Query 033139
Match_columns 126
No_of_seqs 119 out of 1022
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 10:17:59 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033139.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033139hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00134 40S ribosomal protein 100.0 5.6E-49 1.2E-53 293.9 9.0 117 7-123 9-125 (154)
2 PRK04053 rps13p 30S ribosomal 100.0 2.1E-46 4.5E-51 278.8 9.2 118 6-123 3-120 (149)
3 TIGR03629 arch_S13P archaeal r 100.0 8.4E-46 1.8E-50 274.3 9.0 115 8-123 1-115 (144)
4 COG0099 RpsM Ribosomal protein 100.0 9.6E-35 2.1E-39 208.6 6.2 90 12-123 1-90 (121)
5 KOG3311 Ribosomal protein S18 100.0 1.2E-34 2.5E-39 215.0 5.1 124 1-124 1-124 (152)
6 CHL00137 rps13 ribosomal prote 100.0 3E-32 6.6E-37 197.0 6.9 90 12-123 1-90 (122)
7 PRK05179 rpsM 30S ribosomal pr 100.0 4.5E-32 9.7E-37 196.1 7.3 90 12-123 1-90 (122)
8 TIGR03631 bact_S13 30S ribosom 100.0 2.5E-30 5.4E-35 184.8 7.2 88 14-123 1-88 (113)
9 PF00416 Ribosomal_S13: Riboso 100.0 3.2E-30 6.9E-35 182.1 5.9 88 14-123 1-88 (107)
10 PF06831 H2TH: Formamidopyrimi 97.5 9.2E-05 2E-09 50.8 3.1 52 22-73 22-76 (92)
11 PRK01103 formamidopyrimidine/5 97.2 0.00037 8.1E-09 56.1 4.0 52 22-73 154-208 (274)
12 PRK04184 DNA topoisomerase VI 97.1 0.00052 1.1E-08 60.5 4.3 51 23-73 256-306 (535)
13 PRK14810 formamidopyrimidine-D 96.7 0.0021 4.5E-08 51.9 4.4 51 22-72 153-206 (272)
14 TIGR01052 top6b DNA topoisomer 96.7 0.002 4.3E-08 56.3 4.2 51 23-73 247-300 (488)
15 PRK14811 formamidopyrimidine-D 96.5 0.0034 7.5E-08 50.6 4.1 50 22-71 142-194 (269)
16 PRK10445 endonuclease VIII; Pr 96.5 0.0035 7.5E-08 50.3 4.1 51 23-73 151-204 (263)
17 PRK13945 formamidopyrimidine-D 96.3 0.0053 1.2E-07 49.7 4.1 52 22-73 163-217 (282)
18 TIGR00577 fpg formamidopyrimid 96.2 0.0053 1.1E-07 49.5 3.7 52 22-73 154-208 (272)
19 COG1389 DNA topoisomerase VI, 95.5 0.011 2.5E-07 51.6 2.9 52 22-73 255-310 (538)
20 PF05833 FbpA: Fibronectin-bin 95.5 0.0067 1.4E-07 51.3 1.5 50 22-71 185-235 (455)
21 COG0266 Nei Formamidopyrimidin 94.5 0.043 9.3E-07 44.8 3.5 58 15-72 147-207 (273)
22 PF00633 HHH: Helix-hairpin-he 94.3 0.025 5.5E-07 31.4 1.3 18 29-46 12-29 (30)
23 TIGR00275 flavoprotein, HI0933 93.4 0.066 1.4E-06 44.8 2.8 50 22-73 282-331 (400)
24 PF11798 IMS_HHH: IMS family H 93.1 0.05 1.1E-06 30.4 1.1 22 28-50 11-32 (32)
25 PF10391 DNA_pol_lambd_f: Fing 91.9 0.09 2E-06 32.6 1.3 22 29-51 3-24 (52)
26 COG0030 KsgA Dimethyladenosine 91.4 0.17 3.7E-06 41.0 2.7 48 21-73 209-256 (259)
27 PRK00274 ksgA 16S ribosomal RN 91.4 0.21 4.6E-06 39.8 3.3 53 20-73 218-270 (272)
28 PF14520 HHH_5: Helix-hairpin- 91.1 0.034 7.4E-07 34.7 -1.2 26 26-52 3-28 (60)
29 PRK02515 psbU photosystem II c 91.0 0.17 3.8E-06 37.2 2.2 59 15-73 48-109 (132)
30 PF03486 HI0933_like: HI0933-l 89.7 0.47 1E-05 40.4 4.1 51 21-73 288-339 (409)
31 smart00278 HhH1 Helix-hairpin- 89.7 0.21 4.5E-06 26.3 1.3 19 29-47 2-20 (26)
32 COG1293 Predicted RNA-binding 89.3 0.57 1.2E-05 41.6 4.5 49 25-73 187-235 (564)
33 TIGR00755 ksgA dimethyladenosi 89.3 0.39 8.4E-06 37.7 3.1 59 9-71 195-253 (253)
34 cd00080 HhH2_motif Helix-hairp 88.8 0.22 4.8E-06 32.7 1.2 35 6-49 7-43 (75)
35 PF09883 DUF2110: Uncharacteri 88.1 1.9 4.2E-05 34.4 6.2 55 18-73 92-158 (225)
36 PF00398 RrnaAD: Ribosomal RNA 86.7 0.29 6.2E-06 38.8 0.9 62 7-72 200-261 (262)
37 smart00279 HhH2 Helix-hairpin- 86.1 0.49 1.1E-05 27.2 1.4 34 7-47 2-35 (36)
38 COG3743 Uncharacterized conser 86.0 0.49 1.1E-05 34.9 1.7 44 28-72 67-110 (133)
39 PRK14606 ruvA Holliday junctio 85.8 0.42 9E-06 36.8 1.3 21 28-48 108-128 (188)
40 TIGR03252 uncharacterized HhH- 85.7 0.35 7.6E-06 37.2 0.9 32 21-52 108-139 (177)
41 PRK14601 ruvA Holliday junctio 85.3 0.45 9.8E-06 36.6 1.3 20 28-47 108-127 (183)
42 PRK14604 ruvA Holliday junctio 84.5 0.52 1.1E-05 36.5 1.3 21 28-48 108-128 (195)
43 PRK14603 ruvA Holliday junctio 84.4 0.53 1.1E-05 36.5 1.3 19 28-46 107-125 (197)
44 PF14579 HHH_6: Helix-hairpin- 84.2 0.62 1.4E-05 31.3 1.5 27 23-49 22-48 (90)
45 PRK13901 ruvA Holliday junctio 83.9 0.57 1.2E-05 36.5 1.3 21 28-48 107-127 (196)
46 PRK14602 ruvA Holliday junctio 83.3 0.61 1.3E-05 36.3 1.3 19 28-46 109-127 (203)
47 COG0632 RuvA Holliday junction 82.0 0.77 1.7E-05 35.9 1.4 21 28-48 108-128 (201)
48 PF14520 HHH_5: Helix-hairpin- 81.7 1 2.2E-05 27.9 1.6 20 29-48 39-58 (60)
49 PF02042 RWP-RK: RWP-RK domain 80.6 1.3 2.8E-05 27.7 1.8 26 33-58 24-51 (52)
50 PRK14605 ruvA Holliday junctio 80.0 0.51 1.1E-05 36.4 -0.2 38 14-51 59-96 (194)
51 PRK00116 ruvA Holliday junctio 79.1 0.65 1.4E-05 35.6 0.1 59 15-73 60-130 (192)
52 PRK14605 ruvA Holliday junctio 78.2 1.2 2.6E-05 34.3 1.4 18 28-45 108-125 (194)
53 PRK14600 ruvA Holliday junctio 78.1 1.1 2.3E-05 34.5 1.1 18 28-46 108-125 (186)
54 PF12826 HHH_2: Helix-hairpin- 77.5 1 2.2E-05 28.5 0.7 18 32-49 7-24 (64)
55 PF12836 HHH_3: Helix-hairpin- 77.2 1.2 2.5E-05 28.2 0.9 47 23-69 9-62 (65)
56 TIGR01448 recD_rel helicase, p 75.3 3.1 6.7E-05 38.0 3.4 41 32-72 88-138 (720)
57 PF14716 HHH_8: Helix-hairpin- 74.7 1.8 3.8E-05 27.6 1.2 19 29-47 48-66 (68)
58 smart00483 POLXc DNA polymeras 74.0 2 4.2E-05 35.7 1.7 25 27-52 88-112 (334)
59 TIGR00426 competence protein C 73.7 2.6 5.6E-05 26.7 1.8 26 23-48 11-37 (69)
60 cd00056 ENDO3c endonuclease II 73.6 1.7 3.6E-05 31.4 1.0 45 23-71 78-122 (158)
61 PF14490 HHH_4: Helix-hairpin- 73.4 1.7 3.8E-05 29.4 1.0 26 28-53 45-71 (94)
62 TIGR01259 comE comEA protein. 73.3 2.1 4.5E-05 30.5 1.4 31 20-50 60-90 (120)
63 TIGR00084 ruvA Holliday juncti 72.6 1.8 3.8E-05 33.4 1.0 18 28-45 107-124 (191)
64 TIGR00084 ruvA Holliday juncti 72.3 0.7 1.5E-05 35.6 -1.3 37 13-49 57-93 (191)
65 PF02371 Transposase_20: Trans 72.1 2.4 5.3E-05 28.1 1.5 20 29-48 3-22 (87)
66 smart00478 ENDO3c endonuclease 71.6 2.1 4.5E-05 30.6 1.1 42 26-71 70-111 (149)
67 cd00141 NT_POLXc Nucleotidyltr 71.4 2.4 5.2E-05 34.7 1.6 25 27-52 84-108 (307)
68 COG2081 Predicted flavoprotein 71.0 4.6 0.0001 34.9 3.2 50 21-73 283-332 (408)
69 PRK01229 N-glycosylase/DNA lya 70.9 2.8 6E-05 32.9 1.7 44 25-72 115-159 (208)
70 cd00128 XPG Xeroderma pigmento 69.7 2.4 5.2E-05 34.4 1.2 34 7-49 211-244 (316)
71 PF11731 Cdd1: Pathogenicity l 69.5 3.2 6.9E-05 28.8 1.6 37 28-65 12-48 (93)
72 PRK03980 flap endonuclease-1; 69.2 2.8 6E-05 34.3 1.5 59 7-74 177-236 (292)
73 PF01367 5_3_exonuc: 5'-3' exo 69.1 0.92 2E-05 31.7 -1.2 20 30-49 20-39 (101)
74 PRK14602 ruvA Holliday junctio 68.3 1.4 3.1E-05 34.2 -0.3 61 13-73 59-131 (203)
75 PRK12278 50S ribosomal protein 68.3 4.2 9.1E-05 32.3 2.3 55 28-83 158-212 (221)
76 PRK08609 hypothetical protein; 68.3 3.2 7E-05 36.8 1.8 24 28-51 88-111 (570)
77 PRK14600 ruvA Holliday junctio 67.7 1.3 2.7E-05 34.2 -0.8 59 14-73 59-129 (186)
78 TIGR01083 nth endonuclease III 67.5 2.9 6.2E-05 31.7 1.2 23 26-48 104-126 (191)
79 PRK14601 ruvA Holliday junctio 67.0 1.3 2.8E-05 34.1 -0.8 37 13-49 58-94 (183)
80 PRK10702 endonuclease III; Pro 66.8 2.8 6.2E-05 32.6 1.0 29 17-48 101-129 (211)
81 PRK14606 ruvA Holliday junctio 66.7 1.3 2.9E-05 34.1 -0.8 36 14-49 59-94 (188)
82 COG0353 RecR Recombinational D 66.6 2.9 6.4E-05 32.8 1.1 83 25-124 9-104 (198)
83 COG0258 Exo 5'-3' exonuclease 66.4 3.8 8.3E-05 33.3 1.8 33 7-49 184-219 (310)
84 PF11338 DUF3140: Protein of u 65.0 11 0.00024 26.2 3.6 36 33-72 32-67 (92)
85 PRK13901 ruvA Holliday junctio 64.6 1.6 3.4E-05 34.1 -0.8 36 14-49 58-93 (196)
86 PRK14603 ruvA Holliday junctio 64.6 1.5 3.3E-05 33.9 -0.8 61 13-73 57-129 (197)
87 PRK00076 recR recombination pr 64.3 3.7 8E-05 32.1 1.2 40 25-72 8-47 (196)
88 TIGR00615 recR recombination p 63.6 3.4 7.3E-05 32.3 0.9 40 25-72 8-47 (195)
89 TIGR01084 mutY A/G-specific ad 63.4 3.2 6.8E-05 33.7 0.7 30 16-48 96-125 (275)
90 COG0632 RuvA Holliday junction 63.2 1.4 3E-05 34.5 -1.3 38 12-49 57-94 (201)
91 PRK12766 50S ribosomal protein 62.8 3.9 8.4E-05 32.8 1.1 38 29-67 4-41 (232)
92 PTZ00217 flap endonuclease-1; 62.6 4.4 9.5E-05 34.5 1.5 34 7-49 223-256 (393)
93 cd01104 HTH_MlrA-CarA Helix-Tu 62.4 20 0.00044 21.9 4.2 43 30-72 6-52 (68)
94 PRK07373 DNA polymerase III su 61.7 8.6 0.00019 33.4 3.1 48 23-70 109-166 (449)
95 cd00349 Ribosomal_L11 Ribosoma 61.4 25 0.00054 25.6 5.1 63 35-120 61-130 (131)
96 PLN03072 60S ribosomal protein 61.2 13 0.00029 28.3 3.8 62 36-120 74-143 (166)
97 smart00475 53EXOc 5'-3' exonuc 61.2 4.8 0.0001 32.3 1.4 19 31-49 189-207 (259)
98 PRK09482 flap endonuclease-lik 61.2 4.8 0.0001 32.5 1.4 19 31-49 185-203 (256)
99 PF06514 PsbU: Photosystem II 61.1 13 0.00027 26.0 3.3 58 16-73 11-71 (93)
100 cd00008 53EXOc 5'-3' exonuclea 60.7 4.9 0.00011 31.7 1.4 20 30-49 185-204 (240)
101 COG0177 Nth Predicted EndoIII- 60.0 12 0.00025 29.6 3.4 49 17-72 101-149 (211)
102 COG2231 Uncharacterized protei 59.5 6.7 0.00015 31.1 1.9 42 18-59 103-146 (215)
103 PRK13913 3-methyladenine DNA g 59.4 4.7 0.0001 31.8 1.1 24 25-48 118-141 (218)
104 PRK00116 ruvA Holliday junctio 59.4 5.4 0.00012 30.5 1.4 21 29-49 109-129 (192)
105 PHA02564 V virion protein; Pro 59.3 17 0.00038 26.9 4.0 32 41-73 88-119 (141)
106 PRK13844 recombination protein 59.0 5.2 0.00011 31.4 1.2 40 25-72 12-51 (200)
107 PRK14604 ruvA Holliday junctio 58.6 2.2 4.9E-05 33.0 -0.9 61 13-73 58-130 (195)
108 PRK12311 rpsB 30S ribosomal pr 58.3 6.2 0.00013 33.1 1.6 45 28-73 263-307 (326)
109 PRK00558 uvrC excinuclease ABC 58.2 7.8 0.00017 34.8 2.4 44 22-67 537-580 (598)
110 KOG2518 5'-3' exonuclease [Rep 57.9 4.8 0.0001 36.0 0.9 37 5-50 211-247 (556)
111 PRK14976 5'-3' exonuclease; Pr 57.7 5.6 0.00012 32.3 1.3 19 31-49 194-212 (281)
112 PRK14896 ksgA 16S ribosomal RN 57.4 17 0.00036 28.6 3.9 63 9-73 192-256 (258)
113 PF14635 HHH_7: Helix-hairpin- 56.9 6.6 0.00014 27.7 1.4 41 9-49 28-71 (104)
114 TIGR03674 fen_arch flap struct 55.4 6.9 0.00015 32.5 1.5 52 7-74 224-283 (338)
115 PRK10880 adenine DNA glycosyla 54.7 5.8 0.00013 33.4 0.9 29 17-48 101-129 (350)
116 CHL00154 rpl29 ribosomal prote 54.3 7.5 0.00016 25.2 1.2 55 56-121 9-63 (67)
117 TIGR00588 ogg 8-oxoguanine DNA 53.8 6.8 0.00015 32.2 1.2 44 25-71 217-260 (310)
118 PRK13910 DNA glycosylase MutY; 53.5 7.4 0.00016 31.9 1.3 47 18-71 65-111 (289)
119 PTZ00338 dimethyladenosine tra 51.8 20 0.00044 29.2 3.6 33 40-73 256-288 (294)
120 COG1936 Predicted nucleotide k 51.5 10 0.00022 29.4 1.7 25 27-51 2-26 (180)
121 COG0122 AlkA 3-methyladenine D 51.2 7.8 0.00017 31.6 1.1 25 24-48 194-218 (285)
122 KOG2251 Homeobox transcription 50.0 12 0.00026 30.0 1.9 31 59-90 44-92 (228)
123 cd01702 PolY_Pol_eta DNA Polym 49.9 10 0.00022 31.6 1.7 37 29-65 183-221 (359)
124 PRK14669 uvrC excinuclease ABC 49.7 11 0.00024 34.2 1.9 25 25-49 549-573 (624)
125 PRK01143 rpl11p 50S ribosomal 49.2 50 0.0011 25.0 5.1 62 37-121 69-136 (163)
126 PF04760 IF2_N: Translation in 48.6 9.8 0.00021 22.9 1.0 44 29-72 8-52 (54)
127 PRK10308 3-methyl-adenine DNA 48.3 9.1 0.0002 31.1 1.1 30 26-55 205-234 (283)
128 smart00389 HOX Homeodomain. DN 48.0 19 0.00041 21.0 2.3 30 58-88 24-53 (56)
129 PRK13766 Hef nuclease; Provisi 47.8 12 0.00027 33.7 2.0 25 25-49 712-736 (773)
130 TIGR02607 antidote_HigA addict 47.7 23 0.0005 22.2 2.7 29 58-91 44-72 (78)
131 PRK05898 dnaE DNA polymerase I 47.6 24 0.00052 33.8 3.8 47 23-69 747-802 (971)
132 COG1059 Thermostable 8-oxoguan 46.9 10 0.00022 30.0 1.1 27 25-51 118-144 (210)
133 smart00649 RL11 Ribosomal prot 46.7 58 0.0013 23.7 5.0 61 37-120 64-130 (132)
134 cd00427 Ribosomal_L29_HIP Ribo 44.9 15 0.00033 22.7 1.5 53 56-119 3-55 (57)
135 PRK14671 uvrC excinuclease ABC 44.5 9 0.00019 34.6 0.5 49 17-67 558-606 (621)
136 PRK07945 hypothetical protein; 44.2 13 0.00028 30.8 1.4 21 29-49 50-70 (335)
137 KOG0650 WD40 repeat nucleolar 44.1 35 0.00076 31.3 4.1 48 50-104 141-188 (733)
138 KOG0843 Transcription factor E 41.4 34 0.00074 26.8 3.2 40 37-77 84-126 (197)
139 COG0080 RplK Ribosomal protein 41.0 89 0.0019 23.3 5.3 59 38-119 72-136 (141)
140 KOG3802 Transcription factor O 41.0 14 0.00031 31.8 1.2 29 60-89 320-348 (398)
141 PTZ00105 60S ribosomal protein 40.7 55 0.0012 24.2 4.1 60 38-120 50-117 (140)
142 PF13613 HTH_Tnp_4: Helix-turn 40.4 18 0.0004 21.7 1.3 21 28-48 23-43 (53)
143 PRK00306 50S ribosomal protein 40.1 25 0.00055 22.3 2.0 55 56-121 6-60 (66)
144 KOG0844 Transcription factor E 39.7 20 0.00042 30.4 1.8 30 58-88 187-234 (408)
145 COG1555 ComEA DNA uptake prote 39.5 28 0.00061 25.7 2.5 20 29-48 98-117 (149)
146 TIGR03045 PS_II_C550 cytochrom 39.0 36 0.00077 25.7 3.0 17 57-73 130-146 (159)
147 cd00086 homeodomain Homeodomai 38.5 12 0.00027 21.9 0.4 30 58-88 24-53 (59)
148 TIGR00600 rad2 DNA excision re 38.3 17 0.00037 34.9 1.4 35 7-50 854-888 (1034)
149 TIGR01632 L11_bact 50S ribosom 38.3 52 0.0011 24.3 3.7 61 37-120 71-137 (140)
150 PRK14670 uvrC excinuclease ABC 37.9 19 0.0004 32.4 1.5 40 26-67 512-551 (574)
151 PRK14668 uvrC excinuclease ABC 37.9 18 0.00038 32.5 1.4 39 26-66 523-561 (577)
152 CHL00127 rpl11 ribosomal prote 37.6 73 0.0016 23.5 4.4 61 37-120 72-138 (140)
153 PRK12373 NADH dehydrogenase su 37.5 30 0.00064 29.9 2.6 56 28-84 323-378 (400)
154 PRK14667 uvrC excinuclease ABC 37.5 19 0.00041 32.3 1.5 43 23-67 509-551 (567)
155 PRK00419 DNA primase small sub 37.2 16 0.00034 31.2 0.9 20 29-48 222-241 (376)
156 PRK00140 rplK 50S ribosomal pr 36.9 46 0.001 24.5 3.2 60 37-119 72-137 (141)
157 KOG0494 Transcription factor C 36.6 24 0.00051 29.3 1.8 31 58-89 147-195 (332)
158 TIGR00594 polc DNA-directed DN 36.0 27 0.00058 33.5 2.3 47 23-69 819-875 (1022)
159 PRK04301 radA DNA repair and r 35.6 25 0.00055 28.4 1.8 38 28-66 6-43 (317)
160 TIGR00194 uvrC excinuclease AB 35.0 16 0.00036 32.7 0.7 25 25-49 538-562 (574)
161 PF00298 Ribosomal_L11: Riboso 34.9 1.3E+02 0.0027 19.4 5.1 59 38-119 3-67 (69)
162 PF13276 HTH_21: HTH-like doma 34.1 25 0.00055 21.3 1.3 35 20-54 20-56 (60)
163 PRK07279 dnaE DNA polymerase I 34.0 29 0.00063 33.4 2.1 25 23-47 745-769 (1034)
164 PF03118 RNA_pol_A_CTD: Bacter 33.9 25 0.00054 22.4 1.2 20 29-48 45-64 (66)
165 PF00046 Homeobox: Homeobox do 33.9 12 0.00026 22.2 -0.2 29 59-88 25-53 (57)
166 PF01418 HTH_6: Helix-turn-hel 33.7 31 0.00067 22.2 1.7 22 30-51 40-61 (77)
167 PRK06920 dnaE DNA polymerase I 33.2 35 0.00075 33.1 2.6 46 23-68 797-851 (1107)
168 PF10662 PduV-EutP: Ethanolami 32.7 37 0.00079 25.1 2.1 36 38-73 108-143 (143)
169 PF14213 DUF4325: Domain of un 32.7 58 0.0013 20.8 2.9 55 18-72 12-73 (74)
170 cd01401 PncB_like Nicotinate p 32.5 74 0.0016 27.2 4.2 35 39-73 289-327 (377)
171 TIGR00593 pola DNA polymerase 32.2 24 0.00053 33.2 1.3 19 31-49 188-206 (887)
172 PF13331 DUF4093: Domain of un 32.1 17 0.00036 24.7 0.2 40 21-66 45-84 (87)
173 PRK05755 DNA polymerase I; Pro 31.9 24 0.00052 32.9 1.2 20 30-49 189-208 (880)
174 COG2938 Uncharacterized conser 31.8 28 0.0006 24.2 1.3 33 55-88 40-72 (94)
175 KOG2875 8-oxoguanine DNA glyco 31.7 19 0.00042 30.0 0.6 21 26-46 216-236 (323)
176 TIGR02366 DHAK_reg probable di 31.6 23 0.00049 25.5 0.8 27 28-54 13-39 (176)
177 PRK00919 GMP synthase subunit 31.4 90 0.0019 25.8 4.4 48 51-105 155-202 (307)
178 TIGR00608 radc DNA repair prot 31.4 31 0.00066 27.1 1.6 21 30-50 62-82 (218)
179 PF10500 SR-25: Nuclear RNA-sp 31.3 87 0.0019 25.1 4.1 32 56-100 157-188 (225)
180 COG1111 MPH1 ERCC4-like helica 31.2 28 0.00061 31.2 1.5 87 22-122 160-247 (542)
181 TIGR00575 dnlj DNA ligase, NAD 31.2 19 0.00041 32.7 0.4 23 26-49 497-519 (652)
182 PRK14666 uvrC excinuclease ABC 31.0 25 0.00054 32.5 1.2 24 26-49 635-658 (694)
183 PF00542 Ribosomal_L12: Riboso 30.9 22 0.00047 23.0 0.6 45 26-73 16-60 (68)
184 KOG0842 Transcription factor t 30.7 27 0.00058 29.2 1.2 28 58-87 177-205 (307)
185 COG3415 Transposase and inacti 30.4 1E+02 0.0022 22.6 4.2 45 29-73 26-78 (138)
186 PF05155 Phage_X: Phage X fami 30.0 10 0.00022 25.9 -1.1 42 41-84 42-85 (92)
187 TIGR02236 recomb_radA DNA repa 29.9 29 0.00064 27.7 1.3 35 30-65 1-35 (310)
188 TIGR02836 spore_IV_A stage IV 29.8 92 0.002 27.7 4.4 90 22-118 179-277 (492)
189 PF13551 HTH_29: Winged helix- 29.5 1.2E+02 0.0026 19.8 4.1 45 29-73 17-72 (112)
190 PRK02406 DNA polymerase IV; Va 29.5 34 0.00074 27.8 1.7 37 28-65 168-204 (343)
191 PRK00024 hypothetical protein; 28.8 35 0.00077 26.8 1.6 22 29-50 67-88 (224)
192 PRK00461 rpmC 50S ribosomal pr 28.8 44 0.00096 22.8 1.9 53 56-119 5-57 (87)
193 PF11460 DUF3007: Protein of u 28.6 30 0.00065 24.5 1.0 20 53-72 84-103 (104)
194 PRK03352 DNA polymerase IV; Va 28.5 42 0.00091 27.3 2.0 36 29-65 178-213 (346)
195 PRK06266 transcription initiat 28.3 1.1E+02 0.0025 23.1 4.3 49 62-115 51-102 (178)
196 PF00912 Transgly: Transglycos 28.3 36 0.00078 25.9 1.5 38 32-77 120-157 (178)
197 smart00581 PSP proline-rich do 28.2 62 0.0013 20.3 2.3 32 53-89 3-34 (54)
198 PRK07135 dnaE DNA polymerase I 27.9 41 0.00089 32.2 2.1 47 23-69 748-804 (973)
199 PF14229 DUF4332: Domain of un 27.8 26 0.00057 24.8 0.6 36 34-70 1-38 (122)
200 cd00141 NT_POLXc Nucleotidyltr 27.6 22 0.00048 29.1 0.2 31 29-59 46-76 (307)
201 PRK07956 ligA NAD-dependent DN 27.5 23 0.0005 32.3 0.3 35 31-65 448-482 (665)
202 KOG3817 Uncharacterized conser 27.4 50 0.0011 28.7 2.3 50 51-104 309-377 (452)
203 TIGR00575 dnlj DNA ligase, NAD 27.3 27 0.00059 31.7 0.8 33 32-64 436-468 (652)
204 PRK01172 ski2-like helicase; P 27.1 37 0.0008 30.3 1.6 39 28-67 612-650 (674)
205 cd03067 PDI_b_PDIR_N PDIb fami 27.1 56 0.0012 23.4 2.2 30 29-58 43-80 (112)
206 PF00440 TetR_N: Bacterial reg 27.1 34 0.00073 19.8 0.9 21 33-53 11-31 (47)
207 KOG2534 DNA polymerase IV (fam 26.6 30 0.00065 29.3 0.9 14 30-43 99-112 (353)
208 PF00986 DNA_gyraseB_C: DNA gy 26.6 26 0.00055 22.8 0.3 47 26-72 4-50 (65)
209 PRK07956 ligA NAD-dependent DN 26.6 41 0.00089 30.7 1.8 23 26-49 510-532 (665)
210 PRK05672 dnaE2 error-prone DNA 26.5 39 0.00083 32.6 1.6 46 23-69 811-863 (1046)
211 TIGR02663 nifX nitrogen fixati 26.4 1E+02 0.0022 21.4 3.4 48 34-86 70-118 (119)
212 KOG1856 Transcription elongati 26.1 30 0.00066 33.9 0.9 43 9-51 784-829 (1299)
213 smart00483 POLXc DNA polymeras 26.1 40 0.00087 27.9 1.5 22 29-50 49-70 (334)
214 smart00530 HTH_XRE Helix-turn- 26.1 53 0.0012 17.4 1.6 18 35-52 36-53 (56)
215 PF08478 POTRA_1: POTRA domain 26.0 97 0.0021 18.7 3.0 34 32-65 7-40 (69)
216 PF02879 PGM_PMM_II: Phosphogl 25.9 12 0.00026 25.1 -1.4 40 11-50 6-46 (104)
217 PRK14672 uvrC excinuclease ABC 25.9 35 0.00077 31.5 1.2 43 23-67 603-645 (691)
218 TIGR00012 L29 ribosomal protei 25.9 61 0.0013 19.8 2.0 52 56-118 2-53 (55)
219 PRK02362 ski2-like helicase; P 25.8 40 0.00087 30.6 1.6 39 28-67 652-690 (737)
220 KOG0821 Predicted ribosomal RN 25.7 86 0.0019 25.8 3.3 35 39-73 270-304 (326)
221 PRK14539 50S ribosomal protein 25.1 1.4E+02 0.0029 23.5 4.2 61 37-120 69-135 (196)
222 COG1131 CcmA ABC-type multidru 25.0 1E+02 0.0023 24.8 3.7 59 12-70 80-148 (293)
223 PRK00254 ski2-like helicase; P 24.9 33 0.00071 31.1 0.8 39 28-67 645-683 (720)
224 COG0587 DnaE DNA polymerase II 24.7 44 0.00096 32.6 1.7 47 24-70 819-874 (1139)
225 cd02020 CMPK Cytidine monophos 24.5 1.3E+02 0.0029 20.3 3.7 37 28-65 2-39 (147)
226 PF14053 DUF4248: Domain of un 24.4 1.3E+02 0.0029 19.4 3.4 49 24-74 7-69 (69)
227 TIGR00630 uvra excinuclease AB 24.2 66 0.0014 30.6 2.7 30 40-69 321-350 (924)
228 PRK03858 DNA polymerase IV; Va 24.2 57 0.0012 27.0 2.1 35 29-64 174-208 (396)
229 cd00093 HTH_XRE Helix-turn-hel 24.2 62 0.0014 17.3 1.7 17 35-51 38-54 (58)
230 KOG3908 Queuine-tRNA ribosyltr 24.0 16 0.00035 30.9 -1.2 40 7-51 230-269 (396)
231 CHL00133 psbV photosystem II c 23.9 84 0.0018 23.9 2.8 17 57-73 131-147 (163)
232 TIGR00596 rad1 DNA repair prot 23.8 50 0.0011 31.0 1.8 39 26-67 756-794 (814)
233 KOG1014 17 beta-hydroxysteroid 23.7 58 0.0012 27.3 2.0 42 32-78 57-98 (312)
234 PF00832 Ribosomal_L39: Riboso 23.7 39 0.00084 20.3 0.7 36 66-103 4-41 (43)
235 PF13442 Cytochrome_CBB3: Cyto 23.5 1E+02 0.0022 18.6 2.7 14 58-71 54-67 (67)
236 PRK12766 50S ribosomal protein 23.4 56 0.0012 26.3 1.8 21 29-49 37-57 (232)
237 COG1796 POL4 DNA polymerase IV 23.4 47 0.001 28.0 1.4 20 29-48 54-73 (326)
238 PF00392 GntR: Bacterial regul 23.4 66 0.0014 19.6 1.8 29 20-48 19-48 (64)
239 PRK05673 dnaE DNA polymerase I 23.3 47 0.001 32.3 1.6 47 23-69 815-871 (1135)
240 TIGR01405 polC_Gram_pos DNA po 23.3 52 0.0011 32.3 1.8 46 24-69 1146-1197(1213)
241 PF03250 Tropomodulin: Tropomo 23.2 52 0.0011 24.7 1.5 43 45-89 10-54 (147)
242 PF11174 DUF2970: Protein of u 23.2 17 0.00037 22.8 -0.9 22 84-105 19-40 (56)
243 PF04218 CENP-B_N: CENP-B N-te 23.0 47 0.001 20.1 1.0 20 27-46 25-44 (53)
244 PF07700 HNOB: Heme NO binding 22.9 84 0.0018 23.1 2.6 37 37-73 18-57 (171)
245 TIGR02620 cas_VVA1548 putative 22.9 62 0.0013 22.5 1.7 35 38-72 44-86 (93)
246 cd08532 SAM_PNT-PDEF-like Ster 22.8 54 0.0012 21.7 1.4 33 45-81 1-33 (76)
247 PRK07374 dnaE DNA polymerase I 22.8 49 0.0011 32.3 1.6 48 23-70 830-887 (1170)
248 COG1948 MUS81 ERCC4-type nucle 22.7 53 0.0012 26.7 1.6 24 26-49 180-203 (254)
249 PRK03609 umuC DNA polymerase V 22.7 58 0.0013 27.4 1.9 36 29-65 180-215 (422)
250 KOG2519 5'-3' exonuclease [Rep 22.6 69 0.0015 28.2 2.3 34 7-49 217-250 (449)
251 PF09652 Cas_VVA1548: Putative 22.5 76 0.0016 22.1 2.1 35 38-72 44-86 (93)
252 COG3181 Uncharacterized protei 22.2 1.6E+02 0.0035 24.6 4.4 56 56-117 254-311 (319)
253 PF14794 DUF4479: Domain of un 22.1 74 0.0016 20.8 1.9 16 58-73 47-62 (73)
254 PRK08609 hypothetical protein; 21.9 30 0.00066 30.8 0.0 32 29-60 49-80 (570)
255 PRK00349 uvrA excinuclease ABC 21.8 78 0.0017 30.2 2.7 32 39-70 322-353 (943)
256 PTZ00205 DNA polymerase kappa; 21.7 76 0.0016 28.7 2.5 27 29-59 310-336 (571)
257 COG0394 Wzb Protein-tyrosine-p 21.6 1E+02 0.0023 22.3 2.8 27 39-65 48-75 (139)
258 PF12114 Period_C: Period prot 21.5 71 0.0015 25.0 2.0 40 79-118 94-133 (195)
259 PF09397 Ftsk_gamma: Ftsk gamm 21.0 53 0.0011 21.2 1.0 26 23-48 19-44 (65)
260 KOG1647 Vacuolar H+-ATPase V1 20.8 73 0.0016 25.8 2.0 53 43-120 156-208 (255)
261 COG1194 MutY A/G-specific DNA 20.8 55 0.0012 27.7 1.3 34 10-46 98-131 (342)
262 PF00034 Cytochrom_C: Cytochro 20.7 97 0.0021 18.7 2.2 16 58-73 74-89 (91)
263 PRK05416 glmZ(sRNA)-inactivati 20.7 3.5E+02 0.0076 22.0 6.0 44 27-73 8-51 (288)
264 PRK03103 DNA polymerase IV; Re 20.7 74 0.0016 26.6 2.1 35 29-64 182-216 (409)
265 PF01595 DUF21: Domain of unkn 20.7 1.4E+02 0.003 21.5 3.3 42 31-73 134-175 (183)
266 PRK06826 dnaE DNA polymerase I 20.7 57 0.0012 31.8 1.6 47 23-69 819-875 (1151)
267 PHA00439 exonuclease 20.6 47 0.001 27.4 0.9 16 31-47 191-206 (286)
268 PRK14133 DNA polymerase IV; Pr 20.5 67 0.0015 26.2 1.8 36 29-65 174-209 (347)
269 TIGR02019 BchJ bacteriochlorop 20.5 2.4E+02 0.0051 21.8 4.7 38 36-73 18-58 (188)
270 PRK12277 50S ribosomal protein 20.3 87 0.0019 21.4 2.0 28 46-73 50-77 (83)
271 PRK14549 50S ribosomal protein 20.3 82 0.0018 20.3 1.8 54 56-119 9-62 (69)
272 PF13443 HTH_26: Cro/C1-type H 20.3 1.5E+02 0.0034 17.5 3.0 37 29-72 15-51 (63)
273 PRK13620 psbV cytochrome c-550 20.1 1.1E+02 0.0023 24.4 2.7 17 56-72 182-198 (215)
No 1
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=100.00 E-value=5.6e-49 Score=293.88 Aligned_cols=117 Identities=66% Similarity=1.064 Sum_probs=114.9
Q ss_pred cccccchhhccccCCCCeehheehhhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCCccCChhhhhc
Q 033139 7 EDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVANPRQFKIPDWFLNR 86 (126)
Q Consensus 7 ~~~~~mvrI~g~~l~~~K~v~~aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L~~~i~~~~~~~iP~w~~nr 86 (126)
++|+||+||+|+|||++|+|.+||++|||||+++|.+||+++||||++++++||++|+++|+++|++|.+|.+|+||+||
T Consensus 9 ~~~~~mvrI~~~~l~~~K~v~~aLt~I~GIG~~~A~~I~~~lgi~~~~~~~~Lt~~qi~~l~~~i~~~~~~~iP~w~~nr 88 (154)
T PTZ00134 9 DDFQHILRILNTNVDGKRKVPYALTAIKGIGRRFAYLVCKKAGIDVTKRAGELTAEEIEKIVEIIANPLQFKIPDWFLNR 88 (154)
T ss_pred hhhhhhhhccCccCCCCCEEEEeecccccccHHHHHHHHHHcCcCcCCCcccCCHHHHHHHHHHHhccccCCCChhHhhc
Confidence 58999999999999999999999999999999999999999999999999999999999999999988779999999999
Q ss_pred cccccCCccceeehhhHHHHHHHHHHHHHhcccceee
Q 033139 87 QKDYKDGRYSQVVSNALDMKLRDDLERLKKIRYGLVV 123 (126)
Q Consensus 87 ~~d~~tg~~~h~i~~dL~~~~~~dI~rl~~I~sy~~~ 123 (126)
|+|++||+|.|++|+||++.+++||+|+++|+||||+
T Consensus 89 ~kd~~tG~d~h~i~~dL~~~~~~dI~Rl~~I~sYRG~ 125 (154)
T PTZ00134 89 QRDPKDGKNSHLTSNMLDTKLREDLERLKKIRLHRGL 125 (154)
T ss_pred cccccccchhhhhHHHHHHHHHHHHHHHHHhcchhee
Confidence 9999999999999999999999999999999999996
No 2
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=100.00 E-value=2.1e-46 Score=278.85 Aligned_cols=118 Identities=37% Similarity=0.685 Sum_probs=115.5
Q ss_pred ccccccchhhccccCCCCeehheehhhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCCccCChhhhh
Q 033139 6 NEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVANPRQFKIPDWFLN 85 (126)
Q Consensus 6 ~~~~~~mvrI~g~~l~~~K~v~~aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L~~~i~~~~~~~iP~w~~n 85 (126)
+++|+||+||+|+|||++|++.+||++|||||+++|.+||+++||||++++++||++|+++|+++|++|..+++|+||+|
T Consensus 3 ~~~~~~m~rI~~~~i~~~k~i~~aLt~IyGIG~~~a~~Ic~~lgi~~~~~~~~Lt~~qi~~l~~~i~~~~~~~iP~w~~N 82 (149)
T PRK04053 3 EEEFKYIVRIAGTDLDGTKPVEYALTGIKGIGRRTARAIARKLGLDPNAKLGYLSDEEIEKIEEALEDPAEEGIPSWMLN 82 (149)
T ss_pred hhhhhhhHhhcCccCCCCCEEeeeccccccccHHHHHHHHHHcCcCCCCccCcCCHHHHHHHHHHHHhhccccCchhhhc
Confidence 47899999999999999999999999999999999999999999999999999999999999999998878999999999
Q ss_pred ccccccCCccceeehhhHHHHHHHHHHHHHhcccceee
Q 033139 86 RQKDYKDGRYSQVVSNALDMKLRDDLERLKKIRYGLVV 123 (126)
Q Consensus 86 r~~d~~tg~~~h~i~~dL~~~~~~dI~rl~~I~sy~~~ 123 (126)
||+|++||++.|+||+||++.+++||+|+++|+||||.
T Consensus 83 r~~d~~tg~~~~~ie~dLr~~~~~~I~rl~~I~syRG~ 120 (149)
T PRK04053 83 RRKDYETGEDLHLIGSDLILTVREDINRMKKIRSYRGI 120 (149)
T ss_pred cccccccCccceEehHHHHHHHHHHHHHHHHhcceeee
Confidence 99999999999999999999999999999999999996
No 3
>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=8.4e-46 Score=274.27 Aligned_cols=115 Identities=41% Similarity=0.750 Sum_probs=112.6
Q ss_pred ccccchhhccccCCCCeehheehhhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCCccCChhhhhcc
Q 033139 8 DFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVANPRQFKIPDWFLNRQ 87 (126)
Q Consensus 8 ~~~~mvrI~g~~l~~~K~v~~aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L~~~i~~~~~~~iP~w~~nr~ 87 (126)
+|+||+||+|+|||++|++.+||++|||||+++|.+||+++||||++++++||++|+++|+++|++ ..+++|+||+|||
T Consensus 1 ~~~~m~rI~~~~i~~~k~v~~aLt~I~GIG~~~a~~I~~~lgi~~~~~~~~Lt~~qi~~l~~~i~~-~~~~iP~w~~Nr~ 79 (144)
T TIGR03629 1 EFKYIVRIADTDLDGNKPVEYALTGIKGIGRRFARAIARKLGVDPNAKLGYLDDEEIEKLEEAVEN-YEYGIPSWLLNRR 79 (144)
T ss_pred CcceeeeeeCccCCCCCEEEEeecceeccCHHHHHHHHHHcCcCCCCCcccCCHHHHHHHHHHHHh-ccccCCHHHhhcc
Confidence 589999999999999999999999999999999999999999999999999999999999999997 4699999999999
Q ss_pred ccccCCccceeehhhHHHHHHHHHHHHHhcccceee
Q 033139 88 KDYKDGRYSQVVSNALDMKLRDDLERLKKIRYGLVV 123 (126)
Q Consensus 88 ~d~~tg~~~h~i~~dL~~~~~~dI~rl~~I~sy~~~ 123 (126)
+|++||+|.|+||+||++++++||+|+++|+||||+
T Consensus 80 ~d~~tg~~~~~ie~dL~~~~~~dI~rl~~I~~yRG~ 115 (144)
T TIGR03629 80 KDYETGEDLHLIGSDLDMTVREDINRMKKIRSYRGI 115 (144)
T ss_pred cccccCccceEehHHHHHHHHHHHHHHHHhcceeee
Confidence 999999999999999999999999999999999996
No 4
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=9.6e-35 Score=208.55 Aligned_cols=90 Identities=37% Similarity=0.629 Sum_probs=87.9
Q ss_pred chhhccccCCCCeehheehhhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCCccCChhhhhcccccc
Q 033139 12 ILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVANPRQFKIPDWFLNRQKDYK 91 (126)
Q Consensus 12 mvrI~g~~l~~~K~v~~aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L~~~i~~~~~~~iP~w~~nr~~d~~ 91 (126)
|+||+|+|||++|++.+|||+|||||.++|.+||+++||||++++++||++|+++|++++++ .|
T Consensus 1 maRIagvdip~~K~v~iALt~IyGIG~~~a~~I~~~~gi~~~~r~~eLteeei~~ir~~i~~--~~-------------- 64 (121)
T COG0099 1 MARIAGVDIPGNKRVVIALTYIYGIGRRRAKEICKKAGIDPDKRVGELTEEEIERLRDAIQN--KY-------------- 64 (121)
T ss_pred CceecccCCCCCceEeehhhhhccccHHHHHHHHHHcCCCHhHhhccCCHHHHHHHHHHHHh--cC--------------
Confidence 89999999999999999999999999999999999999999999999999999999999996 46
Q ss_pred CCccceeehhhHHHHHHHHHHHHHhcccceee
Q 033139 92 DGRYSQVVSNALDMKLRDDLERLKKIRYGLVV 123 (126)
Q Consensus 92 tg~~~h~i~~dL~~~~~~dI~rl~~I~sy~~~ 123 (126)
+||+||++++++||+||++|+||||+
T Consensus 65 ------~vegDLr~~v~~dIkRl~~i~~YRGi 90 (121)
T COG0099 65 ------LVEGDLRREVRMDIKRLMKIGCYRGI 90 (121)
T ss_pred ------eehhHHHHHHHHHHHHHHHhhhhhhh
Confidence 99999999999999999999999996
No 5
>KOG3311 consensus Ribosomal protein S18 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.2e-34 Score=214.98 Aligned_cols=124 Identities=62% Similarity=1.002 Sum_probs=121.5
Q ss_pred CCCCCccccccchhhccccCCCCeehheehhhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCCccCC
Q 033139 1 MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVANPRQFKIP 80 (126)
Q Consensus 1 ~~~~~~~~~~~mvrI~g~~l~~~K~v~~aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L~~~i~~~~~~~iP 80 (126)
|+++-++.|++|+||+|++++++++|.|||+.|||||...|..+|+++||++.+++++|+++|+..+..++++|..+.+|
T Consensus 1 msl~~~~~~q~i~~il~~~~dg~~~V~fAl~~i~Gig~~~A~~ic~K~~~~~~~r~gelt~~qi~~i~~i~~d~~~~~~~ 80 (152)
T KOG3311|consen 1 MSLVIPEAFQHILRILNTNVDGKRKVTFALTSIKGIGRRYAEIVCKKADLDLTKRAGELTEEQILRILQILNDPRQYKIP 80 (152)
T ss_pred CceecchhHHHHHHHHccCCCCCceeEEEEEEEeeechhhhhhhhhhcCcchhhhhccccHHHHHHHHHHhcCHHHhcCc
Confidence 78998899999999999999999999999999999999999999999999999999999999999999999999899999
Q ss_pred hhhhhccccccCCccceeehhhHHHHHHHHHHHHHhcccceeee
Q 033139 81 DWFLNRQKDYKDGRYSQVVSNALDMKLRDDLERLKKIRYGLVVL 124 (126)
Q Consensus 81 ~w~~nr~~d~~tg~~~h~i~~dL~~~~~~dI~rl~~I~sy~~~~ 124 (126)
.|++||++|.++|...|++++.|...+++||+|+++|.||||+-
T Consensus 81 ~~~l~rq~~~~dG~~~~l~~~~ld~r~r~~ieRlkki~~~RG~r 124 (152)
T KOG3311|consen 81 DWFLNRQKDIIDGKVNHLLGNGLDTRLRADIERLKKIRCHRGLR 124 (152)
T ss_pred hHHHHhhcccccCccccccchhhhhHHHHHHHHHhhhcccccce
Confidence 99999999999999999999999999999999999999999974
No 6
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=99.97 E-value=3e-32 Score=197.03 Aligned_cols=90 Identities=23% Similarity=0.353 Sum_probs=87.9
Q ss_pred chhhccccCCCCeehheehhhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCCccCChhhhhcccccc
Q 033139 12 ILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVANPRQFKIPDWFLNRQKDYK 91 (126)
Q Consensus 12 mvrI~g~~l~~~K~v~~aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L~~~i~~~~~~~iP~w~~nr~~d~~ 91 (126)
||||+|+++|++|+|.+||++|||||+++|.+||+++||||++++++||++|+++|.+++++ +|
T Consensus 1 mvrI~~~~i~~~k~v~~aLt~i~GIG~~~A~~ic~~lgi~~~~~~~~Lt~~qi~~l~~~i~~--~~-------------- 64 (122)
T CHL00137 1 MVRIAGVDLPRNKRIEYALTYIYGIGLTSAKEILEKANIDPDIRTKDLTDEQISALREIIEE--NY-------------- 64 (122)
T ss_pred CceEcCccCCCCCEeeeeecccccccHHHHHHHHHHcCcCcCcCcccCCHHHHHHHHHHHHH--hC--------------
Confidence 89999999999999999999999999999999999999999999999999999999999987 57
Q ss_pred CCccceeehhhHHHHHHHHHHHHHhcccceee
Q 033139 92 DGRYSQVVSNALDMKLRDDLERLKKIRYGLVV 123 (126)
Q Consensus 92 tg~~~h~i~~dL~~~~~~dI~rl~~I~sy~~~ 123 (126)
.+|+||++.+++||+|+++|+||||+
T Consensus 65 ------~i~~dL~~~~~~dI~rl~~I~sYRG~ 90 (122)
T CHL00137 65 ------QVEGDLRRFESLNIKRLMEINCYRGR 90 (122)
T ss_pred ------cchHHHHHHHHHHHHHHHHhCchhcc
Confidence 79999999999999999999999996
No 7
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=99.97 E-value=4.5e-32 Score=196.12 Aligned_cols=90 Identities=24% Similarity=0.398 Sum_probs=87.9
Q ss_pred chhhccccCCCCeehheehhhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCCccCChhhhhcccccc
Q 033139 12 ILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVANPRQFKIPDWFLNRQKDYK 91 (126)
Q Consensus 12 mvrI~g~~l~~~K~v~~aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L~~~i~~~~~~~iP~w~~nr~~d~~ 91 (126)
||||+|+|+|++|+|.+||++|||||+++|.+||+++||||++++++||++|+++|.++|++ +|
T Consensus 1 MvrI~~~~l~~~k~v~~aL~~I~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi~~l~~~i~~--~~-------------- 64 (122)
T PRK05179 1 MARIAGVDIPRNKRVVIALTYIYGIGRTRAKEILAAAGIDPDTRVKDLTDEELDKIREEIDK--NY-------------- 64 (122)
T ss_pred CceecCccCCCCcEEEeeecccccccHHHHHHHHHHhCcCcccccccCCHHHHHHHHHHHHh--hc--------------
Confidence 89999999999999999999999999999999999999999999999999999999999997 46
Q ss_pred CCccceeehhhHHHHHHHHHHHHHhcccceee
Q 033139 92 DGRYSQVVSNALDMKLRDDLERLKKIRYGLVV 123 (126)
Q Consensus 92 tg~~~h~i~~dL~~~~~~dI~rl~~I~sy~~~ 123 (126)
.+|+||++++++||+||++|+||||+
T Consensus 65 ------~i~~dL~~~~~~dI~rl~~I~sYRG~ 90 (122)
T PRK05179 65 ------KVEGDLRREVSMNIKRLMDIGCYRGL 90 (122)
T ss_pred ------cchHHHHHHHHHHHHHHHHhcceeee
Confidence 79999999999999999999999996
No 8
>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=99.96 E-value=2.5e-30 Score=184.83 Aligned_cols=88 Identities=26% Similarity=0.407 Sum_probs=85.6
Q ss_pred hhccccCCCCeehheehhhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCCccCChhhhhccccccCC
Q 033139 14 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVANPRQFKIPDWFLNRQKDYKDG 93 (126)
Q Consensus 14 rI~g~~l~~~K~v~~aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L~~~i~~~~~~~iP~w~~nr~~d~~tg 93 (126)
||+|+|+|++|+|.+||++|||||+.+|.+||+++||||++++++||++|+++|.++|++ +|
T Consensus 1 ri~~~~l~~~k~v~~aL~~i~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi~~l~~~l~~--~~---------------- 62 (113)
T TIGR03631 1 RIAGVDIPNNKRVEIALTYIYGIGRTRARKILEKAGIDPDKRVKDLTEEELNAIREEIEA--KY---------------- 62 (113)
T ss_pred CcCCccCCCCCEEeeeeeeeecccHHHHHHHHHHhCcCcccccccCCHHHHHHHHHHHHh--cC----------------
Confidence 799999999999999999999999999999999999999999999999999999999987 46
Q ss_pred ccceeehhhHHHHHHHHHHHHHhcccceee
Q 033139 94 RYSQVVSNALDMKLRDDLERLKKIRYGLVV 123 (126)
Q Consensus 94 ~~~h~i~~dL~~~~~~dI~rl~~I~sy~~~ 123 (126)
.+|+||++.+++||+|+++|+||||+
T Consensus 63 ----~i~~~L~~~~~~dI~rl~~I~syRG~ 88 (113)
T TIGR03631 63 ----KVEGDLRREVSLNIKRLMDIGCYRGL 88 (113)
T ss_pred ----cchHHHHHHHHHHHHHHHHhcceecc
Confidence 79999999999999999999999996
No 9
>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=99.96 E-value=3.2e-30 Score=182.09 Aligned_cols=88 Identities=39% Similarity=0.674 Sum_probs=83.6
Q ss_pred hhccccCCCCeehheehhhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCCccCChhhhhccccccCC
Q 033139 14 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVANPRQFKIPDWFLNRQKDYKDG 93 (126)
Q Consensus 14 rI~g~~l~~~K~v~~aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L~~~i~~~~~~~iP~w~~nr~~d~~tg 93 (126)
||+||+||++|+|.+||++|||||+++|.+||+++||+|++++++||++|+++|.+++++ ++
T Consensus 1 rI~~~~l~~~k~i~~aLt~IyGIG~~~A~~Ic~~lgi~~~~~~~~Ls~~~i~~l~~~i~~--~~---------------- 62 (107)
T PF00416_consen 1 RILGTNLPGNKPIYIALTKIYGIGRRKAKQICKKLGINPNKKVGDLSDEQIDKLRKIIEK--NH---------------- 62 (107)
T ss_dssp ETTTTCE-TSSBHHHHHTTSTTBCHHHHHHHHHHTTS-SSSBTTTSTHHHHHHHHHHHHT--HS----------------
T ss_pred CcCCCcCCCCcchHhHHhhhhccCHHHHHHHHHHcCCChhhhcccCCHHHHHHHHHHHHH--hc----------------
Confidence 799999999999999999999999999999999999999999999999999999999997 45
Q ss_pred ccceeehhhHHHHHHHHHHHHHhcccceee
Q 033139 94 RYSQVVSNALDMKLRDDLERLKKIRYGLVV 123 (126)
Q Consensus 94 ~~~h~i~~dL~~~~~~dI~rl~~I~sy~~~ 123 (126)
++++||++++++||+|+++|+||||+
T Consensus 63 ----~i~~~L~~~~~~~i~rl~~i~syRG~ 88 (107)
T PF00416_consen 63 ----LIENDLKRQVRENIKRLKKIKSYRGI 88 (107)
T ss_dssp ----TCHHHHHHHHHHHHHHHHHHTTHHHH
T ss_pred ----cccchHHHHHHHHHHHHHHHHHhhcc
Confidence 89999999999999999999999985
No 10
>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=97.51 E-value=9.2e-05 Score=50.85 Aligned_cols=52 Identities=29% Similarity=0.383 Sum_probs=44.2
Q ss_pred CCeehheeh---hhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 033139 22 GKQKIMFAL---TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVAN 73 (126)
Q Consensus 22 ~~K~v~~aL---t~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L~~~i~~ 73 (126)
.+++|..+| +.+-|||.-.|.+||-.+||+|..++++|+++|+.+|.+.+..
T Consensus 22 ~~~~ik~~LlDQ~~iaGiGNiy~~EiLf~a~i~P~~~~~~L~~~~~~~l~~~~~~ 76 (92)
T PF06831_consen 22 RRRPIKAALLDQSVIAGIGNIYADEILFRAGIHPERPASSLSEEELRRLHEAIKR 76 (92)
T ss_dssp CCSBHHHHHHCTTTSTT--HHHHHHHHHHTTB-TTSBGGGSHHHHHHHHHHHHHH
T ss_pred CcchHHHHHhCCCccccCcHHHHHHHHHHcCCCccCccccCCHHHHHHHHHHHHH
Confidence 477888887 6899999999999999999999999999999999998887763
No 11
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=97.23 E-value=0.00037 Score=56.06 Aligned_cols=52 Identities=31% Similarity=0.381 Sum_probs=48.1
Q ss_pred CCeehheeh---hhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 033139 22 GKQKIMFAL---TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVAN 73 (126)
Q Consensus 22 ~~K~v~~aL---t~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L~~~i~~ 73 (126)
.+++|.-+| +-+-|||.-.|.+||-.+||+|.+++++||++|++.|.+.+.+
T Consensus 154 ~~~~Ik~~LLDQ~~iaGiGNiya~EiLf~a~I~P~~~~~~Ls~~~~~~L~~~~~~ 208 (274)
T PRK01103 154 KKTAIKPALLDQTVVVGVGNIYADEALFRAGIHPERPAGSLSRAEAERLVDAIKA 208 (274)
T ss_pred CCccHHHHhhcCCeEecccHhHHHHHHHHcCCCccCccccCCHHHHHHHHHHHHH
Confidence 567899999 8999999999999999999999999999999999998887764
No 12
>PRK04184 DNA topoisomerase VI subunit B; Validated
Probab=97.13 E-value=0.00052 Score=60.47 Aligned_cols=51 Identities=25% Similarity=0.414 Sum_probs=47.1
Q ss_pred CeehheehhhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 033139 23 KQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVAN 73 (126)
Q Consensus 23 ~K~v~~aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L~~~i~~ 73 (126)
..-..|.-..|.+||..+|.+||+.+|+++++++++|+++|+.+|.+++.+
T Consensus 256 ~~l~~fL~~~f~~v~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~ 306 (535)
T PRK04184 256 RTLKEFLVEEFSRVGDKTADEILEKAGLDPNKKPKELTREELERLVEAFKK 306 (535)
T ss_pred CCHHHHHHHhhcccCHHHHHHHHHHcCCCCCCChhhCCHHHHHHHHHHHHh
Confidence 344567778999999999999999999999999999999999999999996
No 13
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=96.75 E-value=0.0021 Score=51.87 Aligned_cols=51 Identities=25% Similarity=0.311 Sum_probs=44.6
Q ss_pred CCeehheehhhh---cccccchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHh
Q 033139 22 GKQKIMFALTSI---KGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVA 72 (126)
Q Consensus 22 ~~K~v~~aLt~I---yGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L~~~i~ 72 (126)
.+.+|.-+|..- -|||.-.|.+||-.+||+|.+++++||++|+++|.+++.
T Consensus 153 ~~~~ik~~Lldq~viaGiGNiya~EiLf~a~i~P~~~~~~l~~~~~~~l~~a~~ 206 (272)
T PRK14810 153 RKTRIKSALLNQTLLRGVGNIYADEALFRAGIRPQRLASSLSRERLRKLHDAIG 206 (272)
T ss_pred CCccHHHHhhcCceeccccHhHHHHHHHHcCCCCCCCcccCCHHHHHHHHHHHH
Confidence 456777777544 999999999999999999999999999999998888554
No 14
>TIGR01052 top6b DNA topoisomerase VI, B subunit. This model describes DNA topoisomerase VI, an archaeal type II DNA topoisomerase (DNA gyrase).
Probab=96.70 E-value=0.002 Score=56.28 Aligned_cols=51 Identities=18% Similarity=0.313 Sum_probs=46.7
Q ss_pred CeehheehhhhcccccchHHHHHHHhCCC---CCCcCCCCCHHHHHHHHHHHhC
Q 033139 23 KQKIMFALTSIKGIGRRLANIVCKKADVD---MNKRAGELSAAELDQLMVVVAN 73 (126)
Q Consensus 23 ~K~v~~aLt~IyGIG~~~A~~Ic~~~gI~---p~~k~~~Ls~~qi~~L~~~i~~ 73 (126)
..-..|.-..|..||..+|.+||+.+|++ +++++++|+++|+.+|.+++.+
T Consensus 247 ~~l~~fL~~~f~~v~~~~a~~~~~~~g~~~~~~~~~~~~l~~~~~~~l~~~~~~ 300 (488)
T TIGR01052 247 STLRSFLVSEFSRIGEKKIKELLEKYGIDVDPLDKKPKELTWDEAEKIVNAFKE 300 (488)
T ss_pred ccHHHHHHHhhcccCHHHHHHHHHHhCCCccccCCChhhCCHHHHHHHHHHHHh
Confidence 34456777899999999999999999999 9999999999999999999997
No 15
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=96.50 E-value=0.0034 Score=50.56 Aligned_cols=50 Identities=20% Similarity=0.237 Sum_probs=43.9
Q ss_pred CCeehheeh---hhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHH
Q 033139 22 GKQKIMFAL---TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVV 71 (126)
Q Consensus 22 ~~K~v~~aL---t~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L~~~i 71 (126)
.+++|.-+| +-|-|||.-.|.+||=.+||+|..++++||++|+++|-+.+
T Consensus 142 ~~~~Ik~~LlDQ~~iaGIGNiyadEiLf~A~I~P~~~~~~Ls~~~~~~L~~~i 194 (269)
T PRK14811 142 TARPVKPWLLSQKPVAGVGNIYADESLWRARIHPARPATSLKAPEARRLYRAI 194 (269)
T ss_pred cCCcHHHHHhcCceeecccHHHHHHHHHHcCCCccCCcccCCHHHHHHHHHHH
Confidence 367888887 56899999999999999999999999999999988884444
No 16
>PRK10445 endonuclease VIII; Provisional
Probab=96.49 E-value=0.0035 Score=50.33 Aligned_cols=51 Identities=22% Similarity=0.298 Sum_probs=45.0
Q ss_pred Ceehheeh---hhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 033139 23 KQKIMFAL---TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVAN 73 (126)
Q Consensus 23 ~K~v~~aL---t~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L~~~i~~ 73 (126)
+++|.-+| +-+-|||.-.|.+||=.+||+|..++++||++|+++|.+.+.+
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 56777666 4688999999999999999999999999999999999887764
No 17
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=96.29 E-value=0.0053 Score=49.68 Aligned_cols=52 Identities=27% Similarity=0.355 Sum_probs=45.5
Q ss_pred CCeehheeh---hhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 033139 22 GKQKIMFAL---TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVAN 73 (126)
Q Consensus 22 ~~K~v~~aL---t~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L~~~i~~ 73 (126)
.+.+|.-+| +-|-|||.-.|.+||=.+||+|..++++||++|++.|.+.+..
T Consensus 163 ~~~~IK~~LLDQ~~vaGIGNiya~EiLf~A~IhP~~~~~~Ls~~~~~~L~~~i~~ 217 (282)
T PRK13945 163 RTRSIKTALLDQSIVAGIGNIYADESLFKAGIHPTTPAGQLKKKQLERLREAIIE 217 (282)
T ss_pred CCccHHHHhhcCCeEeccchhHHHHHHHHcCCCccCccccCCHHHHHHHHHHHHH
Confidence 466777777 5789999999999999999999999999999998888777653
No 18
>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=96.22 E-value=0.0053 Score=49.48 Aligned_cols=52 Identities=31% Similarity=0.355 Sum_probs=45.7
Q ss_pred CCeehheeh---hhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 033139 22 GKQKIMFAL---TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVAN 73 (126)
Q Consensus 22 ~~K~v~~aL---t~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L~~~i~~ 73 (126)
.+++|.-+| +-+-|||.-.|.+||=.+||+|..++++||++|+++|.+.+.+
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 456777777 5678999999999999999999999999999999999887764
No 19
>COG1389 DNA topoisomerase VI, subunit B [DNA replication, recombination, and repair]
Probab=95.48 E-value=0.011 Score=51.57 Aligned_cols=52 Identities=21% Similarity=0.308 Sum_probs=47.9
Q ss_pred CCeehheehhhhcccccchHHHHHHHhCCCCCCcCCCCC----HHHHHHHHHHHhC
Q 033139 22 GKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELS----AAELDQLMVVVAN 73 (126)
Q Consensus 22 ~~K~v~~aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls----~~qi~~L~~~i~~ 73 (126)
...--.|....|..||..+|.++|+.+|++|++++.+|+ .++.++|.+++.+
T Consensus 255 ~~tv~~fL~sef~rig~~ta~e~~e~~g~~~~~~p~~L~~~~~~eea~~lv~a~~~ 310 (538)
T COG1389 255 RSTVREFLVSEFSRIGEKTADELLEYAGFDPDKKPRELTKKKTREEAEKLVEAFKK 310 (538)
T ss_pred hhhHHHHHHHHHHHhhhhhHHHHHHHhcCCcccCHHHhhcccCHHHHHHHHHHHHh
Confidence 455567888999999999999999999999999999999 9999999999986
No 20
>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=95.47 E-value=0.0067 Score=51.30 Aligned_cols=50 Identities=30% Similarity=0.531 Sum_probs=34.6
Q ss_pred CCeehheehh-hhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHH
Q 033139 22 GKQKIMFALT-SIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVV 71 (126)
Q Consensus 22 ~~K~v~~aLt-~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L~~~i 71 (126)
....+.-+|. .+.|+|+..|.++|..+|+++++++.+++++++..|.+.+
T Consensus 185 ~~~~l~~~L~~~~~G~~~~la~ei~~ra~i~~~~~~~~~~~~~~~~l~~~~ 235 (455)
T PF05833_consen 185 KEKTLVKALSKNFQGFGPELAEEILYRAGIDKNKKVEELSDEEIEKLFEAI 235 (455)
T ss_dssp CG-BHHHHHHHHCTT--HHHHHHHHCCCTS-TTSBGGG--HHHHCHHHHHH
T ss_pred CcccHHHHHHHHHHHhHHHHHHHHHHHhCCCCccccccchhhhHHHHHHHH
Confidence 3455555555 4559999999999999999999999999999876655444
No 21
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=94.46 E-value=0.043 Score=44.84 Aligned_cols=58 Identities=26% Similarity=0.362 Sum_probs=47.9
Q ss_pred hccccCCCCeehheeh---hhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHh
Q 033139 15 VLNTNVDGKQKIMFAL---TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVA 72 (126)
Q Consensus 15 I~g~~l~~~K~v~~aL---t~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L~~~i~ 72 (126)
++..-...+++|.-+| +-+-|||.-.|.++|=.+||+|.+..++|+.+|+..|.+++.
T Consensus 147 l~~~l~~~~~~IK~~LLDQ~vvaGvGNIYa~E~Lf~agI~P~~~a~~l~~~~~~~l~~~i~ 207 (273)
T COG0266 147 LAEKLAKKKRRIKTALLDQKVVAGVGNIYADEILFRAGIHPARPAGDLSLAQLALLHEAIK 207 (273)
T ss_pred HHHHHhcCccchHHHhhcCCceecccHHHHHHHHHHcCCCcccCccccCHHHHHHHHHHHH
Confidence 3334445566677777 568999999999999999999999999999999888877765
No 22
>PF00633 HHH: Helix-hairpin-helix motif; InterPro: IPR000445 The HhH motif is an around 20 amino acids domain present in prokaryotic and eukaryotic non-sequence-specific DNA binding proteins [, , ]. The HhH motif is similar to, but distinct from, the HtH motif. Both of these motifs have two helices connected by a short turn. In the HtH motif the second helix binds to DNA with the helix in the major groove. This allows the contact between specific base and residues throughout the protein. In the HhH motif the second helix does not protrude from the surface of the protein and therefore cannot lie in the major groove of the DNA. Crystallographic studies suggest that the interaction of the HhH domain with DNA is mediated by amino acids located in the strongly conserved loop (L-P-G-V) and at the N-terminal end of the second helix []. This interaction could involve the formation of hydrogen bonds between protein backbone nitrogens and DNA phosphate groups []. The structural difference between the HtH and HhH domains is reflected at the functional level: whereas the HtH domain, found primarily in gene regulatory proteins, binds DNA in a sequence specific manner, the HhH domain is rather found in proteins involved in enzymatic activities and binds DNA with no sequence specificity []. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain [].; GO: 0003677 DNA binding; PDB: 3C1Z_A 3C23_A 3C1Y_A 3C21_A 1Z00_A 2A1J_B 1KEA_A 1VRL_A 1RRQ_A 3G0Q_A ....
Probab=94.28 E-value=0.025 Score=31.38 Aligned_cols=18 Identities=33% Similarity=0.565 Sum_probs=15.1
Q ss_pred ehhhhcccccchHHHHHH
Q 033139 29 ALTSIKGIGRRLANIVCK 46 (126)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~ 46 (126)
-|..+.|||+.+|..|+.
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 478999999999999975
No 23
>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=93.37 E-value=0.066 Score=44.79 Aligned_cols=50 Identities=24% Similarity=0.421 Sum_probs=43.7
Q ss_pred CCeehheehhhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 033139 22 GKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVAN 73 (126)
Q Consensus 22 ~~K~v~~aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L~~~i~~ 73 (126)
+++.+.-.|+.+ +-.+++..||+.+||++++++++||++|+++|.+.+++
T Consensus 282 ~~~~~~~~l~~~--l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~lk~ 331 (400)
T TIGR00275 282 PKKTVKNILKGL--LPKRLAELLLEQLGIDPDLPAAQLSKKEIKKLVQLLKN 331 (400)
T ss_pred hhhhHHHHhhhh--hhHHHHHHHHHHcCCCCCCChHHCCHHHHHHHHHHHhC
Confidence 466666666644 78899999999999999999999999999999999986
No 24
>PF11798 IMS_HHH: IMS family HHH motif; InterPro: IPR024728 This helix-hairpin-helix motif is found in proteins belonging to the type-Y family of DNA polymerases []. This type of polymerases are thought to be involved in UV protection and mutation [, ]. ; PDB: 3PZP_B 2OH2_B 2W7O_B 3IN5_B 1T94_A 2W7P_B 2W8K_A 2AGQ_A 1RYR_A 3RAX_A ....
Probab=93.09 E-value=0.05 Score=30.44 Aligned_cols=22 Identities=23% Similarity=0.447 Sum_probs=16.1
Q ss_pred eehhhhcccccchHHHHHHHhCC
Q 033139 28 FALTSIKGIGRRLANIVCKKADV 50 (126)
Q Consensus 28 ~aLt~IyGIG~~~A~~Ic~~~gI 50 (126)
..++.+.|||+.++.+ ++++||
T Consensus 11 lpi~~~~GIG~kt~~k-L~~~GI 32 (32)
T PF11798_consen 11 LPIRKFWGIGKKTAKK-LNKLGI 32 (32)
T ss_dssp SBGGGSTTS-HHHHHH-HHCTT-
T ss_pred CCHHhhCCccHHHHHH-HHHccC
Confidence 3578999999999998 555554
No 25
>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=91.91 E-value=0.09 Score=32.65 Aligned_cols=22 Identities=23% Similarity=0.314 Sum_probs=15.8
Q ss_pred ehhhhcccccchHHHHHHHhCCC
Q 033139 29 ALTSIKGIGRRLANIVCKKADVD 51 (126)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~~gI~ 51 (126)
.+++|+|||+++|++..+ .|+.
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 468999999999999987 6764
No 26
>COG0030 KsgA Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis]
Probab=91.42 E-value=0.17 Score=41.01 Aligned_cols=48 Identities=23% Similarity=0.299 Sum_probs=43.8
Q ss_pred CCCeehheehhhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 033139 21 DGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVAN 73 (126)
Q Consensus 21 ~~~K~v~~aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L~~~i~~ 73 (126)
...|++.-+|+..++ ..++|+.+|++++.|+.+||-+|.-+|.+.+..
T Consensus 209 ~RRKtl~n~l~~~~~-----~~~~l~~~~i~~~~R~e~ls~~~f~~L~~~l~~ 256 (259)
T COG0030 209 QRRKTLRNNLKNLFG-----LEEVLEAAGIDPNARAENLSPEDFLKLANALKG 256 (259)
T ss_pred hhhHHHHHHHHhhhh-----HHHHHHhcCCCcccChhhCCHHHHHHHHHHHhh
Confidence 467888889988888 899999999999999999999999999999874
No 27
>PRK00274 ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed
Probab=91.40 E-value=0.21 Score=39.79 Aligned_cols=53 Identities=23% Similarity=0.284 Sum_probs=42.8
Q ss_pred CCCCeehheehhhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 033139 20 VDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVAN 73 (126)
Q Consensus 20 l~~~K~v~~aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L~~~i~~ 73 (126)
-...|++.-+|..+++. ...+.++++.+|++++.++.+|+.+|..+|.+.+.+
T Consensus 218 ~~rrk~l~~~l~~~~~~-~~~~~~~l~~~~~~~~~r~~~l~~~~~~~L~~~~~~ 270 (272)
T PRK00274 218 AQRRKTLRNNLKNLFGS-KEKLEEALEAAGIDPNRRAETLSVEEFVRLANALAA 270 (272)
T ss_pred hchHHHHHHHHHhhccc-hHHHHHHHHHCCCCcCCCceeCCHHHHHHHHHHHHh
Confidence 34567777777776552 245678899999999999999999999999998864
No 28
>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=91.10 E-value=0.034 Score=34.72 Aligned_cols=26 Identities=27% Similarity=0.404 Sum_probs=21.5
Q ss_pred hheehhhhcccccchHHHHHHHhCCCC
Q 033139 26 IMFALTSIKGIGRRLANIVCKKADVDM 52 (126)
Q Consensus 26 v~~aLt~IyGIG~~~A~~Ic~~~gI~p 52 (126)
++-.|..|.|||+..|..+.+. |+..
T Consensus 3 ~~~~L~~I~Gig~~~a~~L~~~-G~~t 28 (60)
T PF14520_consen 3 VFDDLLSIPGIGPKRAEKLYEA-GIKT 28 (60)
T ss_dssp HHHHHHTSTTCHHHHHHHHHHT-TCSS
T ss_pred HHHhhccCCCCCHHHHHHHHhc-CCCc
Confidence 4557889999999999998877 7764
No 29
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=90.98 E-value=0.17 Score=37.25 Aligned_cols=59 Identities=19% Similarity=0.158 Sum_probs=44.4
Q ss_pred hccccCCCCeehheehhhhcccccchHHHHHHHhCC---CCCCcCCCCCHHHHHHHHHHHhC
Q 033139 15 VLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADV---DMNKRAGELSAAELDQLMVVVAN 73 (126)
Q Consensus 15 I~g~~l~~~K~v~~aLt~IyGIG~~~A~~Ic~~~gI---~p~~k~~~Ls~~qi~~L~~~i~~ 73 (126)
-.|.-++-|..-.-.|+.+.|||+++|.+|++.-.+ +.-..+..+++.|.+.+.+..++
T Consensus 48 ~~~~kIdiN~A~~~el~~lpGigP~~A~~IV~nGpf~sveDL~~V~GIgekqk~~l~k~~~~ 109 (132)
T PRK02515 48 EFGEKIDLNNSSVRAFRQFPGMYPTLAGKIVKNAPYDSVEDVLNLPGLSERQKELLEANLDN 109 (132)
T ss_pred hcCCcccCCccCHHHHHHCCCCCHHHHHHHHHCCCCCCHHHHHcCCCCCHHHHHHHHHhhcc
Confidence 346666666666677999999999999999963322 22345777899999999998875
No 30
>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=89.71 E-value=0.47 Score=40.40 Aligned_cols=51 Identities=27% Similarity=0.402 Sum_probs=44.5
Q ss_pred CCCeehheehhhhcccccchHHHHHHHhCC-CCCCcCCCCCHHHHHHHHHHHhC
Q 033139 21 DGKQKIMFALTSIKGIGRRLANIVCKKADV-DMNKRAGELSAAELDQLMVVVAN 73 (126)
Q Consensus 21 ~~~K~v~~aLt~IyGIG~~~A~~Ic~~~gI-~p~~k~~~Ls~~qi~~L~~~i~~ 73 (126)
.+++.+...|..+ +-++++..+|+.++| ++++++.+++++++.+|.+.+++
T Consensus 288 ~~~~~~~~~l~~~--lp~rl~~~ll~~~~i~~~~~~~~~l~~~~~~~L~~~lk~ 339 (409)
T PF03486_consen 288 NPKRTLKNFLKGL--LPKRLALALLKRAGIKDPDKKVSELSKKERNRLANLLKR 339 (409)
T ss_dssp TTTSBHHHHHTTT--S-HHHHHHHHHHTTS-STTSBGGGS-HHHHHHHHHHHHC
T ss_pred HHhhHHHHHHHHH--hHHHHHHHHHHHcCCCccccchhhcCHHHHHHHHHHHHh
Confidence 4577788888776 889999999999999 99999999999999999999986
No 31
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=89.71 E-value=0.21 Score=26.33 Aligned_cols=19 Identities=26% Similarity=0.468 Sum_probs=16.5
Q ss_pred ehhhhcccccchHHHHHHH
Q 033139 29 ALTSIKGIGRRLANIVCKK 47 (126)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~ 47 (126)
.|..+.|||+.+|..|++.
T Consensus 2 ~L~~i~GiG~k~A~~il~~ 20 (26)
T smart00278 2 ELLKVPGIGPKTAEKILEA 20 (26)
T ss_pred hhhhCCCCCHHHHHHHHHh
Confidence 3678999999999999864
No 32
>COG1293 Predicted RNA-binding protein homologous to eukaryotic snRNP [Transcription]
Probab=89.35 E-value=0.57 Score=41.61 Aligned_cols=49 Identities=22% Similarity=0.314 Sum_probs=44.0
Q ss_pred ehheehhhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 033139 25 KIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVAN 73 (126)
Q Consensus 25 ~v~~aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L~~~i~~ 73 (126)
-+..++..+.|+|+-.|.++|-.+|++++....++.++.+..+...+++
T Consensus 187 ~~~~~~~~~~g~~~~~a~el~~rag~~~~~~~~~~~~~~~~~v~~~~~~ 235 (564)
T COG1293 187 DIVRLLARFLGLGGLLAEELLSRAGLDKKVPAKDLFEEEIKKVREALEE 235 (564)
T ss_pred HHHHHHHHhcCCCHHHHHHHHHhcCCCcCCchhhhhHHHHHHHHHHHHh
Confidence 3456788899999999999999999999999999999999999887654
No 33
>TIGR00755 ksgA dimethyladenosine transferase. Alternate name: S-adenosylmethionine--6-N',N'-adenosyl (rRNA) dimethyltransferase
Probab=89.26 E-value=0.39 Score=37.65 Aligned_cols=59 Identities=17% Similarity=0.251 Sum_probs=44.4
Q ss_pred cccchhhccccCCCCeehheehhhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHH
Q 033139 9 FQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVV 71 (126)
Q Consensus 9 ~~~mvrI~g~~l~~~K~v~~aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L~~~i 71 (126)
|.++++. ..-...|++.-+|..+++- ..+..+++.+|+++++++.+||.+|..+|.+.+
T Consensus 195 ~~~~~~~--~F~~rrk~l~~~l~~~~~~--~~~~~~l~~~~i~~~~r~~~l~~~~~~~l~~~~ 253 (253)
T TIGR00755 195 FEKLLKA--AFSQRRKTLRNNLKQLLKA--SKLEEVLEQLGLDPTARAEQLSPEDFLRLANLL 253 (253)
T ss_pred HHHHHHH--HHccchHHHHHHHhhhcch--hHHHHHHHHCCcCCCCCcccCCHHHHHHHHHhC
Confidence 4455543 2345678888888877442 356678999999999999999999999997753
No 34
>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=88.84 E-value=0.22 Score=32.69 Aligned_cols=35 Identities=20% Similarity=0.356 Sum_probs=27.0
Q ss_pred ccccccchhhcc--ccCCCCeehheehhhhcccccchHHHHHHHhC
Q 033139 6 NEDFQHILRVLN--TNVDGKQKIMFALTSIKGIGRRLANIVCKKAD 49 (126)
Q Consensus 6 ~~~~~~mvrI~g--~~l~~~K~v~~aLt~IyGIG~~~A~~Ic~~~g 49 (126)
.++|.++.=+.| +|- +..+.|||+.+|.+++++.|
T Consensus 7 ~~q~~d~~~L~GD~~D~---------i~gv~giG~k~A~~ll~~~~ 43 (75)
T cd00080 7 PEQFIDLAILVGDKSDN---------IPGVPGIGPKTALKLLKEYG 43 (75)
T ss_pred HHHHHHHHHHcCCcccc---------CCCCCcccHHHHHHHHHHhC
Confidence 466777777777 543 34689999999999998865
No 35
>PF09883 DUF2110: Uncharacterized protein conserved in archaea (DUF2110); InterPro: IPR016757 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=88.11 E-value=1.9 Score=34.38 Aligned_cols=55 Identities=13% Similarity=0.181 Sum_probs=46.7
Q ss_pred ccCCCCeehheehhhhcccccchHHHHHHHhCCCCCCc------------CCCCCHHHHHHHHHHHhC
Q 033139 18 TNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKR------------AGELSAAELDQLMVVVAN 73 (126)
Q Consensus 18 ~~l~~~K~v~~aLt~IyGIG~~~A~~Ic~~~gI~p~~k------------~~~Ls~~qi~~L~~~i~~ 73 (126)
++++ ...+..--..++|+|+...++|.+.+|+=++.+ ...||++|+++|-++.+.
T Consensus 92 ~~v~-G~~~~ip~d~L~~Lg~g~~~Qi~~rFG~V~hlPvev~~v~~~~~~~~rltd~q~d~l~~W~~~ 158 (225)
T PF09883_consen 92 VDVD-GIFVPIPKDELKPLGPGSPRQIRRRFGLVQHLPVEVEFVKVEDGIEARLTDEQVDRLYEWTRD 158 (225)
T ss_pred EEee-cccccCcHHHhcccCCCCHHHHHHHhCcccCCceEEEEEEcccCcccccCHHHHHHHHHHhhC
Confidence 3444 566666667889999999999999999999988 567999999999999986
No 36
>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=86.67 E-value=0.29 Score=38.79 Aligned_cols=62 Identities=24% Similarity=0.297 Sum_probs=48.7
Q ss_pred cccccchhhccccCCCCeehheehhhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHh
Q 033139 7 EDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVA 72 (126)
Q Consensus 7 ~~~~~mvrI~g~~l~~~K~v~~aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L~~~i~ 72 (126)
+.|.++++.+= ....|++.-+|+.+++ ...+..+.+.+||+++.++.+|+.+|..+|.++++
T Consensus 200 ~~~~~~~~~~F--~~rrk~l~~~L~~~~~--~~~~~~~~~~~~i~~~~r~~~ls~~~~~~l~~~l~ 261 (262)
T PF00398_consen 200 DAFEYFVRQLF--SQRRKTLRNSLKSLFP--GEQLEELLEKAGIDPNARAEELSPEQFLKLFKYLN 261 (262)
T ss_dssp HHHHHHHHHHH--TTTTSBHHHHTTCTHH--HHHHHHHHHHCTHTTTTCGGCHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHH--hCcchHHHHHHhhhcC--HHHHHHhhhhcCCCCCCCcccCCHHHHHHHHHHhh
Confidence 34566666543 3588999999887753 33457777889999999999999999999999886
No 37
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=86.06 E-value=0.49 Score=27.15 Aligned_cols=34 Identities=18% Similarity=0.354 Sum_probs=24.2
Q ss_pred cccccchhhccccCCCCeehheehhhhcccccchHHHHHHH
Q 033139 7 EDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKK 47 (126)
Q Consensus 7 ~~~~~mvrI~g~~l~~~K~v~~aLt~IyGIG~~~A~~Ic~~ 47 (126)
++|-++.=+.| |-.+| ...+.|||+.+|.+++++
T Consensus 2 ~q~~~~~~L~G-D~~dn------i~Gv~giG~ktA~~ll~~ 35 (36)
T smart00279 2 EQLIDYAILVG-DYSDN------IPGVKGIGPKTALKLLRE 35 (36)
T ss_pred HHHHHHHHHhC-cCCCC------CCCCCcccHHHHHHHHHh
Confidence 34555666667 44443 367899999999999875
No 38
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=85.99 E-value=0.49 Score=34.94 Aligned_cols=44 Identities=20% Similarity=0.231 Sum_probs=39.2
Q ss_pred eehhhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHh
Q 033139 28 FALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVA 72 (126)
Q Consensus 28 ~aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L~~~i~ 72 (126)
-=|+.|.|||+..+. .++.+||-.-..+-.+|..++..+..+++
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 358999999998875 57899999999999999999999999986
No 39
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=85.79 E-value=0.42 Score=36.84 Aligned_cols=21 Identities=19% Similarity=0.352 Sum_probs=17.8
Q ss_pred eehhhhcccccchHHHHHHHh
Q 033139 28 FALTSIKGIGRRLANIVCKKA 48 (126)
Q Consensus 28 ~aLt~IyGIG~~~A~~Ic~~~ 48 (126)
-+|++++|||+++|.+||-.+
T Consensus 108 ~~L~~vpGIGkKtAerIilEL 128 (188)
T PRK14606 108 EGLSKLPGISKKTAERIVMEL 128 (188)
T ss_pred HHHhhCCCCCHHHHHHHHHHH
Confidence 468999999999999999443
No 40
>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=85.69 E-value=0.35 Score=37.20 Aligned_cols=32 Identities=16% Similarity=0.321 Sum_probs=26.5
Q ss_pred CCCeehheehhhhcccccchHHHHHHHhCCCC
Q 033139 21 DGKQKIMFALTSIKGIGRRLANIVCKKADVDM 52 (126)
Q Consensus 21 ~~~K~v~~aLt~IyGIG~~~A~~Ic~~~gI~p 52 (126)
|++..+.--|..++|||+.+|..+|..+|=-.
T Consensus 108 p~t~~lre~Ll~LpGVG~KTAnvVL~~l~~~~ 139 (177)
T TIGR03252 108 PDGKELLRRLKALPGFGKQKAKIFLALLGKQL 139 (177)
T ss_pred CCcHHHHHHHHcCCCCCHHHHHHHHHHHHHHh
Confidence 66777777899999999999999998776443
No 41
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=85.32 E-value=0.45 Score=36.58 Aligned_cols=20 Identities=25% Similarity=0.410 Sum_probs=17.3
Q ss_pred eehhhhcccccchHHHHHHH
Q 033139 28 FALTSIKGIGRRLANIVCKK 47 (126)
Q Consensus 28 ~aLt~IyGIG~~~A~~Ic~~ 47 (126)
-+|++++|||+++|.+|+-.
T Consensus 108 ~~L~~vpGIGkKtAeRIilE 127 (183)
T PRK14601 108 SVLKKVPGIGPKSAKRIIAE 127 (183)
T ss_pred HHHhhCCCCCHHHHHHHHHH
Confidence 46899999999999999943
No 42
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=84.46 E-value=0.52 Score=36.50 Aligned_cols=21 Identities=24% Similarity=0.433 Sum_probs=17.9
Q ss_pred eehhhhcccccchHHHHHHHh
Q 033139 28 FALTSIKGIGRRLANIVCKKA 48 (126)
Q Consensus 28 ~aLt~IyGIG~~~A~~Ic~~~ 48 (126)
-+|+.++|||+++|.+|+-.+
T Consensus 108 ~~L~kvpGIGkKtAerIilEL 128 (195)
T PRK14604 108 ARLARVPGIGKKTAERIVLEL 128 (195)
T ss_pred HHHhhCCCCCHHHHHHHHHHH
Confidence 478999999999999999443
No 43
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=84.37 E-value=0.53 Score=36.49 Aligned_cols=19 Identities=37% Similarity=0.557 Sum_probs=16.9
Q ss_pred eehhhhcccccchHHHHHH
Q 033139 28 FALTSIKGIGRRLANIVCK 46 (126)
Q Consensus 28 ~aLt~IyGIG~~~A~~Ic~ 46 (126)
-+|++++|||+++|.+||-
T Consensus 107 ~~L~kvpGIGkKtAerIil 125 (197)
T PRK14603 107 RLLTSASGVGKKLAERIAL 125 (197)
T ss_pred HHHhhCCCCCHHHHHHHHH
Confidence 4689999999999999993
No 44
>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=84.25 E-value=0.62 Score=31.29 Aligned_cols=27 Identities=26% Similarity=0.582 Sum_probs=22.1
Q ss_pred CeehheehhhhcccccchHHHHHHHhC
Q 033139 23 KQKIMFALTSIKGIGRRLANIVCKKAD 49 (126)
Q Consensus 23 ~K~v~~aLt~IyGIG~~~A~~Ic~~~g 49 (126)
+..|.++|+.|+|||...|.+|++.-.
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 468999999999999999999998774
No 45
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=83.89 E-value=0.57 Score=36.52 Aligned_cols=21 Identities=29% Similarity=0.501 Sum_probs=17.5
Q ss_pred eehhhhcccccchHHHHHHHh
Q 033139 28 FALTSIKGIGRRLANIVCKKA 48 (126)
Q Consensus 28 ~aLt~IyGIG~~~A~~Ic~~~ 48 (126)
-+|++++|||+++|.+|+-.+
T Consensus 107 ~~L~~vpGIGkKtAeRIIlEL 127 (196)
T PRK13901 107 ELISKVKGIGNKMAGKIFLKL 127 (196)
T ss_pred HHHhhCCCCCHHHHHHHHHHH
Confidence 468999999999999998443
No 46
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=83.30 E-value=0.61 Score=36.28 Aligned_cols=19 Identities=37% Similarity=0.562 Sum_probs=16.7
Q ss_pred eehhhhcccccchHHHHHH
Q 033139 28 FALTSIKGIGRRLANIVCK 46 (126)
Q Consensus 28 ~aLt~IyGIG~~~A~~Ic~ 46 (126)
-+|++++|||+++|.+|+-
T Consensus 109 ~~L~~ipGIGkKtAerIil 127 (203)
T PRK14602 109 AALTRVSGIGKKTAQHIFL 127 (203)
T ss_pred HHHhcCCCcCHHHHHHHHH
Confidence 4689999999999999993
No 47
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=81.98 E-value=0.77 Score=35.93 Aligned_cols=21 Identities=33% Similarity=0.498 Sum_probs=16.7
Q ss_pred eehhhhcccccchHHHHHHHh
Q 033139 28 FALTSIKGIGRRLANIVCKKA 48 (126)
Q Consensus 28 ~aLt~IyGIG~~~A~~Ic~~~ 48 (126)
-+|++++|||+++|.+||-.+
T Consensus 108 ~~L~k~PGIGkKtAerivleL 128 (201)
T COG0632 108 KALSKIPGIGKKTAERIVLEL 128 (201)
T ss_pred HhhhcCCCCCHHHHHHHHHHH
Confidence 468889999999999988443
No 48
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=81.73 E-value=1 Score=27.95 Aligned_cols=20 Identities=35% Similarity=0.561 Sum_probs=17.8
Q ss_pred ehhhhcccccchHHHHHHHh
Q 033139 29 ALTSIKGIGRRLANIVCKKA 48 (126)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~~ 48 (126)
.|..+.|||+.+|.+|++.+
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 48899999999999999865
No 49
>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=80.64 E-value=1.3 Score=27.66 Aligned_cols=26 Identities=8% Similarity=0.190 Sum_probs=20.6
Q ss_pred hcccccchHHHHHHHhCCC--CCCcCCC
Q 033139 33 IKGIGRRLANIVCKKADVD--MNKRAGE 58 (126)
Q Consensus 33 IyGIG~~~A~~Ic~~~gI~--p~~k~~~ 58 (126)
--|||.++-+++|.++||. |-.++++
T Consensus 24 ~Lgv~~T~LKr~CR~~GI~RWP~Rkl~S 51 (52)
T PF02042_consen 24 ELGVSVTTLKRRCRRLGIPRWPYRKLKS 51 (52)
T ss_pred HhCCCHHHHHHHHHHcCCCCCCchhhcc
Confidence 4699999999999999997 4455443
No 50
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=79.98 E-value=0.51 Score=36.41 Aligned_cols=38 Identities=13% Similarity=0.286 Sum_probs=29.2
Q ss_pred hhccccCCCCeehheehhhhcccccchHHHHHHHhCCC
Q 033139 14 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVD 51 (126)
Q Consensus 14 rI~g~~l~~~K~v~~aLt~IyGIG~~~A~~Ic~~~gI~ 51 (126)
.++|-.=...+.++-.|.++.|||+++|..|+..++.+
T Consensus 59 ~LyGF~~~~Er~lF~~Li~V~GIGpK~Al~ILs~~~~~ 96 (194)
T PRK14605 59 SLFGFATTEELSLFETLIDVSGIGPKLGLAMLSAMNAE 96 (194)
T ss_pred eeeCCCCHHHHHHHHHHhCCCCCCHHHHHHHHHhCCHH
Confidence 56676667777888888888888888888888776533
No 51
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=79.08 E-value=0.65 Score=35.59 Aligned_cols=59 Identities=10% Similarity=0.226 Sum_probs=40.8
Q ss_pred hccccCCCCeehheehhhhcccccchHHHHHHHhCCCCC------------CcCCCCCHHHHHHHHHHHhC
Q 033139 15 VLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMN------------KRAGELSAAELDQLMVVVAN 73 (126)
Q Consensus 15 I~g~~l~~~K~v~~aLt~IyGIG~~~A~~Ic~~~gI~p~------------~k~~~Ls~~qi~~L~~~i~~ 73 (126)
+.|-.=...+.+...|..|.|||+++|..|++.+|.+.- .++.-+++...++|...+..
T Consensus 60 l~gF~~~~ek~~f~~L~~i~GIGpk~A~~il~~fg~~~l~~~i~~~d~~~L~~v~Gig~k~A~~I~~~l~~ 130 (192)
T PRK00116 60 LYGFLTKEERELFRLLISVSGVGPKLALAILSGLSPEELVQAIANGDVKALTKVPGIGKKTAERIVLELKD 130 (192)
T ss_pred HcCcCCHHHHHHHHHHhcCCCCCHHHHHHHHHhCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHH
Confidence 355553344555558899999999999999999885211 23555677777777777765
No 52
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=78.17 E-value=1.2 Score=34.34 Aligned_cols=18 Identities=33% Similarity=0.567 Sum_probs=16.0
Q ss_pred eehhhhcccccchHHHHH
Q 033139 28 FALTSIKGIGRRLANIVC 45 (126)
Q Consensus 28 ~aLt~IyGIG~~~A~~Ic 45 (126)
-+|+.++|||+++|.+|+
T Consensus 108 ~~L~~vpGIGkKtAerIi 125 (194)
T PRK14605 108 ELLSTIPGIGKKTASRIV 125 (194)
T ss_pred HHHHhCCCCCHHHHHHHH
Confidence 358999999999999966
No 53
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=78.11 E-value=1.1 Score=34.54 Aligned_cols=18 Identities=39% Similarity=0.650 Sum_probs=14.9
Q ss_pred eehhhhcccccchHHHHHH
Q 033139 28 FALTSIKGIGRRLANIVCK 46 (126)
Q Consensus 28 ~aLt~IyGIG~~~A~~Ic~ 46 (126)
-+| +++|||+++|.+||-
T Consensus 108 ~~L-~vpGIGkKtAerIil 125 (186)
T PRK14600 108 AAL-KVNGIGEKLINRIIT 125 (186)
T ss_pred hhe-ECCCCcHHHHHHHHH
Confidence 456 799999999999983
No 54
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=77.50 E-value=1 Score=28.54 Aligned_cols=18 Identities=28% Similarity=0.589 Sum_probs=14.9
Q ss_pred hhcccccchHHHHHHHhC
Q 033139 32 SIKGIGRRLANIVCKKAD 49 (126)
Q Consensus 32 ~IyGIG~~~A~~Ic~~~g 49 (126)
.|+|||.++|+.+++..|
T Consensus 7 GI~~VG~~~ak~L~~~f~ 24 (64)
T PF12826_consen 7 GIPGVGEKTAKLLAKHFG 24 (64)
T ss_dssp TSTT--HHHHHHHHHCCS
T ss_pred CCCCccHHHHHHHHHHcC
Confidence 699999999999999888
No 55
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=77.24 E-value=1.2 Score=28.25 Aligned_cols=47 Identities=15% Similarity=0.222 Sum_probs=29.6
Q ss_pred CeehheehhhhcccccchHHHHHHHh-------CCCCCCcCCCCCHHHHHHHHH
Q 033139 23 KQKIMFALTSIKGIGRRLANIVCKKA-------DVDMNKRAGELSAAELDQLMV 69 (126)
Q Consensus 23 ~K~v~~aLt~IyGIG~~~A~~Ic~~~-------gI~p~~k~~~Ls~~qi~~L~~ 69 (126)
|..=.--|..++|||+..|..|.+.= .++.-..+..++++.+++|..
T Consensus 9 N~as~~eL~~lpgi~~~~A~~Iv~~R~~~G~f~s~~dL~~v~gi~~~~~~~l~~ 62 (65)
T PF12836_consen 9 NTASAEELQALPGIGPKQAKAIVEYREKNGPFKSLEDLKEVPGIGPKTYEKLKP 62 (65)
T ss_dssp TTS-HHHHHTSTT--HHHHHHHHHHHHHH-S-SSGGGGGGSTT--HHHHHHHCC
T ss_pred ccCCHHHHHHcCCCCHHHHHHHHHHHHhCcCCCCHHHHhhCCCCCHHHHHHHHh
Confidence 34444568899999999999999755 344445666667777777654
No 56
>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=75.28 E-value=3.1 Score=37.97 Aligned_cols=41 Identities=27% Similarity=0.391 Sum_probs=29.2
Q ss_pred hhcccccchHHHHHHHhCCC--------CC--CcCCCCCHHHHHHHHHHHh
Q 033139 32 SIKGIGRRLANIVCKKADVD--------MN--KRAGELSAAELDQLMVVVA 72 (126)
Q Consensus 32 ~IyGIG~~~A~~Ic~~~gI~--------p~--~k~~~Ls~~qi~~L~~~i~ 72 (126)
.|+|||+.+|.+|.+.+|.+ |+ ..+.-+++...+.|.+.++
T Consensus 88 ~~~GIG~~~A~~iv~~fg~~~~~~i~~~~~~L~~v~gi~~~~~~~i~~~~~ 138 (720)
T TIGR01448 88 SIKGVGKKLAQRIVKTFGEAAFDVLDDDPEKLLEVPGISKANLEKFVSQWS 138 (720)
T ss_pred CCCCcCHHHHHHHHHHhCHhHHHHHHhCHHHHhcCCCCCHHHHHHHHHHHH
Confidence 49999999999999999865 21 2334566666666665544
No 57
>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=74.67 E-value=1.8 Score=27.64 Aligned_cols=19 Identities=26% Similarity=0.504 Sum_probs=16.6
Q ss_pred ehhhhcccccchHHHHHHH
Q 033139 29 ALTSIKGIGRRLANIVCKK 47 (126)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~ 47 (126)
+++.++|||.++|.+|-+-
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 58
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=74.03 E-value=2 Score=35.66 Aligned_cols=25 Identities=16% Similarity=0.292 Sum_probs=21.8
Q ss_pred heehhhhcccccchHHHHHHHhCCCC
Q 033139 27 MFALTSIKGIGRRLANIVCKKADVDM 52 (126)
Q Consensus 27 ~~aLt~IyGIG~~~A~~Ic~~~gI~p 52 (126)
...|.+|+|||+++|..+-+ +||..
T Consensus 88 l~~l~~i~GiGpk~a~~l~~-lGi~t 112 (334)
T smart00483 88 LKLFTNVFGVGPKTAAKWYR-KGIRT 112 (334)
T ss_pred HHHHHccCCcCHHHHHHHHH-hCCCC
Confidence 45678999999999999999 99874
No 59
>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=73.67 E-value=2.6 Score=26.69 Aligned_cols=26 Identities=15% Similarity=0.258 Sum_probs=20.3
Q ss_pred Ceehheehhh-hcccccchHHHHHHHh
Q 033139 23 KQKIMFALTS-IKGIGRRLANIVCKKA 48 (126)
Q Consensus 23 ~K~v~~aLt~-IyGIG~~~A~~Ic~~~ 48 (126)
|..-.-.|.. +.|||...|.+|++.-
T Consensus 11 Nta~~~~L~~~ipgig~~~a~~Il~~R 37 (69)
T TIGR00426 11 NTATAEELQRAMNGVGLKKAEAIVSYR 37 (69)
T ss_pred cCCCHHHHHhHCCCCCHHHHHHHHHHH
Confidence 3333446777 9999999999999984
No 60
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=73.64 E-value=1.7 Score=31.38 Aligned_cols=45 Identities=18% Similarity=0.242 Sum_probs=29.8
Q ss_pred CeehheehhhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHH
Q 033139 23 KQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVV 71 (126)
Q Consensus 23 ~K~v~~aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L~~~i 71 (126)
...+.-.|+.++|||+.+|..+|.-. ++++.-+- |-.+.++.+.+
T Consensus 78 ~~~~~~~L~~l~GIG~~tA~~~l~~~-~~~~~~pv---D~~v~r~~~~~ 122 (158)
T cd00056 78 DPDAREELLALPGVGRKTANVVLLFA-LGPDAFPV---DTHVRRVLKRL 122 (158)
T ss_pred CcccHHHHHcCCCCCHHHHHHHHHHH-CCCCCCcc---chhHHHHHHHh
Confidence 35677889999999999999998743 33322222 45555555554
No 61
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=73.44 E-value=1.7 Score=29.36 Aligned_cols=26 Identities=27% Similarity=0.510 Sum_probs=20.1
Q ss_pred eehhh-hcccccchHHHHHHHhCCCCC
Q 033139 28 FALTS-IKGIGRRLANIVCKKADVDMN 53 (126)
Q Consensus 28 ~aLt~-IyGIG~~~A~~Ic~~~gI~p~ 53 (126)
+.|.. |.|||-.+|.+|..++|++++
T Consensus 45 Y~L~~~i~gi~F~~aD~iA~~~g~~~~ 71 (94)
T PF14490_consen 45 YRLIEDIDGIGFKTADKIALKLGIEPD 71 (94)
T ss_dssp TCCCB-SSSSBHHHHHHHHHTTT--TT
T ss_pred HHHHHHccCCCHHHHHHHHHHcCCCCC
Confidence 44544 999999999999999999874
No 62
>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=73.32 E-value=2.1 Score=30.52 Aligned_cols=31 Identities=19% Similarity=0.249 Sum_probs=24.9
Q ss_pred CCCCeehheehhhhcccccchHHHHHHHhCC
Q 033139 20 VDGKQKIMFALTSIKGIGRRLANIVCKKADV 50 (126)
Q Consensus 20 l~~~K~v~~aLt~IyGIG~~~A~~Ic~~~gI 50 (126)
++=|..-.-.|..+.|||+.+|.+|.+.-+-
T Consensus 60 iniNtA~~~eL~~lpGIG~~~A~~Ii~~R~~ 90 (120)
T TIGR01259 60 VNINAASLEELQALPGIGPAKAKAIIEYREE 90 (120)
T ss_pred EeCCcCCHHHHhcCCCCCHHHHHHHHHHHHh
Confidence 4455556667899999999999999998753
No 63
>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=72.64 E-value=1.8 Score=33.35 Aligned_cols=18 Identities=33% Similarity=0.523 Sum_probs=16.3
Q ss_pred eehhhhcccccchHHHHH
Q 033139 28 FALTSIKGIGRRLANIVC 45 (126)
Q Consensus 28 ~aLt~IyGIG~~~A~~Ic 45 (126)
-+|+.++|||+++|.+|+
T Consensus 107 ~~L~~ipGiGkKtAerIi 124 (191)
T TIGR00084 107 KALVKIPGVGKKTAERLL 124 (191)
T ss_pred HHHHhCCCCCHHHHHHHH
Confidence 357899999999999998
No 64
>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=72.33 E-value=0.7 Score=35.59 Aligned_cols=37 Identities=16% Similarity=0.284 Sum_probs=31.1
Q ss_pred hhhccccCCCCeehheehhhhcccccchHHHHHHHhC
Q 033139 13 LRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKAD 49 (126)
Q Consensus 13 vrI~g~~l~~~K~v~~aLt~IyGIG~~~A~~Ic~~~g 49 (126)
..++|-.=...+.++..|.++.|||+++|..|+..++
T Consensus 57 ~~LyGF~~~~Er~lF~~L~~V~GIGpK~Al~iL~~~~ 93 (191)
T TIGR00084 57 ELLFGFNTLEERELFKELIKVNGVGPKLALAILSNMS 93 (191)
T ss_pred ceeeCCCCHHHHHHHHHHhCCCCCCHHHHHHHHhcCC
Confidence 3567777778889999999999999999999976554
No 65
>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=72.07 E-value=2.4 Score=28.13 Aligned_cols=20 Identities=40% Similarity=0.423 Sum_probs=18.3
Q ss_pred ehhhhcccccchHHHHHHHh
Q 033139 29 ALTSIKGIGRRLANIVCKKA 48 (126)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~~ 48 (126)
.|+.|+|||+.+|..|+..+
T Consensus 3 ~l~sipGig~~~a~~llaei 22 (87)
T PF02371_consen 3 LLTSIPGIGPITAATLLAEI 22 (87)
T ss_pred hhcCCCCccHHHHHHHHHHH
Confidence 47899999999999999888
No 66
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=71.62 E-value=2.1 Score=30.63 Aligned_cols=42 Identities=19% Similarity=0.092 Sum_probs=26.8
Q ss_pred hheehhhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHH
Q 033139 26 IMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVV 71 (126)
Q Consensus 26 v~~aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L~~~i 71 (126)
..-.|..++|||+.+|..+|.-.--. ...+.| -.+.++...+
T Consensus 70 ~~~~L~~l~GIG~~tA~~~l~~~~~~-~~~~~D---~~v~r~~~rl 111 (149)
T smart00478 70 DREELLKLPGVGRKTANAVLSFALGK-PFIPVD---THVLRIAKRL 111 (149)
T ss_pred HHHHHHcCCCCcHHHHHHHHHHHCCC-CCCccc---hHHHHHHHHh
Confidence 44567889999999999998775322 233333 3555544444
No 67
>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=71.41 E-value=2.4 Score=34.70 Aligned_cols=25 Identities=16% Similarity=0.396 Sum_probs=21.2
Q ss_pred heehhhhcccccchHHHHHHHhCCCC
Q 033139 27 MFALTSIKGIGRRLANIVCKKADVDM 52 (126)
Q Consensus 27 ~~aLt~IyGIG~~~A~~Ic~~~gI~p 52 (126)
..-|.+|+|||+++|.++- .+|+..
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 3456799999999999999 899873
No 68
>COG2081 Predicted flavoproteins [General function prediction only]
Probab=70.96 E-value=4.6 Score=34.90 Aligned_cols=50 Identities=24% Similarity=0.352 Sum_probs=43.2
Q ss_pred CCCeehheehhhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 033139 21 DGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVAN 73 (126)
Q Consensus 21 ~~~K~v~~aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L~~~i~~ 73 (126)
.++|.+..+|.. .++.+.+..++++.|| |+....+||+.|+++|.+.|+.
T Consensus 283 ~~~kslkn~L~~--~lp~rlv~~~l~~~~i-~~~~~~~ls~~~~~~l~~~ik~ 332 (408)
T COG2081 283 NPKKSLKNALAK--LLPKRLVEFLLERAGI-PDEPLAQLSPKELAQLAAALKA 332 (408)
T ss_pred ChhhHHHHHHHH--HhhhHHHHHHHHhccC-CCcchhhcCHHHHHHHHHHHhc
Confidence 345666666655 5788999999999999 9999999999999999999986
No 69
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=70.87 E-value=2.8 Score=32.92 Aligned_cols=44 Identities=16% Similarity=0.117 Sum_probs=31.0
Q ss_pred ehheehh-hhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHh
Q 033139 25 KIMFALT-SIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVA 72 (126)
Q Consensus 25 ~v~~aLt-~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L~~~i~ 72 (126)
...-.|. +++|||+.+|..|+...|..|-.-+ |.++.++.+-+.
T Consensus 115 ~~R~~Ll~~lpGIG~KTAd~vL~~~~~~~~~iV----DtHv~Ri~~RlG 159 (208)
T PRK01229 115 EAREFLVKNIKGIGYKEASHFLRNVGYEDLAIL----DRHILRFLKRYG 159 (208)
T ss_pred HHHHHHHHcCCCCcHHHHHHHHHHccCCCeeee----eHHHHHHHHHhC
Confidence 4455566 9999999999999976776554333 346777666653
No 70
>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=69.71 E-value=2.4 Score=34.42 Aligned_cols=34 Identities=26% Similarity=0.285 Sum_probs=27.8
Q ss_pred cccccchhhccccCCCCeehheehhhhcccccchHHHHHHHhC
Q 033139 7 EDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKAD 49 (126)
Q Consensus 7 ~~~~~mvrI~g~~l~~~K~v~~aLt~IyGIG~~~A~~Ic~~~g 49 (126)
++|-.+.=++|+|... .|.|||+.+|.+++++.|
T Consensus 211 ~q~id~~~L~G~Dy~~---------gv~giG~k~A~~li~~~~ 244 (316)
T cd00128 211 EKLIDLAILLGCDYTE---------GIPGIGPVTALKLIKKYG 244 (316)
T ss_pred HHHHHHHHhcCCCCCC---------CCCCccHHHHHHHHHHcC
Confidence 5677777788876633 688999999999999987
No 71
>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=69.48 E-value=3.2 Score=28.83 Aligned_cols=37 Identities=22% Similarity=0.138 Sum_probs=27.1
Q ss_pred eehhhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHH
Q 033139 28 FALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELD 65 (126)
Q Consensus 28 ~aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~ 65 (126)
..|+.|.|||+++|.-+- .+||+.=.-+..-+.+++-
T Consensus 12 ~~L~~iP~IG~a~a~DL~-~LGi~s~~~L~g~dP~~Ly 48 (93)
T PF11731_consen 12 SDLTDIPNIGKATAEDLR-LLGIRSPADLKGRDPEELY 48 (93)
T ss_pred HHHhcCCCccHHHHHHHH-HcCCCCHHHHhCCCHHHHH
Confidence 468999999999999976 8999864444444555443
No 72
>PRK03980 flap endonuclease-1; Provisional
Probab=69.22 E-value=2.8 Score=34.32 Aligned_cols=59 Identities=24% Similarity=0.331 Sum_probs=37.2
Q ss_pred cccccchhhccccCCCCeehheehhhhcccccchHHHHHHHhC-CCCCCcCCCCCHHHHHHHHHHHhCC
Q 033139 7 EDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKAD-VDMNKRAGELSAAELDQLMVVVANP 74 (126)
Q Consensus 7 ~~~~~mvrI~g~~l~~~K~v~~aLt~IyGIG~~~A~~Ic~~~g-I~p~~k~~~Ls~~qi~~L~~~i~~~ 74 (126)
++|-.+.=++|+|-.. .|.|||+.+|.+++++.| |+.=....+..-.....+++++.+|
T Consensus 177 ~q~id~~iL~G~Dy~~---------GI~GIG~ktA~kLi~~~~sle~i~~~~~~~~~~~~~~r~~f~~p 236 (292)
T PRK03980 177 EQLIDIAILVGTDYNP---------GIKGIGPKTALKLIKKHGDLEKVLEERGFEIENYDEIREFFLNP 236 (292)
T ss_pred HHHHHHHHhcCCCCCC---------CCCCccHHHHHHHHHHCCCHHHHHHhccCCCCCHHHHHHHhcCC
Confidence 5677777788865533 688999999999999988 1111110001112345677777776
No 73
>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=69.14 E-value=0.92 Score=31.74 Aligned_cols=20 Identities=20% Similarity=0.408 Sum_probs=15.8
Q ss_pred hhhhcccccchHHHHHHHhC
Q 033139 30 LTSIKGIGRRLANIVCKKAD 49 (126)
Q Consensus 30 Lt~IyGIG~~~A~~Ic~~~g 49 (126)
...+.|||+++|.+++++.|
T Consensus 20 IPGV~GIG~KtA~~LL~~yg 39 (101)
T PF01367_consen 20 IPGVPGIGPKTAAKLLQEYG 39 (101)
T ss_dssp B---TTSTCHCCCCCHHHHT
T ss_pred CCCCCCCCHHHHHHHHHHcC
Confidence 34689999999999999998
No 74
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=68.33 E-value=1.4 Score=34.19 Aligned_cols=61 Identities=13% Similarity=0.203 Sum_probs=45.6
Q ss_pred hhhccccCCCCeehheehhhhcccccchHHHHHHHhCCC------------CCCcCCCCCHHHHHHHHHHHhC
Q 033139 13 LRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVD------------MNKRAGELSAAELDQLMVVVAN 73 (126)
Q Consensus 13 vrI~g~~l~~~K~v~~aLt~IyGIG~~~A~~Ic~~~gI~------------p~~k~~~Ls~~qi~~L~~~i~~ 73 (126)
..++|-.=...+.++..|.++.|||+++|..|+..++.+ .-.++.-+.+.--++|.-.++.
T Consensus 59 ~~LyGF~~~~Er~lF~~Li~V~GIGpK~Al~iLs~~~~~~l~~aI~~~D~~~L~~ipGIGkKtAerIilELkd 131 (203)
T PRK14602 59 LELFGFATWDERQTFIVLISISKVGAKTALAILSQFRPDDLRRLVAEEDVAALTRVSGIGKKTAQHIFLELKY 131 (203)
T ss_pred ceeeCCCCHHHHHHHHHHhCCCCcCHHHHHHHHhhCCHHHHHHHHHhCCHHHHhcCCCcCHHHHHHHHHHHHH
Confidence 356777777788899999999999999999999876533 2245556666666666666665
No 75
>PRK12278 50S ribosomal protein L21/unknown domain fusion protein; Provisional
Probab=68.29 E-value=4.2 Score=32.30 Aligned_cols=55 Identities=22% Similarity=0.330 Sum_probs=44.1
Q ss_pred eehhhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCCccCChhh
Q 033139 28 FALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVANPRQFKIPDWF 83 (126)
Q Consensus 28 ~aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L~~~i~~~~~~~iP~w~ 83 (126)
-.|+.|.|||+..+.. +..+|+..-..+-.++++++..+...+.-+....-..|-
T Consensus 158 DDL~~I~GIGp~~a~~-L~eaGi~tfaQIAa~t~a~ia~id~~l~~~gri~rd~Wv 212 (221)
T PRK12278 158 DDLTKITGVGPALAKK-LNEAGVTTFAQIAALTDADIAKIDEKLSFKGRIEKDGWI 212 (221)
T ss_pred chheeccccChHHHHH-HHHcCCCCHHHhhCCChhhhhhhhhcccCCCccCcchHH
Confidence 4589999999999877 688999999999999999999999988654323224453
No 76
>PRK08609 hypothetical protein; Provisional
Probab=68.28 E-value=3.2 Score=36.84 Aligned_cols=24 Identities=21% Similarity=0.346 Sum_probs=21.9
Q ss_pred eehhhhcccccchHHHHHHHhCCC
Q 033139 28 FALTSIKGIGRRLANIVCKKADVD 51 (126)
Q Consensus 28 ~aLt~IyGIG~~~A~~Ic~~~gI~ 51 (126)
..|++|+|||+++|.++-+.+||.
T Consensus 88 ~~l~~i~GiGpk~a~~l~~~lGi~ 111 (570)
T PRK08609 88 LPLLKLPGLGGKKIAKLYKELGVV 111 (570)
T ss_pred HHHhcCCCCCHHHHHHHHHHhCCC
Confidence 467899999999999999999986
No 77
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=67.71 E-value=1.3 Score=34.16 Aligned_cols=59 Identities=8% Similarity=0.150 Sum_probs=43.3
Q ss_pred hhccccCCCCeehheehhhhcccccchHHHHHHHhCCC------------CCCcCCCCCHHHHHHHHHHHhC
Q 033139 14 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVD------------MNKRAGELSAAELDQLMVVVAN 73 (126)
Q Consensus 14 rI~g~~l~~~K~v~~aLt~IyGIG~~~A~~Ic~~~gI~------------p~~k~~~Ls~~qi~~L~~~i~~ 73 (126)
.++|-.=+..+.++..|.++.|||+++|..|+..++.+ .- ++.-+.+.--++|.-.++.
T Consensus 59 ~LyGF~~~~Er~lF~~LisV~GIGpK~Al~iLs~~~~~~l~~aI~~~D~~~L-~vpGIGkKtAerIilELk~ 129 (186)
T PRK14600 59 QLYGFLNREEQDCLRMLVKVSGVNYKTAMSILSKLTPEQLFSAIVNEDKAAL-KVNGIGEKLINRIITELQY 129 (186)
T ss_pred eeeCCCCHHHHHHHHHHhCcCCcCHHHHHHHHccCCHHHHHHHHHcCCHhhe-ECCCCcHHHHHHHHHHHHH
Confidence 57888888889999999999999999999999765422 12 4455555555666655654
No 78
>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=67.45 E-value=2.9 Score=31.70 Aligned_cols=23 Identities=35% Similarity=0.465 Sum_probs=19.1
Q ss_pred hheehhhhcccccchHHHHHHHh
Q 033139 26 IMFALTSIKGIGRRLANIVCKKA 48 (126)
Q Consensus 26 v~~aLt~IyGIG~~~A~~Ic~~~ 48 (126)
..-.|..++|||+.+|..||-..
T Consensus 104 ~~~~L~~l~GIG~ktA~~ill~~ 126 (191)
T TIGR01083 104 DREELVKLPGVGRKTANVVLNVA 126 (191)
T ss_pred HHHHHHhCCCCcHHHHHHHHHHH
Confidence 35568999999999999998544
No 79
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=67.00 E-value=1.3 Score=34.05 Aligned_cols=37 Identities=27% Similarity=0.373 Sum_probs=31.3
Q ss_pred hhhccccCCCCeehheehhhhcccccchHHHHHHHhC
Q 033139 13 LRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKAD 49 (126)
Q Consensus 13 vrI~g~~l~~~K~v~~aLt~IyGIG~~~A~~Ic~~~g 49 (126)
..++|-.=...+.++-.|.++.|||+++|..|+..+.
T Consensus 58 ~~LyGF~~~~Er~lF~~Li~VsGIGpK~Al~ILs~~~ 94 (183)
T PRK14601 58 NKLYGFLDKDEQKMFEMLLKVNGIGANTAMAVCSSLD 94 (183)
T ss_pred ceeeCCCCHHHHHHHHHHhccCCccHHHHHHHHcCCC
Confidence 3567777778889999999999999999999986543
No 80
>PRK10702 endonuclease III; Provisional
Probab=66.77 E-value=2.8 Score=32.64 Aligned_cols=29 Identities=38% Similarity=0.509 Sum_probs=21.7
Q ss_pred cccCCCCeehheehhhhcccccchHHHHHHHh
Q 033139 17 NTNVDGKQKIMFALTSIKGIGRRLANIVCKKA 48 (126)
Q Consensus 17 g~~l~~~K~v~~aLt~IyGIG~~~A~~Ic~~~ 48 (126)
|-++|. ..-.|.+++|||+.+|..|+--+
T Consensus 101 ~~~~p~---~~~~Ll~lpGVG~ktA~~ill~a 129 (211)
T PRK10702 101 NGEVPE---DRAALEALPGVGRKTANVVLNTA 129 (211)
T ss_pred CCCCCc---hHHHHhcCCcccHHHHHHHHHHH
Confidence 444553 35678999999999999987543
No 81
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=66.66 E-value=1.3 Score=34.07 Aligned_cols=36 Identities=17% Similarity=0.346 Sum_probs=30.8
Q ss_pred hhccccCCCCeehheehhhhcccccchHHHHHHHhC
Q 033139 14 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKAD 49 (126)
Q Consensus 14 rI~g~~l~~~K~v~~aLt~IyGIG~~~A~~Ic~~~g 49 (126)
.++|-.=...+.++-.|.++.|||+++|..|+..++
T Consensus 59 ~LyGF~~~~Er~lF~~Li~V~GIGpK~AL~iLs~~~ 94 (188)
T PRK14606 59 TLYGFSNERKKELFLSLTKVSRLGPKTALKIISNED 94 (188)
T ss_pred eeeCCCCHHHHHHHHHHhccCCccHHHHHHHHcCCC
Confidence 567777778888999999999999999999986543
No 82
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=66.59 E-value=2.9 Score=32.78 Aligned_cols=83 Identities=18% Similarity=0.186 Sum_probs=52.5
Q ss_pred ehheehhhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCC-CccC------------Chhhhhcccccc
Q 033139 25 KIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVANPR-QFKI------------PDWFLNRQKDYK 91 (126)
Q Consensus 25 ~v~~aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L~~~i~~~~-~~~i------------P~w~~nr~~d~~ 91 (126)
.+..+|..++|||+++|.++.--+ -+.+++++..|.+++.+.. +... =.-+.+-++|
T Consensus 9 ~LI~~l~kLPGvG~KsA~R~AfhL--------L~~~~~~~~~la~al~~a~~~i~~C~~C~~~te~d~C~ICsd~~Rd-- 78 (198)
T COG0353 9 KLIDALKKLPGVGPKSAQRLAFHL--------LQRDREDVERLAKALLEAKENIKHCSVCGNLTESDPCDICSDESRD-- 78 (198)
T ss_pred HHHHHHhhCCCCChhHHHHHHHHH--------HccCHHHHHHHHHHHHHHHhcCccccccCCcCCCCcCcCcCCcccC--
Confidence 456789999999999999997444 3446777777777765310 1110 1113455555
Q ss_pred CCccceeehhhHHHHHHHHHHHHHhcccceeee
Q 033139 92 DGRYSQVVSNALDMKLRDDLERLKKIRYGLVVL 124 (126)
Q Consensus 92 tg~~~h~i~~dL~~~~~~dI~rl~~I~sy~~~~ 124 (126)
..-.-+|++ -.|+..+=+.+.|+|..
T Consensus 79 -~~~icVVe~------p~Dv~a~E~~~~f~G~Y 104 (198)
T COG0353 79 -KSQLCVVEE------PKDVLALEKTGEFRGLY 104 (198)
T ss_pred -CceEEEEcc------hHHHHHHHHhcccCeeE
Confidence 223445554 35777788888888864
No 83
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=66.44 E-value=3.8 Score=33.30 Aligned_cols=33 Identities=24% Similarity=0.462 Sum_probs=26.4
Q ss_pred cccccchhhcc--c-cCCCCeehheehhhhcccccchHHHHHHHhC
Q 033139 7 EDFQHILRVLN--T-NVDGKQKIMFALTSIKGIGRRLANIVCKKAD 49 (126)
Q Consensus 7 ~~~~~mvrI~g--~-~l~~~K~v~~aLt~IyGIG~~~A~~Ic~~~g 49 (126)
+++.++.=+.| + ++|| ++|||+.+|.++++..|
T Consensus 184 ~qliD~~~L~Gd~sDnipG----------V~GIG~ktA~~Ll~~~g 219 (310)
T COG0258 184 EQLIDLKALVGDSSDNIPG----------VKGIGPKTALKLLQEYG 219 (310)
T ss_pred HHHHHHHHHhCCcccCCCC----------CCCcCHHHHHHHHHHhC
Confidence 45667777778 4 3444 99999999999999999
No 84
>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=65.02 E-value=11 Score=26.18 Aligned_cols=36 Identities=17% Similarity=0.299 Sum_probs=31.7
Q ss_pred hcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHh
Q 033139 33 IKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVA 72 (126)
Q Consensus 33 IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L~~~i~ 72 (126)
=--+|....++|++.++ ++-.+||++++...++.+.
T Consensus 32 ~es~Gh~sGRrIv~IL~----K~k~dltddD~~hMrkVV~ 67 (92)
T PF11338_consen 32 GESVGHESGRRIVEILR----KRKTDLTDDDYEHMRKVVG 67 (92)
T ss_pred CcccCcchhhHHHHHHh----cCcccCCHHHHHHHHHHHH
Confidence 34578999999999998 8889999999999999886
No 85
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=64.64 E-value=1.6 Score=34.11 Aligned_cols=36 Identities=19% Similarity=0.278 Sum_probs=30.9
Q ss_pred hhccccCCCCeehheehhhhcccccchHHHHHHHhC
Q 033139 14 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKAD 49 (126)
Q Consensus 14 rI~g~~l~~~K~v~~aLt~IyGIG~~~A~~Ic~~~g 49 (126)
.++|-.=...+.++-.|.++.|||+++|..|+..+.
T Consensus 58 ~LYGF~t~~Er~lF~~LisVsGIGPK~ALaILs~~~ 93 (196)
T PRK13901 58 KLFGFLNSSEREVFEELIGVDGIGPRAALRVLSGIK 93 (196)
T ss_pred eeeCCCCHHHHHHHHHHhCcCCcCHHHHHHHHcCCC
Confidence 567777778889999999999999999999996543
No 86
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=64.61 E-value=1.5 Score=33.92 Aligned_cols=61 Identities=11% Similarity=0.176 Sum_probs=43.8
Q ss_pred hhhccccCCCCeehheehhhhcccccchHHHHHHHhCC------------CCCCcCCCCCHHHHHHHHHHHhC
Q 033139 13 LRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADV------------DMNKRAGELSAAELDQLMVVVAN 73 (126)
Q Consensus 13 vrI~g~~l~~~K~v~~aLt~IyGIG~~~A~~Ic~~~gI------------~p~~k~~~Ls~~qi~~L~~~i~~ 73 (126)
..++|-.=...+.++..|.++.|||+++|..|+..++. ..-.++.-+.+.--++|.-.++.
T Consensus 57 ~~LyGF~~~~Er~lF~~L~~V~GIGpK~AL~iLs~~~~~~l~~aI~~~D~~~L~kvpGIGkKtAerIilELkd 129 (197)
T PRK14603 57 LSLYGFPDEDSLELFELLLGVSGVGPKLALALLSALPPALLARALLEGDARLLTSASGVGKKLAERIALELKG 129 (197)
T ss_pred ceeeCcCCHHHHHHHHHHhCcCCcCHHHHHHHHcCCCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHH
Confidence 35677777788889999999999999999999876542 12235555556666666666654
No 87
>PRK00076 recR recombination protein RecR; Reviewed
Probab=64.25 E-value=3.7 Score=32.06 Aligned_cols=40 Identities=20% Similarity=0.227 Sum_probs=28.9
Q ss_pred ehheehhhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHh
Q 033139 25 KIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVA 72 (126)
Q Consensus 25 ~v~~aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L~~~i~ 72 (126)
.+.-+|+.++|||+++|.++.-.+=- -.++++..|.+.|.
T Consensus 8 ~Li~~l~~LPGIG~KsA~Rla~~ll~--------~~~~~~~~la~~i~ 47 (196)
T PRK00076 8 KLIEALRKLPGIGPKSAQRLAFHLLQ--------RDREDVLRLAQALE 47 (196)
T ss_pred HHHHHHHHCCCCCHHHHHHHHHHHHc--------CCHHHHHHHHHHHH
Confidence 34567899999999999999765433 34566666666655
No 88
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=63.55 E-value=3.4 Score=32.28 Aligned_cols=40 Identities=20% Similarity=0.255 Sum_probs=28.5
Q ss_pred ehheehhhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHh
Q 033139 25 KIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVA 72 (126)
Q Consensus 25 ~v~~aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L~~~i~ 72 (126)
.+.-+|+.++|||+++|.++.-.+= +-.++++..|.++|.
T Consensus 8 ~Li~~l~~LPGIG~KsA~RlA~~ll--------~~~~~~~~~la~ai~ 47 (195)
T TIGR00615 8 KLIESLKKLPGIGPKSAQRLAFHLL--------KRDPSEVLRLAQALL 47 (195)
T ss_pred HHHHHHHHCCCCCHHHHHHHHHHHH--------cCCHHHHHHHHHHHH
Confidence 4556899999999999999965443 234566666666655
No 89
>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=63.43 E-value=3.2 Score=33.74 Aligned_cols=30 Identities=20% Similarity=0.303 Sum_probs=22.9
Q ss_pred ccccCCCCeehheehhhhcccccchHHHHHHHh
Q 033139 16 LNTNVDGKQKIMFALTSIKGIGRRLANIVCKKA 48 (126)
Q Consensus 16 ~g~~l~~~K~v~~aLt~IyGIG~~~A~~Ic~~~ 48 (126)
.|-.+|.+ .-.|..++|||+.||..||--+
T Consensus 96 ~~g~~p~~---~~~L~~LpGIG~~TA~~Il~~a 125 (275)
T TIGR01084 96 FGGEFPQD---FEDLAALPGVGRYTAGAILSFA 125 (275)
T ss_pred cCCCCcHH---HHHHHhCCCCCHHHHHHHHHHH
Confidence 34456644 5679999999999999998644
No 90
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=63.16 E-value=1.4 Score=34.54 Aligned_cols=38 Identities=21% Similarity=0.308 Sum_probs=32.7
Q ss_pred chhhccccCCCCeehheehhhhcccccchHHHHHHHhC
Q 033139 12 ILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKAD 49 (126)
Q Consensus 12 mvrI~g~~l~~~K~v~~aLt~IyGIG~~~A~~Ic~~~g 49 (126)
...++|-.=...+.++-.|.++-|||+++|..||..+.
T Consensus 57 ~~~LyGF~~~~ER~lF~~LisVnGIGpK~ALaiLs~~~ 94 (201)
T COG0632 57 AHLLYGFLTEEERELFRLLISVNGIGPKLALAILSNLD 94 (201)
T ss_pred HHHHcCCCCHHHHHHHHHHHccCCccHHHHHHHHcCCC
Confidence 45678888888899999999999999999999986543
No 91
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=62.84 E-value=3.9 Score=32.83 Aligned_cols=38 Identities=18% Similarity=0.307 Sum_probs=20.6
Q ss_pred ehhhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHH
Q 033139 29 ALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQL 67 (126)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L 67 (126)
.|..|.|||+.++..+++. ||..-..+..-|.++|..+
T Consensus 4 ~L~~IpGIG~krakkLl~~-GF~Sve~Ik~AS~eEL~~V 41 (232)
T PRK12766 4 ELEDISGVGPSKAEALREA-GFESVEDVRAADQSELAEV 41 (232)
T ss_pred ccccCCCcCHHHHHHHHHc-CCCCHHHHHhCCHHHHHHc
Confidence 3556667777766666544 4544444444444444443
No 92
>PTZ00217 flap endonuclease-1; Provisional
Probab=62.62 E-value=4.4 Score=34.54 Aligned_cols=34 Identities=26% Similarity=0.362 Sum_probs=26.8
Q ss_pred cccccchhhccccCCCCeehheehhhhcccccchHHHHHHHhC
Q 033139 7 EDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKAD 49 (126)
Q Consensus 7 ~~~~~mvrI~g~~l~~~K~v~~aLt~IyGIG~~~A~~Ic~~~g 49 (126)
++|-.+.-+.|+|-. ..|.|||+.+|.+++++.|
T Consensus 223 ~q~id~~iL~G~Dy~---------pgi~GIG~ktA~~Li~~~g 256 (393)
T PTZ00217 223 DQFIDLCILCGCDYC---------DTIKGIGPKTAYKLIKKYK 256 (393)
T ss_pred HHHHHHHHHhCCCCC---------CCCCCccHHHHHHHHHHcC
Confidence 566777778886543 3689999999999998866
No 93
>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=62.36 E-value=20 Score=21.87 Aligned_cols=43 Identities=12% Similarity=0.204 Sum_probs=33.0
Q ss_pred hhhhcccccchHHHHHHHhCCCCCCcC----CCCCHHHHHHHHHHHh
Q 033139 30 LTSIKGIGRRLANIVCKKADVDMNKRA----GELSAAELDQLMVVVA 72 (126)
Q Consensus 30 Lt~IyGIG~~~A~~Ic~~~gI~p~~k~----~~Ls~~qi~~L~~~i~ 72 (126)
+....||...+.+.-.+..|+.+..+- ...+++++..|..+..
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 456789999999998887787664332 3679999998888765
No 94
>PRK07373 DNA polymerase III subunit alpha; Reviewed
Probab=61.70 E-value=8.6 Score=33.40 Aligned_cols=48 Identities=17% Similarity=0.296 Sum_probs=33.5
Q ss_pred CeehheehhhhcccccchHHHHHHHh---C-------CCCCCcCCCCCHHHHHHHHHH
Q 033139 23 KQKIMFALTSIKGIGRRLANIVCKKA---D-------VDMNKRAGELSAAELDQLMVV 70 (126)
Q Consensus 23 ~K~v~~aLt~IyGIG~~~A~~Ic~~~---g-------I~p~~k~~~Ls~~qi~~L~~~ 70 (126)
++.|.|+|..|+|||...+.+|.+.= | +-.....+.++...++.|.++
T Consensus 109 ~~~IrfGL~aIKGVG~~~i~~Iv~eR~~~g~F~sl~DF~~Rvd~~~vnkr~lE~LIka 166 (449)
T PRK07373 109 GEKILFGLSAVRNLGEGAIESILKAREEGGEFKSLADFCDRVDLRVVNRRALETLIYC 166 (449)
T ss_pred CCEEEEcchhcCCCCHHHHHHHHHHHHhcCCCCCHHHHHHHhCcccCCHHHHHHHHHc
Confidence 45799999999999999999998643 2 111223345677777766553
No 95
>cd00349 Ribosomal_L11 Ribosomal protein L11. Ribosomal protein L11, together with proteins L10 and L7/L12, and 23S rRNA, form the L7/L12 stalk on the surface of the large subunit of the ribosome. The homologous eukaryotic cytoplasmic protein is also called 60S ribosomal protein L12, which is distinct from the L12 involved in the formation of the L7/L12 stalk. The C-terminal domain (CTD) of L11 is essential for binding 23S rRNA, while the N-terminal domain (NTD) contains the binding site for the antibiotics thiostrepton and micrococcin. L11 and 23S rRNA form an essential part of the GTPase-associated region (GAR). Based on differences in the relative positions of the L11 NTD and CTD during the translational cycle, L11 is proposed to play a significant role in the binding of initiation factors, elongation factors, and release factors to the ribosome. Several factors, including the class I release factors RF1 and RF2, are known to interact directly with L11. In eukaryotes, L11 has been im
Probab=61.43 E-value=25 Score=25.58 Aligned_cols=63 Identities=8% Similarity=0.191 Sum_probs=48.1
Q ss_pred ccc-cchHHHHHHHhCCCC------CCcCCCCCHHHHHHHHHHHhCCCCccCChhhhhccccccCCccceeehhhHHHHH
Q 033139 35 GIG-RRLANIVCKKADVDM------NKRAGELSAAELDQLMVVVANPRQFKIPDWFLNRQKDYKDGRYSQVVSNALDMKL 107 (126)
Q Consensus 35 GIG-~~~A~~Ic~~~gI~p------~~k~~~Ls~~qi~~L~~~i~~~~~~~iP~w~~nr~~d~~tg~~~h~i~~dL~~~~ 107 (126)
=|+ +.+|.-|.+.+|+.. ...++++|-+|+.+|.+.-.. . +-..+|...+
T Consensus 61 ~v~~Pp~s~ll~ka~g~~kgs~~~~~~~~g~it~~~v~eIA~~K~~---d--------------------l~~~~l~~~v 117 (131)
T cd00349 61 EVKTPPASALLKKAAGIEKGSKKPNKEKVGNITLDQVYEIAKIKLP---D--------------------LNAKTLKSAV 117 (131)
T ss_pred EEcCCCHHHHHHHHhCCCCCCCCCCCeeeeeecHHHHHHHHHHHHh---h--------------------hcchhHHHHH
Confidence 345 889999999999876 345799999999999998764 2 4677888888
Q ss_pred HHHHHHHHhcccc
Q 033139 108 RDDLERLKKIRYG 120 (126)
Q Consensus 108 ~~dI~rl~~I~sy 120 (126)
++=+=--+.+++.
T Consensus 118 k~v~GTa~SmGi~ 130 (131)
T cd00349 118 KEILGTARSMGIT 130 (131)
T ss_pred HHHHhhHhhCeEE
Confidence 8766666666553
No 96
>PLN03072 60S ribosomal protein L12; Provisional
Probab=61.19 E-value=13 Score=28.26 Aligned_cols=62 Identities=13% Similarity=0.144 Sum_probs=46.2
Q ss_pred cccchHHHHHHHhCCCCC--------CcCCCCCHHHHHHHHHHHhCCCCccCChhhhhccccccCCccceeehhhHHHHH
Q 033139 36 IGRRLANIVCKKADVDMN--------KRAGELSAAELDQLMVVVANPRQFKIPDWFLNRQKDYKDGRYSQVVSNALDMKL 107 (126)
Q Consensus 36 IG~~~A~~Ic~~~gI~p~--------~k~~~Ls~~qi~~L~~~i~~~~~~~iP~w~~nr~~d~~tg~~~h~i~~dL~~~~ 107 (126)
+-+.+|.-|.+.+|+... ..+++||-+|+.+|.+.-.. - +-..||+..+
T Consensus 74 v~Pp~s~LLkKa~g~~kgs~~~~~~~~~vG~it~~qv~eIA~~K~~---d--------------------l~a~~l~~av 130 (166)
T PLN03072 74 VVPSAAALVIKALKEPERDRKKVKNIKHNGNISLDDVIEIAKIMRP---R--------------------SMAKELAGTV 130 (166)
T ss_pred eCCCHHHHHHHHhCCCCCCCccCCCCeeeeeecHHHHHHHHHHHHH---H--------------------hCcccHHHHH
Confidence 369999999999999875 57899999999999987553 1 4567777777
Q ss_pred HHHHHHHHhcccc
Q 033139 108 RDDLERLKKIRYG 120 (126)
Q Consensus 108 ~~dI~rl~~I~sy 120 (126)
++=+=--+.+++.
T Consensus 131 k~VlGTarSmGi~ 143 (166)
T PLN03072 131 KEILGTCVSVGCT 143 (166)
T ss_pred HHhHheeeeCeEE
Confidence 7655444444443
No 97
>smart00475 53EXOc 5'-3' exonuclease.
Probab=61.18 E-value=4.8 Score=32.32 Aligned_cols=19 Identities=26% Similarity=0.431 Sum_probs=17.0
Q ss_pred hhhcccccchHHHHHHHhC
Q 033139 31 TSIKGIGRRLANIVCKKAD 49 (126)
Q Consensus 31 t~IyGIG~~~A~~Ic~~~g 49 (126)
..+.|||+++|.+++++.|
T Consensus 189 pGV~GIG~KtA~~Ll~~yg 207 (259)
T smart00475 189 PGVPGIGEKTAAKLLKEFG 207 (259)
T ss_pred CCCCCCCHHHHHHHHHHhC
Confidence 4579999999999999987
No 98
>PRK09482 flap endonuclease-like protein; Provisional
Probab=61.16 E-value=4.8 Score=32.50 Aligned_cols=19 Identities=21% Similarity=0.343 Sum_probs=17.1
Q ss_pred hhhcccccchHHHHHHHhC
Q 033139 31 TSIKGIGRRLANIVCKKAD 49 (126)
Q Consensus 31 t~IyGIG~~~A~~Ic~~~g 49 (126)
..+.|||+++|.+++++.|
T Consensus 185 pGVpGIG~KtA~~LL~~~g 203 (256)
T PRK09482 185 PGVAGIGPKSAAELLNQFR 203 (256)
T ss_pred CCCCCcChHHHHHHHHHhC
Confidence 5689999999999999877
No 99
>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=61.12 E-value=13 Score=25.96 Aligned_cols=58 Identities=21% Similarity=0.146 Sum_probs=42.9
Q ss_pred ccccCCCCeehheehhhhcccccchHHHHHHHhC---CCCCCcCCCCCHHHHHHHHHHHhC
Q 033139 16 LNTNVDGKQKIMFALTSIKGIGRRLANIVCKKAD---VDMNKRAGELSAAELDQLMVVVAN 73 (126)
Q Consensus 16 ~g~~l~~~K~v~~aLt~IyGIG~~~A~~Ic~~~g---I~p~~k~~~Ls~~qi~~L~~~i~~ 73 (126)
+|..|+=|..-..+.+.+.|.=++.|.+|+..+= ++.=..+..||+.|-..|.+..++
T Consensus 11 ~G~KIDlNNa~vr~f~~~pGmYPtlA~kIv~naPY~sveDvl~ipgLse~qK~~lk~~~~~ 71 (93)
T PF06514_consen 11 LGQKIDLNNANVRAFRQFPGMYPTLAGKIVSNAPYKSVEDVLNIPGLSERQKALLKKYEDN 71 (93)
T ss_dssp CCTCEETTSS-GGGGCCSTTTTCCHHHHHHHS---SSGGGGCCSTT--HHHHHHHHHHGGG
T ss_pred cCCceecccHhHHHHHHCCCCCHHHHHHHHhCCCCCCHHHHHhccCCCHHHHHHHHHHhcc
Confidence 4555666666778899999999999999998763 444456678999999999999986
No 100
>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=60.68 E-value=4.9 Score=31.65 Aligned_cols=20 Identities=25% Similarity=0.458 Sum_probs=17.0
Q ss_pred hhhhcccccchHHHHHHHhC
Q 033139 30 LTSIKGIGRRLANIVCKKAD 49 (126)
Q Consensus 30 Lt~IyGIG~~~A~~Ic~~~g 49 (126)
...+.|||+++|.+++++.|
T Consensus 185 ipGv~GiG~ktA~~Ll~~~g 204 (240)
T cd00008 185 IPGVPGIGEKTAAKLLKEYG 204 (240)
T ss_pred CCCCCccCHHHHHHHHHHhC
Confidence 34679999999999998865
No 101
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=60.03 E-value=12 Score=29.61 Aligned_cols=49 Identities=20% Similarity=0.159 Sum_probs=32.8
Q ss_pred cccCCCCeehheehhhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHh
Q 033139 17 NTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVA 72 (126)
Q Consensus 17 g~~l~~~K~v~~aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L~~~i~ 72 (126)
|-++|++ .-.|.+..|||++||.-++..+---|...+.. ++.++.+-+.
T Consensus 101 ~g~vP~~---~~eL~~LPGVGrKTAnvVL~~a~g~p~i~VDT----HV~Rvs~R~g 149 (211)
T COG0177 101 GGEVPDT---REELLSLPGVGRKTANVVLSFAFGIPAIAVDT----HVHRVSNRLG 149 (211)
T ss_pred CCCCCch---HHHHHhCCCcchHHHHHHHHhhcCCCcccccc----hHHHHHHHhC
Confidence 3344443 35789999999999999887744333666554 6666666553
No 102
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=59.54 E-value=6.7 Score=31.15 Aligned_cols=42 Identities=24% Similarity=0.130 Sum_probs=29.9
Q ss_pred ccCCCCeeh--heehhhhcccccchHHHHHHHhCCCCCCcCCCC
Q 033139 18 TNVDGKQKI--MFALTSIKGIGRRLANIVCKKADVDMNKRAGEL 59 (126)
Q Consensus 18 ~~l~~~K~v--~~aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~L 59 (126)
.++.+.++. +--|-+|+|||+.||..|+--+.=-|..-+..-
T Consensus 103 ~~~~~~~~~~~R~~LL~iKGIG~ETaDsILlYa~~rp~FVvD~Y 146 (215)
T COG2231 103 INLESFKSEVLREELLSIKGIGKETADSILLYALDRPVFVVDKY 146 (215)
T ss_pred hhhhccchHHHHHHHHccCCcchhhHHHHHHHHhcCcccchhHH
Confidence 345555555 667889999999999999877765555444433
No 103
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=59.42 E-value=4.7 Score=31.79 Aligned_cols=24 Identities=25% Similarity=0.166 Sum_probs=19.3
Q ss_pred ehheehhhhcccccchHHHHHHHh
Q 033139 25 KIMFALTSIKGIGRRLANIVCKKA 48 (126)
Q Consensus 25 ~v~~aLt~IyGIG~~~A~~Ic~~~ 48 (126)
...-.|.+++|||+.||..|+--+
T Consensus 118 ~~re~Ll~l~GIG~kTAd~iLlya 141 (218)
T PRK13913 118 VTREWLLDQKGIGKESADAILCYV 141 (218)
T ss_pred hHHHHHHcCCCccHHHHHHHHHHH
Confidence 344569999999999999887644
No 104
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=59.41 E-value=5.4 Score=30.50 Aligned_cols=21 Identities=33% Similarity=0.559 Sum_probs=18.5
Q ss_pred ehhhhcccccchHHHHHHHhC
Q 033139 29 ALTSIKGIGRRLANIVCKKAD 49 (126)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~~g 49 (126)
.|+.++|||+++|.+|+..+.
T Consensus 109 ~L~~v~Gig~k~A~~I~~~l~ 129 (192)
T PRK00116 109 ALTKVPGIGKKTAERIVLELK 129 (192)
T ss_pred HHHhCCCCCHHHHHHHHHHHH
Confidence 588999999999999997654
No 105
>PHA02564 V virion protein; Provisional
Probab=59.26 E-value=17 Score=26.93 Aligned_cols=32 Identities=16% Similarity=0.081 Sum_probs=27.4
Q ss_pred HHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 033139 41 ANIVCKKADVDMNKRAGELSAAELDQLMVVVAN 73 (126)
Q Consensus 41 A~~Ic~~~gI~p~~k~~~Ls~~qi~~L~~~i~~ 73 (126)
+..+|+.+|++|+.++.-..+ .+.+|..+|-.
T Consensus 88 i~~Vs~~~GV~~~~~idl~d~-~l~~l~~Aii~ 119 (141)
T PHA02564 88 ATAVANAMGVPPQAGLHLDQD-TLAALVTAIIR 119 (141)
T ss_pred HHHHHHHHCCCCCCcCcCCcH-HHHHHHHHHHH
Confidence 778999999999999986656 88899888864
No 106
>PRK13844 recombination protein RecR; Provisional
Probab=58.99 E-value=5.2 Score=31.38 Aligned_cols=40 Identities=10% Similarity=0.090 Sum_probs=29.0
Q ss_pred ehheehhhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHh
Q 033139 25 KIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVA 72 (126)
Q Consensus 25 ~v~~aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L~~~i~ 72 (126)
.+.-+|+.++|||+++|.++.-.+ =+..++++..|.+.|.
T Consensus 12 ~LI~~l~~LPGIG~KsA~Rla~~l--------L~~~~~~~~~la~~i~ 51 (200)
T PRK13844 12 AVIESLRKLPTIGKKSSQRLALYL--------LDKSPETAIAIANSLL 51 (200)
T ss_pred HHHHHHHHCCCCCHHHHHHHHHHH--------HcCCHHHHHHHHHHHH
Confidence 355688999999999999997544 2335566666666665
No 107
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=58.64 E-value=2.2 Score=32.97 Aligned_cols=61 Identities=10% Similarity=0.201 Sum_probs=42.6
Q ss_pred hhhccccCCCCeehheehhhhcccccchHHHHHHHhCC------------CCCCcCCCCCHHHHHHHHHHHhC
Q 033139 13 LRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADV------------DMNKRAGELSAAELDQLMVVVAN 73 (126)
Q Consensus 13 vrI~g~~l~~~K~v~~aLt~IyGIG~~~A~~Ic~~~gI------------~p~~k~~~Ls~~qi~~L~~~i~~ 73 (126)
..++|-.=...+.++.-|.++.|||+++|..|+..+.. ..-+++.-+...--++|.-.++.
T Consensus 58 ~~LyGF~~~~Er~lF~~Li~V~GIGpK~Al~iLs~~~~~el~~aI~~~D~~~L~kvpGIGkKtAerIilELk~ 130 (195)
T PRK14604 58 LTLYGFSTPAQRQLFELLIGVSGVGPKAALNLLSSGTPDELQLAIAGGDVARLARVPGIGKKTAERIVLELKG 130 (195)
T ss_pred ceeeCCCCHHHHHHHHHHhCcCCcCHHHHHHHHcCCCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHH
Confidence 35677777778888999999999999999999976531 22234555555555566655554
No 108
>PRK12311 rpsB 30S ribosomal protein S2/unknown domain fusion protein; Provisional
Probab=58.25 E-value=6.2 Score=33.05 Aligned_cols=45 Identities=9% Similarity=0.079 Sum_probs=39.4
Q ss_pred eehhhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 033139 28 FALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVAN 73 (126)
Q Consensus 28 ~aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L~~~i~~ 73 (126)
--|+.|.|||+..+.. |..+||..-..+-.+|++++..+...+.-
T Consensus 263 DdL~~I~GiGp~~e~~-L~~~Gi~~f~QiA~~t~~~~a~vd~~l~f 307 (326)
T PRK12311 263 DDLKKLTGVSPQIEKK-LNDLGIFHFWQLAELDPDDAAKIGEELGL 307 (326)
T ss_pred hhhhhhccCChhhhhh-hhhcCCCCHHHhhCCChhhhhhhhhcccC
Confidence 4589999999988765 78999999999999999999988887754
No 109
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=58.24 E-value=7.8 Score=34.77 Aligned_cols=44 Identities=30% Similarity=0.349 Sum_probs=31.2
Q ss_pred CCeehheehhhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHH
Q 033139 22 GKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQL 67 (126)
Q Consensus 22 ~~K~v~~aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L 67 (126)
..+....+|..|.|||+.++..+++..|= -..+.+-|.+++.++
T Consensus 537 ~k~~~~s~L~~IpGIG~k~~k~Ll~~FgS--~~~i~~As~eeL~~v 580 (598)
T PRK00558 537 SKARLTSALDDIPGIGPKRRKALLKHFGS--LKAIKEASVEELAKV 580 (598)
T ss_pred ccchhhhhHhhCCCcCHHHHHHHHHHcCC--HHHHHhCCHHHHhhc
Confidence 34456789999999999999999998873 223344455555443
No 110
>KOG2518 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=57.87 E-value=4.8 Score=35.97 Aligned_cols=37 Identities=22% Similarity=0.372 Sum_probs=32.5
Q ss_pred CccccccchhhccccCCCCeehheehhhhcccccchHHHHHHHhCC
Q 033139 5 ANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADV 50 (126)
Q Consensus 5 ~~~~~~~mvrI~g~~l~~~K~v~~aLt~IyGIG~~~A~~Ic~~~gI 50 (126)
..|.|++|.=+.|.|- |.++.|||-.+|.+++.+...
T Consensus 211 ~~ekfr~mciLSGCDY---------l~slpGvGl~tA~k~l~k~~~ 247 (556)
T KOG2518|consen 211 TEEKFRRMCILSGCDY---------LSSLPGVGLATAHKLLSKYNT 247 (556)
T ss_pred CHHHHHHHHHhcCCcc---------cccCccccHHHHHHHHHhcCc
Confidence 4477999999999997 788999999999999988764
No 111
>PRK14976 5'-3' exonuclease; Provisional
Probab=57.70 E-value=5.6 Score=32.28 Aligned_cols=19 Identities=32% Similarity=0.426 Sum_probs=16.8
Q ss_pred hhhcccccchHHHHHHHhC
Q 033139 31 TSIKGIGRRLANIVCKKAD 49 (126)
Q Consensus 31 t~IyGIG~~~A~~Ic~~~g 49 (126)
..+.|||+++|.+++++.|
T Consensus 194 pGVpGIG~KtA~~LL~~~g 212 (281)
T PRK14976 194 KGVKGIGPKTAIKLLNKYG 212 (281)
T ss_pred CCCCcccHHHHHHHHHHcC
Confidence 4589999999999998877
No 112
>PRK14896 ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Provisional
Probab=57.43 E-value=17 Score=28.62 Aligned_cols=63 Identities=19% Similarity=0.241 Sum_probs=41.6
Q ss_pred cccchhhccccCCCCeehheehhhhcc-cccchHHHHHHHh-CCCCCCcCCCCCHHHHHHHHHHHhC
Q 033139 9 FQHILRVLNTNVDGKQKIMFALTSIKG-IGRRLANIVCKKA-DVDMNKRAGELSAAELDQLMVVVAN 73 (126)
Q Consensus 9 ~~~mvrI~g~~l~~~K~v~~aLt~IyG-IG~~~A~~Ic~~~-gI~p~~k~~~Ls~~qi~~L~~~i~~ 73 (126)
|.++++. ..-...|++.-+|..+.. .+......+...+ ++++++|+.+||.+|..+|.+.+..
T Consensus 192 ~~~~~~~--~F~~rrk~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~R~e~L~~~~~~~l~~~~~~ 256 (258)
T PRK14896 192 FDDFVKA--LFQHRRKTLRNALKNSAHISGKEDIKAVVEALPEELLNKRVFQLSPEEIAELANLLYE 256 (258)
T ss_pred HHHHHHH--HHccccHHHHHHHhhhccccchhHHHHHHHHcCCCCcCCCCccCCHHHHHHHHHHHHh
Confidence 3444443 244567888888877631 1211123345556 5668999999999999999998864
No 113
>PF14635 HHH_7: Helix-hairpin-helix motif ; PDB: 3PSI_A 3PSF_A.
Probab=56.91 E-value=6.6 Score=27.72 Aligned_cols=41 Identities=17% Similarity=0.346 Sum_probs=29.8
Q ss_pred cccchhhccccCC---CCeehheehhhhcccccchHHHHHHHhC
Q 033139 9 FQHILRVLNTNVD---GKQKIMFALTSIKGIGRRLANIVCKKAD 49 (126)
Q Consensus 9 ~~~mvrI~g~~l~---~~K~v~~aLt~IyGIG~~~A~~Ic~~~g 49 (126)
|-.+|--.|+||+ .+......|+++-|.|+++|..+.+.+.
T Consensus 28 ~vd~vN~vGVDIN~a~~~~~~~~~LqfV~GLGPRKA~~Ll~~l~ 71 (104)
T PF14635_consen 28 FVDVVNQVGVDINRAVSHPHLANLLQFVCGLGPRKAQALLKALK 71 (104)
T ss_dssp HHHHHHHH-EEHHHHCT-HHHHGGGGGSTT--HHHHHHHHHHHH
T ss_pred HHHHHHhhCccHHHHhcChHHHhhHhHhcCCChHHHHHHHHHHH
Confidence 4456667788875 4667778999999999999999998776
No 114
>TIGR03674 fen_arch flap structure-specific endonuclease. Endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA
Probab=55.44 E-value=6.9 Score=32.51 Aligned_cols=52 Identities=23% Similarity=0.382 Sum_probs=35.0
Q ss_pred cccccchhhccccCCCCeehheehhhhcccccchHHHHHHHhC--------CCCCCcCCCCCHHHHHHHHHHHhCC
Q 033139 7 EDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKAD--------VDMNKRAGELSAAELDQLMVVVANP 74 (126)
Q Consensus 7 ~~~~~mvrI~g~~l~~~K~v~~aLt~IyGIG~~~A~~Ic~~~g--------I~p~~k~~~Ls~~qi~~L~~~i~~~ 74 (126)
++|-.+.-+.|.|-. ..|.|||+.+|.+++++.| ++.. +. ...+++++..+|
T Consensus 224 ~q~id~~iL~G~dyn---------~Gv~GIG~ktA~kli~~~gsie~il~~~~~~-----~~--~~~~~~~~f~~~ 283 (338)
T TIGR03674 224 EQLIDIAILVGTDYN---------EGVKGIGPKTALKLIKEHGDLEKVLKARGED-----IE--NYDEIREFFLNP 283 (338)
T ss_pred HHHHHHHHhcCCCCC---------CCCCCccHHHHHHHHHHcCCHHHHHHhhcCC-----CC--CHHHHHHHhCCC
Confidence 556666777777432 4789999999999998854 2211 22 246788877765
No 115
>PRK10880 adenine DNA glycosylase; Provisional
Probab=54.68 E-value=5.8 Score=33.42 Aligned_cols=29 Identities=14% Similarity=0.298 Sum_probs=22.4
Q ss_pred cccCCCCeehheehhhhcccccchHHHHHHHh
Q 033139 17 NTNVDGKQKIMFALTSIKGIGRRLANIVCKKA 48 (126)
Q Consensus 17 g~~l~~~K~v~~aLt~IyGIG~~~A~~Ic~~~ 48 (126)
|-.+| ...-.|..++|||+.||..||.-+
T Consensus 101 ~g~~p---~~~~~L~~LpGIG~~TA~aIl~~a 129 (350)
T PRK10880 101 GGEFP---ETFEEVAALPGVGRSTAGAILSLS 129 (350)
T ss_pred CCCch---hhHHHHhcCCCccHHHHHHHHHHH
Confidence 44455 345679999999999999999644
No 116
>CHL00154 rpl29 ribosomal protein L29; Validated
Probab=54.26 E-value=7.5 Score=25.25 Aligned_cols=55 Identities=11% Similarity=0.115 Sum_probs=37.8
Q ss_pred CCCCCHHHHHHHHHHHhCCCCccCChhhhhccccccCCccceeehhhHHHHHHHHHHHHHhcccce
Q 033139 56 AGELSAAELDQLMVVVANPRQFKIPDWFLNRQKDYKDGRYSQVVSNALDMKLRDDLERLKKIRYGL 121 (126)
Q Consensus 56 ~~~Ls~~qi~~L~~~i~~~~~~~iP~w~~nr~~d~~tg~~~h~i~~dL~~~~~~dI~rl~~I~sy~ 121 (126)
+.++|.+|+..-...+.. .+ +|-|.--.|| ++-.+...+.++-||.|++.|-+-+
T Consensus 9 lr~ls~~eL~~~l~elk~--el------f~LRfq~atg---ql~n~~~ir~~RrdIARikTil~ek 63 (67)
T CHL00154 9 IIDLTDSEISEEIIKTKK--EL------FDLRLKKATR---QNFKPHLFKHKKHRLAQLLTLLSSR 63 (67)
T ss_pred HHhCCHHHHHHHHHHHHH--HH------HHHHHHHHhC---cccChHHHHHHHHHHHHHHHHHHHH
Confidence 467888888766666654 23 4555555555 3555666799999999999987654
No 117
>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=53.75 E-value=6.8 Score=32.17 Aligned_cols=44 Identities=14% Similarity=0.132 Sum_probs=29.8
Q ss_pred ehheehhhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHH
Q 033139 25 KIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVV 71 (126)
Q Consensus 25 ~v~~aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L~~~i 71 (126)
.+.-.|+.++|||+.+|..||-..-=.|+.-+- |-.+.++.+.+
T Consensus 217 ~~~~~L~~l~GIG~~tAd~vll~~l~~~d~~Pv---D~~v~r~~~r~ 260 (310)
T TIGR00588 217 DAREALCELPGVGPKVADCICLMGLDKPQAVPV---DVHVWRIANRD 260 (310)
T ss_pred HHHHHHHhCCCccHHHHHHHHHHhCCCCCceee---cHHHHHHHHHH
Confidence 456788999999999999999665444443332 45555555444
No 118
>PRK13910 DNA glycosylase MutY; Provisional
Probab=53.50 E-value=7.4 Score=31.93 Aligned_cols=47 Identities=15% Similarity=0.233 Sum_probs=29.6
Q ss_pred ccCCCCeehheehhhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHH
Q 033139 18 TNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVV 71 (126)
Q Consensus 18 ~~l~~~K~v~~aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L~~~i 71 (126)
-.+|.+ .-.|.++.|||+.||..|+.-+ ++... -.=|..+.++..-+
T Consensus 65 g~~P~~---~~~L~~LpGIG~kTA~aIl~~a-f~~~~---~~VD~nV~RVl~Rl 111 (289)
T PRK13910 65 SQLPND---YQSLLKLPGIGAYTANAILCFG-FREKS---ACVDANIKRVLLRL 111 (289)
T ss_pred CCCChh---HHHHHhCCCCCHHHHHHHHHHH-CCCCc---CcccHHHHHHHHHH
Confidence 345553 5789999999999999998643 33211 13344555555443
No 119
>PTZ00338 dimethyladenosine transferase-like protein; Provisional
Probab=51.85 E-value=20 Score=29.18 Aligned_cols=33 Identities=12% Similarity=0.229 Sum_probs=29.0
Q ss_pred hHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 033139 40 LANIVCKKADVDMNKRAGELSAAELDQLMVVVAN 73 (126)
Q Consensus 40 ~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L~~~i~~ 73 (126)
....+++.+|++ ..|..+||-+|.-+|.+++.+
T Consensus 256 ~~~~~l~~~~~~-~~R~e~l~~~~f~~L~~~~~~ 288 (294)
T PTZ00338 256 FIAEILEDSGMF-EKRSVKLDIDDFLKLLLAFNK 288 (294)
T ss_pred HHHHHHHHcCCc-ccChhhCCHHHHHHHHHHHHH
Confidence 345679999997 799999999999999999985
No 120
>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]
Probab=51.48 E-value=10 Score=29.38 Aligned_cols=25 Identities=16% Similarity=0.360 Sum_probs=22.1
Q ss_pred heehhhhcccccchHHHHHHHhCCC
Q 033139 27 MFALTSIKGIGRRLANIVCKKADVD 51 (126)
Q Consensus 27 ~~aLt~IyGIG~~~A~~Ic~~~gI~ 51 (126)
.+++|..+|+|++++.+.++++|++
T Consensus 2 ~I~ITGTPGvGKTT~~~~L~~lg~~ 26 (180)
T COG1936 2 LIAITGTPGVGKTTVCKLLRELGYK 26 (180)
T ss_pred eEEEeCCCCCchHHHHHHHHHhCCc
Confidence 3688999999999999999988875
No 121
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=51.19 E-value=7.8 Score=31.63 Aligned_cols=25 Identities=28% Similarity=0.364 Sum_probs=20.2
Q ss_pred eehheehhhhcccccchHHHHHHHh
Q 033139 24 QKIMFALTSIKGIGRRLANIVCKKA 48 (126)
Q Consensus 24 K~v~~aLt~IyGIG~~~A~~Ic~~~ 48 (126)
..+.-.|+.|.|||+-||.-+|--.
T Consensus 194 e~a~e~L~~i~GIG~WTAe~~llf~ 218 (285)
T COG0122 194 EEAIEELTALKGIGPWTAEMFLLFG 218 (285)
T ss_pred HHHHHHHHcCCCcCHHHHHHHHHHc
Confidence 3356679999999999999998543
No 122
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=49.96 E-value=12 Score=30.00 Aligned_cols=31 Identities=26% Similarity=0.563 Sum_probs=22.9
Q ss_pred CCHHHHHHHHHHHhCCCCcc------------------CChhhhhccccc
Q 033139 59 LSAAELDQLMVVVANPRQFK------------------IPDWFLNRQKDY 90 (126)
Q Consensus 59 Ls~~qi~~L~~~i~~~~~~~------------------iP~w~~nr~~d~ 90 (126)
.+..|++.|++.+++ ..|. |=.||.|||.+.
T Consensus 44 Ftr~QlevLe~LF~k-TqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~ 92 (228)
T KOG2251|consen 44 FTRKQLEVLEALFAK-TQYPDVFMREELALKLNLPESRVQVWFKNRRAKC 92 (228)
T ss_pred ecHHHHHHHHHHHHh-hcCccHHHHHHHHHHhCCchhhhhhhhccccchh
Confidence 578889888888875 2232 456999999884
No 123
>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=49.87 E-value=10 Score=31.64 Aligned_cols=37 Identities=22% Similarity=0.424 Sum_probs=27.6
Q ss_pred ehhhhcccccchHHHHHHHhCCCCCCcCCCC--CHHHHH
Q 033139 29 ALTSIKGIGRRLANIVCKKADVDMNKRAGEL--SAAELD 65 (126)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~L--s~~qi~ 65 (126)
-+..+.|||+.++.++++.+||..-.-+-.+ +.+++.
T Consensus 183 pv~~l~GiG~~~~~~ll~~~Gi~ti~dl~~~~~~~~~L~ 221 (359)
T cd01702 183 PITSIRGLGGKLGEEIIDLLGLPTEGDVAGFRSSESDLQ 221 (359)
T ss_pred cHHHhCCcCHHHHHHHHHHcCCcCHHHHHhccCCHHHHH
Confidence 5789999999999999999999864444444 444443
No 124
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=49.70 E-value=11 Score=34.20 Aligned_cols=25 Identities=20% Similarity=0.247 Sum_probs=21.7
Q ss_pred ehheehhhhcccccchHHHHHHHhC
Q 033139 25 KIMFALTSIKGIGRRLANIVCKKAD 49 (126)
Q Consensus 25 ~v~~aLt~IyGIG~~~A~~Ic~~~g 49 (126)
...-.|..|.|||+.++.++++..|
T Consensus 549 ~~~S~L~~IpGIG~kr~~~LL~~Fg 573 (624)
T PRK14669 549 DRTSELLEIPGVGAKTVQRLLKHFG 573 (624)
T ss_pred HHHHHHhcCCCCCHHHHHHHHHHcC
Confidence 3456788999999999999999887
No 125
>PRK01143 rpl11p 50S ribosomal protein L11P; Validated
Probab=49.22 E-value=50 Score=25.02 Aligned_cols=62 Identities=11% Similarity=0.207 Sum_probs=47.0
Q ss_pred ccchHHHHHHHhCCCC------CCcCCCCCHHHHHHHHHHHhCCCCccCChhhhhccccccCCccceeehhhHHHHHHHH
Q 033139 37 GRRLANIVCKKADVDM------NKRAGELSAAELDQLMVVVANPRQFKIPDWFLNRQKDYKDGRYSQVVSNALDMKLRDD 110 (126)
Q Consensus 37 G~~~A~~Ic~~~gI~p------~~k~~~Ls~~qi~~L~~~i~~~~~~~iP~w~~nr~~d~~tg~~~h~i~~dL~~~~~~d 110 (126)
-+.+|.-|.+.+|+.. ...++.+|-+|+..|.+.-.. . +...+|+..+++=
T Consensus 69 ~Pp~s~ll~kaag~~kgs~~p~~~~vG~It~~qv~eIA~~K~~--d---------------------~~~~~l~~~vk~V 125 (163)
T PRK01143 69 IPPTTALIKKELGIEKGSGEPGHEVVGNLSFEQVVKIAIMKKD--D---------------------LLSYDLKAAVKEV 125 (163)
T ss_pred CCCHHHHHHHHhCCcCCCCCCCCceeeeecHHHHHHHHHHHhh--h---------------------hccccHHHHHHHH
Confidence 4788888999999954 355799999999999998763 2 2456788888877
Q ss_pred HHHHHhcccce
Q 033139 111 LERLKKIRYGL 121 (126)
Q Consensus 111 I~rl~~I~sy~ 121 (126)
+=--+.++|.+
T Consensus 126 lGTarSmGi~V 136 (163)
T PRK01143 126 LGTCVSMGVTV 136 (163)
T ss_pred HhhHhhceEEE
Confidence 77777776654
No 126
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=48.61 E-value=9.8 Score=22.90 Aligned_cols=44 Identities=11% Similarity=0.074 Sum_probs=32.3
Q ss_pred ehhhhcccccchHHHHH-HHhCCCCCCcCCCCCHHHHHHHHHHHh
Q 033139 29 ALTSIKGIGRRLANIVC-KKADVDMNKRAGELSAAELDQLMVVVA 72 (126)
Q Consensus 29 aLt~IyGIG~~~A~~Ic-~~~gI~p~~k~~~Ls~~qi~~L~~~i~ 72 (126)
-|..-.|+...--.+.| +.+|+.....-..|++++...|.+.+.
T Consensus 8 elAk~l~v~~~~ii~~l~~~~Gi~~~~~~~~ld~e~~~~i~~~~~ 52 (54)
T PF04760_consen 8 ELAKELGVPSKEIIKKLFKELGIMVKSINSSLDEEEAELIAEEFG 52 (54)
T ss_dssp HHHHHHSSSHHHHHHHH-HHHTS---SSSS-EETTGGGHHHHHH-
T ss_pred HHHHHHCcCHHHHHHHHHHhCCcCcCCCCCcCCHHHHHHHHHHhC
Confidence 46677788888888889 559999777788889999999888764
No 127
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=48.34 E-value=9.1 Score=31.08 Aligned_cols=30 Identities=27% Similarity=0.244 Sum_probs=22.8
Q ss_pred hheehhhhcccccchHHHHHHHhCCCCCCc
Q 033139 26 IMFALTSIKGIGRRLANIVCKKADVDMNKR 55 (126)
Q Consensus 26 v~~aLt~IyGIG~~~A~~Ic~~~gI~p~~k 55 (126)
..-.|..++|||+.+|..|+-..==.|+.=
T Consensus 205 ~~~~L~~LpGIGpwTA~~vllr~lg~~D~f 234 (283)
T PRK10308 205 AMKTLQTFPGIGRWTANYFALRGWQAKDVF 234 (283)
T ss_pred HHHHHhcCCCcCHHHHHHHHHHhCCCCCCC
Confidence 456799999999999999986644344543
No 128
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=48.02 E-value=19 Score=21.02 Aligned_cols=30 Identities=23% Similarity=0.364 Sum_probs=19.4
Q ss_pred CCCHHHHHHHHHHHhCCCCccCChhhhhccc
Q 033139 58 ELSAAELDQLMVVVANPRQFKIPDWFLNRQK 88 (126)
Q Consensus 58 ~Ls~~qi~~L~~~i~~~~~~~iP~w~~nr~~ 88 (126)
..+.+++..|.+.+.-+ ...|=.||.|||.
T Consensus 24 ~P~~~~~~~la~~~~l~-~~qV~~WF~nrR~ 53 (56)
T smart00389 24 YPSREEREELAAKLGLS-ERQVKVWFQNRRA 53 (56)
T ss_pred CCCHHHHHHHHHHHCcC-HHHHHHhHHHHhh
Confidence 45667777777776532 2445678888875
No 129
>PRK13766 Hef nuclease; Provisional
Probab=47.77 E-value=12 Score=33.72 Aligned_cols=25 Identities=16% Similarity=0.251 Sum_probs=21.5
Q ss_pred ehheehhhhcccccchHHHHHHHhC
Q 033139 25 KIMFALTSIKGIGRRLANIVCKKAD 49 (126)
Q Consensus 25 ~v~~aLt~IyGIG~~~A~~Ic~~~g 49 (126)
...+.|+.+.|||+.+|..|++.+|
T Consensus 712 ~~~~~L~~ipgig~~~a~~Ll~~fg 736 (773)
T PRK13766 712 QQEYIVESLPDVGPVLARNLLEHFG 736 (773)
T ss_pred HHHHHHhcCCCCCHHHHHHHHHHcC
Confidence 3345799999999999999999987
No 130
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.
Probab=47.69 E-value=23 Score=22.18 Aligned_cols=29 Identities=24% Similarity=0.429 Sum_probs=21.0
Q ss_pred CCCHHHHHHHHHHHhCCCCccCChhhhhcccccc
Q 033139 58 ELSAAELDQLMVVVANPRQFKIPDWFLNRQKDYK 91 (126)
Q Consensus 58 ~Ls~~qi~~L~~~i~~~~~~~iP~w~~nr~~d~~ 91 (126)
.++.+.+.+|.+.+.- -|.|++++++.++
T Consensus 44 ~~~~~~~~~l~~~l~v-----~~~~l~~~~~~~~ 72 (78)
T TIGR02607 44 GITADMALRLAKALGT-----SPEFWLNLQNAYD 72 (78)
T ss_pred CCCHHHHHHHHHHcCC-----CHHHHHHHHHHHH
Confidence 5678888888887752 2788888877643
No 131
>PRK05898 dnaE DNA polymerase III DnaE; Validated
Probab=47.62 E-value=24 Score=33.77 Aligned_cols=47 Identities=23% Similarity=0.350 Sum_probs=33.6
Q ss_pred CeehheehhhhcccccchHHHHHHHhCCCCC---------CcCCCCCHHHHHHHHH
Q 033139 23 KQKIMFALTSIKGIGRRLANIVCKKADVDMN---------KRAGELSAAELDQLMV 69 (126)
Q Consensus 23 ~K~v~~aLt~IyGIG~~~A~~Ic~~~gI~p~---------~k~~~Ls~~qi~~L~~ 69 (126)
+..|.++|+.|+|||...|..|.+.-.-.|- .+...++...++.|.+
T Consensus 747 ~~~Ir~gL~~Ikgig~~~~~~I~~~R~~g~f~~~~df~~r~~~~~i~k~~le~LI~ 802 (971)
T PRK05898 747 KQIIRFGFNTIKGFGDELLKKIKSALQNKTFSDFISYIDALKKNNVSLSNIEILIN 802 (971)
T ss_pred CCeEEecchhcCCcCHHHHHHHHHHHhcCCCCCHHHHHHHhhhcCCCHHHHHHHHH
Confidence 5679999999999999999999865432221 1234567777776665
No 132
>COG1059 Thermostable 8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=46.87 E-value=10 Score=29.95 Aligned_cols=27 Identities=22% Similarity=0.338 Sum_probs=23.2
Q ss_pred ehheehhhhcccccchHHHHHHHhCCC
Q 033139 25 KIMFALTSIKGIGRRLANIVCKKADVD 51 (126)
Q Consensus 25 ~v~~aLt~IyGIG~~~A~~Ic~~~gI~ 51 (126)
.=++.+.+|+|||.+=|..+++..|+.
T Consensus 118 aRE~Lv~nikGiGyKEASHFLRNVG~~ 144 (210)
T COG1059 118 ARELLVENIKGIGYKEASHFLRNVGFE 144 (210)
T ss_pred HHHHHHHHcccccHHHHHHHHHhcChh
Confidence 345677899999999999999999974
No 133
>smart00649 RL11 Ribosomal protein L11/L12.
Probab=46.74 E-value=58 Score=23.68 Aligned_cols=61 Identities=10% Similarity=0.222 Sum_probs=46.9
Q ss_pred ccchHHHHHHHhCCCCC------CcCCCCCHHHHHHHHHHHhCCCCccCChhhhhccccccCCccceeehhhHHHHHHHH
Q 033139 37 GRRLANIVCKKADVDMN------KRAGELSAAELDQLMVVVANPRQFKIPDWFLNRQKDYKDGRYSQVVSNALDMKLRDD 110 (126)
Q Consensus 37 G~~~A~~Ic~~~gI~p~------~k~~~Ls~~qi~~L~~~i~~~~~~~iP~w~~nr~~d~~tg~~~h~i~~dL~~~~~~d 110 (126)
-+.+|.-|.+.+|+... ..++.+|-+|+.+|.+.-.. + +...+|+..+++=
T Consensus 64 ~P~~s~ll~k~~g~~kgs~~p~~~~~g~it~~~v~eIA~~K~~--d---------------------~~~~~l~~~~k~V 120 (132)
T smart00649 64 TPPASFLLKKAAGIEKGSKKPGKKKVGNITLDQVYEIAKIKRP--D---------------------LNAKDLEAAVKEI 120 (132)
T ss_pred CCCHHHHHHHHhCCCCCCCCCCCeeeeEEcHHHHHHHHHHHHH--H---------------------hcchhHHHHHHHH
Confidence 47888889999998854 45789999999999988764 2 3667888888877
Q ss_pred HHHHHhcccc
Q 033139 111 LERLKKIRYG 120 (126)
Q Consensus 111 I~rl~~I~sy 120 (126)
+--.+.+++.
T Consensus 121 ~GTa~SmGi~ 130 (132)
T smart00649 121 LGTARSMGIT 130 (132)
T ss_pred HhhHhcceEE
Confidence 7666666654
No 134
>cd00427 Ribosomal_L29_HIP Ribosomal L29 protein/HIP. L29 is a protein of the large ribosomal Subunit. A homolog, called heparin/heparan sulfate interacting protein (HIP), has also been identified in mammals. L29 is located on the surface of the large ribosomal subunit, where it participates in forming a protein ring that surrounds the polypeptide exit channel, providing structural support for the ribosome. L29 is involved in forming the translocon binding site, along with L19, L22, L23, L24, and L31e. In addition, L29 and L23 form the interaction site for trigger factor (TF) on the ribosomal surface, adjacent to the exit tunnel. L29 forms numerous interactions with L23 and with the 23S rRNA. In some eukaryotes, L29 is referred to as L35, which is distinct from L35 found in bacteria and some eukaryotes (primarily plastids and mitochondria). The mammalian homolog, HIP, is found on the surface of many tissues and cell lines. It is believed to play a role in cell adhesion and modulat
Probab=44.87 E-value=15 Score=22.72 Aligned_cols=53 Identities=21% Similarity=0.259 Sum_probs=34.4
Q ss_pred CCCCCHHHHHHHHHHHhCCCCccCChhhhhccccccCCccceeehhhHHHHHHHHHHHHHhccc
Q 033139 56 AGELSAAELDQLMVVVANPRQFKIPDWFLNRQKDYKDGRYSQVVSNALDMKLRDDLERLKKIRY 119 (126)
Q Consensus 56 ~~~Ls~~qi~~L~~~i~~~~~~~iP~w~~nr~~d~~tg~~~h~i~~dL~~~~~~dI~rl~~I~s 119 (126)
+.++|.+|+......+.+ .+ ++-|..-.||. +-..-..+.++-||.|+..+-+
T Consensus 3 ir~ls~~eL~~~l~~l~~--el------f~Lr~q~~~~~---~~~~~~~~~~Rr~IARi~Til~ 55 (57)
T cd00427 3 LREKSDEELQEKLDELKK--EL------FNLRFQKATGQ---LENPHRIRKVRKDIARIKTVLN 55 (57)
T ss_pred HHHCCHHHHHHHHHHHHH--HH------HHHHHHHHHCC---CcCcHHHHHHHHHHHHHHHHHH
Confidence 456788887766665554 23 34444444554 4445567899999999998754
No 135
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=44.49 E-value=9 Score=34.64 Aligned_cols=49 Identities=22% Similarity=0.377 Sum_probs=34.7
Q ss_pred cccCCCCeehheehhhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHH
Q 033139 17 NTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQL 67 (126)
Q Consensus 17 g~~l~~~K~v~~aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L 67 (126)
+-..-..+...-.|..|.|||+.+|..+++.+| +. ..+..-+.++|.++
T Consensus 558 hr~~r~k~~~~s~L~~I~GIG~k~a~~Ll~~Fg-s~-~~i~~As~eeL~~v 606 (621)
T PRK14671 558 HRKLRSKRTLQTELTDIAGIGEKTAEKLLEHFG-SV-EKVAKASLEELAAV 606 (621)
T ss_pred ChhhHHHHHhhhhhhcCCCcCHHHHHHHHHHcC-CH-HHHHhCCHHHHHHH
Confidence 444545556677789999999999999999996 21 23444466776554
No 136
>PRK07945 hypothetical protein; Provisional
Probab=44.16 E-value=13 Score=30.77 Aligned_cols=21 Identities=33% Similarity=0.623 Sum_probs=18.3
Q ss_pred ehhhhcccccchHHHHHHHhC
Q 033139 29 ALTSIKGIGRRLANIVCKKAD 49 (126)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~~g 49 (126)
.|+.++|||+.+|.+|-+.+.
T Consensus 50 ~l~~~~giG~~~a~~i~e~~~ 70 (335)
T PRK07945 50 SLTSLPGIGPKTAKVIAQALA 70 (335)
T ss_pred CcccCCCcCHHHHHHHHHHHh
Confidence 689999999999999987654
No 137
>KOG0650 consensus WD40 repeat nucleolar protein Bop1, involved in ribosome biogenesis [Translation, ribosomal structure and biogenesis]
Probab=44.14 E-value=35 Score=31.34 Aligned_cols=48 Identities=21% Similarity=0.487 Sum_probs=37.2
Q ss_pred CCCCCcCCCCCHHHHHHHHHHHhCCCCccCChhhhhccccccCCccceeehhhHH
Q 033139 50 VDMNKRAGELSAAELDQLMVVVANPRQFKIPDWFLNRQKDYKDGRYSQVVSNALD 104 (126)
Q Consensus 50 I~p~~k~~~Ls~~qi~~L~~~i~~~~~~~iP~w~~nr~~d~~tg~~~h~i~~dL~ 104 (126)
++-.+-++-...++++++.+.|+.| .+ | ++.+|..||++..++.-|+.
T Consensus 141 ~~gkkI~kp~k~~~ld~fl~~iedp-~~----W--r~v~Dk~tG~dv~LTkEev~ 188 (733)
T KOG0650|consen 141 IDGKKITKPAKGDELDSFLAKIEDP-DY----W--RKVKDKMTGKDVNLTKEEVK 188 (733)
T ss_pred ccccEecCCCccchHHHHHHhhcCc-ch----h--ccccccCCCceeeecHHHHH
Confidence 3334445566678999999999986 35 5 99999999999999877764
No 138
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=41.43 E-value=34 Score=26.79 Aligned_cols=40 Identities=15% Similarity=0.091 Sum_probs=26.2
Q ss_pred ccchHHHHHHHhCCC--CCCcCC-CCCHHHHHHHHHHHhCCCCc
Q 033139 37 GRRLANIVCKKADVD--MNKRAG-ELSAAELDQLMVVVANPRQF 77 (126)
Q Consensus 37 G~~~A~~Ic~~~gI~--p~~k~~-~Ls~~qi~~L~~~i~~~~~~ 77 (126)
|...+..+.-...+. ..+|+. -.|.+|+.+|+.+++.. .|
T Consensus 84 ~~~~~~~~~l~~~~~~~~~kr~RT~ft~~Ql~~LE~~F~~~-~Y 126 (197)
T KOG0843|consen 84 GKDTMLEGFLLLPLRSMRPKRIRTAFTPEQLLKLEHAFEGN-QY 126 (197)
T ss_pred ccchhhhhhccccccccCCCccccccCHHHHHHHHHHHhcC-Ce
Confidence 455555555555555 333443 46999999999999874 35
No 139
>COG0080 RplK Ribosomal protein L11 [Translation, ribosomal structure and biogenesis]
Probab=41.02 E-value=89 Score=23.31 Aligned_cols=59 Identities=12% Similarity=0.233 Sum_probs=43.7
Q ss_pred cchHHHHHHHhCCCC------CCcCCCCCHHHHHHHHHHHhCCCCccCChhhhhccccccCCccceeehhhHHHHHHHHH
Q 033139 38 RRLANIVCKKADVDM------NKRAGELSAAELDQLMVVVANPRQFKIPDWFLNRQKDYKDGRYSQVVSNALDMKLRDDL 111 (126)
Q Consensus 38 ~~~A~~Ic~~~gI~p------~~k~~~Ls~~qi~~L~~~i~~~~~~~iP~w~~nr~~d~~tg~~~h~i~~dL~~~~~~dI 111 (126)
+..|.-|.+.+|+++ ..++++||-+|+..|.+.-.. - +...||...+++=.
T Consensus 72 PPas~LlkKa~g~~~Gs~~p~k~~vG~lt~~qv~eIA~~K~~---d--------------------l~a~~l~aA~k~I~ 128 (141)
T COG0080 72 PPASALLKKAAGIEKGSGKPNKNKVGKLTLAQVREIAKTKMP---D--------------------LNAKDLEAAVKEIL 128 (141)
T ss_pred CCHHHHHHHHhCCCCCCCCCCcceeeeeeHHHHHHHHHHhhh---h--------------------hhhHHHHHHHHHHh
Confidence 667888888999864 367899999999999887553 1 57888988887655
Q ss_pred HHHHhccc
Q 033139 112 ERLKKIRY 119 (126)
Q Consensus 112 ~rl~~I~s 119 (126)
=--+.+++
T Consensus 129 GTa~SMGv 136 (141)
T COG0080 129 GTARSMGV 136 (141)
T ss_pred hhhhhceE
Confidence 44444443
No 140
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=40.96 E-value=14 Score=31.80 Aligned_cols=29 Identities=17% Similarity=0.405 Sum_probs=23.3
Q ss_pred CHHHHHHHHHHHhCCCCccCChhhhhcccc
Q 033139 60 SAAELDQLMVVVANPRQFKIPDWFLNRQKD 89 (126)
Q Consensus 60 s~~qi~~L~~~i~~~~~~~iP~w~~nr~~d 89 (126)
|.+||..|.+.++= .+..|-.||-|||.-
T Consensus 320 t~qEIt~iA~~L~l-eKEVVRVWFCNRRQk 348 (398)
T KOG3802|consen 320 TSQEITHIAESLQL-EKEVVRVWFCNRRQK 348 (398)
T ss_pred CHHHHHHHHHHhcc-ccceEEEEeeccccc
Confidence 66899999999872 256789999999864
No 141
>PTZ00105 60S ribosomal protein L12; Provisional
Probab=40.71 E-value=55 Score=24.16 Aligned_cols=60 Identities=8% Similarity=0.123 Sum_probs=44.4
Q ss_pred cchHHHHHHHhCCCCC----C----cCCCCCHHHHHHHHHHHhCCCCccCChhhhhccccccCCccceeehhhHHHHHHH
Q 033139 38 RRLANIVCKKADVDMN----K----RAGELSAAELDQLMVVVANPRQFKIPDWFLNRQKDYKDGRYSQVVSNALDMKLRD 109 (126)
Q Consensus 38 ~~~A~~Ic~~~gI~p~----~----k~~~Ls~~qi~~L~~~i~~~~~~~iP~w~~nr~~d~~tg~~~h~i~~dL~~~~~~ 109 (126)
+.+|.-|.+.+|+... . .++.||-+|+.+|.+.-.. . +-..+|...+++
T Consensus 50 Pp~s~ll~k~ag~~~~~~~~~~~~~~vG~it~~qv~eIAk~K~~--d---------------------l~~~~l~~a~k~ 106 (140)
T PTZ00105 50 PTASSLLIKALKEPPRDRKKVKNIKHSGNLTFDQVIKIARTMRP--K---------------------SMAKTFKGTVKE 106 (140)
T ss_pred CCHHHHHHHHhCCCCCCCCCCCcceeeeEeeHHHHHHHHHHHHh--h---------------------hCCCcHHHHHHH
Confidence 9999999999998632 2 6889999999999997654 2 346677777776
Q ss_pred HHHHHHhcccc
Q 033139 110 DLERLKKIRYG 120 (126)
Q Consensus 110 dI~rl~~I~sy 120 (126)
=+=--+.+++.
T Consensus 107 V~GTarSmGi~ 117 (140)
T PTZ00105 107 VLGTCVSIGCT 117 (140)
T ss_pred HHhhheeeeEE
Confidence 65555555554
No 142
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=40.40 E-value=18 Score=21.70 Aligned_cols=21 Identities=14% Similarity=0.069 Sum_probs=17.2
Q ss_pred eehhhhcccccchHHHHHHHh
Q 033139 28 FALTSIKGIGRRLANIVCKKA 48 (126)
Q Consensus 28 ~aLt~IyGIG~~~A~~Ic~~~ 48 (126)
.-|...+||+++++.+++...
T Consensus 23 ~~La~~FgIs~stvsri~~~~ 43 (53)
T PF13613_consen 23 QDLAYRFGISQSTVSRIFHEW 43 (53)
T ss_pred hHHhhheeecHHHHHHHHHHH
Confidence 356788999999999998653
No 143
>PRK00306 50S ribosomal protein L29; Reviewed
Probab=40.11 E-value=25 Score=22.34 Aligned_cols=55 Identities=20% Similarity=0.295 Sum_probs=38.1
Q ss_pred CCCCCHHHHHHHHHHHhCCCCccCChhhhhccccccCCccceeehhhHHHHHHHHHHHHHhcccce
Q 033139 56 AGELSAAELDQLMVVVANPRQFKIPDWFLNRQKDYKDGRYSQVVSNALDMKLRDDLERLKKIRYGL 121 (126)
Q Consensus 56 ~~~Ls~~qi~~L~~~i~~~~~~~iP~w~~nr~~d~~tg~~~h~i~~dL~~~~~~dI~rl~~I~sy~ 121 (126)
+.++|.+|+......+.+ .+ ++-|..-.||. +-..-..+.++-||.|+..+-+-+
T Consensus 6 lr~ls~~eL~~~l~~lkk--eL------~~lR~~~~~~~---~~n~~~i~~~rk~IARi~Tvl~er 60 (66)
T PRK00306 6 LRELSVEELNEKLLELKK--EL------FNLRFQKATGQ---LENTHRLREVRRDIARIKTVLRER 60 (66)
T ss_pred HhhCCHHHHHHHHHHHHH--HH------HHHHHHHHhCC---CcCcHHHHHHHHHHHHHHHHHHHH
Confidence 567899998877777765 33 45554445554 344555789999999999876543
No 144
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=39.72 E-value=20 Score=30.44 Aligned_cols=30 Identities=20% Similarity=0.428 Sum_probs=21.6
Q ss_pred CCCHHHHHHHHHHHhCCCCcc------------------CChhhhhccc
Q 033139 58 ELSAAELDQLMVVVANPRQFK------------------IPDWFLNRQK 88 (126)
Q Consensus 58 ~Ls~~qi~~L~~~i~~~~~~~------------------iP~w~~nr~~ 88 (126)
-.|.|||.+|++.+-. .||. |-.||-|||.
T Consensus 187 AFTReQIaRLEKEFyr-ENYVSRprRcELAAaLNLPEtTIKVWFQNRRM 234 (408)
T KOG0844|consen 187 AFTREQIARLEKEFYR-ENYVSRPRRCELAAALNLPETTIKVWFQNRRM 234 (408)
T ss_pred hhhHHHHHHHHHHHHH-hccccCchhhhHHHhhCCCcceeehhhhhchh
Confidence 3588999999987653 1342 4569999985
No 145
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=39.53 E-value=28 Score=25.73 Aligned_cols=20 Identities=25% Similarity=0.439 Sum_probs=17.0
Q ss_pred ehhhhcccccchHHHHHHHh
Q 033139 29 ALTSIKGIGRRLANIVCKKA 48 (126)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~~ 48 (126)
-|+.+.|||+++|.+|.+.=
T Consensus 98 eL~~lpgIG~~kA~aIi~yR 117 (149)
T COG1555 98 ELQALPGIGPKKAQAIIDYR 117 (149)
T ss_pred HHHHCCCCCHHHHHHHHHHH
Confidence 35999999999999998544
No 146
>TIGR03045 PS_II_C550 cytochrome c-550. Members of this protein family are cytochrome c-550, the PsbV extrinsic protein of photosystem II, from both Cyanobacteria and chloroplasts. A paralog to this protein, PsbV2, is found in some species in addition to PsbV itself.
Probab=38.98 E-value=36 Score=25.71 Aligned_cols=17 Identities=12% Similarity=0.128 Sum_probs=15.4
Q ss_pred CCCCHHHHHHHHHHHhC
Q 033139 57 GELSAAELDQLMVVVAN 73 (126)
Q Consensus 57 ~~Ls~~qi~~L~~~i~~ 73 (126)
+.||++|+..|..+|..
T Consensus 130 ~~LsdeEL~avAaYIl~ 146 (159)
T TIGR03045 130 RNLTDEDLRLIAGHILV 146 (159)
T ss_pred CCCCHHHHHHHHHHHHH
Confidence 67999999999999875
No 147
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=38.52 E-value=12 Score=21.93 Aligned_cols=30 Identities=23% Similarity=0.328 Sum_probs=17.4
Q ss_pred CCCHHHHHHHHHHHhCCCCccCChhhhhccc
Q 033139 58 ELSAAELDQLMVVVANPRQFKIPDWFLNRQK 88 (126)
Q Consensus 58 ~Ls~~qi~~L~~~i~~~~~~~iP~w~~nr~~ 88 (126)
..+.+++..|...+.=+ ...|-.||.|||.
T Consensus 24 ~P~~~~~~~la~~~~l~-~~qV~~WF~nrR~ 53 (59)
T cd00086 24 YPSREEREELAKELGLT-ERQVKIWFQNRRA 53 (59)
T ss_pred CCCHHHHHHHHHHHCcC-HHHHHHHHHHHHH
Confidence 34556666666665421 2335668888775
No 148
>TIGR00600 rad2 DNA excision repair protein (rad2). All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=38.35 E-value=17 Score=34.95 Aligned_cols=35 Identities=11% Similarity=0.130 Sum_probs=27.4
Q ss_pred cccccchhhccccCCCCeehheehhhhcccccchHHHHHHHhCC
Q 033139 7 EDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADV 50 (126)
Q Consensus 7 ~~~~~mvrI~g~~l~~~K~v~~aLt~IyGIG~~~A~~Ic~~~gI 50 (126)
++|-.+.-++|+|-. ..|.|||+.+|.+|++..|=
T Consensus 854 ~qli~laiL~G~DY~---------~GI~GIGpktAl~li~~~~~ 888 (1034)
T TIGR00600 854 NKLINLAYLLGSDYT---------EGIPTVGPVSAMEILNEFPG 888 (1034)
T ss_pred HHHHHHHHeeCCCCC---------CCCCcccHHHHHHHHHHcCC
Confidence 455666777777663 36999999999999999873
No 149
>TIGR01632 L11_bact 50S ribosomal protein L11. This model represents bacterial, chloroplast, and most mitochondrial forms of 50S ribosomal protein L11.
Probab=38.30 E-value=52 Score=24.28 Aligned_cols=61 Identities=8% Similarity=0.206 Sum_probs=44.9
Q ss_pred ccchHHHHHHHhCCCCC------CcCCCCCHHHHHHHHHHHhCCCCccCChhhhhccccccCCccceeehhhHHHHHHHH
Q 033139 37 GRRLANIVCKKADVDMN------KRAGELSAAELDQLMVVVANPRQFKIPDWFLNRQKDYKDGRYSQVVSNALDMKLRDD 110 (126)
Q Consensus 37 G~~~A~~Ic~~~gI~p~------~k~~~Ls~~qi~~L~~~i~~~~~~~iP~w~~nr~~d~~tg~~~h~i~~dL~~~~~~d 110 (126)
-+.+|.-|.+.+|+.+. ..++.+|-+|+.+|.+.-.. . +-..+|...+++=
T Consensus 71 ~Pp~s~ll~kaag~~~gs~~p~~~~~G~it~~qv~eIA~~K~~--d---------------------~~~~~l~~~vk~v 127 (140)
T TIGR01632 71 TPPVSYLLKKAAGVEKGSKNPKKEKVGKITRKQVREIAEIKMS--D---------------------LNTKDIEAAMKII 127 (140)
T ss_pred CCCHHHHHHHHhCCCCCCCCCCCeEEeEecHHHHHHHHHHHHH--H---------------------hCcccHHHHHHHh
Confidence 57888999999998776 36799999999999988653 2 3566777777765
Q ss_pred HHHHHhcccc
Q 033139 111 LERLKKIRYG 120 (126)
Q Consensus 111 I~rl~~I~sy 120 (126)
+=--+.+++.
T Consensus 128 ~GTarSmGi~ 137 (140)
T TIGR01632 128 AGTAKSMGIE 137 (140)
T ss_pred heeHeeceEE
Confidence 5555555543
No 150
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=37.95 E-value=19 Score=32.43 Aligned_cols=40 Identities=30% Similarity=0.331 Sum_probs=28.8
Q ss_pred hheehhhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHH
Q 033139 26 IMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQL 67 (126)
Q Consensus 26 v~~aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L 67 (126)
....|..|.|||+.+.+++++..|== ..+..-|.+||.++
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 45688999999999999999987732 33444555555443
No 151
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=37.87 E-value=18 Score=32.51 Aligned_cols=39 Identities=15% Similarity=0.262 Sum_probs=29.0
Q ss_pred hheehhhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHH
Q 033139 26 IMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQ 66 (126)
Q Consensus 26 v~~aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~ 66 (126)
...+|+.|.|||+.++.++++..|= -..+.+-|.+++.+
T Consensus 523 ~~~~L~~IpGIG~kr~~~LL~~FGS--~~~I~~As~eeL~~ 561 (577)
T PRK14668 523 VSTVLDDVPGVGPETRKRLLRRFGS--VEGVREASVEDLRD 561 (577)
T ss_pred HHhHHhcCCCCCHHHHHHHHHHcCC--HHHHHhCCHHHHHh
Confidence 5689999999999999999998862 23344455555543
No 152
>CHL00127 rpl11 ribosomal protein L11; Validated
Probab=37.58 E-value=73 Score=23.49 Aligned_cols=61 Identities=11% Similarity=0.192 Sum_probs=44.4
Q ss_pred ccchHHHHHHHhCCCCC------CcCCCCCHHHHHHHHHHHhCCCCccCChhhhhccccccCCccceeehhhHHHHHHHH
Q 033139 37 GRRLANIVCKKADVDMN------KRAGELSAAELDQLMVVVANPRQFKIPDWFLNRQKDYKDGRYSQVVSNALDMKLRDD 110 (126)
Q Consensus 37 G~~~A~~Ic~~~gI~p~------~k~~~Ls~~qi~~L~~~i~~~~~~~iP~w~~nr~~d~~tg~~~h~i~~dL~~~~~~d 110 (126)
-+.+|.-|.+.+|+... ..+++||-+|+.+|.+.-.. . +...+|...+++=
T Consensus 72 ~Pp~s~ll~ka~gi~~gs~~p~~~~~G~it~~~v~eIA~~K~~--d---------------------~~~~~l~~~vk~v 128 (140)
T CHL00127 72 TPPASVLLAKAAGIKKGSGEPNKKKVGSITIKQLEEIAQIKLP--D---------------------LNTISLSKAIKII 128 (140)
T ss_pred CCCHHHHHHHHhCCCcCCCCCCCeecceecHHHHHHHHHHHhh--h---------------------hccccHHHHHHHh
Confidence 57888888999998754 34789999999999987653 1 3567777777766
Q ss_pred HHHHHhcccc
Q 033139 111 LERLKKIRYG 120 (126)
Q Consensus 111 I~rl~~I~sy 120 (126)
+---+.+++.
T Consensus 129 ~GTa~SmGi~ 138 (140)
T CHL00127 129 EGTAKNMGIS 138 (140)
T ss_pred HeeheeceEE
Confidence 5555555543
No 153
>PRK12373 NADH dehydrogenase subunit E; Provisional
Probab=37.51 E-value=30 Score=29.93 Aligned_cols=56 Identities=14% Similarity=0.161 Sum_probs=44.0
Q ss_pred eehhhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCCccCChhhh
Q 033139 28 FALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVANPRQFKIPDWFL 84 (126)
Q Consensus 28 ~aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L~~~i~~~~~~~iP~w~~ 84 (126)
--|+.|.|||+..+.. +..+||..--.+-.++++++..+...+.-+....--.|--
T Consensus 323 DDLk~I~GIGpk~e~~-Ln~~Gi~~f~QIA~wt~~eia~vd~~l~f~Gri~rd~Wv~ 378 (400)
T PRK12373 323 DDLKLISGVGPKIEAT-LNELGIFTFDQVAAWKKAERAWVDGYLNFKGRIERDDWVK 378 (400)
T ss_pred hhhhhccCCChHHHHH-HHhcCCCCHHHHhCCCHHHhHHhhhcccCCCCcCcchHHH
Confidence 3589999999998765 7899999999999999999999988887543332234543
No 154
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=37.50 E-value=19 Score=32.31 Aligned_cols=43 Identities=26% Similarity=0.267 Sum_probs=30.7
Q ss_pred CeehheehhhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHH
Q 033139 23 KQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQL 67 (126)
Q Consensus 23 ~K~v~~aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L 67 (126)
+....-.|..|.|||+.+.+++++..|== ..++.-|.+||.++
T Consensus 509 k~~~~S~Ld~I~GiG~kr~~~Ll~~Fgs~--~~ik~As~eeL~~v 551 (567)
T PRK14667 509 KEGLKDILDKIKGIGEVKKEIIYRNFKTL--YDFLKADDEELKKL 551 (567)
T ss_pred cccccCccccCCCCCHHHHHHHHHHhCCH--HHHHhCCHHHHHHc
Confidence 34456778999999999999999988732 33445556666544
No 155
>PRK00419 DNA primase small subunit; Reviewed
Probab=37.23 E-value=16 Score=31.25 Aligned_cols=20 Identities=35% Similarity=0.471 Sum_probs=14.6
Q ss_pred ehhhhcccccchHHHHHHHh
Q 033139 29 ALTSIKGIGRRLANIVCKKA 48 (126)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~~ 48 (126)
-|+.+.|||..+|+++++..
T Consensus 222 ~l~~~~gi~~~~~~~~l~~~ 241 (376)
T PRK00419 222 RLEEFDGIGEGTAKKILKAA 241 (376)
T ss_pred hhhhhcccchhHHHHHHHHh
Confidence 45667888888888887653
No 156
>PRK00140 rplK 50S ribosomal protein L11; Validated
Probab=36.92 E-value=46 Score=24.52 Aligned_cols=60 Identities=8% Similarity=0.184 Sum_probs=44.0
Q ss_pred ccchHHHHHHHhCCCCC------CcCCCCCHHHHHHHHHHHhCCCCccCChhhhhccccccCCccceeehhhHHHHHHHH
Q 033139 37 GRRLANIVCKKADVDMN------KRAGELSAAELDQLMVVVANPRQFKIPDWFLNRQKDYKDGRYSQVVSNALDMKLRDD 110 (126)
Q Consensus 37 G~~~A~~Ic~~~gI~p~------~k~~~Ls~~qi~~L~~~i~~~~~~~iP~w~~nr~~d~~tg~~~h~i~~dL~~~~~~d 110 (126)
-+.+|.-|.+.+|+... ..+++||-+|+.+|.+.-.. + +...+|+..+++=
T Consensus 72 ~Pp~s~ll~k~~g~~~gs~~p~~~~vG~it~~~v~eIA~~K~~--d---------------------~~~~~l~~~vk~V 128 (141)
T PRK00140 72 TPPASVLLKKAAGIEKGSGEPNKEKVGKITRAQVREIAETKMP--D---------------------LNAADIEAAMRMI 128 (141)
T ss_pred CCCHHHHHHHHhCCCCCCCCCCCeEEeeEcHHHHHHHHHHHHH--h---------------------hCCCcHHHHHHHh
Confidence 68899999999999874 45689999999999988653 2 3457777777765
Q ss_pred HHHHHhccc
Q 033139 111 LERLKKIRY 119 (126)
Q Consensus 111 I~rl~~I~s 119 (126)
+=--+.+++
T Consensus 129 lGTa~SmGi 137 (141)
T PRK00140 129 AGTARSMGI 137 (141)
T ss_pred heeeeEeeE
Confidence 544444444
No 157
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=36.59 E-value=24 Score=29.30 Aligned_cols=31 Identities=23% Similarity=0.511 Sum_probs=23.4
Q ss_pred CCCHHHHHHHHHHHhCCCCcc------------------CChhhhhcccc
Q 033139 58 ELSAAELDQLMVVVANPRQFK------------------IPDWFLNRQKD 89 (126)
Q Consensus 58 ~Ls~~qi~~L~~~i~~~~~~~------------------iP~w~~nr~~d 89 (126)
-+|..|++.|++++++. .|+ |-.||-|||.-
T Consensus 147 iFT~~Qle~LEkaFkea-HYPDv~Are~la~ktelpEDRIqVWfQNRRAK 195 (332)
T KOG0494|consen 147 IFTSYQLEELEKAFKEA-HYPDVYAREMLADKTELPEDRIQVWFQNRRAK 195 (332)
T ss_pred hhhHHHHHHHHHHHhhc-cCccHHHHHHHhhhccCchhhhhHHhhhhhHH
Confidence 36899999999999863 242 44699998854
No 158
>TIGR00594 polc DNA-directed DNA polymerase III (polc). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=35.96 E-value=27 Score=33.49 Aligned_cols=47 Identities=19% Similarity=0.349 Sum_probs=33.4
Q ss_pred CeehheehhhhcccccchHHHHHHHhCC-CC---------CCcCCCCCHHHHHHHHH
Q 033139 23 KQKIMFALTSIKGIGRRLANIVCKKADV-DM---------NKRAGELSAAELDQLMV 69 (126)
Q Consensus 23 ~K~v~~aLt~IyGIG~~~A~~Ic~~~gI-~p---------~~k~~~Ls~~qi~~L~~ 69 (126)
+..|.++|..|+|||...|..|.+.-.- .| ....+.++..+++.|.+
T Consensus 819 ~~~i~~gl~~Ikgig~~~~~~Iv~~R~~~~~f~s~~Df~~R~~~~~~~~~~le~Li~ 875 (1022)
T TIGR00594 819 DKGIRYGLGAIKGVGESVVKSIIEERNKNGPFKSLFDFINRVDFKKLNKKVLEALIK 875 (1022)
T ss_pred CCEEEechhhcCCCCHHHHHHHHHHHHhCCCCCCHHHHHHHhcccCCCHHHHHHHHH
Confidence 4579999999999999999999865421 11 12234577777777664
No 159
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=35.58 E-value=25 Score=28.41 Aligned_cols=38 Identities=24% Similarity=0.316 Sum_probs=24.9
Q ss_pred eehhhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHH
Q 033139 28 FALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQ 66 (126)
Q Consensus 28 ~aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~ 66 (126)
..|..++|||+.+|..+ .+.||..-.-+-+++.+++.+
T Consensus 6 ~~l~~l~gIg~~~a~~L-~~~Gi~t~~dl~~~~~~~L~~ 43 (317)
T PRK04301 6 KDLEDLPGVGPATAEKL-REAGYDTVEAIAVASPKELSE 43 (317)
T ss_pred ccHhhcCCCCHHHHHHH-HHcCCCCHHHHHcCCHHHHHH
Confidence 45788999998887764 567777555554555555433
No 160
>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=34.98 E-value=16 Score=32.70 Aligned_cols=25 Identities=20% Similarity=0.278 Sum_probs=21.6
Q ss_pred ehheehhhhcccccchHHHHHHHhC
Q 033139 25 KIMFALTSIKGIGRRLANIVCKKAD 49 (126)
Q Consensus 25 ~v~~aLt~IyGIG~~~A~~Ic~~~g 49 (126)
.+.-.|..|.|||+.+.+.+++..|
T Consensus 538 ~~~S~Ld~I~GIG~kr~~~LL~~Fg 562 (574)
T TIGR00194 538 SLQSPLLKIPGVGEKRVQKLLKYFG 562 (574)
T ss_pred HHHHHHhcCCCCCHHHHHHHHHHcC
Confidence 3456788999999999999998877
No 161
>PF00298 Ribosomal_L11: Ribosomal protein L11, RNA binding domain; InterPro: IPR020783 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 L11 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L11 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, ], groups bacteria, plant chloroplast, red algal chloroplast, cyanelle and archaeabacterial L11; and mammalian, plant and yeast L12 (YL15). L11 is a protein of 140 to 165 amino-acid residues. In E. coli, the C-terminal half of L11 has been shown [] to be in an extended and loosely folded conformation and is likely to be buried within the ribosomal structure.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 1VQN_I 2OTJ_I 3G6E_I 3CME_I 1YIJ_I 1YI2_I 3G4S_I 3CMA_I 3I55_I 1VQ7_I ....
Probab=34.91 E-value=1.3e+02 Score=19.45 Aligned_cols=59 Identities=7% Similarity=0.185 Sum_probs=40.8
Q ss_pred cchHHHHHHHhCCCCC------CcCCCCCHHHHHHHHHHHhCCCCccCChhhhhccccccCCccceeehhhHHHHHHHHH
Q 033139 38 RRLANIVCKKADVDMN------KRAGELSAAELDQLMVVVANPRQFKIPDWFLNRQKDYKDGRYSQVVSNALDMKLRDDL 111 (126)
Q Consensus 38 ~~~A~~Ic~~~gI~p~------~k~~~Ls~~qi~~L~~~i~~~~~~~iP~w~~nr~~d~~tg~~~h~i~~dL~~~~~~dI 111 (126)
+.++.-|.+.+|++.. ..++.||-+|+.+|.+.-.. - ..+.||+..+++=+
T Consensus 3 Pp~s~llkkaagi~kGs~~p~~~~vG~it~~~i~eIAk~K~~---d--------------------~~~~~l~~~~k~v~ 59 (69)
T PF00298_consen 3 PPTSWLLKKAAGIKKGSSKPGKEKVGTITLKQIYEIAKIKQK---D--------------------LNAKSLESAVKSVI 59 (69)
T ss_dssp STHHHHHHHHHTTSSSSSSTTTSSSEEEEHHHHHHHHHHHTT---T--------------------SSSSSHHHHHHHHH
T ss_pred CChHHHHHHHhCCCCCCCCCCCceeeeecHHHHHHHHHHhhc---c--------------------cccCCHHHHHHHHH
Confidence 4567778888888432 45889999999999987654 2 35667777776655
Q ss_pred HHHHhccc
Q 033139 112 ERLKKIRY 119 (126)
Q Consensus 112 ~rl~~I~s 119 (126)
---+.+++
T Consensus 60 Gta~SmGi 67 (69)
T PF00298_consen 60 GTARSMGI 67 (69)
T ss_dssp HHHHTTTE
T ss_pred HHHhcCce
Confidence 55554443
No 162
>PF13276 HTH_21: HTH-like domain
Probab=34.07 E-value=25 Score=21.31 Aligned_cols=35 Identities=14% Similarity=0.264 Sum_probs=29.2
Q ss_pred CCCCeehheehhhhcc--cccchHHHHHHHhCCCCCC
Q 033139 20 VDGKQKIMFALTSIKG--IGRRLANIVCKKADVDMNK 54 (126)
Q Consensus 20 l~~~K~v~~aLt~IyG--IG~~~A~~Ic~~~gI~p~~ 54 (126)
..|...+...|..-+| ||..+...|++..||....
T Consensus 20 ~yG~rri~~~L~~~~~~~v~~krV~RlM~~~gL~~~~ 56 (60)
T PF13276_consen 20 TYGYRRIWAELRREGGIRVSRKRVRRLMREMGLRSKR 56 (60)
T ss_pred CeehhHHHHHHhccCcccccHHHHHHHHHHcCCcccC
Confidence 5677888889988876 7999999999999997643
No 163
>PRK07279 dnaE DNA polymerase III DnaE; Reviewed
Probab=33.95 E-value=29 Score=33.44 Aligned_cols=25 Identities=36% Similarity=0.579 Sum_probs=22.5
Q ss_pred CeehheehhhhcccccchHHHHHHH
Q 033139 23 KQKIMFALTSIKGIGRRLANIVCKK 47 (126)
Q Consensus 23 ~K~v~~aLt~IyGIG~~~A~~Ic~~ 47 (126)
++.|.++|..|+|||...+..|.+.
T Consensus 745 ~~~Ir~GL~aIkgvg~~~~~~I~~~ 769 (1034)
T PRK07279 745 NKKIYLGLKNIKGLPRDLAYWIIEN 769 (1034)
T ss_pred CCEEEeehhhcCCCCHHHHHHHHHC
Confidence 5579999999999999999999764
No 164
>PF03118 RNA_pol_A_CTD: Bacterial RNA polymerase, alpha chain C terminal domain; InterPro: IPR011260 The core of the bacterial RNA polymerase (RNAP) consists of four subunits, two alpha, a beta and a beta', which are conserved from bacteria to mammals. The alpha subunit (RpoA) initiates RNAP assembly by dimerising to form a platform on which the beta subunits can interact. The alpha subunit consists of a N-terminal domain (NTD) and a C-terminal domain (CTD), connected by a short linker. The NTD is essential for RNAP assembly, while the CTD is necessary for transcription regulation, interacting with transcription factors and promoter upstream elements. In Escherichia coli, the catabolite activator protein (CAP or CRP) was shown to exert its effect through its interactions with the CTD, where CAP binding to CTD promotes RNAP binding to promoter DNA, thereby stimulating transcription initiation at class I CAP-dependent promoters. At class II CAP-dependent promoters, the interaction of CAP with CTD is one of multiple interactions involved in activation []. The CTD has a compact structure of four helices and two long arms enclosing its hydrophobic core, making its folding topology distinct from most other binding proteins. The upstream promoter element-binding site is formed from helices 1 and 4 [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3N97_B 1XS9_D 3K4G_A 3N4M_B 1COO_A 1LB2_E 3IYD_A 1Z3E_B 3GFK_B 3IHQ_B ....
Probab=33.91 E-value=25 Score=22.43 Aligned_cols=20 Identities=25% Similarity=0.360 Sum_probs=17.2
Q ss_pred ehhhhcccccchHHHHHHHh
Q 033139 29 ALTSIKGIGRRLANIVCKKA 48 (126)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~~ 48 (126)
-|.+++|+|+....+|.+++
T Consensus 45 ~L~~i~n~G~ksl~EI~~~L 64 (66)
T PF03118_consen 45 DLLKIKNFGKKSLEEIKEKL 64 (66)
T ss_dssp HHHTSTTSHHHHHHHHHHHH
T ss_pred HHHhCCCCCHhHHHHHHHHH
Confidence 47899999999999998765
No 165
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=33.88 E-value=12 Score=22.24 Aligned_cols=29 Identities=24% Similarity=0.477 Sum_probs=15.4
Q ss_pred CCHHHHHHHHHHHhCCCCccCChhhhhccc
Q 033139 59 LSAAELDQLMVVVANPRQFKIPDWFLNRQK 88 (126)
Q Consensus 59 Ls~~qi~~L~~~i~~~~~~~iP~w~~nr~~ 88 (126)
.+.++++.|...+.=+ ...|-.||.|||.
T Consensus 25 p~~~~~~~la~~l~l~-~~~V~~WF~nrR~ 53 (57)
T PF00046_consen 25 PSKEEREELAKELGLT-ERQVKNWFQNRRR 53 (57)
T ss_dssp CHHHHHHHHHHHHTSS-HHHHHHHHHHHHH
T ss_pred cccccccccccccccc-ccccccCHHHhHH
Confidence 4455555555555421 2335567877764
No 166
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=33.69 E-value=31 Score=22.22 Aligned_cols=22 Identities=23% Similarity=0.336 Sum_probs=13.9
Q ss_pred hhhhcccccchHHHHHHHhCCC
Q 033139 30 LTSIKGIGRRLANIVCKKADVD 51 (126)
Q Consensus 30 Lt~IyGIG~~~A~~Ic~~~gI~ 51 (126)
|..--|+.+++..++|+++|++
T Consensus 40 lA~~~~vS~sti~Rf~kkLG~~ 61 (77)
T PF01418_consen 40 LAEKAGVSPSTIVRFCKKLGFS 61 (77)
T ss_dssp HHHHCTS-HHHHHHHHHHCTTT
T ss_pred HHHHcCCCHHHHHHHHHHhCCC
Confidence 4455567777777777777765
No 167
>PRK06920 dnaE DNA polymerase III DnaE; Reviewed
Probab=33.23 E-value=35 Score=33.12 Aligned_cols=46 Identities=17% Similarity=0.290 Sum_probs=31.6
Q ss_pred CeehheehhhhcccccchHHHHHHHhCCCCC---------CcCCCCCHHHHHHHH
Q 033139 23 KQKIMFALTSIKGIGRRLANIVCKKADVDMN---------KRAGELSAAELDQLM 68 (126)
Q Consensus 23 ~K~v~~aLt~IyGIG~~~A~~Ic~~~gI~p~---------~k~~~Ls~~qi~~L~ 68 (126)
+..|.++|..|+|||...+..|.+.-.-.|- ...+.++...++.|.
T Consensus 797 ~~~Ir~gL~~Ikgvg~~~~~~Iv~~R~~g~f~s~~Df~~R~~~~~~nk~~le~Li 851 (1107)
T PRK06920 797 GNAIRYSLLSIRNIGMATVTALYEEREKKMFEDLFEFCLRMPSKFVTERNLEAFV 851 (1107)
T ss_pred CCeeEechhhcCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHhccCCCHHHHHHHH
Confidence 4579999999999999999999865422221 122346666666654
No 168
>PF10662 PduV-EutP: Ethanolamine utilisation - propanediol utilisation; InterPro: IPR012381 Members of this family function in ethanolamine [] and propanediol [] degradation pathways. Both pathways require coenzyme B12 (adenosylcobalamin, AdoCbl). Bacteria that harbour these pathways can use ethanolamine as a source of carbon and nitrogen, or propanediol as a sole carbon and energy source, respectively. The exact roles of the EutP and PduV proteins in these respective pathways are not yet determined. Members of this family contain P-loop consensus motifs in the N-terminal part, and are distantly related to various GTPases and ATPases, including ATPase components of transport systems. Propanediol degradation is thought to be important for the natural Salmonella populations, since propanediol is produced by the fermentation of the common plant sugars rhamnose and fucose [, ]. More than 1% of the Salmonella enterica genome is devoted to the utilisation of propanediol and cobalamin biosynthesis. In vivo expression technology has indicated that propanediol utilisation (pdu) genes may be important for growth in host tissues, and competitive index studies with mice have shown that pdu mutations confer a virulence defect [, ]. The pdu operon is contiguous and co-regulated with the cobalamin (B12) biosynthesis cob operon, indicating that propanediol catabolism may be the primary reason for de novo B12 synthesis in Salmonella [, , ]. Please see IPR003207 from INTERPRO, IPR003208 from INTERPRO, IPR009204 from INTERPRO, IPR009191 from INTERPRO, IPR009192 from INTERPRO for more details on the propanediol utilisation pathway and the pdu operon.; GO: 0005524 ATP binding, 0006576 cellular biogenic amine metabolic process
Probab=32.72 E-value=37 Score=25.12 Aligned_cols=36 Identities=14% Similarity=0.072 Sum_probs=31.5
Q ss_pred cchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 033139 38 RRLANIVCKKADVDMNKRAGELSAAELDQLMVVVAN 73 (126)
Q Consensus 38 ~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L~~~i~~ 73 (126)
...|++.++.+|+..=..++..+.+-+++|.++|++
T Consensus 108 i~~a~~~L~~aG~~~if~vS~~~~eGi~eL~~~L~~ 143 (143)
T PF10662_consen 108 IERAKKWLKNAGVKEIFEVSAVTGEGIEELKDYLEE 143 (143)
T ss_pred HHHHHHHHHHcCCCCeEEEECCCCcCHHHHHHHHhC
Confidence 346778899999999999999999999999999863
No 169
>PF14213 DUF4325: Domain of unknown function (DUF4325)
Probab=32.68 E-value=58 Score=20.76 Aligned_cols=55 Identities=7% Similarity=0.149 Sum_probs=41.3
Q ss_pred ccCCCCeehheehhhhcccccchHHHHHH----HhC---CCCCCcCCCCCHHHHHHHHHHHh
Q 033139 18 TNVDGKQKIMFALTSIKGIGRRLANIVCK----KAD---VDMNKRAGELSAAELDQLMVVVA 72 (126)
Q Consensus 18 ~~l~~~K~v~~aLt~IyGIG~~~A~~Ic~----~~g---I~p~~k~~~Ls~~qi~~L~~~i~ 72 (126)
..+..+++|..-+..+.++|.+++.+..- +.| +....++..++++.-..|..+++
T Consensus 12 ~~l~~~~~V~lDF~gv~~~~ssFl~eafg~l~~~~~~~~~~~~l~~~~~~~~~~~~I~~vi~ 73 (74)
T PF14213_consen 12 PALKEGEKVVLDFEGVESITSSFLNEAFGQLVREFGEEEIKKRLKFKNANESIKEMIKRVIE 73 (74)
T ss_pred HHHhcCCeEEEECCCcccccHHHHHHHHHHHHHHcCHHHHhheeEEecCCHHHHHHHHHHHh
Confidence 34556677999999999999999988754 334 45567777888887777777765
No 170
>cd01401 PncB_like Nicotinate phosphoribosyltransferase (NAPRTase), related to PncB. Nicotinate phosphoribosyltransferase catalyses the formation of NAMN and PPi from 5-phosphoribosy -1-pyrophosphate (PRPP) and nicotinic acid, this is the first, and also rate limiting, reaction in the NAD salvage synthesis. This salvage pathway serves to recycle NAD degradation products. This subgroup is present in bacteria, archea and funghi.
Probab=32.54 E-value=74 Score=27.17 Aligned_cols=35 Identities=14% Similarity=0.102 Sum_probs=29.8
Q ss_pred chHHHHHHHhCCCCCCc----CCCCCHHHHHHHHHHHhC
Q 033139 39 RLANIVCKKADVDMNKR----AGELSAAELDQLMVVVAN 73 (126)
Q Consensus 39 ~~A~~Ic~~~gI~p~~k----~~~Ls~~qi~~L~~~i~~ 73 (126)
..+++..+++||+|..| -++|+++.+..|.+..+.
T Consensus 289 ~k~r~~~~~~Gi~p~~K~iv~Sd~Lde~~i~~L~~~~~g 327 (377)
T cd01401 289 EKAIAHYEKLGIDPKTKTLVFSDGLDVEKALELYEYFKG 327 (377)
T ss_pred HHHHHHHHHcCCCCCCcEEEEcCCCCHHHHHHHHHHHcC
Confidence 35677889999999999 679999999999997763
No 171
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=32.17 E-value=24 Score=33.24 Aligned_cols=19 Identities=26% Similarity=0.468 Sum_probs=16.5
Q ss_pred hhhcccccchHHHHHHHhC
Q 033139 31 TSIKGIGRRLANIVCKKAD 49 (126)
Q Consensus 31 t~IyGIG~~~A~~Ic~~~g 49 (126)
..+.|||+++|.+++++.|
T Consensus 188 pGVpGIG~KtA~kLL~~yg 206 (887)
T TIGR00593 188 PGVKGIGEKTAAKLLQEFG 206 (887)
T ss_pred CCCCCcCHHHHHHHHHHcC
Confidence 3489999999999998866
No 172
>PF13331 DUF4093: Domain of unknown function (DUF4093)
Probab=32.11 E-value=17 Score=24.71 Aligned_cols=40 Identities=18% Similarity=0.202 Sum_probs=30.0
Q ss_pred CCCeehheehhhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHH
Q 033139 21 DGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQ 66 (126)
Q Consensus 21 ~~~K~v~~aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~ 66 (126)
++.+.-+-.|....|||+..|++++++++.= ..|.+|+++
T Consensus 45 ~~s~~rR~~l~~~L~iGy~N~KqllkrLN~f------~it~~e~~~ 84 (87)
T PF13331_consen 45 PDSKERREKLGEYLGIGYGNAKQLLKRLNMF------GITREEFEE 84 (87)
T ss_pred ccHHHHHHHHHHHHCCCCCCHHHHHHHHHHc------CCCHHHHHH
Confidence 4557788888999999999999999887632 345555554
No 173
>PRK05755 DNA polymerase I; Provisional
Probab=31.89 E-value=24 Score=32.91 Aligned_cols=20 Identities=20% Similarity=0.429 Sum_probs=17.1
Q ss_pred hhhhcccccchHHHHHHHhC
Q 033139 30 LTSIKGIGRRLANIVCKKAD 49 (126)
Q Consensus 30 Lt~IyGIG~~~A~~Ic~~~g 49 (126)
...+.|||+++|.+++++.|
T Consensus 189 ipGv~GiG~ktA~~Ll~~~g 208 (880)
T PRK05755 189 IPGVPGIGEKTAAKLLQEYG 208 (880)
T ss_pred CCCCCCccHHHHHHHHHHcC
Confidence 35689999999999998866
No 174
>COG2938 Uncharacterized conserved protein [Function unknown]
Probab=31.81 E-value=28 Score=24.22 Aligned_cols=33 Identities=18% Similarity=0.356 Sum_probs=27.2
Q ss_pred cCCCCCHHHHHHHHHHHhCCCCccCChhhhhccc
Q 033139 55 RAGELSAAELDQLMVVVANPRQFKIPDWFLNRQK 88 (126)
Q Consensus 55 k~~~Ls~~qi~~L~~~i~~~~~~~iP~w~~nr~~ 88 (126)
-...||++|+.....+++.+. -.+=.|++|+..
T Consensus 40 ~~~~lsd~el~~f~~LLe~~D-~dL~~Wi~g~~~ 72 (94)
T COG2938 40 EFDSLSDEELDEFERLLECED-NDLFNWIMGHGE 72 (94)
T ss_pred HHhhCCHHHHHHHHHHHcCCc-HHHHHHHhCCCC
Confidence 357899999999999999764 446689999887
No 175
>KOG2875 consensus 8-oxoguanine DNA glycosylase [Replication, recombination and repair]
Probab=31.72 E-value=19 Score=30.02 Aligned_cols=21 Identities=33% Similarity=0.632 Sum_probs=18.8
Q ss_pred hheehhhhcccccchHHHHHH
Q 033139 26 IMFALTSIKGIGRRLANIVCK 46 (126)
Q Consensus 26 v~~aLt~IyGIG~~~A~~Ic~ 46 (126)
+.-+|..+.|||++.|.-||-
T Consensus 216 ar~~L~~lpGVG~KVADCI~L 236 (323)
T KOG2875|consen 216 AREALCSLPGVGPKVADCICL 236 (323)
T ss_pred HHHHHhcCCCCcchHhhhhhh
Confidence 567899999999999999993
No 176
>TIGR02366 DHAK_reg probable dihydroxyacetone kinase regulator. The seed alignment for this family was built from a set of closely related uncharacterized proteins associated with operons for the type of bacterial dihydroxyacetone kinase that transfers PEP-derived phosphate from a phosphoprotein, as in phosphotransferase system transport, rather than from ATP. Members have a TetR transcriptional regulator domain (pfam00440) at the N-terminus and sequence homology throughout.
Probab=31.60 E-value=23 Score=25.45 Aligned_cols=27 Identities=7% Similarity=0.119 Sum_probs=22.5
Q ss_pred eehhhhcccccchHHHHHHHhCCCCCC
Q 033139 28 FALTSIKGIGRRLANIVCKKADVDMNK 54 (126)
Q Consensus 28 ~aLt~IyGIG~~~A~~Ic~~~gI~p~~ 54 (126)
+.|-.-+|...-+..+||+++|++..+
T Consensus 13 ~~Ll~~k~~~~ITV~~I~~~AgvsR~T 39 (176)
T TIGR02366 13 KDLMEVQAFSKISVSDIMSTAQIRRQT 39 (176)
T ss_pred HHHHHHCCCccCCHHHHHHHhCCCHHH
Confidence 345667999999999999999999543
No 177
>PRK00919 GMP synthase subunit B; Validated
Probab=31.40 E-value=90 Score=25.78 Aligned_cols=48 Identities=10% Similarity=0.148 Sum_probs=36.4
Q ss_pred CCCCcCCCCCHHHHHHHHHHHhCCCCccCChhhhhccccccCCccceeehhhHHH
Q 033139 51 DMNKRAGELSAAELDQLMVVVANPRQFKIPDWFLNRQKDYKDGRYSQVVSNALDM 105 (126)
Q Consensus 51 ~p~~k~~~Ls~~qi~~L~~~i~~~~~~~iP~w~~nr~~d~~tg~~~h~i~~dL~~ 105 (126)
..-.++.+|+++|+.++.+ .+++|.|+.+|.+=+..|.-.-+.| ++..
T Consensus 155 ~Ii~PL~~l~K~EVr~la~------~lGLp~~~~~r~p~~~pcLa~Ri~g-~vt~ 202 (307)
T PRK00919 155 KIVEPLRDLYKDEVREVAR------ALGLPEEISERMPFPGPGLAVRIIG-EVTE 202 (307)
T ss_pred CcccCchhCcHHHHHHHHH------HcCCChhhhCCCCCCCCceeEEeec-ccCH
Confidence 3455677799988888876 3678999999999888888777765 5533
No 178
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=31.40 E-value=31 Score=27.12 Aligned_cols=21 Identities=29% Similarity=0.408 Sum_probs=16.9
Q ss_pred hhhhcccccchHHHHHHHhCC
Q 033139 30 LTSIKGIGRRLANIVCKKADV 50 (126)
Q Consensus 30 Lt~IyGIG~~~A~~Ic~~~gI 50 (126)
|+.|+|||+..|.+|.....+
T Consensus 62 L~~i~GiG~aka~~l~a~~El 82 (218)
T TIGR00608 62 LSSVPGIGEAKAIQLKAAVEL 82 (218)
T ss_pred HHhCcCCcHHHHHHHHHHHHH
Confidence 788999999999888655444
No 179
>PF10500 SR-25: Nuclear RNA-splicing-associated protein; InterPro: IPR019532 SR-25, otherwise known as ADP-ribosylation factor-like factor 6-interacting protein 4, is expressed in virtually all tissue types. At the N terminus there is a repeat of serine-arginine (SR repeat), and towards the middle of the protein there are clusters of both serines and of basic amino acids. The presence of many nuclear localisation signals strongly implies that this is a nuclear protein that may contribute to RNA splicing []. SR-25 is also implicated, along with heat-shock-protein-27, as a mediator in the Rac1 (GTPase ras-related C3 botulinum toxin substrate 1; also see IPR019093 from INTERPRO) signalling pathway [].
Probab=31.32 E-value=87 Score=25.10 Aligned_cols=32 Identities=16% Similarity=0.232 Sum_probs=25.0
Q ss_pred CCCCCHHHHHHHHHHHhCCCCccCChhhhhccccccCCccceeeh
Q 033139 56 AGELSAAELDQLMVVVANPRQFKIPDWFLNRQKDYKDGRYSQVVS 100 (126)
Q Consensus 56 ~~~Ls~~qi~~L~~~i~~~~~~~iP~w~~nr~~d~~tg~~~h~i~ 100 (126)
+.-+|.||.+.-...|.. -| |++||...-+-|
T Consensus 157 m~PmTkEEyearQSvIRr--Vv-----------DpETGRtRLIkG 188 (225)
T PF10500_consen 157 MAPMTKEEYEARQSVIRR--VV-----------DPETGRTRLIKG 188 (225)
T ss_pred cCCCCHHHHHHHHhhhee--ee-----------cCCCCceeeecc
Confidence 566788888888888876 45 999999986533
No 180
>COG1111 MPH1 ERCC4-like helicases [DNA replication, recombination, and repair]
Probab=31.18 E-value=28 Score=31.20 Aligned_cols=87 Identities=13% Similarity=0.145 Sum_probs=56.7
Q ss_pred CCeehheehhhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHh-CCCCccCChhhhhccccccCCccceeeh
Q 033139 22 GKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVA-NPRQFKIPDWFLNRQKDYKDGRYSQVVS 100 (126)
Q Consensus 22 ~~K~v~~aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L~~~i~-~~~~~~iP~w~~nr~~d~~tg~~~h~i~ 100 (126)
..++...|||.-+|=-.....++|+.+||+. .-++.=.+.++..=.+-++ ......+|+||..= -
T Consensus 160 ~k~~~ilgLTASPGs~~ekI~eV~~nLgIe~-vevrTE~d~DV~~Yv~~~kve~ikV~lp~e~~~i-------------r 225 (542)
T COG1111 160 AKNPLILGLTASPGSDLEKIQEVVENLGIEK-VEVRTEEDPDVRPYVKKIKVEWIKVDLPEEIKEI-------------R 225 (542)
T ss_pred ccCceEEEEecCCCCCHHHHHHHHHhCCcce-EEEecCCCccHHHhhccceeEEEeccCcHHHHHH-------------H
Confidence 3445899999999999999999999999983 4444444555544443333 11124568887643 3
Q ss_pred hhHHHHHHHHHHHHHhccccee
Q 033139 101 NALDMKLRDDLERLKKIRYGLV 122 (126)
Q Consensus 101 ~dL~~~~~~dI~rl~~I~sy~~ 122 (126)
..|+..++.-.+.|+..+-|.+
T Consensus 226 ~~l~~~l~~~Lk~L~~~g~~~~ 247 (542)
T COG1111 226 DLLRDALKPRLKPLKELGVIES 247 (542)
T ss_pred HHHHHHHHHHHHHHHHcCceec
Confidence 4456666666666666665543
No 181
>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=31.17 E-value=19 Score=32.74 Aligned_cols=23 Identities=30% Similarity=0.520 Sum_probs=17.7
Q ss_pred hheehhhhcccccchHHHHHHHhC
Q 033139 26 IMFALTSIKGIGRRLANIVCKKAD 49 (126)
Q Consensus 26 v~~aLt~IyGIG~~~A~~Ic~~~g 49 (126)
+.+|| .|.|||+.+|+.+++..|
T Consensus 497 ~L~aL-gIpgVG~~~ak~L~~~f~ 519 (652)
T TIGR00575 497 LLFAL-GIRHVGEVTAKNLAKHFG 519 (652)
T ss_pred HHhhc-cCCCcCHHHHHHHHHHhC
Confidence 34444 788999999999988776
No 182
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=31.03 E-value=25 Score=32.45 Aligned_cols=24 Identities=21% Similarity=0.383 Sum_probs=21.5
Q ss_pred hheehhhhcccccchHHHHHHHhC
Q 033139 26 IMFALTSIKGIGRRLANIVCKKAD 49 (126)
Q Consensus 26 v~~aLt~IyGIG~~~A~~Ic~~~g 49 (126)
+.-.|..|.|||+.++..+++.+|
T Consensus 635 ~~s~L~~IPGIGpkr~k~LL~~FG 658 (694)
T PRK14666 635 LTGELQRVEGIGPATARLLWERFG 658 (694)
T ss_pred hHhHHhhCCCCCHHHHHHHHHHhC
Confidence 456788999999999999999988
No 183
>PF00542 Ribosomal_L12: Ribosomal protein L7/L12 C-terminal domain; InterPro: IPR013823 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 [, ]. This entry represents the C-terminal domain of the large subunit ribosomal proteins, known as the L7/L12 family. L7/L12 is present in each 50S subunit in four copies organised as two dimers. The L8 protein complex consisting of two dimers of L7/L12 and L10 in Escherichia coli ribosomes is assembled on the conserved region of 23 S rRNA termed the GTPase-associated domain []. The L7/L12 dimer probably interacts with EF-Tu. L7 and L12 only differ in a single post translational modification of the addition of an acetyl group to the N terminus of L7.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1DD4_B 1DD3_A 1RQU_B 2GYA_5 2GYC_5 1RQS_A 1RQV_A 1CTF_A 2XUX_L.
Probab=30.86 E-value=22 Score=22.98 Aligned_cols=45 Identities=13% Similarity=0.197 Sum_probs=34.3
Q ss_pred hheehhhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 033139 26 IMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVAN 73 (126)
Q Consensus 26 v~~aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L~~~i~~ 73 (126)
+.-.+..+.|+|-.-|+.+++.+ |..=...++.++-+.+.+.++.
T Consensus 16 vIK~vR~~tgl~L~eAK~~vd~~---p~~ik~~v~keeAe~ik~~Le~ 60 (68)
T PF00542_consen 16 VIKEVREITGLGLKEAKKLVDSL---PKVIKEGVSKEEAEEIKKKLEA 60 (68)
T ss_dssp HHHHHHHHC---HHHHHHHHCTT---TEEEEEEE-HHHHHHHHHHHHC
T ss_pred HHHHHHHHhCCcHHHHHHHHHhC---CHHHHcCCCHHHHHHHHHHHHH
Confidence 44567889999999999999998 5555567899999999999986
No 184
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=30.69 E-value=27 Score=29.16 Aligned_cols=28 Identities=46% Similarity=0.732 Sum_probs=15.1
Q ss_pred CCCHHHHHHHHHHHh-CCCCccCChhhhhcc
Q 033139 58 ELSAAELDQLMVVVA-NPRQFKIPDWFLNRQ 87 (126)
Q Consensus 58 ~Ls~~qi~~L~~~i~-~~~~~~iP~w~~nr~ 87 (126)
-||.-|-+.|.+.|. .|.+.+| ||-|||
T Consensus 177 YLSAPERE~LA~~LrLT~TQVKI--WFQNrR 205 (307)
T KOG0842|consen 177 YLSAPEREHLASSLRLTPTQVKI--WFQNRR 205 (307)
T ss_pred ccccHhHHHHHHhcCCCchheee--eeecch
Confidence 344455555555544 3333333 999987
No 185
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=30.43 E-value=1e+02 Score=22.65 Aligned_cols=45 Identities=16% Similarity=0.175 Sum_probs=36.3
Q ss_pred ehhhhcccccchHHHHHHHhC---CC--C---CCcCCCCCHHHHHHHHHHHhC
Q 033139 29 ALTSIKGIGRRLANIVCKKAD---VD--M---NKRAGELSAAELDQLMVVVAN 73 (126)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~~g---I~--p---~~k~~~Ls~~qi~~L~~~i~~ 73 (126)
..+..+|+|.+|+..-.++.. .+ + .=++..|+++|++.|.+.++.
T Consensus 26 e~Ak~~gvs~sTvy~wv~r~~e~G~~l~~~~~~GrP~kl~~~q~~~l~e~~~~ 78 (138)
T COG3415 26 EAAKRFGVSISTVYRWVRRYRETGLDLPPKPRKGRPRKLSEEQLEILLERLRE 78 (138)
T ss_pred HHHHHhCccHHHHHHHHHHhccccccccCccCCCCCcccCHHHHHHHHHHHhc
Confidence 346789999999999987765 33 2 246889999999999999986
No 186
>PF05155 Phage_X: Phage X family ; InterPro: IPR022688 The sequences matched by this entry represent a family of phage and plasmid replication proteins. In bacteriophage IKe and related phage, the full-length protein is designated gene II protein. A much shorter protein of unknown function, translated from a conserved in-frame alternative initiator, is designated gene X protein. Members of this family also include plasmid replication proteins. ; GO: 0006260 DNA replication
Probab=30.03 E-value=10 Score=25.90 Aligned_cols=42 Identities=21% Similarity=0.447 Sum_probs=26.3
Q ss_pred HHHHHHHhCCCCCCc--CCCCCHHHHHHHHHHHhCCCCccCChhhh
Q 033139 41 ANIVCKKADVDMNKR--AGELSAAELDQLMVVVANPRQFKIPDWFL 84 (126)
Q Consensus 41 A~~Ic~~~gI~p~~k--~~~Ls~~qi~~L~~~i~~~~~~~iP~w~~ 84 (126)
.++-+.++|||.... +...+.. +-.+.+.|+-. ...+|+|+.
T Consensus 42 hr~~L~~~GIdia~~~nl~~~~~~-vvp~~r~ie~~-~~~~PdwY~ 85 (92)
T PF05155_consen 42 HRARLLKIGIDIAQLQNLSKFSPN-VVPLVRVIEVK-PLQIPDWYV 85 (92)
T ss_pred HHHHHHHcCCCHHHhcccccCCCC-cCceeEEEecC-CCCCCcccc
Confidence 455577899996554 3333433 56677777731 236899985
No 187
>TIGR02236 recomb_radA DNA repair and recombination protein RadA. This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.
Probab=29.87 E-value=29 Score=27.73 Aligned_cols=35 Identities=26% Similarity=0.305 Sum_probs=21.7
Q ss_pred hhhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHH
Q 033139 30 LTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELD 65 (126)
Q Consensus 30 Lt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~ 65 (126)
|..+.|||+.++..+. +.||..-..+...+.+++.
T Consensus 1 l~~i~gig~~~~~~L~-~~Gi~ti~dl~~~~~~~L~ 35 (310)
T TIGR02236 1 LEDLPGVGPATAEKLR-EAGYDTFEAIAVASPKELS 35 (310)
T ss_pred CcccCCCCHHHHHHHH-HcCCCCHHHHHcCCHHHHH
Confidence 3568899988887764 5666654444444554443
No 188
>TIGR02836 spore_IV_A stage IV sporulation protein A. A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This protein, a member of this panel, is designated stage IV sporulation protein A. It acts in the mother cell compartment and plays a role in spore coat morphogenesis.
Probab=29.76 E-value=92 Score=27.70 Aligned_cols=90 Identities=11% Similarity=0.259 Sum_probs=57.4
Q ss_pred CCeehheehhhhcccccch---HHHHHHHhCCC-CCCcCCCCCHHHHHHHHHHHh-C-C---CCccCChhhhhccccccC
Q 033139 22 GKQKIMFALTSIKGIGRRL---ANIVCKKADVD-MNKRAGELSAAELDQLMVVVA-N-P---RQFKIPDWFLNRQKDYKD 92 (126)
Q Consensus 22 ~~K~v~~aLt~IyGIG~~~---A~~Ic~~~gI~-p~~k~~~Ls~~qi~~L~~~i~-~-~---~~~~iP~w~~nr~~d~~t 92 (126)
-+||....|.+..-..+.+ +.++-++.++. -....-+|++++|..|-+.+= . | -++.+|.|.--=..|
T Consensus 179 ~~kPfiivlN~~dp~~~et~~l~~~l~eky~vpvl~v~c~~l~~~DI~~il~~vL~EFPv~Ei~~~~P~Wve~L~~~--- 255 (492)
T TIGR02836 179 LNKPFIILLNSTHPYHPETEALRQELEEKYDVPVLAMDVESMRESDILSVLEEVLYEFPILEINIDLPSWVEVLDEN--- 255 (492)
T ss_pred cCCCEEEEEECcCCCCchhHHHHHHHHHHhCCceEEEEHHHcCHHHHHHHHHHHHhcCCceEEEeeCchHHHhcCCC---
Confidence 3566666666655332222 34555677765 456778999999997766542 1 1 124479997554444
Q ss_pred CccceeehhhHHHHHHHHHHHHHhcc
Q 033139 93 GRYSQVVSNALDMKLRDDLERLKKIR 118 (126)
Q Consensus 93 g~~~h~i~~dL~~~~~~dI~rl~~I~ 118 (126)
|.+-.++...+++-++.+.+++
T Consensus 256 ----Hwlk~~~~~~i~~~~~~i~~ir 277 (492)
T TIGR02836 256 ----HWLKENFQSSVKETVKDVYRLR 277 (492)
T ss_pred ----chHHHHHHHHHHHHHHhhhHHh
Confidence 8999998888887666665554
No 189
>PF13551 HTH_29: Winged helix-turn helix
Probab=29.47 E-value=1.2e+02 Score=19.76 Aligned_cols=45 Identities=22% Similarity=0.226 Sum_probs=33.4
Q ss_pred ehhhhcccccchHHHHHHHh---C---CCC----CCcCCC-CCHHHHHHHHHHHhC
Q 033139 29 ALTSIKGIGRRLANIVCKKA---D---VDM----NKRAGE-LSAAELDQLMVVVAN 73 (126)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~~---g---I~p----~~k~~~-Ls~~qi~~L~~~i~~ 73 (126)
......|+.+.+.....+.+ | +.+ .-+... |++++...|.+.+.+
T Consensus 17 ~ia~~lg~s~~Tv~r~~~~~~~~G~~~l~~~~~~~g~~~~~l~~~~~~~l~~~~~~ 72 (112)
T PF13551_consen 17 EIARRLGISRRTVYRWLKRYREGGIEGLLPRKPRGGRPRKRLSEEQRAQLIELLRE 72 (112)
T ss_pred HHHHHHCcCHHHHHHHHHHHHcccHHHHHhccccCCCCCCCCCHHHHHHHHHHHHH
Confidence 45677899999999888773 3 333 224444 999999999999986
No 190
>PRK02406 DNA polymerase IV; Validated
Probab=29.46 E-value=34 Score=27.82 Aligned_cols=37 Identities=19% Similarity=0.245 Sum_probs=26.3
Q ss_pred eehhhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHH
Q 033139 28 FALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELD 65 (126)
Q Consensus 28 ~aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~ 65 (126)
.-++.+.|||+.++.++ +.+||..=--+-.++.+++.
T Consensus 168 lpi~~l~giG~~~~~~L-~~~Gi~ti~dl~~l~~~~L~ 204 (343)
T PRK02406 168 LPVEKIPGVGKVTAEKL-HALGIYTCADLQKYDLAELI 204 (343)
T ss_pred CCcchhcCCCHHHHHHH-HHcCCCcHHHHHhCCHHHHH
Confidence 35688999999999985 68999764444444555553
No 191
>PRK00024 hypothetical protein; Reviewed
Probab=28.78 E-value=35 Score=26.75 Aligned_cols=22 Identities=36% Similarity=0.436 Sum_probs=17.5
Q ss_pred ehhhhcccccchHHHHHHHhCC
Q 033139 29 ALTSIKGIGRRLANIVCKKADV 50 (126)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~~gI 50 (126)
.|..+.|||+..|..|+....+
T Consensus 67 eL~~i~GIG~akA~~L~a~~El 88 (224)
T PRK00024 67 ELQSIKGIGPAKAAQLKAALEL 88 (224)
T ss_pred HHhhccCccHHHHHHHHHHHHH
Confidence 3888999999999888755544
No 192
>PRK00461 rpmC 50S ribosomal protein L29; Reviewed
Probab=28.77 E-value=44 Score=22.79 Aligned_cols=53 Identities=17% Similarity=0.255 Sum_probs=34.8
Q ss_pred CCCCCHHHHHHHHHHHhCCCCccCChhhhhccccccCCccceeehhhHHHHHHHHHHHHHhccc
Q 033139 56 AGELSAAELDQLMVVVANPRQFKIPDWFLNRQKDYKDGRYSQVVSNALDMKLRDDLERLKKIRY 119 (126)
Q Consensus 56 ~~~Ls~~qi~~L~~~i~~~~~~~iP~w~~nr~~d~~tg~~~h~i~~dL~~~~~~dI~rl~~I~s 119 (126)
+.++|.+|+......+.. .+ ++-|.--.||. +-..-..+.++-||.|+..+-.
T Consensus 5 lR~lS~eEL~e~L~elkk--EL------f~LR~q~atgq---l~n~~~ir~iRR~IARilTvl~ 57 (87)
T PRK00461 5 LRKKSVEELEKLVIELKA--EL------FTLRFKNATGS---LDQTHKIKEIRKDIARILTILN 57 (87)
T ss_pred HHhCCHHHHHHHHHHHHH--HH------HHHHHHHHhCc---ccccHHHHHHHHHHHHHHHHHH
Confidence 567888888866666654 23 44444444553 3334456899999999988754
No 193
>PF11460 DUF3007: Protein of unknown function (DUF3007); InterPro: IPR021562 This is a family of uncharacterised proteins found in bacteria and eukaryotes.
Probab=28.61 E-value=30 Score=24.54 Aligned_cols=20 Identities=40% Similarity=0.519 Sum_probs=17.3
Q ss_pred CCcCCCCCHHHHHHHHHHHh
Q 033139 53 NKRAGELSAAELDQLMVVVA 72 (126)
Q Consensus 53 ~~k~~~Ls~~qi~~L~~~i~ 72 (126)
.+|+.+||++|+++|.+.++
T Consensus 84 qkRle~l~~eE~~~L~~eie 103 (104)
T PF11460_consen 84 QKRLEELSPEELEALQAEIE 103 (104)
T ss_pred HHHHHhCCHHHHHHHHHHhc
Confidence 46788999999999998876
No 194
>PRK03352 DNA polymerase IV; Validated
Probab=28.51 E-value=42 Score=27.34 Aligned_cols=36 Identities=17% Similarity=0.204 Sum_probs=26.0
Q ss_pred ehhhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHH
Q 033139 29 ALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELD 65 (126)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~ 65 (126)
-+..+.|||+.++.. ++++||..=.-+-.++.+++.
T Consensus 178 pl~~l~gig~~~~~~-L~~~Gi~ti~dl~~l~~~~L~ 213 (346)
T PRK03352 178 PTDALWGVGPKTAKR-LAALGITTVADLAAADPAELA 213 (346)
T ss_pred CHHHcCCCCHHHHHH-HHHcCCccHHHHhcCCHHHHH
Confidence 467889999999998 578999864444445665553
No 195
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=28.28 E-value=1.1e+02 Score=23.09 Aligned_cols=49 Identities=12% Similarity=0.187 Sum_probs=29.2
Q ss_pred HHHHHHHHHHhCCCCccCChhhhhccccccCCccce---eehhhHHHHHHHHHHHHH
Q 033139 62 AELDQLMVVVANPRQFKIPDWFLNRQKDYKDGRYSQ---VVSNALDMKLRDDLERLK 115 (126)
Q Consensus 62 ~qi~~L~~~i~~~~~~~iP~w~~nr~~d~~tg~~~h---~i~~dL~~~~~~dI~rl~ 115 (126)
.++.++-..+.. .++=. ..|++|..+|...+ +-...+...+..++.++.
T Consensus 51 ~~VRk~L~~L~e---~gLv~--~~r~r~~~~Gr~~y~w~l~~~~i~d~ik~~~~~~~ 102 (178)
T PRK06266 51 NTVRKILYKLYD---ARLAD--YKREKDEETNWYTYTWKPELEKLPEIIKKKKMEEL 102 (178)
T ss_pred HHHHHHHHHHHH---CCCeE--EeeeeccCCCcEEEEEEeCHHHHHHHHHHHHHHHH
Confidence 455555555554 22211 36778988999888 444566666666665553
No 196
>PF00912 Transgly: Transglycosylase; InterPro: IPR001264 The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (2.4.1.- from EC) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'. Glycosyltransferase family 51 GT51 from CAZY comprises enzymes with only one known activity; murein polymerases (2.4 from EC). These enzymes utilise MurNAc-GlcNAc-P-P-lipid II as the sugar donor. The family includes the bifunctional penicillin-binding proteins that have a transglycosylase (N terminus) and transpeptidase (C terminus) domain [] and the monofunctional biosynthetic peptidoglycan transglycosylases [].; GO: 0003824 catalytic activity, 0009252 peptidoglycan biosynthetic process, 0009274 peptidoglycan-based cell wall; PDB: 3VMT_A 3VMS_B 3VMQ_A 3VMR_A 3D3H_A 3NB7_A 3NB6_A 2OQO_A 2V2F_A 3HZS_A ....
Probab=28.27 E-value=36 Score=25.93 Aligned_cols=38 Identities=26% Similarity=0.367 Sum_probs=25.8
Q ss_pred hhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCCc
Q 033139 32 SIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVANPRQF 77 (126)
Q Consensus 32 ~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L~~~i~~~~~~ 77 (126)
.+|||...--.-+ ++.+++||..|...|...+.+|..|
T Consensus 120 ~~~Gv~aAs~~yF--------~k~~~~Ls~~eaa~La~l~~~P~~y 157 (178)
T PF00912_consen 120 GIYGVEAASRYYF--------GKSPSDLSLAEAALLAGLLPNPSRY 157 (178)
T ss_dssp TBBSHHHHHHHHH--------SSSCGG--HHHHHHHHHCTTSTTTS
T ss_pred ccchHHHHHHHHh--------CCCHHHCCHHHHHHHhhhccCcccc
Confidence 6667654332222 5568899999999999999998655
No 197
>smart00581 PSP proline-rich domain in spliceosome associated proteins.
Probab=28.22 E-value=62 Score=20.33 Aligned_cols=32 Identities=19% Similarity=0.370 Sum_probs=22.0
Q ss_pred CCcCCCCCHHHHHHHHHHHhCCCCccCChhhhhcccc
Q 033139 53 NKRAGELSAAELDQLMVVVANPRQFKIPDWFLNRQKD 89 (126)
Q Consensus 53 ~~k~~~Ls~~qi~~L~~~i~~~~~~~iP~w~~nr~~d 89 (126)
+.+.+.||++ |++++.=+ ....|.|+.+-|+-
T Consensus 3 ~~kPG~lS~~----LR~ALG~~-~~~pPPWl~~Mq~~ 34 (54)
T smart00581 3 HFKPGRISDE----LREALGLP-PGQPPPWLYRMRRL 34 (54)
T ss_pred CccCCcCCHH----HHHHcCCC-CCCCChHHHHHHHH
Confidence 4677888864 77777632 34589999876653
No 198
>PRK07135 dnaE DNA polymerase III DnaE; Validated
Probab=27.86 E-value=41 Score=32.21 Aligned_cols=47 Identities=19% Similarity=0.292 Sum_probs=33.0
Q ss_pred CeehheehhhhcccccchHHHHHHHhCC-CC---------CCcCCCCCHHHHHHHHH
Q 033139 23 KQKIMFALTSIKGIGRRLANIVCKKADV-DM---------NKRAGELSAAELDQLMV 69 (126)
Q Consensus 23 ~K~v~~aLt~IyGIG~~~A~~Ic~~~gI-~p---------~~k~~~Ls~~qi~~L~~ 69 (126)
++.|.++|+.|+|||...|..|.+.-.- .| ....+.++...++.|.+
T Consensus 748 ~~~Ir~gL~~Ikgvg~~~~~~Iv~~R~~~g~f~s~~Df~~R~~~~~~~k~~le~Li~ 804 (973)
T PRK07135 748 NGKIFLPLIMIKGLGSVAIKKIIDERNKNGKYKNFFDFILRLKFIGISKSIIEKLIK 804 (973)
T ss_pred CCEEEECccccCCcCHHHHHHHHHHHHhCCCCCCHHHHHHhccccCCCHHHHHHHHH
Confidence 4579999999999999999999865421 11 11224577777777664
No 199
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=27.80 E-value=26 Score=24.83 Aligned_cols=36 Identities=25% Similarity=0.255 Sum_probs=28.7
Q ss_pred cccccchHHHHHHHhCCCCCCcCCCCCHHHHHH--HHHH
Q 033139 34 KGIGRRLANIVCKKADVDMNKRAGELSAAELDQ--LMVV 70 (126)
Q Consensus 34 yGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~--L~~~ 70 (126)
.|||+..+.++ +++||+....+-+.++.+..+ |.+.
T Consensus 1 pgi~~~~~~~L-~~~GI~t~~~Ll~~~~~~~~r~~La~~ 38 (122)
T PF14229_consen 1 PGIGPKEAAKL-KAAGIKTTGDLLEAGDTPLGRKALAKK 38 (122)
T ss_pred CCCCHHHHHHH-HHcCCCcHHHHHHcCCCHHHHHHHHHh
Confidence 58999999988 999999877777777777776 5543
No 200
>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=27.63 E-value=22 Score=29.05 Aligned_cols=31 Identities=19% Similarity=0.380 Sum_probs=23.0
Q ss_pred ehhhhcccccchHHHHHHHhCCCCCCcCCCC
Q 033139 29 ALTSIKGIGRRLANIVCKKADVDMNKRAGEL 59 (126)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~L 59 (126)
.++.++|||+++|.+|.+-+.=..-.+..+|
T Consensus 46 ~~~~ipgiG~~ia~kI~E~~~tG~~~~le~l 76 (307)
T cd00141 46 EAKKLPGIGKKIAEKIEEILETGKLRKLEEL 76 (307)
T ss_pred HhcCCCCccHHHHHHHHHHHHcCCHHHHHHH
Confidence 5689999999999999988765443333333
No 201
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=27.47 E-value=23 Score=32.30 Aligned_cols=35 Identities=20% Similarity=0.294 Sum_probs=25.3
Q ss_pred hhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHH
Q 033139 31 TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELD 65 (126)
Q Consensus 31 t~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~ 65 (126)
-.|.|+|++++.++.+..+|..-.-+-.|+.+++.
T Consensus 448 l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~ 482 (665)
T PRK07956 448 MDIDGLGEKIIEQLFEKGLIHDPADLFKLTAEDLL 482 (665)
T ss_pred cCCCCcCHHHHHHHHHcCCCCCHHHHHhcCHHHHh
Confidence 36899999999999999988753334445555443
No 202
>KOG3817 consensus Uncharacterized conserved protein [Function unknown]
Probab=27.41 E-value=50 Score=28.67 Aligned_cols=50 Identities=14% Similarity=0.265 Sum_probs=37.0
Q ss_pred CCCCcCCCCCHH------------HHHHHHHHHhCCCCccCChhhh-------hccccccCCccceeehhhHH
Q 033139 51 DMNKRAGELSAA------------ELDQLMVVVANPRQFKIPDWFL-------NRQKDYKDGRYSQVVSNALD 104 (126)
Q Consensus 51 ~p~~k~~~Ls~~------------qi~~L~~~i~~~~~~~iP~w~~-------nr~~d~~tg~~~h~i~~dL~ 104 (126)
.+-.+.+-||+| ++++|+++.++| .-|+|.. .|=.|+..|.+ |+...+..
T Consensus 309 fkpl~rRlLtEeEYeeQaeveT~kaLaeLReycnkp---d~~~Wkvvgrlrsp~rfA~F~eG~~-Hlt~~Ei~ 377 (452)
T KOG3817|consen 309 FKPLKRRLLTEEEYEEQAEVETSKALAELREYCNKP---DCKQWKVVGRLRSPLRFASFAEGAP-HLTDEEIE 377 (452)
T ss_pred ccccchhhcCHHHHHHHHHHHHHHHHHHHHHHhCCC---CCchhhhhhhccCHHHHHHHhcCCC-CCCHHHHH
Confidence 444677778765 477899999985 4689963 44567889999 99888763
No 203
>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=27.34 E-value=27 Score=31.73 Aligned_cols=33 Identities=21% Similarity=0.296 Sum_probs=23.5
Q ss_pred hhcccccchHHHHHHHhCCCCCCcCCCCCHHHH
Q 033139 32 SIKGIGRRLANIVCKKADVDMNKRAGELSAAEL 64 (126)
Q Consensus 32 ~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi 64 (126)
.|.|+|+.++.++.+..+|..-.-+-.|+.+++
T Consensus 436 ~I~GLG~k~i~~L~~~g~I~~~~Dl~~L~~~~L 468 (652)
T TIGR00575 436 DIEGLGDKVIEQLFEKKLVRSVADLYALKKEDL 468 (652)
T ss_pred CCCCcCHHHHHHHHHcCCcCCHHHHHhcCHHHH
Confidence 689999999999999888864333334444444
No 204
>PRK01172 ski2-like helicase; Provisional
Probab=27.14 E-value=37 Score=30.35 Aligned_cols=39 Identities=18% Similarity=0.184 Sum_probs=31.7
Q ss_pred eehhhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHH
Q 033139 28 FALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQL 67 (126)
Q Consensus 28 ~aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L 67 (126)
..|..+.|+|+..|++ |.++|+..-.-+-+++++++.+|
T Consensus 612 ~~L~~ip~~~~~~a~~-l~~~g~~~~~di~~~~~~~~~~i 650 (674)
T PRK01172 612 IDLVLIPKVGRVRARR-LYDAGFKTVDDIARSSPERIKKI 650 (674)
T ss_pred HhhcCCCCCCHHHHHH-HHHcCCCCHHHHHhCCHHHHHHH
Confidence 4577899999998876 78899998777777788887766
No 205
>cd03067 PDI_b_PDIR_N PDIb family, PDIR subfamily, N-terminal TRX-like b domain; composed of proteins similar to human PDIR (for Protein Disulfide Isomerase Related). PDIR is composed of three redox active TRX (a) domains and an N-terminal redox inactive TRX-like (b) domain. Similar to PDI, it is involved in oxidative protein folding in the endoplasmic reticulum (ER) through its isomerase and chaperone activities. These activities are lower compared to PDI, probably due to PDIR acting only on a subset of proteins. PDIR is preferentially expressed in cells actively secreting proteins and its expression is induced by stress. Similar to PDI, the isomerase and chaperone activities of PDIR are independent; CXXC mutants lacking isomerase activity retain chaperone activity. The TRX-like b domain of PDIR is critical for its chaperone activity.
Probab=27.08 E-value=56 Score=23.41 Aligned_cols=30 Identities=27% Similarity=0.454 Sum_probs=23.4
Q ss_pred ehhhhccccc--------chHHHHHHHhCCCCCCcCCC
Q 033139 29 ALTSIKGIGR--------RLANIVCKKADVDMNKRAGE 58 (126)
Q Consensus 29 aLt~IyGIG~--------~~A~~Ic~~~gI~p~~k~~~ 58 (126)
+-+.++|.|- .=++++|+++.++|+.++..
T Consensus 43 ~A~~vkG~gT~~~vdCgd~e~kKLCKKlKv~~~~kp~~ 80 (112)
T cd03067 43 VAQAVKGQGTIAWIDCGDSESRKLCKKLKVDPSSKPKP 80 (112)
T ss_pred HHHHhcCceeEEEEecCChHHHHHHHHHccCCCCCCCc
Confidence 3456777764 45999999999998888776
No 206
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=27.07 E-value=34 Score=19.75 Aligned_cols=21 Identities=19% Similarity=0.177 Sum_probs=17.9
Q ss_pred hcccccchHHHHHHHhCCCCC
Q 033139 33 IKGIGRRLANIVCKKADVDMN 53 (126)
Q Consensus 33 IyGIG~~~A~~Ic~~~gI~p~ 53 (126)
-.|+...+...||+.+|+++.
T Consensus 11 ~~G~~~~s~~~Ia~~~gvs~~ 31 (47)
T PF00440_consen 11 EKGYEAVSIRDIARRAGVSKG 31 (47)
T ss_dssp HHHTTTSSHHHHHHHHTSCHH
T ss_pred HhCHHhCCHHHHHHHHccchh
Confidence 468888999999999999853
No 207
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=26.61 E-value=30 Score=29.34 Aligned_cols=14 Identities=36% Similarity=0.543 Sum_probs=0.0
Q ss_pred hhhhcccccchHHH
Q 033139 30 LTSIKGIGRRLANI 43 (126)
Q Consensus 30 Lt~IyGIG~~~A~~ 43 (126)
+++|+|||.++|.+
T Consensus 99 FtnifGvG~ktA~~ 112 (353)
T KOG2534|consen 99 FTNIFGVGLKTAEK 112 (353)
T ss_pred HHHHhccCHHHHHH
No 208
>PF00986 DNA_gyraseB_C: DNA gyrase B subunit, carboxyl terminus The Prosite motif does not match this Pfam entry.; InterPro: IPR002288 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils []. Type IIA topoisomerases together manage chromosome integrity and topology in cells. Topoisomerase II (called gyrase in bacteria) primarily introduces negative supercoils into DNA. In bacteria, topoisomerase II consists of two polypeptide subunits, gyrA and gyrB, which form a heterotetramer: (BA)2. In most eukaryotes, topoisomerase II consists of a single polypeptide, where the N- and C-terminal regions correspond to gyrB and gyrA, respectively; this topoisomerase II forms a homodimer that is equivalent to the bacterial heterotetramer. There are four functional domains in topoisomerase II: domain 1 (N-terminal of gyrB) is an ATPase, domain 2 (C-terminal of gyrB) is responsible for subunit interactions, domain 3 (N-terminal of gyrA) is responsible for the breaking-rejoining function through its capacity to form protein-DNA bridges, and domain 4 (C-terminal of gyrA) is able to non-specifically bind DNA []. Topoisomerase IV primarily decatenates DNA and relaxes positive supercoils, which is important in bacteria, where the circular chromosome becomes catenated, or linked, during replication []. Topoisomerase IV consists of two polypeptide subunits, parE and parC, where parC is homologous to gyrA and parE is homologous to gyrB. This entry represents the C-terminal region (C-terminal part of domain 2) of subunit B found in topoisomerase II (gyrB) and topoisomerase IV (parE), which are primarily of bacterial origin. It does not include the topoisomerase II enzymes composed of a single polypeptide, as are found in most eukaryotes. This region is involved in subunit interaction, which accounts for the difference between subunit B and single polypeptide topoisomerase II. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0005524 ATP binding, 0006265 DNA topological change, 0005694 chromosome; PDB: 3LTN_D 3RAF_C 3FOF_C 3RAE_C 3KSA_D 3RAD_C 3FOE_D 3KSB_D 3K9F_D 2XCT_D ....
Probab=26.61 E-value=26 Score=22.77 Aligned_cols=47 Identities=9% Similarity=0.120 Sum_probs=29.6
Q ss_pred hheehhhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHh
Q 033139 26 IMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVA 72 (126)
Q Consensus 26 v~~aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L~~~i~ 72 (126)
-.+-++.++|+|.-.+.++.+-.==..+.++-.++-++.....+.++
T Consensus 4 ~~~~I~RfKGLGEM~p~qL~eTTmdP~~R~L~~V~i~d~~~~~~~~~ 50 (65)
T PF00986_consen 4 KKVEIQRFKGLGEMNPDQLWETTMDPETRRLIRVTIEDAEEADELFE 50 (65)
T ss_dssp TTTEEEESSSGGGS-HHHHHHHHTSTTTTEEEEEEHCCHHHHHHHHH
T ss_pred CCceeEEecccccCCHHHHHHHccCccceEEEEEEECCHHHHHHHHH
Confidence 34567899999999999987655333344455555555555555554
No 209
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=26.59 E-value=41 Score=30.70 Aligned_cols=23 Identities=22% Similarity=0.557 Sum_probs=17.0
Q ss_pred hheehhhhcccccchHHHHHHHhC
Q 033139 26 IMFALTSIKGIGRRLANIVCKKAD 49 (126)
Q Consensus 26 v~~aLt~IyGIG~~~A~~Ic~~~g 49 (126)
+.+|| .|.|||+.+|+.+++..+
T Consensus 510 ~l~al-gi~~IG~~~ak~L~~~f~ 532 (665)
T PRK07956 510 FLYAL-GIRHVGEKAAKALARHFG 532 (665)
T ss_pred hhHhh-hccCcCHHHHHHHHHHcC
Confidence 44455 688889988888887664
No 210
>PRK05672 dnaE2 error-prone DNA polymerase; Validated
Probab=26.49 E-value=39 Score=32.56 Aligned_cols=46 Identities=22% Similarity=0.353 Sum_probs=31.6
Q ss_pred CeehheehhhhcccccchHHHHHHHhCCCCC-------CcCCCCCHHHHHHHHH
Q 033139 23 KQKIMFALTSIKGIGRRLANIVCKKADVDMN-------KRAGELSAAELDQLMV 69 (126)
Q Consensus 23 ~K~v~~aLt~IyGIG~~~A~~Ic~~~gI~p~-------~k~~~Ls~~qi~~L~~ 69 (126)
++.|.++|..|+|||...|..|.+.=.-.|- .|++ ++...++.|.+
T Consensus 811 ~~~I~~gl~~Ikgvg~~~~~~Iv~~R~~g~f~s~~Df~~R~~-~~~~~le~Li~ 863 (1046)
T PRK05672 811 GPAVRLGLRLVRGLGEEAAERIVAARARGPFTSVEDLARRAG-LDRRQLEALAD 863 (1046)
T ss_pred CCcEEechhhcCCCCHHHHHHHHHHhhcCCCCCHHHHHHHhC-CCHHHHHHHHH
Confidence 4679999999999999999999875421111 1222 56666666654
No 211
>TIGR02663 nifX nitrogen fixation protein NifX. Members of this family are NifX proteins encoded within operons for nitrogen fixation in a number of bacteria. NifX, NafY, and the C-terminal region of NifB all belong to the Pfam family pfam02579 and are involved in MoFe cofactor biosynthesis. NifX is a nitrogenase accessory protein with a role in expression of the MoFe cofactor.
Probab=26.35 E-value=1e+02 Score=21.37 Aligned_cols=48 Identities=19% Similarity=0.224 Sum_probs=31.8
Q ss_pred cccccchHHHHHHHhCCCCCCc-CCCCCHHHHHHHHHHHhCCCCccCChhhhhc
Q 033139 34 KGIGRRLANIVCKKADVDMNKR-AGELSAAELDQLMVVVANPRQFKIPDWFLNR 86 (126)
Q Consensus 34 yGIG~~~A~~Ic~~~gI~p~~k-~~~Ls~~qi~~L~~~i~~~~~~~iP~w~~nr 86 (126)
.|||+.- ...++..||.+-.. ...-=++-+++|...+.. .-|+|+-+.
T Consensus 70 ~~IG~~a-~~~L~~~gI~~~~~~~~~~v~eal~~l~~~~~~----~~~~w~~~~ 118 (119)
T TIGR02663 70 LAIGGPA-AAKVVAAKIHPIKVNEPESISELLERLQKMLKG----NPPPWLRKA 118 (119)
T ss_pred hhcCccH-HHHHHHcCCeeEecCCCccHHHHHHHHHHHHcC----CCCHHHHhh
Confidence 4688764 44567799998542 222346677888888854 459998653
No 212
>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]
Probab=26.12 E-value=30 Score=33.85 Aligned_cols=43 Identities=21% Similarity=0.298 Sum_probs=34.0
Q ss_pred cccchhhccccCC---CCeehheehhhhcccccchHHHHHHHhCCC
Q 033139 9 FQHILRVLNTNVD---GKQKIMFALTSIKGIGRRLANIVCKKADVD 51 (126)
Q Consensus 9 ~~~mvrI~g~~l~---~~K~v~~aLt~IyGIG~~~A~~Ic~~~gI~ 51 (126)
|=.++-+-|+||+ .|..-.-+|++|-|.|+++|..+++.+-=+
T Consensus 784 ~Vd~vn~VGVDIN~a~~n~~~~~lLqyI~GlGpRKa~~lLKsl~~~ 829 (1299)
T KOG1856|consen 784 FVDIVNEVGVDINKAANNPYYANLLQYICGLGPRKATSLLKSLKRN 829 (1299)
T ss_pred HHHhHhhhhhhHHHHhcChhhhhhHHHhcCCCcccHHHHHHHHHHc
Confidence 4456677888875 466677889999999999999999877533
No 213
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=26.11 E-value=40 Score=27.89 Aligned_cols=22 Identities=18% Similarity=0.428 Sum_probs=19.1
Q ss_pred ehhhhcccccchHHHHHHHhCC
Q 033139 29 ALTSIKGIGRRLANIVCKKADV 50 (126)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~~gI 50 (126)
-|+.+.|||.++|.+|-+-+.=
T Consensus 49 ~l~~lpgIG~~ia~kI~Eil~t 70 (334)
T smart00483 49 DLKGLPGIGDKIKKKIEEIIET 70 (334)
T ss_pred HHhcCCCccHHHHHHHHHHHHh
Confidence 5789999999999999987653
No 214
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=26.09 E-value=53 Score=17.43 Aligned_cols=18 Identities=11% Similarity=0.036 Sum_probs=9.6
Q ss_pred ccccchHHHHHHHhCCCC
Q 033139 35 GIGRRLANIVCKKADVDM 52 (126)
Q Consensus 35 GIG~~~A~~Ic~~~gI~p 52 (126)
.+...++..+|+.+|+++
T Consensus 36 ~~~~~~~~~i~~~~~~~~ 53 (56)
T smart00530 36 KPSLETLKKLAKALGVSL 53 (56)
T ss_pred CCCHHHHHHHHHHhCCCh
Confidence 344555555555555554
No 215
>PF08478 POTRA_1: POTRA domain, FtsQ-type; InterPro: IPR013685 FtsQ/DivIB bacterial division proteins (IPR005548 from INTERPRO) contain an N-terminal POTRA domain (for polypeptide-transport-associated domain). This is found in different types of proteins, usually associated with a transmembrane beta-barrel. FtsQ/DivIB may have chaperone-like roles, which has also been postulated for the POTRA domain in other contexts []. ; PDB: 2ALJ_A 2VH1_B 3J00_Z 2VH2_B.
Probab=25.96 E-value=97 Score=18.74 Aligned_cols=34 Identities=9% Similarity=0.108 Sum_probs=25.4
Q ss_pred hhcccccchHHHHHHHhCCCCCCcCCCCCHHHHH
Q 033139 32 SIKGIGRRLANIVCKKADVDMNKRAGELSAAELD 65 (126)
Q Consensus 32 ~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~ 65 (126)
.|.|-..-...+|++.+|+.+...+-.++.+++.
T Consensus 7 ~V~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~ 40 (69)
T PF08478_consen 7 EVSGNSYLSKEEILQALGIQKGKNLFSLDLKKIE 40 (69)
T ss_dssp EEES-SSS-HHHHHHHHCTTSTTTCCCSHHHHHH
T ss_pred EEECCCcCCHHHHHHHhCcCCCCeEEEECHHHHH
Confidence 4668888899999999999998888877555444
No 216
>PF02879 PGM_PMM_II: Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II; InterPro: IPR005845 The alpha-D-phosphohexomutase superfamily is composed of four related enzymes, each of which catalyses a phosphoryl transfer on their sugar substrates: phosphoglucomutase (PGM), phosphoglucomutase/phosphomannomutase (PGM/PMM), phosphoglucosamine mutase (PNGM), and phosphoacetylglucosamine mutase (PAGM) []. PGM (5.4.2.2 from EC) converts D-glucose 1-phosphate into D-glucose 6-phosphate, and participates in both the breakdown and synthesis of glucose []. PGM/PMM (5.4.2.2 from EC; 5.4.2.8 from EC) are primarily bacterial enzymes that use either glucose or mannose as substrate, participating in the biosynthesis of a variety of carbohydrates such as lipopolysaccharides and alginate [, ]. Both PNGM (5.4.2.3 from EC) and PAGM (5.4.2.10 from EC) are involved in the biosynthesis of UDP-N-acetylglucosamine [, ]. Despite differences in substrate specificity, these enzymes share a similar catalytic mechanism, converting 1-phospho-sugars to 6-phospho-sugars via a biphosphorylated 1,6-phospho-sugar. The active enzyme is phosphorylated at a conserved serine residue and binds one magnesium ion; residues around the active site serine are well conserved among family members. The reaction mechanism involves phosphoryl transfer from the phosphoserine to the substrate to create a biophosphorylated sugar, followed by a phosphoryl transfer from the substrate back to the enzyme []. The structures of PGM and PGM/PMM have been determined, and were found to be very similar in topology. These enzymes are both composed of four domains and a large central active site cleft, where each domain contains residues essential for catalysis and/or substrate recognition. Domain I contains the catalytic phosphoserine, domain II contains a metal-binding loop to coordinate the magnesium ion, domain III contains the sugar-binding loop that recognises the two different binding orientations of the 1- and 6-phospho-sugars, and domain IV contains a phosphate-binding site required for orienting the incoming phospho-sugar substrate. This entry represents domain II found in alpha-D-phosphohexomutase enzymes. This domain has a 3-layer alpha/beta/alpha topology.; GO: 0016868 intramolecular transferase activity, phosphotransferases, 0005975 carbohydrate metabolic process; PDB: 2F7L_A 3PDK_B 1KFQ_B 1KFI_A 1C47_A 1VKL_B 1LXT_A 1JDY_B 3PMG_A 1C4G_B ....
Probab=25.93 E-value=12 Score=25.08 Aligned_cols=40 Identities=10% Similarity=0.248 Sum_probs=29.6
Q ss_pred cchhhcc-ccCCCCeehheehhhhcccccchHHHHHHHhCC
Q 033139 11 HILRVLN-TNVDGKQKIMFALTSIKGIGRRLANIVCKKADV 50 (126)
Q Consensus 11 ~mvrI~g-~~l~~~K~v~~aLt~IyGIG~~~A~~Ic~~~gI 50 (126)
++...++ ...-..+.+.+.+..-+|.|...+..|++++|.
T Consensus 6 ~l~~~~~~~~~~~~~~~kivvD~~~G~~~~~~~~ll~~lg~ 46 (104)
T PF02879_consen 6 SLLSFIDILEAIKKSGLKIVVDCMNGAGSDILPRLLERLGC 46 (104)
T ss_dssp HHHHTSCHHHHHHHTTCEEEEE-TTSTTHHHHHHHHHHTTC
T ss_pred HHhhhccchhhcccCCCEEEEECCCCHHHHHHHHHHHHcCC
Confidence 3444444 333455567889999999999999999999997
No 217
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=25.91 E-value=35 Score=31.49 Aligned_cols=43 Identities=7% Similarity=0.191 Sum_probs=29.6
Q ss_pred CeehheehhhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHH
Q 033139 23 KQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQL 67 (126)
Q Consensus 23 ~K~v~~aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L 67 (126)
.+...-.|..|.|||+.....+++.+|= -..+..-|.+||.++
T Consensus 603 k~~~~s~L~~IpGiG~kr~~~LL~~FgS--~~~i~~As~eel~~v 645 (691)
T PRK14672 603 KKELVLSFERLPHVGKVRAHRLLAHFGS--FRSLQSATPQDIATA 645 (691)
T ss_pred hhhcccccccCCCCCHHHHHHHHHHhcC--HHHHHhCCHHHHHhC
Confidence 3445578899999999999999988772 233444455555443
No 218
>TIGR00012 L29 ribosomal protein L29. called L29 in prokaryotic (50S) large subunits and L35 in eukaryotic (60S) large subunits.
Probab=25.87 E-value=61 Score=19.84 Aligned_cols=52 Identities=17% Similarity=0.199 Sum_probs=30.4
Q ss_pred CCCCCHHHHHHHHHHHhCCCCccCChhhhhccccccCCccceeehhhHHHHHHHHHHHHHhcc
Q 033139 56 AGELSAAELDQLMVVVANPRQFKIPDWFLNRQKDYKDGRYSQVVSNALDMKLRDDLERLKKIR 118 (126)
Q Consensus 56 ~~~Ls~~qi~~L~~~i~~~~~~~iP~w~~nr~~d~~tg~~~h~i~~dL~~~~~~dI~rl~~I~ 118 (126)
+.++|.+|+......+.+ .+ ++=|..-.||.- -..-..+.++-||.|++.+-
T Consensus 2 lr~~s~~EL~~~l~~lr~--eL------f~Lr~~~~~~~~---~~~~~i~~~Rk~IARi~Tvl 53 (55)
T TIGR00012 2 LREKSKEELAKKLDELKK--EL------FELRFQKATGQL---AKPHRIRQVRRDIARLLTVL 53 (55)
T ss_pred HhhCCHHHHHHHHHHHHH--HH------HHHHHHHHhCCc---ccchHHHHHHHHHHHHHHHH
Confidence 356777777765555543 22 222333333432 24445688999999998864
No 219
>PRK02362 ski2-like helicase; Provisional
Probab=25.85 E-value=40 Score=30.59 Aligned_cols=39 Identities=15% Similarity=0.289 Sum_probs=31.5
Q ss_pred eehhhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHH
Q 033139 28 FALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQL 67 (126)
Q Consensus 28 ~aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L 67 (126)
..|..+.|||+..|+++- .+||..-..+-.++++++.++
T Consensus 652 ~~L~~ip~i~~~~a~~l~-~~gi~s~~dl~~~~~~~l~~~ 690 (737)
T PRK02362 652 LDLVGLRGVGRVRARRLY-NAGIESRADLRAADKSVVLAI 690 (737)
T ss_pred HHHhCCCCCCHHHHHHHH-HcCCCCHHHHHhCCHHHHHHH
Confidence 456789999999997766 599998777777788888775
No 220
>KOG0821 consensus Predicted ribosomal RNA adenine dimethylase [RNA processing and modification]
Probab=25.70 E-value=86 Score=25.81 Aligned_cols=35 Identities=23% Similarity=0.256 Sum_probs=31.1
Q ss_pred chHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 033139 39 RLANIVCKKADVDMNKRAGELSAAELDQLMVVVAN 73 (126)
Q Consensus 39 ~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L~~~i~~ 73 (126)
..|..+++++.|+|..+.-+|+-||...|.+.-+.
T Consensus 270 E~~~~Ll~~~~idpT~r~~~L~iEQf~~LAE~Y~E 304 (326)
T KOG0821|consen 270 ESTGRLLELADIDPTLRPRQLSIEQFKSLAEVYRE 304 (326)
T ss_pred HHHHHHHHHhcCCCccCceeeeHHHHHHHHHHHHH
Confidence 35778999999999999999999999999887654
No 221
>PRK14539 50S ribosomal protein L11/unknown domain fusion protein; Provisional
Probab=25.11 E-value=1.4e+02 Score=23.50 Aligned_cols=61 Identities=7% Similarity=0.086 Sum_probs=43.7
Q ss_pred ccchHHHHHHHhCCCCC------CcCCCCCHHHHHHHHHHHhCCCCccCChhhhhccccccCCccceeehhhHHHHHHHH
Q 033139 37 GRRLANIVCKKADVDMN------KRAGELSAAELDQLMVVVANPRQFKIPDWFLNRQKDYKDGRYSQVVSNALDMKLRDD 110 (126)
Q Consensus 37 G~~~A~~Ic~~~gI~p~------~k~~~Ls~~qi~~L~~~i~~~~~~~iP~w~~nr~~d~~tg~~~h~i~~dL~~~~~~d 110 (126)
-+.+|.-|.+.+|+... ..+++||-+|+..|.+.-.. . +...+|...+++=
T Consensus 69 tPptS~LLkKaagi~kGs~~p~k~~vG~Itl~qv~eIAk~K~~--D---------------------l~~~~Le~avK~V 125 (196)
T PRK14539 69 TAPASFKIKQAAKIKSGSANSKTTIVGTITLSQLEEIAKYKLP--D---------------------LNTDDVEEAMHTI 125 (196)
T ss_pred CCCHHHHHHHHhCCCCCCCCCCCeEEEEecHHHHHHHHHHHhh--h---------------------hCCCcHHHHHHHH
Confidence 35889999999999765 34689999999999987653 1 3456777777765
Q ss_pred HHHHHhcccc
Q 033139 111 LERLKKIRYG 120 (126)
Q Consensus 111 I~rl~~I~sy 120 (126)
+=--+.+++.
T Consensus 126 lGTArSMGI~ 135 (196)
T PRK14539 126 AGTAKNMGVL 135 (196)
T ss_pred HhhheeCeEE
Confidence 5555555543
No 222
>COG1131 CcmA ABC-type multidrug transport system, ATPase component [Defense mechanisms]
Probab=25.05 E-value=1e+02 Score=24.76 Aligned_cols=59 Identities=15% Similarity=0.129 Sum_probs=42.6
Q ss_pred chhhcccc-CCCCeehheeh---hhhcccc----cchHHHHHHHhCCCC--CCcCCCCCHHHHHHHHHH
Q 033139 12 ILRVLNTN-VDGKQKIMFAL---TSIKGIG----RRLANIVCKKADVDM--NKRAGELSAAELDQLMVV 70 (126)
Q Consensus 12 mvrI~g~~-l~~~K~v~~aL---t~IyGIG----~~~A~~Ic~~~gI~p--~~k~~~Ls~~qi~~L~~~ 70 (126)
+-++...+ ++++-++.-.| ..+||.. ...+.++++.+|++. ++++++||..+-.++.=+
T Consensus 80 igy~~~~~~~~~~lT~~e~l~~~~~l~~~~~~~~~~~~~~~l~~~~L~~~~~~~~~~lS~G~kqrl~ia 148 (293)
T COG1131 80 IGYVPQEPSLYPELTVRENLEFFARLYGLSKEEAEERIEELLELFGLEDKANKKVRTLSGGMKQRLSIA 148 (293)
T ss_pred eEEEccCCCCCccccHHHHHHHHHHHhCCChhHHHHHHHHHHHHcCCchhhCcchhhcCHHHHHHHHHH
Confidence 33443333 45566665555 5788887 457889999999998 788999999988876544
No 223
>PRK00254 ski2-like helicase; Provisional
Probab=24.91 E-value=33 Score=31.06 Aligned_cols=39 Identities=21% Similarity=0.188 Sum_probs=30.5
Q ss_pred eehhhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHH
Q 033139 28 FALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQL 67 (126)
Q Consensus 28 ~aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L 67 (126)
..|..+.|||+..|++ |-+.|+..-..+.+.++++|.++
T Consensus 645 ~~L~~ipgig~~~~~~-l~~~g~~s~~~i~~a~~~el~~~ 683 (720)
T PRK00254 645 LELMRLPMIGRKRARA-LYNAGFRSIEDIVNAKPSELLKV 683 (720)
T ss_pred hhhhcCCCCCHHHHHH-HHHccCCCHHHHHhCCHHHHhcC
Confidence 3467899999999998 55778887777777788887665
No 224
>COG0587 DnaE DNA polymerase III, alpha subunit [DNA replication, recombination, and repair]
Probab=24.70 E-value=44 Score=32.60 Aligned_cols=47 Identities=21% Similarity=0.291 Sum_probs=37.5
Q ss_pred eehheehhhhcccccchHHHHHHHh---------CCCCCCcCCCCCHHHHHHHHHH
Q 033139 24 QKIMFALTSIKGIGRRLANIVCKKA---------DVDMNKRAGELSAAELDQLMVV 70 (126)
Q Consensus 24 K~v~~aLt~IyGIG~~~A~~Ic~~~---------gI~p~~k~~~Ls~~qi~~L~~~ 70 (126)
+.|.++|..|+|+|...+..|.+.- .+......+.++...++.|.++
T Consensus 819 ~~I~~gL~~IKGvg~~~i~~Iv~~R~~~~~~~~~df~~r~~~~~l~kr~lE~Lika 874 (1139)
T COG0587 819 KAIRLGLGAIKGVGEDAIEEIVEARKEKPFKSLEDFCDRIDRKGLNKRVLESLIKA 874 (1139)
T ss_pred CcEEEhhhhhcCCcHHHHHHHHHHhhcccCCcHhHHHHHhhhccCCHHHHHHHHHc
Confidence 6999999999999999999988774 3444445556888888888776
No 225
>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=24.47 E-value=1.3e+02 Score=20.31 Aligned_cols=37 Identities=22% Similarity=0.382 Sum_probs=25.2
Q ss_pred eehhhhcccccch-HHHHHHHhCCCCCCcCCCCCHHHHH
Q 033139 28 FALTSIKGIGRRL-ANIVCKKADVDMNKRAGELSAAELD 65 (126)
Q Consensus 28 ~aLt~IyGIG~~~-A~~Ic~~~gI~p~~k~~~Ls~~qi~ 65 (126)
+++...+|-|.++ |..+.+++|+. -...+.+..++..
T Consensus 2 I~i~G~~GsGKst~a~~la~~~~~~-~~~~~~i~~e~~~ 39 (147)
T cd02020 2 IAIDGPAGSGKSTVAKLLAKKLGLP-YLDTGGIRTEEVG 39 (147)
T ss_pred EEEECCCCCCHHHHHHHHHHHhCCc-eeccccCCHHHHH
Confidence 4677889999998 88888888864 2333455555443
No 226
>PF14053 DUF4248: Domain of unknown function (DUF4248)
Probab=24.36 E-value=1.3e+02 Score=19.41 Aligned_cols=49 Identities=8% Similarity=0.056 Sum_probs=35.0
Q ss_pred eehheehhhhcccccchHHHHH--------------HHhCCCCCCcCCCCCHHHHHHHHHHHhCC
Q 033139 24 QKIMFALTSIKGIGRRLANIVC--------------KKADVDMNKRAGELSAAELDQLMVVVANP 74 (126)
Q Consensus 24 K~v~~aLt~IyGIG~~~A~~Ic--------------~~~gI~p~~k~~~Ls~~qi~~L~~~i~~~ 74 (126)
..-+.|+.++.++-+..|..-+ ..+|-.+.. ..+|..|+..|.+.+..|
T Consensus 7 ~k~ELA~lYfP~~~~~sA~r~L~rwI~~~~~L~~~L~~~Gy~~~~--r~~TP~QV~lIv~~LGeP 69 (69)
T PF14053_consen 7 GKSELAQLYFPDLTPSSAVRKLRRWIRRNPELLEELEATGYHPRQ--RSFTPRQVRLIVRYLGEP 69 (69)
T ss_pred cHHHHHHHHcCCCCHHHHHHHHHHHHHHCHHHHHHHHHcCCCCCC--EecCHHHHHHHHHHcCCC
Confidence 3456788888888777776543 345666554 669999999999988653
No 227
>TIGR00630 uvra excinuclease ABC, A subunit. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=24.22 E-value=66 Score=30.63 Aligned_cols=30 Identities=7% Similarity=0.161 Sum_probs=26.3
Q ss_pred hHHHHHHHhCCCCCCcCCCCCHHHHHHHHH
Q 033139 40 LANIVCKKADVDMNKRAGELSAAELDQLMV 69 (126)
Q Consensus 40 ~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L~~ 69 (126)
.-..+|+..|||.+++.++|+++|.+.+-.
T Consensus 321 ~l~~~~~~~g~~~~~p~~~l~~~~~~~ll~ 350 (924)
T TIGR00630 321 MLKSLAEHYGFDLDTPWKDLPEEVQKAVLY 350 (924)
T ss_pred HHHHHHHHcCCCCCCChHHCCHHHHHHHhc
Confidence 345689999999999999999999998864
No 228
>PRK03858 DNA polymerase IV; Validated
Probab=24.16 E-value=57 Score=27.05 Aligned_cols=35 Identities=17% Similarity=0.279 Sum_probs=24.6
Q ss_pred ehhhhcccccchHHHHHHHhCCCCCCcCCCCCHHHH
Q 033139 29 ALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAEL 64 (126)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi 64 (126)
-++.+.|||+.++..+ +++||..=.-+..++.+++
T Consensus 174 pl~~l~Gig~~~~~~L-~~~Gi~t~~dl~~l~~~~L 208 (396)
T PRK03858 174 PVRRLWGVGPVTAAKL-RAHGITTVGDVAELPESAL 208 (396)
T ss_pred ChhhcCCCCHHHHHHH-HHhCCCcHHHHhcCCHHHH
Confidence 4678889999999886 6789986444444454443
No 229
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=24.15 E-value=62 Score=17.29 Aligned_cols=17 Identities=12% Similarity=0.014 Sum_probs=7.7
Q ss_pred ccccchHHHHHHHhCCC
Q 033139 35 GIGRRLANIVCKKADVD 51 (126)
Q Consensus 35 GIG~~~A~~Ic~~~gI~ 51 (126)
.++...+..+|+.+|++
T Consensus 38 ~~~~~~~~~i~~~~~~~ 54 (58)
T cd00093 38 NPSLETLEKLAKALGVS 54 (58)
T ss_pred CCCHHHHHHHHHHhCCC
Confidence 34444444444444444
No 230
>KOG3908 consensus Queuine-tRNA ribosyltransferase [RNA processing and modification]
Probab=23.95 E-value=16 Score=30.89 Aligned_cols=40 Identities=15% Similarity=0.331 Sum_probs=36.4
Q ss_pred cccccchhhccccCCCCeehheehhhhcccccchHHHHHHHhCCC
Q 033139 7 EDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVD 51 (126)
Q Consensus 7 ~~~~~mvrI~g~~l~~~K~v~~aLt~IyGIG~~~A~~Ic~~~gI~ 51 (126)
.+|-.||...-..+|.+|+ .+.-|+|...-..+|-.+|.|
T Consensus 230 ~~Fwr~V~~ct~~LP~dkP-----RYlMGVGya~DlVVCvaLG~D 269 (396)
T KOG3908|consen 230 SEFWRMVAFCTSSLPPDKP-----RYLMGVGYAEDLVVCVALGSD 269 (396)
T ss_pred HHHHHHHHHHHccCCCCCC-----ceeeccCcccceeeeehhCCc
Confidence 5688999999999999998 578999999999999999977
No 231
>CHL00133 psbV photosystem II cytochrome c550; Validated
Probab=23.95 E-value=84 Score=23.85 Aligned_cols=17 Identities=12% Similarity=0.077 Sum_probs=15.1
Q ss_pred CCCCHHHHHHHHHHHhC
Q 033139 57 GELSAAELDQLMVVVAN 73 (126)
Q Consensus 57 ~~Ls~~qi~~L~~~i~~ 73 (126)
+.||++||..|..+|-.
T Consensus 131 ~~LsdeEL~aVAaYIl~ 147 (163)
T CHL00133 131 RSLTDEDLYAIAGHILL 147 (163)
T ss_pred CCCCHHHHHHHHHHHHh
Confidence 57999999999999763
No 232
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=23.81 E-value=50 Score=31.01 Aligned_cols=39 Identities=26% Similarity=0.348 Sum_probs=27.6
Q ss_pred hheehhhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHH
Q 033139 26 IMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQL 67 (126)
Q Consensus 26 v~~aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L 67 (126)
..+ |..++|||+..|..++++.| .=..+-.+|.+++..+
T Consensus 756 q~~-L~~lPgI~~~~a~~ll~~f~--si~~l~~as~eeL~~~ 794 (814)
T TIGR00596 756 QDF-LLKLPGVTKKNYRNLRKKVK--SIRELAKLSQNELNEL 794 (814)
T ss_pred HHH-HHHCCCCCHHHHHHHHHHcC--CHHHHHhCCHHHHHHH
Confidence 456 77999999999999999854 3333445566665543
No 233
>KOG1014 consensus 17 beta-hydroxysteroid dehydrogenase type 3, HSD17B3 [Lipid transport and metabolism]
Probab=23.67 E-value=58 Score=27.32 Aligned_cols=42 Identities=17% Similarity=0.291 Sum_probs=32.0
Q ss_pred hhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCCcc
Q 033139 32 SIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVANPRQFK 78 (126)
Q Consensus 32 ~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L~~~i~~~~~~~ 78 (126)
.-.|||+..|.++++ =|++ .-+=.=|++-++++.+.|+. .++
T Consensus 57 aTDGIGKayA~eLAk-rG~n--vvLIsRt~~KL~~v~kEI~~--~~~ 98 (312)
T KOG1014|consen 57 ATDGIGKAYARELAK-RGFN--VVLISRTQEKLEAVAKEIEE--KYK 98 (312)
T ss_pred CCCcchHHHHHHHHH-cCCE--EEEEeCCHHHHHHHHHHHHH--HhC
Confidence 457999999999998 5766 22222388999999999997 563
No 234
>PF00832 Ribosomal_L39: Ribosomal L39 protein; InterPro: IPR000077 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 [, ]. A number of eukaryotic and archaebacterial large subunit ribosomal proteins can be grouped on the basis of sequence similarities. These proteins are very basic. About 50 residues long, they are the smallest proteins of eukaryotic-type ribosomes.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3CCJ_2 3CME_2 3OW2_1 1YI2_2 1KD1_3 3CXC_1 3G6E_2 1VQ4_2 3CCU_2 3CC7_2 ....
Probab=23.65 E-value=39 Score=20.31 Aligned_cols=36 Identities=14% Similarity=0.189 Sum_probs=18.8
Q ss_pred HHHHHHhCCCCccCChhh--hhccccccCCccceeehhhH
Q 033139 66 QLMVVVANPRQFKIPDWF--LNRQKDYKDGRYSQVVSNAL 103 (126)
Q Consensus 66 ~L~~~i~~~~~~~iP~w~--~nr~~d~~tg~~~h~i~~dL 103 (126)
.|.++..+ +-.+|.|. ...++-.+..+..|.=-++|
T Consensus 4 rLaKa~kq--NrpvP~Wv~~kT~~kiryn~kRRhWRRtkL 41 (43)
T PF00832_consen 4 RLAKAQKQ--NRPVPQWVRMKTGNKIRYNPKRRHWRRTKL 41 (43)
T ss_dssp HHHHHHHH--TS---HHGHHCTTSS-SSGTT---TTTS-S
T ss_pred HHHHHHhc--cCCCCcEEEEeCCCceeeCCCccccccccc
Confidence 46777776 78899996 46666666777777655544
No 235
>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=23.55 E-value=1e+02 Score=18.60 Aligned_cols=14 Identities=29% Similarity=0.522 Sum_probs=12.5
Q ss_pred CCCHHHHHHHHHHH
Q 033139 58 ELSAAELDQLMVVV 71 (126)
Q Consensus 58 ~Ls~~qi~~L~~~i 71 (126)
.||++|+..|..+|
T Consensus 54 ~ls~~e~~~l~~yi 67 (67)
T PF13442_consen 54 QLSDEEIEALAAYI 67 (67)
T ss_dssp TSTHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHC
Confidence 69999999998875
No 236
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=23.44 E-value=56 Score=26.25 Aligned_cols=21 Identities=29% Similarity=0.471 Sum_probs=19.0
Q ss_pred ehhhhcccccchHHHHHHHhC
Q 033139 29 ALTSIKGIGRRLANIVCKKAD 49 (126)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~~g 49 (126)
.|..+.|||...|.+|.+.++
T Consensus 37 EL~~V~GIg~k~AekI~e~l~ 57 (232)
T PRK12766 37 ELAEVDGIGNALAARIKADVG 57 (232)
T ss_pred HHHHccCCCHHHHHHHHHHhc
Confidence 478899999999999999887
No 237
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=23.42 E-value=47 Score=28.04 Aligned_cols=20 Identities=30% Similarity=0.539 Sum_probs=16.5
Q ss_pred ehhhhcccccchHHHHHHHh
Q 033139 29 ALTSIKGIGRRLANIVCKKA 48 (126)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~~ 48 (126)
++|.+.|||+.+|..|-.-+
T Consensus 54 ~~t~l~gIGk~ia~~I~e~l 73 (326)
T COG1796 54 RLTELPGIGKGIAEKISEYL 73 (326)
T ss_pred ccCCCCCccHHHHHHHHHHH
Confidence 58899999999999886543
No 238
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=23.41 E-value=66 Score=19.62 Aligned_cols=29 Identities=14% Similarity=0.130 Sum_probs=20.3
Q ss_pred CCCCee-hheehhhhcccccchHHHHHHHh
Q 033139 20 VDGKQK-IMFALTSIKGIGRRLANIVCKKA 48 (126)
Q Consensus 20 l~~~K~-v~~aLt~IyGIG~~~A~~Ic~~~ 48 (126)
-||.+- -...|...||+++.++++.++.+
T Consensus 19 ~~g~~lps~~~la~~~~vsr~tvr~al~~L 48 (64)
T PF00392_consen 19 PPGDRLPSERELAERYGVSRTTVREALRRL 48 (64)
T ss_dssp -TTSBE--HHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCCCEeCCHHHHHHHhccCCcHHHHHHHHH
Confidence 334444 57889999999999999887765
No 239
>PRK05673 dnaE DNA polymerase III subunit alpha; Validated
Probab=23.29 E-value=47 Score=32.29 Aligned_cols=47 Identities=17% Similarity=0.316 Sum_probs=32.5
Q ss_pred CeehheehhhhcccccchHHHHHHHhCC-CC---------CCcCCCCCHHHHHHHHH
Q 033139 23 KQKIMFALTSIKGIGRRLANIVCKKADV-DM---------NKRAGELSAAELDQLMV 69 (126)
Q Consensus 23 ~K~v~~aLt~IyGIG~~~A~~Ic~~~gI-~p---------~~k~~~Ls~~qi~~L~~ 69 (126)
+..|.++|..|+|||...|..|.+.=.- .| ....+.++...++.|.+
T Consensus 815 ~~~I~~gL~~Ikgvg~~~~~~I~~~R~~~g~f~s~~Df~~R~~~~~~~k~~le~Li~ 871 (1135)
T PRK05673 815 DGDIRYGLGAIKGVGEGAVEAIVEAREEGGPFKDLFDFCARVDLKKVNKRVLESLIK 871 (1135)
T ss_pred CCEEEechhhcCCCCHHHHHHHHHHHHhCCCCCCHHHHHHHhccCCCCHHHHHHHHH
Confidence 4579999999999999999999865421 01 11224466666666654
No 240
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=23.28 E-value=52 Score=32.30 Aligned_cols=46 Identities=15% Similarity=0.301 Sum_probs=31.7
Q ss_pred eehheehhhhcccccchHHHHHHHhCCCCCCcCC------CCCHHHHHHHHH
Q 033139 24 QKIMFALTSIKGIGRRLANIVCKKADVDMNKRAG------ELSAAELDQLMV 69 (126)
Q Consensus 24 K~v~~aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~------~Ls~~qi~~L~~ 69 (126)
+.+.++|..|.|+|...|..|.+.-.-.|-..+. .++...++.|.+
T Consensus 1146 ~~I~~~l~aI~glg~~~a~~Iv~~R~~g~F~s~~Df~~R~~v~k~~le~L~~ 1197 (1213)
T TIGR01405 1146 NTLIPPFNAIPGLGENVANSIVEARNEKPFLSKEDLKKRTKISKTHIEKLDS 1197 (1213)
T ss_pred CEEEeehhhcCCCCHHHHHHHHHHHhhCCCCCHHHHHHHhCCCHHHHHHHHh
Confidence 4689999999999999999999765322322221 346666666654
No 241
>PF03250 Tropomodulin: Tropomodulin; InterPro: IPR004934 Actin filaments have an intrinsic polarity, each with a fast-growing (barbed) end and a slow-growing (pointed) end. To regulate the dynamics at these ends, capping proteins have evolved that specifically bind to either the barbed or the pointed ends of the filament, where they block the association and dissociation of monomers. Pointed ends, for which actin monomers have significantly lower association and dissociation rate-constants than for barbed, are capped by either the Arp2/3 complex or tropomodulins []. Tropomodulin is a novel tropomyosin regulatory protein that binds to the end of erythrocyte tropomyosin and blocks head-to-tail association of tropomyosin along actin filaments []. Limited proteolysis shows this protein is composed of two domains. The unstructured tropomyosin-binding region at the N terminus has an actin pointed-end-capping activity that is dramatically up-regulated by tropomyosin coating of the actin filament[]. The second region is found near the C terminus. This tropomyosin-independent capping-domain caps pure actin. ; GO: 0005523 tropomyosin binding, 0005856 cytoskeleton
Probab=23.25 E-value=52 Score=24.71 Aligned_cols=43 Identities=30% Similarity=0.438 Sum_probs=30.7
Q ss_pred HHHhCCCCCCcCCCCCHHHHHHHHHHHh--CCCCccCChhhhhcccc
Q 033139 45 CKKADVDMNKRAGELSAAELDQLMVVVA--NPRQFKIPDWFLNRQKD 89 (126)
Q Consensus 45 c~~~gI~p~~k~~~Ls~~qi~~L~~~i~--~~~~~~iP~w~~nr~~d 89 (126)
-+.-.||.+--+..||.+++.+|...++ .|.+-.+|+=| ||+|
T Consensus 10 ~~y~DiDeDelL~~LS~EEL~~L~~el~e~DPd~~~lP~g~--Rq~d 54 (147)
T PF03250_consen 10 EKYEDIDEDELLAKLSPEELEELENELEEMDPDNSLLPAGM--RQRD 54 (147)
T ss_pred hhcccCCHHHHHHhCCHHHHHHHHHHHHhhCCCcccCChhh--hccc
Confidence 3445678888889999999999997764 46554467665 4444
No 242
>PF11174 DUF2970: Protein of unknown function (DUF2970); InterPro: IPR021344 This short family is conserved in Proteobacteria. The function is not known.
Probab=23.20 E-value=17 Score=22.83 Aligned_cols=22 Identities=18% Similarity=0.397 Sum_probs=17.6
Q ss_pred hhccccccCCccceeehhhHHH
Q 033139 84 LNRQKDYKDGRYSQVVSNALDM 105 (126)
Q Consensus 84 ~nr~~d~~tg~~~h~i~~dL~~ 105 (126)
.||++|+.+|.-.|.|-.-+..
T Consensus 19 ~~~e~Df~~~~p~~~Ii~gii~ 40 (56)
T PF11174_consen 19 KNRERDFAQGSPVHFIIVGIIL 40 (56)
T ss_pred hhHHHHHHcCCCchHHHHHHHH
Confidence 4899999999999987665543
No 243
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=22.97 E-value=47 Score=20.12 Aligned_cols=20 Identities=15% Similarity=0.182 Sum_probs=13.2
Q ss_pred heehhhhcccccchHHHHHH
Q 033139 27 MFALTSIKGIGRRLANIVCK 46 (126)
Q Consensus 27 ~~aLt~IyGIG~~~A~~Ic~ 46 (126)
..++..-|||+.++...|++
T Consensus 25 ~~~ia~~fgv~~sTv~~I~K 44 (53)
T PF04218_consen 25 KRDIAREFGVSRSTVSTILK 44 (53)
T ss_dssp HHHHHHHHT--CCHHHHHHH
T ss_pred HHHHHHHhCCCHHHHHHHHH
Confidence 45677778888888877765
No 244
>PF07700 HNOB: Heme NO binding; InterPro: IPR011644 This ligand-binding domain is found in soluble guanylate cyclases. In soluble guanylate cyclases this domain binds heme via a covalent linkage to histidine []. Soluble guanylate cyclases are nitric oxide-responsive signaling proteins.; GO: 0020037 heme binding; PDB: 3TFE_A 2O0C_B 3TFA_A 2O09_B 2O0G_B 3L6J_A 3TFG_B 3TF8_A 3TFF_A 3TF9_B ....
Probab=22.93 E-value=84 Score=23.09 Aligned_cols=37 Identities=19% Similarity=0.273 Sum_probs=30.4
Q ss_pred ccchHHHHHHHhCCCC---CCcCCCCCHHHHHHHHHHHhC
Q 033139 37 GRRLANIVCKKADVDM---NKRAGELSAAELDQLMVVVAN 73 (126)
Q Consensus 37 G~~~A~~Ic~~~gI~p---~~k~~~Ls~~qi~~L~~~i~~ 73 (126)
|..+-.+|++++|+++ -...+.-+|+++.+|.+++.+
T Consensus 18 G~~~w~~i~~~~~~~~~~~f~~~~~Y~D~~~~~lv~a~a~ 57 (171)
T PF07700_consen 18 GEEVWDEILERAGLDSDGIFTSHGNYDDEETYKLVEAAAE 57 (171)
T ss_dssp HHHHHHHHHHHTTSSTTSS--TTSBTTHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHhCCCcCCccccccccCHHHHHHHHHHHHH
Confidence 4888999999999993 336677799999999999886
No 245
>TIGR02620 cas_VVA1548 putative CRISPR-associated protein, VVA1548 family. This model represents a conserved domain of about 95 amino acids exclusively in species with CRISPR (Clustered Regularly Interspaced Short Palidromic Repeats). In all bacterial species with members so far (Vibrio vulnificus YJ016, Mannheimia succiniciproducens MBEL55E, and Nitrosomonas europaea ATCC 19718) and but not in the archaeon Methanothermobacter thermautotrophicus str. Delta H, the gene for this protein is in the midst of a cluster of Cas protein gene near CRISPR repeats.
Probab=22.88 E-value=62 Score=22.54 Aligned_cols=35 Identities=29% Similarity=0.348 Sum_probs=29.4
Q ss_pred cchHHHHHH--------HhCCCCCCcCCCCCHHHHHHHHHHHh
Q 033139 38 RRLANIVCK--------KADVDMNKRAGELSAAELDQLMVVVA 72 (126)
Q Consensus 38 ~~~A~~Ic~--------~~gI~p~~k~~~Ls~~qi~~L~~~i~ 72 (126)
...|.++|+ .+.+++..+-.+||.+|+.+.-.-++
T Consensus 44 v~Laa~vc~kGa~y~~l~l~~p~e~rG~Elsae~m~~~ga~l~ 86 (93)
T TIGR02620 44 VSLAADICKKGARYFELSLNVPASVRGTELEAEQLKACDAQLE 86 (93)
T ss_pred HHHHHHHHhCCcEEEEEEccCChHHcCCcccHHHHHhcCcEEE
Confidence 468999998 67899999999999999987665554
No 246
>cd08532 SAM_PNT-PDEF-like Sterile alpha motif (SAM)/Pointed domain of prostate-derived ETS factor. SAM Pointed domain of PDEF-like (Prostate-Derived ETS Factor) subfamily of ETS transcriptional regulators is a putative protein-protein interaction domain. In human males this activator is highly expressed in the prostate gland and enhances androgen-mediated activation of the PSA promoter though interaction with the DNA binding domain of androgen receptor. PDEF may play a role in prostate cancer development as well as in goblet cell formation and mucus production in the epithelial lining of respiratory and intestinal tracts.
Probab=22.80 E-value=54 Score=21.71 Aligned_cols=33 Identities=18% Similarity=0.455 Sum_probs=26.0
Q ss_pred HHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCCccCCh
Q 033139 45 CKKADVDMNKRAGELSAAELDQLMVVVANPRQFKIPD 81 (126)
Q Consensus 45 c~~~gI~p~~k~~~Ls~~qi~~L~~~i~~~~~~~iP~ 81 (126)
|+++||+++ +...|.+|+.+=.....+ +|.+|.
T Consensus 1 c~~L~ip~D--P~~Ws~~~V~~WL~w~~~--ef~L~~ 33 (76)
T cd08532 1 CKLLGISPD--PYQWSPANVQKWLLWTEH--QYRLPP 33 (76)
T ss_pred CCcCCCCCC--hhhcCHHHHHHHHHHHHH--HhCCCC
Confidence 678888865 788999999987777665 688776
No 247
>PRK07374 dnaE DNA polymerase III subunit alpha; Validated
Probab=22.79 E-value=49 Score=32.35 Aligned_cols=48 Identities=19% Similarity=0.333 Sum_probs=33.1
Q ss_pred CeehheehhhhcccccchHHHHHHHhCC-CC---------CCcCCCCCHHHHHHHHHH
Q 033139 23 KQKIMFALTSIKGIGRRLANIVCKKADV-DM---------NKRAGELSAAELDQLMVV 70 (126)
Q Consensus 23 ~K~v~~aLt~IyGIG~~~A~~Ic~~~gI-~p---------~~k~~~Ls~~qi~~L~~~ 70 (126)
+..|.++|..|+|||...|..|.+.=.- .| ....+.++...++.|.++
T Consensus 830 ~~~Ir~GL~aIkgvg~~~~~~Iv~~R~~~g~f~s~~Df~~R~~~~~~nk~~le~LI~a 887 (1170)
T PRK07374 830 GNRILFGLSAVKNLGDGAIRNIIAARDSDGPFKSLADLCDRLPSNVLNRRSLESLIHC 887 (1170)
T ss_pred CCEEEechhhcCCCCHHHHHHHHHHHHhCCCCCCHHHHHHHhccccCCHHHHHHHHHc
Confidence 4569999999999999999999865421 11 112344677777766643
No 248
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=22.70 E-value=53 Score=26.70 Aligned_cols=24 Identities=42% Similarity=0.599 Sum_probs=20.9
Q ss_pred hheehhhhcccccchHHHHHHHhC
Q 033139 26 IMFALTSIKGIGRRLANIVCKKAD 49 (126)
Q Consensus 26 v~~aLt~IyGIG~~~A~~Ic~~~g 49 (126)
-.+-|.++.|||...|..+++..|
T Consensus 180 q~~il~s~pgig~~~a~~ll~~fg 203 (254)
T COG1948 180 QLYILESIPGIGPKLAERLLKKFG 203 (254)
T ss_pred HHHHHHcCCCccHHHHHHHHHHhc
Confidence 346679999999999999998877
No 249
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=22.69 E-value=58 Score=27.44 Aligned_cols=36 Identities=11% Similarity=0.287 Sum_probs=26.9
Q ss_pred ehhhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHH
Q 033139 29 ALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELD 65 (126)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~ 65 (126)
-+..+.|||+.++..+ +++||..-.-+..++.+.+.
T Consensus 180 Pv~~l~GiG~~~~~~L-~~lGi~TigdL~~~~~~~L~ 215 (422)
T PRK03609 180 PVEEVWGVGRRISKKL-NAMGIKTALDLADTNIRFIR 215 (422)
T ss_pred ChhhcCCccHHHHHHH-HHcCCCcHHHHhcCCHHHHH
Confidence 4578999999999887 67999975555555665554
No 250
>KOG2519 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=22.61 E-value=69 Score=28.18 Aligned_cols=34 Identities=24% Similarity=0.353 Sum_probs=25.9
Q ss_pred cccccchhhccccCCCCeehheehhhhcccccchHHHHHHHhC
Q 033139 7 EDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKAD 49 (126)
Q Consensus 7 ~~~~~mvrI~g~~l~~~K~v~~aLt~IyGIG~~~A~~Ic~~~g 49 (126)
++|-.+.=++|.|--.+ |.|||+..|.++.++.+
T Consensus 217 ~~fidL~lLlGCDYc~~---------I~Gig~~~al~lir~~~ 250 (449)
T KOG2519|consen 217 ESFIDLCLLLGCDYCPT---------IRGIGPKKALKLIRQHG 250 (449)
T ss_pred HHHHHHHHHhcCccccc---------ccccChHHHHHHHHHhc
Confidence 33445555667766555 99999999999999998
No 251
>PF09652 Cas_VVA1548: Putative CRISPR-associated protein (Cas_VVA1548); InterPro: IPR013443 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. This entry represents a conserved region of about 95 amino acids found exclusively in species with CRISPR repeats. In all bacterial species that contain this entry, the genes encoding the proteins are in the midst of a cluster of cas genes.
Probab=22.52 E-value=76 Score=22.07 Aligned_cols=35 Identities=31% Similarity=0.410 Sum_probs=27.5
Q ss_pred cchHHHHHHH--------hCCCCCCcCCCCCHHHHHHHHHHHh
Q 033139 38 RRLANIVCKK--------ADVDMNKRAGELSAAELDQLMVVVA 72 (126)
Q Consensus 38 ~~~A~~Ic~~--------~gI~p~~k~~~Ls~~qi~~L~~~i~ 72 (126)
..+|.++|++ +.+++..+-.+||.+|+.+--.-|+
T Consensus 44 vhLaA~vc~kGa~y~~L~l~lp~e~RG~ELsae~m~~~ga~l~ 86 (93)
T PF09652_consen 44 VHLAAEVCEKGARYYHLSLDLPAEQRGRELSAEQMRACGARLE 86 (93)
T ss_pred HHHHHHHHhCCcEEEEEEccCChHHcCCcccHHHHHhcCCEEE
Confidence 3678999955 5688999999999999987654444
No 252
>COG3181 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.18 E-value=1.6e+02 Score=24.62 Aligned_cols=56 Identities=9% Similarity=0.208 Sum_probs=41.1
Q ss_pred CCCCCHHHHHHHHHHHhCCCCccCChhhh--hccccccCCccceeehhhHHHHHHHHHHHHHhc
Q 033139 56 AGELSAAELDQLMVVVANPRQFKIPDWFL--NRQKDYKDGRYSQVVSNALDMKLRDDLERLKKI 117 (126)
Q Consensus 56 ~~~Ls~~qi~~L~~~i~~~~~~~iP~w~~--nr~~d~~tg~~~h~i~~dL~~~~~~dI~rl~~I 117 (126)
...++++++.++.+++++ -..-|.|-- .++-=..+. .-+.+|...++.|+.|...+
T Consensus 254 p~g~~~e~~~~~~~a~kk--~l~s~e~~~~~~~~~~~~~~----~~~eel~a~i~~~~~~~~~~ 311 (319)
T COG3181 254 PAGTPDEIIAKLSAALKK--ALASPEWQKRLKELGLVPSY----LTGEELKAYIEKEIARWGEL 311 (319)
T ss_pred CCCCCHHHHHHHHHHHHH--HhcCHHHHHHHHhcCCCCcc----CCHHHHHHHHHHHHHHHHHH
Confidence 467899999999999997 566799952 222211111 67789999999999988765
No 253
>PF14794 DUF4479: Domain of unknown function (DUF4479); PDB: 3BU2_C.
Probab=22.11 E-value=74 Score=20.85 Aligned_cols=16 Identities=13% Similarity=0.192 Sum_probs=12.4
Q ss_pred CCCHHHHHHHHHHHhC
Q 033139 58 ELSAAELDQLMVVVAN 73 (126)
Q Consensus 58 ~Ls~~qi~~L~~~i~~ 73 (126)
.||++|++.|.++|++
T Consensus 47 ~Lt~eqv~~LN~~l~~ 62 (73)
T PF14794_consen 47 FLTEEQVAKLNQALQK 62 (73)
T ss_dssp ---HHHHHHHHHHHHH
T ss_pred EcCHHHHHHHHHHHHH
Confidence 6899999999999986
No 254
>PRK08609 hypothetical protein; Provisional
Probab=21.85 E-value=30 Score=30.78 Aligned_cols=32 Identities=25% Similarity=0.405 Sum_probs=23.9
Q ss_pred ehhhhcccccchHHHHHHHhCCCCCCcCCCCC
Q 033139 29 ALTSIKGIGRRLANIVCKKADVDMNKRAGELS 60 (126)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls 60 (126)
.|+.|.|||.++|.+|-+-+.=..-.+..+|.
T Consensus 49 ~l~~ipgIG~~ia~kI~Eil~tG~~~~le~l~ 80 (570)
T PRK08609 49 DFTKLKGIGKGTAEVIQEYRETGESSVLQELK 80 (570)
T ss_pred hhccCCCcCHHHHHHHHHHHHhCChHHHHHHH
Confidence 68999999999999998877544444444443
No 255
>PRK00349 uvrA excinuclease ABC subunit A; Reviewed
Probab=21.77 E-value=78 Score=30.22 Aligned_cols=32 Identities=9% Similarity=0.169 Sum_probs=26.7
Q ss_pred chHHHHHHHhCCCCCCcCCCCCHHHHHHHHHH
Q 033139 39 RLANIVCKKADVDMNKRAGELSAAELDQLMVV 70 (126)
Q Consensus 39 ~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L~~~ 70 (126)
..-..+|+..|||++++.++|+++|.+.|-.=
T Consensus 322 ~~l~~~~~~~g~~~~~p~~~l~~~~~~~ll~g 353 (943)
T PRK00349 322 QMLKSLAEHYGFDLDTPWKDLPEEVQDIILYG 353 (943)
T ss_pred HHHHHHHHHcCCCCCCchHHCCHHHHHHHcCC
Confidence 34566899999999999999999998776553
No 256
>PTZ00205 DNA polymerase kappa; Provisional
Probab=21.69 E-value=76 Score=28.71 Aligned_cols=27 Identities=19% Similarity=0.420 Sum_probs=21.4
Q ss_pred ehhhhcccccchHHHHHHHhCCCCCCcCCCC
Q 033139 29 ALTSIKGIGRRLANIVCKKADVDMNKRAGEL 59 (126)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~L 59 (126)
-++.++|||+.++.. ++.+||.. +++|
T Consensus 310 pV~ki~GIG~~t~~~-L~~~GI~T---igDL 336 (571)
T PTZ00205 310 GLRSVPGVGKVTEAL-LKGLGITT---LSDI 336 (571)
T ss_pred CcceeCCcCHHHHHH-HHHcCCCc---HHHH
Confidence 568999999999965 57899985 5554
No 257
>COG0394 Wzb Protein-tyrosine-phosphatase [Signal transduction mechanisms]
Probab=21.64 E-value=1e+02 Score=22.26 Aligned_cols=27 Identities=22% Similarity=0.366 Sum_probs=23.8
Q ss_pred chHHHHHHHhCCCCC-CcCCCCCHHHHH
Q 033139 39 RLANIVCKKADVDMN-KRAGELSAAELD 65 (126)
Q Consensus 39 ~~A~~Ic~~~gI~p~-~k~~~Ls~~qi~ 65 (126)
..|.+++++.||+.+ .+.+.+++++..
T Consensus 48 ~~a~~vl~e~Gid~~~~~~k~i~~~~~~ 75 (139)
T COG0394 48 PRAVEVLAEHGIDISGHRSKQLTEEDFD 75 (139)
T ss_pred HHHHHHHHHcCCCcCCccCccCchhhhh
Confidence 568889999999999 799999999884
No 258
>PF12114 Period_C: Period protein 2/3C-terminal region; InterPro: IPR022728 This domain is found in eukaryotes and is typically between 164 to 200 amino acids in length. Sequences represented by this entry are found C-terminal to PF08447 from PFAM.
Probab=21.53 E-value=71 Score=24.96 Aligned_cols=40 Identities=25% Similarity=0.358 Sum_probs=32.7
Q ss_pred CChhhhhccccccCCccceeehhhHHHHHHHHHHHHHhcc
Q 033139 79 IPDWFLNRQKDYKDGRYSQVVSNALDMKLRDDLERLKKIR 118 (126)
Q Consensus 79 iP~w~~nr~~d~~tg~~~h~i~~dL~~~~~~dI~rl~~I~ 118 (126)
=|.|++..+-|..-==..++=..|+..-+++|.++|+.+.
T Consensus 94 dPiWl~~~~t~~~vmmtYQ~p~R~~e~VLkeD~ekLk~mq 133 (195)
T PF12114_consen 94 DPIWLMMANTDEDVMMTYQMPERDLEEVLKEDREKLKSMQ 133 (195)
T ss_pred CCcchhhccCChhHeEEeecCcccHHHHHHHHHHHHHHHH
Confidence 4999988887766555566778899999999999999875
No 259
>PF09397 Ftsk_gamma: Ftsk gamma domain; InterPro: IPR018541 This domain directs oriented DNA translocation and forms a winged helix structure []. Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding []. ; PDB: 2VE9_B 2VE8_E 2J5O_A 2J5P_A.
Probab=21.02 E-value=53 Score=21.15 Aligned_cols=26 Identities=15% Similarity=0.047 Sum_probs=18.7
Q ss_pred CeehheehhhhcccccchHHHHHHHh
Q 033139 23 KQKIMFALTSIKGIGRRLANIVCKKA 48 (126)
Q Consensus 23 ~K~v~~aLt~IyGIG~~~A~~Ic~~~ 48 (126)
.+.-...|+.-++||+..|..|++.+
T Consensus 19 ~~~S~S~lQR~~rIGynrAariid~L 44 (65)
T PF09397_consen 19 GKASISLLQRKFRIGYNRAARIIDQL 44 (65)
T ss_dssp TCECHHHHHHHHT--HHHHHHHHHHH
T ss_pred CCccHHHHHHHhCCCHHHHHHHHHHH
Confidence 34445568999999999999998765
No 260
>KOG1647 consensus Vacuolar H+-ATPase V1 sector, subunit D [Energy production and conversion]
Probab=20.81 E-value=73 Score=25.78 Aligned_cols=53 Identities=26% Similarity=0.316 Sum_probs=37.8
Q ss_pred HHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCCccCChhhhhccccccCCccceeehhhHHHHHHHHHHHHHhcccc
Q 033139 43 IVCKKADVDMNKRAGELSAAELDQLMVVVANPRQFKIPDWFLNRQKDYKDGRYSQVVSNALDMKLRDDLERLKKIRYG 120 (126)
Q Consensus 43 ~Ic~~~gI~p~~k~~~Ls~~qi~~L~~~i~~~~~~~iP~w~~nr~~d~~tg~~~h~i~~dL~~~~~~dI~rl~~I~sy 120 (126)
.+++.+-...+.+++.|..--|-+|.+.+. | |.++|...-|+|.=||++|..+
T Consensus 156 ~~Lde~ik~TNrRVNAiEhvIIPrlenTi~----Y---------------------I~sELdE~eRedF~RLKKiQ~~ 208 (255)
T KOG1647|consen 156 RTLDEAIKVTNRRVNAIEHVIIPRLENTIA----Y---------------------IVSELDELEREDFYRLKKIQAK 208 (255)
T ss_pred HHHHHHHHHHhhhhhhhhhhhhhhhhhHHH----H---------------------HHHHHHHHHHHHHHHHHHHHHH
Confidence 344444455566666666666666666663 4 8999999999999999998754
No 261
>COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair]
Probab=20.79 E-value=55 Score=27.75 Aligned_cols=34 Identities=15% Similarity=0.310 Sum_probs=26.1
Q ss_pred ccchhhccccCCCCeehheehhhhcccccchHHHHHH
Q 033139 10 QHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCK 46 (126)
Q Consensus 10 ~~mvrI~g~~l~~~K~v~~aLt~IyGIG~~~A~~Ic~ 46 (126)
+.++.-.|-.+|++.. .|..+.|||+.+|.+|+.
T Consensus 98 ~~v~~~~~G~~P~~~~---~l~~LpGiG~yTa~Ail~ 131 (342)
T COG1194 98 QEVVERHGGEFPDDEE---ELAALPGVGPYTAGAILS 131 (342)
T ss_pred HHHHHHcCCCCCCCHH---HHHhCCCCcHHHHHHHHH
Confidence 4566667777887754 456699999999999974
No 262
>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=20.74 E-value=97 Score=18.70 Aligned_cols=16 Identities=25% Similarity=0.306 Sum_probs=14.6
Q ss_pred CCCHHHHHHHHHHHhC
Q 033139 58 ELSAAELDQLMVVVAN 73 (126)
Q Consensus 58 ~Ls~~qi~~L~~~i~~ 73 (126)
.||++|+..|..+|++
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 7999999999999874
No 263
>PRK05416 glmZ(sRNA)-inactivating NTPase; Provisional
Probab=20.73 E-value=3.5e+02 Score=21.95 Aligned_cols=44 Identities=18% Similarity=0.273 Sum_probs=36.9
Q ss_pred heehhhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 033139 27 MFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVAN 73 (126)
Q Consensus 27 ~~aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L~~~i~~ 73 (126)
.+.++...|-|++++.++++..|.. -+..+..+.+..+.+.+++
T Consensus 8 ~i~i~G~~GsGKtt~~~~l~~~g~~---~~d~~~~~L~~~l~~~~~~ 51 (288)
T PRK05416 8 LVIVTGLSGAGKSVALRALEDLGYY---CVDNLPPSLLPKLVELLAQ 51 (288)
T ss_pred EEEEECCCCCcHHHHHHHHHHcCCe---EECCcCHHHHHHHHHHHHh
Confidence 5788999999999999999988874 3788888888888777765
No 264
>PRK03103 DNA polymerase IV; Reviewed
Probab=20.71 E-value=74 Score=26.58 Aligned_cols=35 Identities=11% Similarity=0.281 Sum_probs=24.5
Q ss_pred ehhhhcccccchHHHHHHHhCCCCCCcCCCCCHHHH
Q 033139 29 ALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAEL 64 (126)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi 64 (126)
-+..+.|||+.++.. ++.+||..=.-+-.++.+++
T Consensus 182 pi~~l~gig~~~~~~-L~~~Gi~tigdl~~~~~~~L 216 (409)
T PRK03103 182 PVRKLFGVGSRMEKH-LRRMGIRTIGQLANTPLERL 216 (409)
T ss_pred CHhhcCCccHHHHHH-HHHcCCCCHHHHhcCCHHHH
Confidence 457889999998888 57899975444444455544
No 265
>PF01595 DUF21: Domain of unknown function DUF21; InterPro: IPR002550 This transmembrane region has no known function. Many of the sequences in this family are annotated as hemolysins, however this is due to a similarity to Q54318 from SWISSPROT that does not contain this domain. This domain is found in the N terminus of the proteins adjacent to two intracellular CBS domains (IPR000644 from INTERPRO).
Probab=20.69 E-value=1.4e+02 Score=21.45 Aligned_cols=42 Identities=14% Similarity=0.089 Sum_probs=33.5
Q ss_pred hhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 033139 31 TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVAN 73 (126)
Q Consensus 31 t~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L~~~i~~ 73 (126)
.=+--++...+..+++..|.++ ..-..+|++|+..+.+.-++
T Consensus 134 ~P~~~~l~~i~~~~~~~~~~~~-~~~~~~s~eel~~lv~~~~e 175 (183)
T PF01595_consen 134 YPLVWLLSFISNKILKLFGIEN-EEDPAVSEEELRSLVEEGEE 175 (183)
T ss_pred HHHHHHHHHHHHHHHHHhCCCc-cccCCCCHHHHHHHHHhHHH
Confidence 3344456678889999999998 78888999999998887664
No 266
>PRK06826 dnaE DNA polymerase III DnaE; Reviewed
Probab=20.69 E-value=57 Score=31.82 Aligned_cols=47 Identities=15% Similarity=0.369 Sum_probs=32.7
Q ss_pred CeehheehhhhcccccchHHHHHHHhCC-CC---------CCcCCCCCHHHHHHHHH
Q 033139 23 KQKIMFALTSIKGIGRRLANIVCKKADV-DM---------NKRAGELSAAELDQLMV 69 (126)
Q Consensus 23 ~K~v~~aLt~IyGIG~~~A~~Ic~~~gI-~p---------~~k~~~Ls~~qi~~L~~ 69 (126)
+..|.++|..|+|||...|..|.+.=.- .| ....+.++...++.|.+
T Consensus 819 ~~~Ir~gL~aIkgvg~~~~~~Iv~~R~~~g~f~s~~Df~~R~~~~~~nk~~le~Li~ 875 (1151)
T PRK06826 819 GDKIRFGLAAVKNVGENAIDSIVEEREKKGKFKSLVDFCERVDTSQINKRAVESLIK 875 (1151)
T ss_pred CCEEEechhhcCCCCHHHHHHHHHHHHhCCCCCCHHHHHHHhcccCCCHHHHHHHHH
Confidence 4579999999999999999999865421 11 11233567777776654
No 267
>PHA00439 exonuclease
Probab=20.62 E-value=47 Score=27.40 Aligned_cols=16 Identities=25% Similarity=0.380 Sum_probs=14.4
Q ss_pred hhhcccccchHHHHHHH
Q 033139 31 TSIKGIGRRLANIVCKK 47 (126)
Q Consensus 31 t~IyGIG~~~A~~Ic~~ 47 (126)
..+.||| .+|.++++.
T Consensus 191 PGVpGIG-KTA~kLL~~ 206 (286)
T PHA00439 191 SGIPGWG-DTAEAFLEN 206 (286)
T ss_pred CCCCCcC-HHHHHHHhC
Confidence 4689999 999999987
No 268
>PRK14133 DNA polymerase IV; Provisional
Probab=20.51 E-value=67 Score=26.19 Aligned_cols=36 Identities=17% Similarity=0.241 Sum_probs=26.3
Q ss_pred ehhhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHH
Q 033139 29 ALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELD 65 (126)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~ 65 (126)
-+..+.|||+.++..+ +++||..=.-+-.++.+++.
T Consensus 174 pv~~l~gig~~~~~~L-~~~Gi~ti~dl~~l~~~~L~ 209 (347)
T PRK14133 174 PISKVHGIGKKSVEKL-NNIGIYTIEDLLKLSREFLI 209 (347)
T ss_pred CccccCCCCHHHHHHH-HHcCCccHHHHhhCCHHHHH
Confidence 4577899999999985 78999875555555655553
No 269
>TIGR02019 BchJ bacteriochlorophyll 4-vinyl reductase. This model represents the component of bacteriochlorophyll synthetase responsible for reduction of the B-ring pendant ethylene (4-vinyl) group. It appears that this step must precede the reduction of ring D, at least by the "dark" protochlorophyllide reductase enzymes BchN, BchB and BchL. This family appears to be present in photosynthetic bacteria except for the cyanobacterial clade. Cyanobacteria must use a non-orthologous gene to carry out this required step for the biosynthesis of both bacteriochlorophyll and chlorophyll.
Probab=20.49 E-value=2.4e+02 Score=21.84 Aligned_cols=38 Identities=16% Similarity=0.189 Sum_probs=32.1
Q ss_pred cccchHHHHHHHhCCCC---CCcCCCCCHHHHHHHHHHHhC
Q 033139 36 IGRRLANIVCKKADVDM---NKRAGELSAAELDQLMVVVAN 73 (126)
Q Consensus 36 IG~~~A~~Ic~~~gI~p---~~k~~~Ls~~qi~~L~~~i~~ 73 (126)
.|+..+..+++.+|.+. +..-.-++++++..|.+.++.
T Consensus 18 ~g~~~~~~~~~~~g~~~~~~~~p~~mv~E~~~~aL~~aL~~ 58 (188)
T TIGR02019 18 YGPGAADRALAAAGQGVLRPGPPSGMLPESQFSTLHRWLRD 58 (188)
T ss_pred cCHHHHHHHHHHcCcccccCCCchhcCCHHHHHHHHHHHHH
Confidence 47889999999999994 555566789999999999986
No 270
>PRK12277 50S ribosomal protein L13e; Provisional
Probab=20.32 E-value=87 Score=21.36 Aligned_cols=28 Identities=14% Similarity=0.332 Sum_probs=22.2
Q ss_pred HHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 033139 46 KKADVDMNKRAGELSAAELDQLMVVVAN 73 (126)
Q Consensus 46 ~~~gI~p~~k~~~Ls~~qi~~L~~~i~~ 73 (126)
..+||.-|.+=.+.+++-+++|.++.++
T Consensus 50 rtiGI~VD~RRrn~~~eNVerLk~y~sk 77 (83)
T PRK12277 50 RKLGIRVDKRRKTVHEENVEALKKFLEQ 77 (83)
T ss_pred cccCeeecccccCCCHHHHHHHHHHHHH
Confidence 3446666777888899999999999875
No 271
>PRK14549 50S ribosomal protein L29P; Provisional
Probab=20.31 E-value=82 Score=20.32 Aligned_cols=54 Identities=15% Similarity=0.165 Sum_probs=32.1
Q ss_pred CCCCCHHHHHHHHHHHhCCCCccCChhhhhccccccCCccceeehhhHHHHHHHHHHHHHhccc
Q 033139 56 AGELSAAELDQLMVVVANPRQFKIPDWFLNRQKDYKDGRYSQVVSNALDMKLRDDLERLKKIRY 119 (126)
Q Consensus 56 ~~~Ls~~qi~~L~~~i~~~~~~~iP~w~~nr~~d~~tg~~~h~i~~dL~~~~~~dI~rl~~I~s 119 (126)
+.+||.+|+......+.. .+ +|-|-.-.||.. +-.+-..+.++-||.|+..+-+
T Consensus 9 lr~ls~~eL~~~l~elk~--eL------f~LR~q~~~~~~--l~n~~~ir~~Rk~IARi~Tvl~ 62 (69)
T PRK14549 9 IREMSPEEREEKLEELKL--EL------LKERAQAAMGGA--PENPGRIREIRRTIARILTIQR 62 (69)
T ss_pred HHhCCHHHHHHHHHHHHH--HH------HHHHHHHHhCcC--ccccHHHHHHHHHHHHHHHHHH
Confidence 567788888766666654 23 333333333321 1122346889999999988754
No 272
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=20.28 E-value=1.5e+02 Score=17.48 Aligned_cols=37 Identities=16% Similarity=0.251 Sum_probs=21.5
Q ss_pred ehhhhcccccchHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHh
Q 033139 29 ALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVA 72 (126)
Q Consensus 29 aLt~IyGIG~~~A~~Ic~~~gI~p~~k~~~Ls~~qi~~L~~~i~ 72 (126)
.|..--||.+.+...++. .+...++-+.+.+|.+++.
T Consensus 15 ~La~~~gis~~tl~~~~~-------~~~~~~~~~~l~~ia~~l~ 51 (63)
T PF13443_consen 15 DLARKTGISRSTLSRILN-------GKPSNPSLDTLEKIAKALN 51 (63)
T ss_dssp HHHHHHT--HHHHHHHHT-------TT-----HHHHHHHHHHHT
T ss_pred HHHHHHCcCHHHHHHHHh-------cccccccHHHHHHHHHHcC
Confidence 345566777777777774 2356788899999999886
No 273
>PRK13620 psbV cytochrome c-550; Provisional
Probab=20.11 E-value=1.1e+02 Score=24.44 Aligned_cols=17 Identities=12% Similarity=0.120 Sum_probs=14.6
Q ss_pred CCCCCHHHHHHHHHHHh
Q 033139 56 AGELSAAELDQLMVVVA 72 (126)
Q Consensus 56 ~~~Ls~~qi~~L~~~i~ 72 (126)
+.+||++++..|...|=
T Consensus 182 ~r~LtdedL~aIa~~IL 198 (215)
T PRK13620 182 MRNLTEDDLVAISGHIL 198 (215)
T ss_pred cCCCCHHHHHHHHHHHh
Confidence 57899999999999864
Done!