Query gi|254780625|ref|YP_003065038.1| formamidopyrimidine-DNA glycosylase [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 289
No_of_seqs 122 out of 2796
Neff 7.7
Searched_HMMs 39220
Date Sun May 29 21:20:15 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780625.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR00577 fpg formamidopyrimid 100.0 0 0 610.7 21.0 273 1-288 1-292 (292)
2 PRK01103 formamidopyrimidine-D 100.0 0 0 586.9 24.8 272 1-289 1-272 (273)
3 COG0266 Nei Formamidopyrimidin 100.0 0 0 578.0 25.0 273 1-289 1-273 (273)
4 PRK13945 formamidopyrimidine-D 100.0 0 0 568.3 25.9 273 1-289 1-283 (283)
5 PRK10445 endonuclease VIII; Pr 100.0 0 0 511.3 24.1 260 1-289 1-263 (263)
6 pfam06831 H2TH Formamidopyrimi 100.0 8.4E-31 2.1E-35 217.9 6.6 93 142-240 1-93 (93)
7 pfam01149 Fapy_DNA_glyco Forma 100.0 1.6E-27 4E-32 196.9 14.0 116 2-126 1-117 (117)
8 pfam05833 FbpA Fibronectin-bin 98.0 9.9E-05 2.5E-09 50.5 10.2 79 141-228 162-240 (447)
9 pfam06827 zf-FPG_IleRS Zinc fi 97.7 2.7E-05 6.9E-10 54.1 2.8 29 260-289 1-29 (30)
10 COG1293 Predicted RNA-binding 97.5 0.0024 6.2E-08 41.5 10.3 71 145-226 168-238 (564)
11 PRK04184 DNA topoisomerase VI 97.0 0.003 7.6E-08 41.0 6.7 75 140-224 230-305 (533)
12 PTZ00134 40S ribosomal protein 96.7 0.0036 9.2E-08 40.4 5.2 50 164-222 25-74 (154)
13 pfam00416 Ribosomal_S13 Riboso 96.1 0.01 2.6E-07 37.5 4.6 51 164-223 10-60 (106)
14 PRK04053 rps13p 30S ribosomal 95.9 0.013 3.3E-07 36.8 4.3 53 163-224 19-71 (149)
15 COG0099 RpsM Ribosomal protein 95.5 0.012 3.1E-07 37.1 3.1 48 166-222 14-61 (121)
16 PRK05179 rpsM 30S ribosomal pr 95.5 0.014 3.7E-07 36.6 3.4 49 165-222 13-61 (122)
17 TIGR03629 arch_S13P archaeal r 95.3 0.023 5.8E-07 35.3 4.0 51 164-223 16-66 (144)
18 TIGR03631 bact_S13 30S ribosom 95.1 0.025 6.3E-07 35.1 3.6 48 165-221 11-58 (113)
19 CHL00137 rps13 ribosomal prote 94.8 0.039 1E-06 33.8 3.9 48 165-221 13-60 (122)
20 PRK12495 hypothetical protein; 93.1 0.026 6.5E-07 35.0 0.3 26 259-289 41-66 (221)
21 pfam06677 Auto_anti-p27 Sjogre 91.4 0.11 2.8E-06 30.9 1.8 26 259-288 16-41 (41)
22 COG1645 Uncharacterized Zn-fin 90.4 0.15 3.8E-06 30.0 1.8 24 261-289 29-52 (131)
23 COG1389 DNA topoisomerase VI, 89.5 0.74 1.9E-05 25.6 4.7 105 112-224 206-311 (538)
24 PRK00420 hypothetical protein; 88.9 0.22 5.5E-06 29.0 1.6 25 261-289 20-44 (107)
25 PRK07220 DNA topoisomerase I; 88.0 0.51 1.3E-05 26.6 3.0 29 259-288 634-664 (740)
26 COG1096 Predicted RNA-binding 87.8 0.39 9.8E-06 27.4 2.3 27 254-289 147-173 (188)
27 PRK08413 consensus 85.4 0.89 2.3E-05 25.1 3.1 28 201-228 528-555 (733)
28 PRK08938 DNA topoisomerase I; 84.5 0.84 2.1E-05 25.2 2.7 27 202-228 536-562 (692)
29 PRK05823 consensus 83.2 0.67 1.7E-05 25.8 1.7 78 151-228 485-586 (691)
30 cd04476 RPA1_DBD_C RPA1_DBD_C: 82.2 0.6 1.5E-05 26.1 1.2 20 98-118 69-88 (166)
31 PRK08173 DNA topoisomerase III 79.3 5.1 0.00013 20.2 5.2 24 260-288 624-647 (857)
32 pfam00398 RrnaAD Ribosomal RNA 78.6 2.1 5.4E-05 22.6 3.0 53 158-222 205-257 (258)
33 KOG3311 consensus 78.6 1.7 4.4E-05 23.2 2.5 50 164-222 23-72 (152)
34 pfam08273 Prim_Zn_Ribbon Zinc- 78.3 1 2.6E-05 24.7 1.3 27 261-288 4-33 (39)
35 PRK09137 DNA topoisomerase I; 78.2 2.1 5.5E-05 22.6 2.9 79 150-228 472-574 (761)
36 pfam03486 HI0933_like HI0933-l 77.8 1.7 4.4E-05 23.2 2.3 65 149-224 267-336 (405)
37 PRK07219 DNA topoisomerase I; 76.2 3 7.6E-05 21.7 3.2 25 260-285 716-740 (769)
38 smart00778 Prim_Zn_Ribbon Zinc 72.9 2.6 6.7E-05 22.0 2.2 27 261-288 4-32 (37)
39 smart00661 RPOL9 RNA polymeras 72.6 3.5 9E-05 21.2 2.8 26 262-288 2-27 (52)
40 PRK08665 ribonucleotide-diphos 71.4 5.4 0.00014 20.1 3.5 53 215-287 675-727 (733)
41 PRK00274 ksgA dimethyladenosin 71.4 4.3 0.00011 20.7 3.0 56 158-224 210-265 (267)
42 PRK08620 DNA topoisomerase III 70.3 4.3 0.00011 20.7 2.8 24 260-284 648-671 (726)
43 COG0675 Transposase and inacti 69.7 3 7.5E-05 21.7 1.9 22 260-289 309-330 (364)
44 TIGR00755 ksgA dimethyladenosi 69.1 5.2 0.00013 20.1 3.0 59 156-220 215-276 (277)
45 pfam07282 Transposase_35 Putat 68.7 2.4 6.1E-05 22.3 1.2 27 259-288 27-53 (69)
46 PRK05582 DNA topoisomerase I; 66.9 3.8 9.8E-05 21.0 2.0 79 151-229 457-559 (692)
47 COG2888 Predicted Zn-ribbon RN 63.8 2.7 6.9E-05 22.0 0.7 25 262-287 29-56 (61)
48 PRK07141 DNA topoisomerase I; 63.7 12 0.0003 17.9 5.0 29 259-288 564-597 (622)
49 PRK12366 replication factor A; 63.2 4.1 0.00011 20.8 1.6 23 261-288 534-556 (649)
50 PRK07726 DNA topoisomerase III 63.1 12 0.0003 17.8 5.2 22 262-288 632-658 (716)
51 PRK09521 exosome complex RNA-b 62.6 6.6 0.00017 19.5 2.5 23 262-289 152-174 (187)
52 TIGR00617 rpa1 replication fac 62.3 4.7 0.00012 20.4 1.8 53 230-289 504-562 (671)
53 smart00532 LIGANc Ligase N fam 62.2 6.8 0.00017 19.4 2.5 23 261-286 400-422 (441)
54 TIGR01544 HAD-SF-IE HAD-superf 61.1 5.8 0.00015 19.8 2.0 43 153-202 133-177 (287)
55 COG3024 Uncharacterized protei 60.7 2.3 5.8E-05 22.5 -0.1 27 261-288 8-34 (65)
56 COG2081 Predicted flavoprotein 60.1 8.2 0.00021 18.9 2.7 64 149-224 268-333 (408)
57 COG2956 Predicted N-acetylgluc 59.4 4.4 0.00011 20.6 1.2 20 262-289 356-376 (389)
58 COG1571 Predicted DNA-binding 59.2 4.2 0.00011 20.8 1.0 29 256-288 346-374 (421)
59 COG0272 Lig NAD-dependent DNA 56.3 9.1 0.00023 18.6 2.4 22 262-286 406-427 (667)
60 PRK00432 30S ribosomal protein 55.9 8.2 0.00021 18.9 2.1 28 258-288 21-48 (54)
61 TIGR00575 dnlj DNA ligase, NAD 54.4 7.8 0.0002 19.0 1.8 22 262-286 413-434 (706)
62 COG1656 Uncharacterized conser 54.0 5.5 0.00014 20.0 0.9 28 261-289 98-138 (165)
63 CHL00174 accD acetyl-CoA carbo 53.8 1.8 4.6E-05 23.1 -1.6 28 165-192 143-171 (305)
64 COG0030 KsgA Dimethyladenosine 52.9 12 0.0003 17.9 2.5 52 157-223 204-256 (259)
65 PRK00635 excinuclease ABC subu 51.7 18 0.00047 16.6 3.4 17 191-207 321-337 (1809)
66 PRK03681 hypA hydrogenase nick 50.7 8 0.0002 18.9 1.3 23 262-288 72-94 (114)
67 PRK00564 hypA hydrogenase nick 48.5 7.8 0.0002 19.0 1.0 22 262-288 73-95 (117)
68 pfam10263 SprT-like SprT-like 48.4 19 0.00048 16.5 2.9 26 262-288 121-146 (153)
69 TIGR02159 PA_CoA_Oxy4 phenylac 47.5 9 0.00023 18.6 1.2 32 256-288 107-143 (152)
70 TIGR02483 PFK_mixed phosphofru 47.1 9.2 0.00024 18.5 1.2 22 174-195 259-280 (339)
71 COG1439 Predicted nucleic acid 46.5 17 0.00045 16.8 2.5 26 254-280 147-172 (177)
72 PRK08271 anaerobic ribonucleos 45.9 8.6 0.00022 18.7 0.9 48 176-231 415-462 (625)
73 TIGR00387 glcD glycolate oxida 45.1 23 0.00059 16.0 3.0 80 138-235 296-390 (437)
74 PRK07956 ligA NAD-dependent DN 44.4 21 0.00054 16.2 2.7 23 261-286 405-427 (668)
75 pfam03119 DNA_ligase_ZBD NAD-d 44.3 16 0.0004 17.0 2.0 21 263-286 2-22 (27)
76 pfam08394 Arc_trans_TRASH Arch 44.2 4.9 0.00013 20.3 -0.6 23 267-289 4-31 (37)
77 PRK00349 uvrA excinuclease ABC 44.2 24 0.00061 15.9 4.2 29 179-207 315-346 (944)
78 pfam02591 DUF164 Putative zinc 43.9 4.5 0.00011 20.6 -0.8 30 259-289 21-54 (56)
79 COG3677 Transposase and inacti 43.8 16 0.00042 16.9 2.0 27 261-289 31-61 (129)
80 PRK08174 DNA topoisomerase III 43.6 24 0.00062 15.8 5.3 29 258-288 613-645 (670)
81 COG1997 RPL43A Ribosomal prote 42.8 17 0.00043 16.8 2.0 25 261-288 36-60 (89)
82 TIGR02890 spore_yteA sporulati 42.6 9.1 0.00023 18.6 0.6 107 154-289 4-117 (167)
83 PRK06556 vitamin B12-dependent 42.0 16 0.0004 17.1 1.7 24 259-287 927-950 (957)
84 TIGR00630 uvra excinuclease AB 41.8 9.9 0.00025 18.3 0.7 17 191-207 351-367 (956)
85 COG3350 Uncharacterized conser 41.7 17 0.00043 16.8 1.9 22 265-286 6-33 (53)
86 COG0375 HybF Zn finger protein 40.3 11 0.00028 18.0 0.7 23 261-288 71-93 (115)
87 TIGR03670 rpoB_arch DNA-direct 39.6 23 0.0006 15.9 2.3 73 123-197 366-445 (599)
88 pfam07191 DUF1407 Protein of u 38.6 3.6 9.3E-05 21.1 -2.0 26 261-287 31-56 (70)
89 PRK12860 transcriptional activ 38.4 29 0.00075 15.3 3.9 84 166-288 78-161 (189)
90 TIGR01341 aconitase_1 aconitat 38.0 11 0.00029 18.0 0.5 56 154-239 514-569 (896)
91 PRK07225 DNA-directed RNA poly 37.7 27 0.00069 15.5 2.4 75 123-198 372-452 (605)
92 TIGR01405 polC_Gram_pos DNA po 37.4 11 0.00028 18.1 0.3 13 69-81 544-556 (1264)
93 TIGR02661 MauD methylamine deh 37.3 9.7 0.00025 18.4 0.1 11 212-222 169-179 (189)
94 PRK12380 hydrogenase nickel in 37.0 15 0.00037 17.2 0.9 22 262-288 72-93 (113)
95 pfam08271 TF_Zn_Ribbon TFIIB z 36.8 26 0.00067 15.6 2.2 10 278-287 16-25 (40)
96 pfam01155 HypA Hydrogenase exp 36.2 16 0.00041 17.0 1.0 22 262-288 71-92 (112)
97 PRK12722 transcriptional activ 35.4 33 0.00083 15.0 5.4 84 166-288 78-161 (185)
98 KOG2169 consensus 35.1 17 0.00044 16.8 1.0 12 278-289 342-353 (636)
99 pfam01927 DUF82 Protein of unk 34.8 15 0.00038 17.2 0.7 27 262-289 92-131 (146)
100 PRK06319 DNA topoisomerase I/S 34.8 33 0.00085 15.0 5.1 80 150-230 478-582 (864)
101 PRK11788 hypothetical protein; 34.7 24 0.00061 15.9 1.7 21 261-289 355-376 (389)
102 pfam03811 Ins_element1 Inserti 34.6 22 0.00055 16.1 1.5 12 278-289 26-37 (88)
103 TIGR01206 lysW lysine biosynth 34.6 26 0.00067 15.6 1.9 23 265-287 6-28 (54)
104 TIGR02642 phage_xxxx uncharact 34.5 13 0.00033 17.6 0.3 80 176-288 126-206 (270)
105 cd02967 mauD Methylamine utili 34.4 8.4 0.00021 18.8 -0.7 23 44-66 7-30 (114)
106 TIGR00395 leuS_arch leucyl-tRN 33.3 21 0.00053 16.3 1.2 40 44-83 303-344 (1109)
107 TIGR00469 pheS_mito phenylalan 33.2 23 0.00059 15.9 1.5 43 177-224 292-335 (460)
108 cd01675 RNR_III Class III ribo 32.2 37 0.00094 14.7 2.6 49 176-231 361-409 (555)
109 pfam04919 DUF655 Protein of un 32.1 37 0.00094 14.7 2.7 53 153-206 98-150 (181)
110 KOG3053 consensus 32.0 13 0.00034 17.5 0.1 20 165-184 218-237 (293)
111 COG5216 Uncharacterized conser 31.9 33 0.00083 15.0 2.0 25 262-288 24-51 (67)
112 PRK09194 prolyl-tRNA synthetas 31.4 33 0.00083 15.0 2.0 18 256-274 388-405 (570)
113 pfam08274 PhnA_Zn_Ribbon PhnA 30.8 36 0.00091 14.8 2.1 23 262-288 4-26 (30)
114 pfam09788 Tmemb_55A Transmembr 30.3 32 0.00083 15.0 1.8 27 262-289 161-187 (258)
115 TIGR03655 anti_R_Lar restricti 30.3 25 0.00064 15.7 1.2 27 261-288 2-33 (53)
116 COG1592 Rubrerythrin [Energy p 30.0 16 0.0004 17.1 0.1 21 262-288 136-156 (166)
117 TIGR00354 polC DNA polymerase 29.9 27 0.00068 15.6 1.3 104 166-287 1006-1112(1173)
118 PRK08402 replication factor A; 29.1 18 0.00046 16.7 0.3 24 261-287 215-238 (357)
119 COG1998 RPS31 Ribosomal protei 27.9 24 0.0006 15.9 0.7 27 258-287 17-43 (51)
120 KOG2324 consensus 27.5 21 0.00053 16.3 0.4 26 262-288 229-254 (457)
121 TIGR00019 prfA peptide chain r 26.5 19 0.00049 16.5 0.1 33 165-197 263-295 (373)
122 pfam05280 FlhC Flagellar trans 26.1 47 0.0012 14.0 4.2 84 166-288 78-161 (176)
123 KOG2923 consensus 25.9 30 0.00076 15.3 1.0 25 262-288 24-51 (67)
124 PRK13804 ileS isoleucyl-tRNA s 25.5 27 0.00068 15.6 0.7 10 266-275 554-563 (966)
125 PRK12300 leuS leucyl-tRNA synt 25.2 38 0.00096 14.6 1.4 22 45-66 181-202 (888)
126 pfam09297 zf-NADH-PPase NADH p 25.0 34 0.00087 14.9 1.1 26 261-289 4-29 (32)
127 PRK07418 acetolactate synthase 24.8 31 0.0008 15.1 0.9 21 261-288 592-612 (615)
128 PRK07562 ribonucleotide-diphos 24.8 39 0.00099 14.5 1.4 27 256-287 1143-1170(1177)
129 COG2046 MET3 ATP sulfurylase ( 24.3 29 0.00074 15.3 0.7 11 279-289 318-328 (397)
130 PRK00390 leuS leucyl-tRNA synt 24.1 42 0.0011 14.3 1.5 12 262-274 471-482 (822)
131 PRK06039 ileS isoleucyl-tRNA s 24.1 41 0.0011 14.4 1.4 12 262-274 503-514 (1042)
132 pfam00085 Thioredoxin Thioredo 24.0 21 0.00053 16.3 -0.1 11 57-67 18-28 (104)
133 TIGR00515 accD acetyl-CoA carb 23.7 16 0.00041 17.0 -0.8 10 176-185 117-126 (292)
134 pfam04945 YHS YHS domain. This 23.2 53 0.0013 13.7 2.1 21 265-285 1-26 (44)
135 TIGR02311 HpaI 2,4-dihydroxyhe 23.1 37 0.00094 14.7 1.0 21 165-185 114-134 (249)
136 cd02993 PDI_a_APS_reductase PD 22.9 16 0.00042 16.9 -0.8 24 38-67 8-31 (109)
137 pfam01258 zf-dskA_traR Prokary 22.8 11 0.00029 18.0 -1.7 26 263-289 6-32 (32)
138 PRK05743 ileS isoleucyl-tRNA s 22.4 52 0.0013 13.7 1.7 16 254-270 872-887 (910)
139 TIGR03147 cyt_nit_nrfF cytochr 22.2 31 0.0008 15.1 0.5 32 196-234 44-75 (126)
140 TIGR00959 ffh signal recogniti 22.1 32 0.00081 15.1 0.5 37 148-187 332-370 (439)
141 TIGR02738 TrbB type-F conjugat 22.1 30 0.00076 15.3 0.4 10 60-69 58-67 (176)
142 KOG2846 consensus 22.1 36 0.00093 14.7 0.8 29 258-288 218-249 (328)
143 PRK08565 DNA-directed RNA poly 21.8 56 0.0014 13.5 2.2 59 140-198 884-948 (1101)
144 pfam04423 Rad50_zn_hook Rad50 21.5 35 0.00088 14.9 0.6 10 262-272 22-31 (54)
145 pfam10571 UPF0547 Uncharacteri 21.4 43 0.0011 14.2 1.1 20 262-288 2-21 (26)
146 PRK10144 formate-dependent nit 21.3 34 0.00086 14.9 0.5 32 196-234 44-75 (126)
147 pfam09723 CxxC_CxxC_SSSS Zinc 21.2 58 0.0015 13.4 2.7 25 263-288 8-33 (42)
148 pfam06044 DRP Dam-replacing fa 20.9 44 0.0011 14.2 1.0 13 161-173 179-191 (254)
149 PRK05580 primosome assembly pr 20.8 59 0.0015 13.4 1.7 26 262-288 415-451 (699)
150 PRK13208 valS valyl-tRNA synth 20.7 45 0.0012 14.1 1.1 24 164-189 348-371 (809)
151 COG0419 SbcC ATPase involved i 20.7 38 0.00096 14.6 0.7 13 95-107 70-82 (908)
152 TIGR00385 dsbE periplasmic pro 20.7 33 0.00084 15.0 0.3 49 37-85 41-100 (175)
153 KOG2851 consensus 20.5 45 0.0012 14.1 1.0 15 252-266 329-343 (412)
154 pfam00133 tRNA-synt_1 tRNA syn 20.5 41 0.0011 14.3 0.8 12 262-274 476-487 (606)
155 COG0178 UvrA Excinuclease ATPa 20.4 60 0.0015 13.3 5.1 15 193-207 324-338 (935)
156 KOG2907 consensus 20.4 47 0.0012 14.0 1.1 27 261-288 75-109 (116)
No 1
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase; InterPro: IPR000191 Formamidopyrimidine-DNA glycosylase (3.2.2.23 from EC) (Fapy-DNA glycosylase) (gene fpg) is a bacterial enzyme involved in DNA repair and which excise oxidized purine bases to release 2,6-diamino-4-hydroxy-5N-methylformamido- pyrimidine (Fapy) and 7,8-dihydro-8-oxoguanine (8-OxoG) residues. In addition to its glycosylase activity, FPG can also nick DNA at apurinic/apyrimidinic sites (AP sites). FPG is a monomeric protein of about 32 Kd which binds and require zinc for its activity. The C-terminal region is the zinc binding site in the enzyme where four conserved and essential cysteines are located ..
Probab=100.00 E-value=0 Score=610.67 Aligned_cols=273 Identities=38% Similarity=0.673 Sum_probs=259.6
Q ss_pred CCCCCHHHHHHHHHHHHHCCCEEEEEEECCCC--CCCCCCHHHHHHHCCCEEEEEEECCEEEEEEECCCC------CCCC
Q ss_conf 96764367889889998679778899964833--265787789997289889999605308999503553------1001
Q gi|254780625|r 1 MPELPEVEIIRRNLMMVMKNMTVTDICLHRKN--LRFDFPHHFSAATRGKKIIDVSRRAKYLLIELEGNL------SIIV 72 (289)
Q Consensus 1 MPElPEVe~~~~~l~~~l~g~~I~~V~~~~~~--~~~~~~~~~~~~L~G~~I~~v~r~GK~l~l~l~~~~------~L~~ 72 (289)
|||||||||++|.|++.++|++|.+|.+..++ .++..+++|...|.|++|.++.|||||||++|+++. +|++
T Consensus 1 MPELPEVETvrR~L~~~~~gktI~~V~V~~~~~~~~~~~~~~l~~~L~g~~i~~~~RRGKYLl~~L~~~~~~~~ag~lv~ 80 (292)
T TIGR00577 1 MPELPEVETVRRGLEPLVLGKTIKSVEVVLRRVVKRPAGVEDLQKELLGQTILSIQRRGKYLLFELDDGVFQFMAGALVS 80 (292)
T ss_pred CCCCHHHHHHHHHHHHHHCCCCCCEEEEECCCCCCCCCCHHHHHHHHCCCEEEEECCCEEEEEEEECCCEEECCCEEEEE
T ss_conf 99861289987633434068510148995262100478858999874797688603330456764057700015404788
Q ss_pred CCCCCCEEEEECCCCCCCCCCCCCCEEEEEEECCCCCEEEEEEEECCCCCC--CEECCCCCCHHHCCCCCCCCCCCC-CC
Q ss_conf 525532799814785422458766338999706887604899981587664--100145530100532356555332-21
Q gi|254780625|r 73 HLGMSGSFIIEHTSCAKPIKNPQHNHVTISLTNNTNTKKYRVIYNDPRRFG--FMDLVETSLKYQYPPLRTLGPEPA-DN 149 (289)
Q Consensus 73 HlgM~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~D~R~fG--~~~~~~~~~~~~~~~l~~lGpD~l-~~ 149 (289)
||||+|++++...+... .++|.|+.+.|+||. .|.|.|+|+|| +|.+++....+....+++|||||| |+
T Consensus 81 HLrM~G~y~~~~~~~~~---~~kH~hv~~~f~dG~-----~L~y~D~R~FG~~~~~l~~~~~~~~~~~l~~LGpEPly~~ 152 (292)
T TIGR00577 81 HLRMEGKYRLEEVPDAP---PDKHVHVDFLFDDGT-----ELRYHDPRKFGKVTWLLLDRGEVEASLLLAKLGPEPLYSE 152 (292)
T ss_pred EEEEEEEEEECCCCCCC---CCCCCEEEEEECCCC-----EEEEECCCEEEEEEEEECCCCCHHHHHHHHHHCCCCCCCH
T ss_conf 43312221101178788---888656999986996-----7887557635568987167753012013667288888652
Q ss_pred CCHHHHHHHHHHCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 11067888742014542100111265435641368999999871787783122220010158999999998788767654
Q gi|254780625|r 150 SFNAIYLTHQFHKKNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKVLIDAI 229 (289)
Q Consensus 150 ~~~~~~~~~~l~~~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~~vl~~a~ 229 (289)
+|+.+++.+.+++++++||++||||++|||||||||||+||+|||||.+.+++|+.+| ++.|+++|.+||.+||
T Consensus 153 ~F~~~~l~~~l~~~~r~~K~~LLDQ~~V~G~GNIYADE~LF~A~ihP~~~A~~L~~~~------~~~L~~~i~~vL~~Ai 226 (292)
T TIGR00577 153 DFTAEYLFEKLAKSKRKIKTALLDQRLVAGLGNIYADEVLFRAGIHPERLANQLSKEE------CELLHKAIKEVLRKAI 226 (292)
T ss_pred HCCHHHHHHHHHHCCCHHHHHHHCCCEEEEEHHHHHHHHHHHHCCCCCHHHHCCCHHH------HHHHHHHHHHHHHHHH
T ss_conf 1173899999874040345686548757651010666899873688101000158889------9999999999999998
Q ss_pred HCCCCCCCC--CCCCCCCCCCCHHHEEEECCCCCCCCC-CCCCEEEEEEEC-----CCCEEECCCCC
Q ss_conf 218875531--116778778741331665738771078-778878999987-----81206387767
Q gi|254780625|r 230 DAGGSSLRD--YVHIDGSIGYFQNAFSVYGKTGEPCLS-NCGQMIRRIVQA-----GRSTFYCTYCQ 288 (289)
Q Consensus 230 ~~gG~~~~~--~~~~~g~~g~~~~~~~vy~r~g~~C~~-~CG~~I~~~~~~-----gR~ty~Cp~CQ 288 (289)
+.||||++| |++++|++|+|+..+.||||+|+|| + +||++|++++++ ||+|||||+||
T Consensus 227 e~GGtt~~~q~f~~~~G~~G~fq~~l~VYGrkg~pC-~a~CGt~I~k~~~~LYGkDgRgthfCp~CQ 292 (292)
T TIGR00577 227 EAGGTTIRDQLFVQSDGENGYFQQELQVYGRKGEPC-RARCGTTIEKEKVGLYGKDGRGTHFCPQCQ 292 (292)
T ss_pred HCCCCCCCCEEEEECCCCCCCCCCEEEEECCCCCCC-CCCCCCEEEEEEEECCCCCCCCEECCCCCC
T ss_conf 648970002002304787875344210025638834-367884478876530151675101268889
No 2
>PRK01103 formamidopyrimidine-DNA glycosylase; Validated
Probab=100.00 E-value=0 Score=586.88 Aligned_cols=272 Identities=45% Similarity=0.797 Sum_probs=259.1
Q ss_pred CCCCCHHHHHHHHHHHHHCCCEEEEEEECCCCCCCCCCHHHHHHHCCCEEEEEEECCEEEEEEECCCCCCCCCCCCCCEE
Q ss_conf 96764367889889998679778899964833265787789997289889999605308999503553100152553279
Q gi|254780625|r 1 MPELPEVEIIRRNLMMVMKNMTVTDICLHRKNLRFDFPHHFSAATRGKKIIDVSRRAKYLLIELEGNLSIIVHLGMSGSF 80 (289)
Q Consensus 1 MPElPEVe~~~~~l~~~l~g~~I~~V~~~~~~~~~~~~~~~~~~L~G~~I~~v~r~GK~l~l~l~~~~~L~~HlgM~G~~ 80 (289)
||||||||+++++|++.+.|++|++|++.+++.++..+++|.+.|.|++|.+|+|+||+|+|+||++ +|++||||+|+|
T Consensus 1 MPElPEVe~~~~~l~~~~~g~~I~~v~~~~~~~~~~~~~~~~~~L~G~~i~~v~r~GK~l~~~~~~~-~l~~HlgMtG~~ 79 (273)
T PRK01103 1 MPELPEVETVRRGLEPHVVGKTIERVEVRNPKLRWPVPEDFAERLSGQTILAVGRRGKYLLLDLDDG-TLISHLGMSGSL 79 (273)
T ss_pred CCCHHHHHHHHHHHHHHHCCCEEEEEEECCCCCCCCCCHHHHHHCCCCEEEEEECCCEEEEEECCCC-EEEEEEECCEEE
T ss_conf 9865899999999999848999989998985322788588997748999987871303999981698-289987323379
Q ss_pred EEECCCCCCCCCCCCCCEEEEEEECCCCCEEEEEEEECCCCCCCEECCCCCCHHHCCCCCCCCCCCCCCCCHHHHHHHHH
Q ss_conf 98147854224587663389997068876048999815876641001455301005323565553322111067888742
Q gi|254780625|r 81 IIEHTSCAKPIKNPQHNHVTISLTNNTNTKKYRVIYNDPRRFGFMDLVETSLKYQYPPLRTLGPEPADNSFNAIYLTHQF 160 (289)
Q Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~D~R~fG~~~~~~~~~~~~~~~l~~lGpD~l~~~~~~~~~~~~l 160 (289)
.+...+. ..++|.|+.|.|+++. .++|.|+|+||++.+++..+...++.+++||||||+++|+.++|.+.+
T Consensus 80 ~~~~~~~----~~~k~~~l~l~~~~g~-----~l~f~D~R~fG~i~~~~~~~~~~~~~l~~lGpD~L~~~~~~~~~~~~l 150 (273)
T PRK01103 80 RVLPGET----PPEKHDHVDFVLDDGT-----VLRYNDPRRFGAMLLAEEGDLHAHPLLAKLGPEPLSDAFDGEYLAAKL 150 (273)
T ss_pred EEECCCC----CCCCEEEEEEEECCCC-----EEEEECCCCCEEEEEEECCCCCCCHHHHHCCCCCCCCCCCHHHHHHHH
T ss_conf 9955899----9886328999958995-----899973775317999967750004078766998465557999999876
Q ss_pred HCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC
Q ss_conf 01454210011126543564136899999987178778312222001015899999999878876765421887553111
Q gi|254780625|r 161 HKKNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKVLIDAIDAGGSSLRDYV 240 (289)
Q Consensus 161 ~~~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~~vl~~a~~~gG~~~~~~~ 240 (289)
++++++||++||||++||||||||+|||||+|||||++++++||++| +.+|+++++.||..|++.||+|++||+
T Consensus 151 ~~~~~~Ik~~LlDQ~~iaGiGNiyadEiLf~a~IhP~~~~~~Ls~~e------~~~L~~~~~~vl~~ai~~~G~t~~d~~ 224 (273)
T PRK01103 151 RKKKTAIKPALLDQTIVVGVGNIYADEALFRAGIHPERPAGSLSKAR------AERLVEAIKAVLAEAIEQGGTTLRDYV 224 (273)
T ss_pred HCCCCHHHHHHCCCCEEECCCHHHHHHHHHHCCCCCCCHHCCCCHHH------HHHHHHHHHHHHHHHHHCCCCCCHHCC
T ss_conf 43654266762258846035398999999876487135001179999------999999999999999981897402200
Q ss_pred CCCCCCCCCHHHEEEECCCCCCCCCCCCCEEEEEEECCCCEEECCCCCC
Q ss_conf 6778778741331665738771078778878999987812063877679
Q gi|254780625|r 241 HIDGSIGYFQNAFSVYGKTGEPCLSNCGQMIRRIVQAGRSTFYCTYCQK 289 (289)
Q Consensus 241 ~~~g~~g~~~~~~~vy~r~g~~C~~~CG~~I~~~~~~gR~ty~Cp~CQk 289 (289)
+++|++|+|+++++||+|+|+|| |+||++|++++++||+|||||.|||
T Consensus 225 ~~~g~~G~~~~~~~Vy~r~g~~C-~~Cg~~I~~~~~~gR~t~~CP~CQk 272 (273)
T PRK01103 225 NADGEPGYFQQSLQVYGREGEPC-RRCGTPIEKIKQGGRSTFFCPKCQK 272 (273)
T ss_pred CCCCCCCCCCEEEEECCCCCCCC-CCCCCEEEEEEECCCCCEECCCCCC
T ss_conf 66888675330578808898948-9999967899988971199957618
No 3
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=100.00 E-value=0 Score=578.00 Aligned_cols=273 Identities=47% Similarity=0.804 Sum_probs=261.2
Q ss_pred CCCCCHHHHHHHHHHHHHCCCEEEEEEECCCCCCCCCCHHHHHHHCCCEEEEEEECCEEEEEEECCCCCCCCCCCCCCEE
Q ss_conf 96764367889889998679778899964833265787789997289889999605308999503553100152553279
Q gi|254780625|r 1 MPELPEVEIIRRNLMMVMKNMTVTDICLHRKNLRFDFPHHFSAATRGKKIIDVSRRAKYLLIELEGNLSIIVHLGMSGSF 80 (289)
Q Consensus 1 MPElPEVe~~~~~l~~~l~g~~I~~V~~~~~~~~~~~~~~~~~~L~G~~I~~v~r~GK~l~l~l~~~~~L~~HlgM~G~~ 80 (289)
||||||||++++.|++.+.|++|++|++..+++++..+++|...|.|++|.++.||||||+++|+++.+|++||||+|+|
T Consensus 1 MPELPEVetv~rgL~~~~~G~~I~~v~v~~p~l~~~~~~~~~~~L~G~~I~~v~rRgKyLl~~l~g~~~Li~HLgM~G~~ 80 (273)
T COG0266 1 MPELPEVETVRRGLEPHLVGKTITRVEVRRPRLRWPDSEEFAERLTGQRITSVERRGKYLLIELSGDLTLISHLGMSGSL 80 (273)
T ss_pred CCCCCHHHHHHHHHHHHHCCCEEEEEEECCCCEECCCCHHHHHHCCCCEEEEEECCCCEEEEECCCCCEEEEECCCCEEE
T ss_conf 99874779898766887579878899953875113677778965589698367512125999917994899966764689
Q ss_pred EEECCCCCCCCCCCCCCEEEEEEECCCCCEEEEEEEECCCCCCCEECCCCCCHHHCCCCCCCCCCCCCCCCHHHHHHHHH
Q ss_conf 98147854224587663389997068876048999815876641001455301005323565553322111067888742
Q gi|254780625|r 81 IIEHTSCAKPIKNPQHNHVTISLTNNTNTKKYRVIYNDPRRFGFMDLVETSLKYQYPPLRTLGPEPADNSFNAIYLTHQF 160 (289)
Q Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~D~R~fG~~~~~~~~~~~~~~~l~~lGpD~l~~~~~~~~~~~~l 160 (289)
++...+.+ ..+|+|+.|.|+|+. ..+.|.|+|+||++.+.+..+ ..++.+++||||||+++||.+++.+.+
T Consensus 81 ~~~~~~~~----~~kH~hv~~~~~~g~----~~l~y~D~R~FG~~~~~~~~~-~~~~~l~~LGpePl~~~f~~~~l~~~l 151 (273)
T COG0266 81 RLEARGEP----DEKHDHVDFVLSDGK----DVLRYNDPRRFGTMLLIEDLE-EVHPVLAKLGPEPLSDDFDPEYLAEKL 151 (273)
T ss_pred EEECCCCC----CCCCEEEEEEECCCC----EEEEEECCCCCCEEEEECCCC-CCCHHHHHCCCCCCCCCCCHHHHHHHH
T ss_conf 98517888----886308999975993----599986387674899945665-432779865999885436999999987
Q ss_pred HCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC
Q ss_conf 01454210011126543564136899999987178778312222001015899999999878876765421887553111
Q gi|254780625|r 161 HKKNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKVLIDAIDAGGSSLRDYV 240 (289)
Q Consensus 161 ~~~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~~vl~~a~~~gG~~~~~~~ 240 (289)
++++++||++||||++||||||||+|||||+|||||.+++++|+++| +..|+++|+.||.+|++.||+|++||.
T Consensus 152 ~~~~~~IK~~LLDQ~vvaGvGNIYa~E~Lf~agI~P~~~a~~l~~~~------~~~l~~~i~~vl~~ai~~gGtt~r~~~ 225 (273)
T COG0266 152 AKKKRRIKTALLDQKVVAGVGNIYADEILFRAGIHPARPAGDLSLAQ------LALLHEAIKDVLADAIERGGTTLRDFV 225 (273)
T ss_pred HCCCCCHHHHHHCCCCEECCCHHHHHHHHHHCCCCCCCCCCCCCHHH------HHHHHHHHHHHHHHHHHHCCCCCCCEE
T ss_conf 32764167776407703034178888899873798546703027899------999999999999999981898024324
Q ss_pred CCCCCCCCCHHHEEEECCCCCCCCCCCCCEEEEEEECCCCEEECCCCCC
Q ss_conf 6778778741331665738771078778878999987812063877679
Q gi|254780625|r 241 HIDGSIGYFQNAFSVYGKTGEPCLSNCGQMIRRIVQAGRSTFYCTYCQK 289 (289)
Q Consensus 241 ~~~g~~g~~~~~~~vy~r~g~~C~~~CG~~I~~~~~~gR~ty~Cp~CQk 289 (289)
+.+|+.|+|+..++||+|+|+|| ++||++|++++++||+|||||+|||
T Consensus 226 ~~~g~~G~fq~~l~VYgR~GepC-~~CGt~I~k~~~~gR~t~~CP~CQ~ 273 (273)
T COG0266 226 NADGKPGYFQQELKVYGRAGEPC-RRCGTPIEKIKLGGRSTFYCPVCQK 273 (273)
T ss_pred CCCCCCCCCCEEEEEECCCCCCC-CCCCCEEEEEEECCCCCEECCCCCC
T ss_conf 56898774312689855789988-7458876799986876776878789
No 4
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=100.00 E-value=0 Score=568.33 Aligned_cols=273 Identities=37% Similarity=0.598 Sum_probs=249.4
Q ss_pred CCCCCHHHHHHHHHHHHHCCCEEEEEEECCCCC-CC-CCCHHHHHHHCCCEEEEEEECCEEEEEEECCCC------CCCC
Q ss_conf 967643678898899986797788999648332-65-787789997289889999605308999503553------1001
Q gi|254780625|r 1 MPELPEVEIIRRNLMMVMKNMTVTDICLHRKNL-RF-DFPHHFSAATRGKKIIDVSRRAKYLLIELEGNL------SIIV 72 (289)
Q Consensus 1 MPElPEVe~~~~~l~~~l~g~~I~~V~~~~~~~-~~-~~~~~~~~~L~G~~I~~v~r~GK~l~l~l~~~~------~L~~ 72 (289)
||||||||++++.|++.+.|++|++|++..++. .. ..+++|.+.|.|++|.+|.|+||||+|+|+++. +|++
T Consensus 1 MPELPEVe~~~~~L~~~~~g~~I~~v~~~~~~~~~~~~~~~~f~~~L~G~~i~~v~RrGK~l~~~l~~~~~~~~~~~l~~ 80 (283)
T PRK13945 1 MPELPEVETVRRGLEQLLLNFIIKGVEVLRERTIASPGGVEEFIKGLQGSLIGKWHRRGKYLLASLKKEGSENSAGWLGV 80 (283)
T ss_pred CCCHHHHHHHHHHHHHHHCCCEEEEEEEECCCCCCCCCCHHHHHHHCCCCEEEEEEEEEEEEEEEECCCCCCCCCCEEEE
T ss_conf 98468899999999998689989899990773312889979999764898997887678999998047655566757999
Q ss_pred CCCCCCEEEEECCCCCCCCCCCCCCEEEEEEECCCCCEEEEEEEECCCCCCCEECCCCCC--HHHCCCCCCCCCCCCCCC
Q ss_conf 525532799814785422458766338999706887604899981587664100145530--100532356555332211
Q gi|254780625|r 73 HLGMSGSFIIEHTSCAKPIKNPQHNHVTISLTNNTNTKKYRVIYNDPRRFGFMDLVETSL--KYQYPPLRTLGPEPADNS 150 (289)
Q Consensus 73 HlgM~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~D~R~fG~~~~~~~~~--~~~~~~l~~lGpD~l~~~ 150 (289)
||||||+|.+.+.+ ..+++|.|+.|.|+++. .++|.|+|+||++.++.... ....+.+++||||||+++
T Consensus 81 HLgMtG~~~~~~~~----~~~~kh~~~~l~~~~~~-----~l~f~D~R~FG~v~~~~~~~~~~~~~~~l~~LGpDpl~~~ 151 (283)
T PRK13945 81 HLRMTGQFLWVEQD----TPPCKHTRVRLFNKKNQ-----ELRFVDIRSFGQMWWVPPGLSPESIITGLKKLGPEPFSPE 151 (283)
T ss_pred EEEEEEEEEEECCC----CCCCCCEEEEEEECCCC-----EEEEEEECCCCEEEEECCCCCHHHHHHHHHHCCCCCCCCC
T ss_conf 86312478873687----78998259999979998-----8999970225458995587455666677763398711232
Q ss_pred CHHHHHHHHHHCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 10678887420145421001112654356413689999998717877831222200101589999999987887676542
Q gi|254780625|r 151 FNAIYLTHQFHKKNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKVLIDAID 230 (289)
Q Consensus 151 ~~~~~~~~~l~~~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~~vl~~a~~ 230 (289)
|+.++|.+.+++++++||++||||++||||||||+|||||+|||||.+++++||++| +++|++++++||..|++
T Consensus 152 ~~~~~~~~~l~~~~~~IK~~LlDQ~~iaGIGNiyadEiLf~a~I~P~~~~~~Ls~~e------~~~L~~~i~~vL~~ai~ 225 (283)
T PRK13945 152 FNVEYLKKKLKGRTRSIKTALLDQSIVAGIGNIYADESLFKAGIRPTTEAGTLKKNQ------LERLREAIVEVLKTSIG 225 (283)
T ss_pred CCHHHHHHHHHHCCCCCCEEEECCCEECCCCHHHHHHHHHHCCCCCCCCCCCCCHHH------HHHHHHHHHHHHHHHHH
T ss_conf 689999988752675435177518852345499999999985999778603089999------99999999999999998
Q ss_pred CCCCCCCCCCCCCCCCCCCHHHEEEECCCCCCCCCCCCCEEEEEEECCCCEEECCCCCC
Q ss_conf 18875531116778778741331665738771078778878999987812063877679
Q gi|254780625|r 231 AGGSSLRDYVHIDGSIGYFQNAFSVYGKTGEPCLSNCGQMIRRIVQAGRSTFYCTYCQK 289 (289)
Q Consensus 231 ~gG~~~~~~~~~~g~~g~~~~~~~vy~r~g~~C~~~CG~~I~~~~~~gR~ty~Cp~CQk 289 (289)
.||+|++||++++|..|+|+..++||+|+|+|| ++||++|++++++||+|||||.|||
T Consensus 226 ~ggtt~~d~~~~~g~~g~~~~~~~Vy~r~g~~C-~~Cg~~I~~~~~~gR~t~~CP~CQk 283 (283)
T PRK13945 226 AGGTTFSDFRDLEGVNGNYGGQAWVYRRTGQPC-RKCGTPIERIKLAGRSTHWCPNCQK 283 (283)
T ss_pred CCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCC-CCCCCEEEEEEECCCCCEECCCCCC
T ss_conf 489845013477787688775388967898948-9999888899999975788921149
No 5
>PRK10445 endonuclease VIII; Provisional
Probab=100.00 E-value=0 Score=511.25 Aligned_cols=260 Identities=22% Similarity=0.418 Sum_probs=223.7
Q ss_pred CCCCCHHHHHHHHHHHHHCCCEEEEEEECCCCCCCCCCHHHHHHHCCCEEEEEEECCEEEEEEECCCCCCCCCCCCCCEE
Q ss_conf 96764367889889998679778899964833265787789997289889999605308999503553100152553279
Q gi|254780625|r 1 MPELPEVEIIRRNLMMVMKNMTVTDICLHRKNLRFDFPHHFSAATRGKKIIDVSRRAKYLLIELEGNLSIIVHLGMSGSF 80 (289)
Q Consensus 1 MPElPEVe~~~~~l~~~l~g~~I~~V~~~~~~~~~~~~~~~~~~L~G~~I~~v~r~GK~l~l~l~~~~~L~~HlgM~G~~ 80 (289)
||||||||++++.|++.+.|++|++|.+..+.. ..|.+.|.|++|.+|+|+||||+|+|+++.+|++||||||+|
T Consensus 1 MPELPEVe~v~~~L~~~l~g~~I~~v~~~~~~~-----~~~~~~l~g~~i~~v~RrGK~L~~~~~~~~~L~~HLgMtG~~ 75 (263)
T PRK10445 1 MPEGPEIRRAADNLEAAIKGKPLTDVWFAFPQL-----KPYESQLIGQHVTHIETRGKALLTHFSNGLTLYSHNQLYGVW 75 (263)
T ss_pred CCCHHHHHHHHHHHHHHHCCCEEEEEEECCCCC-----CCHHHHCCCCEEEEEEEEEEEEEEEECCCCEEEEECCEEEEE
T ss_conf 997389999999999985898887999558775-----226876599999699987289999978996899806420699
Q ss_pred EEECCCCCCCCCCCCCCEEEEEEECCCCCEEEEEEEECCCCCCCEECCCCCCHHHCCCCCCCCCCCCCCCCHHHHHHHHH
Q ss_conf 98147854224587663389997068876048999815876641001455301005323565553322111067888742
Q gi|254780625|r 81 IIEHTSCAKPIKNPQHNHVTISLTNNTNTKKYRVIYNDPRRFGFMDLVETSLKYQYPPLRTLGPEPADNSFNAIYLTHQF 160 (289)
Q Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~D~R~fG~~~~~~~~~~~~~~~l~~lGpD~l~~~~~~~~~~~~l 160 (289)
.+.+.+.. ++++.++++.|.++.. ..+.|.+. .+++++......++.+++||||||+++|+.++|.+.+
T Consensus 76 ~~~~~~~~----~~~~~~~~~~~~~~~~---~~~~~~~~----~~~~~~~~~~~~~~~l~~LGPdpL~~~~~~~~~~~~l 144 (263)
T PRK10445 76 RVVDTGEE----PQTTRVLRVRLQTADK---TILLYSAS----DIEMLTAEQLTTHPFLQRVGPDVLDPNLTPEVVKERL 144 (263)
T ss_pred EEECCCCC----CCCCCEEEEEEECCCC---EEEEECCC----EEEEECHHHHHHCHHHHHCCCCCCCCCCCHHHHHHHH
T ss_conf 97469889----9978569999985991---79998498----5899731331106078765986577779999999998
Q ss_pred HC---CCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf 01---454210011126543564136899999987178778312222001015899999999878876765421887553
Q gi|254780625|r 161 HK---KNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKVLIDAIDAGGSSLR 237 (289)
Q Consensus 161 ~~---~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~~vl~~a~~~gG~~~~ 237 (289)
.. ++++||++||||++||||||||+|||||+|||||.+++++||++| +++|++++++||..|++.||++..
T Consensus 145 ~~~~~~~~~IK~~LLDQ~vvaGIGNIYa~EiLf~a~I~P~~~~~~Ls~~~------~~~L~~~i~~vl~~ai~~gG~~~~ 218 (263)
T PRK10445 145 LSPRFRNRQFSGLLLDQAFLAGLGNYLRVEILWQVGLTGQHKAKDLNAAQ------LDALAHALLDIPRLSYATRGQVDE 218 (263)
T ss_pred HHCCCCCCHHHHHHHCCCEEEECCHHHHHHHHHHCCCCCCCCCCCCCHHH------HHHHHHHHHHHHHHHHHHCCCCCC
T ss_conf 63302575076651168867511388998999982899788702099999------999999999999999982993267
Q ss_pred CCCCCCCCCCCCHHHEEEECCCCCCCCCCCCCEEEEEEECCCCEEECCCCCC
Q ss_conf 1116778778741331665738771078778878999987812063877679
Q gi|254780625|r 238 DYVHIDGSIGYFQNAFSVYGKTGEPCLSNCGQMIRRIVQAGRSTFYCTYCQK 289 (289)
Q Consensus 238 ~~~~~~g~~g~~~~~~~vy~r~g~~C~~~CG~~I~~~~~~gR~ty~Cp~CQk 289 (289)
+ ...| .+ ..|+||+|+|+|| ++||++|++++++||+|||||.||-
T Consensus 219 ~--~~~g---~~-~~~~Vy~R~g~~C-~~Cg~~I~~~~~~gRst~~Cp~CQ~ 263 (263)
T PRK10445 219 N--KHHG---AL-FRFKVFHRDGEAC-ERCGGIIEKTTLSSRPFYWCPGCQH 263 (263)
T ss_pred C--CCCC---CE-EEEEEECCCCCCC-CCCCCEEEEEEECCCCCEECCCCCC
T ss_conf 7--7788---66-4689967797938-9999762799988987887956489
No 6
>pfam06831 H2TH Formamidopyrimidine-DNA glycosylase H2TH domain. Formamidopyrimidine-DNA glycosylase (Fpg) is a DNA repair enzyme that excises oxidized purines from damaged DNA. This family is the central domain containing the DNA-binding helix-two turn-helix domain.
Probab=99.97 E-value=8.4e-31 Score=217.90 Aligned_cols=93 Identities=41% Similarity=0.666 Sum_probs=90.6
Q ss_pred CCCCCCCCCCHHHHHHHHHHCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 55533221110678887420145421001112654356413689999998717877831222200101589999999987
Q gi|254780625|r 142 LGPEPADNSFNAIYLTHQFHKKNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEI 221 (289)
Q Consensus 142 lGpD~l~~~~~~~~~~~~l~~~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i 221 (289)
||||||+++|+.++|.+++++++++||.+||||++||||||||+|||||+|||||++++++|+++| +.+||+++
T Consensus 1 LGpDpL~~~~~~~~f~~~l~~~~~~Ik~~LlDQ~~iaGiGNiy~dEiLf~a~I~P~~~~~~Ls~~~------~~~L~~~i 74 (93)
T pfam06831 1 LGPDPLSEPFTADEFAERLAKKKRPIKTALLDQRVVAGIGNIYADEVLFRAGIHPERPASSLSKKE------CEALHTVI 74 (93)
T ss_pred CCCCCCCCCCCHHHHHHHHHCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCHHH------HHHHHHHH
T ss_conf 998989986899999999865875199998667742565399999999991899678706199999------99999999
Q ss_pred HHHHHHHHHCCCCCCCCCC
Q ss_conf 8876765421887553111
Q gi|254780625|r 222 QKVLIDAIDAGGSSLRDYV 240 (289)
Q Consensus 222 ~~vl~~a~~~gG~~~~~~~ 240 (289)
+.||.+|++.||+|++||.
T Consensus 75 ~~vl~~ai~~gGtti~dys 93 (93)
T pfam06831 75 KDVLQKAIEMGGGGIRTFS 93 (93)
T ss_pred HHHHHHHHHCCCCCCCCCC
T ss_conf 9999999994999730184
No 7
>pfam01149 Fapy_DNA_glyco Formamidopyrimidine-DNA glycosylase N-terminal domain. Formamidopyrimidine-DNA glycosylase (Fpg) is a DNA repair enzyme that excises oxidized purines from damaged DNA. This family is the N-terminal domain contains eight beta-strands, forming a beta-sandwich with two alpha-helices parallel to its edges.
Probab=99.95 E-value=1.6e-27 Score=196.88 Aligned_cols=116 Identities=41% Similarity=0.721 Sum_probs=105.3
Q ss_pred CCCCHHHHHHHHHHHHHCCCEEEEEEECCCC-CCCCCCHHHHHHHCCCEEEEEEECCEEEEEEECCCCCCCCCCCCCCEE
Q ss_conf 6764367889889998679778899964833-265787789997289889999605308999503553100152553279
Q gi|254780625|r 2 PELPEVEIIRRNLMMVMKNMTVTDICLHRKN-LRFDFPHHFSAATRGKKIIDVSRRAKYLLIELEGNLSIIVHLGMSGSF 80 (289)
Q Consensus 2 PElPEVe~~~~~l~~~l~g~~I~~V~~~~~~-~~~~~~~~~~~~L~G~~I~~v~r~GK~l~l~l~~~~~L~~HlgM~G~~ 80 (289)
|||||||++++.|++.+.|++|++|++.+++ ++...++.|.+.|.|++|++|+|+||||+++|+++.+|++||||||+|
T Consensus 1 PELPEVe~~~~~l~~~~~g~~I~~v~~~~~~~~~~~~~~~~~~~l~G~~i~~v~RrGK~i~~~l~~~~~l~~HLgMtG~~ 80 (117)
T pfam01149 1 PELPEVETVRRGLEPLLVGRRITKVEVRRPKILRGPEPEEFIEALEGRTITDVRRRGKYLLLELDGGLVLVIHLGMTGRL 80 (117)
T ss_pred CCCCCHHHHHHHHHHHHCCCEEEEEEECCCCCCCCCCHHHHHHHCCCCEEEEEEEEEEEEEEEECCCCEEEEECCCCEEE
T ss_conf 98701999999999985899888999756871467784999977499998469850269999999998899816775689
Q ss_pred EEECCCCCCCCCCCCCCEEEEEEECCCCCEEEEEEEECCCCCCCEE
Q ss_conf 9814785422458766338999706887604899981587664100
Q gi|254780625|r 81 IIEHTSCAKPIKNPQHNHVTISLTNNTNTKKYRVIYNDPRRFGFMD 126 (289)
Q Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~D~R~fG~~~ 126 (289)
.+.... ...++|+|+.|.|+++. .++|.|+|+||+++
T Consensus 81 ~~~~~~----~~~~kh~~v~~~f~~g~-----~l~f~D~R~FG~i~ 117 (117)
T pfam01149 81 RVVEPE----DPPPKHTHVVLHLDDGR-----ELRFVDPRRFGRVR 117 (117)
T ss_pred EECCCC----CCCCCCEEEEEEECCCC-----EEEEECCCCCCCCC
T ss_conf 963787----89998589999979999-----99998588883139
No 8
>pfam05833 FbpA Fibronectin-binding protein A N-terminus (FbpA). This family consists of the N-terminal region of the prokaryotic fibronectin-binding protein. 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.
Probab=98.01 E-value=9.9e-05 Score=50.45 Aligned_cols=79 Identities=16% Similarity=0.200 Sum_probs=60.5
Q ss_pred CCCCCCCCCCCHHHHHHHHHHCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf 65553322111067888742014542100111265435641368999999871787783122220010158999999998
Q gi|254780625|r 141 TLGPEPADNSFNAIYLTHQFHKKNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQE 220 (289)
Q Consensus 141 ~lGpD~l~~~~~~~~~~~~l~~~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~ 220 (289)
..+.||++.+ +.+.|.+.+.....++..+| ++.+.|+|..++.|++++|++++..++..|++.+ +.+|+++
T Consensus 162 ~~k~~p~~~~-~~~~~~~~~~~~~~~l~~~l--~~~~~G~sp~la~El~~rag~~~~~~~~~l~~~~------~~~L~~~ 232 (447)
T pfam05833 162 QDKLNPLEIE-EFEEFKERLSLVPGDLVKAL--VQAFQGLSPLLAEELCYRAGLDKNTPVEELSDED------WERLYEA 232 (447)
T ss_pred CCCCCCCCCC-HHHHHHHHHHCCCCHHHHHH--HHHHCCCCHHHHHHHHHHHCCCCCCCHHHCCHHH------HHHHHHH
T ss_conf 0258955476-47889986411864099999--9982699889999999982898677711249899------9999999
Q ss_pred HHHHHHHH
Q ss_conf 78876765
Q gi|254780625|r 221 IQKVLIDA 228 (289)
Q Consensus 221 i~~vl~~a 228 (289)
+..++.+-
T Consensus 233 ~~~~~~~~ 240 (447)
T pfam05833 233 FKELLNDL 240 (447)
T ss_pred HHHHHHHH
T ss_conf 99999986
No 9
>pfam06827 zf-FPG_IleRS Zinc finger found in FPG and IleRS. This zinc binding domain is found at the C-terminus of isoleucyl tRNA synthetase and the enzyme Formamidopyrimidine-DNA glycosylase EC:3.2.2.23.
Probab=97.68 E-value=2.7e-05 Score=54.06 Aligned_cols=29 Identities=52% Similarity=1.027 Sum_probs=27.4
Q ss_pred CCCCCCCCCCEEEEEEECCCCEEECCCCCC
Q ss_conf 771078778878999987812063877679
Q gi|254780625|r 260 GEPCLSNCGQMIRRIVQAGRSTFYCTYCQK 289 (289)
Q Consensus 260 g~~C~~~CG~~I~~~~~~gR~ty~Cp~CQk 289 (289)
|++| ++|+..|.++..++|.++|||+||+
T Consensus 1 g~kC-~RCw~~~~~~~~~~r~~~~C~rCq~ 29 (30)
T pfam06827 1 GEKC-PRCWTYIEKVGQGGRSTFLCPRCQK 29 (30)
T ss_pred CCCC-CCCCCEEEEEEECCCCCCCCCCCCC
T ss_conf 9827-7479971576855888811805324
No 10
>COG1293 Predicted RNA-binding protein homologous to eukaryotic snRNP [Transcription]
Probab=97.46 E-value=0.0024 Score=41.55 Aligned_cols=71 Identities=15% Similarity=0.219 Sum_probs=47.1
Q ss_pred CCCCCCCHHHHHHHHHHCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 33221110678887420145421001112654356413689999998717877831222200101589999999987887
Q gi|254780625|r 145 EPADNSFNAIYLTHQFHKKNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKV 224 (289)
Q Consensus 145 D~l~~~~~~~~~~~~l~~~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~~v 224 (289)
+|++ ++.+.|.........-+.. -+..+.|+|-.|++|+|++|++.+..++.++...+ +..+..++...
T Consensus 168 ~p~~--~~~~~~~~~~~~~~~~~~~---~~~~~~g~~~~~a~el~~rag~~~~~~~~~~~~~~------~~~v~~~~~~~ 236 (564)
T COG1293 168 NPYE--QSEEDFKELQLNSGADIVR---LLARFLGLGGLLAEELLSRAGLDKKVPAKDLFEEE------IKKVREALEEL 236 (564)
T ss_pred CHHH--CCHHHHHHHHHCCCHHHHH---HHHHHCCCCHHHHHHHHHHCCCCCCCCHHHHHHHH------HHHHHHHHHHH
T ss_conf 9222--6766899986225247778---87875386577899999861787577513440889------99998766665
Q ss_pred HH
Q ss_conf 67
Q gi|254780625|r 225 LI 226 (289)
Q Consensus 225 l~ 226 (289)
+.
T Consensus 237 ~~ 238 (564)
T COG1293 237 LN 238 (564)
T ss_pred HH
T ss_conf 30
No 11
>PRK04184 DNA topoisomerase VI subunit B; Validated
Probab=96.99 E-value=0.003 Score=40.95 Aligned_cols=75 Identities=21% Similarity=0.298 Sum_probs=62.2
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHC-CCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf 56555332211106788874201-45421001112654356413689999998717877831222200101589999999
Q gi|254780625|r 140 RTLGPEPADNSFNAIYLTHQFHK-KNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLI 218 (289)
Q Consensus 140 ~~lGpD~l~~~~~~~~~~~~l~~-~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~ 218 (289)
..+-|-|- ..+...+...++. +++++..+| ++-|++||.-.++||+=.|+|.|..+..+|+++| +.+|+
T Consensus 230 ~eikPHP~--Gvelg~L~~ml~~t~~~tl~~FL--~~eFsrVg~~~A~ei~~~agl~~~~~p~~l~~~e------~~~L~ 299 (533)
T PRK04184 230 KEIKPHPH--GVDLGTLKRMAARTDRSTLSEFL--VSEFSRVGEKTAKEILEYAGLDPNKKPKELTWEE------AERLV 299 (533)
T ss_pred CCCCCCCC--CCCHHHHHHHHHHCCCCCHHHHH--HHHCCCCCHHHHHHHHHHCCCCCCCCCCCCCHHH------HHHHH
T ss_conf 76789986--26588999999875997789999--8543556989999999972899999900189999------99999
Q ss_pred HHHHHH
Q ss_conf 987887
Q gi|254780625|r 219 QEIQKV 224 (289)
Q Consensus 219 ~~i~~v 224 (289)
++++++
T Consensus 300 ~a~~~~ 305 (533)
T PRK04184 300 EAMKKM 305 (533)
T ss_pred HHHHHC
T ss_conf 999847
No 12
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=96.69 E-value=0.0036 Score=40.41 Aligned_cols=50 Identities=20% Similarity=0.331 Sum_probs=41.5
Q ss_pred CCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 54210011126543564136899999987178778312222001015899999999878
Q gi|254780625|r 164 NSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQ 222 (289)
Q Consensus 164 ~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~ 222 (289)
+.+|.-+| +.|-|||.-+|.+||..++|+|.+++++||++| +.+|...|.
T Consensus 25 ~K~v~~aL---t~I~GIG~~~A~~Ic~~~gid~~~r~g~Lteee------i~~i~~~I~ 74 (154)
T PTZ00134 25 REKVTIAL---TAIKGIGRRFATVVCKQAGVDVTKRAGELTQEE------INKIVAIIS 74 (154)
T ss_pred CCEEEEEE---EEECCCCHHHHHHHHHHCCCCCCCCCCCCCHHH------HHHHHHHHC
T ss_conf 95889985---322064899999999980989454216499999------999999972
No 13
>pfam00416 Ribosomal_S13 Ribosomal protein S13/S18. This family includes ribosomal protein S13 from prokaryotes and S18 from eukaryotes.
Probab=96.08 E-value=0.01 Score=37.52 Aligned_cols=51 Identities=20% Similarity=0.298 Sum_probs=41.6
Q ss_pred CCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 542100111265435641368999999871787783122220010158999999998788
Q gi|254780625|r 164 NSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQK 223 (289)
Q Consensus 164 ~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~~ 223 (289)
+.+|.-+|. .|-|||.-.|..||..++|+|..++++||++| +..|-+.+.+
T Consensus 10 ~K~v~~ALt---~I~GIG~~~A~~Ic~~lgi~~~~k~~~Lt~~q------i~~l~~~i~~ 60 (106)
T pfam00416 10 NKKIEIALT---YIKGIGRRKANQILKKAGVDKDKRVGELTEEE------IDRIRDIISN 60 (106)
T ss_pred CCEEEEEEC---CCCCCCHHHHHHHHHHCCCCCCCCCCCCCHHH------HHHHHHHHHH
T ss_conf 968644411---21052899999999991959775715499999------9999999975
No 14
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=95.85 E-value=0.013 Score=36.84 Aligned_cols=53 Identities=19% Similarity=0.219 Sum_probs=42.8
Q ss_pred CCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 45421001112654356413689999998717877831222200101589999999987887
Q gi|254780625|r 163 KNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKV 224 (289)
Q Consensus 163 ~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~~v 224 (289)
.+.+|.-+| +.|-|||.-.|..||-.++|+|..++.+||++| +..|-+.+.+-
T Consensus 19 ~~K~i~~AL---t~IyGIG~~~A~~Ic~~lgId~~~k~~~Lte~q------i~~l~~~i~~~ 71 (149)
T PRK04053 19 GTKPVEYAL---TGIKGIGRRTARAIARKLGLDPHAKLGYLSDEE------IEKIEEALENP 71 (149)
T ss_pred CCCEEEEEC---CCCCCCCHHHHHHHHHHHCCCCCCCCCCCCHHH------HHHHHHHHHHH
T ss_conf 996864441---111484899999999991899877307499999------99999999746
No 15
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=95.52 E-value=0.012 Score=37.05 Aligned_cols=48 Identities=25% Similarity=0.330 Sum_probs=39.5
Q ss_pred CCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 210011126543564136899999987178778312222001015899999999878
Q gi|254780625|r 166 NLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQ 222 (289)
Q Consensus 166 ~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~ 222 (289)
.+.-+| +.|-|||--.+.|||-.++|+|..++.+||++| +.+|-+++.
T Consensus 14 ~v~iAL---t~IyGIG~~~a~~I~~~~gi~~~~r~~~Lteee------i~~ir~~i~ 61 (121)
T COG0099 14 RVVIAL---TYIYGIGRRRAKEICKKAGIDPDKRVGELTEEE------IERLRDAIQ 61 (121)
T ss_pred EEEEHH---HHHCCCCHHHHHHHHHHCCCCHHHHHCCCCHHH------HHHHHHHHH
T ss_conf 576504---630353699999999991988667645299999------999999998
No 16
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=95.50 E-value=0.014 Score=36.56 Aligned_cols=49 Identities=31% Similarity=0.381 Sum_probs=39.3
Q ss_pred CCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 4210011126543564136899999987178778312222001015899999999878
Q gi|254780625|r 165 SNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQ 222 (289)
Q Consensus 165 ~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~ 222 (289)
.+|.-+| +.|-|||.-.|..||-.++|||..++.+||++| +..|-+.|.
T Consensus 13 K~v~~AL---t~I~GIG~~~A~~Ic~~lgId~~~k~g~Ls~~q------i~~I~~~I~ 61 (122)
T PRK05179 13 KRVVIAL---TYIYGIGRTRAKEILAAAGIDPDTRVKDLTDEE------LDKLREEID 61 (122)
T ss_pred CCHHHHH---HHHCCCCHHHHHHHHHHCCCCCCCCHHHCCHHH------HHHHHHHHH
T ss_conf 7868477---300275899999999982999766887656999------999999998
No 17
>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=95.35 E-value=0.023 Score=35.30 Aligned_cols=51 Identities=22% Similarity=0.292 Sum_probs=40.9
Q ss_pred CCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 542100111265435641368999999871787783122220010158999999998788
Q gi|254780625|r 164 NSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQK 223 (289)
Q Consensus 164 ~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~~ 223 (289)
+.+|.-+| +.|-|||.-+|..||-.++|+|..++.+||++| +..|-+.+..
T Consensus 16 ~K~v~~aL---t~I~GIG~~~A~~Ic~~~gid~~~k~~~Lt~~e------i~~i~~~i~~ 66 (144)
T TIGR03629 16 NKPVEYAL---TGIKGIGRRFARAIARKLGVDPNAKLGYLDDEE------IEKLEEAVEN 66 (144)
T ss_pred CCEEEEEE---EEECCCCHHHHHHHHHHHCCCCCCCCCCCCHHH------HHHHHHHHHH
T ss_conf 96898872---212372899999999990999353604199999------9999999985
No 18
>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=95.10 E-value=0.025 Score=35.07 Aligned_cols=48 Identities=25% Similarity=0.410 Sum_probs=38.8
Q ss_pred CCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 421001112654356413689999998717877831222200101589999999987
Q gi|254780625|r 165 SNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEI 221 (289)
Q Consensus 165 ~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i 221 (289)
.+|.-+| +-|-|||--.|..||-.++|+|..++.+||++| +..|-+.+
T Consensus 11 K~v~~AL---t~I~GIG~~~A~~Ic~~lgId~~~k~g~Ls~~q------i~~I~~~I 58 (113)
T TIGR03631 11 KRVEIAL---TYIYGIGRTRARKILEKAGIDPDKRVKDLTEEE------LNAIREEI 58 (113)
T ss_pred CCHHHHH---HCEECCCHHHHHHHHHHCCCCCCCCHHHCCHHH------HHHHHHHH
T ss_conf 6746065---200275899999999992999877864499999------99999999
No 19
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=94.79 E-value=0.039 Score=33.76 Aligned_cols=48 Identities=25% Similarity=0.344 Sum_probs=38.7
Q ss_pred CCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 421001112654356413689999998717877831222200101589999999987
Q gi|254780625|r 165 SNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEI 221 (289)
Q Consensus 165 ~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i 221 (289)
.+|.-+|. .|-|||--.|..||..++|+|..++++||++| +..|-+.+
T Consensus 13 K~v~~aLt---~I~GIG~~~A~~Ic~~lgi~~~~k~~~Ls~~q------i~~i~~~i 60 (122)
T CHL00137 13 KRIEIALT---YIYGIGLTSAKKILEKANIDPDTRTKDLTDEQ------IVSIRQII 60 (122)
T ss_pred CEEEEHHH---HHCCCCHHHHHHHHHHCCCCCCCCCCCCCHHH------HHHHHHHH
T ss_conf 77313111---00061899999999984989885526299999------99999999
No 20
>PRK12495 hypothetical protein; Provisional
Probab=93.11 E-value=0.026 Score=34.96 Aligned_cols=26 Identities=35% Similarity=0.732 Sum_probs=18.8
Q ss_pred CCCCCCCCCCCEEEEEEECCCCEEECCCCCC
Q ss_conf 8771078778878999987812063877679
Q gi|254780625|r 259 TGEPCLSNCGQMIRRIVQAGRSTFYCTYCQK 289 (289)
Q Consensus 259 ~g~~C~~~CG~~I~~~~~~gR~ty~Cp~CQk 289 (289)
++..| ..||.+|=+.. ..-|||.||.
T Consensus 41 TN~HC-~~CGdPIFR~d----GqeFCPTCQ~ 66 (221)
T PRK12495 41 TNAHC-DECGSPIFRHD----GQEFCPTCQH 66 (221)
T ss_pred CCCCC-CCCCCHHHHCC----CCCCCCCCCC
T ss_conf 21200-22367234047----6614864235
No 21
>pfam06677 Auto_anti-p27 Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). This family consists of several Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27) sequences. It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis.
Probab=91.40 E-value=0.11 Score=30.92 Aligned_cols=26 Identities=27% Similarity=0.814 Sum_probs=20.6
Q ss_pred CCCCCCCCCCCEEEEEEECCCCEEECCCCC
Q ss_conf 877107877887899998781206387767
Q gi|254780625|r 259 TGEPCLSNCGQMIRRIVQAGRSTFYCTYCQ 288 (289)
Q Consensus 259 ~g~~C~~~CG~~I~~~~~~gR~ty~Cp~CQ 288 (289)
-++.| |.||+++-+.+.|. .|||.||
T Consensus 16 L~~~C-~~Cg~pLf~~k~g~---~~Cp~C~ 41 (41)
T pfam06677 16 LDEHC-PKCGTPLFRLKDGK---VFCPSCE 41 (41)
T ss_pred HHCCC-CCCCCEEEECCCCC---EECCCCC
T ss_conf 54325-45698305848999---9578779
No 22
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=90.44 E-value=0.15 Score=30.04 Aligned_cols=24 Identities=25% Similarity=0.783 Sum_probs=17.3
Q ss_pred CCCCCCCCCEEEEEEECCCCEEECCCCCC
Q ss_conf 71078778878999987812063877679
Q gi|254780625|r 261 EPCLSNCGQMIRRIVQAGRSTFYCTYCQK 289 (289)
Q Consensus 261 ~~C~~~CG~~I~~~~~~gR~ty~Cp~CQk 289 (289)
..| |.||.++-+ +. .+-|||.|++
T Consensus 29 ~hC-p~Cg~PLF~-Kd---G~v~CPvC~~ 52 (131)
T COG1645 29 KHC-PKCGTPLFR-KD---GEVFCPVCGY 52 (131)
T ss_pred HHC-CCCCCCCEE-EC---CEEECCCCCC
T ss_conf 448-655883163-08---9587777776
No 23
>COG1389 DNA topoisomerase VI, subunit B [DNA replication, recombination, and repair]
Probab=89.46 E-value=0.74 Score=25.58 Aligned_cols=105 Identities=23% Similarity=0.352 Sum_probs=70.3
Q ss_pred EEEEEECCCCCCCEECCCCCCHHHCCCCCCCCCCCCCCCCHHHHHHHHHHC-CCCCCCEEEECCCCCCCCCHHHHHHHHH
Q ss_conf 899981587664100145530100532356555332211106788874201-4542100111265435641368999999
Q gi|254780625|r 112 YRVIYNDPRRFGFMDLVETSLKYQYPPLRTLGPEPADNSFNAIYLTHQFHK-KNSNLKNALLNQKIVAGIGNIYVCEALW 190 (289)
Q Consensus 112 ~~l~~~D~R~fG~~~~~~~~~~~~~~~l~~lGpD~l~~~~~~~~~~~~l~~-~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf 190 (289)
..+.|.||- |.+.+++.....-=++-..+-|-|- ..+.+.+...++. ++.++..+|+ +-|+-||---++|+|=
T Consensus 206 A~I~l~dPd--G~~~vf~r~t~~lP~pP~E~kPHP~--gvd~~~L~~M~~~T~~~tv~~fL~--sef~rig~~ta~e~~e 279 (538)
T COG1389 206 ARIVLKDPD--GNLVVFPRSTDKLPKPPKEIKPHPH--GVDLDTLKKMAHRTRRSTVREFLV--SEFSRIGEKTADELLE 279 (538)
T ss_pred EEEEEECCC--CCEEEECCCHHHCCCCCCCCCCCCC--CCCHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHH
T ss_conf 179998899--8678713314117999300489976--457889999998753435999999--9987762667999999
Q ss_pred HHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 8717877831222200101589999999987887
Q gi|254780625|r 191 RAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKV 224 (289)
Q Consensus 191 ~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~~v 224 (289)
.++.+|..+...|+.+. ..+.+++|.++.+++
T Consensus 280 ~~g~~~~~~p~~L~~~~--~~eea~~lv~a~~~~ 311 (538)
T COG1389 280 YAGFDPDKKPRELTKKK--TREEAEKLVEAFKKM 311 (538)
T ss_pred HHCCCCCCCHHHHHCCC--CHHHHHHHHHHHHHC
T ss_conf 84679654878860345--789999999999858
No 24
>PRK00420 hypothetical protein; Validated
Probab=88.89 E-value=0.22 Score=29.00 Aligned_cols=25 Identities=20% Similarity=0.486 Sum_probs=17.7
Q ss_pred CCCCCCCCCEEEEEEECCCCEEECCCCCC
Q ss_conf 71078778878999987812063877679
Q gi|254780625|r 261 EPCLSNCGQMIRRIVQAGRSTFYCTYCQK 289 (289)
Q Consensus 261 ~~C~~~CG~~I~~~~~~gR~ty~Cp~CQk 289 (289)
.+| |.||.++-+.+-| ..|||.|-|
T Consensus 20 ~~C-~~Cg~plf~~k~G---~~~Cp~cgk 44 (107)
T PRK00420 20 KHC-PVCGLPLFELKDG---EVVCPNHGK 44 (107)
T ss_pred HHC-CCCCCCEEECCCC---CEECCCCCC
T ss_conf 137-6579840574898---776898987
No 25
>PRK07220 DNA topoisomerase I; Validated
Probab=87.97 E-value=0.51 Score=26.61 Aligned_cols=29 Identities=24% Similarity=0.657 Sum_probs=23.8
Q ss_pred CCCCCCCCCCCEEEEEEECCCCEE-E-CCCCC
Q ss_conf 877107877887899998781206-3-87767
Q gi|254780625|r 259 TGEPCLSNCGQMIRRIVQAGRSTF-Y-CTYCQ 288 (289)
Q Consensus 259 ~g~~C~~~CG~~I~~~~~~gR~ty-~-Cp~CQ 288 (289)
.+..| +.||-++.++.-+|+..| . ||.|.
T Consensus 634 ~~~~C-~~~~~~~~~~~~~~~~~~~~~cp~c~ 664 (740)
T PRK07220 634 TDKVC-EAHGLHHIKIINGGKRPWDLGCPQCN 664 (740)
T ss_pred CCCCC-CCCCCEEEEEEECCCCCCCCCCCCCC
T ss_conf 78868-77998379998089875767899877
No 26
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=87.83 E-value=0.39 Score=27.39 Aligned_cols=27 Identities=22% Similarity=0.717 Sum_probs=21.2
Q ss_pred EEECCCCCCCCCCCCCEEEEEEECCCCEEECCCCCC
Q ss_conf 665738771078778878999987812063877679
Q gi|254780625|r 254 SVYGKTGEPCLSNCGQMIRRIVQAGRSTFYCTYCQK 289 (289)
Q Consensus 254 ~vy~r~g~~C~~~CG~~I~~~~~~gR~ty~Cp~CQk 289 (289)
-||.+ | ++|++.+.+ ...+-+||+||.
T Consensus 147 VI~A~----C-srC~~~L~~----~~~~l~Cp~Cg~ 173 (188)
T COG1096 147 VIYAR----C-SRCRAPLVK----KGNMLKCPNCGN 173 (188)
T ss_pred EEEEE----C-CCCCCCEEE----CCCEEECCCCCC
T ss_conf 99998----3-677762088----475998887798
No 27
>PRK08413 consensus
Probab=85.36 E-value=0.89 Score=25.06 Aligned_cols=28 Identities=4% Similarity=0.131 Sum_probs=11.6
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 2222001015899999999878876765
Q gi|254780625|r 201 RSLIQNNGTPKDILYKLIQEIQKVLIDA 228 (289)
Q Consensus 201 ~~Ls~~e~~~~~~~~~L~~~i~~vl~~a 228 (289)
+.+.+.+...++.+...|....+.+.++
T Consensus 528 d~Ia~G~~~~~~~l~~f~~~f~~~i~~~ 555 (733)
T PRK08413 528 DEIAEDKADWQKVLKDFYYPFMDKIEEG 555 (733)
T ss_pred HHHHCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf 9998598659999999999999999999
No 28
>PRK08938 DNA topoisomerase I; Validated
Probab=84.51 E-value=0.84 Score=25.22 Aligned_cols=27 Identities=11% Similarity=0.126 Sum_probs=13.3
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 222001015899999999878876765
Q gi|254780625|r 202 SLIQNNGTPKDILYKLIQEIQKVLIDA 228 (289)
Q Consensus 202 ~Ls~~e~~~~~~~~~L~~~i~~vl~~a 228 (289)
.+.+.+..-.+.+...|....+.+..+
T Consensus 536 ~Ia~G~~~~~~~l~~f~~~f~~~l~~a 562 (692)
T PRK08938 536 EVEEGKEQWVKVIDEFYKPFEKELEKA 562 (692)
T ss_pred HHHCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf 997697429999999999999999999
No 29
>PRK05823 consensus
Probab=83.20 E-value=0.67 Score=25.84 Aligned_cols=78 Identities=12% Similarity=0.113 Sum_probs=35.6
Q ss_pred CHHHHHHHHHHCC-------CCCCCEEEECCCCCCCCCHHHH--------HHHH---HHHHCCCC------CCCCCCCHH
Q ss_conf 1067888742014-------5421001112654356413689--------9999---98717877------831222200
Q gi|254780625|r 151 FNAIYLTHQFHKK-------NSNLKNALLNQKIVAGIGNIYV--------CEAL---WRAKLSPI------RKTRSLIQN 206 (289)
Q Consensus 151 ~~~~~~~~~l~~~-------~~~Ik~~LlDQ~~iaGIGN~y~--------~EiL---f~a~I~P~------~~~~~Ls~~ 206 (289)
||...+.+.+.+. ...|=..|.|-.+|-.-|+-+. .+.| |-.=++|. ...+.+.+.
T Consensus 485 yTEasLi~~ME~~GIGtpATrA~II~~L~~R~Yv~~~~k~l~pT~~G~~l~~~L~~~~~~l~~~~~Ta~~E~~Ld~I~~G 564 (691)
T PRK05823 485 YTQASLIEALEKAGIGRPSTYSTMASINLERGYANLDKRAYIPTDLGEKVNQELSKHFPKIINKEFTKNMEESLDEIAEG 564 (691)
T ss_pred CCHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCEEECCCEEEEHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCC
T ss_conf 89999999999679997576899999887368289519767451899999999987525634977999999988999769
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 1015899999999878876765
Q gi|254780625|r 207 NGTPKDILYKLIQEIQKVLIDA 228 (289)
Q Consensus 207 e~~~~~~~~~L~~~i~~vl~~a 228 (289)
+....+.+...+....+.+..+
T Consensus 565 ~~~~~~~l~~f~~~~~~~~~~~ 586 (691)
T PRK05823 565 KVNWKSFLKTFWPNFKEEVKLA 586 (691)
T ss_pred CCCHHHHHHHHHHHHHHHHHHH
T ss_conf 9889999999999999999999
No 30
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=82.15 E-value=0.6 Score=26.14 Aligned_cols=20 Identities=5% Similarity=0.337 Sum_probs=9.4
Q ss_pred EEEEEEECCCCCEEEEEEEEC
Q ss_conf 389997068876048999815
Q gi|254780625|r 98 HVTISLTNNTNTKKYRVIYND 118 (289)
Q Consensus 98 ~~~~~~~~~~~~~~~~l~~~D 118 (289)
.+.+.+.|++.... ...|.+
T Consensus 69 ~l~~~i~D~Tg~~~-~~~F~~ 88 (166)
T cd04476 69 ILSLNVADHTGEAW-LTLFDE 88 (166)
T ss_pred EEEEEEECCCCCEE-EEEEHH
T ss_conf 99999986889999-998667
No 31
>PRK08173 DNA topoisomerase III; Validated
Probab=79.29 E-value=5.1 Score=20.19 Aligned_cols=24 Identities=38% Similarity=1.027 Sum_probs=13.3
Q ss_pred CCCCCCCCCCEEEEEEECCCCEEECCCCC
Q ss_conf 77107877887899998781206387767
Q gi|254780625|r 260 GEPCLSNCGQMIRRIVQAGRSTFYCTYCQ 288 (289)
Q Consensus 260 g~~C~~~CG~~I~~~~~~gR~ty~Cp~CQ 288 (289)
+.|| |.||..|. .+...|-|..|.
T Consensus 624 ~~~C-P~Cg~~i~----~~~k~y~C~~C~ 647 (857)
T PRK08173 624 QTPC-PNCGGVVK----ENYRRFACTKCD 647 (857)
T ss_pred CCCC-CCCCCEEE----ECCCEEECCCCC
T ss_conf 5788-88895167----556189779997
No 32
>pfam00398 RrnaAD Ribosomal RNA adenine dimethylase.
Probab=78.63 E-value=2.1 Score=22.62 Aligned_cols=53 Identities=15% Similarity=0.141 Sum_probs=38.3
Q ss_pred HHHHCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 74201454210011126543564136899999987178778312222001015899999999878
Q gi|254780625|r 158 HQFHKKNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQ 222 (289)
Q Consensus 158 ~~l~~~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~ 222 (289)
..+..++.+|++.|- +++..-..++|..++|+|...+.+||.+| +.+|++.+.
T Consensus 205 ~~F~~RRK~L~n~L~------~~~~~~~~~~l~~~gi~~~~R~e~Ls~e~------~~~L~~~l~ 257 (258)
T pfam00398 205 KLFNGKGRSLFTSLR------RLFPGGQVQALSKTRINDNALVGKLSPEQ------WLTIFKELA 257 (258)
T ss_pred HHHHCCCHHHHHHHH------HHCCHHHHHHHHHCCCCCCCCCCCCCHHH------HHHHHHHHC
T ss_conf 998116378999998------73880799999987769888861599999------999999970
No 33
>KOG3311 consensus
Probab=78.58 E-value=1.7 Score=23.22 Aligned_cols=50 Identities=20% Similarity=0.368 Sum_probs=41.0
Q ss_pred CCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 54210011126543564136899999987178778312222001015899999999878
Q gi|254780625|r 164 NSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQ 222 (289)
Q Consensus 164 ~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~ 222 (289)
+..|.-+|+- |.|||--||.+++=.+++++...+.+|++.| +..+...+.
T Consensus 23 ~~~V~fAl~~---i~Gig~~~A~~ic~K~~~~~~~r~gelt~~q------i~~i~~i~~ 72 (152)
T KOG3311 23 KRKVTFALTS---IKGIGRRYAEIVCKKADLDLTKRAGELTEEQ------ILRILQILN 72 (152)
T ss_pred CCEEEEEEEE---EEEECHHHHHHHHHHCCCCHHHHHCCCCHHH------HHHHHHHHC
T ss_conf 8006898888---8651122444444203740555413124999------999999861
No 34
>pfam08273 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase.
Probab=78.28 E-value=1 Score=24.66 Aligned_cols=27 Identities=41% Similarity=0.896 Sum_probs=20.9
Q ss_pred CCCCCCCCCEEEEE---EECCCCEEECCCCC
Q ss_conf 71078778878999---98781206387767
Q gi|254780625|r 261 EPCLSNCGQMIRRI---VQAGRSTFYCTYCQ 288 (289)
Q Consensus 261 ~~C~~~CG~~I~~~---~~~gR~ty~Cp~CQ 288 (289)
.|| |.||.+=..- ...+|.+|||-+|-
T Consensus 4 ~pC-P~CGg~Drfr~fdd~~g~G~~~C~~Cg 33 (39)
T pfam08273 4 GPC-PNCGGSDRFRIFDDKDGRGTWFCFSCG 33 (39)
T ss_pred CCC-CCCCCCCCCEECCCCCCCCCEECCCCC
T ss_conf 677-777785752565578997577838887
No 35
>PRK09137 DNA topoisomerase I; Validated
Probab=78.20 E-value=2.1 Score=22.61 Aligned_cols=79 Identities=8% Similarity=0.045 Sum_probs=34.4
Q ss_pred CCHHHHHHHHHHCC-------CCCCCEEEECCCCCCCCCHH--------HHHHHHHH---HHCCCC------CCCCCCCH
Q ss_conf 11067888742014-------54210011126543564136--------89999998---717877------83122220
Q gi|254780625|r 150 SFNAIYLTHQFHKK-------NSNLKNALLNQKIVAGIGNI--------YVCEALWR---AKLSPI------RKTRSLIQ 205 (289)
Q Consensus 150 ~~~~~~~~~~l~~~-------~~~Ik~~LlDQ~~iaGIGN~--------y~~EiLf~---a~I~P~------~~~~~Ls~ 205 (289)
.+|...+.+.+.+. ..+|=..|+|..+|---|+- .-.+.|-. .=++|. ...+.+.+
T Consensus 472 ryTEasLIk~ME~~GIGtpsT~A~II~~L~~R~Yv~~~~k~l~pT~lG~~v~~~L~~~f~~iv~~~~Ta~mE~~Ld~Ia~ 551 (761)
T PRK09137 472 RYTEASLVKALEEYGIGRPSTYASIISTLQQREYVRLDKKRFIPTDVGRIVNKFLTEHFTKYVDYNFTAGLEDELDEIAR 551 (761)
T ss_pred CCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCEEEECCEEEECHHHHHHHHHHHHHCHHHCCHHHHHHHHHHHHHHHC
T ss_conf 88999999999737999623689999989738969965998856467999999998855231596689999998899976
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 01015899999999878876765
Q gi|254780625|r 206 NNGTPKDILYKLIQEIQKVLIDA 228 (289)
Q Consensus 206 ~e~~~~~~~~~L~~~i~~vl~~a 228 (289)
.+..-.+.+...|......+..+
T Consensus 552 G~~~~~~vl~~f~~~f~~~~~~~ 574 (761)
T PRK09137 552 GEKDWIPVLEEFWHPFIELIKEK 574 (761)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHH
T ss_conf 99608999999999999999999
No 36
>pfam03486 HI0933_like HI0933-like protein.
Probab=77.83 E-value=1.7 Score=23.24 Aligned_cols=65 Identities=23% Similarity=0.221 Sum_probs=45.8
Q ss_pred CCCHHHHHHHHHHC-----CCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 11106788874201-----4542100111265435641368999999871787783122220010158999999998788
Q gi|254780625|r 149 NSFNAIYLTHQFHK-----KNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQK 223 (289)
Q Consensus 149 ~~~~~~~~~~~l~~-----~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~~ 223 (289)
|+++.+.+.+.+.. .++.++.+|- .-+=.=+...+|-.++|+|.+++++|+.++ +.+|.+.+++
T Consensus 267 P~~~~~~l~~~l~~~~~~~~~~~~~~~l~-----~~lp~rl~~~ll~~~~i~~~~~~~~l~~~~------~~~l~~~lk~ 335 (405)
T pfam03486 267 PDLDAEELAARLEKPRGAHPKKSLKNALA-----GLLPKRLALFLLEQAGIDPDKKLAQLSKKD------LAALADLLKA 335 (405)
T ss_pred CCCCHHHHHHHHHHHHHHCCHHHHHHHHH-----HHHHHHHHHHHHHHCCCCCCCCHHHCCHHH------HHHHHHHHHC
T ss_conf 99999999999999988682323999888-----775899999999971998688636579999------9999999866
Q ss_pred H
Q ss_conf 7
Q gi|254780625|r 224 V 224 (289)
Q Consensus 224 v 224 (289)
.
T Consensus 336 ~ 336 (405)
T pfam03486 336 W 336 (405)
T ss_pred C
T ss_conf 9
No 37
>PRK07219 DNA topoisomerase I; Validated
Probab=76.18 E-value=3 Score=21.69 Aligned_cols=25 Identities=32% Similarity=0.745 Sum_probs=10.3
Q ss_pred CCCCCCCCCCEEEEEEECCCCEEECC
Q ss_conf 77107877887899998781206387
Q gi|254780625|r 260 GEPCLSNCGQMIRRIVQAGRSTFYCT 285 (289)
Q Consensus 260 g~~C~~~CG~~I~~~~~~gR~ty~Cp 285 (289)
+++| |.||.++...+-+.+.-.+||
T Consensus 716 ~e~C-p~Cg~~~~~~~~~~~~~~~C~ 740 (769)
T PRK07219 716 GEKC-PYCGAPILVLINGRRHWKFCP 740 (769)
T ss_pred CCCC-CCCCCEEEEEECCCCCEEECC
T ss_conf 8847-778983799972784300689
No 38
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=72.87 E-value=2.6 Score=22.04 Aligned_cols=27 Identities=41% Similarity=0.951 Sum_probs=19.8
Q ss_pred CCCCCCCCCEEEEE--EECCCCEEECCCCC
Q ss_conf 71078778878999--98781206387767
Q gi|254780625|r 261 EPCLSNCGQMIRRI--VQAGRSTFYCTYCQ 288 (289)
Q Consensus 261 ~~C~~~CG~~I~~~--~~~gR~ty~Cp~CQ 288 (289)
.|| |.||..=..- .-.||.+|+|-+|-
T Consensus 4 ~pC-P~CGG~Drfrf~dk~g~G~~~C~~Cg 32 (37)
T smart00778 4 GPC-PNCGGSDRFRFDDKDGRGTWFCSVCG 32 (37)
T ss_pred CCC-CCCCCCCCEEEECCCCCEEEECCCCC
T ss_conf 678-86778655367469997407827887
No 39
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=72.60 E-value=3.5 Score=21.22 Aligned_cols=26 Identities=27% Similarity=0.682 Sum_probs=19.1
Q ss_pred CCCCCCCCEEEEEEECCCCEEECCCCC
Q ss_conf 107877887899998781206387767
Q gi|254780625|r 262 PCLSNCGQMIRRIVQAGRSTFYCTYCQ 288 (289)
Q Consensus 262 ~C~~~CG~~I~~~~~~gR~ty~Cp~CQ 288 (289)
-| |.||..+.-..-.+...|.|++|.
T Consensus 2 FC-p~C~n~l~p~~~~~~~~~~C~~C~ 27 (52)
T smart00661 2 FC-PKCGNMLIPKEGKEKRRFVCRKCG 27 (52)
T ss_pred CC-CCCCCEEEEEECCCCEEEECCCCC
T ss_conf 78-652888768536995389748999
No 40
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=71.38 E-value=5.4 Score=20.06 Aligned_cols=53 Identities=23% Similarity=0.430 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHEEEECCCCCCCCCCCCCEEEEEEECCCCEEECCCC
Q ss_conf 9999987887676542188755311167787787413316657387710787788789999878120638776
Q gi|254780625|r 215 YKLIQEIQKVLIDAIDAGGSSLRDYVHIDGSIGYFQNAFSVYGKTGEPCLSNCGQMIRRIVQAGRSTFYCTYC 287 (289)
Q Consensus 215 ~~L~~~i~~vl~~a~~~gG~~~~~~~~~~g~~g~~~~~~~vy~r~g~~C~~~CG~~I~~~~~~gR~ty~Cp~C 287 (289)
..+..+|-++|..-+..++.... .... .-.+.+| |.||.++.+. +| =+.|+.|
T Consensus 675 ~S~~daI~~~L~~~~~~~~~~~~-----~~~~----------~~~~~~C-P~CG~~l~~~--eG--C~~C~~C 727 (733)
T PRK08665 675 LSCPDAIAKVLEKHLLANGYDPV-----EEEA----------DPERGAC-PECGSILEHE--EG--CAVCHSC 727 (733)
T ss_pred CCHHHHHHHHHHHHHHHCCCCCC-----CCCC----------CCCCCCC-CCCCCEEEEC--CC--CCCCCCC
T ss_conf 54999999999999973577766-----5546----------6678979-9998747876--89--8727778
No 41
>PRK00274 ksgA dimethyladenosine transferase; Reviewed
Probab=71.36 E-value=4.3 Score=20.66 Aligned_cols=56 Identities=20% Similarity=0.380 Sum_probs=40.8
Q ss_pred HHHHCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 7420145421001112654356413689999998717877831222200101589999999987887
Q gi|254780625|r 158 HQFHKKNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKV 224 (289)
Q Consensus 158 ~~l~~~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~~v 224 (289)
..+..+++.|++.|- ..+ .+--.+++|-.++|+|...+.+||.+| +.+|++.+...
T Consensus 210 ~~F~~RRK~l~n~Lk--~~~---~~~~~~~~l~~~~i~~~~RpeeLs~~~------~~~L~~~l~~~ 265 (267)
T PRK00274 210 AAFNQRRKTLRNNLK--NLA---GKELLEELLEALGIDPNRRAETLSVEE------FVRLANALADL 265 (267)
T ss_pred HHHHCCHHHHHHHHH--HHC---CHHHHHHHHHHCCCCCCCCHHHCCHHH------HHHHHHHHHHH
T ss_conf 998146489999998--752---888899999986979677824399999------99999999997
No 42
>PRK08620 DNA topoisomerase III; Provisional
Probab=70.27 E-value=4.3 Score=20.67 Aligned_cols=24 Identities=21% Similarity=0.534 Sum_probs=9.2
Q ss_pred CCCCCCCCCCEEEEEEECCCCEEEC
Q ss_conf 7710787788789999878120638
Q gi|254780625|r 260 GEPCLSNCGQMIRRIVQAGRSTFYC 284 (289)
Q Consensus 260 g~~C~~~CG~~I~~~~~~gR~ty~C 284 (289)
|..| |.||..+..-.-+....|.|
T Consensus 648 ~~~C-p~C~~~~~~~~~~~g~~~~c 671 (726)
T PRK08620 648 NARC-PNCKKKLELRGEGEGQIFVC 671 (726)
T ss_pred CCCC-CCCCCEEEEEECCCCCEEEE
T ss_conf 8949-99998568985677878997
No 43
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=69.72 E-value=3 Score=21.71 Aligned_cols=22 Identities=27% Similarity=0.753 Sum_probs=16.7
Q ss_pred CCCCCCCCCCEEEEEEECCCCEEECCCCCC
Q ss_conf 771078778878999987812063877679
Q gi|254780625|r 260 GEPCLSNCGQMIRRIVQAGRSTFYCTYCQK 289 (289)
Q Consensus 260 g~~C~~~CG~~I~~~~~~gR~ty~Cp~CQk 289 (289)
-+.| ++||. -....|.||.|..
T Consensus 309 S~~C-~~cg~-------~~~r~~~C~~cg~ 330 (364)
T COG0675 309 SKTC-PCCGH-------LSGRLFKCPRCGF 330 (364)
T ss_pred CCCC-CCCCC-------CCCCEEECCCCCC
T ss_conf 7778-87787-------4785488899897
No 44
>TIGR00755 ksgA dimethyladenosine transferase; InterPro: IPR011530 This family of proteins represent the rRNA adenine dimethylases (e.g. KsgA). The bacterial enzyme KsgA catalyzes 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 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. 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 .; GO: 0016433 rRNA (adenine) methyltransferase activity, 0006364 rRNA processing.
Probab=69.09 E-value=5.2 Score=20.13 Aligned_cols=59 Identities=20% Similarity=0.260 Sum_probs=47.0
Q ss_pred HHHHHHCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCC---CCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf 887420145421001112654356413689999998717877---83122220010158999999998
Q gi|254780625|r 156 LTHQFHKKNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPI---RKTRSLIQNNGTPKDILYKLIQE 220 (289)
Q Consensus 156 ~~~~l~~~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~---~~~~~Ls~~e~~~~~~~~~L~~~ 220 (289)
....+..|++++.+.|-+-..-..+.+.+..+.|...+|++. +++-+|+-+| +.+|++.
T Consensus 215 ~~~~F~~RRK~l~n~L~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~R~e~L~~~d------f~~L~~~ 276 (277)
T TIGR00755 215 LKAAFSQRRKTLRNNLKNSLKDNLLAKEKLEEVLEQLGLDPTKLNARAEQLSPED------FLRLANL 276 (277)
T ss_pred HHHHHCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCHHCCHHCCCHHH------HHHHHHH
T ss_conf 9998617871015556542221011124566678870888650006611148899------9999960
No 45
>pfam07282 Transposase_35 Putative transposase DNA-binding domain. This putative domain is found at the C-terminus of a large number of transposase proteins. This domain contains four conserved cysteines suggestive of a zinc binding domain. Given the need for transposases to bind DNA as well as the large number of DNA-binding zinc fingers we hypothesize this domain is DNA-binding.
Probab=68.66 E-value=2.4 Score=22.31 Aligned_cols=27 Identities=41% Similarity=0.886 Sum_probs=19.2
Q ss_pred CCCCCCCCCCCEEEEEEECCCCEEECCCCC
Q ss_conf 877107877887899998781206387767
Q gi|254780625|r 259 TGEPCLSNCGQMIRRIVQAGRSTFYCTYCQ 288 (289)
Q Consensus 259 ~g~~C~~~CG~~I~~~~~~gR~ty~Cp~CQ 288 (289)
+-+.| +.||....+ ...+| .|.||.|-
T Consensus 27 TS~~C-~~Cg~~~~~-~~~~r-~~~C~~Cg 53 (69)
T pfam07282 27 TSKTC-SVCGHKNKE-SLSGR-TFKCPNCG 53 (69)
T ss_pred CCCCC-CCCCCCCCC-CCCCC-EEECCCCC
T ss_conf 86427-999899867-48887-89899899
No 46
>PRK05582 DNA topoisomerase I; Validated
Probab=66.90 E-value=3.8 Score=20.98 Aligned_cols=79 Identities=14% Similarity=0.153 Sum_probs=35.8
Q ss_pred CHHHHHHHHHHCC-------CCCCCEEEECCCCCCCCCHHH--------HHHHHHH---HHCCCC------CCCCCCCHH
Q ss_conf 1067888742014-------542100111265435641368--------9999998---717877------831222200
Q gi|254780625|r 151 FNAIYLTHQFHKK-------NSNLKNALLNQKIVAGIGNIY--------VCEALWR---AKLSPI------RKTRSLIQN 206 (289)
Q Consensus 151 ~~~~~~~~~l~~~-------~~~Ik~~LlDQ~~iaGIGN~y--------~~EiLf~---a~I~P~------~~~~~Ls~~ 206 (289)
||...+.+.+... ..+|=..|++..+|.--|+-+ -.|.|-. .=++|. ...+.+.++
T Consensus 457 yTEasLik~ME~~GIGtpATrA~II~~L~~R~Yv~~~~k~l~pT~~G~~v~~~L~~~f~~i~~~~~Ta~~E~~Ld~I~~G 536 (692)
T PRK05582 457 YSEASLIKKLESLGIGRPSTYAPTISTLLSRKYVEREKKQLIPTELGFKVIEILEKHFPQIVDSEFTANMEEKLDEIAEG 536 (692)
T ss_pred CCHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCEEEECCEEEECHHHHHHHHHHHHHCHHHCCHHHHHHHHHHHHHHHCC
T ss_conf 79999999998479986045899998887467099409888475799999999988553322854899999999999859
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 10158999999998788767654
Q gi|254780625|r 207 NGTPKDILYKLIQEIQKVLIDAI 229 (289)
Q Consensus 207 e~~~~~~~~~L~~~i~~vl~~a~ 229 (289)
+..-++.+...|....+.+..+.
T Consensus 537 ~~~~~~~l~~f~~~f~~~i~~~~ 559 (692)
T PRK05582 537 KADWQEVLKDFYYPFMEKIEEAK 559 (692)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHH
T ss_conf 87799999999999999999998
No 47
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=63.76 E-value=2.7 Score=21.96 Aligned_cols=25 Identities=36% Similarity=0.875 Sum_probs=16.7
Q ss_pred CCCCCCC-CEEEEEEEC--CCCEEECCCC
Q ss_conf 1078778-878999987--8120638776
Q gi|254780625|r 262 PCLSNCG-QMIRRIVQA--GRSTFYCTYC 287 (289)
Q Consensus 262 ~C~~~CG-~~I~~~~~~--gR~ty~Cp~C 287 (289)
+| |+|| ..|-|-.-- -..+|-||+|
T Consensus 29 ~C-PnCGe~~I~Rc~~CRk~g~~Y~Cp~C 56 (61)
T COG2888 29 PC-PNCGEVEIYRCAKCRKLGNPYRCPKC 56 (61)
T ss_pred EC-CCCCCEEEEHHHHHHHCCCCEECCCC
T ss_conf 48-99982424105668774994478876
No 48
>PRK07141 DNA topoisomerase I; Validated
Probab=63.69 E-value=12 Score=17.90 Aligned_cols=29 Identities=21% Similarity=0.580 Sum_probs=16.9
Q ss_pred CCCCCCCCCCCEEE--EEEECCCCEEECCC---CC
Q ss_conf 87710787788789--99987812063877---67
Q gi|254780625|r 259 TGEPCLSNCGQMIR--RIVQAGRSTFYCTY---CQ 288 (289)
Q Consensus 259 ~g~~C~~~CG~~I~--~~~~~gR~ty~Cp~---CQ 288 (289)
.|.+| |.||..+. +.+.|+..-|-|.. |.
T Consensus 564 ~~~~C-P~Cg~~l~~r~~~~g~~~F~gCs~yp~Ck 597 (622)
T PRK07141 564 LGESC-PDCNGDLVYRNNRKGDQRFIGCSNFPNCR 597 (622)
T ss_pred CCCCC-CCCCCCEEEEECCCCCCEEEECCCCCCCC
T ss_conf 79988-78998225787368898698789998888
No 49
>PRK12366 replication factor A; Reviewed
Probab=63.18 E-value=4.1 Score=20.77 Aligned_cols=23 Identities=22% Similarity=0.713 Sum_probs=17.4
Q ss_pred CCCCCCCCCEEEEEEECCCCEEECCCCC
Q ss_conf 7107877887899998781206387767
Q gi|254780625|r 261 EPCLSNCGQMIRRIVQAGRSTFYCTYCQ 288 (289)
Q Consensus 261 ~~C~~~CG~~I~~~~~~gR~ty~Cp~CQ 288 (289)
..| |.|+..+.... ..|-||.|-
T Consensus 534 ~~C-P~C~krv~~~e----~~y~C~~cG 556 (649)
T PRK12366 534 TLC-PNCRKRVNLVD----NKYVCEECG 556 (649)
T ss_pred EEC-CCCCCEEEECC----CCEECCCCC
T ss_conf 728-66676056458----825277678
No 50
>PRK07726 DNA topoisomerase III; Provisional
Probab=63.14 E-value=12 Score=17.84 Aligned_cols=22 Identities=23% Similarity=0.664 Sum_probs=15.3
Q ss_pred CCCCCCCCEEEEEEECCCCEEEC-----CCCC
Q ss_conf 10787788789999878120638-----7767
Q gi|254780625|r 262 PCLSNCGQMIRRIVQAGRSTFYC-----TYCQ 288 (289)
Q Consensus 262 ~C~~~CG~~I~~~~~~gR~ty~C-----p~CQ 288 (289)
+| |.||..|.. +...|.| |.|.
T Consensus 632 ~C-P~Cg~~v~~----~~k~~~Cs~y~~~~C~ 658 (716)
T PRK07726 632 SC-KKCDGDVID----KGTFYGCSNYNTTQCD 658 (716)
T ss_pred CC-CCCCCEEEE----CCEEEECCCCCCCCCC
T ss_conf 59-999998377----6758973799899999
No 51
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=62.64 E-value=6.6 Score=19.49 Aligned_cols=23 Identities=26% Similarity=0.667 Sum_probs=18.1
Q ss_pred CCCCCCCCEEEEEEECCCCEEECCCCCC
Q ss_conf 1078778878999987812063877679
Q gi|254780625|r 262 PCLSNCGQMIRRIVQAGRSTFYCTYCQK 289 (289)
Q Consensus 262 ~C~~~CG~~I~~~~~~gR~ty~Cp~CQk 289 (289)
.| +.||.++.. ......||.|.+
T Consensus 152 ~C-~~cg~~m~~----~~~~~~Cp~cg~ 174 (187)
T PRK09521 152 LC-SRCRTPLVK----KGNTLKCPNCGN 174 (187)
T ss_pred EC-CCCCCCEEE----ECCEEECCCCCC
T ss_conf 57-767885867----399999999999
No 52
>TIGR00617 rpa1 replication factor-a protein 1 (rpa1); InterPro: IPR004591 All proteins in this family for which functions are known are part of a multiprotein complex made up of homologs of RPA1, RPA2 and RPA3 that bind single-stranded DNA and function in the recognition of DNA damage for nucleotide excision repair. The complex binds to single-stranded DNA sequences participating in DNA replication in addition to those mediating transcriptional repression and activation, and stimulates the activity of cognate strand exchange protein Sep1. It cooperates with T-AG and DNA topoisomerase I to unwind template DNA containing the Simian virus 40 origin of replication. This family is Replication factor-a protein 1 (RPA1); GO: 0003677 DNA binding, 0006260 DNA replication, 0005634 nucleus.
Probab=62.28 E-value=4.7 Score=20.40 Aligned_cols=53 Identities=28% Similarity=0.718 Sum_probs=29.7
Q ss_pred HCCC-CCCCCCCCCCCCCCCCHHH-EEEECCCCCCCCCC----CCCEEEEEEECCCCEEECCCCCC
Q ss_conf 2188-7553111677877874133-16657387710787----78878999987812063877679
Q gi|254780625|r 230 DAGG-SSLRDYVHIDGSIGYFQNA-FSVYGKTGEPCLSN----CGQMIRRIVQAGRSTFYCTYCQK 289 (289)
Q Consensus 230 ~~gG-~~~~~~~~~~g~~g~~~~~-~~vy~r~g~~C~~~----CG~~I~~~~~~gR~ty~Cp~CQk 289 (289)
..|. +.-.||.-..+..-+.+.. =..| | .|+.. |..+| .-.+-.+|||.+|||
T Consensus 504 ~lG~DsdKPDyfs~kA~I~~~k~~qN~~Y-~---ACp~~~DrPCnKKV---~d~~~g~yRCEKC~k 562 (671)
T TIGR00617 504 NLGKDSDKPDYFSVKATIVYLKKDQNALY-R---ACPKEGDRPCNKKV---VDQGDGTYRCEKCDK 562 (671)
T ss_pred HCCCCCCCCCEEEEEEEEEEECCCCEEEE-C---CCCCCCCCCCCCEE---EECCCCCEEEECCCC
T ss_conf 36898875616999899999716740542-4---67445788866456---745979358612688
No 53
>smart00532 LIGANc Ligase N family.
Probab=62.16 E-value=6.8 Score=19.39 Aligned_cols=23 Identities=26% Similarity=0.668 Sum_probs=16.1
Q ss_pred CCCCCCCCCEEEEEEECCCCEEECCC
Q ss_conf 71078778878999987812063877
Q gi|254780625|r 261 EPCLSNCGQMIRRIVQAGRSTFYCTY 286 (289)
Q Consensus 261 ~~C~~~CG~~I~~~~~~gR~ty~Cp~ 286 (289)
..| |.||+.+.+. ++...++||.
T Consensus 400 ~~C-P~C~s~l~~~--~~~~~~~C~n 422 (441)
T smart00532 400 THC-PSCGSELVRE--EGEVDIRCPN 422 (441)
T ss_pred CCC-CCCCCEEEEC--CCCEEEECCC
T ss_conf 989-8997983843--8987898899
No 54
>TIGR01544 HAD-SF-IE HAD-superfamily (subfamily IE) hydrolase, TIGR01544; InterPro: IPR006434 This family is a small group of metazoan sequences with one sequence from Arabidopsis thaliana. The sequences from mouse are annotated as pyrimidine 5-nucleotidases, apparently in reference to HSPC233, the human homolog. However, no such annotation can currently be found for this gene. This group of sequences was found during searches for members of the haloacid dehalogenase (HAD) superfamily (IPR005834 from INTERPRO). All of the conserved catalytic motifs are found. The placement of the variable domain between motifs 1 and 2 indicates membership in subfamily I of the superfamily, but these sequences are sufficiently different from any of the branches of that subfamily (IA-ID) as to constitute a separate branch to now be called IE. Considering that the closest identifiable hit outside of the noise range is to a phosphoserine phosphatase, this group may be considered to be most closely allied to subfamily IB..
Probab=61.12 E-value=5.8 Score=19.84 Aligned_cols=43 Identities=30% Similarity=0.343 Sum_probs=30.4
Q ss_pred HHHHHHHHHCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHH--CCCCCCCCC
Q ss_conf 67888742014542100111265435641368999999871--787783122
Q gi|254780625|r 153 AIYLTHQFHKKNSNLKNALLNQKIVAGIGNIYVCEALWRAK--LSPIRKTRS 202 (289)
Q Consensus 153 ~~~~~~~l~~~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~--I~P~~~~~~ 202 (289)
.+.|.+.|.+..-| .+. +=|||||++- ++|=||. +||..++=|
T Consensus 133 ~e~Ff~~Lq~h~IP--~~i----FSAGiGn~~e-~vlrQa~Gv~hpNvkvvS 177 (287)
T TIGR01544 133 AEDFFEKLQRHSIP--VLI----FSAGIGNVVE-EVLRQALGVLHPNVKVVS 177 (287)
T ss_pred HHHHHHHHHHCCCC--EEE----EECCCHHHHH-HHHHHHCCCCCCCCEEEE
T ss_conf 16799998745898--999----9357217999-999863588899743886
No 55
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=60.69 E-value=2.3 Score=22.45 Aligned_cols=27 Identities=22% Similarity=0.546 Sum_probs=20.5
Q ss_pred CCCCCCCCCEEEEEEECCCCEEECCCCC
Q ss_conf 7107877887899998781206387767
Q gi|254780625|r 261 EPCLSNCGQMIRRIVQAGRSTFYCTYCQ 288 (289)
Q Consensus 261 ~~C~~~CG~~I~~~~~~gR~ty~Cp~CQ 288 (289)
-+| |.||.++.....+--.-|-|.+||
T Consensus 8 v~C-P~Cgkpv~w~~~s~frPFCSkRCk 34 (65)
T COG3024 8 VPC-PTCGKPVVWGEESPFRPFCSKRCK 34 (65)
T ss_pred CCC-CCCCCCCCCCCCCCCCCCHHHHHH
T ss_conf 538-877883334666776763367662
No 56
>COG2081 Predicted flavoproteins [General function prediction only]
Probab=60.12 E-value=8.2 Score=18.87 Aligned_cols=64 Identities=23% Similarity=0.208 Sum_probs=47.5
Q ss_pred CCCHHHHHHHHHHC--CCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 11106788874201--45421001112654356413689999998717877831222200101589999999987887
Q gi|254780625|r 149 NSFNAIYLTHQFHK--KNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKV 224 (289)
Q Consensus 149 ~~~~~~~~~~~l~~--~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~~v 224 (289)
|+.+.+.+.+.+++ +++++|++|-. .++-=+..=+|=+++| |..+..+||.++ ++.|...++.-
T Consensus 268 P~~~~~~l~~~l~~~~~~kslkn~L~~-----~lp~rlv~~~l~~~~i-~~~~~~~ls~~~------~~~l~~~ik~~ 333 (408)
T COG2081 268 PDVDAEELLRELRRANPKKSLKNALAK-----LLPKRLVEFLLERAGI-PDEPLAQLSPKE------LAQLAAALKAW 333 (408)
T ss_pred CCCCHHHHHHHHHHHCHHHHHHHHHHH-----HHHHHHHHHHHHHCCC-CCCCHHHCCHHH------HHHHHHHHHCC
T ss_conf 999999999999765855689999987-----7326799999985357-874256559888------99999997547
No 57
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=59.37 E-value=4.4 Score=20.58 Aligned_cols=20 Identities=30% Similarity=1.016 Sum_probs=13.4
Q ss_pred CCCCCCCCEEEEEEECCCCEEE-CCCCCC
Q ss_conf 1078778878999987812063-877679
Q gi|254780625|r 262 PCLSNCGQMIRRIVQAGRSTFY-CTYCQK 289 (289)
Q Consensus 262 ~C~~~CG~~I~~~~~~gR~ty~-Cp~CQk 289 (289)
.| ++||-+. ++.|| ||.|-+
T Consensus 356 RC-~~CGF~a-------~~l~W~CPsC~~ 376 (389)
T COG2956 356 RC-QNCGFTA-------HTLYWHCPSCRA 376 (389)
T ss_pred EE-CCCCCCH-------HEEEEECCCCCC
T ss_conf 10-0168631-------013541887565
No 58
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=59.18 E-value=4.2 Score=20.75 Aligned_cols=29 Identities=34% Similarity=0.863 Sum_probs=22.0
Q ss_pred ECCCCCCCCCCCCCEEEEEEECCCCEEECCCCC
Q ss_conf 573877107877887899998781206387767
Q gi|254780625|r 256 YGKTGEPCLSNCGQMIRRIVQAGRSTFYCTYCQ 288 (289)
Q Consensus 256 y~r~g~~C~~~CG~~I~~~~~~gR~ty~Cp~CQ 288 (289)
|-+.+-.| |+||..+ +..||+-|-||+|-
T Consensus 346 ~~~~~p~C-p~Cg~~m---~S~G~~g~rC~kCg 374 (421)
T COG1571 346 YERVNPVC-PRCGGRM---KSAGRNGFRCKKCG 374 (421)
T ss_pred EEECCCCC-CCCCCCH---HHCCCCCCCCCCCC
T ss_conf 67717889-7667713---11678985266426
No 59
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=56.30 E-value=9.1 Score=18.57 Aligned_cols=22 Identities=32% Similarity=0.756 Sum_probs=14.1
Q ss_pred CCCCCCCCEEEEEEECCCCEEECCC
Q ss_conf 1078778878999987812063877
Q gi|254780625|r 262 PCLSNCGQMIRRIVQAGRSTFYCTY 286 (289)
Q Consensus 262 ~C~~~CG~~I~~~~~~gR~ty~Cp~ 286 (289)
.| |.||+.+.+ .-+-...+|+.
T Consensus 406 ~C-P~C~s~l~r--~~~e~~~rC~n 427 (667)
T COG0272 406 HC-PVCGSELVR--EEGEVVIRCTN 427 (667)
T ss_pred CC-CCCCCEEEE--CCCCEEEECCC
T ss_conf 79-889997674--26755686689
No 60
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=55.89 E-value=8.2 Score=18.86 Aligned_cols=28 Identities=21% Similarity=0.578 Sum_probs=20.3
Q ss_pred CCCCCCCCCCCCEEEEEEECCCCEEECCCCC
Q ss_conf 3877107877887899998781206387767
Q gi|254780625|r 258 KTGEPCLSNCGQMIRRIVQAGRSTFYCTYCQ 288 (289)
Q Consensus 258 r~g~~C~~~CG~~I~~~~~~gR~ty~Cp~CQ 288 (289)
|..+.| |+||.-|-.....+| ++|-.|-
T Consensus 21 r~~k~C-PrCG~GvfmA~H~dR--~~CGKCg 48 (54)
T PRK00432 21 RKNKFC-PRCGPGVFMAEHKDR--WACGKCG 48 (54)
T ss_pred ECCCCC-CCCCCCEEEEECCCC--CCCCCCC
T ss_conf 867859-799994640125887--6635866
No 61
>TIGR00575 dnlj DNA ligase, NAD-dependent; InterPro: IPR001679 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalyzing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase: one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC). This family is predominantly composed of NAD-dependent bacterial DNA ligases. They are proteins of about 75 to 85 Kd whose sequence is well conserved , . They also show similarity to yicF, an Escherichia coli hypothetical protein of 63 Kd.; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair.
Probab=54.40 E-value=7.8 Score=19.00 Aligned_cols=22 Identities=32% Similarity=0.691 Sum_probs=11.8
Q ss_pred CCCCCCCCEEEEEEECCCCEEECCC
Q ss_conf 1078778878999987812063877
Q gi|254780625|r 262 PCLSNCGQMIRRIVQAGRSTFYCTY 286 (289)
Q Consensus 262 ~C~~~CG~~I~~~~~~gR~ty~Cp~ 286 (289)
.| |.||+++.++. +-..+|||+
T Consensus 413 ~C-P~C~s~lv~~~--~e~~~rC~N 434 (706)
T TIGR00575 413 HC-PSCGSPLVRIE--EEVDIRCTN 434 (706)
T ss_pred CC-CCCCCEEECCC--CCEEEECCC
T ss_conf 18-88883311157--872165388
No 62
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=54.04 E-value=5.5 Score=19.98 Aligned_cols=28 Identities=18% Similarity=0.612 Sum_probs=18.9
Q ss_pred CCCCCCCCCEEEEEEEC-------------CCCEEECCCCCC
Q ss_conf 71078778878999987-------------812063877679
Q gi|254780625|r 261 EPCLSNCGQMIRRIVQA-------------GRSTFYCTYCQK 289 (289)
Q Consensus 261 ~~C~~~CG~~I~~~~~~-------------gR~ty~Cp~CQk 289 (289)
.-| |.|++.+.+..-. ....|.||+|-|
T Consensus 98 ~RC-p~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~Cgk 138 (165)
T COG1656 98 SRC-PECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGK 138 (165)
T ss_pred CCC-CCCCCEECCCCHHHHHHCCCHHHHHCCCCEEECCCCCC
T ss_conf 327-43497801076777752065244202001467799762
No 63
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=53.76 E-value=1.8 Score=23.11 Aligned_cols=28 Identities=7% Similarity=0.143 Sum_probs=16.9
Q ss_pred CCCCEEEECCCCCCC-CCHHHHHHHHHHH
Q ss_conf 421001112654356-4136899999987
Q gi|254780625|r 165 SNLKNALLNQKIVAG-IGNIYVCEALWRA 192 (289)
Q Consensus 165 ~~Ik~~LlDQ~~iaG-IGN~y~~EiLf~a 192 (289)
.++-...||-.++-| +|-....-|...+
T Consensus 143 ~~vvv~vmDF~FmGGSMGsvvGEki~ra~ 171 (305)
T CHL00174 143 IPVALGVMDFQFMGGSMGSVVGEKITRLI 171 (305)
T ss_pred EEEEEEEEECCCCCCCCHHHHHHHHHHHH
T ss_conf 77999997240115652078899999999
No 64
>COG0030 KsgA Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis]
Probab=52.94 E-value=12 Score=17.85 Aligned_cols=52 Identities=23% Similarity=0.432 Sum_probs=38.7
Q ss_pred HHHHHCCCCCCCEEEECCCCCCCCCHHH-HHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 8742014542100111265435641368-999999871787783122220010158999999998788
Q gi|254780625|r 157 THQFHKKNSNLKNALLNQKIVAGIGNIY-VCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQK 223 (289)
Q Consensus 157 ~~~l~~~~~~Ik~~LlDQ~~iaGIGN~y-~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~~ 223 (289)
...+..+++++.+.|- |++ ..|+|=+++|+|.+.+.+||-+| +.+|++....
T Consensus 204 ~~~F~~RRKtl~n~l~---------~~~~~~~~l~~~~i~~~~R~e~ls~~~------f~~L~~~l~~ 256 (259)
T COG0030 204 KAAFSQRRKTLRNNLK---------NLFGLEEVLEAAGIDPNARAENLSPED------FLKLANALKG 256 (259)
T ss_pred HHHHHHHHHHHHHHHH---------HHHHHHHHHHHCCCCCCCCHHHCCHHH------HHHHHHHHHH
T ss_conf 9998600688999877---------541199999866998113956599999------9999998764
No 65
>PRK00635 excinuclease ABC subunit A; Provisional
Probab=51.68 E-value=18 Score=16.62 Aligned_cols=17 Identities=12% Similarity=-0.027 Sum_probs=12.2
Q ss_pred HHHCCCCCCCCCCCHHH
Q ss_conf 87178778312222001
Q gi|254780625|r 191 RAKLSPIRKTRSLIQNN 207 (289)
Q Consensus 191 ~a~I~P~~~~~~Ls~~e 207 (289)
.-++++.+|..+|++++
T Consensus 321 ~~~~~~d~P~~~L~~~~ 337 (1809)
T PRK00635 321 TLNFSLSTPWKDLSPEI 337 (1809)
T ss_pred HCCCCCCCCHHHCCHHH
T ss_conf 76989899928799999
No 66
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=50.70 E-value=8 Score=18.94 Aligned_cols=23 Identities=22% Similarity=0.544 Sum_probs=13.3
Q ss_pred CCCCCCCCEEEEEEECCCCEEECCCCC
Q ss_conf 107877887899998781206387767
Q gi|254780625|r 262 PCLSNCGQMIRRIVQAGRSTFYCTYCQ 288 (289)
Q Consensus 262 ~C~~~CG~~I~~~~~~gR~ty~Cp~CQ 288 (289)
.| +.||....- -....+.||.|+
T Consensus 72 ~C-~~C~~~~~~---~~~~~~~CP~Cg 94 (114)
T PRK03681 72 WC-ETCQQYVTL---LTQRVRRCPQCH 94 (114)
T ss_pred EC-CCCCCEEEE---CCCCCCCCCCCC
T ss_conf 96-559985540---677677390883
No 67
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=48.53 E-value=7.8 Score=18.99 Aligned_cols=22 Identities=18% Similarity=0.777 Sum_probs=12.2
Q ss_pred CCCCCCCCEEEEEEECCCCEE-ECCCCC
Q ss_conf 107877887899998781206-387767
Q gi|254780625|r 262 PCLSNCGQMIRRIVQAGRSTF-YCTYCQ 288 (289)
Q Consensus 262 ~C~~~CG~~I~~~~~~gR~ty-~Cp~CQ 288 (289)
.| +.||....-. ...| -||.|+
T Consensus 73 ~C-~~Cg~~f~~~----~~~~~~CP~Cg 95 (117)
T PRK00564 73 EC-KDCSHVFKPN----ALDYGVCEKCH 95 (117)
T ss_pred EC-CCCCCEEECC----CCCCCCCCCCC
T ss_conf 91-0089988227----74068590988
No 68
>pfam10263 SprT-like SprT-like family. This family represents a domain found in eukaryotes and prokaryotes. The domain contains a characteristic motif of the zinc metallopeptidases. This family includes the bacterial SprT protein.
Probab=48.37 E-value=19 Score=16.54 Aligned_cols=26 Identities=31% Similarity=0.795 Sum_probs=20.7
Q ss_pred CCCCCCCCEEEEEEECCCCEEECCCCC
Q ss_conf 107877887899998781206387767
Q gi|254780625|r 262 PCLSNCGQMIRRIVQAGRSTFYCTYCQ 288 (289)
Q Consensus 262 ~C~~~CG~~I~~~~~~gR~ty~Cp~CQ 288 (289)
.| ..||..+.+...-++..|.|+.|+
T Consensus 121 ~C-~~C~~~~~r~~~~~~~~y~C~~C~ 146 (153)
T pfam10263 121 RC-TSCGQLYPRKRRIRRHRYRCGRCG 146 (153)
T ss_pred EC-CCCCCEEEEEEECCCCCEECCCCC
T ss_conf 99-999887357874157557755689
No 69
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit; InterPro: IPR011883 Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation , . Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA . .
Probab=47.50 E-value=9 Score=18.61 Aligned_cols=32 Identities=19% Similarity=0.510 Sum_probs=21.7
Q ss_pred ECCCCCCCCCCCCCEEEEE--EECC---CCEEECCCCC
Q ss_conf 5738771078778878999--9878---1206387767
Q gi|254780625|r 256 YGKTGEPCLSNCGQMIRRI--VQAG---RSTFYCTYCQ 288 (289)
Q Consensus 256 y~r~g~~C~~~CG~~I~~~--~~~g---R~ty~Cp~CQ 288 (289)
+-+.--.| ||||..=-+. .+|. |..|+|-.|.
T Consensus 107 ~~~~~v~C-PRCgS~~T~~~s~FG~TaCKaLy~C~aC~ 143 (152)
T TIGR02159 107 LEPPSVQC-PRCGSADTTITSEFGPTACKALYRCRACK 143 (152)
T ss_pred CCCCCCCC-CCCCCCCEEEECCCCCHHHHHHHHCCCCC
T ss_conf 46877788-88775211333034331446754110247
No 70
>TIGR02483 PFK_mixed phosphofructokinase; InterPro: IPR012829 Members of this family that are characterised, save one, are phosphofructokinases dependent on pyrophosphate (2.7.1.90 from EC) rather than ATP (2.7.1.11 from EC). The exception is one of three phosphofructokinases from Streptomyces coelicolor. Family members are both bacterial and archaeal.; GO: 0005524 ATP binding, 0008443 phosphofructokinase activity, 0006002 fructose 6-phosphate metabolic process, 0006096 glycolysis.
Probab=47.06 E-value=9.2 Score=18.53 Aligned_cols=22 Identities=27% Similarity=0.324 Sum_probs=17.8
Q ss_pred CCCCCCCCHHHHHHHHHHHHCC
Q ss_conf 6543564136899999987178
Q gi|254780625|r 174 QKIVAGIGNIYVCEALWRAKLS 195 (289)
Q Consensus 174 Q~~iaGIGN~y~~EiLf~a~I~ 195 (289)
...+.||||++|+||=-+.++.
T Consensus 259 ~~RLGGiG~~lA~~i~~rtg~E 280 (339)
T TIGR02483 259 HVRLGGIGNWLAEEIERRTGIE 280 (339)
T ss_pred CEECCCHHHHHHHHHHHHCCCC
T ss_conf 5001321889999999871982
No 71
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=46.52 E-value=17 Score=16.75 Aligned_cols=26 Identities=23% Similarity=0.539 Sum_probs=18.1
Q ss_pred EEECCCCCCCCCCCCCEEEEEEECCCC
Q ss_conf 665738771078778878999987812
Q gi|254780625|r 254 SVYGKTGEPCLSNCGQMIRRIVQAGRS 280 (289)
Q Consensus 254 ~vy~r~g~~C~~~CG~~I~~~~~~gR~ 280 (289)
.+|--++.-| |.||+++.+...-.++
T Consensus 147 ~~f~~~~~~C-p~CG~~~~~~~~~~~~ 172 (177)
T COG1439 147 RIFPEPKDFC-PICGSPLKRKRVKSRS 172 (177)
T ss_pred EECCCCCCCC-CCCCCCEEEEEECHHH
T ss_conf 2508988807-7899911785500000
No 72
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=45.91 E-value=8.6 Score=18.75 Aligned_cols=48 Identities=15% Similarity=0.016 Sum_probs=23.9
Q ss_pred CCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 43564136899999987178778312222001015899999999878876765421
Q gi|254780625|r 176 IVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKVLIDAIDA 231 (289)
Q Consensus 176 ~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~~vl~~a~~~ 231 (289)
.|+=||=+=..|++-..+++.. ..++ ..+-..++.+.|++.+.+.-+.
T Consensus 415 hFsTIGi~GmnEa~~~~g~~~~------~~~e--g~~fa~~vL~~mr~~~~~~qee 462 (625)
T PRK08271 415 QFLTIGINGMWEAAEFQGLTVG------YNEE--GEAFVQEVLKVIYEANEEASKE 462 (625)
T ss_pred CCCCCCHHHHHHHHHHCCCCCC------CCHH--HHHHHHHHHHHHHHHHHHHHHH
T ss_conf 2766304059999997599878------9989--9999999999999999999999
No 73
>TIGR00387 glcD glycolate oxidase, subunit GlcD; InterPro: IPR004490 The glc locus of Escherichia coli encodes the subunits of glycolate oxidase and the glc regulator protein. The subunit GlcD is similar to that of several D-lactate dehydrogenases, including that of E. coli. Glycolate oxidase has been found to have some D-lactate dehydrogenase activity.; GO: 0008891 glycolate oxidase activity, 0009339 glycolate oxidase complex.
Probab=45.06 E-value=23 Score=15.97 Aligned_cols=80 Identities=21% Similarity=0.148 Sum_probs=48.0
Q ss_pred CCCCCC----CCCCCCCCHH-----HHHHH---HHHCCC--CCCCEEEECCCCC-CCCCHHHHHHHHHHHHCCCCCCCCC
Q ss_conf 235655----5332211106-----78887---420145--4210011126543-5641368999999871787783122
Q gi|254780625|r 138 PLRTLG----PEPADNSFNA-----IYLTH---QFHKKN--SNLKNALLNQKIV-AGIGNIYVCEALWRAKLSPIRKTRS 202 (289)
Q Consensus 138 ~l~~lG----pD~l~~~~~~-----~~~~~---~l~~~~--~~Ik~~LlDQ~~i-aGIGN~y~~EiLf~a~I~P~~~~~~ 202 (289)
.+++++ |+.+-.|.+- ..+.+ .|..+. ..|.++-.- .++ +|=|| +||.-..+.
T Consensus 296 a~~~~~Gtkk~~~~~eD~tVPR~~Lp~~l~~I~~ia~Ky~~~~~ANF~i~-~~gHaGDGN-----------lHP~i~~d~ 363 (437)
T TIGR00387 296 AASKLSGTKKPKYLIEDGTVPRSKLPEVLKGIADIASKYDDLAVANFKIF-IVGHAGDGN-----------LHPLILTDE 363 (437)
T ss_pred HHHHHHCCCCCCEEEECCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEEEE-EEEECCCCC-----------CCCEEECCC
T ss_conf 99874055575525623300456778999999999975186345402677-887417787-----------543222378
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 220010158999999998788767654218875
Q gi|254780625|r 203 LIQNNGTPKDILYKLIQEIQKVLIDAIDAGGSS 235 (289)
Q Consensus 203 Ls~~e~~~~~~~~~L~~~i~~vl~~a~~~gG~~ 235 (289)
=. ++.++|-.+..-+||+.|++.|||-
T Consensus 364 ~~------~~~~er~e~~~~EI~e~a~~LGGti 390 (437)
T TIGR00387 364 ED------KGEMERVEELGGEILELAIELGGTI 390 (437)
T ss_pred CC------HHHHHHHHHHHHHHHHHHHHCCCCE
T ss_conf 86------6689999999999999872227705
No 74
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=44.40 E-value=21 Score=16.24 Aligned_cols=23 Identities=30% Similarity=0.703 Sum_probs=16.3
Q ss_pred CCCCCCCCCEEEEEEECCCCEEECCC
Q ss_conf 71078778878999987812063877
Q gi|254780625|r 261 EPCLSNCGQMIRRIVQAGRSTFYCTY 286 (289)
Q Consensus 261 ~~C~~~CG~~I~~~~~~gR~ty~Cp~ 286 (289)
..| |.||+++.+. .+...++|++
T Consensus 405 ~~C-P~C~s~l~~~--~~~~~~~C~N 427 (668)
T PRK07956 405 THC-PVCGSELVRE--EGEAVLRCTN 427 (668)
T ss_pred CCC-CCCCCEEEEE--CCCEEEECCC
T ss_conf 787-6779857993--6963787789
No 75
>pfam03119 DNA_ligase_ZBD NAD-dependent DNA ligase C4 zinc finger domain. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilising either ATP or NAD(+) as a cofactor. This family is a small zinc binding motif that is presumably DNA binding. IT is found only in NAD dependent DNA ligases.
Probab=44.34 E-value=16 Score=17.02 Aligned_cols=21 Identities=33% Similarity=0.733 Sum_probs=16.6
Q ss_pred CCCCCCCEEEEEEECCCCEEECCC
Q ss_conf 078778878999987812063877
Q gi|254780625|r 263 CLSNCGQMIRRIVQAGRSTFYCTY 286 (289)
Q Consensus 263 C~~~CG~~I~~~~~~gR~ty~Cp~ 286 (289)
| |.||+.+.+. .+...++|+.
T Consensus 2 C-P~C~s~l~r~--~~ev~~rC~n 22 (27)
T pfam03119 2 C-PVCGSPLVRE--EGEVDIRCTN 22 (27)
T ss_pred C-CCCCCEEECC--CCCEEEECCC
T ss_conf 8-8898974856--8978688889
No 76
>pfam08394 Arc_trans_TRASH Archaeal TRASH domain. This region is found in the C-terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module.
Probab=44.19 E-value=4.9 Score=20.29 Aligned_cols=23 Identities=26% Similarity=0.663 Sum_probs=11.3
Q ss_pred CCCEEE----EEEECCCCEEE-CCCCCC
Q ss_conf 788789----99987812063-877679
Q gi|254780625|r 267 CGQMIR----RIVQAGRSTFY-CTYCQK 289 (289)
Q Consensus 267 CG~~I~----~~~~~gR~ty~-Cp~CQk 289 (289)
||..|. ..++++|.-|. ||+||+
T Consensus 4 CG~eI~g~Pi~~k~~nrvYy~CC~tC~~ 31 (37)
T pfam08394 4 CGKEIKGEPITYKVKNRVYYVCCPTCLS 31 (37)
T ss_pred CCCCCCCCCEEEEECCEEEEEECHHHHH
T ss_conf 6775059957999757799998768889
No 77
>PRK00349 uvrA excinuclease ABC subunit A; Reviewed
Probab=44.19 E-value=24 Score=15.88 Aligned_cols=29 Identities=7% Similarity=-0.156 Sum_probs=21.6
Q ss_pred CCCHHHHHHHHHH---HHCCCCCCCCCCCHHH
Q ss_conf 6413689999998---7178778312222001
Q gi|254780625|r 179 GIGNIYVCEALWR---AKLSPIRKTRSLIQNN 207 (289)
Q Consensus 179 GIGN~y~~EiLf~---a~I~P~~~~~~Ls~~e 207 (289)
.-.+||.....-. .++++.+|.++|++++
T Consensus 315 ~~~~~~~~~L~~~a~~~gf~~d~P~~dLs~e~ 346 (944)
T PRK00349 315 KSSSYYFQMLKSLAEHYGFDLDTPWKDLPEEV 346 (944)
T ss_pred CCCHHHHHHHHHHHHHCCCCCCCCHHHCCHHH
T ss_conf 87648999999999975998678146699999
No 78
>pfam02591 DUF164 Putative zinc ribbon domain.
Probab=43.90 E-value=4.5 Score=20.57 Aligned_cols=30 Identities=20% Similarity=0.559 Sum_probs=20.1
Q ss_pred CCCCCCCCCCCEEEEEEE----CCCCEEECCCCCC
Q ss_conf 877107877887899998----7812063877679
Q gi|254780625|r 259 TGEPCLSNCGQMIRRIVQ----AGRSTFYCTYCQK 289 (289)
Q Consensus 259 ~g~~C~~~CG~~I~~~~~----~gR~ty~Cp~CQk 289 (289)
.+..| .-|+..|.-..+ .+....+||.|+|
T Consensus 21 ~~~~C-~gC~~~i~~q~~~~l~~~~~i~~Cp~CgR 54 (56)
T pfam02591 21 EGGAC-GGCRMKLPPQTLNELRKGDEIVRCPHCGR 54 (56)
T ss_pred CCCCC-CCCCEECCHHHHHHHHCCCCEEECCCCCC
T ss_conf 59956-76874739999999986998579979886
No 79
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=43.83 E-value=16 Score=16.95 Aligned_cols=27 Identities=19% Similarity=0.548 Sum_probs=16.8
Q ss_pred CCCCCCCCCEEEEEEECC----CCEEECCCCCC
Q ss_conf 710787788789999878----12063877679
Q gi|254780625|r 261 EPCLSNCGQMIRRIVQAG----RSTFYCTYCQK 289 (289)
Q Consensus 261 ~~C~~~CG~~I~~~~~~g----R~ty~Cp~CQk 289 (289)
..| |.|+..- ..+.|+ ..-|-|+.|++
T Consensus 31 ~~c-P~C~s~~-~~k~g~~~~~~qRyrC~~C~~ 61 (129)
T COG3677 31 VNC-PRCKSSN-VVKIGGIRRGHQRYKCKSCGS 61 (129)
T ss_pred CCC-CCCCCCC-EEEECCCCCCCCCCCCCCCCC
T ss_conf 768-9888511-023777426652535687586
No 80
>PRK08174 DNA topoisomerase III; Validated
Probab=43.62 E-value=24 Score=15.82 Aligned_cols=29 Identities=21% Similarity=0.572 Sum_probs=17.0
Q ss_pred CCCCCCCCCCCCEEEEEEECC-CCEEEC---CCCC
Q ss_conf 387710787788789999878-120638---7767
Q gi|254780625|r 258 KTGEPCLSNCGQMIRRIVQAG-RSTFYC---TYCQ 288 (289)
Q Consensus 258 r~g~~C~~~CG~~I~~~~~~g-R~ty~C---p~CQ 288 (289)
..+.+| |.||..+..- .+. ..-|=| |.|-
T Consensus 613 ~~~~~C-P~Cg~~l~~r-~~k~G~F~gCs~yP~Ck 645 (670)
T PRK08174 613 PPSPAC-PQCGAPTRQR-NGKSGPFWGCSRYPDCK 645 (670)
T ss_pred CCCCCC-CCCCCEEEEE-ECCCCCEEECCCCCCCC
T ss_conf 989978-7899750367-06887378699998888
No 81
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=42.76 E-value=17 Score=16.85 Aligned_cols=25 Identities=20% Similarity=0.656 Sum_probs=17.2
Q ss_pred CCCCCCCCCEEEEEEECCCCEEECCCCC
Q ss_conf 7107877887899998781206387767
Q gi|254780625|r 261 EPCLSNCGQMIRRIVQAGRSTFYCTYCQ 288 (289)
Q Consensus 261 ~~C~~~CG~~I~~~~~~gR~ty~Cp~CQ 288 (289)
-.| |.||.+. .+=.+..+|.|..|-
T Consensus 36 ~~C-p~C~~~~--VkR~a~GIW~C~kCg 60 (89)
T COG1997 36 HVC-PFCGRTT--VKRIATGIWKCRKCG 60 (89)
T ss_pred CCC-CCCCCCC--EEEECCCEEECCCCC
T ss_conf 769-9789740--455236758717888
No 82
>TIGR02890 spore_yteA sporulation protein, yteA family; InterPro: IPR014240 This entry contains predicted regulatory proteins that are found in nearly every species of the endospore-forming bacteria within the Firmicutes (low-GC Gram-positive bacteria), with the exception of Clostridium perfringens. Some (but not all) of these proteins contain an unusual DksA/TraR C4-type zinc finger, where only one of the four key Cys residues is conserved. All members of this entry share an additional C-terminal domain. The function of proteins in this family is unknown. YteA is found in mature spores of Bacillus subtilis and its expression appeasr to be regulated by sigma-K ..
Probab=42.57 E-value=9.1 Score=18.57 Aligned_cols=107 Identities=21% Similarity=0.295 Sum_probs=55.7
Q ss_pred HHHHHHHHCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHC---CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH---
Q ss_conf 78887420145421001112654356413689999998717---877831222200101589999999987887676---
Q gi|254780625|r 154 IYLTHQFHKKNSNLKNALLNQKIVAGIGNIYVCEALWRAKL---SPIRKTRSLIQNNGTPKDILYKLIQEIQKVLID--- 227 (289)
Q Consensus 154 ~~~~~~l~~~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I---~P~~~~~~Ls~~e~~~~~~~~~L~~~i~~vl~~--- 227 (289)
..|++.|...|..+=..|..=..=-|||.....|..=.=-. ||.=.+++|=+.|.. ..|...+...|.+
T Consensus 4 ~~lK~~L~~~K~~l~~~~~~~~~~~~~~~~~~~e~~gELS~YDNHPaD~ATElyEReKD-----~AL~~~~~~~L~~Ie~ 78 (167)
T TIGR02890 4 AELKNALLQEKEELEQRLKQMNKEDGLGEASQRESVGELSSYDNHPADLATELYEREKD-----IALKEHEKRELREIEH 78 (167)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHH-----HHHHHHHHHHHHHHHH
T ss_conf 88999999999999999998752122100023332111001368853344304577532-----6889999999988999
Q ss_pred HHHCCCCCCCCCCCCCCCCCCCHHHEEEECCCCCCCCCCCCCEEEEEEE-CCCCEEECCCCCC
Q ss_conf 5421887553111677877874133166573877107877887899998-7812063877679
Q gi|254780625|r 228 AIDAGGSSLRDYVHIDGSIGYFQNAFSVYGKTGEPCLSNCGQMIRRIVQ-AGRSTFYCTYCQK 289 (289)
Q Consensus 228 a~~~gG~~~~~~~~~~g~~g~~~~~~~vy~r~g~~C~~~CG~~I~~~~~-~gR~ty~Cp~CQk 289 (289)
|+..- ..| -|| -| .+||.+|-.+.. +-=+|-.|-.||+
T Consensus 79 AL~~i------------e~G-------tYG----IC-e~cG~~Ip~ERLEA~P~A~~c~~~~~ 117 (167)
T TIGR02890 79 ALQKI------------ENG-------TYG----IC-EVCGKPIPYERLEALPTATTCVECQN 117 (167)
T ss_pred HHHHH------------HCC-------CCE----EE-CCCCCCCCHHHHHCCHHHHHHHHHHC
T ss_conf 99998------------578-------970----00-44878798444200417889998722
No 83
>PRK06556 vitamin B12-dependent ribonucleotide reductase; Validated
Probab=41.97 E-value=16 Score=17.08 Aligned_cols=24 Identities=29% Similarity=0.822 Sum_probs=17.0
Q ss_pred CCCCCCCCCCCEEEEEEECCCCEEECCCC
Q ss_conf 87710787788789999878120638776
Q gi|254780625|r 259 TGEPCLSNCGQMIRRIVQAGRSTFYCTYC 287 (289)
Q Consensus 259 ~g~~C~~~CG~~I~~~~~~gR~ty~Cp~C 287 (289)
++.+| |.||.++.+ . -+=|.|..|
T Consensus 927 dap~C-peCGs~mvR---n-GgC~kC~~C 950 (957)
T PRK06556 927 DAPLC-PTCGTIMVR---N-GSCYVCEGC 950 (957)
T ss_pred CCCCC-CCCCCCEEE---C-CCCCCCCCC
T ss_conf 89878-755765378---6-874323568
No 84
>TIGR00630 uvra excinuclease ABC, A subunit; InterPro: IPR004602 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain . The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , . The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , . Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). During the process of Escherichia coli nucleotide excision repair, DNA damage recognition and processing are achieved by the action of the uvrA, uvrB, and uvrC gene products . The UvrC protein contain 4 conserved regions: a central region which interact with UvrB (Uvr domain), a Helix hairpin Helix (HhH) domain important for 5 prime incision of damage DNA and the homology regions 1 and 2 of unknown function. UvrC homology region 2 is specific for UvrC proteins, whereas UvrC homology region 1 is also shared by few other nucleases.; GO: 0009381 excinuclease ABC activity, 0006289 nucleotide-excision repair, 0009380 excinuclease repair complex.
Probab=41.80 E-value=9.9 Score=18.35 Aligned_cols=17 Identities=6% Similarity=-0.107 Sum_probs=10.6
Q ss_pred HHHCCCCCCCCCCCHHH
Q ss_conf 87178778312222001
Q gi|254780625|r 191 RAKLSPIRKTRSLIQNN 207 (289)
Q Consensus 191 ~a~I~P~~~~~~Ls~~e 207 (289)
+-+++..+|+.+|++++
T Consensus 351 ~~~Fdl~~P~~~L~~~~ 367 (956)
T TIGR00630 351 HYGFDLDTPWKDLPEEV 367 (956)
T ss_pred HHCCCHHHHHHCCCHHH
T ss_conf 72888646754158667
No 85
>COG3350 Uncharacterized conserved protein [Function unknown]
Probab=41.68 E-value=17 Score=16.83 Aligned_cols=22 Identities=18% Similarity=0.679 Sum_probs=16.6
Q ss_pred CCCCCEEE------EEEECCCCEEECCC
Q ss_conf 87788789------99987812063877
Q gi|254780625|r 265 SNCGQMIR------RIVQAGRSTFYCTY 286 (289)
Q Consensus 265 ~~CG~~I~------~~~~~gR~ty~Cp~ 286 (289)
|+||.+|. +..++|.+=|||..
T Consensus 6 PVcgm~v~~~~a~~k~~Y~GktYYFcse 33 (53)
T COG3350 6 PVCGMKVDNENAEYKSSYGGKTYYFCSE 33 (53)
T ss_pred CCCCCCCCCCCCCEEEEECCEEEEEECH
T ss_conf 7767652665551058758878997089
No 86
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=40.28 E-value=11 Score=18.03 Aligned_cols=23 Identities=26% Similarity=0.592 Sum_probs=13.8
Q ss_pred CCCCCCCCCEEEEEEECCCCEEECCCCC
Q ss_conf 7107877887899998781206387767
Q gi|254780625|r 261 EPCLSNCGQMIRRIVQAGRSTFYCTYCQ 288 (289)
Q Consensus 261 ~~C~~~CG~~I~~~~~~gR~ty~Cp~CQ 288 (289)
..| ..|+..+..... .|+||+|.
T Consensus 71 ~~C-~~C~~~~~~e~~----~~~CP~C~ 93 (115)
T COG0375 71 CWC-LDCGQEVELEEL----DYRCPKCG 93 (115)
T ss_pred EEE-CCCCCEECCHHH----EEECCCCC
T ss_conf 894-239976021553----10888999
No 87
>TIGR03670 rpoB_arch DNA-directed RNA polymerase subunit B. This model represents the archaeal version of DNA-directed RNA polymerase subunit B (rpoB) and is observed in all archaeal genomes.
Probab=39.56 E-value=23 Score=15.93 Aligned_cols=73 Identities=12% Similarity=0.142 Sum_probs=51.0
Q ss_pred CCEECCCCCCHHHCCCC-CCCCCCCC-CC-----CCHHHHHHHHHHCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCC
Q ss_conf 41001455301005323-56555332-21-----1106788874201454210011126543564136899999987178
Q gi|254780625|r 123 GFMDLVETSLKYQYPPL-RTLGPEPA-DN-----SFNAIYLTHQFHKKNSNLKNALLNQKIVAGIGNIYVCEALWRAKLS 195 (289)
Q Consensus 123 G~~~~~~~~~~~~~~~l-~~lGpD~l-~~-----~~~~~~~~~~l~~~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~ 195 (289)
|.+.++-..++ .|+. ..+-||+. +| ++|...+.+.+.++-..+.....|-+-|.+.-.=.-.|.|-.+|.+
T Consensus 366 Gvig~i~~qeD--MPFt~dGi~PDIIiNPHa~PSRMTIGqllE~l~gK~~~~~G~~~d~tpF~~~~~~~~~~~L~~~g~~ 443 (599)
T TIGR03670 366 GVIGMIVPQED--MPFTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPFEGEPEEELRKELLKLGFK 443 (599)
T ss_pred CEEEEECCHHH--CCCCCCCCCCCEEECCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEECCCCCCCHHHHHHHHHHHCCC
T ss_conf 33320126753--9978899987089899878765508999999989999966984224789999999999999981999
Q ss_pred CC
Q ss_conf 77
Q gi|254780625|r 196 PI 197 (289)
Q Consensus 196 P~ 197 (289)
+.
T Consensus 444 ~~ 445 (599)
T TIGR03670 444 PD 445 (599)
T ss_pred CC
T ss_conf 88
No 88
>pfam07191 DUF1407 Protein of unknown function (DUF1407). This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family have 8 highly conserved cysteine residues, which form two zinc ribbon domains.
Probab=38.65 E-value=3.6 Score=21.14 Aligned_cols=26 Identities=23% Similarity=0.791 Sum_probs=20.8
Q ss_pred CCCCCCCCCEEEEEEECCCCEEECCCC
Q ss_conf 710787788789999878120638776
Q gi|254780625|r 261 EPCLSNCGQMIRRIVQAGRSTFYCTYC 287 (289)
Q Consensus 261 ~~C~~~CG~~I~~~~~~gR~ty~Cp~C 287 (289)
.-| |.|+.++++.+-=|-..|||.+|
T Consensus 31 a~C-P~C~~~Lq~LkACGAvdYfC~~c 56 (70)
T pfam07191 31 ALC-PDCHQELEVLKACGAVDYFCNHC 56 (70)
T ss_pred EEC-CCCCCHHHHHHHCCCCCCCCCCC
T ss_conf 989-76243789987727602020679
No 89
>PRK12860 transcriptional activator FlhC; Provisional
Probab=38.43 E-value=29 Score=15.31 Aligned_cols=84 Identities=23% Similarity=0.357 Sum_probs=54.8
Q ss_pred CCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC
Q ss_conf 21001112654356413689999998717877831222200101589999999987887676542188755311167787
Q gi|254780625|r 166 NLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKVLIDAIDAGGSSLRDYVHIDGS 245 (289)
Q Consensus 166 ~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~~vl~~a~~~gG~~~~~~~~~~g~ 245 (289)
.|-..|+.+.-..||--++++==||.--+....- + |.-.+-|-|. |..-++.|
T Consensus 78 niY~~l~~~~~~~~i~A~ikaYrLYlEq~~~~~~-------e--pvLslTRAWt-----LvRF~dsg------------- 130 (189)
T PRK12860 78 NAYRFLVNEARCSGLDALTKGYRLYLEHCCATGT-------E--PVLSLTRAWT-----LVRFFDAG------------- 130 (189)
T ss_pred HHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCC-------C--CHHHHHHHHH-----HHHHHHCC-------------
T ss_conf 9999999706985299999999999996535589-------7--1236888999-----99997458-------------
Q ss_pred CCCCHHHEEEECCCCCCCCCCCCCEEEEEEECCCCEEECCCCC
Q ss_conf 7874133166573877107877887899998781206387767
Q gi|254780625|r 246 IGYFQNAFSVYGKTGEPCLSNCGQMIRRIVQAGRSTFYCTYCQ 288 (289)
Q Consensus 246 ~g~~~~~~~vy~r~g~~C~~~CG~~I~~~~~~gR~ty~Cp~CQ 288 (289)
- + .=.+| ++||+.-......-...|-|.-||
T Consensus 131 --m----L-----~~~~C-~~CgG~FV~ha~d~~~~fvC~lC~ 161 (189)
T PRK12860 131 --M----L-----QLARC-RRCGGKFVTHAHDLRHNFVCGLCQ 161 (189)
T ss_pred --C----E-----EECCC-CCCCCCEECCCCCCCCCCCCCCCC
T ss_conf --7----0-----00677-777881552235678887778988
No 90
>TIGR01341 aconitase_1 aconitate hydratase 1; InterPro: IPR006249 Aconitase (aconitate hydratase; 4.2.1.3 from EC) is an iron-sulphur protein that contains a [4Fe-4S]-cluster and catalyses the interconversion of isocitrate and citrate via a cis-aconitate intermediate. Aconitase functions in both the TCA and glyoxylate cycles, however unlike the majority of iron-sulphur proteins that function as electron carriers, the [4Fe-4S]-cluster of aconitase reacts directly with an enzyme substrate. In eukaryotes there is a cytosolic form (cAcn) and a mitochondrial form (mAcn) of the enzyme. In bacteria there are also 2 forms, aconitase A (AcnA) and B (AcnB). Several aconitases are known to be multi-functional enzymes with a second non-catalytic, but essential function that arises when the cellular environment changes, such as when iron levels drop , . Eukaryotic cAcn and mAcn, and bacterial AcnA have the same domain organisation, consisting of three N-terminal alpha/beta/alpha domains, a linker region, followed by a C-terminal 'swivel' domain with a beta/beta/alpha structure (1-2-3-linker-4), although mAcn is small than cAcn. However, bacterial AcnB has a different organisation: it contains an N-terminal HEAT-like domain, followed by the 'swivel' domain, then the three alpha/beta/alpha domains (HEAT-4-1-2-3) . Below is a description of some of the multi-functional activities associated with different aconitases. Eukaryotic mAcn catalyses the second step of the mitochondrial TCA cycle, which is important for energy production, providing high energy electrons in the form of NADH and FADH2 to the mitochondrial oxidative phosphorylation pathway . The TCA cycle also provides precursors for haem and amino acid production. This enzyme has a second, non-catalytic but essential role in mitochondrial DNA (mtDNA) maintenance: mAcn acts to stabilise mtDNA, forming part of mtDNA protein-DNA complexes known as nucleoids. mAcn is thought to reversibly model nucleoids to directly influence mitochondrial gene expression in response to changes in the cellular environment. Therefore, mAcn can influence the expression of components of the oxidative phosphorylation pathway encoded in mtDNA. Eukaryotic cAcn enzyme balances the amount of citrate and isocitrate in the cytoplasm, which in turn creates a balance between the amount of NADPH generated from isocitrate by isocitrate dehydrogenase with the amount of acetyl-CoA generated from citrate by citrate lyase. Fatty acid synthesis requires both NADPH and acetyl-CoA, as do other metabolic processes, including the need for NADPH to combat oxidative stress. The enzymatic form of cAcn predominates when iron levels are normal, but if they drop sufficiently to cause the disassembly of the [4Fe-4S]-cluster, then cAcn undergoes a conformational change from a compact enzyme to a more open L-shaped protein known as iron regulatory protein 1 (IRP1; or IRE-binding protein 1, IREBP1) , . As IRP1, the catalytic site and the [4Fe-4S]-cluster are lost, and two new RNA-binding sites appear. IRP1 functions in the post-transcriptional regulation of genes involved in iron metabolism - it binds to mRNA iron-responsive elements (IRE), 30-nucleotide stem-loop structures at the 3' or 5' end of specific transcripts. Transcripts containing an IRE include ferritin L and H subunits (iron storage), transferrin (iron plasma chaperone), transferrin receptor (iron uptake into cells), ferroportin (iron exporter), mAcn, succinate dehydrogenase, erythroid aminolevulinic acid synthetase (tetrapyrrole biosynthesis), among others. If the IRE is in the 5'-UTR of the transcript (e.g. in ferritin mRNA), then IRP1-binding prevents its translation by blocking the transcript from binding to the ribosome. If the IRE is in the 3'-UTR of the transcript (e.g. transferrin receptor), then IRP1-binding protects it from endonuclease degradation, thereby prolonging the half-life of the transcript and enabling it to be translated . IRP2 is another IRE-binding protein that binds to the same transcripts as IRP1. However, since IRP1 is predominantly in the enzymatic cAcn form, it is IRP2 that acts as the major metabolic regulator that maintains iron homeostasis . Although IRP2 is homologous to IRP1, IPR2 lacks aconitase activity, and is known only to have a single function in the post-transcriptional regulation of iron metabolism genes . In iron-replete cells, IRP2 activity is regulated primarily by iron-dependent degradation through the ubiquitin-proteasomal system. Bacterial AcnB is also known to be multi-functional. In addition to its role in the TCA cycle, AcnB was shown to be a post-transcriptional regulator of gene expression in Escherichia coli and Salmonella enterica , . In S.enterica, AcnB initiates a regulatory cascade controlling flagella biosynthesis through an interaction with the ftsH transcript, an alternative RNA polymerase sigma factor. This binding lowers the intracellular concentration of FtsH protease, which in turn enhances the amount of RNA polymerase sigma32 factor (normally degraded by FtsH protease), and sigma32 then increases the synthesis of chaperone DnaK, which in turn promotes the synthesis of the flagellar protein FliC. AcnB regulates the synthesis of other proteins as well, such as superoxide dismutase (SodA) and other enzymes involved in oxidative stress. This entry represents bacterial aconitase A (AcnA), eukaryotic cytosolic aconitase (cAcn/IRP1), iron regulatory protein 2 (IRP2), and a few mitochondrial aconitases (certain mAcn proteins, but not the majority of these enzymes). More information about these proteins can be found at Protein of the Month: Aconitase .; GO: 0051539 4 iron 4 sulfur cluster binding, 0008152 metabolic process.
Probab=37.97 E-value=11 Score=17.97 Aligned_cols=56 Identities=18% Similarity=0.265 Sum_probs=35.2
Q ss_pred HHHHHHHHCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf 78887420145421001112654356413689999998717877831222200101589999999987887676542188
Q gi|254780625|r 154 IYLTHQFHKKNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKVLIDAIDAGG 233 (289)
Q Consensus 154 ~~~~~~l~~~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~~vl~~a~~~gG 233 (289)
+.+.+++++-. |.=-+|+||==| |.+||||..|++=|-.. .|.-||+.-|
T Consensus 514 ~~~e~AI~~Nd------L~~~aVLSGNRN-------FEGRIHPLvK~NyLASP-----------------PLVVAYALAG 563 (896)
T TIGR01341 514 EEVEEAIVKND------LVVVAVLSGNRN-------FEGRIHPLVKANYLASP-----------------PLVVAYALAG 563 (896)
T ss_pred HHHHHHHHHCC------EEEEEEEECCCC-------CCCEECCCCCCCCCCCC-----------------HHHHHHHHCC
T ss_conf 88998966288------289998315546-------33201600123534572-----------------5798985148
Q ss_pred CCCCCC
Q ss_conf 755311
Q gi|254780625|r 234 SSLRDY 239 (289)
Q Consensus 234 ~~~~~~ 239 (289)
+..-|+
T Consensus 564 ~~~Inl 569 (896)
T TIGR01341 564 NVDINL 569 (896)
T ss_pred CEEECC
T ss_conf 135545
No 91
>PRK07225 DNA-directed RNA polymerase subunit B'; Validated
Probab=37.66 E-value=27 Score=15.54 Aligned_cols=75 Identities=11% Similarity=0.109 Sum_probs=52.0
Q ss_pred CCEECCCCCCHHHCCCCCCCCCCCC-CC-----CCHHHHHHHHHHCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCC
Q ss_conf 4100145530100532356555332-21-----11067888742014542100111265435641368999999871787
Q gi|254780625|r 123 GFMDLVETSLKYQYPPLRTLGPEPA-DN-----SFNAIYLTHQFHKKNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSP 196 (289)
Q Consensus 123 G~~~~~~~~~~~~~~~l~~lGpD~l-~~-----~~~~~~~~~~l~~~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P 196 (289)
|.+.++-+.++.... -..+-||+. +| ++|...+.+.+.++-..+.....|-+-|.+.-.-.-.|.|-.+|.++
T Consensus 372 Gvig~i~~~eDMPFt-~dGi~PDiIiNPH~~PSRMTIGqllE~l~gK~~~~~G~~~d~tpF~~~~~~~~~~~L~~~g~~~ 450 (605)
T PRK07225 372 GVIGLIVPQEDMPFT-ESGVVPDLIINPHAIPSRMTIGHVLEMIGGKVGSLEGRRVDGTAFSGEPEEDLRESLKKLGFEH 450 (605)
T ss_pred CEEECCCCCCCCCCC-CCCCCCCEEECCCCCCCCCCHHHHHHHHHHHHHHHCCCEEEECCCCCCCHHHHHHHHHHHCCCC
T ss_conf 312110254039938-8999871888988687656089999998778887449635307889988899999999838998
Q ss_pred CC
Q ss_conf 78
Q gi|254780625|r 197 IR 198 (289)
Q Consensus 197 ~~ 198 (289)
.-
T Consensus 451 ~G 452 (605)
T PRK07225 451 TG 452 (605)
T ss_pred CC
T ss_conf 99
No 92
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha subunit, Gram-positive type; InterPro: IPR006308 These are the polypeptide chains of DNA polymerase III. Full-length homologs of this protein are restricted to the Gram-positive lineages, including the Mycoplasmas. This protein is designated alpha chain and given the gene symbol polC, but is not a full-length homolog of other polC genes. The N-terminal region of about 200 amino acids is rich in low-complexity sequence and poorly alignable. ; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication, 0005737 cytoplasm.
Probab=37.40 E-value=11 Score=18.06 Aligned_cols=13 Identities=8% Similarity=0.302 Sum_probs=6.4
Q ss_pred CCCCCCCCCCEEE
Q ss_conf 1001525532799
Q gi|254780625|r 69 SIIVHLGMSGSFI 81 (289)
Q Consensus 69 ~L~~HlgM~G~~~ 81 (289)
+|+.-.|..|.|.
T Consensus 544 il~~s~G~~~~~n 556 (1264)
T TIGR01405 544 ILVASQGLENKLN 556 (1264)
T ss_pred HHCCCCCCCCCCC
T ss_conf 1002778886547
No 93
>TIGR02661 MauD methylamine dehydrogenase accessory protein MauD; InterPro: IPR013478 MauD appears critical to proper formation of the small subunit of methylamine dehydrogenase, which has both an unusual tryptophan tryptophylquinone cofactor and multiple disulphide bonds. MauD shares sequence similarity, including a CPxC motif, with a number of thiol:disulphide interchange proteins. In MauD mutants, the small subunit apparently does not form properly and is rapidly degraded .; GO: 0030416 methylamine metabolic process.
Probab=37.31 E-value=9.7 Score=18.39 Aligned_cols=11 Identities=18% Similarity=0.247 Sum_probs=5.0
Q ss_pred HHHHHHHHHHH
Q ss_conf 99999999878
Q gi|254780625|r 212 DILYKLIQEIQ 222 (289)
Q Consensus 212 ~~~~~L~~~i~ 222 (289)
+.++.|+++++
T Consensus 169 EHlESLlEa~r 179 (189)
T TIGR02661 169 EHLESLLEADR 179 (189)
T ss_pred HHHHHHHHHCC
T ss_conf 88999886200
No 94
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=36.98 E-value=15 Score=17.24 Aligned_cols=22 Identities=23% Similarity=0.605 Sum_probs=12.4
Q ss_pred CCCCCCCCEEEEEEECCCCEEECCCCC
Q ss_conf 107877887899998781206387767
Q gi|254780625|r 262 PCLSNCGQMIRRIVQAGRSTFYCTYCQ 288 (289)
Q Consensus 262 ~C~~~CG~~I~~~~~~gR~ty~Cp~CQ 288 (289)
-| +.||....-. ...+.||.|+
T Consensus 72 ~C-~~C~~~~~~~----~~~~~CP~Cg 93 (113)
T PRK12380 72 WC-WDCSQVVEIH----QHDAQCPHCH 93 (113)
T ss_pred EC-CCCCCEEECC----CCCCCCCCCC
T ss_conf 96-5599987247----8888390697
No 95
>pfam08271 TF_Zn_Ribbon TFIIB zinc-binding. The transcription factor TFIIB contains a zinc-binding motif near the N-terminus. This domain is involved in the interaction with RNA pol II and TFIIF and plays a crucial role in selecting the transcription initiation site. The domain adopts a zinc ribbon like structure.
Probab=36.77 E-value=26 Score=15.63 Aligned_cols=10 Identities=40% Similarity=1.032 Sum_probs=4.6
Q ss_pred CCCEEECCCC
Q ss_conf 8120638776
Q gi|254780625|r 278 GRSTFYCTYC 287 (289)
Q Consensus 278 gR~ty~Cp~C 287 (289)
.|.-+.|+.|
T Consensus 16 ~~Ge~vC~~C 25 (40)
T pfam08271 16 ERGEYVCTEC 25 (40)
T ss_pred CCCCEECCCC
T ss_conf 7897870579
No 96
>pfam01155 HypA Hydrogenase expression/synthesis hypA family. Four conserved cysteines lie either side of the least conserved region.
Probab=36.17 E-value=16 Score=16.96 Aligned_cols=22 Identities=32% Similarity=0.774 Sum_probs=12.7
Q ss_pred CCCCCCCCEEEEEEECCCCEEECCCCC
Q ss_conf 107877887899998781206387767
Q gi|254780625|r 262 PCLSNCGQMIRRIVQAGRSTFYCTYCQ 288 (289)
Q Consensus 262 ~C~~~CG~~I~~~~~~gR~ty~Cp~CQ 288 (289)
.| +.||..-.-. ...+.||.|+
T Consensus 71 ~C-~~Cg~~~~~~----~~~~~CP~Cg 92 (112)
T pfam01155 71 RC-RDCGQEFELE----ERFFRCPKCG 92 (112)
T ss_pred EC-CCCCCEECCC----CCCCCCCCCC
T ss_conf 99-8999714257----7767990897
No 97
>PRK12722 transcriptional activator FlhC; Provisional
Probab=35.40 E-value=33 Score=15.01 Aligned_cols=84 Identities=20% Similarity=0.381 Sum_probs=57.0
Q ss_pred CCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC
Q ss_conf 21001112654356413689999998717877831222200101589999999987887676542188755311167787
Q gi|254780625|r 166 NLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKVLIDAIDAGGSSLRDYVHIDGS 245 (289)
Q Consensus 166 ~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~~vl~~a~~~gG~~~~~~~~~~g~ 245 (289)
.|-..|..+.-+.||--++++==||.--+.+...-.-|| +-|-|.-++- ++.|
T Consensus 78 n~y~~l~~~~~~~~i~alvkaYrLYlE~~~~~~~ep~Ls---------~TRAWtLvrF-----~dsg------------- 130 (185)
T PRK12722 78 NIYRFLLKTGLCSGIDAVIKAYRLYLEQCPLAEEEPLLS---------LTRAWTLVRF-----VDSG------------- 130 (185)
T ss_pred HHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCEEE---------HHHHHHHHHH-----HCCC-------------
T ss_conf 999999981699849999999999999744478985321---------5789999999-----6168-------------
Q ss_pred CCCCHHHEEEECCCCCCCCCCCCCEEEEEEECCCCEEECCCCC
Q ss_conf 7874133166573877107877887899998781206387767
Q gi|254780625|r 246 IGYFQNAFSVYGKTGEPCLSNCGQMIRRIVQAGRSTFYCTYCQ 288 (289)
Q Consensus 246 ~g~~~~~~~vy~r~g~~C~~~CG~~I~~~~~~gR~ty~Cp~CQ 288 (289)
- +. =..| ++||+.-......-...|-|+-||
T Consensus 131 --m----L~-----lt~C-~~CgG~Fv~ha~~~~~~fvC~lC~ 161 (185)
T PRK12722 131 --M----LQ-----LSSC-NCCGGHFVTHAHDPHGSFVCGLCQ 161 (185)
T ss_pred --C----EE-----ECCC-CCCCCCEEECCCCCCCCCCCCCCC
T ss_conf --6----65-----3356-646880253014678886068888
No 98
>KOG2169 consensus
Probab=35.08 E-value=17 Score=16.81 Aligned_cols=12 Identities=42% Similarity=0.952 Sum_probs=10.7
Q ss_pred CCCEEECCCCCC
Q ss_conf 812063877679
Q gi|254780625|r 278 GRSTFYCTYCQK 289 (289)
Q Consensus 278 gR~ty~Cp~CQk 289 (289)
.+.||.||.|||
T Consensus 342 ~~pTW~CPVC~~ 353 (636)
T KOG2169 342 QKPTWRCPVCQK 353 (636)
T ss_pred CCCEEECCCCCC
T ss_conf 687134555766
No 99
>pfam01927 DUF82 Protein of unknown function DUF82. This prokaryotic protein family has no known function. The protein contains four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=34.85 E-value=15 Score=17.20 Aligned_cols=27 Identities=15% Similarity=0.518 Sum_probs=17.2
Q ss_pred CCCCCCCCEEEEEEEC-------------CCCEEECCCCCC
Q ss_conf 1078778878999987-------------812063877679
Q gi|254780625|r 262 PCLSNCGQMIRRIVQA-------------GRSTFYCTYCQK 289 (289)
Q Consensus 262 ~C~~~CG~~I~~~~~~-------------gR~ty~Cp~CQk 289 (289)
-| +.|++++..+.-. ...-|.||.|.|
T Consensus 92 RC-~~CN~~L~~v~k~~v~~~vp~~v~~~~~~F~~C~~Cgk 131 (146)
T pfam01927 92 RC-LKCNGPLEPVSKEEVAGRVPPYVYERYDEFWRCPKCGR 131 (146)
T ss_pred CC-CCCCCCCEECCHHHHHHHCCCHHHHCCCCEEECCCCCC
T ss_conf 56-56798995818789854567202225881477899999
No 100
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=34.85 E-value=33 Score=14.95 Aligned_cols=80 Identities=14% Similarity=0.225 Sum_probs=34.4
Q ss_pred CCHHHHHHHHHHCC-------CCCCCEEEECCCCC---------CCCCHHHHHHHH---HHHHCCCC------CCCCCCC
Q ss_conf 11067888742014-------54210011126543---------564136899999---98717877------8312222
Q gi|254780625|r 150 SFNAIYLTHQFHKK-------NSNLKNALLNQKIV---------AGIGNIYVCEAL---WRAKLSPI------RKTRSLI 204 (289)
Q Consensus 150 ~~~~~~~~~~l~~~-------~~~Ik~~LlDQ~~i---------aGIGN~y~~EiL---f~a~I~P~------~~~~~Ls 204 (289)
.||...+.+.|... ..+|=..|+|-.++ .=+|- ...+.| |-.=+++. ...+.+.
T Consensus 478 RYTEAsLIk~ME~~GIGRPSTyA~II~tL~~R~YV~~e~k~l~PT~lG~-~V~~~L~~~f~~ivd~~fTA~mE~~LD~Ia 556 (864)
T PRK06319 478 RFTEASLVKELEKSGIGRPSTYATIMNKIQSREYTLKENQRLRPTELGK-IISQFLETNFPRIMDIGFTALMEDELELIA 556 (864)
T ss_pred CCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHCCCEEEECCEECCHHHHH-HHHHHHHHHHHHHCCCCHHHHHHHHHHHHH
T ss_conf 9888999999971799950106999998986798810198868007899-999999986464348531789998899997
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 00101589999999987887676542
Q gi|254780625|r 205 QNNGTPKDILYKLIQEIQKVLIDAID 230 (289)
Q Consensus 205 ~~e~~~~~~~~~L~~~i~~vl~~a~~ 230 (289)
+.+..-+..+...|..-...+..+.+
T Consensus 557 ~G~~~w~~vL~~F~~~f~~~l~~a~~ 582 (864)
T PRK06319 557 DNKKPWKLLLQEFWEQFLPVVVTAEK 582 (864)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf 38741999999999999999999986
No 101
>PRK11788 hypothetical protein; Provisional
Probab=34.70 E-value=24 Score=15.90 Aligned_cols=21 Identities=33% Similarity=0.871 Sum_probs=14.2
Q ss_pred CCCCCCCCCEEEEEEECCCC-EEECCCCCC
Q ss_conf 71078778878999987812-063877679
Q gi|254780625|r 261 EPCLSNCGQMIRRIVQAGRS-TFYCTYCQK 289 (289)
Q Consensus 261 ~~C~~~CG~~I~~~~~~gR~-ty~Cp~CQk 289 (289)
=.| ..||-. +++ -|-||.|+.
T Consensus 355 Y~C-~~CGF~-------~~~~~WqCPsC~~ 376 (389)
T PRK11788 355 YRC-RNCGFT-------ARTLYWHCPSCKA 376 (389)
T ss_pred EEC-CCCCCC-------CCCEEEECCCCCC
T ss_conf 769-999998-------8831457909998
No 102
>pfam03811 Ins_element1 Insertion element protein.
Probab=34.63 E-value=22 Score=16.15 Aligned_cols=12 Identities=25% Similarity=0.980 Sum_probs=6.0
Q ss_pred CCCEEECCCCCC
Q ss_conf 812063877679
Q gi|254780625|r 278 GRSTFYCTYCQK 289 (289)
Q Consensus 278 gR~ty~Cp~CQk 289 (289)
|.--|+|..|.|
T Consensus 26 G~QRYrC~~C~r 37 (88)
T pfam03811 26 GHQRYRCRHCRR 37 (88)
T ss_pred CCCCEEECCCCC
T ss_conf 985777277895
No 103
>TIGR01206 lysW lysine biosynthesis protein LysW; InterPro: IPR005906 This very small, poorly characterised protein in Thermus thermophilus has been shown to be essential for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate.; GO: 0019878 lysine biosynthetic process via aminoadipic acid.
Probab=34.62 E-value=26 Score=15.61 Aligned_cols=23 Identities=22% Similarity=0.394 Sum_probs=8.8
Q ss_pred CCCCCEEEEEEECCCCEEECCCC
Q ss_conf 87788789999878120638776
Q gi|254780625|r 265 SNCGQMIRRIVQAGRSTFYCTYC 287 (289)
Q Consensus 265 ~~CG~~I~~~~~~gR~ty~Cp~C 287 (289)
|.||+.|+-...-=...-.|+.|
T Consensus 6 P~~GA~i~L~N~ELg~lV~c~~~ 28 (54)
T TIGR01206 6 PECGAEIELENPELGELVVCDEC 28 (54)
T ss_pred CCCCCEEEECCCCCCCEEECCCC
T ss_conf 87675567408876616752899
No 104
>TIGR02642 phage_xxxx uncharacterized phage protein; InterPro: IPR013464 This uncharacterised protein is found in prophage regions of Shewanella oneidensis MR-1, Vibrio vulnificus (strain YJ016), Yersinia pseudotuberculosis IP 32953, and Aeromonas hydrophila ATCC7966. It appears to have regions of sequence similarity to the phage lambda antitermination protein Q..
Probab=34.54 E-value=13 Score=17.58 Aligned_cols=80 Identities=26% Similarity=0.361 Sum_probs=39.6
Q ss_pred CCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHEEE
Q ss_conf 43564136899999987178778312222001015899999999878876765421887553111677877874133166
Q gi|254780625|r 176 IVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKVLIDAIDAGGSSLRDYVHIDGSIGYFQNAFSV 255 (289)
Q Consensus 176 ~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~~vl~~a~~~gG~~~~~~~~~~g~~g~~~~~~~v 255 (289)
.++|.-|-|+. |-.++.. .|++++ +..|...| +.++.-|++...+++||..... +
T Consensus 126 ~~dgl~~~ik~--Le~~~~~------~l~~g~------I~~L~~~I-~~~~~~I~TE~~~Lrd~a~~~a--~-------- 180 (270)
T TIGR02642 126 VVDGLKKEIKR--LEKEKAE------KLDDGE------IKLLEDEI-KALKAKIDTERRALRDYAVAKA--A-------- 180 (270)
T ss_pred HHHHHHHHHHH--HHHHHHH------HCCCCH------HHHHHHHH-HHHHHHHHHHHHHHHHHHHHHH--H--------
T ss_conf 77423789999--9999986------358233------78999999-9998776777888999999987--4--------
Q ss_pred ECCCCCCCCCCCCCEEEEEEECCCCE-EECCCCC
Q ss_conf 57387710787788789999878120-6387767
Q gi|254780625|r 256 YGKTGEPCLSNCGQMIRRIVQAGRST-FYCTYCQ 288 (289)
Q Consensus 256 y~r~g~~C~~~CG~~I~~~~~~gR~t-y~Cp~CQ 288 (289)
.-..| |+|-++ ...-|+- --|++|.
T Consensus 181 ---~~~~C-P~C~Gt----g~~~~~~P~~C~~C~ 206 (270)
T TIGR02642 181 ---ESRKC-PRCRGT----GLRLRRQPEECDKCA 206 (270)
T ss_pred ---HCCCC-CCCCCC----CCCCCCCCCCCCCCC
T ss_conf ---14887-986566----788897788777778
No 105
>cd02967 mauD Methylamine utilization (mau) D family; mauD protein is the translation product of the mauD gene found in methylotrophic bacteria, which are able to use methylamine as a sole carbon source and a nitrogen source. mauD is an essential accessory protein for the biosynthesis of methylamine dehydrogenase (MADH), the enzyme that catalyzes the oxidation of methylamine and other primary amines. MADH possesses an alpha2beta2 subunit structure; the alpha subunit is also referred to as the large subunit. Each beta (small) subunit contains a tryptophan tryptophylquinone (TTQ) prosthetic group. Accessory proteins are essential for the proper transport of MADH to the periplasm, TTQ synthesis and the formation of several structural disulfide bonds. Bacterial mutants containing an insertion on the mauD gene were unable to grow on methylamine as a sole carbon source, were found to lack the MADH small subunit and had decreased amounts of the MADH large subunit.
Probab=34.37 E-value=8.4 Score=18.81 Aligned_cols=23 Identities=9% Similarity=-0.036 Sum_probs=11.1
Q ss_pred HHCCCEEEEEEE-CCEEEEEEECC
Q ss_conf 728988999960-53089995035
Q gi|254780625|r 44 ATRGKKIIDVSR-RAKYLLIELEG 66 (289)
Q Consensus 44 ~L~G~~I~~v~r-~GK~l~l~l~~ 66 (289)
.|.|+++.=-.- -||..++.|-.
T Consensus 7 ~ldG~~v~L~~~~~gk~vll~Fwa 30 (114)
T cd02967 7 TIDGAPVRIGGISPGRPTLLFFLS 30 (114)
T ss_pred CCCCCEEEECCCCCCCEEEEEEEC
T ss_conf 389986980553699849999978
No 106
>TIGR00395 leuS_arch leucyl-tRNA synthetase; InterPro: IPR004493 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases . Leucyl tRNA synthetase (6.1.1.4 from EC) is an alpha monomer that belongs to class Ia. There are two different families of leucyl-tRNA synthetases. This family includes both archaeal and cytosolic eukaryotic leucyl-tRNA synthetases.; GO: 0000166 nucleotide binding, 0004823 leucine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006429 leucyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=33.26 E-value=21 Score=16.30 Aligned_cols=40 Identities=20% Similarity=0.280 Sum_probs=22.9
Q ss_pred HHCCCEEEEEEECCEEEEEEECCCC--CCCCCCCCCCEEEEE
Q ss_conf 7289889999605308999503553--100152553279981
Q gi|254780625|r 44 ATRGKKIIDVSRRAKYLLIELEGNL--SIIVHLGMSGSFIIE 83 (289)
Q Consensus 44 ~L~G~~I~~v~r~GK~l~l~l~~~~--~L~~HlgM~G~~~~~ 83 (289)
.+-|.|-+-|..---|..++.++.. -=.+.|--+|-|.+.
T Consensus 303 T~yG~Tn~wv~P~~~Yv~~~~~~e~etenGielienGiwi~~ 344 (1109)
T TIGR00395 303 TVYGVTNVWVNPDITYVIAEVGGEKETENGIELIENGIWIVS 344 (1109)
T ss_pred HHHCCEEEEECCCCCEEEEEECCCCCHHHHHHHHHCCHHHHH
T ss_conf 100755355557751689973374001200445542257778
No 107
>TIGR00469 pheS_mito phenylalanyl-tRNA synthetase; InterPro: IPR004530 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases . Phenylalanyl-tRNA synthetase (6.1.1.20 from EC) is an alpha2/beta2 tetramer composed of 2 subunits that belongs to class IIc. In eubacteria, a small subunit (pheS gene) can be designated as beta (E. coli) or alpha subunit (nomenclature adopted in InterPro). Reciprocally the large subunit (pheT gene) can be designated as alpha (E. coli) or beta (see IPR004531 from INTERPRO and IPR004532 from INTERPRO). In all other kingdoms the two subunits have equivalent length in eukaryota, and can be identified by specific signatures. The enzyme from Thermus thermophilus has an alpha 2 beta 2 type quaternary structure and is one of the most complicated members of the synthetase family. Identification of phenylalanyl-tRNA synthetase as a member of class II aaRSs was based only on sequence alignment of the small alpha-subunit with other synthetases . This family describes the mitochondrial phenylalanyl-tRNA synthetases. Unlike all other known phenylalanyl-tRNA synthetases, the mitochondrial form demonstrated from yeast is monomeric. It is similar to but longer than the alpha subunit (PheS) of the alpha 2 beta 2 form found in bacteria, Archaea, and eukaryotes, and shares the characteristic motifs of class II aminoacyl-tRNA ligases.; GO: 0000166 nucleotide binding, 0004826 phenylalanine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006432 phenylalanyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=33.18 E-value=23 Score=15.95 Aligned_cols=43 Identities=21% Similarity=0.217 Sum_probs=27.1
Q ss_pred CCCCCHHHHHHHHHHHHCCCC-CCCCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 356413689999998717877-831222200101589999999987887
Q gi|254780625|r 177 VAGIGNIYVCEALWRAKLSPI-RKTRSLIQNNGTPKDILYKLIQEIQKV 224 (289)
Q Consensus 177 iaGIGN~y~~EiLf~a~I~P~-~~~~~Ls~~e~~~~~~~~~L~~~i~~v 224 (289)
+-|.| +++.|||-+||.||- +-+=... ...+.+.-|.-.|.++
T Consensus 292 ~~GCG-~~R~~~L~R~G~~~SetIGyAFG----~GL~R~AM~LF~IPDI 335 (460)
T TIGR00469 292 LLGCG-LIRQDVLLRAGVKQSETIGYAFG----LGLDRLAMLLFDIPDI 335 (460)
T ss_pred EECCC-HHHHHHHHHCCCCCCCCCCEEEC----CCHHHHHHHHHCCCCE
T ss_conf 51551-46778988458973332200001----0088999887348861
No 108
>cd01675 RNR_III Class III ribonucleotide reductase. Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit w
Probab=32.24 E-value=37 Score=14.68 Aligned_cols=49 Identities=14% Similarity=0.077 Sum_probs=21.8
Q ss_pred CCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 43564136899999987178778312222001015899999999878876765421
Q gi|254780625|r 176 IVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKVLIDAIDA 231 (289)
Q Consensus 176 ~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~~vl~~a~~~ 231 (289)
.+.-||=+=-.|.+-.-....+. .+++ ..+...++.+.+++.+.+.-+.
T Consensus 361 ~~~tIG~iGL~Ea~~~l~G~~~~-----e~~e--~~~f~~~il~~m~~~~~~~~~e 409 (555)
T cd01675 361 HTLTIGFIGLNEAAEALTGKGIG-----ESEE--AREFGIRILEHIRERADEFKEE 409 (555)
T ss_pred EEEECHHHHHHHHHHHHCCCCCC-----CCHH--HHHHHHHHHHHHHHHHHHHHHH
T ss_conf 36831485799999997099978-----9988--9999999999999999999898
No 109
>pfam04919 DUF655 Protein of unknown function, DUF655. This family includes several uncharacterized archaeal proteins.
Probab=32.11 E-value=37 Score=14.67 Aligned_cols=53 Identities=15% Similarity=0.248 Sum_probs=38.7
Q ss_pred HHHHHHHHHCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHH
Q ss_conf 678887420145421001112654356413689999998717877831222200
Q gi|254780625|r 153 AIYLTHQFHKKNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQN 206 (289)
Q Consensus 153 ~~~~~~~l~~~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~ 206 (289)
.+.|.+-+ ++..||..-|--=..++||||-.+.+||=.-+-.|+..-.+|.+.
T Consensus 98 E~~FV~Ff-N~A~pit~rlH~leLLPGIGkK~~~~ileeR~~~~FeSFedi~~R 150 (181)
T pfam04919 98 EDRFVKFF-NEAEPITTRLHQLELLPGIGKKMMWAILEERKKKPFESFEDIKER 150 (181)
T ss_pred HHHHHHHH-HCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCHHHHHHH
T ss_conf 46766765-136874487888875334038999999999655998899999988
No 110
>KOG3053 consensus
Probab=32.00 E-value=13 Score=17.50 Aligned_cols=20 Identities=30% Similarity=0.313 Sum_probs=9.4
Q ss_pred CCCCEEEECCCCCCCCCHHH
Q ss_conf 42100111265435641368
Q gi|254780625|r 165 SNLKNALLNQKIVAGIGNIY 184 (289)
Q Consensus 165 ~~Ik~~LlDQ~~iaGIGN~y 184 (289)
+.++-+|+=.++-.=+||++
T Consensus 218 rv~CgAl~lPTis~~vG~~l 237 (293)
T KOG3053 218 RVLCGALLLPTISTIVGRVL 237 (293)
T ss_pred HHHHHHHHHHHHHHHHHHHH
T ss_conf 33103343006999999999
No 111
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=31.94 E-value=33 Score=15.01 Aligned_cols=25 Identities=28% Similarity=0.804 Sum_probs=16.0
Q ss_pred CCCCCCCCEEEEEE---ECCCCEEECCCCC
Q ss_conf 10787788789999---8781206387767
Q gi|254780625|r 262 PCLSNCGQMIRRIV---QAGRSTFYCTYCQ 288 (289)
Q Consensus 262 ~C~~~CG~~I~~~~---~~gR~ty~Cp~CQ 288 (289)
|| | ||...+-.- ..|-..--||.|-
T Consensus 24 PC-P-CGDRFeIsLeDl~~GE~VArCPSCS 51 (67)
T COG5216 24 PC-P-CGDRFEISLEDLRNGEVVARCPSCS 51 (67)
T ss_pred CC-C-CCCEEEEEHHHHHCCCEEEECCCCE
T ss_conf 47-8-8877578877853986688769851
No 112
>PRK09194 prolyl-tRNA synthetase; Provisional
Probab=31.37 E-value=33 Score=15.01 Aligned_cols=18 Identities=17% Similarity=0.342 Sum_probs=13.2
Q ss_pred ECCCCCCCCCCCCCEEEEE
Q ss_conf 5738771078778878999
Q gi|254780625|r 256 YGKTGEPCLSNCGQMIRRI 274 (289)
Q Consensus 256 y~r~g~~C~~~CG~~I~~~ 274 (289)
.-++|.+| |.||.++...
T Consensus 388 ~v~~GD~C-p~c~~~L~~~ 405 (570)
T PRK09194 388 NVVEGDPS-PDGGGTLKIA 405 (570)
T ss_pred HCCCCCCC-CCCCCEEEEE
T ss_conf 52568889-8899712774
No 113
>pfam08274 PhnA_Zn_Ribbon PhnA Zinc-Ribbon.
Probab=30.81 E-value=36 Score=14.75 Aligned_cols=23 Identities=17% Similarity=0.522 Sum_probs=16.2
Q ss_pred CCCCCCCCEEEEEEECCCCEEECCCCC
Q ss_conf 107877887899998781206387767
Q gi|254780625|r 262 PCLSNCGQMIRRIVQAGRSTFYCTYCQ 288 (289)
Q Consensus 262 ~C~~~CG~~I~~~~~~gR~ty~Cp~CQ 288 (289)
+| |.|+.. .++.....+.||.|-
T Consensus 4 ~C-p~C~se---ytY~d~~~~vCpeC~ 26 (30)
T pfam08274 4 KC-PLCNSE---YTYEDGALLVCPECA 26 (30)
T ss_pred CC-CCCCCC---CEECCCCEEECCCCC
T ss_conf 78-878981---247479997997545
No 114
>pfam09788 Tmemb_55A Transmembrane protein 55A. Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=30.31 E-value=32 Score=15.02 Aligned_cols=27 Identities=19% Similarity=0.447 Sum_probs=17.9
Q ss_pred CCCCCCCCEEEEEEECCCCEEECCCCCC
Q ss_conf 1078778878999987812063877679
Q gi|254780625|r 262 PCLSNCGQMIRRIVQAGRSTFYCTYCQK 289 (289)
Q Consensus 262 ~C~~~CG~~I~~~~~~gR~ty~Cp~CQk 289 (289)
.| ..|..+....+..+++.--||+|.|
T Consensus 161 ~C-gHC~~~Flf~~~~~ntlArCPhCrK 187 (258)
T pfam09788 161 IC-GHCNNTFLWNELTDNTLARCPHCRK 187 (258)
T ss_pred EC-CCCCCCEEECCCCCCCCCCCCCCCC
T ss_conf 83-5789827841567772013887642
No 115
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=30.29 E-value=25 Score=15.73 Aligned_cols=27 Identities=26% Similarity=0.730 Sum_probs=14.9
Q ss_pred CCCCCCCCCEEEEEEE----CCCCEEE-CCCCC
Q ss_conf 7107877887899998----7812063-87767
Q gi|254780625|r 261 EPCLSNCGQMIRRIVQ----AGRSTFY-CTYCQ 288 (289)
Q Consensus 261 ~~C~~~CG~~I~~~~~----~gR~ty~-Cp~CQ 288 (289)
+|| |=||.....+.. .+.+.|+ |-.|+
T Consensus 2 kpC-PFCG~~~~~~~~~~~~~~~~~~~~C~~Cg 33 (53)
T TIGR03655 2 KPC-PFCGGADVYLRRGFDPLDLSHYFECSTCG 33 (53)
T ss_pred CCC-CCCCCCHHHEECCCCCCCCEEEEECCCCC
T ss_conf 888-87897531000257876652688777777
No 116
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=30.01 E-value=16 Score=17.06 Aligned_cols=21 Identities=24% Similarity=0.618 Sum_probs=13.5
Q ss_pred CCCCCCCCEEEEEEECCCCEEECCCCC
Q ss_conf 107877887899998781206387767
Q gi|254780625|r 262 PCLSNCGQMIRRIVQAGRSTFYCTYCQ 288 (289)
Q Consensus 262 ~C~~~CG~~I~~~~~~gR~ty~Cp~CQ 288 (289)
.| ++||.+... -.---||.|-
T Consensus 136 vC-~vCGy~~~g-----e~P~~CPiCg 156 (166)
T COG1592 136 VC-PVCGYTHEG-----EAPEVCPICG 156 (166)
T ss_pred EC-CCCCCCCCC-----CCCCCCCCCC
T ss_conf 76-878881268-----9987699999
No 117
>TIGR00354 polC DNA polymerase II, large subunit DP2; InterPro: IPR004475 This family represents the large subunit, DP2, of a two subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication, 0006308 DNA catabolic process.
Probab=29.87 E-value=27 Score=15.57 Aligned_cols=104 Identities=18% Similarity=0.351 Sum_probs=45.1
Q ss_pred CCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCC---CCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf 210011126543564136899999987178778312---22200101589999999987887676542188755311167
Q gi|254780625|r 166 NLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTR---SLIQNNGTPKDILYKLIQEIQKVLIDAIDAGGSSLRDYVHI 242 (289)
Q Consensus 166 ~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~---~Ls~~e~~~~~~~~~L~~~i~~vl~~a~~~gG~~~~~~~~~ 242 (289)
.+++-|=|.+.+.||+ |.-|. ++|+-.-|++ +|...+--...++ .|++.|+.|=+..+.-+= +..+ ..
T Consensus 1006 ~VedRLgkpeqy~Gl~--ftH~T---srId~GpKvcaYK~L~tM~eKv~sQ~-~lA~kIrAvDerdVaE~V--i~sH-Fl 1076 (1173)
T TIGR00354 1006 KVEDRLGKPEQYEGLF--FTHDT---SRIDAGPKVCAYKSLKTMKEKVESQL-ELAKKIRAVDERDVAEKV--IQSH-FL 1076 (1173)
T ss_pred HHHHHCCCCCCEECCC--EECCC---CHHCCCCCEEECCCCHHHHHHHHHHH-HHHHHHHHCCCCCCCCCH--HHCC-CC
T ss_conf 8886548812244020--20362---00105873321014402578999999-987562001451000201--1103-43
Q ss_pred CCCCCCCHHHEEEECCCCCCCCCCCCCEEEEEEECCCCEEECCCC
Q ss_conf 787787413316657387710787788789999878120638776
Q gi|254780625|r 243 DGSIGYFQNAFSVYGKTGEPCLSNCGQMIRRIVQAGRSTFYCTYC 287 (289)
Q Consensus 243 ~g~~g~~~~~~~vy~r~g~~C~~~CG~~I~~~~~~gR~ty~Cp~C 287 (289)
+.-.|+. ..|.|.---| ++||++=+|+.+.|. ||+|
T Consensus 1077 PD~iGNl----RAFSRQ~vRC-TkCn~KYRRIPL~Gk----C~kC 1112 (1173)
T TIGR00354 1077 PDLIGNL----RAFSRQEVRC-TKCNAKYRRIPLKGK----CLKC 1112 (1173)
T ss_pred HHHHHHH----HHHHCCCCCC-CCCCCCCCCCCCCCC----CCCC
T ss_conf 0255453----1431265101-358684133478664----4466
No 118
>PRK08402 replication factor A; Reviewed
Probab=29.09 E-value=18 Score=16.67 Aligned_cols=24 Identities=17% Similarity=0.573 Sum_probs=16.8
Q ss_pred CCCCCCCCCEEEEEEECCCCEEECCCC
Q ss_conf 710787788789999878120638776
Q gi|254780625|r 261 EPCLSNCGQMIRRIVQAGRSTFYCTYC 287 (289)
Q Consensus 261 ~~C~~~CG~~I~~~~~~gR~ty~Cp~C 287 (289)
..| |.|+..+..- -|-.+|.||.|
T Consensus 215 dAC-PeC~rkvd~d--~~~~~wiCpEh 238 (357)
T PRK08402 215 DAC-PECKKKVDYD--PGTDVWICPEH 238 (357)
T ss_pred HHC-HHHHHCCCCC--CCCCCEECCCC
T ss_conf 748-2431102447--88762667666
No 119
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=27.89 E-value=24 Score=15.92 Aligned_cols=27 Identities=19% Similarity=0.529 Sum_probs=16.7
Q ss_pred CCCCCCCCCCCCEEEEEEECCCCEEECCCC
Q ss_conf 387710787788789999878120638776
Q gi|254780625|r 258 KTGEPCLSNCGQMIRRIVQAGRSTFYCTYC 287 (289)
Q Consensus 258 r~g~~C~~~CG~~I~~~~~~gR~ty~Cp~C 287 (289)
|.+.-| |+||.-+-...... -|+|-.|
T Consensus 17 rk~~~C-PrCG~gvfmA~H~d--R~~CGkC 43 (51)
T COG1998 17 RKNRFC-PRCGPGVFMADHKD--RWACGKC 43 (51)
T ss_pred ECCCCC-CCCCCCCHHHHCCC--EEEECCC
T ss_conf 814528-88888434341576--0674354
No 120
>KOG2324 consensus
Probab=27.48 E-value=21 Score=16.29 Aligned_cols=26 Identities=19% Similarity=0.400 Sum_probs=15.7
Q ss_pred CCCCCCCCEEEEEEECCCCEEECCCCC
Q ss_conf 107877887899998781206387767
Q gi|254780625|r 262 PCLSNCGQMIRRIVQAGRSTFYCTYCQ 288 (289)
Q Consensus 262 ~C~~~CG~~I~~~~~~gR~ty~Cp~CQ 288 (289)
.| +.||-.--.+++..-.+--||.||
T Consensus 229 ~C-~~C~~s~n~e~~~~sk~~~Cp~C~ 254 (457)
T KOG2324 229 SC-PSCGYSKNSEDLDLSKIASCPKCN 254 (457)
T ss_pred EC-CCCCCCCCHHHHCCCCCCCCCCCC
T ss_conf 46-767755760121377656687656
No 121
>TIGR00019 prfA peptide chain release factor 1; InterPro: IPR004373 This family describes peptide chain release factor 1 (PrfA, RF-1), and excludes the related peptide chain release factor 2 (PrfB, RF-2). RF-1 helps recognise and terminate translation at UAA and UAG stop codons. The mitochondrial release factors are prfA-like, although not included above the trusted cut-off for this model. RF-1 does not have a translational frameshift.; GO: 0016149 translation release factor activity codon specific, 0006415 translational termination, 0005737 cytoplasm.
Probab=26.49 E-value=19 Score=16.47 Aligned_cols=33 Identities=15% Similarity=-0.080 Sum_probs=16.4
Q ss_pred CCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCC
Q ss_conf 421001112654356413689999998717877
Q gi|254780625|r 165 SNLKNALLNQKIVAGIGNIYVCEALWRAKLSPI 197 (289)
Q Consensus 165 ~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~ 197 (289)
-|-+=+.--|.==|=.=|==++=-.-+|||.=.
T Consensus 263 LPTGIVV~CQdErSQ~kNK~kAmk~L~ArL~~~ 295 (373)
T TIGR00019 263 LPTGIVVSCQDERSQHKNKDKAMKILRARLYEK 295 (373)
T ss_pred CCCCCEEEEECCCCHHHHHHHHHHHHHHHHHHH
T ss_conf 688417885478520567999999999999999
No 122
>pfam05280 FlhC Flagellar transcriptional activator (FlhC). This family consists of several bacterial flagellar transcriptional activator (FlhC) proteins. FlhC combines with FlhD to form a regulatory complex in E. coli, this complex has been shown to be a global regulator involved in many cellular processes as well as a flagellar transcriptional activator.
Probab=26.14 E-value=47 Score=14.01 Aligned_cols=84 Identities=20% Similarity=0.347 Sum_probs=56.6
Q ss_pred CCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC
Q ss_conf 21001112654356413689999998717877831222200101589999999987887676542188755311167787
Q gi|254780625|r 166 NLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKVLIDAIDAGGSSLRDYVHIDGS 245 (289)
Q Consensus 166 ~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~~vl~~a~~~gG~~~~~~~~~~g~ 245 (289)
.|-..|..+.-..||--++++=-||.--+.+...-.-|+ +-|-|. |..-++.|
T Consensus 78 niy~fl~~~~~~~~i~a~ikaYrLYlEq~~~~~~epvLs---------lTRAWt-----LvRF~dsg------------- 130 (176)
T pfam05280 78 NIYRFLIKHGGCSGIEAVIKAYRLYLEQIPADELEPVLS---------LTRAWT-----LVRFFDSG------------- 130 (176)
T ss_pred HHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCHH---------HHHHHH-----HHHHHHCC-------------
T ss_conf 999999972898519999999999998678768863014---------888999-----99997358-------------
Q ss_pred CCCCHHHEEEECCCCCCCCCCCCCEEEEEEECCCCEEECCCCC
Q ss_conf 7874133166573877107877887899998781206387767
Q gi|254780625|r 246 IGYFQNAFSVYGKTGEPCLSNCGQMIRRIVQAGRSTFYCTYCQ 288 (289)
Q Consensus 246 ~g~~~~~~~vy~r~g~~C~~~CG~~I~~~~~~gR~ty~Cp~CQ 288 (289)
- + .=.+| .+||+.-......-...|.|.-||
T Consensus 131 --m----L-----~~~~C-~~CgG~FV~ha~~~~~~fvC~lC~ 161 (176)
T pfam05280 131 --M----L-----QLTRC-KCCGGHFVTHAHDLQHNFVCGLCQ 161 (176)
T ss_pred --C----E-----ECCCC-CCCCCCEECCCCCCCCCCCCCCCC
T ss_conf --7----1-----00566-777881550013578885567988
No 123
>KOG2923 consensus
Probab=25.92 E-value=30 Score=15.28 Aligned_cols=25 Identities=28% Similarity=0.857 Sum_probs=17.6
Q ss_pred CCCCCCCCEEEEEEE---CCCCEEECCCCC
Q ss_conf 107877887899998---781206387767
Q gi|254780625|r 262 PCLSNCGQMIRRIVQ---AGRSTFYCTYCQ 288 (289)
Q Consensus 262 ~C~~~CG~~I~~~~~---~gR~ty~Cp~CQ 288 (289)
|| | ||..-+-.+- .|+..--||.|-
T Consensus 24 PC-p-CGDrf~It~edL~~ge~Va~CpsCS 51 (67)
T KOG2923 24 PC-P-CGDRFQITLEDLENGEDVARCPSCS 51 (67)
T ss_pred CC-C-CCCEEEECHHHHHCCCEEECCCCCE
T ss_conf 77-7-8873365399986788063189966
No 124
>PRK13804 ileS isoleucyl-tRNA synthetase; Provisional
Probab=25.50 E-value=27 Score=15.57 Aligned_cols=10 Identities=10% Similarity=0.275 Sum_probs=4.3
Q ss_pred CCCCEEEEEE
Q ss_conf 7788789999
Q gi|254780625|r 266 NCGQMIRRIV 275 (289)
Q Consensus 266 ~CG~~I~~~~ 275 (289)
.||...++++
T Consensus 554 ~~~~~~~r~~ 563 (966)
T PRK13804 554 HPGEEWTKVT 563 (966)
T ss_pred CCHHHHEECC
T ss_conf 8745507413
No 125
>PRK12300 leuS leucyl-tRNA synthetase; Reviewed
Probab=25.18 E-value=38 Score=14.62 Aligned_cols=22 Identities=27% Similarity=0.434 Sum_probs=8.7
Q ss_pred HCCCEEEEEEECCEEEEEEECC
Q ss_conf 2898899996053089995035
Q gi|254780625|r 45 TRGKKIIDVSRRAKYLLIELEG 66 (289)
Q Consensus 45 L~G~~I~~v~r~GK~l~l~l~~ 66 (289)
|-|.+...|..-..|+.+..++
T Consensus 181 l~g~ta~~v~Pd~~Yv~~~~~~ 202 (888)
T PRK12300 181 VFGVTNLWVNPDAEYVVAEVDG 202 (888)
T ss_pred HHHHHEEEECCCCCEEEEECCC
T ss_conf 4300003777763234564277
No 126
>pfam09297 zf-NADH-PPase NADH pyrophosphatase zinc ribbon domain. This domain is found in between two duplicated NUDIX domains. It has a zinc ribbon structure.
Probab=25.02 E-value=34 Score=14.90 Aligned_cols=26 Identities=23% Similarity=0.512 Sum_probs=18.0
Q ss_pred CCCCCCCCCEEEEEEECCCCEEECCCCCC
Q ss_conf 71078778878999987812063877679
Q gi|254780625|r 261 EPCLSNCGQMIRRIVQAGRSTFYCTYCQK 289 (289)
Q Consensus 261 ~~C~~~CG~~I~~~~~~gR~ty~Cp~CQk 289 (289)
.-| .+||++.+... +-..-.||.|+.
T Consensus 4 rfC-~~CG~~t~~~~--~g~~r~C~~Cg~ 29 (32)
T pfam09297 4 RFC-GRCGAPTEPAE--GGWARVCPSCGH 29 (32)
T ss_pred CCC-CCCCCCCCCCC--CCCEEECCCCCC
T ss_conf 442-44688475077--851766887676
No 127
>PRK07418 acetolactate synthase 3 catalytic subunit; Reviewed
Probab=24.83 E-value=31 Score=15.12 Aligned_cols=21 Identities=33% Similarity=0.773 Sum_probs=13.6
Q ss_pred CCCCCCCCCEEEEEEECCCCEEECCCCC
Q ss_conf 7107877887899998781206387767
Q gi|254780625|r 261 EPCLSNCGQMIRRIVQAGRSTFYCTYCQ 288 (289)
Q Consensus 261 ~~C~~~CG~~I~~~~~~gR~ty~Cp~CQ 288 (289)
-.| +.||++ .--+--|||.|-
T Consensus 592 ~~~-~~~~~~------~~~~~~~~~~~~ 612 (615)
T PRK07418 592 IYC-SNCGTK------NPSTHKFCPECG 612 (615)
T ss_pred EEC-CCCCCC------CCCCCCCCCCCC
T ss_conf 105-888888------863355364226
No 128
>PRK07562 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=24.79 E-value=39 Score=14.52 Aligned_cols=27 Identities=41% Similarity=0.893 Sum_probs=17.6
Q ss_pred ECCCCCCCCCCCCC-EEEEEEECCCCEEECCCC
Q ss_conf 57387710787788-789999878120638776
Q gi|254780625|r 256 YGKTGEPCLSNCGQ-MIRRIVQAGRSTFYCTYC 287 (289)
Q Consensus 256 y~r~g~~C~~~CG~-~I~~~~~~gR~ty~Cp~C 287 (289)
-+-+|.+| |.||. ++.+. .+-|-|..|
T Consensus 1143 ~g~~g~~C-peCGs~tmvrn----G~C~~C~~C 1170 (1177)
T PRK07562 1143 QGYTGESC-SECGNFTLVRN----GTCLKCDTC 1170 (1177)
T ss_pred CCCCCCCC-CCCCCCCEEEC----CCCCCCCCC
T ss_conf 48889978-88899640735----860310138
No 129
>COG2046 MET3 ATP sulfurylase (sulfate adenylyltransferase) [Inorganic ion transport and metabolism]
Probab=24.35 E-value=29 Score=15.33 Aligned_cols=11 Identities=36% Similarity=1.050 Sum_probs=8.8
Q ss_pred CCEEECCCCCC
Q ss_conf 12063877679
Q gi|254780625|r 279 RSTFYCTYCQK 289 (289)
Q Consensus 279 R~ty~Cp~CQk 289 (289)
+-.||||.|+.
T Consensus 318 ~e~~YC~~c~~ 328 (397)
T COG2046 318 EEFFYCPKCGQ 328 (397)
T ss_pred CCEEECCCCCC
T ss_conf 23164132057
No 130
>PRK00390 leuS leucyl-tRNA synthetase; Validated
Probab=24.10 E-value=42 Score=14.30 Aligned_cols=12 Identities=42% Similarity=0.996 Sum_probs=6.7
Q ss_pred CCCCCCCCEEEEE
Q ss_conf 1078778878999
Q gi|254780625|r 262 PCLSNCGQMIRRI 274 (289)
Q Consensus 262 ~C~~~CG~~I~~~ 274 (289)
.| +.||..-.|+
T Consensus 471 ~c-~~~g~~~~Re 482 (822)
T PRK00390 471 TC-PKCGKPARRE 482 (822)
T ss_pred EC-CCCCCCCEEC
T ss_conf 14-7778721453
No 131
>PRK06039 ileS isoleucyl-tRNA synthetase; Reviewed
Probab=24.06 E-value=41 Score=14.36 Aligned_cols=12 Identities=50% Similarity=1.423 Sum_probs=6.0
Q ss_pred CCCCCCCCEEEEE
Q ss_conf 1078778878999
Q gi|254780625|r 262 PCLSNCGQMIRRI 274 (289)
Q Consensus 262 ~C~~~CG~~I~~~ 274 (289)
+| +.||....++
T Consensus 503 ~~-~~~~~~~~r~ 514 (1042)
T PRK06039 503 PC-PDCGTGMRRV 514 (1042)
T ss_pred CC-CCCCCCCCCC
T ss_conf 58-9986210305
No 132
>pfam00085 Thioredoxin Thioredoxin. Thioredoxins are small enzymes that participate in redox reactions, via the reversible oxidation of an active centre disulfide bond. Some members with only the active site are not separated from the noise.
Probab=24.03 E-value=21 Score=16.29 Aligned_cols=11 Identities=18% Similarity=0.313 Sum_probs=4.6
Q ss_pred CEEEEEEECCC
Q ss_conf 30899950355
Q gi|254780625|r 57 AKYLLIELEGN 67 (289)
Q Consensus 57 GK~l~l~l~~~ 67 (289)
+|-+++.|-.+
T Consensus 18 ~k~vlv~F~a~ 28 (104)
T pfam00085 18 DKPVLVDFYAP 28 (104)
T ss_pred CCCEEEEEECC
T ss_conf 99499999899
No 133
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit; InterPro: IPR000438 Fatty acid synthesis involves a set of reactions, commencing with carboxylation of acetyl-CoA to malonyl-CoA. This is an irreversible reaction, catalysed by the acetyl-CoA carboxylase complex (6.4.1.2 from EC); a heterohexamer of biotin carboxyl carrier protein, biotin carboxylase and two non-identical carboxyl transferase subunits (alpha and beta) in a 2:2 association . The reaction involves two steps: Biotin carrier protein + ATP + HCO_3^- = Carboxybiotin carrier protein + ADP + P_i Carboxybiotin carrier protein + Acetyl-CoA = Malonyl-CoA + Biotin carrier protein In the first step, biotin carboxylase catalyses the carboxylation of the carrier protein to form an intermediate. Next, the transcarboxylase complex transfers the carboxyl group from the intermediate to acetyl-CoA forming malonyl-CoA.; GO: 0003989 acetyl-CoA carboxylase activity, 0006633 fatty acid biosynthetic process, 0009317 acetyl-CoA carboxylase complex.
Probab=23.74 E-value=16 Score=17.01 Aligned_cols=10 Identities=40% Similarity=0.866 Sum_probs=4.4
Q ss_pred CCCCCCHHHH
Q ss_conf 4356413689
Q gi|254780625|r 176 IVAGIGNIYV 185 (289)
Q Consensus 176 ~iaGIGN~y~ 185 (289)
++.|=|.+|.
T Consensus 117 v~tg~G~l~~ 126 (292)
T TIGR00515 117 VVTGKGTLYG 126 (292)
T ss_pred EEEEEEEECC
T ss_conf 6860037548
No 134
>pfam04945 YHS YHS domain. This short presumed domain is about 50 amino acid residues long. It often contains two cysteines that may be functionally important. This domain is found in copper transporting ATPases, some phenol hydroxylases and in a set of uncharacterized membrane proteins. This domain is named after three of the most conserved amino acids it contains. The domain may be metal binding, possibly copper ions. This domain is duplicated in some copper transporting ATPases.
Probab=23.22 E-value=53 Score=13.66 Aligned_cols=21 Identities=24% Similarity=0.793 Sum_probs=13.2
Q ss_pred CCCCCEEE-----EEEECCCCEEECC
Q ss_conf 87788789-----9998781206387
Q gi|254780625|r 265 SNCGQMIR-----RIVQAGRSTFYCT 285 (289)
Q Consensus 265 ~~CG~~I~-----~~~~~gR~ty~Cp 285 (289)
|+||-.|. +...+|++-|||.
T Consensus 1 PVCGM~V~~~~~~~~~y~G~~Y~FCS 26 (44)
T pfam04945 1 PVCGMYVKPRAAYKLEYEGRRYHFCS 26 (44)
T ss_pred CCCCCEECCCCCCCEEECCEEEEEEC
T ss_conf 98887868888871689994899858
No 135
>TIGR02311 HpaI 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase; InterPro: IPR012689 This entry represents the aldolase which performs the final step unique to the 4-hydroxyphenylacetic acid catabolism pathway in which 2,4-dihydroxyhept-2-ene-1,7-dioic acid is split into pyruvate and succinate-semialdehyde. The gene for enzyme is generally found adjacent to other genes for this pathway.; GO: 0018802 24-dihydroxyhept-2-ene-17-dioate aldolase activity, 0010124 phenylacetate catabolic process.
Probab=23.14 E-value=37 Score=14.66 Aligned_cols=21 Identities=14% Similarity=0.055 Sum_probs=12.6
Q ss_pred CCCCEEEECCCCCCCCCHHHH
Q ss_conf 421001112654356413689
Q gi|254780625|r 165 SNLKNALLNQKIVAGIGNIYV 185 (289)
Q Consensus 165 ~~Ik~~LlDQ~~iaGIGN~y~ 185 (289)
|-|.++|-==+.+.=|=||+-
T Consensus 114 RGVGSALARASrwNrIp~Ylq 134 (249)
T TIGR02311 114 RGVGSALARASRWNRIPDYLQ 134 (249)
T ss_pred CCCHHHHHHHHHCCCHHHHHC
T ss_conf 340078776322176125760
No 136
>cd02993 PDI_a_APS_reductase PDIa family, 5'-Adenylylsulfate (APS) reductase subfamily; composed of plant-type APS reductases containing a C-terminal redox active TRX domain and an N-terminal reductase domain which is part of a superfamily that includes N type ATP PPases. APS reductase catalyzes the reduction of activated sulfate to sulfite, a key step in the biosynthesis of sulfur-containing metabolites. Sulfate is first activated by ATP sulfurylase, forming APS, which can be phosphorylated to 3'-phosphoadenosine-5'-phosphosulfate (PAPS). Depending on the organism, either APS or PAPS can be used for sulfate reduction. Prokaryotes and fungi use PAPS, whereas plants use both APS and PAPS. Since plant-type APS reductase uses glutathione (GSH) as its electron donor, the C-terminal domain may function like glutaredoxin, a GSH-dependent member of the TRX superfamily. The flow of reducing equivalents goes from GSH - C-terminal TRX domain - N-terminal reductase domain - APS. Plant-type APS red
Probab=22.95 E-value=16 Score=16.94 Aligned_cols=24 Identities=25% Similarity=0.358 Sum_probs=11.2
Q ss_pred CHHHHHHHCCCEEEEEEECCEEEEEEECCC
Q ss_conf 778999728988999960530899950355
Q gi|254780625|r 38 PHHFSAATRGKKIIDVSRRAKYLLIELEGN 67 (289)
Q Consensus 38 ~~~~~~~L~G~~I~~v~r~GK~l~l~l~~~ 67 (289)
+++|.+.+.|+ ...|..++.|=.+
T Consensus 8 ~~~f~~~v~~~------~~~k~~lV~FYAP 31 (109)
T cd02993 8 RAEIEALAKGE------RRNQSTLVVLYAP 31 (109)
T ss_pred HHHHHHHHHCC------CCCCCEEEEEECC
T ss_conf 77399997043------5699889999999
No 137
>pfam01258 zf-dskA_traR Prokaryotic dksA/traR C4-type zinc finger.
Probab=22.78 E-value=11 Score=17.98 Aligned_cols=26 Identities=27% Similarity=0.658 Sum_probs=18.8
Q ss_pred CCCCCCCEEEEEEECCC-CEEECCCCCC
Q ss_conf 07877887899998781-2063877679
Q gi|254780625|r 263 CLSNCGQMIRRIVQAGR-STFYCTYCQK 289 (289)
Q Consensus 263 C~~~CG~~I~~~~~~gR-~ty~Cp~CQk 289 (289)
| ..||..|.......+ ...+|..||.
T Consensus 6 C-~~CGE~i~~~R~~~~~~~~~C~~C~~ 32 (32)
T pfam01258 6 C-EDCGEPIPEARLEAVPGATLCIECQE 32 (32)
T ss_pred C-CCCCCCCCHHHHHCCCCCCCCHHCCC
T ss_conf 0-51789258999717988787031349
No 138
>PRK05743 ileS isoleucyl-tRNA synthetase; Reviewed
Probab=22.40 E-value=52 Score=13.70 Aligned_cols=16 Identities=31% Similarity=0.588 Sum_probs=7.7
Q ss_pred EEECCCCCCCCCCCCCE
Q ss_conf 66573877107877887
Q gi|254780625|r 254 SVYGKTGEPCLSNCGQM 270 (289)
Q Consensus 254 ~vy~r~g~~C~~~CG~~ 270 (289)
.|..-.|..| +||=.-
T Consensus 872 ~v~~a~g~KC-~RCW~~ 887 (910)
T PRK05743 872 VVEKAEGEKC-ERCWHY 887 (910)
T ss_pred EEEECCCCCC-CCCCCC
T ss_conf 9997999977-130989
No 139
>TIGR03147 cyt_nit_nrfF cytochrome c nitrite reductase, accessory protein NrfF.
Probab=22.20 E-value=31 Score=15.14 Aligned_cols=32 Identities=16% Similarity=0.405 Sum_probs=17.8
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 778312222001015899999999878876765421887
Q gi|254780625|r 196 PIRKTRSLIQNNGTPKDILYKLIQEIQKVLIDAIDAGGS 234 (289)
Q Consensus 196 P~~~~~~Ls~~e~~~~~~~~~L~~~i~~vl~~a~~~gG~ 234 (289)
|.-...++.+.+ ..+.+.++...++.+..|-+
T Consensus 44 pvCq~qsi~~S~-------a~~A~dmR~~I~~~i~~G~s 75 (126)
T TIGR03147 44 PQCQNQNLVESN-------SPIAYDLRHEVYSMVNEGKS 75 (126)
T ss_pred CCCCCCCHHHCC-------HHHHHHHHHHHHHHHHCCCC
T ss_conf 777997740076-------19999999999999985999
No 140
>TIGR00959 ffh signal recognition particle protein; InterPro: IPR004780 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes , . SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor . In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. This entry represents various SRP subunits.; GO: 0008312 7S RNA binding, 0006614 SRP-dependent cotranslational protein targeting to membrane, 0048500 signal recognition particle.
Probab=22.11 E-value=32 Score=15.08 Aligned_cols=37 Identities=22% Similarity=0.397 Sum_probs=28.7
Q ss_pred CCCCHHHHHHHHHHC-CC-CCCCEEEECCCCCCCCCHHHHHH
Q ss_conf 211106788874201-45-42100111265435641368999
Q gi|254780625|r 148 DNSFNAIYLTHQFHK-KN-SNLKNALLNQKIVAGIGNIYVCE 187 (289)
Q Consensus 148 ~~~~~~~~~~~~l~~-~~-~~Ik~~LlDQ~~iaGIGN~y~~E 187 (289)
...||++.|.+.++. +| .++..+| +.+||+|++-.++
T Consensus 332 ~~~FdleDfl~Ql~~~~KMG~l~~L~---~MiPG~g~~~~~~ 370 (439)
T TIGR00959 332 KGQFDLEDFLEQLRQIKKMGPLSSLL---KMIPGMGGMKPSL 370 (439)
T ss_pred CCCCCHHHHHHHHHHHHHCCCHHHHH---HHHCCCCCCCHHH
T ss_conf 05889899999999997227903588---8602202443357
No 141
>TIGR02738 TrbB type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB; InterPro: IPR014109 This entry includes thiol-disulphide isomerase (TrbB), a protein that is involved in conjugative transfer of plasmid DNA, specifically in the F-type system. TrbB has been predicted to contain a thioredoxin fold, it also contains a conserved pair of cysteines and has been shown to function as a thiol disulphide isomerase by complementation of Escherichia coli DsbA mutants . TtbB is believed to be involved in pilin assembly . TrbB is closely related to TraF (IPR014110 from INTERPRO) though somewhat longer lacking the cysteine motif and is apparently not functional as a disulphide bond isomerase..
Probab=22.10 E-value=30 Score=15.27 Aligned_cols=10 Identities=10% Similarity=0.126 Sum_probs=5.6
Q ss_pred EEEEECCCCC
Q ss_conf 9995035531
Q gi|254780625|r 60 LLIELEGNLS 69 (289)
Q Consensus 60 l~l~l~~~~~ 69 (289)
.|+.|++++.
T Consensus 58 ~Wy~Ls~~r~ 67 (176)
T TIGR02738 58 VWYRLSNGRK 67 (176)
T ss_pred EEEEECHHHH
T ss_conf 0011033678
No 142
>KOG2846 consensus
Probab=22.08 E-value=36 Score=14.71 Aligned_cols=29 Identities=28% Similarity=0.555 Sum_probs=16.7
Q ss_pred CCCCCCCCCCC---CEEEEEEECCCCEEECCCCC
Q ss_conf 38771078778---87899998781206387767
Q gi|254780625|r 258 KTGEPCLSNCG---QMIRRIVQAGRSTFYCTYCQ 288 (289)
Q Consensus 258 r~g~~C~~~CG---~~I~~~~~~gR~ty~Cp~CQ 288 (289)
|.+.-| +.|- +...++.+. =.+||||.|-
T Consensus 218 ryALIC-~~C~~HNGla~~ee~~-yi~F~C~~Cn 249 (328)
T KOG2846 218 RYALIC-SQCHHHNGLARKEEYE-YITFRCPHCN 249 (328)
T ss_pred HHHHCC-HHHCCCCCCCCHHHCC-CEEEECCCCC
T ss_conf 054521-2102015867765567-6289875554
No 143
>PRK08565 DNA-directed RNA polymerase subunit beta; Provisional
Probab=21.79 E-value=56 Score=13.48 Aligned_cols=59 Identities=12% Similarity=0.134 Sum_probs=40.6
Q ss_pred CCCCCCCC-CC-----CCHHHHHHHHHHCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCC
Q ss_conf 56555332-21-----1106788874201454210011126543564136899999987178778
Q gi|254780625|r 140 RTLGPEPA-DN-----SFNAIYLTHQFHKKNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIR 198 (289)
Q Consensus 140 ~~lGpD~l-~~-----~~~~~~~~~~l~~~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~ 198 (289)
..+-||+. +| ++|...+.+.+.++-..+.....|-+.|.+...-...|.|..+|.++.-
T Consensus 884 dG~~pDiI~NPhg~PSRMtiGql~E~~~gk~~~~~g~~~d~tpF~~~~~~~~~~~l~~~g~~~~G 948 (1101)
T PRK08565 884 EGIVPDLILNPHAIPSRMTVGQLLEAIAGKVAALTGRFVDATPFEGEPEEELRKELLKLGFKPSG 948 (1101)
T ss_pred CCCCCCEEECCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCC
T ss_conf 99885188789878776709999999876888725973114898998899999999975989999
No 144
>pfam04423 Rad50_zn_hook Rad50 zinc hook motif. The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.
Probab=21.48 E-value=35 Score=14.86 Aligned_cols=10 Identities=30% Similarity=0.876 Sum_probs=6.5
Q ss_pred CCCCCCCCEEE
Q ss_conf 10787788789
Q gi|254780625|r 262 PCLSNCGQMIR 272 (289)
Q Consensus 262 ~C~~~CG~~I~ 272 (289)
.| |+||..+.
T Consensus 22 ~C-PvC~r~l~ 31 (54)
T pfam04423 22 CC-PVCGRPLD 31 (54)
T ss_pred CC-CCCCCCCC
T ss_conf 77-76699766
No 145
>pfam10571 UPF0547 Uncharacterized protein family UPF0547. This domain contains a zinc-ribbon motif.
Probab=21.40 E-value=43 Score=14.24 Aligned_cols=20 Identities=25% Similarity=0.773 Sum_probs=11.4
Q ss_pred CCCCCCCCEEEEEEECCCCEEECCCCC
Q ss_conf 107877887899998781206387767
Q gi|254780625|r 262 PCLSNCGQMIRRIVQAGRSTFYCTYCQ 288 (289)
Q Consensus 262 ~C~~~CG~~I~~~~~~gR~ty~Cp~CQ 288 (289)
.| |.|+..|-. +.-.||.|.
T Consensus 2 ~C-P~C~~~vp~------~~~~Cp~CG 21 (26)
T pfam10571 2 TC-PECGAEVPL------AAKICPHCG 21 (26)
T ss_pred CC-CCCCCCCCH------HCCCCCCCC
T ss_conf 68-755483640------034477888
No 146
>PRK10144 formate-dependent nitrite reductase complex subunit NrfF; Provisional
Probab=21.28 E-value=34 Score=14.93 Aligned_cols=32 Identities=16% Similarity=0.340 Sum_probs=18.0
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 778312222001015899999999878876765421887
Q gi|254780625|r 196 PIRKTRSLIQNNGTPKDILYKLIQEIQKVLIDAIDAGGS 234 (289)
Q Consensus 196 P~~~~~~Ls~~e~~~~~~~~~L~~~i~~vl~~a~~~gG~ 234 (289)
|.-...++.+.+ ..+.+.++...++.++.|-+
T Consensus 44 pvCq~qsi~~S~-------s~iA~dmR~~Ir~~i~~G~s 75 (126)
T PRK10144 44 PQCQNQNLLESN-------APVAVSMRHQVYSMVAEGKS 75 (126)
T ss_pred CCCCCCCHHHCC-------HHHHHHHHHHHHHHHHCCCC
T ss_conf 778998841157-------79999999999999986999
No 147
>pfam09723 CxxC_CxxC_SSSS Zinc ribbon domain. This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=21.17 E-value=58 Score=13.40 Aligned_cols=25 Identities=20% Similarity=0.663 Sum_probs=12.6
Q ss_pred CCCCCCCEEEEEEE-CCCCEEECCCCC
Q ss_conf 07877887899998-781206387767
Q gi|254780625|r 263 CLSNCGQMIRRIVQ-AGRSTFYCTYCQ 288 (289)
Q Consensus 263 C~~~CG~~I~~~~~-~gR~ty~Cp~CQ 288 (289)
| ..||...+...- +.+..--||.|+
T Consensus 8 C-~~Cg~~fe~~~~~~~~~~~~CP~C~ 33 (42)
T pfam09723 8 C-EDCGHTFEVLQKISDAPLATCPECG 33 (42)
T ss_pred E-CCCCCEEEEEEECCCCCCCCCCCCC
T ss_conf 4-8899989999865799887697999
No 148
>pfam06044 DRP Dam-replacing family. Dam-replacing protein (DRP) is an restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis.
Probab=20.91 E-value=44 Score=14.17 Aligned_cols=13 Identities=8% Similarity=0.135 Sum_probs=6.0
Q ss_pred HCCCCCCCEEEEC
Q ss_conf 0145421001112
Q gi|254780625|r 161 HKKNSNLKNALLN 173 (289)
Q Consensus 161 ~~~~~~Ik~~LlD 173 (289)
+.++..-+..+||
T Consensus 179 r~~~~e~rGW~ld 191 (254)
T pfam06044 179 RNQSIESRGWTLD 191 (254)
T ss_pred HHCCCHHCCHHHH
T ss_conf 8511310101899
No 149
>PRK05580 primosome assembly protein PriA; Validated
Probab=20.76 E-value=59 Score=13.35 Aligned_cols=26 Identities=15% Similarity=0.351 Sum_probs=12.5
Q ss_pred CCCCCCCCEEEEEEECC-----------CCEEECCCCC
Q ss_conf 10787788789999878-----------1206387767
Q gi|254780625|r 262 PCLSNCGQMIRRIVQAG-----------RSTFYCTYCQ 288 (289)
Q Consensus 262 ~C~~~CG~~I~~~~~~g-----------R~ty~Cp~CQ 288 (289)
.| ++|+..+...+-.+ ...+-||.|.
T Consensus 415 ~C-~~C~~~L~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg 451 (699)
T PRK05580 415 RC-PHCDGPLTLHRAGRRLRCHHCGYQEPIPRACPECG 451 (699)
T ss_pred EC-CCCCCEEEECCCCCCEECCCCCCCCCCCCCCCCCC
T ss_conf 65-67898634206898332264688365755465679
No 150
>PRK13208 valS valyl-tRNA synthetase; Reviewed
Probab=20.71 E-value=45 Score=14.09 Aligned_cols=24 Identities=13% Similarity=-0.062 Sum_probs=11.6
Q ss_pred CCCCCEEEECCCCCCCCCHHHHHHHH
Q ss_conf 54210011126543564136899999
Q gi|254780625|r 164 NSNLKNALLNQKIVAGIGNIYVCEAL 189 (289)
Q Consensus 164 ~~~Ik~~LlDQ~~iaGIGN~y~~EiL 189 (289)
+.+|--.+.||=++.- . -++++++
T Consensus 348 ~~pi~~~~~~QWfi~~-~-~~k~~~~ 371 (809)
T PRK13208 348 KTPIEILVTRQWFIKV-L-DLKEELL 371 (809)
T ss_pred CCCCEEEECHHHHHHH-H-HHHHHHH
T ss_conf 9721687524566532-7-7788888
No 151
>COG0419 SbcC ATPase involved in DNA repair [DNA replication, recombination, and repair]
Probab=20.70 E-value=38 Score=14.60 Aligned_cols=13 Identities=15% Similarity=0.245 Sum_probs=7.1
Q ss_pred CCCEEEEEEECCC
Q ss_conf 6633899970688
Q gi|254780625|r 95 QHNHVTISLTNNT 107 (289)
Q Consensus 95 ~~~~~~~~~~~~~ 107 (289)
+...+.|.|+.++
T Consensus 70 ~~~~V~l~F~~~g 82 (908)
T COG0419 70 KSASVELEFEVNG 82 (908)
T ss_pred CCEEEEEEEEECC
T ss_conf 6079999999899
No 152
>TIGR00385 dsbE periplasmic protein thiol:disulfide oxidoreductases, DsbE subfamily; InterPro: IPR004799 Periplasmic protein thiol:disulphide oxidoreductase is involved in the biogenesis of c-type cytochromes as well as in disulphide bond formation in some periplasmic proteins. This group defines the DsbE subfamily.; GO: 0015036 disulfide oxidoreductase activity, 0017004 cytochrome complex assembly, 0030288 outer membrane-bounded periplasmic space.
Probab=20.68 E-value=33 Score=14.99 Aligned_cols=49 Identities=22% Similarity=0.263 Sum_probs=26.5
Q ss_pred CCHHHHHHHCC--CEEE-EEEECCEEEEEEE--------CCCCCCCCCCCCCCEEEEECC
Q ss_conf 87789997289--8899-9960530899950--------355310015255327998147
Q gi|254780625|r 37 FPHHFSAATRG--KKII-DVSRRAKYLLIEL--------EGNLSIIVHLGMSGSFIIEHT 85 (289)
Q Consensus 37 ~~~~~~~~L~G--~~I~-~v~r~GK~l~l~l--------~~~~~L~~HlgM~G~~~~~~~ 85 (289)
.|+...+.|.+ +.++ ++.+.||-.++-+ -.++=++..|--+|++.+..-
T Consensus 41 vP~~~~a~L~~~~q~~~~~~~~qG~~~LlNVWAsWCp~CraEHp~L~eLak~Grl~ivG~ 100 (175)
T TIGR00385 41 VPAFGLAALREPLQLYTADIFRQGKPVLLNVWASWCPPCRAEHPYLNELAKEGRLPIVGV 100 (175)
T ss_pred CCCCHHHHCCCCCCCCCHHHHHCCCEEEEEEEECCCCCCHHCCHHHHHHHHCCCCEEEEE
T ss_conf 885112202467861364453089606998840368883100057899975397307886
No 153
>KOG2851 consensus
Probab=20.52 E-value=45 Score=14.09 Aligned_cols=15 Identities=40% Similarity=0.640 Sum_probs=10.7
Q ss_pred HEEEECCCCCCCCCC
Q ss_conf 316657387710787
Q gi|254780625|r 252 AFSVYGKTGEPCLSN 266 (289)
Q Consensus 252 ~~~vy~r~g~~C~~~ 266 (289)
-|-||-++|..|-|.
T Consensus 329 PFcVHP~Tg~VcVPi 343 (412)
T KOG2851 329 PFCVHPKTGRVCVPI 343 (412)
T ss_pred CCCCCCCCCCEEEEC
T ss_conf 742258888667642
No 154
>pfam00133 tRNA-synt_1 tRNA synthetases class I (I, L, M and V). Other tRNA synthetase sub-families are too dissimilar to be included.
Probab=20.46 E-value=41 Score=14.34 Aligned_cols=12 Identities=0% Similarity=-0.130 Sum_probs=6.5
Q ss_pred CCCCCCCCEEEEE
Q ss_conf 1078778878999
Q gi|254780625|r 262 PCLSNCGQMIRRI 274 (289)
Q Consensus 262 ~C~~~CG~~I~~~ 274 (289)
.| +.|+....++
T Consensus 476 ~~-~~~~~~~~re 487 (606)
T pfam00133 476 LL-GKGAGTLEQD 487 (606)
T ss_pred HC-CCCCCCEEEC
T ss_conf 53-5788751567
No 155
>COG0178 UvrA Excinuclease ATPase subunit [DNA replication, recombination, and repair]
Probab=20.43 E-value=60 Score=13.30 Aligned_cols=15 Identities=7% Similarity=-0.022 Sum_probs=11.2
Q ss_pred HCCCCCCCCCCCHHH
Q ss_conf 178778312222001
Q gi|254780625|r 193 KLSPIRKTRSLIQNN 207 (289)
Q Consensus 193 ~I~P~~~~~~Ls~~e 207 (289)
+++...|..+|++++
T Consensus 324 ~~d~~~P~~~L~~e~ 338 (935)
T COG0178 324 GFDLDTPWKDLPEEQ 338 (935)
T ss_pred CCCCCCCHHHCCHHH
T ss_conf 998468536699999
No 156
>KOG2907 consensus
Probab=20.38 E-value=47 Score=14.01 Aligned_cols=27 Identities=22% Similarity=0.635 Sum_probs=14.6
Q ss_pred CCCCCCCCCEE--------EEEEECCCCEEECCCCC
Q ss_conf 71078778878--------99998781206387767
Q gi|254780625|r 261 EPCLSNCGQMI--------RRIVQAGRSTFYCTYCQ 288 (289)
Q Consensus 261 ~~C~~~CG~~I--------~~~~~~gR~ty~Cp~CQ 288 (289)
..| |.||..= +...-|.-.-|-||+|-
T Consensus 75 ~kC-pkCghe~m~Y~T~QlRSADEGQTVFYTC~kC~ 109 (116)
T KOG2907 75 HKC-PKCGHEEMSYHTLQLRSADEGQTVFYTCPKCK 109 (116)
T ss_pred CCC-CCCCCCHHHHHHHHCCCCCCCCEEEEECCCCC
T ss_conf 017-55698312155664023468953899757654
Done!