Query 030930
Match_columns 169
No_of_seqs 126 out of 925
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 06:43:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030930.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030930hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0099 RpsM Ribosomal protein 100.0 3.7E-51 8E-56 313.8 10.1 119 47-165 1-121 (121)
2 CHL00137 rps13 ribosomal prote 100.0 6.3E-49 1.4E-53 302.9 11.6 119 47-165 1-121 (122)
3 PRK05179 rpsM 30S ribosomal pr 100.0 1E-48 2.2E-53 301.7 11.4 119 47-165 1-121 (122)
4 TIGR03629 arch_S13P archaeal r 100.0 1.5E-48 3.3E-53 308.2 11.6 121 39-165 1-144 (144)
5 PTZ00134 40S ribosomal protein 100.0 1E-48 2.2E-53 312.2 10.6 126 34-165 5-154 (154)
6 PRK04053 rps13p 30S ribosomal 100.0 1.3E-48 2.9E-53 310.1 9.9 123 37-165 3-149 (149)
7 TIGR03631 bact_S13 30S ribosom 100.0 5.7E-46 1.2E-50 283.0 10.5 110 49-158 1-112 (113)
8 PF00416 Ribosomal_S13: Riboso 100.0 3.3E-45 7.2E-50 275.1 4.5 105 49-153 1-107 (107)
9 KOG3311 Ribosomal protein S18 100.0 4.4E-38 9.6E-43 249.5 6.4 128 30-165 1-152 (152)
10 PRK01103 formamidopyrimidine/5 94.3 0.047 1E-06 46.9 3.7 52 56-107 153-208 (274)
11 PF06831 H2TH: Formamidopyrimi 94.2 0.059 1.3E-06 39.4 3.5 50 57-106 22-75 (92)
12 PRK14810 formamidopyrimidine-D 92.1 0.17 3.7E-06 43.6 3.7 52 56-107 152-207 (272)
13 PF00633 HHH: Helix-hairpin-he 92.1 0.096 2.1E-06 31.2 1.5 18 64-81 12-29 (30)
14 PRK14811 formamidopyrimidine-D 91.4 0.32 7E-06 41.8 4.7 50 57-106 142-195 (269)
15 PRK10445 endonuclease VIII; Pr 91.1 0.37 8.1E-06 41.3 4.7 50 58-107 151-204 (263)
16 TIGR00577 fpg formamidopyrimid 90.6 0.41 8.8E-06 41.2 4.5 51 57-107 154-208 (272)
17 PRK13945 formamidopyrimidine-D 90.4 0.41 8.9E-06 41.4 4.4 49 58-106 164-216 (282)
18 PF11798 IMS_HHH: IMS family H 88.2 0.3 6.4E-06 29.3 1.3 21 64-85 12-32 (32)
19 PRK04184 DNA topoisomerase VI 86.5 1 2.2E-05 42.8 4.6 50 59-108 256-307 (535)
20 KOG3311 Ribosomal protein S18 85.5 0.15 3.3E-06 41.1 -1.2 46 110-157 70-115 (152)
21 PF05833 FbpA: Fibronectin-bin 84.9 0.23 4.9E-06 44.8 -0.6 51 57-107 185-237 (455)
22 PRK02515 psbU photosystem II c 84.5 0.97 2.1E-05 35.8 2.9 61 51-111 49-113 (132)
23 COG3743 Uncharacterized conser 83.6 1 2.2E-05 35.8 2.6 43 63-106 67-110 (133)
24 smart00278 HhH1 Helix-hairpin- 81.6 1.1 2.5E-05 25.2 1.7 19 64-82 2-20 (26)
25 PF14520 HHH_5: Helix-hairpin- 81.3 0.35 7.6E-06 32.2 -0.6 37 62-99 4-41 (60)
26 PF13035 DUF3896: Protein of u 80.6 3.7 7.9E-05 28.1 4.1 42 77-134 19-61 (61)
27 PF10391 DNA_pol_lambd_f: Fing 79.9 1.2 2.5E-05 29.7 1.5 22 64-86 3-24 (52)
28 PF14579 HHH_6: Helix-hairpin- 79.5 2.1 4.6E-05 30.7 2.9 27 58-84 22-48 (90)
29 PRK14606 ruvA Holliday junctio 79.2 1.1 2.3E-05 37.0 1.4 20 64-83 109-128 (188)
30 PRK14601 ruvA Holliday junctio 77.3 1.3 2.9E-05 36.4 1.4 19 64-82 109-127 (183)
31 PRK14604 ruvA Holliday junctio 76.7 1.4 3E-05 36.5 1.4 21 63-83 108-128 (195)
32 COG0632 RuvA Holliday junction 76.5 1.6 3.4E-05 36.7 1.7 22 63-84 108-129 (201)
33 PRK14603 ruvA Holliday junctio 76.5 1.4 3.1E-05 36.5 1.5 19 64-82 108-126 (197)
34 COG0266 Nei Formamidopyrimidin 76.5 4.1 9E-05 35.7 4.3 53 55-107 152-208 (273)
35 PRK14602 ruvA Holliday junctio 75.9 1.5 3.4E-05 36.4 1.5 18 64-81 110-127 (203)
36 PRK13901 ruvA Holliday junctio 75.1 1.6 3.5E-05 36.4 1.4 19 64-82 108-126 (196)
37 PF11731 Cdd1: Pathogenicity l 74.8 2.6 5.7E-05 31.4 2.3 37 63-100 12-49 (93)
38 TIGR00275 flavoprotein, HI0933 74.7 3.7 8E-05 36.6 3.7 39 71-109 294-333 (400)
39 PF12826 HHH_2: Helix-hairpin- 74.3 0.77 1.7E-05 31.2 -0.6 33 67-100 7-39 (64)
40 COG0353 RecR Recombinational D 73.3 5 0.00011 33.8 3.9 72 61-139 10-108 (198)
41 TIGR03252 uncharacterized HhH- 72.1 1 2.2E-05 37.1 -0.4 29 56-84 108-136 (177)
42 TIGR00615 recR recombination p 71.9 5.9 0.00013 33.2 4.0 72 61-139 9-107 (195)
43 TIGR01052 top6b DNA topoisomer 71.5 6 0.00013 37.3 4.4 49 59-107 247-300 (488)
44 PRK13844 recombination protein 70.9 6.3 0.00014 33.1 4.0 72 61-139 13-111 (200)
45 PRK14600 ruvA Holliday junctio 70.1 3 6.4E-05 34.4 1.9 19 63-82 108-126 (186)
46 PRK00076 recR recombination pr 69.9 6.5 0.00014 32.9 3.9 72 61-139 9-107 (196)
47 PRK00274 ksgA 16S ribosomal RN 68.8 3 6.5E-05 35.4 1.7 47 60-107 223-270 (272)
48 PRK14605 ruvA Holliday junctio 66.5 3.2 6.9E-05 34.2 1.3 17 64-80 109-125 (194)
49 PRK00116 ruvA Holliday junctio 64.9 3.1 6.7E-05 34.0 1.0 38 49-86 59-96 (192)
50 PF03486 HI0933_like: HI0933-l 62.9 5.9 0.00013 36.1 2.5 52 56-109 288-341 (409)
51 PF14716 HHH_8: Helix-hairpin- 62.8 4.9 0.00011 27.4 1.5 19 64-82 48-66 (68)
52 cd00080 HhH2_motif Helix-hairp 62.5 6.5 0.00014 27.5 2.1 20 65-84 24-43 (75)
53 PF14520 HHH_5: Helix-hairpin- 62.1 5.6 0.00012 26.2 1.7 20 64-83 39-58 (60)
54 PF02371 Transposase_20: Trans 60.4 7 0.00015 27.7 2.0 20 64-83 3-22 (87)
55 smart00279 HhH2 Helix-hairpin- 59.7 8 0.00017 23.7 1.9 17 66-82 19-35 (36)
56 PRK07945 hypothetical protein; 58.9 15 0.00032 32.6 4.2 47 64-118 50-96 (335)
57 TIGR00084 ruvA Holliday juncti 57.3 6.2 0.00013 32.5 1.5 18 63-80 107-124 (191)
58 smart00483 POLXc DNA polymeras 57.0 7.3 0.00016 34.5 2.0 39 62-101 88-132 (334)
59 cd00056 ENDO3c endonuclease II 56.2 6.6 0.00014 30.1 1.4 25 58-82 78-102 (158)
60 smart00478 ENDO3c endonuclease 54.6 7.3 0.00016 29.6 1.4 23 61-83 70-92 (149)
61 PRK09482 flap endonuclease-lik 53.8 42 0.00091 29.0 6.1 19 66-84 185-203 (256)
62 TIGR00426 competence protein C 53.2 16 0.00034 24.7 2.7 23 61-83 14-37 (69)
63 cd00141 NT_POLXc Nucleotidyltr 51.7 10 0.00022 33.2 2.0 25 62-87 84-108 (307)
64 PRK10702 endonuclease III; Pro 51.6 8.2 0.00018 32.2 1.4 23 61-83 107-129 (211)
65 TIGR01083 nth endonuclease III 50.9 8.5 0.00018 31.1 1.3 23 61-83 104-126 (191)
66 TIGR00755 ksgA dimethyladenosi 50.7 7.8 0.00017 32.3 1.1 44 59-104 208-252 (253)
67 PRK14605 ruvA Holliday junctio 50.5 4.1 9E-05 33.6 -0.6 39 48-86 58-96 (194)
68 COG0030 KsgA Dimethyladenosine 50.1 7.9 0.00017 33.6 1.0 45 58-107 211-256 (259)
69 PRK08609 hypothetical protein; 50.0 11 0.00025 35.8 2.2 24 63-86 88-111 (570)
70 COG1389 DNA topoisomerase VI, 49.7 18 0.00039 34.5 3.4 43 66-108 264-311 (538)
71 cd00008 53EXOc 5'-3' exonuclea 49.3 40 0.00087 28.3 5.2 20 65-84 185-204 (240)
72 smart00475 53EXOc 5'-3' exonuc 48.1 52 0.0011 28.2 5.7 20 65-84 188-207 (259)
73 COG0258 Exo 5'-3' exonuclease 47.4 42 0.00091 29.1 5.1 18 68-85 203-220 (310)
74 PF12836 HHH_3: Helix-hairpin- 47.4 9.7 0.00021 25.6 1.0 45 59-103 10-62 (65)
75 PRK13913 3-methyladenine DNA g 46.2 11 0.00025 31.7 1.4 22 61-82 119-140 (218)
76 TIGR01259 comE comEA protein. 45.1 19 0.00042 27.3 2.4 32 54-85 59-90 (120)
77 TIGR01084 mutY A/G-specific ad 44.9 12 0.00026 32.5 1.3 28 53-83 98-125 (275)
78 PRK14976 5'-3' exonuclease; Pr 44.4 68 0.0015 27.8 6.0 19 66-84 194-212 (281)
79 PF00398 RrnaAD: Ribosomal RNA 43.7 9.5 0.00021 32.1 0.6 50 56-107 212-262 (262)
80 PRK10308 3-methyl-adenine DNA 43.5 38 0.00083 29.4 4.3 22 61-82 205-226 (283)
81 PRK14666 uvrC excinuclease ABC 43.0 25 0.00054 34.7 3.3 44 57-101 631-674 (694)
82 PRK07373 DNA polymerase III su 43.0 22 0.00047 33.1 2.8 46 58-103 109-165 (449)
83 PRK01229 N-glycosylase/DNA lya 42.4 17 0.00036 30.6 1.8 27 60-86 115-142 (208)
84 TIGR00084 ruvA Holliday juncti 42.3 4.2 9E-05 33.5 -1.8 37 48-84 57-93 (191)
85 COG1293 Predicted RNA-binding 42.0 27 0.00058 33.3 3.3 45 61-105 188-233 (564)
86 PRK10880 adenine DNA glycosyla 41.4 13 0.00028 33.5 1.1 22 61-82 107-128 (350)
87 PRK00558 uvrC excinuclease ABC 41.1 16 0.00035 35.1 1.7 47 54-101 534-580 (598)
88 COG2081 Predicted flavoprotein 40.7 35 0.00075 31.8 3.7 50 58-109 285-334 (408)
89 PRK00116 ruvA Holliday junctio 40.3 16 0.00035 29.8 1.4 21 64-84 109-129 (192)
90 PRK13910 DNA glycosylase MutY; 39.5 16 0.00036 32.0 1.4 21 62-82 71-91 (289)
91 PRK14667 uvrC excinuclease ABC 39.4 21 0.00047 34.2 2.3 47 54-101 505-551 (567)
92 PRK12311 rpsB 30S ribosomal pr 39.2 18 0.00039 32.4 1.7 44 62-106 262-306 (326)
93 COG0177 Nth Predicted EndoIII- 39.1 16 0.00034 30.9 1.2 26 54-82 103-128 (211)
94 PF02318 FYVE_2: FYVE-type zin 38.4 63 0.0014 24.3 4.3 16 92-107 2-17 (118)
95 COG1936 Predicted nucleotide k 38.2 33 0.00071 28.6 2.9 25 62-86 2-26 (180)
96 PRK12766 50S ribosomal protein 38.1 24 0.00053 30.4 2.2 22 64-86 4-25 (232)
97 TIGR01448 recD_rel helicase, p 37.3 61 0.0013 31.8 5.0 39 67-105 88-137 (720)
98 PRK14670 uvrC excinuclease ABC 37.2 23 0.0005 34.1 2.1 40 61-101 512-551 (574)
99 PRK14671 uvrC excinuclease ABC 36.9 28 0.0006 33.7 2.6 50 51-101 557-606 (621)
100 PRK14669 uvrC excinuclease ABC 36.7 27 0.00058 34.0 2.5 46 55-101 544-589 (624)
101 TIGR00588 ogg 8-oxoguanine DNA 36.0 19 0.00042 31.6 1.3 23 61-83 218-240 (310)
102 COG0122 AlkA 3-methyladenine D 35.7 21 0.00045 31.2 1.4 23 60-82 195-217 (285)
103 PRK14602 ruvA Holliday junctio 34.4 7.5 0.00016 32.3 -1.4 38 48-85 59-96 (203)
104 PRK14668 uvrC excinuclease ABC 34.4 24 0.00052 33.9 1.7 40 61-101 523-562 (577)
105 cd01104 HTH_MlrA-CarA Helix-Tu 33.6 89 0.0019 20.2 4.0 42 65-106 6-52 (68)
106 PRK14606 ruvA Holliday junctio 33.0 6 0.00013 32.6 -2.3 37 48-84 58-94 (188)
107 PRK14601 ruvA Holliday junctio 32.8 8.8 0.00019 31.6 -1.3 37 48-84 58-94 (183)
108 cd01199 INT_Tn1545_C Tn1545-re 31.7 69 0.0015 24.4 3.6 16 93-108 2-17 (205)
109 PRK14600 ruvA Holliday junctio 31.0 10 0.00022 31.2 -1.2 38 48-85 58-95 (186)
110 PF14842 FliG_N: FliG N-termin 30.8 71 0.0015 23.6 3.4 37 72-108 7-45 (108)
111 PRK12278 50S ribosomal protein 30.6 42 0.00092 28.6 2.4 43 63-106 158-201 (221)
112 PF02042 RWP-RK: RWP-RK domain 30.6 50 0.0011 22.1 2.3 19 68-86 24-42 (52)
113 PF11338 DUF3140: Protein of u 30.3 65 0.0014 24.1 3.1 33 71-106 35-67 (92)
114 PF06514 PsbU: Photosystem II 29.9 29 0.00062 26.0 1.2 59 52-110 12-74 (93)
115 PRK13901 ruvA Holliday junctio 28.9 12 0.00025 31.4 -1.2 37 48-84 57-93 (196)
116 KOG0437 Leucyl-tRNA synthetase 28.7 66 0.0014 32.8 3.7 61 26-96 387-460 (1080)
117 PRK14603 ruvA Holliday junctio 28.7 11 0.00025 31.1 -1.3 37 48-84 57-93 (197)
118 PF14490 HHH_4: Helix-hairpin- 26.6 40 0.00086 24.2 1.4 24 63-86 45-69 (94)
119 PF14794 DUF4479: Domain of un 25.6 60 0.0013 22.9 2.1 18 91-108 46-63 (73)
120 PF03677 UPF0137: Uncharacteri 25.5 1E+02 0.0023 26.8 3.9 23 91-113 35-57 (243)
121 TIGR00575 dnlj DNA ligase, NAD 25.5 57 0.0012 31.8 2.6 36 66-101 435-471 (652)
122 COG3415 Transposase and inacti 25.2 64 0.0014 25.5 2.4 78 64-143 26-115 (138)
123 PRK05755 DNA polymerase I; Pro 25.2 1.8E+02 0.0039 29.1 6.1 20 65-84 189-208 (880)
124 COG2231 Uncharacterized protei 24.8 20 0.00044 30.6 -0.5 32 53-84 103-136 (215)
125 KOG2534 DNA polymerase IV (fam 24.6 1.3E+02 0.0027 27.6 4.4 25 62-86 55-79 (353)
126 PF04001 Vhr1: Transcription f 24.0 67 0.0014 24.1 2.2 11 76-86 9-19 (95)
127 PF01367 5_3_exonuc: 5'-3' exo 23.7 8.7 0.00019 28.7 -2.6 19 66-84 21-39 (101)
128 PRK14604 ruvA Holliday junctio 23.5 16 0.00035 30.2 -1.3 36 48-83 58-93 (195)
129 cd01702 PolY_Pol_eta DNA Polym 23.4 60 0.0013 29.0 2.2 38 63-100 182-222 (359)
130 TIGR00194 uvrC excinuclease AB 22.7 55 0.0012 31.5 1.9 30 55-84 533-562 (574)
131 PF14635 HHH_7: Helix-hairpin- 22.6 66 0.0014 24.3 2.0 27 58-84 45-71 (104)
132 PTZ00338 dimethyladenosine tra 22.6 95 0.002 27.0 3.2 33 75-107 256-288 (294)
133 PF14229 DUF4332: Domain of un 22.3 1.1E+02 0.0023 23.3 3.1 41 65-106 55-96 (122)
134 PRK07956 ligA NAD-dependent DN 22.1 81 0.0017 30.9 2.9 36 66-101 448-484 (665)
135 PF00034 Cytochrom_C: Cytochro 22.0 92 0.002 20.1 2.4 16 92-107 74-89 (91)
136 cd00128 XPG Xeroderma pigmento 21.9 66 0.0014 27.8 2.1 19 66-84 226-244 (316)
137 PF11460 DUF3007: Protein of u 21.9 51 0.0011 25.2 1.2 19 88-106 85-103 (104)
138 PF13442 Cytochrome_CBB3: Cyto 21.8 84 0.0018 20.4 2.2 16 90-105 52-67 (67)
139 PRK05898 dnaE DNA polymerase I 21.5 83 0.0018 32.4 3.0 25 58-82 747-771 (971)
140 COG0632 RuvA Holliday junction 21.4 33 0.0007 28.8 0.1 69 17-85 21-95 (201)
141 PF09346 SMI1_KNR4: SMI1 / KNR 20.8 1.4E+02 0.003 20.8 3.3 26 93-119 2-27 (130)
142 PLN02200 adenylate kinase fami 20.7 1E+02 0.0022 25.7 3.0 42 54-95 37-79 (234)
143 COG1796 POL4 DNA polymerase IV 20.7 64 0.0014 29.2 1.8 21 64-84 54-74 (326)
144 cd02020 CMPK Cytidine monophos 20.4 3.3E+02 0.0073 19.5 7.3 42 63-104 2-44 (147)
145 cd05124 AFK Actin-Fragmin Kina 20.4 2.7E+02 0.0058 24.2 5.5 49 58-108 23-73 (238)
146 COG1908 FrhD Coenzyme F420-red 20.3 1.1E+02 0.0023 24.4 2.7 34 75-108 82-117 (132)
No 1
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.7e-51 Score=313.78 Aligned_cols=119 Identities=50% Similarity=0.863 Sum_probs=116.3
Q ss_pred eeEEeCccCCCCeEEeEeeccccccCHHHHHHHHHHcCCC-ccccCCCCHHHHHHHHHHHh-hcccchHHHHHHHHHHHH
Q 030930 47 CARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKME-NKITKDMSEEELITIRDEVS-KYMIEGDLRRFNALAIRR 124 (169)
Q Consensus 47 ~vrI~~tni~~~K~i~~ALt~I~GIG~~~A~~Ic~~lgi~-~k~~~~Ls~~el~~L~~~l~-~~~Ie~dLr~~~~~nI~r 124 (169)
|+||+|+|||++|+|++|||+|||||+++|..||+++||| +++++||||||+++|.++++ .|++|+||++++++||+|
T Consensus 1 maRIagvdip~~K~v~iALt~IyGIG~~~a~~I~~~~gi~~~~r~~eLteeei~~ir~~i~~~~~vegDLr~~v~~dIkR 80 (121)
T COG0099 1 MARIAGVDIPGNKRVVIALTYIYGIGRRRAKEICKKAGIDPDKRVGELTEEEIERLRDAIQNKYLVEGDLRREVRMDIKR 80 (121)
T ss_pred CceecccCCCCCceEeehhhhhccccHHHHHHHHHHcCCCHhHhhccCCHHHHHHHHHHHHhcCeehhHHHHHHHHHHHH
Confidence 6999999999999999999999999999999999999999 77899999999999999998 899999999999999999
Q ss_pred HHhhhhcccCccCCCCccCCccCccccccCCCceeeecccc
Q 030930 125 LKEIQCYRGIRHIQGLPCRGQHTKNNCRTLKGKRVAIAGKK 165 (169)
Q Consensus 125 L~~I~sYRG~RH~~GLPVRGQRTrTNarT~Kg~~~gV~~kK 165 (169)
|++|+||||+||.+|||||||||||||||+||.+++|++||
T Consensus 81 l~~i~~YRGiRH~~GLpVRGQrTktnaRtrkG~~~~v~~KK 121 (121)
T COG0099 81 LMKIGCYRGIRHRRGLPVRGQRTKTNARTRKGPRKGVAKKK 121 (121)
T ss_pred HHHhhhhhhhhhhcCCCCCCcccCccccccCCCccccccCC
Confidence 99999999999999999999999999999999999998876
No 2
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=100.00 E-value=6.3e-49 Score=302.87 Aligned_cols=119 Identities=50% Similarity=0.912 Sum_probs=114.7
Q ss_pred eeEEeCccCCCCeEEeEeeccccccCHHHHHHHHHHcCCC-ccccCCCCHHHHHHHHHHHh-hcccchHHHHHHHHHHHH
Q 030930 47 CARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKME-NKITKDMSEEELITIRDEVS-KYMIEGDLRRFNALAIRR 124 (169)
Q Consensus 47 ~vrI~~tni~~~K~i~~ALt~I~GIG~~~A~~Ic~~lgi~-~k~~~~Ls~~el~~L~~~l~-~~~Ie~dLr~~~~~nI~r 124 (169)
|+||+|||||++|+|.+|||+|||||+++|.+||+++||| +.++++|+++|+++|.++|+ +|.+|+||++.+++||+|
T Consensus 1 mvrI~~~~i~~~k~v~~aLt~i~GIG~~~A~~ic~~lgi~~~~~~~~Lt~~qi~~l~~~i~~~~~i~~dL~~~~~~dI~r 80 (122)
T CHL00137 1 MVRIAGVDLPRNKRIEYALTYIYGIGLTSAKEILEKANIDPDIRTKDLTDEQISALREIIEENYQVEGDLRRFESLNIKR 80 (122)
T ss_pred CceEcCccCCCCCEeeeeecccccccHHHHHHHHHHcCcCcCcCcccCCHHHHHHHHHHHHHhCcchHHHHHHHHHHHHH
Confidence 6999999999999999999999999999999999999999 67789999999999999997 699999999999999999
Q ss_pred HHhhhhcccCccCCCCccCCccCccccccCCCceeeecccc
Q 030930 125 LKEIQCYRGIRHIQGLPCRGQHTKNNCRTLKGKRVAIAGKK 165 (169)
Q Consensus 125 L~~I~sYRG~RH~~GLPVRGQRTrTNarT~Kg~~~gV~~kK 165 (169)
|++|+||||+||.+|||||||||||||||+|+....|++||
T Consensus 81 l~~I~sYRG~RH~~gLPVRGQRT~tNarT~k~~~~~~~~kk 121 (122)
T CHL00137 81 LMEINCYRGRRHRLGLPVRGQRTRTNARTRRGAKKTVAGKK 121 (122)
T ss_pred HHHhCchhcccccCCCCCCCCcCCccccccCCCcccccccC
Confidence 99999999999999999999999999999999998888654
No 3
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=100.00 E-value=1e-48 Score=301.68 Aligned_cols=119 Identities=55% Similarity=0.923 Sum_probs=114.5
Q ss_pred eeEEeCccCCCCeEEeEeeccccccCHHHHHHHHHHcCCC-ccccCCCCHHHHHHHHHHHhh-cccchHHHHHHHHHHHH
Q 030930 47 CARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKME-NKITKDMSEEELITIRDEVSK-YMIEGDLRRFNALAIRR 124 (169)
Q Consensus 47 ~vrI~~tni~~~K~i~~ALt~I~GIG~~~A~~Ic~~lgi~-~k~~~~Ls~~el~~L~~~l~~-~~Ie~dLr~~~~~nI~r 124 (169)
|+||+|||||++|+|.+||++|||||+++|.+||+++||| +.++++|+++|+++|.++|++ |.+|+||++++++||+|
T Consensus 1 MvrI~~~~l~~~k~v~~aL~~I~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi~~l~~~i~~~~~i~~dL~~~~~~dI~r 80 (122)
T PRK05179 1 MARIAGVDIPRNKRVVIALTYIYGIGRTRAKEILAAAGIDPDTRVKDLTDEELDKIREEIDKNYKVEGDLRREVSMNIKR 80 (122)
T ss_pred CceecCccCCCCcEEEeeecccccccHHHHHHHHHHhCcCcccccccCCHHHHHHHHHHHHhhccchHHHHHHHHHHHHH
Confidence 7999999999999999999999999999999999999999 677899999999999999985 99999999999999999
Q ss_pred HHhhhhcccCccCCCCccCCccCccccccCCCceeeecccc
Q 030930 125 LKEIQCYRGIRHIQGLPCRGQHTKNNCRTLKGKRVAIAGKK 165 (169)
Q Consensus 125 L~~I~sYRG~RH~~GLPVRGQRTrTNarT~Kg~~~gV~~kK 165 (169)
|++|+||||+||.+|||||||||||||||+||....|..||
T Consensus 81 l~~I~sYRG~RH~~gLPVRGQRT~TNart~k~~~~~~~~kk 121 (122)
T PRK05179 81 LMDIGCYRGLRHRRGLPVRGQRTKTNARTRKGPRKTIAGKK 121 (122)
T ss_pred HHHhcceeeeecccCCCCCCCcCCccccccCCccccccccC
Confidence 99999999999999999999999999999999988887654
No 4
>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=100.00 E-value=1.5e-48 Score=308.18 Aligned_cols=121 Identities=36% Similarity=0.576 Sum_probs=116.4
Q ss_pred CCCCcccceeEEeCccCCCCeEEeEeeccccccCHHHHHHHHHHcCCC-ccccCCCCHHHHHHHHHHHhh----------
Q 030930 39 QYPGLSIQCARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKME-NKITKDMSEEELITIRDEVSK---------- 107 (169)
Q Consensus 39 ~f~~i~~~~vrI~~tni~~~K~i~~ALt~I~GIG~~~A~~Ic~~lgi~-~k~~~~Ls~~el~~L~~~l~~---------- 107 (169)
+|||| +||+|||||++|+|.+||++|||||+++|.+||+++||| +.++++||++|+++|.++|++
T Consensus 1 ~~~~m----~rI~~~~i~~~k~v~~aLt~I~GIG~~~a~~I~~~lgi~~~~~~~~Lt~~qi~~l~~~i~~~~~~iP~w~~ 76 (144)
T TIGR03629 1 EFKYI----VRIADTDLDGNKPVEYALTGIKGIGRRFARAIARKLGVDPNAKLGYLDDEEIEKLEEAVENYEYGIPSWLL 76 (144)
T ss_pred Cccee----eeeeCccCCCCCEEEEeecceeccCHHHHHHHHHHcCcCCCCCcccCCHHHHHHHHHHHHhccccCCHHHh
Confidence 47877 999999999999999999999999999999999999999 778999999999999999975
Q ss_pred ------------cccchHHHHHHHHHHHHHHhhhhcccCccCCCCccCCccCccccccCCCceeeecccc
Q 030930 108 ------------YMIEGDLRRFNALAIRRLKEIQCYRGIRHIQGLPCRGQHTKNNCRTLKGKRVAIAGKK 165 (169)
Q Consensus 108 ------------~~Ie~dLr~~~~~nI~rL~~I~sYRG~RH~~GLPVRGQRTrTNarT~Kg~~~gV~~kK 165 (169)
|.+|+||++.+++||+||++|+||||+||.+||||||||||||||| |+++||++||
T Consensus 77 Nr~~d~~tg~~~~~ie~dL~~~~~~dI~rl~~I~~yRG~RH~~gLpVRGQRTrTNaRt--g~~~gv~~kk 144 (144)
T TIGR03629 77 NRRKDYETGEDLHLIGSDLDMTVREDINRMKKIRSYRGIRHELGLKVRGQRTKSTGRR--GRTVGVSRKK 144 (144)
T ss_pred hcccccccCccceEehHHHHHHHHHHHHHHHHhcceeeeeccCCCCCCCCcCCCCCcC--CCccccccCC
Confidence 6799999999999999999999999999999999999999999998 9999999987
No 5
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=100.00 E-value=1e-48 Score=312.18 Aligned_cols=126 Identities=28% Similarity=0.482 Sum_probs=118.8
Q ss_pred cCCCCCCCCcccceeEEeCccCCCCeEEeEeeccccccCHHHHHHHHHHcCCC-ccccCCCCHHHHHHHHHHHhh---c-
Q 030930 34 VSKQPQYPGLSIQCARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKME-NKITKDMSEEELITIRDEVSK---Y- 108 (169)
Q Consensus 34 ~~~~~~f~~i~~~~vrI~~tni~~~K~i~~ALt~I~GIG~~~A~~Ic~~lgi~-~k~~~~Ls~~el~~L~~~l~~---~- 108 (169)
...+++|||| +||+|||||++|+|.+||++|||||+++|.+||+++||| ++++++||++|+++|.++|++ |
T Consensus 5 ~~~~~~~~~m----vrI~~~~l~~~K~v~~aLt~I~GIG~~~A~~I~~~lgi~~~~~~~~Lt~~qi~~l~~~i~~~~~~~ 80 (154)
T PTZ00134 5 LEKADDFQHI----LRILNTNVDGKRKVPYALTAIKGIGRRFAYLVCKKAGIDVTKRAGELTAEEIEKIVEIIANPLQFK 80 (154)
T ss_pred ccchhhhhhh----hhccCccCCCCCEEEEeecccccccHHHHHHHHHHcCcCcCCCcccCCHHHHHHHHHHHhccccCC
Confidence 3344589999 999999999999999999999999999999999999999 778899999999999999975 5
Q ss_pred -------------------ccchHHHHHHHHHHHHHHhhhhcccCccCCCCccCCccCccccccCCCceeeecccc
Q 030930 109 -------------------MIEGDLRRFNALAIRRLKEIQCYRGIRHIQGLPCRGQHTKNNCRTLKGKRVAIAGKK 165 (169)
Q Consensus 109 -------------------~Ie~dLr~~~~~nI~rL~~I~sYRG~RH~~GLPVRGQRTrTNarT~Kg~~~gV~~kK 165 (169)
.+++||++.+++||+||++|+||||+||.+||||||||||||||| |+++||++||
T Consensus 81 iP~w~~nr~kd~~tG~d~h~i~~dL~~~~~~dI~Rl~~I~sYRG~RH~~GLpVRGQRTkTnaR~--g~~~gv~~kk 154 (154)
T PTZ00134 81 IPDWFLNRQRDPKDGKNSHLTSNMLDTKLREDLERLKKIRLHRGLRHHWGLRVRGQHTKTTGRR--GRTVGVSRKK 154 (154)
T ss_pred CChhHhhccccccccchhhhhHHHHHHHHHHHHHHHHHhcchheeecccCCccCCccCCCCCcc--ccccceeccC
Confidence 369999999999999999999999999999999999999999998 9999999987
No 6
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=100.00 E-value=1.3e-48 Score=310.10 Aligned_cols=123 Identities=36% Similarity=0.574 Sum_probs=117.7
Q ss_pred CCCCCCcccceeEEeCccCCCCeEEeEeeccccccCHHHHHHHHHHcCCC-ccccCCCCHHHHHHHHHHHh---------
Q 030930 37 QPQYPGLSIQCARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKME-NKITKDMSEEELITIRDEVS--------- 106 (169)
Q Consensus 37 ~~~f~~i~~~~vrI~~tni~~~K~i~~ALt~I~GIG~~~A~~Ic~~lgi~-~k~~~~Ls~~el~~L~~~l~--------- 106 (169)
.++|||| +||+|||||++|+|.+||++|||||+++|.+||+++||| +.++++||++|+++|.++|+
T Consensus 3 ~~~~~~m----~rI~~~~i~~~k~i~~aLt~IyGIG~~~a~~Ic~~lgi~~~~~~~~Lt~~qi~~l~~~i~~~~~~~iP~ 78 (149)
T PRK04053 3 EEEFKYI----VRIAGTDLDGTKPVEYALTGIKGIGRRTARAIARKLGLDPNAKLGYLSDEEIEKIEEALEDPAEEGIPS 78 (149)
T ss_pred hhhhhhh----HhhcCccCCCCCEEeeeccccccccHHHHHHHHHHcCcCCCCccCcCCHHHHHHHHHHHHhhccccCch
Confidence 4579998 999999999999999999999999999999999999999 67899999999999999996
Q ss_pred --------------hcccchHHHHHHHHHHHHHHhhhhcccCccCCCCccCCccCccccccCCCceeeecccc
Q 030930 107 --------------KYMIEGDLRRFNALAIRRLKEIQCYRGIRHIQGLPCRGQHTKNNCRTLKGKRVAIAGKK 165 (169)
Q Consensus 107 --------------~~~Ie~dLr~~~~~nI~rL~~I~sYRG~RH~~GLPVRGQRTrTNarT~Kg~~~gV~~kK 165 (169)
+|+||+||++.+++||+||++|+||||+||.+||||||||||||||| |+++||++||
T Consensus 79 w~~Nr~~d~~tg~~~~~ie~dLr~~~~~~I~rl~~I~syRG~RH~~GLPVRGQRTrTNaRt--g~~~gv~~kk 149 (149)
T PRK04053 79 WMLNRRKDYETGEDLHLIGSDLILTVREDINRMKKIRSYRGIRHELGLKVRGQRTRSTGRT--GGTVGVSRKK 149 (149)
T ss_pred hhhccccccccCccceEehHHHHHHHHHHHHHHHHhcceeeecccCCCCCCCCcCCCCCcC--CCccccccCC
Confidence 36799999999999999999999999999999999999999999998 9999999987
No 7
>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=100.00 E-value=5.7e-46 Score=282.99 Aligned_cols=110 Identities=59% Similarity=0.987 Sum_probs=105.8
Q ss_pred EEeCccCCCCeEEeEeeccccccCHHHHHHHHHHcCCC-ccccCCCCHHHHHHHHHHHh-hcccchHHHHHHHHHHHHHH
Q 030930 49 RVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKME-NKITKDMSEEELITIRDEVS-KYMIEGDLRRFNALAIRRLK 126 (169)
Q Consensus 49 rI~~tni~~~K~i~~ALt~I~GIG~~~A~~Ic~~lgi~-~k~~~~Ls~~el~~L~~~l~-~~~Ie~dLr~~~~~nI~rL~ 126 (169)
||+|||||++|+|.+||++|||||.++|.+||+++||| +.++++|+++|++.|.++|+ +|.+|+||++.+++||+||+
T Consensus 1 ri~~~~l~~~k~v~~aL~~i~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi~~l~~~l~~~~~i~~~L~~~~~~dI~rl~ 80 (113)
T TIGR03631 1 RIAGVDIPNNKRVEIALTYIYGIGRTRARKILEKAGIDPDKRVKDLTEEELNAIREEIEAKYKVEGDLRREVSLNIKRLM 80 (113)
T ss_pred CcCCccCCCCCEEeeeeeeeecccHHHHHHHHHHhCcCcccccccCCHHHHHHHHHHHHhcCcchHHHHHHHHHHHHHHH
Confidence 68999999999999999999999999999999999999 67789999999999999996 69999999999999999999
Q ss_pred hhhhcccCccCCCCccCCccCccccccCCCce
Q 030930 127 EIQCYRGIRHIQGLPCRGQHTKNNCRTLKGKR 158 (169)
Q Consensus 127 ~I~sYRG~RH~~GLPVRGQRTrTNarT~Kg~~ 158 (169)
+|+||||+||.+|||||||||||||||+|+..
T Consensus 81 ~I~syRG~RH~~gLpVRGQRT~TNart~k~~~ 112 (113)
T TIGR03631 81 DIGCYRGLRHRRGLPVRGQRTKTNARTRKGPR 112 (113)
T ss_pred HhcceeccccccCCCCCCCcCCccccccCCCC
Confidence 99999999999999999999999999988753
No 8
>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=100.00 E-value=3.3e-45 Score=275.05 Aligned_cols=105 Identities=47% Similarity=0.729 Sum_probs=100.7
Q ss_pred EEeCccCCCCeEEeEeeccccccCHHHHHHHHHHcCCC-ccccCCCCHHHHHHHHHHHhh-cccchHHHHHHHHHHHHHH
Q 030930 49 RVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKME-NKITKDMSEEELITIRDEVSK-YMIEGDLRRFNALAIRRLK 126 (169)
Q Consensus 49 rI~~tni~~~K~i~~ALt~I~GIG~~~A~~Ic~~lgi~-~k~~~~Ls~~el~~L~~~l~~-~~Ie~dLr~~~~~nI~rL~ 126 (169)
||+|||||++|+|.+||++|||||+++|.+||+++||| +.++++|+++|+++|.++|++ |.+++||++++++||++|+
T Consensus 1 rI~~~~l~~~k~i~~aLt~IyGIG~~~A~~Ic~~lgi~~~~~~~~Ls~~~i~~l~~~i~~~~~i~~~L~~~~~~~i~rl~ 80 (107)
T PF00416_consen 1 RILGTNLPGNKPIYIALTKIYGIGRRKAKQICKKLGINPNKKVGDLSDEQIDKLRKIIEKNHLIENDLKRQVRENIKRLK 80 (107)
T ss_dssp ETTTTCE-TSSBHHHHHTTSTTBCHHHHHHHHHHTTS-SSSBTTTSTHHHHHHHHHHHHTHSTCHHHHHHHHHHHHHHHH
T ss_pred CcCCCcCCCCcchHhHHhhhhccCHHHHHHHHHHcCCChhhhcccCCHHHHHHHHHHHHHhccccchHHHHHHHHHHHHH
Confidence 78999999999999999999999999999999999999 578899999999999999997 9999999999999999999
Q ss_pred hhhhcccCccCCCCccCCccCcccccc
Q 030930 127 EIQCYRGIRHIQGLPCRGQHTKNNCRT 153 (169)
Q Consensus 127 ~I~sYRG~RH~~GLPVRGQRTrTNarT 153 (169)
+|+||||+||.+|||||||||||||||
T Consensus 81 ~i~syRG~RH~~gLpvRGQRT~tNarT 107 (107)
T PF00416_consen 81 KIKSYRGIRHRKGLPVRGQRTKTNART 107 (107)
T ss_dssp HHTTHHHHHHHHTSBSSSSTSSSSSHH
T ss_pred HHHHhhcchhhCCCCCCCCCCCCCCCC
Confidence 999999999999999999999999997
No 9
>KOG3311 consensus Ribosomal protein S18 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.4e-38 Score=249.50 Aligned_cols=128 Identities=30% Similarity=0.591 Sum_probs=116.1
Q ss_pred cccccCCCCCCCCcccceeEEeCccCCCCeEEeEeeccccccCHHHHHHHHHHcCCC-ccccCCCCHHHHHHHHHHHhh-
Q 030930 30 LSFPVSKQPQYPGLSIQCARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKME-NKITKDMSEEELITIRDEVSK- 107 (169)
Q Consensus 30 ~~~~~~~~~~f~~i~~~~vrI~~tni~~~K~i~~ALt~I~GIG~~~A~~Ic~~lgi~-~k~~~~Ls~~el~~L~~~l~~- 107 (169)
||+.. +++|||| +||+|+++|++++|.|||++|||||+.+|+.+|+++|+| .+++|+|+++|++.+.+++++
T Consensus 1 msl~~--~~~~q~i----~~il~~~~dg~~~V~fAl~~i~Gig~~~A~~ic~K~~~~~~~r~gelt~~qi~~i~~i~~d~ 74 (152)
T KOG3311|consen 1 MSLVI--PEAFQHI----LRILNTNVDGKRKVTFALTSIKGIGRRYAEIVCKKADLDLTKRAGELTEEQILRILQILNDP 74 (152)
T ss_pred Cceec--chhHHHH----HHHHccCCCCCceeEEEEEEEeeechhhhhhhhhhcCcchhhhhccccHHHHHHHHHHhcCH
Confidence 34443 4569999 999999999999999999999999999999999999999 888999999999999999874
Q ss_pred --c--------------------ccchHHHHHHHHHHHHHHhhhhcccCccCCCCccCCccCccccccCCCceeeecccc
Q 030930 108 --Y--------------------MIEGDLRRFNALAIRRLKEIQCYRGIRHIQGLPCRGQHTKNNCRTLKGKRVAIAGKK 165 (169)
Q Consensus 108 --~--------------------~Ie~dLr~~~~~nI~rL~~I~sYRG~RH~~GLPVRGQRTrTNarT~Kg~~~gV~~kK 165 (169)
| ++.+.+....++||+||++|.||||+||.+|||||||||+|||+ ||++|||++||
T Consensus 75 ~~~~~~~~~l~rq~~~~dG~~~~l~~~~ld~r~r~~ieRlkki~~~RG~rh~~gl~vRGQ~Tkt~~~--~gk~v~Vs~Kk 152 (152)
T KOG3311|consen 75 RQYKIPDWFLNRQKDIIDGKVNHLLGNGLDTRLRADIERLKKIRCHRGLRHFWGLRVRGQRTKTNGR--RGKTVGVSGKK 152 (152)
T ss_pred HHhcCchHHHHhhcccccCccccccchhhhhHHHHHHHHHhhhcccccceeccCCcccCcccccccc--ccceeeecccC
Confidence 2 23456777889999999999999999999999999999999995 69999999987
No 10
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=94.34 E-value=0.047 Score=46.89 Aligned_cols=52 Identities=19% Similarity=0.261 Sum_probs=45.2
Q ss_pred CCCeEEeEee---ccccccCHHHHHHHHHHcCCCcc-ccCCCCHHHHHHHHHHHhh
Q 030930 56 PNNKRIEYSL---QYIHGVGRTRARQILVDLKMENK-ITKDMSEEELITIRDEVSK 107 (169)
Q Consensus 56 ~~~K~i~~AL---t~I~GIG~~~A~~Ic~~lgi~~k-~~~~Ls~~el~~L~~~l~~ 107 (169)
..++.|.-+| +-+-|||.-+|..||-++||+|. .+++||++|++.|.+.+.+
T Consensus 153 ~~~~~Ik~~LLDQ~~iaGiGNiya~EiLf~a~I~P~~~~~~Ls~~~~~~L~~~~~~ 208 (274)
T PRK01103 153 KKKTAIKPALLDQTVVVGVGNIYADEALFRAGIHPERPAGSLSRAEAERLVDAIKA 208 (274)
T ss_pred cCCccHHHHhhcCCeEecccHhHHHHHHHHcCCCccCccccCCHHHHHHHHHHHHH
Confidence 3567888899 88999999999999999999965 4699999999999877644
No 11
>PF06831 H2TH: Formamidopyrimidine-DNA glycosylase H2TH domain; InterPro: IPR015886 This entry represents a helix-2turn-helix DNA-binding domain found in DNA glycosylase/AP lyase enzymes, which are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Most damage to bases in DNA is repaired by the base excision repair pathway []. These enzymes are primarily from bacteria, and have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC). Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines [, ]. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above (3.2.2 from EC, 4.2.99.18 from EC), but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine []. These protein contains three structural domains: an N-terminal catalytic core domain, a central helix-two turn-helix (H2TH) module and a C-terminal zinc finger []. The N-terminal catalytic domain and the C-terminal zinc finger straddle the DNA with the long axis of the protein oriented roughly orthogonal to the helical axis of the DNA. Residues that contact DNA are located in the catalytic domain and in a beta-hairpin loop formed by the zinc finger []. This entry represents the central domain containing the DNA-binding helix-two turn-helix domain [].; GO: 0003684 damaged DNA binding, 0003906 DNA-(apurinic or apyrimidinic site) lyase activity, 0008270 zinc ion binding, 0016799 hydrolase activity, hydrolyzing N-glycosyl compounds, 0006289 nucleotide-excision repair; PDB: 3GQ3_A 3JR5_A 3SAT_A 3GPX_A 2F5Q_A 3SBJ_A 3U6S_A 3SAU_A 3SAR_A 2F5P_A ....
Probab=94.24 E-value=0.059 Score=39.40 Aligned_cols=50 Identities=26% Similarity=0.433 Sum_probs=39.1
Q ss_pred CCeEEeEee---ccccccCHHHHHHHHHHcCCCccc-cCCCCHHHHHHHHHHHh
Q 030930 57 NNKRIEYSL---QYIHGVGRTRARQILVDLKMENKI-TKDMSEEELITIRDEVS 106 (169)
Q Consensus 57 ~~K~i~~AL---t~I~GIG~~~A~~Ic~~lgi~~k~-~~~Ls~~el~~L~~~l~ 106 (169)
.+++|..+| +-+-|||.-++..||-+++|+|.. +.+|+++|+..|-+.+.
T Consensus 22 ~~~~ik~~LlDQ~~iaGiGNiy~~EiLf~a~i~P~~~~~~L~~~~~~~l~~~~~ 75 (92)
T PF06831_consen 22 RRRPIKAALLDQSVIAGIGNIYADEILFRAGIHPERPASSLSEEELRRLHEAIK 75 (92)
T ss_dssp CCSBHHHHHHCTTTSTT--HHHHHHHHHHTTB-TTSBGGGSHHHHHHHHHHHHH
T ss_pred CcchHHHHHhCCCccccCcHHHHHHHHHHcCCCccCccccCCHHHHHHHHHHHH
Confidence 356666666 678999999999999999999654 69999999999977664
No 12
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=92.13 E-value=0.17 Score=43.56 Aligned_cols=52 Identities=23% Similarity=0.408 Sum_probs=42.5
Q ss_pred CCCeEEeEeecc---ccccCHHHHHHHHHHcCCCcc-ccCCCCHHHHHHHHHHHhh
Q 030930 56 PNNKRIEYSLQY---IHGVGRTRARQILVDLKMENK-ITKDMSEEELITIRDEVSK 107 (169)
Q Consensus 56 ~~~K~i~~ALt~---I~GIG~~~A~~Ic~~lgi~~k-~~~~Ls~~el~~L~~~l~~ 107 (169)
..+.+|..+|-. |-|||.-+|..||-++||++. .+++||++|++.|.+.+..
T Consensus 152 ~~~~~ik~~Lldq~viaGiGNiya~EiLf~a~i~P~~~~~~l~~~~~~~l~~a~~~ 207 (272)
T PRK14810 152 GRKTRIKSALLNQTLLRGVGNIYADEALFRAGIRPQRLASSLSRERLRKLHDAIGE 207 (272)
T ss_pred cCCccHHHHhhcCceeccccHhHHHHHHHHcCCCCCCCcccCCHHHHHHHHHHHHH
Confidence 345667777744 499999999999999999955 5799999999999876643
No 13
>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=92.10 E-value=0.096 Score=31.21 Aligned_cols=18 Identities=33% Similarity=0.512 Sum_probs=15.2
Q ss_pred eeccccccCHHHHHHHHH
Q 030930 64 SLQYIHGVGRTRARQILV 81 (169)
Q Consensus 64 ALt~I~GIG~~~A~~Ic~ 81 (169)
.|.+++|||+.+|..|+.
T Consensus 12 eL~~lpGIG~~tA~~I~~ 29 (30)
T PF00633_consen 12 ELMKLPGIGPKTANAILS 29 (30)
T ss_dssp HHHTSTT-SHHHHHHHHH
T ss_pred HHHhCCCcCHHHHHHHHh
Confidence 578999999999999975
No 14
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=91.42 E-value=0.32 Score=41.84 Aligned_cols=50 Identities=14% Similarity=0.201 Sum_probs=42.5
Q ss_pred CCeEEeEee---ccccccCHHHHHHHHHHcCCCccc-cCCCCHHHHHHHHHHHh
Q 030930 57 NNKRIEYSL---QYIHGVGRTRARQILVDLKMENKI-TKDMSEEELITIRDEVS 106 (169)
Q Consensus 57 ~~K~i~~AL---t~I~GIG~~~A~~Ic~~lgi~~k~-~~~Ls~~el~~L~~~l~ 106 (169)
.+++|.-+| +-|-|||.-+|..||=.++|+|.+ +++||++|++.|-+.+.
T Consensus 142 ~~~~Ik~~LlDQ~~iaGIGNiyadEiLf~A~I~P~~~~~~Ls~~~~~~L~~~i~ 195 (269)
T PRK14811 142 TARPVKPWLLSQKPVAGVGNIYADESLWRARIHPARPATSLKAPEARRLYRAIR 195 (269)
T ss_pred cCCcHHHHHhcCceeecccHHHHHHHHHHcCCCccCCcccCCHHHHHHHHHHHH
Confidence 367787777 568899999999999999999655 69999999999976654
No 15
>PRK10445 endonuclease VIII; Provisional
Probab=91.07 E-value=0.37 Score=41.28 Aligned_cols=50 Identities=20% Similarity=0.338 Sum_probs=40.9
Q ss_pred CeEEeEee---ccccccCHHHHHHHHHHcCCCccc-cCCCCHHHHHHHHHHHhh
Q 030930 58 NKRIEYSL---QYIHGVGRTRARQILVDLKMENKI-TKDMSEEELITIRDEVSK 107 (169)
Q Consensus 58 ~K~i~~AL---t~I~GIG~~~A~~Ic~~lgi~~k~-~~~Ls~~el~~L~~~l~~ 107 (169)
+++|.-+| +-+-|||.-+|..||=.++|+|.+ +++||++|++.|-+.+.+
T Consensus 151 ~~~IK~~LLDQ~~vaGIGNiyadEiLf~A~I~P~~~~~~Ls~~~~~~L~~~i~~ 204 (263)
T PRK10445 151 NRQFSGLLLDQAFLAGLGNYLRVEILWQAGLTPQHKAKDLNEAQLDALAHALLD 204 (263)
T ss_pred cccHHHHHhcCCccccccHHHHHHHHHHcCCCcCCCcccCCHHHHHHHHHHHHH
Confidence 45565555 447799999999999999999665 699999999999776643
No 16
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=90.56 E-value=0.41 Score=41.19 Aligned_cols=51 Identities=18% Similarity=0.393 Sum_probs=41.5
Q ss_pred CCeEEeEee---ccccccCHHHHHHHHHHcCCCccc-cCCCCHHHHHHHHHHHhh
Q 030930 57 NNKRIEYSL---QYIHGVGRTRARQILVDLKMENKI-TKDMSEEELITIRDEVSK 107 (169)
Q Consensus 57 ~~K~i~~AL---t~I~GIG~~~A~~Ic~~lgi~~k~-~~~Ls~~el~~L~~~l~~ 107 (169)
.+.+|.-+| +-|-|||.-+|..||=.++|+|.+ +++||++|++.|-+.+..
T Consensus 154 ~~~~Ik~~LlDQ~vvaGIGNiyadEiLf~a~I~P~~~~~~Ls~~~~~~L~~~i~~ 208 (272)
T TIGR00577 154 SKRKIKTALLDQRLVAGIGNIYADEVLFRAGIHPERLANSLSKEECELLHRAIKE 208 (272)
T ss_pred CCCcHHHHHhcCCeEecccHHHHHHHHHHcCCCcchhhccCCHHHHHHHHHHHHH
Confidence 345566666 557799999999999999999655 699999999999776643
No 17
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=90.43 E-value=0.41 Score=41.38 Aligned_cols=49 Identities=16% Similarity=0.363 Sum_probs=41.2
Q ss_pred CeEEeEee---ccccccCHHHHHHHHHHcCCCccc-cCCCCHHHHHHHHHHHh
Q 030930 58 NKRIEYSL---QYIHGVGRTRARQILVDLKMENKI-TKDMSEEELITIRDEVS 106 (169)
Q Consensus 58 ~K~i~~AL---t~I~GIG~~~A~~Ic~~lgi~~k~-~~~Ls~~el~~L~~~l~ 106 (169)
...|.-+| +-|-|||.-+|..||=.++|+|.+ +++||++|++.|.+.+.
T Consensus 164 ~~~IK~~LLDQ~~vaGIGNiya~EiLf~A~IhP~~~~~~Ls~~~~~~L~~~i~ 216 (282)
T PRK13945 164 TRSIKTALLDQSIVAGIGNIYADESLFKAGIHPTTPAGQLKKKQLERLREAII 216 (282)
T ss_pred CccHHHHhhcCCeEeccchhHHHHHHHHcCCCccCccccCCHHHHHHHHHHHH
Confidence 45666666 568899999999999999999655 69999999999977664
No 18
>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=88.17 E-value=0.3 Score=29.30 Aligned_cols=21 Identities=24% Similarity=0.572 Sum_probs=15.3
Q ss_pred eeccccccCHHHHHHHHHHcCC
Q 030930 64 SLQYIHGVGRTRARQILVDLKM 85 (169)
Q Consensus 64 ALt~I~GIG~~~A~~Ic~~lgi 85 (169)
.+++++|||+.++.+ ++++||
T Consensus 12 pi~~~~GIG~kt~~k-L~~~GI 32 (32)
T PF11798_consen 12 PIRKFWGIGKKTAKK-LNKLGI 32 (32)
T ss_dssp BGGGSTTS-HHHHHH-HHCTT-
T ss_pred CHHhhCCccHHHHHH-HHHccC
Confidence 578999999999988 455553
No 19
>PRK04184 DNA topoisomerase VI subunit B; Validated
Probab=86.49 E-value=1 Score=42.78 Aligned_cols=50 Identities=28% Similarity=0.438 Sum_probs=42.6
Q ss_pred eEEeEee-ccccccCHHHHHHHHHHcCCC-ccccCCCCHHHHHHHHHHHhhc
Q 030930 59 KRIEYSL-QYIHGVGRTRARQILVDLKME-NKITKDMSEEELITIRDEVSKY 108 (169)
Q Consensus 59 K~i~~AL-t~I~GIG~~~A~~Ic~~lgi~-~k~~~~Ls~~el~~L~~~l~~~ 108 (169)
+++.--| ..+-.||..+|..||+.+|++ ++..++|+++|+++|.+.+.++
T Consensus 256 ~~l~~fL~~~f~~v~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~~ 307 (535)
T PRK04184 256 RTLKEFLVEEFSRVGDKTADEILEKAGLDPNKKPKELTREELERLVEAFKKY 307 (535)
T ss_pred CCHHHHHHHhhcccCHHHHHHHHHHcCCCCCCChhhCCHHHHHHHHHHHHhc
Confidence 4444444 678899999999999999999 6678999999999999999875
No 20
>KOG3311 consensus Ribosomal protein S18 [Translation, ribosomal structure and biogenesis]
Probab=85.53 E-value=0.15 Score=41.14 Aligned_cols=46 Identities=17% Similarity=0.123 Sum_probs=39.5
Q ss_pred cchHHHHHHHHHHHHHHhhhhcccCccCCCCccCCccCccccccCCCc
Q 030930 110 IEGDLRRFNALAIRRLKEIQCYRGIRHIQGLPCRGQHTKNNCRTLKGK 157 (169)
Q Consensus 110 Ie~dLr~~~~~nI~rL~~I~sYRG~RH~~GLPVRGQRTrTNarT~Kg~ 157 (169)
+.+|.+.+...|+..+.++.+|.|- ..+||+.||+|+.|+.++|.+
T Consensus 70 i~~d~~~~~~~~~~l~rq~~~~dG~--~~~l~~~~ld~r~r~~ieRlk 115 (152)
T KOG3311|consen 70 ILNDPRQYKIPDWFLNRQKDIIDGK--VNHLLGNGLDTRLRADIERLK 115 (152)
T ss_pred HhcCHHHhcCchHHHHhhcccccCc--cccccchhhhhHHHHHHHHHh
Confidence 4567777778889999999999999 999999999999999886643
No 21
>PF05833 FbpA: Fibronectin-binding protein A N-terminus (FbpA); InterPro: IPR008616 This family consists of the N-terminal region of the prokaryotic fibronectin-binding protein, the C-terminal region is IPR008532 from INTERPRO. Fibronectin binding is considered to be an important virulence factor in streptococcal infections. Fibronectin is a dimeric glycoprotein that is present in a soluble form in plasma and extracellular fluids; it is also present in a fibrillar form on cell surfaces. Both the soluble and cellular forms of fibronectin may be incorporated into the extracellular tissue matrix. While fibronectin has critical roles in eukaryotic cellular processes, such as adhesion, migration and differentiation, it is also a substrate for the attachment of bacteria. The binding of pathogenic Streptococcus pyogenes and Staphylococcus aureus to epithelial cells via fibronectin facilitates their internalisation and systemic spread within the host [].; PDB: 3DOA_A 2ZBK_F 2HKJ_A 1Z5B_A 1Z5C_B 1MX0_F 1Z5A_A 1MU5_A 1Z59_A.
Probab=84.93 E-value=0.23 Score=44.78 Aligned_cols=51 Identities=24% Similarity=0.382 Sum_probs=36.5
Q ss_pred CCeEEeEeecccc-ccCHHHHHHHHHHcCCC-ccccCCCCHHHHHHHHHHHhh
Q 030930 57 NNKRIEYSLQYIH-GVGRTRARQILVDLKME-NKITKDMSEEELITIRDEVSK 107 (169)
Q Consensus 57 ~~K~i~~ALt~I~-GIG~~~A~~Ic~~lgi~-~k~~~~Ls~~el~~L~~~l~~ 107 (169)
+...+..+|...+ |+|..+|..+|.++|+| +..+.++++++++.|.+.+.+
T Consensus 185 ~~~~l~~~L~~~~~G~~~~la~ei~~ra~i~~~~~~~~~~~~~~~~l~~~~~~ 237 (455)
T PF05833_consen 185 KEKTLVKALSKNFQGFGPELAEEILYRAGIDKNKKVEELSDEEIEKLFEAIRE 237 (455)
T ss_dssp CG-BHHHHHHHHCTT--HHHHHHHHCCCTS-TTSBGGG--HHHHCHHHHHHHH
T ss_pred CcccHHHHHHHHHHHhHHHHHHHHHHHhCCCCccccccchhhhHHHHHHHHHH
Confidence 4566777786666 99999999999999999 666899999998888666543
No 22
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=84.50 E-value=0.97 Score=35.81 Aligned_cols=61 Identities=15% Similarity=0.163 Sum_probs=47.7
Q ss_pred eCccCCCCeEEeEeeccccccCHHHHHHHHHHcCCCc----cccCCCCHHHHHHHHHHHhhcccc
Q 030930 51 GGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKMEN----KITKDMSEEELITIRDEVSKYMIE 111 (169)
Q Consensus 51 ~~tni~~~K~i~~ALt~I~GIG~~~A~~Ic~~lgi~~----k~~~~Ls~~el~~L~~~l~~~~Ie 111 (169)
.+.-||-|..=..+|+..+|||+..|..|++.-.+.+ ..+..+++.|.+.|.++.++|.+.
T Consensus 49 ~~~kIdiN~A~~~el~~lpGigP~~A~~IV~nGpf~sveDL~~V~GIgekqk~~l~k~~~~ftV~ 113 (132)
T PRK02515 49 FGEKIDLNNSSVRAFRQFPGMYPTLAGKIVKNAPYDSVEDVLNLPGLSERQKELLEANLDNFTVT 113 (132)
T ss_pred cCCcccCCccCHHHHHHCCCCCHHHHHHHHHCCCCCCHHHHHcCCCCCHHHHHHHHHhhcceeeC
Confidence 3556666666677899999999999999997555552 236889999999999999887653
No 23
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=83.57 E-value=1 Score=35.79 Aligned_cols=43 Identities=19% Similarity=0.254 Sum_probs=37.5
Q ss_pred EeeccccccCHHHHHHHHHHcCCC-ccccCCCCHHHHHHHHHHHh
Q 030930 63 YSLQYIHGVGRTRARQILVDLKME-NKITKDMSEEELITIRDEVS 106 (169)
Q Consensus 63 ~ALt~I~GIG~~~A~~Ic~~lgi~-~k~~~~Ls~~el~~L~~~l~ 106 (169)
--||.|.|||..... ++.-+||. ...+-.+|..|+..+.++|+
T Consensus 67 DDLt~I~GIGPk~e~-~Ln~~GI~tfaQIAAwt~~di~~id~~l~ 110 (133)
T COG3743 67 DDLTRISGIGPKLEK-VLNELGIFTFAQIAAWTRADIAWIDDYLN 110 (133)
T ss_pred ccchhhcccCHHHHH-HHHHcCCccHHHHHhcCHHHHHHHHhhcC
Confidence 469999999998765 67889999 77888999999999999885
No 24
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=81.65 E-value=1.1 Score=25.22 Aligned_cols=19 Identities=32% Similarity=0.490 Sum_probs=16.4
Q ss_pred eeccccccCHHHHHHHHHH
Q 030930 64 SLQYIHGVGRTRARQILVD 82 (169)
Q Consensus 64 ALt~I~GIG~~~A~~Ic~~ 82 (169)
.|..|+|||...|..|+..
T Consensus 2 ~L~~i~GiG~k~A~~il~~ 20 (26)
T smart00278 2 ELLKVPGIGPKTAEKILEA 20 (26)
T ss_pred hhhhCCCCCHHHHHHHHHh
Confidence 3678999999999999863
No 25
>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=81.27 E-value=0.35 Score=32.15 Aligned_cols=37 Identities=24% Similarity=0.299 Sum_probs=25.2
Q ss_pred eEeeccccccCHHHHHHHHHHcCCCc-cccCCCCHHHHH
Q 030930 62 EYSLQYIHGVGRTRARQILVDLKMEN-KITKDMSEEELI 99 (169)
Q Consensus 62 ~~ALt~I~GIG~~~A~~Ic~~lgi~~-k~~~~Ls~~el~ 99 (169)
+.+|.+|+|||...|..+.+. |+.+ .-+-..+.+++.
T Consensus 4 ~~~L~~I~Gig~~~a~~L~~~-G~~t~~~l~~a~~~~L~ 41 (60)
T PF14520_consen 4 FDDLLSIPGIGPKRAEKLYEA-GIKTLEDLANADPEELA 41 (60)
T ss_dssp HHHHHTSTTCHHHHHHHHHHT-TCSSHHHHHTSHHHHHH
T ss_pred HHhhccCCCCCHHHHHHHHhc-CCCcHHHHHcCCHHHHh
Confidence 456889999999999998877 7763 223333444433
No 26
>PF13035 DUF3896: Protein of unknown function (DUF3896)
Probab=80.64 E-value=3.7 Score=28.15 Aligned_cols=42 Identities=33% Similarity=0.484 Sum_probs=29.8
Q ss_pred HHHHHHcCCCccccCCCCHHHHHHHHHHHhhcccchHHHHHHHHHHHHHHhhhhc-ccC
Q 030930 77 RQILVDLKMENKITKDMSEEELITIRDEVSKYMIEGDLRRFNALAIRRLKEIQCY-RGI 134 (169)
Q Consensus 77 ~~Ic~~lgi~~k~~~~Ls~~el~~L~~~l~~~~Ie~dLr~~~~~nI~rL~~I~sY-RG~ 134 (169)
.++|++|. --.|+++|-++|.-+|++| +-|-.|++++.| ||+
T Consensus 19 q~lc~kls-----~~~ls~~er~qi~~eidny-----------eyilnlvemnhyergf 61 (61)
T PF13035_consen 19 QQLCKKLS-----SMHLSEKEREQIKLEIDNY-----------EYILNLVEMNHYERGF 61 (61)
T ss_pred HHHHHHHh-----hcccCHHHHHHHHhhhhhH-----------HHHHHHHHHhcccccC
Confidence 45676654 3568888888888888775 445568888888 664
No 27
>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=79.92 E-value=1.2 Score=29.67 Aligned_cols=22 Identities=27% Similarity=0.324 Sum_probs=15.8
Q ss_pred eeccccccCHHHHHHHHHHcCCC
Q 030930 64 SLQYIHGVGRTRARQILVDLKME 86 (169)
Q Consensus 64 ALt~I~GIG~~~A~~Ic~~lgi~ 86 (169)
.++.|+|||..+|..... .|+-
T Consensus 3 ~f~~I~GVG~~tA~~w~~-~G~r 24 (52)
T PF10391_consen 3 LFTGIWGVGPKTARKWYA-KGIR 24 (52)
T ss_dssp HHHTSTT--HHHHHHHHH-TT--
T ss_pred chhhcccccHHHHHHHHH-hCCC
Confidence 368999999999999987 7765
No 28
>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=79.50 E-value=2.1 Score=30.67 Aligned_cols=27 Identities=30% Similarity=0.477 Sum_probs=21.5
Q ss_pred CeEEeEeeccccccCHHHHHHHHHHcC
Q 030930 58 NKRIEYSLQYIHGVGRTRARQILVDLK 84 (169)
Q Consensus 58 ~K~i~~ALt~I~GIG~~~A~~Ic~~lg 84 (169)
+..|.++|+.|+|||...|..|++.-.
T Consensus 22 ~~~Ir~gl~~Ikglg~~~a~~I~~~R~ 48 (90)
T PF14579_consen 22 NNAIRLGLSAIKGLGEEVAEKIVEERE 48 (90)
T ss_dssp -TEEE-BGGGSTTS-HHHHHHHHHHHH
T ss_pred CCEEeehHhhcCCCCHHHHHHHHHhHh
Confidence 468999999999999999999997653
No 29
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=79.20 E-value=1.1 Score=36.98 Aligned_cols=20 Identities=25% Similarity=0.589 Sum_probs=15.1
Q ss_pred eeccccccCHHHHHHHHHHc
Q 030930 64 SLQYIHGVGRTRARQILVDL 83 (169)
Q Consensus 64 ALt~I~GIG~~~A~~Ic~~l 83 (169)
+|++++|||+++|.+|+-.|
T Consensus 109 ~L~~vpGIGkKtAerIilEL 128 (188)
T PRK14606 109 GLSKLPGISKKTAERIVMEL 128 (188)
T ss_pred HHhhCCCCCHHHHHHHHHHH
Confidence 57788888888888888443
No 30
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=77.32 E-value=1.3 Score=36.43 Aligned_cols=19 Identities=26% Similarity=0.630 Sum_probs=13.1
Q ss_pred eeccccccCHHHHHHHHHH
Q 030930 64 SLQYIHGVGRTRARQILVD 82 (169)
Q Consensus 64 ALt~I~GIG~~~A~~Ic~~ 82 (169)
+|++++|||+++|.+|+-.
T Consensus 109 ~L~~vpGIGkKtAeRIilE 127 (183)
T PRK14601 109 VLKKVPGIGPKSAKRIIAE 127 (183)
T ss_pred HHhhCCCCCHHHHHHHHHH
Confidence 5677777777777777733
No 31
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=76.70 E-value=1.4 Score=36.50 Aligned_cols=21 Identities=29% Similarity=0.621 Sum_probs=16.3
Q ss_pred EeeccccccCHHHHHHHHHHc
Q 030930 63 YSLQYIHGVGRTRARQILVDL 83 (169)
Q Consensus 63 ~ALt~I~GIG~~~A~~Ic~~l 83 (169)
.+|++++|||+++|.+|+-.|
T Consensus 108 ~~L~kvpGIGkKtAerIilEL 128 (195)
T PRK14604 108 ARLARVPGIGKKTAERIVLEL 128 (195)
T ss_pred HHHhhCCCCCHHHHHHHHHHH
Confidence 368888888888888888443
No 32
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=76.50 E-value=1.6 Score=36.67 Aligned_cols=22 Identities=36% Similarity=0.677 Sum_probs=18.0
Q ss_pred EeeccccccCHHHHHHHHHHcC
Q 030930 63 YSLQYIHGVGRTRARQILVDLK 84 (169)
Q Consensus 63 ~ALt~I~GIG~~~A~~Ic~~lg 84 (169)
-+|++++|||+++|.+||-.|-
T Consensus 108 ~~L~k~PGIGkKtAerivleLk 129 (201)
T COG0632 108 KALSKIPGIGKKTAERIVLELK 129 (201)
T ss_pred HhhhcCCCCCHHHHHHHHHHHh
Confidence 4789999999999999985543
No 33
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=76.48 E-value=1.4 Score=36.45 Aligned_cols=19 Identities=32% Similarity=0.489 Sum_probs=15.4
Q ss_pred eeccccccCHHHHHHHHHH
Q 030930 64 SLQYIHGVGRTRARQILVD 82 (169)
Q Consensus 64 ALt~I~GIG~~~A~~Ic~~ 82 (169)
+|++++|||+++|.+|+-.
T Consensus 108 ~L~kvpGIGkKtAerIilE 126 (197)
T PRK14603 108 LLTSASGVGKKLAERIALE 126 (197)
T ss_pred HHhhCCCCCHHHHHHHHHH
Confidence 6888888888888888843
No 34
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=76.47 E-value=4.1 Score=35.74 Aligned_cols=53 Identities=23% Similarity=0.388 Sum_probs=42.8
Q ss_pred CCCCeEEeEee---ccccccCHHHHHHHHHHcCCCccc-cCCCCHHHHHHHHHHHhh
Q 030930 55 IPNNKRIEYSL---QYIHGVGRTRARQILVDLKMENKI-TKDMSEEELITIRDEVSK 107 (169)
Q Consensus 55 i~~~K~i~~AL---t~I~GIG~~~A~~Ic~~lgi~~k~-~~~Ls~~el~~L~~~l~~ 107 (169)
...+++|.-+| +-|=|||..+|..+|=++||+|.+ +++|+++|++.|.+.+..
T Consensus 152 ~~~~~~IK~~LLDQ~vvaGvGNIYa~E~Lf~agI~P~~~a~~l~~~~~~~l~~~i~~ 208 (273)
T COG0266 152 AKKKRRIKTALLDQKVVAGVGNIYADEILFRAGIHPARPAGDLSLAQLALLHEAIKD 208 (273)
T ss_pred hcCccchHHHhhcCCceecccHHHHHHHHHHcCCCcccCccccCHHHHHHHHHHHHH
Confidence 34455576666 567899999999999999999655 699999998888777643
No 35
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=75.88 E-value=1.5 Score=36.38 Aligned_cols=18 Identities=28% Similarity=0.704 Sum_probs=14.4
Q ss_pred eeccccccCHHHHHHHHH
Q 030930 64 SLQYIHGVGRTRARQILV 81 (169)
Q Consensus 64 ALt~I~GIG~~~A~~Ic~ 81 (169)
+|++++|||+++|.+|+-
T Consensus 110 ~L~~ipGIGkKtAerIil 127 (203)
T PRK14602 110 ALTRVSGIGKKTAQHIFL 127 (203)
T ss_pred HHhcCCCcCHHHHHHHHH
Confidence 678888888888888873
No 36
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=75.06 E-value=1.6 Score=36.41 Aligned_cols=19 Identities=21% Similarity=0.504 Sum_probs=13.8
Q ss_pred eeccccccCHHHHHHHHHH
Q 030930 64 SLQYIHGVGRTRARQILVD 82 (169)
Q Consensus 64 ALt~I~GIG~~~A~~Ic~~ 82 (169)
+|++++|||+++|.+|+-.
T Consensus 108 ~L~~vpGIGkKtAeRIIlE 126 (196)
T PRK13901 108 LISKVKGIGNKMAGKIFLK 126 (196)
T ss_pred HHhhCCCCCHHHHHHHHHH
Confidence 5777777777777777743
No 37
>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=74.82 E-value=2.6 Score=31.41 Aligned_cols=37 Identities=24% Similarity=0.250 Sum_probs=27.0
Q ss_pred EeeccccccCHHHHHHHHHHcCCC-ccccCCCCHHHHHH
Q 030930 63 YSLQYIHGVGRTRARQILVDLKME-NKITKDMSEEELIT 100 (169)
Q Consensus 63 ~ALt~I~GIG~~~A~~Ic~~lgi~-~k~~~~Ls~~el~~ 100 (169)
..|+.|+|||+.+|.-+. .+||+ ..-...-+.+++..
T Consensus 12 ~~L~~iP~IG~a~a~DL~-~LGi~s~~~L~g~dP~~Ly~ 49 (93)
T PF11731_consen 12 SDLTDIPNIGKATAEDLR-LLGIRSPADLKGRDPEELYE 49 (93)
T ss_pred HHHhcCCCccHHHHHHHH-HcCCCCHHHHhCCCHHHHHH
Confidence 458999999999999887 99999 44443334555443
No 38
>TIGR00275 flavoprotein, HI0933 family. The model when searched with a partial length search brings in proteins with a dinucleotide-binding motif (Rossman fold) over the initial 40 residues of the model, including oxidoreductases and dehydrogenases. Partially characterized members include an FAD-binding protein from Bacillus cereus and flavoprotein HI0933 from Haemophilus influenzae.
Probab=74.68 E-value=3.7 Score=36.63 Aligned_cols=39 Identities=13% Similarity=0.252 Sum_probs=35.0
Q ss_pred cCHHHHHHHHHHcCCC-ccccCCCCHHHHHHHHHHHhhcc
Q 030930 71 VGRTRARQILVDLKME-NKITKDMSEEELITIRDEVSKYM 109 (169)
Q Consensus 71 IG~~~A~~Ic~~lgi~-~k~~~~Ls~~el~~L~~~l~~~~ 109 (169)
+-.+++..+++.+||+ ++.+.+|+++|++.|.+.+.+|.
T Consensus 294 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~lk~~~ 333 (400)
T TIGR00275 294 LPKRLAELLLEQLGIDPDLPAAQLSKKEIKKLVQLLKNWP 333 (400)
T ss_pred hhHHHHHHHHHHcCCCCCCChHHCCHHHHHHHHHHHhCCE
Confidence 6788999999999999 66789999999999999998764
No 39
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=74.33 E-value=0.77 Score=31.22 Aligned_cols=33 Identities=27% Similarity=0.276 Sum_probs=19.8
Q ss_pred cccccCHHHHHHHHHHcCCCccccCCCCHHHHHH
Q 030930 67 YIHGVGRTRARQILVDLKMENKITKDMSEEELIT 100 (169)
Q Consensus 67 ~I~GIG~~~A~~Ic~~lgi~~k~~~~Ls~~el~~ 100 (169)
.|+|||...|+.+++.+| +-.....-+.+|+..
T Consensus 7 GI~~VG~~~ak~L~~~f~-sl~~l~~a~~e~L~~ 39 (64)
T PF12826_consen 7 GIPGVGEKTAKLLAKHFG-SLEALMNASVEELSA 39 (64)
T ss_dssp TSTT--HHHHHHHHHCCS-CHHHHCC--HHHHCT
T ss_pred CCCCccHHHHHHHHHHcC-CHHHHHHcCHHHHhc
Confidence 699999999999999998 412223334444443
No 40
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=73.34 E-value=5 Score=33.82 Aligned_cols=72 Identities=21% Similarity=0.340 Sum_probs=50.3
Q ss_pred EeEeeccccccCHHHHHHHHHHcCCCccccCCCCHHHHHHHHHHHhh-------------cc------cchHHHH-----
Q 030930 61 IEYSLQYIHGVGRTRARQILVDLKMENKITKDMSEEELITIRDEVSK-------------YM------IEGDLRR----- 116 (169)
Q Consensus 61 i~~ALt~I~GIG~~~A~~Ic~~lgi~~k~~~~Ls~~el~~L~~~l~~-------------~~------Ie~dLr~----- 116 (169)
+..+|.+.+|||.+.|.++.--+- +.++++++.|.+.|.+ +. |=.|=+|
T Consensus 10 LI~~l~kLPGvG~KsA~R~AfhLL-------~~~~~~~~~la~al~~a~~~i~~C~~C~~~te~d~C~ICsd~~Rd~~~i 82 (198)
T COG0353 10 LIDALKKLPGVGPKSAQRLAFHLL-------QRDREDVERLAKALLEAKENIKHCSVCGNLTESDPCDICSDESRDKSQL 82 (198)
T ss_pred HHHHHhhCCCCChhHHHHHHHHHH-------ccCHHHHHHHHHHHHHHHhcCccccccCCcCCCCcCcCcCCcccCCceE
Confidence 456899999999999999875543 4567788888776643 10 1011111
Q ss_pred ---HHHHHHHHHHhhhhcccCccCCC
Q 030930 117 ---FNALAIRRLKEIQCYRGIRHIQG 139 (169)
Q Consensus 117 ---~~~~nI~rL~~I~sYRG~RH~~G 139 (169)
.--.|+..+-+.+.|+|.=|.+|
T Consensus 83 cVVe~p~Dv~a~E~~~~f~G~YhVL~ 108 (198)
T COG0353 83 CVVEEPKDVLALEKTGEFRGLYHVLG 108 (198)
T ss_pred EEEcchHHHHHHHHhcccCeeEEEec
Confidence 12468888999999999999877
No 41
>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=72.05 E-value=1 Score=37.14 Aligned_cols=29 Identities=28% Similarity=0.492 Sum_probs=24.3
Q ss_pred CCCeEEeEeeccccccCHHHHHHHHHHcC
Q 030930 56 PNNKRIEYSLQYIHGVGRTRARQILVDLK 84 (169)
Q Consensus 56 ~~~K~i~~ALt~I~GIG~~~A~~Ic~~lg 84 (169)
|+...++..|.+++|||+.+|+.++.-||
T Consensus 108 p~t~~lre~Ll~LpGVG~KTAnvVL~~l~ 136 (177)
T TIGR03252 108 PDGKELLRRLKALPGFGKQKAKIFLALLG 136 (177)
T ss_pred CCcHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence 56666677899999999999999997665
No 42
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=71.94 E-value=5.9 Score=33.17 Aligned_cols=72 Identities=21% Similarity=0.369 Sum_probs=47.5
Q ss_pred EeEeeccccccCHHHHHHHHHHcCCCccccCCCCHHHHHHHHHHHhhc------------ccc-------hHHHH-----
Q 030930 61 IEYSLQYIHGVGRTRARQILVDLKMENKITKDMSEEELITIRDEVSKY------------MIE-------GDLRR----- 116 (169)
Q Consensus 61 i~~ALt~I~GIG~~~A~~Ic~~lgi~~k~~~~Ls~~el~~L~~~l~~~------------~Ie-------~dLr~----- 116 (169)
+..+|.+++|||+++|.++.-.+= +..++++..|.+.|.+. .-+ .|-.|
T Consensus 9 Li~~l~~LPGIG~KsA~RlA~~ll-------~~~~~~~~~la~ai~~~~~~i~~C~~C~~lse~~~C~IC~d~~Rd~~~i 81 (195)
T TIGR00615 9 LIESLKKLPGIGPKSAQRLAFHLL-------KRDPSEVLRLAQALLEAKENLRTCSVCGAISDQEVCNICSDERRDNSVI 81 (195)
T ss_pred HHHHHHHCCCCCHHHHHHHHHHHH-------cCCHHHHHHHHHHHHHHHHcCCcCCCCCCCCCCCcCCCCCCCCCCCCEE
Confidence 445789999999999999864432 33556666666665431 111 11111
Q ss_pred ---HHHHHHHHHHhhhhcccCccCCC
Q 030930 117 ---FNALAIRRLKEIQCYRGIRHIQG 139 (169)
Q Consensus 117 ---~~~~nI~rL~~I~sYRG~RH~~G 139 (169)
..-.|+.-+-+.+.|+|.=|-+|
T Consensus 82 CVVE~~~Dv~aiE~~~~y~G~YhVL~ 107 (195)
T TIGR00615 82 CVVEDPKDVFALEKTKEFRGRYHVLG 107 (195)
T ss_pred EEECCHHHHHHHHhhCccceEEEEcc
Confidence 12467778889999999999986
No 43
>TIGR01052 top6b DNA topoisomerase VI, B subunit. This model describes DNA topoisomerase VI, an archaeal type II DNA topoisomerase (DNA gyrase).
Probab=71.52 E-value=6 Score=37.30 Aligned_cols=49 Identities=14% Similarity=0.295 Sum_probs=41.1
Q ss_pred eEEeEee-ccccccCHHHHHHHHHHcCCC----ccccCCCCHHHHHHHHHHHhh
Q 030930 59 KRIEYSL-QYIHGVGRTRARQILVDLKME----NKITKDMSEEELITIRDEVSK 107 (169)
Q Consensus 59 K~i~~AL-t~I~GIG~~~A~~Ic~~lgi~----~k~~~~Ls~~el~~L~~~l~~ 107 (169)
+.+.--| ..+-.||..+|..||+.+|++ ++...+|+++|+++|.+.+.+
T Consensus 247 ~~l~~fL~~~f~~v~~~~a~~~~~~~g~~~~~~~~~~~~l~~~~~~~l~~~~~~ 300 (488)
T TIGR01052 247 STLRSFLVSEFSRIGEKKIKELLEKYGIDVDPLDKKPKELTWDEAEKIVNAFKE 300 (488)
T ss_pred ccHHHHHHHhhcccCHHHHHHHHHHhCCCccccCCChhhCCHHHHHHHHHHHHh
Confidence 4554444 678899999999999999998 345699999999999999975
No 44
>PRK13844 recombination protein RecR; Provisional
Probab=70.91 E-value=6.3 Score=33.14 Aligned_cols=72 Identities=22% Similarity=0.334 Sum_probs=47.7
Q ss_pred EeEeeccccccCHHHHHHHHHHcCCCccccCCCCHHHHHHHHHHHhhc------------ccc-------hHHHH-----
Q 030930 61 IEYSLQYIHGVGRTRARQILVDLKMENKITKDMSEEELITIRDEVSKY------------MIE-------GDLRR----- 116 (169)
Q Consensus 61 i~~ALt~I~GIG~~~A~~Ic~~lgi~~k~~~~Ls~~el~~L~~~l~~~------------~Ie-------~dLr~----- 116 (169)
+..+|.+.+|||+++|.++.-.+= +..+++++.|.+.|.+. .-| .|-.|
T Consensus 13 LI~~l~~LPGIG~KsA~Rla~~lL-------~~~~~~~~~la~~i~~~~~~i~~C~~C~~lte~~~C~IC~d~~Rd~~~i 85 (200)
T PRK13844 13 VIESLRKLPTIGKKSSQRLALYLL-------DKSPETAIAIANSLLDATANIKKCVYCQALTEDDVCNICSNTNRDDTKL 85 (200)
T ss_pred HHHHHHHCCCCCHHHHHHHHHHHH-------cCCHHHHHHHHHHHHHHHHhCCcCCCCCCCCCCCCCCCCCCCCCCCCEE
Confidence 345789999999999999875432 33566777776666431 111 11111
Q ss_pred ---HHHHHHHHHHhhhhcccCccCCC
Q 030930 117 ---FNALAIRRLKEIQCYRGIRHIQG 139 (169)
Q Consensus 117 ---~~~~nI~rL~~I~sYRG~RH~~G 139 (169)
..-.|+.-+-+.+.|+|.=|-+|
T Consensus 86 CVVE~~~Dv~aiE~t~~y~G~YhVL~ 111 (200)
T PRK13844 86 CIIESMLDMIAIEEAGIYRGKYFVLN 111 (200)
T ss_pred EEECCHHHHHHHHhhCccceEEEEcc
Confidence 12467778889999999999874
No 45
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=70.13 E-value=3 Score=34.36 Aligned_cols=19 Identities=21% Similarity=0.531 Sum_probs=14.1
Q ss_pred EeeccccccCHHHHHHHHHH
Q 030930 63 YSLQYIHGVGRTRARQILVD 82 (169)
Q Consensus 63 ~ALt~I~GIG~~~A~~Ic~~ 82 (169)
.+| +++|||+++|.+|+-.
T Consensus 108 ~~L-~vpGIGkKtAerIilE 126 (186)
T PRK14600 108 AAL-KVNGIGEKLINRIITE 126 (186)
T ss_pred hhe-ECCCCcHHHHHHHHHH
Confidence 467 7888888888888743
No 46
>PRK00076 recR recombination protein RecR; Reviewed
Probab=69.88 E-value=6.5 Score=32.89 Aligned_cols=72 Identities=21% Similarity=0.417 Sum_probs=47.7
Q ss_pred EeEeeccccccCHHHHHHHHHHcCCCccccCCCCHHHHHHHHHHHhhc------------ccchHH-------HH-----
Q 030930 61 IEYSLQYIHGVGRTRARQILVDLKMENKITKDMSEEELITIRDEVSKY------------MIEGDL-------RR----- 116 (169)
Q Consensus 61 i~~ALt~I~GIG~~~A~~Ic~~lgi~~k~~~~Ls~~el~~L~~~l~~~------------~Ie~dL-------r~----- 116 (169)
+..+|.+++|||+++|.++.-.+= +..+++++.|.+.|.+. .-++++ .|
T Consensus 9 Li~~l~~LPGIG~KsA~Rla~~ll-------~~~~~~~~~la~~i~~~~~~i~~C~~C~~lse~~~C~IC~d~~Rd~~~i 81 (196)
T PRK00076 9 LIEALRKLPGIGPKSAQRLAFHLL-------QRDREDVLRLAQALEEAKEKIKHCSVCGNLTEQDPCEICSDPRRDQSLI 81 (196)
T ss_pred HHHHHHHCCCCCHHHHHHHHHHHH-------cCCHHHHHHHHHHHHHHHHcCCcCCCCCCcCCCCcCCCCCCCCCCCCEE
Confidence 345789999999999999885543 33566777776666431 111110 11
Q ss_pred ---HHHHHHHHHHhhhhcccCccCCC
Q 030930 117 ---FNALAIRRLKEIQCYRGIRHIQG 139 (169)
Q Consensus 117 ---~~~~nI~rL~~I~sYRG~RH~~G 139 (169)
..-.|+.-+-+.+.|+|.=|-+|
T Consensus 82 cVVE~~~Dv~aiE~s~~y~G~YhVL~ 107 (196)
T PRK00076 82 CVVESPADVLAIERTGEYRGLYHVLG 107 (196)
T ss_pred EEECCHHHHHHHHhhCcCceEEEEec
Confidence 12457777888899999999887
No 47
>PRK00274 ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed
Probab=68.80 E-value=3 Score=35.42 Aligned_cols=47 Identities=15% Similarity=0.377 Sum_probs=35.0
Q ss_pred EEeEeeccccccCHHHHHHHHHHcCCC-ccccCCCCHHHHHHHHHHHhh
Q 030930 60 RIEYSLQYIHGVGRTRARQILVDLKME-NKITKDMSEEELITIRDEVSK 107 (169)
Q Consensus 60 ~i~~ALt~I~GIG~~~A~~Ic~~lgi~-~k~~~~Ls~~el~~L~~~l~~ 107 (169)
.+..+|..+++. ...+..+++.+|++ +.++.+|+.+|+.+|.+.++.
T Consensus 223 ~l~~~l~~~~~~-~~~~~~~l~~~~~~~~~r~~~l~~~~~~~L~~~~~~ 270 (272)
T PRK00274 223 TLRNNLKNLFGS-KEKLEEALEAAGIDPNRRAETLSVEEFVRLANALAA 270 (272)
T ss_pred HHHHHHHhhccc-hHHHHHHHHHCCCCcCCCceeCCHHHHHHHHHHHHh
Confidence 344455555431 34567889999999 788999999999999887754
No 48
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=66.47 E-value=3.2 Score=34.25 Aligned_cols=17 Identities=35% Similarity=0.618 Sum_probs=9.1
Q ss_pred eeccccccCHHHHHHHH
Q 030930 64 SLQYIHGVGRTRARQIL 80 (169)
Q Consensus 64 ALt~I~GIG~~~A~~Ic 80 (169)
+|++++|||+++|.+|+
T Consensus 109 ~L~~vpGIGkKtAerIi 125 (194)
T PRK14605 109 LLSTIPGIGKKTASRIV 125 (194)
T ss_pred HHHhCCCCCHHHHHHHH
Confidence 35555555555555544
No 49
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=64.92 E-value=3.1 Score=34.01 Aligned_cols=38 Identities=26% Similarity=0.241 Sum_probs=28.0
Q ss_pred EEeCccCCCCeEEeEeeccccccCHHHHHHHHHHcCCC
Q 030930 49 RVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKME 86 (169)
Q Consensus 49 rI~~tni~~~K~i~~ALt~I~GIG~~~A~~Ic~~lgi~ 86 (169)
|+.|-.=...+.++..|..|+|||+.+|..|++.+|.+
T Consensus 59 ~l~gF~~~~ek~~f~~L~~i~GIGpk~A~~il~~fg~~ 96 (192)
T PRK00116 59 LLYGFLTKEERELFRLLISVSGVGPKLALAILSGLSPE 96 (192)
T ss_pred HHcCcCCHHHHHHHHHHhcCCCCCHHHHHHHHHhCCHH
Confidence 34454433334455588999999999999999999964
No 50
>PF03486 HI0933_like: HI0933-like protein; InterPro: IPR004792 This is a family of conserved hypothetical proteins that may include proteins with a dinucleotide-binding motif (Rossman fold), including oxidoreductases and dehydrogenases.; PDB: 2I0Z_A 3V76_A 2GQF_A.
Probab=62.94 E-value=5.9 Score=36.09 Aligned_cols=52 Identities=12% Similarity=0.224 Sum_probs=41.3
Q ss_pred CCCeEEeEeeccccccCHHHHHHHHHHcCC-C-ccccCCCCHHHHHHHHHHHhhcc
Q 030930 56 PNNKRIEYSLQYIHGVGRTRARQILVDLKM-E-NKITKDMSEEELITIRDEVSKYM 109 (169)
Q Consensus 56 ~~~K~i~~ALt~I~GIG~~~A~~Ic~~lgi-~-~k~~~~Ls~~el~~L~~~l~~~~ 109 (169)
.+++.+...|..+ +-++.+..+|+.+++ + ++...+|+++|+.+|.+.|.+|.
T Consensus 288 ~~~~~~~~~l~~~--lp~rl~~~ll~~~~i~~~~~~~~~l~~~~~~~L~~~lk~~~ 341 (409)
T PF03486_consen 288 NPKRTLKNFLKGL--LPKRLALALLKRAGIKDPDKKVSELSKKERNRLANLLKRFP 341 (409)
T ss_dssp TTTSBHHHHHTTT--S-HHHHHHHHHHTTS-STTSBGGGS-HHHHHHHHHHHHCEE
T ss_pred HHhhHHHHHHHHH--hHHHHHHHHHHHcCCCccccchhhcCHHHHHHHHHHHHhCc
Confidence 3455666666665 889999999999999 8 66789999999999999998763
No 51
>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=62.76 E-value=4.9 Score=27.37 Aligned_cols=19 Identities=26% Similarity=0.433 Sum_probs=16.6
Q ss_pred eeccccccCHHHHHHHHHH
Q 030930 64 SLQYIHGVGRTRARQILVD 82 (169)
Q Consensus 64 ALt~I~GIG~~~A~~Ic~~ 82 (169)
+|++|+|||..+|..|-.-
T Consensus 48 ~~~~l~gIG~~ia~kI~E~ 66 (68)
T PF14716_consen 48 DLKKLPGIGKSIAKKIDEI 66 (68)
T ss_dssp HHCTSTTTTHHHHHHHHHH
T ss_pred HHhhCCCCCHHHHHHHHHH
Confidence 6899999999999998654
No 52
>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=62.50 E-value=6.5 Score=27.48 Aligned_cols=20 Identities=20% Similarity=0.406 Sum_probs=17.6
Q ss_pred eccccccCHHHHHHHHHHcC
Q 030930 65 LQYIHGVGRTRARQILVDLK 84 (169)
Q Consensus 65 Lt~I~GIG~~~A~~Ic~~lg 84 (169)
+..|+|||..+|..++...|
T Consensus 24 i~gv~giG~k~A~~ll~~~~ 43 (75)
T cd00080 24 IPGVPGIGPKTALKLLKEYG 43 (75)
T ss_pred CCCCCcccHHHHHHHHHHhC
Confidence 34689999999999999877
No 53
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=62.09 E-value=5.6 Score=26.23 Aligned_cols=20 Identities=30% Similarity=0.476 Sum_probs=17.6
Q ss_pred eeccccccCHHHHHHHHHHc
Q 030930 64 SLQYIHGVGRTRARQILVDL 83 (169)
Q Consensus 64 ALt~I~GIG~~~A~~Ic~~l 83 (169)
.|..|+|||..+|..|+..+
T Consensus 39 ~L~~i~Gig~~~a~~i~~~~ 58 (60)
T PF14520_consen 39 ELAEIPGIGEKTAEKIIEAA 58 (60)
T ss_dssp HHHTSTTSSHHHHHHHHHHH
T ss_pred HHhcCCCCCHHHHHHHHHHH
Confidence 38899999999999998765
No 54
>PF02371 Transposase_20: Transposase IS116/IS110/IS902 family; InterPro: IPR003346 Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This family includes transposases for IS116, IS110 and IS902. It is often found with the transposase IS111A/IS1328/IS1533 family (see IPR002525 from INTERPRO) [, ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=60.39 E-value=7 Score=27.70 Aligned_cols=20 Identities=30% Similarity=0.529 Sum_probs=18.2
Q ss_pred eeccccccCHHHHHHHHHHc
Q 030930 64 SLQYIHGVGRTRARQILVDL 83 (169)
Q Consensus 64 ALt~I~GIG~~~A~~Ic~~l 83 (169)
-|++|+|||..+|..|+..+
T Consensus 3 ~l~sipGig~~~a~~llaei 22 (87)
T PF02371_consen 3 LLTSIPGIGPITAATLLAEI 22 (87)
T ss_pred hhcCCCCccHHHHHHHHHHH
Confidence 47899999999999999887
No 55
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=59.74 E-value=8 Score=23.72 Aligned_cols=17 Identities=24% Similarity=0.472 Sum_probs=15.1
Q ss_pred ccccccCHHHHHHHHHH
Q 030930 66 QYIHGVGRTRARQILVD 82 (169)
Q Consensus 66 t~I~GIG~~~A~~Ic~~ 82 (169)
..|+|||..+|..++++
T Consensus 19 ~Gv~giG~ktA~~ll~~ 35 (36)
T smart00279 19 PGVKGIGPKTALKLLRE 35 (36)
T ss_pred CCCCcccHHHHHHHHHh
Confidence 57899999999999875
No 56
>PRK07945 hypothetical protein; Provisional
Probab=58.92 E-value=15 Score=32.59 Aligned_cols=47 Identities=26% Similarity=0.309 Sum_probs=31.5
Q ss_pred eeccccccCHHHHHHHHHHcCCCccccCCCCHHHHHHHHHHHhhcccchHHHHHH
Q 030930 64 SLQYIHGVGRTRARQILVDLKMENKITKDMSEEELITIRDEVSKYMIEGDLRRFN 118 (169)
Q Consensus 64 ALt~I~GIG~~~A~~Ic~~lgi~~k~~~~Ls~~el~~L~~~l~~~~Ie~dLr~~~ 118 (169)
.|++|+|||+.+|..|-+-+. .|.+ ++++.|.+.++--. +.+|...+
T Consensus 50 ~l~~~~giG~~~a~~i~e~~~-----tg~~--~~l~~l~~~~~~~~-g~~l~~~~ 96 (335)
T PRK07945 50 SLTSLPGIGPKTAKVIAQALA-----GRVP--DYLAELRADAEPLG-GGALRAAL 96 (335)
T ss_pred CcccCCCcCHHHHHHHHHHHh-----cCCH--HHHHHHHHhhcCCc-cHHHHHHH
Confidence 699999999999999988766 4443 35666666553222 44455433
No 57
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=57.35 E-value=6.2 Score=32.46 Aligned_cols=18 Identities=39% Similarity=0.604 Sum_probs=15.5
Q ss_pred EeeccccccCHHHHHHHH
Q 030930 63 YSLQYIHGVGRTRARQIL 80 (169)
Q Consensus 63 ~ALt~I~GIG~~~A~~Ic 80 (169)
-+|++++|||.++|.+|+
T Consensus 107 ~~L~~ipGiGkKtAerIi 124 (191)
T TIGR00084 107 KALVKIPGVGKKTAERLL 124 (191)
T ss_pred HHHHhCCCCCHHHHHHHH
Confidence 357889999999999998
No 58
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=56.99 E-value=7.3 Score=34.52 Aligned_cols=39 Identities=10% Similarity=0.194 Sum_probs=28.8
Q ss_pred eEeeccccccCHHHHHHHHHHcCCCc--cc--c--CCCCHHHHHHH
Q 030930 62 EYSLQYIHGVGRTRARQILVDLKMEN--KI--T--KDMSEEELITI 101 (169)
Q Consensus 62 ~~ALt~I~GIG~~~A~~Ic~~lgi~~--k~--~--~~Ls~~el~~L 101 (169)
...|++|+|||..+|..+.+ +||.+ .. . ..|+.+|+.-|
T Consensus 88 l~~l~~i~GiGpk~a~~l~~-lGi~tl~eL~~a~~~~l~~~q~~gl 132 (334)
T smart00483 88 LKLFTNVFGVGPKTAAKWYR-KGIRTLEELKKNKELKLTKQQKAGL 132 (334)
T ss_pred HHHHHccCCcCHHHHHHHHH-hCCCCHHHHHhcccccCCHHHHHHH
Confidence 45679999999999999999 99983 21 1 25777664433
No 59
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=56.17 E-value=6.6 Score=30.12 Aligned_cols=25 Identities=28% Similarity=0.363 Sum_probs=21.5
Q ss_pred CeEEeEeeccccccCHHHHHHHHHH
Q 030930 58 NKRIEYSLQYIHGVGRTRARQILVD 82 (169)
Q Consensus 58 ~K~i~~ALt~I~GIG~~~A~~Ic~~ 82 (169)
...+...|++++|||+.+|..++..
T Consensus 78 ~~~~~~~L~~l~GIG~~tA~~~l~~ 102 (158)
T cd00056 78 DPDAREELLALPGVGRKTANVVLLF 102 (158)
T ss_pred CcccHHHHHcCCCCCHHHHHHHHHH
Confidence 3557888999999999999998864
No 60
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=54.65 E-value=7.3 Score=29.62 Aligned_cols=23 Identities=30% Similarity=0.294 Sum_probs=19.5
Q ss_pred EeEeeccccccCHHHHHHHHHHc
Q 030930 61 IEYSLQYIHGVGRTRARQILVDL 83 (169)
Q Consensus 61 i~~ALt~I~GIG~~~A~~Ic~~l 83 (169)
....|.+++|||+.+|..+|...
T Consensus 70 ~~~~L~~l~GIG~~tA~~~l~~~ 92 (149)
T smart00478 70 DREELLKLPGVGRKTANAVLSFA 92 (149)
T ss_pred HHHHHHcCCCCcHHHHHHHHHHH
Confidence 45678899999999999988764
No 61
>PRK09482 flap endonuclease-like protein; Provisional
Probab=53.83 E-value=42 Score=29.02 Aligned_cols=19 Identities=21% Similarity=0.476 Sum_probs=17.0
Q ss_pred ccccccCHHHHHHHHHHcC
Q 030930 66 QYIHGVGRTRARQILVDLK 84 (169)
Q Consensus 66 t~I~GIG~~~A~~Ic~~lg 84 (169)
..|+|||..+|..+++..|
T Consensus 185 pGVpGIG~KtA~~LL~~~g 203 (256)
T PRK09482 185 PGVAGIGPKSAAELLNQFR 203 (256)
T ss_pred CCCCCcChHHHHHHHHHhC
Confidence 5689999999999998887
No 62
>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=53.21 E-value=16 Score=24.66 Aligned_cols=23 Identities=30% Similarity=0.365 Sum_probs=19.0
Q ss_pred EeEeecc-ccccCHHHHHHHHHHc
Q 030930 61 IEYSLQY-IHGVGRTRARQILVDL 83 (169)
Q Consensus 61 i~~ALt~-I~GIG~~~A~~Ic~~l 83 (169)
-.-.|.. ++|||...|.+|+..-
T Consensus 14 ~~~~L~~~ipgig~~~a~~Il~~R 37 (69)
T TIGR00426 14 TAEELQRAMNGVGLKKAEAIVSYR 37 (69)
T ss_pred CHHHHHhHCCCCCHHHHHHHHHHH
Confidence 3346778 9999999999999883
No 63
>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=51.69 E-value=10 Score=33.20 Aligned_cols=25 Identities=28% Similarity=0.450 Sum_probs=21.6
Q ss_pred eEeeccccccCHHHHHHHHHHcCCCc
Q 030930 62 EYSLQYIHGVGRTRARQILVDLKMEN 87 (169)
Q Consensus 62 ~~ALt~I~GIG~~~A~~Ic~~lgi~~ 87 (169)
..-|++|+|||+.+|..+. .+|+.+
T Consensus 84 l~~l~~i~GiGpk~a~~l~-~lGi~s 108 (307)
T cd00141 84 LLLLLRVPGVGPKTARKLY-ELGIRT 108 (307)
T ss_pred HHHHHcCCCCCHHHHHHHH-HcCCCC
Confidence 3456899999999999999 999983
No 64
>PRK10702 endonuclease III; Provisional
Probab=51.61 E-value=8.2 Score=32.17 Aligned_cols=23 Identities=30% Similarity=0.390 Sum_probs=19.4
Q ss_pred EeEeeccccccCHHHHHHHHHHc
Q 030930 61 IEYSLQYIHGVGRTRARQILVDL 83 (169)
Q Consensus 61 i~~ALt~I~GIG~~~A~~Ic~~l 83 (169)
....|.+++|||+.+|..|+..+
T Consensus 107 ~~~~Ll~lpGVG~ktA~~ill~a 129 (211)
T PRK10702 107 DRAALEALPGVGRKTANVVLNTA 129 (211)
T ss_pred hHHHHhcCCcccHHHHHHHHHHH
Confidence 36789999999999999998543
No 65
>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=50.87 E-value=8.5 Score=31.11 Aligned_cols=23 Identities=30% Similarity=0.283 Sum_probs=19.1
Q ss_pred EeEeeccccccCHHHHHHHHHHc
Q 030930 61 IEYSLQYIHGVGRTRARQILVDL 83 (169)
Q Consensus 61 i~~ALt~I~GIG~~~A~~Ic~~l 83 (169)
....|.+++|||+.+|..||...
T Consensus 104 ~~~~L~~l~GIG~ktA~~ill~~ 126 (191)
T TIGR01083 104 DREELVKLPGVGRKTANVVLNVA 126 (191)
T ss_pred HHHHHHhCCCCcHHHHHHHHHHH
Confidence 35679999999999999998543
No 66
>TIGR00755 ksgA dimethyladenosine transferase. Alternate name: S-adenosylmethionine--6-N',N'-adenosyl (rRNA) dimethyltransferase
Probab=50.74 E-value=7.8 Score=32.29 Aligned_cols=44 Identities=14% Similarity=0.353 Sum_probs=31.9
Q ss_pred eEEeEeeccccccCHHHHHHHHHHcCCC-ccccCCCCHHHHHHHHHH
Q 030930 59 KRIEYSLQYIHGVGRTRARQILVDLKME-NKITKDMSEEELITIRDE 104 (169)
Q Consensus 59 K~i~~ALt~I~GIG~~~A~~Ic~~lgi~-~k~~~~Ls~~el~~L~~~ 104 (169)
|.+..+|..+++- ..+..++..+|++ ++++.+|+.+|+..|.+.
T Consensus 208 k~l~~~l~~~~~~--~~~~~~l~~~~i~~~~r~~~l~~~~~~~l~~~ 252 (253)
T TIGR00755 208 KTLRNNLKQLLKA--SKLEEVLEQLGLDPTARAEQLSPEDFLRLANL 252 (253)
T ss_pred HHHHHHHhhhcch--hHHHHHHHHCCcCCCCCcccCCHHHHHHHHHh
Confidence 4455556555331 3456778889998 788999999999998764
No 67
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=50.45 E-value=4.1 Score=33.56 Aligned_cols=39 Identities=15% Similarity=0.206 Sum_probs=33.4
Q ss_pred eEEeCccCCCCeEEeEeeccccccCHHHHHHHHHHcCCC
Q 030930 48 ARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKME 86 (169)
Q Consensus 48 vrI~~tni~~~K~i~~ALt~I~GIG~~~A~~Ic~~lgi~ 86 (169)
..++|-.=...+.++.-|.++.|||+.+|..|+..++.+
T Consensus 58 ~~LyGF~~~~Er~lF~~Li~V~GIGpK~Al~ILs~~~~~ 96 (194)
T PRK14605 58 LSLFGFATTEELSLFETLIDVSGIGPKLGLAMLSAMNAE 96 (194)
T ss_pred ceeeCCCCHHHHHHHHHHhCCCCCCHHHHHHHHHhCCHH
Confidence 467787778888899999999999999999999877643
No 68
>COG0030 KsgA Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis]
Probab=50.09 E-value=7.9 Score=33.65 Aligned_cols=45 Identities=16% Similarity=0.401 Sum_probs=37.5
Q ss_pred CeEEeEeeccccccCHHHHHHHHHHcCCC-ccccCCCCHHHHHHHHHHHhh
Q 030930 58 NKRIEYSLQYIHGVGRTRARQILVDLKME-NKITKDMSEEELITIRDEVSK 107 (169)
Q Consensus 58 ~K~i~~ALt~I~GIG~~~A~~Ic~~lgi~-~k~~~~Ls~~el~~L~~~l~~ 107 (169)
.|.+..+|+..++ ...+|..+|+| +.++.+|+.+|+-.|.+.+..
T Consensus 211 RKtl~n~l~~~~~-----~~~~l~~~~i~~~~R~e~ls~~~f~~L~~~l~~ 256 (259)
T COG0030 211 RKTLRNNLKNLFG-----LEEVLEAAGIDPNARAENLSPEDFLKLANALKG 256 (259)
T ss_pred hHHHHHHHHhhhh-----HHHHHHhcCCCcccChhhCCHHHHHHHHHHHhh
Confidence 4666677777766 78999999999 678999999999999888754
No 69
>PRK08609 hypothetical protein; Provisional
Probab=50.04 E-value=11 Score=35.75 Aligned_cols=24 Identities=17% Similarity=0.358 Sum_probs=22.0
Q ss_pred EeeccccccCHHHHHHHHHHcCCC
Q 030930 63 YSLQYIHGVGRTRARQILVDLKME 86 (169)
Q Consensus 63 ~ALt~I~GIG~~~A~~Ic~~lgi~ 86 (169)
..|++|+|||+.+|.++.+.+||.
T Consensus 88 ~~l~~i~GiGpk~a~~l~~~lGi~ 111 (570)
T PRK08609 88 LPLLKLPGLGGKKIAKLYKELGVV 111 (570)
T ss_pred HHHhcCCCCCHHHHHHHHHHhCCC
Confidence 467899999999999999999996
No 70
>COG1389 DNA topoisomerase VI, subunit B [DNA replication, recombination, and repair]
Probab=49.73 E-value=18 Score=34.47 Aligned_cols=43 Identities=16% Similarity=0.302 Sum_probs=37.4
Q ss_pred ccccccCHHHHHHHHHHcCCC-ccccCCCC----HHHHHHHHHHHhhc
Q 030930 66 QYIHGVGRTRARQILVDLKME-NKITKDMS----EEELITIRDEVSKY 108 (169)
Q Consensus 66 t~I~GIG~~~A~~Ic~~lgi~-~k~~~~Ls----~~el~~L~~~l~~~ 108 (169)
..+--||..+|..+|+.+|+| ++...+|+ .+|.++|.+.+.+|
T Consensus 264 sef~rig~~ta~e~~e~~g~~~~~~p~~L~~~~~~eea~~lv~a~~~~ 311 (538)
T COG1389 264 SEFSRIGEKTADELLEYAGFDPDKKPRELTKKKTREEAEKLVEAFKKM 311 (538)
T ss_pred HHHHHhhhhhHHHHHHHhcCCcccCHHHhhcccCHHHHHHHHHHHHhC
Confidence 556679999999999999999 66678888 99999999998764
No 71
>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=49.33 E-value=40 Score=28.30 Aligned_cols=20 Identities=20% Similarity=0.454 Sum_probs=16.6
Q ss_pred eccccccCHHHHHHHHHHcC
Q 030930 65 LQYIHGVGRTRARQILVDLK 84 (169)
Q Consensus 65 Lt~I~GIG~~~A~~Ic~~lg 84 (169)
+..|+|||..+|..++++.|
T Consensus 185 ipGv~GiG~ktA~~Ll~~~g 204 (240)
T cd00008 185 IPGVPGIGEKTAAKLLKEYG 204 (240)
T ss_pred CCCCCccCHHHHHHHHHHhC
Confidence 34678999999999998876
No 72
>smart00475 53EXOc 5'-3' exonuclease.
Probab=48.08 E-value=52 Score=28.21 Aligned_cols=20 Identities=20% Similarity=0.488 Sum_probs=16.1
Q ss_pred eccccccCHHHHHHHHHHcC
Q 030930 65 LQYIHGVGRTRARQILVDLK 84 (169)
Q Consensus 65 Lt~I~GIG~~~A~~Ic~~lg 84 (169)
+..|+|||..+|..++++.|
T Consensus 188 ipGV~GIG~KtA~~Ll~~yg 207 (259)
T smart00475 188 IPGVPGIGEKTAAKLLKEFG 207 (259)
T ss_pred CCCCCCCCHHHHHHHHHHhC
Confidence 34578999999999988877
No 73
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=47.43 E-value=42 Score=29.09 Aligned_cols=18 Identities=22% Similarity=0.486 Sum_probs=17.1
Q ss_pred ccccCHHHHHHHHHHcCC
Q 030930 68 IHGVGRTRARQILVDLKM 85 (169)
Q Consensus 68 I~GIG~~~A~~Ic~~lgi 85 (169)
|+|||..+|..++...|.
T Consensus 203 V~GIG~ktA~~Ll~~~gs 220 (310)
T COG0258 203 VKGIGPKTALKLLQEYGS 220 (310)
T ss_pred CCCcCHHHHHHHHHHhCC
Confidence 999999999999999993
No 74
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=47.40 E-value=9.7 Score=25.64 Aligned_cols=45 Identities=16% Similarity=0.231 Sum_probs=26.5
Q ss_pred eEEeEeeccccccCHHHHHHHHHHc----CCCc----cccCCCCHHHHHHHHH
Q 030930 59 KRIEYSLQYIHGVGRTRARQILVDL----KMEN----KITKDMSEEELITIRD 103 (169)
Q Consensus 59 K~i~~ALt~I~GIG~~~A~~Ic~~l----gi~~----k~~~~Ls~~el~~L~~ 103 (169)
..=...|..++|||...|..|.+.= ++.+ ..+..++++.+++|..
T Consensus 10 ~as~~eL~~lpgi~~~~A~~Iv~~R~~~G~f~s~~dL~~v~gi~~~~~~~l~~ 62 (65)
T PF12836_consen 10 TASAEELQALPGIGPKQAKAIVEYREKNGPFKSLEDLKEVPGIGPKTYEKLKP 62 (65)
T ss_dssp TS-HHHHHTSTT--HHHHHHHHHHHHHH-S-SSGGGGGGSTT--HHHHHHHCC
T ss_pred cCCHHHHHHcCCCCHHHHHHHHHHHHhCcCCCCHHHHhhCCCCCHHHHHHHHh
Confidence 3334568899999999999999654 3331 2246677777777654
No 75
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=46.17 E-value=11 Score=31.73 Aligned_cols=22 Identities=27% Similarity=0.273 Sum_probs=18.5
Q ss_pred EeEeeccccccCHHHHHHHHHH
Q 030930 61 IEYSLQYIHGVGRTRARQILVD 82 (169)
Q Consensus 61 i~~ALt~I~GIG~~~A~~Ic~~ 82 (169)
....|.+++|||+.+|..|+--
T Consensus 119 ~re~Ll~l~GIG~kTAd~iLly 140 (218)
T PRK13913 119 TREWLLDQKGIGKESADAILCY 140 (218)
T ss_pred HHHHHHcCCCccHHHHHHHHHH
Confidence 4467999999999999998853
No 76
>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=45.08 E-value=19 Score=27.33 Aligned_cols=32 Identities=22% Similarity=0.252 Sum_probs=25.9
Q ss_pred cCCCCeEEeEeeccccccCHHHHHHHHHHcCC
Q 030930 54 EIPNNKRIEYSLQYIHGVGRTRARQILVDLKM 85 (169)
Q Consensus 54 ni~~~K~i~~ALt~I~GIG~~~A~~Ic~~lgi 85 (169)
-|+-|..-...|..++|||...|..|++..+-
T Consensus 59 ~iniNtA~~~eL~~lpGIG~~~A~~Ii~~R~~ 90 (120)
T TIGR01259 59 AVNINAASLEELQALPGIGPAKAKAIIEYREE 90 (120)
T ss_pred CEeCCcCCHHHHhcCCCCCHHHHHHHHHHHHh
Confidence 35556666778899999999999999988753
No 77
>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=44.91 E-value=12 Score=32.54 Aligned_cols=28 Identities=36% Similarity=0.367 Sum_probs=21.8
Q ss_pred ccCCCCeEEeEeeccccccCHHHHHHHHHHc
Q 030930 53 VEIPNNKRIEYSLQYIHGVGRTRARQILVDL 83 (169)
Q Consensus 53 tni~~~K~i~~ALt~I~GIG~~~A~~Ic~~l 83 (169)
-.+|.. ...|.+++|||+.+|..|+..+
T Consensus 98 g~~p~~---~~~L~~LpGIG~~TA~~Il~~a 125 (275)
T TIGR01084 98 GEFPQD---FEDLAALPGVGRYTAGAILSFA 125 (275)
T ss_pred CCCcHH---HHHHHhCCCCCHHHHHHHHHHH
Confidence 345543 5689999999999999998643
No 78
>PRK14976 5'-3' exonuclease; Provisional
Probab=44.41 E-value=68 Score=27.81 Aligned_cols=19 Identities=21% Similarity=0.387 Sum_probs=16.4
Q ss_pred ccccccCHHHHHHHHHHcC
Q 030930 66 QYIHGVGRTRARQILVDLK 84 (169)
Q Consensus 66 t~I~GIG~~~A~~Ic~~lg 84 (169)
-.|+|||..+|..+++..|
T Consensus 194 pGVpGIG~KtA~~LL~~~g 212 (281)
T PRK14976 194 KGVKGIGPKTAIKLLNKYG 212 (281)
T ss_pred CCCCcccHHHHHHHHHHcC
Confidence 4589999999999998877
No 79
>PF00398 RrnaAD: Ribosomal RNA adenine dimethylase; InterPro: IPR001737 This family of proteins include rRNA adenine dimethylases (e.g. KsgA) and the Erythromycin resistance methylases (Erm). The bacterial enzyme KsgA catalyses the transfer of a total of four methyl groups from S-adenosyl-l-methionine (S-AdoMet) to two adjacent adenosine bases in 16S rRNA. This enzyme and the resulting modified adenosine bases appear to be conserved in all species of eubacteria, eukaryotes, and archaea, and in eukaryotic organelles. Bacterial resistance to the aminoglycoside antibiotic kasugamycin involves inactivation of KsgA and resulting loss of the dimethylations, with modest consequences to the overall fitness of the organism. In contrast, the yeast ortholog, Dim1, is essential. In Saccharomyces cerevisiae (Baker's yeast), and presumably in other eukaryotes, the enzyme performs a vital role in pre-rRNA processing in addition to its methylating activity. The best conserved region in these enzymes is located in the N-terminal section and corresponds to a region that is probably involved in S-adenosyl methionine (SAM) binding domain. The crystal structure of KsgA from Escherichia coli has been solved to a resolution of 2.1A. It bears a strong similarity to the crystal structure of ErmC' from Bacillus stearothermophilus and a lesser similarity to the yeast mitochondrial transcription factor, sc-mtTFB []. The Erm family of RNA methyltransferases, which methylate a single adenosine base in 23S rRNA confer resistance to the MLS-B group of antibiotics. Despite their sequence similarity, the two enzyme families have strikingly different levels of regulation that remain to be elucidated. Other orthologs, of this family include the yeast and Homo sapiens (Human) mitochondrial transcription factors (MTF1 and h-mtTFB respectively), which are nuclear encoded []. Human-mtTFB is able to stimulate transcription in vitro independently of its S-adenosylmethionine binding and rRNA methyltransferase activity [].; GO: 0000179 rRNA (adenine-N6,N6-)-dimethyltransferase activity, 0008649 rRNA methyltransferase activity, 0000154 rRNA modification; PDB: 3FTF_A 3R9X_B 3FTE_A 3FTC_A 3FTD_A 3GRY_A 3FYC_A 3GRU_A 3FYD_A 3GRV_A ....
Probab=43.74 E-value=9.5 Score=32.12 Aligned_cols=50 Identities=16% Similarity=0.303 Sum_probs=38.7
Q ss_pred CCCeEEeEeeccccccCHHHHHHHHHHcCCC-ccccCCCCHHHHHHHHHHHhh
Q 030930 56 PNNKRIEYSLQYIHGVGRTRARQILVDLKME-NKITKDMSEEELITIRDEVSK 107 (169)
Q Consensus 56 ~~~K~i~~ALt~I~GIG~~~A~~Ic~~lgi~-~k~~~~Ls~~el~~L~~~l~~ 107 (169)
-..|.+..+|..+++ ......+.+.+||+ +.++.+|+.+|+.+|.+++++
T Consensus 212 ~rrk~l~~~L~~~~~--~~~~~~~~~~~~i~~~~r~~~ls~~~~~~l~~~l~k 262 (262)
T PF00398_consen 212 QRRKTLRNSLKSLFP--GEQLEELLEKAGIDPNARAEELSPEQFLKLFKYLNK 262 (262)
T ss_dssp TTTSBHHHHTTCTHH--HHHHHHHHHHCTHTTTTCGGCHHHHHHHHHHHHHHH
T ss_pred CcchHHHHHHhhhcC--HHHHHHhhhhcCCCCCCCcccCCHHHHHHHHHHhhC
Confidence 466777777777653 33456677779999 678999999999999988763
No 80
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=43.52 E-value=38 Score=29.41 Aligned_cols=22 Identities=27% Similarity=0.318 Sum_probs=19.3
Q ss_pred EeEeeccccccCHHHHHHHHHH
Q 030930 61 IEYSLQYIHGVGRTRARQILVD 82 (169)
Q Consensus 61 i~~ALt~I~GIG~~~A~~Ic~~ 82 (169)
+...|+.|+|||+.+|..|+-.
T Consensus 205 ~~~~L~~LpGIGpwTA~~vllr 226 (283)
T PRK10308 205 AMKTLQTFPGIGRWTANYFALR 226 (283)
T ss_pred HHHHHhcCCCcCHHHHHHHHHH
Confidence 4578999999999999998865
No 81
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=43.05 E-value=25 Score=34.75 Aligned_cols=44 Identities=20% Similarity=0.290 Sum_probs=31.6
Q ss_pred CCeEEeEeeccccccCHHHHHHHHHHcCCCccccCCCCHHHHHHH
Q 030930 57 NNKRIEYSLQYIHGVGRTRARQILVDLKMENKITKDMSEEELITI 101 (169)
Q Consensus 57 ~~K~i~~ALt~I~GIG~~~A~~Ic~~lgi~~k~~~~Ls~~el~~L 101 (169)
....+.-.|..|+|||+..+..+++.+| +-..+.+-+.+||..+
T Consensus 631 ~k~~~~s~L~~IPGIGpkr~k~LL~~FG-Sle~I~~AS~eELa~V 674 (694)
T PRK14666 631 AGAALTGELQRVEGIGPATARLLWERFG-SLQAMAAAGEEGLAAV 674 (694)
T ss_pred HhhhhHhHHhhCCCCCHHHHHHHHHHhC-CHHHHHhcCHHHHHhc
Confidence 3444567889999999999999999998 4333444455665444
No 82
>PRK07373 DNA polymerase III subunit alpha; Reviewed
Probab=42.97 E-value=22 Score=33.10 Aligned_cols=46 Identities=15% Similarity=0.231 Sum_probs=31.9
Q ss_pred CeEEeEeeccccccCHHHHHHHHHHc---C-CCc-----cc--cCCCCHHHHHHHHH
Q 030930 58 NKRIEYSLQYIHGVGRTRARQILVDL---K-MEN-----KI--TKDMSEEELITIRD 103 (169)
Q Consensus 58 ~K~i~~ALt~I~GIG~~~A~~Ic~~l---g-i~~-----k~--~~~Ls~~el~~L~~ 103 (169)
++.|+|+|..|+|||...+..|.+.= | +.+ .+ .+.++...++.|..
T Consensus 109 ~~~IrfGL~aIKGVG~~~i~~Iv~eR~~~g~F~sl~DF~~Rvd~~~vnkr~lE~LIk 165 (449)
T PRK07373 109 GEKILFGLSAVRNLGEGAIESILKAREEGGEFKSLADFCDRVDLRVVNRRALETLIY 165 (449)
T ss_pred CCEEEEcchhcCCCCHHHHHHHHHHHHhcCCCCCHHHHHHHhCcccCCHHHHHHHHH
Confidence 34699999999999999999998532 2 111 12 24567766666643
No 83
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=42.36 E-value=17 Score=30.60 Aligned_cols=27 Identities=26% Similarity=0.346 Sum_probs=21.4
Q ss_pred EEeEeec-cccccCHHHHHHHHHHcCCC
Q 030930 60 RIEYSLQ-YIHGVGRTRARQILVDLKME 86 (169)
Q Consensus 60 ~i~~ALt-~I~GIG~~~A~~Ic~~lgi~ 86 (169)
..+..|. +++|||+.+|..|+.-.+..
T Consensus 115 ~~R~~Ll~~lpGIG~KTAd~vL~~~~~~ 142 (208)
T PRK01229 115 EAREFLVKNIKGIGYKEASHFLRNVGYE 142 (208)
T ss_pred HHHHHHHHcCCCCcHHHHHHHHHHccCC
Confidence 4566777 99999999999999655543
No 84
>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=42.28 E-value=4.2 Score=33.47 Aligned_cols=37 Identities=22% Similarity=0.281 Sum_probs=30.9
Q ss_pred eEEeCccCCCCeEEeEeeccccccCHHHHHHHHHHcC
Q 030930 48 ARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLK 84 (169)
Q Consensus 48 vrI~~tni~~~K~i~~ALt~I~GIG~~~A~~Ic~~lg 84 (169)
..+.|-.=...+.++..|.+|.|||+++|..|+..++
T Consensus 57 ~~LyGF~~~~Er~lF~~L~~V~GIGpK~Al~iL~~~~ 93 (191)
T TIGR00084 57 ELLFGFNTLEERELFKELIKVNGVGPKLALAILSNMS 93 (191)
T ss_pred ceeeCCCCHHHHHHHHHHhCCCCCCHHHHHHHHhcCC
Confidence 4677777778888999999999999999999965444
No 85
>COG1293 Predicted RNA-binding protein homologous to eukaryotic snRNP [Transcription]
Probab=42.03 E-value=27 Score=33.35 Aligned_cols=45 Identities=27% Similarity=0.386 Sum_probs=38.0
Q ss_pred EeEeeccccccCHHHHHHHHHHcCCCc-cccCCCCHHHHHHHHHHH
Q 030930 61 IEYSLQYIHGVGRTRARQILVDLKMEN-KITKDMSEEELITIRDEV 105 (169)
Q Consensus 61 i~~ALt~I~GIG~~~A~~Ic~~lgi~~-k~~~~Ls~~el~~L~~~l 105 (169)
+...|..+.|+|.-+|..+|-++|++. ....++.++++..|...+
T Consensus 188 ~~~~~~~~~g~~~~~a~el~~rag~~~~~~~~~~~~~~~~~v~~~~ 233 (564)
T COG1293 188 IVRLLARFLGLGGLLAEELLSRAGLDKKVPAKDLFEEEIKKVREAL 233 (564)
T ss_pred HHHHHHHhcCCCHHHHHHHHHhcCCCcCCchhhhhHHHHHHHHHHH
Confidence 345677789999999999999999994 446999999999997654
No 86
>PRK10880 adenine DNA glycosylase; Provisional
Probab=41.41 E-value=13 Score=33.49 Aligned_cols=22 Identities=32% Similarity=0.318 Sum_probs=19.3
Q ss_pred EeEeeccccccCHHHHHHHHHH
Q 030930 61 IEYSLQYIHGVGRTRARQILVD 82 (169)
Q Consensus 61 i~~ALt~I~GIG~~~A~~Ic~~ 82 (169)
....|.+++|||+.+|..||.-
T Consensus 107 ~~~~L~~LpGIG~~TA~aIl~~ 128 (350)
T PRK10880 107 TFEEVAALPGVGRSTAGAILSL 128 (350)
T ss_pred hHHHHhcCCCccHHHHHHHHHH
Confidence 4578999999999999999963
No 87
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=41.12 E-value=16 Score=35.07 Aligned_cols=47 Identities=28% Similarity=0.399 Sum_probs=34.0
Q ss_pred cCCCCeEEeEeeccccccCHHHHHHHHHHcCCCccccCCCCHHHHHHH
Q 030930 54 EIPNNKRIEYSLQYIHGVGRTRARQILVDLKMENKITKDMSEEELITI 101 (169)
Q Consensus 54 ni~~~K~i~~ALt~I~GIG~~~A~~Ic~~lgi~~k~~~~Ls~~el~~L 101 (169)
.+-....+..+|..|+|||..++..+++.+|= -..+.+-+.+|+..+
T Consensus 534 ~~R~k~~~~s~L~~IpGIG~k~~k~Ll~~FgS-~~~i~~As~eeL~~v 580 (598)
T PRK00558 534 KKRSKARLTSALDDIPGIGPKRRKALLKHFGS-LKAIKEASVEELAKV 580 (598)
T ss_pred cccccchhhhhHhhCCCcCHHHHHHHHHHcCC-HHHHHhCCHHHHhhc
Confidence 45555667899999999999999999999983 222344455565444
No 88
>COG2081 Predicted flavoproteins [General function prediction only]
Probab=40.74 E-value=35 Score=31.75 Aligned_cols=50 Identities=12% Similarity=0.169 Sum_probs=40.9
Q ss_pred CeEEeEeeccccccCHHHHHHHHHHcCCCccccCCCCHHHHHHHHHHHhhcc
Q 030930 58 NKRIEYSLQYIHGVGRTRARQILVDLKMENKITKDMSEEELITIRDEVSKYM 109 (169)
Q Consensus 58 ~K~i~~ALt~I~GIG~~~A~~Ic~~lgi~~k~~~~Ls~~el~~L~~~l~~~~ 109 (169)
+|.+..+|.. .++++.+..++.+.+|.+....+|++.|+++|.+.|..|.
T Consensus 285 ~kslkn~L~~--~lp~rlv~~~l~~~~i~~~~~~~ls~~~~~~l~~~ik~~~ 334 (408)
T COG2081 285 KKSLKNALAK--LLPKRLVEFLLERAGIPDEPLAQLSPKELAQLAAALKAWP 334 (408)
T ss_pred hhHHHHHHHH--HhhhHHHHHHHHhccCCCcchhhcCHHHHHHHHHHHhcCe
Confidence 4445555543 5788999999999999777889999999999999998764
No 89
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=40.33 E-value=16 Score=29.82 Aligned_cols=21 Identities=33% Similarity=0.725 Sum_probs=18.9
Q ss_pred eeccccccCHHHHHHHHHHcC
Q 030930 64 SLQYIHGVGRTRARQILVDLK 84 (169)
Q Consensus 64 ALt~I~GIG~~~A~~Ic~~lg 84 (169)
.|++++|||..+|.+|+..+.
T Consensus 109 ~L~~v~Gig~k~A~~I~~~l~ 129 (192)
T PRK00116 109 ALTKVPGIGKKTAERIVLELK 129 (192)
T ss_pred HHHhCCCCCHHHHHHHHHHHH
Confidence 589999999999999997765
No 90
>PRK13910 DNA glycosylase MutY; Provisional
Probab=39.46 E-value=16 Score=32.04 Aligned_cols=21 Identities=33% Similarity=0.309 Sum_probs=19.0
Q ss_pred eEeeccccccCHHHHHHHHHH
Q 030930 62 EYSLQYIHGVGRTRARQILVD 82 (169)
Q Consensus 62 ~~ALt~I~GIG~~~A~~Ic~~ 82 (169)
...|.+++|||+.+|..|+..
T Consensus 71 ~~~L~~LpGIG~kTA~aIl~~ 91 (289)
T PRK13910 71 YQSLLKLPGIGAYTANAILCF 91 (289)
T ss_pred HHHHHhCCCCCHHHHHHHHHH
Confidence 678999999999999999864
No 91
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=39.41 E-value=21 Score=34.20 Aligned_cols=47 Identities=19% Similarity=0.286 Sum_probs=34.0
Q ss_pred cCCCCeEEeEeeccccccCHHHHHHHHHHcCCCccccCCCCHHHHHHH
Q 030930 54 EIPNNKRIEYSLQYIHGVGRTRARQILVDLKMENKITKDMSEEELITI 101 (169)
Q Consensus 54 ni~~~K~i~~ALt~I~GIG~~~A~~Ic~~lgi~~k~~~~Ls~~el~~L 101 (169)
.+-.+..+.-.|..|+|||..+...+++.+|=- +.+..-|.+|+.++
T Consensus 505 ~~r~k~~~~S~Ld~I~GiG~kr~~~Ll~~Fgs~-~~ik~As~eeL~~v 551 (567)
T PRK14667 505 KLREKEGLKDILDKIKGIGEVKKEIIYRNFKTL-YDFLKADDEELKKL 551 (567)
T ss_pred HHhhcccccCccccCCCCCHHHHHHHHHHhCCH-HHHHhCCHHHHHHc
Confidence 344555667889999999999999999999822 22345566666554
No 92
>PRK12311 rpsB 30S ribosomal protein S2/unknown domain fusion protein; Provisional
Probab=39.23 E-value=18 Score=32.43 Aligned_cols=44 Identities=18% Similarity=0.222 Sum_probs=37.2
Q ss_pred eEeeccccccCHHHHHHHHHHcCCC-ccccCCCCHHHHHHHHHHHh
Q 030930 62 EYSLQYIHGVGRTRARQILVDLKME-NKITKDMSEEELITIRDEVS 106 (169)
Q Consensus 62 ~~ALt~I~GIG~~~A~~Ic~~lgi~-~k~~~~Ls~~el~~L~~~l~ 106 (169)
.--|+.|.|||+.... .|..+|+. ...+-.++++|+..+...+.
T Consensus 262 ~DdL~~I~GiGp~~e~-~L~~~Gi~~f~QiA~~t~~~~a~vd~~l~ 306 (326)
T PRK12311 262 PDDLKKLTGVSPQIEK-KLNDLGIFHFWQLAELDPDDAAKIGEELG 306 (326)
T ss_pred chhhhhhccCChhhhh-hhhhcCCCCHHHhhCCChhhhhhhhhccc
Confidence 3568999999998765 57899999 77889999999999988875
No 93
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=39.08 E-value=16 Score=30.95 Aligned_cols=26 Identities=35% Similarity=0.528 Sum_probs=21.2
Q ss_pred cCCCCeEEeEeeccccccCHHHHHHHHHH
Q 030930 54 EIPNNKRIEYSLQYIHGVGRTRARQILVD 82 (169)
Q Consensus 54 ni~~~K~i~~ALt~I~GIG~~~A~~Ic~~ 82 (169)
++|++ ..+|.+.+|||+.+|+.++..
T Consensus 103 ~vP~~---~~eL~~LPGVGrKTAnvVL~~ 128 (211)
T COG0177 103 EVPDT---REELLSLPGVGRKTANVVLSF 128 (211)
T ss_pred CCCch---HHHHHhCCCcchHHHHHHHHh
Confidence 44544 468999999999999999876
No 94
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=38.41 E-value=63 Score=24.26 Aligned_cols=16 Identities=25% Similarity=0.324 Sum_probs=13.3
Q ss_pred CCCHHHHHHHHHHHhh
Q 030930 92 DMSEEELITIRDEVSK 107 (169)
Q Consensus 92 ~Ls~~el~~L~~~l~~ 107 (169)
.||++|-+.|.++|..
T Consensus 2 ~Lt~eE~~~I~~Vl~R 17 (118)
T PF02318_consen 2 HLTEEEREIILQVLQR 17 (118)
T ss_dssp TS-CHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHh
Confidence 6999999999999964
No 95
>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]
Probab=38.24 E-value=33 Score=28.57 Aligned_cols=25 Identities=24% Similarity=0.363 Sum_probs=22.7
Q ss_pred eEeeccccccCHHHHHHHHHHcCCC
Q 030930 62 EYSLQYIHGVGRTRARQILVDLKME 86 (169)
Q Consensus 62 ~~ALt~I~GIG~~~A~~Ic~~lgi~ 86 (169)
..++|..+|+|+++.-..++.+|++
T Consensus 2 ~I~ITGTPGvGKTT~~~~L~~lg~~ 26 (180)
T COG1936 2 LIAITGTPGVGKTTVCKLLRELGYK 26 (180)
T ss_pred eEEEeCCCCCchHHHHHHHHHhCCc
Confidence 3688999999999999999999987
No 96
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=38.11 E-value=24 Score=30.40 Aligned_cols=22 Identities=32% Similarity=0.484 Sum_probs=13.6
Q ss_pred eeccccccCHHHHHHHHHHcCCC
Q 030930 64 SLQYIHGVGRTRARQILVDLKME 86 (169)
Q Consensus 64 ALt~I~GIG~~~A~~Ic~~lgi~ 86 (169)
.|..|.|||...+..+++. |+.
T Consensus 4 ~L~~IpGIG~krakkLl~~-GF~ 25 (232)
T PRK12766 4 ELEDISGVGPSKAEALREA-GFE 25 (232)
T ss_pred ccccCCCcCHHHHHHHHHc-CCC
Confidence 3566677777777666554 444
No 97
>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=37.30 E-value=61 Score=31.76 Aligned_cols=39 Identities=21% Similarity=0.302 Sum_probs=27.8
Q ss_pred cccccCHHHHHHHHHHcCCC-ccc----------cCCCCHHHHHHHHHHH
Q 030930 67 YIHGVGRTRARQILVDLKME-NKI----------TKDMSEEELITIRDEV 105 (169)
Q Consensus 67 ~I~GIG~~~A~~Ic~~lgi~-~k~----------~~~Ls~~el~~L~~~l 105 (169)
.|+|||+.+|..|.+.+|.+ -.. +..++++..+.|.+.+
T Consensus 88 ~~~GIG~~~A~~iv~~fg~~~~~~i~~~~~~L~~v~gi~~~~~~~i~~~~ 137 (720)
T TIGR01448 88 SIKGVGKKLAQRIVKTFGEAAFDVLDDDPEKLLEVPGISKANLEKFVSQW 137 (720)
T ss_pred CCCCcCHHHHHHHHHHhCHhHHHHHHhCHHHHhcCCCCCHHHHHHHHHHH
Confidence 49999999999999999977 211 2346666666665443
No 98
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=37.17 E-value=23 Score=34.08 Aligned_cols=40 Identities=28% Similarity=0.395 Sum_probs=29.9
Q ss_pred EeEeeccccccCHHHHHHHHHHcCCCccccCCCCHHHHHHH
Q 030930 61 IEYSLQYIHGVGRTRARQILVDLKMENKITKDMSEEELITI 101 (169)
Q Consensus 61 i~~ALt~I~GIG~~~A~~Ic~~lgi~~k~~~~Ls~~el~~L 101 (169)
....|..|+|||+.+...+++.+|== +.+..-|.+|+.++
T Consensus 512 ~~s~L~~I~GiG~kr~~~LL~~Fgs~-~~I~~As~eeL~~v 551 (574)
T PRK14670 512 IKLNYTKIKGIGEKKAKKILKSLGTY-KDILLLNEDEIAEK 551 (574)
T ss_pred cccccccCCCCCHHHHHHHHHHhCCH-HHHHhCCHHHHHhC
Confidence 55689999999999999999999822 22345566666554
No 99
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=36.93 E-value=28 Score=33.75 Aligned_cols=50 Identities=20% Similarity=0.296 Sum_probs=36.5
Q ss_pred eCccCCCCeEEeEeeccccccCHHHHHHHHHHcCCCccccCCCCHHHHHHH
Q 030930 51 GGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKMENKITKDMSEEELITI 101 (169)
Q Consensus 51 ~~tni~~~K~i~~ALt~I~GIG~~~A~~Ic~~lgi~~k~~~~Ls~~el~~L 101 (169)
.+-..-..+.+.-.|..|+|||..++..+++.+| +-..+..-+.+|+..+
T Consensus 557 yhr~~r~k~~~~s~L~~I~GIG~k~a~~Ll~~Fg-s~~~i~~As~eeL~~v 606 (621)
T PRK14671 557 YHRKLRSKRTLQTELTDIAGIGEKTAEKLLEHFG-SVEKVAKASLEELAAV 606 (621)
T ss_pred hChhhHHHHHhhhhhhcCCCcCHHHHHHHHHHcC-CHHHHHhCCHHHHHHH
Confidence 5566667777888899999999999999999996 2122233366666554
No 100
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=36.69 E-value=27 Score=33.97 Aligned_cols=46 Identities=17% Similarity=0.248 Sum_probs=32.7
Q ss_pred CCCCeEEeEeeccccccCHHHHHHHHHHcCCCccccCCCCHHHHHHH
Q 030930 55 IPNNKRIEYSLQYIHGVGRTRARQILVDLKMENKITKDMSEEELITI 101 (169)
Q Consensus 55 i~~~K~i~~ALt~I~GIG~~~A~~Ic~~lgi~~k~~~~Ls~~el~~L 101 (169)
+-....+.-.|.+|+|||..++..+++.+|= -+.+..-|.+||.++
T Consensus 544 ~R~k~~~~S~L~~IpGIG~kr~~~LL~~FgS-i~~I~~As~eeL~~v 589 (624)
T PRK14669 544 RRETRDRTSELLEIPGVGAKTVQRLLKHFGS-LERVRAATETQLAAV 589 (624)
T ss_pred HhhHHHHHHHHhcCCCCCHHHHHHHHHHcCC-HHHHHhCCHHHHHHH
Confidence 3344455677899999999999999999982 122355566777554
No 101
>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=36.01 E-value=19 Score=31.55 Aligned_cols=23 Identities=26% Similarity=0.133 Sum_probs=19.8
Q ss_pred EeEeeccccccCHHHHHHHHHHc
Q 030930 61 IEYSLQYIHGVGRTRARQILVDL 83 (169)
Q Consensus 61 i~~ALt~I~GIG~~~A~~Ic~~l 83 (169)
+.-.|+.++|||+.+|..||-..
T Consensus 218 ~~~~L~~l~GIG~~tAd~vll~~ 240 (310)
T TIGR00588 218 AREALCELPGVGPKVADCICLMG 240 (310)
T ss_pred HHHHHHhCCCccHHHHHHHHHHh
Confidence 56789999999999999998553
No 102
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=35.66 E-value=21 Score=31.19 Aligned_cols=23 Identities=22% Similarity=0.225 Sum_probs=19.7
Q ss_pred EEeEeeccccccCHHHHHHHHHH
Q 030930 60 RIEYSLQYIHGVGRTRARQILVD 82 (169)
Q Consensus 60 ~i~~ALt~I~GIG~~~A~~Ic~~ 82 (169)
.+.-.|++|+|||+-+|..++-.
T Consensus 195 ~a~e~L~~i~GIG~WTAe~~llf 217 (285)
T COG0122 195 EAIEELTALKGIGPWTAEMFLLF 217 (285)
T ss_pred HHHHHHHcCCCcCHHHHHHHHHH
Confidence 36778999999999999998854
No 103
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=34.44 E-value=7.5 Score=32.29 Aligned_cols=38 Identities=21% Similarity=0.181 Sum_probs=31.8
Q ss_pred eEEeCccCCCCeEEeEeeccccccCHHHHHHHHHHcCC
Q 030930 48 ARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKM 85 (169)
Q Consensus 48 vrI~~tni~~~K~i~~ALt~I~GIG~~~A~~Ic~~lgi 85 (169)
..++|-.=...+.++.-|.++.|||+.+|..|+..++.
T Consensus 59 ~~LyGF~~~~Er~lF~~Li~V~GIGpK~Al~iLs~~~~ 96 (203)
T PRK14602 59 LELFGFATWDERQTFIVLISISKVGAKTALAILSQFRP 96 (203)
T ss_pred ceeeCCCCHHHHHHHHHHhCCCCcCHHHHHHHHhhCCH
Confidence 46677777778888888999999999999999976653
No 104
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=34.38 E-value=24 Score=33.89 Aligned_cols=40 Identities=20% Similarity=0.331 Sum_probs=29.7
Q ss_pred EeEeeccccccCHHHHHHHHHHcCCCccccCCCCHHHHHHH
Q 030930 61 IEYSLQYIHGVGRTRARQILVDLKMENKITKDMSEEELITI 101 (169)
Q Consensus 61 i~~ALt~I~GIG~~~A~~Ic~~lgi~~k~~~~Ls~~el~~L 101 (169)
...+|..|+|||..++..+++.+| +...+.+-+.+|+..+
T Consensus 523 ~~~~L~~IpGIG~kr~~~LL~~FG-S~~~I~~As~eeL~~v 562 (577)
T PRK14668 523 VSTVLDDVPGVGPETRKRLLRRFG-SVEGVREASVEDLRDV 562 (577)
T ss_pred HHhHHhcCCCCCHHHHHHHHHHcC-CHHHHHhCCHHHHHhC
Confidence 568999999999999999999997 2223345556666444
No 105
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=33.56 E-value=89 Score=20.24 Aligned_cols=42 Identities=14% Similarity=0.109 Sum_probs=31.3
Q ss_pred eccccccCHHHHHHHHHHcCCC-ccc----cCCCCHHHHHHHHHHHh
Q 030930 65 LQYIHGVGRTRARQILVDLKME-NKI----TKDMSEEELITIRDEVS 106 (169)
Q Consensus 65 Lt~I~GIG~~~A~~Ic~~lgi~-~k~----~~~Ls~~el~~L~~~l~ 106 (169)
+.+..||...+.....+..|+. +.+ ....+++|+..|..+..
T Consensus 6 va~~~gvs~~tlr~w~~~~g~~~~~r~~~~~r~yt~~~v~~l~~i~~ 52 (68)
T cd01104 6 VARLTGVSPDTLRAWERRYGLPAPQRTDGGHRLYSEADVARLRLIRR 52 (68)
T ss_pred HHHHHCcCHHHHHHHHHhCCCCCCCcCCCCCeecCHHHHHHHHHHHH
Confidence 3467889999999888877886 433 24788999988877653
No 106
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=33.01 E-value=6 Score=32.60 Aligned_cols=37 Identities=19% Similarity=0.225 Sum_probs=31.4
Q ss_pred eEEeCccCCCCeEEeEeeccccccCHHHHHHHHHHcC
Q 030930 48 ARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLK 84 (169)
Q Consensus 48 vrI~~tni~~~K~i~~ALt~I~GIG~~~A~~Ic~~lg 84 (169)
..++|-.=...+.++.-|.++.|||+++|..|+..++
T Consensus 58 ~~LyGF~~~~Er~lF~~Li~V~GIGpK~AL~iLs~~~ 94 (188)
T PRK14606 58 ITLYGFSNERKKELFLSLTKVSRLGPKTALKIISNED 94 (188)
T ss_pred ceeeCCCCHHHHHHHHHHhccCCccHHHHHHHHcCCC
Confidence 4667777778888899999999999999999996554
No 107
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=32.84 E-value=8.8 Score=31.57 Aligned_cols=37 Identities=16% Similarity=0.256 Sum_probs=31.4
Q ss_pred eEEeCccCCCCeEEeEeeccccccCHHHHHHHHHHcC
Q 030930 48 ARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLK 84 (169)
Q Consensus 48 vrI~~tni~~~K~i~~ALt~I~GIG~~~A~~Ic~~lg 84 (169)
..++|-.=...+.++.-|.++.|||+++|..|+..+.
T Consensus 58 ~~LyGF~~~~Er~lF~~Li~VsGIGpK~Al~ILs~~~ 94 (183)
T PRK14601 58 NKLYGFLDKDEQKMFEMLLKVNGIGANTAMAVCSSLD 94 (183)
T ss_pred ceeeCCCCHHHHHHHHHHhccCCccHHHHHHHHcCCC
Confidence 4677877788888999999999999999999995543
No 108
>cd01199 INT_Tn1545_C Tn1545-related conjugative transposon integrases, site-specific recombinases, DNA breaking-rejoining enzymes, C-terminal catalytic domain. This CD includes bacterial (gram positive) and phage integrases, including those similar to Tn1545, Tn5252, and Tn5276 conjugative transposon integrases and Lactobacillus phage phi adh integrase.
Probab=31.67 E-value=69 Score=24.37 Aligned_cols=16 Identities=25% Similarity=0.526 Sum_probs=13.7
Q ss_pred CCHHHHHHHHHHHhhc
Q 030930 93 MSEEELITIRDEVSKY 108 (169)
Q Consensus 93 Ls~~el~~L~~~l~~~ 108 (169)
||++|+..|.+.+..+
T Consensus 2 lt~ee~~~l~~~~~~~ 17 (205)
T cd01199 2 LEKNELKALLDVLNSY 17 (205)
T ss_pred CCHHHHHHHHHHHHhc
Confidence 7899999999988654
No 109
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=30.98 E-value=10 Score=31.17 Aligned_cols=38 Identities=21% Similarity=0.159 Sum_probs=31.9
Q ss_pred eEEeCccCCCCeEEeEeeccccccCHHHHHHHHHHcCC
Q 030930 48 ARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKM 85 (169)
Q Consensus 48 vrI~~tni~~~K~i~~ALt~I~GIG~~~A~~Ic~~lgi 85 (169)
..++|-.=+..+.++.-|.++.|||+.+|..|+..++.
T Consensus 58 ~~LyGF~~~~Er~lF~~LisV~GIGpK~Al~iLs~~~~ 95 (186)
T PRK14600 58 TQLYGFLNREEQDCLRMLVKVSGVNYKTAMSILSKLTP 95 (186)
T ss_pred ceeeCCCCHHHHHHHHHHhCcCCcCHHHHHHHHccCCH
Confidence 35677777888888999999999999999999976543
No 110
>PF14842 FliG_N: FliG N-terminal domain; PDB: 3HJL_A 3AJC_A 3USY_B.
Probab=30.83 E-value=71 Score=23.59 Aligned_cols=37 Identities=32% Similarity=0.478 Sum_probs=25.9
Q ss_pred CHHHHHHHHHHcCCC-c-cccCCCCHHHHHHHHHHHhhc
Q 030930 72 GRTRARQILVDLKME-N-KITKDMSEEELITIRDEVSKY 108 (169)
Q Consensus 72 G~~~A~~Ic~~lgi~-~-k~~~~Ls~~el~~L~~~l~~~ 108 (169)
|...|-.++-.+|-+ . +..+.|+++|+++|...+.+.
T Consensus 7 g~~KAAilLl~Lgee~Aa~vlk~l~~~ei~~i~~~ma~l 45 (108)
T PF14842_consen 7 GIQKAAILLLALGEEAAAEVLKHLDEEEIERISREMAKL 45 (108)
T ss_dssp HHHHHHHHHHHS-HHHHHHHHHHS-HHHHHHHHHHHHT-
T ss_pred HHHHHHHHHHHHCHHHHHHHHccCCHHHHHHHHHHHHcc
Confidence 456677788888877 3 345889999999998888753
No 111
>PRK12278 50S ribosomal protein L21/unknown domain fusion protein; Provisional
Probab=30.60 E-value=42 Score=28.58 Aligned_cols=43 Identities=21% Similarity=0.346 Sum_probs=36.6
Q ss_pred EeeccccccCHHHHHHHHHHcCCC-ccccCCCCHHHHHHHHHHHh
Q 030930 63 YSLQYIHGVGRTRARQILVDLKME-NKITKDMSEEELITIRDEVS 106 (169)
Q Consensus 63 ~ALt~I~GIG~~~A~~Ic~~lgi~-~k~~~~Ls~~el~~L~~~l~ 106 (169)
-.|+.|.|||...+.. +..+|++ ...+-.++++++..+...+.
T Consensus 158 DDL~~I~GIGp~~a~~-L~eaGi~tfaQIAa~t~a~ia~id~~l~ 201 (221)
T PRK12278 158 DDLTKITGVGPALAKK-LNEAGVTTFAQIAALTDADIAKIDEKLS 201 (221)
T ss_pred chheeccccChHHHHH-HHHcCCCCHHHhhCCChhhhhhhhhccc
Confidence 4589999999998876 5789999 77889999999999988874
No 112
>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].
Probab=30.57 E-value=50 Score=22.08 Aligned_cols=19 Identities=21% Similarity=0.139 Sum_probs=17.6
Q ss_pred ccccCHHHHHHHHHHcCCC
Q 030930 68 IHGVGRTRARQILVDLKME 86 (169)
Q Consensus 68 I~GIG~~~A~~Ic~~lgi~ 86 (169)
--||+.+.-+.+|+++||.
T Consensus 24 ~Lgv~~T~LKr~CR~~GI~ 42 (52)
T PF02042_consen 24 ELGVSVTTLKRRCRRLGIP 42 (52)
T ss_pred HhCCCHHHHHHHHHHcCCC
Confidence 4699999999999999998
No 113
>PF11338 DUF3140: Protein of unknown function (DUF3140); InterPro: IPR021487 Some members in this family of proteins are annotated as DNA binding proteins. No function is currently known.
Probab=30.28 E-value=65 Score=24.05 Aligned_cols=33 Identities=27% Similarity=0.491 Sum_probs=27.4
Q ss_pred cCHHHHHHHHHHcCCCccccCCCCHHHHHHHHHHHh
Q 030930 71 VGRTRARQILVDLKMENKITKDMSEEELITIRDEVS 106 (169)
Q Consensus 71 IG~~~A~~Ic~~lgi~~k~~~~Ls~~el~~L~~~l~ 106 (169)
+|......|+..|+ ++..+||+++++.+++++.
T Consensus 35 ~Gh~sGRrIv~IL~---K~k~dltddD~~hMrkVV~ 67 (92)
T PF11338_consen 35 VGHESGRRIVEILR---KRKTDLTDDDYEHMRKVVG 67 (92)
T ss_pred cCcchhhHHHHHHh---cCcccCCHHHHHHHHHHHH
Confidence 56777788888887 7789999999999988774
No 114
>PF06514 PsbU: Photosystem II 12 kDa extrinsic protein (PsbU); InterPro: IPR010527 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. In PSII, the oxygen-evolving complex (OEC) is responsible for catalysing the splitting of water to O(2) and 4H+. The OEC is composed of a cluster of manganese, calcium and chloride ions bound to extrinsic proteins. In cyanobacteria there are five extrinsic proteins in OEC (PsbO, PsbP-like, PsbQ-like, PsbU and PsbV), while in plants there are only three (PsbO, PsbP and PsbQ), PsbU and PsbV having been lost during the evolution of green plants []. This family represents the PSII extrinsic protein PsbU, which forms part of the OEC in cyanobacteria and red algae. PsbU acts to stabilise the oxygen-evolving machinery of PSII against heat-induced inactivation, which is crucial for cellular thermo-tolerance [].; GO: 0015979 photosynthesis, 0042549 photosystem II stabilization, 0009523 photosystem II, 0009654 oxygen evolving complex, 0019898 extrinsic to membrane; PDB: 3BZ1_U 3KZI_U 3PRQ_U 2AXT_u 3BZ2_U 4FBY_U 3PRR_U 1S5L_U 3A0H_U 3ARC_U ....
Probab=29.92 E-value=29 Score=26.04 Aligned_cols=59 Identities=15% Similarity=0.227 Sum_probs=41.7
Q ss_pred CccCCCCeEEeEeeccccccCHHHHHHHHHHcCCC--ccc--cCCCCHHHHHHHHHHHhhccc
Q 030930 52 GVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKME--NKI--TKDMSEEELITIRDEVSKYMI 110 (169)
Q Consensus 52 ~tni~~~K~i~~ALt~I~GIG~~~A~~Ic~~lgi~--~k~--~~~Ls~~el~~L~~~l~~~~I 110 (169)
|..||-|..-..+.++.+|.=+..|..|+.-.=.+ ... +..||+.|-+.|..+.++|.+
T Consensus 12 G~KIDlNNa~vr~f~~~pGmYPtlA~kIv~naPY~sveDvl~ipgLse~qK~~lk~~~~~Ftv 74 (93)
T PF06514_consen 12 GQKIDLNNANVRAFRQFPGMYPTLAGKIVSNAPYKSVEDVLNIPGLSERQKALLKKYEDNFTV 74 (93)
T ss_dssp CTCEETTSS-GGGGCCSTTTTCCHHHHHHHS---SSGGGGCCSTT--HHHHHHHHHHGGGEE-
T ss_pred CCceecccHhHHHHHHCCCCCHHHHHHHHhCCCCCCHHHHHhccCCCHHHHHHHHHHhcccee
Confidence 34455555556788999999999999999988776 232 478999999999999998865
No 115
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=28.90 E-value=12 Score=31.37 Aligned_cols=37 Identities=19% Similarity=0.284 Sum_probs=31.3
Q ss_pred eEEeCccCCCCeEEeEeeccccccCHHHHHHHHHHcC
Q 030930 48 ARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLK 84 (169)
Q Consensus 48 vrI~~tni~~~K~i~~ALt~I~GIG~~~A~~Ic~~lg 84 (169)
+.++|-.=...+.++.-|.++.|||+++|..|+..++
T Consensus 57 ~~LYGF~t~~Er~lF~~LisVsGIGPK~ALaILs~~~ 93 (196)
T PRK13901 57 LKLFGFLNSSEREVFEELIGVDGIGPRAALRVLSGIK 93 (196)
T ss_pred ceeeCCCCHHHHHHHHHHhCcCCcCHHHHHHHHcCCC
Confidence 4667777788888999999999999999999996544
No 116
>KOG0437 consensus Leucyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=28.73 E-value=66 Score=32.84 Aligned_cols=61 Identities=23% Similarity=0.412 Sum_probs=41.0
Q ss_pred CCCccccccCCCCCCCCcccceeEEeCccCCCCeEEeEeec------------cccccCHHHHHHHHHHcCCC-ccccCC
Q 030930 26 TNASLSFPVSKQPQYPGLSIQCARVGGVEIPNNKRIEYSLQ------------YIHGVGRTRARQILVDLKME-NKITKD 92 (169)
Q Consensus 26 ~~~~~~~~~~~~~~f~~i~~~~vrI~~tni~~~K~i~~ALt------------~I~GIG~~~A~~Ic~~lgi~-~k~~~~ 92 (169)
+--..|+|...|+.|..+ .+|.....+ ++|+ .|.|.|.-.|..||..+.|. ++-...
T Consensus 387 TGvVtsVpsdsPDDf~al---------~dL~kK~~l-Yg~~~ew~~~E~vPii~~~~fGdl~ae~vc~~lKiqs~~dk~k 456 (1080)
T KOG0437|consen 387 TGVVTSVPSDSPDDFAAL---------QDLKKKPEL-YGLKPEWVLFEIVPIIRIPGFGDLAAEVVCDELKIQSPNDKKK 456 (1080)
T ss_pred ceeEEeCCCCCchhhhHH---------Hhhhhcccc-cCCChhhccccccceeeccccchhhHHHHHHHHhccCchhHHH
Confidence 334567777777766654 444444333 4544 79999999999999999999 444444
Q ss_pred CCHH
Q 030930 93 MSEE 96 (169)
Q Consensus 93 Ls~~ 96 (169)
|-|.
T Consensus 457 laea 460 (1080)
T KOG0437|consen 457 LAEA 460 (1080)
T ss_pred HHHh
Confidence 4443
No 117
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=28.67 E-value=11 Score=31.13 Aligned_cols=37 Identities=22% Similarity=0.161 Sum_probs=30.7
Q ss_pred eEEeCccCCCCeEEeEeeccccccCHHHHHHHHHHcC
Q 030930 48 ARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLK 84 (169)
Q Consensus 48 vrI~~tni~~~K~i~~ALt~I~GIG~~~A~~Ic~~lg 84 (169)
..++|-.=...+.++.-|.++.|||+++|..|+..++
T Consensus 57 ~~LyGF~~~~Er~lF~~L~~V~GIGpK~AL~iLs~~~ 93 (197)
T PRK14603 57 LSLYGFPDEDSLELFELLLGVSGVGPKLALALLSALP 93 (197)
T ss_pred ceeeCcCCHHHHHHHHHHhCcCCcCHHHHHHHHcCCC
Confidence 4667777778888888999999999999999985443
No 118
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=26.61 E-value=40 Score=24.22 Aligned_cols=24 Identities=38% Similarity=0.585 Sum_probs=18.9
Q ss_pred Eeecc-ccccCHHHHHHHHHHcCCC
Q 030930 63 YSLQY-IHGVGRTRARQILVDLKME 86 (169)
Q Consensus 63 ~ALt~-I~GIG~~~A~~Ic~~lgi~ 86 (169)
|-|.. |.|||-.+|-.|..++|++
T Consensus 45 Y~L~~~i~gi~F~~aD~iA~~~g~~ 69 (94)
T PF14490_consen 45 YRLIEDIDGIGFKTADKIALKLGIE 69 (94)
T ss_dssp TCCCB-SSSSBHHHHHHHHHTTT--
T ss_pred HHHHHHccCCCHHHHHHHHHHcCCC
Confidence 44544 9999999999999999987
No 119
>PF14794 DUF4479: Domain of unknown function (DUF4479); PDB: 3BU2_C.
Probab=25.55 E-value=60 Score=22.93 Aligned_cols=18 Identities=17% Similarity=0.281 Sum_probs=12.6
Q ss_pred CCCCHHHHHHHHHHHhhc
Q 030930 91 KDMSEEELITIRDEVSKY 108 (169)
Q Consensus 91 ~~Ls~~el~~L~~~l~~~ 108 (169)
=.||+++++.|.+.|.+-
T Consensus 46 V~Lt~eqv~~LN~~l~~~ 63 (73)
T PF14794_consen 46 VFLTEEQVAKLNQALQKA 63 (73)
T ss_dssp ----HHHHHHHHHHHHHT
T ss_pred EEcCHHHHHHHHHHHHHc
Confidence 579999999999999863
No 120
>PF03677 UPF0137: Uncharacterised protein family (UPF0137); InterPro: IPR005350 This family of bacterial proteins includes a number of plasmid-encoded virulence proteins.
Probab=25.49 E-value=1e+02 Score=26.78 Aligned_cols=23 Identities=17% Similarity=0.315 Sum_probs=20.1
Q ss_pred CCCCHHHHHHHHHHHhhcccchH
Q 030930 91 KDMSEEELITIRDEVSKYMIEGD 113 (169)
Q Consensus 91 ~~Ls~~el~~L~~~l~~~~Ie~d 113 (169)
-+|+++|-++|.+.+++|.++++
T Consensus 35 ~~Ls~~E~~~le~Ll~~y~~~d~ 57 (243)
T PF03677_consen 35 ISLSSKEKQRLENLLEKYNFSDE 57 (243)
T ss_pred ccCCHHHHHHHHHHHHhcCCccc
Confidence 56999999999999999887765
No 121
>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=25.47 E-value=57 Score=31.80 Aligned_cols=36 Identities=17% Similarity=0.249 Sum_probs=27.7
Q ss_pred ccccccCHHHHHHHHHHcCCC-ccccCCCCHHHHHHH
Q 030930 66 QYIHGVGRTRARQILVDLKME-NKITKDMSEEELITI 101 (169)
Q Consensus 66 t~I~GIG~~~A~~Ic~~lgi~-~k~~~~Ls~~el~~L 101 (169)
-.|.|+|..++.++.+..+|. ..-.-.|+++++..|
T Consensus 435 l~I~GLG~k~i~~L~~~g~I~~~~Dl~~L~~~~L~~L 471 (652)
T TIGR00575 435 MDIEGLGDKVIEQLFEKKLVRSVADLYALKKEDLLEL 471 (652)
T ss_pred cCCCCcCHHHHHHHHHcCCcCCHHHHHhcCHHHHhhc
Confidence 369999999999999999887 333347777766655
No 122
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=25.20 E-value=64 Score=25.51 Aligned_cols=78 Identities=17% Similarity=0.221 Sum_probs=49.0
Q ss_pred eeccccccCHHHHHHHHHHcC---CC--cc----ccCCCCHHHHHHHHHHHhhcccchHHHHH-HHHHHHHHH--hhhhc
Q 030930 64 SLQYIHGVGRTRARQILVDLK---ME--NK----ITKDMSEEELITIRDEVSKYMIEGDLRRF-NALAIRRLK--EIQCY 131 (169)
Q Consensus 64 ALt~I~GIG~~~A~~Ic~~lg---i~--~k----~~~~Ls~~el~~L~~~l~~~~Ie~dLr~~-~~~nI~rL~--~I~sY 131 (169)
...+++|+|..++..-..+.. .+ +. +...|+++|++.|.+.+..-. -.|+.. .....++-+ ..+++
T Consensus 26 e~Ak~~gvs~sTvy~wv~r~~e~G~~l~~~~~~GrP~kl~~~q~~~l~e~~~~k~--wTl~~~~~~l~~e~gv~y~~~~v 103 (138)
T COG3415 26 EAAKRFGVSISTVYRWVRRYRETGLDLPPKPRKGRPRKLSEEQLEILLERLREKD--WTLKELVEELGLEFGVWYHASAV 103 (138)
T ss_pred HHHHHhCccHHHHHHHHHHhccccccccCccCCCCCcccCHHHHHHHHHHHhccc--chHHHHHHHHhhhcCeEEeHHHH
Confidence 356889999999999998876 22 22 258999999999999986411 222211 000111222 22356
Q ss_pred ccCccCCCCccC
Q 030930 132 RGIRHIQGLPCR 143 (169)
Q Consensus 132 RG~RH~~GLPVR 143 (169)
+=+.|..||+-.
T Consensus 104 ~~~l~~~Glsyk 115 (138)
T COG3415 104 RRLLHELGLSYK 115 (138)
T ss_pred HHHHHHcCCCcC
Confidence 667788888765
No 123
>PRK05755 DNA polymerase I; Provisional
Probab=25.17 E-value=1.8e+02 Score=29.11 Aligned_cols=20 Identities=20% Similarity=0.458 Sum_probs=17.6
Q ss_pred eccccccCHHHHHHHHHHcC
Q 030930 65 LQYIHGVGRTRARQILVDLK 84 (169)
Q Consensus 65 Lt~I~GIG~~~A~~Ic~~lg 84 (169)
+..|+|||..+|..++++.|
T Consensus 189 ipGv~GiG~ktA~~Ll~~~g 208 (880)
T PRK05755 189 IPGVPGIGEKTAAKLLQEYG 208 (880)
T ss_pred CCCCCCccHHHHHHHHHHcC
Confidence 45689999999999999988
No 124
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=24.77 E-value=20 Score=30.56 Aligned_cols=32 Identities=25% Similarity=0.336 Sum_probs=24.6
Q ss_pred ccCCCCeEE--eEeeccccccCHHHHHHHHHHcC
Q 030930 53 VEIPNNKRI--EYSLQYIHGVGRTRARQILVDLK 84 (169)
Q Consensus 53 tni~~~K~i--~~ALt~I~GIG~~~A~~Ic~~lg 84 (169)
.++++.++. +--|-+|+|||.-+|..|+--+.
T Consensus 103 ~~~~~~~~~~~R~~LL~iKGIG~ETaDsILlYa~ 136 (215)
T COG2231 103 INLESFKSEVLREELLSIKGIGKETADSILLYAL 136 (215)
T ss_pred hhhhccchHHHHHHHHccCCcchhhHHHHHHHHh
Confidence 355666665 67789999999999999886544
No 125
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=24.63 E-value=1.3e+02 Score=27.61 Aligned_cols=25 Identities=20% Similarity=0.198 Sum_probs=20.1
Q ss_pred eEeeccccccCHHHHHHHHHHcCCC
Q 030930 62 EYSLQYIHGVGRTRARQILVDLKME 86 (169)
Q Consensus 62 ~~ALt~I~GIG~~~A~~Ic~~lgi~ 86 (169)
.--+.+++|||...|..|-..|.=.
T Consensus 55 ~~ea~~lP~iG~kia~ki~EiletG 79 (353)
T KOG2534|consen 55 GEEAEKLPGIGPKIAEKIQEILETG 79 (353)
T ss_pred HHHhcCCCCCCHHHHHHHHHHHHcC
Confidence 3346779999999999999888744
No 126
>PF04001 Vhr1: Transcription factor Vhr1; InterPro: IPR007147 This is a family of proteins of unknown function found in yeast.
Probab=24.01 E-value=67 Score=24.08 Aligned_cols=11 Identities=18% Similarity=0.314 Sum_probs=5.9
Q ss_pred HHHHHHHcCCC
Q 030930 76 ARQILVDLKME 86 (169)
Q Consensus 76 A~~Ic~~lgi~ 86 (169)
.+.|-++|++.
T Consensus 9 Th~IR~~LnF~ 19 (95)
T PF04001_consen 9 THKIREQLNFH 19 (95)
T ss_pred hHHHHHHhCCc
Confidence 34555555555
No 127
>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=23.73 E-value=8.7 Score=28.74 Aligned_cols=19 Identities=21% Similarity=0.410 Sum_probs=15.5
Q ss_pred ccccccCHHHHHHHHHHcC
Q 030930 66 QYIHGVGRTRARQILVDLK 84 (169)
Q Consensus 66 t~I~GIG~~~A~~Ic~~lg 84 (169)
-.|+|||..+|..++.++|
T Consensus 21 PGV~GIG~KtA~~LL~~yg 39 (101)
T PF01367_consen 21 PGVPGIGPKTAAKLLQEYG 39 (101)
T ss_dssp ---TTSTCHCCCCCHHHHT
T ss_pred CCCCCCCHHHHHHHHHHcC
Confidence 4689999999999999998
No 128
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=23.50 E-value=16 Score=30.21 Aligned_cols=36 Identities=22% Similarity=0.261 Sum_probs=29.7
Q ss_pred eEEeCccCCCCeEEeEeeccccccCHHHHHHHHHHc
Q 030930 48 ARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDL 83 (169)
Q Consensus 48 vrI~~tni~~~K~i~~ALt~I~GIG~~~A~~Ic~~l 83 (169)
..++|-.=...+.++.-|.++.|||+++|..|+..+
T Consensus 58 ~~LyGF~~~~Er~lF~~Li~V~GIGpK~Al~iLs~~ 93 (195)
T PRK14604 58 LTLYGFSTPAQRQLFELLIGVSGVGPKAALNLLSSG 93 (195)
T ss_pred ceeeCCCCHHHHHHHHHHhCcCCcCHHHHHHHHcCC
Confidence 456777777778888889999999999999999654
No 129
>cd01702 PolY_Pol_eta DNA Polymerase eta. Pol eta, also called Rad30A, 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. Unlike other Y-family members, Pol eta can efficiently and accurately replicate DNA past UV-induced lesions. Its activity is initiated by two simultaneous interactions: the PIP box in pol eta interacting with PCNA, and the UBZ (ubiquitin-binding zinc finger) in pol eta interacting with monoubiquitin attached to PCNA. Pol eta is more efficient in copying damaged DNA than undamaged DNA and seems to recognize when a lesion has been passed, facilitating a lesion-dependent dissociation from the DNA.
Probab=23.39 E-value=60 Score=28.98 Aligned_cols=38 Identities=21% Similarity=0.312 Sum_probs=28.2
Q ss_pred EeeccccccCHHHHHHHHHHcCCCcc-ccCCC--CHHHHHH
Q 030930 63 YSLQYIHGVGRTRARQILVDLKMENK-ITKDM--SEEELIT 100 (169)
Q Consensus 63 ~ALt~I~GIG~~~A~~Ic~~lgi~~k-~~~~L--s~~el~~ 100 (169)
.-+..++|||..++..++..+||.+- -+-.+ +.+++.+
T Consensus 182 lpv~~l~GiG~~~~~~ll~~~Gi~ti~dl~~~~~~~~~L~~ 222 (359)
T cd01702 182 LPITSIRGLGGKLGEEIIDLLGLPTEGDVAGFRSSESDLQE 222 (359)
T ss_pred CcHHHhCCcCHHHHHHHHHHcCCcCHHHHHhccCCHHHHHH
Confidence 35789999999999999999999842 23344 5665554
No 130
>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=22.67 E-value=55 Score=31.46 Aligned_cols=30 Identities=23% Similarity=0.318 Sum_probs=24.6
Q ss_pred CCCCeEEeEeeccccccCHHHHHHHHHHcC
Q 030930 55 IPNNKRIEYSLQYIHGVGRTRARQILVDLK 84 (169)
Q Consensus 55 i~~~K~i~~ALt~I~GIG~~~A~~Ic~~lg 84 (169)
+-....+.-.|..|+|||+.+...+++.+|
T Consensus 533 ~r~k~~~~S~Ld~I~GIG~kr~~~LL~~Fg 562 (574)
T TIGR00194 533 KRLKASLQSPLLKIPGVGEKRVQKLLKYFG 562 (574)
T ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHHHHcC
Confidence 334444567889999999999999999988
No 131
>PF14635 HHH_7: Helix-hairpin-helix motif ; PDB: 3PSI_A 3PSF_A.
Probab=22.60 E-value=66 Score=24.34 Aligned_cols=27 Identities=30% Similarity=0.573 Sum_probs=19.9
Q ss_pred CeEEeEeeccccccCHHHHHHHHHHcC
Q 030930 58 NKRIEYSLQYIHGVGRTRARQILVDLK 84 (169)
Q Consensus 58 ~K~i~~ALt~I~GIG~~~A~~Ic~~lg 84 (169)
+......|+.|-|.|++.|..+.+.+.
T Consensus 45 ~~~~~~~LqfV~GLGPRKA~~Ll~~l~ 71 (104)
T PF14635_consen 45 HPHLANLLQFVCGLGPRKAQALLKALK 71 (104)
T ss_dssp -HHHHGGGGGSTT--HHHHHHHHHHHH
T ss_pred ChHHHhhHhHhcCCChHHHHHHHHHHH
Confidence 334466789999999999999998775
No 132
>PTZ00338 dimethyladenosine transferase-like protein; Provisional
Probab=22.60 E-value=95 Score=27.04 Aligned_cols=33 Identities=18% Similarity=0.192 Sum_probs=28.0
Q ss_pred HHHHHHHHcCCCccccCCCCHHHHHHHHHHHhh
Q 030930 75 RARQILVDLKMENKITKDMSEEELITIRDEVSK 107 (169)
Q Consensus 75 ~A~~Ic~~lgi~~k~~~~Ls~~el~~L~~~l~~ 107 (169)
....++..+|+++.++.+|+-+|+-.|...+.+
T Consensus 256 ~~~~~l~~~~~~~~R~e~l~~~~f~~L~~~~~~ 288 (294)
T PTZ00338 256 FIAEILEDSGMFEKRSVKLDIDDFLKLLLAFNK 288 (294)
T ss_pred HHHHHHHHcCCcccChhhCCHHHHHHHHHHHHH
Confidence 344678999999888999999999999888865
No 133
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=22.32 E-value=1.1e+02 Score=23.27 Aligned_cols=41 Identities=17% Similarity=0.208 Sum_probs=29.7
Q ss_pred eccccccCHHHHHHHHHHcCCC-ccccCCCCHHHHHHHHHHHh
Q 030930 65 LQYIHGVGRTRARQILVDLKME-NKITKDMSEEELITIRDEVS 106 (169)
Q Consensus 65 Lt~I~GIG~~~A~~Ic~~lgi~-~k~~~~Ls~~el~~L~~~l~ 106 (169)
|..|.|||..+|. ++..+||+ -....+.+.+++..-...++
T Consensus 55 L~ri~gi~~~~a~-LL~~AGv~Tv~~LA~~~p~~L~~~l~~~n 96 (122)
T PF14229_consen 55 LMRIPGIGPQYAE-LLEHAGVDTVEELAQRNPQNLHQKLGRLN 96 (122)
T ss_pred hhhcCCCCHHHHH-HHHHhCcCcHHHHHhCCHHHHHHHHHHHH
Confidence 4589999999986 56789998 44556677777666555543
No 134
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=22.08 E-value=81 Score=30.87 Aligned_cols=36 Identities=17% Similarity=0.240 Sum_probs=27.5
Q ss_pred ccccccCHHHHHHHHHHcCCC-ccccCCCCHHHHHHH
Q 030930 66 QYIHGVGRTRARQILVDLKME-NKITKDMSEEELITI 101 (169)
Q Consensus 66 t~I~GIG~~~A~~Ic~~lgi~-~k~~~~Ls~~el~~L 101 (169)
-.|.|+|..++.++.+..+|. ..-.-.|+++++..|
T Consensus 448 l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l 484 (665)
T PRK07956 448 MDIDGLGEKIIEQLFEKGLIHDPADLFKLTAEDLLGL 484 (665)
T ss_pred cCCCCcCHHHHHHHHHcCCCCCHHHHHhcCHHHHhcC
Confidence 479999999999999999987 322347777666554
No 135
>PF00034 Cytochrom_C: Cytochrome c; InterPro: IPR003088 Cytochromes c (cytC) can be defined as electron-transfer proteins having one or several haem c groups, bound to the protein by one or, more generally, two thioether bonds involving sulphydryl groups of cysteine residues. The fifth haem iron ligand is always provided by a histidine residue. CytC possess a wide range of properties and function in a large number of different redox processes. Ambler [] recognised four classes of cytC. Class I includes the low-spin soluble cytC of mitochondria and bacteria, with the haem-attachment site towards the N terminus, and the sixth ligand provided by a methionine residue about 40 residues further on towards the C terminus. On the basis of sequence similarity, class I cytC were further subdivided into five classes, IA to IE. Class IB includes the eukaryotic mitochondrial cytC and prokaryotic 'short' cyt c2 exemplified by Rhodopila globiformis cyt c2; class IA includes 'long' cyt c2, such as Rhodospirillum rubrum cyt c2 and Aquaspirillum itersonii cyt c-550, which have several extra loops by comparison with class IB cytC.; GO: 0005506 iron ion binding, 0009055 electron carrier activity, 0020037 heme binding; PDB: 1YNR_B 2AI5_A 1AYG_A 3O5C_C 1YEA_A 3CXH_W 1YTC_A 1YEB_A 2YBB_Y 2B4Z_A ....
Probab=22.03 E-value=92 Score=20.08 Aligned_cols=16 Identities=19% Similarity=0.293 Sum_probs=14.2
Q ss_pred CCCHHHHHHHHHHHhh
Q 030930 92 DMSEEELITIRDEVSK 107 (169)
Q Consensus 92 ~Ls~~el~~L~~~l~~ 107 (169)
.||++|+..|..+|..
T Consensus 74 ~ls~~e~~~l~ayl~s 89 (91)
T PF00034_consen 74 ILSDEEIADLAAYLRS 89 (91)
T ss_dssp TSSHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHH
Confidence 7999999999999864
No 136
>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=21.94 E-value=66 Score=27.78 Aligned_cols=19 Identities=21% Similarity=0.366 Sum_probs=17.4
Q ss_pred ccccccCHHHHHHHHHHcC
Q 030930 66 QYIHGVGRTRARQILVDLK 84 (169)
Q Consensus 66 t~I~GIG~~~A~~Ic~~lg 84 (169)
..|+|||..+|..++++.|
T Consensus 226 ~gv~giG~k~A~~li~~~~ 244 (316)
T cd00128 226 EGIPGIGPVTALKLIKKYG 244 (316)
T ss_pred CCCCCccHHHHHHHHHHcC
Confidence 3689999999999999988
No 137
>PF11460 DUF3007: Protein of unknown function (DUF3007); InterPro: IPR021562 This is a family of uncharacterised proteins found in bacteria and eukaryotes.
Probab=21.91 E-value=51 Score=25.20 Aligned_cols=19 Identities=32% Similarity=0.490 Sum_probs=14.2
Q ss_pred cccCCCCHHHHHHHHHHHh
Q 030930 88 KITKDMSEEELITIRDEVS 106 (169)
Q Consensus 88 k~~~~Ls~~el~~L~~~l~ 106 (169)
++..+||+||+++|...|+
T Consensus 85 kRle~l~~eE~~~L~~eie 103 (104)
T PF11460_consen 85 KRLEELSPEELEALQAEIE 103 (104)
T ss_pred HHHHhCCHHHHHHHHHHhc
Confidence 4567888888888877664
No 138
>PF13442 Cytochrome_CBB3: Cytochrome C oxidase, cbb3-type, subunit III ; PDB: 1KB0_A 2DGE_D 2CE1_A 2CE0_A 2V07_A 1W2L_A 2ZOO_A 2ZBO_G 1DVV_A 2EXV_A ....
Probab=21.79 E-value=84 Score=20.40 Aligned_cols=16 Identities=19% Similarity=0.347 Sum_probs=13.7
Q ss_pred cCCCCHHHHHHHHHHH
Q 030930 90 TKDMSEEELITIRDEV 105 (169)
Q Consensus 90 ~~~Ls~~el~~L~~~l 105 (169)
.+.||++|+..|..+|
T Consensus 52 ~~~ls~~e~~~l~~yi 67 (67)
T PF13442_consen 52 GGQLSDEEIEALAAYI 67 (67)
T ss_dssp TTTSTHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHC
Confidence 4589999999998875
No 139
>PRK05898 dnaE DNA polymerase III DnaE; Validated
Probab=21.55 E-value=83 Score=32.38 Aligned_cols=25 Identities=20% Similarity=0.395 Sum_probs=22.5
Q ss_pred CeEEeEeeccccccCHHHHHHHHHH
Q 030930 58 NKRIEYSLQYIHGVGRTRARQILVD 82 (169)
Q Consensus 58 ~K~i~~ALt~I~GIG~~~A~~Ic~~ 82 (169)
+..|.++|+.|+|||...+..|.+.
T Consensus 747 ~~~Ir~gL~~Ikgig~~~~~~I~~~ 771 (971)
T PRK05898 747 KQIIRFGFNTIKGFGDELLKKIKSA 771 (971)
T ss_pred CCeEEecchhcCCcCHHHHHHHHHH
Confidence 5679999999999999999999864
No 140
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=21.42 E-value=33 Score=28.81 Aligned_cols=69 Identities=14% Similarity=0.123 Sum_probs=45.4
Q ss_pred ecCccCCCCCCCccccccCCC-CCCC-----CcccceeEEeCccCCCCeEEeEeeccccccCHHHHHHHHHHcCC
Q 030930 17 CNGHNNNLLTNASLSFPVSKQ-PQYP-----GLSIQCARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKM 85 (169)
Q Consensus 17 ~~~~~~~~~~~~~~~~~~~~~-~~f~-----~i~~~~vrI~~tni~~~K~i~~ALt~I~GIG~~~A~~Ic~~lgi 85 (169)
++|.----..|.+....++.+ +.++ +++=....++|-.=...+.++.-|.++-|||.++|..|+..++.
T Consensus 21 ~~GVGY~i~~~~~~~~~l~~~g~~~~l~t~~~vREd~~~LyGF~~~~ER~lF~~LisVnGIGpK~ALaiLs~~~~ 95 (201)
T COG0632 21 VNGVGYEINVPMRTLAELPEVGEEVKLFTHLVVREDAHLLYGFLTEEERELFRLLISVNGIGPKLALAILSNLDP 95 (201)
T ss_pred eCCEEEEEEcChHHHhhcccCCCeEEEEEEEeehhhHHHHcCCCCHHHHHHHHHHHccCCccHHHHHHHHcCCCH
Confidence 555443334566666655221 2222 22223355777777788889999999999999999999965543
No 141
>PF09346 SMI1_KNR4: SMI1 / KNR4 family (SUKH-1); InterPro: IPR018958 Proteins in this family are involved in the regulation of 1,3-beta-glucan synthase activity and cell-wall formation [, ]. Yeast members of this family are involved in the regulation of cell wall assembly. Saccharomyces cerevisiae (Baker's yeast) protein KNR4 (SMI1) has a regulatory role in chitin deposition and in cell wall assembly []. It was originally identified as a regulator of chitin synthase expression (acting as a repressor) [] and of 1,3-beta-glucan synthase levels []. It was shown to localise in patches at presumptive bud sites in unbudded cells and at the incipient bud site during bud emergence []. KNR4 is believed to connect the PKC1-SLT2 MAPK pathway with cell proliferation. It has been shown to interact with BCK2, a gene involved in cell cycle progression in S. cerevisiae (forming a complex) to allow PKC1 to coordinate the cell cycle (cell proliferation) with cell wall integrity [, ]. PKC1 plays an essential role in cell wall integrity and cell proliferation through a bifurcated PKC1/mitogen-activated protein (MAP) kinase pathway. KNR4 also interacts with the tyrosine-tRNA synthetase protein encoded by TYS1 and is involved in sporulation process []. Note: previously reported evidence that KNR4 may interact with nuclear matrix-association region [] may be due to an artefact [].; PDB: 3D5P_A 2ICG_A.
Probab=20.75 E-value=1.4e+02 Score=20.78 Aligned_cols=26 Identities=19% Similarity=0.420 Sum_probs=16.7
Q ss_pred CCHHHHHHHHHHHhhcccchHHHHHHH
Q 030930 93 MSEEELITIRDEVSKYMIEGDLRRFNA 119 (169)
Q Consensus 93 Ls~~el~~L~~~l~~~~Ie~dLr~~~~ 119 (169)
+|+++|..+++.+. +.++.++|..++
T Consensus 2 ~t~~~I~~~E~~lg-~~LP~~yk~fl~ 27 (130)
T PF09346_consen 2 ATEEEIQELEEKLG-VRLPDDYKEFLK 27 (130)
T ss_dssp --HHHHHHHHHHHT-S---HHHHHHHH
T ss_pred CCHHHHHHHHHHhC-CCCcHHHHHHHH
Confidence 68999999999884 478999986544
No 142
>PLN02200 adenylate kinase family protein
Probab=20.74 E-value=1e+02 Score=25.66 Aligned_cols=42 Identities=10% Similarity=0.069 Sum_probs=30.7
Q ss_pred cCCCCeEEeEeeccccccCHHHH-HHHHHHcCCCccccCCCCH
Q 030930 54 EIPNNKRIEYSLQYIHGVGRTRA-RQILVDLKMENKITKDMSE 95 (169)
Q Consensus 54 ni~~~K~i~~ALt~I~GIG~~~A-~~Ic~~lgi~~k~~~~Ls~ 95 (169)
..+...+..+.+...+|-|+.+. ..+++++|+..-..++|=.
T Consensus 37 ~~~~~~~~ii~I~G~PGSGKsT~a~~La~~~g~~his~gdllR 79 (234)
T PLN02200 37 SSKEKTPFITFVLGGPGSGKGTQCEKIVETFGFKHLSAGDLLR 79 (234)
T ss_pred CccCCCCEEEEEECCCCCCHHHHHHHHHHHhCCeEEEccHHHH
Confidence 34444557789999999999995 8899999987544455443
No 143
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=20.67 E-value=64 Score=29.21 Aligned_cols=21 Identities=29% Similarity=0.387 Sum_probs=18.1
Q ss_pred eeccccccCHHHHHHHHHHcC
Q 030930 64 SLQYIHGVGRTRARQILVDLK 84 (169)
Q Consensus 64 ALt~I~GIG~~~A~~Ic~~lg 84 (169)
++|.++|||+.+|..|-.-+.
T Consensus 54 ~~t~l~gIGk~ia~~I~e~l~ 74 (326)
T COG1796 54 RLTELPGIGKGIAEKISEYLD 74 (326)
T ss_pred ccCCCCCccHHHHHHHHHHHH
Confidence 699999999999999876554
No 144
>cd02020 CMPK Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine monophosphate (CMP) to produce cytidine diphosphate (CDP), using ATP as the preferred phosphoryl donor.
Probab=20.42 E-value=3.3e+02 Score=19.49 Aligned_cols=42 Identities=19% Similarity=0.234 Sum_probs=30.3
Q ss_pred EeeccccccCHHH-HHHHHHHcCCCccccCCCCHHHHHHHHHH
Q 030930 63 YSLQYIHGVGRTR-ARQILVDLKMENKITKDMSEEELITIRDE 104 (169)
Q Consensus 63 ~ALt~I~GIG~~~-A~~Ic~~lgi~~k~~~~Ls~~el~~L~~~ 104 (169)
+++...+|-|.++ |..+.+.+|+.---.+.+.++++....+.
T Consensus 2 I~i~G~~GsGKst~a~~la~~~~~~~~~~~~i~~e~~~~~~~~ 44 (147)
T cd02020 2 IAIDGPAGSGKSTVAKLLAKKLGLPYLDTGGIRTEEVGKLASE 44 (147)
T ss_pred EEEECCCCCCHHHHHHHHHHHhCCceeccccCCHHHHHHHHHH
Confidence 4678889999998 88899999987333346777766555443
No 145
>cd05124 AFK Actin-Fragmin Kinase (AFK); catalytic domain. The AFK catalytic domain is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase (PI3K). AFK is found in slime molds, ciliates, and flowering plants. It catalyzes the transfer of the gamma-phosphoryl group from ATP specifically to threonine residues in the actin-fragmin complex. The phosphorylation sites are located at a minor contact site for DNase I and at an actin-actin contact site. Fragmin is an actin-binding protein that functions as a regulator of the microfilament system. It interferes with the growth of F-actin by severing actin filaments and capping their ends. The phosphorylation of the actin-fragmin complex inhibits its nucleation activity and results in calcium-dependent capping activity. Thus, AFK plays a role in regulating ac
Probab=20.36 E-value=2.7e+02 Score=24.17 Aligned_cols=49 Identities=10% Similarity=0.083 Sum_probs=36.8
Q ss_pred CeEEeEeeccccccCHHHHHHHHHHcCCC-ccc-cCCCCHHHHHHHHHHHhhc
Q 030930 58 NKRIEYSLQYIHGVGRTRARQILVDLKME-NKI-TKDMSEEELITIRDEVSKY 108 (169)
Q Consensus 58 ~K~i~~ALt~I~GIG~~~A~~Ic~~lgi~-~k~-~~~Ls~~el~~L~~~l~~~ 108 (169)
+.-|...-+.| ....++.+++..||+. |.. +=+.++.|+..+...|...
T Consensus 23 ~a~ViK~s~ti--~~E~~~~~La~~LgVpiPq~rvi~~~~~E~~e~~~~L~~a 73 (238)
T cd05124 23 GAIVVKSSPNI--ASEYFLSKLAKILGLPIPQMRVLEWNSSEFTEMSENLLKA 73 (238)
T ss_pred cEEEEEcCccH--HHHHHHHHHHHHhCCCCCceeeeecCCHHHHHHHHHHHHH
Confidence 34444444666 7889999999999999 764 5777788888888877653
No 146
>COG1908 FrhD Coenzyme F420-reducing hydrogenase, delta subunit [Energy production and conversion]
Probab=20.33 E-value=1.1e+02 Score=24.36 Aligned_cols=34 Identities=15% Similarity=0.227 Sum_probs=26.4
Q ss_pred HHHHHHHHcCCCcccc--CCCCHHHHHHHHHHHhhc
Q 030930 75 RARQILVDLKMENKIT--KDMSEEELITIRDEVSKY 108 (169)
Q Consensus 75 ~A~~Ic~~lgi~~k~~--~~Ls~~el~~L~~~l~~~ 108 (169)
..+.+++.+||++.++ -..|..|.+++.+.+++|
T Consensus 82 ~lke~l~elgie~eRv~~~wiSa~E~ekf~e~~~ef 117 (132)
T COG1908 82 LLKELLKELGIEPERVRVLWISAAEGEKFAETINEF 117 (132)
T ss_pred HHHHHHHHhCCCcceEEEEEEehhhHHHHHHHHHHH
Confidence 3567888999997764 777888999988877653
Done!