Query 014334
Match_columns 426
No_of_seqs 282 out of 1528
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 04:07:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/014334.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/014334hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2875 8-oxoguanine DNA glyco 100.0 2.3E-48 5.1E-53 375.5 19.1 241 33-382 46-298 (323)
2 TIGR00588 ogg 8-oxoguanine DNA 100.0 4.8E-43 1E-47 350.2 26.9 259 6-386 28-306 (310)
3 PRK10308 3-methyl-adenine DNA 100.0 5.5E-37 1.2E-41 303.2 25.7 242 11-390 32-276 (283)
4 COG0122 AlkA 3-methyladenine D 100.0 4E-37 8.7E-42 304.3 20.6 215 66-392 60-276 (285)
5 cd00056 ENDO3c endonuclease II 99.9 8.2E-25 1.8E-29 197.0 14.4 120 253-388 31-157 (158)
6 PRK10702 endonuclease III; Pro 99.9 6.7E-23 1.4E-27 195.2 16.5 108 250-372 56-169 (211)
7 KOG1918 3-methyladenine DNA gl 99.9 4.2E-23 9.2E-28 194.7 11.7 132 250-392 108-243 (254)
8 TIGR01083 nth endonuclease III 99.9 4.5E-22 9.8E-27 186.2 17.8 111 251-377 54-170 (191)
9 PRK13913 3-methyladenine DNA g 99.9 9.8E-22 2.1E-26 188.0 15.6 109 251-370 65-178 (218)
10 TIGR01084 mutY A/G-specific ad 99.9 2E-21 4.3E-26 191.8 17.7 157 251-422 54-225 (275)
11 COG0177 Nth Predicted EndoIII- 99.9 6.8E-21 1.5E-25 180.9 15.9 108 249-371 55-168 (211)
12 PRK10880 adenine DNA glycosyla 99.8 5.2E-20 1.1E-24 187.1 18.0 148 251-416 58-223 (350)
13 smart00478 ENDO3c endonuclease 99.8 5.1E-20 1.1E-24 164.5 14.7 119 252-387 21-146 (149)
14 PRK13910 DNA glycosylase MutY; 99.8 2E-18 4.3E-23 171.6 12.4 154 244-412 14-177 (289)
15 PRK01229 N-glycosylase/DNA lya 99.8 9.2E-18 2E-22 159.6 14.7 113 260-381 68-195 (208)
16 PF00730 HhH-GPD: HhH-GPD supe 99.5 1.5E-13 3.2E-18 116.3 12.1 75 252-372 27-108 (108)
17 TIGR03252 uncharacterized HhH- 99.5 2.9E-13 6.3E-18 125.8 12.0 79 253-335 50-137 (177)
18 COG1194 MutY A/G-specific DNA 99.5 4.3E-13 9.4E-18 135.3 13.0 156 248-422 59-234 (342)
19 COG2231 Uncharacterized protei 99.5 2.8E-12 6E-17 121.0 16.4 103 255-368 63-171 (215)
20 KOG1921 Endonuclease III [Repl 99.3 3.7E-11 8.1E-16 115.9 13.4 103 254-370 110-220 (286)
21 PF07934 OGG_N: 8-oxoguanine D 98.4 3E-07 6.5E-12 79.6 5.7 80 34-127 38-117 (117)
22 KOG2457 A/G-specific adenine D 98.2 7.9E-06 1.7E-10 83.8 9.3 137 249-403 151-303 (555)
23 COG1059 Thermostable 8-oxoguan 97.6 0.0012 2.6E-08 62.4 12.7 88 254-356 72-164 (210)
24 PF00633 HHH: Helix-hairpin-he 97.3 0.00019 4E-09 48.5 2.7 20 311-330 9-28 (30)
25 PF06029 AlkA_N: AlkA N-termin 96.0 0.03 6.4E-07 49.1 7.6 82 12-120 33-114 (116)
26 smart00278 HhH1 Helix-hairpin- 93.9 0.037 8E-07 35.8 1.7 17 314-330 2-18 (26)
27 PRK13901 ruvA Holliday junctio 92.2 0.46 9.9E-06 45.5 7.1 67 247-330 57-124 (196)
28 PRK14606 ruvA Holliday junctio 89.7 3.9 8.4E-05 38.8 10.7 108 247-370 58-168 (188)
29 PRK14601 ruvA Holliday junctio 89.6 2.6 5.6E-05 39.9 9.4 107 247-369 58-166 (183)
30 PF12826 HHH_2: Helix-hairpin- 89.4 0.51 1.1E-05 36.9 3.8 37 283-330 16-52 (64)
31 PF14716 HHH_8: Helix-hairpin- 88.9 1.7 3.6E-05 34.2 6.5 50 266-330 14-64 (68)
32 smart00483 POLXc DNA polymeras 87.6 1.4 3E-05 45.3 6.6 62 264-336 48-111 (334)
33 TIGR00084 ruvA Holliday juncti 86.0 1.7 3.8E-05 41.2 5.9 67 247-330 57-124 (191)
34 PF14520 HHH_5: Helix-hairpin- 85.3 2.2 4.8E-05 32.6 5.2 50 265-331 6-56 (60)
35 PRK14605 ruvA Holliday junctio 85.1 11 0.00024 35.8 10.9 67 247-330 58-125 (194)
36 PRK00076 recR recombination pr 84.3 0.89 1.9E-05 43.5 3.1 30 307-336 5-35 (196)
37 COG0632 RuvA Holliday junction 83.9 1.4 3E-05 42.4 4.2 67 248-330 59-125 (201)
38 COG0353 RecR Recombinational D 83.9 0.95 2.1E-05 43.3 3.1 30 307-336 6-36 (198)
39 TIGR00615 recR recombination p 83.9 0.99 2.1E-05 43.2 3.2 30 307-336 5-35 (195)
40 PRK13844 recombination protein 83.2 1 2.3E-05 43.2 3.1 30 307-336 9-39 (200)
41 PRK14600 ruvA Holliday junctio 82.3 2.6 5.6E-05 40.0 5.4 66 248-330 59-124 (186)
42 PF02371 Transposase_20: Trans 82.1 1.1 2.4E-05 36.8 2.5 35 313-347 2-36 (87)
43 PRK14603 ruvA Holliday junctio 81.9 2 4.3E-05 41.0 4.5 68 247-330 57-124 (197)
44 PRK14604 ruvA Holliday junctio 80.0 2.2 4.9E-05 40.7 4.1 68 247-330 58-125 (195)
45 PRK00116 ruvA Holliday junctio 79.5 16 0.00035 34.5 9.7 67 248-331 59-126 (192)
46 cd00141 NT_POLXc Nucleotidyltr 79.4 5 0.00011 40.6 6.7 61 265-336 46-107 (307)
47 PRK14602 ruvA Holliday junctio 79.3 2.3 5E-05 40.8 3.9 68 247-330 59-126 (203)
48 PRK14605 ruvA Holliday junctio 77.6 1.7 3.8E-05 41.3 2.6 29 307-335 67-95 (194)
49 PRK08609 hypothetical protein; 77.6 3.9 8.4E-05 45.0 5.6 61 265-335 49-110 (570)
50 TIGR00575 dnlj DNA ligase, NAD 75.5 8.4 0.00018 43.2 7.5 79 253-335 455-552 (652)
51 PRK00116 ruvA Holliday junctio 73.6 3.3 7.2E-05 39.2 3.3 25 310-334 70-94 (192)
52 PRK07956 ligA NAD-dependent DN 73.4 9.6 0.00021 42.9 7.3 80 252-335 467-565 (665)
53 TIGR00084 ruvA Holliday juncti 70.9 3.6 7.8E-05 39.1 2.9 24 307-330 66-89 (191)
54 COG0632 RuvA Holliday junction 70.7 2.6 5.7E-05 40.5 1.9 67 308-376 68-135 (201)
55 PF14520 HHH_5: Helix-hairpin- 69.2 7 0.00015 29.8 3.6 33 252-284 26-59 (60)
56 TIGR00426 competence protein C 68.3 5.3 0.00012 31.2 2.9 54 257-330 9-64 (69)
57 TIGR01259 comE comEA protein. 66.5 12 0.00027 32.8 5.1 58 253-330 57-115 (120)
58 PRK14601 ruvA Holliday junctio 66.1 3.5 7.5E-05 39.1 1.7 26 308-333 68-93 (183)
59 PF03352 Adenine_glyco: Methyl 65.6 79 0.0017 30.0 10.6 39 115-153 17-56 (179)
60 TIGR00608 radc DNA repair prot 65.5 7.6 0.00017 37.7 3.9 51 269-330 23-77 (218)
61 PF10391 DNA_pol_lambd_f: Fing 64.9 4.8 0.0001 30.5 1.9 22 313-334 2-24 (52)
62 PRK13901 ruvA Holliday junctio 64.5 4.4 9.6E-05 38.8 2.1 26 307-332 66-91 (196)
63 PF11731 Cdd1: Pathogenicity l 63.4 5.1 0.00011 34.1 2.0 27 309-335 8-35 (93)
64 PRK14350 ligA NAD-dependent DN 63.1 15 0.00033 41.4 6.2 22 313-334 541-562 (669)
65 PRK02515 psbU photosystem II c 63.0 16 0.00036 33.0 5.2 56 251-330 48-104 (132)
66 PRK14603 ruvA Holliday junctio 63.0 4.1 8.8E-05 38.9 1.5 26 308-333 67-92 (197)
67 PRK00024 hypothetical protein; 62.1 10 0.00022 36.9 4.1 50 269-329 33-82 (224)
68 PF11798 IMS_HHH: IMS family H 61.6 5.2 0.00011 27.2 1.4 15 315-329 13-27 (32)
69 PRK14602 ruvA Holliday junctio 61.4 5.2 0.00011 38.4 2.0 27 308-334 69-95 (203)
70 PRK14604 ruvA Holliday junctio 61.3 4.7 0.0001 38.5 1.6 25 307-331 67-91 (195)
71 PF09674 DUF2400: Protein of u 60.8 6.1 0.00013 38.8 2.4 19 338-356 176-194 (232)
72 PRK14606 ruvA Holliday junctio 60.6 5 0.00011 38.1 1.7 27 307-333 67-93 (188)
73 PRK14351 ligA NAD-dependent DN 58.2 26 0.00056 39.7 7.0 81 253-335 485-582 (689)
74 PF12836 HHH_3: Helix-hairpin- 57.6 16 0.00034 28.4 3.8 52 258-329 8-60 (65)
75 PF12836 HHH_3: Helix-hairpin- 57.4 9.4 0.0002 29.7 2.5 19 312-330 13-31 (65)
76 cd00080 HhH2_motif Helix-hairp 57.1 6.2 0.00013 31.8 1.4 23 313-335 22-44 (75)
77 PRK14600 ruvA Holliday junctio 57.0 8.9 0.00019 36.4 2.7 26 308-333 68-93 (186)
78 smart00279 HhH2 Helix-hairpin- 56.1 8.1 0.00018 27.1 1.7 17 314-330 17-33 (36)
79 TIGR02757 conserved hypothetic 55.7 8.4 0.00018 37.9 2.3 19 338-356 173-191 (229)
80 TIGR01259 comE comEA protein. 54.5 11 0.00023 33.2 2.6 19 312-330 67-85 (120)
81 PRK08097 ligB NAD-dependent DN 52.4 39 0.00085 37.4 7.0 83 251-335 446-542 (562)
82 COG1555 ComEA DNA uptake prote 52.2 10 0.00022 34.7 2.2 19 312-330 96-114 (149)
83 COG1796 POL4 DNA polymerase IV 51.0 27 0.00059 36.0 5.2 46 270-330 22-70 (326)
84 PRK02515 psbU photosystem II c 49.6 14 0.0003 33.4 2.5 19 312-330 60-78 (132)
85 PRK07945 hypothetical protein; 48.7 26 0.00056 36.0 4.7 53 265-330 12-66 (335)
86 PRK14973 DNA topoisomerase I; 48.7 26 0.00056 41.1 5.2 82 250-340 821-905 (936)
87 COG2003 RadC DNA repair protei 45.8 19 0.00042 35.3 3.1 49 270-329 34-82 (224)
88 smart00483 POLXc DNA polymeras 45.4 34 0.00074 35.1 5.0 42 273-330 24-65 (334)
89 COG1948 MUS81 ERCC4-type nucle 45.4 43 0.00092 33.5 5.4 75 253-334 117-203 (254)
90 PF00416 Ribosomal_S13: Riboso 45.0 22 0.00049 30.5 3.1 43 309-351 11-57 (107)
91 COG1555 ComEA DNA uptake prote 43.3 55 0.0012 29.9 5.5 52 258-329 91-143 (149)
92 PRK12766 50S ribosomal protein 42.9 44 0.00096 33.0 5.1 26 312-337 35-60 (232)
93 PF01367 5_3_exonuc: 5'-3' exo 41.8 4.1 8.9E-05 35.0 -2.0 27 313-339 18-44 (101)
94 cd00141 NT_POLXc Nucleotidyltr 41.5 53 0.0012 33.3 5.6 44 271-330 19-62 (307)
95 KOG2841 Structure-specific end 40.3 28 0.00061 34.5 3.2 38 248-285 211-249 (254)
96 TIGR01448 recD_rel helicase, p 39.5 55 0.0012 37.2 5.9 29 307-335 76-106 (720)
97 TIGR00426 competence protein C 39.0 28 0.00061 27.1 2.5 19 312-330 15-34 (69)
98 TIGR00624 tag DNA-3-methyladen 37.7 3.6E+02 0.0079 25.6 12.2 39 115-153 21-60 (179)
99 COG0272 Lig NAD-dependent DNA 33.2 91 0.002 35.3 6.2 37 312-355 542-578 (667)
100 PRK07758 hypothetical protein; 33.2 79 0.0017 27.1 4.4 39 280-329 44-83 (95)
101 PRK14976 5'-3' exonuclease; Pr 33.1 28 0.00061 35.0 2.1 24 313-336 191-214 (281)
102 PF03118 RNA_pol_A_CTD: Bacter 32.6 42 0.00091 26.4 2.6 46 270-331 17-62 (66)
103 PRK09482 flap endonuclease-lik 31.8 28 0.0006 34.7 1.8 24 313-336 182-205 (256)
104 KOG2534 DNA polymerase IV (fam 31.0 1.3E+02 0.0029 31.2 6.4 40 274-329 33-72 (353)
105 TIGR01954 nusA_Cterm_rpt trans 30.6 1.1E+02 0.0023 21.8 4.3 35 251-285 13-48 (50)
106 TIGR01448 recD_rel helicase, p 30.4 6.8E+02 0.015 28.6 12.7 37 317-353 185-223 (720)
107 smart00475 53EXOc 5'-3' exonuc 29.7 33 0.00071 34.1 1.9 24 313-336 186-209 (259)
108 COG4277 Predicted DNA-binding 29.3 39 0.00083 35.0 2.3 21 312-332 329-349 (404)
109 KOG2534 DNA polymerase IV (fam 29.0 1.1E+02 0.0024 31.8 5.5 75 250-337 46-122 (353)
110 cd00008 53EXOc 5'-3' exonuclea 28.4 40 0.00086 32.9 2.2 24 313-336 183-206 (240)
111 PRK14671 uvrC excinuclease ABC 27.3 90 0.002 35.0 5.0 31 309-339 565-595 (621)
112 CHL00137 rps13 ribosomal prote 26.7 40 0.00087 29.9 1.7 27 309-335 13-39 (122)
113 PRK13482 DNA integrity scannin 26.0 88 0.0019 32.8 4.3 42 249-290 304-346 (352)
114 PRK13482 DNA integrity scannin 26.0 85 0.0018 32.9 4.2 39 281-330 298-336 (352)
115 PF12826 HHH_2: Helix-hairpin- 25.5 61 0.0013 25.1 2.4 34 249-282 20-54 (64)
116 PRK05179 rpsM 30S ribosomal pr 24.4 48 0.001 29.4 1.8 27 309-335 13-39 (122)
117 PRK08609 hypothetical protein; 24.3 1.4E+02 0.0031 32.9 5.8 48 266-329 16-64 (570)
118 COG1415 Uncharacterized conser 23.9 2E+02 0.0043 30.2 6.3 20 310-329 275-294 (373)
119 PTZ00134 40S ribosomal protein 23.6 48 0.001 30.7 1.7 27 309-335 26-52 (154)
120 PRK10353 3-methyl-adenine DNA 23.6 6.5E+02 0.014 24.0 11.0 39 115-153 22-61 (187)
121 PF09597 IGR: IGR protein moti 22.8 1.3E+02 0.0029 23.4 3.7 39 250-289 17-57 (57)
122 TIGR00596 rad1 DNA repair prot 22.5 78 0.0017 36.7 3.4 29 307-335 751-779 (814)
123 TIGR03631 bact_S13 30S ribosom 22.1 52 0.0011 28.8 1.5 27 309-335 11-37 (113)
124 PRK14666 uvrC excinuclease ABC 21.9 72 0.0016 36.3 2.9 29 309-337 633-661 (694)
125 COG2117 Predicted subunit of t 20.6 99 0.0021 29.4 3.1 54 263-325 127-181 (198)
126 PF14229 DUF4332: Domain of un 20.1 2E+02 0.0044 25.2 4.9 32 289-330 39-70 (122)
127 TIGR03629 arch_S13P archaeal r 20.0 62 0.0013 29.6 1.6 27 309-335 17-43 (144)
No 1
>KOG2875 consensus 8-oxoguanine DNA glycosylase [Replication, recombination and repair]
Probab=100.00 E-value=2.3e-48 Score=375.48 Aligned_cols=241 Identities=20% Similarity=0.260 Sum_probs=197.1
Q ss_pred eEEEEEeccCCCCCceEEEEeccCCCCCCCCCHHHHHHHHHHHHHHhcCCchhhHhhHHHHHHHHHHHhhhchhhhcccC
Q 014334 33 SVDVTICQPQQDPHSLRIEVRNSASGSAPSLSQEQQDALLAQVKRMLRLSEADERNVRDFKRIVRQVAQEEGEESQYMTD 112 (426)
Q Consensus 33 ~~~v~i~q~~~~~~~L~~~v~~~~~~~~~~ls~~~~~~i~~~v~r~l~Ld~d~~~~~~~f~~~~~~~~~~~~~~~~~~~~ 112 (426)
.-+|++.|. ++....|++.-+ +.+..+.+. +.|+.||+||++|..++..|-..+.+|..+++
T Consensus 46 ~~v~~L~Q~--ee~~~~y~~~~s----~~~p~~del----~~i~~yf~ldv~L~~l~~~W~~~D~~F~~la~-------- 107 (323)
T KOG2875|consen 46 DQVWTLTQT--EEQCTVYRGDKS----ASRPTPDEL----EAISKYFQLDVTLAQLYHHWGSVDDHFQELAQ-------- 107 (323)
T ss_pred cEEEEEEec--CCceEEEEeecC----CCCCChHHH----HHHHHHHhheeeHHHHHHHhCcCChHHHHHHH--------
Confidence 346788886 444577777663 223334332 35789999999999999999999999988873
Q ss_pred CcccccCCCChHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhhhhcCCCCCCCCCCCCCCCcchhhhhhhhhhhhhhhhhh
Q 014334 113 FSGRVFRSPTLFEDMVKCMLLCNCQWPRTLSMARALCELQWELQHCSPSISEDFIPQTPAGKESKRRQKVSKVASKLTSR 192 (426)
Q Consensus 113 ~ggRvlr~p~~fE~lv~~I~s~N~~~~r~~~m~~~Lc~~~g~l~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~ 192 (426)
.|.|+||| ||||||++|||||||||+||++|+++||..+|+. |+
T Consensus 108 qgvRlLrQ-dP~E~lfSFiCSSNNNIaRIT~Mve~fc~~fG~~----------------i~------------------- 151 (323)
T KOG2875|consen 108 QGVRLLRQ-DPIECLFSFICSSNNNIARITGMVERFCQAFGPR----------------II------------------- 151 (323)
T ss_pred hhhHHHhc-CcHHHHHHHHhcCCCcHHHHHHHHHHHHHhhCcc----------------eE-------------------
Confidence 47899998 8999999999999999999999999999999873 32
Q ss_pred hhhhhcchhhhhhhhcccccccccCCCCCCCCCCcccccccccCCCCCCCCcccccccCCCCHHHHhcC-CHHHHHHHCc
Q 014334 193 IAESKASSEDYMNLKLDCAGVLEENVQPSFPQNDIESDLHGLNELSTTDPPSARDRIGNFPSPRELANL-DESFLAKRCN 271 (426)
Q Consensus 193 ~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~FPtpe~La~~-~~e~Lr~~~g 271 (426)
.+||. .+|.|||.+.|+.. .+++||+ .|
T Consensus 152 -------------------------------------~~dg~-------------~~h~FPsl~~L~g~~~Ea~LR~-~g 180 (323)
T KOG2875|consen 152 -------------------------------------QLDGV-------------DYHGFPSLQALAGPEVEAELRK-LG 180 (323)
T ss_pred -------------------------------------eecCc-------------ccccCccHHHhcCcHhHHHHHH-cC
Confidence 45664 78999999999964 4557997 99
Q ss_pred CcHHHHHHHHHHHHHHhCCCChhHHHhhhhhcccccHHHHHHHHhcCCCcCHHHHHHH-HHHhCCCCccccchHHHHHHH
Q 014334 272 LGYRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNV-LVCIGFYHVIPTDSETIRHLK 350 (426)
Q Consensus 272 ~GyRAkyI~~lA~~i~eg~ldLe~L~~l~~~~~~~~~eea~e~L~~L~GIGpkTAd~I-L~~Lg~~dvfPvDthV~Ril~ 350 (426)
|||||+||.++|++|.+..--++.|..+++ .+||++++.|+.+||||||+|||| ||+|+.+.++|||+|++||++
T Consensus 181 fGYRAkYI~~ta~~l~~~~g~~~wLqsl~~----~~yeear~~L~~lpGVG~KVADCI~Lm~l~~~~~VPVDvHi~ria~ 256 (323)
T KOG2875|consen 181 FGYRAKYISATARALQEKQGGLAWLQSLRK----SSYEEAREALCSLPGVGPKVADCICLMSLDKLSAVPVDVHIWRIAQ 256 (323)
T ss_pred cchhHHHHHHHHHHHHHhcccchHHHHHhc----ccHHHHHHHHhcCCCCcchHhhhhhhhhcCCCCcccchhhHHHHhh
Confidence 999999999999999985443344444322 399999999999999999999999 599999999999999999999
Q ss_pred HhhccC------CC---HHHHHHHHHHHhcCCChH-HHHHHH
Q 014334 351 QVHARN------CT---SKTVQMIAESIYGKYAPF-QFLAYW 382 (426)
Q Consensus 351 rly~~~------~t---~k~i~~~~~e~~g~~agw-q~l~fw 382 (426)
.++..+ .+ +.++..++++.||+|||| |.++|-
T Consensus 257 ~y~l~~~~g~k~l~~ki~~ev~~~f~~~~G~YAGwAQ~~lfs 298 (323)
T KOG2875|consen 257 DYILPGLSGAKELTPKINGEVSNFFRSLWGEYAGWAQAVLFS 298 (323)
T ss_pred cccCCCccccccCCcchhHHHHHHHHHHhcccccchhheeec
Confidence 554433 12 467889999999999999 999884
No 2
>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=100.00 E-value=4.8e-43 Score=350.19 Aligned_cols=259 Identities=22% Similarity=0.280 Sum_probs=201.1
Q ss_pred ccc--ccccccccceecCCCCCCCCCCCceEEEEEeccCCCCCceEEEEeccCCCCCCCCCHHHHHHHHHHHHHHhcCCc
Q 014334 6 RWD--PLSRSLSRPLHLSNSLDNTDIPSVSVDVTICQPQQDPHSLRIEVRNSASGSAPSLSQEQQDALLAQVKRMLRLSE 83 (426)
Q Consensus 6 ~wd--~~~~~~~r~lr~~~~~~~~~~~~~~~~v~i~q~~~~~~~L~~~v~~~~~~~~~~ls~~~~~~i~~~v~r~l~Ld~ 83 (426)
+|. ...+.|.|.+.+++. + .+.+.|+ ++.+.+.+..+ .. .+.+.+.+.|++||+||.
T Consensus 28 rw~~~~~~~~y~~~~~~~~~---------~-~~~~~q~---~~~~~~~~~~~-----~~---~~~~~~~~~ir~~f~Ld~ 86 (310)
T TIGR00588 28 RWRWEESPAHWSGLLVIADQ---------P-VWTLTQT---EEQLLCTVYRG-----DK---PTQDELETKLEKYFQLDV 86 (310)
T ss_pred cCceeCCCCeEEEEEEECCe---------e-EEEEEEc---CCceEEEEecC-----CC---ccHHHHHHHHHHHhcCCC
Confidence 564 556789999999875 3 4456675 33454444431 11 145678889999999999
Q ss_pred hhhHhhHHHHHHH-HHHHhhhchhhhcccCCcccccCCCChHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhhhhcCCCCC
Q 014334 84 ADERNVRDFKRIV-RQVAQEEGEESQYMTDFSGRVFRSPTLFEDMVKCMLLCNCQWPRTLSMARALCELQWELQHCSPSI 162 (426)
Q Consensus 84 d~~~~~~~f~~~~-~~~~~~~~~~~~~~~~~ggRvlr~p~~fE~lv~~I~s~N~~~~r~~~m~~~Lc~~~g~l~~~~~~~ 162 (426)
| +.+|+... ..++.++... .. ..|.|++++ |+||++|+||||||+|++++.+|.++||+.||+
T Consensus 87 d----~~~i~~~~~~~D~~l~~~~-~~--~~GlRi~~~-d~fE~lv~~IlsQq~si~~a~~~~~rL~~~~G~-------- 150 (310)
T TIGR00588 87 S----LAQLYTHWGSVDKHFQYVA-QK--FQGVRLLRQ-DPFECLISFICSSNNNIARITRMVERLCQAFGP-------- 150 (310)
T ss_pred C----HHHHHHHHhhcCHHHHHHH-Hh--CCCCCCCCC-CHHHHHHHHHHhCCCCHHHHHHHHHHHHHHhCC--------
Confidence 9 66666553 3344444221 11 135699999 999999999999999999999999999999986
Q ss_pred CCCCCCCCCCcchhhhhhhhhhhhhhhhhhhhhhhcchhhhhhhhcccccccccCCCCCCCCCCcccccccccCCCCCCC
Q 014334 163 SEDFIPQTPAGKESKRRQKVSKVASKLTSRIAESKASSEDYMNLKLDCAGVLEENVQPSFPQNDIESDLHGLNELSTTDP 242 (426)
Q Consensus 163 ~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 242 (426)
++. .++|
T Consensus 151 --------~~~--------------------------------------------------------~~~g--------- 157 (310)
T TIGR00588 151 --------RLI--------------------------------------------------------TLDG--------- 157 (310)
T ss_pred --------Ccc--------------------------------------------------------cCCC---------
Confidence 111 1122
Q ss_pred CcccccccCCCCHHHHhcCCHH-HHHHHCcCcHHHHHHHHHHHHHHhCCC---ChhHHHhhhhhcccccHHHHHHHHhcC
Q 014334 243 PSARDRIGNFPSPRELANLDES-FLAKRCNLGYRAGRILKLARGIVDGQI---QLRELEDMCNEASLTAYVKLAEQLSQI 318 (426)
Q Consensus 243 p~~~~~~~~FPtpe~La~~~~e-~Lr~~~g~GyRAkyI~~lA~~i~eg~l---dLe~L~~l~~~~~~~~~eea~e~L~~L 318 (426)
..++.||||++|+..+.+ .|+. +|+||||+||+++|+++.+|.. +++.|.++ ++++++++|++|
T Consensus 158 ----~~~~~FPtp~~La~~~~e~~Lr~-~G~g~Ra~~I~~~A~~i~~~~~~~~~l~~l~~~-------~~~~~~~~L~~l 225 (310)
T TIGR00588 158 ----VTYHGFPSLHALTGPEAEAHLRK-LGLGYRARYIRETARALLEEQGGRAWLQQIRGA-------SYEDAREALCEL 225 (310)
T ss_pred ----cccccCCCHHHHhCCChHHHHHH-cCCHHHHHHHHHHHHHHHhccCCchhHHhhccC-------ChHHHHHHHHhC
Confidence 257899999999997654 7886 9999999999999999999754 45566665 899999999999
Q ss_pred CCcCHHHHHHHH-HHhCCCCccccchHHHHHHHHhhccC-----------CCHHHHHHHHHHHhcCCChH-HHHHHHHHH
Q 014334 319 NGFGPFTRNNVL-VCIGFYHVIPTDSETIRHLKQVHARN-----------CTSKTVQMIAESIYGKYAPF-QFLAYWSEL 385 (426)
Q Consensus 319 ~GIGpkTAd~IL-~~Lg~~dvfPvDthV~Ril~rly~~~-----------~t~k~i~~~~~e~~g~~agw-q~l~fw~~L 385 (426)
|||||||||||| |+|+++++||+|+||+|+++++|+.. .+++++.++++++|++|+|| |.++|.+++
T Consensus 226 ~GIG~~tAd~vll~~l~~~d~~PvD~~v~r~~~r~y~~~~~~~~~~~~~~~~~~~i~~~~~~~~g~~ag~aq~~lf~~~~ 305 (310)
T TIGR00588 226 PGVGPKVADCICLMGLDKPQAVPVDVHVWRIANRDYPWHPKTSRAKGPSPFARKELGNFFRSLWGPYAGWAQAVLFSADL 305 (310)
T ss_pred CCccHHHHHHHHHHhCCCCCceeecHHHHHHHHHHhcccccccccccCChhHHHHHHHHHHHHhcCcchHHHHHHHHHHh
Confidence 999999999996 89999999999999999999999753 23577888899999999999 888875544
Q ss_pred H
Q 014334 386 W 386 (426)
Q Consensus 386 w 386 (426)
.
T Consensus 306 ~ 306 (310)
T TIGR00588 306 R 306 (310)
T ss_pred h
Confidence 3
No 3
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=100.00 E-value=5.5e-37 Score=303.16 Aligned_cols=242 Identities=18% Similarity=0.203 Sum_probs=192.0
Q ss_pred ccccccceecCCCCCCCCCCCceEEEEEeccCCCCCceEEEEeccCCCCCCCCCHHHHHHHHHHHHHHhcCCchhhHhhH
Q 014334 11 SRSLSRPLHLSNSLDNTDIPSVSVDVTICQPQQDPHSLRIEVRNSASGSAPSLSQEQQDALLAQVKRMLRLSEADERNVR 90 (426)
Q Consensus 11 ~~~~~r~lr~~~~~~~~~~~~~~~~v~i~q~~~~~~~L~~~v~~~~~~~~~~ls~~~~~~i~~~v~r~l~Ld~d~~~~~~ 90 (426)
.+.|.|++++++. ...|+|++. .....|.+++... +. .....+++.|+|||+||.| +.
T Consensus 32 ~~~y~R~~~~~~~---------~~~~~v~~~-~~~~~l~~~~~~~-------~~-~~~~~~~~~vrr~fdLd~d----~~ 89 (283)
T PRK10308 32 EGYYARSLAVGEH---------RGVVTVIPD-IARHTLHINLSAG-------LE-PVAAECLAKMSRLFDLQCN----PQ 89 (283)
T ss_pred CCEEEEEEEECCc---------cEEEEEEEc-CCCceEEEEEcCC-------cc-ccHHHHHHHHHHHcCCCCC----HH
Confidence 3689999999976 788888875 1233577777652 11 2345689999999999999 88
Q ss_pred HHHHHHHHHHhhhchhhhcccCCcccccCCCChHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhhhhcCCCCCCCCCCCCC
Q 014334 91 DFKRIVRQVAQEEGEESQYMTDFSGRVFRSPTLFEDMVKCMLLCNCQWPRTLSMARALCELQWELQHCSPSISEDFIPQT 170 (426)
Q Consensus 91 ~f~~~~~~~~~~~~~~~~~~~~~ggRvlr~p~~fE~lv~~I~s~N~~~~r~~~m~~~Lc~~~g~l~~~~~~~~~~~~~~~ 170 (426)
.|+......... ..|.|+++.+|+||++|++||+||+++.++.++..+||+.||+
T Consensus 90 ~i~~~L~~~~~~---------~~GlR~p~~~d~fE~lv~aIigQqisv~~a~~~~~rlv~~~G~---------------- 144 (283)
T PRK10308 90 IVNGALGKLGAA---------RPGLRLPGSVDAFEQGVRAILGQLVSVAMAAKLTAKVAQLYGE---------------- 144 (283)
T ss_pred HHHHHHHHHHHh---------CCCCcCCCCCCHHHHHHHHHHHhHHHHHHHHHHHHHHHHHhCc----------------
Confidence 776544322111 1477999989999999999999999999999999999999986
Q ss_pred CCcchhhhhhhhhhhhhhhhhhhhhhhcchhhhhhhhcccccccccCCCCCCCCCCcccccccccCCCCCCCCccccccc
Q 014334 171 PAGKESKRRQKVSKVASKLTSRIAESKASSEDYMNLKLDCAGVLEENVQPSFPQNDIESDLHGLNELSTTDPPSARDRIG 250 (426)
Q Consensus 171 p~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~ 250 (426)
++. ++ ..++
T Consensus 145 ~l~----------------------------------------------------------~~-------------~~~~ 153 (283)
T PRK10308 145 RLD----------------------------------------------------------DF-------------PEYV 153 (283)
T ss_pred ccc----------------------------------------------------------CC-------------CCcc
Confidence 110 00 1368
Q ss_pred CCCCHHHHhcCCHHHHHHHCcCcH-HHHHHHHHHHHHHhCCCChhHHHhhhhhcccccHHHHHHHHhcCCCcCHHHHHHH
Q 014334 251 NFPSPRELANLDESFLAKRCNLGY-RAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNV 329 (426)
Q Consensus 251 ~FPtpe~La~~~~e~Lr~~~g~Gy-RAkyI~~lA~~i~eg~ldLe~L~~l~~~~~~~~~eea~e~L~~L~GIGpkTAd~I 329 (426)
.||||++|+++++++|+. ||+++ ||+||+++|+++.+|.++++.+ .++++++++|++|||||||||+||
T Consensus 154 ~FPtpe~La~~~~~eL~~-~Gl~~~Ra~~L~~lA~~i~~g~l~l~~~---------~~~~~~~~~L~~LpGIGpwTA~~v 223 (283)
T PRK10308 154 CFPTPERLAAADPQALKA-LGMPLKRAEALIHLANAALEGTLPLTIP---------GDVEQAMKTLQTFPGIGRWTANYF 223 (283)
T ss_pred CCCCHHHHHcCCHHHHHH-CCCCHHHHHHHHHHHHHHHcCCCCcccc---------CCHHHHHHHHhcCCCcCHHHHHHH
Confidence 999999999999999997 99985 9999999999999999987642 266899999999999999999999
Q ss_pred H-HHhCCCCccc-cchHHHHHHHHhhccCCCHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHH
Q 014334 330 L-VCIGFYHVIP-TDSETIRHLKQVHARNCTSKTVQMIAESIYGKYAPFQFLAYWSELWHFYE 390 (426)
Q Consensus 330 L-~~Lg~~dvfP-vDthV~Ril~rly~~~~t~k~i~~~~~e~~g~~agwq~l~fw~~Lw~~y~ 390 (426)
| |+||++|+|| +|++++|.+. . .+++++.+ +...|+||++++. .+||+...
T Consensus 224 llr~lg~~D~fp~~D~~l~~~~~---~--~~~~~~~~----~a~~w~P~rsya~-~~LW~~~~ 276 (283)
T PRK10308 224 ALRGWQAKDVFLPDDYLIKQRFP---G--MTPAQIRR----YAERWKPWRSYAL-LHIWYTEG 276 (283)
T ss_pred HHHhCCCCCCCCcccHHHHHhcc---c--CCHHHHHH----HHHhcCCHHHHHH-HHHHHcCC
Confidence 6 8999999997 9999998652 2 34455544 4457999999987 56998744
No 4
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=100.00 E-value=4e-37 Score=304.34 Aligned_cols=215 Identities=21% Similarity=0.340 Sum_probs=184.9
Q ss_pred HHHHHHHHHHHHHhcCCchhhHhhHHHHHHHHHHHhhhchhhhcccCCcccccCCCChHHHHHHHHHhcCCCHHHHHHHH
Q 014334 66 EQQDALLAQVKRMLRLSEADERNVRDFKRIVRQVAQEEGEESQYMTDFSGRVFRSPTLFEDMVKCMLLCNCQWPRTLSMA 145 (426)
Q Consensus 66 ~~~~~i~~~v~r~l~Ld~d~~~~~~~f~~~~~~~~~~~~~~~~~~~~~ggRvlr~p~~fE~lv~~I~s~N~~~~r~~~m~ 145 (426)
...+.+...++++|+||.+ +.++......++.... +|+|++..+|+||+||++||+||+++.++.+|.
T Consensus 60 ~~~~~~~~~~~~~~~lD~~----l~~i~~~~~~~~~~~~--------~g~~~~~~~d~fe~lv~aI~~QqvS~~~A~~i~ 127 (285)
T COG0122 60 PVAEDIEAALRRLFDLDPD----LAPIIDALGPLPLLRA--------PGLRLPLAPDPFEALVRAILSQQVSVAAAAKIW 127 (285)
T ss_pred hhhHHHHHHHHHHHhcCCc----HHHHHHhcCccccccc--------cCcccCCCCCHHHHHHHHHHHhHhhHHHHHHHH
Confidence 3567788889999999999 8888887776655441 578888778999999999999999999999999
Q ss_pred HHHHHHhhhhhcCCCCCCCCCCCCCCCcchhhhhhhhhhhhhhhhhhhhhhhcchhhhhhhhcccccccccCCCCCCCCC
Q 014334 146 RALCELQWELQHCSPSISEDFIPQTPAGKESKRRQKVSKVASKLTSRIAESKASSEDYMNLKLDCAGVLEENVQPSFPQN 225 (426)
Q Consensus 146 ~~Lc~~~g~l~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 225 (426)
.+|++.||+- +
T Consensus 128 ~rl~~~~g~~----------------~----------------------------------------------------- 138 (285)
T COG0122 128 ARLVSLYGNA----------------L----------------------------------------------------- 138 (285)
T ss_pred HHHHHHhCCc----------------c-----------------------------------------------------
Confidence 9999998861 1
Q ss_pred CcccccccccCCCCCCCCcccccccCCCCHHHHhcCCHHHHHHHCcCcHHHHHHHHHHHHHHhCCCChhHHHhhhhhccc
Q 014334 226 DIESDLHGLNELSTTDPPSARDRIGNFPSPRELANLDESFLAKRCNLGYRAGRILKLARGIVDGQIQLRELEDMCNEASL 305 (426)
Q Consensus 226 ~~~~~~~~~~~~~~~~~p~~~~~~~~FPtpe~La~~~~e~Lr~~~g~GyRAkyI~~lA~~i~eg~ldLe~L~~l~~~~~~ 305 (426)
..+|.|||||+|++++++.|+..++.+|||+||+++|+++.+|.+++..+..+
T Consensus 139 ---------------------~~~~~fptpe~l~~~~~~~l~~~g~s~~Ka~yi~~~A~~~~~g~~~~~~l~~~------ 191 (285)
T COG0122 139 ---------------------EIYHSFPTPEQLAAADEEALRRCGLSGRKAEYIISLARAAAEGELDLSELKPL------ 191 (285)
T ss_pred ---------------------ccccCCCCHHHHHhcCHHHHHHhCCcHHHHHHHHHHHHHHHcCCccHHHhccC------
Confidence 14799999999999999999985668999999999999999999999999988
Q ss_pred ccHHHHHHHHhcCCCcCHHHHHHHH-HHhCCCCccc-cchHHHHHHHHhhccCCCHHHHHHHHHHHhcCCChHHHHHHHH
Q 014334 306 TAYVKLAEQLSQINGFGPFTRNNVL-VCIGFYHVIP-TDSETIRHLKQVHARNCTSKTVQMIAESIYGKYAPFQFLAYWS 383 (426)
Q Consensus 306 ~~~eea~e~L~~L~GIGpkTAd~IL-~~Lg~~dvfP-vDthV~Ril~rly~~~~t~k~i~~~~~e~~g~~agwq~l~fw~ 383 (426)
+++++++.|++|+|||||||+|+| |+||++|+|| +|+++++.++++|..+. ......++++.++|+||++++.++
T Consensus 192 -~~e~a~e~L~~i~GIG~WTAe~~llf~lgr~dvfP~~D~~lr~~~~~~~~~~~--~~~~~~~~~~~e~w~p~rs~A~~y 268 (285)
T COG0122 192 -SDEEAIEELTALKGIGPWTAEMFLLFGLGRPDVFPADDLGLRRAIKKLYRLPT--RPTEKEVRELAERWGPYRSYAALY 268 (285)
T ss_pred -CHHHHHHHHHcCCCcCHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhcCCC--CchHHHHHHHHhcccCHHHHHHHH
Confidence 899999999999999999999997 8999999999 89999999999994332 222334566778899999998755
Q ss_pred HHHHHHHHh
Q 014334 384 ELWHFYEKR 392 (426)
Q Consensus 384 ~Lw~~y~~~ 392 (426)
||+.+...
T Consensus 269 -Lw~~~~~~ 276 (285)
T COG0122 269 -LWRYARAT 276 (285)
T ss_pred -HHHhhhcc
Confidence 99987643
No 5
>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=8.2e-25 Score=197.00 Aligned_cols=120 Identities=28% Similarity=0.315 Sum_probs=98.2
Q ss_pred CCHHHHhcCCHHHHHHHCcCc----HHHHHHHHHHHHHHhCCCChhHHHhhhhhcccccHHHHHHHHhcCCCcCHHHHHH
Q 014334 253 PSPRELANLDESFLAKRCNLG----YRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNN 328 (426)
Q Consensus 253 Ptpe~La~~~~e~Lr~~~g~G----yRAkyI~~lA~~i~eg~ldLe~L~~l~~~~~~~~~eea~e~L~~L~GIGpkTAd~ 328 (426)
|||++|+.+++++|++ ++.+ +||++|+++|+.+.++..++.. +++++++.|++|||||||||+|
T Consensus 31 pt~~~l~~~~~~~l~~-~~~~~G~~~kA~~i~~~a~~~~~~~~~~~~-----------~~~~~~~~L~~l~GIG~~tA~~ 98 (158)
T cd00056 31 PTPEALAAADEEELRE-LIRSLGYRRKAKYLKELARAIVEGFGGLVL-----------DDPDAREELLALPGVGRKTANV 98 (158)
T ss_pred CCHHHHHCCCHHHHHH-HHHhcChHHHHHHHHHHHHHHHHHcCCccC-----------CCcccHHHHHcCCCCCHHHHHH
Confidence 8999999999999997 5443 6999999999999987765332 4478899999999999999999
Q ss_pred HH-HHhCCCCccccchHHHHHHHHhhccC--CCHHHHHHHHHHHhcCCChHHHHHHHHHHHHH
Q 014334 329 VL-VCIGFYHVIPTDSETIRHLKQVHARN--CTSKTVQMIAESIYGKYAPFQFLAYWSELWHF 388 (426)
Q Consensus 329 IL-~~Lg~~dvfPvDthV~Ril~rly~~~--~t~k~i~~~~~e~~g~~agwq~l~fw~~Lw~~ 388 (426)
|| ++++ .++||+|+|+.|+++++|..+ .+++++.+.+..+++ .+|.+++.++ ||.+
T Consensus 99 ~l~~~~~-~~~~pvD~~v~r~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~-l~~~ 157 (158)
T cd00056 99 VLLFALG-PDAFPVDTHVRRVLKRLGLIPKKKTPEELEELLEELLP--KPYWGEANQA-LMDL 157 (158)
T ss_pred HHHHHCC-CCCCccchhHHHHHHHhCCCCCCCCHHHHHHHHHHHCC--HHHHHHHHHH-HHHc
Confidence 97 8999 899999999999999999843 566777776665554 3677777644 7764
No 6
>PRK10702 endonuclease III; Provisional
Probab=99.90 E-value=6.7e-23 Score=195.22 Aligned_cols=108 Identities=17% Similarity=0.198 Sum_probs=89.1
Q ss_pred cCCCCHHHHhcCCHHHHHHHC-cCcH---HHHHHHHHHHHHHhCCCChhHHHhhhhhcccccHHHHHHHHhcCCCcCHHH
Q 014334 250 GNFPSPRELANLDESFLAKRC-NLGY---RAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFT 325 (426)
Q Consensus 250 ~~FPtpe~La~~~~e~Lr~~~-g~Gy---RAkyI~~lA~~i~eg~ldLe~L~~l~~~~~~~~~eea~e~L~~L~GIGpkT 325 (426)
..||||++|+++++++|++.+ ++|| ||++|+++|+.+.+..- .++++.++.|++|||||+||
T Consensus 56 ~~~pt~e~l~~a~~~~l~~~i~~~G~y~~kA~~l~~~a~~i~~~~~--------------~~~p~~~~~Ll~lpGVG~kt 121 (211)
T PRK10702 56 PVANTPAAMLELGVEGVKTYIKTIGLYNSKAENVIKTCRILLEQHN--------------GEVPEDRAALEALPGVGRKT 121 (211)
T ss_pred HHcCCHHHHHCCCHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHcC--------------CCCCchHHHHhcCCcccHHH
Confidence 369999999999999999843 5674 99999999999986321 13456799999999999999
Q ss_pred HHHHH-HHhCCCCccccchHHHHHHHHhhccC-CCHHHHHHHHHHHhcC
Q 014334 326 RNNVL-VCIGFYHVIPTDSETIRHLKQVHARN-CTSKTVQMIAESIYGK 372 (426)
Q Consensus 326 Ad~IL-~~Lg~~dvfPvDthV~Ril~rly~~~-~t~k~i~~~~~e~~g~ 372 (426)
||||| +++++ ++||||+||+|+++|+|... .+++++++.+.+.+..
T Consensus 122 A~~ill~a~~~-~~~~VDt~v~Rv~~r~g~~~~~~~~~~~~~l~~~lp~ 169 (211)
T PRK10702 122 ANVVLNTAFGW-PTIAVDTHIFRVCNRTQFAPGKNVEQVEEKLLKVVPA 169 (211)
T ss_pred HHHHHHHHcCC-CcccccchHHHHHHHhCCCCCCCHHHHHHHHHHhCCc
Confidence 99997 99999 58999999999999998754 4567777777776643
No 7
>KOG1918 consensus 3-methyladenine DNA glycosidase [Replication, recombination and repair]
Probab=99.89 E-value=4.2e-23 Score=194.70 Aligned_cols=132 Identities=25% Similarity=0.418 Sum_probs=115.4
Q ss_pred cCCCCHHHHhcCCHHHHHHHCcC-cHHHHHHHHHHHHHHhCCC-ChhHHHhhhhhcccccHHHHHHHHhcCCCcCHHHHH
Q 014334 250 GNFPSPRELANLDESFLAKRCNL-GYRAGRILKLARGIVDGQI-QLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRN 327 (426)
Q Consensus 250 ~~FPtpe~La~~~~e~Lr~~~g~-GyRAkyI~~lA~~i~eg~l-dLe~L~~l~~~~~~~~~eea~e~L~~L~GIGpkTAd 327 (426)
+.||+|+.+..++.++|++ ||| +.|+.||+.+|++..+|.+ ..+...++ +.+++.+.|+.++|||+||+.
T Consensus 108 ~~~~~pe~i~~~~~~~lrk-cG~S~rK~~yLh~lA~~~~ng~I~s~~~i~~m-------seEeL~~~LT~VKGIg~Wtv~ 179 (254)
T KOG1918|consen 108 EKFPTPEFIDPLDCEELRK-CGFSKRKASYLHSLAEAYTNGYIPSKSGIEKM-------SEEELIERLTNVKGIGRWTVE 179 (254)
T ss_pred cCCCCchhcCcCCHHHHHH-hCcchhhHHHHHHHHHHHhcCCCCchHHHhhc-------CHHHHHHHHHhccCccceeee
Confidence 6899999999999999998 997 5789999999999999954 44556666 889999999999999999999
Q ss_pred HHH-HHhCCCCccc-cchHHHHHHHHhhccCCCHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHHHh
Q 014334 328 NVL-VCIGFYHVIP-TDSETIRHLKQVHARNCTSKTVQMIAESIYGKYAPFQFLAYWSELWHFYEKR 392 (426)
Q Consensus 328 ~IL-~~Lg~~dvfP-vDthV~Ril~rly~~~~t~k~i~~~~~e~~g~~agwq~l~fw~~Lw~~y~~~ 392 (426)
++| |+|+|+|++| .|.+|++.++.+++... .+...++.++-+.|+||++++.|+ ||+.++-.
T Consensus 180 MflIfsL~R~DVmp~dDlgir~g~k~l~gl~~--~p~~~evekl~e~~kpyRtvaawY-lWki~~~~ 243 (254)
T KOG1918|consen 180 MFLIFSLHRPDVMPADDLGIRNGVKKLLGLKP--LPLPKEVEKLCEKCKPYRTVAAWY-LWKIIKLD 243 (254)
T ss_pred eeeeeccCCCcccCchhhhHHHHHHHHhCCCC--CCchHHHHHHhhhccchHHHHHHH-HHhhhhhh
Confidence 998 9999999999 78999999999999863 223445567778999999999999 99998765
No 8
>TIGR01083 nth endonuclease III. This equivalog model identifes nth members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=99.89 E-value=4.5e-22 Score=186.20 Aligned_cols=111 Identities=23% Similarity=0.246 Sum_probs=87.9
Q ss_pred CCCCHHHHhcCCHHHHHHH---CcC-cHHHHHHHHHHHHHHhCCCChhHHHhhhhhcccccHHHHHHHHhcCCCcCHHHH
Q 014334 251 NFPSPRELANLDESFLAKR---CNL-GYRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTR 326 (426)
Q Consensus 251 ~FPtpe~La~~~~e~Lr~~---~g~-GyRAkyI~~lA~~i~eg~ldLe~L~~l~~~~~~~~~eea~e~L~~L~GIGpkTA 326 (426)
.||||++|+++++++|.+. +|+ ..||+||+++|+.+.++.. . +.++.++.|++|||||+|||
T Consensus 54 ~~pt~~~l~~~~~~~L~~~ir~~G~~~~Ka~~i~~~a~~i~~~~~-------~-------~~~~~~~~L~~l~GIG~ktA 119 (191)
T TIGR01083 54 VYPTPQALAQAGLEELEEYIKSIGLYRNKAKNIIALCRILVERYG-------G-------EVPEDREELVKLPGVGRKTA 119 (191)
T ss_pred HCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHcC-------C-------CCchHHHHHHhCCCCcHHHH
Confidence 5899999999999998653 444 2399999999999987521 0 33567899999999999999
Q ss_pred HHHH-HHhCCCCccccchHHHHHHHHhhccC-CCHHHHHHHHHHHhcCCChHH
Q 014334 327 NNVL-VCIGFYHVIPTDSETIRHLKQVHARN-CTSKTVQMIAESIYGKYAPFQ 377 (426)
Q Consensus 327 d~IL-~~Lg~~dvfPvDthV~Ril~rly~~~-~t~k~i~~~~~e~~g~~agwq 377 (426)
+||| ++++++ .||+|+||.|+++|++... .+++++.+.+.++++ +..|.
T Consensus 120 ~~ill~~~~~~-~~~vD~~v~Ri~~r~g~~~~~~~~~~~~~l~~~~p-~~~~~ 170 (191)
T TIGR01083 120 NVVLNVAFGIP-AIAVDTHVFRVSNRLGLSKGKDPDKVEEELLKLIP-REFWT 170 (191)
T ss_pred HHHHHHHcCCC-ccccchhHHHHHHHcCCCCCCCHHHHHHHHHHHCC-chhHH
Confidence 9997 899997 5999999999999987654 456777777766653 33343
No 9
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=99.87 E-value=9.8e-22 Score=188.01 Aligned_cols=109 Identities=17% Similarity=0.133 Sum_probs=89.6
Q ss_pred CCCCHHHHhcCCHHHHHHHC---cCc-HHHHHHHHHHHHHHhCCCChhHHHhhhhhcccccHHHHHHHHhcCCCcCHHHH
Q 014334 251 NFPSPRELANLDESFLAKRC---NLG-YRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTR 326 (426)
Q Consensus 251 ~FPtpe~La~~~~e~Lr~~~---g~G-yRAkyI~~lA~~i~eg~ldLe~L~~l~~~~~~~~~eea~e~L~~L~GIGpkTA 326 (426)
.||||+.|+++++++|++.+ |+. .||+||+++|+.+.++..+++. + ..++.++.|+++||||+|||
T Consensus 65 ~~~t~e~L~~a~~eeL~~~Irp~Gf~~~KA~~Lk~la~~i~~~~g~~~~---~-------~~~~~re~Ll~l~GIG~kTA 134 (218)
T PRK13913 65 DEINLKKIAYIEFSKLAECVRPSGFYNQKAKRLIDLSENILKDFGSFEN---F-------KQEVTREWLLDQKGIGKESA 134 (218)
T ss_pred cCCCHHHHHcCCHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHcCCchh---c-------cCchHHHHHHcCCCccHHHH
Confidence 68999999999999999853 442 3899999999999875444332 2 22467899999999999999
Q ss_pred HHHH-HHhCCCCccccchHHHHHHHHhhccCCCHHHHHHHHHHHh
Q 014334 327 NNVL-VCIGFYHVIPTDSETIRHLKQVHARNCTSKTVQMIAESIY 370 (426)
Q Consensus 327 d~IL-~~Lg~~dvfPvDthV~Ril~rly~~~~t~k~i~~~~~e~~ 370 (426)
|+|| ++++++ +||||+|++|+++|++....+|.++++.+.+..
T Consensus 135 d~iLlya~~rp-~fvVDty~~Rv~~RlG~~~~~y~~~~~~~~~~l 178 (218)
T PRK13913 135 DAILCYVCAKE-VMVVDKYSYLFLKKLGIEIEDYDELQHFFEKGV 178 (218)
T ss_pred HHHHHHHcCCC-ccccchhHHHHHHHcCCCCCCHHHHHHHHHHhh
Confidence 9997 899996 899999999999998766567888888776643
No 10
>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=99.87 E-value=2e-21 Score=191.84 Aligned_cols=157 Identities=24% Similarity=0.243 Sum_probs=107.0
Q ss_pred CCCCHHHHhcCCHHHHHHH-CcCcH--HHHHHHHHHHHHHhCCCChhHHHhhhhhcccccHHHHHHHHhcCCCcCHHHHH
Q 014334 251 NFPSPRELANLDESFLAKR-CNLGY--RAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRN 327 (426)
Q Consensus 251 ~FPtpe~La~~~~e~Lr~~-~g~Gy--RAkyI~~lA~~i~eg~ldLe~L~~l~~~~~~~~~eea~e~L~~L~GIGpkTAd 327 (426)
.||||++|+++++++|.+. .|+|| ||++|+++|+.|.+.... ..++.++.|++|||||+|||+
T Consensus 54 ~fpt~~~La~a~~eeL~~~~~~lG~y~RAr~L~~~A~~i~~~~~g--------------~~p~~~~~L~~LpGIG~~TA~ 119 (275)
T TIGR01084 54 RFPTVQALANAPQDEVLKLWEGLGYYARARNLHKAAQEVVEEFGG--------------EFPQDFEDLAALPGVGRYTAG 119 (275)
T ss_pred hCCCHHHHHCcCHHHHHHHHHHCCcHHHHHHHHHHHHHHHHHcCC--------------CCcHHHHHHHhCCCCCHHHHH
Confidence 5899999999999999764 36676 999999999999873110 223558999999999999999
Q ss_pred HHH-HHhCCCCccccchHHHHHHHHhhccC--CCHHHHHHH----HHHHhcCCChHHHHHHHHHHHHHHHH-hhCCCCCC
Q 014334 328 NVL-VCIGFYHVIPTDSETIRHLKQVHARN--CTSKTVQMI----AESIYGKYAPFQFLAYWSELWHFYEK-RFGKLSEM 399 (426)
Q Consensus 328 ~IL-~~Lg~~dvfPvDthV~Ril~rly~~~--~t~k~i~~~----~~e~~g~~agwq~l~fw~~Lw~~y~~-~~g~~~~~ 399 (426)
||| ++|++++ ++||+||+|++.|+|+.+ .+++++.+. +.+++....+-.+-...+++=+.++. +...|..|
T Consensus 120 ~Il~~a~~~~~-~~vD~~v~RVl~Rl~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~~~n~alm~lG~~vC~~~~P~C~~C 198 (275)
T TIGR01084 120 AILSFALNKPY-PILDGNVKRVLSRLFAVEGWPGKKKVENRLWTLAESLLPKADPEAFNQALMDLGAMICTRKKPKCDLC 198 (275)
T ss_pred HHHHHHCCCCC-CcchHhHHHHHHHHccCcCCCCHHHHHHHHHHHHHHHCChhhHHHHHHHHHHHhHHHcCCCCCCCCCC
Confidence 997 8999974 559999999999999875 233444444 55555432211111112345455554 45666666
Q ss_pred C----CccchhhhhcccCccccccccc
Q 014334 400 P----YSDYKLITASNMGIKNIRKVKR 422 (426)
Q Consensus 400 ~----~s~~~~~~~~~~~~~~~~~~~~ 422 (426)
| |..|+..+...+-.++++|+++
T Consensus 199 pl~~~C~~~~~~~~~~~p~~~~~~~~~ 225 (275)
T TIGR01084 199 PLQDFCLAYQQGTWEEYPVKKPKAAPP 225 (275)
T ss_pred CChhhCHHHHcCCHhhcCCCCCCCCCC
Confidence 6 4445555555555555444433
No 11
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=99.86 E-value=6.8e-21 Score=180.92 Aligned_cols=108 Identities=25% Similarity=0.274 Sum_probs=92.3
Q ss_pred ccCCCCHHHHhcCCHHHHHHHC---cCc-HHHHHHHHHHHHHHhCCCChhHHHhhhhhcccccHHHHHHHHhcCCCcCHH
Q 014334 249 IGNFPSPRELANLDESFLAKRC---NLG-YRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPF 324 (426)
Q Consensus 249 ~~~FPtpe~La~~~~e~Lr~~~---g~G-yRAkyI~~lA~~i~eg~ldLe~L~~l~~~~~~~~~eea~e~L~~L~GIGpk 324 (426)
+-.|||||+|+++++++|.+.+ ||. .||++|+++|+.|.+.... ..++.+++|++|||||+|
T Consensus 55 f~~~~t~e~l~~a~~~~l~~~I~~iGlyr~KAk~I~~~~~~l~e~~~g--------------~vP~~~~eL~~LPGVGrK 120 (211)
T COG0177 55 FKRYPTPEDLLNADEEELEELIKSIGLYRNKAKNIKELARILLEKFGG--------------EVPDTREELLSLPGVGRK 120 (211)
T ss_pred HHHcCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHcCC--------------CCCchHHHHHhCCCcchH
Confidence 4578899999999999888743 443 2899999999999974211 346679999999999999
Q ss_pred HHHHHH-HHhCCCCccccchHHHHHHHHhhccC-CCHHHHHHHHHHHhc
Q 014334 325 TRNNVL-VCIGFYHVIPTDSETIRHLKQVHARN-CTSKTVQMIAESIYG 371 (426)
Q Consensus 325 TAd~IL-~~Lg~~dvfPvDthV~Ril~rly~~~-~t~k~i~~~~~e~~g 371 (426)
||++|| +++|.+ +|||||||.|+.+|++..+ .++.+++..+.++++
T Consensus 121 TAnvVL~~a~g~p-~i~VDTHV~Rvs~R~gl~~~~~p~~ve~~L~~~iP 168 (211)
T COG0177 121 TANVVLSFAFGIP-AIAVDTHVHRVSNRLGLVPGKTPEEVEEALMKLIP 168 (211)
T ss_pred HHHHHHHhhcCCC-cccccchHHHHHHHhCCCCCCCHHHHHHHHHHHCC
Confidence 999998 999999 9999999999999999876 678899988888875
No 12
>PRK10880 adenine DNA glycosylase; Provisional
Probab=99.84 E-value=5.2e-20 Score=187.13 Aligned_cols=148 Identities=22% Similarity=0.192 Sum_probs=104.0
Q ss_pred CCCCHHHHhcCCHHHHHHH-CcCcH--HHHHHHHHHHHHHhCCCChhHHHhhhhhcccccHHHHHHHHhcCCCcCHHHHH
Q 014334 251 NFPSPRELANLDESFLAKR-CNLGY--RAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRN 327 (426)
Q Consensus 251 ~FPtpe~La~~~~e~Lr~~-~g~Gy--RAkyI~~lA~~i~eg~ldLe~L~~l~~~~~~~~~eea~e~L~~L~GIGpkTAd 327 (426)
.|||+++|+++++++|.+. .|+|| ||++|+++|+.|.+... ...++.++.|++|||||+|||+
T Consensus 58 ~fPt~~~La~a~~eel~~~~~glGyy~RAr~L~~~A~~i~~~~~--------------g~~p~~~~~L~~LpGIG~~TA~ 123 (350)
T PRK10880 58 RFPTVTDLANAPLDEVLHLWTGLGYYARARNLHKAAQQVATLHG--------------GEFPETFEEVAALPGVGRSTAG 123 (350)
T ss_pred HCcCHHHHHCcCHHHHHHHHHcCChHHHHHHHHHHHHHHHHHhC--------------CCchhhHHHHhcCCCccHHHHH
Confidence 5899999999999999874 48898 99999999999976311 0345678999999999999999
Q ss_pred HHH-HHhCCCCccccchHHHHHHHHhhccC--CCHHHHHHHH----HHHhcC--CChH-HHHHHHHHHHHHHHH-hhCCC
Q 014334 328 NVL-VCIGFYHVIPTDSETIRHLKQVHARN--CTSKTVQMIA----ESIYGK--YAPF-QFLAYWSELWHFYEK-RFGKL 396 (426)
Q Consensus 328 ~IL-~~Lg~~dvfPvDthV~Ril~rly~~~--~t~k~i~~~~----~e~~g~--~agw-q~l~fw~~Lw~~y~~-~~g~~ 396 (426)
||| ++++++ .++||+||+|++.|+|+.. .+++++.+.+ .++... +.-+ |.+ +++=+.++. +..+|
T Consensus 124 aIl~~af~~~-~~iVD~nV~RV~~Rl~~i~~~~~~~~~~~~l~~~~~~l~p~~~~~~~nqal---m~lGa~vC~p~~P~C 199 (350)
T PRK10880 124 AILSLSLGKH-FPILDGNVKRVLARCYAVSGWPGKKEVENRLWQLSEQVTPAVGVERFNQAM---MDLGAMVCTRSKPKC 199 (350)
T ss_pred HHHHHHCCCC-eecccHHHHHHHHHHhcccCCCChHHHHHHHHHHHHHhCChhHHHHHHHHH---HHhhHHhccCCCCCC
Confidence 997 899984 3448999999999998865 3344444433 333332 2222 222 345555664 45677
Q ss_pred CCCC----CccchhhhhcccCccc
Q 014334 397 SEMP----YSDYKLITASNMGIKN 416 (426)
Q Consensus 397 ~~~~----~s~~~~~~~~~~~~~~ 416 (426)
..|| |..|+..+-..+-.+.
T Consensus 200 ~~Cpl~~~C~~~~~~~~~~~P~k~ 223 (350)
T PRK10880 200 ELCPLQNGCIAYANHSWALYPGKK 223 (350)
T ss_pred CCCccHhhhHHHHcCCHhhCCCCC
Confidence 7776 4456655544443333
No 13
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=99.84 E-value=5.1e-20 Score=164.50 Aligned_cols=119 Identities=27% Similarity=0.349 Sum_probs=91.3
Q ss_pred CCCHHHHhcCCHHHHHHH---CcCc-HHHHHHHHHHHHHHhCCCChhHHHhhhhhcccccHHHHHHHHhcCCCcCHHHHH
Q 014334 252 FPSPRELANLDESFLAKR---CNLG-YRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRN 327 (426)
Q Consensus 252 FPtpe~La~~~~e~Lr~~---~g~G-yRAkyI~~lA~~i~eg~ldLe~L~~l~~~~~~~~~eea~e~L~~L~GIGpkTAd 327 (426)
||||++|+++++++|.+. +|+. .||+||+++|+.+.+... .+.++.++.|++|||||||||+
T Consensus 21 ~~~~~~l~~~~~~eL~~~l~~~g~~~~ka~~i~~~a~~~~~~~~--------------~~~~~~~~~L~~l~GIG~~tA~ 86 (149)
T smart00478 21 FPTPEDLAAADEEELEELIRPLGFYRRKAKYLIELARILVEEYG--------------GEVPDDREELLKLPGVGRKTAN 86 (149)
T ss_pred CCCHHHHHCCCHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHC--------------CCccHHHHHHHcCCCCcHHHHH
Confidence 679999999999988442 5653 499999999999887321 0234678999999999999999
Q ss_pred HHH-HHhCCCCccccchHHHHHHHHhhccC--CCHHHHHHHHHHHhcCCChHHHHHHHHHHHH
Q 014334 328 NVL-VCIGFYHVIPTDSETIRHLKQVHARN--CTSKTVQMIAESIYGKYAPFQFLAYWSELWH 387 (426)
Q Consensus 328 ~IL-~~Lg~~dvfPvDthV~Ril~rly~~~--~t~k~i~~~~~e~~g~~agwq~l~fw~~Lw~ 387 (426)
||| |++++ +++|+|+|+.|+++++|+.+ .+++++.+.++++++. ..|+.++.+ .+|.
T Consensus 87 ~~l~~~~~~-~~~~~D~~v~r~~~rl~~~~~~~~~~~~~~~~~~~~p~-~~~~~~~~~-~l~~ 146 (149)
T smart00478 87 AVLSFALGK-PFIPVDTHVLRIAKRLGLVDKKSTPEEVEKLLEKLLPK-EDWRELNLL-LIDF 146 (149)
T ss_pred HHHHHHCCC-CCCccchHHHHHHHHhCCCCCCCCHHHHHHHHHHHCCH-HHHHHHHHH-HHHH
Confidence 996 89999 78889999999999999864 3467777777666543 336655542 3543
No 14
>PRK13910 DNA glycosylase MutY; Provisional
Probab=99.77 E-value=2e-18 Score=171.56 Aligned_cols=154 Identities=19% Similarity=0.153 Sum_probs=106.6
Q ss_pred cccccccCCCCHHHHhcCCHHHHHHH-CcCcH--HHHHHHHHHHHHHhCCCChhHHHhhhhhcccccHHHHHHHHhcCCC
Q 014334 244 SARDRIGNFPSPRELANLDESFLAKR-CNLGY--RAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQING 320 (426)
Q Consensus 244 ~~~~~~~~FPtpe~La~~~~e~Lr~~-~g~Gy--RAkyI~~lA~~i~eg~ldLe~L~~l~~~~~~~~~eea~e~L~~L~G 320 (426)
++......|||+++|+++++++|.+. .|+|| ||++|+++|+.|.++... ..+..++.|++|||
T Consensus 14 yy~rf~~~fPt~e~La~a~~~el~~~~~glGyy~RAr~L~~~A~~i~~~~~g--------------~~P~~~~~L~~LpG 79 (289)
T PRK13910 14 FYSPFLEAFPTLKDLANAPLEEVLLLWRGLGYYSRAKNLKKSAEICVKEHHS--------------QLPNDYQSLLKLPG 79 (289)
T ss_pred HHHHHHHHCCCHHHHHCCCHHHHHHHHHcCCcHHHHHHHHHHHHHHHHHhCC--------------CCChhHHHHHhCCC
Confidence 34456789999999999999999875 47888 999999999999863210 11234899999999
Q ss_pred cCHHHHHHHH-HHhCCCCccccchHHHHHHHHhhccC--CCHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHHHhhCCCC
Q 014334 321 FGPFTRNNVL-VCIGFYHVIPTDSETIRHLKQVHARN--CTSKTVQMIAESIYGKYAPFQFLAYWSELWHFYEKRFGKLS 397 (426)
Q Consensus 321 IGpkTAd~IL-~~Lg~~dvfPvDthV~Ril~rly~~~--~t~k~i~~~~~e~~g~~agwq~l~fw~~Lw~~y~~~~g~~~ 397 (426)
||+|||+||| +++|++ ++|||+||+|++.|+++.. .+++++.....++...-.++..-...+++=+.++.....|.
T Consensus 80 IG~kTA~aIl~~af~~~-~~~VD~nV~RVl~Rl~g~~~~~~~~~l~~~~~~~l~~~~~~~~nqaLm~~Ga~iC~~~P~C~ 158 (289)
T PRK13910 80 IGAYTANAILCFGFREK-SACVDANIKRVLLRLFGLDPNIHAKDLQIKANDFLNLNESFNHNQALIDLGALICSPKPKCA 158 (289)
T ss_pred CCHHHHHHHHHHHCCCC-cCcccHHHHHHHHHHhcCCCCccHHHHHHHHHHhCCccchHHHHHHHHHHhHHHcCCCCCCC
Confidence 9999999997 999986 6789999999999998775 33455544444444332222211111234444554445677
Q ss_pred CCC----Cccchhhhhccc
Q 014334 398 EMP----YSDYKLITASNM 412 (426)
Q Consensus 398 ~~~----~s~~~~~~~~~~ 412 (426)
.|| |..|+..+...+
T Consensus 159 ~CPl~~~C~~~~~~~~~~~ 177 (289)
T PRK13910 159 ICPLNPYCLGKNNPEKHTL 177 (289)
T ss_pred CCcChhhhhhhhcCCcccc
Confidence 776 444554444433
No 15
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=99.76 E-value=9.2e-18 Score=159.62 Aligned_cols=113 Identities=19% Similarity=0.177 Sum_probs=82.6
Q ss_pred cCCHHHHHHH---CcCcH---HHHHHHHHHHHHHhCCCChhHHHhhhhhcccccHHHHHHHHh-cCCCcCHHHHHHHHHH
Q 014334 260 NLDESFLAKR---CNLGY---RAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLS-QINGFGPFTRNNVLVC 332 (426)
Q Consensus 260 ~~~~e~Lr~~---~g~Gy---RAkyI~~lA~~i~eg~ldLe~L~~l~~~~~~~~~eea~e~L~-~L~GIGpkTAd~IL~~ 332 (426)
.+++++|.+. +|-|| ||+||+++++.+ |. +..+... ..+.+++++.|+ ++||||+|||+|||+.
T Consensus 68 ~~~~eeL~~~Ir~~Gygf~~~KAk~I~~~~~~~--~~--l~~~~~~-----~~~~~~~R~~Ll~~lpGIG~KTAd~vL~~ 138 (208)
T PRK01229 68 YLSEEELEEKLKEVGHRFYNKRAEYIVEARKLY--GK--LKEIIKA-----DKDQFEAREFLVKNIKGIGYKEASHFLRN 138 (208)
T ss_pred CCCHHHHHHHHHHhhcccHHHHHHHHHHHHHHH--HH--HHHHHhc-----cCCchHHHHHHHHcCCCCcHHHHHHHHHH
Confidence 3455555443 44233 899999999986 22 2222200 025689999999 9999999999999965
Q ss_pred hCCCCccccchHHHHHHHHhhccC--------CCHHHHHHHHHHHhcCCChHHHHHH
Q 014334 333 IGFYHVIPTDSETIRHLKQVHARN--------CTSKTVQMIAESIYGKYAPFQFLAY 381 (426)
Q Consensus 333 Lg~~dvfPvDthV~Ril~rly~~~--------~t~k~i~~~~~e~~g~~agwq~l~f 381 (426)
.+..++|+||+||.|+++|++..+ .+|.+++..+.+++..+.-+.+.+-
T Consensus 139 ~~~~~~~iVDtHv~Ri~~RlG~~~~~~~~lt~~~y~~~E~~l~~~~~~~~~~~~~Ld 195 (208)
T PRK01229 139 VGYEDLAILDRHILRFLKRYGLIEEIPKTLSKKRYLEIEEILREIAEELGISLGELD 195 (208)
T ss_pred ccCCCeeeeeHHHHHHHHHhCCCcccccccCcCCHHHHHHHHHHHHHHcCCCHHHHH
Confidence 555679999999999999998765 2588899999998887765555554
No 16
>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=99.52 E-value=1.5e-13 Score=116.35 Aligned_cols=75 Identities=27% Similarity=0.373 Sum_probs=62.5
Q ss_pred CCCHHHHhcCCHHHHHHH---CcCc-HHHHHHHHHHHHHHhCCCChhHHHhhhhhcccccHHHHHHHHhcCCCcCHHHHH
Q 014334 252 FPSPRELANLDESFLAKR---CNLG-YRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRN 327 (426)
Q Consensus 252 FPtpe~La~~~~e~Lr~~---~g~G-yRAkyI~~lA~~i~eg~ldLe~L~~l~~~~~~~~~eea~e~L~~L~GIGpkTAd 327 (426)
||||++|+++++++|++. +|++ +||+||+++|+.+.
T Consensus 27 ~pt~~~l~~~~~~el~~~i~~~G~~~~ka~~i~~~a~~~~---------------------------------------- 66 (108)
T PF00730_consen 27 FPTPEALAEASEEELRELIRPLGFSRRKAKYIIELARAIL---------------------------------------- 66 (108)
T ss_dssp CSSHHHHHCSHHHHHHHHHTTSTSHHHHHHHHHHHHHHHH----------------------------------------
T ss_pred CCCHHHHHhCCHHHHHHHhhccCCCHHHHHHHHHHHHHhh----------------------------------------
Confidence 999999999999999883 4887 89999999999774
Q ss_pred HHHHHhCCCC-ccccchHHHHHHHHhhccCC--CHHHHHHHHHHHhcC
Q 014334 328 NVLVCIGFYH-VIPTDSETIRHLKQVHARNC--TSKTVQMIAESIYGK 372 (426)
Q Consensus 328 ~IL~~Lg~~d-vfPvDthV~Ril~rly~~~~--t~k~i~~~~~e~~g~ 372 (426)
|+++ ++|+|+|+.|+++++|+.+. +++++.+.+.+.|+|
T Consensus 67 ------~~~d~~~~~D~~v~r~~~r~~~~~~~~~~~~~~~~~~e~~~p 108 (108)
T PF00730_consen 67 ------GRPDPFPPVDTHVRRVLQRLGGIPEKKTKEETEKKLEELWPP 108 (108)
T ss_dssp ------C-SSSS-TTSHHHHHHHHHHTSSSSSTTHHHHHHHHHHHGTT
T ss_pred ------hcccceecCcHHHHHHHHHHcCCCCCCCHHHHHHHHHhhCcC
Confidence 6777 66699999999999999873 678888888777764
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=99.48 E-value=2.9e-13 Score=125.76 Aligned_cols=79 Identities=19% Similarity=0.180 Sum_probs=61.0
Q ss_pred CCHHHHhcCCHHHHHHHCc-C----cH---HHHHHHHHHHHHHh-CCCChhHHHhhhhhcccccHHHHHHHHhcCCCcCH
Q 014334 253 PSPRELANLDESFLAKRCN-L----GY---RAGRILKLARGIVD-GQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGP 323 (426)
Q Consensus 253 Ptpe~La~~~~e~Lr~~~g-~----Gy---RAkyI~~lA~~i~e-g~ldLe~L~~l~~~~~~~~~eea~e~L~~L~GIGp 323 (426)
+||+.|++++.++|.+.+. . || ||++|+++|+.|.+ -..+++.|.... ..+..++++.|++||||||
T Consensus 50 ~tp~~La~a~~eeL~~lI~~~pal~Gfy~~KAk~Lk~~a~~iie~y~G~v~~L~~~~----~p~t~~lre~Ll~LpGVG~ 125 (177)
T TIGR03252 50 LDAEDIAKYDPQAFVALFSERPAVHRFPGSMAKRVQALAQYVVDTYDGDATAVWTEG----DPDGKELLRRLKALPGFGK 125 (177)
T ss_pred CCHHHHHcCCHHHHHHHHhcCccccCchHHHHHHHHHHHHHHHHHhCCChhhhhccc----CCCcHHHHHHHHcCCCCCH
Confidence 6899999999999988663 2 54 89999999999985 233555555410 1256788999999999999
Q ss_pred HHHHHHHHHhCC
Q 014334 324 FTRNNVLVCIGF 335 (426)
Q Consensus 324 kTAd~IL~~Lg~ 335 (426)
|||++||.-||.
T Consensus 126 KTAnvVL~~l~~ 137 (177)
T TIGR03252 126 QKAKIFLALLGK 137 (177)
T ss_pred HHHHHHHHHHHH
Confidence 999999855554
No 18
>COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair]
Probab=99.47 E-value=4.3e-13 Score=135.27 Aligned_cols=156 Identities=26% Similarity=0.314 Sum_probs=112.7
Q ss_pred cccCCCCHHHHhcCCHHHHHH-HCcCcH--HHHHHHHHHHHHHh---CCCChhHHHhhhhhcccccHHHHHHHHhcCCCc
Q 014334 248 RIGNFPSPRELANLDESFLAK-RCNLGY--RAGRILKLARGIVD---GQIQLRELEDMCNEASLTAYVKLAEQLSQINGF 321 (426)
Q Consensus 248 ~~~~FPtpe~La~~~~e~Lr~-~~g~Gy--RAkyI~~lA~~i~e---g~ldLe~L~~l~~~~~~~~~eea~e~L~~L~GI 321 (426)
....|||+++||+++.+++.+ +.|+|| ||+.|+..|+.|.+ |.+. +..+.|.+||||
T Consensus 59 fl~rfPti~~LA~A~~~evl~~W~gLGYysRArnL~~~A~~v~~~~~G~~P-----------------~~~~~l~~LpGi 121 (342)
T COG1194 59 FLERFPTIKALAAAPEDEVLKAWEGLGYYSRARNLHKAAQEVVERHGGEFP-----------------DDEEELAALPGV 121 (342)
T ss_pred HHHhCCCHHHHhcCCHHHHHHHHHhcChHHHHHHHHHHHHHHHHHcCCCCC-----------------CCHHHHHhCCCC
Confidence 567899999999999887665 579996 99999999999996 4432 225778889999
Q ss_pred CHHHHHHHH-HHhCCCCccc-cchHHHHHHHHhhccCC------CHHHHHHHHHHHhcCCC-hHHHHHHHHHHHHHHHHh
Q 014334 322 GPFTRNNVL-VCIGFYHVIP-TDSETIRHLKQVHARNC------TSKTVQMIAESIYGKYA-PFQFLAYWSELWHFYEKR 392 (426)
Q Consensus 322 GpkTAd~IL-~~Lg~~dvfP-vDthV~Ril~rly~~~~------t~k~i~~~~~e~~g~~a-gwq~l~fw~~Lw~~y~~~ 392 (426)
|++||..|| ++++++ +| +|.+|.|++.|++.+.. +.+++...++++.-+-. +-++....++|=..-+..
T Consensus 122 G~yTa~Ail~~a~~~~--~~~lDgNV~RVl~R~f~i~~~~~~~~~~~~~~~~~~~ll~p~~~~~~fnqammdlGA~ICt~ 199 (342)
T COG1194 122 GPYTAGAILSFAFNQP--EPVLDGNVKRVLSRLFAISGDIGKPKTKKELWELAEQLLTPDRRPGDFNQAMMDLGATICTA 199 (342)
T ss_pred cHHHHHHHHHHHhCCC--CceeecchheeehhhhcccccccccchhHHHHHHHHHhcCCCCChHHHHHHHHHhhhHhhcC
Confidence 999999998 899874 67 89999999999998862 34555666666444444 222222224565555554
Q ss_pred -hCCCCCCC----CccchhhhhcccCccccccccc
Q 014334 393 -FGKLSEMP----YSDYKLITASNMGIKNIRKVKR 422 (426)
Q Consensus 393 -~g~~~~~~----~s~~~~~~~~~~~~~~~~~~~~ 422 (426)
..+|+.|| |..|+..+-...-.+.++++++
T Consensus 200 ~~P~C~~CPl~~~c~a~~~g~~~~~P~k~~k~~~~ 234 (342)
T COG1194 200 KKPKCSLCPLRDNCAAYRNGTPEKYPVKKPKKKLP 234 (342)
T ss_pred CCCCCCcCcchHHHHHHHcCCcccCCCcCcccccc
Confidence 37777777 3446666666666666666665
No 19
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=99.45 E-value=2.8e-12 Score=121.03 Aligned_cols=103 Identities=24% Similarity=0.313 Sum_probs=83.9
Q ss_pred HHHHhcCCHHHHHHHC-cCcH---HHHHHHHHHHHHHhCCCChhHHHhhhhhcccccHHHHHHHHhcCCCcCHHHHHHHH
Q 014334 255 PRELANLDESFLAKRC-NLGY---RAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNVL 330 (426)
Q Consensus 255 pe~La~~~~e~Lr~~~-g~Gy---RAkyI~~lA~~i~eg~ldLe~L~~l~~~~~~~~~eea~e~L~~L~GIGpkTAd~IL 330 (426)
++.|..++.++|.+++ +.|| ||+||+++.+.++.--..++.... ...|+.|++|+|||+-|||.||
T Consensus 63 l~~I~~~~~~~L~elIrpsGFYnqKa~rLk~l~k~l~~~~~~~~~~~~----------~~~R~~LL~iKGIG~ETaDsIL 132 (215)
T COG2231 63 LKKILKLDEEELAELIRPSGFYNQKAKRLKALSKNLAKFFINLESFKS----------EVLREELLSIKGIGKETADSIL 132 (215)
T ss_pred HHHHhcCCHHHHHHHHhccchHHHHHHHHHHHHHHHHHHhhhhhccch----------HHHHHHHHccCCcchhhHHHHH
Confidence 8999999999998865 3564 899998888888764444443322 3379999999999999999997
Q ss_pred -HHhCCCCccccchHHHHHHHHhhccCC-CHHHHHHHHHH
Q 014334 331 -VCIGFYHVIPTDSETIRHLKQVHARNC-TSKTVQMIAES 368 (426)
Q Consensus 331 -~~Lg~~dvfPvDthV~Ril~rly~~~~-t~k~i~~~~~e 368 (426)
++++++ +|+||...+|++.|+++... +++++.+.+++
T Consensus 133 lYa~~rp-~FVvD~Yt~R~l~rlg~i~~k~ydeik~~fe~ 171 (215)
T COG2231 133 LYALDRP-VFVVDKYTRRLLSRLGGIEEKKYDEIKELFEE 171 (215)
T ss_pred HHHhcCc-ccchhHHHHHHHHHhcccccccHHHHHHHHHh
Confidence 899996 89999999999999998874 57778777664
No 20
>KOG1921 consensus Endonuclease III [Replication, recombination and repair]
Probab=99.29 E-value=3.7e-11 Score=115.88 Aligned_cols=103 Identities=17% Similarity=0.164 Sum_probs=84.5
Q ss_pred CHHHHhcCCHHHHHHHC-cCcH---HHHHHHHHHHHHHhCCCChhHHHhhhhhcccccHHHHHHHHhcCCCcCHHHHHHH
Q 014334 254 SPRELANLDESFLAKRC-NLGY---RAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNV 329 (426)
Q Consensus 254 tpe~La~~~~e~Lr~~~-g~Gy---RAkyI~~lA~~i~eg~ldLe~L~~l~~~~~~~~~eea~e~L~~L~GIGpkTAd~I 329 (426)
|+|.+.+.++..|.+++ .+|| ||+||+++|+.+.+.-. .|.....+.|++|||||||.|..+
T Consensus 110 T~e~v~~~de~~l~~LI~~VgFy~rKA~ylkkta~IL~d~f~--------------gDIP~~v~dLlsLPGVGPKMa~L~ 175 (286)
T KOG1921|consen 110 TLEAVLKIDEPTLNELIYPVGFYTRKAKYLKKTAKILQDKFD--------------GDIPDTVEDLLSLPGVGPKMAHLT 175 (286)
T ss_pred CHHHHhccChHhHHhhhhhccchHHHHHHHHHHHHHHHHHhC--------------CCCchhHHHHhcCCCCchHHHHHH
Confidence 89999999998888754 3564 79999999998887421 155667899999999999999999
Q ss_pred H-HHhCCCCccccchHHHHHHHHhhccC---CCHHHHHHHHHHHh
Q 014334 330 L-VCIGFYHVIPTDSETIRHLKQVHARN---CTSKTVQMIAESIY 370 (426)
Q Consensus 330 L-~~Lg~~dvfPvDthV~Ril~rly~~~---~t~k~i~~~~~e~~ 370 (426)
| -+.|.-.-+-|||||+|+.+|+++.+ .++++++.+++.+.
T Consensus 176 m~~AWn~i~GI~VDtHVHRi~nrlgWv~~ktkspE~TR~aLq~wL 220 (286)
T KOG1921|consen 176 MQVAWNKIVGICVDTHVHRICNRLGWVDTKTKSPEQTRVALQQWL 220 (286)
T ss_pred HHHHhccceeEEeehHHHHHHHHhcccccccCCHHHHHHHHHHhC
Confidence 8 69998878889999999999999987 34777777765543
No 21
>PF07934 OGG_N: 8-oxoguanine DNA glycosylase, N-terminal domain; InterPro: IPR012904 The presence of 8-oxoguanine residues in DNA can give rise to G-C to T-A transversion mutations. This enzyme is found in archaeal, bacterial and eukaryotic species, and is specifically responsible for the process which leads to the removal of 8-oxoguanine residues. It has DNA glycosylase activity (3.2.2.23 from EC) and DNA lyase activity (4.2.99.18 from EC) []. The region featured in this family is the N-terminal domain, which is organised into a single copy of a TBP-like fold. The domain contributes residues to the 8-oxoguanine binding pocket []. ; GO: 0003684 damaged DNA binding, 0008534 oxidized purine base lesion DNA N-glycosylase activity, 0006289 nucleotide-excision repair; PDB: 3F0Z_A 3I0X_A 3F10_A 3I0W_A 1N39_A 1LWV_A 1YQM_A 2NOL_A 1YQL_A 1LWY_A ....
Probab=98.44 E-value=3e-07 Score=79.62 Aligned_cols=80 Identities=16% Similarity=0.169 Sum_probs=48.4
Q ss_pred EEEEEeccCCCCCceEEEEeccCCCCCCCCCHHHHHHHHHHHHHHhcCCchhhHhhHHHHHHHHHHHhhhchhhhcccCC
Q 014334 34 VDVTICQPQQDPHSLRIEVRNSASGSAPSLSQEQQDALLAQVKRMLRLSEADERNVRDFKRIVRQVAQEEGEESQYMTDF 113 (426)
Q Consensus 34 ~~v~i~q~~~~~~~L~~~v~~~~~~~~~~ls~~~~~~i~~~v~r~l~Ld~d~~~~~~~f~~~~~~~~~~~~~~~~~~~~~ 113 (426)
.+|.|+|. ++.+.+++...+ ........+.+...+++||+||.|+...++.|.+.++.+..... ++ .
T Consensus 38 ~~~~l~q~---~~~~~~~~~~~~----~~~~~~~~~~~~~~l~~YF~Ld~dl~~l~~~~~~~D~~l~~~~~----~~--~ 104 (117)
T PF07934_consen 38 RVVQLRQD---DDNLLYRCLSSA----EPSNSSSEEDIEEFLRDYFDLDVDLEKLYEDWSKKDPRLAKAID----KY--R 104 (117)
T ss_dssp EEEEEEEE---TTEEEEECE--T----TS---S-HHHHHHCHHHHTTTTS-HHHHHHHHCCHSHHHHHHHH----CT--T
T ss_pred eEEEEEEC---CCEEEEEEecCC----CcccccchhhHHHHHHHHhcCCccHHHHHHHHhhhCHHHHHHHh----cC--C
Confidence 56678884 788999998732 23334456778888999999999988888788766766654441 11 3
Q ss_pred cccccCCCChHHHH
Q 014334 114 SGRVFRSPTLFEDM 127 (426)
Q Consensus 114 ggRvlr~p~~fE~l 127 (426)
|.||+|| ||||+|
T Consensus 105 GlRiLrQ-dp~E~L 117 (117)
T PF07934_consen 105 GLRILRQ-DPFETL 117 (117)
T ss_dssp T--------HHHHH
T ss_pred CcEEECC-ChhhhC
Confidence 6699997 899997
No 22
>KOG2457 consensus A/G-specific adenine DNA glycosylase [Replication, recombination and repair]
Probab=98.16 E-value=7.9e-06 Score=83.82 Aligned_cols=137 Identities=23% Similarity=0.312 Sum_probs=92.8
Q ss_pred ccCCCCHHHHhcCCHH-HHHH-HCcCcH--HHHHHHHHHHHHHhCCCChhHHHhhhhhcccccHHHHHHHHhc-CCCcCH
Q 014334 249 IGNFPSPRELANLDES-FLAK-RCNLGY--RAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQ-INGFGP 323 (426)
Q Consensus 249 ~~~FPtpe~La~~~~e-~Lr~-~~g~Gy--RAkyI~~lA~~i~eg~ldLe~L~~l~~~~~~~~~eea~e~L~~-L~GIGp 323 (426)
.-..||..+|+.++.+ +... +.|+|| |+++|++-|++++.|.-. .....-+.|++ +||||+
T Consensus 151 MqkwPTl~dla~Asl~~eVn~lWaGlGyY~R~rrL~ega~~vv~~~~g--------------e~Prta~~l~kgvpGVG~ 216 (555)
T KOG2457|consen 151 MQKWPTLYDLAQASLEKEVNELWAGLGYYRRARRLLEGAKMVVAGTEG--------------EFPRTASSLMKGVPGVGQ 216 (555)
T ss_pred HHhCchHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhCCC--------------CCCChHHHHHhhCCCCCc
Confidence 4579999999998874 4444 469997 899999999999975311 11222356665 999999
Q ss_pred HHHHHHH-HHhCCCCccccchHHHHHHHHhhccCCCH------HHHHHHHHHHhcCCCh--H-HHHHHHHHHHHHH-HHh
Q 014334 324 FTRNNVL-VCIGFYHVIPTDSETIRHLKQVHARNCTS------KTVQMIAESIYGKYAP--F-QFLAYWSELWHFY-EKR 392 (426)
Q Consensus 324 kTAd~IL-~~Lg~~dvfPvDthV~Ril~rly~~~~t~------k~i~~~~~e~~g~~ag--w-q~l~fw~~Lw~~y-~~~ 392 (426)
+||..|+ .+++.... -||-+|.|++.|...+..+. ..+-+.+.++-.+-+| + |++.. |=.-. ...
T Consensus 217 YTAGAiaSIAf~q~tG-iVDGNVirvlsRalAIhsDcSkgk~~q~~wkLA~qLVDP~RPGDFNQalME---LGAt~CTpq 292 (555)
T KOG2457|consen 217 YTAGAIASIAFNQVTG-IVDGNVIRVLSRALAIHSDCSKGKFFQSSWKLAAQLVDPSRPGDFNQALME---LGATLCTPQ 292 (555)
T ss_pred cchhhhhhhhhcCccc-ccccchHHHhHHhHhhcCCcchhhHHHHHHHHHHHhcCCCCCCcHHHHHHH---hcCeeccCC
Confidence 9999998 78887532 28999999999988776321 2233455566666655 4 66653 32222 222
Q ss_pred hCCCCCCCCcc
Q 014334 393 FGKLSEMPYSD 403 (426)
Q Consensus 393 ~g~~~~~~~s~ 403 (426)
...|+.||-|.
T Consensus 293 ~P~CS~CPvss 303 (555)
T KOG2457|consen 293 KPSCSSCPVSS 303 (555)
T ss_pred CCCcCCCCcHH
Confidence 45667776554
No 23
>COG1059 Thermostable 8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=97.59 E-value=0.0012 Score=62.41 Aligned_cols=88 Identities=24% Similarity=0.279 Sum_probs=63.7
Q ss_pred CHHHHhcCCHHHHHHHCcCcH---HHHHHHHHHHHHHhCCCChhHHHhhhhhcccccHHH-HHHHHh-cCCCcCHHHHHH
Q 014334 254 SPRELANLDESFLAKRCNLGY---RAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVK-LAEQLS-QINGFGPFTRNN 328 (426)
Q Consensus 254 tpe~La~~~~e~Lr~~~g~Gy---RAkyI~~lA~~i~eg~ldLe~L~~l~~~~~~~~~ee-a~e~L~-~L~GIGpkTAd~ 328 (426)
+-|+| .|.|+. +|-.| ||+||...=+.+-+ +..+-+. .+.+. +|+.|. .++|||-|-|..
T Consensus 72 ~~eEL----~e~Lk~-~g~Rf~n~raeyIVeaR~~~~~----lk~~v~~------~~~~~vaRE~Lv~nikGiGyKEASH 136 (210)
T COG1059 72 SEEEL----REKLKE-VGYRFYNVRAEYIVEAREKFDD----LKIIVKA------DENEKVARELLVENIKGIGYKEASH 136 (210)
T ss_pred CHHHH----HHHHHH-hcchhcccchHHHHHHHHHHHH----HHHHHhc------CcchHHHHHHHHHHcccccHHHHHH
Confidence 55555 345554 54333 89999988777653 2233332 12233 888888 999999999999
Q ss_pred HHHHhCCCCccccchHHHHHHHHhhccC
Q 014334 329 VLVCIGFYHVIPTDSETIRHLKQVHARN 356 (426)
Q Consensus 329 IL~~Lg~~dvfPvDthV~Ril~rly~~~ 356 (426)
+|+-.|..|+--.|-|+.|-+.+++..+
T Consensus 137 FLRNVG~~D~AIlDrHIlr~l~r~g~i~ 164 (210)
T COG1059 137 FLRNVGFEDLAILDRHILRWLVRYGLID 164 (210)
T ss_pred HHHhcChhHHHHHHHHHHHHHHHhcccc
Confidence 9998888775558999999999998876
No 24
>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=97.32 E-value=0.00019 Score=48.52 Aligned_cols=20 Identities=40% Similarity=0.657 Sum_probs=17.4
Q ss_pred HHHHHhcCCCcCHHHHHHHH
Q 014334 311 LAEQLSQINGFGPFTRNNVL 330 (426)
Q Consensus 311 a~e~L~~L~GIGpkTAd~IL 330 (426)
..++|++||||||+||+.|+
T Consensus 9 s~eeL~~lpGIG~~tA~~I~ 28 (30)
T PF00633_consen 9 SIEELMKLPGIGPKTANAIL 28 (30)
T ss_dssp SHHHHHTSTT-SHHHHHHHH
T ss_pred CHHHHHhCCCcCHHHHHHHH
Confidence 47899999999999999996
No 25
>PF06029 AlkA_N: AlkA N-terminal domain; InterPro: IPR010316 This domain is found at the N terminus of bacterial AlkA 3.2.2.21 from EC. AlkA (3-methyladenine-DNA glycosylase II) is a base excision repair glycosylase from Escherichia coli. It removes a variety of alkylated bases from DNA, primarily by removing alkylation damage from duplex and single stranded DNA. AlkA flips a 1-azaribose abasic nucleotide out of DNA. This produces a 66 degrees bend in the DNA and a marked widening of the minor groove []. This groove is a large hydrophobic cleft, which is unusually rich in aromatic residues. AlkA recognises electron-deficient methylated bases through pi-donor/acceptor interactions involving the electron-rich aromatic cleft. AlkA is similar in fold and active site location to the bifunctional glycosylase/lyase endonuclease III. This suggests that the two may use similar mechanisms for base excision []. The structural analysis of the AlkA and AlkA-hypoxanthine structures indicate that free hypoxanthine binding in the active site may inhibit glycosylase activity [].; GO: 0003905 alkylbase DNA N-glycosylase activity; PDB: 1MPG_B 3CWS_D 3CW7_C 3CWA_B 3D4V_A 3CWT_C 3CWU_B 3OGD_A 3CVS_C 1PVS_A ....
Probab=95.98 E-value=0.03 Score=49.14 Aligned_cols=82 Identities=16% Similarity=0.154 Sum_probs=46.2
Q ss_pred cccccceecCCCCCCCCCCCceEEEEEeccCCCCCceEEEEeccCCCCCCCCCHHHHHHHHHHHHHHhcCCchhhHhhHH
Q 014334 12 RSLSRPLHLSNSLDNTDIPSVSVDVTICQPQQDPHSLRIEVRNSASGSAPSLSQEQQDALLAQVKRMLRLSEADERNVRD 91 (426)
Q Consensus 12 ~~~~r~lr~~~~~~~~~~~~~~~~v~i~q~~~~~~~L~~~v~~~~~~~~~~ls~~~~~~i~~~v~r~l~Ld~d~~~~~~~ 91 (426)
++|.|+++++.. .-.|+|+.. ...++|.+++..+ ...+...+.+.|+|||+||.| ...
T Consensus 33 ~~Y~Rt~~l~~~---------~g~v~v~~~-~~~~~l~v~~~~~--------~~~~l~~~~~rvRrlfDLdaD----p~~ 90 (116)
T PF06029_consen 33 GSYRRTFRLGGG---------PGWVSVRHD-PEKNHLRVTLSLS--------DLRDLPAVIARVRRLFDLDAD----PQA 90 (116)
T ss_dssp SEEEEEEEETTE---------EEEEEEEEE-TTTTEEEEEE-GG--------GGGGHHHHHHHHHHHTTTT------HHH
T ss_pred CeEEEEEEeCCe---------EEEEEEEEc-CCCCEEEEEEEcc--------cHHHHHHHHHHHHHHhCCCCC----HHH
Confidence 489999999986 566777664 1357899999873 124567899999999999999 555
Q ss_pred HHHHHHHHHhhhchhhhcccCCcccccCC
Q 014334 92 FKRIVRQVAQEEGEESQYMTDFSGRVFRS 120 (426)
Q Consensus 92 f~~~~~~~~~~~~~~~~~~~~~ggRvlr~ 120 (426)
..+.- ++.++... ...-|.|+++.
T Consensus 91 I~~~L--dp~l~p~~---~~~pGLRlPG~ 114 (116)
T PF06029_consen 91 IEAHL--DPLLAPLV---AARPGLRLPGA 114 (116)
T ss_dssp HHHHH------GGGG---TS-TT------
T ss_pred HHHHH--hhcccccc---cCCCCCcCCCc
Confidence 54333 33333221 11236688763
No 26
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=93.89 E-value=0.037 Score=35.78 Aligned_cols=17 Identities=35% Similarity=0.716 Sum_probs=15.9
Q ss_pred HHhcCCCcCHHHHHHHH
Q 014334 314 QLSQINGFGPFTRNNVL 330 (426)
Q Consensus 314 ~L~~L~GIGpkTAd~IL 330 (426)
.|++++|||+|+|+.++
T Consensus 2 ~L~~i~GiG~k~A~~il 18 (26)
T smart00278 2 ELLKVPGIGPKTAEKIL 18 (26)
T ss_pred hhhhCCCCCHHHHHHHH
Confidence 58899999999999997
No 27
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=92.21 E-value=0.46 Score=45.48 Aligned_cols=67 Identities=24% Similarity=0.267 Sum_probs=41.8
Q ss_pred ccccCCCCHHHHhcCCHHHHHHHCcCcHH-HHHHHHHHHHHHhCCCChhHHHhhhhhcccccHHHHHHHHhcCCCcCHHH
Q 014334 247 DRIGNFPSPRELANLDESFLAKRCNLGYR-AGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFT 325 (426)
Q Consensus 247 ~~~~~FPtpe~La~~~~e~Lr~~~g~GyR-AkyI~~lA~~i~eg~ldLe~L~~l~~~~~~~~~eea~e~L~~L~GIGpkT 325 (426)
...|-|.|.++..- -+.|...-|+|-| |-.|. +. ++.+.|... =..+..+.|.++||||+||
T Consensus 57 ~~LYGF~t~~Er~l--F~~LisVsGIGPK~ALaIL-------s~-~~~~el~~a-------I~~~D~~~L~~vpGIGkKt 119 (196)
T PRK13901 57 LKLFGFLNSSEREV--FEELIGVDGIGPRAALRVL-------SG-IKYNEFRDA-------IDREDIELISKVKGIGNKM 119 (196)
T ss_pred ceeeCCCCHHHHHH--HHHHhCcCCcCHHHHHHHH-------cC-CCHHHHHHH-------HHhCCHHHHhhCCCCCHHH
Confidence 35799999888532 3445554588987 43333 21 233333322 0112258999999999999
Q ss_pred HHHHH
Q 014334 326 RNNVL 330 (426)
Q Consensus 326 Ad~IL 330 (426)
|+-|.
T Consensus 120 AeRII 124 (196)
T PRK13901 120 AGKIF 124 (196)
T ss_pred HHHHH
Confidence 99994
No 28
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=89.67 E-value=3.9 Score=38.83 Aligned_cols=108 Identities=18% Similarity=0.172 Sum_probs=57.1
Q ss_pred ccccCCCCHHHHhcCCHHHHHHHCcCcHHHHHHHHHHHHHHhCCCChhHHHhhhhhcccccHHHHHHHHhcCCCcCHHHH
Q 014334 247 DRIGNFPSPRELANLDESFLAKRCNLGYRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTR 326 (426)
Q Consensus 247 ~~~~~FPtpe~La~~~~e~Lr~~~g~GyRAkyI~~lA~~i~eg~ldLe~L~~l~~~~~~~~~eea~e~L~~L~GIGpkTA 326 (426)
...|-|.|.++..- -+.|...-|+|-|. |-.|.++ ++.+.|... =..+..+.|+++||||+|||
T Consensus 58 ~~LyGF~~~~Er~l--F~~Li~V~GIGpK~------AL~iLs~-~~~~el~~a-------I~~~D~~~L~~vpGIGkKtA 121 (188)
T PRK14606 58 ITLYGFSNERKKEL--FLSLTKVSRLGPKT------ALKIISN-EDAETLVTM-------IASQDVEGLSKLPGISKKTA 121 (188)
T ss_pred ceeeCCCCHHHHHH--HHHHhccCCccHHH------HHHHHcC-CCHHHHHHH-------HHhCCHHHHhhCCCCCHHHH
Confidence 46789999887532 23455445788874 2223332 333333332 11222589999999999999
Q ss_pred HHHHHHhC-CCCccc-cc-hHHHHHHHHhhccCCCHHHHHHHHHHHh
Q 014334 327 NNVLVCIG-FYHVIP-TD-SETIRHLKQVHARNCTSKTVQMIAESIY 370 (426)
Q Consensus 327 d~IL~~Lg-~~dvfP-vD-thV~Ril~rly~~~~t~k~i~~~~~e~~ 370 (426)
+-|..-|. +...+. .+ .....++..+-.++.+++++...+.+..
T Consensus 122 erIilELkdK~~~~~~~~~~~~~e~~~AL~~LGy~~~ea~~av~~~~ 168 (188)
T PRK14606 122 ERIVMELKDEFESAGIKDMRIYHESLEALVSLGYPEKQAREAVKHVY 168 (188)
T ss_pred HHHHHHHHHhhccccCCCcccHHHHHHHHHHcCCCHHHHHHHHHHHh
Confidence 99943222 211111 11 1123344444444445566666665554
No 29
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=89.64 E-value=2.6 Score=39.94 Aligned_cols=107 Identities=11% Similarity=0.176 Sum_probs=57.2
Q ss_pred ccccCCCCHHHHhcCCHHHHHHHCcCcHHHHHHHHHHHHHHhCCCChhHHHhhhhhcccccHHHHHHHHhcCCCcCHHHH
Q 014334 247 DRIGNFPSPRELANLDESFLAKRCNLGYRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTR 326 (426)
Q Consensus 247 ~~~~~FPtpe~La~~~~e~Lr~~~g~GyRAkyI~~lA~~i~eg~ldLe~L~~l~~~~~~~~~eea~e~L~~L~GIGpkTA 326 (426)
...|-|-|.++..- -+.|...-|.|-|. |-.|.+. ++.+.|... =..+..+.|.++||||+|||
T Consensus 58 ~~LyGF~~~~Er~l--F~~Li~VsGIGpK~------Al~ILs~-~~~~el~~a-------I~~~D~~~L~~vpGIGkKtA 121 (183)
T PRK14601 58 NKLYGFLDKDEQKM--FEMLLKVNGIGANT------AMAVCSS-LDVNSFYKA-------LSLGDESVLKKVPGIGPKSA 121 (183)
T ss_pred ceeeCCCCHHHHHH--HHHHhccCCccHHH------HHHHHcC-CCHHHHHHH-------HHhCCHHHHhhCCCCCHHHH
Confidence 35789999888532 34455545888874 2223332 334444432 11222589999999999999
Q ss_pred HHHHHHh-CCCCcc-ccchHHHHHHHHhhccCCCHHHHHHHHHHH
Q 014334 327 NNVLVCI-GFYHVI-PTDSETIRHLKQVHARNCTSKTVQMIAESI 369 (426)
Q Consensus 327 d~IL~~L-g~~dvf-PvDthV~Ril~rly~~~~t~k~i~~~~~e~ 369 (426)
+-|+.-| ++.... +.......++..+-.++.+.+++.+.+.++
T Consensus 122 eRIilELkdK~~~~~~~~~~~~ea~~AL~~LGy~~~ea~~a~~~~ 166 (183)
T PRK14601 122 KRIIAELSDAKTKLENVSDDKSEALAALLTLGFKQEKIIKVLASC 166 (183)
T ss_pred HHHHHHHHHHhhccCCCCccHHHHHHHHHHcCCCHHHHHHHHHhc
Confidence 9994222 221111 111122344444444444555555555443
No 30
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=89.42 E-value=0.51 Score=36.87 Aligned_cols=37 Identities=27% Similarity=0.373 Sum_probs=24.6
Q ss_pred HHHHHhCCCChhHHHhhhhhcccccHHHHHHHHhcCCCcCHHHHHHHH
Q 014334 283 ARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNVL 330 (426)
Q Consensus 283 A~~i~eg~ldLe~L~~l~~~~~~~~~eea~e~L~~L~GIGpkTAd~IL 330 (426)
|+.+++.--+++.|.+. + .++|.+++|||+.+|+.|.
T Consensus 16 ak~L~~~f~sl~~l~~a-------~----~e~L~~i~gIG~~~A~si~ 52 (64)
T PF12826_consen 16 AKLLAKHFGSLEALMNA-------S----VEELSAIPGIGPKIAQSIY 52 (64)
T ss_dssp HHHHHHCCSCHHHHCC-------------HHHHCTSTT--HHHHHHHH
T ss_pred HHHHHHHcCCHHHHHHc-------C----HHHHhccCCcCHHHHHHHH
Confidence 44555554566666654 3 4689999999999999996
No 31
>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=88.91 E-value=1.7 Score=34.23 Aligned_cols=50 Identities=18% Similarity=0.149 Sum_probs=34.8
Q ss_pred HHHHC-cCcHHHHHHHHHHHHHHhCCCChhHHHhhhhhcccccHHHHHHHHhcCCCcCHHHHHHHH
Q 014334 266 LAKRC-NLGYRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNVL 330 (426)
Q Consensus 266 Lr~~~-g~GyRAkyI~~lA~~i~eg~ldLe~L~~l~~~~~~~~~eea~e~L~~L~GIGpkTAd~IL 330 (426)
+.+.. +-.||+..-...|..|..-..++ ....+.|.+|||||+.+|.-|-
T Consensus 14 ~~~~~~~~~~r~~aY~~Aa~~i~~l~~~i---------------~~~~~~~~~l~gIG~~ia~kI~ 64 (68)
T PF14716_consen 14 LYELQGGDPFRARAYRRAAAAIKALPYPI---------------TSGEEDLKKLPGIGKSIAKKID 64 (68)
T ss_dssp HHHHTSTSHHHHHHHHHHHHHHHHSSS-H---------------HSHHHHHCTSTTTTHHHHHHHH
T ss_pred HHHHhhCCcHHHHHHHHHHHHHHhCCHhH---------------hhHHHHHhhCCCCCHHHHHHHH
Confidence 33334 56689998999999887743322 2221259999999999999883
No 32
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=87.56 E-value=1.4 Score=45.26 Aligned_cols=62 Identities=19% Similarity=0.236 Sum_probs=41.0
Q ss_pred HHHHHHCcCcHH-HHHHHHHHHHHHhCCCC-hhHHHhhhhhcccccHHHHHHHHhcCCCcCHHHHHHHHHHhCCC
Q 014334 264 SFLAKRCNLGYR-AGRILKLARGIVDGQIQ-LRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNVLVCIGFY 336 (426)
Q Consensus 264 e~Lr~~~g~GyR-AkyI~~lA~~i~eg~ld-Le~L~~l~~~~~~~~~eea~e~L~~L~GIGpkTAd~IL~~Lg~~ 336 (426)
++|.+.-|+|-+ |+-|.++ +..|.+. +..... .+.......|++++||||++|.-+-. +|..
T Consensus 48 ~~l~~lpgIG~~ia~kI~Ei---l~tG~~~~~~e~l~-------~~~p~~l~~l~~i~GiGpk~a~~l~~-lGi~ 111 (334)
T smart00483 48 KDLKGLPGIGDKIKKKIEEI---IETGKSSKVLEILN-------DEVYKSLKLFTNVFGVGPKTAAKWYR-KGIR 111 (334)
T ss_pred HHHhcCCCccHHHHHHHHHH---HHhCcHHHHHHHhc-------CcHHHHHHHHHccCCcCHHHHHHHHH-hCCC
Confidence 356654588876 4444444 4468765 222222 26788899999999999999977754 6653
No 33
>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=85.98 E-value=1.7 Score=41.20 Aligned_cols=67 Identities=21% Similarity=0.167 Sum_probs=42.4
Q ss_pred ccccCCCCHHHHhcCCHHHHHHHCcCcHH-HHHHHHHHHHHHhCCCChhHHHhhhhhcccccHHHHHHHHhcCCCcCHHH
Q 014334 247 DRIGNFPSPRELANLDESFLAKRCNLGYR-AGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFT 325 (426)
Q Consensus 247 ~~~~~FPtpe~La~~~~e~Lr~~~g~GyR-AkyI~~lA~~i~eg~ldLe~L~~l~~~~~~~~~eea~e~L~~L~GIGpkT 325 (426)
...|-|.|.++..- -..|...-|+|-| |..| .+ ..+.+.|... =..+....|.++||||+||
T Consensus 57 ~~LyGF~~~~Er~l--F~~L~~V~GIGpK~Al~i-------L~-~~~~~el~~a-------I~~~d~~~L~~ipGiGkKt 119 (191)
T TIGR00084 57 ELLFGFNTLEEREL--FKELIKVNGVGPKLALAI-------LS-NMSPEEFVYA-------IETEEVKALVKIPGVGKKT 119 (191)
T ss_pred ceeeCCCCHHHHHH--HHHHhCCCCCCHHHHHHH-------Hh-cCCHHHHHHH-------HHhCCHHHHHhCCCCCHHH
Confidence 36799999988532 2445554588976 4444 22 2344444432 0112247799999999999
Q ss_pred HHHHH
Q 014334 326 RNNVL 330 (426)
Q Consensus 326 Ad~IL 330 (426)
|+-|+
T Consensus 120 AerIi 124 (191)
T TIGR00084 120 AERLL 124 (191)
T ss_pred HHHHH
Confidence 99995
No 34
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=85.33 E-value=2.2 Score=32.56 Aligned_cols=50 Identities=24% Similarity=0.365 Sum_probs=31.8
Q ss_pred HHHHHCcCcHHHHHHHHHHHHHHh-CCCChhHHHhhhhhcccccHHHHHHHHhcCCCcCHHHHHHHHH
Q 014334 265 FLAKRCNLGYRAGRILKLARGIVD-GQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNVLV 331 (426)
Q Consensus 265 ~Lr~~~g~GyRAkyI~~lA~~i~e-g~ldLe~L~~l~~~~~~~~~eea~e~L~~L~GIGpkTAd~IL~ 331 (426)
+|.+.-|+|-+ +|+.+.+ |-.+++.|... + .+.|.+++|||+++|+-+..
T Consensus 6 ~L~~I~Gig~~------~a~~L~~~G~~t~~~l~~a-------~----~~~L~~i~Gig~~~a~~i~~ 56 (60)
T PF14520_consen 6 DLLSIPGIGPK------RAEKLYEAGIKTLEDLANA-------D----PEELAEIPGIGEKTAEKIIE 56 (60)
T ss_dssp HHHTSTTCHHH------HHHHHHHTTCSSHHHHHTS-------H----HHHHHTSTTSSHHHHHHHHH
T ss_pred hhccCCCCCHH------HHHHHHhcCCCcHHHHHcC-------C----HHHHhcCCCCCHHHHHHHHH
Confidence 44443466654 2223333 55566666654 2 36799999999999999863
No 35
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=85.10 E-value=11 Score=35.83 Aligned_cols=67 Identities=21% Similarity=0.233 Sum_probs=40.5
Q ss_pred ccccCCCCHHHHhcCCHHHHHHHCcCcHH-HHHHHHHHHHHHhCCCChhHHHhhhhhcccccHHHHHHHHhcCCCcCHHH
Q 014334 247 DRIGNFPSPRELANLDESFLAKRCNLGYR-AGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFT 325 (426)
Q Consensus 247 ~~~~~FPtpe~La~~~~e~Lr~~~g~GyR-AkyI~~lA~~i~eg~ldLe~L~~l~~~~~~~~~eea~e~L~~L~GIGpkT 325 (426)
...|-|-+.++-.- -+.|...-|+|-| |-.| .+. ++.+.|... =..+..+.|.++||||+||
T Consensus 58 ~~LyGF~~~~Er~l--F~~Li~V~GIGpK~Al~I-------Ls~-~~~~~l~~a-------I~~~D~~~L~~vpGIGkKt 120 (194)
T PRK14605 58 LSLFGFATTEELSL--FETLIDVSGIGPKLGLAM-------LSA-MNAEALASA-------IISGNAELLSTIPGIGKKT 120 (194)
T ss_pred ceeeCCCCHHHHHH--HHHHhCCCCCCHHHHHHH-------HHh-CCHHHHHHH-------HHhCCHHHHHhCCCCCHHH
Confidence 35789998887532 2345544578876 4333 332 233333221 0022257899999999999
Q ss_pred HHHHH
Q 014334 326 RNNVL 330 (426)
Q Consensus 326 Ad~IL 330 (426)
|+-|.
T Consensus 121 AerIi 125 (194)
T PRK14605 121 ASRIV 125 (194)
T ss_pred HHHHH
Confidence 99973
No 36
>PRK00076 recR recombination protein RecR; Reviewed
Probab=84.33 E-value=0.89 Score=43.54 Aligned_cols=30 Identities=23% Similarity=0.312 Sum_probs=25.9
Q ss_pred cHHHHHHHHhcCCCcCHHHHHHHH-HHhCCC
Q 014334 307 AYVKLAEQLSQINGFGPFTRNNVL-VCIGFY 336 (426)
Q Consensus 307 ~~eea~e~L~~L~GIGpkTAd~IL-~~Lg~~ 336 (426)
+.+++.+.|..|||||+|+|.-+. +-|.++
T Consensus 5 ~~~~Li~~l~~LPGIG~KsA~Rla~~ll~~~ 35 (196)
T PRK00076 5 PIEKLIEALRKLPGIGPKSAQRLAFHLLQRD 35 (196)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHHHcCC
Confidence 578899999999999999999995 667665
No 37
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=83.91 E-value=1.4 Score=42.44 Aligned_cols=67 Identities=21% Similarity=0.232 Sum_probs=42.5
Q ss_pred cccCCCCHHHHhcCCHHHHHHHCcCcHHHHHHHHHHHHHHhCCCChhHHHhhhhhcccccHHHHHHHHhcCCCcCHHHHH
Q 014334 248 RIGNFPSPRELANLDESFLAKRCNLGYRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRN 327 (426)
Q Consensus 248 ~~~~FPtpe~La~~~~e~Lr~~~g~GyRAkyI~~lA~~i~eg~ldLe~L~~l~~~~~~~~~eea~e~L~~L~GIGpkTAd 327 (426)
..|-|.|.++-.- -..|.+.-|+|=|. |-+|.+. ++.+.|.+. =..+..+.|.++||||+|||+
T Consensus 59 ~LyGF~~~~ER~l--F~~LisVnGIGpK~------ALaiLs~-~~~~~l~~a-------I~~~d~~~L~k~PGIGkKtAe 122 (201)
T COG0632 59 LLYGFLTEEEREL--FRLLISVNGIGPKL------ALAILSN-LDPEELAQA-------IANEDVKALSKIPGIGKKTAE 122 (201)
T ss_pred HHcCCCCHHHHHH--HHHHHccCCccHHH------HHHHHcC-CCHHHHHHH-------HHhcChHhhhcCCCCCHHHHH
Confidence 4677888776321 23454445778764 2234443 455666654 123346899999999999999
Q ss_pred HHH
Q 014334 328 NVL 330 (426)
Q Consensus 328 ~IL 330 (426)
-|+
T Consensus 123 riv 125 (201)
T COG0632 123 RIV 125 (201)
T ss_pred HHH
Confidence 994
No 38
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=83.90 E-value=0.95 Score=43.33 Aligned_cols=30 Identities=20% Similarity=0.296 Sum_probs=26.0
Q ss_pred cHHHHHHHHhcCCCcCHHHHHHHH-HHhCCC
Q 014334 307 AYVKLAEQLSQINGFGPFTRNNVL-VCIGFY 336 (426)
Q Consensus 307 ~~eea~e~L~~L~GIGpkTAd~IL-~~Lg~~ 336 (426)
..+.+.+.|..|||||||+|.-+. +.|.+.
T Consensus 6 ~i~~LI~~l~kLPGvG~KsA~R~AfhLL~~~ 36 (198)
T COG0353 6 PIEKLIDALKKLPGVGPKSAQRLAFHLLQRD 36 (198)
T ss_pred HHHHHHHHHhhCCCCChhHHHHHHHHHHccC
Confidence 568889999999999999999996 567664
No 39
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=83.88 E-value=0.99 Score=43.21 Aligned_cols=30 Identities=23% Similarity=0.329 Sum_probs=25.8
Q ss_pred cHHHHHHHHhcCCCcCHHHHHHHH-HHhCCC
Q 014334 307 AYVKLAEQLSQINGFGPFTRNNVL-VCIGFY 336 (426)
Q Consensus 307 ~~eea~e~L~~L~GIGpkTAd~IL-~~Lg~~ 336 (426)
+.+++.+.|..|||||+|+|.-+. +-|.++
T Consensus 5 ~~~~Li~~l~~LPGIG~KsA~RlA~~ll~~~ 35 (195)
T TIGR00615 5 PISKLIESLKKLPGIGPKSAQRLAFHLLKRD 35 (195)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHHHcCC
Confidence 468889999999999999999994 667665
No 40
>PRK13844 recombination protein RecR; Provisional
Probab=83.20 E-value=1 Score=43.21 Aligned_cols=30 Identities=10% Similarity=0.114 Sum_probs=25.9
Q ss_pred cHHHHHHHHhcCCCcCHHHHHHHH-HHhCCC
Q 014334 307 AYVKLAEQLSQINGFGPFTRNNVL-VCIGFY 336 (426)
Q Consensus 307 ~~eea~e~L~~L~GIGpkTAd~IL-~~Lg~~ 336 (426)
..+++.+.|..|||||+|+|.-+. +-|.++
T Consensus 9 ~~~~LI~~l~~LPGIG~KsA~Rla~~lL~~~ 39 (200)
T PRK13844 9 KISAVIESLRKLPTIGKKSSQRLALYLLDKS 39 (200)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHHHcCC
Confidence 568889999999999999999994 677665
No 41
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=82.34 E-value=2.6 Score=39.96 Aligned_cols=66 Identities=20% Similarity=0.273 Sum_probs=40.2
Q ss_pred cccCCCCHHHHhcCCHHHHHHHCcCcHHHHHHHHHHHHHHhCCCChhHHHhhhhhcccccHHHHHHHHhcCCCcCHHHHH
Q 014334 248 RIGNFPSPRELANLDESFLAKRCNLGYRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRN 327 (426)
Q Consensus 248 ~~~~FPtpe~La~~~~e~Lr~~~g~GyRAkyI~~lA~~i~eg~ldLe~L~~l~~~~~~~~~eea~e~L~~L~GIGpkTAd 327 (426)
..|-|-|.++..- -+.|...-|+|-|. |-.+.+. ++.+.|... =..+..+.| ++||||+|||+
T Consensus 59 ~LyGF~~~~Er~l--F~~LisV~GIGpK~------Al~iLs~-~~~~~l~~a-------I~~~D~~~L-~vpGIGkKtAe 121 (186)
T PRK14600 59 QLYGFLNREEQDC--LRMLVKVSGVNYKT------AMSILSK-LTPEQLFSA-------IVNEDKAAL-KVNGIGEKLIN 121 (186)
T ss_pred eeeCCCCHHHHHH--HHHHhCcCCcCHHH------HHHHHcc-CCHHHHHHH-------HHcCCHhhe-ECCCCcHHHHH
Confidence 5799999888532 24455545889874 1223332 333444332 001123788 99999999999
Q ss_pred HHH
Q 014334 328 NVL 330 (426)
Q Consensus 328 ~IL 330 (426)
-|+
T Consensus 122 rIi 124 (186)
T PRK14600 122 RII 124 (186)
T ss_pred HHH
Confidence 994
No 42
>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=82.10 E-value=1.1 Score=36.82 Aligned_cols=35 Identities=29% Similarity=0.410 Sum_probs=27.2
Q ss_pred HHHhcCCCcCHHHHHHHHHHhCCCCccccchHHHH
Q 014334 313 EQLSQINGFGPFTRNNVLVCIGFYHVIPTDSETIR 347 (426)
Q Consensus 313 e~L~~L~GIGpkTAd~IL~~Lg~~dvfPvDthV~R 347 (426)
+.|++|||||+-||..++--+|.++.|+-.-++..
T Consensus 2 ~~l~sipGig~~~a~~llaeigd~~rF~~~~~l~~ 36 (87)
T PF02371_consen 2 ELLTSIPGIGPITAATLLAEIGDISRFKSAKQLAS 36 (87)
T ss_pred chhcCCCCccHHHHHHHHHHHcCchhcccchhhhh
Confidence 46899999999999999865687778885544433
No 43
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=81.92 E-value=2 Score=41.04 Aligned_cols=68 Identities=16% Similarity=0.156 Sum_probs=41.3
Q ss_pred ccccCCCCHHHHhcCCHHHHHHHCcCcHHHHHHHHHHHHHHhCCCChhHHHhhhhhcccccHHHHHHHHhcCCCcCHHHH
Q 014334 247 DRIGNFPSPRELANLDESFLAKRCNLGYRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTR 326 (426)
Q Consensus 247 ~~~~~FPtpe~La~~~~e~Lr~~~g~GyRAkyI~~lA~~i~eg~ldLe~L~~l~~~~~~~~~eea~e~L~~L~GIGpkTA 326 (426)
...|-|-|.++..- -+.|...-|+|-|. |-.|.++ ++.+.|... =.....+.|.++||||+|||
T Consensus 57 ~~LyGF~~~~Er~l--F~~L~~V~GIGpK~------AL~iLs~-~~~~~l~~a-------I~~~D~~~L~kvpGIGkKtA 120 (197)
T PRK14603 57 LSLYGFPDEDSLEL--FELLLGVSGVGPKL------ALALLSA-LPPALLARA-------LLEGDARLLTSASGVGKKLA 120 (197)
T ss_pred ceeeCcCCHHHHHH--HHHHhCcCCcCHHH------HHHHHcC-CCHHHHHHH-------HHhCCHHHHhhCCCCCHHHH
Confidence 35788988877432 23455445788773 2223332 333444332 11222589999999999999
Q ss_pred HHHH
Q 014334 327 NNVL 330 (426)
Q Consensus 327 d~IL 330 (426)
+-|.
T Consensus 121 erIi 124 (197)
T PRK14603 121 ERIA 124 (197)
T ss_pred HHHH
Confidence 9994
No 44
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=80.00 E-value=2.2 Score=40.65 Aligned_cols=68 Identities=18% Similarity=0.185 Sum_probs=41.7
Q ss_pred ccccCCCCHHHHhcCCHHHHHHHCcCcHHHHHHHHHHHHHHhCCCChhHHHhhhhhcccccHHHHHHHHhcCCCcCHHHH
Q 014334 247 DRIGNFPSPRELANLDESFLAKRCNLGYRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTR 326 (426)
Q Consensus 247 ~~~~~FPtpe~La~~~~e~Lr~~~g~GyRAkyI~~lA~~i~eg~ldLe~L~~l~~~~~~~~~eea~e~L~~L~GIGpkTA 326 (426)
...|-|-|.++..- -..|...-|.|-|. |-.|.+. ++.+.|... =..+..+.|.++||||+|||
T Consensus 58 ~~LyGF~~~~Er~l--F~~Li~V~GIGpK~------Al~iLs~-~~~~el~~a-------I~~~D~~~L~kvpGIGkKtA 121 (195)
T PRK14604 58 LTLYGFSTPAQRQL--FELLIGVSGVGPKA------ALNLLSS-GTPDELQLA-------IAGGDVARLARVPGIGKKTA 121 (195)
T ss_pred ceeeCCCCHHHHHH--HHHHhCcCCcCHHH------HHHHHcC-CCHHHHHHH-------HHhCCHHHHhhCCCCCHHHH
Confidence 35788988877432 23455545888874 2223332 333444332 11222589999999999999
Q ss_pred HHHH
Q 014334 327 NNVL 330 (426)
Q Consensus 327 d~IL 330 (426)
+-|+
T Consensus 122 erIi 125 (195)
T PRK14604 122 ERIV 125 (195)
T ss_pred HHHH
Confidence 9994
No 45
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=79.48 E-value=16 Score=34.51 Aligned_cols=67 Identities=19% Similarity=0.187 Sum_probs=37.7
Q ss_pred cccCCCCHHHHhcCCHHHHHHHCcCcHH-HHHHHHHHHHHHhCCCChhHHHhhhhhcccccHHHHHHHHhcCCCcCHHHH
Q 014334 248 RIGNFPSPRELANLDESFLAKRCNLGYR-AGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTR 326 (426)
Q Consensus 248 ~~~~FPtpe~La~~~~e~Lr~~~g~GyR-AkyI~~lA~~i~eg~ldLe~L~~l~~~~~~~~~eea~e~L~~L~GIGpkTA 326 (426)
.++.|-+.++-.- ...|...-|+|-| |..|.+. +..+.|... =..+-.+.|.++||||+++|
T Consensus 59 ~l~gF~~~~ek~~--f~~L~~i~GIGpk~A~~il~~--------fg~~~l~~~-------i~~~d~~~L~~v~Gig~k~A 121 (192)
T PRK00116 59 LLYGFLTKEEREL--FRLLISVSGVGPKLALAILSG--------LSPEELVQA-------IANGDVKALTKVPGIGKKTA 121 (192)
T ss_pred HHcCcCCHHHHHH--HHHHhcCCCCCHHHHHHHHHh--------CCHHHHHHH-------HHhCCHHHHHhCCCCCHHHH
Confidence 4567765554322 4455544478875 6555321 111222211 00112468999999999999
Q ss_pred HHHHH
Q 014334 327 NNVLV 331 (426)
Q Consensus 327 d~IL~ 331 (426)
+-|+.
T Consensus 122 ~~I~~ 126 (192)
T PRK00116 122 ERIVL 126 (192)
T ss_pred HHHHH
Confidence 99963
No 46
>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=79.43 E-value=5 Score=40.65 Aligned_cols=61 Identities=23% Similarity=0.316 Sum_probs=40.6
Q ss_pred HHHHHCcCcHH-HHHHHHHHHHHHhCCCChhHHHhhhhhcccccHHHHHHHHhcCCCcCHHHHHHHHHHhCCC
Q 014334 265 FLAKRCNLGYR-AGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNVLVCIGFY 336 (426)
Q Consensus 265 ~Lr~~~g~GyR-AkyI~~lA~~i~eg~ldLe~L~~l~~~~~~~~~eea~e~L~~L~GIGpkTAd~IL~~Lg~~ 336 (426)
++.+.=|+|-+ |+.|.++. ..|.+ ..|..+.. +.......|++++||||++|.-+. .+|..
T Consensus 46 ~~~~ipgiG~~ia~kI~E~~---~tG~~--~~le~l~~-----~~~~~l~~l~~i~GiGpk~a~~l~-~lGi~ 107 (307)
T cd00141 46 EAKKLPGIGKKIAEKIEEIL---ETGKL--RKLEELRE-----DVPPGLLLLLRVPGVGPKTARKLY-ELGIR 107 (307)
T ss_pred HhcCCCCccHHHHHHHHHHH---HcCCH--HHHHHHhc-----cchHHHHHHHcCCCCCHHHHHHHH-HcCCC
Confidence 44443378875 55555553 35654 45555522 467888999999999999998886 56653
No 47
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=79.28 E-value=2.3 Score=40.80 Aligned_cols=68 Identities=16% Similarity=0.218 Sum_probs=40.3
Q ss_pred ccccCCCCHHHHhcCCHHHHHHHCcCcHHHHHHHHHHHHHHhCCCChhHHHhhhhhcccccHHHHHHHHhcCCCcCHHHH
Q 014334 247 DRIGNFPSPRELANLDESFLAKRCNLGYRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTR 326 (426)
Q Consensus 247 ~~~~~FPtpe~La~~~~e~Lr~~~g~GyRAkyI~~lA~~i~eg~ldLe~L~~l~~~~~~~~~eea~e~L~~L~GIGpkTA 326 (426)
...|-|-|.++..- -+.|...-|+|-|. |-.|.+. ++.+.|... =.....+.|.++||||+|||
T Consensus 59 ~~LyGF~~~~Er~l--F~~Li~V~GIGpK~------Al~iLs~-~~~~~l~~a-------I~~~D~~~L~~ipGIGkKtA 122 (203)
T PRK14602 59 LELFGFATWDERQT--FIVLISISKVGAKT------ALAILSQ-FRPDDLRRL-------VAEEDVAALTRVSGIGKKTA 122 (203)
T ss_pred ceeeCCCCHHHHHH--HHHHhCCCCcCHHH------HHHHHhh-CCHHHHHHH-------HHhCCHHHHhcCCCcCHHHH
Confidence 35788998887532 23455445788773 1122221 223333322 01122589999999999999
Q ss_pred HHHH
Q 014334 327 NNVL 330 (426)
Q Consensus 327 d~IL 330 (426)
+-|+
T Consensus 123 erIi 126 (203)
T PRK14602 123 QHIF 126 (203)
T ss_pred HHHH
Confidence 9994
No 48
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=77.62 E-value=1.7 Score=41.29 Aligned_cols=29 Identities=24% Similarity=0.348 Sum_probs=24.2
Q ss_pred cHHHHHHHHhcCCCcCHHHHHHHHHHhCC
Q 014334 307 AYVKLAEQLSQINGFGPFTRNNVLVCIGF 335 (426)
Q Consensus 307 ~~eea~e~L~~L~GIGpkTAd~IL~~Lg~ 335 (426)
.-.++.+.|++++|||||+|-.||-.++-
T Consensus 67 ~Er~lF~~Li~V~GIGpK~Al~ILs~~~~ 95 (194)
T PRK14605 67 EELSLFETLIDVSGIGPKLGLAMLSAMNA 95 (194)
T ss_pred HHHHHHHHHhCCCCCCHHHHHHHHHhCCH
Confidence 33578899999999999999999865553
No 49
>PRK08609 hypothetical protein; Provisional
Probab=77.57 E-value=3.9 Score=45.02 Aligned_cols=61 Identities=16% Similarity=0.116 Sum_probs=37.7
Q ss_pred HHHHHCcCcHH-HHHHHHHHHHHHhCCCChhHHHhhhhhcccccHHHHHHHHhcCCCcCHHHHHHHHHHhCC
Q 014334 265 FLAKRCNLGYR-AGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNVLVCIGF 335 (426)
Q Consensus 265 ~Lr~~~g~GyR-AkyI~~lA~~i~eg~ldLe~L~~l~~~~~~~~~eea~e~L~~L~GIGpkTAd~IL~~Lg~ 335 (426)
+|.+.-|+|-+ |+.|. +.+..|.+ ..|..++. ..++....|++++||||++|.-+---+|-
T Consensus 49 ~l~~ipgIG~~ia~kI~---Eil~tG~~--~~le~l~~-----~~p~~~~~l~~i~GiGpk~a~~l~~~lGi 110 (570)
T PRK08609 49 DFTKLKGIGKGTAEVIQ---EYRETGES--SVLQELKK-----EVPEGLLPLLKLPGLGGKKIAKLYKELGV 110 (570)
T ss_pred hhccCCCcCHHHHHHHH---HHHHhCCh--HHHHHHHh-----hCcHHHHHHhcCCCCCHHHHHHHHHHhCC
Confidence 56665688877 44443 33445764 34444422 33445668999999999999777434553
No 50
>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=75.48 E-value=8.4 Score=43.21 Aligned_cols=79 Identities=20% Similarity=0.238 Sum_probs=43.7
Q ss_pred CCHHHHhcCCHHHHHHHCcCcHH-HHHHHHHHHHHHhCCCChhHH-Hh-------------hhhhcccccHHHH----HH
Q 014334 253 PSPRELANLDESFLAKRCNLGYR-AGRILKLARGIVDGQIQLREL-ED-------------MCNEASLTAYVKL----AE 313 (426)
Q Consensus 253 Ptpe~La~~~~e~Lr~~~g~GyR-AkyI~~lA~~i~eg~ldLe~L-~~-------------l~~~~~~~~~eea----~e 313 (426)
-++++|-.++.++|.++-|+|-| |..|.+..+.-.... ++.+ .. +.. .-.+.+++ .+
T Consensus 455 ~~~~Dl~~L~~~~L~~L~GfG~Ksa~nIl~~Ie~sk~~~--l~r~L~aLgIpgVG~~~ak~L~~--~f~sl~~l~~As~e 530 (652)
T TIGR00575 455 RSVADLYALKKEDLLELEGFGEKSAQNLLNAIEKSKEKP--LARLLFALGIRHVGEVTAKNLAK--HFGTLDKLKAASLE 530 (652)
T ss_pred CCHHHHHhcCHHHHhhccCccHHHHHHHHHHHHHhccCc--HHHHHhhccCCCcCHHHHHHHHH--HhCCHHHHHhCCHH
Confidence 47788888888888874578865 555555444322211 1110 00 000 00022222 24
Q ss_pred HHhcCCCcCHHHHHHHHHHhCC
Q 014334 314 QLSQINGFGPFTRNNVLVCIGF 335 (426)
Q Consensus 314 ~L~~L~GIGpkTAd~IL~~Lg~ 335 (426)
+|.+++|||+++|+.|+--|..
T Consensus 531 eL~~i~GIG~~~A~~I~~ff~~ 552 (652)
T TIGR00575 531 ELLSVEGVGPKVAESIVNFFHD 552 (652)
T ss_pred HHhcCCCcCHHHHHHHHHHHhh
Confidence 7889999999999999744443
No 51
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=73.58 E-value=3.3 Score=39.16 Aligned_cols=25 Identities=24% Similarity=0.372 Sum_probs=20.9
Q ss_pred HHHHHHhcCCCcCHHHHHHHHHHhC
Q 014334 310 KLAEQLSQINGFGPFTRNNVLVCIG 334 (426)
Q Consensus 310 ea~e~L~~L~GIGpkTAd~IL~~Lg 334 (426)
+....|..++||||++|..+|-.++
T Consensus 70 ~~f~~L~~i~GIGpk~A~~il~~fg 94 (192)
T PRK00116 70 ELFRLLISVSGVGPKLALAILSGLS 94 (192)
T ss_pred HHHHHHhcCCCCCHHHHHHHHHhCC
Confidence 4478999999999999999985454
No 52
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=73.37 E-value=9.6 Score=42.86 Aligned_cols=80 Identities=16% Similarity=0.269 Sum_probs=44.9
Q ss_pred CCCHHHHhcCCHHHHHHHCcCcHH-HHHHHHHHHHHHhCCCChhHH-Hh-------------hhhhcccccHHHH----H
Q 014334 252 FPSPRELANLDESFLAKRCNLGYR-AGRILKLARGIVDGQIQLREL-ED-------------MCNEASLTAYVKL----A 312 (426)
Q Consensus 252 FPtpe~La~~~~e~Lr~~~g~GyR-AkyI~~lA~~i~eg~ldLe~L-~~-------------l~~~~~~~~~eea----~ 312 (426)
--++++|-.+..++|..+-|+|-| +..|.+-.+...+- .|+.+ .. +.. .-.+.+++ .
T Consensus 467 I~~i~DL~~L~~~~L~~l~gfG~Ksa~~ll~~Ie~sk~~--~l~R~l~algi~~IG~~~ak~L~~--~f~sl~~l~~As~ 542 (665)
T PRK07956 467 IHDPADLFKLTAEDLLGLEGFGEKSAQNLLDAIEKSKET--SLARFLYALGIRHVGEKAAKALAR--HFGSLEALRAASE 542 (665)
T ss_pred CCCHHHHHhcCHHHHhcCcCcchHHHHHHHHHHHHhhcC--CHHHhhHhhhccCcCHHHHHHHHH--HcCCHHHHHhCCH
Confidence 357888888888888875588875 55554433322221 11110 00 000 00122222 3
Q ss_pred HHHhcCCCcCHHHHHHHHHHhCC
Q 014334 313 EQLSQINGFGPFTRNNVLVCIGF 335 (426)
Q Consensus 313 e~L~~L~GIGpkTAd~IL~~Lg~ 335 (426)
++|.+++|||+++|..|.-.|..
T Consensus 543 eeL~~i~GIG~~~A~sI~~ff~~ 565 (665)
T PRK07956 543 EELAAVEGVGEVVAQSIVEFFAV 565 (665)
T ss_pred HHHhccCCcCHHHHHHHHHHHhh
Confidence 57999999999999999744443
No 53
>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=70.89 E-value=3.6 Score=39.07 Aligned_cols=24 Identities=29% Similarity=0.434 Sum_probs=20.9
Q ss_pred cHHHHHHHHhcCCCcCHHHHHHHH
Q 014334 307 AYVKLAEQLSQINGFGPFTRNNVL 330 (426)
Q Consensus 307 ~~eea~e~L~~L~GIGpkTAd~IL 330 (426)
.-.++...|++++|||||+|-.||
T Consensus 66 ~Er~lF~~L~~V~GIGpK~Al~iL 89 (191)
T TIGR00084 66 EERELFKELIKVNGVGPKLALAIL 89 (191)
T ss_pred HHHHHHHHHhCCCCCCHHHHHHHH
Confidence 346788999999999999998886
No 54
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=70.73 E-value=2.6 Score=40.54 Aligned_cols=67 Identities=24% Similarity=0.319 Sum_probs=38.8
Q ss_pred HHHHHHHHhcCCCcCHHHHHHHHHHhCCCCccc-cchHHHHHHHHhhccCCCHHHHHHHHHHHhcCCChH
Q 014334 308 YVKLAEQLSQINGFGPFTRNNVLVCIGFYHVIP-TDSETIRHLKQVHARNCTSKTVQMIAESIYGKYAPF 376 (426)
Q Consensus 308 ~eea~e~L~~L~GIGpkTAd~IL~~Lg~~dvfP-vDthV~Ril~rly~~~~t~k~i~~~~~e~~g~~agw 376 (426)
-.+....|+++.|||||+|=.||-.+.-.+..- ++..=...+.+.=|++ +|.-++.+.++=+++..|
T Consensus 68 ER~lF~~LisVnGIGpK~ALaiLs~~~~~~l~~aI~~~d~~~L~k~PGIG--kKtAerivleLk~K~~~~ 135 (201)
T COG0632 68 ERELFRLLISVNGIGPKLALAILSNLDPEELAQAIANEDVKALSKIPGIG--KKTAERIVLELKGKLAAF 135 (201)
T ss_pred HHHHHHHHHccCCccHHHHHHHHcCCCHHHHHHHHHhcChHhhhcCCCCC--HHHHHHHHHHHhhhhhhh
Confidence 357789999999999999999984333222111 3333334444443433 244444455555555555
No 55
>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=69.20 E-value=7 Score=29.76 Aligned_cols=33 Identities=33% Similarity=0.399 Sum_probs=28.0
Q ss_pred CCCHHHHhcCCHHHHHHHCcCcH-HHHHHHHHHH
Q 014334 252 FPSPRELANLDESFLAKRCNLGY-RAGRILKLAR 284 (426)
Q Consensus 252 FPtpe~La~~~~e~Lr~~~g~Gy-RAkyI~~lA~ 284 (426)
|.|+++|+.+++++|.+.-|+|- +|+.|+.-++
T Consensus 26 ~~t~~~l~~a~~~~L~~i~Gig~~~a~~i~~~~~ 59 (60)
T PF14520_consen 26 IKTLEDLANADPEELAEIPGIGEKTAEKIIEAAR 59 (60)
T ss_dssp CSSHHHHHTSHHHHHHTSTTSSHHHHHHHHHHHH
T ss_pred CCcHHHHHcCCHHHHhcCCCCCHHHHHHHHHHHh
Confidence 88999999999999998669997 4887777665
No 56
>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=68.29 E-value=5.3 Score=31.18 Aligned_cols=54 Identities=20% Similarity=0.274 Sum_probs=33.5
Q ss_pred HHhcCCHHHHHH-HCcCcHH-HHHHHHHHHHHHhCCCChhHHHhhhhhcccccHHHHHHHHhcCCCcCHHHHHHHH
Q 014334 257 ELANLDESFLAK-RCNLGYR-AGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNVL 330 (426)
Q Consensus 257 ~La~~~~e~Lr~-~~g~GyR-AkyI~~lA~~i~eg~ldLe~L~~l~~~~~~~~~eea~e~L~~L~GIGpkTAd~IL 330 (426)
.|-.++.++|.. .-|+|.+ |+.|.+-=. ..|.+ + -.++|.+++|||.++++-|+
T Consensus 9 nvNta~~~~L~~~ipgig~~~a~~Il~~R~--~~g~~-----------------~-s~~dL~~v~gi~~~~~~~i~ 64 (69)
T TIGR00426 9 NINTATAEELQRAMNGVGLKKAEAIVSYRE--EYGPF-----------------K-TVEDLKQVPGIGNSLVEKNL 64 (69)
T ss_pred ECcCCCHHHHHhHCCCCCHHHHHHHHHHHH--HcCCc-----------------C-CHHHHHcCCCCCHHHHHHHH
Confidence 444567778876 4588874 443332211 01211 1 24778899999999999885
No 57
>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=66.55 E-value=12 Score=32.80 Aligned_cols=58 Identities=14% Similarity=0.265 Sum_probs=40.9
Q ss_pred CCHHHHhcCCHHHHHHHCcCcH-HHHHHHHHHHHHHhCCCChhHHHhhhhhcccccHHHHHHHHhcCCCcCHHHHHHHH
Q 014334 253 PSPRELANLDESFLAKRCNLGY-RAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNVL 330 (426)
Q Consensus 253 Ptpe~La~~~~e~Lr~~~g~Gy-RAkyI~~lA~~i~eg~ldLe~L~~l~~~~~~~~~eea~e~L~~L~GIGpkTAd~IL 330 (426)
+.+-.|-.++.++|...-|+|. +|+.|+.-=.. +|.+ . + .++|..++|||+++++-|.
T Consensus 57 ~~~iniNtA~~~eL~~lpGIG~~~A~~Ii~~R~~--~g~f-----~---------s----~eeL~~V~GIg~k~~~~i~ 115 (120)
T TIGR01259 57 LAAVNINAASLEELQALPGIGPAKAKAIIEYREE--NGAF-----K---------S----VDDLTKVSGIGEKSLEKLK 115 (120)
T ss_pred CCCEeCCcCCHHHHhcCCCCCHHHHHHHHHHHHh--cCCc-----C---------C----HHHHHcCCCCCHHHHHHHH
Confidence 3455677789999987568886 67766654432 3332 1 2 4778999999999998874
No 58
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=66.07 E-value=3.5 Score=39.08 Aligned_cols=26 Identities=31% Similarity=0.348 Sum_probs=22.0
Q ss_pred HHHHHHHHhcCCCcCHHHHHHHHHHh
Q 014334 308 YVKLAEQLSQINGFGPFTRNNVLVCI 333 (426)
Q Consensus 308 ~eea~e~L~~L~GIGpkTAd~IL~~L 333 (426)
-.+..+.|+++.|||||+|=.||-.+
T Consensus 68 Er~lF~~Li~VsGIGpK~Al~ILs~~ 93 (183)
T PRK14601 68 EQKMFEMLLKVNGIGANTAMAVCSSL 93 (183)
T ss_pred HHHHHHHHhccCCccHHHHHHHHcCC
Confidence 35778999999999999999998433
No 59
>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=65.59 E-value=79 Score=29.97 Aligned_cols=39 Identities=23% Similarity=0.263 Sum_probs=29.1
Q ss_pred ccccCCC-ChHHHHHHHHHhcCCCHHHHHHHHHHHHHHhh
Q 014334 115 GRVFRSP-TLFEDMVKCMLLCNCQWPRTLSMARALCELQW 153 (426)
Q Consensus 115 gRvlr~p-~~fE~lv~~I~s~N~~~~r~~~m~~~Lc~~~g 153 (426)
||....+ .+||.|+-.+.-+--+|.-|++--.++.+.|-
T Consensus 17 G~P~~dD~~LFe~L~Le~fQaGLsW~~Il~Kr~~~r~aF~ 56 (179)
T PF03352_consen 17 GRPVHDDRKLFEMLTLEGFQAGLSWSTILKKREAFREAFA 56 (179)
T ss_dssp TSS---HHHHHHHHHHHHHTTTS-HHHHHHTHHHHHHHTG
T ss_pred CCcccCHHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHH
Confidence 5555443 68999999999999999999998888887753
No 60
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=65.48 E-value=7.6 Score=37.69 Aligned_cols=51 Identities=24% Similarity=0.302 Sum_probs=38.0
Q ss_pred HCcCcHHHH-HHHHHHHHHHhCC---CChhHHHhhhhhcccccHHHHHHHHhcCCCcCHHHHHHHH
Q 014334 269 RCNLGYRAG-RILKLARGIVDGQ---IQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNVL 330 (426)
Q Consensus 269 ~~g~GyRAk-yI~~lA~~i~eg~---ldLe~L~~l~~~~~~~~~eea~e~L~~L~GIGpkTAd~IL 330 (426)
.++.|.+-+ -...+|+.+.+.- .++..|... + .++|++++|||+-.|..++
T Consensus 23 lL~~g~~~~~~~~~lA~~ll~~f~~~g~l~~l~~a-------~----~~eL~~i~GiG~aka~~l~ 77 (218)
T TIGR00608 23 ILRTGTPKGLDVLSLSKRLLDVFGRQDSLGHLLSA-------P----PEELSSVPGIGEAKAIQLK 77 (218)
T ss_pred HHhCCCCCCCCHHHHHHHHHHHhcccCCHHHHHhC-------C----HHHHHhCcCCcHHHHHHHH
Confidence 357777766 7889999998753 356666665 4 4679999999997777763
No 61
>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=64.92 E-value=4.8 Score=30.52 Aligned_cols=22 Identities=27% Similarity=0.302 Sum_probs=15.2
Q ss_pred HHHhcCCCcCHHHHHHHH-HHhC
Q 014334 313 EQLSQINGFGPFTRNNVL-VCIG 334 (426)
Q Consensus 313 e~L~~L~GIGpkTAd~IL-~~Lg 334 (426)
+.++.+.||||.||.-.. +|+.
T Consensus 2 ~~f~~I~GVG~~tA~~w~~~G~r 24 (52)
T PF10391_consen 2 KLFTGIWGVGPKTARKWYAKGIR 24 (52)
T ss_dssp HHHHTSTT--HHHHHHHHHTT--
T ss_pred cchhhcccccHHHHHHHHHhCCC
Confidence 678999999999999885 4554
No 62
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=64.47 E-value=4.4 Score=38.85 Aligned_cols=26 Identities=27% Similarity=0.376 Sum_probs=22.0
Q ss_pred cHHHHHHHHhcCCCcCHHHHHHHHHH
Q 014334 307 AYVKLAEQLSQINGFGPFTRNNVLVC 332 (426)
Q Consensus 307 ~~eea~e~L~~L~GIGpkTAd~IL~~ 332 (426)
.-.++.+.|+++.|||||+|=.||-.
T Consensus 66 ~Er~lF~~LisVsGIGPK~ALaILs~ 91 (196)
T PRK13901 66 SEREVFEELIGVDGIGPRAALRVLSG 91 (196)
T ss_pred HHHHHHHHHhCcCCcCHHHHHHHHcC
Confidence 33577899999999999999999843
No 63
>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=63.43 E-value=5.1 Score=34.12 Aligned_cols=27 Identities=19% Similarity=0.154 Sum_probs=21.4
Q ss_pred HHHHHHHhcCCCcCHHHHHHHH-HHhCC
Q 014334 309 VKLAEQLSQINGFGPFTRNNVL-VCIGF 335 (426)
Q Consensus 309 eea~e~L~~L~GIGpkTAd~IL-~~Lg~ 335 (426)
.+....|+.|||||+.+|.-+. .|+..
T Consensus 8 ~~~~~~L~~iP~IG~a~a~DL~~LGi~s 35 (93)
T PF11731_consen 8 RAGLSDLTDIPNIGKATAEDLRLLGIRS 35 (93)
T ss_pred HHHHHHHhcCCCccHHHHHHHHHcCCCC
Confidence 4567899999999999999884 44443
No 64
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=63.12 E-value=15 Score=41.42 Aligned_cols=22 Identities=23% Similarity=0.392 Sum_probs=18.4
Q ss_pred HHHhcCCCcCHHHHHHHHHHhC
Q 014334 313 EQLSQINGFGPFTRNNVLVCIG 334 (426)
Q Consensus 313 e~L~~L~GIGpkTAd~IL~~Lg 334 (426)
++|++++|||+.+|..|.-.|.
T Consensus 541 e~l~~i~giG~~~a~si~~ff~ 562 (669)
T PRK14350 541 SKLLKIKGIGEKIALNIIEAFN 562 (669)
T ss_pred HHHhhCCCccHHHHHHHHHHHc
Confidence 4799999999999999973344
No 65
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=62.98 E-value=16 Score=32.97 Aligned_cols=56 Identities=14% Similarity=0.178 Sum_probs=40.1
Q ss_pred CCCCHHHHhcCCHHHHHHHCcCcH-HHHHHHHHHHHHHhCCCChhHHHhhhhhcccccHHHHHHHHhcCCCcCHHHHHHH
Q 014334 251 NFPSPRELANLDESFLAKRCNLGY-RAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNV 329 (426)
Q Consensus 251 ~FPtpe~La~~~~e~Lr~~~g~Gy-RAkyI~~lA~~i~eg~ldLe~L~~l~~~~~~~~~eea~e~L~~L~GIGpkTAd~I 329 (426)
.+-..=+|-.++.++|.+.=|+|= +|+.|. .+|... + .+.|.+++|||+++.+.+
T Consensus 48 ~~~~kIdiN~A~~~el~~lpGigP~~A~~IV------~nGpf~--------------s----veDL~~V~GIgekqk~~l 103 (132)
T PRK02515 48 EFGEKIDLNNSSVRAFRQFPGMYPTLAGKIV------KNAPYD--------------S----VEDVLNLPGLSERQKELL 103 (132)
T ss_pred hcCCcccCCccCHHHHHHCCCCCHHHHHHHH------HCCCCC--------------C----HHHHHcCCCCCHHHHHHH
Confidence 344555677788999987558884 688776 255432 2 477899999999987777
Q ss_pred H
Q 014334 330 L 330 (426)
Q Consensus 330 L 330 (426)
-
T Consensus 104 ~ 104 (132)
T PRK02515 104 E 104 (132)
T ss_pred H
Confidence 4
No 66
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=62.96 E-value=4.1 Score=38.94 Aligned_cols=26 Identities=27% Similarity=0.388 Sum_probs=22.0
Q ss_pred HHHHHHHHhcCCCcCHHHHHHHHHHh
Q 014334 308 YVKLAEQLSQINGFGPFTRNNVLVCI 333 (426)
Q Consensus 308 ~eea~e~L~~L~GIGpkTAd~IL~~L 333 (426)
-.++.+.|+++.|||||+|=.||-.+
T Consensus 67 Er~lF~~L~~V~GIGpK~AL~iLs~~ 92 (197)
T PRK14603 67 SLELFELLLGVSGVGPKLALALLSAL 92 (197)
T ss_pred HHHHHHHHhCcCCcCHHHHHHHHcCC
Confidence 35778999999999999999998433
No 67
>PRK00024 hypothetical protein; Reviewed
Probab=62.13 E-value=10 Score=36.87 Aligned_cols=50 Identities=30% Similarity=0.442 Sum_probs=37.4
Q ss_pred HCcCcHHHHHHHHHHHHHHhCCCChhHHHhhhhhcccccHHHHHHHHhcCCCcCHHHHHHH
Q 014334 269 RCNLGYRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNV 329 (426)
Q Consensus 269 ~~g~GyRAkyI~~lA~~i~eg~ldLe~L~~l~~~~~~~~~eea~e~L~~L~GIGpkTAd~I 329 (426)
.++.|.+-+-...+|+.+.+...++..+... + .++|++++|||+..|-.+
T Consensus 33 lL~~g~~~~~~~~LA~~LL~~fgsL~~l~~a-------s----~~eL~~i~GIG~akA~~L 82 (224)
T PRK00024 33 LLRTGTKGKSVLDLARELLQRFGSLRGLLDA-------S----LEELQSIKGIGPAKAAQL 82 (224)
T ss_pred HHcCCCCCCCHHHHHHHHHHHcCCHHHHHhC-------C----HHHHhhccCccHHHHHHH
Confidence 3677777667788999988744456666654 4 467899999999988777
No 68
>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=61.60 E-value=5.2 Score=27.19 Aligned_cols=15 Identities=20% Similarity=0.381 Sum_probs=11.8
Q ss_pred HhcCCCcCHHHHHHH
Q 014334 315 LSQINGFGPFTRNNV 329 (426)
Q Consensus 315 L~~L~GIGpkTAd~I 329 (426)
+..++|||++|+.-+
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 468999999998865
No 69
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=61.36 E-value=5.2 Score=38.35 Aligned_cols=27 Identities=19% Similarity=0.017 Sum_probs=22.5
Q ss_pred HHHHHHHHhcCCCcCHHHHHHHHHHhC
Q 014334 308 YVKLAEQLSQINGFGPFTRNNVLVCIG 334 (426)
Q Consensus 308 ~eea~e~L~~L~GIGpkTAd~IL~~Lg 334 (426)
-.++.+.|+++.|||||+|=.||-.+.
T Consensus 69 Er~lF~~Li~V~GIGpK~Al~iLs~~~ 95 (203)
T PRK14602 69 ERQTFIVLISISKVGAKTALAILSQFR 95 (203)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHHhhCC
Confidence 357789999999999999999984443
No 70
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=61.29 E-value=4.7 Score=38.51 Aligned_cols=25 Identities=36% Similarity=0.432 Sum_probs=21.6
Q ss_pred cHHHHHHHHhcCCCcCHHHHHHHHH
Q 014334 307 AYVKLAEQLSQINGFGPFTRNNVLV 331 (426)
Q Consensus 307 ~~eea~e~L~~L~GIGpkTAd~IL~ 331 (426)
.-.++.+.|+++.|||||+|=.||-
T Consensus 67 ~Er~lF~~Li~V~GIGpK~Al~iLs 91 (195)
T PRK14604 67 AQRQLFELLIGVSGVGPKAALNLLS 91 (195)
T ss_pred HHHHHHHHHhCcCCcCHHHHHHHHc
Confidence 3467889999999999999999983
No 71
>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=60.85 E-value=6.1 Score=38.83 Aligned_cols=19 Identities=21% Similarity=0.431 Sum_probs=16.8
Q ss_pred ccccchHHHHHHHHhhccC
Q 014334 338 VIPTDSETIRHLKQVHARN 356 (426)
Q Consensus 338 vfPvDthV~Ril~rly~~~ 356 (426)
++|.||||.|+.++++...
T Consensus 176 iiPLDtHv~~var~LGL~~ 194 (232)
T PF09674_consen 176 IIPLDTHVFRVARKLGLLK 194 (232)
T ss_pred cccchHhHHHHHHHcCCcc
Confidence 4899999999999998765
No 72
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=60.62 E-value=5 Score=38.08 Aligned_cols=27 Identities=19% Similarity=0.235 Sum_probs=22.4
Q ss_pred cHHHHHHHHhcCCCcCHHHHHHHHHHh
Q 014334 307 AYVKLAEQLSQINGFGPFTRNNVLVCI 333 (426)
Q Consensus 307 ~~eea~e~L~~L~GIGpkTAd~IL~~L 333 (426)
.-.++.+.|+++.|||||+|=.||-.+
T Consensus 67 ~Er~lF~~Li~V~GIGpK~AL~iLs~~ 93 (188)
T PRK14606 67 RKKELFLSLTKVSRLGPKTALKIISNE 93 (188)
T ss_pred HHHHHHHHHhccCCccHHHHHHHHcCC
Confidence 346788999999999999999998433
No 73
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=58.24 E-value=26 Score=39.72 Aligned_cols=81 Identities=16% Similarity=0.183 Sum_probs=41.2
Q ss_pred CCHHHHhcCCHHHHHHHCcCcHH-HHHHHHHHHHHHhCCCChhHH-Hhhhh-----------hcccccHHHH----HHHH
Q 014334 253 PSPRELANLDESFLAKRCNLGYR-AGRILKLARGIVDGQIQLREL-EDMCN-----------EASLTAYVKL----AEQL 315 (426)
Q Consensus 253 Ptpe~La~~~~e~Lr~~~g~GyR-AkyI~~lA~~i~eg~ldLe~L-~~l~~-----------~~~~~~~eea----~e~L 315 (426)
-++.+|-.++.++|..+-|+|.| |..|.+-.+.- ...+|+.+ ..+.= ...-.+.+++ .++|
T Consensus 485 ~~~~Dl~~L~~~~L~~l~g~g~Ksa~~Ll~~Ie~s--k~~~l~r~l~ALgIpgIG~~~ak~L~~~F~si~~L~~As~eeL 562 (689)
T PRK14351 485 ESLADLYDLTVADLAELEGWGETSAENLLAELEAS--REPPLADFLVALGIPEVGPTTARNLAREFGTFEAIMDADEEAL 562 (689)
T ss_pred CCHHHHHHcCHHHHhcCcCcchhHHHHHHHHHHHH--ccCCHHHHHHHcCCCCcCHHHHHHHHHHhCCHHHHHhCCHHHH
Confidence 46777777788888764478875 44443332211 11222210 00000 0000012222 3568
Q ss_pred hcCCCcCHHHHHHHHHHhCC
Q 014334 316 SQINGFGPFTRNNVLVCIGF 335 (426)
Q Consensus 316 ~~L~GIGpkTAd~IL~~Lg~ 335 (426)
.+++|||+++|+.|.-.|..
T Consensus 563 ~~i~GIG~k~A~sI~~ff~~ 582 (689)
T PRK14351 563 RAVDDVGPTVAEEIREFFDS 582 (689)
T ss_pred hccCCcCHHHHHHHHHHHhh
Confidence 88999999999888634443
No 74
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=57.57 E-value=16 Score=28.40 Aligned_cols=52 Identities=21% Similarity=0.338 Sum_probs=30.1
Q ss_pred HhcCCHHHHHHHCcCcH-HHHHHHHHHHHHHhCCCChhHHHhhhhhcccccHHHHHHHHhcCCCcCHHHHHHH
Q 014334 258 LANLDESFLAKRCNLGY-RAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNV 329 (426)
Q Consensus 258 La~~~~e~Lr~~~g~Gy-RAkyI~~lA~~i~eg~ldLe~L~~l~~~~~~~~~eea~e~L~~L~GIGpkTAd~I 329 (426)
|-.++.++|...-|+|. .|+.|.+.=+.. |.+. + .++|..++|||+.+.+-+
T Consensus 8 iN~as~~eL~~lpgi~~~~A~~Iv~~R~~~--G~f~--------------s----~~dL~~v~gi~~~~~~~l 60 (65)
T PF12836_consen 8 INTASAEELQALPGIGPKQAKAIVEYREKN--GPFK--------------S----LEDLKEVPGIGPKTYEKL 60 (65)
T ss_dssp TTTS-HHHHHTSTT--HHHHHHHHHHHHHH---S-S--------------S----GGGGGGSTT--HHHHHHH
T ss_pred CccCCHHHHHHcCCCCHHHHHHHHHHHHhC--cCCC--------------C----HHHHhhCCCCCHHHHHHH
Confidence 44578889987448886 477666544332 4431 1 477889999999998766
No 75
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=57.40 E-value=9.4 Score=29.68 Aligned_cols=19 Identities=32% Similarity=0.648 Sum_probs=15.6
Q ss_pred HHHHhcCCCcCHHHHHHHH
Q 014334 312 AEQLSQINGFGPFTRNNVL 330 (426)
Q Consensus 312 ~e~L~~L~GIGpkTAd~IL 330 (426)
.++|.++||||++.|+.|+
T Consensus 13 ~~eL~~lpgi~~~~A~~Iv 31 (65)
T PF12836_consen 13 AEELQALPGIGPKQAKAIV 31 (65)
T ss_dssp HHHHHTSTT--HHHHHHHH
T ss_pred HHHHHHcCCCCHHHHHHHH
Confidence 5789999999999999996
No 76
>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=57.08 E-value=6.2 Score=31.77 Aligned_cols=23 Identities=26% Similarity=0.439 Sum_probs=18.5
Q ss_pred HHHhcCCCcCHHHHHHHHHHhCC
Q 014334 313 EQLSQINGFGPFTRNNVLVCIGF 335 (426)
Q Consensus 313 e~L~~L~GIGpkTAd~IL~~Lg~ 335 (426)
+.+..+||||+|+|.-++.-++-
T Consensus 22 D~i~gv~giG~k~A~~ll~~~~~ 44 (75)
T cd00080 22 DNIPGVPGIGPKTALKLLKEYGS 44 (75)
T ss_pred ccCCCCCcccHHHHHHHHHHhCC
Confidence 45668999999999999855554
No 77
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=57.04 E-value=8.9 Score=36.35 Aligned_cols=26 Identities=15% Similarity=0.116 Sum_probs=22.1
Q ss_pred HHHHHHHHhcCCCcCHHHHHHHHHHh
Q 014334 308 YVKLAEQLSQINGFGPFTRNNVLVCI 333 (426)
Q Consensus 308 ~eea~e~L~~L~GIGpkTAd~IL~~L 333 (426)
-.++.+.|+++.|||||+|=.||-.+
T Consensus 68 Er~lF~~LisV~GIGpK~Al~iLs~~ 93 (186)
T PRK14600 68 EQDCLRMLVKVSGVNYKTAMSILSKL 93 (186)
T ss_pred HHHHHHHHhCcCCcCHHHHHHHHccC
Confidence 35778999999999999999998433
No 78
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=56.08 E-value=8.1 Score=27.05 Aligned_cols=17 Identities=29% Similarity=0.604 Sum_probs=14.0
Q ss_pred HHhcCCCcCHHHHHHHH
Q 014334 314 QLSQINGFGPFTRNNVL 330 (426)
Q Consensus 314 ~L~~L~GIGpkTAd~IL 330 (426)
-+..+||||+|+|--+|
T Consensus 17 ni~Gv~giG~ktA~~ll 33 (36)
T smart00279 17 NIPGVKGIGPKTALKLL 33 (36)
T ss_pred CCCCCCcccHHHHHHHH
Confidence 34689999999998775
No 79
>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=55.73 E-value=8.4 Score=37.85 Aligned_cols=19 Identities=21% Similarity=0.450 Sum_probs=16.1
Q ss_pred ccccchHHHHHHHHhhccC
Q 014334 338 VIPTDSETIRHLKQVHARN 356 (426)
Q Consensus 338 vfPvDthV~Ril~rly~~~ 356 (426)
++|.|||+.|++++++...
T Consensus 173 iiPLDtH~~rvar~LgL~~ 191 (229)
T TIGR02757 173 ILPLDTHVFRIAKKLKLLK 191 (229)
T ss_pred eeechHhHHHHHHHhCCcc
Confidence 3899999999999987654
No 80
>TIGR01259 comE comEA protein. This model describes the ComEA protein in bacteria. The com E locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. Lesions in the loci has been variously described for the appearance of competence-related pheonotypes and impairment of competence, suggesting their intimate functional role in bacterial transformation.
Probab=54.52 E-value=11 Score=33.22 Aligned_cols=19 Identities=26% Similarity=0.621 Sum_probs=17.8
Q ss_pred HHHHhcCCCcCHHHHHHHH
Q 014334 312 AEQLSQINGFGPFTRNNVL 330 (426)
Q Consensus 312 ~e~L~~L~GIGpkTAd~IL 330 (426)
.++|+++||||++.|.-|+
T Consensus 67 ~~eL~~lpGIG~~~A~~Ii 85 (120)
T TIGR01259 67 LEELQALPGIGPAKAKAII 85 (120)
T ss_pred HHHHhcCCCCCHHHHHHHH
Confidence 5789999999999999998
No 81
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=52.37 E-value=39 Score=37.43 Aligned_cols=83 Identities=14% Similarity=0.123 Sum_probs=45.6
Q ss_pred CCCCHHHHhcCCHHHHHHHCcCcHH-HHHHHHHHHHHHhCCCChhHHH-hh-----hhh---cccccHHHH----HHHHh
Q 014334 251 NFPSPRELANLDESFLAKRCNLGYR-AGRILKLARGIVDGQIQLRELE-DM-----CNE---ASLTAYVKL----AEQLS 316 (426)
Q Consensus 251 ~FPtpe~La~~~~e~Lr~~~g~GyR-AkyI~~lA~~i~eg~ldLe~L~-~l-----~~~---~~~~~~eea----~e~L~ 316 (426)
..-++.+|-.++.++|.+.-|+|-| ++.|.+..+.- ...+|+.+- .+ ... ..-.+.+++ .+.|.
T Consensus 446 ~i~~~~Diy~L~~~~l~~l~gfgeks~~nll~aIe~s--k~~~l~r~l~aLGI~~vG~~~ak~~~~~i~~l~~a~~e~l~ 523 (562)
T PRK08097 446 LFEHLFSWLALTPEQLANTPGIGKARAEQLWHQFNLA--RQQPFSRWLKALGIPLPQAALNALDDRSWQQLLSRSEQQWQ 523 (562)
T ss_pred CcCCHHHHhcCCHHHHhcCcCccHHHHHHHHHHHHHH--cCCCHHHHHHHcCCccHHHHHHHHhcCCHHHHHcCCHHHHh
Confidence 4567888888888888764477764 55444433321 122222210 00 000 000012222 25799
Q ss_pred cCCCcCHHHHHHHHHHhCC
Q 014334 317 QINGFGPFTRNNVLVCIGF 335 (426)
Q Consensus 317 ~L~GIGpkTAd~IL~~Lg~ 335 (426)
+++|||+.+|+.|.-.|..
T Consensus 524 ~i~gIG~~~a~si~~~f~~ 542 (562)
T PRK08097 524 QLPGIGEGRARQLIAFLQH 542 (562)
T ss_pred cCCCchHHHHHHHHHHHcC
Confidence 9999999999999744443
No 82
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=52.16 E-value=10 Score=34.68 Aligned_cols=19 Identities=32% Similarity=0.665 Sum_probs=16.9
Q ss_pred HHHHhcCCCcCHHHHHHHH
Q 014334 312 AEQLSQINGFGPFTRNNVL 330 (426)
Q Consensus 312 ~e~L~~L~GIGpkTAd~IL 330 (426)
.++|..|||||++.|..|.
T Consensus 96 ~eeL~~lpgIG~~kA~aIi 114 (149)
T COG1555 96 AEELQALPGIGPKKAQAII 114 (149)
T ss_pred HHHHHHCCCCCHHHHHHHH
Confidence 4667999999999999996
No 83
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=51.00 E-value=27 Score=36.01 Aligned_cols=46 Identities=13% Similarity=0.188 Sum_probs=34.3
Q ss_pred CcCc-HHHHHHHHHHHHHHhCCCChhHHHhhhhhcccccHHHHHHH--HhcCCCcCHHHHHHHH
Q 014334 270 CNLG-YRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQ--LSQINGFGPFTRNNVL 330 (426)
Q Consensus 270 ~g~G-yRAkyI~~lA~~i~eg~ldLe~L~~l~~~~~~~~~eea~e~--L~~L~GIGpkTAd~IL 330 (426)
.|-. ||++.-...|+.+.+-.- +++++.+. ++.|||||+-+|+.|-
T Consensus 22 ~Gen~fk~~aYr~Aa~sle~~~e---------------~~~ei~e~~~~t~l~gIGk~ia~~I~ 70 (326)
T COG1796 22 EGENPFKIRAYRKAAQSLENLTE---------------DLEEIEERGRLTELPGIGKGIAEKIS 70 (326)
T ss_pred cCCCccchHHHHHHHHhhhhccc---------------chHHHHhhcccCCCCCccHHHHHHHH
Confidence 4544 888888888887765332 45555666 9999999999999994
No 84
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=49.57 E-value=14 Score=33.42 Aligned_cols=19 Identities=16% Similarity=0.329 Sum_probs=17.0
Q ss_pred HHHHhcCCCcCHHHHHHHH
Q 014334 312 AEQLSQINGFGPFTRNNVL 330 (426)
Q Consensus 312 ~e~L~~L~GIGpkTAd~IL 330 (426)
.++|.++|||||..|.-|.
T Consensus 60 ~~el~~lpGigP~~A~~IV 78 (132)
T PRK02515 60 VRAFRQFPGMYPTLAGKIV 78 (132)
T ss_pred HHHHHHCCCCCHHHHHHHH
Confidence 4668899999999999997
No 85
>PRK07945 hypothetical protein; Provisional
Probab=48.68 E-value=26 Score=36.01 Aligned_cols=53 Identities=25% Similarity=0.302 Sum_probs=35.4
Q ss_pred HHHHHCc-CcHHHHHHHHHHHHHHhCCCChhHHHhhhhhcccccHHHHHH-HHhcCCCcCHHHHHHHH
Q 014334 265 FLAKRCN-LGYRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAE-QLSQINGFGPFTRNNVL 330 (426)
Q Consensus 265 ~Lr~~~g-~GyRAkyI~~lA~~i~eg~ldLe~L~~l~~~~~~~~~eea~e-~L~~L~GIGpkTAd~IL 330 (426)
+|.+..| --||++.-.+.|+.|..-.-+ .+..+ . .+ .|.+|||||.-+|..|.
T Consensus 12 ~lle~~~~n~frv~ayr~aa~~~~~~~~~--~~~~~-------~----~~g~l~~~~giG~~~a~~i~ 66 (335)
T PRK07945 12 FLLERARADTYRVRAFRRAADVVEALDAA--ERARR-------A----RAGSLTSLPGIGPKTAKVIA 66 (335)
T ss_pred HHHHHcCCChhhHHHHHHHHHHHHhcChh--HHHHH-------H----hcCCcccCCCcCHHHHHHHH
Confidence 3444345 349999999999988653222 12222 0 12 69999999999999984
No 86
>PRK14973 DNA topoisomerase I; Provisional
Probab=48.65 E-value=26 Score=41.10 Aligned_cols=82 Identities=16% Similarity=0.248 Sum_probs=47.9
Q ss_pred cCCCCHHHHhcCCHHHHHHHCcCcH-HHHHHHHHHH-HHHhCCCChhHHHhhhhhcccccHHHHHHHHhcCCCcCHHHHH
Q 014334 250 GNFPSPRELANLDESFLAKRCNLGY-RAGRILKLAR-GIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRN 327 (426)
Q Consensus 250 ~~FPtpe~La~~~~e~Lr~~~g~Gy-RAkyI~~lA~-~i~eg~ldLe~L~~l~~~~~~~~~eea~e~L~~L~GIGpkTAd 327 (426)
.-|=++++++.+++++|...-|++= .+..+...|. .+. .-+-....+. -.+.-+.+|+.++|||++|++
T Consensus 821 ~G~~~~~d~~~a~p~~La~~~g~~~~~~~~~~~~~~~~~~--~~~~~~~~~~-------~~~~~~~el~~vkg~ge~t~~ 891 (936)
T PRK14973 821 AGFDTPEDFCSVHPAYLALKTGISPETICRHAKLVCEKLG--RPVPEKISKA-------AFERGRAELLSVPGLGETTLE 891 (936)
T ss_pred hcCCCHHHHHhcCHHHHhcCCCCChhhHHHHHHHHHHHhc--CCCchhhhhh-------hhcccchhhhhccCCCHHHHH
Confidence 4699999999999999986445542 3333333333 222 1111222221 223445569999999999997
Q ss_pred HH-HHHhCCCCccc
Q 014334 328 NV-LVCIGFYHVIP 340 (426)
Q Consensus 328 ~I-L~~Lg~~dvfP 340 (426)
-. +-|.-..+.+-
T Consensus 892 ~l~~ag~~~~e~l~ 905 (936)
T PRK14973 892 KLYLAGVYDGDLLV 905 (936)
T ss_pred HHHHcCCCCHHHhc
Confidence 66 34444443333
No 87
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=45.84 E-value=19 Score=35.27 Aligned_cols=49 Identities=24% Similarity=0.362 Sum_probs=37.3
Q ss_pred CcCcHHHHHHHHHHHHHHhCCCChhHHHhhhhhcccccHHHHHHHHhcCCCcCHHHHHHH
Q 014334 270 CNLGYRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNV 329 (426)
Q Consensus 270 ~g~GyRAkyI~~lA~~i~eg~ldLe~L~~l~~~~~~~~~eea~e~L~~L~GIGpkTAd~I 329 (426)
++.|-|-+-...+|+.+.+.-..|..|.+. + .++|++++|||+-.|--+
T Consensus 34 LrtG~~~~~~~~la~~lL~~fg~L~~l~~a-------~----~~el~~v~GiG~aka~~l 82 (224)
T COG2003 34 LRTGTKGESVLDLAKELLQEFGSLAELLKA-------S----VEELSSVKGIGLAKAIQI 82 (224)
T ss_pred HhcCCCCCCHHHHHHHHHHHcccHHHHHhC-------C----HHHHhhCCCccHHHHHHH
Confidence 567877778899999999854446666654 3 588999999998766555
No 88
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=45.41 E-value=34 Score=35.11 Aligned_cols=42 Identities=12% Similarity=0.170 Sum_probs=31.4
Q ss_pred cHHHHHHHHHHHHHHhCCCChhHHHhhhhhcccccHHHHHHHHhcCCCcCHHHHHHHH
Q 014334 273 GYRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNVL 330 (426)
Q Consensus 273 GyRAkyI~~lA~~i~eg~ldLe~L~~l~~~~~~~~~eea~e~L~~L~GIGpkTAd~IL 330 (426)
-||+.+....|..|..-..+++ + .++|.+|||||+.+|+-|-
T Consensus 24 ~~k~~ay~~Aa~~i~~l~~~i~------------~----~~~l~~lpgIG~~ia~kI~ 65 (334)
T smart00483 24 KRKCSYFRKAASVLKSLPFPIN------------S----MKDLKGLPGIGDKIKKKIE 65 (334)
T ss_pred HHHHHHHHHHHHHHHhCCCCCC------------C----HHHHhcCCCccHHHHHHHH
Confidence 4788888888888876443322 2 1368899999999999993
No 89
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=45.36 E-value=43 Score=33.52 Aligned_cols=75 Identities=21% Similarity=0.194 Sum_probs=44.2
Q ss_pred CCHHHHhcCCHHHHHHHCcCc--------HHHHHHHHHHHHHHh-CCCC--hhHHHhhhhhcccccHHHHH-HHHhcCCC
Q 014334 253 PSPRELANLDESFLAKRCNLG--------YRAGRILKLARGIVD-GQIQ--LRELEDMCNEASLTAYVKLA-EQLSQING 320 (426)
Q Consensus 253 Ptpe~La~~~~e~Lr~~~g~G--------yRAkyI~~lA~~i~e-g~ld--Le~L~~l~~~~~~~~~eea~-e~L~~L~G 320 (426)
-.|+++..+-....-+ .|+. .=|..|+.+|+.... ++-. ...... ..++.+.. ..|.++||
T Consensus 117 i~~~av~~al~s~~vd-fg~~vi~t~~~~~Ta~~i~~la~req~e~~r~v~~~~~~~------~~t~~e~q~~il~s~pg 189 (254)
T COG1948 117 IHPNAVRGALASLAVD-FGLPVIWTRSPEETAELIHELARREQEERKRSVNPHGKKK------AKTLKELQLYILESIPG 189 (254)
T ss_pred cCHHHHHHHHHHHHhh-cCceEEEeCCHHHHHHHHHHHHHHHHHhcccccccccccc------ccchHHHHHHHHHcCCC
Confidence 3677776643333222 2332 248899999998883 2211 111111 12555554 56689999
Q ss_pred cCHHHHHHHHHHhC
Q 014334 321 FGPFTRNNVLVCIG 334 (426)
Q Consensus 321 IGpkTAd~IL~~Lg 334 (426)
||++.|.-+|--+|
T Consensus 190 ig~~~a~~ll~~fg 203 (254)
T COG1948 190 IGPKLAERLLKKFG 203 (254)
T ss_pred ccHHHHHHHHHHhc
Confidence 99999999984444
No 90
>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=45.04 E-value=22 Score=30.48 Aligned_cols=43 Identities=16% Similarity=0.156 Sum_probs=28.3
Q ss_pred HHHHHHHhcCCCcCHHHHHHHHHHhCCCCccc----cchHHHHHHHH
Q 014334 309 VKLAEQLSQINGFGPFTRNNVLVCIGFYHVIP----TDSETIRHLKQ 351 (426)
Q Consensus 309 eea~e~L~~L~GIGpkTAd~IL~~Lg~~dvfP----vDthV~Ril~r 351 (426)
..+.-.|..|.|||+.+|..|+.-+|...-.. .|.++.++..-
T Consensus 11 k~i~~aLt~IyGIG~~~A~~Ic~~lgi~~~~~~~~Ls~~~i~~l~~~ 57 (107)
T PF00416_consen 11 KPIYIALTKIYGIGRRKAKQICKKLGINPNKKVGDLSDEQIDKLRKI 57 (107)
T ss_dssp SBHHHHHTTSTTBCHHHHHHHHHHTTS-SSSBTTTSTHHHHHHHHHH
T ss_pred cchHhHHhhhhccCHHHHHHHHHHcCCChhhhcccCCHHHHHHHHHH
Confidence 45678999999999999999975555433222 24445444443
No 91
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=43.32 E-value=55 Score=29.89 Aligned_cols=52 Identities=21% Similarity=0.388 Sum_probs=35.4
Q ss_pred HhcCCHHHHHHHCcCc-HHHHHHHHHHHHHHhCCCChhHHHhhhhhcccccHHHHHHHHhcCCCcCHHHHHHH
Q 014334 258 LANLDESFLAKRCNLG-YRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNV 329 (426)
Q Consensus 258 La~~~~e~Lr~~~g~G-yRAkyI~~lA~~i~eg~ldLe~L~~l~~~~~~~~~eea~e~L~~L~GIGpkTAd~I 329 (426)
|-.++.|+|+.+-|+| .+|+.|++-=+ ..|.. ...+.|...+|||+++.+-+
T Consensus 91 iNtAs~eeL~~lpgIG~~kA~aIi~yRe--~~G~f------------------~sv~dL~~v~GiG~~~~ekl 143 (149)
T COG1555 91 INTASAEELQALPGIGPKKAQAIIDYRE--ENGPF------------------KSVDDLAKVKGIGPKTLEKL 143 (149)
T ss_pred ccccCHHHHHHCCCCCHHHHHHHHHHHH--HcCCC------------------CcHHHHHhccCCCHHHHHHH
Confidence 4457889997655788 47877754332 23432 11478899999999998765
No 92
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=42.89 E-value=44 Score=32.97 Aligned_cols=26 Identities=15% Similarity=0.331 Sum_probs=15.7
Q ss_pred HHHHhcCCCcCHHHHHHHHHHhCCCC
Q 014334 312 AEQLSQINGFGPFTRNNVLVCIGFYH 337 (426)
Q Consensus 312 ~e~L~~L~GIGpkTAd~IL~~Lg~~d 337 (426)
.++|.+++|||.++|+-|.-.|+.++
T Consensus 35 ~eEL~~V~GIg~k~AekI~e~l~~~~ 60 (232)
T PRK12766 35 QSELAEVDGIGNALAARIKADVGGLE 60 (232)
T ss_pred HHHHHHccCCCHHHHHHHHHHhcccc
Confidence 35666677777777777654444443
No 93
>PF01367 5_3_exonuc: 5'-3' exonuclease, C-terminal SAM fold; InterPro: IPR020045 This entry represents the C-terminal domain of 5' to 3' exonucleases. The 5'-3' exonucleases are conserved in organisms as diverse as bacteriophage and mammals. It adopts a SAM fold consisting of 4-5 helices packed into a bundle of two orthogonally packed alpha-hairpins. This domain is involved in interactions with DNA and proteins. 5' to 3' exonucleases that contain this domain include: Bacteriophage T4 RNase H, which has sequence similarity to the RAD2 family of eukaryotic proteins []. 5' to 3' exonuclease domain of DNA polymerase Taq, which is homologous to Escherichia coli DNA polymerase I (pol I) [, ]. Bacteriophage T5 5'-exonuclease, which are structure-specific endonucleases []. Flap endonuclease-1 (Fen-1 nuclease), a structure specific nuclease that is an essential enzyme for eukaryotic DNA replication and repair []. ; GO: 0003677 DNA binding, 0003824 catalytic activity; PDB: 1TAQ_A 1BGX_T 1TAU_A 1XO1_B 1EXN_A 1UT8_A 1UT5_B.
Probab=41.76 E-value=4.1 Score=35.01 Aligned_cols=27 Identities=26% Similarity=0.437 Sum_probs=18.2
Q ss_pred HHHhcCCCcCHHHHHHHHHHhCCCCcc
Q 014334 313 EQLSQINGFGPFTRNNVLVCIGFYHVI 339 (426)
Q Consensus 313 e~L~~L~GIGpkTAd~IL~~Lg~~dvf 339 (426)
+-+..+||||+|||.-+|.-+|-.+.+
T Consensus 18 DNIPGV~GIG~KtA~~LL~~ygsle~i 44 (101)
T PF01367_consen 18 DNIPGVPGIGPKTAAKLLQEYGSLENI 44 (101)
T ss_dssp CTB---TTSTCHCCCCCHHHHTSCHCC
T ss_pred cCCCCCCCCCHHHHHHHHHHcCCHHHH
Confidence 456789999999999998666655433
No 94
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this
Probab=41.46 E-value=53 Score=33.30 Aligned_cols=44 Identities=16% Similarity=0.203 Sum_probs=32.2
Q ss_pred cCcHHHHHHHHHHHHHHhCCCChhHHHhhhhhcccccHHHHHHHHhcCCCcCHHHHHHHH
Q 014334 271 NLGYRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNVL 330 (426)
Q Consensus 271 g~GyRAkyI~~lA~~i~eg~ldLe~L~~l~~~~~~~~~eea~e~L~~L~GIGpkTAd~IL 330 (426)
+--||++.-...|..|..-..++. + .+++.+|||||+.+|+.|-
T Consensus 19 ~~~~r~~aY~~Aa~~l~~l~~~i~------------~----~~~~~~ipgiG~~ia~kI~ 62 (307)
T cd00141 19 GNPFRVRAYRKAARALESLPEPIE------------S----LEEAKKLPGIGKKIAEKIE 62 (307)
T ss_pred CCcchHHHHHHHHHHHHhCCcccC------------C----HHHhcCCCCccHHHHHHHH
Confidence 345888888888888876443322 2 2356899999999999994
No 95
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair]
Probab=40.25 E-value=28 Score=34.53 Aligned_cols=38 Identities=26% Similarity=0.329 Sum_probs=32.5
Q ss_pred cccCCCCHHHHhcCCHHHHHHHCcCcH-HHHHHHHHHHH
Q 014334 248 RIGNFPSPRELANLDESFLAKRCNLGY-RAGRILKLARG 285 (426)
Q Consensus 248 ~~~~FPtpe~La~~~~e~Lr~~~g~Gy-RAkyI~~lA~~ 285 (426)
....|+|.++|..++.++|....|+|- ||+.|++....
T Consensus 211 LL~~FgsLq~~~~AS~~ele~~~G~G~~kak~l~~~l~~ 249 (254)
T KOG2841|consen 211 LLQKFGSLQQISNASEGELEQCPGLGPAKAKRLHKFLHQ 249 (254)
T ss_pred HHHhcccHHHHHhcCHhHHHhCcCcCHHHHHHHHHHHhc
Confidence 367899999999999999998669995 79999887653
No 96
>TIGR01448 recD_rel helicase, putative, RecD/TraA family. This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.
Probab=39.52 E-value=55 Score=37.21 Aligned_cols=29 Identities=21% Similarity=0.269 Sum_probs=20.4
Q ss_pred cHHHHHHHHhc--CCCcCHHHHHHHHHHhCC
Q 014334 307 AYVKLAEQLSQ--INGFGPFTRNNVLVCIGF 335 (426)
Q Consensus 307 ~~eea~e~L~~--L~GIGpkTAd~IL~~Lg~ 335 (426)
+.+.+...|.+ ++||||++|.-|...||.
T Consensus 76 ~~~~i~~yL~s~~~~GIG~~~A~~iv~~fg~ 106 (720)
T TIGR01448 76 SKEGIVAYLSSRSIKGVGKKLAQRIVKTFGE 106 (720)
T ss_pred CHHHHHHHHhcCCCCCcCHHHHHHHHHHhCH
Confidence 44566777764 888888888888655553
No 97
>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region. Members of the subfamily recognized by this model include competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model.
Probab=39.02 E-value=28 Score=27.07 Aligned_cols=19 Identities=32% Similarity=0.569 Sum_probs=16.6
Q ss_pred HHHHhc-CCCcCHHHHHHHH
Q 014334 312 AEQLSQ-INGFGPFTRNNVL 330 (426)
Q Consensus 312 ~e~L~~-L~GIGpkTAd~IL 330 (426)
.+.|.. ++|||+.+|..|+
T Consensus 15 ~~~L~~~ipgig~~~a~~Il 34 (69)
T TIGR00426 15 AEELQRAMNGVGLKKAEAIV 34 (69)
T ss_pred HHHHHhHCCCCCHHHHHHHH
Confidence 357777 9999999999997
No 98
>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=37.69 E-value=3.6e+02 Score=25.56 Aligned_cols=39 Identities=23% Similarity=0.206 Sum_probs=30.6
Q ss_pred ccccC-CCChHHHHHHHHHhcCCCHHHHHHHHHHHHHHhh
Q 014334 115 GRVFR-SPTLFEDMVKCMLLCNCQWPRTLSMARALCELQW 153 (426)
Q Consensus 115 gRvlr-~p~~fE~lv~~I~s~N~~~~r~~~m~~~Lc~~~g 153 (426)
|+... ...|||.|+-.+.-+-.+|.-|++--+++.+.|.
T Consensus 21 G~p~~dd~~LFE~L~Le~fQAGLSW~tIL~Kr~~fr~aF~ 60 (179)
T TIGR00624 21 GVPLRDSVALFERMSLEGFQAGLSWITVLRKRENYRRAFS 60 (179)
T ss_pred CCcCcCCHHHHHHHHHHHHhCcCCHHHHHHhHHHHHHHHc
Confidence 44444 3379999999999999999999988888877653
No 99
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=33.18 E-value=91 Score=35.29 Aligned_cols=37 Identities=19% Similarity=0.381 Sum_probs=25.9
Q ss_pred HHHHhcCCCcCHHHHHHHHHHhCCCCccccchHHHHHHHHhhcc
Q 014334 312 AEQLSQINGFGPFTRNNVLVCIGFYHVIPTDSETIRHLKQVHAR 355 (426)
Q Consensus 312 ~e~L~~L~GIGpkTAd~IL~~Lg~~dvfPvDthV~Ril~rly~~ 355 (426)
.++|.+++|||+.+|..|---|. +.+.+..+.++...
T Consensus 542 ~e~l~~i~giG~~vA~si~~ff~-------~~~~~~li~~L~~~ 578 (667)
T COG0272 542 EEELASIPGIGEVVARSIIEFFA-------NEENRELIDELLAA 578 (667)
T ss_pred HHHHhhccchhHHHHHHHHHHHc-------CHHHHHHHHHHHHc
Confidence 46888999999999999963333 34556666665544
No 100
>PRK07758 hypothetical protein; Provisional
Probab=33.16 E-value=79 Score=27.15 Aligned_cols=39 Identities=18% Similarity=0.403 Sum_probs=0.0
Q ss_pred HHHHHHHHh-CCCChhHHHhhhhhcccccHHHHHHHHhcCCCcCHHHHHHH
Q 014334 280 LKLARGIVD-GQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNV 329 (426)
Q Consensus 280 ~~lA~~i~e-g~ldLe~L~~l~~~~~~~~~eea~e~L~~L~GIGpkTAd~I 329 (426)
....+.+.. |--.++.|.++ + .++|++|+|||+++.+-|
T Consensus 44 vRA~N~Lk~AGI~TL~dLv~~-------t----e~ELl~iknlGkKSL~EI 83 (95)
T PRK07758 44 APARRALEHHGIHTVEELSKY-------S----EKEILKLHGMGPASLPKL 83 (95)
T ss_pred HHHHHHHHHcCCCcHHHHHcC-------C----HHHHHHccCCCHHHHHHH
No 101
>PRK14976 5'-3' exonuclease; Provisional
Probab=33.12 E-value=28 Score=34.96 Aligned_cols=24 Identities=25% Similarity=0.425 Sum_probs=19.3
Q ss_pred HHHhcCCCcCHHHHHHHHHHhCCC
Q 014334 313 EQLSQINGFGPFTRNNVLVCIGFY 336 (426)
Q Consensus 313 e~L~~L~GIGpkTAd~IL~~Lg~~ 336 (426)
+-+..+||||||||.-+|--+|-.
T Consensus 191 DnipGVpGIG~KtA~~LL~~~gsl 214 (281)
T PRK14976 191 DNIKGVKGIGPKTAIKLLNKYGNI 214 (281)
T ss_pred CCCCCCCcccHHHHHHHHHHcCCH
Confidence 456789999999999998666654
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=32.62 E-value=42 Score=26.43 Aligned_cols=46 Identities=26% Similarity=0.304 Sum_probs=28.3
Q ss_pred CcCcHHHHHHHHHHHHHHhCCCChhHHHhhhhhcccccHHHHHHHHhcCCCcCHHHHHHHHH
Q 014334 270 CNLGYRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNVLV 331 (426)
Q Consensus 270 ~g~GyRAkyI~~lA~~i~eg~ldLe~L~~l~~~~~~~~~eea~e~L~~L~GIGpkTAd~IL~ 331 (426)
+++..||.....- .|--.+..|-.+ + .+.|+.++|+|+++.+-|..
T Consensus 17 L~LS~Ra~n~L~~-----~~I~tv~dL~~~-------s----~~~L~~i~n~G~ksl~EI~~ 62 (66)
T PF03118_consen 17 LGLSVRAYNCLKR-----AGIHTVGDLVKY-------S----EEDLLKIKNFGKKSLEEIKE 62 (66)
T ss_dssp STSBHHHHHHHHC-----TT--BHHHHHCS------------HHHHHTSTTSHHHHHHHHHH
T ss_pred hCCCHHHHHHHHH-----hCCcCHHHHHhC-------C----HHHHHhCCCCCHhHHHHHHH
Confidence 4677776433221 133344555554 3 36899999999999998853
No 103
>PRK09482 flap endonuclease-like protein; Provisional
Probab=31.81 E-value=28 Score=34.71 Aligned_cols=24 Identities=17% Similarity=0.350 Sum_probs=19.5
Q ss_pred HHHhcCCCcCHHHHHHHHHHhCCC
Q 014334 313 EQLSQINGFGPFTRNNVLVCIGFY 336 (426)
Q Consensus 313 e~L~~L~GIGpkTAd~IL~~Lg~~ 336 (426)
+-+..+||||||||--+|--+|-.
T Consensus 182 DnIpGVpGIG~KtA~~LL~~~gsl 205 (256)
T PRK09482 182 SKIPGVAGIGPKSAAELLNQFRSL 205 (256)
T ss_pred cCCCCCCCcChHHHHHHHHHhCCH
Confidence 456789999999999998666654
No 104
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=31.04 E-value=1.3e+02 Score=31.21 Aligned_cols=40 Identities=18% Similarity=0.268 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHHHHhCCCChhHHHhhhhhcccccHHHHHHHHhcCCCcCHHHHHHH
Q 014334 274 YRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNV 329 (426)
Q Consensus 274 yRAkyI~~lA~~i~eg~ldLe~L~~l~~~~~~~~~eea~e~L~~L~GIGpkTAd~I 329 (426)
.|+..-...|..+..=..... + .+++..||||||++|.-|
T Consensus 33 ~r~~~y~~Aasvlk~~p~~I~------------S----~~ea~~lP~iG~kia~ki 72 (353)
T KOG2534|consen 33 DRARAYRRAASVLKSLPFPIT------------S----GEEAEKLPGIGPKIAEKI 72 (353)
T ss_pred HHHHHHHHHHHHHHhCCCCcc------------c----HHHhcCCCCCCHHHHHHH
Confidence 577666666666655322211 2 366777999999999999
No 105
>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=30.60 E-value=1.1e+02 Score=21.85 Aligned_cols=35 Identities=20% Similarity=0.200 Sum_probs=28.2
Q ss_pred CCCCHHHHhcCCHHHHHHHCcCcH-HHHHHHHHHHH
Q 014334 251 NFPSPRELANLDESFLAKRCNLGY-RAGRILKLARG 285 (426)
Q Consensus 251 ~FPtpe~La~~~~e~Lr~~~g~Gy-RAkyI~~lA~~ 285 (426)
-|=|.++|+.+++++|....|++. ++..|+..|+.
T Consensus 13 G~~s~e~la~~~~~eL~~i~g~~~e~a~~ii~~a~~ 48 (50)
T TIGR01954 13 GFTTVEDLAYVPIDELLSIEGFDEETAKELINRARN 48 (50)
T ss_pred CCCCHHHHHccCHHHHhcCCCCCHHHHHHHHHHHHH
Confidence 577999999999999998667775 77777776663
No 106
>TIGR01448 recD_rel helicase, putative, RecD/TraA family. This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.
Probab=30.41 E-value=6.8e+02 Score=28.57 Aligned_cols=37 Identities=19% Similarity=0.326 Sum_probs=23.3
Q ss_pred cCCCcCHHHHHHHHHHhCCCCccc--cchHHHHHHHHhh
Q 014334 317 QINGFGPFTRNNVLVCIGFYHVIP--TDSETIRHLKQVH 353 (426)
Q Consensus 317 ~L~GIGpkTAd~IL~~Lg~~dvfP--vDthV~Ril~rly 353 (426)
.++|||-++||.|...+|...-=| +...+..++.+..
T Consensus 185 ~i~gigF~~aD~iA~~~g~~~~d~~Ri~a~i~~~L~~~~ 223 (720)
T TIGR01448 185 DVKGIGFLTADQLAQALGIALNDPRRITAGLVYSLQQAC 223 (720)
T ss_pred hcCCCCHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHh
Confidence 689999999999954455431112 4455555555544
No 107
>smart00475 53EXOc 5'-3' exonuclease.
Probab=29.72 E-value=33 Score=34.08 Aligned_cols=24 Identities=21% Similarity=0.369 Sum_probs=19.0
Q ss_pred HHHhcCCCcCHHHHHHHHHHhCCC
Q 014334 313 EQLSQINGFGPFTRNNVLVCIGFY 336 (426)
Q Consensus 313 e~L~~L~GIGpkTAd~IL~~Lg~~ 336 (426)
+-+..+||||||||--+|.-+|-.
T Consensus 186 DnipGV~GIG~KtA~~Ll~~ygsl 209 (259)
T smart00475 186 DNIPGVPGIGEKTAAKLLKEFGSL 209 (259)
T ss_pred cCCCCCCCCCHHHHHHHHHHhCCH
Confidence 446789999999999998656643
No 108
>COG4277 Predicted DNA-binding protein with the Helix-hairpin-helix motif [General function prediction only]
Probab=29.34 E-value=39 Score=34.96 Aligned_cols=21 Identities=14% Similarity=0.365 Sum_probs=18.6
Q ss_pred HHHHhcCCCcCHHHHHHHHHH
Q 014334 312 AEQLSQINGFGPFTRNNVLVC 332 (426)
Q Consensus 312 ~e~L~~L~GIGpkTAd~IL~~ 332 (426)
.+.|+.+||||+++|.-|+|.
T Consensus 329 ~~~llRVPGiG~ksa~rIv~~ 349 (404)
T COG4277 329 YKELLRVPGIGVKSARRIVMT 349 (404)
T ss_pred HHHhcccCCCChHHHHHHHHH
Confidence 578999999999999999753
No 109
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=29.00 E-value=1.1e+02 Score=31.76 Aligned_cols=75 Identities=21% Similarity=0.230 Sum_probs=45.1
Q ss_pred cCCCCHHHHhcCCHHHHHHHCcCcHH-HHHHHHHHHHHHhCCCChhHHHhhhhhcccccHHHHHHHHhcCCCcCHHHHHH
Q 014334 250 GNFPSPRELANLDESFLAKRCNLGYR-AGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNN 328 (426)
Q Consensus 250 ~~FPtpe~La~~~~e~Lr~~~g~GyR-AkyI~~lA~~i~eg~ldLe~L~~l~~~~~~~~~eea~e~L~~L~GIGpkTAd~ 328 (426)
.+||.|=. +-+++..+=|+|-| |+-|.++++ .|.+ ..|...++ .+..+..+.+.++-|||++||+-
T Consensus 46 k~~p~~I~----S~~ea~~lP~iG~kia~ki~Eile---tG~l--~ele~v~~----de~~~~lklFtnifGvG~ktA~~ 112 (353)
T KOG2534|consen 46 KSLPFPIT----SGEEAEKLPGIGPKIAEKIQEILE---TGVL--RELEAVRN----DERSQSLKLFTNIFGVGLKTAEK 112 (353)
T ss_pred HhCCCCcc----cHHHhcCCCCCCHHHHHHHHHHHH---cCCc--hhHHHHhc----chhHHHHHHHHHHhccCHHHHHH
Confidence 45554422 34455443468877 555554433 4654 23333322 14467789999999999999998
Q ss_pred H-HHHhCCCC
Q 014334 329 V-LVCIGFYH 337 (426)
Q Consensus 329 I-L~~Lg~~d 337 (426)
- .+|+.-.+
T Consensus 113 Wy~~GfrTle 122 (353)
T KOG2534|consen 113 WYREGFRTLE 122 (353)
T ss_pred HHHhhhhHHH
Confidence 8 46765443
No 110
>cd00008 53EXOc 5'-3' exonuclease; T5 type 5'-3' exonuclease domains may co-occur with DNA polymerase I (Pol I) domains, or be part of Pol I containing complexes. They digest dsDNA and ssDNA, releasing mono-,di- and tri-nucleotides, as well as oligonucleotides, and have also been reported to possess RNase H activity. Also called 5' nuclease family, involved in structure-specific cleavage of flaps formed by Pol I activity (similar to mammalian flap endonuclease I, FEN-1). A single nucleic acid strand may be threaded through the 5' nuclease enzyme before cleavage occurs. The domain binds two divalent metal ions which are necessary for activity.
Probab=28.36 E-value=40 Score=32.90 Aligned_cols=24 Identities=21% Similarity=0.346 Sum_probs=18.8
Q ss_pred HHHhcCCCcCHHHHHHHHHHhCCC
Q 014334 313 EQLSQINGFGPFTRNNVLVCIGFY 336 (426)
Q Consensus 313 e~L~~L~GIGpkTAd~IL~~Lg~~ 336 (426)
+-+..+||||||||.-+|.-+|-.
T Consensus 183 DnipGv~GiG~ktA~~Ll~~~gsl 206 (240)
T cd00008 183 DNIPGVPGIGEKTAAKLLKEYGSL 206 (240)
T ss_pred cCCCCCCccCHHHHHHHHHHhCCH
Confidence 456789999999998888555543
No 111
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=27.30 E-value=90 Score=35.02 Aligned_cols=31 Identities=26% Similarity=0.385 Sum_probs=24.1
Q ss_pred HHHHHHHhcCCCcCHHHHHHHHHHhCCCCcc
Q 014334 309 VKLAEQLSQINGFGPFTRNNVLVCIGFYHVI 339 (426)
Q Consensus 309 eea~e~L~~L~GIGpkTAd~IL~~Lg~~dvf 339 (426)
......|..|+|||+++|..+|..+|-.+.+
T Consensus 565 ~~~~s~L~~I~GIG~k~a~~Ll~~Fgs~~~i 595 (621)
T PRK14671 565 RTLQTELTDIAGIGEKTAEKLLEHFGSVEKV 595 (621)
T ss_pred HHhhhhhhcCCCcCHHHHHHHHHHcCCHHHH
Confidence 4456788999999999999998667644433
No 112
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=26.73 E-value=40 Score=29.94 Aligned_cols=27 Identities=19% Similarity=0.281 Sum_probs=21.5
Q ss_pred HHHHHHHhcCCCcCHHHHHHHHHHhCC
Q 014334 309 VKLAEQLSQINGFGPFTRNNVLVCIGF 335 (426)
Q Consensus 309 eea~e~L~~L~GIGpkTAd~IL~~Lg~ 335 (426)
..+.-.|..|.|||+.+|..|+.-+|-
T Consensus 13 k~v~~aLt~i~GIG~~~A~~ic~~lgi 39 (122)
T CHL00137 13 KRIEYALTYIYGIGLTSAKEILEKANI 39 (122)
T ss_pred CEeeeeecccccccHHHHHHHHHHcCc
Confidence 445678999999999999999844443
No 113
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=26.04 E-value=88 Score=32.76 Aligned_cols=42 Identities=19% Similarity=0.156 Sum_probs=36.1
Q ss_pred ccCCCCHHHHhcCCHHHHHHHCcCc-HHHHHHHHHHHHHHhCC
Q 014334 249 IGNFPSPRELANLDESFLAKRCNLG-YRAGRILKLARGIVDGQ 290 (426)
Q Consensus 249 ~~~FPtpe~La~~~~e~Lr~~~g~G-yRAkyI~~lA~~i~eg~ 290 (426)
...|.+.+.|.+++.++|.+.-|+| .||+.|.+.++.+.+..
T Consensus 304 l~~FGSL~~Il~As~eeL~~VeGIGe~rA~~I~e~l~Rl~e~~ 346 (352)
T PRK13482 304 VEHFGSLQGLLAASIEDLDEVEGIGEVRARAIREGLSRLAEQS 346 (352)
T ss_pred HHHcCCHHHHHcCCHHHHhhCCCcCHHHHHHHHHHHHHHHHHH
Confidence 5679999999999999999855899 48999999999887643
No 114
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=26.00 E-value=85 Score=32.87 Aligned_cols=39 Identities=18% Similarity=0.308 Sum_probs=28.0
Q ss_pred HHHHHHHhCCCChhHHHhhhhhcccccHHHHHHHHhcCCCcCHHHHHHHH
Q 014334 281 KLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNVL 330 (426)
Q Consensus 281 ~lA~~i~eg~ldLe~L~~l~~~~~~~~~eea~e~L~~L~GIGpkTAd~IL 330 (426)
.+|+.+.+.-.++..+-+. + .++|..++|||++.|..|.
T Consensus 298 ~iAk~Ll~~FGSL~~Il~A-------s----~eeL~~VeGIGe~rA~~I~ 336 (352)
T PRK13482 298 AVIENLVEHFGSLQGLLAA-------S----IEDLDEVEGIGEVRARAIR 336 (352)
T ss_pred HHHHHHHHHcCCHHHHHcC-------C----HHHHhhCCCcCHHHHHHHH
Confidence 5677777755556655553 3 4679999999999998874
No 115
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=25.52 E-value=61 Score=25.11 Aligned_cols=34 Identities=24% Similarity=0.225 Sum_probs=23.0
Q ss_pred ccCCCCHHHHhcCCHHHHHHHCcCcHH-HHHHHHH
Q 014334 249 IGNFPSPRELANLDESFLAKRCNLGYR-AGRILKL 282 (426)
Q Consensus 249 ~~~FPtpe~La~~~~e~Lr~~~g~GyR-AkyI~~l 282 (426)
...|+|.+.|.+++.|+|...-|+|-. |+.|.+.
T Consensus 20 ~~~f~sl~~l~~a~~e~L~~i~gIG~~~A~si~~f 54 (64)
T PF12826_consen 20 AKHFGSLEALMNASVEELSAIPGIGPKIAQSIYEF 54 (64)
T ss_dssp HHCCSCHHHHCC--HHHHCTSTT--HHHHHHHHHH
T ss_pred HHHcCCHHHHHHcCHHHHhccCCcCHHHHHHHHHH
Confidence 358999999999999999874489975 6655543
No 116
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=24.41 E-value=48 Score=29.45 Aligned_cols=27 Identities=22% Similarity=0.407 Sum_probs=21.3
Q ss_pred HHHHHHHhcCCCcCHHHHHHHHHHhCC
Q 014334 309 VKLAEQLSQINGFGPFTRNNVLVCIGF 335 (426)
Q Consensus 309 eea~e~L~~L~GIGpkTAd~IL~~Lg~ 335 (426)
..+.-.|..|.|||+.+|..|+.-+|-
T Consensus 13 k~v~~aL~~I~GIG~~~a~~i~~~lgi 39 (122)
T PRK05179 13 KRVVIALTYIYGIGRTRAKEILAAAGI 39 (122)
T ss_pred cEEEeeecccccccHHHHHHHHHHhCc
Confidence 445678999999999999999844443
No 117
>PRK08609 hypothetical protein; Provisional
Probab=24.25 E-value=1.4e+02 Score=32.92 Aligned_cols=48 Identities=10% Similarity=0.165 Sum_probs=34.2
Q ss_pred HHHHCc-CcHHHHHHHHHHHHHHhCCCChhHHHhhhhhcccccHHHHHHHHhcCCCcCHHHHHHH
Q 014334 266 LAKRCN-LGYRAGRILKLARGIVDGQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNV 329 (426)
Q Consensus 266 Lr~~~g-~GyRAkyI~~lA~~i~eg~ldLe~L~~l~~~~~~~~~eea~e~L~~L~GIGpkTAd~I 329 (426)
|.+..| -.||++.-...|+.|..-.-+ ..+ ...|.+|||||+.+|+.|
T Consensus 16 ~le~~g~n~fr~~aYr~Aa~~i~~l~~~---------------i~~-~~~l~~ipgIG~~ia~kI 64 (570)
T PRK08609 16 YMELKGENPFKISAFRKAAQALELDERS---------------LSE-IDDFTKLKGIGKGTAEVI 64 (570)
T ss_pred HHHhcCCCcHHHHHHHHHHHHHHhCchh---------------hhh-hhhhccCCCcCHHHHHHH
Confidence 333345 459999899999887664322 222 247899999999999999
No 118
>COG1415 Uncharacterized conserved protein [Function unknown]
Probab=23.92 E-value=2e+02 Score=30.25 Aligned_cols=20 Identities=30% Similarity=0.390 Sum_probs=17.3
Q ss_pred HHHHHHhcCCCcCHHHHHHH
Q 014334 310 KLAEQLSQINGFGPFTRNNV 329 (426)
Q Consensus 310 ea~e~L~~L~GIGpkTAd~I 329 (426)
+..++|+-+|||||.|+-.+
T Consensus 275 ~Df~elLl~~GiGpstvRAL 294 (373)
T COG1415 275 DDFEELLLVPGIGPSTVRAL 294 (373)
T ss_pred ccHHHHHhccCCCHHHHHHH
Confidence 44688999999999999887
No 119
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=23.57 E-value=48 Score=30.70 Aligned_cols=27 Identities=26% Similarity=0.219 Sum_probs=21.9
Q ss_pred HHHHHHHhcCCCcCHHHHHHHHHHhCC
Q 014334 309 VKLAEQLSQINGFGPFTRNNVLVCIGF 335 (426)
Q Consensus 309 eea~e~L~~L~GIGpkTAd~IL~~Lg~ 335 (426)
..+.-.|..|.|||+.+|..|+..+|-
T Consensus 26 K~v~~aLt~I~GIG~~~A~~I~~~lgi 52 (154)
T PTZ00134 26 RKVPYALTAIKGIGRRFAYLVCKKAGI 52 (154)
T ss_pred CEEEEeecccccccHHHHHHHHHHcCc
Confidence 445678999999999999999855554
No 120
>PRK10353 3-methyl-adenine DNA glycosylase I; Provisional
Probab=23.56 E-value=6.5e+02 Score=24.04 Aligned_cols=39 Identities=18% Similarity=0.077 Sum_probs=30.1
Q ss_pred ccccC-CCChHHHHHHHHHhcCCCHHHHHHHHHHHHHHhh
Q 014334 115 GRVFR-SPTLFEDMVKCMLLCNCQWPRTLSMARALCELQW 153 (426)
Q Consensus 115 gRvlr-~p~~fE~lv~~I~s~N~~~~r~~~m~~~Lc~~~g 153 (426)
|+... ...+||.|+=-+.-+-.+|.-|++--+++.+.|.
T Consensus 22 G~P~~dd~~LFE~L~Le~~QAGLSW~tIL~Kre~fr~aF~ 61 (187)
T PRK10353 22 GVPETDSKKLFEMICLEGQQAGLSWITVLKKRENYRACFH 61 (187)
T ss_pred CCcCCCcHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHc
Confidence 44443 3478999998888889999999988888887653
No 121
>PF09597 IGR: IGR protein motif; InterPro: IPR019083 This entry is found in fungal and plant proteins and contains a conserved IGR motif. Its function is unknown.
Probab=22.83 E-value=1.3e+02 Score=23.37 Aligned_cols=39 Identities=21% Similarity=0.198 Sum_probs=31.5
Q ss_pred cCCCC-HHHHhcCCHHHHHHHCcCcHH-HHHHHHHHHHHHhC
Q 014334 250 GNFPS-PRELANLDESFLAKRCNLGYR-AGRILKLARGIVDG 289 (426)
Q Consensus 250 ~~FPt-pe~La~~~~e~Lr~~~g~GyR-AkyI~~lA~~i~eg 289 (426)
-.|++ +++|-..+-..|++ .|+--| -+||....+.+..|
T Consensus 17 ~kf~~~w~~lf~~~s~~LK~-~GIp~r~RryiL~~~ek~r~G 57 (57)
T PF09597_consen 17 EKFESDWEKLFTTSSKQLKE-LGIPVRQRRYILRWREKYRQG 57 (57)
T ss_pred HHHHHHHHHHHhcCHHHHHH-CCCCHHHHHHHHHHHHHHhCc
Confidence 36899 99999999999998 787665 57998888776554
No 122
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=22.49 E-value=78 Score=36.69 Aligned_cols=29 Identities=10% Similarity=-0.066 Sum_probs=23.9
Q ss_pred cHHHHHHHHhcCCCcCHHHHHHHHHHhCC
Q 014334 307 AYVKLAEQLSQINGFGPFTRNNVLVCIGF 335 (426)
Q Consensus 307 ~~eea~e~L~~L~GIGpkTAd~IL~~Lg~ 335 (426)
...+..+.|.+|||||++.|..+|..+|-
T Consensus 751 ~~~~~q~~L~~lPgI~~~~a~~ll~~f~s 779 (814)
T TIGR00596 751 FNDGPQDFLLKLPGVTKKNYRNLRKKVKS 779 (814)
T ss_pred ccHHHHHHHHHCCCCCHHHHHHHHHHcCC
Confidence 45677888999999999999999855553
No 123
>TIGR03631 bact_S13 30S ribosomal protein S13. This model describes bacterial ribosomal protein S13, to the exclusion of the homologous archaeal S13P and eukaryotic ribosomal protein S18. This model identifies some (but not all) instances of chloroplast and mitochondrial S13, which is of bacterial type.
Probab=22.12 E-value=52 Score=28.82 Aligned_cols=27 Identities=22% Similarity=0.333 Sum_probs=21.3
Q ss_pred HHHHHHHhcCCCcCHHHHHHHHHHhCC
Q 014334 309 VKLAEQLSQINGFGPFTRNNVLVCIGF 335 (426)
Q Consensus 309 eea~e~L~~L~GIGpkTAd~IL~~Lg~ 335 (426)
..+.-.|..|.|||+.+|..|+.-+|-
T Consensus 11 k~v~~aL~~i~GIG~~~a~~i~~~lgi 37 (113)
T TIGR03631 11 KRVEIALTYIYGIGRTRARKILEKAGI 37 (113)
T ss_pred CEEeeeeeeeecccHHHHHHHHHHhCc
Confidence 345678899999999999999844443
No 124
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=21.93 E-value=72 Score=36.30 Aligned_cols=29 Identities=24% Similarity=0.422 Sum_probs=22.8
Q ss_pred HHHHHHHhcCCCcCHHHHHHHHHHhCCCC
Q 014334 309 VKLAEQLSQINGFGPFTRNNVLVCIGFYH 337 (426)
Q Consensus 309 eea~e~L~~L~GIGpkTAd~IL~~Lg~~d 337 (426)
......|..+|||||+++.-+|..||-.+
T Consensus 633 ~~~~s~L~~IPGIGpkr~k~LL~~FGSle 661 (694)
T PRK14666 633 AALTGELQRVEGIGPATARLLWERFGSLQ 661 (694)
T ss_pred hhhHhHHhhCCCCCHHHHHHHHHHhCCHH
Confidence 34567899999999999999986666433
No 125
>COG2117 Predicted subunit of tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]
Probab=20.56 E-value=99 Score=29.38 Aligned_cols=54 Identities=20% Similarity=0.281 Sum_probs=34.3
Q ss_pred HHHHHHHCcCcHHHHHHHHHHHHHHh-CCCChhHHHhhhhhcccccHHHHHHHHhcCCCcCHHH
Q 014334 263 ESFLAKRCNLGYRAGRILKLARGIVD-GQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFT 325 (426)
Q Consensus 263 ~e~Lr~~~g~GyRAkyI~~lA~~i~e-g~ldLe~L~~l~~~~~~~~~eea~e~L~~L~GIGpkT 325 (426)
++-++.+.|+|||+ |..+|.++.. .+..-+.+.+ .|||.-...|+.-+|+-|+.
T Consensus 127 v~Yi~PL~G~G~kt--i~~Lv~~~f~~e~~~Se~~~k-------~DYEaElR~lL~erg~~~~~ 181 (198)
T COG2117 127 VQYIRPLLGLGYKT--IRRLVSAIFILEEGPSEKIEK-------ADYEAELRYLLRERGTAPED 181 (198)
T ss_pred ceeecccccccHHH--HHHHHHHHeeeeccccccccc-------cchHHHHHHHHHHcCCChHH
Confidence 33444457999986 7777777653 1111122233 38998888888888887765
No 126
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=20.14 E-value=2e+02 Score=25.16 Aligned_cols=32 Identities=25% Similarity=0.201 Sum_probs=24.4
Q ss_pred CCCChhHHHhhhhhcccccHHHHHHHHhcCCCcCHHHHHHHH
Q 014334 289 GQIQLRELEDMCNEASLTAYVKLAEQLSQINGFGPFTRNNVL 330 (426)
Q Consensus 289 g~ldLe~L~~l~~~~~~~~~eea~e~L~~L~GIGpkTAd~IL 330 (426)
..++...+.++ ..+..|+.++|||+..|..++
T Consensus 39 ~~i~~~~l~~w----------~~~AdL~ri~gi~~~~a~LL~ 70 (122)
T PF14229_consen 39 LGISERNLLKW----------VNQADLMRIPGIGPQYAELLE 70 (122)
T ss_pred cCCCHHHHHHH----------HhHHHhhhcCCCCHHHHHHHH
Confidence 44666666665 336889999999999988775
No 127
>TIGR03629 arch_S13P archaeal ribosomal protein S13P. This model describes exclusively the archaeal ribosomal protein S13P. It excludes the homologous eukaryotic 40S ribosomal protein S18 and bacterial 30S ribosomal protein S13.
Probab=20.01 E-value=62 Score=29.61 Aligned_cols=27 Identities=19% Similarity=0.246 Sum_probs=21.1
Q ss_pred HHHHHHHhcCCCcCHHHHHHHHHHhCC
Q 014334 309 VKLAEQLSQINGFGPFTRNNVLVCIGF 335 (426)
Q Consensus 309 eea~e~L~~L~GIGpkTAd~IL~~Lg~ 335 (426)
..+.-.|..|.|||+..|..|+.-+|-
T Consensus 17 k~v~~aLt~I~GIG~~~a~~I~~~lgi 43 (144)
T TIGR03629 17 KPVEYALTGIKGIGRRFARAIARKLGV 43 (144)
T ss_pred CEEEEeecceeccCHHHHHHHHHHcCc
Confidence 344568899999999999999854443
Done!