Query psy1365
Match_columns 140
No_of_seqs 120 out of 943
Neff 5.9
Searched_HMMs 46136
Date Fri Aug 16 16:43:57 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1365.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1365hhsearch_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 2.4E-62 5.2E-67 372.4 10.3 137 1-140 18-154 (154)
2 PRK04053 rps13p 30S ribosomal 100.0 2.8E-61 6.1E-66 365.0 11.6 137 1-140 13-149 (149)
3 TIGR03629 arch_S13P archaeal r 100.0 3.9E-61 8.4E-66 362.6 11.5 136 1-140 9-144 (144)
4 COG0099 RpsM Ribosomal protein 100.0 1.5E-50 3.3E-55 295.0 8.2 115 1-140 5-121 (121)
5 CHL00137 rps13 ribosomal prote 100.0 3.2E-47 6.9E-52 280.0 9.6 107 1-132 5-111 (122)
6 TIGR03631 bact_S13 30S ribosom 100.0 7E-47 1.5E-51 275.0 9.9 109 1-134 3-111 (113)
7 PRK05179 rpsM 30S ribosomal pr 100.0 6.9E-47 1.5E-51 278.3 9.9 107 1-132 5-111 (122)
8 KOG3311|consensus 100.0 8.1E-47 1.8E-51 284.5 7.5 137 1-140 16-152 (152)
9 PF00416 Ribosomal_S13: Riboso 100.0 3.6E-46 7.8E-51 268.3 3.9 105 1-130 3-107 (107)
10 PF06831 H2TH: Formamidopyrimi 97.2 0.00031 6.7E-09 49.1 2.8 50 8-57 23-75 (92)
11 PRK01103 formamidopyrimidine/5 97.0 0.0007 1.5E-08 55.6 3.5 52 7-58 154-208 (274)
12 PRK14810 formamidopyrimidine-D 96.5 0.0027 5.9E-08 52.2 3.6 50 8-57 154-206 (272)
13 PRK14811 formamidopyrimidine-D 96.3 0.0049 1.1E-07 50.7 4.1 50 8-57 143-195 (269)
14 PRK10445 endonuclease VIII; Pr 96.2 0.0057 1.2E-07 50.1 3.9 51 8-58 151-204 (263)
15 PRK13945 formamidopyrimidine-D 96.2 0.0063 1.4E-07 50.2 4.2 49 9-57 165-216 (282)
16 TIGR00577 fpg formamidopyrimid 96.1 0.0065 1.4E-07 49.9 3.7 50 9-58 156-208 (272)
17 PRK04184 DNA topoisomerase VI 95.9 0.0085 1.8E-07 53.9 3.7 49 11-59 259-307 (535)
18 TIGR01052 top6b DNA topoisomer 94.4 0.04 8.6E-07 49.2 3.5 54 11-65 250-306 (488)
19 PF05833 FbpA: Fibronectin-bin 93.8 0.019 4E-07 49.6 0.2 49 9-57 187-236 (455)
20 COG0266 Nei Formamidopyrimidin 93.7 0.083 1.8E-06 44.0 3.8 49 9-57 156-207 (273)
21 PF00633 HHH: Helix-hairpin-he 93.6 0.031 6.7E-07 31.5 0.8 18 14-31 12-29 (30)
22 COG1389 DNA topoisomerase VI, 92.5 0.1 2.2E-06 46.7 2.7 48 12-59 260-311 (538)
23 KOG3311|consensus 91.9 0.025 5.5E-07 43.3 -1.4 48 83-132 66-113 (152)
24 PF11798 IMS_HHH: IMS family H 90.3 0.13 2.8E-06 29.2 0.8 21 14-35 12-32 (32)
25 PF14520 HHH_5: Helix-hairpin- 88.1 0.042 9.2E-07 34.9 -2.6 36 11-47 3-38 (60)
26 PF10391 DNA_pol_lambd_f: Fing 88.0 0.23 5E-06 31.3 0.9 22 14-36 3-24 (52)
27 PRK00274 ksgA 16S ribosomal RN 87.8 0.34 7.3E-06 39.4 1.9 49 9-58 222-270 (272)
28 COG3743 Uncharacterized conser 87.2 0.37 8E-06 36.2 1.6 43 14-57 68-110 (133)
29 TIGR00275 flavoprotein, HI0933 86.6 0.63 1.4E-05 39.7 3.0 49 9-59 284-332 (400)
30 smart00278 HhH1 Helix-hairpin- 86.2 0.37 8.1E-06 25.8 0.9 19 14-32 2-20 (26)
31 PRK02515 psbU photosystem II c 86.1 0.31 6.7E-06 36.6 0.7 55 5-59 53-110 (132)
32 COG0030 KsgA Dimethyladenosine 85.9 0.44 9.5E-06 39.4 1.6 46 8-58 211-256 (259)
33 PRK14606 ruvA Holliday junctio 82.7 0.56 1.2E-05 36.8 0.8 21 13-33 108-128 (188)
34 PF14579 HHH_6: Helix-hairpin- 82.1 1.1 2.5E-05 30.6 2.1 27 8-34 22-48 (90)
35 PF09883 DUF2110: Uncharacteri 81.8 4.2 9E-05 33.1 5.5 51 8-58 96-158 (225)
36 TIGR00755 ksgA dimethyladenosi 81.7 0.85 1.8E-05 36.5 1.6 46 8-55 207-252 (253)
37 PRK14601 ruvA Holliday junctio 81.7 0.64 1.4E-05 36.4 0.8 21 13-33 108-128 (183)
38 PF03486 HI0933_like: HI0933-l 81.5 1.4 2.9E-05 38.4 2.9 50 7-58 289-339 (409)
39 PRK14603 ruvA Holliday junctio 80.7 0.72 1.6E-05 36.4 0.8 20 13-32 107-126 (197)
40 PRK14604 ruvA Holliday junctio 80.4 0.75 1.6E-05 36.3 0.8 21 13-33 108-128 (195)
41 PRK13901 ruvA Holliday junctio 79.9 0.79 1.7E-05 36.4 0.8 21 13-33 107-127 (196)
42 PRK14602 ruvA Holliday junctio 79.5 0.85 1.8E-05 36.2 0.9 19 14-32 110-128 (203)
43 COG0632 RuvA Holliday junction 79.4 0.92 2E-05 36.2 1.1 21 13-33 108-128 (201)
44 TIGR03252 uncharacterized HhH- 79.4 0.51 1.1E-05 37.0 -0.3 30 6-35 108-137 (177)
45 PF00398 RrnaAD: Ribosomal RNA 79.3 0.6 1.3E-05 37.7 -0.0 49 7-57 213-261 (262)
46 COG1293 Predicted RNA-binding 78.9 2 4.3E-05 39.0 3.2 47 12-58 189-235 (564)
47 PRK14600 ruvA Holliday junctio 74.7 1.5 3.2E-05 34.4 1.0 19 13-32 108-126 (186)
48 PRK14605 ruvA Holliday junctio 73.0 1.5 3.3E-05 34.4 0.8 17 14-30 109-125 (194)
49 PF14520 HHH_5: Helix-hairpin- 72.6 2 4.3E-05 27.1 1.1 20 14-33 39-58 (60)
50 PF12836 HHH_3: Helix-hairpin- 71.8 1.1 2.5E-05 28.8 -0.2 43 11-53 12-61 (65)
51 PRK12278 50S ribosomal protein 70.8 3.2 7E-05 33.6 2.2 54 13-67 158-211 (221)
52 cd00080 HhH2_motif Helix-hairp 70.6 2.5 5.4E-05 28.1 1.3 20 15-34 24-43 (75)
53 PF11731 Cdd1: Pathogenicity l 70.6 2.6 5.7E-05 29.8 1.4 37 13-50 12-48 (93)
54 PRK00116 ruvA Holliday junctio 70.5 2.2 4.9E-05 33.2 1.2 25 11-35 71-95 (192)
55 smart00279 HhH2 Helix-hairpin- 68.7 2.9 6.3E-05 24.3 1.1 17 16-32 19-35 (36)
56 PRK12311 rpsB 30S ribosomal pr 68.5 2.5 5.4E-05 36.0 1.1 44 13-57 263-306 (326)
57 PF02371 Transposase_20: Trans 68.4 2.9 6.4E-05 28.3 1.3 23 14-37 3-25 (87)
58 PF14716 HHH_8: Helix-hairpin- 68.2 2.5 5.5E-05 27.4 0.9 20 14-33 48-67 (68)
59 cd00056 ENDO3c endonuclease II 67.8 2.2 4.8E-05 31.4 0.6 24 9-32 79-102 (158)
60 PF02042 RWP-RK: RWP-RK domain 66.6 4.4 9.5E-05 25.7 1.7 26 18-43 24-51 (52)
61 PF11338 DUF3140: Protein of u 66.3 9.6 0.00021 26.9 3.5 35 19-57 33-67 (92)
62 smart00478 ENDO3c endonuclease 66.2 2.7 6E-05 30.6 0.8 22 12-33 71-92 (149)
63 TIGR01259 comE comEA protein. 65.8 3.1 6.8E-05 30.2 1.1 29 7-35 62-90 (120)
64 PF14490 HHH_4: Helix-hairpin- 65.1 3.1 6.8E-05 28.6 0.9 23 16-38 49-71 (94)
65 TIGR00084 ruvA Holliday juncti 64.8 3 6.6E-05 32.7 0.9 19 13-31 107-125 (191)
66 smart00483 POLXc DNA polymeras 64.5 3.5 7.6E-05 34.9 1.2 25 12-37 88-112 (334)
67 PRK01229 N-glycosylase/DNA lya 63.8 3.8 8.2E-05 32.8 1.2 41 12-56 117-158 (208)
68 PF12826 HHH_2: Helix-hairpin- 63.7 2.9 6.4E-05 26.9 0.5 18 17-34 7-24 (64)
69 TIGR00426 competence protein C 62.8 3.1 6.7E-05 26.8 0.5 22 12-33 15-37 (69)
70 cd00141 NT_POLXc Nucleotidyltr 62.3 4.2 9E-05 34.0 1.3 24 13-37 85-108 (307)
71 PRK10702 endonuclease III; Pro 61.7 4 8.6E-05 32.5 1.0 22 12-33 108-129 (211)
72 TIGR01083 nth endonuclease III 61.6 3.5 7.6E-05 31.9 0.7 22 12-33 105-126 (191)
73 PRK14605 ruvA Holliday junctio 61.3 1.6 3.5E-05 34.3 -1.2 27 8-34 68-94 (194)
74 COG2231 Uncharacterized protei 60.8 6.7 0.00015 31.7 2.2 40 4-43 104-145 (215)
75 PRK08609 hypothetical protein; 58.4 5.8 0.00013 36.0 1.6 24 13-36 88-111 (570)
76 PHA02564 V virion protein; Pro 58.2 17 0.00036 27.5 3.8 32 25-57 87-118 (141)
77 COG2081 Predicted flavoprotein 57.0 12 0.00025 33.1 3.2 38 20-58 295-332 (408)
78 PRK12766 50S ribosomal protein 55.2 6.2 0.00013 32.2 1.1 38 14-52 4-41 (232)
79 TIGR01084 mutY A/G-specific ad 54.4 6.3 0.00014 32.6 1.1 22 12-33 104-125 (275)
80 PRK13913 3-methyladenine DNA g 53.5 9 0.0002 30.8 1.8 28 12-39 120-147 (218)
81 COG0353 RecR Recombinational D 52.4 9.3 0.0002 30.5 1.7 86 11-116 10-108 (198)
82 PRK10880 adenine DNA glycosyla 51.7 6.6 0.00014 33.7 0.8 23 11-33 107-129 (350)
83 PF01367 5_3_exonuc: 5'-3' exo 51.6 2.5 5.5E-05 30.0 -1.5 19 16-34 21-39 (101)
84 PRK13910 DNA glycosylase MutY; 51.4 6.7 0.00015 32.8 0.8 22 12-33 71-92 (289)
85 COG0258 Exo 5'-3' exonuclease 51.3 9.6 0.00021 31.6 1.7 17 18-34 203-219 (310)
86 PRK00076 recR recombination pr 50.8 8.9 0.00019 30.5 1.4 40 11-58 9-48 (196)
87 TIGR00084 ruvA Holliday juncti 50.1 1.9 4.2E-05 33.8 -2.5 25 8-32 67-91 (191)
88 TIGR00615 recR recombination p 50.1 9.3 0.0002 30.4 1.4 39 11-57 9-47 (195)
89 TIGR01448 recD_rel helicase, p 49.9 14 0.00031 34.4 2.7 41 17-57 88-138 (720)
90 PRK14602 ruvA Holliday junctio 49.1 4.2 9.2E-05 32.2 -0.7 26 9-34 70-95 (203)
91 PRK00116 ruvA Holliday junctio 48.6 8.1 0.00018 30.1 0.8 21 14-34 109-129 (192)
92 TIGR00588 ogg 8-oxoguanine DNA 47.5 8.2 0.00018 32.3 0.7 30 11-40 218-247 (310)
93 PRK13844 recombination protein 47.0 11 0.00024 30.1 1.3 40 11-58 13-52 (200)
94 PRK10308 3-methyl-adenine DNA 46.5 11 0.00024 31.2 1.4 33 11-43 205-238 (283)
95 PRK12373 NADH dehydrogenase su 46.4 15 0.00032 32.3 2.2 54 14-68 324-377 (400)
96 COG0177 Nth Predicted EndoIII- 45.0 23 0.00051 28.4 2.9 40 13-56 109-148 (211)
97 cd01104 HTH_MlrA-CarA Helix-Tu 44.6 43 0.00093 20.7 3.7 43 15-57 6-52 (68)
98 PRK07373 DNA polymerase III su 43.8 16 0.00034 32.4 1.9 25 8-32 109-133 (449)
99 PRK14606 ruvA Holliday junctio 43.6 2.6 5.6E-05 33.1 -2.7 26 8-33 68-93 (188)
100 COG0122 AlkA 3-methyladenine D 43.4 11 0.00023 31.5 0.8 23 11-33 196-218 (285)
101 PRK14601 ruvA Holliday junctio 41.9 4.1 8.8E-05 31.9 -1.8 25 8-32 68-92 (183)
102 PF01698 FLO_LFY: Floricaula / 41.8 8.6 0.00019 33.6 0.0 41 17-59 56-96 (386)
103 PRK14600 ruvA Holliday junctio 41.6 4.2 9.1E-05 31.9 -1.8 26 8-33 68-93 (186)
104 smart00475 53EXOc 5'-3' exonuc 41.6 15 0.00032 30.1 1.3 20 15-34 188-207 (259)
105 cd00008 53EXOc 5'-3' exonuclea 41.6 15 0.00032 29.5 1.3 20 15-34 185-204 (240)
106 PRK14603 ruvA Holliday junctio 41.4 4.1 9E-05 32.1 -1.9 26 8-33 67-92 (197)
107 smart00389 HOX Homeodomain. DN 40.8 9.9 0.00022 22.7 0.2 30 43-73 24-53 (56)
108 PRK09482 flap endonuclease-lik 40.0 16 0.00036 30.0 1.4 20 15-34 184-203 (256)
109 PRK00558 uvrC excinuclease ABC 39.8 18 0.00039 33.1 1.7 43 8-52 538-580 (598)
110 PRK14604 ruvA Holliday junctio 39.4 13 0.00028 29.3 0.7 24 9-32 69-92 (195)
111 PRK05898 dnaE DNA polymerase I 39.0 45 0.00097 32.6 4.3 46 8-53 747-801 (971)
112 PRK13901 ruvA Holliday junctio 38.1 5.1 0.00011 31.8 -1.8 26 8-33 67-92 (196)
113 COG1936 Predicted nucleotide k 38.0 24 0.00051 27.9 1.9 25 12-36 2-26 (180)
114 PRK14976 5'-3' exonuclease; Pr 37.6 18 0.00039 29.9 1.3 19 16-34 194-212 (281)
115 PRK14671 uvrC excinuclease ABC 36.7 19 0.00042 33.2 1.5 42 9-52 565-606 (621)
116 PF14635 HHH_7: Helix-hairpin- 36.7 20 0.00043 25.7 1.2 25 10-34 47-71 (104)
117 cd01702 PolY_Pol_eta DNA Polym 35.7 20 0.00043 30.5 1.3 37 14-50 183-221 (359)
118 KOG0843|consensus 34.2 84 0.0018 25.1 4.4 50 22-72 84-154 (197)
119 PRK14896 ksgA 16S ribosomal RN 34.0 35 0.00076 27.3 2.4 31 28-58 225-256 (258)
120 COG1555 ComEA DNA uptake prote 32.6 30 0.00065 26.1 1.7 30 14-43 98-128 (149)
121 COG0632 RuvA Holliday junction 32.6 5.1 0.00011 32.0 -2.6 26 8-33 68-93 (201)
122 COG2938 Uncharacterized conser 32.5 68 0.0015 22.7 3.4 33 40-73 40-72 (94)
123 COG2145 ThiM Hydroxyethylthiaz 31.8 60 0.0013 27.1 3.4 57 40-110 62-119 (265)
124 PRK07945 hypothetical protein; 31.7 25 0.00055 29.7 1.3 21 14-34 50-70 (335)
125 PTZ00338 dimethyladenosine tra 31.5 43 0.00093 27.8 2.6 32 26-58 257-288 (294)
126 PF13442 Cytochrome_CBB3: Cyto 31.3 47 0.001 20.6 2.2 14 43-56 54-67 (67)
127 cd00086 homeodomain Homeodomai 30.6 13 0.00029 22.2 -0.4 28 44-72 25-52 (59)
128 PF04760 IF2_N: Translation in 30.6 19 0.00041 22.0 0.2 44 14-57 8-52 (54)
129 PF06514 PsbU: Photosystem II 30.1 41 0.00088 23.8 1.9 58 2-59 12-72 (93)
130 PF00046 Homeobox: Homeobox do 29.5 10 0.00022 23.0 -1.1 14 44-57 7-20 (57)
131 KOG0492|consensus 29.1 59 0.0013 26.6 2.9 60 28-104 134-212 (246)
132 cd00128 XPG Xeroderma pigmento 28.6 31 0.00067 28.5 1.2 19 16-34 226-244 (316)
133 PRK13766 Hef nuclease; Provisi 28.5 29 0.00063 32.0 1.2 23 12-34 714-736 (773)
134 PRK14669 uvrC excinuclease ABC 28.4 33 0.00071 31.8 1.5 24 11-34 550-573 (624)
135 COG1111 MPH1 ERCC4-like helica 28.4 64 0.0014 29.5 3.2 86 7-112 160-249 (542)
136 PF02318 FYVE_2: FYVE-type zin 28.3 69 0.0015 22.9 2.9 17 42-58 1-17 (118)
137 PRK14667 uvrC excinuclease ABC 28.2 31 0.00068 31.5 1.3 43 8-52 509-551 (567)
138 PF00542 Ribosomal_L12: Riboso 28.0 23 0.00051 23.3 0.4 45 11-58 16-60 (68)
139 PRK00919 GMP synthase subunit 27.9 1.7E+02 0.0037 24.6 5.6 80 35-120 154-237 (307)
140 PRK14670 uvrC excinuclease ABC 27.1 34 0.00073 31.4 1.3 40 11-52 512-551 (574)
141 KOG2875|consensus 27.0 25 0.00054 29.9 0.5 22 11-32 216-237 (323)
142 COG1059 Thermostable 8-oxoguan 27.0 21 0.00046 28.6 0.0 25 12-36 120-144 (210)
143 PRK03980 flap endonuclease-1; 26.6 34 0.00074 28.5 1.2 18 17-34 193-210 (292)
144 KOG0650|consensus 26.6 1.1E+02 0.0024 28.7 4.5 40 39-85 145-184 (733)
145 PF14794 DUF4479: Domain of un 26.5 54 0.0012 21.9 1.9 16 43-58 47-62 (73)
146 PF02697 DUF217: Uncharacteriz 26.3 48 0.001 22.1 1.6 47 11-57 10-61 (71)
147 PF14053 DUF4248: Domain of un 24.8 1E+02 0.0022 20.3 3.0 45 12-58 10-68 (69)
148 PF11460 DUF3007: Protein of u 24.1 44 0.00095 24.1 1.2 20 38-57 84-103 (104)
149 TIGR02714 amido_AtzD_TrzD ring 24.1 1.4E+02 0.0031 26.0 4.5 29 27-58 270-298 (366)
150 PF00034 Cytochrom_C: Cytochro 24.1 75 0.0016 19.6 2.3 16 43-58 74-89 (91)
151 PF14213 DUF4325: Domain of un 23.7 1.5E+02 0.0033 19.1 3.7 53 5-57 14-73 (74)
152 TIGR03674 fen_arch flap struct 23.5 42 0.0009 28.4 1.2 19 16-34 239-257 (338)
153 COG1131 CcmA ABC-type multidru 23.5 2.3E+02 0.0049 23.3 5.5 38 16-53 103-146 (293)
154 cd00349 Ribosomal_L11 Ribosoma 23.5 2.6E+02 0.0056 20.6 5.3 37 21-57 62-105 (131)
155 TIGR00608 radc DNA repair prot 23.4 41 0.00089 26.9 1.1 22 14-35 61-82 (218)
156 PF00986 DNA_gyraseB_C: DNA gy 23.4 46 0.00099 22.0 1.1 43 13-56 6-49 (65)
157 PF09346 SMI1_KNR4: SMI1 / KNR 23.2 1.2E+02 0.0026 20.2 3.3 18 44-65 2-19 (130)
158 PRK14668 uvrC excinuclease ABC 22.9 40 0.00087 30.9 1.0 39 11-51 523-561 (577)
159 TIGR02236 recomb_radA DNA repa 22.7 50 0.0011 27.0 1.5 36 15-51 1-36 (310)
160 PRK14666 uvrC excinuclease ABC 22.6 38 0.00083 31.9 0.8 24 11-34 635-658 (694)
161 PF10662 PduV-EutP: Ethanolami 22.4 75 0.0016 23.9 2.2 35 23-57 108-142 (143)
162 cd00141 NT_POLXc Nucleotidyltr 22.4 31 0.00067 28.8 0.2 31 14-44 46-76 (307)
163 PRK06920 dnaE DNA polymerase I 22.4 80 0.0017 31.3 3.0 26 8-33 797-822 (1107)
164 PF14229 DUF4332: Domain of un 22.3 75 0.0016 22.9 2.2 42 15-57 55-96 (122)
165 PRK13620 psbV cytochrome c-550 22.3 93 0.002 25.2 2.8 16 41-56 182-197 (215)
166 COG0272 Lig NAD-dependent DNA 22.2 2.5E+02 0.0055 26.5 6.0 23 14-36 544-566 (667)
167 PF10500 SR-25: Nuclear RNA-sp 22.0 2E+02 0.0044 23.5 4.8 32 41-85 157-188 (225)
168 PTZ00217 flap endonuclease-1; 21.7 49 0.0011 28.8 1.3 19 16-34 238-256 (393)
169 PF13276 HTH_21: HTH-like doma 21.4 32 0.0007 21.2 0.1 33 6-38 21-55 (60)
170 COG1636 Uncharacterized protei 21.3 97 0.0021 24.9 2.7 82 32-136 117-198 (204)
171 KOG0844|consensus 21.3 60 0.0013 28.1 1.7 13 44-56 188-200 (408)
172 PRK00024 hypothetical protein; 21.0 50 0.0011 26.4 1.1 22 14-35 67-88 (224)
173 KOG4302|consensus 21.0 2.9E+02 0.0062 26.1 6.1 19 25-43 189-207 (660)
174 smart00483 POLXc DNA polymeras 20.9 46 0.00099 28.1 0.9 23 14-36 49-71 (334)
175 TIGR00575 dnlj DNA ligase, NAD 20.9 44 0.00096 31.0 0.9 35 16-50 435-469 (652)
176 PF06207 DUF1002: Protein of u 20.8 1.8E+02 0.0038 23.6 4.2 29 26-61 181-209 (225)
177 COG1194 MutY A/G-specific DNA 20.8 44 0.00095 28.9 0.8 19 14-32 114-132 (342)
178 TIGR00575 dnlj DNA ligase, NAD 20.6 39 0.00084 31.4 0.4 22 12-34 498-519 (652)
179 PRK07956 ligA NAD-dependent DN 20.4 39 0.00084 31.5 0.4 35 16-50 448-482 (665)
180 cd01401 PncB_like Nicotinate p 20.3 1.7E+02 0.0037 25.5 4.3 33 25-57 290-326 (377)
181 PRK05672 dnaE2 error-prone DNA 20.1 67 0.0015 31.6 1.9 45 8-53 811-862 (1046)
182 PRK12766 50S ribosomal protein 20.1 57 0.0012 26.7 1.2 21 14-34 37-57 (232)
183 PF04201 TPD52: Tumour protein 20.1 58 0.0013 25.3 1.2 16 42-57 24-39 (162)
No 1
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=100.00 E-value=2.4e-62 Score=372.42 Aligned_cols=137 Identities=72% Similarity=1.122 Sum_probs=134.8
Q ss_pred CCccCCCCeeeeeecccccccCcchHHHHHhHhCCCCCCccCCCCHHHHHHHHHHHhCCCCcCCCcccccccccccCCce
Q psy1365 1 MSTNIDGKRKVMFALTAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKIITIMTNPRQYKIPDWFLNRQKDIVDGKY 80 (140)
Q Consensus 1 ~~t~l~~~k~v~~ALt~IyGIG~~~A~~Ic~~lGI~~~~~~~~Ls~~qi~~L~~~I~~~~~~~i~~w~~nr~~d~~tg~~ 80 (140)
+|||||++|+|.+||++|||||+++|.+||++|||||++++++||++|+++|.++|++|.+|.+|+||+|||+|++||+|
T Consensus 18 ~~~~l~~~K~v~~aLt~I~GIG~~~A~~I~~~lgi~~~~~~~~Lt~~qi~~l~~~i~~~~~~~iP~w~~nr~kd~~tG~d 97 (154)
T PTZ00134 18 LNTNVDGKRKVPYALTAIKGIGRRFAYLVCKKAGIDVTKRAGELTAEEIEKIVEIIANPLQFKIPDWFLNRQRDPKDGKN 97 (154)
T ss_pred cCccCCCCCEEEEeecccccccHHHHHHHHHHcCcCcCCCcccCCHHHHHHHHHHHhccccCCCChhHhhccccccccch
Confidence 68999999999999999999999999999999999999999999999999999999987779999999999999999999
Q ss_pred eEeeccchhHHHHHHHHHHHHHHhhhheeccCCCCCCccCCccccccCCCccceeeeccC
Q psy1365 81 SQILLTSTAQLDSKLREDLERLKKIRAHRGMRHYWGLRVRGQHTKTTGRRGRTVGVSKKK 140 (140)
Q Consensus 81 ~~l~~~~~~~L~~~~~~~I~rl~~i~syRG~RH~~gLpVRGQRTrtN~rt~~~~gv~~kk 140 (140)
.|+++ +||++++++||+||++|+||||+||++||||||||||||||+|+++||++||
T Consensus 98 ~h~i~---~dL~~~~~~dI~Rl~~I~sYRG~RH~~GLpVRGQRTkTnaR~g~~~gv~~kk 154 (154)
T PTZ00134 98 SHLTS---NMLDTKLREDLERLKKIRLHRGLRHHWGLRVRGQHTKTTGRRGRTVGVSRKK 154 (154)
T ss_pred hhhhH---HHHHHHHHHHHHHHHHhcchheeecccCCccCCccCCCCCccccccceeccC
Confidence 99999 9999999999999999999999999999999999999999999999999997
No 2
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=100.00 E-value=2.8e-61 Score=365.01 Aligned_cols=137 Identities=46% Similarity=0.760 Sum_probs=135.1
Q ss_pred CCccCCCCeeeeeecccccccCcchHHHHHhHhCCCCCCccCCCCHHHHHHHHHHHhCCCCcCCCcccccccccccCCce
Q psy1365 1 MSTNIDGKRKVMFALTAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKIITIMTNPRQYKIPDWFLNRQKDIVDGKY 80 (140)
Q Consensus 1 ~~t~l~~~k~v~~ALt~IyGIG~~~A~~Ic~~lGI~~~~~~~~Ls~~qi~~L~~~I~~~~~~~i~~w~~nr~~d~~tg~~ 80 (140)
+|||||++|+|.+||++|||||+++|.+||+++||||++++++||++|+++|.++|++|..+.+|+||+||++|++||++
T Consensus 13 ~~~~i~~~k~i~~aLt~IyGIG~~~a~~Ic~~lgi~~~~~~~~Lt~~qi~~l~~~i~~~~~~~iP~w~~Nr~~d~~tg~~ 92 (149)
T PRK04053 13 AGTDLDGTKPVEYALTGIKGIGRRTARAIARKLGLDPNAKLGYLSDEEIEKIEEALEDPAEEGIPSWMLNRRKDYETGED 92 (149)
T ss_pred cCccCCCCCEEeeeccccccccHHHHHHHHHHcCcCCCCccCcCCHHHHHHHHHHHHhhccccCchhhhccccccccCcc
Confidence 68999999999999999999999999999999999999999999999999999999988889999999999999999999
Q ss_pred eEeeccchhHHHHHHHHHHHHHHhhhheeccCCCCCCccCCccccccCCCccceeeeccC
Q psy1365 81 SQILLTSTAQLDSKLREDLERLKKIRAHRGMRHYWGLRVRGQHTKTTGRRGRTVGVSKKK 140 (140)
Q Consensus 81 ~~l~~~~~~~L~~~~~~~I~rl~~i~syRG~RH~~gLpVRGQRTrtN~rt~~~~gv~~kk 140 (140)
.|+++ +||++++++||+||++|+||||+||.+||||||||||||||||+++||+|||
T Consensus 93 ~~~ie---~dLr~~~~~~I~rl~~I~syRG~RH~~GLPVRGQRTrTNaRtg~~~gv~~kk 149 (149)
T PRK04053 93 LHLIG---SDLILTVREDINRMKKIRSYRGIRHELGLKVRGQRTRSTGRTGGTVGVSRKK 149 (149)
T ss_pred ceEeh---HHHHHHHHHHHHHHHHhcceeeecccCCCCCCCCcCCCCCcCCCccccccCC
Confidence 99999 9999999999999999999999999999999999999999999999999997
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=3.9e-61 Score=362.60 Aligned_cols=136 Identities=49% Similarity=0.839 Sum_probs=133.7
Q ss_pred CCccCCCCeeeeeecccccccCcchHHHHHhHhCCCCCCccCCCCHHHHHHHHHHHhCCCCcCCCcccccccccccCCce
Q psy1365 1 MSTNIDGKRKVMFALTAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKIITIMTNPRQYKIPDWFLNRQKDIVDGKY 80 (140)
Q Consensus 1 ~~t~l~~~k~v~~ALt~IyGIG~~~A~~Ic~~lGI~~~~~~~~Ls~~qi~~L~~~I~~~~~~~i~~w~~nr~~d~~tg~~ 80 (140)
+|||||++|+|.+||++|||||+++|.+||+++||||++++++||++|+++|.++|++ ..|.+|+||+||++|++||++
T Consensus 9 ~~~~i~~~k~v~~aLt~I~GIG~~~a~~I~~~lgi~~~~~~~~Lt~~qi~~l~~~i~~-~~~~iP~w~~Nr~~d~~tg~~ 87 (144)
T TIGR03629 9 ADTDLDGNKPVEYALTGIKGIGRRFARAIARKLGVDPNAKLGYLDDEEIEKLEEAVEN-YEYGIPSWLLNRRKDYETGED 87 (144)
T ss_pred eCccCCCCCEEEEeecceeccCHHHHHHHHHHcCcCCCCCcccCCHHHHHHHHHHHHh-ccccCCHHHhhcccccccCcc
Confidence 6899999999999999999999999999999999999999999999999999999988 579999999999999999999
Q ss_pred eEeeccchhHHHHHHHHHHHHHHhhhheeccCCCCCCccCCccccccCCCccceeeeccC
Q psy1365 81 SQILLTSTAQLDSKLREDLERLKKIRAHRGMRHYWGLRVRGQHTKTTGRRGRTVGVSKKK 140 (140)
Q Consensus 81 ~~l~~~~~~~L~~~~~~~I~rl~~i~syRG~RH~~gLpVRGQRTrtN~rt~~~~gv~~kk 140 (140)
.|+++ +||++++++||+||++|+||||+||.+||||||||||||||||+++||++||
T Consensus 88 ~~~ie---~dL~~~~~~dI~rl~~I~~yRG~RH~~gLpVRGQRTrTNaRtg~~~gv~~kk 144 (144)
T TIGR03629 88 LHLIG---SDLDMTVREDINRMKKIRSYRGIRHELGLKVRGQRTKSTGRRGRTVGVSRKK 144 (144)
T ss_pred ceEeh---HHHHHHHHHHHHHHHHhcceeeeeccCCCCCCCCcCCCCCcCCCccccccCC
Confidence 99999 9999999999999999999999999999999999999999999999999997
No 4
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.5e-50 Score=294.95 Aligned_cols=115 Identities=45% Similarity=0.697 Sum_probs=110.7
Q ss_pred CCccCCCCeeeeeecccccccCcchHHHHHhHhCCCCCCccCCCCHHHHHHHHHHHhCCCCcCCCcccccccccccCCce
Q psy1365 1 MSTNIDGKRKVMFALTAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKIITIMTNPRQYKIPDWFLNRQKDIVDGKY 80 (140)
Q Consensus 1 ~~t~l~~~k~v~~ALt~IyGIG~~~A~~Ic~~lGI~~~~~~~~Ls~~qi~~L~~~I~~~~~~~i~~w~~nr~~d~~tg~~ 80 (140)
+|+|||++|+|.+|||+|||||.++|.+||+++||||++++++|||+|+++|.++|++ .|.++
T Consensus 5 agvdip~~K~v~iALt~IyGIG~~~a~~I~~~~gi~~~~r~~eLteeei~~ir~~i~~--~~~ve--------------- 67 (121)
T COG0099 5 AGVDIPGNKRVVIALTYIYGIGRRRAKEICKKAGIDPDKRVGELTEEEIERLRDAIQN--KYLVE--------------- 67 (121)
T ss_pred cccCCCCCceEeehhhhhccccHHHHHHHHHHcCCCHhHhhccCCHHHHHHHHHHHHh--cCeeh---------------
Confidence 5899999999999999999999999999999999999999999999999999999986 46555
Q ss_pred eEeeccchhHHHHHHHHHHHHHHhhhheeccCCCCCCccCCccccccCCC--ccceeeeccC
Q psy1365 81 SQILLTSTAQLDSKLREDLERLKKIRAHRGMRHYWGLRVRGQHTKTTGRR--GRTVGVSKKK 140 (140)
Q Consensus 81 ~~l~~~~~~~L~~~~~~~I~rl~~i~syRG~RH~~gLpVRGQRTrtN~rt--~~~~gv~~kk 140 (140)
+||++++++||+||++|+||||+||.+||||||||||||||| |.++||++||
T Consensus 68 --------gDLr~~v~~dIkRl~~i~~YRGiRH~~GLpVRGQrTktnaRtrkG~~~~v~~KK 121 (121)
T COG0099 68 --------GDLRREVRMDIKRLMKIGCYRGIRHRRGLPVRGQRTKTNARTRKGPRKGVAKKK 121 (121)
T ss_pred --------hHHHHHHHHHHHHHHHhhhhhhhhhhcCCCCCCcccCccccccCCCccccccCC
Confidence 899999999999999999999999999999999999999999 9999999987
No 5
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=100.00 E-value=3.2e-47 Score=280.05 Aligned_cols=107 Identities=31% Similarity=0.519 Sum_probs=103.1
Q ss_pred CCccCCCCeeeeeecccccccCcchHHHHHhHhCCCCCCccCCCCHHHHHHHHHHHhCCCCcCCCcccccccccccCCce
Q psy1365 1 MSTNIDGKRKVMFALTAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKIITIMTNPRQYKIPDWFLNRQKDIVDGKY 80 (140)
Q Consensus 1 ~~t~l~~~k~v~~ALt~IyGIG~~~A~~Ic~~lGI~~~~~~~~Ls~~qi~~L~~~I~~~~~~~i~~w~~nr~~d~~tg~~ 80 (140)
+|||||++|+|.+||++|||||+++|.+||+++||||++++++||++|+++|.++|++ +|.++
T Consensus 5 ~~~~i~~~k~v~~aLt~i~GIG~~~A~~ic~~lgi~~~~~~~~Lt~~qi~~l~~~i~~--~~~i~--------------- 67 (122)
T CHL00137 5 AGVDLPRNKRIEYALTYIYGIGLTSAKEILEKANIDPDIRTKDLTDEQISALREIIEE--NYQVE--------------- 67 (122)
T ss_pred cCccCCCCCEeeeeecccccccHHHHHHHHHHcCcCcCcCcccCCHHHHHHHHHHHHH--hCcch---------------
Confidence 6899999999999999999999999999999999999999999999999999999986 46555
Q ss_pred eEeeccchhHHHHHHHHHHHHHHhhhheeccCCCCCCccCCccccccCCCcc
Q psy1365 81 SQILLTSTAQLDSKLREDLERLKKIRAHRGMRHYWGLRVRGQHTKTTGRRGR 132 (140)
Q Consensus 81 ~~l~~~~~~~L~~~~~~~I~rl~~i~syRG~RH~~gLpVRGQRTrtN~rt~~ 132 (140)
+||++.+++||+||++|+||||+||.+|||||||||||||||++
T Consensus 68 --------~dL~~~~~~dI~rl~~I~sYRG~RH~~gLPVRGQRT~tNarT~k 111 (122)
T CHL00137 68 --------GDLRRFESLNIKRLMEINCYRGRRHRLGLPVRGQRTRTNARTRR 111 (122)
T ss_pred --------HHHHHHHHHHHHHHHHhCchhcccccCCCCCCCCcCCccccccC
Confidence 89999999999999999999999999999999999999999997
No 6
>TIGR03631 bact_S13 30S ribosomal protein S13. This model describes bacterial ribosomal protein S13, to the exclusion of the homologous archaeal S13P and eukaryotic ribosomal protein S18. This model identifies some (but not all) instances of chloroplast and mitochondrial S13, which is of bacterial type.
Probab=100.00 E-value=7e-47 Score=274.98 Aligned_cols=109 Identities=37% Similarity=0.544 Sum_probs=103.7
Q ss_pred CCccCCCCeeeeeecccccccCcchHHHHHhHhCCCCCCccCCCCHHHHHHHHHHHhCCCCcCCCcccccccccccCCce
Q psy1365 1 MSTNIDGKRKVMFALTAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKIITIMTNPRQYKIPDWFLNRQKDIVDGKY 80 (140)
Q Consensus 1 ~~t~l~~~k~v~~ALt~IyGIG~~~A~~Ic~~lGI~~~~~~~~Ls~~qi~~L~~~I~~~~~~~i~~w~~nr~~d~~tg~~ 80 (140)
+|||||++|+|.+||++|||||+++|.+||+++||||++++++|+++|+++|.++|+++ |.++
T Consensus 3 ~~~~l~~~k~v~~aL~~i~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi~~l~~~l~~~--~~i~--------------- 65 (113)
T TIGR03631 3 AGVDIPNNKRVEIALTYIYGIGRTRARKILEKAGIDPDKRVKDLTEEELNAIREEIEAK--YKVE--------------- 65 (113)
T ss_pred CCccCCCCCEEeeeeeeeecccHHHHHHHHHHhCcCcccccccCCHHHHHHHHHHHHhc--Ccch---------------
Confidence 68999999999999999999999999999999999999999999999999999999863 5444
Q ss_pred eEeeccchhHHHHHHHHHHHHHHhhhheeccCCCCCCccCCccccccCCCccce
Q psy1365 81 SQILLTSTAQLDSKLREDLERLKKIRAHRGMRHYWGLRVRGQHTKTTGRRGRTV 134 (140)
Q Consensus 81 ~~l~~~~~~~L~~~~~~~I~rl~~i~syRG~RH~~gLpVRGQRTrtN~rt~~~~ 134 (140)
+||++.+++||+||++|+||||+||++|||||||||||||||++..
T Consensus 66 --------~~L~~~~~~dI~rl~~I~syRG~RH~~gLpVRGQRT~TNart~k~~ 111 (113)
T TIGR03631 66 --------GDLRREVSLNIKRLMDIGCYRGLRHRRGLPVRGQRTKTNARTRKGP 111 (113)
T ss_pred --------HHHHHHHHHHHHHHHHhcceeccccccCCCCCCCcCCccccccCCC
Confidence 9999999999999999999999999999999999999999999854
No 7
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=100.00 E-value=6.9e-47 Score=278.28 Aligned_cols=107 Identities=36% Similarity=0.566 Sum_probs=102.8
Q ss_pred CCccCCCCeeeeeecccccccCcchHHHHHhHhCCCCCCccCCCCHHHHHHHHHHHhCCCCcCCCcccccccccccCCce
Q psy1365 1 MSTNIDGKRKVMFALTAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKIITIMTNPRQYKIPDWFLNRQKDIVDGKY 80 (140)
Q Consensus 1 ~~t~l~~~k~v~~ALt~IyGIG~~~A~~Ic~~lGI~~~~~~~~Ls~~qi~~L~~~I~~~~~~~i~~w~~nr~~d~~tg~~ 80 (140)
+|||||++|+|.+||++|||||+++|.+||+++||||++++++||++|+++|.++|+++ |.++
T Consensus 5 ~~~~l~~~k~v~~aL~~I~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi~~l~~~i~~~--~~i~--------------- 67 (122)
T PRK05179 5 AGVDIPRNKRVVIALTYIYGIGRTRAKEILAAAGIDPDTRVKDLTDEELDKIREEIDKN--YKVE--------------- 67 (122)
T ss_pred cCccCCCCcEEEeeecccccccHHHHHHHHHHhCcCcccccccCCHHHHHHHHHHHHhh--ccch---------------
Confidence 68999999999999999999999999999999999999999999999999999999873 5444
Q ss_pred eEeeccchhHHHHHHHHHHHHHHhhhheeccCCCCCCccCCccccccCCCcc
Q psy1365 81 SQILLTSTAQLDSKLREDLERLKKIRAHRGMRHYWGLRVRGQHTKTTGRRGR 132 (140)
Q Consensus 81 ~~l~~~~~~~L~~~~~~~I~rl~~i~syRG~RH~~gLpVRGQRTrtN~rt~~ 132 (140)
+||++++++||+||++|+||||+||++|||||||||||||||++
T Consensus 68 --------~dL~~~~~~dI~rl~~I~sYRG~RH~~gLPVRGQRT~TNart~k 111 (122)
T PRK05179 68 --------GDLRREVSMNIKRLMDIGCYRGLRHRRGLPVRGQRTKTNARTRK 111 (122)
T ss_pred --------HHHHHHHHHHHHHHHHhcceeeeecccCCCCCCCcCCccccccC
Confidence 89999999999999999999999999999999999999999998
No 8
>KOG3311|consensus
Probab=100.00 E-value=8.1e-47 Score=284.54 Aligned_cols=137 Identities=69% Similarity=1.162 Sum_probs=135.3
Q ss_pred CCccCCCCeeeeeecccccccCcchHHHHHhHhCCCCCCccCCCCHHHHHHHHHHHhCCCCcCCCcccccccccccCCce
Q psy1365 1 MSTNIDGKRKVMFALTAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKIITIMTNPRQYKIPDWFLNRQKDIVDGKY 80 (140)
Q Consensus 1 ~~t~l~~~k~v~~ALt~IyGIG~~~A~~Ic~~lGI~~~~~~~~Ls~~qi~~L~~~I~~~~~~~i~~w~~nr~~d~~tg~~ 80 (140)
|||++|++++|.|||++|||||...|..+|++++|++.+++++|+++|++.+.+++++|..|.+|.|++|+++|.++|+.
T Consensus 16 l~~~~dg~~~V~fAl~~i~Gig~~~A~~ic~K~~~~~~~r~gelt~~qi~~i~~i~~d~~~~~~~~~~l~rq~~~~dG~~ 95 (152)
T KOG3311|consen 16 LNTNVDGKRKVTFALTSIKGIGRRYAEIVCKKADLDLTKRAGELTEEQILRILQILNDPRQYKIPDWFLNRQKDIIDGKV 95 (152)
T ss_pred HccCCCCCceeEEEEEEEeeechhhhhhhhhhcCcchhhhhccccHHHHHHHHHHhcCHHHhcCchHHHHhhcccccCcc
Confidence 68999999999999999999999999999999999999999999999999999999999899999999999999999999
Q ss_pred eEeeccchhHHHHHHHHHHHHHHhhhheeccCCCCCCccCCccccccCCCccceeeeccC
Q psy1365 81 SQILLTSTAQLDSKLREDLERLKKIRAHRGMRHYWGLRVRGQHTKTTGRRGRTVGVSKKK 140 (140)
Q Consensus 81 ~~l~~~~~~~L~~~~~~~I~rl~~i~syRG~RH~~gLpVRGQRTrtN~rt~~~~gv~~kk 140 (140)
.||++ +.|+..++++|+|+++|.||||+||.+|||||||||+|||+.|++|||++||
T Consensus 96 ~~l~~---~~ld~r~r~~ieRlkki~~~RG~rh~~gl~vRGQ~Tkt~~~~gk~v~Vs~Kk 152 (152)
T KOG3311|consen 96 NHLLG---NGLDTRLRADIERLKKIRCHRGLRHFWGLRVRGQRTKTNGRRGKTVGVSGKK 152 (152)
T ss_pred ccccc---hhhhhHHHHHHHHHhhhcccccceeccCCcccCccccccccccceeeecccC
Confidence 99999 9999999999999999999999999999999999999999999999999997
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=100.00 E-value=3.6e-46 Score=268.33 Aligned_cols=105 Identities=43% Similarity=0.682 Sum_probs=98.7
Q ss_pred CCccCCCCeeeeeecccccccCcchHHHHHhHhCCCCCCccCCCCHHHHHHHHHHHhCCCCcCCCcccccccccccCCce
Q psy1365 1 MSTNIDGKRKVMFALTAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKIITIMTNPRQYKIPDWFLNRQKDIVDGKY 80 (140)
Q Consensus 1 ~~t~l~~~k~v~~ALt~IyGIG~~~A~~Ic~~lGI~~~~~~~~Ls~~qi~~L~~~I~~~~~~~i~~w~~nr~~d~~tg~~ 80 (140)
+|||||++|+|.+||++|||||+++|.+||+++||+|++++++|+++|+++|.++|++ .|.++
T Consensus 3 ~~~~l~~~k~i~~aLt~IyGIG~~~A~~Ic~~lgi~~~~~~~~Ls~~~i~~l~~~i~~--~~~i~--------------- 65 (107)
T PF00416_consen 3 LGTNLPGNKPIYIALTKIYGIGRRKAKQICKKLGINPNKKVGDLSDEQIDKLRKIIEK--NHLIE--------------- 65 (107)
T ss_dssp TTTCE-TSSBHHHHHTTSTTBCHHHHHHHHHHTTS-SSSBTTTSTHHHHHHHHHHHHT--HSTCH---------------
T ss_pred CCCcCCCCcchHhHHhhhhccCHHHHHHHHHHcCCChhhhcccCCHHHHHHHHHHHHH--hcccc---------------
Confidence 6999999999999999999999999999999999999999999999999999999986 34444
Q ss_pred eEeeccchhHHHHHHHHHHHHHHhhhheeccCCCCCCccCCccccccCCC
Q psy1365 81 SQILLTSTAQLDSKLREDLERLKKIRAHRGMRHYWGLRVRGQHTKTTGRR 130 (140)
Q Consensus 81 ~~l~~~~~~~L~~~~~~~I~rl~~i~syRG~RH~~gLpVRGQRTrtN~rt 130 (140)
+||++++++||++|++|+||||+||.+|||||||||||||||
T Consensus 66 --------~~L~~~~~~~i~rl~~i~syRG~RH~~gLpvRGQRT~tNarT 107 (107)
T PF00416_consen 66 --------NDLKRQVRENIKRLKKIKSYRGIRHRKGLPVRGQRTKTNART 107 (107)
T ss_dssp --------HHHHHHHHHHHHHHHHHTTHHHHHHHHTSBSSSSTSSSSSHH
T ss_pred --------chHHHHHHHHHHHHHHHHHhhcchhhCCCCCCCCCCCCCCCC
Confidence 999999999999999999999999999999999999999986
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=97.18 E-value=0.00031 Score=49.12 Aligned_cols=50 Identities=28% Similarity=0.456 Sum_probs=39.9
Q ss_pred Ceeeeeec---ccccccCcchHHHHHhHhCCCCCCccCCCCHHHHHHHHHHHh
Q psy1365 8 KRKVMFAL---TAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKIITIMT 57 (140)
Q Consensus 8 ~k~v~~AL---t~IyGIG~~~A~~Ic~~lGI~~~~~~~~Ls~~qi~~L~~~I~ 57 (140)
+++|..+| +.+-|||.-.+..||-.+||+|..++.+|+++|+..|-+.+.
T Consensus 23 ~~~ik~~LlDQ~~iaGiGNiy~~EiLf~a~i~P~~~~~~L~~~~~~~l~~~~~ 75 (92)
T PF06831_consen 23 RRPIKAALLDQSVIAGIGNIYADEILFRAGIHPERPASSLSEEELRRLHEAIK 75 (92)
T ss_dssp CSBHHHHHHCTTTSTT--HHHHHHHHHHTTB-TTSBGGGSHHHHHHHHHHHHH
T ss_pred cchHHHHHhCCCccccCcHHHHHHHHHHcCCCccCccccCCHHHHHHHHHHHH
Confidence 34455555 568999999999999999999999999999999999877664
No 11
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=96.98 E-value=0.0007 Score=55.58 Aligned_cols=52 Identities=25% Similarity=0.413 Sum_probs=46.9
Q ss_pred CCeeeeeec---ccccccCcchHHHHHhHhCCCCCCccCCCCHHHHHHHHHHHhC
Q psy1365 7 GKRKVMFAL---TAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKIITIMTN 58 (140)
Q Consensus 7 ~~k~v~~AL---t~IyGIG~~~A~~Ic~~lGI~~~~~~~~Ls~~qi~~L~~~I~~ 58 (140)
.+++|.-+| +-|-|||.-.|..||-.+||||..++++||++|++.|-+.+.+
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 456788888 8899999999999999999999999999999999999777753
No 12
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=96.49 E-value=0.0027 Score=52.21 Aligned_cols=50 Identities=24% Similarity=0.363 Sum_probs=43.0
Q ss_pred Ceeeeeeccc---ccccCcchHHHHHhHhCCCCCCccCCCCHHHHHHHHHHHh
Q psy1365 8 KRKVMFALTA---IKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKIITIMT 57 (140)
Q Consensus 8 ~k~v~~ALt~---IyGIG~~~A~~Ic~~lGI~~~~~~~~Ls~~qi~~L~~~I~ 57 (140)
+.+|.-+|.. |-|||.-.|..||-.+||||..++++||++|++.|.+.+.
T Consensus 154 ~~~ik~~Lldq~viaGiGNiya~EiLf~a~i~P~~~~~~l~~~~~~~l~~a~~ 206 (272)
T PRK14810 154 KTRIKSALLNQTLLRGVGNIYADEALFRAGIRPQRLASSLSRERLRKLHDAIG 206 (272)
T ss_pred CccHHHHhhcCceeccccHhHHHHHHHHcCCCCCCCcccCCHHHHHHHHHHHH
Confidence 4456666644 4999999999999999999999999999999999887664
No 13
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=96.32 E-value=0.0049 Score=50.68 Aligned_cols=50 Identities=20% Similarity=0.263 Sum_probs=42.1
Q ss_pred Ceeeeeec---ccccccCcchHHHHHhHhCCCCCCccCCCCHHHHHHHHHHHh
Q psy1365 8 KRKVMFAL---TAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKIITIMT 57 (140)
Q Consensus 8 ~k~v~~AL---t~IyGIG~~~A~~Ic~~lGI~~~~~~~~Ls~~qi~~L~~~I~ 57 (140)
+.+|.-+| +-|-|||.-.|..||-.+||+|..++.+||++|++.|-+.+.
T Consensus 143 ~~~Ik~~LlDQ~~iaGIGNiyadEiLf~A~I~P~~~~~~Ls~~~~~~L~~~i~ 195 (269)
T PRK14811 143 ARPVKPWLLSQKPVAGVGNIYADESLWRARIHPARPATSLKAPEARRLYRAIR 195 (269)
T ss_pred CCcHHHHHhcCceeecccHHHHHHHHHHcCCCccCCcccCCHHHHHHHHHHHH
Confidence 34555555 458899999999999999999999999999999999865554
No 14
>PRK10445 endonuclease VIII; Provisional
Probab=96.21 E-value=0.0057 Score=50.09 Aligned_cols=51 Identities=18% Similarity=0.280 Sum_probs=43.3
Q ss_pred Ceeeeeec---ccccccCcchHHHHHhHhCCCCCCccCCCCHHHHHHHHHHHhC
Q psy1365 8 KRKVMFAL---TAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKIITIMTN 58 (140)
Q Consensus 8 ~k~v~~AL---t~IyGIG~~~A~~Ic~~lGI~~~~~~~~Ls~~qi~~L~~~I~~ 58 (140)
+++|.-+| +-|-|||.-.|..||=.++|||..++++||++|++.|-+.+.+
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 34555555 4478999999999999999999999999999999999777753
No 15
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=96.20 E-value=0.0063 Score=50.24 Aligned_cols=49 Identities=22% Similarity=0.403 Sum_probs=42.2
Q ss_pred eeeeeec---ccccccCcchHHHHHhHhCCCCCCccCCCCHHHHHHHHHHHh
Q psy1365 9 RKVMFAL---TAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKIITIMT 57 (140)
Q Consensus 9 k~v~~AL---t~IyGIG~~~A~~Ic~~lGI~~~~~~~~Ls~~qi~~L~~~I~ 57 (140)
.+|.-+| +-|-|||.-.|..||=.+||+|..++++||++|++.|-+.+.
T Consensus 165 ~~IK~~LLDQ~~vaGIGNiya~EiLf~A~IhP~~~~~~Ls~~~~~~L~~~i~ 216 (282)
T PRK13945 165 RSIKTALLDQSIVAGIGNIYADESLFKAGIHPTTPAGQLKKKQLERLREAII 216 (282)
T ss_pred ccHHHHhhcCCeEeccchhHHHHHHHHcCCCccCccccCCHHHHHHHHHHHH
Confidence 3444555 568899999999999999999999999999999999877765
No 16
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=96.09 E-value=0.0065 Score=49.94 Aligned_cols=50 Identities=28% Similarity=0.397 Sum_probs=42.4
Q ss_pred eeeeeec---ccccccCcchHHHHHhHhCCCCCCccCCCCHHHHHHHHHHHhC
Q psy1365 9 RKVMFAL---TAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKIITIMTN 58 (140)
Q Consensus 9 k~v~~AL---t~IyGIG~~~A~~Ic~~lGI~~~~~~~~Ls~~qi~~L~~~I~~ 58 (140)
.+|.-+| +-|-|||.-.|..||-.++|+|..++.+||++|++.|-+.+.+
T Consensus 156 ~~Ik~~LlDQ~vvaGIGNiyadEiLf~a~I~P~~~~~~Ls~~~~~~L~~~i~~ 208 (272)
T TIGR00577 156 RKIKTALLDQRLVAGIGNIYADEVLFRAGIHPERLANSLSKEECELLHRAIKE 208 (272)
T ss_pred CcHHHHHhcCCeEecccHHHHHHHHHHcCCCcchhhccCCHHHHHHHHHHHHH
Confidence 3444444 4578999999999999999999999999999999999777653
No 17
>PRK04184 DNA topoisomerase VI subunit B; Validated
Probab=95.87 E-value=0.0085 Score=53.94 Aligned_cols=49 Identities=22% Similarity=0.424 Sum_probs=45.0
Q ss_pred eeeecccccccCcchHHHHHhHhCCCCCCccCCCCHHHHHHHHHHHhCC
Q psy1365 11 VMFALTAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKIITIMTNP 59 (140)
Q Consensus 11 v~~ALt~IyGIG~~~A~~Ic~~lGI~~~~~~~~Ls~~qi~~L~~~I~~~ 59 (140)
..|.-..|-.||..+|..||..+|++|+++..+|+++|+..|.+++.+.
T Consensus 259 ~~fL~~~f~~v~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~~ 307 (535)
T PRK04184 259 KEFLVEEFSRVGDKTADEILEKAGLDPNKKPKELTREELERLVEAFKKY 307 (535)
T ss_pred HHHHHHhhcccCHHHHHHHHHHcCCCCCCChhhCCHHHHHHHHHHHHhc
Confidence 3456688999999999999999999999999999999999999999864
No 18
>TIGR01052 top6b DNA topoisomerase VI, B subunit. This model describes DNA topoisomerase VI, an archaeal type II DNA topoisomerase (DNA gyrase).
Probab=94.44 E-value=0.04 Score=49.20 Aligned_cols=54 Identities=24% Similarity=0.409 Sum_probs=46.9
Q ss_pred eeeecccccccCcchHHHHHhHhCCC---CCCccCCCCHHHHHHHHHHHhCCCCcCCC
Q psy1365 11 VMFALTAIKGCGRRFSNIVLKKADID---LNKRAGECSEEEVDKIITIMTNPRQYKIP 65 (140)
Q Consensus 11 v~~ALt~IyGIG~~~A~~Ic~~lGI~---~~~~~~~Ls~~qi~~L~~~I~~~~~~~i~ 65 (140)
..|.-..|-.||..+|..||..+|++ |+++..+|+++|++.|.+++.+. .+.-|
T Consensus 250 ~~fL~~~f~~v~~~~a~~~~~~~g~~~~~~~~~~~~l~~~~~~~l~~~~~~~-~~~~P 306 (488)
T TIGR01052 250 RSFLVSEFSRIGEKKIKELLEKYGIDVDPLDKKPKELTWDEAEKIVNAFKEM-KFMAP 306 (488)
T ss_pred HHHHHHhhcccCHHHHHHHHHHhCCCccccCCChhhCCHHHHHHHHHHHHhc-CCCCC
Confidence 34555889999999999999999999 99999999999999999999864 45444
No 19
>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=93.82 E-value=0.019 Score=49.64 Aligned_cols=49 Identities=31% Similarity=0.489 Sum_probs=34.5
Q ss_pred eeeeeeccccc-ccCcchHHHHHhHhCCCCCCccCCCCHHHHHHHHHHHh
Q psy1365 9 RKVMFALTAIK-GCGRRFSNIVLKKADIDLNKRAGECSEEEVDKIITIMT 57 (140)
Q Consensus 9 k~v~~ALt~Iy-GIG~~~A~~Ic~~lGI~~~~~~~~Ls~~qi~~L~~~I~ 57 (140)
..+.-+|...+ |+|+..|..||.++|+++++.+.+|+++++..|.+.+.
T Consensus 187 ~~l~~~L~~~~~G~~~~la~ei~~ra~i~~~~~~~~~~~~~~~~l~~~~~ 236 (455)
T PF05833_consen 187 KTLVKALSKNFQGFGPELAEEILYRAGIDKNKKVEELSDEEIEKLFEAIR 236 (455)
T ss_dssp -BHHHHHHHHCTT--HHHHHHHHCCCTS-TTSBGGG--HHHHCHHHHHHH
T ss_pred ccHHHHHHHHHHHhHHHHHHHHHHHhCCCCccccccchhhhHHHHHHHHH
Confidence 44555565555 99999999999999999999999999999777655543
No 20
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=93.68 E-value=0.083 Score=43.98 Aligned_cols=49 Identities=22% Similarity=0.400 Sum_probs=42.0
Q ss_pred eeeeeec---ccccccCcchHHHHHhHhCCCCCCccCCCCHHHHHHHHHHHh
Q psy1365 9 RKVMFAL---TAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKIITIMT 57 (140)
Q Consensus 9 k~v~~AL---t~IyGIG~~~A~~Ic~~lGI~~~~~~~~Ls~~qi~~L~~~I~ 57 (140)
++|.-+| +-|-|||.-.|..+|=++||+|...+++|+.+|+..|.++|.
T Consensus 156 ~~IK~~LLDQ~vvaGvGNIYa~E~Lf~agI~P~~~a~~l~~~~~~~l~~~i~ 207 (273)
T COG0266 156 RRIKTALLDQKVVAGVGNIYADEILFRAGIHPARPAGDLSLAQLALLHEAIK 207 (273)
T ss_pred cchHHHhhcCCceecccHHHHHHHHHHcCCCcccCccccCHHHHHHHHHHHH
Confidence 3455555 558899999999999999999999999999999888877775
No 21
>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=93.59 E-value=0.031 Score=31.52 Aligned_cols=18 Identities=28% Similarity=0.523 Sum_probs=15.1
Q ss_pred ecccccccCcchHHHHHh
Q psy1365 14 ALTAIKGCGRRFSNIVLK 31 (140)
Q Consensus 14 ALt~IyGIG~~~A~~Ic~ 31 (140)
.|.+++|||+++|..|+.
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 22
>COG1389 DNA topoisomerase VI, subunit B [DNA replication, recombination, and repair]
Probab=92.50 E-value=0.1 Score=46.68 Aligned_cols=48 Identities=21% Similarity=0.381 Sum_probs=43.7
Q ss_pred eeecccccccCcchHHHHHhHhCCCCCCccCCCC----HHHHHHHHHHHhCC
Q psy1365 12 MFALTAIKGCGRRFSNIVLKKADIDLNKRAGECS----EEEVDKIITIMTNP 59 (140)
Q Consensus 12 ~~ALt~IyGIG~~~A~~Ic~~lGI~~~~~~~~Ls----~~qi~~L~~~I~~~ 59 (140)
.|....|--||..+|..+|+.+|++|++.+.+|+ .++.+.|.+++.+.
T Consensus 260 ~fL~sef~rig~~ta~e~~e~~g~~~~~~p~~L~~~~~~eea~~lv~a~~~~ 311 (538)
T COG1389 260 EFLVSEFSRIGEKTADELLEYAGFDPDKKPRELTKKKTREEAEKLVEAFKKM 311 (538)
T ss_pred HHHHHHHHHhhhhhHHHHHHHhcCCcccCHHHhhcccCHHHHHHHHHHHHhC
Confidence 4556778899999999999999999999999999 99999999999864
No 23
>KOG3311|consensus
Probab=91.94 E-value=0.025 Score=43.25 Aligned_cols=48 Identities=15% Similarity=-0.036 Sum_probs=42.0
Q ss_pred eeccchhHHHHHHHHHHHHHHhhhheeccCCCCCCccCCccccccCCCcc
Q psy1365 83 ILLTSTAQLDSKLREDLERLKKIRAHRGMRHYWGLRVRGQHTKTTGRRGR 132 (140)
Q Consensus 83 l~~~~~~~L~~~~~~~I~rl~~i~syRG~RH~~gLpVRGQRTrtN~rt~~ 132 (140)
-+.+|++|.+.+.-.++...+++.+|.|. ..+||+.||.|+.|+.+.+
T Consensus 66 ~i~~i~~d~~~~~~~~~~l~rq~~~~dG~--~~~l~~~~ld~r~r~~ieR 113 (152)
T KOG3311|consen 66 RILQILNDPRQYKIPDWFLNRQKDIIDGK--VNHLLGNGLDTRLRADIER 113 (152)
T ss_pred HHHHHhcCHHHhcCchHHHHhhcccccCc--cccccchhhhhHHHHHHHH
Confidence 34456788899999999999999999999 9999999999999987665
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=90.34 E-value=0.13 Score=29.20 Aligned_cols=21 Identities=24% Similarity=0.414 Sum_probs=15.5
Q ss_pred ecccccccCcchHHHHHhHhCC
Q psy1365 14 ALTAIKGCGRRFSNIVLKKADI 35 (140)
Q Consensus 14 ALt~IyGIG~~~A~~Ic~~lGI 35 (140)
.+++++|||+.++.. ++.+||
T Consensus 12 pi~~~~GIG~kt~~k-L~~~GI 32 (32)
T PF11798_consen 12 PIRKFWGIGKKTAKK-LNKLGI 32 (32)
T ss_dssp BGGGSTTS-HHHHHH-HHCTT-
T ss_pred CHHhhCCccHHHHHH-HHHccC
Confidence 678999999999988 555554
No 25
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=88.15 E-value=0.042 Score=34.94 Aligned_cols=36 Identities=19% Similarity=0.243 Sum_probs=25.1
Q ss_pred eeeecccccccCcchHHHHHhHhCCCCCCccCCCCHH
Q psy1365 11 VMFALTAIKGCGRRFSNIVLKKADIDLNKRAGECSEE 47 (140)
Q Consensus 11 v~~ALt~IyGIG~~~A~~Ic~~lGI~~~~~~~~Ls~~ 47 (140)
++-+|.+|.|||+..|..+... |+..-..+-..+.+
T Consensus 3 ~~~~L~~I~Gig~~~a~~L~~~-G~~t~~~l~~a~~~ 38 (60)
T PF14520_consen 3 VFDDLLSIPGIGPKRAEKLYEA-GIKTLEDLANADPE 38 (60)
T ss_dssp HHHHHHTSTTCHHHHHHHHHHT-TCSSHHHHHTSHHH
T ss_pred HHHhhccCCCCCHHHHHHHHhc-CCCcHHHHHcCCHH
Confidence 3457899999999999998877 77743333333333
No 26
>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=88.05 E-value=0.23 Score=31.32 Aligned_cols=22 Identities=23% Similarity=0.256 Sum_probs=15.8
Q ss_pred ecccccccCcchHHHHHhHhCCC
Q psy1365 14 ALTAIKGCGRRFSNIVLKKADID 36 (140)
Q Consensus 14 ALt~IyGIG~~~A~~Ic~~lGI~ 36 (140)
.+++|+|||+.+|....+ .|+.
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 478999999999999987 6765
No 27
>PRK00274 ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed
Probab=87.78 E-value=0.34 Score=39.44 Aligned_cols=49 Identities=24% Similarity=0.291 Sum_probs=37.5
Q ss_pred eeeeeecccccccCcchHHHHHhHhCCCCCCccCCCCHHHHHHHHHHHhC
Q psy1365 9 RKVMFALTAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKIITIMTN 58 (140)
Q Consensus 9 k~v~~ALt~IyGIG~~~A~~Ic~~lGI~~~~~~~~Ls~~qi~~L~~~I~~ 58 (140)
|++..+|..+++. ...+..+++.+|++|+.++.+|+.+|...|.+.+..
T Consensus 222 k~l~~~l~~~~~~-~~~~~~~l~~~~~~~~~r~~~l~~~~~~~L~~~~~~ 270 (272)
T PRK00274 222 KTLRNNLKNLFGS-KEKLEEALEAAGIDPNRRAETLSVEEFVRLANALAA 270 (272)
T ss_pred HHHHHHHHhhccc-hHHHHHHHHHCCCCcCCCceeCCHHHHHHHHHHHHh
Confidence 4444555555431 245678899999999999999999999999888764
No 28
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=87.18 E-value=0.37 Score=36.21 Aligned_cols=43 Identities=21% Similarity=0.262 Sum_probs=38.8
Q ss_pred ecccccccCcchHHHHHhHhCCCCCCccCCCCHHHHHHHHHHHh
Q psy1365 14 ALTAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKIITIMT 57 (140)
Q Consensus 14 ALt~IyGIG~~~A~~Ic~~lGI~~~~~~~~Ls~~qi~~L~~~I~ 57 (140)
=||.|.|||+... ..|+-+||--...+-.+|..++..+..+++
T Consensus 68 DLt~I~GIGPk~e-~~Ln~~GI~tfaQIAAwt~~di~~id~~l~ 110 (133)
T COG3743 68 DLTRISGIGPKLE-KVLNELGIFTFAQIAAWTRADIAWIDDYLN 110 (133)
T ss_pred cchhhcccCHHHH-HHHHHcCCccHHHHHhcCHHHHHHHHhhcC
Confidence 5899999999876 567899999999999999999999999885
No 29
>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=86.64 E-value=0.63 Score=39.74 Aligned_cols=49 Identities=22% Similarity=0.415 Sum_probs=40.2
Q ss_pred eeeeeecccccccCcchHHHHHhHhCCCCCCccCCCCHHHHHHHHHHHhCC
Q psy1365 9 RKVMFALTAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKIITIMTNP 59 (140)
Q Consensus 9 k~v~~ALt~IyGIG~~~A~~Ic~~lGI~~~~~~~~Ls~~qi~~L~~~I~~~ 59 (140)
+.+...|..+ +-.+++..||+.+||++++++.+|+++|++.|.+.+.+.
T Consensus 284 ~~~~~~l~~~--l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~lk~~ 332 (400)
T TIGR00275 284 KTVKNILKGL--LPKRLAELLLEQLGIDPDLPAAQLSKKEIKKLVQLLKNW 332 (400)
T ss_pred hhHHHHhhhh--hhHHHHHHHHHHcCCCCCCChHHCCHHHHHHHHHHHhCC
Confidence 3344444432 678899999999999999999999999999999999863
No 30
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=86.23 E-value=0.37 Score=25.77 Aligned_cols=19 Identities=21% Similarity=0.427 Sum_probs=16.5
Q ss_pred ecccccccCcchHHHHHhH
Q psy1365 14 ALTAIKGCGRRFSNIVLKK 32 (140)
Q Consensus 14 ALt~IyGIG~~~A~~Ic~~ 32 (140)
.|..|.|||+++|..|+..
T Consensus 2 ~L~~i~GiG~k~A~~il~~ 20 (26)
T smart00278 2 ELLKVPGIGPKTAEKILEA 20 (26)
T ss_pred hhhhCCCCCHHHHHHHHHh
Confidence 3678999999999999863
No 31
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=86.14 E-value=0.31 Score=36.59 Aligned_cols=55 Identities=16% Similarity=0.101 Sum_probs=39.2
Q ss_pred CCCCeeeeeecccccccCcchHHHHHhHhCC---CCCCccCCCCHHHHHHHHHHHhCC
Q psy1365 5 IDGKRKVMFALTAIKGCGRRFSNIVLKKADI---DLNKRAGECSEEEVDKIITIMTNP 59 (140)
Q Consensus 5 l~~~k~v~~ALt~IyGIG~~~A~~Ic~~lGI---~~~~~~~~Ls~~qi~~L~~~I~~~ 59 (140)
+|=|..-..+|+.++|||+..|..|++.-.+ +.-..+.-+++.|.+.|.++.+++
T Consensus 53 IdiN~A~~~el~~lpGigP~~A~~IV~nGpf~sveDL~~V~GIgekqk~~l~k~~~~f 110 (132)
T PRK02515 53 IDLNNSSVRAFRQFPGMYPTLAGKIVKNAPYDSVEDVLNLPGLSERQKELLEANLDNF 110 (132)
T ss_pred ccCCccCHHHHHHCCCCCHHHHHHHHHCCCCCCHHHHHcCCCCCHHHHHHHHHhhcce
Confidence 4444445567899999999999999963222 222346667899999998888763
No 32
>COG0030 KsgA Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis]
Probab=85.86 E-value=0.44 Score=39.37 Aligned_cols=46 Identities=28% Similarity=0.340 Sum_probs=39.5
Q ss_pred CeeeeeecccccccCcchHHHHHhHhCCCCCCccCCCCHHHHHHHHHHHhC
Q psy1365 8 KRKVMFALTAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKIITIMTN 58 (140)
Q Consensus 8 ~k~v~~ALt~IyGIG~~~A~~Ic~~lGI~~~~~~~~Ls~~qi~~L~~~I~~ 58 (140)
.|.+..+|...++ ...+|..+|++++.++.+||.+|+-.|.+++..
T Consensus 211 RKtl~n~l~~~~~-----~~~~l~~~~i~~~~R~e~ls~~~f~~L~~~l~~ 256 (259)
T COG0030 211 RKTLRNNLKNLFG-----LEEVLEAAGIDPNARAENLSPEDFLKLANALKG 256 (259)
T ss_pred hHHHHHHHHhhhh-----HHHHHHhcCCCcccChhhCCHHHHHHHHHHHhh
Confidence 4556667777776 889999999999999999999999999988864
No 33
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=82.67 E-value=0.56 Score=36.84 Aligned_cols=21 Identities=10% Similarity=0.257 Sum_probs=18.0
Q ss_pred eecccccccCcchHHHHHhHh
Q psy1365 13 FALTAIKGCGRRFSNIVLKKA 33 (140)
Q Consensus 13 ~ALt~IyGIG~~~A~~Ic~~l 33 (140)
-+|++++|||+++|.+||-.|
T Consensus 108 ~~L~~vpGIGkKtAerIilEL 128 (188)
T PRK14606 108 EGLSKLPGISKKTAERIVMEL 128 (188)
T ss_pred HHHhhCCCCCHHHHHHHHHHH
Confidence 368999999999999999543
No 34
>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=82.08 E-value=1.1 Score=30.57 Aligned_cols=27 Identities=22% Similarity=0.514 Sum_probs=21.7
Q ss_pred CeeeeeecccccccCcchHHHHHhHhC
Q psy1365 8 KRKVMFALTAIKGCGRRFSNIVLKKAD 34 (140)
Q Consensus 8 ~k~v~~ALt~IyGIG~~~A~~Ic~~lG 34 (140)
+..|.++|+.|+|||...|..|++.-.
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 368999999999999999999997664
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=81.82 E-value=4.2 Score=33.06 Aligned_cols=51 Identities=12% Similarity=0.126 Sum_probs=42.7
Q ss_pred CeeeeeecccccccCcchHHHHHhHhCCCCCCc------------cCCCCHHHHHHHHHHHhC
Q psy1365 8 KRKVMFALTAIKGCGRRFSNIVLKKADIDLNKR------------AGECSEEEVDKIITIMTN 58 (140)
Q Consensus 8 ~k~v~~ALt~IyGIG~~~A~~Ic~~lGI~~~~~------------~~~Ls~~qi~~L~~~I~~ 58 (140)
...+..---.++|+|+....||..++|+=++++ -..||++|++.|-++...
T Consensus 96 G~~~~ip~d~L~~Lg~g~~~Qi~~rFG~V~hlPvev~~v~~~~~~~~rltd~q~d~l~~W~~~ 158 (225)
T PF09883_consen 96 GIFVPIPKDELKPLGPGSPRQIRRRFGLVQHLPVEVEFVKVEDGIEARLTDEQVDRLYEWTRD 158 (225)
T ss_pred cccccCcHHHhcccCCCCHHHHHHHhCcccCCceEEEEEEcccCcccccCHHHHHHHHHHhhC
Confidence 444555556778999999999999999999998 457999999999998875
No 36
>TIGR00755 ksgA dimethyladenosine transferase. Alternate name: S-adenosylmethionine--6-N',N'-adenosyl (rRNA) dimethyltransferase
Probab=81.68 E-value=0.85 Score=36.46 Aligned_cols=46 Identities=17% Similarity=0.231 Sum_probs=34.6
Q ss_pred CeeeeeecccccccCcchHHHHHhHhCCCCCCccCCCCHHHHHHHHHH
Q psy1365 8 KRKVMFALTAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKIITI 55 (140)
Q Consensus 8 ~k~v~~ALt~IyGIG~~~A~~Ic~~lGI~~~~~~~~Ls~~qi~~L~~~ 55 (140)
.|++.-+|..+++- ..+..++..+|+++++++.+||.+|...|.+.
T Consensus 207 rk~l~~~l~~~~~~--~~~~~~l~~~~i~~~~r~~~l~~~~~~~l~~~ 252 (253)
T TIGR00755 207 RKTLRNNLKQLLKA--SKLEEVLEQLGLDPTARAEQLSPEDFLRLANL 252 (253)
T ss_pred hHHHHHHHhhhcch--hHHHHHHHHCCcCCCCCcccCCHHHHHHHHHh
Confidence 34555566655331 34567888999999999999999999998654
No 37
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=81.66 E-value=0.64 Score=36.45 Aligned_cols=21 Identities=14% Similarity=0.313 Sum_probs=17.9
Q ss_pred eecccccccCcchHHHHHhHh
Q psy1365 13 FALTAIKGCGRRFSNIVLKKA 33 (140)
Q Consensus 13 ~ALt~IyGIG~~~A~~Ic~~l 33 (140)
-+|++++|||+++|.+|+-.|
T Consensus 108 ~~L~~vpGIGkKtAeRIilEL 128 (183)
T PRK14601 108 SVLKKVPGIGPKSAKRIIAEL 128 (183)
T ss_pred HHHhhCCCCCHHHHHHHHHHH
Confidence 368999999999999999443
No 38
>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=81.55 E-value=1.4 Score=38.39 Aligned_cols=50 Identities=26% Similarity=0.423 Sum_probs=40.8
Q ss_pred CCeeeeeecccccccCcchHHHHHhHhCC-CCCCccCCCCHHHHHHHHHHHhC
Q psy1365 7 GKRKVMFALTAIKGCGRRFSNIVLKKADI-DLNKRAGECSEEEVDKIITIMTN 58 (140)
Q Consensus 7 ~~k~v~~ALt~IyGIG~~~A~~Ic~~lGI-~~~~~~~~Ls~~qi~~L~~~I~~ 58 (140)
+++.+...|..+ +-.+++..+|+.++| +++.++.+|+.+++..|.+.|.+
T Consensus 289 ~~~~~~~~l~~~--lp~rl~~~ll~~~~i~~~~~~~~~l~~~~~~~L~~~lk~ 339 (409)
T PF03486_consen 289 PKRTLKNFLKGL--LPKRLALALLKRAGIKDPDKKVSELSKKERNRLANLLKR 339 (409)
T ss_dssp TTSBHHHHHTTT--S-HHHHHHHHHHTTS-STTSBGGGS-HHHHHHHHHHHHC
T ss_pred HhhHHHHHHHHH--hHHHHHHHHHHHcCCCccccchhhcCHHHHHHHHHHHHh
Confidence 344555556555 778899999999999 99999999999999999999986
No 39
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=80.66 E-value=0.72 Score=36.41 Aligned_cols=20 Identities=20% Similarity=0.396 Sum_probs=17.4
Q ss_pred eecccccccCcchHHHHHhH
Q psy1365 13 FALTAIKGCGRRFSNIVLKK 32 (140)
Q Consensus 13 ~ALt~IyGIG~~~A~~Ic~~ 32 (140)
.+|++++|||+++|.+||-.
T Consensus 107 ~~L~kvpGIGkKtAerIilE 126 (197)
T PRK14603 107 RLLTSASGVGKKLAERIALE 126 (197)
T ss_pred HHHhhCCCCCHHHHHHHHHH
Confidence 36899999999999999943
No 40
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=80.41 E-value=0.75 Score=36.32 Aligned_cols=21 Identities=14% Similarity=0.339 Sum_probs=18.0
Q ss_pred eecccccccCcchHHHHHhHh
Q psy1365 13 FALTAIKGCGRRFSNIVLKKA 33 (140)
Q Consensus 13 ~ALt~IyGIG~~~A~~Ic~~l 33 (140)
.+|++++|||+++|.+|+-.|
T Consensus 108 ~~L~kvpGIGkKtAerIilEL 128 (195)
T PRK14604 108 ARLARVPGIGKKTAERIVLEL 128 (195)
T ss_pred HHHhhCCCCCHHHHHHHHHHH
Confidence 368999999999999999543
No 41
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=79.88 E-value=0.79 Score=36.41 Aligned_cols=21 Identities=19% Similarity=0.417 Sum_probs=17.9
Q ss_pred eecccccccCcchHHHHHhHh
Q psy1365 13 FALTAIKGCGRRFSNIVLKKA 33 (140)
Q Consensus 13 ~ALt~IyGIG~~~A~~Ic~~l 33 (140)
-+|++++|||+++|.+|+-.|
T Consensus 107 ~~L~~vpGIGkKtAeRIIlEL 127 (196)
T PRK13901 107 ELISKVKGIGNKMAGKIFLKL 127 (196)
T ss_pred HHHhhCCCCCHHHHHHHHHHH
Confidence 368999999999999999443
No 42
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=79.47 E-value=0.85 Score=36.16 Aligned_cols=19 Identities=26% Similarity=0.538 Sum_probs=17.0
Q ss_pred ecccccccCcchHHHHHhH
Q psy1365 14 ALTAIKGCGRRFSNIVLKK 32 (140)
Q Consensus 14 ALt~IyGIG~~~A~~Ic~~ 32 (140)
+|++++|||+++|.+|+-.
T Consensus 110 ~L~~ipGIGkKtAerIilE 128 (203)
T PRK14602 110 ALTRVSGIGKKTAQHIFLE 128 (203)
T ss_pred HHhcCCCcCHHHHHHHHHH
Confidence 6899999999999999943
No 43
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=79.45 E-value=0.92 Score=36.17 Aligned_cols=21 Identities=24% Similarity=0.403 Sum_probs=18.2
Q ss_pred eecccccccCcchHHHHHhHh
Q psy1365 13 FALTAIKGCGRRFSNIVLKKA 33 (140)
Q Consensus 13 ~ALt~IyGIG~~~A~~Ic~~l 33 (140)
-+|++++|||+++|.+||-.|
T Consensus 108 ~~L~k~PGIGkKtAerivleL 128 (201)
T COG0632 108 KALSKIPGIGKKTAERIVLEL 128 (201)
T ss_pred HhhhcCCCCCHHHHHHHHHHH
Confidence 368999999999999999553
No 44
>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=79.45 E-value=0.51 Score=36.97 Aligned_cols=30 Identities=20% Similarity=0.327 Sum_probs=23.3
Q ss_pred CCCeeeeeecccccccCcchHHHHHhHhCC
Q psy1365 6 DGKRKVMFALTAIKGCGRRFSNIVLKKADI 35 (140)
Q Consensus 6 ~~~k~v~~ALt~IyGIG~~~A~~Ic~~lGI 35 (140)
++...+.-.|.+++|||+.+|..+|.-||=
T Consensus 108 p~t~~lre~Ll~LpGVG~KTAnvVL~~l~~ 137 (177)
T TIGR03252 108 PDGKELLRRLKALPGFGKQKAKIFLALLGK 137 (177)
T ss_pred CCcHHHHHHHHcCCCCCHHHHHHHHHHHHH
Confidence 344445567999999999999999976653
No 45
>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=79.26 E-value=0.6 Score=37.71 Aligned_cols=49 Identities=27% Similarity=0.289 Sum_probs=38.2
Q ss_pred CCeeeeeecccccccCcchHHHHHhHhCCCCCCccCCCCHHHHHHHHHHHh
Q psy1365 7 GKRKVMFALTAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKIITIMT 57 (140)
Q Consensus 7 ~~k~v~~ALt~IyGIG~~~A~~Ic~~lGI~~~~~~~~Ls~~qi~~L~~~I~ 57 (140)
..|++.-+|..+++ ......+.+.+||+++.++.+|+.+|...|.++++
T Consensus 213 rrk~l~~~L~~~~~--~~~~~~~~~~~~i~~~~r~~~ls~~~~~~l~~~l~ 261 (262)
T PF00398_consen 213 RRKTLRNSLKSLFP--GEQLEELLEKAGIDPNARAEELSPEQFLKLFKYLN 261 (262)
T ss_dssp TTSBHHHHTTCTHH--HHHHHHHHHHCTHTTTTCGGCHHHHHHHHHHHHHH
T ss_pred cchHHHHHHhhhcC--HHHHHHhhhhcCCCCCCCcccCCHHHHHHHHHHhh
Confidence 45666666766653 33456677779999999999999999999988875
No 46
>COG1293 Predicted RNA-binding protein homologous to eukaryotic snRNP [Transcription]
Probab=78.91 E-value=2 Score=39.01 Aligned_cols=47 Identities=23% Similarity=0.323 Sum_probs=42.1
Q ss_pred eeecccccccCcchHHHHHhHhCCCCCCccCCCCHHHHHHHHHHHhC
Q psy1365 12 MFALTAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKIITIMTN 58 (140)
Q Consensus 12 ~~ALt~IyGIG~~~A~~Ic~~lGI~~~~~~~~Ls~~qi~~L~~~I~~ 58 (140)
..+|..+.|+|.-.|..+|-++|++++..+.++.++++..+...+.+
T Consensus 189 ~~~~~~~~g~~~~~a~el~~rag~~~~~~~~~~~~~~~~~v~~~~~~ 235 (564)
T COG1293 189 VRLLARFLGLGGLLAEELLSRAGLDKKVPAKDLFEEEIKKVREALEE 235 (564)
T ss_pred HHHHHHhcCCCHHHHHHHHHhcCCCcCCchhhhhHHHHHHHHHHHHh
Confidence 45577899999999999999999999999999999999999877644
No 47
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=74.73 E-value=1.5 Score=34.41 Aligned_cols=19 Identities=26% Similarity=0.555 Sum_probs=16.4
Q ss_pred eecccccccCcchHHHHHhH
Q psy1365 13 FALTAIKGCGRRFSNIVLKK 32 (140)
Q Consensus 13 ~ALt~IyGIG~~~A~~Ic~~ 32 (140)
.+| +++|||+++|.+||-.
T Consensus 108 ~~L-~vpGIGkKtAerIilE 126 (186)
T PRK14600 108 AAL-KVNGIGEKLINRIITE 126 (186)
T ss_pred hhe-ECCCCcHHHHHHHHHH
Confidence 467 8999999999999944
No 48
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=72.96 E-value=1.5 Score=34.40 Aligned_cols=17 Identities=24% Similarity=0.552 Sum_probs=15.5
Q ss_pred ecccccccCcchHHHHH
Q psy1365 14 ALTAIKGCGRRFSNIVL 30 (140)
Q Consensus 14 ALt~IyGIG~~~A~~Ic 30 (140)
+|++++|||+++|..|+
T Consensus 109 ~L~~vpGIGkKtAerIi 125 (194)
T PRK14605 109 LLSTIPGIGKKTASRIV 125 (194)
T ss_pred HHHhCCCCCHHHHHHHH
Confidence 58999999999999966
No 49
>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=72.56 E-value=2 Score=27.09 Aligned_cols=20 Identities=25% Similarity=0.501 Sum_probs=17.4
Q ss_pred ecccccccCcchHHHHHhHh
Q psy1365 14 ALTAIKGCGRRFSNIVLKKA 33 (140)
Q Consensus 14 ALt~IyGIG~~~A~~Ic~~l 33 (140)
.|..++|||+.+|..|+..+
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 47889999999999998765
No 50
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=71.78 E-value=1.1 Score=28.80 Aligned_cols=43 Identities=14% Similarity=0.192 Sum_probs=27.1
Q ss_pred eeeecccccccCcchHHHHHhHh-------CCCCCCccCCCCHHHHHHHH
Q psy1365 11 VMFALTAIKGCGRRFSNIVLKKA-------DIDLNKRAGECSEEEVDKII 53 (140)
Q Consensus 11 v~~ALt~IyGIG~~~A~~Ic~~l-------GI~~~~~~~~Ls~~qi~~L~ 53 (140)
=...|..++|||+..|.+|.+.= .++.-..+..++++.+++|.
T Consensus 12 s~~eL~~lpgi~~~~A~~Iv~~R~~~G~f~s~~dL~~v~gi~~~~~~~l~ 61 (65)
T PF12836_consen 12 SAEELQALPGIGPKQAKAIVEYREKNGPFKSLEDLKEVPGIGPKTYEKLK 61 (65)
T ss_dssp -HHHHHTSTT--HHHHHHHHHHHHHH-S-SSGGGGGGSTT--HHHHHHHC
T ss_pred CHHHHHHcCCCCHHHHHHHHHHHHhCcCCCCHHHHhhCCCCCHHHHHHHH
Confidence 34458899999999999999764 34444555556777777764
No 51
>PRK12278 50S ribosomal protein L21/unknown domain fusion protein; Provisional
Probab=70.85 E-value=3.2 Score=33.58 Aligned_cols=54 Identities=19% Similarity=0.306 Sum_probs=43.0
Q ss_pred eecccccccCcchHHHHHhHhCCCCCCccCCCCHHHHHHHHHHHhCCCCcCCCcc
Q psy1365 13 FALTAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKIITIMTNPRQYKIPDW 67 (140)
Q Consensus 13 ~ALt~IyGIG~~~A~~Ic~~lGI~~~~~~~~Ls~~qi~~L~~~I~~~~~~~i~~w 67 (140)
-.|+.|.|||+..+.. +..+|+.....+-.++++++..+...+.-+....-+.|
T Consensus 158 DDL~~I~GIGp~~a~~-L~eaGi~tfaQIAa~t~a~ia~id~~l~~~gri~rd~W 211 (221)
T PRK12278 158 DDLTKITGVGPALAKK-LNEAGVTTFAQIAALTDADIAKIDEKLSFKGRIEKDGW 211 (221)
T ss_pred chheeccccChHHHHH-HHHcCCCCHHHhhCCChhhhhhhhhcccCCCccCcchH
Confidence 4589999999998765 67899999999999999999999888853322223445
No 52
>cd00080 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) motif. HhH2 domains are found in Rad2 family of prokaryotic and eukaryotic replication and repair nucleases, i.e., DNA polymerase I, Taq DNA polymerase, DNA repair protein Rad2 endonuclease, flap endonuclease, exonuclease I and IX, 5'-3' exonuclease and also bacteriophage Rnase H. These nucleases degrade RNA-DNA or DNA-DNA duplexes, or both and play essential roles in DNA duplication, repair, and recombination.
Probab=70.64 E-value=2.5 Score=28.14 Aligned_cols=20 Identities=20% Similarity=0.363 Sum_probs=17.2
Q ss_pred cccccccCcchHHHHHhHhC
Q psy1365 15 LTAIKGCGRRFSNIVLKKAD 34 (140)
Q Consensus 15 Lt~IyGIG~~~A~~Ic~~lG 34 (140)
+..|.|||+.+|..|+...|
T Consensus 24 i~gv~giG~k~A~~ll~~~~ 43 (75)
T cd00080 24 IPGVPGIGPKTALKLLKEYG 43 (75)
T ss_pred CCCCCcccHHHHHHHHHHhC
Confidence 45799999999999998855
No 53
>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=70.63 E-value=2.6 Score=29.76 Aligned_cols=37 Identities=19% Similarity=0.073 Sum_probs=28.4
Q ss_pred eecccccccCcchHHHHHhHhCCCCCCccCCCCHHHHH
Q psy1365 13 FALTAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVD 50 (140)
Q Consensus 13 ~ALt~IyGIG~~~A~~Ic~~lGI~~~~~~~~Ls~~qi~ 50 (140)
..|+.|+|||+++|.-+. .+||+.=..+..-+++++-
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 468999999999999887 8999875555555555554
No 54
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=70.53 E-value=2.2 Score=33.24 Aligned_cols=25 Identities=16% Similarity=0.319 Sum_probs=21.6
Q ss_pred eeeecccccccCcchHHHHHhHhCC
Q psy1365 11 VMFALTAIKGCGRRFSNIVLKKADI 35 (140)
Q Consensus 11 v~~ALt~IyGIG~~~A~~Ic~~lGI 35 (140)
+...|..|+|||+++|..|++.+|.
T Consensus 71 ~f~~L~~i~GIGpk~A~~il~~fg~ 95 (192)
T PRK00116 71 LFRLLISVSGVGPKLALAILSGLSP 95 (192)
T ss_pred HHHHHhcCCCCCHHHHHHHHHhCCH
Confidence 4447889999999999999998886
No 55
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=68.66 E-value=2.9 Score=24.27 Aligned_cols=17 Identities=24% Similarity=0.477 Sum_probs=15.0
Q ss_pred ccccccCcchHHHHHhH
Q psy1365 16 TAIKGCGRRFSNIVLKK 32 (140)
Q Consensus 16 t~IyGIG~~~A~~Ic~~ 32 (140)
..|.|||+.+|..++++
T Consensus 19 ~Gv~giG~ktA~~ll~~ 35 (36)
T smart00279 19 PGVKGIGPKTALKLLRE 35 (36)
T ss_pred CCCCcccHHHHHHHHHh
Confidence 57899999999999875
No 56
>PRK12311 rpsB 30S ribosomal protein S2/unknown domain fusion protein; Provisional
Probab=68.53 E-value=2.5 Score=36.05 Aligned_cols=44 Identities=16% Similarity=0.091 Sum_probs=38.8
Q ss_pred eecccccccCcchHHHHHhHhCCCCCCccCCCCHHHHHHHHHHHh
Q psy1365 13 FALTAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKIITIMT 57 (140)
Q Consensus 13 ~ALt~IyGIG~~~A~~Ic~~lGI~~~~~~~~Ls~~qi~~L~~~I~ 57 (140)
--|+.|.|||+..+ ..|..+||.-...+..++++++..+...+.
T Consensus 263 DdL~~I~GiGp~~e-~~L~~~Gi~~f~QiA~~t~~~~a~vd~~l~ 306 (326)
T PRK12311 263 DDLKKLTGVSPQIE-KKLNDLGIFHFWQLAELDPDDAAKIGEELG 306 (326)
T ss_pred hhhhhhccCChhhh-hhhhhcCCCCHHHhhCCChhhhhhhhhccc
Confidence 45899999999876 467899999999999999999999988775
No 57
>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=68.38 E-value=2.9 Score=28.27 Aligned_cols=23 Identities=30% Similarity=0.369 Sum_probs=19.8
Q ss_pred ecccccccCcchHHHHHhHhCCCC
Q psy1365 14 ALTAIKGCGRRFSNIVLKKADIDL 37 (140)
Q Consensus 14 ALt~IyGIG~~~A~~Ic~~lGI~~ 37 (140)
.|++|+|||..+|..|+..+ -|+
T Consensus 3 ~l~sipGig~~~a~~llaei-gd~ 25 (87)
T PF02371_consen 3 LLTSIPGIGPITAATLLAEI-GDI 25 (87)
T ss_pred hhcCCCCccHHHHHHHHHHH-cCc
Confidence 47899999999999999888 444
No 58
>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=68.19 E-value=2.5 Score=27.40 Aligned_cols=20 Identities=15% Similarity=0.302 Sum_probs=16.9
Q ss_pred ecccccccCcchHHHHHhHh
Q psy1365 14 ALTAIKGCGRRFSNIVLKKA 33 (140)
Q Consensus 14 ALt~IyGIG~~~A~~Ic~~l 33 (140)
+++.|+|||.++|..|-..+
T Consensus 48 ~~~~l~gIG~~ia~kI~E~l 67 (68)
T PF14716_consen 48 DLKKLPGIGKSIAKKIDEIL 67 (68)
T ss_dssp HHCTSTTTTHHHHHHHHHHH
T ss_pred HHhhCCCCCHHHHHHHHHHH
Confidence 58999999999999986543
No 59
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=67.79 E-value=2.2 Score=31.39 Aligned_cols=24 Identities=33% Similarity=0.415 Sum_probs=20.6
Q ss_pred eeeeeecccccccCcchHHHHHhH
Q psy1365 9 RKVMFALTAIKGCGRRFSNIVLKK 32 (140)
Q Consensus 9 k~v~~ALt~IyGIG~~~A~~Ic~~ 32 (140)
..+...|++++|||+.+|..+|..
T Consensus 79 ~~~~~~L~~l~GIG~~tA~~~l~~ 102 (158)
T cd00056 79 PDAREELLALPGVGRKTANVVLLF 102 (158)
T ss_pred cccHHHHHcCCCCCHHHHHHHHHH
Confidence 446678999999999999999875
No 60
>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=66.58 E-value=4.4 Score=25.66 Aligned_cols=26 Identities=8% Similarity=-0.026 Sum_probs=19.5
Q ss_pred ccccCcchHHHHHhHhCCC--CCCccCC
Q psy1365 18 IKGCGRRFSNIVLKKADID--LNKRAGE 43 (140)
Q Consensus 18 IyGIG~~~A~~Ic~~lGI~--~~~~~~~ 43 (140)
--||+.+.-+.+|.++||. |..++.+
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 3589999999999999997 4444443
No 61
>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=66.28 E-value=9.6 Score=26.94 Aligned_cols=35 Identities=9% Similarity=0.291 Sum_probs=31.1
Q ss_pred cccCcchHHHHHhHhCCCCCCccCCCCHHHHHHHHHHHh
Q psy1365 19 KGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKIITIMT 57 (140)
Q Consensus 19 yGIG~~~A~~Ic~~lGI~~~~~~~~Ls~~qi~~L~~~I~ 57 (140)
--+|......|+..|+ ++-.+||+++++.+.+++.
T Consensus 33 es~Gh~sGRrIv~IL~----K~k~dltddD~~hMrkVV~ 67 (92)
T PF11338_consen 33 ESVGHESGRRIVEILR----KRKTDLTDDDYEHMRKVVG 67 (92)
T ss_pred cccCcchhhHHHHHHh----cCcccCCHHHHHHHHHHHH
Confidence 3478899999999998 7789999999999999886
No 62
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=66.16 E-value=2.7 Score=30.62 Aligned_cols=22 Identities=36% Similarity=0.425 Sum_probs=18.7
Q ss_pred eeecccccccCcchHHHHHhHh
Q psy1365 12 MFALTAIKGCGRRFSNIVLKKA 33 (140)
Q Consensus 12 ~~ALt~IyGIG~~~A~~Ic~~l 33 (140)
...|..++|||+.+|..+|...
T Consensus 71 ~~~L~~l~GIG~~tA~~~l~~~ 92 (149)
T smart00478 71 REELLKLPGVGRKTANAVLSFA 92 (149)
T ss_pred HHHHHcCCCCcHHHHHHHHHHH
Confidence 4567899999999999998775
No 63
>TIGR01259 comE comEA protein. This model describes the ComEA protein in bacteria. The com E locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. Lesions in the loci has been variously described for the appearance of competence-related pheonotypes and impairment of competence, suggesting their intimate functional role in bacterial transformation.
Probab=65.79 E-value=3.1 Score=30.15 Aligned_cols=29 Identities=14% Similarity=0.170 Sum_probs=22.8
Q ss_pred CCeeeeeecccccccCcchHHHHHhHhCC
Q psy1365 7 GKRKVMFALTAIKGCGRRFSNIVLKKADI 35 (140)
Q Consensus 7 ~~k~v~~ALt~IyGIG~~~A~~Ic~~lGI 35 (140)
=|..-.-.|..++|||+.+|..|++.-.-
T Consensus 62 iNtA~~~eL~~lpGIG~~~A~~Ii~~R~~ 90 (120)
T TIGR01259 62 INAASLEELQALPGIGPAKAKAIIEYREE 90 (120)
T ss_pred CCcCCHHHHhcCCCCCHHHHHHHHHHHHh
Confidence 34444557889999999999999988753
No 64
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=65.13 E-value=3.1 Score=28.63 Aligned_cols=23 Identities=22% Similarity=0.338 Sum_probs=17.5
Q ss_pred ccccccCcchHHHHHhHhCCCCC
Q psy1365 16 TAIKGCGRRFSNIVLKKADIDLN 38 (140)
Q Consensus 16 t~IyGIG~~~A~~Ic~~lGI~~~ 38 (140)
..|.|||-.+|..|..++|++++
T Consensus 49 ~~i~gi~F~~aD~iA~~~g~~~~ 71 (94)
T PF14490_consen 49 EDIDGIGFKTADKIALKLGIEPD 71 (94)
T ss_dssp B-SSSSBHHHHHHHHHTTT--TT
T ss_pred HHccCCCHHHHHHHHHHcCCCCC
Confidence 34899999999999999998864
No 65
>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=64.76 E-value=3 Score=32.66 Aligned_cols=19 Identities=32% Similarity=0.454 Sum_probs=16.7
Q ss_pred eecccccccCcchHHHHHh
Q psy1365 13 FALTAIKGCGRRFSNIVLK 31 (140)
Q Consensus 13 ~ALt~IyGIG~~~A~~Ic~ 31 (140)
-+|+.++|||+++|..|+-
T Consensus 107 ~~L~~ipGiGkKtAerIil 125 (191)
T TIGR00084 107 KALVKIPGVGKKTAERLLL 125 (191)
T ss_pred HHHHhCCCCCHHHHHHHHH
Confidence 3588999999999999983
No 66
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=64.52 E-value=3.5 Score=34.86 Aligned_cols=25 Identities=16% Similarity=0.215 Sum_probs=21.9
Q ss_pred eeecccccccCcchHHHHHhHhCCCC
Q psy1365 12 MFALTAIKGCGRRFSNIVLKKADIDL 37 (140)
Q Consensus 12 ~~ALt~IyGIG~~~A~~Ic~~lGI~~ 37 (140)
...|++|+|||+++|..+-+ +||..
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 34578999999999999998 99975
No 67
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=63.78 E-value=3.8 Score=32.79 Aligned_cols=41 Identities=15% Similarity=0.122 Sum_probs=29.0
Q ss_pred eeecc-cccccCcchHHHHHhHhCCCCCCccCCCCHHHHHHHHHHH
Q psy1365 12 MFALT-AIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKIITIM 56 (140)
Q Consensus 12 ~~ALt-~IyGIG~~~A~~Ic~~lGI~~~~~~~~Ls~~qi~~L~~~I 56 (140)
.-.|. +++|||+.+|..|+.-.|+.|-.-+. ..+.++..-+
T Consensus 117 R~~Ll~~lpGIG~KTAd~vL~~~~~~~~~iVD----tHv~Ri~~Rl 158 (208)
T PRK01229 117 REFLVKNIKGIGYKEASHFLRNVGYEDLAILD----RHILRFLKRY 158 (208)
T ss_pred HHHHHHcCCCCcHHHHHHHHHHccCCCeeeee----HHHHHHHHHh
Confidence 34566 99999999999999766765544443 4666665555
No 68
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=63.70 E-value=2.9 Score=26.89 Aligned_cols=18 Identities=22% Similarity=0.462 Sum_probs=14.9
Q ss_pred cccccCcchHHHHHhHhC
Q psy1365 17 AIKGCGRRFSNIVLKKAD 34 (140)
Q Consensus 17 ~IyGIG~~~A~~Ic~~lG 34 (140)
.|+|||...|+.+++..|
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 699999999999999887
No 69
>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=62.79 E-value=3.1 Score=26.82 Aligned_cols=22 Identities=14% Similarity=0.244 Sum_probs=18.6
Q ss_pred eeeccc-ccccCcchHHHHHhHh
Q psy1365 12 MFALTA-IKGCGRRFSNIVLKKA 33 (140)
Q Consensus 12 ~~ALt~-IyGIG~~~A~~Ic~~l 33 (140)
.-.|.. +.|||...|.+|+..-
T Consensus 15 ~~~L~~~ipgig~~~a~~Il~~R 37 (69)
T TIGR00426 15 AEELQRAMNGVGLKKAEAIVSYR 37 (69)
T ss_pred HHHHHhHCCCCCHHHHHHHHHHH
Confidence 335777 9999999999999884
No 70
>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=62.27 E-value=4.2 Score=33.96 Aligned_cols=24 Identities=17% Similarity=0.304 Sum_probs=21.2
Q ss_pred eecccccccCcchHHHHHhHhCCCC
Q psy1365 13 FALTAIKGCGRRFSNIVLKKADIDL 37 (140)
Q Consensus 13 ~ALt~IyGIG~~~A~~Ic~~lGI~~ 37 (140)
..|.+|+|||+++|..+- .+|+..
T Consensus 85 ~~l~~i~GiGpk~a~~l~-~lGi~s 108 (307)
T cd00141 85 LLLLRVPGVGPKTARKLY-ELGIRT 108 (307)
T ss_pred HHHHcCCCCCHHHHHHHH-HcCCCC
Confidence 457899999999999999 999984
No 71
>PRK10702 endonuclease III; Provisional
Probab=61.74 E-value=4 Score=32.45 Aligned_cols=22 Identities=45% Similarity=0.667 Sum_probs=18.7
Q ss_pred eeecccccccCcchHHHHHhHh
Q psy1365 12 MFALTAIKGCGRRFSNIVLKKA 33 (140)
Q Consensus 12 ~~ALt~IyGIG~~~A~~Ic~~l 33 (140)
.-.|.+++|||+++|..|+..+
T Consensus 108 ~~~Ll~lpGVG~ktA~~ill~a 129 (211)
T PRK10702 108 RAALEALPGVGRKTANVVLNTA 129 (211)
T ss_pred HHHHhcCCcccHHHHHHHHHHH
Confidence 4578999999999999998654
No 72
>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=61.59 E-value=3.5 Score=31.86 Aligned_cols=22 Identities=36% Similarity=0.539 Sum_probs=18.7
Q ss_pred eeecccccccCcchHHHHHhHh
Q psy1365 12 MFALTAIKGCGRRFSNIVLKKA 33 (140)
Q Consensus 12 ~~ALt~IyGIG~~~A~~Ic~~l 33 (140)
...|.+++|||+.+|..||...
T Consensus 105 ~~~L~~l~GIG~ktA~~ill~~ 126 (191)
T TIGR01083 105 REELVKLPGVGRKTANVVLNVA 126 (191)
T ss_pred HHHHHhCCCCcHHHHHHHHHHH
Confidence 4568999999999999999654
No 73
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=61.25 E-value=1.6 Score=34.26 Aligned_cols=27 Identities=15% Similarity=0.308 Sum_probs=22.5
Q ss_pred CeeeeeecccccccCcchHHHHHhHhC
Q psy1365 8 KRKVMFALTAIKGCGRRFSNIVLKKAD 34 (140)
Q Consensus 8 ~k~v~~ALt~IyGIG~~~A~~Ic~~lG 34 (140)
.+.++..|.+|.|||+++|..|+..++
T Consensus 68 Er~lF~~Li~V~GIGpK~Al~ILs~~~ 94 (194)
T PRK14605 68 ELSLFETLIDVSGIGPKLGLAMLSAMN 94 (194)
T ss_pred HHHHHHHHhCCCCCCHHHHHHHHHhCC
Confidence 345666789999999999999998765
No 74
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=60.76 E-value=6.7 Score=31.68 Aligned_cols=40 Identities=20% Similarity=0.135 Sum_probs=28.3
Q ss_pred cCCCCeee--eeecccccccCcchHHHHHhHhCCCCCCccCC
Q psy1365 4 NIDGKRKV--MFALTAIKGCGRRFSNIVLKKADIDLNKRAGE 43 (140)
Q Consensus 4 ~l~~~k~v--~~ALt~IyGIG~~~A~~Ic~~lGI~~~~~~~~ 43 (140)
++++.++. .--|-+|+|||.-+|..|+--+.=-|..-+..
T Consensus 104 ~~~~~~~~~~R~~LL~iKGIG~ETaDsILlYa~~rp~FVvD~ 145 (215)
T COG2231 104 NLESFKSEVLREELLSIKGIGKETADSILLYALDRPVFVVDK 145 (215)
T ss_pred hhhccchHHHHHHHHccCCcchhhHHHHHHHHhcCcccchhH
Confidence 34444444 45678999999999999998776666555444
No 75
>PRK08609 hypothetical protein; Provisional
Probab=58.41 E-value=5.8 Score=35.96 Aligned_cols=24 Identities=17% Similarity=0.252 Sum_probs=21.7
Q ss_pred eecccccccCcchHHHHHhHhCCC
Q psy1365 13 FALTAIKGCGRRFSNIVLKKADID 36 (140)
Q Consensus 13 ~ALt~IyGIG~~~A~~Ic~~lGI~ 36 (140)
..|++|+|||+++|..+-+.+||.
T Consensus 88 ~~l~~i~GiGpk~a~~l~~~lGi~ 111 (570)
T PRK08609 88 LPLLKLPGLGGKKIAKLYKELGVV 111 (570)
T ss_pred HHHhcCCCCCHHHHHHHHHHhCCC
Confidence 457899999999999999999985
No 76
>PHA02564 V virion protein; Provisional
Probab=58.24 E-value=17 Score=27.51 Aligned_cols=32 Identities=6% Similarity=0.128 Sum_probs=27.0
Q ss_pred hHHHHHhHhCCCCCCccCCCCHHHHHHHHHHHh
Q psy1365 25 FSNIVLKKADIDLNKRAGECSEEEVDKIITIMT 57 (140)
Q Consensus 25 ~A~~Ic~~lGI~~~~~~~~Ls~~qi~~L~~~I~ 57 (140)
.+..||+.+|++|+.++.-.++ .+..|..+|.
T Consensus 87 Yi~~Vs~~~GV~~~~~idl~d~-~l~~l~~Aii 118 (141)
T PHA02564 87 YATAVANAMGVPPQAGLHLDQD-TLAALVTAII 118 (141)
T ss_pred HHHHHHHHHCCCCCCcCcCCcH-HHHHHHHHHH
Confidence 4788999999999999996555 8888888874
No 77
>COG2081 Predicted flavoproteins [General function prediction only]
Probab=57.04 E-value=12 Score=33.07 Aligned_cols=38 Identities=16% Similarity=0.288 Sum_probs=35.6
Q ss_pred ccCcchHHHHHhHhCCCCCCccCCCCHHHHHHHHHHHhC
Q psy1365 20 GCGRRFSNIVLKKADIDLNKRAGECSEEEVDKIITIMTN 58 (140)
Q Consensus 20 GIG~~~A~~Ic~~lGI~~~~~~~~Ls~~qi~~L~~~I~~ 58 (140)
.++.+.+..++.+.|| |+..+.+||+.|+++|.+.|+.
T Consensus 295 ~lp~rlv~~~l~~~~i-~~~~~~~ls~~~~~~l~~~ik~ 332 (408)
T COG2081 295 LLPKRLVEFLLERAGI-PDEPLAQLSPKELAQLAAALKA 332 (408)
T ss_pred HhhhHHHHHHHHhccC-CCcchhhcCHHHHHHHHHHHhc
Confidence 4788999999999999 9999999999999999999985
No 78
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=55.25 E-value=6.2 Score=32.25 Aligned_cols=38 Identities=13% Similarity=0.264 Sum_probs=21.4
Q ss_pred ecccccccCcchHHHHHhHhCCCCCCccCCCCHHHHHHH
Q psy1365 14 ALTAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKI 52 (140)
Q Consensus 14 ALt~IyGIG~~~A~~Ic~~lGI~~~~~~~~Ls~~qi~~L 52 (140)
.|..|.|||+..+..+++. ||..-..+..-|.++|..+
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 4666777777777766544 5554444444444444443
No 79
>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=54.37 E-value=6.3 Score=32.63 Aligned_cols=22 Identities=32% Similarity=0.418 Sum_probs=18.8
Q ss_pred eeecccccccCcchHHHHHhHh
Q psy1365 12 MFALTAIKGCGRRFSNIVLKKA 33 (140)
Q Consensus 12 ~~ALt~IyGIG~~~A~~Ic~~l 33 (140)
.-.|.+++|||+.+|..||..+
T Consensus 104 ~~~L~~LpGIG~~TA~~Il~~a 125 (275)
T TIGR01084 104 FEDLAALPGVGRYTAGAILSFA 125 (275)
T ss_pred HHHHHhCCCCCHHHHHHHHHHH
Confidence 4578999999999999999654
No 80
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=53.53 E-value=9 Score=30.79 Aligned_cols=28 Identities=18% Similarity=0.024 Sum_probs=20.6
Q ss_pred eeecccccccCcchHHHHHhHhCCCCCC
Q psy1365 12 MFALTAIKGCGRRFSNIVLKKADIDLNK 39 (140)
Q Consensus 12 ~~ALt~IyGIG~~~A~~Ic~~lGI~~~~ 39 (140)
.-.|.+++|||+.+|..|+--+-=.|..
T Consensus 120 re~Ll~l~GIG~kTAd~iLlya~~rp~f 147 (218)
T PRK13913 120 REWLLDQKGIGKESADAILCYVCAKEVM 147 (218)
T ss_pred HHHHHcCCCccHHHHHHHHHHHcCCCcc
Confidence 3468999999999999988654333333
No 81
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=52.38 E-value=9.3 Score=30.55 Aligned_cols=86 Identities=19% Similarity=0.271 Sum_probs=53.1
Q ss_pred eeeecccccccCcchHHHHHhHhCCCCCCccCCCCHHHHHHHHHHHhCCC-CcCC-C-----------cccccccccccC
Q psy1365 11 VMFALTAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKIITIMTNPR-QYKI-P-----------DWFLNRQKDIVD 77 (140)
Q Consensus 11 v~~ALt~IyGIG~~~A~~Ic~~lGI~~~~~~~~Ls~~qi~~L~~~I~~~~-~~~i-~-----------~w~~nr~~d~~t 77 (140)
+..+|..++|||++.|..+.--|- +.+++++..|.++|.+-. +... . .-+.+-++|..
T Consensus 10 LI~~l~kLPGvG~KsA~R~AfhLL--------~~~~~~~~~la~al~~a~~~i~~C~~C~~~te~d~C~ICsd~~Rd~~- 80 (198)
T COG0353 10 LIDALKKLPGVGPKSAQRLAFHLL--------QRDREDVERLAKALLEAKENIKHCSVCGNLTESDPCDICSDESRDKS- 80 (198)
T ss_pred HHHHHhhCCCCChhHHHHHHHHHH--------ccCHHHHHHHHHHHHHHHhcCccccccCCcCCCCcCcCcCCcccCCc-
Confidence 456899999999999999885543 346778888877775321 1110 0 11233334432
Q ss_pred CceeEeeccchhHHHHHHHHHHHHHHhhhheeccCCCCC
Q psy1365 78 GKYSQILLTSTAQLDSKLREDLERLKKIRAHRGMRHYWG 116 (140)
Q Consensus 78 g~~~~l~~~~~~~L~~~~~~~I~rl~~i~syRG~RH~~g 116 (140)
.+-+++ .-.|+..|=+.+.|+|.=|..|
T Consensus 81 --~icVVe---------~p~Dv~a~E~~~~f~G~YhVL~ 108 (198)
T COG0353 81 --QLCVVE---------EPKDVLALEKTGEFRGLYHVLG 108 (198)
T ss_pred --eEEEEc---------chHHHHHHHHhcccCeeEEEec
Confidence 344444 2346666777888888888765
No 82
>PRK10880 adenine DNA glycosylase; Provisional
Probab=51.66 E-value=6.6 Score=33.70 Aligned_cols=23 Identities=22% Similarity=0.394 Sum_probs=19.3
Q ss_pred eeeecccccccCcchHHHHHhHh
Q psy1365 11 VMFALTAIKGCGRRFSNIVLKKA 33 (140)
Q Consensus 11 v~~ALt~IyGIG~~~A~~Ic~~l 33 (140)
..-.|.+++|||+++|..||..+
T Consensus 107 ~~~~L~~LpGIG~~TA~aIl~~a 129 (350)
T PRK10880 107 TFEEVAALPGVGRSTAGAILSLS 129 (350)
T ss_pred hHHHHhcCCCccHHHHHHHHHHH
Confidence 34578999999999999999753
No 83
>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=51.56 E-value=2.5 Score=30.05 Aligned_cols=19 Identities=16% Similarity=0.350 Sum_probs=15.1
Q ss_pred ccccccCcchHHHHHhHhC
Q psy1365 16 TAIKGCGRRFSNIVLKKAD 34 (140)
Q Consensus 16 t~IyGIG~~~A~~Ic~~lG 34 (140)
-.+.|||+++|..+++..|
T Consensus 21 PGV~GIG~KtA~~LL~~yg 39 (101)
T PF01367_consen 21 PGVPGIGPKTAAKLLQEYG 39 (101)
T ss_dssp ---TTSTCHCCCCCHHHHT
T ss_pred CCCCCCCHHHHHHHHHHcC
Confidence 4689999999999999877
No 84
>PRK13910 DNA glycosylase MutY; Provisional
Probab=51.41 E-value=6.7 Score=32.80 Aligned_cols=22 Identities=23% Similarity=0.243 Sum_probs=18.9
Q ss_pred eeecccccccCcchHHHHHhHh
Q psy1365 12 MFALTAIKGCGRRFSNIVLKKA 33 (140)
Q Consensus 12 ~~ALt~IyGIG~~~A~~Ic~~l 33 (140)
.-.|.+++|||+++|..|+..+
T Consensus 71 ~~~L~~LpGIG~kTA~aIl~~a 92 (289)
T PRK13910 71 YQSLLKLPGIGAYTANAILCFG 92 (289)
T ss_pred HHHHHhCCCCCHHHHHHHHHHH
Confidence 4678999999999999998643
No 85
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=51.30 E-value=9.6 Score=31.59 Aligned_cols=17 Identities=24% Similarity=0.401 Sum_probs=16.6
Q ss_pred ccccCcchHHHHHhHhC
Q psy1365 18 IKGCGRRFSNIVLKKAD 34 (140)
Q Consensus 18 IyGIG~~~A~~Ic~~lG 34 (140)
|+|||+.+|..++...|
T Consensus 203 V~GIG~ktA~~Ll~~~g 219 (310)
T COG0258 203 VKGIGPKTALKLLQEYG 219 (310)
T ss_pred CCCcCHHHHHHHHHHhC
Confidence 99999999999999999
No 86
>PRK00076 recR recombination protein RecR; Reviewed
Probab=50.77 E-value=8.9 Score=30.49 Aligned_cols=40 Identities=15% Similarity=0.182 Sum_probs=29.4
Q ss_pred eeeecccccccCcchHHHHHhHhCCCCCCccCCCCHHHHHHHHHHHhC
Q psy1365 11 VMFALTAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKIITIMTN 58 (140)
Q Consensus 11 v~~ALt~IyGIG~~~A~~Ic~~lGI~~~~~~~~Ls~~qi~~L~~~I~~ 58 (140)
+..+|..++|||+++|..+.-.+=- -+++++..|.+.|.+
T Consensus 9 Li~~l~~LPGIG~KsA~Rla~~ll~--------~~~~~~~~la~~i~~ 48 (196)
T PRK00076 9 LIEALRKLPGIGPKSAQRLAFHLLQ--------RDREDVLRLAQALEE 48 (196)
T ss_pred HHHHHHHCCCCCHHHHHHHHHHHHc--------CCHHHHHHHHHHHHH
Confidence 4457899999999999999865533 346677777766653
No 87
>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=50.14 E-value=1.9 Score=33.76 Aligned_cols=25 Identities=20% Similarity=0.486 Sum_probs=20.1
Q ss_pred CeeeeeecccccccCcchHHHHHhH
Q psy1365 8 KRKVMFALTAIKGCGRRFSNIVLKK 32 (140)
Q Consensus 8 ~k~v~~ALt~IyGIG~~~A~~Ic~~ 32 (140)
.+.++..|.+|.|||+++|..|+..
T Consensus 67 Er~lF~~L~~V~GIGpK~Al~iL~~ 91 (191)
T TIGR00084 67 ERELFKELIKVNGVGPKLALAILSN 91 (191)
T ss_pred HHHHHHHHhCCCCCCHHHHHHHHhc
Confidence 3456677899999999999999543
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=50.10 E-value=9.3 Score=30.41 Aligned_cols=39 Identities=13% Similarity=0.129 Sum_probs=28.4
Q ss_pred eeeecccccccCcchHHHHHhHhCCCCCCccCCCCHHHHHHHHHHHh
Q psy1365 11 VMFALTAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKIITIMT 57 (140)
Q Consensus 11 v~~ALt~IyGIG~~~A~~Ic~~lGI~~~~~~~~Ls~~qi~~L~~~I~ 57 (140)
+..+|..++|||+++|..+.-.+=- .+++++..|.++|.
T Consensus 9 Li~~l~~LPGIG~KsA~RlA~~ll~--------~~~~~~~~la~ai~ 47 (195)
T TIGR00615 9 LIESLKKLPGIGPKSAQRLAFHLLK--------RDPSEVLRLAQALL 47 (195)
T ss_pred HHHHHHHCCCCCHHHHHHHHHHHHc--------CCHHHHHHHHHHHH
Confidence 4557899999999999999754432 34667777766664
No 89
>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=49.86 E-value=14 Score=34.41 Aligned_cols=41 Identities=17% Similarity=0.344 Sum_probs=28.8
Q ss_pred cccccCcchHHHHHhHhCCCC--------C--CccCCCCHHHHHHHHHHHh
Q psy1365 17 AIKGCGRRFSNIVLKKADIDL--------N--KRAGECSEEEVDKIITIMT 57 (140)
Q Consensus 17 ~IyGIG~~~A~~Ic~~lGI~~--------~--~~~~~Ls~~qi~~L~~~I~ 57 (140)
.|+|||+.+|..|.+.+|.+. + ..+.-++++..+.|.+.+.
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 499999999999999988662 1 1233466666666655553
No 90
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=49.06 E-value=4.2 Score=32.18 Aligned_cols=26 Identities=19% Similarity=0.339 Sum_probs=21.3
Q ss_pred eeeeeecccccccCcchHHHHHhHhC
Q psy1365 9 RKVMFALTAIKGCGRRFSNIVLKKAD 34 (140)
Q Consensus 9 k~v~~ALt~IyGIG~~~A~~Ic~~lG 34 (140)
+.++..|.++.|||+++|..|+..++
T Consensus 70 r~lF~~Li~V~GIGpK~Al~iLs~~~ 95 (203)
T PRK14602 70 RQTFIVLISISKVGAKTALAILSQFR 95 (203)
T ss_pred HHHHHHHhCCCCcCHHHHHHHHhhCC
Confidence 44566789999999999999997653
No 91
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=48.57 E-value=8.1 Score=30.08 Aligned_cols=21 Identities=24% Similarity=0.464 Sum_probs=18.4
Q ss_pred ecccccccCcchHHHHHhHhC
Q psy1365 14 ALTAIKGCGRRFSNIVLKKAD 34 (140)
Q Consensus 14 ALt~IyGIG~~~A~~Ic~~lG 34 (140)
.|+.++|||+++|..|+..+.
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 92
>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=47.54 E-value=8.2 Score=32.33 Aligned_cols=30 Identities=13% Similarity=0.082 Sum_probs=23.4
Q ss_pred eeeecccccccCcchHHHHHhHhCCCCCCc
Q psy1365 11 VMFALTAIKGCGRRFSNIVLKKADIDLNKR 40 (140)
Q Consensus 11 v~~ALt~IyGIG~~~A~~Ic~~lGI~~~~~ 40 (140)
+.-.|+.++|||+.+|..||-..-=.|+.-
T Consensus 218 ~~~~L~~l~GIG~~tAd~vll~~l~~~d~~ 247 (310)
T TIGR00588 218 AREALCELPGVGPKVADCICLMGLDKPQAV 247 (310)
T ss_pred HHHHHHhCCCccHHHHHHHHHHhCCCCCce
Confidence 456789999999999999997755455443
No 93
>PRK13844 recombination protein RecR; Provisional
Probab=46.99 E-value=11 Score=30.13 Aligned_cols=40 Identities=18% Similarity=0.119 Sum_probs=29.1
Q ss_pred eeeecccccccCcchHHHHHhHhCCCCCCccCCCCHHHHHHHHHHHhC
Q psy1365 11 VMFALTAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKIITIMTN 58 (140)
Q Consensus 11 v~~ALt~IyGIG~~~A~~Ic~~lGI~~~~~~~~Ls~~qi~~L~~~I~~ 58 (140)
+.-+|..++|||+++|..+.-.+= +.+++++..|.+.|.+
T Consensus 13 LI~~l~~LPGIG~KsA~Rla~~lL--------~~~~~~~~~la~~i~~ 52 (200)
T PRK13844 13 VIESLRKLPTIGKKSSQRLALYLL--------DKSPETAIAIANSLLD 52 (200)
T ss_pred HHHHHHHCCCCCHHHHHHHHHHHH--------cCCHHHHHHHHHHHHH
Confidence 445789999999999999885542 2356777777777653
No 94
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=46.53 E-value=11 Score=31.15 Aligned_cols=33 Identities=18% Similarity=0.152 Sum_probs=25.0
Q ss_pred eeeecccccccCcchHHHHHhHhCCCCCCc-cCC
Q psy1365 11 VMFALTAIKGCGRRFSNIVLKKADIDLNKR-AGE 43 (140)
Q Consensus 11 v~~ALt~IyGIG~~~A~~Ic~~lGI~~~~~-~~~ 43 (140)
+.-.|+.|+|||+.+|..|+-..-=+|+.- .+|
T Consensus 205 ~~~~L~~LpGIGpwTA~~vllr~lg~~D~fp~~D 238 (283)
T PRK10308 205 AMKTLQTFPGIGRWTANYFALRGWQAKDVFLPDD 238 (283)
T ss_pred HHHHHhcCCCcCHHHHHHHHHHhCCCCCCCCccc
Confidence 456799999999999999997744455554 444
No 95
>PRK12373 NADH dehydrogenase subunit E; Provisional
Probab=46.42 E-value=15 Score=32.31 Aligned_cols=54 Identities=17% Similarity=0.232 Sum_probs=43.0
Q ss_pred ecccccccCcchHHHHHhHhCCCCCCccCCCCHHHHHHHHHHHhCCCCcCCCccc
Q psy1365 14 ALTAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKIITIMTNPRQYKIPDWF 68 (140)
Q Consensus 14 ALt~IyGIG~~~A~~Ic~~lGI~~~~~~~~Ls~~qi~~L~~~I~~~~~~~i~~w~ 68 (140)
-|+.|.|||+..+. .|..+||.....+-.++++++..+...+.-+....-..|.
T Consensus 324 DLk~I~GIGpk~e~-~Ln~~Gi~~f~QIA~wt~~eia~vd~~l~f~Gri~rd~Wv 377 (400)
T PRK12373 324 DLKLISGVGPKIEA-TLNELGIFTFDQVAAWKKAERAWVDGYLNFKGRIERDDWV 377 (400)
T ss_pred hhhhccCCChHHHH-HHHhcCCCCHHHHhCCCHHHhHHhhhcccCCCCcCcchHH
Confidence 58999999998765 5789999999999999999999998888633223335564
No 96
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=44.97 E-value=23 Score=28.43 Aligned_cols=40 Identities=23% Similarity=0.220 Sum_probs=28.0
Q ss_pred eecccccccCcchHHHHHhHhCCCCCCccCCCCHHHHHHHHHHH
Q psy1365 13 FALTAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKIITIM 56 (140)
Q Consensus 13 ~ALt~IyGIG~~~A~~Ic~~lGI~~~~~~~~Ls~~qi~~L~~~I 56 (140)
.+|.+..|||+++|+.++..+---|...|.- .|.++.+-+
T Consensus 109 ~eL~~LPGVGrKTAnvVL~~a~g~p~i~VDT----HV~Rvs~R~ 148 (211)
T COG0177 109 EELLSLPGVGRKTANVVLSFAFGIPAIAVDT----HVHRVSNRL 148 (211)
T ss_pred HHHHhCCCcchHHHHHHHHhhcCCCcccccc----hHHHHHHHh
Confidence 4689999999999999887733333555553 566665544
No 97
>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=44.65 E-value=43 Score=20.74 Aligned_cols=43 Identities=14% Similarity=0.169 Sum_probs=32.3
Q ss_pred cccccccCcchHHHHHhHhCCCCCCcc----CCCCHHHHHHHHHHHh
Q psy1365 15 LTAIKGCGRRFSNIVLKKADIDLNKRA----GECSEEEVDKIITIMT 57 (140)
Q Consensus 15 Lt~IyGIG~~~A~~Ic~~lGI~~~~~~----~~Ls~~qi~~L~~~I~ 57 (140)
+....||...+...-.+..|+.+..+- ...+++|+..|..+..
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 356789999999988887787664332 3679999998877764
No 98
>PRK07373 DNA polymerase III subunit alpha; Reviewed
Probab=43.85 E-value=16 Score=32.44 Aligned_cols=25 Identities=28% Similarity=0.526 Sum_probs=22.1
Q ss_pred CeeeeeecccccccCcchHHHHHhH
Q psy1365 8 KRKVMFALTAIKGCGRRFSNIVLKK 32 (140)
Q Consensus 8 ~k~v~~ALt~IyGIG~~~A~~Ic~~ 32 (140)
+..|.|+|..|+|||...+.+|++.
T Consensus 109 ~~~IrfGL~aIKGVG~~~i~~Iv~e 133 (449)
T PRK07373 109 GEKILFGLSAVRNLGEGAIESILKA 133 (449)
T ss_pred CCEEEEcchhcCCCCHHHHHHHHHH
Confidence 3469999999999999999999864
No 99
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=43.62 E-value=2.6 Score=33.08 Aligned_cols=26 Identities=15% Similarity=0.378 Sum_probs=21.1
Q ss_pred CeeeeeecccccccCcchHHHHHhHh
Q psy1365 8 KRKVMFALTAIKGCGRRFSNIVLKKA 33 (140)
Q Consensus 8 ~k~v~~ALt~IyGIG~~~A~~Ic~~l 33 (140)
.+.++..|.++.|||+++|..|+..+
T Consensus 68 Er~lF~~Li~V~GIGpK~AL~iLs~~ 93 (188)
T PRK14606 68 KKELFLSLTKVSRLGPKTALKIISNE 93 (188)
T ss_pred HHHHHHHHhccCCccHHHHHHHHcCC
Confidence 34566778999999999999998543
No 100
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=43.37 E-value=11 Score=31.45 Aligned_cols=23 Identities=30% Similarity=0.359 Sum_probs=19.7
Q ss_pred eeeecccccccCcchHHHHHhHh
Q psy1365 11 VMFALTAIKGCGRRFSNIVLKKA 33 (140)
Q Consensus 11 v~~ALt~IyGIG~~~A~~Ic~~l 33 (140)
+.-.|++|.|||+-+|..+|-..
T Consensus 196 a~e~L~~i~GIG~WTAe~~llf~ 218 (285)
T COG0122 196 AIEELTALKGIGPWTAEMFLLFG 218 (285)
T ss_pred HHHHHHcCCCcCHHHHHHHHHHc
Confidence 45679999999999999999663
No 101
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=41.94 E-value=4.1 Score=31.92 Aligned_cols=25 Identities=20% Similarity=0.275 Sum_probs=20.5
Q ss_pred CeeeeeecccccccCcchHHHHHhH
Q psy1365 8 KRKVMFALTAIKGCGRRFSNIVLKK 32 (140)
Q Consensus 8 ~k~v~~ALt~IyGIG~~~A~~Ic~~ 32 (140)
.+.++..|.++.|||+++|..||..
T Consensus 68 Er~lF~~Li~VsGIGpK~Al~ILs~ 92 (183)
T PRK14601 68 EQKMFEMLLKVNGIGANTAMAVCSS 92 (183)
T ss_pred HHHHHHHHhccCCccHHHHHHHHcC
Confidence 3456667899999999999999854
No 102
>PF01698 FLO_LFY: Floricaula / Leafy protein; InterPro: IPR002910 This family consists of various plant development proteins which are homologues of Floricaula (FLO) and leafy (LFY) proteins which are floral meristem identity proteins. Mutations in the sequences of these proteins affect flower and leaf development.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2VY1_A 2VY2_A.
Probab=41.80 E-value=8.6 Score=33.63 Aligned_cols=41 Identities=10% Similarity=0.149 Sum_probs=0.0
Q ss_pred cccccCcchHHHHHhHhCCCCCCccCCCCHHHHHHHHHHHhCC
Q psy1365 17 AIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKIITIMTNP 59 (140)
Q Consensus 17 ~IyGIG~~~A~~Ic~~lGI~~~~~~~~Ls~~qi~~L~~~I~~~ 59 (140)
.=|||-++++..|. .|||--++-++ ++|+||+.+.+.|...
T Consensus 56 ~~YGVRy~T~AKIa-ElGFTvsTLl~-M~deELDdmM~sL~~i 96 (386)
T PF01698_consen 56 QGYGVRYYTAAKIA-ELGFTVSTLLN-MTDEELDDMMNSLSQI 96 (386)
T ss_dssp -------------------------------------------
T ss_pred hhccccHHHHHHHH-HhcccHHHHhc-ccHHHHHHHHHHHHHH
Confidence 45899999998886 68999888776 7999999999888763
No 103
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=41.64 E-value=4.2 Score=31.87 Aligned_cols=26 Identities=15% Similarity=0.270 Sum_probs=21.0
Q ss_pred CeeeeeecccccccCcchHHHHHhHh
Q psy1365 8 KRKVMFALTAIKGCGRRFSNIVLKKA 33 (140)
Q Consensus 8 ~k~v~~ALt~IyGIG~~~A~~Ic~~l 33 (140)
.+.++.-|.++.|||+++|..|+..+
T Consensus 68 Er~lF~~LisV~GIGpK~Al~iLs~~ 93 (186)
T PRK14600 68 EQDCLRMLVKVSGVNYKTAMSILSKL 93 (186)
T ss_pred HHHHHHHHhCcCCcCHHHHHHHHccC
Confidence 34556678999999999999998654
No 104
>smart00475 53EXOc 5'-3' exonuclease.
Probab=41.63 E-value=15 Score=30.10 Aligned_cols=20 Identities=20% Similarity=0.428 Sum_probs=17.5
Q ss_pred cccccccCcchHHHHHhHhC
Q psy1365 15 LTAIKGCGRRFSNIVLKKAD 34 (140)
Q Consensus 15 Lt~IyGIG~~~A~~Ic~~lG 34 (140)
+..+.|||+++|..++++.|
T Consensus 188 ipGV~GIG~KtA~~Ll~~yg 207 (259)
T smart00475 188 IPGVPGIGEKTAAKLLKEFG 207 (259)
T ss_pred CCCCCCCCHHHHHHHHHHhC
Confidence 35689999999999998877
No 105
>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=41.59 E-value=15 Score=29.50 Aligned_cols=20 Identities=20% Similarity=0.429 Sum_probs=17.0
Q ss_pred cccccccCcchHHHHHhHhC
Q psy1365 15 LTAIKGCGRRFSNIVLKKAD 34 (140)
Q Consensus 15 Lt~IyGIG~~~A~~Ic~~lG 34 (140)
+..|+|||+++|..++++.|
T Consensus 185 ipGv~GiG~ktA~~Ll~~~g 204 (240)
T cd00008 185 IPGVPGIGEKTAAKLLKEYG 204 (240)
T ss_pred CCCCCccCHHHHHHHHHHhC
Confidence 45689999999999998864
No 106
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=41.39 E-value=4.1 Score=32.11 Aligned_cols=26 Identities=15% Similarity=0.289 Sum_probs=20.9
Q ss_pred CeeeeeecccccccCcchHHHHHhHh
Q psy1365 8 KRKVMFALTAIKGCGRRFSNIVLKKA 33 (140)
Q Consensus 8 ~k~v~~ALt~IyGIG~~~A~~Ic~~l 33 (140)
.+.++..|.++.|||+++|..|+..+
T Consensus 67 Er~lF~~L~~V~GIGpK~AL~iLs~~ 92 (197)
T PRK14603 67 SLELFELLLGVSGVGPKLALALLSAL 92 (197)
T ss_pred HHHHHHHHhCcCCcCHHHHHHHHcCC
Confidence 34566678999999999999998543
No 107
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=40.76 E-value=9.9 Score=22.74 Aligned_cols=30 Identities=23% Similarity=0.398 Sum_probs=17.0
Q ss_pred CCCHHHHHHHHHHHhCCCCcCCCcccccccc
Q psy1365 43 ECSEEEVDKIITIMTNPRQYKIPDWFLNRQK 73 (140)
Q Consensus 43 ~Ls~~qi~~L~~~I~~~~~~~i~~w~~nr~~ 73 (140)
..+.+++..|...+.-+ ...|-.||-|+|.
T Consensus 24 ~P~~~~~~~la~~~~l~-~~qV~~WF~nrR~ 53 (56)
T smart00389 24 YPSREEREELAAKLGLS-ERQVKVWFQNRRA 53 (56)
T ss_pred CCCHHHHHHHHHHHCcC-HHHHHHhHHHHhh
Confidence 34566666666665422 2345568777763
No 108
>PRK09482 flap endonuclease-like protein; Provisional
Probab=40.02 E-value=16 Score=29.99 Aligned_cols=20 Identities=15% Similarity=0.348 Sum_probs=17.2
Q ss_pred cccccccCcchHHHHHhHhC
Q psy1365 15 LTAIKGCGRRFSNIVLKKAD 34 (140)
Q Consensus 15 Lt~IyGIG~~~A~~Ic~~lG 34 (140)
+..++|||+++|..+++..|
T Consensus 184 IpGVpGIG~KtA~~LL~~~g 203 (256)
T PRK09482 184 IPGVAGIGPKSAAELLNQFR 203 (256)
T ss_pred CCCCCCcChHHHHHHHHHhC
Confidence 35689999999999998876
No 109
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=39.75 E-value=18 Score=33.14 Aligned_cols=43 Identities=33% Similarity=0.361 Sum_probs=30.8
Q ss_pred CeeeeeecccccccCcchHHHHHhHhCCCCCCccCCCCHHHHHHH
Q psy1365 8 KRKVMFALTAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKI 52 (140)
Q Consensus 8 ~k~v~~ALt~IyGIG~~~A~~Ic~~lGI~~~~~~~~Ls~~qi~~L 52 (140)
......+|..|.|||+..+..|++.+|= -..+.+-|.+++..+
T Consensus 538 k~~~~s~L~~IpGIG~k~~k~Ll~~FgS--~~~i~~As~eeL~~v 580 (598)
T PRK00558 538 KARLTSALDDIPGIGPKRRKALLKHFGS--LKAIKEASVEELAKV 580 (598)
T ss_pred cchhhhhHhhCCCcCHHHHHHHHHHcCC--HHHHHhCCHHHHhhc
Confidence 3446789999999999999999998873 223344455555443
No 110
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=39.41 E-value=13 Score=29.30 Aligned_cols=24 Identities=21% Similarity=0.357 Sum_probs=20.0
Q ss_pred eeeeeecccccccCcchHHHHHhH
Q psy1365 9 RKVMFALTAIKGCGRRFSNIVLKK 32 (140)
Q Consensus 9 k~v~~ALt~IyGIG~~~A~~Ic~~ 32 (140)
+.++.-|.++.|||+++|..|+..
T Consensus 69 r~lF~~Li~V~GIGpK~Al~iLs~ 92 (195)
T PRK14604 69 RQLFELLIGVSGVGPKAALNLLSS 92 (195)
T ss_pred HHHHHHHhCcCCcCHHHHHHHHcC
Confidence 445667899999999999999964
No 111
>PRK05898 dnaE DNA polymerase III DnaE; Validated
Probab=39.02 E-value=45 Score=32.62 Aligned_cols=46 Identities=17% Similarity=0.301 Sum_probs=32.2
Q ss_pred CeeeeeecccccccCcchHHHHHhHhCCCCCC---------ccCCCCHHHHHHHH
Q psy1365 8 KRKVMFALTAIKGCGRRFSNIVLKKADIDLNK---------RAGECSEEEVDKII 53 (140)
Q Consensus 8 ~k~v~~ALt~IyGIG~~~A~~Ic~~lGI~~~~---------~~~~Ls~~qi~~L~ 53 (140)
+..|.++|+.|+|||...+..|.+.-.-.|.. ....++...++.|.
T Consensus 747 ~~~Ir~gL~~Ikgig~~~~~~I~~~R~~g~f~~~~df~~r~~~~~i~k~~le~LI 801 (971)
T PRK05898 747 KQIIRFGFNTIKGFGDELLKKIKSALQNKTFSDFISYIDALKKNNVSLSNIEILI 801 (971)
T ss_pred CCeEEecchhcCCcCHHHHHHHHHHHhcCCCCCHHHHHHHhhhcCCCHHHHHHHH
Confidence 45799999999999999999998643322321 23445666666664
No 112
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=38.06 E-value=5.1 Score=31.80 Aligned_cols=26 Identities=31% Similarity=0.394 Sum_probs=20.9
Q ss_pred CeeeeeecccccccCcchHHHHHhHh
Q psy1365 8 KRKVMFALTAIKGCGRRFSNIVLKKA 33 (140)
Q Consensus 8 ~k~v~~ALt~IyGIG~~~A~~Ic~~l 33 (140)
.+.++.-|.++.|||+++|..||..+
T Consensus 67 Er~lF~~LisVsGIGPK~ALaILs~~ 92 (196)
T PRK13901 67 EREVFEELIGVDGIGPRAALRVLSGI 92 (196)
T ss_pred HHHHHHHHhCcCCcCHHHHHHHHcCC
Confidence 34556678999999999999998543
No 113
>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]
Probab=38.03 E-value=24 Score=27.85 Aligned_cols=25 Identities=20% Similarity=0.372 Sum_probs=22.4
Q ss_pred eeecccccccCcchHHHHHhHhCCC
Q psy1365 12 MFALTAIKGCGRRFSNIVLKKADID 36 (140)
Q Consensus 12 ~~ALt~IyGIG~~~A~~Ic~~lGI~ 36 (140)
.+|+|..+|+|+++....++.+|++
T Consensus 2 ~I~ITGTPGvGKTT~~~~L~~lg~~ 26 (180)
T COG1936 2 LIAITGTPGVGKTTVCKLLRELGYK 26 (180)
T ss_pred eEEEeCCCCCchHHHHHHHHHhCCc
Confidence 4789999999999999999988876
No 114
>PRK14976 5'-3' exonuclease; Provisional
Probab=37.60 E-value=18 Score=29.93 Aligned_cols=19 Identities=26% Similarity=0.396 Sum_probs=16.6
Q ss_pred ccccccCcchHHHHHhHhC
Q psy1365 16 TAIKGCGRRFSNIVLKKAD 34 (140)
Q Consensus 16 t~IyGIG~~~A~~Ic~~lG 34 (140)
-.++|||+++|..+++..|
T Consensus 194 pGVpGIG~KtA~~LL~~~g 212 (281)
T PRK14976 194 KGVKGIGPKTAIKLLNKYG 212 (281)
T ss_pred CCCCcccHHHHHHHHHHcC
Confidence 4589999999999998766
No 115
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=36.75 E-value=19 Score=33.18 Aligned_cols=42 Identities=24% Similarity=0.404 Sum_probs=29.7
Q ss_pred eeeeeecccccccCcchHHHHHhHhCCCCCCccCCCCHHHHHHH
Q psy1365 9 RKVMFALTAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKI 52 (140)
Q Consensus 9 k~v~~ALt~IyGIG~~~A~~Ic~~lGI~~~~~~~~Ls~~qi~~L 52 (140)
+.+.-.|..|.|||+.+|..|++.+| +. ..+..-|.+++.++
T Consensus 565 ~~~~s~L~~I~GIG~k~a~~Ll~~Fg-s~-~~i~~As~eeL~~v 606 (621)
T PRK14671 565 RTLQTELTDIAGIGEKTAEKLLEHFG-SV-EKVAKASLEELAAV 606 (621)
T ss_pred HHhhhhhhcCCCcCHHHHHHHHHHcC-CH-HHHHhCCHHHHHHH
Confidence 34556788999999999999999995 21 23344466666554
No 116
>PF14635 HHH_7: Helix-hairpin-helix motif ; PDB: 3PSI_A 3PSF_A.
Probab=36.69 E-value=20 Score=25.74 Aligned_cols=25 Identities=24% Similarity=0.275 Sum_probs=19.0
Q ss_pred eeeeecccccccCcchHHHHHhHhC
Q psy1365 10 KVMFALTAIKGCGRRFSNIVLKKAD 34 (140)
Q Consensus 10 ~v~~ALt~IyGIG~~~A~~Ic~~lG 34 (140)
.....|+.+-|.|+++|..+.+.+.
T Consensus 47 ~~~~~LqfV~GLGPRKA~~Ll~~l~ 71 (104)
T PF14635_consen 47 HLANLLQFVCGLGPRKAQALLKALK 71 (104)
T ss_dssp HHHGGGGGSTT--HHHHHHHHHHHH
T ss_pred HHHhhHhHhcCCChHHHHHHHHHHH
Confidence 3456789999999999999998765
No 117
>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=35.68 E-value=20 Score=30.53 Aligned_cols=37 Identities=16% Similarity=0.373 Sum_probs=28.1
Q ss_pred ecccccccCcchHHHHHhHhCCCCCCccCCC--CHHHHH
Q psy1365 14 ALTAIKGCGRRFSNIVLKKADIDLNKRAGEC--SEEEVD 50 (140)
Q Consensus 14 ALt~IyGIG~~~A~~Ic~~lGI~~~~~~~~L--s~~qi~ 50 (140)
-+..+.|||..++..+++.+||..-.-+-.+ +.+++.
T Consensus 183 pv~~l~GiG~~~~~~ll~~~Gi~ti~dl~~~~~~~~~L~ 221 (359)
T cd01702 183 PITSIRGLGGKLGEEIIDLLGLPTEGDVAGFRSSESDLQ 221 (359)
T ss_pred cHHHhCCcCHHHHHHHHHHcCCcCHHHHHhccCCHHHHH
Confidence 5688999999999999999999864444444 555544
No 118
>KOG0843|consensus
Probab=34.16 E-value=84 Score=25.06 Aligned_cols=50 Identities=18% Similarity=0.244 Sum_probs=33.7
Q ss_pred CcchHHHHHhHhCCC---CCCccCCCCHHHHHHHHHHHhCCCCcCC------------------Cccccccc
Q psy1365 22 GRRFSNIVLKKADID---LNKRAGECSEEEVDKIITIMTNPRQYKI------------------PDWFLNRQ 72 (140)
Q Consensus 22 G~~~A~~Ic~~lGI~---~~~~~~~Ls~~qi~~L~~~I~~~~~~~i------------------~~w~~nr~ 72 (140)
|...+..+.-.+.+. |...--.+|.+|+.+|+.+++.. .|.+ -.||-|||
T Consensus 84 ~~~~~~~~~l~~~~~~~~~kr~RT~ft~~Ql~~LE~~F~~~-~Yvvg~eR~~LA~~L~LsetQVkvWFQNRR 154 (197)
T KOG0843|consen 84 GKDTMLEGFLLLPLRSMRPKRIRTAFTPEQLLKLEHAFEGN-QYVVGAERKQLAQSLSLSETQVKVWFQNRR 154 (197)
T ss_pred ccchhhhhhccccccccCCCccccccCHHHHHHHHHHHhcC-CeeechHHHHHHHHcCCChhHhhhhhhhhh
Confidence 445555555555555 33334457999999999999865 4533 35999998
No 119
>PRK14896 ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Provisional
Probab=33.96 E-value=35 Score=27.32 Aligned_cols=31 Identities=26% Similarity=0.333 Sum_probs=25.0
Q ss_pred HHHhHh-CCCCCCccCCCCHHHHHHHHHHHhC
Q psy1365 28 IVLKKA-DIDLNKRAGECSEEEVDKIITIMTN 58 (140)
Q Consensus 28 ~Ic~~l-GI~~~~~~~~Ls~~qi~~L~~~I~~ 58 (140)
.+...+ ++++++++.+||.+|+..|.+.+..
T Consensus 225 ~~~~~~~~~~~~~R~e~L~~~~~~~l~~~~~~ 256 (258)
T PRK14896 225 AVVEALPEELLNKRVFQLSPEEIAELANLLYE 256 (258)
T ss_pred HHHHHcCCCCcCCCCccCCHHHHHHHHHHHHh
Confidence 345555 5668999999999999999988854
No 120
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=32.60 E-value=30 Score=26.06 Aligned_cols=30 Identities=17% Similarity=0.297 Sum_probs=20.8
Q ss_pred ecccccccCcchHHHHHhHhCCC-CCCccCC
Q psy1365 14 ALTAIKGCGRRFSNIVLKKADID-LNKRAGE 43 (140)
Q Consensus 14 ALt~IyGIG~~~A~~Ic~~lGI~-~~~~~~~ 43 (140)
-|..+.|||++.|.+|.+--.-+ |..-+.+
T Consensus 98 eL~~lpgIG~~kA~aIi~yRe~~G~f~sv~d 128 (149)
T COG1555 98 ELQALPGIGPKKAQAIIDYREENGPFKSVDD 128 (149)
T ss_pred HHHHCCCCCHHHHHHHHHHHHHcCCCCcHHH
Confidence 45899999999999999653211 4444443
No 121
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=32.58 E-value=5.1 Score=31.95 Aligned_cols=26 Identities=19% Similarity=0.443 Sum_probs=21.2
Q ss_pred CeeeeeecccccccCcchHHHHHhHh
Q psy1365 8 KRKVMFALTAIKGCGRRFSNIVLKKA 33 (140)
Q Consensus 8 ~k~v~~ALt~IyGIG~~~A~~Ic~~l 33 (140)
.+.++..|.++-|||+++|.+||..+
T Consensus 68 ER~lF~~LisVnGIGpK~ALaiLs~~ 93 (201)
T COG0632 68 ERELFRLLISVNGIGPKLALAILSNL 93 (201)
T ss_pred HHHHHHHHHccCCccHHHHHHHHcCC
Confidence 34566678999999999999998543
No 122
>COG2938 Uncharacterized conserved protein [Function unknown]
Probab=32.51 E-value=68 Score=22.67 Aligned_cols=33 Identities=15% Similarity=0.377 Sum_probs=25.2
Q ss_pred ccCCCCHHHHHHHHHHHhCCCCcCCCcccccccc
Q psy1365 40 RAGECSEEEVDKIITIMTNPRQYKIPDWFLNRQK 73 (140)
Q Consensus 40 ~~~~Ls~~qi~~L~~~I~~~~~~~i~~w~~nr~~ 73 (140)
...+||++|+..+..+++.+. -.+=.|++|+..
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 456899999999999997642 234468888886
No 123
>COG2145 ThiM Hydroxyethylthiazole kinase, sugar kinase family [Coenzyme metabolism]
Probab=31.82 E-value=60 Score=27.10 Aligned_cols=57 Identities=25% Similarity=0.294 Sum_probs=42.4
Q ss_pred ccCCCCHHHHHHHHHHHhCCCCcCCCccccccccccc-CCceeEeeccchhHHHHHHHHHHHHHHhhhheec
Q psy1365 40 RAGECSEEEVDKIITIMTNPRQYKIPDWFLNRQKDIV-DGKYSQILLTSTAQLDSKLREDLERLKKIRAHRG 110 (140)
Q Consensus 40 ~~~~Ls~~qi~~L~~~I~~~~~~~i~~w~~nr~~d~~-tg~~~~l~~~~~~~L~~~~~~~I~rl~~i~syRG 110 (140)
.+|.|+++.++.+..+++..-+...| |.+ ||+ -| .+.+|+++-.++-...+.-..||
T Consensus 62 NIGTL~~~~~~~m~~A~~~An~~~~P-vvL----DPVgvg---------At~~R~~~~~~LL~~~~~~~IrG 119 (265)
T COG2145 62 NIGTLSAERIQAMRAAIKAANESGKP-VVL----DPVGVG---------ATKFRTKFALELLAEVKPAAIRG 119 (265)
T ss_pred eeccCChHHHHHHHHHHHHHHhcCCC-EEe----cCccCC---------chHHHHHHHHHHHHhcCCcEEec
Confidence 48999999999999888643356777 444 775 12 16799999988888877777776
No 124
>PRK07945 hypothetical protein; Provisional
Probab=31.68 E-value=25 Score=29.65 Aligned_cols=21 Identities=19% Similarity=0.463 Sum_probs=18.0
Q ss_pred ecccccccCcchHHHHHhHhC
Q psy1365 14 ALTAIKGCGRRFSNIVLKKAD 34 (140)
Q Consensus 14 ALt~IyGIG~~~A~~Ic~~lG 34 (140)
.|++|+|||..+|..|-+.+.
T Consensus 50 ~l~~~~giG~~~a~~i~e~~~ 70 (335)
T PRK07945 50 SLTSLPGIGPKTAKVIAQALA 70 (335)
T ss_pred CcccCCCcCHHHHHHHHHHHh
Confidence 599999999999999886643
No 125
>PTZ00338 dimethyladenosine transferase-like protein; Provisional
Probab=31.52 E-value=43 Score=27.79 Aligned_cols=32 Identities=13% Similarity=0.194 Sum_probs=28.0
Q ss_pred HHHHHhHhCCCCCCccCCCCHHHHHHHHHHHhC
Q psy1365 26 SNIVLKKADIDLNKRAGECSEEEVDKIITIMTN 58 (140)
Q Consensus 26 A~~Ic~~lGI~~~~~~~~Ls~~qi~~L~~~I~~ 58 (140)
...++..+|++ +.|..+||.+|.-.|.+.+.+
T Consensus 257 ~~~~l~~~~~~-~~R~e~l~~~~f~~L~~~~~~ 288 (294)
T PTZ00338 257 IAEILEDSGMF-EKRSVKLDIDDFLKLLLAFNK 288 (294)
T ss_pred HHHHHHHcCCc-ccChhhCCHHHHHHHHHHHHH
Confidence 34678999997 799999999999999998864
No 126
>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=31.29 E-value=47 Score=20.60 Aligned_cols=14 Identities=21% Similarity=0.527 Sum_probs=12.6
Q ss_pred CCCHHHHHHHHHHH
Q psy1365 43 ECSEEEVDKIITIM 56 (140)
Q Consensus 43 ~Ls~~qi~~L~~~I 56 (140)
.||++|+..|.++|
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 79999999998876
No 127
>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=30.62 E-value=13 Score=22.23 Aligned_cols=28 Identities=25% Similarity=0.436 Sum_probs=13.7
Q ss_pred CCHHHHHHHHHHHhCCCCcCCCccccccc
Q psy1365 44 CSEEEVDKIITIMTNPRQYKIPDWFLNRQ 72 (140)
Q Consensus 44 Ls~~qi~~L~~~I~~~~~~~i~~w~~nr~ 72 (140)
.+.++++.|...+.=+ ...|-.||-|+|
T Consensus 25 P~~~~~~~la~~~~l~-~~qV~~WF~nrR 52 (59)
T cd00086 25 PSREEREELAKELGLT-ERQVKIWFQNRR 52 (59)
T ss_pred CCHHHHHHHHHHHCcC-HHHHHHHHHHHH
Confidence 3445555555554311 223445777665
No 128
>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=30.59 E-value=19 Score=22.02 Aligned_cols=44 Identities=20% Similarity=0.115 Sum_probs=30.2
Q ss_pred ecccccccCcchHHHHH-hHhCCCCCCccCCCCHHHHHHHHHHHh
Q psy1365 14 ALTAIKGCGRRFSNIVL-KKADIDLNKRAGECSEEEVDKIITIMT 57 (140)
Q Consensus 14 ALt~IyGIG~~~A~~Ic-~~lGI~~~~~~~~Ls~~qi~~L~~~I~ 57 (140)
-|..-.||-..--...| ..+|+.....-..|+++++..|.+.++
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 35566677777778888 559999777778889999998887764
No 129
>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=30.06 E-value=41 Score=23.83 Aligned_cols=58 Identities=14% Similarity=0.067 Sum_probs=40.8
Q ss_pred CccCCCCeeeeeecccccccCcchHHHHHhHhC---CCCCCccCCCCHHHHHHHHHHHhCC
Q psy1365 2 STNIDGKRKVMFALTAIKGCGRRFSNIVLKKAD---IDLNKRAGECSEEEVDKIITIMTNP 59 (140)
Q Consensus 2 ~t~l~~~k~v~~ALt~IyGIG~~~A~~Ic~~lG---I~~~~~~~~Ls~~qi~~L~~~I~~~ 59 (140)
|..||=|-.-..+.+++.|.=+..|..|+.-.= ++.=..+..||+.|-+.|.+..+++
T Consensus 12 G~KIDlNNa~vr~f~~~pGmYPtlA~kIv~naPY~sveDvl~ipgLse~qK~~lk~~~~~F 72 (93)
T PF06514_consen 12 GQKIDLNNANVRAFRQFPGMYPTLAGKIVSNAPYKSVEDVLNIPGLSERQKALLKKYEDNF 72 (93)
T ss_dssp CTCEETTSS-GGGGCCSTTTTCCHHHHHHHS---SSGGGGCCSTT--HHHHHHHHHHGGGE
T ss_pred CCceecccHhHHHHHHCCCCCHHHHHHHHhCCCCCCHHHHHhccCCCHHHHHHHHHHhccc
Confidence 344455555667889999999999999998753 3334456678999999999999863
No 130
>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=29.49 E-value=10 Score=22.99 Aligned_cols=14 Identities=7% Similarity=0.209 Sum_probs=7.6
Q ss_pred CCHHHHHHHHHHHh
Q psy1365 44 CSEEEVDKIITIMT 57 (140)
Q Consensus 44 Ls~~qi~~L~~~I~ 57 (140)
+|++|+..|.++..
T Consensus 7 ~t~~q~~~L~~~f~ 20 (57)
T PF00046_consen 7 FTKEQLKVLEEYFQ 20 (57)
T ss_dssp SSHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHH
Confidence 45555555555554
No 131
>KOG0492|consensus
Probab=29.11 E-value=59 Score=26.57 Aligned_cols=60 Identities=20% Similarity=0.324 Sum_probs=37.2
Q ss_pred HHHhHhCCCCCCccC-CCCHHHHHHHHHHHhCCCCc-C-----------------CCcccccccccccCCceeEeeccch
Q psy1365 28 IVLKKADIDLNKRAG-ECSEEEVDKIITIMTNPRQY-K-----------------IPDWFLNRQKDIVDGKYSQILLTST 88 (140)
Q Consensus 28 ~Ic~~lGI~~~~~~~-~Ls~~qi~~L~~~I~~~~~~-~-----------------i~~w~~nr~~d~~tg~~~~l~~~~~ 88 (140)
.+|..----+|.+.. -+|..|+..|+..+... +| . +--||-|||
T Consensus 134 ~~C~LrKhk~nRkPRtPFTtqQLlaLErkfrek-qYLSiaEraefSsSL~LTeTqVKIWFQNRR---------------- 196 (246)
T KOG0492|consen 134 TTCTLRKHKPNRKPRTPFTTQQLLALERKFREK-QYLSIAERAEFSSSLELTETQVKIWFQNRR---------------- 196 (246)
T ss_pred ccchhcccCCCCCCCCCCCHHHHHHHHHHHhHh-hhhhHHHHHhhhhhhhhhhhheehhhhhhh----------------
Confidence 345444444444433 46888888888777543 33 2 235999999
Q ss_pred hHHHHHHHHHHHHHHh
Q psy1365 89 AQLDSKLREDLERLKK 104 (140)
Q Consensus 89 ~~L~~~~~~~I~rl~~ 104 (140)
..-+|..++.++.++.
T Consensus 197 AKaKRlQeae~Ek~km 212 (246)
T KOG0492|consen 197 AKAKRLQEAELEKLKM 212 (246)
T ss_pred HHHHHHHHHHHHHhhh
Confidence 5556777777776654
No 132
>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=28.55 E-value=31 Score=28.53 Aligned_cols=19 Identities=26% Similarity=0.277 Sum_probs=17.2
Q ss_pred ccccccCcchHHHHHhHhC
Q psy1365 16 TAIKGCGRRFSNIVLKKAD 34 (140)
Q Consensus 16 t~IyGIG~~~A~~Ic~~lG 34 (140)
..|+|||+.+|..+++..|
T Consensus 226 ~gv~giG~k~A~~li~~~~ 244 (316)
T cd00128 226 EGIPGIGPVTALKLIKKYG 244 (316)
T ss_pred CCCCCccHHHHHHHHHHcC
Confidence 3689999999999999987
No 133
>PRK13766 Hef nuclease; Provisional
Probab=28.45 E-value=29 Score=32.03 Aligned_cols=23 Identities=9% Similarity=0.250 Sum_probs=20.4
Q ss_pred eeecccccccCcchHHHHHhHhC
Q psy1365 12 MFALTAIKGCGRRFSNIVLKKAD 34 (140)
Q Consensus 12 ~~ALt~IyGIG~~~A~~Ic~~lG 34 (140)
.+.|..|.|||...|..|++.+|
T Consensus 714 ~~~L~~ipgig~~~a~~Ll~~fg 736 (773)
T PRK13766 714 EYIVESLPDVGPVLARNLLEHFG 736 (773)
T ss_pred HHHHhcCCCCCHHHHHHHHHHcC
Confidence 34689999999999999999876
No 134
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=28.44 E-value=33 Score=31.80 Aligned_cols=24 Identities=25% Similarity=0.259 Sum_probs=21.1
Q ss_pred eeeecccccccCcchHHHHHhHhC
Q psy1365 11 VMFALTAIKGCGRRFSNIVLKKAD 34 (140)
Q Consensus 11 v~~ALt~IyGIG~~~A~~Ic~~lG 34 (140)
..-.|.+|+|||+..+..+++.+|
T Consensus 550 ~~S~L~~IpGIG~kr~~~LL~~Fg 573 (624)
T PRK14669 550 RTSELLEIPGVGAKTVQRLLKHFG 573 (624)
T ss_pred HHHHHhcCCCCCHHHHHHHHHHcC
Confidence 445688999999999999999887
No 135
>COG1111 MPH1 ERCC4-like helicases [DNA replication, recombination, and repair]
Probab=28.43 E-value=64 Score=29.54 Aligned_cols=86 Identities=16% Similarity=0.231 Sum_probs=60.8
Q ss_pred CCeeeeeecccccccCcchHHHHHhHhCCCCCCccCCCCHHHHHHHHHHHhCCC----CcCCCcccccccccccCCceeE
Q psy1365 7 GKRKVMFALTAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKIITIMTNPR----QYKIPDWFLNRQKDIVDGKYSQ 82 (140)
Q Consensus 7 ~~k~v~~ALt~IyGIG~~~A~~Ic~~lGI~~~~~~~~Ls~~qi~~L~~~I~~~~----~~~i~~w~~nr~~d~~tg~~~~ 82 (140)
..++...|||.-+|=-......+|+.|||+ +.-+..=.+.+| ..++.... +..+|.||..=|
T Consensus 160 ~k~~~ilgLTASPGs~~ekI~eV~~nLgIe-~vevrTE~d~DV---~~Yv~~~kve~ikV~lp~e~~~ir---------- 225 (542)
T COG1111 160 AKNPLILGLTASPGSDLEKIQEVVENLGIE-KVEVRTEEDPDV---RPYVKKIKVEWIKVDLPEEIKEIR---------- 225 (542)
T ss_pred ccCceEEEEecCCCCCHHHHHHHHHhCCcc-eEEEecCCCccH---HHhhccceeEEEeccCcHHHHHHH----------
Confidence 455689999999999999999999999998 344443333333 44443221 234666654322
Q ss_pred eeccchhHHHHHHHHHHHHHHhhhheeccC
Q psy1365 83 ILLTSTAQLDSKLREDLERLKKIRAHRGMR 112 (140)
Q Consensus 83 l~~~~~~~L~~~~~~~I~rl~~i~syRG~R 112 (140)
..|+..++.-.+.|++.+-|.+..
T Consensus 226 ------~~l~~~l~~~Lk~L~~~g~~~~~~ 249 (542)
T COG1111 226 ------DLLRDALKPRLKPLKELGVIESSS 249 (542)
T ss_pred ------HHHHHHHHHHHHHHHHcCceeccC
Confidence 678888888899999999888876
No 136
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=28.29 E-value=69 Score=22.85 Aligned_cols=17 Identities=24% Similarity=0.456 Sum_probs=13.8
Q ss_pred CCCCHHHHHHHHHHHhC
Q psy1365 42 GECSEEEVDKIITIMTN 58 (140)
Q Consensus 42 ~~Ls~~qi~~L~~~I~~ 58 (140)
+.||++|-+.|.++|..
T Consensus 1 s~Lt~eE~~~I~~Vl~R 17 (118)
T PF02318_consen 1 SHLTEEEREIILQVLQR 17 (118)
T ss_dssp TTS-CHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHh
Confidence 46999999999999975
No 137
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=28.15 E-value=31 Score=31.54 Aligned_cols=43 Identities=23% Similarity=0.251 Sum_probs=29.7
Q ss_pred CeeeeeecccccccCcchHHHHHhHhCCCCCCccCCCCHHHHHHH
Q psy1365 8 KRKVMFALTAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKI 52 (140)
Q Consensus 8 ~k~v~~ALt~IyGIG~~~A~~Ic~~lGI~~~~~~~~Ls~~qi~~L 52 (140)
+......|..|+|||+.+..++++.+|== ..+..-|.+|+.++
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 34456788999999999999999887632 33444455555443
No 138
>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=28.03 E-value=23 Score=23.26 Aligned_cols=45 Identities=18% Similarity=0.214 Sum_probs=33.5
Q ss_pred eeeecccccccCcchHHHHHhHhCCCCCCccCCCCHHHHHHHHHHHhC
Q psy1365 11 VMFALTAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKIITIMTN 58 (140)
Q Consensus 11 v~~ALt~IyGIG~~~A~~Ic~~lGI~~~~~~~~Ls~~qi~~L~~~I~~ 58 (140)
+.-++..+.|+|..-|+.+++.+ |..-...++.++-+.|.+.|+.
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 34467888999999999999998 6666667899999999998875
No 139
>PRK00919 GMP synthase subunit B; Validated
Probab=27.92 E-value=1.7e+02 Score=24.63 Aligned_cols=80 Identities=14% Similarity=0.078 Sum_probs=52.3
Q ss_pred CCCCCccCCCCHHHHHHHHHHHhCCCCcCCCcccccccccccCCceeEeeccchhH----HHHHHHHHHHHHHhhhheec
Q psy1365 35 IDLNKRAGECSEEEVDKIITIMTNPRQYKIPDWFLNRQKDIVDGKYSQILLTSTAQ----LDSKLREDLERLKKIRAHRG 110 (140)
Q Consensus 35 I~~~~~~~~Ls~~qi~~L~~~I~~~~~~~i~~w~~nr~~d~~tg~~~~l~~~~~~~----L~~~~~~~I~rl~~i~syRG 110 (140)
+..-.++.+|+.+||-.+...+ .+|.|+.+|.+=+-.|.-+-++|.||.+ ++..-.-=++.|.+-+-|..
T Consensus 154 ~~Ii~PL~~l~K~EVr~la~~l------GLp~~~~~r~p~~~pcLa~Ri~g~vt~e~l~~v~~ae~~~~~~~~~~~~~~~ 227 (307)
T PRK00919 154 LKIVEPLRDLYKDEVREVARAL------GLPEEISERMPFPGPGLAVRIIGEVTEEKLEIVREANAIVEEEVEKYGPDKW 227 (307)
T ss_pred CCcccCchhCcHHHHHHHHHHc------CCChhhhCCCCCCCCceeEEeecccCHHHHHHHHHHHHHHHHHHHhcCCccc
Confidence 3455667789999998887654 5788988888777777666667777666 33333333566777777763
Q ss_pred cCCCCCCccC
Q psy1365 111 MRHYWGLRVR 120 (140)
Q Consensus 111 ~RH~~gLpVR 120 (140)
-=.+-=|||+
T Consensus 228 q~~~~~~~~~ 237 (307)
T PRK00919 228 QYFAALLGVK 237 (307)
T ss_pred ceEEEEcCce
Confidence 3333345654
No 140
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=27.11 E-value=34 Score=31.40 Aligned_cols=40 Identities=25% Similarity=0.305 Sum_probs=28.5
Q ss_pred eeeecccccccCcchHHHHHhHhCCCCCCccCCCCHHHHHHH
Q psy1365 11 VMFALTAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKI 52 (140)
Q Consensus 11 v~~ALt~IyGIG~~~A~~Ic~~lGI~~~~~~~~Ls~~qi~~L 52 (140)
....|..|+|||+.....+++.+|== ..+..-|.+|+.++
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 55689999999999999999887632 33444455555443
No 141
>KOG2875|consensus
Probab=27.05 E-value=25 Score=29.91 Aligned_cols=22 Identities=18% Similarity=0.291 Sum_probs=19.0
Q ss_pred eeeecccccccCcchHHHHHhH
Q psy1365 11 VMFALTAIKGCGRRFSNIVLKK 32 (140)
Q Consensus 11 v~~ALt~IyGIG~~~A~~Ic~~ 32 (140)
+.-||+.++|||++.|.-||-.
T Consensus 216 ar~~L~~lpGVG~KVADCI~Lm 237 (323)
T KOG2875|consen 216 AREALCSLPGVGPKVADCICLM 237 (323)
T ss_pred HHHHHhcCCCCcchHhhhhhhh
Confidence 4568999999999999999943
No 142
>COG1059 Thermostable 8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=27.00 E-value=21 Score=28.64 Aligned_cols=25 Identities=20% Similarity=0.372 Sum_probs=21.8
Q ss_pred eeecccccccCcchHHHHHhHhCCC
Q psy1365 12 MFALTAIKGCGRRFSNIVLKKADID 36 (140)
Q Consensus 12 ~~ALt~IyGIG~~~A~~Ic~~lGI~ 36 (140)
.+.+.+|||||.+-|...++..|+.
T Consensus 120 E~Lv~nikGiGyKEASHFLRNVG~~ 144 (210)
T COG1059 120 ELLVENIKGIGYKEASHFLRNVGFE 144 (210)
T ss_pred HHHHHHcccccHHHHHHHHHhcChh
Confidence 3456799999999999999999985
No 143
>PRK03980 flap endonuclease-1; Provisional
Probab=26.63 E-value=34 Score=28.50 Aligned_cols=18 Identities=33% Similarity=0.477 Sum_probs=16.7
Q ss_pred cccccCcchHHHHHhHhC
Q psy1365 17 AIKGCGRRFSNIVLKKAD 34 (140)
Q Consensus 17 ~IyGIG~~~A~~Ic~~lG 34 (140)
.|+|||+.+|..+++..|
T Consensus 193 GI~GIG~ktA~kLi~~~~ 210 (292)
T PRK03980 193 GIKGIGPKTALKLIKKHG 210 (292)
T ss_pred CCCCccHHHHHHHHHHCC
Confidence 688999999999999887
No 144
>KOG0650|consensus
Probab=26.60 E-value=1.1e+02 Score=28.74 Aligned_cols=40 Identities=23% Similarity=0.440 Sum_probs=30.4
Q ss_pred CccCCCCHHHHHHHHHHHhCCCCcCCCcccccccccccCCceeEeec
Q psy1365 39 KRAGECSEEEVDKIITIMTNPRQYKIPDWFLNRQKDIVDGKYSQILL 85 (140)
Q Consensus 39 ~~~~~Ls~~qi~~L~~~I~~~~~~~i~~w~~nr~~d~~tg~~~~l~~ 85 (140)
+-......++++++.+.|+.| +.| ++.+|+.||++..|.-
T Consensus 145 kI~kp~k~~~ld~fl~~iedp-----~~W--r~v~Dk~tG~dv~LTk 184 (733)
T KOG0650|consen 145 KITKPAKGDELDSFLAKIEDP-----DYW--RKVKDKMTGKDVNLTK 184 (733)
T ss_pred EecCCCccchHHHHHHhhcCc-----chh--ccccccCCCceeeecH
Confidence 334555668899888888764 457 8999999999888754
No 145
>PF14794 DUF4479: Domain of unknown function (DUF4479); PDB: 3BU2_C.
Probab=26.55 E-value=54 Score=21.91 Aligned_cols=16 Identities=25% Similarity=0.295 Sum_probs=12.2
Q ss_pred CCCHHHHHHHHHHHhC
Q psy1365 43 ECSEEEVDKIITIMTN 58 (140)
Q Consensus 43 ~Ls~~qi~~L~~~I~~ 58 (140)
.||++|++.|.++|.+
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 4899999999999975
No 146
>PF02697 DUF217: Uncharacterized ACR, COG1753; InterPro: IPR003847 This entry is represented by Natrialba phage PhiCh1, Orf96. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=26.25 E-value=48 Score=22.09 Aligned_cols=47 Identities=26% Similarity=0.297 Sum_probs=35.8
Q ss_pred eeeecccccccCcchHHHHHhHhC-----CCCCCccCCCCHHHHHHHHHHHh
Q psy1365 11 VMFALTAIKGCGRRFSNIVLKKAD-----IDLNKRAGECSEEEVDKIITIMT 57 (140)
Q Consensus 11 v~~ALt~IyGIG~~~A~~Ic~~lG-----I~~~~~~~~Ls~~qi~~L~~~I~ 57 (140)
++-.|..++.=|.+++..|+..+. -+...-+|.|++++.+.+.+.+.
T Consensus 10 vY~rL~~~K~~~eSFSdvI~rli~~~~~~~~l~~~~g~l~deea~~~~~~i~ 61 (71)
T PF02697_consen 10 VYERLKKLKREDESFSDVIERLIEKEKKRRDLMDYFGILSDEEADEMEKDIK 61 (71)
T ss_pred HHHHHHHHhcCCCCHHHHHHHHHhcccchhHHHHHhccCChhhHHHHHHHHH
Confidence 345677888889999999999988 33344577888888888877775
No 147
>PF14053 DUF4248: Domain of unknown function (DUF4248)
Probab=24.78 E-value=1e+02 Score=20.30 Aligned_cols=45 Identities=9% Similarity=0.018 Sum_probs=31.4
Q ss_pred eeecccccccCcchHHHHH--------------hHhCCCCCCccCCCCHHHHHHHHHHHhC
Q psy1365 12 MFALTAIKGCGRRFSNIVL--------------KKADIDLNKRAGECSEEEVDKIITIMTN 58 (140)
Q Consensus 12 ~~ALt~IyGIG~~~A~~Ic--------------~~lGI~~~~~~~~Ls~~qi~~L~~~I~~ 58 (140)
+.|+.++.++-+..|..-+ ..+|.++.. ..+|+.||..|.+.+..
T Consensus 10 ELA~lYfP~~~~~sA~r~L~rwI~~~~~L~~~L~~~Gy~~~~--r~~TP~QV~lIv~~LGe 68 (69)
T PF14053_consen 10 ELAQLYFPDLTPSSAVRKLRRWIRRNPELLEELEATGYHPRQ--RSFTPRQVRLIVRYLGE 68 (69)
T ss_pred HHHHHHcCCCCHHHHHHHHHHHHHHCHHHHHHHHHcCCCCCC--EecCHHHHHHHHHHcCC
Confidence 4566677777665554433 456777666 55999999999888764
No 148
>PF11460 DUF3007: Protein of unknown function (DUF3007); InterPro: IPR021562 This is a family of uncharacterised proteins found in bacteria and eukaryotes.
Probab=24.09 E-value=44 Score=24.13 Aligned_cols=20 Identities=30% Similarity=0.383 Sum_probs=16.7
Q ss_pred CCccCCCCHHHHHHHHHHHh
Q psy1365 38 NKRAGECSEEEVDKIITIMT 57 (140)
Q Consensus 38 ~~~~~~Ls~~qi~~L~~~I~ 57 (140)
.+++.+||++|+++|.+-|+
T Consensus 84 qkRle~l~~eE~~~L~~eie 103 (104)
T PF11460_consen 84 QKRLEELSPEELEALQAEIE 103 (104)
T ss_pred HHHHHhCCHHHHHHHHHHhc
Confidence 46788999999999987765
No 149
>TIGR02714 amido_AtzD_TrzD ring-opening amidohydrolases. Members of this family are are ring-opening amidohydrolases, including cyanuric acid amidohydrolase (EC 3.5.2.15) (AtzD and TrzD) and barbiturase. Note that barbiturase does not act as defined for EC 3.5.2.1 (barbiturate + water = malonate + urea) but rather catalyzes the ring-opening of barbituric acid to ureidomalonic acid (see Soong, et al., PubMed:11485332).
Probab=24.09 E-value=1.4e+02 Score=25.95 Aligned_cols=29 Identities=10% Similarity=0.450 Sum_probs=23.1
Q ss_pred HHHHhHhCCCCCCccCCCCHHHHHHHHHHHhC
Q psy1365 27 NIVLKKADIDLNKRAGECSEEEVDKIITIMTN 58 (140)
Q Consensus 27 ~~Ic~~lGI~~~~~~~~Ls~~qi~~L~~~I~~ 58 (140)
...++.+|++.. +.++++|..+|.+++-+
T Consensus 270 ~~al~~~Gl~~~---~~~~~~~~~rlv~VfaK 298 (366)
T TIGR02714 270 RAAIRDAGLELP---ERPHSDDLDQLVNVFAK 298 (366)
T ss_pred HHHHHHhCCCCC---CCCChHHHHHHHHHHhh
Confidence 456678999874 67788999999998865
No 150
>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=24.05 E-value=75 Score=19.64 Aligned_cols=16 Identities=19% Similarity=0.347 Sum_probs=14.2
Q ss_pred CCCHHHHHHHHHHHhC
Q psy1365 43 ECSEEEVDKIITIMTN 58 (140)
Q Consensus 43 ~Ls~~qi~~L~~~I~~ 58 (140)
.||++|+..|..+|..
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 7999999999999863
No 151
>PF14213 DUF4325: Domain of unknown function (DUF4325)
Probab=23.74 E-value=1.5e+02 Score=19.09 Aligned_cols=53 Identities=13% Similarity=0.207 Sum_probs=38.5
Q ss_pred CCCCeeeeeecccccccCcchHHHHHhH----hC---CCCCCccCCCCHHHHHHHHHHHh
Q psy1365 5 IDGKRKVMFALTAIKGCGRRFSNIVLKK----AD---IDLNKRAGECSEEEVDKIITIMT 57 (140)
Q Consensus 5 l~~~k~v~~ALt~IyGIG~~~A~~Ic~~----lG---I~~~~~~~~Ls~~qi~~L~~~I~ 57 (140)
+..+++|..-+..|.+++.+++....-. .| +.....+..++++.-..|..+++
T Consensus 14 l~~~~~V~lDF~gv~~~~ssFl~eafg~l~~~~~~~~~~~~l~~~~~~~~~~~~I~~vi~ 73 (74)
T PF14213_consen 14 LKEGEKVVLDFEGVESITSSFLNEAFGQLVREFGEEEIKKRLKFKNANESIKEMIKRVIE 73 (74)
T ss_pred HhcCCeEEEECCCcccccHHHHHHHHHHHHHHcCHHHHhheeEEecCCHHHHHHHHHHHh
Confidence 4456679999999999999999887643 33 34456667777777777766664
No 152
>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=23.51 E-value=42 Score=28.44 Aligned_cols=19 Identities=21% Similarity=0.399 Sum_probs=16.4
Q ss_pred ccccccCcchHHHHHhHhC
Q psy1365 16 TAIKGCGRRFSNIVLKKAD 34 (140)
Q Consensus 16 t~IyGIG~~~A~~Ic~~lG 34 (140)
..|+|||+.+|..+++..|
T Consensus 239 ~Gv~GIG~ktA~kli~~~g 257 (338)
T TIGR03674 239 EGVKGIGPKTALKLIKEHG 257 (338)
T ss_pred CCCCCccHHHHHHHHHHcC
Confidence 5799999999999997743
No 153
>COG1131 CcmA ABC-type multidrug transport system, ATPase component [Defense mechanisms]
Probab=23.51 E-value=2.3e+02 Score=23.26 Aligned_cols=38 Identities=13% Similarity=0.117 Sum_probs=31.3
Q ss_pred ccccccC----cchHHHHHhHhCCCC--CCccCCCCHHHHHHHH
Q psy1365 16 TAIKGCG----RRFSNIVLKKADIDL--NKRAGECSEEEVDKII 53 (140)
Q Consensus 16 t~IyGIG----~~~A~~Ic~~lGI~~--~~~~~~Ls~~qi~~L~ 53 (140)
..+||.. ...+..+++.+|++. +.+++.||--+-.++.
T Consensus 103 ~~l~~~~~~~~~~~~~~~l~~~~L~~~~~~~~~~lS~G~kqrl~ 146 (293)
T COG1131 103 ARLYGLSKEEAEERIEELLELFGLEDKANKKVRTLSGGMKQRLS 146 (293)
T ss_pred HHHhCCChhHHHHHHHHHHHHcCCchhhCcchhhcCHHHHHHHH
Confidence 5678876 457889999999999 7889999988877663
No 154
>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=23.49 E-value=2.6e+02 Score=20.59 Aligned_cols=37 Identities=22% Similarity=0.270 Sum_probs=30.0
Q ss_pred cC-cchHHHHHhHhCCCC------CCccCCCCHHHHHHHHHHHh
Q psy1365 21 CG-RRFSNIVLKKADIDL------NKRAGECSEEEVDKIITIMT 57 (140)
Q Consensus 21 IG-~~~A~~Ic~~lGI~~------~~~~~~Ls~~qi~~L~~~I~ 57 (140)
|+ +.+|..|.+.+|+.. ...+++||-+|+..|.++-.
T Consensus 62 v~~Pp~s~ll~ka~g~~kgs~~~~~~~~g~it~~~v~eIA~~K~ 105 (131)
T cd00349 62 VKTPPASALLKKAAGIEKGSKKPNKEKVGNITLDQVYEIAKIKL 105 (131)
T ss_pred EcCCCHHHHHHHHhCCCCCCCCCCCeeeeeecHHHHHHHHHHHH
Confidence 44 788888888888876 45589999999999977764
No 155
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=23.40 E-value=41 Score=26.91 Aligned_cols=22 Identities=14% Similarity=0.283 Sum_probs=17.4
Q ss_pred ecccccccCcchHHHHHhHhCC
Q psy1365 14 ALTAIKGCGRRFSNIVLKKADI 35 (140)
Q Consensus 14 ALt~IyGIG~~~A~~Ic~~lGI 35 (140)
.|++|+|||+..|.+|+....+
T Consensus 61 eL~~i~GiG~aka~~l~a~~El 82 (218)
T TIGR00608 61 ELSSVPGIGEAKAIQLKAAVEL 82 (218)
T ss_pred HHHhCcCCcHHHHHHHHHHHHH
Confidence 3889999999999888755443
No 156
>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=23.39 E-value=46 Score=21.97 Aligned_cols=43 Identities=14% Similarity=0.247 Sum_probs=26.4
Q ss_pred eecccccccCcchHHHHHhHhCCCCCC-ccCCCCHHHHHHHHHHH
Q psy1365 13 FALTAIKGCGRRFSNIVLKKADIDLNK-RAGECSEEEVDKIITIM 56 (140)
Q Consensus 13 ~ALt~IyGIG~~~A~~Ic~~lGI~~~~-~~~~Ls~~qi~~L~~~I 56 (140)
+-++.++|+|.--+.++-.-. +||.. ++-.++-++.....+++
T Consensus 6 ~~I~RfKGLGEM~p~qL~eTT-mdP~~R~L~~V~i~d~~~~~~~~ 49 (65)
T PF00986_consen 6 VEIQRFKGLGEMNPDQLWETT-MDPETRRLIRVTIEDAEEADELF 49 (65)
T ss_dssp TEEEESSSGGGS-HHHHHHHH-TSTTTTEEEEEEHCCHHHHHHHH
T ss_pred ceeEEecccccCCHHHHHHHc-cCccceEEEEEEECCHHHHHHHH
Confidence 457899999999999987654 34444 45444444444444444
No 157
>PF09346 SMI1_KNR4: SMI1 / KNR4 family (SUKH-1); InterPro: IPR018958 Proteins in this family are involved in the regulation of 1,3-beta-glucan synthase activity and cell-wall formation [, ]. Yeast members of this family are involved in the regulation of cell wall assembly. Saccharomyces cerevisiae (Baker's yeast) protein KNR4 (SMI1) has a regulatory role in chitin deposition and in cell wall assembly []. It was originally identified as a regulator of chitin synthase expression (acting as a repressor) [] and of 1,3-beta-glucan synthase levels []. It was shown to localise in patches at presumptive bud sites in unbudded cells and at the incipient bud site during bud emergence []. KNR4 is believed to connect the PKC1-SLT2 MAPK pathway with cell proliferation. It has been shown to interact with BCK2, a gene involved in cell cycle progression in S. cerevisiae (forming a complex) to allow PKC1 to coordinate the cell cycle (cell proliferation) with cell wall integrity [, ]. PKC1 plays an essential role in cell wall integrity and cell proliferation through a bifurcated PKC1/mitogen-activated protein (MAP) kinase pathway. KNR4 also interacts with the tyrosine-tRNA synthetase protein encoded by TYS1 and is involved in sporulation process []. Note: previously reported evidence that KNR4 may interact with nuclear matrix-association region [] may be due to an artefact [].; PDB: 3D5P_A 2ICG_A.
Probab=23.20 E-value=1.2e+02 Score=20.15 Aligned_cols=18 Identities=22% Similarity=0.549 Sum_probs=11.4
Q ss_pred CCHHHHHHHHHHHhCCCCcCCC
Q psy1365 44 CSEEEVDKIITIMTNPRQYKIP 65 (140)
Q Consensus 44 Ls~~qi~~L~~~I~~~~~~~i~ 65 (140)
+|+++|..+.+.+. +.+|
T Consensus 2 ~t~~~I~~~E~~lg----~~LP 19 (130)
T PF09346_consen 2 ATEEEIQELEEKLG----VRLP 19 (130)
T ss_dssp --HHHHHHHHHHHT----S---
T ss_pred CCHHHHHHHHHHhC----CCCc
Confidence 68999999999995 5788
No 158
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=22.94 E-value=40 Score=30.89 Aligned_cols=39 Identities=21% Similarity=0.267 Sum_probs=27.7
Q ss_pred eeeecccccccCcchHHHHHhHhCCCCCCccCCCCHHHHHH
Q psy1365 11 VMFALTAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDK 51 (140)
Q Consensus 11 v~~ALt~IyGIG~~~A~~Ic~~lGI~~~~~~~~Ls~~qi~~ 51 (140)
...+|..|.|||+.++..+++.+|=- ..+-+.|.+++..
T Consensus 523 ~~~~L~~IpGIG~kr~~~LL~~FGS~--~~I~~As~eeL~~ 561 (577)
T PRK14668 523 VSTVLDDVPGVGPETRKRLLRRFGSV--EGVREASVEDLRD 561 (577)
T ss_pred HHhHHhcCCCCCHHHHHHHHHHcCCH--HHHHhCCHHHHHh
Confidence 45789999999999999999887622 2333445555533
No 159
>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=22.71 E-value=50 Score=26.96 Aligned_cols=36 Identities=19% Similarity=0.252 Sum_probs=23.0
Q ss_pred cccccccCcchHHHHHhHhCCCCCCccCCCCHHHHHH
Q psy1365 15 LTAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDK 51 (140)
Q Consensus 15 Lt~IyGIG~~~A~~Ic~~lGI~~~~~~~~Ls~~qi~~ 51 (140)
|..++|||+.++..+. ..||..-..+..++++++..
T Consensus 1 l~~i~gig~~~~~~L~-~~Gi~ti~dl~~~~~~~L~~ 36 (310)
T TIGR02236 1 LEDLPGVGPATAEKLR-EAGYDTFEAIAVASPKELSE 36 (310)
T ss_pred CcccCCCCHHHHHHHH-HcCCCCHHHHHcCCHHHHHh
Confidence 4578899988877654 56666555555555555544
No 160
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=22.64 E-value=38 Score=31.89 Aligned_cols=24 Identities=13% Similarity=0.267 Sum_probs=21.4
Q ss_pred eeeecccccccCcchHHHHHhHhC
Q psy1365 11 VMFALTAIKGCGRRFSNIVLKKAD 34 (140)
Q Consensus 11 v~~ALt~IyGIG~~~A~~Ic~~lG 34 (140)
+.-.|..|.|||+..+..+++.+|
T Consensus 635 ~~s~L~~IPGIGpkr~k~LL~~FG 658 (694)
T PRK14666 635 LTGELQRVEGIGPATARLLWERFG 658 (694)
T ss_pred hHhHHhhCCCCCHHHHHHHHHHhC
Confidence 445788999999999999999988
No 161
>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=22.41 E-value=75 Score=23.90 Aligned_cols=35 Identities=11% Similarity=0.110 Sum_probs=28.2
Q ss_pred cchHHHHHhHhCCCCCCccCCCCHHHHHHHHHHHh
Q psy1365 23 RRFSNIVLKKADIDLNKRAGECSEEEVDKIITIMT 57 (140)
Q Consensus 23 ~~~A~~Ic~~lGI~~~~~~~~Ls~~qi~~L~~~I~ 57 (140)
...|.+.++.+|+.+=-.++.++.+-++.|.++|+
T Consensus 108 i~~a~~~L~~aG~~~if~vS~~~~eGi~eL~~~L~ 142 (143)
T PF10662_consen 108 IERAKKWLKNAGVKEIFEVSAVTGEGIEELKDYLE 142 (143)
T ss_pred HHHHHHHHHHcCCCCeEEEECCCCcCHHHHHHHHh
Confidence 34677788888888888888888888888888875
No 162
>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=22.39 E-value=31 Score=28.77 Aligned_cols=31 Identities=10% Similarity=0.216 Sum_probs=23.0
Q ss_pred ecccccccCcchHHHHHhHhCCCCCCccCCC
Q psy1365 14 ALTAIKGCGRRFSNIVLKKADIDLNKRAGEC 44 (140)
Q Consensus 14 ALt~IyGIG~~~A~~Ic~~lGI~~~~~~~~L 44 (140)
.+++++|||.++|..|...+.=..-..+.+|
T Consensus 46 ~~~~ipgiG~~ia~kI~E~~~tG~~~~le~l 76 (307)
T cd00141 46 EAKKLPGIGKKIAEKIEEILETGKLRKLEEL 76 (307)
T ss_pred HhcCCCCccHHHHHHHHHHHHcCCHHHHHHH
Confidence 5689999999999999988765543333333
No 163
>PRK06920 dnaE DNA polymerase III DnaE; Reviewed
Probab=22.37 E-value=80 Score=31.34 Aligned_cols=26 Identities=12% Similarity=0.266 Sum_probs=22.6
Q ss_pred CeeeeeecccccccCcchHHHHHhHh
Q psy1365 8 KRKVMFALTAIKGCGRRFSNIVLKKA 33 (140)
Q Consensus 8 ~k~v~~ALt~IyGIG~~~A~~Ic~~l 33 (140)
+..|.++|..|+|||...+..|.+.=
T Consensus 797 ~~~Ir~gL~~Ikgvg~~~~~~Iv~~R 822 (1107)
T PRK06920 797 GNAIRYSLLSIRNIGMATVTALYEER 822 (1107)
T ss_pred CCeeEechhhcCCCCHHHHHHHHHHh
Confidence 45799999999999999999998653
No 164
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=22.34 E-value=75 Score=22.91 Aligned_cols=42 Identities=17% Similarity=0.382 Sum_probs=31.7
Q ss_pred cccccccCcchHHHHHhHhCCCCCCccCCCCHHHHHHHHHHHh
Q psy1365 15 LTAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKIITIMT 57 (140)
Q Consensus 15 Lt~IyGIG~~~A~~Ic~~lGI~~~~~~~~Ls~~qi~~L~~~I~ 57 (140)
|..|.|||...|. ++..+||+.-..+.+.+++++..-..-++
T Consensus 55 L~ri~gi~~~~a~-LL~~AGv~Tv~~LA~~~p~~L~~~l~~~n 96 (122)
T PF14229_consen 55 LMRIPGIGPQYAE-LLEHAGVDTVEELAQRNPQNLHQKLGRLN 96 (122)
T ss_pred hhhcCCCCHHHHH-HHHHhCcCcHHHHHhCCHHHHHHHHHHHH
Confidence 4589999999985 66789999877777777777765544443
No 165
>PRK13620 psbV cytochrome c-550; Provisional
Probab=22.28 E-value=93 Score=25.23 Aligned_cols=16 Identities=13% Similarity=0.171 Sum_probs=14.1
Q ss_pred cCCCCHHHHHHHHHHH
Q psy1365 41 AGECSEEEVDKIITIM 56 (140)
Q Consensus 41 ~~~Ls~~qi~~L~~~I 56 (140)
+.+|||+|+..|..+|
T Consensus 182 ~r~LtdedL~aIa~~I 197 (215)
T PRK13620 182 MRNLTEDDLVAISGHI 197 (215)
T ss_pred cCCCCHHHHHHHHHHH
Confidence 4679999999999887
No 166
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=22.18 E-value=2.5e+02 Score=26.48 Aligned_cols=23 Identities=17% Similarity=0.297 Sum_probs=18.3
Q ss_pred ecccccccCcchHHHHHhHhCCC
Q psy1365 14 ALTAIKGCGRRFSNIVLKKADID 36 (140)
Q Consensus 14 ALt~IyGIG~~~A~~Ic~~lGI~ 36 (140)
.|..+.|||...|..|+..+.-+
T Consensus 544 ~l~~i~giG~~vA~si~~ff~~~ 566 (667)
T COG0272 544 ELASIPGIGEVVARSIIEFFANE 566 (667)
T ss_pred HHhhccchhHHHHHHHHHHHcCH
Confidence 46778999999999998887633
No 167
>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=22.05 E-value=2e+02 Score=23.47 Aligned_cols=32 Identities=16% Similarity=0.132 Sum_probs=21.9
Q ss_pred cCCCCHHHHHHHHHHHhCCCCcCCCcccccccccccCCceeEeec
Q psy1365 41 AGECSEEEVDKIITIMTNPRQYKIPDWFLNRQKDIVDGKYSQILL 85 (140)
Q Consensus 41 ~~~Ls~~qi~~L~~~I~~~~~~~i~~w~~nr~~d~~tg~~~~l~~ 85 (140)
+..+|.||.+.-..+|-. -=||+||-...+-|
T Consensus 157 m~PmTkEEyearQSvIRr-------------VvDpETGRtRLIkG 188 (225)
T PF10500_consen 157 MAPMTKEEYEARQSVIRR-------------VVDPETGRTRLIKG 188 (225)
T ss_pred cCCCCHHHHHHHHhhhee-------------eecCCCCceeeecc
Confidence 445666777766666643 33899998887766
No 168
>PTZ00217 flap endonuclease-1; Provisional
Probab=21.73 E-value=49 Score=28.79 Aligned_cols=19 Identities=32% Similarity=0.464 Sum_probs=16.7
Q ss_pred ccccccCcchHHHHHhHhC
Q psy1365 16 TAIKGCGRRFSNIVLKKAD 34 (140)
Q Consensus 16 t~IyGIG~~~A~~Ic~~lG 34 (140)
..|.|||+.+|..+++..|
T Consensus 238 pgi~GIG~ktA~~Li~~~g 256 (393)
T PTZ00217 238 DTIKGIGPKTAYKLIKKYK 256 (393)
T ss_pred CCCCCccHHHHHHHHHHcC
Confidence 4699999999999998765
No 169
>PF13276 HTH_21: HTH-like domain
Probab=21.45 E-value=32 Score=21.21 Aligned_cols=33 Identities=15% Similarity=0.259 Sum_probs=23.7
Q ss_pred CCCeeeeeecccccc--cCcchHHHHHhHhCCCCC
Q psy1365 6 DGKRKVMFALTAIKG--CGRRFSNIVLKKADIDLN 38 (140)
Q Consensus 6 ~~~k~v~~ALt~IyG--IG~~~A~~Ic~~lGI~~~ 38 (140)
.|...|..+|..-+| ||..+...|++.+||...
T Consensus 21 yG~rri~~~L~~~~~~~v~~krV~RlM~~~gL~~~ 55 (60)
T PF13276_consen 21 YGYRRIWAELRREGGIRVSRKRVRRLMREMGLRSK 55 (60)
T ss_pred eehhHHHHHHhccCcccccHHHHHHHHHHcCCccc
Confidence 355566667777665 688888888888888654
No 170
>COG1636 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.30 E-value=97 Score=24.90 Aligned_cols=82 Identities=16% Similarity=0.124 Sum_probs=54.0
Q ss_pred HhCCCCCCccCCCCHHHHHHHHHHHhCCCCcCCCcccccccccccCCceeEeeccchhHHHHHHHHHHHHHHhhhheecc
Q psy1365 32 KADIDLNKRAGECSEEEVDKIITIMTNPRQYKIPDWFLNRQKDIVDGKYSQILLTSTAQLDSKLREDLERLKKIRAHRGM 111 (140)
Q Consensus 32 ~lGI~~~~~~~~Ls~~qi~~L~~~I~~~~~~~i~~w~~nr~~d~~tg~~~~l~~~~~~~L~~~~~~~I~rl~~i~syRG~ 111 (140)
.|+++|.+.+ .||..+-.-++++ |.++.|..|.||.-- .. +.+...-+..+==.+|=|+
T Consensus 117 tL~iSp~Kn~-----~qin~~G~~~~k~--y~V~yl~~dfrK~gg-------------~~-r~~elske~~~YrQ~YCGC 175 (204)
T COG1636 117 TLLISPKKNM-----NQINEIGERAAKP--YGVVYLPSNFRKNGG-------------YQ-RSIELSKEENIYRQEYCGC 175 (204)
T ss_pred heecCcccCH-----HHHHHHhHHhhcc--cCceecCcccccccc-------------hH-HHHHHHHHHhHHHhhccch
Confidence 4566665544 4677777777764 889999999885432 23 2333332333333578776
Q ss_pred CCCCCCccCCccccccCCCccceee
Q psy1365 112 RHYWGLRVRGQHTKTTGRRGRTVGV 136 (140)
Q Consensus 112 RH~~gLpVRGQRTrtN~rt~~~~gv 136 (140)
.++|.-.+|+-++++|-...+|.
T Consensus 176 --vysl~~q~~~~~~~~r~~~~~~~ 198 (204)
T COG1636 176 --VYSLKDQNEDRKEVNRQAIPFGK 198 (204)
T ss_pred --hhhHhhhcchhhhhchhhhhHHh
Confidence 47888899999999988777664
No 171
>KOG0844|consensus
Probab=21.26 E-value=60 Score=28.06 Aligned_cols=13 Identities=8% Similarity=0.284 Sum_probs=10.7
Q ss_pred CCHHHHHHHHHHH
Q psy1365 44 CSEEEVDKIITIM 56 (140)
Q Consensus 44 Ls~~qi~~L~~~I 56 (140)
+|-|||.+|++.+
T Consensus 188 FTReQIaRLEKEF 200 (408)
T KOG0844|consen 188 FTREQIARLEKEF 200 (408)
T ss_pred hhHHHHHHHHHHH
Confidence 5789999998766
No 172
>PRK00024 hypothetical protein; Reviewed
Probab=20.98 E-value=50 Score=26.42 Aligned_cols=22 Identities=23% Similarity=0.330 Sum_probs=17.6
Q ss_pred ecccccccCcchHHHHHhHhCC
Q psy1365 14 ALTAIKGCGRRFSNIVLKKADI 35 (140)
Q Consensus 14 ALt~IyGIG~~~A~~Ic~~lGI 35 (140)
.|.+|+|||+..|.+|+....+
T Consensus 67 eL~~i~GIG~akA~~L~a~~El 88 (224)
T PRK00024 67 ELQSIKGIGPAKAAQLKAALEL 88 (224)
T ss_pred HHhhccCccHHHHHHHHHHHHH
Confidence 4789999999999888755444
No 173
>KOG4302|consensus
Probab=20.96 E-value=2.9e+02 Score=26.08 Aligned_cols=19 Identities=5% Similarity=0.027 Sum_probs=15.1
Q ss_pred hHHHHHhHhCCCCCCccCC
Q psy1365 25 FSNIVLKKADIDLNKRAGE 43 (140)
Q Consensus 25 ~A~~Ic~~lGI~~~~~~~~ 43 (140)
....+|..||+++...+.+
T Consensus 189 ~I~~l~~~Lg~~~~~~vt~ 207 (660)
T KOG4302|consen 189 EIKSLCSVLGLDFSMTVTD 207 (660)
T ss_pred HHHHHHHHhCCCcccchhh
Confidence 3567899999999988743
No 174
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=20.88 E-value=46 Score=28.12 Aligned_cols=23 Identities=13% Similarity=0.315 Sum_probs=19.6
Q ss_pred ecccccccCcchHHHHHhHhCCC
Q psy1365 14 ALTAIKGCGRRFSNIVLKKADID 36 (140)
Q Consensus 14 ALt~IyGIG~~~A~~Ic~~lGI~ 36 (140)
.|+.|+|||...|..|-..+.=.
T Consensus 49 ~l~~lpgIG~~ia~kI~Eil~tG 71 (334)
T smart00483 49 DLKGLPGIGDKIKKKIEEIIETG 71 (334)
T ss_pred HHhcCCCccHHHHHHHHHHHHhC
Confidence 47899999999999999886644
No 175
>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=20.86 E-value=44 Score=30.99 Aligned_cols=35 Identities=14% Similarity=0.154 Sum_probs=24.9
Q ss_pred ccccccCcchHHHHHhHhCCCCCCccCCCCHHHHH
Q psy1365 16 TAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVD 50 (140)
Q Consensus 16 t~IyGIG~~~A~~Ic~~lGI~~~~~~~~Ls~~qi~ 50 (140)
-.|.|+|+.++.++.+..+|..-.-+-.|+.+++.
T Consensus 435 l~I~GLG~k~i~~L~~~g~I~~~~Dl~~L~~~~L~ 469 (652)
T TIGR00575 435 MDIEGLGDKVIEQLFEKKLVRSVADLYALKKEDLL 469 (652)
T ss_pred cCCCCcCHHHHHHHHHcCCcCCHHHHHhcCHHHHh
Confidence 46899999999999998888653334445554443
No 176
>PF06207 DUF1002: Protein of unknown function (DUF1002); InterPro: IPR009343 This protein family has no known function. Its members are about 300 amino acids in length. It has so far been detected in Firmicute bacteria and some archaebacteria.
Probab=20.82 E-value=1.8e+02 Score=23.58 Aligned_cols=29 Identities=28% Similarity=0.513 Sum_probs=22.3
Q ss_pred HHHHHhHhCCCCCCccCCCCHHHHHHHHHHHhCCCC
Q psy1365 26 SNIVLKKADIDLNKRAGECSEEEVDKIITIMTNPRQ 61 (140)
Q Consensus 26 A~~Ic~~lGI~~~~~~~~Ls~~qi~~L~~~I~~~~~ 61 (140)
...+++.+||+ ||++|+..|..++.+..+
T Consensus 181 V~~~~~~~~i~-------ls~~q~~~i~~l~~~~~~ 209 (225)
T PF06207_consen 181 VNNVLNNYNIN-------LSDEQIQQIVNLMKKIQN 209 (225)
T ss_pred HHHHHHHcCCC-------CCHHHHHHHHHHHHHHHc
Confidence 34566777777 899999999999986533
No 177
>COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair]
Probab=20.78 E-value=44 Score=28.86 Aligned_cols=19 Identities=26% Similarity=0.389 Sum_probs=16.1
Q ss_pred ecccccccCcchHHHHHhH
Q psy1365 14 ALTAIKGCGRRFSNIVLKK 32 (140)
Q Consensus 14 ALt~IyGIG~~~A~~Ic~~ 32 (140)
.|..+.|||.++|.+|+..
T Consensus 114 ~l~~LpGiG~yTa~Ail~~ 132 (342)
T COG1194 114 ELAALPGVGPYTAGAILSF 132 (342)
T ss_pred HHHhCCCCcHHHHHHHHHH
Confidence 4667999999999999854
No 178
>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=20.62 E-value=39 Score=31.38 Aligned_cols=22 Identities=27% Similarity=0.397 Sum_probs=17.2
Q ss_pred eeecccccccCcchHHHHHhHhC
Q psy1365 12 MFALTAIKGCGRRFSNIVLKKAD 34 (140)
Q Consensus 12 ~~ALt~IyGIG~~~A~~Ic~~lG 34 (140)
.+|| .|+|||+..|..+++.++
T Consensus 498 L~aL-gIpgVG~~~ak~L~~~f~ 519 (652)
T TIGR00575 498 LFAL-GIRHVGEVTAKNLAKHFG 519 (652)
T ss_pred Hhhc-cCCCcCHHHHHHHHHHhC
Confidence 3444 789999999999888776
No 179
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=20.43 E-value=39 Score=31.49 Aligned_cols=35 Identities=17% Similarity=0.183 Sum_probs=26.0
Q ss_pred ccccccCcchHHHHHhHhCCCCCCccCCCCHHHHH
Q psy1365 16 TAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVD 50 (140)
Q Consensus 16 t~IyGIG~~~A~~Ic~~lGI~~~~~~~~Ls~~qi~ 50 (140)
-.|.|+|++++.++.+..+|..-.-+-.|+++++.
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 47899999999999999988754444455555554
No 180
>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=20.28 E-value=1.7e+02 Score=25.47 Aligned_cols=33 Identities=12% Similarity=0.084 Sum_probs=28.0
Q ss_pred hHHHHHhHhCCCCCCc----cCCCCHHHHHHHHHHHh
Q psy1365 25 FSNIVLKKADIDLNKR----AGECSEEEVDKIITIMT 57 (140)
Q Consensus 25 ~A~~Ic~~lGI~~~~~----~~~Ls~~qi~~L~~~I~ 57 (140)
.+....+++||+|..+ -++|+++.+..|.+..+
T Consensus 290 k~r~~~~~~Gi~p~~K~iv~Sd~Lde~~i~~L~~~~~ 326 (377)
T cd01401 290 KAIAHYEKLGIDPKTKTLVFSDGLDVEKALELYEYFK 326 (377)
T ss_pred HHHHHHHHcCCCCCCcEEEEcCCCCHHHHHHHHHHHc
Confidence 4667778999999888 67899999999988775
No 181
>PRK05672 dnaE2 error-prone DNA polymerase; Validated
Probab=20.10 E-value=67 Score=31.59 Aligned_cols=45 Identities=16% Similarity=0.294 Sum_probs=31.0
Q ss_pred CeeeeeecccccccCcchHHHHHhHhCCCCC-------CccCCCCHHHHHHHH
Q psy1365 8 KRKVMFALTAIKGCGRRFSNIVLKKADIDLN-------KRAGECSEEEVDKII 53 (140)
Q Consensus 8 ~k~v~~ALt~IyGIG~~~A~~Ic~~lGI~~~-------~~~~~Ls~~qi~~L~ 53 (140)
+..|.++|..|+|||...|..|.+.=.-.|. .+++ ++...++.|.
T Consensus 811 ~~~I~~gl~~Ikgvg~~~~~~Iv~~R~~g~f~s~~Df~~R~~-~~~~~le~Li 862 (1046)
T PRK05672 811 GPAVRLGLRLVRGLGEEAAERIVAARARGPFTSVEDLARRAG-LDRRQLEALA 862 (1046)
T ss_pred CCcEEechhhcCCCCHHHHHHHHHHhhcCCCCCHHHHHHHhC-CCHHHHHHHH
Confidence 4679999999999999999999864321121 1222 5666666664
No 182
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=20.08 E-value=57 Score=26.73 Aligned_cols=21 Identities=14% Similarity=0.346 Sum_probs=18.9
Q ss_pred ecccccccCcchHHHHHhHhC
Q psy1365 14 ALTAIKGCGRRFSNIVLKKAD 34 (140)
Q Consensus 14 ALt~IyGIG~~~A~~Ic~~lG 34 (140)
.|..+.|||...|..|...++
T Consensus 37 EL~~V~GIg~k~AekI~e~l~ 57 (232)
T PRK12766 37 ELAEVDGIGNALAARIKADVG 57 (232)
T ss_pred HHHHccCCCHHHHHHHHHHhc
Confidence 478899999999999999987
No 183
>PF04201 TPD52: Tumour protein D52 family; InterPro: IPR007327 The hD52 gene was originally identified through its elevated expression level in human breast carcinoma. Cloning of D52 homologues from other species has indicated that D52 may play roles in calcium-mediated signal transduction and cell proliferation. Two human homologues of hD52, hD53 and hD54, have also been identified, demonstrating the existence of a novel gene/protein family []. These proteins have an N-terminal coiled-coil that allows members to form homo- and heterodimers with each other [].
Probab=20.06 E-value=58 Score=25.28 Aligned_cols=16 Identities=25% Similarity=0.302 Sum_probs=10.7
Q ss_pred CCCCHHHHHHHHHHHh
Q psy1365 42 GECSEEEVDKIITIMT 57 (140)
Q Consensus 42 ~~Ls~~qi~~L~~~I~ 57 (140)
..|+++|-+.|...|.
T Consensus 24 ~~LsEeE~eeLr~EL~ 39 (162)
T PF04201_consen 24 EGLSEEEREELRSELA 39 (162)
T ss_pred ccCCHHHHHHHHHHHH
Confidence 4677777776666664
Done!