Query 016147
Match_columns 394
No_of_seqs 167 out of 513
Neff 7.1
Searched_HMMs 46136
Date Fri Mar 29 04:13:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016147.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016147hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1498 26S proteasome regulat 100.0 2E-103 4E-108 759.9 32.8 365 5-392 74-438 (439)
2 COG5071 RPN5 26S proteasome re 100.0 2.6E-89 5.7E-94 642.2 27.4 366 5-393 74-439 (439)
3 KOG1497 COP9 signalosome, subu 100.0 9.8E-56 2.1E-60 418.0 28.7 317 31-383 72-389 (399)
4 KOG0687 26S proteasome regulat 100.0 1.2E-28 2.6E-33 234.9 23.8 300 38-382 81-392 (393)
5 KOG1464 COP9 signalosome, subu 99.9 4.4E-24 9.5E-29 200.2 16.5 270 66-374 149-435 (440)
6 COG5187 RPN7 26S proteasome re 99.9 7E-23 1.5E-27 193.1 22.8 300 37-381 91-405 (412)
7 KOG1463 26S proteasome regulat 99.8 3.4E-19 7.3E-24 171.3 24.0 299 19-354 85-393 (411)
8 COG5159 RPN6 26S proteasome re 99.7 1.4E-15 3.1E-20 143.8 21.7 299 17-353 80-390 (421)
9 PF01399 PCI: PCI domain; Int 99.7 1.1E-15 2.4E-20 125.4 11.4 104 242-352 1-105 (105)
10 KOG0686 COP9 signalosome, subu 99.6 2.7E-13 5.8E-18 133.6 20.9 257 61-356 149-414 (466)
11 smart00753 PAM PCI/PINT associ 99.5 1.7E-13 3.8E-18 109.7 10.2 72 285-356 2-73 (88)
12 smart00088 PINT motif in prote 99.5 1.7E-13 3.8E-18 109.7 10.2 72 285-356 2-73 (88)
13 KOG2908 26S proteasome regulat 99.4 9.1E-10 2E-14 106.8 27.2 280 66-381 79-378 (380)
14 PF10602 RPN7: 26S proteasome 99.3 5.8E-11 1.3E-15 107.8 13.0 154 46-230 22-176 (177)
15 KOG2581 26S proteasome regulat 99.1 8.9E-08 1.9E-12 95.0 26.1 279 58-377 165-451 (493)
16 KOG2582 COP9 signalosome, subu 98.7 8E-07 1.7E-11 87.3 15.7 175 163-353 180-361 (422)
17 KOG2758 Translation initiation 98.0 0.015 3.3E-07 56.9 26.9 79 303-383 345-423 (432)
18 KOG1076 Translation initiation 97.7 0.00013 2.8E-09 77.1 9.0 68 287-354 694-765 (843)
19 KOG2753 Uncharacterized conser 97.6 0.023 4.9E-07 55.8 21.5 193 166-370 165-368 (378)
20 PF10255 Paf67: RNA polymerase 96.6 0.15 3.3E-06 52.1 18.0 205 93-329 111-343 (404)
21 KOG2072 Translation initiation 96.6 0.072 1.6E-06 57.8 16.0 73 280-352 420-493 (988)
22 PF10075 PCI_Csn8: COP9 signal 95.7 0.067 1.5E-06 46.6 8.7 46 286-331 76-121 (143)
23 PF09976 TPR_21: Tetratricopep 95.6 0.31 6.7E-06 42.1 12.5 114 41-192 31-144 (145)
24 COG2956 Predicted N-acetylgluc 94.8 2.4 5.2E-05 42.1 17.1 157 4-194 73-242 (389)
25 PF09012 FeoC: FeoC like trans 93.7 0.16 3.4E-06 38.6 5.1 48 298-345 5-52 (69)
26 KOG2688 Transcription-associat 93.2 0.69 1.5E-05 47.0 10.2 171 166-354 205-386 (394)
27 COG3107 LppC Putative lipoprot 92.8 1.6 3.5E-05 45.8 12.2 105 58-193 59-163 (604)
28 KOG2076 RNA polymerase III tra 92.4 6.2 0.00014 43.8 16.7 142 10-195 129-270 (895)
29 COG5600 Transcription-associat 92.1 2.7 5.9E-05 42.4 12.4 171 166-354 220-405 (413)
30 PF14938 SNAP: Soluble NSF att 91.9 12 0.00027 36.0 17.6 111 60-194 112-224 (282)
31 PF08784 RPA_C: Replication pr 91.9 0.21 4.7E-06 40.8 4.0 37 307-343 65-101 (102)
32 PF14938 SNAP: Soluble NSF att 90.5 7.4 0.00016 37.6 13.8 74 58-131 151-225 (282)
33 PF04348 LppC: LppC putative l 90.4 0.081 1.8E-06 56.2 0.0 106 59-194 21-126 (536)
34 PF09295 ChAPs: ChAPs (Chs5p-A 89.6 6.3 0.00014 40.4 12.9 93 23-131 171-263 (395)
35 PF13424 TPR_12: Tetratricopep 89.6 3.2 7E-05 31.3 8.5 69 61-130 4-74 (78)
36 TIGR02795 tol_pal_ybgF tol-pal 88.9 5.1 0.00011 32.0 9.8 102 64-195 4-105 (119)
37 PF09976 TPR_21: Tetratricopep 88.7 12 0.00025 32.1 12.4 61 61-128 84-144 (145)
38 PF09756 DDRGK: DDRGK domain; 88.0 0.75 1.6E-05 42.2 4.5 76 304-381 110-187 (188)
39 PF13432 TPR_16: Tetratricopep 87.2 3.2 6.9E-05 30.1 6.8 58 67-130 2-59 (65)
40 PF04733 Coatomer_E: Coatomer 86.5 6.9 0.00015 38.3 10.6 161 25-236 70-232 (290)
41 cd00189 TPR Tetratricopeptide 85.2 12 0.00026 27.0 10.3 94 65-194 3-96 (100)
42 KOG1586 Protein required for f 83.8 42 0.00092 32.2 14.9 28 282-309 233-263 (288)
43 PRK11788 tetratricopeptide rep 83.4 24 0.00052 34.9 13.3 101 63-194 108-208 (389)
44 PRK11788 tetratricopeptide rep 82.8 52 0.0011 32.5 18.3 102 62-194 141-242 (389)
45 PF12895 Apc3: Anaphase-promot 82.4 7.5 0.00016 29.9 7.3 60 62-128 25-84 (84)
46 PF14559 TPR_19: Tetratricopep 82.3 3.6 7.9E-05 30.0 5.2 53 73-131 2-54 (68)
47 cd00090 HTH_ARSR Arsenical Res 81.5 9.6 0.00021 27.7 7.4 45 308-352 21-65 (78)
48 PF12802 MarR_2: MarR family; 80.5 9.5 0.00021 27.5 6.8 51 295-345 7-59 (62)
49 PF13414 TPR_11: TPR repeat; P 79.9 3.5 7.6E-05 30.2 4.4 64 60-129 1-65 (69)
50 TIGR03504 FimV_Cterm FimV C-te 79.7 3.7 8E-05 28.5 4.1 26 65-90 2-27 (44)
51 PF12569 NARP1: NMDA receptor- 77.5 19 0.00042 38.2 10.6 65 100-194 2-66 (517)
52 PRK15431 ferrous iron transpor 76.5 6.7 0.00015 30.7 5.1 39 301-339 10-48 (78)
53 PRK02603 photosystem I assembl 76.5 40 0.00087 29.6 11.0 71 58-131 31-101 (172)
54 PF13424 TPR_12: Tetratricopep 75.9 18 0.00038 27.1 7.4 70 102-194 5-74 (78)
55 TIGR02521 type_IV_pilW type IV 75.2 56 0.0012 28.5 15.2 101 60-196 29-129 (234)
56 TIGR02521 type_IV_pilW type IV 75.0 57 0.0012 28.5 14.1 99 63-195 100-198 (234)
57 KOG1840 Kinesin light chain [C 74.7 63 0.0014 34.3 13.4 126 46-194 225-353 (508)
58 PF01047 MarR: MarR family; I 74.2 13 0.00029 26.5 6.0 49 297-345 7-55 (59)
59 TIGR03879 near_KaiC_dom probab 74.1 5 0.00011 31.1 3.8 41 297-337 22-62 (73)
60 PF04703 FaeA: FaeA-like prote 74.0 8.8 0.00019 28.7 5.0 34 305-338 13-46 (62)
61 smart00550 Zalpha Z-DNA-bindin 73.8 13 0.00028 28.0 6.1 32 308-339 23-54 (68)
62 PF13412 HTH_24: Winged helix- 73.6 16 0.00034 25.1 6.0 33 305-337 15-47 (48)
63 COG3355 Predicted transcriptio 73.5 34 0.00073 29.4 9.1 70 307-376 42-120 (126)
64 PF02082 Rrf2: Transcriptional 73.2 23 0.00049 27.6 7.6 59 295-353 11-71 (83)
65 TIGR01764 excise DNA binding d 72.7 12 0.00025 25.2 5.2 47 308-365 2-48 (49)
66 KOG1497 COP9 signalosome, subu 72.5 9.7 0.00021 37.9 6.2 75 54-178 136-210 (399)
67 smart00418 HTH_ARSR helix_turn 71.8 18 0.00038 25.4 6.3 47 305-351 8-54 (66)
68 PF13176 TPR_7: Tetratricopept 71.7 5.5 0.00012 25.8 3.1 22 66-87 3-24 (36)
69 smart00419 HTH_CRP helix_turn_ 71.7 8.6 0.00019 26.0 4.3 32 307-338 8-39 (48)
70 smart00347 HTH_MARR helix_turn 71.1 46 0.001 25.8 9.7 65 307-371 24-89 (101)
71 PF08220 HTH_DeoR: DeoR-like h 70.9 18 0.00039 26.2 6.0 45 303-351 10-54 (57)
72 PRK10049 pgaA outer membrane p 70.4 1.7E+02 0.0038 32.4 16.4 101 65-195 313-422 (765)
73 PF12728 HTH_17: Helix-turn-he 70.3 16 0.00034 25.5 5.5 47 308-365 2-48 (51)
74 cd00092 HTH_CRP helix_turn_hel 69.6 9 0.0002 27.9 4.3 34 306-339 24-57 (67)
75 PF13174 TPR_6: Tetratricopept 69.5 11 0.00023 23.1 4.0 26 65-90 3-28 (33)
76 PF13428 TPR_14: Tetratricopep 68.9 9.4 0.0002 25.8 3.9 26 64-89 3-28 (44)
77 PF02259 FAT: FAT domain; Int 68.0 1.2E+02 0.0026 29.3 14.9 173 17-194 101-286 (352)
78 TIGR00990 3a0801s09 mitochondr 67.9 1.5E+02 0.0033 31.8 15.0 99 61-195 330-428 (615)
79 PF13181 TPR_8: Tetratricopept 67.6 12 0.00026 23.2 4.0 26 62-87 1-26 (34)
80 COG1497 Predicted transcriptio 67.2 34 0.00075 32.6 8.4 66 304-374 22-87 (260)
81 KOG3081 Vesicle coat complex C 66.5 1.3E+02 0.0029 29.3 13.5 126 66-236 112-238 (299)
82 cd05804 StaR_like StaR_like; a 66.0 71 0.0015 31.1 11.1 66 62-129 148-213 (355)
83 TIGR02552 LcrH_SycD type III s 65.3 76 0.0016 26.0 12.8 98 62-195 17-114 (135)
84 PF07721 TPR_4: Tetratricopept 64.6 9.7 0.00021 22.8 3.0 24 63-86 2-25 (26)
85 KOG2076 RNA polymerase III tra 64.6 24 0.00051 39.4 7.8 84 43-131 395-478 (895)
86 KOG4414 COP9 signalosome, subu 64.1 18 0.00039 31.9 5.5 43 286-328 111-153 (197)
87 KOG3060 Uncharacterized conser 64.0 22 0.00049 34.3 6.6 29 62-90 154-182 (289)
88 KOG1840 Kinesin light chain [C 64.0 2E+02 0.0043 30.6 14.4 113 59-194 280-395 (508)
89 PF12895 Apc3: Anaphase-promot 63.7 63 0.0014 24.6 9.4 50 74-127 1-50 (84)
90 smart00345 HTH_GNTR helix_turn 63.6 18 0.00039 25.3 4.8 32 307-338 19-51 (60)
91 TIGR03302 OM_YfiO outer membra 63.6 86 0.0019 28.6 10.6 73 56-131 27-99 (235)
92 PF03399 SAC3_GANP: SAC3/GANP/ 63.5 45 0.00098 30.1 8.6 142 165-319 55-204 (204)
93 PF00325 Crp: Bacterial regula 63.1 16 0.00036 23.6 3.9 30 308-337 3-32 (32)
94 PF13371 TPR_9: Tetratricopept 63.0 24 0.00051 25.9 5.6 58 68-131 1-58 (73)
95 TIGR02795 tol_pal_ybgF tol-pal 62.6 40 0.00087 26.6 7.3 67 62-131 39-105 (119)
96 smart00344 HTH_ASNC helix_turn 62.3 24 0.00053 28.5 5.9 40 305-344 15-57 (108)
97 smart00420 HTH_DEOR helix_turn 61.7 23 0.00049 24.1 4.9 34 306-339 13-46 (53)
98 PRK11179 DNA-binding transcrip 61.5 13 0.00029 32.5 4.5 38 306-343 22-62 (153)
99 TIGR02010 IscR iron-sulfur clu 61.3 50 0.0011 28.2 8.0 53 296-348 12-66 (135)
100 PRK14574 hmsH outer membrane p 60.6 1.3E+02 0.0028 34.0 13.0 97 62-195 102-198 (822)
101 cd07377 WHTH_GntR Winged helix 60.2 30 0.00066 24.7 5.6 30 309-338 27-56 (66)
102 KOG1129 TPR repeat-containing 59.8 1.2E+02 0.0027 30.5 11.1 97 65-198 226-322 (478)
103 TIGR00373 conserved hypothetic 59.7 1.3E+02 0.0027 26.7 10.7 68 306-373 27-96 (158)
104 cd05804 StaR_like StaR_like; a 59.7 96 0.0021 30.1 10.8 99 64-194 116-214 (355)
105 PF09339 HTH_IclR: IclR helix- 59.6 20 0.00044 25.2 4.4 38 301-338 12-49 (52)
106 PRK03573 transcriptional regul 59.5 78 0.0017 26.9 8.9 44 307-350 46-89 (144)
107 TIGR00990 3a0801s09 mitochondr 59.4 2.5E+02 0.0054 30.1 15.6 98 62-195 399-496 (615)
108 PF13404 HTH_AsnC-type: AsnC-t 58.3 15 0.00032 25.1 3.3 26 306-331 16-41 (42)
109 PLN03218 maturation of RBCL 1; 58.1 3.6E+02 0.0078 31.5 20.6 94 69-194 549-642 (1060)
110 KOG1155 Anaphase-promoting com 58.1 89 0.0019 32.8 10.1 63 66-130 470-535 (559)
111 PF13545 HTH_Crp_2: Crp-like h 58.0 24 0.00051 26.5 4.8 33 306-338 27-59 (76)
112 cd00189 TPR Tetratricopeptide 57.0 67 0.0015 22.7 9.6 62 63-130 35-96 (100)
113 PF06163 DUF977: Bacterial pro 56.8 18 0.00039 31.0 4.2 70 287-370 11-81 (127)
114 KOG2003 TPR repeat-containing 56.1 1.5E+02 0.0032 31.2 11.2 112 62-209 521-635 (840)
115 TIGR02944 suf_reg_Xantho FeS a 55.7 21 0.00046 30.1 4.7 36 306-341 24-59 (130)
116 PF07719 TPR_2: Tetratricopept 55.6 27 0.00059 21.3 4.1 25 63-87 2-26 (34)
117 PRK09954 putative kinase; Prov 55.5 46 0.001 33.1 7.8 47 305-351 15-64 (362)
118 PRK10049 pgaA outer membrane p 54.9 2E+02 0.0044 32.0 13.3 98 61-194 358-455 (765)
119 TIGR00738 rrf2_super rrf2 fami 54.7 58 0.0013 27.3 7.2 52 295-346 11-64 (132)
120 PLN03081 pentatricopeptide (PP 54.5 2.4E+02 0.0052 30.8 13.7 24 66-89 364-387 (697)
121 PF01325 Fe_dep_repress: Iron 54.2 53 0.0012 24.1 5.9 34 305-338 20-53 (60)
122 PF04545 Sigma70_r4: Sigma-70, 53.5 48 0.001 22.9 5.4 31 302-332 15-45 (50)
123 PF11873 DUF3393: Domain of un 53.4 11 0.00024 35.1 2.6 63 206-271 110-172 (204)
124 PLN03088 SGT1, suppressor of 53.0 1.7E+02 0.0036 29.3 11.3 94 66-195 6-99 (356)
125 PF13374 TPR_10: Tetratricopep 52.7 30 0.00065 22.1 4.1 27 62-88 2-28 (42)
126 PF13432 TPR_16: Tetratricopep 52.3 72 0.0016 22.7 6.5 59 106-194 1-59 (65)
127 COG2956 Predicted N-acetylgluc 52.1 2.7E+02 0.0058 28.2 17.0 88 31-129 47-134 (389)
128 PRK10857 DNA-binding transcrip 51.4 71 0.0015 28.5 7.5 42 307-348 25-66 (164)
129 PF14559 TPR_19: Tetratricopep 51.2 22 0.00049 25.6 3.6 30 62-91 25-54 (68)
130 PRK15359 type III secretion sy 51.0 1.6E+02 0.0034 25.2 10.8 92 67-194 29-120 (144)
131 COG1959 Predicted transcriptio 50.8 72 0.0016 28.0 7.3 57 293-349 9-67 (150)
132 PRK06266 transcription initiat 49.7 1.3E+02 0.0028 27.3 9.0 66 306-371 35-102 (178)
133 PF08279 HTH_11: HTH domain; 49.5 29 0.00064 24.4 3.9 28 308-335 16-43 (55)
134 TIGR01610 phage_O_Nterm phage 49.3 80 0.0017 25.3 6.8 46 304-351 44-89 (95)
135 TIGR02552 LcrH_SycD type III s 49.2 47 0.001 27.3 5.7 64 62-131 51-114 (135)
136 PLN03081 pentatricopeptide (PP 49.1 3E+02 0.0065 30.0 13.4 91 67-195 467-557 (697)
137 PF03704 BTAD: Bacterial trans 48.8 1.4E+02 0.0031 25.0 8.9 72 56-133 56-127 (146)
138 PF13429 TPR_15: Tetratricopep 48.8 18 0.00039 34.4 3.5 60 66-130 12-72 (280)
139 PRK10747 putative protoheme IX 48.8 2E+02 0.0044 29.0 11.3 100 64-194 265-389 (398)
140 PF12793 SgrR_N: Sugar transpo 47.8 50 0.0011 27.7 5.5 33 305-337 17-49 (115)
141 TIGR02917 PEP_TPR_lipo putativ 47.7 3.9E+02 0.0085 28.8 21.9 100 59-194 122-221 (899)
142 PF13414 TPR_11: TPR repeat; P 47.4 62 0.0013 23.3 5.5 64 101-194 2-66 (69)
143 PRK11169 leucine-responsive tr 47.4 53 0.0012 29.0 6.0 42 302-343 23-67 (164)
144 PF13463 HTH_27: Winged helix 47.1 74 0.0016 23.0 5.9 48 303-350 14-64 (68)
145 KOG1128 Uncharacterized conser 47.1 1E+02 0.0022 34.0 8.9 139 60-227 396-557 (777)
146 PRK10141 DNA-binding transcrip 47.0 1.7E+02 0.0038 24.6 9.3 70 307-378 30-104 (117)
147 PF04967 HTH_10: HTH DNA bindi 46.9 67 0.0014 23.2 5.3 30 303-332 16-48 (53)
148 PRK11447 cellulose synthase su 46.7 3.3E+02 0.0072 31.8 13.9 116 5-130 608-739 (1157)
149 PF13601 HTH_34: Winged helix 46.1 1.4E+02 0.003 23.2 7.6 42 305-346 12-53 (80)
150 KOG3054 Uncharacterized conser 46.0 38 0.00083 32.3 4.9 50 303-352 210-259 (299)
151 PF01022 HTH_5: Bacterial regu 45.8 59 0.0013 22.3 4.8 33 306-338 14-46 (47)
152 KOG1538 Uncharacterized conser 45.5 2.5E+02 0.0054 31.0 11.2 141 9-195 654-833 (1081)
153 PRK10370 formate-dependent nit 45.1 2.4E+02 0.0052 25.6 15.4 98 62-195 73-173 (198)
154 PF13730 HTH_36: Helix-turn-he 44.7 34 0.00075 24.0 3.6 29 309-337 27-55 (55)
155 COG1522 Lrp Transcriptional re 44.6 36 0.00078 29.2 4.4 37 307-343 22-61 (154)
156 smart00874 B5 tRNA synthetase 44.4 51 0.0011 24.5 4.7 62 307-380 5-68 (71)
157 PRK10046 dpiA two-component re 44.0 52 0.0011 30.2 5.6 45 298-342 168-212 (225)
158 PHA02360 hypothetical protein 43.9 24 0.00052 26.5 2.6 47 41-87 8-59 (70)
159 PF00392 GntR: Bacterial regul 43.6 59 0.0013 23.7 4.8 35 305-339 21-56 (64)
160 PRK03902 manganese transport t 43.6 1.5E+02 0.0032 25.4 8.1 34 305-338 20-53 (142)
161 PLN03077 Protein ECB2; Provisi 43.5 5.2E+02 0.011 29.0 17.2 195 68-335 329-584 (857)
162 PRK10747 putative protoheme IX 43.4 2.3E+02 0.0051 28.6 10.8 94 67-195 89-182 (398)
163 smart00346 HTH_ICLR helix_turn 43.3 1.5E+02 0.0033 22.7 8.4 43 307-351 20-62 (91)
164 PRK11189 lipoprotein NlpI; Pro 42.9 2.3E+02 0.0049 27.4 10.2 100 59-194 61-160 (296)
165 PRK11920 rirA iron-responsive 42.8 87 0.0019 27.5 6.6 52 297-348 13-65 (153)
166 KOG2908 26S proteasome regulat 42.8 3.4E+02 0.0074 27.5 11.1 116 3-127 59-182 (380)
167 PRK11014 transcriptional repre 42.7 64 0.0014 27.7 5.6 47 306-352 24-70 (141)
168 PHA02943 hypothetical protein; 42.5 1.8E+02 0.0039 25.9 8.2 84 305-392 22-115 (165)
169 PF13429 TPR_15: Tetratricopep 42.0 72 0.0016 30.2 6.5 94 66-195 82-175 (280)
170 PRK09782 bacteriophage N4 rece 42.0 2.5E+02 0.0054 32.5 11.6 91 66-196 48-138 (987)
171 TIGR02917 PEP_TPR_lipo putativ 41.9 4.7E+02 0.01 28.1 22.9 26 169-194 773-798 (899)
172 PRK11512 DNA-binding transcrip 41.7 99 0.0022 26.4 6.7 45 305-349 52-96 (144)
173 PF01978 TrmB: Sugar-specific 41.6 68 0.0015 23.6 5.0 39 305-343 20-58 (68)
174 KOG1070 rRNA processing protei 41.1 7.3E+02 0.016 30.0 16.0 60 66-131 1534-1593(1710)
175 PF12854 PPR_1: PPR repeat 41.0 35 0.00075 21.8 2.8 22 67-88 12-33 (34)
176 COG5051 RPL36A Ribosomal prote 40.2 99 0.0021 24.8 5.6 70 10-87 27-96 (97)
177 TIGR02337 HpaR homoprotocatech 40.0 2.1E+02 0.0045 23.4 10.3 42 305-346 40-81 (118)
178 PF04492 Phage_rep_O: Bacterio 39.0 48 0.001 27.2 4.0 35 303-337 50-84 (100)
179 cd07311 terB_like_1 tellurium 38.9 79 0.0017 27.9 5.6 99 31-131 14-119 (150)
180 PRK10803 tol-pal system protei 38.6 3.7E+02 0.0079 25.8 11.3 85 41-132 163-247 (263)
181 PF12840 HTH_20: Helix-turn-he 38.4 75 0.0016 23.0 4.7 37 303-339 20-56 (61)
182 TIGR02702 SufR_cyano iron-sulf 38.2 1.4E+02 0.0031 27.2 7.5 47 305-351 13-64 (203)
183 PF09613 HrpB1_HrpK: Bacterial 37.9 3E+02 0.0065 24.6 9.5 82 18-107 8-89 (160)
184 PF08281 Sigma70_r4_2: Sigma-7 37.7 63 0.0014 22.5 4.0 31 301-331 20-50 (54)
185 PF08679 DsrD: Dissimilatory s 37.2 61 0.0013 24.7 3.9 33 305-337 17-50 (67)
186 smart00421 HTH_LUXR helix_turn 37.2 96 0.0021 21.0 5.0 29 304-332 15-43 (58)
187 PF09743 DUF2042: Uncharacteri 37.0 1.5E+02 0.0034 28.7 7.8 39 306-344 129-167 (272)
188 KOG3250 COP9 signalosome, subu 36.1 61 0.0013 30.5 4.6 76 301-376 103-189 (258)
189 PRK10870 transcriptional repre 35.1 2.6E+02 0.0056 25.0 8.6 42 307-348 71-112 (176)
190 PF10345 Cohesin_load: Cohesin 34.7 6.1E+02 0.013 27.3 17.0 129 46-202 43-175 (608)
191 PF12569 NARP1: NMDA receptor- 34.4 1.2E+02 0.0025 32.4 7.0 65 60-130 2-66 (517)
192 PF12964 DUF3853: Protein of u 33.7 31 0.00068 28.1 2.0 41 309-353 47-87 (96)
193 PF13613 HTH_Tnp_4: Helix-turn 33.3 1E+02 0.0022 21.8 4.5 40 294-333 6-45 (53)
194 CHL00033 ycf3 photosystem I as 33.2 3.2E+02 0.0069 23.6 12.6 69 60-131 33-101 (168)
195 cd06170 LuxR_C_like C-terminal 33.1 1.2E+02 0.0025 20.7 4.9 29 304-332 12-40 (57)
196 TIGR00540 hemY_coli hemY prote 33.0 3.4E+02 0.0073 27.5 10.0 95 66-195 122-216 (409)
197 PF08672 APC2: Anaphase promot 32.9 51 0.0011 24.4 2.9 24 317-340 31-54 (60)
198 PF05584 Sulfolobus_pRN: Sulfo 32.9 2.2E+02 0.0048 22.0 6.4 44 295-340 8-51 (72)
199 COG3063 PilF Tfp pilus assembl 32.6 4.6E+02 0.0099 25.2 13.3 139 59-237 32-171 (250)
200 KOG1900 Nuclear pore complex, 31.7 4.7E+02 0.01 31.0 11.4 57 166-223 1007-1063(1311)
201 KOG2047 mRNA splicing factor [ 31.4 3.2E+02 0.0069 30.1 9.5 163 63-229 388-572 (835)
202 cd08312 Death_MyD88 Death doma 30.9 1.1E+02 0.0023 23.8 4.7 46 311-378 20-70 (79)
203 PRK14165 winged helix-turn-hel 30.9 2.7E+02 0.0059 26.1 8.2 48 305-352 19-66 (217)
204 PF08221 HTH_9: RNA polymerase 30.7 2.2E+02 0.0048 20.9 6.7 35 304-338 24-58 (62)
205 PF00515 TPR_1: Tetratricopept 30.6 1.2E+02 0.0025 18.6 4.1 25 63-87 2-26 (34)
206 COG3629 DnrI DNA-binding trans 30.5 2.2E+02 0.0047 27.9 7.7 70 55-131 139-216 (280)
207 COG5481 Uncharacterized conser 30.5 1.4E+02 0.0031 22.1 4.8 31 60-90 5-35 (67)
208 PF06971 Put_DNA-bind_N: Putat 30.4 66 0.0014 22.9 3.1 26 304-329 25-50 (50)
209 PRK15174 Vi polysaccharide exp 30.2 7.5E+02 0.016 27.0 13.3 98 62-195 284-381 (656)
210 PF10078 DUF2316: Uncharacteri 30.2 59 0.0013 26.2 3.1 25 305-329 21-45 (89)
211 PF04760 IF2_N: Translation in 30.0 31 0.00067 24.5 1.3 22 307-328 3-24 (54)
212 COG5308 NUP170 Nuclear pore co 29.7 2E+02 0.0044 32.7 7.9 100 167-270 969-1089(1263)
213 CHL00033 ycf3 photosystem I as 29.6 2.7E+02 0.0059 24.0 7.7 70 61-130 71-141 (168)
214 COG2345 Predicted transcriptio 29.2 97 0.0021 29.1 4.8 39 302-340 20-58 (218)
215 PRK13918 CRP/FNR family transc 29.0 1.7E+02 0.0036 26.1 6.3 33 306-338 148-180 (202)
216 PF14394 DUF4423: Domain of un 28.9 3E+02 0.0066 24.6 7.9 42 298-339 29-73 (171)
217 PRK10411 DNA-binding transcrip 28.8 1.3E+02 0.0029 28.4 5.8 36 304-339 15-50 (240)
218 KOG3060 Uncharacterized conser 28.3 5.7E+02 0.012 25.0 17.2 62 103-194 52-114 (289)
219 PRK14720 transcript cleavage f 28.2 5.1E+02 0.011 29.7 11.0 122 60-219 29-163 (906)
220 PRK13509 transcriptional repre 27.8 1.5E+02 0.0033 28.1 6.1 36 303-338 15-50 (251)
221 PRK14720 transcript cleavage f 27.8 9.8E+02 0.021 27.5 13.5 64 64-134 118-181 (906)
222 PF13518 HTH_28: Helix-turn-he 27.1 1.1E+02 0.0023 20.9 3.7 44 300-344 5-48 (52)
223 KOG1585 Protein required for f 27.0 6E+02 0.013 24.8 12.8 61 168-235 192-252 (308)
224 PF12324 HTH_15: Helix-turn-he 26.7 79 0.0017 24.8 3.1 28 305-332 36-63 (77)
225 KOG1861 Leucine permease trans 26.7 7.9E+02 0.017 26.1 15.0 57 76-132 321-378 (540)
226 PF10345 Cohesin_load: Cohesin 26.7 8.3E+02 0.018 26.3 14.1 87 78-191 37-124 (608)
227 KOG1931 Putative transmembrane 26.6 1E+03 0.022 27.8 12.7 29 64-92 217-245 (1156)
228 COG1729 Uncharacterized protei 26.1 1.1E+02 0.0024 29.7 4.7 66 63-132 179-245 (262)
229 PRK10434 srlR DNA-bindng trans 26.1 1.6E+02 0.0035 28.0 5.9 40 298-337 10-49 (256)
230 KOG1466 Translation initiation 25.5 2.7E+02 0.0058 27.2 7.0 88 22-125 12-102 (313)
231 TIGR01884 cas_HTH CRISPR locus 25.4 2.5E+02 0.0055 25.5 6.9 39 306-344 156-194 (203)
232 TIGR00540 hemY_coli hemY prote 25.1 6.6E+02 0.014 25.3 10.6 100 61-195 83-182 (409)
233 PF01535 PPR: PPR repeat; Int 25.1 95 0.0021 18.2 2.8 22 68-89 6-27 (31)
234 PF01726 LexA_DNA_bind: LexA D 24.8 1.5E+02 0.0032 22.2 4.2 31 308-338 26-57 (65)
235 PF07848 PaaX: PaaX-like prote 24.6 88 0.0019 23.8 3.1 30 310-339 26-55 (70)
236 PRK13777 transcriptional regul 24.5 5.4E+02 0.012 23.4 10.0 53 295-347 47-99 (185)
237 PF01984 dsDNA_bind: Double-st 24.5 44 0.00095 27.8 1.4 22 321-342 61-82 (107)
238 TIGR01889 Staph_reg_Sar staphy 24.2 3.9E+02 0.0084 21.6 9.2 41 306-346 42-82 (109)
239 PF13542 HTH_Tnp_ISL3: Helix-t 24.1 1.3E+02 0.0028 20.7 3.7 27 305-331 25-51 (52)
240 KOG2002 TPR-containing nuclear 23.6 9.8E+02 0.021 27.6 11.8 113 64-216 272-387 (1018)
241 PRK04424 fatty acid biosynthes 23.3 1.3E+02 0.0029 27.2 4.5 43 295-337 9-51 (185)
242 COG4367 Uncharacterized protei 23.0 1E+02 0.0022 24.8 3.2 26 304-329 20-45 (97)
243 PF13371 TPR_9: Tetratricopept 23.0 2.7E+02 0.0058 20.0 5.5 29 61-89 28-56 (73)
244 TIGR00952 S15_bact ribosomal p 22.7 2E+02 0.0043 23.0 4.8 35 37-71 2-36 (86)
245 PF00440 TetR_N: Bacterial reg 22.6 2E+02 0.0043 19.5 4.4 22 303-324 12-33 (47)
246 PF03484 B5: tRNA synthetase B 22.4 1E+02 0.0022 23.2 3.0 60 307-380 5-67 (70)
247 smart00028 TPR Tetratricopepti 22.4 1.3E+02 0.0028 16.3 3.1 22 66-87 5-26 (34)
248 TIGR03697 NtcA_cyano global ni 22.4 1.4E+02 0.003 26.3 4.5 33 307-339 143-175 (193)
249 COG2886 Uncharacterized small 22.2 2.4E+02 0.0052 22.7 5.2 26 306-331 40-65 (88)
250 PF13217 DUF4025: Protein of u 21.8 45 0.00097 24.4 0.9 24 322-345 31-54 (55)
251 PF04539 Sigma70_r3: Sigma-70 21.8 1E+02 0.0023 23.2 3.1 36 306-345 19-54 (78)
252 TIGR03826 YvyF flagellar opero 21.3 2.4E+02 0.0051 24.6 5.4 39 305-347 42-82 (137)
253 PF13431 TPR_17: Tetratricopep 21.2 1.2E+02 0.0026 19.2 2.8 21 62-82 13-33 (34)
254 PF14123 DUF4290: Domain of un 21.1 1.3E+02 0.0028 27.3 3.9 29 18-50 17-45 (176)
255 KOG2376 Signal recognition par 21.0 1.1E+03 0.024 25.7 13.5 110 66-194 114-252 (652)
256 PF02002 TFIIE_alpha: TFIIE al 21.0 1.4E+02 0.0029 24.2 3.8 35 306-340 26-60 (105)
257 PRK04214 rbn ribonuclease BN/u 21.0 4.7E+02 0.01 26.7 8.6 66 306-376 309-391 (412)
258 PRK10265 chaperone-modulator p 20.9 2.4E+02 0.0052 22.9 5.1 41 306-350 6-46 (101)
259 COG3118 Thioredoxin domain-con 20.8 8.3E+02 0.018 24.2 12.2 48 174-224 244-291 (304)
260 PHA02591 hypothetical protein; 20.7 1.1E+02 0.0024 24.0 2.9 24 307-330 59-82 (83)
261 PRK11753 DNA-binding transcrip 20.7 1.4E+02 0.0031 26.6 4.3 32 307-338 168-199 (211)
262 TIGR00498 lexA SOS regulatory 20.6 1.8E+02 0.0039 26.3 4.9 40 308-347 26-66 (199)
263 PRK05626 rpsO 30S ribosomal pr 20.4 2.4E+02 0.0051 22.7 4.9 36 36-71 4-39 (89)
264 PF07064 RIC1: RIC1; InterPro 20.4 4.1E+02 0.0089 25.5 7.5 62 68-129 185-247 (258)
265 KOG2041 WD40 repeat protein [G 20.4 1.1E+03 0.023 26.6 11.0 80 75-196 747-826 (1189)
266 PF08280 HTH_Mga: M protein tr 20.3 1.6E+02 0.0034 21.3 3.6 28 305-332 17-44 (59)
267 KOG2114 Vacuolar assembly/sort 20.3 6.4E+02 0.014 28.6 9.5 68 58-129 364-458 (933)
268 COG3413 Predicted DNA binding 20.2 1.2E+02 0.0026 28.0 3.7 27 306-332 177-203 (215)
269 PF13182 DUF4007: Protein of u 20.2 2.5E+02 0.0054 27.4 6.0 72 289-362 198-284 (286)
270 PRK10906 DNA-binding transcrip 20.1 2.5E+02 0.0055 26.7 6.0 35 303-337 15-49 (252)
271 PF10771 DUF2582: Protein of u 20.0 1.9E+02 0.0041 21.8 4.0 44 305-350 20-63 (65)
272 smart00531 TFIIE Transcription 20.0 5.7E+02 0.012 22.1 7.9 33 305-337 13-45 (147)
No 1
>KOG1498 consensus 26S proteasome regulatory complex, subunit RPN5/PSMD12 [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2e-103 Score=759.89 Aligned_cols=365 Identities=57% Similarity=0.879 Sum_probs=353.7
Q ss_pred HHHHHHhhhchhHHHHHHHHHHHHHhccCCCChHHHHHHHHHhhhhcCCcchHHHHHHHHHHHHHHHHHHhcCHHHHHHH
Q 016147 5 LLLFIIRSVYLFLQAVTAMVQQAMQYIDQTPDLDTRIELIKTLNSVSAGKIYVEIERARLIKKLAKIKEEQGLIAEAADL 84 (394)
Q Consensus 5 ~~~~l~k~r~q~k~ai~~~v~~~~~~~~~~~d~~~k~~~i~~L~~vt~gki~~E~era~l~~~La~i~e~~gd~~eAa~i 84 (394)
.+.+|||||||+|+||++|||+||+|+|++||.++|+++|+|||+||+||||||+||||+|..||+++|++||+.+||++
T Consensus 74 ~i~~Lskkrgqlk~ai~~Mvq~~~~y~~~~~d~~~k~~li~tLr~VtegkIyvEvERarlTk~L~~ike~~Gdi~~Aa~i 153 (439)
T KOG1498|consen 74 QIRLLSKKRGQLKQAIQSMVQQAMTYIDGTPDLETKIKLIETLRTVTEGKIYVEVERARLTKMLAKIKEEQGDIAEAADI 153 (439)
T ss_pred HHHHHHHHhhHHHHHHHHHHHHHHHhccCCCCchhHHHHHHHHHHhhcCceEEeehHHHHHHHHHHHHHHcCCHHHHHHH
Confidence 36789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCccccCCCCccccCCCCCCCcccccCCCCccchHHH
Q 016147 85 MQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPRVFDADPSKEKKKPKEGDNVVEEAPADIPSLLEL 164 (394)
Q Consensus 85 L~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~ 164 (394)
|+++||||||+|+.+||++|+||||||||.++||++|+++++||+.++|+.+ +.+++
T Consensus 154 l~el~VETygsm~~~ekV~fiLEQmrKOG~~~D~vra~i~skKI~~K~F~~~-----------------------~~~~l 210 (439)
T KOG1498|consen 154 LCELQVETYGSMEKSEKVAFILEQMRLCLLRLDYVRAQIISKKINKKFFEKP-----------------------DVQEL 210 (439)
T ss_pred HHhcchhhhhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhHHhcCCc-----------------------cHHHH
Confidence 9999999999999999999999999999999999999999999999999753 56899
Q ss_pred HHHHHHHHHHHHHhhhhHHHHHHHHHHHhccCCCCCChhcHHHHHHHHHHHHHhCCCChhchHhhhhhhcccCcCCChhH
Q 016147 165 KRIYYELMIRYYSHNNDYLEICRCYKAIYEIPYIKEDPAQWMPVLRKICWYLVLAPHDPMQSSLLNSTLEDKNLSEIPNF 244 (394)
Q Consensus 165 klk~~~~~~~~~~~~~~flea~k~y~ei~~t~~i~~d~~~~~~~L~~av~~~ILap~~~~rs~ll~~l~~d~~l~~ip~~ 244 (394)
|++||++|++++.|++.||++|++|+++|+||.+++||++|..+|.++|+|++|||++|+|+++++++..|+.++++|.|
T Consensus 211 KlkyY~lmI~l~lh~~~Yl~v~~~Yraiy~t~~vk~d~~kw~~vL~~iv~f~~LAp~dneQsdll~~is~dKkL~e~p~~ 290 (439)
T KOG1498|consen 211 KLKYYELMIRLGLHDRAYLNVCRSYRAIYDTGNVKEDPEKWIEVLRSIVSFCVLAPHDNEQSDLLARISNDKKLSELPDY 290 (439)
T ss_pred HHHHHHHHHHhcccccchhhHHHHHHHHhcccccccChhhhhhhhhhheeEEeecCCCcHHHHHHHHHhcccccccCccH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhcchhcccchhhHHHHHHhhhhhhhhcCCchhhhhHHHHHHHHHHHHHHHHHhhcCcccHHHHHHHhCCCHHHH
Q 016147 245 RLLLKQLVTMEVIQWTSLWNTYKDEFENETNMLGGSLGAKAAEDLRQRIIEHNILVVSKYYSRITLKRLAELLCLSIQEA 324 (394)
Q Consensus 245 ~~L~k~f~~~eli~~~~~~~~~~~~l~~~~~~~~d~~~~~~~~~L~~~viEHNI~visk~Y~~Isl~rLa~lL~ls~~e~ 324 (394)
..++++|++.+|++|+.+.+.|++.+.....+..+..|++||++|+.||+|||||++++||+|||+.|||+++|+|++++
T Consensus 291 k~lLklfv~~EL~rw~s~~~~yg~~l~~~~~~~~~~~gek~~~dL~~RIiEHNiRiiA~yYSrIt~~rl~eLLdl~~ee~ 370 (439)
T KOG1498|consen 291 KELLKLFVTMELIRWVSLVESYGDELRTNDFFDGGEEGEKRWSDLKLRIIEHNIRIIAKYYSRITLKRLAELLDLPVEEM 370 (439)
T ss_pred HHHHHHHHhcceeeehhHhhhhHHHHhhcccccccchhhhHHHHHHHHHHHHHHHHHHHHHhhccHHHHHHHhCCCHHHH
Confidence 99999999999999998889999999876434455679999999999999999999999999999999999999999999
Q ss_pred HHHHHHhHhcCcEEEEeccCCCEEEEecCCChHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHhhhhcc
Q 016147 325 EKHLSDMVVSKALVAKIDRPQGIVCFQVAKDSNDILNSWAMNLEKLLDLVEKSCHQIHKETMVHKTAL 392 (394)
Q Consensus 325 E~~ls~MI~~g~l~akIDq~~giV~F~~~k~~~~~L~~W~~~I~~l~~~V~k~~~lI~ke~~~~~~~~ 392 (394)
|++||+||+.|+++||||||+|||.|..++++++.||+|+.|+.+|+++++|+||||+||+|||+++.
T Consensus 371 E~~LS~lv~t~ti~aKidrpsgII~F~k~K~~~~~LneW~~nve~L~~ll~K~~HLI~KEemmhsi~~ 438 (439)
T KOG1498|consen 371 EKFLSDLVVTGTIYAKIDRPSGIINFQKVKDSNEILNEWASNVEKLLGLLEKVSHLIHKEEMMHSIQK 438 (439)
T ss_pred HHHHHHHHhccceEEEecCCCceEEEEecccHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 99999999999999999999999999999999999999999999999999999999999999999864
No 2
>COG5071 RPN5 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2.6e-89 Score=642.15 Aligned_cols=366 Identities=39% Similarity=0.659 Sum_probs=352.7
Q ss_pred HHHHHHhhhchhHHHHHHHHHHHHHhccCCCChHHHHHHHHHhhhhcCCcchHHHHHHHHHHHHHHHHHHhcCHHHHHHH
Q 016147 5 LLLFIIRSVYLFLQAVTAMVQQAMQYIDQTPDLDTRIELIKTLNSVSAGKIYVEIERARLIKKLAKIKEEQGLIAEAADL 84 (394)
Q Consensus 5 ~~~~l~k~r~q~k~ai~~~v~~~~~~~~~~~d~~~k~~~i~~L~~vt~gki~~E~era~l~~~La~i~e~~gd~~eAa~i 84 (394)
+++.|+|||||+|+||++|+|++|+|++...|..++..+++||++||||+||||+||||+|..|.++||.+||+.+|+++
T Consensus 74 ql~~L~kKhGQlk~sI~~MIq~vmEylKg~~dl~t~i~~ietlr~VtEgkIFvEvERariT~~L~~ikee~Gdi~sA~Di 153 (439)
T COG5071 74 QLVSLFKKHGQLKQSITSMIQHVMEYLKGIDDLKTKINLIETLRTVTEGKIFVEVERARLTQLLSQIKEEQGDIKSAQDI 153 (439)
T ss_pred HHHHHHHHcchHHHHHHHHHHHHHHhccCcccccchHhHHHHHHHHhcCceEEehhHHHHHHHHHHHHHHhcchhHHHHH
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCccccCCCCccccCCCCCCCcccccCCCCccchHHH
Q 016147 85 MQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPRVFDADPSKEKKKPKEGDNVVEEAPADIPSLLEL 164 (394)
Q Consensus 85 L~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~ 164 (394)
|+++||||||+|+..+|+.|+|||||||+.++||.+|.++++||+.++|..+ +...+
T Consensus 154 lcn~pVETygs~~~Sekv~fiLEQ~rL~vl~~Dy~~A~~~~kKI~KK~Fe~~-----------------------d~~sl 210 (439)
T COG5071 154 LCNEPVETYGSFDLSEKVAFILEQVRLFLLRSDYYMASTYTKKINKKFFEKE-----------------------DVQSL 210 (439)
T ss_pred HhcCchhhccchhHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHhccc-----------------------cHHHH
Confidence 9999999999999999999999999999999999999999999999999753 56799
Q ss_pred HHHHHHHHHHHHHhhhhHHHHHHHHHHHhccCCCCCChhcHHHHHHHHHHHHHhCCCChhchHhhhhhhcccCcCCChhH
Q 016147 165 KRIYYELMIRYYSHNNDYLEICRCYKAIYEIPYIKEDPAQWMPVLRKICWYLVLAPHDPMQSSLLNSTLEDKNLSEIPNF 244 (394)
Q Consensus 165 klk~~~~~~~~~~~~~~flea~k~y~ei~~t~~i~~d~~~~~~~L~~av~~~ILap~~~~rs~ll~~l~~d~~l~~ip~~ 244 (394)
|++||++..+++.|.|.|+++|++|+++|+|..+++|++.|..+|+++++|++|+|+++++.++++++..|.++..+|.-
T Consensus 211 KlkyYeL~V~i~Lh~R~Yl~v~~y~~~vY~t~~~~~d~Akwk~VLS~~v~F~iLtpy~neq~dlvhKi~~d~kl~sl~~~ 290 (439)
T COG5071 211 KLKYYELKVRIGLHDRAYLDVCKYYRAVYDTAVVQEDPAKWKEVLSNVVCFALLTPYDNEQADLLHKINADHKLNSLPLL 290 (439)
T ss_pred HHHHHHHhheeecccHHHHHHHHHHHHHHHHHHhccCcccccchhhcceeeEEecccccHHHHHHHHhhhhhhhccchhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhcchhcccchhhHHHHHHhhhhhhhhcCCchhhhhHHHHHHHHHHHHHHHHHhhcCcccHHHHHHHhCCCHHHH
Q 016147 245 RLLLKQLVTMEVIQWTSLWNTYKDEFENETNMLGGSLGAKAAEDLRQRIIEHNILVVSKYYSRITLKRLAELLCLSIQEA 324 (394)
Q Consensus 245 ~~L~k~f~~~eli~~~~~~~~~~~~l~~~~~~~~d~~~~~~~~~L~~~viEHNI~visk~Y~~Isl~rLa~lL~ls~~e~ 324 (394)
..++++|..+++++||.+...|++.+....--|++..++.||.+|++||+|||+|+|+.||+||++.||+.++++|++++
T Consensus 291 ~~lVk~f~vNelmrwp~V~~~y~~~l~~~~faF~~e~~~~~w~DL~krviEHN~RvI~~yYSrI~~~rl~~lld~~~s~t 370 (439)
T COG5071 291 QQLVKCFIVNELMRWPKVAEIYGSALRSNVFAFNDEKGEKRWSDLRKRVIEHNIRVIANYYSRIHCSRLGVLLDMSPSET 370 (439)
T ss_pred hhHHHHHHHHHHHhhhHHHHHhHHHHHhhhhhhccchhhhhHHHHHHHHHHhhHhHHHHHhhhhhHHHHHHHHcCCHHHH
Confidence 99999999999999999999999988654223466678899999999999999999999999999999999999999999
Q ss_pred HHHHHHhHhcCcEEEEeccCCCEEEEecCCChHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHhhhhccc
Q 016147 325 EKHLSDMVVSKALVAKIDRPQGIVCFQVAKDSNDILNSWAMNLEKLLDLVEKSCHQIHKETMVHKTALK 393 (394)
Q Consensus 325 E~~ls~MI~~g~l~akIDq~~giV~F~~~k~~~~~L~~W~~~I~~l~~~V~k~~~lI~ke~~~~~~~~~ 393 (394)
|+.+|+||++|.++|||+||+|||.|+++++..+.||.|+.|++.+|+.++++.|||.||+|+|+++.|
T Consensus 371 e~~ISdlVN~G~~yaKiNrpa~Ii~FEK~~n~~~~lneW~~NV~ellgklek~~HLI~KEe~m~siqak 439 (439)
T COG5071 371 EQFISDLVNKGHFYAKINRPAQIISFEKSQNVQEQLNEWGSNVTELLGKLEKVRHLIIKEEMMNSIQAK 439 (439)
T ss_pred HHHHHHHHhcCcEEEEecCccceEEeeccccHHHHHHHhcccHHHHHHHHHHHhHHHhHHHHHhhhccC
Confidence 999999999999999999999999999999999999999999999999999999999999999998754
No 3
>KOG1497 consensus COP9 signalosome, subunit CSN4 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=100.00 E-value=9.8e-56 Score=418.02 Aligned_cols=317 Identities=22% Similarity=0.295 Sum_probs=285.0
Q ss_pred ccCCCChHHHHHHHHHhhhhcCCcchHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHhhhhhc-ccCcHHHHHHHHHHHH
Q 016147 31 IDQTPDLDTRIELIKTLNSVSAGKIYVEIERARLIKKLAKIKEEQGLIAEAADLMQEVAVETF-GAMAKTEKIAFILEQV 109 (394)
Q Consensus 31 ~~~~~d~~~k~~~i~~L~~vt~gki~~E~era~l~~~La~i~e~~gd~~eAa~iL~~i~vEt~-~~m~~~eK~e~~Leq~ 109 (394)
++.+|+.-.|.-.-+||..|+++.|++|++.+-++.+||.+||++|+|..||.+|.+|+.||+ ...+.+.|+..++++.
T Consensus 72 l~~l~~e~~Kei~~~~l~~iq~rvisfeEqv~~irl~LAsiYE~Eq~~~~aaq~L~~I~~~tg~~~~d~~~kl~l~iria 151 (399)
T KOG1497|consen 72 LSILEDELRKEISHFTLEKIQPRVISFEEQVASIRLHLASIYEKEQNWRDAAQVLVGIPLDTGQKAYDVEQKLLLCIRIA 151 (399)
T ss_pred hccCCHHHHHHHHHHHHHhcccccccHHHHHHHHHHHHHHHHHHhhhHHHHHHHHhccCcccchhhhhhHHHHHHHHHHH
Confidence 566676555665666999999999999999999999999999999999999999999999996 4789999999999999
Q ss_pred HHHhccCChHHHHHHHHhhCccccCCCCccccCCCCCCCcccccCCCCccchHHHHHHHHHHHHHHHHhhhhHHHHHHHH
Q 016147 110 RLCLDRQDYVRAQILSRKISPRVFDADPSKEKKKPKEGDNVVEEAPADIPSLLELKRIYYELMIRYYSHNNDYLEICRCY 189 (394)
Q Consensus 110 rL~L~~~D~~~a~~~~~Ki~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~~~~flea~k~y 189 (394)
||||+.+|.+.|+++.+|+|...-.. ...++.+.|.-|.+|..+..|+|+|||++|
T Consensus 152 rlyLe~~d~veae~~inRaSil~a~~------------------------~Ne~Lqie~kvc~ARvlD~krkFlEAAqrY 207 (399)
T KOG1497|consen 152 RLYLEDDDKVEAEAYINRASILQAES------------------------SNEQLQIEYKVCYARVLDYKRKFLEAAQRY 207 (399)
T ss_pred HHHHhcCcHHHHHHHHHHHHHhhhcc------------------------cCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999753211 236888999999999999999999999999
Q ss_pred HHHhccCCCCCChhcHHHHHHHHHHHHHhCCCChhchHhhhhhhcccCcCCChhHHHHHHHhcchhcccchhhHHHHHHh
Q 016147 190 KAIYEIPYIKEDPAQWMPVLRKICWYLVLAPHDPMQSSLLNSTLEDKNLSEIPNFRLLLKQLVTMEVIQWTSLWNTYKDE 269 (394)
Q Consensus 190 ~ei~~t~~i~~d~~~~~~~L~~av~~~ILap~~~~rs~ll~~l~~d~~l~~ip~~~~L~k~f~~~eli~~~~~~~~~~~~ 269 (394)
++++.+.-+ |+.++.++|+.|+.|++||.+||+|+++|+.+++||+++++|.|..+.|+|+. ++|+.+++.++-...
T Consensus 208 yels~~ki~--~e~~~~~aL~~a~~CtlLA~~gpqrsr~Latlfkder~~~l~~y~ileKmyl~-riI~k~el~ef~~~L 284 (399)
T KOG1497|consen 208 YELSQRKIV--DESERLEALKKALQCTLLASAGPQRSRMLATLFKDERCQKLPAYGILEKMYLE-RIIRKEELQEFEAFL 284 (399)
T ss_pred HHHHHHHhc--chHHHHHHHHHhHhheeecCCChHHHHHHHHHhcCcccccccchHHHHHHHHH-HHhcchhHHHHHHHh
Confidence 999987765 45678999999999999999999999999999999999999999999999997 799999986544344
Q ss_pred hhhhhhhcCCchhhhhHHHHHHHHHHHHHHHHHhhcCcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEEeccCCCEEE
Q 016147 270 FENETNMLGGSLGAKAAEDLRQRIIEHNILVVSKYYSRITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKIDRPQGIVC 349 (394)
Q Consensus 270 l~~~~~~~~d~~~~~~~~~L~~~viEHNI~visk~Y~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~akIDq~~giV~ 349 (394)
.+|+.....| +...+.++++||||..+|++|++|||+.||.+|++|++.+|+++++||.+||++|.|||.+|||+
T Consensus 285 ~pHQka~~~d-----gssil~ra~~EhNlls~Skly~nisf~~Lg~ll~i~~ekaekiaa~MI~qeRmng~IDQ~egiih 359 (399)
T KOG1497|consen 285 QPHQKAHTMD-----GSSILDRAVIEHNLLSASKLYNNISFEELGALLKIDAEKAEKIAAQMITQERMNGSIDQIEGIIH 359 (399)
T ss_pred cchhhhcccC-----cchhhhhHHHHHhHHHHHHHHHhccHHHHHHHhCCCHHHHHHHHHHHHhHHHhccchHhhcceEe
Confidence 4566554222 34779999999999999999999999999999999999999999999999999999999999999
Q ss_pred EecCCChHHHHHHHHHHHHHHHHHHHHHHhhhhH
Q 016147 350 FQVAKDSNDILNSWAMNLEKLLDLVEKSCHQIHK 383 (394)
Q Consensus 350 F~~~k~~~~~L~~W~~~I~~l~~~V~k~~~lI~k 383 (394)
|.++ +.+..|+.+|.+||+.||++.+.|.+
T Consensus 360 Fe~~----e~l~~wdkqi~sl~~qvNki~~~i~~ 389 (399)
T KOG1497|consen 360 FEDR----EELPQWDKQIQSLCNQVNKILDKISH 389 (399)
T ss_pred ecch----hhhhhhhHHHHHHHHHHHHHHHHHHH
Confidence 9985 67999999999999999999999876
No 4
>KOG0687 consensus 26S proteasome regulatory complex, subunit RPN7/PSMD6 [Posttranslational modification, protein turnover, chaperones]
Probab=99.97 E-value=1.2e-28 Score=234.88 Aligned_cols=300 Identities=17% Similarity=0.183 Sum_probs=250.5
Q ss_pred HHHHHHHH-HhhhhcCCcchHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHhhhhhcc-cCcHHHHHHHHHHHHHHHhcc
Q 016147 38 DTRIELIK-TLNSVSAGKIYVEIERARLIKKLAKIKEEQGLIAEAADLMQEVAVETFG-AMAKTEKIAFILEQVRLCLDR 115 (394)
Q Consensus 38 ~~k~~~i~-~L~~vt~gki~~E~era~l~~~La~i~e~~gd~~eAa~iL~~i~vEt~~-~m~~~eK~e~~Leq~rL~L~~ 115 (394)
+.|++=++ .+.+..++.. |-|..+.....|.+|.+.||.+.|.+.+.. |++ +++.+.|+++.+..+||.+..
T Consensus 81 eeki~eld~~iedaeenlG--E~ev~ea~~~kaeYycqigDkena~~~~~~----t~~ktvs~g~kiDVvf~~iRlglfy 154 (393)
T KOG0687|consen 81 EEKIKELDEKIEDAEENLG--ESEVREAMLRKAEYYCQIGDKENALEALRK----TYEKTVSLGHKIDVVFYKIRLGLFY 154 (393)
T ss_pred HHHHHHHHHHHHHHHHhcc--hHHHHHHHHHHHHHHHHhccHHHHHHHHHH----HHHHHhhcccchhhHHHHHHHHHhh
Confidence 55555555 4455666666 889999999999999999999999999987 875 799999999999999999999
Q ss_pred CChHHHHHHHHhhCccccCCCCccccCCCCCCCcccccCCCCccchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhcc
Q 016147 116 QDYVRAQILSRKISPRVFDADPSKEKKKPKEGDNVVEEAPADIPSLLELKRIYYELMIRYYSHNNDYLEICRCYKAIYEI 195 (394)
Q Consensus 116 ~D~~~a~~~~~Ki~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~~~~flea~k~y~ei~~t 195 (394)
.|..-....+.|++..+-.+ ++||-|.|++-+.+.|.++.+||.+|+..|.++..|
T Consensus 155 ~D~~lV~~~iekak~liE~G------------------------gDWeRrNRlKvY~Gly~msvR~Fk~Aa~Lfld~vsT 210 (393)
T KOG0687|consen 155 LDHDLVTESIEKAKSLIEEG------------------------GDWERRNRLKVYQGLYCMSVRNFKEAADLFLDSVST 210 (393)
T ss_pred ccHHHHHHHHHHHHHHHHhC------------------------CChhhhhhHHHHHHHHHHHHHhHHHHHHHHHHHccc
Confidence 99999999999999886443 468999999999999999999999999999999999
Q ss_pred CCCCCChhcHHHHHHHHHHHHHhCC-CChhchHhhhhhhcccC----cCCChhHHHHHHHhcchhcccchhhHHHHHHhh
Q 016147 196 PYIKEDPAQWMPVLRKICWYLVLAP-HDPMQSSLLNSTLEDKN----LSEIPNFRLLLKQLVTMEVIQWTSLWNTYKDEF 270 (394)
Q Consensus 196 ~~i~~d~~~~~~~L~~av~~~ILap-~~~~rs~ll~~l~~d~~----l~~ip~~~~L~k~f~~~eli~~~~~~~~~~~~l 270 (394)
++.- +.. -+..+|.|+|++. ...+|.++-.++.+.|. +.++|....++..++. |.|..+|
T Consensus 211 FtS~----El~-~Y~~~v~Ytv~~g~i~leR~dlktKVi~~~Evl~vl~~l~~~~q~l~SLY~----------C~Y~~Ff 275 (393)
T KOG0687|consen 211 FTSY----ELM-SYETFVRYTVITGLIALERVDLKTKVIKCPEVLEVLHKLPSVSQLLNSLYE----------CDYSDFF 275 (393)
T ss_pred ccce----ecc-cHHHHHHHHHHHhhheeccchHHhhhcCcHHHHHHhhcCchHHHHHHHHHh----------ccHHHHH
Confidence 8763 333 3677888888876 67899999999999875 5567777777766654 6787777
Q ss_pred hhhhhhcCCchhhhhHHHHHHH--HHHHHHHHHHhh---cCcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEEeccCC
Q 016147 271 ENETNMLGGSLGAKAAEDLRQR--IIEHNILVVSKY---YSRITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKIDRPQ 345 (394)
Q Consensus 271 ~~~~~~~~d~~~~~~~~~L~~~--viEHNI~visk~---Y~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~akIDq~~ 345 (394)
.+...+.......+++-..|-+ ++|--+++.+|+ |.++|++.||+.||+|++.++..|+++|.+|+++|||||++
T Consensus 276 ~~L~~~~~~~lk~D~~l~~h~~yyvREMR~rvY~QlLESYrsl~l~~MA~aFgVSVefiDreL~rFI~~grL~ckIDrVn 355 (393)
T KOG0687|consen 276 NDLAAVEAKQLKDDRYLGPHYRYYVREMRRRVYAQLLESYRSLTLESMAKAFGVSVEFIDRELGRFIAAGRLHCKIDRVN 355 (393)
T ss_pred HHHHHHHHHhhccchhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCchHHHHHhHHHHhhccCceeeeeeccc
Confidence 6543222112222333333433 677777888876 99999999999999999999999999999999999999999
Q ss_pred CEEEEecCCChHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 016147 346 GIVCFQVAKDSNDILNSWAMNLEKLLDLVEKSCHQIH 382 (394)
Q Consensus 346 giV~F~~~k~~~~~L~~W~~~I~~l~~~V~k~~~lI~ 382 (394)
|||..++|.+.|-+...-..+.+-|++.|+|++..|+
T Consensus 356 GVVEtNrpD~KN~qyq~vikqGd~LLnriQK~~rvi~ 392 (393)
T KOG0687|consen 356 GVVETNRPDEKNAQYQAVIKQGDLLLNRIQKLSRVIN 392 (393)
T ss_pred ceeecCCccccchHHHHHHhhhHHHHHHHHHHHHHhc
Confidence 9999999999998999999999999999999999886
No 5
>KOG1464 consensus COP9 signalosome, subunit CSN2 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=99.92 E-value=4.4e-24 Score=200.16 Aligned_cols=270 Identities=15% Similarity=0.233 Sum_probs=224.9
Q ss_pred HHHHHHHHHhcCHHHHHHHHHHhhhhhcc--cCcHHHHHHHHHHH----HHHHhccCChHHHHHHHHhhCc-cccCCCCc
Q 016147 66 KKLAKIKEEQGLIAEAADLMQEVAVETFG--AMAKTEKIAFILEQ----VRLCLDRQDYVRAQILSRKISP-RVFDADPS 138 (394)
Q Consensus 66 ~~La~i~e~~gd~~eAa~iL~~i~vEt~~--~m~~~eK~e~~Leq----~rL~L~~~D~~~a~~~~~Ki~~-~~~~~~~~ 138 (394)
.+|+++|...|++..-.++|.++++.|.. .-++..|-...||+ +++|-+.+|-.+...+..++-. +.....|.
T Consensus 149 tKLgkl~fd~~e~~kl~KIlkqLh~SCq~edGedD~kKGtQLLEiYAlEIQmYT~qKnNKkLK~lYeqalhiKSAIPHPl 228 (440)
T KOG1464|consen 149 TKLGKLYFDRGEYTKLQKILKQLHQSCQTEDGEDDQKKGTQLLEIYALEIQMYTEQKNNKKLKALYEQALHIKSAIPHPL 228 (440)
T ss_pred chHhhhheeHHHHHHHHHHHHHHHHHhccccCchhhhccchhhhhHhhHhhhhhhhcccHHHHHHHHHHHHhhccCCchH
Confidence 57999999999999999999999998863 44555565555555 8899999998888887776643 22222332
Q ss_pred cccCCCCCCCcccccCCCCccchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhccCCCCCChhcHHHHHHHHHHHHHh
Q 016147 139 KEKKKPKEGDNVVEEAPADIPSLLELKRIYYELMIRYYSHNNDYLEICRCYKAIYEIPYIKEDPAQWMPVLRKICWYLVL 218 (394)
Q Consensus 139 ~~~~~~~~~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~~~~flea~k~y~ei~~t~~i~~d~~~~~~~L~~av~~~IL 218 (394)
+++.+++|+ .|+....+++-.+.-+|+||++.|.+.++ ..+.+||++.|+.-+|
T Consensus 229 -----------ImGvIRECG-------GKMHlreg~fe~AhTDFFEAFKNYDEsGs--------pRRttCLKYLVLANML 282 (440)
T KOG1464|consen 229 -----------IMGVIRECG-------GKMHLREGEFEKAHTDFFEAFKNYDESGS--------PRRTTCLKYLVLANML 282 (440)
T ss_pred -----------HHhHHHHcC-------CccccccchHHHHHhHHHHHHhcccccCC--------cchhHHHHHHHHHHHH
Confidence 677777787 45566777888899999999999999886 5788999998888887
Q ss_pred C-----CCChhchHhhhhhhcccCcCCChhHHHHHHHhcchhcccchhhHHHHHHhhh-hhhhhcCCchhhhhHHHHHHH
Q 016147 219 A-----PHDPMQSSLLNSTLEDKNLSEIPNFRLLLKQLVTMEVIQWTSLWNTYKDEFE-NETNMLGGSLGAKAAEDLRQR 292 (394)
Q Consensus 219 a-----p~~~~rs~ll~~l~~d~~l~~ip~~~~L~k~f~~~eli~~~~~~~~~~~~l~-~~~~~~~d~~~~~~~~~L~~~ 292 (394)
. |++.+.. +.|+++ +++.++..|+.+|.+++|+. |+..+. |+..+++||++.+|.++|.+.
T Consensus 283 mkS~iNPFDsQEA----KPyKNd--PEIlAMTnlv~aYQ~NdI~e-------FE~Il~~~~~~IM~DpFIReh~EdLl~n 349 (440)
T KOG1464|consen 283 MKSGINPFDSQEA----KPYKND--PEILAMTNLVAAYQNNDIIE-------FERILKSNRSNIMDDPFIREHIEDLLRN 349 (440)
T ss_pred HHcCCCCCccccc----CCCCCC--HHHHHHHHHHHHHhcccHHH-------HHHHHHhhhccccccHHHHHHHHHHHHH
Confidence 5 5555544 677655 68889999999999998864 555565 678899999999999999999
Q ss_pred HHHHHHHHHHhhcCcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEEeccCCCEEEEecCCCh----HHHHHHHHHHHH
Q 016147 293 IIEHNILVVSKYYSRITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKIDRPQGIVCFQVAKDS----NDILNSWAMNLE 368 (394)
Q Consensus 293 viEHNI~visk~Y~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~akIDq~~giV~F~~~k~~----~~~L~~W~~~I~ 368 (394)
|+...+..+.+||++|.+..+++.|++++.+++..+...|.+.+|.|+||+++|++...+.++. -..|..|++++.
T Consensus 350 iRTQVLlkLIkPYt~i~Ipfis~~Lnv~~~dV~~LLV~~ILD~~i~g~Ide~n~~l~~~~~~~s~~k~~~al~kW~~ql~ 429 (440)
T KOG1464|consen 350 IRTQVLLKLIKPYTNIGIPFISKELNVPEADVESLLVSCILDDTIDGRIDEVNQYLELDKSKNSGSKLYKALDKWNNQLK 429 (440)
T ss_pred HHHHHHHHHhccccccCchhhHhhcCCCHHHHHHHHHHHHhccccccchHHhhhHhccCccCCcchHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999999887653 368999999999
Q ss_pred HHHHHH
Q 016147 369 KLLDLV 374 (394)
Q Consensus 369 ~l~~~V 374 (394)
+|-..|
T Consensus 430 Sl~~~i 435 (440)
T KOG1464|consen 430 SLQSNI 435 (440)
T ss_pred HHHHHH
Confidence 987654
No 6
>COG5187 RPN7 26S proteasome regulatory complex component, contains PCI domain [Posttranslational modification, protein turnover, chaperones]
Probab=99.91 E-value=7e-23 Score=193.08 Aligned_cols=300 Identities=15% Similarity=0.144 Sum_probs=239.0
Q ss_pred hHHHHHHH-HHhhhhcCCcchHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHhhhhhc-ccCcHHHHHHHHHHHHHHHhc
Q 016147 37 LDTRIELI-KTLNSVSAGKIYVEIERARLIKKLAKIKEEQGLIAEAADLMQEVAVETF-GAMAKTEKIAFILEQVRLCLD 114 (394)
Q Consensus 37 ~~~k~~~i-~~L~~vt~gki~~E~era~l~~~La~i~e~~gd~~eAa~iL~~i~vEt~-~~m~~~eK~e~~Leq~rL~L~ 114 (394)
.+.|++-+ +.+++..+... |.|-++....+|++|.+.+|.+.+.+.+.. ++ ..|+.+-|++++|..+||.+.
T Consensus 91 neeki~Elde~i~~~eedng--E~e~~ea~~n~aeyY~qi~D~~ng~~~~~~----~~~~a~stg~KiDv~l~kiRlg~~ 164 (412)
T COG5187 91 NEEKIEELDERIREKEEDNG--ETEGSEADRNIAEYYCQIMDIQNGFEWMRR----LMRDAMSTGLKIDVFLCKIRLGLI 164 (412)
T ss_pred hHHHHHHHHHHHHHHhhccc--chHHHHHHHHHHHHHHHHhhhhhHHHHHHH----HHHHHHhcccchhhHHHHHHHHHh
Confidence 46676666 68888887776 899999999999999999999999998887 55 478999999999999999999
Q ss_pred cCChHHHHHHHHhhCccccCCCCccccCCCCCCCcccccCCCCccchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhc
Q 016147 115 RQDYVRAQILSRKISPRVFDADPSKEKKKPKEGDNVVEEAPADIPSLLELKRIYYELMIRYYSHNNDYLEICRCYKAIYE 194 (394)
Q Consensus 115 ~~D~~~a~~~~~Ki~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~~~~flea~k~y~ei~~ 194 (394)
.+|-.-.+..+.++++.+-.+ ++|+.|.+|+.+.+.+.+..+||.+|+..+.++..
T Consensus 165 y~d~~vV~e~lE~~~~~iEkG------------------------gDWeRrNRyK~Y~Gi~~m~~RnFkeAa~Ll~d~l~ 220 (412)
T COG5187 165 YGDRKVVEESLEVADDIIEKG------------------------GDWERRNRYKVYKGIFKMMRRNFKEAAILLSDILP 220 (412)
T ss_pred hccHHHHHHHHHHHHHHHHhC------------------------CCHHhhhhHHHHHHHHHHHHHhhHHHHHHHHHHhc
Confidence 999999999999999876443 46899999999999999999999999999999999
Q ss_pred cCCCCCChhcHHHHHHHHHHHHHhCC-CChhchHhhhhhhcccC----cCCChhHHHHHHHhcchhcccchhhHHHHHHh
Q 016147 195 IPYIKEDPAQWMPVLRKICWYLVLAP-HDPMQSSLLNSTLEDKN----LSEIPNFRLLLKQLVTMEVIQWTSLWNTYKDE 269 (394)
Q Consensus 195 t~~i~~d~~~~~~~L~~av~~~ILap-~~~~rs~ll~~l~~d~~----l~~ip~~~~L~k~f~~~eli~~~~~~~~~~~~ 269 (394)
|++.. +. ..+..+|.|++.+. ...+|.++..++.+.|+ +.+...+..|..+-.+ ...+.|+..
T Consensus 221 tF~S~----El-~sY~~~vrYa~~~Gl~~leR~diktki~dspevl~vi~~~e~l~sl~~l~~S-------Ly~cdY~~~ 288 (412)
T COG5187 221 TFESS----EL-ISYSRAVRYAIFCGLLRLERRDIKTKILDSPEVLDVIGSSEKLGSLVQLATS-------LYECDYGGD 288 (412)
T ss_pred ccccc----cc-ccHHHHHHHHHHhhhheeehhhhhhhhcCCHHHHHhccchhhhhhHHHHHHH-------HHHhccchh
Confidence 98753 33 23667777777776 67899999999999874 2333334444443322 123556655
Q ss_pred hhhhhhhc-----CCchhhhhHHHHHHHHHHHHHHHHHhh---cCcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEEe
Q 016147 270 FENETNML-----GGSLGAKAAEDLRQRIIEHNILVVSKY---YSRITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKI 341 (394)
Q Consensus 270 l~~~~~~~-----~d~~~~~~~~~L~~~viEHNI~visk~---Y~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~akI 341 (394)
|.+...++ +|.+.-.|..- -|+|--.|+.+|. |...+++.||+.||+|++-++.-+..+|.+|+++|.|
T Consensus 289 F~~ll~~~~n~L~~d~fl~rh~d~---fvREMRrrvYaQlLESYr~lsl~sMA~tFgVSV~yvdrDLg~FIp~~~LncvI 365 (412)
T COG5187 289 FMNLLYLFCNSLQDDVFLGRHVDL---FVREMRRRVYAQLLESYRLLSLESMAQTFGVSVEYVDRDLGEFIPEGRLNCVI 365 (412)
T ss_pred hHHHHHHHHhhccchHHHHHHHHH---HHHHHHHHHHHHHHHHHHHhhHHHHHHHhCccHHHHhhhHHhhCCCCceeeee
Confidence 55432222 22222222222 2566677777765 9999999999999999999999999999999999999
Q ss_pred ccCCCEEEEecCCChHHHHHHHHHHHHHHHHHHHHHHhhh
Q 016147 342 DRPQGIVCFQVAKDSNDILNSWAMNLEKLLDLVEKSCHQI 381 (394)
Q Consensus 342 Dq~~giV~F~~~k~~~~~L~~W~~~I~~l~~~V~k~~~lI 381 (394)
||++|+|...+|...|.....-..+.+.|+..++|..-.+
T Consensus 366 DRvnGvVetnrpdekn~qy~~vVkqGd~ll~klqKy~atv 405 (412)
T COG5187 366 DRVNGVVETNRPDEKNQQYSSVVKQGDDLLRKLQKYVATV 405 (412)
T ss_pred ecccceEeccCcchhhhhHHHHHhcchHHHHHHHHHHHHH
Confidence 9999999999999888999999999999999999976544
No 7
>KOG1463 consensus 26S proteasome regulatory complex, subunit RPN6/PSMD11 [Posttranslational modification, protein turnover, chaperones]
Probab=99.85 E-value=3.4e-19 Score=171.33 Aligned_cols=299 Identities=14% Similarity=0.206 Sum_probs=230.2
Q ss_pred HHHHHHHHHHHhccCCCCh-HHHHHHHHHhhh-hc-CCcchHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHhhhhhccc
Q 016147 19 AVTAMVQQAMQYIDQTPDL-DTRIELIKTLNS-VS-AGKIYVEIERARLIKKLAKIKEEQGLIAEAADLMQEVAVETFGA 95 (394)
Q Consensus 19 ai~~~v~~~~~~~~~~~d~-~~k~~~i~~L~~-vt-~gki~~E~era~l~~~La~i~e~~gd~~eAa~iL~~i~vEt~~~ 95 (394)
=.+++|+...+....+||. +.++.+....-+ .+ +.+-| -|..|.-.|+.+|...+++.+|....+++--|--.-
T Consensus 85 kaaKlvR~Lvd~~~~~~~~~~~~i~l~~~cIeWA~~ekRtF---LRq~Learli~Ly~d~~~YteAlaL~~~L~rElKKl 161 (411)
T KOG1463|consen 85 KAAKLVRSLVDMFLKIDDGTGDQIELCTECIEWAKREKRTF---LRQSLEARLIRLYNDTKRYTEALALINDLLRELKKL 161 (411)
T ss_pred HHHHHHHHHHHHHccCCCCcchHHHHHHHHHHHHHHHhHHH---HHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhc
Confidence 3456677666666666643 455555553333 22 33333 367777889999999999999999999998887655
Q ss_pred CcHHHHHHHHHHHHHHHhccCChHHHHH--HHHhhCccccCCCCccccCCCCCCCcccccCCCCccchHHHHHHHHHHHH
Q 016147 96 MAKTEKIAFILEQVRLCLDRQDYVRAQI--LSRKISPRVFDADPSKEKKKPKEGDNVVEEAPADIPSLLELKRIYYELMI 173 (394)
Q Consensus 96 m~~~eK~e~~Leq~rL~L~~~D~~~a~~--~~~Ki~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~klk~~~~~~ 173 (394)
-++.-=+++.|.--..|..-++..+|+. .+.|++ ++++|++.+.. ...-...+
T Consensus 162 DDK~lLvev~llESK~y~~l~Nl~KakasLTsART~-----------------AnaiYcpPqlQ--------a~lDLqSG 216 (411)
T KOG1463|consen 162 DDKILLVEVHLLESKAYHALRNLPKAKASLTSARTT-----------------ANAIYCPPQLQ--------ATLDLQSG 216 (411)
T ss_pred ccccceeeehhhhhHHHHHHhcchhHHHHHHHHHHh-----------------hcccccCHHHH--------HHHHHhcc
Confidence 5666778999999999999999988887 444444 45677554332 22233667
Q ss_pred HHHHhhhhHHHHHHHHHHHhccCCCCCChhcHHHHHHHHHHHHHhCCCChhchHhhhhh----hcccCcCCChhHHHHHH
Q 016147 174 RYYSHNNDYLEICRCYKAIYEIPYIKEDPAQWMPVLRKICWYLVLAPHDPMQSSLLNST----LEDKNLSEIPNFRLLLK 249 (394)
Q Consensus 174 ~~~~~~~~flea~k~y~ei~~t~~i~~d~~~~~~~L~~av~~~ILap~~~~rs~ll~~l----~~d~~l~~ip~~~~L~k 249 (394)
.+|..++||.-|+.+|+|.++.+....++.+....|+++++|-|...-..+-..++..- |.+ +.+..++....
T Consensus 217 Ilha~ekDykTafSYFyEAfEgf~s~~~~v~A~~sLKYMlLcKIMln~~ddv~~lls~K~~l~y~g---~~i~AmkavAe 293 (411)
T KOG1463|consen 217 ILHAAEKDYKTAFSYFYEAFEGFDSLDDDVKALTSLKYMLLCKIMLNLPDDVAALLSAKLALKYAG---RDIDAMKAVAE 293 (411)
T ss_pred ceeecccccchHHHHHHHHHccccccCCcHHHHHHHHHHHHHHHHhcCHHHHHHHHhhHHHHhccC---cchHHHHHHHH
Confidence 89999999999999999999988765555567889999999999987655544444311 333 46788899999
Q ss_pred HhcchhcccchhhHHHHHHhhhhhhhhcCCchhhhhHHHHHHHHHHHHHHHHHhhcCcccHHHHHHHhCCCHHHHHHHHH
Q 016147 250 QLVTMEVIQWTSLWNTYKDEFENETNMLGGSLGAKAAEDLRQRIIEHNILVVSKYYSRITLKRLAELLCLSIQEAEKHLS 329 (394)
Q Consensus 250 ~f~~~eli~~~~~~~~~~~~l~~~~~~~~d~~~~~~~~~L~~~viEHNI~visk~Y~~Isl~rLa~lL~ls~~e~E~~ls 329 (394)
+|-++.+-.+...-..| ...+.+|++...|...|.+.+.|.|+..|..||++|.++.+|+++|++...+|+-||
T Consensus 294 A~~nRSLkdF~~AL~~y------k~eL~~D~ivr~Hl~~Lyd~lLEknl~riIEPyS~Vei~hIA~~IGl~~~~VEkKLs 367 (411)
T KOG1463|consen 294 AFGNRSLKDFEKALADY------KKELAEDPIVRSHLQSLYDNLLEKNLCRIIEPYSRVEISHIAEVIGLDVPQVEKKLS 367 (411)
T ss_pred HhcCCcHHHHHHHHHHh------HHHHhcChHHHHHHHHHHHHHHHHhHHHHcCchhhhhHHHHHHHHCCCcHHHHHHHH
Confidence 99998775443332333 345668889999999999999999999999999999999999999999999999999
Q ss_pred HhHhcCcEEEEeccCCCE-EEEecCC
Q 016147 330 DMVVSKALVAKIDRPQGI-VCFQVAK 354 (394)
Q Consensus 330 ~MI~~g~l~akIDq~~gi-V~F~~~k 354 (394)
+||.++.++|.+||.+|. |.|+.|.
T Consensus 368 qMILDKkf~G~LDQg~g~Liv~~e~~ 393 (411)
T KOG1463|consen 368 QMILDKKFYGTLDQGEGCLIVFEEPP 393 (411)
T ss_pred HHHHHHHhhcccccCCCeEEEeCCCC
Confidence 999999999999999998 7777664
No 8
>COG5159 RPN6 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=99.71 E-value=1.4e-15 Score=143.83 Aligned_cols=299 Identities=13% Similarity=0.181 Sum_probs=222.3
Q ss_pred HHHHHHHHHHHHHhccCCCCh-HHHHHHHHHhhhh--cCCcchHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHhhhhhc
Q 016147 17 LQAVTAMVQQAMQYIDQTPDL-DTRIELIKTLNSV--SAGKIYVEIERARLIKKLAKIKEEQGLIAEAADLMQEVAVETF 93 (394)
Q Consensus 17 k~ai~~~v~~~~~~~~~~~d~-~~k~~~i~~L~~v--t~gki~~E~era~l~~~La~i~e~~gd~~eAa~iL~~i~vEt~ 93 (394)
|.-++++|+..++..+..||. +..+++.+.+-+. .|.+.|+ |..|.-+|+-.+.+.|.+.+|...+..+.-|--
T Consensus 80 k~k~~KiirtLiekf~~~~dsl~dqi~v~~~~iewA~rEkr~fL---r~~Le~Kli~l~y~~~~YsdalalIn~ll~ElK 156 (421)
T COG5159 80 KPKITKIIRTLIEKFPYSSDSLEDQIKVLTALIEWADREKRKFL---RLELECKLIYLLYKTGKYSDALALINPLLHELK 156 (421)
T ss_pred chhHHHHHHHHHHhcCCCCccHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHH
Confidence 344677888888888887764 7777777766663 3445554 455667788899999999999999998887765
Q ss_pred ccCcHHHHHHHHHHHHHHHhccCChHHHHH--HHHhhCccccCCCCccccCCCCCCCcccccCCCCccchHHHHHHHHHH
Q 016147 94 GAMAKTEKIAFILEQVRLCLDRQDYVRAQI--LSRKISPRVFDADPSKEKKKPKEGDNVVEEAPADIPSLLELKRIYYEL 171 (394)
Q Consensus 94 ~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~--~~~Ki~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~klk~~~~ 171 (394)
.--++---++++|-.-..|.+-++..+++. .+.|+. ++++|||... ....-.+
T Consensus 157 k~DDK~~Li~vhllESKvyh~irnv~KskaSLTaArt~-----------------Ans~YCPpql--------qa~lDL~ 211 (421)
T COG5159 157 KYDDKINLITVHLLESKVYHEIRNVSKSKASLTAARTL-----------------ANSAYCPPQL--------QAQLDLL 211 (421)
T ss_pred hhcCccceeehhhhhHHHHHHHHhhhhhhhHHHHHHHH-----------------hhccCCCHHH--------HHHHHHh
Confidence 444555667788888888888888776655 334433 4556765333 2223335
Q ss_pred HHHHHHhhhhHHHHHHHHHHHhccCCCCCChhcHHHHHHHHHHHHHhCCCChhchHhhhhhhcccC------cCCChhHH
Q 016147 172 MIRYYSHNNDYLEICRCYKAIYEIPYIKEDPAQWMPVLRKICWYLVLAPHDPMQSSLLNSTLEDKN------LSEIPNFR 245 (394)
Q Consensus 172 ~~~~~~~~~~flea~k~y~ei~~t~~i~~d~~~~~~~L~~av~~~ILap~~~~rs~ll~~l~~d~~------l~~ip~~~ 245 (394)
.+.++..+++|.-|+.+|.|.++.++...+..+.-..|+++++--|.+.. +.+.. .+..++. -+.+..+.
T Consensus 212 sGIlhcdd~dyktA~SYF~Ea~Egft~l~~d~kAc~sLkYmlLSkIMlN~---~~evk-~vl~~K~t~~~y~~r~I~am~ 287 (421)
T COG5159 212 SGILHCDDRDYKTASSYFIEALEGFTLLKMDVKACVSLKYMLLSKIMLNR---REEVK-AVLRNKNTLKHYDDRMIRAML 287 (421)
T ss_pred ccceeeccccchhHHHHHHHHHhccccccchHHHHHHHHHHHHHHHHHhh---HHHHH-HHHccchhHhhhhhhhHHHHH
Confidence 66889999999999999999999887755445556677766555555433 23222 2222221 13577888
Q ss_pred HHHHHhcchhcccchhhHHHHHHhhhhhhhhcCCchhhhhHHHHHHHHHHHHHHHHHhhcCcccHHHHHHHhCCCHHHHH
Q 016147 246 LLLKQLVTMEVIQWTSLWNTYKDEFENETNMLGGSLGAKAAEDLRQRIIEHNILVVSKYYSRITLKRLAELLCLSIQEAE 325 (394)
Q Consensus 246 ~L~k~f~~~eli~~~~~~~~~~~~l~~~~~~~~d~~~~~~~~~L~~~viEHNI~visk~Y~~Isl~rLa~lL~ls~~e~E 325 (394)
....+|-|+.+..+...-.+|++ .+..|+++..|...|...+.|.|+..|..||+++.++.+|.++|++..++|
T Consensus 288 avaea~~NRsL~df~~aL~qY~~------el~~D~~iRsHl~~LYD~LLe~Nl~kiiEPfs~VeishIa~viGldt~qvE 361 (421)
T COG5159 288 AVAEAFGNRSLKDFSDALAQYSD------ELHQDSFIRSHLQYLYDVLLEKNLVKIIEPFSVVEISHIADVIGLDTNQVE 361 (421)
T ss_pred HHHHHhCCCcHhhHHHHHHHhhH------HhccCHHHHHHHHHHHHHHHHhhhhhhcCcceeeehhHHHHHhcccHHHHH
Confidence 89999999988776655555554 455788889999999999999999999999999999999999999999999
Q ss_pred HHHHHhHhcCcEEEEeccCCCEE-EEecC
Q 016147 326 KHLSDMVVSKALVAKIDRPQGIV-CFQVA 353 (394)
Q Consensus 326 ~~ls~MI~~g~l~akIDq~~giV-~F~~~ 353 (394)
.-+++||.++-++|..||.+|.. .++.|
T Consensus 362 gKLsqMILDKifyG~LDqg~gcLivy~ep 390 (421)
T COG5159 362 GKLSQMILDKIFYGTLDQGDGCLIVYGEP 390 (421)
T ss_pred HHHHHHHHHHHHHhhhccCCceEEEeCCc
Confidence 99999999999999999999984 44444
No 9
>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=99.65 E-value=1.1e-15 Score=125.37 Aligned_cols=104 Identities=28% Similarity=0.456 Sum_probs=86.9
Q ss_pred hhHHHHHHHhcchhcccchhhHHHHHHhhhhh-hhhcCCchhhhhHHHHHHHHHHHHHHHHHhhcCcccHHHHHHHhCCC
Q 016147 242 PNFRLLLKQLVTMEVIQWTSLWNTYKDEFENE-TNMLGGSLGAKAAEDLRQRIIEHNILVVSKYYSRITLKRLAELLCLS 320 (394)
Q Consensus 242 p~~~~L~k~f~~~eli~~~~~~~~~~~~l~~~-~~~~~d~~~~~~~~~L~~~viEHNI~visk~Y~~Isl~rLa~lL~ls 320 (394)
|.|..|+++|.+.++-.+ ...+..+ ..++.++....+++.+...+++++++.++++|++|+++++|++|+++
T Consensus 1 ~~~~~l~~~~~~~~~~~~-------~~~l~~~~~~~~~~~~l~~~~~~l~~~i~~~~l~~l~~~y~~i~~~~ia~~l~~~ 73 (105)
T PF01399_consen 1 PPYSELLRAFRSGDLQEF-------EEFLEKHSESLFKDPFLAEYVEQLKEKIRRRNLRQLSKPYSSISISEIAKALQLS 73 (105)
T ss_dssp HHHHHHHHHHHCT-HHHH-------HHHHHHTCHHHHHCTTHHHHHHHHHHHHHHHHHHHHHHC-SEEEHHHHHHHHTCC
T ss_pred CHHHHHHHHHHhCCHHHH-------HHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHHHHHHHhcccchHHHHHHhccc
Confidence 789999999998876443 3333322 34445555667889999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhHhcCcEEEEeccCCCEEEEec
Q 016147 321 IQEAEKHLSDMVVSKALVAKIDRPQGIVCFQV 352 (394)
Q Consensus 321 ~~e~E~~ls~MI~~g~l~akIDq~~giV~F~~ 352 (394)
.+++|..+++||.+|.|.|+||+++|+|.|++
T Consensus 74 ~~~vE~~l~~~I~~~~i~~~ID~~~~~v~~~k 105 (105)
T PF01399_consen 74 EEEVESILIDLISNGLIKAKIDQVNGVVVFSK 105 (105)
T ss_dssp HHHHHHHHHHHHHTTSSEEEEETTTTEEEE-S
T ss_pred hHHHHHHHHHHHHCCCEEEEEECCCCEEEecC
Confidence 99999999999999999999999999999974
No 10
>KOG0686 consensus COP9 signalosome, subunit CSN1 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=99.57 E-value=2.7e-13 Score=133.59 Aligned_cols=257 Identities=15% Similarity=0.114 Sum_probs=188.1
Q ss_pred HHHHHHHHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCccccCCCCccc
Q 016147 61 RARLIKKLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPRVFDADPSKE 140 (394)
Q Consensus 61 ra~l~~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~~~~~~~~~~ 140 (394)
..+.-..|++.|...|+++.|.+...-+.-- --+.++-+.+++..|++.+.-+||.+...+++|+...- .+..
T Consensus 149 iRra~~Dl~dhy~~cG~l~~Alr~YsR~RdY---CTs~khvInm~ln~i~VSI~~~nw~hv~sy~~~A~st~-~~~~--- 221 (466)
T KOG0686|consen 149 IRRALEDLGDHYLDCGQLDNALRCYSRARDY---CTSAKHVINMCLNLILVSIYMGNWGHVLSYISKAESTP-DANE--- 221 (466)
T ss_pred HHHHHHHHHHHHHHhccHHHHHhhhhhhhhh---hcchHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHhCc-hhhh---
Confidence 3455589999999999999999955442211 13567899999999999999999999999999997642 1100
Q ss_pred cCCCCCCCcccccCCCCccchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhccCCCCCChhcHHHHHHHHHHHHHh-C
Q 016147 141 KKKPKEGDNVVEEAPADIPSLLELKRIYYELMIRYYSHNNDYLEICRCYKAIYEIPYIKEDPAQWMPVLRKICWYLVL-A 219 (394)
Q Consensus 141 ~~~~~~~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~~~~flea~k~y~ei~~t~~i~~d~~~~~~~L~~av~~~IL-a 219 (394)
+. +..--.|++- +.+.-+...++|..|+++|...--+. . |. .+...=+.+.+|+.| |
T Consensus 222 --------~~--------~q~v~~kl~C--~agLa~L~lkkyk~aa~~fL~~~~~~-~--d~-~~ivtpsdv~iYggLcA 279 (466)
T KOG0686|consen 222 --------NL--------AQEVPAKLKC--AAGLANLLLKKYKSAAKYFLLAEFDH-C--DY-PEIVTPSDVAIYGGLCA 279 (466)
T ss_pred --------hH--------HHhcCcchHH--HHHHHHHHHHHHHHHHHHHHhCCCCc-c--Cc-cceecchhhHHHHhhHh
Confidence 00 0001123333 33455566679999999998665321 1 11 111112233344444 4
Q ss_pred CCChhchHhhhhhhccc----CcCCChhHHHHHHHhcchhcccchhhHHHHHHhhhh----hhhhcCCchhhhhHHHHHH
Q 016147 220 PHDPMQSSLLNSTLEDK----NLSEIPNFRLLLKQLVTMEVIQWTSLWNTYKDEFEN----ETNMLGGSLGAKAAEDLRQ 291 (394)
Q Consensus 220 p~~~~rs~ll~~l~~d~----~l~~ip~~~~L~k~f~~~eli~~~~~~~~~~~~l~~----~~~~~~d~~~~~~~~~L~~ 291 (394)
-++..|.++...+..+. .++..|.+..++..|++. .|..+|.- .+.+.-|.....|.+.|-.
T Consensus 280 LAtfdr~~Lk~~vi~n~~Fk~flel~Pqlr~il~~fy~s----------ky~~cl~~L~~~k~~llLD~yLaphVd~Ly~ 349 (466)
T KOG0686|consen 280 LATFDRQDLKLNVIKNESFKLFLELEPQLREILFKFYSS----------KYASCLELLREIKPRLLLDMYLAPHVDNLYS 349 (466)
T ss_pred hccCCHHHHHHHHHcchhhhhHHhcChHHHHHHHHHhhh----------hHHHHHHHHHHhccceeechhcchhHHHHHH
Confidence 46777888887777654 367789999999999873 68887762 3456667778888888888
Q ss_pred HHHHHHHHHHHhhcCcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEEeccCCCEEEEecCCCh
Q 016147 292 RIIEHNILVVSKYYSRITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKIDRPQGIVCFQVAKDS 356 (394)
Q Consensus 292 ~viEHNI~visk~Y~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~akIDq~~giV~F~~~k~~ 356 (394)
-|++.-+...-.+|+++.+++||..||.|+.+.|+.+-++|.+|.|+||||+.+|||.-....+.
T Consensus 350 ~IR~r~llqy~~py~s~~m~~mA~af~~sv~~le~~l~~LI~~~~i~~rIDs~~ki~~~~~~~~e 414 (466)
T KOG0686|consen 350 LIRNRALLQYLSPYSSADMSKMAEAFNTSVAILESELLELILEGKISGRIDSHNKILYARDADSE 414 (466)
T ss_pred HHHHhhHHHhcCccccchHHHHHHHhcccHHHHHHHHHHHHHccchheeeccccceeeecccccc
Confidence 88888887777899999999999999999999999999999999999999999999998776544
No 11
>smart00753 PAM PCI/PINT associated module.
Probab=99.49 E-value=1.7e-13 Score=109.72 Aligned_cols=72 Identities=39% Similarity=0.511 Sum_probs=68.0
Q ss_pred hHHHHHHHHHHHHHHHHHhhcCcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEEeccCCCEEEEecCCCh
Q 016147 285 AAEDLRQRIIEHNILVVSKYYSRITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKIDRPQGIVCFQVAKDS 356 (394)
Q Consensus 285 ~~~~L~~~viEHNI~visk~Y~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~akIDq~~giV~F~~~k~~ 356 (394)
++..+.+.++.+|+..++++|++|++++||+.|++|.+++|..+++||.+|.|.|+|||++|+|.|.+..+.
T Consensus 2 ~~~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~~~r 73 (88)
T smart00753 2 LVERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEVDPR 73 (88)
T ss_pred hHHHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCCchh
Confidence 467899999999999999999999999999999999999999999999999999999999999999987543
No 12
>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=99.49 E-value=1.7e-13 Score=109.72 Aligned_cols=72 Identities=39% Similarity=0.511 Sum_probs=68.0
Q ss_pred hHHHHHHHHHHHHHHHHHhhcCcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEEeccCCCEEEEecCCCh
Q 016147 285 AAEDLRQRIIEHNILVVSKYYSRITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKIDRPQGIVCFQVAKDS 356 (394)
Q Consensus 285 ~~~~L~~~viEHNI~visk~Y~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~akIDq~~giV~F~~~k~~ 356 (394)
++..+.+.++.+|+..++++|++|++++||+.|++|.+++|..+++||.+|.|.|+|||++|+|.|.+..+.
T Consensus 2 ~~~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~~~r 73 (88)
T smart00088 2 LVERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEVDPR 73 (88)
T ss_pred hHHHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCCchh
Confidence 467899999999999999999999999999999999999999999999999999999999999999987543
No 13
>KOG2908 consensus 26S proteasome regulatory complex, subunit RPN9/PSMD13 [Posttranslational modification, protein turnover, chaperones]
Probab=99.36 E-value=9.1e-10 Score=106.76 Aligned_cols=280 Identities=19% Similarity=0.252 Sum_probs=183.3
Q ss_pred HHHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCccccCCCCccccCCCC
Q 016147 66 KKLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPRVFDADPSKEKKKPK 145 (394)
Q Consensus 66 ~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~~~~~~~~~~~~~~~ 145 (394)
..+-...+..+|..+|.+.|.++--.+-..-.+..-.-...+++|++|+.+|...++..+.......-..+
T Consensus 79 ei~l~~~~~~~D~~~al~~Le~i~~~~~~~~e~~av~~~~t~~~r~~L~i~DLk~~kk~ldd~~~~ld~~~--------- 149 (380)
T KOG2908|consen 79 EILLVVSEQISDKDEALEFLEKIIEKLKEYKEPDAVIYILTEIARLKLEINDLKEIKKLLDDLKSMLDSLD--------- 149 (380)
T ss_pred HHHHHHHHHhccHHHHHHHHHHHHHHHHhhccchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHhccc---------
Confidence 44445567778999999999998765544444556777788999999999999999998887765321100
Q ss_pred CCCcccccCCCCccchHH-HHHHHHHHHHHHHHhhhhHHHHHHH---HHHHhccCCCCCChhcHHHHHHHHHHHHHhCC-
Q 016147 146 EGDNVVEEAPADIPSLLE-LKRIYYELMIRYYSHNNDYLEICRC---YKAIYEIPYIKEDPAQWMPVLRKICWYLVLAP- 220 (394)
Q Consensus 146 ~~~~~~~~~~~~~~~~~d-~klk~~~~~~~~~~~~~~flea~k~---y~ei~~t~~i~~d~~~~~~~L~~av~~~ILap- 220 (394)
++.. ..-.||.....||...++|-...++ |....+...+.+ +++...---..++++|+.
T Consensus 150 --------------~v~~~Vh~~fY~lssqYyk~~~d~a~yYr~~L~YL~~~d~~~l~~--se~~~lA~~L~~aALLGe~ 213 (380)
T KOG2908|consen 150 --------------GVTSNVHSSFYSLSSQYYKKIGDFASYYRHALLYLGCSDIDDLSE--SEKQDLAFDLSLAALLGEN 213 (380)
T ss_pred --------------CCChhhhhhHHHHHHHHHHHHHhHHHHHHHHHHHhccccccccCH--HHHHHHHHHHHHHHHhccc
Confidence 1222 5678999999999999998775554 444443333322 333332223446777775
Q ss_pred CChhchHhhh-hhhcccCcCCChhHHHHHHHhcchhcccchhhHHHHHHhhhhhhhhcCCchhhhhHHHHHHHHHHHHH-
Q 016147 221 HDPMQSSLLN-STLEDKNLSEIPNFRLLLKQLVTMEVIQWTSLWNTYKDEFENETNMLGGSLGAKAAEDLRQRIIEHNI- 298 (394)
Q Consensus 221 ~~~~rs~ll~-~l~~d~~l~~ip~~~~L~k~f~~~eli~~~~~~~~~~~~l~~~~~~~~d~~~~~~~~~L~~~viEHNI- 298 (394)
.-|. ..+|+ -+.+.=.-........++.+|...++-++..+...+.. ++.+ ..+-.-|...+.---+
T Consensus 214 iyNf-GELL~HPilesL~gT~~eWL~dll~Afn~Gdl~~f~~l~~~~~~----~p~L------~~~e~~L~qKI~LmaLi 282 (380)
T KOG2908|consen 214 IYNF-GELLAHPILESLKGTNREWLKDLLIAFNSGDLKRFESLKGVWGK----QPDL------ASNEDFLLQKIRLLALI 282 (380)
T ss_pred cccH-HHHHhhHHHHHhcCCcHHHHHHHHHHhccCCHHHHHHHHHHhcc----CchH------HHHHHHHHHHHHHHHHH
Confidence 2222 23333 22221111233456788889988877655544333322 1111 1111222222111000
Q ss_pred -HHHHh--hcCcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEEeccCCCEEEEecCCCh----------HHHHHHHHH
Q 016147 299 -LVVSK--YYSRITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKIDRPQGIVCFQVAKDS----------NDILNSWAM 365 (394)
Q Consensus 299 -~visk--~Y~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~akIDq~~giV~F~~~k~~----------~~~L~~W~~ 365 (394)
.+.++ -=..|||+.+|+...+|.+++|-.+.+..+-|-|.|.|||++|+|+|.+..+. .+.+..|.+
T Consensus 283 Ei~F~rpa~~R~lsf~~Ia~~tkip~~eVE~LVMKAlslgLikG~Idqv~~~v~~swvqPRvl~~~qI~~Mk~rl~~W~~ 362 (380)
T KOG2908|consen 283 EITFSRPANERTLSFKEIAEATKIPNKEVELLVMKALSLGLIKGSIDQVEGVVYMSWVQPRVLDRSQIVKMKDRLDEWNK 362 (380)
T ss_pred HHHhcCcchhccccHHHHHHHhCCCHHHHHHHHHHHHhccceeeeecccccEEEEecccccccCHHHHHhHHHHHHHHHH
Confidence 11223 13459999999999999999999999999999999999999999999986542 378999999
Q ss_pred HHHHHHHHHHHHHhhh
Q 016147 366 NLEKLLDLVEKSCHQI 381 (394)
Q Consensus 366 ~I~~l~~~V~k~~~lI 381 (394)
+|.++-+.|+.-+|-|
T Consensus 363 ~v~~me~~ve~~~~~i 378 (380)
T KOG2908|consen 363 DVKSMEGLVEHRGHEI 378 (380)
T ss_pred HHHHHHHHHHHhcccc
Confidence 9999999999888765
No 14
>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=99.27 E-value=5.8e-11 Score=107.78 Aligned_cols=154 Identities=12% Similarity=0.005 Sum_probs=123.4
Q ss_pred HhhhhcCCcchHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHH
Q 016147 46 TLNSVSAGKIYVEIERARLIKKLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILS 125 (394)
Q Consensus 46 ~L~~vt~gki~~E~era~l~~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~ 125 (394)
-|..-.++-| +++..+....||++|.+.||+++|.+.+....- ...+.+.|++++|.++|++++.+||..+..++
T Consensus 22 elk~~~~n~~--kesir~~~~~l~~~~~~~Gd~~~A~k~y~~~~~---~~~~~~~~id~~l~~irv~i~~~d~~~v~~~i 96 (177)
T PF10602_consen 22 ELKDAKSNLG--KESIRMALEDLADHYCKIGDLEEALKAYSRARD---YCTSPGHKIDMCLNVIRVAIFFGDWSHVEKYI 96 (177)
T ss_pred HHHHHHhccc--hHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHhh---hcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHH
Confidence 4555566666 889999999999999999999999998887332 36789999999999999999999999999999
Q ss_pred HhhCccccCCCCccccCCCCCCCcccccCCCCccchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhccCCCCCChhcH
Q 016147 126 RKISPRVFDADPSKEKKKPKEGDNVVEEAPADIPSLLELKRIYYELMIRYYSHNNDYLEICRCYKAIYEIPYIKEDPAQW 205 (394)
Q Consensus 126 ~Ki~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~~~~flea~k~y~ei~~t~~i~~d~~~~ 205 (394)
.|+....-. .++++.+.|+.-+.+.++++.++|.+||+.|.++..|+... +..+.
T Consensus 97 ~ka~~~~~~------------------------~~d~~~~nrlk~~~gL~~l~~r~f~~AA~~fl~~~~t~~~~-~~~el 151 (177)
T PF10602_consen 97 EKAESLIEK------------------------GGDWERRNRLKVYEGLANLAQRDFKEAAELFLDSLSTFTSL-QYTEL 151 (177)
T ss_pred HHHHHHHhc------------------------cchHHHHHHHHHHHHHHHHHhchHHHHHHHHHccCcCCCCC-chhhh
Confidence 999976432 14578999999999999999999999999999999877531 11222
Q ss_pred HHHHHHHHHHHHhCC-CChhchHhhh
Q 016147 206 MPVLRKICWYLVLAP-HDPMQSSLLN 230 (394)
Q Consensus 206 ~~~L~~av~~~ILap-~~~~rs~ll~ 230 (394)
-....+++|++|+. ++..|++|..
T Consensus 152 -~s~~d~a~Y~~l~aLat~~R~eLk~ 176 (177)
T PF10602_consen 152 -ISYNDFAIYGGLCALATLDRSELKK 176 (177)
T ss_pred -cCHHHHHHHHHHHHHHhCCHHHHcc
Confidence 23556666666665 7788887754
No 15
>KOG2581 consensus 26S proteasome regulatory complex, subunit RPN3/PSMD3 [Posttranslational modification, protein turnover, chaperones]
Probab=99.09 E-value=8.9e-08 Score=94.97 Aligned_cols=279 Identities=19% Similarity=0.218 Sum_probs=179.5
Q ss_pred HHHHHHHHHHHHHHHHHhcCHHHHHHHHHHhhhhhcccCc-HHH-HHHHHHHHHHHHhccCChHHHHHHHHhhCccccCC
Q 016147 58 EIERARLIKKLAKIKEEQGLIAEAADLMQEVAVETFGAMA-KTE-KIAFILEQVRLCLDRQDYVRAQILSRKISPRVFDA 135 (394)
Q Consensus 58 E~era~l~~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~-~~e-K~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~~~~~ 135 (394)
..=.|.+-.-++-.||.+|+...--..|....- | .++- +.+ +.-.+--..|.||-.+-|.+|...+.|..- ...
T Consensus 165 D~i~ak~~fy~~l~~E~~~~l~~~rs~l~~~lr-t-AtLrhd~e~qavLiN~LLr~yL~n~lydqa~~lvsK~~~--pe~ 240 (493)
T KOG2581|consen 165 DLIAAKLYFYLYLSYELEGRLADIRSFLHALLR-T-ATLRHDEEGQAVLINLLLRNYLHNKLYDQADKLVSKSVY--PEA 240 (493)
T ss_pred HHHHHHHHHHHHHHHHhhcchHHHHHHHHHHHH-H-hhhcCcchhHHHHHHHHHHHHhhhHHHHHHHHHhhcccC--ccc
Confidence 334466777888889999886555444443321 1 1221 222 333344458999999999999999888762 111
Q ss_pred CCccccCCCCCCCcccccCCCCccchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhc-cCCCCCChhcHHHHHHHHHH
Q 016147 136 DPSKEKKKPKEGDNVVEEAPADIPSLLELKRIYYELMIRYYSHNNDYLEICRCYKAIYE-IPYIKEDPAQWMPVLRKICW 214 (394)
Q Consensus 136 ~~~~~~~~~~~~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~~~~flea~k~y~ei~~-t~~i~~d~~~~~~~L~~av~ 214 (394)
.. +. .--||.=+.+++...+.+|-+|.+++....- .|.... -.-+.++-+.+++
T Consensus 241 ~s----------------------nn--e~ARY~yY~GrIkaiqldYssA~~~~~qa~rkapq~~a-lGf~q~v~k~~iv 295 (493)
T KOG2581|consen 241 AS----------------------NN--EWARYLYYLGRIKAIQLDYSSALEYFLQALRKAPQHAA-LGFRQQVNKLMIV 295 (493)
T ss_pred cc----------------------cH--HHHHHHHHHhhHHHhhcchhHHHHHHHHHHHhCcchhh-hhHHHHHHHHHHH
Confidence 10 12 2246666677999999999999999998774 221100 0122344444444
Q ss_pred HHHhCCCChhchHhhhhhhcccCcCC-ChhHHHHHHHhcchhcccchhhHHHHHHhhhhhhhhcCCchhhhhHHHHHHHH
Q 016147 215 YLVLAPHDPMQSSLLNSTLEDKNLSE-IPNFRLLLKQLVTMEVIQWTSLWNTYKDEFENETNMLGGSLGAKAAEDLRQRI 293 (394)
Q Consensus 215 ~~ILap~~~~rs~ll~~l~~d~~l~~-ip~~~~L~k~f~~~eli~~~~~~~~~~~~l~~~~~~~~d~~~~~~~~~L~~~v 293 (394)
-..|...-|+|+ ++.-|.+++ +-.|-.|.+.--..+|-++.+..+.|++.|... ++. .-.--|+..|
T Consensus 296 v~ll~geiPers-----~F~Qp~~~ksL~~Yf~Lt~AVr~gdlkkF~~~leq~k~~f~~D-----~ty--~LivRLR~NV 363 (493)
T KOG2581|consen 296 VELLLGEIPERS-----VFRQPGMRKSLRPYFKLTQAVRLGDLKKFNETLEQFKDKFQAD-----GTY--TLIVRLRHNV 363 (493)
T ss_pred HHHHcCCCcchh-----hhcCccHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHhhC-----Ccc--hHHHHHHHHH
Confidence 455555568887 333333332 444556666665556766665556666655421 110 0124478889
Q ss_pred HHHHHHHHHhhcCcccHHHHHHHhCCCH-HHHHHHHHHhHhcCcEEEEeccCCCEEEEecCC---ChHHHHHHHHHHHHH
Q 016147 294 IEHNILVVSKYYSRITLKRLAELLCLSI-QEAEKHLSDMVVSKALVAKIDRPQGIVCFQVAK---DSNDILNSWAMNLEK 369 (394)
Q Consensus 294 iEHNI~visk~Y~~Isl~rLa~lL~ls~-~e~E~~ls~MI~~g~l~akIDq~~giV~F~~~k---~~~~~L~~W~~~I~~ 369 (394)
|..-||.||--|+|||+..+|.-|+++. +++|-++++.|.+|-|.|+||-.+|.+.-...- ++++.=..++..|.-
T Consensus 364 IkTgIR~ISlsYSRISl~DIA~kL~l~Seed~EyiVakAIRDGvIea~Id~~~g~m~skE~~diy~t~epQ~~f~~rI~f 443 (493)
T KOG2581|consen 364 IKTGIRKISLSYSRISLQDIAKKLGLNSEEDAEYIVAKAIRDGVIEAKIDHEDGFMQSKETFDIYSTREPQTAFDERIRF 443 (493)
T ss_pred HHHhhhheeeeeeeccHHHHHHHhcCCCchhHHHHHHHHHHhccceeeeccccCceehhhhhhhhccCCchhhHhHHHHH
Confidence 9999999999999999999999999965 459999999999999999999999976544321 112333457777777
Q ss_pred HHHHHHHH
Q 016147 370 LLDLVEKS 377 (394)
Q Consensus 370 l~~~V~k~ 377 (394)
.+++=|..
T Consensus 444 Cl~LhN~~ 451 (493)
T KOG2581|consen 444 CLQLHNEA 451 (493)
T ss_pred HHHHHHHH
Confidence 77665543
No 16
>KOG2582 consensus COP9 signalosome, subunit CSN3 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=98.66 E-value=8e-07 Score=87.27 Aligned_cols=175 Identities=14% Similarity=0.126 Sum_probs=116.3
Q ss_pred HHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhccCCCCCChhcHHHHHH-HHHHHHHhCCC----ChhchHhhhhhhcccC
Q 016147 163 ELKRIYYELMIRYYSHNNDYLEICRCYKAIYEIPYIKEDPAQWMPVLR-KICWYLVLAPH----DPMQSSLLNSTLEDKN 237 (394)
Q Consensus 163 d~klk~~~~~~~~~~~~~~flea~k~y~ei~~t~~i~~d~~~~~~~L~-~av~~~ILap~----~~~rs~ll~~l~~d~~ 237 (394)
..-+.|+.+.+-++...++|-.|---|..+.-+|.-.... --.++++ ...+++|+..- +..-+.-..+..+
T Consensus 180 k~fL~Y~yYgg~iciglk~fe~Al~~~e~~v~~Pa~~vs~-~hlEaYkkylLvsLI~~GK~~ql~k~ts~~~~r~~K--- 255 (422)
T KOG2582|consen 180 KYFLLYLYYGGMICIGLKRFERALYLLEICVTTPAMAVSH-IHLEAYKKYLLVSLILTGKVFQLPKNTSQNAGRFFK--- 255 (422)
T ss_pred HHHHHHHHhcceeeeccccHHHHHHHHHHHHhcchhHHHH-HHHHHHHHHHHHHhhhcCceeeccccchhhhHHhcc---
Confidence 4557788888888888999988888888888888653221 1223333 44556666531 1122233334444
Q ss_pred cCCChhHHHHHHHhcchhcccchhhHHHHHHhhh-hhhhhcCCchhhhhHHHHHHHHHHHHHHHHHhhcCcccHHHHHHH
Q 016147 238 LSEIPNFRLLLKQLVTMEVIQWTSLWNTYKDEFE-NETNMLGGSLGAKAAEDLRQRIIEHNILVVSKYYSRITLKRLAEL 316 (394)
Q Consensus 238 l~~ip~~~~L~k~f~~~eli~~~~~~~~~~~~l~-~~~~~~~d~~~~~~~~~L~~~viEHNI~visk~Y~~Isl~rLa~l 316 (394)
...|.|.++.++|.++ ... ..+.+.. |...+..|.. ..-.+..-..+--|||....|-|++++++.+|++
T Consensus 256 -~ms~pY~ef~~~Y~~~-~~~------eLr~lVk~~~~rF~kDnn-t~l~k~av~sl~k~nI~rltktF~sLsL~dIA~~ 326 (422)
T KOG2582|consen 256 -PMSNPYHEFLNVYLKD-SST------ELRTLVKKHSERFTKDNN-TGLAKQAVSSLYKKNIQRLTKTFLSLSLSDIASR 326 (422)
T ss_pred -cCCchHHHHHHHHhcC-CcH------HHHHHHHHHHHHHhhcCc-HHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHH
Confidence 4577899999999874 221 1222221 2222322211 1112334445678999999999999999999998
Q ss_pred hCC-CHHHHHHHHHHhHhcCcEEEEeccCCCEEEEecC
Q 016147 317 LCL-SIQEAEKHLSDMVVSKALVAKIDRPQGIVCFQVA 353 (394)
Q Consensus 317 L~l-s~~e~E~~ls~MI~~g~l~akIDq~~giV~F~~~ 353 (394)
..+ +++|+|+++-+||.+|+++|.|| |.|.|...
T Consensus 327 vQLa~~qevek~Ilqmie~~~i~a~iN---G~v~f~~n 361 (422)
T KOG2582|consen 327 VQLASAQEVEKYILQMIEDGEIFASIN---GMVFFTDN 361 (422)
T ss_pred HHhcchHHHHHHHHHHhccCceEEEec---ceEEEecC
Confidence 888 58899999999999999999999 99999653
No 17
>KOG2758 consensus Translation initiation factor 3, subunit e (eIF-3e) [Translation, ribosomal structure and biogenesis]
Probab=97.96 E-value=0.015 Score=56.92 Aligned_cols=79 Identities=23% Similarity=0.229 Sum_probs=60.8
Q ss_pred hhcCcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEEeccCCCEEEEecCCChHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 016147 303 KYYSRITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKIDRPQGIVCFQVAKDSNDILNSWAMNLEKLLDLVEKSCHQIH 382 (394)
Q Consensus 303 k~Y~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~akIDq~~giV~F~~~k~~~~~L~~W~~~I~~l~~~V~k~~~lI~ 382 (394)
+.-++||++-||.-|+++++++|.-+.++|.+.+|.||||...|-|..+.+.. .....-.++..+|.-.-+++...|.
T Consensus 345 RIHqcIti~mLA~kLnm~~eeaErwivnlIr~~rl~AkidSklg~Vvmg~~~~--s~~qQ~ie~tksLS~rsq~la~~le 422 (432)
T KOG2758|consen 345 RIHQCITIDMLADKLNMDPEEAERWIVNLIRTARLDAKIDSKLGHVVMGHPTV--SPHQQLIEKTKSLSFRSQNLAQQLE 422 (432)
T ss_pred HHHHheeHHHHHHHhcCCHHHHHHHHHHHHHHhhhhhhhccccCceeecCCCC--CHHHHHHHhccccchhHHHHHHHHH
Confidence 45678999999999999999999999999999999999999999999987653 2333344455555544444444444
Q ss_pred H
Q 016147 383 K 383 (394)
Q Consensus 383 k 383 (394)
|
T Consensus 423 k 423 (432)
T KOG2758|consen 423 K 423 (432)
T ss_pred H
Confidence 3
No 18
>KOG1076 consensus Translation initiation factor 3, subunit c (eIF-3c) [Translation, ribosomal structure and biogenesis]
Probab=97.71 E-value=0.00013 Score=77.05 Aligned_cols=68 Identities=24% Similarity=0.446 Sum_probs=62.2
Q ss_pred HHHHHHHHHHHHHH----HHhhcCcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEEeccCCCEEEEecCC
Q 016147 287 EDLRQRIIEHNILV----VSKYYSRITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKIDRPQGIVCFQVAK 354 (394)
Q Consensus 287 ~~L~~~viEHNI~v----isk~Y~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~akIDq~~giV~F~~~k 354 (394)
..|.++|.|.-+|. .|.+|++||++.||++|+||+..+-.++|+||.+..|.|+.|||.++|.|++..
T Consensus 694 ~Ml~~rIqEEsLRTYLftYss~Y~SvSl~~LA~mFdLp~~~VhsIiSkmiineEl~AslDqpt~~iv~hrvE 765 (843)
T KOG1076|consen 694 DMLTERIQEESLRTYLFTYSSVYDSVSLAKLADMFDLPEPKVHSIISKMIINEELHASLDQPTQCIVMHRVE 765 (843)
T ss_pred HHHHHHHHHHHHHHHHHHhhhhhhhccHHHHHHHhCCCchhHHHHHHHHHHHHHhhhccCCCcceEEEeecc
Confidence 45678888888876 568899999999999999999999999999999999999999999999999854
No 19
>KOG2753 consensus Uncharacterized conserved protein, contains PCI domain [General function prediction only]
Probab=97.57 E-value=0.023 Score=55.84 Aligned_cols=193 Identities=17% Similarity=0.171 Sum_probs=111.0
Q ss_pred HHHHHHHHHHHHhhhhHHHHHHHHHHHhccCCCCCChhcHHHHHHHHHHHHHhCCCChhchHhhhhhhcccCcCCChhHH
Q 016147 166 RIYYELMIRYYSHNNDYLEICRCYKAIYEIPYIKEDPAQWMPVLRKICWYLVLAPHDPMQSSLLNSTLEDKNLSEIPNFR 245 (394)
Q Consensus 166 lk~~~~~~~~~~~~~~flea~k~y~ei~~t~~i~~d~~~~~~~L~~av~~~ILap~~~~rs~ll~~l~~d~~l~~ip~~~ 245 (394)
..++.+..+.....+.--++++.+-+...|.+-+ |......---..|.-++-+|....=..++. +.-=..++.-+ +.
T Consensus 165 rel~r~v~~al~~~k~~~~s~kvmt~lLgtyt~d-nas~AredA~rcV~~av~dP~~F~fD~Ll~-L~pV~qLE~d~-i~ 241 (378)
T KOG2753|consen 165 RELLRAVHKALKDNKSVDESSKVMTELLGTYTED-NASEAREDAMRCVVEAVKDPKIFLFDHLLT-LPPVKQLEGDL-IH 241 (378)
T ss_pred HHHHHHHHHHHHhcchhhhHHHHHHHHHHHhccc-chhHHHHHHHHHHHHHHcCCceeccchhcc-CchHHHhccch-HH
Confidence 3555555544444444446777777777766542 222222222234444555664322221221 11101133333 55
Q ss_pred HHHHHhcchhcccchhhHHHHHHhhhhhhhhcCCchhhhhHHHHHHHHHHHHHHHHHhhcCcccHHHHHHHhCCCHHHHH
Q 016147 246 LLLKQLVTMEVIQWTSLWNTYKDEFENETNMLGGSLGAKAAEDLRQRIIEHNILVVSKYYSRITLKRLAELLCLSIQEAE 325 (394)
Q Consensus 246 ~L~k~f~~~eli~~~~~~~~~~~~l~~~~~~~~d~~~~~~~~~L~~~viEHNI~visk~Y~~Isl~rLa~lL~ls~~e~E 325 (394)
.|++.|.+..+ ..|-.+-..+.++..+ .|-.+ ++.-+.++---+..++..=..||++.|++-|++.++|+|
T Consensus 242 qLL~IF~s~~L-------~aYveF~~~N~~Fvqs-~gl~~-E~~~~KMRLLTlm~LA~es~eisy~~l~k~LqI~edeVE 312 (378)
T KOG2753|consen 242 QLLKIFVSGKL-------DAYVEFVAANSGFVQS-QGLVH-EQNMAKMRLLTLMSLAEESNEISYDTLAKELQINEDEVE 312 (378)
T ss_pred HHHHHHHhcch-------HHHHHHHHhChHHHHH-hcccH-HHHHHHHHHHHHHHHhccCCCCCHHHHHHHhccCHHHHH
Confidence 78899988655 2343333222222111 01110 233344444445556667889999999999999999999
Q ss_pred HHHHHhHhcCcEEEEeccCCCEEEEecCCC----------hHHHHHHHH-HHHHHH
Q 016147 326 KHLSDMVVSKALVAKIDRPQGIVCFQVAKD----------SNDILNSWA-MNLEKL 370 (394)
Q Consensus 326 ~~ls~MI~~g~l~akIDq~~giV~F~~~k~----------~~~~L~~W~-~~I~~l 370 (394)
..+.+.|..|-+.|||||.++.|.-.+..- -.+.|+.|. ++++.+
T Consensus 313 ~fVIdaI~aklV~~kidq~~~~viVs~~~hR~FG~~qW~~L~~kL~aw~k~~~stv 368 (378)
T KOG2753|consen 313 LFVIDAIRAKLVEGKIDQMNRTVIVSSSTHRTFGKQQWQQLRDKLAAWGKQNLSTV 368 (378)
T ss_pred HHHHHHHHHHHHHhhHHhhcceEEeehhhhhhcccHHHHHHHHHHHHHHhhhhHHH
Confidence 999999999999999999999988765311 135788894 444433
No 20
>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=96.65 E-value=0.15 Score=52.07 Aligned_cols=205 Identities=17% Similarity=0.220 Sum_probs=105.8
Q ss_pred cccCcHHHHHHH--HHHHHHHHhccCChHHHHHHHHhhCccccCCCCccccCCCCCCCcccccCCCCccchHHHHHHHHH
Q 016147 93 FGAMAKTEKIAF--ILEQVRLCLDRQDYVRAQILSRKISPRVFDADPSKEKKKPKEGDNVVEEAPADIPSLLELKRIYYE 170 (394)
Q Consensus 93 ~~~m~~~eK~e~--~Leq~rL~L~~~D~~~a~~~~~Ki~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~klk~~~ 170 (394)
+|+-+....+=| ++-..|++..-|||..|-..+.=|..- . .+++...+.|. +..+=
T Consensus 111 ~g~~~l~~~LGYFSligLlRvh~LLGDY~~Alk~l~~idl~---~------------~~l~~~V~~~~-------is~~Y 168 (404)
T PF10255_consen 111 YGSSPLYKMLGYFSLIGLLRVHCLLGDYYQALKVLENIDLN---K------------KGLYTKVPACH-------ISTYY 168 (404)
T ss_pred cccccHHHHhhHHHHHHHHHHHHhccCHHHHHHHhhccCcc---c------------chhhccCcchh-------eehHH
Confidence 344444444444 455589999999999998876655431 0 11333334443 34444
Q ss_pred HHHHHHHhhhhHHHHHHHHHHHhcc----C------CCCCCh--hcHHHHHHHHHHHHHhCCC--Ch-hchHhhhhhhcc
Q 016147 171 LMIRYYSHNNDYLEICRCYKAIYEI----P------YIKEDP--AQWMPVLRKICWYLVLAPH--DP-MQSSLLNSTLED 235 (394)
Q Consensus 171 ~~~~~~~~~~~flea~k~y~ei~~t----~------~i~~d~--~~~~~~L~~av~~~ILap~--~~-~rs~ll~~l~~d 235 (394)
+.+.-|+.-|+|.||.+.|..+... . +.+-|. ...-.++.-..+|..|+|- +. -.+.+-.+ +.|
T Consensus 169 yvGFaylMlrRY~DAir~f~~iL~yi~r~k~~~~~~~~q~d~i~K~~eqMyaLlAic~~l~p~~lde~i~~~lkek-y~e 247 (404)
T PF10255_consen 169 YVGFAYLMLRRYADAIRTFSQILLYIQRTKNQYHQRSYQYDQINKKNEQMYALLAICLSLCPQRLDESISSQLKEK-YGE 247 (404)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhccccchhhHHHhHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHH-HHH
Confidence 5567777778888888888776642 1 111111 0112344456678888884 21 12222222 322
Q ss_pred c--Cc--CCChhHHHHHHHhcchhcccch---hhH---HHHH-HhhhhhhhhcCCchhhhhHHHHHHHHHHHHHHHHHhh
Q 016147 236 K--NL--SEIPNFRLLLKQLVTMEVIQWT---SLW---NTYK-DEFENETNMLGGSLGAKAAEDLRQRIIEHNILVVSKY 304 (394)
Q Consensus 236 ~--~l--~~ip~~~~L~k~f~~~eli~~~---~~~---~~~~-~~l~~~~~~~~d~~~~~~~~~L~~~viEHNI~visk~ 304 (394)
. ++ ..++.|.+|... -.|..|.+. ... ..+. +-..++..+ ...+++....-.+||..-|.
T Consensus 248 k~~kmq~gd~~~f~elF~~-acPKFIsp~~pp~~~~~~~~~~~e~~~~Ql~~--------Fl~eV~~q~~l~~lRSyLKL 318 (404)
T PF10255_consen 248 KMEKMQRGDEEAFEELFSF-ACPKFISPVSPPDYDGPSQNKNKEPYRRQLKL--------FLDEVKQQQKLPTLRSYLKL 318 (404)
T ss_pred HHHHHHccCHHHHHHHHHh-hCCCccCCCCCCCcccccchhhhhHHHHHHHH--------HHHHHHHhhhhhHHHHHHHh
Confidence 1 01 123333332220 122222211 000 0000 000111111 12344555556688999999
Q ss_pred cCcccHHHHHHHhCCCHHHHHHHHH
Q 016147 305 YSRITLKRLAELLCLSIQEAEKHLS 329 (394)
Q Consensus 305 Y~~Isl~rLa~lL~ls~~e~E~~ls 329 (394)
|++|+++.||.+++++++++-..|.
T Consensus 319 Ytti~l~KLA~fl~vd~~~lr~~Ll 343 (404)
T PF10255_consen 319 YTTIPLEKLASFLDVDEEELRSQLL 343 (404)
T ss_pred hcCCCHHHHHHHcCCCHHHHHHHHH
Confidence 9999999999999999997665543
No 21
>KOG2072 consensus Translation initiation factor 3, subunit a (eIF-3a) [Translation, ribosomal structure and biogenesis]
Probab=96.62 E-value=0.072 Score=57.76 Aligned_cols=73 Identities=26% Similarity=0.288 Sum_probs=66.6
Q ss_pred chhhhhHHHHHHHHHHHHHHHHHhhcCcccHHHHHHHhC-CCHHHHHHHHHHhHhcCcEEEEeccCCCEEEEec
Q 016147 280 SLGAKAAEDLRQRIIEHNILVVSKYYSRITLKRLAELLC-LSIQEAEKHLSDMVVSKALVAKIDRPQGIVCFQV 352 (394)
Q Consensus 280 ~~~~~~~~~L~~~viEHNI~visk~Y~~Isl~rLa~lL~-ls~~e~E~~ls~MI~~g~l~akIDq~~giV~F~~ 352 (394)
+....+...|+..++-.-+..+|+.|.+|++++|.+|.- +++-++|+.+.+.+..+-+..+||-..+.|+|++
T Consensus 420 ~~~~QYI~sLq~v~~~RllqQvSqiY~sIs~~~l~~La~F~~~~~lEk~~v~a~k~~~v~iriDH~~~~v~Fgs 493 (988)
T KOG2072|consen 420 PDKSQYIPSLQDVIILRLLQQVSQIYESISFERLYKLAPFFSAFELEKLLVEAAKHNDVSIRIDHESNSVSFGS 493 (988)
T ss_pred CCccccchhHHHHHHHHHHHHHHHHHHHHhHHHHHHHHhhcCHHHHHHHHHHHHhccceeEEeccccceeeecc
Confidence 334567788999999999999999999999999999877 5899999999999999999999999999999984
No 22
>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=95.70 E-value=0.067 Score=46.57 Aligned_cols=46 Identities=37% Similarity=0.444 Sum_probs=38.1
Q ss_pred HHHHHHHHHHHHHHHHHhhcCcccHHHHHHHhCCCHHHHHHHHHHh
Q 016147 286 AEDLRQRIIEHNILVVSKYYSRITLKRLAELLCLSIQEAEKHLSDM 331 (394)
Q Consensus 286 ~~~L~~~viEHNI~visk~Y~~Isl~rLa~lL~ls~~e~E~~ls~M 331 (394)
...|+..|++.-...+++-|++|+++.++++||++++++++++.+-
T Consensus 76 v~~~~~~iR~~i~~~i~~aY~sIs~~~la~~Lg~~~~el~~~~~~~ 121 (143)
T PF10075_consen 76 VPGFEDTIRERIAHLISKAYSSISLSDLAEMLGLSEEELEKFIKSR 121 (143)
T ss_dssp STTHHHHHHHHHHHHHHHH-SEE-HHHHHHHTTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHhHcCHHHHHHHhCCCHHHHHHHHHHc
Confidence 3557899999999999999999999999999999988888876665
No 23
>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=95.59 E-value=0.31 Score=42.13 Aligned_cols=114 Identities=23% Similarity=0.195 Sum_probs=85.9
Q ss_pred HHHHHHhhhhcCCcchHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHH
Q 016147 41 IELIKTLNSVSAGKIYVEIERARLIKKLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVR 120 (394)
Q Consensus 41 ~~~i~~L~~vt~gki~~E~era~l~~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~ 120 (394)
...++.|..--++..| .....+.+|+++...|++++|...|+.+.-.+ -++.-+--..|+.+++++..++|..
T Consensus 31 ~~~~~~l~~~~~~s~y----a~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~---~d~~l~~~a~l~LA~~~~~~~~~d~ 103 (145)
T PF09976_consen 31 EAAAEQLAKDYPSSPY----AALAALQLAKAAYEQGDYDEAKAALEKALANA---PDPELKPLARLRLARILLQQGQYDE 103 (145)
T ss_pred HHHHHHHHHHCCCChH----HHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhC---CCHHHHHHHHHHHHHHHHHcCCHHH
Confidence 4456666665566643 24566789999999999999999999876532 3445566668888999999999999
Q ss_pred HHHHHHhhCccccCCCCccccCCCCCCCcccccCCCCccchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHH
Q 016147 121 AQILSRKISPRVFDADPSKEKKKPKEGDNVVEEAPADIPSLLELKRIYYELMIRYYSHNNDYLEICRCYKAI 192 (394)
Q Consensus 121 a~~~~~Ki~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~~~~flea~k~y~ei 192 (394)
|...+..+... ..+-.+..+.+.++...+++-+|-..|...
T Consensus 104 Al~~L~~~~~~-------------------------------~~~~~~~~~~Gdi~~~~g~~~~A~~~y~~A 144 (145)
T PF09976_consen 104 ALATLQQIPDE-------------------------------AFKALAAELLGDIYLAQGDYDEARAAYQKA 144 (145)
T ss_pred HHHHHHhccCc-------------------------------chHHHHHHHHHHHHHHCCCHHHHHHHHHHh
Confidence 99998764321 123346778889999999999999998754
No 24
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=94.84 E-value=2.4 Score=42.11 Aligned_cols=157 Identities=19% Similarity=0.170 Sum_probs=107.1
Q ss_pred HHHHHHHhhhchhHHHHHHHHHHHHHhccCCCChHHHHHHHHHhhh--hcCC------cchHH----HHH-HHHHHHHHH
Q 016147 4 LLLLFIIRSVYLFLQAVTAMVQQAMQYIDQTPDLDTRIELIKTLNS--VSAG------KIYVE----IER-ARLIKKLAK 70 (394)
Q Consensus 4 ~~~~~l~k~r~q~k~ai~~~v~~~~~~~~~~~d~~~k~~~i~~L~~--vt~g------ki~~E----~er-a~l~~~La~ 70 (394)
|-|+.|-++||-...||. |.+..---++++ .+.|.-.+..|.. ...| .||.. -|. -.....|..
T Consensus 73 ltLGnLfRsRGEvDRAIR--iHQ~L~~spdlT-~~qr~lAl~qL~~Dym~aGl~DRAE~~f~~L~de~efa~~AlqqLl~ 149 (389)
T COG2956 73 LTLGNLFRSRGEVDRAIR--IHQTLLESPDLT-FEQRLLALQQLGRDYMAAGLLDRAEDIFNQLVDEGEFAEGALQQLLN 149 (389)
T ss_pred HHHHHHHHhcchHHHHHH--HHHHHhcCCCCc-hHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHhcchhhhHHHHHHHHH
Confidence 568999999999999996 333333233333 3667666665543 2222 23322 122 345578999
Q ss_pred HHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCccccCCCCccccCCCCCCCcc
Q 016147 71 IKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPRVFDADPSKEKKKPKEGDNV 150 (394)
Q Consensus 71 i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~~~~~~~~~~~~~~~~~~~~ 150 (394)
||.++.+|++|.++-..+..=+. .--.-+-..||-|-+.-++..+|..+|...++|+-.- ++.
T Consensus 150 IYQ~treW~KAId~A~~L~k~~~-q~~~~eIAqfyCELAq~~~~~~~~d~A~~~l~kAlqa----~~~------------ 212 (389)
T COG2956 150 IYQATREWEKAIDVAERLVKLGG-QTYRVEIAQFYCELAQQALASSDVDRARELLKKALQA----DKK------------ 212 (389)
T ss_pred HHHHhhHHHHHHHHHHHHHHcCC-ccchhHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHhh----Ccc------------
Confidence 99999999999998776654322 2223578889999999999999999999999998642 111
Q ss_pred cccCCCCccchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhc
Q 016147 151 VEEAPADIPSLLELKRIYYELMIRYYSHNNDYLEICRCYKAIYE 194 (394)
Q Consensus 151 ~~~~~~~~~~~~d~klk~~~~~~~~~~~~~~flea~k~y~ei~~ 194 (394)
| .+--..+++.+...++|-.|-+.|..+..
T Consensus 213 ------c--------vRAsi~lG~v~~~~g~y~~AV~~~e~v~e 242 (389)
T COG2956 213 ------C--------VRASIILGRVELAKGDYQKAVEALERVLE 242 (389)
T ss_pred ------c--------eehhhhhhHHHHhccchHHHHHHHHHHHH
Confidence 1 11123556788888888888888888876
No 25
>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=93.66 E-value=0.16 Score=38.63 Aligned_cols=48 Identities=17% Similarity=0.094 Sum_probs=36.0
Q ss_pred HHHHHhhcCcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEEeccCC
Q 016147 298 ILVVSKYYSRITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKIDRPQ 345 (394)
Q Consensus 298 I~visk~Y~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~akIDq~~ 345 (394)
|+-+-+--.++|+..||..|++|++.+|.+|..||..|+|...-+...
T Consensus 5 i~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~~~~~~~ 52 (69)
T PF09012_consen 5 IRDYLRERGRVSLAELAREFGISPEAVEAMLEQLIRKGYIRKVDMSSC 52 (69)
T ss_dssp HHHHHHHS-SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCEEEEEE--
T ss_pred HHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEecCCCC
Confidence 344445567899999999999999999999999999999985554443
No 26
>KOG2688 consensus Transcription-associated recombination protein - Thp1p [Cell cycle control, cell division, chromosome partitioning]
Probab=93.22 E-value=0.69 Score=46.98 Aligned_cols=171 Identities=16% Similarity=0.176 Sum_probs=96.9
Q ss_pred HHHHHHHHHHHHhhhhHHHHHHHHHHHhc-cCCCCCChhcHHHHHHHHHHHHHhCCCChhchHhhhhhhcccCcCCChhH
Q 016147 166 RIYYELMIRYYSHNNDYLEICRCYKAIYE-IPYIKEDPAQWMPVLRKICWYLVLAPHDPMQSSLLNSTLEDKNLSEIPNF 244 (394)
Q Consensus 166 lk~~~~~~~~~~~~~~flea~k~y~ei~~-t~~i~~d~~~~~~~L~~av~~~ILap~~~~rs~ll~~l~~d~~l~~ip~~ 244 (394)
..|.-+.++++.++.||.+|..+..+.+. .|...- ......|.+.|-.+++-...|.. .++.+.- +..|
T Consensus 205 v~y~YylGr~a~~~~d~~~A~~~L~~af~~cp~~~~--~n~~~iliylip~~~llg~~Pt~-~lL~~~~-------~~~~ 274 (394)
T KOG2688|consen 205 VVYHYYLGRYAMFESDFLNAFLQLNEAFRLCPDLLL--KNKRLILIYLIPTGLLLGRIPTK-ELLDFYT-------LDKY 274 (394)
T ss_pred eeeeeeeeeehhhhhhHHHHHHHHHHHHHhCcHHHH--hhhhhHHHHHhHHHHHhccCcch-hhHhHhh-------HHhH
Confidence 44444555999999999999999888874 221100 01112455555555555554442 2222221 2234
Q ss_pred HHHHHHhcchhcccchhhHHHHHHhhhhhhhhcCCchhhhhHHHHHHHHHHHH-HHHHHhhc---CcccHHHHHHHhCCC
Q 016147 245 RLLLKQLVTMEVIQWTSLWNTYKDEFENETNMLGGSLGAKAAEDLRQRIIEHN-ILVVSKYY---SRITLKRLAELLCLS 320 (394)
Q Consensus 245 ~~L~k~f~~~eli~~~~~~~~~~~~l~~~~~~~~d~~~~~~~~~L~~~viEHN-I~visk~Y---~~Isl~rLa~lL~ls 320 (394)
..|++.--...+- .|...+..+...+.....---...+.- +.=|| ++.+.+.- ++++++++-..+..+
T Consensus 275 ~~lv~aVr~Gnl~-------~f~~al~~~E~~f~~~gi~l~l~~l~l-v~yrnL~kkv~~~~~~~~~lpls~~~~al~~~ 346 (394)
T KOG2688|consen 275 SPLVQAVRSGNLR-------LFDLALADNERFFIRSGIYLTLEKLPL-VVYRNLFKKVIQLWGKTSQLPLSRFLTALQFS 346 (394)
T ss_pred HHHHHHHHhccHH-------HHHHHHhhhHHHHHHhccHHHhhhhhH-HHHHHHHHHHHHHhCCCCCCCHHHHHHHHhhc
Confidence 4444444333331 222222221111111000000122222 22333 35555666 889999988887654
Q ss_pred ------HHHHHHHHHHhHhcCcEEEEeccCCCEEEEecCC
Q 016147 321 ------IQEAEKHLSDMVVSKALVAKIDRPQGIVCFQVAK 354 (394)
Q Consensus 321 ------~~e~E~~ls~MI~~g~l~akIDq~~giV~F~~~k 354 (394)
.+|+|-.++.+|..|+|.|.|+....-+.|.+..
T Consensus 347 ~~~~~~~deveciLa~lI~~G~ikgYish~~~~~V~sK~~ 386 (394)
T KOG2688|consen 347 GVTDVDLDEVECILANLIDLGRIKGYISHQLQTLVFSKKD 386 (394)
T ss_pred CCCCCchhhHHHHHHhhhhhccccchhchhhheEEEecCC
Confidence 6999999999999999999999999999998753
No 27
>COG3107 LppC Putative lipoprotein [General function prediction only]
Probab=92.76 E-value=1.6 Score=45.81 Aligned_cols=105 Identities=16% Similarity=0.172 Sum_probs=91.3
Q ss_pred HHHHHHHHHHHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCccccCCCC
Q 016147 58 EIERARLIKKLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPRVFDADP 137 (394)
Q Consensus 58 E~era~l~~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~~~~~~~ 137 (394)
++|.+.....=++..-++|+...|..+|.++++ .+++..|.+.-|--++|.+.++++..|..+..+.+.-.+.
T Consensus 59 ~~~~~~~~llAa~al~~e~k~~qA~~Ll~ql~~----~Ltd~Q~~~~~LL~ael~la~~q~~~Al~~L~~~~~~~ls--- 131 (604)
T COG3107 59 GEQQNDWLLLAARALVEEGKTAQAQALLNQLPQ----ELTDAQRAEKSLLAAELALAQKQPAAALQQLAKLLPADLS--- 131 (604)
T ss_pred chhhhhHHHHHHHHHHHcCChHHHHHHHHhccc----cCCHHHHHHHHHHHHHHHHhccChHHHHHHHhhcchhhcC---
Confidence 367788888888999999999999999999987 6899999999999999999999999999999998864331
Q ss_pred ccccCCCCCCCcccccCCCCccchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHh
Q 016147 138 SKEKKKPKEGDNVVEEAPADIPSLLELKRIYYELMIRYYSHNNDYLEICRCYKAIY 193 (394)
Q Consensus 138 ~~~~~~~~~~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~~~~flea~k~y~ei~ 193 (394)
+-.+.|||...+....+.++-++++|..-...
T Consensus 132 ------------------------~~Qq~Ry~q~~a~a~ea~~~~~~a~rari~~~ 163 (604)
T COG3107 132 ------------------------QNQQARYYQARADALEARGDSIDAARARIAQD 163 (604)
T ss_pred ------------------------HHHHHHHHHHHHHHHhcccchHHHHHHHHHhh
Confidence 22578999999999999999999998776554
No 28
>KOG2076 consensus RNA polymerase III transcription factor TFIIIC [Transcription]
Probab=92.43 E-value=6.2 Score=43.79 Aligned_cols=142 Identities=14% Similarity=0.166 Sum_probs=95.9
Q ss_pred HhhhchhHHHHHHHHHHHHHhccCCCChHHHHHHHHHhhhhcCCcchHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHhh
Q 016147 10 IRSVYLFLQAVTAMVQQAMQYIDQTPDLDTRIELIKTLNSVSAGKIYVEIERARLIKKLAKIKEEQGLIAEAADLMQEVA 89 (394)
Q Consensus 10 ~k~r~q~k~ai~~~v~~~~~~~~~~~d~~~k~~~i~~L~~vt~gki~~E~era~l~~~La~i~e~~gd~~eAa~iL~~i~ 89 (394)
+++++++..++..|.-+|-.---. .+.+.-.++...+-..-+.. ...-..||.+||..||.++|...---
T Consensus 129 ~r~~~~l~~~l~~ll~eAN~lfar-g~~eeA~~i~~EvIkqdp~~-------~~ay~tL~~IyEqrGd~eK~l~~~ll-- 198 (895)
T KOG2076|consen 129 SRGKSKLAPELRQLLGEANNLFAR-GDLEEAEEILMEVIKQDPRN-------PIAYYTLGEIYEQRGDIEKALNFWLL-- 198 (895)
T ss_pred CCcccccCHHHHHHHHHHHHHHHh-CCHHHHHHHHHHHHHhCccc-------hhhHHHHHHHHHHcccHHHHHHHHHH--
Confidence 356788999999998887554333 44454444444222222332 23447899999999999999862110
Q ss_pred hhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCccccCCCCccccCCCCCCCcccccCCCCccchHHHHHHHH
Q 016147 90 VETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPRVFDADPSKEKKKPKEGDNVVEEAPADIPSLLELKRIYY 169 (394)
Q Consensus 90 vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~klk~~ 169 (394)
-.-+.+..+ ++|.....+....+++.+|..+..|+-.. .| ..++++ |-
T Consensus 199 ---AAHL~p~d~-e~W~~ladls~~~~~i~qA~~cy~rAI~~----~p----------------------~n~~~~--~e 246 (895)
T KOG2076|consen 199 ---AAHLNPKDY-ELWKRLADLSEQLGNINQARYCYSRAIQA----NP----------------------SNWELI--YE 246 (895)
T ss_pred ---HHhcCCCCh-HHHHHHHHHHHhcccHHHHHHHHHHHHhc----CC----------------------cchHHH--HH
Confidence 023555566 99999999999999999999999998653 22 122222 22
Q ss_pred HHHHHHHHhhhhHHHHHHHHHHHhcc
Q 016147 170 ELMIRYYSHNNDYLEICRCYKAIYEI 195 (394)
Q Consensus 170 ~~~~~~~~~~~~flea~k~y~ei~~t 195 (394)
. ..+|...|++..|...|..++..
T Consensus 247 r--s~L~~~~G~~~~Am~~f~~l~~~ 270 (895)
T KOG2076|consen 247 R--SSLYQKTGDLKRAMETFLQLLQL 270 (895)
T ss_pred H--HHHHHHhChHHHHHHHHHHHHhh
Confidence 2 25566678999999999999964
No 29
>COG5600 Transcription-associated recombination protein [DNA replication, recombination, and repair]
Probab=92.06 E-value=2.7 Score=42.37 Aligned_cols=171 Identities=14% Similarity=0.145 Sum_probs=93.4
Q ss_pred HHHHHHHHHHHHhhhhHHHHHHHHHHHhc-cCCCCCChhcHHHHHHHHH-HHHHhCCCChhchHhhhhhhcccCcCCChh
Q 016147 166 RIYYELMIRYYSHNNDYLEICRCYKAIYE-IPYIKEDPAQWMPVLRKIC-WYLVLAPHDPMQSSLLNSTLEDKNLSEIPN 243 (394)
Q Consensus 166 lk~~~~~~~~~~~~~~flea~k~y~ei~~-t~~i~~d~~~~~~~L~~av-~~~ILap~~~~rs~ll~~l~~d~~l~~ip~ 243 (394)
.-|.=+.++||.+..+|-+|+-++.+++. .|.... -...-++...+ +++++-...|-+. +|.+.. + +..
T Consensus 220 v~f~YYLG~~~l~~en~heA~~~L~~aFl~c~~l~~--~n~~rIl~~~ipt~Llv~~~~Ptk~-~L~r~~---~---~s~ 290 (413)
T COG5600 220 VVFHYYLGIYYLLNENFHEAFLHLNEAFLQCPWLIT--RNRKRILPYYIPTSLLVNKFPPTKD-LLERFK---R---CSV 290 (413)
T ss_pred eehhhHHHHHHHHHHhHHHHHHHHHHHHHhChhhhh--cchheehhHHhhHHHHhCCCCCchH-HHHhcc---c---cch
Confidence 34455566999999999999999988874 333100 01122233333 3444444555544 444332 2 445
Q ss_pred HHHHHHHhcchhcccchhhHHHHHHhhhhhhhhcCCchhhhhHHHHHHHHHHHHHHHHHhh----c--Cc--ccHHHHHH
Q 016147 244 FRLLLKQLVTMEVIQWTSLWNTYKDEFENETNMLGGSLGAKAAEDLRQRIIEHNILVVSKY----Y--SR--ITLKRLAE 315 (394)
Q Consensus 244 ~~~L~k~f~~~eli~~~~~~~~~~~~l~~~~~~~~d~~~~~~~~~L~~~viEHNI~visk~----Y--~~--Isl~rLa~ 315 (394)
|.-|.+.--+..| ..|...++.+...+.+...--.......-|.-.|+.. +- . ++ .++-..+.
T Consensus 291 ~~~LvkavrsGni-------~~~~~~l~~ner~~~~~~l~ltl~~~~~~V~~RNL~r--k~w~~~~~qsrlp~sil~~~~ 361 (413)
T COG5600 291 YSPLVKAVRSGNI-------EDFDLALSRNERKFAKRGLYLTLLAHYPLVCFRNLFR--KIWRLHGKQSRLPLSILLIVL 361 (413)
T ss_pred hHHHHHHHHcCCH-------HHHHHHHHHhHHHHHHcchHHHHHhhccHHHHHHHHH--HHHhhccccccCcHHHHHHHH
Confidence 6667776665544 2344444322222211100000111111233344433 22 2 23 23333444
Q ss_pred HhCC-C----HHHHHHHHHHhHhcCcEEEEeccCCCEEEEecCC
Q 016147 316 LLCL-S----IQEAEKHLSDMVVSKALVAKIDRPQGIVCFQVAK 354 (394)
Q Consensus 316 lL~l-s----~~e~E~~ls~MI~~g~l~akIDq~~giV~F~~~k 354 (394)
.+.. + .+++|-.++.||..|.+.|.|-.-...|.|.+..
T Consensus 362 qls~~dn~~~~~~VEciL~tlI~~G~lrgYis~s~~~vV~sk~~ 405 (413)
T COG5600 362 QLSAIDNFHSFKEVECILVTLIGLGLLRGYISHSRRTVVFSKKD 405 (413)
T ss_pred HccCCCcccChHHHHHHHHHHHhhhhhhheecccceEEEEecCC
Confidence 4443 3 7899999999999999999999999999998754
No 30
>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A.
Probab=91.95 E-value=12 Score=36.00 Aligned_cols=111 Identities=19% Similarity=0.237 Sum_probs=78.5
Q ss_pred HHHHHHHHHHHHHHHh-cCHHHHHHHHHHhhhhhcc-cCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCccccCCCC
Q 016147 60 ERARLIKKLAKIKEEQ-GLIAEAADLMQEVAVETFG-AMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPRVFDADP 137 (394)
Q Consensus 60 era~l~~~La~i~e~~-gd~~eAa~iL~~i~vEt~~-~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~~~~~~~ 137 (394)
.-|++-..+|++||.. |++++|.+.++.- +|.|. .-....-.+.++..+.++...++|..|-.+..++.......+.
T Consensus 112 ~aA~~~~~lA~~ye~~~~d~e~Ai~~Y~~A-~~~y~~e~~~~~a~~~~~~~A~l~~~l~~y~~A~~~~e~~~~~~l~~~l 190 (282)
T PF14938_consen 112 QAAKCLKELAEIYEEQLGDYEKAIEYYQKA-AELYEQEGSPHSAAECLLKAADLYARLGRYEEAIEIYEEVAKKCLENNL 190 (282)
T ss_dssp HHHHHHHHHHHHHCCTT--HHHHHHHHHHH-HHHHHHTT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTCCCHCT
T ss_pred HHHHHHHHHHHHHHHHcCCHHHHHHHHHHH-HHHHHHCCChhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhhcccc
Confidence 4588889999999999 9999999988773 34443 2356777889999999999999999999999998765443210
Q ss_pred ccccCCCCCCCcccccCCCCccchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhc
Q 016147 138 SKEKKKPKEGDNVVEEAPADIPSLLELKRIYYELMIRYYSHNNDYLEICRCYKAIYE 194 (394)
Q Consensus 138 ~~~~~~~~~~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~~~~flea~k~y~ei~~ 194 (394)
. ....| +|+-..+..+++.+|+..|-+.|....+
T Consensus 191 ~----------------------~~~~~-~~~l~a~l~~L~~~D~v~A~~~~~~~~~ 224 (282)
T PF14938_consen 191 L----------------------KYSAK-EYFLKAILCHLAMGDYVAARKALERYCS 224 (282)
T ss_dssp T----------------------GHHHH-HHHHHHHHHHHHTT-HHHHHHHHHHHGT
T ss_pred c----------------------chhHH-HHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence 0 01232 3555567788888899888888777654
No 31
>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=91.95 E-value=0.21 Score=40.78 Aligned_cols=37 Identities=22% Similarity=0.276 Sum_probs=34.3
Q ss_pred cccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEEecc
Q 016147 307 RITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKIDR 343 (394)
Q Consensus 307 ~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~akIDq 343 (394)
=|+++.|++.|+++..+++..+-.|+.+|.||..||-
T Consensus 65 Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd 101 (102)
T PF08784_consen 65 GVHVDEIAQQLGMSENEVRKALDFLSNEGHIYSTIDD 101 (102)
T ss_dssp TEEHHHHHHHSTS-HHHHHHHHHHHHHTTSEEESSST
T ss_pred cccHHHHHHHhCcCHHHHHHHHHHHHhCCeEecccCC
Confidence 4999999999999999999999999999999999994
No 32
>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A.
Probab=90.50 E-value=7.4 Score=37.57 Aligned_cols=74 Identities=22% Similarity=0.266 Sum_probs=57.0
Q ss_pred HHHHHHHHHHHHHHHHHhcCHHHHHHHHHHhhhhhc-ccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCcc
Q 016147 58 EIERARLIKKLAKIKEEQGLIAEAADLMQEVAVETF-GAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPR 131 (394)
Q Consensus 58 E~era~l~~~La~i~e~~gd~~eAa~iL~~i~vEt~-~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~ 131 (394)
......+...+|.++...|++.+|.+++.++--..- ..+.+-.--+++|..+=++|..+|++.|....++....
T Consensus 151 ~~~a~~~~~~~A~l~~~l~~y~~A~~~~e~~~~~~l~~~l~~~~~~~~~l~a~l~~L~~~D~v~A~~~~~~~~~~ 225 (282)
T PF14938_consen 151 PHSAAECLLKAADLYARLGRYEEAIEIYEEVAKKCLENNLLKYSAKEYFLKAILCHLAMGDYVAARKALERYCSQ 225 (282)
T ss_dssp HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTCCCHCTTGHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHGTT
T ss_pred hhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhhcccccchhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence 456688889999999999999999999998654322 23444444568899999999999999999999987643
No 33
>PF04348 LppC: LppC putative lipoprotein; InterPro: IPR007443 This entry includes several bacterial outer membrane antigens, whose molecular function is unknown.; PDB: 3CKM_A.
Probab=90.38 E-value=0.081 Score=56.23 Aligned_cols=106 Identities=22% Similarity=0.223 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCccccCCCCc
Q 016147 59 IERARLIKKLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPRVFDADPS 138 (394)
Q Consensus 59 ~era~l~~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~~~~~~~~ 138 (394)
.+++++...-++.+-++|++..|..+|.+|.. ..++...+.++.|-.+++.+..+++..|....+......+.
T Consensus 21 ~~~~~~~L~Aa~a~l~~g~~~~A~~ll~~l~~---~~L~~~q~~~~~Ll~A~lal~~~~~~~Al~~L~~~~~~~l~---- 93 (536)
T PF04348_consen 21 EQRAQLLLLAARALLQEGDWAQAQALLNQLDP---QQLSPSQQARYQLLRARLALAQGDPEQALSLLNAQDLWQLP---- 93 (536)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred HhHHHHHHHHHHHHHhCCCHHHHHHHHHhccc---ccCChHHHHHHHHHHHHHHHhcCCHHHHHHHhccCCcccCC----
Confidence 57888889999999999999999999999885 35778899999999999999999999999988775433221
Q ss_pred cccCCCCCCCcccccCCCCccchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhc
Q 016147 139 KEKKKPKEGDNVVEEAPADIPSLLELKRIYYELMIRYYSHNNDYLEICRCYKAIYE 194 (394)
Q Consensus 139 ~~~~~~~~~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~~~~flea~k~y~ei~~ 194 (394)
.....+|+.+.+..+...++.+++++.+..+..
T Consensus 94 -----------------------~~~~~~~~~l~A~a~~~~~~~l~Aa~~~i~l~~ 126 (536)
T PF04348_consen 94 -----------------------PEQQARYHQLRAQAYEQQGDPLAAARERIALDP 126 (536)
T ss_dssp --------------------------------------------------------
T ss_pred -----------------------HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhh
Confidence 345678999999999999999999999887664
No 34
>PF09295 ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); InterPro: IPR015374 ChAPs (Chs5p-Arf1p-binding proteins) are required for the export of specialised cargo from the Golgi. They physically interact with Chs3, Chs5 and the small GTPase Arf1, and they also form interactions with each other [].
Probab=89.65 E-value=6.3 Score=40.40 Aligned_cols=93 Identities=22% Similarity=0.249 Sum_probs=66.9
Q ss_pred HHHHHHHhccCCCChHHHHHHHHHhhhhcCCcchHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHH
Q 016147 23 MVQQAMQYIDQTPDLDTRIELIKTLNSVSAGKIYVEIERARLIKKLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKI 102 (394)
Q Consensus 23 ~v~~~~~~~~~~~d~~~k~~~i~~L~~vt~gki~~E~era~l~~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~ 102 (394)
+|.-.+.++..++.-+.-..+++.|.+-.+. +...||+++-..++-.+|.++|.+.--+.. .+ .
T Consensus 171 Lv~~Ll~~l~~t~~~~~ai~lle~L~~~~pe----------v~~~LA~v~l~~~~E~~AI~ll~~aL~~~p--~d----~ 234 (395)
T PF09295_consen 171 LVDTLLKYLSLTQRYDEAIELLEKLRERDPE----------VAVLLARVYLLMNEEVEAIRLLNEALKENP--QD----S 234 (395)
T ss_pred HHHHHHHHHhhcccHHHHHHHHHHHHhcCCc----------HHHHHHHHHHhcCcHHHHHHHHHHHHHhCC--CC----H
Confidence 4445555655555555555666666554433 224588888888888999999988553322 22 8
Q ss_pred HHHHHHHHHHhccCChHHHHHHHHhhCcc
Q 016147 103 AFILEQVRLCLDRQDYVRAQILSRKISPR 131 (394)
Q Consensus 103 e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~ 131 (394)
+....|++.++.++++..|..+++|+-..
T Consensus 235 ~LL~~Qa~fLl~k~~~~lAL~iAk~av~l 263 (395)
T PF09295_consen 235 ELLNLQAEFLLSKKKYELALEIAKKAVEL 263 (395)
T ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHHHHh
Confidence 89999999999999999999999998764
No 35
>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=89.58 E-value=3.2 Score=31.29 Aligned_cols=69 Identities=20% Similarity=0.210 Sum_probs=53.6
Q ss_pred HHHHHHHHHHHHHHhcCHHHHHHHHHHhh-h-hhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCc
Q 016147 61 RARLIKKLAKIKEEQGLIAEAADLMQEVA-V-ETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISP 130 (394)
Q Consensus 61 ra~l~~~La~i~e~~gd~~eAa~iL~~i~-v-Et~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~ 130 (394)
.+.+-..+|.+|...|++++|.+.++..- + +.+|. +....+..+.....++...||+..|..+..|+-.
T Consensus 4 ~a~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~-~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al~ 74 (78)
T PF13424_consen 4 TANAYNNLARVYRELGRYDEALDYYEKALDIEEQLGD-DHPDTANTLNNLGECYYRLGDYEEALEYYQKALD 74 (78)
T ss_dssp HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTT-HHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCC-CCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence 46677899999999999999999887632 2 12222 3345688899999999999999999999998753
No 36
>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=88.88 E-value=5.1 Score=32.01 Aligned_cols=102 Identities=10% Similarity=-0.098 Sum_probs=72.4
Q ss_pred HHHHHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCccccCCCCccccCC
Q 016147 64 LIKKLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPRVFDADPSKEKKK 143 (394)
Q Consensus 64 l~~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~~~~~~~~~~~~~ 143 (394)
....+|..+...|++.+|.+.+..+.-...+. ....+..+...+++...+++..|..+.+++....- +++
T Consensus 4 ~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~---~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p-~~~------ 73 (119)
T TIGR02795 4 AYYDAALLVLKAGDYADAIQAFQAFLKKYPKS---TYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKYP-KSP------ 73 (119)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCc---cccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHCC-CCC------
Confidence 45778999999999999999998875322111 12345677789999999999999999998875421 110
Q ss_pred CCCCCcccccCCCCccchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhcc
Q 016147 144 PKEGDNVVEEAPADIPSLLELKRIYYELMIRYYSHNNDYLEICRCYKAIYEI 195 (394)
Q Consensus 144 ~~~~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~~~~flea~k~y~ei~~t 195 (394)
.. ...+..++..+...+++-+|.+.|.++...
T Consensus 74 ----------------~~----~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~ 105 (119)
T TIGR02795 74 ----------------KA----PDALLKLGMSLQELGDKEKAKATLQQVIKR 105 (119)
T ss_pred ----------------cc----cHHHHHHHHHHHHhCChHHHHHHHHHHHHH
Confidence 00 112344556677789999999999888864
No 37
>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=88.74 E-value=12 Score=32.12 Aligned_cols=61 Identities=25% Similarity=0.184 Sum_probs=48.6
Q ss_pred HHHHHHHHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhh
Q 016147 61 RARLIKKLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKI 128 (394)
Q Consensus 61 ra~l~~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki 128 (394)
+...+..||.++...|++++|...|..++-+. .+-.+..-...+++..||+..|.....++
T Consensus 84 ~~~a~l~LA~~~~~~~~~d~Al~~L~~~~~~~-------~~~~~~~~~Gdi~~~~g~~~~A~~~y~~A 144 (145)
T PF09976_consen 84 KPLARLRLARILLQQGQYDEALATLQQIPDEA-------FKALAAELLGDIYLAQGDYDEARAAYQKA 144 (145)
T ss_pred HHHHHHHHHHHHHHcCCHHHHHHHHHhccCcc-------hHHHHHHHHHHHHHHCCCHHHHHHHHHHh
Confidence 45667789999999999999999997754332 34445666789999999999999987764
No 38
>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=87.97 E-value=0.75 Score=42.20 Aligned_cols=76 Identities=14% Similarity=0.197 Sum_probs=35.2
Q ss_pred hcCcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEEeccCCCEEEEecCCChHHHHHHHHHHHH--HHHHHHHHHHhhh
Q 016147 304 YYSRITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKIDRPQGIVCFQVAKDSNDILNSWAMNLE--KLLDLVEKSCHQI 381 (394)
Q Consensus 304 ~Y~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~akIDq~~giV~F~~~k~~~~~L~~W~~~I~--~l~~~V~k~~~lI 381 (394)
-=.-+.|+.||..||++++++..-|-.|..+|+|.|-||--...|+-.... -+.+..+...-+ ++-+++..++.+|
T Consensus 110 ~~Kvv~ledla~~f~l~t~~~i~ri~~L~~~g~ltGv~DdrGkfIyIs~eE--~~~va~fi~~rGRvsi~el~~~~N~~i 187 (188)
T PF09756_consen 110 EHKVVNLEDLAAEFGLRTQDVINRIQELEAEGRLTGVIDDRGKFIYISEEE--MEAVAKFIKQRGRVSISELAQESNRLI 187 (188)
T ss_dssp H-SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-EEE-TT--EEE----------------------------------
T ss_pred HcceeeHHHHHHHcCCCHHHHHHHHHHHHHCCCceeeEcCCCCeEEecHHH--HHHHHHHHHHcCCccHHHHHHHHHhhc
Confidence 345689999999999999999999999999999999999977777766432 123333433222 3344444555554
No 39
>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B.
Probab=87.17 E-value=3.2 Score=30.14 Aligned_cols=58 Identities=16% Similarity=0.095 Sum_probs=48.0
Q ss_pred HHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCc
Q 016147 67 KLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISP 130 (394)
Q Consensus 67 ~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~ 130 (394)
.+|..+...|++++|.+.++.+--.. ..-.+.++...+++...|++..|..+..++-.
T Consensus 2 ~~a~~~~~~g~~~~A~~~~~~~l~~~------P~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~ 59 (65)
T PF13432_consen 2 ALARALYQQGDYDEAIAAFEQALKQD------PDNPEAWYLLGRILYQQGRYDEALAYYERALE 59 (65)
T ss_dssp HHHHHHHHCTHHHHHHHHHHHHHCCS------TTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred hHHHHHHHcCCHHHHHHHHHHHHHHC------CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence 68899999999999999999865322 23678888999999999999999999988754
No 40
>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=86.47 E-value=6.9 Score=38.27 Aligned_cols=161 Identities=11% Similarity=0.067 Sum_probs=98.4
Q ss_pred HHHHHhccCCCChHHHHHHHHHhhh-hcCCcchHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHH
Q 016147 25 QQAMQYIDQTPDLDTRIELIKTLNS-VSAGKIYVEIERARLIKKLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIA 103 (394)
Q Consensus 25 ~~~~~~~~~~~d~~~k~~~i~~L~~-vt~gki~~E~era~l~~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e 103 (394)
+....|+.... .|...+..|.+ +.++.. ..-.-+....|.++..+|++++|.++|... .-+|
T Consensus 70 ~~la~y~~~~~---~~e~~l~~l~~~~~~~~~---~~~~~~~~~~A~i~~~~~~~~~AL~~l~~~-----------~~lE 132 (290)
T PF04733_consen 70 RLLAEYLSSPS---DKESALEELKELLADQAG---ESNEIVQLLAATILFHEGDYEEALKLLHKG-----------GSLE 132 (290)
T ss_dssp HHHHHHHCTST---THHCHHHHHHHCCCTS------CHHHHHHHHHHHHCCCCHHHHHHCCCTTT-----------TCHH
T ss_pred HHHHHHHhCcc---chHHHHHHHHHHHHhccc---cccHHHHHHHHHHHHHcCCHHHHHHHHHcc-----------Cccc
Confidence 34455554322 34555666655 333322 111235567778899999999999977641 3367
Q ss_pred HHHHHHHHHhccCChHHHHHHHHhhCccccCCCCccccCCCCCCCcccccCCCCccchHHHHHHHHHHHHHHHHhhhhHH
Q 016147 104 FILEQVRLCLDRQDYVRAQILSRKISPRVFDADPSKEKKKPKEGDNVVEEAPADIPSLLELKRIYYELMIRYYSHNNDYL 183 (394)
Q Consensus 104 ~~Leq~rL~L~~~D~~~a~~~~~Ki~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~~~~fl 183 (394)
...-.+.++|..+.++.|+..+++.... .. ...-....+..+.++....+|-
T Consensus 133 ~~al~Vqi~L~~~R~dlA~k~l~~~~~~--~e--------------------------D~~l~qLa~awv~l~~g~e~~~ 184 (290)
T PF04733_consen 133 LLALAVQILLKMNRPDLAEKELKNMQQI--DE--------------------------DSILTQLAEAWVNLATGGEKYQ 184 (290)
T ss_dssp HHHHHHHHHHHTT-HHHHHHHHHHHHCC--SC--------------------------CHHHHHHHHHHHHHHHTTTCCC
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHHhc--CC--------------------------cHHHHHHHHHHHHHHhCchhHH
Confidence 7788899999999999999999887643 11 1333455666677777778899
Q ss_pred HHHHHHHHHhccCCCCCChhcHHHHHHHHHHHHHhCC-CChhchHhhhhhhccc
Q 016147 184 EICRCYKAIYEIPYIKEDPAQWMPVLRKICWYLVLAP-HDPMQSSLLNSTLEDK 236 (394)
Q Consensus 184 ea~k~y~ei~~t~~i~~d~~~~~~~L~~av~~~ILap-~~~~rs~ll~~l~~d~ 236 (394)
+|+..|.|+.+++. ..+. .|....+|.+... ++.-..-+...+..||
T Consensus 185 ~A~y~f~El~~~~~-----~t~~-~lng~A~~~l~~~~~~eAe~~L~~al~~~~ 232 (290)
T PF04733_consen 185 DAFYIFEELSDKFG-----STPK-LLNGLAVCHLQLGHYEEAEELLEEALEKDP 232 (290)
T ss_dssp HHHHHHHHHHCCS-------SHH-HHHHHHHHHHHCT-HHHHHHHHHHHCCC-C
T ss_pred HHHHHHHHHHhccC-----CCHH-HHHHHHHHHHHhCCHHHHHHHHHHHHHhcc
Confidence 99999999998652 1223 3443344455444 4333444444444554
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=85.15 E-value=12 Score=26.96 Aligned_cols=94 Identities=14% Similarity=0.010 Sum_probs=64.3
Q ss_pred HHHHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCccccCCCCccccCCC
Q 016147 65 IKKLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPRVFDADPSKEKKKP 144 (394)
Q Consensus 65 ~~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~~~~~~~~~~~~~~ 144 (394)
...+|..+...|++.+|.+.+....-.. . ... ..+.....++...+++..|..+.+++.....
T Consensus 3 ~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~---~~~--~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~----------- 65 (100)
T cd00189 3 LLNLGNLYYKLGDYDEALEYYEKALELD-P---DNA--DAYYNLAAAYYKLGKYEEALEDYEKALELDP----------- 65 (100)
T ss_pred HHHHHHHHHHHhcHHHHHHHHHHHHhcC-C---ccH--HHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC-----------
Confidence 4578889999999999999988754221 1 111 6677888889999999999999888765311
Q ss_pred CCCCcccccCCCCccchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhc
Q 016147 145 KEGDNVVEEAPADIPSLLELKRIYYELMIRYYSHNNDYLEICRCYKAIYE 194 (394)
Q Consensus 145 ~~~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~~~~flea~k~y~ei~~ 194 (394)
... ..+...+..+...+++-+|...+..+..
T Consensus 66 ---------------~~~----~~~~~~~~~~~~~~~~~~a~~~~~~~~~ 96 (100)
T cd00189 66 ---------------DNA----KAYYNLGLAYYKLGKYEEALEAYEKALE 96 (100)
T ss_pred ---------------cch----hHHHHHHHHHHHHHhHHHHHHHHHHHHc
Confidence 011 2234445666667777777777766553
No 42
>KOG1586 consensus Protein required for fusion of vesicles in vesicular transport, alpha-SNAP [Intracellular trafficking, secretion, and vesicular transport]
Probab=83.75 E-value=42 Score=32.18 Aligned_cols=28 Identities=29% Similarity=0.337 Sum_probs=20.2
Q ss_pred hhhhHHHHHHHHHHHHHHHHH---hhcCccc
Q 016147 282 GAKAAEDLRQRIIEHNILVVS---KYYSRIT 309 (394)
Q Consensus 282 ~~~~~~~L~~~viEHNI~vis---k~Y~~Is 309 (394)
-.+..++|..+|-|.|+-..+ +-|.+||
T Consensus 233 Eckflk~L~~aieE~d~e~fte~vkefDsis 263 (288)
T KOG1586|consen 233 ECKFLKDLLDAIEEQDIEKFTEVVKEFDSIS 263 (288)
T ss_pred HHHHHHHHHHHHhhhhHHHHHHHHHhhhccc
Confidence 345678899999999997765 3466654
No 43
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=83.44 E-value=24 Score=34.85 Aligned_cols=101 Identities=13% Similarity=0.099 Sum_probs=53.7
Q ss_pred HHHHHHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCccccCCCCccccC
Q 016147 63 RLIKKLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPRVFDADPSKEKK 142 (394)
Q Consensus 63 ~l~~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~~~~~~~~~~~~ 142 (394)
.....|+..|...|++++|.+.+....-. ...-...+...+.++...++|.+|.....++.... +.
T Consensus 108 ~~~~~La~~~~~~g~~~~A~~~~~~~l~~------~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~----~~---- 173 (389)
T PRK11788 108 LALQELGQDYLKAGLLDRAEELFLQLVDE------GDFAEGALQQLLEIYQQEKDWQKAIDVAERLEKLG----GD---- 173 (389)
T ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHHcC------CcchHHHHHHHHHHHHHhchHHHHHHHHHHHHHhc----CC----
Confidence 34455666666666666666655553211 01122344555566666666666666665544221 00
Q ss_pred CCCCCCcccccCCCCccchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhc
Q 016147 143 KPKEGDNVVEEAPADIPSLLELKRIYYELMIRYYSHNNDYLEICRCYKAIYE 194 (394)
Q Consensus 143 ~~~~~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~~~~flea~k~y~ei~~ 194 (394)
........|+..++..+...+++-+|.+.|.+...
T Consensus 174 -----------------~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~al~ 208 (389)
T PRK11788 174 -----------------SLRVEIAHFYCELAQQALARGDLDAARALLKKALA 208 (389)
T ss_pred -----------------cchHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHh
Confidence 00111223455556666677888888888877765
No 44
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=82.75 E-value=52 Score=32.46 Aligned_cols=102 Identities=19% Similarity=0.167 Sum_probs=74.6
Q ss_pred HHHHHHHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCccccCCCCcccc
Q 016147 62 ARLIKKLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPRVFDADPSKEK 141 (394)
Q Consensus 62 a~l~~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~~~~~~~~~~~ 141 (394)
......|+.++...|++++|.+.+..+.- ....-.......++...+++++..+++..|..+.+++-... +
T Consensus 141 ~~~~~~la~~~~~~g~~~~A~~~~~~~~~-~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~----p---- 211 (389)
T PRK11788 141 EGALQQLLEIYQQEKDWQKAIDVAERLEK-LGGDSLRVEIAHFYCELAQQALARGDLDAARALLKKALAAD----P---- 211 (389)
T ss_pred HHHHHHHHHHHHHhchHHHHHHHHHHHHH-hcCCcchHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhHC----c----
Confidence 45667899999999999999999887642 11111222345567788899999999999999999986531 1
Q ss_pred CCCCCCCcccccCCCCccchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhc
Q 016147 142 KKPKEGDNVVEEAPADIPSLLELKRIYYELMIRYYSHNNDYLEICRCYKAIYE 194 (394)
Q Consensus 142 ~~~~~~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~~~~flea~k~y~ei~~ 194 (394)
+.. .-+...+..+...++|-+|-..|.++..
T Consensus 212 ------------------~~~----~~~~~la~~~~~~g~~~~A~~~~~~~~~ 242 (389)
T PRK11788 212 ------------------QCV----RASILLGDLALAQGDYAAAIEALERVEE 242 (389)
T ss_pred ------------------CCH----HHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 111 1234566778889999999999998885
No 45
>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A.
Probab=82.44 E-value=7.5 Score=29.87 Aligned_cols=60 Identities=22% Similarity=0.205 Sum_probs=44.3
Q ss_pred HHHHHHHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhh
Q 016147 62 ARLIKKLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKI 128 (394)
Q Consensus 62 a~l~~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki 128 (394)
......||..+...|++++|..+++...+. ... .+...-.++.+++.++|..|.....|+
T Consensus 25 ~~~~~~la~~~~~~~~y~~A~~~~~~~~~~------~~~-~~~~~l~a~~~~~l~~y~eAi~~l~~~ 84 (84)
T PF12895_consen 25 SAYLYNLAQCYFQQGKYEEAIELLQKLKLD------PSN-PDIHYLLARCLLKLGKYEEAIKALEKA 84 (84)
T ss_dssp HHHHHHHHHHHHHTTHHHHHHHHHHCHTHH------HCH-HHHHHHHHHHHHHTT-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHhCCC------CCC-HHHHHHHHHHHHHhCCHHHHHHHHhcC
Confidence 445677999999999999999999873222 111 333334499999999999999988764
No 46
>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=82.35 E-value=3.6 Score=29.96 Aligned_cols=53 Identities=19% Similarity=0.187 Sum_probs=42.2
Q ss_pred HHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCcc
Q 016147 73 EEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPR 131 (394)
Q Consensus 73 e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~ 131 (394)
-+.|++++|.+.++.+--... .-.++.+..+++++..|++.+|..+.+++...
T Consensus 2 l~~~~~~~A~~~~~~~l~~~p------~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~ 54 (68)
T PF14559_consen 2 LKQGDYDEAIELLEKALQRNP------DNPEARLLLAQCYLKQGQYDEAEELLERLLKQ 54 (68)
T ss_dssp HHTTHHHHHHHHHHHHHHHTT------TSHHHHHHHHHHHHHTT-HHHHHHHHHCCHGG
T ss_pred hhccCHHHHHHHHHHHHHHCC------CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence 468999999999998754322 24577788999999999999999999988754
No 47
>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=81.52 E-value=9.6 Score=27.72 Aligned_cols=45 Identities=20% Similarity=0.231 Sum_probs=38.9
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEEeccCCCEEEEec
Q 016147 308 ITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKIDRPQGIVCFQV 352 (394)
Q Consensus 308 Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~akIDq~~giV~F~~ 352 (394)
++.+.+++.+|++...+-..+..|+..|-+.+.-+...+...+..
T Consensus 21 ~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~~~~~~~~~~~~~~ 65 (78)
T cd00090 21 LTVSELAERLGLSQSTVSRHLKKLEEAGLVESRREGRRVYYSLTD 65 (78)
T ss_pred cCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEEEEeccEEEEEeCC
Confidence 999999999999999999999999999999887666555555554
No 48
>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=80.48 E-value=9.5 Score=27.46 Aligned_cols=51 Identities=16% Similarity=0.141 Sum_probs=38.3
Q ss_pred HHHHHHHHhhcCc--ccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEEeccCC
Q 016147 295 EHNILVVSKYYSR--ITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKIDRPQ 345 (394)
Q Consensus 295 EHNI~visk~Y~~--Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~akIDq~~ 345 (394)
+..+..+-..+.. ++...||+.++++..-+-..+.+|+..|-+.-.-|.-+
T Consensus 7 q~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~r~~~~~D 59 (62)
T PF12802_consen 7 QFRVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEKKGLVERERDPGD 59 (62)
T ss_dssp HHHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE-SSS
T ss_pred HHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCCCCC
Confidence 3344444444454 99999999999999999999999999998876666544
No 49
>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=79.88 E-value=3.5 Score=30.21 Aligned_cols=64 Identities=19% Similarity=0.100 Sum_probs=49.9
Q ss_pred HHHHHHHHHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccC-ChHHHHHHHHhhC
Q 016147 60 ERARLIKKLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQ-DYVRAQILSRKIS 129 (394)
Q Consensus 60 era~l~~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~-D~~~a~~~~~Ki~ 129 (394)
|.|..-..+|.++...|++++|...+...- .+++. -...+......+...+ ++.+|....+|+-
T Consensus 1 e~a~~~~~~g~~~~~~~~~~~A~~~~~~ai-----~~~p~-~~~~~~~~g~~~~~~~~~~~~A~~~~~~al 65 (69)
T PF13414_consen 1 ENAEAWYNLGQIYFQQGDYEEAIEYFEKAI-----ELDPN-NAEAYYNLGLAYMKLGKDYEEAIEDFEKAL 65 (69)
T ss_dssp TSHHHHHHHHHHHHHTTHHHHHHHHHHHHH-----HHSTT-HHHHHHHHHHHHHHTTTHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHcCCHHHHHHHHHHHH-----HcCCC-CHHHHHHHHHHHHHhCccHHHHHHHHHHHH
Confidence 346777889999999999999999777521 12222 3568888999999999 7999999988874
No 50
>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=79.72 E-value=3.7 Score=28.52 Aligned_cols=26 Identities=31% Similarity=0.313 Sum_probs=23.7
Q ss_pred HHHHHHHHHHhcCHHHHHHHHHHhhh
Q 016147 65 IKKLAKIKEEQGLIAEAADLMQEVAV 90 (394)
Q Consensus 65 ~~~La~i~e~~gd~~eAa~iL~~i~v 90 (394)
+..||+.|.+.||.+.|-++|.++.-
T Consensus 2 kLdLA~ayie~Gd~e~Ar~lL~evl~ 27 (44)
T TIGR03504 2 KLDLARAYIEMGDLEGARELLEEVIE 27 (44)
T ss_pred chHHHHHHHHcCChHHHHHHHHHHHH
Confidence 46899999999999999999999883
No 51
>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=77.48 E-value=19 Score=38.20 Aligned_cols=65 Identities=17% Similarity=0.155 Sum_probs=40.0
Q ss_pred HHHHHHHHHHHHHhccCChHHHHHHHHhhCccccCCCCccccCCCCCCCcccccCCCCccchHHHHHHHHHHHHHHHHhh
Q 016147 100 EKIAFILEQVRLCLDRQDYVRAQILSRKISPRVFDADPSKEKKKPKEGDNVVEEAPADIPSLLELKRIYYELMIRYYSHN 179 (394)
Q Consensus 100 eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~~ 179 (394)
|.-|++|.++.+..+.|++.+|-.++.+....+.+ |+.+++..+.++..-
T Consensus 2 E~SE~lLY~~~il~e~g~~~~AL~~L~~~~~~I~D------------------------------k~~~~E~rA~ll~kL 51 (517)
T PF12569_consen 2 EHSELLLYKNSILEEAGDYEEALEHLEKNEKQILD------------------------------KLAVLEKRAELLLKL 51 (517)
T ss_pred cHHHHHHHHHHHHHHCCCHHHHHHHHHhhhhhCCC------------------------------HHHHHHHHHHHHHHc
Confidence 34566666666666666666666666655443321 245566666666666
Q ss_pred hhHHHHHHHHHHHhc
Q 016147 180 NDYLEICRCYKAIYE 194 (394)
Q Consensus 180 ~~flea~k~y~ei~~ 194 (394)
+++-+|...|..+.+
T Consensus 52 g~~~eA~~~y~~Li~ 66 (517)
T PF12569_consen 52 GRKEEAEKIYRELID 66 (517)
T ss_pred CCHHHHHHHHHHHHH
Confidence 777777777777665
No 52
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=76.49 E-value=6.7 Score=30.75 Aligned_cols=39 Identities=10% Similarity=0.075 Sum_probs=34.8
Q ss_pred HHhhcCcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEE
Q 016147 301 VSKYYSRITLKRLAELLCLSIQEAEKHLSDMVVSKALVA 339 (394)
Q Consensus 301 isk~Y~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~a 339 (394)
.-.-+-+.+...||..|+.|++-+|.+|..++.-|++.-
T Consensus 10 ~l~~~gr~s~~~Ls~~~~~p~~~VeaMLe~l~~kGkver 48 (78)
T PRK15431 10 LLALRGRMEAAQISQTLNTPQPMINAMLQQLESMGKAVR 48 (78)
T ss_pred HHHHcCcccHHHHHHHHCcCHHHHHHHHHHHHHCCCeEe
Confidence 334578999999999999999999999999999999854
No 53
>PRK02603 photosystem I assembly protein Ycf3; Provisional
Probab=76.46 E-value=40 Score=29.61 Aligned_cols=71 Identities=10% Similarity=-0.012 Sum_probs=55.2
Q ss_pred HHHHHHHHHHHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCcc
Q 016147 58 EIERARLIKKLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPR 131 (394)
Q Consensus 58 E~era~l~~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~ 131 (394)
....+.....+|..+...|++++|...+....-... +..+....+.....++...|++..|..++.++-..
T Consensus 31 ~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~---~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~ 101 (172)
T PRK02603 31 KAKEAFVYYRDGMSAQADGEYAEALENYEEALKLEE---DPNDRSYILYNMGIIYASNGEHDKALEYYHQALEL 101 (172)
T ss_pred HhhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhh---ccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence 445677789999999999999999998887532111 11234567888899999999999999999988753
No 54
>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=75.92 E-value=18 Score=27.11 Aligned_cols=70 Identities=13% Similarity=-0.031 Sum_probs=52.8
Q ss_pred HHHHHHHHHHHhccCChHHHHHHHHhhCccccCCCCccccCCCCCCCcccccCCCCccchHHHHHHHHHHHHHHHHhhhh
Q 016147 102 IAFILEQVRLCLDRQDYVRAQILSRKISPRVFDADPSKEKKKPKEGDNVVEEAPADIPSLLELKRIYYELMIRYYSHNND 181 (394)
Q Consensus 102 ~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~~~~ 181 (394)
...+.....++...++|.+|..+.+|+... ....+ .........+..++..+...++
T Consensus 5 a~~~~~la~~~~~~~~~~~A~~~~~~al~~-~~~~~----------------------~~~~~~a~~~~~lg~~~~~~g~ 61 (78)
T PF13424_consen 5 ANAYNNLARVYRELGRYDEALDYYEKALDI-EEQLG----------------------DDHPDTANTLNNLGECYYRLGD 61 (78)
T ss_dssp HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-HHHTT----------------------THHHHHHHHHHHHHHHHHHTTH
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHHHHHH-HHHHC----------------------CCCHHHHHHHHHHHHHHHHcCC
Confidence 355677889999999999999999999876 32111 1122336778888899999999
Q ss_pred HHHHHHHHHHHhc
Q 016147 182 YLEICRCYKAIYE 194 (394)
Q Consensus 182 flea~k~y~ei~~ 194 (394)
|-+|-..|....+
T Consensus 62 ~~~A~~~~~~al~ 74 (78)
T PF13424_consen 62 YEEALEYYQKALD 74 (78)
T ss_dssp HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHh
Confidence 9999999987764
No 55
>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=75.23 E-value=56 Score=28.54 Aligned_cols=101 Identities=14% Similarity=0.094 Sum_probs=73.6
Q ss_pred HHHHHHHHHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCccccCCCCcc
Q 016147 60 ERARLIKKLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPRVFDADPSK 139 (394)
Q Consensus 60 era~l~~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~~~~~~~~~ 139 (394)
..+.....+|..+...|++++|...+....-.. ..-...+.....++...+|+..|..+.+++-... +
T Consensus 29 ~~~~~~~~la~~~~~~~~~~~A~~~~~~~l~~~------p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~----~-- 96 (234)
T TIGR02521 29 KAAKIRVQLALGYLEQGDLEVAKENLDKALEHD------PDDYLAYLALALYYQQLGELEKAEDSFRRALTLN----P-- 96 (234)
T ss_pred cHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC------cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC----C--
Confidence 346777889999999999999999888753211 1124567778999999999999999999887531 1
Q ss_pred ccCCCCCCCcccccCCCCccchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhccC
Q 016147 140 EKKKPKEGDNVVEEAPADIPSLLELKRIYYELMIRYYSHNNDYLEICRCYKAIYEIP 196 (394)
Q Consensus 140 ~~~~~~~~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~~~~flea~k~y~ei~~t~ 196 (394)
...+ .+...+..+...++|-+|-..|..+...+
T Consensus 97 --------------------~~~~----~~~~~~~~~~~~g~~~~A~~~~~~~~~~~ 129 (234)
T TIGR02521 97 --------------------NNGD----VLNNYGTFLCQQGKYEQAMQQFEQAIEDP 129 (234)
T ss_pred --------------------CCHH----HHHHHHHHHHHcccHHHHHHHHHHHHhcc
Confidence 1111 23344566677889999999999888644
No 56
>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=75.03 E-value=57 Score=28.51 Aligned_cols=99 Identities=9% Similarity=0.053 Sum_probs=63.4
Q ss_pred HHHHHHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCccccCCCCccccC
Q 016147 63 RLIKKLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPRVFDADPSKEKK 142 (394)
Q Consensus 63 ~l~~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~~~~~~~~~~~~ 142 (394)
.....++.++...|++++|.+.+....-. -........+.....++...+++..|..+..++.... +
T Consensus 100 ~~~~~~~~~~~~~g~~~~A~~~~~~~~~~----~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~----~----- 166 (234)
T TIGR02521 100 DVLNNYGTFLCQQGKYEQAMQQFEQAIED----PLYPQPARSLENAGLCALKAGDFDKAEKYLTRALQID----P----- 166 (234)
T ss_pred HHHHHHHHHHHHcccHHHHHHHHHHHHhc----cccccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC----c-----
Confidence 35567788888888888888888775321 0111223445556778888889998888888876431 1
Q ss_pred CCCCCCcccccCCCCccchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhcc
Q 016147 143 KPKEGDNVVEEAPADIPSLLELKRIYYELMIRYYSHNNDYLEICRCYKAIYEI 195 (394)
Q Consensus 143 ~~~~~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~~~~flea~k~y~ei~~t 195 (394)
... ..+..++..+...++|-+|...|......
T Consensus 167 -----------------~~~----~~~~~la~~~~~~~~~~~A~~~~~~~~~~ 198 (234)
T TIGR02521 167 -----------------QRP----ESLLELAELYYLRGQYKDARAYLERYQQT 198 (234)
T ss_pred -----------------CCh----HHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence 001 12335566777788888877777766653
No 57
>KOG1840 consensus Kinesin light chain [Cytoskeleton]
Probab=74.72 E-value=63 Score=34.30 Aligned_cols=126 Identities=16% Similarity=0.117 Sum_probs=86.2
Q ss_pred HhhhhcCCcchHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHH---hhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHH
Q 016147 46 TLNSVSAGKIYVEIERARLIKKLAKIKEEQGLIAEAADLMQE---VAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQ 122 (394)
Q Consensus 46 ~L~~vt~gki~~E~era~l~~~La~i~e~~gd~~eAa~iL~~---i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~ 122 (394)
+|+.+..++..-.--.+.....+|.+|-..|++.+|+.++++ |..+++|.+. ..-..++...+-+|...++|..|+
T Consensus 225 Al~~l~k~~G~~hl~va~~l~~~a~~y~~~~k~~eAv~ly~~AL~i~e~~~G~~h-~~va~~l~nLa~ly~~~GKf~EA~ 303 (508)
T KOG1840|consen 225 ALRILEKTSGLKHLVVASMLNILALVYRSLGKYDEAVNLYEEALTIREEVFGEDH-PAVAATLNNLAVLYYKQGKFAEAE 303 (508)
T ss_pred HHHHHHHccCccCHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHhcCCCC-HHHHHHHHHHHHHHhccCChHHHH
Confidence 555555554434445566666899999999999999999886 4445556543 345667778899999999999999
Q ss_pred HHHHhhCccccCCCCccccCCCCCCCcccccCCCCccchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhc
Q 016147 123 ILSRKISPRVFDADPSKEKKKPKEGDNVVEEAPADIPSLLELKRIYYELMIRYYSHNNDYLEICRCYKAIYE 194 (394)
Q Consensus 123 ~~~~Ki~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~~~~flea~k~y~ei~~ 194 (394)
.+..++-...-... .+...+..-. +.-.+..+.+.++|-+|.+.|.....
T Consensus 304 ~~~e~Al~I~~~~~---------------------~~~~~~v~~~-l~~~~~~~~~~~~~Eea~~l~q~al~ 353 (508)
T KOG1840|consen 304 EYCERALEIYEKLL---------------------GASHPEVAAQ-LSELAAILQSMNEYEEAKKLLQKALK 353 (508)
T ss_pred HHHHHHHHHHHHhh---------------------ccChHHHHHH-HHHHHHHHHHhcchhHHHHHHHHHHH
Confidence 99999876532211 0123344433 33445566778889998888875553
No 58
>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=74.17 E-value=13 Score=26.50 Aligned_cols=49 Identities=20% Similarity=0.150 Sum_probs=39.6
Q ss_pred HHHHHHhhcCcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEEeccCC
Q 016147 297 NILVVSKYYSRITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKIDRPQ 345 (394)
Q Consensus 297 NI~visk~Y~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~akIDq~~ 345 (394)
.+..+..-+-.++...||+.++++..-+=..+.+|+..|-|.-..|.-+
T Consensus 7 ~iL~~l~~~~~~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~r~~~~~D 55 (59)
T PF01047_consen 7 RILRILYENGGITQSELAEKLGISRSTVTRIIKRLEKKGLIERERDPDD 55 (59)
T ss_dssp HHHHHHHHHSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTE
T ss_pred HHHHHHHHcCCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEeccCCCC
Confidence 3344444567799999999999999999999999999999987777654
No 59
>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=74.08 E-value=5 Score=31.09 Aligned_cols=41 Identities=20% Similarity=0.143 Sum_probs=35.2
Q ss_pred HHHHHHhhcCcccHHHHHHHhCCCHHHHHHHHHHhHhcCcE
Q 016147 297 NILVVSKYYSRITLKRLAELLCLSIQEAEKHLSDMVVSKAL 337 (394)
Q Consensus 297 NI~visk~Y~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l 337 (394)
.+-.+++++...|...+|+.+|+|+.-+...+..+...|.+
T Consensus 22 ~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~~~~~~~~ 62 (73)
T TIGR03879 22 AAAALAREEAGKTASEIAEELGRTEQTVRNHLKGETKAGGL 62 (73)
T ss_pred HHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcCcccchH
Confidence 34445578899999999999999999999999988888865
No 60
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=74.01 E-value=8.8 Score=28.72 Aligned_cols=34 Identities=21% Similarity=0.224 Sum_probs=30.3
Q ss_pred cCcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEE
Q 016147 305 YSRITLKRLAELLCLSIQEAEKHLSDMVVSKALV 338 (394)
Q Consensus 305 Y~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~ 338 (394)
..-++..++|+.+|+|.-.+..+|..|..+|.+.
T Consensus 13 ~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~ 46 (62)
T PF04703_consen 13 NGPLKTREIADALGLSIYQARYYLEKLEKEGKVE 46 (62)
T ss_dssp TS-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEE
T ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEE
Confidence 6779999999999999999999999999999884
No 61
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=73.83 E-value=13 Score=28.02 Aligned_cols=32 Identities=22% Similarity=0.173 Sum_probs=30.2
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEE
Q 016147 308 ITLKRLAELLCLSIQEAEKHLSDMVVSKALVA 339 (394)
Q Consensus 308 Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~a 339 (394)
++...||+.||++...+.+.|..|...|.+..
T Consensus 23 ~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~ 54 (68)
T smart00550 23 STALQLAKNLGLPKKEVNRVLYSLEKKGKVCK 54 (68)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence 99999999999999999999999999998754
No 62
>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=73.58 E-value=16 Score=25.15 Aligned_cols=33 Identities=30% Similarity=0.310 Sum_probs=28.3
Q ss_pred cCcccHHHHHHHhCCCHHHHHHHHHHhHhcCcE
Q 016147 305 YSRITLKRLAELLCLSIQEAEKHLSDMVVSKAL 337 (394)
Q Consensus 305 Y~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l 337 (394)
=..+|..+||+.+|+|..-+-..+.+|+..|-|
T Consensus 15 ~~~~t~~ela~~~~is~~tv~~~l~~L~~~g~I 47 (48)
T PF13412_consen 15 NPRITQKELAEKLGISRSTVNRYLKKLEEKGLI 47 (48)
T ss_dssp CTTS-HHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred cCCCCHHHHHHHhCCCHHHHHHHHHHHHHCcCc
Confidence 345999999999999999999999999999976
No 63
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=73.46 E-value=34 Score=29.38 Aligned_cols=70 Identities=21% Similarity=0.359 Sum_probs=50.5
Q ss_pred cccHHHHHHHhCCCHHHHHHHHHHhHhcCcEE-EEec-cCCCEEEEecCCChH-------HHHHHHHHHHHHHHHHHHH
Q 016147 307 RITLKRLAELLCLSIQEAEKHLSDMVVSKALV-AKID-RPQGIVCFQVAKDSN-------DILNSWAMNLEKLLDLVEK 376 (394)
Q Consensus 307 ~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~-akID-q~~giV~F~~~k~~~-------~~L~~W~~~I~~l~~~V~k 376 (394)
-.|.+.||+-|+.+-.-+.+-+-+++.-|-+. -|+. +..|..+-=.+-+++ ..+++|..++.++....++
T Consensus 42 ~~tvdelae~lnr~rStv~rsl~~L~~~GlV~Rek~~~~~Ggy~yiY~~i~~ee~k~~i~~~l~~w~~~~~~~i~~~~~ 120 (126)
T COG3355 42 PLTVDELAEILNRSRSTVYRSLQNLLEAGLVEREKVNLKGGGYYYLYKPIDPEEIKKKILKDLDEWYDKMKQLIEEFEK 120 (126)
T ss_pred CcCHHHHHHHHCccHHHHHHHHHHHHHcCCeeeeeeccCCCceeEEEecCCHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 35788999999999999999999999999873 4444 334443333344443 4688888888877766543
No 64
>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=73.23 E-value=23 Score=27.57 Aligned_cols=59 Identities=17% Similarity=0.117 Sum_probs=42.3
Q ss_pred HHHHHHHHhhcC--cccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEEeccCCCEEEEecC
Q 016147 295 EHNILVVSKYYS--RITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKIDRPQGIVCFQVA 353 (394)
Q Consensus 295 EHNI~visk~Y~--~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~akIDq~~giV~F~~~ 353 (394)
-|-+..++.... .+|.+.||+.+++|+..+++.+..|...|-+...=-+..|+.--.++
T Consensus 11 l~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s~~G~~GGy~L~~~~ 71 (83)
T PF02082_consen 11 LRILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKAGLIESSRGRGGGYRLARPP 71 (83)
T ss_dssp HHHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETSTTSEEEESS-C
T ss_pred HHHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEecCCCCCceeecCCH
Confidence 344444554443 39999999999999999999999999999887765555555444443
No 65
>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=72.67 E-value=12 Score=25.25 Aligned_cols=47 Identities=15% Similarity=0.085 Sum_probs=34.2
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEEeccCCCEEEEecCCChHHHHHHHHH
Q 016147 308 ITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKIDRPQGIVCFQVAKDSNDILNSWAM 365 (394)
Q Consensus 308 Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~akIDq~~giV~F~~~k~~~~~L~~W~~ 365 (394)
+|++.+|++||+|..-+ -+++.+|.+.+... .|...|.. +.+..|-+
T Consensus 2 lt~~e~a~~lgis~~ti----~~~~~~g~i~~~~~--g~~~~~~~-----~~l~~~~~ 48 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTV----YRLIHEGELPAYRV--GRHYRIPR-----EDVDEYLE 48 (49)
T ss_pred CCHHHHHHHHCCCHHHH----HHHHHcCCCCeEEe--CCeEEEeH-----HHHHHHHh
Confidence 47899999999998754 46778999876543 46666764 45777754
No 66
>KOG1497 consensus COP9 signalosome, subunit CSN4 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=72.54 E-value=9.7 Score=37.85 Aligned_cols=75 Identities=20% Similarity=0.253 Sum_probs=52.2
Q ss_pred cchHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCcccc
Q 016147 54 KIYVEIERARLIKKLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPRVF 133 (394)
Q Consensus 54 ki~~E~era~l~~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~~~ 133 (394)
+-+=+++...++.++|+.|-+.||..+|+-.... | |+. .+.+.|..
T Consensus 136 ~~~d~~~kl~l~iriarlyLe~~d~veae~~inR----a--Sil--------------------------~a~~~Ne~-- 181 (399)
T KOG1497|consen 136 KAYDVEQKLLLCIRIARLYLEDDDKVEAEAYINR----A--SIL--------------------------QAESSNEQ-- 181 (399)
T ss_pred hhhhhHHHHHHHHHHHHHHHhcCcHHHHHHHHHH----H--HHh--------------------------hhcccCHH--
Confidence 5555678899999999999999999998765443 1 100 01111211
Q ss_pred CCCCccccCCCCCCCcccccCCCCccchHHHHHHHHHHHHHHHHh
Q 016147 134 DADPSKEKKKPKEGDNVVEEAPADIPSLLELKRIYYELMIRYYSH 178 (394)
Q Consensus 134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~ 178 (394)
+...+++|+++..|.|.||.+++.+||..
T Consensus 182 ----------------Lqie~kvc~ARvlD~krkFlEAAqrYyel 210 (399)
T KOG1497|consen 182 ----------------LQIEYKVCYARVLDYKRKFLEAAQRYYEL 210 (399)
T ss_pred ----------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 11234678889999999999999999975
No 67
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=71.80 E-value=18 Score=25.44 Aligned_cols=47 Identities=17% Similarity=0.208 Sum_probs=37.7
Q ss_pred cCcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEEeccCCCEEEEe
Q 016147 305 YSRITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKIDRPQGIVCFQ 351 (394)
Q Consensus 305 Y~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~akIDq~~giV~F~ 351 (394)
-..+++..+++.+|+|...+-+.+..|...|-+...-+...+...+.
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~~~~~~~~~~~~~~ 54 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLREAGLVESRREGKRVYYSLT 54 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeeecCCEEEEEEc
Confidence 45689999999999999999999999999999976555444444433
No 68
>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A.
Probab=71.71 E-value=5.5 Score=25.81 Aligned_cols=22 Identities=23% Similarity=0.397 Sum_probs=18.7
Q ss_pred HHHHHHHHHhcCHHHHHHHHHH
Q 016147 66 KKLAKIKEEQGLIAEAADLMQE 87 (394)
Q Consensus 66 ~~La~i~e~~gd~~eAa~iL~~ 87 (394)
..||.+|...|+|++|.++.+.
T Consensus 3 ~~Lg~~~~~~g~~~~Ai~~y~~ 24 (36)
T PF13176_consen 3 NNLGRIYRQQGDYEKAIEYYEQ 24 (36)
T ss_dssp HHHHHHHHHCT-HHHHHHHHHH
T ss_pred HHHHHHHHHcCCHHHHHHHHHH
Confidence 4689999999999999998876
No 69
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=71.68 E-value=8.6 Score=25.98 Aligned_cols=32 Identities=22% Similarity=0.304 Sum_probs=29.9
Q ss_pred cccHHHHHHHhCCCHHHHHHHHHHhHhcCcEE
Q 016147 307 RITLKRLAELLCLSIQEAEKHLSDMVVSKALV 338 (394)
Q Consensus 307 ~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~ 338 (394)
.++...||+.+|+|...+-+.+..|...|-+.
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L~~~g~l~ 39 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRLEKEGLIS 39 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 47889999999999999999999999999885
No 70
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=71.09 E-value=46 Score=25.76 Aligned_cols=65 Identities=11% Similarity=0.131 Sum_probs=45.6
Q ss_pred cccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEEeccCCCE-EEEecCCChHHHHHHHHHHHHHHH
Q 016147 307 RITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKIDRPQGI-VCFQVAKDSNDILNSWAMNLEKLL 371 (394)
Q Consensus 307 ~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~akIDq~~gi-V~F~~~k~~~~~L~~W~~~I~~l~ 371 (394)
.++.+.|++.++++...+-..+.+|+..|-+...-|+.++- ..+.-.......+..+...+....
T Consensus 24 ~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~~~~~~~~~r~~~~~lT~~g~~~~~~~~~~~~~~~ 89 (101)
T smart00347 24 PLSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRLPSPEDRRSVLVSLTEEGRELIEELLEARHETL 89 (101)
T ss_pred CcCHHHHHHHHCCCchhHHHHHHHHHHCCCeEecCCCCCCCeEEEEECHhHHHHHHHHHHHHHHHH
Confidence 58999999999999999999999999999998776643322 222222333455555555555444
No 71
>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=70.92 E-value=18 Score=26.23 Aligned_cols=45 Identities=22% Similarity=0.294 Sum_probs=37.0
Q ss_pred hhcCcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEEeccCCCEEEEe
Q 016147 303 KYYSRITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKIDRPQGIVCFQ 351 (394)
Q Consensus 303 k~Y~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~akIDq~~giV~F~ 351 (394)
+--..+|++.||+.||+|+.-+-.-+..|...|. |.|.-|=+.+.
T Consensus 10 ~~~~~~s~~ela~~~~VS~~TiRRDl~~L~~~g~----i~r~~GG~~~~ 54 (57)
T PF08220_consen 10 KEKGKVSVKELAEEFGVSEMTIRRDLNKLEKQGL----IKRTHGGAVLN 54 (57)
T ss_pred HHcCCEEHHHHHHHHCcCHHHHHHHHHHHHHCCC----EEEEcCEEEeC
Confidence 4467899999999999999999999999999996 55555555543
No 72
>PRK10049 pgaA outer membrane protein PgaA; Provisional
Probab=70.36 E-value=1.7e+02 Score=32.43 Aligned_cols=101 Identities=9% Similarity=-0.066 Sum_probs=73.9
Q ss_pred HHHHHHHHHHhcCHHHHHHHHHHhhhhhc---------ccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCccccCC
Q 016147 65 IKKLAKIKEEQGLIAEAADLMQEVAVETF---------GAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPRVFDA 135 (394)
Q Consensus 65 ~~~La~i~e~~gd~~eAa~iL~~i~vEt~---------~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~~~~~ 135 (394)
...|+..+.+.|++++|...+..+.-... ...+.....+.++..+.++...+|+..|.....++....
T Consensus 313 ~~~L~~a~~~~g~~~eA~~~l~~~~~~~P~~~~~~~~~~~~p~~~~~~a~~~~a~~l~~~g~~~eA~~~l~~al~~~--- 389 (765)
T PRK10049 313 LADLFYSLLESENYPGALTVTAHTINNSPPFLRLYGSPTSIPNDDWLQGQSLLSQVAKYSNDLPQAEMRARELAYNA--- 389 (765)
T ss_pred HHHHHHHHHhcccHHHHHHHHHHHhhcCCceEeecCCCCCCCCchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC---
Confidence 45667778899999999999887764321 123445677888888999999999999999999886542
Q ss_pred CCccccCCCCCCCcccccCCCCccchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhcc
Q 016147 136 DPSKEKKKPKEGDNVVEEAPADIPSLLELKRIYYELMIRYYSHNNDYLEICRCYKAIYEI 195 (394)
Q Consensus 136 ~~~~~~~~~~~~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~~~~flea~k~y~ei~~t 195 (394)
| +..++ ....+..+...+++-+|-..|..+...
T Consensus 390 -P----------------------~n~~l----~~~lA~l~~~~g~~~~A~~~l~~al~l 422 (765)
T PRK10049 390 -P----------------------GNQGL----RIDYASVLQARGWPRAAENELKKAEVL 422 (765)
T ss_pred -C----------------------CCHHH----HHHHHHHHHhcCCHHHHHHHHHHHHhh
Confidence 1 11222 344456777888999999999888863
No 73
>PF12728 HTH_17: Helix-turn-helix domain
Probab=70.32 E-value=16 Score=25.45 Aligned_cols=47 Identities=19% Similarity=0.164 Sum_probs=35.0
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEEeccCCCEEEEecCCChHHHHHHHHH
Q 016147 308 ITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKIDRPQGIVCFQVAKDSNDILNSWAM 365 (394)
Q Consensus 308 Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~akIDq~~giV~F~~~k~~~~~L~~W~~ 365 (394)
+|.+.+|++||+|..-+ -+|+.+|.+.+- ++.+-+.|.. +.+++|-+
T Consensus 2 lt~~e~a~~l~is~~tv----~~~~~~g~i~~~--~~g~~~~~~~-----~~l~~~~~ 48 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTV----YRWIRQGKIPPF--KIGRKWRIPK-----SDLDRWLE 48 (51)
T ss_pred CCHHHHHHHHCcCHHHH----HHHHHcCCCCeE--EeCCEEEEeH-----HHHHHHHH
Confidence 47899999999998764 467889999665 3666677765 45777764
No 74
>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=69.60 E-value=9 Score=27.91 Aligned_cols=34 Identities=15% Similarity=0.239 Sum_probs=31.1
Q ss_pred CcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEE
Q 016147 306 SRITLKRLAELLCLSIQEAEKHLSDMVVSKALVA 339 (394)
Q Consensus 306 ~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~a 339 (394)
..+|...||+.+|+|..-+.+.+..|...|-|..
T Consensus 24 ~~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~~ 57 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSRTLKELEEEGLISR 57 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence 3589999999999999999999999999998764
No 75
>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A.
Probab=69.45 E-value=11 Score=23.05 Aligned_cols=26 Identities=23% Similarity=0.254 Sum_probs=22.2
Q ss_pred HHHHHHHHHHhcCHHHHHHHHHHhhh
Q 016147 65 IKKLAKIKEEQGLIAEAADLMQEVAV 90 (394)
Q Consensus 65 ~~~La~i~e~~gd~~eAa~iL~~i~v 90 (394)
...+|.++...|++++|.+.++.+--
T Consensus 3 ~~~~a~~~~~~g~~~~A~~~~~~~~~ 28 (33)
T PF13174_consen 3 LYRLARCYYKLGDYDEAIEYFQRLIK 28 (33)
T ss_dssp HHHHHHHHHHHCHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHccCHHHHHHHHHHHHH
Confidence 46789999999999999999988754
No 76
>PF13428 TPR_14: Tetratricopeptide repeat
Probab=68.86 E-value=9.4 Score=25.77 Aligned_cols=26 Identities=23% Similarity=0.198 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHhcCHHHHHHHHHHhh
Q 016147 64 LIKKLAKIKEEQGLIAEAADLMQEVA 89 (394)
Q Consensus 64 l~~~La~i~e~~gd~~eAa~iL~~i~ 89 (394)
+...||..|...|++++|.++++.+-
T Consensus 3 ~~~~la~~~~~~G~~~~A~~~~~~~l 28 (44)
T PF13428_consen 3 AWLALARAYRRLGQPDEAERLLRRAL 28 (44)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence 45678888888888888888887644
No 77
>PF02259 FAT: FAT domain; InterPro: IPR003151 The FAT domain is a domain present in the PIK-related kinases. Members of the family of PIK-related kinases may act as intracellular sensors that govern radial and horizontal pathways [].; GO: 0005515 protein binding
Probab=67.98 E-value=1.2e+02 Score=29.32 Aligned_cols=173 Identities=14% Similarity=0.111 Sum_probs=103.6
Q ss_pred HHHHHHHHHHHHHhccCCCC-hHHHHHHHHHhhhhcCCcchHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHhhhhhccc
Q 016147 17 LQAVTAMVQQAMQYIDQTPD-LDTRIELIKTLNSVSAGKIYVEIERARLIKKLAKIKEEQGLIAEAADLMQEVAVETFGA 95 (394)
Q Consensus 17 k~ai~~~v~~~~~~~~~~~d-~~~k~~~i~~L~~vt~gki~~E~era~l~~~La~i~e~~gd~~eAa~iL~~i~vEt~~~ 95 (394)
.+....+++.=..-++.+++ .+....++ .+|.+.-+.+....+.+.....+|++.-..|.+.-|...|..+.-- ..
T Consensus 101 ~~~~~~l~~~W~~Rl~~~~~~~~~~~~il-~~R~~~l~~~~~~~~~~~~~l~~a~~aRk~g~~~~A~~~l~~~~~~--~~ 177 (352)
T PF02259_consen 101 PQDLKSLLKRWRSRLPNMQDDFSVWEPIL-SLRRLVLSLILLPEELAETWLKFAKLARKAGNFQLALSALNRLFQL--NP 177 (352)
T ss_pred HHHHHHHHHHHHHHHHHhccchHHHHHHH-HHHHHHHhcccchhHHHHHHHHHHHHHHHCCCcHHHHHHHHHHhcc--CC
Confidence 33444444433334444433 23333333 5566555656778899999999999999999999999988875531 11
Q ss_pred CcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCccccCCC-CccccCCCCCCCcc----ccc-CCCCccchHHHHHHHH
Q 016147 96 MAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPRVFDAD-PSKEKKKPKEGDNV----VEE-APADIPSLLELKRIYY 169 (394)
Q Consensus 96 m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~~~~~~-~~~~~~~~~~~~~~----~~~-~~~~~~~~~d~klk~~ 169 (394)
....-...+.++.+++.-..|+...|-..++..-...+... .... ........ ... .........+.+-+.+
T Consensus 178 ~~~~~~~~v~~e~akllw~~g~~~~Ai~~L~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~ 255 (352)
T PF02259_consen 178 SSESLLPRVFLEYAKLLWAQGEQEEAIQKLRELLKCRLSKNIDSIS--NAELKSGLLESLEVISSTNLDKESKELKAKAF 255 (352)
T ss_pred cccCCCcchHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhhcccccc--HHHHhhccccccccccccchhhhhHHHHHHHH
Confidence 11112678889999999999999888887665544111111 0000 00000000 000 0000123457777888
Q ss_pred HHHHHHHHhh------hhHHHHHHHHHHHhc
Q 016147 170 ELMIRYYSHN------NDYLEICRCYKAIYE 194 (394)
Q Consensus 170 ~~~~~~~~~~------~~flea~k~y~ei~~ 194 (394)
...+.|.... .++-++.+.|.+...
T Consensus 256 l~~a~w~~~~~~~~~~~~~~~~~~~~~~a~~ 286 (352)
T PF02259_consen 256 LLLAKWLDELYSKLSSESSDEILKYYKEATK 286 (352)
T ss_pred HHHHHHHHhhccccccccHHHHHHHHHHHHH
Confidence 8888888887 777888888887775
No 78
>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=67.86 E-value=1.5e+02 Score=31.75 Aligned_cols=99 Identities=12% Similarity=0.030 Sum_probs=69.6
Q ss_pred HHHHHHHHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCccccCCCCccc
Q 016147 61 RARLIKKLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPRVFDADPSKE 140 (394)
Q Consensus 61 ra~l~~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~~~~~~~~~~ 140 (394)
.+.....++.++...|++++|...+...- +... .-...++....+++..+++..|..+..++-.. +|
T Consensus 330 ~a~a~~~lg~~~~~~g~~~eA~~~~~kal-~l~P-----~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~----~p--- 396 (615)
T TIGR00990 330 EAIALNLRGTFKCLKGKHLEALADLSKSI-ELDP-----RVTQSYIKRASMNLELGDPDKAEEDFDKALKL----NS--- 396 (615)
T ss_pred hHHHHHHHHHHHHHcCCHHHHHHHHHHHH-HcCC-----CcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh----CC---
Confidence 34556778888889999999998887642 1111 12346677788888999999999999888532 11
Q ss_pred cCCCCCCCcccccCCCCccchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhcc
Q 016147 141 KKKPKEGDNVVEEAPADIPSLLELKRIYYELMIRYYSHNNDYLEICRCYKAIYEI 195 (394)
Q Consensus 141 ~~~~~~~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~~~~flea~k~y~ei~~t 195 (394)
...+ .+...+..+...++|-+|..+|......
T Consensus 397 -------------------~~~~----~~~~lg~~~~~~g~~~~A~~~~~kal~l 428 (615)
T TIGR00990 397 -------------------EDPD----IYYHRAQLHFIKGEFAQAGKDYQKSIDL 428 (615)
T ss_pred -------------------CCHH----HHHHHHHHHHHcCCHHHHHHHHHHHHHc
Confidence 1112 2445567777889999999999988863
No 79
>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=67.58 E-value=12 Score=23.21 Aligned_cols=26 Identities=31% Similarity=0.345 Sum_probs=19.4
Q ss_pred HHHHHHHHHHHHHhcCHHHHHHHHHH
Q 016147 62 ARLIKKLAKIKEEQGLIAEAADLMQE 87 (394)
Q Consensus 62 a~l~~~La~i~e~~gd~~eAa~iL~~ 87 (394)
|++-..+|.+|...|++++|.+.+..
T Consensus 1 a~~~~~lg~~y~~~~~~~~A~~~~~~ 26 (34)
T PF13181_consen 1 AEAYYNLGKIYEQLGDYEEALEYFEK 26 (34)
T ss_dssp -HHHHHHHHHHHHTTSHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence 34556788888888888888887664
No 80
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=67.21 E-value=34 Score=32.63 Aligned_cols=66 Identities=18% Similarity=0.315 Sum_probs=54.5
Q ss_pred hcCcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEEeccCCCEEEEecCCChHHHHHHHHHHHHHHHHHH
Q 016147 304 YYSRITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKIDRPQGIVCFQVAKDSNDILNSWAMNLEKLLDLV 374 (394)
Q Consensus 304 ~Y~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~akIDq~~giV~F~~~k~~~~~L~~W~~~I~~l~~~V 374 (394)
+=-+++-+.+|.-||+|++-+-.++-+||.+|-+.- .|-.++.=.+...+.+-+|..+++...+.+
T Consensus 22 ~qp~v~q~eIA~~lgiT~QaVsehiK~Lv~eG~i~~-----~gR~~Y~iTkkG~e~l~~~~~dlr~f~~ev 87 (260)
T COG1497 22 RQPRVKQKEIAKKLGITLQAVSEHIKELVKEGLIEK-----EGRGEYEITKKGAEWLLEQLSDLRRFSEEV 87 (260)
T ss_pred hCCCCCHHHHHHHcCCCHHHHHHHHHHHHhccceee-----cCCeeEEEehhHHHHHHHHHHHHHHHHHHH
Confidence 446789999999999999999999999999997654 444455444556789999999999998888
No 81
>KOG3081 consensus Vesicle coat complex COPI, epsilon subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=66.54 E-value=1.3e+02 Score=29.33 Aligned_cols=126 Identities=14% Similarity=0.084 Sum_probs=84.7
Q ss_pred HHHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCccccCCCCccccCCCC
Q 016147 66 KKLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPRVFDADPSKEKKKPK 145 (394)
Q Consensus 66 ~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~~~~~~~~~~~~~~~ 145 (394)
..=|.+|...|++++|.+.+.. .+-+|...-.+.+.+...-+.-|+..++|.... ++
T Consensus 112 l~aa~i~~~~~~~deAl~~~~~-----------~~~lE~~Al~VqI~lk~~r~d~A~~~lk~mq~i--de---------- 168 (299)
T KOG3081|consen 112 LLAAIIYMHDGDFDEALKALHL-----------GENLEAAALNVQILLKMHRFDLAEKELKKMQQI--DE---------- 168 (299)
T ss_pred HHhhHHhhcCCChHHHHHHHhc-----------cchHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc--ch----------
Confidence 4445788999999999997764 234566677777777777778888888877742 10
Q ss_pred CCCcccccCCCCccchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhc-cCCCCCChhcHHHHHHHHHHHHHhCCCChh
Q 016147 146 EGDNVVEEAPADIPSLLELKRIYYELMIRYYSHNNDYLEICRCYKAIYE-IPYIKEDPAQWMPVLRKICWYLVLAPHDPM 224 (394)
Q Consensus 146 ~~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~~~~flea~k~y~ei~~-t~~i~~d~~~~~~~L~~av~~~ILap~~~~ 224 (394)
...-...-...+.+.....++-+|+..|.+..+ || ..+......||.+..+-.+..-
T Consensus 169 ----------------d~tLtQLA~awv~la~ggek~qdAfyifeE~s~k~~------~T~~llnG~Av~~l~~~~~eeA 226 (299)
T KOG3081|consen 169 ----------------DATLTQLAQAWVKLATGGEKIQDAFYIFEELSEKTP------PTPLLLNGQAVCHLQLGRYEEA 226 (299)
T ss_pred ----------------HHHHHHHHHHHHHHhccchhhhhHHHHHHHHhcccC------CChHHHccHHHHHHHhcCHHHH
Confidence 111122455666777778888999999999987 54 2455666677777666666555
Q ss_pred chHhhhhhhccc
Q 016147 225 QSSLLNSTLEDK 236 (394)
Q Consensus 225 rs~ll~~l~~d~ 236 (394)
.+-+...+.+|+
T Consensus 227 e~lL~eaL~kd~ 238 (299)
T KOG3081|consen 227 ESLLEEALDKDA 238 (299)
T ss_pred HHHHHHHHhccC
Confidence 555555555554
No 82
>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=66.03 E-value=71 Score=31.08 Aligned_cols=66 Identities=18% Similarity=0.164 Sum_probs=51.3
Q ss_pred HHHHHHHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhC
Q 016147 62 ARLIKKLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKIS 129 (394)
Q Consensus 62 a~l~~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~ 129 (394)
...-..+|.++...|++++|...+....-- ... +.......+...+++++..||+..|..+.+++.
T Consensus 148 ~~~~~~la~i~~~~g~~~eA~~~l~~~l~~-~~~-~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~~~ 213 (355)
T cd05804 148 AWAVHAVAHVLEMQGRFKEGIAFMESWRDT-WDC-SSMLRGHNWWHLALFYLERGDYEAALAIYDTHI 213 (355)
T ss_pred cHHHHHHHHHHHHcCCHHHHHHHHHhhhhc-cCC-CcchhHHHHHHHHHHHHHCCCHHHHHHHHHHHh
Confidence 345678999999999999999998874321 111 234445677788999999999999999999873
No 83
>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=65.31 E-value=76 Score=26.02 Aligned_cols=98 Identities=18% Similarity=0.037 Sum_probs=69.6
Q ss_pred HHHHHHHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCccccCCCCcccc
Q 016147 62 ARLIKKLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPRVFDADPSKEK 141 (394)
Q Consensus 62 a~l~~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~~~~~~~~~~~ 141 (394)
......+|..+...|++.+|...++.+.- .. . .-.+++.....++...+++..|..+.+++.... |
T Consensus 17 ~~~~~~~a~~~~~~~~~~~A~~~~~~~~~-~~-p----~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~----p---- 82 (135)
T TIGR02552 17 LEQIYALAYNLYQQGRYDEALKLFQLLAA-YD-P----YNSRYWLGLAACCQMLKEYEEAIDAYALAAALD----P---- 82 (135)
T ss_pred HHHHHHHHHHHHHcccHHHHHHHHHHHHH-hC-C----CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC----C----
Confidence 34467889999999999999999877531 11 1 124677788889999999999999998876431 1
Q ss_pred CCCCCCCcccccCCCCccchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhcc
Q 016147 142 KKPKEGDNVVEEAPADIPSLLELKRIYYELMIRYYSHNNDYLEICRCYKAIYEI 195 (394)
Q Consensus 142 ~~~~~~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~~~~flea~k~y~ei~~t 195 (394)
...+ ++...+..+...++|-+|.+.|..+...
T Consensus 83 ------------------~~~~----~~~~la~~~~~~g~~~~A~~~~~~al~~ 114 (135)
T TIGR02552 83 ------------------DDPR----PYFHAAECLLALGEPESALKALDLAIEI 114 (135)
T ss_pred ------------------CChH----HHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence 1111 2233445667788999999999888864
No 84
>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=64.63 E-value=9.7 Score=22.84 Aligned_cols=24 Identities=33% Similarity=0.257 Sum_probs=20.5
Q ss_pred HHHHHHHHHHHHhcCHHHHHHHHH
Q 016147 63 RLIKKLAKIKEEQGLIAEAADLMQ 86 (394)
Q Consensus 63 ~l~~~La~i~e~~gd~~eAa~iL~ 86 (394)
+....||..+-..|++++|..++.
T Consensus 2 ~a~~~la~~~~~~G~~~eA~~~l~ 25 (26)
T PF07721_consen 2 RARLALARALLAQGDPDEAERLLR 25 (26)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHh
Confidence 456789999999999999998764
No 85
>KOG2076 consensus RNA polymerase III transcription factor TFIIIC [Transcription]
Probab=64.60 E-value=24 Score=39.44 Aligned_cols=84 Identities=15% Similarity=0.106 Sum_probs=66.6
Q ss_pred HHHHhhhhcCCcchHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHH
Q 016147 43 LIKTLNSVSAGKIYVEIERARLIKKLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQ 122 (394)
Q Consensus 43 ~i~~L~~vt~gki~~E~era~l~~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~ 122 (394)
+.+.|.....-..+-..++..+-..+|+.|-..|.+.+|.+.|..|--. +.-.-..+++.++|++.+.+.+..|.
T Consensus 395 ~~e~ll~~l~~~n~~~~d~~dL~~d~a~al~~~~~~~~Al~~l~~i~~~-----~~~~~~~vw~~~a~c~~~l~e~e~A~ 469 (895)
T KOG2076|consen 395 LLEALLHFLVEDNVWVSDDVDLYLDLADALTNIGKYKEALRLLSPITNR-----EGYQNAFVWYKLARCYMELGEYEEAI 469 (895)
T ss_pred hHHHHHHHHHHhcCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHhcC-----ccccchhhhHHHHHHHHHHhhHHHHH
Confidence 3455555554445457788999999999999999999999999876521 11222789999999999999999999
Q ss_pred HHHHhhCcc
Q 016147 123 ILSRKISPR 131 (394)
Q Consensus 123 ~~~~Ki~~~ 131 (394)
...+|+-..
T Consensus 470 e~y~kvl~~ 478 (895)
T KOG2076|consen 470 EFYEKVLIL 478 (895)
T ss_pred HHHHHHHhc
Confidence 999999753
No 86
>KOG4414 consensus COP9 signalosome, subunit CSN8 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=64.09 E-value=18 Score=31.89 Aligned_cols=43 Identities=21% Similarity=0.295 Sum_probs=35.4
Q ss_pred HHHHHHHHHHHHHHHHHhhcCcccHHHHHHHhCCCHHHHHHHH
Q 016147 286 AEDLRQRIIEHNILVVSKYYSRITLKRLAELLCLSIQEAEKHL 328 (394)
Q Consensus 286 ~~~L~~~viEHNI~visk~Y~~Isl~rLa~lL~ls~~e~E~~l 328 (394)
...++......-...+++-|++|+...+|-.+|++++++-+.+
T Consensus 111 maAf~D~~~kR~FaLl~qAYssI~~~D~A~FlGl~~ddAtk~i 153 (197)
T KOG4414|consen 111 MAAFRDATRKRAFALLLQAYSSIIADDFAAFLGLPEDDATKGI 153 (197)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHH
Confidence 3456666666777788899999999999999999999987654
No 87
>KOG3060 consensus Uncharacterized conserved protein [Function unknown]
Probab=64.00 E-value=22 Score=34.31 Aligned_cols=29 Identities=24% Similarity=0.251 Sum_probs=23.9
Q ss_pred HHHHHHHHHHHHHhcCHHHHHHHHHHhhh
Q 016147 62 ARLIKKLAKIKEEQGLIAEAADLMQEVAV 90 (394)
Q Consensus 62 a~l~~~La~i~e~~gd~~eAa~iL~~i~v 90 (394)
......||+||-.+|+++.|+=++.++-.
T Consensus 154 ~EAW~eLaeiY~~~~~f~kA~fClEE~ll 182 (289)
T KOG3060|consen 154 QEAWHELAEIYLSEGDFEKAAFCLEELLL 182 (289)
T ss_pred HHHHHHHHHHHHhHhHHHHHHHHHHHHHH
Confidence 34567899999999999999988888654
No 88
>KOG1840 consensus Kinesin light chain [Cytoskeleton]
Probab=63.99 E-value=2e+02 Score=30.60 Aligned_cols=113 Identities=22% Similarity=0.228 Sum_probs=80.7
Q ss_pred HHHHHHHHHHHHHHHHhcCHHHHHHHHHHhhhhhcc---cCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCccccCC
Q 016147 59 IERARLIKKLAKIKEEQGLIAEAADLMQEVAVETFG---AMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPRVFDA 135 (394)
Q Consensus 59 ~era~l~~~La~i~e~~gd~~eAa~iL~~i~vEt~~---~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~~~~~ 135 (394)
.-++-.-..||..|...|+++||...+.. -+|-+. .-+..+--..+.+..-++--.+++..|..+..|+...+...
T Consensus 280 ~~va~~l~nLa~ly~~~GKf~EA~~~~e~-Al~I~~~~~~~~~~~v~~~l~~~~~~~~~~~~~Eea~~l~q~al~i~~~~ 358 (508)
T KOG1840|consen 280 PAVAATLNNLAVLYYKQGKFAEAEEYCER-ALEIYEKLLGASHPEVAAQLSELAAILQSMNEYEEAKKLLQKALKIYLDA 358 (508)
T ss_pred HHHHHHHHHHHHHHhccCChHHHHHHHHH-HHHHHHHhhccChHHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhh
Confidence 45677778999999999999998865443 222221 13444555667777888888899999999999888766532
Q ss_pred CCccccCCCCCCCcccccCCCCccchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhc
Q 016147 136 DPSKEKKKPKEGDNVVEEAPADIPSLLELKRIYYELMIRYYSHNNDYLEICRCYKAIYE 194 (394)
Q Consensus 136 ~~~~~~~~~~~~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~~~~flea~k~y~ei~~ 194 (394)
.+. ++ -.--++|.-++..|.+.|+|-||-..|.++..
T Consensus 359 ~g~--------~~--------------~~~a~~~~nl~~l~~~~gk~~ea~~~~k~ai~ 395 (508)
T KOG1840|consen 359 PGE--------DN--------------VNLAKIYANLAELYLKMGKYKEAEELYKKAIQ 395 (508)
T ss_pred ccc--------cc--------------hHHHHHHHHHHHHHHHhcchhHHHHHHHHHHH
Confidence 211 11 13356788888889999999999888888775
No 89
>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A.
Probab=63.70 E-value=63 Score=24.55 Aligned_cols=50 Identities=16% Similarity=0.187 Sum_probs=38.9
Q ss_pred HhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHh
Q 016147 74 EQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRK 127 (394)
Q Consensus 74 ~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~K 127 (394)
..|++++|...+..+.-.... ...-.+++..++.+...++|.+|-.++++
T Consensus 1 ~~~~y~~Ai~~~~k~~~~~~~----~~~~~~~~~la~~~~~~~~y~~A~~~~~~ 50 (84)
T PF12895_consen 1 DQGNYENAIKYYEKLLELDPT----NPNSAYLYNLAQCYFQQGKYEEAIELLQK 50 (84)
T ss_dssp HTT-HHHHHHHHHHHHHHHCG----THHHHHHHHHHHHHHHTTHHHHHHHHHHC
T ss_pred CCccHHHHHHHHHHHHHHCCC----ChhHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence 368999999988876543222 22666888899999999999999999988
No 90
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=63.62 E-value=18 Score=25.35 Aligned_cols=32 Identities=19% Similarity=0.227 Sum_probs=29.5
Q ss_pred cc-cHHHHHHHhCCCHHHHHHHHHHhHhcCcEE
Q 016147 307 RI-TLKRLAELLCLSIQEAEKHLSDMVVSKALV 338 (394)
Q Consensus 307 ~I-sl~rLa~lL~ls~~e~E~~ls~MI~~g~l~ 338 (394)
.+ |...||+.+|+|..-+.+.+..|...|-+.
T Consensus 19 ~l~s~~~la~~~~vs~~tv~~~l~~L~~~g~i~ 51 (60)
T smart00345 19 KLPSERELAAQLGVSRTTVREALSRLEAEGLVQ 51 (60)
T ss_pred cCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 45 899999999999999999999999999775
No 91
>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=63.62 E-value=86 Score=28.61 Aligned_cols=73 Identities=16% Similarity=0.014 Sum_probs=56.5
Q ss_pred hHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCcc
Q 016147 56 YVEIERARLIKKLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPR 131 (394)
Q Consensus 56 ~~E~era~l~~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~ 131 (394)
.+.++.+.....++..+...|++++|...+..+.-....+ ..-.+.++..+.++...++|..|....+++...
T Consensus 27 ~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~p~~---~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~ 99 (235)
T TIGR03302 27 PVEEWPAEELYEEAKEALDSGDYTEAIKYFEALESRYPFS---PYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRL 99 (235)
T ss_pred CcccCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCc---hhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Confidence 4456777888999999999999999999998864321111 123345677789999999999999999998765
No 92
>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=63.52 E-value=45 Score=30.09 Aligned_cols=142 Identities=20% Similarity=0.203 Sum_probs=66.7
Q ss_pred HHHHHHHHHHHHHhhhhHHHHHHHH---HHHhccCCCCCChhcHHHHHHHHHHHHHhCCCChhchHhhhhhhcccCcCCC
Q 016147 165 KRIYYELMIRYYSHNNDYLEICRCY---KAIYEIPYIKEDPAQWMPVLRKICWYLVLAPHDPMQSSLLNSTLEDKNLSEI 241 (394)
Q Consensus 165 klk~~~~~~~~~~~~~~flea~k~y---~ei~~t~~i~~d~~~~~~~L~~av~~~ILap~~~~rs~ll~~l~~d~~l~~i 241 (394)
-+..|+..++++...++.-+-.+++ ...|+............+.....++|.+.....++-...+..+- +....-
T Consensus 55 ~i~v~E~~ar~~i~~~d~~qf~~c~~~L~~lY~~~~~~~~~~~~~ef~~y~lL~~l~~~~~~~~~~~l~~l~--~~~~~~ 132 (204)
T PF03399_consen 55 AIKVYERIARFAIESGDLEQFNQCLSQLKELYDDLRDLPPSPNEAEFIAYYLLYLLCQNNIPDFHMELELLP--SEILSS 132 (204)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT---TTHHHHHHHHHHHTT-T---THHHHHHTTS---HHHHTS
T ss_pred HHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHhhccCCCCCCHHHHHHHHHHHHHHcccchHHHHHHHHCc--hhhhcC
Confidence 4677888888888776654322222 22222110000012234555555555543332223222232221 113344
Q ss_pred hhHHH---HHHHhcchhcccchhhHHHHHHhhhhhhhhcCCchhhhhH-HHHHHHHHHHHHHHHHhhcCc-ccHHHHHHH
Q 016147 242 PNFRL---LLKQLVTMEVIQWTSLWNTYKDEFENETNMLGGSLGAKAA-EDLRQRIIEHNILVVSKYYSR-ITLKRLAEL 316 (394)
Q Consensus 242 p~~~~---L~k~f~~~eli~~~~~~~~~~~~l~~~~~~~~d~~~~~~~-~~L~~~viEHNI~visk~Y~~-Isl~rLa~l 316 (394)
|.++. +.+++.+. .|..+|.-... ...+...... ..+-.+++.+=+..+++-|.+ |+++.|+++
T Consensus 133 ~~i~~al~l~~a~~~g----------ny~~ff~l~~~-~~~~~l~~~l~~~~~~~iR~~al~~i~~ay~~~i~l~~l~~~ 201 (204)
T PF03399_consen 133 PYIQFALELCRALMEG----------NYVRFFRLYRS-KSAPYLFACLMERFFNRIRLRALQSISKAYRSSIPLSFLAEL 201 (204)
T ss_dssp HHHHHHHHHHHHH--T----------THHHHHHHHT--TTS-HHHHHHHGGGHHHHHHHHHHHHHHHS-T-EEHHHHHHH
T ss_pred HHHHHHHHHHHHHHcC----------CHHHHHHHHhc-cCCChHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence 55543 34455443 23333321100 0111111222 225678899999999999999 999999999
Q ss_pred hCC
Q 016147 317 LCL 319 (394)
Q Consensus 317 L~l 319 (394)
|+.
T Consensus 202 L~F 204 (204)
T PF03399_consen 202 LGF 204 (204)
T ss_dssp TT-
T ss_pred cCC
Confidence 974
No 93
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=63.12 E-value=16 Score=23.57 Aligned_cols=30 Identities=17% Similarity=0.264 Sum_probs=24.4
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHhHhcCcE
Q 016147 308 ITLKRLAELLCLSIQEAEKHLSDMVVSKAL 337 (394)
Q Consensus 308 Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l 337 (394)
+|-..+|..+|++++-+=+.++++-.+|-|
T Consensus 3 mtr~diA~~lG~t~ETVSR~l~~l~~~glI 32 (32)
T PF00325_consen 3 MTRQDIADYLGLTRETVSRILKKLERQGLI 32 (32)
T ss_dssp --HHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred cCHHHHHHHhCCcHHHHHHHHHHHHHcCCC
Confidence 567889999999999999999999888854
No 94
>PF13371 TPR_9: Tetratricopeptide repeat
Probab=63.04 E-value=24 Score=25.88 Aligned_cols=58 Identities=16% Similarity=0.075 Sum_probs=45.7
Q ss_pred HHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCcc
Q 016147 68 LAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPR 131 (394)
Q Consensus 68 La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~ 131 (394)
|+.+|...|++++|.+++..+-.-.. .-...++.-.+++...|+|..|.....++-..
T Consensus 1 l~~~~~~~~~~~~A~~~~~~~l~~~p------~~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~~ 58 (73)
T PF13371_consen 1 LKQIYLQQEDYEEALEVLERALELDP------DDPELWLQRARCLFQLGRYEEALEDLERALEL 58 (73)
T ss_pred CHHHHHhCCCHHHHHHHHHHHHHhCc------ccchhhHHHHHHHHHhccHHHHHHHHHHHHHH
Confidence 56789999999999998887543211 24566777899999999999999999988753
No 95
>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=62.61 E-value=40 Score=26.62 Aligned_cols=67 Identities=16% Similarity=0.040 Sum_probs=51.5
Q ss_pred HHHHHHHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCcc
Q 016147 62 ARLIKKLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPR 131 (394)
Q Consensus 62 a~l~~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~ 131 (394)
......+|.++.+.|++.+|.+.+..+.-...+. ....+.++...+++...+++..|..+.+++...
T Consensus 39 ~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~---~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~ 105 (119)
T TIGR02795 39 PNAHYWLGEAYYAQGKYADAAKAFLAVVKKYPKS---PKAPDALLKLGMSLQELGDKEKAKATLQQVIKR 105 (119)
T ss_pred HHHHHHHHHHHHhhccHHHHHHHHHHHHHHCCCC---CcccHHHHHHHHHHHHhCChHHHHHHHHHHHHH
Confidence 3456779999999999999999999866422111 123456777778888999999999999988765
No 96
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=62.34 E-value=24 Score=28.48 Aligned_cols=40 Identities=23% Similarity=0.249 Sum_probs=34.8
Q ss_pred cCcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEE---EEeccC
Q 016147 305 YSRITLKRLAELLCLSIQEAEKHLSDMVVSKALV---AKIDRP 344 (394)
Q Consensus 305 Y~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~---akIDq~ 344 (394)
-.++|++.||+.+|+|+..+-+.+.+|..+|-+. +.+|+.
T Consensus 15 ~~~~~~~~la~~l~~s~~tv~~~l~~L~~~g~i~~~~~~~~~~ 57 (108)
T smart00344 15 DARISLAELAKKVGLSPSTVHNRVKRLEEEGVIKGYTAVINPK 57 (108)
T ss_pred hCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeceEEEeCHH
Confidence 4689999999999999999999999999999765 556643
No 97
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=61.68 E-value=23 Score=24.10 Aligned_cols=34 Identities=24% Similarity=0.351 Sum_probs=30.8
Q ss_pred CcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEE
Q 016147 306 SRITLKRLAELLCLSIQEAEKHLSDMVVSKALVA 339 (394)
Q Consensus 306 ~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~a 339 (394)
..++...|++.|++|+.-+...+..|...|.|..
T Consensus 13 ~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~~ 46 (53)
T smart00420 13 GKVSVEELAELLGVSEMTIRRDLNKLEEQGLLTR 46 (53)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 3489999999999999999999999999988754
No 98
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=61.48 E-value=13 Score=32.49 Aligned_cols=38 Identities=13% Similarity=0.184 Sum_probs=34.9
Q ss_pred CcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEE---EEecc
Q 016147 306 SRITLKRLAELLCLSIQEAEKHLSDMVVSKALV---AKIDR 343 (394)
Q Consensus 306 ~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~---akIDq 343 (394)
.++|.+.||+.+|+|+..+-.-+.+|..+|-|. |-+|.
T Consensus 22 ~R~s~~eiA~~lglS~~tV~~Ri~rL~~~GvI~~~~~~v~~ 62 (153)
T PRK11179 22 ARTPYAELAKQFGVSPGTIHVRVEKMKQAGIITGTRVDVNP 62 (153)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeEEEEECH
Confidence 899999999999999999999999999999884 56774
No 99
>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=61.32 E-value=50 Score=28.18 Aligned_cols=53 Identities=13% Similarity=0.109 Sum_probs=40.4
Q ss_pred HHHHHHHhhcC--cccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEEeccCCCEE
Q 016147 296 HNILVVSKYYS--RITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKIDRPQGIV 348 (394)
Q Consensus 296 HNI~visk~Y~--~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~akIDq~~giV 348 (394)
|-+..++.... .+|.+.||+.+++|+..+++.+..|...|-+...=....|+.
T Consensus 12 ~~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~glv~s~~G~~Ggy~ 66 (135)
T TIGR02010 12 TAMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLRKAGLVKSVRGPGGGYQ 66 (135)
T ss_pred HHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEeCCCCCEe
Confidence 33444554433 499999999999999999999999999998876545445543
No 100
>PRK14574 hmsH outer membrane protein; Provisional
Probab=60.62 E-value=1.3e+02 Score=33.97 Aligned_cols=97 Identities=9% Similarity=-0.013 Sum_probs=70.9
Q ss_pred HHHHHHHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCccccCCCCcccc
Q 016147 62 ARLIKKLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPRVFDADPSKEK 141 (394)
Q Consensus 62 a~l~~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~~~~~~~~~~~ 141 (394)
.+....+|.++...|++.+|.++++.+.-.. +.. .+.++-.+.++...+.+..|...++++....-
T Consensus 102 ~~~llalA~ly~~~gdyd~Aiely~kaL~~d----P~n--~~~l~gLa~~y~~~~q~~eAl~~l~~l~~~dp-------- 167 (822)
T PRK14574 102 SRGLASAARAYRNEKRWDQALALWQSSLKKD----PTN--PDLISGMIMTQADAGRGGVVLKQATELAERDP-------- 167 (822)
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC----CCC--HHHHHHHHHHHhhcCCHHHHHHHHHHhcccCc--------
Confidence 4556677899999999999999999875321 122 34445668999999999999999999986421
Q ss_pred CCCCCCCcccccCCCCccchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhcc
Q 016147 142 KKPKEGDNVVEEAPADIPSLLELKRIYYELMIRYYSHNNDYLEICRCYKAIYEI 195 (394)
Q Consensus 142 ~~~~~~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~~~~flea~k~y~ei~~t 195 (394)
+ ..++...+..+...+++.+|...|.++...
T Consensus 168 ---------------------~--~~~~l~layL~~~~~~~~~AL~~~ekll~~ 198 (822)
T PRK14574 168 ---------------------T--VQNYMTLSYLNRATDRNYDALQASSEAVRL 198 (822)
T ss_pred ---------------------c--hHHHHHHHHHHHhcchHHHHHHHHHHHHHh
Confidence 1 333445555555577888899999999874
No 101
>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=60.19 E-value=30 Score=24.69 Aligned_cols=30 Identities=20% Similarity=0.210 Sum_probs=28.0
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHhHhcCcEE
Q 016147 309 TLKRLAELLCLSIQEAEKHLSDMVVSKALV 338 (394)
Q Consensus 309 sl~rLa~lL~ls~~e~E~~ls~MI~~g~l~ 338 (394)
+...||+.+|+|..-+-+.+..|...|-|.
T Consensus 27 ~~~~la~~~~is~~~v~~~l~~L~~~G~i~ 56 (66)
T cd07377 27 SERELAEELGVSRTTVREALRELEAEGLVE 56 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 489999999999999999999999999775
No 102
>KOG1129 consensus TPR repeat-containing protein [General function prediction only]
Probab=59.81 E-value=1.2e+02 Score=30.52 Aligned_cols=97 Identities=12% Similarity=0.075 Sum_probs=78.7
Q ss_pred HHHHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCccccCCCCccccCCC
Q 016147 65 IKKLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPRVFDADPSKEKKKP 144 (394)
Q Consensus 65 ~~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~~~~~~~~~~~~~~ 144 (394)
..++++.|..-|-..+|.+.|+. +++..+-.|.+|--.+.|-.-+.+.+|-..+.-.-..+ .
T Consensus 226 k~Q~gkCylrLgm~r~Aekqlqs-------sL~q~~~~dTfllLskvY~ridQP~~AL~~~~~gld~f-P---------- 287 (478)
T KOG1129|consen 226 KQQMGKCYLRLGMPRRAEKQLQS-------SLTQFPHPDTFLLLSKVYQRIDQPERALLVIGEGLDSF-P---------- 287 (478)
T ss_pred HHHHHHHHHHhcChhhhHHHHHH-------HhhcCCchhHHHHHHHHHHHhccHHHHHHHHhhhhhcC-C----------
Confidence 47899999999999999998884 66667778889999999999999999988766444332 1
Q ss_pred CCCCcccccCCCCccchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhccCCC
Q 016147 145 KEGDNVVEEAPADIPSLLELKRIYYELMIRYYSHNNDYLEICRCYKAIYEIPYI 198 (394)
Q Consensus 145 ~~~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~~~~flea~k~y~ei~~t~~i 198 (394)
.-..|.-.++|++.+-+++-++.+.|..+.....+
T Consensus 288 -------------------~~VT~l~g~ARi~eam~~~~~a~~lYk~vlk~~~~ 322 (478)
T KOG1129|consen 288 -------------------FDVTYLLGQARIHEAMEQQEDALQLYKLVLKLHPI 322 (478)
T ss_pred -------------------chhhhhhhhHHHHHHHHhHHHHHHHHHHHHhcCCc
Confidence 11567788999999999999999999999975443
No 103
>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=59.75 E-value=1.3e+02 Score=26.72 Aligned_cols=68 Identities=15% Similarity=0.117 Sum_probs=46.8
Q ss_pred CcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEE-EEe-ccCCCEEEEecCCChHHHHHHHHHHHHHHHHH
Q 016147 306 SRITLKRLAELLCLSIQEAEKHLSDMVVSKALV-AKI-DRPQGIVCFQVAKDSNDILNSWAMNLEKLLDL 373 (394)
Q Consensus 306 ~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~-akI-Dq~~giV~F~~~k~~~~~L~~W~~~I~~l~~~ 373 (394)
.-+|-+.||++||++..++-+.+..|...|-+. -+. |-..|-..+-..-+..++...-...+..+...
T Consensus 27 ~~~tdEeLa~~Lgi~~~~VRk~L~~L~e~~Lv~~~r~r~~~~gw~~Y~w~i~~~~i~d~Ik~~~~~~~~~ 96 (158)
T TIGR00373 27 GEFTDEEISLELGIKLNEVRKALYALYDAGLADYKRRKDDETGWYEYTWRINYEKALDVLKRKLEETAKK 96 (158)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCceeeeeeecCCCcEEEEEEeCHHHHHHHHHHHHHHHHHH
Confidence 348999999999999999999999999999873 222 33446666554334445555545444444443
No 104
>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=59.71 E-value=96 Score=30.11 Aligned_cols=99 Identities=12% Similarity=0.029 Sum_probs=71.3
Q ss_pred HHHHHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCccccCCCCccccCC
Q 016147 64 LIKKLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPRVFDADPSKEKKK 143 (394)
Q Consensus 64 l~~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~~~~~~~~~~~~~ 143 (394)
....+|.++...|++++|...+...- ..-+.. ...+.....++.+.|++..|..+..+.....-.
T Consensus 116 ~~~~~a~~~~~~G~~~~A~~~~~~al----~~~p~~--~~~~~~la~i~~~~g~~~eA~~~l~~~l~~~~~--------- 180 (355)
T cd05804 116 LLGMLAFGLEEAGQYDRAEEAARRAL----ELNPDD--AWAVHAVAHVLEMQGRFKEGIAFMESWRDTWDC--------- 180 (355)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHH----hhCCCC--cHHHHHHHHHHHHcCCHHHHHHHHHhhhhccCC---------
Confidence 44578889999999999999887632 111111 445666688999999999999999988753211
Q ss_pred CCCCCcccccCCCCccchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhc
Q 016147 144 PKEGDNVVEEAPADIPSLLELKRIYYELMIRYYSHNNDYLEICRCYKAIYE 194 (394)
Q Consensus 144 ~~~~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~~~~flea~k~y~ei~~ 194 (394)
..+.....+-..+.++...+++-+|-..|.+...
T Consensus 181 -----------------~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~~~~ 214 (355)
T cd05804 181 -----------------SSMLRGHNWWHLALFYLERGDYEAALAIYDTHIA 214 (355)
T ss_pred -----------------CcchhHHHHHHHHHHHHHCCCHHHHHHHHHHHhc
Confidence 1123334455677889999999999999988754
No 105
>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=59.62 E-value=20 Score=25.17 Aligned_cols=38 Identities=18% Similarity=0.203 Sum_probs=31.7
Q ss_pred HHhhcCcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEE
Q 016147 301 VSKYYSRITLKRLAELLCLSIQEAEKHLSDMVVSKALV 338 (394)
Q Consensus 301 isk~Y~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~ 338 (394)
++.-=..+++..||+.+|++..-+-.++..|+..|-+.
T Consensus 12 l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~~g~v~ 49 (52)
T PF09339_consen 12 LAESGGPLTLSEIARALGLPKSTVHRLLQTLVEEGYVE 49 (52)
T ss_dssp HHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCcCee
Confidence 44445568999999999999999999999999999764
No 106
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=59.47 E-value=78 Score=26.95 Aligned_cols=44 Identities=7% Similarity=-0.013 Sum_probs=37.7
Q ss_pred cccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEEeccCCCEEEE
Q 016147 307 RITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKIDRPQGIVCF 350 (394)
Q Consensus 307 ~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~akIDq~~giV~F 350 (394)
.+|.+.||+.++++..-+=..+.+|+..|-|.-.-|..++=+..
T Consensus 46 ~~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~r~~~~~DrR~~~ 89 (144)
T PRK03573 46 EQSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQTCASDRRAKR 89 (144)
T ss_pred CCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeeecCCCCcCeee
Confidence 47889999999999999999999999999998887766655433
No 107
>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=59.44 E-value=2.5e+02 Score=30.08 Aligned_cols=98 Identities=12% Similarity=0.068 Sum_probs=57.5
Q ss_pred HHHHHHHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCccccCCCCcccc
Q 016147 62 ARLIKKLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPRVFDADPSKEK 141 (394)
Q Consensus 62 a~l~~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~~~~~~~~~~~ 141 (394)
..+...+|.++...|++++|...+...-- +.+ .-...++....++...|++..|....+++-... |
T Consensus 399 ~~~~~~lg~~~~~~g~~~~A~~~~~kal~-----l~P-~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~----P---- 464 (615)
T TIGR00990 399 PDIYYHRAQLHFIKGEFAQAGKDYQKSID-----LDP-DFIFSHIQLGVTQYKEGSIASSMATFRRCKKNF----P---- 464 (615)
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHHHHH-----cCc-cCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC----C----
Confidence 34455666667777777777766654321 111 112334455666666777777777766665321 1
Q ss_pred CCCCCCCcccccCCCCccchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhcc
Q 016147 142 KKPKEGDNVVEEAPADIPSLLELKRIYYELMIRYYSHNNDYLEICRCYKAIYEI 195 (394)
Q Consensus 142 ~~~~~~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~~~~flea~k~y~ei~~t 195 (394)
... ..+...+..+...++|-+|-..|......
T Consensus 465 ------------------~~~----~~~~~lg~~~~~~g~~~~A~~~~~~Al~l 496 (615)
T TIGR00990 465 ------------------EAP----DVYNYYGELLLDQNKFDEAIEKFDTAIEL 496 (615)
T ss_pred ------------------CCh----HHHHHHHHHHHHccCHHHHHHHHHHHHhc
Confidence 111 12444566777788999999999887753
No 108
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=58.29 E-value=15 Score=25.08 Aligned_cols=26 Identities=27% Similarity=0.333 Sum_probs=21.1
Q ss_pred CcccHHHHHHHhCCCHHHHHHHHHHh
Q 016147 306 SRITLKRLAELLCLSIQEAEKHLSDM 331 (394)
Q Consensus 306 ~~Isl~rLa~lL~ls~~e~E~~ls~M 331 (394)
.+.++..||+.+|+|+..+-.-+.+|
T Consensus 16 ~r~s~~~la~~lglS~~~v~~Ri~rL 41 (42)
T PF13404_consen 16 GRRSYAELAEELGLSESTVRRRIRRL 41 (42)
T ss_dssp TTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCccHHHHHHHHCcCHHHHHHHHHHh
Confidence 89999999999999999988776655
No 109
>PLN03218 maturation of RBCL 1; Provisional
Probab=58.13 E-value=3.6e+02 Score=31.48 Aligned_cols=94 Identities=15% Similarity=0.169 Sum_probs=52.0
Q ss_pred HHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCccccCCCCccccCCCCCCC
Q 016147 69 AKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPRVFDADPSKEKKKPKEGD 148 (394)
Q Consensus 69 a~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~~~~~~~~~~~~~~~~~~ 148 (394)
...|.+.|++++|.+++.++..+..|-.++ ...+--.+..|...|++.+|..+..+....-+..
T Consensus 549 I~a~~k~G~~deA~~lf~eM~~~~~gi~PD---~vTynaLI~ay~k~G~ldeA~elf~~M~e~gi~p------------- 612 (1060)
T PLN03218 549 ISACGQSGAVDRAFDVLAEMKAETHPIDPD---HITVGALMKACANAGQVDRAKEVYQMIHEYNIKG------------- 612 (1060)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHhcCCCCCc---HHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCC-------------
Confidence 334444455555555555443321111111 1233344556667777777777776665432110
Q ss_pred cccccCCCCccchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhc
Q 016147 149 NVVEEAPADIPSLLELKRIYYELMIRYYSHNNDYLEICRCYKAIYE 194 (394)
Q Consensus 149 ~~~~~~~~~~~~~~d~klk~~~~~~~~~~~~~~flea~k~y~ei~~ 194 (394)
+ ...|..++..|...+++-+|.+.|.++..
T Consensus 613 ------------~----~~tynsLI~ay~k~G~~deAl~lf~eM~~ 642 (1060)
T PLN03218 613 ------------T----PEVYTIAVNSCSQKGDWDFALSIYDDMKK 642 (1060)
T ss_pred ------------C----hHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Confidence 0 13467777777788888888888888775
No 110
>KOG1155 consensus Anaphase-promoting complex (APC), Cdc23 subunit [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=58.06 E-value=89 Score=32.84 Aligned_cols=63 Identities=25% Similarity=0.285 Sum_probs=47.2
Q ss_pred HHHHHHHHHhcCHHHHHHHHHH-hhhhh-cccCcH-HHHHHHHHHHHHHHhccCChHHHHHHHHhhCc
Q 016147 66 KKLAKIKEEQGLIAEAADLMQE-VAVET-FGAMAK-TEKIAFILEQVRLCLDRQDYVRAQILSRKISP 130 (394)
Q Consensus 66 ~~La~i~e~~gd~~eAa~iL~~-i~vEt-~~~m~~-~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~ 130 (394)
..||++||+-+|.++||..... |.+++ -|..++ -.|...+| ++-+...+||.+|..|..+++.
T Consensus 470 ~~LakLye~l~d~~eAa~~yek~v~~~~~eg~~~~~t~ka~~fL--A~~f~k~~~~~~As~Ya~~~~~ 535 (559)
T KOG1155|consen 470 VRLAKLYEELKDLNEAAQYYEKYVEVSELEGEIDDETIKARLFL--AEYFKKMKDFDEASYYATLVLK 535 (559)
T ss_pred HHHHHHHHHHHhHHHHHHHHHHHHHHHHhhcccchHHHHHHHHH--HHHHHhhcchHHHHHHHHHHhc
Confidence 5799999999999999987653 23222 244443 56666664 5678889999999999998874
No 111
>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=58.00 E-value=24 Score=26.48 Aligned_cols=33 Identities=15% Similarity=0.206 Sum_probs=30.2
Q ss_pred CcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEE
Q 016147 306 SRITLKRLAELLCLSIQEAEKHLSDMVVSKALV 338 (394)
Q Consensus 306 ~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~ 338 (394)
-.+|-+.||.++|+|.+.+-+.+..|..+|-|.
T Consensus 27 ~~lt~~~iA~~~g~sr~tv~r~l~~l~~~g~I~ 59 (76)
T PF13545_consen 27 LPLTQEEIADMLGVSRETVSRILKRLKDEGIIE 59 (76)
T ss_dssp EESSHHHHHHHHTSCHHHHHHHHHHHHHTTSEE
T ss_pred ecCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 457899999999999999999999999999775
No 112
>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=57.00 E-value=67 Score=22.71 Aligned_cols=62 Identities=13% Similarity=-0.075 Sum_probs=46.6
Q ss_pred HHHHHHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCc
Q 016147 63 RLIKKLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISP 130 (394)
Q Consensus 63 ~l~~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~ 130 (394)
.+...+|.++...|++++|.+.+....-- . +... +.+...+.++...+|+..|..+..++..
T Consensus 35 ~~~~~~~~~~~~~~~~~~a~~~~~~~~~~-~---~~~~--~~~~~~~~~~~~~~~~~~a~~~~~~~~~ 96 (100)
T cd00189 35 DAYYNLAAAYYKLGKYEEALEDYEKALEL-D---PDNA--KAYYNLGLAYYKLGKYEEALEAYEKALE 96 (100)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhC-C---Ccch--hHHHHHHHHHHHHHhHHHHHHHHHHHHc
Confidence 44567888899999999999988764321 1 1111 6778888999999999999998887653
No 113
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=56.82 E-value=18 Score=30.98 Aligned_cols=70 Identities=27% Similarity=0.408 Sum_probs=52.1
Q ss_pred HHHHHHHHHHHHHHHHhhcCcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEEeccCCCE-EEEecCCChHHHHHHHHH
Q 016147 287 EDLRQRIIEHNILVVSKYYSRITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKIDRPQGI-VCFQVAKDSNDILNSWAM 365 (394)
Q Consensus 287 ~~L~~~viEHNI~visk~Y~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~akIDq~~gi-V~F~~~k~~~~~L~~W~~ 365 (394)
..+..+|+| +.+-=-++|+..|...+|+|-.-+..++.+||..|.|+- .|. =.|.+ +.+..+|.+
T Consensus 11 ~eLk~rIvE-----lVRe~GRiTi~ql~~~TGasR~Tvk~~lreLVa~G~l~~-----~G~~GvF~s----eqA~~dw~~ 76 (127)
T PF06163_consen 11 EELKARIVE-----LVREHGRITIKQLVAKTGASRNTVKRYLRELVARGDLYR-----HGRSGVFPS----EQARKDWDK 76 (127)
T ss_pred HHHHHHHHH-----HHHHcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCCeEe-----CCCcccccc----HHHHHHHHH
Confidence 344444444 334568999999999999999999999999999999864 122 23433 367889988
Q ss_pred HHHHH
Q 016147 366 NLEKL 370 (394)
Q Consensus 366 ~I~~l 370 (394)
.-.++
T Consensus 77 ~~~~~ 81 (127)
T PF06163_consen 77 ARKKL 81 (127)
T ss_pred hHHhh
Confidence 87766
No 114
>KOG2003 consensus TPR repeat-containing protein [General function prediction only]
Probab=56.13 E-value=1.5e+02 Score=31.22 Aligned_cols=112 Identities=15% Similarity=0.203 Sum_probs=0.0
Q ss_pred HHHHHHHHHH---HHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCccccCCCCc
Q 016147 62 ARLIKKLAKI---KEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPRVFDADPS 138 (394)
Q Consensus 62 a~l~~~La~i---~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~~~~~~~~ 138 (394)
+.++..|-.| +++.|++++|.+.+-.++. =-.--+++...++.+|=.-.|..+|-.++..++..+
T Consensus 521 asc~ealfniglt~e~~~~ldeald~f~klh~------il~nn~evl~qianiye~led~aqaie~~~q~~sli------ 588 (840)
T KOG2003|consen 521 ASCTEALFNIGLTAEALGNLDEALDCFLKLHA------ILLNNAEVLVQIANIYELLEDPAQAIELLMQANSLI------ 588 (840)
T ss_pred hHHHHHHHHhcccHHHhcCHHHHHHHHHHHHH------HHHhhHHHHHHHHHHHHHhhCHHHHHHHHHHhcccC------
Q ss_pred cccCCCCCCCcccccCCCCccchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhccCCCCCChhcHHHHH
Q 016147 139 KEKKKPKEGDNVVEEAPADIPSLLELKRIYYELMIRYYSHNNDYLEICRCYKAIYEIPYIKEDPAQWMPVL 209 (394)
Q Consensus 139 ~~~~~~~~~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~~~~flea~k~y~ei~~t~~i~~d~~~~~~~L 209 (394)
+.+... ..-.+.+|+.+++=-.|++||++.|..+...-..-+|+.++
T Consensus 589 --------------------p~dp~i----lskl~dlydqegdksqafq~~ydsyryfp~nie~iewl~ay 635 (840)
T KOG2003|consen 589 --------------------PNDPAI----LSKLADLYDQEGDKSQAFQCHYDSYRYFPCNIETIEWLAAY 635 (840)
T ss_pred --------------------CCCHHH----HHHHHHHhhcccchhhhhhhhhhcccccCcchHHHHHHHHH
No 115
>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=55.70 E-value=21 Score=30.09 Aligned_cols=36 Identities=17% Similarity=0.182 Sum_probs=32.9
Q ss_pred CcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEEe
Q 016147 306 SRITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKI 341 (394)
Q Consensus 306 ~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~akI 341 (394)
..+|...||+.+|+|+.-+.+.+..|...|-+.+.-
T Consensus 24 ~~~s~~eia~~l~is~~~v~~~l~~L~~~Gli~~~~ 59 (130)
T TIGR02944 24 QPYSAAEIAEQTGLNAPTVSKILKQLSLAGIVTSKR 59 (130)
T ss_pred CCccHHHHHHHHCcCHHHHHHHHHHHHHCCcEEecC
Confidence 458999999999999999999999999999997753
No 116
>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=55.62 E-value=27 Score=21.35 Aligned_cols=25 Identities=16% Similarity=0.122 Sum_probs=17.4
Q ss_pred HHHHHHHHHHHHhcCHHHHHHHHHH
Q 016147 63 RLIKKLAKIKEEQGLIAEAADLMQE 87 (394)
Q Consensus 63 ~l~~~La~i~e~~gd~~eAa~iL~~ 87 (394)
..-..+|.++...|++++|.+.++.
T Consensus 2 ~~~~~lg~~~~~~~~~~~A~~~~~~ 26 (34)
T PF07719_consen 2 EAWYYLGQAYYQLGNYEEAIEYFEK 26 (34)
T ss_dssp HHHHHHHHHHHHTT-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHH
Confidence 4456778888888888888876654
No 117
>PRK09954 putative kinase; Provisional
Probab=55.50 E-value=46 Score=33.12 Aligned_cols=47 Identities=15% Similarity=0.185 Sum_probs=40.7
Q ss_pred cCcccHHHHHHHhCCCHHHHHHHHHHhHhcCcE---EEEeccCCCEEEEe
Q 016147 305 YSRITLKRLAELLCLSIQEAEKHLSDMVVSKAL---VAKIDRPQGIVCFQ 351 (394)
Q Consensus 305 Y~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l---~akIDq~~giV~F~ 351 (394)
-.+||.+.||+.||+|...+-..+.+|..+|.+ -..+|+..+++.+.
T Consensus 15 ~~~~s~~~la~~l~~s~~~v~~~i~~L~~~g~i~~~~~~l~~~~~v~viG 64 (362)
T PRK09954 15 NPLIQQNEIADILQISRSRVAAHIMDLMRKGRIKGKGYILTEQEYCVVVG 64 (362)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCcCCcEEEEcCCccEEEEE
Confidence 358999999999999999999999999999977 35678888777664
No 118
>PRK10049 pgaA outer membrane protein PgaA; Provisional
Probab=54.89 E-value=2e+02 Score=31.95 Aligned_cols=98 Identities=8% Similarity=-0.050 Sum_probs=74.2
Q ss_pred HHHHHHHHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCccccCCCCccc
Q 016147 61 RARLIKKLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPRVFDADPSKE 140 (394)
Q Consensus 61 ra~l~~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~~~~~~~~~~ 140 (394)
.......+|.++...|++++|.+.|+++.-.. +.. .+.++..+.++...|++.+|...++++.... |
T Consensus 358 ~~~a~~~~a~~l~~~g~~~eA~~~l~~al~~~----P~n--~~l~~~lA~l~~~~g~~~~A~~~l~~al~l~----P--- 424 (765)
T PRK10049 358 WLQGQSLLSQVAKYSNDLPQAEMRARELAYNA----PGN--QGLRIDYASVLQARGWPRAAENELKKAEVLE----P--- 424 (765)
T ss_pred HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC----CCC--HHHHHHHHHHHHhcCCHHHHHHHHHHHHhhC----C---
Confidence 44566789999999999999999999875322 222 4688999999999999999999999998642 1
Q ss_pred cCCCCCCCcccccCCCCccchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhc
Q 016147 141 KKKPKEGDNVVEEAPADIPSLLELKRIYYELMIRYYSHNNDYLEICRCYKAIYE 194 (394)
Q Consensus 141 ~~~~~~~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~~~~flea~k~y~ei~~ 194 (394)
+. ..+.| ..+..+...++|-+|-..+..+..
T Consensus 425 -------------------d~--~~l~~--~~a~~al~~~~~~~A~~~~~~ll~ 455 (765)
T PRK10049 425 -------------------RN--INLEV--EQAWTALDLQEWRQMDVLTDDVVA 455 (765)
T ss_pred -------------------CC--hHHHH--HHHHHHHHhCCHHHHHHHHHHHHH
Confidence 11 22333 444567778889888888888886
No 119
>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=54.67 E-value=58 Score=27.26 Aligned_cols=52 Identities=17% Similarity=0.100 Sum_probs=39.6
Q ss_pred HHHHHHHHhhcC--cccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEEeccCCC
Q 016147 295 EHNILVVSKYYS--RITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKIDRPQG 346 (394)
Q Consensus 295 EHNI~visk~Y~--~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~akIDq~~g 346 (394)
-|-+..+++.-. .+|.+.||+.+|+|+..+.+.+..|+..|-|...-....|
T Consensus 11 l~~l~~la~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~~~gli~~~~g~~gg 64 (132)
T TIGR00738 11 LRALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLRRAGLVESVRGPGGG 64 (132)
T ss_pred HHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEEeccCCCCC
Confidence 344455555433 6999999999999999999999999999988764334344
No 120
>PLN03081 pentatricopeptide (PPR) repeat-containing protein; Provisional
Probab=54.55 E-value=2.4e+02 Score=30.79 Aligned_cols=24 Identities=13% Similarity=0.333 Sum_probs=19.0
Q ss_pred HHHHHHHHHhcCHHHHHHHHHHhh
Q 016147 66 KKLAKIKEEQGLIAEAADLMQEVA 89 (394)
Q Consensus 66 ~~La~i~e~~gd~~eAa~iL~~i~ 89 (394)
..|.+.|.+.|++++|.+++.+++
T Consensus 364 ~~Li~~y~k~G~~~~A~~vf~~m~ 387 (697)
T PLN03081 364 TALVDLYSKWGRMEDARNVFDRMP 387 (697)
T ss_pred HHHHHHHHHCCCHHHHHHHHHhCC
Confidence 457778888888888888887764
No 121
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=54.19 E-value=53 Score=24.11 Aligned_cols=34 Identities=18% Similarity=0.121 Sum_probs=29.8
Q ss_pred cCcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEE
Q 016147 305 YSRITLKRLAELLCLSIQEAEKHLSDMVVSKALV 338 (394)
Q Consensus 305 Y~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~ 338 (394)
=..++...||+.||+++.-+=..+.+|...|-+.
T Consensus 20 ~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~GlV~ 53 (60)
T PF01325_consen 20 GGPVRTKDIAERLGVSPPTVTEMLKRLAEKGLVE 53 (60)
T ss_dssp TSSBBHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred CCCccHHHHHHHHCCChHHHHHHHHHHHHCCCEE
Confidence 3679999999999999999999999999998664
No 122
>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=53.53 E-value=48 Score=22.90 Aligned_cols=31 Identities=26% Similarity=0.440 Sum_probs=25.2
Q ss_pred HhhcCcccHHHHHHHhCCCHHHHHHHHHHhH
Q 016147 302 SKYYSRITLKRLAELLCLSIQEAEKHLSDMV 332 (394)
Q Consensus 302 sk~Y~~Isl~rLa~lL~ls~~e~E~~ls~MI 332 (394)
-.||..-|++.+|+.+|+|..-+-....+.+
T Consensus 15 ~~y~~~~t~~eIa~~lg~s~~~V~~~~~~al 45 (50)
T PF04545_consen 15 LRYFEGLTLEEIAERLGISRSTVRRILKRAL 45 (50)
T ss_dssp HHHTST-SHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred HHhcCCCCHHHHHHHHCCcHHHHHHHHHHHH
Confidence 3569999999999999999998887766654
No 123
>PF11873 DUF3393: Domain of unknown function (DUF3393); InterPro: IPR024570 Membrane-bound lytic murein transglycosylase C (also known as murein hydrolase C), is a murein-degrading enzyme that may play a role in the recycling of muropeptides during cell elongation and/or cell division. This entry represents the N-terminal domain, whose function is currently not known.
Probab=53.45 E-value=11 Score=35.07 Aligned_cols=63 Identities=24% Similarity=0.276 Sum_probs=51.4
Q ss_pred HHHHHHHHHHHHhCCCChhchHhhhhhhcccCcCCChhHHHHHHHhcchhcccchhhHHHHHHhhh
Q 016147 206 MPVLRKICWYLVLAPHDPMQSSLLNSTLEDKNLSEIPNFRLLLKQLVTMEVIQWTSLWNTYKDEFE 271 (394)
Q Consensus 206 ~~~L~~av~~~ILap~~~~rs~ll~~l~~d~~l~~ip~~~~L~k~f~~~eli~~~~~~~~~~~~l~ 271 (394)
...|+.||+-++|.|.+|...|+... ++..++.-|++.-.+....+ .-|+|+--...|++.|-
T Consensus 110 ~~~Lk~AIv~TLL~~~Dp~~vDl~Sd--~~i~l~g~PFLygqVlD~~g-~~I~~~wRA~ryAdYLi 172 (204)
T PF11873_consen 110 KAHLKQAIVTTLLTPDDPSSVDLFSD--KDIPLSGEPFLYGQVLDQDG-QPIRWEWRANRYADYLI 172 (204)
T ss_pred HHHHHHHHHHHhcCCCCCccccCccC--CCCccCCCceehheeecCCC-CeEeeHhHHHHHHHHHH
Confidence 57799999999999999999988874 56678888988776766665 68899876778887764
No 124
>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional
Probab=52.95 E-value=1.7e+02 Score=29.33 Aligned_cols=94 Identities=14% Similarity=0.012 Sum_probs=68.0
Q ss_pred HHHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCccccCCCCccccCCCC
Q 016147 66 KKLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPRVFDADPSKEKKKPK 145 (394)
Q Consensus 66 ~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~~~~~~~~~~~~~~~ 145 (394)
...|.-....|++.+|...+...--... .-...++..+.+++..+++..|...+.++-... |
T Consensus 6 ~~~a~~a~~~~~~~~Ai~~~~~Al~~~P------~~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~----P-------- 67 (356)
T PLN03088 6 EDKAKEAFVDDDFALAVDLYTQAIDLDP------NNAELYADRAQANIKLGNFTEAVADANKAIELD----P-------- 67 (356)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHhCC------CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC----c--------
Confidence 3457778889999999998876432111 124577888999999999999999999986531 1
Q ss_pred CCCcccccCCCCccchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhcc
Q 016147 146 EGDNVVEEAPADIPSLLELKRIYYELMIRYYSHNNDYLEICRCYKAIYEI 195 (394)
Q Consensus 146 ~~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~~~~flea~k~y~ei~~t 195 (394)
.. ...|...+..+.+.++|-+|...|......
T Consensus 68 --------------~~----~~a~~~lg~~~~~lg~~~eA~~~~~~al~l 99 (356)
T PLN03088 68 --------------SL----AKAYLRKGTACMKLEEYQTAKAALEKGASL 99 (356)
T ss_pred --------------CC----HHHHHHHHHHHHHhCCHHHHHHHHHHHHHh
Confidence 11 122445567777889999999999988863
No 125
>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A.
Probab=52.68 E-value=30 Score=22.07 Aligned_cols=27 Identities=33% Similarity=0.448 Sum_probs=21.5
Q ss_pred HHHHHHHHHHHHHhcCHHHHHHHHHHh
Q 016147 62 ARLIKKLAKIKEEQGLIAEAADLMQEV 88 (394)
Q Consensus 62 a~l~~~La~i~e~~gd~~eAa~iL~~i 88 (394)
+.....||..|...|++++|.+++++.
T Consensus 2 a~~~~~la~~~~~~g~~~~A~~~~~~a 28 (42)
T PF13374_consen 2 ASALNNLANAYRAQGRYEEALELLEEA 28 (42)
T ss_dssp HHHHHHHHHHHHHCT-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhhhhcchhhHHHHHH
Confidence 445678999999999999999988764
No 126
>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B.
Probab=52.29 E-value=72 Score=22.70 Aligned_cols=59 Identities=19% Similarity=0.154 Sum_probs=43.8
Q ss_pred HHHHHHHhccCChHHHHHHHHhhCccccCCCCccccCCCCCCCcccccCCCCccchHHHHHHHHHHHHHHHHhhhhHHHH
Q 016147 106 LEQVRLCLDRQDYVRAQILSRKISPRVFDADPSKEKKKPKEGDNVVEEAPADIPSLLELKRIYYELMIRYYSHNNDYLEI 185 (394)
Q Consensus 106 Leq~rL~L~~~D~~~a~~~~~Ki~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~~~~flea 185 (394)
+..++.++..|||..|....+++-... | +. ...+...+..+...++|-+|
T Consensus 1 ~~~a~~~~~~g~~~~A~~~~~~~l~~~----P----------------------~~----~~a~~~lg~~~~~~g~~~~A 50 (65)
T PF13432_consen 1 YALARALYQQGDYDEAIAAFEQALKQD----P----------------------DN----PEAWYLLGRILYQQGRYDEA 50 (65)
T ss_dssp HHHHHHHHHCTHHHHHHHHHHHHHCCS----T----------------------TH----HHHHHHHHHHHHHTT-HHHH
T ss_pred ChHHHHHHHcCCHHHHHHHHHHHHHHC----C----------------------CC----HHHHHHHHHHHHHcCCHHHH
Confidence 356788999999999999999988642 1 11 23345556777789999999
Q ss_pred HHHHHHHhc
Q 016147 186 CRCYKAIYE 194 (394)
Q Consensus 186 ~k~y~ei~~ 194 (394)
...|..+..
T Consensus 51 ~~~~~~a~~ 59 (65)
T PF13432_consen 51 LAYYERALE 59 (65)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHHHHH
Confidence 998888764
No 127
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=52.13 E-value=2.7e+02 Score=28.15 Aligned_cols=88 Identities=13% Similarity=0.129 Sum_probs=66.4
Q ss_pred ccCCCChHHHHHHHHHhhhhcCCcchHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHH
Q 016147 31 IDQTPDLDTRIELIKTLNSVSAGKIYVEIERARLIKKLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVR 110 (394)
Q Consensus 31 ~~~~~d~~~k~~~i~~L~~vt~gki~~E~era~l~~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~r 110 (394)
|+.-||+.+. .+++.+ .+.+-.||. -..|+++|.+.|+.+.|.++=|.+- ....++..+|+-...+-.|
T Consensus 47 Ls~Q~dKAvd-lF~e~l---~~d~~t~e~-----~ltLGnLfRsRGEvDRAIRiHQ~L~--~spdlT~~qr~lAl~qL~~ 115 (389)
T COG2956 47 LSNQPDKAVD-LFLEML---QEDPETFEA-----HLTLGNLFRSRGEVDRAIRIHQTLL--ESPDLTFEQRLLALQQLGR 115 (389)
T ss_pred hhcCcchHHH-HHHHHH---hcCchhhHH-----HHHHHHHHHhcchHHHHHHHHHHHh--cCCCCchHHHHHHHHHHHH
Confidence 3555665432 233333 355655564 4679999999999999999999865 2346899999999999999
Q ss_pred HHhccCChHHHHHHHHhhC
Q 016147 111 LCLDRQDYVRAQILSRKIS 129 (394)
Q Consensus 111 L~L~~~D~~~a~~~~~Ki~ 129 (394)
=|+..|=++||+.+.+-.-
T Consensus 116 Dym~aGl~DRAE~~f~~L~ 134 (389)
T COG2956 116 DYMAAGLLDRAEDIFNQLV 134 (389)
T ss_pred HHHHhhhhhHHHHHHHHHh
Confidence 9999999999999876443
No 128
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=51.44 E-value=71 Score=28.50 Aligned_cols=42 Identities=14% Similarity=0.147 Sum_probs=36.6
Q ss_pred cccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEEeccCCCEE
Q 016147 307 RITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKIDRPQGIV 348 (394)
Q Consensus 307 ~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~akIDq~~giV 348 (394)
.+|.+.||+.+|+|+..+++++..|...|-+.+.=....|+.
T Consensus 25 ~vs~~eIA~~~~ip~~~l~kIl~~L~~aGLv~s~rG~~GGy~ 66 (164)
T PRK10857 25 PVPLADISERQGISLSYLEQLFSRLRKNGLVSSVRGPGGGYL 66 (164)
T ss_pred cCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeCCCCCCCee
Confidence 599999999999999999999999999999887555555543
No 129
>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=51.25 E-value=22 Score=25.59 Aligned_cols=30 Identities=23% Similarity=0.234 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHHHhcCHHHHHHHHHHhhhh
Q 016147 62 ARLIKKLAKIKEEQGLIAEAADLMQEVAVE 91 (394)
Q Consensus 62 a~l~~~La~i~e~~gd~~eAa~iL~~i~vE 91 (394)
..++..||.+|.+.|++++|..+|..+.-.
T Consensus 25 ~~~~~~la~~~~~~g~~~~A~~~l~~~~~~ 54 (68)
T PF14559_consen 25 PEARLLLAQCYLKQGQYDEAEELLERLLKQ 54 (68)
T ss_dssp HHHHHHHHHHHHHTT-HHHHHHHHHCCHGG
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence 456678999999999999999999987653
No 130
>PRK15359 type III secretion system chaperone protein SscB; Provisional
Probab=51.01 E-value=1.6e+02 Score=25.18 Aligned_cols=92 Identities=5% Similarity=-0.177 Sum_probs=68.1
Q ss_pred HHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCccccCCCCccccCCCCC
Q 016147 67 KLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPRVFDADPSKEKKKPKE 146 (394)
Q Consensus 67 ~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~~~~~~~~~~~~~~~~ 146 (394)
.+|..+...|++++|...+...--- + -.-.+++..-..++...|++..|....+++.... |.
T Consensus 29 ~~g~~~~~~g~~~~A~~~~~~al~~-----~-P~~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l~----p~-------- 90 (144)
T PRK15359 29 ASGYASWQEGDYSRAVIDFSWLVMA-----Q-PWSWRAHIALAGTWMMLKEYTTAINFYGHALMLD----AS-------- 90 (144)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHc-----C-CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC----CC--------
Confidence 4688899999999999987764321 1 1246788888999999999999999999998642 11
Q ss_pred CCcccccCCCCccchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhc
Q 016147 147 GDNVVEEAPADIPSLLELKRIYYELMIRYYSHNNDYLEICRCYKAIYE 194 (394)
Q Consensus 147 ~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~~~~flea~k~y~ei~~ 194 (394)
.. ..+...+..+...+++-+|...|.....
T Consensus 91 --------------~~----~a~~~lg~~l~~~g~~~eAi~~~~~Al~ 120 (144)
T PRK15359 91 --------------HP----EPVYQTGVCLKMMGEPGLAREAFQTAIK 120 (144)
T ss_pred --------------Cc----HHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence 11 1234455666778999999999988875
No 131
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=50.75 E-value=72 Score=27.96 Aligned_cols=57 Identities=16% Similarity=0.072 Sum_probs=45.5
Q ss_pred HHHHHHHHHHhhcC--cccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEEeccCCCEEE
Q 016147 293 IIEHNILVVSKYYS--RITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKIDRPQGIVC 349 (394)
Q Consensus 293 viEHNI~visk~Y~--~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~akIDq~~giV~ 349 (394)
+.-|-+..++.-.. -+|.+.+|+..|+|+..++++++.|...|-+...==...|+.-
T Consensus 9 yal~~L~~LA~~~~~~~~s~~~IA~~~~is~~~L~kil~~L~kaGlV~S~rG~~GGy~L 67 (150)
T COG1959 9 YALRALLYLALLPGGGPVSSAEIAERQGISPSYLEKILSKLRKAGLVKSVRGKGGGYRL 67 (150)
T ss_pred HHHHHHHHHHhCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHHcCCEEeecCCCCCccC
Confidence 34566666776555 6889999999999999999999999999998876655555543
No 132
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=49.70 E-value=1.3e+02 Score=27.27 Aligned_cols=66 Identities=11% Similarity=0.077 Sum_probs=44.9
Q ss_pred CcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEEecc--CCCEEEEecCCChHHHHHHHHHHHHHHH
Q 016147 306 SRITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKIDR--PQGIVCFQVAKDSNDILNSWAMNLEKLL 371 (394)
Q Consensus 306 ~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~akIDq--~~giV~F~~~k~~~~~L~~W~~~I~~l~ 371 (394)
.-+|-+.||..||++..++-+.|..|-.+|-+..+-=+ ..|-.++-+.-+...+...-...+..+.
T Consensus 35 g~~tdeeLA~~Lgi~~~~VRk~L~~L~e~gLv~~~r~r~~~~Gr~~y~w~l~~~~i~d~ik~~~~~~~ 102 (178)
T PRK06266 35 GEVTDEEIAEQTGIKLNTVRKILYKLYDARLADYKREKDEETNWYTYTWKPELEKLPEIIKKKKMEEL 102 (178)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEeeeeccCCCcEEEEEEeCHHHHHHHHHHHHHHHH
Confidence 35899999999999999999999999999988643322 3455666544444444433333343333
No 133
>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=49.54 E-value=29 Score=24.38 Aligned_cols=28 Identities=29% Similarity=0.286 Sum_probs=26.1
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHhHhcC
Q 016147 308 ITLKRLAELLCLSIQEAEKHLSDMVVSK 335 (394)
Q Consensus 308 Isl~rLa~lL~ls~~e~E~~ls~MI~~g 335 (394)
||.+.||+.||+|..-+.+.+..+-..|
T Consensus 16 it~~eLa~~l~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 16 ITAKELAEELGVSRRTIRRDIKELREWG 43 (55)
T ss_dssp BEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred cCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 9999999999999999999999998888
No 134
>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=49.27 E-value=80 Score=25.29 Aligned_cols=46 Identities=22% Similarity=0.257 Sum_probs=37.5
Q ss_pred hcCcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEEeccCCCEEEEe
Q 016147 304 YYSRITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKIDRPQGIVCFQ 351 (394)
Q Consensus 304 ~Y~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~akIDq~~giV~F~ 351 (394)
.-..+|-+.||+++|++.+-+-+.|.+|...|-|.- ++..|.|.-.
T Consensus 44 ~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~GlI~r--~~~~~~~~~n 89 (95)
T TIGR01610 44 KQDRVTATVIAELTGLSRTHVSDAIKSLARRRIIFR--QGMMGIVGVN 89 (95)
T ss_pred cCCccCHHHHHHHHCcCHHHHHHHHHHHHHCCCeee--ecCCceeecC
Confidence 567899999999999999999999999999998862 3334555444
No 135
>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=49.23 E-value=47 Score=27.30 Aligned_cols=64 Identities=14% Similarity=-0.061 Sum_probs=50.1
Q ss_pred HHHHHHHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCcc
Q 016147 62 ARLIKKLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPR 131 (394)
Q Consensus 62 a~l~~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~ 131 (394)
......+|..+...|++++|.+.+....- +. ..-.+++.....++...||+.+|..+.+++...
T Consensus 51 ~~~~~~la~~~~~~~~~~~A~~~~~~~~~-----~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~ 114 (135)
T TIGR02552 51 SRYWLGLAACCQMLKEYEEAIDAYALAAA-----LD-PDDPRPYFHAAECLLALGEPESALKALDLAIEI 114 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHh-----cC-CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence 45667899999999999999998886431 11 123566677788999999999999999988865
No 136
>PLN03081 pentatricopeptide (PPR) repeat-containing protein; Provisional
Probab=49.06 E-value=3e+02 Score=30.03 Aligned_cols=91 Identities=12% Similarity=0.260 Sum_probs=67.0
Q ss_pred HHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCccccCCCCccccCCCCC
Q 016147 67 KLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPRVFDADPSKEKKKPKE 146 (394)
Q Consensus 67 ~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~~~~~~~~~~~~~~~~ 146 (394)
.+.+.|...|++++|.+++.+.+.+. -...|--.+..|-..+++..|+...++.... +|..
T Consensus 467 ~li~~l~r~G~~~eA~~~~~~~~~~p--------~~~~~~~Ll~a~~~~g~~~~a~~~~~~l~~~----~p~~------- 527 (697)
T PLN03081 467 CMIELLGREGLLDEAYAMIRRAPFKP--------TVNMWAALLTACRIHKNLELGRLAAEKLYGM----GPEK------- 527 (697)
T ss_pred hHHHHHHhcCCHHHHHHHHHHCCCCC--------CHHHHHHHHHHHHHcCCcHHHHHHHHHHhCC----CCCC-------
Confidence 46678899999999999988755321 1234667778888999999999988887532 1110
Q ss_pred CCcccccCCCCccchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhcc
Q 016147 147 GDNVVEEAPADIPSLLELKRIYYELMIRYYSHNNDYLEICRCYKAIYEI 195 (394)
Q Consensus 147 ~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~~~~flea~k~y~ei~~t 195 (394)
...|.+++..|...+++-+|.+.+.++-..
T Consensus 528 -------------------~~~y~~L~~~y~~~G~~~~A~~v~~~m~~~ 557 (697)
T PLN03081 528 -------------------LNNYVVLLNLYNSSGRQAEAAKVVETLKRK 557 (697)
T ss_pred -------------------CcchHHHHHHHHhCCCHHHHHHHHHHHHHc
Confidence 123678888899999999999999877753
No 137
>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=48.81 E-value=1.4e+02 Score=25.01 Aligned_cols=72 Identities=17% Similarity=0.039 Sum_probs=51.8
Q ss_pred hHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCcccc
Q 016147 56 YVEIERARLIKKLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPRVF 133 (394)
Q Consensus 56 ~~E~era~l~~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~~~ 133 (394)
+++.....+...++..+...|++++|...++.+--. -+-.| +.+..-|+.+...|+...|.....+......
T Consensus 56 ~l~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~l~~----dP~~E--~~~~~lm~~~~~~g~~~~A~~~Y~~~~~~l~ 127 (146)
T PF03704_consen 56 RLRELYLDALERLAEALLEAGDYEEALRLLQRALAL----DPYDE--EAYRLLMRALAAQGRRAEALRVYERYRRRLR 127 (146)
T ss_dssp HHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH----STT-H--HHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHhccCHHHHHHHHHHHHhc----CCCCH--HHHHHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 344555566678888899999999999988874421 12222 4566779999999999999999999887543
No 138
>PF13429 TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2_B.
Probab=48.79 E-value=18 Score=34.41 Aligned_cols=60 Identities=17% Similarity=0.205 Sum_probs=0.0
Q ss_pred HHHHHHHHHhcCHHHHHHHHHH-hhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCc
Q 016147 66 KKLAKIKEEQGLIAEAADLMQE-VAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISP 130 (394)
Q Consensus 66 ~~La~i~e~~gd~~eAa~iL~~-i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~ 130 (394)
..+|.++...|++++|.++|.. +. ...+..-.+|+.-.+.|+-..+|+..|...+.++-.
T Consensus 12 l~~A~~~~~~~~~~~Al~~L~~~~~-----~~~~~~~~~~~~~~a~La~~~~~~~~A~~ay~~l~~ 72 (280)
T PF13429_consen 12 LRLARLLYQRGDYEKALEVLKKAAQ-----KIAPPDDPEYWRLLADLAWSLGDYDEAIEAYEKLLA 72 (280)
T ss_dssp ------------------------------------------------------------------
T ss_pred ccccccccccccccccccccccccc-----cccccccccccccccccccccccccccccccccccc
Confidence 4679999999999999999953 22 221223337887788999999999999999888754
No 139
>PRK10747 putative protoheme IX biogenesis protein; Provisional
Probab=48.78 E-value=2e+02 Score=29.04 Aligned_cols=100 Identities=11% Similarity=0.071 Sum_probs=70.8
Q ss_pred HHHHHHHHHHHhcCHHHHHHHHHHhhhhhc--------ccC--cHHHH---------------HHHHHHHHHHHhccCCh
Q 016147 64 LIKKLAKIKEEQGLIAEAADLMQEVAVETF--------GAM--AKTEK---------------IAFILEQVRLCLDRQDY 118 (394)
Q Consensus 64 l~~~La~i~e~~gd~~eAa~iL~~i~vEt~--------~~m--~~~eK---------------~e~~Leq~rL~L~~~D~ 118 (394)
+...+|..+...|+.++|.++|.+..-... +.+ ++..+ .+..+-..|+|+..++|
T Consensus 265 ~~~~~A~~l~~~g~~~~A~~~L~~~l~~~~~~~l~~l~~~l~~~~~~~al~~~e~~lk~~P~~~~l~l~lgrl~~~~~~~ 344 (398)
T PRK10747 265 LQVAMAEHLIECDDHDTAQQIILDGLKRQYDERLVLLIPRLKTNNPEQLEKVLRQQIKQHGDTPLLWSTLGQLLMKHGEW 344 (398)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCHHHHHHHhhccCCChHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHCCCH
Confidence 455678889999999999999987543221 111 22122 33455669999999999
Q ss_pred HHHHHHHHhhCccccCCCCccccCCCCCCCcccccCCCCccchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhc
Q 016147 119 VRAQILSRKISPRVFDADPSKEKKKPKEGDNVVEEAPADIPSLLELKRIYYELMIRYYSHNNDYLEICRCYKAIYE 194 (394)
Q Consensus 119 ~~a~~~~~Ki~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~~~~flea~k~y~ei~~ 194 (394)
.+|+.+..++-.. .| +..+ +..+++.+.+.++--+|+.+|.+...
T Consensus 345 ~~A~~~le~al~~----~P----------------------~~~~-----~~~La~~~~~~g~~~~A~~~~~~~l~ 389 (398)
T PRK10747 345 QEASLAFRAALKQ----RP----------------------DAYD-----YAWLADALDRLHKPEEAAAMRRDGLM 389 (398)
T ss_pred HHHHHHHHHHHhc----CC----------------------CHHH-----HHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence 9999999988753 11 1122 34677888999999999999987754
No 140
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=47.83 E-value=50 Score=27.74 Aligned_cols=33 Identities=33% Similarity=0.299 Sum_probs=30.7
Q ss_pred cCcccHHHHHHHhCCCHHHHHHHHHHhHhcCcE
Q 016147 305 YSRITLKRLAELLCLSIQEAEKHLSDMVVSKAL 337 (394)
Q Consensus 305 Y~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l 337 (394)
-..+|++.||..|..|+-.+-..|.+|...|=|
T Consensus 17 ~~~vtl~elA~~l~cS~Rn~r~lLkkm~~~gWi 49 (115)
T PF12793_consen 17 PVEVTLDELAELLFCSRRNARTLLKKMQEEGWI 49 (115)
T ss_pred CcceeHHHHHHHhCCCHHHHHHHHHHHHHCCCe
Confidence 457899999999999999999999999999977
No 141
>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=47.65 E-value=3.9e+02 Score=28.78 Aligned_cols=100 Identities=13% Similarity=0.013 Sum_probs=65.2
Q ss_pred HHHHHHHHHHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCccccCCCCc
Q 016147 59 IERARLIKKLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPRVFDADPS 138 (394)
Q Consensus 59 ~era~l~~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~~~~~~~~ 138 (394)
.+.+.+...++..+...|++++|.+.+..+.-.... -.+.++..+++++..+++..|.....++... .|
T Consensus 122 ~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~------~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~----~~- 190 (899)
T TIGR02917 122 EGAAELLALRGLAYLGLGQLELAQKSYEQALAIDPR------SLYAKLGLAQLALAENRFDEARALIDEVLTA----DP- 190 (899)
T ss_pred hhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCC------ChhhHHHHHHHHHHCCCHHHHHHHHHHHHHh----CC-
Confidence 344566667777777778888887777764311111 1345667778888888888888888776432 11
Q ss_pred cccCCCCCCCcccccCCCCccchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhc
Q 016147 139 KEKKKPKEGDNVVEEAPADIPSLLELKRIYYELMIRYYSHNNDYLEICRCYKAIYE 194 (394)
Q Consensus 139 ~~~~~~~~~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~~~~flea~k~y~ei~~ 194 (394)
.. ...+...+.++...++|-+|...|..+..
T Consensus 191 ---------------------~~----~~~~~~~~~~~~~~g~~~~A~~~~~~a~~ 221 (899)
T TIGR02917 191 ---------------------GN----VDALLLKGDLLLSLGNIELALAAYRKAIA 221 (899)
T ss_pred ---------------------CC----hHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Confidence 11 12344456777788899999999988875
No 142
>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=47.41 E-value=62 Score=23.30 Aligned_cols=64 Identities=16% Similarity=0.081 Sum_probs=46.0
Q ss_pred HHHHHHHHHHHHhccCChHHHHHHHHhhCccccCCCCccccCCCCCCCcccccCCCCccchHHHHHHHHHHHHHHHHhhh
Q 016147 101 KIAFILEQVRLCLDRQDYVRAQILSRKISPRVFDADPSKEKKKPKEGDNVVEEAPADIPSLLELKRIYYELMIRYYSHNN 180 (394)
Q Consensus 101 K~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~~~ 180 (394)
..+.+......++..+||..|..+..++-... | +.. ..+..++..+...+
T Consensus 2 ~a~~~~~~g~~~~~~~~~~~A~~~~~~ai~~~----p----------------------~~~----~~~~~~g~~~~~~~ 51 (69)
T PF13414_consen 2 NAEAWYNLGQIYFQQGDYEEAIEYFEKAIELD----P----------------------NNA----EAYYNLGLAYMKLG 51 (69)
T ss_dssp SHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHS----T----------------------THH----HHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC----C----------------------CCH----HHHHHHHHHHHHhC
Confidence 35678888999999999999999999988641 1 111 23445556666666
Q ss_pred -hHHHHHHHHHHHhc
Q 016147 181 -DYLEICRCYKAIYE 194 (394)
Q Consensus 181 -~flea~k~y~ei~~ 194 (394)
+|-+|-+.|..+..
T Consensus 52 ~~~~~A~~~~~~al~ 66 (69)
T PF13414_consen 52 KDYEEAIEDFEKALK 66 (69)
T ss_dssp THHHHHHHHHHHHHH
T ss_pred ccHHHHHHHHHHHHH
Confidence 78888888876654
No 143
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=47.39 E-value=53 Score=29.02 Aligned_cols=42 Identities=14% Similarity=0.094 Sum_probs=36.7
Q ss_pred HhhcCcccHHHHHHHhCCCHHHHHHHHHHhHhcCcE---EEEecc
Q 016147 302 SKYYSRITLKRLAELLCLSIQEAEKHLSDMVVSKAL---VAKIDR 343 (394)
Q Consensus 302 sk~Y~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l---~akIDq 343 (394)
-+-=.++|...||+.+|+|+.-+-.-+.+|..+|-| .|.+|.
T Consensus 23 Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~GvI~~~~~~v~p 67 (164)
T PRK11169 23 LQKDGRISNVELSKRVGLSPTPCLERVRRLERQGFIQGYTALLNP 67 (164)
T ss_pred hccCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEEEECH
Confidence 345779999999999999999999999999999987 466773
No 144
>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=47.14 E-value=74 Score=23.02 Aligned_cols=48 Identities=15% Similarity=0.091 Sum_probs=34.8
Q ss_pred hhcCcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEE---eccCCCEEEE
Q 016147 303 KYYSRITLKRLAELLCLSIQEAEKHLSDMVVSKALVAK---IDRPQGIVCF 350 (394)
Q Consensus 303 k~Y~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~ak---IDq~~giV~F 350 (394)
.-...++...|++.++++...+-..+.+|+..|-+.=. -|+...++.+
T Consensus 14 ~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv~~~~~~~d~R~~~~~L 64 (68)
T PF13463_consen 14 HSDGPMTQSDLAERLGISKSTVSRIIKKLEEKGLVEKERDPHDKRSKRYRL 64 (68)
T ss_dssp --TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEESSCTTSEEEEE
T ss_pred ccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEecCCCCcCCeeEEEe
Confidence 45788999999999999999999999999999988433 3444444544
No 145
>KOG1128 consensus Uncharacterized conserved protein, contains TPR repeats [General function prediction only]
Probab=47.09 E-value=1e+02 Score=34.04 Aligned_cols=139 Identities=14% Similarity=0.101 Sum_probs=84.7
Q ss_pred HHHHHHHHHHHHHHHhcCHHHHHHHHHHhh-----hhhcccCcHHHHHHHHHHH-------HHHHhccCChHHHHHHHHh
Q 016147 60 ERARLIKKLAKIKEEQGLIAEAADLMQEVA-----VETFGAMAKTEKIAFILEQ-------VRLCLDRQDYVRAQILSRK 127 (394)
Q Consensus 60 era~l~~~La~i~e~~gd~~eAa~iL~~i~-----vEt~~~m~~~eK~e~~Leq-------~rL~L~~~D~~~a~~~~~K 127 (394)
++.++.+.||.++-+.|=..+|..+...+. ++||..+....|.+-++.| .|+|-..||...=..+..|
T Consensus 396 p~Wq~q~~laell~slGitksAl~I~Erlemw~~vi~CY~~lg~~~kaeei~~q~lek~~d~~lyc~LGDv~~d~s~yEk 475 (777)
T KOG1128|consen 396 PIWQLQRLLAELLLSLGITKSALVIFERLEMWDPVILCYLLLGQHGKAEEINRQELEKDPDPRLYCLLGDVLHDPSLYEK 475 (777)
T ss_pred CcchHHHHHHHHHHHcchHHHHHHHHHhHHHHHHHHHHHHHhcccchHHHHHHHHhcCCCcchhHHHhhhhccChHHHHH
Confidence 567888999999999999999998887665 3566667788888888887 6677777775544444444
Q ss_pred hCccccCCCCccccCCCCCCCcccccCCCCccchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhccCCCCCCh-----
Q 016147 128 ISPRVFDADPSKEKKKPKEGDNVVEEAPADIPSLLELKRIYYELMIRYYSHNNDYLEICRCYKAIYEIPYIKEDP----- 202 (394)
Q Consensus 128 i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~~~~flea~k~y~ei~~t~~i~~d~----- 202 (394)
+...+- ..-.|-++| .+.....+++|-++-+++.........+.+.
T Consensus 476 awElsn---------------------------~~sarA~r~--~~~~~~~~~~fs~~~~hle~sl~~nplq~~~wf~~G 526 (777)
T KOG1128|consen 476 AWELSN---------------------------YISARAQRS--LALLILSNKDFSEADKHLERSLEINPLQLGTWFGLG 526 (777)
T ss_pred HHHHhh---------------------------hhhHHHHHh--hccccccchhHHHHHHHHHHHhhcCccchhHHHhcc
Confidence 432210 000111111 1111233567777777777666544332211
Q ss_pred ------hcHHHHHHHHHHHHHhCCCChhchH
Q 016147 203 ------AQWMPVLRKICWYLVLAPHDPMQSS 227 (394)
Q Consensus 203 ------~~~~~~L~~av~~~ILap~~~~rs~ 227 (394)
.++..+.+.+-.|+=|.|.+.+-..
T Consensus 527 ~~ALqlek~q~av~aF~rcvtL~Pd~~eaWn 557 (777)
T KOG1128|consen 527 CAALQLEKEQAAVKAFHRCVTLEPDNAEAWN 557 (777)
T ss_pred HHHHHHhhhHHHHHHHHHHhhcCCCchhhhh
Confidence 2455666777778888887655433
No 146
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=47.01 E-value=1.7e+02 Score=24.57 Aligned_cols=70 Identities=16% Similarity=0.208 Sum_probs=49.2
Q ss_pred cccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEEeccCCCEEEEecCCChHHHHH-----HHHHHHHHHHHHHHHHH
Q 016147 307 RITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKIDRPQGIVCFQVAKDSNDILN-----SWAMNLEKLLDLVEKSC 378 (394)
Q Consensus 307 ~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~akIDq~~giV~F~~~k~~~~~L~-----~W~~~I~~l~~~V~k~~ 378 (394)
..+...|++.+|+|..-+-..+..|...|-+..+-+-.. +.|.-..+..+.+. .|....+.+-..+++++
T Consensus 30 ~~~v~ela~~l~lsqstvS~HL~~L~~AGLV~~~r~Gr~--~~Y~l~~~~~~~~~~~~~~~w~~~~~~l~~~l~~l~ 104 (117)
T PRK10141 30 ELCVCDLCTALDQSQPKISRHLALLRESGLLLDRKQGKW--VHYRLSPHIPAWAAKIIEQAWLCEQEDVQAIVRNLA 104 (117)
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEEEcCE--EEEEECchHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 578889999999999999999999999999988766443 33433222222222 47766666666666553
No 147
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=46.92 E-value=67 Score=23.21 Aligned_cols=30 Identities=40% Similarity=0.553 Sum_probs=24.6
Q ss_pred hhcC---cccHHHHHHHhCCCHHHHHHHHHHhH
Q 016147 303 KYYS---RITLKRLAELLCLSIQEAEKHLSDMV 332 (394)
Q Consensus 303 k~Y~---~Isl~rLa~lL~ls~~e~E~~ls~MI 332 (394)
-||. .+|++.||+.||+|..-+...|.+..
T Consensus 16 GYfd~PR~~tl~elA~~lgis~st~~~~LRrae 48 (53)
T PF04967_consen 16 GYFDVPRRITLEELAEELGISKSTVSEHLRRAE 48 (53)
T ss_pred CCCCCCCcCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 3666 89999999999999988877776543
No 148
>PRK11447 cellulose synthase subunit BcsC; Provisional
Probab=46.67 E-value=3.3e+02 Score=31.83 Aligned_cols=116 Identities=13% Similarity=0.033 Sum_probs=73.5
Q ss_pred HHHHHHhhhchhHHHHHHHHHHHHHhccCCCChHHHHHHHHHh----------------hhhcCCcchHHHHHHHHHHHH
Q 016147 5 LLLFIIRSVYLFLQAVTAMVQQAMQYIDQTPDLDTRIELIKTL----------------NSVSAGKIYVEIERARLIKKL 68 (394)
Q Consensus 5 ~~~~l~k~r~q~k~ai~~~v~~~~~~~~~~~d~~~k~~~i~~L----------------~~vt~gki~~E~era~l~~~L 68 (394)
.+..+-.++|+..+|+.. .+.+...=+.- .+....+...+ ....+.. ......+
T Consensus 608 ~La~~~~~~g~~~~A~~~-y~~al~~~P~~--~~a~~~la~~~~~~g~~~eA~~~l~~ll~~~p~~-------~~~~~~l 677 (1157)
T PRK11447 608 TLADWAQQRGDYAAARAA-YQRVLTREPGN--ADARLGLIEVDIAQGDLAAARAQLAKLPATANDS-------LNTQRRV 677 (1157)
T ss_pred HHHHHHHHcCCHHHHHHH-HHHHHHhCCCC--HHHHHHHHHHHHHCCCHHHHHHHHHHHhccCCCC-------hHHHHHH
Confidence 345556778888888865 55555543321 23333333222 2121211 2334567
Q ss_pred HHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCc
Q 016147 69 AKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISP 130 (394)
Q Consensus 69 a~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~ 130 (394)
|.++.+.|++++|...+..+.-......+......++...++++...+++.+|..+.+++-.
T Consensus 678 a~~~~~~g~~~eA~~~~~~al~~~~~~~~~~~~a~~~~~~a~~~~~~G~~~~A~~~y~~Al~ 739 (1157)
T PRK11447 678 ALAWAALGDTAAAQRTFNRLIPQAKSQPPSMESALVLRDAARFEAQTGQPQQALETYKDAMV 739 (1157)
T ss_pred HHHHHhCCCHHHHHHHHHHHhhhCccCCcchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence 88999999999999999886543222233333456666779999999999999999998853
No 149
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=46.13 E-value=1.4e+02 Score=23.17 Aligned_cols=42 Identities=19% Similarity=0.138 Sum_probs=33.5
Q ss_pred cCcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEEeccCCC
Q 016147 305 YSRITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKIDRPQG 346 (394)
Q Consensus 305 Y~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~akIDq~~g 346 (394)
-..++|+.|.+.+|+|...+-..+..|..+|-+..+-.-..+
T Consensus 12 ~~~~~f~~L~~~l~lt~g~Ls~hL~~Le~~GyV~~~k~~~~~ 53 (80)
T PF13601_consen 12 NEEATFSELKEELGLTDGNLSKHLKKLEEAGYVEVEKEFEGR 53 (80)
T ss_dssp HSEEEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEE-SSS
T ss_pred cCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEEEeccCC
Confidence 467999999999999999999999999999999766544333
No 150
>KOG3054 consensus Uncharacterized conserved protein [Function unknown]
Probab=46.00 E-value=38 Score=32.30 Aligned_cols=50 Identities=16% Similarity=0.265 Sum_probs=46.0
Q ss_pred hhcCcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEEeccCCCEEEEec
Q 016147 303 KYYSRITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKIDRPQGIVCFQV 352 (394)
Q Consensus 303 k~Y~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~akIDq~~giV~F~~ 352 (394)
|--+.+.|+.||..|||-.+++-.-+-+++.+|.|.|-||--...|+...
T Consensus 210 k~nKvV~ledLas~f~Lrtqd~inriq~~l~eg~ltGVmDDRGKfIYIS~ 259 (299)
T KOG3054|consen 210 KKNKVVPLEDLASEFGLRTQDSINRIQELLAEGLLTGVMDDRGKFIYISM 259 (299)
T ss_pred HhcCeeeHHHHHHHhCccHHHHHHHHHHHHHhhhheeeecCCCceEEecH
Confidence 34678999999999999999999999999999999999999999998774
No 151
>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=45.85 E-value=59 Score=22.29 Aligned_cols=33 Identities=27% Similarity=0.303 Sum_probs=29.2
Q ss_pred CcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEE
Q 016147 306 SRITLKRLAELLCLSIQEAEKHLSDMVVSKALV 338 (394)
Q Consensus 306 ~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~ 338 (394)
...+...|++.+|+|...+-..+..|...|-+.
T Consensus 14 ~~~~~~el~~~l~~s~~~vs~hL~~L~~~glV~ 46 (47)
T PF01022_consen 14 GPLTVSELAEELGLSQSTVSHHLKKLREAGLVE 46 (47)
T ss_dssp SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred CCCchhhHHHhccccchHHHHHHHHHHHCcCee
Confidence 668899999999999999999999999999763
No 152
>KOG1538 consensus Uncharacterized conserved protein WDR10, contains WD40 repeats [General function prediction only]
Probab=45.49 E-value=2.5e+02 Score=31.00 Aligned_cols=141 Identities=17% Similarity=0.218 Sum_probs=79.5
Q ss_pred HHhhhchhHHHHH-----HHHHHHHHhccCCCChHHHHHHHH----HhhhhcCCcchHHHHHHHHHHHHHHHHHHhcCHH
Q 016147 9 IIRSVYLFLQAVT-----AMVQQAMQYIDQTPDLDTRIELIK----TLNSVSAGKIYVEIERARLIKKLAKIKEEQGLIA 79 (394)
Q Consensus 9 l~k~r~q~k~ai~-----~~v~~~~~~~~~~~d~~~k~~~i~----~L~~vt~gki~~E~era~l~~~La~i~e~~gd~~ 79 (394)
|-||-||-..|.- .|-+.+-+|+..-.+.+.|+ ++. --+.+.+-|+ -|+++-+.|+..
T Consensus 654 lFk~~G~enRAlEmyTDlRMFD~aQE~~~~g~~~eKKm-L~RKRA~WAr~~kePka------------AAEmLiSaGe~~ 720 (1081)
T KOG1538|consen 654 LFKRSGHENRALEMYTDLRMFDYAQEFLGSGDPKEKKM-LIRKRADWARNIKEPKA------------AAEMLISAGEHV 720 (1081)
T ss_pred HHHHcCchhhHHHHHHHHHHHHHHHHHhhcCChHHHHH-HHHHHHHHhhhcCCcHH------------HHHHhhcccchh
Confidence 4577788887764 46666777776655544443 332 1233443333 456777888888
Q ss_pred HHHHHHHH-----hhhhhcccCcHHH-----HHHHHH--------------------HHHHHHhccCChHHHHHHHHhhC
Q 016147 80 EAADLMQE-----VAVETFGAMAKTE-----KIAFIL--------------------EQVRLCLDRQDYVRAQILSRKIS 129 (394)
Q Consensus 80 eAa~iL~~-----i~vEt~~~m~~~e-----K~e~~L--------------------eq~rL~L~~~D~~~a~~~~~Ki~ 129 (394)
+|+.+..+ +..|-...++..+ ++..+| .+++|.++.++|..|-.+..|-
T Consensus 721 KAi~i~~d~gW~d~lidI~rkld~~ere~l~~~a~ylk~l~~~gLAaeIF~k~gD~ksiVqlHve~~~W~eAFalAe~h- 799 (1081)
T KOG1538|consen 721 KAIEICGDHGWVDMLIDIARKLDKAEREPLLLCATYLKKLDSPGLAAEIFLKMGDLKSLVQLHVETQRWDEAFALAEKH- 799 (1081)
T ss_pred hhhhhhhcccHHHHHHHHHhhcchhhhhHHHHHHHHHhhccccchHHHHHHHhccHHHHhhheeecccchHhHhhhhhC-
Confidence 88877643 3333333332222 222222 1245555555555555554332
Q ss_pred ccccCCCCccccCCCCCCCcccccCCCCccchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhcc
Q 016147 130 PRVFDADPSKEKKKPKEGDNVVEEAPADIPSLLELKRIYYELMIRYYSHNNDYLEICRCYKAIYEI 195 (394)
Q Consensus 130 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~~~~flea~k~y~ei~~t 195 (394)
++++-..|.-.++|......|.||-+.|+..+-+
T Consensus 800 --------------------------------Pe~~~dVy~pyaqwLAE~DrFeEAqkAfhkAGr~ 833 (1081)
T KOG1538|consen 800 --------------------------------PEFKDDVYMPYAQWLAENDRFEEAQKAFHKAGRQ 833 (1081)
T ss_pred --------------------------------ccccccccchHHHHhhhhhhHHHHHHHHHHhcch
Confidence 2222233555678888888999999999988754
No 153
>PRK10370 formate-dependent nitrite reductase complex subunit NrfG; Provisional
Probab=45.12 E-value=2.4e+02 Score=25.61 Aligned_cols=98 Identities=7% Similarity=-0.009 Sum_probs=70.4
Q ss_pred HHHHHHHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHH-HhccCC--hHHHHHHHHhhCccccCCCCc
Q 016147 62 ARLIKKLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRL-CLDRQD--YVRAQILSRKISPRVFDADPS 138 (394)
Q Consensus 62 a~l~~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL-~L~~~D--~~~a~~~~~Ki~~~~~~~~~~ 138 (394)
+.....||.+|...|++++|...+...- . +. ....+++...+.. +...|+ +..|...++++-..- |
T Consensus 73 ~~~w~~Lg~~~~~~g~~~~A~~a~~~Al----~-l~-P~~~~~~~~lA~aL~~~~g~~~~~~A~~~l~~al~~d----P- 141 (198)
T PRK10370 73 SEQWALLGEYYLWRNDYDNALLAYRQAL----Q-LR-GENAELYAALATVLYYQAGQHMTPQTREMIDKALALD----A- 141 (198)
T ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHHH----H-hC-CCCHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHhC----C-
Confidence 4577899999999999999999887522 1 11 1356677777764 566666 589999999988642 1
Q ss_pred cccCCCCCCCcccccCCCCccchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhcc
Q 016147 139 KEKKKPKEGDNVVEEAPADIPSLLELKRIYYELMIRYYSHNNDYLEICRCYKAIYEI 195 (394)
Q Consensus 139 ~~~~~~~~~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~~~~flea~k~y~ei~~t 195 (394)
+. ...+...+..+...++|-+|-.+|..+...
T Consensus 142 ---------------------~~----~~al~~LA~~~~~~g~~~~Ai~~~~~aL~l 173 (198)
T PRK10370 142 ---------------------NE----VTALMLLASDAFMQADYAQAIELWQKVLDL 173 (198)
T ss_pred ---------------------CC----hhHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence 11 123455567777899999999999998864
No 154
>PF13730 HTH_36: Helix-turn-helix domain
Probab=44.66 E-value=34 Score=24.01 Aligned_cols=29 Identities=14% Similarity=0.213 Sum_probs=26.6
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHhHhcCcE
Q 016147 309 TLKRLAELLCLSIQEAEKHLSDMVVSKAL 337 (394)
Q Consensus 309 sl~rLa~lL~ls~~e~E~~ls~MI~~g~l 337 (394)
|.+.||+.+|++..-+.+.+..++..|-|
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHCcCC
Confidence 78999999999999999999999988853
No 155
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=44.62 E-value=36 Score=29.22 Aligned_cols=37 Identities=24% Similarity=0.272 Sum_probs=34.0
Q ss_pred cccHHHHHHHhCCCHHHHHHHHHHhHhcCcE---EEEecc
Q 016147 307 RITLKRLAELLCLSIQEAEKHLSDMVVSKAL---VAKIDR 343 (394)
Q Consensus 307 ~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l---~akIDq 343 (394)
++++..||+.+|+|+..+-.-+-+|..+|-| .|.+|.
T Consensus 22 r~~~~eia~~lglS~~~v~~Ri~~L~~~GiI~~~~~~v~~ 61 (154)
T COG1522 22 RISNAELAERVGLSPSTVLRRIKRLEEEGVIKGYTAVLDP 61 (154)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHCCceeeEEEEECH
Confidence 4999999999999999999999999999966 678885
No 156
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=44.39 E-value=51 Score=24.51 Aligned_cols=62 Identities=19% Similarity=0.288 Sum_probs=43.2
Q ss_pred cccHHHHHHHhCC--CHHHHHHHHHHhHhcCcEEEEeccCCCEEEEecCCChHHHHHHHHHHHHHHHHHHHHHHhh
Q 016147 307 RITLKRLAELLCL--SIQEAEKHLSDMVVSKALVAKIDRPQGIVCFQVAKDSNDILNSWAMNLEKLLDLVEKSCHQ 380 (394)
Q Consensus 307 ~Isl~rLa~lL~l--s~~e~E~~ls~MI~~g~l~akIDq~~giV~F~~~k~~~~~L~~W~~~I~~l~~~V~k~~~l 380 (394)
.++.+++.+++|+ +.+++.+.|.+|= +.+..+..++.+.+.-|. |-.+|..-++.++.+.+.
T Consensus 5 ~~~~~~i~~llG~~i~~~ei~~~L~~lg----~~~~~~~~~~~~~v~~P~--------~R~Di~~~~DliEei~r~ 68 (71)
T smart00874 5 TLRRERINRLLGLDLSAEEIEEILKRLG----FEVEVSGDDDTLEVTVPS--------YRFDILIEADLIEEVARI 68 (71)
T ss_pred EecHHHHHHHHCCCCCHHHHHHHHHHCC----CeEEecCCCCeEEEECCC--------CccccCcccHHHHHHHHH
Confidence 4678899999996 5778888877773 333333335667777663 667777778888877664
No 157
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=44.04 E-value=52 Score=30.18 Aligned_cols=45 Identities=18% Similarity=0.118 Sum_probs=37.9
Q ss_pred HHHHHhhcCcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEEec
Q 016147 298 ILVVSKYYSRITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKID 342 (394)
Q Consensus 298 I~visk~Y~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~akID 342 (394)
+..++..+...|.+.+|+.||+|+.-++.+++.++..|.+...++
T Consensus 168 l~~~~~g~~g~s~~eIa~~l~iS~~Tv~~~~~~~~~~~~~~~~~~ 212 (225)
T PRK10046 168 RKLFKEPGVQHTAETVAQALTISRTTARRYLEYCASRHLIIAEIV 212 (225)
T ss_pred HHHHHcCCCCcCHHHHHHHhCccHHHHHHHHHHHHhCCeEEEEee
Confidence 445566666789999999999999999999999999998865543
No 158
>PHA02360 hypothetical protein
Probab=43.94 E-value=24 Score=26.47 Aligned_cols=47 Identities=23% Similarity=0.428 Sum_probs=37.8
Q ss_pred HHHHHHhhhhcCCcchHHHHHHHHHHHHHHHHHHhc-----CHHHHHHHHHH
Q 016147 41 IELIKTLNSVSAGKIYVEIERARLIKKLAKIKEEQG-----LIAEAADLMQE 87 (394)
Q Consensus 41 ~~~i~~L~~vt~gki~~E~era~l~~~La~i~e~~g-----d~~eAa~iL~~ 87 (394)
.+-+.+|+....+++|+.+|--.+-.+.-++||++| +..|--++|.+
T Consensus 8 ~~d~~iL~~A~~r~l~LDveyPklY~~i~k~YEe~gidFyG~~dEDYDILld 59 (70)
T PHA02360 8 KKDLQILRAAANRELFLDVEYPKLYKKIRKYYEEEGIDFYGEPDEDYDILLD 59 (70)
T ss_pred HHHHHHHHHHhcchheeecccHHHHHHHHHHHHHcCCcccCCcchhHHHHHH
Confidence 345678999999999999999999999999999875 44555555544
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=43.63 E-value=59 Score=23.74 Aligned_cols=35 Identities=17% Similarity=0.161 Sum_probs=30.0
Q ss_pred cCcc-cHHHHHHHhCCCHHHHHHHHHHhHhcCcEEE
Q 016147 305 YSRI-TLKRLAELLCLSIQEAEKHLSDMVVSKALVA 339 (394)
Q Consensus 305 Y~~I-sl~rLa~lL~ls~~e~E~~ls~MI~~g~l~a 339 (394)
=+++ |...||+.+|+|..-+-+.+..|..+|-+.-
T Consensus 21 g~~lps~~~la~~~~vsr~tvr~al~~L~~~g~i~~ 56 (64)
T PF00392_consen 21 GDRLPSERELAERYGVSRTTVREALRRLEAEGLIER 56 (64)
T ss_dssp TSBE--HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred CCEeCCHHHHHHHhccCCcHHHHHHHHHHHCCcEEE
Confidence 3688 9999999999999999999999999997754
No 160
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=43.59 E-value=1.5e+02 Score=25.36 Aligned_cols=34 Identities=15% Similarity=0.172 Sum_probs=30.5
Q ss_pred cCcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEE
Q 016147 305 YSRITLKRLAELLCLSIQEAEKHLSDMVVSKALV 338 (394)
Q Consensus 305 Y~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~ 338 (394)
-..++++.||+.|++|+.-+=..+.+|...|-|.
T Consensus 20 ~~~~~~~ela~~l~vs~~svs~~l~~L~~~Gli~ 53 (142)
T PRK03902 20 KGYARVSDIAEALSVHPSSVTKMVQKLDKDEYLI 53 (142)
T ss_pred CCCcCHHHHHHHhCCChhHHHHHHHHHHHCCCEE
Confidence 3456889999999999999999999999999886
No 161
>PLN03077 Protein ECB2; Provisional
Probab=43.45 E-value=5.2e+02 Score=28.97 Aligned_cols=195 Identities=12% Similarity=0.050 Sum_probs=0.0
Q ss_pred HHHHHHHhcCHHHHHHHHHHhh----------hhhcccCcHHHHHHHHHHHH----------------------------
Q 016147 68 LAKIKEEQGLIAEAADLMQEVA----------VETFGAMAKTEKIAFILEQV---------------------------- 109 (394)
Q Consensus 68 La~i~e~~gd~~eAa~iL~~i~----------vEt~~~m~~~eK~e~~Leq~---------------------------- 109 (394)
|...|.+.|++++|.+++.+++ +..|.....-++..-+++.|
T Consensus 329 Li~~y~k~g~~~~A~~vf~~m~~~d~~s~n~li~~~~~~g~~~~A~~lf~~M~~~g~~Pd~~t~~~ll~a~~~~g~~~~a 408 (857)
T PLN03077 329 LIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVG 408 (857)
T ss_pred HHHHHHhcCCHHHHHHHHhhCCCCCeeeHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCCCceeHHHHHHHHhccchHHHH
Q ss_pred -----------------------HHHhccCChHHHHHHHHhhCccccCCCCccccCCCCCCCcccccCCCCccchHHHHH
Q 016147 110 -----------------------RLCLDRQDYVRAQILSRKISPRVFDADPSKEKKKPKEGDNVVEEAPADIPSLLELKR 166 (394)
Q Consensus 110 -----------------------rL~L~~~D~~~a~~~~~Ki~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~kl 166 (394)
..|...|++..|..+.++...+....
T Consensus 409 ~~l~~~~~~~g~~~~~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~d~vs------------------------------- 457 (857)
T PLN03077 409 VKLHELAERKGLISYVVVANALIEMYSKCKCIDKALEVFHNIPEKDVIS------------------------------- 457 (857)
T ss_pred HHHHHHHHHhCCCcchHHHHHHHHHHHHcCCHHHHHHHHHhCCCCCeee-------------------------------
Q ss_pred HHHHHHHHHHHhhhhHHHHHHHHHHHhccCCCCCChhcHHHHHHHHHHHHHhCCCChhchHhhhhhhcccCcCCChhHHH
Q 016147 167 IYYELMIRYYSHNNDYLEICRCYKAIYEIPYIKEDPAQWMPVLRKICWYLVLAPHDPMQSSLLNSTLEDKNLSEIPNFRL 246 (394)
Q Consensus 167 k~~~~~~~~~~~~~~flea~k~y~ei~~t~~i~~d~~~~~~~L~~av~~~ILap~~~~rs~ll~~l~~d~~l~~ip~~~~ 246 (394)
|..++.-|...+++.+|...|.+.... +..|...+..+|.. |+-++.. ..-.++...+.+..-......+..
T Consensus 458 --~~~mi~~~~~~g~~~eA~~lf~~m~~~--~~pd~~t~~~lL~a---~~~~g~l-~~~~~i~~~~~~~g~~~~~~~~na 529 (857)
T PLN03077 458 --WTSIIAGLRLNNRCFEALIFFRQMLLT--LKPNSVTLIAALSA---CARIGAL-MCGKEIHAHVLRTGIGFDGFLPNA 529 (857)
T ss_pred --HHHHHHHHHHCCCHHHHHHHHHHHHhC--CCCCHhHHHHHHHH---HhhhchH-HHhHHHHHHHHHhCCCccceechH
Q ss_pred HHHHhcchhcccchhhHHHHHHhhhhhhhhcCCchhhhhHHHHHHHHHHHHHHHHHhhcCcccHHHHHHHhCCCHHHHHH
Q 016147 247 LLKQLVTMEVIQWTSLWNTYKDEFENETNMLGGSLGAKAAEDLRQRIIEHNILVVSKYYSRITLKRLAELLCLSIQEAEK 326 (394)
Q Consensus 247 L~k~f~~~eli~~~~~~~~~~~~l~~~~~~~~d~~~~~~~~~L~~~viEHNI~visk~Y~~Isl~rLa~lL~ls~~e~E~ 326 (394)
|+.+|.. ...+...+...... ......|+.+-.....|.- .+++..
T Consensus 530 Li~~y~k---------~G~~~~A~~~f~~~---~~d~~s~n~lI~~~~~~G~----------------------~~~A~~ 575 (857)
T PLN03077 530 LLDLYVR---------CGRMNYAWNQFNSH---EKDVVSWNILLTGYVAHGK----------------------GSMAVE 575 (857)
T ss_pred HHHHHHH---------cCCHHHHHHHHHhc---CCChhhHHHHHHHHHHcCC----------------------HHHHHH
Q ss_pred HHHHhHhcC
Q 016147 327 HLSDMVVSK 335 (394)
Q Consensus 327 ~ls~MI~~g 335 (394)
...+|+..|
T Consensus 576 lf~~M~~~g 584 (857)
T PLN03077 576 LFNRMVESG 584 (857)
T ss_pred HHHHHHHcC
No 162
>PRK10747 putative protoheme IX biogenesis protein; Provisional
Probab=43.37 E-value=2.3e+02 Score=28.60 Aligned_cols=94 Identities=15% Similarity=0.064 Sum_probs=55.6
Q ss_pred HHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCccccCCCCccccCCCCC
Q 016147 67 KLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPRVFDADPSKEKKKPKE 146 (394)
Q Consensus 67 ~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~~~~~~~~~~~~~~~~ 146 (394)
.-+-+...+|||..|.+.+..-+-. .+...-+++--++.....||+.+|..+..++.... +
T Consensus 89 ~~gl~a~~eGd~~~A~k~l~~~~~~------~~~p~l~~llaA~aA~~~g~~~~A~~~l~~A~~~~----~--------- 149 (398)
T PRK10747 89 EQALLKLAEGDYQQVEKLMTRNADH------AEQPVVNYLLAAEAAQQRGDEARANQHLERAAELA----D--------- 149 (398)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHhc------ccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC----C---------
Confidence 3344455678888888777652210 11234446666777788888888888888876421 1
Q ss_pred CCcccccCCCCccchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhcc
Q 016147 147 GDNVVEEAPADIPSLLELKRIYYELMIRYYSHNNDYLEICRCYKAIYEI 195 (394)
Q Consensus 147 ~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~~~~flea~k~y~ei~~t 195 (394)
+..+--....++++...++|-.|-..+......
T Consensus 150 ----------------~~~~~~~l~~a~l~l~~g~~~~Al~~l~~~~~~ 182 (398)
T PRK10747 150 ----------------NDQLPVEITRVRIQLARNENHAARHGVDKLLEV 182 (398)
T ss_pred ----------------cchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc
Confidence 010111112356777777777777777776653
No 163
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=43.26 E-value=1.5e+02 Score=22.73 Aligned_cols=43 Identities=26% Similarity=0.206 Sum_probs=35.1
Q ss_pred cccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEEeccCCCEEEEe
Q 016147 307 RITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKIDRPQGIVCFQ 351 (394)
Q Consensus 307 ~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~akIDq~~giV~F~ 351 (394)
.+++..||+.+|+|..-+-+.+..|...|-+... ...|.....
T Consensus 20 ~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~~--~~~~~y~l~ 62 (91)
T smart00346 20 GLTLAELAERLGLSKSTAHRLLNTLQELGYVEQD--GQNGRYRLG 62 (91)
T ss_pred CcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeeec--CCCCceeec
Confidence 5999999999999999999999999999988652 234544443
No 164
>PRK11189 lipoprotein NlpI; Provisional
Probab=42.88 E-value=2.3e+02 Score=27.38 Aligned_cols=100 Identities=14% Similarity=-0.041 Sum_probs=71.3
Q ss_pred HHHHHHHHHHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCccccCCCCc
Q 016147 59 IERARLIKKLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPRVFDADPS 138 (394)
Q Consensus 59 ~era~l~~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~~~~~~~~ 138 (394)
.++++.-..+|.+|...|++++|...+...-- +.+. -.+.+.....++...+|+..|....+++.... |.
T Consensus 61 ~~~a~~~~~~g~~~~~~g~~~~A~~~~~~Al~-----l~P~-~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~----P~ 130 (296)
T PRK11189 61 EERAQLHYERGVLYDSLGLRALARNDFSQALA-----LRPD-MADAYNYLGIYLTQAGNFDAAYEAFDSVLELD----PT 130 (296)
T ss_pred HhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHH-----cCCC-CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC----CC
Confidence 47788889999999999999999987665221 1111 14677888899999999999999999987531 11
Q ss_pred cccCCCCCCCcccccCCCCccchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhc
Q 016147 139 KEKKKPKEGDNVVEEAPADIPSLLELKRIYYELMIRYYSHNNDYLEICRCYKAIYE 194 (394)
Q Consensus 139 ~~~~~~~~~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~~~~flea~k~y~ei~~ 194 (394)
... .+...+..+...++|-+|...|...+.
T Consensus 131 ----------------------~~~----a~~~lg~~l~~~g~~~eA~~~~~~al~ 160 (296)
T PRK11189 131 ----------------------YNY----AYLNRGIALYYGGRYELAQDDLLAFYQ 160 (296)
T ss_pred ----------------------CHH----HHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 111 123334445567889998888888775
No 165
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=42.84 E-value=87 Score=27.51 Aligned_cols=52 Identities=13% Similarity=0.036 Sum_probs=39.4
Q ss_pred HHHHHHhhcC-cccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEEeccCCCEE
Q 016147 297 NILVVSKYYS-RITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKIDRPQGIV 348 (394)
Q Consensus 297 NI~visk~Y~-~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~akIDq~~giV 348 (394)
-+..++.... .++.+.||+..++|+..+++.+..|...|-+...==+..|+.
T Consensus 13 ~L~~LA~~~~~~~s~~eIA~~~~is~~~L~kIl~~L~~aGlv~S~rG~~GGy~ 65 (153)
T PRK11920 13 MLMYCAANDGKLSRIPEIARAYGVSELFLFKILQPLVEAGLVETVRGRNGGVR 65 (153)
T ss_pred HHHHHHhCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeecCCCCCee
Confidence 3344444333 379999999999999999999999999998876655444443
No 166
>KOG2908 consensus 26S proteasome regulatory complex, subunit RPN9/PSMD13 [Posttranslational modification, protein turnover, chaperones]
Probab=42.81 E-value=3.4e+02 Score=27.46 Aligned_cols=116 Identities=16% Similarity=0.205 Sum_probs=77.6
Q ss_pred hHHHHHHHhhhchhHHHHHHHHHHHHHhccCCCChHHHHHHHHHh-hhhcC-----CcchHHHHHHHHHHHHHHHHHHhc
Q 016147 3 ALLLLFIIRSVYLFLQAVTAMVQQAMQYIDQTPDLDTRIELIKTL-NSVSA-----GKIYVEIERARLIKKLAKIKEEQG 76 (394)
Q Consensus 3 ~~~~~~l~k~r~q~k~ai~~~v~~~~~~~~~~~d~~~k~~~i~~L-~~vt~-----gki~~E~era~l~~~La~i~e~~g 76 (394)
-+-..|++.=+++..+ -..|+-+....+++.|.+.-++.++.+ +.+.+ +.++.+.|.+|+.. ..|
T Consensus 59 ~lY~NFvsefe~kINp--lslvei~l~~~~~~~D~~~al~~Le~i~~~~~~~~e~~av~~~~t~~~r~~L-------~i~ 129 (380)
T KOG2908|consen 59 QLYLNFVSEFETKINP--LSLVEILLVVSEQISDKDEALEFLEKIIEKLKEYKEPDAVIYILTEIARLKL-------EIN 129 (380)
T ss_pred HHHHHHHHHHhhccCh--HHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHhhccchhHHHHHHHHHHHHH-------hcc
Confidence 3455666666665543 244666667777888888777777743 33333 44555655555544 778
Q ss_pred CHHHHHHHHHHhhh--hhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHh
Q 016147 77 LIAEAADLMQEVAV--ETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRK 127 (394)
Q Consensus 77 d~~eAa~iL~~i~v--Et~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~K 127 (394)
|..++-++|-+..- +.-+.|+..--..||.--.++|=..+|+..+-..+=+
T Consensus 130 DLk~~kk~ldd~~~~ld~~~~v~~~Vh~~fY~lssqYyk~~~d~a~yYr~~L~ 182 (380)
T KOG2908|consen 130 DLKEIKKLLDDLKSMLDSLDGVTSNVHSSFYSLSSQYYKKIGDFASYYRHALL 182 (380)
T ss_pred cHHHHHHHHHHHHHHHhcccCCChhhhhhHHHHHHHHHHHHHhHHHHHHHHHH
Confidence 88888888887664 2235678877788888888888889998777665443
No 167
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=42.68 E-value=64 Score=27.70 Aligned_cols=47 Identities=13% Similarity=0.101 Sum_probs=40.1
Q ss_pred CcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEEeccCCCEEEEec
Q 016147 306 SRITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKIDRPQGIVCFQV 352 (394)
Q Consensus 306 ~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~akIDq~~giV~F~~ 352 (394)
..+|.+.||+.+|+|..-+.+.+..|...|-+..+=-+..|+.....
T Consensus 24 ~~~s~~~ia~~~~is~~~vrk~l~~L~~~Glv~s~~G~~GG~~l~~~ 70 (141)
T PRK11014 24 RMTSISEVTEVYGVSRNHMVKIINQLSRAGYVTAVRGKNGGIRLGKP 70 (141)
T ss_pred CccCHHHHHHHHCcCHHHHHHHHHHHHhCCEEEEecCCCCCeeecCC
Confidence 36899999999999999999999999999988887777677655443
No 168
>PHA02943 hypothetical protein; Provisional
Probab=42.48 E-value=1.8e+02 Score=25.92 Aligned_cols=84 Identities=18% Similarity=0.094 Sum_probs=55.0
Q ss_pred cCcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEEeccCCCEEEEecCCChHHHHHHHHHHHHHHHHHHH---------
Q 016147 305 YSRITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKIDRPQGIVCFQVAKDSNDILNSWAMNLEKLLDLVE--------- 375 (394)
Q Consensus 305 Y~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~akIDq~~giV~F~~~k~~~~~L~~W~~~I~~l~~~V~--------- 375 (394)
.-.-|.+++|+.||+|-.+++-.|--+=.+|.+.- +-+..--+.+-.+ +...|.-.+=.+.+-..|.
T Consensus 22 ~G~~TtseIAkaLGlS~~qa~~~LyvLErEG~Vkr-V~~G~~tyw~l~~---day~~~v~~~~Relwrlv~s~~~kfi~p 97 (165)
T PHA02943 22 DGCKTTSRIANKLGVSHSMARNALYQLAKEGMVLK-VEIGRAAIWCLDE---DAYTNLVFEIKRELWRLVCNSRLKFITP 97 (165)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHHcCceEE-EeecceEEEEECh---HHHHHHHHHHHHHHHHHHHhccccccCh
Confidence 45567899999999999999999999999998854 3344444555444 2333332222333333332
Q ss_pred -HHHhhhhHHHHhhhhcc
Q 016147 376 -KSCHQIHKETMVHKTAL 392 (394)
Q Consensus 376 -k~~~lI~ke~~~~~~~~ 392 (394)
..-+||.|..-.|++-.
T Consensus 98 ~~l~~li~kd~~a~~~~a 115 (165)
T PHA02943 98 SRLLRLIAKDTEAHNIFA 115 (165)
T ss_pred HHHHHHHHhCHHHHHHHH
Confidence 34578888888777644
No 169
>PF13429 TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2_B.
Probab=42.02 E-value=72 Score=30.22 Aligned_cols=94 Identities=19% Similarity=0.287 Sum_probs=42.4
Q ss_pred HHHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCccccCCCCccccCCCC
Q 016147 66 KKLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPRVFDADPSKEKKKPK 145 (394)
Q Consensus 66 ~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~~~~~~~~~~~~~~~ 145 (394)
..|+.+ ...|+..+|++++.. .+. .....+++...+.++...+||.++...++++... ...
T Consensus 82 ~~l~~l-~~~~~~~~A~~~~~~----~~~---~~~~~~~l~~~l~~~~~~~~~~~~~~~l~~~~~~--~~~--------- 142 (280)
T PF13429_consen 82 ERLIQL-LQDGDPEEALKLAEK----AYE---RDGDPRYLLSALQLYYRLGDYDEAEELLEKLEEL--PAA--------- 142 (280)
T ss_dssp --------------------------------------------H-HHHTT-HHHHHHHHHHHHH---T-----------
T ss_pred cccccc-ccccccccccccccc----ccc---cccccchhhHHHHHHHHHhHHHHHHHHHHHHHhc--cCC---------
Confidence 456666 688899999988764 222 1223456666778889999999999999986631 100
Q ss_pred CCCcccccCCCCccchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhcc
Q 016147 146 EGDNVVEEAPADIPSLLELKRIYYELMIRYYSHNNDYLEICRCYKAIYEI 195 (394)
Q Consensus 146 ~~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~~~~flea~k~y~ei~~t 195 (394)
..--.|+...+.++...|++-+|-+.|......
T Consensus 143 -----------------~~~~~~~~~~a~~~~~~G~~~~A~~~~~~al~~ 175 (280)
T PF13429_consen 143 -----------------PDSARFWLALAEIYEQLGDPDKALRDYRKALEL 175 (280)
T ss_dssp ------------------T-HHHHHHHHHHHHHCCHHHHHHHHHHHHHHH
T ss_pred -----------------CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc
Confidence 011356778889999999999999999999873
No 170
>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional
Probab=41.97 E-value=2.5e+02 Score=32.52 Aligned_cols=91 Identities=11% Similarity=-0.019 Sum_probs=66.8
Q ss_pred HHHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCccccCCCCccccCCCC
Q 016147 66 KKLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPRVFDADPSKEKKKPK 145 (394)
Q Consensus 66 ~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~~~~~~~~~~~~~~~ 145 (394)
...|..+...||+.+|...++... ..++.. .+..+..+++++..|++..|..+++|+-.. +|.
T Consensus 48 f~~a~~~~~~Gd~~~A~~~l~~Al-----~~dP~n-~~~~~~LA~~yl~~g~~~~A~~~~~kAv~l----dP~------- 110 (987)
T PRK09782 48 LDKALKAQKNNDEATAIREFEYIH-----QQVPDN-IPLTLYLAEAYRHFGHDDRARLLLEDQLKR----HPG------- 110 (987)
T ss_pred HHHHHHHHhCCCHHHHHHHHHHHH-----HhCCCC-HHHHHHHHHHHHHCCCHHHHHHHHHHHHhc----Ccc-------
Confidence 455667778899999999888743 223333 677799999999999999999999999864 211
Q ss_pred CCCcccccCCCCccchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhccC
Q 016147 146 EGDNVVEEAPADIPSLLELKRIYYELMIRYYSHNNDYLEICRCYKAIYEIP 196 (394)
Q Consensus 146 ~~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~~~~flea~k~y~ei~~t~ 196 (394)
+ ..|+...+.+ ++|-+|...|.++....
T Consensus 111 ---------------n----~~~~~~La~i----~~~~kA~~~ye~l~~~~ 138 (987)
T PRK09782 111 ---------------D----ARLERSLAAI----PVEVKSVTTVEELLAQQ 138 (987)
T ss_pred ---------------c----HHHHHHHHHh----ccChhHHHHHHHHHHhC
Confidence 1 1233333333 88999999999999743
No 171
>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=41.93 E-value=4.7e+02 Score=28.13 Aligned_cols=26 Identities=15% Similarity=0.376 Sum_probs=15.9
Q ss_pred HHHHHHHHHhhhhHHHHHHHHHHHhc
Q 016147 169 YELMIRYYSHNNDYLEICRCYKAIYE 194 (394)
Q Consensus 169 ~~~~~~~~~~~~~flea~k~y~ei~~ 194 (394)
+...+..+...+++.+|...|..+..
T Consensus 773 ~~~la~~~~~~g~~~~A~~~~~~~~~ 798 (899)
T TIGR02917 773 RTALAELYLAQKDYDKAIKHYRTVVK 798 (899)
T ss_pred HHHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 33444556666667777766666664
No 172
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=41.73 E-value=99 Score=26.41 Aligned_cols=45 Identities=13% Similarity=0.072 Sum_probs=39.2
Q ss_pred cCcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEEeccCCCEEE
Q 016147 305 YSRITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKIDRPQGIVC 349 (394)
Q Consensus 305 Y~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~akIDq~~giV~ 349 (394)
-..+|.+.||+.+++++.-+=..+.+|+..|-|.-..|..++=+.
T Consensus 52 ~~~~t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~R~~~~~DrR~~ 96 (144)
T PRK11512 52 AACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNPNDKRGV 96 (144)
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCcccCCee
Confidence 357999999999999999999999999999999888876665433
No 173
>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=41.57 E-value=68 Score=23.63 Aligned_cols=39 Identities=18% Similarity=0.124 Sum_probs=34.2
Q ss_pred cCcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEEecc
Q 016147 305 YSRITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKIDR 343 (394)
Q Consensus 305 Y~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~akIDq 343 (394)
....|...||+.+|+|...+-..+..|...|-+.-.-.+
T Consensus 20 ~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~~~~~ 58 (68)
T PF01978_consen 20 NGPATAEEIAEELGISRSTVYRALKSLEEKGLVEREEGR 58 (68)
T ss_dssp HCHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEEEC
T ss_pred cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcCc
Confidence 567899999999999999999999999999988655444
No 174
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=41.07 E-value=7.3e+02 Score=30.03 Aligned_cols=60 Identities=20% Similarity=0.199 Sum_probs=49.7
Q ss_pred HHHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCcc
Q 016147 66 KKLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPR 131 (394)
Q Consensus 66 ~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~ 131 (394)
..|++||+.-+++.+|.++|+.+-- -|+ +....|+.-+...|..++...|+.+++|+-..
T Consensus 1534 ~~L~~iy~k~ek~~~A~ell~~m~K-KF~-----q~~~vW~~y~~fLl~~ne~~aa~~lL~rAL~~ 1593 (1710)
T KOG1070|consen 1534 LKLLGIYEKSEKNDEADELLRLMLK-KFG-----QTRKVWIMYADFLLRQNEAEAARELLKRALKS 1593 (1710)
T ss_pred HHHHHHHHHhhcchhHHHHHHHHHH-Hhc-----chhhHHHHHHHHHhcccHHHHHHHHHHHHHhh
Confidence 6899999999999999999987432 232 66778888888889999999999999998753
No 175
>PF12854 PPR_1: PPR repeat
Probab=41.01 E-value=35 Score=21.82 Aligned_cols=22 Identities=27% Similarity=0.312 Sum_probs=18.6
Q ss_pred HHHHHHHHhcCHHHHHHHHHHh
Q 016147 67 KLAKIKEEQGLIAEAADLMQEV 88 (394)
Q Consensus 67 ~La~i~e~~gd~~eAa~iL~~i 88 (394)
.|-+-|.+.|++++|.+++.++
T Consensus 12 ~lI~~~Ck~G~~~~A~~l~~~M 33 (34)
T PF12854_consen 12 TLIDGYCKAGRVDEAFELFDEM 33 (34)
T ss_pred HHHHHHHHCCCHHHHHHHHHhC
Confidence 4567789999999999999875
No 176
>COG5051 RPL36A Ribosomal protein L36E [Translation, ribosomal structure and biogenesis]
Probab=40.24 E-value=99 Score=24.77 Aligned_cols=70 Identities=16% Similarity=0.224 Sum_probs=49.1
Q ss_pred HhhhchhHHHHHHHHHHHHHhccCCCChHHHHHHHHHhhhhcCCcchHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHH
Q 016147 10 IRSVYLFLQAVTAMVQQAMQYIDQTPDLDTRIELIKTLNSVSAGKIYVEIERARLIKKLAKIKEEQGLIAEAADLMQE 87 (394)
Q Consensus 10 ~k~r~q~k~ai~~~v~~~~~~~~~~~d~~~k~~~i~~L~~vt~gki~~E~era~l~~~La~i~e~~gd~~eAa~iL~~ 87 (394)
|.|+||+..- +.+|+....-+..+..-| .++|+.|+.-.+.+ -|--++..|+.+..+.+++++-+.++++
T Consensus 27 s~kkgq~s~R-t~fvrsivrEiaGlsPyE--rr~i~Lirns~~kr-----ArKlakKRLGs~kRAkaKvEel~~~i~~ 96 (97)
T COG5051 27 SRKKGQLSKR-TEFVRSIVREIAGLSPYE--RRVIELIRNSQDKR-----ARKLAKKRLGSLKRAKAKVEELTSVIQS 96 (97)
T ss_pred chhhhccccH-HHHHHHHHHHHccCCHHH--HHHHHHHHhcccHH-----HHHHHHHHhhhHHHHHHHHHHHHHHHhc
Confidence 5677887543 235666555566666556 56777777766654 3455778899999999999999998874
No 177
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=40.04 E-value=2.1e+02 Score=23.41 Aligned_cols=42 Identities=10% Similarity=0.094 Sum_probs=37.1
Q ss_pred cCcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEEeccCCC
Q 016147 305 YSRITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKIDRPQG 346 (394)
Q Consensus 305 Y~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~akIDq~~g 346 (394)
...++.+.||+.+|++..-+=..+.+|...|-|...-|..++
T Consensus 40 ~~~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~~~~~D~ 81 (118)
T TIGR02337 40 QGSMEFTQLANQACILRPSLTGILARLERDGLVTRLKASNDQ 81 (118)
T ss_pred cCCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEeccCCCCC
Confidence 467999999999999999999999999999999887765554
No 178
>PF04492 Phage_rep_O: Bacteriophage replication protein O ; InterPro: IPR006497 This entry is represented by the N-terminal domain of Bacteriophage lambda, GpO. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; GO: 0006260 DNA replication
Probab=39.04 E-value=48 Score=27.21 Aligned_cols=35 Identities=26% Similarity=0.377 Sum_probs=33.4
Q ss_pred hhcCcccHHHHHHHhCCCHHHHHHHHHHhHhcCcE
Q 016147 303 KYYSRITLKRLAELLCLSIQEAEKHLSDMVVSKAL 337 (394)
Q Consensus 303 k~Y~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l 337 (394)
|...+||.+.++++.|++...+.+.+..+|..|-|
T Consensus 50 Kk~d~Is~sq~~e~tg~~~~~V~~al~~Li~~~vI 84 (100)
T PF04492_consen 50 KKMDRISNSQIAEMTGLSRDHVSKALNELIRRGVI 84 (100)
T ss_pred CccceeeHHHHHHHHCcCHHHHHHHHHHHHHCCCE
Confidence 56789999999999999999999999999999988
No 179
>cd07311 terB_like_1 tellurium resistance terB-like protein, subgroup 1. This family includes several uncharacterized bacterial proteins. The prototype of this CD is tellurite resistance protein from Nostoc punctiforme that belongs to COG3793. Its precise biological function and its mechanism responsible for tellurium resistance still remains rather poorly understood.
Probab=38.90 E-value=79 Score=27.86 Aligned_cols=99 Identities=17% Similarity=0.294 Sum_probs=63.0
Q ss_pred ccCCCChHHHHHHHHHhhhhc--CCcchHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHhhhhhc----ccCcHHHHHHH
Q 016147 31 IDQTPDLDTRIELIKTLNSVS--AGKIYVEIERARLIKKLAKIKEEQGLIAEAADLMQEVAVETF----GAMAKTEKIAF 104 (394)
Q Consensus 31 ~~~~~d~~~k~~~i~~L~~vt--~gki~~E~era~l~~~La~i~e~~gd~~eAa~iL~~i~vEt~----~~m~~~eK~e~ 104 (394)
++++|..++.......|-++. +|.+. |.|+..++..+.++.-......+|.+...+-.++.+ ...+. ..-.+
T Consensus 14 ~~~~~~~~~~~~~~~~Ll~iAkADG~Vs-e~Ei~~~~~~m~~~~L~~e~~~~aie~~~~~~L~~~~~~~~~~~~-~~~~l 91 (150)
T cd07311 14 FDQIPTNQDKLAYLKALLVCAKGDGVIS-PEERDWAIGYAAARGGDADMVEELKEYTADEDLEEVDFRSPNIKS-SRRAL 91 (150)
T ss_pred cccCCCcccHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHHcCCCHHHHHHHHHhCccccHHHHHHHHHhcch-hHHHH
Confidence 588998888888888776644 77664 788888888888762222234444444222222222 11222 23345
Q ss_pred HHHHHHHHhccCChHHHHH-HHHhhCcc
Q 016147 105 ILEQVRLCLDRQDYVRAQI-LSRKISPR 131 (394)
Q Consensus 105 ~Leq~rL~L~~~D~~~a~~-~~~Ki~~~ 131 (394)
+++++++...+|.+..++. ++.++...
T Consensus 92 l~~~l~vA~ADG~l~~~E~~lL~~iA~~ 119 (150)
T cd07311 92 LYDAIQVCAADGELSPGEVAAVRKAASL 119 (150)
T ss_pred HHHHHHHHHcCCCCCHHHHHHHHHHHHH
Confidence 5779999999999999887 66666654
No 180
>PRK10803 tol-pal system protein YbgF; Provisional
Probab=38.58 E-value=3.7e+02 Score=25.84 Aligned_cols=85 Identities=12% Similarity=0.149 Sum_probs=58.7
Q ss_pred HHHHHHhhhhcCCcchHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHH
Q 016147 41 IELIKTLNSVSAGKIYVEIERARLIKKLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVR 120 (394)
Q Consensus 41 ~~~i~~L~~vt~gki~~E~era~l~~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~ 120 (394)
...++.+-+.-|+.-|. ......||..|...|++.+|...+..+-- .|. +....-+.++....++...||+..
T Consensus 163 i~af~~fl~~yP~s~~a----~~A~y~LG~~y~~~g~~~~A~~~f~~vv~-~yP--~s~~~~dAl~klg~~~~~~g~~~~ 235 (263)
T PRK10803 163 IVAFQNFVKKYPDSTYQ----PNANYWLGQLNYNKGKKDDAAYYFASVVK-NYP--KSPKAADAMFKVGVIMQDKGDTAK 235 (263)
T ss_pred HHHHHHHHHHCcCCcch----HHHHHHHHHHHHHcCCHHHHHHHHHHHHH-HCC--CCcchhHHHHHHHHHHHHcCCHHH
Confidence 33444444444544322 24457999999999999999998877542 221 113445667778888889999999
Q ss_pred HHHHHHhhCccc
Q 016147 121 AQILSRKISPRV 132 (394)
Q Consensus 121 a~~~~~Ki~~~~ 132 (394)
|..+++++-..+
T Consensus 236 A~~~~~~vi~~y 247 (263)
T PRK10803 236 AKAVYQQVIKKY 247 (263)
T ss_pred HHHHHHHHHHHC
Confidence 999999887654
No 181
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=38.40 E-value=75 Score=22.95 Aligned_cols=37 Identities=22% Similarity=0.210 Sum_probs=32.4
Q ss_pred hhcCcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEE
Q 016147 303 KYYSRITLKRLAELLCLSIQEAEKHLSDMVVSKALVA 339 (394)
Q Consensus 303 k~Y~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~a 339 (394)
.--...|...||+.+|++..-+-..+..|...|-|..
T Consensus 20 ~~~~~~t~~ela~~l~~~~~t~s~hL~~L~~aGli~~ 56 (61)
T PF12840_consen 20 ASNGPMTVSELAEELGISQSTVSYHLKKLEEAGLIEV 56 (61)
T ss_dssp HHCSTBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred hcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEE
Confidence 4578899999999999999999999999999997754
No 182
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=38.21 E-value=1.4e+02 Score=27.21 Aligned_cols=47 Identities=28% Similarity=0.320 Sum_probs=38.6
Q ss_pred cCcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEE-----eccCCCEEEEe
Q 016147 305 YSRITLKRLAELLCLSIQEAEKHLSDMVVSKALVAK-----IDRPQGIVCFQ 351 (394)
Q Consensus 305 Y~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~ak-----IDq~~giV~F~ 351 (394)
...+|...||+.+|+++.-+-..+..|...|-|.-. .+||..++...
T Consensus 13 ~~~~t~~eLA~~lgis~~tV~~~L~~Le~~GlV~r~~~~~~~gRp~~~y~LT 64 (203)
T TIGR02702 13 QGQATAAALAEALAISPQAVRRHLKDLETEGLIEYEAVVQGMGRPQYHYQLS 64 (203)
T ss_pred cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEeecccCCCCCceEEEEC
Confidence 467999999999999999999999999999999655 45665544443
No 183
>PF09613 HrpB1_HrpK: Bacterial type III secretion protein (HrpB1_HrpK); InterPro: IPR013394 This family of proteins is encoded by genes found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia.
Probab=37.94 E-value=3e+02 Score=24.64 Aligned_cols=82 Identities=16% Similarity=0.070 Sum_probs=53.9
Q ss_pred HHHHHHHHHHHHhccCCCChHHHHHHHHHhhhhcCCcchHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHhhhhhcccCc
Q 016147 18 QAVTAMVQQAMQYIDQTPDLDTRIELIKTLNSVSAGKIYVEIERARLIKKLAKIKEEQGLIAEAADLMQEVAVETFGAMA 97 (394)
Q Consensus 18 ~ai~~~v~~~~~~~~~~~d~~~k~~~i~~L~~vt~gki~~E~era~l~~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~ 97 (394)
..+..++.-.+--+... +.+.-..++..|+...|+..- +..--+-++-..|+|.+|..+|.++.-.+.+.--
T Consensus 8 ~iv~gLie~~~~al~~~-~~~D~e~lL~ALrvLRP~~~e-------~~~~~~~l~i~r~~w~dA~rlLr~l~~~~~~~p~ 79 (160)
T PF09613_consen 8 EIVGGLIEVLSVALRLG-DPDDAEALLDALRVLRPEFPE-------LDLFDGWLHIVRGDWDDALRLLRELEERAPGFPY 79 (160)
T ss_pred HHHHHHHHHHHHHHccC-ChHHHHHHHHHHHHhCCCchH-------HHHHHHHHHHHhCCHHHHHHHHHHHhccCCCChH
Confidence 45556666655555443 445557889999999999753 3356677888999999999999997544333222
Q ss_pred HHHHHHHHHH
Q 016147 98 KTEKIAFILE 107 (394)
Q Consensus 98 ~~eK~e~~Le 107 (394)
-+.=+-++|.
T Consensus 80 ~kALlA~CL~ 89 (160)
T PF09613_consen 80 AKALLALCLY 89 (160)
T ss_pred HHHHHHHHHH
Confidence 2344445553
No 184
>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=37.72 E-value=63 Score=22.53 Aligned_cols=31 Identities=19% Similarity=0.451 Sum_probs=23.0
Q ss_pred HHhhcCcccHHHHHHHhCCCHHHHHHHHHHh
Q 016147 301 VSKYYSRITLKRLAELLCLSIQEAEKHLSDM 331 (394)
Q Consensus 301 isk~Y~~Isl~rLa~lL~ls~~e~E~~ls~M 331 (394)
.-.|+...|...+|+.+|+|+..+...+.+-
T Consensus 20 ~l~~~~g~s~~eIa~~l~~s~~~v~~~l~ra 50 (54)
T PF08281_consen 20 LLRYFQGMSYAEIAEILGISESTVKRRLRRA 50 (54)
T ss_dssp HHHHTS---HHHHHHHCTS-HHHHHHHHHHH
T ss_pred HHHHHHCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 3358999999999999999999999887764
No 185
>PF08679 DsrD: Dissimilatory sulfite reductase D (DsrD); InterPro: IPR014793 The structure of the dissimilatory sulphite reductase D (DsrD) protein has shown it to contain a winged-helix motif similar to those found in DNA binding proteins []. The structure suggests a possible role for DsrD in transcription or translation of genes, which catalyse dissimilatory sulphite reduction. ; PDB: 1WQ2_B 1UCR_B.
Probab=37.22 E-value=61 Score=24.65 Aligned_cols=33 Identities=18% Similarity=0.205 Sum_probs=25.9
Q ss_pred cCcccHHHHHH-HhCCCHHHHHHHHHHhHhcCcE
Q 016147 305 YSRITLKRLAE-LLCLSIQEAEKHLSDMVVSKAL 337 (394)
Q Consensus 305 Y~~Isl~rLa~-lL~ls~~e~E~~ls~MI~~g~l 337 (394)
=+...|..+.. ..+..+-++-+.+..||++|++
T Consensus 17 KskfYfkD~~k~~pd~k~R~vKKi~~~LV~Eg~l 50 (67)
T PF08679_consen 17 KSKFYFKDFYKAFPDAKPREVKKIVNELVNEGKL 50 (67)
T ss_dssp SS-EEHHHHHHH-TTS-HHHHHHHHHHHHHTTSE
T ss_pred CCceeHHHHHHHCCCcCHHHHHHHHHHHHhhCeE
Confidence 34556778888 6788999999999999999987
No 186
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=37.20 E-value=96 Score=21.00 Aligned_cols=29 Identities=31% Similarity=0.405 Sum_probs=25.0
Q ss_pred hcCcccHHHHHHHhCCCHHHHHHHHHHhH
Q 016147 304 YYSRITLKRLAELLCLSIQEAEKHLSDMV 332 (394)
Q Consensus 304 ~Y~~Isl~rLa~lL~ls~~e~E~~ls~MI 332 (394)
++...+...+|+.+|+|..-+...+.++.
T Consensus 15 ~~~g~s~~eia~~l~is~~tv~~~~~~~~ 43 (58)
T smart00421 15 LAEGLTNKEIAERLGISEKTVKTHLSNIM 43 (58)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 45678999999999999999999888763
No 187
>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=37.01 E-value=1.5e+02 Score=28.71 Aligned_cols=39 Identities=15% Similarity=0.246 Sum_probs=34.2
Q ss_pred CcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEEeccC
Q 016147 306 SRITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKIDRP 344 (394)
Q Consensus 306 ~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~akIDq~ 344 (394)
-.|+++.||+-+++|.+.+-..+......+.|+|++|..
T Consensus 129 G~vsi~eLa~~~~Lp~efl~~~li~~~lg~~I~g~~d~~ 167 (272)
T PF09743_consen 129 GQVSISELAKQYDLPSEFLKEELISKRLGKIIKGRLDGD 167 (272)
T ss_pred CeEeHHHHHHhcCCcHHHHHHHHhhhhcCcceeEEEeCC
Confidence 679999999999999999996666667788899999988
No 188
>KOG3250 consensus COP9 signalosome, subunit CSN7 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=36.13 E-value=61 Score=30.51 Aligned_cols=76 Identities=21% Similarity=0.322 Sum_probs=57.7
Q ss_pred HHhhcCcccHHHHHHHhCCC-HHHHHHHHHHhHhcCcEEEEeccCCCEEE--Eec-----CCCh---HHHHHHHHHHHHH
Q 016147 301 VSKYYSRITLKRLAELLCLS-IQEAEKHLSDMVVSKALVAKIDRPQGIVC--FQV-----AKDS---NDILNSWAMNLEK 369 (394)
Q Consensus 301 isk~Y~~Isl~rLa~lL~ls-~~e~E~~ls~MI~~g~l~akIDq~~giV~--F~~-----~k~~---~~~L~~W~~~I~~ 369 (394)
.+.+-+.|.-.-|-.++.++ +-++|.++.+.+..+-+.|||||.+...+ |.- +++- --.|.+|.+.-..
T Consensus 103 las~~k~lpy~~Ll~~l~~~nvrelEd~iieamya~IlrGkldqr~q~leV~faigRdlr~k~i~nm~~TL~~w~~~cen 182 (258)
T KOG3250|consen 103 LASFEKCLPYLVLLRLLPSRNVRELEDLIIEAMYADILRGKLDQRNQTLEVDFAIGRDLRSKDIDNMKYTLDEWCEGCEN 182 (258)
T ss_pred hhhhchhhhHHHHHhhccCCchhHHHHHHHHHHHHHHHHhhHHhhcceEeechhhcccccHhHHHHHHHHHHHHHHHHHH
Confidence 33556677777788888874 78999999999999999999999999854 432 2221 2468889888888
Q ss_pred HHHHHHH
Q 016147 370 LLDLVEK 376 (394)
Q Consensus 370 l~~~V~k 376 (394)
++-.|+.
T Consensus 183 vL~~ie~ 189 (258)
T KOG3250|consen 183 VLFGIEA 189 (258)
T ss_pred HHHHHHh
Confidence 8877765
No 189
>PRK10870 transcriptional repressor MprA; Provisional
Probab=35.09 E-value=2.6e+02 Score=25.00 Aligned_cols=42 Identities=12% Similarity=0.000 Sum_probs=37.1
Q ss_pred cccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEEeccCCCEE
Q 016147 307 RITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKIDRPQGIV 348 (394)
Q Consensus 307 ~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~akIDq~~giV 348 (394)
.++...||+.++++..-+=..+.+|+..|-|.-.-|..++=+
T Consensus 71 ~it~~eLa~~l~l~~~tvsr~v~rLe~kGlV~R~~~~~DrR~ 112 (176)
T PRK10870 71 SIQPSELSCALGSSRTNATRIADELEKRGWIERRESDNDRRC 112 (176)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCCCCCe
Confidence 589999999999999999999999999999987777766443
No 190
>PF10345 Cohesin_load: Cohesin loading factor; InterPro: IPR019440 Cohesin loading factor is a conserved protein that has been characterised in fungi. It is associated with the cohesin complex and is required in G1 for cohesin binding to chromosomes, but is dispensable in G2 when cohesion has been established. It is often referred to as Ssl3 in Schizosaccharomyces pombe (Fission yeast), and Scc4 in Saccharomyces cerevisiae (Baker's yeast). It complexes with Mis4 [].
Probab=34.74 E-value=6.1e+02 Score=27.31 Aligned_cols=129 Identities=17% Similarity=0.134 Sum_probs=82.3
Q ss_pred Hhhhhc-CCcchHHHHHHHHHHHHHHHH-HHhcCHHHHHHHHHHhhhhhc-ccC-cHHHHHHHHHHHHHHHhccCChHHH
Q 016147 46 TLNSVS-AGKIYVEIERARLIKKLAKIK-EEQGLIAEAADLMQEVAVETF-GAM-AKTEKIAFILEQVRLCLDRQDYVRA 121 (394)
Q Consensus 46 ~L~~vt-~gki~~E~era~l~~~La~i~-e~~gd~~eAa~iL~~i~vEt~-~~m-~~~eK~e~~Leq~rL~L~~~D~~~a 121 (394)
.|+.+. ..++..+ +.|+++.+||.++ ++..++++|-..|..--.=+. ..+ +-+..+++.| +|++-..+-.. |
T Consensus 43 CL~~~~~~~~l~p~-~ea~~~l~la~iL~~eT~n~~~Ae~~L~k~~~l~~~~~~~d~k~~~~~ll--~~i~~~~~~~~-a 118 (608)
T PF10345_consen 43 CLEAVLKQFKLSPR-QEARVRLRLASILLEETENLDLAETYLEKAILLCERHRLTDLKFRCQFLL--ARIYFKTNPKA-A 118 (608)
T ss_pred HHHHHhccCCCCHH-HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhccccchHHHHHHHHHHH--HHHHHhcCHHH-H
Confidence 555544 6677765 6699999999997 477799999988885322222 223 3356666666 88888887776 7
Q ss_pred HHHHHhhCccccCCCCccccCCCCCCCcccccCCCCccchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhccCCCCCC
Q 016147 122 QILSRKISPRVFDADPSKEKKKPKEGDNVVEEAPADIPSLLELKRIYYELMIRYYSHNNDYLEICRCYKAIYEIPYIKED 201 (394)
Q Consensus 122 ~~~~~Ki~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~~~~flea~k~y~ei~~t~~i~~d 201 (394)
..+.++.-...-..+ ...+-.-.+|... .++...+++-.|+..+..+...+....|
T Consensus 119 ~~~l~~~I~~~~~~~----------------------~~~w~~~frll~~--~l~~~~~d~~~Al~~L~~~~~~a~~~~d 174 (608)
T PF10345_consen 119 LKNLDKAIEDSETYG----------------------HSAWYYAFRLLKI--QLALQHKDYNAALENLQSIAQLANQRGD 174 (608)
T ss_pred HHHHHHHHHHHhccC----------------------chhHHHHHHHHHH--HHHHhcccHHHHHHHHHHHHHHhhhcCC
Confidence 777777554321100 0123344455433 4443348999999999999987764444
Q ss_pred h
Q 016147 202 P 202 (394)
Q Consensus 202 ~ 202 (394)
+
T Consensus 175 ~ 175 (608)
T PF10345_consen 175 P 175 (608)
T ss_pred H
Confidence 4
No 191
>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=34.37 E-value=1.2e+02 Score=32.43 Aligned_cols=65 Identities=22% Similarity=0.227 Sum_probs=52.1
Q ss_pred HHHHHHHHHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCc
Q 016147 60 ERARLIKKLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISP 130 (394)
Q Consensus 60 era~l~~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~ 130 (394)
|.+.+-+-.+.++++.|++++|.+.|.+..- ..-.|+.+.-..+++++.-|++..|+.+..+.-.
T Consensus 2 E~SE~lLY~~~il~e~g~~~~AL~~L~~~~~------~I~Dk~~~~E~rA~ll~kLg~~~eA~~~y~~Li~ 66 (517)
T PF12569_consen 2 EHSELLLYKNSILEEAGDYEEALEHLEKNEK------QILDKLAVLEKRAELLLKLGRKEEAEKIYRELID 66 (517)
T ss_pred cHHHHHHHHHHHHHHCCCHHHHHHHHHhhhh------hCCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence 5667778889999999999999999976221 2235677777889999999999999998887643
No 192
>PF12964 DUF3853: Protein of unknown function (DUF3853); InterPro: IPR024363 This entry represents a family of uncharacterised proteins that were found by clustering human gut metagenomic sequences [].
Probab=33.73 E-value=31 Score=28.11 Aligned_cols=41 Identities=20% Similarity=0.169 Sum_probs=35.6
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEEeccCCCEEEEecC
Q 016147 309 TLKRLAELLCLSIQEAEKHLSDMVVSKALVAKIDRPQGIVCFQVA 353 (394)
Q Consensus 309 sl~rLa~lL~ls~~e~E~~ls~MI~~g~l~akIDq~~giV~F~~~ 353 (394)
-++.||++||.|.. .++++..+|.|+--|=|..+.|.|+..
T Consensus 47 G~~GlAklfgcSv~----Ta~RiK~sG~id~AI~Q~Gr~IivD~~ 87 (96)
T PF12964_consen 47 GLKGLAKLFGCSVP----TANRIKKSGKIDPAITQIGRKIIVDAD 87 (96)
T ss_pred hHHHHHHHhCCCch----hHHHHHhcCCccHHHHHcCCEEEEeHH
Confidence 57889999999986 457888999999999999999999864
No 193
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=33.30 E-value=1e+02 Score=21.81 Aligned_cols=40 Identities=13% Similarity=0.156 Sum_probs=33.2
Q ss_pred HHHHHHHHHhhcCcccHHHHHHHhCCCHHHHHHHHHHhHh
Q 016147 294 IEHNILVVSKYYSRITLKRLAELLCLSIQEAEKHLSDMVV 333 (394)
Q Consensus 294 iEHNI~visk~Y~~Isl~rLa~lL~ls~~e~E~~ls~MI~ 333 (394)
.++-+.+..+.=.+.+...||..+|+|..-+-+.+..++.
T Consensus 6 ~d~lll~L~~LR~~~~~~~La~~FgIs~stvsri~~~~~~ 45 (53)
T PF13613_consen 6 EDQLLLTLMYLRLNLTFQDLAYRFGISQSTVSRIFHEWIP 45 (53)
T ss_pred HHHHHHHHHHHHcCCcHhHHhhheeecHHHHHHHHHHHHH
Confidence 4556677788889999999999999999988888777653
No 194
>CHL00033 ycf3 photosystem I assembly protein Ycf3
Probab=33.18 E-value=3.2e+02 Score=23.56 Aligned_cols=69 Identities=12% Similarity=-0.016 Sum_probs=53.2
Q ss_pred HHHHHHHHHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCcc
Q 016147 60 ERARLIKKLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPR 131 (394)
Q Consensus 60 era~l~~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~ 131 (394)
..+.....++..+...|++++|...+...--... +.......+.....++...+++..|..+..++-..
T Consensus 33 ~~a~~~~~~g~~~~~~g~~~~A~~~~~~al~l~~---~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~~ 101 (168)
T CHL00033 33 KEAFTYYRDGMSAQSEGEYAEALQNYYEAMRLEI---DPYDRSYILYNIGLIHTSNGEHTKALEYYFQALER 101 (168)
T ss_pred HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhccc---cchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence 4677778999999999999999998876532211 11223457788899999999999999999988754
No 195
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=33.11 E-value=1.2e+02 Score=20.68 Aligned_cols=29 Identities=24% Similarity=0.368 Sum_probs=24.8
Q ss_pred hcCcccHHHHHHHhCCCHHHHHHHHHHhH
Q 016147 304 YYSRITLKRLAELLCLSIQEAEKHLSDMV 332 (394)
Q Consensus 304 ~Y~~Isl~rLa~lL~ls~~e~E~~ls~MI 332 (394)
++...+...+|+.+|+|+.-+...+.++.
T Consensus 12 ~~~~~s~~eia~~l~~s~~tv~~~~~~~~ 40 (57)
T cd06170 12 LAEGKTNKEIADILGISEKTVKTHLRNIM 40 (57)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 46778999999999999999998877653
No 196
>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=32.98 E-value=3.4e+02 Score=27.49 Aligned_cols=95 Identities=19% Similarity=0.215 Sum_probs=65.4
Q ss_pred HHHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCccccCCCCccccCCCC
Q 016147 66 KKLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPRVFDADPSKEKKKPK 145 (394)
Q Consensus 66 ~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~~~~~~~~~~~~~~~ 145 (394)
...|.+....|+.+.|.+.|.... +. .+...+.+-+..+++.+..+|+..|.....+..... |
T Consensus 122 llaA~aa~~~g~~~~A~~~l~~a~-~~----~p~~~l~~~~~~a~l~l~~~~~~~Al~~l~~l~~~~----P-------- 184 (409)
T TIGR00540 122 IKAAEAAQQRGDEARANQHLEEAA-EL----AGNDNILVEIARTRILLAQNELHAARHGVDKLLEMA----P-------- 184 (409)
T ss_pred HHHHHHHHHCCCHHHHHHHHHHHH-Hh----CCcCchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC----C--------
Confidence 356788888999999999888742 21 222334445556999999999999999988877542 1
Q ss_pred CCCcccccCCCCccchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhcc
Q 016147 146 EGDNVVEEAPADIPSLLELKRIYYELMIRYYSHNNDYLEICRCYKAIYEI 195 (394)
Q Consensus 146 ~~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~~~~flea~k~y~ei~~t 195 (394)
+..+. +.+....+...+++-++-..+......
T Consensus 185 --------------~~~~~----l~ll~~~~~~~~d~~~a~~~l~~l~k~ 216 (409)
T TIGR00540 185 --------------RHKEV----LKLAEEAYIRSGAWQALDDIIDNMAKA 216 (409)
T ss_pred --------------CCHHH----HHHHHHHHHHHhhHHHHHHHHHHHHHc
Confidence 11222 445667778888888777777666643
No 197
>PF08672 APC2: Anaphase promoting complex (APC) subunit 2; InterPro: IPR014786 The anaphase-promoting complex (APC) or cyclosome is a multi-subunit E3 protein ubiquitin ligase that regulates important events in mitosis such as the initiation of anaphase and exit from telophase. The APC, in conjunction with other enzymes, assembles multi-ubiquitin chains on a variety of regulatory proteins, thereby targeting them for proteolysis by the 26S proteasome. Anaphase is initiated when the APC triggers the destruction of securin, thereby allowing the protease, separase, to disrupt sister-chromatid cohesion. Securin ubiquitination by the APC is inhibited by cyclin-dependent kinase 1 (Cdk1)-dependent phosphorylation []. Forkhead Box M1 (FoxM1), which is a transcription factor that is over-expressed in many cancers, is degraded in late mitosis and early G1 phase by the APC/cyclosome (APC/C) E3 ubiquitin ligase []. The APC/C targets mitotic cyclins for destruction in mitosis and G1 phase and is then inactivated at S phase. It thereby generates alternating states of high and low cyclin-Cdk activity, which is required for the alternation of mitosis and DNA replication []. The APC/C is composed of at least 13 subunits that stay tightly associated throughout the cell cycle: APC1, APC2, APC4, APC5, APC9, APC11, CDC16, CDC23, CDC26, CDC27, DOC1, MND2 and SWM1[], []. In fission yeast the 13 subunits are known as: Apc1, Apc2, Nuc2, Apc4, Apc5, Cut9, Apc8, Apc10, Apc11, Hcn1, Apc13, Apc14 and Apc15 []. This entry represents a C-terminal domain found in APC subunit 2. ; PDB: 1LDD_A.
Probab=32.95 E-value=51 Score=24.42 Aligned_cols=24 Identities=21% Similarity=0.299 Sum_probs=18.3
Q ss_pred hCCCHHHHHHHHHHhHhcCcEEEE
Q 016147 317 LCLSIQEAEKHLSDMVVSKALVAK 340 (394)
Q Consensus 317 L~ls~~e~E~~ls~MI~~g~l~ak 340 (394)
.+.|.++++.++..+|.+|++.+.
T Consensus 31 ~~~s~~eL~~fL~~lv~e~~L~~~ 54 (60)
T PF08672_consen 31 YDISLEELQEFLDRLVEEGKLECS 54 (60)
T ss_dssp TT--HHHHHHHHHHHHHTTSEE--
T ss_pred CCCCHHHHHHHHHHHHHCCcEEec
Confidence 567889999999999999999764
No 198
>PF05584 Sulfolobus_pRN: Sulfolobus plasmid regulatory protein; InterPro: IPR008848 This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus.
Probab=32.85 E-value=2.2e+02 Score=22.00 Aligned_cols=44 Identities=23% Similarity=0.189 Sum_probs=36.9
Q ss_pred HHHHHHHHhhcCcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEE
Q 016147 295 EHNILVVSKYYSRITLKRLAELLCLSIQEAEKHLSDMVVSKALVAK 340 (394)
Q Consensus 295 EHNI~visk~Y~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~ak 340 (394)
+.-+.++|+- ++|++.|-+-.|++-..+-..+++|...|-|.-+
T Consensus 8 ~~IL~~ls~~--c~TLeeL~ekTgi~k~~LlV~LsrL~k~GiI~Rk 51 (72)
T PF05584_consen 8 QKILIILSKR--CCTLEELEEKTGISKNTLLVYLSRLAKRGIIERK 51 (72)
T ss_pred HHHHHHHHhc--cCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeeee
Confidence 3344556665 9999999999999999999999999999988543
No 199
>COG3063 PilF Tfp pilus assembly protein PilF [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=32.58 E-value=4.6e+02 Score=25.17 Aligned_cols=139 Identities=16% Similarity=0.021 Sum_probs=94.6
Q ss_pred HHHHHHHHHHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCccccCCCCc
Q 016147 59 IERARLIKKLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPRVFDADPS 138 (394)
Q Consensus 59 ~era~l~~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~~~~~~~~ 138 (394)
.|.+..+..||-=|-+.||...|-+-|.+.- +.-.+ --.-++--+-+|-..|+.+.|....+|+-..--.++
T Consensus 32 ~~aa~arlqLal~YL~~gd~~~A~~nlekAL-~~DPs-----~~~a~~~~A~~Yq~~Ge~~~A~e~YrkAlsl~p~~G-- 103 (250)
T COG3063 32 NEAAKARLQLALGYLQQGDYAQAKKNLEKAL-EHDPS-----YYLAHLVRAHYYQKLGENDLADESYRKALSLAPNNG-- 103 (250)
T ss_pred HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH-HhCcc-----cHHHHHHHHHHHHHcCChhhHHHHHHHHHhcCCCcc--
Confidence 4778889999999999999999988666521 11111 122344445667778999999999999875422221
Q ss_pred cccCCCCCCCcccccCCCCccchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhccCCCCCChhcHHHHHHHHHHHHHh
Q 016147 139 KEKKKPKEGDNVVEEAPADIPSLLELKRIYYELMIRYYSHNNDYLEICRCYKAIYEIPYIKEDPAQWMPVLRKICWYLVL 218 (394)
Q Consensus 139 ~~~~~~~~~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~~~~flea~k~y~ei~~t~~i~~d~~~~~~~L~~av~~~IL 218 (394)
++.- =.+-+.-..+.|-+|-..|....+.|...+- ...+.++++|..=
T Consensus 104 ---------------------dVLN-------NYG~FLC~qg~~~eA~q~F~~Al~~P~Y~~~----s~t~eN~G~Cal~ 151 (250)
T COG3063 104 ---------------------DVLN-------NYGAFLCAQGRPEEAMQQFERALADPAYGEP----SDTLENLGLCALK 151 (250)
T ss_pred ---------------------chhh-------hhhHHHHhCCChHHHHHHHHHHHhCCCCCCc----chhhhhhHHHHhh
Confidence 1211 2234455577899999999999998887532 3458899999886
Q ss_pred CC-CChhchHhhhhhhcccC
Q 016147 219 AP-HDPMQSSLLNSTLEDKN 237 (394)
Q Consensus 219 ap-~~~~rs~ll~~l~~d~~ 237 (394)
+. ++.-+..+-..+..||.
T Consensus 152 ~gq~~~A~~~l~raL~~dp~ 171 (250)
T COG3063 152 AGQFDQAEEYLKRALELDPQ 171 (250)
T ss_pred cCCchhHHHHHHHHHHhCcC
Confidence 65 55556666667777763
No 200
>KOG1900 consensus Nuclear pore complex, Nup155 component (D Nup154, sc Nup157/Nup170) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=31.66 E-value=4.7e+02 Score=30.99 Aligned_cols=57 Identities=9% Similarity=0.186 Sum_probs=44.3
Q ss_pred HHHHHHHHHHHHhhhhHHHHHHHHHHHhccCCCCCChhcHHHHHHHHHHHHHhCCCCh
Q 016147 166 RIYYELMIRYYSHNNDYLEICRCYKAIYEIPYIKEDPAQWMPVLRKICWYLVLAPHDP 223 (394)
Q Consensus 166 lk~~~~~~~~~~~~~~flea~k~y~ei~~t~~i~~d~~~~~~~L~~av~~~ILap~~~ 223 (394)
+|+.++.-+||.-.+.|.+||.-.+.+- |-...-.-+++++.|.+|+.|+=-+..+.
T Consensus 1007 lk~~dLLw~YY~K~e~~~~AA~VL~rLA-t~~~~itLeqRiEyLsRA~~~~~s~s~~s 1063 (1311)
T KOG1900|consen 1007 LKIFDLLWKYYEKREQFSQAAHVLYRLA-TSSFDITLEQRIEYLSRAVGFAKSSSPSS 1063 (1311)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHh-hcCCCccHHHHHHHHHHHhhhcccCCCch
Confidence 7899999999999999999999888776 33222223688999999998876665443
No 201
>KOG2047 consensus mRNA splicing factor [RNA processing and modification]
Probab=31.41 E-value=3.2e+02 Score=30.14 Aligned_cols=163 Identities=15% Similarity=0.187 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCc--------cccC
Q 016147 63 RLIKKLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISP--------RVFD 134 (394)
Q Consensus 63 ~l~~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~--------~~~~ 134 (394)
+|.-.+|++||..|+++.|-.++..-.-=.|+ ...+-.++++.-+.+-|..+++..|-.+..++-. .+-.
T Consensus 388 ~Lw~~faklYe~~~~l~~aRvifeka~~V~y~--~v~dLa~vw~~waemElrh~~~~~Al~lm~~A~~vP~~~~~~~yd~ 465 (835)
T KOG2047|consen 388 TLWVEFAKLYENNGDLDDARVIFEKATKVPYK--TVEDLAEVWCAWAEMELRHENFEAALKLMRRATHVPTNPELEYYDN 465 (835)
T ss_pred hHHHHHHHHHHhcCcHHHHHHHHHHhhcCCcc--chHHHHHHHHHHHHHHHhhhhHHHHHHHHHhhhcCCCchhhhhhcC
Q ss_pred CCCccccCCCC-----------CCCcccccCCCCccchHHHHHHHHHHHHHHHHh--hhhHHH-HHHHHHHHhccCCCCC
Q 016147 135 ADPSKEKKKPK-----------EGDNVVEEAPADIPSLLELKRIYYELMIRYYSH--NNDYLE-ICRCYKAIYEIPYIKE 200 (394)
Q Consensus 135 ~~~~~~~~~~~-----------~~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~--~~~fle-a~k~y~ei~~t~~i~~ 200 (394)
..|.+-..+-- |.-+...-.+..++++.|+|+--=+..+.|... +++|++ +++.|..-...+.-+.
T Consensus 466 ~~pvQ~rlhrSlkiWs~y~DleEs~gtfestk~vYdriidLriaTPqii~NyAmfLEeh~yfeesFk~YErgI~LFk~p~ 545 (835)
T KOG2047|consen 466 SEPVQARLHRSLKIWSMYADLEESLGTFESTKAVYDRIIDLRIATPQIIINYAMFLEEHKYFEESFKAYERGISLFKWPN 545 (835)
T ss_pred CCcHHHHHHHhHHHHHHHHHHHHHhccHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhhHHHHHHHHHHHcCCccCCCcc
Q ss_pred ChhcHHHHHHHHHHHHHhCCCChhchHhh
Q 016147 201 DPAQWMPVLRKICWYLVLAPHDPMQSSLL 229 (394)
Q Consensus 201 d~~~~~~~L~~av~~~ILap~~~~rs~ll 229 (394)
-.+-|.+-|..++- =.+.-.++|.+-|
T Consensus 546 v~diW~tYLtkfi~--rygg~klEraRdL 572 (835)
T KOG2047|consen 546 VYDIWNTYLTKFIK--RYGGTKLERARDL 572 (835)
T ss_pred HHHHHHHHHHHHHH--HhcCCCHHHHHHH
No 202
>cd08312 Death_MyD88 Death domain of Myeloid Differentation primary response protein MyD88. Death Domain (DD) of Myeloid Differentiation primary response protein 88 (MyD88). MyD88 is an adaptor protein involved in interleukin-1 receptor (IL-1R)- and Toll-like receptor (TLR)-induced activation of nuclear factor-kappaB (NF-kB) and mitogen activated protein kinase pathways that lead to the induction of proinflammatory cytokines. It is a key component in the signaling pathway of pathogen recognition in the innate immune system. MyD88 contains an N-terminal DD and a C-terminal Toll/IL-1 Receptor (TIR) homology domain that mediates interaction with TLRs and IL-1R. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and
Probab=30.94 E-value=1.1e+02 Score=23.78 Aligned_cols=46 Identities=24% Similarity=0.387 Sum_probs=30.2
Q ss_pred HHHHHHhCCCHHHHHHHHHHhHhcCcEEEEeccCCCEEEEecCCChHHHHHHHHHH-----HHHHHHHHHHHH
Q 016147 311 KRLAELLCLSIQEAEKHLSDMVVSKALVAKIDRPQGIVCFQVAKDSNDILNSWAMN-----LEKLLDLVEKSC 378 (394)
Q Consensus 311 ~rLa~lL~ls~~e~E~~ls~MI~~g~l~akIDq~~giV~F~~~k~~~~~L~~W~~~-----I~~l~~~V~k~~ 378 (394)
..||+.||++..++..+-. .+.++...|+.|... |..|+..+.++.
T Consensus 20 r~LA~~Lg~~~~~I~~f~~----------------------~~sPt~~lL~~W~~r~~~atv~~L~~~L~~~~ 70 (79)
T cd08312 20 TALAEEMGFEYLEIRNFET----------------------KPSPTEKVLEDWETRPDGATVGNLLELLEKLE 70 (79)
T ss_pred HHHHHHcCCCHHHHHHHcc----------------------CCChHHHHHHHHHhcCCCCcHHHHHHHHHHcC
Confidence 4578888888777653311 124557899999655 777777666544
No 203
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=30.91 E-value=2.7e+02 Score=26.08 Aligned_cols=48 Identities=13% Similarity=0.080 Sum_probs=41.4
Q ss_pred cCcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEEeccCCCEEEEec
Q 016147 305 YSRITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKIDRPQGIVCFQV 352 (394)
Q Consensus 305 Y~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~akIDq~~giV~F~~ 352 (394)
...||.+.||+.+++|..-+=+.+.+|...|-|.-.+|.....|....
T Consensus 19 ~~~IS~~eLA~~L~iS~~Tvsr~Lk~LEe~GlI~R~~~~r~~~v~LTe 66 (217)
T PRK14165 19 TVKISSSEFANHTGTSSKTAARILKQLEDEGYITRTIVPRGQLITITE 66 (217)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEEcCCceEEEECH
Confidence 347899999999999999999999999999999988887655566554
No 204
>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and 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 []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa []. This region is probably a DNA-binding helix-turn-helix.; PDB: 2XV4_S 2XUB_A.
Probab=30.65 E-value=2.2e+02 Score=20.93 Aligned_cols=35 Identities=20% Similarity=0.252 Sum_probs=29.1
Q ss_pred hcCcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEE
Q 016147 304 YYSRITLKRLAELLCLSIQEAEKHLSDMVVSKALV 338 (394)
Q Consensus 304 ~Y~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~ 338 (394)
-+-+.|+.++.+..++|+.++-+-++-||.-|-+.
T Consensus 24 ~~G~ltl~~i~~~t~l~~~~Vk~~L~~LiQh~~v~ 58 (62)
T PF08221_consen 24 SRGRLTLREIVRRTGLSPKQVKKALVVLIQHNLVQ 58 (62)
T ss_dssp HC-SEEHHHHHHHHT--HHHHHHHHHHHHHTTSEE
T ss_pred HcCCcCHHHHHHHhCCCHHHHHHHHHHHHHcCCee
Confidence 57899999999999999999999999999988653
No 205
>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=30.64 E-value=1.2e+02 Score=18.56 Aligned_cols=25 Identities=20% Similarity=0.110 Sum_probs=15.0
Q ss_pred HHHHHHHHHHHHhcCHHHHHHHHHH
Q 016147 63 RLIKKLAKIKEEQGLIAEAADLMQE 87 (394)
Q Consensus 63 ~l~~~La~i~e~~gd~~eAa~iL~~ 87 (394)
++-..+|..|...|++++|...++.
T Consensus 2 ~~~~~~g~~~~~~~~~~~A~~~~~~ 26 (34)
T PF00515_consen 2 EAYYNLGNAYFQLGDYEEALEYYQR 26 (34)
T ss_dssp HHHHHHHHHHHHTT-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHhCCchHHHHHHHH
Confidence 3445666777777777777665543
No 206
>COG3629 DnrI DNA-binding transcriptional activator of the SARP family [Signal transduction mechanisms]
Probab=30.54 E-value=2.2e+02 Score=27.89 Aligned_cols=70 Identities=16% Similarity=0.133 Sum_probs=55.7
Q ss_pred chHHHHHHHHHHH-------HHHHHHHhcCHHHHHHHHHHhh-hhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHH
Q 016147 55 IYVEIERARLIKK-------LAKIKEEQGLIAEAADLMQEVA-VETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSR 126 (394)
Q Consensus 55 i~~E~era~l~~~-------La~i~e~~gd~~eAa~iL~~i~-vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~ 126 (394)
-||.++|.+++.. |++.+...|+++.+...++.+- .++| .| ..+...|+.|+..|+...|...++
T Consensus 139 ~WV~~~R~~l~e~~~~~l~~lae~~~~~~~~~~~~~~l~~Li~~dp~-----~E--~~~~~lm~~y~~~g~~~~ai~~y~ 211 (280)
T COG3629 139 EWVLEQRRALEELFIKALTKLAEALIACGRADAVIEHLERLIELDPY-----DE--PAYLRLMEAYLVNGRQSAAIRAYR 211 (280)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHhcCcc-----ch--HHHHHHHHHHHHcCCchHHHHHHH
Confidence 4677888888877 8888888999999998888753 2222 22 357888999999999999999999
Q ss_pred hhCcc
Q 016147 127 KISPR 131 (394)
Q Consensus 127 Ki~~~ 131 (394)
+.+..
T Consensus 212 ~l~~~ 216 (280)
T COG3629 212 QLKKT 216 (280)
T ss_pred HHHHH
Confidence 98875
No 207
>COG5481 Uncharacterized conserved small protein containing a coiled-coil domain [Function unknown]
Probab=30.53 E-value=1.4e+02 Score=22.13 Aligned_cols=31 Identities=19% Similarity=0.315 Sum_probs=26.5
Q ss_pred HHHHHHHHHHHHHHHhcCHHHHHHHHHHhhh
Q 016147 60 ERARLIKKLAKIKEEQGLIAEAADLMQEVAV 90 (394)
Q Consensus 60 era~l~~~La~i~e~~gd~~eAa~iL~~i~v 90 (394)
+-|.+++.+|.+.++..|++.|.+.+.+.+-
T Consensus 5 dqaeirl~~arLrqeH~D~DaaInAmi~~~c 35 (67)
T COG5481 5 DQAEIRLTLARLRQEHADFDAAINAMIATGC 35 (67)
T ss_pred cHHHHHHHHHHHHHHHhhHHHHHHHHHHhCC
Confidence 4567899999999999999999999987443
No 208
>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=30.43 E-value=66 Score=22.94 Aligned_cols=26 Identities=31% Similarity=0.367 Sum_probs=19.5
Q ss_pred hcCcccHHHHHHHhCCCHHHHHHHHH
Q 016147 304 YYSRITLKRLAELLCLSIQEAEKHLS 329 (394)
Q Consensus 304 ~Y~~Isl~rLa~lL~ls~~e~E~~ls 329 (394)
-..+||-..||+.+|+++.++-+=+|
T Consensus 25 G~~~vSS~~La~~~gi~~~qVRKDlS 50 (50)
T PF06971_consen 25 GVERVSSQELAEALGITPAQVRKDLS 50 (50)
T ss_dssp T-SEE-HHHHHHHHTS-HHHHHHHHH
T ss_pred CCeeECHHHHHHHHCCCHHHhcccCC
Confidence 36789999999999999999876543
No 209
>PRK15174 Vi polysaccharide export protein VexE; Provisional
Probab=30.23 E-value=7.5e+02 Score=26.95 Aligned_cols=98 Identities=11% Similarity=0.013 Sum_probs=67.9
Q ss_pred HHHHHHHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCccccCCCCcccc
Q 016147 62 ARLIKKLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPRVFDADPSKEK 141 (394)
Q Consensus 62 a~l~~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~~~~~~~~~~~ 141 (394)
+++...||.++...|++++|...++..-- .. +.. .+......+++...|++..|.....++... +|
T Consensus 284 ~~a~~~lg~~l~~~g~~~eA~~~l~~al~-l~---P~~--~~a~~~La~~l~~~G~~~eA~~~l~~al~~----~P---- 349 (656)
T PRK15174 284 VRIVTLYADALIRTGQNEKAIPLLQQSLA-TH---PDL--PYVRAMYARALRQVGQYTAASDEFVQLARE----KG---- 349 (656)
T ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHHHH-hC---CCC--HHHHHHHHHHHHHCCCHHHHHHHHHHHHHh----Cc----
Confidence 45678899999999999999998887442 21 111 233445678888999999999999887653 11
Q ss_pred CCCCCCCcccccCCCCccchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhcc
Q 016147 142 KKPKEGDNVVEEAPADIPSLLELKRIYYELMIRYYSHNNDYLEICRCYKAIYEI 195 (394)
Q Consensus 142 ~~~~~~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~~~~flea~k~y~ei~~t 195 (394)
... .++...+..+...+++-+|-..|......
T Consensus 350 ------------------~~~----~~~~~~a~al~~~G~~deA~~~l~~al~~ 381 (656)
T PRK15174 350 ------------------VTS----KWNRYAAAALLQAGKTSEAESVFEHYIQA 381 (656)
T ss_pred ------------------cch----HHHHHHHHHHHHCCCHHHHHHHHHHHHHh
Confidence 111 12333345566788899999888887753
No 210
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=30.21 E-value=59 Score=26.21 Aligned_cols=25 Identities=28% Similarity=0.303 Sum_probs=22.1
Q ss_pred cCcccHHHHHHHhCCCHHHHHHHHH
Q 016147 305 YSRITLKRLAELLCLSIQEAEKHLS 329 (394)
Q Consensus 305 Y~~Isl~rLa~lL~ls~~e~E~~ls 329 (394)
-+.+|.+.+|.-||+|++++|.++.
T Consensus 21 ~~~ls~~~ia~dL~~s~~~le~vL~ 45 (89)
T PF10078_consen 21 LSGLSLEQIAADLGTSPEHLEQVLN 45 (89)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 4678999999999999999998864
No 211
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=29.95 E-value=31 Score=24.53 Aligned_cols=22 Identities=32% Similarity=0.386 Sum_probs=19.0
Q ss_pred cccHHHHHHHhCCCHHHHHHHH
Q 016147 307 RITLKRLAELLCLSIQEAEKHL 328 (394)
Q Consensus 307 ~Isl~rLa~lL~ls~~e~E~~l 328 (394)
.+++..||+.+|+++.++-..+
T Consensus 3 ~i~V~elAk~l~v~~~~ii~~l 24 (54)
T PF04760_consen 3 KIRVSELAKELGVPSKEIIKKL 24 (54)
T ss_dssp EE-TTHHHHHHSSSHHHHHHHH
T ss_pred ceEHHHHHHHHCcCHHHHHHHH
Confidence 5788999999999999988877
No 212
>COG5308 NUP170 Nuclear pore complex subunit [Intracellular trafficking and secretion]
Probab=29.75 E-value=2e+02 Score=32.70 Aligned_cols=100 Identities=21% Similarity=0.341 Sum_probs=64.6
Q ss_pred HHHHHHHHHHHhhhhHHHHHHHHHHHhccCCCCCChhcHHHHHHHHHHHH-HhCCCC-------------------hhch
Q 016147 167 IYYELMIRYYSHNNDYLEICRCYKAIYEIPYIKEDPAQWMPVLRKICWYL-VLAPHD-------------------PMQS 226 (394)
Q Consensus 167 k~~~~~~~~~~~~~~flea~k~y~ei~~t~~i~~d~~~~~~~L~~av~~~-ILap~~-------------------~~rs 226 (394)
|--++.=.||.-..+|++|+...+++-.+. .+-.-++++++|..|-=++ .-.|.+ .-|.
T Consensus 969 kIsnLlW~Yy~kre~f~eaa~vLy~LAtsn-fd~sLeeRIE~L~rAngfc~s~~p~sqk~~~vql~~~v~e~levAsIQd 1047 (1263)
T COG5308 969 KISNLLWKYYVKREDFVEAAQVLYELATSN-FDVSLEERIELLRRANGFCSSHVPNSQKHVNVQLFNEVKERLEVASIQD 1047 (1263)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHhhcC-CCccHHHHHHHHHHhccccccCCcchhHHHHHHHHHHHHHHhhhhhhHH
Confidence 344556688888999999999998887532 1112357888888765332 112222 1278
Q ss_pred HhhhhhhcccCcCCChhHH-HHHHHhcchhcccchhhHHHHHHhh
Q 016147 227 SLLNSTLEDKNLSEIPNFR-LLLKQLVTMEVIQWTSLWNTYKDEF 270 (394)
Q Consensus 227 ~ll~~l~~d~~l~~ip~~~-~L~k~f~~~eli~~~~~~~~~~~~l 270 (394)
|+|..++.|+|++.- ++ +|.+..- .+|++-+++-..|+.-+
T Consensus 1048 DiL~lvr~d~rId~~--~r~eL~k~Ld-G~il~lseLFNdyAdPl 1089 (1263)
T COG5308 1048 DILRLVRVDPRIDNN--KREELSKQLD-GEILSLSELFNDYADPL 1089 (1263)
T ss_pred HHHHHhccCCccCch--HHHHHHhhcC-CeeeeHHHHhhhccccc
Confidence 888889999887663 33 4666554 47888777665565333
No 213
>CHL00033 ycf3 photosystem I assembly protein Ycf3
Probab=29.62 E-value=2.7e+02 Score=24.00 Aligned_cols=70 Identities=10% Similarity=0.022 Sum_probs=46.4
Q ss_pred HHHHHHHHHHHHHHhcCHHHHHHHHHHhhhhhcccC-cHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCc
Q 016147 61 RARLIKKLAKIKEEQGLIAEAADLMQEVAVETFGAM-AKTEKIAFILEQVRLCLDRQDYVRAQILSRKISP 130 (394)
Q Consensus 61 ra~l~~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m-~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~ 130 (394)
.+..-..+|.++...|++++|.+.+....--..... +-.....++..+.|.+...+|+..|.....++..
T Consensus 71 ~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~~~~~~~~~~~~la~i~~~~~~~~~~~g~~~~A~~~~~~a~~ 141 (168)
T CHL00033 71 RSYILYNIGLIHTSNGEHTKALEYYFQALERNPFLPQALNNMAVICHYRGEQAIEQGDSEIAEAWFDQAAE 141 (168)
T ss_pred hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCcHHHHHHHHHHHHHhhHHHHHcccHHHHHHHHHHHHH
Confidence 455678899999999999999998876431111111 1123334455567777799999888777666543
No 214
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=29.25 E-value=97 Score=29.15 Aligned_cols=39 Identities=23% Similarity=0.258 Sum_probs=34.7
Q ss_pred HhhcCcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEE
Q 016147 302 SKYYSRITLKRLAELLCLSIQEAEKHLSDMVVSKALVAK 340 (394)
Q Consensus 302 sk~Y~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~ak 340 (394)
-+-=.-+|...||+.||+|+..+-..+-+++.+|-+...
T Consensus 20 L~~~g~~sa~elA~~Lgis~~avR~HL~~Le~~Glv~~~ 58 (218)
T COG2345 20 LKKSGPVSADELAEELGISPMAVRRHLDDLEAEGLVEVE 58 (218)
T ss_pred HhccCCccHHHHHHHhCCCHHHHHHHHHHHHhCcceeee
Confidence 344567899999999999999999999999999988777
No 215
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=29.00 E-value=1.7e+02 Score=26.05 Aligned_cols=33 Identities=12% Similarity=0.031 Sum_probs=30.0
Q ss_pred CcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEE
Q 016147 306 SRITLKRLAELLCLSIQEAEKHLSDMVVSKALV 338 (394)
Q Consensus 306 ~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~ 338 (394)
-.+|-+.||..+|++.+-+=+.+++|-.+|-|.
T Consensus 148 ~~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~ 180 (202)
T PRK13918 148 IYATHDELAAAVGSVRETVTKVIGELSREGYIR 180 (202)
T ss_pred ecCCHHHHHHHhCccHHHHHHHHHHHHHCCCEE
Confidence 357889999999999999999999999999775
No 216
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=28.90 E-value=3e+02 Score=24.61 Aligned_cols=42 Identities=14% Similarity=0.029 Sum_probs=33.5
Q ss_pred HHHHHhhcCcc-cHHHHHHHh--CCCHHHHHHHHHHhHhcCcEEE
Q 016147 298 ILVVSKYYSRI-TLKRLAELL--CLSIQEAEKHLSDMVVSKALVA 339 (394)
Q Consensus 298 I~visk~Y~~I-sl~rLa~lL--~ls~~e~E~~ls~MI~~g~l~a 339 (394)
||.+.....-- ....||+.| ++|++++++-|..|+.-|-|.=
T Consensus 29 ir~l~~l~~~~~d~~~iak~l~p~is~~ev~~sL~~L~~~gli~k 73 (171)
T PF14394_consen 29 IRELLPLMPFAPDPEWIAKRLRPKISAEEVRDSLEFLEKLGLIKK 73 (171)
T ss_pred HHHHhhcCCCCCCHHHHHHHhcCCCCHHHHHHHHHHHHHCCCeEE
Confidence 34444443333 889999999 9999999999999999998743
No 217
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=28.79 E-value=1.3e+02 Score=28.35 Aligned_cols=36 Identities=19% Similarity=0.286 Sum_probs=32.4
Q ss_pred hcCcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEE
Q 016147 304 YYSRITLKRLAELLCLSIQEAEKHLSDMVVSKALVA 339 (394)
Q Consensus 304 ~Y~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~a 339 (394)
-...++.+.||+.||+|+.-+.+.+..|...|.+..
T Consensus 15 ~~~~~~~~eLa~~l~VS~~TiRRdL~~L~~~~~l~r 50 (240)
T PRK10411 15 NHTSLTTEALAEQLNVSKETIRRDLNELQTQGKILR 50 (240)
T ss_pred HcCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence 467899999999999999999999999999887753
No 218
>KOG3060 consensus Uncharacterized conserved protein [Function unknown]
Probab=28.25 E-value=5.7e+02 Score=24.95 Aligned_cols=62 Identities=24% Similarity=0.253 Sum_probs=40.5
Q ss_pred HHHHHHHH-HHhccCChHHHHHHHHhhCccccCCCCccccCCCCCCCcccccCCCCccchHHHHHHHHHHHHHHHHhhhh
Q 016147 103 AFILEQVR-LCLDRQDYVRAQILSRKISPRVFDADPSKEKKKPKEGDNVVEEAPADIPSLLELKRIYYELMIRYYSHNND 181 (394)
Q Consensus 103 e~~Leq~r-L~L~~~D~~~a~~~~~Ki~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~~~~ 181 (394)
-+++||+- -.+..+..+-|+...+..+..+ .+. .++..+|.-+++. .++
T Consensus 52 w~l~EqV~IAAld~~~~~lAq~C~~~L~~~f-p~S----------------------~RV~~lkam~lEa-------~~~ 101 (289)
T KOG3060|consen 52 WTLYEQVFIAALDTGRDDLAQKCINQLRDRF-PGS----------------------KRVGKLKAMLLEA-------TGN 101 (289)
T ss_pred HHHHHHHHHHHHHhcchHHHHHHHHHHHHhC-CCC----------------------hhHHHHHHHHHHH-------hhc
Confidence 34556543 3566788889999999888775 211 2455555555544 666
Q ss_pred HHHHHHHHHHHhc
Q 016147 182 YLEICRCYKAIYE 194 (394)
Q Consensus 182 flea~k~y~ei~~ 194 (394)
|-+|-..|..+.+
T Consensus 102 ~~~A~e~y~~lL~ 114 (289)
T KOG3060|consen 102 YKEAIEYYESLLE 114 (289)
T ss_pred hhhHHHHHHHHhc
Confidence 6777778888776
No 219
>PRK14720 transcript cleavage factor/unknown domain fusion protein; Provisional
Probab=28.16 E-value=5.1e+02 Score=29.73 Aligned_cols=122 Identities=12% Similarity=0.189 Sum_probs=71.4
Q ss_pred HHHHHHHHHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCccccCCCCcc
Q 016147 60 ERARLIKKLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPRVFDADPSK 139 (394)
Q Consensus 60 era~l~~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~~~~~~~~~ 139 (394)
.....+..|...+-..|++++|..++.+ .++.+. ..+++++--.-|++..+++..+-.. ++-..+-. +
T Consensus 29 ~n~~a~~~Li~~~~~~~~~deai~i~~~-~l~~~P-----~~i~~yy~~G~l~~q~~~~~~~~lv--~~l~~~~~-~--- 96 (906)
T PRK14720 29 SKFKELDDLIDAYKSENLTDEAKDICEE-HLKEHK-----KSISALYISGILSLSRRPLNDSNLL--NLIDSFSQ-N--- 96 (906)
T ss_pred chHHHHHHHHHHHHhcCCHHHHHHHHHH-HHHhCC-----cceehHHHHHHHHHhhcchhhhhhh--hhhhhccc-c---
Confidence 3456778999999999999999998884 333322 2334444444488888887777666 33322211 1
Q ss_pred ccCCCCCCCcccccCCCCccchHHHHHHHHHHHHHHHHhh-------------hhHHHHHHHHHHHhccCCCCCChhcHH
Q 016147 140 EKKKPKEGDNVVEEAPADIPSLLELKRIYYELMIRYYSHN-------------NDYLEICRCYKAIYEIPYIKEDPAQWM 206 (394)
Q Consensus 140 ~~~~~~~~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~~-------------~~flea~k~y~ei~~t~~i~~d~~~~~ 206 (394)
..+..---|+.++..++.+. +++-++...|.++... ||.. .
T Consensus 97 --------------------~~~~~ve~~~~~i~~~~~~k~Al~~LA~~Ydk~g~~~ka~~~yer~L~~-----D~~n-~ 150 (906)
T PRK14720 97 --------------------LKWAIVEHICDKILLYGENKLALRTLAEAYAKLNENKKLKGVWERLVKA-----DRDN-P 150 (906)
T ss_pred --------------------cchhHHHHHHHHHHhhhhhhHHHHHHHHHHHHcCChHHHHHHHHHHHhc-----Cccc-H
Confidence 11233344566666666666 5666666666665542 2222 3
Q ss_pred HHHHHHHHHHHhC
Q 016147 207 PVLRKICWYLVLA 219 (394)
Q Consensus 207 ~~L~~av~~~ILa 219 (394)
.+|.+..++.-..
T Consensus 151 ~aLNn~AY~~ae~ 163 (906)
T PRK14720 151 EIVKKLATSYEEE 163 (906)
T ss_pred HHHHHHHHHHHHh
Confidence 4566655555544
No 220
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=27.78 E-value=1.5e+02 Score=28.10 Aligned_cols=36 Identities=19% Similarity=0.224 Sum_probs=32.3
Q ss_pred hhcCcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEE
Q 016147 303 KYYSRITLKRLAELLCLSIQEAEKHLSDMVVSKALV 338 (394)
Q Consensus 303 k~Y~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~ 338 (394)
+-...++.+.||+.||+|+.-+.+-|..|-..|.+.
T Consensus 15 ~~~~~~~~~ela~~l~vS~~TirRdL~~Le~~g~i~ 50 (251)
T PRK13509 15 AQLGFVTVEKVIERLGISPATARRDINKLDESGKLK 50 (251)
T ss_pred HHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 346889999999999999999999999999988773
No 221
>PRK14720 transcript cleavage factor/unknown domain fusion protein; Provisional
Probab=27.77 E-value=9.8e+02 Score=27.52 Aligned_cols=64 Identities=14% Similarity=0.079 Sum_probs=41.9
Q ss_pred HHHHHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCccccC
Q 016147 64 LIKKLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPRVFD 134 (394)
Q Consensus 64 l~~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~~~~ 134 (394)
+-..||..|...|+.++|..++..+-.=......---.+-+++... |..+|..+++|+-..+.+
T Consensus 118 Al~~LA~~Ydk~g~~~ka~~~yer~L~~D~~n~~aLNn~AY~~ae~-------dL~KA~~m~~KAV~~~i~ 181 (906)
T PRK14720 118 ALRTLAEAYAKLNENKKLKGVWERLVKADRDNPEIVKKLATSYEEE-------DKEKAITYLKKAIYRFIK 181 (906)
T ss_pred HHHHHHHHHHHcCChHHHHHHHHHHHhcCcccHHHHHHHHHHHHHh-------hHHHHHHHHHHHHHHHHh
Confidence 5578999999999999999988875532222222222333333332 888888888888666553
No 222
>PF13518 HTH_28: Helix-turn-helix domain
Probab=27.10 E-value=1.1e+02 Score=20.88 Aligned_cols=44 Identities=9% Similarity=0.127 Sum_probs=32.6
Q ss_pred HHHhhcCcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEEeccC
Q 016147 300 VVSKYYSRITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKIDRP 344 (394)
Q Consensus 300 visk~Y~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~akIDq~ 344 (394)
+|..+-..-|...+|..+|+|...+...+...=..| +.|-.+++
T Consensus 5 iv~~~~~g~s~~~~a~~~gis~~tv~~w~~~y~~~G-~~~l~~~~ 48 (52)
T PF13518_consen 5 IVELYLEGESVREIAREFGISRSTVYRWIKRYREGG-IEGLKPKK 48 (52)
T ss_pred HHHHHHcCCCHHHHHHHHCCCHhHHHHHHHHHHhcC-HHHhccCC
Confidence 344455667999999999999999988888777766 45554444
No 223
>KOG1585 consensus Protein required for fusion of vesicles in vesicular transport, gamma-SNAP [Intracellular trafficking, secretion, and vesicular transport]
Probab=27.04 E-value=6e+02 Score=24.79 Aligned_cols=61 Identities=21% Similarity=0.356 Sum_probs=36.7
Q ss_pred HHHHHHHHHHhhhhHHHHHHHHHHHhccCCCCCChhcHHHHHHHHHHHHHhCCCChhchHhhhhhhcc
Q 016147 168 YYELMIRYYSHNNDYLEICRCYKAIYEIPYIKEDPAQWMPVLRKICWYLVLAPHDPMQSSLLNSTLED 235 (394)
Q Consensus 168 ~~~~~~~~~~~~~~flea~k~y~ei~~t~~i~~d~~~~~~~L~~av~~~ILap~~~~rs~ll~~l~~d 235 (394)
-|-.++..|++.++|..+=++|++.+..|.... +++ ..+|++ +|..|+.+..+...++...
T Consensus 192 ~~va~ilv~L~~~Dyv~aekc~r~~~qip~f~~-sed-~r~len-----LL~ayd~gD~E~~~kvl~s 252 (308)
T KOG1585|consen 192 AYVAAILVYLYAHDYVQAEKCYRDCSQIPAFLK-SED-SRSLEN-----LLTAYDEGDIEEIKKVLSS 252 (308)
T ss_pred HHHHHHHHHhhHHHHHHHHHHhcchhcCccccC-hHH-HHHHHH-----HHHHhccCCHHHHHHHHcC
Confidence 355667777888888888888888777766532 222 233543 2344555555555555553
No 224
>PF12324 HTH_15: Helix-turn-helix domain of alkylmercury lyase; InterPro: IPR024259 Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This entry represents the N-terminal helix-turn-helix domain.; PDB: 3FN8_B 3F2G_B 3F0P_A 3F2F_B 3F2H_A 3F0O_B 1S6L_A.
Probab=26.72 E-value=79 Score=24.78 Aligned_cols=28 Identities=25% Similarity=0.326 Sum_probs=21.0
Q ss_pred cCcccHHHHHHHhCCCHHHHHHHHHHhH
Q 016147 305 YSRITLKRLAELLCLSIQEAEKHLSDMV 332 (394)
Q Consensus 305 Y~~Isl~rLa~lL~ls~~e~E~~ls~MI 332 (394)
=.-+|...||..+|.+.+++...+..|-
T Consensus 36 G~PVt~~~LA~a~g~~~e~v~~~L~~~p 63 (77)
T PF12324_consen 36 GQPVTVEQLAAALGWPVEEVRAALAAMP 63 (77)
T ss_dssp TS-B-HHHHHHHHT--HHHHHHHHHH-T
T ss_pred CCCcCHHHHHHHHCCCHHHHHHHHHhCC
Confidence 5669999999999999999999999885
No 225
>KOG1861 consensus Leucine permease transcriptional regulator [Transcription]
Probab=26.70 E-value=7.9e+02 Score=26.05 Aligned_cols=57 Identities=9% Similarity=0.099 Sum_probs=35.6
Q ss_pred cCHHHHHHHHHHhhhhhc-ccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCccc
Q 016147 76 GLIAEAADLMQEVAVETF-GAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPRV 132 (394)
Q Consensus 76 gd~~eAa~iL~~i~vEt~-~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~~ 132 (394)
.++.=+++-+..|.-+-. ..+-...=+++|=--+|+.||.||.......-..+..++
T Consensus 321 ~~Y~y~CdQ~KSiRQDLTVQ~IrneFTveVYEtHARIALEkGD~~EfNQCQtQLk~LY 378 (540)
T KOG1861|consen 321 ANYAYLCDQFKSIRQDLTVQRIRNEFTVEVYETHARIALEKGDLEEFNQCQTQLKALY 378 (540)
T ss_pred ccHHHHHHHHHHHhhhhhhheeccceeeeeehhhhHHHHhcCCHHHHHHHHHHHHHHH
Confidence 567666665554443322 344455566777777999999999666555555554444
No 226
>PF10345 Cohesin_load: Cohesin loading factor; InterPro: IPR019440 Cohesin loading factor is a conserved protein that has been characterised in fungi. It is associated with the cohesin complex and is required in G1 for cohesin binding to chromosomes, but is dispensable in G2 when cohesion has been established. It is often referred to as Ssl3 in Schizosaccharomyces pombe (Fission yeast), and Scc4 in Saccharomyces cerevisiae (Baker's yeast). It complexes with Mis4 [].
Probab=26.67 E-value=8.3e+02 Score=26.30 Aligned_cols=87 Identities=17% Similarity=0.091 Sum_probs=63.5
Q ss_pred HHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHh-ccCChHHHHHHHHhhCccccCCCCccccCCCCCCCcccccCCC
Q 016147 78 IAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCL-DRQDYVRAQILSRKISPRVFDADPSKEKKKPKEGDNVVEEAPA 156 (394)
Q Consensus 78 ~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L-~~~D~~~a~~~~~Ki~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 156 (394)
+.-|.+.|+-+-- ...++++......|+.+++++ +..++..|+.+..|+-...-.
T Consensus 37 I~~ai~CL~~~~~--~~~l~p~~ea~~~l~la~iL~~eT~n~~~Ae~~L~k~~~l~~~---------------------- 92 (608)
T PF10345_consen 37 IATAIKCLEAVLK--QFKLSPRQEARVRLRLASILLEETENLDLAETYLEKAILLCER---------------------- 92 (608)
T ss_pred HHHHHHHHHHHhc--cCCCCHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhccc----------------------
Confidence 5567777776543 347999999999999999999 789999999999988654321
Q ss_pred CccchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHH
Q 016147 157 DIPSLLELKRIYYELMIRYYSHNNDYLEICRCYKA 191 (394)
Q Consensus 157 ~~~~~~d~klk~~~~~~~~~~~~~~flea~k~y~e 191 (394)
.+..|+|....-+.++++...+-.. |-+.-..
T Consensus 93 --~~~~d~k~~~~~ll~~i~~~~~~~~-a~~~l~~ 124 (608)
T PF10345_consen 93 --HRLTDLKFRCQFLLARIYFKTNPKA-ALKNLDK 124 (608)
T ss_pred --cchHHHHHHHHHHHHHHHHhcCHHH-HHHHHHH
Confidence 1457888877777777776555444 4444443
No 227
>KOG1931 consensus Putative transmembrane protein [General function prediction only]
Probab=26.56 E-value=1e+03 Score=27.79 Aligned_cols=29 Identities=31% Similarity=0.204 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHhcCHHHHHHHHHHhhhhh
Q 016147 64 LIKKLAKIKEEQGLIAEAADLMQEVAVET 92 (394)
Q Consensus 64 l~~~La~i~e~~gd~~eAa~iL~~i~vEt 92 (394)
.++.||-+||.-.-+++|..-+.++..+-
T Consensus 217 ~kE~LA~iFe~l~l~edAL~qydel~a~~ 245 (1156)
T KOG1931|consen 217 TKEKLAFIFEMLNLLEDALLQYDELDAEF 245 (1156)
T ss_pred HHHHHHHHHHHHhhhHHHHHHHHHHHHHH
Confidence 34789999999999999999888887643
No 228
>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.10 E-value=1.1e+02 Score=29.65 Aligned_cols=66 Identities=17% Similarity=0.015 Sum_probs=56.0
Q ss_pred HHHHHHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHH-HHHHHHHHHHhccCChHHHHHHHHhhCccc
Q 016147 63 RLIKKLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKI-AFILEQVRLCLDRQDYVRAQILSRKISPRV 132 (394)
Q Consensus 63 ~l~~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~-e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~~ 132 (394)
.....|++.+...||+++|+.++..+. ...++.-|. |-+|......-+.++...|..+...+-..+
T Consensus 179 nA~yWLGe~~y~qg~y~~Aa~~f~~~~----k~~P~s~KApdallKlg~~~~~l~~~d~A~atl~qv~k~Y 245 (262)
T COG1729 179 NAYYWLGESLYAQGDYEDAAYIFARVV----KDYPKSPKAPDALLKLGVSLGRLGNTDEACATLQQVIKRY 245 (262)
T ss_pred hhHHHHHHHHHhcccchHHHHHHHHHH----HhCCCCCCChHHHHHHHHHHHHhcCHHHHHHHHHHHHHHC
Confidence 445889999999999999999888744 456677777 889999999999999999999998887765
No 229
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=26.05 E-value=1.6e+02 Score=28.01 Aligned_cols=40 Identities=15% Similarity=0.120 Sum_probs=34.0
Q ss_pred HHHHHhhcCcccHHHHHHHhCCCHHHHHHHHHHhHhcCcE
Q 016147 298 ILVVSKYYSRITLKRLAELLCLSIQEAEKHLSDMVVSKAL 337 (394)
Q Consensus 298 I~visk~Y~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l 337 (394)
|.-.-+-..+++++.||+.||+|+.-+-+-|..|-.+|.+
T Consensus 10 Il~~L~~~~~v~v~eLa~~l~VS~~TIRRDL~~Le~~g~l 49 (256)
T PRK10434 10 ILEYLQKQGKTSVEELAQYFDTTGTTIRKDLVILEHAGTV 49 (256)
T ss_pred HHHHHHHcCCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCE
Confidence 3334445788999999999999999999999999999955
No 230
>KOG1466 consensus Translation initiation factor 2B, alpha subunit (eIF-2Balpha/GCN3) [Translation, ribosomal structure and biogenesis]
Probab=25.51 E-value=2.7e+02 Score=27.15 Aligned_cols=88 Identities=16% Similarity=0.273 Sum_probs=63.3
Q ss_pred HHHHHHHHhccCCCChHHHHHHHHHhhhhcCCcchHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHhhhhhc-ccCcHHH
Q 016147 22 AMVQQAMQYIDQTPDLDTRIELIKTLNSVSAGKIYVEIERARLIKKLAKIKEEQGLIAEAADLMQEVAVETF-GAMAKTE 100 (394)
Q Consensus 22 ~~v~~~~~~~~~~~d~~~k~~~i~~L~~vt~gki~~E~era~l~~~La~i~e~~gd~~eAa~iL~~i~vEt~-~~m~~~e 100 (394)
.+|+.-..|+++-||...-...|++|-.+-.++= -..+-|-+....+|...|.. +- .+.+-+-
T Consensus 12 ~iie~f~~~l~eDpd~a~~vAAIraL~~vL~~s~------------a~Ti~el~~~l~~a~~tL~~----~d~ss~Sl~a 75 (313)
T KOG1466|consen 12 SIIEYFLSFLQEDPDLAMAVAAIRALLEVLRRSQ------------ATTIAELENELKSASATLKK----TDTSSISLRA 75 (313)
T ss_pred hHHHHHHHHHhcCchhhhHHHHHHHHHHHHhhcc------------cchHHHHHHHHHHHHHHHHc----cCccchhhhh
Confidence 3567778899999999999999998876654431 12334445567777777775 32 4567777
Q ss_pred HHHHHHHHHHHH--hccCChHHHHHHH
Q 016147 101 KIAFILEQVRLC--LDRQDYVRAQILS 125 (394)
Q Consensus 101 K~e~~Leq~rL~--L~~~D~~~a~~~~ 125 (394)
-.|.+.+=+-+. ++.+||.++..+.
T Consensus 76 gcdlF~Rfvtr~slld~~Df~~ck~~l 102 (313)
T KOG1466|consen 76 GCDLFMRFVTRASLLDYEDFEQCKQHL 102 (313)
T ss_pred hhHHHHHHHHhhhhhhhhHHHHHHHHH
Confidence 888888887776 8999999887743
No 231
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein. Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.
Probab=25.44 E-value=2.5e+02 Score=25.53 Aligned_cols=39 Identities=18% Similarity=0.221 Sum_probs=33.9
Q ss_pred CcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEEeccC
Q 016147 306 SRITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKIDRP 344 (394)
Q Consensus 306 ~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~akIDq~ 344 (394)
..++...+|+.+|+|..-+-+.+..|...|-+.-.-+|.
T Consensus 156 g~~s~~eia~~l~is~stv~r~L~~Le~~GlI~r~~~r~ 194 (203)
T TIGR01884 156 GEKSVKNIAKKLGKSLSTISRHLRELEKKGLVEQKGRKG 194 (203)
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcCCc
Confidence 469999999999999999999999999999887654433
No 232
>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=25.13 E-value=6.6e+02 Score=25.32 Aligned_cols=100 Identities=17% Similarity=0.113 Sum_probs=68.3
Q ss_pred HHHHHHHHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCccccCCCCccc
Q 016147 61 RARLIKKLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPRVFDADPSKE 140 (394)
Q Consensus 61 ra~l~~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~~~~~~~~~~ 140 (394)
+++-...-|-+-..+|||..|-+.+....- . + ..-.-.++-.++.....||+.+|..+++++.... .+
T Consensus 83 k~~~~~~~glla~~~g~~~~A~~~l~~~~~----~-~-~~~~~~~llaA~aa~~~g~~~~A~~~l~~a~~~~-p~----- 150 (409)
T TIGR00540 83 KAQKQTEEALLKLAEGDYAKAEKLIAKNAD----H-A-AEPVLNLIKAAEAAQQRGDEARANQHLEEAAELA-GN----- 150 (409)
T ss_pred HHHHHHHHHHHHHhCCCHHHHHHHHHHHhh----c-C-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-Cc-----
Confidence 344445556677899999999999976321 1 1 1235667788999999999999999999986432 10
Q ss_pred cCCCCCCCcccccCCCCccchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhcc
Q 016147 141 KKKPKEGDNVVEEAPADIPSLLELKRIYYELMIRYYSHNNDYLEICRCYKAIYEI 195 (394)
Q Consensus 141 ~~~~~~~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~~~~flea~k~y~ei~~t 195 (394)
..+-.....++++...++|-.|-..+......
T Consensus 151 -----------------------~~l~~~~~~a~l~l~~~~~~~Al~~l~~l~~~ 182 (409)
T TIGR00540 151 -----------------------DNILVEIARTRILLAQNELHAARHGVDKLLEM 182 (409)
T ss_pred -----------------------CchHHHHHHHHHHHHCCCHHHHHHHHHHHHHh
Confidence 00111222367778888888888777777764
No 233
>PF01535 PPR: PPR repeat; InterPro: IPR002885 This entry represents the PPR repeat. Pentatricopeptide repeat (PPR) proteins are characterised by tandem repeats of a degenerate 35 amino acid motif []. Most of PPR proteins have roles in mitochondria or plastid []. PPR repeats were discovered while screening Arabidopsis proteins for those predicted to be targeted to mitochondria or chloroplast [, ]. Some of these proteins have been shown to play a role in post-transcriptional processes within organelles and they are thought to be sequence-specific RNA-binding proteins [, , ]. Plant genomes have between one hundred to five hundred PPR genes per genome whereas non-plant genomes encode two to six PPR proteins. Although no PPR structures are yet known, the motif is predicted to fold into a helix-turn-helix structure similar to those found in the tetratricopeptide repeat (TPR) family (see PDOC50005 from PROSITEDOC) []. The plant PPR protein family has been divided in two subfamilies on the basis of their motif content and organisation [, ]. Examples of PPR repeat-containing proteins include PET309 P32522 from SWISSPROT, which may be involved in RNA stabilisation [], and crp1, which is involved in RNA processing []. The repeat is associated with a predicted plant protein O49549 from SWISSPROT that has a domain organisation similar to the human BRCA1 protein.
Probab=25.09 E-value=95 Score=18.19 Aligned_cols=22 Identities=23% Similarity=0.249 Sum_probs=17.6
Q ss_pred HHHHHHHhcCHHHHHHHHHHhh
Q 016147 68 LAKIKEEQGLIAEAADLMQEVA 89 (394)
Q Consensus 68 La~i~e~~gd~~eAa~iL~~i~ 89 (394)
+-+.|...|++++|.+++.++.
T Consensus 6 li~~~~~~~~~~~a~~~~~~M~ 27 (31)
T PF01535_consen 6 LISGYCKMGQFEEALEVFDEMR 27 (31)
T ss_pred HHHHHHccchHHHHHHHHHHHh
Confidence 4566788899999999888765
No 234
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=24.77 E-value=1.5e+02 Score=22.21 Aligned_cols=31 Identities=23% Similarity=0.311 Sum_probs=26.9
Q ss_pred ccHHHHHHHhCCC-HHHHHHHHHHhHhcCcEE
Q 016147 308 ITLKRLAELLCLS-IQEAEKHLSDMVVSKALV 338 (394)
Q Consensus 308 Isl~rLa~lL~ls-~~e~E~~ls~MI~~g~l~ 338 (394)
=|+.+||+.||++ +.-+-..|..|...|.|.
T Consensus 26 Pt~rEIa~~~g~~S~~tv~~~L~~Le~kG~I~ 57 (65)
T PF01726_consen 26 PTVREIAEALGLKSTSTVQRHLKALERKGYIR 57 (65)
T ss_dssp --HHHHHHHHTSSSHHHHHHHHHHHHHTTSEE
T ss_pred CCHHHHHHHhCCCChHHHHHHHHHHHHCcCcc
Confidence 5899999999996 999999999999999774
No 235
>PF07848 PaaX: PaaX-like protein; InterPro: IPR012906 This entry describes the N-terminal region of proteins that are similar to, and nclude, the product of the paaX gene of Escherichia coli (P76086 from SWISSPROT). PaaX is a transcriptional regulator that is always found in association with operons believed to be involved in the degradation of phenylacetic acid []. The gene product has been shown to bind to the promoter sites and repress their transcription []. ; PDB: 3KFW_X 3L09_B.
Probab=24.62 E-value=88 Score=23.85 Aligned_cols=30 Identities=27% Similarity=0.201 Sum_probs=24.1
Q ss_pred HHHHHHHhCCCHHHHHHHHHHhHhcCcEEE
Q 016147 310 LKRLAELLCLSIQEAEKHLSDMVVSKALVA 339 (394)
Q Consensus 310 l~rLa~lL~ls~~e~E~~ls~MI~~g~l~a 339 (394)
+-++...||+++.-+-.-+++|+.+|-+..
T Consensus 26 Li~ll~~~Gv~e~avR~alsRl~~~G~L~~ 55 (70)
T PF07848_consen 26 LIRLLAAFGVSESAVRTALSRLVRRGWLES 55 (70)
T ss_dssp HHHHHCCTT--HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHcCCChHHHHHHHHHHHHcCceee
Confidence 446677889999999999999999999854
No 236
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=24.49 E-value=5.4e+02 Score=23.40 Aligned_cols=53 Identities=13% Similarity=0.125 Sum_probs=40.7
Q ss_pred HHHHHHHHhhcCcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEEeccCCCE
Q 016147 295 EHNILVVSKYYSRITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKIDRPQGI 347 (394)
Q Consensus 295 EHNI~visk~Y~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~akIDq~~gi 347 (394)
|+-+..+..-...+|.+.||+.++++..-+=..+.+|...|-|.=..|..++=
T Consensus 47 q~~iL~~L~~~~~itq~eLa~~l~l~~sTvtr~l~rLE~kGlI~R~~~~~DrR 99 (185)
T PRK13777 47 EHHILWIAYHLKGASISEIAKFGVMHVSTAFNFSKKLEERGYLTFSKKEDDKR 99 (185)
T ss_pred HHHHHHHHHhCCCcCHHHHHHHHCCCHhhHHHHHHHHHHCCCEEecCCCCCCC
Confidence 33444443345679999999999999999999999999999887666555544
No 237
>PF01984 dsDNA_bind: Double-stranded DNA-binding domain; InterPro: IPR002836 This protein family is found in archaea and eukaryota. The human TFAR19 (TF-1 cell apoptosis-related protein 19) encodes a protein which shares significant homology to the corresponding proteins of species ranging from yeast to mice. TFAR19 exhibits a ubiquitous expression pattern and its expression is up-regulated in the tumour cells undergoing apoptosis. TFAR19 may play a general role in the apoptotic process []. Also included in this family is a DNA-binding protein from the archaea, Methanobacterium thermoautotrophicum.; GO: 0003677 DNA binding; PDB: 1EIJ_A 2K6B_A 2CRU_A 1YYB_A 2JXN_A 2FH0_A.
Probab=24.47 E-value=44 Score=27.81 Aligned_cols=22 Identities=32% Similarity=0.424 Sum_probs=18.0
Q ss_pred HHHHHHHHHHhHhcCcEEEEec
Q 016147 321 IQEAEKHLSDMVVSKALVAKID 342 (394)
Q Consensus 321 ~~e~E~~ls~MI~~g~l~akID 342 (394)
...+|.+|..|...|+|.++||
T Consensus 61 A~~VE~~Liqlaq~G~l~~kI~ 82 (107)
T PF01984_consen 61 ARQVENQLIQLAQSGQLRGKID 82 (107)
T ss_dssp HHHHHHHHHHHHHCTSSSS-B-
T ss_pred HHHHHHHHHHHHHcCCCCCCcC
Confidence 4578999999999999999887
No 238
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=24.18 E-value=3.9e+02 Score=21.62 Aligned_cols=41 Identities=12% Similarity=0.155 Sum_probs=35.5
Q ss_pred CcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEEeccCCC
Q 016147 306 SRITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKIDRPQG 346 (394)
Q Consensus 306 ~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~akIDq~~g 346 (394)
..++...||..++++..-+=..+.+|+..|-|.-.-|..++
T Consensus 42 ~~~t~~eL~~~l~~~~stvs~~i~~Le~kg~I~r~~~~~D~ 82 (109)
T TIGR01889 42 GKLTLKEIIKEILIKQSALVKIIKKLSKKGYLSKERSEDDE 82 (109)
T ss_pred CcCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEeccCCcccC
Confidence 35999999999999999999999999999998755555544
No 239
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=24.13 E-value=1.3e+02 Score=20.68 Aligned_cols=27 Identities=15% Similarity=0.142 Sum_probs=22.0
Q ss_pred cCcccHHHHHHHhCCCHHHHHHHHHHh
Q 016147 305 YSRITLKRLAELLCLSIQEAEKHLSDM 331 (394)
Q Consensus 305 Y~~Isl~rLa~lL~ls~~e~E~~ls~M 331 (394)
-...|+..+|+.+|+|..-+...+-+.
T Consensus 25 ~~~~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 25 RESRSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred hhcCCHHHHHHHHCCCHHHHHHHHHhh
Confidence 334799999999999999988876543
No 240
>KOG2002 consensus TPR-containing nuclear phosphoprotein that regulates K(+) uptake [Inorganic ion transport and metabolism]
Probab=23.64 E-value=9.8e+02 Score=27.64 Aligned_cols=113 Identities=17% Similarity=0.084 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHH---HHHhhCccccCCCCccc
Q 016147 64 LIKKLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQI---LSRKISPRVFDADPSKE 140 (394)
Q Consensus 64 l~~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~---~~~Ki~~~~~~~~~~~~ 140 (394)
+-..||.+|...||+..+..+....-.-| -.+..+.+-+.-..|-+...|||.+|.. -+.|+++-.|..+
T Consensus 272 ~l~~LAn~fyfK~dy~~v~~la~~ai~~t---~~~~~~aes~Y~~gRs~Ha~Gd~ekA~~yY~~s~k~~~d~~~l~---- 344 (1018)
T KOG2002|consen 272 ALNHLANHFYFKKDYERVWHLAEHAIKNT---ENKSIKAESFYQLGRSYHAQGDFEKAFKYYMESLKADNDNFVLP---- 344 (1018)
T ss_pred HHHHHHHHHhhcccHHHHHHHHHHHHHhh---hhhHHHHHHHHHHHHHHHhhccHHHHHHHHHHHHccCCCCcccc----
Q ss_pred cCCCCCCCcccccCCCCccchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhccCCCCCChhcHHHHHHHHHHHH
Q 016147 141 KKKPKEGDNVVEEAPADIPSLLELKRIYYELMIRYYSHNNDYLEICRCYKAIYEIPYIKEDPAQWMPVLRKICWYL 216 (394)
Q Consensus 141 ~~~~~~~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~~~~flea~k~y~ei~~t~~i~~d~~~~~~~L~~av~~~ 216 (394)
+-..++.+.+.+++-++..||..++.+. +|..+.+.+|.+ +|+
T Consensus 345 ----------------------------~~GlgQm~i~~~dle~s~~~fEkv~k~~---p~~~etm~iLG~--Lya 387 (1018)
T KOG2002|consen 345 ----------------------------LVGLGQMYIKRGDLEESKFCFEKVLKQL---PNNYETMKILGC--LYA 387 (1018)
T ss_pred ----------------------------ccchhHHHHHhchHHHHHHHHHHHHHhC---cchHHHHHHHHh--HHH
No 241
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=23.25 E-value=1.3e+02 Score=27.22 Aligned_cols=43 Identities=19% Similarity=0.126 Sum_probs=35.0
Q ss_pred HHHHHHHHhhcCcccHHHHHHHhCCCHHHHHHHHHHhHhcCcE
Q 016147 295 EHNILVVSKYYSRITLKRLAELLCLSIQEAEKHLSDMVVSKAL 337 (394)
Q Consensus 295 EHNI~visk~Y~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l 337 (394)
+..|.-.-+-...++...||+.||+|+.=+-+-+..|..+|.+
T Consensus 9 ~~~Il~~l~~~~~~~~~~La~~~~vS~~TiRRDl~~L~~~g~~ 51 (185)
T PRK04424 9 QKALQELIEENPFITDEELAEKFGVSIQTIRLDRMELGIPELR 51 (185)
T ss_pred HHHHHHHHHHCCCEEHHHHHHHHCcCHHHHHHHHHHHhcchHH
Confidence 3444444555888999999999999999999999999888855
No 242
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.99 E-value=1e+02 Score=24.77 Aligned_cols=26 Identities=19% Similarity=0.129 Sum_probs=23.0
Q ss_pred hcCcccHHHHHHHhCCCHHHHHHHHH
Q 016147 304 YYSRITLKRLAELLCLSIQEAEKHLS 329 (394)
Q Consensus 304 ~Y~~Isl~rLa~lL~ls~~e~E~~ls 329 (394)
--++.|.+.+|..|++|+..+|+.+.
T Consensus 20 el~~LS~~~iA~~Ln~t~~~lekil~ 45 (97)
T COG4367 20 ELCPLSDEEIATALNWTEVKLEKILQ 45 (97)
T ss_pred hhccccHHHHHHHhCCCHHHHHHHHH
Confidence 35788999999999999999999874
No 243
>PF13371 TPR_9: Tetratricopeptide repeat
Probab=22.96 E-value=2.7e+02 Score=19.98 Aligned_cols=29 Identities=17% Similarity=0.105 Sum_probs=25.1
Q ss_pred HHHHHHHHHHHHHHhcCHHHHHHHHHHhh
Q 016147 61 RARLIKKLAKIKEEQGLIAEAADLMQEVA 89 (394)
Q Consensus 61 ra~l~~~La~i~e~~gd~~eAa~iL~~i~ 89 (394)
...+...+|.++...|++.+|...++...
T Consensus 28 ~~~~~~~~a~~~~~~g~~~~A~~~l~~~l 56 (73)
T PF13371_consen 28 DPELWLQRARCLFQLGRYEEALEDLERAL 56 (73)
T ss_pred cchhhHHHHHHHHHhccHHHHHHHHHHHH
Confidence 45667889999999999999999998765
No 244
>TIGR00952 S15_bact ribosomal protein S15, bacterial/organelle. This model is built to recognize specifically bacterial, chloroplast, and mitochondrial ribosomal protein S15. The homologous proteins of Archaea and Eukarya are designated S13.
Probab=22.71 E-value=2e+02 Score=22.96 Aligned_cols=35 Identities=17% Similarity=0.244 Sum_probs=27.8
Q ss_pred hHHHHHHHHHhhhhcCCcchHHHHHHHHHHHHHHH
Q 016147 37 LDTRIELIKTLNSVSAGKIYVEIERARLIKKLAKI 71 (394)
Q Consensus 37 ~~~k~~~i~~L~~vt~gki~~E~era~l~~~La~i 71 (394)
.+.|-++|.....-.....+.|+|.|-+|...-.+
T Consensus 2 ~~~k~~li~~~~~~~~DtGS~eVQiA~LT~rI~~L 36 (86)
T TIGR00952 2 KERKQEIIKEFQLHEKDTGSPEVQIALLTERINQL 36 (86)
T ss_pred HHHHHHHHHHHcCCCCCCCCHHHHHHHHHHHHHHH
Confidence 35677788877777778899999999999776655
No 245
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=22.60 E-value=2e+02 Score=19.46 Aligned_cols=22 Identities=18% Similarity=0.235 Sum_probs=19.2
Q ss_pred hhcCcccHHHHHHHhCCCHHHH
Q 016147 303 KYYSRITLKRLAELLCLSIQEA 324 (394)
Q Consensus 303 k~Y~~Isl~rLa~lL~ls~~e~ 324 (394)
+-|..+|+.++|+..|+|..-+
T Consensus 12 ~G~~~~s~~~Ia~~~gvs~~~~ 33 (47)
T PF00440_consen 12 KGYEAVSIRDIARRAGVSKGSF 33 (47)
T ss_dssp HHTTTSSHHHHHHHHTSCHHHH
T ss_pred hCHHhCCHHHHHHHHccchhhH
Confidence 5699999999999999997644
No 246
>PF03484 B5: tRNA synthetase B5 domain; InterPro: IPR005147 Domain B5 is found in phenylalanine-tRNA synthetase beta subunits. This domain has been shown to bind DNA through a winged helix-turn-helix motif []. Phenylalanine-tRNA synthetase may influence common cellular processes via DNA binding, in addition to its aminoacylation function.; GO: 0000287 magnesium ion binding, 0003723 RNA binding, 0005524 ATP binding, 0006432 phenylalanyl-tRNA aminoacylation; PDB: 2AKW_B 1B70_B 1B7Y_B 2ALY_B 2IY5_B 2AMC_B 3PCO_D 2CXI_C 1JJC_B 1EIY_B ....
Probab=22.44 E-value=1e+02 Score=23.17 Aligned_cols=60 Identities=22% Similarity=0.346 Sum_probs=41.1
Q ss_pred cccHHHHHHHhCC--CHHHHHHHHHHhHhcCcEEEEecc-CCCEEEEecCCChHHHHHHHHHHHHHHHHHHHHHHhh
Q 016147 307 RITLKRLAELLCL--SIQEAEKHLSDMVVSKALVAKIDR-PQGIVCFQVAKDSNDILNSWAMNLEKLLDLVEKSCHQ 380 (394)
Q Consensus 307 ~Isl~rLa~lL~l--s~~e~E~~ls~MI~~g~l~akIDq-~~giV~F~~~k~~~~~L~~W~~~I~~l~~~V~k~~~l 380 (394)
.++.+++.+++|+ +.+++.+.|.+|= .+++. -.+.+.+..|. |-.+|..-++.++.+.+.
T Consensus 5 ~~~~~~i~~~lG~~i~~~~i~~~L~~lg------~~~~~~~~~~~~v~vP~--------~R~Di~~~~DliEEiaR~ 67 (70)
T PF03484_consen 5 TLSLDKINKLLGIDISPEEIIKILKRLG------FKVEKIDGDTLEVTVPS--------YRFDIEHEEDLIEEIARI 67 (70)
T ss_dssp EEEHHHHHHHHTS---HHHHHHHHHHTT-------EEEE-CTTEEEEEEET--------TSTT-SSHHHHHHHHHHH
T ss_pred EecHHHHHHHhCCCCCHHHHHHHHHHCC------CEEEECCCCEEEEEcCC--------CcCCcCcccHHHHHHHHH
Confidence 4678999999995 6788888877763 23333 56666776663 777788888888877664
No 247
>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=22.44 E-value=1.3e+02 Score=16.35 Aligned_cols=22 Identities=18% Similarity=0.149 Sum_probs=16.5
Q ss_pred HHHHHHHHHhcCHHHHHHHHHH
Q 016147 66 KKLAKIKEEQGLIAEAADLMQE 87 (394)
Q Consensus 66 ~~La~i~e~~gd~~eAa~iL~~ 87 (394)
..+|..+...|++++|...++.
T Consensus 5 ~~~a~~~~~~~~~~~a~~~~~~ 26 (34)
T smart00028 5 YNLGNAYLKLGDYDEALEYYEK 26 (34)
T ss_pred HHHHHHHHHHhhHHHHHHHHHH
Confidence 4677778888888888876654
No 248
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial. Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.
Probab=22.38 E-value=1.4e+02 Score=26.25 Aligned_cols=33 Identities=18% Similarity=0.234 Sum_probs=30.3
Q ss_pred cccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEE
Q 016147 307 RITLKRLAELLCLSIQEAEKHLSDMVVSKALVA 339 (394)
Q Consensus 307 ~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~a 339 (394)
.+|-+.||.++|+|.+-+=+.+++|-.+|-|..
T Consensus 143 ~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~ 175 (193)
T TIGR03697 143 RLSHQAIAEAIGSTRVTITRLLGDLRKKKLISI 175 (193)
T ss_pred CCCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEe
Confidence 578899999999999999999999999998854
No 249
>COG2886 Uncharacterized small protein [Function unknown]
Probab=22.24 E-value=2.4e+02 Score=22.69 Aligned_cols=26 Identities=35% Similarity=0.452 Sum_probs=23.9
Q ss_pred CcccHHHHHHHhCCCHHHHHHHHHHh
Q 016147 306 SRITLKRLAELLCLSIQEAEKHLSDM 331 (394)
Q Consensus 306 ~~Isl~rLa~lL~ls~~e~E~~ls~M 331 (394)
..|||.+.|++.++|..+.+..+++=
T Consensus 40 g~vSlg~Aaela~~sl~ef~~eL~~R 65 (88)
T COG2886 40 GAVSLGRAAELAGMSLNEFEEELRKR 65 (88)
T ss_pred hhhHHHHHHHHhcCCHHHHHHHHHHh
Confidence 88999999999999999999988763
No 250
>PF13217 DUF4025: Protein of unknown function (DUF4025)
Probab=21.84 E-value=45 Score=24.39 Aligned_cols=24 Identities=21% Similarity=0.318 Sum_probs=20.3
Q ss_pred HHHHHHHHHhHhcCcEEEEeccCC
Q 016147 322 QEAEKHLSDMVVSKALVAKIDRPQ 345 (394)
Q Consensus 322 ~e~E~~ls~MI~~g~l~akIDq~~ 345 (394)
..+...+|+...+|+|.|+||+.+
T Consensus 31 A~ThEQVSD~Y~EGTiD~~l~~~~ 54 (55)
T PF13217_consen 31 AVTHEQVSDTYAEGTIDAKLDQEN 54 (55)
T ss_pred HHHHHHHHHHHhhhhHhhhhhccc
Confidence 355667899999999999999875
No 251
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 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 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; 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: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=21.82 E-value=1e+02 Score=23.15 Aligned_cols=36 Identities=25% Similarity=0.254 Sum_probs=24.4
Q ss_pred CcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEEeccCC
Q 016147 306 SRITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKIDRPQ 345 (394)
Q Consensus 306 ~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~akIDq~~ 345 (394)
..-|...||+.||+|++++...+...-. ...+|.+.
T Consensus 19 r~Pt~eEiA~~lgis~~~v~~~l~~~~~----~~Sl~~~~ 54 (78)
T PF04539_consen 19 REPTDEEIAEELGISVEEVRELLQASRR----PVSLDLPV 54 (78)
T ss_dssp S--BHHHHHHHHTS-HHHHHHHHHHHSC----CEESSHCC
T ss_pred CCCCHHHHHHHHcccHHHHHHHHHhCCC----CeEEeeee
Confidence 4578899999999999999988864322 34555553
No 252
>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=21.30 E-value=2.4e+02 Score=24.59 Aligned_cols=39 Identities=15% Similarity=0.012 Sum_probs=30.5
Q ss_pred cCc--ccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEEeccCCCE
Q 016147 305 YSR--ITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKIDRPQGI 347 (394)
Q Consensus 305 Y~~--Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~akIDq~~gi 347 (394)
+-+ -|+..+++.+|+|++.+. ++|.+|||.-.-+..-|+
T Consensus 42 ~p~~~ati~eV~e~tgVs~~~I~----~~IreGRL~~~~~~nl~~ 82 (137)
T TIGR03826 42 HENRQATVSEIVEETGVSEKLIL----KFIREGRLQLKHFPNLGY 82 (137)
T ss_pred CCCCCCCHHHHHHHHCcCHHHHH----HHHHcCCeeccCCCCCcC
Confidence 445 899999999999987655 679999998766555544
No 253
>PF13431 TPR_17: Tetratricopeptide repeat
Probab=21.16 E-value=1.2e+02 Score=19.23 Aligned_cols=21 Identities=33% Similarity=0.292 Sum_probs=17.8
Q ss_pred HHHHHHHHHHHHHhcCHHHHH
Q 016147 62 ARLIKKLAKIKEEQGLIAEAA 82 (394)
Q Consensus 62 a~l~~~La~i~e~~gd~~eAa 82 (394)
+.....||.+|...|++++|.
T Consensus 13 ~~a~~nla~~~~~~g~~~~A~ 33 (34)
T PF13431_consen 13 AEAYNNLANLYLNQGDYEEAI 33 (34)
T ss_pred HHHHHHHHHHHHHCcCHHhhc
Confidence 456688999999999999984
No 254
>PF14123 DUF4290: Domain of unknown function (DUF4290)
Probab=21.09 E-value=1.3e+02 Score=27.31 Aligned_cols=29 Identities=21% Similarity=0.298 Sum_probs=22.4
Q ss_pred HHHHHHHHHHHHhccCCCChHHHHHHHHHhhhh
Q 016147 18 QAVTAMVQQAMQYIDQTPDLDTRIELIKTLNSV 50 (394)
Q Consensus 18 ~ai~~~v~~~~~~~~~~~d~~~k~~~i~~L~~v 50 (394)
.-|+.||..|++ ++|.+.|-++.+++-.|
T Consensus 17 R~IQ~MVd~~~t----ieDreeR~~~A~~II~i 45 (176)
T PF14123_consen 17 RNIQKMVDYAVT----IEDREERNRCAETIIEI 45 (176)
T ss_pred HHHHHHHHHHHh----CCCHHHHHHHHHHHHHH
Confidence 358889999888 89999888777766543
No 255
>KOG2376 consensus Signal recognition particle, subunit Srp72 [Intracellular trafficking, secretion, and vesicular transport]
Probab=21.05 E-value=1.1e+03 Score=25.73 Aligned_cols=110 Identities=15% Similarity=0.135 Sum_probs=62.3
Q ss_pred HHHHHHHHHhcCHHHHHHHHHHhhhhhcccCcH-------------------------HHHHHHHHHHHHHHhccCChHH
Q 016147 66 KKLAKIKEEQGLIAEAADLMQEVAVETFGAMAK-------------------------TEKIAFILEQVRLCLDRQDYVR 120 (394)
Q Consensus 66 ~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~-------------------------~eK~e~~Leq~rL~L~~~D~~~ 120 (394)
+--|++++..|++++|.++.+.+.--+..-.+. ..=-+.+..-+=.+++.++|..
T Consensus 114 ~L~AQvlYrl~~ydealdiY~~L~kn~~dd~d~~~r~nl~a~~a~l~~~~~q~v~~v~e~syel~yN~Ac~~i~~gky~q 193 (652)
T KOG2376|consen 114 ELRAQVLYRLERYDEALDIYQHLAKNNSDDQDEERRANLLAVAAALQVQLLQSVPEVPEDSYELLYNTACILIENGKYNQ 193 (652)
T ss_pred HHHHHHHHHHhhHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHhhhHHHHHhccCCCcchHHHHHHHHHHHHhcccHHH
Confidence 344677888889999999988873211100000 0112344455667889999999
Q ss_pred HHHHHHhh----CccccCCCCccccCCCCCCCcccccCCCCccchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhc
Q 016147 121 AQILSRKI----SPRVFDADPSKEKKKPKEGDNVVEEAPADIPSLLELKRIYYELMIRYYSHNNDYLEICRCYKAIYE 194 (394)
Q Consensus 121 a~~~~~Ki----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~klk~~~~~~~~~~~~~~flea~k~y~ei~~ 194 (394)
|.....|+ ..++.+++.. + +..+..-.--.-.++-.+...|+--||...|-.+..
T Consensus 194 A~elL~kA~~~~~e~l~~~d~~-e------------------Eeie~el~~IrvQlayVlQ~~Gqt~ea~~iy~~~i~ 252 (652)
T KOG2376|consen 194 AIELLEKALRICREKLEDEDTN-E------------------EEIEEELNPIRVQLAYVLQLQGQTAEASSIYVDIIK 252 (652)
T ss_pred HHHHHHHHHHHHHHhhcccccc-h------------------hhHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHHHH
Confidence 99999888 3332222221 1 011111111122333445557888888888887775
No 256
>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=21.01 E-value=1.4e+02 Score=24.20 Aligned_cols=35 Identities=23% Similarity=0.197 Sum_probs=26.7
Q ss_pred CcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEE
Q 016147 306 SRITLKRLAELLCLSIQEAEKHLSDMVVSKALVAK 340 (394)
Q Consensus 306 ~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~ak 340 (394)
..++-+.||+.+|+++.++-+.+..|-.+|-+..+
T Consensus 26 ~~l~de~la~~~~l~~~~vRkiL~~L~~~~lv~~~ 60 (105)
T PF02002_consen 26 GELTDEDLAKKLGLKPKEVRKILYKLYEDGLVSYR 60 (105)
T ss_dssp --B-HHHHHHTT-S-HHHHHHHHHHHHHHSS-EEE
T ss_pred CCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeEEE
Confidence 45888999999999999999999999999988443
No 257
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=20.99 E-value=4.7e+02 Score=26.73 Aligned_cols=66 Identities=12% Similarity=0.219 Sum_probs=48.3
Q ss_pred CcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEEeccCCCEEEEecCCChH-----HHH------------HHHHHHHH
Q 016147 306 SRITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKIDRPQGIVCFQVAKDSN-----DIL------------NSWAMNLE 368 (394)
Q Consensus 306 ~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~akIDq~~giV~F~~~k~~~-----~~L------------~~W~~~I~ 368 (394)
.-+|.++|++.++++++.+++.+..|...|-+. +-++ .+ |...++++ +++ ..|..++.
T Consensus 309 ~~~t~~~La~~l~~~~~~v~~iL~~L~~agLI~-~~~~-g~---~~l~rd~~~itL~dv~~~~~~~~~~~~~~~~~~~~~ 383 (412)
T PRK04214 309 KALDVDEIRRLEPMGYDELGELLCELARIGLLR-RGER-GQ---WVLARDLDSVPLAELYELFVLRPLPCRDDHVGQAAD 383 (412)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHhCCCeE-ecCC-Cc---eEecCCHHhCcHHHHHHhCCCCcCCCccchHHHHHH
Confidence 467999999999999999999999999999885 3332 22 33333332 111 27889998
Q ss_pred HHHHHHHH
Q 016147 369 KLLDLVEK 376 (394)
Q Consensus 369 ~l~~~V~k 376 (394)
.+++.++.
T Consensus 384 ~~l~~~~~ 391 (412)
T PRK04214 384 AALTQLRQ 391 (412)
T ss_pred HHHHHHHH
Confidence 88887764
No 258
>PRK10265 chaperone-modulator protein CbpM; Provisional
Probab=20.88 E-value=2.4e+02 Score=22.93 Aligned_cols=41 Identities=12% Similarity=0.020 Sum_probs=30.5
Q ss_pred CcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEEeccCCCEEEE
Q 016147 306 SRITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKIDRPQGIVCF 350 (394)
Q Consensus 306 ~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~akIDq~~giV~F 350 (394)
.++|+..+++..|++++.++ +||..|-|....+.+.+....
T Consensus 6 ~~lt~~Elc~~~gi~~~~l~----eLve~GlIep~~~~~~~~~F~ 46 (101)
T PRK10265 6 VTFTITEFCLHTGVSEEELN----EIVGLGVIEPREIQETTWVFD 46 (101)
T ss_pred EEeeHHHHHHHHCcCHHHHH----HHHHCCCeecCCCCcccceEC
Confidence 46899999999999998655 688899887655554444433
No 259
>COG3118 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]
Probab=20.80 E-value=8.3e+02 Score=24.20 Aligned_cols=48 Identities=15% Similarity=0.093 Sum_probs=31.9
Q ss_pred HHHHhhhhHHHHHHHHHHHhccCCCCCChhcHHHHHHHHHHHHHhCCCChh
Q 016147 174 RYYSHNNDYLEICRCYKAIYEIPYIKEDPAQWMPVLRKICWYLVLAPHDPM 224 (394)
Q Consensus 174 ~~~~~~~~flea~k~y~ei~~t~~i~~d~~~~~~~L~~av~~~ILap~~~~ 224 (394)
..+.+.+++-+|+-+...+.....--+|..-+.+.+. +|..+.|.+|.
T Consensus 244 ~~~~~~g~~e~Ale~Ll~~l~~d~~~~d~~~Rk~lle---~f~~~g~~Dp~ 291 (304)
T COG3118 244 DQLHLVGRNEAALEHLLALLRRDRGFEDGEARKTLLE---LFEAFGPADPL 291 (304)
T ss_pred HHHHHcCCHHHHHHHHHHHHHhcccccCcHHHHHHHH---HHHhcCCCCHH
Confidence 4455678888888888888865444444445566665 56677777764
No 260
>PHA02591 hypothetical protein; Provisional
Probab=20.75 E-value=1.1e+02 Score=24.05 Aligned_cols=24 Identities=25% Similarity=0.488 Sum_probs=20.1
Q ss_pred cccHHHHHHHhCCCHHHHHHHHHH
Q 016147 307 RITLKRLAELLCLSIQEAEKHLSD 330 (394)
Q Consensus 307 ~Isl~rLa~lL~ls~~e~E~~ls~ 330 (394)
-.|.+++|++||+|.+.+-+++..
T Consensus 59 GlSqeqIA~~LGVsqetVrKYL~~ 82 (83)
T PHA02591 59 GFTVEKIASLLGVSVRKVRRYLES 82 (83)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHhc
Confidence 358899999999999998887653
No 261
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=20.75 E-value=1.4e+02 Score=26.60 Aligned_cols=32 Identities=13% Similarity=0.127 Sum_probs=29.8
Q ss_pred cccHHHHHHHhCCCHHHHHHHHHHhHhcCcEE
Q 016147 307 RITLKRLAELLCLSIQEAEKHLSDMVVSKALV 338 (394)
Q Consensus 307 ~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~ 338 (394)
++|-..||+.+|++++-+-+.+.+|-.+|-|.
T Consensus 168 ~~t~~~lA~~lG~tr~tvsR~l~~l~~~gii~ 199 (211)
T PRK11753 168 KITRQEIGRIVGCSREMVGRVLKMLEDQGLIS 199 (211)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEE
Confidence 68889999999999999999999999999774
No 262
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=20.58 E-value=1.8e+02 Score=26.28 Aligned_cols=40 Identities=20% Similarity=0.316 Sum_probs=35.1
Q ss_pred ccHHHHHHHhCCC-HHHHHHHHHHhHhcCcEEEEeccCCCE
Q 016147 308 ITLKRLAELLCLS-IQEAEKHLSDMVVSKALVAKIDRPQGI 347 (394)
Q Consensus 308 Isl~rLa~lL~ls-~~e~E~~ls~MI~~g~l~akIDq~~gi 347 (394)
.|...||+.+|++ ..-+-..+..|...|-|...=.+..|+
T Consensus 26 ~~~~ela~~~~~~s~~tv~~~l~~L~~~g~i~~~~~~~~~~ 66 (199)
T TIGR00498 26 PSIREIARAVGLRSPSAAEEHLKALERKGYIERDPGKPRAI 66 (199)
T ss_pred CcHHHHHHHhCCCChHHHHHHHHHHHHCCCEecCCCCCCeE
Confidence 7899999999998 999999999999999987766665555
No 263
>PRK05626 rpsO 30S ribosomal protein S15; Reviewed
Probab=20.44 E-value=2.4e+02 Score=22.69 Aligned_cols=36 Identities=17% Similarity=0.250 Sum_probs=29.1
Q ss_pred ChHHHHHHHHHhhhhcCCcchHHHHHHHHHHHHHHH
Q 016147 36 DLDTRIELIKTLNSVSAGKIYVEIERARLIKKLAKI 71 (394)
Q Consensus 36 d~~~k~~~i~~L~~vt~gki~~E~era~l~~~La~i 71 (394)
+.+.|-.+|.....-.....+.|+|.|-+|.....+
T Consensus 4 ~~~~k~~li~~f~~~~~DTGS~eVQiA~LT~rI~~L 39 (89)
T PRK05626 4 TKEKKAEIIKEYGRHEGDTGSPEVQVALLTERINHL 39 (89)
T ss_pred CHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHHHHHH
Confidence 346777888888777777899999999999877665
No 264
>PF07064 RIC1: RIC1; InterPro: IPR009771 This entry represents RIC1 (Ribosomal control protein1) and has been identified in yeast as a Golgi protein involved in retrograde transport to the cis-Golgi network. It forms a heterodimer with Rgp1 and functions as a guanyl-nucleotide exchange factor [] which activates YPT6 by exchanging bound GDP for free GTP. RIC1 is thereby required for efficient fusion of endosome-derived vesicles with the Golgi. The RIC1-RGP1 complex participates in the recycling of SNC1, presumably by mediating fusion of endosomal vesicles with the Golgi compartment and may also be indirectly involved in the transcription of both ribosomal protein genes and ribosomal RNA [, , ].
Probab=20.40 E-value=4.1e+02 Score=25.52 Aligned_cols=62 Identities=19% Similarity=0.172 Sum_probs=46.7
Q ss_pred HHHHHHHhcCHHHHHHHHHHhh-hhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhC
Q 016147 68 LAKIKEEQGLIAEAADLMQEVA-VETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKIS 129 (394)
Q Consensus 68 La~i~e~~gd~~eAa~iL~~i~-vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~ 129 (394)
|=+-.-+.|+.+.|+..|-=++ .|....+...+-.+..++.++..++.+||.-|..+++=..
T Consensus 185 Lf~~cl~~~~l~tAa~yLlVl~~~e~~~~~~~~~~~~~al~LL~~a~~~~~w~Lc~eL~RFL~ 247 (258)
T PF07064_consen 185 LFEECLENGNLKTAASYLLVLQNLEGSSVVKDEESRQCALRLLVMALESGDWDLCFELVRFLK 247 (258)
T ss_pred HHHHHHHcCcHHHHHHHHHHHHhcCCcchhhhHHHHHHHHHHHHHHHhcccHHHHHHHHHHHH
Confidence 3344456899999999888776 2222233467778899999999999999999999877444
No 265
>KOG2041 consensus WD40 repeat protein [General function prediction only]
Probab=20.39 E-value=1.1e+03 Score=26.62 Aligned_cols=80 Identities=16% Similarity=0.130 Sum_probs=50.5
Q ss_pred hcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHHHHHHhccCChHHHHHHHHhhCccccCCCCccccCCCCCCCcccccC
Q 016147 75 QGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPRVFDADPSKEKKKPKEGDNVVEEA 154 (394)
Q Consensus 75 ~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq~rL~L~~~D~~~a~~~~~Ki~~~~~~~~~~~~~~~~~~~~~~~~~~ 154 (394)
-|+++||-++.- -++++.- -+.|++.-+||-|.-.+++-=+ +.
T Consensus 747 ~g~feeaek~yl--------d~drrDL------Aielr~klgDwfrV~qL~r~g~-------~d---------------- 789 (1189)
T KOG2041|consen 747 YGEFEEAEKLYL--------DADRRDL------AIELRKKLGDWFRVYQLIRNGG-------SD---------------- 789 (1189)
T ss_pred hcchhHhhhhhh--------ccchhhh------hHHHHHhhhhHHHHHHHHHccC-------CC----------------
Confidence 378888888433 3443321 2456777899999888866222 11
Q ss_pred CCCccchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhccC
Q 016147 155 PADIPSLLELKRIYYELMIRYYSHNNDYLEICRCYKAIYEIP 196 (394)
Q Consensus 155 ~~~~~~~~d~klk~~~~~~~~~~~~~~flea~k~y~ei~~t~ 196 (394)
.+.+.+-.=...++.++..-....+|+++|....++.
T Consensus 790 -----~dD~~~e~A~r~ig~~fa~~~~We~A~~yY~~~~~~e 826 (1189)
T KOG2041|consen 790 -----DDDEGKEDAFRNIGETFAEMMEWEEAAKYYSYCGDTE 826 (1189)
T ss_pred -----cchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccchH
Confidence 1223344445667777777888899999988777643
No 266
>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=20.34 E-value=1.6e+02 Score=21.33 Aligned_cols=28 Identities=29% Similarity=0.373 Sum_probs=23.4
Q ss_pred cCcccHHHHHHHhCCCHHHHHHHHHHhH
Q 016147 305 YSRITLKRLAELLCLSIQEAEKHLSDMV 332 (394)
Q Consensus 305 Y~~Isl~rLa~lL~ls~~e~E~~ls~MI 332 (394)
-..++++.||+.+|+|.--+-..+..+=
T Consensus 17 ~~~~~~~ela~~l~~S~rti~~~i~~L~ 44 (59)
T PF08280_consen 17 NKWITLKELAKKLNISERTIKNDINELN 44 (59)
T ss_dssp HTSBBHHHHHHHCTS-HHHHHHHHHHHH
T ss_pred CCCCcHHHHHHHHCCCHHHHHHHHHHHH
Confidence 5678999999999999998888887764
No 267
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=20.27 E-value=6.4e+02 Score=28.60 Aligned_cols=68 Identities=22% Similarity=0.220 Sum_probs=53.1
Q ss_pred HHHHHHHHHHHHHHHHHhcCHHHHHHHHHHhhhhhcccCcHHHHHHHHHHH---------------------------HH
Q 016147 58 EIERARLIKKLAKIKEEQGLIAEAADLMQEVAVETFGAMAKTEKIAFILEQ---------------------------VR 110 (394)
Q Consensus 58 E~era~l~~~La~i~e~~gd~~eAa~iL~~i~vEt~~~m~~~eK~e~~Leq---------------------------~r 110 (394)
+.=++.+-++-|+.+...||+++|..-..+ |-|.+++.+-+..+|+- +-
T Consensus 364 ~d~~~~i~~kYgd~Ly~Kgdf~~A~~qYI~----tI~~le~s~Vi~kfLdaq~IknLt~YLe~L~~~gla~~dhttlLLn 439 (933)
T KOG2114|consen 364 EDTLAEIHRKYGDYLYGKGDFDEATDQYIE----TIGFLEPSEVIKKFLDAQRIKNLTSYLEALHKKGLANSDHTTLLLN 439 (933)
T ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHH----HcccCChHHHHHHhcCHHHHHHHHHHHHHHHHcccccchhHHHHHH
Confidence 456788899999999999999999986654 77888888877666543 44
Q ss_pred HHhccCChHHHHHHHHhhC
Q 016147 111 LCLDRQDYVRAQILSRKIS 129 (394)
Q Consensus 111 L~L~~~D~~~a~~~~~Ki~ 129 (394)
+|.+-+|-.+...+++|..
T Consensus 440 cYiKlkd~~kL~efI~~~~ 458 (933)
T KOG2114|consen 440 CYIKLKDVEKLTEFISKCD 458 (933)
T ss_pred HHHHhcchHHHHHHHhcCC
Confidence 4777788888888877776
No 268
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=20.24 E-value=1.2e+02 Score=27.98 Aligned_cols=27 Identities=33% Similarity=0.407 Sum_probs=23.1
Q ss_pred CcccHHHHHHHhCCCHHHHHHHHHHhH
Q 016147 306 SRITLKRLAELLCLSIQEAEKHLSDMV 332 (394)
Q Consensus 306 ~~Isl~rLa~lL~ls~~e~E~~ls~MI 332 (394)
.++++..||+.||+|+.-+...|.+..
T Consensus 177 R~~~l~dLA~~lGISkst~~ehLRrAe 203 (215)
T COG3413 177 RRVSLKDLAKELGISKSTLSEHLRRAE 203 (215)
T ss_pred ccCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 589999999999999988887776643
No 269
>PF13182 DUF4007: Protein of unknown function (DUF4007)
Probab=20.17 E-value=2.5e+02 Score=27.40 Aligned_cols=72 Identities=17% Similarity=0.224 Sum_probs=53.1
Q ss_pred HHHHHHHHHHHHHH----hhcCcccHHHH-------HHHhCCCHHHHHHHHHHhHhc-CcEEEEeccCCCE--EEEec-C
Q 016147 289 LRQRIIEHNILVVS----KYYSRITLKRL-------AELLCLSIQEAEKHLSDMVVS-KALVAKIDRPQGI--VCFQV-A 353 (394)
Q Consensus 289 L~~~viEHNI~vis----k~Y~~Isl~rL-------a~lL~ls~~e~E~~ls~MI~~-g~l~akIDq~~gi--V~F~~-~ 353 (394)
|.-.|+-.-+.-.. .-.++|++++| +..|+|+++.+...|..+-.. |.| ++.+.+|+ |.+.. .
T Consensus 198 l~~~i~~YaL~~~~~~~~~~~~sis~~~L~~~~~sPGriF~L~~~~l~~~L~~l~~~~g~i--~~~~TaGl~qv~~~~~~ 275 (286)
T PF13182_consen 198 LPPEIFLYALLDFAERESPGRNSISFDELLNEPGSPGRIFKLDEESLAERLEQLEEIYGFI--SWSDTAGLDQVYLKDEE 275 (286)
T ss_pred CCHHHHHHHHHHHHHHhCCCCcEEEHHHHhcCCCCcceEeccCHHHHHHHHHHHHhhcCcE--EEEEcCCCeEEEecccc
Confidence 44445555554433 45889999998 689999999999999999988 655 46778884 77777 5
Q ss_pred CChHHHHHH
Q 016147 354 KDSNDILNS 362 (394)
Q Consensus 354 k~~~~~L~~ 362 (394)
.++.++|++
T Consensus 276 ~~~~~~L~~ 284 (286)
T PF13182_consen 276 LDAWDVLKQ 284 (286)
T ss_pred CCHHHHHHH
Confidence 566666654
No 270
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=20.14 E-value=2.5e+02 Score=26.66 Aligned_cols=35 Identities=20% Similarity=0.305 Sum_probs=32.1
Q ss_pred hhcCcccHHHHHHHhCCCHHHHHHHHHHhHhcCcE
Q 016147 303 KYYSRITLKRLAELLCLSIQEAEKHLSDMVVSKAL 337 (394)
Q Consensus 303 k~Y~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l 337 (394)
+-...++...||+.|++|++-+-+-|..|-.+|.+
T Consensus 15 ~~~~~~~~~ela~~l~vS~~TiRRdL~~Le~~g~l 49 (252)
T PRK10906 15 KQQGYVSTEELVEHFSVSPQTIRRDLNDLAEQNKI 49 (252)
T ss_pred HHcCCEeHHHHHHHhCCCHHHHHHHHHHHHHCCCE
Confidence 45778999999999999999999999999999976
No 271
>PF10771 DUF2582: Protein of unknown function (DUF2582); InterPro: IPR019707 This entry represents conserved proteins found in bacteria and archaea. The function is not known. ; PDB: 2L02_B 2L01_A.
Probab=20.03 E-value=1.9e+02 Score=21.81 Aligned_cols=44 Identities=11% Similarity=0.105 Sum_probs=36.4
Q ss_pred cCcccHHHHHHHhCCCHHHHHHHHHHhHhcCcEEEEeccCCCEEEE
Q 016147 305 YSRITLKRLAELLCLSIQEAEKHLSDMVVSKALVAKIDRPQGIVCF 350 (394)
Q Consensus 305 Y~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l~akIDq~~giV~F 350 (394)
-...|+++|++..+++..++-.-|.=+..+++|. |++.+|.+.|
T Consensus 20 ~~~~s~~el~k~~~l~~~~~~~AiGWLarE~KI~--~~~~~~~~~v 63 (65)
T PF10771_consen 20 NGEWSVSELKKATGLSDKEVYLAIGWLARENKIE--FEEKNGELYV 63 (65)
T ss_dssp SSSEEHHHHHHHCT-SCHHHHHHHHHHHCTTSEE--EEEETTEEEE
T ss_pred CCCcCHHHHHHHhCcCHHHHHHHHHHHhccCcee--EEeeCCEEEE
Confidence 3568999999999999999999999999999984 5577776665
No 272
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=20.02 E-value=5.7e+02 Score=22.05 Aligned_cols=33 Identities=27% Similarity=0.232 Sum_probs=29.4
Q ss_pred cCcccHHHHHHHhCCCHHHHHHHHHHhHhcCcE
Q 016147 305 YSRITLKRLAELLCLSIQEAEKHLSDMVVSKAL 337 (394)
Q Consensus 305 Y~~Isl~rLa~lL~ls~~e~E~~ls~MI~~g~l 337 (394)
..-+|=+.||+++|++..++-+.|..|-.+|.+
T Consensus 13 ~~~~~dedLa~~l~i~~n~vRkiL~~L~ed~~~ 45 (147)
T smart00531 13 NGCVTEEDLAELLGIKQKQLRKILYLLYDEKLI 45 (147)
T ss_pred cCCcCHHHHHHHhCCCHHHHHHHHHHHHhhhcc
Confidence 355899999999999999999999999997764
Done!