glyco 99.6 2.7E-15 6E-20 159.0 11.4 139 381-530 116-258 (323)
21 PF00730 HhH-GPD: HhH-GPD supe 99.5 6E-14 1.3E-18 129.0 9.6 107 387-551 1-107 (108)
22 KOG1918 3-methyladenine DNA gl 99.4 1.5E-13 3.3E-18 141.9 8.1 166 376-562 69-238 (254)
23 PF15629 Perm-CXXC: Permuted s 99.1 1.3E-11 2.8E-16 92.4 0.8 32 799-830 1-32 (32)
24 COG1059 Thermostable 8-oxoguan 98.3 1.4E-06 3E-11 89.5 7.3 122 382-535 39-165 (210)
25 PF00633 HHH: Helix-hairpin-he 97.6 1.6E-05 3.4E-10 59.6 0.9 26 483-510 5-30 (30)
26 PF10576 EndIII_4Fe-2S: Iron-s 96.9 0.00034 7.3E-09 46.5 0.9 17 587-603 1-17 (17)
27 PF09674 DUF2400: Protein of u 96.7 0.0014 3E-08 70.1 3.8 88 456-583 142-229 (232)
28 TIGR02757 conserved hypothetic 96.2 0.0043 9.2E-08 66.3 3.9 85 458-584 142-227 (229)
29 smart00525 FES FES domain. iro 96.0 0.0035 7.5E-08 45.2 1.4 22 586-607 1-22 (26)
30 smart00278 HhH1 Helix-hairpin- 91.3 0.14 3.1E-06 36.9 2.0 20 492-511 2-21 (26)
31 PF12826 HHH_2: Helix-hairpin- 90.6 0.34 7.3E-06 42.0 4.0 40 465-510 15-54 (64)
32 PRK13901 ruvA Holliday junctio 87.3 2 4.3E-05 45.4 7.7 66 428-514 59-130 (196)
33 PF14716 HHH_8: Helix-hairpin- 85.5 3.2 7E-05 36.2 6.9 58 443-510 9-66 (68)
34 TIGR00426 competence protein C 83.2 1.6 3.5E-05 37.9 4.0 58 436-510 9-66 (69)
35 PRK02515 psbU photosystem II c 83.0 1.8 3.9E-05 43.2 4.7 53 435-509 53-105 (132)
36 PF14520 HHH_5: Helix-hairpin- 82.2 3.7 8.1E-05 34.8 5.8 30 477-510 28-57 (60)
37 PF09171 DUF1886: Domain of un 82.1 3.9 8.5E-05 44.7 7.2 133 443-589 77-232 (246)
38 PRK14601 ruvA Holliday junctio 79.8 6.4 0.00014 41.2 7.6 70 428-514 60-131 (183)
39 PRK00076 recR recombination pr 79.5 1.7 3.7E-05 45.9 3.4 28 487-514 7-34 (196)
40 PRK13844 recombination protein 79.2 1.8 3.9E-05 45.9 3.4 28 487-514 11-38 (200)
41 PRK14606 ruvA Holliday junctio 79.1 6.9 0.00015 41.1 7.6 66 428-514 60-131 (188)
42 TIGR00615 recR recombination p 78.9 1.9 4E-05 45.7 3.4 28 487-514 7-34 (195)
43 PRK10353 3-methyl-adenine DNA 78.5 2.6 5.6E-05 44.4 4.3 47 429-475 60-111 (187)
44 PF03352 Adenine_glyco: Methyl 78.4 7.4 0.00016 40.7 7.6 47 429-475 55-106 (179)
45 PRK00024 hypothetical protein; 78.4 3.6 7.9E-05 44.0 5.5 61 439-508 23-83 (224)
46 PF14520 HHH_5: Helix-hairpin- 77.6 2.1 4.5E-05 36.3 2.8 27 489-515 3-29 (60)
47 TIGR00608 radc DNA repair prot 77.2 4.4 9.5E-05 43.4 5.7 61 439-508 13-77 (218)
48 PRK14602 ruvA Holliday junctio 75.5 8.8 0.00019 40.7 7.3 70 428-514 61-132 (203)
49 COG0353 RecR Recombinational D 75.5 2.5 5.5E-05 44.7 3.2 28 487-514 8-35 (198)
50 PRK14605 ruvA Holliday junctio 75.0 9.8 0.00021 40.0 7.5 65 428-509 60-126 (194)
51 PRK14600 ruvA Holliday junctio 74.6 7.2 0.00016 40.9 6.3 69 428-514 60-130 (186)
52 PRK00116 ruvA Holliday junctio 74.6 5.2 0.00011 41.8 5.3 22 490-511 107-128 (192)
53 TIGR00624 tag DNA-3-methyladen 74.3 4.4 9.5E-05 42.4 4.6 43 429-471 59-103 (179)
54 PRK14604 ruvA Holliday junctio 74.0 9.9 0.00021 40.1 7.2 69 429-514 61-131 (195)
55 COG1555 ComEA DNA uptake prote 73.0 5 0.00011 40.6 4.6 56 437-510 91-146 (149)
56 COG0632 RuvA Holliday junction 70.8 3 6.4E-05 44.3 2.5 70 429-513 61-130 (201)
57 TIGR00084 ruvA Holliday juncti 70.5 6.4 0.00014 41.3 4.8 66 428-510 59-126 (191)
58 PRK14973 DNA topoisomerase I; 69.8 8.1 0.00018 49.4 6.4 97 429-533 821-919 (936)
59 PF12836 HHH_3: Helix-hairpin- 69.3 5.6 0.00012 34.5 3.4 53 438-508 9-61 (65)
60 PRK14603 ruvA Holliday junctio 69.3 9.5 0.00021 40.3 5.8 24 490-513 106-129 (197)
61 PRK00116 ruvA Holliday junctio 68.3 4.7 0.0001 42.1 3.3 42 490-532 72-116 (192)
62 TIGR00575 dnlj DNA ligase, NAD 66.0 17 0.00038 44.8 7.9 62 432-509 455-516 (652)
63 TIGR01259 comE comEA protein. 65.8 8.5 0.00019 37.5 4.3 59 434-510 59-117 (120)
64 PRK07956 ligA NAD-dependent DN 64.3 18 0.00038 44.8 7.6 34 432-468 468-501 (665)
65 PF14229 DUF4332: Domain of un 63.0 27 0.00058 34.1 7.2 76 430-530 15-92 (122)
66 PRK14350 ligA NAD-dependent DN 62.8 19 0.00042 44.6 7.5 29 433-464 460-488 (669)
67 PF14490 HHH_4: Helix-hairpin- 59.9 14 0.00029 34.3 4.3 57 441-509 7-64 (94)
68 PF11731 Cdd1: Pathogenicity l 59.8 9 0.00019 36.3 3.1 27 489-515 10-36 (93)
69 COG2003 RadC DNA repair protei 59.7 20 0.00042 39.0 6.0 90 439-549 23-116 (224)
70 PF02371 Transposase_20: Trans 58.1 7.3 0.00016 35.5 2.2 42 491-535 2-43 (87)
71 PF12836 HHH_3: Helix-hairpin- 57.8 9.7 0.00021 33.0 2.8 21 490-510 13-33 (65)
72 TIGR00084 ruvA Holliday juncti 56.7 8.7 0.00019 40.3 2.8 22 488-509 69-90 (191)
73 COG1555 ComEA DNA uptake prote 55.4 9.4 0.0002 38.7 2.7 21 490-510 96-116 (149)
74 PRK08609 hypothetical protein; 55.4 32 0.00069 41.8 7.6 49 452-507 54-104 (570)
75 PRK14605 ruvA Holliday junctio 54.9 9.9 0.00021 40.0 2.8 44 488-532 70-116 (194)
76 PF05559 DUF763: Protein of un 54.7 30 0.00066 39.3 6.7 29 485-515 265-296 (319)
77 COG2818 Tag 3-methyladenine DN 53.9 49 0.0011 35.2 7.6 47 430-476 62-113 (188)
78 TIGR01259 comE comEA protein. 52.1 12 0.00026 36.4 2.8 21 490-510 67-87 (120)
79 PRK14351 ligA NAD-dependent DN 52.0 39 0.00084 42.2 7.6 60 432-509 485-546 (689)
80 PRK07945 hypothetical protein; 49.8 25 0.00053 39.9 5.1 61 443-510 8-68 (335)
81 COG0272 Lig NAD-dependent DNA 49.0 28 0.0006 43.1 5.7 57 444-510 506-562 (667)
82 smart00483 POLXc DNA polymeras 47.6 42 0.0009 38.1 6.5 57 443-510 11-67 (334)
83 PF11798 IMS_HHH: IMS family H 47.2 13 0.00028 28.4 1.7 15 493-507 13-27 (32)
84 smart00483 POLXc DNA polymeras 46.7 27 0.00058 39.6 4.8 48 453-507 55-105 (334)
85 KOG2841 Structure-specific end 46.6 66 0.0014 35.5 7.4 95 342-469 156-250 (254)
86 PRK08097 ligB NAD-dependent DN 42.7 74 0.0016 38.9 7.9 70 432-510 448-539 (562)
87 PRK13482 DNA integrity scannin 42.6 30 0.00065 39.9 4.4 59 443-507 275-335 (352)
88 smart00279 HhH2 Helix-hairpin- 41.3 18 0.0004 28.4 1.8 17 493-509 18-34 (36)
89 cd00141 NT_POLXc Nucleotidyltr 39.1 55 0.0012 36.7 5.7 16 490-505 84-99 (307)
90 TIGR00426 competence protein C 38.7 30 0.00064 30.1 2.9 21 490-510 15-36 (69)
91 cd00141 NT_POLXc Nucleotidyltr 38.4 40 0.00086 37.8 4.5 57 443-510 8-64 (307)
92 PRK14600 ruvA Holliday junctio 37.4 24 0.00052 37.1 2.5 23 488-510 70-92 (186)
93 PRK13901 ruvA Holliday junctio 37.4 26 0.00057 37.3 2.7 23 488-510 69-91 (196)
94 PRK14601 ruvA Holliday junctio 36.3 27 0.0006 36.6 2.7 23 488-510 70-92 (183)
95 PRK14606 ruvA Holliday junctio 35.5 29 0.00063 36.5 2.7 23 487-509 69-91 (188)
96 PRK14603 ruvA Holliday junctio 35.3 29 0.00062 36.8 2.7 22 488-509 69-90 (197)
97 PRK14602 ruvA Holliday junctio 35.1 30 0.00065 36.8 2.7 23 488-510 71-93 (203)
98 cd00080 HhH2_motif Helix-hairp 34.4 19 0.00041 32.3 1.0 19 492-510 23-41 (75)
99 PF11372 DUF3173: Domain of un 33.8 1E+02 0.0022 27.3 5.2 43 452-496 12-57 (59)
100 PRK14604 ruvA Holliday junctio 33.7 30 0.00064 36.6 2.4 23 488-510 70-92 (195)
101 PF10391 DNA_pol_lambd_f: Fing 33.4 38 0.00082 28.8 2.5 18 491-508 2-19 (52)
102 PF03118 RNA_pol_A_CTD: Bacter 31.7 62 0.0013 28.6 3.7 28 477-508 34-61 (66)
103 PRK00254 ski2-like helicase; P 31.4 87 0.0019 38.9 6.3 59 461-532 628-686 (720)
104 COG1796 POL4 DNA polymerase IV 30.7 79 0.0017 36.2 5.2 60 443-510 13-72 (326)
105 PRK02515 psbU photosystem II c 30.3 40 0.00087 34.0 2.6 20 490-509 60-79 (132)
106 COG0632 RuvA Holliday junction 29.6 38 0.00083 36.2 2.4 43 488-530 70-113 (201)
107 PRK07758 hypothetical protein; 28.6 84 0.0018 30.2 4.2 28 477-508 57-84 (95)
108 PF00416 Ribosomal_S13: Riboso 28.3 52 0.0011 31.5 2.9 22 488-509 12-33 (107)
109 PRK12766 50S ribosomal protein 25.4 37 0.00081 37.1 1.5 23 492-514 4-26 (232)
110 KOG0028 Ca2+-binding protein ( 24.3 2.1E+02 0.0045 30.1 6.5 98 437-546 47-148 (172)
111 PRK08609 hypothetical protein; 23.4 1.3E+02 0.0028 36.8 5.6 57 443-510 11-67 (570)
112 PF13592 HTH_33: Winged helix- 23.1 1.1E+02 0.0023 26.3 3.5 35 500-536 3-40 (60)
113 PRK12766 50S ribosomal protein 22.9 1.5E+02 0.0033 32.6 5.5 30 477-510 26-55 (232)
114 PRK14469 ribosomal RNA large s 22.0 1.4E+02 0.003 34.0 5.2 54 437-495 4-57 (343)
115 PRK01172 ski2-like helicase; P 21.6 2E+02 0.0043 35.4 6.8 43 428-473 630-672 (674)
116 COG4277 Predicted DNA-binding 21.6 61 0.0013 37.0 2.2 21 490-510 329-349 (404)
117 KOG0400 40S ribosomal protein 21.1 1.1E+02 0.0024 31.1 3.6 65 479-546 24-92 (151)
118 PF00730 HhH-GPD: HhH-GPD supe 20.6 1.6E+02 0.0034 27.2 4.4 54 457-511 9-62 (108)
119 TIGR01954 nusA_Cterm_rpt trans 20.5 2E+02 0.0044 23.0 4.5 36 430-468 13-48 (50)
120 PRK00558 uvrC excinuclease ABC 20.5 1.3E+02 0.0028 37.1 4.8 13 100-112 143-155 (598)
121 PRK13280 N-glycosylase/DNA lya 20.4 3.6E+02 0.0078 30.4 7.8 134 443-586 87-242 (269)
122 COG1948 MUS81 ERCC4-type nucle 20.4 1.2E+02 0.0026 33.7 4.2 17 348-364 86-102 (254)
123 PRK13890 conjugal transfer pro 20.2 3.9E+02 0.0084 26.1 7.2 80 433-534 23-102 (120)
124 COG2019 AdkA Archaeal adenylat 20.2 2.3E+02 0.0051 30.2 5.9 42 493-534 9-51 (189)
No 1
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=100.00 E-value=4.2e-53 Score=434.12 Aligned_cols=209 Identities=27% Similarity=0.413 Sum_probs=195.4
Q ss_pred CcHHHHHHHHHhHHhhcCCCccccCCCCchhhhhccccccchhhHHhhcccccccccccccccChHHHHHHHHhccCccc
Q 002604 344 MLAEKTRNLGDDISVANKLSDNKLIEPNSVEQVLSAHKVYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQE 423 (901)
Q Consensus 344 ~~~~~~~~i~~rl~~~~~~p~~~~~~~~~~~~~~~~~~~~~lLia~iLSaq~~d~~vnk~qnT~W~~L~kal~n~gLk~~ 423 (901)
|.++++.+|++||...||.|.++ ++| .++|++|||+|||||+||+.+|++ | .+||+.
T Consensus 1 ~~~~~~~~i~~~l~~~~p~~~~~---l~~-------~~pf~lLva~iLSaqttD~~vn~a--t--~~Lf~~--------- 57 (211)
T COG0177 1 LNKKKALEILDRLRELYPEPKTE---LDF-------KDPFELLVAVILSAQTTDEVVNKA--T--PALFKR--------- 57 (211)
T ss_pred CcHhhHHHHHHHHHHHCCCCCCc---cCc-------CCcHHHHHHHHHhccCchHHHHHH--H--HHHHHH---------
Confidence 46788999999999999999977 555 688999999999999999999976 5 888765
Q ss_pred cccCcCCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCCchhhhcCCchHHHHHHHhCCCCcHhH
Q 002604 424 RSRDRMDSLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKS 503 (901)
Q Consensus 424 r~~~~~~~pTpeaLa~A~~eELeelIR~~Gfyn~KAk~Ik~lAr~Lve~yGglDLe~L~~VP~deaRe~LLsLPGIG~KT 503 (901)
++||++|+.|++++|+++|+++|||++||++|+++|+.|+++||| ++|.+ +++|++|||||+||
T Consensus 58 -------~~t~e~l~~a~~~~l~~~I~~iGlyr~KAk~I~~~~~~l~e~~~g-------~vP~~--~~eL~~LPGVGrKT 121 (211)
T COG0177 58 -------YPTPEDLLNADEEELEELIKSIGLYRNKAKNIKELARILLEKFGG-------EVPDT--REELLSLPGVGRKT 121 (211)
T ss_pred -------cCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHcCC-------CCCch--HHHHHhCCCcchHH
Confidence 779999999999999999999999999999999999999999999 89988 99999999999999
Q ss_pred HHHHHHHhcCCceeecchHHHHHHHHhCCCCCCCCHHHHHHHHHHhcCchHHHHHhhhhhhhcCChhhHHHHHHHHHHHh
Q 002604 504 VECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQPLPESLQLHLLELYPVLESIQKYLWPRLCKLDQRTLYELHYQLITFG 583 (901)
Q Consensus 504 Ad~ILlfafgrpafpVDTHV~RVl~RLGlv~~~~tpekvEk~L~~llP~~e~Iqk~lW~~l~~ld~e~~~efH~~LI~fG 583 (901)
|++||+++||+|+|+|||||+||++||||++ .++|+++++.|++++| +.. +.++|++||.||
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------KEL-----------WTDLHHWLILHG 183 (211)
T ss_pred HHHHHHhhcCCCcccccchHHHHHHHhCCCC-CCCHHHHHHHHHHHCC------HHH-----------HHHHHHHHHHhh
Confidence 9999999999999999999999999999999 5899999999999999 334 468999999999
Q ss_pred HhhcccCCCCCCCCCCchhchhhhhh
Q 002604 584 KVFCTKSKPNCNACPMRGECRHFASA 609 (901)
Q Consensus 584 R~ICkarkP~C~~CPLrdlC~y~~~~ 609 (901)
|++|+||+|+|+.|||+++|+++.+.
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 2
>PF15628 RRM_DME: RRM in Demeter
Probab=100.00 E-value=1e-47 Score=348.99 Aligned_cols=69 Identities=84% Similarity=1.420 Sum_probs=68.0
Q ss_pred eeEeeeccccccCCccCCCcceeeceeeecccCCCCCcccchhhhccCCceEEEeccCcchhccCCCCC
Q 002604 833 GTLLIPCRTAMRGSFPLNGTYFQVNEVFADHDSSLNPIDVPREWLWNLPRRMVYFGTSVSSIFKGETDN 901 (901)
Q Consensus 833 gTiLiPCRTAmrg~FPLnGTYFQvnEVFaDh~Ss~~Pi~vpr~~iw~L~rr~vyfGtsv~sI~kg~t~~ 901 (901)
|||||||||||||+|||||||||||||||||+||+|||+|||+|||+|+||+|||||||+|||||||++
T Consensus 1 gtiLiPCrtAmrg~FPLnGTYFQ~nEVFaD~~Ss~~Pi~vpr~~iw~L~rr~vYfGtsv~SIfrGls~~ 69 (103)
T PF15628_consen 1 GTILIPCRTAMRGSFPLNGTYFQVNEVFADHESSRNPIDVPRELIWNLPRRIVYFGTSVSSIFRGLSRE 69 (103)
T ss_pred CceEeeehhhhCCccccCceEEEEEEEEeccccccCCeeccHHHhhcCCceEEEecCcHHHHhcccCHH
Confidence 899999999999999999999999999999999999999999999999999999999999999999975
No 3
>PRK10702 endonuclease III; Provisional
Probab=100.00 E-value=5.6e-44 Score=367.91 Aligned_cols=208 Identities=21% Similarity=0.269 Sum_probs=184.2
Q ss_pred CcHHHHHHHHHhHHhhcCCCccccCCCCchhhhhccccccchhhHHhhcccccccccccccccChHHHHHHHHhccCccc
Q 002604 344 MLAEKTRNLGDDISVANKLSDNKLIEPNSVEQVLSAHKVYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQE 423 (901)
Q Consensus 344 ~~~~~~~~i~~rl~~~~~~p~~~~~~~~~~~~~~~~~~~~~lLia~iLSaq~~d~~vnk~qnT~W~~L~kal~n~gLk~~ 423 (901)
|++++..+|+++|.+.||.+... +.+ .++|+.||++|||+|+++..++++ +.+|+.
T Consensus 1 ~~~~~~~~i~~~l~~~~~~~~~~---~~~-------~~p~e~lvs~iLsq~t~~~~v~~~----~~~L~~---------- 56 (211)
T PRK10702 1 MNKAKRLEILTRLRDNNPHPTTE---LNF-------SSPFELLIAVLLSAQATDVSVNKA----TAKLYP---------- 56 (211)
T ss_pred CCHHHHHHHHHHHHHHCCCCCCC---CCC-------CChHHHHHHHHHHhhcCHHHHHHH----HHHHHH----------
Confidence 34567899999999999976633 333 678999999999999999988754 355542
Q ss_pred cccCcCCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCCchhhhcCCchHHHHHHHhCCCCcHhH
Q 002604 424 RSRDRMDSLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKS 503 (901)
Q Consensus 424 r~~~~~~~pTpeaLa~A~~eELeelIR~~Gfyn~KAk~Ik~lAr~Lve~yGglDLe~L~~VP~deaRe~LLsLPGIG~KT 503 (901)
.++||++|++|+.++|+++||++|||++||++|+++|+.++++||| .+|.+ +++|++|||||+||
T Consensus 57 ------~~pt~e~l~~a~~~~l~~~i~~~G~y~~kA~~l~~~a~~i~~~~~~-------~~p~~--~~~Ll~lpGVG~kt 121 (211)
T PRK10702 57 ------VANTPAAMLELGVEGVKTYIKTIGLYNSKAENVIKTCRILLEQHNG-------EVPED--RAALEALPGVGRKT 121 (211)
T ss_pred ------HcCCHHHHHCCCHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHcCC-------CCCch--HHHHhcCCcccHHH
Confidence 2899999999999999999999999999999999999999999988 67876 99999999999999
Q ss_pred HHHHHHHhcCCceeecchHHHHHHHHhCCCCCCCCHHHHHHHHHHhcCchHHHHHhhhhhhhcCChhhHHHHHHHHHHHh
Q 002604 504 VECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQPLPESLQLHLLELYPVLESIQKYLWPRLCKLDQRTLYELHYQLITFG 583 (901)
Q Consensus 504 Ad~ILlfafgrpafpVDTHV~RVl~RLGlv~~~~tpekvEk~L~~llP~~e~Iqk~lW~~l~~ld~e~~~efH~~LI~fG 583 (901)
|++||+|+||+++|+||+||.||+.|+||.+. .+++++++.+++.+|. .. +.++|++||+||
T Consensus 122 A~~ill~a~~~~~~~VDt~v~Rv~~r~g~~~~-~~~~~~~~~l~~~lp~------~~-----------~~~~~~~li~~G 183 (211)
T PRK10702 122 ANVVLNTAFGWPTIAVDTHIFRVCNRTQFAPG-KNVEQVEEKLLKVVPA------EF-----------KVDCHHWLILHG 183 (211)
T ss_pred HHHHHHHHcCCCcccccchHHHHHHHhCCCCC-CCHHHHHHHHHHhCCc------hH-----------HHHHHHHHHHHh
Confidence 99999999999999999999999999999875 6899999999998883 22 358999999999
Q ss_pred HhhcccCCCCCCCCCCchhchhhhh
Q 002604 584 KVFCTKSKPNCNACPMRGECRHFAS 608 (901)
Q Consensus 584 R~ICkarkP~C~~CPLrdlC~y~~~ 608 (901)
|.+|++++|+|+.|||++.|+|+.+
T Consensus 184 r~~C~~~~P~C~~Cpl~~~C~~~~~ 208 (211)
T PRK10702 184 RYTCIARKPRCGSCIIEDLCEYKEK 208 (211)
T ss_pred HHHcCCCCCCCCCCcChhhcCcccc
Confidence 9999999999999999999998654
No 4
>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=1.6e-36 Score=307.00 Aligned_cols=190 Identities=25% Similarity=0.328 Sum_probs=166.5
Q ss_pred HHHHHHHhHHhhcCCCccccCCCCchhhhhccccccchhhHHhhcccccccccccccccChHHHHHHHHhccCccccccC
Q 002604 348 KTRNLGDDISVANKLSDNKLIEPNSVEQVLSAHKVYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQERSRD 427 (901)
Q Consensus 348 ~~~~i~~rl~~~~~~p~~~~~~~~~~~~~~~~~~~~~lLia~iLSaq~~d~~vnk~qnT~W~~L~kal~n~gLk~~r~~~ 427 (901)
+..+|+++|.+.||.+... .. ..++|+.||+.|||+|+++..+.++ |.+|+.
T Consensus 2 ~~~~i~~~l~~~~~~~~~~---~~-------~~dpf~~Li~~ILsqqt~~~~~~~~----~~~l~~-------------- 53 (191)
T TIGR01083 2 KAQEILERLRKNYPHPTTE---LD-------YNNPFELLVATILSAQATDKSVNKA----TKKLFE-------------- 53 (191)
T ss_pred hHHHHHHHHHHHCCCCCcc---cC-------CCCHHHHHHHHHHHhhCcHHHHHHH----HHHHHH--------------
Confidence 4678999999999977632 11 2577999999999999998877633 455542
Q ss_pred cCCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCCchhhhcCCchHHHHHHHhCCCCcHhHHHHH
Q 002604 428 RMDSLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECV 507 (901)
Q Consensus 428 ~~~~pTpeaLa~A~~eELeelIR~~Gfyn~KAk~Ik~lAr~Lve~yGglDLe~L~~VP~deaRe~LLsLPGIG~KTAd~I 507 (901)
.++||++|++++.++|+++|+++||+++||++|+++|+.+.++|++ .+|.. ++.|++|||||+|||++|
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 56644 999999999999999999
Q ss_pred HHHhcCCceeecchHHHHHHHHhCCCCCCCCHHHHHHHHHHhcCchHHHHHhhhhhhhcCChhhHHHHHHHHHHHhHhhc
Q 002604 508 RLLTLHHLAFPVDTNVGRIAVRLGWVPLQPLPESLQLHLLELYPVLESIQKYLWPRLCKLDQRTLYELHYQLITFGKVFC 587 (901)
Q Consensus 508 LlfafgrpafpVDTHV~RVl~RLGlv~~~~tpekvEk~L~~llP~~e~Iqk~lW~~l~~ld~e~~~efH~~LI~fGR~IC 587 (901)
|+|+||+|+|+||+||.||+.|+||... ++++++++.++.++|. ..+.+||.+||+|||.+|
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 002604 588 TKSKPNC 594 (901)
Q Consensus 588 karkP~C 594 (901)
++++|+|
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=8.2e-37 Score=325.82 Aligned_cols=199 Identities=21% Similarity=0.287 Sum_probs=169.8
Q ss_pred hhccccccchhhHHhhcccccccccccccccChHHHHHHHHhccCccccccCcCCCCCHHHHHcCCHHHHHHHHHhcCCc
Q 002604 376 VLSAHKVYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQERSRDRMDSLDYEALRCANVKEISEAIKERGMN 455 (901)
Q Consensus 376 ~~~~~~~~~lLia~iLSaq~~d~~vnk~qnT~W~~L~kal~n~gLk~~r~~~~~~~pTpeaLa~A~~eELeelIR~~Gfy 455 (901)
+....++|+.||+.||++|++++.+.. .|.++.+ .+|||++|++|++++|.++|+++|||
T Consensus 20 Wr~~~dpy~vlvseIL~QQT~v~~v~~----~~~rl~~----------------~fpt~~~La~a~~eeL~~~~~~lG~y 79 (275)
T TIGR01084 20 WRQNKTPYRVWLSEVMLQQTQVATVIP----YFERFLE----------------RFPTVQALANAPQDEVLKLWEGLGYY 79 (275)
T ss_pred CCCCCCHHHHHHHHHHHhhccHHHHHH----HHHHHHH----------------hCCCHHHHHCcCHHHHHHHHHHCCcH
Confidence 344578899999999999999887763 3555543 28999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhhCCCCchhhhcCCchHHHHHHHhCCCCcHhHHHHHHHHhcCCceeecchHHHHHHHHhCCCCC
Q 002604 456 NMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPL 535 (901)
Q Consensus 456 n~KAk~Ik~lAr~Lve~yGglDLe~L~~VP~deaRe~LLsLPGIG~KTAd~ILlfafgrpafpVDTHV~RVl~RLGlv~~ 535 (901)
+||++|+++|+.|.++||| .+|.+ +++|++|||||+|||++||+|+||+++++||+||.||+.|++....
T Consensus 80 -~RAr~L~~~A~~i~~~~~g-------~~p~~--~~~L~~LpGIG~~TA~~Il~~a~~~~~~~vD~~v~RVl~Rl~~~~~ 149 (275)
T TIGR01084 80 -ARARNLHKAAQEVVEEFGG-------EFPQD--FEDLAALPGVGRYTAGAILSFALNKPYPILDGNVKRVLSRLFAVEG 149 (275)
T ss_pred -HHHHHHHHHHHHHHHHcCC-------CCcHH--HHHHHhCCCCCHHHHHHHHHHHCCCCCCcchHhHHHHHHHHccCcC
Confidence 5999999999999999998 67866 9999999999999999999999999999999999999999976654
Q ss_pred CCCHHHHHHHH----HHhcCchHHHHHhhhhhhhcCChhhHHHHHHHHHHHhHhhcccCCCCCCCCCCchhchhhhhhhc
Q 002604 536 QPLPESLQLHL----LELYPVLESIQKYLWPRLCKLDQRTLYELHYQLITFGKVFCTKSKPNCNACPMRGECRHFASAFA 611 (901)
Q Consensus 536 ~~tpekvEk~L----~~llP~~e~Iqk~lW~~l~~ld~e~~~efH~~LI~fGR~ICkarkP~C~~CPLrdlC~y~~~~~~ 611 (901)
..++.++++.+ ++++| ...+.+||++||+||+.+|++++|+|+.|||++.|.++...
T Consensus 150 ~~~~~~~~~~l~~~~~~~lp-----------------~~~~~~~n~alm~lG~~vC~~~~P~C~~Cpl~~~C~~~~~~-- 210 (275)
T TIGR01084 150 WPGKKKVENRLWTLAESLLP-----------------KADPEAFNQALMDLGAMICTRKKPKCDLCPLQDFCLAYQQG-- 210 (275)
T ss_pred CCCHHHHHHHHHHHHHHHCC-----------------hhhHHHHHHHHHHHhHHHcCCCCCCCCCCCChhhCHHHHcC--
Confidence 45666666664 33343 34678999999999999999999999999999999998865
Q ss_pred ccccccCCCcccc
Q 002604 612 SARLALPGPEEKS 624 (901)
Q Consensus 612 sa~~alP~~~~~~ 624 (901)
....+|.+..+.
T Consensus 211 -~~~~~p~~~~~~ 222 (275)
T TIGR01084 211 -TWEEYPVKKPKA 222 (275)
T ss_pred -CHhhcCCCCCCC
Confidence 456688776544
No 6
>PRK10880 adenine DNA glycosylase; Provisional
Probab=100.00 E-value=1e-36 Score=334.26 Aligned_cols=202 Identities=19% Similarity=0.269 Sum_probs=169.5
Q ss_pred hccccccchhhHHhhcccccccccccccccChHHHHHHHHhccCccccccCcCCCCCHHHHHcCCHHHHHHHHHhcCCcH
Q 002604 377 LSAHKVYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQERSRDRMDSLDYEALRCANVKEISEAIKERGMNN 456 (901)
Q Consensus 377 ~~~~~~~~lLia~iLSaq~~d~~vnk~qnT~W~~L~kal~n~gLk~~r~~~~~~~pTpeaLa~A~~eELeelIR~~Gfyn 456 (901)
+...++|..||+.||++|++++.+.. .|.++.+. +||+++|++|++++|.++|+++|||+
T Consensus 25 r~~~dpy~ilVseILlQQT~v~~v~~----~~~rl~~~----------------fPt~~~La~a~~eel~~~~~glGyy~ 84 (350)
T PRK10880 25 QIDKTPYKVWLSEVMLQQTQVATVIP----YFERFMAR----------------FPTVTDLANAPLDEVLHLWTGLGYYA 84 (350)
T ss_pred CCCCCHHHHHHHHHHHhhccHHHHHH----HHHHHHHH----------------CcCHHHHHCcCHHHHHHHHHcCChHH
Confidence 34468899999999999999988874 34565432 89999999999999999999999995
Q ss_pred HHHHHHHHHHHHHHHhhCCCCchhhhcCCchHHHHHHHhCCCCcHhHHHHHHHHhcCCceeecchHHHHHHHHhCCCCCC
Q 002604 457 MLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQ 536 (901)
Q Consensus 457 ~KAk~Ik~lAr~Lve~yGglDLe~L~~VP~deaRe~LLsLPGIG~KTAd~ILlfafgrpafpVDTHV~RVl~RLGlv~~~ 536 (901)
||++|+++|+.++++|+| .+|.+ +++|++|||||+|||++||+|+||+++++||+||+||+.|++.+...
T Consensus 85 -RAr~L~~~A~~i~~~~~g-------~~p~~--~~~L~~LpGIG~~TA~aIl~~af~~~~~iVD~nV~RV~~Rl~~i~~~ 154 (350)
T PRK10880 85 -RARNLHKAAQQVATLHGG-------EFPET--FEEVAALPGVGRSTAGAILSLSLGKHFPILDGNVKRVLARCYAVSGW 154 (350)
T ss_pred -HHHHHHHHHHHHHHHhCC-------Cchhh--HHHHhcCCCccHHHHHHHHHHHCCCCeecccHHHHHHHHHHhcccCC
Confidence 999999999999999998 67866 99999999999999999999999999999999999999998554433
Q ss_pred CCHHHHHHHHHHhcCchHHHHHhhhhhhhcCChhhHHHHHHHHHHHhHhhcccCCCCCCCCCCchhchhhhhhhcccccc
Q 002604 537 PLPESLQLHLLELYPVLESIQKYLWPRLCKLDQRTLYELHYQLITFGKVFCTKSKPNCNACPMRGECRHFASAFASARLA 616 (901)
Q Consensus 537 ~tpekvEk~L~~llP~~e~Iqk~lW~~l~~ld~e~~~efH~~LI~fGR~ICkarkP~C~~CPLrdlC~y~~~~~~sa~~a 616 (901)
..+.++++.+.++.. . .++.+.+.+||++||+||+.+|++++|+|..|||++.|.+|... ....
T Consensus 155 ~~~~~~~~~l~~~~~-------~------l~p~~~~~~~nqalm~lGa~vC~p~~P~C~~Cpl~~~C~~~~~~---~~~~ 218 (350)
T PRK10880 155 PGKKEVENRLWQLSE-------Q------VTPAVGVERFNQAMMDLGAMVCTRSKPKCELCPLQNGCIAYANH---SWAL 218 (350)
T ss_pred CChHHHHHHHHHHHH-------H------hCChhHHHHHHHHHHHhhHHhccCCCCCCCCCccHhhhHHHHcC---CHhh
Confidence 456666665543221 0 12335678999999999999999999999999999999999875 4566
Q ss_pred cCCCcccc
Q 002604 617 LPGPEEKS 624 (901)
Q Consensus 617 lP~~~~~~ 624 (901)
+|.+..+.
T Consensus 219 ~P~k~~k~ 226 (350)
T PRK10880 219 YPGKKPKQ 226 (350)
T ss_pred CCCCCCCC
Confidence 88876554
No 7
>KOG1921 consensus Endonuclease III [Replication, recombination and repair]
Probab=100.00 E-value=8.2e-34 Score=293.40 Aligned_cols=183 Identities=27% Similarity=0.436 Sum_probs=163.1
Q ss_pred ccccchhhHHhhcccccccccccccccChHHHHHHHHhccCccccccCcCCCCCHHHHHcCCHHHHHHHHHhcCCcHHHH
Q 002604 380 HKVYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQERSRDRMDSLDYEALRCANVKEISEAIKERGMNNMLA 459 (901)
Q Consensus 380 ~~~~~lLia~iLSaq~~d~~vnk~qnT~W~~L~kal~n~gLk~~r~~~~~~~pTpeaLa~A~~eELeelIR~~Gfyn~KA 459 (901)
.-.|+.||+.|||+|++|.....+ -.+| ++ .+.+|+++|+++++..|.++|.++|||++||
T Consensus 76 ~~RfqvLv~lmLSSQTKDevt~~A----m~rL---------~~------~~gLT~e~v~~~de~~l~~LI~~VgFy~rKA 136 (286)
T KOG1921|consen 76 ERRFQVLVGLMLSSQTKDEVTAAA----MLRL---------KE------YGGLTLEAVLKIDEPTLNELIYPVGFYTRKA 136 (286)
T ss_pred hHhHHHHHHHHHhcchHHHHHHHH----HHHH---------HH------hcCCCHHHHhccChHhHHhhhhhccchHHHH
Confidence 346899999999999999755421 1222 21 2468999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhhCCCCchhhhcCCchHHHHHHHhCCCCcHhHHHHHHHHhcCCc-eeecchHHHHHHHHhCCCCCC-C
Q 002604 460 ERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLLTLHHL-AFPVDTNVGRIAVRLGWVPLQ-P 537 (901)
Q Consensus 460 k~Ik~lAr~Lve~yGglDLe~L~~VP~deaRe~LLsLPGIG~KTAd~ILlfafgrp-afpVDTHV~RVl~RLGlv~~~-~ 537 (901)
+||+.+|+.+.++|+| ++|++ .+.|++|||||+|.|..+|..|||+- .|.||+||+||++||||++.+ +
T Consensus 137 ~ylkkta~IL~d~f~g-------DIP~~--v~dLlsLPGVGPKMa~L~m~~AWn~i~GI~VDtHVHRi~nrlgWv~~ktk 207 (286)
T KOG1921|consen 137 KYLKKTAKILQDKFDG-------DIPDT--VEDLLSLPGVGPKMAHLTMQVAWNKIVGICVDTHVHRICNRLGWVDTKTK 207 (286)
T ss_pred HHHHHHHHHHHHHhCC-------CCchh--HHHHhcCCCCchHHHHHHHHHHhccceeEEeehHHHHHHHHhcccccccC
Confidence 9999999999999999 89999 99999999999999999999999985 899999999999999999853 3
Q ss_pred CHHHHHHHHHHhcCchHHHHHhhhhhhhcCChhhHHHHHHHHHHHhHhhcccCCCCCCCCCC-chhchhhh
Q 002604 538 LPESLQLHLLELYPVLESIQKYLWPRLCKLDQRTLYELHYQLITFGKVFCTKSKPNCNACPM-RGECRHFA 607 (901)
Q Consensus 538 tpekvEk~L~~llP~~e~Iqk~lW~~l~~ld~e~~~efH~~LI~fGR~ICkarkP~C~~CPL-rdlC~y~~ 607 (901)
+|++++.+|+.|+| +.+| .++|++||.||+.||++++|+|+.|.+ ++.|+..-
T Consensus 208 spE~TR~aLq~wLP------k~lW-----------~eIN~lLVGFGQ~iC~p~~prC~~C~~~~~~Cpss~ 261 (286)
T KOG1921|consen 208 SPEQTRVALQQWLP------KSLW-----------VEINHLLVGFGQTICTPRRPRCGLCLLSRDLCPSSF 261 (286)
T ss_pred CHHHHHHHHHHhCc------HHHH-----------hhhhceeecccceeeecCCCCccccccCcccCchhh
Confidence 59999999999999 5666 589999999999999999999999999 69999743
No 8
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=100.00 E-value=6.5e-33 Score=287.28 Aligned_cols=189 Identities=15% Similarity=0.211 Sum_probs=147.0
Q ss_pred cccccchhhHHhhcccccccccccccccChHHHHHHHHhccCccccccCcCCCCCHHHHHcCCHHHHHHHHHhcCCcHHH
Q 002604 379 AHKVYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQERSRDRMDSLDYEALRCANVKEISEAIKERGMNNML 458 (901)
Q Consensus 379 ~~~~~~lLia~iLSaq~~d~~vnk~qnT~W~~L~kal~n~gLk~~r~~~~~~~pTpeaLa~A~~eELeelIR~~Gfyn~K 458 (901)
..++|+.||++||++| |.|.++.+++.+ +++....+..+++||++|++++.++|+++||++|||++|
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 3678999999999998 556666666544 332211111246799999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhhCCCCchhhhcCCchHHHHHHHhCCCCcHhHHHHHHHHhcCCceeecchHHHHHHHHhCCCCCCCC
Q 002604 459 AERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQPL 538 (901)
Q Consensus 459 Ak~Ik~lAr~Lve~yGglDLe~L~~VP~deaRe~LLsLPGIG~KTAd~ILlfafgrpafpVDTHV~RVl~RLGlv~~~~t 538 (901)
|++|+++|+++.++||++ +.+. ..++|++|++|||||+|||++||+|+||+|+|+||+|++||+.|+||.. .+
T Consensus 94 A~~Lk~la~~i~~~~g~~--~~~~---~~~~re~Ll~l~GIG~kTAd~iLlya~~rp~fvVDty~~Rv~~RlG~~~--~~ 166 (218)
T PRK13913 94 AKRLIDLSENILKDFGSF--ENFK---QEVTREWLLDQKGIGKESADAILCYVCAKEVMVVDKYSYLFLKKLGIEI--ED 166 (218)
T ss_pred HHHHHHHHHHHHHHcCCc--hhcc---CchHHHHHHcCCCccHHHHHHHHHHHcCCCccccchhHHHHHHHcCCCC--CC
Confidence 999999999999998873 3332 2346999999999999999999999999999999999999999999975 57
Q ss_pred HHHHHHHHHHhcCch-HHHHHhhhhhhhcCChhhHHHHHHHHHHHhHhhccc
Q 002604 539 PESLQLHLLELYPVL-ESIQKYLWPRLCKLDQRTLYELHYQLITFGKVFCTK 589 (901)
Q Consensus 539 pekvEk~L~~llP~~-e~Iqk~lW~~l~~ld~e~~~efH~~LI~fGR~ICka 589 (901)
|++++..++..++.. ..+... .+.. ..+.+.+.+||.+||+|||..|.-
T Consensus 167 y~~~~~~~~~~l~~~~~~~~~~-~~~~-~~~~~~~~~~Halive~~k~~~~~ 216 (218)
T PRK13913 167 YDELQHFFEKGVQENLNSALAL-YENT-ISLAQLYARFHGKIVEFSKQKLEL 216 (218)
T ss_pred HHHHHHHHHHhhhhhhhhhhcc-cccc-chHHHHHHHHHHHHHHHHHHhhhc
Confidence 999999998876421 000000 0000 001257899999999999999964
No 9
>PRK13910 DNA glycosylase MutY; Provisional
Probab=100.00 E-value=1.2e-32 Score=295.62 Aligned_cols=150 Identities=24% Similarity=0.398 Sum_probs=132.7
Q ss_pred CCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCCchhhhcCCchHHHHHHHhCCCCcHhHHHHHHHH
Q 002604 431 SLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLL 510 (901)
Q Consensus 431 ~pTpeaLa~A~~eELeelIR~~Gfyn~KAk~Ik~lAr~Lve~yGglDLe~L~~VP~deaRe~LLsLPGIG~KTAd~ILlf 510 (901)
+||+++|++|++++|.++|+++||| +||++|+++|+.+.++|+| .+|.+ +++|++|||||+|||++||+|
T Consensus 22 fPt~e~La~a~~~el~~~~~glGyy-~RAr~L~~~A~~i~~~~~g-------~~P~~--~~~L~~LpGIG~kTA~aIl~~ 91 (289)
T PRK13910 22 FPTLKDLANAPLEEVLLLWRGLGYY-SRAKNLKKSAEICVKEHHS-------QLPND--YQSLLKLPGIGAYTANAILCF 91 (289)
T ss_pred CCCHHHHHCCCHHHHHHHHHcCCcH-HHHHHHHHHHHHHHHHhCC-------CCChh--HHHHHhCCCCCHHHHHHHHHH
Confidence 8999999999999999999999999 5999999999999999988 78887 999999999999999999999
Q ss_pred hcCCceeecchHHHHHHHHh-CCCCCCCCHHHHHHHHHHhcCchHHHHHhhhhhhhcCChhhHHHHHHHHHHHhHhhccc
Q 002604 511 TLHHLAFPVDTNVGRIAVRL-GWVPLQPLPESLQLHLLELYPVLESIQKYLWPRLCKLDQRTLYELHYQLITFGKVFCTK 589 (901)
Q Consensus 511 afgrpafpVDTHV~RVl~RL-Glv~~~~tpekvEk~L~~llP~~e~Iqk~lW~~l~~ld~e~~~efH~~LI~fGR~ICka 589 (901)
+||+++++||+||+||+.|+ |+... .++.+++.....++| ...+.++|++||+||+.+|++
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 445554443334444 245679999999999999999
Q ss_pred CCCCCCCCCCchhchhhhhh
Q 002604 590 SKPNCNACPMRGECRHFASA 609 (901)
Q Consensus 590 rkP~C~~CPLrdlC~y~~~~ 609 (901)
+|+|..|||++.|.++...
T Consensus 154 -~P~C~~CPl~~~C~~~~~~ 172 (289)
T PRK13910 154 -KPKCAICPLNPYCLGKNNP 172 (289)
T ss_pred -CCCCCCCcChhhhhhhhcC
Confidence 7999999999999998864
No 10
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=100.00 E-value=2.8e-32 Score=277.15 Aligned_cols=209 Identities=23% Similarity=0.396 Sum_probs=175.3
Q ss_pred HHHHHHHHhHHhhcCCCccccCCCCchhhhhccccccchhhHHhhcccccccccccccccChHHHHHHHHhccCcccccc
Q 002604 347 EKTRNLGDDISVANKLSDNKLIEPNSVEQVLSAHKVYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQERSR 426 (901)
Q Consensus 347 ~~~~~i~~rl~~~~~~p~~~~~~~~~~~~~~~~~~~~~lLia~iLSaq~~d~~vnk~qnT~W~~L~kal~n~gLk~~r~~ 426 (901)
.....|++-|-..|+... +-..++.++.+|.+|| .|||.|++|.++++| |+.+
T Consensus 6 ~~~~~iy~~L~~~yg~q~-----------WWp~~~~~EiiigAIL-----------tQNT~WknvekAlen--Lk~~--- 58 (215)
T COG2231 6 ENITKIYKELLRLYGDQG-----------WWPADNKDEIIIGAIL-----------TQNTSWKNVEKALEN--LKNE--- 58 (215)
T ss_pred HHHHHHHHHHHHHcCCcc-----------CCCCCCchhHHHHHHH-----------hccccHHHHHHHHHH--HHHc---
Confidence 345677777777777544 1122444577777776 378999999999987 7764
Q ss_pred CcCCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCCchhhhcCCchHHHHHHHhCCCCcHhHHHH
Q 002604 427 DRMDSLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVEC 506 (901)
Q Consensus 427 ~~~~~pTpeaLa~A~~eELeelIR~~Gfyn~KAk~Ik~lAr~Lve~yGglDLe~L~~VP~deaRe~LLsLPGIG~KTAd~ 506 (901)
+..++++|..++.++|+++|||.|||++||+||+++.+.++..|.++ + .+-...+|++|++++|||..|||+
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 56789999999999999999999999999999999999999877653 2 333444799999999999999999
Q ss_pred HHHHhcCCceeecchHHHHHHHHhCCCCCCCCHHHHHHHHHHhcCchHHHHHhhhhhhhcCChhhHHHHHHHHHHHhHhh
Q 002604 507 VRLLTLHHLAFPVDTNVGRIAVRLGWVPLQPLPESLQLHLLELYPVLESIQKYLWPRLCKLDQRTLYELHYQLITFGKVF 586 (901)
Q Consensus 507 ILlfafgrpafpVDTHV~RVl~RLGlv~~~~tpekvEk~L~~llP~~e~Iqk~lW~~l~~ld~e~~~efH~~LI~fGR~I 586 (901)
||+|||++|+|+||.|.+|++.|+|.+.. ++|+++++.+++.+|. +...+.+||.+|+.|||.+
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 4899999999988873 2245789999999999999
Q ss_pred cccCCCCCCCCCCchhchhhh
Q 002604 587 CTKSKPNCNACPMRGECRHFA 607 (901)
Q Consensus 587 CkarkP~C~~CPLrdlC~y~~ 607 (901)
|+. +|.|+.|||...|.++.
T Consensus 195 ~~k-~~~~~~cpL~~~~~~~~ 214 (215)
T COG2231 195 CKK-KPLCEKCPLKEKCKKYR 214 (215)
T ss_pred ccC-CcCCCCchHHHHHhhcc
Confidence 986 69999999999998764
No 11
>COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair]
Probab=99.96 E-value=1.1e-28 Score=267.77 Aligned_cols=200 Identities=20% Similarity=0.287 Sum_probs=162.0
Q ss_pred hhccccccchhhHHhhcccccccccccccccChHHHHHHHHhccCccccccCcCCCCCHHHHHcCCHHHHHHHHHhcCCc
Q 002604 376 VLSAHKVYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQERSRDRMDSLDYEALRCANVKEISEAIKERGMN 455 (901)
Q Consensus 376 ~~~~~~~~~lLia~iLSaq~~d~~vnk~qnT~W~~L~kal~n~gLk~~r~~~~~~~pTpeaLa~A~~eELeelIR~~Gfy 455 (901)
++....+|..+|+.++.+|++-++|-. -|.+ -++ .+||+++||+|+.+||..+|.++|||
T Consensus 28 WR~~~~PY~VwvSEiMLQQT~v~~Vi~----yy~~---fl~-------------rfPti~~LA~A~~~evl~~W~gLGYy 87 (342)
T COG1194 28 WRETKDPYRVWVSEIMLQQTQVATVIP----YYER---FLE-------------RFPTIKALAAAPEDEVLKAWEGLGYY 87 (342)
T ss_pred CCCCCCcceehhHHHHhhhccHhhhhh----hHHH---HHH-------------hCCCHHHHhcCCHHHHHHHHHhcChH
Confidence 344466899999999999999887762 2233 232 39999999999999999999999987
Q ss_pred HHHHHHHHHHHHHHHHhhCCCCchhhhcCCchHHHHHHHhCCCCcHhHHHHHHHHhcCCceeecchHHHHHHHHhCCCCC
Q 002604 456 NMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPL 535 (901)
Q Consensus 456 n~KAk~Ik~lAr~Lve~yGglDLe~L~~VP~deaRe~LLsLPGIG~KTAd~ILlfafgrpafpVDTHV~RVl~RLGlv~~ 535 (901)
+||++|+++|+.++++||| .+|++ .+.|.+|||||++||.+||.++|+++..+||+||.||+.|+.-+..
T Consensus 88 -sRArnL~~~A~~v~~~~~G-------~~P~~--~~~l~~LpGiG~yTa~Ail~~a~~~~~~~lDgNV~RVl~R~f~i~~ 157 (342)
T COG1194 88 -SRARNLHKAAQEVVERHGG-------EFPDD--EEELAALPGVGPYTAGAILSFAFNQPEPVLDGNVKRVLSRLFAISG 157 (342)
T ss_pred -HHHHHHHHHHHHHHHHcCC-------CCCCC--HHHHHhCCCCcHHHHHHHHHHHhCCCCceeecchheeehhhhcccc
Confidence 7999999999999999999 89999 8999999999999999999999999999999999999999954443
Q ss_pred CCC----HHHHHHHHHHhcCchHHHHHhhhhhhhcCChhhHHHHHHHHHHHhHhhcccCCCCCCCCCCchhchhhhhhhc
Q 002604 536 QPL----PESLQLHLLELYPVLESIQKYLWPRLCKLDQRTLYELHYQLITFGKVFCTKSKPNCNACPMRGECRHFASAFA 611 (901)
Q Consensus 536 ~~t----pekvEk~L~~llP~~e~Iqk~lW~~l~~ld~e~~~efH~~LI~fGR~ICkarkP~C~~CPLrdlC~y~~~~~~ 611 (901)
... ...++..++.++. ....+.+|+++||++|+.||++++|+|..|||++.|..|...
T Consensus 158 ~~~~~~~~~~~~~~~~~ll~----------------p~~~~~~fnqammdlGA~ICt~~~P~C~~CPl~~~c~a~~~g-- 219 (342)
T COG1194 158 DIGKPKTKKELWELAEQLLT----------------PDRRPGDFNQAMMDLGATICTAKKPKCSLCPLRDNCAAYRNG-- 219 (342)
T ss_pred cccccchhHHHHHHHHHhcC----------------CCCChHHHHHHHHHhhhHhhcCCCCCCCcCcchHHHHHHHcC--
Confidence 221 2223333333111 112378999999999999999999999999999999998875
Q ss_pred ccccccCCCcccc
Q 002604 612 SARLALPGPEEKS 624 (901)
Q Consensus 612 sa~~alP~~~~~~ 624 (901)
....+|.+..+.
T Consensus 220 -~~~~~P~k~~k~ 231 (342)
T COG1194 220 -TPEKYPVKKPKK 231 (342)
T ss_pred -CcccCCCcCccc
Confidence 334577665543
No 12
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=99.92 E-value=1.1e-24 Score=210.84 Aligned_cols=129 Identities=34% Similarity=0.469 Sum_probs=117.8
Q ss_pred CCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCCchhhhcCCchHHHHHHHhCCCCcHhHHHHHHHH
Q 002604 431 SLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLL 510 (901)
Q Consensus 431 ~pTpeaLa~A~~eELeelIR~~Gfyn~KAk~Ik~lAr~Lve~yGglDLe~L~~VP~deaRe~LLsLPGIG~KTAd~ILlf 510 (901)
++||++|++++.++|.++|+++||+++||++|+++++.+.+.+++ .+|. .+++|++|||||+|||++||+|
T Consensus 21 ~~~~~~l~~~~~~eL~~~l~~~g~~~~ka~~i~~~a~~~~~~~~~-------~~~~--~~~~L~~l~GIG~~tA~~~l~~ 91 (149)
T smart00478 21 FPTPEDLAAADEEELEELIRPLGFYRRKAKYLIELARILVEEYGG-------EVPD--DREELLKLPGVGRKTANAVLSF 91 (149)
T ss_pred CCCHHHHHCCCHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHCC-------CccH--HHHHHHcCCCCcHHHHHHHHHH
Confidence 789999999999999999999999999999999999999998876 4553 4899999999999999999999
Q ss_pred hcCCceeecchHHHHHHHHhCCCCCCCCHHHHHHHHHHhcCchHHHHHhhhhhhhcCChhhHHHHHHHHHHHhHh
Q 002604 511 TLHHLAFPVDTNVGRIAVRLGWVPLQPLPESLQLHLLELYPVLESIQKYLWPRLCKLDQRTLYELHYQLITFGKV 585 (901)
Q Consensus 511 afgrpafpVDTHV~RVl~RLGlv~~~~tpekvEk~L~~llP~~e~Iqk~lW~~l~~ld~e~~~efH~~LI~fGR~ 585 (901)
+|++++++||+||.|++.|+|+++..+++.+++++++.++|. ..++.+|.++++||+.
T Consensus 92 ~~~~~~~~~D~~v~r~~~rl~~~~~~~~~~~~~~~~~~~~p~-----------------~~~~~~~~~~l~~g~~ 149 (149)
T smart00478 92 ALGKPFIPVDTHVLRIAKRLGLVDKKSTPEEVEKLLEKLLPK-----------------EDWRELNLLLIDFGRT 149 (149)
T ss_pred HCCCCCCccchHHHHHHHHhCCCCCCCCHHHHHHHHHHHCCH-----------------HHHHHHHHHHHHHcCC
Confidence 999999999999999999999998767899999999998882 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=9.6e-25 Score=212.74 Aligned_cols=158 Identities=30% Similarity=0.415 Sum_probs=136.4
Q ss_pred cchhhHHhhcccccccccccccccChHHHHHHHHhccCccccccCcCCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHH
Q 002604 383 YDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQERSRDRMDSLDYEALRCANVKEISEAIKERGMNNMLAERM 462 (901)
Q Consensus 383 ~~lLia~iLSaq~~d~~vnk~qnT~W~~L~kal~n~gLk~~r~~~~~~~pTpeaLa~A~~eELeelIR~~Gfyn~KAk~I 462 (901)
|+.|++.||++|++.+.+. ..|.+|.+.+ .|||++|+.++.++|++++.+.| +++||++|
T Consensus 1 ~e~Li~~il~q~~s~~~a~----~~~~~l~~~~---------------gpt~~~l~~~~~~~l~~~~~~~G-~~~kA~~i 60 (158)
T cd00056 1 FEVLVSEILSQQTTDKAVN----KAYERLFERY---------------GPTPEALAAADEEELRELIRSLG-YRRKAKYL 60 (158)
T ss_pred CHHHHHHHHHhcccHHHHH----HHHHHHHHHh---------------CCCHHHHHCCCHHHHHHHHHhcC-hHHHHHHH
Confidence 6789999999999988776 3356665431 18999999999999999999999 88999999
Q ss_pred HHHHHHHHHhhCCCCchhhhcCCchHHHHHHHhCCCCcHhHHHHHHHHhcCCceeecchHHHHHHHHhCCCCCCCCHHHH
Q 002604 463 KDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQPLPESL 542 (901)
Q Consensus 463 k~lAr~Lve~yGglDLe~L~~VP~deaRe~LLsLPGIG~KTAd~ILlfafgrpafpVDTHV~RVl~RLGlv~~~~tpekv 542 (901)
+++|+.+.+++++... +.+++++.|++|||||+|||++||+|++|.++||||+|+.|++.|+|+.+..++++++
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 9999999998877422 5677899999999999999999999999988999999999999999996666789999
Q ss_pred HHHHHHhcCchHHHHHhhhhhhhcCChhhHHHHHHHHHHHh
Q 002604 543 QLHLLELYPVLESIQKYLWPRLCKLDQRTLYELHYQLITFG 583 (901)
Q Consensus 543 Ek~L~~llP~~e~Iqk~lW~~l~~ld~e~~~efH~~LI~fG 583 (901)
+..+..++|. .....+|+.|+.||
T Consensus 135 ~~~~~~~~~~-----------------~~~~~~~~~l~~~g 158 (158)
T cd00056 135 EELLEELLPK-----------------PYWGEANQALMDLG 158 (158)
T ss_pred HHHHHHHCCH-----------------HHHHHHHHHHHHcC
Confidence 9999888761 23467999999987
No 14
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=99.91 E-value=3e-24 Score=221.48 Aligned_cols=137 Identities=20% Similarity=0.196 Sum_probs=112.2
Q ss_pred ccccchhhHHhhcccccccccccccccChHHHHHHHHhccCccccccCcCCCCCHHHHHcCCHHHHHHHHHhcC--CcHH
Q 002604 380 HKVYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQERSRDRMDSLDYEALRCANVKEISEAIKERG--MNNM 457 (901)
Q Consensus 380 ~~~~~lLia~iLSaq~~d~~vnk~qnT~W~~L~kal~n~gLk~~r~~~~~~~pTpeaLa~A~~eELeelIR~~G--fyn~ 457 (901)
.++|++||++|||||+++..+++ ++.+ +.++.+ .++.++|+++||++| ||++
T Consensus 35 ~~~f~~Lv~~ILsqnT~~~~v~~-----------a~~~--------------L~~~~l-~~~~eeL~~~Ir~~Gygf~~~ 88 (208)
T PRK01229 35 EDLFSELSFCILTANSSAEGGIK-----------AQKE--------------IGDGFL-YLSEEELEEKLKEVGHRFYNK 88 (208)
T ss_pred CChHHHHHHHHhcCcCcHHHHHH-----------HHHh--------------cCHHHc-CCCHHHHHHHHHHhhcccHHH
Confidence 67899999999999777766553 3322 134556 899999999999995 9999
Q ss_pred HHHHHHHHHHH---HHHhh--CCCCchhhhcCCchHHHHHHH-hCCCCcHhHHHHHHHHhcCCceeecchHHHHHHHHhC
Q 002604 458 LAERMKDFLNR---LVREH--GSIDLEWLRDVPPDKAKDYLL-SIRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLG 531 (901)
Q Consensus 458 KAk~Ik~lAr~---Lve~y--GglDLe~L~~VP~deaRe~LL-sLPGIG~KTAd~ILlfafgrpafpVDTHV~RVl~RLG 531 (901)
||++|++++++ +.+.+ ++ ++| ++|++|+ +|||||+|||++||++++.+|+|+||+||.|+++|+|
T Consensus 89 KAk~I~~~~~~~~~l~~~~~~~~-------~~~--~~R~~Ll~~lpGIG~KTAd~vL~~~~~~~~~iVDtHv~Ri~~RlG 159 (208)
T PRK01229 89 RAEYIVEARKLYGKLKEIIKADK-------DQF--EAREFLVKNIKGIGYKEASHFLRNVGYEDLAILDRHILRFLKRYG 159 (208)
T ss_pred HHHHHHHHHHHHHHHHHHHhccC-------Cch--HHHHHHHHcCCCCcHHHHHHHHHHccCCCeeeeeHHHHHHHHHhC
Confidence 99999999988 44433 22 344 5699999 9999999999999976655999999999999999999
Q ss_pred CCCC------CCCHHHHHHHHHHhcC
Q 002604 532 WVPL------QPLPESLQLHLLELYP 551 (901)
Q Consensus 532 lv~~------~~tpekvEk~L~~llP 551 (901)
+++. ..+|.+++..|.+..+
T Consensus 160 ~~~~~~~~lt~~~y~~~E~~l~~~~~ 185 (208)
T PRK01229 160 LIEEIPKTLSKKRYLEIEEILREIAE 185 (208)
T ss_pred CCcccccccCcCCHHHHHHHHHHHHH
Confidence 9875 2589999999887655
No 15
>TIGR00588 ogg 8-oxoguanine DNA-glycosylase (ogg). All proteins in this family for which functions are known are 8-oxo-guanaine DNA glycosylases that function in base excision repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is distantly realted to the Nth-MutY superfamily.
Probab=99.83 E-value=4e-20 Score=200.92 Aligned_cols=142 Identities=23% Similarity=0.275 Sum_probs=115.2
Q ss_pred cccchhhHHhhcccccccccccccccChHHHHHHHHhccCcccc--ccCcCCCCCHHHHHcCCHHHHHHHHHhcCCcHHH
Q 002604 381 KVYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQER--SRDRMDSLDYEALRCANVKEISEAIKERGMNNML 458 (901)
Q Consensus 381 ~~~~lLia~iLSaq~~d~~vnk~qnT~W~~L~kal~n~gLk~~r--~~~~~~~pTpeaLa~A~~eELeelIR~~Gfyn~K 458 (901)
++|+.||++|+|+|.+.+.+. +.+.+|.+. +|-+... ......+|+|++|+.++.+ +.||.+||. .|
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----RMVERLCQA---FGPRLITLDGVTYHGFPSLHALTGPEAE---AHLRKLGLG-YR 186 (310)
T ss_pred CHHHHHHHHHHhCCCCHHHHH----HHHHHHHHH---hCCCcccCCCcccccCCCHHHHhCCChH---HHHHHcCCH-HH
Confidence 679999999999999998776 334666543 3422110 0113458999999997654 357789994 58
Q ss_pred HHHHHHHHHHHHHhhCCC-CchhhhcCCchHHHHHHHhCCCCcHhHHHHHHHHhcCCc-eeecchHHHHHHHHh-CCC
Q 002604 459 AERMKDFLNRLVREHGSI-DLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLLTLHHL-AFPVDTNVGRIAVRL-GWV 533 (901)
Q Consensus 459 Ak~Ik~lAr~Lve~yGgl-DLe~L~~VP~deaRe~LLsLPGIG~KTAd~ILlfafgrp-afpVDTHV~RVl~RL-Glv 533 (901)
|++|+++|+.+.+.+++. +++.|..++.++++++|++|||||+|||+|||+|+||++ +||||+||+|++.|+ |+.
T Consensus 187 a~~I~~~A~~i~~~~~~~~~l~~l~~~~~~~~~~~L~~l~GIG~~tAd~vll~~l~~~d~~PvD~~v~r~~~r~y~~~ 264 (310)
T TIGR00588 187 ARYIRETARALLEEQGGRAWLQQIRGASYEDAREALCELPGVGPKVADCICLMGLDKPQAVPVDVHVWRIANRDYPWH 264 (310)
T ss_pred HHHHHHHHHHHHhccCCchhHHhhccCChHHHHHHHHhCCCccHHHHHHHHHHhCCCCCceeecHHHHHHHHHHhccc
Confidence 999999999999987665 677888999999999999999999999999999999998 899999999999998 553
No 16
>KOG2457 consensus A/G-specific adenine DNA glycosylase [Replication, recombination and repair]
Probab=99.83 E-value=7.7e-21 Score=206.67 Aligned_cols=184 Identities=21% Similarity=0.295 Sum_probs=150.5
Q ss_pred cccchhhHHhhcccccccccccccccChHHHHHHHHhccCccccccCcCCCCCHHHHHcCCH-HHHHHHHHhcCCcHHHH
Q 002604 381 KVYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQERSRDRMDSLDYEALRCANV-KEISEAIKERGMNNMLA 459 (901)
Q Consensus 381 ~~~~lLia~iLSaq~~d~~vnk~qnT~W~~L~kal~n~gLk~~r~~~~~~~pTpeaLa~A~~-eELeelIR~~Gfyn~KA 459 (901)
--|+.+|+-|.-+|++-.+|-+- -| +-++ .+||..+|+.|+. ++|.++|.++||| +|+
T Consensus 124 RaYeVwVSEiMLQQTrV~TV~~Y-Yt------~WMq-------------kwPTl~dla~Asl~~eVn~lWaGlGyY-~R~ 182 (555)
T KOG2457|consen 124 RAYEVWVSEIMLQQTRVQTVMKY-YT------RWMQ-------------KWPTLYDLAQASLEKEVNELWAGLGYY-RRA 182 (555)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH-HH------HHHH-------------hCchHHHHHHHHHHHHHHHHHhhhhHH-HHH
Confidence 34888999999999887666421 11 1122 4899999999999 8999999999999 699
Q ss_pred HHHHHHHHHHHHhhCCCCchhhhcCCchHHHHHHHh-CCCCcHhHHHHHHHHhcCCceeecchHHHHHHHHhCCCCCCCC
Q 002604 460 ERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLS-IRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQPL 538 (901)
Q Consensus 460 k~Ik~lAr~Lve~yGglDLe~L~~VP~deaRe~LLs-LPGIG~KTAd~ILlfafgrpafpVDTHV~RVl~RLGlv~~~~t 538 (901)
++|++.|+.+++.++| .+|.. -+.|.+ +||||+|||.+|+.+||+++.=+||.||.||+.|.--+....+
T Consensus 183 rrL~ega~~vv~~~~g-------e~Prt--a~~l~kgvpGVG~YTAGAiaSIAf~q~tGiVDGNVirvlsRalAIhsDcS 253 (555)
T KOG2457|consen 183 RRLLEGAKMVVAGTEG-------EFPRT--ASSLMKGVPGVGQYTAGAIASIAFNQVTGIVDGNVIRVLSRALAIHSDCS 253 (555)
T ss_pred HHHHHHHHHHHHhCCC-------CCCCh--HHHHHhhCCCCCccchhhhhhhhhcCcccccccchHHHhHHhHhhcCCcc
Confidence 9999999999999998 89987 556666 9999999999999999999999999999999999744443333
Q ss_pred HHHHHHHHHHhcCchHHHHHhhhhhh-hcCChhhHHHHHHHHHHHhHhhcccCCCCCCCCCCchhchhhhh
Q 002604 539 PESLQLHLLELYPVLESIQKYLWPRL-CKLDQRTLYELHYQLITFGKVFCTKSKPNCNACPMRGECRHFAS 608 (901)
Q Consensus 539 pekvEk~L~~llP~~e~Iqk~lW~~l-~~ld~e~~~efH~~LI~fGR~ICkarkP~C~~CPLrdlC~y~~~ 608 (901)
..++-.. +|... -..|+..+.+||++||++|..+|++.+|.|..||+...|+.|.-
T Consensus 254 kgk~~q~--------------~wkLA~qLVDP~RPGDFNQalMELGAt~CTpq~P~CS~CPvss~CrA~q~ 310 (555)
T KOG2457|consen 254 KGKFFQS--------------SWKLAAQLVDPSRPGDFNQALMELGATLCTPQKPSCSSCPVSSQCRAFQL 310 (555)
T ss_pred hhhHHHH--------------HHHHHHHhcCCCCCCcHHHHHHHhcCeeccCCCCCcCCCCcHHHHHHHhH
Confidence 3333222 34332 24577888999999999999999999999999999999999874
No 17
>TIGR03252 uncharacterized HhH-GPD family protein. This model describes a small, well-conserved bacterial protein family. Its sequence largely consists of a domain, HhH-GPD, found in a variety of related base excision DNA repair enzymes (see pfam00730).
Probab=99.82 E-value=4.6e-20 Score=186.08 Aligned_cols=112 Identities=13% Similarity=0.120 Sum_probs=97.2
Q ss_pred ccccchhhHHhhcccccccccccccccChHHHHHHHHhccCccccccCcCCCCCHHHHHcCCHHHHHHHHHhc----CCc
Q 002604 380 HKVYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQERSRDRMDSLDYEALRCANVKEISEAIKER----GMN 455 (901)
Q Consensus 380 ~~~~~lLia~iLSaq~~d~~vnk~qnT~W~~L~kal~n~gLk~~r~~~~~~~pTpeaLa~A~~eELeelIR~~----Gfy 455 (901)
.++|++||++|||||++|..++++ +.+|++.+ +.+||++|++++.++|+++|++. |||
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 678999999999999999988855 36665442 34799999999999999999876 999
Q ss_pred HHHHHHHHHHHHHHHHhhCCCCchhhhc---CCchHHHHHHHhCCCCcHhHHHHHHHH
Q 002604 456 NMLAERMKDFLNRLVREHGSIDLEWLRD---VPPDKAKDYLLSIRGLGLKSVECVRLL 510 (901)
Q Consensus 456 n~KAk~Ik~lAr~Lve~yGglDLe~L~~---VP~deaRe~LLsLPGIG~KTAd~ILlf 510 (901)
++||++|+++|++|+++|+| +++.|.. .+..++|++|++|||||+|||++||++
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 18
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=99.75 E-value=7e-18 Score=181.77 Aligned_cols=167 Identities=19% Similarity=0.244 Sum_probs=132.1
Q ss_pred ccccchhhHHhhcccccccccccccccChHHHHHHHHhccCccccccCcCCCCCHHHHHcCCHHHHHHHHHhcCCcHHHH
Q 002604 380 HKVYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQERSRDRMDSLDYEALRCANVKEISEAIKERGMNNMLA 459 (901)
Q Consensus 380 ~~~~~lLia~iLSaq~~d~~vnk~qnT~W~~L~kal~n~gLk~~r~~~~~~~pTpeaLa~A~~eELeelIR~~Gfyn~KA 459 (901)
.++|+-||..|+|+|-+.+... +.|.+|...+ |-. +.....+|||++|+.++++.|. .+|+...||
T Consensus 103 ~d~fe~lv~aI~~QqvS~~~A~----~i~~rl~~~~---g~~---~~~~~~fptpe~l~~~~~~~l~----~~g~s~~Ka 168 (285)
T COG0122 103 PDPFEALVRAILSQQVSVAAAA----KIWARLVSLY---GNA---LEIYHSFPTPEQLAAADEEALR----RCGLSGRKA 168 (285)
T ss_pred CCHHHHHHHHHHHhHhhHHHHH----HHHHHHHHHh---CCc---cccccCCCCHHHHHhcCHHHHH----HhCCcHHHH
Confidence 5789999999999999887776 6788887664 211 1123458999999999999975 599999999
Q ss_pred HHHHHHHHHHHHhhCCCCchhhhcCCchHHHHHHHhCCCCcHhHHHHHHHHhcCCc-eee-cchHHHHHHHHhCCCCCCC
Q 002604 460 ERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLLTLHHL-AFP-VDTNVGRIAVRLGWVPLQP 537 (901)
Q Consensus 460 k~Ik~lAr~Lve~yGglDLe~L~~VP~deaRe~LLsLPGIG~KTAd~ILlfafgrp-afp-VDTHV~RVl~RLGlv~~~~ 537 (901)
+||+.+|+.+.+ |.+|+..+..++.+++++.|.+|+|||+|||+|||+|++|++ +|| .|.+++|.+.+++..+...
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 5778888888887333333
Q ss_pred CHHHHHHHHHHhcCchHHHHHhhhh
Q 002604 538 LPESLQLHLLELYPVLESIQKYLWP 562 (901)
Q Consensus 538 tpekvEk~L~~llP~~e~Iqk~lW~ 562 (901)
+...++...+.+-|.-...+-++|.
T Consensus 247 ~~~~~~~~~e~w~p~rs~A~~yLw~ 271 (285)
T COG0122 247 TEKEVRELAERWGPYRSYAALYLWR 271 (285)
T ss_pred hHHHHHHHHhcccCHHHHHHHHHHH
Confidence 3333555555665532244556664
No 19
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=99.67 E-value=1.3e-15 Score=164.15 Aligned_cols=151 Identities=15% Similarity=0.090 Sum_probs=116.3
Q ss_pred ccccchhhHHhhcccccccccccccccChHHHHHHHHhccCccccccCcCCCCCHHHHHcCCHHHHHHHHHhcCCcHHHH
Q 002604 380 HKVYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQERSRDRMDSLDYEALRCANVKEISEAIKERGMNNMLA 459 (901)
Q Consensus 380 ~~~~~lLia~iLSaq~~d~~vnk~qnT~W~~L~kal~n~gLk~~r~~~~~~~pTpeaLa~A~~eELeelIR~~Gfyn~KA 459 (901)
-++|+.||..|+++|.+-+... +.+.+|... +|-+-........||||++|++++.++|+ .+||+++||
T Consensus 111 ~d~fE~lv~aIigQqisv~~a~----~~~~rlv~~---~G~~l~~~~~~~~FPtpe~La~~~~~eL~----~~Gl~~~Ra 179 (283)
T PRK10308 111 VDAFEQGVRAILGQLVSVAMAA----KLTAKVAQL---YGERLDDFPEYVCFPTPERLAAADPQALK----ALGMPLKRA 179 (283)
T ss_pred CCHHHHHHHHHHHhHHHHHHHH----HHHHHHHHH---hCccccCCCCccCCCCHHHHHcCCHHHHH----HCCCCHHHH
Confidence 4679999999999998776665 334555433 34321100113468999999999999975 589999999
Q ss_pred HHHHHHHHHHHHhhCCCCchhhhcCCchHHHHHHHhCCCCcHhHHHHHHHHhcCCc-ee-ecchHHHHHHHHhCCCCCCC
Q 002604 460 ERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLLTLHHL-AF-PVDTNVGRIAVRLGWVPLQP 537 (901)
Q Consensus 460 k~Ik~lAr~Lve~yGglDLe~L~~VP~deaRe~LLsLPGIG~KTAd~ILlfafgrp-af-pVDTHV~RVl~RLGlv~~~~ 537 (901)
++|+++|+.+.+ |.++++... +.+++++.|++|||||+|||++|++++||++ +| ++|.+++|.+ + ..
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 999999999997 666665443 4567899999999999999999999999997 77 7899998744 2 24
Q ss_pred CHHHHHHHHHHhcCc
Q 002604 538 LPESLQLHLLELYPV 552 (901)
Q Consensus 538 tpekvEk~L~~llP~ 552 (901)
++.+++...+.+-|.
T Consensus 249 ~~~~~~~~a~~w~P~ 263 (283)
T PRK10308 249 TPAQIRRYAERWKPW 263 (283)
T ss_pred CHHHHHHHHHhcCCH
Confidence 677888888777773
No 20
>KOG2875 consensus 8-oxoguanine DNA glycosylase [Replication, recombination and repair]
Probab=99.61 E-value=2.7e-15 Score=159.00 Aligned_cols=139 Identities=23% Similarity=0.285 Sum_probs=114.8
Q ss_pred cccchhhHHhhcccccccccccccccChHHHHHHHHhccCcccc--ccCcCCCCCHHHHHcCCHHHHHHHHHhcCCcHHH
Q 002604 381 KVYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQER--SRDRMDSLDYEALRCANVKEISEAIKERGMNNML 458 (901)
Q Consensus 381 ~~~~lLia~iLSaq~~d~~vnk~qnT~W~~L~kal~n~gLk~~r--~~~~~~~pTpeaLa~A~~eELeelIR~~Gfyn~K 458 (901)
.|++-|++.|-|....++.+. .-+...+.++|.+--. ..+..+||+.++|+. .++++-+|.+||. .|
T Consensus 116 dP~E~lfSFiCSSNNNIaRIT-------~Mve~fc~~fG~~i~~~dg~~~h~FPsl~~L~g---~~~Ea~LR~~gfG-YR 184 (323)
T KOG2875|consen 116 DPIECLFSFICSSNNNIARIT-------GMVERFCQAFGPRIIQLDGVDYHGFPSLQALAG---PEVEAELRKLGFG-YR 184 (323)
T ss_pred CcHHHHHHHHhcCCCcHHHHH-------HHHHHHHHhhCcceEeecCcccccCccHHHhcC---cHhHHHHHHcCcc-hh
Confidence 458889999999888777665 3455567777755222 234568999999987 7788889999997 79
Q ss_pred HHHHHHHHHHHHHhhCCC-CchhhhcCCchHHHHHHHhCCCCcHhHHHHHHHHhcCCc-eeecchHHHHHHHHh
Q 002604 459 AERMKDFLNRLVREHGSI-DLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLLTLHHL-AFPVDTNVGRIAVRL 530 (901)
Q Consensus 459 Ak~Ik~lAr~Lve~yGgl-DLe~L~~VP~deaRe~LLsLPGIG~KTAd~ILlfafgrp-afpVDTHV~RVl~RL 530 (901)
||||.+.|+.|.+++|+. .|-.|++++.+++|+.|..|||||+|+||||+++++|+. ++|||+||.||+.-.
T Consensus 185 AkYI~~ta~~l~~~~g~~~wLqsl~~~~yeear~~L~~lpGVG~KVADCI~Lm~l~~~~~VPVDvHi~ria~~y 258 (323)
T KOG2875|consen 185 AKYISATARALQEKQGGLAWLQSLRKSSYEEAREALCSLPGVGPKVADCICLMSLDKLSAVPVDVHIWRIAQDY 258 (323)
T ss_pred HHHHHHHHHHHHHhcccchHHHHHhcccHHHHHHHHhcCCCCcchHhhhhhhhhcCCCCcccchhhHHHHhhcc
Confidence 999999999999999882 233456889999999999999999999999999999997 999999999999943
No 21
>PF00730 HhH-GPD: HhH-GPD superfamily base excision DNA repair protein This entry corresponds to Endonuclease III This entry corresponds to Alkylbase DNA glycosidase; InterPro: IPR003265 Endonuclease III (4.2.99.18 from EC) is a DNA repair enzyme which removes a number of damaged pyrimidines from DNA via its glycosylase activity and also cleaves the phosphodiester backbone at apurinic / apyrimidinic sites via a beta-elimination mechanism [, ]. The structurally related DNA glycosylase MutY recognises and excises the mutational intermediate 8-oxoguanine-adenine mispair []. The 3-D structures of Escherichia coli endonuclease III [] and catalytic domain of MutY [] have been determined. The structures contain two all-alpha domains: a sequence-continuous, six-helix domain (residues 22-132) and a Greek-key, four-helix domain formed by one N-terminal and three C-terminal helices (residues 1-21 and 133-211) together with the [Fe4S4] cluster. The cluster is bound entirely within the C-terminal loop by four cysteine residues with a ligation pattern Cys-(Xaa)6-Cys-(Xaa)2-Cys-(Xaa)5-Cys which is distinct from all other known Fe4S4 proteins. This structural motif is referred to as a [Fe4S4] cluster loop (FCL) []. Two DNA-binding motifs have been proposed, one at either end of the interdomain groove: the helix-hairpin-helix (HhH) and FCL motifs (see IPR003651 from INTERPRO). The primary role of the iron-sulphur cluster appears to involve positioning conserved basic residues for interaction with the DNA phosphate backbone by forming the loop of the FCL motif [, ]. The HhH-GPD domain gets its name from its hallmark helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate. This domain is found in a diverse range of structurally related DNA repair proteins that include: endonuclease III, 4.2.99.18 from EC and DNA glycosylase MutY, an A/G-specific adenine glycosylase. Both of these enzymes have a C-terminal iron-sulphur cluster loop (FCL). The methyl-CPG binding protein (MBD4) also contain a related domain that is a thymine DNA glycosylase. The family also includes DNA-3-methyladenine glycosylase II 3.2.2.21 from EC, 8-oxoguanine DNA glycosylases and other members of the AlkA family.; GO: 0006284 base-excision repair; PDB: 3F0Z_A 3I0X_A 3F10_A 3I0W_A 3S6I_D 3N5N_Y 1PU7_A 1PU8_B 1PU6_B 1NGN_A ....
Probab=99.51 E-value=6e-14 Score=129.03 Aligned_cols=107 Identities=24% Similarity=0.260 Sum_probs=89.1
Q ss_pred hHHhhcccccccccccccccChHHHHHHHHhccCccccccCcCCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHH
Q 002604 387 NPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQERSRDRMDSLDYEALRCANVKEISEAIKERGMNNMLAERMKDFL 466 (901)
Q Consensus 387 ia~iLSaq~~d~~vnk~qnT~W~~L~kal~n~gLk~~r~~~~~~~pTpeaLa~A~~eELeelIR~~Gfyn~KAk~Ik~lA 466 (901)
|+.||++|++...+. ..|.+|.+.+ ++|||++|+.+++++|+++|+++||+++||++|+++|
T Consensus 1 V~~Il~qq~s~~~a~----~~~~~l~~~~--------------g~pt~~~l~~~~~~el~~~i~~~G~~~~ka~~i~~~a 62 (108)
T PF00730_consen 1 VRAILSQQTSIKAAR----KIYRRLFERY--------------GFPTPEALAEASEEELRELIRPLGFSRRKAKYIIELA 62 (108)
T ss_dssp HHHHHCTTS-HHHHH----HHHHHHHHHH--------------SCSSHHHHHCSHHHHHHHHHTTSTSHHHHHHHHHHHH
T ss_pred CeeeecCcCcHHHHH----HHHHHHHHHh--------------cCCCHHHHHhCCHHHHHHHhhccCCCHHHHHHHHHHH
Confidence 678999999998777 3456665542 4899999999999999999999999999999999999
Q ss_pred HHHHHhhCCCCchhhhcCCchHHHHHHHhCCCCcHhHHHHHHHHhcCCceeecchHHHHHHHHhCCCCCCCCHHHHHHHH
Q 002604 467 NRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQPLPESLQLHL 546 (901)
Q Consensus 467 r~Lve~yGglDLe~L~~VP~deaRe~LLsLPGIG~KTAd~ILlfafgrpafpVDTHV~RVl~RLGlv~~~~tpekvEk~L 546 (901)
+.+. ++..++++||+|+.|++.|+|+.+..++++++++.+
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 222358999999999999999998767999999988
Q ss_pred HHhcC
Q 002604 547 LELYP 551 (901)
Q Consensus 547 ~~llP 551 (901)
++++|
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=99.44 E-value=1.5e-13 Score=141.88 Aligned_cols=166 Identities=15% Similarity=0.249 Sum_probs=130.2
Q ss_pred hhccccccchhhHHhhcccccccccccccccChHHHHHHHHhccCccccccCcCCCCCHHHHHcCCHHHHHHHHHhcCCc
Q 002604 376 VLSAHKVYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQERSRDRMDSLDYEALRCANVKEISEAIKERGMN 455 (901)
Q Consensus 376 ~~~~~~~~~lLia~iLSaq~~d~~vnk~qnT~W~~L~kal~n~gLk~~r~~~~~~~pTpeaLa~A~~eELeelIR~~Gfy 455 (901)
++....||.-||.+|||+|-.++..| .+.+++. .+.+.| ..+++|+.+..++.++|.+ +||.
T Consensus 69 ~~~~q~Pf~~LiraIlsQQLs~kAan----sI~~Rfv-sl~~g~---------~~~~~pe~i~~~~~~~lrk----cG~S 130 (254)
T KOG1918|consen 69 FKETQTPFERLIRAILSQQLSGKAAN----SIYNRFV-SLCGGA---------EKFPTPEFIDPLDCEELRK----CGFS 130 (254)
T ss_pred cccccCcHHHHHHHHHHHHHHHHHHH----HHHHHHH-HHhCCC---------cCCCCchhcCcCCHHHHHH----hCcc
Confidence 56678899999999999999887666 4455554 444322 2489999999999999754 9999
Q ss_pred HHHHHHHHHHHHHHHHhhCCCCchhhhcCCchHHHHHHHhCCCCcHhHHHHHHHHhcCCc-eeecchH-HHHHHHHh-CC
Q 002604 456 NMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLLTLHHL-AFPVDTN-VGRIAVRL-GW 532 (901)
Q Consensus 456 n~KAk~Ik~lAr~Lve~yGglDLe~L~~VP~deaRe~LLsLPGIG~KTAd~ILlfafgrp-afpVDTH-V~RVl~RL-Gl 532 (901)
.+|+.+|+.+|++..+.| =...+.+.++..+++.+.|..++|||+|||.++|.|+++|+ +||+|.- |+|=+..| |+
T Consensus 131 ~rK~~yLh~lA~~~~ng~-I~s~~~i~~mseEeL~~~LT~VKGIg~Wtv~MflIfsL~R~DVmp~dDlgir~g~k~l~gl 209 (254)
T KOG1918|consen 131 KRKASYLHSLAEAYTNGY-IPSKSGIEKMSEEELIERLTNVKGIGRWTVEMFLIFSLHRPDVMPADDLGIRNGVKKLLGL 209 (254)
T ss_pred hhhHHHHHHHHHHHhcCC-CCchHHHhhcCHHHHHHHHHhccCccceeeeeeeeeccCCCcccCchhhhHHHHHHHHhCC
Confidence 999999999999998743 12566778999999999999999999999999999999998 9999754 55545544 66
Q ss_pred CCCCCCHHHHHHHHHHhcCchHHH-HHhhhh
Q 002604 533 VPLQPLPESLQLHLLELYPVLESI-QKYLWP 562 (901)
Q Consensus 533 v~~~~tpekvEk~L~~llP~~e~I-qk~lW~ 562 (901)
-+. +.+.++++..+.+-| ++.+ ..|+|.
T Consensus 210 ~~~-p~~~evekl~e~~kp-yRtvaawYlWk 238 (254)
T KOG1918|consen 210 KPL-PLPKEVEKLCEKCKP-YRTVAAWYLWK 238 (254)
T ss_pred CCC-CchHHHHHHhhhccc-hHHHHHHHHHh
Confidence 553 678889888877766 4443 355564
No 23
>PF15629 Perm-CXXC: Permuted single zf-CXXC unit
Probab=99.12 E-value=1.3e-11 Score=92.36 Aligned_cols=32 Identities=81% Similarity=1.405 Sum_probs=30.9
Q ss_pred chhhhccccccCccCcCcccccccccccccee
Q 002604 799 PESRCRSKESGKLCDEKTCFSCNSMRETNSQT 830 (901)
Q Consensus 799 p~~~c~~~~~~~~c~~~~~~~c~~~~e~~~~~ 830 (901)
|+++|++|++|+||+++|||+||||||+++|+
T Consensus 1 Pe~~C~sqe~gkLC~~~tCfsCNsiREa~sQ~ 32 (32)
T PF15629_consen 1 PERRCNSQESGKLCDEETCFSCNSIREANSQT 32 (32)
T ss_pred CcccccccccccccCCccccccccHhHHhccC
Confidence 89999999999999999999999999999985
No 24
>COG1059 Thermostable 8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=98.30 E-value=1.4e-06 Score=89.50 Aligned_cols=122 Identities=20% Similarity=0.268 Sum_probs=89.6
Q ss_pred ccchhhHHhhcccccccccccccccChHHHHHHHHhccCccccccCcCCCCCHHHHHcCCHHHHHHHHHhcC--CcHHHH
Q 002604 382 VYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGKQERSRDRMDSLDYEALRCANVKEISEAIKERG--MNNMLA 459 (901)
Q Consensus 382 ~~~lLia~iLSaq~~d~~vnk~qnT~W~~L~kal~n~gLk~~r~~~~~~~pTpeaLa~A~~eELeelIR~~G--fyn~KA 459 (901)
-|..|.=.||-|+++....-++| +. +. +.+..++.+||++.++.+| ||+.||
T Consensus 39 lf~ELsFCILTANsSA~~~~~~q--------~~-----lG-------------~gfly~~~eEL~e~Lk~~g~Rf~n~ra 92 (210)
T COG1059 39 LFKELSFCILTANSSATMGLRAQ--------NE-----LG-------------DGFLYLSEEELREKLKEVGYRFYNVRA 92 (210)
T ss_pred HHHHHHHHhccccchHHHHHHHH--------HH-----hc-------------cccccCCHHHHHHHHHHhcchhcccch
Confidence 37788888888887654433221 11 11 3456678999999999995 799999
Q ss_pred HHHHHHHHHHHHhhCCCCchhhhcCCchH--HHHHHH-hCCCCcHhHHHHHHHHhcCCceeecchHHHHHHHHhCCCCC
Q 002604 460 ERMKDFLNRLVREHGSIDLEWLRDVPPDK--AKDYLL-SIRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPL 535 (901)
Q Consensus 460 k~Ik~lAr~Lve~yGglDLe~L~~VP~de--aRe~LL-sLPGIG~KTAd~ILlfafgrpafpVDTHV~RVl~RLGlv~~ 535 (901)
+||..+-+.+. ++..+-+.+..+ +|+.|+ .++|||-|-|..+|...--....++|.||.|.+.|.|++..
T Consensus 93 eyIVeaR~~~~------~lk~~v~~~~~~~vaRE~Lv~nikGiGyKEASHFLRNVG~~D~AIlDrHIlr~l~r~g~i~e 165 (210)
T COG1059 93 EYIVEAREKFD------DLKIIVKADENEKVARELLVENIKGIGYKEASHFLRNVGFEDLAILDRHILRWLVRYGLIDE 165 (210)
T ss_pred HHHHHHHHHHH------HHHHHHhcCcchHHHHHHHHHHcccccHHHHHHHHHhcChhHHHHHHHHHHHHHHHhccccc
Confidence 99998655553 234444444333 899999 89999999999998553336788899999999999999764
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=97.65 E-value=1.6e-05 Score=59.62 Aligned_cols=26 Identities=19% Similarity=0.448 Sum_probs=22.0
Q ss_pred cCCchHHHHHHHhCCCCcHhHHHHHHHH
Q 002604 483 DVPPDKAKDYLLSIRGLGLKSVECVRLL 510 (901)
Q Consensus 483 ~VP~deaRe~LLsLPGIG~KTAd~ILlf 510 (901)
.+|.+ +++|++|||||+|||++|+.|
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=96.92 E-value=0.00034 Score=46.48 Aligned_cols=17 Identities=47% Similarity=1.323 Sum_probs=11.6
Q ss_pred cccCCCCCCCCCCchhc
Q 002604 587 CTKSKPNCNACPMRGEC 603 (901)
Q Consensus 587 CkarkP~C~~CPLrdlC 603 (901)
|++|+|+|+.|||+++|
T Consensus 1 Ctar~P~C~~Cpl~~~C 17 (17)
T PF10576_consen 1 CTARKPKCEECPLADYC 17 (17)
T ss_dssp S-SSS--GGG-TTGGG-
T ss_pred CcCCCCccccCCCcccC
Confidence 89999999999999998
No 27
>PF09674 DUF2400: Protein of unknown function (DUF2400); InterPro: IPR014127 Members of this uncharacterised protein family are found sporadically, so far only among spirochetes, epsilon and delta proteobacteria, and Bacteroides. The function is unknown and its gene neighbourhoods show little conservation.
Probab=96.67 E-value=0.0014 Score=70.08 Aligned_cols=88 Identities=24% Similarity=0.399 Sum_probs=60.5
Q ss_pred HHHHHHHHHHHHHHHHhhCCCCchhhhcCCchHHHHHHHhCCCCcHhHHHHHHHHhcCCceeecchHHHHHHHHhCCCCC
Q 002604 456 NMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPL 535 (901)
Q Consensus 456 n~KAk~Ik~lAr~Lve~yGglDLe~L~~VP~deaRe~LLsLPGIG~KTAd~ILlfafgrpafpVDTHV~RVl~RLGlv~~ 535 (901)
++-+|+|--++||++++..++|+.-...+++.++ .+|+||||.||+.+||+...
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 3467999999999998766699987777887643 68999999999999999876
Q ss_pred CCCHHHHHHHHHHhcCchHHHHHhhhhhhhcCChhhHHHHHHHHHHHh
Q 002604 536 QPLPESLQLHLLELYPVLESIQKYLWPRLCKLDQRTLYELHYQLITFG 583 (901)
Q Consensus 536 ~~tpekvEk~L~~llP~~e~Iqk~lW~~l~~ld~e~~~efH~~LI~fG 583 (901)
+..--++...+-+. +..+++.++..+..+|-.+|
T Consensus 196 k~~d~k~A~elT~~--------------lr~~~p~DPvKYDFAL~~~G 229 (232)
T PF09674_consen 196 KSADWKAARELTEA--------------LREFDPDDPVKYDFALFRLG 229 (232)
T ss_pred CCccHHHHHHHHHH--------------HHhcCCCCCcchhhhcccCC
Confidence 42211222212111 11244566667777776666
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=96.18 E-value=0.0043 Score=66.33 Aligned_cols=85 Identities=24% Similarity=0.391 Sum_probs=58.3
Q ss_pred HHHHHHHHHHHHHHhhCCCCchhhhcCCchHHHHHHHhCCCCcHhHHHHHHHHhcCCceeecchHHHHHHHHhCCCCCCC
Q 002604 458 LAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQP 537 (901)
Q Consensus 458 KAk~Ik~lAr~Lve~yGglDLe~L~~VP~deaRe~LLsLPGIG~KTAd~ILlfafgrpafpVDTHV~RVl~RLGlv~~~~ 537 (901)
-+|+|--++||++++ +++|+.-...+++.++ ++|+||||.||+.+||+...+
T Consensus 142 a~KR~nMFLRWMVR~-d~VD~GlW~~i~ps~L--------------------------iiPLDtH~~rvar~LgL~~Rk- 193 (229)
T TIGR02757 142 PLKRLNMFLRWMIRK-DEVDLGIWESFKPSDL--------------------------ILPLDTHVFRIAKKLKLLKRK- 193 (229)
T ss_pred hHHHHHHHHHhhccC-CCCCCcCCCCCCHHHc--------------------------eeechHhHHHHHHHhCCcccC-
Confidence 458999999999985 4489887777877643 799999999999999998853
Q ss_pred CH-HHHHHHHHHhcCchHHHHHhhhhhhhcCChhhHHHHHHHHHHHhH
Q 002604 538 LP-ESLQLHLLELYPVLESIQKYLWPRLCKLDQRTLYELHYQLITFGK 584 (901)
Q Consensus 538 tp-ekvEk~L~~llP~~e~Iqk~lW~~l~~ld~e~~~efH~~LI~fGR 584 (901)
++ -++...+-+ .+.++++.++..+..+|-.+|.
T Consensus 194 ~~d~kaa~ElT~--------------~Lr~~dp~DPvKYDFAL~~lGi 227 (229)
T TIGR02757 194 SYDLKAAIEITE--------------ALRELNPEDPIKYDFALFRLGQ 227 (229)
T ss_pred chhHHHHHHHHH--------------HHHhcCCCCCcchhhhcccCCc
Confidence 32 111111111 1223555677777777766663
No 29
>smart00525 FES FES domain. iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3)
Probab=95.96 E-value=0.0035 Score=45.20 Aligned_cols=22 Identities=36% Similarity=1.141 Sum_probs=20.0
Q ss_pred hcccCCCCCCCCCCchhchhhh
Q 002604 586 FCTKSKPNCNACPMRGECRHFA 607 (901)
Q Consensus 586 ICkarkP~C~~CPLrdlC~y~~ 607 (901)
+|++++|+|+.|||++.|++|.
T Consensus 1 vC~ar~P~C~~Cpl~~~C~~~~ 22 (26)
T smart00525 1 ICTARKPRCDECPLKDLCPAYX 22 (26)
T ss_pred CccCCCCCCCCCcCHHHhhhhh
Confidence 6999999999999999999754
No 30
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=91.32 E-value=0.14 Score=36.94 Aligned_cols=20 Identities=30% Similarity=0.338 Sum_probs=17.6
Q ss_pred HHHhCCCCcHhHHHHHHHHh
Q 002604 492 YLLSIRGLGLKSVECVRLLT 511 (901)
Q Consensus 492 ~LLsLPGIG~KTAd~ILlfa 511 (901)
.|.++||||+|+|..|+.+.
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=90.60 E-value=0.34 Score=42.02 Aligned_cols=40 Identities=28% Similarity=0.351 Sum_probs=28.3
Q ss_pred HHHHHHHhhCCCCchhhhcCCchHHHHHHHhCCCCcHhHHHHHHHH
Q 002604 465 FLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLL 510 (901)
Q Consensus 465 lAr~Lve~yGglDLe~L~~VP~deaRe~LLsLPGIG~KTAd~ILlf 510 (901)
.|+.|.+.||. ++.|.... .++|.+++|||+++|..|..|
T Consensus 15 ~ak~L~~~f~s--l~~l~~a~----~e~L~~i~gIG~~~A~si~~f 54 (64)
T PF12826_consen 15 TAKLLAKHFGS--LEALMNAS----VEELSAIPGIGPKIAQSIYEF 54 (64)
T ss_dssp HHHHHHHCCSC--HHHHCC------HHHHCTSTT--HHHHHHHHHH
T ss_pred HHHHHHHHcCC--HHHHHHcC----HHHHhccCCcCHHHHHHHHHH
Confidence 45667777774 67776543 678999999999999999776
No 32
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=87.32 E-value=2 Score=45.44 Aligned_cols=66 Identities=20% Similarity=0.233 Sum_probs=44.7
Q ss_pred cCCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHH------HHHHHHHHhhCCCCchhhhcCCchHHHHHHHhCCCCcH
Q 002604 428 RMDSLDYEALRCANVKEISEAIKERGMNNMLAERMK------DFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGL 501 (901)
Q Consensus 428 ~~~~pTpeaLa~A~~eELeelIR~~Gfyn~KAk~Ik------~lAr~Lve~yGglDLe~L~~VP~deaRe~LLsLPGIG~ 501 (901)
.+||.|.++. +-.+.+|.-.|.-...|-.|. +++++|.. + | .+.|.++||||+
T Consensus 59 LYGF~t~~Er-----~lF~~LisVsGIGPK~ALaILs~~~~~el~~aI~~--~------------D--~~~L~~vpGIGk 117 (196)
T PRK13901 59 LFGFLNSSER-----EVFEELIGVDGIGPRAALRVLSGIKYNEFRDAIDR--E------------D--IELISKVKGIGN 117 (196)
T ss_pred eeCCCCHHHH-----HHHHHHhCcCCcCHHHHHHHHcCCCHHHHHHHHHh--C------------C--HHHHhhCCCCCH
Confidence 3677777764 334555655677777776666 44555543 2 2 668999999999
Q ss_pred hHHHHHHHHhcCC
Q 002604 502 KSVECVRLLTLHH 514 (901)
Q Consensus 502 KTAd~ILlfafgr 514 (901)
|||.-|.+---++
T Consensus 118 KtAeRIIlELkdK 130 (196)
T PRK13901 118 KMAGKIFLKLRGK 130 (196)
T ss_pred HHHHHHHHHHHHh
Confidence 9999888654444
No 33
>PF14716 HHH_8: Helix-hairpin-helix domain; PDB: 2W9M_A 1HUZ_A 1HUO_A 2BPG_B 2BPF_A 1DK3_A 1BPE_A 1BNO_A 1BNP_A 1DK2_A ....
Probab=85.51 E-value=3.2 Score=36.24 Aligned_cols=58 Identities=12% Similarity=0.188 Sum_probs=38.5
Q ss_pred HHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCCchhhhcCCchHHHHHHHhCCCCcHhHHHHHHHH
Q 002604 443 KEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLL 510 (901)
Q Consensus 443 eELeelIR~~Gfyn~KAk~Ik~lAr~Lve~yGglDLe~L~~VP~deaRe~LLsLPGIG~KTAd~ILlf 510 (901)
+++.++..-.|=...|++.-...+..|.. ++. |-+...+.|.+|||||.++|..|--|
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 45555555565445688888888888875 332 22222225999999999999988543
No 34
>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region. Members of the subfamily recognized by this model include competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model.
Probab=83.24 E-value=1.6 Score=37.91 Aligned_cols=58 Identities=22% Similarity=0.318 Sum_probs=37.5
Q ss_pred HHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCCchhhhcCCchHHHHHHHhCCCCcHhHHHHHHHH
Q 002604 436 ALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLL 510 (901)
Q Consensus 436 aLa~A~~eELeelIR~~Gfyn~KAk~Ik~lAr~Lve~yGglDLe~L~~VP~deaRe~LLsLPGIG~KTAd~ILlf 510 (901)
+|-.|+.++|..++.++|. .+|+.|++.- ..+|++ .+ .++|..++|||.++|+-|+.+
T Consensus 9 nvNta~~~~L~~~ipgig~--~~a~~Il~~R----~~~g~~---------~s--~~dL~~v~gi~~~~~~~i~~~ 66 (69)
T TIGR00426 9 NINTATAEELQRAMNGVGL--KKAEAIVSYR----EEYGPF---------KT--VEDLKQVPGIGNSLVEKNLAV 66 (69)
T ss_pred ECcCCCHHHHHhHCCCCCH--HHHHHHHHHH----HHcCCc---------CC--HHHHHcCCCCCHHHHHHHHhh
Confidence 3445777787776555554 4555554321 124543 13 678999999999999998866
No 35
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=83.03 E-value=1.8 Score=43.21 Aligned_cols=53 Identities=19% Similarity=0.289 Sum_probs=39.0
Q ss_pred HHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCCchhhhcCCchHHHHHHHhCCCCcHhHHHHHHH
Q 002604 435 EALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRL 509 (901)
Q Consensus 435 eaLa~A~~eELeelIR~~Gfyn~KAk~Ik~lAr~Lve~yGglDLe~L~~VP~deaRe~LLsLPGIG~KTAd~ILl 509 (901)
=+|-.|+.+++..+ -|++..+|+.|+ .+|.+ .+ .++|+.+||||+++...+--
T Consensus 53 IdiN~A~~~el~~l---pGigP~~A~~IV--------~nGpf---------~s--veDL~~V~GIgekqk~~l~k 105 (132)
T PRK02515 53 IDLNNSSVRAFRQF---PGMYPTLAGKIV--------KNAPY---------DS--VEDVLNLPGLSERQKELLEA 105 (132)
T ss_pred ccCCccCHHHHHHC---CCCCHHHHHHHH--------HCCCC---------CC--HHHHHcCCCCCHHHHHHHHH
Confidence 35667788887653 688888998887 25553 12 77899999999998876654
No 36
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=82.20 E-value=3.7 Score=34.81 Aligned_cols=30 Identities=30% Similarity=0.317 Sum_probs=22.8
Q ss_pred CchhhhcCCchHHHHHHHhCCCCcHhHHHHHHHH
Q 002604 477 DLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLL 510 (901)
Q Consensus 477 DLe~L~~VP~deaRe~LLsLPGIG~KTAd~ILlf 510 (901)
+++.|...+ .+.|.+++|||+++|+-|...
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 566666543 457999999999999987654
No 37
>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=82.14 E-value=3.9 Score=44.71 Aligned_cols=133 Identities=16% Similarity=0.130 Sum_probs=74.1
Q ss_pred HHHHHHHHhc----CCcHHHHHHHHHHHHHHHHhhCCCCchhhhc--CCchHHHHHHHhCCCCc--HhH-------HHHH
Q 002604 443 KEISEAIKER----GMNNMLAERMKDFLNRLVREHGSIDLEWLRD--VPPDKAKDYLLSIRGLG--LKS-------VECV 507 (901)
Q Consensus 443 eELeelIR~~----Gfyn~KAk~Ik~lAr~Lve~yGglDLe~L~~--VP~deaRe~LLsLPGIG--~KT-------Ad~I 507 (901)
+++.+.+... -+.++|.++|.+++..+.. +.+..+.. -.-..+++.|..+=|-. .|| +...
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 4555556543 3467899999988776643 21221111 12234566666654443 233 3334
Q ss_pred HHHhcCC--c-----eeecchHHHHHHHHhCCCCCCCCHHHHHHHHHHhcCchHHHHHhhhhhhhcCChhhHHHHHHHHH
Q 002604 508 RLLTLHH--L-----AFPVDTNVGRIAVRLGWVPLQPLPESLQLHLLELYPVLESIQKYLWPRLCKLDQRTLYELHYQLI 580 (901)
Q Consensus 508 Llfafgr--p-----afpVDTHV~RVl~RLGlv~~~~tpekvEk~L~~llP~~e~Iqk~lW~~l~~ld~e~~~efH~~LI 580 (901)
+..+||. | -||||.||.++..++|++.. .++. .. .. +......|..++....-.+.+++..||
T Consensus 153 ~r~~~g~~~~~p~~IpIPvD~Rva~~T~~sGi~~~--~~~~---~~--~~---~~~v~~~W~~Va~~sgIpplhLDs~lW 222 (246)
T PF09171_consen 153 CRIAFGEFRPYPEEIPIPVDYRVAKLTKRSGIIEC--EREE---MM--RT---REEVQKAWREVAKESGIPPLHLDSLLW 222 (246)
T ss_dssp HHHHCTS-----TTS-----HHHHHHHHCTTS-SS---HHH---HH--CT---CCHHHHHHHHHHHHHT--HHHHHHHHH
T ss_pred HHHhcCCCCCCcccCCCCccHHHHHHHHHhccccc--cHHh---hh--cc---HHHHHHHHHHHHhhcCCCchhhhhHHH
Confidence 4445564 2 68999999999999999764 2221 11 11 223345798887777777899999999
Q ss_pred -HHhHhhccc
Q 002604 581 -TFGKVFCTK 589 (901)
Q Consensus 581 -~fGR~ICka 589 (901)
.+|+..+..
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 38
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=79.75 E-value=6.4 Score=41.21 Aligned_cols=70 Identities=20% Similarity=0.181 Sum_probs=41.2
Q ss_pred cCCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCCchhhhcC--CchHHHHHHHhCCCCcHhHHH
Q 002604 428 RMDSLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDV--PPDKAKDYLLSIRGLGLKSVE 505 (901)
Q Consensus 428 ~~~~pTpeaLa~A~~eELeelIR~~Gfyn~KAk~Ik~lAr~Lve~yGglDLe~L~~V--P~deaRe~LLsLPGIG~KTAd 505 (901)
.++|.|.++. +-.+.+|+-.|.-...|-.|.. .++.+.|... ..| .+.|.++||||+|||+
T Consensus 60 LyGF~~~~Er-----~lF~~Li~VsGIGpK~Al~ILs----------~~~~~el~~aI~~~D--~~~L~~vpGIGkKtAe 122 (183)
T PRK14601 60 LYGFLDKDEQ-----KMFEMLLKVNGIGANTAMAVCS----------SLDVNSFYKALSLGD--ESVLKKVPGIGPKSAK 122 (183)
T ss_pred eeCCCCHHHH-----HHHHHHhccCCccHHHHHHHHc----------CCCHHHHHHHHHhCC--HHHHhhCCCCCHHHHH
Confidence 3577777653 3344455556776555544442 1222222211 123 6789999999999999
Q ss_pred HHHHHhcCC
Q 002604 506 CVRLLTLHH 514 (901)
Q Consensus 506 ~ILlfafgr 514 (901)
-|++---++
T Consensus 123 RIilELkdK 131 (183)
T PRK14601 123 RIIAELSDA 131 (183)
T ss_pred HHHHHHHHH
Confidence 988655454
No 39
>PRK00076 recR recombination protein RecR; Reviewed
Probab=79.48 E-value=1.7 Score=45.93 Aligned_cols=28 Identities=25% Similarity=0.375 Sum_probs=22.1
Q ss_pred hHHHHHHHhCCCCcHhHHHHHHHHhcCC
Q 002604 487 DKAKDYLLSIRGLGLKSVECVRLLTLHH 514 (901)
Q Consensus 487 deaRe~LLsLPGIG~KTAd~ILlfafgr 514 (901)
+++.+.|.+|||||+|||.-+..+.+.+
T Consensus 7 ~~Li~~l~~LPGIG~KsA~Rla~~ll~~ 34 (196)
T PRK00076 7 EKLIEALRKLPGIGPKSAQRLAFHLLQR 34 (196)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHHHcC
Confidence 4678899999999999997666554443
No 40
>PRK13844 recombination protein RecR; Provisional
Probab=79.17 E-value=1.8 Score=45.93 Aligned_cols=28 Identities=21% Similarity=0.260 Sum_probs=22.3
Q ss_pred hHHHHHHHhCCCCcHhHHHHHHHHhcCC
Q 002604 487 DKAKDYLLSIRGLGLKSVECVRLLTLHH 514 (901)
Q Consensus 487 deaRe~LLsLPGIG~KTAd~ILlfafgr 514 (901)
+++.+.|.+|||||+|+|.-+..+.+.+
T Consensus 11 ~~LI~~l~~LPGIG~KsA~Rla~~lL~~ 38 (200)
T PRK13844 11 SAVIESLRKLPTIGKKSSQRLALYLLDK 38 (200)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHHHcC
Confidence 5678899999999999997766654443
No 41
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=79.14 E-value=6.9 Score=41.06 Aligned_cols=66 Identities=11% Similarity=0.062 Sum_probs=40.2
Q ss_pred cCCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHH------HHHHHHHhhCCCCchhhhcCCchHHHHHHHhCCCCcH
Q 002604 428 RMDSLDYEALRCANVKEISEAIKERGMNNMLAERMKD------FLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGL 501 (901)
Q Consensus 428 ~~~~pTpeaLa~A~~eELeelIR~~Gfyn~KAk~Ik~------lAr~Lve~yGglDLe~L~~VP~deaRe~LLsLPGIG~ 501 (901)
.+||.|.++. +-.+.+|.-.|.-...|-.|.. ++++|.. .| .+.|.++||||+
T Consensus 60 LyGF~~~~Er-----~lF~~Li~V~GIGpK~AL~iLs~~~~~el~~aI~~--------------~D--~~~L~~vpGIGk 118 (188)
T PRK14606 60 LYGFSNERKK-----ELFLSLTKVSRLGPKTALKIISNEDAETLVTMIAS--------------QD--VEGLSKLPGISK 118 (188)
T ss_pred eeCCCCHHHH-----HHHHHHhccCCccHHHHHHHHcCCCHHHHHHHHHh--------------CC--HHHHhhCCCCCH
Confidence 3567776653 2334445446776656655542 2333322 12 668999999999
Q ss_pred hHHHHHHHHhcCC
Q 002604 502 KSVECVRLLTLHH 514 (901)
Q Consensus 502 KTAd~ILlfafgr 514 (901)
|||+-|.+---++
T Consensus 119 KtAerIilELkdK 131 (188)
T PRK14606 119 KTAERIVMELKDE 131 (188)
T ss_pred HHHHHHHHHHHHh
Confidence 9999888654443
No 42
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=78.93 E-value=1.9 Score=45.66 Aligned_cols=28 Identities=25% Similarity=0.347 Sum_probs=21.9
Q ss_pred hHHHHHHHhCCCCcHhHHHHHHHHhcCC
Q 002604 487 DKAKDYLLSIRGLGLKSVECVRLLTLHH 514 (901)
Q Consensus 487 deaRe~LLsLPGIG~KTAd~ILlfafgr 514 (901)
+++.+.|.+|||||+|||.-+..+.+.+
T Consensus 7 ~~Li~~l~~LPGIG~KsA~RlA~~ll~~ 34 (195)
T TIGR00615 7 SKLIESLKKLPGIGPKSAQRLAFHLLKR 34 (195)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHHHcC
Confidence 5678899999999999997665554433
No 43
>PRK10353 3-methyl-adenine DNA glycosylase I; Provisional
Probab=78.51 E-value=2.6 Score=44.37 Aligned_cols=47 Identities=4% Similarity=0.116 Sum_probs=35.8
Q ss_pred CCCCCHHHHHcCCHHHHHHHHHhcCCcH--HHHHHHHHHHHHHHH---hhCC
Q 002604 429 MDSLDYEALRCANVKEISEAIKERGMNN--MLAERMKDFLNRLVR---EHGS 475 (901)
Q Consensus 429 ~~~pTpeaLa~A~~eELeelIR~~Gfyn--~KAk~Ik~lAr~Lve---~yGg 475 (901)
...++|+.+|..++++|+.++..-|.-| .|.+.++.=|+.+++ ++|+
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 4578999999999999999999999854 455567775666553 4554
No 44
>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=78.44 E-value=7.4 Score=40.74 Aligned_cols=47 Identities=17% Similarity=0.319 Sum_probs=34.4
Q ss_pred CCCCCHHHHHcCCHHHHHHHHHhcCC--cHHHHHHHHHHHHHHHH---hhCC
Q 002604 429 MDSLDYEALRCANVKEISEAIKERGM--NNMLAERMKDFLNRLVR---EHGS 475 (901)
Q Consensus 429 ~~~pTpeaLa~A~~eELeelIR~~Gf--yn~KAk~Ik~lAr~Lve---~yGg 475 (901)
+..++|+.|+..++++|++++..-|. .+.|.+.++.=|+.+++ +||+
T Consensus 55 F~~Fd~~~vA~~~e~~ie~l~~d~~iIRnr~KI~Avi~NA~~~l~i~~e~gs 106 (179)
T PF03352_consen 55 FAGFDPEKVAKMDEEDIERLMQDPGIIRNRRKIRAVINNARAILKIQEEFGS 106 (179)
T ss_dssp TGGGHHHHHHT--HHHHHHHTTSTTSS--HHHHHHHHHHHHHHHHHHHTTS-
T ss_pred HHCCCHHHHHcCCHHHHHHHhcCcchhhhHHHHHHHHHHHHHHHHHHHhcCC
Confidence 34689999999999999999999998 55677777777776663 4555
No 45
>PRK00024 hypothetical protein; Reviewed
Probab=78.38 E-value=3.6 Score=44.04 Aligned_cols=61 Identities=23% Similarity=0.351 Sum_probs=44.5
Q ss_pred cCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCCchhhhcCCchHHHHHHHhCCCCcHhHHHHHH
Q 002604 439 CANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVR 508 (901)
Q Consensus 439 ~A~~eELeelIR~~Gfyn~KAk~Ik~lAr~Lve~yGglDLe~L~~VP~deaRe~LLsLPGIG~KTAd~IL 508 (901)
.++..||.++|=..|.. -+..+.+|+.++++||+ +..+...+ .++|.+++|||+..|-.++
T Consensus 23 ~Lsd~ELLa~lL~~g~~---~~~~~~LA~~LL~~fgs--L~~l~~as----~~eL~~i~GIG~akA~~L~ 83 (224)
T PRK00024 23 ALSDAELLAILLRTGTK---GKSVLDLARELLQRFGS--LRGLLDAS----LEELQSIKGIGPAKAAQLK 83 (224)
T ss_pred cCCHHHHHHHHHcCCCC---CCCHHHHHHHHHHHcCC--HHHHHhCC----HHHHhhccCccHHHHHHHH
Confidence 44567777776556655 34567889999988885 66666665 4579999999999886654
No 46
>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=77.58 E-value=2.1 Score=36.34 Aligned_cols=27 Identities=37% Similarity=0.391 Sum_probs=22.6
Q ss_pred HHHHHHhCCCCcHhHHHHHHHHhcCCc
Q 002604 489 AKDYLLSIRGLGLKSVECVRLLTLHHL 515 (901)
Q Consensus 489 aRe~LLsLPGIG~KTAd~ILlfafgrp 515 (901)
+.+.|+++||||+++|..+...+|+-.
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 467899999999999998887766654
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=77.16 E-value=4.4 Score=43.40 Aligned_cols=61 Identities=21% Similarity=0.260 Sum_probs=44.6
Q ss_pred cCCHHHHHHHHHhcCCcHHHHH-HHHHHHHHHHHhh---CCCCchhhhcCCchHHHHHHHhCCCCcHhHHHHHH
Q 002604 439 CANVKEISEAIKERGMNNMLAE-RMKDFLNRLVREH---GSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVR 508 (901)
Q Consensus 439 ~A~~eELeelIR~~Gfyn~KAk-~Ik~lAr~Lve~y---GglDLe~L~~VP~deaRe~LLsLPGIG~KTAd~IL 508 (901)
.++..||.++|=..|..+ + ..+.+|+.|+++| |+ |..+...+ .++|.+++|||+..|-.++
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--LGHLLSAP----PEELSSVPGIGEAKAIQLK 77 (218)
T ss_pred cCCHHHHHHHHHhCCCCC---CCCHHHHHHHHHHHhcccCC--HHHHHhCC----HHHHHhCcCCcHHHHHHHH
Confidence 446677777765566653 3 6778999999888 64 67777765 4579999999997776554
No 48
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=75.53 E-value=8.8 Score=40.66 Aligned_cols=70 Identities=16% Similarity=0.106 Sum_probs=39.9
Q ss_pred cCCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCCchhhhc-C-CchHHHHHHHhCCCCcHhHHH
Q 002604 428 RMDSLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRD-V-PPDKAKDYLLSIRGLGLKSVE 505 (901)
Q Consensus 428 ~~~~pTpeaLa~A~~eELeelIR~~Gfyn~KAk~Ik~lAr~Lve~yGglDLe~L~~-V-P~deaRe~LLsLPGIG~KTAd 505 (901)
.+||.|.++. +-...+|.-.|.-...|-.|... ++.+.|.. + ..| .+.|.++||||+|||+
T Consensus 61 LyGF~~~~Er-----~lF~~Li~V~GIGpK~Al~iLs~----------~~~~~l~~aI~~~D--~~~L~~ipGIGkKtAe 123 (203)
T PRK14602 61 LFGFATWDER-----QTFIVLISISKVGAKTALAILSQ----------FRPDDLRRLVAEED--VAALTRVSGIGKKTAQ 123 (203)
T ss_pred eeCCCCHHHH-----HHHHHHhCCCCcCHHHHHHHHhh----------CCHHHHHHHHHhCC--HHHHhcCCCcCHHHHH
Confidence 3567666653 23334455567766666555442 11221111 1 123 6789999999999999
Q ss_pred HHHHHhcCC
Q 002604 506 CVRLLTLHH 514 (901)
Q Consensus 506 ~ILlfafgr 514 (901)
-|++---++
T Consensus 124 rIilELkdK 132 (203)
T PRK14602 124 HIFLELKYK 132 (203)
T ss_pred HHHHHHHHh
Confidence 888644333
No 49
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=75.49 E-value=2.5 Score=44.72 Aligned_cols=28 Identities=29% Similarity=0.388 Sum_probs=21.6
Q ss_pred hHHHHHHHhCCCCcHhHHHHHHHHhcCC
Q 002604 487 DKAKDYLLSIRGLGLKSVECVRLLTLHH 514 (901)
Q Consensus 487 deaRe~LLsLPGIG~KTAd~ILlfafgr 514 (901)
+++++.|.+|||||+|+|.-+..+.+.+
T Consensus 8 ~~LI~~l~kLPGvG~KsA~R~AfhLL~~ 35 (198)
T COG0353 8 EKLIDALKKLPGVGPKSAQRLAFHLLQR 35 (198)
T ss_pred HHHHHHHhhCCCCChhHHHHHHHHHHcc
Confidence 4678899999999999996665554443
No 50
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=74.98 E-value=9.8 Score=40.01 Aligned_cols=65 Identities=22% Similarity=0.262 Sum_probs=38.9
Q ss_pred cCCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCCchhhh-cC-CchHHHHHHHhCCCCcHhHHH
Q 002604 428 RMDSLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLR-DV-PPDKAKDYLLSIRGLGLKSVE 505 (901)
Q Consensus 428 ~~~~pTpeaLa~A~~eELeelIR~~Gfyn~KAk~Ik~lAr~Lve~yGglDLe~L~-~V-P~deaRe~LLsLPGIG~KTAd 505 (901)
.+||.+.++- +-...+|+--|.....|..|... ++.+.|. .+ ..| .+.|.++||||+|||+
T Consensus 60 LyGF~~~~Er-----~lF~~Li~V~GIGpK~Al~ILs~----------~~~~~l~~aI~~~D--~~~L~~vpGIGkKtAe 122 (194)
T PRK14605 60 LFGFATTEEL-----SLFETLIDVSGIGPKLGLAMLSA----------MNAEALASAIISGN--AELLSTIPGIGKKTAS 122 (194)
T ss_pred eeCCCCHHHH-----HHHHHHhCCCCCCHHHHHHHHHh----------CCHHHHHHHHHhCC--HHHHHhCCCCCHHHHH
Confidence 3567776653 33444555567776666555542 1122211 11 223 5679999999999999
Q ss_pred HHHH
Q 002604 506 CVRL 509 (901)
Q Consensus 506 ~ILl 509 (901)
-|++
T Consensus 123 rIil 126 (194)
T PRK14605 123 RIVL 126 (194)
T ss_pred HHHH
Confidence 9664
No 51
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=74.60 E-value=7.2 Score=40.87 Aligned_cols=69 Identities=20% Similarity=0.164 Sum_probs=39.6
Q ss_pred cCCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCCchhhhc-C-CchHHHHHHHhCCCCcHhHHH
Q 002604 428 RMDSLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRD-V-PPDKAKDYLLSIRGLGLKSVE 505 (901)
Q Consensus 428 ~~~~pTpeaLa~A~~eELeelIR~~Gfyn~KAk~Ik~lAr~Lve~yGglDLe~L~~-V-P~deaRe~LLsLPGIG~KTAd 505 (901)
.+||.|.++. +-.+.+|+-.|.-...|-.|... ++.+.|.. + ..| .+.| ++||||+|||+
T Consensus 60 LyGF~~~~Er-----~lF~~LisV~GIGpK~Al~iLs~----------~~~~~l~~aI~~~D--~~~L-~vpGIGkKtAe 121 (186)
T PRK14600 60 LYGFLNREEQ-----DCLRMLVKVSGVNYKTAMSILSK----------LTPEQLFSAIVNED--KAAL-KVNGIGEKLIN 121 (186)
T ss_pred eeCCCCHHHH-----HHHHHHhCcCCcCHHHHHHHHcc----------CCHHHHHHHHHcCC--Hhhe-ECCCCcHHHHH
Confidence 3577777663 33444555567766666555442 11222211 1 112 4678 99999999999
Q ss_pred HHHHHhcCC
Q 002604 506 CVRLLTLHH 514 (901)
Q Consensus 506 ~ILlfafgr 514 (901)
-|++---++
T Consensus 122 rIilELk~K 130 (186)
T PRK14600 122 RIITELQYK 130 (186)
T ss_pred HHHHHHHHH
Confidence 988644443
No 52
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=74.59 E-value=5.2 Score=41.79 Aligned_cols=22 Identities=27% Similarity=0.345 Sum_probs=18.8
Q ss_pred HHHHHhCCCCcHhHHHHHHHHh
Q 002604 490 KDYLLSIRGLGLKSVECVRLLT 511 (901)
Q Consensus 490 Re~LLsLPGIG~KTAd~ILlfa 511 (901)
.+.|.++||||+|+|+.|+..-
T Consensus 107 ~~~L~~v~Gig~k~A~~I~~~l 128 (192)
T PRK00116 107 VKALTKVPGIGKKTAERIVLEL 128 (192)
T ss_pred HHHHHhCCCCCHHHHHHHHHHH
Confidence 5679999999999999998653
No 53
>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=74.28 E-value=4.4 Score=42.38 Aligned_cols=43 Identities=7% Similarity=0.109 Sum_probs=34.5
Q ss_pred CCCCCHHHHHcCCHHHHHHHHHhcCCcHHHH--HHHHHHHHHHHH
Q 002604 429 MDSLDYEALRCANVKEISEAIKERGMNNMLA--ERMKDFLNRLVR 471 (901)
Q Consensus 429 ~~~pTpeaLa~A~~eELeelIR~~Gfyn~KA--k~Ik~lAr~Lve 471 (901)
...++|+.++..++++|+.++..-|.-|.|+ +.++.=|+.+++
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 4578999999999999999999999876554 456666666664
No 54
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=73.98 E-value=9.9 Score=40.14 Aligned_cols=69 Identities=16% Similarity=0.019 Sum_probs=39.9
Q ss_pred CCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCCchhhhcC--CchHHHHHHHhCCCCcHhHHHH
Q 002604 429 MDSLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDV--PPDKAKDYLLSIRGLGLKSVEC 506 (901)
Q Consensus 429 ~~~pTpeaLa~A~~eELeelIR~~Gfyn~KAk~Ik~lAr~Lve~yGglDLe~L~~V--P~deaRe~LLsLPGIG~KTAd~ 506 (901)
+||.|.++. +-...+|.-.|.-.+.|-.|... ++.+.|... ..| .+.|.++||||+|||+-
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 567666653 33344455567766666555431 122222111 122 67899999999999998
Q ss_pred HHHHhcCC
Q 002604 507 VRLLTLHH 514 (901)
Q Consensus 507 ILlfafgr 514 (901)
|++---++
T Consensus 124 IilELk~K 131 (195)
T PRK14604 124 IVLELKGK 131 (195)
T ss_pred HHHHHHHH
Confidence 88654443
No 55
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=73.02 E-value=5 Score=40.61 Aligned_cols=56 Identities=25% Similarity=0.403 Sum_probs=38.2
Q ss_pred HHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCCchhhhcCCchHHHHHHHhCCCCcHhHHHHHHHH
Q 002604 437 LRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLL 510 (901)
Q Consensus 437 La~A~~eELeelIR~~Gfyn~KAk~Ik~lAr~Lve~yGglDLe~L~~VP~deaRe~LLsLPGIG~KTAd~ILlf 510 (901)
|-.|+.++| ..|.++|- .||+.|++ ..+.+|.+ .+ .+.|..++|||++|.+-+.-+
T Consensus 91 iNtAs~eeL-~~lpgIG~--~kA~aIi~----yRe~~G~f---------~s--v~dL~~v~GiG~~~~ekl~~~ 146 (149)
T COG1555 91 INTASAEEL-QALPGIGP--KKAQAIID----YREENGPF---------KS--VDDLAKVKGIGPKTLEKLKDY 146 (149)
T ss_pred ccccCHHHH-HHCCCCCH--HHHHHHHH----HHHHcCCC---------Cc--HHHHHhccCCCHHHHHHHHhh
Confidence 446777888 55555664 58877764 34556653 12 678999999999998876543
No 56
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=70.77 E-value=3 Score=44.35 Aligned_cols=70 Identities=23% Similarity=0.200 Sum_probs=39.6
Q ss_pred CCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCCchhhhcCCchHHHHHHHhCCCCcHhHHHHHH
Q 002604 429 MDSLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVR 508 (901)
Q Consensus 429 ~~~pTpeaLa~A~~eELeelIR~~Gfyn~KAk~Ik~lAr~Lve~yGglDLe~L~~VP~deaRe~LLsLPGIG~KTAd~IL 508 (901)
+||.|.++- +=...+|+-.|.-.+-|-.| +. .+|++.|...=..+-...|.++||||.|||+-|+
T Consensus 61 yGF~~~~ER-----~lF~~LisVnGIGpK~ALai-------Ls---~~~~~~l~~aI~~~d~~~L~k~PGIGkKtAeriv 125 (201)
T COG0632 61 YGFLTEEER-----ELFRLLISVNGIGPKLALAI-------LS---NLDPEELAQAIANEDVKALSKIPGIGKKTAERIV 125 (201)
T ss_pred cCCCCHHHH-----HHHHHHHccCCccHHHHHHH-------Hc---CCCHHHHHHHHHhcChHhhhcCCCCCHHHHHHHH
Confidence 355555442 33455566667664333332 22 2344444322111227789999999999999887
Q ss_pred HHhcC
Q 002604 509 LLTLH 513 (901)
Q Consensus 509 lfafg 513 (901)
+---|
T Consensus 126 leLk~ 130 (201)
T COG0632 126 LELKG 130 (201)
T ss_pred HHHhh
Confidence 64433
No 57
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=70.46 E-value=6.4 Score=41.27 Aligned_cols=66 Identities=23% Similarity=0.190 Sum_probs=41.4
Q ss_pred cCCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCCchhhhc-CC-chHHHHHHHhCCCCcHhHHH
Q 002604 428 RMDSLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRD-VP-PDKAKDYLLSIRGLGLKSVE 505 (901)
Q Consensus 428 ~~~~pTpeaLa~A~~eELeelIR~~Gfyn~KAk~Ik~lAr~Lve~yGglDLe~L~~-VP-~deaRe~LLsLPGIG~KTAd 505 (901)
.+||.|.++- +-...+|+--|.-..+|..|... ++++.|.. +- .| ...|.++||||+|||+
T Consensus 59 LyGF~~~~Er-----~lF~~L~~V~GIGpK~Al~iL~~----------~~~~el~~aI~~~d--~~~L~~ipGiGkKtAe 121 (191)
T TIGR00084 59 LFGFNTLEER-----ELFKELIKVNGVGPKLALAILSN----------MSPEEFVYAIETEE--VKALVKIPGVGKKTAE 121 (191)
T ss_pred eeCCCCHHHH-----HHHHHHhCCCCCCHHHHHHHHhc----------CCHHHHHHHHHhCC--HHHHHhCCCCCHHHHH
Confidence 3577777663 34455666678887777666332 22322221 11 12 4679999999999999
Q ss_pred HHHHH
Q 002604 506 CVRLL 510 (901)
Q Consensus 506 ~ILlf 510 (901)
-|++-
T Consensus 122 rIile 126 (191)
T TIGR00084 122 RLLLE 126 (191)
T ss_pred HHHHH
Confidence 99854
No 58
>PRK14973 DNA topoisomerase I; Provisional
Probab=69.81 E-value=8.1 Score=49.41 Aligned_cols=97 Identities=16% Similarity=0.122 Sum_probs=64.0
Q ss_pred CCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHH-HHHHhhCCCCchhhhcCCchHHHHHHHhCCCCcHhHHHHH
Q 002604 429 MDSLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLN-RLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECV 507 (901)
Q Consensus 429 ~~~pTpeaLa~A~~eELeelIR~~Gfyn~KAk~Ik~lAr-~Lve~yGglDLe~L~~VP~deaRe~LLsLPGIG~KTAd~I 507 (901)
.|+-++++++.|++++|..+ -|+.--.+..+...+. .+... +.+.+.+-..+.-+.+|++++|||++|+.-.
T Consensus 821 ~G~~~~~d~~~a~p~~La~~---~g~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~el~~vkg~ge~t~~~l 893 (936)
T PRK14973 821 AGFDTPEDFCSVHPAYLALK---TGISPETICRHAKLVCEKLGRP----VPEKISKAAFERGRAELLSVPGLGETTLEKL 893 (936)
T ss_pred hcCCCHHHHHhcCHHHHhcC---CCCChhhHHHHHHHHHHHhcCC----CchhhhhhhhcccchhhhhccCCCHHHHHHH
Confidence 47889999999999999764 7998666666655555 54431 2222222222333566999999999999655
Q ss_pred HHHhcCCc-eeecchHHHHHHHHhCCC
Q 002604 508 RLLTLHHL-AFPVDTNVGRIAVRLGWV 533 (901)
Q Consensus 508 Llfafgrp-afpVDTHV~RVl~RLGlv 533 (901)
-.-+.-.+ .+..+ -..|++.+.|+-
T Consensus 894 ~~ag~~~~e~l~~~-d~~~la~~~~i~ 919 (936)
T PRK14973 894 YLAGVYDGDLLVSA-DPKKLAKVTGID 919 (936)
T ss_pred HHcCCCCHHHhccC-CHHHHhhhcCCC
Confidence 44444444 33333 677888888773
No 59
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=69.27 E-value=5.6 Score=34.48 Aligned_cols=53 Identities=19% Similarity=0.374 Sum_probs=30.4
Q ss_pred HcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCCchhhhcCCchHHHHHHHhCCCCcHhHHHHHH
Q 002604 438 RCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVR 508 (901)
Q Consensus 438 a~A~~eELeelIR~~Gfyn~KAk~Ik~lAr~Lve~yGglDLe~L~~VP~deaRe~LLsLPGIG~KTAd~IL 508 (901)
-.|+.++|..+ -|+....|+.|++.= +.+|++ .+ .++|..++|||+++.+-+.
T Consensus 9 N~as~~eL~~l---pgi~~~~A~~Iv~~R----~~~G~f---------~s--~~dL~~v~gi~~~~~~~l~ 61 (65)
T PF12836_consen 9 NTASAEELQAL---PGIGPKQAKAIVEYR----EKNGPF---------KS--LEDLKEVPGIGPKTYEKLK 61 (65)
T ss_dssp TTS-HHHHHTS---TT--HHHHHHHHHHH----HHH-S----------SS--GGGGGGSTT--HHHHHHHC
T ss_pred ccCCHHHHHHc---CCCCHHHHHHHHHHH----HhCcCC---------CC--HHHHhhCCCCCHHHHHHHH
Confidence 35666676542 388778888887533 334553 11 5679999999999987663
No 60
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=69.27 E-value=9.5 Score=40.29 Aligned_cols=24 Identities=29% Similarity=0.246 Sum_probs=19.7
Q ss_pred HHHHHhCCCCcHhHHHHHHHHhcC
Q 002604 490 KDYLLSIRGLGLKSVECVRLLTLH 513 (901)
Q Consensus 490 Re~LLsLPGIG~KTAd~ILlfafg 513 (901)
.+.|.++||||+|||+-|++---+
T Consensus 106 ~~~L~kvpGIGkKtAerIilELkd 129 (197)
T PRK14603 106 ARLLTSASGVGKKLAERIALELKG 129 (197)
T ss_pred HHHHhhCCCCCHHHHHHHHHHHHH
Confidence 678999999999999988754333
No 61
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=68.35 E-value=4.7 Score=42.07 Aligned_cols=42 Identities=19% Similarity=0.194 Sum_probs=26.2
Q ss_pred HHHHHhCCCCcHhHHHHHHHHhcCCcee---ecchHHHHHHHHhCC
Q 002604 490 KDYLLSIRGLGLKSVECVRLLTLHHLAF---PVDTNVGRIAVRLGW 532 (901)
Q Consensus 490 Re~LLsLPGIG~KTAd~ILlfafgrpaf---pVDTHV~RVl~RLGl 532 (901)
...|+.+||||+|||..||. .||-..+ +.+....++..--|+
T Consensus 72 f~~L~~i~GIGpk~A~~il~-~fg~~~l~~~i~~~d~~~L~~v~Gi 116 (192)
T PRK00116 72 FRLLISVSGVGPKLALAILS-GLSPEELVQAIANGDVKALTKVPGI 116 (192)
T ss_pred HHHHhcCCCCCHHHHHHHHH-hCCHHHHHHHHHhCCHHHHHhCCCC
Confidence 45788999999999998864 3443322 334455554333255
No 62
>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=66.02 E-value=17 Score=44.76 Aligned_cols=62 Identities=15% Similarity=0.208 Sum_probs=38.0
Q ss_pred CCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCCchhhhcCCchHHHHHHHhCCCCcHhHHHHHHH
Q 002604 432 LDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRL 509 (901)
Q Consensus 432 pTpeaLa~A~~eELeelIR~~Gfyn~KAk~Ik~lAr~Lve~yGglDLe~L~~VP~deaRe~LLsLPGIG~KTAd~ILl 509 (901)
-++.+|..+..++|.++ -||...+|.+|++..+.-.. .+-+. .-..+.|||||+++|..++.
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------------KPLAR-LLFALGIRHVGEVTAKNLAK 516 (652)
T ss_pred CCHHHHHhcCHHHHhhc---cCccHHHHHHHHHHHHHhcc------------CcHHH-HHhhccCCCcCHHHHHHHHH
Confidence 38889999988887653 47777778877765554321 11111 12334567777777765553
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=65.83 E-value=8.5 Score=37.48 Aligned_cols=59 Identities=20% Similarity=0.383 Sum_probs=39.4
Q ss_pred HHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCCchhhhcCCchHHHHHHHhCCCCcHhHHHHHHHH
Q 002604 434 YEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLL 510 (901)
Q Consensus 434 peaLa~A~~eELeelIR~~Gfyn~KAk~Ik~lAr~Lve~yGglDLe~L~~VP~deaRe~LLsLPGIG~KTAd~ILlf 510 (901)
+-.|-.|+.++|.. | -|....+|+.|++.-.. +|.+ .+ .++|..++|||+|+++-|.-|
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--PGIGPAKAKAIIEYREE----NGAF---------KS--VDDLTKVSGIGEKSLEKLKDY 117 (120)
T ss_pred CEeCCcCCHHHHhc-C--CCCCHHHHHHHHHHHHh----cCCc---------CC--HHHHHcCCCCCHHHHHHHHhc
Confidence 34566677777765 3 45555678777653322 3442 22 678999999999999988755
No 64
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=64.26 E-value=18 Score=44.81 Aligned_cols=34 Identities=15% Similarity=0.195 Sum_probs=23.4
Q ss_pred CCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHH
Q 002604 432 LDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNR 468 (901)
Q Consensus 432 pTpeaLa~A~~eELeelIR~~Gfyn~KAk~Ik~lAr~ 468 (901)
-++.+|..+..++|..+ -||...+|.+|++..+.
T Consensus 468 ~~i~DL~~L~~~~L~~l---~gfG~Ksa~~ll~~Ie~ 501 (665)
T PRK07956 468 HDPADLFKLTAEDLLGL---EGFGEKSAQNLLDAIEK 501 (665)
T ss_pred CCHHHHHhcCHHHHhcC---cCcchHHHHHHHHHHHH
Confidence 48888888887776553 37777777776654443
No 65
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=62.96 E-value=27 Score=34.13 Aligned_cols=76 Identities=14% Similarity=0.180 Sum_probs=46.4
Q ss_pred CCCCHHHHHcCCHHHHHH--HHHhcCCcHHHHHHHHHHHHHHHHhhCCCCchhhhcCCchHHHHHHHhCCCCcHhHHHHH
Q 002604 430 DSLDYEALRCANVKEISE--AIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECV 507 (901)
Q Consensus 430 ~~pTpeaLa~A~~eELee--lIR~~Gfyn~KAk~Ik~lAr~Lve~yGglDLe~L~~VP~deaRe~LLsLPGIG~KTAd~I 507 (901)
|..|+++|+.++...+.. +.+..|.. +++|.++. .+..|..++|||+..|..+
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 455888998888877766 55555555 22332211 1556889999999999887
Q ss_pred HHHhcCCceeecchHHHHHHHHh
Q 002604 508 RLLTLHHLAFPVDTNVGRIAVRL 530 (901)
Q Consensus 508 LlfafgrpafpVDTHV~RVl~RL 530 (901)
+--++.-..=....+..++..++
T Consensus 70 ~~AGv~Tv~~LA~~~p~~L~~~l 92 (122)
T PF14229_consen 70 EHAGVDTVEELAQRNPQNLHQKL 92 (122)
T ss_pred HHhCcCcHHHHHhCCHHHHHHHH
Confidence 76665543222334444444444
No 66
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=62.84 E-value=19 Score=44.55 Aligned_cols=29 Identities=14% Similarity=0.187 Sum_probs=18.7
Q ss_pred CHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHH
Q 002604 433 DYEALRCANVKEISEAIKERGMNNMLAERMKD 464 (901)
Q Consensus 433 TpeaLa~A~~eELeelIR~~Gfyn~KAk~Ik~ 464 (901)
++.+|..+..++|.++ =||...+|.+|++
T Consensus 460 ~~~Dly~L~~~~l~~l---~g~geksa~nl~~ 488 (669)
T PRK14350 460 SEIDLYTFNFDRLINL---KGFKDKRINNLKR 488 (669)
T ss_pred CHHHHhhCCHHHHhhc---cCccHHHHHHHHH
Confidence 6777777777666553 3666666666654
No 67
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=59.85 E-value=14 Score=34.33 Aligned_cols=57 Identities=28% Similarity=0.540 Sum_probs=35.0
Q ss_pred CHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCCchhhhcCCchHHHHHHHh-CCCCcHhHHHHHHH
Q 002604 441 NVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLS-IRGLGLKSVECVRL 509 (901)
Q Consensus 441 ~~eELeelIR~~Gfyn~KAk~Ik~lAr~Lve~yGglDLe~L~~VP~deaRe~LLs-LPGIG~KTAd~ILl 509 (901)
...++...+...|+....|. +|.+.||.-.++.|++=|.. |+. ++|||-++||-|..
T Consensus 7 ~~~~~~~~L~~~gl~~~~a~-------kl~~~yg~~ai~~l~~nPY~-----L~~~i~gi~F~~aD~iA~ 64 (94)
T PF14490_consen 7 GLRELMAFLQEYGLSPKLAM-------KLYKKYGDDAIEILKENPYR-----LIEDIDGIGFKTADKIAL 64 (94)
T ss_dssp --HHHHHHHHHTT--HHHHH-------HHHHHH-TTHHHHHHH-STC-----CCB-SSSSBHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCCHHHHH-------HHHHHHhHHHHHHHHHChHH-----HHHHccCCCHHHHHHHHH
Confidence 34677777888999865554 44455676455556555554 555 89999999987743
No 68
>PF11731 Cdd1: Pathogenicity locus; InterPro: IPR021725 Cdd1 is expressed as part of the pathogenicity locus operon in several different orders of bacteria []. Many members of the family are annotated as being putative mitomycin resistance proteins but this could not be confirmed.
Probab=59.80 E-value=9 Score=36.33 Aligned_cols=27 Identities=26% Similarity=0.322 Sum_probs=22.2
Q ss_pred HHHHHHhCCCCcHhHHHHHHHHhcCCc
Q 002604 489 AKDYLLSIRGLGLKSVECVRLLTLHHL 515 (901)
Q Consensus 489 aRe~LLsLPGIG~KTAd~ILlfafgrp 515 (901)
....|..|||||+.+|.-+...++..+
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 466799999999999988877776654
No 69
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=59.74 E-value=20 Score=38.99 Aligned_cols=90 Identities=26% Similarity=0.322 Sum_probs=58.4
Q ss_pred cCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCCchhhhcCCchHHHHHHHhCCCCcHhHHHHHH-HHhcCCcee
Q 002604 439 CANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVR-LLTLHHLAF 517 (901)
Q Consensus 439 ~A~~eELeelIR~~Gfyn~KAk~Ik~lAr~Lve~yGglDLe~L~~VP~deaRe~LLsLPGIG~KTAd~IL-lfafgrpaf 517 (901)
.++..||-+++=..|-. -+..+.+|+.++.+||+ |..|...+ .++|.+++|||.--|--+. +.-+
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 34557777777667754 56788999999999987 56666655 5689999999976553332 2222
Q ss_pred ecchHHHHHHHHh---CCCCCCCCHHHHHHHHHHh
Q 002604 518 PVDTNVGRIAVRL---GWVPLQPLPESLQLHLLEL 549 (901)
Q Consensus 518 pVDTHV~RVl~RL---Glv~~~~tpekvEk~L~~l 549 (901)
..|++.+- |.+- .+|+++.+.+...
T Consensus 89 -----~~R~~~~~~~~~~~i--~sp~~~~~~l~~~ 116 (224)
T COG2003 89 -----GKRILAERLREGVVI--TSPEAVAEYLRAE 116 (224)
T ss_pred -----HHHHHHHHhccCCcc--CCHHHHHHHHHHH
Confidence 23444432 3322 4677777776543
No 70
>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=58.06 E-value=7.3 Score=35.48 Aligned_cols=42 Identities=21% Similarity=0.239 Sum_probs=30.0
Q ss_pred HHHHhCCCCcHhHHHHHHHHhcCCceeecchHHHHHHHHhCCCCC
Q 002604 491 DYLLSIRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPL 535 (901)
Q Consensus 491 e~LLsLPGIG~KTAd~ILlfafgrpafpVDTHV~RVl~RLGlv~~ 535 (901)
+.|+++||||+-||..++....+...|. +...+..-+|+.|.
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 3589999999999999998773333554 33445556688774
No 71
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=57.76 E-value=9.7 Score=32.99 Aligned_cols=21 Identities=19% Similarity=0.354 Sum_probs=17.1
Q ss_pred HHHHHhCCCCcHhHHHHHHHH
Q 002604 490 KDYLLSIRGLGLKSVECVRLL 510 (901)
Q Consensus 490 Re~LLsLPGIG~KTAd~ILlf 510 (901)
.++|.++||||++.|..|+.+
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 678999999999999999766
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=56.68 E-value=8.7 Score=40.30 Aligned_cols=22 Identities=18% Similarity=0.232 Sum_probs=19.1
Q ss_pred HHHHHHHhCCCCcHhHHHHHHH
Q 002604 488 KAKDYLLSIRGLGLKSVECVRL 509 (901)
Q Consensus 488 eaRe~LLsLPGIG~KTAd~ILl 509 (901)
++...|++++|||||+|-.||.
T Consensus 69 ~lF~~L~~V~GIGpK~Al~iL~ 90 (191)
T TIGR00084 69 ELFKELIKVNGVGPKLALAILS 90 (191)
T ss_pred HHHHHHhCCCCCCHHHHHHHHh
Confidence 5677899999999999988865
No 73
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=55.41 E-value=9.4 Score=38.68 Aligned_cols=21 Identities=19% Similarity=0.335 Sum_probs=18.9
Q ss_pred HHHHHhCCCCcHhHHHHHHHH
Q 002604 490 KDYLLSIRGLGLKSVECVRLL 510 (901)
Q Consensus 490 Re~LLsLPGIG~KTAd~ILlf 510 (901)
-++|..|||||+|.|.+|..+
T Consensus 96 ~eeL~~lpgIG~~kA~aIi~y 116 (149)
T COG1555 96 AEELQALPGIGPKKAQAIIDY 116 (149)
T ss_pred HHHHHHCCCCCHHHHHHHHHH
Confidence 567899999999999999876
No 74
>PRK08609 hypothetical protein; Provisional
Probab=55.37 E-value=32 Score=41.78 Aligned_cols=49 Identities=29% Similarity=0.443 Sum_probs=29.6
Q ss_pred cCCcHHHHHHHHHHHHHHHHhhCCC-Cchhhh-cCCchHHHHHHHhCCCCcHhHHHHH
Q 002604 452 RGMNNMLAERMKDFLNRLVREHGSI-DLEWLR-DVPPDKAKDYLLSIRGLGLKSVECV 507 (901)
Q Consensus 452 ~Gfyn~KAk~Ik~lAr~Lve~yGgl-DLe~L~-~VP~deaRe~LLsLPGIG~KTAd~I 507 (901)
-|....-|+.|.++.+ -|.+ -++.|+ ++|.. ..+|+++||||+|||..+
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 3555555555555442 1332 244554 45554 557999999999999544
No 75
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=54.91 E-value=9.9 Score=40.01 Aligned_cols=44 Identities=16% Similarity=0.187 Sum_probs=28.4
Q ss_pred HHHHHHHhCCCCcHhHHHHHHHHhcCCcee--ec-chHHHHHHHHhCC
Q 002604 488 KAKDYLLSIRGLGLKSVECVRLLTLHHLAF--PV-DTNVGRIAVRLGW 532 (901)
Q Consensus 488 eaRe~LLsLPGIG~KTAd~ILlfafgrpaf--pV-DTHV~RVl~RLGl 532 (901)
++.+.|++++|||+|+|-.||.. |+-..+ +| ...+.++..==|+
T Consensus 70 ~lF~~Li~V~GIGpK~Al~ILs~-~~~~~l~~aI~~~D~~~L~~vpGI 116 (194)
T PRK14605 70 SLFETLIDVSGIGPKLGLAMLSA-MNAEALASAIISGNAELLSTIPGI 116 (194)
T ss_pred HHHHHHhCCCCCCHHHHHHHHHh-CCHHHHHHHHHhCCHHHHHhCCCC
Confidence 56778999999999999999874 443322 33 4455553332254
No 76
>PF05559 DUF763: Protein of unknown function (DUF763); InterPro: IPR008482 This family consists of several uncharacterised bacterial and archaeal proteins of unknown function.
Probab=54.67 E-value=30 Score=39.32 Aligned_cols=29 Identities=28% Similarity=0.457 Sum_probs=22.7
Q ss_pred CchHHHHHHHhCCCCcHhHHHHHHHH---hcCCc
Q 002604 485 PPDKAKDYLLSIRGLGLKSVECVRLL---TLHHL 515 (901)
Q Consensus 485 P~deaRe~LLsLPGIG~KTAd~ILlf---afgrp 515 (901)
|.+ .++|+.++|||++|..++.+. .+|.|
T Consensus 265 p~~--feeLL~~~GvGp~TlRALaLvaelIyg~p 296 (319)
T PF05559_consen 265 PSD--FEELLLIKGVGPSTLRALALVAELIYGVP 296 (319)
T ss_pred ccC--HHHHHhcCCCCHHHHHHHHHHHHHHcCCC
Confidence 456 889999999999999887664 35543
No 77
>COG2818 Tag 3-methyladenine DNA glycosylase [DNA replication, recombination, and repair]
Probab=53.87 E-value=49 Score=35.18 Aligned_cols=47 Identities=13% Similarity=0.256 Sum_probs=35.6
Q ss_pred CCCCHHHHHcCCHHHHHHHHHhcCCcHHHH--HHHHHHHHHHH---HhhCCC
Q 002604 430 DSLDYEALRCANVKEISEAIKERGMNNMLA--ERMKDFLNRLV---REHGSI 476 (901)
Q Consensus 430 ~~pTpeaLa~A~~eELeelIR~~Gfyn~KA--k~Ik~lAr~Lv---e~yGgl 476 (901)
..++|+.+|..+.++|+.++.-.|.-|.|. +.++.=|+.++ ++||++
T Consensus 62 ~~Fd~~kVA~~~~~dverLl~d~gIIR~r~KI~A~i~NA~~~l~l~~e~Gsf 113 (188)
T COG2818 62 HGFDPEKVAAMTEEDVERLLADAGIIRNRGKIKATINNARAVLELQKEFGSF 113 (188)
T ss_pred hcCCHHHHHcCCHHHHHHHHhCcchhhhHHHHHHHHHHHHHHHHHHHHcCCH
Confidence 468999999999999999999999866544 45555555554 456663
No 78
>TIGR01259 comE comEA protein. This model describes the ComEA protein in bacteria. The com E locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. Lesions in the loci has been variously described for the appearance of competence-related pheonotypes and impairment of competence, suggesting their intimate functional role in bacterial transformation.
Probab=52.13 E-value=12 Score=36.42 Aligned_cols=21 Identities=14% Similarity=0.262 Sum_probs=19.2
Q ss_pred HHHHHhCCCCcHhHHHHHHHH
Q 002604 490 KDYLLSIRGLGLKSVECVRLL 510 (901)
Q Consensus 490 Re~LLsLPGIG~KTAd~ILlf 510 (901)
.+.|.+|||||++.|..|+.+
T Consensus 67 ~~eL~~lpGIG~~~A~~Ii~~ 87 (120)
T TIGR01259 67 LEELQALPGIGPAKAKAIIEY 87 (120)
T ss_pred HHHHhcCCCCCHHHHHHHHHH
Confidence 678999999999999999876
No 79
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=51.99 E-value=39 Score=42.16 Aligned_cols=60 Identities=22% Similarity=0.263 Sum_probs=35.8
Q ss_pred CCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCCchhhhcCCchHHHHHH--HhCCCCcHhHHHHHHH
Q 002604 432 LDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYL--LSIRGLGLKSVECVRL 509 (901)
Q Consensus 432 pTpeaLa~A~~eELeelIR~~Gfyn~KAk~Ik~lAr~Lve~yGglDLe~L~~VP~deaRe~L--LsLPGIG~KTAd~ILl 509 (901)
-++.+|..+..++|..+ -||...+|.+|++..+.-. .+|-. ..| +.|||||.++|..++.
T Consensus 485 ~~~~Dl~~L~~~~L~~l---~g~g~Ksa~~Ll~~Ie~sk------------~~~l~---r~l~ALgIpgIG~~~ak~L~~ 546 (689)
T PRK14351 485 ESLADLYDLTVADLAEL---EGWGETSAENLLAELEASR------------EPPLA---DFLVALGIPEVGPTTARNLAR 546 (689)
T ss_pred CCHHHHHHcCHHHHhcC---cCcchhHHHHHHHHHHHHc------------cCCHH---HHHHHcCCCCcCHHHHHHHHH
Confidence 37888888888776543 4777777776655443221 12222 223 2467777777776653
No 80
>PRK07945 hypothetical protein; Provisional
Probab=49.81 E-value=25 Score=39.87 Aligned_cols=61 Identities=10% Similarity=0.103 Sum_probs=38.9
Q ss_pred HHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCCchhhhcCCchHHHHHHHhCCCCcHhHHHHHHHH
Q 002604 443 KEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLL 510 (901)
Q Consensus 443 eELeelIR~~Gfyn~KAk~Ik~lAr~Lve~yGglDLe~L~~VP~deaRe~LLsLPGIG~KTAd~ILlf 510 (901)
++++.++.-.|=..-|++..+++|+.|.. .+. + .+..+.. ...|.+|||||.-||..|.-+
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 45566666667555678888888888764 121 1 1222211 115889999999999988755
No 81
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=48.96 E-value=28 Score=43.09 Aligned_cols=57 Identities=21% Similarity=0.296 Sum_probs=35.1
Q ss_pred HHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCCchhhhcCCchHHHHHHHhCCCCcHhHHHHHHHH
Q 002604 444 EISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLL 510 (901)
Q Consensus 444 ELeelIR~~Gfyn~KAk~Ik~lAr~Lve~yGglDLe~L~~VP~deaRe~LLsLPGIG~KTAd~ILlf 510 (901)
.|..+|-.+|....-... |+.|...|+. ++.|...+ .+.|.+++|||.+.|..|..|
T Consensus 506 ~l~r~l~aLGIr~VG~~~----Ak~La~~f~s--l~~l~~a~----~e~l~~i~giG~~vA~si~~f 562 (667)
T COG0272 506 PLARFLYALGIRHVGETT----AKSLARHFGT--LEALLAAS----EEELASIPGIGEVVARSIIEF 562 (667)
T ss_pred CHHHHHHHcCCchhhHHH----HHHHHHHhhh--HHHHHhcC----HHHHhhccchhHHHHHHHHHH
Confidence 344455555655433322 3333344443 66666554 557889999999999988766
No 82
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=47.57 E-value=42 Score=38.10 Aligned_cols=57 Identities=14% Similarity=0.120 Sum_probs=36.4
Q ss_pred HHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCCchhhhcCCchHHHHHHHhCCCCcHhHHHHHHHH
Q 002604 443 KEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLL 510 (901)
Q Consensus 443 eELeelIR~~Gfyn~KAk~Ik~lAr~Lve~yGglDLe~L~~VP~deaRe~LLsLPGIG~KTAd~ILlf 510 (901)
+++++++.-.|=...|+++..++++.|.. ++. + + +. .+.|.+|||||.++|+.|--+
T Consensus 11 ~~la~l~el~gen~~k~~ay~~Aa~~i~~-l~~-~------i--~~-~~~l~~lpgIG~~ia~kI~Ei 67 (334)
T smart00483 11 EILAENYEVFGENKRKCSYFRKAASVLKS-LPF-P------I--NS-MKDLKGLPGIGDKIKKKIEEI 67 (334)
T ss_pred HHHHHHHHHhcccHHHHHHHHHHHHHHHh-CCC-C------C--CC-HHHHhcCCCccHHHHHHHHHH
Confidence 34445444456544577777777777754 222 1 2 22 247899999999999988743
No 83
>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=47.22 E-value=13 Score=28.43 Aligned_cols=15 Identities=20% Similarity=0.424 Sum_probs=11.1
Q ss_pred HHhCCCCcHhHHHHH
Q 002604 493 LLSIRGLGLKSVECV 507 (901)
Q Consensus 493 LLsLPGIG~KTAd~I 507 (901)
+..++|||++|+.-+
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 84
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=46.65 E-value=27 Score=39.58 Aligned_cols=48 Identities=21% Similarity=0.433 Sum_probs=29.6
Q ss_pred CCcHHHHHHHHHHHHHHHHhhCCCC--chhhh-cCCchHHHHHHHhCCCCcHhHHHHH
Q 002604 453 GMNNMLAERMKDFLNRLVREHGSID--LEWLR-DVPPDKAKDYLLSIRGLGLKSVECV 507 (901)
Q Consensus 453 Gfyn~KAk~Ik~lAr~Lve~yGglD--Le~L~-~VP~deaRe~LLsLPGIG~KTAd~I 507 (901)
|....-|+.|.++.+ .|.+. ++.+. .+| ....+|+.+||||+|||..+
T Consensus 55 gIG~~ia~kI~Eil~-----tG~~~~~~e~l~~~~p--~~l~~l~~i~GiGpk~a~~l 105 (334)
T smart00483 55 GIGDKIKKKIEEIIE-----TGKSSKVLEILNDEVY--KSLKLFTNVFGVGPKTAAKW 105 (334)
T ss_pred CccHHHHHHHHHHHH-----hCcHHHHHHHhcCcHH--HHHHHHHccCCcCHHHHHHH
Confidence 555555666655433 25544 22232 334 34889999999999999554
No 85
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair]
Probab=46.56 E-value=66 Score=35.48 Aligned_cols=95 Identities=14% Similarity=0.083 Sum_probs=63.0
Q ss_pred CcCcHHHHHHHHHhHHhhcCCCccccCCCCchhhhhccccccchhhHHhhcccccccccccccccChHHHHHHHHhccCc
Q 002604 342 GSMLAEKTRNLGDDISVANKLSDNKLIEPNSVEQVLSAHKVYDETNPNISKSKKRKADGEKKNAIDWESLRKEVQRNSGK 421 (901)
Q Consensus 342 ~~~~~~~~~~i~~rl~~~~~~p~~~~~~~~~~~~~~~~~~~~~lLia~iLSaq~~d~~vnk~qnT~W~~L~kal~n~gLk 421 (901)
+.-+.+.+..+.+-+...-..|.+- -. ...+ ..+.+.++..=++..+|||.++ ..| |.
T Consensus 156 lA~s~EeaaryIE~~k~~ek~p~dl----i~----~~~~---~d~ls~~~~~Lt~i~~VnKtda---~~L---L~----- 213 (254)
T KOG2841|consen 156 LAWSMEEAARYIETYKEYEKKPIDL----IM----ERKD---RDLLSSLLGFLTTIPGVNKTDA---QLL---LQ----- 213 (254)
T ss_pred eeccHHHHHHHHHHHHHhhcCCchh----hh----hccc---ccHHHHHHHHHHhCCCCCcccH---HHH---HH-----
Confidence 3456788888888777774444422 11 0111 1223366677778888988522 222 22
Q ss_pred cccccCcCCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHH
Q 002604 422 QERSRDRMDSLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRL 469 (901)
Q Consensus 422 ~~r~~~~~~~pTpeaLa~A~~eELeelIR~~Gfyn~KAk~Ik~lAr~L 469 (901)
.|.+.+.|..|+.++|+.+ -|+..+||++|+++....
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 3789999999999999874 788899999999877543
No 86
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=42.66 E-value=74 Score=38.91 Aligned_cols=70 Identities=10% Similarity=0.113 Sum_probs=44.6
Q ss_pred CCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHH----------------------hhCCCCchhhhcCCchHH
Q 002604 432 LDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVR----------------------EHGSIDLEWLRDVPPDKA 489 (901)
Q Consensus 432 pTpeaLa~A~~eELeelIR~~Gfyn~KAk~Ik~lAr~Lve----------------------~yGglDLe~L~~VP~dea 489 (901)
-++.+|..+..++|.++ -||...+|++|++..+.-.. .|+ +++.|... +
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--SWQQLLSR--S-- 518 (562)
T ss_pred CCHHHHhcCCHHHHhcC---cCccHHHHHHHHHHHHHHcCCCHHHHHHHcCCccHHHHHHHHhcC--CHHHHHcC--C--
Confidence 47888888887776553 47777777777654332111 111 23444332 2
Q ss_pred HHHHHhCCCCcHhHHHHHHHH
Q 002604 490 KDYLLSIRGLGLKSVECVRLL 510 (901)
Q Consensus 490 Re~LLsLPGIG~KTAd~ILlf 510 (901)
.+.|.+++|||+++|+.|..|
T Consensus 519 ~e~l~~i~gIG~~~a~si~~~ 539 (562)
T PRK08097 519 EQQWQQLPGIGEGRARQLIAF 539 (562)
T ss_pred HHHHhcCCCchHHHHHHHHHH
Confidence 457889999999999988776
No 87
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=42.58 E-value=30 Score=39.90 Aligned_cols=59 Identities=20% Similarity=0.340 Sum_probs=39.7
Q ss_pred HHHHHHHHhcCCcH-HHHHHH-HHHHHHHHHhhCCCCchhhhcCCchHHHHHHHhCCCCcHhHHHHH
Q 002604 443 KEISEAIKERGMNN-MLAERM-KDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECV 507 (901)
Q Consensus 443 eELeelIR~~Gfyn-~KAk~I-k~lAr~Lve~yGglDLe~L~~VP~deaRe~LLsLPGIG~KTAd~I 507 (901)
+.+...+.|.||.- .|..+| +.+|+.|+++||+ |..+...+ .++|.+++|||++.|..|
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 34555566666531 122223 5788999999986 56665544 568999999999999764
No 88
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=41.31 E-value=18 Score=28.44 Aligned_cols=17 Identities=18% Similarity=0.335 Sum_probs=13.3
Q ss_pred HHhCCCCcHhHHHHHHH
Q 002604 493 LLSIRGLGLKSVECVRL 509 (901)
Q Consensus 493 LLsLPGIG~KTAd~ILl 509 (901)
+-.+||||+|||--+|.
T Consensus 18 i~Gv~giG~ktA~~ll~ 34 (36)
T smart00279 18 IPGVKGIGPKTALKLLR 34 (36)
T ss_pred CCCCCcccHHHHHHHHH
Confidence 34689999999987653
No 89
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this
Probab=39.08 E-value=55 Score=36.66 Aligned_cols=16 Identities=31% Similarity=0.455 Sum_probs=8.9
Q ss_pred HHHHHhCCCCcHhHHH
Q 002604 490 KDYLLSIRGLGLKSVE 505 (901)
Q Consensus 490 Re~LLsLPGIG~KTAd 505 (901)
...|++++|||+|||.
T Consensus 84 l~~l~~i~GiGpk~a~ 99 (307)
T cd00141 84 LLLLLRVPGVGPKTAR 99 (307)
T ss_pred HHHHHcCCCCCHHHHH
Confidence 5555555555555553
No 90
>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region. Members of the subfamily recognized by this model include competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model.
Probab=38.69 E-value=30 Score=30.07 Aligned_cols=21 Identities=29% Similarity=0.479 Sum_probs=18.3
Q ss_pred HHHHHh-CCCCcHhHHHHHHHH
Q 002604 490 KDYLLS-IRGLGLKSVECVRLL 510 (901)
Q Consensus 490 Re~LLs-LPGIG~KTAd~ILlf 510 (901)
.+.|.. +||||.++|..|+.+
T Consensus 15 ~~~L~~~ipgig~~~a~~Il~~ 36 (69)
T TIGR00426 15 AEELQRAMNGVGLKKAEAIVSY 36 (69)
T ss_pred HHHHHhHCCCCCHHHHHHHHHH
Confidence 457888 999999999999876
No 91
>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=38.42 E-value=40 Score=37.79 Aligned_cols=57 Identities=16% Similarity=0.215 Sum_probs=36.1
Q ss_pred HHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCCchhhhcCCchHHHHHHHhCCCCcHhHHHHHHHH
Q 002604 443 KEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLL 510 (901)
Q Consensus 443 eELeelIR~~Gfyn~KAk~Ik~lAr~Lve~yGglDLe~L~~VP~deaRe~LLsLPGIG~KTAd~ILlf 510 (901)
++|+.++.-.|=..-|++....+|..|.. ... |-+. .+++.+|||||.++|+.|--+
T Consensus 8 ~~ia~~~e~~~~~~~r~~aY~~Aa~~l~~-l~~---------~i~~-~~~~~~ipgiG~~ia~kI~E~ 64 (307)
T cd00141 8 EELADLLELLGGNPFRVRAYRKAARALES-LPE---------PIES-LEEAKKLPGIGKKIAEKIEEI 64 (307)
T ss_pred HHHHHHHHhccCCcchHHHHHHHHHHHHh-CCc---------ccCC-HHHhcCCCCccHHHHHHHHHH
Confidence 34555555454333467667777777764 222 1222 346799999999999998754
No 92
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=37.41 E-value=24 Score=37.06 Aligned_cols=23 Identities=13% Similarity=0.228 Sum_probs=19.7
Q ss_pred HHHHHHHhCCCCcHhHHHHHHHH
Q 002604 488 KAKDYLLSIRGLGLKSVECVRLL 510 (901)
Q Consensus 488 eaRe~LLsLPGIG~KTAd~ILlf 510 (901)
++.+.|+++.|||||+|=.||..
T Consensus 70 ~lF~~LisV~GIGpK~Al~iLs~ 92 (186)
T PRK14600 70 DCLRMLVKVSGVNYKTAMSILSK 92 (186)
T ss_pred HHHHHHhCcCCcCHHHHHHHHcc
Confidence 45778999999999999998873
No 93
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=37.35 E-value=26 Score=37.26 Aligned_cols=23 Identities=17% Similarity=0.224 Sum_probs=19.6
Q ss_pred HHHHHHHhCCCCcHhHHHHHHHH
Q 002604 488 KAKDYLLSIRGLGLKSVECVRLL 510 (901)
Q Consensus 488 eaRe~LLsLPGIG~KTAd~ILlf 510 (901)
++.+.|+++.|||||+|=.||..
T Consensus 69 ~lF~~LisVsGIGPK~ALaILs~ 91 (196)
T PRK13901 69 EVFEELIGVDGIGPRAALRVLSG 91 (196)
T ss_pred HHHHHHhCcCCcCHHHHHHHHcC
Confidence 46778999999999999888853
No 94
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=36.30 E-value=27 Score=36.62 Aligned_cols=23 Identities=26% Similarity=0.377 Sum_probs=19.6
Q ss_pred HHHHHHHhCCCCcHhHHHHHHHH
Q 002604 488 KAKDYLLSIRGLGLKSVECVRLL 510 (901)
Q Consensus 488 eaRe~LLsLPGIG~KTAd~ILlf 510 (901)
++.+.|+++.|||||+|=.||..
T Consensus 70 ~lF~~Li~VsGIGpK~Al~ILs~ 92 (183)
T PRK14601 70 KMFEMLLKVNGIGANTAMAVCSS 92 (183)
T ss_pred HHHHHHhccCCccHHHHHHHHcC
Confidence 56778999999999999888853
No 95
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=35.55 E-value=29 Score=36.52 Aligned_cols=23 Identities=17% Similarity=0.033 Sum_probs=19.7
Q ss_pred hHHHHHHHhCCCCcHhHHHHHHH
Q 002604 487 DKAKDYLLSIRGLGLKSVECVRL 509 (901)
Q Consensus 487 deaRe~LLsLPGIG~KTAd~ILl 509 (901)
.++.+.|+++.|||||+|=.||.
T Consensus 69 r~lF~~Li~V~GIGpK~AL~iLs 91 (188)
T PRK14606 69 KELFLSLTKVSRLGPKTALKIIS 91 (188)
T ss_pred HHHHHHHhccCCccHHHHHHHHc
Confidence 35677899999999999988885
No 96
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=35.33 E-value=29 Score=36.76 Aligned_cols=22 Identities=23% Similarity=0.301 Sum_probs=19.5
Q ss_pred HHHHHHHhCCCCcHhHHHHHHH
Q 002604 488 KAKDYLLSIRGLGLKSVECVRL 509 (901)
Q Consensus 488 eaRe~LLsLPGIG~KTAd~ILl 509 (901)
++.+.|+++.|||||+|=.||.
T Consensus 69 ~lF~~L~~V~GIGpK~AL~iLs 90 (197)
T PRK14603 69 ELFELLLGVSGVGPKLALALLS 90 (197)
T ss_pred HHHHHHhCcCCcCHHHHHHHHc
Confidence 4677899999999999998887
No 97
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=35.05 E-value=30 Score=36.77 Aligned_cols=23 Identities=22% Similarity=0.183 Sum_probs=19.9
Q ss_pred HHHHHHHhCCCCcHhHHHHHHHH
Q 002604 488 KAKDYLLSIRGLGLKSVECVRLL 510 (901)
Q Consensus 488 eaRe~LLsLPGIG~KTAd~ILlf 510 (901)
++.+.|+++.|||||+|=.||..
T Consensus 71 ~lF~~Li~V~GIGpK~Al~iLs~ 93 (203)
T PRK14602 71 QTFIVLISISKVGAKTALAILSQ 93 (203)
T ss_pred HHHHHHhCCCCcCHHHHHHHHhh
Confidence 46778999999999999888874
No 98
>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=34.38 E-value=19 Score=32.29 Aligned_cols=19 Identities=16% Similarity=0.165 Sum_probs=15.2
Q ss_pred HHHhCCCCcHhHHHHHHHH
Q 002604 492 YLLSIRGLGLKSVECVRLL 510 (901)
Q Consensus 492 ~LLsLPGIG~KTAd~ILlf 510 (901)
.+-.+||||+|||.-++.-
T Consensus 23 ~i~gv~giG~k~A~~ll~~ 41 (75)
T cd00080 23 NIPGVPGIGPKTALKLLKE 41 (75)
T ss_pred cCCCCCcccHHHHHHHHHH
Confidence 5667999999999777643
No 99
>PF11372 DUF3173: Domain of unknown function (DUF3173); InterPro: IPR021512 This family of proteins with unknown function appears to be restricted to Firmicutes.
Probab=33.79 E-value=1e+02 Score=27.32 Aligned_cols=43 Identities=21% Similarity=0.274 Sum_probs=30.3
Q ss_pred cCCcHHHHHHHHHHHHHHHHhhCCCC---chhhhcCCchHHHHHHHhC
Q 002604 452 RGMNNMLAERMKDFLNRLVREHGSID---LEWLRDVPPDKAKDYLLSI 496 (901)
Q Consensus 452 ~Gfyn~KAk~Ik~lAr~Lve~yGglD---Le~L~~VP~deaRe~LLsL 496 (901)
+||....|+.|+.-|+.++-.. |++ =..|..+|.. +.++|+.+
T Consensus 12 lGf~~~tA~~IIrqAK~~lV~~-G~~~Y~nkRlg~VP~~-~VEeiLG~ 57 (59)
T PF11372_consen 12 LGFSESTARDIIRQAKALLVQK-GFSFYNNKRLGRVPAS-AVEEILGI 57 (59)
T ss_pred cCCCHHHHHHHHHHHHHHHHHc-CCCcccCCccCcccHH-HHHHHHCC
Confidence 7999999999999998887542 332 2356667765 56667654
No 100
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=33.67 E-value=30 Score=36.65 Aligned_cols=23 Identities=17% Similarity=0.258 Sum_probs=20.0
Q ss_pred HHHHHHHhCCCCcHhHHHHHHHH
Q 002604 488 KAKDYLLSIRGLGLKSVECVRLL 510 (901)
Q Consensus 488 eaRe~LLsLPGIG~KTAd~ILlf 510 (901)
++.+.|+++.|||||+|=.||..
T Consensus 70 ~lF~~Li~V~GIGpK~Al~iLs~ 92 (195)
T PRK14604 70 QLFELLIGVSGVGPKAALNLLSS 92 (195)
T ss_pred HHHHHHhCcCCcCHHHHHHHHcC
Confidence 46778999999999999998874
No 101
>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=33.40 E-value=38 Score=28.82 Aligned_cols=18 Identities=22% Similarity=0.274 Sum_probs=12.8
Q ss_pred HHHHhCCCCcHhHHHHHH
Q 002604 491 DYLLSIRGLGLKSVECVR 508 (901)
Q Consensus 491 e~LLsLPGIG~KTAd~IL 508 (901)
+.|..+.|||+.||.-..
T Consensus 2 ~~f~~I~GVG~~tA~~w~ 19 (52)
T PF10391_consen 2 KLFTGIWGVGPKTARKWY 19 (52)
T ss_dssp HHHHTSTT--HHHHHHHH
T ss_pred cchhhcccccHHHHHHHH
Confidence 468899999999996553
No 102
>PF03118 RNA_pol_A_CTD: Bacterial RNA polymerase, alpha chain C terminal domain; InterPro: IPR011260 The core of the bacterial RNA polymerase (RNAP) consists of four subunits, two alpha, a beta and a beta', which are conserved from bacteria to mammals. The alpha subunit (RpoA) initiates RNAP assembly by dimerising to form a platform on which the beta subunits can interact. The alpha subunit consists of a N-terminal domain (NTD) and a C-terminal domain (CTD), connected by a short linker. The NTD is essential for RNAP assembly, while the CTD is necessary for transcription regulation, interacting with transcription factors and promoter upstream elements. In Escherichia coli, the catabolite activator protein (CAP or CRP) was shown to exert its effect through its interactions with the CTD, where CAP binding to CTD promotes RNAP binding to promoter DNA, thereby stimulating transcription initiation at class I CAP-dependent promoters. At class II CAP-dependent promoters, the interaction of CAP with CTD is one of multiple interactions involved in activation []. The CTD has a compact structure of four helices and two long arms enclosing its hydrophobic core, making its folding topology distinct from most other binding proteins. The upstream promoter element-binding site is formed from helices 1 and 4 [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3N97_B 1XS9_D 3K4G_A 3N4M_B 1COO_A 1LB2_E 3IYD_A 1Z3E_B 3GFK_B 3IHQ_B ....
Probab=31.65 E-value=62 Score=28.55 Aligned_cols=28 Identities=29% Similarity=0.406 Sum_probs=21.5
Q ss_pred CchhhhcCCchHHHHHHHhCCCCcHhHHHHHH
Q 002604 477 DLEWLRDVPPDKAKDYLLSIRGLGLKSVECVR 508 (901)
Q Consensus 477 DLe~L~~VP~deaRe~LLsLPGIG~KTAd~IL 508 (901)
.+..|..++ .+.|++++|+|+++.+-|.
T Consensus 34 tv~dL~~~s----~~~L~~i~n~G~ksl~EI~ 61 (66)
T PF03118_consen 34 TVGDLVKYS----EEDLLKIKNFGKKSLEEIK 61 (66)
T ss_dssp BHHHHHCS-----HHHHHTSTTSHHHHHHHHH
T ss_pred CHHHHHhCC----HHHHHhCCCCCHhHHHHHH
Confidence 556666665 4589999999999998764
No 103
>PRK00254 ski2-like helicase; Provisional
Probab=31.37 E-value=87 Score=38.87 Aligned_cols=59 Identities=12% Similarity=0.092 Sum_probs=33.1
Q ss_pred HHHHHHHHHHHhhCCCCchhhhcCCchHHHHHHHhCCCCcHhHHHHHHHHhcCCceeecchHHHHHHHHhCC
Q 002604 461 RMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGW 532 (901)
Q Consensus 461 ~Ik~lAr~Lve~yGglDLe~L~~VP~deaRe~LLsLPGIG~KTAd~ILlfafgrpafpVDTHV~RVl~RLGl 532 (901)
.|..++++|.. | ++.+ --.|..|||||++.|..++..+|+-..=..+.....+..=.|+
T Consensus 628 ~l~~l~~rl~~---g--------~~~~--~~~L~~ipgig~~~~~~l~~~g~~s~~~i~~a~~~el~~~~gi 686 (720)
T PRK00254 628 YLETLHLRVKH---G--------VREE--LLELMRLPMIGRKRARALYNAGFRSIEDIVNAKPSELLKVEGI 686 (720)
T ss_pred HHHHHHHHHHc---C--------CCHH--HhhhhcCCCCCHHHHHHHHHccCCCHHHHHhCCHHHHhcCCCC
Confidence 44566666652 2 3444 2346778888888888877777775533333334444333244
No 104
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=30.70 E-value=79 Score=36.21 Aligned_cols=60 Identities=18% Similarity=0.250 Sum_probs=36.6
Q ss_pred HHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCCchhhhcCCchHHHHHHHhCCCCcHhHHHHHHHH
Q 002604 443 KEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLL 510 (901)
Q Consensus 443 eELeelIR~~Gfyn~KAk~Ik~lAr~Lve~yGglDLe~L~~VP~deaRe~LLsLPGIG~KTAd~ILlf 510 (901)
++++.++.-.|=..-|++.-+.+|+.|-.. ..|++.+.+ +..|..|||||+.+|+.|.-|
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 455555555554444666666667776542 223332222 224889999999999998765
No 105
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=30.26 E-value=40 Score=33.98 Aligned_cols=20 Identities=5% Similarity=-0.122 Sum_probs=17.3
Q ss_pred HHHHHhCCCCcHhHHHHHHH
Q 002604 490 KDYLLSIRGLGLKSVECVRL 509 (901)
Q Consensus 490 Re~LLsLPGIG~KTAd~ILl 509 (901)
.++|.+|||||+..|..|..
T Consensus 60 ~~el~~lpGigP~~A~~IV~ 79 (132)
T PRK02515 60 VRAFRQFPGMYPTLAGKIVK 79 (132)
T ss_pred HHHHHHCCCCCHHHHHHHHH
Confidence 45689999999999999973
No 106
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=29.55 E-value=38 Score=36.20 Aligned_cols=43 Identities=16% Similarity=0.180 Sum_probs=27.1
Q ss_pred HHHHHHHhCCCCcHhHHHHHHHH-hcCCceeecchHHHHHHHHh
Q 002604 488 KAKDYLLSIRGLGLKSVECVRLL-TLHHLAFPVDTNVGRIAVRL 530 (901)
Q Consensus 488 eaRe~LLsLPGIG~KTAd~ILlf-afgrpafpVDTHV~RVl~RL 530 (901)
++...|+++-|||+|+|=+||.. ....-+-++++-=...+.|+
T Consensus 70 ~lF~~LisVnGIGpK~ALaiLs~~~~~~l~~aI~~~d~~~L~k~ 113 (201)
T COG0632 70 ELFRLLISVNGIGPKLALAILSNLDPEELAQAIANEDVKALSKI 113 (201)
T ss_pred HHHHHHHccCCccHHHHHHHHcCCCHHHHHHHHHhcChHhhhcC
Confidence 56778999999999999888865 33333333333323334444
No 107
>PRK07758 hypothetical protein; Provisional
Probab=28.57 E-value=84 Score=30.18 Aligned_cols=28 Identities=25% Similarity=0.412 Sum_probs=21.1
Q ss_pred CchhhhcCCchHHHHHHHhCCCCcHhHHHHHH
Q 002604 477 DLEWLRDVPPDKAKDYLLSIRGLGLKSVECVR 508 (901)
Q Consensus 477 DLe~L~~VP~deaRe~LLsLPGIG~KTAd~IL 508 (901)
.++.|..+. .++|++|+|+|+|+.+-|.
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 455555554 5589999999999998764
No 108
>PF00416 Ribosomal_S13: Ribosomal protein S13/S18; InterPro: IPR001892 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S13 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S13 is known to be involved in binding fMet-tRNA and, hence, in the initiation of translation. It is a basic protein of 115 to 177 amino-acid residues that contains thee helices and a beta-hairpin in the core of the protein, forming a helix-two turns-helix (H2TH) motif, and a non-globular C-terminal extension. This family of ribosomal proteins is present in prokaryotes, eukaryotes and archaea [, ].; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3BBN_M 2QBB_M 3I1M_M 3OFP_M 3OFX_M 3OFO_M 1VS5_M 3OAQ_M 2QAL_M 3J18_M ....
Probab=28.29 E-value=52 Score=31.46 Aligned_cols=22 Identities=18% Similarity=0.151 Sum_probs=18.0
Q ss_pred HHHHHHHhCCCCcHhHHHHHHH
Q 002604 488 KAKDYLLSIRGLGLKSVECVRL 509 (901)
Q Consensus 488 eaRe~LLsLPGIG~KTAd~ILl 509 (901)
.+.-.|.++.|||+++|..|+.
T Consensus 12 ~i~~aLt~IyGIG~~~A~~Ic~ 33 (107)
T PF00416_consen 12 PIYIALTKIYGIGRRKAKQICK 33 (107)
T ss_dssp BHHHHHTTSTTBCHHHHHHHHH
T ss_pred chHhHHhhhhccCHHHHHHHHH
Confidence 3567899999999999977654
No 109
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=25.36 E-value=37 Score=37.08 Aligned_cols=23 Identities=26% Similarity=0.342 Sum_probs=19.8
Q ss_pred HHHhCCCCcHhHHHHHHHHhcCC
Q 002604 492 YLLSIRGLGLKSVECVRLLTLHH 514 (901)
Q Consensus 492 ~LLsLPGIG~KTAd~ILlfafgr 514 (901)
.|..|||||+++|..++..+|+-
T Consensus 4 ~L~~IpGIG~krakkLl~~GF~S 26 (232)
T PRK12766 4 ELEDISGVGPSKAEALREAGFES 26 (232)
T ss_pred ccccCCCcCHHHHHHHHHcCCCC
Confidence 57889999999999999887774
No 110
>KOG0028 consensus Ca2+-binding protein (centrin/caltractin), EF-Hand superfamily protein [Cytoskeleton; Cell cycle control, cell division, chromosome partitioning]
Probab=24.29 E-value=2.1e+02 Score=30.15 Aligned_cols=98 Identities=21% Similarity=0.167 Sum_probs=52.7
Q ss_pred HHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCCchhhhcCCchHHHHHHHhCCCCcHhHHH----HHHHHhc
Q 002604 437 LRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVE----CVRLLTL 512 (901)
Q Consensus 437 La~A~~eELeelIR~~Gfyn~KAk~Ik~lAr~Lve~yGglDLe~L~~VP~deaRe~LLsLPGIG~KTAd----~ILlfaf 512 (901)
=-.++.++|.-+++..||--.|....+-++..=.+--|.|+++.+. .-....=|.+. |-+ ++.++-+
T Consensus 47 ~g~iD~~EL~vAmralGFE~~k~ei~kll~d~dk~~~g~i~fe~f~--------~~mt~k~~e~d-t~eEi~~afrl~D~ 117 (172)
T KOG0028|consen 47 AGKIDVEELKVAMRALGFEPKKEEILKLLADVDKEGSGKITFEDFR--------RVMTVKLGERD-TKEEIKKAFRLFDD 117 (172)
T ss_pred CCcccHHHHHHHHHHcCCCcchHHHHHHHHhhhhccCceechHHHH--------HHHHHHHhccC-cHHHHHHHHHcccc
Confidence 3456788998889999999766654443333322222444444333 22222233333 222 2333333
Q ss_pred CCceeecchHHHHHHHHhCCCCCCCCHHHHHHHH
Q 002604 513 HHLAFPVDTNVGRIAVRLGWVPLQPLPESLQLHL 546 (901)
Q Consensus 513 grpafpVDTHV~RVl~RLGlv~~~~tpekvEk~L 546 (901)
....-+-=.+..||+.+||=. -+-++++.-+
T Consensus 118 D~~Gkis~~~lkrvakeLgen---ltD~El~eMI 148 (172)
T KOG0028|consen 118 DKTGKISQRNLKRVAKELGEN---LTDEELMEMI 148 (172)
T ss_pred cCCCCcCHHHHHHHHHHhCcc---ccHHHHHHHH
Confidence 344444557899999999853 2344444433
No 111
>PRK08609 hypothetical protein; Provisional
Probab=23.40 E-value=1.3e+02 Score=36.76 Aligned_cols=57 Identities=14% Similarity=0.272 Sum_probs=36.6
Q ss_pred HHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCCchhhhcCCchHHHHHHHhCCCCcHhHHHHHHHH
Q 002604 443 KEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLL 510 (901)
Q Consensus 443 eELeelIR~~Gfyn~KAk~Ik~lAr~Lve~yGglDLe~L~~VP~deaRe~LLsLPGIG~KTAd~ILlf 510 (901)
++++.++.-.|=..-|++.-.++|+.|... .. + + .+ ...|.+|||||..+|..|--+
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-S------L--SE-IDDFTKLKGIGKGTAEVIQEY 67 (570)
T ss_pred HHHHHHHHhcCCCcHHHHHHHHHHHHHHhC-ch-h------h--hh-hhhhccCCCcCHHHHHHHHHH
Confidence 455555555564335677777777777642 21 1 1 11 246899999999999988754
No 112
>PF13592 HTH_33: Winged helix-turn helix
Probab=23.12 E-value=1.1e+02 Score=26.25 Aligned_cols=35 Identities=17% Similarity=0.157 Sum_probs=22.8
Q ss_pred cHhHHHHHHHHh---cCCceeecchHHHHHHHHhCCCCCC
Q 002604 500 GLKSVECVRLLT---LHHLAFPVDTNVGRIAVRLGWVPLQ 536 (901)
Q Consensus 500 G~KTAd~ILlfa---fgrpafpVDTHV~RVl~RLGlv~~~ 536 (901)
|.||+.-|..+. ||... -..+|.|+|.|+||....
T Consensus 3 ~~wt~~~i~~~I~~~fgv~y--s~~~v~~lL~r~G~s~~k 40 (60)
T PF13592_consen 3 GRWTLKEIAAYIEEEFGVKY--SPSGVYRLLKRLGFSYQK 40 (60)
T ss_pred CcccHHHHHHHHHHHHCCEE--cHHHHHHHHHHcCCcccc
Confidence 445555555443 44332 568999999999997643
No 113
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=22.91 E-value=1.5e+02 Score=32.56 Aligned_cols=30 Identities=17% Similarity=0.229 Sum_probs=23.5
Q ss_pred CchhhhcCCchHHHHHHHhCCCCcHhHHHHHHHH
Q 002604 477 DLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLL 510 (901)
Q Consensus 477 DLe~L~~VP~deaRe~LLsLPGIG~KTAd~ILlf 510 (901)
+++.|..-+ .++|.+++|||.++|..|..+
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 355555443 568999999999999999876
No 114
>PRK14469 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=22.01 E-value=1.4e+02 Score=33.97 Aligned_cols=54 Identities=13% Similarity=0.289 Sum_probs=42.2
Q ss_pred HHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCCchhhhcCCchHHHHHHHh
Q 002604 437 LRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLS 495 (901)
Q Consensus 437 La~A~~eELeelIR~~Gfyn~KAk~Ik~lAr~Lve~yGglDLe~L~~VP~deaRe~LLs 495 (901)
|..++.++|++++...|+...+|+.|. +|+-.+ +..|++.+.++|.+ +|+.|..
T Consensus 4 ~~~~~~~~~~~~~~~~g~~~~r~~qi~---~~~~~~-~~~~~~~~~~~~~~-~r~~l~~ 57 (343)
T PRK14469 4 ILDLSYEELVSEITELGLEKYRADQIL---DWIYKK-KVFNFDEMTNLSKD-HRALLSE 57 (343)
T ss_pred cccCCHHHHHHHHHHcCCCchHHHHHH---HHHHhc-CCCCHHHhccccHH-HHHHHhh
Confidence 567889999999999999877777665 577664 44588999999876 6777765
No 115
>PRK01172 ski2-like helicase; Provisional
Probab=21.64 E-value=2e+02 Score=35.44 Aligned_cols=43 Identities=9% Similarity=0.110 Sum_probs=37.3
Q ss_pred cCCCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhh
Q 002604 428 RMDSLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREH 473 (901)
Q Consensus 428 ~~~~pTpeaLa~A~~eELeelIR~~Gfyn~KAk~Ik~lAr~Lve~y 473 (901)
..|+-|+.+|+.++.+++.++ .|+...+|+.|++-|+.+++-|
T Consensus 630 ~~g~~~~~di~~~~~~~~~~i---~~~~~~~~~~i~~~~~~~~~~~ 672 (674)
T PRK01172 630 DAGFKTVDDIARSSPERIKKI---YGFSDTLANAIVNRAMKISSMY 672 (674)
T ss_pred HcCCCCHHHHHhCCHHHHHHH---hccCHHHHHHHHHHHHHHHHHh
Confidence 356779999999999999876 5899999999999999998754
No 116
>COG4277 Predicted DNA-binding protein with the Helix-hairpin-helix motif [General function prediction only]
Probab=21.60 E-value=61 Score=37.02 Aligned_cols=21 Identities=29% Similarity=0.474 Sum_probs=18.5
Q ss_pred HHHHHhCCCCcHhHHHHHHHH
Q 002604 490 KDYLLSIRGLGLKSVECVRLL 510 (901)
Q Consensus 490 Re~LLsLPGIG~KTAd~ILlf 510 (901)
+++|+.+||||.|+|.-|++.
T Consensus 329 ~~~llRVPGiG~ksa~rIv~~ 349 (404)
T COG4277 329 YKELLRVPGIGVKSARRIVMT 349 (404)
T ss_pred HHHhcccCCCChHHHHHHHHH
Confidence 789999999999999887653
No 117
>KOG0400 consensus 40S ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=21.09 E-value=1.1e+02 Score=31.14 Aligned_cols=65 Identities=22% Similarity=0.397 Sum_probs=47.0
Q ss_pred hhhhcCCchHHHHHHHhC--CCCcHhHHHHHHHHhcCC--ceeecchHHHHHHHHhCCCCCCCCHHHHHHHH
Q 002604 479 EWLRDVPPDKAKDYLLSI--RGLGLKSVECVRLLTLHH--LAFPVDTNVGRIAVRLGWVPLQPLPESLQLHL 546 (901)
Q Consensus 479 e~L~~VP~deaRe~LLsL--PGIG~KTAd~ILlfafgr--pafpVDTHV~RVl~RLGlv~~~~tpekvEk~L 546 (901)
.||. +..|+..+.+.++ +|+-+--..++|.-+.|. -.++...-+.||+.+-|++|. -|+.++..+
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 3553 4445677777765 888888888888766554 478889999999999999984 566554433
No 118
>PF00730 HhH-GPD: HhH-GPD superfamily base excision DNA repair protein This entry corresponds to Endonuclease III This entry corresponds to Alkylbase DNA glycosidase; InterPro: IPR003265 Endonuclease III (4.2.99.18 from EC) is a DNA repair enzyme which removes a number of damaged pyrimidines from DNA via its glycosylase activity and also cleaves the phosphodiester backbone at apurinic / apyrimidinic sites via a beta-elimination mechanism [, ]. The structurally related DNA glycosylase MutY recognises and excises the mutational intermediate 8-oxoguanine-adenine mispair []. The 3-D structures of Escherichia coli endonuclease III [] and catalytic domain of MutY [] have been determined. The structures contain two all-alpha domains: a sequence-continuous, six-helix domain (residues 22-132) and a Greek-key, four-helix domain formed by one N-terminal and three C-terminal helices (residues 1-21 and 133-211) together with the [Fe4S4] cluster. The cluster is bound entirely within the C-terminal loop by four cysteine residues with a ligation pattern Cys-(Xaa)6-Cys-(Xaa)2-Cys-(Xaa)5-Cys which is distinct from all other known Fe4S4 proteins. This structural motif is referred to as a [Fe4S4] cluster loop (FCL) []. Two DNA-binding motifs have been proposed, one at either end of the interdomain groove: the helix-hairpin-helix (HhH) and FCL motifs (see IPR003651 from INTERPRO). The primary role of the iron-sulphur cluster appears to involve positioning conserved basic residues for interaction with the DNA phosphate backbone by forming the loop of the FCL motif [, ]. The HhH-GPD domain gets its name from its hallmark helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate. This domain is found in a diverse range of structurally related DNA repair proteins that include: endonuclease III, 4.2.99.18 from EC and DNA glycosylase MutY, an A/G-specific adenine glycosylase. Both of these enzymes have a C-terminal iron-sulphur cluster loop (FCL). The methyl-CPG binding protein (MBD4) also contain a related domain that is a thymine DNA glycosylase. The family also includes DNA-3-methyladenine glycosylase II 3.2.2.21 from EC, 8-oxoguanine DNA glycosylases and other members of the AlkA family.; GO: 0006284 base-excision repair; PDB: 3F0Z_A 3I0X_A 3F10_A 3I0W_A 3S6I_D 3N5N_Y 1PU7_A 1PU8_B 1PU6_B 1NGN_A ....
Probab=20.64 E-value=1.6e+02 Score=27.22 Aligned_cols=54 Identities=15% Similarity=0.225 Sum_probs=39.7
Q ss_pred HHHHHHHHHHHHHHHhhCCCCchhhhcCCchHHHHHHHhCCCCcHhHHHHHHHHh
Q 002604 457 MLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLLT 511 (901)
Q Consensus 457 ~KAk~Ik~lAr~Lve~yGglDLe~L~~VP~deaRe~LLsLPGIG~KTAd~ILlfa 511 (901)
.+.+....+...|.+.||..+.+.|...+.+++++ ++.--|.+..=|..|...+
T Consensus 9 ~s~~~a~~~~~~l~~~~g~pt~~~l~~~~~~el~~-~i~~~G~~~~ka~~i~~~a 62 (108)
T PF00730_consen 9 TSIKAARKIYRRLFERYGFPTPEALAEASEEELRE-LIRPLGFSRRKAKYIIELA 62 (108)
T ss_dssp S-HHHHHHHHHHHHHHHSCSSHHHHHCSHHHHHHH-HHTTSTSHHHHHHHHHHHH
T ss_pred CcHHHHHHHHHHHHHHhcCCCHHHHHhCCHHHHHH-HhhccCCCHHHHHHHHHHH
Confidence 45677778888999999877999999988776554 4444788877777776553
No 119
>TIGR01954 nusA_Cterm_rpt transcription termination factor NusA, C-terminal duplication. NusA is a bacterial transcription termination factor. It is named for its interaction with phage lambda protein N, as part of the N utilization substance. Some members of the NusA family have a long C-terminal extension. This model represents an acidic 50-residue region found in two copies toward the C-terminus of most Proteobacterial NusA proteins, spaced about 26 residues apart. Analogous C-terminal extensions in some other bacterial lineages lack apparent homology but appear similarly acidic.
Probab=20.52 E-value=2e+02 Score=22.95 Aligned_cols=36 Identities=14% Similarity=0.179 Sum_probs=30.2
Q ss_pred CCCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHH
Q 002604 430 DSLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNR 468 (901)
Q Consensus 430 ~~pTpeaLa~A~~eELeelIR~~Gfyn~KAk~Ik~lAr~ 468 (901)
|+-+.++|+.++.++|... .|+...++..|+..++.
T Consensus 13 G~~s~e~la~~~~~eL~~i---~g~~~e~a~~ii~~a~~ 48 (50)
T TIGR01954 13 GFTTVEDLAYVPIDELLSI---EGFDEETAKELINRARN 48 (50)
T ss_pred CCCCHHHHHccCHHHHhcC---CCCCHHHHHHHHHHHHH
Confidence 5779999999999999773 67888889888877764
No 120
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=20.51 E-value=1.3e+02 Score=37.10 Aligned_cols=13 Identities=38% Similarity=0.514 Sum_probs=7.9
Q ss_pred hhcCCccccccCC
Q 002604 100 LQSNGGIRSCSGS 112 (901)
Q Consensus 100 ~q~~~~irs~sgs 112 (901)
++..=.+|+|+.+
T Consensus 143 l~~~f~lr~c~~~ 155 (598)
T PRK00558 143 LQKLFPLRTCEDS 155 (598)
T ss_pred HHHhCCCCCCCCc
Confidence 3344478888654
No 121
>PRK13280 N-glycosylase/DNA lyase; Provisional
Probab=20.45 E-value=3.6e+02 Score=30.36 Aligned_cols=134 Identities=14% Similarity=0.099 Sum_probs=74.0
Q ss_pred HHHHHHHHhc----CCcHHHHHHHHHHHHHHHHhhCCCCchhhhc--CCchHHHHHHHhCCCCc--Hh-------HHHHH
Q 002604 443 KEISEAIKER----GMNNMLAERMKDFLNRLVREHGSIDLEWLRD--VPPDKAKDYLLSIRGLG--LK-------SVECV 507 (901)
Q Consensus 443 eELeelIR~~----Gfyn~KAk~Ik~lAr~Lve~yGglDLe~L~~--VP~deaRe~LLsLPGIG--~K-------TAd~I 507 (901)
+++...+... -+..+|-++|..++..+-+ +.+..+.. ..-+++++.|..+=|-- .| .+...
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 3555556554 2345688888887665432 22222221 12244566666554432 23 33333
Q ss_pred HHHhcCC--c-----eeecchHHHHHHHHhCCCCCCCCHHHHHHHHHHhcCchHHHHHhhhhhhhcCChhhHHHHHHHHH
Q 002604 508 RLLTLHH--L-----AFPVDTNVGRIAVRLGWVPLQPLPESLQLHLLELYPVLESIQKYLWPRLCKLDQRTLYELHYQLI 580 (901)
Q Consensus 508 Llfafgr--p-----afpVDTHV~RVl~RLGlv~~~~tpekvEk~L~~llP~~e~Iqk~lW~~l~~ld~e~~~efH~~LI 580 (901)
...+++. | -||||.-|..+....|++.+..........+.. ......|..++..+.--+..+...||
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 3334443 3 489999999999999999863221111111111 11235688776666556677788888
Q ss_pred HHhHhh
Q 002604 581 TFGKVF 586 (901)
Q Consensus 581 ~fGR~I 586 (901)
..|+..
T Consensus 237 ~~~g~~ 242 (269)
T PRK13280 237 LVLGAL 242 (269)
T ss_pred hhcCCc
Confidence 777654
No 122
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=20.42 E-value=1.2e+02 Score=33.71 Aligned_cols=17 Identities=0% Similarity=-0.083 Sum_probs=12.3
Q ss_pred HHHHHHHhHHhhcCCCc
Q 002604 348 KTRNLGDDISVANKLSD 364 (901)
Q Consensus 348 ~~~~i~~rl~~~~~~p~ 364 (901)
+..+=..||+..|+.|.
T Consensus 86 RlfeQ~~rL~~~y~rpv 102 (254)
T COG1948 86 RLFEQAKRLKKSYERPV 102 (254)
T ss_pred hHHHHHHHHHhcCCccE
Confidence 44455578888888877
No 123
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=20.24 E-value=3.9e+02 Score=26.11 Aligned_cols=80 Identities=14% Similarity=0.084 Sum_probs=48.6
Q ss_pred CHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhhCCCCchhhhcCCchHHHHHHHhCCCCcHhHHHHHHHHhc
Q 002604 433 DYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLLTL 512 (901)
Q Consensus 433 TpeaLa~A~~eELeelIR~~Gfyn~KAk~Ik~lAr~Lve~yGglDLe~L~~VP~deaRe~LLsLPGIG~KTAd~ILlfaf 512 (901)
.....+..+...|..+.++..- -....|..+|+.+ ++++++|....+++ ++.|..|.|.-.
T Consensus 23 eLA~~~Gis~~~is~iE~g~~~--ps~~~l~kIa~aL-----~v~~~~L~~~~~~~-~~~l~~la~~~~----------- 83 (120)
T PRK13890 23 ELSERSGVSISFLSDLTTGKAN--PSLKVMEAIADAL-----ETPLPLLLESTDLD-KEALDALAGGKA----------- 83 (120)
T ss_pred HHHHHHCcCHHHHHHHHcCCCC--CCHHHHHHHHHHH-----CCCHHHHhccCccC-HHHHHHHcCCCC-----------
Confidence 4455556688888877765543 3567788888776 36667665443332 555555555211
Q ss_pred CCceeecchHHHHHHHHhCCCC
Q 002604 513 HHLAFPVDTNVGRIAVRLGWVP 534 (901)
Q Consensus 513 grpafpVDTHV~RVl~RLGlv~ 534 (901)
.-.|.-.+.|++.+|.-.|
T Consensus 84 ---~~~~~~~~~~lld~L~~~P 102 (120)
T PRK13890 84 ---PRSLPPGFERVAAVLPEHQ 102 (120)
T ss_pred ---CCCCChHHHHHHHHcCCcc
Confidence 2245567899999985433
No 124
>COG2019 AdkA Archaeal adenylate kinase [Nucleotide transport and metabolism]
Probab=20.18 E-value=2.3e+02 Score=30.20 Aligned_cols=42 Identities=24% Similarity=0.282 Sum_probs=32.9
Q ss_pred HHhCCCCcHhHHHHHHHHhc-CCceeecchHHHHHHHHhCCCC
Q 002604 493 LLSIRGLGLKSVECVRLLTL-HHLAFPVDTNVGRIAVRLGWVP 534 (901)
Q Consensus 493 LLsLPGIG~KTAd~ILlfaf-grpafpVDTHV~RVl~RLGlv~ 534 (901)
+..+||||.-|+=-++.-.+ +...+-.-+.+.+++.+.|++.
T Consensus 9 itGVpGvGKTTVl~~~~~~l~~~~ivNyG~~Mle~A~k~glve 51 (189)
T COG2019 9 ITGVPGVGKTTVLKIALKELVKHKIVNYGDLMLEIAKKKGLVE 51 (189)
T ss_pred EEcCCCCChHHHHHHHHHHHhhceeeeHhHHHHHHHHHhCCcc
Confidence 45789999999855554444 5667777889999999999986
Done!