Query 033363
Match_columns 121
No_of_seqs 189 out of 1029
Neff 6.8
Searched_HMMs 46136
Date Fri Mar 29 12:58:56 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033363.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033363hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0177 Nth Predicted EndoIII- 100.0 4.9E-30 1.1E-34 193.1 12.1 103 3-107 32-141 (211)
2 PRK10702 endonuclease III; Pro 100.0 1.2E-28 2.7E-33 185.8 13.2 110 3-114 32-148 (211)
3 PRK13913 3-methyladenine DNA g 100.0 2.3E-27 5E-32 179.7 14.0 109 4-114 34-160 (218)
4 TIGR01083 nth endonuclease III 99.9 5.5E-27 1.2E-31 173.9 13.4 109 4-114 30-145 (191)
5 PRK10880 adenine DNA glycosyla 99.9 3.3E-26 7.2E-31 183.5 13.6 112 4-118 30-152 (350)
6 TIGR01084 mutY A/G-specific ad 99.9 1E-25 2.2E-30 175.8 13.7 111 5-118 27-148 (275)
7 PRK13910 DNA glycosylase MutY; 99.9 1.2E-25 2.7E-30 176.3 11.7 102 12-116 4-113 (289)
8 smart00478 ENDO3c endonuclease 99.9 4.3E-25 9.3E-30 156.8 11.7 104 11-116 3-113 (149)
9 cd00056 ENDO3c endonuclease II 99.9 3.5E-24 7.6E-29 153.3 13.3 111 3-116 3-124 (158)
10 COG1194 MutY A/G-specific DNA 99.9 1E-22 2.2E-27 162.0 10.0 113 4-119 34-157 (342)
11 COG0122 AlkA 3-methyladenine D 99.9 4.3E-22 9.4E-27 156.1 13.3 109 3-115 108-240 (285)
12 PRK10308 3-methyl-adenine DNA 99.9 3E-21 6.6E-26 151.1 11.7 81 27-111 153-245 (283)
13 TIGR00588 ogg 8-oxoguanine DNA 99.9 5.9E-21 1.3E-25 151.1 11.3 108 4-116 123-262 (310)
14 TIGR03252 uncharacterized HhH- 99.8 3.5E-20 7.5E-25 136.4 10.5 93 4-96 22-138 (177)
15 PRK01229 N-glycosylase/DNA lya 99.8 1.9E-19 4.1E-24 135.7 10.4 101 2-114 43-158 (208)
16 COG2231 Uncharacterized protei 99.8 6E-19 1.3E-23 131.9 12.3 110 5-116 35-156 (215)
17 KOG1921 Endonuclease III [Repl 99.8 5E-19 1.1E-23 135.5 11.3 113 4-116 82-204 (286)
18 KOG1918 3-methyladenine DNA gl 99.7 4.3E-18 9.3E-23 128.6 7.3 107 7-118 83-210 (254)
19 PF00730 HhH-GPD: HhH-GPD supe 99.7 2.7E-16 5.8E-21 106.0 8.2 85 9-119 5-91 (108)
20 KOG2457 A/G-specific adenine D 99.6 4.3E-15 9.2E-20 120.3 10.1 107 3-112 124-243 (555)
21 KOG2875 8-oxoguanine DNA glyco 99.6 3.8E-15 8.1E-20 116.0 6.5 87 27-118 159-264 (323)
22 PF00633 HHH: Helix-hairpin-he 98.7 1.9E-08 4.1E-13 54.0 2.8 24 69-92 7-30 (30)
23 COG1059 Thermostable 8-oxoguan 97.4 0.00078 1.7E-08 50.5 7.4 58 33-90 66-138 (210)
24 PF14716 HHH_8: Helix-hairpin- 97.0 0.0063 1.4E-07 37.9 7.4 52 41-92 9-66 (68)
25 smart00278 HhH1 Helix-hairpin- 97.0 0.00059 1.3E-08 35.0 1.9 21 74-94 2-22 (26)
26 PRK13901 ruvA Holliday junctio 96.9 0.0029 6.2E-08 47.6 6.0 53 44-96 72-130 (196)
27 PF12826 HHH_2: Helix-hairpin- 96.9 0.0012 2.6E-08 40.8 3.4 24 71-94 33-56 (64)
28 PRK14606 ruvA Holliday junctio 96.5 0.0032 7E-08 46.9 3.7 50 47-96 76-131 (188)
29 PRK14601 ruvA Holliday junctio 96.5 0.0033 7.1E-08 46.8 3.7 51 46-96 75-131 (183)
30 PRK14602 ruvA Holliday junctio 96.4 0.0041 8.8E-08 46.8 3.8 50 47-96 77-132 (203)
31 PRK14603 ruvA Holliday junctio 96.3 0.0047 1E-07 46.4 3.8 43 50-92 78-126 (197)
32 COG0632 RuvA Holliday junction 96.3 0.0046 1E-07 46.7 3.7 54 44-97 73-132 (201)
33 PRK14604 ruvA Holliday junctio 96.3 0.005 1.1E-07 46.1 3.7 50 47-96 76-131 (195)
34 PRK14605 ruvA Holliday junctio 96.2 0.014 3.1E-07 43.6 5.7 46 45-90 74-125 (194)
35 TIGR00084 ruvA Holliday juncti 96.0 0.024 5.2E-07 42.3 5.9 51 44-94 72-128 (191)
36 PRK14600 ruvA Holliday junctio 95.9 0.0081 1.8E-07 44.7 3.2 49 47-96 76-130 (186)
37 PF14520 HHH_5: Helix-hairpin- 95.8 0.068 1.5E-06 32.2 6.6 21 71-91 36-56 (60)
38 PF02371 Transposase_20: Trans 95.8 0.0081 1.8E-07 39.0 2.4 40 73-114 2-41 (87)
39 PRK02515 psbU photosystem II c 95.8 0.023 5E-07 40.2 4.8 65 18-92 39-106 (132)
40 PRK00116 ruvA Holliday junctio 95.6 0.032 7E-07 41.5 5.3 50 47-96 76-131 (192)
41 TIGR00426 competence protein C 95.3 0.027 5.8E-07 34.9 3.5 58 33-92 8-66 (69)
42 PF12836 HHH_3: Helix-hairpin- 95.1 0.032 6.8E-07 34.4 3.4 51 35-89 8-60 (65)
43 PF14520 HHH_5: Helix-hairpin- 94.6 0.096 2.1E-06 31.5 4.6 42 21-65 17-59 (60)
44 TIGR00615 recR recombination p 94.3 0.054 1.2E-06 40.7 3.4 29 69-97 7-35 (195)
45 PRK00076 recR recombination pr 94.2 0.055 1.2E-06 40.7 3.4 29 69-97 7-35 (196)
46 PRK14973 DNA topoisomerase I; 94.2 0.25 5.5E-06 44.9 8.0 88 27-117 821-933 (936)
47 PF14490 HHH_4: Helix-hairpin- 94.2 0.35 7.5E-06 31.8 6.8 61 40-105 8-73 (94)
48 PRK13844 recombination protein 94.1 0.059 1.3E-06 40.7 3.4 29 69-97 11-39 (200)
49 TIGR01259 comE comEA protein. 94.1 0.073 1.6E-06 36.8 3.6 58 32-92 59-117 (120)
50 smart00483 POLXc DNA polymeras 94.1 0.17 3.7E-06 40.7 6.2 52 42-93 12-68 (334)
51 COG0353 RecR Recombinational D 93.9 0.06 1.3E-06 40.6 3.1 29 69-97 8-36 (198)
52 PF11731 Cdd1: Pathogenicity l 93.8 0.065 1.4E-06 35.8 2.7 31 70-100 9-39 (93)
53 cd00141 NT_POLXc Nucleotidyltr 93.7 0.2 4.4E-06 39.7 5.9 44 51-96 52-106 (307)
54 KOG2841 Structure-specific end 93.5 0.13 2.8E-06 39.9 4.3 42 22-66 208-249 (254)
55 PF12836 HHH_3: Helix-hairpin- 93.4 0.086 1.9E-06 32.4 2.7 23 71-93 12-34 (65)
56 PRK07956 ligA NAD-dependent DN 93.4 0.53 1.1E-05 41.3 8.5 69 22-93 458-563 (665)
57 PF11798 IMS_HHH: IMS family H 93.4 0.06 1.3E-06 28.9 1.7 16 74-89 12-27 (32)
58 TIGR00575 dnlj DNA ligase, NAD 93.4 0.53 1.1E-05 41.3 8.3 69 22-93 445-550 (652)
59 PRK07945 hypothetical protein; 93.1 0.31 6.7E-06 39.2 6.1 54 41-94 8-70 (335)
60 COG1555 ComEA DNA uptake prote 92.6 0.21 4.6E-06 35.8 4.2 53 35-90 91-144 (149)
61 PRK08097 ligB NAD-dependent DN 92.6 0.78 1.7E-05 39.6 8.2 71 21-94 437-541 (562)
62 PF05559 DUF763: Protein of un 92.6 0.46 9.9E-06 38.3 6.3 40 58-97 251-296 (319)
63 COG1555 ComEA DNA uptake prote 92.6 0.11 2.5E-06 37.3 2.6 24 71-94 95-118 (149)
64 TIGR01259 comE comEA protein. 92.4 0.14 3E-06 35.4 2.8 23 71-93 66-88 (120)
65 PF10391 DNA_pol_lambd_f: Fing 92.0 0.14 3.1E-06 30.5 2.2 24 72-95 1-24 (52)
66 PRK14350 ligA NAD-dependent DN 92.0 0.35 7.6E-06 42.5 5.4 24 71-94 539-562 (669)
67 COG0272 Lig NAD-dependent DNA 91.5 0.45 9.6E-06 41.8 5.4 24 71-94 541-564 (667)
68 PRK13482 DNA integrity scannin 91.1 0.75 1.6E-05 37.6 6.1 48 20-70 298-345 (352)
69 TIGR00084 ruvA Holliday juncti 90.9 0.2 4.2E-06 37.4 2.5 22 70-91 69-90 (191)
70 PRK00116 ruvA Holliday junctio 90.8 0.2 4.4E-06 37.2 2.4 31 50-91 61-91 (192)
71 PRK08609 hypothetical protein; 90.7 0.74 1.6E-05 39.6 6.1 20 71-90 86-105 (570)
72 PF03352 Adenine_glyco: Methyl 90.4 2.3 5.1E-05 31.5 7.8 52 18-69 44-99 (179)
73 PF14229 DUF4332: Domain of un 90.2 1 2.3E-05 31.1 5.5 58 29-95 16-75 (122)
74 PRK14605 ruvA Holliday junctio 90.0 0.28 6E-06 36.7 2.6 22 70-91 70-91 (194)
75 smart00279 HhH2 Helix-hairpin- 90.0 0.25 5.4E-06 27.2 1.8 17 74-90 17-33 (36)
76 PRK00024 hypothetical protein; 90.0 0.46 9.9E-06 36.2 3.8 51 37-90 23-83 (224)
77 PRK12766 50S ribosomal protein 89.6 0.77 1.7E-05 35.5 4.8 40 23-65 17-57 (232)
78 PF12826 HHH_2: Helix-hairpin- 89.4 1.5 3.2E-05 26.8 5.2 43 20-65 14-56 (64)
79 smart00483 POLXc DNA polymeras 89.0 0.55 1.2E-05 37.8 3.8 21 71-91 87-107 (334)
80 cd00141 NT_POLXc Nucleotidyltr 88.6 0.64 1.4E-05 36.9 3.9 53 42-94 9-66 (307)
81 PRK02515 psbU photosystem II c 88.5 0.39 8.5E-06 34.0 2.3 21 71-91 59-79 (132)
82 PRK00024 hypothetical protein; 88.3 0.76 1.6E-05 35.0 4.0 49 15-66 40-88 (224)
83 cd00080 HhH2_motif Helix-hairp 87.4 0.35 7.6E-06 30.6 1.4 25 71-96 20-44 (75)
84 PRK14351 ligA NAD-dependent DN 87.3 0.82 1.8E-05 40.4 4.1 69 21-92 474-579 (689)
85 KOG2534 DNA polymerase IV (fam 87.2 1.1 2.4E-05 36.3 4.4 41 54-94 32-77 (353)
86 COG1796 POL4 DNA polymerase IV 86.9 2.3 5E-05 34.4 6.1 53 41-93 13-73 (326)
87 PF03118 RNA_pol_A_CTD: Bacter 86.0 1.3 2.8E-05 27.4 3.4 43 47-90 14-61 (66)
88 TIGR00426 competence protein C 85.7 0.92 2E-05 27.9 2.7 22 71-92 14-36 (69)
89 PRK00254 ski2-like helicase; P 84.6 3.1 6.8E-05 36.5 6.4 43 50-92 651-697 (720)
90 PRK13901 ruvA Holliday junctio 83.8 0.88 1.9E-05 34.2 2.3 22 70-91 69-90 (196)
91 TIGR00608 radc DNA repair prot 83.8 2 4.3E-05 32.7 4.3 47 17-66 33-82 (218)
92 PRK14600 ruvA Holliday junctio 83.7 0.88 1.9E-05 33.9 2.2 22 70-91 70-91 (186)
93 PRK14601 ruvA Holliday junctio 83.5 0.92 2E-05 33.7 2.2 22 70-91 70-91 (183)
94 PRK14606 ruvA Holliday junctio 82.7 1.1 2.4E-05 33.4 2.4 21 71-91 71-91 (188)
95 PRK14603 ruvA Holliday junctio 82.5 1.1 2.4E-05 33.6 2.4 21 71-91 70-90 (197)
96 PRK14602 ruvA Holliday junctio 82.5 1.2 2.6E-05 33.5 2.5 21 71-91 72-92 (203)
97 PRK09482 flap endonuclease-lik 82.4 1.5 3.3E-05 34.2 3.2 30 66-96 175-204 (256)
98 PF09597 IGR: IGR protein moti 81.9 4.5 9.7E-05 24.6 4.5 43 22-68 12-55 (57)
99 PRK12766 50S ribosomal protein 81.8 3.4 7.5E-05 31.9 4.8 47 50-97 9-59 (232)
100 PRK14604 ruvA Holliday junctio 81.5 1.3 2.7E-05 33.2 2.3 21 71-91 71-91 (195)
101 PRK14351 ligA NAD-dependent DN 81.5 7.2 0.00016 34.6 7.3 14 77-90 532-545 (689)
102 TIGR01954 nusA_Cterm_rpt trans 81.4 4.3 9.4E-05 22.8 4.2 37 27-66 12-48 (50)
103 TIGR01448 recD_rel helicase, p 80.7 12 0.00025 33.3 8.4 60 41-105 144-208 (720)
104 PF00416 Ribosomal_S13: Riboso 79.6 2 4.3E-05 29.0 2.6 23 72-94 14-36 (107)
105 PRK14973 DNA topoisomerase I; 79.4 8.7 0.00019 35.3 7.3 71 20-94 755-856 (936)
106 PRK14667 uvrC excinuclease ABC 78.8 3.7 8E-05 35.6 4.6 21 70-91 543-563 (567)
107 PRK14672 uvrC excinuclease ABC 78.5 1.9 4.1E-05 38.2 2.8 38 25-65 624-661 (691)
108 PF01367 5_3_exonuc: 5'-3' exo 77.8 0.41 8.8E-06 32.3 -1.2 20 73-92 18-37 (101)
109 TIGR00608 radc DNA repair prot 77.5 9.7 0.00021 29.0 6.1 52 37-90 13-77 (218)
110 COG0632 RuvA Holliday junction 76.8 1.9 4.1E-05 32.6 2.1 22 71-92 71-92 (201)
111 PRK01172 ski2-like helicase; P 76.1 9.6 0.00021 33.1 6.4 39 28-69 632-670 (674)
112 PRK14666 uvrC excinuclease ABC 76.0 7.4 0.00016 34.6 5.7 22 70-91 666-687 (694)
113 COG1948 MUS81 ERCC4-type nucle 75.6 7.9 0.00017 30.3 5.2 21 71-91 212-232 (254)
114 TIGR02236 recomb_radA DNA repa 74.1 11 0.00024 29.4 5.9 42 21-65 11-53 (310)
115 PRK14976 5'-3' exonuclease; Pr 73.8 1.7 3.8E-05 34.1 1.2 26 70-96 188-213 (281)
116 PRK10353 3-methyl-adenine DNA 73.1 20 0.00043 26.8 6.7 47 23-69 54-104 (187)
117 COG2003 RadC DNA repair protei 72.9 5.3 0.00012 30.7 3.6 47 38-87 24-80 (224)
118 cd00008 53EXOc 5'-3' exonuclea 72.0 2.7 5.8E-05 32.1 1.9 31 70-101 180-210 (240)
119 PRK07758 hypothetical protein; 71.6 4.3 9.3E-05 27.2 2.5 23 68-90 62-84 (95)
120 smart00475 53EXOc 5'-3' exonuc 71.5 2.7 5.9E-05 32.7 1.8 22 70-91 183-204 (259)
121 COG4277 Predicted DNA-binding 71.2 3.4 7.3E-05 33.7 2.3 22 71-92 328-349 (404)
122 TIGR00596 rad1 DNA repair prot 69.9 9.5 0.00021 34.5 5.0 42 20-65 768-809 (814)
123 COG2003 RadC DNA repair protei 69.1 9.9 0.00021 29.3 4.4 50 15-67 40-89 (224)
124 PRK14669 uvrC excinuclease ABC 69.0 9.3 0.0002 33.5 4.7 36 23-63 566-601 (624)
125 TIGR00624 tag DNA-3-methyladen 68.9 30 0.00065 25.7 6.8 48 22-69 52-103 (179)
126 PRK04301 radA DNA repair and r 68.8 19 0.0004 28.4 6.1 43 21-66 18-61 (317)
127 PRK00558 uvrC excinuclease ABC 68.8 6.8 0.00015 34.1 3.8 23 70-92 572-594 (598)
128 TIGR03674 fen_arch flap struct 68.5 6.7 0.00015 31.6 3.5 41 45-91 214-254 (338)
129 PRK08609 hypothetical protein; 68.3 25 0.00054 30.4 7.1 62 29-90 73-140 (570)
130 PRK14670 uvrC excinuclease ABC 68.2 12 0.00026 32.5 5.2 26 67-92 540-565 (574)
131 PF00570 HRDC: HRDC domain Blo 67.3 11 0.00023 22.5 3.5 30 58-88 30-59 (68)
132 PF14635 HHH_7: Helix-hairpin- 66.7 4.5 9.8E-05 27.5 1.9 39 49-87 55-95 (104)
133 CHL00137 rps13 ribosomal prote 66.3 3.8 8.3E-05 28.5 1.5 21 73-93 17-37 (122)
134 PTZ00217 flap endonuclease-1; 66.3 6.6 0.00014 32.4 3.1 41 45-91 213-253 (393)
135 COG1796 POL4 DNA polymerase IV 65.6 11 0.00023 30.6 4.1 68 19-94 78-149 (326)
136 PRK14668 uvrC excinuclease ABC 64.5 16 0.00034 31.8 5.2 21 70-90 554-574 (577)
137 PRK14670 uvrC excinuclease ABC 64.2 11 0.00024 32.7 4.2 17 74-90 515-531 (574)
138 COG1491 Predicted RNA-binding 63.9 5.5 0.00012 30.0 2.0 26 71-96 128-153 (202)
139 COG2818 Tag 3-methyladenine DN 63.4 17 0.00036 27.3 4.5 49 20-69 55-105 (188)
140 cd00128 XPG Xeroderma pigmento 63.4 8 0.00017 30.5 3.0 39 47-91 203-241 (316)
141 PRK13482 DNA integrity scannin 63.4 11 0.00023 31.0 3.8 20 71-90 317-336 (352)
142 PRK14350 ligA NAD-dependent DN 63.3 52 0.0011 29.2 8.2 68 20-90 447-519 (669)
143 COG0272 Lig NAD-dependent DNA 63.0 39 0.00085 30.0 7.3 74 19-96 455-533 (667)
144 PRK05179 rpsM 30S ribosomal pr 62.7 4.8 0.0001 28.0 1.5 21 73-93 17-37 (122)
145 PTZ00035 Rad51 protein; Provis 62.7 17 0.00036 29.3 4.8 45 22-69 36-81 (337)
146 TIGR02238 recomb_DMC1 meiotic 62.7 16 0.00036 29.0 4.7 45 22-69 14-59 (313)
147 PLN03187 meiotic recombination 62.5 28 0.00062 28.2 6.1 45 22-69 44-89 (344)
148 COG1415 Uncharacterized conser 62.4 7.4 0.00016 31.9 2.7 24 70-93 275-298 (373)
149 PF13543 KSR1-SAM: SAM like do 62.4 39 0.00084 23.8 6.0 38 25-62 86-123 (129)
150 PRK13766 Hef nuclease; Provisi 62.3 22 0.00048 31.3 5.9 44 50-93 721-767 (773)
151 PF04904 NCD1: NAB conserved r 62.0 41 0.00089 21.8 7.3 53 15-68 18-71 (82)
152 PF04919 DUF655: Protein of un 61.0 6.8 0.00015 29.2 2.1 21 72-92 115-135 (181)
153 PRK14668 uvrC excinuclease ABC 61.0 16 0.00035 31.7 4.7 38 21-62 537-575 (577)
154 PRK13766 Hef nuclease; Provisi 60.7 20 0.00044 31.5 5.3 17 75-91 717-733 (773)
155 PRK03980 flap endonuclease-1; 60.7 8.8 0.00019 30.4 2.8 42 44-91 166-207 (292)
156 PRK14666 uvrC excinuclease ABC 60.6 57 0.0012 29.2 7.9 43 21-66 649-691 (694)
157 TIGR03629 arch_S13P archaeal r 59.7 5.6 0.00012 28.5 1.4 20 73-92 21-40 (144)
158 TIGR03631 bact_S13 30S ribosom 59.3 5.6 0.00012 27.3 1.3 21 73-93 15-35 (113)
159 PRK14469 ribosomal RNA large s 59.1 13 0.00029 29.8 3.6 45 35-79 4-48 (343)
160 PTZ00134 40S ribosomal protein 58.9 6.2 0.00013 28.6 1.5 23 71-93 28-50 (154)
161 COG0703 AroK Shikimate kinase 58.6 24 0.00052 26.0 4.6 43 75-119 7-53 (172)
162 COG3547 Transposase and inacti 58.1 81 0.0017 24.0 8.7 16 75-90 190-205 (303)
163 PRK00254 ski2-like helicase; P 57.3 26 0.00056 30.9 5.4 42 21-65 657-699 (720)
164 PRK04053 rps13p 30S ribosomal 56.9 6.8 0.00015 28.2 1.5 22 71-92 23-44 (149)
165 COG0099 RpsM Ribosomal protein 55.7 8.2 0.00018 27.0 1.6 20 74-93 18-37 (121)
166 PRK00558 uvrC excinuclease ABC 55.4 31 0.00067 30.1 5.5 39 21-63 555-594 (598)
167 PRK07956 ligA NAD-dependent DN 53.9 52 0.0011 29.1 6.7 56 23-82 525-581 (665)
168 PF04558 tRNA_synt_1c_R1: Glut 52.8 42 0.00092 24.4 5.1 56 38-94 1-59 (164)
169 PRK14669 uvrC excinuclease ABC 52.5 11 0.00023 33.2 2.2 23 72-95 551-573 (624)
170 PF13297 Telomere_Sde2_2: Telo 52.2 20 0.00043 22.1 2.7 26 27-52 4-29 (60)
171 PF14056 DUF4250: Domain of un 51.8 41 0.00089 20.2 4.1 31 23-53 14-47 (55)
172 PRK14455 ribosomal RNA large s 51.7 20 0.00044 29.0 3.6 46 34-79 12-57 (356)
173 PRK14463 ribosomal RNA large s 51.7 22 0.00047 28.9 3.7 46 34-79 6-51 (349)
174 TIGR00575 dnlj DNA ligase, NAD 51.6 63 0.0014 28.5 6.8 57 22-82 511-568 (652)
175 PRK14671 uvrC excinuclease ABC 50.6 11 0.00025 32.9 2.1 24 72-96 568-591 (621)
176 TIGR00593 pola DNA polymerase 50.4 15 0.00032 33.6 2.8 22 70-91 182-203 (887)
177 PRK14467 ribosomal RNA large s 50.3 23 0.0005 28.8 3.7 45 35-79 4-48 (348)
178 COG0322 UvrC Nuclease subunit 50.1 27 0.00058 30.5 4.2 23 67-90 556-578 (581)
179 COG1623 Predicted nucleic-acid 49.9 29 0.00064 28.1 4.1 19 71-89 323-341 (349)
180 TIGR00194 uvrC excinuclease AB 49.6 13 0.00028 32.3 2.2 22 73-95 541-562 (574)
181 PRK14454 ribosomal RNA large s 49.5 24 0.00052 28.5 3.7 42 35-79 4-48 (342)
182 PRK02362 ski2-like helicase; P 49.2 32 0.00069 30.4 4.7 39 57-95 633-674 (737)
183 COG0258 Exo 5'-3' exonuclease 49.2 11 0.00025 29.6 1.7 24 71-95 196-219 (310)
184 PF12990 DUF3874: Domain of un 49.0 21 0.00045 22.7 2.6 37 18-56 28-64 (73)
185 PF14579 HHH_6: Helix-hairpin- 48.6 17 0.00036 23.4 2.2 20 74-93 28-47 (90)
186 PHA00439 exonuclease 48.1 12 0.00025 29.8 1.6 22 70-92 185-206 (286)
187 PF12482 DUF3701: Phage integr 47.7 57 0.0012 21.8 4.7 50 43-97 25-74 (96)
188 PRK14456 ribosomal RNA large s 47.7 26 0.00057 28.6 3.7 43 34-79 19-64 (368)
189 COG3743 Uncharacterized conser 46.6 10 0.00022 27.0 0.9 18 73-90 67-84 (133)
190 TIGR00596 rad1 DNA repair prot 45.7 17 0.00036 33.0 2.4 22 71-92 755-776 (814)
191 PRK14465 ribosomal RNA large s 45.6 28 0.00061 28.2 3.5 45 35-79 7-51 (342)
192 PRK11194 ribosomal RNA large s 44.9 32 0.0007 28.2 3.8 43 34-79 7-52 (372)
193 PF13174 TPR_6: Tetratricopept 44.8 30 0.00065 16.8 2.5 16 16-31 17-32 (33)
194 PRK14459 ribosomal RNA large s 44.8 28 0.0006 28.7 3.4 43 34-79 23-68 (373)
195 PRK14460 ribosomal RNA large s 44.5 32 0.00069 27.9 3.7 45 35-79 4-49 (354)
196 TIGR00048 radical SAM enzyme, 44.3 30 0.00064 28.1 3.5 43 34-79 8-53 (355)
197 smart00611 SEC63 Domain of unk 44.1 42 0.0009 26.0 4.2 41 49-90 125-168 (312)
198 KOG3337 Protein similar to pre 43.0 19 0.00041 27.0 2.0 31 19-49 16-46 (201)
199 PRK14672 uvrC excinuclease ABC 42.9 36 0.00078 30.4 4.0 29 68-96 635-663 (691)
200 PRK05755 DNA polymerase I; Pro 42.7 15 0.00034 33.2 1.7 22 70-91 184-205 (880)
201 PRK14457 ribosomal RNA large s 42.1 34 0.00074 27.7 3.5 46 34-79 3-48 (345)
202 PRK14466 ribosomal RNA large s 41.9 35 0.00075 27.8 3.5 45 35-79 7-51 (345)
203 PRK14461 ribosomal RNA large s 41.2 36 0.00079 28.1 3.5 43 34-79 9-54 (371)
204 PRK08311 putative RNA polymera 41.0 1.6E+02 0.0035 22.4 7.5 83 21-115 136-233 (237)
205 PF08625 Utp13: Utp13 specific 40.7 54 0.0012 23.2 4.0 52 33-85 53-109 (141)
206 PRK14671 uvrC excinuclease ABC 40.6 70 0.0015 28.1 5.4 19 71-91 599-617 (621)
207 PRK00419 DNA primase small sub 40.2 38 0.00082 28.0 3.5 41 51-91 199-239 (376)
208 KOG2534 DNA polymerase IV (fam 39.9 39 0.00084 27.6 3.4 26 71-96 95-120 (353)
209 TIGR02239 recomb_RAD51 DNA rep 39.7 61 0.0013 25.8 4.6 44 23-69 15-59 (316)
210 TIGR01448 recD_rel helicase, p 39.0 70 0.0015 28.5 5.2 55 36-91 73-135 (720)
211 COG1701 Uncharacterized protei 38.8 64 0.0014 25.0 4.3 54 11-67 193-246 (256)
212 PRK14667 uvrC excinuclease ABC 37.7 55 0.0012 28.5 4.2 34 24-61 529-562 (567)
213 PLN03186 DNA repair protein RA 37.7 67 0.0014 26.0 4.5 43 24-69 43-86 (342)
214 PRK14470 ribosomal RNA large s 37.4 40 0.00086 27.2 3.2 43 36-79 2-44 (336)
215 PF14964 DUF4507: Domain of un 36.8 1E+02 0.0022 25.4 5.5 71 47-117 129-217 (362)
216 COG5346 Predicted membrane pro 36.5 1.5E+02 0.0033 20.9 5.6 77 9-96 17-101 (136)
217 PRK14453 chloramphenicol/florf 36.2 57 0.0012 26.5 3.9 43 37-79 4-46 (347)
218 PF06568 DUF1127: Domain of un 36.2 50 0.0011 18.1 2.6 29 22-54 7-35 (40)
219 cd01703 PolY_Pol_iota DNA Poly 36.1 24 0.00051 28.9 1.7 22 74-95 173-194 (379)
220 PF06744 DUF1215: Protein of u 35.6 34 0.00074 23.3 2.2 36 18-53 43-80 (125)
221 KOG1201 Hydroxysteroid 17-beta 35.5 1E+02 0.0022 24.8 5.2 81 13-95 96-197 (300)
222 PF03081 Exo70: Exo70 exocyst 35.4 39 0.00086 26.8 2.9 35 16-50 333-371 (371)
223 PF04994 TfoX_C: TfoX C-termin 35.3 30 0.00065 22.1 1.8 22 73-94 3-24 (81)
224 PRK13761 hypothetical protein; 34.7 86 0.0019 24.5 4.4 41 10-53 189-229 (248)
225 COG1031 Uncharacterized Fe-S o 34.3 28 0.00061 29.9 1.9 21 71-91 514-534 (560)
226 COG1948 MUS81 ERCC4-type nucle 34.1 46 0.001 26.1 3.0 36 22-60 195-230 (254)
227 COG1379 PHP family phosphoeste 33.9 53 0.0011 27.1 3.3 32 15-46 320-352 (403)
228 KOG3835 Transcriptional corepr 33.6 2E+02 0.0044 24.2 6.7 55 14-69 19-74 (495)
229 PF08823 PG_binding_2: Putativ 33.3 40 0.00088 21.3 2.1 26 29-54 4-32 (74)
230 PF02889 Sec63: Sec63 Brl doma 33.2 66 0.0014 24.8 3.8 36 56-91 128-166 (314)
231 PF02961 BAF: Barrier to autoi 33.0 29 0.00062 23.0 1.4 25 73-97 19-43 (89)
232 PLN03103 GDP-L-galactose-hexos 31.5 63 0.0014 27.0 3.5 52 15-66 340-393 (403)
233 PF07900 DUF1670: Protein of u 31.4 1.5E+02 0.0033 22.8 5.3 53 38-90 70-126 (220)
234 PF07499 RuvA_C: RuvA, C-termi 31.3 93 0.002 17.5 3.3 23 41-63 4-26 (47)
235 TIGR02236 recomb_radA DNA repa 30.8 1.2E+02 0.0025 23.6 4.8 43 52-94 7-53 (310)
236 TIGR00600 rad2 DNA excision re 30.5 47 0.001 31.1 2.8 41 45-91 844-884 (1034)
237 PRK00625 shikimate kinase; Pro 30.2 81 0.0018 22.7 3.6 33 75-109 5-37 (173)
238 TIGR02895 spore_sigI RNA polym 29.7 2.4E+02 0.0051 21.3 6.2 31 57-87 151-194 (218)
239 KOG2841 Structure-specific end 29.1 69 0.0015 25.1 3.1 41 52-92 203-246 (254)
240 PF05082 Rop-like: Rop-like; 29.0 56 0.0012 20.4 2.2 47 41-90 5-51 (66)
241 PF01706 FliG_C: FliG C-termin 28.1 1.1E+02 0.0025 20.1 3.8 48 20-68 10-57 (110)
242 PHA02698 hypothetical protein; 27.8 1.8E+02 0.0038 18.9 4.5 19 30-48 33-51 (89)
243 PRK03352 DNA polymerase IV; Va 27.8 40 0.00087 26.7 1.8 23 74-96 178-200 (346)
244 COG0133 TrpB Tryptophan syntha 27.3 91 0.002 25.8 3.6 46 72-120 300-345 (396)
245 cd01701 PolY_Rev1 DNA polymera 27.1 41 0.00089 27.5 1.7 23 74-96 223-245 (404)
246 PTZ00205 DNA polymerase kappa; 27.1 36 0.00077 29.7 1.4 21 74-94 310-330 (571)
247 PLN00138 large subunit ribosom 26.9 1.4E+02 0.003 20.4 4.1 38 38-76 18-55 (113)
248 smart00341 HRDC Helicase and R 26.4 90 0.002 18.9 2.9 28 58-86 33-60 (81)
249 PRK04301 radA DNA repair and r 26.2 1.4E+02 0.003 23.4 4.5 32 64-95 30-61 (317)
250 COG3392 Adenine-specific DNA m 25.7 94 0.002 25.0 3.4 49 5-53 245-299 (330)
251 COG2183 Tex Transcriptional ac 25.6 55 0.0012 29.7 2.3 43 50-92 515-558 (780)
252 PF04924 Pox_A6: Poxvirus A6 p 25.5 1.9E+02 0.0041 23.9 5.1 49 2-50 263-314 (371)
253 PF05402 PqqD: Coenzyme PQQ sy 25.3 1.1E+02 0.0024 17.9 3.1 34 18-51 32-65 (68)
254 KOG0898 40S ribosomal protein 24.9 1.4E+02 0.003 21.5 3.8 47 19-65 16-69 (152)
255 COG4168 SapB ABC-type antimicr 24.8 44 0.00095 26.6 1.4 23 73-95 260-282 (321)
256 PF10975 DUF2802: Protein of u 24.4 98 0.0021 19.2 2.7 32 32-64 37-68 (70)
257 PF06992 Phage_lambda_P: Repli 23.9 2.3E+02 0.0051 21.9 5.2 39 17-66 39-77 (233)
258 KOG2518 5'-3' exonuclease [Rep 23.9 49 0.0011 28.7 1.6 20 72-91 224-243 (556)
259 PRK03858 DNA polymerase IV; Va 23.8 58 0.0013 26.3 2.0 23 74-96 174-196 (396)
260 PRK01172 ski2-like helicase; P 23.5 1.6E+02 0.0034 25.7 4.7 41 57-97 593-636 (674)
261 cd00424 PolY Y-family of DNA p 23.2 59 0.0013 25.8 1.9 66 29-96 112-196 (343)
262 cd04755 Commd7 COMM_Domain con 23.1 1.3E+02 0.0028 22.3 3.6 27 36-62 67-93 (180)
263 TIGR00375 conserved hypothetic 22.9 2E+02 0.0044 23.7 5.0 32 15-46 313-345 (374)
264 KOG2653 6-phosphogluconate deh 22.8 4.7E+02 0.01 22.2 7.1 77 34-115 210-297 (487)
265 PF10759 DUF2587: Protein of u 22.7 3.1E+02 0.0068 20.0 7.1 47 68-116 63-113 (169)
266 PRK14552 C/D box methylation g 22.2 1.5E+02 0.0033 24.8 4.2 20 74-95 265-284 (414)
267 cd04752 Commd4 COMM_Domain con 22.2 2.8E+02 0.006 20.0 5.2 25 38-62 60-84 (174)
268 PRK04460 nickel responsive reg 22.0 1.7E+02 0.0036 20.6 3.8 28 41-69 15-42 (137)
269 PF05166 YcgL: YcgL domain; I 21.9 54 0.0012 20.9 1.2 21 33-53 48-68 (74)
270 KOG2520 5'-3' exonuclease [Rep 21.9 1.6E+02 0.0036 26.9 4.5 79 19-117 518-596 (815)
271 PF01202 SKI: Shikimate kinase 21.8 85 0.0018 21.8 2.3 30 79-110 1-30 (158)
272 KOG2344 Exocyst component prot 21.3 1.2E+02 0.0027 26.6 3.6 37 14-50 569-611 (623)
273 PF08328 ASL_C: Adenylosuccina 21.2 1.8E+02 0.004 20.1 3.7 24 38-61 84-107 (115)
274 cd01700 PolY_Pol_V_umuC umuC s 21.1 63 0.0014 25.6 1.7 22 74-95 177-198 (344)
275 COG1324 CutA Uncharacterized p 21.0 38 0.00083 23.0 0.4 24 94-117 78-102 (104)
276 PF09957 DUF2191: Uncharacteri 21.0 1.8E+02 0.0039 16.6 4.6 40 37-77 6-46 (47)
277 cd01067 globin_like superfamil 21.0 1.2E+02 0.0026 19.9 2.8 20 18-37 3-22 (117)
278 PF10343 DUF2419: Protein of u 20.8 4.4E+02 0.0096 21.0 6.8 47 23-69 57-110 (287)
279 PRK02406 DNA polymerase IV; Va 20.7 62 0.0014 25.6 1.6 22 74-95 169-190 (343)
280 PF02006 DUF137: Protein of un 20.7 1.2E+02 0.0025 22.6 2.9 38 10-50 128-165 (178)
281 PRK01216 DNA polymerase IV; Va 20.6 65 0.0014 26.0 1.7 23 74-96 179-201 (351)
282 TIGR01766 tspaseT_teng_C trans 20.4 2.2E+02 0.0047 17.3 4.5 56 54-119 3-70 (82)
283 PRK01810 DNA polymerase IV; Va 20.4 70 0.0015 26.0 1.8 22 74-95 180-201 (407)
284 PF12339 DNAJ_related: DNA-J r 20.3 1E+02 0.0022 21.7 2.4 29 21-49 98-126 (132)
285 PRK05686 fliG flagellar motor 20.2 4.5E+02 0.0098 21.0 8.2 73 17-89 97-182 (339)
286 PRK13948 shikimate kinase; Pro 20.2 1.5E+02 0.0033 21.5 3.4 34 75-110 15-48 (182)
287 PF03131 bZIP_Maf: bZIP Maf tr 20.1 2E+02 0.0043 18.5 3.7 35 31-67 2-36 (92)
288 PF13735 tRNA_NucTran2_2: tRNA 20.1 1.6E+02 0.0035 20.0 3.4 34 36-69 17-50 (149)
No 1
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=99.97 E-value=4.9e-30 Score=193.11 Aligned_cols=103 Identities=22% Similarity=0.345 Sum_probs=95.3
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH-------hhHHHh
Q 033363 3 QIYSIRLKEIAILLKAGRVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG-------ESWTHV 75 (121)
Q Consensus 3 ~~~si~~~~~~~~~~v~~v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-------~~~~~L 75 (121)
.+.++.+|+++||+.|++++.+||++||||++++++++++|++.|+++|||++||++|+++|+++++ +++++|
T Consensus 32 lLva~iLSaqttD~~vn~at~~Lf~~~~t~e~l~~a~~~~l~~~I~~iGlyr~KAk~I~~~~~~l~e~~~g~vP~~~~eL 111 (211)
T COG0177 32 LLVAVILSAQTTDEVVNKATPALFKRYPTPEDLLNADEEELEELIKSIGLYRNKAKNIKELARILLEKFGGEVPDTREEL 111 (211)
T ss_pred HHHHHHHhccCchHHHHHHHHHHHHHcCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHcCCCCCchHHHH
Confidence 3567788888999999999999999999999999999999999999999999999999999999999 489999
Q ss_pred ccCCCCcHHHHHHHHHHhcCCCCccCcchHHH
Q 033363 76 TQLHGVGKYAADAFAIFCTGKWDRVRPTDHML 107 (121)
Q Consensus 76 ~~lpGIG~~tA~~vl~f~~~~~~~v~p~D~~l 107 (121)
.+|||||+|||++||.++||.| .+|+|+++
T Consensus 112 ~~LPGVGrKTAnvVL~~a~g~p--~i~VDTHV 141 (211)
T COG0177 112 LSLPGVGRKTANVVLSFAFGIP--AIAVDTHV 141 (211)
T ss_pred HhCCCcchHHHHHHHHhhcCCC--cccccchH
Confidence 9999999999999999999998 56666544
No 2
>PRK10702 endonuclease III; Provisional
Probab=99.96 E-value=1.2e-28 Score=185.80 Aligned_cols=110 Identities=17% Similarity=0.207 Sum_probs=100.4
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH-------hhHHHh
Q 033363 3 QIYSIRLKEIAILLKAGRVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG-------ESWTHV 75 (121)
Q Consensus 3 ~~~si~~~~~~~~~~v~~v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-------~~~~~L 75 (121)
++.|..+++.+++.+|++++.+|+.+||||++|+++++++|+++|+++||+++||++|+++|+.+.+ +++++|
T Consensus 32 ~lvs~iLsq~t~~~~v~~~~~~L~~~~pt~e~l~~a~~~~l~~~i~~~G~y~~kA~~l~~~a~~i~~~~~~~~p~~~~~L 111 (211)
T PRK10702 32 LLIAVLLSAQATDVSVNKATAKLYPVANTPAAMLELGVEGVKTYIKTIGLYNSKAENVIKTCRILLEQHNGEVPEDRAAL 111 (211)
T ss_pred HHHHHHHHhhcCHHHHHHHHHHHHHHcCCHHHHHCCCHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHcCCCCCchHHHH
Confidence 4556666666778889999999999999999999999999999999999999999999999999987 489999
Q ss_pred ccCCCCcHHHHHHHHHHhcCCCCccCcchHHHHHHHHHH
Q 033363 76 TQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFL 114 (121)
Q Consensus 76 ~~lpGIG~~tA~~vl~f~~~~~~~v~p~D~~l~~~~~wl 114 (121)
++|||||+|||++|++|+||++ .+|+|.+++|....+
T Consensus 112 l~lpGVG~ktA~~ill~a~~~~--~~~VDt~v~Rv~~r~ 148 (211)
T PRK10702 112 EALPGVGRKTANVVLNTAFGWP--TIAVDTHIFRVCNRT 148 (211)
T ss_pred hcCCcccHHHHHHHHHHHcCCC--cccccchHHHHHHHh
Confidence 9999999999999999999996 799999998887665
No 3
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=99.95 E-value=2.3e-27 Score=179.67 Aligned_cols=109 Identities=16% Similarity=0.202 Sum_probs=97.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHH-------hCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH-------
Q 033363 4 IYSIRLKEIAILLKAGRVISDLFT-------LCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG------- 69 (121)
Q Consensus 4 ~~si~~~~~~~~~~v~~v~~~l~~-------~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~------- 69 (121)
+.+..++|.|+.++|++++.+|++ +||||++|++++.++|+++|+|+||+++||++|+++|+.+.+
T Consensus 34 LV~aILsQqT~~~~v~~a~~~L~~~~~~~~~~~~t~e~L~~a~~eeL~~~Irp~Gf~~~KA~~Lk~la~~i~~~~g~~~~ 113 (218)
T PRK13913 34 LLGAVLTQNTKFEAVEKSLENLKNAFILENDDEINLKKIAYIEFSKLAECVRPSGFYNQKAKRLIDLSENILKDFGSFEN 113 (218)
T ss_pred HHHHHHHhhhhHHHHHHHHHHHHHhcccccccCCCHHHHHcCCHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHcCCchh
Confidence 455566666888899999999987 467999999999999999999999999999999999999976
Q ss_pred ----hhHHHhccCCCCcHHHHHHHHHHhcCCCCccCcchHHHHHHHHHH
Q 033363 70 ----ESWTHVTQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFL 114 (121)
Q Consensus 70 ----~~~~~L~~lpGIG~~tA~~vl~f~~~~~~~v~p~D~~l~~~~~wl 114 (121)
..+++|+++||||+||||+||+|++++| +||+|.+++|..+.+
T Consensus 114 ~~~~~~re~Ll~l~GIG~kTAd~iLlya~~rp--~fvVDty~~Rv~~Rl 160 (218)
T PRK13913 114 FKQEVTREWLLDQKGIGKESADAILCYVCAKE--VMVVDKYSYLFLKKL 160 (218)
T ss_pred ccCchHHHHHHcCCCccHHHHHHHHHHHcCCC--ccccchhHHHHHHHc
Confidence 2678999999999999999999999997 799999888776554
No 4
>TIGR01083 nth endonuclease III. This equivalog model identifes nth members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=99.95 E-value=5.5e-27 Score=173.89 Aligned_cols=109 Identities=20% Similarity=0.260 Sum_probs=97.5
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH-------hhHHHhc
Q 033363 4 IYSIRLKEIAILLKAGRVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG-------ESWTHVT 76 (121)
Q Consensus 4 ~~si~~~~~~~~~~v~~v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-------~~~~~L~ 76 (121)
+.+..+++.++.+++.+++.+|++.||||++|+++++++|+++|+++||+++||++|+++|+.+.+ +.+++|+
T Consensus 30 Li~~ILsqqt~~~~~~~~~~~l~~~~pt~~~l~~~~~~~L~~~ir~~G~~~~Ka~~i~~~a~~i~~~~~~~~~~~~~~L~ 109 (191)
T TIGR01083 30 LVATILSAQATDKSVNKATKKLFEVYPTPQALAQAGLEELEEYIKSIGLYRNKAKNIIALCRILVERYGGEVPEDREELV 109 (191)
T ss_pred HHHHHHHhhCcHHHHHHHHHHHHHHCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHcCCCCchHHHHHH
Confidence 345555566667788999999999999999999999999999999999999999999999999986 4789999
Q ss_pred cCCCCcHHHHHHHHHHhcCCCCccCcchHHHHHHHHHH
Q 033363 77 QLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFL 114 (121)
Q Consensus 77 ~lpGIG~~tA~~vl~f~~~~~~~v~p~D~~l~~~~~wl 114 (121)
+|||||+|||+++++|++++| .+|+|.++.|.+.++
T Consensus 110 ~l~GIG~ktA~~ill~~~~~~--~~~vD~~v~Ri~~r~ 145 (191)
T TIGR01083 110 KLPGVGRKTANVVLNVAFGIP--AIAVDTHVFRVSNRL 145 (191)
T ss_pred hCCCCcHHHHHHHHHHHcCCC--ccccchhHHHHHHHc
Confidence 999999999999999999997 488888888887665
No 5
>PRK10880 adenine DNA glycosylase; Provisional
Probab=99.94 E-value=3.3e-26 Score=183.54 Aligned_cols=112 Identities=19% Similarity=0.245 Sum_probs=100.2
Q ss_pred hHHHHHHHHH----HHHHHHHHHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH-------hhH
Q 033363 4 IYSIRLKEIA----ILLKAGRVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG-------ESW 72 (121)
Q Consensus 4 ~~si~~~~~~----~~~~v~~v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-------~~~ 72 (121)
-|.|++++|+ +.++|.++|.+|+++|||+++|+++++++|.++|+++|||+ ||++|+++|+.+.+ .++
T Consensus 30 py~ilVseILlQQT~v~~v~~~~~rl~~~fPt~~~La~a~~eel~~~~~glGyy~-RAr~L~~~A~~i~~~~~g~~p~~~ 108 (350)
T PRK10880 30 PYKVWLSEVMLQQTQVATVIPYFERFMARFPTVTDLANAPLDEVLHLWTGLGYYA-RARNLHKAAQQVATLHGGEFPETF 108 (350)
T ss_pred HHHHHHHHHHHhhccHHHHHHHHHHHHHHCcCHHHHHCcCHHHHHHHHHcCChHH-HHHHHHHHHHHHHHHhCCCchhhH
Confidence 3677777775 45788999999999999999999999999999999999995 99999999999976 478
Q ss_pred HHhccCCCCcHHHHHHHHHHhcCCCCccCcchHHHHHHHHHHHHhh
Q 033363 73 THVTQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFLVSTK 118 (121)
Q Consensus 73 ~~L~~lpGIG~~tA~~vl~f~~~~~~~v~p~D~~l~~~~~wl~~~~ 118 (121)
++|++|||||+|||++|++|+||++ ++++|.+++|.++.+..-.
T Consensus 109 ~~L~~LpGIG~~TA~aIl~~af~~~--~~iVD~nV~RV~~Rl~~i~ 152 (350)
T PRK10880 109 EEVAALPGVGRSTAGAILSLSLGKH--FPILDGNVKRVLARCYAVS 152 (350)
T ss_pred HHHhcCCCccHHHHHHHHHHHCCCC--eecccHHHHHHHHHHhccc
Confidence 9999999999999999999999996 7889999999888775433
No 6
>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=99.94 E-value=1e-25 Score=175.75 Aligned_cols=111 Identities=21% Similarity=0.307 Sum_probs=98.6
Q ss_pred HHHHHHHH----HHHHHHHHHHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH-------hhHH
Q 033363 5 YSIRLKEI----AILLKAGRVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG-------ESWT 73 (121)
Q Consensus 5 ~si~~~~~----~~~~~v~~v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-------~~~~ 73 (121)
|.+++++| ++.++|.++|.+|+++||||++|+++++++|.++|+++||+ +||++|+++|+.+.+ .+++
T Consensus 27 y~vlvseIL~QQT~v~~v~~~~~rl~~~fpt~~~La~a~~eeL~~~~~~lG~y-~RAr~L~~~A~~i~~~~~g~~p~~~~ 105 (275)
T TIGR01084 27 YRVWLSEVMLQQTQVATVIPYFERFLERFPTVQALANAPQDEVLKLWEGLGYY-ARARNLHKAAQEVVEEFGGEFPQDFE 105 (275)
T ss_pred HHHHHHHHHHhhccHHHHHHHHHHHHHhCCCHHHHHCcCHHHHHHHHHHCCcH-HHHHHHHHHHHHHHHHcCCCCcHHHH
Confidence 55555555 45678899999999999999999999999999999999999 699999999999987 4789
Q ss_pred HhccCCCCcHHHHHHHHHHhcCCCCccCcchHHHHHHHHHHHHhh
Q 033363 74 HVTQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFLVSTK 118 (121)
Q Consensus 74 ~L~~lpGIG~~tA~~vl~f~~~~~~~v~p~D~~l~~~~~wl~~~~ 118 (121)
+|++|||||+|||++|++|+||++ .+++|.+++|.++.+....
T Consensus 106 ~L~~LpGIG~~TA~~Il~~a~~~~--~~~vD~~v~RVl~Rl~~~~ 148 (275)
T TIGR01084 106 DLAALPGVGRYTAGAILSFALNKP--YPILDGNVKRVLSRLFAVE 148 (275)
T ss_pred HHHhCCCCCHHHHHHHHHHHCCCC--CCcchHhHHHHHHHHccCc
Confidence 999999999999999999999998 5779999999988876543
No 7
>PRK13910 DNA glycosylase MutY; Provisional
Probab=99.93 E-value=1.2e-25 Score=176.31 Aligned_cols=102 Identities=20% Similarity=0.227 Sum_probs=91.8
Q ss_pred HHHHHHHH-HHHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH-------hhHHHhccCCCCcH
Q 033363 12 IAILLKAG-RVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG-------ESWTHVTQLHGVGK 83 (121)
Q Consensus 12 ~~~~~~v~-~v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-------~~~~~L~~lpGIG~ 83 (121)
+|+.++|. ++|.+|+++|||+++|++++++||+++|+++||| +||++|+++|+.+.+ .++++|++|||||+
T Consensus 4 QT~v~~v~~~yy~rf~~~fPt~e~La~a~~~el~~~~~glGyy-~RAr~L~~~A~~i~~~~~g~~P~~~~~L~~LpGIG~ 82 (289)
T PRK13910 4 QTQINTVVERFYSPFLEAFPTLKDLANAPLEEVLLLWRGLGYY-SRAKNLKKSAEICVKEHHSQLPNDYQSLLKLPGIGA 82 (289)
T ss_pred CCcHHHhHHHHHHHHHHHCCCHHHHHCCCHHHHHHHHHcCCcH-HHHHHHHHHHHHHHHHhCCCCChhHHHHHhCCCCCH
Confidence 44555675 4999999999999999999999999999999999 599999999999987 37999999999999
Q ss_pred HHHHHHHHHhcCCCCccCcchHHHHHHHHHHHH
Q 033363 84 YAADAFAIFCTGKWDRVRPTDHMLNYYWEFLVS 116 (121)
Q Consensus 84 ~tA~~vl~f~~~~~~~v~p~D~~l~~~~~wl~~ 116 (121)
|||++|++|+||++ ++|+|.+++|.++.+.+
T Consensus 83 kTA~aIl~~af~~~--~~~VD~nV~RVl~Rl~g 113 (289)
T PRK13910 83 YTANAILCFGFREK--SACVDANIKRVLLRLFG 113 (289)
T ss_pred HHHHHHHHHHCCCC--cCcccHHHHHHHHHHhc
Confidence 99999999999997 67999999988877643
No 8
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=99.93 E-value=4.3e-25 Score=156.83 Aligned_cols=104 Identities=22% Similarity=0.331 Sum_probs=94.6
Q ss_pred HHHHHHHHHHHHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH-------hhHHHhccCCCCcH
Q 033363 11 EIAILLKAGRVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG-------ESWTHVTQLHGVGK 83 (121)
Q Consensus 11 ~~~~~~~v~~v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-------~~~~~L~~lpGIG~ 83 (121)
+.++.+++.+++.+|.+.||||++++++++++|.++|+++||+++|+++|+++|+.+.+ +.+++|++|||||+
T Consensus 3 qq~~~~~a~~~~~~l~~~~~~~~~l~~~~~~eL~~~l~~~g~~~~ka~~i~~~a~~~~~~~~~~~~~~~~~L~~l~GIG~ 82 (149)
T smart00478 3 QQTSDEAVNKATERLFEKFPTPEDLAAADEEELEELIRPLGFYRRKAKYLIELARILVEEYGGEVPDDREELLKLPGVGR 82 (149)
T ss_pred CcccHHHHHHHHHHHHHHCCCHHHHHCCCHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHCCCccHHHHHHHcCCCCcH
Confidence 34445688899999999999999999999999999999999999999999999999887 37899999999999
Q ss_pred HHHHHHHHHhcCCCCccCcchHHHHHHHHHHHH
Q 033363 84 YAADAFAIFCTGKWDRVRPTDHMLNYYWEFLVS 116 (121)
Q Consensus 84 ~tA~~vl~f~~~~~~~v~p~D~~l~~~~~wl~~ 116 (121)
|||+++++|++++ .++|+|.++.|..+++..
T Consensus 83 ~tA~~~l~~~~~~--~~~~~D~~v~r~~~rl~~ 113 (149)
T smart00478 83 KTANAVLSFALGK--PFIPVDTHVLRIAKRLGL 113 (149)
T ss_pred HHHHHHHHHHCCC--CCCccchHHHHHHHHhCC
Confidence 9999999999999 389999999998887653
No 9
>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=3.5e-24 Score=153.28 Aligned_cols=111 Identities=22% Similarity=0.344 Sum_probs=100.0
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHhC-CCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH----------hh
Q 033363 3 QIYSIRLKEIAILLKAGRVISDLFTLC-PDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG----------ES 71 (121)
Q Consensus 3 ~~~si~~~~~~~~~~v~~v~~~l~~~~-pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~----------~~ 71 (121)
++.+..++++++.+++..++.+|.+.| |||++|+++++++|.+++.++| +++||++|+++|+.+.+ +.
T Consensus 3 ~Li~~il~q~~s~~~a~~~~~~l~~~~gpt~~~l~~~~~~~l~~~~~~~G-~~~kA~~i~~~a~~~~~~~~~~~~~~~~~ 81 (158)
T cd00056 3 VLVSEILSQQTTDKAVNKAYERLFERYGPTPEALAAADEEELRELIRSLG-YRRKAKYLKELARAIVEGFGGLVLDDPDA 81 (158)
T ss_pred HHHHHHHHhcccHHHHHHHHHHHHHHhCCCHHHHHCCCHHHHHHHHHhcC-hHHHHHHHHHHHHHHHHHcCCccCCCccc
Confidence 456666677777778999999999999 9999999999999999999999 78999999999999986 36
Q ss_pred HHHhccCCCCcHHHHHHHHHHhcCCCCccCcchHHHHHHHHHHHH
Q 033363 72 WTHVTQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFLVS 116 (121)
Q Consensus 72 ~~~L~~lpGIG~~tA~~vl~f~~~~~~~v~p~D~~l~~~~~wl~~ 116 (121)
+++|+++||||||||+++++|+++ ++ ++|.|.+++|..+++..
T Consensus 82 ~~~L~~l~GIG~~tA~~~l~~~~~-~~-~~pvD~~v~r~~~~~~~ 124 (158)
T cd00056 82 REELLALPGVGRKTANVVLLFALG-PD-AFPVDTHVRRVLKRLGL 124 (158)
T ss_pred HHHHHcCCCCCHHHHHHHHHHHCC-CC-CCccchhHHHHHHHhCC
Confidence 789999999999999999999999 55 88889999999988764
No 10
>COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair]
Probab=99.88 E-value=1e-22 Score=162.04 Aligned_cols=113 Identities=21% Similarity=0.263 Sum_probs=103.6
Q ss_pred hHHHHHHHHHH----HHHHHHHHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH-------hhH
Q 033363 4 IYSIRLKEIAI----LLKAGRVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG-------ESW 72 (121)
Q Consensus 4 ~~si~~~~~~~----~~~v~~v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-------~~~ 72 (121)
-|.|++|||+. -++|.++|.+|.++|||+++||+|+.+|+.+++.++|+| +||++|+++|+.+.+ ++.
T Consensus 34 PY~VwvSEiMLQQT~v~~Vi~yy~~fl~rfPti~~LA~A~~~evl~~W~gLGYy-sRArnL~~~A~~v~~~~~G~~P~~~ 112 (342)
T COG1194 34 PYRVWVSEIMLQQTQVATVIPYYERFLERFPTIKALAAAPEDEVLKAWEGLGYY-SRARNLHKAAQEVVERHGGEFPDDE 112 (342)
T ss_pred cceehhHHHHhhhccHhhhhhhHHHHHHhCCCHHHHhcCCHHHHHHHHHhcChH-HHHHHHHHHHHHHHHHcCCCCCCCH
Confidence 58899999975 356888999999999999999999999999999999987 899999999999998 489
Q ss_pred HHhccCCCCcHHHHHHHHHHhcCCCCccCcchHHHHHHHHHHHHhhc
Q 033363 73 THVTQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFLVSTKG 119 (121)
Q Consensus 73 ~~L~~lpGIG~~tA~~vl~f~~~~~~~v~p~D~~l~~~~~wl~~~~~ 119 (121)
++|.+|||||+|||.+|++|++|++ .+..|.+++|.++.++.-++
T Consensus 113 ~~l~~LpGiG~yTa~Ail~~a~~~~--~~~lDgNV~RVl~R~f~i~~ 157 (342)
T COG1194 113 EELAALPGVGPYTAGAILSFAFNQP--EPVLDGNVKRVLSRLFAISG 157 (342)
T ss_pred HHHHhCCCCcHHHHHHHHHHHhCCC--Cceeecchheeehhhhcccc
Confidence 9999999999999999999999997 78899999999888776554
No 11
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=99.88 E-value=4.3e-22 Score=156.08 Aligned_cols=109 Identities=21% Similarity=0.318 Sum_probs=92.2
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHh----------CCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHHh--
Q 033363 3 QIYSIRLKEIAILLKAGRVISDLFTL----------CPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGE-- 70 (121)
Q Consensus 3 ~~~si~~~~~~~~~~v~~v~~~l~~~----------~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~~-- 70 (121)
|+-|..++|+...+.+.+++.+|... ||||++|++++++. ++.+|++.+|+++|+++|+.+.++
T Consensus 108 ~lv~aI~~QqvS~~~A~~i~~rl~~~~g~~~~~~~~fptpe~l~~~~~~~----l~~~g~s~~Ka~yi~~~A~~~~~g~~ 183 (285)
T COG0122 108 ALVRAILSQQVSVAAAAKIWARLVSLYGNALEIYHSFPTPEQLAAADEEA----LRRCGLSGRKAEYIISLARAAAEGEL 183 (285)
T ss_pred HHHHHHHHhHhhHHHHHHHHHHHHHHhCCccccccCCCCHHHHHhcCHHH----HHHhCCcHHHHHHHHHHHHHHHcCCc
Confidence 45555566655555667777777642 89999999999998 568999999999999999999983
Q ss_pred ------------hHHHhccCCCCcHHHHHHHHHHhcCCCCccCcchHHHHHHHHHHH
Q 033363 71 ------------SWTHVTQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFLV 115 (121)
Q Consensus 71 ------------~~~~L~~lpGIG~~tA~~vl~f~~~~~~~v~p~D~~l~~~~~wl~ 115 (121)
.+++|++|||||||||+|+++|++|++|.++++|+.+++..+|++
T Consensus 184 ~~~~l~~~~~e~a~e~L~~i~GIG~WTAe~~llf~lgr~dvfP~~D~~lr~~~~~~~ 240 (285)
T COG0122 184 DLSELKPLSDEEAIEELTALKGIGPWTAEMFLLFGLGRPDVFPADDLGLRRAIKKLY 240 (285)
T ss_pred cHHHhccCCHHHHHHHHHcCCCcCHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHh
Confidence 589999999999999999999999999844559999999999987
No 12
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=99.86 E-value=3e-21 Score=151.11 Aligned_cols=81 Identities=20% Similarity=0.356 Sum_probs=73.5
Q ss_pred HhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHHh------------hHHHhccCCCCcHHHHHHHHHHhc
Q 033363 27 TLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGE------------SWTHVTQLHGVGKYAADAFAIFCT 94 (121)
Q Consensus 27 ~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~~------------~~~~L~~lpGIG~~tA~~vl~f~~ 94 (121)
..||||++|+++++++ |+++|++++|+++|+++|+.+.++ .+++|++|||||||||++|++|++
T Consensus 153 ~~FPtpe~La~~~~~e----L~~~Gl~~~Ra~~L~~lA~~i~~g~l~l~~~~~~~~~~~~L~~LpGIGpwTA~~vllr~l 228 (283)
T PRK10308 153 VCFPTPERLAAADPQA----LKALGMPLKRAEALIHLANAALEGTLPLTIPGDVEQAMKTLQTFPGIGRWTANYFALRGW 228 (283)
T ss_pred cCCCCHHHHHcCCHHH----HHHCCCCHHHHHHHHHHHHHHHcCCCCccccCCHHHHHHHHhcCCCcCHHHHHHHHHHhC
Confidence 4689999999999999 567999999999999999999872 478999999999999999999999
Q ss_pred CCCCccCcchHHHHHHH
Q 033363 95 GKWDRVRPTDHMLNYYW 111 (121)
Q Consensus 95 ~~~~~v~p~D~~l~~~~ 111 (121)
|++|.++|+|.++++.+
T Consensus 229 g~~D~fp~~D~~l~~~~ 245 (283)
T PRK10308 229 QAKDVFLPDDYLIKQRF 245 (283)
T ss_pred CCCCCCCcccHHHHHhc
Confidence 99996678999998754
No 13
>TIGR00588 ogg 8-oxoguanine DNA-glycosylase (ogg). All proteins in this family for which functions are known are 8-oxo-guanaine DNA glycosylases that function in base excision repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is distantly realted to the Nth-MutY superfamily.
Probab=99.85 E-value=5.9e-21 Score=151.08 Aligned_cols=108 Identities=22% Similarity=0.227 Sum_probs=86.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHH---------------HhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHH
Q 033363 4 IYSIRLKEIAILLKAGRVISDLF---------------TLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYL 68 (121)
Q Consensus 4 ~~si~~~~~~~~~~v~~v~~~l~---------------~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~ 68 (121)
+.+..+++.+..+++.++..+|. ..||||++|++++.++ .|+++||+ .||++|+++|+.+.
T Consensus 123 lv~~IlsQq~si~~a~~~~~rL~~~~G~~~~~~~g~~~~~FPtp~~La~~~~e~---~Lr~~G~g-~Ra~~I~~~A~~i~ 198 (310)
T TIGR00588 123 LISFICSSNNNIARITRMVERLCQAFGPRLITLDGVTYHGFPSLHALTGPEAEA---HLRKLGLG-YRARYIRETARALL 198 (310)
T ss_pred HHHHHHhCCCCHHHHHHHHHHHHHHhCCCcccCCCcccccCCCHHHHhCCChHH---HHHHcCCH-HHHHHHHHHHHHHH
Confidence 34444444444456667777774 3599999999976553 48899995 68999999999998
Q ss_pred Hh-----------------hHHHhccCCCCcHHHHHHHHHHhcCCCCccCcchHHHHHHHHHHHH
Q 033363 69 GE-----------------SWTHVTQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFLVS 116 (121)
Q Consensus 69 ~~-----------------~~~~L~~lpGIG~~tA~~vl~f~~~~~~~v~p~D~~l~~~~~wl~~ 116 (121)
++ .+++|++|||||||||+||++|+++++| ++|.|.+++|....++.
T Consensus 199 ~~~~~~~~l~~l~~~~~~~~~~~L~~l~GIG~~tAd~vll~~l~~~d-~~PvD~~v~r~~~r~y~ 262 (310)
T TIGR00588 199 EEQGGRAWLQQIRGASYEDAREALCELPGVGPKVADCICLMGLDKPQ-AVPVDVHVWRIANRDYP 262 (310)
T ss_pred hccCCchhHHhhccCChHHHHHHHHhCCCccHHHHHHHHHHhCCCCC-ceeecHHHHHHHHHHhc
Confidence 72 4689999999999999999999999997 78889999988877764
No 14
>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=99.83 E-value=3.5e-20 Score=136.39 Aligned_cols=93 Identities=15% Similarity=0.150 Sum_probs=81.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhC--CCHHHHhcCCHHHHHHHHhhc----CChhHHHHHHHHHHHHHHHh-------
Q 033363 4 IYSIRLKEIAILLKAGRVISDLFTLC--PDAKTATEVDAEEIEKIISTL----GLQKKRAPMIKRFSQEYLGE------- 70 (121)
Q Consensus 4 ~~si~~~~~~~~~~v~~v~~~l~~~~--pt~~~la~a~~~eL~~~i~~~----Gl~~~Ka~~i~~~a~~i~~~------- 70 (121)
+.+..+++.+++++|++++.+|++++ +||++|++++.++|+++|++. ||+++||++|+++|+.+.++
T Consensus 22 LVa~ILSQqTtd~nv~kA~~~L~~~~g~~tp~~La~a~~eeL~~lI~~~pal~Gfy~~KAk~Lk~~a~~iie~y~G~v~~ 101 (177)
T TIGR03252 22 LTGMLLDQQVPMERAFAGPHKIARRMGSLDAEDIAKYDPQAFVALFSERPAVHRFPGSMAKRVQALAQYVVDTYDGDATA 101 (177)
T ss_pred HHHHHHhccCcHHHHHHHHHHHHHHhCCCCHHHHHcCCHHHHHHHHhcCccccCchHHHHHHHHHHHHHHHHHhCCChhh
Confidence 55666677777789999999998765 799999999999999999876 99999999999999999861
Q ss_pred --------h---HHHhccCCCCcHHHHHHHHHHhcCC
Q 033363 71 --------S---WTHVTQLHGVGKYAADAFAIFCTGK 96 (121)
Q Consensus 71 --------~---~~~L~~lpGIG~~tA~~vl~f~~~~ 96 (121)
+ +++|++||||||||||+||.+.-.+
T Consensus 102 L~~~~~p~t~~lre~Ll~LpGVG~KTAnvVL~~l~~~ 138 (177)
T TIGR03252 102 VWTEGDPDGKELLRRLKALPGFGKQKAKIFLALLGKQ 138 (177)
T ss_pred hhcccCCCcHHHHHHHHcCCCCCHHHHHHHHHHHHHH
Confidence 1 5799999999999999999977654
No 15
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=99.81 E-value=1.9e-19 Score=135.67 Aligned_cols=101 Identities=15% Similarity=0.101 Sum_probs=80.5
Q ss_pred chhHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHhcCCHHHHHHHHhhcC--ChhHHHHHHHHHHHH---HHH-------
Q 033363 2 AQIYSIRLKEIAILLKAGRVISDLFTLCPDAKTATEVDAEEIEKIISTLG--LQKKRAPMIKRFSQE---YLG------- 69 (121)
Q Consensus 2 ~~~~si~~~~~~~~~~v~~v~~~l~~~~pt~~~la~a~~~eL~~~i~~~G--l~~~Ka~~i~~~a~~---i~~------- 69 (121)
+||+|+ .++++++++++.+|. ++.+ +++.++|+++|+++| |+++||++|+++++. +.+
T Consensus 43 ~~ILsq----nT~~~~v~~a~~~L~-----~~~l-~~~~eeL~~~Ir~~Gygf~~~KAk~I~~~~~~~~~l~~~~~~~~~ 112 (208)
T PRK01229 43 FCILTA----NSSAEGGIKAQKEIG-----DGFL-YLSEEELEEKLKEVGHRFYNKRAEYIVEARKLYGKLKEIIKADKD 112 (208)
T ss_pred HHHhcC----cCcHHHHHHHHHhcC-----HHHc-CCCHHHHHHHHHHhhcccHHHHHHHHHHHHHHHHHHHHHHhccCC
Confidence 345554 445557778888883 5667 999999999999995 999999999999986 221
Q ss_pred --hhHHHhc-cCCCCcHHHHHHHHHHhcCCCCccCcchHHHHHHHHHH
Q 033363 70 --ESWTHVT-QLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFL 114 (121)
Q Consensus 70 --~~~~~L~-~lpGIG~~tA~~vl~f~~~~~~~v~p~D~~l~~~~~wl 114 (121)
+.+++|+ ++||||+|||+++|..+..++ ++|+|.++.|+...+
T Consensus 113 ~~~~R~~Ll~~lpGIG~KTAd~vL~~~~~~~--~~iVDtHv~Ri~~Rl 158 (208)
T PRK01229 113 QFEAREFLVKNIKGIGYKEASHFLRNVGYED--LAILDRHILRFLKRY 158 (208)
T ss_pred chHHHHHHHHcCCCCcHHHHHHHHHHccCCC--eeeeeHHHHHHHHHh
Confidence 4789999 999999999999997555443 899998888876554
No 16
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=99.81 E-value=6e-19 Score=131.93 Aligned_cols=110 Identities=17% Similarity=0.221 Sum_probs=93.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhC-CCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH-----------hhH
Q 033363 5 YSIRLKEIAILLKAGRVISDLFTLC-PDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG-----------ESW 72 (121)
Q Consensus 5 ~si~~~~~~~~~~v~~v~~~l~~~~-pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-----------~~~ 72 (121)
.+..+.|-|.=++|+++..++.... -+++++.+.|.++|+++|||.|||++||++|+.+++.+.. ..+
T Consensus 35 igAILtQNT~WknvekAlenLk~~~~~~l~~I~~~~~~~L~elIrpsGFYnqKa~rLk~l~k~l~~~~~~~~~~~~~~~R 114 (215)
T COG2231 35 IGAILTQNTSWKNVEKALENLKNEGILNLKKILKLDEEELAELIRPSGFYNQKAKRLKALSKNLAKFFINLESFKSEVLR 114 (215)
T ss_pred HHHHHhccccHHHHHHHHHHHHHcccCCHHHHhcCCHHHHHHHHhccchHHHHHHHHHHHHHHHHHHhhhhhccchHHHH
Confidence 3344444444578999999998765 4799999999999999999999999999999777776665 248
Q ss_pred HHhccCCCCcHHHHHHHHHHhcCCCCccCcchHHHHHHHHHHHH
Q 033363 73 THVTQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFLVS 116 (121)
Q Consensus 73 ~~L~~lpGIG~~tA~~vl~f~~~~~~~v~p~D~~l~~~~~wl~~ 116 (121)
++|++++|||+.|||++|+|++++| +||+|..-+|.+..+-.
T Consensus 115 ~~LL~iKGIG~ETaDsILlYa~~rp--~FVvD~Yt~R~l~rlg~ 156 (215)
T COG2231 115 EELLSIKGIGKETADSILLYALDRP--VFVVDKYTRRLLSRLGG 156 (215)
T ss_pred HHHHccCCcchhhHHHHHHHHhcCc--ccchhHHHHHHHHHhcc
Confidence 9999999999999999999999997 89999999998876543
No 17
>KOG1921 consensus Endonuclease III [Replication, recombination and repair]
Probab=99.80 E-value=5e-19 Score=135.45 Aligned_cols=113 Identities=12% Similarity=0.145 Sum_probs=97.9
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhC-CCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH-------hhHHHh
Q 033363 4 IYSIRLKEIAILLKAGRVISDLFTLC-PDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG-------ESWTHV 75 (121)
Q Consensus 4 ~~si~~~~~~~~~~v~~v~~~l~~~~-pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-------~~~~~L 75 (121)
+.++.++-++.++....+..+|.+.. -|++++.++|+.+|.++|.++|||++||+||+++|+++.+ .++++|
T Consensus 82 Lv~lmLSSQTKDevt~~Am~rL~~~~gLT~e~v~~~de~~l~~LI~~VgFy~rKA~ylkkta~IL~d~f~gDIP~~v~dL 161 (286)
T KOG1921|consen 82 LVGLMLSSQTKDEVTAAAMLRLKEYGGLTLEAVLKIDEPTLNELIYPVGFYTRKAKYLKKTAKILQDKFDGDIPDTVEDL 161 (286)
T ss_pred HHHHHHhcchHHHHHHHHHHHHHHhcCCCHHHHhccChHhHHhhhhhccchHHHHHHHHHHHHHHHHHhCCCCchhHHHH
Confidence 44556666666666678889999887 7999999999999999999999999999999999999998 389999
Q ss_pred ccCCCCcHHHHHHHHHHhcCCCCccCcchHH--HHHHHHHHHH
Q 033363 76 TQLHGVGKYAADAFAIFCTGKWDRVRPTDHM--LNYYWEFLVS 116 (121)
Q Consensus 76 ~~lpGIG~~tA~~vl~f~~~~~~~v~p~D~~--l~~~~~wl~~ 116 (121)
++|||||||+|..+|..++|+--++.+|.|. +++.++|+..
T Consensus 162 lsLPGVGPKMa~L~m~~AWn~i~GI~VDtHVHRi~nrlgWv~~ 204 (286)
T KOG1921|consen 162 LSLPGVGPKMAHLTMQVAWNKIVGICVDTHVHRICNRLGWVDT 204 (286)
T ss_pred hcCCCCchHHHHHHHHHHhccceeEEeehHHHHHHHHhccccc
Confidence 9999999999999999999998777777754 4577888753
No 18
>KOG1918 consensus 3-methyladenine DNA glycosidase [Replication, recombination and repair]
Probab=99.74 E-value=4.3e-18 Score=128.57 Aligned_cols=107 Identities=19% Similarity=0.335 Sum_probs=90.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHH------hCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHHh----------
Q 033363 7 IRLKEIAILLKAGRVISDLFT------LCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGE---------- 70 (121)
Q Consensus 7 i~~~~~~~~~~v~~v~~~l~~------~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~~---------- 70 (121)
|..||++ .++++.+|.+|.. .||+|+.+..++.++ |+.|||+.+|+.+|+.+|+.+.++
T Consensus 83 IlsQQLs-~kAansI~~Rfvsl~~g~~~~~~pe~i~~~~~~~----lrkcG~S~rK~~yLh~lA~~~~ng~I~s~~~i~~ 157 (254)
T KOG1918|consen 83 ILSQQLS-GKAANSIYNRFVSLCGGAEKFPTPEFIDPLDCEE----LRKCGFSKRKASYLHSLAEAYTNGYIPSKSGIEK 157 (254)
T ss_pred HHHHHHH-HHHHHHHHHHHHHHhCCCcCCCCchhcCcCCHHH----HHHhCcchhhHHHHHHHHHHHhcCCCCchHHHhh
Confidence 3333333 4478899999984 589999999999999 788999999999999999999872
Q ss_pred -----hHHHhccCCCCcHHHHHHHHHHhcCCCCccCcchHHHHHHHHHHHHhh
Q 033363 71 -----SWTHVTQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFLVSTK 118 (121)
Q Consensus 71 -----~~~~L~~lpGIG~~tA~~vl~f~~~~~~~v~p~D~~l~~~~~wl~~~~ 118 (121)
.++.|+.++|||+||+.++++|+++|+|..+|+|..+++-++.+++.+
T Consensus 158 mseEeL~~~LT~VKGIg~Wtv~MflIfsL~R~DVmp~dDlgir~g~k~l~gl~ 210 (254)
T KOG1918|consen 158 MSEEELIERLTNVKGIGRWTVEMFLIFSLHRPDVMPADDLGIRNGVKKLLGLK 210 (254)
T ss_pred cCHHHHHHHHHhccCccceeeeeeeeeccCCCcccCchhhhHHHHHHHHhCCC
Confidence 467899999999999999999999999966778899988877776543
No 19
>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=99.67 E-value=2.7e-16 Score=105.98 Aligned_cols=85 Identities=22% Similarity=0.375 Sum_probs=72.8
Q ss_pred HHHHHHHHHHHHHHHHHHHh--CCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHHhhHHHhccCCCCcHHHH
Q 033363 9 LKEIAILLKAGRVISDLFTL--CPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLHGVGKYAA 86 (121)
Q Consensus 9 ~~~~~~~~~v~~v~~~l~~~--~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~~~~~~L~~lpGIG~~tA 86 (121)
++++++.+++.+++.+|++. ||||++|+++++++|.++|+++||+++||++|+++|+.+.
T Consensus 5 l~qq~s~~~a~~~~~~l~~~~g~pt~~~l~~~~~~el~~~i~~~G~~~~ka~~i~~~a~~~~------------------ 66 (108)
T PF00730_consen 5 LSQQTSIKAARKIYRRLFERYGFPTPEALAEASEEELRELIRPLGFSRRKAKYIIELARAIL------------------ 66 (108)
T ss_dssp HCTTS-HHHHHHHHHHHHHHHSCSSHHHHHCSHHHHHHHHHTTSTSHHHHHHHHHHHHHHHH------------------
T ss_pred ecCcCcHHHHHHHHHHHHHHhcCCCHHHHHhCCHHHHHHHhhccCCCHHHHHHHHHHHHHhh------------------
Confidence 34444556788999999998 5999999999999999999999999999999999999996
Q ss_pred HHHHHHhcCCCCccCcchHHHHHHHHHHHHhhc
Q 033363 87 DAFAIFCTGKWDRVRPTDHMLNYYWEFLVSTKG 119 (121)
Q Consensus 87 ~~vl~f~~~~~~~v~p~D~~l~~~~~wl~~~~~ 119 (121)
|++|.++|+|.+++|.+.|+...+.
T Consensus 67 --------~~~d~~~~~D~~v~r~~~r~~~~~~ 91 (108)
T PF00730_consen 67 --------GRPDPFPPVDTHVRRVLQRLGGIPE 91 (108)
T ss_dssp --------C-SSSS-TTSHHHHHHHHHHTSSSS
T ss_pred --------hcccceecCcHHHHHHHHHHcCCCC
Confidence 8887799999999999999876554
No 20
>KOG2457 consensus A/G-specific adenine DNA glycosylase [Replication, recombination and repair]
Probab=99.61 E-value=4.3e-15 Score=120.30 Aligned_cols=107 Identities=16% Similarity=0.228 Sum_probs=93.3
Q ss_pred hhHHHHHHHHHHH----HHHHHHHHHHHHhCCCHHHHhcCCH-HHHHHHHhhcCChhHHHHHHHHHHHHHHH-------h
Q 033363 3 QIYSIRLKEIAIL----LKAGRVISDLFTLCPDAKTATEVDA-EEIEKIISTLGLQKKRAPMIKRFSQEYLG-------E 70 (121)
Q Consensus 3 ~~~si~~~~~~~~----~~v~~v~~~l~~~~pt~~~la~a~~-~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-------~ 70 (121)
-.|.++++||+.. ..|.+.|.+.++++||..+++.|+. +|+.+++.++||| +|+++|.+-|+++++ +
T Consensus 124 RaYeVwVSEiMLQQTrV~TV~~YYt~WMqkwPTl~dla~Asl~~eVn~lWaGlGyY-~R~rrL~ega~~vv~~~~ge~Pr 202 (555)
T KOG2457|consen 124 RAYEVWVSEIMLQQTRVQTVMKYYTRWMQKWPTLYDLAQASLEKEVNELWAGLGYY-RRARRLLEGAKMVVAGTEGEFPR 202 (555)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHHHHhhhhHH-HHHHHHHHHHHHHHHhCCCCCCC
Confidence 3699999999863 3467789999999999999999998 8899999999999 899999999999998 3
Q ss_pred hHHHhcc-CCCCcHHHHHHHHHHhcCCCCccCcchHHHHHHHH
Q 033363 71 SWTHVTQ-LHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWE 112 (121)
Q Consensus 71 ~~~~L~~-lpGIG~~tA~~vl~f~~~~~~~v~p~D~~l~~~~~ 112 (121)
+-+.|.+ +||||+|||.+|+..+||.+ --.+|.++-|.+.
T Consensus 203 ta~~l~kgvpGVG~YTAGAiaSIAf~q~--tGiVDGNVirvls 243 (555)
T KOG2457|consen 203 TASSLMKGVPGVGQYTAGAIASIAFNQV--TGIVDGNVIRVLS 243 (555)
T ss_pred hHHHHHhhCCCCCccchhhhhhhhhcCc--ccccccchHHHhH
Confidence 5677877 99999999999999999997 4667777766654
No 21
>KOG2875 consensus 8-oxoguanine DNA glycosylase [Replication, recombination and repair]
Probab=99.57 E-value=3.8e-15 Score=116.03 Aligned_cols=87 Identities=22% Similarity=0.264 Sum_probs=73.1
Q ss_pred HhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH-----------------hhHHHhccCCCCcHHHHHHH
Q 033363 27 TLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG-----------------ESWTHVTQLHGVGKYAADAF 89 (121)
Q Consensus 27 ~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-----------------~~~~~L~~lpGIG~~tA~~v 89 (121)
+.|||.+.++. .+++.-+|.+||. .|||||...|+.+.+ +.++.|+.+||||+|+||||
T Consensus 159 h~FPsl~~L~g---~~~Ea~LR~~gfG-YRAkYI~~ta~~l~~~~g~~~wLqsl~~~~yeear~~L~~lpGVG~KVADCI 234 (323)
T KOG2875|consen 159 HGFPSLQALAG---PEVEAELRKLGFG-YRAKYISATARALQEKQGGLAWLQSLRKSSYEEAREALCSLPGVGPKVADCI 234 (323)
T ss_pred ccCccHHHhcC---cHhHHHHHHcCcc-hhHHHHHHHHHHHHHhcccchHHHHHhcccHHHHHHHHhcCCCCcchHhhhh
Confidence 56999999986 5677779999998 999999999999998 26889999999999999999
Q ss_pred HHHhcCCCCccCcchHHHHHHHH--HHHHhh
Q 033363 90 AIFCTGKWDRVRPTDHMLNYYWE--FLVSTK 118 (121)
Q Consensus 90 l~f~~~~~~~v~p~D~~l~~~~~--wl~~~~ 118 (121)
++++++.. .+.|+|.++-+... |+.+..
T Consensus 235 ~Lm~l~~~-~~VPVDvHi~ria~~y~l~~~~ 264 (323)
T KOG2875|consen 235 CLMSLDKL-SAVPVDVHIWRIAQDYILPGLS 264 (323)
T ss_pred hhhhcCCC-CcccchhhHHHHhhcccCCCcc
Confidence 99999998 47777777655543 544443
No 22
>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=98.67 E-value=1.9e-08 Score=54.04 Aligned_cols=24 Identities=29% Similarity=0.430 Sum_probs=20.8
Q ss_pred HhhHHHhccCCCCcHHHHHHHHHH
Q 033363 69 GESWTHVTQLHGVGKYAADAFAIF 92 (121)
Q Consensus 69 ~~~~~~L~~lpGIG~~tA~~vl~f 92 (121)
..++++|.++||||||||++|+.|
T Consensus 7 pas~eeL~~lpGIG~~tA~~I~~~ 30 (30)
T PF00633_consen 7 PASIEELMKLPGIGPKTANAILSF 30 (30)
T ss_dssp TSSHHHHHTSTT-SHHHHHHHHHH
T ss_pred CCCHHHHHhCCCcCHHHHHHHHhC
Confidence 357899999999999999999976
No 23
>COG1059 Thermostable 8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=97.43 E-value=0.00078 Score=50.52 Aligned_cols=58 Identities=16% Similarity=0.250 Sum_probs=48.1
Q ss_pred HHHhcCCHHHHHHHHhhc--CChhHHHHHHHHHHHHHHH-----------h-hHHHhc-cCCCCcHHHHHHHH
Q 033363 33 KTATEVDAEEIEKIISTL--GLQKKRAPMIKRFSQEYLG-----------E-SWTHVT-QLHGVGKYAADAFA 90 (121)
Q Consensus 33 ~~la~a~~~eL~~~i~~~--Gl~~~Ka~~i~~~a~~i~~-----------~-~~~~L~-~lpGIG~~tA~~vl 90 (121)
+.+..++.+||.+.++.+ .|++.||++|.+.=+.+-+ . .++.|. .++|+|-|-|.-+|
T Consensus 66 ~gfly~~~eEL~e~Lk~~g~Rf~n~raeyIVeaR~~~~~lk~~v~~~~~~~vaRE~Lv~nikGiGyKEASHFL 138 (210)
T COG1059 66 DGFLYLSEEELREKLKEVGYRFYNVRAEYIVEAREKFDDLKIIVKADENEKVARELLVENIKGIGYKEASHFL 138 (210)
T ss_pred cccccCCHHHHHHHHHHhcchhcccchHHHHHHHHHHHHHHHHHhcCcchHHHHHHHHHHcccccHHHHHHHH
Confidence 456677899999999999 5899999999997666533 1 567777 99999999999887
No 24
>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=97.03 E-value=0.0063 Score=37.89 Aligned_cols=52 Identities=23% Similarity=0.262 Sum_probs=38.7
Q ss_pred HHHHHHHhhcCChhHHHHHHHHHHHHHHH-----hhHHH-hccCCCCcHHHHHHHHHH
Q 033363 41 EEIEKIISTLGLQKKRAPMIKRFSQEYLG-----ESWTH-VTQLHGVGKYAADAFAIF 92 (121)
Q Consensus 41 ~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-----~~~~~-L~~lpGIG~~tA~~vl~f 92 (121)
+++.+...-.|=...|+..-.+.+..+.. .+.++ +.+|||||+.++.-|--|
T Consensus 9 ~~la~~~~~~~~~~~r~~aY~~Aa~~i~~l~~~i~~~~~~~~~l~gIG~~ia~kI~E~ 66 (68)
T PF14716_consen 9 EELADLYELQGGDPFRARAYRRAAAAIKALPYPITSGEEDLKKLPGIGKSIAKKIDEI 66 (68)
T ss_dssp HHHHHHHHHTSTSHHHHHHHHHHHHHHHHSSS-HHSHHHHHCTSTTTTHHHHHHHHHH
T ss_pred HHHHHHHHHhhCCcHHHHHHHHHHHHHHhCCHhHhhHHHHHhhCCCCCHHHHHHHHHH
Confidence 44555555554446889999999988877 35566 999999999999987543
No 25
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=96.95 E-value=0.00059 Score=34.97 Aligned_cols=21 Identities=14% Similarity=0.208 Sum_probs=18.1
Q ss_pred HhccCCCCcHHHHHHHHHHhc
Q 033363 74 HVTQLHGVGKYAADAFAIFCT 94 (121)
Q Consensus 74 ~L~~lpGIG~~tA~~vl~f~~ 94 (121)
.|.++||||+++|+.++.+..
T Consensus 2 ~L~~i~GiG~k~A~~il~~~~ 22 (26)
T smart00278 2 ELLKVPGIGPKTAEKILEAXX 22 (26)
T ss_pred hhhhCCCCCHHHHHHHHHhcc
Confidence 588999999999999987543
No 26
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=96.91 E-value=0.0029 Score=47.59 Aligned_cols=53 Identities=21% Similarity=0.323 Sum_probs=42.0
Q ss_pred HHHHhhcCChhHHHHHHH------HHHHHHHHhhHHHhccCCCCcHHHHHHHHHHhcCC
Q 033363 44 EKIISTLGLQKKRAPMIK------RFSQEYLGESWTHVTQLHGVGKYAADAFAIFCTGK 96 (121)
Q Consensus 44 ~~~i~~~Gl~~~Ka~~i~------~~a~~i~~~~~~~L~~lpGIG~~tA~~vl~f~~~~ 96 (121)
+.+++--|...+.|-.|. +++++|.+++.+.|.++||||+|||+=+.+---++
T Consensus 72 ~~LisVsGIGPK~ALaILs~~~~~el~~aI~~~D~~~L~~vpGIGkKtAeRIIlELkdK 130 (196)
T PRK13901 72 EELIGVDGIGPRAALRVLSGIKYNEFRDAIDREDIELISKVKGIGNKMAGKIFLKLRGK 130 (196)
T ss_pred HHHhCcCCcCHHHHHHHHcCCCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHHh
Confidence 344555677777787777 67888888999999999999999999888654444
No 27
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=96.91 E-value=0.0012 Score=40.82 Aligned_cols=24 Identities=21% Similarity=0.338 Sum_probs=17.4
Q ss_pred hHHHhccCCCCcHHHHHHHHHHhc
Q 033363 71 SWTHVTQLHGVGKYAADAFAIFCT 94 (121)
Q Consensus 71 ~~~~L~~lpGIG~~tA~~vl~f~~ 94 (121)
+.++|.++||||+.+|+.+..|--
T Consensus 33 ~~e~L~~i~gIG~~~A~si~~ff~ 56 (64)
T PF12826_consen 33 SVEELSAIPGIGPKIAQSIYEFFQ 56 (64)
T ss_dssp -HHHHCTSTT--HHHHHHHHHHHH
T ss_pred CHHHHhccCCcCHHHHHHHHHHHC
Confidence 456789999999999999987643
No 28
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=96.51 E-value=0.0032 Score=46.92 Aligned_cols=50 Identities=16% Similarity=0.145 Sum_probs=36.7
Q ss_pred HhhcCChhHHHHHHH------HHHHHHHHhhHHHhccCCCCcHHHHHHHHHHhcCC
Q 033363 47 ISTLGLQKKRAPMIK------RFSQEYLGESWTHVTQLHGVGKYAADAFAIFCTGK 96 (121)
Q Consensus 47 i~~~Gl~~~Ka~~i~------~~a~~i~~~~~~~L~~lpGIG~~tA~~vl~f~~~~ 96 (121)
++--|...+.|-.|. +++++|.+++.+.|+++||||+|||+-+.+---++
T Consensus 76 i~V~GIGpK~AL~iLs~~~~~el~~aI~~~D~~~L~~vpGIGkKtAerIilELkdK 131 (188)
T PRK14606 76 TKVSRLGPKTALKIISNEDAETLVTMIASQDVEGLSKLPGISKKTAERIVMELKDE 131 (188)
T ss_pred hccCCccHHHHHHHHcCCCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHHh
Confidence 333455555555554 46777778999999999999999999988554444
No 29
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=96.51 E-value=0.0033 Score=46.76 Aligned_cols=51 Identities=12% Similarity=0.146 Sum_probs=37.2
Q ss_pred HHhhcCChhHHHHHHH------HHHHHHHHhhHHHhccCCCCcHHHHHHHHHHhcCC
Q 033363 46 IISTLGLQKKRAPMIK------RFSQEYLGESWTHVTQLHGVGKYAADAFAIFCTGK 96 (121)
Q Consensus 46 ~i~~~Gl~~~Ka~~i~------~~a~~i~~~~~~~L~~lpGIG~~tA~~vl~f~~~~ 96 (121)
+++--|...+.|-.|. ++.++|.+++.+.|.++||||+|||+=+.+---++
T Consensus 75 Li~VsGIGpK~Al~ILs~~~~~el~~aI~~~D~~~L~~vpGIGkKtAeRIilELkdK 131 (183)
T PRK14601 75 LLKVNGIGANTAMAVCSSLDVNSFYKALSLGDESVLKKVPGIGPKSAKRIIAELSDA 131 (183)
T ss_pred HhccCCccHHHHHHHHcCCCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHHH
Confidence 3444555555555444 46777777999999999999999999988655444
No 30
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=96.41 E-value=0.0041 Score=46.85 Aligned_cols=50 Identities=24% Similarity=0.195 Sum_probs=35.7
Q ss_pred HhhcCChhHHHHHHHH------HHHHHHHhhHHHhccCCCCcHHHHHHHHHHhcCC
Q 033363 47 ISTLGLQKKRAPMIKR------FSQEYLGESWTHVTQLHGVGKYAADAFAIFCTGK 96 (121)
Q Consensus 47 i~~~Gl~~~Ka~~i~~------~a~~i~~~~~~~L~~lpGIG~~tA~~vl~f~~~~ 96 (121)
+.--|...+.|-.|.. ++++|.+++.+.|.++||||+|||+-+..---++
T Consensus 77 i~V~GIGpK~Al~iLs~~~~~~l~~aI~~~D~~~L~~ipGIGkKtAerIilELkdK 132 (203)
T PRK14602 77 ISISKVGAKTALAILSQFRPDDLRRLVAEEDVAALTRVSGIGKKTAQHIFLELKYK 132 (203)
T ss_pred hCCCCcCHHHHHHHHhhCCHHHHHHHHHhCCHHHHhcCCCcCHHHHHHHHHHHHHh
Confidence 3444555555555543 4567777899999999999999999988544333
No 31
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=96.34 E-value=0.0047 Score=46.36 Aligned_cols=43 Identities=26% Similarity=0.248 Sum_probs=32.3
Q ss_pred cCChhHHHHHHH------HHHHHHHHhhHHHhccCCCCcHHHHHHHHHH
Q 033363 50 LGLQKKRAPMIK------RFSQEYLGESWTHVTQLHGVGKYAADAFAIF 92 (121)
Q Consensus 50 ~Gl~~~Ka~~i~------~~a~~i~~~~~~~L~~lpGIG~~tA~~vl~f 92 (121)
-|...+.|-.|. +++++|.+++.+.|.++||||+|||+-+..-
T Consensus 78 ~GIGpK~AL~iLs~~~~~~l~~aI~~~D~~~L~kvpGIGkKtAerIilE 126 (197)
T PRK14603 78 SGVGPKLALALLSALPPALLARALLEGDARLLTSASGVGKKLAERIALE 126 (197)
T ss_pred CCcCHHHHHHHHcCCCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHH
Confidence 445544554443 4677777799999999999999999988743
No 32
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=96.33 E-value=0.0046 Score=46.66 Aligned_cols=54 Identities=26% Similarity=0.371 Sum_probs=37.6
Q ss_pred HHHHhhcCChhHHHHHH------HHHHHHHHHhhHHHhccCCCCcHHHHHHHHHHhcCCC
Q 033363 44 EKIISTLGLQKKRAPMI------KRFSQEYLGESWTHVTQLHGVGKYAADAFAIFCTGKW 97 (121)
Q Consensus 44 ~~~i~~~Gl~~~Ka~~i------~~~a~~i~~~~~~~L~~lpGIG~~tA~~vl~f~~~~~ 97 (121)
..+|+--|...+=|-.| -+++++|..++.+.|.++||||+|||+-+++---++.
T Consensus 73 ~~LisVnGIGpK~ALaiLs~~~~~~l~~aI~~~d~~~L~k~PGIGkKtAerivleLk~K~ 132 (201)
T COG0632 73 RLLISVNGIGPKLALAILSNLDPEELAQAIANEDVKALSKIPGIGKKTAERIVLELKGKL 132 (201)
T ss_pred HHHHccCCccHHHHHHHHcCCCHHHHHHHHHhcChHhhhcCCCCCHHHHHHHHHHHhhhh
Confidence 33444455554334333 3457777778999999999999999999887655543
No 33
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=96.31 E-value=0.005 Score=46.15 Aligned_cols=50 Identities=22% Similarity=0.333 Sum_probs=35.9
Q ss_pred HhhcCChhHHHHHHH------HHHHHHHHhhHHHhccCCCCcHHHHHHHHHHhcCC
Q 033363 47 ISTLGLQKKRAPMIK------RFSQEYLGESWTHVTQLHGVGKYAADAFAIFCTGK 96 (121)
Q Consensus 47 i~~~Gl~~~Ka~~i~------~~a~~i~~~~~~~L~~lpGIG~~tA~~vl~f~~~~ 96 (121)
++--|...+.|-.|. +++++|.+++.+.|.++||||+|||+=+..---++
T Consensus 76 i~V~GIGpK~Al~iLs~~~~~el~~aI~~~D~~~L~kvpGIGkKtAerIilELk~K 131 (195)
T PRK14604 76 IGVSGVGPKAALNLLSSGTPDELQLAIAGGDVARLARVPGIGKKTAERIVLELKGK 131 (195)
T ss_pred hCcCCcCHHHHHHHHcCCCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHHH
Confidence 333455555555544 45667777899999999999999999888654444
No 34
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=96.20 E-value=0.014 Score=43.57 Aligned_cols=46 Identities=15% Similarity=0.281 Sum_probs=35.4
Q ss_pred HHHhhcCChhHHHHHHHH------HHHHHHHhhHHHhccCCCCcHHHHHHHH
Q 033363 45 KIISTLGLQKKRAPMIKR------FSQEYLGESWTHVTQLHGVGKYAADAFA 90 (121)
Q Consensus 45 ~~i~~~Gl~~~Ka~~i~~------~a~~i~~~~~~~L~~lpGIG~~tA~~vl 90 (121)
.+++--|.....|..|.+ +++.+.+++.+.|.++||||+|||+-+.
T Consensus 74 ~Li~V~GIGpK~Al~ILs~~~~~~l~~aI~~~D~~~L~~vpGIGkKtAerIi 125 (194)
T PRK14605 74 TLIDVSGIGPKLGLAMLSAMNAEALASAIISGNAELLSTIPGIGKKTASRIV 125 (194)
T ss_pred HHhCCCCCCHHHHHHHHHhCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHH
Confidence 334445667677777766 3666777899999999999999999954
No 35
>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=95.96 E-value=0.024 Score=42.27 Aligned_cols=51 Identities=24% Similarity=0.273 Sum_probs=36.3
Q ss_pred HHHHhhcCChhHHHHHHHH------HHHHHHHhhHHHhccCCCCcHHHHHHHHHHhc
Q 033363 44 EKIISTLGLQKKRAPMIKR------FSQEYLGESWTHVTQLHGVGKYAADAFAIFCT 94 (121)
Q Consensus 44 ~~~i~~~Gl~~~Ka~~i~~------~a~~i~~~~~~~L~~lpGIG~~tA~~vl~f~~ 94 (121)
..+++--|...++|..|.. +.+++.+++.+.|.++||||+|||+-+++---
T Consensus 72 ~~L~~V~GIGpK~Al~iL~~~~~~el~~aI~~~d~~~L~~ipGiGkKtAerIileLk 128 (191)
T TIGR00084 72 KELIKVNGVGPKLALAILSNMSPEEFVYAIETEEVKALVKIPGVGKKTAERLLLELK 128 (191)
T ss_pred HHHhCCCCCCHHHHHHHHhcCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHH
Confidence 3344555677677776654 34455557889999999999999999984433
No 36
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.90 E-value=0.0081 Score=44.72 Aligned_cols=49 Identities=16% Similarity=0.200 Sum_probs=34.4
Q ss_pred HhhcCChhHHHHHHH------HHHHHHHHhhHHHhccCCCCcHHHHHHHHHHhcCC
Q 033363 47 ISTLGLQKKRAPMIK------RFSQEYLGESWTHVTQLHGVGKYAADAFAIFCTGK 96 (121)
Q Consensus 47 i~~~Gl~~~Ka~~i~------~~a~~i~~~~~~~L~~lpGIG~~tA~~vl~f~~~~ 96 (121)
++--|...+.|-.|. ++.++|.+++.+.| ++||||+|||+-+.+---++
T Consensus 76 isV~GIGpK~Al~iLs~~~~~~l~~aI~~~D~~~L-~vpGIGkKtAerIilELk~K 130 (186)
T PRK14600 76 VKVSGVNYKTAMSILSKLTPEQLFSAIVNEDKAAL-KVNGIGEKLINRIITELQYK 130 (186)
T ss_pred hCcCCcCHHHHHHHHccCCHHHHHHHHHcCCHhhe-ECCCCcHHHHHHHHHHHHHH
Confidence 344455555555444 35667777899999 99999999999988544443
No 37
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=95.83 E-value=0.068 Score=32.21 Aligned_cols=21 Identities=14% Similarity=0.316 Sum_probs=13.7
Q ss_pred hHHHhccCCCCcHHHHHHHHH
Q 033363 71 SWTHVTQLHGVGKYAADAFAI 91 (121)
Q Consensus 71 ~~~~L~~lpGIG~~tA~~vl~ 91 (121)
+.++|.++||||+++|+-+..
T Consensus 36 ~~~~L~~i~Gig~~~a~~i~~ 56 (60)
T PF14520_consen 36 DPEELAEIPGIGEKTAEKIIE 56 (60)
T ss_dssp HHHHHHTSTTSSHHHHHHHHH
T ss_pred CHHHHhcCCCCCHHHHHHHHH
Confidence 445677777777777766553
No 38
>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=95.75 E-value=0.0081 Score=39.04 Aligned_cols=40 Identities=18% Similarity=0.204 Sum_probs=32.6
Q ss_pred HHhccCCCCcHHHHHHHHHHhcCCCCccCcchHHHHHHHHHH
Q 033363 73 THVTQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFL 114 (121)
Q Consensus 73 ~~L~~lpGIG~~tA~~vl~f~~~~~~~v~p~D~~l~~~~~wl 114 (121)
+.|+++||||+-||..++... +.++ -|+....+..|.++-
T Consensus 2 ~~l~sipGig~~~a~~llaei-gd~~-rF~~~~~l~~~~Gl~ 41 (87)
T PF02371_consen 2 ELLTSIPGIGPITAATLLAEI-GDIS-RFKSAKQLASYAGLA 41 (87)
T ss_pred chhcCCCCccHHHHHHHHHHH-cCch-hcccchhhhhccccc
Confidence 458999999999999999877 6653 688888888886653
No 39
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=95.75 E-value=0.023 Score=40.21 Aligned_cols=65 Identities=12% Similarity=0.089 Sum_probs=47.9
Q ss_pred HHHHHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH---hhHHHhccCCCCcHHHHHHHHHH
Q 033363 18 AGRVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG---ESWTHVTQLHGVGKYAADAFAIF 92 (121)
Q Consensus 18 v~~v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~---~~~~~L~~lpGIG~~tA~~vl~f 92 (121)
+|++=.++- .+...=++-.++.+++++ + =|++..+|+.|.+ . .+.++|..+||||+++.+.+--+
T Consensus 39 ~N~~d~kl~-~~~~kIdiN~A~~~el~~-l--pGigP~~A~~IV~------nGpf~sveDL~~V~GIgekqk~~l~k~ 106 (132)
T PRK02515 39 QNVADAKLG-EFGEKIDLNNSSVRAFRQ-F--PGMYPTLAGKIVK------NAPYDSVEDVLNLPGLSERQKELLEAN 106 (132)
T ss_pred cChhhHHHH-hcCCcccCCccCHHHHHH-C--CCCCHHHHHHHHH------CCCCCCHHHHHcCCCCCHHHHHHHHHh
Confidence 344445555 566677788888888776 3 4777889988872 3 48899999999999988776654
No 40
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=95.58 E-value=0.032 Score=41.46 Aligned_cols=50 Identities=26% Similarity=0.237 Sum_probs=36.3
Q ss_pred HhhcCChhHHHHHHHHH------HHHHHHhhHHHhccCCCCcHHHHHHHHHHhcCC
Q 033363 47 ISTLGLQKKRAPMIKRF------SQEYLGESWTHVTQLHGVGKYAADAFAIFCTGK 96 (121)
Q Consensus 47 i~~~Gl~~~Ka~~i~~~------a~~i~~~~~~~L~~lpGIG~~tA~~vl~f~~~~ 96 (121)
+.-=|....+|+.|.+. .+.+.+++.++|.++||||+++|+.+...--+.
T Consensus 76 ~~i~GIGpk~A~~il~~fg~~~l~~~i~~~d~~~L~~v~Gig~k~A~~I~~~l~~~ 131 (192)
T PRK00116 76 ISVSGVGPKLALAILSGLSPEELVQAIANGDVKALTKVPGIGKKTAERIVLELKDK 131 (192)
T ss_pred hcCCCCCHHHHHHHHHhCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHHH
Confidence 33456667788877664 233555788999999999999999998654443
No 41
>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=95.30 E-value=0.027 Score=34.90 Aligned_cols=58 Identities=21% Similarity=0.334 Sum_probs=39.2
Q ss_pred HHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHH-HhhHHHhccCCCCcHHHHHHHHHH
Q 033363 33 KTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYL-GESWTHVTQLHGVGKYAADAFAIF 92 (121)
Q Consensus 33 ~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~-~~~~~~L~~lpGIG~~tA~~vl~f 92 (121)
=++-.++.++|..++. |+...+++.|.+-=...- -.+.++|.++||||+++++-+.-+
T Consensus 8 invNta~~~~L~~~ip--gig~~~a~~Il~~R~~~g~~~s~~dL~~v~gi~~~~~~~i~~~ 66 (69)
T TIGR00426 8 VNINTATAEELQRAMN--GVGLKKAEAIVSYREEYGPFKTVEDLKQVPGIGNSLVEKNLAV 66 (69)
T ss_pred eECcCCCHHHHHhHCC--CCCHHHHHHHHHHHHHcCCcCCHHHHHcCCCCCHHHHHHHHhh
Confidence 3455678888776554 455456666655422110 047899999999999999988765
No 42
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=95.13 E-value=0.032 Score=34.39 Aligned_cols=51 Identities=22% Similarity=0.378 Sum_probs=31.3
Q ss_pred HhcCCHHHHHHHHhhc-CChhHHHHHHHHHHHHHHH-hhHHHhccCCCCcHHHHHHH
Q 033363 35 ATEVDAEEIEKIISTL-GLQKKRAPMIKRFSQEYLG-ESWTHVTQLHGVGKYAADAF 89 (121)
Q Consensus 35 la~a~~~eL~~~i~~~-Gl~~~Ka~~i~~~a~~i~~-~~~~~L~~lpGIG~~tA~~v 89 (121)
+-.|+.+|| ..+ |++...|+.|.+.=+..-. .+.++|..++|||+.+.+-+
T Consensus 8 iN~as~~eL----~~lpgi~~~~A~~Iv~~R~~~G~f~s~~dL~~v~gi~~~~~~~l 60 (65)
T PF12836_consen 8 INTASAEEL----QALPGIGPKQAKAIVEYREKNGPFKSLEDLKEVPGIGPKTYEKL 60 (65)
T ss_dssp TTTS-HHHH----HTSTT--HHHHHHHHHHHHHH-S-SSGGGGGGSTT--HHHHHHH
T ss_pred CccCCHHHH----HHcCCCCHHHHHHHHHHHHhCcCCCCHHHHhhCCCCCHHHHHHH
Confidence 345677774 344 8888888888765444311 47889999999999987754
No 43
>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=94.62 E-value=0.096 Score=31.54 Aligned_cols=42 Identities=21% Similarity=0.303 Sum_probs=33.3
Q ss_pred HHHHHHHh-CCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHH
Q 033363 21 VISDLFTL-CPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQ 65 (121)
Q Consensus 21 v~~~l~~~-~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~ 65 (121)
...+|.+. |.|+++++.+++++|.++ -|+...+++.|++-++
T Consensus 17 ~a~~L~~~G~~t~~~l~~a~~~~L~~i---~Gig~~~a~~i~~~~~ 59 (60)
T PF14520_consen 17 RAEKLYEAGIKTLEDLANADPEELAEI---PGIGEKTAEKIIEAAR 59 (60)
T ss_dssp HHHHHHHTTCSSHHHHHTSHHHHHHTS---TTSSHHHHHHHHHHHH
T ss_pred HHHHHHhcCCCcHHHHHcCCHHHHhcC---CCCCHHHHHHHHHHHh
Confidence 34456666 999999999999997653 5888899999988765
No 44
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=94.27 E-value=0.054 Score=40.74 Aligned_cols=29 Identities=17% Similarity=0.232 Sum_probs=24.9
Q ss_pred HhhHHHhccCCCCcHHHHHHHHHHhcCCC
Q 033363 69 GESWTHVTQLHGVGKYAADAFAIFCTGKW 97 (121)
Q Consensus 69 ~~~~~~L~~lpGIG~~tA~~vl~f~~~~~ 97 (121)
++..+.|.+|||||+|+|.=+..+-+..+
T Consensus 7 ~~Li~~l~~LPGIG~KsA~RlA~~ll~~~ 35 (195)
T TIGR00615 7 SKLIESLKKLPGIGPKSAQRLAFHLLKRD 35 (195)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHHHcCC
Confidence 45678899999999999999998888764
No 45
>PRK00076 recR recombination protein RecR; Reviewed
Probab=94.20 E-value=0.055 Score=40.71 Aligned_cols=29 Identities=17% Similarity=0.209 Sum_probs=24.9
Q ss_pred HhhHHHhccCCCCcHHHHHHHHHHhcCCC
Q 033363 69 GESWTHVTQLHGVGKYAADAFAIFCTGKW 97 (121)
Q Consensus 69 ~~~~~~L~~lpGIG~~tA~~vl~f~~~~~ 97 (121)
++..+.|.+|||||+|+|.=+..+-+.++
T Consensus 7 ~~Li~~l~~LPGIG~KsA~Rla~~ll~~~ 35 (196)
T PRK00076 7 EKLIEALRKLPGIGPKSAQRLAFHLLQRD 35 (196)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHHHcCC
Confidence 45678899999999999999998888764
No 46
>PRK14973 DNA topoisomerase I; Provisional
Probab=94.18 E-value=0.25 Score=44.92 Aligned_cols=88 Identities=8% Similarity=0.046 Sum_probs=59.8
Q ss_pred HhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHH-HHHH------------hhHHHhccCCCCcHHHHHHHHHHh
Q 033363 27 TLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQ-EYLG------------ESWTHVTQLHGVGKYAADAFAIFC 93 (121)
Q Consensus 27 ~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~-~i~~------------~~~~~L~~lpGIG~~tA~~vl~f~ 93 (121)
..|-++++++.+++++|.. --|++..-...+...+. .... ....+|.+++|||++|.+-.-.-+
T Consensus 821 ~G~~~~~d~~~a~p~~La~---~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~el~~vkg~ge~t~~~l~~ag 897 (936)
T PRK14973 821 AGFDTPEDFCSVHPAYLAL---KTGISPETICRHAKLVCEKLGRPVPEKISKAAFERGRAELLSVPGLGETTLEKLYLAG 897 (936)
T ss_pred hcCCCHHHHHhcCHHHHhc---CCCCChhhHHHHHHHHHHHhcCCCchhhhhhhhcccchhhhhccCCCHHHHHHHHHcC
Confidence 4588999999999999864 47898767666655554 3332 245669999999999997766655
Q ss_pred cCCCCccCcch------------HHHHHHHHHHHHh
Q 033363 94 TGKWDRVRPTD------------HMLNYYWEFLVST 117 (121)
Q Consensus 94 ~~~~~~v~p~D------------~~l~~~~~wl~~~ 117 (121)
.-.++.+.-.| ..+|.+.+|+.-.
T Consensus 898 ~~~~e~l~~~d~~~la~~~~i~~k~~~~~~~~~~~~ 933 (936)
T PRK14973 898 VYDGDLLVSADPKKLAKVTGIDEKKLRNLQAYAKKV 933 (936)
T ss_pred CCCHHHhccCCHHHHhhhcCCCHHHHHHHHHHHhhh
Confidence 54433232223 3567777776543
No 47
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=94.16 E-value=0.35 Score=31.78 Aligned_cols=61 Identities=21% Similarity=0.329 Sum_probs=36.2
Q ss_pred HHHHHHHHhhcCChhHHHHHHHHHHH-----HHHHhhHHHhccCCCCcHHHHHHHHHHhcCCCCccCcchH
Q 033363 40 AEEIEKIISTLGLQKKRAPMIKRFSQ-----EYLGESWTHVTQLHGVGKYAADAFAIFCTGKWDRVRPTDH 105 (121)
Q Consensus 40 ~~eL~~~i~~~Gl~~~Ka~~i~~~a~-----~i~~~~~~~L~~lpGIG~~tA~~vl~f~~~~~~~v~p~D~ 105 (121)
..++...|.+.|++...+..|.+.-. .+.++...-+..++|||-++||.+... +| +.++|.
T Consensus 8 ~~~~~~~L~~~gl~~~~a~kl~~~yg~~ai~~l~~nPY~L~~~i~gi~F~~aD~iA~~-~g----~~~~d~ 73 (94)
T PF14490_consen 8 LRELMAFLQEYGLSPKLAMKLYKKYGDDAIEILKENPYRLIEDIDGIGFKTADKIALK-LG----IEPDDP 73 (94)
T ss_dssp -HHHHHHHHHTT--HHHHHHHHHHH-TTHHHHHHH-STCCCB-SSSSBHHHHHHHHHT-TT------TT-H
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHhHHHHHHHHHChHHHHHHccCCCHHHHHHHHHH-cC----CCCCCH
Confidence 45666678899999888887776522 222233333444999999999999874 44 566664
No 48
>PRK13844 recombination protein RecR; Provisional
Probab=94.12 E-value=0.059 Score=40.69 Aligned_cols=29 Identities=17% Similarity=0.289 Sum_probs=25.1
Q ss_pred HhhHHHhccCCCCcHHHHHHHHHHhcCCC
Q 033363 69 GESWTHVTQLHGVGKYAADAFAIFCTGKW 97 (121)
Q Consensus 69 ~~~~~~L~~lpGIG~~tA~~vl~f~~~~~ 97 (121)
++..+.|.+|||||+|+|.=+..+-+..+
T Consensus 11 ~~LI~~l~~LPGIG~KsA~Rla~~lL~~~ 39 (200)
T PRK13844 11 SAVIESLRKLPTIGKKSSQRLALYLLDKS 39 (200)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHHHcCC
Confidence 45678899999999999999998888764
No 49
>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=94.11 E-value=0.073 Score=36.81 Aligned_cols=58 Identities=19% Similarity=0.311 Sum_probs=39.5
Q ss_pred HHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHH-HhhHHHhccCCCCcHHHHHHHHHH
Q 033363 32 AKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYL-GESWTHVTQLHGVGKYAADAFAIF 92 (121)
Q Consensus 32 ~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~-~~~~~~L~~lpGIG~~tA~~vl~f 92 (121)
+-++-.|+.++|+.+ -|+...+|+.|.+-=+.-- -.++++|..+||||+++++-+.-|
T Consensus 59 ~iniNtA~~~eL~~l---pGIG~~~A~~Ii~~R~~~g~f~s~eeL~~V~GIg~k~~~~i~~~ 117 (120)
T TIGR01259 59 AVNINAASLEELQAL---PGIGPAKAKAIIEYREENGAFKSVDDLTKVSGIGEKSLEKLKDY 117 (120)
T ss_pred CEeCCcCCHHHHhcC---CCCCHHHHHHHHHHHHhcCCcCCHHHHHcCCCCCHHHHHHHHhc
Confidence 445667777777653 4666678877766543210 147889999999999998877644
No 50
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=94.09 E-value=0.17 Score=40.65 Aligned_cols=52 Identities=12% Similarity=0.218 Sum_probs=37.7
Q ss_pred HHHHHHhhcCChhHHHHHHHHHHHHHHH-----hhHHHhccCCCCcHHHHHHHHHHh
Q 033363 42 EIEKIISTLGLQKKRAPMIKRFSQEYLG-----ESWTHVTQLHGVGKYAADAFAIFC 93 (121)
Q Consensus 42 eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-----~~~~~L~~lpGIG~~tA~~vl~f~ 93 (121)
++.+++.-.|=...|.++..++|..+.. .+.++|.+|||||+.+|+-|--+.
T Consensus 12 ~la~l~el~gen~~k~~ay~~Aa~~i~~l~~~i~~~~~l~~lpgIG~~ia~kI~Eil 68 (334)
T smart00483 12 ILAENYEVFGENKRKCSYFRKAASVLKSLPFPINSMKDLKGLPGIGDKIKKKIEEII 68 (334)
T ss_pred HHHHHHHHhcccHHHHHHHHHHHHHHHhCCCCCCCHHHHhcCCCccHHHHHHHHHHH
Confidence 3444444455555677888888887765 466789999999999999887553
No 51
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=93.94 E-value=0.06 Score=40.56 Aligned_cols=29 Identities=21% Similarity=0.217 Sum_probs=24.5
Q ss_pred HhhHHHhccCCCCcHHHHHHHHHHhcCCC
Q 033363 69 GESWTHVTQLHGVGKYAADAFAIFCTGKW 97 (121)
Q Consensus 69 ~~~~~~L~~lpGIG~~tA~~vl~f~~~~~ 97 (121)
++.++.|.+|||||+|+|.=+..+-+.+.
T Consensus 8 ~~LI~~l~kLPGvG~KsA~R~AfhLL~~~ 36 (198)
T COG0353 8 EKLIDALKKLPGVGPKSAQRLAFHLLQRD 36 (198)
T ss_pred HHHHHHHhhCCCCChhHHHHHHHHHHccC
Confidence 45678899999999999999888877663
No 52
>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=93.76 E-value=0.065 Score=35.80 Aligned_cols=31 Identities=13% Similarity=0.259 Sum_probs=25.7
Q ss_pred hhHHHhccCCCCcHHHHHHHHHHhcCCCCcc
Q 033363 70 ESWTHVTQLHGVGKYAADAFAIFCTGKWDRV 100 (121)
Q Consensus 70 ~~~~~L~~lpGIG~~tA~~vl~f~~~~~~~v 100 (121)
+...+|+.|||||+.+|.-+...++..++.+
T Consensus 9 ~~~~~L~~iP~IG~a~a~DL~~LGi~s~~~L 39 (93)
T PF11731_consen 9 AGLSDLTDIPNIGKATAEDLRLLGIRSPADL 39 (93)
T ss_pred HHHHHHhcCCCccHHHHHHHHHcCCCCHHHH
Confidence 4577899999999999999998888765433
No 53
>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=93.66 E-value=0.2 Score=39.72 Aligned_cols=44 Identities=23% Similarity=0.234 Sum_probs=28.0
Q ss_pred CChhHHHHHHHHHHHH--HHH---------hhHHHhccCCCCcHHHHHHHHHHhcCC
Q 033363 51 GLQKKRAPMIKRFSQE--YLG---------ESWTHVTQLHGVGKYAADAFAIFCTGK 96 (121)
Q Consensus 51 Gl~~~Ka~~i~~~a~~--i~~---------~~~~~L~~lpGIG~~tA~~vl~f~~~~ 96 (121)
|....-++.|.++.+. +.. ..+.+|+++|||||++|..+- .+|-
T Consensus 52 giG~~ia~kI~E~~~tG~~~~le~l~~~~~~~l~~l~~i~GiGpk~a~~l~--~lGi 106 (307)
T cd00141 52 GIGKKIAEKIEEILETGKLRKLEELREDVPPGLLLLLRVPGVGPKTARKLY--ELGI 106 (307)
T ss_pred CccHHHHHHHHHHHHcCCHHHHHHHhccchHHHHHHHcCCCCCHHHHHHHH--HcCC
Confidence 6665556666555442 000 145688899999999998776 4443
No 54
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair]
Probab=93.52 E-value=0.13 Score=39.91 Aligned_cols=42 Identities=17% Similarity=0.260 Sum_probs=35.3
Q ss_pred HHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHH
Q 033363 22 ISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQE 66 (121)
Q Consensus 22 ~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~ 66 (121)
...|...|+|.+.+.+|+.+||+++ -|+..+||+.|++..++
T Consensus 208 a~~LL~~FgsLq~~~~AS~~ele~~---~G~G~~kak~l~~~l~~ 249 (254)
T KOG2841|consen 208 AQLLLQKFGSLQQISNASEGELEQC---PGLGPAKAKRLHKFLHQ 249 (254)
T ss_pred HHHHHHhcccHHHHHhcCHhHHHhC---cCcCHHHHHHHHHHHhc
Confidence 3467788999999999999998876 68888999999887654
No 55
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=93.45 E-value=0.086 Score=32.39 Aligned_cols=23 Identities=26% Similarity=0.341 Sum_probs=18.3
Q ss_pred hHHHhccCCCCcHHHHHHHHHHh
Q 033363 71 SWTHVTQLHGVGKYAADAFAIFC 93 (121)
Q Consensus 71 ~~~~L~~lpGIG~~tA~~vl~f~ 93 (121)
+.++|.++||||++.|+.+..+=
T Consensus 12 s~~eL~~lpgi~~~~A~~Iv~~R 34 (65)
T PF12836_consen 12 SAEELQALPGIGPKQAKAIVEYR 34 (65)
T ss_dssp -HHHHHTSTT--HHHHHHHHHHH
T ss_pred CHHHHHHcCCCCHHHHHHHHHHH
Confidence 67899999999999999998875
No 56
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=93.42 E-value=0.53 Score=41.35 Aligned_cols=69 Identities=22% Similarity=0.282 Sum_probs=45.3
Q ss_pred HHHHHHh--CCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH------------------------------
Q 033363 22 ISDLFTL--CPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG------------------------------ 69 (121)
Q Consensus 22 ~~~l~~~--~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~------------------------------ 69 (121)
...|++. -.++++|.++..++|.++ =||...+++.|.+.-+...+
T Consensus 458 i~~L~~~g~I~~i~DL~~L~~~~L~~l---~gfG~Ksa~~ll~~Ie~sk~~~l~R~l~algi~~IG~~~ak~L~~~f~sl 534 (665)
T PRK07956 458 IEQLFEKGLIHDPADLFKLTAEDLLGL---EGFGEKSAQNLLDAIEKSKETSLARFLYALGIRHVGEKAAKALARHFGSL 534 (665)
T ss_pred HHHHHHcCCCCCHHHHHhcCHHHHhcC---cCcchHHHHHHHHHHHHhhcCCHHHhhHhhhccCcCHHHHHHHHHHcCCH
Confidence 3445543 358888888887775442 26776677666554443322
Q ss_pred -----hhHHHhccCCCCcHHHHHHHHHHh
Q 033363 70 -----ESWTHVTQLHGVGKYAADAFAIFC 93 (121)
Q Consensus 70 -----~~~~~L~~lpGIG~~tA~~vl~f~ 93 (121)
.+.++|.+++|||+++|..+..|-
T Consensus 535 ~~l~~As~eeL~~i~GIG~~~A~sI~~ff 563 (665)
T PRK07956 535 EALRAASEEELAAVEGVGEVVAQSIVEFF 563 (665)
T ss_pred HHHHhCCHHHHhccCCcCHHHHHHHHHHH
Confidence 145788889999999998887664
No 57
>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=93.36 E-value=0.06 Score=28.86 Aligned_cols=16 Identities=25% Similarity=0.563 Sum_probs=12.7
Q ss_pred HhccCCCCcHHHHHHH
Q 033363 74 HVTQLHGVGKYAADAF 89 (121)
Q Consensus 74 ~L~~lpGIG~~tA~~v 89 (121)
.+.++||||++|+.-+
T Consensus 12 pi~~~~GIG~kt~~kL 27 (32)
T PF11798_consen 12 PIRKFWGIGKKTAKKL 27 (32)
T ss_dssp BGGGSTTS-HHHHHHH
T ss_pred CHHhhCCccHHHHHHH
Confidence 5789999999999764
No 58
>TIGR00575 dnlj DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.
Probab=93.35 E-value=0.53 Score=41.25 Aligned_cols=69 Identities=19% Similarity=0.257 Sum_probs=42.8
Q ss_pred HHHHHHhC--CCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH------------------------------
Q 033363 22 ISDLFTLC--PDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG------------------------------ 69 (121)
Q Consensus 22 ~~~l~~~~--pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~------------------------------ 69 (121)
...|++.. -++.+|..++.++|.++ =||....++.|.+..+....
T Consensus 445 i~~L~~~g~I~~~~Dl~~L~~~~L~~L---~GfG~Ksa~nIl~~Ie~sk~~~l~r~L~aLgIpgVG~~~ak~L~~~f~sl 521 (652)
T TIGR00575 445 IEQLFEKKLVRSVADLYALKKEDLLEL---EGFGEKSAQNLLNAIEKSKEKPLARLLFALGIRHVGEVTAKNLAKHFGTL 521 (652)
T ss_pred HHHHHHcCCcCCHHHHHhcCHHHHhhc---cCccHHHHHHHHHHHHHhccCcHHHHHhhccCCCcCHHHHHHHHHHhCCH
Confidence 34455432 47888888887775542 26666677766665554332
Q ss_pred -----hhHHHhccCCCCcHHHHHHHHHHh
Q 033363 70 -----ESWTHVTQLHGVGKYAADAFAIFC 93 (121)
Q Consensus 70 -----~~~~~L~~lpGIG~~tA~~vl~f~ 93 (121)
.+.++|.++||||+++|..+..|-
T Consensus 522 ~~l~~As~eeL~~i~GIG~~~A~~I~~ff 550 (652)
T TIGR00575 522 DKLKAASLEELLSVEGVGPKVAESIVNFF 550 (652)
T ss_pred HHHHhCCHHHHhcCCCcCHHHHHHHHHHH
Confidence 134567777777777777776653
No 59
>PRK07945 hypothetical protein; Provisional
Probab=93.12 E-value=0.31 Score=39.18 Aligned_cols=54 Identities=17% Similarity=0.179 Sum_probs=38.8
Q ss_pred HHHHHHHhhcCChhHHHHHHHHHHHHHHHh--h-HH------HhccCCCCcHHHHHHHHHHhc
Q 033363 41 EEIEKIISTLGLQKKRAPMIKRFSQEYLGE--S-WT------HVTQLHGVGKYAADAFAIFCT 94 (121)
Q Consensus 41 ~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~~--~-~~------~L~~lpGIG~~tA~~vl~f~~ 94 (121)
+++..++.--|=..-|.+.-++.|+.+..- . .+ +|.+|||||+-||..+.-+.-
T Consensus 8 ~~~a~lle~~~~n~frv~ayr~aa~~~~~~~~~~~~~~~~~g~l~~~~giG~~~a~~i~e~~~ 70 (335)
T PRK07945 8 RRIAFLLERARADTYRVRAFRRAADVVEALDAAERARRARAGSLTSLPGIGPKTAKVIAQALA 70 (335)
T ss_pred HHHHHHHHHcCCChhhHHHHHHHHHHHHhcChhHHHHHHhcCCcccCCCcCHHHHHHHHHHHh
Confidence 344445555565566888888888887762 1 11 689999999999999887754
No 60
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=92.65 E-value=0.21 Score=35.85 Aligned_cols=53 Identities=19% Similarity=0.333 Sum_probs=30.5
Q ss_pred HhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH-hhHHHhccCCCCcHHHHHHHH
Q 033363 35 ATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG-ESWTHVTQLHGVGKYAADAFA 90 (121)
Q Consensus 35 la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-~~~~~L~~lpGIG~~tA~~vl 90 (121)
+-.|+.+|| +.|..+ ...||+.|++--+.--. .++++|...+|||+++-+-..
T Consensus 91 iNtAs~eeL-~~lpgI--G~~kA~aIi~yRe~~G~f~sv~dL~~v~GiG~~~~ekl~ 144 (149)
T COG1555 91 INTASAEEL-QALPGI--GPKKAQAIIDYREENGPFKSVDDLAKVKGIGPKTLEKLK 144 (149)
T ss_pred ccccCHHHH-HHCCCC--CHHHHHHHHHHHHHcCCCCcHHHHHhccCCCHHHHHHHH
Confidence 445566666 334433 44577666553332211 367788888888888776544
No 61
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=92.61 E-value=0.78 Score=39.63 Aligned_cols=71 Identities=18% Similarity=0.127 Sum_probs=47.1
Q ss_pred HHHHHHHh--CCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH-----------------------------
Q 033363 21 VISDLFTL--CPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG----------------------------- 69 (121)
Q Consensus 21 v~~~l~~~--~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~----------------------------- 69 (121)
....|++. ..++.+|..++.++|.++ =||...+++.|.+.-+.-.+
T Consensus 437 ~i~~L~~~G~i~~~~Diy~L~~~~l~~l---~gfgeks~~nll~aIe~sk~~~l~r~l~aLGI~~vG~~~ak~~~~~i~~ 513 (562)
T PRK08097 437 TWRALHQTGLFEHLFSWLALTPEQLANT---PGIGKARAEQLWHQFNLARQQPFSRWLKALGIPLPQAALNALDDRSWQQ 513 (562)
T ss_pred HHHHHHHcCCcCCHHHHhcCCHHHHhcC---cCccHHHHHHHHHHHHHHcCCCHHHHHHHcCCccHHHHHHHHhcCCHHH
Confidence 34455543 367888888887765442 26666666666554332222
Q ss_pred ---hhHHHhccCCCCcHHHHHHHHHHhc
Q 033363 70 ---ESWTHVTQLHGVGKYAADAFAIFCT 94 (121)
Q Consensus 70 ---~~~~~L~~lpGIG~~tA~~vl~f~~ 94 (121)
.+.++|.+++|||+.+|+++..|--
T Consensus 514 l~~a~~e~l~~i~gIG~~~a~si~~~f~ 541 (562)
T PRK08097 514 LLSRSEQQWQQLPGIGEGRARQLIAFLQ 541 (562)
T ss_pred HHcCCHHHHhcCCCchHHHHHHHHHHHc
Confidence 1457899999999999999987744
No 62
>PF05559 DUF763: Protein of unknown function (DUF763); InterPro: IPR008482 This family consists of several uncharacterised bacterial and archaeal proteins of unknown function.
Probab=92.56 E-value=0.46 Score=38.28 Aligned_cols=40 Identities=15% Similarity=0.215 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHH---hhHHHhccCCCCcHHHHHHHHHHh---cCCC
Q 033363 58 PMIKRFSQEYLG---ESWTHVTQLHGVGKYAADAFAIFC---TGKW 97 (121)
Q Consensus 58 ~~i~~~a~~i~~---~~~~~L~~lpGIG~~tA~~vl~f~---~~~~ 97 (121)
+.+.++.+.+.+ ++.++|+.+|||||+|..++.+.+ +|.|
T Consensus 251 ~~~~~~l~~~~e~~p~~feeLL~~~GvGp~TlRALaLvaelIyg~p 296 (319)
T PF05559_consen 251 RRLWKVLEKAYERQPSDFEELLLIKGVGPSTLRALALVAELIYGVP 296 (319)
T ss_pred HHHHHHHHHHhhCCccCHHHHHhcCCCCHHHHHHHHHHHHHHcCCC
Confidence 344455555555 689999999999999999988876 4554
No 63
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=92.55 E-value=0.11 Score=37.27 Aligned_cols=24 Identities=25% Similarity=0.300 Sum_probs=21.6
Q ss_pred hHHHhccCCCCcHHHHHHHHHHhc
Q 033363 71 SWTHVTQLHGVGKYAADAFAIFCT 94 (121)
Q Consensus 71 ~~~~L~~lpGIG~~tA~~vl~f~~ 94 (121)
+.++|..|||||++.|..|..+--
T Consensus 95 s~eeL~~lpgIG~~kA~aIi~yRe 118 (149)
T COG1555 95 SAEELQALPGIGPKKAQAIIDYRE 118 (149)
T ss_pred CHHHHHHCCCCCHHHHHHHHHHHH
Confidence 678999999999999999998763
No 64
>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=92.36 E-value=0.14 Score=35.43 Aligned_cols=23 Identities=26% Similarity=0.365 Sum_probs=21.0
Q ss_pred hHHHhccCCCCcHHHHHHHHHHh
Q 033363 71 SWTHVTQLHGVGKYAADAFAIFC 93 (121)
Q Consensus 71 ~~~~L~~lpGIG~~tA~~vl~f~ 93 (121)
+.++|.++||||++.|..++.+-
T Consensus 66 ~~~eL~~lpGIG~~~A~~Ii~~R 88 (120)
T TIGR01259 66 SLEELQALPGIGPAKAKAIIEYR 88 (120)
T ss_pred CHHHHhcCCCCCHHHHHHHHHHH
Confidence 67899999999999999999874
No 65
>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=92.05 E-value=0.14 Score=30.51 Aligned_cols=24 Identities=21% Similarity=0.155 Sum_probs=17.0
Q ss_pred HHHhccCCCCcHHHHHHHHHHhcC
Q 033363 72 WTHVTQLHGVGKYAADAFAIFCTG 95 (121)
Q Consensus 72 ~~~L~~lpGIG~~tA~~vl~f~~~ 95 (121)
++.++.+.||||.||.-....++.
T Consensus 1 l~~f~~I~GVG~~tA~~w~~~G~r 24 (52)
T PF10391_consen 1 LKLFTGIWGVGPKTARKWYAKGIR 24 (52)
T ss_dssp HHHHHTSTT--HHHHHHHHHTT--
T ss_pred CcchhhcccccHHHHHHHHHhCCC
Confidence 367899999999999998876654
No 66
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=91.98 E-value=0.35 Score=42.50 Aligned_cols=24 Identities=13% Similarity=0.217 Sum_probs=20.3
Q ss_pred hHHHhccCCCCcHHHHHHHHHHhc
Q 033363 71 SWTHVTQLHGVGKYAADAFAIFCT 94 (121)
Q Consensus 71 ~~~~L~~lpGIG~~tA~~vl~f~~ 94 (121)
+.++|.+++|||+.+|+.+..|--
T Consensus 539 ~~e~l~~i~giG~~~a~si~~ff~ 562 (669)
T PRK14350 539 ALSKLLKIKGIGEKIALNIIEAFN 562 (669)
T ss_pred CHHHHhhCCCccHHHHHHHHHHHc
Confidence 556899999999999999987653
No 67
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=91.45 E-value=0.45 Score=41.81 Aligned_cols=24 Identities=21% Similarity=0.369 Sum_probs=20.8
Q ss_pred hHHHhccCCCCcHHHHHHHHHHhc
Q 033363 71 SWTHVTQLHGVGKYAADAFAIFCT 94 (121)
Q Consensus 71 ~~~~L~~lpGIG~~tA~~vl~f~~ 94 (121)
+.++|.++||||+.+|..+.-|--
T Consensus 541 ~~e~l~~i~giG~~vA~si~~ff~ 564 (667)
T COG0272 541 SEEELASIPGIGEVVARSIIEFFA 564 (667)
T ss_pred CHHHHhhccchhHHHHHHHHHHHc
Confidence 678999999999999999987644
No 68
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=91.06 E-value=0.75 Score=37.58 Aligned_cols=48 Identities=17% Similarity=0.250 Sum_probs=38.7
Q ss_pred HHHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHHh
Q 033363 20 RVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGE 70 (121)
Q Consensus 20 ~v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~~ 70 (121)
++..++.++|.|.+.+.+|+.++|.++ . |+...||+.|++.++.+.+.
T Consensus 298 ~iAk~Ll~~FGSL~~Il~As~eeL~~V-e--GIGe~rA~~I~e~l~Rl~e~ 345 (352)
T PRK13482 298 AVIENLVEHFGSLQGLLAASIEDLDEV-E--GIGEVRARAIREGLSRLAEQ 345 (352)
T ss_pred HHHHHHHHHcCCHHHHHcCCHHHHhhC-C--CcCHHHHHHHHHHHHHHHHH
Confidence 667788899999999999999997653 3 56678899999988887664
No 69
>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=90.95 E-value=0.2 Score=37.38 Aligned_cols=22 Identities=27% Similarity=0.347 Sum_probs=18.5
Q ss_pred hhHHHhccCCCCcHHHHHHHHH
Q 033363 70 ESWTHVTQLHGVGKYAADAFAI 91 (121)
Q Consensus 70 ~~~~~L~~lpGIG~~tA~~vl~ 91 (121)
+....|.++||||||+|-.++.
T Consensus 69 ~lF~~L~~V~GIGpK~Al~iL~ 90 (191)
T TIGR00084 69 ELFKELIKVNGVGPKLALAILS 90 (191)
T ss_pred HHHHHHhCCCCCCHHHHHHHHh
Confidence 3467899999999999988854
No 70
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=90.79 E-value=0.2 Score=37.19 Aligned_cols=31 Identities=23% Similarity=0.288 Sum_probs=23.3
Q ss_pred cCChhHHHHHHHHHHHHHHHhhHHHhccCCCCcHHHHHHHHH
Q 033363 50 LGLQKKRAPMIKRFSQEYLGESWTHVTQLHGVGKYAADAFAI 91 (121)
Q Consensus 50 ~Gl~~~Ka~~i~~~a~~i~~~~~~~L~~lpGIG~~tA~~vl~ 91 (121)
.||.+.+.+.+ ...|.++|||||++|..++.
T Consensus 61 ~gF~~~~ek~~-----------f~~L~~i~GIGpk~A~~il~ 91 (192)
T PRK00116 61 YGFLTKEEREL-----------FRLLISVSGVGPKLALAILS 91 (192)
T ss_pred cCcCCHHHHHH-----------HHHHhcCCCCCHHHHHHHHH
Confidence 67775544433 44689999999999998875
No 71
>PRK08609 hypothetical protein; Provisional
Probab=90.72 E-value=0.74 Score=39.63 Aligned_cols=20 Identities=15% Similarity=0.200 Sum_probs=16.7
Q ss_pred hHHHhccCCCCcHHHHHHHH
Q 033363 71 SWTHVTQLHGVGKYAADAFA 90 (121)
Q Consensus 71 ~~~~L~~lpGIG~~tA~~vl 90 (121)
...+|+++|||||+||..+-
T Consensus 86 ~~~~l~~i~GiGpk~a~~l~ 105 (570)
T PRK08609 86 GLLPLLKLPGLGGKKIAKLY 105 (570)
T ss_pred HHHHHhcCCCCCHHHHHHHH
Confidence 56789999999999996665
No 72
>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=90.45 E-value=2.3 Score=31.52 Aligned_cols=52 Identities=13% Similarity=0.280 Sum_probs=37.7
Q ss_pred HHHHHHHHHHhCC--CHHHHhcCCHHHHHHHHhhcCC--hhHHHHHHHHHHHHHHH
Q 033363 18 AGRVISDLFTLCP--DAKTATEVDAEEIEKIISTLGL--QKKRAPMIKRFSQEYLG 69 (121)
Q Consensus 18 v~~v~~~l~~~~p--t~~~la~a~~~eL~~~i~~~Gl--~~~Ka~~i~~~a~~i~~ 69 (121)
+.+=.+.|.+.|- +|+.++..++++++++++.-|+ .+.|.+.++.=|+.+.+
T Consensus 44 Il~Kr~~~r~aF~~Fd~~~vA~~~e~~ie~l~~d~~iIRnr~KI~Avi~NA~~~l~ 99 (179)
T PF03352_consen 44 ILKKREAFREAFAGFDPEKVAKMDEEDIERLMQDPGIIRNRRKIRAVINNARAILK 99 (179)
T ss_dssp HHHTHHHHHHHTGGGHHHHHHT--HHHHHHHTTSTTSS--HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHCCCHHHHHcCCHHHHHHHhcCcchhhhHHHHHHHHHHHHHHHH
Confidence 3344455556665 6899999999999999998888 66777778877887776
No 73
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=90.24 E-value=1 Score=31.05 Aligned_cols=58 Identities=10% Similarity=0.171 Sum_probs=42.4
Q ss_pred CCCHHHHhcCCHHHHHH--HHhhcCChhHHHHHHHHHHHHHHHhhHHHhccCCCCcHHHHHHHHHHhcC
Q 033363 29 CPDAKTATEVDAEEIEK--IISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLHGVGKYAADAFAIFCTG 95 (121)
Q Consensus 29 ~pt~~~la~a~~~eL~~--~i~~~Gl~~~Ka~~i~~~a~~i~~~~~~~L~~lpGIG~~tA~~vl~f~~~ 95 (121)
.-|+++|.+.+.+...+ +.+..|...+.-..+. .+.+|..+||||+..|..+.--+..
T Consensus 16 I~t~~~Ll~~~~~~~~r~~La~~~~i~~~~l~~w~---------~~AdL~ri~gi~~~~a~LL~~AGv~ 75 (122)
T PF14229_consen 16 IKTTGDLLEAGDTPLGRKALAKKLGISERNLLKWV---------NQADLMRIPGIGPQYAELLEHAGVD 75 (122)
T ss_pred CCcHHHHHHcCCCHHHHHHHHHhcCCCHHHHHHHH---------hHHHhhhcCCCCHHHHHHHHHhCcC
Confidence 35888888888887776 6777888743333332 3457889999999999888876664
No 74
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=89.99 E-value=0.28 Score=36.65 Aligned_cols=22 Identities=14% Similarity=0.228 Sum_probs=19.4
Q ss_pred hhHHHhccCCCCcHHHHHHHHH
Q 033363 70 ESWTHVTQLHGVGKYAADAFAI 91 (121)
Q Consensus 70 ~~~~~L~~lpGIG~~tA~~vl~ 91 (121)
+....|.+++||||++|-.++.
T Consensus 70 ~lF~~Li~V~GIGpK~Al~ILs 91 (194)
T PRK14605 70 SLFETLIDVSGIGPKLGLAMLS 91 (194)
T ss_pred HHHHHHhCCCCCCHHHHHHHHH
Confidence 3467899999999999999987
No 75
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=89.99 E-value=0.25 Score=27.20 Aligned_cols=17 Identities=18% Similarity=0.370 Sum_probs=13.9
Q ss_pred HhccCCCCcHHHHHHHH
Q 033363 74 HVTQLHGVGKYAADAFA 90 (121)
Q Consensus 74 ~L~~lpGIG~~tA~~vl 90 (121)
-+..+||||++||--++
T Consensus 17 ni~Gv~giG~ktA~~ll 33 (36)
T smart00279 17 NIPGVKGIGPKTALKLL 33 (36)
T ss_pred CCCCCCcccHHHHHHHH
Confidence 35689999999998665
No 76
>PRK00024 hypothetical protein; Reviewed
Probab=89.96 E-value=0.46 Score=36.23 Aligned_cols=51 Identities=18% Similarity=0.324 Sum_probs=34.2
Q ss_pred cCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH----------hhHHHhccCCCCcHHHHHHHH
Q 033363 37 EVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG----------ESWTHVTQLHGVGKYAADAFA 90 (121)
Q Consensus 37 ~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~----------~~~~~L~~lpGIG~~tA~~vl 90 (121)
..+..||.+++=..|.. .+..+.+|+.+.+ -+.++|.+++|||+..|..++
T Consensus 23 ~Lsd~ELLa~lL~~g~~---~~~~~~LA~~LL~~fgsL~~l~~as~~eL~~i~GIG~akA~~L~ 83 (224)
T PRK00024 23 ALSDAELLAILLRTGTK---GKSVLDLARELLQRFGSLRGLLDASLEELQSIKGIGPAKAAQLK 83 (224)
T ss_pred cCCHHHHHHHHHcCCCC---CCCHHHHHHHHHHHcCCHHHHHhCCHHHHhhccCccHHHHHHHH
Confidence 34566777666444543 3455666776665 267899999999999885543
No 77
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=89.57 E-value=0.77 Score=35.46 Aligned_cols=40 Identities=18% Similarity=0.160 Sum_probs=24.9
Q ss_pred HHHHHh-CCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHH
Q 033363 23 SDLFTL-CPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQ 65 (121)
Q Consensus 23 ~~l~~~-~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~ 65 (121)
..|++. |.|.++|..|+.++|.++ -|++..+|+.|++...
T Consensus 17 kkLl~~GF~Sve~Ik~AS~eEL~~V---~GIg~k~AekI~e~l~ 57 (232)
T PRK12766 17 EALREAGFESVEDVRAADQSELAEV---DGIGNALAARIKADVG 57 (232)
T ss_pred HHHHHcCCCCHHHHHhCCHHHHHHc---cCCCHHHHHHHHHHhc
Confidence 345555 777777777777775432 3666666666666554
No 78
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=89.45 E-value=1.5 Score=26.79 Aligned_cols=43 Identities=23% Similarity=0.207 Sum_probs=29.5
Q ss_pred HHHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHH
Q 033363 20 RVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQ 65 (121)
Q Consensus 20 ~v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~ 65 (121)
..-..|.+.|+|.+.+.+++.++|.++ =|+....|+.|.+.-+
T Consensus 14 ~~ak~L~~~f~sl~~l~~a~~e~L~~i---~gIG~~~A~si~~ff~ 56 (64)
T PF12826_consen 14 KTAKLLAKHFGSLEALMNASVEELSAI---PGIGPKIAQSIYEFFQ 56 (64)
T ss_dssp HHHHHHHHCCSCHHHHCC--HHHHCTS---TT--HHHHHHHHHHHH
T ss_pred HHHHHHHHHcCCHHHHHHcCHHHHhcc---CCcCHHHHHHHHHHHC
Confidence 345678899999999999999996542 3677778888876544
No 79
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=89.01 E-value=0.55 Score=37.76 Aligned_cols=21 Identities=29% Similarity=0.317 Sum_probs=18.3
Q ss_pred hHHHhccCCCCcHHHHHHHHH
Q 033363 71 SWTHVTQLHGVGKYAADAFAI 91 (121)
Q Consensus 71 ~~~~L~~lpGIG~~tA~~vl~ 91 (121)
.+.+|+++|||||+||..+--
T Consensus 87 ~l~~l~~i~GiGpk~a~~l~~ 107 (334)
T smart00483 87 SLKLFTNVFGVGPKTAAKWYR 107 (334)
T ss_pred HHHHHHccCCcCHHHHHHHHH
Confidence 578999999999999977754
No 80
>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=88.57 E-value=0.64 Score=36.91 Aligned_cols=53 Identities=21% Similarity=0.311 Sum_probs=38.9
Q ss_pred HHHHHHhhcCChhHHHHHHHHHHHHHHH-----hhHHHhccCCCCcHHHHHHHHHHhc
Q 033363 42 EIEKIISTLGLQKKRAPMIKRFSQEYLG-----ESWTHVTQLHGVGKYAADAFAIFCT 94 (121)
Q Consensus 42 eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-----~~~~~L~~lpGIG~~tA~~vl~f~~ 94 (121)
++..++.--|=-..|++.-.++|..+.. .+.+++.++||||+.+|+.|--+.-
T Consensus 9 ~ia~~~e~~~~~~~r~~aY~~Aa~~l~~l~~~i~~~~~~~~ipgiG~~ia~kI~E~~~ 66 (307)
T cd00141 9 ELADLLELLGGNPFRVRAYRKAARALESLPEPIESLEEAKKLPGIGKKIAEKIEEILE 66 (307)
T ss_pred HHHHHHHhccCCcchHHHHHHHHHHHHhCCcccCCHHHhcCCCCccHHHHHHHHHHHH
Confidence 3444444444334688888888888776 7778999999999999999877654
No 81
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=88.48 E-value=0.39 Score=34.02 Aligned_cols=21 Identities=19% Similarity=0.061 Sum_probs=19.2
Q ss_pred hHHHhccCCCCcHHHHHHHHH
Q 033363 71 SWTHVTQLHGVGKYAADAFAI 91 (121)
Q Consensus 71 ~~~~L~~lpGIG~~tA~~vl~ 91 (121)
+.++|.++|||||..|..|..
T Consensus 59 ~~~el~~lpGigP~~A~~IV~ 79 (132)
T PRK02515 59 SVRAFRQFPGMYPTLAGKIVK 79 (132)
T ss_pred CHHHHHHCCCCCHHHHHHHHH
Confidence 678999999999999999984
No 82
>PRK00024 hypothetical protein; Reviewed
Probab=88.28 E-value=0.76 Score=35.02 Aligned_cols=49 Identities=14% Similarity=0.137 Sum_probs=37.5
Q ss_pred HHHHHHHHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHH
Q 033363 15 LLKAGRVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQE 66 (121)
Q Consensus 15 ~~~v~~v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~ 66 (121)
+..|.+...+++++|++...+.+++++||.+ + -|+...||..|..+.+.
T Consensus 40 ~~~~~~LA~~LL~~fgsL~~l~~as~~eL~~-i--~GIG~akA~~L~a~~El 88 (224)
T PRK00024 40 GKSVLDLARELLQRFGSLRGLLDASLEELQS-I--KGIGPAKAAQLKAALEL 88 (224)
T ss_pred CCCHHHHHHHHHHHcCCHHHHHhCCHHHHhh-c--cCccHHHHHHHHHHHHH
Confidence 3457788999999999999999999999765 3 46666788766554443
No 83
>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=87.40 E-value=0.35 Score=30.62 Aligned_cols=25 Identities=16% Similarity=0.183 Sum_probs=19.5
Q ss_pred hHHHhccCCCCcHHHHHHHHHHhcCC
Q 033363 71 SWTHVTQLHGVGKYAADAFAIFCTGK 96 (121)
Q Consensus 71 ~~~~L~~lpGIG~~tA~~vl~f~~~~ 96 (121)
.-+.+..+||||++||.-++. -++.
T Consensus 20 ~~D~i~gv~giG~k~A~~ll~-~~~~ 44 (75)
T cd00080 20 KSDNIPGVPGIGPKTALKLLK-EYGS 44 (75)
T ss_pred ccccCCCCCcccHHHHHHHHH-HhCC
Confidence 456688999999999998885 3443
No 84
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=87.31 E-value=0.82 Score=40.39 Aligned_cols=69 Identities=10% Similarity=0.112 Sum_probs=39.8
Q ss_pred HHHHHHHhC--CCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH-----------------------------
Q 033363 21 VISDLFTLC--PDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG----------------------------- 69 (121)
Q Consensus 21 v~~~l~~~~--pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~----------------------------- 69 (121)
....|++.. -++.+|..+..++|.++ -||...+++.|.+--+.-.+
T Consensus 474 ~i~~L~~~g~V~~~~Dl~~L~~~~L~~l---~g~g~Ksa~~Ll~~Ie~sk~~~l~r~l~ALgIpgIG~~~ak~L~~~F~s 550 (689)
T PRK14351 474 RVQQLVDAGLVESLADLYDLTVADLAEL---EGWGETSAENLLAELEASREPPLADFLVALGIPEVGPTTARNLAREFGT 550 (689)
T ss_pred HHHHHHHcCCCCCHHHHHHcCHHHHhcC---cCcchhHHHHHHHHHHHHccCCHHHHHHHcCCCCcCHHHHHHHHHHhCC
Confidence 344455432 47777777777664432 25555555554443332221
Q ss_pred ------hhHHHhccCCCCcHHHHHHHHHH
Q 033363 70 ------ESWTHVTQLHGVGKYAADAFAIF 92 (121)
Q Consensus 70 ------~~~~~L~~lpGIG~~tA~~vl~f 92 (121)
.+.++|.+++|||+++|+.+..|
T Consensus 551 i~~L~~As~eeL~~i~GIG~k~A~sI~~f 579 (689)
T PRK14351 551 FEAIMDADEEALRAVDDVGPTVAEEIREF 579 (689)
T ss_pred HHHHHhCCHHHHhccCCcCHHHHHHHHHH
Confidence 14567778888888888777665
No 85
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=87.15 E-value=1.1 Score=36.30 Aligned_cols=41 Identities=20% Similarity=0.222 Sum_probs=31.1
Q ss_pred hHHHHHHHHHHHHHHH-----hhHHHhccCCCCcHHHHHHHHHHhc
Q 033363 54 KKRAPMIKRFSQEYLG-----ESWTHVTQLHGVGKYAADAFAIFCT 94 (121)
Q Consensus 54 ~~Ka~~i~~~a~~i~~-----~~~~~L~~lpGIG~~tA~~vl~f~~ 94 (121)
.-|+..-..++..+.. .+.+++.+|||||+++|..|--|.-
T Consensus 32 ~~r~~~y~~Aasvlk~~p~~I~S~~ea~~lP~iG~kia~ki~Eile 77 (353)
T KOG2534|consen 32 EDRARAYRRAASVLKSLPFPITSGEEAEKLPGIGPKIAEKIQEILE 77 (353)
T ss_pred HHHHHHHHHHHHHHHhCCCCcccHHHhcCCCCCCHHHHHHHHHHHH
Confidence 3566666666666655 4789999999999999999876653
No 86
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=86.88 E-value=2.3 Score=34.38 Aligned_cols=53 Identities=19% Similarity=0.217 Sum_probs=38.1
Q ss_pred HHHHHHHhhcCChhHHHHHHHHHHHHHHHh------hHH--HhccCCCCcHHHHHHHHHHh
Q 033363 41 EEIEKIISTLGLQKKRAPMIKRFSQEYLGE------SWT--HVTQLHGVGKYAADAFAIFC 93 (121)
Q Consensus 41 ~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~~------~~~--~L~~lpGIG~~tA~~vl~f~ 93 (121)
+++...+.-.|=..-|++.-++.|+.+.+. ..+ .+++|||||+-+|+.+.-|-
T Consensus 13 e~iA~~me~~Gen~fk~~aYr~Aa~sle~~~e~~~ei~e~~~~t~l~gIGk~ia~~I~e~l 73 (326)
T COG1796 13 ERIADYMELEGENPFKIRAYRKAAQSLENLTEDLEEIEERGRLTELPGIGKGIAEKISEYL 73 (326)
T ss_pred HHHHHHHHhcCCCccchHHHHHHHHhhhhcccchHHHHhhcccCCCCCccHHHHHHHHHHH
Confidence 445555555666557888888888887761 222 38899999999999987665
No 87
>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=85.98 E-value=1.3 Score=27.44 Aligned_cols=43 Identities=21% Similarity=0.244 Sum_probs=27.5
Q ss_pred HhhcCChhHHHHHHHHHHH-----HHHHhhHHHhccCCCCcHHHHHHHH
Q 033363 47 ISTLGLQKKRAPMIKRFSQ-----EYLGESWTHVTQLHGVGKYAADAFA 90 (121)
Q Consensus 47 i~~~Gl~~~Ka~~i~~~a~-----~i~~~~~~~L~~lpGIG~~tA~~vl 90 (121)
|..+||+ .|+.+...-+. .++.-+.++|.++||+|+++.+-+.
T Consensus 14 I~~L~LS-~Ra~n~L~~~~I~tv~dL~~~s~~~L~~i~n~G~ksl~EI~ 61 (66)
T PF03118_consen 14 IEDLGLS-VRAYNCLKRAGIHTVGDLVKYSEEDLLKIKNFGKKSLEEIK 61 (66)
T ss_dssp GGGSTSB-HHHHHHHHCTT--BHHHHHCS-HHHHHTSTTSHHHHHHHHH
T ss_pred HHHhCCC-HHHHHHHHHhCCcCHHHHHhCCHHHHHhCCCCCHhHHHHHH
Confidence 5568898 55544433222 1222367899999999999988664
No 88
>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=85.74 E-value=0.92 Score=27.85 Aligned_cols=22 Identities=23% Similarity=0.447 Sum_probs=19.5
Q ss_pred hHHHhcc-CCCCcHHHHHHHHHH
Q 033363 71 SWTHVTQ-LHGVGKYAADAFAIF 92 (121)
Q Consensus 71 ~~~~L~~-lpGIG~~tA~~vl~f 92 (121)
..++|.. +||||+.+|..++.+
T Consensus 14 ~~~~L~~~ipgig~~~a~~Il~~ 36 (69)
T TIGR00426 14 TAEELQRAMNGVGLKKAEAIVSY 36 (69)
T ss_pred CHHHHHhHCCCCCHHHHHHHHHH
Confidence 4568888 999999999999987
No 89
>PRK00254 ski2-like helicase; Provisional
Probab=84.63 E-value=3.1 Score=36.50 Aligned_cols=43 Identities=12% Similarity=0.189 Sum_probs=28.5
Q ss_pred cCChhHHHHHHHHH----HHHHHHhhHHHhccCCCCcHHHHHHHHHH
Q 033363 50 LGLQKKRAPMIKRF----SQEYLGESWTHVTQLHGVGKYAADAFAIF 92 (121)
Q Consensus 50 ~Gl~~~Ka~~i~~~----a~~i~~~~~~~L~~lpGIG~~tA~~vl~f 92 (121)
-|+.+.|++.+.+. -..+.+.+.++|.++||||+++|..+..+
T Consensus 651 pgig~~~~~~l~~~g~~s~~~i~~a~~~el~~~~gi~~~~a~~i~~~ 697 (720)
T PRK00254 651 PMIGRKRARALYNAGFRSIEDIVNAKPSELLKVEGIGAKIVEGIFKH 697 (720)
T ss_pred CCCCHHHHHHHHHccCCCHHHHHhCCHHHHhcCCCCCHHHHHHHHHH
Confidence 36666666666655 22333346777888888888888887665
No 90
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=83.85 E-value=0.88 Score=34.23 Aligned_cols=22 Identities=23% Similarity=0.306 Sum_probs=19.0
Q ss_pred hhHHHhccCCCCcHHHHHHHHH
Q 033363 70 ESWTHVTQLHGVGKYAADAFAI 91 (121)
Q Consensus 70 ~~~~~L~~lpGIG~~tA~~vl~ 91 (121)
+..+.|.++.|||||+|=.+|.
T Consensus 69 ~lF~~LisVsGIGPK~ALaILs 90 (196)
T PRK13901 69 EVFEELIGVDGIGPRAALRVLS 90 (196)
T ss_pred HHHHHHhCcCCcCHHHHHHHHc
Confidence 3467899999999999988884
No 91
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=83.80 E-value=2 Score=32.68 Aligned_cols=47 Identities=13% Similarity=0.164 Sum_probs=36.5
Q ss_pred HHHHHHHHHHHhC---CCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHH
Q 033363 17 KAGRVISDLFTLC---PDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQE 66 (121)
Q Consensus 17 ~v~~v~~~l~~~~---pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~ 66 (121)
.+.+...+++++| ++...+.+++++||.+ ++ |....||..|..+.+.
T Consensus 33 ~~~~lA~~ll~~f~~~g~l~~l~~a~~~eL~~-i~--GiG~aka~~l~a~~El 82 (218)
T TIGR00608 33 DVLSLSKRLLDVFGRQDSLGHLLSAPPEELSS-VP--GIGEAKAIQLKAAVEL 82 (218)
T ss_pred CHHHHHHHHHHHhcccCCHHHHHhCCHHHHHh-Cc--CCcHHHHHHHHHHHHH
Confidence 5778888999998 8999999999999876 34 5555688777655443
No 92
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=83.70 E-value=0.88 Score=33.85 Aligned_cols=22 Identities=14% Similarity=0.166 Sum_probs=19.0
Q ss_pred hhHHHhccCCCCcHHHHHHHHH
Q 033363 70 ESWTHVTQLHGVGKYAADAFAI 91 (121)
Q Consensus 70 ~~~~~L~~lpGIG~~tA~~vl~ 91 (121)
+..+.|.++.|||||+|=.+|.
T Consensus 70 ~lF~~LisV~GIGpK~Al~iLs 91 (186)
T PRK14600 70 DCLRMLVKVSGVNYKTAMSILS 91 (186)
T ss_pred HHHHHHhCcCCcCHHHHHHHHc
Confidence 3467899999999999988886
No 93
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=83.47 E-value=0.92 Score=33.70 Aligned_cols=22 Identities=18% Similarity=0.345 Sum_probs=18.9
Q ss_pred hhHHHhccCCCCcHHHHHHHHH
Q 033363 70 ESWTHVTQLHGVGKYAADAFAI 91 (121)
Q Consensus 70 ~~~~~L~~lpGIG~~tA~~vl~ 91 (121)
+..+.|.++.|||||+|=.+|.
T Consensus 70 ~lF~~Li~VsGIGpK~Al~ILs 91 (183)
T PRK14601 70 KMFEMLLKVNGIGANTAMAVCS 91 (183)
T ss_pred HHHHHHhccCCccHHHHHHHHc
Confidence 3567899999999999988885
No 94
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=82.74 E-value=1.1 Score=33.37 Aligned_cols=21 Identities=14% Similarity=0.146 Sum_probs=18.3
Q ss_pred hHHHhccCCCCcHHHHHHHHH
Q 033363 71 SWTHVTQLHGVGKYAADAFAI 91 (121)
Q Consensus 71 ~~~~L~~lpGIG~~tA~~vl~ 91 (121)
..+.|.++.|||||+|=.+|.
T Consensus 71 lF~~Li~V~GIGpK~AL~iLs 91 (188)
T PRK14606 71 LFLSLTKVSRLGPKTALKIIS 91 (188)
T ss_pred HHHHHhccCCccHHHHHHHHc
Confidence 467899999999999988884
No 95
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=82.51 E-value=1.1 Score=33.55 Aligned_cols=21 Identities=24% Similarity=0.210 Sum_probs=18.6
Q ss_pred hHHHhccCCCCcHHHHHHHHH
Q 033363 71 SWTHVTQLHGVGKYAADAFAI 91 (121)
Q Consensus 71 ~~~~L~~lpGIG~~tA~~vl~ 91 (121)
....|.++.|||||+|=.+|.
T Consensus 70 lF~~L~~V~GIGpK~AL~iLs 90 (197)
T PRK14603 70 LFELLLGVSGVGPKLALALLS 90 (197)
T ss_pred HHHHHhCcCCcCHHHHHHHHc
Confidence 467899999999999988886
No 96
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=82.51 E-value=1.2 Score=33.53 Aligned_cols=21 Identities=19% Similarity=0.197 Sum_probs=18.6
Q ss_pred hHHHhccCCCCcHHHHHHHHH
Q 033363 71 SWTHVTQLHGVGKYAADAFAI 91 (121)
Q Consensus 71 ~~~~L~~lpGIG~~tA~~vl~ 91 (121)
....|.++.|||||+|=.+|.
T Consensus 72 lF~~Li~V~GIGpK~Al~iLs 92 (203)
T PRK14602 72 TFIVLISISKVGAKTALAILS 92 (203)
T ss_pred HHHHHhCCCCcCHHHHHHHHh
Confidence 466799999999999998886
No 97
>PRK09482 flap endonuclease-like protein; Provisional
Probab=82.40 E-value=1.5 Score=34.20 Aligned_cols=30 Identities=17% Similarity=0.173 Sum_probs=22.1
Q ss_pred HHHHhhHHHhccCCCCcHHHHHHHHHHhcCC
Q 033363 66 EYLGESWTHVTQLHGVGKYAADAFAIFCTGK 96 (121)
Q Consensus 66 ~i~~~~~~~L~~lpGIG~~tA~~vl~f~~~~ 96 (121)
.+..++-+-+..+||||||||.-++. -+|-
T Consensus 175 aL~GD~sDnIpGVpGIG~KtA~~LL~-~~gs 204 (256)
T PRK09482 175 GLAGISSSKIPGVAGIGPKSAAELLN-QFRS 204 (256)
T ss_pred HHhCCCccCCCCCCCcChHHHHHHHH-HhCC
Confidence 34445667789999999999988775 3443
No 98
>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=81.86 E-value=4.5 Score=24.59 Aligned_cols=43 Identities=12% Similarity=0.224 Sum_probs=33.6
Q ss_pred HHHHHHhCCC-HHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHH
Q 033363 22 ISDLFTLCPD-AKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYL 68 (121)
Q Consensus 22 ~~~l~~~~pt-~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~ 68 (121)
......+|++ |+++..++-.+ ++..|..-+--+||....+.+.
T Consensus 12 ~~~~~~kf~~~w~~lf~~~s~~----LK~~GIp~r~RryiL~~~ek~r 55 (57)
T PF09597_consen 12 CEEHAEKFESDWEKLFTTSSKQ----LKELGIPVRQRRYILRWREKYR 55 (57)
T ss_pred HHHHHHHHHHHHHHHHhcCHHH----HHHCCCCHHHHHHHHHHHHHHh
Confidence 3455567888 99999999988 6778998777788887776653
No 99
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=81.78 E-value=3.4 Score=31.92 Aligned_cols=47 Identities=13% Similarity=0.244 Sum_probs=37.1
Q ss_pred cCChhHHHHHHHHH----HHHHHHhhHHHhccCCCCcHHHHHHHHHHhcCCC
Q 033363 50 LGLQKKRAPMIKRF----SQEYLGESWTHVTQLHGVGKYAADAFAIFCTGKW 97 (121)
Q Consensus 50 ~Gl~~~Ka~~i~~~----a~~i~~~~~~~L~~lpGIG~~tA~~vl~f~~~~~ 97 (121)
-|....+++.|.+. .+.+...+.++|.++||||+.+|..+..+ ++.+
T Consensus 9 pGIG~krakkLl~~GF~Sve~Ik~AS~eEL~~V~GIg~k~AekI~e~-l~~~ 59 (232)
T PRK12766 9 SGVGPSKAEALREAGFESVEDVRAADQSELAEVDGIGNALAARIKAD-VGGL 59 (232)
T ss_pred CCcCHHHHHHHHHcCCCCHHHHHhCCHHHHHHccCCCHHHHHHHHHH-hccc
Confidence 46667788888776 55666678999999999999999999877 4443
No 100
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=81.53 E-value=1.3 Score=33.24 Aligned_cols=21 Identities=24% Similarity=0.235 Sum_probs=18.7
Q ss_pred hHHHhccCCCCcHHHHHHHHH
Q 033363 71 SWTHVTQLHGVGKYAADAFAI 91 (121)
Q Consensus 71 ~~~~L~~lpGIG~~tA~~vl~ 91 (121)
....|.++.|||||+|=.+|.
T Consensus 71 lF~~Li~V~GIGpK~Al~iLs 91 (195)
T PRK14604 71 LFELLIGVSGVGPKAALNLLS 91 (195)
T ss_pred HHHHHhCcCCcCHHHHHHHHc
Confidence 467899999999999988886
No 101
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=81.52 E-value=7.2 Score=34.60 Aligned_cols=14 Identities=29% Similarity=0.339 Sum_probs=9.7
Q ss_pred cCCCCcHHHHHHHH
Q 033363 77 QLHGVGKYAADAFA 90 (121)
Q Consensus 77 ~lpGIG~~tA~~vl 90 (121)
.+||||+++|..++
T Consensus 532 gIpgIG~~~ak~L~ 545 (689)
T PRK14351 532 GIPEVGPTTARNLA 545 (689)
T ss_pred CCCCcCHHHHHHHH
Confidence 37777777777655
No 102
>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=81.42 E-value=4.3 Score=22.84 Aligned_cols=37 Identities=14% Similarity=0.138 Sum_probs=30.7
Q ss_pred HhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHH
Q 033363 27 TLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQE 66 (121)
Q Consensus 27 ~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~ 66 (121)
..|-|.++++.+++++|.++ -|+...++..|+..++.
T Consensus 12 ~G~~s~e~la~~~~~eL~~i---~g~~~e~a~~ii~~a~~ 48 (50)
T TIGR01954 12 EGFTTVEDLAYVPIDELLSI---EGFDEETAKELINRARN 48 (50)
T ss_pred cCCCCHHHHHccCHHHHhcC---CCCCHHHHHHHHHHHHH
Confidence 35889999999999998764 67888899998887764
No 103
>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=80.65 E-value=12 Score=33.26 Aligned_cols=60 Identities=20% Similarity=0.245 Sum_probs=38.4
Q ss_pred HHHHHHHhhcCChhHHHHHHHH-----HHHHHHHhhHHHhccCCCCcHHHHHHHHHHhcCCCCccCcchH
Q 033363 41 EEIEKIISTLGLQKKRAPMIKR-----FSQEYLGESWTHVTQLHGVGKYAADAFAIFCTGKWDRVRPTDH 105 (121)
Q Consensus 41 ~eL~~~i~~~Gl~~~Ka~~i~~-----~a~~i~~~~~~~L~~lpGIG~~tA~~vl~f~~~~~~~v~p~D~ 105 (121)
.++...|.+.|++...+..|.+ ..+.+.++...-+.+++|||.++||-+... +| +.|+|.
T Consensus 144 ~~~~~~L~~~gi~~~~a~ki~~~yg~~~~~~i~~nPY~L~~~i~gigF~~aD~iA~~-~g----~~~~d~ 208 (720)
T TIGR01448 144 RRLLAGLQGLGIGIKLAQRIYKFYQADTLDRVEKDPYLLAEDVKGIGFLTADQLAQA-LG----IALNDP 208 (720)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHhHHHHHHHHhCchhhhhhcCCCCHHHHHHHHHH-cC----CCCCCH
Confidence 4444556677777666666655 223333345544557999999999998754 55 456664
No 104
>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=79.56 E-value=2 Score=28.98 Aligned_cols=23 Identities=17% Similarity=0.322 Sum_probs=19.2
Q ss_pred HHHhccCCCCcHHHHHHHHHHhc
Q 033363 72 WTHVTQLHGVGKYAADAFAIFCT 94 (121)
Q Consensus 72 ~~~L~~lpGIG~~tA~~vl~f~~ 94 (121)
.-.|.+++|||+.+|..++...-
T Consensus 14 ~~aLt~IyGIG~~~A~~Ic~~lg 36 (107)
T PF00416_consen 14 YIALTKIYGIGRRKAKQICKKLG 36 (107)
T ss_dssp HHHHTTSTTBCHHHHHHHHHHTT
T ss_pred HhHHhhhhccCHHHHHHHHHHcC
Confidence 45799999999999999886543
No 105
>PRK14973 DNA topoisomerase I; Provisional
Probab=79.37 E-value=8.7 Score=35.26 Aligned_cols=71 Identities=11% Similarity=0.136 Sum_probs=50.7
Q ss_pred HHHHHHHHh-CCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHHh----------------------------
Q 033363 20 RVISDLFTL-CPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGE---------------------------- 70 (121)
Q Consensus 20 ~v~~~l~~~-~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~~---------------------------- 70 (121)
++...|... ..+.++|+.|++.. |+..|++..+++.+.+-|+.++..
T Consensus 755 ~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~sE~~~~~~~~~a~~~~~~~~~~~~gv~~~~~~~~~~~G~~~~~d~~ 830 (936)
T PRK14973 755 KIMKALISSGINDIAALARADPAD----LKKAGLSEAEAASLLAEAKSLCNISRLKEIGVPAVSLKKYQEAGFDTPEDFC 830 (936)
T ss_pred HHHHHHHhcCcchHHHHhhCCHHH----HHHcCCCHHHHHHHHHHHHHHHHHHhhcccCCCHHHHHHHHHhcCCCHHHHH
Confidence 344444443 35789999999998 677899999999999999655531
Q ss_pred --hHHHhccCCCCcHHHHHHHHHHhc
Q 033363 71 --SWTHVTQLHGVGKYAADAFAIFCT 94 (121)
Q Consensus 71 --~~~~L~~lpGIG~~tA~~vl~f~~ 94 (121)
..++|.+++||.+-|+......+.
T Consensus 831 ~a~p~~La~~~g~~~~~~~~~~~~~~ 856 (936)
T PRK14973 831 SVHPAYLALKTGISPETICRHAKLVC 856 (936)
T ss_pred hcCHHHHhcCCCCChhhHHHHHHHHH
Confidence 346777888887777766543333
No 106
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=78.75 E-value=3.7 Score=35.57 Aligned_cols=21 Identities=10% Similarity=0.110 Sum_probs=11.3
Q ss_pred hhHHHhccCCCCcHHHHHHHHH
Q 033363 70 ESWTHVTQLHGVGKYAADAFAI 91 (121)
Q Consensus 70 ~~~~~L~~lpGIG~~tA~~vl~ 91 (121)
.+.++|.++ |||+++|..+..
T Consensus 543 As~eeL~~v-gi~~~~A~~I~~ 563 (567)
T PRK14667 543 ADDEELKKL-GIPPSVKQEVKK 563 (567)
T ss_pred CCHHHHHHc-CCCHHHHHHHHH
Confidence 345555555 555555555543
No 107
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=78.48 E-value=1.9 Score=38.16 Aligned_cols=38 Identities=11% Similarity=0.154 Sum_probs=16.6
Q ss_pred HHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHH
Q 033363 25 LFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQ 65 (121)
Q Consensus 25 l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~ 65 (121)
|++.|.|.+.|.+|+.+||.++ -|++...|+.|+..|.
T Consensus 624 LL~~FgS~~~i~~As~eel~~v---~gi~~~~A~~i~~~~~ 661 (691)
T PRK14672 624 LLAHFGSFRSLQSATPQDIATA---IHIPLTQAHTILHAAT 661 (691)
T ss_pred HHHHhcCHHHHHhCCHHHHHhC---CCCCHHHHHHHHHHhh
Confidence 3444445555555554443221 1444444444444443
No 108
>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=77.78 E-value=0.41 Score=32.32 Aligned_cols=20 Identities=15% Similarity=0.252 Sum_probs=13.3
Q ss_pred HHhccCCCCcHHHHHHHHHH
Q 033363 73 THVTQLHGVGKYAADAFAIF 92 (121)
Q Consensus 73 ~~L~~lpGIG~~tA~~vl~f 92 (121)
+-+-.+||||+|||.-++.-
T Consensus 18 DNIPGV~GIG~KtA~~LL~~ 37 (101)
T PF01367_consen 18 DNIPGVPGIGPKTAAKLLQE 37 (101)
T ss_dssp CTB---TTSTCHCCCCCHHH
T ss_pred cCCCCCCCCCHHHHHHHHHH
Confidence 44667899999999877653
No 109
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=77.54 E-value=9.7 Score=28.95 Aligned_cols=52 Identities=19% Similarity=0.224 Sum_probs=31.1
Q ss_pred cCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH-------------hhHHHhccCCCCcHHHHHHHH
Q 033363 37 EVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG-------------ESWTHVTQLHGVGKYAADAFA 90 (121)
Q Consensus 37 ~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-------------~~~~~L~~lpGIG~~tA~~vl 90 (121)
.++..||.+++=..|..+. ...+.+|+.+.+ -+.++|.+++|||+..|..++
T Consensus 13 ~Lsd~ELLailL~~g~~~~--~~~~~lA~~ll~~f~~~g~l~~l~~a~~~eL~~i~GiG~aka~~l~ 77 (218)
T TIGR00608 13 ALSDYELLAIILRTGTPKG--LDVLSLSKRLLDVFGRQDSLGHLLSAPPEELSSVPGIGEAKAIQLK 77 (218)
T ss_pred cCCHHHHHHHHHhCCCCCC--CCHHHHHHHHHHHhcccCCHHHHHhCCHHHHHhCcCCcHHHHHHHH
Confidence 3455666666645555432 044444544442 367899999999996554443
No 110
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=76.77 E-value=1.9 Score=32.56 Aligned_cols=22 Identities=18% Similarity=0.182 Sum_probs=18.8
Q ss_pred hHHHhccCCCCcHHHHHHHHHH
Q 033363 71 SWTHVTQLHGVGKYAADAFAIF 92 (121)
Q Consensus 71 ~~~~L~~lpGIG~~tA~~vl~f 92 (121)
....|.++.||||++|=++|.-
T Consensus 71 lF~~LisVnGIGpK~ALaiLs~ 92 (201)
T COG0632 71 LFRLLISVNGIGPKLALAILSN 92 (201)
T ss_pred HHHHHHccCCccHHHHHHHHcC
Confidence 4678999999999999888753
No 111
>PRK01172 ski2-like helicase; Provisional
Probab=76.08 E-value=9.6 Score=33.13 Aligned_cols=39 Identities=18% Similarity=0.152 Sum_probs=29.8
Q ss_pred hCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH
Q 033363 28 LCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG 69 (121)
Q Consensus 28 ~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~ 69 (121)
.+-|+.++++++++++.++ +|+.+.+++.|++-|+.+++
T Consensus 632 g~~~~~di~~~~~~~~~~i---~~~~~~~~~~i~~~~~~~~~ 670 (674)
T PRK01172 632 GFKTVDDIARSSPERIKKI---YGFSDTLANAIVNRAMKISS 670 (674)
T ss_pred CCCCHHHHHhCCHHHHHHH---hccCHHHHHHHHHHHHHHHH
Confidence 3668888888888888776 47888888888887777653
No 112
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=76.03 E-value=7.4 Score=34.61 Aligned_cols=22 Identities=18% Similarity=0.205 Sum_probs=13.4
Q ss_pred hhHHHhccCCCCcHHHHHHHHH
Q 033363 70 ESWTHVTQLHGVGKYAADAFAI 91 (121)
Q Consensus 70 ~~~~~L~~lpGIG~~tA~~vl~ 91 (121)
.+.++|.+++|||++.|..|.-
T Consensus 666 AS~eELa~V~Gig~k~Ae~I~~ 687 (694)
T PRK14666 666 AGEEGLAAVPGIGPARAAALHE 687 (694)
T ss_pred cCHHHHHhcCCcCHHHHHHHHH
Confidence 3455566666666666666653
No 113
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=75.58 E-value=7.9 Score=30.34 Aligned_cols=21 Identities=19% Similarity=0.268 Sum_probs=11.8
Q ss_pred hHHHhccCCCCcHHHHHHHHH
Q 033363 71 SWTHVTQLHGVGKYAADAFAI 91 (121)
Q Consensus 71 ~~~~L~~lpGIG~~tA~~vl~ 91 (121)
+..+|.+++|||++.|.-+.-
T Consensus 212 s~~eL~~v~gig~k~A~~I~~ 232 (254)
T COG1948 212 SEEELMKVKGIGEKKAREIYR 232 (254)
T ss_pred CHHHHHHhcCccHHHHHHHHH
Confidence 445566666666666655543
No 114
>TIGR02236 recomb_radA DNA repair and recombination protein RadA. This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.
Probab=74.08 E-value=11 Score=29.36 Aligned_cols=42 Identities=14% Similarity=0.183 Sum_probs=34.1
Q ss_pred HHHHHHHh-CCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHH
Q 033363 21 VISDLFTL-CPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQ 65 (121)
Q Consensus 21 v~~~l~~~-~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~ 65 (121)
...+|.+. |-|.++|+.+++++|.+. +|+...++..|++.+.
T Consensus 11 ~~~~L~~~Gi~ti~dl~~~~~~~L~~~---~g~~~~~a~~l~~~~~ 53 (310)
T TIGR02236 11 TAEKLREAGYDTFEAIAVASPKELSEI---AGISEGTAAKIIQAAR 53 (310)
T ss_pred HHHHHHHcCCCCHHHHHcCCHHHHHhc---cCCCHHHHHHHHHHHH
Confidence 34566666 899999999999998654 5888788888888876
No 115
>PRK14976 5'-3' exonuclease; Provisional
Probab=73.81 E-value=1.7 Score=34.13 Aligned_cols=26 Identities=19% Similarity=0.264 Sum_probs=20.2
Q ss_pred hhHHHhccCCCCcHHHHHHHHHHhcCC
Q 033363 70 ESWTHVTQLHGVGKYAADAFAIFCTGK 96 (121)
Q Consensus 70 ~~~~~L~~lpGIG~~tA~~vl~f~~~~ 96 (121)
++-+-+-.+||||||||.-++. -+|-
T Consensus 188 D~sDnipGVpGIG~KtA~~LL~-~~gs 213 (281)
T PRK14976 188 DSSDNIKGVKGIGPKTAIKLLN-KYGN 213 (281)
T ss_pred CccCCCCCCCcccHHHHHHHHH-HcCC
Confidence 4567789999999999998774 4443
No 116
>PRK10353 3-methyl-adenine DNA glycosylase I; Provisional
Probab=73.07 E-value=20 Score=26.78 Aligned_cols=47 Identities=17% Similarity=0.346 Sum_probs=33.5
Q ss_pred HHHHHhCC--CHHHHhcCCHHHHHHHHhhcCChhHH--HHHHHHHHHHHHH
Q 033363 23 SDLFTLCP--DAKTATEVDAEEIEKIISTLGLQKKR--APMIKRFSQEYLG 69 (121)
Q Consensus 23 ~~l~~~~p--t~~~la~a~~~eL~~~i~~~Gl~~~K--a~~i~~~a~~i~~ 69 (121)
+.|.+.|- +|+.++..+++++++++..-|+-+.| .+.+++=|+.+.+
T Consensus 54 e~fr~aF~~Fd~~~VA~~~e~die~Ll~d~~IIRnr~KI~Avi~NA~~~l~ 104 (187)
T PRK10353 54 ENYRACFHQFDPVKVAAMQEEDVERLVQDAGIIRHRGKIQAIIGNARAYLQ 104 (187)
T ss_pred HHHHHHHcCCCHHHHhCCCHHHHHHHhcCchhHHhHHHHHHHHHHHHHHHH
Confidence 33444443 78999999999999999999985544 4466665666554
No 117
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=72.95 E-value=5.3 Score=30.74 Aligned_cols=47 Identities=19% Similarity=0.306 Sum_probs=33.5
Q ss_pred CCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH----------hhHHHhccCCCCcHHHHH
Q 033363 38 VDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG----------ESWTHVTQLHGVGKYAAD 87 (121)
Q Consensus 38 a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~----------~~~~~L~~lpGIG~~tA~ 87 (121)
++..||.+++=..|- |-+..+.+|+.+.. .+.++|+++||||+--|-
T Consensus 24 Lsd~ELLailLrtG~---~~~~~~~la~~lL~~fg~L~~l~~a~~~el~~v~GiG~aka~ 80 (224)
T COG2003 24 LSDAELLAILLRTGT---KGESVLDLAKELLQEFGSLAELLKASVEELSSVKGIGLAKAI 80 (224)
T ss_pred cchHHHHHHHHhcCC---CCCCHHHHHHHHHHHcccHHHHHhCCHHHHhhCCCccHHHHH
Confidence 345666666645554 45677888888887 268999999999975543
No 118
>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=71.98 E-value=2.7 Score=32.14 Aligned_cols=31 Identities=16% Similarity=0.279 Sum_probs=22.0
Q ss_pred hhHHHhccCCCCcHHHHHHHHHHhcCCCCccC
Q 033363 70 ESWTHVTQLHGVGKYAADAFAIFCTGKWDRVR 101 (121)
Q Consensus 70 ~~~~~L~~lpGIG~~tA~~vl~f~~~~~~~v~ 101 (121)
+.-+-+..+||||||||.-++. -+|-.+.+.
T Consensus 180 D~sDnipGv~GiG~ktA~~Ll~-~~gsle~i~ 210 (240)
T cd00008 180 DSSDNIPGVPGIGEKTAAKLLK-EYGSLEGIL 210 (240)
T ss_pred CcccCCCCCCccCHHHHHHHHH-HhCCHHHHH
Confidence 3467788999999999987774 455444343
No 119
>PRK07758 hypothetical protein; Provisional
Probab=71.59 E-value=4.3 Score=27.22 Aligned_cols=23 Identities=22% Similarity=0.263 Sum_probs=18.7
Q ss_pred HHhhHHHhccCCCCcHHHHHHHH
Q 033363 68 LGESWTHVTQLHGVGKYAADAFA 90 (121)
Q Consensus 68 ~~~~~~~L~~lpGIG~~tA~~vl 90 (121)
+.-+.++|.+++|+|+++.+-+.
T Consensus 62 v~~te~ELl~iknlGkKSL~EIk 84 (95)
T PRK07758 62 SKYSEKEILKLHGMGPASLPKLR 84 (95)
T ss_pred HcCCHHHHHHccCCCHHHHHHHH
Confidence 33578899999999999988754
No 120
>smart00475 53EXOc 5'-3' exonuclease.
Probab=71.48 E-value=2.7 Score=32.66 Aligned_cols=22 Identities=18% Similarity=0.336 Sum_probs=18.1
Q ss_pred hhHHHhccCCCCcHHHHHHHHH
Q 033363 70 ESWTHVTQLHGVGKYAADAFAI 91 (121)
Q Consensus 70 ~~~~~L~~lpGIG~~tA~~vl~ 91 (121)
+.-+-+..+||||||||.-++.
T Consensus 183 D~sDnipGV~GIG~KtA~~Ll~ 204 (259)
T smart00475 183 DSSDNIPGVPGIGEKTAAKLLK 204 (259)
T ss_pred CcccCCCCCCCCCHHHHHHHHH
Confidence 3456789999999999987774
No 121
>COG4277 Predicted DNA-binding protein with the Helix-hairpin-helix motif [General function prediction only]
Probab=71.18 E-value=3.4 Score=33.66 Aligned_cols=22 Identities=14% Similarity=0.368 Sum_probs=19.2
Q ss_pred hHHHhccCCCCcHHHHHHHHHH
Q 033363 71 SWTHVTQLHGVGKYAADAFAIF 92 (121)
Q Consensus 71 ~~~~L~~lpGIG~~tA~~vl~f 92 (121)
..++|+.+||||+++|.-|++.
T Consensus 328 ~~~~llRVPGiG~ksa~rIv~~ 349 (404)
T COG4277 328 PYKELLRVPGIGVKSARRIVMT 349 (404)
T ss_pred CHHHhcccCCCChHHHHHHHHH
Confidence 5789999999999999887753
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=69.87 E-value=9.5 Score=34.50 Aligned_cols=42 Identities=12% Similarity=0.289 Sum_probs=33.8
Q ss_pred HHHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHH
Q 033363 20 RVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQ 65 (121)
Q Consensus 20 ~v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~ 65 (121)
.-+.+++++|.|.++|++++.+||.++ +| ...+|+.|.++.+
T Consensus 768 ~~a~~ll~~f~si~~l~~as~eeL~~~---iG-~~~~A~~i~~fl~ 809 (814)
T TIGR00596 768 KNYRNLRKKVKSIRELAKLSQNELNEL---IG-DEEAAKRLYDFLR 809 (814)
T ss_pred HHHHHHHHHcCCHHHHHhCCHHHHHHH---hC-CHHHHHHHHHHhc
Confidence 346678889999999999999998875 56 4678999887754
No 123
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=69.09 E-value=9.9 Score=29.28 Aligned_cols=50 Identities=16% Similarity=0.105 Sum_probs=38.6
Q ss_pred HHHHHHHHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHH
Q 033363 15 LLKAGRVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEY 67 (121)
Q Consensus 15 ~~~v~~v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i 67 (121)
...|.+...++...|.+...+.+++.+++.+ ++++|. .|+-.|+.+.+.-
T Consensus 40 ~~~~~~la~~lL~~fg~L~~l~~a~~~el~~-v~GiG~--aka~~l~a~~El~ 89 (224)
T COG2003 40 GESVLDLAKELLQEFGSLAELLKASVEELSS-VKGIGL--AKAIQIKAAIELG 89 (224)
T ss_pred CCCHHHHHHHHHHHcccHHHHHhCCHHHHhh-CCCccH--HHHHHHHHHHHHH
Confidence 3557788999999999999999999999876 455554 6877776655543
No 124
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=69.05 E-value=9.3 Score=33.54 Aligned_cols=36 Identities=8% Similarity=0.132 Sum_probs=20.5
Q ss_pred HHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHH
Q 033363 23 SDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRF 63 (121)
Q Consensus 23 ~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~ 63 (121)
.+|++.|.|.+++.+|+.+||.++ +...+|+.|.+.
T Consensus 566 ~~LL~~FgSi~~I~~As~eeL~~v-----i~~k~A~~I~~~ 601 (624)
T PRK14669 566 QRLLKHFGSLERVRAATETQLAAV-----VGRAAAEAIIAH 601 (624)
T ss_pred HHHHHHcCCHHHHHhCCHHHHHHH-----hCHHHHHHHHHH
Confidence 345566677777777776665443 334455555443
No 125
>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=68.85 E-value=30 Score=25.66 Aligned_cols=48 Identities=10% Similarity=0.179 Sum_probs=34.3
Q ss_pred HHHHHHhCC--CHHHHhcCCHHHHHHHHhhcCChhHHHH--HHHHHHHHHHH
Q 033363 22 ISDLFTLCP--DAKTATEVDAEEIEKIISTLGLQKKRAP--MIKRFSQEYLG 69 (121)
Q Consensus 22 ~~~l~~~~p--t~~~la~a~~~eL~~~i~~~Gl~~~Ka~--~i~~~a~~i~~ 69 (121)
.+.|.+.|- +|+.++..+++++++++..-|+-+.|.| .+++=|+.+.+
T Consensus 52 r~~fr~aF~~Fd~~~VA~~~e~~ie~L~~d~~IIRnr~KI~Avi~NA~~~l~ 103 (179)
T TIGR00624 52 RENYRRAFSGFDIVKVARMTDADVERLLQDDGIIRNRGKIEATIANARAALQ 103 (179)
T ss_pred HHHHHHHHcCCCHHHHhCCCHHHHHHHhcCccchhhHHHHHHHHHHHHHHHH
Confidence 344444443 7999999999999999999888776654 35555555543
No 126
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=68.80 E-value=19 Score=28.36 Aligned_cols=43 Identities=14% Similarity=0.179 Sum_probs=34.3
Q ss_pred HHHHHHHh-CCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHH
Q 033363 21 VISDLFTL-CPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQE 66 (121)
Q Consensus 21 v~~~l~~~-~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~ 66 (121)
....|.+. +-|.++++++++++|.+. .|+...++..|++.++.
T Consensus 18 ~a~~L~~~Gi~t~~dl~~~~~~~L~~~---~g~~~~~a~~l~~~a~~ 61 (317)
T PRK04301 18 TAEKLREAGYDTVEAIAVASPKELSEA---AGIGESTAAKIIEAARE 61 (317)
T ss_pred HHHHHHHcCCCCHHHHHcCCHHHHHHh---cCCCHHHHHHHHHHHHH
Confidence 34556554 889999999999998665 58888899999888875
No 127
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=68.79 E-value=6.8 Score=34.08 Aligned_cols=23 Identities=22% Similarity=0.231 Sum_probs=17.3
Q ss_pred hhHHHhccCCCCcHHHHHHHHHH
Q 033363 70 ESWTHVTQLHGVGKYAADAFAIF 92 (121)
Q Consensus 70 ~~~~~L~~lpGIG~~tA~~vl~f 92 (121)
.+.++|.++||||+++|..+..+
T Consensus 572 As~eeL~~v~Gig~~~A~~I~~~ 594 (598)
T PRK00558 572 ASVEELAKVPGISKKLAEAIYEA 594 (598)
T ss_pred CCHHHHhhcCCcCHHHHHHHHHH
Confidence 45677888888888888877654
No 128
>TIGR03674 fen_arch flap structure-specific endonuclease. Endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA
Probab=68.48 E-value=6.7 Score=31.58 Aligned_cols=41 Identities=15% Similarity=0.241 Sum_probs=26.0
Q ss_pred HHHhhcCChhHHHHHHHHHHHHHHHhhHHHhccCCCCcHHHHHHHHH
Q 033363 45 KIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLHGVGKYAADAFAI 91 (121)
Q Consensus 45 ~~i~~~Gl~~~Ka~~i~~~a~~i~~~~~~~L~~lpGIG~~tA~~vl~ 91 (121)
+++..+|+.+ +.+..+|-.+ ++ +.-..+||||++||--++-
T Consensus 214 ~v~~~lgl~~---~q~id~~iL~--G~-dyn~Gv~GIG~ktA~kli~ 254 (338)
T TIGR03674 214 EVLSELGITR---EQLIDIAILV--GT-DYNEGVKGIGPKTALKLIK 254 (338)
T ss_pred HHHHHhCCCH---HHHHHHHHhc--CC-CCCCCCCCccHHHHHHHHH
Confidence 3455667753 3444444433 44 4458999999999977663
No 129
>PRK08609 hypothetical protein; Provisional
Probab=68.34 E-value=25 Score=30.39 Aligned_cols=62 Identities=15% Similarity=0.142 Sum_probs=41.0
Q ss_pred CCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHH-----HHHHHhh-HHHhccCCCCcHHHHHHHH
Q 033363 29 CPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFS-----QEYLGES-WTHVTQLHGVGKYAADAFA 90 (121)
Q Consensus 29 ~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a-----~~i~~~~-~~~L~~lpGIG~~tA~~vl 90 (121)
.+-.+.|.+-.++.+.++++-=|+...+++.+.+-. ..+.+.. -..+..+||+|+||.+.++
T Consensus 73 ~~~le~l~~~~p~~~~~l~~i~GiGpk~a~~l~~~lGi~tl~~L~~a~~~~~~~~~~gfg~k~~~~il 140 (570)
T PRK08609 73 SSVLQELKKEVPEGLLPLLKLPGLGGKKIAKLYKELGVVDKESLKEACENGKVQALAGFGKKTEEKIL 140 (570)
T ss_pred hHHHHHHHhhCcHHHHHHhcCCCCCHHHHHHHHHHhCCCCHHHHHHHHHhCChhhccCcchhHHHHHH
Confidence 344666666566677777777788878888877422 2222111 2247799999999988873
No 130
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=68.25 E-value=12 Score=32.53 Aligned_cols=26 Identities=12% Similarity=0.010 Sum_probs=21.4
Q ss_pred HHHhhHHHhccCCCCcHHHHHHHHHH
Q 033363 67 YLGESWTHVTQLHGVGKYAADAFAIF 92 (121)
Q Consensus 67 i~~~~~~~L~~lpGIG~~tA~~vl~f 92 (121)
|.+.+.++|.++||||+++|..+.-+
T Consensus 540 I~~As~eeL~~v~gi~~~~A~~I~~~ 565 (574)
T PRK14670 540 ILLLNEDEIAEKMKINIKMAKKIKKF 565 (574)
T ss_pred HHhCCHHHHHhCCCCCHHHHHHHHHH
Confidence 33467899999999999999998765
No 131
>PF00570 HRDC: HRDC domain Bloom syndrome. Werner syndrome.; InterPro: IPR002121 The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic acid binding. Mutations in the HRDC domain associated with the human BLM gene result in Bloom Syndrome (BS), an autosomal recessive disorder characterised by proportionate pre- and postnatal growth deficiency; sun-sensitive, telangiectatic, hypo- and hyperpigmented skin; predisposition to malignancy; and chromosomal instability [].; GO: 0003676 nucleic acid binding, 0005622 intracellular; PDB: 3SAG_B 3SAH_B 2CPR_A 3SAF_B 3CYM_A 1WUD_A 2HBK_A 2HBJ_A 2HBM_A 2HBL_A ....
Probab=67.25 E-value=11 Score=22.55 Aligned_cols=30 Identities=20% Similarity=0.302 Sum_probs=20.4
Q ss_pred HHHHHHHHHHHHhhHHHhccCCCCcHHHHHH
Q 033363 58 PMIKRFSQEYLGESWTHVTQLHGVGKYAADA 88 (121)
Q Consensus 58 ~~i~~~a~~i~~~~~~~L~~lpGIG~~tA~~ 88 (121)
..|.++|+. .-.+.++|.+++|+|++-.+-
T Consensus 30 ~~L~~ia~~-~P~s~~~L~~i~g~~~~~~~~ 59 (68)
T PF00570_consen 30 EALLEIAKR-LPTSIEELLQIPGMGKRKVRK 59 (68)
T ss_dssp HHHHHHHHH---SSHHHHHTSTTCGHHHHHH
T ss_pred HHHHHHHHh-CCCCHHHHHHccCCCHHHHHH
Confidence 455555555 335788999999999887653
No 132
>PF14635 HHH_7: Helix-hairpin-helix motif ; PDB: 3PSI_A 3PSF_A.
Probab=66.70 E-value=4.5 Score=27.48 Aligned_cols=39 Identities=15% Similarity=0.143 Sum_probs=26.2
Q ss_pred hcCChhHHHHHHHHHHHHHHH--hhHHHhccCCCCcHHHHH
Q 033363 49 TLGLQKKRAPMIKRFSQEYLG--ESWTHVTQLHGVGKYAAD 87 (121)
Q Consensus 49 ~~Gl~~~Ka~~i~~~a~~i~~--~~~~~L~~lpGIG~~tA~ 87 (121)
-+||..+||..+.+..+..-. .++++|.+...+||++-.
T Consensus 55 V~GLGPRKA~~Ll~~l~~~g~~l~~R~~Lv~~~~~g~~Vf~ 95 (104)
T PF14635_consen 55 VCGLGPRKAQALLKALKQNGGRLENRSQLVTKCLMGPKVFI 95 (104)
T ss_dssp STT--HHHHHHHHHHHHHC-S----TTHHHHTTSS-HHHHH
T ss_pred hcCCChHHHHHHHHHHHHcCCccccHHHHHhcCCCCCeEEE
Confidence 389999999999988875322 478888888889997643
No 133
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=66.30 E-value=3.8 Score=28.50 Aligned_cols=21 Identities=19% Similarity=0.178 Sum_probs=18.0
Q ss_pred HHhccCCCCcHHHHHHHHHHh
Q 033363 73 THVTQLHGVGKYAADAFAIFC 93 (121)
Q Consensus 73 ~~L~~lpGIG~~tA~~vl~f~ 93 (121)
-.|+.+.|||+.+|..++...
T Consensus 17 ~aLt~i~GIG~~~A~~ic~~l 37 (122)
T CHL00137 17 YALTYIYGIGLTSAKEILEKA 37 (122)
T ss_pred eeecccccccHHHHHHHHHHc
Confidence 468999999999999988653
No 134
>PTZ00217 flap endonuclease-1; Provisional
Probab=66.30 E-value=6.6 Score=32.41 Aligned_cols=41 Identities=15% Similarity=0.207 Sum_probs=25.5
Q ss_pred HHHhhcCChhHHHHHHHHHHHHHHHhhHHHhccCCCCcHHHHHHHHH
Q 033363 45 KIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLHGVGKYAADAFAI 91 (121)
Q Consensus 45 ~~i~~~Gl~~~Ka~~i~~~a~~i~~~~~~~L~~lpGIG~~tA~~vl~ 91 (121)
+++..+|+.+ ..+..+|-.+ + -+.+..+||||++||--++-
T Consensus 213 ~v~~~~gl~~---~q~id~~iL~--G-~Dy~pgi~GIG~ktA~~Li~ 253 (393)
T PTZ00217 213 TVLEELGLSM---DQFIDLCILC--G-CDYCDTIKGIGPKTAYKLIK 253 (393)
T ss_pred HHHHHhCCCH---HHHHHHHHHh--C-CCCCCCCCCccHHHHHHHHH
Confidence 3455567753 3344443332 2 35577999999999987763
No 135
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=65.63 E-value=11 Score=30.61 Aligned_cols=68 Identities=13% Similarity=0.181 Sum_probs=41.0
Q ss_pred HHHHHHHHHhCCC----HHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHHhhHHHhccCCCCcHHHHHHHHHHhc
Q 033363 19 GRVISDLFTLCPD----AKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLHGVGKYAADAFAIFCT 94 (121)
Q Consensus 19 ~~v~~~l~~~~pt----~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~~~~~~L~~lpGIG~~tA~~vl~f~~ 94 (121)
.+-+..|...||- ...+...+++.+..+++.+|+- .+ +.+++.++ .-.+..|+|.|++.+.-++-...
T Consensus 78 ~~~le~lk~~~P~gl~~Ll~v~GlGpkKi~~Ly~elgi~-~~-e~l~~a~~------~~~~~~l~GfG~kse~~il~~i~ 149 (326)
T COG1796 78 VKKLEALKKEVPEGLEPLLKVPGLGPKKIVSLYKELGIK-DL-EELQEALE------NGKIRGLRGFGKKSEAKILENIE 149 (326)
T ss_pred cHHHHHHHHhCCcchHHHhhCCCCCcHHHHHHHHHHCcc-cH-HHHHHHHH------hCCccccCCccchhHHHHHHHHH
Confidence 3456677777773 2333344566666666666653 22 23333332 23578899999999999886543
No 136
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=64.54 E-value=16 Score=31.81 Aligned_cols=21 Identities=24% Similarity=0.406 Sum_probs=13.8
Q ss_pred hhHHHhccCCCCcHHHHHHHH
Q 033363 70 ESWTHVTQLHGVGKYAADAFA 90 (121)
Q Consensus 70 ~~~~~L~~lpGIG~~tA~~vl 90 (121)
.+.++|.++||||++.|..+.
T Consensus 554 As~eeL~~vpGi~~~~A~~I~ 574 (577)
T PRK14668 554 ASVEDLRDVPGVGEKTAETIR 574 (577)
T ss_pred CCHHHHHhCCCCCHHHHHHHH
Confidence 455667777777777766654
No 137
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=64.17 E-value=11 Score=32.74 Aligned_cols=17 Identities=24% Similarity=0.487 Sum_probs=10.4
Q ss_pred HhccCCCCcHHHHHHHH
Q 033363 74 HVTQLHGVGKYAADAFA 90 (121)
Q Consensus 74 ~L~~lpGIG~~tA~~vl 90 (121)
.|.++|||||++...++
T Consensus 515 ~L~~I~GiG~kr~~~LL 531 (574)
T PRK14670 515 NYTKIKGIGEKKAKKIL 531 (574)
T ss_pred ccccCCCCCHHHHHHHH
Confidence 46666666666665554
No 138
>COG1491 Predicted RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=63.87 E-value=5.5 Score=29.99 Aligned_cols=26 Identities=23% Similarity=0.139 Sum_probs=20.7
Q ss_pred hHHHhccCCCCcHHHHHHHHHHhcCC
Q 033363 71 SWTHVTQLHGVGKYAADAFAIFCTGK 96 (121)
Q Consensus 71 ~~~~L~~lpGIG~~tA~~vl~f~~~~ 96 (121)
-+..|.-|||||.|+...++---=.+
T Consensus 128 RLH~LELLpGiGkK~m~~ILeERkkk 153 (202)
T COG1491 128 RLHQLELLPGIGKKTMWAILEERKKK 153 (202)
T ss_pred HHHHHHhcccccHHHHHHHHHHHhcC
Confidence 35689999999999999998654433
No 139
>COG2818 Tag 3-methyladenine DNA glycosylase [DNA replication, recombination, and repair]
Probab=63.44 E-value=17 Score=27.30 Aligned_cols=49 Identities=14% Similarity=0.329 Sum_probs=34.9
Q ss_pred HHHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHH--HHHHHHHHHHHH
Q 033363 20 RVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRA--PMIKRFSQEYLG 69 (121)
Q Consensus 20 ~v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka--~~i~~~a~~i~~ 69 (121)
+.|++-|..| +|+.++..+++++++++..-|.-+.|. +.++.=|+.+.+
T Consensus 55 e~freaF~~F-d~~kVA~~~~~dverLl~d~gIIR~r~KI~A~i~NA~~~l~ 105 (188)
T COG2818 55 EAFREAFHGF-DPEKVAAMTEEDVERLLADAGIIRNRGKIKATINNARAVLE 105 (188)
T ss_pred HHHHHHHhcC-CHHHHHcCCHHHHHHHHhCcchhhhHHHHHHHHHHHHHHHH
Confidence 3344333333 899999999999999999999876654 445555666665
No 140
>cd00128 XPG Xeroderma pigmentosum G N- and I-regions (XPGN, XPGI); contains the HhH2 motif; domain in nucleases. XPG is a eukaryotic enzyme that functions in nucleotide-excision repair and transcription-coupled repair of oxidative DNA damage. Functionally/structurally related to FEN-1; divalent metal ion-dependent exo- and endonuclease, and bacterial and bacteriophage 5'3' exonucleases.
Probab=63.42 E-value=8 Score=30.47 Aligned_cols=39 Identities=15% Similarity=0.223 Sum_probs=24.3
Q ss_pred HhhcCChhHHHHHHHHHHHHHHHhhHHHhccCCCCcHHHHHHHHH
Q 033363 47 ISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLHGVGKYAADAFAI 91 (121)
Q Consensus 47 i~~~Gl~~~Ka~~i~~~a~~i~~~~~~~L~~lpGIG~~tA~~vl~ 91 (121)
.+.+|+.. +.+..+|-.+ + -+.+..+||||++||--++.
T Consensus 203 ~~~lgl~~---~q~id~~~L~--G-~Dy~~gv~giG~k~A~~li~ 241 (316)
T cd00128 203 LKELGLTR---EKLIDLAILL--G-CDYTEGIPGIGPVTALKLIK 241 (316)
T ss_pred HHHcCCCH---HHHHHHHHhc--C-CCCCCCCCCccHHHHHHHHH
Confidence 44556653 3344444333 2 34567999999999987764
No 141
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=63.38 E-value=11 Score=30.97 Aligned_cols=20 Identities=25% Similarity=0.453 Sum_probs=16.5
Q ss_pred hHHHhccCCCCcHHHHHHHH
Q 033363 71 SWTHVTQLHGVGKYAADAFA 90 (121)
Q Consensus 71 ~~~~L~~lpGIG~~tA~~vl 90 (121)
+.++|.+++|||++.|..+.
T Consensus 317 s~eeL~~VeGIGe~rA~~I~ 336 (352)
T PRK13482 317 SIEDLDEVEGIGEVRARAIR 336 (352)
T ss_pred CHHHHhhCCCcCHHHHHHHH
Confidence 57889999999999988754
No 142
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=63.26 E-value=52 Score=29.24 Aligned_cols=68 Identities=13% Similarity=0.181 Sum_probs=46.6
Q ss_pred HHHHHHHHh--CCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHHhhHH---HhccCCCCcHHHHHHHH
Q 033363 20 RVISDLFTL--CPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWT---HVTQLHGVGKYAADAFA 90 (121)
Q Consensus 20 ~v~~~l~~~--~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~~~~~---~L~~lpGIG~~tA~~vl 90 (121)
.....|++. .-+|.+|..++.++|.++ =||...+++.|.+--+.-.+.... .=+.+|+||+.+|..+.
T Consensus 447 ~~i~~L~~~G~i~~~~Dly~L~~~~l~~l---~g~geksa~nl~~~Ie~sk~~~l~r~l~ALGI~~vG~~~ak~La 519 (669)
T PRK14350 447 KTIEFLFEKKFISSEIDLYTFNFDRLINL---KGFKDKRINNLKRSIEASKKRPFSKLLLSMGIKDLGENTILLLI 519 (669)
T ss_pred HHHHHHHHcCCcCCHHHHhhCCHHHHhhc---cCccHHHHHHHHHHHHHHhCCCHHHHHHHcCCCchhHHHHHHHH
Confidence 345566654 368999999998876543 388888888877755544332222 22459999999998777
No 143
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=62.95 E-value=39 Score=30.05 Aligned_cols=74 Identities=18% Similarity=0.230 Sum_probs=51.3
Q ss_pred HHHHHHHHHh--CCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHHhhHH---HhccCCCCcHHHHHHHHHHh
Q 033363 19 GRVISDLFTL--CPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWT---HVTQLHGVGKYAADAFAIFC 93 (121)
Q Consensus 19 ~~v~~~l~~~--~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~~~~~---~L~~lpGIG~~tA~~vl~f~ 93 (121)
.++...|++. .-++.+|..++.+++.++ -|+.+.+++.|.+.-+.-.+.... .=+.+|.||+.||..+.. .
T Consensus 455 ~k~i~~L~e~~lI~~~~Dly~Lt~~~l~~l---~~~~~ks~~nLl~aIe~sK~~~l~r~l~aLGIr~VG~~~Ak~La~-~ 530 (667)
T COG0272 455 EKIIEQLFEKGLIKDIADLYTLTEEDLLSL---EGFGEKSAENLLNAIEKSKKQPLARFLYALGIRHVGETTAKSLAR-H 530 (667)
T ss_pred HHHHHHHHHcCccCCHHHHHhCCHHHHhhc---cchhhhHHHHHHHHHHHhccCCHHHHHHHcCCchhhHHHHHHHHH-H
Confidence 3556677754 569999999999997653 344466667666655555444433 346899999999998876 6
Q ss_pred cCC
Q 033363 94 TGK 96 (121)
Q Consensus 94 ~~~ 96 (121)
|+-
T Consensus 531 f~s 533 (667)
T COG0272 531 FGT 533 (667)
T ss_pred hhh
Confidence 663
No 144
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=62.73 E-value=4.8 Score=27.97 Aligned_cols=21 Identities=19% Similarity=0.294 Sum_probs=17.9
Q ss_pred HHhccCCCCcHHHHHHHHHHh
Q 033363 73 THVTQLHGVGKYAADAFAIFC 93 (121)
Q Consensus 73 ~~L~~lpGIG~~tA~~vl~f~ 93 (121)
-.|..+.|||+.+|..++...
T Consensus 17 ~aL~~I~GIG~~~a~~i~~~l 37 (122)
T PRK05179 17 IALTYIYGIGRTRAKEILAAA 37 (122)
T ss_pred eeecccccccHHHHHHHHHHh
Confidence 468999999999999988653
No 145
>PTZ00035 Rad51 protein; Provisional
Probab=62.66 E-value=17 Score=29.29 Aligned_cols=45 Identities=13% Similarity=0.171 Sum_probs=36.9
Q ss_pred HHHHHH-hCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH
Q 033363 22 ISDLFT-LCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG 69 (121)
Q Consensus 22 ~~~l~~-~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~ 69 (121)
..+|.+ .|-|.++++.+++++|.++ .|++..|++.|++.++....
T Consensus 36 ~~kL~~~g~~t~~~~~~~~~~~L~~~---~gis~~~~~~i~~~~~~~~~ 81 (337)
T PTZ00035 36 IKKLKEAGICTVESVAYATKKDLCNI---KGISEAKVEKIKEAASKLVP 81 (337)
T ss_pred HHHHHHcCCCcHHHHHhCCHHHHHHh---hCCCHHHHHHHHHHHHHhcc
Confidence 444554 4889999999999998654 79999999999998888764
No 146
>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1. This model describes DMC1, a subfamily of a larger family of DNA repair and recombination proteins. It is eukaryotic only and most closely related to eukaryotic RAD51. It also resembles archaeal RadA (TIGR02236) and RadB (TIGR02237) and bacterial RecA (TIGR02012). It has been characterized for human as a recombinase active only in meiosis.
Probab=62.65 E-value=16 Score=29.04 Aligned_cols=45 Identities=18% Similarity=0.171 Sum_probs=36.8
Q ss_pred HHHHHH-hCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH
Q 033363 22 ISDLFT-LCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG 69 (121)
Q Consensus 22 ~~~l~~-~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~ 69 (121)
..+|.+ .|-|.++++.+++++|.++ .|++..++..|++.+.....
T Consensus 14 ~~~L~~~g~~t~~~~~~~~~~~L~~~---~gls~~~~~~i~~~~~~~~~ 59 (313)
T TIGR02238 14 IKKLKSAGICTVNGVIMTTRRALCKI---KGLSEAKVDKIKEAASKIIN 59 (313)
T ss_pred HHHHHHcCCCcHHHHHhCCHHHHHHh---cCCCHHHHHHHHHHHHhhhc
Confidence 344554 4889999999999998654 89999999999998887764
No 147
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=62.55 E-value=28 Score=28.21 Aligned_cols=45 Identities=11% Similarity=0.087 Sum_probs=36.6
Q ss_pred HHHHHH-hCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH
Q 033363 22 ISDLFT-LCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG 69 (121)
Q Consensus 22 ~~~l~~-~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~ 69 (121)
..+|.+ .|-|.++++.+++.||.+ -.|++..++..|++.++....
T Consensus 44 ~~kL~~~g~~tv~~~~~~~~~~L~~---~~g~s~~~~~ki~~~a~~~~~ 89 (344)
T PLN03187 44 VKKLQDAGIYTCNGLMMHTKKNLTG---IKGLSEAKVDKICEAAEKLLN 89 (344)
T ss_pred HHHHHHcCCCcHHHHHhCCHHHHHH---hcCCCHHHHHHHHHHHHHhhc
Confidence 444554 478999999999999865 479999999999998888774
No 148
>COG1415 Uncharacterized conserved protein [Function unknown]
Probab=62.43 E-value=7.4 Score=31.95 Aligned_cols=24 Identities=17% Similarity=0.433 Sum_probs=21.0
Q ss_pred hhHHHhccCCCCcHHHHHHHHHHh
Q 033363 70 ESWTHVTQLHGVGKYAADAFAIFC 93 (121)
Q Consensus 70 ~~~~~L~~lpGIG~~tA~~vl~f~ 93 (121)
.+.++|+-.|||||.|..+..+.+
T Consensus 275 ~Df~elLl~~GiGpstvRALalVA 298 (373)
T COG1415 275 DDFEELLLVPGIGPSTVRALALVA 298 (373)
T ss_pred ccHHHHHhccCCCHHHHHHHHHHH
Confidence 589999999999999999887654
No 149
>PF13543 KSR1-SAM: SAM like domain present in kinase suppressor RAS 1
Probab=62.40 E-value=39 Score=23.82 Aligned_cols=38 Identities=16% Similarity=0.318 Sum_probs=27.0
Q ss_pred HHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHH
Q 033363 25 LFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKR 62 (121)
Q Consensus 25 l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~ 62 (121)
+....-|.+++.+++++|+.+++..+|.+.-=.+++.+
T Consensus 86 i~~~~~tLe~Llemsd~el~~~l~~~g~~~EE~rRL~~ 123 (129)
T PF13543_consen 86 ILSKVLTLEALLEMSDEELKEILNRCGAREEECRRLCR 123 (129)
T ss_pred HHHhhcCHHHHHhCCHHHHHHHHHHhCCCHHHHHHHHH
Confidence 33456688889999999999988888876544444433
No 150
>PRK13766 Hef nuclease; Provisional
Probab=62.35 E-value=22 Score=31.25 Aligned_cols=44 Identities=11% Similarity=0.117 Sum_probs=30.8
Q ss_pred cCChhHHHHHHHHH---HHHHHHhhHHHhccCCCCcHHHHHHHHHHh
Q 033363 50 LGLQKKRAPMIKRF---SQEYLGESWTHVTQLHGVGKYAADAFAIFC 93 (121)
Q Consensus 50 ~Gl~~~Ka~~i~~~---a~~i~~~~~~~L~~lpGIG~~tA~~vl~f~ 93 (121)
-|....+++.|.+- .+.+.+...++|.++||+|+++|..+..|.
T Consensus 721 pgig~~~a~~Ll~~fgs~~~i~~as~~~L~~i~Gig~~~a~~i~~~~ 767 (773)
T PRK13766 721 PDVGPVLARNLLEHFGSVEAVMTASEEELMEVEGIGEKTAKRIREVV 767 (773)
T ss_pred CCCCHHHHHHHHHHcCCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHH
Confidence 35555667666653 334444677889999999999999877643
No 151
>PF04904 NCD1: NAB conserved region 1 (NCD1); InterPro: IPR006988 Nab1 and Nab2 are co-repressors that specifically interact with and repress transcription mediated by the three members of the NGFI-A (Egr-1, Krox24, zif/268) family of eukaryotic (metazoa) transcription factors []. This entry represents the N-terminal NAB domain, which interacts with the EGR1 inhibitory domain (R1) []. It may also mediate multimerisation.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=62.01 E-value=41 Score=21.82 Aligned_cols=53 Identities=13% Similarity=0.221 Sum_probs=41.2
Q ss_pred HHHHHHHHHHHHHhCC-CHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHH
Q 033363 15 LLKAGRVISDLFTLCP-DAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYL 68 (121)
Q Consensus 15 ~~~v~~v~~~l~~~~p-t~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~ 68 (121)
+...-..|..|+.... +.+.+..++++|..+++.-+|+. .|--.++++-+.+.
T Consensus 18 rAnLl~Yyd~fi~~GgDDvqQL~~~~e~eF~eim~lvGM~-sKPLHVrRlqKAL~ 71 (82)
T PF04904_consen 18 RANLLQYYDTFIAQGGDDVQQLCEAGEEEFLEIMALVGMA-SKPLHVRRLQKALQ 71 (82)
T ss_pred HhhHHHHHHHHHHHcChhHHHHHhcChHHHHHHHHHhCcc-CccHHHHHHHHHHH
Confidence 4455678999988754 68999999999999999999997 67666665555543
No 152
>PF04919 DUF655: Protein of unknown function (DUF655); InterPro: IPR007003 This family includes several uncharacterised archaeal proteins.; PDB: 2I5H_A.
Probab=61.01 E-value=6.8 Score=29.21 Aligned_cols=21 Identities=19% Similarity=0.109 Sum_probs=15.7
Q ss_pred HHHhccCCCCcHHHHHHHHHH
Q 033363 72 WTHVTQLHGVGKYAADAFAIF 92 (121)
Q Consensus 72 ~~~L~~lpGIG~~tA~~vl~f 92 (121)
+..|.=|||||.|+...++--
T Consensus 115 lH~LeLLPGIGKK~m~~ILeE 135 (181)
T PF04919_consen 115 LHSLELLPGIGKKTMWKILEE 135 (181)
T ss_dssp SBGGGGSTT--HHHHHHHHHH
T ss_pred HHHHhhcccccHHHHHHHHHH
Confidence 457888999999999999853
No 153
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=60.99 E-value=16 Score=31.71 Aligned_cols=38 Identities=18% Similarity=0.302 Sum_probs=30.7
Q ss_pred HHHHHHHhCCCHHHHhcCCHHHHHHHHhhc-CChhHHHHHHHH
Q 033363 21 VISDLFTLCPDAKTATEVDAEEIEKIISTL-GLQKKRAPMIKR 62 (121)
Q Consensus 21 v~~~l~~~~pt~~~la~a~~~eL~~~i~~~-Gl~~~Ka~~i~~ 62 (121)
-..+|++.|.|++++.+++.++| ..+ |+....|+.|.+
T Consensus 537 r~~~LL~~FGS~~~I~~As~eeL----~~vpGi~~~~A~~I~~ 575 (577)
T PRK14668 537 TRKRLLRRFGSVEGVREASVEDL----RDVPGVGEKTAETIRE 575 (577)
T ss_pred HHHHHHHHcCCHHHHHhCCHHHH----HhCCCCCHHHHHHHHH
Confidence 35578899999999999999995 455 888788877754
No 154
>PRK13766 Hef nuclease; Provisional
Probab=60.74 E-value=20 Score=31.52 Aligned_cols=17 Identities=29% Similarity=0.266 Sum_probs=14.5
Q ss_pred hccCCCCcHHHHHHHHH
Q 033363 75 VTQLHGVGKYAADAFAI 91 (121)
Q Consensus 75 L~~lpGIG~~tA~~vl~ 91 (121)
|..+||||+.+|..++.
T Consensus 717 L~~ipgig~~~a~~Ll~ 733 (773)
T PRK13766 717 VESLPDVGPVLARNLLE 733 (773)
T ss_pred HhcCCCCCHHHHHHHHH
Confidence 78999999999887765
No 155
>PRK03980 flap endonuclease-1; Provisional
Probab=60.68 E-value=8.8 Score=30.38 Aligned_cols=42 Identities=14% Similarity=0.217 Sum_probs=26.0
Q ss_pred HHHHhhcCChhHHHHHHHHHHHHHHHhhHHHhccCCCCcHHHHHHHHH
Q 033363 44 EKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLHGVGKYAADAFAI 91 (121)
Q Consensus 44 ~~~i~~~Gl~~~Ka~~i~~~a~~i~~~~~~~L~~lpGIG~~tA~~vl~ 91 (121)
++++..+|+.+ +.+..+|-.+ + -+....+||||++||--++.
T Consensus 166 ~~vl~~lgl~~---~q~id~~iL~--G-~Dy~~GI~GIG~ktA~kLi~ 207 (292)
T PRK03980 166 EEVLKELGITR---EQLIDIAILV--G-TDYNPGIKGIGPKTALKLIK 207 (292)
T ss_pred HHHHHHhCCCH---HHHHHHHHhc--C-CCCCCCCCCccHHHHHHHHH
Confidence 33455677753 4444444333 2 24456999999999977663
No 156
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=60.58 E-value=57 Score=29.22 Aligned_cols=43 Identities=12% Similarity=0.176 Sum_probs=27.9
Q ss_pred HHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHH
Q 033363 21 VISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQE 66 (121)
Q Consensus 21 v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~ 66 (121)
...+|++.|.|++++.+++.++|.++ -|+...+|+.|++..+.
T Consensus 649 r~k~LL~~FGSle~I~~AS~eELa~V---~Gig~k~Ae~I~~~L~~ 691 (694)
T PRK14666 649 TARLLWERFGSLQAMAAAGEEGLAAV---PGIGPARAAALHEHLKT 691 (694)
T ss_pred HHHHHHHHhCCHHHHHhcCHHHHHhc---CCcCHHHHHHHHHHHHH
Confidence 34566677777777777777775432 36666777777665544
No 157
>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=59.69 E-value=5.6 Score=28.49 Aligned_cols=20 Identities=30% Similarity=0.353 Sum_probs=17.0
Q ss_pred HHhccCCCCcHHHHHHHHHH
Q 033363 73 THVTQLHGVGKYAADAFAIF 92 (121)
Q Consensus 73 ~~L~~lpGIG~~tA~~vl~f 92 (121)
-.|+++.|||+.+|..++..
T Consensus 21 ~aLt~I~GIG~~~a~~I~~~ 40 (144)
T TIGR03629 21 YALTGIKGIGRRFARAIARK 40 (144)
T ss_pred EeecceeccCHHHHHHHHHH
Confidence 46899999999999988653
No 158
>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=59.31 E-value=5.6 Score=27.25 Aligned_cols=21 Identities=19% Similarity=0.229 Sum_probs=17.8
Q ss_pred HHhccCCCCcHHHHHHHHHHh
Q 033363 73 THVTQLHGVGKYAADAFAIFC 93 (121)
Q Consensus 73 ~~L~~lpGIG~~tA~~vl~f~ 93 (121)
-.|.++.|||+.+|..++-..
T Consensus 15 ~aL~~i~GIG~~~a~~i~~~l 35 (113)
T TIGR03631 15 IALTYIYGIGRTRARKILEKA 35 (113)
T ss_pred eeeeeeecccHHHHHHHHHHh
Confidence 368999999999999888653
No 159
>PRK14469 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=59.13 E-value=13 Score=29.79 Aligned_cols=45 Identities=27% Similarity=0.293 Sum_probs=32.1
Q ss_pred HhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHHhhHHHhccCC
Q 033363 35 ATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLH 79 (121)
Q Consensus 35 la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~~~~~~L~~lp 79 (121)
+...+.++|++.+.+.|+...|++.|.+-.-.=...+++++..||
T Consensus 4 ~~~~~~~~~~~~~~~~g~~~~r~~qi~~~~~~~~~~~~~~~~~~~ 48 (343)
T PRK14469 4 ILDLSYEELVSEITELGLEKYRADQILDWIYKKKVFNFDEMTNLS 48 (343)
T ss_pred cccCCHHHHHHHHHHcCCCchHHHHHHHHHHhcCCCCHHHhcccc
Confidence 667889999999999999988988886543221114566666665
No 160
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=58.90 E-value=6.2 Score=28.64 Aligned_cols=23 Identities=17% Similarity=0.115 Sum_probs=18.9
Q ss_pred hHHHhccCCCCcHHHHHHHHHHh
Q 033363 71 SWTHVTQLHGVGKYAADAFAIFC 93 (121)
Q Consensus 71 ~~~~L~~lpGIG~~tA~~vl~f~ 93 (121)
..-.|+.+.|||+.+|..++.-.
T Consensus 28 v~~aLt~I~GIG~~~A~~I~~~l 50 (154)
T PTZ00134 28 VPYALTAIKGIGRRFAYLVCKKA 50 (154)
T ss_pred EEEeecccccccHHHHHHHHHHc
Confidence 34579999999999999888643
No 161
>COG0703 AroK Shikimate kinase [Amino acid transport and metabolism]
Probab=58.55 E-value=24 Score=26.00 Aligned_cols=43 Identities=14% Similarity=0.064 Sum_probs=35.5
Q ss_pred hccCCCCcHHHHHHHHHHhcCCCCccCcchHHHHHH----HHHHHHhhc
Q 033363 75 VTQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYY----WEFLVSTKG 119 (121)
Q Consensus 75 L~~lpGIG~~tA~~vl~f~~~~~~~v~p~D~~l~~~----~~wl~~~~~ 119 (121)
|..++|.|+-|..-.+.-.+|.+ +.-.|+.+.+. ..|++...|
T Consensus 7 LiG~mGaGKSTIGr~LAk~L~~~--F~D~D~~Ie~~~g~sI~eIF~~~G 53 (172)
T COG0703 7 LIGFMGAGKSTIGRALAKALNLP--FIDTDQEIEKRTGMSIAEIFEEEG 53 (172)
T ss_pred EEcCCCCCHhHHHHHHHHHcCCC--cccchHHHHHHHCcCHHHHHHHHh
Confidence 67899999999999999999986 77788887544 677777666
No 162
>COG3547 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=58.12 E-value=81 Score=23.97 Aligned_cols=16 Identities=31% Similarity=0.632 Sum_probs=15.2
Q ss_pred hccCCCCcHHHHHHHH
Q 033363 75 VTQLHGVGKYAADAFA 90 (121)
Q Consensus 75 L~~lpGIG~~tA~~vl 90 (121)
|.++||||+-+|..+.
T Consensus 190 l~~~pgig~~~a~~i~ 205 (303)
T COG3547 190 LASIPGIGELTAAAIA 205 (303)
T ss_pred HHhCCCccHHHHHHHH
Confidence 8899999999999988
No 163
>PRK00254 ski2-like helicase; Provisional
Probab=57.34 E-value=26 Score=30.87 Aligned_cols=42 Identities=14% Similarity=0.143 Sum_probs=33.1
Q ss_pred HHHHHHHh-CCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHH
Q 033363 21 VISDLFTL-CPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQ 65 (121)
Q Consensus 21 v~~~l~~~-~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~ 65 (121)
...++++. |.|++++.+++.++|.++ .|+.+..|+.|++..+
T Consensus 657 ~~~~l~~~g~~s~~~i~~a~~~el~~~---~gi~~~~a~~i~~~~~ 699 (720)
T PRK00254 657 RARALYNAGFRSIEDIVNAKPSELLKV---EGIGAKIVEGIFKHLG 699 (720)
T ss_pred HHHHHHHccCCCHHHHHhCCHHHHhcC---CCCCHHHHHHHHHHhc
Confidence 34556666 999999999999996443 3888899999988755
No 164
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=56.95 E-value=6.8 Score=28.22 Aligned_cols=22 Identities=27% Similarity=0.285 Sum_probs=18.2
Q ss_pred hHHHhccCCCCcHHHHHHHHHH
Q 033363 71 SWTHVTQLHGVGKYAADAFAIF 92 (121)
Q Consensus 71 ~~~~L~~lpGIG~~tA~~vl~f 92 (121)
..-.|+++.|||+.+|..++.-
T Consensus 23 i~~aLt~IyGIG~~~a~~Ic~~ 44 (149)
T PRK04053 23 VEYALTGIKGIGRRTARAIARK 44 (149)
T ss_pred EeeeccccccccHHHHHHHHHH
Confidence 3457999999999999988654
No 165
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=55.69 E-value=8.2 Score=26.97 Aligned_cols=20 Identities=20% Similarity=0.310 Sum_probs=17.6
Q ss_pred HhccCCCCcHHHHHHHHHHh
Q 033363 74 HVTQLHGVGKYAADAFAIFC 93 (121)
Q Consensus 74 ~L~~lpGIG~~tA~~vl~f~ 93 (121)
.|+.++|||+.+|..|+.-+
T Consensus 18 ALt~IyGIG~~~a~~I~~~~ 37 (121)
T COG0099 18 ALTYIYGIGRRRAKEICKKA 37 (121)
T ss_pred hhhhhccccHHHHHHHHHHc
Confidence 68999999999999998644
No 166
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=55.43 E-value=31 Score=30.08 Aligned_cols=39 Identities=26% Similarity=0.274 Sum_probs=31.6
Q ss_pred HHHHHHHhCCCHHHHhcCCHHHHHHHHhhc-CChhHHHHHHHHH
Q 033363 21 VISDLFTLCPDAKTATEVDAEEIEKIISTL-GLQKKRAPMIKRF 63 (121)
Q Consensus 21 v~~~l~~~~pt~~~la~a~~~eL~~~i~~~-Gl~~~Ka~~i~~~ 63 (121)
....|.+.|+|++.+.+++.++| ..+ |++...|+.|.+.
T Consensus 555 ~~k~Ll~~FgS~~~i~~As~eeL----~~v~Gig~~~A~~I~~~ 594 (598)
T PRK00558 555 RRKALLKHFGSLKAIKEASVEEL----AKVPGISKKLAEAIYEA 594 (598)
T ss_pred HHHHHHHHcCCHHHHHhCCHHHH----hhcCCcCHHHHHHHHHH
Confidence 34578899999999999999995 445 8888888888664
No 167
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=53.93 E-value=52 Score=29.13 Aligned_cols=56 Identities=18% Similarity=0.148 Sum_probs=39.6
Q ss_pred HHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH-hhHHHhccCCCCc
Q 033363 23 SDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG-ESWTHVTQLHGVG 82 (121)
Q Consensus 23 ~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-~~~~~L~~lpGIG 82 (121)
..|.+.|+|++++.+++.++|.++ -|+....|+.|++.-..-.. +.++.|.+ .||.
T Consensus 525 k~L~~~f~sl~~l~~As~eeL~~i---~GIG~~~A~sI~~ff~~~~~~~~i~~L~~-~gv~ 581 (665)
T PRK07956 525 KALARHFGSLEALRAASEEELAAV---EGVGEVVAQSIVEFFAVEENRELIDELLE-AGVN 581 (665)
T ss_pred HHHHHHcCCHHHHHhCCHHHHhcc---CCcCHHHHHHHHHHHhhhhHHHHHHHHHH-cCCC
Confidence 356678999999999999996542 47778899888776543221 35566666 3775
No 168
>PF04558 tRNA_synt_1c_R1: Glutaminyl-tRNA synthetase, non-specific RNA binding region part 1 ; InterPro: IPR007639 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This is a domain found N-terminal to the catalytic domain of glutaminyl-tRNA synthetase (6.1.1.18 from EC) in eukaryotes but not in Escherichia coli. This domain is thought to bind RNA in a non-specific manner, enhancing interactions between the tRNA and enzyme, but is not essential for enzyme function [].; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 3TL4_X.
Probab=52.81 E-value=42 Score=24.38 Aligned_cols=56 Identities=18% Similarity=0.247 Sum_probs=29.3
Q ss_pred CCHHHHHHHHhhcCChhHHHHHHHH---HHHHHHHhhHHHhccCCCCcHHHHHHHHHHhc
Q 033363 38 VDAEEIEKIISTLGLQKKRAPMIKR---FSQEYLGESWTHVTQLHGVGKYAADAFAIFCT 94 (121)
Q Consensus 38 a~~~eL~~~i~~~Gl~~~Ka~~i~~---~a~~i~~~~~~~L~~lpGIG~~tA~~vl~f~~ 94 (121)
++.+++.+++..+||..+||+-+.+ ++..+. ..+++-..-.|+-..+...+...+-
T Consensus 1 ~s~eel~~lF~~iGL~e~kAket~KN~kls~~L~-~iI~ea~~~~~~dk~~g~LLy~lAt 59 (164)
T PF04558_consen 1 MSEEELIELFKSIGLSEKKAKETLKNKKLSASLK-AIINEAGVDSGCDKKQGNLLYQLAT 59 (164)
T ss_dssp --HHHHHHHHHHTT--HHHHHHHTTSHHHHHHHH-HHHHTS-TT----HHHHHHHHHHHH
T ss_pred CChHHHHHHHHHcCCChhhHHHHHhCHHHHHHHH-HHHHHhcccCCCCHHHHHHHHHHHH
Confidence 3678999999999999999987643 222221 1222222224677777766666555
No 169
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=52.48 E-value=11 Score=33.16 Aligned_cols=23 Identities=17% Similarity=0.280 Sum_probs=19.0
Q ss_pred HHHhccCCCCcHHHHHHHHHHhcC
Q 033363 72 WTHVTQLHGVGKYAADAFAIFCTG 95 (121)
Q Consensus 72 ~~~L~~lpGIG~~tA~~vl~f~~~ 95 (121)
...|.++||||++++..++- .||
T Consensus 551 ~S~L~~IpGIG~kr~~~LL~-~Fg 573 (624)
T PRK14669 551 TSELLEIPGVGAKTVQRLLK-HFG 573 (624)
T ss_pred HHHHhcCCCCCHHHHHHHHH-HcC
Confidence 36799999999999998875 555
No 170
>PF13297 Telomere_Sde2_2: Telomere stability C-terminal
Probab=52.23 E-value=20 Score=22.06 Aligned_cols=26 Identities=15% Similarity=0.319 Sum_probs=22.9
Q ss_pred HhCCCHHHHhcCCHHHHHHHHhhcCC
Q 033363 27 TLCPDAKTATEVDAEEIEKIISTLGL 52 (121)
Q Consensus 27 ~~~pt~~~la~a~~~eL~~~i~~~Gl 52 (121)
..|.|+++|...+.|.|.+.+...|+
T Consensus 4 ~~f~sa~eLe~lGldrLK~~L~a~GL 29 (60)
T PF13297_consen 4 DAFSSAEELEALGLDRLKSALMALGL 29 (60)
T ss_pred hhcCCHHHHHHhCHHHHHHHHHHcCC
Confidence 46889999999999999999988776
No 171
>PF14056 DUF4250: Domain of unknown function (DUF4250)
Probab=51.85 E-value=41 Score=20.23 Aligned_cols=31 Identities=19% Similarity=0.370 Sum_probs=26.2
Q ss_pred HHHHHhCCCHHHHh---cCCHHHHHHHHhhcCCh
Q 033363 23 SDLFTLCPDAKTAT---EVDAEEIEKIISTLGLQ 53 (121)
Q Consensus 23 ~~l~~~~pt~~~la---~a~~~eL~~~i~~~Gl~ 53 (121)
.+|+..|+|.+++. +++.++|.+-++..||.
T Consensus 14 ~kLRD~~~sLd~Lc~~~~id~~~l~~kL~~~Gy~ 47 (55)
T PF14056_consen 14 MKLRDEYSSLDELCYDYDIDKEELEEKLASIGYE 47 (55)
T ss_pred HHHHhccCCHHHHHHHhCCCHHHHHHHHHHcCCe
Confidence 36778899998876 57899999999999985
No 172
>PRK14455 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=51.74 E-value=20 Score=29.05 Aligned_cols=46 Identities=20% Similarity=0.223 Sum_probs=32.8
Q ss_pred HHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHHhhHHHhccCC
Q 033363 34 TATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLH 79 (121)
Q Consensus 34 ~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~~~~~~L~~lp 79 (121)
.+...+.+||++.+.+.|....|++.|.+-.-.=.-.++++++.||
T Consensus 12 ~~~~~~~~~l~~~~~~~g~~~~r~~qi~~~~~~~~~~~~~~m~~l~ 57 (356)
T PRK14455 12 SIYSLTLDELQEWLVEQGEKKFRATQIWDWLYRKRVQSFEEMTNLS 57 (356)
T ss_pred ccccCCHHHHHHHHHHcCCCchHHHHHHHHHHHcCCCCHHHhcccC
Confidence 3788899999999999999999988886543221113566666665
No 173
>PRK14463 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=51.65 E-value=22 Score=28.86 Aligned_cols=46 Identities=20% Similarity=0.297 Sum_probs=31.9
Q ss_pred HHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHHhhHHHhccCC
Q 033363 34 TATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLH 79 (121)
Q Consensus 34 ~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~~~~~~L~~lp 79 (121)
.+...+.+||++.+.+.|....|++.|.+-.-.=.-.++++++.||
T Consensus 6 ~~~~~~~~~l~~~~~~~g~~~~r~~qi~~~~~~~~~~~~~~m~~l~ 51 (349)
T PRK14463 6 DIKNLTLQELEAFLAGQGKERFRAKQIFKWLYQRDARSFAEMTNLS 51 (349)
T ss_pred ccccCCHHHHHHHHHHcCCCchHHHHHHHHHHHhCCCCHHHhcccC
Confidence 4678899999999999999999998885532211113455555554
No 174
>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=51.62 E-value=63 Score=28.52 Aligned_cols=57 Identities=18% Similarity=0.160 Sum_probs=39.0
Q ss_pred HHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH-hhHHHhccCCCCc
Q 033363 22 ISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG-ESWTHVTQLHGVG 82 (121)
Q Consensus 22 ~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-~~~~~L~~lpGIG 82 (121)
...|.+.|+|++++.+++.++|.++ -|+...+|+.|.+.-+.-.. ..++.|.+ .||-
T Consensus 511 ak~L~~~f~sl~~l~~As~eeL~~i---~GIG~~~A~~I~~ff~~~~~~~~i~~L~~-~gv~ 568 (652)
T TIGR00575 511 AKNLAKHFGTLDKLKAASLEELLSV---EGVGPKVAESIVNFFHDPNNRQLIKKLEE-LGVE 568 (652)
T ss_pred HHHHHHHhCCHHHHHhCCHHHHhcC---CCcCHHHHHHHHHHHhhhhHHHHHHHHHH-cCCC
Confidence 3456678999999999999986542 37777888888776543222 34566666 3664
No 175
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=50.60 E-value=11 Score=32.92 Aligned_cols=24 Identities=25% Similarity=0.410 Sum_probs=19.2
Q ss_pred HHHhccCCCCcHHHHHHHHHHhcCC
Q 033363 72 WTHVTQLHGVGKYAADAFAIFCTGK 96 (121)
Q Consensus 72 ~~~L~~lpGIG~~tA~~vl~f~~~~ 96 (121)
...|..+||||++++..++. .||-
T Consensus 568 ~s~L~~I~GIG~k~a~~Ll~-~Fgs 591 (621)
T PRK14671 568 QTELTDIAGIGEKTAEKLLE-HFGS 591 (621)
T ss_pred hhhhhcCCCcCHHHHHHHHH-HcCC
Confidence 46789999999999997764 5553
No 176
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=50.40 E-value=15 Score=33.56 Aligned_cols=22 Identities=18% Similarity=0.365 Sum_probs=17.8
Q ss_pred hhHHHhccCCCCcHHHHHHHHH
Q 033363 70 ESWTHVTQLHGVGKYAADAFAI 91 (121)
Q Consensus 70 ~~~~~L~~lpGIG~~tA~~vl~ 91 (121)
+.-+-+-.+||||||||.-++.
T Consensus 182 D~sDnIpGVpGIG~KtA~kLL~ 203 (887)
T TIGR00593 182 DSSDNIPGVKGIGEKTAAKLLQ 203 (887)
T ss_pred CcccCCCCCCCcCHHHHHHHHH
Confidence 3456788899999999987774
No 177
>PRK14467 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=50.31 E-value=23 Score=28.77 Aligned_cols=45 Identities=24% Similarity=0.373 Sum_probs=30.8
Q ss_pred HhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHHhhHHHhccCC
Q 033363 35 ATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLH 79 (121)
Q Consensus 35 la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~~~~~~L~~lp 79 (121)
+...+.+||++.+.+.|+...|++.|.+-.-.=...++++++.||
T Consensus 4 l~~~~~~~l~~~~~~~g~~~~r~~qi~~~~~~~~~~~~~~m~~l~ 48 (348)
T PRK14467 4 IKNYNLEELEEFVVELGWEKYRAKQIAKWVYKKKVTDFDEMTDLS 48 (348)
T ss_pred cccCCHHHHHHHHHHcCCCchHHHHHHHHHHhcCCCCHHHhcccc
Confidence 567888999999999999888888875432221113556666655
No 178
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=50.07 E-value=27 Score=30.52 Aligned_cols=23 Identities=17% Similarity=0.244 Sum_probs=14.1
Q ss_pred HHHhhHHHhccCCCCcHHHHHHHH
Q 033363 67 YLGESWTHVTQLHGVGKYAADAFA 90 (121)
Q Consensus 67 i~~~~~~~L~~lpGIG~~tA~~vl 90 (121)
+.+.+.++|.++ ||++..|..|.
T Consensus 556 i~~As~eel~~v-gi~~~~a~~i~ 578 (581)
T COG0322 556 IKSASVEELAKV-GISKKLAEKIY 578 (581)
T ss_pred HHhcCHHHHHHc-CCCHHHHHHHH
Confidence 333456667777 77776666553
No 179
>COG1623 Predicted nucleic-acid-binding protein (contains the HHH domain) [General function prediction only]
Probab=49.85 E-value=29 Score=28.08 Aligned_cols=19 Identities=26% Similarity=0.403 Sum_probs=10.1
Q ss_pred hHHHhccCCCCcHHHHHHH
Q 033363 71 SWTHVTQLHGVGKYAADAF 89 (121)
Q Consensus 71 ~~~~L~~lpGIG~~tA~~v 89 (121)
+.++|.++.|||..=|..+
T Consensus 323 s~edL~~VeGIGe~rAr~i 341 (349)
T COG1623 323 SAEDLDAVEGIGEARARAI 341 (349)
T ss_pred cHhHHhhhcchhHHHHHHH
Confidence 4445555555555555444
No 180
>TIGR00194 uvrC excinuclease ABC, C subunit. This family consists of the DNA repair enzyme UvrC, an ABC excinuclease subunit which interacts with the UvrA/UvrB complex to excise UV-damaged nucleotide segments.
Probab=49.61 E-value=13 Score=32.32 Aligned_cols=22 Identities=18% Similarity=0.341 Sum_probs=18.0
Q ss_pred HHhccCCCCcHHHHHHHHHHhcC
Q 033363 73 THVTQLHGVGKYAADAFAIFCTG 95 (121)
Q Consensus 73 ~~L~~lpGIG~~tA~~vl~f~~~ 95 (121)
..|.++|||||++...++- -||
T Consensus 541 S~Ld~I~GIG~kr~~~LL~-~Fg 562 (574)
T TIGR00194 541 SPLLKIPGVGEKRVQKLLK-YFG 562 (574)
T ss_pred HHHhcCCCCCHHHHHHHHH-HcC
Confidence 5799999999999988774 344
No 181
>PRK14454 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=49.49 E-value=24 Score=28.51 Aligned_cols=42 Identities=19% Similarity=0.204 Sum_probs=30.8
Q ss_pred HhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH---hhHHHhccCC
Q 033363 35 ATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG---ESWTHVTQLH 79 (121)
Q Consensus 35 la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~---~~~~~L~~lp 79 (121)
+...+.+||++.+.+.|....|++.|.+ ++.. .++++++.||
T Consensus 4 ~~~~~~~~l~~~~~~~g~~~~r~~qi~~---~~~~~~~~~~~~m~~l~ 48 (342)
T PRK14454 4 ILDFTLEELKEWMKENGEKKFRAKQIFD---WIYKKGVTDFDEMTNIP 48 (342)
T ss_pred cccCCHHHHHHHHHHcCCCchHHHHHHH---HHHHcCCCCHHHhcccc
Confidence 5678889999999999999889888854 3333 3455555554
No 182
>PRK02362 ski2-like helicase; Provisional
Probab=49.24 E-value=32 Score=30.38 Aligned_cols=39 Identities=15% Similarity=0.112 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHHHh---hHHHhccCCCCcHHHHHHHHHHhcC
Q 033363 57 APMIKRFSQEYLGE---SWTHVTQLHGVGKYAADAFAIFCTG 95 (121)
Q Consensus 57 a~~i~~~a~~i~~~---~~~~L~~lpGIG~~tA~~vl~f~~~ 95 (121)
+..+..+++.+..+ ..-+|.+|||||++.|......++.
T Consensus 633 ~~~~~~l~~~l~~gv~~~~~~L~~ip~i~~~~a~~l~~~gi~ 674 (737)
T PRK02362 633 ARAARELEKRVEYGVREELLDLVGLRGVGRVRARRLYNAGIE 674 (737)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHhCCCCCCHHHHHHHHHcCCC
Confidence 55566666666663 4567999999999999776654443
No 183
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=49.19 E-value=11 Score=29.64 Aligned_cols=24 Identities=21% Similarity=0.235 Sum_probs=17.7
Q ss_pred hHHHhccCCCCcHHHHHHHHHHhcC
Q 033363 71 SWTHVTQLHGVGKYAADAFAIFCTG 95 (121)
Q Consensus 71 ~~~~L~~lpGIG~~tA~~vl~f~~~ 95 (121)
.-+.+-.+||||||||--++ ..+|
T Consensus 196 ~sDnipGV~GIG~ktA~~Ll-~~~g 219 (310)
T COG0258 196 SSDNIPGVKGIGPKTALKLL-QEYG 219 (310)
T ss_pred cccCCCCCCCcCHHHHHHHH-HHhC
Confidence 35567779999999997766 3444
No 184
>PF12990 DUF3874: Domain of unknonw function from B. Theta Gene description (DUF3874); InterPro: IPR024450 This domain of unknown function if found in uncharacterised proteins from Bacteroides thetaiotaomicron and other Bacteroidetes.
Probab=49.02 E-value=21 Score=22.69 Aligned_cols=37 Identities=22% Similarity=0.423 Sum_probs=27.7
Q ss_pred HHHHHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHH
Q 033363 18 AGRVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKR 56 (121)
Q Consensus 18 v~~v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~K 56 (121)
+..++..|.+++|.. |.......+-++|+.+|+.+.+
T Consensus 28 a~~If~~L~k~~~~~--l~~~~~~~FGriL~~~gi~~kh 64 (73)
T PF12990_consen 28 AAEIFERLQKKSPAA--LRGSNPNHFGRILQKLGIPRKH 64 (73)
T ss_pred HHHHHHHHHHhCccc--cccCCHHHHHHHHHHcCCCccc
Confidence 456777888877764 7777888888888888886544
No 185
>PF14579 HHH_6: Helix-hairpin-helix motif; PDB: 2HPM_A 2HPI_A 3E0D_A 3F2C_A 3F2B_A 3F2D_A 2HQA_A 2HNH_A.
Probab=48.56 E-value=17 Score=23.40 Aligned_cols=20 Identities=15% Similarity=0.263 Sum_probs=15.5
Q ss_pred HhccCCCCcHHHHHHHHHHh
Q 033363 74 HVTQLHGVGKYAADAFAIFC 93 (121)
Q Consensus 74 ~L~~lpGIG~~tA~~vl~f~ 93 (121)
-|..++|||+.+|..+..--
T Consensus 28 gl~~Ikglg~~~a~~I~~~R 47 (90)
T PF14579_consen 28 GLSAIKGLGEEVAEKIVEER 47 (90)
T ss_dssp BGGGSTTS-HHHHHHHHHHH
T ss_pred hHhhcCCCCHHHHHHHHHhH
Confidence 38899999999999877543
No 186
>PHA00439 exonuclease
Probab=48.07 E-value=12 Score=29.85 Aligned_cols=22 Identities=27% Similarity=0.259 Sum_probs=18.5
Q ss_pred hhHHHhccCCCCcHHHHHHHHHH
Q 033363 70 ESWTHVTQLHGVGKYAADAFAIF 92 (121)
Q Consensus 70 ~~~~~L~~lpGIG~~tA~~vl~f 92 (121)
+.-+-+-.+|||| |||.-++.-
T Consensus 185 DsSDNIPGVpGIG-KTA~kLL~~ 206 (286)
T PHA00439 185 DSTDGYSGIPGWG-DTAEAFLEN 206 (286)
T ss_pred ccccCCCCCCCcC-HHHHHHHhC
Confidence 4567788999999 999998865
No 187
>PF12482 DUF3701: Phage integrase protein; InterPro: IPR022169 This domain family is found in bacteria, and is approximately 100 amino acids in length. The family is found in association with PF00589 from PFAM.
Probab=47.74 E-value=57 Score=21.77 Aligned_cols=50 Identities=8% Similarity=0.159 Sum_probs=33.4
Q ss_pred HHHHHhhcCChhHHHHHHHHHHHHHHHhhHHHhccCCCCcHHHHHHHHHHhcCCC
Q 033363 43 IEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLHGVGKYAADAFAIFCTGKW 97 (121)
Q Consensus 43 L~~~i~~~Gl~~~Ka~~i~~~a~~i~~~~~~~L~~lpGIG~~tA~~vl~f~~~~~ 97 (121)
+.+-|+..|+. +|-++-..+-..-...-.++||+|+.-|..|..|--..+
T Consensus 25 va~~L~aaGi~-----TL~dL~~~i~~rg~~Wwr~vpglG~~~A~~I~awLa~h~ 74 (96)
T PF12482_consen 25 VARRLAAAGIR-----TLADLVDRINRRGGRWWRAVPGLGAAGARRIEAWLAAHP 74 (96)
T ss_pred HHHHHHHcCCc-----hHHHHHHHHHHccchHHHhCcccchHHHHHHHHHHHHhH
Confidence 33445566663 455555555444446789999999999999988765443
No 188
>PRK14456 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=47.73 E-value=26 Score=28.64 Aligned_cols=43 Identities=19% Similarity=0.322 Sum_probs=33.0
Q ss_pred HHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH---hhHHHhccCC
Q 033363 34 TATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG---ESWTHVTQLH 79 (121)
Q Consensus 34 ~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~---~~~~~L~~lp 79 (121)
.+...+.+||++.+...|....|++.|.+ ++.. .++++.+.||
T Consensus 19 ~~~~~~~~el~~~~~~~g~~~~r~~qi~~---w~y~~~~~~~~~m~~l~ 64 (368)
T PRK14456 19 NIRNLRRQELTELLARLGEPAWRAAQLHQ---WLFSHRALSFEEMTTLS 64 (368)
T ss_pred CcccCCHHHHHHHHHHcCCCchHHHHHHH---HHHHcCCCCHHHhcccc
Confidence 48899999999999999999999988854 4433 3566666665
No 189
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=46.58 E-value=10 Score=26.96 Aligned_cols=18 Identities=17% Similarity=0.436 Sum_probs=15.7
Q ss_pred HHhccCCCCcHHHHHHHH
Q 033363 73 THVTQLHGVGKYAADAFA 90 (121)
Q Consensus 73 ~~L~~lpGIG~~tA~~vl 90 (121)
++|+.|.||||+.+..+-
T Consensus 67 DDLt~I~GIGPk~e~~Ln 84 (133)
T COG3743 67 DDLTRISGIGPKLEKVLN 84 (133)
T ss_pred ccchhhcccCHHHHHHHH
Confidence 789999999999987654
No 190
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=45.70 E-value=17 Score=32.97 Aligned_cols=22 Identities=18% Similarity=0.084 Sum_probs=19.0
Q ss_pred hHHHhccCCCCcHHHHHHHHHH
Q 033363 71 SWTHVTQLHGVGKYAADAFAIF 92 (121)
Q Consensus 71 ~~~~L~~lpGIG~~tA~~vl~f 92 (121)
..+.|.+|||||++.|..++.-
T Consensus 755 ~q~~L~~lPgI~~~~a~~ll~~ 776 (814)
T TIGR00596 755 PQDFLLKLPGVTKKNYRNLRKK 776 (814)
T ss_pred HHHHHHHCCCCCHHHHHHHHHH
Confidence 4566999999999999999875
No 191
>PRK14465 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=45.63 E-value=28 Score=28.24 Aligned_cols=45 Identities=24% Similarity=0.257 Sum_probs=31.2
Q ss_pred HhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHHhhHHHhccCC
Q 033363 35 ATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLH 79 (121)
Q Consensus 35 la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~~~~~~L~~lp 79 (121)
+...+.+||++.+...|....|++.|.+-.-.=.-.++++++.||
T Consensus 7 ~~~~~~~~l~~~~~~~g~~~fra~Qi~~wiy~~~~~~~~~mt~l~ 51 (342)
T PRK14465 7 LKGRTLKELSEIMVSLGEKKFRAKQIYHGLYVNRYETWDQFTTFS 51 (342)
T ss_pred cccCCHHHHHHHHHHcCCCchHHHHHHHHHHHcCCCCHHHhcccc
Confidence 677889999999999999999988886532221113455555554
No 192
>PRK11194 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=44.94 E-value=32 Score=28.24 Aligned_cols=43 Identities=12% Similarity=0.307 Sum_probs=32.3
Q ss_pred HHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH---hhHHHhccCC
Q 033363 34 TATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG---ESWTHVTQLH 79 (121)
Q Consensus 34 ~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~---~~~~~L~~lp 79 (121)
.|...+.+||++.+.+.|....||+.|.+ ++.. .++++++.||
T Consensus 7 ~l~~~~~~el~~~~~~~g~~~~ra~qi~~---w~y~~~~~~~~~mt~l~ 52 (372)
T PRK11194 7 NLLDLNRQQMREFFAELGEKPFRADQVMK---WIYHYGCDDFDEMTNIN 52 (372)
T ss_pred CcccCCHHHHHHHHHHcCCCchHHHHHHH---HHHhcCCCCHHHhcccc
Confidence 36788999999999999999999988855 3433 3556666654
No 193
>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A.
Probab=44.77 E-value=30 Score=16.81 Aligned_cols=16 Identities=25% Similarity=0.210 Sum_probs=13.8
Q ss_pred HHHHHHHHHHHHhCCC
Q 033363 16 LKAGRVISDLFTLCPD 31 (121)
Q Consensus 16 ~~v~~v~~~l~~~~pt 31 (121)
.++...+.++...||+
T Consensus 17 ~~A~~~~~~~~~~~P~ 32 (33)
T PF13174_consen 17 DEAIEYFQRLIKRYPD 32 (33)
T ss_dssp HHHHHHHHHHHHHSTT
T ss_pred HHHHHHHHHHHHHCcC
Confidence 5678899999999995
No 194
>PRK14459 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=44.75 E-value=28 Score=28.66 Aligned_cols=43 Identities=26% Similarity=0.430 Sum_probs=33.4
Q ss_pred HHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH---hhHHHhccCC
Q 033363 34 TATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG---ESWTHVTQLH 79 (121)
Q Consensus 34 ~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~---~~~~~L~~lp 79 (121)
.|...+.+||++.+..+|....||+.|.+ ++.. .++++.+.||
T Consensus 23 ~l~~l~~~el~~~~~~~g~~~~ra~Qi~~---wiy~~~~~~~~~mt~l~ 68 (373)
T PRK14459 23 HLADLTPAERREAVAELGLPAFRAKQLAR---HYFGRLTADPAQMTDLP 68 (373)
T ss_pred CcccCCHHHHHHHHHHcCCCcHHHHHHHH---HHHhcCCCCHHHhcccC
Confidence 58899999999999999999999988854 4433 3566666665
No 195
>PRK14460 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=44.54 E-value=32 Score=27.93 Aligned_cols=45 Identities=20% Similarity=0.248 Sum_probs=30.6
Q ss_pred HhcCCHHHHHHHHh-hcCChhHHHHHHHHHHHHHHHhhHHHhccCC
Q 033363 35 ATEVDAEEIEKIIS-TLGLQKKRAPMIKRFSQEYLGESWTHVTQLH 79 (121)
Q Consensus 35 la~a~~~eL~~~i~-~~Gl~~~Ka~~i~~~a~~i~~~~~~~L~~lp 79 (121)
+...+.+||++.+. +.|....|++.|.+-.-.=...++++++.||
T Consensus 4 ~~~~~~~~l~~~~~~~~g~~~~r~~qi~~~~~~~~~~~~~~m~~l~ 49 (354)
T PRK14460 4 ILNLTYPELEAFITAELGEPRFRARQIWQWLWQKGARDFDSMTNVS 49 (354)
T ss_pred cccCCHHHHHHHHHHhcCCCchHHHHHHHHHHHcCCCCHHHhcccc
Confidence 56788899999999 9999988888875532211113455555554
No 196
>TIGR00048 radical SAM enzyme, Cfr family. A Staphylococcus sciuri plasmid-borne member of this family, Cfr, has been identified as essential to transferrable resistance to chloramphenicol and florfenicol by an unknown mechanism. A 14-15 residue cluster with four perfectly conserved Cys residues suggests this protein may be an enzyme with an iron-sulfur cluster. The Cys cluster is part of the radical SAM domain, suggested to provide a general mechanism by which the Fe-S center cleaves S-adenosylmethionine to initiate radical-based catalysis. Members of this family lack apparent transmembrane domains.
Probab=44.30 E-value=30 Score=28.11 Aligned_cols=43 Identities=21% Similarity=0.312 Sum_probs=31.8
Q ss_pred HHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH---hhHHHhccCC
Q 033363 34 TATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG---ESWTHVTQLH 79 (121)
Q Consensus 34 ~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~---~~~~~L~~lp 79 (121)
.+...+.+||++.+...|....|++.|.+ ++.. .++++++.||
T Consensus 8 ~~~~~~~~~l~~~~~~~g~~~~r~~qi~~---~~~~~~~~~~~~m~~l~ 53 (355)
T TIGR00048 8 SLYDLTLQELRQWLKDLGEKPFRAKQIYK---WLYHKGKDSFDDMTNLS 53 (355)
T ss_pred CcccCCHHHHHHHHHHcCCCchhHHHHHH---HHHHcCCCCHHHccccC
Confidence 47888999999999999999999988854 3433 3455555554
No 197
>smart00611 SEC63 Domain of unknown function in Sec63p, Brr2p and other proteins.
Probab=44.10 E-value=42 Score=25.98 Aligned_cols=41 Identities=17% Similarity=0.157 Sum_probs=30.4
Q ss_pred hcCChhHHHHHHHHHHHHHHHhhH---HHhccCCCCcHHHHHHHH
Q 033363 49 TLGLQKKRAPMIKRFSQEYLGESW---THVTQLHGVGKYAADAFA 90 (121)
Q Consensus 49 ~~Gl~~~Ka~~i~~~a~~i~~~~~---~~L~~lpGIG~~tA~~vl 90 (121)
..|.. .-+..+.++++.+..+.+ ..|.+|||||+..+..+-
T Consensus 125 ~~~~~-~~~~~~l~L~q~i~q~~w~~~~~L~Qlp~i~~~~~~~l~ 168 (312)
T smart00611 125 ERGWL-STALNALNLSQMIIQALWPTDSPLLQLPHLPEEILKRLE 168 (312)
T ss_pred hcchH-HHHHHHHHHHHHHHHhhCCCCCccccCCCCCHHHHHHHH
Confidence 34554 347788888888877433 469999999999888665
No 198
>KOG3337 consensus Protein similar to predicted member of the intramitochondrial sorting protein family [Intracellular trafficking, secretion, and vesicular transport]
Probab=43.01 E-value=19 Score=26.96 Aligned_cols=31 Identities=13% Similarity=0.313 Sum_probs=25.7
Q ss_pred HHHHHHHHHhCCCHHHHhcCCHHHHHHHHhh
Q 033363 19 GRVISDLFTLCPDAKTATEVDAEEIEKIIST 49 (121)
Q Consensus 19 ~~v~~~l~~~~pt~~~la~a~~~eL~~~i~~ 49 (121)
+.|..+|+.+||+|.+.-=.+.+-|++-+.+
T Consensus 16 d~VssAfw~RYPNpySkHVlSeDvleR~Vt~ 46 (201)
T KOG3337|consen 16 DQVSSAFWQRYPNPYSKHVLSEDVLEREVTD 46 (201)
T ss_pred HHHHHHHHHhCCCccccccccHHHHhhhcCc
Confidence 5788899999999988877888888877653
No 199
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=42.94 E-value=36 Score=30.41 Aligned_cols=29 Identities=7% Similarity=-0.081 Sum_probs=23.9
Q ss_pred HHhhHHHhccCCCCcHHHHHHHHHHhcCC
Q 033363 68 LGESWTHVTQLHGVGKYAADAFAIFCTGK 96 (121)
Q Consensus 68 ~~~~~~~L~~lpGIG~~tA~~vl~f~~~~ 96 (121)
.+.+.++|.++||||+++|..+.--+...
T Consensus 635 ~~As~eel~~v~gi~~~~A~~i~~~~~~~ 663 (691)
T PRK14672 635 QSATPQDIATAIHIPLTQAHTILHAATRS 663 (691)
T ss_pred HhCCHHHHHhCCCCCHHHHHHHHHHhhcc
Confidence 33588999999999999999998766543
No 200
>PRK05755 DNA polymerase I; Provisional
Probab=42.67 E-value=15 Score=33.16 Aligned_cols=22 Identities=18% Similarity=0.339 Sum_probs=18.2
Q ss_pred hhHHHhccCCCCcHHHHHHHHH
Q 033363 70 ESWTHVTQLHGVGKYAADAFAI 91 (121)
Q Consensus 70 ~~~~~L~~lpGIG~~tA~~vl~ 91 (121)
+.-+-+..+||||||||.-++.
T Consensus 184 D~sDnipGv~GiG~ktA~~Ll~ 205 (880)
T PRK05755 184 DSSDNIPGVPGIGEKTAAKLLQ 205 (880)
T ss_pred CccCCCCCCCCccHHHHHHHHH
Confidence 3456789999999999988774
No 201
>PRK14457 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=42.08 E-value=34 Score=27.71 Aligned_cols=46 Identities=13% Similarity=0.051 Sum_probs=30.8
Q ss_pred HHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHHhhHHHhccCC
Q 033363 34 TATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLH 79 (121)
Q Consensus 34 ~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~~~~~~L~~lp 79 (121)
.+...+.+||++.+...|....|++.|.+-.-.=...+.++.+.||
T Consensus 3 ~~~~~~~~~l~~~~~~~g~~~~r~~qi~~w~~~~~~~~~~~m~~l~ 48 (345)
T PRK14457 3 PLLGRSLAELEDWAVAQGQPAFRGRQLHDWLYNKGVRSLDEISVLP 48 (345)
T ss_pred ccccCCHHHHHHHHHHcCCCchHHHHHHHHHHhcCCCCHHHcCccC
Confidence 3677888999999999999988988885432221113455555554
No 202
>PRK14466 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=41.87 E-value=35 Score=27.84 Aligned_cols=45 Identities=18% Similarity=0.204 Sum_probs=31.4
Q ss_pred HhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHHhhHHHhccCC
Q 033363 35 ATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLH 79 (121)
Q Consensus 35 la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~~~~~~L~~lp 79 (121)
+...+.+||++.+...|....||+.|.+-.-.=.-.++++++.||
T Consensus 7 l~~l~~~el~~~~~~~g~~~fra~Qi~~wi~~~~~~~~~~mt~l~ 51 (345)
T PRK14466 7 LLGMTLEELQSVAKRLGMPAFAAKQIASWLYDKKVTSIDEMTNIS 51 (345)
T ss_pred cccCCHHHHHHHHHHcCCCchHHHHHHHHHHhcCCCCHHHHhhhh
Confidence 678889999999999999999998885432221113455555554
No 203
>PRK14461 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=41.21 E-value=36 Score=28.07 Aligned_cols=43 Identities=19% Similarity=0.268 Sum_probs=32.4
Q ss_pred HHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH---hhHHHhccCC
Q 033363 34 TATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG---ESWTHVTQLH 79 (121)
Q Consensus 34 ~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~---~~~~~L~~lp 79 (121)
.+...+.+||++.+...|....||+.|.+ ++.. .++++.+.||
T Consensus 9 ~l~~l~~~el~~~~~~~g~~~fRa~Qi~~---wiy~~~~~~~~~mtnlp 54 (371)
T PRK14461 9 NLYDLNLAELTELLTAWGQPAFRARQLYR---HLYVNLADSVLAMTDLP 54 (371)
T ss_pred CcccCCHHHHHHHHHHcCCCchHHHHHHH---HHHHcCCCCHHHccccC
Confidence 37888999999999999999999888854 4333 3556666655
No 204
>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed
Probab=41.02 E-value=1.6e+02 Score=22.45 Aligned_cols=83 Identities=5% Similarity=-0.034 Sum_probs=52.4
Q ss_pred HHHHHHHhCC-CHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHHh-------------hHHHhccCCCCcHHHH
Q 033363 21 VISDLFTLCP-DAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGE-------------SWTHVTQLHGVGKYAA 86 (121)
Q Consensus 21 v~~~l~~~~p-t~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~~-------------~~~~L~~lpGIG~~tA 86 (121)
.|.+-+..|. |.++|.+.+|.. +.--+..+++|+.+.++ .+++|.+.-||-+||-
T Consensus 136 ~~~~~L~~~gi~~~dL~~~sPkh-----------~d~r~~~i~ia~~~~~~~~l~~~l~~kk~LP~k~l~~~~~v~rkti 204 (237)
T PRK08311 136 EFKKELKEFGITFEDLVKESPKH-----------RDTRENAIKIAKTIAENEELLEKLKRKKKLPLKELEKRVKVSRKTL 204 (237)
T ss_pred HHHHHHHHcCCcHHHHhhcCCCC-----------HHHHHHHHHHHHHHHcCHHHHHHHHHhCCCCHHHHHHHcCCCHHHH
Confidence 3444455564 888888888764 22236778889988872 5789999999999987
Q ss_pred HHHHHHhcCCCCccCcch-HHHHHHHHHHH
Q 033363 87 DAFAIFCTGKWDRVRPTD-HMLNYYWEFLV 115 (121)
Q Consensus 87 ~~vl~f~~~~~~~v~p~D-~~l~~~~~wl~ 115 (121)
+=-.-|-.... -++..| ..++.|+.+..
T Consensus 205 er~rkyIia~~-li~~~~~~~l~~y~~~~~ 233 (237)
T PRK08311 205 ERNRKYIIAVA-IILAGDYPYLKEYIRGEE 233 (237)
T ss_pred HhhhHHHHHHH-HHHcCCcHHHHHHHhhhc
Confidence 64333322221 122233 46777776643
No 205
>PF08625 Utp13: Utp13 specific WD40 associated domain; InterPro: IPR013934 A large ribonuclear protein complex is required for the processing of the small-ribosomal-subunit rRNA - the small-subunit (SSU) processome [, ]. This preribosomal complex contains the U3 snoRNA and at least 40 proteins, which have the following properties: They are nucleolar. They are able to coimmunoprecipitate with the U3 snoRNA and Mpp10 (a protein specific to the SSU processome). They are required for 18S rRNA biogenesis. There appears to be a linkage between polymerase I transcription and the formation of the SSU processome; as some, but not all, of the SSU processome components are required for pre-rRNA transcription initiation. These SSU processome components have been termed t-Utps. They form a pre-complex with pre-18S rRNA in the absence of snoRNA U3 and other SSU processome components. It has been proposed that the t-Utp complex proteins are both rDNA and rRNA binding proteins that are involved in the initiation of pre18S rRNA transcription. Initially binding to rDNA then associating with the 5' end of the nascent pre18S rRNA. The t-Utpcomplex forms the nucleus around which the rest of the SSU processome components, including snoRNA U3, assemble []. From electron microscopy the SSU processome may correspond to the terminal knobs visualized at the 5' ends of nascent 18S rRNA. Utp13 is a nucleolar protein and component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA []. Upt13 is also a component of the Pwp2 complex that forms part of a stable particle subunit independent of the U3 small nucleolar ribonucleoprotein that is essential for the initial assembly steps of the 90S pre-ribosome []. Components of the Pwp2 complex are: Utp1 (Pwp2), Utp6, Utp12 (Dip2), Utp13, Utp18, and Utp21. The relationship between the Pwp2 complex and the t-Utps complex [] that also associates with the 5' end of nascent pre-18S rRNA is unclear. ; GO: 0006364 rRNA processing, 0032040 small-subunit processome
Probab=40.65 E-value=54 Score=23.18 Aligned_cols=52 Identities=13% Similarity=0.224 Sum_probs=33.8
Q ss_pred HHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH-----hhHHHhccCCCCcHHH
Q 033363 33 KTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG-----ESWTHVTQLHGVGKYA 85 (121)
Q Consensus 33 ~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-----~~~~~L~~lpGIG~~t 85 (121)
+.+...+.+++..+++-+.-++..+|+-. +|+.+.. -..++|.++||+..-.
T Consensus 53 ~~i~~L~~~~l~~LL~~ir~WNTNsr~~~-vAQ~vL~~il~~~~~~~L~~~~~~~~~l 109 (141)
T PF08625_consen 53 EVIKKLDDEQLEKLLRFIRDWNTNSRTSH-VAQRVLNAILKSHPPEELLKIPGLKEIL 109 (141)
T ss_pred HHHHhcCHHHHHHHHHHHHHhhcccccHH-HHHHHHHHHHHhCCHHHHHccccHHHHH
Confidence 34566667777777776666666666543 3554444 3678899999986544
No 206
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=40.57 E-value=70 Score=28.13 Aligned_cols=19 Identities=16% Similarity=0.221 Sum_probs=9.5
Q ss_pred hHHHhccCCCCcHHHHHHHHH
Q 033363 71 SWTHVTQLHGVGKYAADAFAI 91 (121)
Q Consensus 71 ~~~~L~~lpGIG~~tA~~vl~ 91 (121)
+.++|.++ ||+++|..+..
T Consensus 599 s~eeL~~v--ig~k~A~~I~~ 617 (621)
T PRK14671 599 SLEELAAV--AGPKTAETIYR 617 (621)
T ss_pred CHHHHHHH--hCHHHHHHHHH
Confidence 34444444 55555555543
No 207
>PRK00419 DNA primase small subunit; Reviewed
Probab=40.24 E-value=38 Score=28.00 Aligned_cols=41 Identities=15% Similarity=0.234 Sum_probs=25.0
Q ss_pred CChhHHHHHHHHHHHHHHHhhHHHhccCCCCcHHHHHHHHH
Q 033363 51 GLQKKRAPMIKRFSQEYLGESWTHVTQLHGVGKYAADAFAI 91 (121)
Q Consensus 51 Gl~~~Ka~~i~~~a~~i~~~~~~~L~~lpGIG~~tA~~vl~ 91 (121)
|..++=++++......+.+...+.|.++.|||..+|.-++-
T Consensus 199 Gw~~R~~~~~~~~~~~l~~~~~~~l~~~~gi~~~~~~~~l~ 239 (376)
T PRK00419 199 GWGRRFARRLGYFIDHLRELALERLEEFDGIGEGTAKKILK 239 (376)
T ss_pred cHHHHHHHHHHHHHHHHhhhhhhhhhhhcccchhHHHHHHH
Confidence 44444444444443444444444788888999988887773
No 208
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=39.91 E-value=39 Score=27.63 Aligned_cols=26 Identities=23% Similarity=0.174 Sum_probs=22.6
Q ss_pred hHHHhccCCCCcHHHHHHHHHHhcCC
Q 033363 71 SWTHVTQLHGVGKYAADAFAIFCTGK 96 (121)
Q Consensus 71 ~~~~L~~lpGIG~~tA~~vl~f~~~~ 96 (121)
.++-+..+.|||.+||+-+-..++.-
T Consensus 95 ~lklFtnifGvG~ktA~~Wy~~GfrT 120 (353)
T KOG2534|consen 95 SLKLFTNIFGVGLKTAEKWYREGFRT 120 (353)
T ss_pred HHHHHHHHhccCHHHHHHHHHhhhhH
Confidence 57789999999999999998888754
No 209
>TIGR02239 recomb_RAD51 DNA repair protein RAD51. This eukaryotic sequence family consists of RAD51, a protein involved in DNA homologous recombination and repair. It is similar in sequence the exclusively meiotic recombinase DMC1 (TIGR02238), to archaeal families RadA (TIGR02236) and RadB (TIGR02237), and to bacterial RecA (TIGR02012).
Probab=39.73 E-value=61 Score=25.77 Aligned_cols=44 Identities=11% Similarity=0.112 Sum_probs=34.5
Q ss_pred HHHH-HhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH
Q 033363 23 SDLF-TLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG 69 (121)
Q Consensus 23 ~~l~-~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~ 69 (121)
.+|. ..|.|.++++.+++++|.++ .|++..+++.+...+..+..
T Consensus 15 ~~l~~~g~~t~~~~~~~~~~~L~~i---~~ls~~~~~~~~~~~~~~~~ 59 (316)
T TIGR02239 15 KKLQEAGLHTVESVAYAPKKQLLEI---KGISEAKADKILAEAAKLVP 59 (316)
T ss_pred HHHHHcCCCcHHHHHhCCHHHHHHH---hCCCHHHHHHHHHHHHHhcc
Confidence 3444 35899999999999999775 68888999888876665544
No 210
>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=38.99 E-value=70 Score=28.48 Aligned_cols=55 Identities=20% Similarity=0.235 Sum_probs=35.6
Q ss_pred hcCCHHHHHHHHhh---cCChhHHHHHHHHH-----HHHHHHhhHHHhccCCCCcHHHHHHHHH
Q 033363 36 TEVDAEEIEKIIST---LGLQKKRAPMIKRF-----SQEYLGESWTHVTQLHGVGKYAADAFAI 91 (121)
Q Consensus 36 a~a~~~eL~~~i~~---~Gl~~~Ka~~i~~~-----a~~i~~~~~~~L~~lpGIG~~tA~~vl~ 91 (121)
.-.+.+.+...|.+ =|..+..|+.|.+. ...+ ++..+.|.++||||++.++.+..
T Consensus 73 ~p~~~~~i~~yL~s~~~~GIG~~~A~~iv~~fg~~~~~~i-~~~~~~L~~v~gi~~~~~~~i~~ 135 (720)
T TIGR01448 73 APTSKEGIVAYLSSRSIKGVGKKLAQRIVKTFGEAAFDVL-DDDPEKLLEVPGISKANLEKFVS 135 (720)
T ss_pred CCCCHHHHHHHHhcCCCCCcCHHHHHHHHHHhCHhHHHHH-HhCHHHHhcCCCCCHHHHHHHHH
Confidence 33455666666653 24556677777643 2222 24577899999999999987765
No 211
>COG1701 Uncharacterized protein conserved in archaea [Function unknown]
Probab=38.79 E-value=64 Score=25.05 Aligned_cols=54 Identities=20% Similarity=0.299 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHH
Q 033363 11 EIAILLKAGRVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEY 67 (121)
Q Consensus 11 ~~~~~~~v~~v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i 67 (121)
.|++-.++.++++++.+ -...+.+.+.+|++++++..--.+.=++.|+.+.+.+
T Consensus 193 sItIVDnivRA~p~li~---~~~em~~~~reel~~iv~~ydN~~~l~eal~~I~~rL 246 (256)
T COG1701 193 SITIVDNIVRAVPNLIE---FVKEMKNASREELEEIVENYDNKEVLAEALKHIAERL 246 (256)
T ss_pred ceeeeHHHHHHHHHHHH---HHHHHhccCHHHHHHHHHhhccHHHHHHHHHHHHHHH
Confidence 33333344555555554 3567889999999999875444333344444444433
No 212
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=37.75 E-value=55 Score=28.50 Aligned_cols=34 Identities=21% Similarity=0.267 Sum_probs=15.9
Q ss_pred HHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHH
Q 033363 24 DLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIK 61 (121)
Q Consensus 24 ~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~ 61 (121)
.|++.|.|.+.+.+|+.|||.+ +|++...|+.|+
T Consensus 529 ~Ll~~Fgs~~~ik~As~eeL~~----vgi~~~~A~~I~ 562 (567)
T PRK14667 529 IIYRNFKTLYDFLKADDEELKK----LGIPPSVKQEVK 562 (567)
T ss_pred HHHHHhCCHHHHHhCCHHHHHH----cCCCHHHHHHHH
Confidence 3444455555555555555332 244444444443
No 213
>PLN03186 DNA repair protein RAD51 homolog; Provisional
Probab=37.70 E-value=67 Score=26.00 Aligned_cols=43 Identities=9% Similarity=0.114 Sum_probs=34.1
Q ss_pred HHHH-hCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH
Q 033363 24 DLFT-LCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG 69 (121)
Q Consensus 24 ~l~~-~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~ 69 (121)
+|.+ .|.|.++++.+++.+|.++ .|++..|++.+...+.....
T Consensus 43 kL~~~g~~T~~~~~~~~~~~L~~i---~~is~~~~~~~~~~~~~~~~ 86 (342)
T PLN03186 43 KLKDAGIHTVESLAYAPKKDLLQI---KGISEAKVEKILEAASKLVP 86 (342)
T ss_pred HHHHcCCCcHHHHHhCCHHHHHHh---cCCCHHHHHHHHHHHHHhcc
Confidence 4443 4899999999999998765 78999999888887765543
No 214
>PRK14470 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=37.41 E-value=40 Score=27.25 Aligned_cols=43 Identities=7% Similarity=0.050 Sum_probs=27.8
Q ss_pred hcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHHhhHHHhccCC
Q 033363 36 TEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLH 79 (121)
Q Consensus 36 a~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~~~~~~L~~lp 79 (121)
.+.+.+||++.+...|....||+.|.+-.-.=... +++.+.||
T Consensus 2 ~~~~~~~~~~~~~~~g~~~~r~~qi~~~~~~~~~~-~~~m~~l~ 44 (336)
T PRK14470 2 LHLSGQDSRALARPAGISLEDARRITGAVIGRGAP-LRSARNVR 44 (336)
T ss_pred CCCCHHHHHHHHHHcCCCcHHHHHHHHHHHhCCCC-HHHhccCC
Confidence 35678888888988999888888775532211112 55555554
No 215
>PF14964 DUF4507: Domain of unknown function (DUF4507)
Probab=36.79 E-value=1e+02 Score=25.42 Aligned_cols=71 Identities=17% Similarity=0.195 Sum_probs=50.3
Q ss_pred HhhcCChhHH----HHHHHHHHHHHHH-------hhHHHhccCCCCcHHHHHHHHHHhcCCCC-------ccCcchHHHH
Q 033363 47 ISTLGLQKKR----APMIKRFSQEYLG-------ESWTHVTQLHGVGKYAADAFAIFCTGKWD-------RVRPTDHMLN 108 (121)
Q Consensus 47 i~~~Gl~~~K----a~~i~~~a~~i~~-------~~~~~L~~lpGIG~~tA~~vl~f~~~~~~-------~v~p~D~~l~ 108 (121)
|...|.+=++ ..+-.++++.+++ +..+.|..++.+.|--+..++...-...+ ...|-+.-+.
T Consensus 129 L~~a~~Wmqq~g~~s~~s~~La~~iv~dy~~l~p~~~~~L~~l~~~sP~F~a~fitavt~ly~~~~~~~~~~~PP~~LLe 208 (362)
T PF14964_consen 129 LNCAATWMQQLGCSSSYSLRLAQMIVEDYCCLSPGSQETLKQLPNVSPRFCANFITAVTSLYDNPQRSSYEKPPPPSLLE 208 (362)
T ss_pred HHHHHHHHHHcCCCcHHHHHHHHHHHHHHhccCCccHHHHHHhhccChHHHHHHHHHHHHHccCcccccccCCCCHHHHH
Confidence 3344444444 5688888998888 47899999999999888777754432221 2577788888
Q ss_pred HHHHHHHHh
Q 033363 109 YYWEFLVST 117 (121)
Q Consensus 109 ~~~~wl~~~ 117 (121)
-..+|+.+.
T Consensus 209 vI~~Wi~~n 217 (362)
T PF14964_consen 209 VITEWISEN 217 (362)
T ss_pred HHHHHHhCC
Confidence 888888654
No 216
>COG5346 Predicted membrane protein [Function unknown]
Probab=36.55 E-value=1.5e+02 Score=20.91 Aligned_cols=77 Identities=10% Similarity=0.025 Sum_probs=46.5
Q ss_pred HHHHHHHHHHHHHHHHHH-HhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH---hhHHHhccC-CC---
Q 033363 9 LKEIAILLKAGRVISDLF-TLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG---ESWTHVTQL-HG--- 80 (121)
Q Consensus 9 ~~~~~~~~~v~~v~~~l~-~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~---~~~~~L~~l-pG--- 80 (121)
.++++.+++++..+.+-| +.-|.|..|+.- +. |- ..-++.|..+|+.=.+ .....+.++ .-
T Consensus 17 a~~~~~~e~~~n~~~k~F~~~LPpp~~l~qY--ns----I~-----pnt~~rimaMAekEQahrH~~~~k~~~~q~r~~~ 85 (136)
T COG5346 17 AKTFSSNEPDNNFYRKKFEHILPPPDLLSQY--NS----IY-----PNTLQRIMAMAEKEQAHRHAIDLKNLKIQRRGQL 85 (136)
T ss_pred HHHHhhccHHHHHHHHHhcccCCCHHHHHHH--Hh----hc-----CCHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHH
Confidence 445566777777766555 456888887752 22 22 2445778888876544 111111111 12
Q ss_pred CcHHHHHHHHHHhcCC
Q 033363 81 VGKYAADAFAIFCTGK 96 (121)
Q Consensus 81 IG~~tA~~vl~f~~~~ 96 (121)
+|++++-+.++|++.-
T Consensus 86 ~~~~tril~liFgi~L 101 (136)
T COG5346 86 YAKLTRILLLIFGIFL 101 (136)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 7899999999999864
No 217
>PRK14453 chloramphenicol/florfenicol resistance protein; Provisional
Probab=36.18 E-value=57 Score=26.47 Aligned_cols=43 Identities=16% Similarity=0.183 Sum_probs=28.0
Q ss_pred cCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHHhhHHHhccCC
Q 033363 37 EVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLH 79 (121)
Q Consensus 37 ~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~~~~~~L~~lp 79 (121)
+.+.+||++.+...|....|++.|.+-.-.=...++++++.||
T Consensus 4 ~~~~~~l~~~~~~~g~~~~r~~qi~~~~~~~~~~~~~~m~~l~ 46 (347)
T PRK14453 4 KTKYGKMKQILSNLKLPDYRYEQITKAIFKQRIDNFEDMHILP 46 (347)
T ss_pred cCCHHHHHHHHHHcCCCcHHHHHHHHHHHhcCCCCHHHhccCC
Confidence 4567888888989999888888875532211113556666555
No 218
>PF06568 DUF1127: Domain of unknown function (DUF1127); InterPro: IPR009506 This family is found in several hypothetical bacterial proteins. In some cases it represents it represents the C-terminal region whereas in others it represents the whole sequence.
Probab=36.16 E-value=50 Score=18.09 Aligned_cols=29 Identities=10% Similarity=0.255 Sum_probs=21.0
Q ss_pred HHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChh
Q 033363 22 ISDLFTLCPDAKTATEVDAEEIEKIISTLGLQK 54 (121)
Q Consensus 22 ~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~ 54 (121)
+.+..+..-+-.+|..++..+ |+.+|+++
T Consensus 7 ~~~~~~~rrtr~~L~~Lsd~~----L~DIGl~R 35 (40)
T PF06568_consen 7 LRRWRRRRRTRRELAELSDRQ----LADIGLTR 35 (40)
T ss_pred HHHHHHHHHHHHHHccCCHHH----HHHcCCCH
Confidence 334445556778999999998 56789974
No 219
>cd01703 PolY_Pol_iota DNA Polymerase iota. Pol iota, also called Rad30B, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Pol iota is thought to be one of the least efficient polymerases, particularly when opposite pyrimidines; it can incorporate the correct nucleotide opposite a purine much more efficiently than opposite a pyrimidine, and prefers to insert guanosine instead of adenosine opposite thymidine. Pol iota is believed to use Hoogsteen rather than Watson-Crick base pairing, which may explain the varying efficiency for different template nucleotides.
Probab=36.09 E-value=24 Score=28.89 Aligned_cols=22 Identities=14% Similarity=0.282 Sum_probs=18.7
Q ss_pred HhccCCCCcHHHHHHHHHHhcC
Q 033363 74 HVTQLHGVGKYAADAFAIFCTG 95 (121)
Q Consensus 74 ~L~~lpGIG~~tA~~vl~f~~~ 95 (121)
.+.+|||||++|+.-+..++..
T Consensus 173 pv~~l~GiG~~~~~kL~~~GI~ 194 (379)
T cd01703 173 DLRKIPGIGYKTAAKLEAHGIS 194 (379)
T ss_pred CccccCCcCHHHHHHHHHcCCC
Confidence 4789999999999988877654
No 220
>PF06744 DUF1215: Protein of unknown function (DUF1215); InterPro: IPR010623 This domain represents a conserved region situated towards the C-terminal end of several hypothetical bacterial proteins of unknown function. A few members resemble the ImcF protein, which has been proposed [] to be involved in Vibrio cholerae cell surface reorganisation that results in increased adherence to epithelial cells line and increased conjugation frequency.
Probab=35.56 E-value=34 Score=23.28 Aligned_cols=36 Identities=11% Similarity=0.222 Sum_probs=28.0
Q ss_pred HHHHHHH-HHHhCC-CHHHHhcCCHHHHHHHHhhcCCh
Q 033363 18 AGRVISD-LFTLCP-DAKTATEVDAEEIEKIISTLGLQ 53 (121)
Q Consensus 18 v~~v~~~-l~~~~p-t~~~la~a~~~eL~~~i~~~Gl~ 53 (121)
|-..|.+ +..+|| ++.+-.+++.+|+++++.|-|.-
T Consensus 43 V~~~~~~~i~gRYPF~~~s~~dv~l~Df~~fF~p~G~l 80 (125)
T PF06744_consen 43 VYPFCRQAIAGRYPFDPDSSRDVSLADFARFFGPGGVL 80 (125)
T ss_pred HHHHHHHHhcCCCCCCCCCcccCCHHHHHHHhcCCCcH
Confidence 4444444 335899 77899999999999999999875
No 221
>KOG1201 consensus Hydroxysteroid 17-beta dehydrogenase 11 [Secondary metabolites biosynthesis, transport and catabolism]
Probab=35.50 E-value=1e+02 Score=24.77 Aligned_cols=81 Identities=19% Similarity=0.126 Sum_probs=54.2
Q ss_pred HHHHHHHHHHHHHHHhCC------------CHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH---------hh
Q 033363 13 AILLKAGRVISDLFTLCP------------DAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG---------ES 71 (121)
Q Consensus 13 ~~~~~v~~v~~~l~~~~p------------t~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~---------~~ 71 (121)
+.++.+...-.++.+.+. +...+.+.+.+||++.+. ++.- .--.++++++-...+ ..
T Consensus 96 s~~eei~~~a~~Vk~e~G~V~ILVNNAGI~~~~~ll~~~d~ei~k~~~-vN~~-~~f~t~kaFLP~M~~~~~GHIV~IaS 173 (300)
T KOG1201|consen 96 SDREEIYRLAKKVKKEVGDVDILVNNAGIVTGKKLLDCSDEEIQKTFD-VNTI-AHFWTTKAFLPKMLENNNGHIVTIAS 173 (300)
T ss_pred CCHHHHHHHHHHHHHhcCCceEEEeccccccCCCccCCCHHHHHHHHH-HhhH-HHHHHHHHHhHHHHhcCCceEEEehh
Confidence 334555555666665543 345677788999888653 2221 223455566665555 26
Q ss_pred HHHhccCCCCcHHHHHHHHHHhcC
Q 033363 72 WTHVTQLHGVGKYAADAFAIFCTG 95 (121)
Q Consensus 72 ~~~L~~lpGIG~~tA~~vl~f~~~ 95 (121)
..-+...||+++|+|.=..+++|.
T Consensus 174 ~aG~~g~~gl~~YcaSK~a~vGfh 197 (300)
T KOG1201|consen 174 VAGLFGPAGLADYCASKFAAVGFH 197 (300)
T ss_pred hhcccCCccchhhhhhHHHHHHHH
Confidence 678999999999999999998884
No 222
>PF03081 Exo70: Exo70 exocyst complex subunit; InterPro: IPR004140 The Exo70 protein forms one subunit of the exocyst complex. First discovered in Saccharomyces cerevisiae [], Exo70 and other exocyst proteins have been observed in several other eukaryotes, including humans. In S. cerevisiae, the exocyst complex is involved in the late stages of exocytosis, and is localized at the tip of the bud, the major site of exocytosis in yeast []. Exo70 interacts with the Rho3 GTPase []. This interaction mediates one of the three known functions of Rho3 in cell polarity: vesicle docking and fusion with the plasma membrane (the other two functions are regulation of actin polarity and transport of exocytic vesicles from the mother cell to the bud) []. In humans, the functions of Exo70 and the exocyst complex are less well characterised: Exo70 is expressed in several tissues and is thought to also be involved in exocytosis [].; GO: 0006887 exocytosis, 0000145 exocyst; PDB: 2PFV_A 2B7M_B 2B1E_A 2PFT_A.
Probab=35.35 E-value=39 Score=26.80 Aligned_cols=35 Identities=11% Similarity=0.234 Sum_probs=25.8
Q ss_pred HHHHHHHHHHHHhCCCH----HHHhcCCHHHHHHHHhhc
Q 033363 16 LKAGRVISDLFTLCPDA----KTATEVDAEEIEKIISTL 50 (121)
Q Consensus 16 ~~v~~v~~~l~~~~pt~----~~la~a~~~eL~~~i~~~ 50 (121)
+.|.++|.+|.++|+.. +.-..-++++|++.|..+
T Consensus 333 ~~v~p~Y~~F~~~~~~~~~~~~Kyikyt~~~le~~l~~L 371 (371)
T PF03081_consen 333 EKVVPAYRRFYERYRNSQFNPEKYIKYTPEDLENMLNEL 371 (371)
T ss_dssp HHHHHHHHHHHHHCCCCSSSHCCC-SS-HHHHHHHHHTC
T ss_pred HHHHHHHHHHHHHhcccccCCCCCCccCHHHHHHHHHcC
Confidence 56899999999998754 346677899999888653
No 223
>PF04994 TfoX_C: TfoX C-terminal domain; InterPro: IPR007077 This domain is found in a number of bacterial proteins including the TfoX gene product of Haemophilus influenzae. TfoX may play a key role in the development of genetic competence by regulating the expression of late competence-specific genes []. This family corresponds to the C-terminal presumed domain of TfoX. The domain is found in association with the N-terminal domain in some, but not all members of this group, suggesting this is an autonomous and functionally unrelated domain. For example it is found associated with Q9JZR1 from SWISSPROT in IPR002125 from INTERPRO.; PDB: 3BQT_A 3MAB_A.
Probab=35.27 E-value=30 Score=22.12 Aligned_cols=22 Identities=14% Similarity=0.215 Sum_probs=13.9
Q ss_pred HHhccCCCCcHHHHHHHHHHhc
Q 033363 73 THVTQLHGVGKYAADAFAIFCT 94 (121)
Q Consensus 73 ~~L~~lpGIG~~tA~~vl~f~~ 94 (121)
..|.+||.+|+++.....-.+-
T Consensus 3 ~~l~~LpNig~~~e~~L~~vGI 24 (81)
T PF04994_consen 3 NRLKDLPNIGPKSERMLAKVGI 24 (81)
T ss_dssp --GCGSTT--HHHHHHHHHTT-
T ss_pred cchhhCCCCCHHHHHHHHHcCC
Confidence 4689999999999987765443
No 224
>PRK13761 hypothetical protein; Provisional
Probab=34.71 E-value=86 Score=24.48 Aligned_cols=41 Identities=22% Similarity=0.340 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHHHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCCh
Q 033363 10 KEIAILLKAGRVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQ 53 (121)
Q Consensus 10 ~~~~~~~~v~~v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~ 53 (121)
+++++-.++.++++.+.+ -..++.+.+.++++++++...-.
T Consensus 189 A~itIVDni~RA~p~m~~---~~~elk~~~~~el~~iv~~~dN~ 229 (248)
T PRK13761 189 ATITIVDNITRAVPNMTE---YARELKKKDREELEEIVENYDNK 229 (248)
T ss_pred CceeeehhHHHHHHHHHH---HHHHHhcCCHHHHHHHHHhcCcH
Confidence 334333344444444443 36678889999999999865443
No 225
>COG1031 Uncharacterized Fe-S oxidoreductase [Energy production and conversion]
Probab=34.34 E-value=28 Score=29.94 Aligned_cols=21 Identities=19% Similarity=0.238 Sum_probs=18.3
Q ss_pred hHHHhccCCCCcHHHHHHHHH
Q 033363 71 SWTHVTQLHGVGKYAADAFAI 91 (121)
Q Consensus 71 ~~~~L~~lpGIG~~tA~~vl~ 91 (121)
..+.|.++||||.+++.-|+.
T Consensus 514 s~~vl~~ipgig~~~~~~I~~ 534 (560)
T COG1031 514 SKDVLRAIPGIGKKTLRKILA 534 (560)
T ss_pred cHHHHHhcccchhhhHHHHHh
Confidence 367899999999999998875
No 226
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=34.10 E-value=46 Score=26.10 Aligned_cols=36 Identities=22% Similarity=0.307 Sum_probs=15.9
Q ss_pred HHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHH
Q 033363 22 ISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMI 60 (121)
Q Consensus 22 ~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i 60 (121)
+.+++..|.|.+++..++++||..+ -|....||..|
T Consensus 195 a~~ll~~fgS~~~~~tas~~eL~~v---~gig~k~A~~I 230 (254)
T COG1948 195 AERLLKKFGSVEDVLTASEEELMKV---KGIGEKKAREI 230 (254)
T ss_pred HHHHHHHhcCHHHHhhcCHHHHHHh---cCccHHHHHHH
Confidence 3344444555555555554443322 24434444444
No 227
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=33.93 E-value=53 Score=27.10 Aligned_cols=32 Identities=13% Similarity=0.141 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHHHhCCC-HHHHhcCCHHHHHHH
Q 033363 15 LLKAGRVISDLFTLCPD-AKTATEVDAEEIEKI 46 (121)
Q Consensus 15 ~~~v~~v~~~l~~~~pt-~~~la~a~~~eL~~~ 46 (121)
.+.|..+|.+|.+.|.| .+.|.+++.|+|.++
T Consensus 320 tK~V~~~we~lv~~FGtEi~vLi~a~~e~La~V 352 (403)
T COG1379 320 TKAVKRTWERLVRAFGTEIDVLIDAPIEELARV 352 (403)
T ss_pred chhHHHHHHHHHHHhcchhhhHhcCCHHHHhhh
Confidence 45789999999999986 688999999997554
No 228
>KOG3835 consensus Transcriptional corepressor NAB1 [Transcription]
Probab=33.61 E-value=2e+02 Score=24.24 Aligned_cols=55 Identities=13% Similarity=0.158 Sum_probs=42.3
Q ss_pred HHHHHHHHHHHHHHhCC-CHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH
Q 033363 14 ILLKAGRVISDLFTLCP-DAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG 69 (121)
Q Consensus 14 ~~~~v~~v~~~l~~~~p-t~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~ 69 (121)
.+.+...+|+.|+.... +.+.|.++.++|..++..=+|+. .|--.++++-+++.+
T Consensus 19 qkANLlsYyd~FIqQGGDDvqQlceagEeEFLEIMaLVGMa-~KPLHVRRlQkALre 74 (495)
T KOG3835|consen 19 QKANLLSYYDVFIQQGGDDVQQLCEAGEEEFLEIMALVGMA-PKPLHVRRLQKALRE 74 (495)
T ss_pred HHhhHHHHHHHHHHhcchHHHHHHHhhHHHHHHHHHHhccC-CcchhHHHHHHHHHH
Confidence 34456688999998765 68999999999999999999997 565555555555544
No 229
>PF08823 PG_binding_2: Putative peptidoglycan binding domain; InterPro: IPR014927 This entry may be a peptidoglycan binding domain.
Probab=33.32 E-value=40 Score=21.26 Aligned_cols=26 Identities=23% Similarity=0.436 Sum_probs=19.4
Q ss_pred CCCHHHHhcCCH---HHHHHHHhhcCChh
Q 033363 29 CPDAKTATEVDA---EEIEKIISTLGLQK 54 (121)
Q Consensus 29 ~pt~~~la~a~~---~eL~~~i~~~Gl~~ 54 (121)
.|.|+++...+. ++|++.|+.+|+++
T Consensus 4 ~~~p~~~~~l~~~~~~evq~~L~~lGyy~ 32 (74)
T PF08823_consen 4 KPRPEELLPLDGDVAREVQEALKRLGYYK 32 (74)
T ss_pred CCCchhhccCcHHHHHHHHHHHHHcCCcc
Confidence 367777777775 46778899999953
No 230
>PF02889 Sec63: Sec63 Brl domain; InterPro: IPR004179 This domain was named after the yeast Sec63 (or NPL1) (also known as the Brl domain) protein in which it was found. This protein is required for assembly of functional endoplasmic reticulum translocons [, ]. Other yeast proteins containing this domain include pre-mRNA splicing helicase BRR2, HFM1 protein and putative helicases. ; PDB: 3IM2_A 3IM1_A 3HIB_A 2Q0Z_X.
Probab=33.21 E-value=66 Score=24.77 Aligned_cols=36 Identities=19% Similarity=0.229 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHHHHhhH---HHhccCCCCcHHHHHHHHH
Q 033363 56 RAPMIKRFSQEYLGESW---THVTQLHGVGKYAADAFAI 91 (121)
Q Consensus 56 Ka~~i~~~a~~i~~~~~---~~L~~lpGIG~~tA~~vl~ 91 (121)
=+..+..+++.+..+.| ..|.+|||||+..+..+.-
T Consensus 128 ~~~~~l~l~q~i~q~~w~~~~~L~Qlp~i~~~~~~~l~~ 166 (314)
T PF02889_consen 128 TALNALELSQCIVQALWDSDSPLLQLPHIGEESLKKLEK 166 (314)
T ss_dssp HHHHHHHHHHHHHHTS-TTS-GGGGSTT--HHHHHHHHH
T ss_pred HHHHHHHHHHHHHhhcCCCCChhhcCCCCCHHHHHHHhc
Confidence 45667777777776544 4799999999999887776
No 231
>PF02961 BAF: Barrier to autointegration factor; InterPro: IPR004122 Barrier-to-autointegration factor (BAF) is an essential protein that is highly conserved in metazoan evolution, and which may act as a DNA-bridging protein []. BAF binds directly to double-stranded DNA, to transcription activators, and to inner nuclear membrane proteins, including lamin A filament proteins that anchor nuclear-pore complexes in place, and nuclear LEM-domain proteins that bind to laminins filaments and chromatin. New findings suggest that BAF has structural roles in nuclear assembly and chromatin organisation, represses gene expression and might interlink chromatin structure, nuclear architecture and gene regulation in metazoans []. BAF can be exploited by retroviruses to act as a host component of pre-integration complexes, which promote the integration of the retroviral DNA into the host chromosome by preventing autointegration of retroviral DNA []. BAF might contribute to the assembly or activity of retroviral pre-integration complexes through direct binding to the retroviral proteins p55 Gag and matrix, as well as to DNA.; GO: 0003677 DNA binding; PDB: 2ODG_A 2BZF_A 2EZX_B 2EZY_B 1QCK_B 1CI4_B 2EZZ_B.
Probab=33.04 E-value=29 Score=23.02 Aligned_cols=25 Identities=24% Similarity=0.203 Sum_probs=16.8
Q ss_pred HHhccCCCCcHHHHHHHHHHhcCCC
Q 033363 73 THVTQLHGVGKYAADAFAIFCTGKW 97 (121)
Q Consensus 73 ~~L~~lpGIG~~tA~~vl~f~~~~~ 97 (121)
+....||||||--+.-+---+|++.
T Consensus 19 K~V~~laGIG~~lg~~L~~~GfdKA 43 (89)
T PF02961_consen 19 KPVTELAGIGPVLGKRLEEKGFDKA 43 (89)
T ss_dssp -BGGGSTT--HHHHHHHHHTT--BH
T ss_pred CCccccCCcCHHHHHHHHHCCCcHH
Confidence 5688999999999988887777764
No 232
>PLN03103 GDP-L-galactose-hexose-1-phosphate guanyltransferase; Provisional
Probab=31.51 E-value=63 Score=27.04 Aligned_cols=52 Identities=8% Similarity=0.077 Sum_probs=41.7
Q ss_pred HHHHHHHHHHHHHhC--CCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHH
Q 033363 15 LLKAGRVISDLFTLC--PDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQE 66 (121)
Q Consensus 15 ~~~v~~v~~~l~~~~--pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~ 66 (121)
..++++++.++-..+ |+-++.-.++++++.++|+.+.++..+.+.+++....
T Consensus 340 ~s~~NPA~~EmsG~l~~~~~eDfe~lTE~~~~~il~EvsLse~~f~ev~~~i~~ 393 (403)
T PLN03103 340 DTQVNPAVWEISGHIVLKRKEDYERATEEYAWRLLAEVSLSEERFQEVKALCFA 393 (403)
T ss_pred hccCChhhHhhcceeeecchHhhhhcCHHHHHHHHHHccCCHHHHHHHHHHHHh
Confidence 346778888887765 4678999999999999999999998887776665544
No 233
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=31.36 E-value=1.5e+02 Score=22.80 Aligned_cols=53 Identities=25% Similarity=0.295 Sum_probs=38.6
Q ss_pred CCHHHHHHHHhhcCChhHHHHHHHHHHHHHHHh----hHHHhccCCCCcHHHHHHHH
Q 033363 38 VDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGE----SWTHVTQLHGVGKYAADAFA 90 (121)
Q Consensus 38 a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~~----~~~~L~~lpGIG~~tA~~vl 90 (121)
.++||++......|+...|...|.++++..-+. +.++|..|=|+-+.|...-+
T Consensus 70 ~~~ED~e~~~~~~~~~elr~~rIvRl~~EAy~QgglLT~~Dla~LL~~S~~TI~~~i 126 (220)
T PF07900_consen 70 VDPEDIEMRNEKYGLSELRKHRIVRLTNEAYDQGGLLTQEDLAMLLGISPRTISKDI 126 (220)
T ss_pred cCHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHcCCcccHHHHHHHHCCCHHHHHHHH
Confidence 357888887777899999999998888877662 45566666666666665544
No 234
>PF07499 RuvA_C: RuvA, C-terminal domain; InterPro: IPR011114 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. The domain represents the C-terminal domain III of RuvA. This domain plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB []. Within the Holliday junction, this domain makes no interaction with the DNA.; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination, 0009379 Holliday junction helicase complex; PDB: 1HJP_A 1CUK_A 1C7Y_A 1IXS_A 1IXR_B 1BVS_E 2ZTC_A 2ZTD_B 2H5X_A.
Probab=31.26 E-value=93 Score=17.49 Aligned_cols=23 Identities=22% Similarity=0.210 Sum_probs=14.9
Q ss_pred HHHHHHHhhcCChhHHHHHHHHH
Q 033363 41 EEIEKIISTLGLQKKRAPMIKRF 63 (121)
Q Consensus 41 ~eL~~~i~~~Gl~~~Ka~~i~~~ 63 (121)
+|+.+.|-.+||.+.-+....+-
T Consensus 4 ~d~~~AL~~LGy~~~e~~~av~~ 26 (47)
T PF07499_consen 4 EDALEALISLGYSKAEAQKAVSK 26 (47)
T ss_dssp HHHHHHHHHTTS-HHHHHHHHHH
T ss_pred HHHHHHHHHcCCCHHHHHHHHHH
Confidence 56677788999986665554443
No 235
>TIGR02236 recomb_radA DNA repair and recombination protein RadA. This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.
Probab=30.78 E-value=1.2e+02 Score=23.58 Aligned_cols=43 Identities=9% Similarity=0.064 Sum_probs=29.1
Q ss_pred ChhHHHHHHHHH----HHHHHHhhHHHhccCCCCcHHHHHHHHHHhc
Q 033363 52 LQKKRAPMIKRF----SQEYLGESWTHVTQLHGVGKYAADAFAIFCT 94 (121)
Q Consensus 52 l~~~Ka~~i~~~----a~~i~~~~~~~L~~lpGIG~~tA~~vl~f~~ 94 (121)
..+.+++.|.+. .+.+...+.++|.+++|+++..|+-+...+.
T Consensus 7 ig~~~~~~L~~~Gi~ti~dl~~~~~~~L~~~~g~~~~~a~~l~~~~~ 53 (310)
T TIGR02236 7 VGPATAEKLREAGYDTFEAIAVASPKELSEIAGISEGTAAKIIQAAR 53 (310)
T ss_pred CCHHHHHHHHHcCCCCHHHHHcCCHHHHHhccCCCHHHHHHHHHHHH
Confidence 334444444444 4444456788999999999988888877665
No 236
>TIGR00600 rad2 DNA excision repair protein (rad2). All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=30.55 E-value=47 Score=31.06 Aligned_cols=41 Identities=17% Similarity=0.117 Sum_probs=25.9
Q ss_pred HHHhhcCChhHHHHHHHHHHHHHHHhhHHHhccCCCCcHHHHHHHHH
Q 033363 45 KIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLHGVGKYAADAFAI 91 (121)
Q Consensus 45 ~~i~~~Gl~~~Ka~~i~~~a~~i~~~~~~~L~~lpGIG~~tA~~vl~ 91 (121)
.+++.+|+.+ ..++.+|-.+- -+....|||||++||--++.
T Consensus 844 ~i~~~lglt~---~qli~laiL~G---~DY~~GI~GIGpktAl~li~ 884 (1034)
T TIGR00600 844 DIHNQLGLDR---NKLINLAYLLG---SDYTEGIPTVGPVSAMEILN 884 (1034)
T ss_pred HHHHHhCCCH---HHHHHHHHeeC---CCCCCCCCcccHHHHHHHHH
Confidence 3455678763 44555544431 23356999999999977664
No 237
>PRK00625 shikimate kinase; Provisional
Probab=30.22 E-value=81 Score=22.73 Aligned_cols=33 Identities=18% Similarity=0.011 Sum_probs=25.1
Q ss_pred hccCCCCcHHHHHHHHHHhcCCCCccCcchHHHHH
Q 033363 75 VTQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNY 109 (121)
Q Consensus 75 L~~lpGIG~~tA~~vl~f~~~~~~~v~p~D~~l~~ 109 (121)
|..+||.|+-|..-.+.--++.+ +.-.|..++.
T Consensus 5 LiG~pGsGKTT~~k~La~~l~~~--~id~D~~I~~ 37 (173)
T PRK00625 5 LCGLPTVGKTSFGKALAKFLSLP--FFDTDDLIVS 37 (173)
T ss_pred EECCCCCCHHHHHHHHHHHhCCC--EEEhhHHHHH
Confidence 56799999999888887777764 5666766653
No 238
>TIGR02895 spore_sigI RNA polymerase sigma-I factor. Members of this sigma factor protein family are strictly limited to endospore-forming species in the Firmicutes lineage of bacteria, but are not universally present among such species. Sigma-I was shown to be induced by heat shock (PubMed:11157964) in Bacillus subtilis and is suggested by its phylogenetic profile to be connected to the program of sporulation (PubMed:16311624).
Probab=29.74 E-value=2.4e+02 Score=21.33 Aligned_cols=31 Identities=0% Similarity=0.059 Sum_probs=25.4
Q ss_pred HHHHHHHHHHHHHh-------------hHHHhccCCCCcHHHHH
Q 033363 57 APMIKRFSQEYLGE-------------SWTHVTQLHGVGKYAAD 87 (121)
Q Consensus 57 a~~i~~~a~~i~~~-------------~~~~L~~lpGIG~~tA~ 87 (121)
-+..+++|+.+.++ .+++|.+.-||-+||-+
T Consensus 151 r~~~i~ia~~~~~~~~l~~~l~~kk~LP~k~l~~~~~v~rktie 194 (218)
T TIGR02895 151 RKKAIKIAKVIVENEELLEYLIRKKKLPIKEIEERVRISRKTIE 194 (218)
T ss_pred HHHHHHHHHHHhcCHHHHHHHHHhCCCCHHHHHHHcCCCHHHHH
Confidence 46778889998873 57899999999999865
No 239
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair]
Probab=29.09 E-value=69 Score=25.11 Aligned_cols=41 Identities=22% Similarity=0.234 Sum_probs=28.1
Q ss_pred ChhHHHHHHHHH---HHHHHHhhHHHhccCCCCcHHHHHHHHHH
Q 033363 52 LQKKRAPMIKRF---SQEYLGESWTHVTQLHGVGKYAADAFAIF 92 (121)
Q Consensus 52 l~~~Ka~~i~~~---a~~i~~~~~~~L~~lpGIG~~tA~~vl~f 92 (121)
..+.+|..|..- .+.+....+++|..+||+||--|.-+.-|
T Consensus 203 VnKtda~~LL~~FgsLq~~~~AS~~ele~~~G~G~~kak~l~~~ 246 (254)
T KOG2841|consen 203 VNKTDAQLLLQKFGSLQQISNASEGELEQCPGLGPAKAKRLHKF 246 (254)
T ss_pred CCcccHHHHHHhcccHHHHHhcCHhHHHhCcCcCHHHHHHHHHH
Confidence 344555555432 33444567899999999999999877654
No 240
>PF05082 Rop-like: Rop-like; InterPro: IPR007774 This family contains several uncharacterised bacterial proteins. These proteins are found in nitrogen fixation operons, so are likely to play a role in this process.; PDB: 3CSX_A 2JS5_B.
Probab=28.97 E-value=56 Score=20.43 Aligned_cols=47 Identities=23% Similarity=0.273 Sum_probs=27.8
Q ss_pred HHHHHHHhhcCChhHHHHHHHHHHHHHHHhhHHHhccCCCCcHHHHHHHH
Q 033363 41 EEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLHGVGKYAADAFA 90 (121)
Q Consensus 41 ~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~~~~~~L~~lpGIG~~tA~~vl 90 (121)
++|..-++.+ ++||-..+.=...+.|+....-.+||+|..+|=+++.
T Consensus 5 ~eLk~evkKL---~~~A~~~kmdLHDLaEdLP~~w~~i~~vA~~ty~a~~ 51 (66)
T PF05082_consen 5 EELKKEVKKL---NRKATQAKMDLHDLAEDLPTNWEEIPEVAQKTYDAYA 51 (66)
T ss_dssp HHHHHHHHHH---HHHHHHHHHHHHHHHHCTTTTGGGHHHHHHHHHHHHH
T ss_pred HHHHHHHHHH---HHHHHHHHHHHHHHHHccchhHHHHHHHHHHHHHHHH
Confidence 4444444444 3455555554555555555566778888888877665
No 241
>PF01706 FliG_C: FliG C-terminal domain; InterPro: IPR023087 The flagellar motor switch in Escherichia coli and Salmonella typhimurium regulates the direction of flagellar rotation and hence controls swimming behaviour []. The switch is a complex apparatus that responds to signals transduced by the chemotaxis sensory signalling system during chemotactic behaviour []. CheY, the chemotaxis response regulator, is believed to act directly on the switch to induce tumbles in the swimming pattern, but no physical interactions of CheY and switch proteins have yet been demonstrated. The switch complex comprises at least three proteins - FliG, FliM and FliN. It has been shown that FliG interacts with FliM, FliM interacts with itself, and FliM interacts with FliN []. Several residues within the middle third of FliG appear to be strongly involved in the FliG-FliM interaction, with residues near the N- or C-termini being less important []. Such clustering suggests that FliG-FliM interaction plays a central role in switching. Analysis of the FliG, FliM and FliN sequences shows that none are especially hydrophobic or appear to be integral membrane proteins []. This result is consistent with other evidence suggesting that the proteins may be peripheral to the membrane, possibly mounted on the basal body M ring [, ]. FliG is present in about 25 copies per flagellum. This entry represents the C-terminal domain of FliG, the structure of which is known. This domain functions specifically in motor rotation [].; PDB: 3USY_B 3USW_A 3HJL_A 3AJC_A 1LKV_X 1QC7_B.
Probab=28.13 E-value=1.1e+02 Score=20.15 Aligned_cols=48 Identities=13% Similarity=0.146 Sum_probs=32.6
Q ss_pred HHHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHH
Q 033363 20 RVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYL 68 (121)
Q Consensus 20 ~v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~ 68 (121)
....++.+..-+.++|...|...|..+++.++.. .=+..|+.....+.
T Consensus 10 ~la~~ir~~~f~F~dl~~l~~~~l~~ll~~v~~~-~la~ALkga~~e~~ 57 (110)
T PF01706_consen 10 ELAEKIREKMFTFDDLVRLDDRDLQKLLREVDPD-DLALALKGASEELR 57 (110)
T ss_dssp HHHHHHHHHCS-GGGGGGS-HHHHHHHHTTS-HH-HHHHHHCTS-HHHH
T ss_pred HHHHHHHHHhhhHHHHHcCCHHHHHHHHHHCCHh-HHHHHHccCCHHHH
Confidence 4556777888899999999999999999998854 45555555544443
No 242
>PHA02698 hypothetical protein; Provisional
Probab=27.80 E-value=1.8e+02 Score=18.89 Aligned_cols=19 Identities=11% Similarity=0.475 Sum_probs=15.7
Q ss_pred CCHHHHhcCCHHHHHHHHh
Q 033363 30 PDAKTATEVDAEEIEKIIS 48 (121)
Q Consensus 30 pt~~~la~a~~~eL~~~i~ 48 (121)
|+|+.+...++++..+++.
T Consensus 33 p~peeV~~CsPEdMs~mLD 51 (89)
T PHA02698 33 PTPEEVPQCSPEDMSDMLD 51 (89)
T ss_pred CChhhhccCCHHHHHHHHH
Confidence 5788999999999877664
No 243
>PRK03352 DNA polymerase IV; Validated
Probab=27.77 E-value=40 Score=26.68 Aligned_cols=23 Identities=26% Similarity=0.302 Sum_probs=18.6
Q ss_pred HhccCCCCcHHHHHHHHHHhcCC
Q 033363 74 HVTQLHGVGKYAADAFAIFCTGK 96 (121)
Q Consensus 74 ~L~~lpGIG~~tA~~vl~f~~~~ 96 (121)
.+.++||||++|++-...++...
T Consensus 178 pl~~l~gig~~~~~~L~~~Gi~t 200 (346)
T PRK03352 178 PTDALWGVGPKTAKRLAALGITT 200 (346)
T ss_pred CHHHcCCCCHHHHHHHHHcCCcc
Confidence 47788999999999987766654
No 244
>COG0133 TrpB Tryptophan synthase beta chain [Amino acid transport and metabolism]
Probab=27.28 E-value=91 Score=25.82 Aligned_cols=46 Identities=22% Similarity=0.114 Sum_probs=33.3
Q ss_pred HHHhccCCCCcHHHHHHHHHHhcCCCCccCcchHHHHHHHHHHHHhhcC
Q 033363 72 WTHVTQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFLVSTKGN 120 (121)
Q Consensus 72 ~~~L~~lpGIG~~tA~~vl~f~~~~~~~v~p~D~~l~~~~~wl~~~~~~ 120 (121)
+..=+..|||||.-|- + ...||..-+.+.|..--..+..|++.+|-
T Consensus 300 ISAGLDYPgVGPeha~--l-~~~gRa~y~~itD~EAl~af~~L~r~EGI 345 (396)
T COG0133 300 ISAGLDYPGVGPEHAY--L-KDIGRAEYVSITDEEALEAFQLLSRLEGI 345 (396)
T ss_pred eccCCCCCCCChhHHH--H-HhcCceeEEecChHHHHHHHHHHHHhcCc
Confidence 4556789999998773 2 45677665677787777777778888774
No 245
>cd01701 PolY_Rev1 DNA polymerase Rev1. Rev1 is a translesion synthesis (TLS) polymerase found in eukaryotes. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Rev1 has both structural and enzymatic roles. Structurally, it is believed to interact with other nonclassical polymerases and replication machinery to act as a scaffold. Enzymatically, it catalyzes the specific insertion of dCMP opposite abasic sites. Rev1 interacts with the Rev7 subunit of the B-family TLS polymerase Pol zeta (Rev3/Rev7). Rev1 is known to actively promote the introduction of mutations, potentially making it a significant target for cancer treatment.
Probab=27.08 E-value=41 Score=27.52 Aligned_cols=23 Identities=26% Similarity=0.368 Sum_probs=19.1
Q ss_pred HhccCCCCcHHHHHHHHHHhcCC
Q 033363 74 HVTQLHGVGKYAADAFAIFCTGK 96 (121)
Q Consensus 74 ~L~~lpGIG~~tA~~vl~f~~~~ 96 (121)
.+..|||||++|++-+..++...
T Consensus 223 Pv~~l~GIG~~~~~~L~~~Gi~t 245 (404)
T cd01701 223 KVGDLPGVGSSLAEKLVKLFGDT 245 (404)
T ss_pred CHhHhCCCCHHHHHHHHHcCCcc
Confidence 47788999999999988777654
No 246
>PTZ00205 DNA polymerase kappa; Provisional
Probab=27.07 E-value=36 Score=29.74 Aligned_cols=21 Identities=19% Similarity=0.246 Sum_probs=16.2
Q ss_pred HhccCCCCcHHHHHHHHHHhc
Q 033363 74 HVTQLHGVGKYAADAFAIFCT 94 (121)
Q Consensus 74 ~L~~lpGIG~~tA~~vl~f~~ 94 (121)
.+.++||||+.|+.-...++.
T Consensus 310 pV~ki~GIG~~t~~~L~~~GI 330 (571)
T PTZ00205 310 GLRSVPGVGKVTEALLKGLGI 330 (571)
T ss_pred CcceeCCcCHHHHHHHHHcCC
Confidence 477899999999986655443
No 247
>PLN00138 large subunit ribosomal protein LP2; Provisional
Probab=26.92 E-value=1.4e+02 Score=20.44 Aligned_cols=38 Identities=21% Similarity=0.344 Sum_probs=30.6
Q ss_pred CCHHHHHHHHhhcCChhHHHHHHHHHHHHHHHhhHHHhc
Q 033363 38 VDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVT 76 (121)
Q Consensus 38 a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~~~~~~L~ 76 (121)
-+.++|..+|+..|. ..-..++..+++.+...++++|.
T Consensus 18 pta~dI~~IL~AaGv-evd~~~~~~f~~~L~gK~i~eLI 55 (113)
T PLN00138 18 PSAEDLKDILGSVGA-DADDDRIELLLSEVKGKDITELI 55 (113)
T ss_pred CCHHHHHHHHHHcCC-cccHHHHHHHHHHHcCCCHHHHH
Confidence 456778888999998 48888999999988777777766
No 248
>smart00341 HRDC Helicase and RNase D C-terminal. Hypothetical role in nucleic acid binding. Mutations in the HRDC domain cause human disease.
Probab=26.40 E-value=90 Score=18.87 Aligned_cols=28 Identities=14% Similarity=0.286 Sum_probs=17.9
Q ss_pred HHHHHHHHHHHHhhHHHhccCCCCcHHHH
Q 033363 58 PMIKRFSQEYLGESWTHVTQLHGVGKYAA 86 (121)
Q Consensus 58 ~~i~~~a~~i~~~~~~~L~~lpGIG~~tA 86 (121)
+.|.++|+.. -.+.++|.+++|+|++-.
T Consensus 33 ~~L~~ia~~~-P~~~~~L~~i~g~~~~~~ 60 (81)
T smart00341 33 ETLIKMAAAL-PTNVSELLAIDGVGEEKA 60 (81)
T ss_pred HHHHHHHHHC-CCCHHHHhcCCCCCHHHH
Confidence 5555555542 136778888888886644
No 249
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=26.18 E-value=1.4e+02 Score=23.44 Aligned_cols=32 Identities=13% Similarity=0.094 Sum_probs=25.0
Q ss_pred HHHHHHhhHHHhccCCCCcHHHHHHHHHHhcC
Q 033363 64 SQEYLGESWTHVTQLHGVGKYAADAFAIFCTG 95 (121)
Q Consensus 64 a~~i~~~~~~~L~~lpGIG~~tA~~vl~f~~~ 95 (121)
++.+..-+.++|.+++|++++.|..+...+.+
T Consensus 30 ~~dl~~~~~~~L~~~~g~~~~~a~~l~~~a~~ 61 (317)
T PRK04301 30 VEAIAVASPKELSEAAGIGESTAAKIIEAARE 61 (317)
T ss_pred HHHHHcCCHHHHHHhcCCCHHHHHHHHHHHHH
Confidence 33444456789999999999999998887765
No 250
>COG3392 Adenine-specific DNA methylase [DNA replication, recombination, and repair]
Probab=25.65 E-value=94 Score=25.04 Aligned_cols=49 Identities=18% Similarity=0.190 Sum_probs=38.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHh------CCCHHHHhcCCHHHHHHHHhhcCCh
Q 033363 5 YSIRLKEIAILLKAGRVISDLFTL------CPDAKTATEVDAEEIEKIISTLGLQ 53 (121)
Q Consensus 5 ~si~~~~~~~~~~v~~v~~~l~~~------~pt~~~la~a~~~eL~~~i~~~Gl~ 53 (121)
||-+-+..++++|+..++..|+.. +-|-.....++.+++.+++...|=+
T Consensus 245 ~~~~KSsfcs~~~a~~af~eLI~d~k~kyIlLSYNneg~~s~e~i~eiL~k~G~~ 299 (330)
T COG3392 245 YSWQKSSFCSRKQATQAFEELISDAKFKYILLSYNNEGLMSEEEILEILEKYGKY 299 (330)
T ss_pred hhhhhhhhhHHHHHHHHHHHHHhhcCccEEEEecCccccccHHHHHHHHHhcCcE
Confidence 444556778899999999999864 3467777888999999999887743
No 251
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=25.59 E-value=55 Score=29.66 Aligned_cols=43 Identities=23% Similarity=0.269 Sum_probs=30.3
Q ss_pred cCChhHHHHHHHHHHHHHHH-hhHHHhccCCCCcHHHHHHHHHH
Q 033363 50 LGLQKKRAPMIKRFSQEYLG-ESWTHVTQLHGVGKYAADAFAIF 92 (121)
Q Consensus 50 ~Gl~~~Ka~~i~~~a~~i~~-~~~~~L~~lpGIG~~tA~~vl~f 92 (121)
.||..++|++|.+.-+..-. ..+++|.+.|..|+|+=.-..-|
T Consensus 515 sGL~kt~A~nIv~~r~~~g~f~~Rk~L~kv~rlg~k~Feq~aGF 558 (780)
T COG2183 515 SGLNKTLAKNIVAYRDENGAFDNRKQLKKVPRLGPKAFEQCAGF 558 (780)
T ss_pred hhhchhHHHHHHHHHhhcCCcccHHHHhcCCCcChhhhhhccee
Confidence 57777777777664443321 47999999999999986655443
No 252
>PF04924 Pox_A6: Poxvirus A6 protein ; InterPro: IPR007008 This is a family of poxvirus A6 proteins have no known function.
Probab=25.45 E-value=1.9e+02 Score=23.89 Aligned_cols=49 Identities=10% Similarity=0.258 Sum_probs=33.7
Q ss_pred chhHHHHHHHHHHHHHHHHHHHHHHHhC---CCHHHHhcCCHHHHHHHHhhc
Q 033363 2 AQIYSIRLKEIAILLKAGRVISDLFTLC---PDAKTATEVDAEEIEKIISTL 50 (121)
Q Consensus 2 ~~~~si~~~~~~~~~~v~~v~~~l~~~~---pt~~~la~a~~~eL~~~i~~~ 50 (121)
+-+|++..+|+.|...+.......+..+ -++++|...+...|+.+|+-.
T Consensus 263 sKLy~liy~e~ktN~~l~~L~~dvldS~k~KiS~ddlKq~gV~NlQsLi~~I 314 (371)
T PF04924_consen 263 SKLYVLIYNEFKTNPELGYLLRDVLDSIKTKISVDDLKQKGVNNLQSLIRYI 314 (371)
T ss_pred HHHHHHHHHHHhcCHHHHHHHHHHHHHHhhcCCHHHHHHhcchhHHHHHHHH
Confidence 4589999999988766655555555443 367777777777777766643
No 253
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=25.29 E-value=1.1e+02 Score=17.92 Aligned_cols=34 Identities=18% Similarity=0.184 Sum_probs=17.6
Q ss_pred HHHHHHHHHHhCCCHHHHhcCCHHHHHHHHhhcC
Q 033363 18 AGRVISDLFTLCPDAKTATEVDAEEIEKIISTLG 51 (121)
Q Consensus 18 v~~v~~~l~~~~pt~~~la~a~~~eL~~~i~~~G 51 (121)
+..+...+.+.|+-+.+-+..+..++.+.|+..|
T Consensus 32 ~~ei~~~l~~~y~~~~~~~~~dv~~fl~~L~~~g 65 (68)
T PF05402_consen 32 VEEIVDALAEEYDVDPEEAEEDVEEFLEQLREKG 65 (68)
T ss_dssp HHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHCc
Confidence 4566667777777555544444444444444444
No 254
>KOG0898 consensus 40S ribosomal protein S15 [Translation, ribosomal structure and biogenesis]
Probab=24.92 E-value=1.4e+02 Score=21.48 Aligned_cols=47 Identities=19% Similarity=0.333 Sum_probs=33.0
Q ss_pred HHHHHHHHHhCCCHHHHhcCCHHHHHHHHh-------hcCChhHHHHHHHHHHH
Q 033363 19 GRVISDLFTLCPDAKTATEVDAEEIEKIIS-------TLGLQKKRAPMIKRFSQ 65 (121)
Q Consensus 19 ~~v~~~l~~~~pt~~~la~a~~~eL~~~i~-------~~Gl~~~Ka~~i~~~a~ 65 (121)
.+.|.+|..+.-+.++|++++.+++.++.. .-||.+.-...|+++-+
T Consensus 16 KRTFrkftyrGVdld~Lldms~~~~~~l~~ar~rrR~~RGL~~k~~~liKklrk 69 (152)
T KOG0898|consen 16 KRTFRKFTYRGVDLDQLLDMSTEQLVKLFPARQRRRLNRGLTRKPHSLIKKLRK 69 (152)
T ss_pred hhhhhhccccCCCHHHHhcCCHHHHHHHHHHHHHHHHHcccccchHHHHHHHHH
Confidence 456777777777999999999999977653 24666555555555533
No 255
>COG4168 SapB ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]
Probab=24.79 E-value=44 Score=26.61 Aligned_cols=23 Identities=17% Similarity=0.221 Sum_probs=19.1
Q ss_pred HHhccCCCCcHHHHHHHHHHhcC
Q 033363 73 THVTQLHGVGKYAADAFAIFCTG 95 (121)
Q Consensus 73 ~~L~~lpGIG~~tA~~vl~f~~~ 95 (121)
|..-.=||||+|--|++...-++
T Consensus 260 Es~f~WPGiGRWLi~Ai~qqDy~ 282 (321)
T COG4168 260 ESVFGWPGIGRWLINAIRQQDYA 282 (321)
T ss_pred HHHcCCCchhHHHHHHHHhhhhH
Confidence 55667899999999999877665
No 256
>PF10975 DUF2802: Protein of unknown function (DUF2802); InterPro: IPR021244 This bacterial family of proteins has no known function.
Probab=24.42 E-value=98 Score=19.24 Aligned_cols=32 Identities=16% Similarity=0.321 Sum_probs=21.7
Q ss_pred HHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHH
Q 033363 32 AKTATEVDAEEIEKIISTLGLQKKRAPMIKRFS 64 (121)
Q Consensus 32 ~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a 64 (121)
+-.|+..+ -+++++++.||+++.=|+.|..+-
T Consensus 37 A~klv~~G-a~~~el~~~CgL~~aEAeLl~~Lh 68 (70)
T PF10975_consen 37 AIKLVRQG-ASVEELMEECGLSRAEAELLLSLH 68 (70)
T ss_pred HHHHHHcC-CCHHHHHHHcCCCHHHHHHHHHHh
Confidence 44455544 345556889999988888877654
No 257
>PF06992 Phage_lambda_P: Replication protein P; InterPro: IPR009731 This family consists of several Bacteriophage lambda replication protein P like proteins. The bacteriophage lambda P protein promoters replication of the phage chromosome by recruiting a key component of the cellular replication machinery to the viral origin. Specifically, P protein delivers one or more molecules of Escherichia coli DnaB helicase to a nucleoprotein structure formed by the lambda O initiator at the lambda replication origin [].; GO: 0006270 DNA-dependent DNA replication initiation
Probab=23.95 E-value=2.3e+02 Score=21.94 Aligned_cols=39 Identities=23% Similarity=0.429 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHH
Q 033363 17 KAGRVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQE 66 (121)
Q Consensus 17 ~v~~v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~ 66 (121)
-||.+|.+|...||-+. +.-+.+++.+ .|...|..+++.
T Consensus 39 ~vd~lF~~L~aifPa~~--a~~~~~~~~~---------aKr~Wi~~f~en 77 (233)
T PF06992_consen 39 LVDRLFRQLKAIFPAWR--ANPDQEELNE---------AKRQWIKAFAEN 77 (233)
T ss_pred HHHHHHHHHHHhCchhc--cCCCHHHHHH---------HHHHHHHHHHHc
Confidence 47888999999999874 4566666433 477777777653
No 258
>KOG2518 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=23.89 E-value=49 Score=28.71 Aligned_cols=20 Identities=25% Similarity=0.293 Sum_probs=16.9
Q ss_pred HHHhccCCCCcHHHHHHHHH
Q 033363 72 WTHVTQLHGVGKYAADAFAI 91 (121)
Q Consensus 72 ~~~L~~lpGIG~~tA~~vl~ 91 (121)
-+.|.+|||||-.||.-++.
T Consensus 224 CDYl~slpGvGl~tA~k~l~ 243 (556)
T KOG2518|consen 224 CDYLSSLPGVGLATAHKLLS 243 (556)
T ss_pred CcccccCccccHHHHHHHHH
Confidence 46799999999999987664
No 259
>PRK03858 DNA polymerase IV; Validated
Probab=23.82 E-value=58 Score=26.26 Aligned_cols=23 Identities=26% Similarity=0.304 Sum_probs=18.7
Q ss_pred HhccCCCCcHHHHHHHHHHhcCC
Q 033363 74 HVTQLHGVGKYAADAFAIFCTGK 96 (121)
Q Consensus 74 ~L~~lpGIG~~tA~~vl~f~~~~ 96 (121)
.+..|||||+.|++-+..++...
T Consensus 174 pl~~l~Gig~~~~~~L~~~Gi~t 196 (396)
T PRK03858 174 PVRRLWGVGPVTAAKLRAHGITT 196 (396)
T ss_pred ChhhcCCCCHHHHHHHHHhCCCc
Confidence 47788999999999988776654
No 260
>PRK01172 ski2-like helicase; Provisional
Probab=23.54 E-value=1.6e+02 Score=25.69 Aligned_cols=41 Identities=7% Similarity=-0.042 Sum_probs=27.6
Q ss_pred HHHHHHHHHHHHHh---hHHHhccCCCCcHHHHHHHHHHhcCCC
Q 033363 57 APMIKRFSQEYLGE---SWTHVTQLHGVGKYAADAFAIFCTGKW 97 (121)
Q Consensus 57 a~~i~~~a~~i~~~---~~~~L~~lpGIG~~tA~~vl~f~~~~~ 97 (121)
+..+..+...+..+ ..-.|.+|||||+..|......++.-+
T Consensus 593 ~~~l~~~~~rl~~gv~~~~~~L~~ip~~~~~~a~~l~~~g~~~~ 636 (674)
T PRK01172 593 RRKLEILNIRIKEGIREDLIDLVLIPKVGRVRARRLYDAGFKTV 636 (674)
T ss_pred HHHHHHHHHHHHcCCCHHHHhhcCCCCCCHHHHHHHHHcCCCCH
Confidence 45566666666654 344677888888888877776666543
No 261
>cd00424 PolY Y-family of DNA polymerases. Y-family DNA polymerases are a specialized subset of polymerases that facilitate translesion synthesis (TLS), a process that allows the bypass of a variety of DNA lesions. Unlike replicative polymerases, TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. The active sites of TLS polymerases are large and flexible to allow the accomodation of distorted bases. Most TLS polymerases are members of the Y-family, including Pol eta, Pol kappa/IV, Pol iota, Rev1, and Pol V, which is found exclusively in bacteria. In eukaryotes, the B-family polymerase Pol zeta also functions as a TLS polymerase. Expression of Y-family polymerases is often induced by DNA damage and is believed to be highly regulated. TLS is likely induced by the monoubiquitination of the replication clamp PCNA, which provides a scaffold for TLS polymerases to bind in ord
Probab=23.16 E-value=59 Score=25.76 Aligned_cols=66 Identities=14% Similarity=0.244 Sum_probs=37.7
Q ss_pred CCCHHHHhcCCHHHHHHHHh----hcCChhHHHHHHHHHHHHHHH---------hhH------HHhccCCCCcHHHHHHH
Q 033363 29 CPDAKTATEVDAEEIEKIIS----TLGLQKKRAPMIKRFSQEYLG---------ESW------THVTQLHGVGKYAADAF 89 (121)
Q Consensus 29 ~pt~~~la~a~~~eL~~~i~----~~Gl~~~Ka~~i~~~a~~i~~---------~~~------~~L~~lpGIG~~tA~~v 89 (121)
|.++.+++..=.++|.+... ++|.+. .+.+-++|..... +.. -.+.++||||+++++-+
T Consensus 112 ~~~~~~la~~i~~~i~~~~ggl~~siGia~--n~~lAKlAs~~~KP~g~~v~~~~~~~~~L~~lpi~~l~giG~~~~~~L 189 (343)
T cd00424 112 LGLGSEVALRIKRHIAEQLGGITASIGIAS--NKLLAKLAAKYAKPDGLTILDPEDLPGFLSKLPLTDLPGIGAVTAKRL 189 (343)
T ss_pred cCCHHHHHHHHHHHHHHHhCCceEEEeecc--cHHHHHHHhccCCCCCEEEEcHHHHHHHHhcCChhhcCCCCHHHHHHH
Confidence 45566666544455544333 455553 3344445544331 111 14677999999999998
Q ss_pred HHHhcCC
Q 033363 90 AIFCTGK 96 (121)
Q Consensus 90 l~f~~~~ 96 (121)
..++...
T Consensus 190 ~~~Gi~t 196 (343)
T cd00424 190 EAVGINP 196 (343)
T ss_pred HHcCCCc
Confidence 8766653
No 262
>cd04755 Commd7 COMM_Domain containing protein 7. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=23.12 E-value=1.3e+02 Score=22.31 Aligned_cols=27 Identities=22% Similarity=0.443 Sum_probs=21.9
Q ss_pred hcCCHHHHHHHHhhcCChhHHHHHHHH
Q 033363 36 TEVDAEEIEKIISTLGLQKKRAPMIKR 62 (121)
Q Consensus 36 a~a~~~eL~~~i~~~Gl~~~Ka~~i~~ 62 (121)
.+.+++.|.+-+..+|+++-||..+.+
T Consensus 67 ~nv~~~~L~~eL~~lgL~~eka~~~~~ 93 (180)
T cd04755 67 RNLTAEQLREDLIQLGLSEEKASYFSE 93 (180)
T ss_pred cCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence 567788888888999999999996543
No 263
>TIGR00375 conserved hypothetical protein TIGR00375. The member of this family from Methanococcus jannaschii, MJ0043, is considerably longer and appears to contain an intein N-terminal to the region of homology.
Probab=22.91 E-value=2e+02 Score=23.73 Aligned_cols=32 Identities=9% Similarity=0.092 Sum_probs=25.6
Q ss_pred HHHHHHHHHHHHHhCCC-HHHHhcCCHHHHHHH
Q 033363 15 LLKAGRVISDLFTLCPD-AKTATEVDAEEIEKI 46 (121)
Q Consensus 15 ~~~v~~v~~~l~~~~pt-~~~la~a~~~eL~~~ 46 (121)
.+.|...|.+|+++|.| .+-|.+++.+||.++
T Consensus 313 ~k~v~~~~~~l~~~fG~E~~iL~~~~~eel~~~ 345 (374)
T TIGR00375 313 TKAVQSLWEKLKKAFGTEIAVLHEAAEEDLARV 345 (374)
T ss_pred cHHHHHHHHHHHHHhccHHHHHhcCCHHHHHHH
Confidence 35788999999999865 678889999986543
No 264
>KOG2653 consensus 6-phosphogluconate dehydrogenase [Carbohydrate transport and metabolism]
Probab=22.85 E-value=4.7e+02 Score=22.16 Aligned_cols=77 Identities=12% Similarity=0.150 Sum_probs=44.4
Q ss_pred HHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH----------hhHHHhccCCCCcHHHHHHHHHHhcCCCCccCcc
Q 033363 34 TATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG----------ESWTHVTQLHGVGKYAADAFAIFCTGKWDRVRPT 103 (121)
Q Consensus 34 ~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~----------~~~~~L~~lpGIG~~tA~~vl~f~~~~~~~v~p~ 103 (121)
.+..++.+|+.+++..-+=. .=-.+|+++...|.. +.+.+-..-+|-|.||+-.-+- +|.| ++-.
T Consensus 210 ~~~gls~~eia~vF~~WN~g-eleSfLieIT~dIlk~~d~~G~~lv~kI~D~aGqKGTGkwt~~~Ale--~g~P--v~lI 284 (487)
T KOG2653|consen 210 SVLGLSNDEIAEVFDDWNKG-ELESFLIEITADILKFKDEDGKPLVDKILDKAGQKGTGKWTVISALE--LGVP--VTLI 284 (487)
T ss_pred HhcCCcHHHHHHHHHhhccc-chhHHHHHHhHHHhheeccCCChHHHHHHhhhcCCCccHHHHHHHHH--hCCC--hHHH
Confidence 44455566665555432222 122467777777765 2345667789999999976664 4443 3332
Q ss_pred -hHHHHHHHHHHH
Q 033363 104 -DHMLNYYWEFLV 115 (121)
Q Consensus 104 -D~~l~~~~~wl~ 115 (121)
.....|+++.+.
T Consensus 285 ~eavfaRclS~lK 297 (487)
T KOG2653|consen 285 GEAVFARCLSALK 297 (487)
T ss_pred HHHHHHHHHHHHH
Confidence 234466766654
No 265
>PF10759 DUF2587: Protein of unknown function (DUF2587); InterPro: IPR019695 This entry represents proteins found Actinobacteria sp. The function is not known.
Probab=22.68 E-value=3.1e+02 Score=20.04 Aligned_cols=47 Identities=13% Similarity=0.131 Sum_probs=36.2
Q ss_pred HHhhHHHhccCCCCcHHHHHHHHHHhcCCCCccCcchHHHHH----HHHHHHH
Q 033363 68 LGESWTHVTQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNY----YWEFLVS 116 (121)
Q Consensus 68 ~~~~~~~L~~lpGIG~~tA~~vl~f~~~~~~~v~p~D~~l~~----~~~wl~~ 116 (121)
++.++++|.+ |.+|...+-+.-+++--.+...|.|..||. .++|+.+
T Consensus 63 H~~SI~ELed--gLaPeL~eEL~RlslPF~~~~~PSdaELRIAQAQLVGWLEG 113 (169)
T PF10759_consen 63 HERSIKELED--GLAPELREELERLSLPFTEDSTPSDAELRIAQAQLVGWLEG 113 (169)
T ss_pred HHHHHHHHHH--hcCHHHHHHHHHcCCCCCCCCCCchHHHHHHHHHHHHHHHH
Confidence 3345666664 899999999988888877778999998864 4788764
No 266
>PRK14552 C/D box methylation guide ribonucleoprotein complex aNOP56 subunit; Provisional
Probab=22.19 E-value=1.5e+02 Score=24.75 Aligned_cols=20 Identities=25% Similarity=0.378 Sum_probs=15.0
Q ss_pred HhccCCCCcHHHHHHHHHHhcC
Q 033363 74 HVTQLHGVGKYAADAFAIFCTG 95 (121)
Q Consensus 74 ~L~~lpGIG~~tA~~vl~f~~~ 95 (121)
-|++| ||+-+|.-++..+-+
T Consensus 265 NLtaL--VG~~lAArLIa~AGs 284 (414)
T PRK14552 265 NLTAL--VGPSLGARLISLAGG 284 (414)
T ss_pred HHHHH--HhhHHHHHHHHHhCC
Confidence 46777 999999877776533
No 267
>cd04752 Commd4 COMM_Domain containing protein 4. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=22.19 E-value=2.8e+02 Score=20.00 Aligned_cols=25 Identities=36% Similarity=0.547 Sum_probs=14.0
Q ss_pred CCHHHHHHHHhhcCChhHHHHHHHH
Q 033363 38 VDAEEIEKIISTLGLQKKRAPMIKR 62 (121)
Q Consensus 38 a~~~eL~~~i~~~Gl~~~Ka~~i~~ 62 (121)
.+++++.+-|..+||++.++..+.+
T Consensus 60 ~~~~~l~~eL~~lglp~e~~~~l~~ 84 (174)
T cd04752 60 VDGESLSSELQQLGLPKEHATSLCR 84 (174)
T ss_pred CCHHHHHHHHHHcCCCHHHHHHHHH
Confidence 4555555555666666555555544
No 268
>PRK04460 nickel responsive regulator; Provisional
Probab=21.98 E-value=1.7e+02 Score=20.65 Aligned_cols=28 Identities=25% Similarity=0.546 Sum_probs=23.0
Q ss_pred HHHHHHHhhcCChhHHHHHHHHHHHHHHH
Q 033363 41 EEIEKIISTLGLQKKRAPMIKRFSQEYLG 69 (121)
Q Consensus 41 ~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~ 69 (121)
+++.++++.-||. .|++.|..+.+..+.
T Consensus 15 ~~lD~~~~~~gy~-sRSe~ird~ir~~l~ 42 (137)
T PRK04460 15 EKFDELIEEKGYQ-NRSEAIRDLIRDFLV 42 (137)
T ss_pred HHHHHHHHHcCCC-CHHHHHHHHHHHHHH
Confidence 4677778899996 799999999986664
No 269
>PF05166 YcgL: YcgL domain; InterPro: IPR007840 This family of proteins formerly called DUF709 includes the Escherichia coli gene ycgL. Homologues of YcgL are found in gammaproteobacteria. The structure of this protein shows a novel alpha/beta/alpha sandwich structure []. The proteins in this entry are functionally uncharacterised.; PDB: 2H7A_A.
Probab=21.93 E-value=54 Score=20.90 Aligned_cols=21 Identities=19% Similarity=0.349 Sum_probs=15.9
Q ss_pred HHHhcCCHHHHHHHHhhcCCh
Q 033363 33 KTATEVDAEEIEKIISTLGLQ 53 (121)
Q Consensus 33 ~~la~a~~~eL~~~i~~~Gl~ 53 (121)
..|+.+|.+++.+.|..-||+
T Consensus 48 r~La~~d~~~V~~~l~~~Gfy 68 (74)
T PF05166_consen 48 RKLARADAEKVLAALEEQGFY 68 (74)
T ss_dssp ---SSS-HHHHHHHHHHTSEE
T ss_pred ceeccCCHHHHHHHHHhCCEE
Confidence 459999999999999999987
No 270
>KOG2520 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=21.86 E-value=1.6e+02 Score=26.92 Aligned_cols=79 Identities=22% Similarity=0.281 Sum_probs=50.2
Q ss_pred HHHHHHHHHhCCCHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHHhhHHHhccCCCCcHHHHHHHHHHhcCCCC
Q 033363 19 GRVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHVTQLHGVGKYAADAFAIFCTGKWD 98 (121)
Q Consensus 19 ~~v~~~l~~~~pt~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~~~~~~L~~lpGIG~~tA~~vl~f~~~~~~ 98 (121)
..||..+|..---.+.. ..+++ -+.+|+.+ ..|+.+|.-+-. +.-..++|||+=+|--++.
T Consensus 518 ~~VYrn~F~knk~ve~y---~~~di---~kel~l~R---~~lI~lA~LlGs---DYt~Gl~giGpV~AlEil~------- 578 (815)
T KOG2520|consen 518 TRVYRNFFNKNKYVEKY---QLDDI---EKELGLDR---PNLISLAQLLGS---DYTEGLKGIGPVSALEILA------- 578 (815)
T ss_pred chhhHHHhhcCccceee---ehHHH---HHHHccCc---hhhHHHHHhccc---ccccCCCcccchHHHHHHH-------
Confidence 35888888643322221 12333 35578874 457777776533 2345699999999977764
Q ss_pred ccCcchHHHHHHHHHHHHh
Q 033363 99 RVRPTDHMLNYYWEFLVST 117 (121)
Q Consensus 99 ~v~p~D~~l~~~~~wl~~~ 117 (121)
-||.|.++.++-.|+..+
T Consensus 579 -Efp~~~~l~~f~~w~~~~ 596 (815)
T KOG2520|consen 579 -EFPGDENLLKFKKWVQQT 596 (815)
T ss_pred -HcCCcchhHHHHHHHHHh
Confidence 366667788888888754
No 271
>PF01202 SKI: Shikimate kinase; InterPro: IPR000623 Shikimate kinase (2.7.1.71 from EC) catalyses the fifth step in the biosynthesis of aromatic amino acids from chorismate (the so-called shikimate pathway) []. The enzyme catalyses the following reaction: ATP + shikimate = ADP + shikimate-3-phosphate The protein is found in bacteria (gene aroK or aroL), plants and fungi (where it is part of a multifunctional enzyme that catalyses five consecutive steps in this pathway). In 1994, the 3D structure of shikimate kinase was predicted to be very close to that of adenylate kinase, suggesting a functional similarity as well as an evolutionary relationship []. This prediction has since been confirmed experimentally. The protein is reported to possess an alpha/beta fold, consisting of a central sheet of five parallel beta-strands flanked by alpha-helices. Such a topology is very similar to that of adenylate kinase [].; GO: 0004765 shikimate kinase activity, 0005524 ATP binding; PDB: 3VAA_C 1KO8_B 1KO4_B 1KO1_A 1KOF_A 1KNQ_A 1KO5_A 1KAG_A 2PT5_D 1SHK_A ....
Probab=21.79 E-value=85 Score=21.81 Aligned_cols=30 Identities=17% Similarity=0.092 Sum_probs=24.5
Q ss_pred CCCcHHHHHHHHHHhcCCCCccCcchHHHHHH
Q 033363 79 HGVGKYAADAFAIFCTGKWDRVRPTDHMLNYY 110 (121)
Q Consensus 79 pGIG~~tA~~vl~f~~~~~~~v~p~D~~l~~~ 110 (121)
||.|+-|..-.+.-.+|.+ +.-.|..+.+.
T Consensus 1 ~GsGKStvg~~lA~~L~~~--fiD~D~~i~~~ 30 (158)
T PF01202_consen 1 MGSGKSTVGKLLAKRLGRP--FIDLDDEIEER 30 (158)
T ss_dssp TTSSHHHHHHHHHHHHTSE--EEEHHHHHHHH
T ss_pred CCCcHHHHHHHHHHHhCCC--ccccCHHHHHH
Confidence 7999999999999999986 66667766443
No 272
>KOG2344 consensus Exocyst component protein and related proteins [Intracellular trafficking, secretion, and vesicular transport]
Probab=21.31 E-value=1.2e+02 Score=26.65 Aligned_cols=37 Identities=16% Similarity=0.214 Sum_probs=28.9
Q ss_pred HHHHHHHHHHHHHHhCC------CHHHHhcCCHHHHHHHHhhc
Q 033363 14 ILLKAGRVISDLFTLCP------DAKTATEVDAEEIEKIISTL 50 (121)
Q Consensus 14 ~~~~v~~v~~~l~~~~p------t~~~la~a~~~eL~~~i~~~ 50 (121)
+.+.+.|+|.+|+.+|. .++.-..-++++|+..|..+
T Consensus 569 i~~~v~P~Yr~F~~r~~~~~~~k~~~kyikYtpedlE~~L~dL 611 (623)
T KOG2344|consen 569 ISEKVVPAYRSFYGRYRNSVSGKNPEKYIKYTPEDLENYLSDL 611 (623)
T ss_pred HHHHHHHHHHHHHHHhccccCCCCCCcccccCHHHHHHHHHHH
Confidence 34678999999999854 46777778899999988754
No 273
>PF08328 ASL_C: Adenylosuccinate lyase C-terminal; InterPro: IPR013539 This domain is found at the C terminus of adenylosuccinate lyase(ASL; PurB in Escherichia coli). It has been identified in bacteria, eukaryotes and archaea and is found together with the lyase domain IPR000362 from INTERPRO. ASL catalyses the cleavage of succinylaminoimidazole carboxamide ribotide to aminoimidazole carboxamide ribotide and fumarate and the cleavage of adenylosuccinate to adenylate and fumarate []. ; GO: 0004018 N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity, 0006188 IMP biosynthetic process; PDB: 2HVG_A 2QGA_C 2PTS_A 2PTR_A 2PTQ_B 3BHG_A 3GZH_A.
Probab=21.16 E-value=1.8e+02 Score=20.10 Aligned_cols=24 Identities=13% Similarity=0.383 Sum_probs=11.6
Q ss_pred CCHHHHHHHHhhcCChhHHHHHHH
Q 033363 38 VDAEEIEKIISTLGLQKKRAPMIK 61 (121)
Q Consensus 38 a~~~eL~~~i~~~Gl~~~Ka~~i~ 61 (121)
.+.+++.+.|..+.++..-...|+
T Consensus 84 it~~~l~~fI~~L~ip~~~k~~L~ 107 (115)
T PF08328_consen 84 ITKEDLREFIESLDIPEEAKARLL 107 (115)
T ss_dssp --HHHHHHHHHTSSS-HHHHHHHH
T ss_pred CCHHHHHHHHHhCCCCHHHHHHHH
Confidence 345666666666666544433333
No 274
>cd01700 PolY_Pol_V_umuC umuC subunit of DNA Polymerase V. umuC subunit of Pol V. Pol V is a bacterial translesion synthesis (TLS) polymerase that consists of the heterotrimer of one umuC and two umuD subunits. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Pol V, RecA, single stranded DNA-binding protein, beta sliding clamp, and gamma clamp loading complex are responsible for inducing the SOS response in bacteria to repair UV-induced DNA damage.
Probab=21.14 E-value=63 Score=25.55 Aligned_cols=22 Identities=18% Similarity=0.333 Sum_probs=17.5
Q ss_pred HhccCCCCcHHHHHHHHHHhcC
Q 033363 74 HVTQLHGVGKYAADAFAIFCTG 95 (121)
Q Consensus 74 ~L~~lpGIG~~tA~~vl~f~~~ 95 (121)
.+.++||||++|.+-+..++..
T Consensus 177 pl~~l~gig~~~~~~L~~~Gi~ 198 (344)
T cd01700 177 PVGDVWGIGRRTAKKLNAMGIH 198 (344)
T ss_pred ChhhcCccCHHHHHHHHHcCCC
Confidence 3677899999999987766554
No 275
>COG1324 CutA Uncharacterized protein involved in tolerance to divalent cations [Inorganic ion transport and metabolism]
Probab=21.04 E-value=38 Score=23.04 Aligned_cols=24 Identities=25% Similarity=0.216 Sum_probs=17.7
Q ss_pred cCCCCc-cCcchHHHHHHHHHHHHh
Q 033363 94 TGKWDR-VRPTDHMLNYYWEFLVST 117 (121)
Q Consensus 94 ~~~~~~-v~p~D~~l~~~~~wl~~~ 117 (121)
+.-|.. ++|.|...+.|++|+...
T Consensus 78 YevPeIi~i~v~~g~~eYL~Wl~~~ 102 (104)
T COG1324 78 YEVPEIIALPVDNGLPEYLEWLNEE 102 (104)
T ss_pred CCCceEEEEEeccCCHHHHHHHHHh
Confidence 444432 377899999999999864
No 276
>PF09957 DUF2191: Uncharacterized protein conserved in bacteria (DUF2191); InterPro: IPR019239 This entry, found in various hypothetical prokaryotic proteins, has no known function.
Probab=20.96 E-value=1.8e+02 Score=16.58 Aligned_cols=40 Identities=10% Similarity=0.252 Sum_probs=27.6
Q ss_pred cCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH-hhHHHhcc
Q 033363 37 EVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG-ESWTHVTQ 77 (121)
Q Consensus 37 ~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~-~~~~~L~~ 77 (121)
+.|.+-+++..+-.|.. .|...|....+.++. ....+|.+
T Consensus 6 ~iDd~Ll~eA~~l~g~~-tk~~~V~~ALr~~i~r~~~~~l~~ 46 (47)
T PF09957_consen 6 DIDDELLAEAMRLTGTK-TKKEAVNEALRELIRRRKRRELLE 46 (47)
T ss_pred eeCHHHHHHHHHHhCCC-CHHHHHHHHHHHHHHHHHHHHHHc
Confidence 45666777777778865 788888888887776 33444443
No 277
>cd01067 globin_like superfamily containing globins and truncated hemoglobins
Probab=20.95 E-value=1.2e+02 Score=19.86 Aligned_cols=20 Identities=15% Similarity=0.210 Sum_probs=16.4
Q ss_pred HHHHHHHHHHhCCCHHHHhc
Q 033363 18 AGRVISDLFTLCPDAKTATE 37 (121)
Q Consensus 18 v~~v~~~l~~~~pt~~~la~ 37 (121)
|+..|.+|++.+|....+-+
T Consensus 3 v~~fy~~lf~~~P~~~~~F~ 22 (117)
T cd01067 3 VDDFYKHLFENYPPLRKYFK 22 (117)
T ss_pred HHHHHHHHHHhChhHHHHCC
Confidence 56788999999988887765
No 278
>PF10343 DUF2419: Protein of unknown function (DUF2419); InterPro: IPR019438 This entry contains proteins that have no known function.
Probab=20.80 E-value=4.4e+02 Score=21.03 Aligned_cols=47 Identities=23% Similarity=0.354 Sum_probs=38.7
Q ss_pred HHHHHhCC--CHHHHhcCCHHHHHHHHhh-----cCChhHHHHHHHHHHHHHHH
Q 033363 23 SDLFTLCP--DAKTATEVDAEEIEKIIST-----LGLQKKRAPMIKRFSQEYLG 69 (121)
Q Consensus 23 ~~l~~~~p--t~~~la~a~~~eL~~~i~~-----~Gl~~~Ka~~i~~~a~~i~~ 69 (121)
.++-+..| +|+-+.+.+.++|..++++ +-+-..|.+.|+++.+.+.+
T Consensus 57 rAl~~~~pi~~~~~~~~~t~~~l~~if~s~~~~~iPll~eR~~~L~E~G~vL~~ 110 (287)
T PF10343_consen 57 RALDEGIPITDPKYYAKMTDEELRHIFRSDTEEEIPLLEERARLLREVGRVLLE 110 (287)
T ss_pred HHHhcCCCCcCHHHHHhCCHHHHHHHhcCCCCCcCCCHHHHHHHHHHHHHHHHH
Confidence 34445667 7999999999999999985 44667899999999999887
No 279
>PRK02406 DNA polymerase IV; Validated
Probab=20.73 E-value=62 Score=25.56 Aligned_cols=22 Identities=27% Similarity=0.383 Sum_probs=17.9
Q ss_pred HhccCCCCcHHHHHHHHHHhcC
Q 033363 74 HVTQLHGVGKYAADAFAIFCTG 95 (121)
Q Consensus 74 ~L~~lpGIG~~tA~~vl~f~~~ 95 (121)
.+.++||||+.++.-...++..
T Consensus 169 pi~~l~giG~~~~~~L~~~Gi~ 190 (343)
T PRK02406 169 PVEKIPGVGKVTAEKLHALGIY 190 (343)
T ss_pred CcchhcCCCHHHHHHHHHcCCC
Confidence 4788899999999998766554
No 280
>PF02006 DUF137: Protein of unknown function DUF137; InterPro: IPR002855 The archaeal proteins in this family have no known function.
Probab=20.68 E-value=1.2e+02 Score=22.62 Aligned_cols=38 Identities=26% Similarity=0.399 Sum_probs=24.3
Q ss_pred HHHHHHHHHHHHHHHHHHhCCCHHHHhcCCHHHHHHHHhhc
Q 033363 10 KEIAILLKAGRVISDLFTLCPDAKTATEVDAEEIEKIISTL 50 (121)
Q Consensus 10 ~~~~~~~~v~~v~~~l~~~~pt~~~la~a~~~eL~~~i~~~ 50 (121)
+.+++-.++.++++.+.+ -..++.+.+.++++++++..
T Consensus 128 AtitIVDni~RA~p~~~~---~~~~lk~~~~~el~~iv~~~ 165 (178)
T PF02006_consen 128 ATITIVDNITRAIPNMIE---FARELKKKDREELEEIVKNY 165 (178)
T ss_pred CceeeehhHHHHHHHHHH---HHHHHhcCCHHHHHHHHHhc
Confidence 334333344455555544 46788889999999999754
No 281
>PRK01216 DNA polymerase IV; Validated
Probab=20.64 E-value=65 Score=25.99 Aligned_cols=23 Identities=17% Similarity=0.453 Sum_probs=18.4
Q ss_pred HhccCCCCcHHHHHHHHHHhcCC
Q 033363 74 HVTQLHGVGKYAADAFAIFCTGK 96 (121)
Q Consensus 74 ~L~~lpGIG~~tA~~vl~f~~~~ 96 (121)
.+.++||||++|+.-..-++...
T Consensus 179 Pi~~l~giG~~~~~~L~~~Gi~T 201 (351)
T PRK01216 179 DIADIPGIGDITAEKLKKLGVNK 201 (351)
T ss_pred CcccccCCCHHHHHHHHHcCCCc
Confidence 47788999999998887766543
No 282
>TIGR01766 tspaseT_teng_C transposase, IS605 OrfB family, central region. This model represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by pfam model pfam01385, and other proteins.
Probab=20.41 E-value=2.2e+02 Score=17.34 Aligned_cols=56 Identities=11% Similarity=0.182 Sum_probs=31.1
Q ss_pred hHHHHHHHHHHHHHHHhh--------HHHhccCCC----CcHHHHHHHHHHhcCCCCccCcchHHHHHHHHHHHHhhc
Q 033363 54 KKRAPMIKRFSQEYLGES--------WTHVTQLHG----VGKYAADAFAIFCTGKWDRVRPTDHMLNYYWEFLVSTKG 119 (121)
Q Consensus 54 ~~Ka~~i~~~a~~i~~~~--------~~~L~~lpG----IG~~tA~~vl~f~~~~~~~v~p~D~~l~~~~~wl~~~~~ 119 (121)
+++..+++++|+.+++.. ++.|..+++ -|.+.+..+..+++++ ++.+++|.....|
T Consensus 3 ~~~~d~~hk~a~~iv~~~~~~~~~Ivie~L~~~~~~~~~~~~~~~~~~~~~~~~~----------~~~~l~yka~~~G 70 (82)
T TIGR01766 3 NKVEDFLHKIVKQIVEYAKENNGTIVLEDLKNIKEMVDKKSKYLRRKLHQWSFRK----------LISKIKYKAEEYG 70 (82)
T ss_pred cHHHHHHHHHHHHHHHHHHHcCCEEEECCccchhhhcchhhHHHHHHHHhhhHHH----------HHHHHHHHHHHcC
Confidence 456677888888887732 233333333 3344555555555543 4566666665554
No 283
>PRK01810 DNA polymerase IV; Validated
Probab=20.36 E-value=70 Score=25.98 Aligned_cols=22 Identities=23% Similarity=0.419 Sum_probs=17.6
Q ss_pred HhccCCCCcHHHHHHHHHHhcC
Q 033363 74 HVTQLHGVGKYAADAFAIFCTG 95 (121)
Q Consensus 74 ~L~~lpGIG~~tA~~vl~f~~~ 95 (121)
.+.+|||||+.+++-+..++..
T Consensus 180 pv~~l~giG~~~~~~L~~~Gi~ 201 (407)
T PRK01810 180 PVGEMHGIGEKTAEKLKDIGIQ 201 (407)
T ss_pred CHhhcCCcCHHHHHHHHHcCCC
Confidence 4667899999999988766654
No 284
>PF12339 DNAJ_related: DNA-J related protein ; InterPro: IPR021059 This domain family is approximately 130 amino acids in length and contains a conserved YYLD sequence motif. The proteins have a C-terminal DNA-J domain PF00226 from PFAM and most of the sequences are annotated as DNA-J related proteins, other annotations include: DnaJ-class molecular chaperon and formate dehydrogenase; but there is currently no publications to support these annotations.
Probab=20.30 E-value=1e+02 Score=21.67 Aligned_cols=29 Identities=17% Similarity=0.208 Sum_probs=25.0
Q ss_pred HHHHHHHhCCCHHHHhcCCHHHHHHHHhh
Q 033363 21 VISDLFTLCPDAKTATEVDAEEIEKIIST 49 (121)
Q Consensus 21 v~~~l~~~~pt~~~la~a~~~eL~~~i~~ 49 (121)
....+.+-|-+|..+.++++++|+++|.+
T Consensus 98 ~~d~Lr~YYLDw~n~~~t~~~~V~~LL~~ 126 (132)
T PF12339_consen 98 EDDPLREYYLDWQNYEETSEAEVERLLNS 126 (132)
T ss_pred ccchHHHHHccHHHHhhcCHHHHHHHHHH
Confidence 35677788999999999999999999864
No 285
>PRK05686 fliG flagellar motor switch protein G; Validated
Probab=20.25 E-value=4.5e+02 Score=20.95 Aligned_cols=73 Identities=15% Similarity=0.252 Sum_probs=47.4
Q ss_pred HHHHHHHHHHHhC--CCHHHHhcCCHHHHHHHHhhc----------CC-hhHHHHHHHHHHHHHHHhhHHHhccCCCCcH
Q 033363 17 KAGRVISDLFTLC--PDAKTATEVDAEEIEKIISTL----------GL-QKKRAPMIKRFSQEYLGESWTHVTQLHGVGK 83 (121)
Q Consensus 17 ~v~~v~~~l~~~~--pt~~~la~a~~~eL~~~i~~~----------Gl-~~~Ka~~i~~~a~~i~~~~~~~L~~lpGIG~ 83 (121)
++..++.++...- ..|+.|..++++.|..+|+.. ++ ...+++.+..+......+....+..+..|-+
T Consensus 97 ~a~~il~~i~~~~~~~~fe~L~~ld~~~l~~lL~~EhpqtiA~iLs~l~~~~aa~vL~~l~~~~~~~v~~ria~l~~v~~ 176 (339)
T PRK05686 97 KADSILERILESLGTSGFDFLRKMDPQQLANFIRNEHPQTIALILSYLKPDQAAEILSLLPEELRADVMMRIATLEGVSP 176 (339)
T ss_pred HHHHHHHHHhccccCchHHHHhcCCHHHHHHHHHhcCHHHHHHHHhCCCHHHHHHHHHhCCHHHHHHHHHHHHccCCCCH
Confidence 4555666655432 378999999999988888742 11 1245555555665555566677777778877
Q ss_pred HHHHHH
Q 033363 84 YAADAF 89 (121)
Q Consensus 84 ~tA~~v 89 (121)
....-+
T Consensus 177 ~~~~~i 182 (339)
T PRK05686 177 EALKEV 182 (339)
T ss_pred HHHHHH
Confidence 766655
No 286
>PRK13948 shikimate kinase; Provisional
Probab=20.15 E-value=1.5e+02 Score=21.54 Aligned_cols=34 Identities=15% Similarity=0.001 Sum_probs=26.4
Q ss_pred hccCCCCcHHHHHHHHHHhcCCCCccCcchHHHHHH
Q 033363 75 VTQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYY 110 (121)
Q Consensus 75 L~~lpGIG~~tA~~vl~f~~~~~~~v~p~D~~l~~~ 110 (121)
|..++|.|+-|..-.+.-.+|.+ +.-.|..+.+.
T Consensus 15 LiG~~GsGKSTvg~~La~~lg~~--~iD~D~~ie~~ 48 (182)
T PRK13948 15 LAGFMGTGKSRIGWELSRALMLH--FIDTDRYIERV 48 (182)
T ss_pred EECCCCCCHHHHHHHHHHHcCCC--EEECCHHHHHH
Confidence 67889999999999998888875 55566655443
No 287
>PF03131 bZIP_Maf: bZIP Maf transcription factor; InterPro: IPR004826 There are several different types of Maf transcription factors with different roles in the cell. MafG and MafH are small Mafs which lack a putative transactivation domain. They behave as transcriptional repressors when they dimerize among themselves. However they also serve as transcriptional activators by dimerizing with other (usually larger) basic-zipper proteins and recruiting them to specific DNA-binding sites. Maf transcription factors contain a conserved basic region leucine zipper (bZIP) domain, which mediates their dimerization and DNA binding property. Neural retina-specific leucine zipper proteins also belong to this family. Together with the basic region, the Maf extended homology region (EHR), conserved only within the Maf family, defines the DNA binding specific to Mafs. This structure enables Mafs to make a broader area of contact with DNA and to recognise longer DNA sequences. In particular, the two residues at the beginning of helix H2 are positioned to recognise the flanking region []. Small Maf proteins heterodimerize with Fos and may act as competitive repressors of the NF2-E2 transcription factor. In mouse, Maf1 may play an early role in axial patterning. Defects in these proteins are a cause of autosomal dominant retinitis pigmentosa. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2KZ5_A 3A5T_A 1K1V_A 1SKN_P 2WT7_B 2WTY_B.
Probab=20.14 E-value=2e+02 Score=18.51 Aligned_cols=35 Identities=11% Similarity=0.311 Sum_probs=21.5
Q ss_pred CHHHHhcCCHHHHHHHHhhcCChhHHHHHHHHHHHHH
Q 033363 31 DAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEY 67 (121)
Q Consensus 31 t~~~la~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i 67 (121)
|-+.|.+++.+|+..++ -||+..-...|+..=+..
T Consensus 2 s~eeL~~m~v~efn~~L--~~lt~~q~~~lK~~RRr~ 36 (92)
T PF03131_consen 2 SDEELVSMSVREFNRLL--RGLTEEQIAELKQRRRRL 36 (92)
T ss_dssp -HHHHHHS-HHHHHHHC--TTS-HHHHHHHHHHHHHH
T ss_pred CHHHHhhCCHHHHHHHH--HcCCHHHHHHHHHHHHHH
Confidence 45678888888888877 677766666665544433
No 288
>PF13735 tRNA_NucTran2_2: tRNA nucleotidyltransferase domain 2 putative; PDB: 1MIY_A 1MIV_B 1MIW_B.
Probab=20.10 E-value=1.6e+02 Score=20.01 Aligned_cols=34 Identities=18% Similarity=0.258 Sum_probs=22.7
Q ss_pred hcCCHHHHHHHHhhcCChhHHHHHHHHHHHHHHH
Q 033363 36 TEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLG 69 (121)
Q Consensus 36 a~a~~~eL~~~i~~~Gl~~~Ka~~i~~~a~~i~~ 69 (121)
...++++..+.++.+.|++...+.+..+.+....
T Consensus 17 ~~~~~~~a~~~L~~lk~Sn~~i~~v~~l~~~~~~ 50 (149)
T PF13735_consen 17 LGLDPEEAREILKRLKFSNKEIKRVLSLVELHMR 50 (149)
T ss_dssp TT---S-HHHHHHHTT--HHHHHHHHHHHHHHHH
T ss_pred hccHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 3456677888899999999888888888887665
Done!