Query 031787
Match_columns 153
No_of_seqs 115 out of 1037
Neff 6.1
Searched_HMMs 46136
Date Fri Mar 29 05:20:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031787.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031787hhsearch_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 1.5E-65 3.3E-70 394.5 11.5 148 6-153 7-154 (154)
2 PRK04053 rps13p 30S ribosomal 100.0 1.1E-64 2.3E-69 388.3 11.1 148 6-153 2-149 (149)
3 TIGR03629 arch_S13P archaeal r 100.0 7.2E-64 1.6E-68 381.9 9.6 144 9-153 1-144 (144)
4 COG0099 RpsM Ribosomal protein 100.0 3.5E-51 7.6E-56 301.2 7.3 119 13-153 1-121 (121)
5 KOG3311 Ribosomal protein S18 100.0 3E-50 6.4E-55 306.3 7.1 152 2-153 1-152 (152)
6 CHL00137 rps13 ribosomal prote 100.0 7.5E-48 1.6E-52 286.7 9.0 111 13-145 1-111 (122)
7 PRK05179 rpsM 30S ribosomal pr 100.0 1E-47 2.2E-52 286.0 9.5 111 13-145 1-111 (122)
8 TIGR03631 bact_S13 30S ribosom 100.0 3.3E-46 7.2E-51 274.7 9.6 111 15-147 1-111 (113)
9 PF00416 Ribosomal_S13: Riboso 100.0 2.2E-46 4.7E-51 272.9 4.1 107 15-143 1-107 (107)
10 PRK04184 DNA topoisomerase VI 98.5 1.5E-07 3.2E-12 85.2 4.7 91 24-123 256-350 (535)
11 COG1389 DNA topoisomerase VI, 98.4 1.6E-07 3.4E-12 83.4 4.0 92 23-123 255-354 (538)
12 TIGR01052 top6b DNA topoisomer 98.4 4E-07 8.8E-12 81.6 5.0 91 24-123 247-344 (488)
13 PF06831 H2TH: Formamidopyrimi 97.3 0.00025 5.4E-09 50.2 3.3 52 23-74 22-76 (92)
14 PRK01103 formamidopyrimidine/5 97.1 0.00074 1.6E-08 56.3 4.4 53 22-74 153-208 (274)
15 PRK14810 formamidopyrimidine-D 96.5 0.0036 7.7E-08 52.2 4.2 52 23-74 153-207 (272)
16 PRK14811 formamidopyrimidine-D 96.4 0.0045 9.7E-08 51.6 4.6 51 24-74 143-196 (269)
17 PRK10445 endonuclease VIII; Pr 96.3 0.0047 1E-07 51.3 4.2 51 24-74 151-204 (263)
18 PRK13945 formamidopyrimidine-D 96.3 0.0058 1.3E-07 51.2 4.5 52 23-74 163-217 (282)
19 TIGR00577 fpg formamidopyrimid 96.3 0.0055 1.2E-07 51.1 4.2 52 23-74 154-208 (272)
20 COG0266 Nei Formamidopyrimidin 94.1 0.16 3.5E-06 42.8 6.3 60 15-74 146-208 (273)
21 PF05833 FbpA: Fibronectin-bin 93.8 0.023 4.9E-07 49.9 0.7 51 23-73 185-236 (455)
22 PF00633 HHH: Helix-hairpin-he 93.7 0.045 9.7E-07 31.1 1.6 18 30-47 12-29 (30)
23 PRK14867 DNA topoisomerase VI 92.5 0.16 3.5E-06 47.5 4.2 81 33-123 410-494 (659)
24 TIGR00275 flavoprotein, HI0933 91.6 0.13 2.8E-06 44.6 2.5 50 23-74 282-331 (400)
25 cd00080 HhH2_motif Helix-hairp 90.2 0.26 5.7E-06 33.3 2.4 37 5-50 5-43 (75)
26 PF11798 IMS_HHH: IMS family H 89.6 0.2 4.4E-06 28.7 1.3 22 29-51 11-32 (32)
27 PF14520 HHH_5: Helix-hairpin- 89.3 0.042 9.1E-07 35.4 -2.0 36 28-64 4-39 (60)
28 PF10391 DNA_pol_lambd_f: Fing 88.5 0.32 6.9E-06 31.0 1.7 22 30-52 3-24 (52)
29 PRK00274 ksgA 16S ribosomal RN 88.4 0.38 8.2E-06 39.7 2.6 63 9-74 208-270 (272)
30 smart00278 HhH1 Helix-hairpin- 87.5 0.43 9.3E-06 25.8 1.6 20 30-49 2-21 (26)
31 COG3743 Uncharacterized conser 86.4 0.48 1E-05 36.0 1.9 44 29-73 67-110 (133)
32 PRK14601 ruvA Holliday junctio 86.0 0.47 1E-05 37.7 1.8 35 6-49 94-128 (183)
33 COG0030 KsgA Dimethyladenosine 85.6 0.53 1.1E-05 39.4 2.0 48 22-74 209-256 (259)
34 PRK02515 psbU photosystem II c 85.2 0.56 1.2E-05 35.6 1.8 59 16-74 48-109 (132)
35 PRK14606 ruvA Holliday junctio 84.0 0.61 1.3E-05 37.1 1.6 22 29-50 108-129 (188)
36 KOG3311 Ribosomal protein S18 83.1 0.19 4.2E-06 38.9 -1.5 45 100-146 70-114 (152)
37 PF03486 HI0933_like: HI0933-l 83.1 1.4 3E-05 38.9 3.6 51 22-74 288-339 (409)
38 PRK14603 ruvA Holliday junctio 82.5 0.76 1.6E-05 36.8 1.6 20 29-48 107-126 (197)
39 PRK14604 ruvA Holliday junctio 82.1 0.8 1.7E-05 36.6 1.6 21 29-49 108-128 (195)
40 TIGR00755 ksgA dimethyladenosi 82.0 1 2.3E-05 36.5 2.2 59 9-71 194-252 (253)
41 PRK13901 ruvA Holliday junctio 81.5 0.87 1.9E-05 36.6 1.6 21 29-49 107-127 (196)
42 COG0632 RuvA Holliday junction 81.4 0.9 2E-05 36.7 1.6 21 29-49 108-128 (201)
43 PF00398 RrnaAD: Ribosomal RNA 81.1 0.61 1.3E-05 38.2 0.6 62 8-73 200-261 (262)
44 TIGR03252 uncharacterized HhH- 81.1 0.7 1.5E-05 36.7 0.9 29 22-50 108-136 (177)
45 PRK14602 ruvA Holliday junctio 80.9 0.92 2E-05 36.4 1.5 20 29-48 109-128 (203)
46 COG1293 Predicted RNA-binding 80.7 1.5 3.2E-05 40.4 2.9 50 25-74 186-235 (564)
47 smart00279 HhH2 Helix-hairpin- 80.6 2.1 4.4E-05 25.2 2.6 34 8-48 2-35 (36)
48 PF14579 HHH_6: Helix-hairpin- 78.4 2.3 5E-05 29.4 2.7 27 24-50 22-48 (90)
49 PF09883 DUF2110: Uncharacteri 76.0 5.1 0.00011 32.9 4.5 52 24-75 96-159 (225)
50 PRK14600 ruvA Holliday junctio 75.3 1.6 3.5E-05 34.7 1.4 20 29-49 108-127 (186)
51 PF11731 Cdd1: Pathogenicity l 75.2 2.2 4.7E-05 30.5 1.9 37 29-66 12-48 (93)
52 PF12836 HHH_3: Helix-hairpin- 75.1 1.3 2.9E-05 28.8 0.8 47 24-70 9-62 (65)
53 PF14520 HHH_5: Helix-hairpin- 74.8 2.4 5.2E-05 27.0 1.9 20 30-49 39-58 (60)
54 PRK14605 ruvA Holliday junctio 74.8 1.8 3.9E-05 34.5 1.6 18 29-46 108-125 (194)
55 TIGR00426 competence protein C 73.8 2.2 4.8E-05 27.9 1.6 26 24-49 11-37 (69)
56 PRK14605 ruvA Holliday junctio 73.6 0.75 1.6E-05 36.7 -0.9 37 15-51 59-95 (194)
57 PRK01229 N-glycosylase/DNA lya 72.9 11 0.00024 30.4 5.8 69 27-109 116-185 (208)
58 PRK00116 ruvA Holliday junctio 72.3 2.5 5.5E-05 33.4 1.9 60 15-74 59-130 (192)
59 PF02042 RWP-RK: RWP-RK domain 71.4 3.9 8.4E-05 26.2 2.2 25 34-58 24-50 (52)
60 PRK14868 DNA topoisomerase VI 71.1 4.2 9E-05 39.1 3.2 54 61-123 482-539 (795)
61 TIGR03674 fen_arch flap struct 71.0 3.2 6.9E-05 35.7 2.3 36 6-50 222-257 (338)
62 PF14716 HHH_8: Helix-hairpin- 70.8 2.8 6.1E-05 27.5 1.6 20 30-49 48-67 (68)
63 TIGR01259 comE comEA protein. 70.7 2.3 5E-05 31.2 1.2 32 20-51 59-90 (120)
64 smart00483 POLXc DNA polymeras 68.0 3.7 8E-05 35.2 2.1 25 28-53 88-112 (334)
65 PF02371 Transposase_20: Trans 67.2 4.1 9E-05 27.9 1.8 21 30-50 3-23 (87)
66 PRK12278 50S ribosomal protein 66.9 4.3 9.2E-05 33.3 2.1 45 29-74 158-202 (221)
67 cd00056 ENDO3c endonuclease II 65.9 3.6 7.9E-05 30.7 1.5 44 25-72 79-122 (158)
68 TIGR00084 ruvA Holliday juncti 65.9 3.8 8.2E-05 32.5 1.6 20 29-48 107-126 (191)
69 smart00478 ENDO3c endonuclease 65.7 3.7 8E-05 30.4 1.5 23 27-49 70-92 (149)
70 cd00128 XPG Xeroderma pigmento 65.3 5.1 0.00011 33.7 2.4 36 6-50 209-244 (316)
71 PF12826 HHH_2: Helix-hairpin- 64.9 3.3 7.1E-05 27.0 0.9 18 33-50 7-24 (64)
72 PF12826 HHH_2: Helix-hairpin- 64.8 4.7 0.0001 26.2 1.6 21 30-50 36-56 (64)
73 cd00141 NT_POLXc Nucleotidyltr 64.2 4.9 0.00011 34.0 2.1 25 28-53 84-108 (307)
74 PTZ00217 flap endonuclease-1; 63.9 5.6 0.00012 35.0 2.4 36 6-50 221-256 (393)
75 PF14490 HHH_4: Helix-hairpin- 63.7 4.2 9E-05 28.4 1.3 26 29-54 45-71 (94)
76 COG0353 RecR Recombinational D 63.7 8.1 0.00018 31.2 3.1 86 27-129 10-108 (198)
77 PRK03980 flap endonuclease-1; 63.0 5.8 0.00013 33.5 2.3 36 6-50 175-210 (292)
78 PRK08609 hypothetical protein; 62.7 5.6 0.00012 36.6 2.3 25 29-53 88-112 (570)
79 COG0632 RuvA Holliday junction 62.3 1.3 2.7E-05 35.8 -1.7 38 13-50 57-94 (201)
80 PRK10702 endonuclease III; Pro 62.2 5 0.00011 32.3 1.7 23 27-49 107-129 (211)
81 TIGR00615 recR recombination p 62.2 5.6 0.00012 32.0 2.0 86 27-129 9-107 (195)
82 PRK12311 rpsB 30S ribosomal pr 62.1 4.3 9.3E-05 35.1 1.4 44 29-73 263-306 (326)
83 PRK00076 recR recombination pr 61.8 5.7 0.00012 32.0 1.9 86 27-129 9-107 (196)
84 TIGR01083 nth endonuclease III 61.5 5.5 0.00012 31.2 1.8 23 27-49 104-126 (191)
85 TIGR00084 ruvA Holliday juncti 61.5 1.1 2.5E-05 35.5 -2.1 35 15-49 58-92 (191)
86 TIGR01084 mutY A/G-specific ad 60.5 5.3 0.00011 33.5 1.6 29 18-49 97-125 (275)
87 KOG2518 5'-3' exonuclease [Rep 59.5 6.6 0.00014 36.2 2.1 60 6-74 211-277 (556)
88 COG2081 Predicted flavoprotein 59.3 11 0.00025 33.5 3.5 49 23-74 284-332 (408)
89 PRK13844 recombination protein 59.1 6.8 0.00015 31.7 2.0 39 28-74 14-52 (200)
90 PRK14602 ruvA Holliday junctio 59.0 2.1 4.7E-05 34.3 -0.9 37 15-51 60-96 (203)
91 PRK14606 ruvA Holliday junctio 58.9 1.6 3.6E-05 34.6 -1.6 35 15-49 59-93 (188)
92 PHA02564 V virion protein; Pro 58.6 19 0.00042 27.5 4.3 34 40-74 86-119 (141)
93 cd00008 53EXOc 5'-3' exonuclea 58.4 8.4 0.00018 31.4 2.4 37 7-50 168-204 (240)
94 PRK14601 ruvA Holliday junctio 58.2 1.7 3.8E-05 34.4 -1.6 35 15-49 59-93 (183)
95 cd01104 HTH_MlrA-CarA Helix-Tu 58.0 28 0.00062 21.9 4.5 43 31-73 6-52 (68)
96 TIGR01448 recD_rel helicase, p 57.8 11 0.00024 35.7 3.4 42 33-74 88-139 (720)
97 COG0177 Nth Predicted EndoIII- 57.7 24 0.00052 28.7 4.9 40 28-72 108-148 (211)
98 PRK14600 ruvA Holliday junctio 57.5 1.9 4.1E-05 34.2 -1.5 36 15-50 59-94 (186)
99 PRK13901 ruvA Holliday junctio 56.4 2 4.3E-05 34.6 -1.5 35 15-49 58-92 (196)
100 PRK14603 ruvA Holliday junctio 55.4 2.1 4.4E-05 34.3 -1.6 35 15-49 58-92 (197)
101 smart00475 53EXOc 5'-3' exonuc 54.0 13 0.00028 30.9 2.8 36 8-50 172-207 (259)
102 PRK12766 50S ribosomal protein 53.4 7.6 0.00017 32.1 1.4 20 31-50 38-57 (232)
103 PRK13910 DNA glycosylase MutY; 53.3 8.1 0.00018 32.7 1.6 22 28-49 71-92 (289)
104 PF11338 DUF3140: Protein of u 53.2 22 0.00047 25.4 3.5 35 35-73 33-67 (92)
105 COG0258 Exo 5'-3' exonuclease 52.5 14 0.00031 31.0 3.0 34 7-50 183-219 (310)
106 PRK13913 3-methyladenine DNA g 52.2 8.3 0.00018 31.4 1.4 23 27-49 119-141 (218)
107 PRK14667 uvrC excinuclease ABC 52.1 8 0.00017 35.8 1.4 43 24-68 509-551 (567)
108 PRK10880 adenine DNA glycosyla 52.0 9.3 0.0002 33.2 1.8 23 27-49 107-129 (350)
109 PRK00116 ruvA Holliday junctio 50.8 11 0.00023 29.8 1.8 21 30-50 109-129 (192)
110 PRK14976 5'-3' exonuclease; Pr 49.4 16 0.00035 30.6 2.8 36 8-50 177-212 (281)
111 PF01698 FLO_LFY: Floricaula / 49.2 5.6 0.00012 35.2 0.0 77 33-127 56-132 (386)
112 PRK14670 uvrC excinuclease ABC 48.9 9 0.0002 35.5 1.3 40 27-68 512-551 (574)
113 PRK10308 3-methyl-adenine DNA 48.4 33 0.00071 28.8 4.5 30 27-56 205-234 (283)
114 PF01367 5_3_exonuc: 5'-3' exo 47.8 2.8 6.1E-05 30.2 -1.7 20 31-50 20-39 (101)
115 TIGR00588 ogg 8-oxoguanine DNA 47.6 11 0.00023 32.1 1.4 43 27-72 218-260 (310)
116 PRK14604 ruvA Holliday junctio 47.4 3.3 7.1E-05 33.1 -1.6 35 15-49 59-93 (195)
117 PRK00558 uvrC excinuclease ABC 47.2 14 0.00031 34.2 2.3 43 23-67 537-579 (598)
118 PF14635 HHH_7: Helix-hairpin- 46.7 4.9 0.00011 29.2 -0.6 42 9-50 27-71 (104)
119 PRK14669 uvrC excinuclease ABC 46.5 13 0.00027 35.0 1.8 41 26-68 549-589 (624)
120 PF09239 Topo-VIb_trans: Topoi 44.7 9.2 0.0002 29.9 0.6 35 87-123 1-39 (160)
121 KOG0494 Transcription factor C 42.9 11 0.00024 32.0 0.8 32 59-91 147-196 (332)
122 TIGR00600 rad2 DNA excision re 42.3 17 0.00038 36.1 2.1 36 7-51 853-888 (1034)
123 COG2938 Uncharacterized conser 41.7 15 0.00032 26.3 1.2 34 55-89 39-72 (94)
124 PTZ00338 dimethyladenosine tra 41.5 32 0.0007 28.9 3.4 34 40-74 255-288 (294)
125 PF04760 IF2_N: Translation in 40.6 16 0.00034 22.7 1.1 44 30-73 8-52 (54)
126 PRK09482 flap endonuclease-lik 40.5 19 0.0004 30.1 1.8 20 31-50 184-203 (256)
127 COG0122 AlkA 3-methyladenine D 40.4 16 0.00035 30.8 1.4 23 27-49 196-218 (285)
128 PRK14668 uvrC excinuclease ABC 39.3 15 0.00032 34.1 1.1 39 27-67 523-561 (577)
129 COG3415 Transposase and inacti 38.7 63 0.0014 24.5 4.3 45 30-74 26-78 (138)
130 PRK12373 NADH dehydrogenase su 38.4 25 0.00054 31.4 2.3 45 29-74 323-367 (400)
131 COG1555 ComEA DNA uptake prote 37.5 32 0.00069 26.2 2.6 22 28-49 96-117 (149)
132 PRK14896 ksgA 16S ribosomal RN 37.4 37 0.00079 27.6 3.1 64 9-74 191-256 (258)
133 PRK14671 uvrC excinuclease ABC 37.1 22 0.00049 33.2 1.9 49 18-68 558-606 (621)
134 PRK14672 uvrC excinuclease ABC 36.7 17 0.00036 34.6 1.0 43 23-67 602-644 (691)
135 cd01702 PolY_Pol_eta DNA Polym 36.2 24 0.00051 30.5 1.9 38 29-66 182-221 (359)
136 KOG2251 Homeobox transcription 35.4 27 0.00059 28.8 2.0 32 59-91 43-92 (228)
137 PRK13766 Hef nuclease; Provisi 35.1 26 0.00056 32.9 2.1 23 28-50 714-736 (773)
138 PRK07373 DNA polymerase III su 34.6 32 0.00069 30.9 2.5 25 24-48 109-133 (449)
139 COG2231 Uncharacterized protei 33.9 30 0.00065 28.3 2.0 36 20-55 104-141 (215)
140 PF06514 PsbU: Photosystem II 33.4 46 0.001 23.8 2.6 58 17-74 11-71 (93)
141 COG1948 MUS81 ERCC4-type nucle 33.0 28 0.00061 29.2 1.7 38 28-67 181-218 (254)
142 COG1059 Thermostable 8-oxoguan 32.7 22 0.00047 28.9 0.9 25 28-52 120-144 (210)
143 PF00542 Ribosomal_L12: Riboso 32.1 20 0.00043 23.9 0.6 44 28-74 17-60 (68)
144 PRK07945 hypothetical protein; 32.0 29 0.00063 29.7 1.7 21 30-50 50-70 (335)
145 PF13442 Cytochrome_CBB3: Cyto 31.4 46 0.001 20.9 2.2 14 59-72 54-67 (67)
146 PF02318 FYVE_2: FYVE-type zin 30.1 58 0.0013 23.5 2.8 17 58-74 1-17 (118)
147 TIGR00575 dnlj DNA ligase, NAD 28.9 28 0.0006 32.8 1.1 36 32-67 435-470 (652)
148 KOG2875 8-oxoguanine DNA glyco 28.8 24 0.00052 30.3 0.6 22 27-48 216-237 (323)
149 PRK14666 uvrC excinuclease ABC 28.8 31 0.00066 32.9 1.4 40 26-67 634-673 (694)
150 cd00141 NT_POLXc Nucleotidyltr 28.5 23 0.00049 30.0 0.5 24 30-53 46-69 (307)
151 COG1936 Predicted nucleotide k 27.8 48 0.001 26.4 2.2 24 29-52 3-26 (180)
152 smart00483 POLXc DNA polymeras 27.8 34 0.00073 29.3 1.4 22 30-51 49-70 (334)
153 KOG0650 WD40 repeat nucleolar 27.7 77 0.0017 30.1 3.7 48 52-106 142-189 (733)
154 COG1636 Uncharacterized protei 27.6 46 0.001 27.0 2.0 82 48-149 117-198 (204)
155 PRK05898 dnaE DNA polymerase I 27.4 1.1E+02 0.0023 30.5 4.8 26 24-49 747-772 (971)
156 TIGR00194 uvrC excinuclease AB 27.2 40 0.00087 31.3 1.9 25 26-50 538-562 (574)
157 PF06394 Pepsin-I3: Pepsin inh 27.0 38 0.00082 23.3 1.3 21 54-74 34-54 (76)
158 PF15614 WHIM3: WSTF, HB1, Itc 26.4 1.2E+02 0.0027 18.8 3.4 37 61-118 6-42 (46)
159 PRK04301 radA DNA repair and r 26.2 49 0.0011 27.7 2.1 38 29-67 6-43 (317)
160 PF13551 HTH_29: Winged helix- 26.2 1.5E+02 0.0032 20.0 4.3 46 30-75 17-73 (112)
161 PF03118 RNA_pol_A_CTD: Bacter 25.4 48 0.001 21.7 1.5 20 30-49 45-64 (66)
162 PF00986 DNA_gyraseB_C: DNA gy 25.1 31 0.00066 23.0 0.5 43 29-72 6-49 (65)
163 smart00389 HOX Homeodomain. DN 25.0 51 0.0011 19.7 1.5 29 59-88 24-52 (56)
164 TIGR02663 nifX nitrogen fixati 24.6 82 0.0018 22.6 2.8 47 35-86 70-117 (119)
165 PF06207 DUF1002: Protein of u 24.5 1.5E+02 0.0034 24.2 4.6 30 42-78 181-210 (225)
166 TIGR00608 radc DNA repair prot 24.3 37 0.00081 27.5 1.0 22 30-51 61-82 (218)
167 PF12558 DUF3744: ATP-binding 23.9 72 0.0016 21.3 2.2 41 33-73 6-48 (74)
168 TIGR02236 recomb_radA DNA repa 23.9 50 0.0011 27.3 1.7 36 31-67 1-36 (310)
169 COG0322 UvrC Nuclease subunit 23.8 39 0.00084 31.5 1.1 43 24-68 525-567 (581)
170 PF13276 HTH_21: HTH-like doma 23.7 42 0.00091 21.0 0.9 35 21-55 20-56 (60)
171 PF13613 HTH_Tnp_4: Helix-turn 23.0 60 0.0013 20.0 1.6 21 29-49 23-43 (53)
172 PF14794 DUF4479: Domain of un 22.8 70 0.0015 21.6 1.9 24 50-74 39-62 (73)
173 PF02879 PGM_PMM_II: Phosphogl 22.7 29 0.00063 23.9 0.1 40 12-51 6-46 (104)
174 COG1194 MutY A/G-specific DNA 22.7 51 0.0011 28.8 1.5 36 10-48 97-132 (342)
175 PRK05755 DNA polymerase I; Pro 22.6 73 0.0016 30.8 2.8 36 8-50 173-208 (880)
176 PRK07956 ligA NAD-dependent DN 22.5 36 0.00078 32.1 0.6 35 32-66 448-482 (665)
177 TIGR00596 rad1 DNA repair prot 22.5 55 0.0012 31.7 1.9 38 28-68 757-794 (814)
178 PF11460 DUF3007: Protein of u 22.5 45 0.00097 24.3 1.0 20 54-73 84-103 (104)
179 KOG0821 Predicted ribosomal RN 22.0 1.2E+02 0.0026 25.7 3.5 35 40-74 270-304 (326)
180 PRK02362 ski2-like helicase; P 21.8 58 0.0013 30.6 1.9 39 29-68 652-690 (737)
181 PF00034 Cytochrom_C: Cytochro 21.8 88 0.0019 19.6 2.3 16 59-74 74-89 (91)
182 PRK00024 hypothetical protein; 21.6 45 0.00097 27.0 1.0 22 30-51 67-88 (224)
183 PRK12766 50S ribosomal protein 21.5 71 0.0015 26.5 2.1 38 30-68 4-41 (232)
184 KOG2519 5'-3' exonuclease [Rep 21.5 1.1E+02 0.0023 27.8 3.4 35 7-50 216-250 (449)
185 cd01401 PncB_like Nicotinate p 21.2 1.7E+02 0.0036 25.9 4.5 35 40-74 289-327 (377)
186 PF10662 PduV-EutP: Ethanolami 21.2 82 0.0018 24.0 2.3 37 38-74 107-143 (143)
187 COG1111 MPH1 ERCC4-like helica 20.9 63 0.0014 29.9 1.8 85 24-125 161-249 (542)
188 smart00530 HTH_XRE Helix-turn- 20.8 91 0.002 17.0 2.0 18 36-53 36-53 (56)
189 COG1796 POL4 DNA polymerase IV 20.8 63 0.0014 28.1 1.7 20 30-49 54-73 (326)
190 KOG0843 Transcription factor E 20.7 78 0.0017 25.5 2.1 52 38-89 84-155 (197)
191 PRK08609 hypothetical protein; 20.6 36 0.00078 31.4 0.2 24 30-53 49-72 (570)
No 1
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=100.00 E-value=1.5e-65 Score=394.49 Aligned_cols=148 Identities=72% Similarity=1.171 Sum_probs=145.0
Q ss_pred CccchhhhhhhcCccCCCCeeeeeehhhccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCCccCCcccc
Q 031787 6 ANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFL 85 (153)
Q Consensus 6 ~~~~~~~~vri~~~~l~~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~L~~~i~~~~~~~ip~w~~ 85 (153)
.+++|+||+||+|||||++|+|.+||++|||||..+|.+||+.+||||++++++||++|++.|.++|++|.+|.+|+||+
T Consensus 7 ~~~~~~~mvrI~~~~l~~~K~v~~aLt~I~GIG~~~A~~I~~~lgi~~~~~~~~Lt~~qi~~l~~~i~~~~~~~iP~w~~ 86 (154)
T PTZ00134 7 KADDFQHILRILNTNVDGKRKVPYALTAIKGIGRRFAYLVCKKAGIDVTKRAGELTAEEIEKIVEIIANPLQFKIPDWFL 86 (154)
T ss_pred chhhhhhhhhccCccCCCCCEEEEeecccccccHHHHHHHHHHcCcCcCCCcccCCHHHHHHHHHHHhccccCCCChhHh
Confidence 33689999999999999999999999999999999999999999999999999999999999999999987899999999
Q ss_pred CccCCcCCCcchhhhhhhHHHHHHHhhhhhhccceeecccCCCCCccCCcCCcccCCCccceeeeccC
Q 031787 86 NRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 153 (153)
Q Consensus 86 nr~kd~~tg~~~~li~~dL~~~~~~~I~rl~~i~syRG~RH~~gLpvRGQRT~tNart~~~~~v~~~~ 153 (153)
|||+|+.||+|.|+||+||++++++||+||++|+||||+||++||||||||||||||||+++||++||
T Consensus 87 nr~kd~~tG~d~h~i~~dL~~~~~~dI~Rl~~I~sYRG~RH~~GLpVRGQRTkTnaR~g~~~gv~~kk 154 (154)
T PTZ00134 87 NRQRDPKDGKNSHLTSNMLDTKLREDLERLKKIRLHRGLRHHWGLRVRGQHTKTTGRRGRTVGVSRKK 154 (154)
T ss_pred hccccccccchhhhhHHHHHHHHHHHHHHHHHhcchheeecccCCccCCccCCCCCccccccceeccC
Confidence 99999999999999999999999999999999999999999999999999999999999999999997
No 2
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=100.00 E-value=1.1e-64 Score=388.25 Aligned_cols=148 Identities=44% Similarity=0.797 Sum_probs=145.5
Q ss_pred CccchhhhhhhcCccCCCCeeeeeehhhccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCCccCCcccc
Q 031787 6 ANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFL 85 (153)
Q Consensus 6 ~~~~~~~~vri~~~~l~~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~L~~~i~~~~~~~ip~w~~ 85 (153)
.+++|+||+||+|||||++|+|.+||++|||||+++|.+||+.+||||++++++||++|+++|.++|++|..+.+|+||+
T Consensus 2 ~~~~~~~m~rI~~~~i~~~k~i~~aLt~IyGIG~~~a~~Ic~~lgi~~~~~~~~Lt~~qi~~l~~~i~~~~~~~iP~w~~ 81 (149)
T PRK04053 2 MEEEFKYIVRIAGTDLDGTKPVEYALTGIKGIGRRTARAIARKLGLDPNAKLGYLSDEEIEKIEEALEDPAEEGIPSWML 81 (149)
T ss_pred chhhhhhhHhhcCccCCCCCEEeeeccccccccHHHHHHHHHHcCcCCCCccCcCCHHHHHHHHHHHHhhccccCchhhh
Confidence 35789999999999999999999999999999999999999999999999999999999999999999988899999999
Q ss_pred CccCCcCCCcchhhhhhhHHHHHHHhhhhhhccceeecccCCCCCccCCcCCcccCCCccceeeeccC
Q 031787 86 NRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 153 (153)
Q Consensus 86 nr~kd~~tg~~~~li~~dL~~~~~~~I~rl~~i~syRG~RH~~gLpvRGQRT~tNart~~~~~v~~~~ 153 (153)
||++|+.||+|.|+||+||++++++||+||++|+||||+||.+||||||||||||||||+++||+|||
T Consensus 82 Nr~~d~~tg~~~~~ie~dLr~~~~~~I~rl~~I~syRG~RH~~GLPVRGQRTrTNaRtg~~~gv~~kk 149 (149)
T PRK04053 82 NRRKDYETGEDLHLIGSDLILTVREDINRMKKIRSYRGIRHELGLKVRGQRTRSTGRTGGTVGVSRKK 149 (149)
T ss_pred ccccccccCccceEehHHHHHHHHHHHHHHHHhcceeeecccCCCCCCCCcCCCCCcCCCccccccCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999997
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=7.2e-64 Score=381.94 Aligned_cols=144 Identities=49% Similarity=0.880 Sum_probs=141.9
Q ss_pred chhhhhhhcCccCCCCeeeeeehhhccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCCccCCccccCcc
Q 031787 9 DFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQ 88 (153)
Q Consensus 9 ~~~~~vri~~~~l~~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~L~~~i~~~~~~~ip~w~~nr~ 88 (153)
+|+||+||+||+||++|+|.+||++|||||+++|.+||+.+||||++++++||++|++.|.++|++ ..|.+|+||+||+
T Consensus 1 ~~~~m~rI~~~~i~~~k~v~~aLt~I~GIG~~~a~~I~~~lgi~~~~~~~~Lt~~qi~~l~~~i~~-~~~~iP~w~~Nr~ 79 (144)
T TIGR03629 1 EFKYIVRIADTDLDGNKPVEYALTGIKGIGRRFARAIARKLGVDPNAKLGYLDDEEIEKLEEAVEN-YEYGIPSWLLNRR 79 (144)
T ss_pred CcceeeeeeCccCCCCCEEEEeecceeccCHHHHHHHHHHcCcCCCCCcccCCHHHHHHHHHHHHh-ccccCCHHHhhcc
Confidence 589999999999999999999999999999999999999999999999999999999999999998 6799999999999
Q ss_pred CCcCCCcchhhhhhhHHHHHHHhhhhhhccceeecccCCCCCccCCcCCcccCCCccceeeeccC
Q 031787 89 KDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 153 (153)
Q Consensus 89 kd~~tg~~~~li~~dL~~~~~~~I~rl~~i~syRG~RH~~gLpvRGQRT~tNart~~~~~v~~~~ 153 (153)
+|+.||+|.|+||+||++++++||+||++|+||||+||.+||||||||||||||||+++||++||
T Consensus 80 ~d~~tg~~~~~ie~dL~~~~~~dI~rl~~I~~yRG~RH~~gLpVRGQRTrTNaRtg~~~gv~~kk 144 (144)
T TIGR03629 80 KDYETGEDLHLIGSDLDMTVREDINRMKKIRSYRGIRHELGLKVRGQRTKSTGRRGRTVGVSRKK 144 (144)
T ss_pred cccccCccceEehHHHHHHHHHHHHHHHHhcceeeeeccCCCCCCCCcCCCCCcCCCccccccCC
Confidence 99999999999999999999999999999999999999999999999999999999999999997
No 4
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.5e-51 Score=301.20 Aligned_cols=119 Identities=44% Similarity=0.701 Sum_probs=115.3
Q ss_pred hhhhcCccCCCCeeeeeehhhccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCCccCCccccCccCCcC
Q 031787 13 ILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYK 92 (153)
Q Consensus 13 ~vri~~~~l~~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~L~~~i~~~~~~~ip~w~~nr~kd~~ 92 (153)
|+||+|+|||++|.|.+|||+|||||..+|.+||+.+||||++++++|||||+++|.++|++
T Consensus 1 maRIagvdip~~K~v~iALt~IyGIG~~~a~~I~~~~gi~~~~r~~eLteeei~~ir~~i~~------------------ 62 (121)
T COG0099 1 MARIAGVDIPGNKRVVIALTYIYGIGRRRAKEICKKAGIDPDKRVGELTEEEIERLRDAIQN------------------ 62 (121)
T ss_pred CceecccCCCCCceEeehhhhhccccHHHHHHHHHHcCCCHhHhhccCCHHHHHHHHHHHHh------------------
Confidence 79999999999999999999999999999999999999999999999999999999999985
Q ss_pred CCcchhhhhhhHHHHHHHhhhhhhccceeecccCCCCCccCCcCCcccCCC--ccceeeeccC
Q 031787 93 DGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGRR--GKTVGVSKKR 153 (153)
Q Consensus 93 tg~~~~li~~dL~~~~~~~I~rl~~i~syRG~RH~~gLpvRGQRT~tNart--~~~~~v~~~~ 153 (153)
.|+||+||++++++||+||++|+||||+||.+|||||||||+||||| |.++||++||
T Consensus 63 ----~~~vegDLr~~v~~dIkRl~~i~~YRGiRH~~GLpVRGQrTktnaRtrkG~~~~v~~KK 121 (121)
T COG0099 63 ----KYLVEGDLRREVRMDIKRLMKIGCYRGIRHRRGLPVRGQRTKTNARTRKGPRKGVAKKK 121 (121)
T ss_pred ----cCeehhHHHHHHHHHHHHHHHhhhhhhhhhhcCCCCCCcccCccccccCCCccccccCC
Confidence 24679999999999999999999999999999999999999999999 9999999887
No 5
>KOG3311 consensus Ribosomal protein S18 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3e-50 Score=306.27 Aligned_cols=152 Identities=69% Similarity=1.128 Sum_probs=150.5
Q ss_pred ccCCCccchhhhhhhcCccCCCCeeeeeehhhccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCCccCC
Q 031787 2 KSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIP 81 (153)
Q Consensus 2 ~~~~~~~~~~~~vri~~~~l~~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~L~~~i~~~~~~~ip 81 (153)
|||+-++.||||+||+|++++++++|.|||+.|+|||..+|..+|+++|+|+.+++++|+++|++.+.+++++|.++.+|
T Consensus 1 msl~~~~~~q~i~~il~~~~dg~~~V~fAl~~i~Gig~~~A~~ic~K~~~~~~~r~gelt~~qi~~i~~i~~d~~~~~~~ 80 (152)
T KOG3311|consen 1 MSLVIPEAFQHILRILNTNVDGKRKVTFALTSIKGIGRRYAEIVCKKADLDLTKRAGELTEEQILRILQILNDPRQYKIP 80 (152)
T ss_pred CceecchhHHHHHHHHccCCCCCceeEEEEEEEeeechhhhhhhhhhcCcchhhhhccccHHHHHHHHHHhcCHHHhcCc
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccCccCCcCCCcchhhhhhhHHHHHHHhhhhhhccceeecccCCCCCccCCcCCcccCCCccceeeeccC
Q 031787 82 DWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 153 (153)
Q Consensus 82 ~w~~nr~kd~~tg~~~~li~~dL~~~~~~~I~rl~~i~syRG~RH~~gLpvRGQRT~tNart~~~~~v~~~~ 153 (153)
.|++|+++|..+|+..|++.+.++..++++|+||++|.||||+||.+|||||||||+|||+.|++|||++||
T Consensus 81 ~~~l~rq~~~~dG~~~~l~~~~ld~r~r~~ieRlkki~~~RG~rh~~gl~vRGQ~Tkt~~~~gk~v~Vs~Kk 152 (152)
T KOG3311|consen 81 DWFLNRQKDIIDGKVNHLLGNGLDTRLRADIERLKKIRCHRGLRHFWGLRVRGQRTKTNGRRGKTVGVSGKK 152 (152)
T ss_pred hHHHHhhcccccCccccccchhhhhHHHHHHHHHhhhcccccceeccCCcccCccccccccccceeeecccC
Confidence 999999999999999999999999999999999999999999999999999999999999999999999997
No 6
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=100.00 E-value=7.5e-48 Score=286.71 Aligned_cols=111 Identities=31% Similarity=0.499 Sum_probs=107.2
Q ss_pred hhhhcCccCCCCeeeeeehhhccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCCccCCccccCccCCcC
Q 031787 13 ILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYK 92 (153)
Q Consensus 13 ~vri~~~~l~~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~L~~~i~~~~~~~ip~w~~nr~kd~~ 92 (153)
|+||+||+||++|+|.+||++|||||+++|.+||+.+||||++++++|+++|++.|.++|++ +|.
T Consensus 1 mvrI~~~~i~~~k~v~~aLt~i~GIG~~~A~~ic~~lgi~~~~~~~~Lt~~qi~~l~~~i~~--~~~------------- 65 (122)
T CHL00137 1 MVRIAGVDLPRNKRIEYALTYIYGIGLTSAKEILEKANIDPDIRTKDLTDEQISALREIIEE--NYQ------------- 65 (122)
T ss_pred CceEcCccCCCCCEeeeeecccccccHHHHHHHHHHcCcCcCcCcccCCHHHHHHHHHHHHH--hCc-------------
Confidence 78999999999999999999999999999999999999999999999999999999999986 243
Q ss_pred CCcchhhhhhhHHHHHHHhhhhhhccceeecccCCCCCccCCcCCcccCCCcc
Q 031787 93 DGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGRRGK 145 (153)
Q Consensus 93 tg~~~~li~~dL~~~~~~~I~rl~~i~syRG~RH~~gLpvRGQRT~tNart~~ 145 (153)
||+||++.+++||+||++|+||||+||.+|||||||||||||||++
T Consensus 66 -------i~~dL~~~~~~dI~rl~~I~sYRG~RH~~gLPVRGQRT~tNarT~k 111 (122)
T CHL00137 66 -------VEGDLRRFESLNIKRLMEINCYRGRRHRLGLPVRGQRTRTNARTRR 111 (122)
T ss_pred -------chHHHHHHHHHHHHHHHHhCchhcccccCCCCCCCCcCCccccccC
Confidence 6999999999999999999999999999999999999999999997
No 7
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=100.00 E-value=1e-47 Score=286.03 Aligned_cols=111 Identities=34% Similarity=0.527 Sum_probs=107.6
Q ss_pred hhhhcCccCCCCeeeeeehhhccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCCccCCccccCccCCcC
Q 031787 13 ILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYK 92 (153)
Q Consensus 13 ~vri~~~~l~~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~L~~~i~~~~~~~ip~w~~nr~kd~~ 92 (153)
||||+||+||++|+|.+||++|||||+.+|.+||+.+||||++++++|+++|++.|.++|+++ |
T Consensus 1 MvrI~~~~l~~~k~v~~aL~~I~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi~~l~~~i~~~--~-------------- 64 (122)
T PRK05179 1 MARIAGVDIPRNKRVVIALTYIYGIGRTRAKEILAAAGIDPDTRVKDLTDEELDKIREEIDKN--Y-------------- 64 (122)
T ss_pred CceecCccCCCCcEEEeeecccccccHHHHHHHHHHhCcCcccccccCCHHHHHHHHHHHHhh--c--------------
Confidence 799999999999999999999999999999999999999999999999999999999999873 3
Q ss_pred CCcchhhhhhhHHHHHHHhhhhhhccceeecccCCCCCccCCcCCcccCCCcc
Q 031787 93 DGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGRRGK 145 (153)
Q Consensus 93 tg~~~~li~~dL~~~~~~~I~rl~~i~syRG~RH~~gLpvRGQRT~tNart~~ 145 (153)
.+|+||++++++||+||++|+||||+||.+|||||||||||||||++
T Consensus 65 ------~i~~dL~~~~~~dI~rl~~I~sYRG~RH~~gLPVRGQRT~TNart~k 111 (122)
T PRK05179 65 ------KVEGDLRREVSMNIKRLMDIGCYRGLRHRRGLPVRGQRTKTNARTRK 111 (122)
T ss_pred ------cchHHHHHHHHHHHHHHHHhcceeeeecccCCCCCCCcCCccccccC
Confidence 36999999999999999999999999999999999999999999998
No 8
>TIGR03631 bact_S13 30S ribosomal protein S13. This model describes bacterial ribosomal protein S13, to the exclusion of the homologous archaeal S13P and eukaryotic ribosomal protein S18. This model identifies some (but not all) instances of chloroplast and mitochondrial S13, which is of bacterial type.
Probab=100.00 E-value=3.3e-46 Score=274.66 Aligned_cols=111 Identities=35% Similarity=0.519 Sum_probs=106.4
Q ss_pred hhcCccCCCCeeeeeehhhccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCCccCCccccCccCCcCCC
Q 031787 15 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYKDG 94 (153)
Q Consensus 15 ri~~~~l~~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~L~~~i~~~~~~~ip~w~~nr~kd~~tg 94 (153)
||+|||||++|+|.+||++|||||..+|.+||+.+||||++++++|+++|++.|.++|+++ |
T Consensus 1 ri~~~~l~~~k~v~~aL~~i~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi~~l~~~l~~~--~---------------- 62 (113)
T TIGR03631 1 RIAGVDIPNNKRVEIALTYIYGIGRTRARKILEKAGIDPDKRVKDLTEEELNAIREEIEAK--Y---------------- 62 (113)
T ss_pred CcCCccCCCCCEEeeeeeeeecccHHHHHHHHHHhCcCcccccccCCHHHHHHHHHHHHhc--C----------------
Confidence 7999999999999999999999999999999999999999999999999999999999873 3
Q ss_pred cchhhhhhhHHHHHHHhhhhhhccceeecccCCCCCccCCcCCcccCCCccce
Q 031787 95 KYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGRRGKTV 147 (153)
Q Consensus 95 ~~~~li~~dL~~~~~~~I~rl~~i~syRG~RH~~gLpvRGQRT~tNart~~~~ 147 (153)
.||+||+..+++||+||++|+||||+||++|||||||||||||||+++.
T Consensus 63 ----~i~~~L~~~~~~dI~rl~~I~syRG~RH~~gLpVRGQRT~TNart~k~~ 111 (113)
T TIGR03631 63 ----KVEGDLRREVSLNIKRLMDIGCYRGLRHRRGLPVRGQRTKTNARTRKGP 111 (113)
T ss_pred ----cchHHHHHHHHHHHHHHHHhcceeccccccCCCCCCCcCCccccccCCC
Confidence 3699999999999999999999999999999999999999999999864
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=2.2e-46 Score=272.89 Aligned_cols=107 Identities=45% Similarity=0.768 Sum_probs=101.8
Q ss_pred hhcCccCCCCeeeeeehhhccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCCccCCccccCccCCcCCC
Q 031787 15 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYKDG 94 (153)
Q Consensus 15 ri~~~~l~~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~L~~~i~~~~~~~ip~w~~nr~kd~~tg 94 (153)
||+||+||++|+|.+||++|||||+++|.+||+.+||||+.++++|+++|+++|.++|++
T Consensus 1 rI~~~~l~~~k~i~~aLt~IyGIG~~~A~~Ic~~lgi~~~~~~~~Ls~~~i~~l~~~i~~-------------------- 60 (107)
T PF00416_consen 1 RILGTNLPGNKPIYIALTKIYGIGRRKAKQICKKLGINPNKKVGDLSDEQIDKLRKIIEK-------------------- 60 (107)
T ss_dssp ETTTTCE-TSSBHHHHHTTSTTBCHHHHHHHHHHTTS-SSSBTTTSTHHHHHHHHHHHHT--------------------
T ss_pred CcCCCcCCCCcchHhHHhhhhccCHHHHHHHHHHcCCChhhhcccCCHHHHHHHHHHHHH--------------------
Confidence 799999999999999999999999999999999999999999999999999999999987
Q ss_pred cchhhhhhhHHHHHHHhhhhhhccceeecccCCCCCccCCcCCcccCCC
Q 031787 95 KYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGRR 143 (153)
Q Consensus 95 ~~~~li~~dL~~~~~~~I~rl~~i~syRG~RH~~gLpvRGQRT~tNart 143 (153)
.|++|+||++++++||+||++|+||||+||.+|||||||||||||||
T Consensus 61 --~~~i~~~L~~~~~~~i~rl~~i~syRG~RH~~gLpvRGQRT~tNarT 107 (107)
T PF00416_consen 61 --NHLIENDLKRQVRENIKRLKKIKSYRGIRHRKGLPVRGQRTKTNART 107 (107)
T ss_dssp --HSTCHHHHHHHHHHHHHHHHHHTTHHHHHHHHTSBSSSSTSSSSSHH
T ss_pred --hccccchHHHHHHHHHHHHHHHHHhhcchhhCCCCCCCCCCCCCCCC
Confidence 34689999999999999999999999999999999999999999986
No 10
>PRK04184 DNA topoisomerase VI subunit B; Validated
Probab=98.47 E-value=1.5e-07 Score=85.21 Aligned_cols=91 Identities=21% Similarity=0.329 Sum_probs=80.1
Q ss_pred CeeeeeehhhccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCCccCCccccCccCCcCCCcchhhhhhh
Q 031787 24 KQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNA 103 (153)
Q Consensus 24 ~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~L~~~i~~~~~~~ip~w~~nr~kd~~tg~~~~li~~d 103 (153)
.....|+-..|.+||..+|.+||+.+|+++++++.+|+++|+++|.+++.+ +++ +.|+.|+++|.+..+|+..
T Consensus 256 ~~l~~fL~~~f~~v~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~---~~~----~~pp~~~lspige~~i~~g 328 (535)
T PRK04184 256 RTLKEFLVEEFSRVGDKTADEILEKAGLDPNKKPKELTREELERLVEAFKK---YKF----MAPPTACLSPIGEELIEKG 328 (535)
T ss_pred CCHHHHHHHhhcccCHHHHHHHHHHcCCCCCCChhhCCHHHHHHHHHHHHh---ccC----cCCCCccCCCCCHHHHHHH
Confidence 344567778999999999999999999999999999999999999999987 544 5678889999999999999
Q ss_pred HHHHHHH----hhhhhhccceeec
Q 031787 104 LDMKLRD----DLERLKKIRNHRG 123 (153)
Q Consensus 104 L~~~~~~----~I~rl~~i~syRG 123 (153)
|+..++. .++| +.+.|+|
T Consensus 329 l~~~~~p~f~~~~tr--~p~~y~g 350 (535)
T PRK04184 329 LKKILKPEFVAAVTR--KPKVYSG 350 (535)
T ss_pred HHHhcCccEEEEecc--CCcccCC
Confidence 9998777 4666 8888876
No 11
>COG1389 DNA topoisomerase VI, subunit B [DNA replication, recombination, and repair]
Probab=98.44 E-value=1.6e-07 Score=83.44 Aligned_cols=92 Identities=22% Similarity=0.295 Sum_probs=83.2
Q ss_pred CCeeeeeehhhccccchhhHHHHHHHhCCCCCCcCCCCC----HHHHHHHHHHHhCCCCccCCccccCccCCcCCCcchh
Q 031787 23 GKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELS----AAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQ 98 (153)
Q Consensus 23 ~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls----~~ei~~L~~~i~~~~~~~ip~w~~nr~kd~~tg~~~~ 98 (153)
..+.-.|+..+|..||..+|..+|+.+|++|++++.+|+ ++|.++|.+++.+ ++ |+.|+.|++++.+..
T Consensus 255 ~~tv~~fL~sef~rig~~ta~e~~e~~g~~~~~~p~~L~~~~~~eea~~lv~a~~~---~~----fm~Pptd~LsPIGee 327 (538)
T COG1389 255 RSTVREFLVSEFSRIGEKTADELLEYAGFDPDKKPRELTKKKTREEAEKLVEAFKK---MK----FMAPPTDGLSPIGEE 327 (538)
T ss_pred hhhHHHHHHHHHHHhhhhhHHHHHHHhcCCcccCHHHhhcccCHHHHHHHHHHHHh---Cc----ccCCCccccCcccHH
Confidence 444457888999999999999999999999999999999 9999999999987 54 378899999999999
Q ss_pred hhhhhHHHHHHH----hhhhhhccceeec
Q 031787 99 VVSNALDMKLRD----DLERLKKIRNHRG 123 (153)
Q Consensus 99 li~~dL~~~~~~----~I~rl~~i~syRG 123 (153)
+|+..|+..++. .+.| +.+.|+|
T Consensus 328 ~ie~gLk~~~~pefv~avTR--kPkvy~G 354 (538)
T COG1389 328 LIEKGLKSILNPEFVAAVTR--KPKVYRG 354 (538)
T ss_pred HHHHHHHHhcCchheeeecc--CccccCC
Confidence 999999999876 6788 9999999
No 12
>TIGR01052 top6b DNA topoisomerase VI, B subunit. This model describes DNA topoisomerase VI, an archaeal type II DNA topoisomerase (DNA gyrase).
Probab=98.38 E-value=4e-07 Score=81.59 Aligned_cols=91 Identities=18% Similarity=0.262 Sum_probs=80.0
Q ss_pred CeeeeeehhhccccchhhHHHHHHHhCCC---CCCcCCCCCHHHHHHHHHHHhCCCCccCCccccCccCCcCCCcchhhh
Q 031787 24 KQKIMFALTSIKGIGRRLANIVCKKADVD---MNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVV 100 (153)
Q Consensus 24 ~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~---~~~kv~~Ls~~ei~~L~~~i~~~~~~~ip~w~~nr~kd~~tg~~~~li 100 (153)
.....|+-..|..||..+|.+||+.+|++ +++++.+|+++|++.|.+++.+ .+| +.|+.|+++|.+..+|
T Consensus 247 ~~l~~fL~~~f~~v~~~~a~~~~~~~g~~~~~~~~~~~~l~~~~~~~l~~~~~~---~~~----~~P~~~~lspige~~i 319 (488)
T TIGR01052 247 STLRSFLVSEFSRIGEKKIKELLEKYGIDVDPLDKKPKELTWDEAEKIVNAFKE---MKF----MAPPTDGLSPIGEENI 319 (488)
T ss_pred ccHHHHHHHhhcccCHHHHHHHHHHhCCCccccCCChhhCCHHHHHHHHHHHHh---cCC----CCCCccccCCCCHHHH
Confidence 34446777889999999999999999999 9999999999999999999987 333 6778999999999999
Q ss_pred hhhHHHHHHH----hhhhhhccceeec
Q 031787 101 SNALDMKLRD----DLERLKKIRNHRG 123 (153)
Q Consensus 101 ~~dL~~~~~~----~I~rl~~i~syRG 123 (153)
+..|+..++. .++| +.+.|+|
T Consensus 320 ~~gl~~~~~p~f~~~~tr--~p~~y~g 344 (488)
T TIGR01052 320 EKGLKEILQPEFVGAVTR--SPKTYRG 344 (488)
T ss_pred HHHHHHhcCccEEEEecc--CCccccC
Confidence 9999998777 5677 8888887
No 13
>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=97.29 E-value=0.00025 Score=50.18 Aligned_cols=52 Identities=29% Similarity=0.376 Sum_probs=43.0
Q ss_pred CCeeeeeeh---hhccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 031787 23 GKQKIMFAL---TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 74 (153)
Q Consensus 23 ~~k~i~~aL---t~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~L~~~i~~ 74 (153)
.+++|..+| +.+-|||...|.+||-.+||+|..++++|+++|+..|.+.+..
T Consensus 22 ~~~~ik~~LlDQ~~iaGiGNiy~~EiLf~a~i~P~~~~~~L~~~~~~~l~~~~~~ 76 (92)
T PF06831_consen 22 RRRPIKAALLDQSVIAGIGNIYADEILFRAGIHPERPASSLSEEELRRLHEAIKR 76 (92)
T ss_dssp CCSBHHHHHHCTTTSTT--HHHHHHHHHHTTB-TTSBGGGSHHHHHHHHHHHHHH
T ss_pred CcchHHHHHhCCCccccCcHHHHHHHHHHcCCCccCccccCCHHHHHHHHHHHHH
Confidence 467776666 5699999999999999999999999999999999998887753
No 14
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=97.07 E-value=0.00074 Score=56.26 Aligned_cols=53 Identities=30% Similarity=0.369 Sum_probs=48.5
Q ss_pred CCCeeeeeeh---hhccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 031787 22 DGKQKIMFAL---TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 74 (153)
Q Consensus 22 ~~~k~i~~aL---t~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~L~~~i~~ 74 (153)
..++.|.-+| +-+-|||.-.|.+||-++||+|..++++||++|++.|.+.+.+
T Consensus 153 ~~~~~Ik~~LLDQ~~iaGiGNiya~EiLf~a~I~P~~~~~~Ls~~~~~~L~~~~~~ 208 (274)
T PRK01103 153 KKKTAIKPALLDQTVVVGVGNIYADEALFRAGIHPERPAGSLSRAEAERLVDAIKA 208 (274)
T ss_pred cCCccHHHHhhcCCeEecccHhHHHHHHHHcCCCccCccccCCHHHHHHHHHHHHH
Confidence 3567888888 8899999999999999999999999999999999999888864
No 15
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=96.47 E-value=0.0036 Score=52.23 Aligned_cols=52 Identities=25% Similarity=0.337 Sum_probs=45.0
Q ss_pred CCeeeeeehhh---ccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 031787 23 GKQKIMFALTS---IKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 74 (153)
Q Consensus 23 ~~k~i~~aLt~---I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~L~~~i~~ 74 (153)
.+.+|.-+|-. |-|||.-.|.+||-++||+|..++++||++|++.|.+++.+
T Consensus 153 ~~~~ik~~Lldq~viaGiGNiya~EiLf~a~i~P~~~~~~l~~~~~~~l~~a~~~ 207 (272)
T PRK14810 153 RKTRIKSALLNQTLLRGVGNIYADEALFRAGIRPQRLASSLSRERLRKLHDAIGE 207 (272)
T ss_pred CCccHHHHhhcCceeccccHhHHHHHHHHcCCCCCCCcccCCHHHHHHHHHHHHH
Confidence 45567666744 59999999999999999999999999999999999887754
No 16
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=96.44 E-value=0.0045 Score=51.62 Aligned_cols=51 Identities=20% Similarity=0.234 Sum_probs=44.7
Q ss_pred Ceeeeeeh---hhccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 031787 24 KQKIMFAL---TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 74 (153)
Q Consensus 24 ~k~i~~aL---t~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~L~~~i~~ 74 (153)
+++|.-+| +-|-|||.-.|.+||-.+||+|..++++||++|++.|-+++..
T Consensus 143 ~~~Ik~~LlDQ~~iaGIGNiyadEiLf~A~I~P~~~~~~Ls~~~~~~L~~~i~~ 196 (269)
T PRK14811 143 ARPVKPWLLSQKPVAGVGNIYADESLWRARIHPARPATSLKAPEARRLYRAIRE 196 (269)
T ss_pred CCcHHHHHhcCceeecccHHHHHHHHHHcCCCccCCcccCCHHHHHHHHHHHHH
Confidence 66776666 4589999999999999999999999999999999999777654
No 17
>PRK10445 endonuclease VIII; Provisional
Probab=96.34 E-value=0.0047 Score=51.31 Aligned_cols=51 Identities=22% Similarity=0.298 Sum_probs=44.1
Q ss_pred Ceeeeeeh---hhccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 031787 24 KQKIMFAL---TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 74 (153)
Q Consensus 24 ~k~i~~aL---t~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~L~~~i~~ 74 (153)
+++|.-+| +-+-|||.-.|.+||-.+||+|..++++||++|++.|.+.+.+
T Consensus 151 ~~~IK~~LLDQ~~vaGIGNiyadEiLf~A~I~P~~~~~~Ls~~~~~~L~~~i~~ 204 (263)
T PRK10445 151 NRQFSGLLLDQAFLAGLGNYLRVEILWQAGLTPQHKAKDLNEAQLDALAHALLD 204 (263)
T ss_pred cccHHHHHhcCCccccccHHHHHHHHHHcCCCcCCCcccCCHHHHHHHHHHHHH
Confidence 45565555 3478999999999999999999999999999999999888865
No 18
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=96.29 E-value=0.0058 Score=51.18 Aligned_cols=52 Identities=27% Similarity=0.347 Sum_probs=45.4
Q ss_pred CCeeeeeeh---hhccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 031787 23 GKQKIMFAL---TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 74 (153)
Q Consensus 23 ~~k~i~~aL---t~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~L~~~i~~ 74 (153)
.+.+|.-+| +-|-|||.-.|.+||=.+||+|..++++||++|++.|.+.+..
T Consensus 163 ~~~~IK~~LLDQ~~vaGIGNiya~EiLf~A~IhP~~~~~~Ls~~~~~~L~~~i~~ 217 (282)
T PRK13945 163 RTRSIKTALLDQSIVAGIGNIYADESLFKAGIHPTTPAGQLKKKQLERLREAIIE 217 (282)
T ss_pred CCccHHHHhhcCCeEeccchhHHHHHHHHcCCCccCccccCCHHHHHHHHHHHHH
Confidence 356676666 4589999999999999999999999999999999999888754
No 19
>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=96.26 E-value=0.0055 Score=51.06 Aligned_cols=52 Identities=31% Similarity=0.346 Sum_probs=45.4
Q ss_pred CCeeeeeeh---hhccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 031787 23 GKQKIMFAL---TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 74 (153)
Q Consensus 23 ~~k~i~~aL---t~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~L~~~i~~ 74 (153)
.+.+|.-+| +-|-|||.-.|.+||-.++|+|..++++||++|++.|.+.+.+
T Consensus 154 ~~~~Ik~~LlDQ~vvaGIGNiyadEiLf~a~I~P~~~~~~Ls~~~~~~L~~~i~~ 208 (272)
T TIGR00577 154 SKRKIKTALLDQRLVAGIGNIYADEVLFRAGIHPERLANSLSKEECELLHRAIKE 208 (272)
T ss_pred CCCcHHHHHhcCCeEecccHHHHHHHHHHcCCCcchhhccCCHHHHHHHHHHHHH
Confidence 456666666 4588999999999999999999999999999999999888754
No 20
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=94.10 E-value=0.16 Score=42.83 Aligned_cols=60 Identities=25% Similarity=0.345 Sum_probs=48.2
Q ss_pred hhcCccCCCCeeeeeeh---hhccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 031787 15 RVLNTNVDGKQKIMFAL---TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 74 (153)
Q Consensus 15 ri~~~~l~~~k~i~~aL---t~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~L~~~i~~ 74 (153)
++...-...+++|.-+| +-+-|||...|.++|=++||+|...+++|+..|++.|.+++.+
T Consensus 146 ~l~~~l~~~~~~IK~~LLDQ~vvaGvGNIYa~E~Lf~agI~P~~~a~~l~~~~~~~l~~~i~~ 208 (273)
T COG0266 146 YLAEKLAKKKRRIKTALLDQKVVAGVGNIYADEILFRAGIHPARPAGDLSLAQLALLHEAIKD 208 (273)
T ss_pred HHHHHHhcCccchHHHhhcCCceecccHHHHHHHHHHcCCCcccCccccCHHHHHHHHHHHHH
Confidence 33444445555665555 4589999999999999999999999999999999988887753
No 21
>PF05833 FbpA: Fibronectin-binding protein A N-terminus (FbpA); InterPro: IPR008616 This family consists of the N-terminal region of the prokaryotic fibronectin-binding protein, the C-terminal region is IPR008532 from INTERPRO. Fibronectin binding is considered to be an important virulence factor in streptococcal infections. Fibronectin is a dimeric glycoprotein that is present in a soluble form in plasma and extracellular fluids; it is also present in a fibrillar form on cell surfaces. Both the soluble and cellular forms of fibronectin may be incorporated into the extracellular tissue matrix. While fibronectin has critical roles in eukaryotic cellular processes, such as adhesion, migration and differentiation, it is also a substrate for the attachment of bacteria. The binding of pathogenic Streptococcus pyogenes and Staphylococcus aureus to epithelial cells via fibronectin facilitates their internalisation and systemic spread within the host [].; PDB: 3DOA_A 2ZBK_F 2HKJ_A 1Z5B_A 1Z5C_B 1MX0_F 1Z5A_A 1MU5_A 1Z59_A.
Probab=93.77 E-value=0.023 Score=49.90 Aligned_cols=51 Identities=29% Similarity=0.503 Sum_probs=35.4
Q ss_pred CCeeeeeeh-hhccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHh
Q 031787 23 GKQKIMFAL-TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVA 73 (153)
Q Consensus 23 ~~k~i~~aL-t~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~L~~~i~ 73 (153)
+...+.-+| ..+.|+|+..|..+|.++|++++.++.++++++++.|.+.+.
T Consensus 185 ~~~~l~~~L~~~~~G~~~~la~ei~~ra~i~~~~~~~~~~~~~~~~l~~~~~ 236 (455)
T PF05833_consen 185 KEKTLVKALSKNFQGFGPELAEEILYRAGIDKNKKVEELSDEEIEKLFEAIR 236 (455)
T ss_dssp CG-BHHHHHHHHCTT--HHHHHHHHCCCTS-TTSBGGG--HHHHCHHHHHHH
T ss_pred CcccHHHHHHHHHHHhHHHHHHHHHHHhCCCCccccccchhhhHHHHHHHHH
Confidence 444555555 445699999999999999999999999999998777665554
No 22
>PF00633 HHH: Helix-hairpin-helix motif; InterPro: IPR000445 The HhH motif is an around 20 amino acids domain present in prokaryotic and eukaryotic non-sequence-specific DNA binding proteins [, , ]. The HhH motif is similar to, but distinct from, the HtH motif. Both of these motifs have two helices connected by a short turn. In the HtH motif the second helix binds to DNA with the helix in the major groove. This allows the contact between specific base and residues throughout the protein. In the HhH motif the second helix does not protrude from the surface of the protein and therefore cannot lie in the major groove of the DNA. Crystallographic studies suggest that the interaction of the HhH domain with DNA is mediated by amino acids located in the strongly conserved loop (L-P-G-V) and at the N-terminal end of the second helix []. This interaction could involve the formation of hydrogen bonds between protein backbone nitrogens and DNA phosphate groups []. The structural difference between the HtH and HhH domains is reflected at the functional level: whereas the HtH domain, found primarily in gene regulatory proteins, binds DNA in a sequence specific manner, the HhH domain is rather found in proteins involved in enzymatic activities and binds DNA with no sequence specificity []. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain [].; GO: 0003677 DNA binding; PDB: 3C1Z_A 3C23_A 3C1Y_A 3C21_A 1Z00_A 2A1J_B 1KEA_A 1VRL_A 1RRQ_A 3G0Q_A ....
Probab=93.73 E-value=0.045 Score=31.14 Aligned_cols=18 Identities=33% Similarity=0.565 Sum_probs=15.2
Q ss_pred ehhhccccchhhHHHHHH
Q 031787 30 ALTSIKGIGRRLANIVCK 47 (153)
Q Consensus 30 aLt~I~GIG~~~A~~Ic~ 47 (153)
.|.+++|||+++|..|+.
T Consensus 12 eL~~lpGIG~~tA~~I~~ 29 (30)
T PF00633_consen 12 ELMKLPGIGPKTANAILS 29 (30)
T ss_dssp HHHTSTT-SHHHHHHHHH
T ss_pred HHHhCCCcCHHHHHHHHh
Confidence 578999999999999975
No 23
>PRK14867 DNA topoisomerase VI subunit B; Provisional
Probab=92.47 E-value=0.16 Score=47.52 Aligned_cols=81 Identities=14% Similarity=0.128 Sum_probs=60.6
Q ss_pred hccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCCccCCccccCccCCcCCCcchhhhhhhHHHHHHH--
Q 031787 33 SIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRD-- 110 (153)
Q Consensus 33 ~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~L~~~i~~~~~~~ip~w~~nr~kd~~tg~~~~li~~dL~~~~~~-- 110 (153)
.+-++-...+..+.+.+-=-+++.+.+|+++|++.|.+++.+ ..| +.|+.|+++|.+..+|+..| ..++.
T Consensus 410 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~a~~~---~~~----~aP~t~~LsPige~~i~~gl-~~~~pef 481 (659)
T PRK14867 410 DKAMVSDEELEKYRKEIKDLLKKNPKEMTWKEAELIVNVLQD---MDF----MAPSTTGLRPIGAENIEKSL-ETLEPDF 481 (659)
T ss_pred hhhhhhhhhhhhhhhhhhhhccCChhhCCHHHHHHHHHHHHh---cCC----CCCCccccCCCCHHHHHHHH-HhcCcce
Confidence 334444444444443322226889999999999999999987 333 56789999999999999999 77776
Q ss_pred --hhhhhhccceeec
Q 031787 111 --DLERLKKIRNHRG 123 (153)
Q Consensus 111 --~I~rl~~i~syRG 123 (153)
.++| +.+.|+|
T Consensus 482 ~~a~tR--~p~~y~g 494 (659)
T PRK14867 482 LKTLTR--KPKTYKG 494 (659)
T ss_pred EEEecc--CcccccC
Confidence 5677 8889986
No 24
>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=91.63 E-value=0.13 Score=44.59 Aligned_cols=50 Identities=24% Similarity=0.416 Sum_probs=43.4
Q ss_pred CCeeeeeehhhccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 031787 23 GKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 74 (153)
Q Consensus 23 ~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~L~~~i~~ 74 (153)
+++.+...|..+ +-.+.+..||+.+||++++++++|+++|++.|.+.|.+
T Consensus 282 ~~~~~~~~l~~~--l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~lk~ 331 (400)
T TIGR00275 282 PKKTVKNILKGL--LPKRLAELLLEQLGIDPDLPAAQLSKKEIKKLVQLLKN 331 (400)
T ss_pred hhhhHHHHhhhh--hhHHHHHHHHHHcCCCCCCChHHCCHHHHHHHHHHHhC
Confidence 456666666643 78999999999999999999999999999999999987
No 25
>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=90.17 E-value=0.26 Score=33.34 Aligned_cols=37 Identities=19% Similarity=0.375 Sum_probs=30.4
Q ss_pred CCccchhhhhhhcC--ccCCCCeeeeeehhhccccchhhHHHHHHHhC
Q 031787 5 VANEDFQHILRVLN--TNVDGKQKIMFALTSIKGIGRRLANIVCKKAD 50 (153)
Q Consensus 5 ~~~~~~~~~vri~~--~~l~~~k~i~~aLt~I~GIG~~~A~~Ic~~lg 50 (153)
+++++|..+.=+.| +| -+..++|||+++|.+|+...|
T Consensus 5 ~~~~q~~d~~~L~GD~~D---------~i~gv~giG~k~A~~ll~~~~ 43 (75)
T cd00080 5 LTPEQFIDLAILVGDKSD---------NIPGVPGIGPKTALKLLKEYG 43 (75)
T ss_pred cCHHHHHHHHHHcCCccc---------cCCCCCcccHHHHHHHHHHhC
Confidence 35678888888888 66 345799999999999998866
No 26
>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=89.61 E-value=0.2 Score=28.67 Aligned_cols=22 Identities=23% Similarity=0.496 Sum_probs=15.5
Q ss_pred eehhhccccchhhHHHHHHHhCC
Q 031787 29 FALTSIKGIGRRLANIVCKKADV 51 (153)
Q Consensus 29 ~aLt~I~GIG~~~A~~Ic~~lgi 51 (153)
..+++|+|||++++..+ +.+||
T Consensus 11 lpi~~~~GIG~kt~~kL-~~~GI 32 (32)
T PF11798_consen 11 LPIRKFWGIGKKTAKKL-NKLGI 32 (32)
T ss_dssp SBGGGSTTS-HHHHHHH-HCTT-
T ss_pred CCHHhhCCccHHHHHHH-HHccC
Confidence 35789999999999984 44443
No 27
>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=89.35 E-value=0.042 Score=35.38 Aligned_cols=36 Identities=22% Similarity=0.276 Sum_probs=25.2
Q ss_pred eeehhhccccchhhHHHHHHHhCCCCCCcCCCCCHHH
Q 031787 28 MFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAE 64 (153)
Q Consensus 28 ~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~e 64 (153)
+-.|.+|.|||+..|..+.+. |+..-..+-..+.++
T Consensus 4 ~~~L~~I~Gig~~~a~~L~~~-G~~t~~~l~~a~~~~ 39 (60)
T PF14520_consen 4 FDDLLSIPGIGPKRAEKLYEA-GIKTLEDLANADPEE 39 (60)
T ss_dssp HHHHHTSTTCHHHHHHHHHHT-TCSSHHHHHTSHHHH
T ss_pred HHhhccCCCCCHHHHHHHHhc-CCCcHHHHHcCCHHH
Confidence 457889999999999999877 776433333333333
No 28
>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=88.49 E-value=0.32 Score=31.01 Aligned_cols=22 Identities=23% Similarity=0.314 Sum_probs=16.0
Q ss_pred ehhhccccchhhHHHHHHHhCCC
Q 031787 30 ALTSIKGIGRRLANIVCKKADVD 52 (153)
Q Consensus 30 aLt~I~GIG~~~A~~Ic~~lgi~ 52 (153)
.+++|+|||+.+|.+..+ .|+.
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 478999999999999997 7764
No 29
>PRK00274 ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed
Probab=88.45 E-value=0.38 Score=39.73 Aligned_cols=63 Identities=21% Similarity=0.256 Sum_probs=45.8
Q ss_pred chhhhhhhcCccCCCCeeeeeehhhccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 031787 9 DFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 74 (153)
Q Consensus 9 ~~~~~vri~~~~l~~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~L~~~i~~ 74 (153)
.|..+++.+ .....|.+.-+|..+++. ...+.++++.+|++++.++.+|+.+|+.+|.+.+.+
T Consensus 208 ~~~~~~~~~--F~~rrk~l~~~l~~~~~~-~~~~~~~l~~~~~~~~~r~~~l~~~~~~~L~~~~~~ 270 (272)
T PRK00274 208 LFFRVVKAA--FAQRRKTLRNNLKNLFGS-KEKLEEALEAAGIDPNRRAETLSVEEFVRLANALAA 270 (272)
T ss_pred HHHHHHHHH--HhchHHHHHHHHHhhccc-hHHHHHHHHHCCCCcCCCceeCCHHHHHHHHHHHHh
Confidence 344555433 233456666677666442 345678899999999999999999999999988764
No 30
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=87.49 E-value=0.43 Score=25.78 Aligned_cols=20 Identities=25% Similarity=0.434 Sum_probs=17.0
Q ss_pred ehhhccccchhhHHHHHHHh
Q 031787 30 ALTSIKGIGRRLANIVCKKA 49 (153)
Q Consensus 30 aLt~I~GIG~~~A~~Ic~~l 49 (153)
.|..++|||.++|..|+...
T Consensus 2 ~L~~i~GiG~k~A~~il~~~ 21 (26)
T smart00278 2 ELLKVPGIGPKTAEKILEAX 21 (26)
T ss_pred hhhhCCCCCHHHHHHHHHhc
Confidence 36789999999999999743
No 31
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=86.40 E-value=0.48 Score=35.97 Aligned_cols=44 Identities=20% Similarity=0.225 Sum_probs=39.1
Q ss_pred eehhhccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHh
Q 031787 29 FALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVA 73 (153)
Q Consensus 29 ~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~L~~~i~ 73 (153)
-=|+.|.|||+..+. .+..+||-....+-.+|..++..+..+|+
T Consensus 67 DDLt~I~GIGPk~e~-~Ln~~GI~tfaQIAAwt~~di~~id~~l~ 110 (133)
T COG3743 67 DDLTRISGIGPKLEK-VLNELGIFTFAQIAAWTRADIAWIDDYLN 110 (133)
T ss_pred ccchhhcccCHHHHH-HHHHcCCccHHHHHhcCHHHHHHHHhhcC
Confidence 458999999998876 46789999999999999999999999984
No 32
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=86.05 E-value=0.47 Score=37.69 Aligned_cols=35 Identities=20% Similarity=0.293 Sum_probs=25.5
Q ss_pred CccchhhhhhhcCccCCCCeeeeeehhhccccchhhHHHHHHHh
Q 031787 6 ANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKA 49 (153)
Q Consensus 6 ~~~~~~~~vri~~~~l~~~k~i~~aLt~I~GIG~~~A~~Ic~~l 49 (153)
+.++|..++.--++ -+|++++|||+++|.+|+-.|
T Consensus 94 ~~~el~~aI~~~D~---------~~L~~vpGIGkKtAeRIilEL 128 (183)
T PRK14601 94 DVNSFYKALSLGDE---------SVLKKVPGIGPKSAKRIIAEL 128 (183)
T ss_pred CHHHHHHHHHhCCH---------HHHhhCCCCCHHHHHHHHHHH
Confidence 34555555544444 489999999999999999554
No 33
>COG0030 KsgA Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis]
Probab=85.62 E-value=0.53 Score=39.39 Aligned_cols=48 Identities=23% Similarity=0.295 Sum_probs=42.3
Q ss_pred CCCeeeeeehhhccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 031787 22 DGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 74 (153)
Q Consensus 22 ~~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~L~~~i~~ 74 (153)
...|.+.-+|+..++ ..++|+.+|+|++.++.+|+.+|+-.|.+++..
T Consensus 209 ~RRKtl~n~l~~~~~-----~~~~l~~~~i~~~~R~e~ls~~~f~~L~~~l~~ 256 (259)
T COG0030 209 QRRKTLRNNLKNLFG-----LEEVLEAAGIDPNARAENLSPEDFLKLANALKG 256 (259)
T ss_pred hhhHHHHHHHHhhhh-----HHHHHHhcCCCcccChhhCCHHHHHHHHHHHhh
Confidence 356777788888777 899999999999999999999999999998864
No 34
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=85.22 E-value=0.56 Score=35.56 Aligned_cols=59 Identities=19% Similarity=0.150 Sum_probs=44.3
Q ss_pred hcCccCCCCeeeeeehhhccccchhhHHHHHHHhCC---CCCCcCCCCCHHHHHHHHHHHhC
Q 031787 16 VLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADV---DMNKRAGELSAAELDNLMVVVAN 74 (153)
Q Consensus 16 i~~~~l~~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi---~~~~kv~~Ls~~ei~~L~~~i~~ 74 (153)
-.+.-|+-|..-...|+.++|||+..|.+|++.-.+ +.-..+..+++.|.+.|.+..++
T Consensus 48 ~~~~kIdiN~A~~~el~~lpGigP~~A~~IV~nGpf~sveDL~~V~GIgekqk~~l~k~~~~ 109 (132)
T PRK02515 48 EFGEKIDLNNSSVRAFRQFPGMYPTLAGKIVKNAPYDSVEDVLNLPGLSERQKELLEANLDN 109 (132)
T ss_pred hcCCcccCCccCHHHHHHCCCCCHHHHHHHHHCCCCCCHHHHHcCCCCCHHHHHHHHHhhcc
Confidence 356666767777778999999999999999963222 22235777899999999998876
No 35
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=84.04 E-value=0.61 Score=37.10 Aligned_cols=22 Identities=18% Similarity=0.344 Sum_probs=18.9
Q ss_pred eehhhccccchhhHHHHHHHhC
Q 031787 29 FALTSIKGIGRRLANIVCKKAD 50 (153)
Q Consensus 29 ~aLt~I~GIG~~~A~~Ic~~lg 50 (153)
-+|++++|||+++|.+||-.|.
T Consensus 108 ~~L~~vpGIGkKtAerIilELk 129 (188)
T PRK14606 108 EGLSKLPGISKKTAERIVMELK 129 (188)
T ss_pred HHHhhCCCCCHHHHHHHHHHHH
Confidence 4799999999999999995543
No 36
>KOG3311 consensus Ribosomal protein S18 [Translation, ribosomal structure and biogenesis]
Probab=83.14 E-value=0.19 Score=38.87 Aligned_cols=45 Identities=13% Similarity=-0.073 Sum_probs=37.9
Q ss_pred hhhhHHHHHHHhhhhhhccceeecccCCCCCccCCcCCcccCCCccc
Q 031787 100 VSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGRRGKT 146 (153)
Q Consensus 100 i~~dL~~~~~~~I~rl~~i~syRG~RH~~gLpvRGQRT~tNart~~~ 146 (153)
+.+|.+.....++..+.++.+|.|- ..+||+.||.|+.|+.+.+.
T Consensus 70 i~~d~~~~~~~~~~l~rq~~~~dG~--~~~l~~~~ld~r~r~~ieRl 114 (152)
T KOG3311|consen 70 ILNDPRQYKIPDWFLNRQKDIIDGK--VNHLLGNGLDTRLRADIERL 114 (152)
T ss_pred HhcCHHHhcCchHHHHhhcccccCc--cccccchhhhhHHHHHHHHH
Confidence 4456666677799999999999999 99999999999999876653
No 37
>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=83.13 E-value=1.4 Score=38.90 Aligned_cols=51 Identities=27% Similarity=0.394 Sum_probs=44.1
Q ss_pred CCCeeeeeehhhccccchhhHHHHHHHhCC-CCCCcCCCCCHHHHHHHHHHHhC
Q 031787 22 DGKQKIMFALTSIKGIGRRLANIVCKKADV-DMNKRAGELSAAELDNLMVVVAN 74 (153)
Q Consensus 22 ~~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi-~~~~kv~~Ls~~ei~~L~~~i~~ 74 (153)
.+++.+...|..+ +-.+.+..+|+.++| +++.++++|+++++..|.+.|.+
T Consensus 288 ~~~~~~~~~l~~~--lp~rl~~~ll~~~~i~~~~~~~~~l~~~~~~~L~~~lk~ 339 (409)
T PF03486_consen 288 NPKRTLKNFLKGL--LPKRLALALLKRAGIKDPDKKVSELSKKERNRLANLLKR 339 (409)
T ss_dssp TTTSBHHHHHTTT--S-HHHHHHHHHHTTS-STTSBGGGS-HHHHHHHHHHHHC
T ss_pred HHhhHHHHHHHHH--hHHHHHHHHHHHcCCCccccchhhcCHHHHHHHHHHHHh
Confidence 4567777777776 889999999999999 99999999999999999999987
No 38
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=82.49 E-value=0.76 Score=36.78 Aligned_cols=20 Identities=35% Similarity=0.549 Sum_probs=17.8
Q ss_pred eehhhccccchhhHHHHHHH
Q 031787 29 FALTSIKGIGRRLANIVCKK 48 (153)
Q Consensus 29 ~aLt~I~GIG~~~A~~Ic~~ 48 (153)
-+|++++|||+++|.+||-.
T Consensus 107 ~~L~kvpGIGkKtAerIilE 126 (197)
T PRK14603 107 RLLTSASGVGKKLAERIALE 126 (197)
T ss_pred HHHhhCCCCCHHHHHHHHHH
Confidence 48999999999999999944
No 39
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=82.13 E-value=0.8 Score=36.63 Aligned_cols=21 Identities=24% Similarity=0.433 Sum_probs=18.4
Q ss_pred eehhhccccchhhHHHHHHHh
Q 031787 29 FALTSIKGIGRRLANIVCKKA 49 (153)
Q Consensus 29 ~aLt~I~GIG~~~A~~Ic~~l 49 (153)
.+|++++|||+++|.+|+-.|
T Consensus 108 ~~L~kvpGIGkKtAerIilEL 128 (195)
T PRK14604 108 ARLARVPGIGKKTAERIVLEL 128 (195)
T ss_pred HHHhhCCCCCHHHHHHHHHHH
Confidence 489999999999999999553
No 40
>TIGR00755 ksgA dimethyladenosine transferase. Alternate name: S-adenosylmethionine--6-N',N'-adenosyl (rRNA) dimethyltransferase
Probab=81.95 E-value=1 Score=36.50 Aligned_cols=59 Identities=17% Similarity=0.202 Sum_probs=43.4
Q ss_pred chhhhhhhcCccCCCCeeeeeehhhccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHH
Q 031787 9 DFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVV 71 (153)
Q Consensus 9 ~~~~~vri~~~~l~~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~L~~~ 71 (153)
.|.++++.+ .-...|.+.-+|..+++- ..+..+++.+|+++++++.+|+.+|+..|.+.
T Consensus 194 ~~~~~~~~~--F~~rrk~l~~~l~~~~~~--~~~~~~l~~~~i~~~~r~~~l~~~~~~~l~~~ 252 (253)
T TIGR00755 194 LFEKLLKAA--FSQRRKTLRNNLKQLLKA--SKLEEVLEQLGLDPTARAEQLSPEDFLRLANL 252 (253)
T ss_pred HHHHHHHHH--HccchHHHHHHHhhhcch--hHHHHHHHHCCcCCCCCcccCCHHHHHHHHHh
Confidence 355666542 234567777777776442 35567888999999999999999999998765
No 41
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=81.51 E-value=0.87 Score=36.62 Aligned_cols=21 Identities=29% Similarity=0.501 Sum_probs=18.4
Q ss_pred eehhhccccchhhHHHHHHHh
Q 031787 29 FALTSIKGIGRRLANIVCKKA 49 (153)
Q Consensus 29 ~aLt~I~GIG~~~A~~Ic~~l 49 (153)
-+|++++|||+++|.+|+-.|
T Consensus 107 ~~L~~vpGIGkKtAeRIIlEL 127 (196)
T PRK13901 107 ELISKVKGIGNKMAGKIFLKL 127 (196)
T ss_pred HHHhhCCCCCHHHHHHHHHHH
Confidence 489999999999999999554
No 42
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=81.39 E-value=0.9 Score=36.67 Aligned_cols=21 Identities=33% Similarity=0.498 Sum_probs=18.1
Q ss_pred eehhhccccchhhHHHHHHHh
Q 031787 29 FALTSIKGIGRRLANIVCKKA 49 (153)
Q Consensus 29 ~aLt~I~GIG~~~A~~Ic~~l 49 (153)
-+|++++|||+++|.+||-.|
T Consensus 108 ~~L~k~PGIGkKtAerivleL 128 (201)
T COG0632 108 KALSKIPGIGKKTAERIVLEL 128 (201)
T ss_pred HhhhcCCCCCHHHHHHHHHHH
Confidence 479999999999999999554
No 43
>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=81.14 E-value=0.61 Score=38.21 Aligned_cols=62 Identities=24% Similarity=0.307 Sum_probs=48.3
Q ss_pred cchhhhhhhcCccCCCCeeeeeehhhccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHh
Q 031787 8 EDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVA 73 (153)
Q Consensus 8 ~~~~~~vri~~~~l~~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~L~~~i~ 73 (153)
+.|.++++.+=. ...|.+.-+|..+++ ...+..+.+.+||+++.++.+|+.+|+..|.++|+
T Consensus 200 ~~~~~~~~~~F~--~rrk~l~~~L~~~~~--~~~~~~~~~~~~i~~~~r~~~ls~~~~~~l~~~l~ 261 (262)
T PF00398_consen 200 DAFEYFVRQLFS--QRRKTLRNSLKSLFP--GEQLEELLEKAGIDPNARAEELSPEQFLKLFKYLN 261 (262)
T ss_dssp HHHHHHHHHHHT--TTTSBHHHHTTCTHH--HHHHHHHHHHCTHTTTTCGGCHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHh--CcchHHHHHHhhhcC--HHHHHHhhhhcCCCCCCCcccCCHHHHHHHHHHhh
Confidence 467777766533 578888888887653 33456677779999999999999999999999875
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=81.05 E-value=0.7 Score=36.65 Aligned_cols=29 Identities=17% Similarity=0.331 Sum_probs=23.8
Q ss_pred CCCeeeeeehhhccccchhhHHHHHHHhC
Q 031787 22 DGKQKIMFALTSIKGIGRRLANIVCKKAD 50 (153)
Q Consensus 22 ~~~k~i~~aLt~I~GIG~~~A~~Ic~~lg 50 (153)
++...+...|.+++|||+++|..+|..||
T Consensus 108 p~t~~lre~Ll~LpGVG~KTAnvVL~~l~ 136 (177)
T TIGR03252 108 PDGKELLRRLKALPGFGKQKAKIFLALLG 136 (177)
T ss_pred CCcHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence 44555567799999999999999998776
No 45
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=80.92 E-value=0.92 Score=36.43 Aligned_cols=20 Identities=35% Similarity=0.554 Sum_probs=17.7
Q ss_pred eehhhccccchhhHHHHHHH
Q 031787 29 FALTSIKGIGRRLANIVCKK 48 (153)
Q Consensus 29 ~aLt~I~GIG~~~A~~Ic~~ 48 (153)
-+|++++|||+++|.+|+-.
T Consensus 109 ~~L~~ipGIGkKtAerIilE 128 (203)
T PRK14602 109 AALTRVSGIGKKTAQHIFLE 128 (203)
T ss_pred HHHhcCCCcCHHHHHHHHHH
Confidence 47999999999999999944
No 46
>COG1293 Predicted RNA-binding protein homologous to eukaryotic snRNP [Transcription]
Probab=80.70 E-value=1.5 Score=40.43 Aligned_cols=50 Identities=22% Similarity=0.302 Sum_probs=44.5
Q ss_pred eeeeeehhhccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 031787 25 QKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 74 (153)
Q Consensus 25 k~i~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~L~~~i~~ 74 (153)
.-+..++..+.|+|.-.|..+|-++|++++....++.++++..+...+.+
T Consensus 186 ~~~~~~~~~~~g~~~~~a~el~~rag~~~~~~~~~~~~~~~~~v~~~~~~ 235 (564)
T COG1293 186 ADIVRLLARFLGLGGLLAEELLSRAGLDKKVPAKDLFEEEIKKVREALEE 235 (564)
T ss_pred hHHHHHHHHhcCCCHHHHHHHHHhcCCCcCCchhhhhHHHHHHHHHHHHh
Confidence 33557788899999999999999999999999999999999999887654
No 47
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=80.61 E-value=2.1 Score=25.18 Aligned_cols=34 Identities=18% Similarity=0.354 Sum_probs=24.3
Q ss_pred cchhhhhhhcCccCCCCeeeeeehhhccccchhhHHHHHHH
Q 031787 8 EDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKK 48 (153)
Q Consensus 8 ~~~~~~vri~~~~l~~~k~i~~aLt~I~GIG~~~A~~Ic~~ 48 (153)
++|-.+.=+.| |-.++ ...+.|||.++|.+++++
T Consensus 2 ~q~~~~~~L~G-D~~dn------i~Gv~giG~ktA~~ll~~ 35 (36)
T smart00279 2 EQLIDYAILVG-DYSDN------IPGVKGIGPKTALKLLRE 35 (36)
T ss_pred HHHHHHHHHhC-cCCCC------CCCCCcccHHHHHHHHHh
Confidence 45666666777 53332 367899999999999875
No 48
>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=78.36 E-value=2.3 Score=29.41 Aligned_cols=27 Identities=26% Similarity=0.582 Sum_probs=21.8
Q ss_pred CeeeeeehhhccccchhhHHHHHHHhC
Q 031787 24 KQKIMFALTSIKGIGRRLANIVCKKAD 50 (153)
Q Consensus 24 ~k~i~~aLt~I~GIG~~~A~~Ic~~lg 50 (153)
+..|.++|+.|+|||...|..|++.-.
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 368999999999999999999997764
No 49
>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=75.98 E-value=5.1 Score=32.92 Aligned_cols=52 Identities=10% Similarity=0.107 Sum_probs=43.3
Q ss_pred CeeeeeehhhccccchhhHHHHHHHhCCCCCCc------------CCCCCHHHHHHHHHHHhCC
Q 031787 24 KQKIMFALTSIKGIGRRLANIVCKKADVDMNKR------------AGELSAAELDNLMVVVANP 75 (153)
Q Consensus 24 ~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~~~~k------------v~~Ls~~ei~~L~~~i~~~ 75 (153)
...+..--..++|+|+....+|.+++|+=+..+ ...||++|+++|-++.+.+
T Consensus 96 G~~~~ip~d~L~~Lg~g~~~Qi~~rFG~V~hlPvev~~v~~~~~~~~rltd~q~d~l~~W~~~~ 159 (225)
T PF09883_consen 96 GIFVPIPKDELKPLGPGSPRQIRRRFGLVQHLPVEVEFVKVEDGIEARLTDEQVDRLYEWTRDG 159 (225)
T ss_pred cccccCcHHHhcccCCCCHHHHHHHhCcccCCceEEEEEEcccCcccccCHHHHHHHHHHhhCC
Confidence 444445556778999999999999999998888 5679999999999998763
No 50
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=75.27 E-value=1.6 Score=34.66 Aligned_cols=20 Identities=35% Similarity=0.586 Sum_probs=16.7
Q ss_pred eehhhccccchhhHHHHHHHh
Q 031787 29 FALTSIKGIGRRLANIVCKKA 49 (153)
Q Consensus 29 ~aLt~I~GIG~~~A~~Ic~~l 49 (153)
.+| +++|||+++|.+||-.|
T Consensus 108 ~~L-~vpGIGkKtAerIilEL 127 (186)
T PRK14600 108 AAL-KVNGIGEKLINRIITEL 127 (186)
T ss_pred hhe-ECCCCcHHHHHHHHHHH
Confidence 467 89999999999999443
No 51
>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=75.23 E-value=2.2 Score=30.50 Aligned_cols=37 Identities=22% Similarity=0.138 Sum_probs=28.2
Q ss_pred eehhhccccchhhHHHHHHHhCCCCCCcCCCCCHHHHH
Q 031787 29 FALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELD 66 (153)
Q Consensus 29 ~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~ 66 (153)
..|+.|+|||+++|.-+. .+||+.-..+..-+++++-
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 468999999999999987 8999875555544555543
No 52
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=75.06 E-value=1.3 Score=28.81 Aligned_cols=47 Identities=15% Similarity=0.217 Sum_probs=29.1
Q ss_pred CeeeeeehhhccccchhhHHHHHHHh-------CCCCCCcCCCCCHHHHHHHHH
Q 031787 24 KQKIMFALTSIKGIGRRLANIVCKKA-------DVDMNKRAGELSAAELDNLMV 70 (153)
Q Consensus 24 ~k~i~~aLt~I~GIG~~~A~~Ic~~l-------gi~~~~kv~~Ls~~ei~~L~~ 70 (153)
|+.-...|..++|||...|.+|.+.= .++.-..+..++++.+++|..
T Consensus 9 N~as~~eL~~lpgi~~~~A~~Iv~~R~~~G~f~s~~dL~~v~gi~~~~~~~l~~ 62 (65)
T PF12836_consen 9 NTASAEELQALPGIGPKQAKAIVEYREKNGPFKSLEDLKEVPGIGPKTYEKLKP 62 (65)
T ss_dssp TTS-HHHHHTSTT--HHHHHHHHHHHHHH-S-SSGGGGGGSTT--HHHHHHHCC
T ss_pred ccCCHHHHHHcCCCCHHHHHHHHHHHHhCcCCCCHHHHhhCCCCCHHHHHHHHh
Confidence 33344568899999999999999764 333444666677777777654
No 53
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=74.83 E-value=2.4 Score=27.00 Aligned_cols=20 Identities=35% Similarity=0.561 Sum_probs=17.8
Q ss_pred ehhhccccchhhHHHHHHHh
Q 031787 30 ALTSIKGIGRRLANIVCKKA 49 (153)
Q Consensus 30 aLt~I~GIG~~~A~~Ic~~l 49 (153)
.|..++|||+.+|..|++.+
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 48899999999999999765
No 54
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=74.79 E-value=1.8 Score=34.45 Aligned_cols=18 Identities=33% Similarity=0.567 Sum_probs=16.0
Q ss_pred eehhhccccchhhHHHHH
Q 031787 29 FALTSIKGIGRRLANIVC 46 (153)
Q Consensus 29 ~aLt~I~GIG~~~A~~Ic 46 (153)
-+|++++|||+++|.+|+
T Consensus 108 ~~L~~vpGIGkKtAerIi 125 (194)
T PRK14605 108 ELLSTIPGIGKKTASRIV 125 (194)
T ss_pred HHHHhCCCCCHHHHHHHH
Confidence 468999999999999966
No 55
>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region. Members of the subfamily recognized by this model include competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model.
Probab=73.75 E-value=2.2 Score=27.85 Aligned_cols=26 Identities=15% Similarity=0.258 Sum_probs=20.6
Q ss_pred Ceeeeeehhh-ccccchhhHHHHHHHh
Q 031787 24 KQKIMFALTS-IKGIGRRLANIVCKKA 49 (153)
Q Consensus 24 ~k~i~~aLt~-I~GIG~~~A~~Ic~~l 49 (153)
|..-.-.|.. +.|||...|.+|++.-
T Consensus 11 Nta~~~~L~~~ipgig~~~a~~Il~~R 37 (69)
T TIGR00426 11 NTATAEELQRAMNGVGLKKAEAIVSYR 37 (69)
T ss_pred cCCCHHHHHhHCCCCCHHHHHHHHHHH
Confidence 3344446778 9999999999999884
No 56
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=73.56 E-value=0.75 Score=36.67 Aligned_cols=37 Identities=14% Similarity=0.269 Sum_probs=30.4
Q ss_pred hhcCccCCCCeeeeeehhhccccchhhHHHHHHHhCC
Q 031787 15 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADV 51 (153)
Q Consensus 15 ri~~~~l~~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi 51 (153)
.++|-.=...+.++..|.++.|||+++|..|+..++.
T Consensus 59 ~LyGF~~~~Er~lF~~Li~V~GIGpK~Al~ILs~~~~ 95 (194)
T PRK14605 59 SLFGFATTEELSLFETLIDVSGIGPKLGLAMLSAMNA 95 (194)
T ss_pred eeeCCCCHHHHHHHHHHhCCCCCCHHHHHHHHHhCCH
Confidence 4566666667778888999999999999999987763
No 57
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=72.87 E-value=11 Score=30.45 Aligned_cols=69 Identities=13% Similarity=0.057 Sum_probs=43.7
Q ss_pred eeeehh-hccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCCccCCccccCccCCcCCCcchhhhhhhHH
Q 031787 27 IMFALT-SIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALD 105 (153)
Q Consensus 27 i~~aLt-~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~L~~~i~~~~~~~ip~w~~nr~kd~~tg~~~~li~~dL~ 105 (153)
....|. +++|||+++|..|+...|..|..-+ |-.+.++..-+. + .....+..|..+..-+|..|.
T Consensus 116 ~R~~Ll~~lpGIG~KTAd~vL~~~~~~~~~iV----DtHv~Ri~~RlG------~----~~~~~~~lt~~~y~~~E~~l~ 181 (208)
T PRK01229 116 AREFLVKNIKGIGYKEASHFLRNVGYEDLAIL----DRHILRFLKRYG------L----IEEIPKTLSKKRYLEIEEILR 181 (208)
T ss_pred HHHHHHHcCCCCcHHHHHHHHHHccCCCeeee----eHHHHHHHHHhC------C----CcccccccCcCCHHHHHHHHH
Confidence 345566 9999999999999976776553333 457777766552 1 001112456667777788776
Q ss_pred HHHH
Q 031787 106 MKLR 109 (153)
Q Consensus 106 ~~~~ 109 (153)
....
T Consensus 182 ~~~~ 185 (208)
T PRK01229 182 EIAE 185 (208)
T ss_pred HHHH
Confidence 5444
No 58
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=72.34 E-value=2.5 Score=33.39 Aligned_cols=60 Identities=10% Similarity=0.203 Sum_probs=39.6
Q ss_pred hhcCccCCCCeeeeeehhhccccchhhHHHHHHHhCCCCC------------CcCCCCCHHHHHHHHHHHhC
Q 031787 15 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMN------------KRAGELSAAELDNLMVVVAN 74 (153)
Q Consensus 15 ri~~~~l~~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~~~------------~kv~~Ls~~ei~~L~~~i~~ 74 (153)
|+.|-.=...+.++..|..|+|||+++|..|++.+|.+.- .++.-+++...++|...+.+
T Consensus 59 ~l~gF~~~~ek~~f~~L~~i~GIGpk~A~~il~~fg~~~l~~~i~~~d~~~L~~v~Gig~k~A~~I~~~l~~ 130 (192)
T PRK00116 59 LLYGFLTKEERELFRLLISVSGVGPKLALAILSGLSPEELVQAIANGDVKALTKVPGIGKKTAERIVLELKD 130 (192)
T ss_pred HHcCcCCHHHHHHHHHHhcCCCCCHHHHHHHHHhCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHH
Confidence 3355553334455558899999999999999999986221 13444566666666666654
No 59
>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=71.40 E-value=3.9 Score=26.17 Aligned_cols=25 Identities=8% Similarity=0.195 Sum_probs=19.5
Q ss_pred ccccchhhHHHHHHHhCCC--CCCcCC
Q 031787 34 IKGIGRRLANIVCKKADVD--MNKRAG 58 (153)
Q Consensus 34 I~GIG~~~A~~Ic~~lgi~--~~~kv~ 58 (153)
--||+..+-+.+|+++||. |-.++.
T Consensus 24 ~Lgv~~T~LKr~CR~~GI~RWP~Rkl~ 50 (52)
T PF02042_consen 24 ELGVSVTTLKRRCRRLGIPRWPYRKLK 50 (52)
T ss_pred HhCCCHHHHHHHHHHcCCCCCCchhhc
Confidence 4689999999999999997 444443
No 60
>PRK14868 DNA topoisomerase VI subunit B; Provisional
Probab=71.10 E-value=4.2 Score=39.08 Aligned_cols=54 Identities=15% Similarity=0.216 Sum_probs=45.3
Q ss_pred CHHHHHHHHHHHhCCCCccCCccccCccCCcCCCcchhhhhhhHHHHHHH----hhhhhhccceeec
Q 031787 61 SAAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRD----DLERLKKIRNHRG 123 (153)
Q Consensus 61 s~~ei~~L~~~i~~~~~~~ip~w~~nr~kd~~tg~~~~li~~dL~~~~~~----~I~rl~~i~syRG 123 (153)
+.++.+.|.+++.+ ..| +.|+.|+++|.+..+|+..|+..+.. .++| +.+.|+|
T Consensus 482 ~~~~a~~L~~am~~---~~~----~aP~t~cLsPIgee~i~~Gl~k~~~peF~aa~TR--~p~vy~G 539 (795)
T PRK14868 482 DRDAASDLLEAMRE---TDI----IAPPTDCLSPISAELVEAGLRKEFDADFYAAATR--DAEVHGG 539 (795)
T ss_pred CHHHHHHHHHHHHh---cCC----CCCCccccCcCCHHHHHHHHHhhcCcceEEEecc--CCcccCC
Confidence 68899999999987 333 56789999999999999999998777 5666 7888876
No 61
>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=70.97 E-value=3.2 Score=35.71 Aligned_cols=36 Identities=25% Similarity=0.425 Sum_probs=28.9
Q ss_pred CccchhhhhhhcCccCCCCeeeeeehhhccccchhhHHHHHHHhC
Q 031787 6 ANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKAD 50 (153)
Q Consensus 6 ~~~~~~~~vri~~~~l~~~k~i~~aLt~I~GIG~~~A~~Ic~~lg 50 (153)
+.++|-.+.=++|++ +. ..|+|||+++|..+++..|
T Consensus 222 ~~~q~id~~iL~G~d--------yn-~Gv~GIG~ktA~kli~~~g 257 (338)
T TIGR03674 222 TREQLIDIAILVGTD--------YN-EGVKGIGPKTALKLIKEHG 257 (338)
T ss_pred CHHHHHHHHHhcCCC--------CC-CCCCCccHHHHHHHHHHcC
Confidence 446788888888886 44 6899999999999998743
No 62
>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=70.83 E-value=2.8 Score=27.51 Aligned_cols=20 Identities=25% Similarity=0.459 Sum_probs=17.5
Q ss_pred ehhhccccchhhHHHHHHHh
Q 031787 30 ALTSIKGIGRRLANIVCKKA 49 (153)
Q Consensus 30 aLt~I~GIG~~~A~~Ic~~l 49 (153)
.++.++|||.++|..|-+.+
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 68999999999999997654
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=70.72 E-value=2.3 Score=31.24 Aligned_cols=32 Identities=19% Similarity=0.238 Sum_probs=25.6
Q ss_pred cCCCCeeeeeehhhccccchhhHHHHHHHhCC
Q 031787 20 NVDGKQKIMFALTSIKGIGRRLANIVCKKADV 51 (153)
Q Consensus 20 ~l~~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi 51 (153)
.++=|..-.-.|..++|||+.+|.+|.+..+-
T Consensus 59 ~iniNtA~~~eL~~lpGIG~~~A~~Ii~~R~~ 90 (120)
T TIGR01259 59 AVNINAASLEELQALPGIGPAKAKAIIEYREE 90 (120)
T ss_pred CEeCCcCCHHHHhcCCCCCHHHHHHHHHHHHh
Confidence 34455556678899999999999999998753
No 64
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=68.02 E-value=3.7 Score=35.22 Aligned_cols=25 Identities=16% Similarity=0.292 Sum_probs=22.4
Q ss_pred eeehhhccccchhhHHHHHHHhCCCC
Q 031787 28 MFALTSIKGIGRRLANIVCKKADVDM 53 (153)
Q Consensus 28 ~~aLt~I~GIG~~~A~~Ic~~lgi~~ 53 (153)
...|.+|+|||+++|..+.+ +||..
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 46689999999999999999 99975
No 65
>PF02371 Transposase_20: Transposase IS116/IS110/IS902 family; InterPro: IPR003346 Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This family includes transposases for IS116, IS110 and IS902. It is often found with the transposase IS111A/IS1328/IS1533 family (see IPR002525 from INTERPRO) [, ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=67.16 E-value=4.1 Score=27.88 Aligned_cols=21 Identities=38% Similarity=0.404 Sum_probs=19.0
Q ss_pred ehhhccccchhhHHHHHHHhC
Q 031787 30 ALTSIKGIGRRLANIVCKKAD 50 (153)
Q Consensus 30 aLt~I~GIG~~~A~~Ic~~lg 50 (153)
.|++|+|||..+|..|+..+|
T Consensus 3 ~l~sipGig~~~a~~llaeig 23 (87)
T PF02371_consen 3 LLTSIPGIGPITAATLLAEIG 23 (87)
T ss_pred hhcCCCCccHHHHHHHHHHHc
Confidence 588999999999999999883
No 66
>PRK12278 50S ribosomal protein L21/unknown domain fusion protein; Provisional
Probab=66.86 E-value=4.3 Score=33.29 Aligned_cols=45 Identities=24% Similarity=0.290 Sum_probs=40.0
Q ss_pred eehhhccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 031787 29 FALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 74 (153)
Q Consensus 29 ~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~L~~~i~~ 74 (153)
--|+.|.|||+..+.. +..+|+..-..+-.++++++..+...+.-
T Consensus 158 DDL~~I~GIGp~~a~~-L~eaGi~tfaQIAa~t~a~ia~id~~l~~ 202 (221)
T PRK12278 158 DDLTKITGVGPALAKK-LNEAGVTTFAQIAALTDADIAKIDEKLSF 202 (221)
T ss_pred chheeccccChHHHHH-HHHcCCCCHHHhhCCChhhhhhhhhcccC
Confidence 4689999999999877 56899999999999999999999988853
No 67
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=65.88 E-value=3.6 Score=30.65 Aligned_cols=44 Identities=18% Similarity=0.191 Sum_probs=29.1
Q ss_pred eeeeeehhhccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHH
Q 031787 25 QKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVV 72 (153)
Q Consensus 25 k~i~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~L~~~i 72 (153)
..+...|++++|||+.+|..++.... +++.-+- |-.+.++...+
T Consensus 79 ~~~~~~L~~l~GIG~~tA~~~l~~~~-~~~~~pv---D~~v~r~~~~~ 122 (158)
T cd00056 79 PDAREELLALPGVGRKTANVVLLFAL-GPDAFPV---DTHVRRVLKRL 122 (158)
T ss_pred cccHHHHHcCCCCCHHHHHHHHHHHC-CCCCCcc---chhHHHHHHHh
Confidence 55778899999999999999987532 2322222 44555554443
No 68
>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=65.88 E-value=3.8 Score=32.54 Aligned_cols=20 Identities=30% Similarity=0.456 Sum_probs=17.2
Q ss_pred eehhhccccchhhHHHHHHH
Q 031787 29 FALTSIKGIGRRLANIVCKK 48 (153)
Q Consensus 29 ~aLt~I~GIG~~~A~~Ic~~ 48 (153)
-+|++++|||+++|.+|+-.
T Consensus 107 ~~L~~ipGiGkKtAerIile 126 (191)
T TIGR00084 107 KALVKIPGVGKKTAERLLLE 126 (191)
T ss_pred HHHHhCCCCCHHHHHHHHHH
Confidence 46889999999999999933
No 69
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=65.70 E-value=3.7 Score=30.37 Aligned_cols=23 Identities=35% Similarity=0.356 Sum_probs=19.3
Q ss_pred eeeehhhccccchhhHHHHHHHh
Q 031787 27 IMFALTSIKGIGRRLANIVCKKA 49 (153)
Q Consensus 27 i~~aLt~I~GIG~~~A~~Ic~~l 49 (153)
....|.+++|||+.+|..+|...
T Consensus 70 ~~~~L~~l~GIG~~tA~~~l~~~ 92 (149)
T smart00478 70 DREELLKLPGVGRKTANAVLSFA 92 (149)
T ss_pred HHHHHHcCCCCcHHHHHHHHHHH
Confidence 34567889999999999998775
No 70
>cd00128 XPG Xeroderma pigmentosum G N- and I-regions (XPGN, XPGI); contains the HhH2 motif; domain in nucleases. XPG is a eukaryotic enzyme that functions in nucleotide-excision repair and transcription-coupled repair of oxidative DNA damage. Functionally/structurally related to FEN-1; divalent metal ion-dependent exo- and endonuclease, and bacterial and bacteriophage 5'3' exonucleases.
Probab=65.30 E-value=5.1 Score=33.67 Aligned_cols=36 Identities=25% Similarity=0.284 Sum_probs=29.3
Q ss_pred CccchhhhhhhcCccCCCCeeeeeehhhccccchhhHHHHHHHhC
Q 031787 6 ANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKAD 50 (153)
Q Consensus 6 ~~~~~~~~vri~~~~l~~~k~i~~aLt~I~GIG~~~A~~Ic~~lg 50 (153)
+.++|-.+.=++|+|-. ..++|||.++|.++++..|
T Consensus 209 ~~~q~id~~~L~G~Dy~---------~gv~giG~k~A~~li~~~~ 244 (316)
T cd00128 209 TREKLIDLAILLGCDYT---------EGIPGIGPVTALKLIKKYG 244 (316)
T ss_pred CHHHHHHHHHhcCCCCC---------CCCCCccHHHHHHHHHHcC
Confidence 34678888888887732 3799999999999999987
No 71
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=64.91 E-value=3.3 Score=26.97 Aligned_cols=18 Identities=28% Similarity=0.589 Sum_probs=14.9
Q ss_pred hccccchhhHHHHHHHhC
Q 031787 33 SIKGIGRRLANIVCKKAD 50 (153)
Q Consensus 33 ~I~GIG~~~A~~Ic~~lg 50 (153)
.|+|||..+|+.|++.+|
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 689999999999999888
No 72
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=64.76 E-value=4.7 Score=26.24 Aligned_cols=21 Identities=29% Similarity=0.512 Sum_probs=16.6
Q ss_pred ehhhccccchhhHHHHHHHhC
Q 031787 30 ALTSIKGIGRRLANIVCKKAD 50 (153)
Q Consensus 30 aLt~I~GIG~~~A~~Ic~~lg 50 (153)
.|+.++|||+.+|..|.+.+.
T Consensus 36 ~L~~i~gIG~~~A~si~~ff~ 56 (64)
T PF12826_consen 36 ELSAIPGIGPKIAQSIYEFFQ 56 (64)
T ss_dssp HHCTSTT--HHHHHHHHHHHH
T ss_pred HHhccCCcCHHHHHHHHHHHC
Confidence 689999999999999988764
No 73
>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=64.21 E-value=4.9 Score=34.00 Aligned_cols=25 Identities=16% Similarity=0.396 Sum_probs=21.6
Q ss_pred eeehhhccccchhhHHHHHHHhCCCC
Q 031787 28 MFALTSIKGIGRRLANIVCKKADVDM 53 (153)
Q Consensus 28 ~~aLt~I~GIG~~~A~~Ic~~lgi~~ 53 (153)
...|.+|+|||+++|..+. .+|+..
T Consensus 84 l~~l~~i~GiGpk~a~~l~-~lGi~s 108 (307)
T cd00141 84 LLLLLRVPGVGPKTARKLY-ELGIRT 108 (307)
T ss_pred HHHHHcCCCCCHHHHHHHH-HcCCCC
Confidence 3467899999999999999 999875
No 74
>PTZ00217 flap endonuclease-1; Provisional
Probab=63.86 E-value=5.6 Score=35.05 Aligned_cols=36 Identities=25% Similarity=0.405 Sum_probs=29.1
Q ss_pred CccchhhhhhhcCccCCCCeeeeeehhhccccchhhHHHHHHHhC
Q 031787 6 ANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKAD 50 (153)
Q Consensus 6 ~~~~~~~~vri~~~~l~~~k~i~~aLt~I~GIG~~~A~~Ic~~lg 50 (153)
+.++|-.+.=++|+| + +..|.|||+.+|..|++..|
T Consensus 221 ~~~q~id~~iL~G~D--------y-~pgi~GIG~ktA~~Li~~~g 256 (393)
T PTZ00217 221 SMDQFIDLCILCGCD--------Y-CDTIKGIGPKTAYKLIKKYK 256 (393)
T ss_pred CHHHHHHHHHHhCCC--------C-CCCCCCccHHHHHHHHHHcC
Confidence 446788888888977 2 34799999999999998865
No 75
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=63.74 E-value=4.2 Score=28.37 Aligned_cols=26 Identities=27% Similarity=0.514 Sum_probs=19.4
Q ss_pred eehh-hccccchhhHHHHHHHhCCCCC
Q 031787 29 FALT-SIKGIGRRLANIVCKKADVDMN 54 (153)
Q Consensus 29 ~aLt-~I~GIG~~~A~~Ic~~lgi~~~ 54 (153)
|.|. .|.|||-++|-+|...+|++++
T Consensus 45 Y~L~~~i~gi~F~~aD~iA~~~g~~~~ 71 (94)
T PF14490_consen 45 YRLIEDIDGIGFKTADKIALKLGIEPD 71 (94)
T ss_dssp TCCCB-SSSSBHHHHHHHHHTTT--TT
T ss_pred HHHHHHccCCCHHHHHHHHHHcCCCCC
Confidence 4444 4999999999999999998763
No 76
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=63.74 E-value=8.1 Score=31.23 Aligned_cols=86 Identities=22% Similarity=0.320 Sum_probs=53.3
Q ss_pred eeeehhhccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCC-cc------------CCccccCccCCcCC
Q 031787 27 IMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQ-FK------------IPDWFLNRQKDYKD 93 (153)
Q Consensus 27 i~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~L~~~i~~~~~-~~------------ip~w~~nr~kd~~t 93 (153)
+..+|.+++|||+++|.++.--+- +.++++++.|.++|.+... .. .=.-+.++++|..+
T Consensus 10 LI~~l~kLPGvG~KsA~R~AfhLL--------~~~~~~~~~la~al~~a~~~i~~C~~C~~~te~d~C~ICsd~~Rd~~~ 81 (198)
T COG0353 10 LIDALKKLPGVGPKSAQRLAFHLL--------QRDREDVERLAKALLEAKENIKHCSVCGNLTESDPCDICSDESRDKSQ 81 (198)
T ss_pred HHHHHhhCCCCChhHHHHHHHHHH--------ccCHHHHHHHHHHHHHHHhcCccccccCCcCCCCcCcCcCCcccCCce
Confidence 446899999999999999986654 3467777777777654210 11 11122345555431
Q ss_pred CcchhhhhhhHHHHHHHhhhhhhccceeecccCCCC
Q 031787 94 GKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWG 129 (153)
Q Consensus 94 g~~~~li~~dL~~~~~~~I~rl~~i~syRG~RH~~g 129 (153)
.-+||.. .|+..+-+.+.|+|.=|-.|
T Consensus 82 ---icVVe~p------~Dv~a~E~~~~f~G~YhVL~ 108 (198)
T COG0353 82 ---LCVVEEP------KDVLALEKTGEFRGLYHVLG 108 (198)
T ss_pred ---EEEEcch------HHHHHHHHhcccCeeEEEec
Confidence 2234433 35666667888888888766
No 77
>PRK03980 flap endonuclease-1; Provisional
Probab=63.03 E-value=5.8 Score=33.53 Aligned_cols=36 Identities=31% Similarity=0.372 Sum_probs=29.1
Q ss_pred CccchhhhhhhcCccCCCCeeeeeehhhccccchhhHHHHHHHhC
Q 031787 6 ANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKAD 50 (153)
Q Consensus 6 ~~~~~~~~vri~~~~l~~~k~i~~aLt~I~GIG~~~A~~Ic~~lg 50 (153)
+.++|-.+.=++|+|- ...|+|||+++|..|++..|
T Consensus 175 ~~~q~id~~iL~G~Dy---------~~GI~GIG~ktA~kLi~~~~ 210 (292)
T PRK03980 175 TREQLIDIAILVGTDY---------NPGIKGIGPKTALKLIKKHG 210 (292)
T ss_pred CHHHHHHHHHhcCCCC---------CCCCCCccHHHHHHHHHHCC
Confidence 3467888888888762 23789999999999999887
No 78
>PRK08609 hypothetical protein; Provisional
Probab=62.66 E-value=5.6 Score=36.62 Aligned_cols=25 Identities=20% Similarity=0.292 Sum_probs=22.2
Q ss_pred eehhhccccchhhHHHHHHHhCCCC
Q 031787 29 FALTSIKGIGRRLANIVCKKADVDM 53 (153)
Q Consensus 29 ~aLt~I~GIG~~~A~~Ic~~lgi~~ 53 (153)
..|++|+|||+++|.++.+.+||..
T Consensus 88 ~~l~~i~GiGpk~a~~l~~~lGi~t 112 (570)
T PRK08609 88 LPLLKLPGLGGKKIAKLYKELGVVD 112 (570)
T ss_pred HHHhcCCCCCHHHHHHHHHHhCCCC
Confidence 4678999999999999999999853
No 79
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=62.27 E-value=1.3 Score=35.83 Aligned_cols=38 Identities=21% Similarity=0.308 Sum_probs=31.8
Q ss_pred hhhhcCccCCCCeeeeeehhhccccchhhHHHHHHHhC
Q 031787 13 ILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKAD 50 (153)
Q Consensus 13 ~vri~~~~l~~~k~i~~aLt~I~GIG~~~A~~Ic~~lg 50 (153)
...++|-.=...+.++..|.++.|||+++|.+|+..++
T Consensus 57 ~~~LyGF~~~~ER~lF~~LisVnGIGpK~ALaiLs~~~ 94 (201)
T COG0632 57 AHLLYGFLTEEERELFRLLISVNGIGPKLALAILSNLD 94 (201)
T ss_pred HHHHcCCCCHHHHHHHHHHHccCCccHHHHHHHHcCCC
Confidence 35677777778888899999999999999999996544
No 80
>PRK10702 endonuclease III; Provisional
Probab=62.21 E-value=5 Score=32.31 Aligned_cols=23 Identities=39% Similarity=0.562 Sum_probs=19.3
Q ss_pred eeeehhhccccchhhHHHHHHHh
Q 031787 27 IMFALTSIKGIGRRLANIVCKKA 49 (153)
Q Consensus 27 i~~aLt~I~GIG~~~A~~Ic~~l 49 (153)
..-.|.+++|||+++|..|+..+
T Consensus 107 ~~~~Ll~lpGVG~ktA~~ill~a 129 (211)
T PRK10702 107 DRAALEALPGVGRKTANVVLNTA 129 (211)
T ss_pred hHHHHhcCCcccHHHHHHHHHHH
Confidence 35779999999999999998554
No 81
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=62.15 E-value=5.6 Score=32.01 Aligned_cols=86 Identities=20% Similarity=0.298 Sum_probs=49.5
Q ss_pred eeeehhhccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCC-ccC------------CccccCccCCcCC
Q 031787 27 IMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQ-FKI------------PDWFLNRQKDYKD 93 (153)
Q Consensus 27 i~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~L~~~i~~~~~-~~i------------p~w~~nr~kd~~t 93 (153)
+..+|++++|||+++|.++.-.+= ...++++..|.++|.+..+ ... =+-+.++.+|..
T Consensus 9 Li~~l~~LPGIG~KsA~RlA~~ll--------~~~~~~~~~la~ai~~~~~~i~~C~~C~~lse~~~C~IC~d~~Rd~~- 79 (195)
T TIGR00615 9 LIESLKKLPGIGPKSAQRLAFHLL--------KRDPSEVLRLAQALLEAKENLRTCSVCGAISDQEVCNICSDERRDNS- 79 (195)
T ss_pred HHHHHHHCCCCCHHHHHHHHHHHH--------cCCHHHHHHHHHHHHHHHHcCCcCCCCCCCCCCCcCCCCCCCCCCCC-
Confidence 446789999999999999975543 2356667777666654210 111 011122333221
Q ss_pred CcchhhhhhhHHHHHHHhhhhhhccceeecccCCCC
Q 031787 94 GKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWG 129 (153)
Q Consensus 94 g~~~~li~~dL~~~~~~~I~rl~~i~syRG~RH~~g 129 (153)
-.-+||+. .|+.-+-+.+.|+|.=|-.|
T Consensus 80 --~iCVVE~~------~Dv~aiE~~~~y~G~YhVL~ 107 (195)
T TIGR00615 80 --VICVVEDP------KDVFALEKTKEFRGRYHVLG 107 (195)
T ss_pred --EEEEECCH------HHHHHHHhhCccceEEEEcc
Confidence 12245554 24445556788888888775
No 82
>PRK12311 rpsB 30S ribosomal protein S2/unknown domain fusion protein; Provisional
Probab=62.11 E-value=4.3 Score=35.09 Aligned_cols=44 Identities=9% Similarity=0.098 Sum_probs=39.0
Q ss_pred eehhhccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHh
Q 031787 29 FALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVA 73 (153)
Q Consensus 29 ~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~L~~~i~ 73 (153)
--|+.|.|||+..+.. |..+||..-..+..++++++..+...+.
T Consensus 263 DdL~~I~GiGp~~e~~-L~~~Gi~~f~QiA~~t~~~~a~vd~~l~ 306 (326)
T PRK12311 263 DDLKKLTGVSPQIEKK-LNDLGIFHFWQLAELDPDDAAKIGEELG 306 (326)
T ss_pred hhhhhhccCChhhhhh-hhhcCCCCHHHhhCCChhhhhhhhhccc
Confidence 5689999999988765 7889999999999999999999888774
No 83
>PRK00076 recR recombination protein RecR; Reviewed
Probab=61.80 E-value=5.7 Score=31.98 Aligned_cols=86 Identities=20% Similarity=0.266 Sum_probs=50.6
Q ss_pred eeeehhhccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCC-cc------------CCccccCccCCcCC
Q 031787 27 IMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQ-FK------------IPDWFLNRQKDYKD 93 (153)
Q Consensus 27 i~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~L~~~i~~~~~-~~------------ip~w~~nr~kd~~t 93 (153)
+..+|.+++|||+++|.++.-.+=- ..++++..|.++|.+..+ .. +=+-+.++.+|..
T Consensus 9 Li~~l~~LPGIG~KsA~Rla~~ll~--------~~~~~~~~la~~i~~~~~~i~~C~~C~~lse~~~C~IC~d~~Rd~~- 79 (196)
T PRK00076 9 LIEALRKLPGIGPKSAQRLAFHLLQ--------RDREDVLRLAQALEEAKEKIKHCSVCGNLTEQDPCEICSDPRRDQS- 79 (196)
T ss_pred HHHHHHHCCCCCHHHHHHHHHHHHc--------CCHHHHHHHHHHHHHHHHcCCcCCCCCCcCCCCcCCCCCCCCCCCC-
Confidence 3467899999999999999866532 356677777766654211 11 0011122333321
Q ss_pred CcchhhhhhhHHHHHHHhhhhhhccceeecccCCCC
Q 031787 94 GKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWG 129 (153)
Q Consensus 94 g~~~~li~~dL~~~~~~~I~rl~~i~syRG~RH~~g 129 (153)
-.-+||+- .|+.-+-+.+.|+|.=|-.|
T Consensus 80 --~icVVE~~------~Dv~aiE~s~~y~G~YhVL~ 107 (196)
T PRK00076 80 --LICVVESP------ADVLAIERTGEYRGLYHVLG 107 (196)
T ss_pred --EEEEECCH------HHHHHHHhhCcCceEEEEec
Confidence 12245554 25555556788888888776
No 84
>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=61.53 E-value=5.5 Score=31.17 Aligned_cols=23 Identities=35% Similarity=0.465 Sum_probs=19.3
Q ss_pred eeeehhhccccchhhHHHHHHHh
Q 031787 27 IMFALTSIKGIGRRLANIVCKKA 49 (153)
Q Consensus 27 i~~aLt~I~GIG~~~A~~Ic~~l 49 (153)
....|.+++|||+.+|..||-..
T Consensus 104 ~~~~L~~l~GIG~ktA~~ill~~ 126 (191)
T TIGR01083 104 DREELVKLPGVGRKTANVVLNVA 126 (191)
T ss_pred HHHHHHhCCCCcHHHHHHHHHHH
Confidence 35678999999999999999554
No 85
>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=61.53 E-value=1.1 Score=35.53 Aligned_cols=35 Identities=17% Similarity=0.322 Sum_probs=27.3
Q ss_pred hhcCccCCCCeeeeeehhhccccchhhHHHHHHHh
Q 031787 15 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKA 49 (153)
Q Consensus 15 ri~~~~l~~~k~i~~aLt~I~GIG~~~A~~Ic~~l 49 (153)
.++|-.=...+.++..|.++.|||+++|..|+..+
T Consensus 58 ~LyGF~~~~Er~lF~~L~~V~GIGpK~Al~iL~~~ 92 (191)
T TIGR00084 58 LLFGFNTLEERELFKELIKVNGVGPKLALAILSNM 92 (191)
T ss_pred eeeCCCCHHHHHHHHHHhCCCCCCHHHHHHHHhcC
Confidence 45555556677778889999999999999995443
No 86
>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=60.51 E-value=5.3 Score=33.53 Aligned_cols=29 Identities=21% Similarity=0.290 Sum_probs=22.3
Q ss_pred CccCCCCeeeeeehhhccccchhhHHHHHHHh
Q 031787 18 NTNVDGKQKIMFALTSIKGIGRRLANIVCKKA 49 (153)
Q Consensus 18 ~~~l~~~k~i~~aLt~I~GIG~~~A~~Ic~~l 49 (153)
|-.+|.. .-.|.+++|||+++|..|+...
T Consensus 97 ~g~~p~~---~~~L~~LpGIG~~TA~~Il~~a 125 (275)
T TIGR01084 97 GGEFPQD---FEDLAALPGVGRYTAGAILSFA 125 (275)
T ss_pred CCCCcHH---HHHHHhCCCCCHHHHHHHHHHH
Confidence 3445543 5679999999999999999654
No 87
>KOG2518 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=59.53 E-value=6.6 Score=36.16 Aligned_cols=60 Identities=15% Similarity=0.203 Sum_probs=43.8
Q ss_pred CccchhhhhhhcCccCCCCeeeeeehhhccccchhhHHHHHHHhCCCCCC-------cCCCCCHHHHHHHHHHHhC
Q 031787 6 ANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNK-------RAGELSAAELDNLMVVVAN 74 (153)
Q Consensus 6 ~~~~~~~~vri~~~~l~~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~~~~-------kv~~Ls~~ei~~L~~~i~~ 74 (153)
+.|.|++|.=+.|+| -|.++.|||..+|.++..+...-... +--...++.++....+...
T Consensus 211 ~~ekfr~mciLSGCD---------Yl~slpGvGl~tA~k~l~k~~~~d~vi~~~~~~~~l~Vpd~y~~~F~~A~~t 277 (556)
T KOG2518|consen 211 TEEKFRRMCILSGCD---------YLSSLPGVGLATAHKLLSKYNTPDRVIISHLLKKKLTVPDDYIENFERANLT 277 (556)
T ss_pred CHHHHHHHHHhcCCc---------ccccCccccHHHHHHHHHhcCcHHHHHHHHHhccCCcCCHHHHHHHHHHHHh
Confidence 558999999999999 46779999999999999775532111 1124567777777776654
No 88
>COG2081 Predicted flavoproteins [General function prediction only]
Probab=59.35 E-value=11 Score=33.53 Aligned_cols=49 Identities=22% Similarity=0.331 Sum_probs=41.9
Q ss_pred CCeeeeeehhhccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 031787 23 GKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 74 (153)
Q Consensus 23 ~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~L~~~i~~ 74 (153)
+++.+.-+|.. .++.+.+..++++.|| |+....+|++.|+++|.+.|+.
T Consensus 284 ~~kslkn~L~~--~lp~rlv~~~l~~~~i-~~~~~~~ls~~~~~~l~~~ik~ 332 (408)
T COG2081 284 PKKSLKNALAK--LLPKRLVEFLLERAGI-PDEPLAQLSPKELAQLAAALKA 332 (408)
T ss_pred hhhHHHHHHHH--HhhhHHHHHHHHhccC-CCcchhhcCHHHHHHHHHHHhc
Confidence 45555555544 5789999999999999 9999999999999999999987
No 89
>PRK13844 recombination protein RecR; Provisional
Probab=59.14 E-value=6.8 Score=31.67 Aligned_cols=39 Identities=10% Similarity=0.090 Sum_probs=29.3
Q ss_pred eeehhhccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 031787 28 MFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 74 (153)
Q Consensus 28 ~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~L~~~i~~ 74 (153)
..+|++++|||+++|.++.-.+= +..+++++.|.++|.+
T Consensus 14 I~~l~~LPGIG~KsA~Rla~~lL--------~~~~~~~~~la~~i~~ 52 (200)
T PRK13844 14 IESLRKLPTIGKKSSQRLALYLL--------DKSPETAIAIANSLLD 52 (200)
T ss_pred HHHHHHCCCCCHHHHHHHHHHHH--------cCCHHHHHHHHHHHHH
Confidence 46789999999999999986542 2456677777777654
No 90
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=59.02 E-value=2.1 Score=34.31 Aligned_cols=37 Identities=14% Similarity=0.180 Sum_probs=29.2
Q ss_pred hhcCccCCCCeeeeeehhhccccchhhHHHHHHHhCC
Q 031787 15 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADV 51 (153)
Q Consensus 15 ri~~~~l~~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi 51 (153)
.++|-.=...+.++..|.++.|||+++|..|+..++.
T Consensus 60 ~LyGF~~~~Er~lF~~Li~V~GIGpK~Al~iLs~~~~ 96 (203)
T PRK14602 60 ELFGFATWDERQTFIVLISISKVGAKTALAILSQFRP 96 (203)
T ss_pred eeeCCCCHHHHHHHHHHhCCCCcCHHHHHHHHhhCCH
Confidence 4555555566777788999999999999999987653
No 91
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=58.94 E-value=1.6 Score=34.62 Aligned_cols=35 Identities=14% Similarity=0.311 Sum_probs=27.9
Q ss_pred hhcCccCCCCeeeeeehhhccccchhhHHHHHHHh
Q 031787 15 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKA 49 (153)
Q Consensus 15 ri~~~~l~~~k~i~~aLt~I~GIG~~~A~~Ic~~l 49 (153)
.++|-.=...+.++..|.++.|||+++|..|+..+
T Consensus 59 ~LyGF~~~~Er~lF~~Li~V~GIGpK~AL~iLs~~ 93 (188)
T PRK14606 59 TLYGFSNERKKELFLSLTKVSRLGPKTALKIISNE 93 (188)
T ss_pred eeeCCCCHHHHHHHHHHhccCCccHHHHHHHHcCC
Confidence 45565556677778889999999999999998554
No 92
>PHA02564 V virion protein; Provisional
Probab=58.65 E-value=19 Score=27.51 Aligned_cols=34 Identities=15% Similarity=0.070 Sum_probs=28.2
Q ss_pred hhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 031787 40 RLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 74 (153)
Q Consensus 40 ~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~L~~~i~~ 74 (153)
..+..+|+.+|++|+.++.-.++ .+..|..+|..
T Consensus 86 aYi~~Vs~~~GV~~~~~idl~d~-~l~~l~~Aii~ 119 (141)
T PHA02564 86 AYATAVANAMGVPPQAGLHLDQD-TLAALVTAIIR 119 (141)
T ss_pred HHHHHHHHHHCCCCCCcCcCCcH-HHHHHHHHHHH
Confidence 35889999999999999986555 88888888864
No 93
>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=58.42 E-value=8.4 Score=31.36 Aligned_cols=37 Identities=16% Similarity=0.297 Sum_probs=25.1
Q ss_pred ccchhhhhhhcCccCCCCeeeeeehhhccccchhhHHHHHHHhC
Q 031787 7 NEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKAD 50 (153)
Q Consensus 7 ~~~~~~~vri~~~~l~~~k~i~~aLt~I~GIG~~~A~~Ic~~lg 50 (153)
+++|-.+.=+.|-..| .+..++|||+++|..+++..|
T Consensus 168 p~q~~d~~~L~GD~sD-------nipGv~GiG~ktA~~Ll~~~g 204 (240)
T cd00008 168 PAQIIDYKALMGDSSD-------NIPGVPGIGEKTAAKLLKEYG 204 (240)
T ss_pred HHHHHHHHHHcCCccc-------CCCCCCccCHHHHHHHHHHhC
Confidence 3455555556662221 345689999999999998865
No 94
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=58.24 E-value=1.7 Score=34.43 Aligned_cols=35 Identities=26% Similarity=0.378 Sum_probs=28.0
Q ss_pred hhcCccCCCCeeeeeehhhccccchhhHHHHHHHh
Q 031787 15 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKA 49 (153)
Q Consensus 15 ri~~~~l~~~k~i~~aLt~I~GIG~~~A~~Ic~~l 49 (153)
.++|-.=...+.++..|.++.|||+++|..|+..+
T Consensus 59 ~LyGF~~~~Er~lF~~Li~VsGIGpK~Al~ILs~~ 93 (183)
T PRK14601 59 KLYGFLDKDEQKMFEMLLKVNGIGANTAMAVCSSL 93 (183)
T ss_pred eeeCCCCHHHHHHHHHHhccCCccHHHHHHHHcCC
Confidence 45566666677778889999999999999998543
No 95
>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=57.99 E-value=28 Score=21.89 Aligned_cols=43 Identities=12% Similarity=0.195 Sum_probs=32.6
Q ss_pred hhhccccchhhHHHHHHHhCCCCCCcC----CCCCHHHHHHHHHHHh
Q 031787 31 LTSIKGIGRRLANIVCKKADVDMNKRA----GELSAAELDNLMVVVA 73 (153)
Q Consensus 31 Lt~I~GIG~~~A~~Ic~~lgi~~~~kv----~~Ls~~ei~~L~~~i~ 73 (153)
+.+..||...+...-.+..|+.+..+- ...+++++..|..+..
T Consensus 6 va~~~gvs~~tlr~w~~~~g~~~~~r~~~~~r~yt~~~v~~l~~i~~ 52 (68)
T cd01104 6 VARLTGVSPDTLRAWERRYGLPAPQRTDGGHRLYSEADVARLRLIRR 52 (68)
T ss_pred HHHHHCcCHHHHHHHHHhCCCCCCCcCCCCCeecCHHHHHHHHHHHH
Confidence 456789999999998887787664332 3679999998887764
No 96
>TIGR01448 recD_rel helicase, putative, RecD/TraA family. This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.
Probab=57.81 E-value=11 Score=35.70 Aligned_cols=42 Identities=26% Similarity=0.396 Sum_probs=29.6
Q ss_pred hccccchhhHHHHHHHhCCCC--------C--CcCCCCCHHHHHHHHHHHhC
Q 031787 33 SIKGIGRRLANIVCKKADVDM--------N--KRAGELSAAELDNLMVVVAN 74 (153)
Q Consensus 33 ~I~GIG~~~A~~Ic~~lgi~~--------~--~kv~~Ls~~ei~~L~~~i~~ 74 (153)
.|+|||+.+|..|++.+|.+. . ..+..+++..++.|.+.+.+
T Consensus 88 ~~~GIG~~~A~~iv~~fg~~~~~~i~~~~~~L~~v~gi~~~~~~~i~~~~~~ 139 (720)
T TIGR01448 88 SIKGVGKKLAQRIVKTFGEAAFDVLDDDPEKLLEVPGISKANLEKFVSQWSQ 139 (720)
T ss_pred CCCCcCHHHHHHHHHHhCHhHHHHHHhCHHHHhcCCCCCHHHHHHHHHHHHH
Confidence 499999999999999988662 1 23345666666666665543
No 97
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=57.73 E-value=24 Score=28.73 Aligned_cols=40 Identities=20% Similarity=0.253 Sum_probs=29.7
Q ss_pred eeehhhccccchhhHHHHHHH-hCCCCCCcCCCCCHHHHHHHHHHH
Q 031787 28 MFALTSIKGIGRRLANIVCKK-ADVDMNKRAGELSAAELDNLMVVV 72 (153)
Q Consensus 28 ~~aLt~I~GIG~~~A~~Ic~~-lgi~~~~kv~~Ls~~ei~~L~~~i 72 (153)
...|.+.+|||++||+-++.. +|++ ...|-. .+.++.+-+
T Consensus 108 ~~eL~~LPGVGrKTAnvVL~~a~g~p-~i~VDT----HV~Rvs~R~ 148 (211)
T COG0177 108 REELLSLPGVGRKTANVVLSFAFGIP-AIAVDT----HVHRVSNRL 148 (211)
T ss_pred HHHHHhCCCcchHHHHHHHHhhcCCC-cccccc----hHHHHHHHh
Confidence 357999999999999999887 4544 555543 777766654
No 98
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=57.49 E-value=1.9 Score=34.24 Aligned_cols=36 Identities=14% Similarity=0.155 Sum_probs=29.3
Q ss_pred hhcCccCCCCeeeeeehhhccccchhhHHHHHHHhC
Q 031787 15 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKAD 50 (153)
Q Consensus 15 ri~~~~l~~~k~i~~aLt~I~GIG~~~A~~Ic~~lg 50 (153)
.++|-.=...+.++..|.++.|||+++|.+|+..++
T Consensus 59 ~LyGF~~~~Er~lF~~LisV~GIGpK~Al~iLs~~~ 94 (186)
T PRK14600 59 QLYGFLNREEQDCLRMLVKVSGVNYKTAMSILSKLT 94 (186)
T ss_pred eeeCCCCHHHHHHHHHHhCcCCcCHHHHHHHHccCC
Confidence 456666667778888899999999999999986543
No 99
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=56.38 E-value=2 Score=34.55 Aligned_cols=35 Identities=20% Similarity=0.282 Sum_probs=28.1
Q ss_pred hhcCccCCCCeeeeeehhhccccchhhHHHHHHHh
Q 031787 15 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKA 49 (153)
Q Consensus 15 ri~~~~l~~~k~i~~aLt~I~GIG~~~A~~Ic~~l 49 (153)
.++|-.=...+.++..|.++.|||+++|.+|+..+
T Consensus 58 ~LYGF~t~~Er~lF~~LisVsGIGPK~ALaILs~~ 92 (196)
T PRK13901 58 KLFGFLNSSEREVFEELIGVDGIGPRAALRVLSGI 92 (196)
T ss_pred eeeCCCCHHHHHHHHHHhCcCCcCHHHHHHHHcCC
Confidence 45666666677788889999999999999999554
No 100
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=55.44 E-value=2.1 Score=34.29 Aligned_cols=35 Identities=14% Similarity=0.227 Sum_probs=27.9
Q ss_pred hhcCccCCCCeeeeeehhhccccchhhHHHHHHHh
Q 031787 15 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKA 49 (153)
Q Consensus 15 ri~~~~l~~~k~i~~aLt~I~GIG~~~A~~Ic~~l 49 (153)
.++|-.=...+.++..|.++.|||+++|.+|+..+
T Consensus 58 ~LyGF~~~~Er~lF~~L~~V~GIGpK~AL~iLs~~ 92 (197)
T PRK14603 58 SLYGFPDEDSLELFELLLGVSGVGPKLALALLSAL 92 (197)
T ss_pred eeeCcCCHHHHHHHHHHhCcCCcCHHHHHHHHcCC
Confidence 45565556677778889999999999999998654
No 101
>smart00475 53EXOc 5'-3' exonuclease.
Probab=53.97 E-value=13 Score=30.86 Aligned_cols=36 Identities=19% Similarity=0.346 Sum_probs=24.6
Q ss_pred cchhhhhhhcCccCCCCeeeeeehhhccccchhhHHHHHHHhC
Q 031787 8 EDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKAD 50 (153)
Q Consensus 8 ~~~~~~vri~~~~l~~~k~i~~aLt~I~GIG~~~A~~Ic~~lg 50 (153)
++|-.+.=+.|-.-| .+..++|||+++|.++++..|
T Consensus 172 ~q~~d~~aL~GD~sD-------nipGV~GIG~KtA~~Ll~~yg 207 (259)
T smart00475 172 EQIIDYKALMGDSSD-------NIPGVPGIGEKTAAKLLKEFG 207 (259)
T ss_pred HHHHHHHHHhCCccc-------CCCCCCCCCHHHHHHHHHHhC
Confidence 455555556661111 245589999999999999887
No 102
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=53.38 E-value=7.6 Score=32.11 Aligned_cols=20 Identities=30% Similarity=0.494 Sum_probs=9.3
Q ss_pred hhhccccchhhHHHHHHHhC
Q 031787 31 LTSIKGIGRRLANIVCKKAD 50 (153)
Q Consensus 31 Lt~I~GIG~~~A~~Ic~~lg 50 (153)
|..+.|||...|..|.+.++
T Consensus 38 L~~V~GIg~k~AekI~e~l~ 57 (232)
T PRK12766 38 LAEVDGIGNALAARIKADVG 57 (232)
T ss_pred HHHccCCCHHHHHHHHHHhc
Confidence 34444444444444444443
No 103
>PRK13910 DNA glycosylase MutY; Provisional
Probab=53.27 E-value=8.1 Score=32.74 Aligned_cols=22 Identities=27% Similarity=0.277 Sum_probs=19.3
Q ss_pred eeehhhccccchhhHHHHHHHh
Q 031787 28 MFALTSIKGIGRRLANIVCKKA 49 (153)
Q Consensus 28 ~~aLt~I~GIG~~~A~~Ic~~l 49 (153)
.-.|.+++|||+++|..|+..+
T Consensus 71 ~~~L~~LpGIG~kTA~aIl~~a 92 (289)
T PRK13910 71 YQSLLKLPGIGAYTANAILCFG 92 (289)
T ss_pred HHHHHhCCCCCHHHHHHHHHHH
Confidence 5789999999999999998643
No 104
>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=53.23 E-value=22 Score=25.40 Aligned_cols=35 Identities=17% Similarity=0.350 Sum_probs=30.7
Q ss_pred cccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHh
Q 031787 35 KGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVA 73 (153)
Q Consensus 35 ~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~L~~~i~ 73 (153)
--+|......|++.|+ ++-.+||+++++.+.+++.
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 4578899999999998 7789999999999999875
No 105
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=52.54 E-value=14 Score=31.01 Aligned_cols=34 Identities=21% Similarity=0.424 Sum_probs=27.1
Q ss_pred ccchhhhhhhcC--cc-CCCCeeeeeehhhccccchhhHHHHHHHhC
Q 031787 7 NEDFQHILRVLN--TN-VDGKQKIMFALTSIKGIGRRLANIVCKKAD 50 (153)
Q Consensus 7 ~~~~~~~vri~~--~~-l~~~k~i~~aLt~I~GIG~~~A~~Ic~~lg 50 (153)
.+++..+.=+.| +| +|| ++|||+++|.++++..|
T Consensus 183 p~qliD~~~L~Gd~sDnipG----------V~GIG~ktA~~Ll~~~g 219 (310)
T COG0258 183 PEQLIDLKALVGDSSDNIPG----------VKGIGPKTALKLLQEYG 219 (310)
T ss_pred HHHHHHHHHHhCCcccCCCC----------CCCcCHHHHHHHHHHhC
Confidence 346777777888 43 344 99999999999999998
No 106
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=52.20 E-value=8.3 Score=31.39 Aligned_cols=23 Identities=26% Similarity=0.198 Sum_probs=18.6
Q ss_pred eeeehhhccccchhhHHHHHHHh
Q 031787 27 IMFALTSIKGIGRRLANIVCKKA 49 (153)
Q Consensus 27 i~~aLt~I~GIG~~~A~~Ic~~l 49 (153)
..-.|.+++|||+.||..|+-.+
T Consensus 119 ~re~Ll~l~GIG~kTAd~iLlya 141 (218)
T PRK13913 119 TREWLLDQKGIGKESADAILCYV 141 (218)
T ss_pred HHHHHHcCCCccHHHHHHHHHHH
Confidence 34569999999999999887544
No 107
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=52.08 E-value=8 Score=35.81 Aligned_cols=43 Identities=26% Similarity=0.264 Sum_probs=33.0
Q ss_pred CeeeeeehhhccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHH
Q 031787 24 KQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNL 68 (153)
Q Consensus 24 ~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~L 68 (153)
+......|..|+|||+...+++++.+| .-..+..-|.||+.++
T Consensus 509 k~~~~S~Ld~I~GiG~kr~~~Ll~~Fg--s~~~ik~As~eeL~~v 551 (567)
T PRK14667 509 KEGLKDILDKIKGIGEVKKEIIYRNFK--TLYDFLKADDEELKKL 551 (567)
T ss_pred cccccCccccCCCCCHHHHHHHHHHhC--CHHHHHhCCHHHHHHc
Confidence 444567889999999999999999998 3445666667777554
No 108
>PRK10880 adenine DNA glycosylase; Provisional
Probab=52.03 E-value=9.3 Score=33.25 Aligned_cols=23 Identities=17% Similarity=0.364 Sum_probs=19.9
Q ss_pred eeeehhhccccchhhHHHHHHHh
Q 031787 27 IMFALTSIKGIGRRLANIVCKKA 49 (153)
Q Consensus 27 i~~aLt~I~GIG~~~A~~Ic~~l 49 (153)
..-.|.+++|||+++|..||..+
T Consensus 107 ~~~~L~~LpGIG~~TA~aIl~~a 129 (350)
T PRK10880 107 TFEEVAALPGVGRSTAGAILSLS 129 (350)
T ss_pred hHHHHhcCCCccHHHHHHHHHHH
Confidence 45789999999999999999754
No 109
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=50.75 E-value=11 Score=29.80 Aligned_cols=21 Identities=33% Similarity=0.559 Sum_probs=18.7
Q ss_pred ehhhccccchhhHHHHHHHhC
Q 031787 30 ALTSIKGIGRRLANIVCKKAD 50 (153)
Q Consensus 30 aLt~I~GIG~~~A~~Ic~~lg 50 (153)
.|++++|||+++|.+|+..+.
T Consensus 109 ~L~~v~Gig~k~A~~I~~~l~ 129 (192)
T PRK00116 109 ALTKVPGIGKKTAERIVLELK 129 (192)
T ss_pred HHHhCCCCCHHHHHHHHHHHH
Confidence 689999999999999997754
No 110
>PRK14976 5'-3' exonuclease; Provisional
Probab=49.38 E-value=16 Score=30.65 Aligned_cols=36 Identities=19% Similarity=0.308 Sum_probs=24.1
Q ss_pred cchhhhhhhcCccCCCCeeeeeehhhccccchhhHHHHHHHhC
Q 031787 8 EDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKAD 50 (153)
Q Consensus 8 ~~~~~~vri~~~~l~~~k~i~~aLt~I~GIG~~~A~~Ic~~lg 50 (153)
++|-.+.=+.|--.| ....++|||+++|.++++..|
T Consensus 177 ~q~~d~~aL~GD~sD-------nipGVpGIG~KtA~~LL~~~g 212 (281)
T PRK14976 177 KQIIDYKGLVGDSSD-------NIKGVKGIGPKTAIKLLNKYG 212 (281)
T ss_pred HHHHHHHHHhCCccC-------CCCCCCcccHHHHHHHHHHcC
Confidence 455555555661111 234589999999999998876
No 111
>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=49.22 E-value=5.6 Score=35.16 Aligned_cols=77 Identities=19% Similarity=0.293 Sum_probs=0.0
Q ss_pred hccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCCccCCccccCccCCcCCCcchhhhhhhHHHHHHHhh
Q 031787 33 SIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDL 112 (153)
Q Consensus 33 ~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~L~~~i~~~~~~~ip~w~~nr~kd~~tg~~~~li~~dL~~~~~~~I 112 (153)
.=|||-++||..|. .+|+--+.-++ ++|+||+.+.+.|+.. |-+ |.+=|+.+ +++..++..-
T Consensus 56 ~~YGVRy~T~AKIa-ElGFTvsTLl~-M~deELDdmM~sL~~i--fRw---------dLLVGERY-----GIKAAvRAER 117 (386)
T PF01698_consen 56 QGYGVRYYTAAKIA-ELGFTVSTLLN-MTDEELDDMMNSLSQI--FRW---------DLLVGERY-----GIKAAVRAER 117 (386)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred hhccccHHHHHHHH-HhcccHHHHhc-ccHHHHHHHHHHHHHH--hhh---------hhhhhhhh-----hHHHHHHHHH
Confidence 45899999999886 58888766665 7999999999998763 222 44445544 5677777777
Q ss_pred hhhhccceeecccCC
Q 031787 113 ERLKKIRNHRGLRHY 127 (153)
Q Consensus 113 ~rl~~i~syRG~RH~ 127 (153)
.||-.....+..||.
T Consensus 118 RRl~e~~~~~rR~hl 132 (386)
T PF01698_consen 118 RRLEEEEESRRRRHL 132 (386)
T ss_dssp ---------------
T ss_pred HHhhcchhhhhhhcc
Confidence 777776555666653
No 112
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=48.94 E-value=9 Score=35.52 Aligned_cols=40 Identities=30% Similarity=0.331 Sum_probs=31.2
Q ss_pred eeeehhhccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHH
Q 031787 27 IMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNL 68 (153)
Q Consensus 27 i~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~L 68 (153)
....|..|+|||+....++++.+| .-..+..-|.||+.++
T Consensus 512 ~~s~L~~I~GiG~kr~~~LL~~Fg--s~~~I~~As~eeL~~v 551 (574)
T PRK14670 512 IKLNYTKIKGIGEKKAKKILKSLG--TYKDILLLNEDEIAEK 551 (574)
T ss_pred cccccccCCCCCHHHHHHHHHHhC--CHHHHHhCCHHHHHhC
Confidence 456899999999999999999988 3445666666776553
No 113
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=48.41 E-value=33 Score=28.79 Aligned_cols=30 Identities=27% Similarity=0.244 Sum_probs=22.8
Q ss_pred eeeehhhccccchhhHHHHHHHhCCCCCCc
Q 031787 27 IMFALTSIKGIGRRLANIVCKKADVDMNKR 56 (153)
Q Consensus 27 i~~aLt~I~GIG~~~A~~Ic~~lgi~~~~k 56 (153)
+...|..++|||+.+|..|+-+.==+|+.-
T Consensus 205 ~~~~L~~LpGIGpwTA~~vllr~lg~~D~f 234 (283)
T PRK10308 205 AMKTLQTFPGIGRWTANYFALRGWQAKDVF 234 (283)
T ss_pred HHHHHhcCCCcCHHHHHHHHHHhCCCCCCC
Confidence 346789999999999999987643355553
No 114
>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=47.84 E-value=2.8 Score=30.15 Aligned_cols=20 Identities=20% Similarity=0.408 Sum_probs=15.6
Q ss_pred hhhccccchhhHHHHHHHhC
Q 031787 31 LTSIKGIGRRLANIVCKKAD 50 (153)
Q Consensus 31 Lt~I~GIG~~~A~~Ic~~lg 50 (153)
...++|||+++|..+++..|
T Consensus 20 IPGV~GIG~KtA~~LL~~yg 39 (101)
T PF01367_consen 20 IPGVPGIGPKTAAKLLQEYG 39 (101)
T ss_dssp B---TTSTCHCCCCCHHHHT
T ss_pred CCCCCCCCHHHHHHHHHHcC
Confidence 45689999999999999987
No 115
>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=47.64 E-value=11 Score=32.09 Aligned_cols=43 Identities=14% Similarity=0.122 Sum_probs=29.5
Q ss_pred eeeehhhccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHH
Q 031787 27 IMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVV 72 (153)
Q Consensus 27 i~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~L~~~i 72 (153)
+.-.|+.++|||+.+|..||-..==.|+.-+. |--+.++.+-+
T Consensus 218 ~~~~L~~l~GIG~~tAd~vll~~l~~~d~~Pv---D~~v~r~~~r~ 260 (310)
T TIGR00588 218 AREALCELPGVGPKVADCICLMGLDKPQAVPV---DVHVWRIANRD 260 (310)
T ss_pred HHHHHHhCCCccHHHHHHHHHHhCCCCCceee---cHHHHHHHHHH
Confidence 45778999999999999999775444444332 45566655443
No 116
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=47.40 E-value=3.3 Score=33.11 Aligned_cols=35 Identities=11% Similarity=0.247 Sum_probs=27.1
Q ss_pred hhcCccCCCCeeeeeehhhccccchhhHHHHHHHh
Q 031787 15 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKA 49 (153)
Q Consensus 15 ri~~~~l~~~k~i~~aLt~I~GIG~~~A~~Ic~~l 49 (153)
.++|-.=...+.++..|.++.|||+++|..|+..+
T Consensus 59 ~LyGF~~~~Er~lF~~Li~V~GIGpK~Al~iLs~~ 93 (195)
T PRK14604 59 TLYGFSTPAQRQLFELLIGVSGVGPKAALNLLSSG 93 (195)
T ss_pred eeeCCCCHHHHHHHHHHhCcCCcCHHHHHHHHcCC
Confidence 34555555566777889999999999999999654
No 117
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=47.17 E-value=14 Score=34.23 Aligned_cols=43 Identities=30% Similarity=0.338 Sum_probs=31.4
Q ss_pred CCeeeeeehhhccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHH
Q 031787 23 GKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDN 67 (153)
Q Consensus 23 ~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~ 67 (153)
.+..+..+|..|.|||..++..|++.+|= -..+.+-+.+|+..
T Consensus 537 ~k~~~~s~L~~IpGIG~k~~k~Ll~~FgS--~~~i~~As~eeL~~ 579 (598)
T PRK00558 537 SKARLTSALDDIPGIGPKRRKALLKHFGS--LKAIKEASVEELAK 579 (598)
T ss_pred ccchhhhhHhhCCCcCHHHHHHHHHHcCC--HHHHHhCCHHHHhh
Confidence 34456789999999999999999999882 23344455666544
No 118
>PF14635 HHH_7: Helix-hairpin-helix motif ; PDB: 3PSI_A 3PSF_A.
Probab=46.65 E-value=4.9 Score=29.20 Aligned_cols=42 Identities=17% Similarity=0.325 Sum_probs=30.5
Q ss_pred chhhhhhhcCccCCC---CeeeeeehhhccccchhhHHHHHHHhC
Q 031787 9 DFQHILRVLNTNVDG---KQKIMFALTSIKGIGRRLANIVCKKAD 50 (153)
Q Consensus 9 ~~~~~vri~~~~l~~---~k~i~~aLt~I~GIG~~~A~~Ic~~lg 50 (153)
.|-.+|-..|+||+. +......|+.+-|.|+++|..+.+.+.
T Consensus 27 ~~vd~vN~vGVDIN~a~~~~~~~~~LqfV~GLGPRKA~~Ll~~l~ 71 (104)
T PF14635_consen 27 AFVDVVNQVGVDINRAVSHPHLANLLQFVCGLGPRKAQALLKALK 71 (104)
T ss_dssp HHHHHHHHH-EEHHHHCT-HHHHGGGGGSTT--HHHHHHHHHHHH
T ss_pred HHHHHHHhhCccHHHHhcChHHHhhHhHhcCCChHHHHHHHHHHH
Confidence 456667777888864 555678899999999999999998775
No 119
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=46.45 E-value=13 Score=34.96 Aligned_cols=41 Identities=17% Similarity=0.220 Sum_probs=30.6
Q ss_pred eeeeehhhccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHH
Q 031787 26 KIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNL 68 (153)
Q Consensus 26 ~i~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~L 68 (153)
...-.|..|+|||+..+.++++.+| .-..+..-|.+|+.++
T Consensus 549 ~~~S~L~~IpGIG~kr~~~LL~~Fg--Si~~I~~As~eeL~~v 589 (624)
T PRK14669 549 DRTSELLEIPGVGAKTVQRLLKHFG--SLERVRAATETQLAAV 589 (624)
T ss_pred HHHHHHhcCCCCCHHHHHHHHHHcC--CHHHHHhCCHHHHHHH
Confidence 3456788999999999999999998 2344555666666554
No 120
>PF09239 Topo-VIb_trans: Topoisomerase VI B subunit, transducer; InterPro: IPR015320 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 []. This entry represents subunit B of topoisomerase VI, an ATP-dependent type IIB enzyme. Members of this family adopt a structure consisting of a four-stranded beta-sheet backed by three alpha-helices, the last of which is over 50 amino acids long and extends from the body of the protein by several turns. This domain has been proposed to mediate intersubunit communication by structurally transducing signals from the ATP binding and hydrolysis domains to the DNA binding and cleavage domains of the gyrase holoenzyme []. 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, 0006265 DNA topological change, 0005694 chromosome; PDB: 2ZBK_F 2HKJ_A 1Z5B_A 1Z5C_B 1MX0_F 1Z5A_A 1MU5_A 1Z59_A 2Q2E_B.
Probab=44.67 E-value=9.2 Score=29.93 Aligned_cols=35 Identities=17% Similarity=0.179 Sum_probs=20.6
Q ss_pred ccCCcCCCcchhhhhhhHHHHHHH----hhhhhhccceeec
Q 031787 87 RQKDYKDGKYSQVVSNALDMKLRD----DLERLKKIRNHRG 123 (153)
Q Consensus 87 r~kd~~tg~~~~li~~dL~~~~~~----~I~rl~~i~syRG 123 (153)
|+.|++++.+..+|+..|+..++. .++| +.+.|+|
T Consensus 1 P~~~cLsPiGe~~i~~Gl~k~l~pefv~avtR--~p~vy~G 39 (160)
T PF09239_consen 1 PPTDCLSPIGEELIEKGLKKELNPEFVAAVTR--KPSVYSG 39 (160)
T ss_dssp --SCCS----HHHHHHHHHHHC--SEEEEEE-----EEETT
T ss_pred CCCcccCccCHHHHHHHHHHhcCccEEEEEcc--CCceecC
Confidence 467999999999999999998888 4566 7778876
No 121
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=42.90 E-value=11 Score=32.05 Aligned_cols=32 Identities=22% Similarity=0.523 Sum_probs=24.8
Q ss_pred CCCHHHHHHHHHHHhCCCCcc------------------CCccccCccCCc
Q 031787 59 ELSAAELDNLMVVVANPRQFK------------------IPDWFLNRQKDY 91 (153)
Q Consensus 59 ~Ls~~ei~~L~~~i~~~~~~~------------------ip~w~~nr~kd~ 91 (153)
-+|+.|++.|++++++.. |. |..||.|||.-|
T Consensus 147 iFT~~Qle~LEkaFkeaH-YPDv~Are~la~ktelpEDRIqVWfQNRRAKW 196 (332)
T KOG0494|consen 147 IFTSYQLEELEKAFKEAH-YPDVYAREMLADKTELPEDRIQVWFQNRRAKW 196 (332)
T ss_pred hhhHHHHHHHHHHHhhcc-CccHHHHHHHhhhccCchhhhhHHhhhhhHHh
Confidence 378999999999987643 32 678999998644
No 122
>TIGR00600 rad2 DNA excision repair protein (rad2). All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=42.30 E-value=17 Score=36.06 Aligned_cols=36 Identities=11% Similarity=0.174 Sum_probs=29.6
Q ss_pred ccchhhhhhhcCccCCCCeeeeeehhhccccchhhHHHHHHHhCC
Q 031787 7 NEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADV 51 (153)
Q Consensus 7 ~~~~~~~vri~~~~l~~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi 51 (153)
.++|-.+.-++|+| | ...|+|||+.+|..|++..|=
T Consensus 853 ~~qli~laiL~G~D--------Y-~~GI~GIGpktAl~li~~~~~ 888 (1034)
T TIGR00600 853 RNKLINLAYLLGSD--------Y-TEGIPTVGPVSAMEILNEFPG 888 (1034)
T ss_pred HHHHHHHHHeeCCC--------C-CCCCCcccHHHHHHHHHHcCC
Confidence 46677778888888 4 257999999999999999873
No 123
>COG2938 Uncharacterized conserved protein [Function unknown]
Probab=41.74 E-value=15 Score=26.33 Aligned_cols=34 Identities=21% Similarity=0.369 Sum_probs=27.4
Q ss_pred CcCCCCCHHHHHHHHHHHhCCCCccCCccccCccC
Q 031787 55 KRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQK 89 (153)
Q Consensus 55 ~kv~~Ls~~ei~~L~~~i~~~~~~~ip~w~~nr~k 89 (153)
....+||++|++.+..+++.+. -.+-.|+.|+..
T Consensus 39 ~~~~~lsd~el~~f~~LLe~~D-~dL~~Wi~g~~~ 72 (94)
T COG2938 39 KEFDSLSDEELDEFERLLECED-NDLFNWIMGHGE 72 (94)
T ss_pred HHHhhCCHHHHHHHHHHHcCCc-HHHHHHHhCCCC
Confidence 3467899999999999998753 456679998877
No 124
>PTZ00338 dimethyladenosine transferase-like protein; Provisional
Probab=41.46 E-value=32 Score=28.94 Aligned_cols=34 Identities=12% Similarity=0.219 Sum_probs=29.2
Q ss_pred hhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 031787 40 RLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 74 (153)
Q Consensus 40 ~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~L~~~i~~ 74 (153)
.....+++.+|++ +.|+.+|+-+|+-.|..++.+
T Consensus 255 ~~~~~~l~~~~~~-~~R~e~l~~~~f~~L~~~~~~ 288 (294)
T PTZ00338 255 EFIAEILEDSGMF-EKRSVKLDIDDFLKLLLAFNK 288 (294)
T ss_pred HHHHHHHHHcCCc-ccChhhCCHHHHHHHHHHHHH
Confidence 3445678999997 799999999999999999875
No 125
>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=40.62 E-value=16 Score=22.65 Aligned_cols=44 Identities=11% Similarity=0.064 Sum_probs=31.8
Q ss_pred ehhhccccchhhHHHHH-HHhCCCCCCcCCCCCHHHHHHHHHHHh
Q 031787 30 ALTSIKGIGRRLANIVC-KKADVDMNKRAGELSAAELDNLMVVVA 73 (153)
Q Consensus 30 aLt~I~GIG~~~A~~Ic-~~lgi~~~~kv~~Ls~~ei~~L~~~i~ 73 (153)
-|.+-.|+...-....| ..+|+.....-..|++++++.|.+.+.
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 45667788888888888 559999777788889999998888763
No 126
>PRK09482 flap endonuclease-like protein; Provisional
Probab=40.47 E-value=19 Score=30.05 Aligned_cols=20 Identities=20% Similarity=0.373 Sum_probs=17.5
Q ss_pred hhhccccchhhHHHHHHHhC
Q 031787 31 LTSIKGIGRRLANIVCKKAD 50 (153)
Q Consensus 31 Lt~I~GIG~~~A~~Ic~~lg 50 (153)
...++|||+++|..+++..|
T Consensus 184 IpGVpGIG~KtA~~LL~~~g 203 (256)
T PRK09482 184 IPGVAGIGPKSAAELLNQFR 203 (256)
T ss_pred CCCCCCcChHHHHHHHHHhC
Confidence 45689999999999998877
No 127
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=40.40 E-value=16 Score=30.77 Aligned_cols=23 Identities=30% Similarity=0.354 Sum_probs=19.4
Q ss_pred eeeehhhccccchhhHHHHHHHh
Q 031787 27 IMFALTSIKGIGRRLANIVCKKA 49 (153)
Q Consensus 27 i~~aLt~I~GIG~~~A~~Ic~~l 49 (153)
+.-.|++|.|||+-+|..++-..
T Consensus 196 a~e~L~~i~GIG~WTAe~~llf~ 218 (285)
T COG0122 196 AIEELTALKGIGPWTAEMFLLFG 218 (285)
T ss_pred HHHHHHcCCCcCHHHHHHHHHHc
Confidence 45678999999999999998653
No 128
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=39.29 E-value=15 Score=34.10 Aligned_cols=39 Identities=15% Similarity=0.270 Sum_probs=30.4
Q ss_pred eeeehhhccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHH
Q 031787 27 IMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDN 67 (153)
Q Consensus 27 i~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~ 67 (153)
...+|+.|.|||..++.++++.+| .-..+-+-+.+|+..
T Consensus 523 ~~~~L~~IpGIG~kr~~~LL~~FG--S~~~I~~As~eeL~~ 561 (577)
T PRK14668 523 VSTVLDDVPGVGPETRKRLLRRFG--SVEGVREASVEDLRD 561 (577)
T ss_pred HHhHHhcCCCCCHHHHHHHHHHcC--CHHHHHhCCHHHHHh
Confidence 458899999999999999999987 334555566666644
No 129
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=38.75 E-value=63 Score=24.53 Aligned_cols=45 Identities=16% Similarity=0.168 Sum_probs=36.4
Q ss_pred ehhhccccchhhHHHHHHHhC---CC--CC---CcCCCCCHHHHHHHHHHHhC
Q 031787 30 ALTSIKGIGRRLANIVCKKAD---VD--MN---KRAGELSAAELDNLMVVVAN 74 (153)
Q Consensus 30 aLt~I~GIG~~~A~~Ic~~lg---i~--~~---~kv~~Ls~~ei~~L~~~i~~ 74 (153)
...+++|||.+++..-..+.. .+ +. -+++.|+++|++.|.+.+..
T Consensus 26 e~Ak~~gvs~sTvy~wv~r~~e~G~~l~~~~~~GrP~kl~~~q~~~l~e~~~~ 78 (138)
T COG3415 26 EAAKRFGVSISTVYRWVRRYRETGLDLPPKPRKGRPRKLSEEQLEILLERLRE 78 (138)
T ss_pred HHHHHhCccHHHHHHHHHHhccccccccCccCCCCCcccCHHHHHHHHHHHhc
Confidence 457889999999999998764 33 33 37889999999999999875
No 130
>PRK12373 NADH dehydrogenase subunit E; Provisional
Probab=38.35 E-value=25 Score=31.37 Aligned_cols=45 Identities=13% Similarity=0.076 Sum_probs=39.6
Q ss_pred eehhhccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 031787 29 FALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 74 (153)
Q Consensus 29 ~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~L~~~i~~ 74 (153)
--|+.|.|||+..+.. +..+||.....+-.++++++..+...+.-
T Consensus 323 DDLk~I~GIGpk~e~~-Ln~~Gi~~f~QIA~wt~~eia~vd~~l~f 367 (400)
T PRK12373 323 DDLKLISGVGPKIEAT-LNELGIFTFDQVAAWKKAERAWVDGYLNF 367 (400)
T ss_pred hhhhhccCCChHHHHH-HHhcCCCCHHHHhCCCHHHhHHhhhcccC
Confidence 4689999999998765 67899999999999999999999888753
No 131
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=37.50 E-value=32 Score=26.24 Aligned_cols=22 Identities=23% Similarity=0.330 Sum_probs=18.4
Q ss_pred eeehhhccccchhhHHHHHHHh
Q 031787 28 MFALTSIKGIGRRLANIVCKKA 49 (153)
Q Consensus 28 ~~aLt~I~GIG~~~A~~Ic~~l 49 (153)
.--|..++|||+++|.+|.+.-
T Consensus 96 ~eeL~~lpgIG~~kA~aIi~yR 117 (149)
T COG1555 96 AEELQALPGIGPKKAQAIIDYR 117 (149)
T ss_pred HHHHHHCCCCCHHHHHHHHHHH
Confidence 3456999999999999999664
No 132
>PRK14896 ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Provisional
Probab=37.37 E-value=37 Score=27.63 Aligned_cols=64 Identities=20% Similarity=0.237 Sum_probs=40.8
Q ss_pred chhhhhhhcCccCCCCeeeeeehhhccc-cchhhHHHHHHHh-CCCCCCcCCCCCHHHHHHHHHHHhC
Q 031787 9 DFQHILRVLNTNVDGKQKIMFALTSIKG-IGRRLANIVCKKA-DVDMNKRAGELSAAELDNLMVVVAN 74 (153)
Q Consensus 9 ~~~~~vri~~~~l~~~k~i~~aLt~I~G-IG~~~A~~Ic~~l-gi~~~~kv~~Ls~~ei~~L~~~i~~ 74 (153)
.|.++++.+ .-...|.+.-+|..+.. .+......+...+ ++++++++.+||.+|+..|.+.+..
T Consensus 191 ~~~~~~~~~--F~~rrk~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~R~e~L~~~~~~~l~~~~~~ 256 (258)
T PRK14896 191 FFDDFVKAL--FQHRRKTLRNALKNSAHISGKEDIKAVVEALPEELLNKRVFQLSPEEIAELANLLYE 256 (258)
T ss_pred HHHHHHHHH--HccccHHHHHHHhhhccccchhHHHHHHHHcCCCCcCCCCccCCHHHHHHHHHHHHh
Confidence 355555542 33456777777776531 1211123345556 5668999999999999999998854
No 133
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=37.12 E-value=22 Score=33.22 Aligned_cols=49 Identities=22% Similarity=0.377 Sum_probs=34.5
Q ss_pred CccCCCCeeeeeehhhccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHH
Q 031787 18 NTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNL 68 (153)
Q Consensus 18 ~~~l~~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~L 68 (153)
+-..-..+.+.-.|..|.|||+++|..|++.+| +. ..+..-+.+++.++
T Consensus 558 hr~~r~k~~~~s~L~~I~GIG~k~a~~Ll~~Fg-s~-~~i~~As~eeL~~v 606 (621)
T PRK14671 558 HRKLRSKRTLQTELTDIAGIGEKTAEKLLEHFG-SV-EKVAKASLEELAAV 606 (621)
T ss_pred ChhhHHHHHhhhhhhcCCCcCHHHHHHHHHHcC-CH-HHHHhCCHHHHHHH
Confidence 444445556677889999999999999999996 11 33444566676554
No 134
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=36.70 E-value=17 Score=34.63 Aligned_cols=43 Identities=7% Similarity=0.193 Sum_probs=32.1
Q ss_pred CCeeeeeehhhccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHH
Q 031787 23 GKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDN 67 (153)
Q Consensus 23 ~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~ 67 (153)
..+.+...|..|+|||+.....+++.+| .-..+..-|.+||..
T Consensus 602 ~k~~~~s~L~~IpGiG~kr~~~LL~~Fg--S~~~i~~As~eel~~ 644 (691)
T PRK14672 602 TKKELVLSFERLPHVGKVRAHRLLAHFG--SFRSLQSATPQDIAT 644 (691)
T ss_pred hhhhcccccccCCCCCHHHHHHHHHHhc--CHHHHHhCCHHHHHh
Confidence 3444567899999999999999999988 334555556666654
No 135
>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=36.20 E-value=24 Score=30.51 Aligned_cols=38 Identities=21% Similarity=0.430 Sum_probs=28.4
Q ss_pred eehhhccccchhhHHHHHHHhCCCCCCcCCCC--CHHHHH
Q 031787 29 FALTSIKGIGRRLANIVCKKADVDMNKRAGEL--SAAELD 66 (153)
Q Consensus 29 ~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~L--s~~ei~ 66 (153)
.-+..+.|||.+++..+++.+||..-.-+-.+ +.+++.
T Consensus 182 lpv~~l~GiG~~~~~~ll~~~Gi~ti~dl~~~~~~~~~L~ 221 (359)
T cd01702 182 LPITSIRGLGGKLGEEIIDLLGLPTEGDVAGFRSSESDLQ 221 (359)
T ss_pred CcHHHhCCcCHHHHHHHHHHcCCcCHHHHHhccCCHHHHH
Confidence 35789999999999999999999864444444 555443
No 136
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=35.42 E-value=27 Score=28.79 Aligned_cols=32 Identities=25% Similarity=0.540 Sum_probs=22.3
Q ss_pred CCCHHHHHHHHHHHhCCCCcc------------------CCccccCccCCc
Q 031787 59 ELSAAELDNLMVVVANPRQFK------------------IPDWFLNRQKDY 91 (153)
Q Consensus 59 ~Ls~~ei~~L~~~i~~~~~~~------------------ip~w~~nr~kd~ 91 (153)
.++.+|++.|++.+++- .|. |-.||.|||+++
T Consensus 43 tFtr~QlevLe~LF~kT-qYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~ 92 (228)
T KOG2251|consen 43 TFTRKQLEVLEALFAKT-QYPDVFMREELALKLNLPESRVQVWFKNRRAKC 92 (228)
T ss_pred eecHHHHHHHHHHHHhh-cCccHHHHHHHHHHhCCchhhhhhhhccccchh
Confidence 36778888888877652 332 567999988744
No 137
>PRK13766 Hef nuclease; Provisional
Probab=35.12 E-value=26 Score=32.87 Aligned_cols=23 Identities=17% Similarity=0.278 Sum_probs=20.6
Q ss_pred eeehhhccccchhhHHHHHHHhC
Q 031787 28 MFALTSIKGIGRRLANIVCKKAD 50 (153)
Q Consensus 28 ~~aLt~I~GIG~~~A~~Ic~~lg 50 (153)
.+.|..|.|||...|..|++.+|
T Consensus 714 ~~~L~~ipgig~~~a~~Ll~~fg 736 (773)
T PRK13766 714 EYIVESLPDVGPVLARNLLEHFG 736 (773)
T ss_pred HHHHhcCCCCCHHHHHHHHHHcC
Confidence 34689999999999999999987
No 138
>PRK07373 DNA polymerase III subunit alpha; Reviewed
Probab=34.62 E-value=32 Score=30.92 Aligned_cols=25 Identities=24% Similarity=0.550 Sum_probs=22.0
Q ss_pred CeeeeeehhhccccchhhHHHHHHH
Q 031787 24 KQKIMFALTSIKGIGRRLANIVCKK 48 (153)
Q Consensus 24 ~k~i~~aLt~I~GIG~~~A~~Ic~~ 48 (153)
+..|.|+|..|+|||...+.+|.+.
T Consensus 109 ~~~IrfGL~aIKGVG~~~i~~Iv~e 133 (449)
T PRK07373 109 GEKILFGLSAVRNLGEGAIESILKA 133 (449)
T ss_pred CCEEEEcchhcCCCCHHHHHHHHHH
Confidence 4469999999999999999999754
No 139
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=33.94 E-value=30 Score=28.31 Aligned_cols=36 Identities=28% Similarity=0.162 Sum_probs=26.7
Q ss_pred cCCCCeee--eeehhhccccchhhHHHHHHHhCCCCCC
Q 031787 20 NVDGKQKI--MFALTSIKGIGRRLANIVCKKADVDMNK 55 (153)
Q Consensus 20 ~l~~~k~i--~~aLt~I~GIG~~~A~~Ic~~lgi~~~~ 55 (153)
++++.++. .--|-+|+|||..+|..|+-.+.=-|.-
T Consensus 104 ~~~~~~~~~~R~~LL~iKGIG~ETaDsILlYa~~rp~F 141 (215)
T COG2231 104 NLESFKSEVLREELLSIKGIGKETADSILLYALDRPVF 141 (215)
T ss_pred hhhccchHHHHHHHHccCCcchhhHHHHHHHHhcCccc
Confidence 45555555 5678899999999999998777644443
No 140
>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=33.37 E-value=46 Score=23.80 Aligned_cols=58 Identities=19% Similarity=0.100 Sum_probs=41.3
Q ss_pred cCccCCCCeeeeeehhhccccchhhHHHHHHHhCCC---CCCcCCCCCHHHHHHHHHHHhC
Q 031787 17 LNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVD---MNKRAGELSAAELDNLMVVVAN 74 (153)
Q Consensus 17 ~~~~l~~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~---~~~kv~~Ls~~ei~~L~~~i~~ 74 (153)
+|..||=|..-..+.+++.|.=+..|..|+.-.=.+ .=..+..||+.|-+.|.+.+++
T Consensus 11 ~G~KIDlNNa~vr~f~~~pGmYPtlA~kIv~naPY~sveDvl~ipgLse~qK~~lk~~~~~ 71 (93)
T PF06514_consen 11 LGQKIDLNNANVRAFRQFPGMYPTLAGKIVSNAPYKSVEDVLNIPGLSERQKALLKKYEDN 71 (93)
T ss_dssp CCTCEETTSS-GGGGCCSTTTTCCHHHHHHHS---SSGGGGCCSTT--HHHHHHHHHHGGG
T ss_pred cCCceecccHhHHHHHHCCCCCHHHHHHHHhCCCCCCHHHHHhccCCCHHHHHHHHHHhcc
Confidence 345555566667889999999999999999765333 3335667999999999999986
No 141
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=33.01 E-value=28 Score=29.16 Aligned_cols=38 Identities=34% Similarity=0.393 Sum_probs=27.8
Q ss_pred eeehhhccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHH
Q 031787 28 MFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDN 67 (153)
Q Consensus 28 ~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~ 67 (153)
.+.|.+|+|||...|..+++.+|= -..+-..+++|+..
T Consensus 181 ~~il~s~pgig~~~a~~ll~~fgS--~~~~~tas~~eL~~ 218 (254)
T COG1948 181 LYILESIPGIGPKLAERLLKKFGS--VEDVLTASEEELMK 218 (254)
T ss_pred HHHHHcCCCccHHHHHHHHHHhcC--HHHHhhcCHHHHHH
Confidence 577899999999999999988872 33444455554443
No 142
>COG1059 Thermostable 8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=32.65 E-value=22 Score=28.92 Aligned_cols=25 Identities=24% Similarity=0.403 Sum_probs=22.0
Q ss_pred eeehhhccccchhhHHHHHHHhCCC
Q 031787 28 MFALTSIKGIGRRLANIVCKKADVD 52 (153)
Q Consensus 28 ~~aLt~I~GIG~~~A~~Ic~~lgi~ 52 (153)
.+.+.+|+|||++-|.-.++-.|+.
T Consensus 120 E~Lv~nikGiGyKEASHFLRNVG~~ 144 (210)
T COG1059 120 ELLVENIKGIGYKEASHFLRNVGFE 144 (210)
T ss_pred HHHHHHcccccHHHHHHHHHhcChh
Confidence 4667799999999999999999974
No 143
>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=32.06 E-value=20 Score=23.86 Aligned_cols=44 Identities=14% Similarity=0.172 Sum_probs=32.7
Q ss_pred eeehhhccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 031787 28 MFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 74 (153)
Q Consensus 28 ~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~L~~~i~~ 74 (153)
.-.+..+.|+|..-|+.+++.+ |..-...++.++.+.+.+.|..
T Consensus 17 IK~vR~~tgl~L~eAK~~vd~~---p~~ik~~v~keeAe~ik~~Le~ 60 (68)
T PF00542_consen 17 IKEVREITGLGLKEAKKLVDSL---PKVIKEGVSKEEAEEIKKKLEA 60 (68)
T ss_dssp HHHHHHHC---HHHHHHHHCTT---TEEEEEEE-HHHHHHHHHHHHC
T ss_pred HHHHHHHhCCcHHHHHHHHHhC---CHHHHcCCCHHHHHHHHHHHHH
Confidence 4567889999999999999988 4555556889999999998875
No 144
>PRK07945 hypothetical protein; Provisional
Probab=31.97 E-value=29 Score=29.71 Aligned_cols=21 Identities=33% Similarity=0.623 Sum_probs=18.6
Q ss_pred ehhhccccchhhHHHHHHHhC
Q 031787 30 ALTSIKGIGRRLANIVCKKAD 50 (153)
Q Consensus 30 aLt~I~GIG~~~A~~Ic~~lg 50 (153)
.|++++|||..+|..|-+.+.
T Consensus 50 ~l~~~~giG~~~a~~i~e~~~ 70 (335)
T PRK07945 50 SLTSLPGIGPKTAKVIAQALA 70 (335)
T ss_pred CcccCCCcCHHHHHHHHHHHh
Confidence 699999999999999987654
No 145
>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=31.39 E-value=46 Score=20.92 Aligned_cols=14 Identities=29% Similarity=0.520 Sum_probs=12.7
Q ss_pred CCCHHHHHHHHHHH
Q 031787 59 ELSAAELDNLMVVV 72 (153)
Q Consensus 59 ~Ls~~ei~~L~~~i 72 (153)
.||++|+..|..+|
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 69999999999876
No 146
>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=30.14 E-value=58 Score=23.54 Aligned_cols=17 Identities=18% Similarity=0.335 Sum_probs=13.8
Q ss_pred CCCCHHHHHHHHHHHhC
Q 031787 58 GELSAAELDNLMVVVAN 74 (153)
Q Consensus 58 ~~Ls~~ei~~L~~~i~~ 74 (153)
+.||++|-+.|.+.|..
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 46999999999999965
No 147
>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=28.90 E-value=28 Score=32.78 Aligned_cols=36 Identities=19% Similarity=0.237 Sum_probs=26.8
Q ss_pred hhccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHH
Q 031787 32 TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDN 67 (153)
Q Consensus 32 t~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~ 67 (153)
-+|.|+|++++.++.+..+|..-.-+-.|+.+++..
T Consensus 435 l~I~GLG~k~i~~L~~~g~I~~~~Dl~~L~~~~L~~ 470 (652)
T TIGR00575 435 MDIEGLGDKVIEQLFEKKLVRSVADLYALKKEDLLE 470 (652)
T ss_pred cCCCCcCHHHHHHHHHcCCcCCHHHHHhcCHHHHhh
Confidence 368999999999999998886544455666555544
No 148
>KOG2875 consensus 8-oxoguanine DNA glycosylase [Replication, recombination and repair]
Probab=28.84 E-value=24 Score=30.34 Aligned_cols=22 Identities=32% Similarity=0.582 Sum_probs=19.0
Q ss_pred eeeehhhccccchhhHHHHHHH
Q 031787 27 IMFALTSIKGIGRRLANIVCKK 48 (153)
Q Consensus 27 i~~aLt~I~GIG~~~A~~Ic~~ 48 (153)
+.-+|..++|||++.|..||-.
T Consensus 216 ar~~L~~lpGVG~KVADCI~Lm 237 (323)
T KOG2875|consen 216 AREALCSLPGVGPKVADCICLM 237 (323)
T ss_pred HHHHHhcCCCCcchHhhhhhhh
Confidence 4568999999999999999954
No 149
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=28.77 E-value=31 Score=32.93 Aligned_cols=40 Identities=15% Similarity=0.212 Sum_probs=28.2
Q ss_pred eeeeehhhccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHH
Q 031787 26 KIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDN 67 (153)
Q Consensus 26 ~i~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~ 67 (153)
.+.-.|..|.|||+..+..|++.+| .-..+..-+.++|..
T Consensus 634 ~~~s~L~~IPGIGpkr~k~LL~~FG--Sle~I~~AS~eELa~ 673 (694)
T PRK14666 634 ALTGELQRVEGIGPATARLLWERFG--SLQAMAAAGEEGLAA 673 (694)
T ss_pred hhHhHHhhCCCCCHHHHHHHHHHhC--CHHHHHhcCHHHHHh
Confidence 3456789999999999999999988 223344445555433
No 150
>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=28.46 E-value=23 Score=29.98 Aligned_cols=24 Identities=17% Similarity=0.379 Sum_probs=20.2
Q ss_pred ehhhccccchhhHHHHHHHhCCCC
Q 031787 30 ALTSIKGIGRRLANIVCKKADVDM 53 (153)
Q Consensus 30 aLt~I~GIG~~~A~~Ic~~lgi~~ 53 (153)
.+++++|||..+|..|.+.+.=..
T Consensus 46 ~~~~ipgiG~~ia~kI~E~~~tG~ 69 (307)
T cd00141 46 EAKKLPGIGKKIAEKIEEILETGK 69 (307)
T ss_pred HhcCCCCccHHHHHHHHHHHHcCC
Confidence 568999999999999998876433
No 151
>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]
Probab=27.83 E-value=48 Score=26.45 Aligned_cols=24 Identities=17% Similarity=0.336 Sum_probs=21.4
Q ss_pred eehhhccccchhhHHHHHHHhCCC
Q 031787 29 FALTSIKGIGRRLANIVCKKADVD 52 (153)
Q Consensus 29 ~aLt~I~GIG~~~A~~Ic~~lgi~ 52 (153)
.++|..+|+|+.++...++.+|++
T Consensus 3 I~ITGTPGvGKTT~~~~L~~lg~~ 26 (180)
T COG1936 3 IAITGTPGVGKTTVCKLLRELGYK 26 (180)
T ss_pred EEEeCCCCCchHHHHHHHHHhCCc
Confidence 678999999999999999988875
No 152
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=27.76 E-value=34 Score=29.34 Aligned_cols=22 Identities=18% Similarity=0.428 Sum_probs=19.5
Q ss_pred ehhhccccchhhHHHHHHHhCC
Q 031787 30 ALTSIKGIGRRLANIVCKKADV 51 (153)
Q Consensus 30 aLt~I~GIG~~~A~~Ic~~lgi 51 (153)
-|++++|||..+|..|.+.+.=
T Consensus 49 ~l~~lpgIG~~ia~kI~Eil~t 70 (334)
T smart00483 49 DLKGLPGIGDKIKKKIEEIIET 70 (334)
T ss_pred HHhcCCCccHHHHHHHHHHHHh
Confidence 5889999999999999988763
No 153
>KOG0650 consensus WD40 repeat nucleolar protein Bop1, involved in ribosome biogenesis [Translation, ribosomal structure and biogenesis]
Probab=27.69 E-value=77 Score=30.08 Aligned_cols=48 Identities=23% Similarity=0.428 Sum_probs=35.5
Q ss_pred CCCCcCCCCCHHHHHHHHHHHhCCCCccCCccccCccCCcCCCcchhhhhhhHHH
Q 031787 52 DMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDM 106 (153)
Q Consensus 52 ~~~~kv~~Ls~~ei~~L~~~i~~~~~~~ip~w~~nr~kd~~tg~~~~li~~dL~~ 106 (153)
+..+-..-...++++++...|+.| +.| ++.+|..||++..|...+++.
T Consensus 142 ~gkkI~kp~k~~~ld~fl~~iedp-----~~W--r~v~Dk~tG~dv~LTkEev~l 189 (733)
T KOG0650|consen 142 DGKKITKPAKGDELDSFLAKIEDP-----DYW--RKVKDKMTGKDVNLTKEEVKL 189 (733)
T ss_pred cccEecCCCccchHHHHHHhhcCc-----chh--ccccccCCCceeeecHHHHHH
Confidence 333444455667899988888874 346 889999999999888877643
No 154
>COG1636 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.56 E-value=46 Score=26.99 Aligned_cols=82 Identities=13% Similarity=0.222 Sum_probs=51.4
Q ss_pred HhCCCCCCcCCCCCHHHHHHHHHHHhCCCCccCCccccCccCCcCCCcchhhhhhhHHHHHHHhhhhhhccceeecccCC
Q 031787 48 KADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHY 127 (153)
Q Consensus 48 ~lgi~~~~kv~~Ls~~ei~~L~~~i~~~~~~~ip~w~~nr~kd~~tg~~~~li~~dL~~~~~~~I~rl~~i~syRG~RH~ 127 (153)
.|+|+|.+.+ .||+.+-.-++++ |.++.|..|.+|..-+ .......-..+|-| .+|=|+ .
T Consensus 117 tL~iSp~Kn~-----~qin~~G~~~~k~--y~V~yl~~dfrK~gg~-------~r~~elske~~~Yr----Q~YCGC--v 176 (204)
T COG1636 117 TLLISPKKNM-----NQINEIGERAAKP--YGVVYLPSNFRKNGGY-------QRSIELSKEENIYR----QEYCGC--V 176 (204)
T ss_pred heecCcccCH-----HHHHHHhHHhhcc--cCceecCcccccccch-------HHHHHHHHHHhHHH----hhccch--h
Confidence 3455554433 4777777777775 8899999998874332 11111122223333 577776 4
Q ss_pred CCCccCCcCCcccCCCccceee
Q 031787 128 WGLRVRGQHTKTTGRRGKTVGV 149 (153)
Q Consensus 128 ~gLpvRGQRT~tNart~~~~~v 149 (153)
.+|.-.+|+-++++|-...+|.
T Consensus 177 ysl~~q~~~~~~~~r~~~~~~~ 198 (204)
T COG1636 177 YSLKDQNEDRKEVNRQAIPFGK 198 (204)
T ss_pred hhHhhhcchhhhhchhhhhHHh
Confidence 6788888888888887776664
No 155
>PRK05898 dnaE DNA polymerase III DnaE; Validated
Probab=27.41 E-value=1.1e+02 Score=30.51 Aligned_cols=26 Identities=35% Similarity=0.506 Sum_probs=22.8
Q ss_pred CeeeeeehhhccccchhhHHHHHHHh
Q 031787 24 KQKIMFALTSIKGIGRRLANIVCKKA 49 (153)
Q Consensus 24 ~k~i~~aLt~I~GIG~~~A~~Ic~~l 49 (153)
+..|.++|..|+|||...|..|.+.-
T Consensus 747 ~~~Ir~gL~~Ikgig~~~~~~I~~~R 772 (971)
T PRK05898 747 KQIIRFGFNTIKGFGDELLKKIKSAL 772 (971)
T ss_pred CCeEEecchhcCCcCHHHHHHHHHHH
Confidence 45799999999999999999998643
No 156
>TIGR00194 uvrC excinuclease ABC, C subunit. This family consists of the DNA repair enzyme UvrC, an ABC excinuclease subunit which interacts with the UvrA/UvrB complex to excise UV-damaged nucleotide segments.
Probab=27.19 E-value=40 Score=31.28 Aligned_cols=25 Identities=20% Similarity=0.278 Sum_probs=21.8
Q ss_pred eeeeehhhccccchhhHHHHHHHhC
Q 031787 26 KIMFALTSIKGIGRRLANIVCKKAD 50 (153)
Q Consensus 26 ~i~~aLt~I~GIG~~~A~~Ic~~lg 50 (153)
.+.-.|..|+|||++....+++.+|
T Consensus 538 ~~~S~Ld~I~GIG~kr~~~LL~~Fg 562 (574)
T TIGR00194 538 SLQSPLLKIPGVGEKRVQKLLKYFG 562 (574)
T ss_pred HHHHHHhcCCCCCHHHHHHHHHHcC
Confidence 3456789999999999999999887
No 157
>PF06394 Pepsin-I3: Pepsin inhibitor-3-like repeated domain; InterPro: IPR010480 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. The members of this group of proteins belong to MEROPS inhibitor family I33, clan IR; the nematode aspartyl protease inhibitors or Aspins. They are restricted to parasitic nematode species. Structural features common to the nematode Aspins include the presence of a signal peptide sequence and the conservation of all four cysteine residues in the mature protein. The Y[V.A]RDLT sequence motif has been suggested as being of crucial functional importance in several filarial nematode inhibitors [], this sequence is not conserved in Tco-API-1 from Trichostrongylus colubriformis (Black scour worm) and it has been demonstrated that Tco-API-1, is not an Aspin as it does not inhibit porcine pepsin []. Related inhibitors from Onchocerca volvulus, Ov33 [] and Ascaris suum (Pig roundworm), PI-3 [] inhibit the in vitro activity of aspartyl proteases such as pepsin and cathepsin E (MEROPS peptidase family A1). Aspin may facilitate the safe passage of the eggs of Ascaris through the host stomach without digestion by pepsin [, ]. The other parasitic nematodes known to express homologous proteins do not pass through the stomach of their hosts []. Several proteins in the family are potent allergens in mammals. The three-dimensional structures of pepsin inhibitor-3 (PI-3) from A. suum and of the complex between PI-3 and porcine pepsin at 1. 75 A and 2.45 A resolution, respectively, have revealed the mechanism of aspartic protease inhibition. PI-3 has a new fold consisting of two identical domains, each comprising an antiparallel beta-sheet flanked by an alpha-helix. In the enzyme-inhibitor complex, the N-terminal beta-strand of PI-3 pairs with one strand of the 'active site flap' (residues 70-82) of pepsin, thus forming an eight-stranded beta-sheet that spans the two proteins. PI-3 has a novel mode of inhibition, using its N-terminal residues to occupy and therefore block the first three binding pockets in pepsin for substrate residues C-terminal to the scissile bond (S1'-S3') [].; PDB: 1F32_A 1F34_B.
Probab=27.02 E-value=38 Score=23.29 Aligned_cols=21 Identities=24% Similarity=0.249 Sum_probs=15.9
Q ss_pred CCcCCCCCHHHHHHHHHHHhC
Q 031787 54 NKRAGELSAAELDNLMVVVAN 74 (153)
Q Consensus 54 ~~kv~~Ls~~ei~~L~~~i~~ 74 (153)
...+.+||++|..+|.++-++
T Consensus 34 g~~~R~Lt~~E~~eL~~y~~~ 54 (76)
T PF06394_consen 34 GKYARDLTPDEQQELKTYQKK 54 (76)
T ss_dssp TCEEEE--HHHHHHHHHHHHH
T ss_pred CEeeccCCHHHHHHHHHHHHH
Confidence 456889999999999998765
No 158
>PF15614 WHIM3: WSTF, HB1, Itc1p, MBD9 motif 3
Probab=26.41 E-value=1.2e+02 Score=18.82 Aligned_cols=37 Identities=24% Similarity=0.293 Sum_probs=23.2
Q ss_pred CHHHHHHHHHHHhCCCCccCCccccCccCCcCCCcchhhhhhhHHHHHHHhhhhhhcc
Q 031787 61 SAAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKI 118 (153)
Q Consensus 61 s~~ei~~L~~~i~~~~~~~ip~w~~nr~kd~~tg~~~~li~~dL~~~~~~~I~rl~~i 118 (153)
+++|++.|.+++.+| -++ =|..|+..+....+.+-.|
T Consensus 6 ~~e~ld~L~~aL~~p--rG~-------------------RE~~L~~~L~~~~k~~~~~ 42 (46)
T PF15614_consen 6 DPEELDELLKALENP--RGK-------------------RESKLKKELDKHRKGPLEI 42 (46)
T ss_pred CHHHHHHHHHHHcCc--ccH-------------------hHHHHHHHHHHHhcchhhh
Confidence 578999999888554 222 3667776666655444333
No 159
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=26.25 E-value=49 Score=27.71 Aligned_cols=38 Identities=24% Similarity=0.309 Sum_probs=25.6
Q ss_pred eehhhccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHH
Q 031787 29 FALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDN 67 (153)
Q Consensus 29 ~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~ 67 (153)
..|..++|||+.+|..+ ...||..-.-+-+++++++.+
T Consensus 6 ~~l~~l~gIg~~~a~~L-~~~Gi~t~~dl~~~~~~~L~~ 43 (317)
T PRK04301 6 KDLEDLPGVGPATAEKL-REAGYDTVEAIAVASPKELSE 43 (317)
T ss_pred ccHhhcCCCCHHHHHHH-HHcCCCCHHHHHcCCHHHHHH
Confidence 46789999998887765 466777555555555555433
No 160
>PF13551 HTH_29: Winged helix-turn helix
Probab=26.17 E-value=1.5e+02 Score=19.97 Aligned_cols=46 Identities=20% Similarity=0.220 Sum_probs=33.1
Q ss_pred ehhhccccchhhHHHHHHH---hC---CCC----CCcCCC-CCHHHHHHHHHHHhCC
Q 031787 30 ALTSIKGIGRRLANIVCKK---AD---VDM----NKRAGE-LSAAELDNLMVVVANP 75 (153)
Q Consensus 30 aLt~I~GIG~~~A~~Ic~~---lg---i~~----~~kv~~-Ls~~ei~~L~~~i~~~ 75 (153)
.+....||++.+.....+. -| +.+ .-+... |++++.+.|.+++.++
T Consensus 17 ~ia~~lg~s~~Tv~r~~~~~~~~G~~~l~~~~~~~g~~~~~l~~~~~~~l~~~~~~~ 73 (112)
T PF13551_consen 17 EIARRLGISRRTVYRWLKRYREGGIEGLLPRKPRGGRPRKRLSEEQRAQLIELLREN 73 (112)
T ss_pred HHHHHHCcCHHHHHHHHHHHHcccHHHHHhccccCCCCCCCCCHHHHHHHHHHHHHC
Confidence 4566788999999888877 23 333 123444 9999999999999763
No 161
>PF03118 RNA_pol_A_CTD: Bacterial RNA polymerase, alpha chain C terminal domain; InterPro: IPR011260 The core of the bacterial RNA polymerase (RNAP) consists of four subunits, two alpha, a beta and a beta', which are conserved from bacteria to mammals. The alpha subunit (RpoA) initiates RNAP assembly by dimerising to form a platform on which the beta subunits can interact. The alpha subunit consists of a N-terminal domain (NTD) and a C-terminal domain (CTD), connected by a short linker. The NTD is essential for RNAP assembly, while the CTD is necessary for transcription regulation, interacting with transcription factors and promoter upstream elements. In Escherichia coli, the catabolite activator protein (CAP or CRP) was shown to exert its effect through its interactions with the CTD, where CAP binding to CTD promotes RNAP binding to promoter DNA, thereby stimulating transcription initiation at class I CAP-dependent promoters. At class II CAP-dependent promoters, the interaction of CAP with CTD is one of multiple interactions involved in activation []. The CTD has a compact structure of four helices and two long arms enclosing its hydrophobic core, making its folding topology distinct from most other binding proteins. The upstream promoter element-binding site is formed from helices 1 and 4 [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3N97_B 1XS9_D 3K4G_A 3N4M_B 1COO_A 1LB2_E 3IYD_A 1Z3E_B 3GFK_B 3IHQ_B ....
Probab=25.37 E-value=48 Score=21.70 Aligned_cols=20 Identities=25% Similarity=0.360 Sum_probs=17.2
Q ss_pred ehhhccccchhhHHHHHHHh
Q 031787 30 ALTSIKGIGRRLANIVCKKA 49 (153)
Q Consensus 30 aLt~I~GIG~~~A~~Ic~~l 49 (153)
-|.+|+|+|......|.+.+
T Consensus 45 ~L~~i~n~G~ksl~EI~~~L 64 (66)
T PF03118_consen 45 DLLKIKNFGKKSLEEIKEKL 64 (66)
T ss_dssp HHHTSTTSHHHHHHHHHHHH
T ss_pred HHHhCCCCCHhHHHHHHHHH
Confidence 57899999999999988765
No 162
>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=25.07 E-value=31 Score=23.04 Aligned_cols=43 Identities=12% Similarity=0.196 Sum_probs=26.4
Q ss_pred eehhhccccchhhHHHHHHHhCCCCCC-cCCCCCHHHHHHHHHHH
Q 031787 29 FALTSIKGIGRRLANIVCKKADVDMNK-RAGELSAAELDNLMVVV 72 (153)
Q Consensus 29 ~aLt~I~GIG~~~A~~Ic~~lgi~~~~-kv~~Ls~~ei~~L~~~i 72 (153)
+.++.++|+|...|.++.+-.= ||.. ++-.++-++.....+.+
T Consensus 6 ~~I~RfKGLGEM~p~qL~eTTm-dP~~R~L~~V~i~d~~~~~~~~ 49 (65)
T PF00986_consen 6 VEIQRFKGLGEMNPDQLWETTM-DPETRRLIRVTIEDAEEADELF 49 (65)
T ss_dssp TEEEESSSGGGS-HHHHHHHHT-STTTTEEEEEEHCCHHHHHHHH
T ss_pred ceeEEecccccCCHHHHHHHcc-CccceEEEEEEECCHHHHHHHH
Confidence 5578999999999999987653 4444 44444444444444443
No 163
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=24.96 E-value=51 Score=19.75 Aligned_cols=29 Identities=24% Similarity=0.371 Sum_probs=14.9
Q ss_pred CCCHHHHHHHHHHHhCCCCccCCccccCcc
Q 031787 59 ELSAAELDNLMVVVANPRQFKIPDWFLNRQ 88 (153)
Q Consensus 59 ~Ls~~ei~~L~~~i~~~~~~~ip~w~~nr~ 88 (153)
..+.++++.|.+.+.-+ ...|-.||-|+|
T Consensus 24 ~P~~~~~~~la~~~~l~-~~qV~~WF~nrR 52 (56)
T smart00389 24 YPSREEREELAAKLGLS-ERQVKVWFQNRR 52 (56)
T ss_pred CCCHHHHHHHHHHHCcC-HHHHHHhHHHHh
Confidence 34556666666665321 223445666555
No 164
>TIGR02663 nifX nitrogen fixation protein NifX. Members of this family are NifX proteins encoded within operons for nitrogen fixation in a number of bacteria. NifX, NafY, and the C-terminal region of NifB all belong to the Pfam family pfam02579 and are involved in MoFe cofactor biosynthesis. NifX is a nitrogenase accessory protein with a role in expression of the MoFe cofactor.
Probab=24.65 E-value=82 Score=22.57 Aligned_cols=47 Identities=21% Similarity=0.263 Sum_probs=29.8
Q ss_pred cccchhhHHHHHHHhCCCCCC-cCCCCCHHHHHHHHHHHhCCCCccCCccccC
Q 031787 35 KGIGRRLANIVCKKADVDMNK-RAGELSAAELDNLMVVVANPRQFKIPDWFLN 86 (153)
Q Consensus 35 ~GIG~~~A~~Ic~~lgi~~~~-kv~~Ls~~ei~~L~~~i~~~~~~~ip~w~~n 86 (153)
.|||..-+. .+..+||.+-. ....-=++-++.|+..+.. .-|+||.+
T Consensus 70 ~~IG~~a~~-~L~~~gI~~~~~~~~~~v~eal~~l~~~~~~----~~~~w~~~ 117 (119)
T TIGR02663 70 LAIGGPAAA-KVVAAKIHPIKVNEPESISELLERLQKMLKG----NPPPWLRK 117 (119)
T ss_pred hhcCccHHH-HHHHcCCeeEecCCCccHHHHHHHHHHHHcC----CCCHHHHh
Confidence 367766444 45668998854 2222346677788888743 46889864
No 165
>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=24.52 E-value=1.5e+02 Score=24.21 Aligned_cols=30 Identities=13% Similarity=0.329 Sum_probs=20.5
Q ss_pred HHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCCCc
Q 031787 42 ANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQF 78 (153)
Q Consensus 42 A~~Ic~~lgi~~~~kv~~Ls~~ei~~L~~~i~~~~~~ 78 (153)
...+++.++|+ ||++|++.|..++.+..+.
T Consensus 181 V~~~~~~~~i~-------ls~~q~~~i~~l~~~~~~~ 210 (225)
T PF06207_consen 181 VNNVLNNYNIN-------LSDEQIQQIVNLMKKIQNL 210 (225)
T ss_pred HHHHHHHcCCC-------CCHHHHHHHHHHHHHHHcC
Confidence 34455666665 8888888888888774333
No 166
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=24.25 E-value=37 Score=27.50 Aligned_cols=22 Identities=27% Similarity=0.389 Sum_probs=17.3
Q ss_pred ehhhccccchhhHHHHHHHhCC
Q 031787 30 ALTSIKGIGRRLANIVCKKADV 51 (153)
Q Consensus 30 aLt~I~GIG~~~A~~Ic~~lgi 51 (153)
.|.+|+|||...|.+|.....+
T Consensus 61 eL~~i~GiG~aka~~l~a~~El 82 (218)
T TIGR00608 61 ELSSVPGIGEAKAIQLKAAVEL 82 (218)
T ss_pred HHHhCcCCcHHHHHHHHHHHHH
Confidence 3889999999999888655443
No 167
>PF12558 DUF3744: ATP-binding cassette cobalt transporter; InterPro: IPR022216 This domain family is found in bacteria, and is approximately 70 amino acids in length. The family is found in association with PF00005 from PFAM. There is a conserved REP sequence motif. There is a single completely conserved residue P that may be functionally important. The proteins in this family are frequently annotated as ABC Cobalt transporters however there is little accompanying literature to confirm this. ; GO: 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances
Probab=23.92 E-value=72 Score=21.30 Aligned_cols=41 Identities=24% Similarity=0.300 Sum_probs=28.4
Q ss_pred hccccchhhHHHHHHHhCCCCCC--cCCCCCHHHHHHHHHHHh
Q 031787 33 SIKGIGRRLANIVCKKADVDMNK--RAGELSAAELDNLMVVVA 73 (153)
Q Consensus 33 ~I~GIG~~~A~~Ic~~lgi~~~~--kv~~Ls~~ei~~L~~~i~ 73 (153)
.=.||-+......++.+|+|-+. .+.+|+.=.++.+...|.
T Consensus 6 ~~~GIREPLYitALk~ag~~l~~~~~l~~l~~l~~~~~~~~l~ 48 (74)
T PF12558_consen 6 EQNGIREPLYITALKYAGVDLTKEDHLSDLDNLDLSDVKEKLQ 48 (74)
T ss_pred hhcCCCccHHHHHHHHcCCCcccCCCccCHHHCCcHHHHHHHH
Confidence 34799999999999999998665 445555444555444443
No 168
>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=23.86 E-value=50 Score=27.35 Aligned_cols=36 Identities=25% Similarity=0.305 Sum_probs=23.5
Q ss_pred hhhccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHH
Q 031787 31 LTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDN 67 (153)
Q Consensus 31 Lt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~ 67 (153)
+..++|||+.++..+. ..||..-..+...+++++..
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 4578999998888765 56666555555555555543
No 169
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=23.81 E-value=39 Score=31.53 Aligned_cols=43 Identities=26% Similarity=0.271 Sum_probs=33.0
Q ss_pred CeeeeeehhhccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHH
Q 031787 24 KQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNL 68 (153)
Q Consensus 24 ~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~L 68 (153)
+..+...|-.|.|||+....++++.+| .-..+.+-|.+|+..+
T Consensus 525 k~~~~s~Ld~I~GiG~~r~~~LL~~Fg--s~~~i~~As~eel~~v 567 (581)
T COG0322 525 KAMLQSSLDDIPGIGPKRRKALLKHFG--SLKGIKSASVEELAKV 567 (581)
T ss_pred hhhhcCccccCCCcCHHHHHHHHHHhh--CHHHHHhcCHHHHHHc
Confidence 334567788999999999999999988 3455666677777664
No 170
>PF13276 HTH_21: HTH-like domain
Probab=23.68 E-value=42 Score=20.97 Aligned_cols=35 Identities=14% Similarity=0.264 Sum_probs=28.7
Q ss_pred CCCCeeeeeehhhccc--cchhhHHHHHHHhCCCCCC
Q 031787 21 VDGKQKIMFALTSIKG--IGRRLANIVCKKADVDMNK 55 (153)
Q Consensus 21 l~~~k~i~~aLt~I~G--IG~~~A~~Ic~~lgi~~~~ 55 (153)
.-|...|...|..-+| ||.+++..|++.+||....
T Consensus 20 ~yG~rri~~~L~~~~~~~v~~krV~RlM~~~gL~~~~ 56 (60)
T PF13276_consen 20 TYGYRRIWAELRREGGIRVSRKRVRRLMREMGLRSKR 56 (60)
T ss_pred CeehhHHHHHHhccCcccccHHHHHHHHHHcCCcccC
Confidence 5677788888888776 7999999999999997643
No 171
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=23.01 E-value=60 Score=19.99 Aligned_cols=21 Identities=14% Similarity=0.069 Sum_probs=17.1
Q ss_pred eehhhccccchhhHHHHHHHh
Q 031787 29 FALTSIKGIGRRLANIVCKKA 49 (153)
Q Consensus 29 ~aLt~I~GIG~~~A~~Ic~~l 49 (153)
.-|...+||+.++|.+++..+
T Consensus 23 ~~La~~FgIs~stvsri~~~~ 43 (53)
T PF13613_consen 23 QDLAYRFGISQSTVSRIFHEW 43 (53)
T ss_pred hHHhhheeecHHHHHHHHHHH
Confidence 456788999999999998653
No 172
>PF14794 DUF4479: Domain of unknown function (DUF4479); PDB: 3BU2_C.
Probab=22.83 E-value=70 Score=21.60 Aligned_cols=24 Identities=13% Similarity=0.248 Sum_probs=12.4
Q ss_pred CCCCCCcCCCCCHHHHHHHHHHHhC
Q 031787 50 DVDMNKRAGELSAAELDNLMVVVAN 74 (153)
Q Consensus 50 gi~~~~kv~~Ls~~ei~~L~~~i~~ 74 (153)
.|..+=.+ .||+++++.|.++|.+
T Consensus 39 ~i~~~G~V-~Lt~eqv~~LN~~l~~ 62 (73)
T PF14794_consen 39 EIEGNGQV-FLTEEQVAKLNQALQK 62 (73)
T ss_dssp ------------HHHHHHHHHHHHH
T ss_pred eecCCcCE-EcCHHHHHHHHHHHHH
Confidence 33333334 4999999999999986
No 173
>PF02879 PGM_PMM_II: Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II; InterPro: IPR005845 The alpha-D-phosphohexomutase superfamily is composed of four related enzymes, each of which catalyses a phosphoryl transfer on their sugar substrates: phosphoglucomutase (PGM), phosphoglucomutase/phosphomannomutase (PGM/PMM), phosphoglucosamine mutase (PNGM), and phosphoacetylglucosamine mutase (PAGM) []. PGM (5.4.2.2 from EC) converts D-glucose 1-phosphate into D-glucose 6-phosphate, and participates in both the breakdown and synthesis of glucose []. PGM/PMM (5.4.2.2 from EC; 5.4.2.8 from EC) are primarily bacterial enzymes that use either glucose or mannose as substrate, participating in the biosynthesis of a variety of carbohydrates such as lipopolysaccharides and alginate [, ]. Both PNGM (5.4.2.3 from EC) and PAGM (5.4.2.10 from EC) are involved in the biosynthesis of UDP-N-acetylglucosamine [, ]. Despite differences in substrate specificity, these enzymes share a similar catalytic mechanism, converting 1-phospho-sugars to 6-phospho-sugars via a biphosphorylated 1,6-phospho-sugar. The active enzyme is phosphorylated at a conserved serine residue and binds one magnesium ion; residues around the active site serine are well conserved among family members. The reaction mechanism involves phosphoryl transfer from the phosphoserine to the substrate to create a biophosphorylated sugar, followed by a phosphoryl transfer from the substrate back to the enzyme []. The structures of PGM and PGM/PMM have been determined, and were found to be very similar in topology. These enzymes are both composed of four domains and a large central active site cleft, where each domain contains residues essential for catalysis and/or substrate recognition. Domain I contains the catalytic phosphoserine, domain II contains a metal-binding loop to coordinate the magnesium ion, domain III contains the sugar-binding loop that recognises the two different binding orientations of the 1- and 6-phospho-sugars, and domain IV contains a phosphate-binding site required for orienting the incoming phospho-sugar substrate. This entry represents domain II found in alpha-D-phosphohexomutase enzymes. This domain has a 3-layer alpha/beta/alpha topology.; GO: 0016868 intramolecular transferase activity, phosphotransferases, 0005975 carbohydrate metabolic process; PDB: 2F7L_A 3PDK_B 1KFQ_B 1KFI_A 1C47_A 1VKL_B 1LXT_A 1JDY_B 3PMG_A 1C4G_B ....
Probab=22.73 E-value=29 Score=23.93 Aligned_cols=40 Identities=10% Similarity=0.248 Sum_probs=29.3
Q ss_pred hhhhhcC-ccCCCCeeeeeehhhccccchhhHHHHHHHhCC
Q 031787 12 HILRVLN-TNVDGKQKIMFALTSIKGIGRRLANIVCKKADV 51 (153)
Q Consensus 12 ~~vri~~-~~l~~~k~i~~aLt~I~GIG~~~A~~Ic~~lgi 51 (153)
++...++ ...-....+...+...+|.|...+..|++++|.
T Consensus 6 ~l~~~~~~~~~~~~~~~kivvD~~~G~~~~~~~~ll~~lg~ 46 (104)
T PF02879_consen 6 SLLSFIDILEAIKKSGLKIVVDCMNGAGSDILPRLLERLGC 46 (104)
T ss_dssp HHHHTSCHHHHHHHTTCEEEEE-TTSTTHHHHHHHHHHTTC
T ss_pred HHhhhccchhhcccCCCEEEEECCCCHHHHHHHHHHHHcCC
Confidence 3444444 333345556788889999999999999999998
No 174
>COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair]
Probab=22.69 E-value=51 Score=28.84 Aligned_cols=36 Identities=14% Similarity=0.194 Sum_probs=27.2
Q ss_pred hhhhhhhcCccCCCCeeeeeehhhccccchhhHHHHHHH
Q 031787 10 FQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKK 48 (153)
Q Consensus 10 ~~~~vri~~~~l~~~k~i~~aLt~I~GIG~~~A~~Ic~~ 48 (153)
.+.++.-.|-.+|++. -.|..++|||.++|.+|+..
T Consensus 97 A~~v~~~~~G~~P~~~---~~l~~LpGiG~yTa~Ail~~ 132 (342)
T COG1194 97 AQEVVERHGGEFPDDE---EELAALPGVGPYTAGAILSF 132 (342)
T ss_pred HHHHHHHcCCCCCCCH---HHHHhCCCCcHHHHHHHHHH
Confidence 3566677777777765 45677999999999999853
No 175
>PRK05755 DNA polymerase I; Provisional
Probab=22.62 E-value=73 Score=30.82 Aligned_cols=36 Identities=19% Similarity=0.387 Sum_probs=24.3
Q ss_pred cchhhhhhhcCccCCCCeeeeeehhhccccchhhHHHHHHHhC
Q 031787 8 EDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKAD 50 (153)
Q Consensus 8 ~~~~~~vri~~~~l~~~k~i~~aLt~I~GIG~~~A~~Ic~~lg 50 (153)
++|-.+.=+.|-.-| .+..++|||+++|..+++..|
T Consensus 173 ~q~~d~~~L~GD~sD-------nipGv~GiG~ktA~~Ll~~~g 208 (880)
T PRK05755 173 EQIIDYLALMGDSSD-------NIPGVPGIGEKTAAKLLQEYG 208 (880)
T ss_pred HHHHHHHHHhCCccC-------CCCCCCCccHHHHHHHHHHcC
Confidence 445555555662211 245689999999999998866
No 176
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=22.55 E-value=36 Score=32.13 Aligned_cols=35 Identities=20% Similarity=0.294 Sum_probs=25.2
Q ss_pred hhccccchhhHHHHHHHhCCCCCCcCCCCCHHHHH
Q 031787 32 TSIKGIGRRLANIVCKKADVDMNKRAGELSAAELD 66 (153)
Q Consensus 32 t~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~ 66 (153)
-+|.|+|++++.++.+..+|..-.-+-.|+.+++.
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 46899999999999999988753334445544443
No 177
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=22.51 E-value=55 Score=31.72 Aligned_cols=38 Identities=26% Similarity=0.367 Sum_probs=28.5
Q ss_pred eeehhhccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHH
Q 031787 28 MFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNL 68 (153)
Q Consensus 28 ~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~L 68 (153)
.| |.+++|||+..|..|++.+| .=..+-.++.+|+..+
T Consensus 757 ~~-L~~lPgI~~~~a~~ll~~f~--si~~l~~as~eeL~~~ 794 (814)
T TIGR00596 757 DF-LLKLPGVTKKNYRNLRKKVK--SIRELAKLSQNELNEL 794 (814)
T ss_pred HH-HHHCCCCCHHHHHHHHHHcC--CHHHHHhCCHHHHHHH
Confidence 45 77999999999999999865 3345556666666553
No 178
>PF11460 DUF3007: Protein of unknown function (DUF3007); InterPro: IPR021562 This is a family of uncharacterised proteins found in bacteria and eukaryotes.
Probab=22.48 E-value=45 Score=24.34 Aligned_cols=20 Identities=40% Similarity=0.517 Sum_probs=16.1
Q ss_pred CCcCCCCCHHHHHHHHHHHh
Q 031787 54 NKRAGELSAAELDNLMVVVA 73 (153)
Q Consensus 54 ~~kv~~Ls~~ei~~L~~~i~ 73 (153)
.+|..+||+||+++|.+-|+
T Consensus 84 qkRle~l~~eE~~~L~~eie 103 (104)
T PF11460_consen 84 QKRLEELSPEELEALQAEIE 103 (104)
T ss_pred HHHHHhCCHHHHHHHHHHhc
Confidence 45778899999999888764
No 179
>KOG0821 consensus Predicted ribosomal RNA adenine dimethylase [RNA processing and modification]
Probab=21.97 E-value=1.2e+02 Score=25.70 Aligned_cols=35 Identities=23% Similarity=0.263 Sum_probs=31.6
Q ss_pred hhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 031787 40 RLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 74 (153)
Q Consensus 40 ~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~L~~~i~~ 74 (153)
..+..+++++.|||+.+.-+|+-||...|.+..+.
T Consensus 270 E~~~~Ll~~~~idpT~r~~~L~iEQf~~LAE~Y~E 304 (326)
T KOG0821|consen 270 ESTGRLLELADIDPTLRPRQLSIEQFKSLAEVYRE 304 (326)
T ss_pred HHHHHHHHHhcCCCccCceeeeHHHHHHHHHHHHH
Confidence 46778999999999999999999999999998765
No 180
>PRK02362 ski2-like helicase; Provisional
Probab=21.84 E-value=58 Score=30.65 Aligned_cols=39 Identities=15% Similarity=0.288 Sum_probs=31.2
Q ss_pred eehhhccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHH
Q 031787 29 FALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNL 68 (153)
Q Consensus 29 ~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~L 68 (153)
..|..++|||+..|.++-+ +||..-..+-.++++++..|
T Consensus 652 ~~L~~ip~i~~~~a~~l~~-~gi~s~~dl~~~~~~~l~~~ 690 (737)
T PRK02362 652 LDLVGLRGVGRVRARRLYN-AGIESRADLRAADKSVVLAI 690 (737)
T ss_pred HHHhCCCCCCHHHHHHHHH-cCCCCHHHHHhCCHHHHHHH
Confidence 4567899999999977765 99988777777777777775
No 181
>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=21.82 E-value=88 Score=19.62 Aligned_cols=16 Identities=25% Similarity=0.333 Sum_probs=14.5
Q ss_pred CCCHHHHHHHHHHHhC
Q 031787 59 ELSAAELDNLMVVVAN 74 (153)
Q Consensus 59 ~Ls~~ei~~L~~~i~~ 74 (153)
.||++|+..|..+|.+
T Consensus 74 ~ls~~e~~~l~ayl~s 89 (91)
T PF00034_consen 74 ILSDEEIADLAAYLRS 89 (91)
T ss_dssp TSSHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHH
Confidence 7999999999999864
No 182
>PRK00024 hypothetical protein; Reviewed
Probab=21.60 E-value=45 Score=27.04 Aligned_cols=22 Identities=36% Similarity=0.436 Sum_probs=17.6
Q ss_pred ehhhccccchhhHHHHHHHhCC
Q 031787 30 ALTSIKGIGRRLANIVCKKADV 51 (153)
Q Consensus 30 aLt~I~GIG~~~A~~Ic~~lgi 51 (153)
.|.+++|||+..|..|+....+
T Consensus 67 eL~~i~GIG~akA~~L~a~~El 88 (224)
T PRK00024 67 ELQSIKGIGPAKAAQLKAALEL 88 (224)
T ss_pred HHhhccCccHHHHHHHHHHHHH
Confidence 4889999999999888755444
No 183
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=21.50 E-value=71 Score=26.47 Aligned_cols=38 Identities=18% Similarity=0.300 Sum_probs=27.3
Q ss_pred ehhhccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHH
Q 031787 30 ALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNL 68 (153)
Q Consensus 30 aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~L 68 (153)
.|..|.|||...+..|++. ||..-..+..-+.++|..+
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 5788999999999999876 5555555555555555554
No 184
>KOG2519 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=21.49 E-value=1.1e+02 Score=27.82 Aligned_cols=35 Identities=23% Similarity=0.346 Sum_probs=27.8
Q ss_pred ccchhhhhhhcCccCCCCeeeeeehhhccccchhhHHHHHHHhC
Q 031787 7 NEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKAD 50 (153)
Q Consensus 7 ~~~~~~~vri~~~~l~~~k~i~~aLt~I~GIG~~~A~~Ic~~lg 50 (153)
.++|=.+-=++|+|-... |.|||+..|..+.+..+
T Consensus 216 ~~~fidL~lLlGCDYc~~---------I~Gig~~~al~lir~~~ 250 (449)
T KOG2519|consen 216 RESFIDLCLLLGCDYCPT---------IRGIGPKKALKLIRQHG 250 (449)
T ss_pred HHHHHHHHHHhcCccccc---------ccccChHHHHHHHHHhc
Confidence 356666667788885444 99999999999999988
No 185
>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=21.23 E-value=1.7e+02 Score=25.88 Aligned_cols=35 Identities=14% Similarity=0.095 Sum_probs=29.0
Q ss_pred hhHHHHHHHhCCCCCCc----CCCCCHHHHHHHHHHHhC
Q 031787 40 RLANIVCKKADVDMNKR----AGELSAAELDNLMVVVAN 74 (153)
Q Consensus 40 ~~A~~Ic~~lgi~~~~k----v~~Ls~~ei~~L~~~i~~ 74 (153)
..+....+++||+|..+ -++|+++.+..|.+..+.
T Consensus 289 ~k~r~~~~~~Gi~p~~K~iv~Sd~Lde~~i~~L~~~~~g 327 (377)
T cd01401 289 EKAIAHYEKLGIDPKTKTLVFSDGLDVEKALELYEYFKG 327 (377)
T ss_pred HHHHHHHHHcCCCCCCcEEEEcCCCCHHHHHHHHHHHcC
Confidence 35677788999999888 678999999999987654
No 186
>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=21.16 E-value=82 Score=23.98 Aligned_cols=37 Identities=14% Similarity=0.066 Sum_probs=30.1
Q ss_pred chhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhC
Q 031787 38 GRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 74 (153)
Q Consensus 38 G~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~L~~~i~~ 74 (153)
....|.+.++.+|+..=-.++.++.+-++.|.++|++
T Consensus 107 ~i~~a~~~L~~aG~~~if~vS~~~~eGi~eL~~~L~~ 143 (143)
T PF10662_consen 107 NIERAKKWLKNAGVKEIFEVSAVTGEGIEELKDYLEE 143 (143)
T ss_pred hHHHHHHHHHHcCCCCeEEEECCCCcCHHHHHHHHhC
Confidence 4456778888899988888888999999999888753
No 187
>COG1111 MPH1 ERCC4-like helicases [DNA replication, recombination, and repair]
Probab=20.89 E-value=63 Score=29.91 Aligned_cols=85 Identities=14% Similarity=0.201 Sum_probs=60.8
Q ss_pred CeeeeeehhhccccchhhHHHHHHHhCCCCCCcCCCCCHHHHHHHHHHHhCCC----CccCCccccCccCCcCCCcchhh
Q 031787 24 KQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPR----QFKIPDWFLNRQKDYKDGKYSQV 99 (153)
Q Consensus 24 ~k~i~~aLt~I~GIG~~~A~~Ic~~lgi~~~~kv~~Ls~~ei~~L~~~i~~~~----~~~ip~w~~nr~kd~~tg~~~~l 99 (153)
.++...|||.-+|=-......+|+-|||.. .-+..=.+.++.. ++.... +..+|.|+- .
T Consensus 161 k~~~ilgLTASPGs~~ekI~eV~~nLgIe~-vevrTE~d~DV~~---Yv~~~kve~ikV~lp~e~~-------------~ 223 (542)
T COG1111 161 KNPLILGLTASPGSDLEKIQEVVENLGIEK-VEVRTEEDPDVRP---YVKKIKVEWIKVDLPEEIK-------------E 223 (542)
T ss_pred cCceEEEEecCCCCCHHHHHHHHHhCCcce-EEEecCCCccHHH---hhccceeEEEeccCcHHHH-------------H
Confidence 344889999999999999999999999973 4444333444444 554311 122465544 3
Q ss_pred hhhhHHHHHHHhhhhhhccceeeccc
Q 031787 100 VSNALDMKLRDDLERLKKIRNHRGLR 125 (153)
Q Consensus 100 i~~dL~~~~~~~I~rl~~i~syRG~R 125 (153)
|-..|+..+++-.+.|++.+-|.+..
T Consensus 224 ir~~l~~~l~~~Lk~L~~~g~~~~~~ 249 (542)
T COG1111 224 IRDLLRDALKPRLKPLKELGVIESSS 249 (542)
T ss_pred HHHHHHHHHHHHHHHHHHcCceeccC
Confidence 67788888888999999999998876
No 188
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=20.83 E-value=91 Score=17.04 Aligned_cols=18 Identities=11% Similarity=0.036 Sum_probs=9.0
Q ss_pred ccchhhHHHHHHHhCCCC
Q 031787 36 GIGRRLANIVCKKADVDM 53 (153)
Q Consensus 36 GIG~~~A~~Ic~~lgi~~ 53 (153)
.+...++..||+.+|+++
T Consensus 36 ~~~~~~~~~i~~~~~~~~ 53 (56)
T smart00530 36 KPSLETLKKLAKALGVSL 53 (56)
T ss_pred CCCHHHHHHHHHHhCCCh
Confidence 334455555555555543
No 189
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=20.82 E-value=63 Score=28.10 Aligned_cols=20 Identities=30% Similarity=0.539 Sum_probs=17.3
Q ss_pred ehhhccccchhhHHHHHHHh
Q 031787 30 ALTSIKGIGRRLANIVCKKA 49 (153)
Q Consensus 30 aLt~I~GIG~~~A~~Ic~~l 49 (153)
++|.++|||+.+|..|-..+
T Consensus 54 ~~t~l~gIGk~ia~~I~e~l 73 (326)
T COG1796 54 RLTELPGIGKGIAEKISEYL 73 (326)
T ss_pred ccCCCCCccHHHHHHHHHHH
Confidence 58999999999999987654
No 190
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=20.71 E-value=78 Score=25.50 Aligned_cols=52 Identities=13% Similarity=0.150 Sum_probs=30.4
Q ss_pred chhhHHHHHHHhCCC---CCCcCCCCCHHHHHHHHHHHhCCCCcc-----------------CCccccCccC
Q 031787 38 GRRLANIVCKKADVD---MNKRAGELSAAELDNLMVVVANPRQFK-----------------IPDWFLNRQK 89 (153)
Q Consensus 38 G~~~A~~Ic~~lgi~---~~~kv~~Ls~~ei~~L~~~i~~~~~~~-----------------ip~w~~nr~k 89 (153)
+...+..+.-.+.++ |...--.+|.+|+.+|+.+++....+. +-.||.|||.
T Consensus 84 ~~~~~~~~~l~~~~~~~~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRt 155 (197)
T KOG0843|consen 84 GKDTMLEGFLLLPLRSMRPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRT 155 (197)
T ss_pred ccchhhhhhccccccccCCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhH
Confidence 333344444444444 333334579999999999887642111 4569999873
No 191
>PRK08609 hypothetical protein; Provisional
Probab=20.59 E-value=36 Score=31.35 Aligned_cols=24 Identities=25% Similarity=0.477 Sum_probs=20.3
Q ss_pred ehhhccccchhhHHHHHHHhCCCC
Q 031787 30 ALTSIKGIGRRLANIVCKKADVDM 53 (153)
Q Consensus 30 aLt~I~GIG~~~A~~Ic~~lgi~~ 53 (153)
.|++|+|||..+|..|.+.+.=..
T Consensus 49 ~l~~ipgIG~~ia~kI~Eil~tG~ 72 (570)
T PRK08609 49 DFTKLKGIGKGTAEVIQEYRETGE 72 (570)
T ss_pred hhccCCCcCHHHHHHHHHHHHhCC
Confidence 689999999999999998876333
Done!