Query psy17612
Match_columns 449
No_of_seqs 243 out of 362
Neff 4.7
Searched_HMMs 46136
Date Fri Aug 16 18:32:59 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17612.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17612hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2758|consensus 100.0 5E-109 1E-113 819.5 30.5 310 6-330 120-430 (432)
2 KOG0687|consensus 100.0 4E-48 8.6E-53 385.7 24.1 281 11-322 100-392 (393)
3 KOG1464|consensus 100.0 1.9E-41 4.2E-46 333.5 17.4 267 19-324 149-438 (440)
4 COG5187 RPN7 26S proteasome re 100.0 1.5E-35 3.4E-40 293.0 21.9 281 11-321 111-405 (412)
5 KOG2758|consensus 99.9 1.4E-26 3E-31 231.6 8.2 83 351-433 346-429 (432)
6 PF01399 PCI: PCI domain; Int 99.6 1.6E-15 3.4E-20 125.6 11.1 104 176-293 1-104 (105)
7 KOG0686|consensus 99.6 1.6E-14 3.4E-19 149.0 20.2 279 7-322 142-447 (466)
8 PF10602 RPN7: 26S proteasome 99.4 3.6E-13 7.8E-18 125.6 9.7 140 7-158 28-173 (177)
9 smart00753 PAM PCI/PINT associ 99.4 6.2E-13 1.3E-17 109.0 8.9 72 213-297 1-72 (88)
10 smart00088 PINT motif in prote 99.4 6.2E-13 1.3E-17 109.0 8.9 72 213-297 1-72 (88)
11 KOG1463|consensus 99.1 1.4E-09 3E-14 111.0 15.6 264 19-310 132-408 (411)
12 COG5159 RPN6 26S proteasome re 98.5 6.5E-06 1.4E-10 83.4 18.2 267 19-312 129-408 (421)
13 KOG2908|consensus 98.4 0.00024 5.3E-09 73.2 26.0 254 22-317 82-364 (380)
14 smart00753 PAM PCI/PINT associ 98.1 3.5E-06 7.6E-11 69.0 5.1 45 358-402 29-73 (88)
15 smart00088 PINT motif in prote 98.1 3.5E-06 7.6E-11 69.0 5.1 45 358-402 29-73 (88)
16 KOG1498|consensus 97.8 0.0022 4.8E-08 67.3 19.1 275 19-319 135-428 (439)
17 PF01399 PCI: PCI domain; Int 97.8 3.1E-05 6.8E-10 63.9 4.4 40 358-397 65-104 (105)
18 KOG1497|consensus 97.6 0.0093 2E-07 61.6 20.0 70 253-324 321-390 (399)
19 KOG2753|consensus 97.5 0.013 2.7E-07 60.7 18.9 92 207-311 262-361 (378)
20 COG5071 RPN5 26S proteasome re 97.4 0.038 8.3E-07 57.0 20.9 273 12-321 128-427 (439)
21 PF10075 PCI_Csn8: COP9 signal 96.8 0.0043 9.3E-08 55.7 7.7 103 152-273 15-121 (143)
22 KOG2581|consensus 96.6 0.0099 2.1E-07 63.0 9.2 89 187-293 329-422 (493)
23 KOG2072|consensus 96.3 0.59 1.3E-05 53.5 20.9 260 17-294 182-493 (988)
24 KOG1076|consensus 96.1 0.026 5.7E-07 63.0 9.5 153 160-331 634-797 (843)
25 KOG2688|consensus 95.0 0.11 2.5E-06 54.9 9.0 141 131-299 227-389 (394)
26 PF13424 TPR_12: Tetratricopep 94.1 0.29 6.3E-06 38.4 7.5 73 12-84 2-77 (78)
27 PF09012 FeoC: FeoC like trans 93.9 0.066 1.4E-06 42.7 3.5 45 225-282 3-47 (69)
28 PF13174 TPR_6: Tetratricopept 93.2 0.14 3E-06 33.6 3.6 32 16-47 1-32 (33)
29 PF13432 TPR_16: Tetratricopep 92.4 0.87 1.9E-05 34.4 7.6 59 19-81 1-59 (65)
30 KOG2582|consensus 92.3 2.4 5.3E-05 44.9 12.9 139 141-299 224-368 (422)
31 PF10255 Paf67: RNA polymerase 92.0 3.1 6.6E-05 44.5 13.6 110 138-272 214-344 (404)
32 PF09756 DDRGK: DDRGK domain; 91.9 0.29 6.3E-06 47.1 5.4 58 224-295 101-158 (188)
33 PRK10803 tol-pal system protei 91.8 0.71 1.5E-05 46.1 8.2 81 4-85 169-249 (263)
34 PRK15331 chaperone protein Sic 91.5 0.52 1.1E-05 44.6 6.5 64 7-74 29-92 (165)
35 PF09976 TPR_21: Tetratricopep 91.0 1.2 2.5E-05 39.5 7.9 74 4-78 37-110 (145)
36 PF13414 TPR_11: TPR repeat; P 90.9 1.3 2.8E-05 33.7 7.2 63 15-81 3-66 (69)
37 PF07719 TPR_2: Tetratricopept 90.6 0.55 1.2E-05 30.9 4.3 32 16-47 2-33 (34)
38 PF12895 Apc3: Anaphase-promot 89.4 0.93 2E-05 36.3 5.5 60 14-78 24-83 (84)
39 TIGR02795 tol_pal_ybgF tol-pal 89.3 2.8 6E-05 34.1 8.4 68 15-83 2-69 (119)
40 TIGR02521 type_IV_pilW type IV 89.1 15 0.00033 32.3 16.4 168 13-204 29-198 (234)
41 cd00189 TPR Tetratricopeptide 88.8 1.9 4.1E-05 31.4 6.4 60 17-80 2-61 (100)
42 PRK15363 pathogenicity island 88.7 1.7 3.6E-05 40.9 7.3 63 8-74 27-90 (157)
43 TIGR02795 tol_pal_ybgF tol-pal 88.3 3.3 7.2E-05 33.7 8.2 69 15-84 39-107 (119)
44 KOG0687|consensus 88.0 0.95 2E-05 47.4 5.6 71 355-425 318-391 (393)
45 TIGR03504 FimV_Cterm FimV C-te 87.3 0.77 1.7E-05 34.3 3.4 26 19-44 3-28 (44)
46 TIGR02917 PEP_TPR_lipo putativ 87.1 39 0.00085 36.5 17.5 66 11-80 121-186 (899)
47 PF14559 TPR_19: Tetratricopep 87.1 0.84 1.8E-05 34.6 3.6 37 11-47 21-57 (68)
48 PRK15431 ferrous iron transpor 86.4 1 2.2E-05 37.8 4.0 53 224-290 4-57 (78)
49 PRK11189 lipoprotein NlpI; Pro 86.4 27 0.00059 34.8 15.0 69 9-81 92-160 (296)
50 PF13176 TPR_7: Tetratricopept 85.6 0.84 1.8E-05 31.6 2.7 30 17-46 1-30 (36)
51 KOG2581|consensus 85.4 0.61 1.3E-05 49.9 2.7 42 354-395 377-420 (493)
52 PF13525 YfiO: Outer membrane 85.0 6 0.00013 37.4 9.0 71 14-85 4-74 (203)
53 cd00189 TPR Tetratricopeptide 84.2 4.8 0.0001 29.2 6.5 64 12-79 31-94 (100)
54 PF14853 Fis1_TPR_C: Fis1 C-te 83.9 1.9 4E-05 33.4 4.2 36 15-50 1-36 (53)
55 PF13181 TPR_8: Tetratricopept 83.7 1.9 4.1E-05 28.5 3.7 31 16-46 2-32 (34)
56 PF13428 TPR_14: Tetratricopep 83.2 2.3 5E-05 30.5 4.2 33 16-48 2-34 (44)
57 TIGR02552 LcrH_SycD type III s 83.2 7.6 0.00016 32.9 8.1 68 9-81 11-79 (135)
58 PF08220 HTH_DeoR: DeoR-like h 81.9 4.4 9.5E-05 31.2 5.6 54 223-293 1-54 (57)
59 PF12569 NARP1: NMDA receptor- 81.8 72 0.0016 35.3 16.8 222 12-239 35-293 (517)
60 TIGR02521 type_IV_pilW type IV 81.2 6.7 0.00015 34.6 7.4 66 13-82 133-198 (234)
61 PF13371 TPR_9: Tetratricopept 81.1 1.9 4.1E-05 33.1 3.3 35 12-46 26-60 (73)
62 KOG1464|consensus 81.0 1.7 3.8E-05 44.8 3.9 69 358-427 369-437 (440)
63 PF13432 TPR_16: Tetratricopep 80.4 3.2 6.9E-05 31.3 4.3 37 11-47 27-63 (65)
64 PF00515 TPR_1: Tetratricopept 79.3 4.1 9E-05 27.0 4.1 31 16-46 2-32 (34)
65 PF13374 TPR_10: Tetratricopep 78.6 3.3 7.2E-05 28.0 3.6 31 15-45 2-32 (42)
66 PF08279 HTH_11: HTH domain; 78.5 5.1 0.00011 29.8 4.9 47 226-288 5-51 (55)
67 PRK10747 putative protoheme IX 78.1 84 0.0018 32.7 15.3 96 20-126 158-253 (398)
68 TIGR03302 OM_YfiO outer membra 77.9 12 0.00026 35.0 8.3 62 19-81 170-231 (235)
69 PRK11788 tetratricopeptide rep 77.5 81 0.0018 31.5 18.9 66 15-84 107-172 (389)
70 PRK10866 outer membrane biogen 76.8 15 0.00033 36.0 8.9 44 5-48 59-102 (243)
71 PF03399 SAC3_GANP: SAC3/GANP/ 76.2 6.1 0.00013 36.7 5.8 102 138-261 97-204 (204)
72 TIGR03302 OM_YfiO outer membra 76.2 13 0.00028 34.8 8.0 75 10-85 28-102 (235)
73 PF13431 TPR_17: Tetratricopep 76.1 1.4 3.1E-05 30.5 1.1 27 9-35 7-33 (34)
74 KOG1498|consensus 76.0 3.3 7.3E-05 44.2 4.3 67 358-424 358-429 (439)
75 TIGR02917 PEP_TPR_lipo putativ 75.9 1.2E+02 0.0027 32.8 19.3 61 15-80 567-628 (899)
76 COG5600 Transcription-associat 74.9 33 0.00072 36.7 11.2 161 115-299 237-408 (413)
77 smart00028 TPR Tetratricopepti 72.7 7.2 0.00016 23.0 3.7 31 16-46 2-32 (34)
78 TIGR02552 LcrH_SycD type III s 72.3 18 0.00038 30.7 7.2 71 10-84 46-116 (135)
79 PRK12370 invasion protein regu 72.3 1E+02 0.0022 33.7 14.7 69 10-82 333-401 (553)
80 PF13371 TPR_9: Tetratricopept 72.2 14 0.0003 28.1 6.0 57 21-81 1-57 (73)
81 PRK15359 type III secretion sy 71.0 18 0.0004 32.2 7.3 28 18-45 27-54 (144)
82 KOG1126|consensus 70.2 2E+02 0.0044 32.9 16.3 184 16-216 354-598 (638)
83 PF13424 TPR_12: Tetratricopep 69.6 6.4 0.00014 30.7 3.6 33 12-44 43-75 (78)
84 smart00345 HTH_GNTR helix_turn 69.0 6.7 0.00015 28.8 3.4 47 221-280 4-51 (60)
85 cd05804 StaR_like StaR_like; a 68.6 16 0.00036 36.1 7.1 69 11-79 144-212 (355)
86 PRK02603 photosystem I assembl 67.8 36 0.00079 30.8 8.7 69 11-81 31-100 (172)
87 PF10668 Phage_terminase: Phag 67.7 6.2 0.00014 31.6 3.1 37 223-272 9-45 (60)
88 PRK06266 transcription initiat 67.7 25 0.00055 33.4 7.8 104 205-328 4-112 (178)
89 TIGR02944 suf_reg_Xantho FeS a 67.6 15 0.00032 32.3 5.9 80 211-308 4-84 (130)
90 PF12862 Apc5: Anaphase-promot 67.4 43 0.00093 27.9 8.4 60 26-85 9-73 (94)
91 KOG1861|consensus 67.1 37 0.00081 37.4 9.7 102 141-265 388-494 (540)
92 PRK11788 tetratricopeptide rep 66.9 1.4E+02 0.0031 29.8 18.7 72 9-81 63-135 (389)
93 KOG0686|consensus 66.7 7.7 0.00017 41.8 4.5 70 359-428 371-449 (466)
94 TIGR03826 YvyF flagellar opero 65.4 7 0.00015 36.0 3.5 43 226-285 34-78 (137)
95 PRK11189 lipoprotein NlpI; Pro 64.6 26 0.00055 35.0 7.6 69 10-82 58-127 (296)
96 KOG2003|consensus 64.1 22 0.00048 39.2 7.3 78 11-88 520-607 (840)
97 PF14559 TPR_19: Tetratricopep 62.9 16 0.00035 27.4 4.6 51 26-80 2-52 (68)
98 TIGR00990 3a0801s09 mitochondr 61.5 2.5E+02 0.0055 30.8 18.4 68 10-81 360-427 (615)
99 PF02082 Rrf2: Transcriptional 60.6 35 0.00075 27.8 6.5 65 219-297 8-72 (83)
100 KOG4234|consensus 60.4 37 0.00079 34.1 7.5 67 13-79 93-160 (271)
101 PLN03088 SGT1, suppressor of 60.0 37 0.0008 35.1 8.0 67 11-81 32-98 (356)
102 PF14938 SNAP: Soluble NSF att 59.6 1.9E+02 0.0041 28.7 15.4 42 178-220 238-279 (282)
103 PF13525 YfiO: Outer membrane 59.2 40 0.00087 31.8 7.5 45 5-49 32-76 (203)
104 CHL00033 ycf3 photosystem I as 59.0 63 0.0014 29.0 8.5 71 15-85 72-145 (168)
105 PRK11014 transcriptional repre 58.9 19 0.00042 32.2 5.1 58 221-291 10-67 (141)
106 smart00420 HTH_DEOR helix_turn 58.4 15 0.00033 26.1 3.6 28 253-280 18-45 (53)
107 TIGR02010 IscR iron-sulfur clu 58.1 26 0.00056 31.2 5.7 61 222-296 11-71 (135)
108 PF08784 RPA_C: Replication pr 57.9 16 0.00034 30.9 4.1 42 231-285 60-101 (102)
109 PF13414 TPR_11: TPR repeat; P 57.8 13 0.00027 28.2 3.2 37 10-46 32-69 (69)
110 PF14938 SNAP: Soluble NSF att 57.6 82 0.0018 31.2 9.7 124 7-136 106-234 (282)
111 PF13412 HTH_24: Winged helix- 57.1 18 0.0004 26.2 3.8 44 222-279 4-47 (48)
112 PRK10857 DNA-binding transcrip 55.7 26 0.00056 32.8 5.5 62 221-296 10-71 (164)
113 PLN03098 LPA1 LOW PSII ACCUMUL 55.2 49 0.0011 36.2 8.1 71 10-82 70-141 (453)
114 PRK10049 pgaA outer membrane p 55.1 63 0.0014 36.8 9.5 13 168-180 499-511 (765)
115 PF03704 BTAD: Bacterial trans 54.9 66 0.0014 28.0 7.7 71 12-86 59-129 (146)
116 PRK11447 cellulose synthase su 54.6 4.5E+02 0.0098 31.6 17.2 73 10-82 298-380 (1157)
117 PRK11447 cellulose synthase su 54.6 3.8E+02 0.0082 32.2 16.1 70 12-85 25-94 (1157)
118 PF13512 TPR_18: Tetratricopep 53.9 87 0.0019 29.1 8.5 70 15-85 10-79 (142)
119 cd00090 HTH_ARSR Arsenical Res 53.8 56 0.0012 24.2 6.2 40 253-292 24-63 (78)
120 PRK10866 outer membrane biogen 53.6 69 0.0015 31.5 8.3 71 14-85 31-101 (243)
121 CHL00033 ycf3 photosystem I as 53.4 1.1E+02 0.0025 27.3 9.2 72 9-82 29-101 (168)
122 COG1849 Uncharacterized protei 52.2 25 0.00054 30.4 4.3 34 12-45 38-71 (90)
123 PF12895 Apc3: Anaphase-promot 51.6 15 0.00033 29.2 2.9 33 8-40 51-83 (84)
124 COG1349 GlpR Transcriptional r 51.2 36 0.00078 33.8 6.0 60 221-297 4-63 (253)
125 PRK04424 fatty acid biosynthes 50.2 19 0.00042 34.1 3.8 46 221-279 6-51 (185)
126 PLN03088 SGT1, suppressor of 50.2 66 0.0014 33.3 8.0 63 16-82 3-65 (356)
127 PF01047 MarR: MarR family; I 50.2 29 0.00062 26.0 4.0 47 229-288 10-56 (59)
128 cd07377 WHTH_GntR Winged helix 49.6 30 0.00064 25.8 4.1 27 253-279 29-55 (66)
129 PF09012 FeoC: FeoC like trans 49.6 7.9 0.00017 30.7 0.9 38 353-391 13-51 (69)
130 TIGR00990 3a0801s09 mitochondr 49.3 3.9E+02 0.0086 29.3 19.5 68 10-81 326-393 (615)
131 PRK10370 formate-dependent nit 49.3 36 0.00078 32.2 5.5 74 9-86 101-177 (198)
132 KOG2753|consensus 49.0 12 0.00025 39.5 2.2 58 358-415 299-361 (378)
133 PRK11920 rirA iron-responsive 48.7 45 0.00097 30.7 5.8 73 221-308 10-83 (153)
134 KOG1840|consensus 48.3 73 0.0016 35.3 8.3 75 11-85 279-357 (508)
135 smart00550 Zalpha Z-DNA-bindin 48.2 21 0.00046 28.4 3.2 28 253-280 26-53 (68)
136 PRK10681 DNA-binding transcrip 48.1 34 0.00075 33.7 5.3 41 220-273 5-45 (252)
137 PF13518 HTH_28: Helix-turn-he 48.1 34 0.00073 24.7 4.0 30 253-283 16-45 (52)
138 PRK10906 DNA-binding transcrip 46.8 36 0.00077 33.8 5.2 46 221-279 4-49 (252)
139 KOG4414|consensus 46.7 28 0.0006 33.0 4.1 45 215-272 111-155 (197)
140 PF11972 HTH_13: HTH DNA bindi 46.4 25 0.00055 27.7 3.2 32 229-273 6-37 (54)
141 KOG1463|consensus 46.4 49 0.0011 35.3 6.3 73 343-415 329-409 (411)
142 PF03374 ANT: Phage antirepres 46.3 32 0.00069 29.3 4.2 58 224-308 12-70 (111)
143 PF07720 TPR_3: Tetratricopept 46.3 46 0.00099 23.7 4.3 25 15-39 1-25 (36)
144 PLN03083 E3 UFM1-protein ligas 46.0 2.2E+02 0.0048 33.4 11.9 174 177-381 76-295 (803)
145 COG4105 ComL DNA uptake lipopr 45.1 76 0.0016 32.2 7.2 78 6-85 62-145 (254)
146 PF07721 TPR_4: Tetratricopept 45.0 31 0.00068 22.2 3.1 23 17-39 3-25 (26)
147 PRK10434 srlR DNA-bindng trans 45.0 34 0.00073 33.9 4.7 46 221-279 4-49 (256)
148 TIGR03879 near_KaiC_dom probab 44.7 19 0.00041 29.9 2.4 35 232-279 28-62 (73)
149 TIGR03315 Se_ygfK putative sel 44.6 58 0.0013 39.0 7.2 105 256-366 213-341 (1012)
150 PRK10803 tol-pal system protei 43.6 27 0.00059 35.0 3.8 46 4-49 206-251 (263)
151 COG1729 Uncharacterized protei 43.5 81 0.0018 32.1 7.2 81 4-85 167-247 (262)
152 KOG1726|consensus 43.0 80 0.0017 31.5 6.9 24 215-239 100-123 (225)
153 PRK09802 DNA-binding transcrip 43.0 43 0.00094 33.5 5.2 49 219-280 14-62 (269)
154 PRK09853 putative selenate red 42.4 63 0.0014 38.7 7.0 105 256-366 215-343 (1019)
155 PRK10411 DNA-binding transcrip 41.9 38 0.00082 33.3 4.5 54 221-291 3-56 (240)
156 KOG3054|consensus 41.7 48 0.001 33.7 5.2 54 227-293 205-258 (299)
157 PF04733 Coatomer_E: Coatomer 41.5 88 0.0019 31.7 7.2 165 19-214 106-275 (290)
158 COG2976 Uncharacterized protei 41.5 68 0.0015 31.7 6.0 62 15-77 89-150 (207)
159 PF00392 GntR: Bacterial regul 41.4 53 0.0011 25.3 4.4 51 216-279 3-54 (64)
160 PF13384 HTH_23: Homeodomain-l 41.3 22 0.00049 25.8 2.2 40 222-277 6-45 (50)
161 TIGR00738 rrf2_super rrf2 fami 41.0 55 0.0012 28.4 5.0 43 253-296 29-71 (132)
162 PRK15359 type III secretion sy 40.8 1.7E+02 0.0037 26.0 8.2 69 9-81 52-120 (144)
163 PRK10370 formate-dependent nit 40.7 1.3E+02 0.0028 28.5 7.7 72 9-85 67-142 (198)
164 PRK09954 putative kinase; Prov 40.3 55 0.0012 33.4 5.6 52 229-293 10-64 (362)
165 COG3071 HemY Uncharacterized e 40.3 5.2E+02 0.011 28.1 14.6 110 13-134 151-261 (400)
166 PF08831 MHCassoc_trimer: Clas 40.2 54 0.0012 27.3 4.4 36 71-114 26-61 (72)
167 PF09339 HTH_IclR: IclR helix- 40.2 46 0.001 24.7 3.8 42 225-279 7-48 (52)
168 PRK02603 photosystem I assembl 40.1 2E+02 0.0044 25.9 8.7 34 14-47 71-104 (172)
169 COG5071 RPN5 26S proteasome re 40.0 56 0.0012 34.5 5.4 51 358-409 358-408 (439)
170 PF12569 NARP1: NMDA receptor- 39.9 5.7E+02 0.012 28.4 14.3 66 13-82 192-257 (517)
171 smart00346 HTH_ICLR helix_turn 39.5 77 0.0017 25.4 5.3 29 253-281 24-52 (91)
172 TIGR00373 conserved hypothetic 39.5 1.7E+02 0.0036 27.3 8.1 102 209-329 2-105 (158)
173 PRK13509 transcriptional repre 38.9 40 0.00087 33.3 4.2 45 222-279 5-49 (251)
174 PF09743 DUF2042: Uncharacteri 38.3 1.8E+02 0.0038 29.7 8.7 60 209-286 108-167 (272)
175 PF11817 Foie-gras_1: Foie gra 38.1 1.2E+02 0.0026 29.7 7.3 60 15-74 178-239 (247)
176 KOG2582|consensus 38.0 68 0.0015 34.5 5.8 125 268-400 228-362 (422)
177 KOG2114|consensus 37.1 2.2E+02 0.0049 33.7 10.0 160 5-167 357-548 (933)
178 PF04733 Coatomer_E: Coatomer 36.6 74 0.0016 32.2 5.8 57 18-78 166-226 (290)
179 PF12487 DUF3703: Protein of u 36.4 2.7E+02 0.006 25.0 8.6 67 15-81 9-75 (112)
180 PRK12370 invasion protein regu 35.8 1.2E+02 0.0027 33.1 7.7 67 10-80 367-433 (553)
181 PF13429 TPR_15: Tetratricopep 35.5 1E+02 0.0023 29.8 6.5 65 15-83 146-210 (280)
182 PF13545 HTH_Crp_2: Crp-like h 35.5 70 0.0015 24.9 4.4 48 243-294 22-69 (76)
183 PF04703 FaeA: FaeA-like prote 35.2 67 0.0015 25.7 4.1 33 234-279 13-45 (62)
184 PF01022 HTH_5: Bacterial regu 34.2 1.1E+02 0.0024 22.3 4.9 43 221-278 2-44 (47)
185 PRK14584 hmsS hemin storage sy 33.6 82 0.0018 29.7 5.0 46 103-152 23-73 (153)
186 PF09976 TPR_21: Tetratricopep 33.6 2E+02 0.0043 25.3 7.4 53 17-76 87-141 (145)
187 cd06171 Sigma70_r4 Sigma70, re 33.6 82 0.0018 21.7 4.1 23 253-275 30-52 (55)
188 smart00419 HTH_CRP helix_turn_ 33.5 66 0.0014 22.5 3.6 30 251-280 10-39 (48)
189 PF08281 Sigma70_r4_2: Sigma-7 33.2 91 0.002 22.9 4.4 44 215-274 8-51 (54)
190 KOG1497|consensus 33.2 88 0.0019 33.2 5.7 48 357-406 321-368 (399)
191 PRK09782 bacteriophage N4 rece 33.2 8.5E+02 0.018 29.3 14.3 60 16-80 543-603 (987)
192 PF11972 HTH_13: HTH DNA bindi 32.9 41 0.00088 26.6 2.5 25 353-377 12-37 (54)
193 COG1666 Uncharacterized protei 32.5 63 0.0014 30.7 4.1 41 374-414 112-152 (165)
194 KOG3364|consensus 32.5 41 0.0009 31.5 2.9 39 10-48 66-104 (149)
195 KOG0547|consensus 32.3 99 0.0021 34.6 6.1 59 17-79 117-175 (606)
196 PF05527 DUF758: Domain of unk 31.8 3E+02 0.0064 26.8 8.6 33 11-45 35-67 (186)
197 PRK14574 hmsH outer membrane p 31.5 9.2E+02 0.02 28.4 14.4 70 7-80 26-95 (822)
198 TIGR02844 spore_III_D sporulat 30.4 57 0.0012 27.4 3.1 32 223-268 7-38 (80)
199 PF13429 TPR_15: Tetratricopep 30.4 5.1E+02 0.011 25.0 11.6 179 11-221 74-260 (280)
200 COG1959 Predicted transcriptio 30.1 1E+02 0.0022 28.4 5.0 62 221-296 10-71 (150)
201 KOG1126|consensus 30.1 1.3E+02 0.0028 34.3 6.7 75 8-86 516-590 (638)
202 cd00092 HTH_CRP helix_turn_hel 29.9 53 0.0011 24.7 2.7 28 253-280 29-56 (67)
203 PF14276 DUF4363: Domain of un 29.8 3.5E+02 0.0075 23.5 8.2 75 11-85 24-109 (121)
204 cd00131 PAX Paired Box domain 28.8 89 0.0019 28.0 4.3 44 222-281 22-65 (128)
205 PF04010 DUF357: Protein of un 28.7 1.1E+02 0.0023 25.4 4.4 34 12-45 32-65 (75)
206 COG5187 RPN7 26S proteasome re 28.4 1.1E+02 0.0023 32.4 5.3 70 355-424 332-404 (412)
207 PF13512 TPR_18: Tetratricopep 27.5 2.4E+02 0.0052 26.2 7.0 42 7-48 39-80 (142)
208 PRK15174 Vi polysaccharide exp 27.4 2E+02 0.0044 32.3 7.7 70 9-82 278-347 (656)
209 PF01978 TrmB: Sugar-specific 27.0 1.1E+02 0.0024 23.6 4.2 41 226-280 13-53 (68)
210 PF04049 APC8: Anaphase promot 26.9 41 0.0009 30.8 1.9 25 16-40 75-99 (142)
211 COG1654 BirA Biotin operon rep 26.6 1.2E+02 0.0025 25.5 4.4 56 344-402 9-67 (79)
212 PRK03837 transcriptional regul 26.6 1.6E+02 0.0036 27.9 6.0 64 215-293 15-79 (241)
213 KOG3060|consensus 26.4 2.4E+02 0.0052 29.2 7.3 64 15-86 154-217 (289)
214 PF04545 Sigma70_r4: Sigma-70, 26.1 1.1E+02 0.0023 22.4 3.7 29 234-275 18-46 (50)
215 cd00086 homeodomain Homeodomai 25.6 68 0.0015 23.5 2.6 20 253-272 31-50 (59)
216 smart00351 PAX Paired Box doma 25.5 1.2E+02 0.0026 26.9 4.5 28 253-280 37-64 (125)
217 PF14561 TPR_20: Tetratricopep 25.4 1.6E+02 0.0035 24.7 5.1 36 11-46 18-53 (90)
218 PF14178 YppF: YppF-like prote 25.2 40 0.00087 27.2 1.3 31 3-33 9-39 (60)
219 PF00046 Homeobox: Homeobox do 24.9 1.2E+02 0.0026 22.5 3.8 19 358-376 32-50 (57)
220 PF08280 HTH_Mga: M protein tr 24.3 1.1E+02 0.0024 23.5 3.7 36 224-273 8-43 (59)
221 KOG2796|consensus 24.3 8.6E+02 0.019 25.7 12.9 171 17-215 179-364 (366)
222 PF00046 Homeobox: Homeobox do 23.9 78 0.0017 23.5 2.6 20 253-272 31-50 (57)
223 PF10300 DUF3808: Protein of u 23.8 2E+02 0.0043 31.2 6.6 64 18-81 270-333 (468)
224 PRK10072 putative transcriptio 23.7 1.8E+02 0.0038 25.2 5.0 27 232-271 42-68 (96)
225 COG1654 BirA Biotin operon rep 23.7 1.9E+02 0.004 24.3 5.0 45 249-296 19-65 (79)
226 PF14226 DIOX_N: non-haem diox 23.7 90 0.002 26.2 3.3 26 3-28 30-55 (116)
227 cd00092 HTH_CRP helix_turn_hel 23.7 1.5E+02 0.0032 22.2 4.2 37 358-397 30-66 (67)
228 PF05843 Suf: Suppressor of fo 23.5 2.8E+02 0.0061 27.6 7.3 69 15-85 70-139 (280)
229 PF09743 DUF2042: Uncharacteri 23.4 1.8E+02 0.004 29.5 5.9 67 203-285 162-228 (272)
230 TIGR01764 excise DNA binding d 23.4 74 0.0016 22.2 2.3 28 251-282 3-30 (49)
231 smart00418 HTH_ARSR helix_turn 23.4 1.7E+02 0.0036 20.9 4.3 32 253-284 14-45 (66)
232 TIGR01636 phage_rinA phage tra 23.2 1.4E+02 0.003 26.9 4.5 50 211-274 76-125 (134)
233 PF06971 Put_DNA-bind_N: Putat 23.2 1.2E+02 0.0026 23.4 3.5 36 223-271 10-50 (50)
234 PF13463 HTH_27: Winged helix 23.1 2.6E+02 0.0056 21.1 5.5 45 225-282 7-51 (68)
235 PF12802 MarR_2: MarR family; 22.9 1.3E+02 0.0029 22.3 3.8 33 253-285 25-57 (62)
236 KOG2002|consensus 22.9 1.4E+03 0.031 27.7 14.1 155 11-215 160-346 (1018)
237 TIGR01610 phage_O_Nterm phage 22.8 2.5E+02 0.0055 23.6 5.8 41 253-295 51-91 (95)
238 PRK14574 hmsH outer membrane p 22.7 1.3E+03 0.028 27.2 17.8 50 190-239 263-320 (822)
239 PF13011 LZ_Tnp_IS481: leucine 22.7 99 0.0022 26.4 3.3 31 253-284 29-59 (85)
240 KOG2376|consensus 22.5 5.9E+02 0.013 29.2 9.9 77 10-86 105-212 (652)
241 TIGR00540 hemY_coli hemY prote 22.4 8.9E+02 0.019 25.2 15.5 164 15-208 118-296 (409)
242 PRK05412 putative nucleotide-b 22.3 1.3E+02 0.0029 28.6 4.3 52 362-414 97-148 (161)
243 PF12862 Apc5: Anaphase-promot 22.2 1.7E+02 0.0037 24.2 4.6 33 14-46 40-72 (94)
244 TIGR00540 hemY_coli hemY prote 22.0 9.1E+02 0.02 25.1 18.7 61 18-82 156-216 (409)
245 smart00344 HTH_ASNC helix_turn 21.5 96 0.0021 25.9 3.0 39 233-284 14-55 (108)
246 KOG2076|consensus 21.3 1.5E+03 0.032 27.3 14.1 254 9-274 235-510 (895)
247 PF13730 HTH_36: Helix-turn-he 21.2 1E+02 0.0023 22.7 2.8 26 253-278 29-54 (55)
248 cd00155 RasGEF Guanine nucleot 20.9 2.8E+02 0.0061 26.5 6.4 62 12-85 75-136 (237)
249 PF02002 TFIIE_alpha: TFIIE al 20.8 1.4E+02 0.003 25.3 3.9 44 225-282 17-60 (105)
250 smart00389 HOX Homeodomain. DN 20.8 92 0.002 22.8 2.4 19 358-376 32-50 (56)
251 PF05559 DUF763: Protein of un 20.4 53 0.0012 34.3 1.4 26 358-390 104-129 (319)
252 cd00086 homeodomain Homeodomai 20.2 99 0.0021 22.6 2.5 19 358-376 32-50 (59)
253 TIGR03338 phnR_burk phosphonat 20.1 2.6E+02 0.0056 26.1 5.9 64 216-294 14-77 (212)
254 TIGR02997 Sig70-cyanoRpoD RNA 20.0 8.9E+02 0.019 24.3 10.1 33 253-285 181-213 (298)
No 1
>KOG2758|consensus
Probab=100.00 E-value=5.4e-109 Score=819.49 Aligned_cols=310 Identities=68% Similarity=1.133 Sum_probs=303.9
Q ss_pred eccCCCHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHHHHHHHhc
Q psy17612 6 FFFQFKMDMMESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNKLREYIDG 85 (449)
Q Consensus 6 ~~~~~~~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLke~id~ 85 (449)
.+|||++|++++|||||||+|+||||+.|+++||+|+.++++.++++++++|||+|+||+++|||.|++++.||||+||+
T Consensus 120 e~ynf~~e~i~~lykyakfqyeCGNY~gAs~yLY~~r~l~~~~d~n~lsalwGKlASEIL~qnWd~A~edL~rLre~IDs 199 (432)
T KOG2758|consen 120 EHYNFTPERIETLYKYAKFQYECGNYSGASDYLYFYRALVSDPDRNYLSALWGKLASEILTQNWDGALEDLTRLREYIDS 199 (432)
T ss_pred HhcCCCHHHHHHHHHHHHHHHhccCcccHHHHHHHHHHhcCCcchhhHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHcc
Confidence 57999999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred CCCCCCChHHHHHHHHHHHHHHHHHHhcCccchhhHHHHhcCCchhhhHHHhhhhHHHHHHHHHHHhc-cccccchHHHH
Q psy17612 86 GSANFESPLHLLQQRTWLIHWSLFVFFNHVKGRDLIIDMFLNRPHYLNAIQTMCPHILRYLATAVIIN-RSKRNALKDLV 164 (449)
Q Consensus 86 ~~~~~~~pl~~l~qR~WliHwsLf~ffn~~~g~~~~iD~F~~~~~yl~aIqt~cp~lLRYlvvA~Il~-~~r~~~l~dlv 164 (449)
+.|.+|..+++|||||+|||||+|||||+|++.++|+|+++|.|+|||||+|||+||||++|+++| ++|++.++|+|
T Consensus 200 --~~f~~~~~~l~qRtWLiHWslfv~fnhpkgrd~iid~fly~p~YLNaIQt~cPhllRYLatAvvtnk~~rr~~lkdlv 277 (432)
T KOG2758|consen 200 --KSFSTSAQQLQQRTWLIHWSLFVFFNHPKGRDTIIDMFLYQPPYLNAIQTSCPHLLRYLATAVVTNKRRRRNRLKDLV 277 (432)
T ss_pred --cccccHHHHHHHHHHHHHHHHHhhccCCChhhHHHHHHccCHHHHHHHHhhCHHHHHHHHHHhhcchHhhHHHHHHHH
Confidence 788999999999999999999999999999999999999999999999999999999999999999 67788999999
Q ss_pred HHHhhhccCCCchHHHHHHHHhhcccHHHHHHHHHHHhhhcccccchHHhHHHHHHHHHHHHHHHhhhhceeeEeecccc
Q psy17612 165 KVIQQESYTYKDPITEFLEHLYVSFDFESAREKLTECTEVLDNDFFLVACLDEFVENARLMIFETFCRIHQCISIQKESN 244 (449)
Q Consensus 165 ~vi~qE~~~Y~DpiT~fv~~lYv~fdf~~aq~~L~~~~~vl~~DfFL~~~~d~fvenaR~~ife~ycriy~~IsI~~~~~ 244 (449)
+||+||+|+|+||+|+|++|+|++|||++||++|++|++||.|||||++|.++|+|+||++|||+|||||+||+|
T Consensus 278 kVIqqE~ysYkDPiteFl~clyvn~DFdgAq~kl~eCeeVl~nDfFLva~l~~F~E~ARl~ifEtfCRIHqcIti----- 352 (432)
T KOG2758|consen 278 KVIQQESYSYKDPITEFLECLYVNYDFDGAQKKLRECEEVLVNDFFLVALLDEFLENARLLIFETFCRIHQCITI----- 352 (432)
T ss_pred HHHHHhccccCCcHHHHHHHHhhccchHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHHHHHHHHHHHHheeH-----
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccccchhhHHhhcCCCHHHHHHHHHHHHHcccccceecccCCEEEeCCCCCChHHHHHHhhhhhhhHHHHHHHHHHHH
Q psy17612 245 VIDKIFDGQMLASKLNMGTDEAECWIVNLIRNARLDAKIDSKLGHVIMGTQPLSPYQQLLEKIDTLSVRSEALQALIERK 324 (449)
Q Consensus 245 ~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rLdaKIDs~~G~V~m~~~~~s~Yqqviek~d~L~~R~q~L~~~i~~~ 324 (449)
+|||++|||+++|+|+||||+||++||+|||||+.|+|+|++|+.|+|||+|++|+.|++|+|.|+..++++
T Consensus 353 --------~mLA~kLnm~~eeaErwivnlIr~~rl~AkidSklg~Vvmg~~~~s~~qQ~ie~tksLS~rsq~la~~lek~ 424 (432)
T KOG2758|consen 353 --------DMLADKLNMDPEEAERWIVNLIRTARLDAKIDSKLGHVVMGHPTVSPHQQLIEKTKSLSFRSQNLAQQLEKK 424 (432)
T ss_pred --------HHHHHHhcCCHHHHHHHHHHHHHHhhhhhhhccccCceeecCCCCCHHHHHHHhccccchhHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhhcC
Q psy17612 325 VKVRNN 330 (449)
Q Consensus 325 ~~~~~~ 330 (449)
.++.+.
T Consensus 425 ~~~~~~ 430 (432)
T KOG2758|consen 425 IQQKKH 430 (432)
T ss_pred HHHhhc
Confidence 776643
No 2
>KOG0687|consensus
Probab=100.00 E-value=4e-48 Score=385.75 Aligned_cols=281 Identities=18% Similarity=0.283 Sum_probs=258.1
Q ss_pred CHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHHHHHHHhcCCCCC
Q psy17612 11 KMDMMESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNKLREYIDGGSANF 90 (449)
Q Consensus 11 ~~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLke~id~~~~~~ 90 (449)
+.|+++++.+.|.|||++||.++|.+.+......+.+.|.+ ++.++.+++.+++..|.+...+.+.|++++|++||||+
T Consensus 100 E~ev~ea~~~kaeYycqigDkena~~~~~~t~~ktvs~g~k-iDVvf~~iRlglfy~D~~lV~~~iekak~liE~GgDWe 178 (393)
T KOG0687|consen 100 ESEVREAMLRKAEYYCQIGDKENALEALRKTYEKTVSLGHK-IDVVFYKIRLGLFYLDHDLVTESIEKAKSLIEEGGDWE 178 (393)
T ss_pred hHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHhhcccc-hhhHHHHHHHHHhhccHHHHHHHHHHHHHHHHhCCChh
Confidence 68999999999999999999999999999999999888887 99999999999999999999999999999999999999
Q ss_pred -CChHHHHHHHHHHHHHHHHHHh--cCccchhhHHHHhcCCchhhhHHHhhhhHHHHHHHHHHHhccccccc----h--H
Q psy17612 91 -ESPLHLLQQRTWLIHWSLFVFF--NHVKGRDLIIDMFLNRPHYLNAIQTMCPHILRYLATAVIINRSKRNA----L--K 161 (449)
Q Consensus 91 -~~pl~~l~qR~WliHwsLf~ff--n~~~g~~~~iD~F~~~~~yl~aIqt~cp~lLRYlvvA~Il~~~r~~~----l--~ 161 (449)
+|+++.|+ ++|.+. ||++|.++|+|... ||++...+.++.++||+|++++++..|.++ + +
T Consensus 179 RrNRlKvY~--------Gly~msvR~Fk~Aa~Lfld~vs---TFtS~El~~Y~~~v~Ytv~~g~i~leR~dlktKVi~~~ 247 (393)
T KOG0687|consen 179 RRNRLKVYQ--------GLYCMSVRNFKEAADLFLDSVS---TFTSYELMSYETFVRYTVITGLIALERVDLKTKVIKCP 247 (393)
T ss_pred hhhhHHHHH--------HHHHHHHHhHHHHHHHHHHHcc---cccceecccHHHHHHHHHHHhhheeccchHHhhhcCcH
Confidence 89999777 999888 79999999999999 999999999999999999999999988654 3 7
Q ss_pred HHHHHHhhhccCCCchHHHHHHHHhhcccHHHHHHHHHHH-hhhcccccchHHhHHHHHHHHHHHHHHHhhhhceeeEee
Q psy17612 162 DLVKVIQQESYTYKDPITEFLEHLYVSFDFESAREKLTEC-TEVLDNDFFLVACLDEFVENARLMIFETFCRIHQCISIQ 240 (449)
Q Consensus 162 dlv~vi~qE~~~Y~DpiT~fv~~lYv~fdf~~aq~~L~~~-~~vl~~DfFL~~~~d~fvenaR~~ife~ycriy~~IsI~ 240 (449)
||+.++.+- .|+.+|+.++|. +|+..|+..|... ...+..|.||.+|.++|+|++|+.+|.|++.+|++++|
T Consensus 248 Evl~vl~~l-----~~~~q~l~SLY~-C~Y~~Ff~~L~~~~~~~lk~D~~l~~h~~yyvREMR~rvY~QlLESYrsl~l- 320 (393)
T KOG0687|consen 248 EVLEVLHKL-----PSVSQLLNSLYE-CDYSDFFNDLAAVEAKQLKDDRYLGPHYRYYVREMRRRVYAQLLESYRSLTL- 320 (393)
T ss_pred HHHHHhhcC-----chHHHHHHHHHh-ccHHHHHHHHHHHHHHhhccchhcchHHHHHHHHHHHHHHHHHHHHHHHHHH-
Confidence 777777663 345555555555 5666667888655 77899999999999999999999999999999999999
Q ss_pred ccccccccccchhhHHhhcCCCHHHHHHHHHHHHHcccccceecccCCEEEeCCCC--CChHHHHHHhhhhhhhHHHHHH
Q psy17612 241 KESNVIDKIFDGQMLASKLNMGTDEAECWIVNLIRNARLDAKIDSKLGHVIMGTQP--LSPYQQLLEKIDTLSVRSEALQ 318 (449)
Q Consensus 241 ~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rLdaKIDs~~G~V~m~~~~--~s~Yqqviek~d~L~~R~q~L~ 318 (449)
++||+.||||.+++|+.|.+||.+|||+||||.|+|+|++|+|+ +.+||.+|++||.|+||+||++
T Consensus 321 ------------~~MA~aFgVSVefiDreL~rFI~~grL~ckIDrVnGVVEtNrpD~KN~qyq~vikqGd~LLnriQK~~ 388 (393)
T KOG0687|consen 321 ------------ESMAKAFGVSVEFIDRELGRFIAAGRLHCKIDRVNGVVETNRPDEKNAQYQAVIKQGDLLLNRIQKLS 388 (393)
T ss_pred ------------HHHHHHhCchHHHHHhHHHHhhccCceeeeeecccceeecCCccccchHHHHHHhhhHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999997 5779999999999999999999
Q ss_pred HHHH
Q psy17612 319 ALIE 322 (449)
Q Consensus 319 ~~i~ 322 (449)
++|.
T Consensus 389 rvi~ 392 (393)
T KOG0687|consen 389 RVIN 392 (393)
T ss_pred HHhc
Confidence 9884
No 3
>KOG1464|consensus
Probab=100.00 E-value=1.9e-41 Score=333.49 Aligned_cols=267 Identities=21% Similarity=0.283 Sum_probs=248.0
Q ss_pred HHHHHHHHhcCChhhHHHHHHHHHhcCC----CcchhhHHHHHHHHHHhHhhcChHHHHHHHHHHHHHHhcCC---CCCC
Q psy17612 19 YKLAKFRYECGNYSITTSYLYFYLLVMP----TSDRHYLAVLWGKLASEILVQNWDLALEDLNKLREYIDGGS---ANFE 91 (449)
Q Consensus 19 yk~Akf~y~~GdY~~A~~~L~~~~~l~~----~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLke~id~~~---~~~~ 91 (449)
.|+|++|+++|+|.+..++|.+++..|. .+|++++++|++++|+||+|+ ++.++.++||.+|+++. +.++
T Consensus 149 tKLgkl~fd~~e~~kl~KIlkqLh~SCq~edGedD~kKGtQLLEiYAlEIQmY---T~qKnNKkLK~lYeqalhiKSAIP 225 (440)
T KOG1464|consen 149 TKLGKLYFDRGEYTKLQKILKQLHQSCQTEDGEDDQKKGTQLLEIYALEIQMY---TEQKNNKKLKALYEQALHIKSAIP 225 (440)
T ss_pred chHhhhheeHHHHHHHHHHHHHHHHHhccccCchhhhccchhhhhHhhHhhhh---hhhcccHHHHHHHHHHHHhhccCC
Confidence 5899999999999999999999999997 357889999999999999999 99999999999999863 5678
Q ss_pred ChH-----------HHHHHHHHHHHHHHHHHhcCccchhhHHHHhcCCchhhhHHHhhhhHHHHHHHHHHHhccccccch
Q psy17612 92 SPL-----------HLLQQRTWLIHWSLFVFFNHVKGRDLIIDMFLNRPHYLNAIQTMCPHILRYLATAVIINRSKRNAL 160 (449)
Q Consensus 92 ~pl-----------~~l~qR~WliHwsLf~ffn~~~g~~~~iD~F~~~~~yl~aIqt~cp~lLRYlvvA~Il~~~r~~~l 160 (449)
||+ |+|.++.|. +|..+|||+|. .|..+......+||+|||+|+|+++|.+|||
T Consensus 226 HPlImGvIRECGGKMHlreg~fe------------~AhTDFFEAFK---NYDEsGspRRttCLKYLVLANMLmkS~iNPF 290 (440)
T KOG1464|consen 226 HPLIMGVIRECGGKMHLREGEFE------------KAHTDFFEAFK---NYDESGSPRRTTCLKYLVLANMLMKSGINPF 290 (440)
T ss_pred chHHHhHHHHcCCccccccchHH------------HHHhHHHHHHh---cccccCCcchhHHHHHHHHHHHHHHcCCCCC
Confidence 887 677777777 68999999999 6888877777799999999999999999999
Q ss_pred HHHHHHHhhhccCCC-ch----HHHHHHHHhhcccHHHHHHHHHHHhhhcccccchHHhHHHHHHHHHHHHHHHhhhhce
Q psy17612 161 KDLVKVIQQESYTYK-DP----ITEFLEHLYVSFDFESAREKLTECTEVLDNDFFLVACLDEFVENARLMIFETFCRIHQ 235 (449)
Q Consensus 161 ~dlv~vi~qE~~~Y~-Dp----iT~fv~~lYv~fdf~~aq~~L~~~~~vl~~DfFL~~~~d~fvenaR~~ife~ycriy~ 235 (449)
+ +||++||+ || +|+++ ++|++.|+.+|+++|+.....|+.|+|+..|++++++++|++++-..+|||+
T Consensus 291 D------sQEAKPyKNdPEIlAMTnlv-~aYQ~NdI~eFE~Il~~~~~~IM~DpFIReh~EdLl~niRTQVLlkLIkPYt 363 (440)
T KOG1464|consen 291 D------SQEAKPYKNDPEILAMTNLV-AAYQNNDIIEFERILKSNRSNIMDDPFIREHIEDLLRNIRTQVLLKLIKPYT 363 (440)
T ss_pred c------ccccCCCCCCHHHHHHHHHH-HHHhcccHHHHHHHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence 9 99999999 99 89999 8899999999999999999999999999999999999999999999999999
Q ss_pred eeEeeccccccccccchhhHHhhcCCCHHHHHHHHHHHHHcccccceecccCCEEEeCCCCCChHHHHHHhhhhhhhHHH
Q psy17612 236 CISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLIRNARLDAKIDSKLGHVIMGTQPLSPYQQLLEKIDTLSVRSE 315 (449)
Q Consensus 236 ~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rLdaKIDs~~G~V~m~~~~~s~Yqqviek~d~L~~R~q 315 (449)
.|.| +++|++||+++.+++..||.+|.+.+++++||.+++.++++...++- ..+.+..|.+.++++
T Consensus 364 ~i~I-------------pfis~~Lnv~~~dV~~LLV~~ILD~~i~g~Ide~n~~l~~~~~~~s~-~k~~~al~kW~~ql~ 429 (440)
T KOG1464|consen 364 NIGI-------------PFISKELNVPEADVESLLVSCILDDTIDGRIDEVNQYLELDKSKNSG-SKLYKALDKWNNQLK 429 (440)
T ss_pred ccCc-------------hhhHhhcCCCHHHHHHHHHHHHhccccccchHHhhhHhccCccCCcc-hHHHHHHHHHHHHHH
Confidence 9999 99999999999999999999999999999999999999999887654 246777889999999
Q ss_pred HHHHHHHHH
Q psy17612 316 ALQALIERK 324 (449)
Q Consensus 316 ~L~~~i~~~ 324 (449)
.|+.+|..+
T Consensus 430 Sl~~~i~sr 438 (440)
T KOG1464|consen 430 SLQSNIVSR 438 (440)
T ss_pred HHHHHHHhh
Confidence 999998765
No 4
>COG5187 RPN7 26S proteasome regulatory complex component, contains PCI domain [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.5e-35 Score=292.95 Aligned_cols=281 Identities=15% Similarity=0.196 Sum_probs=252.5
Q ss_pred CHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHHHHHHHhcCCCCC
Q psy17612 11 KMDMMESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNKLREYIDGGSANF 90 (449)
Q Consensus 11 ~~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLke~id~~~~~~ 90 (449)
+.|..++.-.+|.||+.+||.+++.+++..........+.| ++.++.+++++.+.+|--...+-+++++.+|++||||+
T Consensus 111 E~e~~ea~~n~aeyY~qi~D~~ng~~~~~~~~~~a~stg~K-iDv~l~kiRlg~~y~d~~vV~e~lE~~~~~iEkGgDWe 189 (412)
T COG5187 111 ETEGSEADRNIAEYYCQIMDIQNGFEWMRRLMRDAMSTGLK-IDVFLCKIRLGLIYGDRKVVEESLEVADDIIEKGGDWE 189 (412)
T ss_pred chHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhcccc-hhhHHHHHHHHHhhccHHHHHHHHHHHHHHHHhCCCHH
Confidence 56788999999999999999999999999888777777887 99999999999999999889999999999999999999
Q ss_pred -CChHHHHHHHHHHHHHHHHHHh--cCccchhhHHHHhcCCchhhhHHHhhhhHHHHHHHHHHHhccccccc----h--H
Q psy17612 91 -ESPLHLLQQRTWLIHWSLFVFF--NHVKGRDLIIDMFLNRPHYLNAIQTMCPHILRYLATAVIINRSKRNA----L--K 161 (449)
Q Consensus 91 -~~pl~~l~qR~WliHwsLf~ff--n~~~g~~~~iD~F~~~~~yl~aIqt~cp~lLRYlvvA~Il~~~r~~~----l--~ 161 (449)
+|+.+.++ ++|.+. ||+.|..+|.|... ||.++..+.+..+.||.+++.+++..|+++ + |
T Consensus 190 RrNRyK~Y~--------Gi~~m~~RnFkeAa~Ll~d~l~---tF~S~El~sY~~~vrYa~~~Gl~~leR~diktki~dsp 258 (412)
T COG5187 190 RRNRYKVYK--------GIFKMMRRNFKEAAILLSDILP---TFESSELISYSRAVRYAIFCGLLRLERRDIKTKILDSP 258 (412)
T ss_pred hhhhHHHHH--------HHHHHHHHhhHHHHHHHHHHhc---cccccccccHHHHHHHHHHhhhheeehhhhhhhhcCCH
Confidence 79999666 999887 79999999999998 999999999999999999999999888655 3 8
Q ss_pred HHHHHHhhhccCC--CchHHHHHHHHhhcccHHHHHHHHHH-HhhhcccccchHHhHHHHHHHHHHHHHHHhhhhceeeE
Q psy17612 162 DLVKVIQQESYTY--KDPITEFLEHLYVSFDFESAREKLTE-CTEVLDNDFFLVACLDEFVENARLMIFETFCRIHQCIS 238 (449)
Q Consensus 162 dlv~vi~qE~~~Y--~DpiT~fv~~lYv~fdf~~aq~~L~~-~~~vl~~DfFL~~~~d~fvenaR~~ife~ycriy~~Is 238 (449)
+++.||++...-- ....|++++|-|--| +..|.. -..++..|.||..|.|+|+|++|..+|.|.+.+|+.++
T Consensus 259 evl~vi~~~e~l~sl~~l~~SLy~cdY~~~-----F~~ll~~~~n~L~~d~fl~rh~d~fvREMRrrvYaQlLESYr~ls 333 (412)
T COG5187 259 EVLDVIGSSEKLGSLVQLATSLYECDYGGD-----FMNLLYLFCNSLQDDVFLGRHVDLFVREMRRRVYAQLLESYRLLS 333 (412)
T ss_pred HHHHhccchhhhhhHHHHHHHHHHhccchh-----hHHHHHHHHhhccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 8999998876421 144677777766633 355544 44589999999999999999999999999999999999
Q ss_pred eeccccccccccchhhHHhhcCCCHHHHHHHHHHHHHcccccceecccCCEEEeCCCC--CChHHHHHHhhhhhhhHHHH
Q psy17612 239 IQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLIRNARLDAKIDSKLGHVIMGTQP--LSPYQQLLEKIDTLSVRSEA 316 (449)
Q Consensus 239 I~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rLdaKIDs~~G~V~m~~~~--~s~Yqqviek~d~L~~R~q~ 316 (449)
| ++||+.||||.+.+|+-|..||.++||+|+||.+||+|++++|+ +.+||.++++||.|++|+|+
T Consensus 334 l-------------~sMA~tFgVSV~yvdrDLg~FIp~~~LncvIDRvnGvVetnrpdekn~qy~~vVkqGd~ll~klqK 400 (412)
T COG5187 334 L-------------ESMAQTFGVSVEYVDRDLGEFIPEGRLNCVIDRVNGVVETNRPDEKNQQYSSVVKQGDDLLRKLQK 400 (412)
T ss_pred H-------------HHHHHHhCccHHHHhhhHHhhCCCCceeeeeecccceEeccCcchhhhhHHHHHhcchHHHHHHHH
Confidence 9 99999999999999999999999999999999999999999997 58999999999999999999
Q ss_pred HHHHH
Q psy17612 317 LQALI 321 (449)
Q Consensus 317 L~~~i 321 (449)
-...+
T Consensus 401 y~atv 405 (412)
T COG5187 401 YVATV 405 (412)
T ss_pred HHHHH
Confidence 98776
No 5
>KOG2758|consensus
Probab=99.93 E-value=1.4e-26 Score=231.62 Aligned_cols=83 Identities=60% Similarity=0.864 Sum_probs=80.3
Q ss_pred hhhhHHH-HHHhhcCCChHHHHHHHHHHhhhcccccccccCCCeEEecCCCCChhHHHHHhhhcccchHHHHHHHHHHHH
Q psy17612 351 DLNVITI-MLASKLNMGTDEAECWIVNLIRNARLDAKIDSKLGHVIMGTQPLSPYQQLLEKIDTLSVRSEALQALIERKV 429 (449)
Q Consensus 351 ~~~~~~~-~la~kLnm~~~eaE~WIvnLIr~~~ldAKIDs~~~~v~m~~~~~svyqqviektk~l~~rt~~l~~~~~~~~ 429 (449)
+|++|++ |||+||||+++|||+|||||||++|+||||||+.|+|+||++++|+|||||||||+|+|||+.|+++++++.
T Consensus 346 IHqcIti~mLA~kLnm~~eeaErwivnlIr~~rl~AkidSklg~Vvmg~~~~s~~qQ~ie~tksLS~rsq~la~~lek~~ 425 (432)
T KOG2758|consen 346 IHQCITIDMLADKLNMDPEEAERWIVNLIRTARLDAKIDSKLGHVVMGHPTVSPHQQLIEKTKSLSFRSQNLAQQLEKKI 425 (432)
T ss_pred HHHheeHHHHHHHhcCCHHHHHHHHHHHHHHhhhhhhhccccCceeecCCCCCHHHHHHHhccccchhHHHHHHHHHHHH
Confidence 8999999 999999999999999999999999999999999999999999999999999999999999999999999997
Q ss_pred hhhc
Q psy17612 430 KVRN 433 (449)
Q Consensus 430 ~~~~ 433 (449)
.+..
T Consensus 426 ~~~~ 429 (432)
T KOG2758|consen 426 QQKK 429 (432)
T ss_pred HHhh
Confidence 6654
No 6
>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.
Probab=99.64 E-value=1.6e-15 Score=125.57 Aligned_cols=104 Identities=29% Similarity=0.412 Sum_probs=95.8
Q ss_pred chHHHHHHHHhhcccHHHHHHHHHHHhhhcccccchHHhHHHHHHHHHHHHHHHhhhhceeeEeeccccccccccchhhH
Q psy17612 176 DPITEFLEHLYVSFDFESAREKLTECTEVLDNDFFLVACLDEFVENARLMIFETFCRIHQCISIQKESNVIDKIFDGQML 255 (449)
Q Consensus 176 DpiT~fv~~lYv~fdf~~aq~~L~~~~~vl~~DfFL~~~~d~fvenaR~~ife~ycriy~~IsI~~~~~~~~~~~~~~~L 255 (449)
+|+++++++ |...|+..+.+.+..+++.+..|.++..|.+.+.+.+|...+.+++++|++|++ +.+
T Consensus 1 ~~~~~l~~~-~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~~l~~~i~~~~l~~l~~~y~~i~~-------------~~i 66 (105)
T PF01399_consen 1 PPYSELLRA-FRSGDLQEFEEFLEKHSESLFKDPFLAEYVEQLKEKIRRRNLRQLSKPYSSISI-------------SEI 66 (105)
T ss_dssp HHHHHHHHH-HHCT-HHHHHHHHHHTCHHHHHCTTHHHHHHHHHHHHHHHHHHHHHHC-SEEEH-------------HHH
T ss_pred CHHHHHHHH-HHhCCHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHHHHHHHhcccch-------------HHH
Confidence 468889954 777889999999999988888999999999999999999999999999999999 999
Q ss_pred HhhcCCCHHHHHHHHHHHHHcccccceecccCCEEEeC
Q psy17612 256 ASKLNMGTDEAECWIVNLIRNARLDAKIDSKLGHVIMG 293 (449)
Q Consensus 256 A~~Lnms~~e~E~wIVnlIr~~rLdaKIDs~~G~V~m~ 293 (449)
|+.|+++.+++|.||+++|.+|+|+||||+++|+|+++
T Consensus 67 a~~l~~~~~~vE~~l~~~I~~~~i~~~ID~~~~~v~~~ 104 (105)
T PF01399_consen 67 AKALQLSEEEVESILIDLISNGLIKAKIDQVNGVVVFS 104 (105)
T ss_dssp HHHHTCCHHHHHHHHHHHHHTTSSEEEEETTTTEEEE-
T ss_pred HHHhccchHHHHHHHHHHHHCCCEEEEEECCCCEEEec
Confidence 99999999999999999999999999999999999986
No 7
>KOG0686|consensus
Probab=99.64 E-value=1.6e-14 Score=148.96 Aligned_cols=279 Identities=16% Similarity=0.226 Sum_probs=198.8
Q ss_pred ccCCCHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHHHHHHHhcC
Q psy17612 7 FFQFKMDMMESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNKLREYIDGG 86 (449)
Q Consensus 7 ~~~~~~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLke~id~~ 86 (449)
.-++..-++.++-++|.+|++||+.+.|.+.+-..|.-|++. .+.++.....+..-|.++||--..-...+++..-+..
T Consensus 142 ~n~iKEsiRra~~Dl~dhy~~cG~l~~Alr~YsR~RdYCTs~-khvInm~ln~i~VSI~~~nw~hv~sy~~~A~st~~~~ 220 (466)
T KOG0686|consen 142 DNLIKESIRRALEDLGDHYLDCGQLDNALRCYSRARDYCTSA-KHVINMCLNLILVSIYMGNWGHVLSYISKAESTPDAN 220 (466)
T ss_pred cchhhHHHHHHHHHHHHHHHHhccHHHHHhhhhhhhhhhcch-HHHHHHHHHHHHHHHhhcchhhhhhHHHHHHhCchhh
Confidence 446777889999999999999999999999999999999865 5568999999999999999999999998888775321
Q ss_pred C---CCCCChHH------HHHHHHHHHHHHHHHHhcCccchhhHHHHhcCCchhhhHHHhhhh-HHHHHHHHHHHhcccc
Q psy17612 87 S---ANFESPLH------LLQQRTWLIHWSLFVFFNHVKGRDLIIDMFLNRPHYLNAIQTMCP-HILRYLATAVIINRSK 156 (449)
Q Consensus 87 ~---~~~~~pl~------~l~qR~WliHwsLf~ffn~~~g~~~~iD~F~~~~~yl~aIqt~cp-~lLRYlvvA~Il~~~r 156 (449)
. ...+.|+. .|..|..- .+..-|+..-.+.-.|-. ...| .+-=|--++++-+-+|
T Consensus 221 ~~~~q~v~~kl~C~agLa~L~lkkyk------------~aa~~fL~~~~~~~d~~~---ivtpsdv~iYggLcALAtfdr 285 (466)
T KOG0686|consen 221 ENLAQEVPAKLKCAAGLANLLLKKYK------------SAAKYFLLAEFDHCDYPE---IVTPSDVAIYGGLCALATFDR 285 (466)
T ss_pred hhHHHhcCcchHHHHHHHHHHHHHHH------------HHHHHHHhCCCCccCccc---eecchhhHHHHhhHhhccCCH
Confidence 1 11234432 23333211 111222222111000000 1112 3555888888888888
Q ss_pred ccchHHHHHHHhhhcc-CCC--ch-----HHHHHHHHhhcccHHHHHHHHHHHhhhcccccchHHhHHHHHHHHHHHHHH
Q psy17612 157 RNALKDLVKVIQQESY-TYK--DP-----ITEFLEHLYVSFDFESAREKLTECTEVLDNDFFLVACLDEFVENARLMIFE 228 (449)
Q Consensus 157 ~~~l~dlv~vi~qE~~-~Y~--Dp-----iT~fv~~lYv~fdf~~aq~~L~~~~~vl~~DfFL~~~~d~fvenaR~~ife 228 (449)
.+... .||..++. .+. +| +-.|+++-|. .-.+.|++.+.-+.-|+||++|++.+..-+|-...-
T Consensus 286 ~~Lk~---~vi~n~~Fk~flel~Pqlr~il~~fy~sky~-----~cl~~L~~~k~~llLD~yLaphVd~Ly~~IR~r~ll 357 (466)
T KOG0686|consen 286 QDLKL---NVIKNESFKLFLELEPQLREILFKFYSSKYA-----SCLELLREIKPRLLLDMYLAPHVDNLYSLIRNRALL 357 (466)
T ss_pred HHHHH---HHHcchhhhhHHhcChHHHHHHHHHhhhhHH-----HHHHHHHHhccceeechhcchhHHHHHHHHHHhhHH
Confidence 55443 34445542 122 33 4455555554 446899999999999999999999999999999999
Q ss_pred HhhhhceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHHHHHcccccceecccCCEEEeCCCC--CChHHHH---
Q psy17612 229 TFCRIHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLIRNARLDAKIDSKLGHVIMGTQP--LSPYQQL--- 303 (449)
Q Consensus 229 ~ycriy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rLdaKIDs~~G~V~m~~~~--~s~Yqqv--- 303 (449)
+|..||.++++ .-||..||+|..+.|..+-.||.+|++.||||+-+++|.+-..+ +...+.+
T Consensus 358 qy~~py~s~~m-------------~~mA~af~~sv~~le~~l~~LI~~~~i~~rIDs~~ki~~~~~~~~en~~fe~~~~~ 424 (466)
T KOG0686|consen 358 QYLSPYSSADM-------------SKMAEAFNTSVAILESELLELILEGKISGRIDSHNKILYARDADSENATFERVLPM 424 (466)
T ss_pred HhcCccccchH-------------HHHHHHhcccHHHHHHHHHHHHHccchheeeccccceeeecccccccchhhhcchh
Confidence 99999999999 99999999999999999999999999999999999999987653 2222222
Q ss_pred ----HHhhhhhhhHHHHHHHHHH
Q psy17612 304 ----LEKIDTLSVRSEALQALIE 322 (449)
Q Consensus 304 ----iek~d~L~~R~q~L~~~i~ 322 (449)
-.+.+.|+-|+.++.+.+.
T Consensus 425 ~~~~~~~~kal~lr~~~~~~~~h 447 (466)
T KOG0686|consen 425 GKRSQLEAKALLLRAALLKNKIH 447 (466)
T ss_pred hHHHHHHHHHHHHHHHHHhcccc
Confidence 2334455555555544443
No 8
>PF10602 RPN7: 26S proteasome subunit RPN7; InterPro: IPR019585 This entry represents the regulatory subunit RPN7 (known as the non-ATPase regulatory subunit 6 in higher eukaryotes) of the 26S proteasome. This entry also matches the evolutionarily related subunit 1 of the COP9 signalosome complex (CSN) from Arabidopsis []. The 26S proteasome plays a major role in ATP-dependent degradation of ubiquitinated proteins. Substrate specificity is conferred by the regulatory particle (RP), which can dissociate into stable lid and base subcomplexes. The regulatory subunit RPN7 is one of the lid subunits of the 26S proteasome and has been shown in Saccharomyces cerevisiae (Baker's yeast) to be required for structural integrity []. The COP9 signalosome is a conserved protein complex composed of eight subunits, where Individual subunits of the complex have been linked to various signal transduction pathways leading to gene expression and cell cycle control []. The overall organisation and the amino acid sequences of the COP9 signalosome subunits resemble the lid subcomplex of the 19 S regulatory particle for the 26 S proteasome []. COP9 subunit 1 (CSN1 or GPS1) of the COP9 complex is an essential subunit of the complex with regard to both structural integrity and functionality. The N-terminal region of subunit 1 (CSN1-N) can inhibit c-fos expression from either a transfected template or a chromosomal transgene (fos-lacZ), and may contain the activity domain that confers most of the repression functions of CSN1. The C-terminal region of subunit 1 (CSN1-C) allows integration of the protein into the COP9 signalosome.
Probab=99.44 E-value=3.6e-13 Score=125.59 Aligned_cols=140 Identities=10% Similarity=0.097 Sum_probs=125.3
Q ss_pred ccCCCHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHHHHHHHhcC
Q psy17612 7 FFQFKMDMMESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNKLREYIDGG 86 (449)
Q Consensus 7 ~~~~~~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLke~id~~ 86 (449)
+-.++.++++++.++|.||+++||+++|.+.+...+..|++.+.+ ++..+..++..|+.+||+.+...+.|++.+++.+
T Consensus 28 ~n~~kesir~~~~~l~~~~~~~Gd~~~A~k~y~~~~~~~~~~~~~-id~~l~~irv~i~~~d~~~v~~~i~ka~~~~~~~ 106 (177)
T PF10602_consen 28 SNLGKESIRMALEDLADHYCKIGDLEEALKAYSRARDYCTSPGHK-IDMCLNVIRVAIFFGDWSHVEKYIEKAESLIEKG 106 (177)
T ss_pred hccchHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHhhhcCCHHHH-HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhcc
Confidence 456789999999999999999999999999999999999987665 9999999999999999999999999999999999
Q ss_pred CCCC-CChHHHHHHHHHHHHHHHHHHh--cCccchhhHHHHhcCCchhhh---HHHhhhhHHHHHHHHHHHhcccccc
Q psy17612 87 SANF-ESPLHLLQQRTWLIHWSLFVFF--NHVKGRDLIIDMFLNRPHYLN---AIQTMCPHILRYLATAVIINRSKRN 158 (449)
Q Consensus 87 ~~~~-~~pl~~l~qR~WliHwsLf~ff--n~~~g~~~~iD~F~~~~~yl~---aIqt~cp~lLRYlvvA~Il~~~r~~ 158 (449)
++|. +|+++.++ +|+.+. ++..|...|++.-. +|.+ ..-.....+..|.+++++.+.+|..
T Consensus 107 ~d~~~~nrlk~~~--------gL~~l~~r~f~~AA~~fl~~~~---t~~~~~~~el~s~~d~a~Y~~l~aLat~~R~e 173 (177)
T PF10602_consen 107 GDWERRNRLKVYE--------GLANLAQRDFKEAAELFLDSLS---TFTSLQYTELISYNDFAIYGGLCALATLDRSE 173 (177)
T ss_pred chHHHHHHHHHHH--------HHHHHHhchHHHHHHHHHccCc---CCCCCchhhhcCHHHHHHHHHHHHHHhCCHHH
Confidence 9998 78888665 888887 47899999999987 7765 5556666999999999999998844
No 9
>smart00753 PAM PCI/PINT associated module.
Probab=99.43 E-value=6.2e-13 Score=108.95 Aligned_cols=72 Identities=24% Similarity=0.260 Sum_probs=69.3
Q ss_pred HhHHHHHHHHHHHHHHHhhhhceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHHHHHcccccceecccCCEEEe
Q psy17612 213 ACLDEFVENARLMIFETFCRIHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLIRNARLDAKIDSKLGHVIM 292 (449)
Q Consensus 213 ~~~d~fvenaR~~ife~ycriy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rLdaKIDs~~G~V~m 292 (449)
+|.+.+.+.+|...+.+||++|++|++ +.||+.|+++.+++|.+|+++|++|.|+||||+.+|+|.+
T Consensus 1 ~~~~~l~~~~~~~~l~~l~~~y~~i~~-------------~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~ 67 (88)
T smart00753 1 QLVERLQRKIRLTNLLQLSEPYSSISL-------------SDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEF 67 (88)
T ss_pred ChHHHHHHHHHHHHHHHHhHHhceeeH-------------HHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEE
Confidence 478899999999999999999999999 9999999999999999999999999999999999999999
Q ss_pred CCCCC
Q psy17612 293 GTQPL 297 (449)
Q Consensus 293 ~~~~~ 297 (449)
++.++
T Consensus 68 ~~~~~ 72 (88)
T smart00753 68 EEVDP 72 (88)
T ss_pred CCCch
Confidence 98765
No 10
>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15. Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.
Probab=99.43 E-value=6.2e-13 Score=108.95 Aligned_cols=72 Identities=24% Similarity=0.260 Sum_probs=69.3
Q ss_pred HhHHHHHHHHHHHHHHHhhhhceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHHHHHcccccceecccCCEEEe
Q psy17612 213 ACLDEFVENARLMIFETFCRIHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLIRNARLDAKIDSKLGHVIM 292 (449)
Q Consensus 213 ~~~d~fvenaR~~ife~ycriy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rLdaKIDs~~G~V~m 292 (449)
+|.+.+.+.+|...+.+||++|++|++ +.||+.|+++.+++|.+|+++|++|.|+||||+.+|+|.+
T Consensus 1 ~~~~~l~~~~~~~~l~~l~~~y~~i~~-------------~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~ 67 (88)
T smart00088 1 QLVERLQRKIRLTNLLQLSEPYSSISL-------------SDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEF 67 (88)
T ss_pred ChHHHHHHHHHHHHHHHHhHHhceeeH-------------HHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEE
Confidence 478899999999999999999999999 9999999999999999999999999999999999999999
Q ss_pred CCCCC
Q psy17612 293 GTQPL 297 (449)
Q Consensus 293 ~~~~~ 297 (449)
++.++
T Consensus 68 ~~~~~ 72 (88)
T smart00088 68 EEVDP 72 (88)
T ss_pred CCCch
Confidence 98765
No 11
>KOG1463|consensus
Probab=99.12 E-value=1.4e-09 Score=111.00 Aligned_cols=264 Identities=13% Similarity=0.147 Sum_probs=179.2
Q ss_pred HHHHHHHHhcCChhhHHHHHHHHH-hcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHHHHHHHhcCC---C-CCCCh
Q psy17612 19 YKLAKFRYECGNYSITTSYLYFYL-LVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNKLREYIDGGS---A-NFESP 93 (449)
Q Consensus 19 yk~Akf~y~~GdY~~A~~~L~~~~-~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLke~id~~~---~-~~~~p 93 (449)
-+++.+|++.|+|.+|......+. ++-.-+|+- .|-++.-.|-=.+ -++.++.|.|.-+-... + ..-+|
T Consensus 132 arli~Ly~d~~~YteAlaL~~~L~rElKKlDDK~---lLvev~llESK~y---~~l~Nl~KakasLTsART~AnaiYcpP 205 (411)
T KOG1463|consen 132 ARLIRLYNDTKRYTEALALINDLLRELKKLDDKI---LLVEVHLLESKAY---HALRNLPKAKASLTSARTTANAIYCPP 205 (411)
T ss_pred HHHHHHHHhhHHHHHHHHHHHHHHHHHHhccccc---ceeeehhhhhHHH---HHHhcchhHHHHHHHHHHhhcccccCH
Confidence 467889999999999998776533 332223332 2222222222222 35566666666665432 2 22455
Q ss_pred HHHHHHHHHHHHHHHHHHh--cCccchhhHHHHhcCCchhhhHHH-hhhhHHHHHHHHHHHhccccccchHHHHHHHhhh
Q psy17612 94 LHLLQQRTWLIHWSLFVFF--NHVKGRDLIIDMFLNRPHYLNAIQ-TMCPHILRYLATAVIINRSKRNALKDLVKVIQQE 170 (449)
Q Consensus 94 l~~l~qR~WliHwsLf~ff--n~~~g~~~~iD~F~~~~~yl~aIq-t~cp~lLRYlvvA~Il~~~r~~~l~dlv~vi~qE 170 (449)
..|-+ --|. =++..-- ++.-|..=|+|+|= +|.+-.- ..+-.-|||..++-|.- ++.+-+.-+++ ...
T Consensus 206 qlQa~--lDLq-SGIlha~ekDykTafSYFyEAfE---gf~s~~~~v~A~~sLKYMlLcKIMl-n~~ddv~~lls--~K~ 276 (411)
T KOG1463|consen 206 QLQAT--LDLQ-SGILHAAEKDYKTAFSYFYEAFE---GFDSLDDDVKALTSLKYMLLCKIML-NLPDDVAALLS--AKL 276 (411)
T ss_pred HHHHH--HHHh-ccceeecccccchHHHHHHHHHc---cccccCCcHHHHHHHHHHHHHHHHh-cCHHHHHHHHh--hHH
Confidence 43211 0000 0000000 12334455678887 5655432 23346899998876643 23233333333 344
Q ss_pred ccCCCchHHH---HHHHHhhcccHHHHHHHHHHHhhhcccccchHHhHHHHHHHHHHHHHHHhhhhceeeEeeccccccc
Q psy17612 171 SYTYKDPITE---FLEHLYVSFDFESAREKLTECTEVLDNDFFLVACLDEFVENARLMIFETFCRIHQCISIQKESNVID 247 (449)
Q Consensus 171 ~~~Y~DpiT~---fv~~lYv~fdf~~aq~~L~~~~~vl~~DfFL~~~~d~fvenaR~~ife~ycriy~~IsI~~~~~~~~ 247 (449)
+..|.+|..+ =+-..|.+-+..+|+..|++....|..|++++.|...+-+++=-.=+-..+.||.+|.|
T Consensus 277 ~l~y~g~~i~AmkavAeA~~nRSLkdF~~AL~~yk~eL~~D~ivr~Hl~~Lyd~lLEknl~riIEPyS~Vei-------- 348 (411)
T KOG1463|consen 277 ALKYAGRDIDAMKAVAEAFGNRSLKDFEKALADYKKELAEDPIVRSHLQSLYDNLLEKNLCRIIEPYSRVEI-------- 348 (411)
T ss_pred HHhccCcchHHHHHHHHHhcCCcHHHHHHHHHHhHHHHhcChHHHHHHHHHHHHHHHHhHHHHcCchhhhhH--------
Confidence 4457777432 23357889999999999999999999999999999999999888888888899999999
Q ss_pred cccchhhHHhhcCCCHHHHHHHHHHHHHcccccceecccCCEEEeCCCC--CChHHHHHHhhhhh
Q psy17612 248 KIFDGQMLASKLNMGTDEAECWIVNLIRNARLDAKIDSKLGHVIMGTQP--LSPYQQLLEKIDTL 310 (449)
Q Consensus 248 ~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rLdaKIDs~~G~V~m~~~~--~s~Yqqviek~d~L 310 (449)
..+|+-.|++.+.+|+-|+..|.+.++.+-+|+-+|+++.-..+ .+.|+..+|....+
T Consensus 349 -----~hIA~~IGl~~~~VEkKLsqMILDKkf~G~LDQg~g~Liv~~e~~~d~~y~~aLetI~~m 408 (411)
T KOG1463|consen 349 -----SHIAEVIGLDVPQVEKKLSQMILDKKFYGTLDQGEGCLIVFEEPPADNTYDAALETIQNM 408 (411)
T ss_pred -----HHHHHHHCCCcHHHHHHHHHHHHHHHhhcccccCCCeEEEeCCCCcchHHHHHHHHHHhc
Confidence 99999999999999999999999999999999999999987654 58899999876654
No 12
>COG5159 RPN6 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=98.52 E-value=6.5e-06 Score=83.41 Aligned_cols=267 Identities=16% Similarity=0.212 Sum_probs=170.3
Q ss_pred HHHHHHHHhcCChhhHHHHHHHHH-hcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHHHHHHHhcCC---C-CCCCh
Q psy17612 19 YKLAKFRYECGNYSITTSYLYFYL-LVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNKLREYIDGGS---A-NFESP 93 (449)
Q Consensus 19 yk~Akf~y~~GdY~~A~~~L~~~~-~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLke~id~~~---~-~~~~p 93 (449)
.|++.++|+.|.|..|...+..+. ++-.-+|+- .|-...-.|--.+ -+.+++.|.|.-+-... + ..-+|
T Consensus 129 ~Kli~l~y~~~~YsdalalIn~ll~ElKk~DDK~---~Li~vhllESKvy---h~irnv~KskaSLTaArt~Ans~YCPp 202 (421)
T COG5159 129 CKLIYLLYKTGKYSDALALINPLLHELKKYDDKI---NLITVHLLESKVY---HEIRNVSKSKASLTAARTLANSAYCPP 202 (421)
T ss_pred HHHHHHHHhcccHHHHHHHHHHHHHHHHhhcCcc---ceeehhhhhHHHH---HHHHhhhhhhhHHHHHHHHhhccCCCH
Confidence 467889999999999998887643 332222221 1111111222121 23333344333333211 1 12233
Q ss_pred HHHHHHHHHHHHHHHHHHh--cCccchhhHHHHhcCCchhhhHH-HhhhhHHHHHHHHHHHhccccccchHHHHHHHhhh
Q psy17612 94 LHLLQQRTWLIHWSLFVFF--NHVKGRDLIIDMFLNRPHYLNAI-QTMCPHILRYLATAVIINRSKRNALKDLVKVIQQE 170 (449)
Q Consensus 94 l~~l~qR~WliHwsLf~ff--n~~~g~~~~iD~F~~~~~yl~aI-qt~cp~lLRYlvvA~Il~~~r~~~l~dlv~vi~qE 170 (449)
. +|..--|+ =+++..= ++.-|..-|+|+|- +|++-- -..+-..|||+.+.-|.-. |+.-++.+++-=..
T Consensus 203 q--lqa~lDL~-sGIlhcdd~dyktA~SYF~Ea~E---gft~l~~d~kAc~sLkYmlLSkIMlN-~~~evk~vl~~K~t- 274 (421)
T COG5159 203 Q--LQAQLDLL-SGILHCDDRDYKTASSYFIEALE---GFTLLKMDVKACVSLKYMLLSKIMLN-RREEVKAVLRNKNT- 274 (421)
T ss_pred H--HHHHHHHh-ccceeeccccchhHHHHHHHHHh---ccccccchHHHHHHHHHHHHHHHHHh-hHHHHHHHHccchh-
Confidence 2 22111111 0111110 23455667888887 554421 1122248999988766532 32333333331111
Q ss_pred ccCCCchHH---HHHHHHhhcccHHHHHHHHHHHhhhcccccchHHhHHHHHHHHHHHHHHHhhhhceeeEeeccccccc
Q psy17612 171 SYTYKDPIT---EFLEHLYVSFDFESAREKLTECTEVLDNDFFLVACLDEFVENARLMIFETFCRIHQCISIQKESNVID 247 (449)
Q Consensus 171 ~~~Y~DpiT---~fv~~lYv~fdf~~aq~~L~~~~~vl~~DfFL~~~~d~fvenaR~~ife~ycriy~~IsI~~~~~~~~ 247 (449)
...|.|-+. .=+-..|.+-+..+|...|++.+..+..|.|+.+|..++-.+.=-.-+-..+.||.+|.|
T Consensus 275 ~~~y~~r~I~am~avaea~~NRsL~df~~aL~qY~~el~~D~~iRsHl~~LYD~LLe~Nl~kiiEPfs~Vei-------- 346 (421)
T COG5159 275 LKHYDDRMIRAMLAVAEAFGNRSLKDFSDALAQYSDELHQDSFIRSHLQYLYDVLLEKNLVKIIEPFSVVEI-------- 346 (421)
T ss_pred HhhhhhhhHHHHHHHHHHhCCCcHhhHHHHHHHhhHHhccCHHHHHHHHHHHHHHHHhhhhhhcCcceeeeh--------
Confidence 113554422 223456888899999999999999999999999999999888877778888999999999
Q ss_pred cccchhhHHhhcCCCHHHHHHHHHHHHHcccccceecccCCEEEeCCCC--CChHHHHHHhhhhhhh
Q psy17612 248 KIFDGQMLASKLNMGTDEAECWIVNLIRNARLDAKIDSKLGHVIMGTQP--LSPYQQLLEKIDTLSV 312 (449)
Q Consensus 248 ~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rLdaKIDs~~G~V~m~~~~--~s~Yqqviek~d~L~~ 312 (449)
..+|+-+|.+...+|.-++..|.+.-..+..|+-+|+++....| .+.|...+|....|..
T Consensus 347 -----shIa~viGldt~qvEgKLsqMILDKifyG~LDqg~gcLivy~ep~qd~tyd~ale~v~~l~~ 408 (421)
T COG5159 347 -----SHIADVIGLDTNQVEGKLSQMILDKIFYGTLDQGDGCLIVYGEPAQDNTYDEALEQVEALDC 408 (421)
T ss_pred -----hHHHHHhcccHHHHHHHHHHHHHHHHHHhhhccCCceEEEeCCccccchHHHHHHHHHHhhh
Confidence 99999999999999999999999999999999999999887665 5889988888766543
No 13
>KOG2908|consensus
Probab=98.39 E-value=0.00024 Score=73.18 Aligned_cols=254 Identities=16% Similarity=0.160 Sum_probs=160.5
Q ss_pred HHHHHhcCChhhHHHHHHHHHhcCCCcch--hhHHHHHHHHHHhHhhcChHHHHHHHHHHHHHHhcCCCCCCChHHHHHH
Q psy17612 22 AKFRYECGNYSITTSYLYFYLLVMPTSDR--HYLAVLWGKLASEILVQNWDLALEDLNKLREYIDGGSANFESPLHLLQQ 99 (449)
Q Consensus 22 Akf~y~~GdY~~A~~~L~~~~~l~~~~~~--k~ls~lwgkla~eIl~~dwd~a~~~l~kLke~id~~~~~~~~pl~~l~q 99 (449)
-.+-=+++|..+|.++|..........+. ...-+.-++-++-+..+|-..+.+-+..++..+|+-. ..+...+..-
T Consensus 82 l~~~~~~~D~~~al~~Le~i~~~~~~~~e~~av~~~~t~~~r~~L~i~DLk~~kk~ldd~~~~ld~~~-~v~~~Vh~~f- 159 (380)
T KOG2908|consen 82 LVVSEQISDKDEALEFLEKIIEKLKEYKEPDAVIYILTEIARLKLEINDLKEIKKLLDDLKSMLDSLD-GVTSNVHSSF- 159 (380)
T ss_pred HHHHHHhccHHHHHHHHHHHHHHHHhhccchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHhccc-CCChhhhhhH-
Confidence 34455788999999999998887753333 3344555666666677788888888888888888742 2211111000
Q ss_pred HHHHHHHHHHHHhcCccchhhHHHHhcCCchhhhHHHhhhhHHHHHHHHHHHhccccc---cchHH--HHHHHhhhccCC
Q psy17612 100 RTWLIHWSLFVFFNHVKGRDLIIDMFLNRPHYLNAIQTMCPHILRYLATAVIINRSKR---NALKD--LVKVIQQESYTY 174 (449)
Q Consensus 100 R~WliHwsLf~ffn~~~g~~~~iD~F~~~~~yl~aIqt~cp~lLRYlvvA~Il~~~r~---~~l~d--lv~vi~qE~~~Y 174 (449)
+|.=+-++. ....|-+. +-|+|+|+-+.-+-..++. +...+ +-..++.+-|.|
T Consensus 160 -----Y~lssqYyk---~~~d~a~y--------------Yr~~L~YL~~~d~~~l~~se~~~lA~~L~~aALLGe~iyNf 217 (380)
T KOG2908|consen 160 -----YSLSSQYYK---KIGDFASY--------------YRHALLYLGCSDIDDLSESEKQDLAFDLSLAALLGENIYNF 217 (380)
T ss_pred -----HHHHHHHHH---HHHhHHHH--------------HHHHHHHhccccccccCHHHHHHHHHHHHHHHHhccccccH
Confidence 011111111 11111111 2255666655443332221 11111 111233333333
Q ss_pred ----CchH------------HHHHHHHhhcccHHHHHHHHHHHhhhcccccchHHhHHHHHHHHHHHHHH--Hhhh--hc
Q psy17612 175 ----KDPI------------TEFLEHLYVSFDFESAREKLTECTEVLDNDFFLVACLDEFVENARLMIFE--TFCR--IH 234 (449)
Q Consensus 175 ----~Dpi------------T~fv~~lYv~fdf~~aq~~L~~~~~vl~~DfFL~~~~d~fvenaR~~ife--~ycr--iy 234 (449)
..|+ -+++ -+|..=|++.|++.-.. ...=|-|.++.+.+.+-+|++.+- +|.| ..
T Consensus 218 GELL~HPilesL~gT~~eWL~dll-~Afn~Gdl~~f~~l~~~----~~~~p~L~~~e~~L~qKI~LmaLiEi~F~rpa~~ 292 (380)
T KOG2908|consen 218 GELLAHPILESLKGTNREWLKDLL-IAFNSGDLKRFESLKGV----WGKQPDLASNEDFLLQKIRLLALIEITFSRPANE 292 (380)
T ss_pred HHHHhhHHHHHhcCCcHHHHHHHH-HHhccCCHHHHHHHHHH----hccCchHHHHHHHHHHHHHHHHHHHHHhcCcchh
Confidence 2442 3333 35666788888765444 334677899999999999998775 5668 78
Q ss_pred eeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHHHHHcccccceecccCCEEEeCCCCC--ChHHHHHHhhhhhhh
Q psy17612 235 QCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLIRNARLDAKIDSKLGHVIMGTQPL--SPYQQLLEKIDTLSV 312 (449)
Q Consensus 235 ~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rLdaKIDs~~G~V~m~~~~~--s~Yqqviek~d~L~~ 312 (449)
+.||. +-+|++..+|.++||-.+.+.+..|-+.+.||.|+|+|.|+.-.| ..-+|+..=.+.+..
T Consensus 293 R~lsf-------------~~Ia~~tkip~~eVE~LVMKAlslgLikG~Idqv~~~v~~swvqPRvl~~~qI~~Mk~rl~~ 359 (380)
T KOG2908|consen 293 RTLSF-------------KEIAEATKIPNKEVELLVMKALSLGLIKGSIDQVEGVVYMSWVQPRVLDRSQIVKMKDRLDE 359 (380)
T ss_pred ccccH-------------HHHHHHhCCCHHHHHHHHHHHHhccceeeeecccccEEEEecccccccCHHHHHhHHHHHHH
Confidence 99999 999999999999999999999999999999999999999986433 556677766665555
Q ss_pred HHHHH
Q psy17612 313 RSEAL 317 (449)
Q Consensus 313 R~q~L 317 (449)
+-+..
T Consensus 360 W~~~v 364 (380)
T KOG2908|consen 360 WNKDV 364 (380)
T ss_pred HHHHH
Confidence 54443
No 14
>smart00753 PAM PCI/PINT associated module.
Probab=98.13 E-value=3.5e-06 Score=68.98 Aligned_cols=45 Identities=29% Similarity=0.296 Sum_probs=42.4
Q ss_pred HHHhhcCCChHHHHHHHHHHhhhcccccccccCCCeEEecCCCCC
Q psy17612 358 MLASKLNMGTDEAECWIVNLIRNARLDAKIDSKLGHVIMGTQPLS 402 (449)
Q Consensus 358 ~la~kLnm~~~eaE~WIvnLIr~~~ldAKIDs~~~~v~m~~~~~s 402 (449)
.||+.++++.+++|.||+++|+++.++||||..+|+|.++..++.
T Consensus 29 ~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~~~r 73 (88)
T smart00753 29 DLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEVDPR 73 (88)
T ss_pred HHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCCchh
Confidence 669999999999999999999999999999999999999988763
No 15
>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15. Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.
Probab=98.13 E-value=3.5e-06 Score=68.98 Aligned_cols=45 Identities=29% Similarity=0.296 Sum_probs=42.4
Q ss_pred HHHhhcCCChHHHHHHHHHHhhhcccccccccCCCeEEecCCCCC
Q psy17612 358 MLASKLNMGTDEAECWIVNLIRNARLDAKIDSKLGHVIMGTQPLS 402 (449)
Q Consensus 358 ~la~kLnm~~~eaE~WIvnLIr~~~ldAKIDs~~~~v~m~~~~~s 402 (449)
.||+.++++.+++|.||+++|+++.++||||..+|+|.++..++.
T Consensus 29 ~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~~~r 73 (88)
T smart00088 29 DLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEVDPR 73 (88)
T ss_pred HHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCCchh
Confidence 669999999999999999999999999999999999999988763
No 16
>KOG1498|consensus
Probab=97.77 E-value=0.0022 Score=67.34 Aligned_cols=275 Identities=19% Similarity=0.186 Sum_probs=156.0
Q ss_pred HHHHHHHHhcCChhhHHHHHHHHHhcCCCc--chhhHHHHHHHHHHhHhhcChHHHHHHHHHHHHHHhcCCCCCCChHHH
Q psy17612 19 YKLAKFRYECGNYSITTSYLYFYLLVMPTS--DRHYLAVLWGKLASEILVQNWDLALEDLNKLREYIDGGSANFESPLHL 96 (449)
Q Consensus 19 yk~Akf~y~~GdY~~A~~~L~~~~~l~~~~--~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLke~id~~~~~~~~pl~~ 96 (449)
-.+++.+=++||-..|++.+-++..-+-++ -.-+....++-+++-++-.||-.|.=-.+|+.--+-...+ ...
T Consensus 135 k~L~~ike~~Gdi~~Aa~il~el~VETygsm~~~ekV~fiLEQmrKOG~~~D~vra~i~skKI~~K~F~~~~-----~~~ 209 (439)
T KOG1498|consen 135 KMLAKIKEEQGDIAEAADILCELQVETYGSMEKSEKVAFILEQMRLCLLRLDYVRAQIISKKINKKFFEKPD-----VQE 209 (439)
T ss_pred HHHHHHHHHcCCHHHHHHHHHhcchhhhhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhHHhcCCcc-----HHH
Confidence 357899999999999999998776655332 2235889999999999999998887766776553333111 111
Q ss_pred HHHHHHHHHHHHHHHhc-CccchhhHHHHhcCCchhh-hHHHhh---hhHHHHHHHHHHHhccccccchHHHHHHHhhhc
Q psy17612 97 LQQRTWLIHWSLFVFFN-HVKGRDLIIDMFLNRPHYL-NAIQTM---CPHILRYLATAVIINRSKRNALKDLVKVIQQES 171 (449)
Q Consensus 97 l~qR~WliHwsLf~ffn-~~~g~~~~iD~F~~~~~yl-~aIqt~---cp~lLRYlvvA~Il~~~r~~~l~dlv~vi~qE~ 171 (449)
+. |.++-|.+=.. |..+.-.....+.. -|. -.+++. -...|+=.|..++++- -.+.-.|++.-++...
T Consensus 210 lK----lkyY~lmI~l~lh~~~Yl~v~~~Yra--iy~t~~vk~d~~kw~~vL~~iv~f~~LAp-~dneQsdll~~is~dK 282 (439)
T KOG1498|consen 210 LK----LKYYELMIRLGLHDRAYLNVCRSYRA--IYDTGNVKEDPEKWIEVLRSIVSFCVLAP-HDNEQSDLLARISNDK 282 (439)
T ss_pred HH----HHHHHHHHHhcccccchhhHHHHHHH--HhcccccccChhhhhhhhhhheeEEeecC-CCcHHHHHHHHHhccc
Confidence 11 12222222111 22222222222220 010 011110 0122333333333321 1122355666565333
Q ss_pred cCCC-chHHHHHHHHhhcccHHHHHHHHHHHhhhcc-cccch-HHhHHHHHHHHHHHHHHHhh----hhceeeEeecccc
Q psy17612 172 YTYK-DPITEFLEHLYVSFDFESAREKLTECTEVLD-NDFFL-VACLDEFVENARLMIFETFC----RIHQCISIQKESN 244 (449)
Q Consensus 172 ~~Y~-DpiT~fv~~lYv~fdf~~aq~~L~~~~~vl~-~DfFL-~~~~d~fvenaR~~ife~yc----riy~~IsI~~~~~ 244 (449)
..+ .|-+.=+--+|++-.--..-..-+.-..++. +|||- ..+-+--.+.++..|+|-=+ +-|+||+.
T Consensus 283 -kL~e~p~~k~lLklfv~~EL~rw~s~~~~yg~~l~~~~~~~~~~~gek~~~dL~~RIiEHNiRiiA~yYSrIt~----- 356 (439)
T KOG1498|consen 283 -KLSELPDYKELLKLFVTMELIRWVSLVESYGDELRTNDFFDGGEEGEKRWSDLKLRIIEHNIRIIAKYYSRITL----- 356 (439)
T ss_pred -ccccCccHHHHHHHHHhcceeeehhHhhhhHHHHhhcccccccchhhhHHHHHHHHHHHHHHHHHHHHHhhccH-----
Confidence 333 5633222233333221111111111122232 35554 34455566666666666544 45999999
Q ss_pred ccccccchhhHHhhcCCCHHHHHHHHHHHHHcccccceecccCCEEEeCCCCCCh-----HHHHHHhhhhhhhHHHHHHH
Q psy17612 245 VIDKIFDGQMLASKLNMGTDEAECWIVNLIRNARLDAKIDSKLGHVIMGTQPLSP-----YQQLLEKIDTLSVRSEALQA 319 (449)
Q Consensus 245 ~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rLdaKIDs~~G~V~m~~~~~s~-----Yqqviek~d~L~~R~q~L~~ 319 (449)
..||+.|++++++.|..|++++.+|-+-||||..+|+|.-..+..+. .-+-+++.=.+++|+..|-.
T Consensus 357 --------~rl~eLLdl~~ee~E~~LS~lv~t~ti~aKidrpsgII~F~k~K~~~~~LneW~~nve~L~~ll~K~~HLI~ 428 (439)
T KOG1498|consen 357 --------KRLAELLDLPVEEMEKFLSDLVVTGTIYAKIDRPSGIINFQKVKDSNEILNEWASNVEKLLGLLEKVSHLIH 428 (439)
T ss_pred --------HHHHHHhCCCHHHHHHHHHHHHhccceEEEecCCCceEEEEecccHHHHHHHHHhhHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999998887544 34556665566666555543
No 17
>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.
Probab=97.76 E-value=3.1e-05 Score=63.90 Aligned_cols=40 Identities=33% Similarity=0.527 Sum_probs=37.7
Q ss_pred HHHhhcCCChHHHHHHHHHHhhhcccccccccCCCeEEec
Q psy17612 358 MLASKLNMGTDEAECWIVNLIRNARLDAKIDSKLGHVIMG 397 (449)
Q Consensus 358 ~la~kLnm~~~eaE~WIvnLIr~~~ldAKIDs~~~~v~m~ 397 (449)
.+|+.|+++.+++|.|++++|+++++.||||..+|+|+++
T Consensus 65 ~ia~~l~~~~~~vE~~l~~~I~~~~i~~~ID~~~~~v~~~ 104 (105)
T PF01399_consen 65 EIAKALQLSEEEVESILIDLISNGLIKAKIDQVNGVVVFS 104 (105)
T ss_dssp HHHHHHTCCHHHHHHHHHHHHHTTSSEEEEETTTTEEEE-
T ss_pred HHHHHhccchHHHHHHHHHHHHCCCEEEEEECCCCEEEec
Confidence 5599999999999999999999999999999999999986
No 18
>KOG1497|consensus
Probab=97.59 E-value=0.0093 Score=61.59 Aligned_cols=70 Identities=19% Similarity=0.254 Sum_probs=61.8
Q ss_pred hhHHhhcCCCHHHHHHHHHHHHHcccccceecccCCEEEeCCCCCChHHHHHHhhhhhhhHHHHHHHHHHHH
Q psy17612 253 QMLASKLNMGTDEAECWIVNLIRNARLDAKIDSKLGHVIMGTQPLSPYQQLLEKIDTLSVRSEALQALIERK 324 (449)
Q Consensus 253 ~~LA~~Lnms~~e~E~wIVnlIr~~rLdaKIDs~~G~V~m~~~~~s~Yqqviek~d~L~~R~q~L~~~i~~~ 324 (449)
+-|+.-|+++++.+|+.-++.|..+|++|-||+.+|+|.--. ..+|+|-=++...|.+-+++++-.|...
T Consensus 321 ~~Lg~ll~i~~ekaekiaa~MI~qeRmng~IDQ~egiihFe~--~e~l~~wdkqi~sl~~qvNki~~~i~~~ 390 (399)
T KOG1497|consen 321 EELGALLKIDAEKAEKIAAQMITQERMNGSIDQIEGIIHFED--REELPQWDKQIQSLCNQVNKILDKISHY 390 (399)
T ss_pred HHHHHHhCCCHHHHHHHHHHHHhHHHhccchHhhcceEeecc--hhhhhhhhHHHHHHHHHHHHHHHHHHHh
Confidence 889999999999999999999999999999999999998644 6778777777888999999888777554
No 19
>KOG2753|consensus
Probab=97.45 E-value=0.013 Score=60.71 Aligned_cols=92 Identities=25% Similarity=0.381 Sum_probs=78.4
Q ss_pred cccchHHh---HHHHHHHHHHHHHHHhhhhceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHHHHHccccccee
Q psy17612 207 NDFFLVAC---LDEFVENARLMIFETFCRIHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLIRNARLDAKI 283 (449)
Q Consensus 207 ~DfFL~~~---~d~fvenaR~~ife~ycriy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rLdaKI 283 (449)
|--|+..| -+..++-+|++-|-....+-..|+. +.|++.|.+.++|+|-|++..|+.+-+.|||
T Consensus 262 N~~Fvqs~gl~~E~~~~KMRLLTlm~LA~es~eisy-------------~~l~k~LqI~edeVE~fVIdaI~aklV~~ki 328 (378)
T KOG2753|consen 262 NSGFVQSQGLVHEQNMAKMRLLTLMSLAEESNEISY-------------DTLAKELQINEDEVELFVIDAIRAKLVEGKI 328 (378)
T ss_pred ChHHHHHhcccHHHHHHHHHHHHHHHHhccCCCCCH-------------HHHHHHhccCHHHHHHHHHHHHHHHHHHhhH
Confidence 44455444 3578899999999999999999999 9999999999999999999999999999999
Q ss_pred cccCCEEEeCCCC-----CChHHHHHHhhhhhh
Q psy17612 284 DSKLGHVIMGTQP-----LSPYQQLLEKIDTLS 311 (449)
Q Consensus 284 Ds~~G~V~m~~~~-----~s~Yqqviek~d~L~ 311 (449)
|+.+.+|+..+.. ..+.||+-++...+.
T Consensus 329 dq~~~~viVs~~~hR~FG~~qW~~L~~kL~aw~ 361 (378)
T KOG2753|consen 329 DQMNRTVIVSSSTHRTFGKQQWQQLRDKLAAWG 361 (378)
T ss_pred HhhcceEEeehhhhhhcccHHHHHHHHHHHHHH
Confidence 9999999887652 467888887766664
No 20
>COG5071 RPN5 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=97.36 E-value=0.038 Score=56.98 Aligned_cols=273 Identities=14% Similarity=0.117 Sum_probs=154.2
Q ss_pred HHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCC--cchhhHHHHHHHHHHhHhhcChHHHHHHHHHHHHHHhcCCCC
Q psy17612 12 MDMMESMYKLAKFRYECGNYSITTSYLYFYLLVMPT--SDRHYLAVLWGKLASEILVQNWDLALEDLNKLREYIDGGSAN 89 (449)
Q Consensus 12 ~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~--~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLke~id~~~~~ 89 (449)
.|-...--.+.+.+=+|||-..|.+.|-....-+-+ .-.-+..-.++.+++-++-.||-.|.-..+|++.-+-...+.
T Consensus 128 vERariT~~L~~ikee~Gdi~sA~Dilcn~pVETygs~~~Sekv~fiLEQ~rL~vl~~Dy~~A~~~~kKI~KK~Fe~~d~ 207 (439)
T COG5071 128 VERARLTQLLSQIKEEQGDIKSAQDILCNEPVETYGSFDLSEKVAFILEQVRLFLLRSDYYMASTYTKKINKKFFEKEDV 207 (439)
T ss_pred hhHHHHHHHHHHHHHHhcchhHHHHHHhcCchhhccchhHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHhccccH
Confidence 333444456778889999999999988654443321 122347889999999999999999988888876654442222
Q ss_pred CCChHHHHHHHHHHHHHHHHHHhcCccchhhHHHHhcCCchhhhHHH-------hhhh---HHHHHHHHH-----HHhcc
Q psy17612 90 FESPLHLLQQRTWLIHWSLFVFFNHVKGRDLIIDMFLNRPHYLNAIQ-------TMCP---HILRYLATA-----VIINR 154 (449)
Q Consensus 90 ~~~pl~~l~qR~WliHwsLf~ffn~~~g~~~~iD~F~~~~~yl~aIq-------t~cp---~lLRYlvvA-----~Il~~ 154 (449)
..-.++.|. +.+-.-+++..|+++-| |... .-=-|-|+. ++++
T Consensus 208 ~slKlkyYe---------------------L~V~i~Lh~R~Yl~v~~y~~~vY~t~~~~~d~Akwk~VLS~~v~F~iLt- 265 (439)
T COG5071 208 QSLKLKYYE---------------------LKVRIGLHDRAYLDVCKYYRAVYDTAVVQEDPAKWKEVLSNVVCFALLT- 265 (439)
T ss_pred HHHHHHHHH---------------------HhheeecccHHHHHHHHHHHHHHHHHHhccCcccccchhhcceeeEEec-
Confidence 222222222 11111112222322211 0000 000022222 1121
Q ss_pred ccccchHHHHHHHhhhccCCC-chHHHHHHHHhhcccHHHHHHHHHHHhhhcccccc-hH-----HhHHHHHHHHHHHHH
Q psy17612 155 SKRNALKDLVKVIQQESYTYK-DPITEFLEHLYVSFDFESAREKLTECTEVLDNDFF-LV-----ACLDEFVENARLMIF 227 (449)
Q Consensus 155 ~r~~~l~dlv~vi~qE~~~Y~-DpiT~fv~~lYv~fdf~~aq~~L~~~~~vl~~DfF-L~-----~~~d~fvenaR~~if 227 (449)
+=-+...|++--|+...+--+ |...+++.| |+...|=.--..=+....++..|.| +. .|.+++....=-.-|
T Consensus 266 py~neq~dlvhKi~~d~kl~sl~~~~~lVk~-f~vNelmrwp~V~~~y~~~l~~~~faF~~e~~~~~w~DL~krviEHN~ 344 (439)
T COG5071 266 PYDNEQADLLHKINADHKLNSLPLLQQLVKC-FIVNELMRWPKVAEIYGSALRSNVFAFNDEKGEKRWSDLRKRVIEHNI 344 (439)
T ss_pred ccccHHHHHHHHhhhhhhhccchhhhhHHHH-HHHHHHHhhhHHHHHhHHHHHhhhhhhccchhhhhHHHHHHHHHHhhH
Confidence 112334556665555544334 334556644 3323222211112223445555533 32 345555444333334
Q ss_pred HHhhhhceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHHHHHcccccceecccCCEEEeCCCCCChHHHHHHhh
Q psy17612 228 ETFCRIHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLIRNARLDAKIDSKLGHVIMGTQPLSPYQQLLEKI 307 (449)
Q Consensus 228 e~ycriy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rLdaKIDs~~G~V~m~~~~~s~Yqqviek~ 307 (449)
...-+-|++|++ ..|+.-+.+|+++.|..|+.++-+|-.-|||....|+|.-..|.++. |++-|=+
T Consensus 345 RvI~~yYSrI~~-------------~rl~~lld~~~s~te~~ISdlVN~G~~yaKiNrpa~Ii~FEK~~n~~-~~lneW~ 410 (439)
T COG5071 345 RVIANYYSRIHC-------------SRLGVLLDMSPSETEQFISDLVNKGHFYAKINRPAQIISFEKSQNVQ-EQLNEWG 410 (439)
T ss_pred hHHHHHhhhhhH-------------HHHHHHHcCCHHHHHHHHHHHHhcCcEEEEecCccceEEeeccccHH-HHHHHhc
Confidence 445566999999 99999999999999999999999999999999999999988877654 4554444
Q ss_pred h---hhhhHHHHHHHHH
Q psy17612 308 D---TLSVRSEALQALI 321 (449)
Q Consensus 308 d---~L~~R~q~L~~~i 321 (449)
+ .|+-.+.+....|
T Consensus 411 ~NV~ellgklek~~HLI 427 (439)
T COG5071 411 SNVTELLGKLEKVRHLI 427 (439)
T ss_pred ccHHHHHHHHHHHhHHH
Confidence 3 3444444444443
No 21
>PF10075 PCI_Csn8: COP9 signalosome, subunit CSN8; InterPro: IPR019280 The photomorphogenic 9 (COP9) signalosome or CSN complex is composed of eight subunits: Cops1/GPS1, Cops2, Cops3, Cops4, Cops5, Cop6, Cops7 (Cops7A or Cops7B) and Cops8. In the complex, Cops8, which is the smallest subunit, probably interacts directly with Cops3, Cops4 and Cops7 (Cops7A or Cops7B). This signalosome is homologous to the lid subcomplex of the 26S proteasome and regulates the ubiquitin-proteasome pathway. It functions as a structural scaffold for subunit-subunit interactions within the complex and is a key regulator of photomorphogenic development [].; PDB: 1RZ4_A.
Probab=96.84 E-value=0.0043 Score=55.71 Aligned_cols=103 Identities=19% Similarity=0.163 Sum_probs=68.1
Q ss_pred hccccccchHHHHHHHhhhccCCCch----HHHHHHHHhhcccHHHHHHHHHHHhhhcccccchHHhHHHHHHHHHHHHH
Q psy17612 152 INRSKRNALKDLVKVIQQESYTYKDP----ITEFLEHLYVSFDFESAREKLTECTEVLDNDFFLVACLDEFVENARLMIF 227 (449)
Q Consensus 152 l~~~r~~~l~dlv~vi~qE~~~Y~Dp----iT~fv~~lYv~fdf~~aq~~L~~~~~vl~~DfFL~~~~d~fvenaR~~if 227 (449)
|...+...++-+.+.|.++... .|| +..+... ..+.||.++-..++... -...+.+.+..|.+++|..++
T Consensus 15 L~~~~~~df~~~~~rip~~~~~-~~~~i~~i~~l~~~-L~~~~~~~~~~~~~~~~----~~~~~~~~v~~~~~~iR~~i~ 88 (143)
T PF10075_consen 15 LMQNDLSDFRLLWKRIPEELKQ-SDPEIKAIWSLGQA-LWEGDYSKFWQALRSNP----WSPDYKPFVPGFEDTIRERIA 88 (143)
T ss_dssp HHTTTSTHHHHHHHTS-HHHHT-S-TTHHHHHHHHHH-HHTT-HHHHHHHS-TT--------HHHHTSTTHHHHHHHHHH
T ss_pred HHcCCchHHHHHHHcCCHHHHh-hhHHHHHHHHHHHH-HHCCCHHHHHHHHHhcc----chHHHHHHHHHHHHHHHHHHH
Confidence 3344444455555555555432 244 4455533 44578888886555431 124677788899999999999
Q ss_pred HHhhhhceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHHH
Q psy17612 228 ETFCRIHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNL 273 (449)
Q Consensus 228 e~ycriy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnl 273 (449)
...-+.|++|++ +.+|+-||++.+++++++.+.
T Consensus 89 ~~i~~aY~sIs~-------------~~la~~Lg~~~~el~~~~~~~ 121 (143)
T PF10075_consen 89 HLISKAYSSISL-------------SDLAEMLGLSEEELEKFIKSR 121 (143)
T ss_dssp HHHHHH-SEE-H-------------HHHHHHTTS-HHHHHHHHHHH
T ss_pred HHHHHHHhHcCH-------------HHHHHHhCCCHHHHHHHHHHc
Confidence 999999999999 999999999999999999875
No 22
>KOG2581|consensus
Probab=96.58 E-value=0.0099 Score=62.96 Aligned_cols=89 Identities=26% Similarity=0.299 Sum_probs=70.2
Q ss_pred hcccHHHHHHHHHHHhhhcccccchHHhHHHHHHHHHHHHHHHhhh----hceeeEeeccccccccccchhhHHhhcCCC
Q psy17612 187 VSFDFESAREKLTECTEVLDNDFFLVACLDEFVENARLMIFETFCR----IHQCISIQKESNVIDKIFDGQMLASKLNMG 262 (449)
Q Consensus 187 v~fdf~~aq~~L~~~~~vl~~DfFL~~~~d~fvenaR~~ife~ycr----iy~~IsI~~~~~~~~~~~~~~~LA~~Lnms 262 (449)
..-|.+.|.+.|....+.++.| +.=.++-..|.-+..|=+| .|++|++ ..+|.+||++
T Consensus 329 r~gdlkkF~~~leq~k~~f~~D-----~ty~LivRLR~NVIkTgIR~ISlsYSRISl-------------~DIA~kL~l~ 390 (493)
T KOG2581|consen 329 RLGDLKKFNETLEQFKDKFQAD-----GTYTLIVRLRHNVIKTGIRKISLSYSRISL-------------QDIAKKLGLN 390 (493)
T ss_pred HHhhHHHHHHHHHHHHHHHhhC-----CcchHHHHHHHHHHHHhhhheeeeeeeccH-------------HHHHHHhcCC
Confidence 4467777777777766555444 4444555677777777666 5999999 9999999998
Q ss_pred HHH-HHHHHHHHHHcccccceecccCCEEEeC
Q psy17612 263 TDE-AECWIVNLIRNARLDAKIDSKLGHVIMG 293 (449)
Q Consensus 263 ~~e-~E~wIVnlIr~~rLdaKIDs~~G~V~m~ 293 (449)
.++ +|-..++.||+|-++||||...|.++..
T Consensus 391 Seed~EyiVakAIRDGvIea~Id~~~g~m~sk 422 (493)
T KOG2581|consen 391 SEEDAEYIVAKAIRDGVIEAKIDHEDGFMQSK 422 (493)
T ss_pred CchhHHHHHHHHHHhccceeeeccccCceehh
Confidence 776 9999999999999999999999988765
No 23
>KOG2072|consensus
Probab=96.26 E-value=0.59 Score=53.46 Aligned_cols=260 Identities=17% Similarity=0.202 Sum_probs=162.6
Q ss_pred HHHHHHHHHHhcCChhhHHHHHHHHHhcC-------C-------CcchhhHHHHHHHHHHhHhhcChHHHHHHHHHHHHH
Q psy17612 17 SMYKLAKFRYECGNYSITTSYLYFYLLVM-------P-------TSDRHYLAVLWGKLASEILVQNWDLALEDLNKLREY 82 (449)
Q Consensus 17 ~lyk~Akf~y~~GdY~~A~~~L~~~~~l~-------~-------~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLke~ 82 (449)
.-+++|.=|-+.-+|-..-+.|..-+.-. . .+-+.+++.=+-.|-..|.|.=|..|-+-++-+.-+
T Consensus 182 ~aFqFCLkYqRktEFRrLCe~LR~HL~~i~k~~nq~~~v~Ln~~Etlql~LDtRf~QLdvAi~lELWQEAyrSiEDIhgL 261 (988)
T KOG2072|consen 182 KAFQFCLKYQRKTEFRRLCELLRMHLDNINKHQNQSTRVDLNDPETLQLYLDTRFQQLDVAIELELWQEAYRSIEDIHGL 261 (988)
T ss_pred HHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhhccCcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33455555555555655555554322211 1 112446777788889999999999998776666666
Q ss_pred HhcCCCCC-CChHH----------------HHHHHHHHHHHHHHHHhcCccchhhHHHHhcCCchhhhHHHhh-------
Q psy17612 83 IDGGSANF-ESPLH----------------LLQQRTWLIHWSLFVFFNHVKGRDLIIDMFLNRPHYLNAIQTM------- 138 (449)
Q Consensus 83 id~~~~~~-~~pl~----------------~l~qR~WliHwsLf~ffn~~~g~~~~iD~F~~~~~yl~aIqt~------- 138 (449)
+.-...+. +.-++ .++.=+|+-.+.|+-=+|-+-..+.|..+-. .-+|+|+.+-
T Consensus 262 m~lSKrtPkp~~laNYY~KL~~VF~~sgn~LfHAaAw~k~f~l~k~~~K~~Tqde~q~~as--~VlLaaLSIP~~~~~~~ 339 (988)
T KOG2072|consen 262 MKLSKRTPKPSTLANYYEKLAKVFWKSGNPLFHAAAWLKLFKLYKNMNKNLTQDELQRMAS--RVLLAALSIPIPDARSD 339 (988)
T ss_pred HHHhcCCCchhHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHhcccccHHHHHHHHH--HHHHHHhcCCCCCcccc
Confidence 55321222 22222 2344466643333322332222233322211 1233332211
Q ss_pred ------hh--HHHHHHHHHHHhccc----cccchHHHHHHHhhhccCCCch-HHHHHHHHhhcccHHHHHHHHHHHhhhc
Q psy17612 139 ------CP--HILRYLATAVIINRS----KRNALKDLVKVIQQESYTYKDP-ITEFLEHLYVSFDFESAREKLTECTEVL 205 (449)
Q Consensus 139 ------cp--~lLRYlvvA~Il~~~----r~~~l~dlv~vi~qE~~~Y~Dp-iT~fv~~lYv~fdf~~aq~~L~~~~~vl 205 (449)
.+ +.=+=+-+|++|+.+ |..+++++|+ -.-+.+-|+ +.+||.-|=++|+--..-+.|..+-.-+
T Consensus 340 ~~r~~e~e~~~~ek~~rla~LL~L~~~PTR~~ll~e~v~---~gV~~~v~qe~kdLY~iLEveF~PL~l~k~lq~ll~~l 416 (988)
T KOG2072|consen 340 SARLIEIEDIGKEKNLRLANLLGLPAPPTRKGLLKEAVR---EGVLSKVDQEVKDLYNILEVEFHPLKLCKKLQPLLDKL 416 (988)
T ss_pred cccccccccchhhHHHHHHHHhCCCCCccHHHHHHHHHH---hccHhhhhHHHHHHHHHHHhcCCHHHHHHHHHHHHHHH
Confidence 01 233445566777653 4556677776 222234455 8899999999998776666666666666
Q ss_pred ccccchHHhHHHHHHHHHHHHHHHhhhhceeeEeeccccccccccchhhHHhhcC-CCHHHHHHHHHHHHHcccccceec
Q psy17612 206 DNDFFLVACLDEFVENARLMIFETFCRIHQCISIQKESNVIDKIFDGQMLASKLN-MGTDEAECWIVNLIRNARLDAKID 284 (449)
Q Consensus 206 ~~DfFL~~~~d~fvenaR~~ife~ycriy~~IsI~~~~~~~~~~~~~~~LA~~Ln-ms~~e~E~wIVnlIr~~rLdaKID 284 (449)
.+-+.-++|+..+-..+=+.+|.|.-.||++|++ +.|.+--- ++.-++|+.||+..+++-+..+||
T Consensus 417 s~~~~~~QYI~sLq~v~~~RllqQvSqiY~sIs~-------------~~l~~La~F~~~~~lEk~~v~a~k~~~v~iriD 483 (988)
T KOG2072|consen 417 SESPDKSQYIPSLQDVIILRLLQQVSQIYESISF-------------ERLYKLAPFFSAFELEKLLVEAAKHNDVSIRID 483 (988)
T ss_pred HcCCCccccchhHHHHHHHHHHHHHHHHHHHHhH-------------HHHHHHHhhcCHHHHHHHHHHHHhccceeEEec
Confidence 6656668888888889999999999999999999 65443111 677899999999999999999999
Q ss_pred ccCCEEEeCC
Q psy17612 285 SKLGHVIMGT 294 (449)
Q Consensus 285 s~~G~V~m~~ 294 (449)
-..|+|.-|+
T Consensus 484 H~~~~v~Fgs 493 (988)
T KOG2072|consen 484 HESNSVSFGS 493 (988)
T ss_pred cccceeeecc
Confidence 9999998884
No 24
>KOG1076|consensus
Probab=96.11 E-value=0.026 Score=63.02 Aligned_cols=153 Identities=18% Similarity=0.229 Sum_probs=98.7
Q ss_pred hHHHHHHHhhhccCCC-ch--HHHHHHHH---hhcccHHHHHHHHHHHhhh----cccccchHHhHHHHHH-HHHHHHHH
Q psy17612 160 LKDLVKVIQQESYTYK-DP--ITEFLEHL---YVSFDFESAREKLTECTEV----LDNDFFLVACLDEFVE-NARLMIFE 228 (449)
Q Consensus 160 l~dlv~vi~qE~~~Y~-Dp--iT~fv~~l---Yv~fdf~~aq~~L~~~~~v----l~~DfFL~~~~d~fve-naR~~ife 228 (449)
|.-.++.....+ +. .| +.+.|-++ -.+-||..+++-+...-++ -..|.-+....+.+-| ..|+. +-
T Consensus 634 frr~Le~serqs--f~gPPEn~RehVvaAsKAm~~Gnw~~c~~fi~nn~KvW~Lfpn~d~V~~Ml~~rIqEEsLRTY-Lf 710 (843)
T KOG1076|consen 634 FRRQLEHSERQS--FTGPPENTREHVVAASKAMQKGNWQKCFEFIVNNIKVWDLFPNADTVLDMLTERIQEESLRTY-LF 710 (843)
T ss_pred HHHHHHHHhhcc--ccCCchhHHHHHHHHHHHHhcCCHHHHHHHHHhhhhHHHhcccHHHHHHHHHHHHHHHHHHHH-HH
Confidence 444555444333 44 44 44555332 3445666666544442222 1235555555555544 44554 45
Q ss_pred HhhhhceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHHHHHcccccceecccCCEEEeCCCCCChHHHHHHhhh
Q psy17612 229 TFCRIHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLIRNARLDAKIDSKLGHVIMGTQPLSPYQQLLEKID 308 (449)
Q Consensus 229 ~ycriy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rLdaKIDs~~G~V~m~~~~~s~Yqqviek~d 308 (449)
+|-..|.+||+ +.||+-|.+|+..|-..|+..|.+--|.|+.|..+++|+|.+..++--|.+.=+
T Consensus 711 tYss~Y~SvSl-------------~~LA~mFdLp~~~VhsIiSkmiineEl~AslDqpt~~iv~hrvE~srlq~La~q-- 775 (843)
T KOG1076|consen 711 TYSSVYDSVSL-------------AKLADMFDLPEPKVHSIISKMIINEELHASLDQPTQCIVMHRVEPSRLQSLAVQ-- 775 (843)
T ss_pred HhhhhhhhccH-------------HHHHHHhCCCchhHHHHHHHHHHHHHhhhccCCCcceEEEeeccchHHHHHHHH--
Confidence 89999999999 999999999999999999999999999999999999999999766554443322
Q ss_pred hhhhHHHHHHHHHHHHHhhhcCC
Q psy17612 309 TLSVRSEALQALIERKVKVRNNS 331 (449)
Q Consensus 309 ~L~~R~q~L~~~i~~~~~~~~~~ 331 (449)
|..+...|+.+-++....+.++
T Consensus 776 -L~eKl~~L~E~NE~~~e~ktg~ 797 (843)
T KOG1076|consen 776 -LSEKLAILAENNEKVFESKTGG 797 (843)
T ss_pred -HHHHHHHHHHhccchhccccCC
Confidence 3334444555555555555543
No 25
>KOG2688|consensus
Probab=94.96 E-value=0.11 Score=54.89 Aligned_cols=141 Identities=20% Similarity=0.339 Sum_probs=86.5
Q ss_pred hhhHHHhhhh--------HHHHHHHHHHHhccccccchHHHHHHHhhhc-cCCCchHHHHHHHHhhcccHHHHHHHHHHH
Q psy17612 131 YLNAIQTMCP--------HILRYLATAVIINRSKRNALKDLVKVIQQES-YTYKDPITEFLEHLYVSFDFESAREKLTEC 201 (449)
Q Consensus 131 yl~aIqt~cp--------~lLRYlvvA~Il~~~r~~~l~dlv~vi~qE~-~~Y~DpiT~fv~~lYv~fdf~~aq~~L~~~ 201 (449)
+++.--..|| -++-|++...++.++ -|-+.++. +++ -.|.+-+...-. =+...+...|+..
T Consensus 227 ~L~~af~~cp~~~~~n~~~iliylip~~~llg~--~Pt~~lL~---~~~~~~~~~lv~aVr~-----Gnl~~f~~al~~~ 296 (394)
T KOG2688|consen 227 QLNEAFRLCPDLLLKNKRLILIYLIPTGLLLGR--IPTKELLD---FYTLDKYSPLVQAVRS-----GNLRLFDLALADN 296 (394)
T ss_pred HHHHHHHhCcHHHHhhhhhHHHHHhHHHHHhcc--CcchhhHh---HhhHHhHHHHHHHHHh-----ccHHHHHHHHhhh
Confidence 4444445666 288899999998765 22332322 221 112222233333 4444445788887
Q ss_pred hhhcccccchHHhHHHHHHHHHHHHHHHhh----hhc---eeeEeeccccccccccchhhHHhhcC------CCHHHHHH
Q psy17612 202 TEVLDNDFFLVACLDEFVENARLMIFETFC----RIH---QCISIQKESNVIDKIFDGQMLASKLN------MGTDEAEC 268 (449)
Q Consensus 202 ~~vl~~DfFL~~~~d~fvenaR~~ife~yc----riy---~~IsI~~~~~~~~~~~~~~~LA~~Ln------ms~~e~E~ 268 (449)
| .+|+..=+=--++..|...|.... +++ +++++ +.+-..+- ++.+|+|+
T Consensus 297 E-----~~f~~~gi~l~l~~l~lv~yrnL~kkv~~~~~~~~~lpl-------------s~~~~al~~~~~~~~~~devec 358 (394)
T KOG2688|consen 297 E-----RFFIRSGIYLTLEKLPLVVYRNLFKKVIQLWGKTSQLPL-------------SRFLTALQFSGVTDVDLDEVEC 358 (394)
T ss_pred H-----HHHHHhccHHHhhhhhHHHHHHHHHHHHHHhCCCCCCCH-------------HHHHHHHhhcCCCCCchhhHHH
Confidence 7 344433333334445655554432 344 45555 66665554 44699999
Q ss_pred HHHHHHHcccccceecccCCEEEeCCCCCCh
Q psy17612 269 WIVNLIRNARLDAKIDSKLGHVIMGTQPLSP 299 (449)
Q Consensus 269 wIVnlIr~~rLdaKIDs~~G~V~m~~~~~s~ 299 (449)
-||++|..|+|+|-|+.....++....++-|
T Consensus 359 iLa~lI~~G~ikgYish~~~~~V~sK~~pfp 389 (394)
T KOG2688|consen 359 ILANLIDLGRIKGYISHQLQTLVFSKKDPFP 389 (394)
T ss_pred HHHhhhhhccccchhchhhheEEEecCCCCC
Confidence 9999999999999999999999998877544
No 26
>PF13424 TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 4A1S_B 3CEQ_B 3EDT_H ....
Probab=94.09 E-value=0.29 Score=38.36 Aligned_cols=73 Identities=18% Similarity=0.128 Sum_probs=50.9
Q ss_pred HHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCC--C-cchhhHHHHHHHHHHhHhhcChHHHHHHHHHHHHHHh
Q psy17612 12 MDMMESMYKLAKFRYECGNYSITTSYLYFYLLVMP--T-SDRHYLAVLWGKLASEILVQNWDLALEDLNKLREYID 84 (449)
Q Consensus 12 ~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~--~-~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLke~id 84 (449)
|++...+..+|..|++.|+|+.|.+++........ + +......++.+.=.+--..++.+.|++-+++.-++.+
T Consensus 2 ~~~a~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al~i~~ 77 (78)
T PF13424_consen 2 PDTANAYNNLARVYRELGRYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYRLGDYEEALEYYQKALDIFE 77 (78)
T ss_dssp HHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhhc
Confidence 67888999999999999999999999998877742 2 2222233333333344445688888888887766554
No 27
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=93.90 E-value=0.066 Score=42.66 Aligned_cols=45 Identities=18% Similarity=0.294 Sum_probs=38.1
Q ss_pred HHHHHhhhhceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHHHHHcccccce
Q psy17612 225 MIFETFCRIHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLIRNARLDAK 282 (449)
Q Consensus 225 ~ife~ycriy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rLdaK 282 (449)
....+|++-+.++|+ ..||..||+|++.+|..|-.+|+-|++..-
T Consensus 3 ~~i~~~l~~~~~~S~-------------~eLa~~~~~s~~~ve~mL~~l~~kG~I~~~ 47 (69)
T PF09012_consen 3 QEIRDYLRERGRVSL-------------AELAREFGISPEAVEAMLEQLIRKGYIRKV 47 (69)
T ss_dssp HHHHHHHHHS-SEEH-------------HHHHHHTT--HHHHHHHHHHHHCCTSCEEE
T ss_pred HHHHHHHHHcCCcCH-------------HHHHHHHCcCHHHHHHHHHHHHHCCcEEEe
Confidence 346789999999999 999999999999999999999999999843
No 28
>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A.
Probab=93.18 E-value=0.14 Score=33.58 Aligned_cols=32 Identities=25% Similarity=0.591 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHhcCChhhHHHHHHHHHhcCCC
Q psy17612 16 ESMYKLAKFRYECGNYSITTSYLYFYLLVMPT 47 (449)
Q Consensus 16 d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~ 47 (449)
|++|.+|..+++.|++++|.+++..+...-|+
T Consensus 1 ~a~~~~a~~~~~~g~~~~A~~~~~~~~~~~P~ 32 (33)
T PF13174_consen 1 DALYRLARCYYKLGDYDEAIEYFQRLIKRYPD 32 (33)
T ss_dssp HHHHHHHHHHHHHCHHHHHHHHHHHHHHHSTT
T ss_pred CHHHHHHHHHHHccCHHHHHHHHHHHHHHCcC
Confidence 68999999999999999999999998877664
No 29
>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B.
Probab=92.40 E-value=0.87 Score=34.42 Aligned_cols=59 Identities=20% Similarity=0.140 Sum_probs=46.2
Q ss_pred HHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHHHHH
Q psy17612 19 YKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNKLRE 81 (449)
Q Consensus 19 yk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLke 81 (449)
|.+|..+++.|+|+.|.+.+..+...-|. ...++++.=.+....++++.|.+.+.++-+
T Consensus 1 ~~~a~~~~~~g~~~~A~~~~~~~l~~~P~----~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~ 59 (65)
T PF13432_consen 1 YALARALYQQGDYDEAIAAFEQALKQDPD----NPEAWYLLGRILYQQGRYDEALAYYERALE 59 (65)
T ss_dssp HHHHHHHHHCTHHHHHHHHHHHHHCCSTT----HHHHHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred ChHHHHHHHcCCHHHHHHHHHHHHHHCCC----CHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence 67899999999999999999988888763 245666666667778899999877776644
No 30
>KOG2582|consensus
Probab=92.28 E-value=2.4 Score=44.90 Aligned_cols=139 Identities=20% Similarity=0.270 Sum_probs=92.0
Q ss_pred HHHHHHHHHHHhccccccchHH-HHHHHhhhccCCCchHHHHHHHHhhcccHHHHHHHHHHHhhhcccccchHHhHHHHH
Q psy17612 141 HILRYLATAVIINRSKRNALKD-LVKVIQQESYTYKDPITEFLEHLYVSFDFESAREKLTECTEVLDNDFFLVACLDEFV 219 (449)
Q Consensus 141 ~lLRYlvvA~Il~~~r~~~l~d-lv~vi~qE~~~Y~DpiT~fv~~lYv~fdf~~aq~~L~~~~~vl~~DfFL~~~~d~fv 219 (449)
-.=+|+.+..|++..-. .++. --+.+..--+++..|--+|.++ |-+-.-.+-+..+.+..+.+..|-=+ ..+.+-+
T Consensus 224 aYkkylLvsLI~~GK~~-ql~k~ts~~~~r~~K~ms~pY~ef~~~-Y~~~~~~eLr~lVk~~~~rF~kDnnt-~l~k~av 300 (422)
T KOG2582|consen 224 AYKKYLLVSLILTGKVF-QLPKNTSQNAGRFFKPMSNPYHEFLNV-YLKDSSTELRTLVKKHSERFTKDNNT-GLAKQAV 300 (422)
T ss_pred HHHHHHHHHhhhcCcee-eccccchhhhHHhcccCCchHHHHHHH-HhcCCcHHHHHHHHHHHHHHhhcCcH-HHHHHHH
Confidence 34578888888776442 3332 2233344445678889999966 55444444555566665555555432 1233334
Q ss_pred HHHHHHHHHHhhhhceeeEeeccccccccccchhhHHh--hcCCCHHHHHHHHHHHHHcccccceecccCCEEEeCCCC-
Q psy17612 220 ENARLMIFETFCRIHQCISIQKESNVIDKIFDGQMLAS--KLNMGTDEAECWIVNLIRNARLDAKIDSKLGHVIMGTQP- 296 (449)
Q Consensus 220 enaR~~ife~ycriy~~IsI~~~~~~~~~~~~~~~LA~--~Lnms~~e~E~wIVnlIr~~rLdaKIDs~~G~V~m~~~~- 296 (449)
+..-..=....-|-|.+++| +.+|+ +|+ ++.|||+.|-+.|-+|++-|.|| |.|.-...+
T Consensus 301 ~sl~k~nI~rltktF~sLsL-------------~dIA~~vQLa-~~qevek~Ilqmie~~~i~a~iN---G~v~f~~n~e 363 (422)
T KOG2582|consen 301 SSLYKKNIQRLTKTFLSLSL-------------SDIASRVQLA-SAQEVEKYILQMIEDGEIFASIN---GMVFFTDNPE 363 (422)
T ss_pred HHHHHHHHHHHHHHHHHhhH-------------HHHHHHHHhc-chHHHHHHHHHHhccCceEEEec---ceEEEecCcc
Confidence 44444445566788999999 99999 565 46789999999999999999999 888766543
Q ss_pred --CCh
Q psy17612 297 --LSP 299 (449)
Q Consensus 297 --~s~ 299 (449)
+|+
T Consensus 364 ~~~Sp 368 (422)
T KOG2582|consen 364 KYNSP 368 (422)
T ss_pred cCCCH
Confidence 555
No 31
>PF10255 Paf67: RNA polymerase I-associated factor PAF67; InterPro: IPR019382 RNA polymerase I is a multi-subunit enzyme and its transcription competence is dependent on the presence of PAF67 [].
Probab=92.02 E-value=3.1 Score=44.51 Aligned_cols=110 Identities=15% Similarity=0.274 Sum_probs=71.1
Q ss_pred hhhHHHHHHHHHHHhccccccchHH-HHHHHhhhccCCCchHHHHHHHHhhcccHHHHHHHHHHHhh-hcc-c-------
Q psy17612 138 MCPHILRYLATAVIINRSKRNALKD-LVKVIQQESYTYKDPITEFLEHLYVSFDFESAREKLTECTE-VLD-N------- 207 (449)
Q Consensus 138 ~cp~lLRYlvvA~Il~~~r~~~l~d-lv~vi~qE~~~Y~DpiT~fv~~lYv~fdf~~aq~~L~~~~~-vl~-~------- 207 (449)
.+....--++++..++..| ++| +...+ .|. |.|-+..+- +.|.+.|.+.+..|.. -|. .
T Consensus 214 ~~eqMyaLlAic~~l~p~~---lde~i~~~l-kek--y~ek~~kmq-----~gd~~~f~elF~~acPKFIsp~~pp~~~~ 282 (404)
T PF10255_consen 214 KNEQMYALLAICLSLCPQR---LDESISSQL-KEK--YGEKMEKMQ-----RGDEEAFEELFSFACPKFISPVSPPDYDG 282 (404)
T ss_pred HHHHHHHHHHHHHHhCCCC---CCHHHHHHH-HHH--HHHHHHHHH-----ccCHHHHHHHHHhhCCCccCCCCCCCccc
Confidence 3334555555666665444 666 44444 443 676665544 3477777777766553 222 1
Q ss_pred -------ccchHHhHHHHHHHH----HHHHHHHhhhhceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHH
Q psy17612 208 -------DFFLVACLDEFVENA----RLMIFETFCRIHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVN 272 (449)
Q Consensus 208 -------DfFL~~~~d~fvena----R~~ife~ycriy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVn 272 (449)
|++. .+++-|++++ .+.-+..|++.|++|++ +-||.-++|+++++-.+|..
T Consensus 283 ~~~~~~~e~~~-~Ql~~Fl~eV~~q~~l~~lRSyLKLYtti~l-------------~KLA~fl~vd~~~lr~~Ll~ 344 (404)
T PF10255_consen 283 PSQNKNKEPYR-RQLKLFLDEVKQQQKLPTLRSYLKLYTTIPL-------------EKLASFLDVDEEELRSQLLC 344 (404)
T ss_pred ccchhhhhHHH-HHHHHHHHHHHHhhhhhHHHHHHHhhcCCCH-------------HHHHHHcCCCHHHHHHHHHH
Confidence 3332 2345555554 45578999999999999 99999999999999988863
No 32
>PF09756 DDRGK: DDRGK domain; InterPro: IPR019153 This is a family of proteins of approximately 300 residues. They contain a highly conserved DDRGK motif. The function is unknown. ; PDB: 1WI9_A.
Probab=91.92 E-value=0.29 Score=47.09 Aligned_cols=58 Identities=24% Similarity=0.402 Sum_probs=42.2
Q ss_pred HHHHHHhhhhceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHHHHHcccccceecccCCEEEeCCC
Q psy17612 224 LMIFETFCRIHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLIRNARLDAKIDSKLGHVIMGTQ 295 (449)
Q Consensus 224 ~~ife~ycriy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rLdaKIDs~~G~V~m~~~ 295 (449)
+.-|..|++-+++|.| +.||..|||++.++-.-|-.|..+|+|.+-||-. |..+.-+|
T Consensus 101 L~~Fi~yIK~~Kvv~l-------------edla~~f~l~t~~~i~ri~~L~~~g~ltGv~Ddr-GkfIyIs~ 158 (188)
T PF09756_consen 101 LQEFINYIKEHKVVNL-------------EDLAAEFGLRTQDVINRIQELEAEGRLTGVIDDR-GKFIYISE 158 (188)
T ss_dssp HHHHHHHHHH-SEE-H-------------HHHHHHH-S-HHHHHHHHHHHHHHSSS-EEE-TT---EEE---
T ss_pred HHHHHHHHHHcceeeH-------------HHHHHHcCCCHHHHHHHHHHHHHCCCceeeEcCC-CCeEEecH
Confidence 4557789999999999 9999999999999999999999999999999994 55544444
No 33
>PRK10803 tol-pal system protein YbgF; Provisional
Probab=91.79 E-value=0.71 Score=46.14 Aligned_cols=81 Identities=12% Similarity=0.045 Sum_probs=60.1
Q ss_pred eeeccCCCHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHHHHHHH
Q psy17612 4 FIFFFQFKMDMMESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNKLREYI 83 (449)
Q Consensus 4 ~~~~~~~~~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLke~i 83 (449)
|+.+|-=++-.-+++|.+|..||..|+|..|..++..+...-|++ .+..++++..-.+-.-.++++.|.+.++++-+.+
T Consensus 169 fl~~yP~s~~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP~s-~~~~dAl~klg~~~~~~g~~~~A~~~~~~vi~~y 247 (263)
T PRK10803 169 FVKKYPDSTYQPNANYWLGQLNYNKGKKDDAAYYFASVVKNYPKS-PKAADAMFKVGVIMQDKGDTAKAKAVYQQVIKKY 247 (263)
T ss_pred HHHHCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCC-cchhHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC
Confidence 344554444556899999999999999999999998888877754 4446676655444556688999988888776665
Q ss_pred hc
Q psy17612 84 DG 85 (449)
Q Consensus 84 d~ 85 (449)
.+
T Consensus 248 P~ 249 (263)
T PRK10803 248 PG 249 (263)
T ss_pred cC
Confidence 54
No 34
>PRK15331 chaperone protein SicA; Provisional
Probab=91.50 E-value=0.52 Score=44.57 Aligned_cols=64 Identities=19% Similarity=0.219 Sum_probs=47.2
Q ss_pred ccCCCHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHH
Q psy17612 7 FFQFKMDMMESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALE 74 (449)
Q Consensus 7 ~~~~~~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~ 74 (449)
-+||+++.++.+|.+|.-+|..|+|+.|..++..+...-+. +.+ -..|.=+|-=+..+|+.|..
T Consensus 29 l~gis~~~le~iY~~Ay~~y~~Gk~~eA~~~F~~L~~~d~~-n~~---Y~~GLaa~~Q~~k~y~~Ai~ 92 (165)
T PRK15331 29 VHGIPQDMMDGLYAHAYEFYNQGRLDEAETFFRFLCIYDFY-NPD---YTMGLAAVCQLKKQFQKACD 92 (165)
T ss_pred HhCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcC-cHH---HHHHHHHHHHHHHHHHHHHH
Confidence 37999999999999999999999999999877665554442 233 35566666655556655544
No 35
>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=90.97 E-value=1.2 Score=39.54 Aligned_cols=74 Identities=19% Similarity=0.114 Sum_probs=54.5
Q ss_pred eeeccCCCHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHH
Q psy17612 4 FIFFFQFKMDMMESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNK 78 (449)
Q Consensus 4 ~~~~~~~~~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~k 78 (449)
|+.+|+=++-...+.+.+|+.+++.|+|++|.+.|..+....++...+ --+.+..-.+.+..++++.|++.+..
T Consensus 37 l~~~~~~s~ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~~d~~l~-~~a~l~LA~~~~~~~~~d~Al~~L~~ 110 (145)
T PF09976_consen 37 LAKDYPSSPYAALAALQLAKAAYEQGDYDEAKAALEKALANAPDPELK-PLARLRLARILLQQGQYDEALATLQQ 110 (145)
T ss_pred HHHHCCCChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCHHHH-HHHHHHHHHHHHHcCCHHHHHHHHHh
Confidence 345666666677888999999999999999999999998887543333 22344444555666789999887754
No 36
>PF13414 TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2PL2_B 3IEG_B 2FBN_A ....
Probab=90.90 E-value=1.3 Score=33.66 Aligned_cols=63 Identities=17% Similarity=0.339 Sum_probs=47.6
Q ss_pred HHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhc-ChHHHHHHHHHHHH
Q psy17612 15 MESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQ-NWDLALEDLNKLRE 81 (449)
Q Consensus 15 ~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~-dwd~a~~~l~kLke 81 (449)
-+.++.+|..+++.|+|+.|..++.......|+. ..++..+=.+-..++ +++.|.++.++.-+
T Consensus 3 a~~~~~~g~~~~~~~~~~~A~~~~~~ai~~~p~~----~~~~~~~g~~~~~~~~~~~~A~~~~~~al~ 66 (69)
T PF13414_consen 3 AEAWYNLGQIYFQQGDYEEAIEYFEKAIELDPNN----AEAYYNLGLAYMKLGKDYEEAIEDFEKALK 66 (69)
T ss_dssp HHHHHHHHHHHHHTTHHHHHHHHHHHHHHHSTTH----HHHHHHHHHHHHHTTTHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCC----HHHHHHHHHHHHHhCccHHHHHHHHHHHHH
Confidence 4678999999999999999999999999887642 224444444444555 58999998887654
No 37
>PF07719 TPR_2: Tetratricopeptide repeat; InterPro: IPR013105 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]. It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. This repeat includes outlying Tetratricopeptide-like repeats (TPR) that are not matched by IPR001440 from INTERPRO.; PDB: 1XNF_B 3Q15_A 4ABN_A 1OUV_A 3U4T_A 3MA5_C 2KCV_A 2KCL_A 2XEV_A 3NF1_A ....
Probab=90.59 E-value=0.55 Score=30.93 Aligned_cols=32 Identities=31% Similarity=0.469 Sum_probs=27.6
Q ss_pred HHHHHHHHHHHhcCChhhHHHHHHHHHhcCCC
Q psy17612 16 ESMYKLAKFRYECGNYSITTSYLYFYLLVMPT 47 (449)
Q Consensus 16 d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~ 47 (449)
+.++.+|..++..|+|+.|.+++.....+.|+
T Consensus 2 ~~~~~lg~~~~~~~~~~~A~~~~~~al~l~p~ 33 (34)
T PF07719_consen 2 EAWYYLGQAYYQLGNYEEAIEYFEKALELDPN 33 (34)
T ss_dssp HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHHHHCcC
Confidence 46899999999999999999999998887763
No 38
>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A.
Probab=89.41 E-value=0.93 Score=36.31 Aligned_cols=60 Identities=17% Similarity=0.212 Sum_probs=42.6
Q ss_pred HHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHH
Q psy17612 14 MMESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNK 78 (449)
Q Consensus 14 ~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~k 78 (449)
.-..++.+|..+|+.|+|++|.+++.. .... .......|-.=.|=+..++|+.|.+-+.+
T Consensus 24 ~~~~~~~la~~~~~~~~y~~A~~~~~~-~~~~----~~~~~~~~l~a~~~~~l~~y~eAi~~l~~ 83 (84)
T PF12895_consen 24 NSAYLYNLAQCYFQQGKYEEAIELLQK-LKLD----PSNPDIHYLLARCLLKLGKYEEAIKALEK 83 (84)
T ss_dssp HHHHHHHHHHHHHHTTHHHHHHHHHHC-HTHH----HCHHHHHHHHHHHHHHTT-HHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHCCCHHHHHHHHHH-hCCC----CCCHHHHHHHHHHHHHhCCHHHHHHHHhc
Confidence 344677789999999999999999987 2221 22245555555666777899999887765
No 39
>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF. Members of this protein family are the product of one of seven genes regularly clustered in operons to encode the proteins of the tol-pal system, which is critical for maintaining the integrity of the bacterial outer membrane. The gene for this periplasmic protein has been designated orf2 and ybgF. All members of the seed alignment were from unique tol-pal gene regions from completed bacterial genomes. The architecture of this protein is a signal sequence, a low-complexity region usually rich in Asn and Gln, a well-conserved region with tandem repeats that resemble the tetratricopeptide (TPR) repeat, involved in protein-protein interaction.
Probab=89.32 E-value=2.8 Score=34.13 Aligned_cols=68 Identities=13% Similarity=0.075 Sum_probs=50.2
Q ss_pred HHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHHHHHHH
Q psy17612 15 MESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNKLREYI 83 (449)
Q Consensus 15 ~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLke~i 83 (449)
.+.+|.+|..+++.|+|+.|.+.+..+....++.. ....+.+..-.+-...++++.|.+.++++-...
T Consensus 2 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~ 69 (119)
T TIGR02795 2 EEAYYDAALLVLKAGDYADAIQAFQAFLKKYPKST-YAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKY 69 (119)
T ss_pred cHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCcc-ccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHC
Confidence 36789999999999999999999999887776432 223344444445556678899988888776543
No 40
>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW. Members of this family are designated PilF in ref (PubMed:8973346) and PilW in ref (PubMed:15612916). This outer membrane protein is required both for pilus stability and for pilus function such as adherence to human cells. Members of this family contain copies of the TPR (tetratricopeptide repeat) domain.
Probab=89.06 E-value=15 Score=32.34 Aligned_cols=168 Identities=14% Similarity=0.082 Sum_probs=88.4
Q ss_pred HHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHHHHHHHhcCCCCCCC
Q psy17612 13 DMMESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNKLREYIDGGSANFES 92 (449)
Q Consensus 13 e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLke~id~~~~~~~~ 92 (449)
...+..+.+|..+++.|+|+.|.+.+.......|.. ...+...-.+-...++++.|.+...+.-+.... +
T Consensus 29 ~~~~~~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~----~~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~------~ 98 (234)
T TIGR02521 29 KAAKIRVQLALGYLEQGDLEVAKENLDKALEHDPDD----YLAYLALALYYQQLGELEKAEDSFRRALTLNPN------N 98 (234)
T ss_pred cHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCccc----HHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCC------C
Confidence 457889999999999999999999999887665532 223333334445567899888888777554322 2
Q ss_pred hHHHHHHHHHHHHHHHHHHh--cCccchhhHHHHhcCCchhhhHHHhhhhHHHHHHHHHHHhccccccchHHHHHHHhhh
Q psy17612 93 PLHLLQQRTWLIHWSLFVFF--NHVKGRDLIIDMFLNRPHYLNAIQTMCPHILRYLATAVIINRSKRNALKDLVKVIQQE 170 (449)
Q Consensus 93 pl~~l~qR~WliHwsLf~ff--n~~~g~~~~iD~F~~~~~yl~aIqt~cp~lLRYlvvA~Il~~~r~~~l~dlv~vi~qE 170 (449)
+.. +... +...+. +..++.+.+-.... .+.+ ...+....-+..+..-...-....+.+-+.+...
T Consensus 99 ~~~-~~~~------~~~~~~~g~~~~A~~~~~~~~~-~~~~-----~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~ 165 (234)
T TIGR02521 99 GDV-LNNY------GTFLCQQGKYEQAMQQFEQAIE-DPLY-----PQPARSLENAGLCALKAGDFDKAEKYLTRALQID 165 (234)
T ss_pred HHH-HHHH------HHHHHHcccHHHHHHHHHHHHh-cccc-----ccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC
Confidence 211 1111 111111 11222222222221 1100 1122222222222221111122333344444443
Q ss_pred ccCCCchHHHHHHHHhhcccHHHHHHHHHHHhhh
Q psy17612 171 SYTYKDPITEFLEHLYVSFDFESAREKLTECTEV 204 (449)
Q Consensus 171 ~~~Y~DpiT~fv~~lYv~fdf~~aq~~L~~~~~v 204 (449)
+. ..+....+-...+..-++++|.+.+.++.+.
T Consensus 166 ~~-~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~ 198 (234)
T TIGR02521 166 PQ-RPESLLELAELYYLRGQYKDARAYLERYQQT 198 (234)
T ss_pred cC-ChHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence 32 2234556667778889999999988887765
No 41
>cd00189 TPR Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and C
Probab=88.79 E-value=1.9 Score=31.43 Aligned_cols=60 Identities=22% Similarity=0.331 Sum_probs=40.8
Q ss_pred HHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHHHH
Q psy17612 17 SMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNKLR 80 (449)
Q Consensus 17 ~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLk 80 (449)
.++.+|..+++.|+++.|.+++.......+... ......-.+-...++++.|.+.+.++-
T Consensus 2 ~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~a~~~~~~~~ 61 (100)
T cd00189 2 ALLNLGNLYYKLGDYDEALEYYEKALELDPDNA----DAYYNLAAAYYKLGKYEEALEDYEKAL 61 (100)
T ss_pred HHHHHHHHHHHHhcHHHHHHHHHHHHhcCCccH----HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 578999999999999999999998887776432 222222223333466777776655543
No 42
>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional
Probab=88.72 E-value=1.7 Score=40.87 Aligned_cols=63 Identities=8% Similarity=0.102 Sum_probs=42.6
Q ss_pred cCCC-HHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHH
Q psy17612 8 FQFK-MDMMESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALE 74 (449)
Q Consensus 8 ~~~~-~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~ 74 (449)
.+++ +|.++.+|.+|..+|+.|+|+.|.+.+..+...-+. . ..-..|.=+|-=.+++|+.|.+
T Consensus 27 ~~~~~~~~l~~lY~~A~~ly~~G~l~~A~~~f~~L~~~Dp~---~-~~y~~gLG~~~Q~~g~~~~AI~ 90 (157)
T PRK15363 27 LDDDVTQPLNTLYRYAMQLMEVKEFAGAARLFQLLTIYDAW---S-FDYWFRLGECCQAQKHWGEAIY 90 (157)
T ss_pred HCCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcc---c-HHHHHHHHHHHHHHhhHHHHHH
Confidence 3688 999999999999999999999999877555444332 1 2233343344434445555544
No 43
>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF. Members of this protein family are the product of one of seven genes regularly clustered in operons to encode the proteins of the tol-pal system, which is critical for maintaining the integrity of the bacterial outer membrane. The gene for this periplasmic protein has been designated orf2 and ybgF. All members of the seed alignment were from unique tol-pal gene regions from completed bacterial genomes. The architecture of this protein is a signal sequence, a low-complexity region usually rich in Asn and Gln, a well-conserved region with tandem repeats that resemble the tetratricopeptide (TPR) repeat, involved in protein-protein interaction.
Probab=88.30 E-value=3.3 Score=33.66 Aligned_cols=69 Identities=16% Similarity=0.081 Sum_probs=49.3
Q ss_pred HHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHHHHHHHh
Q psy17612 15 MESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNKLREYID 84 (449)
Q Consensus 15 ~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLke~id 84 (449)
.++.+.+|..+++.|+|+.|.+++..+....|+.. ....+++..-.+-...++++.|.+.+.++.+...
T Consensus 39 ~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~-~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~p 107 (119)
T TIGR02795 39 PNAHYWLGEAYYAQGKYADAAKAFLAVVKKYPKSP-KAPDALLKLGMSLQELGDKEKAKATLQQVIKRYP 107 (119)
T ss_pred HHHHHHHHHHHHhhccHHHHHHHHHHHHHHCCCCC-cccHHHHHHHHHHHHhCChHHHHHHHHHHHHHCc
Confidence 56789999999999999999999999988876432 2123333333344456788888887777665533
No 44
>KOG0687|consensus
Probab=87.98 E-value=0.95 Score=47.37 Aligned_cols=71 Identities=24% Similarity=0.295 Sum_probs=63.0
Q ss_pred HHH-HHHhhcCCChHHHHHHHHHHhhhcccccccccCCCeEEecCCCCCh--hHHHHHhhhcccchHHHHHHHH
Q psy17612 355 ITI-MLASKLNMGTDEAECWIVNLIRNARLDAKIDSKLGHVIMGTQPLSP--YQQLLEKIDTLSVRSEALQALI 425 (449)
Q Consensus 355 ~~~-~la~kLnm~~~eaE~WIvnLIr~~~ldAKIDs~~~~v~m~~~~~sv--yqqviektk~l~~rt~~l~~~~ 425 (449)
++. ++|+-+|.|.+=.++=+..+|-++||.+|||-.+|.|..++|..-- ||-||-.-..|-.|-|.++..|
T Consensus 318 l~l~~MA~aFgVSVefiDreL~rFI~~grL~ckIDrVnGVVEtNrpD~KN~qyq~vikqGd~LLnriQK~~rvi 391 (393)
T KOG0687|consen 318 LTLESMAKAFGVSVEFIDRELGRFIAAGRLHCKIDRVNGVVETNRPDEKNAQYQAVIKQGDLLLNRIQKLSRVI 391 (393)
T ss_pred HHHHHHHHHhCchHHHHHhHHHHhhccCceeeeeecccceeecCCccccchHHHHHHhhhHHHHHHHHHHHHHh
Confidence 444 8899999999999999999999999999999999999999998777 9999999888888888777654
No 45
>TIGR03504 FimV_Cterm FimV C-terminal domain. This protein is found at the extreme C-terminus of FimV from Pseudomonas aeruginosa, and of TspA of Neisseria meningitidis. Disruption of the former blocks twitching motility from type IV pili; Semmler, et al. suggest a role in peptidoglycan layer remodelling required by type IV fimbrial systems.
Probab=87.34 E-value=0.77 Score=34.30 Aligned_cols=26 Identities=19% Similarity=0.092 Sum_probs=23.7
Q ss_pred HHHHHHHHhcCChhhHHHHHHHHHhc
Q psy17612 19 YKLAKFRYECGNYSITTSYLYFYLLV 44 (449)
Q Consensus 19 yk~Akf~y~~GdY~~A~~~L~~~~~l 44 (449)
|++|+-|.+.||++.|.+.|......
T Consensus 3 LdLA~ayie~Gd~e~Ar~lL~evl~~ 28 (44)
T TIGR03504 3 LDLARAYIEMGDLEGARELLEEVIEE 28 (44)
T ss_pred hHHHHHHHHcCChHHHHHHHHHHHHc
Confidence 68999999999999999999988843
No 46
>TIGR02917 PEP_TPR_lipo putative PEP-CTERM system TPR-repeat lipoprotein. This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.
Probab=87.08 E-value=39 Score=36.52 Aligned_cols=66 Identities=14% Similarity=0.050 Sum_probs=37.4
Q ss_pred CHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHHHH
Q psy17612 11 KMDMMESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNKLR 80 (449)
Q Consensus 11 ~~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLk 80 (449)
+++....++..|..++..|+|+.|.+.+.......|.. ...+.+.-.+-...++++.|.+.+.++.
T Consensus 121 ~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~----~~~~~~la~~~~~~~~~~~A~~~~~~~~ 186 (899)
T TIGR02917 121 DEGAAELLALRGLAYLGLGQLELAQKSYEQALAIDPRS----LYAKLGLAQLALAENRFDEARALIDEVL 186 (899)
T ss_pred chhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCC----hhhHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence 45555666677777777777777777666665554422 2233333333444456666666555543
No 47
>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A ....
Probab=87.08 E-value=0.84 Score=34.56 Aligned_cols=37 Identities=24% Similarity=0.184 Sum_probs=28.1
Q ss_pred CHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCC
Q psy17612 11 KMDMMESMYKLAKFRYECGNYSITTSYLYFYLLVMPT 47 (449)
Q Consensus 11 ~~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~ 47 (449)
.|+..+..+.+|+++++.|+|+.|.++|..+....++
T Consensus 21 ~p~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~ 57 (68)
T PF14559_consen 21 NPDNPEARLLLAQCYLKQGQYDEAEELLERLLKQDPD 57 (68)
T ss_dssp TTTSHHHHHHHHHHHHHTT-HHHHHHHHHCCHGGGTT
T ss_pred CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcC
Confidence 4666777888888888888888888888877777664
No 48
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=86.43 E-value=1 Score=37.80 Aligned_cols=53 Identities=11% Similarity=0.146 Sum_probs=44.3
Q ss_pred HHHHHHhhhhceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHHHHHcccccceec-ccCCEE
Q psy17612 224 LMIFETFCRIHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLIRNARLDAKID-SKLGHV 290 (449)
Q Consensus 224 ~~ife~ycriy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rLdaKID-s~~G~V 290 (449)
++-...|++-|.+++. ..||..|++|++-+|..|..+++-||+. ||+ ...|+.
T Consensus 4 L~qlRd~l~~~gr~s~-------------~~Ls~~~~~p~~~VeaMLe~l~~kGkve-rv~~~~~gC~ 57 (78)
T PRK15431 4 LIQVRDLLALRGRMEA-------------AQISQTLNTPQPMINAMLQQLESMGKAV-RIQEEPDGCL 57 (78)
T ss_pred HHHHHHHHHHcCcccH-------------HHHHHHHCcCHHHHHHHHHHHHHCCCeE-eeccCCCCCC
Confidence 4556789999999999 9999999999999999999999999986 443 333443
No 49
>PRK11189 lipoprotein NlpI; Provisional
Probab=86.43 E-value=27 Score=34.81 Aligned_cols=69 Identities=17% Similarity=0.189 Sum_probs=50.4
Q ss_pred CCCHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHHHHH
Q psy17612 9 QFKMDMMESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNKLRE 81 (449)
Q Consensus 9 ~~~~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLke 81 (449)
.+.|+..++++.+|..+...|+|+.|.+.+.....+-|+. ..+++.+-.+-...++++.|.+.++++-+
T Consensus 92 ~l~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~P~~----~~a~~~lg~~l~~~g~~~eA~~~~~~al~ 160 (296)
T PRK11189 92 ALRPDMADAYNYLGIYLTQAGNFDAAYEAFDSVLELDPTY----NYAYLNRGIALYYGGRYELAQDDLLAFYQ 160 (296)
T ss_pred HcCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCC----HHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3566777888999999999999999998888888776642 22444444445556788888888877654
No 50
>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A.
Probab=85.59 E-value=0.84 Score=31.64 Aligned_cols=30 Identities=17% Similarity=0.284 Sum_probs=24.8
Q ss_pred HHHHHHHHHHhcCChhhHHHHHHHHHhcCC
Q psy17612 17 SMYKLAKFRYECGNYSITTSYLYFYLLVMP 46 (449)
Q Consensus 17 ~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~ 46 (449)
++..+|.+|.+.|+|++|.+++.....+..
T Consensus 1 al~~Lg~~~~~~g~~~~Ai~~y~~aL~l~~ 30 (36)
T PF13176_consen 1 ALNNLGRIYRQQGDYEKAIEYYEQALALAR 30 (36)
T ss_dssp HHHHHHHHHHHCT-HHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHcCCHHHHHHHHHHHHHhcc
Confidence 577899999999999999999998665554
No 51
>KOG2581|consensus
Probab=85.36 E-value=0.61 Score=49.89 Aligned_cols=42 Identities=33% Similarity=0.525 Sum_probs=35.3
Q ss_pred hHHH-HHHhhcCCChHH-HHHHHHHHhhhcccccccccCCCeEE
Q psy17612 354 VITI-MLASKLNMGTDE-AECWIVNLIRNARLDAKIDSKLGHVI 395 (449)
Q Consensus 354 ~~~~-~la~kLnm~~~e-aE~WIvnLIr~~~ldAKIDs~~~~v~ 395 (449)
.||. ++|+|||++.+| ||--...-||++-.+||||-+.|.++
T Consensus 377 RISl~DIA~kL~l~Seed~EyiVakAIRDGvIea~Id~~~g~m~ 420 (493)
T KOG2581|consen 377 RISLQDIAKKLGLNSEEDAEYIVAKAIRDGVIEAKIDHEDGFMQ 420 (493)
T ss_pred eccHHHHHHHhcCCCchhHHHHHHHHHHhccceeeeccccCcee
Confidence 3455 789999999887 77666699999999999999999654
No 52
>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A.
Probab=85.04 E-value=6 Score=37.36 Aligned_cols=71 Identities=11% Similarity=0.078 Sum_probs=55.2
Q ss_pred HHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHHHHHHHhc
Q psy17612 14 MMESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNKLREYIDG 85 (449)
Q Consensus 14 ~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLke~id~ 85 (449)
.-+.+|..|.-.++.|+|+.|.+.|..+...-|++... -.+.+...-+-...++++.|....+++-+.+-+
T Consensus 4 ~~~~lY~~a~~~~~~g~y~~Ai~~f~~l~~~~P~s~~a-~~A~l~la~a~y~~~~y~~A~~~~~~fi~~yP~ 74 (203)
T PF13525_consen 4 TAEALYQKALEALQQGDYEEAIKLFEKLIDRYPNSPYA-PQAQLMLAYAYYKQGDYEEAIAAYERFIKLYPN 74 (203)
T ss_dssp -HHHHHHHHHHHHHCT-HHHHHHHHHHHHHH-TTSTTH-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT
T ss_pred CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCChHH-HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCC
Confidence 45789999999999999999999999999998865544 566777777778888999998888887766665
No 53
>cd00189 TPR Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and C
Probab=84.17 E-value=4.8 Score=29.20 Aligned_cols=64 Identities=20% Similarity=0.214 Sum_probs=43.7
Q ss_pred HHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHHH
Q psy17612 12 MDMMESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNKL 79 (449)
Q Consensus 12 ~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kL 79 (449)
+..-..++.+|..++..|+++.|.+++.......+... ...+..-.+-...++++.|.+.+.++
T Consensus 31 ~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~a~~~~~~~ 94 (100)
T cd00189 31 PDNADAYYNLAAAYYKLGKYEEALEDYEKALELDPDNA----KAYYNLGLAYYKLGKYEEALEAYEKA 94 (100)
T ss_pred CccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcch----hHHHHHHHHHHHHHhHHHHHHHHHHH
Confidence 33347789999999999999999999988877765432 23333333444456677776665554
No 54
>PF14853 Fis1_TPR_C: Fis1 C-terminal tetratricopeptide repeat; PDB: 1IYG_A 1PC2_A 1NZN_A 3UUX_C 1Y8M_A 2PQR_A 2PQN_A 3O48_A.
Probab=83.92 E-value=1.9 Score=33.39 Aligned_cols=36 Identities=25% Similarity=0.405 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcch
Q psy17612 15 MESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDR 50 (449)
Q Consensus 15 ~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~ 50 (449)
+|.+|-+|--+|+.|||++|.+++..+...-|++.+
T Consensus 1 Rd~lY~lAig~ykl~~Y~~A~~~~~~lL~~eP~N~Q 36 (53)
T PF14853_consen 1 RDCLYYLAIGHYKLGEYEKARRYCDALLEIEPDNRQ 36 (53)
T ss_dssp HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHTTS-HH
T ss_pred ChhHHHHHHHHHHhhhHHHHHHHHHHHHhhCCCcHH
Confidence 578999999999999999999999999999886543
No 55
>PF13181 TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_C 2KCV_A 2KCL_A 3FP3_A 3LCA_A 3FP4_A 3FP2_A 1W3B_B 1ELW_A ....
Probab=83.66 E-value=1.9 Score=28.52 Aligned_cols=31 Identities=29% Similarity=0.443 Sum_probs=27.6
Q ss_pred HHHHHHHHHHHhcCChhhHHHHHHHHHhcCC
Q psy17612 16 ESMYKLAKFRYECGNYSITTSYLYFYLLVMP 46 (449)
Q Consensus 16 d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~ 46 (449)
+.++.+|.++.+.|+++.|.+++.......+
T Consensus 2 ~~~~~lg~~y~~~~~~~~A~~~~~~a~~~~~ 32 (34)
T PF13181_consen 2 EAYYNLGKIYEQLGDYEEALEYFEKALELNP 32 (34)
T ss_dssp HHHHHHHHHHHHTTSHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHHhhCC
Confidence 5688999999999999999999998877665
No 56
>PF13428 TPR_14: Tetratricopeptide repeat
Probab=83.18 E-value=2.3 Score=30.49 Aligned_cols=33 Identities=18% Similarity=0.109 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCc
Q psy17612 16 ESMYKLAKFRYECGNYSITTSYLYFYLLVMPTS 48 (449)
Q Consensus 16 d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~ 48 (449)
+.++.+|..|.+.|+++.|.+++.......|++
T Consensus 2 ~~~~~la~~~~~~G~~~~A~~~~~~~l~~~P~~ 34 (44)
T PF13428_consen 2 AAWLALARAYRRLGQPDEAERLLRRALALDPDD 34 (44)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCC
Confidence 467899999999999999999999999998843
No 57
>TIGR02552 LcrH_SycD type III secretion low calcium response chaperone LcrH/SycD. ScyD/LcrH contains three central tetratricopeptide-like repeats that are predicted to fold into an all-alpha-helical array.
Probab=83.17 E-value=7.6 Score=32.94 Aligned_cols=68 Identities=18% Similarity=0.292 Sum_probs=49.0
Q ss_pred CCCHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHH-HhHhhcChHHHHHHHHHHHH
Q psy17612 9 QFKMDMMESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLA-SEILVQNWDLALEDLNKLRE 81 (449)
Q Consensus 9 ~~~~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla-~eIl~~dwd~a~~~l~kLke 81 (449)
.++|+..+.++.+|..++..|+|+.|.+.+......-+.+ . ..|..++ +-...++++.|.+.+.++-+
T Consensus 11 ~~~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~p~~----~-~~~~~la~~~~~~~~~~~A~~~~~~~~~ 79 (135)
T TIGR02552 11 GLDSEQLEQIYALAYNLYQQGRYDEALKLFQLLAAYDPYN----S-RYWLGLAACCQMLKEYEEAIDAYALAAA 79 (135)
T ss_pred cCChhhHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCCCc----H-HHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4678888999999999999999999999998877765532 1 2333333 33445678888777665543
No 58
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=81.90 E-value=4.4 Score=31.23 Aligned_cols=54 Identities=13% Similarity=0.145 Sum_probs=43.2
Q ss_pred HHHHHHHhhhhceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHHHHHcccccceecccCCEEEeC
Q psy17612 223 RLMIFETFCRIHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLIRNARLDAKIDSKLGHVIMG 293 (449)
Q Consensus 223 R~~ife~ycriy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rLdaKIDs~~G~V~m~ 293 (449)
|......|++-+..+++ +.||+.||+|+.=+.+.|..|-..|. |...-|-++..
T Consensus 1 R~~~Il~~l~~~~~~s~-------------~ela~~~~VS~~TiRRDl~~L~~~g~----i~r~~GG~~~~ 54 (57)
T PF08220_consen 1 RQQQILELLKEKGKVSV-------------KELAEEFGVSEMTIRRDLNKLEKQGL----IKRTHGGAVLN 54 (57)
T ss_pred CHHHHHHHHHHcCCEEH-------------HHHHHHHCcCHHHHHHHHHHHHHCCC----EEEEcCEEEeC
Confidence 44556678899999999 99999999999999999999977774 55555555543
No 59
>PF12569 NARP1: NMDA receptor-regulated protein 1 ; InterPro: IPR021183 This group represents N-terminal acetyltransferase A (NatA) auxiliary subunit and represents a non-catalytic component of the NatA N-terminal acetyltransferase, which catalyzes acetylation of proteins beginning with Met-Ser, Met-Gly and Met-Ala. N-terminal acetylation plays a role in normal eukaryotic translation and processing, protect against proteolytic degradation and protein turnover. NAT1 anchors ARD1 and NAT5 to the ribosome and may present the N- terminal of nascent polypeptides for acetylation [], [].
Probab=81.77 E-value=72 Score=35.28 Aligned_cols=222 Identities=17% Similarity=0.176 Sum_probs=118.4
Q ss_pred HHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhc--ChHHHHHHHHHHHHHHhcCCCC
Q psy17612 12 MDMMESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQ--NWDLALEDLNKLREYIDGGSAN 89 (449)
Q Consensus 12 ~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~--dwd~a~~~l~kLke~id~~~~~ 89 (449)
.+....+-..|.++...|+++.|...+..+....|++ ..+...|+..+....... +.+...+-...+.+.+..+ ++
T Consensus 35 ~Dk~~~~E~rA~ll~kLg~~~eA~~~y~~Li~rNPdn-~~Yy~~L~~~~g~~~~~~~~~~~~~~~~y~~l~~~yp~s-~~ 112 (517)
T PF12569_consen 35 LDKLAVLEKRAELLLKLGRKEEAEKIYRELIDRNPDN-YDYYRGLEEALGLQLQLSDEDVEKLLELYDELAEKYPRS-DA 112 (517)
T ss_pred CCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCc-HHHHHHHHHHHhhhcccccccHHHHHHHHHHHHHhCccc-cc
Confidence 4455667788999999999999999999988888754 445666666654443111 1111122223333333221 12
Q ss_pred C-CChHHH-----HHH--HHHH---HH---HHHHHHhc----CccchhhHHHHhcCCchhhhHHH------------hhh
Q psy17612 90 F-ESPLHL-----LQQ--RTWL---IH---WSLFVFFN----HVKGRDLIIDMFLNRPHYLNAIQ------------TMC 139 (449)
Q Consensus 90 ~-~~pl~~-----l~q--R~Wl---iH---wsLf~ffn----~~~g~~~~iD~F~~~~~yl~aIq------------t~c 139 (449)
. +-||.. +.. ..++ ++ +|||.-.. .+.-...+.+.+. .|.+..+ .--
T Consensus 113 ~~rl~L~~~~g~~F~~~~~~yl~~~l~KgvPslF~~lk~Ly~d~~K~~~i~~l~~---~~~~~l~~~~~~~~~~~~~~~~ 189 (517)
T PF12569_consen 113 PRRLPLDFLEGDEFKERLDEYLRPQLRKGVPSLFSNLKPLYKDPEKAAIIESLVE---EYVNSLESNGSFSNGDDEEKEP 189 (517)
T ss_pred hhHhhcccCCHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHcChhHHHHHHHHHH---HHHHhhcccCCCCCccccccCC
Confidence 1 222211 110 1111 12 35553332 1211222222222 2222211 112
Q ss_pred ----hHHHHHHHHHHHhccccccchHHHHHHHhhhccCCCchHHHHHHHHhhcccHHHHHHHHHHHhhhcccccchH-Hh
Q psy17612 140 ----PHILRYLATAVIINRSKRNALKDLVKVIQQESYTYKDPITEFLEHLYVSFDFESAREKLTECTEVLDNDFFLV-AC 214 (449)
Q Consensus 140 ----p~lLRYlvvA~Il~~~r~~~l~dlv~vi~qE~~~Y~DpiT~fv~~lYv~fdf~~aq~~L~~~~~vl~~DfFL~-~~ 214 (449)
.|++-|++-.---.++....+.-|=+.|...|. .-|...-=-..+-..-||++|-+.+.++++.=..|+||. .|
T Consensus 190 p~~~lw~~~~lAqhyd~~g~~~~Al~~Id~aI~htPt-~~ely~~KarilKh~G~~~~Aa~~~~~Ar~LD~~DRyiNsK~ 268 (517)
T PF12569_consen 190 PSTLLWTLYFLAQHYDYLGDYEKALEYIDKAIEHTPT-LVELYMTKARILKHAGDLKEAAEAMDEARELDLADRYINSKC 268 (517)
T ss_pred chHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhcCCC-cHHHHHHHHHHHHHCCCHHHHHHHHHHHHhCChhhHHHHHHH
Confidence 256655543332223333444434445554431 112211111233456899999999999999999999995 67
Q ss_pred HHHHHHHHHHHHHHHhhhhceeeEe
Q psy17612 215 LDEFVENARLMIFETFCRIHQCISI 239 (449)
Q Consensus 215 ~d~fvenaR~~ife~ycriy~~IsI 239 (449)
..+.+|+=+.--=+.-|..+++-+.
T Consensus 269 aKy~LRa~~~e~A~~~~~~Ftr~~~ 293 (517)
T PF12569_consen 269 AKYLLRAGRIEEAEKTASLFTREDV 293 (517)
T ss_pred HHHHHHCCCHHHHHHHHHhhcCCCC
Confidence 9999999888888888888877664
No 60
>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW. Members of this family are designated PilF in ref (PubMed:8973346) and PilW in ref (PubMed:15612916). This outer membrane protein is required both for pilus stability and for pilus function such as adherence to human cells. Members of this family contain copies of the TPR (tetratricopeptide repeat) domain.
Probab=81.22 E-value=6.7 Score=34.63 Aligned_cols=66 Identities=15% Similarity=0.129 Sum_probs=46.9
Q ss_pred HHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHHHHHH
Q psy17612 13 DMMESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNKLREY 82 (449)
Q Consensus 13 e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLke~ 82 (449)
.....++.+|..+++.|+++.|.+++.......+.. ...++..-.+-...++++.|.+.+++..+.
T Consensus 133 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~----~~~~~~la~~~~~~~~~~~A~~~~~~~~~~ 198 (234)
T TIGR02521 133 QPARSLENAGLCALKAGDFDKAEKYLTRALQIDPQR----PESLLELAELYYLRGQYKDARAYLERYQQT 198 (234)
T ss_pred cchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCC----hHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence 345667888999999999999999888877766532 223334444445567888888888887766
No 61
>PF13371 TPR_9: Tetratricopeptide repeat
Probab=81.10 E-value=1.9 Score=33.08 Aligned_cols=35 Identities=23% Similarity=0.174 Sum_probs=16.5
Q ss_pred HHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCC
Q psy17612 12 MDMMESMYKLAKFRYECGNYSITTSYLYFYLLVMP 46 (449)
Q Consensus 12 ~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~ 46 (449)
|+....++.+|.+++..|+|+.|.+.+..+...+|
T Consensus 26 p~~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~~~p 60 (73)
T PF13371_consen 26 PDDPELWLQRARCLFQLGRYEEALEDLERALELSP 60 (73)
T ss_pred cccchhhHHHHHHHHHhccHHHHHHHHHHHHHHCC
Confidence 33444444444444444444444444444444444
No 62
>KOG1464|consensus
Probab=81.04 E-value=1.7 Score=44.79 Aligned_cols=69 Identities=20% Similarity=0.284 Sum_probs=51.3
Q ss_pred HHHhhcCCChHHHHHHHHHHhhhcccccccccCCCeEEecCCCCChhHHHHHhhhcccchHHHHHHHHHH
Q psy17612 358 MLASKLNMGTDEAECWIVNLIRNARLDAKIDSKLGHVIMGTQPLSPYQQLLEKIDTLSVRSEALQALIER 427 (449)
Q Consensus 358 ~la~kLnm~~~eaE~WIvnLIr~~~ldAKIDs~~~~v~m~~~~~svyqqviektk~l~~rt~~l~~~~~~ 427 (449)
.+|++||.++.|.|.-+|.+|-+.+++++||-.++.+.|+....|--. .+.-.+..+-+-..|..+|..
T Consensus 369 fis~~Lnv~~~dV~~LLV~~ILD~~i~g~Ide~n~~l~~~~~~~s~~k-~~~al~kW~~ql~Sl~~~i~s 437 (440)
T KOG1464|consen 369 FISKELNVPEADVESLLVSCILDDTIDGRIDEVNQYLELDKSKNSGSK-LYKALDKWNNQLKSLQSNIVS 437 (440)
T ss_pred hhHhhcCCCHHHHHHHHHHHHhccccccchHHhhhHhccCccCCcchH-HHHHHHHHHHHHHHHHHHHHh
Confidence 558999999999999999999999999999999999999887764332 222222244444445555543
No 63
>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B.
Probab=80.39 E-value=3.2 Score=31.28 Aligned_cols=37 Identities=27% Similarity=0.370 Sum_probs=32.7
Q ss_pred CHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCC
Q psy17612 11 KMDMMESMYKLAKFRYECGNYSITTSYLYFYLLVMPT 47 (449)
Q Consensus 11 ~~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~ 47 (449)
.|+..++++.+|.+++..|+|+.|.+++..+....|+
T Consensus 27 ~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~~P~ 63 (65)
T PF13432_consen 27 DPDNPEAWYLLGRILYQQGRYDEALAYYERALELDPD 63 (65)
T ss_dssp STTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT
T ss_pred CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcC
Confidence 4788999999999999999999999999998887764
No 64
>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]. It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. The X-ray structure of a domain containing three TPRs from protein phosphatase 5 revealed that TPR adopts a helix-turn-helix arrangement, with adjacent TPR motifs packing in a parallel fashion, resulting in a spiral of repeating anti-parallel alpha-helices []. The two helices are denoted helix A and helix B. The packing angle between helix A and helix B is ~24 degrees; within a single TPR and generates a right-handed superhelical shape. Helix A interacts with helix B and with helix A' of the next TPR. Two protein surfaces are generated: the inner concave surface is contributed to mainly by residue on helices A, and the other surface presents residues from both helices A and B. ; GO: 0005515 protein binding; PDB: 3SF4_C 2LNI_A 1ELW_A 2C0M_A 1FCH_B 3R9A_B 2J9Q_A 2C0L_A 1KT1_A 3FWV_A ....
Probab=79.28 E-value=4.1 Score=27.00 Aligned_cols=31 Identities=26% Similarity=0.447 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHhcCChhhHHHHHHHHHhcCC
Q psy17612 16 ESMYKLAKFRYECGNYSITTSYLYFYLLVMP 46 (449)
Q Consensus 16 d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~ 46 (449)
++++.+|..++..|+|+.|.+++.....+-|
T Consensus 2 ~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p 32 (34)
T PF00515_consen 2 EAYYNLGNAYFQLGDYEEALEYYQRALELDP 32 (34)
T ss_dssp HHHHHHHHHHHHTT-HHHHHHHHHHHHHHST
T ss_pred HHHHHHHHHHHHhCCchHHHHHHHHHHHHCc
Confidence 5789999999999999999999998877765
No 65
>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A.
Probab=78.65 E-value=3.3 Score=28.02 Aligned_cols=31 Identities=19% Similarity=0.123 Sum_probs=26.0
Q ss_pred HHHHHHHHHHHHhcCChhhHHHHHHHHHhcC
Q psy17612 15 MESMYKLAKFRYECGNYSITTSYLYFYLLVM 45 (449)
Q Consensus 15 ~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~ 45 (449)
..++..+|.+|+..|+|++|..++.......
T Consensus 2 a~~~~~la~~~~~~g~~~~A~~~~~~al~~~ 32 (42)
T PF13374_consen 2 ASALNNLANAYRAQGRYEEALELLEEALEIR 32 (42)
T ss_dssp HHHHHHHHHHHHHCT-HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhhhhcchhhHHHHHHHHHH
Confidence 5678999999999999999999998866554
No 66
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=78.50 E-value=5.1 Score=29.84 Aligned_cols=47 Identities=23% Similarity=0.225 Sum_probs=34.1
Q ss_pred HHHHhhhhceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHHHHHcccccceecccCC
Q psy17612 226 IFETFCRIHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLIRNARLDAKIDSKLG 288 (449)
Q Consensus 226 ife~ycriy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rLdaKIDs~~G 288 (449)
++..++.-...|+. +.||+.||||..-+.+.|..|-..+ +.|.++.|
T Consensus 5 il~~L~~~~~~it~-------------~eLa~~l~vS~rTi~~~i~~L~~~~---~~I~~~~~ 51 (55)
T PF08279_consen 5 ILKLLLESKEPITA-------------KELAEELGVSRRTIRRDIKELREWG---IPIESKRG 51 (55)
T ss_dssp HHHHHHHTTTSBEH-------------HHHHHHCTS-HHHHHHHHHHHHHTT----EEEEETT
T ss_pred HHHHHHHcCCCcCH-------------HHHHHHhCCCHHHHHHHHHHHHHCC---CeEEeeCC
Confidence 34444455555899 9999999999999999999986666 66666554
No 67
>PRK10747 putative protoheme IX biogenesis protein; Provisional
Probab=78.08 E-value=84 Score=32.72 Aligned_cols=96 Identities=17% Similarity=0.156 Sum_probs=56.3
Q ss_pred HHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHHHHHHHhcCCCCCCChHHHHHH
Q psy17612 20 KLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNKLREYIDGGSANFESPLHLLQQ 99 (449)
Q Consensus 20 k~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLke~id~~~~~~~~pl~~l~q 99 (449)
-.|.++...|+|+.|.+.+.......|.+ .. ++--...+-...+||+.|.+-+.+++..... .+..+..+.+
T Consensus 158 ~~a~l~l~~g~~~~Al~~l~~~~~~~P~~-~~---al~ll~~~~~~~gdw~~a~~~l~~l~k~~~~----~~~~~~~l~~ 229 (398)
T PRK10747 158 TRVRIQLARNENHAARHGVDKLLEVAPRH-PE---VLRLAEQAYIRTGAWSSLLDILPSMAKAHVG----DEEHRAMLEQ 229 (398)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHhcCCCC-HH---HHHHHHHHHHHHHhHHHHHHHHHHHHHcCCC----CHHHHHHHHH
Confidence 34889999999999999998888887643 22 2222233334558999998877777664322 1122344556
Q ss_pred HHHHHHHHHHHHhcCccchhhHHHHhc
Q psy17612 100 RTWLIHWSLFVFFNHVKGRDLIIDMFL 126 (449)
Q Consensus 100 R~WliHwsLf~ffn~~~g~~~~iD~F~ 126 (449)
++|+ .+..--...++.+.+...+.
T Consensus 230 ~a~~---~l~~~~~~~~~~~~l~~~w~ 253 (398)
T PRK10747 230 QAWI---GLMDQAMADQGSEGLKRWWK 253 (398)
T ss_pred HHHH---HHHHHHHHhcCHHHHHHHHH
Confidence 6665 22222222344555555544
No 68
>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO. Members of this protein family include YfiO, a near-essential protein of the outer membrane, part of a complex involved in protein insertion into the bacterial outer membrane. Many proteins in this family are annotated as ComL, based on the involvement of this protein in natural transformation with exogenous DNA in Neisseria gonorrhoeae. This protein family shows sequence similarity to, but is distinct from, the tol-pal system protein YbgF (TIGR02795).
Probab=77.91 E-value=12 Score=35.01 Aligned_cols=62 Identities=16% Similarity=0.111 Sum_probs=51.0
Q ss_pred HHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHHHHH
Q psy17612 19 YKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNKLRE 81 (449)
Q Consensus 19 yk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLke 81 (449)
+..|.+|++.|+|..|...+..+....|+.. ....+++..-.+-...++++.|.+....|..
T Consensus 170 ~~~a~~~~~~g~~~~A~~~~~~al~~~p~~~-~~~~a~~~l~~~~~~lg~~~~A~~~~~~l~~ 231 (235)
T TIGR03302 170 LYVARFYLKRGAYVAAINRFETVVENYPDTP-ATEEALARLVEAYLKLGLKDLAQDAAAVLGA 231 (235)
T ss_pred HHHHHHHHHcCChHHHHHHHHHHHHHCCCCc-chHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence 5779999999999999999999998887543 3366777777888888999999987777654
No 69
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=77.48 E-value=81 Score=31.52 Aligned_cols=66 Identities=11% Similarity=0.066 Sum_probs=46.8
Q ss_pred HHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHHHHHHHh
Q psy17612 15 MESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNKLREYID 84 (449)
Q Consensus 15 ~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLke~id 84 (449)
...+..+|..++..|+|+.|.+++.......+.. ...+-....+-...++|+.|.+...++.+.-.
T Consensus 107 ~~~~~~La~~~~~~g~~~~A~~~~~~~l~~~~~~----~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~ 172 (389)
T PRK11788 107 LLALQELGQDYLKAGLLDRAEELFLQLVDEGDFA----EGALQQLLEIYQQEKDWQKAIDVAERLEKLGG 172 (389)
T ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCcch----HHHHHHHHHHHHHhchHHHHHHHHHHHHHhcC
Confidence 4578889999999999999999998887664421 22333333344456789999888888876543
No 70
>PRK10866 outer membrane biogenesis protein BamD; Provisional
Probab=76.76 E-value=15 Score=36.03 Aligned_cols=44 Identities=11% Similarity=0.115 Sum_probs=33.8
Q ss_pred eeccCCCHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCc
Q psy17612 5 IFFFQFKMDMMESMYKLAKFRYECGNYSITTSYLYFYLLVMPTS 48 (449)
Q Consensus 5 ~~~~~~~~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~ 48 (449)
+..|-.++....+++.+|..+|+.|+|+.|..++..+...-|++
T Consensus 59 ~~~yP~s~~a~~a~l~la~ayy~~~~y~~A~~~~e~fi~~~P~~ 102 (243)
T PRK10866 59 DNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTH 102 (243)
T ss_pred HHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCcCC
Confidence 44566677777788888888888888888888888888777754
No 71
>PF03399 SAC3_GANP: SAC3/GANP/Nin1/mts3/eIF-3 p25 family; InterPro: IPR005062 This large family includes diverse proteins involved in large complexes [, , ]. The alignment contains one highly conserved negatively charged residue and one highly conserved positively charged residue that are probably important for the function of these proteins. The family includes the yeast nuclear export factor Sac3 [], and mammalian GANP/MCM3-associated proteins, which facilitate the nuclear localisation of MCM3, a protein that associates with chromatin in the G1 phase of the cell-cycle. The 26S protease (or 26S proteasome) is responsible for degrading ubiquitin conjugates. It consists of 19S regulatory complexes associated with the ends of 20S proteasomes. The 19S regulatory complex is composed of about 20 different polypeptides and confers ATP-dependence and substrate specificity to the 26S enzyme. The conserved region occurs at the C-terminal of the Nin1-like regulatory subunit [, , ]. This family includes several eukaryotic translation initiation factor 3 subunit 11 (eIF-3 p25) proteins. Eukaryotic initiation factor 3 (eIF3) is a multisubunit complex that is required for binding of mRNA to 40 S ribosomal subunits, stabilisation of ternary complex binding to 40 S subunits, and dissociation of 40 and 60 S subunits [].; PDB: 3T5V_D.
Probab=76.21 E-value=6.1 Score=36.74 Aligned_cols=102 Identities=16% Similarity=0.251 Sum_probs=61.4
Q ss_pred hhhHHHHHHHHHHHhccccccchHHHHHHHhhhc-cCCCchHHHH---HHHHhhcccHHHHHHHHHHHhhhcccccchHH
Q psy17612 138 MCPHILRYLATAVIINRSKRNALKDLVKVIQQES-YTYKDPITEF---LEHLYVSFDFESAREKLTECTEVLDNDFFLVA 213 (449)
Q Consensus 138 ~cp~lLRYlvvA~Il~~~r~~~l~dlv~vi~qE~-~~Y~DpiT~f---v~~lYv~fdf~~aq~~L~~~~~vl~~DfFL~~ 213 (449)
.-+.+.-|.++..+.+.+. .++...+..-+ ...++|.-.+ +..++...+|..+.+.+.. ...+++..
T Consensus 97 ~~~ef~~y~lL~~l~~~~~----~~~~~~l~~l~~~~~~~~~i~~al~l~~a~~~gny~~ff~l~~~-----~~~~~l~~ 167 (204)
T PF03399_consen 97 NEAEFIAYYLLYLLCQNNI----PDFHMELELLPSEILSSPYIQFALELCRALMEGNYVRFFRLYRS-----KSAPYLFA 167 (204)
T ss_dssp THHHHHHHHHHHTT-T-------THHHHHHTTS-HHHHTSHHHHHHHHHHHHH--TTHHHHHHHHT------TTS-HHHH
T ss_pred CHHHHHHHHHHHHHHcccc----hHHHHHHHHCchhhhcCHHHHHHHHHHHHHHcCCHHHHHHHHhc-----cCCChHHH
Confidence 3346777887776654322 22222222211 1234663322 2256777888888876622 46777777
Q ss_pred hHH-HHHHHHHHHHHHHhhhhcee-eEeeccccccccccchhhHHhhcCC
Q psy17612 214 CLD-EFVENARLMIFETFCRIHQC-ISIQKESNVIDKIFDGQMLASKLNM 261 (449)
Q Consensus 214 ~~d-~fvenaR~~ife~ycriy~~-IsI~~~~~~~~~~~~~~~LA~~Lnm 261 (449)
|+- -|+..+|..+....++.|.+ |++ +.+++-||.
T Consensus 168 ~l~~~~~~~iR~~al~~i~~ay~~~i~l-------------~~l~~~L~F 204 (204)
T PF03399_consen 168 CLMERFFNRIRLRALQSISKAYRSSIPL-------------SFLAELLGF 204 (204)
T ss_dssp HHHGGGHHHHHHHHHHHHHHHS-T-EEH-------------HHHHHHTT-
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCCCCH-------------HHHHHHcCC
Confidence 744 49999999999999999999 999 999988873
No 72
>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO. Members of this protein family include YfiO, a near-essential protein of the outer membrane, part of a complex involved in protein insertion into the bacterial outer membrane. Many proteins in this family are annotated as ComL, based on the involvement of this protein in natural transformation with exogenous DNA in Neisseria gonorrhoeae. This protein family shows sequence similarity to, but is distinct from, the tol-pal system protein YbgF (TIGR02795).
Probab=76.16 E-value=13 Score=34.81 Aligned_cols=75 Identities=13% Similarity=0.072 Sum_probs=55.1
Q ss_pred CCHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHHHHHHHhc
Q psy17612 10 FKMDMMESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNKLREYIDG 85 (449)
Q Consensus 10 ~~~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLke~id~ 85 (449)
.++...+.+|.+|..++..|+|+.|...+..+...-|++. ....+....--+-...++|+.|.+.++++-+...+
T Consensus 28 ~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~p~~~-~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~~p~ 102 (235)
T TIGR03302 28 VEEWPAEELYEEAKEALDSGDYTEAIKYFEALESRYPFSP-YAEQAQLDLAYAYYKSGDYAEAIAAADRFIRLHPN 102 (235)
T ss_pred cccCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCch-hHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcC
Confidence 5567788999999999999999999999999888776432 21223333333445567999999888877665543
No 73
>PF13431 TPR_17: Tetratricopeptide repeat
Probab=76.13 E-value=1.4 Score=30.50 Aligned_cols=27 Identities=19% Similarity=0.314 Sum_probs=24.2
Q ss_pred CCCHHHHHHHHHHHHHHHhcCChhhHH
Q psy17612 9 QFKMDMMESMYKLAKFRYECGNYSITT 35 (449)
Q Consensus 9 ~~~~e~~d~lyk~Akf~y~~GdY~~A~ 35 (449)
.++|+--++++.+|.+++..|+++.|.
T Consensus 7 e~~P~n~~a~~nla~~~~~~g~~~~A~ 33 (34)
T PF13431_consen 7 ELNPNNAEAYNNLANLYLNQGDYEEAI 33 (34)
T ss_pred HHCCCCHHHHHHHHHHHHHCcCHHhhc
Confidence 357888999999999999999999985
No 74
>KOG1498|consensus
Probab=76.00 E-value=3.3 Score=44.23 Aligned_cols=67 Identities=24% Similarity=0.207 Sum_probs=52.2
Q ss_pred HHHhhcCCChHHHHHHHHHHhhhcccccccccCCCeEEecCCCCChhH-----HHHHhhhcccchHHHHHHH
Q psy17612 358 MLASKLNMGTDEAECWIVNLIRNARLDAKIDSKLGHVIMGTQPLSPYQ-----QLLEKIDTLSVRSEALQAL 424 (449)
Q Consensus 358 ~la~kLnm~~~eaE~WIvnLIr~~~ldAKIDs~~~~v~m~~~~~svyq-----qviektk~l~~rt~~l~~~ 424 (449)
.||+.|++++++.|+.|.+|+-+.-.-||||-.+|.|....+..+.|+ +-+|+.=++.-|+..|-+.
T Consensus 358 rl~eLLdl~~ee~E~~LS~lv~t~ti~aKidrpsgII~F~k~K~~~~~LneW~~nve~L~~ll~K~~HLI~K 429 (439)
T KOG1498|consen 358 RLAELLDLPVEEMEKFLSDLVVTGTIYAKIDRPSGIINFQKVKDSNEILNEWASNVEKLLGLLEKVSHLIHK 429 (439)
T ss_pred HHHHHhCCCHHHHHHHHHHHHhccceEEEecCCCceEEEEecccHHHHHHHHHhhHHHHHHHHHHHHHHHHH
Confidence 789999999999999999999999999999999999888777655443 4455555555555554443
No 75
>TIGR02917 PEP_TPR_lipo putative PEP-CTERM system TPR-repeat lipoprotein. This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.
Probab=75.91 E-value=1.2e+02 Score=32.77 Aligned_cols=61 Identities=20% Similarity=0.249 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHH-HhHhhcChHHHHHHHHHHH
Q psy17612 15 MESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLA-SEILVQNWDLALEDLNKLR 80 (449)
Q Consensus 15 ~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla-~eIl~~dwd~a~~~l~kLk 80 (449)
.+..+.+|.++.+.|+++.|.+++.......+.+ . ..|..++ +-...++++.|.+..+++-
T Consensus 567 ~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~-~----~~~~~l~~~~~~~~~~~~A~~~~~~~~ 628 (899)
T TIGR02917 567 IEPALALAQYYLGKGQLKKALAILNEAADAAPDS-P----EAWLMLGRAQLAAGDLNKAVSSFKKLL 628 (899)
T ss_pred hhHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCC-H----HHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence 3444555555555666665555555544433321 1 1222222 2223355666665555443
No 76
>COG5600 Transcription-associated recombination protein [DNA replication, recombination, and repair]
Probab=74.92 E-value=33 Score=36.74 Aligned_cols=161 Identities=18% Similarity=0.150 Sum_probs=89.2
Q ss_pred ccchhhHHHHhcCCchhhhHHHhhhhHHHHHHHHHHHhccccccchHHHHHHHhhhc-cCCCchHHHHHHHHhhcccHHH
Q psy17612 115 VKGRDLIIDMFLNRPHYLNAIQTMCPHILRYLATAVIINRSKRNALKDLVKVIQQES-YTYKDPITEFLEHLYVSFDFES 193 (449)
Q Consensus 115 ~~g~~~~iD~F~~~~~yl~aIqt~cp~lLRYlvvA~Il~~~r~~~l~dlv~vi~qE~-~~Y~DpiT~fv~~lYv~fdf~~ 193 (449)
.+|...|-++|+. ...-++-.-.-++=|.+.++++..+. -|.++ ++.+.+ -.+-.|++.=+ ..=++++
T Consensus 237 heA~~~L~~aFl~---c~~l~~~n~~rIl~~~ipt~Llv~~~-~Ptk~---~L~r~~~~s~~~~Lvkav----rsGni~~ 305 (413)
T COG5600 237 HEAFLHLNEAFLQ---CPWLITRNRKRILPYYIPTSLLVNKF-PPTKD---LLERFKRCSVYSPLVKAV----RSGNIED 305 (413)
T ss_pred HHHHHHHHHHHHh---ChhhhhcchheehhHHhhHHHHhCCC-CCchH---HHHhccccchhHHHHHHH----HcCCHHH
Confidence 3466667777772 11112222233666777777765433 25555 344544 22334444333 3355666
Q ss_pred HHHHHHHHhhh-cccccchH--Hh-HHHHHHHHHHHHH-HHhhhhceeeEeeccccccccccchhhHHhhcCCC-----H
Q psy17612 194 AREKLTECTEV-LDNDFFLV--AC-LDEFVENARLMIF-ETFCRIHQCISIQKESNVIDKIFDGQMLASKLNMG-----T 263 (449)
Q Consensus 194 aq~~L~~~~~v-l~~DfFL~--~~-~d~fvenaR~~if-e~ycriy~~IsI~~~~~~~~~~~~~~~LA~~Lnms-----~ 263 (449)
+...|+..+.. +..--++. .| -.=+.||.-..++ -..|.+-=.++| -..+.++..+ .
T Consensus 306 ~~~~l~~ner~~~~~~l~ltl~~~~~~V~~RNL~rk~w~~~~~qsrlp~si-------------l~~~~qls~~dn~~~~ 372 (413)
T COG5600 306 FDLALSRNERKFAKRGLYLTLLAHYPLVCFRNLFRKIWRLHGKQSRLPLSI-------------LLIVLQLSAIDNFHSF 372 (413)
T ss_pred HHHHHHHhHHHHHHcchHHHHHhhccHHHHHHHHHHHHhhccccccCcHHH-------------HHHHHHccCCCcccCh
Confidence 67888888863 23333332 21 1122333322222 222222112344 4455555543 6
Q ss_pred HHHHHHHHHHHHcccccceecccCCEEEeCCCCCCh
Q psy17612 264 DEAECWIVNLIRNARLDAKIDSKLGHVIMGTQPLSP 299 (449)
Q Consensus 264 ~e~E~wIVnlIr~~rLdaKIDs~~G~V~m~~~~~s~ 299 (449)
+++|+.+|++|.-|.|.|-|-.....|+....++-|
T Consensus 373 ~~VEciL~tlI~~G~lrgYis~s~~~vV~sk~~pFp 408 (413)
T COG5600 373 KEVECILVTLIGLGLLRGYISHSRRTVVFSKKDPFP 408 (413)
T ss_pred HHHHHHHHHHHhhhhhhheecccceEEEEecCCCCC
Confidence 899999999999999999999999999888776543
No 77
>smart00028 TPR Tetratricopeptide repeats. Repeats present in 4 or more copies in proteins. Contain a minimum of 34 amino acids each and self-associate via a "knobs and holes" mechanism.
Probab=72.69 E-value=7.2 Score=22.98 Aligned_cols=31 Identities=26% Similarity=0.411 Sum_probs=25.7
Q ss_pred HHHHHHHHHHHhcCChhhHHHHHHHHHhcCC
Q psy17612 16 ESMYKLAKFRYECGNYSITTSYLYFYLLVMP 46 (449)
Q Consensus 16 d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~ 46 (449)
+.++.+|..++..|+|+.|..++.......+
T Consensus 2 ~~~~~~a~~~~~~~~~~~a~~~~~~~~~~~~ 32 (34)
T smart00028 2 EALYNLGNAYLKLGDYDEALEYYEKALELDP 32 (34)
T ss_pred hHHHHHHHHHHHHhhHHHHHHHHHHHHccCC
Confidence 4678899999999999999999987665443
No 78
>TIGR02552 LcrH_SycD type III secretion low calcium response chaperone LcrH/SycD. ScyD/LcrH contains three central tetratricopeptide-like repeats that are predicted to fold into an all-alpha-helical array.
Probab=72.26 E-value=18 Score=30.67 Aligned_cols=71 Identities=11% Similarity=0.002 Sum_probs=50.9
Q ss_pred CCHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHHHHHHHh
Q psy17612 10 FKMDMMESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNKLREYID 84 (449)
Q Consensus 10 ~~~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLke~id 84 (449)
..|...+..+.+|.+++..|+|+.|.+++.......+.+. ......=-+-...++++.|.+.++++-++..
T Consensus 46 ~~p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~p~~~----~~~~~la~~~~~~g~~~~A~~~~~~al~~~p 116 (135)
T TIGR02552 46 YDPYNSRYWLGLAACCQMLKEYEEAIDAYALAAALDPDDP----RPYFHAAECLLALGEPESALKALDLAIEICG 116 (135)
T ss_pred hCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCh----HHHHHHHHHHHHcCCHHHHHHHHHHHHHhcc
Confidence 3455678889999999999999999999998777765332 1222222345566899999988877766443
No 79
>PRK12370 invasion protein regulator; Provisional
Probab=72.26 E-value=1e+02 Score=33.67 Aligned_cols=69 Identities=12% Similarity=0.076 Sum_probs=48.6
Q ss_pred CCHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHHHHHH
Q psy17612 10 FKMDMMESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNKLREY 82 (449)
Q Consensus 10 ~~~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLke~ 82 (449)
++|+.-+++..+|..+...|+++.|..++.....+.|+... ++...=.+-...++++.|.+.+.++-++
T Consensus 333 ldP~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~P~~~~----a~~~lg~~l~~~G~~~eAi~~~~~Al~l 401 (553)
T PRK12370 333 LDHNNPQALGLLGLINTIHSEYIVGSLLFKQANLLSPISAD----IKYYYGWNLFMAGQLEEALQTINECLKL 401 (553)
T ss_pred cCCCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCHH----HHHHHHHHHHHCCCHHHHHHHHHHHHhc
Confidence 45666777888899999999999999999988888874322 2222222334567888888887776553
No 80
>PF13371 TPR_9: Tetratricopeptide repeat
Probab=72.16 E-value=14 Score=28.15 Aligned_cols=57 Identities=19% Similarity=0.207 Sum_probs=45.2
Q ss_pred HHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHHHHH
Q psy17612 21 LAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNKLRE 81 (449)
Q Consensus 21 ~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLke 81 (449)
++..+...|+|+.|.+++.....+-|.+ ....+.+=.+-...++|+.|.+++.+.-+
T Consensus 1 l~~~~~~~~~~~~A~~~~~~~l~~~p~~----~~~~~~~a~~~~~~g~~~~A~~~l~~~l~ 57 (73)
T PF13371_consen 1 LKQIYLQQEDYEEALEVLERALELDPDD----PELWLQRARCLFQLGRYEEALEDLERALE 57 (73)
T ss_pred CHHHHHhCCCHHHHHHHHHHHHHhCccc----chhhHHHHHHHHHhccHHHHHHHHHHHHH
Confidence 3578899999999999999988887642 33566666677788899999999887754
No 81
>PRK15359 type III secretion system chaperone protein SscB; Provisional
Probab=70.98 E-value=18 Score=32.22 Aligned_cols=28 Identities=14% Similarity=0.304 Sum_probs=14.4
Q ss_pred HHHHHHHHHhcCChhhHHHHHHHHHhcC
Q psy17612 18 MYKLAKFRYECGNYSITTSYLYFYLLVM 45 (449)
Q Consensus 18 lyk~Akf~y~~GdY~~A~~~L~~~~~l~ 45 (449)
++.+|..++..|+|+.|.+++.......
T Consensus 27 ~~~~g~~~~~~g~~~~A~~~~~~al~~~ 54 (144)
T PRK15359 27 VYASGYASWQEGDYSRAVIDFSWLVMAQ 54 (144)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHcC
Confidence 4445555555555555555555444443
No 82
>KOG1126|consensus
Probab=70.18 E-value=2e+02 Score=32.87 Aligned_cols=184 Identities=18% Similarity=0.294 Sum_probs=100.4
Q ss_pred HHHHHHHHHHHhcCChhhHHHHHHHHHhcCC----CcchhhHHHHHH--------HHHHhHhhc----------------
Q psy17612 16 ESMYKLAKFRYECGNYSITTSYLYFYLLVMP----TSDRHYLAVLWG--------KLASEILVQ---------------- 67 (449)
Q Consensus 16 d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~----~~~~k~ls~lwg--------kla~eIl~~---------------- 67 (449)
=.+.++|+.||+.++|.+|.+++..+|.+.| +.+ -+.+.||- -||-|+...
T Consensus 354 wvl~q~GrayFEl~~Y~~a~~~F~~~r~~~p~rv~~me-iyST~LWHLq~~v~Ls~Laq~Li~~~~~sPesWca~GNcfS 432 (638)
T KOG1126|consen 354 WVLSQLGRAYFELIEYDQAERIFSLVRRIEPYRVKGME-IYSTTLWHLQDEVALSYLAQDLIDTDPNSPESWCALGNCFS 432 (638)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccchh-HHHHHHHHHHhhHHHHHHHHHHHhhCCCCcHHHHHhcchhh
Confidence 3578899999999999999999999999987 222 24666663 345444432
Q ss_pred ---ChHHHHHHHHHHHH--------------------HHhcCCCCC-----CChHHHHHHHHHHHHHHHHHHhcCccchh
Q psy17612 68 ---NWDLALEDLNKLRE--------------------YIDGGSANF-----ESPLHLLQQRTWLIHWSLFVFFNHVKGRD 119 (449)
Q Consensus 68 ---dwd~a~~~l~kLke--------------------~id~~~~~~-----~~pl~~l~qR~WliHwsLf~ffn~~~g~~ 119 (449)
|-++|.|..+++-. .+|++-.-+ .+|.+ .|+|- +|=..+ -+.++-
T Consensus 433 LQkdh~~Aik~f~RAiQldp~faYayTLlGhE~~~~ee~d~a~~~fr~Al~~~~rh---YnAwY---GlG~vy-~Kqek~ 505 (638)
T KOG1126|consen 433 LQKDHDTAIKCFKRAIQLDPRFAYAYTLLGHESIATEEFDKAMKSFRKALGVDPRH---YNAWY---GLGTVY-LKQEKL 505 (638)
T ss_pred hhhHHHHHHHHHHHhhccCCccchhhhhcCChhhhhHHHHhHHHHHHhhhcCCchh---hHHHH---hhhhhe-eccchh
Confidence 34666666655422 112110011 12322 35564 443322 233444
Q ss_pred hHHHHhcCCchhhhHHHhhhhHHHHHHHH-HHHhcc-cc-ccchHHHHHHHhhhccCCCchHHHHHH--HHhhcccHHHH
Q psy17612 120 LIIDMFLNRPHYLNAIQTMCPHILRYLAT-AVIINR-SK-RNALKDLVKVIQQESYTYKDPITEFLE--HLYVSFDFESA 194 (449)
Q Consensus 120 ~~iD~F~~~~~yl~aIqt~cp~lLRYlvv-A~Il~~-~r-~~~l~dlv~vi~qE~~~Y~DpiT~fv~--~lYv~fdf~~a 194 (449)
++-|.++. -|++ .-|.=..-++. ..+..+ .+ .+.|.-+=+++.- .++||+..|-. -+|--+++++|
T Consensus 506 e~Ae~~fq-----kA~~-INP~nsvi~~~~g~~~~~~k~~d~AL~~~~~A~~l---d~kn~l~~~~~~~il~~~~~~~ea 576 (638)
T KOG1126|consen 506 EFAEFHFQ-----KAVE-INPSNSVILCHIGRIQHQLKRKDKALQLYEKAIHL---DPKNPLCKYHRASILFSLGRYVEA 576 (638)
T ss_pred hHHHHHHH-----hhhc-CCccchhHHhhhhHHHHHhhhhhHHHHHHHHHHhc---CCCCchhHHHHHHHHHhhcchHHH
Confidence 44454441 1222 22211111222 222222 11 2223322233333 46899877753 36778999999
Q ss_pred HHHHHHHhhhcccccchHHhHH
Q psy17612 195 REKLTECTEVLDNDFFLVACLD 216 (449)
Q Consensus 195 q~~L~~~~~vl~~DfFL~~~~d 216 (449)
.+.|.+.++....+-+....+.
T Consensus 577 l~~LEeLk~~vP~es~v~~llg 598 (638)
T KOG1126|consen 577 LQELEELKELVPQESSVFALLG 598 (638)
T ss_pred HHHHHHHHHhCcchHHHHHHHH
Confidence 9999999998888766544433
No 83
>PF13424 TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 4A1S_B 3CEQ_B 3EDT_H ....
Probab=69.62 E-value=6.4 Score=30.65 Aligned_cols=33 Identities=21% Similarity=0.332 Sum_probs=29.2
Q ss_pred HHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhc
Q psy17612 12 MDMMESMYKLAKFRYECGNYSITTSYLYFYLLV 44 (449)
Q Consensus 12 ~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l 44 (449)
+++...+..+|.+++..|+|+.|.+++......
T Consensus 43 ~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al~i 75 (78)
T PF13424_consen 43 PDTANTLNNLGECYYRLGDYEEALEYYQKALDI 75 (78)
T ss_dssp HHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence 467999999999999999999999999876544
No 84
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=69.00 E-value=6.7 Score=28.75 Aligned_cols=47 Identities=17% Similarity=0.074 Sum_probs=36.8
Q ss_pred HHHHHHHHHhhhhceee-EeeccccccccccchhhHHhhcCCCHHHHHHHHHHHHHccccc
Q psy17612 221 NARLMIFETFCRIHQCI-SIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLIRNARLD 280 (449)
Q Consensus 221 naR~~ife~ycriy~~I-sI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rLd 280 (449)
..|..+....+.+...+ ++ ..||+.||+|..-+.+.+-.|...|-+.
T Consensus 4 ~l~~~i~~~~~~~~~~l~s~-------------~~la~~~~vs~~tv~~~l~~L~~~g~i~ 51 (60)
T smart00345 4 RLREDIVSGELRPGDKLPSE-------------RELAAQLGVSRTTVREALSRLEAEGLVQ 51 (60)
T ss_pred HHHHHHHcCCCCCCCcCcCH-------------HHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 34555555555666677 77 9999999999999999999998887653
No 85
>cd05804 StaR_like StaR_like; a well-conserved protein found in bacteria, plants, and animals. A family member from Streptomyces toyocaensis, StaR is part of a gene cluster involved in the biosynthesis of glycopeptide antibiotics (GPAs), specifically A47934. It has been speculated that StaR could be a flavoprotein hydroxylating a tyrosine sidechain. Some family members have been annotated as proteins containing tetratricopeptide (TPR) repeats, which may at least indicate mostly alpha-helical secondary structure.
Probab=68.61 E-value=16 Score=36.06 Aligned_cols=69 Identities=10% Similarity=-0.009 Sum_probs=49.5
Q ss_pred CHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHHH
Q psy17612 11 KMDMMESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNKL 79 (449)
Q Consensus 11 ~~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kL 79 (449)
.|+....+.-+|..+++.|++++|..++.......+..........|..-.+-+..++++.|.+.++++
T Consensus 144 ~p~~~~~~~~la~i~~~~g~~~eA~~~l~~~l~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~~ 212 (355)
T cd05804 144 NPDDAWAVHAVAHVLEMQGRFKEGIAFMESWRDTWDCSSMLRGHNWWHLALFYLERGDYEAALAIYDTH 212 (355)
T ss_pred CCCCcHHHHHHHHHHHHcCCHHHHHHHHHhhhhccCCCcchhHHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence 344455677788899999999999988888777665322222445666667777788888888877776
No 86
>PRK02603 photosystem I assembly protein Ycf3; Provisional
Probab=67.79 E-value=36 Score=30.80 Aligned_cols=69 Identities=14% Similarity=0.006 Sum_probs=46.9
Q ss_pred CHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHH-hHhhcChHHHHHHHHHHHH
Q psy17612 11 KMDMMESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLAS-EILVQNWDLALEDLNKLRE 81 (449)
Q Consensus 11 ~~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~-eIl~~dwd~a~~~l~kLke 81 (449)
.+.....++.+|..++..|+|+.|.+++.......++.... . ..|..++. -...++++.|.+.+.+.-+
T Consensus 31 ~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~-~-~~~~~la~~~~~~g~~~~A~~~~~~al~ 100 (172)
T PRK02603 31 KAKEAFVYYRDGMSAQADGEYAEALENYEEALKLEEDPNDR-S-YILYNMGIIYASNGEHDKALEYYHQALE 100 (172)
T ss_pred HhhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhccchH-H-HHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence 44566788999999999999999999999887766532221 2 23333332 2334688888877665544
No 87
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=67.67 E-value=6.2 Score=31.57 Aligned_cols=37 Identities=22% Similarity=0.323 Sum_probs=33.2
Q ss_pred HHHHHHHhhhhceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHH
Q psy17612 223 RLMIFETFCRIHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVN 272 (449)
Q Consensus 223 R~~ife~ycriy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVn 272 (449)
|-.+|+-|...=..|++ ..+|++||||+.-+-+|=..
T Consensus 9 rdkA~e~y~~~~g~i~l-------------kdIA~~Lgvs~~tIr~WK~~ 45 (60)
T PF10668_consen 9 RDKAFEIYKESNGKIKL-------------KDIAEKLGVSESTIRKWKSR 45 (60)
T ss_pred HHHHHHHHHHhCCCccH-------------HHHHHHHCCCHHHHHHHhhh
Confidence 56789999888889999 99999999999999999765
No 88
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=67.67 E-value=25 Score=33.40 Aligned_cols=104 Identities=8% Similarity=0.083 Sum_probs=74.1
Q ss_pred cccccchHHhHHHHH--HHHHHHHHHHhhhhceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHHHHHcccccce
Q psy17612 205 LDNDFFLVACLDEFV--ENARLMIFETFCRIHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLIRNARLDAK 282 (449)
Q Consensus 205 l~~DfFL~~~~d~fv--enaR~~ife~ycriy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rLdaK 282 (449)
+.+|+.+...+.+++ ...+..|+... ..|..++- +.||+.|||+..++-+-|..|-.+|-+..+
T Consensus 4 ~~~~~~v~~~l~~~~~~~~~~~~Vl~~L-~~~g~~td-------------eeLA~~Lgi~~~~VRk~L~~L~e~gLv~~~ 69 (178)
T PRK06266 4 MLNNPLVQKVLFEIMEGDEEGFEVLKAL-IKKGEVTD-------------EEIAEQTGIKLNTVRKILYKLYDARLADYK 69 (178)
T ss_pred hhcCHHHHHHHHHHhcCCccHhHHHHHH-HHcCCcCH-------------HHHHHHHCCCHHHHHHHHHHHHHCCCeEEe
Confidence 348888888888888 44467777764 57788999 999999999999999999999888766543
Q ss_pred ecccCCEEEeCCCCC---ChHHHHHHhhhhhhhHHHHHHHHHHHHHhhh
Q psy17612 283 IDSKLGHVIMGTQPL---SPYQQLLEKIDTLSVRSEALQALIERKVKVR 328 (449)
Q Consensus 283 IDs~~G~V~m~~~~~---s~Yqqviek~d~L~~R~q~L~~~i~~~~~~~ 328 (449)
--+..| +|+|.- -.|.+++ +.+..|..++...+...+...
T Consensus 70 r~r~~~---~Gr~~y~w~l~~~~i~---d~ik~~~~~~~~klk~~l~~e 112 (178)
T PRK06266 70 REKDEE---TNWYTYTWKPELEKLP---EIIKKKKMEELKKLKEQLEEE 112 (178)
T ss_pred eeeccC---CCcEEEEEEeCHHHHH---HHHHHHHHHHHHHHHHHhhhc
Confidence 322212 244432 3456666 446678888887777766544
No 89
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
Probab=67.63 E-value=15 Score=32.26 Aligned_cols=80 Identities=10% Similarity=0.035 Sum_probs=51.8
Q ss_pred hHHhHHHHHHHHHHHHHHHhhhhceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHHHHHcccccceecccCCEE
Q psy17612 211 LVACLDEFVENARLMIFETFCRIHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLIRNARLDAKIDSKLGHV 290 (449)
Q Consensus 211 L~~~~d~fvenaR~~ife~ycriy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rLdaKIDs~~G~V 290 (449)
|+...++-++-+..++- ..-..+++ ..||+++|+|+..+.+-+..|.+.|-+...-.. .|..
T Consensus 4 ls~~~~yal~~l~~la~----~~~~~~s~-------------~eia~~l~is~~~v~~~l~~L~~~Gli~~~~g~-~ggy 65 (130)
T TIGR02944 4 ISKLTDYATLVLTTLAQ----NDSQPYSA-------------AEIAEQTGLNAPTVSKILKQLSLAGIVTSKRGV-EGGY 65 (130)
T ss_pred cchHHhHHHHHHHHHHh----CCCCCccH-------------HHHHHHHCcCHHHHHHHHHHHHHCCcEEecCCC-CCCh
Confidence 34445555555444432 23457889 999999999999999999999999887654332 3434
Q ss_pred EeCCCC-CChHHHHHHhhh
Q psy17612 291 IMGTQP-LSPYQQLLEKID 308 (449)
Q Consensus 291 ~m~~~~-~s~Yqqviek~d 308 (449)
..++++ .-...++++..+
T Consensus 66 ~l~~~~~~it~~~v~~~l~ 84 (130)
T TIGR02944 66 TLARAPRDITVADIVKAVE 84 (130)
T ss_pred hhcCCccccCHHHHHHHHc
Confidence 444444 233555555443
No 90
>PF12862 Apc5: Anaphase-promoting complex subunit 5
Probab=67.43 E-value=43 Score=27.88 Aligned_cols=60 Identities=17% Similarity=0.139 Sum_probs=43.4
Q ss_pred HhcCChhhHHHHHHHHHhcCCCcchh-----hHHHHHHHHHHhHhhcChHHHHHHHHHHHHHHhc
Q psy17612 26 YECGNYSITTSYLYFYLLVMPTSDRH-----YLAVLWGKLASEILVQNWDLALEDLNKLREYIDG 85 (449)
Q Consensus 26 y~~GdY~~A~~~L~~~~~l~~~~~~k-----~ls~lwgkla~eIl~~dwd~a~~~l~kLke~id~ 85 (449)
.++|||..|.+.|..+...+...+.. .-.++...-..-..+++++.|.+.+++.-.+-..
T Consensus 9 ~~~~dy~~A~d~L~~~fD~~~~~~~~~~~~~~~~all~lA~~~~~~G~~~~A~~~l~eAi~~Are 73 (94)
T PF12862_consen 9 LRSGDYSEALDALHRYFDYAKQSNNSSSNSGLAYALLNLAELHRRFGHYEEALQALEEAIRLARE 73 (94)
T ss_pred HHcCCHHHHHHHHHHHHHHHhhcccchhhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHH
Confidence 57899999999999988887643322 2345555666677778999998877766555554
No 91
>KOG1861|consensus
Probab=67.12 E-value=37 Score=37.35 Aligned_cols=102 Identities=16% Similarity=0.222 Sum_probs=64.4
Q ss_pred HHHHHHHHHHHhccccccchHHHHHHHhhhccCCCchHHHHH---HHHhhcccHHHHHHHHHHHhhhcccccchHHh-HH
Q psy17612 141 HILRYLATAVIINRSKRNALKDLVKVIQQESYTYKDPITEFL---EHLYVSFDFESAREKLTECTEVLDNDFFLVAC-LD 216 (449)
Q Consensus 141 ~lLRYlvvA~Il~~~r~~~l~dlv~vi~qE~~~Y~DpiT~fv---~~lYv~fdf~~aq~~L~~~~~vl~~DfFL~~~-~d 216 (449)
.++-|-++..|++..+.+.+. +++-+..|-+ .||-..+. ..+-.--++..|++.- ..=+=+..| +|
T Consensus 388 EF~AYriLY~i~tkN~~di~s-ll~~lt~E~k--ed~~V~hAL~vR~A~~~GNY~kFFrLY-------~~AP~M~~yLmd 457 (540)
T KOG1861|consen 388 EFTAYRILYYIFTKNYPDILS-LLRDLTEEDK--EDEAVAHALEVRSAVTLGNYHKFFRLY-------LTAPNMSGYLMD 457 (540)
T ss_pred hHHHHHHHHHHHhcCchHHHH-HHHhccHhhc--cCHHHHHHHHHHHHHHhccHHHHHHHH-------hhcccchhHHHH
Confidence 577788999999987743222 3333334432 37732221 1221222222223321 122334556 79
Q ss_pred HHHHHHHHHHHHHhhhhce-eeEeeccccccccccchhhHHhhcCCCHHH
Q psy17612 217 EFVENARLMIFETFCRIHQ-CISIQKESNVIDKIFDGQMLASKLNMGTDE 265 (449)
Q Consensus 217 ~fvenaR~~ife~ycriy~-~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e 265 (449)
-|++-.|..++...|+.|. +|++ +++++.|.+..-|
T Consensus 458 lF~erER~~Al~ii~KsyrP~i~~-------------~fi~~~laf~~~e 494 (540)
T KOG1861|consen 458 LFLERERKKALTIICKSYRPTITV-------------DFIASELAFDSME 494 (540)
T ss_pred HHHHHHHHHHHHHHHHHcCCCccH-------------HHHhhhhhhchHH
Confidence 9999999999999999998 9999 9999999987554
No 92
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=66.86 E-value=1.4e+02 Score=29.77 Aligned_cols=72 Identities=13% Similarity=0.030 Sum_probs=50.0
Q ss_pred CCCHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHh-HhhcChHHHHHHHHHHHH
Q psy17612 9 QFKMDMMESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASE-ILVQNWDLALEDLNKLRE 81 (449)
Q Consensus 9 ~~~~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~e-Il~~dwd~a~~~l~kLke 81 (449)
...|+..+.++.+|.++...|+|+.|.+++..........+.. ....|..++.. ...++++.|.+.+.++.+
T Consensus 63 ~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~-~~~~~~~La~~~~~~g~~~~A~~~~~~~l~ 135 (389)
T PRK11788 63 KVDPETVELHLALGNLFRRRGEVDRAIRIHQNLLSRPDLTREQ-RLLALQELGQDYLKAGLLDRAEELFLQLVD 135 (389)
T ss_pred hcCcccHHHHHHHHHHHHHcCcHHHHHHHHHHHhcCCCCCHHH-HHHHHHHHHHHHHHCCCHHHHHHHHHHHHc
Confidence 3567778899999999999999999999998877643222222 12334444433 334689999887777654
No 93
>KOG0686|consensus
Probab=66.72 E-value=7.7 Score=41.82 Aligned_cols=70 Identities=20% Similarity=0.217 Sum_probs=55.8
Q ss_pred HHhhcCCChHHHHHHHHHHhhhcccccccccCCCeEEecCC---------CCChhHHHHHhhhcccchHHHHHHHHHHH
Q psy17612 359 LASKLNMGTDEAECWIVNLIRNARLDAKIDSKLGHVIMGTQ---------PLSPYQQLLEKIDTLSVRSEALQALIERK 428 (449)
Q Consensus 359 la~kLnm~~~eaE~WIvnLIr~~~ldAKIDs~~~~v~m~~~---------~~svyqqviektk~l~~rt~~l~~~~~~~ 428 (449)
+|+-+|++..+-|+=+..||-+.++.|||||..+.|.|-+. +...-++---++|++..|+.++.+.+...
T Consensus 371 mA~af~~sv~~le~~l~~LI~~~~i~~rIDs~~ki~~~~~~~~en~~fe~~~~~~~~~~~~~kal~lr~~~~~~~~ht~ 449 (466)
T KOG0686|consen 371 MAEAFNTSVAILESELLELILEGKISGRIDSHNKILYARDADSENATFERVLPMGKRSQLEAKALLLRAALLKNKIHTK 449 (466)
T ss_pred HHHHhcccHHHHHHHHHHHHHccchheeeccccceeeecccccccchhhhcchhhHHHHHHHHHHHHHHHHHhccccCC
Confidence 48999999999999999999999999999999999999765 22223344456777788887777766644
No 94
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=65.41 E-value=7 Score=35.98 Aligned_cols=43 Identities=21% Similarity=0.299 Sum_probs=35.3
Q ss_pred HHHHhhhhcee--eEeeccccccccccchhhHHhhcCCCHHHHHHHHHHHHHcccccceecc
Q psy17612 226 IFETFCRIHQC--ISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLIRNARLDAKIDS 285 (449)
Q Consensus 226 ife~ycriy~~--IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rLdaKIDs 285 (449)
....|+|=|+. -++ ..+|+.+|||++. |-.||++|||.-.-++
T Consensus 34 kV~~yLr~~p~~~ati-------------~eV~e~tgVs~~~----I~~~IreGRL~~~~~~ 78 (137)
T TIGR03826 34 KVYKFLRKHENRQATV-------------SEIVEETGVSEKL----ILKFIREGRLQLKHFP 78 (137)
T ss_pred HHHHHHHHCCCCCCCH-------------HHHHHHHCcCHHH----HHHHHHcCCeeccCCC
Confidence 34578888888 999 9999999999886 6677899999765554
No 95
>PRK11189 lipoprotein NlpI; Provisional
Probab=64.56 E-value=26 Score=35.01 Aligned_cols=69 Identities=13% Similarity=0.042 Sum_probs=43.5
Q ss_pred CCHHH-HHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHHHHHH
Q psy17612 10 FKMDM-MESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNKLREY 82 (449)
Q Consensus 10 ~~~e~-~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLke~ 82 (449)
.+++. -+.++.+|..+...|+++.|...+.....+-|+. . .++...=..-...++++.|.+...++-++
T Consensus 58 ~~~~~~a~~~~~~g~~~~~~g~~~~A~~~~~~Al~l~P~~-~---~a~~~lg~~~~~~g~~~~A~~~~~~Al~l 127 (296)
T PRK11189 58 LTDEERAQLHYERGVLYDSLGLRALARNDFSQALALRPDM-A---DAYNYLGIYLTQAGNFDAAYEAFDSVLEL 127 (296)
T ss_pred CCcHhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCC-H---HHHHHHHHHHHHCCCHHHHHHHHHHHHHh
Confidence 44444 5678888888888888888888887777766532 1 12222222234456788887776666543
No 96
>KOG2003|consensus
Probab=64.12 E-value=22 Score=39.21 Aligned_cols=78 Identities=17% Similarity=0.172 Sum_probs=45.5
Q ss_pred CHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchh--hHHHHHHHH-----HHhHhhcCh---HHHHHHHHHHH
Q psy17612 11 KMDMMESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRH--YLAVLWGKL-----ASEILVQNW---DLALEDLNKLR 80 (449)
Q Consensus 11 ~~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k--~ls~lwgkl-----a~eIl~~dw---d~a~~~l~kLk 80 (449)
+....++||..|--+-..|+.+.|.++++.++...-++-+- .+..+.+.+ |+|.+|+-- +.--.-|.||-
T Consensus 520 dasc~ealfniglt~e~~~~ldeald~f~klh~il~nn~evl~qianiye~led~aqaie~~~q~~slip~dp~ilskl~ 599 (840)
T KOG2003|consen 520 DASCTEALFNIGLTAEALGNLDEALDCFLKLHAILLNNAEVLVQIANIYELLEDPAQAIELLMQANSLIPNDPAILSKLA 599 (840)
T ss_pred chHHHHHHHHhcccHHHhcCHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhhCHHHHHHHHHHhcccCCCCHHHHHHHH
Confidence 44566777877777777888888888887777665432111 122222222 455555411 00112368888
Q ss_pred HHHhcCCC
Q psy17612 81 EYIDGGSA 88 (449)
Q Consensus 81 e~id~~~~ 88 (449)
++||++|+
T Consensus 600 dlydqegd 607 (840)
T KOG2003|consen 600 DLYDQEGD 607 (840)
T ss_pred HHhhcccc
Confidence 99998763
No 97
>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A ....
Probab=62.92 E-value=16 Score=27.38 Aligned_cols=51 Identities=20% Similarity=0.092 Sum_probs=37.9
Q ss_pred HhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHHHH
Q psy17612 26 YECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNKLR 80 (449)
Q Consensus 26 y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLk 80 (449)
++.|+|+.|.+++.......|++ ..+..+.-.|-+..++++.|.+.++++.
T Consensus 2 l~~~~~~~A~~~~~~~l~~~p~~----~~~~~~la~~~~~~g~~~~A~~~l~~~~ 52 (68)
T PF14559_consen 2 LKQGDYDEAIELLEKALQRNPDN----PEARLLLAQCYLKQGQYDEAEELLERLL 52 (68)
T ss_dssp HHTTHHHHHHHHHHHHHHHTTTS----HHHHHHHHHHHHHTT-HHHHHHHHHCCH
T ss_pred hhccCHHHHHHHHHHHHHHCCCC----HHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence 57899999999999998888742 3455566667777788888877666553
No 98
>TIGR00990 3a0801s09 mitochondrial precursor proteins import receptor (72 kDa mitochondrial outermembrane protein) (mitochondrial import receptor for the ADP/ATP carrier) (translocase of outermembrane tom70).
Probab=61.54 E-value=2.5e+02 Score=30.80 Aligned_cols=68 Identities=13% Similarity=0.109 Sum_probs=39.4
Q ss_pred CCHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHHHHH
Q psy17612 10 FKMDMMESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNKLRE 81 (449)
Q Consensus 10 ~~~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLke 81 (449)
++|...+.++.+|..+++.|+|+.|.+++......-|.. ..++..+-.+-...++++.|.+..+++-+
T Consensus 360 l~P~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~p~~----~~~~~~lg~~~~~~g~~~~A~~~~~kal~ 427 (615)
T TIGR00990 360 LDPRVTQSYIKRASMNLELGDPDKAEEDFDKALKLNSED----PDIYYHRAQLHFIKGEFAQAGKDYQKSID 427 (615)
T ss_pred cCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCC----HHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence 455556667777777777777777777776665554321 12222222233445667777766666544
No 99
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=60.64 E-value=35 Score=27.81 Aligned_cols=65 Identities=11% Similarity=0.129 Sum_probs=44.8
Q ss_pred HHHHHHHHHHHhhhhceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHHHHHcccccceecccCCEEEeCCCCC
Q psy17612 219 VENARLMIFETFCRIHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLIRNARLDAKIDSKLGHVIMGTQPL 297 (449)
Q Consensus 219 venaR~~ife~ycriy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rLdaKIDs~~G~V~m~~~~~ 297 (449)
--..|.+++-..-.--+.+++ +.||+.+|+|+..+++.+..|.++|-+..+= -.+|-....+++.
T Consensus 8 ~~Al~~l~~la~~~~~~~~s~-------------~eiA~~~~i~~~~l~kil~~L~~~Gli~s~~-G~~GGy~L~~~~~ 72 (83)
T PF02082_consen 8 DYALRILLYLARHPDGKPVSS-------------KEIAERLGISPSYLRKILQKLKKAGLIESSR-GRGGGYRLARPPE 72 (83)
T ss_dssp HHHHHHHHHHHCTTTSC-BEH-------------HHHHHHHTS-HHHHHHHHHHHHHTTSEEEET-STTSEEEESS-CC
T ss_pred HHHHHHHHHHHhCCCCCCCCH-------------HHHHHHHCcCHHHHHHHHHHHhhCCeeEecC-CCCCceeecCCHH
Confidence 334566666544443344999 9999999999999999999999998765432 2356677777663
No 100
>KOG4234|consensus
Probab=60.39 E-value=37 Score=34.07 Aligned_cols=67 Identities=22% Similarity=0.336 Sum_probs=49.5
Q ss_pred HHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHH-HHhHhhcChHHHHHHHHHH
Q psy17612 13 DMMESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKL-ASEILVQNWDLALEDLNKL 79 (449)
Q Consensus 13 e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkl-a~eIl~~dwd~a~~~l~kL 79 (449)
+-.+.|-+=|.=+|.-|+|+.|.+-+......||+...+.-++|++-= ||-|-..-|+.|.++-.|.
T Consensus 93 ~kad~lK~EGN~~F~ngdyeeA~skY~~Ale~cp~~~~e~rsIly~Nraaa~iKl~k~e~aI~dcsKa 160 (271)
T KOG4234|consen 93 EKADSLKKEGNELFKNGDYEEANSKYQEALESCPSTSTEERSILYSNRAAALIKLRKWESAIEDCSKA 160 (271)
T ss_pred HHHHHHHHHHHHhhhcccHHHHHHHHHHHHHhCccccHHHHHHHHhhhHHHHHHhhhHHHHHHHHHhh
Confidence 345667788899999999999999999999999976665555555543 4444445677777766655
No 101
>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional
Probab=59.98 E-value=37 Score=35.14 Aligned_cols=67 Identities=13% Similarity=0.085 Sum_probs=36.9
Q ss_pred CHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHHHHH
Q psy17612 11 KMDMMESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNKLRE 81 (449)
Q Consensus 11 ~~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLke 81 (449)
.|+....++.+|..++..|+|+.|...+.....+.+.... +++.+=.+-...++++.|.+.+.++-+
T Consensus 32 ~P~~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~P~~~~----a~~~lg~~~~~lg~~~eA~~~~~~al~ 98 (356)
T PLN03088 32 DPNNAELYADRAQANIKLGNFTEAVADANKAIELDPSLAK----AYLRKGTACMKLEEYQTAKAALEKGAS 98 (356)
T ss_pred CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCCHH----HHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence 3444556666777777777777777776666666553211 222222233344566666666655544
No 102
>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A.
Probab=59.62 E-value=1.9e+02 Score=28.66 Aligned_cols=42 Identities=19% Similarity=0.229 Sum_probs=30.7
Q ss_pred HHHHHHHHhhcccHHHHHHHHHHHhhhcccccchHHhHHHHHH
Q psy17612 178 ITEFLEHLYVSFDFESAREKLTECTEVLDNDFFLVACLDEFVE 220 (449)
Q Consensus 178 iT~fv~~lYv~fdf~~aq~~L~~~~~vl~~DfFL~~~~d~fve 220 (449)
+.+++ ..|.+-|.+.+...+.+-..+-.-|.+....+-..-+
T Consensus 238 ~~~l~-~A~~~~D~e~f~~av~~~d~~~~ld~w~~~~l~~~k~ 279 (282)
T PF14938_consen 238 LEDLL-EAYEEGDVEAFTEAVAEYDSISRLDNWKTKMLLKIKK 279 (282)
T ss_dssp HHHHH-HHHHTT-CCCHHHHCHHHTTSS---HHHHHHHHHHHH
T ss_pred HHHHH-HHHHhCCHHHHHHHHHHHcccCccHHHHHHHHHHHHh
Confidence 66777 5599999999999999999999999998776554433
No 103
>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A.
Probab=59.22 E-value=40 Score=31.76 Aligned_cols=45 Identities=18% Similarity=0.159 Sum_probs=36.3
Q ss_pred eeccCCCHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcc
Q psy17612 5 IFFFQFKMDMMESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSD 49 (449)
Q Consensus 5 ~~~~~~~~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~ 49 (449)
+..|-.++-.-++++.+|..+|..|+|..|...+..|...-|.+.
T Consensus 32 ~~~~P~s~~a~~A~l~la~a~y~~~~y~~A~~~~~~fi~~yP~~~ 76 (203)
T PF13525_consen 32 IDRYPNSPYAPQAQLMLAYAYYKQGDYEEAIAAYERFIKLYPNSP 76 (203)
T ss_dssp HHH-TTSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-T
T ss_pred HHHCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCc
Confidence 345667788889999999999999999999999999999988543
No 104
>CHL00033 ycf3 photosystem I assembly protein Ycf3
Probab=59.01 E-value=63 Score=28.98 Aligned_cols=71 Identities=15% Similarity=0.149 Sum_probs=38.3
Q ss_pred HHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchh--hHHHHHHHH-HHhHhhcChHHHHHHHHHHHHHHhc
Q psy17612 15 MESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRH--YLAVLWGKL-ASEILVQNWDLALEDLNKLREYIDG 85 (449)
Q Consensus 15 ~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k--~ls~lwgkl-a~eIl~~dwd~a~~~l~kLke~id~ 85 (449)
..+++.+|..+...|+++.|.+++......-+..... .+..+...+ ...+..++++.|.....+..+.+.+
T Consensus 72 ~~~~~~lg~~~~~~g~~~eA~~~~~~Al~~~~~~~~~~~~la~i~~~~~~~~~~~g~~~~A~~~~~~a~~~~~~ 145 (168)
T CHL00033 72 SYILYNIGLIHTSNGEHTKALEYYFQALERNPFLPQALNNMAVICHYRGEQAIEQGDSEIAEAWFDQAAEYWKQ 145 (168)
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCcHHHHHHHHHHHHHhhHHHHHcccHHHHHHHHHHHHHHHHH
Confidence 3466777777777777777777776666554422111 011111111 1122455677777777666666665
No 105
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=58.92 E-value=19 Score=32.24 Aligned_cols=58 Identities=16% Similarity=0.097 Sum_probs=44.9
Q ss_pred HHHHHHHHHhhhhceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHHHHHcccccceecccCCEEE
Q psy17612 221 NARLMIFETFCRIHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLIRNARLDAKIDSKLGHVI 291 (449)
Q Consensus 221 naR~~ife~ycriy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rLdaKIDs~~G~V~ 291 (449)
..|.+++.....+-+.+++ ..||+.+|+|+..+++-+..|-++|=+..+=-...|...
T Consensus 10 Al~~~i~la~~~~g~~~s~-------------~~ia~~~~is~~~vrk~l~~L~~~Glv~s~~G~~GG~~l 67 (141)
T PRK11014 10 GLRALIYMASLPEGRMTSI-------------SEVTEVYGVSRNHMVKIINQLSRAGYVTAVRGKNGGIRL 67 (141)
T ss_pred HHHHHHHHhcCCCCCccCH-------------HHHHHHHCcCHHHHHHHHHHHHhCCEEEEecCCCCCeee
Confidence 4677777777777778899 999999999999999999999888866554444334333
No 106
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=58.44 E-value=15 Score=26.07 Aligned_cols=28 Identities=18% Similarity=0.070 Sum_probs=25.8
Q ss_pred hhHHhhcCCCHHHHHHHHHHHHHccccc
Q psy17612 253 QMLASKLNMGTDEAECWIVNLIRNARLD 280 (449)
Q Consensus 253 ~~LA~~Lnms~~e~E~wIVnlIr~~rLd 280 (449)
..||+.||+++.-+.+.|.+|...|.+.
T Consensus 18 ~~l~~~l~~s~~tv~~~l~~L~~~g~i~ 45 (53)
T smart00420 18 EELAELLGVSEMTIRRDLNKLEEQGLLT 45 (53)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 9999999999999999999998887664
No 107
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=58.05 E-value=26 Score=31.20 Aligned_cols=61 Identities=8% Similarity=0.064 Sum_probs=42.8
Q ss_pred HHHHHHHHhhhhceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHHHHHcccccceecccCCEEEeCCCC
Q psy17612 222 ARLMIFETFCRIHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLIRNARLDAKIDSKLGHVIMGTQP 296 (449)
Q Consensus 222 aR~~ife~ycriy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rLdaKIDs~~G~V~m~~~~ 296 (449)
+|.+++-....-.+.+++ +.||+.+++|+.++++.+..|-+.|=+..+=.. .|-....+++
T Consensus 11 l~~l~~La~~~~~~~~s~-------------~~ia~~~~ip~~~l~kil~~L~~~glv~s~~G~-~Ggy~l~~~~ 71 (135)
T TIGR02010 11 VTAMLDLALNAETGPVTL-------------ADISERQGISLSYLEQLFAKLRKAGLVKSVRGP-GGGYQLGRPA 71 (135)
T ss_pred HHHHHHHHhCCCCCcCcH-------------HHHHHHHCcCHHHHHHHHHHHHHCCceEEEeCC-CCCEeccCCH
Confidence 455555554444456888 999999999999999999999888877653333 3334444444
No 108
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=57.93 E-value=16 Score=30.88 Aligned_cols=42 Identities=17% Similarity=0.223 Sum_probs=34.7
Q ss_pred hhhceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHHHHHcccccceecc
Q psy17612 231 CRIHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLIRNARLDAKIDS 285 (449)
Q Consensus 231 criy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rLdaKIDs 285 (449)
|..=.-|++ +.++++|+|+.++++.-|-.|+.+|.|=..||-
T Consensus 60 ~~~~~Gv~v-------------~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd 101 (102)
T PF08784_consen 60 PNSEEGVHV-------------DEIAQQLGMSENEVRKALDFLSNEGHIYSTIDD 101 (102)
T ss_dssp ---TTTEEH-------------HHHHHHSTS-HHHHHHHHHHHHHTTSEEESSST
T ss_pred CCCCCcccH-------------HHHHHHhCcCHHHHHHHHHHHHhCCeEecccCC
Confidence 344457999 999999999999999999999999999888874
No 109
>PF13414 TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2PL2_B 3IEG_B 2FBN_A ....
Probab=57.82 E-value=13 Score=28.17 Aligned_cols=37 Identities=19% Similarity=0.217 Sum_probs=31.9
Q ss_pred CCHHHHHHHHHHHHHHHhcC-ChhhHHHHHHHHHhcCC
Q psy17612 10 FKMDMMESMYKLAKFRYECG-NYSITTSYLYFYLLVMP 46 (449)
Q Consensus 10 ~~~e~~d~lyk~Akf~y~~G-dY~~A~~~L~~~~~l~~ 46 (449)
++|+-...++.+|..++..| +|..|.+.+.....+-|
T Consensus 32 ~~p~~~~~~~~~g~~~~~~~~~~~~A~~~~~~al~l~P 69 (69)
T PF13414_consen 32 LDPNNAEAYYNLGLAYMKLGKDYEEAIEDFEKALKLDP 69 (69)
T ss_dssp HSTTHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHST
T ss_pred cCCCCHHHHHHHHHHHHHhCccHHHHHHHHHHHHHcCc
Confidence 46777889999999999999 79999999988776643
No 110
>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A.
Probab=57.65 E-value=82 Score=31.20 Aligned_cols=124 Identities=10% Similarity=0.088 Sum_probs=68.8
Q ss_pred ccCCCHHHHHHHHHHHHHHHhc-CChhhHHHHHHHHHhcCCCcch--hhHHHHHHHHHHhHhhcChHHHHHHHHHHHHHH
Q psy17612 7 FFQFKMDMMESMYKLAKFRYEC-GNYSITTSYLYFYLLVMPTSDR--HYLAVLWGKLASEILVQNWDLALEDLNKLREYI 83 (449)
Q Consensus 7 ~~~~~~e~~d~lyk~Akf~y~~-GdY~~A~~~L~~~~~l~~~~~~--k~ls~lwgkla~eIl~~dwd~a~~~l~kLke~i 83 (449)
..|-....-..+.++|++|-+. |+|+.|.+++..........+. ....++...-.+-+..++++.|.+-..++-...
T Consensus 106 ~~G~~~~aA~~~~~lA~~ye~~~~d~e~Ai~~Y~~A~~~y~~e~~~~~a~~~~~~~A~l~~~l~~y~~A~~~~e~~~~~~ 185 (282)
T PF14938_consen 106 EAGRFSQAAKCLKELAEIYEEQLGDYEKAIEYYQKAAELYEQEGSPHSAAECLLKAADLYARLGRYEEAIEIYEEVAKKC 185 (282)
T ss_dssp HCT-HHHHHHHHHHHHHHHCCTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTC
T ss_pred hcCcHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHh
Confidence 4455566778899999999999 9999999999887777653332 224445555555666678888877766553321
Q ss_pred hcCCCCCCChHHHHHHHHHHHHHHHHHHhc-CccchhhHHHHhcC-CchhhhHHH
Q psy17612 84 DGGSANFESPLHLLQQRTWLIHWSLFVFFN-HVKGRDLIIDMFLN-RPHYLNAIQ 136 (449)
Q Consensus 84 d~~~~~~~~pl~~l~qR~WliHwsLf~ffn-~~~g~~~~iD~F~~-~~~yl~aIq 136 (449)
..+|+..+.-|..++-=.|-.+.. -+-+....++.+.. .|+|..+-.
T Consensus 186 ------l~~~l~~~~~~~~~l~a~l~~L~~~D~v~A~~~~~~~~~~~~~F~~s~E 234 (282)
T PF14938_consen 186 ------LENNLLKYSAKEYFLKAILCHLAMGDYVAARKALERYCSQDPSFASSRE 234 (282)
T ss_dssp ------CCHCTTGHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHGTTSTTSTTSHH
T ss_pred ------hcccccchhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCCCcHH
Confidence 224444444444332122222221 22234445555553 456666544
No 111
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=57.09 E-value=18 Score=26.23 Aligned_cols=44 Identities=18% Similarity=0.291 Sum_probs=33.7
Q ss_pred HHHHHHHHhhhhceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHHHHHcccc
Q psy17612 222 ARLMIFETFCRIHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLIRNARL 279 (449)
Q Consensus 222 aR~~ife~ycriy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rL 279 (449)
.+..|+ .++.-++.++. ..+|+++|+|..-+-+-|-.|+..|-+
T Consensus 4 ~~~~Il-~~l~~~~~~t~-------------~ela~~~~is~~tv~~~l~~L~~~g~I 47 (48)
T PF13412_consen 4 TQRKIL-NYLRENPRITQ-------------KELAEKLGISRSTVNRYLKKLEEKGLI 47 (48)
T ss_dssp HHHHHH-HHHHHCTTS-H-------------HHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHH-HHHHHcCCCCH-------------HHHHHHhCCCHHHHHHHHHHHHHCcCc
Confidence 344555 45555888999 999999999999999999999887744
No 112
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=55.71 E-value=26 Score=32.80 Aligned_cols=62 Identities=10% Similarity=0.107 Sum_probs=46.0
Q ss_pred HHHHHHHHHhhhhceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHHHHHcccccceecccCCEEEeCCCC
Q psy17612 221 NARLMIFETFCRIHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLIRNARLDAKIDSKLGHVIMGTQP 296 (449)
Q Consensus 221 naR~~ife~ycriy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rLdaKIDs~~G~V~m~~~~ 296 (449)
..|.+++-.+..-.+.+++ +.||+++|+|+..+++.+..|-+.|=+...=...-| ....+++
T Consensus 10 Al~~l~~lA~~~~~~~vs~-------------~eIA~~~~ip~~~l~kIl~~L~~aGLv~s~rG~~GG-y~Lar~p 71 (164)
T PRK10857 10 AVTAMLDVALNSEAGPVPL-------------ADISERQGISLSYLEQLFSRLRKNGLVSSVRGPGGG-YLLGKDA 71 (164)
T ss_pred HHHHHHHHHhCCCCCcCcH-------------HHHHHHHCcCHHHHHHHHHHHHHCCCEEeCCCCCCC-eeccCCH
Confidence 3556666666666677999 999999999999999999999888877663333333 4445554
No 113
>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional
Probab=55.19 E-value=49 Score=36.18 Aligned_cols=71 Identities=13% Similarity=0.001 Sum_probs=54.7
Q ss_pred CCHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhh-cChHHHHHHHHHHHHH
Q psy17612 10 FKMDMMESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILV-QNWDLALEDLNKLREY 82 (449)
Q Consensus 10 ~~~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~-~dwd~a~~~l~kLke~ 82 (449)
-+|+..++.+.+|..++..|+|++|...+.....+-|++.. ....|.-+||-... ++.+.|.+.+.++-++
T Consensus 70 ~dP~~a~a~~NLG~AL~~lGryeEAIa~f~rALeL~Pd~ae--A~~A~yNLAcaya~LGr~dEAla~LrrALel 141 (453)
T PLN03098 70 ADVKTAEDAVNLGLSLFSKGRVKDALAQFETALELNPNPDE--AQAAYYNKACCHAYREEGKKAADCLRTALRD 141 (453)
T ss_pred CCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCchH--HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence 45677899999999999999999999999999988875431 22455666655444 5788998888887664
No 114
>PRK10049 pgaA outer membrane protein PgaA; Provisional
Probab=55.10 E-value=63 Score=36.80 Aligned_cols=13 Identities=15% Similarity=0.496 Sum_probs=9.4
Q ss_pred hhhccCCCchHHH
Q psy17612 168 QQESYTYKDPITE 180 (449)
Q Consensus 168 ~qE~~~Y~DpiT~ 180 (449)
+.+++-|+.|+.+
T Consensus 499 ~~~~~~ys~~~~~ 511 (765)
T PRK10049 499 DITTILYSPPLAD 511 (765)
T ss_pred cceeEEecCccCC
Confidence 5677778888753
No 115
>PF03704 BTAD: Bacterial transcriptional activator domain; InterPro: IPR005158 Found in the DNRI/REDD/AFSR family of regulators, this region of AFSR (P25941 from SWISSPROT) along with the C-terminal region is capable of independently directing actinorhodin production. It is important for the formation of secondary metabolites.; PDB: 2FF4_B 2FEZ_A.
Probab=54.88 E-value=66 Score=28.03 Aligned_cols=71 Identities=15% Similarity=0.127 Sum_probs=55.3
Q ss_pred HHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHHHHHHHhcC
Q psy17612 12 MDMMESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNKLREYIDGG 86 (449)
Q Consensus 12 ~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLke~id~~ 86 (449)
...++++.+++..+.+.|+|+.|...+......-|.+.. ..-..+.+-...++...|++--.+++..+...
T Consensus 59 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~l~~dP~~E~----~~~~lm~~~~~~g~~~~A~~~Y~~~~~~l~~e 129 (146)
T PF03704_consen 59 ELYLDALERLAEALLEAGDYEEALRLLQRALALDPYDEE----AYRLLMRALAAQGRRAEALRVYERYRRRLREE 129 (146)
T ss_dssp HHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HH----HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHhccCHHHHHHHHHHHHhcCCCCHH----HHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 345788899999999999999999999988888875432 34445667777889999999999998888864
No 116
>PRK11447 cellulose synthase subunit BcsC; Provisional
Probab=54.63 E-value=4.5e+02 Score=31.57 Aligned_cols=73 Identities=14% Similarity=0.084 Sum_probs=47.9
Q ss_pred CCHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchh-hH------HHHHHHHH---HhHhhcChHHHHHHHHHH
Q psy17612 10 FKMDMMESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRH-YL------AVLWGKLA---SEILVQNWDLALEDLNKL 79 (449)
Q Consensus 10 ~~~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k-~l------s~lwgkla---~eIl~~dwd~a~~~l~kL 79 (449)
..|+..++++.+|..++..|+|++|.+++.......+..... +. ...|..+. +.+-.++++.|.+.++++
T Consensus 298 ~~P~~~~a~~~Lg~~~~~~g~~~eA~~~l~~Al~~~p~~~~~~~~~~ll~~~~~~~~~~~g~~~~~~g~~~eA~~~~~~A 377 (1157)
T PRK11447 298 ANPKDSEALGALGQAYSQQGDRARAVAQFEKALALDPHSSNRDKWESLLKVNRYWLLIQQGDAALKANNLAQAERLYQQA 377 (1157)
T ss_pred hCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCccchhHHHHHHHhhhHHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence 456667889999999999999999999999988877643221 01 11222221 122345777777766665
Q ss_pred HHH
Q psy17612 80 REY 82 (449)
Q Consensus 80 ke~ 82 (449)
-+.
T Consensus 378 l~~ 380 (1157)
T PRK11447 378 RQV 380 (1157)
T ss_pred HHh
Confidence 543
No 117
>PRK11447 cellulose synthase subunit BcsC; Provisional
Probab=54.59 E-value=3.8e+02 Score=32.23 Aligned_cols=70 Identities=13% Similarity=0.123 Sum_probs=57.9
Q ss_pred HHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHHHHHHHhc
Q psy17612 12 MDMMESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNKLREYIDG 85 (449)
Q Consensus 12 ~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLke~id~ 85 (449)
++..+.|++-++++-..|+++.|.+.|+.+...-|++ ..++.....+....++-+.|.+.++++.+.--+
T Consensus 25 ~~~~~~Ll~q~~~~~~~~~~d~a~~~l~kl~~~~p~~----p~~~~~~~~~~l~~g~~~~A~~~l~~l~~~~P~ 94 (1157)
T PRK11447 25 PTAQQQLLEQVRLGEATHREDLVRQSLYRLELIDPNN----PDVIAARFRLLLRQGDSDGAQKLLDRLSQLAPD 94 (1157)
T ss_pred CCHHHHHHHHHHHHHhhCChHHHHHHHHHHHccCCCC----HHHHHHHHHHHHhCCCHHHHHHHHHHHHhhCCC
Confidence 4567789999999999999999999999888887643 346677777778889999999999999775443
No 118
>PF13512 TPR_18: Tetratricopeptide repeat
Probab=53.86 E-value=87 Score=29.06 Aligned_cols=70 Identities=14% Similarity=0.070 Sum_probs=53.7
Q ss_pred HHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHHHHHHHhc
Q psy17612 15 MESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNKLREYIDG 85 (449)
Q Consensus 15 ~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLke~id~ 85 (449)
-..||.-|.--++.|+|..|.+.|..+..--|...-..-..||-.+ +=....+++.|.....+.-++--+
T Consensus 10 ~~~ly~~a~~~l~~~~Y~~A~~~le~L~~ryP~g~ya~qAqL~l~y-ayy~~~~y~~A~a~~~rFirLhP~ 79 (142)
T PF13512_consen 10 PQELYQEAQEALQKGNYEEAIKQLEALDTRYPFGEYAEQAQLDLAY-AYYKQGDYEEAIAAYDRFIRLHPT 79 (142)
T ss_pred HHHHHHHHHHHHHhCCHHHHHHHHHHHHhcCCCCcccHHHHHHHHH-HHHHccCHHHHHHHHHHHHHhCCC
Confidence 4679999999999999999999999999988854433233444444 366778999999988887766554
No 119
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=53.76 E-value=56 Score=24.15 Aligned_cols=40 Identities=10% Similarity=0.155 Sum_probs=32.5
Q ss_pred hhHHhhcCCCHHHHHHHHHHHHHcccccceecccCCEEEe
Q psy17612 253 QMLASKLNMGTDEAECWIVNLIRNARLDAKIDSKLGHVIM 292 (449)
Q Consensus 253 ~~LA~~Lnms~~e~E~wIVnlIr~~rLdaKIDs~~G~V~m 292 (449)
+.+|+.+|++...+.+.+-.|...|-+.+.-+...+....
T Consensus 24 ~ei~~~~~i~~~~i~~~l~~L~~~g~i~~~~~~~~~~~~~ 63 (78)
T cd00090 24 SELAERLGLSQSTVSRHLKKLEEAGLVESRREGRRVYYSL 63 (78)
T ss_pred HHHHHHHCcCHhHHHHHHHHHHHCCCeEEEEeccEEEEEe
Confidence 9999999999999999999999999887765553344333
No 120
>PRK10866 outer membrane biogenesis protein BamD; Provisional
Probab=53.56 E-value=69 Score=31.48 Aligned_cols=71 Identities=13% Similarity=0.057 Sum_probs=53.7
Q ss_pred HHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHHHHHHHhc
Q psy17612 14 MMESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNKLREYIDG 85 (449)
Q Consensus 14 ~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLke~id~ 85 (449)
..+.+|..|.-.++.|+|+.|.+.+..+...-|.+... ..+....--+-....+++.|....++.-+...+
T Consensus 31 ~~~~~Y~~A~~~~~~g~y~~Ai~~f~~l~~~yP~s~~a-~~a~l~la~ayy~~~~y~~A~~~~e~fi~~~P~ 101 (243)
T PRK10866 31 PPSEIYATAQQKLQDGNWKQAITQLEALDNRYPFGPYS-QQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPT 101 (243)
T ss_pred CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCChHH-HHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCcC
Confidence 45679999999999999999999999999988865433 344444444566678899998877776554443
No 121
>CHL00033 ycf3 photosystem I assembly protein Ycf3
Probab=53.37 E-value=1.1e+02 Score=27.31 Aligned_cols=72 Identities=11% Similarity=-0.052 Sum_probs=49.0
Q ss_pred CCCHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHH-HHhHhhcChHHHHHHHHHHHHH
Q psy17612 9 QFKMDMMESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKL-ASEILVQNWDLALEDLNKLREY 82 (449)
Q Consensus 9 ~~~~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkl-a~eIl~~dwd~a~~~l~kLke~ 82 (449)
.-.......++..|..+...|+|+.|...+.......++.... . ..|..+ .+-...++.+.|.+...++-++
T Consensus 29 ~~~~~~a~~~~~~g~~~~~~g~~~~A~~~~~~al~l~~~~~~~-~-~~~~~lg~~~~~~g~~~eA~~~~~~Al~~ 101 (168)
T CHL00033 29 TSGEKEAFTYYRDGMSAQSEGEYAEALQNYYEAMRLEIDPYDR-S-YILYNIGLIHTSNGEHTKALEYYFQALER 101 (168)
T ss_pred CchhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhccccchhh-H-HHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence 3344557778999999999999999999999888776532111 2 233333 3334456788888877766553
No 122
>COG1849 Uncharacterized protein conserved in archaea [Function unknown]
Probab=52.23 E-value=25 Score=30.42 Aligned_cols=34 Identities=29% Similarity=0.367 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcC
Q psy17612 12 MDMMESMYKLAKFRYECGNYSITTSYLYFYLLVM 45 (449)
Q Consensus 12 ~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~ 45 (449)
.++..+.++=|++|++.|||..|..++...+.+.
T Consensus 38 ~~ma~~Y~~Dakyf~ekGD~vtAfa~~sYa~g~l 71 (90)
T COG1849 38 VDMAESYFEDAKYFLEKGDYVTAFAALSYAHGWL 71 (90)
T ss_pred HHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHH
Confidence 4678889999999999999999999887766654
No 123
>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A.
Probab=51.61 E-value=15 Score=29.21 Aligned_cols=33 Identities=18% Similarity=0.196 Sum_probs=26.7
Q ss_pred cCCCHHHHHHHHHHHHHHHhcCChhhHHHHHHH
Q psy17612 8 FQFKMDMMESMYKLAKFRYECGNYSITTSYLYF 40 (449)
Q Consensus 8 ~~~~~e~~d~lyk~Akf~y~~GdY~~A~~~L~~ 40 (449)
.++++...+..+-+|+.+++.|+|++|.++|..
T Consensus 51 ~~~~~~~~~~~~l~a~~~~~l~~y~eAi~~l~~ 83 (84)
T PF12895_consen 51 LKLDPSNPDIHYLLARCLLKLGKYEEAIKALEK 83 (84)
T ss_dssp HTHHHCHHHHHHHHHHHHHHTT-HHHHHHHHHH
T ss_pred hCCCCCCHHHHHHHHHHHHHhCCHHHHHHHHhc
Confidence 345566678888889999999999999999875
No 124
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=51.20 E-value=36 Score=33.76 Aligned_cols=60 Identities=12% Similarity=0.045 Sum_probs=48.6
Q ss_pred HHHHHHHHHhhhhceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHHHHHcccccceecccCCEEEeCCCCC
Q psy17612 221 NARLMIFETFCRIHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLIRNARLDAKIDSKLGHVIMGTQPL 297 (449)
Q Consensus 221 naR~~ife~ycriy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rLdaKIDs~~G~V~m~~~~~ 297 (449)
.-|+.....+++-+..|++ +.||+.||||+.=+-|.|..|=..|.| -.+-|-+....++.
T Consensus 4 ~eR~~~Il~~l~~~g~v~v-------------~eLa~~~~VS~~TIRRDL~~Le~~g~l----~R~hGGa~~~~~~~ 63 (253)
T COG1349 4 EERHQKILELLKEKGKVSV-------------EELAELFGVSEMTIRRDLNELEEQGLL----LRVHGGAVLPDSES 63 (253)
T ss_pred HHHHHHHHHHHHHcCcEEH-------------HHHHHHhCCCHHHHHHhHHHHHHCCcE----EEEeCCEecCCCcc
Confidence 3488899999999999999 999999999999999999998776644 45555555555443
No 125
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=50.24 E-value=19 Score=34.07 Aligned_cols=46 Identities=13% Similarity=0.037 Sum_probs=40.4
Q ss_pred HHHHHHHHHhhhhceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHHHHHcccc
Q psy17612 221 NARLMIFETFCRIHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLIRNARL 279 (449)
Q Consensus 221 naR~~ife~ycriy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rL 279 (449)
.-|......+++-++.+++ +.||+.||+|++=+-+.|..|-..|.+
T Consensus 6 ~~R~~~Il~~l~~~~~~~~-------------~~La~~~~vS~~TiRRDl~~L~~~g~~ 51 (185)
T PRK04424 6 KERQKALQELIEENPFITD-------------EELAEKFGVSIQTIRLDRMELGIPELR 51 (185)
T ss_pred HHHHHHHHHHHHHCCCEEH-------------HHHHHHHCcCHHHHHHHHHHHhcchHH
Confidence 3488888999999999999 999999999999999999988665544
No 126
>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional
Probab=50.22 E-value=66 Score=33.30 Aligned_cols=63 Identities=16% Similarity=0.192 Sum_probs=49.5
Q ss_pred HHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHHHHHH
Q psy17612 16 ESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNKLREY 82 (449)
Q Consensus 16 d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLke~ 82 (449)
..|.+.|.-.+..|+|..|.+++.......+.. ..++..+-.+-+..++++.|..++.++-++
T Consensus 3 ~~l~~~a~~a~~~~~~~~Ai~~~~~Al~~~P~~----~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l 65 (356)
T PLN03088 3 KDLEDKAKEAFVDDDFALAVDLYTQAIDLDPNN----AELYADRAQANIKLGNFTEAVADANKAIEL 65 (356)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCC----HHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence 458889999999999999999999998887743 234455555566678999999998887654
No 127
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=50.19 E-value=29 Score=25.95 Aligned_cols=47 Identities=17% Similarity=0.131 Sum_probs=38.9
Q ss_pred HhhhhceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHHHHHcccccceecccCC
Q psy17612 229 TFCRIHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLIRNARLDAKIDSKLG 288 (449)
Q Consensus 229 ~ycriy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rLdaKIDs~~G 288 (449)
.++.-++.+++ ..||+.+++++.-+=+.+-+|+..|-+.-..|+..+
T Consensus 10 ~~l~~~~~~~~-------------~~la~~~~~~~~~~t~~i~~L~~~g~I~r~~~~~D~ 56 (59)
T PF01047_consen 10 RILYENGGITQ-------------SELAEKLGISRSTVTRIIKRLEKKGLIERERDPDDR 56 (59)
T ss_dssp HHHHHHSSEEH-------------HHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTET
T ss_pred HHHHHcCCCCH-------------HHHHHHHCCChhHHHHHHHHHHHCCCEEeccCCCCC
Confidence 34556788999 999999999999999999999999988777766543
No 128
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=49.62 E-value=30 Score=25.76 Aligned_cols=27 Identities=15% Similarity=0.134 Sum_probs=24.8
Q ss_pred hhHHhhcCCCHHHHHHHHHHHHHcccc
Q psy17612 253 QMLASKLNMGTDEAECWIVNLIRNARL 279 (449)
Q Consensus 253 ~~LA~~Lnms~~e~E~wIVnlIr~~rL 279 (449)
..||+.+|+|..-+.+.|..|-..|=+
T Consensus 29 ~~la~~~~is~~~v~~~l~~L~~~G~i 55 (66)
T cd07377 29 RELAEELGVSRTTVREALRELEAEGLV 55 (66)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCE
Confidence 899999999999999999999887754
No 129
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=49.61 E-value=7.9 Score=30.69 Aligned_cols=38 Identities=21% Similarity=0.408 Sum_probs=28.5
Q ss_pred hhHHH-HHHhhcCCChHHHHHHHHHHhhhcccccccccCC
Q psy17612 353 NVITI-MLASKLNMGTDEAECWIVNLIRNARLDAKIDSKL 391 (449)
Q Consensus 353 ~~~~~-~la~kLnm~~~eaE~WIvnLIr~~~ldAKIDs~~ 391 (449)
+.+|. +||..||++++..|-=|.-|||.+++. |++...
T Consensus 13 ~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~-~~~~~~ 51 (69)
T PF09012_consen 13 GRVSLAELAREFGISPEAVEAMLEQLIRKGYIR-KVDMSS 51 (69)
T ss_dssp -SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCE-EEEEE-
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEE-EecCCC
Confidence 44555 889999999999999999999999997 555443
No 130
>TIGR00990 3a0801s09 mitochondrial precursor proteins import receptor (72 kDa mitochondrial outermembrane protein) (mitochondrial import receptor for the ADP/ATP carrier) (translocase of outermembrane tom70).
Probab=49.34 E-value=3.9e+02 Score=29.32 Aligned_cols=68 Identities=13% Similarity=0.051 Sum_probs=46.5
Q ss_pred CCHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHHHHH
Q psy17612 10 FKMDMMESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNKLRE 81 (449)
Q Consensus 10 ~~~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLke 81 (449)
..+....+++.+|.+++..|+|+.|.+.+.....+.|.... .....-.+-...++++.|.+.+.++-+
T Consensus 326 ~~~~~a~a~~~lg~~~~~~g~~~eA~~~~~kal~l~P~~~~----~~~~la~~~~~~g~~~eA~~~~~~al~ 393 (615)
T TIGR00990 326 LGEKEAIALNLRGTFKCLKGKHLEALADLSKSIELDPRVTQ----SYIKRASMNLELGDPDKAEEDFDKALK 393 (615)
T ss_pred CChhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCcHH----HHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 35667778889999999999999999999888877653221 222222222345688888888777643
No 131
>PRK10370 formate-dependent nitrite reductase complex subunit NrfG; Provisional
Probab=49.31 E-value=36 Score=32.23 Aligned_cols=74 Identities=16% Similarity=0.124 Sum_probs=54.1
Q ss_pred CCCHHHHHHHHHHHHH-HHhcCC--hhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHHHHHHHhc
Q psy17612 9 QFKMDMMESMYKLAKF-RYECGN--YSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNKLREYIDG 85 (449)
Q Consensus 9 ~~~~e~~d~lyk~Akf-~y~~Gd--Y~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLke~id~ 85 (449)
.+.|+..+.++.+|.. ++..|+ ++.|.+.+......-+++ .. +++..=.+....++++.|....+++-++...
T Consensus 101 ~l~P~~~~~~~~lA~aL~~~~g~~~~~~A~~~l~~al~~dP~~-~~---al~~LA~~~~~~g~~~~Ai~~~~~aL~l~~~ 176 (198)
T PRK10370 101 QLRGENAELYAALATVLYYQAGQHMTPQTREMIDKALALDANE-VT---ALMLLASDAFMQADYAQAIELWQKVLDLNSP 176 (198)
T ss_pred HhCCCCHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHhCCCC-hh---HHHHHHHHHHHcCCHHHHHHHHHHHHhhCCC
Confidence 4667788889999995 578888 599999999888887743 22 3333333344578999999999998887766
Q ss_pred C
Q psy17612 86 G 86 (449)
Q Consensus 86 ~ 86 (449)
+
T Consensus 177 ~ 177 (198)
T PRK10370 177 R 177 (198)
T ss_pred C
Confidence 3
No 132
>KOG2753|consensus
Probab=48.98 E-value=12 Score=39.54 Aligned_cols=58 Identities=29% Similarity=0.473 Sum_probs=46.0
Q ss_pred HHHhhcCCChHHHHHHHHHHhhhcccccccccCCCeEEecCCC-----CChhHHHHHhhhccc
Q psy17612 358 MLASKLNMGTDEAECWIVNLIRNARLDAKIDSKLGHVIMGTQP-----LSPYQQLLEKIDTLS 415 (449)
Q Consensus 358 ~la~kLnm~~~eaE~WIvnLIr~~~ldAKIDs~~~~v~m~~~~-----~svyqqviektk~l~ 415 (449)
.|++.|-.+.||.|-||+..||-.-..+|||--.-+|++++.. .--.||+-+|.+...
T Consensus 299 ~l~k~LqI~edeVE~fVIdaI~aklV~~kidq~~~~viVs~~~hR~FG~~qW~~L~~kL~aw~ 361 (378)
T KOG2753|consen 299 TLAKELQINEDEVELFVIDAIRAKLVEGKIDQMNRTVIVSSSTHRTFGKQQWQQLRDKLAAWG 361 (378)
T ss_pred HHHHHhccCHHHHHHHHHHHHHHHHHHhhHHhhcceEEeehhhhhhcccHHHHHHHHHHHHHH
Confidence 4599999999999999999999988899999888888886542 123566777666553
No 133
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=48.73 E-value=45 Score=30.68 Aligned_cols=73 Identities=10% Similarity=0.064 Sum_probs=48.3
Q ss_pred HHHHHHHHHhhhhceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHHHHHcccccceecccCCEEEeCCCCC-Ch
Q psy17612 221 NARLMIFETFCRIHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLIRNARLDAKIDSKLGHVIMGTQPL-SP 299 (449)
Q Consensus 221 naR~~ife~ycriy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rLdaKIDs~~G~V~m~~~~~-s~ 299 (449)
.+|.+++-... ....+++ +.||++.|+|+.++++.+..|.+.|=+..+=-. +|=....+++. -.
T Consensus 10 Alr~L~~LA~~-~~~~~s~-------------~eIA~~~~is~~~L~kIl~~L~~aGlv~S~rG~-~GGy~La~~p~eIt 74 (153)
T PRK11920 10 AIRMLMYCAAN-DGKLSRI-------------PEIARAYGVSELFLFKILQPLVEAGLVETVRGR-NGGVRLGRPAADIS 74 (153)
T ss_pred HHHHHHHHHhC-CCCcCcH-------------HHHHHHHCcCHHHHHHHHHHHHHCCCEEeecCC-CCCeeecCCHHHCc
Confidence 45666666533 3445788 999999999999999999999998877655543 33444555542 12
Q ss_pred HHHHHHhhh
Q psy17612 300 YQQLLEKID 308 (449)
Q Consensus 300 Yqqviek~d 308 (449)
-.+|++..+
T Consensus 75 l~dIi~ave 83 (153)
T PRK11920 75 LFDVVRVTE 83 (153)
T ss_pred HHHHHHHHc
Confidence 234444443
No 134
>KOG1840|consensus
Probab=48.27 E-value=73 Score=35.25 Aligned_cols=75 Identities=17% Similarity=0.110 Sum_probs=59.7
Q ss_pred CHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCC----CcchhhHHHHHHHHHHhHhhcChHHHHHHHHHHHHHHhc
Q psy17612 11 KMDMMESMYKLAKFRYECGNYSITTSYLYFYLLVMP----TSDRHYLAVLWGKLASEILVQNWDLALEDLNKLREYIDG 85 (449)
Q Consensus 11 ~~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~----~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLke~id~ 85 (449)
.|.+...|-.+|..|+..|.|..|..++........ ..+....+.+-...+..=.+...+.|.+.+.++-++|.+
T Consensus 279 h~~va~~l~nLa~ly~~~GKf~EA~~~~e~Al~I~~~~~~~~~~~v~~~l~~~~~~~~~~~~~Eea~~l~q~al~i~~~ 357 (508)
T KOG1840|consen 279 HPAVAATLNNLAVLYYKQGKFAEAEEYCERALEIYEKLLGASHPEVAAQLSELAAILQSMNEYEEAKKLLQKALKIYLD 357 (508)
T ss_pred CHHHHHHHHHHHHHHhccCChHHHHHHHHHHHHHHHHhhccChHHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHh
Confidence 466777888999999999999999998877555432 344555667777777777788899999999999999985
No 135
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=48.20 E-value=21 Score=28.42 Aligned_cols=28 Identities=18% Similarity=0.239 Sum_probs=26.2
Q ss_pred hhHHhhcCCCHHHHHHHHHHHHHccccc
Q psy17612 253 QMLASKLNMGTDEAECWIVNLIRNARLD 280 (449)
Q Consensus 253 ~~LA~~Lnms~~e~E~wIVnlIr~~rLd 280 (449)
..||++||++...+.+-|.+|...|.+.
T Consensus 26 ~eLa~~lgl~~~~v~r~L~~L~~~G~V~ 53 (68)
T smart00550 26 LQLAKNLGLPKKEVNRVLYSLEKKGKVC 53 (68)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 9999999999999999999999988764
No 136
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=48.12 E-value=34 Score=33.70 Aligned_cols=41 Identities=7% Similarity=-0.028 Sum_probs=37.2
Q ss_pred HHHHHHHHHHhhhhceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHHH
Q psy17612 220 ENARLMIFETFCRIHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNL 273 (449)
Q Consensus 220 enaR~~ife~ycriy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnl 273 (449)
.+-|....-.+++-|..|++ +.||+.||||++=+-|.|-.|
T Consensus 5 ~~eR~~~I~~~l~~~~~v~v-------------~eLa~~~~VS~~TIRRDL~~L 45 (252)
T PRK10681 5 RDERIGQLLQALKRSDKLHL-------------KDAAALLGVSEMTIRRDLNAH 45 (252)
T ss_pred HHHHHHHHHHHHHHcCCCcH-------------HHHHHHhCCCHHHHHHHHHHh
Confidence 34588888999999999999 999999999999999999875
No 137
>PF13518 HTH_28: Helix-turn-helix domain
Probab=48.06 E-value=34 Score=24.72 Aligned_cols=30 Identities=10% Similarity=0.267 Sum_probs=24.9
Q ss_pred hhHHhhcCCCHHHHHHHHHHHHHccccccee
Q psy17612 253 QMLASKLNMGTDEAECWIVNLIRNARLDAKI 283 (449)
Q Consensus 253 ~~LA~~Lnms~~e~E~wIVnlIr~~rLdaKI 283 (449)
..+|..||||+.-+.+|+-.+=..| +++-.
T Consensus 16 ~~~a~~~gis~~tv~~w~~~y~~~G-~~~l~ 45 (52)
T PF13518_consen 16 REIAREFGISRSTVYRWIKRYREGG-IEGLK 45 (52)
T ss_pred HHHHHHHCCCHhHHHHHHHHHHhcC-HHHhc
Confidence 9999999999999999999986655 44433
No 138
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=46.76 E-value=36 Score=33.76 Aligned_cols=46 Identities=9% Similarity=0.144 Sum_probs=40.8
Q ss_pred HHHHHHHHHhhhhceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHHHHHcccc
Q psy17612 221 NARLMIFETFCRIHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLIRNARL 279 (449)
Q Consensus 221 naR~~ife~ycriy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rL 279 (449)
.-|....-.+++-++.+++ ..||+.||||++-+-|.|..|-..|.|
T Consensus 4 ~~R~~~Il~~l~~~~~~~~-------------~ela~~l~vS~~TiRRdL~~Le~~g~l 49 (252)
T PRK10906 4 TQRHDAIIELVKQQGYVST-------------EELVEHFSVSPQTIRRDLNDLAEQNKI 49 (252)
T ss_pred HHHHHHHHHHHHHcCCEeH-------------HHHHHHhCCCHHHHHHHHHHHHHCCCE
Confidence 3477777778899999999 999999999999999999999888765
No 139
>KOG4414|consensus
Probab=46.71 E-value=28 Score=33.04 Aligned_cols=45 Identities=20% Similarity=0.240 Sum_probs=38.9
Q ss_pred HHHHHHHHHHHHHHHhhhhceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHH
Q psy17612 215 LDEFVENARLMIFETFCRIHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVN 272 (449)
Q Consensus 215 ~d~fvenaR~~ife~ycriy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVn 272 (449)
...|-..-|..+|.-.+..|++|.+ +.+|-.+||++|++-+-|+.
T Consensus 111 maAf~D~~~kR~FaLl~qAYssI~~-------------~D~A~FlGl~~ddAtk~ilE 155 (197)
T KOG4414|consen 111 MAAFRDATRKRAFALLLQAYSSIIA-------------DDFAAFLGLPEDDATKGILE 155 (197)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH-------------HHHHHHhCCCHHHHHHHHHH
Confidence 4456667788899999999999999 99999999999998887764
No 140
>PF11972 HTH_13: HTH DNA binding domain; InterPro: IPR021068 The proteins in this entry have not been characterised. They contain a C-terminal helix-turn-helix DNA binding domain.
Probab=46.43 E-value=25 Score=27.68 Aligned_cols=32 Identities=22% Similarity=0.268 Sum_probs=27.3
Q ss_pred HhhhhceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHHH
Q psy17612 229 TFCRIHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNL 273 (449)
Q Consensus 229 ~ycriy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnl 273 (449)
..+-.++-||. .|+|+.||+|+.-+.+++..|
T Consensus 6 dll~~~P~Vsa-------------~mva~~L~vT~~~A~~li~eL 37 (54)
T PF11972_consen 6 DLLLSRPLVSA-------------PMVAKELGVTPQAAQRLIAEL 37 (54)
T ss_pred HHHHhCccccH-------------HHHHHHhCCCHHHHHHHHHHh
Confidence 45566788888 999999999999999988765
No 141
>KOG1463|consensus
Probab=46.41 E-value=49 Score=35.27 Aligned_cols=73 Identities=16% Similarity=0.299 Sum_probs=58.7
Q ss_pred hHHhhhhc-----hhhhHHH-HHHhhcCCChHHHHHHHHHHhhhcccccccccCCCeEEecCC--CCChhHHHHHhhhcc
Q psy17612 343 KEMLASKA-----DLNVITI-MLASKLNMGTDEAECWIVNLIRNARLDAKIDSKLGHVIMGTQ--PLSPYQQLLEKIDTL 414 (449)
Q Consensus 343 ~~~~~~~~-----~~~~~~~-~la~kLnm~~~eaE~WIvnLIr~~~ldAKIDs~~~~v~m~~~--~~svyqqviektk~l 414 (449)
+++++.|+ ..-+|-+ -+|+-+||+....|+=+...|-+-++..-+|--+|++++... +.+.|+..+|-.+++
T Consensus 329 d~lLEknl~riIEPyS~Vei~hIA~~IGl~~~~VEkKLsqMILDKkf~G~LDQg~g~Liv~~e~~~d~~y~~aLetI~~m 408 (411)
T KOG1463|consen 329 DNLLEKNLCRIIEPYSRVEISHIAEVIGLDVPQVEKKLSQMILDKKFYGTLDQGEGCLIVFEEPPADNTYDAALETIQNM 408 (411)
T ss_pred HHHHHHhHHHHcCchhhhhHHHHHHHHCCCcHHHHHHHHHHHHHHHhhcccccCCCeEEEeCCCCcchHHHHHHHHHHhc
Confidence 46666665 3344444 779999999999999999999999999999999999999654 457888888877665
Q ss_pred c
Q psy17612 415 S 415 (449)
Q Consensus 415 ~ 415 (449)
+
T Consensus 409 ~ 409 (411)
T KOG1463|consen 409 G 409 (411)
T ss_pred c
Confidence 3
No 142
>PF03374 ANT: Phage antirepressor protein KilAC domain; InterPro: IPR005039 This entry is represented by Bacteriophage P1, Ant1 C-terminal domain, which represents the processed Ant2 chain. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Prophages P1 and P7 exist as unit copy DNA plasmids in the bacterial cell. Maintenance of the prophage state requires the continuous expression of two repressors: (i) C1 is a protein which negatively regulates the expression of lytic genes including the C1 inactivator gene coi, and (ii) C4 is an antisense RNA which specifically inhibits the synthesis of an anti-repressor Ant.; GO: 0003677 DNA binding
Probab=46.31 E-value=32 Score=29.29 Aligned_cols=58 Identities=19% Similarity=0.334 Sum_probs=44.7
Q ss_pred HHHHHHhhhhceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHHHHHcccccceecccCCEEEe-CCCCCChHHH
Q psy17612 224 LMIFETFCRIHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLIRNARLDAKIDSKLGHVIM-GTQPLSPYQQ 302 (449)
Q Consensus 224 ~~ife~ycriy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rLdaKIDs~~G~V~m-~~~~~s~Yqq 302 (449)
.-++++|...-.++++ ...|+.|||++...=.||.. .|.+.- ....+.|||+
T Consensus 12 a~~~d~~~~~~~~~ti-------------~~~AK~L~i~~~~l~~~Lr~--------------~g~l~~~~~~~~~p~q~ 64 (111)
T PF03374_consen 12 AEFYDAFVDSDGLYTI-------------REAAKLLGIGRNKLFQWLRE--------------KGWLYRRGKGRNLPYQK 64 (111)
T ss_pred hHHHHHHHcCCCCccH-------------HHHHHHhCCCHHHHHHHHHh--------------CCceEECCCCCcccChh
Confidence 3567888888899999 99999999999988888765 344544 2335788888
Q ss_pred HHHhhh
Q psy17612 303 LLEKID 308 (449)
Q Consensus 303 viek~d 308 (449)
.+++|-
T Consensus 65 ~~~~G~ 70 (111)
T PF03374_consen 65 YIDAGY 70 (111)
T ss_pred hhccce
Confidence 887754
No 143
>PF07720 TPR_3: Tetratricopeptide repeat; InterPro: IPR011716 This entry includes tetratricopeptide-like repeats found in the LcrH/SycD-like chaperones [].; PDB: 3KS2_O 3GZ2_A 3GZ1_A 3GYZ_A 4AM9_A 2VGX_A 2VGY_A.
Probab=46.25 E-value=46 Score=23.70 Aligned_cols=25 Identities=28% Similarity=0.424 Sum_probs=21.1
Q ss_pred HHHHHHHHHHHHhcCChhhHHHHHH
Q psy17612 15 MESMYKLAKFRYECGNYSITTSYLY 39 (449)
Q Consensus 15 ~d~lyk~Akf~y~~GdY~~A~~~L~ 39 (449)
.|.++.+|-.+|..|+|++|.+++.
T Consensus 1 ~e~~y~~a~~~y~~~ky~~A~~~~~ 25 (36)
T PF07720_consen 1 PEYLYGLAYNFYQKGKYDEAIHFFQ 25 (36)
T ss_dssp HHHHHHHHHHHHHTT-HHHHHHHHH
T ss_pred CcHHHHHHHHHHHHhhHHHHHHHHH
Confidence 3678999999999999999999854
No 144
>PLN03083 E3 UFM1-protein ligase 1 homolog; Provisional
Probab=45.99 E-value=2.2e+02 Score=33.40 Aligned_cols=174 Identities=14% Similarity=0.221 Sum_probs=0.0
Q ss_pred hHHHHHHHHhhcccHHHHHHHHHHHhhhcccccch---------HHhHHHHHHHHHHHHHHHhhhhceeeEeeccccccc
Q psy17612 177 PITEFLEHLYVSFDFESAREKLTECTEVLDNDFFL---------VACLDEFVENARLMIFETFCRIHQCISIQKESNVID 247 (449)
Q Consensus 177 piT~fv~~lYv~fdf~~aq~~L~~~~~vl~~DfFL---------~~~~d~fvenaR~~ife~ycriy~~IsI~~~~~~~~ 247 (449)
+++++=..|=|+|+ .+=+.++.++..|+=+ ..|++-..+++ ..-++=--.|+|
T Consensus 76 nlvdLa~~LnVD~~-----hiEr~~~~iv~~d~~~~l~~GeLit~~Yld~iaeEI-----ne~LqE~G~isI-------- 137 (803)
T PLN03083 76 SLVDLADTIGVDLY-----HVERQAQQVVSDDPGLMLVQGEIISQSYWDSIAEEI-----NERLQECSQIAL-------- 137 (803)
T ss_pred eHHHHhhhcCCCHH-----HHHHHHHHHhcCCCceEEecCEecchHHHHHHHHHH-----HHHHHHcCcChH--------
Q ss_pred cccchhhHHhhcCCCHHHHHHHHHHHHHcccccceecccCCEEEeC------------------CCCC-----ChHHHHH
Q psy17612 248 KIFDGQMLASKLNMGTDEAECWIVNLIRNARLDAKIDSKLGHVIMG------------------TQPL-----SPYQQLL 304 (449)
Q Consensus 248 ~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rLdaKIDs~~G~V~m~------------------~~~~-----s~Yqqvi 304 (449)
..||++|+++.|++-..|..- ..+.++|++ ..|.+.+. +|.+ +.|||.+
T Consensus 138 -----~eLa~~~~Lpsefl~~~l~~r-lG~iI~g~~--~g~~lyT~aYv~r~~a~vRG~l~AiT~Pt~~s~l~~~~q~~l 209 (803)
T PLN03083 138 -----AELARQLQVGSELVTSMLEPR-LGTIVKARL--EGGQLYTPAYVARVTAMVRGAARGITVPTNLSSLWNSLQQLL 209 (803)
T ss_pred -----HHHHHhcCChHHHHHHHHHHH-hccceEEEe--cCCEEecHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHhh
Q ss_pred Hhhhhh---hhHHHHHHHHHHHHHhhhcCCCCCCCCCccch-----------hHHhhhhchhhhHHHHHHhhcCCChHHH
Q psy17612 305 EKIDTL---SVRSEALQALIERKVKVRNNSANAGGENSWAS-----------KEMLASKADLNVITIMLASKLNMGTDEA 370 (449)
Q Consensus 305 ek~d~L---~~R~q~L~~~i~~~~~~~~~~~~~~~~~~~~~-----------~~~~~~~~~~~~~~~~la~kLnm~~~ea 370 (449)
.-.+.. ..+-+.....++..++...-...-.+...|.+ .+|+..|--+.+- ..+|||.+ ++
T Consensus 210 ~~~~~~~~v~~~~~lf~~~l~~Li~~~~l~G~~~~~~~yvP~vy~~~Q~~~V~sfy~QNgyIeyd---~l~kLgIs--dp 284 (803)
T PLN03083 210 REMDGAGGVTVEGSFFQSIFNGLVKEEEVLGSLRAGTHWTPAVFAHAQKESVDAFFSQNSYITYD---TLQKLGIS--QP 284 (803)
T ss_pred ccccccccccchHHHHHHHHHHHHhcCcccceeecCcEEccHHHHHHHHHHHHHHHHhcCcEeHH---HHHHhCCC--ch
Q ss_pred HHHHHHHhhhc
Q psy17612 371 ECWIVNLIRNA 381 (449)
Q Consensus 371 E~WIvnLIr~~ 381 (449)
...|-+...++
T Consensus 285 k~~l~~~~~~~ 295 (803)
T PLN03083 285 KQFLQSRYPDG 295 (803)
T ss_pred HHHHHHhCcCC
No 145
>COG4105 ComL DNA uptake lipoprotein [General function prediction only]
Probab=45.06 E-value=76 Score=32.24 Aligned_cols=78 Identities=14% Similarity=0.201 Sum_probs=55.8
Q ss_pred eccCCCHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHH-hHh-----hcChHHHHHHHHHH
Q psy17612 6 FFFQFKMDMMESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLAS-EIL-----VQNWDLALEDLNKL 79 (449)
Q Consensus 6 ~~~~~~~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~-eIl-----~~dwd~a~~~l~kL 79 (449)
..|-+++-.-.+++.+|.-+|+.|+|+.|..++..|..+-|+. ++ .+-+.-...+ -.. ..|-..+.+-+..+
T Consensus 62 ~~~p~s~~~~qa~l~l~yA~Yk~~~y~~A~~~~drFi~lyP~~-~n-~dY~~YlkgLs~~~~i~~~~rDq~~~~~A~~~f 139 (254)
T COG4105 62 SRHPFSPYSEQAQLDLAYAYYKNGEYDLALAYIDRFIRLYPTH-PN-ADYAYYLKGLSYFFQIDDVTRDQSAARAAFAAF 139 (254)
T ss_pred HcCCCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHhCCCC-CC-hhHHHHHHHHHHhccCCccccCHHHHHHHHHHH
Confidence 5688899999999999999999999999999999999998853 33 2222211111 111 13445566677888
Q ss_pred HHHHhc
Q psy17612 80 REYIDG 85 (449)
Q Consensus 80 ke~id~ 85 (449)
++++++
T Consensus 140 ~~~i~r 145 (254)
T COG4105 140 KELVQR 145 (254)
T ss_pred HHHHHH
Confidence 888876
No 146
>PF07721 TPR_4: Tetratricopeptide repeat; InterPro: IPR011717 This entry includes tetratricopeptide-like repeats not detected by the IPR001440 from INTERPRO, IPR013105 from INTERPRO and IPR011716 from INTERPRO models. The tetratricopeptide repeat (TPR) motif is a protein-protein interaction module found in multiple copies in a number of functionally different proteins that facilitates specific interactions with a partner protein(s) [].; GO: 0042802 identical protein binding
Probab=45.04 E-value=31 Score=22.22 Aligned_cols=23 Identities=17% Similarity=0.106 Sum_probs=20.2
Q ss_pred HHHHHHHHHHhcCChhhHHHHHH
Q psy17612 17 SMYKLAKFRYECGNYSITTSYLY 39 (449)
Q Consensus 17 ~lyk~Akf~y~~GdY~~A~~~L~ 39 (449)
+.+.+|..++..|+.+.|...+.
T Consensus 3 a~~~la~~~~~~G~~~eA~~~l~ 25 (26)
T PF07721_consen 3 ARLALARALLAQGDPDEAERLLR 25 (26)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHh
Confidence 56789999999999999998764
No 147
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=45.01 E-value=34 Score=33.90 Aligned_cols=46 Identities=13% Similarity=0.068 Sum_probs=41.5
Q ss_pred HHHHHHHHHhhhhceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHHHHHcccc
Q psy17612 221 NARLMIFETFCRIHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLIRNARL 279 (449)
Q Consensus 221 naR~~ife~ycriy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rL 279 (449)
+-|....-.+++-+..|++ +.||+.||||++=+-+-|..|-..|.+
T Consensus 4 ~eR~~~Il~~L~~~~~v~v-------------~eLa~~l~VS~~TIRRDL~~Le~~g~l 49 (256)
T PRK10434 4 RQRQAAILEYLQKQGKTSV-------------EELAQYFDTTGTTIRKDLVILEHAGTV 49 (256)
T ss_pred HHHHHHHHHHHHHcCCEEH-------------HHHHHHHCCCHHHHHHHHHHHHHCCCE
Confidence 3488888899999999999 999999999999999999999887754
No 148
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=44.69 E-value=19 Score=29.85 Aligned_cols=35 Identities=11% Similarity=0.077 Sum_probs=31.7
Q ss_pred hhceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHHHHHcccc
Q psy17612 232 RIHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLIRNARL 279 (449)
Q Consensus 232 riy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rL 279 (449)
+-++..|+ ..+|+.||+|+.-+..++.++.++|.|
T Consensus 28 R~~eGlS~-------------kEIAe~LGIS~~TVk~~l~~~~~~~~~ 62 (73)
T TIGR03879 28 REEAGKTA-------------SEIAEELGRTEQTVRNHLKGETKAGGL 62 (73)
T ss_pred HHHcCCCH-------------HHHHHHHCcCHHHHHHHHhcCcccchH
Confidence 66688899 999999999999999999998888766
No 149
>TIGR03315 Se_ygfK putative selenate reductase, YgfK subunit. Members of this protein family are YgfK, predicted to be one subunit of a three-subunit, molybdopterin-containing selenate reductase. This enzyme is found, typically, in genomic regions associated with xanthine dehydrogenase homologs predicted to belong to the selenium-dependent molybdenum hydroxylases (SDMH). Therefore, the selenate reductase is suggested to play a role in furnishing selenide for SelD, the selenophosphate synthase.
Probab=44.62 E-value=58 Score=38.95 Aligned_cols=105 Identities=18% Similarity=0.173 Sum_probs=62.8
Q ss_pred HhhcCCCHHHHHHHHHHHHHccccccee--ccc-------------C--CEEEeCCC---CCChHHHHHHhhhhhhhHHH
Q psy17612 256 ASKLNMGTDEAECWIVNLIRNARLDAKI--DSK-------------L--GHVIMGTQ---PLSPYQQLLEKIDTLSVRSE 315 (449)
Q Consensus 256 A~~Lnms~~e~E~wIVnlIr~~rLdaKI--Ds~-------------~--G~V~m~~~---~~s~Yqqviek~d~L~~R~q 315 (449)
|.--|.+|+|+|+...-||.+.+|+.-| ++- . ..|..+.. +.-+|. ..-..+.|.+
T Consensus 213 st~hgcp~~eie~i~~~~~~~k~~~~~~k~nptllg~~~~r~~~~~~g~~~~~~~~~~f~~dl~~~----~~~~~~~~l~ 288 (1012)
T TIGR03315 213 STMHGCPPDEIEAICRYLLEEKGLHTFVKLNPTLLGYKFVRDTMDEMGFDYIVLKEESFSHDLQYE----DAVAMLQRLQ 288 (1012)
T ss_pred hhccCCCHHHHHHHHHHHHhccCCceEEeeCcccccHHHHHHHHHhcCCceEecchhhcccccchh----HHHHHHHHHH
Confidence 6668999999999999999999998744 110 0 11111111 112333 3445666777
Q ss_pred HHHHHHHHHHhhhcCCCCCCC----CCccchhHHhhhhchhhhHHHHHHhhcCCC
Q psy17612 316 ALQALIERKVKVRNNSANAGG----ENSWASKEMLASKADLNVITIMLASKLNMG 366 (449)
Q Consensus 316 ~L~~~i~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~la~kLnm~ 366 (449)
+|+..-.-..+.+ ..|... .+.--+++||-||--|=-+|+.||.+|--.
T Consensus 289 ~~~~~~~~~fgvk--~~nt~~~~~~~~~~p~~~my~sg~~l~~~~~~~~~~l~~~ 341 (1012)
T TIGR03315 289 LLAKEKGLGFGVK--LTNTLPVTIAKGELPGEEMYMSGRALFPLSINLAAKLSRE 341 (1012)
T ss_pred HHHHHcCCeeeEE--EecccceeecCCCCCcccccccCCccccchHHHHHhhHHh
Confidence 7765433221111 111111 122345789999999999999888887433
No 150
>PRK10803 tol-pal system protein YbgF; Provisional
Probab=43.64 E-value=27 Score=34.98 Aligned_cols=46 Identities=11% Similarity=0.164 Sum_probs=39.9
Q ss_pred eeeccCCCHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcc
Q psy17612 4 FIFFFQFKMDMMESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSD 49 (449)
Q Consensus 4 ~~~~~~~~~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~ 49 (449)
++.+|--++..-++++++|..+.+.|++..|.+++..+...-|++.
T Consensus 206 vv~~yP~s~~~~dAl~klg~~~~~~g~~~~A~~~~~~vi~~yP~s~ 251 (263)
T PRK10803 206 VVKNYPKSPKAADAMFKVGVIMQDKGDTAKAKAVYQQVIKKYPGTD 251 (263)
T ss_pred HHHHCCCCcchhHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCCH
Confidence 3566777888999999999999999999999999998888887543
No 151
>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=43.50 E-value=81 Score=32.12 Aligned_cols=81 Identities=20% Similarity=0.098 Sum_probs=53.5
Q ss_pred eeeccCCCHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHHHHHHH
Q psy17612 4 FIFFFQFKMDMMESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNKLREYI 83 (449)
Q Consensus 4 ~~~~~~~~~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLke~i 83 (449)
|+.+|-=.+=.-++.|=||+.+|..|+|..|...+-.+..--|.. ++--+.|+-.=-|.--.++-|.|..-+..+-.-|
T Consensus 167 fi~~YP~s~~~~nA~yWLGe~~y~qg~y~~Aa~~f~~~~k~~P~s-~KApdallKlg~~~~~l~~~d~A~atl~qv~k~Y 245 (262)
T COG1729 167 FIKKYPNSTYTPNAYYWLGESLYAQGDYEDAAYIFARVVKDYPKS-PKAPDALLKLGVSLGRLGNTDEACATLQQVIKRY 245 (262)
T ss_pred HHHcCCCCcccchhHHHHHHHHHhcccchHHHHHHHHHHHhCCCC-CCChHHHHHHHHHHHHhcCHHHHHHHHHHHHHHC
Confidence 444554444556788999999999999999998887777666543 4434566555445444567777777666554444
Q ss_pred hc
Q psy17612 84 DG 85 (449)
Q Consensus 84 d~ 85 (449)
-+
T Consensus 246 P~ 247 (262)
T COG1729 246 PG 247 (262)
T ss_pred CC
Confidence 43
No 152
>KOG1726|consensus
Probab=43.03 E-value=80 Score=31.53 Aligned_cols=24 Identities=13% Similarity=0.325 Sum_probs=21.4
Q ss_pred HHHHHHHHHHHHHHHhhhhceeeEe
Q psy17612 215 LDEFVENARLMIFETFCRIHQCISI 239 (449)
Q Consensus 215 ~d~fvenaR~~ife~ycriy~~IsI 239 (449)
+|.++..+|...+++.|.++++. +
T Consensus 100 id~~l~~~k~~~~~~a~~~~~r~-l 123 (225)
T KOG1726|consen 100 IDRMLVEAKERVYDAAVSILKRA-L 123 (225)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH-H
Confidence 68899999999999999998876 5
No 153
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=42.99 E-value=43 Score=33.48 Aligned_cols=49 Identities=10% Similarity=-0.038 Sum_probs=43.5
Q ss_pred HHHHHHHHHHHhhhhceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHHHHHccccc
Q psy17612 219 VENARLMIFETFCRIHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLIRNARLD 280 (449)
Q Consensus 219 venaR~~ife~ycriy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rLd 280 (449)
-+.-|+...-.+++-+..|++ +.||+.||+|+.=+.|.|..|=..|.+.
T Consensus 14 ~~~eR~~~Il~~L~~~~~vtv-------------~eLa~~l~VS~~TIRRDL~~Le~~G~l~ 62 (269)
T PRK09802 14 GTSERREQIIQRLRQQGSVQV-------------NDLSALYGVSTVTIRNDLAFLEKQGIAV 62 (269)
T ss_pred cHHHHHHHHHHHHHHcCCEeH-------------HHHHHHHCCCHHHHHHHHHHHHhCCCeE
Confidence 345688889999999999999 9999999999999999999997777664
No 154
>PRK09853 putative selenate reductase subunit YgfK; Provisional
Probab=42.35 E-value=63 Score=38.73 Aligned_cols=105 Identities=18% Similarity=0.117 Sum_probs=62.6
Q ss_pred HhhcCCCHHHHHHHHHHHHHccccccee--ccc-------C--------CEEEeCCC---CCChHHHHHHhhhhhhhHHH
Q psy17612 256 ASKLNMGTDEAECWIVNLIRNARLDAKI--DSK-------L--------GHVIMGTQ---PLSPYQQLLEKIDTLSVRSE 315 (449)
Q Consensus 256 A~~Lnms~~e~E~wIVnlIr~~rLdaKI--Ds~-------~--------G~V~m~~~---~~s~Yqqviek~d~L~~R~q 315 (449)
|.--|.+|+|+|+...-||.+.+|+.-| ++- . ..|..+.. +.-+|. .....+.|.+
T Consensus 215 st~hgcp~~eie~i~~~~~~~k~~~~~~k~nptllg~~~~r~~~d~~g~~~~~~~~~~f~~dl~~~----~a~~m~~~l~ 290 (1019)
T PRK09853 215 STMHGCPPHEIEAIARYLLEEKGLNTFVKLNPTLLGYERVREILDKMGFDYIGLKEEHFDHDLQYT----DAVEMLERLM 290 (1019)
T ss_pred hhccCCCHHHHHHHHHHHHhccCCceEEeeCcccccHHHHHHHHHhcCCceEecchhhcccccchh----HHHHHHHHHH
Confidence 6668999999999999999999998744 110 0 11121111 112333 3445666777
Q ss_pred HHHHHHHHHHhhhcCCCCCCC----CCccchhHHhhhhchhhhHHHHHHhhcCCC
Q psy17612 316 ALQALIERKVKVRNNSANAGG----ENSWASKEMLASKADLNVITIMLASKLNMG 366 (449)
Q Consensus 316 ~L~~~i~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~la~kLnm~ 366 (449)
.|+..-.-..+.+ ..|... .+.--+++||-||--|=-+|+.||.+|--.
T Consensus 291 ~~~~~~~~~fgvk--~tnt~~~~~~~~~lp~~~mymsg~~l~pl~i~~a~~l~~~ 343 (1019)
T PRK09853 291 ALAKEKGLGFGVK--LTNTLPVINNKGELPGEEMYMSGRALFPLSINLAAKLSRE 343 (1019)
T ss_pred HHHHHcCceeeEE--EecccceeecCCCCCcccccccCCcccceeHHHHHhhHHh
Confidence 7765433211111 111111 123345789999999999999888877433
No 155
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=41.86 E-value=38 Score=33.34 Aligned_cols=54 Identities=17% Similarity=0.197 Sum_probs=44.0
Q ss_pred HHHHHHHHHhhhhceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHHHHHcccccceecccCCEEE
Q psy17612 221 NARLMIFETFCRIHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLIRNARLDAKIDSKLGHVI 291 (449)
Q Consensus 221 naR~~ife~ycriy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rLdaKIDs~~G~V~ 291 (449)
+.|....-.+++-++.++. +.||+.||+|+.=+.+.|..|-..+++. ...|..+
T Consensus 3 ~~R~~~Il~~l~~~~~~~~-------------~eLa~~l~VS~~TiRRdL~~L~~~~~l~----r~~Gga~ 56 (240)
T PRK10411 3 AARQQAIVDLLLNHTSLTT-------------EALAEQLNVSKETIRRDLNELQTQGKIL----RNHGRAK 56 (240)
T ss_pred hHHHHHHHHHHHHcCCCcH-------------HHHHHHHCcCHHHHHHHHHHHHHCCCEE----EecCeEE
Confidence 4577778888888999999 9999999999999999999997766553 3455543
No 156
>KOG3054|consensus
Probab=41.71 E-value=48 Score=33.72 Aligned_cols=54 Identities=17% Similarity=0.335 Sum_probs=47.2
Q ss_pred HHHhhhhceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHHHHHcccccceecccCCEEEeC
Q psy17612 227 FETFCRIHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLIRNARLDAKIDSKLGHVIMG 293 (449)
Q Consensus 227 fe~ycriy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rLdaKIDs~~G~V~m~ 293 (449)
|.+|++--++|-| +.||..||+-..++-.-|-+|+.+|-|.+-||--.-.|.++
T Consensus 205 Fv~YIk~nKvV~l-------------edLas~f~Lrtqd~inriq~~l~eg~ltGVmDDRGKfIYIS 258 (299)
T KOG3054|consen 205 FVEYIKKNKVVPL-------------EDLASEFGLRTQDSINRIQELLAEGLLTGVMDDRGKFIYIS 258 (299)
T ss_pred HHHHHHhcCeeeH-------------HHHHHHhCccHHHHHHHHHHHHHhhhheeeecCCCceEEec
Confidence 5578899999999 99999999999999889999999999999999865555553
No 157
>PF04733 Coatomer_E: Coatomer epsilon subunit; InterPro: IPR006822 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the epsilon subunit of the coatomer complex, which is involved in the regulation of intracellular protein trafficking between the endoplasmic reticulum and the Golgi complex []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006890 retrograde vesicle-mediated transport, Golgi to ER, 0030126 COPI vesicle coat; PDB: 3MV2_B 3MV3_F 3MKR_A.
Probab=41.55 E-value=88 Score=31.68 Aligned_cols=165 Identities=18% Similarity=0.228 Sum_probs=81.6
Q ss_pred HHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHHHHHHHhcCCCCCCChHHHHH
Q psy17612 19 YKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNKLREYIDGGSANFESPLHLLQ 98 (449)
Q Consensus 19 yk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLke~id~~~~~~~~pl~~l~ 98 (449)
+--|.+++..|+|+.|.+.+.. +.+ +.++--.+-+=+.++..|.|.+.++++++.-| .+.+.++-
T Consensus 106 ~~~A~i~~~~~~~~~AL~~l~~--------~~~-lE~~al~Vqi~L~~~R~dlA~k~l~~~~~~~e------D~~l~qLa 170 (290)
T PF04733_consen 106 LLAATILFHEGDYEEALKLLHK--------GGS-LELLALAVQILLKMNRPDLAEKELKNMQQIDE------DSILTQLA 170 (290)
T ss_dssp HHHHHHHCCCCHHHHHHCCCTT--------TTC-HHHHHHHHHHHHHTT-HHHHHHHHHHHHCCSC------CHHHHHHH
T ss_pred HHHHHHHHHcCCHHHHHHHHHc--------cCc-ccHHHHHHHHHHHcCCHHHHHHHHHHHHhcCC------cHHHHHHH
Confidence 3346677788888887766642 122 34443334444556788999888887765322 23444443
Q ss_pred HHHHHHHHHHHHHhcCccchhhHHHHhcCCchhhhHHHh--hhhHHHHHHHHHHHhccccccchHHHHHHHhhhccCCCc
Q psy17612 99 QRTWLIHWSLFVFFNHVKGRDLIIDMFLNRPHYLNAIQT--MCPHILRYLATAVIINRSKRNALKDLVKVIQQESYTYKD 176 (449)
Q Consensus 99 qR~WliHwsLf~ffn~~~g~~~~iD~F~~~~~yl~aIqt--~cp~lLRYlvvA~Il~~~r~~~l~dlv~vi~qE~~~Y~D 176 (449)
-+|+ -+. .|.+.+-++|. -|-.--++ .-|.++--.+++.|..++=...-..+.+.+...+ .|
T Consensus 171 -~awv------~l~---~g~e~~~~A~y---~f~El~~~~~~t~~~lng~A~~~l~~~~~~eAe~~L~~al~~~~---~~ 234 (290)
T PF04733_consen 171 -EAWV------NLA---TGGEKYQDAFY---IFEELSDKFGSTPKLLNGLAVCHLQLGHYEEAEELLEEALEKDP---ND 234 (290)
T ss_dssp -HHHH------HHH---HTTTCCCHHHH---HHHHHHCCS--SHHHHHHHHHHHHHCT-HHHHHHHHHHHCCC-C---CH
T ss_pred -HHHH------HHH---hCchhHHHHHH---HHHHHHhccCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhcc---CC
Confidence 2443 222 24444444443 22221111 1235555566666654322222222223332222 23
Q ss_pred h--HHHHHHH-HhhcccHHHHHHHHHHHhhhcccccchHHh
Q psy17612 177 P--ITEFLEH-LYVSFDFESAREKLTECTEVLDNDFFLVAC 214 (449)
Q Consensus 177 p--iT~fv~~-lYv~fdf~~aq~~L~~~~~vl~~DfFL~~~ 214 (449)
| +.+++.| .+..-+-+.+.+.+.+..++-.+-+|+..+
T Consensus 235 ~d~LaNliv~~~~~gk~~~~~~~~l~qL~~~~p~h~~~~~~ 275 (290)
T PF04733_consen 235 PDTLANLIVCSLHLGKPTEAAERYLSQLKQSNPNHPLVKDL 275 (290)
T ss_dssp HHHHHHHHHHHHHTT-TCHHHHHHHHHCHHHTTTSHHHHHH
T ss_pred HHHHHHHHHHHHHhCCChhHHHHHHHHHHHhCCCChHHHHH
Confidence 3 4455543 455555466777777777776666676655
No 158
>COG2976 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=41.50 E-value=68 Score=31.67 Aligned_cols=62 Identities=19% Similarity=0.126 Sum_probs=39.5
Q ss_pred HHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHH
Q psy17612 15 MESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLN 77 (449)
Q Consensus 15 ~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~ 77 (449)
.-+.+.+||-++|+|+++.|...|......+.++..+-+ +-.-.=+.-++.+..|.|++-|.
T Consensus 89 ~laaL~lAk~~ve~~~~d~A~aqL~~~l~~t~De~lk~l-~~lRLArvq~q~~k~D~AL~~L~ 150 (207)
T COG2976 89 VLAALELAKAEVEANNLDKAEAQLKQALAQTKDENLKAL-AALRLARVQLQQKKADAALKTLD 150 (207)
T ss_pred HHHHHHHHHHHHhhccHHHHHHHHHHHHccchhHHHHHH-HHHHHHHHHHHhhhHHHHHHHHh
Confidence 345678999999999999999999988877764433311 11222223344445666665443
No 159
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=41.41 E-value=53 Score=25.34 Aligned_cols=51 Identities=12% Similarity=0.094 Sum_probs=39.4
Q ss_pred HHHHHHHHHHHHHHhhhhceee-EeeccccccccccchhhHHhhcCCCHHHHHHHHHHHHHcccc
Q psy17612 216 DEFVENARLMIFETFCRIHQCI-SIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLIRNARL 279 (449)
Q Consensus 216 d~fvenaR~~ife~ycriy~~I-sI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rL 279 (449)
+...+..+..|..--.++-+.+ +. ..||+.||+|..-+.+-+-.|...|-+
T Consensus 3 ~~i~~~l~~~I~~g~~~~g~~lps~-------------~~la~~~~vsr~tvr~al~~L~~~g~i 54 (64)
T PF00392_consen 3 EQIYDQLRQAILSGRLPPGDRLPSE-------------RELAERYGVSRTTVREALRRLEAEGLI 54 (64)
T ss_dssp HHHHHHHHHHHHTTSS-TTSBE--H-------------HHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHHHHHHcCCCCCCCEeCCH-------------HHHHHHhccCCcHHHHHHHHHHHCCcE
Confidence 3455666677777777788888 88 999999999999999999999888865
No 160
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=41.32 E-value=22 Score=25.80 Aligned_cols=40 Identities=20% Similarity=0.286 Sum_probs=23.0
Q ss_pred HHHHHHHHhhhhceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHHHHHcc
Q psy17612 222 ARLMIFETFCRIHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLIRNA 277 (449)
Q Consensus 222 aR~~ife~ycriy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~ 277 (449)
-|..++.-+.. ..+. ..+|+.||+|+.-+-+|+-++=..|
T Consensus 6 ~R~~ii~l~~~---G~s~-------------~~ia~~lgvs~~Tv~~w~kr~~~~G 45 (50)
T PF13384_consen 6 RRAQIIRLLRE---GWSI-------------REIAKRLGVSRSTVYRWIKRYREEG 45 (50)
T ss_dssp ----HHHHHHH---T--H-------------HHHHHHHTS-HHHHHHHHT------
T ss_pred HHHHHHHHHHC---CCCH-------------HHHHHHHCcCHHHHHHHHHHccccc
Confidence 35556666655 6677 9999999999999999998875444
No 161
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=40.99 E-value=55 Score=28.42 Aligned_cols=43 Identities=14% Similarity=0.152 Sum_probs=32.6
Q ss_pred hhHHhhcCCCHHHHHHHHHHHHHcccccceecccCCEEEeCCCC
Q psy17612 253 QMLASKLNMGTDEAECWIVNLIRNARLDAKIDSKLGHVIMGTQP 296 (449)
Q Consensus 253 ~~LA~~Lnms~~e~E~wIVnlIr~~rLdaKIDs~~G~V~m~~~~ 296 (449)
+.||+.+|+++..+.+.+..|.+.|-+...- ...|-...++++
T Consensus 29 ~eia~~~~i~~~~v~~il~~L~~~gli~~~~-g~~ggy~l~~~~ 71 (132)
T TIGR00738 29 KEIAERQGISRSYLEKILRTLRRAGLVESVR-GPGGGYRLARPP 71 (132)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHCCcEEecc-CCCCCccCCCCH
Confidence 9999999999999999999999988775532 223434444444
No 162
>PRK15359 type III secretion system chaperone protein SscB; Provisional
Probab=40.76 E-value=1.7e+02 Score=25.99 Aligned_cols=69 Identities=10% Similarity=0.001 Sum_probs=53.7
Q ss_pred CCCHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHHHHH
Q psy17612 9 QFKMDMMESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNKLRE 81 (449)
Q Consensus 9 ~~~~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLke 81 (449)
.++|...++++.+|..+...|+|+.|.+.+.....+.|++ ...++..=.|=...++.+.|.+...++-+
T Consensus 52 ~~~P~~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l~p~~----~~a~~~lg~~l~~~g~~~eAi~~~~~Al~ 120 (144)
T PRK15359 52 MAQPWSWRAHIALAGTWMMLKEYTTAINFYGHALMLDASH----PEPVYQTGVCLKMMGEPGLAREAFQTAIK 120 (144)
T ss_pred HcCCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCC----cHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence 3567788999999999999999999999999988887643 23445544555667889888888777644
No 163
>PRK10370 formate-dependent nitrite reductase complex subunit NrfG; Provisional
Probab=40.73 E-value=1.3e+02 Score=28.53 Aligned_cols=72 Identities=13% Similarity=0.009 Sum_probs=51.6
Q ss_pred CCCHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhH-hh-cC--hHHHHHHHHHHHHHHh
Q psy17612 9 QFKMDMMESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEI-LV-QN--WDLALEDLNKLREYID 84 (449)
Q Consensus 9 ~~~~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eI-l~-~d--wd~a~~~l~kLke~id 84 (449)
..+|+..+..+.+|..+...|+|+.|.+++.....+-|++. .+|.-+|.-. .. ++ -+.|.+-+.++-+.-.
T Consensus 67 ~~~P~~~~~w~~Lg~~~~~~g~~~~A~~a~~~Al~l~P~~~-----~~~~~lA~aL~~~~g~~~~~~A~~~l~~al~~dP 141 (198)
T PRK10370 67 RANPQNSEQWALLGEYYLWRNDYDNALLAYRQALQLRGENA-----ELYAALATVLYYQAGQHMTPQTREMIDKALALDA 141 (198)
T ss_pred HHCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCH-----HHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHhCC
Confidence 34677788999999999999999999999999999887432 2344444322 12 23 3778887777766555
Q ss_pred c
Q psy17612 85 G 85 (449)
Q Consensus 85 ~ 85 (449)
+
T Consensus 142 ~ 142 (198)
T PRK10370 142 N 142 (198)
T ss_pred C
Confidence 4
No 164
>PRK09954 putative kinase; Provisional
Probab=40.34 E-value=55 Score=33.41 Aligned_cols=52 Identities=19% Similarity=0.320 Sum_probs=43.0
Q ss_pred HhhhhceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHHHHHccccc---ceecccCCEEEeC
Q psy17612 229 TFCRIHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLIRNARLD---AKIDSKLGHVIMG 293 (449)
Q Consensus 229 ~ycriy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rLd---aKIDs~~G~V~m~ 293 (449)
.+++=+++++. ..||+.||||+.-+.+.|.+|...|.+. ..+|...++++.|
T Consensus 10 ~~l~~~~~~s~-------------~~la~~l~~s~~~v~~~i~~L~~~g~i~~~~~~l~~~~~v~viG 64 (362)
T PRK09954 10 AILRRNPLIQQ-------------NEIADILQISRSRVAAHIMDLMRKGRIKGKGYILTEQEYCVVVG 64 (362)
T ss_pred HHHHHCCCCCH-------------HHHHHHHCCCHHHHHHHHHHHHHCCCcCCcEEEEcCCccEEEEE
Confidence 34455678888 9999999999999999999999999875 3677777777666
No 165
>COG3071 HemY Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]
Probab=40.33 E-value=5.2e+02 Score=28.09 Aligned_cols=110 Identities=21% Similarity=0.276 Sum_probs=74.8
Q ss_pred HHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHHHHHHHhcCCCCCCC
Q psy17612 13 DMMESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNKLREYIDGGSANFES 92 (449)
Q Consensus 13 e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLke~id~~~~~~~~ 92 (449)
+..-..+..++++...|||..|.+-+..+....|-. +. .+-=...+=|-.++|+....-+.+|++ .+ ...+
T Consensus 151 ~~l~v~ltrarlll~~~d~~aA~~~v~~ll~~~pr~-~~---vlrLa~r~y~~~g~~~~ll~~l~~L~k----a~-~l~~ 221 (400)
T COG3071 151 DTLAVELTRARLLLNRRDYPAARENVDQLLEMTPRH-PE---VLRLALRAYIRLGAWQALLAILPKLRK----AG-LLSD 221 (400)
T ss_pred chHHHHHHHHHHHHhCCCchhHHHHHHHHHHhCcCC-hH---HHHHHHHHHHHhccHHHHHHHHHHHHH----cc-CCCh
Confidence 445667788999999999999999999888887632 22 333344555667899888777776654 21 2223
Q ss_pred h-HHHHHHHHHHHHHHHHHHhcCccchhhHHHHhcCCchhhhH
Q psy17612 93 P-LHLLQQRTWLIHWSLFVFFNHVKGRDLIIDMFLNRPHYLNA 134 (449)
Q Consensus 93 p-l~~l~qR~WliHwsLf~ffn~~~g~~~~iD~F~~~~~yl~a 134 (449)
+ ...+++++|- ++.-=-.+++|.+.+.+.+.+.|+-+.+
T Consensus 222 ~e~~~le~~a~~---glL~q~~~~~~~~gL~~~W~~~pr~lr~ 261 (400)
T COG3071 222 EEAARLEQQAWE---GLLQQARDDNGSEGLKTWWKNQPRKLRN 261 (400)
T ss_pred HHHHHHHHHHHH---HHHHHHhccccchHHHHHHHhccHHhhc
Confidence 3 4678888887 4443334778888888888865554433
No 166
>PF08831 MHCassoc_trimer: Class II MHC-associated invariant chain trimerisation domain; InterPro: IPR011988 This entry represents the trimerisation domain of the MHC class II-associated invariant chain (Ii). Ii plays a critical role in the assembly of the MHC, as well as in MHC II antigen processing by stabilising peptide-free class II alpha/beta heterodimers in a complex soon after their synthesis and directing transport of the complex from the endoplasmic reticulum to compartments where peptide loading of class II takes place []. In antigen-presenting cells (APCs), loading of MHC II molecules with peptides is regulated by Ii, which blocks MHC II antigen-binding sites in pre-endosomal compartments []. Several molecules then act upon MHC II molecules in endosomes to facilitate peptide loading: Ii-degrading proteases, the peptide exchange factor, human leukocyte antigen-DM (HLA-DM), and its modulator, HLA-DO (DO). The Invariant chain contains a single transmembrane domain. Ii first assembles into a trimer and then associates with three class II alpha/beta MHC heterodimers. Although the membrane-proximal region of the Ii luminal domain is structurally disordered, the C-terminal segment of the luminal domain is largely alpha-helical and contains a major interaction site for the Ii trimer []. More information about these proteins can be found at Protein of the Month: MHC [].; GO: 0042289 MHC class II protein binding, 0006886 intracellular protein transport, 0006955 immune response, 0019882 antigen processing and presentation, 0016020 membrane; PDB: 1IIE_C.
Probab=40.21 E-value=54 Score=27.33 Aligned_cols=36 Identities=22% Similarity=0.502 Sum_probs=25.7
Q ss_pred HHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHHHhcC
Q psy17612 71 LALEDLNKLREYIDGGSANFESPLHLLQQRTWLIHWSLFVFFNH 114 (449)
Q Consensus 71 ~a~~~l~kLke~id~~~~~~~~pl~~l~qR~WliHwsLf~ffn~ 114 (449)
+-+++++.||..++.. +| -.--+|+-||.||-+...
T Consensus 26 tf~~NL~~LK~~M~~~-~W-------k~FEsWM~~WLlFqMaq~ 61 (72)
T PF08831_consen 26 TFLENLKHLKNQMNES-DW-------KSFESWMHQWLLFQMAQN 61 (72)
T ss_dssp -HHHHHHHHHHHS-HH-HH-------HHHHHHHHHHHHHHHHT-
T ss_pred HHHHHHHHHHHhcchh-hH-------HHHHHHHHHHHHHHHHhc
Confidence 5567889999888862 23 445699999999998753
No 167
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=40.17 E-value=46 Score=24.74 Aligned_cols=42 Identities=12% Similarity=0.227 Sum_probs=33.8
Q ss_pred HHHHHhhhhceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHHHHHcccc
Q psy17612 225 MIFETFCRIHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLIRNARL 279 (449)
Q Consensus 225 ~ife~ycriy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rL 279 (449)
.|++.+.+--..+++ ..||+++|++..-+-+.+..|...|=+
T Consensus 7 ~iL~~l~~~~~~~t~-------------~eia~~~gl~~stv~r~L~tL~~~g~v 48 (52)
T PF09339_consen 7 RILEALAESGGPLTL-------------SEIARALGLPKSTVHRLLQTLVEEGYV 48 (52)
T ss_dssp HHHHCHHCTBSCEEH-------------HHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHcCCCCCCH-------------HHHHHHHCcCHHHHHHHHHHHHHCcCe
Confidence 456666666666899 999999999999999999999877743
No 168
>PRK02603 photosystem I assembly protein Ycf3; Provisional
Probab=40.12 E-value=2e+02 Score=25.92 Aligned_cols=34 Identities=15% Similarity=0.129 Sum_probs=29.5
Q ss_pred HHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCC
Q psy17612 14 MMESMYKLAKFRYECGNYSITTSYLYFYLLVMPT 47 (449)
Q Consensus 14 ~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~ 47 (449)
....++.+|..++..|+|+.|.+++.......+.
T Consensus 71 ~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~ 104 (172)
T PRK02603 71 RSYILYNMGIIYASNGEHDKALEYYHQALELNPK 104 (172)
T ss_pred HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcc
Confidence 4568999999999999999999999888777653
No 169
>COG5071 RPN5 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=39.99 E-value=56 Score=34.54 Aligned_cols=51 Identities=25% Similarity=0.322 Sum_probs=43.0
Q ss_pred HHHhhcCCChHHHHHHHHHHhhhcccccccccCCCeEEecCCCCChhHHHHH
Q psy17612 358 MLASKLNMGTDEAECWIVNLIRNARLDAKIDSKLGHVIMGTQPLSPYQQLLE 409 (449)
Q Consensus 358 ~la~kLnm~~~eaE~WIvnLIr~~~ldAKIDs~~~~v~m~~~~~svyqqvie 409 (449)
.|+.-|.|++++.|+.|..|+.++..-|||+-..|.|....+. |+-||+=|
T Consensus 358 rl~~lld~~~s~te~~ISdlVN~G~~yaKiNrpa~Ii~FEK~~-n~~~~lne 408 (439)
T COG5071 358 RLGVLLDMSPSETEQFISDLVNKGHFYAKINRPAQIISFEKSQ-NVQEQLNE 408 (439)
T ss_pred HHHHHHcCCHHHHHHHHHHHHhcCcEEEEecCccceEEeeccc-cHHHHHHH
Confidence 5678899999999999999999999999999999988877653 56666544
No 170
>PF12569 NARP1: NMDA receptor-regulated protein 1 ; InterPro: IPR021183 This group represents N-terminal acetyltransferase A (NatA) auxiliary subunit and represents a non-catalytic component of the NatA N-terminal acetyltransferase, which catalyzes acetylation of proteins beginning with Met-Ser, Met-Gly and Met-Ala. N-terminal acetylation plays a role in normal eukaryotic translation and processing, protect against proteolytic degradation and protein turnover. NAT1 anchors ARD1 and NAT5 to the ribosome and may present the N- terminal of nascent polypeptides for acetylation [], [].
Probab=39.89 E-value=5.7e+02 Score=28.43 Aligned_cols=66 Identities=20% Similarity=0.211 Sum_probs=53.4
Q ss_pred HHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHHHHHH
Q psy17612 13 DMMESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNKLREY 82 (449)
Q Consensus 13 e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLke~ 82 (449)
-.+=++|=+|++|...|+|+.|.+++......+|+. .+.+.-|-++=--.++...|.+.+..+|++
T Consensus 192 ~~lw~~~~lAqhyd~~g~~~~Al~~Id~aI~htPt~----~ely~~KarilKh~G~~~~Aa~~~~~Ar~L 257 (517)
T PF12569_consen 192 TLLWTLYFLAQHYDYLGDYEKALEYIDKAIEHTPTL----VELYMTKARILKHAGDLKEAAEAMDEAREL 257 (517)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhcCCCc----HHHHHHHHHHHHHCCCHHHHHHHHHHHHhC
Confidence 346688899999999999999999999999988753 445555655555668999999999988874
No 171
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=39.54 E-value=77 Score=25.42 Aligned_cols=29 Identities=17% Similarity=0.217 Sum_probs=26.7
Q ss_pred hhHHhhcCCCHHHHHHHHHHHHHcccccc
Q psy17612 253 QMLASKLNMGTDEAECWIVNLIRNARLDA 281 (449)
Q Consensus 253 ~~LA~~Lnms~~e~E~wIVnlIr~~rLda 281 (449)
..||+.+|++..-+-+.|..|...|-+.-
T Consensus 24 ~~ia~~l~i~~~tv~r~l~~L~~~g~l~~ 52 (91)
T smart00346 24 AELAERLGLSKSTAHRLLNTLQELGYVEQ 52 (91)
T ss_pred HHHHHHhCCCHHHHHHHHHHHHHCCCeee
Confidence 99999999999999999999998887753
No 172
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=39.49 E-value=1.7e+02 Score=27.25 Aligned_cols=102 Identities=15% Similarity=0.133 Sum_probs=66.2
Q ss_pred cchHHhHHHHHHHHHHHHHHHhhhhceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHHHHHccccccee--ccc
Q psy17612 209 FFLVACLDEFVENARLMIFETFCRIHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLIRNARLDAKI--DSK 286 (449)
Q Consensus 209 fFL~~~~d~fvenaR~~ife~ycriy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rLdaKI--Ds~ 286 (449)
+.+..++..|+..-=..++...+ .|.-++- +.||+.|||+..++-+-|-.|-.+|=+.-+= |..
T Consensus 2 ~~~~~~~~~~~g~~~v~Vl~aL~-~~~~~td-------------EeLa~~Lgi~~~~VRk~L~~L~e~~Lv~~~r~r~~~ 67 (158)
T TIGR00373 2 ELLNEVVGRAAEEEVGLVLFSLG-IKGEFTD-------------EEISLELGIKLNEVRKALYALYDAGLADYKRRKDDE 67 (158)
T ss_pred hHHHHHHHHHcChhHHHHHHHHh-ccCCCCH-------------HHHHHHHCCCHHHHHHHHHHHHHCCCceeeeeeecC
Confidence 33445555666544466777655 5677888 9999999999999999999987777653221 223
Q ss_pred CCEEEeCCCCCChHHHHHHhhhhhhhHHHHHHHHHHHHHhhhc
Q psy17612 287 LGHVIMGTQPLSPYQQLLEKIDTLSVRSEALQALIERKVKVRN 329 (449)
Q Consensus 287 ~G~V~m~~~~~s~Yqqviek~d~L~~R~q~L~~~i~~~~~~~~ 329 (449)
+|-..-- =.-.|.++++ .+..|..++...+...+....
T Consensus 68 ~gw~~Y~--w~i~~~~i~d---~Ik~~~~~~~~~lk~~l~~e~ 105 (158)
T TIGR00373 68 TGWYEYT--WRINYEKALD---VLKRKLEETAKKLREKLEFET 105 (158)
T ss_pred CCcEEEE--EEeCHHHHHH---HHHHHHHHHHHHHHHHHhhcc
Confidence 3321100 0134566664 466788888888887766554
No 173
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=38.87 E-value=40 Score=33.29 Aligned_cols=45 Identities=16% Similarity=0.184 Sum_probs=39.7
Q ss_pred HHHHHHHHhhhhceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHHHHHcccc
Q psy17612 222 ARLMIFETFCRIHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLIRNARL 279 (449)
Q Consensus 222 aR~~ife~ycriy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rL 279 (449)
-|......+++-+..+++ +.||+.||+|+.=+.+.|..|-..|.+
T Consensus 5 ~R~~~Il~~l~~~~~~~~-------------~ela~~l~vS~~TirRdL~~Le~~g~i 49 (251)
T PRK13509 5 QRHQILLELLAQLGFVTV-------------EKVIERLGISPATARRDINKLDESGKL 49 (251)
T ss_pred HHHHHHHHHHHHcCCcCH-------------HHHHHHHCcCHHHHHHHHHHHHHCCCE
Confidence 477777888899999999 999999999999999999998766655
No 174
>PF09743 DUF2042: Uncharacterized conserved protein (DUF2042); InterPro: IPR018611 The ubiquitin fold modifier 1 (Ufm1) is the most recently discovered ubiquitin-like modifier whose conjugation (ufmylation) system is conserved in multicellular organisms. Ufm1 is known to covalently attach with cellular protein(s) via a specific E1-activating enzyme (Uba5), an E2-conjugating enzyme (Ufc1), and a E3-ligating enzyme []. This entry represents E3 UFM1-protein ligase 1.
Probab=38.26 E-value=1.8e+02 Score=29.67 Aligned_cols=60 Identities=13% Similarity=0.184 Sum_probs=47.8
Q ss_pred cchHHhHHHHHHHHHHHHHHHhhhhceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHHHHHcccccceeccc
Q psy17612 209 FFLVACLDEFVENARLMIFETFCRIHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLIRNARLDAKIDSK 286 (449)
Q Consensus 209 fFL~~~~d~fvenaR~~ife~ycriy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rLdaKIDs~ 286 (449)
.+-..|+|...++++-.. +-.-.|+| ..||+++++|.+++-..++.-...+.++|++|..
T Consensus 108 lit~~Yld~l~~Eine~L-----qe~G~vsi-------------~eLa~~~~Lp~efl~~~li~~~lg~~I~g~~d~~ 167 (272)
T PF09743_consen 108 LITDSYLDSLAEEINEKL-----QESGQVSI-------------SELAKQYDLPSEFLKEELISKRLGKIIKGRLDGD 167 (272)
T ss_pred EccHHHHHHHHHHHHHHH-----HHcCeEeH-------------HHHHHhcCCcHHHHHHHHhhhhcCcceeEEEeCC
Confidence 333566676666665544 44489999 9999999999999998888888888899999985
No 175
>PF11817 Foie-gras_1: Foie gras liver health family 1; InterPro: IPR021773 Mutating the gene foie gras in zebrafish has been shown to affect development; the mutants develop large, lipid-filled hepatocytes in the liver, resembling those in individuals with fatty liver disease []. Foie-gras protein is long and has several well-defined domains though none of them has a known function. We have annotated this one as the first []. THe C terminus of this region contains TPR repeats.
Probab=38.07 E-value=1.2e+02 Score=29.72 Aligned_cols=60 Identities=15% Similarity=0.104 Sum_probs=42.3
Q ss_pred HHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcc--hhhHHHHHHHHHHhHhhcChHHHHH
Q psy17612 15 MESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSD--RHYLAVLWGKLASEILVQNWDLALE 74 (449)
Q Consensus 15 ~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~--~k~ls~lwgkla~eIl~~dwd~a~~ 74 (449)
..-.+++|+.|+..|||++|.++|.........++ .-.-.++|..+.|-...+|.+..+.
T Consensus 178 ~~l~~~~A~ey~~~g~~~~A~~~l~~~~~~yr~egW~~l~~~~l~~l~~Ca~~~~~~~~~l~ 239 (247)
T PF11817_consen 178 SYLSLEMAEEYFRLGDYDKALKLLEPAASSYRREGWWSLLTEVLWRLLECAKRLGDVEDYLT 239 (247)
T ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhCCcHHHHHHHHHHHHHHHHHhCCHHHHHH
Confidence 33456899999999999999999998743332221 1125677888888888887665544
No 176
>KOG2582|consensus
Probab=38.04 E-value=68 Score=34.47 Aligned_cols=125 Identities=19% Similarity=0.263 Sum_probs=69.9
Q ss_pred HHHHHHHHcccccceecccCCEEEe--CCCCCChHHHHHHhhhhhhhHHHHHHHHHHHHHhhhcCCCCCCCCCccchhHH
Q psy17612 268 CWIVNLIRNARLDAKIDSKLGHVIM--GTQPLSPYQQLLEKIDTLSVRSEALQALIERKVKVRNNSANAGGENSWASKEM 345 (449)
Q Consensus 268 ~wIVnlIr~~rLdaKIDs~~G~V~m--~~~~~s~Yqqviek~d~L~~R~q~L~~~i~~~~~~~~~~~~~~~~~~~~~~~~ 345 (449)
-.+|.+|..|+.- .+|+-+...+. -++..++|.+..+- -+.++.-=.+.+-++...+=.-.|.-+-.-.+-..+
T Consensus 228 ylLvsLI~~GK~~-ql~k~ts~~~~r~~K~ms~pY~ef~~~---Y~~~~~~eLr~lVk~~~~rF~kDnnt~l~k~av~sl 303 (422)
T KOG2582|consen 228 YLLVSLILTGKVF-QLPKNTSQNAGRFFKPMSNPYHEFLNV---YLKDSSTELRTLVKKHSERFTKDNNTGLAKQAVSSL 303 (422)
T ss_pred HHHHHhhhcCcee-eccccchhhhHHhcccCCchHHHHHHH---HhcCCcHHHHHHHHHHHHHHhhcCcHHHHHHHHHHH
Confidence 4679999999886 66665433222 23446799988753 333333323333333322221000000111122233
Q ss_pred hhhhc-----hhhhHHH-HHHh--hcCCChHHHHHHHHHHhhhcccccccccCCCeEEecCCC
Q psy17612 346 LASKA-----DLNVITI-MLAS--KLNMGTDEAECWIVNLIRNARLDAKIDSKLGHVIMGTQP 400 (449)
Q Consensus 346 ~~~~~-----~~~~~~~-~la~--kLnm~~~eaE~WIvnLIr~~~ldAKIDs~~~~v~m~~~~ 400 (449)
+..+| -.-.++. .+|+ .|. +++|||+-|-++|.+.+.-|-|| |.|.....|
T Consensus 304 ~k~nI~rltktF~sLsL~dIA~~vQLa-~~qevek~Ilqmie~~~i~a~iN---G~v~f~~n~ 362 (422)
T KOG2582|consen 304 YKKNIQRLTKTFLSLSLSDIASRVQLA-SAQEVEKYILQMIEDGEIFASIN---GMVFFTDNP 362 (422)
T ss_pred HHHHHHHHHHHHHHhhHHHHHHHHHhc-chHHHHHHHHHHhccCceEEEec---ceEEEecCc
Confidence 33333 1112233 5677 343 46799999999999999999998 999987765
No 177
>KOG2114|consensus
Probab=37.09 E-value=2.2e+02 Score=33.65 Aligned_cols=160 Identities=19% Similarity=0.293 Sum_probs=90.0
Q ss_pred eeccCCCHHHHHH-HHHHHHHHHhcCChhhHHHHHHHHHhcCCC--------cc---hhhHHHHHHHHHHhHhhcChH--
Q psy17612 5 IFFFQFKMDMMES-MYKLAKFRYECGNYSITTSYLYFYLLVMPT--------SD---RHYLAVLWGKLASEILVQNWD-- 70 (449)
Q Consensus 5 ~~~~~~~~e~~d~-lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~--------~~---~k~ls~lwgkla~eIl~~dwd-- 70 (449)
.++++.+++-+.. +.|||.+.|..|||++|...+-+......+ +. ++-.+.||...+-.+-..|--
T Consensus 357 Ak~~~~d~d~~~~i~~kYgd~Ly~Kgdf~~A~~qYI~tI~~le~s~Vi~kfLdaq~IknLt~YLe~L~~~gla~~dhttl 436 (933)
T KOG2114|consen 357 AKSQHLDEDTLAEIHRKYGDYLYGKGDFDEATDQYIETIGFLEPSEVIKKFLDAQRIKNLTSYLEALHKKGLANSDHTTL 436 (933)
T ss_pred HHhcCCCHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHcccCChHHHHHHhcCHHHHHHHHHHHHHHHHcccccchhHHH
Confidence 3567777776655 678999999999999999876655544421 11 122445666666665554422
Q ss_pred -----HHHHHHHHHHHHHhcCC--CCC---CChHHHHHHHHHHHHHHHHHH-h-cCccchhhHHHHhcCCchhhhHHH--
Q psy17612 71 -----LALEDLNKLREYIDGGS--ANF---ESPLHLLQQRTWLIHWSLFVF-F-NHVKGRDLIIDMFLNRPHYLNAIQ-- 136 (449)
Q Consensus 71 -----~a~~~l~kLke~id~~~--~~~---~~pl~~l~qR~WliHwsLf~f-f-n~~~g~~~~iD~F~~~~~yl~aIq-- 136 (449)
.-+++..||.+.|+++. .|+ ..-+..+.+=..+-|-.+..- | +|+...+-+++..- .|..|++
T Consensus 437 LLncYiKlkd~~kL~efI~~~~~g~~~fd~e~al~Ilr~snyl~~a~~LA~k~~~he~vl~ille~~~---ny~eAl~yi 513 (933)
T KOG2114|consen 437 LLNCYIKLKDVEKLTEFISKCDKGEWFFDVETALEILRKSNYLDEAELLATKFKKHEWVLDILLEDLH---NYEEALRYI 513 (933)
T ss_pred HHHHHHHhcchHHHHHHHhcCCCcceeeeHHHHHHHHHHhChHHHHHHHHHHhccCHHHHHHHHHHhc---CHHHHHHHH
Confidence 33578899999999863 344 233455554444444333221 2 35555666666665 4555543
Q ss_pred hhhh--HHHHHHHHHHH--hccccccchHHHHHHH
Q psy17612 137 TMCP--HILRYLATAVI--INRSKRNALKDLVKVI 167 (449)
Q Consensus 137 t~cp--~lLRYlvvA~I--l~~~r~~~l~dlv~vi 167 (449)
..|| .+||=+.-... +...+....+.+++.+
T Consensus 514 ~slp~~e~l~~l~kyGk~Ll~h~P~~t~~ili~~~ 548 (933)
T KOG2114|consen 514 SSLPISELLRTLNKYGKILLEHDPEETMKILIELI 548 (933)
T ss_pred hcCCHHHHHHHHHHHHHHHHhhChHHHHHHHHHHH
Confidence 2333 55555544332 2223323334445544
No 178
>PF04733 Coatomer_E: Coatomer epsilon subunit; InterPro: IPR006822 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the epsilon subunit of the coatomer complex, which is involved in the regulation of intracellular protein trafficking between the endoplasmic reticulum and the Golgi complex []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006890 retrograde vesicle-mediated transport, Golgi to ER, 0030126 COPI vesicle coat; PDB: 3MV2_B 3MV3_F 3MKR_A.
Probab=36.64 E-value=74 Score=32.22 Aligned_cols=57 Identities=16% Similarity=0.103 Sum_probs=33.2
Q ss_pred HHHHHHHH--HhcCC--hhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHH
Q psy17612 18 MYKLAKFR--YECGN--YSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNK 78 (449)
Q Consensus 18 lyk~Akf~--y~~Gd--Y~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~k 78 (449)
++.+|.-| +-.|. |..|.-++.++...+ +.. ...+-|+..|.++.++|+.|.+.+..
T Consensus 166 l~qLa~awv~l~~g~e~~~~A~y~f~El~~~~---~~t-~~~lng~A~~~l~~~~~~eAe~~L~~ 226 (290)
T PF04733_consen 166 LTQLAEAWVNLATGGEKYQDAFYIFEELSDKF---GST-PKLLNGLAVCHLQLGHYEEAEELLEE 226 (290)
T ss_dssp HHHHHHHHHHHHHTTTCCCHHHHHHHHHHCCS-----S-HHHHHHHHHHHHHCT-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHhCchhHHHHHHHHHHHHhcc---CCC-HHHHHHHHHHHHHhCCHHHHHHHHHH
Confidence 45555533 33453 555554444433332 233 45678999999999999999876554
No 179
>PF12487 DUF3703: Protein of unknown function (DUF3703) ; InterPro: IPR022172 This family of proteins is found in bacteria. Proteins in this family are typically between 113 and 135 amino acids in length.
Probab=36.42 E-value=2.7e+02 Score=24.96 Aligned_cols=67 Identities=13% Similarity=0.054 Sum_probs=55.0
Q ss_pred HHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHHHHH
Q psy17612 15 MESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNKLRE 81 (449)
Q Consensus 15 ~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLke 81 (449)
.+.-+..|+--+..||+..|-..|+..+.+.+...--..-.-|-.|+..+...||-++.-.+-+|--
T Consensus 9 ~~~el~~a~~a~~~~~~~~aw~hLErAHIlgQ~~~~~H~~~H~~ML~~a~r~rd~rEv~GQ~~Rl~~ 75 (112)
T PF12487_consen 9 YDAELEAAREALAAGDLQQAWRHLERAHILGQPYPWLHTRVHWAMLRFALRQRDRREVLGQLLRLIV 75 (112)
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHhhHHhcCCchhHHHHHHHHHHHHHHHccCHHHHHHHHHHHHH
Confidence 4556677888899999999999999999999754433478999999999999999888877766533
No 180
>PRK12370 invasion protein regulator; Provisional
Probab=35.79 E-value=1.2e+02 Score=33.06 Aligned_cols=67 Identities=16% Similarity=0.017 Sum_probs=48.4
Q ss_pred CCHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHHHH
Q psy17612 10 FKMDMMESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNKLR 80 (449)
Q Consensus 10 ~~~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLk 80 (449)
+.|+..++++.+|..++..|++++|.+.+.....+.|....- .+..+..-...++++.|.+...++.
T Consensus 367 l~P~~~~a~~~lg~~l~~~G~~~eAi~~~~~Al~l~P~~~~~----~~~~~~~~~~~g~~eeA~~~~~~~l 433 (553)
T PRK12370 367 LSPISADIKYYYGWNLFMAGQLEEALQTINECLKLDPTRAAA----GITKLWITYYHTGIDDAIRLGDELR 433 (553)
T ss_pred hCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCChhh----HHHHHHHHHhccCHHHHHHHHHHHH
Confidence 456677889999999999999999999999999998753221 1112223344577888877665543
No 181
>PF13429 TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2_B.
Probab=35.53 E-value=1e+02 Score=29.80 Aligned_cols=65 Identities=20% Similarity=0.138 Sum_probs=36.3
Q ss_pred HHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHHHHHHH
Q psy17612 15 MESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNKLREYI 83 (449)
Q Consensus 15 ~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLke~i 83 (449)
...++.+|.++.+.|+++.|.+++.....+-|++..-....+| +-|-.++.+.+.+-++.+.+..
T Consensus 146 ~~~~~~~a~~~~~~G~~~~A~~~~~~al~~~P~~~~~~~~l~~----~li~~~~~~~~~~~l~~~~~~~ 210 (280)
T PF13429_consen 146 ARFWLALAEIYEQLGDPDKALRDYRKALELDPDDPDARNALAW----LLIDMGDYDEAREALKRLLKAA 210 (280)
T ss_dssp HHHHHHHHHHHHHCCHHHHHHHHHHHHHHH-TT-HHHHHHHHH----HHCTTCHHHHHHHHHHHHHHH-
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHH----HHHHCCChHHHHHHHHHHHHHC
Confidence 4456677777777777777777777777777643322222333 2344455555555555555544
No 182
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=35.51 E-value=70 Score=24.88 Aligned_cols=48 Identities=15% Similarity=0.170 Sum_probs=37.3
Q ss_pred ccccccccchhhHHhhcCCCHHHHHHHHHHHHHcccccceecccCCEEEeCC
Q psy17612 243 SNVIDKIFDGQMLASKLNMGTDEAECWIVNLIRNARLDAKIDSKLGHVIMGT 294 (449)
Q Consensus 243 ~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rLdaKIDs~~G~V~m~~ 294 (449)
...+..-+.-+.||+.+|+|.+-+-+-|..|...|-| +...|.++...
T Consensus 22 ~~~~~~~lt~~~iA~~~g~sr~tv~r~l~~l~~~g~I----~~~~~~i~I~d 69 (76)
T PF13545_consen 22 GIRIPLPLTQEEIADMLGVSRETVSRILKRLKDEGII----EVKRGKIIILD 69 (76)
T ss_dssp EEEEEEESSHHHHHHHHTSCHHHHHHHHHHHHHTTSE----EEETTEEEESS
T ss_pred CceEEecCCHHHHHHHHCCCHHHHHHHHHHHHHCCCE----EEcCCEEEECC
Confidence 3345556777999999999999999999999888854 45666666543
No 183
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=35.18 E-value=67 Score=25.73 Aligned_cols=33 Identities=12% Similarity=0.285 Sum_probs=28.5
Q ss_pred ceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHHHHHcccc
Q psy17612 234 HQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLIRNARL 279 (449)
Q Consensus 234 y~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rL 279 (449)
+.-++- ..+|+.+|+|.-.+..+|..|-.+|++
T Consensus 13 ~~p~~T-------------~eiA~~~gls~~~aR~yL~~Le~eG~V 45 (62)
T PF04703_consen 13 NGPLKT-------------REIADALGLSIYQARYYLEKLEKEGKV 45 (62)
T ss_dssp TS-EEH-------------HHHHHHHTS-HHHHHHHHHHHHHCTSE
T ss_pred CCCCCH-------------HHHHHHhCCCHHHHHHHHHHHHHCCCE
Confidence 777888 999999999999999999999888866
No 184
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=34.23 E-value=1.1e+02 Score=22.33 Aligned_cols=43 Identities=16% Similarity=0.254 Sum_probs=34.4
Q ss_pred HHHHHHHHHhhhhceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHHHHHccc
Q psy17612 221 NARLMIFETFCRIHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLIRNAR 278 (449)
Q Consensus 221 naR~~ife~ycriy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~r 278 (449)
..|+.|....+. ...++ ..+|+.||+++..+-+-|-.|..+|-
T Consensus 2 ~~R~~Il~~L~~--~~~~~-------------~el~~~l~~s~~~vs~hL~~L~~~gl 44 (47)
T PF01022_consen 2 PTRLRILKLLSE--GPLTV-------------SELAEELGLSQSTVSHHLKKLREAGL 44 (47)
T ss_dssp HHHHHHHHHHTT--SSEEH-------------HHHHHHHTS-HHHHHHHHHHHHHTTS
T ss_pred HHHHHHHHHHHh--CCCch-------------hhHHHhccccchHHHHHHHHHHHCcC
Confidence 357777777777 66788 99999999999999999988876663
No 185
>PRK14584 hmsS hemin storage system protein; Provisional
Probab=33.57 E-value=82 Score=29.73 Aligned_cols=46 Identities=26% Similarity=0.343 Sum_probs=31.1
Q ss_pred HHHHHHHHHhcCccchhhHHHHhcCCch-----hhhHHHhhhhHHHHHHHHHHHh
Q psy17612 103 LIHWSLFVFFNHVKGRDLIIDMFLNRPH-----YLNAIQTMCPHILRYLATAVII 152 (449)
Q Consensus 103 liHwsLf~ffn~~~g~~~~iD~F~~~~~-----yl~aIqt~cp~lLRYlvvA~Il 152 (449)
++-|..|.||- ...|+++|.+++. +...+-..+..++-|+++|++-
T Consensus 23 ~~aW~gfi~l~----~~~~~~~~~~~~~~gp~~~~~~~~s~~~tl~~yl~ial~n 73 (153)
T PRK14584 23 ALAWFGFLFLL----VRGLLEMISRAPHMGPIPLRIYILSGLTTIALYLAIAAFN 73 (153)
T ss_pred HHHHHHHHHHH----HHHHHHHhccCcccCCcchhHHHhhhHHHHHHHHHHHHHH
Confidence 35688887762 3346777764333 4566667788899999888764
No 186
>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=33.57 E-value=2e+02 Score=25.26 Aligned_cols=53 Identities=21% Similarity=0.269 Sum_probs=33.2
Q ss_pred HHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhh--cChHHHHHHH
Q psy17612 17 SMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILV--QNWDLALEDL 76 (449)
Q Consensus 17 ~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~--~dwd~a~~~l 76 (449)
+.+.+|++++..|+|+.|.+.|.. .++... ....+. +.-+|+. ++++.|.+--
T Consensus 87 a~l~LA~~~~~~~~~d~Al~~L~~----~~~~~~--~~~~~~-~~Gdi~~~~g~~~~A~~~y 141 (145)
T PF09976_consen 87 ARLRLARILLQQGQYDEALATLQQ----IPDEAF--KALAAE-LLGDIYLAQGDYDEARAAY 141 (145)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHh----ccCcch--HHHHHH-HHHHHHHHCCCHHHHHHHH
Confidence 577899999999999999999854 221111 122222 3335554 5677665543
No 187
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=33.56 E-value=82 Score=21.70 Aligned_cols=23 Identities=9% Similarity=0.182 Sum_probs=20.4
Q ss_pred hhHHhhcCCCHHHHHHHHHHHHH
Q psy17612 253 QMLASKLNMGTDEAECWIVNLIR 275 (449)
Q Consensus 253 ~~LA~~Lnms~~e~E~wIVnlIr 275 (449)
..+|+.+|+|..-+-+|+.+...
T Consensus 30 ~~ia~~~~~s~~~i~~~~~~~~~ 52 (55)
T cd06171 30 EEIAEILGISRSTVRQRLHRALK 52 (55)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHH
Confidence 99999999999999999987643
No 188
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=33.52 E-value=66 Score=22.55 Aligned_cols=30 Identities=13% Similarity=0.158 Sum_probs=27.0
Q ss_pred chhhHHhhcCCCHHHHHHHHHHHHHccccc
Q psy17612 251 DGQMLASKLNMGTDEAECWIVNLIRNARLD 280 (449)
Q Consensus 251 ~~~~LA~~Lnms~~e~E~wIVnlIr~~rLd 280 (449)
....||+.+|+|+..+-+.|..|...|-+.
T Consensus 10 s~~~la~~l~~s~~tv~~~l~~L~~~g~l~ 39 (48)
T smart00419 10 TRQEIAELLGLTRETVSRTLKRLEKEGLIS 39 (48)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 348999999999999999999999988774
No 189
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=33.18 E-value=91 Score=22.92 Aligned_cols=44 Identities=16% Similarity=0.207 Sum_probs=27.6
Q ss_pred HHHHHHHHHHHHHHHhhhhceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHHHH
Q psy17612 215 LDEFVENARLMIFETFCRIHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLI 274 (449)
Q Consensus 215 ~d~fvenaR~~ife~ycriy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlI 274 (449)
+..+=+.-|..+...| +...+. ..+|+.+|+|+.-+..++.+..
T Consensus 8 l~~L~~~~r~i~~l~~---~~g~s~-------------~eIa~~l~~s~~~v~~~l~ra~ 51 (54)
T PF08281_consen 8 LAQLPERQREIFLLRY---FQGMSY-------------AEIAEILGISESTVKRRLRRAR 51 (54)
T ss_dssp HHCS-HHHHHHHHHHH---TS---H-------------HHHHHHCTS-HHHHHHHHHHHH
T ss_pred HHCCCHHHHHHHHHHH---HHCcCH-------------HHHHHHHCcCHHHHHHHHHHHH
Confidence 3333444455554444 355566 8899999999999999998764
No 190
>KOG1497|consensus
Probab=33.16 E-value=88 Score=33.23 Aligned_cols=48 Identities=21% Similarity=0.278 Sum_probs=43.1
Q ss_pred HHHHhhcCCChHHHHHHHHHHhhhcccccccccCCCeEEecCCCCChhHH
Q psy17612 357 IMLASKLNMGTDEAECWIVNLIRNARLDAKIDSKLGHVIMGTQPLSPYQQ 406 (449)
Q Consensus 357 ~~la~kLnm~~~eaE~WIvnLIr~~~ldAKIDs~~~~v~m~~~~~svyqq 406 (449)
+.|+.-|+++++.||+--.+.|-..||.+-||-.+|.|+..+ .+.|+|
T Consensus 321 ~~Lg~ll~i~~ekaekiaa~MI~qeRmng~IDQ~egiihFe~--~e~l~~ 368 (399)
T KOG1497|consen 321 EELGALLKIDAEKAEKIAAQMITQERMNGSIDQIEGIIHFED--REELPQ 368 (399)
T ss_pred HHHHHHhCCCHHHHHHHHHHHHhHHHhccchHhhcceEeecc--hhhhhh
Confidence 389999999999999999999999999999999999999876 556644
No 191
>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional
Probab=33.16 E-value=8.5e+02 Score=29.35 Aligned_cols=60 Identities=22% Similarity=0.208 Sum_probs=41.4
Q ss_pred HHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHH-HhHhhcChHHHHHHHHHHH
Q psy17612 16 ESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLA-SEILVQNWDLALEDLNKLR 80 (449)
Q Consensus 16 d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla-~eIl~~dwd~a~~~l~kLk 80 (449)
...+.+|..+.+.|+++.|.+++.......+... ...+ .++ .-...++++.|...+.++-
T Consensus 543 ~a~~~la~all~~Gd~~eA~~~l~qAL~l~P~~~----~l~~-~La~~l~~~Gr~~eAl~~~~~AL 603 (987)
T PRK09782 543 EDLLAAANTAQAAGNGAARDRWLQQAEQRGLGDN----ALYW-WLHAQRYIPGQPELALNDLTRSL 603 (987)
T ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCccH----HHHH-HHHHHHHhCCCHHHHHHHHHHHH
Confidence 4578889999999999999999999888765331 1222 222 1223478888887766654
No 192
>PF11972 HTH_13: HTH DNA binding domain; InterPro: IPR021068 The proteins in this entry have not been characterised. They contain a C-terminal helix-turn-helix DNA binding domain.
Probab=32.90 E-value=41 Score=26.56 Aligned_cols=25 Identities=24% Similarity=0.409 Sum_probs=21.8
Q ss_pred hhHHH-HHHhhcCCChHHHHHHHHHH
Q psy17612 353 NVITI-MLASKLNMGTDEAECWIVNL 377 (449)
Q Consensus 353 ~~~~~-~la~kLnm~~~eaE~WIvnL 377 (449)
-+||. |+++.||.|+..|.+.|..|
T Consensus 12 P~Vsa~mva~~L~vT~~~A~~li~eL 37 (54)
T PF11972_consen 12 PLVSAPMVAKELGVTPQAAQRLIAEL 37 (54)
T ss_pred ccccHHHHHHHhCCCHHHHHHHHHHh
Confidence 45777 99999999999999998766
No 193
>COG1666 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.52 E-value=63 Score=30.69 Aligned_cols=41 Identities=17% Similarity=0.263 Sum_probs=33.3
Q ss_pred HHHHhhhcccccccccCCCeEEecCCCCChhHHHHHhhhcc
Q psy17612 374 IVNLIRNARLDAKIDSKLGHVIMGTQPLSPYQQLLEKIDTL 414 (449)
Q Consensus 374 IvnLIr~~~ldAKIDs~~~~v~m~~~~~svyqqviektk~l 414 (449)
|+.|||+++|--+=--...+|.++.-...-.|+||--.|+.
T Consensus 112 I~KlIkDsklKVqaqIQGdqVRVtgK~rDDLQaVialvr~~ 152 (165)
T COG1666 112 IVKLIKDSKLKVQAQIQGDQVRVTGKKRDDLQAVIALVRGA 152 (165)
T ss_pred HHHHHHhcccceeeeeccceEEEeccchhhHHHHHHHHHhc
Confidence 89999999995333346889999999999999999876654
No 194
>KOG3364|consensus
Probab=32.46 E-value=41 Score=31.50 Aligned_cols=39 Identities=26% Similarity=0.284 Sum_probs=32.1
Q ss_pred CCHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCc
Q psy17612 10 FKMDMMESMYKLAKFRYECGNYSITTSYLYFYLLVMPTS 48 (449)
Q Consensus 10 ~~~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~ 48 (449)
=+.+-++.+|=+|-=+|+.|+|+.+..|+.-+...-|++
T Consensus 66 ~~~~rRe~lyYLAvg~yRlkeY~~s~~yvd~ll~~e~~n 104 (149)
T KOG3364|consen 66 HPERRRECLYYLAVGHYRLKEYSKSLRYVDALLETEPNN 104 (149)
T ss_pred CcccchhhhhhhHHHHHHHhhHHHHHHHHHHHHhhCCCc
Confidence 356678888999999999999999999998777666543
No 195
>KOG0547|consensus
Probab=32.26 E-value=99 Score=34.57 Aligned_cols=59 Identities=14% Similarity=0.196 Sum_probs=41.0
Q ss_pred HHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHHH
Q psy17612 17 SMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNKL 79 (449)
Q Consensus 17 ~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kL 79 (449)
+|-..|+-+|..|.|+.|.+|+.....+||+.. - -.=.+-||=+..++|..+.++-.+.
T Consensus 117 ~lK~~GN~~f~~kkY~eAIkyY~~AI~l~p~ep-i---FYsNraAcY~~lgd~~~Vied~TkA 175 (606)
T KOG0547|consen 117 ALKTKGNKFFRNKKYDEAIKYYTQAIELCPDEP-I---FYSNRAACYESLGDWEKVIEDCTKA 175 (606)
T ss_pred HHHhhhhhhhhcccHHHHHHHHHHHHhcCCCCc-h---hhhhHHHHHHHHhhHHHHHHHHHHH
Confidence 345578889999999999999999999998641 1 1112335555666776666655544
No 196
>PF05527 DUF758: Domain of unknown function (DUF758) ; InterPro: IPR008477 This is a family of eukaryotic proteins with unknown function, which are induced by tumour necrosis factor.; PDB: 3F4M_A.
Probab=31.79 E-value=3e+02 Score=26.82 Aligned_cols=33 Identities=15% Similarity=0.299 Sum_probs=25.5
Q ss_pred CHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcC
Q psy17612 11 KMDMMESMYKLAKFRYECGNYSITTSYLYFYLLVM 45 (449)
Q Consensus 11 ~~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~ 45 (449)
..|++|.||+++|-|. |+...|.+++.......
T Consensus 35 sselLD~ly~l~K~~t--~~kkeA~ki~KniIKi~ 67 (186)
T PF05527_consen 35 SSELLDELYRLLKEYT--GNKKEAEKIIKNIIKIV 67 (186)
T ss_dssp HHHHHHHHHHHHHHHH--S-HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHh--cCHHHHHHHHHHHHHHH
Confidence 3578999999999765 78999999887665544
No 197
>PRK14574 hmsH outer membrane protein; Provisional
Probab=31.55 E-value=9.2e+02 Score=28.42 Aligned_cols=70 Identities=13% Similarity=0.075 Sum_probs=48.1
Q ss_pred ccCCCHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHHHH
Q psy17612 7 FFQFKMDMMESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNKLR 80 (449)
Q Consensus 7 ~~~~~~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLk 80 (449)
---.-|+..+..|..|-..++.|||..|.+.|.++...-|....- +. ..+.+-...++.+.|...+++.-
T Consensus 26 ~~~~~p~~~~~~y~~aii~~r~Gd~~~Al~~L~qaL~~~P~~~~a-v~---dll~l~~~~G~~~~A~~~~eka~ 95 (822)
T PRK14574 26 GFVVNPAMADTQYDSLIIRARAGDTAPVLDYLQEESKAGPLQSGQ-VD---DWLQIAGWAGRDQEVIDVYERYQ 95 (822)
T ss_pred ccccCccchhHHHHHHHHHHhCCCHHHHHHHHHHHHhhCccchhh-HH---HHHHHHHHcCCcHHHHHHHHHhc
Confidence 334456778899999999999999999999999988887754222 11 22222223377777777666553
No 198
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID. Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.
Probab=30.43 E-value=57 Score=27.43 Aligned_cols=32 Identities=6% Similarity=0.094 Sum_probs=27.4
Q ss_pred HHHHHHHhhhhceeeEeeccccccccccchhhHHhhcCCCHHHHHH
Q psy17612 223 RLMIFETFCRIHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAEC 268 (449)
Q Consensus 223 R~~ife~ycriy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~ 268 (449)
|+.....+++- +.++| ..+|+.+|+|..=+-+
T Consensus 7 R~~~I~e~l~~-~~~ti-------------~dvA~~~gvS~~TVsr 38 (80)
T TIGR02844 7 RVLEIGKYIVE-TKATV-------------RETAKVFGVSKSTVHK 38 (80)
T ss_pred HHHHHHHHHHH-CCCCH-------------HHHHHHhCCCHHHHHH
Confidence 77777777777 99999 9999999999987655
No 199
>PF13429 TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2_B.
Probab=30.42 E-value=5.1e+02 Score=25.03 Aligned_cols=179 Identities=16% Similarity=0.088 Sum_probs=58.5
Q ss_pred CHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHHHHHHHhcCCCCC
Q psy17612 11 KMDMMESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNKLREYIDGGSANF 90 (449)
Q Consensus 11 ~~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLke~id~~~~~~ 90 (449)
++.....+..++.+ +..|+|.+|.+++.......+ +.. .+...+.+-...++|+.+.+-++++.+... ..
T Consensus 74 ~~~~~~~~~~l~~l-~~~~~~~~A~~~~~~~~~~~~--~~~---~l~~~l~~~~~~~~~~~~~~~l~~~~~~~~----~~ 143 (280)
T PF13429_consen 74 DKANPQDYERLIQL-LQDGDPEEALKLAEKAYERDG--DPR---YLLSALQLYYRLGDYDEAEELLEKLEELPA----AP 143 (280)
T ss_dssp --------------------------------------------------H-HHHTT-HHHHHHHHHHHHH-T-------
T ss_pred cccccccccccccc-ccccccccccccccccccccc--ccc---hhhHHHHHHHHHhHHHHHHHHHHHHHhccC----CC
Confidence 44445556677777 788999999988765444332 222 222333344556789888888888764221 11
Q ss_pred CChHHHHHHHHHHHHHHHHHHhcCccc-----hhhHHHHhcCCchhhhHHHhhhhHHHHHHHHHHHhccccccchHHHHH
Q psy17612 91 ESPLHLLQQRTWLIHWSLFVFFNHVKG-----RDLIIDMFLNRPHYLNAIQTMCPHILRYLATAVIINRSKRNALKDLVK 165 (449)
Q Consensus 91 ~~pl~~l~qR~WliHwsLf~ffn~~~g-----~~~~iD~F~~~~~yl~aIqt~cp~lLRYlvvA~Il~~~r~~~l~dlv~ 165 (449)
.+|.. |.....+....| ...+-....-.| .-|.++..++-.. +...+.+-++++++
T Consensus 144 ~~~~~----------~~~~a~~~~~~G~~~~A~~~~~~al~~~P--------~~~~~~~~l~~~l-i~~~~~~~~~~~l~ 204 (280)
T PF13429_consen 144 DSARF----------WLALAEIYEQLGDPDKALRDYRKALELDP--------DDPDARNALAWLL-IDMGDYDEAREALK 204 (280)
T ss_dssp T-HHH----------HHHHHHHHHHCCHHHHHHHHHHHHHHH-T--------T-HHHHHHHHHHH-CTTCHHHHHHHHHH
T ss_pred CCHHH----------HHHHHHHHHHcCCHHHHHHHHHHHHHcCC--------CCHHHHHHHHHHH-HHCCChHHHHHHHH
Confidence 23322 222222211122 222222222122 2223443443333 33333333444444
Q ss_pred HHhhhc---cCCCchHHHHHHHHhhcccHHHHHHHHHHHhhhcccccchHHhHHHHHHH
Q psy17612 166 VIQQES---YTYKDPITEFLEHLYVSFDFESAREKLTECTEVLDNDFFLVACLDEFVEN 221 (449)
Q Consensus 166 vi~qE~---~~Y~DpiT~fv~~lYv~fdf~~aq~~L~~~~~vl~~DfFL~~~~d~fven 221 (449)
...... ..+.+++ -.+.+.--+.++|...+.+.-..-.+|+-...++.+.++.
T Consensus 205 ~~~~~~~~~~~~~~~l---a~~~~~lg~~~~Al~~~~~~~~~~p~d~~~~~~~a~~l~~ 260 (280)
T PF13429_consen 205 RLLKAAPDDPDLWDAL---AAAYLQLGRYEEALEYLEKALKLNPDDPLWLLAYADALEQ 260 (280)
T ss_dssp HHHHH-HTSCCHCHHH---HHHHHHHT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHT-
T ss_pred HHHHHCcCHHHHHHHH---HHHhcccccccccccccccccccccccccccccccccccc
Confidence 332221 0122333 3333444677888888888777777888877776666543
No 200
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=30.14 E-value=1e+02 Score=28.38 Aligned_cols=62 Identities=11% Similarity=0.106 Sum_probs=41.8
Q ss_pred HHHHHHHHHhhhhceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHHHHHcccccceecccCCEEEeCCCC
Q psy17612 221 NARLMIFETFCRIHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLIRNARLDAKIDSKLGHVIMGTQP 296 (449)
Q Consensus 221 naR~~ife~ycriy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rLdaKIDs~~G~V~m~~~~ 296 (449)
..|.+++-.--..-.-+++ +.+|+..|+|+.++++.+..|-++|=+...=-+.-| ...++|+
T Consensus 10 al~~L~~LA~~~~~~~~s~-------------~~IA~~~~is~~~L~kil~~L~kaGlV~S~rG~~GG-y~Lar~~ 71 (150)
T COG1959 10 ALRALLYLALLPGGGPVSS-------------AEIAERQGISPSYLEKILSKLRKAGLVKSVRGKGGG-YRLARPP 71 (150)
T ss_pred HHHHHHHHHhCCCCCcccH-------------HHHHHHhCcCHHHHHHHHHHHHHcCCEEeecCCCCC-ccCCCCh
Confidence 3455554443333335778 999999999999999999999887766554444333 3344444
No 201
>KOG1126|consensus
Probab=30.10 E-value=1.3e+02 Score=34.28 Aligned_cols=75 Identities=8% Similarity=0.092 Sum_probs=57.1
Q ss_pred cCCCHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHHHHHHHhcC
Q psy17612 8 FQFKMDMMESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNKLREYIDGG 86 (449)
Q Consensus 8 ~~~~~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLke~id~~ 86 (449)
..|.|--.--+...|+++.++|.+++|..++.....+-+.+ .-+-+.+-.+-+.+.+.+.|+.+|++||++.-+.
T Consensus 516 ~~INP~nsvi~~~~g~~~~~~k~~d~AL~~~~~A~~ld~kn----~l~~~~~~~il~~~~~~~eal~~LEeLk~~vP~e 590 (638)
T KOG1126|consen 516 VEINPSNSVILCHIGRIQHQLKRKDKALQLYEKAIHLDPKN----PLCKYHRASILFSLGRYVEALQELEELKELVPQE 590 (638)
T ss_pred hcCCccchhHHhhhhHHHHHhhhhhHHHHHHHHHHhcCCCC----chhHHHHHHHHHhhcchHHHHHHHHHHHHhCcch
Confidence 35666666777888999999999999998888766655432 2245666666677788999999999999998874
No 202
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=29.86 E-value=53 Score=24.73 Aligned_cols=28 Identities=14% Similarity=0.164 Sum_probs=26.0
Q ss_pred hhHHhhcCCCHHHHHHHHHHHHHccccc
Q psy17612 253 QMLASKLNMGTDEAECWIVNLIRNARLD 280 (449)
Q Consensus 253 ~~LA~~Lnms~~e~E~wIVnlIr~~rLd 280 (449)
..||+.+|+++.-+.+.|..|...|-+.
T Consensus 29 ~ela~~~g~s~~tv~r~l~~L~~~g~i~ 56 (67)
T cd00092 29 QEIADYLGLTRETVSRTLKELEEEGLIS 56 (67)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 9999999999999999999999888664
No 203
>PF14276 DUF4363: Domain of unknown function (DUF4363)
Probab=29.81 E-value=3.5e+02 Score=23.48 Aligned_cols=75 Identities=13% Similarity=0.102 Sum_probs=55.9
Q ss_pred CHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCC-----------cchhhHHHHHHHHHHhHhhcChHHHHHHHHHH
Q psy17612 11 KMDMMESMYKLAKFRYECGNYSITTSYLYFYLLVMPT-----------SDRHYLAVLWGKLASEILVQNWDLALEDLNKL 79 (449)
Q Consensus 11 ~~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~-----------~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kL 79 (449)
..+.+.....-+.-..+.+||+.|.+.+..+...... ++-..++.-..++..-|..+|-+.++.++..+
T Consensus 24 ~~~~i~~~l~~i~~~i~~~dW~~A~~~~~~l~~~W~k~~~~~~~~~~h~eid~i~~sl~rl~~~i~~~dk~~~l~el~~l 103 (121)
T PF14276_consen 24 STDSIEEQLEQIEEAIENEDWEKAYKETEELEKEWDKNKKRWSILIEHQEIDNIDISLARLKGYIEAKDKSESLAELAEL 103 (121)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhhchheeeeecHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence 3556667777788888999999999888776655421 11223677778888888888888888888888
Q ss_pred HHHHhc
Q psy17612 80 REYIDG 85 (449)
Q Consensus 80 ke~id~ 85 (449)
|.+++.
T Consensus 104 k~~i~~ 109 (121)
T PF14276_consen 104 KELIEH 109 (121)
T ss_pred HHHHHH
Confidence 888875
No 204
>cd00131 PAX Paired Box domain
Probab=28.81 E-value=89 Score=27.96 Aligned_cols=44 Identities=11% Similarity=0.064 Sum_probs=35.0
Q ss_pred HHHHHHHHhhhhceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHHHHHcccccc
Q psy17612 222 ARLMIFETFCRIHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLIRNARLDA 281 (449)
Q Consensus 222 aR~~ife~ycriy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rLda 281 (449)
.|..|+.-| ....+. ..+|+.||+|...+-+|+-++-..|.+..
T Consensus 22 ~R~rIv~~~---~~G~s~-------------~~iA~~~~Vs~~tV~r~i~r~~e~G~v~p 65 (128)
T cd00131 22 IRQRIVELA---QSGIRP-------------CDISRQLRVSHGCVSKILNRYYETGSIRP 65 (128)
T ss_pred HHHHHHHHH---HcCCCH-------------HHHHHHHCcCHHHHHHHHHHHHHcCCcCC
Confidence 455565444 356677 99999999999999999999988887653
No 205
>PF04010 DUF357: Protein of unknown function (DUF357); InterPro: IPR023140 This domain is found in a family of proteins, which have no known function.; PDB: 2OO2_A 2PMR_A.
Probab=28.72 E-value=1.1e+02 Score=25.39 Aligned_cols=34 Identities=21% Similarity=0.275 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcC
Q psy17612 12 MDMMESMYKLAKFRYECGNYSITTSYLYFYLLVM 45 (449)
Q Consensus 12 ~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~ 45 (449)
.+|..+.++=|++|++.||+.+|...+..-+.+.
T Consensus 32 ~~mA~~Y~~D~~~fl~~gD~v~Ala~~sYa~GwL 65 (75)
T PF04010_consen 32 LEMAESYLEDGKYFLEKGDYVNALACFSYAHGWL 65 (75)
T ss_dssp HHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 3678889999999999999999998887655443
No 206
>COG5187 RPN7 26S proteasome regulatory complex component, contains PCI domain [Posttranslational modification, protein turnover, chaperones]
Probab=28.44 E-value=1.1e+02 Score=32.39 Aligned_cols=70 Identities=17% Similarity=0.234 Sum_probs=53.2
Q ss_pred HHH-HHHhhcCCChHHHHHHHHHHhhhcccccccccCCCeEEecCCCC--ChhHHHHHhhhcccchHHHHHHH
Q psy17612 355 ITI-MLASKLNMGTDEAECWIVNLIRNARLDAKIDSKLGHVIMGTQPL--SPYQQLLEKIDTLSVRSEALQAL 424 (449)
Q Consensus 355 ~~~-~la~kLnm~~~eaE~WIvnLIr~~~ldAKIDs~~~~v~m~~~~~--svyqqviektk~l~~rt~~l~~~ 424 (449)
+|. .+|+.+|.|.+=.++=+...|-+.||..+||-.+|.|..+.|.. --|+.|.---.+|--|-|.-+.+
T Consensus 332 lsl~sMA~tFgVSV~yvdrDLg~FIp~~~LncvIDRvnGvVetnrpdekn~qy~~vVkqGd~ll~klqKy~at 404 (412)
T COG5187 332 LSLESMAQTFGVSVEYVDRDLGEFIPEGRLNCVIDRVNGVVETNRPDEKNQQYSSVVKQGDDLLRKLQKYVAT 404 (412)
T ss_pred hhHHHHHHHhCccHHHHhhhHHhhCCCCceeeeeecccceEeccCcchhhhhHHHHHhcchHHHHHHHHHHHH
Confidence 444 67889999999999999999999999999999999999887764 45666665555554444443333
No 207
>PF13512 TPR_18: Tetratricopeptide repeat
Probab=27.54 E-value=2.4e+02 Score=26.22 Aligned_cols=42 Identities=19% Similarity=0.258 Sum_probs=35.3
Q ss_pred ccCCCHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCc
Q psy17612 7 FFQFKMDMMESMYKLAKFRYECGNYSITTSYLYFYLLVMPTS 48 (449)
Q Consensus 7 ~~~~~~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~ 48 (449)
.|-+.+=.-.+-+++|..||+.|+|+.|...+..|..+-|..
T Consensus 39 ryP~g~ya~qAqL~l~yayy~~~~y~~A~a~~~rFirLhP~h 80 (142)
T PF13512_consen 39 RYPFGEYAEQAQLDLAYAYYKQGDYEEAIAAYDRFIRLHPTH 80 (142)
T ss_pred cCCCCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCC
Confidence 344555556788999999999999999999999999999853
No 208
>PRK15174 Vi polysaccharide export protein VexE; Provisional
Probab=27.36 E-value=2e+02 Score=32.28 Aligned_cols=70 Identities=19% Similarity=0.250 Sum_probs=0.0
Q ss_pred CCCHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHHHHHH
Q psy17612 9 QFKMDMMESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNKLREY 82 (449)
Q Consensus 9 ~~~~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLke~ 82 (449)
.+.|+...++..+|..+.+.|+++.|..++.....+.| +....-..+|..... .++++.|.+.+.++-+.
T Consensus 278 ~l~P~~~~a~~~lg~~l~~~g~~~eA~~~l~~al~l~P--~~~~a~~~La~~l~~--~G~~~eA~~~l~~al~~ 347 (656)
T PRK15174 278 QFNSDNVRIVTLYADALIRTGQNEKAIPLLQQSLATHP--DLPYVRAMYARALRQ--VGQYTAASDEFVQLARE 347 (656)
T ss_pred hhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCC--CCHHHHHHHHHHHHH--CCCHHHHHHHHHHHHHh
No 209
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=26.98 E-value=1.1e+02 Score=23.65 Aligned_cols=41 Identities=7% Similarity=0.117 Sum_probs=34.2
Q ss_pred HHHHhhhhceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHHHHHccccc
Q psy17612 226 IFETFCRIHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLIRNARLD 280 (449)
Q Consensus 226 ife~ycriy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rLd 280 (449)
+|...+ -+...+. ..+|+.+|++...+-+.|-+|.+.|-+.
T Consensus 13 vy~~Ll-~~~~~t~-------------~eIa~~l~i~~~~v~~~L~~L~~~GlV~ 53 (68)
T PF01978_consen 13 VYLALL-KNGPATA-------------EEIAEELGISRSTVYRALKSLEEKGLVE 53 (68)
T ss_dssp HHHHHH-HHCHEEH-------------HHHHHHHTSSHHHHHHHHHHHHHTTSEE
T ss_pred HHHHHH-HcCCCCH-------------HHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 444444 6788888 9999999999999999999998888653
No 210
>PF04049 APC8: Anaphase promoting complex subunit 8 / Cdc23 ; InterPro: IPR007192 The anaphase-promoting complex is composed of eight protein subunits, including BimE (APC1), CDC27 (APC3), CDC16 (APC6), and CDC23 (APC8). This entry is for CDC23.; GO: 0030071 regulation of mitotic metaphase/anaphase transition, 0005680 anaphase-promoting complex
Probab=26.86 E-value=41 Score=30.75 Aligned_cols=25 Identities=28% Similarity=0.393 Sum_probs=22.1
Q ss_pred HHHHHHHHHHHhcCChhhHHHHHHH
Q psy17612 16 ESMYKLAKFRYECGNYSITTSYLYF 40 (449)
Q Consensus 16 d~lyk~Akf~y~~GdY~~A~~~L~~ 40 (449)
...|-+||-||+|++|..|.-+|..
T Consensus 75 ~d~yllAksyFD~kEy~RaA~~L~~ 99 (142)
T PF04049_consen 75 YDKYLLAKSYFDCKEYDRAAHVLKD 99 (142)
T ss_pred HHHHHHHHHHhchhHHHHHHHHHcc
Confidence 4788999999999999999977764
No 211
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=26.61 E-value=1.2e+02 Score=25.52 Aligned_cols=56 Identities=21% Similarity=0.164 Sum_probs=37.6
Q ss_pred HHhhhhchhhhHHH-HHHhhcCCChHHHHHHHHHHhhhcccccccccC--CCeEEecCCCCC
Q psy17612 344 EMLASKADLNVITI-MLASKLNMGTDEAECWIVNLIRNARLDAKIDSK--LGHVIMGTQPLS 402 (449)
Q Consensus 344 ~~~~~~~~~~~~~~-~la~kLnm~~~eaE~WIvnLIr~~~ldAKIDs~--~~~v~m~~~~~s 402 (449)
..+...++-+-+|. .||++||||.....|-|-.| |+-.+ .|||. .|......+.-.
T Consensus 9 ~~ll~~~~~~~~SGe~La~~LgiSRtaVwK~Iq~L-r~~G~--~I~s~~~kGY~L~~~~~ll 67 (79)
T COG1654 9 LLLLLLLTGNFVSGEKLAEELGISRTAVWKHIQQL-REEGV--DIESVRGKGYLLPQLPDLL 67 (79)
T ss_pred HHHHHHcCCCcccHHHHHHHHCccHHHHHHHHHHH-HHhCC--ceEecCCCceeccCccccC
Confidence 33334445555677 89999999999999988886 67777 45554 455555554433
No 212
>PRK03837 transcriptional regulator NanR; Provisional
Probab=26.60 E-value=1.6e+02 Score=27.93 Aligned_cols=64 Identities=14% Similarity=0.030 Sum_probs=54.9
Q ss_pred HHHHHHHHHHHHHHHhhhhceee-EeeccccccccccchhhHHhhcCCCHHHHHHHHHHHHHcccccceecccCCEEEeC
Q psy17612 215 LDEFVENARLMIFETFCRIHQCI-SIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLIRNARLDAKIDSKLGHVIMG 293 (449)
Q Consensus 215 ~d~fvenaR~~ife~ycriy~~I-sI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rLdaKIDs~~G~V~m~ 293 (449)
.+...+..|..|..-.++|=.++ +. ..||++||||..=+-.-|..|-..|-++- -...|.++..
T Consensus 15 ~~~v~~~l~~~I~~g~l~pG~~Lp~E-------------~~Lae~~gVSRt~VREAL~~L~~eGlv~~--~~~~G~~V~~ 79 (241)
T PRK03837 15 SEEVEERLEQMIRSGEFGPGDQLPSE-------------RELMAFFGVGRPAVREALQALKRKGLVQI--SHGERARVSR 79 (241)
T ss_pred HHHHHHHHHHHHHhCCCCCCCCCCCH-------------HHHHHHhCCCHHHHHHHHHHHHHCCCEEE--ecCCceeEec
Confidence 46788999999999999999999 89 99999999999999999999988887643 4556776654
No 213
>KOG3060|consensus
Probab=26.44 E-value=2.4e+02 Score=29.17 Aligned_cols=64 Identities=25% Similarity=0.372 Sum_probs=48.8
Q ss_pred HHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHHHHHHHhcC
Q psy17612 15 MESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNKLREYIDGG 86 (449)
Q Consensus 15 ~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLke~id~~ 86 (449)
-++...+|.+|..-|+|++|.=++.++....|.+ ..+++.|| |++.. ..-.+++.-.|+++.++
T Consensus 154 ~EAW~eLaeiY~~~~~f~kA~fClEE~ll~~P~n-----~l~f~rla-e~~Yt--~gg~eN~~~arkyy~~a 217 (289)
T KOG3060|consen 154 QEAWHELAEIYLSEGDFEKAAFCLEELLLIQPFN-----PLYFQRLA-EVLYT--QGGAENLELARKYYERA 217 (289)
T ss_pred HHHHHHHHHHHHhHhHHHHHHHHHHHHHHcCCCc-----HHHHHHHH-HHHHH--HhhHHHHHHHHHHHHHH
Confidence 4567789999999999999999999988887732 36788888 55543 14466777778888873
No 214
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=26.15 E-value=1.1e+02 Score=22.39 Aligned_cols=29 Identities=7% Similarity=0.280 Sum_probs=24.2
Q ss_pred ceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHHHHH
Q psy17612 234 HQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLIR 275 (449)
Q Consensus 234 y~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr 275 (449)
+...++ ..+|+.||+|..-+-++..+.+.
T Consensus 18 ~~~~t~-------------~eIa~~lg~s~~~V~~~~~~al~ 46 (50)
T PF04545_consen 18 FEGLTL-------------EEIAERLGISRSTVRRILKRALK 46 (50)
T ss_dssp TST-SH-------------HHHHHHHTSCHHHHHHHHHHHHH
T ss_pred cCCCCH-------------HHHHHHHCCcHHHHHHHHHHHHH
Confidence 667778 99999999999999988887664
No 215
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=25.63 E-value=68 Score=23.53 Aligned_cols=20 Identities=25% Similarity=0.543 Sum_probs=18.8
Q ss_pred hhHHhhcCCCHHHHHHHHHH
Q psy17612 253 QMLASKLNMGTDEAECWIVN 272 (449)
Q Consensus 253 ~~LA~~Lnms~~e~E~wIVn 272 (449)
..||..+||++..|..|.-|
T Consensus 31 ~~la~~~~l~~~qV~~WF~n 50 (59)
T cd00086 31 EELAKELGLTERQVKIWFQN 50 (59)
T ss_pred HHHHHHHCcCHHHHHHHHHH
Confidence 89999999999999999876
No 216
>smart00351 PAX Paired Box domain.
Probab=25.54 E-value=1.2e+02 Score=26.93 Aligned_cols=28 Identities=4% Similarity=-0.006 Sum_probs=25.1
Q ss_pred hhHHhhcCCCHHHHHHHHHHHHHccccc
Q psy17612 253 QMLASKLNMGTDEAECWIVNLIRNARLD 280 (449)
Q Consensus 253 ~~LA~~Lnms~~e~E~wIVnlIr~~rLd 280 (449)
..+|+.||+|+.-+-+|+-++-..|.+.
T Consensus 37 ~~iA~~~gvs~~tV~kwi~r~~~~G~~~ 64 (125)
T smart00351 37 CDISRQLCVSHGCVSKILGRYYETGSIR 64 (125)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHcCCcC
Confidence 9999999999999999999997777543
No 217
>PF14561 TPR_20: Tetratricopeptide repeat; PDB: 3QOU_A 2R5S_A 3QDN_B.
Probab=25.38 E-value=1.6e+02 Score=24.74 Aligned_cols=36 Identities=19% Similarity=0.199 Sum_probs=27.9
Q ss_pred CHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCC
Q psy17612 11 KMDMMESMYKLAKFRYECGNYSITTSYLYFYLLVMP 46 (449)
Q Consensus 11 ~~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~ 46 (449)
+|+-.++.|.+|..+...|+|+.|.+.|-.....-+
T Consensus 18 ~P~D~~ar~~lA~~~~~~g~~e~Al~~Ll~~v~~dr 53 (90)
T PF14561_consen 18 NPDDLDARYALADALLAAGDYEEALDQLLELVRRDR 53 (90)
T ss_dssp STT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHCC-T
T ss_pred CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCc
Confidence 567789999999999999999999988866555544
No 218
>PF14178 YppF: YppF-like protein
Probab=25.18 E-value=40 Score=27.16 Aligned_cols=31 Identities=23% Similarity=0.316 Sum_probs=27.7
Q ss_pred ceeeccCCCHHHHHHHHHHHHHHHhcCChhh
Q psy17612 3 LFIFFFQFKMDMMESMYKLAKFRYECGNYSI 33 (449)
Q Consensus 3 ~~~~~~~~~~e~~d~lyk~Akf~y~~GdY~~ 33 (449)
.|+.+++.+|+.++.|+++|+..|=.|+-..
T Consensus 9 ~F~~~k~y~p~~~NeLLDFar~~Yi~gei~i 39 (60)
T PF14178_consen 9 KFMQKKKYEPEDMNELLDFARKLYIQGEISI 39 (60)
T ss_pred HHHHHhccCcccHHHHHHHHHHHHHhCcccH
Confidence 4888999999999999999999998887654
No 219
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=24.86 E-value=1.2e+02 Score=22.49 Aligned_cols=19 Identities=26% Similarity=0.529 Sum_probs=17.6
Q ss_pred HHHhhcCCChHHHHHHHHH
Q psy17612 358 MLASKLNMGTDEAECWIVN 376 (449)
Q Consensus 358 ~la~kLnm~~~eaE~WIvn 376 (449)
.||+.|||+......|.-|
T Consensus 32 ~la~~l~l~~~~V~~WF~n 50 (57)
T PF00046_consen 32 ELAKELGLTERQVKNWFQN 50 (57)
T ss_dssp HHHHHHTSSHHHHHHHHHH
T ss_pred cccccccccccccccCHHH
Confidence 7899999999999999876
No 220
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=24.33 E-value=1.1e+02 Score=23.50 Aligned_cols=36 Identities=28% Similarity=0.394 Sum_probs=28.5
Q ss_pred HHHHHHhhhhceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHHH
Q psy17612 224 LMIFETFCRIHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNL 273 (449)
Q Consensus 224 ~~ife~ycriy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnl 273 (449)
+.+++-+.. -+.+++ +.||+++|+|+--+-..|..+
T Consensus 8 ~~Ll~~L~~-~~~~~~-------------~ela~~l~~S~rti~~~i~~L 43 (59)
T PF08280_consen 8 LKLLELLLK-NKWITL-------------KELAKKLNISERTIKNDINEL 43 (59)
T ss_dssp HHHHHHHHH-HTSBBH-------------HHHHHHCTS-HHHHHHHHHHH
T ss_pred HHHHHHHHc-CCCCcH-------------HHHHHHHCCCHHHHHHHHHHH
Confidence 344555556 889999 999999999999988888775
No 221
>KOG2796|consensus
Probab=24.30 E-value=8.6e+02 Score=25.67 Aligned_cols=171 Identities=20% Similarity=0.302 Sum_probs=93.0
Q ss_pred HHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHHHH---HHHhcCCCCCCCh
Q psy17612 17 SMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNKLR---EYIDGGSANFESP 93 (449)
Q Consensus 17 ~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLk---e~id~~~~~~~~p 93 (449)
.+|-++.+..-.|+|+-..+.+..++..-++.++. +..-+|.++ .+.+|-.+|.....+.. ..+++ ..+.
T Consensus 179 Vmy~~~~~llG~kEy~iS~d~~~~vi~~~~e~~p~-L~s~Lgr~~--MQ~GD~k~a~~yf~~vek~~~kL~~----~q~~ 251 (366)
T KOG2796|consen 179 VMYSMANCLLGMKEYVLSVDAYHSVIKYYPEQEPQ-LLSGLGRIS--MQIGDIKTAEKYFQDVEKVTQKLDG----LQGK 251 (366)
T ss_pred HHHHHHHHHhcchhhhhhHHHHHHHHHhCCcccHH-HHHHHHHHH--HhcccHHHHHHHHHHHHHHHhhhhc----cchh
Confidence 46778889999999999999999999977665555 555555554 55677766665444322 22222 1122
Q ss_pred HHHHHHHHHHHHHHHHHHhcCccchhhHHHHhc-------CCchhhhHHHhhhhHHHHHHHHHHHhccccccchHHHHHH
Q psy17612 94 LHLLQQRTWLIHWSLFVFFNHVKGRDLIIDMFL-------NRPHYLNAIQTMCPHILRYLATAVIINRSKRNALKDLVKV 166 (449)
Q Consensus 94 l~~l~qR~WliHwsLf~ffn~~~g~~~~iD~F~-------~~~~yl~aIqt~cp~lLRYlvvA~Il~~~r~~~l~dlv~v 166 (449)
.++..... ++|+ |.+.+.+... .++.-..++.+. --|+-|+ ++-.+.+|.+-.+
T Consensus 252 ~~V~~n~a-----~i~l------g~nn~a~a~r~~~~i~~~D~~~~~a~NnK-ALcllYl-------g~l~DAiK~~e~~ 312 (366)
T KOG2796|consen 252 IMVLMNSA-----FLHL------GQNNFAEAHRFFTEILRMDPRNAVANNNK-ALCLLYL-------GKLKDALKQLEAM 312 (366)
T ss_pred HHHHhhhh-----hhee------cccchHHHHHHHhhccccCCCchhhhchH-HHHHHHH-------HHHHHHHHHHHHH
Confidence 22222111 2232 3333333322 122111121111 0234443 3334566666666
Q ss_pred HhhhccCCCch-----HHHHHHHHhhcccHHHHHHHHHHHhhhcccccchHHhH
Q psy17612 167 IQQESYTYKDP-----ITEFLEHLYVSFDFESAREKLTECTEVLDNDFFLVACL 215 (449)
Q Consensus 167 i~qE~~~Y~Dp-----iT~fv~~lYv~fdf~~aq~~L~~~~~vl~~DfFL~~~~ 215 (449)
.++.|-+|-.- ++..+|-.|++-- +-.+.|.+.-.-...|-|=++|.
T Consensus 313 ~~~~P~~~l~es~~~nL~tmyEL~Ys~~~--~~k~~l~~~ia~~~~d~f~~~c~ 364 (366)
T KOG2796|consen 313 VQQDPRHYLHESVLFNLTTMYELEYSRSM--QKKQALLEAVAGKEGDSFNTQCL 364 (366)
T ss_pred hccCCccchhhhHHHHHHHHHHHHhhhhh--hHHHHHHHHHhccCCCcccchhh
Confidence 67777666644 6778888888653 12233444444466777877775
No 222
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=23.92 E-value=78 Score=23.50 Aligned_cols=20 Identities=25% Similarity=0.531 Sum_probs=18.5
Q ss_pred hhHHhhcCCCHHHHHHHHHH
Q psy17612 253 QMLASKLNMGTDEAECWIVN 272 (449)
Q Consensus 253 ~~LA~~Lnms~~e~E~wIVn 272 (449)
..||..+||++..|..|.-|
T Consensus 31 ~~la~~l~l~~~~V~~WF~n 50 (57)
T PF00046_consen 31 EELAKELGLTERQVKNWFQN 50 (57)
T ss_dssp HHHHHHHTSSHHHHHHHHHH
T ss_pred ccccccccccccccccCHHH
Confidence 88999999999999999865
No 223
>PF10300 DUF3808: Protein of unknown function (DUF3808); InterPro: IPR019412 This entry represents a family of proteins conserved from fungi to humans. In humans this protein is expressed in primary breast carcinomas but not in normal breast tissue, and has a putative eukaryotic RNP-1 RNA binding region and a candidate anchoring transmembrane domain. The human protein is coordinately regulated with oestrogen receptor, but is not necessarily oestradiol-responsive []. Members of this family carry a tetratricopeptide repeat (IPR013105 from INTERPRO) at their C terminus.
Probab=23.78 E-value=2e+02 Score=31.15 Aligned_cols=64 Identities=9% Similarity=0.073 Sum_probs=49.3
Q ss_pred HHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHHHHH
Q psy17612 18 MYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNKLRE 81 (449)
Q Consensus 18 lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLke 81 (449)
++-.|+++.-.||-+.|.+.+.........-.+-..=++|+.-=+-.+.+||+.|.+...+|.+
T Consensus 270 l~~~gR~~~~~g~~~~Ai~~~~~a~~~q~~~~Ql~~l~~~El~w~~~~~~~w~~A~~~f~~L~~ 333 (468)
T PF10300_consen 270 LFFEGRLERLKGNLEEAIESFERAIESQSEWKQLHHLCYFELAWCHMFQHDWEEAAEYFLRLLK 333 (468)
T ss_pred HHHHHHHHHHhcCHHHHHHHHHHhccchhhHHhHHHHHHHHHHHHHHHHchHHHHHHHHHHHHh
Confidence 4556889999999999999998655332222222345899999999999999999998888866
No 224
>PRK10072 putative transcriptional regulator; Provisional
Probab=23.73 E-value=1.8e+02 Score=25.21 Aligned_cols=27 Identities=19% Similarity=0.241 Sum_probs=22.0
Q ss_pred hhceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHH
Q psy17612 232 RIHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIV 271 (449)
Q Consensus 232 riy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIV 271 (449)
|-...++- ..+|+.+|+|..-+-+|..
T Consensus 42 R~~~glTQ-------------~elA~~lGvS~~TVs~WE~ 68 (96)
T PRK10072 42 RKGTGLKI-------------DDFARVLGVSVAMVKEWES 68 (96)
T ss_pred HHHcCCCH-------------HHHHHHhCCCHHHHHHHHc
Confidence 34467788 9999999999998888864
No 225
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=23.71 E-value=1.9e+02 Score=24.32 Aligned_cols=45 Identities=20% Similarity=0.233 Sum_probs=31.9
Q ss_pred ccchhhHHhhcCCCHHHHHHHHHHHHHcccccceecccC--CEEEeCCCC
Q psy17612 249 IFDGQMLASKLNMGTDEAECWIVNLIRNARLDAKIDSKL--GHVIMGTQP 296 (449)
Q Consensus 249 ~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rLdaKIDs~~--G~V~m~~~~ 296 (449)
...|+.||++||||...+.+-|=.|=..| ..||++. |......|+
T Consensus 19 ~~SGe~La~~LgiSRtaVwK~Iq~Lr~~G---~~I~s~~~kGY~L~~~~~ 65 (79)
T COG1654 19 FVSGEKLAEELGISRTAVWKHIQQLREEG---VDIESVRGKGYLLPQLPD 65 (79)
T ss_pred cccHHHHHHHHCccHHHHHHHHHHHHHhC---CceEecCCCceeccCccc
Confidence 45679999999999999999887763222 4677665 455554444
No 226
>PF14226 DIOX_N: non-haem dioxygenase in morphine synthesis N-terminal; PDB: 3OOX_A 1BK0_A 1IPS_B 1QIQ_A 1OC1_A 2Y86_A 2Y60_A 1W03_A 2VE1_A 1QJF_A ....
Probab=23.69 E-value=90 Score=26.22 Aligned_cols=26 Identities=4% Similarity=0.289 Sum_probs=23.3
Q ss_pred ceeeccCCCHHHHHHHHHHHHHHHhc
Q psy17612 3 LFIFFFQFKMDMMESMYKLAKFRYEC 28 (449)
Q Consensus 3 ~~~~~~~~~~e~~d~lyk~Akf~y~~ 28 (449)
..+.+||++.+.++.+++.++=+|+.
T Consensus 30 f~l~nhGi~~~l~~~~~~~~~~fF~l 55 (116)
T PF14226_consen 30 FYLVNHGIPQELIDRVFAAAREFFAL 55 (116)
T ss_dssp EEEESSSSSHHHHHHHHHHHHHHHCS
T ss_pred EEEecccccchhhHHHHHHHHHHHHh
Confidence 56899999999999999999988854
No 227
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=23.66 E-value=1.5e+02 Score=22.20 Aligned_cols=37 Identities=11% Similarity=0.154 Sum_probs=27.9
Q ss_pred HHHhhcCCChHHHHHHHHHHhhhcccccccccCCCeEEec
Q psy17612 358 MLASKLNMGTDEAECWIVNLIRNARLDAKIDSKLGHVIMG 397 (449)
Q Consensus 358 ~la~kLnm~~~eaE~WIvnLIr~~~ldAKIDs~~~~v~m~ 397 (449)
.||+.+|+++..+.+-|-.|....-+... . .|.+.++
T Consensus 30 ela~~~g~s~~tv~r~l~~L~~~g~i~~~--~-~~~~~l~ 66 (67)
T cd00092 30 EIADYLGLTRETVSRTLKELEEEGLISRR--G-RGKYRVN 66 (67)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHCCCEEec--C-CCeEEeC
Confidence 78999999999999999999777655421 1 3566554
No 228
>PF05843 Suf: Suppressor of forked protein (Suf); InterPro: IPR008847 This domain consists of several eukaryotic suppressor of forked (Suf) like proteins. The Drosophila melanogaster suppressor of forked [Su(f)] protein shares homology with the Saccharomyces cerevisiae RNA14 protein and the 77 kDa subunit of Homo sapiens cleavage stimulation factor, which are proteins involved in mRNA 3' end formation. This suggests a role for Su(f) in mRNA 3' end formation in Drosophila. The su(f) gene produces three transcripts; two of them are polyadenylated at the end of the transcription unit, and one is a truncated transcript, polyadenylated in intron 4. It is thought that su(f) plays a role in the regulation of poly(A) site utilisation and the GU-rich sequence is important for this regulation to occur [].; GO: 0006397 mRNA processing, 0005634 nucleus; PDB: 2L9B_B 2OND_B 2OOE_A 4E85_B 4EBA_C 4E6H_A 2UY1_B.
Probab=23.53 E-value=2.8e+02 Score=27.61 Aligned_cols=69 Identities=9% Similarity=0.116 Sum_probs=49.6
Q ss_pred HHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHH-HHhHhhcChHHHHHHHHHHHHHHhc
Q psy17612 15 MESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKL-ASEILVQNWDLALEDLNKLREYIDG 85 (449)
Q Consensus 15 ~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkl-a~eIl~~dwd~a~~~l~kLke~id~ 85 (449)
.+-++.|..|..+.||..+|..+++......+.. .+ ...+|.++ .-|-..+|++.+.+=-++..+++..
T Consensus 70 ~~~~~~Y~~~l~~~~d~~~aR~lfer~i~~l~~~-~~-~~~iw~~~i~fE~~~Gdl~~v~~v~~R~~~~~~~ 139 (280)
T PF05843_consen 70 PDFWLEYLDFLIKLNDINNARALFERAISSLPKE-KQ-SKKIWKKFIEFESKYGDLESVRKVEKRAEELFPE 139 (280)
T ss_dssp HHHHHHHHHHHHHTT-HHHHHHHHHHHCCTSSCH-HH-CHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHTTT
T ss_pred HHHHHHHHHHHHHhCcHHHHHHHHHHHHHhcCch-hH-HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhh
Confidence 4557788899999999999999998877776533 21 56788875 4577777888777777777777665
No 229
>PF09743 DUF2042: Uncharacterized conserved protein (DUF2042); InterPro: IPR018611 The ubiquitin fold modifier 1 (Ufm1) is the most recently discovered ubiquitin-like modifier whose conjugation (ufmylation) system is conserved in multicellular organisms. Ufm1 is known to covalently attach with cellular protein(s) via a specific E1-activating enzyme (Uba5), an E2-conjugating enzyme (Ufc1), and a E3-ligating enzyme []. This entry represents E3 UFM1-protein ligase 1.
Probab=23.42 E-value=1.8e+02 Score=29.55 Aligned_cols=67 Identities=18% Similarity=0.250 Sum_probs=57.9
Q ss_pred hhcccccchHHhHHHHHHHHHHHHHHHhhhhceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHHHHHcccccce
Q psy17612 203 EVLDNDFFLVACLDEFVENARLMIFETFCRIHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLIRNARLDAK 282 (449)
Q Consensus 203 ~vl~~DfFL~~~~d~fvenaR~~ife~ycriy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rLdaK 282 (449)
..+.+| .=|...|+...|..+=..++.+=+-+.+ +.|.+.+|++..-+-..+-+||..|++.++
T Consensus 162 g~~d~~---~lyT~ayv~r~ka~iRG~l~a~T~Pt~l-------------~~l~~~~~~~~~l~~~il~~Li~~~~l~G~ 225 (272)
T PF09743_consen 162 GRLDGD---VLYTEAYVARQKARIRGALSAITRPTPL-------------SSLLKRYGFEEKLFQSILEELIKSGELPGS 225 (272)
T ss_pred EEEeCC---EEecHHHHHHHHHHHHHHHhcCccceEH-------------HHHHHHhCCcHHHHHHHHHHHHhcCcceEE
Confidence 345566 3467789999999999999999999999 999999999999999999999999999987
Q ss_pred ecc
Q psy17612 283 IDS 285 (449)
Q Consensus 283 IDs 285 (449)
|-.
T Consensus 226 i~G 228 (272)
T PF09743_consen 226 IVG 228 (272)
T ss_pred EEC
Confidence 765
No 230
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=23.42 E-value=74 Score=22.16 Aligned_cols=28 Identities=21% Similarity=0.137 Sum_probs=22.2
Q ss_pred chhhHHhhcCCCHHHHHHHHHHHHHcccccce
Q psy17612 251 DGQMLASKLNMGTDEAECWIVNLIRNARLDAK 282 (449)
Q Consensus 251 ~~~~LA~~Lnms~~e~E~wIVnlIr~~rLdaK 282 (449)
+.+.+|+.||+|+.-+.+| +++|++.+.
T Consensus 3 t~~e~a~~lgis~~ti~~~----~~~g~i~~~ 30 (49)
T TIGR01764 3 TVEEAAEYLGVSKDTVYRL----IHEGELPAY 30 (49)
T ss_pred CHHHHHHHHCCCHHHHHHH----HHcCCCCeE
Confidence 3488999999999987766 477888763
No 231
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=23.41 E-value=1.7e+02 Score=20.95 Aligned_cols=32 Identities=13% Similarity=0.177 Sum_probs=27.7
Q ss_pred hhHHhhcCCCHHHHHHHHHHHHHcccccceec
Q psy17612 253 QMLASKLNMGTDEAECWIVNLIRNARLDAKID 284 (449)
Q Consensus 253 ~~LA~~Lnms~~e~E~wIVnlIr~~rLdaKID 284 (449)
..+++.||+++..+-+-|-.|...|-+...-+
T Consensus 14 ~~i~~~l~is~~~v~~~l~~L~~~g~i~~~~~ 45 (66)
T smart00418 14 CELAEILGLSQSTVSHHLKKLREAGLVESRRE 45 (66)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCeeeeec
Confidence 99999999999999999999998887764433
No 232
>TIGR01636 phage_rinA phage transcriptional activator, RinA family. This model represents a family of phage proteins, including RinA, a transcriptional activator in staphylococcal phage phi 11. This family shows similarity to ArpU, a phage-related putative autolysin regulator, and to some sporulation-specific sigma factors.
Probab=23.19 E-value=1.4e+02 Score=26.85 Aligned_cols=50 Identities=24% Similarity=0.363 Sum_probs=39.9
Q ss_pred hHHhHHHHHHHHHHHHHHHhhhhceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHHHH
Q psy17612 211 LVACLDEFVENARLMIFETFCRIHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLI 274 (449)
Q Consensus 211 L~~~~d~fvenaR~~ife~ycriy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlI 274 (449)
+..+++.+-+.-|..|...|++..+ .+. ..+|..||||..-+-++--+++
T Consensus 76 I~~~l~~Ld~~er~II~~rY~~~~~-~t~-------------~~Ia~~l~iS~~t~~r~r~~~l 125 (134)
T TIGR01636 76 IENCLNEADEQTRVIIQELYMKKRP-LTL-------------VGLAQQLFISKSTAYRLRNHII 125 (134)
T ss_pred HHHHHHhCCHHHHHHHHHHHccCCC-CCH-------------HHHHHHhCCCHHHHHHHHHHHH
Confidence 4445666677789999999998877 788 9999999999998877655543
No 233
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=23.15 E-value=1.2e+02 Score=23.36 Aligned_cols=36 Identities=19% Similarity=0.212 Sum_probs=24.9
Q ss_pred HHHHHHHhhhhce-----eeEeeccccccccccchhhHHhhcCCCHHHHHHHHH
Q psy17612 223 RLMIFETFCRIHQ-----CISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIV 271 (449)
Q Consensus 223 R~~ife~ycriy~-----~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIV 271 (449)
|+..|-.+++-.+ .|+= ..||+.+|+++..+-+.++
T Consensus 10 RL~~Y~r~L~~l~~~G~~~vSS-------------~~La~~~gi~~~qVRKDlS 50 (50)
T PF06971_consen 10 RLPLYLRYLEQLKEEGVERVSS-------------QELAEALGITPAQVRKDLS 50 (50)
T ss_dssp HHHHHHHHHHHHHHTT-SEE-H-------------HHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHHHHHHHcCCeeECH-------------HHHHHHHCCCHHHhcccCC
Confidence 5556666655443 4555 9999999999999888764
No 234
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=23.12 E-value=2.6e+02 Score=21.05 Aligned_cols=45 Identities=11% Similarity=0.184 Sum_probs=32.4
Q ss_pred HHHHHhhhhceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHHHHHcccccce
Q psy17612 225 MIFETFCRIHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLIRNARLDAK 282 (449)
Q Consensus 225 ~ife~ycriy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rLdaK 282 (449)
.++...+..+..+++ ..||+.+|++..-+-+.|-+|+..|=+.=.
T Consensus 7 ~vL~~l~~~~~~~t~-------------~~l~~~~~~~~~~vs~~i~~L~~~glv~~~ 51 (68)
T PF13463_consen 7 QVLRALAHSDGPMTQ-------------SDLAERLGISKSTVSRIIKKLEEKGLVEKE 51 (68)
T ss_dssp HHHHHHT--TS-BEH-------------HHHHHHTT--HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHccCCCcCH-------------HHHHHHHCcCHHHHHHHHHHHHHCCCEEec
Confidence 344444457788899 999999999999999999999999977433
No 235
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=22.91 E-value=1.3e+02 Score=22.27 Aligned_cols=33 Identities=15% Similarity=0.246 Sum_probs=27.2
Q ss_pred hhHHhhcCCCHHHHHHHHHHHHHcccccceecc
Q psy17612 253 QMLASKLNMGTDEAECWIVNLIRNARLDAKIDS 285 (449)
Q Consensus 253 ~~LA~~Lnms~~e~E~wIVnlIr~~rLdaKIDs 285 (449)
..||+.+++++.-+-+-|.+|+..|=+.-.-|.
T Consensus 25 ~~la~~l~~~~~~vs~~v~~L~~~Glv~r~~~~ 57 (62)
T PF12802_consen 25 SELAERLGISKSTVSRIVKRLEKKGLVERERDP 57 (62)
T ss_dssp HHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE-S
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCCC
Confidence 999999999999999999999998876554443
No 236
>KOG2002|consensus
Probab=22.88 E-value=1.4e+03 Score=27.74 Aligned_cols=155 Identities=19% Similarity=0.210 Sum_probs=0.0
Q ss_pred CHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCC--Ccch------------------------------hhHHHHHH
Q psy17612 11 KMDMMESMYKLAKFRYECGNYSITTSYLYFYLLVMP--TSDR------------------------------HYLAVLWG 58 (449)
Q Consensus 11 ~~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~--~~~~------------------------------k~ls~lwg 58 (449)
.|.-+=+|+=.|.+-|..|||..|..|+..+...+| ..|. . .+++-|
T Consensus 160 sp~Nil~LlGkA~i~ynkkdY~~al~yyk~al~inp~~~aD~rIgig~Cf~kl~~~~~a~~a~~ralqLdp~~-v~alv~ 238 (1018)
T KOG2002|consen 160 SPDNILALLGKARIAYNKKDYRGALKYYKKALRINPACKADVRIGIGHCFWKLGMSEKALLAFERALQLDPTC-VSALVA 238 (1018)
T ss_pred CCcchHHHHHHHHHHhccccHHHHHHHHHHHHhcCcccCCCccchhhhHHHhccchhhHHHHHHHHHhcChhh-HHHHHH
Q ss_pred HHHHhHhhcChHHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHHHhcCccchhhHHHHhcCCchhhhHHHhh
Q psy17612 59 KLASEILVQNWDLALEDLNKLREYIDGGSANFESPLHLLQQRTWLIHWSLFVFFNHVKGRDLIIDMFLNRPHYLNAIQTM 138 (449)
Q Consensus 59 kla~eIl~~dwd~a~~~l~kLke~id~~~~~~~~pl~~l~qR~WliHwsLf~ffn~~~g~~~~iD~F~~~~~yl~aIqt~ 138 (449)
.--....++|-+.-.+.+..+-..+.- ...||.- |.|-+=++||. .--..+...
T Consensus 239 L~~~~l~~~d~~s~~~~~~ll~~ay~~---n~~nP~~-------l~~LAn~fyfK----------------~dy~~v~~l 292 (1018)
T KOG2002|consen 239 LGEVDLNFNDSDSYKKGVQLLQRAYKE---NNENPVA-------LNHLANHFYFK----------------KDYERVWHL 292 (1018)
T ss_pred HHHHHHHccchHHHHHHHHHHHHHHhh---cCCCcHH-------HHHHHHHHhhc----------------ccHHHHHHH
Q ss_pred hhHHHHHHHHHHHhccccccchHHHHHHHhhhccCCCchHHHHHHHHhhcccHHHHHHHHHHHhhhcccccchHHhH
Q psy17612 139 CPHILRYLATAVIINRSKRNALKDLVKVIQQESYTYKDPITEFLEHLYVSFDFESAREKLTECTEVLDNDFFLVACL 215 (449)
Q Consensus 139 cp~lLRYlvvA~Il~~~r~~~l~dlv~vi~qE~~~Y~DpiT~fv~~lYv~fdf~~aq~~L~~~~~vl~~DfFL~~~~ 215 (449)
+-|.+.++..-+|.+.+--..-+ |-+..=||++|.+.--+..+ ..+|.|+-+|.
T Consensus 293 a~~ai~~t~~~~~~aes~Y~~gR----------------------s~Ha~Gd~ekA~~yY~~s~k-~~~d~~~l~~~ 346 (1018)
T KOG2002|consen 293 AEHAIKNTENKSIKAESFYQLGR----------------------SYHAQGDFEKAFKYYMESLK-ADNDNFVLPLV 346 (1018)
T ss_pred HHHHHHhhhhhHHHHHHHHHHHH----------------------HHHhhccHHHHHHHHHHHHc-cCCCCcccccc
No 237
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=22.82 E-value=2.5e+02 Score=23.61 Aligned_cols=41 Identities=17% Similarity=0.128 Sum_probs=35.2
Q ss_pred hhHHhhcCCCHHHHHHHHHHHHHcccccceecccCCEEEeCCC
Q psy17612 253 QMLASKLNMGTDEAECWIVNLIRNARLDAKIDSKLGHVIMGTQ 295 (449)
Q Consensus 253 ~~LA~~Lnms~~e~E~wIVnlIr~~rLdaKIDs~~G~V~m~~~ 295 (449)
..||+.+|++++-+-+-|..|...|-|. .+...|.+-+|.+
T Consensus 51 ~eLa~~~g~sr~tVsr~L~~Le~~GlI~--r~~~~~~~~~n~~ 91 (95)
T TIGR01610 51 TVIAELTGLSRTHVSDAIKSLARRRIIF--RQGMMGIVGVNTP 91 (95)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHCCCee--eecCCceeecCCC
Confidence 9999999999999999999999999884 4555688877754
No 238
>PRK14574 hmsH outer membrane protein; Provisional
Probab=22.73 E-value=1.3e+03 Score=27.21 Aligned_cols=50 Identities=14% Similarity=0.155 Sum_probs=39.0
Q ss_pred cHHHHHHHHHHHhhhcc---ccc-----chHHhHHHHHHHHHHHHHHHhhhhceeeEe
Q psy17612 190 DFESAREKLTECTEVLD---NDF-----FLVACLDEFVENARLMIFETFCRIHQCISI 239 (449)
Q Consensus 190 df~~aq~~L~~~~~vl~---~Df-----FL~~~~d~fvenaR~~ife~ycriy~~IsI 239 (449)
-|..+.+.|++.+..+. .++ |.....|.++=-...-=+.+-++-|+++..
T Consensus 263 r~~~~d~ala~~~~l~~~~~~~p~~~~~~~~~~~Drl~aL~~r~r~~~vi~~y~~l~~ 320 (822)
T PRK14574 263 RFDIADKALADYQNLLTRWGKDPEAQADYQRARIDRLGALLVRHQTADLIKEYEAMEA 320 (822)
T ss_pred hHHHHHHHHHHHHHHHhhccCCCccchHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhh
Confidence 35577788999888876 555 788888888877777778888888888876
No 239
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=22.68 E-value=99 Score=26.44 Aligned_cols=31 Identities=13% Similarity=0.215 Sum_probs=25.8
Q ss_pred hhHHhhcCCCHHHHHHHHHHHHHcccccceec
Q psy17612 253 QMLASKLNMGTDEAECWIVNLIRNARLDAKID 284 (449)
Q Consensus 253 ~~LA~~Lnms~~e~E~wIVnlIr~~rLdaKID 284 (449)
.-.|+.||||..-+.+|+.++-.+|. .+-.|
T Consensus 29 a~aA~~~gVS~~Ta~kW~~Ryra~G~-~GL~D 59 (85)
T PF13011_consen 29 AHAAAEFGVSRRTAYKWLARYRAEGE-AGLQD 59 (85)
T ss_pred HHHHHHhCCCHHHHHHHHHHHHHcCc-ccccc
Confidence 89999999999999999999977663 33444
No 240
>KOG2376|consensus
Probab=22.55 E-value=5.9e+02 Score=29.22 Aligned_cols=77 Identities=16% Similarity=0.108 Sum_probs=50.2
Q ss_pred CCHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCC-cc--------------------------hhhHHHHHHHHHH
Q psy17612 10 FKMDMMESMYKLAKFRYECGNYSITTSYLYFYLLVMPT-SD--------------------------RHYLAVLWGKLAS 62 (449)
Q Consensus 10 ~~~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~-~~--------------------------~k~ls~lwgkla~ 62 (449)
.+.+....+-=.|++.|+.|+|+.|.+++.++.....+ .+ ..--+.++..--+
T Consensus 105 ~~~~~~~ll~L~AQvlYrl~~ydealdiY~~L~kn~~dd~d~~~r~nl~a~~a~l~~~~~q~v~~v~e~syel~yN~Ac~ 184 (652)
T KOG2376|consen 105 LDRLDDKLLELRAQVLYRLERYDEALDIYQHLAKNNSDDQDEERRANLLAVAAALQVQLLQSVPEVPEDSYELLYNTACI 184 (652)
T ss_pred ccccchHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHhhhHHHHHhccCCCcchHHHHHHHHHH
Confidence 34444445566799999999999999998887333221 00 0012344444445
Q ss_pred hHhhcChHHHHHHHHHH----HHHHhcC
Q psy17612 63 EILVQNWDLALEDLNKL----REYIDGG 86 (449)
Q Consensus 63 eIl~~dwd~a~~~l~kL----ke~id~~ 86 (449)
.|-.++|+.|.+-|.+. +|-+..+
T Consensus 185 ~i~~gky~qA~elL~kA~~~~~e~l~~~ 212 (652)
T KOG2376|consen 185 LIENGKYNQAIELLEKALRICREKLEDE 212 (652)
T ss_pred HHhcccHHHHHHHHHHHHHHHHHhhccc
Confidence 56668999999999999 5555554
No 241
>TIGR00540 hemY_coli hemY protein. This is an uncharacterized protein encoded next to a heme-biosynthetic enzyme in two gamma division proteobacteria (E. coli and H. influenzae). It is known in no other species. The gene symbol hemY is unfortunate in that an unrelated protein, protoporphyrinogen oxidase, is designated as HemG in E. coli but as HemY in Bacillus subtilis.
Probab=22.39 E-value=8.9e+02 Score=25.18 Aligned_cols=164 Identities=15% Similarity=0.132 Sum_probs=86.2
Q ss_pred HHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHHHHHHHhcCCCCCCChH
Q psy17612 15 MESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNKLREYIDGGSANFESPL 94 (449)
Q Consensus 15 ~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLke~id~~~~~~~~pl 94 (449)
.-.++-.|......|+++.|.++|.......++.+.. ...... .+-+..++++.|.+.+.++.+.-.+ ||-
T Consensus 118 ~~~~llaA~aa~~~g~~~~A~~~l~~a~~~~p~~~l~-~~~~~a--~l~l~~~~~~~Al~~l~~l~~~~P~------~~~ 188 (409)
T TIGR00540 118 VLNLIKAAEAAQQRGDEARANQHLEEAAELAGNDNIL-VEIART--RILLAQNELHAARHGVDKLLEMAPR------HKE 188 (409)
T ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCcCchH-HHHHHH--HHHHHCCCHHHHHHHHHHHHHhCCC------CHH
Confidence 3345567899999999999999999887766543222 222222 2233456899898887776654322 331
Q ss_pred -------HHHHHHHHHHHHHHHHHhcCccchhhHHHHhcC----CchhhhHHHhhhhHHHHHHHHHHHhcc-ccccchHH
Q psy17612 95 -------HLLQQRTWLIHWSLFVFFNHVKGRDLIIDMFLN----RPHYLNAIQTMCPHILRYLATAVIINR-SKRNALKD 162 (449)
Q Consensus 95 -------~~l~qR~WliHwsLf~ffn~~~g~~~~iD~F~~----~~~yl~aIqt~cp~lLRYlvvA~Il~~-~r~~~l~d 162 (449)
.++++..|- +...+++.+.. ++.... -++..+....+.. ....-...
T Consensus 189 ~l~ll~~~~~~~~d~~-------------~a~~~l~~l~k~~~~~~~~~~--------~l~~~a~~~~l~~~~~~~~~~~ 247 (409)
T TIGR00540 189 VLKLAEEAYIRSGAWQ-------------ALDDIIDNMAKAGLFDDEEFA--------DLEQKAEIGLLDEAMADEGIDG 247 (409)
T ss_pred HHHHHHHHHHHHhhHH-------------HHHHHHHHHHHcCCCCHHHHH--------HHHHHHHHHHHHHHHHhcCHHH
Confidence 223333332 22233333331 111111 1222222222211 11122334
Q ss_pred HHHHHhhhccCCC-ch--HHHHHHHHhhcccHHHHHHHHHHHhhhcccc
Q psy17612 163 LVKVIQQESYTYK-DP--ITEFLEHLYVSFDFESAREKLTECTEVLDND 208 (449)
Q Consensus 163 lv~vi~qE~~~Y~-Dp--iT~fv~~lYv~fdf~~aq~~L~~~~~vl~~D 208 (449)
+.+...+.+..++ +| ...+...+...-++++|.+.|.+.-+.-.+|
T Consensus 248 L~~~~~~~p~~~~~~~~l~~~~a~~l~~~g~~~~A~~~l~~~l~~~pd~ 296 (409)
T TIGR00540 248 LLNWWKNQPRHRRHNIALKIALAEHLIDCDDHDSAQEIIFDGLKKLGDD 296 (409)
T ss_pred HHHHHHHCCHHHhCCHHHHHHHHHHHHHCCChHHHHHHHHHHHhhCCCc
Confidence 4445555554344 55 4455566677788889988888877765555
No 242
>PRK05412 putative nucleotide-binding protein; Reviewed
Probab=22.31 E-value=1.3e+02 Score=28.64 Aligned_cols=52 Identities=17% Similarity=0.247 Sum_probs=39.1
Q ss_pred hcCCChHHHHHHHHHHhhhcccccccccCCCeEEecCCCCChhHHHHHhhhcc
Q psy17612 362 KLNMGTDEAECWIVNLIRNARLDAKIDSKLGHVIMGTQPLSPYQQLLEKIDTL 414 (449)
Q Consensus 362 kLnm~~~eaE~WIvnLIr~~~ldAKIDs~~~~v~m~~~~~svyqqviektk~l 414 (449)
+=|++.|.|.+ ||.+|+++++-.+---....|.++.-...-.|+||--.|..
T Consensus 97 k~GI~~e~AKk-IvK~IKd~klKVqa~IQGd~vRVtgKkrDDLQ~viallk~~ 148 (161)
T PRK05412 97 KQGIDQELAKK-IVKLIKDSKLKVQAQIQGDQVRVTGKKRDDLQAVIALLRKA 148 (161)
T ss_pred hhccCHHHHHH-HHHHHHhcCCceeEEecCcEEEEecCCHhHHHHHHHHHHhc
Confidence 44677776665 99999999984332236889999888889999999776653
No 243
>PF12862 Apc5: Anaphase-promoting complex subunit 5
Probab=22.18 E-value=1.7e+02 Score=24.24 Aligned_cols=33 Identities=15% Similarity=0.189 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCC
Q psy17612 14 MMESMYKLAKFRYECGNYSITTSYLYFYLLVMP 46 (449)
Q Consensus 14 ~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~ 46 (449)
..-+++.+|.+++.-|+++.|.+.+.+...+..
T Consensus 40 ~~~all~lA~~~~~~G~~~~A~~~l~eAi~~Ar 72 (94)
T PF12862_consen 40 LAYALLNLAELHRRFGHYEEALQALEEAIRLAR 72 (94)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHH
Confidence 456789999999999999999999999888875
No 244
>TIGR00540 hemY_coli hemY protein. This is an uncharacterized protein encoded next to a heme-biosynthetic enzyme in two gamma division proteobacteria (E. coli and H. influenzae). It is known in no other species. The gene symbol hemY is unfortunate in that an unrelated protein, protoporphyrinogen oxidase, is designated as HemG in E. coli but as HemY in Bacillus subtilis.
Probab=22.01 E-value=9.1e+02 Score=25.12 Aligned_cols=61 Identities=10% Similarity=0.045 Sum_probs=45.7
Q ss_pred HHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHHHHHH
Q psy17612 18 MYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNKLREY 82 (449)
Q Consensus 18 lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLke~ 82 (449)
-..+|+++.+.|+|+.|.+.+.......|.+ .. ++--...+-+..+||+.|.+.+.++.+.
T Consensus 156 ~~~~a~l~l~~~~~~~Al~~l~~l~~~~P~~-~~---~l~ll~~~~~~~~d~~~a~~~l~~l~k~ 216 (409)
T TIGR00540 156 EIARTRILLAQNELHAARHGVDKLLEMAPRH-KE---VLKLAEEAYIRSGAWQALDDIIDNMAKA 216 (409)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHHHHhCCCC-HH---HHHHHHHHHHHHhhHHHHHHHHHHHHHc
Confidence 3445999999999999999999999888743 33 2222333346678999999988887764
No 245
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=21.50 E-value=96 Score=25.90 Aligned_cols=39 Identities=21% Similarity=0.245 Sum_probs=33.2
Q ss_pred hceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHHHHHccccc---ceec
Q psy17612 233 IHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLIRNARLD---AKID 284 (449)
Q Consensus 233 iy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rLd---aKID 284 (449)
-..+++. ..||+.+|+|+.-+-+.|-+|..+|-+. +.+|
T Consensus 14 ~~~~~~~-------------~~la~~l~~s~~tv~~~l~~L~~~g~i~~~~~~~~ 55 (108)
T smart00344 14 KDARISL-------------AELAKKVGLSPSTVHNRVKRLEEEGVIKGYTAVIN 55 (108)
T ss_pred HhCCCCH-------------HHHHHHHCcCHHHHHHHHHHHHHCCCeeceEEEeC
Confidence 3567888 9999999999999999999999999554 4555
No 246
>KOG2076|consensus
Probab=21.30 E-value=1.5e+03 Score=27.29 Aligned_cols=254 Identities=13% Similarity=0.084 Sum_probs=130.9
Q ss_pred CCCHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCc-chhhHHHHHHHHHHhHhhcChHHHHHHHHHHHHHHhcCC
Q psy17612 9 QFKMDMMESMYKLAKFRYECGNYSITTSYLYFYLLVMPTS-DRHYLAVLWGKLASEILVQNWDLALEDLNKLREYIDGGS 87 (449)
Q Consensus 9 ~~~~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~-~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLke~id~~~ 87 (449)
...|....-+++++.+|-+.|++..|.+...+...++|+. ..+..+..|++....+-+.+-+.|. +.|-..+.+++
T Consensus 235 ~~~p~n~~~~~ers~L~~~~G~~~~Am~~f~~l~~~~p~~d~er~~d~i~~~~~~~~~~~~~e~a~---~~le~~~s~~~ 311 (895)
T KOG2076|consen 235 QANPSNWELIYERSSLYQKTGDLKRAMETFLQLLQLDPPVDIERIEDLIRRVAHYFITHNERERAA---KALEGALSKEK 311 (895)
T ss_pred hcCCcchHHHHHHHHHHHHhChHHHHHHHHHHHHhhCCchhHHHHHHHHHHHHHHHHHhhHHHHHH---HHHHHHHhhcc
Confidence 3467778899999999999999999999999999998844 3556788888888887777554443 44444555443
Q ss_pred CCCCCh-HH-----HHHHHHHHHHHHHHH--HhcC----ccchhhHHHHhcC-CchhhhHHHhhhhHHHHH-HHHHHHhc
Q psy17612 88 ANFESP-LH-----LLQQRTWLIHWSLFV--FFNH----VKGRDLIIDMFLN-RPHYLNAIQTMCPHILRY-LATAVIIN 153 (449)
Q Consensus 88 ~~~~~p-l~-----~l~qR~WliHwsLf~--ffn~----~~g~~~~iD~F~~-~~~yl~aIqt~cp~lLRY-lvvA~Il~ 153 (449)
+-+..| +. .|....|-. ++.. .+.+ ++.++...+-+.. ++.++..+--.-+.-||- -+..+++.
T Consensus 312 ~~~~~ed~ni~ael~l~~~q~d~--~~~~i~~~~~r~~e~d~~e~~~~~~~~~~~~~~~~~~~~~s~~l~v~rl~icL~~ 389 (895)
T KOG2076|consen 312 DEASLEDLNILAELFLKNKQSDK--ALMKIVDDRNRESEKDDSEWDTDERRREEPNALCEVGKELSYDLRVIRLMICLVH 389 (895)
T ss_pred ccccccHHHHHHHHHHHhHHHHH--hhHHHHHHhccccCCChhhhhhhhhccccccccccCCCCCCccchhHhHhhhhhc
Confidence 433333 21 122222211 1110 0101 1111112222221 223333333333334443 33455666
Q ss_pred cccccchHHHHHHHhhhc--cCCC-chHHHHHHHHhhcccHHHHHHHHHHHhhhcccccchHHhHHHHHHHHHHHH----
Q psy17612 154 RSKRNALKDLVKVIQQES--YTYK-DPITEFLEHLYVSFDFESAREKLTECTEVLDNDFFLVACLDEFVENARLMI---- 226 (449)
Q Consensus 154 ~~r~~~l~dlv~vi~qE~--~~Y~-DpiT~fv~~lYv~fdf~~aq~~L~~~~~vl~~DfFL~~~~d~fvenaR~~i---- 226 (449)
.+-.++..-+.....+.. -.+. |.+++..+.+-..-.|+.|-.-|..+.. ++.+= +...|.+-+|+..
T Consensus 390 L~~~e~~e~ll~~l~~~n~~~~d~~dL~~d~a~al~~~~~~~~Al~~l~~i~~---~~~~~--~~~vw~~~a~c~~~l~e 464 (895)
T KOG2076|consen 390 LKERELLEALLHFLVEDNVWVSDDVDLYLDLADALTNIGKYKEALRLLSPITN---REGYQ--NAFVWYKLARCYMELGE 464 (895)
T ss_pred ccccchHHHHHHHHHHhcCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHhc---Ccccc--chhhhHHHHHHHHHHhh
Confidence 655566544444333322 1222 5578888777676777777777665433 22221 1333444444332
Q ss_pred HHHhhhhceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHHHH
Q psy17612 227 FETFCRIHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLI 274 (449)
Q Consensus 227 fe~ycriy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlI 274 (449)
+++=...|..|=+ -.+.-+|--+.-..|=+++|=.+ ++-.-|.+.+
T Consensus 465 ~e~A~e~y~kvl~-~~p~~~D~Ri~Lasl~~~~g~~E-kalEtL~~~~ 510 (895)
T KOG2076|consen 465 YEEAIEFYEKVLI-LAPDNLDARITLASLYQQLGNHE-KALETLEQII 510 (895)
T ss_pred HHHHHHHHHHHHh-cCCCchhhhhhHHHHHHhcCCHH-HHHHHHhccc
Confidence 1111222222211 12233344444488888888665 4444566655
No 247
>PF13730 HTH_36: Helix-turn-helix domain
Probab=21.15 E-value=1e+02 Score=22.67 Aligned_cols=26 Identities=19% Similarity=0.180 Sum_probs=23.8
Q ss_pred hhHHhhcCCCHHHHHHHHHHHHHccc
Q psy17612 253 QMLASKLNMGTDEAECWIVNLIRNAR 278 (449)
Q Consensus 253 ~~LA~~Lnms~~e~E~wIVnlIr~~r 278 (449)
+.||+.+|+|+.-+.+.|-.|...|-
T Consensus 29 ~~la~~~g~s~~Tv~~~i~~L~~~G~ 54 (55)
T PF13730_consen 29 ETLAKDLGVSRRTVQRAIKELEEKGL 54 (55)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHCcC
Confidence 99999999999999999999987763
No 248
>cd00155 RasGEF Guanine nucleotide exchange factor for Ras-like small GTPases. Small GTP-binding proteins of the Ras superfamily function as molecular switches in fundamental events such as signal transduction, cytoskeleton dynamics and intracellular trafficking. Guanine-nucleotide-exchange factors (GEFs) positively regulate these GTP-binding proteins in response to a variety of signals. GEFs catalyze the dissociation of GDP from the inactive GTP-binding proteins. GTP can then bind and induce structural changes that allow interaction with effectors.
Probab=20.87 E-value=2.8e+02 Score=26.46 Aligned_cols=62 Identities=18% Similarity=0.206 Sum_probs=45.4
Q ss_pred HHHHHHHHHHHHHHHhcCChhhHHHHHHHHHhcCCCcchhhHHHHHHHHHHhHhhcChHHHHHHHHHHHHHHhc
Q psy17612 12 MDMMESMYKLAKFRYECGNYSITTSYLYFYLLVMPTSDRHYLAVLWGKLASEILVQNWDLALEDLNKLREYIDG 85 (449)
Q Consensus 12 ~e~~d~lyk~Akf~y~~GdY~~A~~~L~~~~~l~~~~~~k~ls~lwgkla~eIl~~dwd~a~~~l~kLke~id~ 85 (449)
.+++....+.|...++.|||..+..++.-+...+. .++...|..+.-+ .++.+.+|++++..
T Consensus 75 ~~~i~~~I~ia~~l~~l~Nfns~~aI~~~L~~~~I----~RL~~tw~~l~~~--------~~~~~~~l~~l~~~ 136 (237)
T cd00155 75 ARLLSKFIQVAKHCRELNNFNSLMAIVSALSSSPI----SRLKKTWEVLSSK--------LKKLFEELEELVDP 136 (237)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCccc----hhHHHHHHHCCHH--------HHHHHHHHHHHhCc
Confidence 57788999999999999999999988765543332 3488899987643 34555666666654
No 249
>PF02002 TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024550 The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation, together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits, TFIIE-alpha and TFIIE-beta, and joins the preinitiation complex after RNA polymerase II and TFIIF []. This entry represents a helix-turn-helix (HTH) domain found in eukaryotic TFIIE-alpha []. It is also found in proteins from archaebacteria that are presumed to be TFIIE-alpha subunits [], the transcriptional regulator SarR, and also DNA-directed RNA polymerase III subunit Rpc3.; PDB: 1VD4_A 1Q1H_A.
Probab=20.79 E-value=1.4e+02 Score=25.28 Aligned_cols=44 Identities=18% Similarity=0.259 Sum_probs=30.7
Q ss_pred HHHHHhhhhceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHHHHHcccccce
Q psy17612 225 MIFETFCRIHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLIRNARLDAK 282 (449)
Q Consensus 225 ~ife~ycriy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rLdaK 282 (449)
.|+..+++ |..++= +.||+.+||++.++-+.|..|-.++=+..+
T Consensus 17 ~Il~~L~~-~~~l~d-------------e~la~~~~l~~~~vRkiL~~L~~~~lv~~~ 60 (105)
T PF02002_consen 17 RILDALLR-KGELTD-------------EDLAKKLGLKPKEVRKILYKLYEDGLVSYR 60 (105)
T ss_dssp HHHHHHHH-H--B-H-------------HHHHHTT-S-HHHHHHHHHHHHHHSS-EEE
T ss_pred HHHHHHHH-cCCcCH-------------HHHHHHhCCCHHHHHHHHHHHHHCCCeEEE
Confidence 45555554 678888 999999999999999999999888766543
No 250
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=20.79 E-value=92 Score=22.76 Aligned_cols=19 Identities=32% Similarity=0.639 Sum_probs=17.9
Q ss_pred HHHhhcCCChHHHHHHHHH
Q psy17612 358 MLASKLNMGTDEAECWIVN 376 (449)
Q Consensus 358 ~la~kLnm~~~eaE~WIvn 376 (449)
.||+.+||+......|..|
T Consensus 32 ~la~~~~l~~~qV~~WF~n 50 (56)
T smart00389 32 ELAAKLGLSERQVKVWFQN 50 (56)
T ss_pred HHHHHHCcCHHHHHHhHHH
Confidence 7799999999999999987
No 251
>PF05559 DUF763: Protein of unknown function (DUF763); InterPro: IPR008482 This family consists of several uncharacterised bacterial and archaeal proteins of unknown function.
Probab=20.38 E-value=53 Score=34.34 Aligned_cols=26 Identities=31% Similarity=0.556 Sum_probs=20.5
Q ss_pred HHHhhcCCChHHHHHHHHHHhhhcccccccccC
Q psy17612 358 MLASKLNMGTDEAECWIVNLIRNARLDAKIDSK 390 (449)
Q Consensus 358 ~la~kLnm~~~eaE~WIvnLIr~~~ldAKIDs~ 390 (449)
.+++++|++. ..|+|.+||-||+|+.
T Consensus 104 ~~~~~~gld~-------~~L~~~SRL~AKVDn~ 129 (319)
T PF05559_consen 104 EIAERFGLDA-------EELVRASRLVAKVDNA 129 (319)
T ss_pred HHHHHhCCCH-------HHHHHHHHHHHhhhhH
Confidence 4466777765 4689999999999986
No 252
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=20.17 E-value=99 Score=22.65 Aligned_cols=19 Identities=26% Similarity=0.541 Sum_probs=17.7
Q ss_pred HHHhhcCCChHHHHHHHHH
Q psy17612 358 MLASKLNMGTDEAECWIVN 376 (449)
Q Consensus 358 ~la~kLnm~~~eaE~WIvn 376 (449)
.||+.+||+......|.-|
T Consensus 32 ~la~~~~l~~~qV~~WF~n 50 (59)
T cd00086 32 ELAKELGLTERQVKIWFQN 50 (59)
T ss_pred HHHHHHCcCHHHHHHHHHH
Confidence 6799999999999999887
No 253
>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter.
Probab=20.15 E-value=2.6e+02 Score=26.10 Aligned_cols=64 Identities=8% Similarity=-0.008 Sum_probs=54.0
Q ss_pred HHHHHHHHHHHHHHhhhhceeeEeeccccccccccchhhHHhhcCCCHHHHHHHHHHHHHcccccceecccCCEEEeCC
Q psy17612 216 DEFVENARLMIFETFCRIHQCISIQKESNVIDKIFDGQMLASKLNMGTDEAECWIVNLIRNARLDAKIDSKLGHVIMGT 294 (449)
Q Consensus 216 d~fvenaR~~ife~ycriy~~IsI~~~~~~~~~~~~~~~LA~~Lnms~~e~E~wIVnlIr~~rLdaKIDs~~G~V~m~~ 294 (449)
+...+..|-.|..--++|=.+++- ..||+.||||..=+-.-|-.|-..|-++ +-...|.++..-
T Consensus 14 ~~v~~~l~~~I~~g~l~pG~~L~e-------------~~La~~lgVSRtpVReAL~~L~~eGlv~--~~~~~G~~V~~~ 77 (212)
T TIGR03338 14 TLVQDEIERAILSGELPPGAKLNE-------------SDIAARLGVSRGPVREAFRALEEAGLVR--NEKNRGVFVREI 77 (212)
T ss_pred HHHHHHHHHHHHcCCCCCCCEecH-------------HHHHHHhCCChHHHHHHHHHHHHCCCEE--EecCCCeEEecC
Confidence 556688899999999999999999 9999999999999999999999888774 345567777653
No 254
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).
Probab=20.02 E-value=8.9e+02 Score=24.31 Aligned_cols=33 Identities=15% Similarity=0.241 Sum_probs=26.0
Q ss_pred hhHHhhcCCCHHHHHHHHHHHHHcccccceecc
Q psy17612 253 QMLASKLNMGTDEAECWIVNLIRNARLDAKIDS 285 (449)
Q Consensus 253 ~~LA~~Lnms~~e~E~wIVnlIr~~rLdaKIDs 285 (449)
..+|+.+|+++++++..+.-.-+..-||+.++.
T Consensus 181 ~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~ 213 (298)
T TIGR02997 181 AEIAEALELEPEQVRELLQRARQPVSLDAPVGD 213 (298)
T ss_pred HHHHHHhCCCHHHHHHHHHHcccCcccCCCcCC
Confidence 899999999999999987655455567776644
Done!