Query psy1676
Match_columns 343
No_of_seqs 242 out of 811
Neff 7.2
Searched_HMMs 46136
Date Fri Aug 16 21:18:12 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1676.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1676hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2581|consensus 100.0 2.5E-96 6E-101 695.6 31.0 340 2-342 154-493 (493)
2 KOG2688|consensus 100.0 4.6E-34 9.9E-39 275.1 15.7 242 32-285 131-391 (394)
3 COG5600 Transcription-associat 100.0 1.7E-31 3.6E-36 252.5 19.2 244 30-284 143-409 (413)
4 KOG2582|consensus 100.0 9.6E-29 2.1E-33 232.9 20.1 284 13-306 92-391 (422)
5 PF08375 Rpn3_C: Proteasome re 99.9 6.4E-28 1.4E-32 177.9 6.7 68 274-341 1-68 (68)
6 KOG1497|consensus 99.8 2.2E-17 4.8E-22 154.0 21.1 272 16-303 102-387 (399)
7 PF01399 PCI: PCI domain; Int 99.8 7.5E-18 1.6E-22 135.0 12.1 104 167-271 1-105 (105)
8 KOG1498|consensus 99.7 3.4E-16 7.3E-21 149.6 20.5 276 17-298 131-422 (439)
9 KOG1463|consensus 99.7 1.4E-15 3E-20 143.2 19.5 212 62-274 173-393 (411)
10 KOG1464|consensus 99.6 2.5E-14 5.5E-19 131.8 17.0 228 58-292 192-431 (440)
11 KOG2908|consensus 99.6 2.5E-12 5.5E-17 121.4 28.4 242 52-298 110-367 (380)
12 COG5159 RPN6 26S proteasome re 99.5 1.3E-12 2.8E-17 121.1 17.8 184 90-274 201-391 (421)
13 COG5071 RPN5 26S proteasome re 99.5 7.1E-13 1.5E-17 123.4 14.1 271 16-294 130-418 (439)
14 smart00753 PAM PCI/PINT associ 99.3 3.4E-11 7.3E-16 94.0 9.1 86 203-291 2-87 (88)
15 smart00088 PINT motif in prote 99.3 3.4E-11 7.3E-16 94.0 9.1 86 203-291 2-87 (88)
16 KOG1076|consensus 98.3 0.00014 2.9E-09 75.1 21.2 248 13-272 482-764 (843)
17 KOG0687|consensus 98.2 0.00037 8E-09 66.4 20.1 204 63-272 147-363 (393)
18 COG5187 RPN7 26S proteasome re 98.0 0.0017 3.7E-08 61.2 21.2 174 93-272 190-377 (412)
19 PF10255 Paf67: RNA polymerase 98.0 0.00045 9.8E-09 68.4 18.2 184 58-248 123-343 (404)
20 KOG0686|consensus 97.8 0.0017 3.7E-08 63.6 17.2 207 64-272 194-411 (466)
21 KOG2753|consensus 97.6 0.0056 1.2E-07 58.6 17.1 117 169-291 240-359 (378)
22 KOG2758|consensus 97.4 0.001 2.2E-08 63.5 9.3 95 178-273 301-396 (432)
23 PF14938 SNAP: Soluble NSF att 97.3 0.0069 1.5E-07 57.3 14.3 148 51-199 108-268 (282)
24 KOG2072|consensus 97.2 0.39 8.4E-06 51.1 29.1 69 203-271 425-493 (988)
25 PF10075 PCI_Csn8: COP9 signal 96.2 0.029 6.2E-07 47.7 8.5 106 141-250 10-121 (143)
26 PF09976 TPR_21: Tetratricopep 96.0 0.16 3.6E-06 42.7 12.2 100 15-122 46-145 (145)
27 PF13371 TPR_9: Tetratricopept 95.8 0.032 6.9E-07 40.9 6.0 60 63-128 1-62 (73)
28 PF13432 TPR_16: Tetratricopep 95.7 0.053 1.1E-06 38.9 6.7 61 63-127 3-63 (65)
29 PF07719 TPR_2: Tetratricopept 95.6 0.032 6.8E-07 34.5 4.8 32 96-127 2-33 (34)
30 TIGR02552 LcrH_SycD type III s 95.5 0.41 8.9E-06 39.1 12.3 99 20-128 20-118 (135)
31 PRK15359 type III secretion sy 95.4 0.33 7.2E-06 41.1 11.8 99 20-128 27-125 (144)
32 cd00189 TPR Tetratricopeptide 95.4 0.3 6.6E-06 35.0 10.3 96 19-126 2-99 (100)
33 PF13424 TPR_12: Tetratricopep 95.4 0.084 1.8E-06 39.3 7.2 65 57-123 5-74 (78)
34 TIGR02795 tol_pal_ybgF tol-pal 94.9 0.64 1.4E-05 36.5 11.4 106 17-128 2-109 (119)
35 PF12895 Apc3: Anaphase-promot 94.7 0.33 7.1E-06 36.7 8.9 58 58-121 27-84 (84)
36 PF13414 TPR_11: TPR repeat; P 94.4 0.12 2.7E-06 37.3 5.7 64 58-126 4-69 (69)
37 PRK11788 tetratricopeptide rep 94.2 5.1 0.00011 38.7 18.2 103 18-127 108-212 (389)
38 PF09012 FeoC: FeoC like trans 93.8 0.12 2.7E-06 38.2 4.7 47 216-263 5-51 (69)
39 TIGR03302 OM_YfiO outer membra 93.6 4 8.6E-05 36.7 15.3 118 4-127 17-147 (235)
40 PF14938 SNAP: Soluble NSF att 93.5 2.6 5.6E-05 39.7 14.2 200 16-216 34-250 (282)
41 PF00515 TPR_1: Tetratricopept 93.4 0.22 4.7E-06 30.9 4.7 32 96-127 2-33 (34)
42 PF03399 SAC3_GANP: SAC3/GANP/ 93.2 1.7 3.6E-05 38.6 11.8 63 171-237 140-204 (204)
43 PF13424 TPR_12: Tetratricopep 93.1 0.89 1.9E-05 33.6 8.5 70 14-83 2-72 (78)
44 PF10602 RPN7: 26S proteasome 92.8 2.8 6.1E-05 36.9 12.4 89 59-148 75-168 (177)
45 CHL00033 ycf3 photosystem I as 92.7 2.7 5.9E-05 36.0 12.1 105 16-123 34-141 (168)
46 TIGR00990 3a0801s09 mitochondr 92.6 6.2 0.00013 41.3 16.8 62 16-83 364-425 (615)
47 PRK11788 tetratricopeptide rep 92.3 4.6 0.0001 39.0 14.6 101 19-126 37-138 (389)
48 PRK02603 photosystem I assembl 92.2 2.8 6.1E-05 36.2 11.7 88 14-110 32-121 (172)
49 PRK11189 lipoprotein NlpI; Pro 92.1 1.7 3.7E-05 41.2 11.0 100 17-128 64-165 (296)
50 PRK10370 formate-dependent nit 91.9 3.4 7.3E-05 37.0 12.1 100 17-127 73-176 (198)
51 TIGR02917 PEP_TPR_lipo putativ 91.9 6.2 0.00013 41.7 16.0 103 14-128 122-226 (899)
52 TIGR02521 type_IV_pilW type IV 91.5 8.4 0.00018 33.1 17.3 97 16-124 30-128 (234)
53 PF13181 TPR_8: Tetratricopept 91.2 0.41 9E-06 29.5 3.9 31 96-126 2-32 (34)
54 TIGR03302 OM_YfiO outer membra 91.2 2.9 6.4E-05 37.6 11.1 65 61-128 37-103 (235)
55 PF08784 RPA_C: Replication pr 90.8 0.24 5.2E-06 39.4 3.1 38 224-262 64-101 (102)
56 KOG4162|consensus 90.3 1.7 3.6E-05 46.3 9.4 104 10-124 677-783 (799)
57 TIGR02521 type_IV_pilW type IV 90.2 4.3 9.3E-05 35.0 11.0 103 16-127 64-167 (234)
58 PF04733 Coatomer_E: Coatomer 89.9 2.2 4.7E-05 40.7 9.3 90 58-153 132-253 (290)
59 PRK12370 invasion protein regu 89.5 28 0.00061 36.0 18.2 180 62-256 343-538 (553)
60 PF13429 TPR_15: Tetratricopep 89.3 5.4 0.00012 37.0 11.5 101 16-128 145-247 (280)
61 cd00189 TPR Tetratricopeptide 89.3 2.2 4.7E-05 30.3 7.1 61 62-128 5-67 (100)
62 TIGR02917 PEP_TPR_lipo putativ 89.2 5.3 0.00011 42.2 12.6 103 15-126 54-156 (899)
63 KOG1840|consensus 89.1 9.6 0.00021 39.3 13.7 144 9-153 191-343 (508)
64 PF13174 TPR_6: Tetratricopept 88.8 0.75 1.6E-05 27.8 3.6 30 98-127 3-32 (33)
65 TIGR00990 3a0801s09 mitochondr 88.2 8 0.00017 40.5 13.0 104 13-128 327-432 (615)
66 PRK15174 Vi polysaccharide exp 88.0 5.9 0.00013 42.1 12.0 257 17-291 284-581 (656)
67 PF09295 ChAPs: ChAPs (Chs5p-A 86.6 5.3 0.00012 39.9 10.0 90 20-119 203-292 (395)
68 KOG2002|consensus 86.4 4.3 9.3E-05 44.3 9.6 69 58-127 271-339 (1018)
69 cd05804 StaR_like StaR_like; a 86.3 9.6 0.00021 36.3 11.5 96 20-123 117-214 (355)
70 PRK10803 tol-pal system protei 86.3 24 0.00051 33.2 13.7 105 17-128 142-250 (263)
71 PF12688 TPR_5: Tetratrico pep 85.9 18 0.0004 29.8 12.3 114 17-140 1-116 (120)
72 PRK15363 pathogenicity island 85.7 3 6.6E-05 36.2 6.8 80 64-153 42-121 (157)
73 PF14559 TPR_19: Tetratricopep 84.5 1.9 4.1E-05 30.7 4.3 54 68-127 2-57 (68)
74 PF09756 DDRGK: DDRGK domain; 84.4 1.8 4E-05 38.7 4.9 48 223-271 111-158 (188)
75 KOG2076|consensus 84.2 70 0.0015 35.1 19.9 105 12-128 168-274 (895)
76 PF14853 Fis1_TPR_C: Fis1 C-te 84.1 4.2 9.1E-05 28.6 5.7 33 96-128 2-34 (53)
77 PRK12370 invasion protein regu 84.1 8.9 0.00019 39.8 10.7 100 13-124 334-435 (553)
78 PLN03088 SGT1, suppressor of 83.8 14 0.00031 36.1 11.5 89 29-128 14-103 (356)
79 PRK11179 DNA-binding transcrip 83.7 2.9 6.4E-05 35.7 5.9 38 224-262 22-62 (153)
80 PF13176 TPR_7: Tetratricopept 83.6 2 4.4E-05 27.2 3.7 25 99-123 3-27 (36)
81 KOG2300|consensus 83.5 42 0.00091 34.5 14.4 73 54-126 401-476 (629)
82 PF13412 HTH_24: Winged helix- 83.4 4.3 9.3E-05 27.3 5.5 34 223-257 15-48 (48)
83 KOG1173|consensus 82.9 64 0.0014 33.6 20.6 110 9-123 241-374 (611)
84 CHL00033 ycf3 photosystem I as 82.2 21 0.00045 30.4 10.7 75 50-127 28-104 (168)
85 PF02082 Rrf2: Transcriptional 81.3 3.6 7.9E-05 31.3 5.0 47 225-272 25-71 (83)
86 smart00028 TPR Tetratricopepti 80.9 4.1 9E-05 22.8 4.2 30 97-126 3-32 (34)
87 PF13414 TPR_11: TPR repeat; P 80.6 4 8.6E-05 29.1 4.8 34 95-128 3-36 (69)
88 PF13428 TPR_14: Tetratricopep 80.0 3.7 8E-05 27.1 4.1 31 98-128 4-34 (44)
89 PF01726 LexA_DNA_bind: LexA D 79.8 3.5 7.5E-05 30.3 4.2 33 225-257 25-57 (65)
90 PRK02603 photosystem I assembl 79.7 13 0.00029 31.9 8.6 74 52-128 30-105 (172)
91 PF12802 MarR_2: MarR family; 79.0 4.8 0.0001 28.3 4.7 38 226-264 22-59 (62)
92 PRK10803 tol-pal system protei 79.0 20 0.00043 33.7 10.1 68 58-128 144-213 (263)
93 TIGR02552 LcrH_SycD type III s 79.0 12 0.00027 30.1 7.9 65 58-128 18-84 (135)
94 TIGR02795 tol_pal_ybgF tol-pal 78.7 13 0.00029 28.7 7.7 63 63-128 8-72 (119)
95 COG1522 Lrp Transcriptional re 78.5 5.6 0.00012 33.5 5.8 38 222-260 19-56 (154)
96 smart00550 Zalpha Z-DNA-bindin 78.3 7.2 0.00016 28.7 5.6 32 225-257 22-53 (68)
97 PRK11169 leucine-responsive tr 77.8 5.8 0.00013 34.3 5.8 40 219-259 22-61 (164)
98 PRK10049 pgaA outer membrane p 77.5 1.1E+02 0.0024 33.1 18.8 165 23-199 278-461 (765)
99 PRK15359 type III secretion sy 76.6 15 0.00033 30.8 7.9 81 63-153 30-110 (144)
100 PRK10049 pgaA outer membrane p 76.6 35 0.00076 36.9 12.5 99 18-128 360-460 (765)
101 PRK10866 outer membrane biogen 76.5 63 0.0014 29.8 14.9 62 64-128 39-102 (243)
102 PF13429 TPR_15: Tetratricopep 76.4 5.9 0.00013 36.8 5.8 69 58-128 111-179 (280)
103 PRK15179 Vi polysaccharide bio 76.0 57 0.0012 35.1 13.6 100 17-126 86-185 (694)
104 PF00392 GntR: Bacterial regul 75.3 23 0.00049 25.3 7.5 42 223-267 21-63 (64)
105 PF09339 HTH_IclR: IclR helix- 74.1 7.6 0.00017 26.7 4.5 38 219-257 12-49 (52)
106 PLN03081 pentatricopeptide (PP 73.3 1.3E+02 0.0029 31.9 25.0 230 58-309 361-610 (697)
107 PLN03077 Protein ECB2; Provisi 72.7 1.5E+02 0.0033 32.3 20.5 254 26-309 498-773 (857)
108 PRK09782 bacteriophage N4 rece 72.3 33 0.00072 38.5 11.1 92 23-127 582-675 (987)
109 PRK11447 cellulose synthase su 71.8 30 0.00064 39.4 10.9 106 17-128 303-418 (1157)
110 PRK15331 chaperone protein Sic 71.7 70 0.0015 28.0 11.9 103 8-126 33-136 (165)
111 PF01047 MarR: MarR family; I 71.6 9.1 0.0002 26.7 4.5 41 223-264 15-55 (59)
112 PLN03081 pentatricopeptide (PP 71.3 69 0.0015 34.1 13.1 61 57-124 158-218 (697)
113 PRK15431 ferrous iron transpor 71.3 10 0.00022 29.0 4.8 41 219-260 10-50 (78)
114 cd07377 WHTH_GntR Winged helix 70.9 31 0.00067 24.0 7.3 33 224-257 23-56 (66)
115 PLN03077 Protein ECB2; Provisi 70.4 1.3E+02 0.0028 32.9 15.2 60 58-124 223-282 (857)
116 smart00419 HTH_CRP helix_turn_ 70.1 9.5 0.00021 25.0 4.2 32 225-257 8-39 (48)
117 PRK11447 cellulose synthase su 69.8 85 0.0018 35.7 14.0 91 20-126 576-668 (1157)
118 PRK15174 Vi polysaccharide exp 69.6 41 0.00089 35.7 10.8 102 18-127 247-350 (656)
119 TIGR02944 suf_reg_Xantho FeS a 68.3 8.1 0.00018 31.9 4.2 44 224-268 24-67 (130)
120 KOG1126|consensus 67.6 35 0.00076 36.0 9.3 103 19-127 491-623 (638)
121 TIGR02010 IscR iron-sulfur clu 67.2 13 0.00028 31.0 5.3 63 224-288 24-86 (135)
122 PRK11906 transcriptional regul 66.9 85 0.0018 32.0 11.7 58 67-128 348-405 (458)
123 PF12569 NARP1: NMDA receptor- 66.8 27 0.00058 36.2 8.4 126 58-193 195-337 (517)
124 TIGR00540 hemY_coli hemY prote 66.4 65 0.0014 31.9 11.0 101 18-127 264-369 (409)
125 cd00092 HTH_CRP helix_turn_hel 66.2 12 0.00026 26.5 4.2 34 224-258 24-57 (67)
126 KOG3250|consensus 66.1 26 0.00055 32.2 7.0 124 166-298 59-186 (258)
127 PF13432 TPR_16: Tetratricopep 65.9 18 0.0004 25.3 5.2 49 99-153 1-49 (65)
128 PF00325 Crp: Bacterial regula 65.7 14 0.0003 23.3 3.8 31 225-256 2-32 (32)
129 PF13374 TPR_10: Tetratricopep 65.4 15 0.00033 22.9 4.3 27 97-123 4-30 (42)
130 smart00418 HTH_ARSR helix_turn 65.3 21 0.00046 24.3 5.4 39 223-262 8-46 (66)
131 PF07719 TPR_2: Tetratricopept 64.6 17 0.00038 21.7 4.3 29 17-45 1-29 (34)
132 smart00344 HTH_ASNC helix_turn 63.7 17 0.00037 28.6 5.2 33 224-257 16-48 (108)
133 TIGR00738 rrf2_super rrf2 fami 63.7 13 0.00028 30.5 4.5 44 224-268 24-67 (132)
134 PRK14574 hmsH outer membrane p 62.1 2.5E+02 0.0055 30.9 16.0 90 29-128 46-135 (822)
135 PF09976 TPR_21: Tetratricopep 61.6 92 0.002 25.7 9.6 64 56-120 46-110 (145)
136 smart00345 HTH_GNTR helix_turn 61.2 34 0.00073 23.2 5.8 33 224-257 18-51 (60)
137 KOG1155|consensus 61.2 1E+02 0.0022 31.7 10.8 100 19-124 434-536 (559)
138 PF01325 Fe_dep_repress: Iron 60.6 33 0.00072 24.5 5.7 36 221-257 18-53 (60)
139 KOG4414|consensus 60.5 14 0.00031 31.7 4.2 44 202-246 109-152 (197)
140 COG3063 PilF Tfp pilus assembl 60.3 1.5E+02 0.0032 27.7 11.7 91 58-153 36-157 (250)
141 KOG0543|consensus 60.3 35 0.00077 34.0 7.5 67 58-128 258-324 (397)
142 cd05804 StaR_like StaR_like; a 59.8 1.5E+02 0.0033 27.9 11.9 27 100-126 119-145 (355)
143 cd00090 HTH_ARSR Arsenical Res 59.6 34 0.00074 24.0 5.8 41 226-267 21-61 (78)
144 PF14394 DUF4423: Domain of un 59.5 79 0.0017 27.7 9.0 96 202-308 19-118 (171)
145 PRK11189 lipoprotein NlpI; Pro 58.8 55 0.0012 30.9 8.5 70 52-127 59-130 (296)
146 PF10602 RPN7: 26S proteasome 58.8 1.3E+02 0.0027 26.4 13.6 82 42-124 21-102 (177)
147 PRK10857 DNA-binding transcrip 58.5 18 0.00038 31.6 4.6 47 224-271 24-70 (164)
148 PF10300 DUF3808: Protein of u 57.6 2.2E+02 0.0049 28.9 14.1 120 20-151 230-356 (468)
149 PF09986 DUF2225: Uncharacteri 57.6 1.4E+02 0.0031 27.0 10.6 77 46-124 106-194 (214)
150 COG1497 Predicted transcriptio 57.5 15 0.00033 34.1 4.2 50 208-258 7-57 (260)
151 PRK04841 transcriptional regul 56.9 1.7E+02 0.0036 31.9 13.0 106 18-123 532-640 (903)
152 COG1729 Uncharacterized protei 56.7 56 0.0012 30.8 7.9 66 59-128 144-211 (262)
153 KOG2003|consensus 56.6 2.4E+02 0.0052 29.0 16.5 97 18-126 525-623 (840)
154 PF13281 DUF4071: Domain of un 56.4 2.2E+02 0.0047 28.4 15.3 69 58-127 143-214 (374)
155 PF09999 DUF2240: Uncharacteri 56.1 14 0.00031 31.6 3.5 74 224-301 16-106 (144)
156 smart00420 HTH_DEOR helix_turn 55.9 24 0.00053 23.3 4.1 34 224-258 13-46 (53)
157 PRK11920 rirA iron-responsive 55.8 41 0.0009 28.8 6.5 48 224-272 23-70 (153)
158 PF01978 TrmB: Sugar-specific 55.2 40 0.00087 24.2 5.5 38 222-260 19-56 (68)
159 PF13404 HTH_AsnC-type: AsnC-t 54.9 34 0.00073 22.7 4.5 26 224-250 16-41 (42)
160 PF13463 HTH_27: Winged helix 54.6 45 0.00096 23.6 5.6 42 220-262 13-54 (68)
161 PRK09782 bacteriophage N4 rece 54.6 1.7E+02 0.0038 32.9 12.6 95 19-128 44-141 (987)
162 PF09202 Rio2_N: Rio2, N-termi 53.7 40 0.00087 25.9 5.4 51 215-266 14-64 (82)
163 KOG3054|consensus 53.6 23 0.00049 33.0 4.6 48 223-271 212-259 (299)
164 KOG1173|consensus 53.3 69 0.0015 33.5 8.4 28 229-256 510-538 (611)
165 PRK15363 pathogenicity island 52.0 1.6E+02 0.0035 25.6 13.1 86 30-126 48-134 (157)
166 PF08279 HTH_11: HTH domain; 51.8 74 0.0016 21.6 6.4 38 216-254 6-43 (55)
167 PF13181 TPR_8: Tetratricopept 51.3 45 0.00097 19.9 4.5 30 17-46 1-30 (34)
168 TIGR01610 phage_O_Nterm phage 51.2 47 0.001 26.0 5.6 46 222-270 44-89 (95)
169 PF13730 HTH_36: Helix-turn-he 50.8 28 0.00062 23.8 3.9 29 227-256 27-55 (55)
170 TIGR02147 Fsuc_second hypothet 50.7 2.2E+02 0.0048 26.9 12.2 107 192-308 107-216 (271)
171 PF04703 FaeA: FaeA-like prote 50.1 35 0.00077 24.8 4.3 34 223-257 13-46 (62)
172 TIGR02337 HpaR homoprotocatech 49.9 1.2E+02 0.0026 24.2 8.0 42 223-265 40-81 (118)
173 PF07721 TPR_4: Tetratricopept 49.8 26 0.00055 20.3 3.0 23 97-119 3-25 (26)
174 PLN03088 SGT1, suppressor of 49.7 54 0.0012 32.0 7.0 59 64-128 9-69 (356)
175 PF13545 HTH_Crp_2: Crp-like h 49.7 33 0.00071 25.0 4.3 42 224-270 27-68 (76)
176 PRK10153 DNA-binding transcrip 49.5 1.1E+02 0.0023 31.8 9.4 56 67-127 430-485 (517)
177 KOG4234|consensus 49.2 70 0.0015 29.4 6.9 97 98-200 98-200 (271)
178 PRK10747 putative protoheme IX 49.0 1.6E+02 0.0034 29.1 10.3 33 95-127 328-360 (398)
179 PRK11014 transcriptional repre 48.7 35 0.00075 28.6 4.8 47 224-271 24-70 (141)
180 COG1959 Predicted transcriptio 48.7 29 0.00063 29.7 4.3 71 225-297 25-97 (150)
181 PF12840 HTH_20: Helix-turn-he 48.7 67 0.0014 22.6 5.6 37 221-258 20-56 (61)
182 COG2345 Predicted transcriptio 48.5 51 0.0011 30.2 6.1 49 213-262 13-61 (218)
183 KOG2076|consensus 47.0 65 0.0014 35.3 7.4 68 58-128 415-482 (895)
184 COG0173 AspS Aspartyl-tRNA syn 46.7 5 0.00011 41.4 -0.8 101 137-238 176-286 (585)
185 KOG3081|consensus 45.9 1.1E+02 0.0025 29.1 8.0 80 103-192 215-296 (299)
186 PF01022 HTH_5: Bacterial regu 45.4 66 0.0014 21.4 4.9 33 224-257 14-46 (47)
187 PRK14574 hmsH outer membrane p 45.4 4.6E+02 0.01 28.9 17.9 69 60-128 370-449 (822)
188 PF12895 Apc3: Anaphase-promot 45.0 70 0.0015 23.6 5.6 60 16-82 24-83 (84)
189 PLN03098 LPA1 LOW PSII ACCUMUL 44.6 72 0.0016 32.4 7.0 64 58-124 76-141 (453)
190 PRK04841 transcriptional regul 44.6 4.5E+02 0.0097 28.6 15.5 107 19-125 493-603 (903)
191 PRK09954 putative kinase; Prov 44.6 40 0.00086 32.7 5.2 49 222-271 14-65 (362)
192 KOG1840|consensus 44.5 3.8E+02 0.0083 27.8 18.8 131 22-153 246-385 (508)
193 KOG1129|consensus 44.5 2.5E+02 0.0055 27.7 10.3 57 62-124 261-319 (478)
194 KOG1127|consensus 42.7 3.4E+02 0.0073 30.7 11.9 129 58-198 527-660 (1238)
195 PF13812 PPR_3: Pentatricopept 41.8 37 0.00079 20.1 3.0 24 59-82 3-26 (34)
196 PHA02943 hypothetical protein; 41.3 41 0.00089 29.1 4.0 36 222-258 21-56 (165)
197 TIGR01764 excise DNA binding d 40.8 47 0.001 21.5 3.6 31 226-261 2-32 (49)
198 PF10300 DUF3808: Protein of u 40.3 2.5E+02 0.0053 28.7 10.3 86 19-111 269-356 (468)
199 PF08220 HTH_DeoR: DeoR-like h 39.8 86 0.0019 22.0 5.0 35 221-256 10-44 (57)
200 PRK11512 DNA-binding transcrip 39.7 51 0.0011 27.5 4.5 42 224-266 53-94 (144)
201 PF01535 PPR: PPR repeat; Int 39.2 28 0.00061 20.1 2.1 25 59-83 2-26 (31)
202 KOG0495|consensus 38.5 5.5E+02 0.012 27.9 13.2 167 20-200 587-788 (913)
203 PF05331 DUF742: Protein of un 38.0 73 0.0016 26.1 4.9 33 225-258 55-87 (114)
204 PRK06266 transcription initiat 37.2 2.9E+02 0.0063 24.3 9.8 48 224-272 35-84 (178)
205 KOG1174|consensus 37.1 1.4E+02 0.0031 30.3 7.5 63 59-128 440-504 (564)
206 PF08898 DUF1843: Domain of un 36.9 90 0.0019 22.0 4.4 39 171-209 6-45 (53)
207 KOG0495|consensus 36.9 2.5E+02 0.0053 30.3 9.5 107 18-137 686-794 (913)
208 PRK10370 formate-dependent nit 36.9 3E+02 0.0064 24.3 12.5 36 93-128 71-106 (198)
209 PF09940 DUF2172: Domain of un 36.7 46 0.001 33.0 4.1 65 192-257 319-386 (386)
210 TIGR00373 conserved hypothetic 36.2 2.1E+02 0.0045 24.7 7.8 67 224-294 27-95 (158)
211 PRK14165 winged helix-turn-hel 36.1 84 0.0018 28.8 5.5 50 223-273 19-68 (217)
212 COG4700 Uncharacterized protei 35.9 1.5E+02 0.0032 27.0 6.8 62 62-127 129-192 (251)
213 COG4367 Uncharacterized protei 35.8 44 0.00096 26.1 3.1 24 224-248 22-45 (97)
214 PF08221 HTH_9: RNA polymerase 35.0 1.7E+02 0.0037 21.0 6.4 35 222-257 24-58 (62)
215 KOG1156|consensus 34.8 4.2E+02 0.0091 28.4 10.8 88 100-193 80-171 (700)
216 PF14559 TPR_19: Tetratricopep 34.7 1E+02 0.0022 21.4 4.8 42 106-153 2-43 (68)
217 KOG0542|consensus 34.6 1.2E+02 0.0026 28.5 6.2 64 193-256 155-244 (280)
218 PF12862 Apc5: Anaphase-promot 34.6 2.1E+02 0.0046 21.9 7.4 63 66-128 7-74 (94)
219 PF12324 HTH_15: Helix-turn-he 34.6 99 0.0021 23.6 4.7 39 211-251 25-63 (77)
220 PF12569 NARP1: NMDA receptor- 34.5 5.5E+02 0.012 26.7 12.4 105 19-123 196-333 (517)
221 KOG2796|consensus 34.5 3.9E+02 0.0084 25.7 9.6 23 102-124 259-281 (366)
222 KOG3364|consensus 34.2 94 0.002 26.6 5.0 40 89-128 65-104 (149)
223 KOG1861|consensus 33.9 5.5E+02 0.012 26.5 12.9 136 98-242 351-495 (540)
224 PF04545 Sigma70_r4: Sigma-70, 32.9 1.3E+02 0.0028 20.0 4.9 29 223-252 18-46 (50)
225 smart00346 HTH_ICLR helix_turn 32.9 2.1E+02 0.0045 21.3 6.9 34 224-258 19-52 (91)
226 PF04049 APC8: Anaphase promot 32.7 69 0.0015 27.1 4.1 45 62-113 79-123 (142)
227 PF12793 SgrR_N: Sugar transpo 32.6 1.3E+02 0.0029 24.5 5.7 65 222-295 16-83 (115)
228 PF12854 PPR_1: PPR repeat 32.6 70 0.0015 19.8 3.2 25 58-82 8-32 (34)
229 PRK14720 transcript cleavage f 32.3 5.2E+02 0.011 28.9 11.6 107 12-127 26-148 (906)
230 TIGR00756 PPR pentatricopeptid 32.2 48 0.001 19.4 2.3 25 59-83 2-26 (35)
231 COG4496 Uncharacterized protei 32.0 68 0.0015 25.2 3.5 38 246-298 48-85 (100)
232 COG1321 TroR Mn-dependent tran 31.7 1.1E+02 0.0025 26.2 5.4 41 216-257 15-55 (154)
233 PRK03902 manganese transport t 31.7 1.3E+02 0.0028 25.1 5.6 36 221-257 18-53 (142)
234 PF10557 Cullin_Nedd8: Cullin 31.6 1.2E+02 0.0026 22.0 4.8 53 205-257 2-61 (68)
235 PF08631 SPO22: Meiosis protei 31.6 4.3E+02 0.0093 24.6 11.8 59 67-125 3-66 (278)
236 PF13512 TPR_18: Tetratricopep 31.4 68 0.0015 27.4 3.8 62 63-127 53-131 (142)
237 PF07729 FCD: FCD domain; Int 31.1 2.4E+02 0.0052 21.5 9.1 29 163-191 94-122 (125)
238 COG3071 HemY Uncharacterized e 31.1 88 0.0019 31.2 5.0 71 58-128 264-361 (400)
239 TIGR03879 near_KaiC_dom probab 30.8 68 0.0015 24.2 3.3 35 221-256 28-62 (73)
240 KOG2300|consensus 30.5 3.2E+02 0.0069 28.4 8.9 66 60-126 91-158 (629)
241 PF02064 MAS20: MAS20 protein 30.3 1.5E+02 0.0032 24.6 5.6 29 100-128 68-96 (121)
242 PRK03573 transcriptional regul 30.3 1.6E+02 0.0034 24.4 6.0 40 225-265 46-85 (144)
243 KOG3252|consensus 30.2 2.3E+02 0.005 25.5 7.0 89 168-269 100-188 (217)
244 PLN03098 LPA1 LOW PSII ACCUMUL 30.2 2.9E+02 0.0063 28.2 8.6 60 91-153 71-130 (453)
245 KOG3677|consensus 29.9 6.1E+02 0.013 25.8 12.1 217 58-289 236-497 (525)
246 PF05843 Suf: Suppressor of fo 29.8 4.7E+02 0.01 24.4 12.1 136 19-199 3-141 (280)
247 PF13601 HTH_34: Winged helix 29.8 2.4E+02 0.0053 21.2 7.3 40 223-263 12-51 (80)
248 PF13041 PPR_2: PPR repeat fam 29.6 74 0.0016 21.1 3.2 26 58-83 4-29 (50)
249 PF10078 DUF2316: Uncharacteri 29.5 62 0.0013 25.4 3.0 24 224-248 22-45 (89)
250 PRK10046 dpiA two-component re 29.2 1.6E+02 0.0034 26.2 6.2 46 217-263 169-214 (225)
251 KOG1125|consensus 29.0 86 0.0019 32.7 4.7 87 33-123 410-526 (579)
252 COG1510 Predicted transcriptio 28.9 3.2E+02 0.007 24.2 7.6 33 224-257 40-72 (177)
253 PRK11534 DNA-binding transcrip 28.8 2.6E+02 0.0056 24.9 7.5 60 208-270 9-72 (224)
254 TIGR00498 lexA SOS regulatory 28.3 1.8E+02 0.0039 25.6 6.3 36 225-260 25-60 (199)
255 PF07389 DUF1500: Protein of u 28.2 1.4E+02 0.003 23.4 4.6 46 209-256 32-77 (100)
256 COG5010 TadD Flp pilus assembl 28.1 4.2E+02 0.009 25.0 8.7 66 58-127 101-166 (257)
257 PF10516 SHNi-TPR: SHNi-TPR; 28.0 96 0.0021 20.1 3.3 25 99-123 5-29 (38)
258 PRK15418 transcriptional regul 27.7 2.6E+02 0.0057 26.9 7.7 60 220-295 23-83 (318)
259 PF09295 ChAPs: ChAPs (Chs5p-A 27.4 4.7E+02 0.01 26.2 9.6 62 58-128 170-233 (395)
260 PLN03218 maturation of RBCL 1; 27.0 9.8E+02 0.021 27.3 19.2 65 58-123 543-607 (1060)
261 TIGR01889 Staph_reg_Sar staphy 26.6 1.2E+02 0.0025 24.1 4.3 40 224-264 42-81 (109)
262 TIGR02431 pcaR_pcaU beta-ketoa 26.4 1.4E+02 0.0029 27.4 5.3 35 222-257 21-55 (248)
263 COG2976 Uncharacterized protei 26.3 5E+02 0.011 23.6 10.5 63 58-125 126-189 (207)
264 PRK09990 DNA-binding transcrip 26.0 4.9E+02 0.011 23.5 9.3 49 222-273 27-76 (251)
265 PF12728 HTH_17: Helix-turn-he 25.7 1E+02 0.0023 20.5 3.4 29 226-259 2-30 (51)
266 PF13431 TPR_17: Tetratricopep 25.6 86 0.0019 19.4 2.7 21 95-115 13-33 (34)
267 cd04762 HTH_MerR-trunc Helix-T 25.6 1.6E+02 0.0034 18.7 4.2 29 226-259 1-29 (49)
268 PRK10163 DNA-binding transcrip 25.3 1.5E+02 0.0032 27.7 5.4 36 221-257 36-71 (271)
269 KOG1550|consensus 25.2 3.2E+02 0.007 28.4 8.4 52 72-126 308-359 (552)
270 KOG1156|consensus 25.2 3.9E+02 0.0085 28.6 8.7 60 60-123 374-433 (700)
271 KOG4626|consensus 25.1 4.1E+02 0.0089 28.6 8.7 60 61-126 358-419 (966)
272 PF03444 HrcA_DNA-bdg: Winged 25.0 1.8E+02 0.0039 22.2 4.7 49 221-270 19-67 (78)
273 PF02002 TFIIE_alpha: TFIIE al 24.8 98 0.0021 24.4 3.5 35 224-259 26-60 (105)
274 smart00668 CTLH C-terminal to 24.7 1.8E+02 0.0038 19.7 4.5 31 170-200 6-36 (58)
275 TIGR03338 phnR_burk phosphonat 24.7 3.4E+02 0.0073 23.8 7.5 47 222-271 31-77 (212)
276 TIGR01716 RGG_Cterm transcript 24.6 3.5E+02 0.0075 23.8 7.6 64 58-123 130-196 (220)
277 PF06969 HemN_C: HemN C-termin 24.4 1.8E+02 0.0038 20.5 4.6 45 223-271 18-62 (66)
278 PRK11569 transcriptional repre 24.4 3E+02 0.0064 25.7 7.3 37 220-257 38-74 (274)
279 KOG1126|consensus 24.3 96 0.0021 32.8 4.1 62 67-128 431-522 (638)
280 PRK00215 LexA repressor; Valid 24.1 3.9E+02 0.0084 23.5 7.7 40 224-263 22-61 (205)
281 COG4565 CitB Response regulato 23.8 5E+02 0.011 23.9 8.2 103 157-263 105-210 (224)
282 TIGR00540 hemY_coli hemY prote 23.8 7E+02 0.015 24.5 13.0 26 102-127 160-185 (409)
283 PF04190 DUF410: Protein of un 23.6 6E+02 0.013 23.6 16.5 38 172-209 198-236 (260)
284 KOG4056|consensus 23.4 1.4E+02 0.0031 25.3 4.3 46 100-158 86-131 (143)
285 PF12645 HTH_16: Helix-turn-he 22.9 1.5E+02 0.0032 21.6 3.9 49 171-219 2-61 (65)
286 PRK10870 transcriptional repre 22.8 1.5E+02 0.0032 25.9 4.6 41 224-265 70-110 (176)
287 COG1849 Uncharacterized protei 22.7 1.8E+02 0.0039 22.8 4.4 32 92-123 38-69 (90)
288 PRK05657 RNA polymerase sigma 22.7 4.4E+02 0.0094 25.4 8.2 22 226-248 190-211 (325)
289 PRK03837 transcriptional regul 22.5 4.3E+02 0.0092 23.6 7.8 60 209-271 16-80 (241)
290 PF10007 DUF2250: Uncharacteri 22.3 1.3E+02 0.0028 23.7 3.6 28 229-257 25-52 (92)
291 PRK15481 transcriptional regul 22.3 7.6E+02 0.016 24.3 10.8 45 222-269 25-70 (431)
292 TIGR02702 SufR_cyano iron-sulf 22.2 5.5E+02 0.012 22.7 9.0 36 223-259 13-48 (203)
293 KOG2316|consensus 21.3 74 0.0016 29.4 2.4 42 220-262 117-163 (277)
294 PF14947 HTH_45: Winged helix- 21.3 3.4E+02 0.0073 20.1 5.7 34 223-257 17-50 (77)
295 PF08679 DsrD: Dissimilatory s 21.0 2.1E+02 0.0046 21.2 4.2 35 222-256 16-50 (67)
296 COG1414 IclR Transcriptional r 20.8 1.3E+02 0.0029 27.7 4.1 31 226-257 20-50 (246)
297 PF04967 HTH_10: HTH DNA bindi 20.6 1.7E+02 0.0036 20.5 3.6 27 224-251 22-48 (53)
298 COG4235 Cytochrome c biogenesi 20.4 7.6E+02 0.016 23.6 12.1 99 20-128 159-260 (287)
299 PRK15090 DNA-binding transcrip 20.4 1.4E+02 0.003 27.5 4.1 33 224-257 27-59 (257)
300 PF09114 MotA_activ: Transcrip 20.2 1.6E+02 0.0034 23.2 3.6 47 226-276 31-79 (96)
No 1
>KOG2581|consensus
Probab=100.00 E-value=2.5e-96 Score=695.60 Aligned_cols=340 Identities=68% Similarity=1.028 Sum_probs=335.3
Q ss_pred cccchhccchhHHHHHHHHHHHHHHHhhcccHHHHHHHHHHHHHHhhhcCCcchhHHHHHHHHHHHHhhccHHHHHhhhh
Q psy1676 2 SKITSENRRTSDLIAAKCYFYHSRVHELTNNLDKVRSFLNARLRIATLRNDFEGQAVLINCLLRNYLHYNLYDQADKLVK 81 (343)
Q Consensus 2 ~~~~~~~~~~~d~~~a~~~~y~~~~~e~~~~~~~~~~~l~~~~r~a~~~~~~~~~~~l~n~Llr~yl~~~~~~~a~~li~ 81 (343)
..+...|||++|.++||+|||++++||..+++..+|++|++.+|||+++||.+||++++|+|||+|+..+.|++|.++++
T Consensus 154 ~~i~~~nrRtlD~i~ak~~fy~~l~~E~~~~l~~~rs~l~~~lrtAtLrhd~e~qavLiN~LLr~yL~n~lydqa~~lvs 233 (493)
T KOG2581|consen 154 ASISIQNRRTLDLIAAKLYFYLYLSYELEGRLADIRSFLHALLRTATLRHDEEGQAVLINLLLRNYLHNKLYDQADKLVS 233 (493)
T ss_pred HHHHhcchhhHHHHHHHHHHHHHHHHHhhcchHHHHHHHHHHHHHhhhcCcchhHHHHHHHHHHHHhhhHHHHHHHHHhh
Confidence 34677899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcCCCCCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCccchHHHHHHHHHHHHHHHHhcCCCCChhhhhhHh
Q psy1676 82 KSAFPENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQTAAVGFRQTTQKLAVVVELLLGDIPDRQIFRQAV 161 (343)
Q Consensus 82 k~~~p~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~sa~~~~~~i~K~li~v~LL~G~iP~~~~~~~~~ 161 (343)
|+.+|+.+++++++||+||.|+|.+++++|+.|.++|.+|++++|+..+.||++++.||+|++.|++|+||++++|.+|.
T Consensus 234 K~~~pe~~snne~ARY~yY~GrIkaiqldYssA~~~~~qa~rkapq~~alGf~q~v~k~~ivv~ll~geiPers~F~Qp~ 313 (493)
T KOG2581|consen 234 KSVYPEAASNNEWARYLYYLGRIKAIQLDYSSALEYFLQALRKAPQHAALGFRQQVNKLMIVVELLLGEIPERSVFRQPG 313 (493)
T ss_pred cccCccccccHHHHHHHHHHhhHHHhhcchhHHHHHHHHHHHhCcchhhhhHHHHHHHHHHHHHHHcCCCcchhhhcCcc
Confidence 99999999999999999999999999999999999999999999988789999999999999999999999999999999
Q ss_pred HhhhhhhhHHHHHHHHhCCHHHHHHHHHhccccccccccHHHHHHHHHHHHHHHHHHHhhcccccChHHHHHHhCCCCHH
Q psy1676 162 LRRALSPYFQLTQAVRMGELQKFNEVLTTYGNQFRTDYTFKLILRLRHNVIKTAIRSIGASYSRITPTKIAEKLGLESPE 241 (343)
Q Consensus 162 l~~~l~~Y~~L~~Av~~Gdl~~f~~~l~~~~~~f~~d~~~~Lv~~l~~~v~r~~ir~i~~~ys~Isl~dIa~~l~l~s~~ 241 (343)
+++.|.||..|++||+.||+++|+++++++...|..||+|.|+.|||++||+++||+|+.+|||||+.|||++|+++|++
T Consensus 314 ~~ksL~~Yf~Lt~AVr~gdlkkF~~~leq~k~~f~~D~ty~LivRLR~NVIkTgIR~ISlsYSRISl~DIA~kL~l~See 393 (493)
T KOG2581|consen 314 MRKSLRPYFKLTQAVRLGDLKKFNETLEQFKDKFQADGTYTLIVRLRHNVIKTGIRKISLSYSRISLQDIAKKLGLNSEE 393 (493)
T ss_pred HHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHhhCCcchHHHHHHHHHHHHhhhheeeeeeeccHHHHHHHhcCCCch
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhHHcCCceEEeeCCCceEEEccCccccccccchHHHHHHHHHHHHhhHHHhhhcCCCCCCCCcchhhHHHHH
Q psy1676 242 DAEFIIAKAIRDGVIEATLDREKGYMQSKESADIYCTVEPQLAFHQRIAFCLDLHNQSVKAMRYPPKSYGKDLESAEERR 321 (343)
Q Consensus 242 e~E~ila~lI~~G~I~a~Id~~~g~v~~~~~~~v~s~~ep~~~~~~rI~~cl~l~~~~~~am~~~~~~~~~~~~~~~~~~ 321 (343)
++|+||+++|+||.|+|+|||++|+|++++..++|+|.+|+.+|+.||+||++|||++|+||||||+.| +++|++|++|
T Consensus 394 d~EyiVakAIRDGvIea~Id~~~g~m~skE~~diy~t~epQ~~f~~rI~fCl~LhN~~vkamRyPp~~~-~~~Es~E~~r 472 (493)
T KOG2581|consen 394 DAEYIVAKAIRDGVIEAKIDHEDGFMQSKETFDIYSTREPQTAFDERIRFCLQLHNEAVKAMRYPPKKK-KDLESAEKRR 472 (493)
T ss_pred hHHHHHHHHHHhccceeeeccccCceehhhhhhhhccCCchhhHhHHHHHHHHHHHHHHHHhcCCCcch-hhHHHHHHhh
Confidence 999999999999999999999999999999999999999999999999999999999999999999999 9999999999
Q ss_pred HhhHhhHHHHHHhccccCCCC
Q psy1676 322 EREQQDLELAKEMAEEDDDGF 342 (343)
Q Consensus 322 ~~~~~~~~~~~~~~~~~~~~~ 342 (343)
||||||+|+||||+|||||||
T Consensus 473 ereqq~~e~akemae~Ddd~F 493 (493)
T KOG2581|consen 473 EREQQELELAKEMAEEDDDDF 493 (493)
T ss_pred hhhhhHHHHHHHhhhcccCCC
Confidence 999999999999999999998
No 2
>KOG2688|consensus
Probab=100.00 E-value=4.6e-34 Score=275.15 Aligned_cols=242 Identities=18% Similarity=0.280 Sum_probs=212.9
Q ss_pred cHHHHHHHHHHHHHHhhhcC-------CcchhHHHHHHHHHHHHhhccHHHHHhhhhhcCCC----CCCChHHHHHHHHH
Q psy1676 32 NLDKVRSFLNARLRIATLRN-------DFEGQAVLINCLLRNYLHYNLYDQADKLVKKSAFP----ENASNNEWARFHFY 100 (343)
Q Consensus 32 ~~~~~~~~l~~~~r~a~~~~-------~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~~~p----~~~~~~~~~~Y~YY 100 (343)
.++.+...++.+++++..+. .+++..+++|+++++||+.+.+++|+++++...-+ ...+.+++++|+||
T Consensus 131 ~le~~s~~i~~~f~~cl~d~~~~~~~~kk~~~~~i~n~lf~Iyfri~~~~L~k~l~ra~~~~~~~~~~~~l~~~v~y~Yy 210 (394)
T KOG2688|consen 131 LLEAASRTISRLFSSCLSDRRADLEESKKVAMLYIVNQLFQIYFRIEKLLLCKNLIRAFDQSGSDISDFPLAQLVVYHYY 210 (394)
T ss_pred HHHHHHHHHHHHHHHHhCccccccccchhhHHHHHHHHHHHHHHHHhhHHHhHHHHHHhhccccchhhcccccceeeeee
Confidence 37888899999888776552 23456699999999999999999999999976322 12456899999999
Q ss_pred HHHHHHHhhCHHHHHHHHHHHHhhCCccchHHHHHHHHHHHHHHHHhcCCCCChhhhhhHhHhhhhhhhHHHHHHHHhCC
Q psy1676 101 LGRIKAVRLEYSTAHKNLVQALRKAPQTAAVGFRQTTQKLAVVVELLLGDIPDRQIFRQAVLRRALSPYFQLTQAVRMGE 180 (343)
Q Consensus 101 ~Gri~~~~~~y~~A~~~L~~A~~~~~~~sa~~~~~~i~K~li~v~LL~G~iP~~~~~~~~~l~~~l~~Y~~L~~Av~~Gd 180 (343)
.|++++++.||.+|+.+|..||+.||... ..+++.+++|++|+.+++|++|..+++.. ..+..|..+++||+.||
T Consensus 211 lGr~a~~~~d~~~A~~~L~~af~~cp~~~-~~n~~~iliylip~~~llg~~Pt~~lL~~----~~~~~~~~lv~aVr~Gn 285 (394)
T KOG2688|consen 211 LGRYAMFESDFLNAFLQLNEAFRLCPDLL-LKNKRLILIYLIPTGLLLGRIPTKELLDF----YTLDKYSPLVQAVRSGN 285 (394)
T ss_pred eeeehhhhhhHHHHHHHHHHHHHhCcHHH-HhhhhhHHHHHhHHHHHhccCcchhhHhH----hhHHhHHHHHHHHHhcc
Confidence 99999999999999999999999999863 55799999999999999999999888873 34778999999999999
Q ss_pred HHHHHHHHHhccccccccccHHHHHHHHHHHHHHHHHHHhhcc---cccChHHHHHHhCCCC-----HHHHHHHHHHhHH
Q psy1676 181 LQKFNEVLTTYGNQFRTDYTFKLILRLRHNVIKTAIRSIGASY---SRITPTKIAEKLGLES-----PEDAEFIIAKAIR 252 (343)
Q Consensus 181 l~~f~~~l~~~~~~f~~d~~~~Lv~~l~~~v~r~~ir~i~~~y---s~Isl~dIa~~l~l~s-----~~e~E~ila~lI~ 252 (343)
+..|+.++++|+..|.+.|.|..++.++..|+|+++++++... +++|++.+..++++.+ .+|+||++|++|.
T Consensus 286 l~~f~~al~~~E~~f~~~gi~l~l~~l~lv~yrnL~kkv~~~~~~~~~lpls~~~~al~~~~~~~~~~deveciLa~lI~ 365 (394)
T KOG2688|consen 286 LRLFDLALADNERFFIRSGIYLTLEKLPLVVYRNLFKKVIQLWGKTSQLPLSRFLTALQFSGVTDVDLDEVECILANLID 365 (394)
T ss_pred HHHHHHHHhhhHHHHHHhccHHHhhhhhHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHhhcCCCCCchhhHHHHHHhhhh
Confidence 9999999999999999999999999999999999999999988 9999999999998764 8999999999999
Q ss_pred cCCceEEeeCCCceEEEccCccccccccchHHH
Q psy1676 253 DGVIEATLDREKGYMQSKESADIYCTVEPQLAF 285 (343)
Q Consensus 253 ~G~I~a~Id~~~g~v~~~~~~~v~s~~ep~~~~ 285 (343)
+|.|+|+|+|....++ +|+.+|||..
T Consensus 366 ~G~ikgYish~~~~~V-------~sK~~pfp~~ 391 (394)
T KOG2688|consen 366 LGRIKGYISHQLQTLV-------FSKKDPFPHL 391 (394)
T ss_pred hccccchhchhhheEE-------EecCCCCCCC
Confidence 9999888888876554 5566788754
No 3
>COG5600 Transcription-associated recombination protein [DNA replication, recombination, and repair]
Probab=99.98 E-value=1.7e-31 Score=252.53 Aligned_cols=244 Identities=20% Similarity=0.301 Sum_probs=203.7
Q ss_pred cccHHHHHHHHHHHHHHhhhcCC-------cchhHHHHHHHHHHHHhhccHHHHHhhhhhcC---CCCC--CChHHHHHH
Q psy1676 30 TNNLDKVRSFLNARLRIATLRND-------FEGQAVLINCLLRNYLHYNLYDQADKLVKKSA---FPEN--ASNNEWARF 97 (343)
Q Consensus 30 ~~~~~~~~~~l~~~~r~a~~~~~-------~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~~---~p~~--~~~~~~~~Y 97 (343)
.+.++++.+.+..+|..+..... ++|..+++|+|+.+||+.+++++|+++++... .|+. .+.+|++.|
T Consensus 143 ~d~l~~~sr~l~R~Fn~il~dR~p~ln~skk~g~y~iaNlL~~iY~Rl~~~~l~~n~lka~~~vs~~Di~~~~~sq~v~f 222 (413)
T COG5600 143 QDNLSKISRLLTRMFNSILNDRSPALNPSKKVGLYYIANLLFQIYLRLGRFKLCENFLKASKEVSMPDISEYQKSQVVVF 222 (413)
T ss_pred HhhHHHHHHHHHHHHHHhcCCcCccCChhhHHHHHHHHHHHHHHHHHhccHHHHHHHHHhcccccccccchhhhcceeeh
Confidence 35778888888888876665433 35666999999999999999999999999653 3432 357899999
Q ss_pred HHHHHHHHHHhhCHHHHHHHHHHHHhhCCccchHHHHHHHHHHHHHHHHhcCCCCC-hhhhhhHhHhhhhhhhHHHHHHH
Q psy1676 98 HFYLGRIKAVRLEYSTAHKNLVQALRKAPQTAAVGFRQTTQKLAVVVELLLGDIPD-RQIFRQAVLRRALSPYFQLTQAV 176 (343)
Q Consensus 98 ~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~sa~~~~~~i~K~li~v~LL~G~iP~-~~~~~~~~l~~~l~~Y~~L~~Av 176 (343)
+||+|++|+.+.++.+|+.+|..||..||.. -.++.+.+.-|.||..|+.|+.|+ ++++... + .+..|..|++|+
T Consensus 223 ~YYLG~~~l~~en~heA~~~L~~aFl~c~~l-~~~n~~rIl~~~ipt~Llv~~~~Ptk~~L~r~--~-~~s~~~~Lvkav 298 (413)
T COG5600 223 HYYLGIYYLLNENFHEAFLHLNEAFLQCPWL-ITRNRKRILPYYIPTSLLVNKFPPTKDLLERF--K-RCSVYSPLVKAV 298 (413)
T ss_pred hhHHHHHHHHHHhHHHHHHHHHHHHHhChhh-hhcchheehhHHhhHHHHhCCCCCchHHHHhc--c-ccchhHHHHHHH
Confidence 9999999999999999999999999999974 356688899999999999888654 5655421 2 277899999999
Q ss_pred HhCCHHHHHHHHHhccccccccccH-HHHHHHHHHHHHHHHHHHhhcc---cccChHHHHHHhCCC------CHHHHHHH
Q psy1676 177 RMGELQKFNEVLTTYGNQFRTDYTF-KLILRLRHNVIKTAIRSIGASY---SRITPTKIAEKLGLE------SPEDAEFI 246 (343)
Q Consensus 177 ~~Gdl~~f~~~l~~~~~~f~~d~~~-~Lv~~l~~~v~r~~ir~i~~~y---s~Isl~dIa~~l~l~------s~~e~E~i 246 (343)
+.||++.|+.++++|+..|.+.|.| +|..+++..++|+++|+++..- +++|++-+...++++ +.++|||+
T Consensus 299 rsGni~~~~~~l~~ner~~~~~~l~ltl~~~~~~V~~RNL~rk~w~~~~~qsrlp~sil~~~~qls~~dn~~~~~~VEci 378 (413)
T COG5600 299 RSGNIEDFDLALSRNERKFAKRGLYLTLLAHYPLVCFRNLFRKIWRLHGKQSRLPLSILLIVLQLSAIDNFHSFKEVECI 378 (413)
T ss_pred HcCCHHHHHHHHHHhHHHHHHcchHHHHHhhccHHHHHHHHHHHHhhccccccCcHHHHHHHHHccCCCcccChHHHHHH
Confidence 9999999999999999999999999 5667899999999999988754 788888877777664 48999999
Q ss_pred HHHhHHcCCceEEeeCCCceEEEccCccccccccchHH
Q psy1676 247 IAKAIRDGVIEATLDREKGYMQSKESADIYCTVEPQLA 284 (343)
Q Consensus 247 la~lI~~G~I~a~Id~~~g~v~~~~~~~v~s~~ep~~~ 284 (343)
+++||..|+++|+|+|...+|+|+ +.+|||.
T Consensus 379 L~tlI~~G~lrgYis~s~~~vV~s-------k~~pFp~ 409 (413)
T COG5600 379 LVTLIGLGLLRGYISHSRRTVVFS-------KKDPFPV 409 (413)
T ss_pred HHHHHhhhhhhheecccceEEEEe-------cCCCCCC
Confidence 999999999999999988877665 4567764
No 4
>KOG2582|consensus
Probab=99.96 E-value=9.6e-29 Score=232.86 Aligned_cols=284 Identities=16% Similarity=0.242 Sum_probs=228.7
Q ss_pred HHHHHHHHHHHHHHHhhcccHH----HHH--HHHHHHHHHhhhcCCcchhHHHHHHHHHHHHhhccHHHHHhhhhhc--C
Q psy1676 13 DLIAAKCYFYHSRVHELTNNLD----KVR--SFLNARLRIATLRNDFEGQAVLINCLLRNYLHYNLYDQADKLVKKS--A 84 (343)
Q Consensus 13 d~~~a~~~~y~~~~~e~~~~~~----~~~--~~l~~~~r~a~~~~~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~--~ 84 (343)
.++.=-.+++++.++.+...+. ..+ +.++.++-.. +..+...+.++..++.+|++.++|....+.++-- .
T Consensus 92 eqlr~as~~f~~lc~~l~~~~~~~~~p~~gi~ii~~av~k~--~~~~~qlT~~H~~l~~~~L~ak~y~~~~p~ld~dive 169 (422)
T KOG2582|consen 92 EQLRLASEIFFPLCHDLTEAVVKKNKPLRGIRIIMQAVDKM--QPSNGQLTSIHADLLQLCLEAKDYASVLPYLDDDIVE 169 (422)
T ss_pred HHHhhHHHHHHHHHHHHHHHHHhcCCccccchHHHHHHHHh--ccCccchhhhHHHHHHHHHHhhcccccCCccchhHHH
Confidence 3444455677777776655332 122 2333333221 2222234478889999999999999999888732 1
Q ss_pred C---CCCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHh-hCCccchHHHHHHHHHHHHHHHHhcCC---CCC-hhh
Q psy1676 85 F---PENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALR-KAPQTAAVGFRQTTQKLAVVVELLLGD---IPD-RQI 156 (343)
Q Consensus 85 ~---p~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~-~~~~~sa~~~~~~i~K~li~v~LL~G~---iP~-~~~ 156 (343)
+ ..+.+....+.|+||+|+|++..++|++|..+|..++. |+.+.+.+. .++++||+++..++.|+ +|+ .+.
T Consensus 170 i~~~n~h~~~k~fL~Y~yYgg~iciglk~fe~Al~~~e~~v~~Pa~~vs~~h-lEaYkkylLvsLI~~GK~~ql~k~ts~ 248 (422)
T KOG2582|consen 170 ICKANPHLDPKYFLLYLYYGGMICIGLKRFERALYLLEICVTTPAMAVSHIH-LEAYKKYLLVSLILTGKVFQLPKNTSQ 248 (422)
T ss_pred HhccCCCCCHHHHHHHHHhcceeeeccccHHHHHHHHHHHHhcchhHHHHHH-HHHHHHHHHHHhhhcCceeeccccchh
Confidence 1 12346679999999999999999999999999999999 666555455 99999999999999999 466 334
Q ss_pred hhhHhHhhhhhhhHHHHHHHHhCCHHHHHHHHHhccccccccccHHHHHHHHHHHHHHHHHHHhhcccccChHHHHHHhC
Q psy1676 157 FRQAVLRRALSPYFQLTQAVRMGELQKFNEVLTTYGNQFRTDYTFKLILRLRHNVIKTAIRSIGASYSRITPTKIAEKLG 236 (343)
Q Consensus 157 ~~~~~l~~~l~~Y~~L~~Av~~Gdl~~f~~~l~~~~~~f~~d~~~~Lv~~l~~~v~r~~ir~i~~~ys~Isl~dIa~~l~ 236 (343)
-..|.++....||.++.+++-++....++.++.+|.+.|.+|++.++++++....++++|.+++++|++|+|+|||++.+
T Consensus 249 ~~~r~~K~ms~pY~ef~~~Y~~~~~~eLr~lVk~~~~rF~kDnnt~l~k~av~sl~k~nI~rltktF~sLsL~dIA~~vQ 328 (422)
T KOG2582|consen 249 NAGRFFKPMSNPYHEFLNVYLKDSSTELRTLVKKHSERFTKDNNTGLAKQAVSSLYKKNIQRLTKTFLSLSLSDIASRVQ 328 (422)
T ss_pred hhHHhcccCCchHHHHHHHHhcCCcHHHHHHHHHHHHHHhhcCcHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHH
Confidence 45556565566999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCHHHHHHHHHHhHHcCCceEEeeCCCceEEEccCccccccccchHHHHHHHHHHHHhhHHHhhhcCCC
Q psy1676 237 LESPEDAEFIIAKAIRDGVIEATLDREKGYMQSKESADIYCTVEPQLAFHQRIAFCLDLHNQSVKAMRYP 306 (343)
Q Consensus 237 l~s~~e~E~ila~lI~~G~I~a~Id~~~g~v~~~~~~~v~s~~ep~~~~~~rI~~cl~l~~~~~~am~~~ 306 (343)
|.+.+|||..|.+||.+|.|.|+|+ |+|.|.+.+.-|-++|+ ++..|..|.+| ++..++|.=.
T Consensus 329 La~~qevek~Ilqmie~~~i~a~iN---G~v~f~~n~e~~~SpeM---~~nk~~~~~~L-~e~l~~~e~s 391 (422)
T KOG2582|consen 329 LASAQEVEKYILQMIEDGEIFASIN---GMVFFTDNPEKYNSPEM---HENKIDLCIQL-IEALKAMEES 391 (422)
T ss_pred hcchHHHHHHHHHHhccCceEEEec---ceEEEecCcccCCCHHH---HhhHHHHHHHH-HHHHHhcchh
Confidence 9999999999999999999999997 99999998877766665 34489999999 5559999533
No 5
>PF08375 Rpn3_C: Proteasome regulatory subunit C-terminal; InterPro: IPR013586 Intracellular proteins, including short-lived proteins such as cyclin, Mos, Myc, p53, NF-kappaB, and IkappaB, are degraded by the ubiquitin-proteasome system. The 26S proteasome is a self-compartmentalising protease responsible for the regulated degradation of intracellular proteins in eukaryotes [, ]. This giant intracellular protease is formed by several subunits arranged into two 19S polar caps, where protein recognition and ATP-dependent unfolding occur, flanking a 20S central barrel-shaped structure with an inner proteolytic chamber. This overall structure is highly conserved among eukaryotes and is essential for cell viability. Proteins targeted to the 26S proteasome are conjugated with a polyubiquitin chain by an enzymatic cascade before delivery to the 26S proteasome for degradation into oligopeptides. The 19S component is divided into a "base" subunit containing six ATPases (Rpt proteins) and two non-ATPases (Rpn1, Rpn2), and a "lid" subunit composed of eight stoichiometric proteins (Rpn3, Rpn5, Rpn6, Rpn7, Rpn8, Rpn9, Rpn11, Rpn12) []. Additional non-essential and species specific proteins may also be present. The 19S unit performs several essential functions including binding the specific protein substrates, unfolding them, cleaving the attached ubiquitin chains, opening the 20S subunit, and driving the unfolded polypeptide into the proteolytic chamber for degradation. The 26s proteasome and 19S regulator are of medical interest due to their involvement in burn rehabilitation []. This eukaryotic domain is found at the C terminus of 26S proteasome regulatory subunits such as the non-ATPase Rpn3 subunit which is essential for proteasomal function []. It occurs together with the PCI/PINT domain (IPR000717 from INTERPRO). ; GO: 0030234 enzyme regulator activity, 0042176 regulation of protein catabolic process, 0000502 proteasome complex
Probab=99.95 E-value=6.4e-28 Score=177.87 Aligned_cols=68 Identities=72% Similarity=1.053 Sum_probs=65.8
Q ss_pred cccccccchHHHHHHHHHHHHhhHHHhhhcCCCCCCCCcchhhHHHHHHhhHhhHHHHHHhccccCCC
Q psy1676 274 DIYCTVEPQLAFHQRIAFCLDLHNQSVKAMRYPPKSYGKDLESAEERREREQQDLELAKEMAEEDDDG 341 (343)
Q Consensus 274 ~v~s~~ep~~~~~~rI~~cl~l~~~~~~am~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 341 (343)
|||||.+|+.+||+||+|||+|||+|||||||||++|++++++++++|+|+++++|+|++++|+|+||
T Consensus 1 DvYsT~ePq~aF~~RI~FCL~lHneaVkAMRyP~~~~~~~~~~~~~~~ere~~e~el~~e~~e~D~DD 68 (68)
T PF08375_consen 1 DVYSTNEPQEAFHQRIAFCLQLHNEAVKAMRYPPDAHKKELESAEERREREQQEEELAKEIEEGDLDD 68 (68)
T ss_pred CCcchhhHHHHHHHHHHHHHHHHHHHHHHhcCCCCccchhhhhHHHHHHHHHHHHHHHHHHhccCCCC
Confidence 69999999999999999999999999999999999999999999999999999999999999997775
No 6
>KOG1497|consensus
Probab=99.78 E-value=2.2e-17 Score=154.00 Aligned_cols=272 Identities=18% Similarity=0.244 Sum_probs=208.1
Q ss_pred HHHHHHHHHHHHhhcccHHHHHHHHHHHHH-HhhhcCCcchhHHHHHHHHHHHHhhccHHHHHhhhhhcCCCCCC--ChH
Q psy1676 16 AAKCYFYHSRVHELTNNLDKVRSFLNARLR-IATLRNDFEGQAVLINCLLRNYLHYNLYDQADKLVKKSAFPENA--SNN 92 (343)
Q Consensus 16 ~a~~~~y~~~~~e~~~~~~~~~~~l~~~~r-~a~~~~~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~~~p~~~--~~~ 92 (343)
.+-+.+-++-+||..+++..+...|...-- |..-..|.+....+.-.+-|+|++.++...|..+++++++|... +..
T Consensus 102 v~~irl~LAsiYE~Eq~~~~aaq~L~~I~~~tg~~~~d~~~kl~l~iriarlyLe~~d~veae~~inRaSil~a~~~Ne~ 181 (399)
T KOG1497|consen 102 VASIRLHLASIYEKEQNWRDAAQVLVGIPLDTGQKAYDVEQKLLLCIRIARLYLEDDDKVEAEAYINRASILQAESSNEQ 181 (399)
T ss_pred HHHHHHHHHHHHHHhhhHHHHHHHHhccCcccchhhhhhHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHhhhcccCHH
Confidence 456788899999999999988887754221 11111122223345556889999999999999999999887433 334
Q ss_pred HHHHHHHHHHHHHHHhhCHHHHHHHHHHHHh-hCCccchHHHHHHHHHHHHHHHHhcCCCCChhhhhhHhHh----hhhh
Q psy1676 93 EWARFHFYLGRIKAVRLEYSTAHKNLVQALR-KAPQTAAVGFRQTTQKLAVVVELLLGDIPDRQIFRQAVLR----RALS 167 (343)
Q Consensus 93 ~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~-~~~~~sa~~~~~~i~K~li~v~LL~G~iP~~~~~~~~~l~----~~l~ 167 (343)
.++.|.-+.+|+.-..++|-+|...+.+... +-.. ..-+...++-.+.|.+|.+-.|.++.+-+..++ +.+.
T Consensus 182 Lqie~kvc~ARvlD~krkFlEAAqrYyels~~ki~~---e~~~~~aL~~a~~CtlLA~~gpqrsr~Latlfkder~~~l~ 258 (399)
T KOG1497|consen 182 LQIEYKVCYARVLDYKRKFLEAAQRYYELSQRKIVD---ESERLEALKKALQCTLLASAGPQRSRMLATLFKDERCQKLP 258 (399)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc---hHHHHHHHHHhHhheeecCCChHHHHHHHHHhcCccccccc
Confidence 6788888999999999999999777665544 3321 223566777788999999999997655332222 1233
Q ss_pred hhH-----HHHHHHHhCCHHHHHHHHHhccccccccccHHHHHHHHHHHHHHHHHHHhhcccccChHHHHHHhCCCCHHH
Q psy1676 168 PYF-----QLTQAVRMGELQKFNEVLTTYGNQFRTDYTFKLILRLRHNVIKTAIRSIGASYSRITPTKIAEKLGLESPED 242 (343)
Q Consensus 168 ~Y~-----~L~~Av~~Gdl~~f~~~l~~~~~~f~~d~~~~Lv~~l~~~v~r~~ir~i~~~ys~Isl~dIa~~l~l~s~~e 242 (343)
.|. -+.+.++..++..|...+..|+..=..||. ..+ -..+++|++.-+++-|..||++.+++.++++ ++.
T Consensus 259 ~y~ileKmyl~riI~k~el~ef~~~L~pHQka~~~dgs-sil---~ra~~EhNlls~Skly~nisf~~Lg~ll~i~-~ek 333 (399)
T KOG1497|consen 259 AYGILEKMYLERIIRKEELQEFEAFLQPHQKAHTMDGS-SIL---DRAVIEHNLLSASKLYNNISFEELGALLKID-AEK 333 (399)
T ss_pred chHHHHHHHHHHHhcchhHHHHHHHhcchhhhcccCcc-hhh---hhHHHHHhHHHHHHHHHhccHHHHHHHhCCC-HHH
Confidence 333 255677888999999999999987777775 333 3578999999999999999999999999996 999
Q ss_pred HHHHHHHhHHcCCceEEeeCCCceEEEccCccccccccchHHHHHHHH-HHHHhhHHHhhhc
Q psy1676 243 AEFIIAKAIRDGVIEATLDREKGYMQSKESADIYCTVEPQLAFHQRIA-FCLDLHNQSVKAM 303 (343)
Q Consensus 243 ~E~ila~lI~~G~I~a~Id~~~g~v~~~~~~~v~s~~ep~~~~~~rI~-~cl~l~~~~~~am 303 (343)
+|.++++||.+|.++|+|||.+|+|.|.+ .+|.|.|+++|+ -|-++++- ...|
T Consensus 334 aekiaa~MI~qeRmng~IDQ~egiihFe~-------~e~l~~wdkqi~sl~~qvNki-~~~i 387 (399)
T KOG1497|consen 334 AEKIAAQMITQERMNGSIDQIEGIIHFED-------REELPQWDKQIQSLCNQVNKI-LDKI 387 (399)
T ss_pred HHHHHHHHHhHHHhccchHhhcceEeecc-------hhhhhhhhHHHHHHHHHHHHH-HHHH
Confidence 99999999999999999999999999986 268999999999 59999544 4444
No 7
>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=99.76 E-value=7.5e-18 Score=135.04 Aligned_cols=104 Identities=29% Similarity=0.529 Sum_probs=96.4
Q ss_pred hhhHHHHHHHHhCCHHHHHHHHHhc-cccccccccHHHHHHHHHHHHHHHHHHHhhcccccChHHHHHHhCCCCHHHHHH
Q psy1676 167 SPYFQLTQAVRMGELQKFNEVLTTY-GNQFRTDYTFKLILRLRHNVIKTAIRSIGASYSRITPTKIAEKLGLESPEDAEF 245 (343)
Q Consensus 167 ~~Y~~L~~Av~~Gdl~~f~~~l~~~-~~~f~~d~~~~Lv~~l~~~v~r~~ir~i~~~ys~Isl~dIa~~l~l~s~~e~E~ 245 (343)
+||.+|.+++.+||+..|.+.++++ ...|.++++..+++.++..++++.+++++..|++||++++|+.++++ .+++|.
T Consensus 1 ~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~~l~~~i~~~~l~~l~~~y~~i~~~~ia~~l~~~-~~~vE~ 79 (105)
T PF01399_consen 1 PPYSELLRAFRSGDLQEFEEFLEKHSESLFKDPFLAEYVEQLKEKIRRRNLRQLSKPYSSISISEIAKALQLS-EEEVES 79 (105)
T ss_dssp HHHHHHHHHHHCT-HHHHHHHHHHTCHHHHHCTTHHHHHHHHHHHHHHHHHHHHHHC-SEEEHHHHHHHHTCC-HHHHHH
T ss_pred CHHHHHHHHHHhCCHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHHHHHHHhcccchHHHHHHhccc-hHHHHH
Confidence 3789999999999999999999999 77888888889999999999999999999999999999999999996 899999
Q ss_pred HHHHhHHcCCceEEeeCCCceEEEcc
Q psy1676 246 IIAKAIRDGVIEATLDREKGYMQSKE 271 (343)
Q Consensus 246 ila~lI~~G~I~a~Id~~~g~v~~~~ 271 (343)
+|++||.+|.|+|+|||.+|+|+|++
T Consensus 80 ~l~~~I~~~~i~~~ID~~~~~v~~~k 105 (105)
T PF01399_consen 80 ILIDLISNGLIKAKIDQVNGVVVFSK 105 (105)
T ss_dssp HHHHHHHTTSSEEEEETTTTEEEE-S
T ss_pred HHHHHHHCCCEEEEEECCCCEEEecC
Confidence 99999999999999999999999974
No 8
>KOG1498|consensus
Probab=99.73 E-value=3.4e-16 Score=149.64 Aligned_cols=276 Identities=19% Similarity=0.220 Sum_probs=208.1
Q ss_pred HHHHHHHHHHHhhcccHHHHHHHHHHHHH-HhhhcCCcchhHHHHHHHHHHHHhhccHHHHHhhhhhcC---CCCCCChH
Q psy1676 17 AKCYFYHSRVHELTNNLDKVRSFLNARLR-IATLRNDFEGQAVLINCLLRNYLHYNLYDQADKLVKKSA---FPENASNN 92 (343)
Q Consensus 17 a~~~~y~~~~~e~~~~~~~~~~~l~~~~r-~a~~~~~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~~---~p~~~~~~ 92 (343)
|++=--++++.|..|.+.++...|.+..- |-..-...+...+++.+ +|+|+..++|-+|..+.+|+. |.+.....
T Consensus 131 arlTk~L~~ike~~Gdi~~Aa~il~el~VETygsm~~~ekV~fiLEQ-mrKOG~~~D~vra~i~skKI~~K~F~~~~~~~ 209 (439)
T KOG1498|consen 131 ARLTKMLAKIKEEQGDIAEAADILCELQVETYGSMEKSEKVAFILEQ-MRLCLLRLDYVRAQIISKKINKKFFEKPDVQE 209 (439)
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHhcchhhhhhhHHHHHHHHHHHH-HHHHHHhhhHHHHHHHHHHhhHHhcCCccHHH
Confidence 44555678999999999999998876432 21111123445577777 999999999999999999884 43333446
Q ss_pred HHHHHHHHHHHHHHHhhCHHHHHHHHHHHHh-hCCccchHHHHHHHHHHHHHHHHhcCCCCCh-hhhhhHhHh---hhhh
Q psy1676 93 EWARFHFYLGRIKAVRLEYSTAHKNLVQALR-KAPQTAAVGFRQTTQKLAVVVELLLGDIPDR-QIFRQAVLR---RALS 167 (343)
Q Consensus 93 ~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~-~~~~~sa~~~~~~i~K~li~v~LL~G~iP~~-~~~~~~~l~---~~l~ 167 (343)
..+.||+.+-++..+++.|-++.+++...+. ++.+....+|.+.+. -++...+|.-.-+.. .++...... ..+.
T Consensus 210 lKlkyY~lmI~l~lh~~~Yl~v~~~Yraiy~t~~vk~d~~kw~~vL~-~iv~f~~LAp~dneQsdll~~is~dKkL~e~p 288 (439)
T KOG1498|consen 210 LKLKYYELMIRLGLHDRAYLNVCRSYRAIYDTGNVKEDPEKWIEVLR-SIVSFCVLAPHDNEQSDLLARISNDKKLSELP 288 (439)
T ss_pred HHHHHHHHHHHhcccccchhhHHHHHHHHhcccccccChhhhhhhhh-hheeEEeecCCCcHHHHHHHHHhcccccccCc
Confidence 7888999999999999999999999998887 333221122222111 111112222222222 222211111 2356
Q ss_pred hhHHHHHHHHhCCHHHHHHHHHhccccccccccH-------HHHHHHHHHHHHHHHHHHhhcccccChHHHHHHhCCCCH
Q psy1676 168 PYFQLTQAVRMGELQKFNEVLTTYGNQFRTDYTF-------KLILRLRHNVIKTAIRSIGASYSRITPTKIAEKLGLESP 240 (343)
Q Consensus 168 ~Y~~L~~Av~~Gdl~~f~~~l~~~~~~f~~d~~~-------~Lv~~l~~~v~r~~ir~i~~~ys~Isl~dIa~~l~l~s~ 240 (343)
.|..+++.|.+|.+..|....+.+...+..++++ .-++.|+..+++|++|.++..||+|++.+++..++++ +
T Consensus 289 ~~k~lLklfv~~EL~rw~s~~~~yg~~l~~~~~~~~~~~gek~~~dL~~RIiEHNiRiiA~yYSrIt~~rl~eLLdl~-~ 367 (439)
T KOG1498|consen 289 DYKELLKLFVTMELIRWVSLVESYGDELRTNDFFDGGEEGEKRWSDLKLRIIEHNIRIIAKYYSRITLKRLAELLDLP-V 367 (439)
T ss_pred cHHHHHHHHHhcceeeehhHhhhhHHHHhhcccccccchhhhHHHHHHHHHHHHHHHHHHHHHhhccHHHHHHHhCCC-H
Confidence 7999999999999999999999998888777433 5689999999999999999999999999999999996 9
Q ss_pred HHHHHHHHHhHHcCCceEEeeCCCceEEEccCccccccccchHHHHHHHHHHHHhhHH
Q psy1676 241 EDAEFIIAKAIRDGVIEATLDREKGYMQSKESADIYCTVEPQLAFHQRIAFCLDLHNQ 298 (343)
Q Consensus 241 ~e~E~ila~lI~~G~I~a~Id~~~g~v~~~~~~~v~s~~ep~~~~~~rI~~cl~l~~~ 298 (343)
+++|..++.|+..|.|.|+||++.|.+.|...++ .++-++.|...+...+.+-+.
T Consensus 368 ee~E~~LS~lv~t~ti~aKidrpsgII~F~k~K~---~~~~LneW~~nve~L~~ll~K 422 (439)
T KOG1498|consen 368 EEMEKFLSDLVVTGTIYAKIDRPSGIINFQKVKD---SNEILNEWASNVEKLLGLLEK 422 (439)
T ss_pred HHHHHHHHHHHhccceEEEecCCCceEEEEeccc---HHHHHHHHHhhHHHHHHHHHH
Confidence 9999999999999999999999999999998776 567899999999998888665
No 9
>KOG1463|consensus
Probab=99.70 E-value=1.4e-15 Score=143.18 Aligned_cols=212 Identities=19% Similarity=0.234 Sum_probs=169.5
Q ss_pred HHHHHHHhhccHHHHHhhhhhc-CC--CCCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCccchHHHHHHHH
Q psy1676 62 CLLRNYLHYNLYDQADKLVKKS-AF--PENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQTAAVGFRQTTQ 138 (343)
Q Consensus 62 ~Llr~yl~~~~~~~a~~li~k~-~~--p~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~sa~~~~~~i~ 138 (343)
+-=+.|+..++...|+.-+..+ +- .-..|+..+.+-.-.+|.+++.++||..|+.+|.+||............-..+
T Consensus 173 lESK~y~~l~Nl~KakasLTsART~AnaiYcpPqlQa~lDLqSGIlha~ekDykTafSYFyEAfEgf~s~~~~v~A~~sL 252 (411)
T KOG1463|consen 173 LESKAYHALRNLPKAKASLTSARTTANAIYCPPQLQATLDLQSGILHAAEKDYKTAFSYFYEAFEGFDSLDDDVKALTSL 252 (411)
T ss_pred hhhHHHHHHhcchhHHHHHHHHHHhhcccccCHHHHHHHHHhccceeecccccchHHHHHHHHHccccccCCcHHHHHHH
Confidence 3346666666666666554422 11 11246678899999999999999999999999999999433221112244579
Q ss_pred HHHHHHHHhcCCCCC-hhhhhhHh-H---hhhhhhhHHHHHHHHhCCHHHHHHHHHhccccccccccH-HHHHHHHHHHH
Q psy1676 139 KLAVVVELLLGDIPD-RQIFRQAV-L---RRALSPYFQLTQAVRMGELQKFNEVLTTYGNQFRTDYTF-KLILRLRHNVI 212 (343)
Q Consensus 139 K~li~v~LL~G~iP~-~~~~~~~~-l---~~~l~~Y~~L~~Av~~Gdl~~f~~~l~~~~~~f~~d~~~-~Lv~~l~~~v~ 212 (343)
||+++|.++++..-+ ..++..+. + .+.+.....+++|+.+.++..|+.++..|..++..|... ..+..|..++.
T Consensus 253 KYMlLcKIMln~~ddv~~lls~K~~l~y~g~~i~AmkavAeA~~nRSLkdF~~AL~~yk~eL~~D~ivr~Hl~~Lyd~lL 332 (411)
T KOG1463|consen 253 KYMLLCKIMLNLPDDVAALLSAKLALKYAGRDIDAMKAVAEAFGNRSLKDFEKALADYKKELAEDPIVRSHLQSLYDNLL 332 (411)
T ss_pred HHHHHHHHHhcCHHHHHHHHhhHHHHhccCcchHHHHHHHHHhcCCcHHHHHHHHHHhHHHHhcChHHHHHHHHHHHHHH
Confidence 999999999988544 34444332 1 134567788999999999999999999999999999987 67899999999
Q ss_pred HHHHHHHhhcccccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEeeCCCceEEEccCcc
Q psy1676 213 KTAIRSIGASYSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLDREKGYMQSKESAD 274 (343)
Q Consensus 213 r~~ir~i~~~ys~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~Id~~~g~v~~~~~~~ 274 (343)
..++-||..+||++-++.||+.+|++ ...||.-+++||-|....|++||.+|++...+.++
T Consensus 333 Eknl~riIEPyS~Vei~hIA~~IGl~-~~~VEkKLsqMILDKkf~G~LDQg~g~Liv~~e~~ 393 (411)
T KOG1463|consen 333 EKNLCRIIEPYSRVEISHIAEVIGLD-VPQVEKKLSQMILDKKFYGTLDQGEGCLIVFEEPP 393 (411)
T ss_pred HHhHHHHcCchhhhhHHHHHHHHCCC-cHHHHHHHHHHHHHHHhhcccccCCCeEEEeCCCC
Confidence 99999999999999999999999996 99999999999999999999999999998776554
No 10
>KOG1464|consensus
Probab=99.61 E-value=2.5e-14 Score=131.77 Aligned_cols=228 Identities=17% Similarity=0.233 Sum_probs=166.7
Q ss_pred HHHHHHHHHHHhhcc-------HHHHHhhhhhcCCCCCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCccch
Q psy1676 58 VLINCLLRNYLHYNL-------YDQADKLVKKSAFPENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQTAA 130 (343)
Q Consensus 58 ~l~n~Llr~yl~~~~-------~~~a~~li~k~~~p~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~sa 130 (343)
-+..+-+.+|-..++ |++|..+- +.+|. +--.-.-+-++|..++..++|.+|+.-|-.||.+......
T Consensus 192 EiYAlEIQmYT~qKnNKkLK~lYeqalhiK--SAIPH---PlImGvIRECGGKMHlreg~fe~AhTDFFEAFKNYDEsGs 266 (440)
T KOG1464|consen 192 EIYALEIQMYTEQKNNKKLKALYEQALHIK--SAIPH---PLIMGVIRECGGKMHLREGEFEKAHTDFFEAFKNYDESGS 266 (440)
T ss_pred hhHhhHhhhhhhhcccHHHHHHHHHHHHhh--ccCCc---hHHHhHHHHcCCccccccchHHHHHhHHHHHHhcccccCC
Confidence 555566778876655 44444432 23332 1133345668999999999999999999999996554322
Q ss_pred HHHHHHHHHHHHHHHHhcCC-C-CChhhhhhHh-HhhhhhhhHHHHHHHHhCCHHHHHHHHHhccccccccccH-HHHHH
Q psy1676 131 VGFRQTTQKLAVVVELLLGD-I-PDRQIFRQAV-LRRALSPYFQLTQAVRMGELQKFNEVLTTYGNQFRTDYTF-KLILR 206 (343)
Q Consensus 131 ~~~~~~i~K~li~v~LL~G~-i-P~~~~~~~~~-l~~~l~~Y~~L~~Av~~Gdl~~f~~~l~~~~~~f~~d~~~-~Lv~~ 206 (343)
.. +..++||+++..+|+.. | |-.+.-..|. -.+.+.....|+.|+...|+.+|++++..|++....|+.. ..++.
T Consensus 267 pR-RttCLKYLVLANMLmkS~iNPFDsQEAKPyKNdPEIlAMTnlv~aYQ~NdI~eFE~Il~~~~~~IM~DpFIReh~Ed 345 (440)
T KOG1464|consen 267 PR-RTTCLKYLVLANMLMKSGINPFDSQEAKPYKNDPEILAMTNLVAAYQNNDIIEFERILKSNRSNIMDDPFIREHIED 345 (440)
T ss_pred cc-hhHHHHHHHHHHHHHHcCCCCCcccccCCCCCCHHHHHHHHHHHHHhcccHHHHHHHHHhhhccccccHHHHHHHHH
Confidence 33 77899999999988654 3 3222111111 0234556788999999999999999999999888877765 34555
Q ss_pred HHHHHHHHHHHHHhhcccccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEeeCCCceEEEccCcccccc-ccchHHH
Q psy1676 207 LRHNVIKTAIRSIGASYSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLDREKGYMQSKESADIYCT-VEPQLAF 285 (343)
Q Consensus 207 l~~~v~r~~ir~i~~~ys~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~Id~~~g~v~~~~~~~v~s~-~ep~~~~ 285 (343)
|..++.-.-+.++.++|++|.++-|++.|+++ +.+||.+++.+|-|..|+|.||+.++++...+....=|+ -..+..|
T Consensus 346 Ll~niRTQVLlkLIkPYt~i~Ipfis~~Lnv~-~~dV~~LLV~~ILD~~i~g~Ide~n~~l~~~~~~~s~~k~~~al~kW 424 (440)
T KOG1464|consen 346 LLRNIRTQVLLKLIKPYTNIGIPFISKELNVP-EADVESLLVSCILDDTIDGRIDEVNQYLELDKSKNSGSKLYKALDKW 424 (440)
T ss_pred HHHHHHHHHHHHHhccccccCchhhHhhcCCC-HHHHHHHHHHHHhccccccchHHhhhHhccCccCCcchHHHHHHHHH
Confidence 55555445556777899999999999999996 999999999999999999999999999988765553333 3567778
Q ss_pred HHHHHHH
Q psy1676 286 HQRIAFC 292 (343)
Q Consensus 286 ~~rI~~c 292 (343)
..||...
T Consensus 425 ~~ql~Sl 431 (440)
T KOG1464|consen 425 NNQLKSL 431 (440)
T ss_pred HHHHHHH
Confidence 8887753
No 11
>KOG2908|consensus
Probab=99.59 E-value=2.5e-12 Score=121.37 Aligned_cols=242 Identities=15% Similarity=0.218 Sum_probs=167.5
Q ss_pred CcchhHHHHHHHHHHHHhhccHHHHHhhhhhc--CCC--CCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCc
Q psy1676 52 DFEGQAVLINCLLRNYLHYNLYDQADKLVKKS--AFP--ENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQ 127 (343)
Q Consensus 52 ~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~--~~p--~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~ 127 (343)
.|+...++.....|+++..|+...|+.++... ... ...+.+-...|+-.+..+|-..++|..++++...-+. |..
T Consensus 110 e~~av~~~~t~~~r~~L~i~DLk~~kk~ldd~~~~ld~~~~v~~~Vh~~fY~lssqYyk~~~d~a~yYr~~L~YL~-~~d 188 (380)
T KOG2908|consen 110 EPDAVIYILTEIARLKLEINDLKEIKKLLDDLKSMLDSLDGVTSNVHSSFYSLSSQYYKKIGDFASYYRHALLYLG-CSD 188 (380)
T ss_pred cchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHhcccCCChhhhhhHHHHHHHHHHHHHhHHHHHHHHHHHhc-ccc
Confidence 44566788888999999999999999998853 222 1244456677888888888899999888877665554 221
Q ss_pred --cchHHHHHHHHHHHHHHHHhcCC-CCC-hhhhhhHhHhhh----hhhhHHHHHHHHhCCHHHHHHHHHhccc--cccc
Q psy1676 128 --TAAVGFRQTTQKLAVVVELLLGD-IPD-RQIFRQAVLRRA----LSPYFQLTQAVRMGELQKFNEVLTTYGN--QFRT 197 (343)
Q Consensus 128 --~sa~~~~~~i~K~li~v~LL~G~-iP~-~~~~~~~~l~~~----l~~Y~~L~~Av~~Gdl~~f~~~l~~~~~--~f~~ 197 (343)
......++... +-+...-++|+ +-+ ..++.+|.++.. -.|..++..||++||+.+|++....+.. .|.+
T Consensus 189 ~~~l~~se~~~lA-~~L~~aALLGe~iyNfGELL~HPilesL~gT~~eWL~dll~Afn~Gdl~~f~~l~~~~~~~p~L~~ 267 (380)
T KOG2908|consen 189 IDDLSESEKQDLA-FDLSLAALLGENIYNFGELLAHPILESLKGTNREWLKDLLIAFNSGDLKRFESLKGVWGKQPDLAS 267 (380)
T ss_pred ccccCHHHHHHHH-HHHHHHHHhccccccHHHHHhhHHHHHhcCCcHHHHHHHHHHhccCCHHHHHHHHHHhccCchHHH
Confidence 11122233333 34444556676 877 678888988743 3578899999999999999999887765 3332
Q ss_pred cccHHHHHHHHHHHHHHHHHHHhhcccccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEeeCCCceEEEcc-Ccccc
Q psy1676 198 DYTFKLILRLRHNVIKTAIRSIGASYSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLDREKGYMQSKE-SADIY 276 (343)
Q Consensus 198 d~~~~Lv~~l~~~v~r~~ir~i~~~ys~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~Id~~~g~v~~~~-~~~v~ 276 (343)
..- .|.++.+..+.-..+=.-...-.+||+++||++.+++ .++||.+|+++++.|.|+|.||+..|.|.+.+ .+.|+
T Consensus 268 ~e~-~L~qKI~LmaLiEi~F~rpa~~R~lsf~~Ia~~tkip-~~eVE~LVMKAlslgLikG~Idqv~~~v~~swvqPRvl 345 (380)
T KOG2908|consen 268 NED-FLLQKIRLLALIEITFSRPANERTLSFKEIAEATKIP-NKEVELLVMKALSLGLIKGSIDQVEGVVYMSWVQPRVL 345 (380)
T ss_pred HHH-HHHHHHHHHHHHHHHhcCcchhccccHHHHHHHhCCC-HHHHHHHHHHHHhccceeeeecccccEEEEeccccccc
Confidence 211 2333333322211110001123579999999999996 99999999999999999999999999999988 45566
Q ss_pred ccccchHHHHHHHHH-HHHhhHH
Q psy1676 277 CTVEPQLAFHQRIAF-CLDLHNQ 298 (343)
Q Consensus 277 s~~ep~~~~~~rI~~-cl~l~~~ 298 (343)
+.++ .....+|+.. |-++++-
T Consensus 346 ~~~q-I~~Mk~rl~~W~~~v~~m 367 (380)
T KOG2908|consen 346 DRSQ-IVKMKDRLDEWNKDVKSM 367 (380)
T ss_pred CHHH-HHhHHHHHHHHHHHHHHH
Confidence 5544 6667777765 6565443
No 12
>COG5159 RPN6 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=99.50 E-value=1.3e-12 Score=121.15 Aligned_cols=184 Identities=17% Similarity=0.263 Sum_probs=154.0
Q ss_pred ChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCccchHHHHHHHHHHHHHHHHhcCCCCC-hhhhhhHhHh-----
Q psy1676 90 SNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQTAAVGFRQTTQKLAVVVELLLGDIPD-RQIFRQAVLR----- 163 (343)
Q Consensus 90 ~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~sa~~~~~~i~K~li~v~LL~G~iP~-~~~~~~~~l~----- 163 (343)
|+..+..-....|.+++-.++|..|+.+|..|+...+......-.-..+||++++.++++.+.+ .++++.+...
T Consensus 201 Ppqlqa~lDL~sGIlhcdd~dyktA~SYF~Ea~Egft~l~~d~kAc~sLkYmlLSkIMlN~~~evk~vl~~K~t~~~y~~ 280 (421)
T COG5159 201 PPQLQAQLDLLSGILHCDDRDYKTASSYFIEALEGFTLLKMDVKACVSLKYMLLSKIMLNRREEVKAVLRNKNTLKHYDD 280 (421)
T ss_pred CHHHHHHHHHhccceeeccccchhHHHHHHHHHhccccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHccchhHhhhhh
Confidence 5678888899999999999999999999999999544321111122368999999999988665 4555443222
Q ss_pred hhhhhhHHHHHHHHhCCHHHHHHHHHhccccccccccH-HHHHHHHHHHHHHHHHHHhhcccccChHHHHHHhCCCCHHH
Q psy1676 164 RALSPYFQLTQAVRMGELQKFNEVLTTYGNQFRTDYTF-KLILRLRHNVIKTAIRSIGASYSRITPTKIAEKLGLESPED 242 (343)
Q Consensus 164 ~~l~~Y~~L~~Av~~Gdl~~f~~~l~~~~~~f~~d~~~-~Lv~~l~~~v~r~~ir~i~~~ys~Isl~dIa~~l~l~s~~e 242 (343)
..+.....+++|+.+.++..|+.++.+|..++..|... ..+.-|.......++-+|..+|+++.++.||..+|++ ...
T Consensus 281 r~I~am~avaea~~NRsL~df~~aL~qY~~el~~D~~iRsHl~~LYD~LLe~Nl~kiiEPfs~VeishIa~viGld-t~q 359 (421)
T COG5159 281 RMIRAMLAVAEAFGNRSLKDFSDALAQYSDELHQDSFIRSHLQYLYDVLLEKNLVKIIEPFSVVEISHIADVIGLD-TNQ 359 (421)
T ss_pred hhHHHHHHHHHHhCCCcHhhHHHHHHHhhHHhccCHHHHHHHHHHHHHHHHhhhhhhcCcceeeehhHHHHHhccc-HHH
Confidence 24556778999999999999999999999999999876 6788899999999999999999999999999999996 999
Q ss_pred HHHHHHHhHHcCCceEEeeCCCceEEEccCcc
Q psy1676 243 AEFIIAKAIRDGVIEATLDREKGYMQSKESAD 274 (343)
Q Consensus 243 ~E~ila~lI~~G~I~a~Id~~~g~v~~~~~~~ 274 (343)
+|.-+++||-|....|.+||.+||+...+.+.
T Consensus 360 vEgKLsqMILDKifyG~LDqg~gcLivy~ep~ 391 (421)
T COG5159 360 VEGKLSQMILDKIFYGTLDQGDGCLIVYGEPA 391 (421)
T ss_pred HHHHHHHHHHHHHHHhhhccCCceEEEeCCcc
Confidence 99999999999999999999999998776543
No 13
>COG5071 RPN5 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=99.47 E-value=7.1e-13 Score=123.37 Aligned_cols=271 Identities=20% Similarity=0.221 Sum_probs=189.8
Q ss_pred HHHHHHHHHHHHhhcccHHHHHHHHHHHHH-HhhhcCCcchhHHHHHHHHHHHHhhccHHHHHhhhhhc---CCCCCCCh
Q psy1676 16 AAKCYFYHSRVHELTNNLDKVRSFLNARLR-IATLRNDFEGQAVLINCLLRNYLHYNLYDQADKLVKKS---AFPENASN 91 (343)
Q Consensus 16 ~a~~~~y~~~~~e~~~~~~~~~~~l~~~~r-~a~~~~~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~---~~p~~~~~ 91 (343)
.|++---+++++|.+|.+.++...+-+..- |-..-.......+++.+ +|+|+..++|-+|....+|+ .|.+....
T Consensus 130 RariT~~L~~ikee~Gdi~sA~Dilcn~pVETygs~~~Sekv~fiLEQ-~rL~vl~~Dy~~A~~~~kKI~KK~Fe~~d~~ 208 (439)
T COG5071 130 RARLTQLLSQIKEEQGDIKSAQDILCNEPVETYGSFDLSEKVAFILEQ-VRLFLLRSDYYMASTYTKKINKKFFEKEDVQ 208 (439)
T ss_pred HHHHHHHHHHHHHHhcchhHHHHHHhcCchhhccchhHHHHHHHHHHH-HHHHHhccchHHHHHHHHHHHHHHhccccHH
Confidence 345556678999999999999888865331 11111112233366666 89999999999999998877 46554455
Q ss_pred HHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCC-cc-chHHHHHHHHHHHHHHHHhcCCCCC--hhhhhhH--hHh-h
Q psy1676 92 NEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAP-QT-AAVGFRQTTQKLAVVVELLLGDIPD--RQIFRQA--VLR-R 164 (343)
Q Consensus 92 ~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~-~~-sa~~~~~~i~K~li~v~LL~G~iP~--~~~~~~~--~l~-~ 164 (343)
+..+.|+-..-+|.+.++.|-++..+|+..+.... .. .|.. +. ++-.++...+ +.-.-+ ..++-.. ..+ .
T Consensus 209 slKlkyYeL~V~i~Lh~R~Yl~v~~y~~~vY~t~~~~~d~Akw-k~-VLS~~v~F~i-Ltpy~neq~dlvhKi~~d~kl~ 285 (439)
T COG5071 209 SLKLKYYELKVRIGLHDRAYLDVCKYYRAVYDTAVVQEDPAKW-KE-VLSNVVCFAL-LTPYDNEQADLLHKINADHKLN 285 (439)
T ss_pred HHHHHHHHHhheeecccHHHHHHHHHHHHHHHHHHhccCcccc-cc-hhhcceeeEE-ecccccHHHHHHHHhhhhhhhc
Confidence 78899999999999999999999999998887322 11 1111 11 1110000011 111100 1111100 000 1
Q ss_pred hhhhhHHHHHHHHhCCHHHHHHHHHhcccccccc-------ccHHHHHHHHHHHHHHHHHHHhhcccccChHHHHHHhCC
Q psy1676 165 ALSPYFQLTQAVRMGELQKFNEVLTTYGNQFRTD-------YTFKLILRLRHNVIKTAIRSIGASYSRITPTKIAEKLGL 237 (343)
Q Consensus 165 ~l~~Y~~L~~Av~~Gdl~~f~~~l~~~~~~f~~d-------~~~~Lv~~l~~~v~r~~ir~i~~~ys~Isl~dIa~~l~l 237 (343)
.+..-.+++..+....+..|..+-+.+++.+..+ ..---+..|+..|+.|++|.|...||+|++.++...+++
T Consensus 286 sl~~~~~lVk~f~vNelmrwp~V~~~y~~~l~~~~faF~~e~~~~~w~DL~krviEHN~RvI~~yYSrI~~~rl~~lld~ 365 (439)
T COG5071 286 SLPLLQQLVKCFIVNELMRWPKVAEIYGSALRSNVFAFNDEKGEKRWSDLRKRVIEHNIRVIANYYSRIHCSRLGVLLDM 365 (439)
T ss_pred cchhhhhHHHHHHHHHHHhhhHHHHHhHHHHHhhhhhhccchhhhhHHHHHHHHHHhhHhHHHHHhhhhhHHHHHHHHcC
Confidence 2333457888888888888888888777655554 222458899999999999999999999999999999999
Q ss_pred CCHHHHHHHHHHhHHcCCceEEeeCCCceEEEccCccccccccchHHHHHHHHHHHH
Q psy1676 238 ESPEDAEFIIAKAIRDGVIEATLDREKGYMQSKESADIYCTVEPQLAFHQRIAFCLD 294 (343)
Q Consensus 238 ~s~~e~E~ila~lI~~G~I~a~Id~~~g~v~~~~~~~v~s~~ep~~~~~~rI~~cl~ 294 (343)
+ ++++|..++.|++.|.+.|+|+++.|+|.|.+...+ .+.+++|...+...|.
T Consensus 366 ~-~s~te~~ISdlVN~G~~yaKiNrpa~Ii~FEK~~n~---~~~lneW~~NV~ellg 418 (439)
T COG5071 366 S-PSETEQFISDLVNKGHFYAKINRPAQIISFEKSQNV---QEQLNEWGSNVTELLG 418 (439)
T ss_pred C-HHHHHHHHHHHHhcCcEEEEecCccceEEeeccccH---HHHHHHhcccHHHHHH
Confidence 6 999999999999999999999999999999987653 4567888887776554
No 14
>smart00753 PAM PCI/PINT associated module.
Probab=99.25 E-value=3.4e-11 Score=94.05 Aligned_cols=86 Identities=30% Similarity=0.467 Sum_probs=75.5
Q ss_pred HHHHHHHHHHHHHHHHHhhcccccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEeeCCCceEEEccCccccccccch
Q psy1676 203 LILRLRHNVIKTAIRSIGASYSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLDREKGYMQSKESADIYCTVEPQ 282 (343)
Q Consensus 203 Lv~~l~~~v~r~~ir~i~~~ys~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~Id~~~g~v~~~~~~~v~s~~ep~ 282 (343)
.+..+...+.++.+..++.+|++|++++|++.++++ .+++|..|.+||.+|.|.|+|||.+|+|.+.++..-+ .++.
T Consensus 2 ~~~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~-~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~~~r~--~~~~ 78 (88)
T smart00753 2 LVERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLS-VPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEVDPRR--SEPL 78 (88)
T ss_pred hHHHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcC-HHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCCchhh--hhHH
Confidence 356778888899999999999999999999999996 7899999999999999999999999999999876554 4677
Q ss_pred HHHHHHHHH
Q psy1676 283 LAFHQRIAF 291 (343)
Q Consensus 283 ~~~~~rI~~ 291 (343)
+.+.+++..
T Consensus 79 ~~~~~~l~~ 87 (88)
T smart00753 79 AQFAETLKK 87 (88)
T ss_pred HHHHHHhhc
Confidence 778777653
No 15
>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15. Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.
Probab=99.25 E-value=3.4e-11 Score=94.05 Aligned_cols=86 Identities=30% Similarity=0.467 Sum_probs=75.5
Q ss_pred HHHHHHHHHHHHHHHHHhhcccccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEeeCCCceEEEccCccccccccch
Q psy1676 203 LILRLRHNVIKTAIRSIGASYSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLDREKGYMQSKESADIYCTVEPQ 282 (343)
Q Consensus 203 Lv~~l~~~v~r~~ir~i~~~ys~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~Id~~~g~v~~~~~~~v~s~~ep~ 282 (343)
.+..+...+.++.+..++.+|++|++++|++.++++ .+++|..|.+||.+|.|.|+|||.+|+|.+.++..-+ .++.
T Consensus 2 ~~~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~-~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~~~r~--~~~~ 78 (88)
T smart00088 2 LVERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLS-VPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEVDPRR--SEPL 78 (88)
T ss_pred hHHHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcC-HHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCCchhh--hhHH
Confidence 356778888899999999999999999999999996 7899999999999999999999999999999876554 4677
Q ss_pred HHHHHHHHH
Q psy1676 283 LAFHQRIAF 291 (343)
Q Consensus 283 ~~~~~rI~~ 291 (343)
+.+.+++..
T Consensus 79 ~~~~~~l~~ 87 (88)
T smart00088 79 AQFAETLKK 87 (88)
T ss_pred HHHHHHhhc
Confidence 778777653
No 16
>KOG1076|consensus
Probab=98.29 E-value=0.00014 Score=75.05 Aligned_cols=248 Identities=15% Similarity=0.186 Sum_probs=150.8
Q ss_pred HHHHHHHHHHHHHHHhhcccHHHHHHHHHHHH-HHhhhcCCcchhH----HHHHHHHHHHHhhccHHHHHhhhhhcCCCC
Q psy1676 13 DLIAAKCYFYHSRVHELTNNLDKVRSFLNARL-RIATLRNDFEGQA----VLINCLLRNYLHYNLYDQADKLVKKSAFPE 87 (343)
Q Consensus 13 d~~~a~~~~y~~~~~e~~~~~~~~~~~l~~~~-r~a~~~~~~~~~~----~l~n~Llr~yl~~~~~~~a~~li~k~~~p~ 87 (343)
|.+.+++.-++=.-|-+.+++-.+|..|+-++ .+..-..|+.+|. +++. |=-+-|+.|....|-..+....-
T Consensus 482 ~r~rtRAmLchIYh~AL~d~f~~ARDlLLMSHlQdnI~h~D~stQIL~NRtmvQ-LGLCAFR~Gmi~EaH~~L~dl~s-- 558 (843)
T KOG1076|consen 482 DRLRTRAMLCHIYHHALHDNFYTARDLLLMSHLQDNIQHADISTQILFNRTMVQ-LGLCAFRQGMIKEAHQCLSDLQS-- 558 (843)
T ss_pred HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhhccChhHHHHHHHHHHH-HHHHHHHcccHHHHHHHHHHHHh--
Confidence 55555553333333447778889998876665 6666677888776 3332 23344788888877777764311
Q ss_pred CCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHh-hCCccchHHHHHHHHHHHHHHHHhcCCCCChhh--------hh
Q psy1676 88 NASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALR-KAPQTAAVGFRQTTQKLAVVVELLLGDIPDRQI--------FR 158 (343)
Q Consensus 88 ~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~-~~~~~sa~~~~~~i~K~li~v~LL~G~iP~~~~--------~~ 158 (343)
+..++=..=.|...-.+++.+.-.......-. |.|.+ -|.+.+--..++|.||+ +||.-.- ..
T Consensus 559 ----t~r~kELLgQgv~~~~~he~t~eQe~~eR~rQlPyHmH---INLELlEcVyLtcaMLl-EIP~MAA~~~d~Rrr~i 630 (843)
T KOG1076|consen 559 ----TGRVKELLGQGVLQRRQHEKTAEQEKIERRRQLPYHMH---INLELLECVYLTCAMLL-EIPYMAAHESDARRRMI 630 (843)
T ss_pred ----cchHHHHHhhhhhhhhhhccChhhHHHHHhhcCchhhh---ccHHHHHHHHHHHHHHH-hhhHHhhhhhhhhcccc
Confidence 12222222233333333333333333333333 22222 23555555555666665 4443100 00
Q ss_pred hHhHh---------------hhhhhhH-HHHHHHHhCCHHHHHHHHHhccccccc----cccH-HHHHHHHHHHHHHHHH
Q psy1676 159 QAVLR---------------RALSPYF-QLTQAVRMGELQKFNEVLTTYGNQFRT----DYTF-KLILRLRHNVIKTAIR 217 (343)
Q Consensus 159 ~~~l~---------------~~l~~Y~-~L~~Av~~Gdl~~f~~~l~~~~~~f~~----d~~~-~Lv~~l~~~v~r~~ir 217 (343)
++.+. .....|- .-++|...||+..-.+.+-.+...|.- |.+. .|.++++.--+|+-+-
T Consensus 631 Sk~frr~Le~serqsf~gPPEn~RehVvaAsKAm~~Gnw~~c~~fi~nn~KvW~Lfpn~d~V~~Ml~~rIqEEsLRTYLf 710 (843)
T KOG1076|consen 631 SKSFRRQLEHSERQSFTGPPENTREHVVAASKAMQKGNWQKCFEFIVNNIKVWDLFPNADTVLDMLTERIQEESLRTYLF 710 (843)
T ss_pred cHHHHHHHHHHhhccccCCchhHHHHHHHHHHHHhcCCHHHHHHHHHhhhhHHHhcccHHHHHHHHHHHHHHHHHHHHHH
Confidence 00111 1122332 457899999999988866555544432 2222 3456666666677776
Q ss_pred HHhhcccccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEeeCCCceEEEccC
Q psy1676 218 SIGASYSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLDREKGYMQSKES 272 (343)
Q Consensus 218 ~i~~~ys~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~Id~~~g~v~~~~~ 272 (343)
.-+..|..||++.+|....|+ +..|-.||++||-...|.|++|++.++++++++
T Consensus 711 tYss~Y~SvSl~~LA~mFdLp-~~~VhsIiSkmiineEl~AslDqpt~~iv~hrv 764 (843)
T KOG1076|consen 711 TYSSVYDSVSLAKLADMFDLP-EPKVHSIISKMIINEELHASLDQPTQCIVMHRV 764 (843)
T ss_pred HhhhhhhhccHHHHHHHhCCC-chhHHHHHHHHHHHHHhhhccCCCcceEEEeec
Confidence 677788999999999999996 899999999999999999999999999999974
No 17
>KOG0687|consensus
Probab=98.17 E-value=0.00037 Score=66.44 Aligned_cols=204 Identities=17% Similarity=0.230 Sum_probs=133.0
Q ss_pred HHHHHHhhccHHHHHhhhhhc--CCCCCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCccchHHHHHHHHHH
Q psy1676 63 LLRNYLHYNLYDQADKLVKKS--AFPENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQTAAVGFRQTTQKL 140 (343)
Q Consensus 63 Llr~yl~~~~~~~a~~li~k~--~~p~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~sa~~~~~~i~K~ 140 (343)
.+|+=|-.++.+.-...+.++ .+.+.-.=.-.=||.-|.|++.+.-++|.+|...|..++..-... -..--..+..|
T Consensus 147 ~iRlglfy~D~~lV~~~iekak~liE~GgDWeRrNRlKvY~Gly~msvR~Fk~Aa~Lfld~vsTFtS~-El~~Y~~~v~Y 225 (393)
T KOG0687|consen 147 KIRLGLFYLDHDLVTESIEKAKSLIEEGGDWERRNRLKVYQGLYCMSVRNFKEAADLFLDSVSTFTSY-ELMSYETFVRY 225 (393)
T ss_pred HHHHHHhhccHHHHHHHHHHHHHHHHhCCChhhhhhHHHHHHHHHHHHHhHHHHHHHHHHHcccccce-ecccHHHHHHH
Confidence 355555555555555555543 122211222445778899999999999999999999998743321 11224556678
Q ss_pred HHHHHHhcCCCCC--hhhhhhHhHh---hhhhhhHHHHHHHHhCCHHHHHHHHHhc-cccccccccH-----HHHHHHHH
Q psy1676 141 AVVVELLLGDIPD--RQIFRQAVLR---RALSPYFQLTQAVRMGELQKFNEVLTTY-GNQFRTDYTF-----KLILRLRH 209 (343)
Q Consensus 141 li~v~LL~G~iP~--~~~~~~~~l~---~~l~~Y~~L~~Av~~Gdl~~f~~~l~~~-~~~f~~d~~~-----~Lv~~l~~ 209 (343)
.+++.++.=+-|+ ..++..|.+- ..+.+-.+++.++=.-|...|-..+... ...+..|..+ --+...|.
T Consensus 226 tv~~g~i~leR~dlktKVi~~~Evl~vl~~l~~~~q~l~SLY~C~Y~~Ff~~L~~~~~~~lk~D~~l~~h~~yyvREMR~ 305 (393)
T KOG0687|consen 226 TVITGLIALERVDLKTKVIKCPEVLEVLHKLPSVSQLLNSLYECDYSDFFNDLAAVEAKQLKDDRYLGPHYRYYVREMRR 305 (393)
T ss_pred HHHHhhheeccchHHhhhcCcHHHHHHhhcCchHHHHHHHHHhccHHHHHHHHHHHHHHhhccchhcchHHHHHHHHHHH
Confidence 8888876555444 2233333221 1233444555555556666666655333 4455555432 22455555
Q ss_pred HHHHHHHHHHhhcccccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEeeCCCceEEEccC
Q psy1676 210 NVIKTAIRSIGASYSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLDREKGYMQSKES 272 (343)
Q Consensus 210 ~v~r~~ir~i~~~ys~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~Id~~~g~v~~~~~ 272 (343)
.++-..+ .+|..+++.-.|+..|+ |++=++.=+++.|..|.++++||+.+|.|....+
T Consensus 306 rvY~QlL----ESYrsl~l~~MA~aFgV-SVefiDreL~rFI~~grL~ckIDrVnGVVEtNrp 363 (393)
T KOG0687|consen 306 RVYAQLL----ESYRSLTLESMAKAFGV-SVEFIDRELGRFIAAGRLHCKIDRVNGVVETNRP 363 (393)
T ss_pred HHHHHHH----HHHHHHHHHHHHHHhCc-hHHHHHhHHHHhhccCceeeeeecccceeecCCc
Confidence 5554444 69999999999999999 5999999999999999999999999999887654
No 18
>COG5187 RPN7 26S proteasome regulatory complex component, contains PCI domain [Posttranslational modification, protein turnover, chaperones]
Probab=98.03 E-value=0.0017 Score=61.24 Aligned_cols=174 Identities=19% Similarity=0.313 Sum_probs=117.5
Q ss_pred HHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCccchHHHHHHHHHHHHHHHHhcCCCCC--hhhhhhHhH------hh
Q psy1676 93 EWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQTAAVGFRQTTQKLAVVVELLLGDIPD--RQIFRQAVL------RR 164 (343)
Q Consensus 93 ~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~sa~~~~~~i~K~li~v~LL~G~iP~--~~~~~~~~l------~~ 164 (343)
-.=+|.-|.|+..+..++|++|...|..++......--+. -..+..|.+++.++.=+--+ ..++..|.+ ..
T Consensus 190 RrNRyK~Y~Gi~~m~~RnFkeAa~Ll~d~l~tF~S~El~s-Y~~~vrYa~~~Gl~~leR~diktki~dspevl~vi~~~e 268 (412)
T COG5187 190 RRNRYKVYKGIFKMMRRNFKEAAILLSDILPTFESSELIS-YSRAVRYAIFCGLLRLERRDIKTKILDSPEVLDVIGSSE 268 (412)
T ss_pred hhhhHHHHHHHHHHHHHhhHHHHHHHHHHhcccccccccc-HHHHHHHHHHhhhheeehhhhhhhhcCCHHHHHhccchh
Confidence 4457889999999999999999999999887433221122 34467789999886432100 122222211 11
Q ss_pred hhhhhHHHHHHHHhCCHH-HHHHHHHhccccccccccHH-----HHHHHHHHHHHHHHHHHhhcccccChHHHHHHhCCC
Q psy1676 165 ALSPYFQLTQAVRMGELQ-KFNEVLTTYGNQFRTDYTFK-----LILRLRHNVIKTAIRSIGASYSRITPTKIAEKLGLE 238 (343)
Q Consensus 165 ~l~~Y~~L~~Av~~Gdl~-~f~~~l~~~~~~f~~d~~~~-----Lv~~l~~~v~r~~ir~i~~~ys~Isl~dIa~~l~l~ 238 (343)
.+....+++...=..|.. -|...+..+...+..|...+ .+...|..|+- .+-.+|..+|+...|+..|+
T Consensus 269 ~l~sl~~l~~SLy~cdY~~~F~~ll~~~~n~L~~d~fl~rh~d~fvREMRrrvYa----QlLESYr~lsl~sMA~tFgV- 343 (412)
T COG5187 269 KLGSLVQLATSLYECDYGGDFMNLLYLFCNSLQDDVFLGRHVDLFVREMRRRVYA----QLLESYRLLSLESMAQTFGV- 343 (412)
T ss_pred hhhhHHHHHHHHHHhccchhhHHHHHHHHhhccchHHHHHHHHHHHHHHHHHHHH----HHHHHHHHhhHHHHHHHhCc-
Confidence 233334455555444544 67777777777666665432 23333444443 34468999999999999999
Q ss_pred CHHHHHHHHHHhHHcCCceEEeeCCCceEEEccC
Q psy1676 239 SPEDAEFIIAKAIRDGVIEATLDREKGYMQSKES 272 (343)
Q Consensus 239 s~~e~E~ila~lI~~G~I~a~Id~~~g~v~~~~~ 272 (343)
|++-++.-+++-|-+|.++..||+.+|.|....+
T Consensus 344 SV~yvdrDLg~FIp~~~LncvIDRvnGvVetnrp 377 (412)
T COG5187 344 SVEYVDRDLGEFIPEGRLNCVIDRVNGVVETNRP 377 (412)
T ss_pred cHHHHhhhHHhhCCCCceeeeeecccceEeccCc
Confidence 5999999999999999999999999998876643
No 19
>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=98.01 E-value=0.00045 Score=68.44 Aligned_cols=184 Identities=17% Similarity=0.161 Sum_probs=121.7
Q ss_pred HHHHHHHHHHHhhccHHHHHhhhhhcCCCCC----CChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhC---C----
Q psy1676 58 VLINCLLRNYLHYNLYDQADKLVKKSAFPEN----ASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKA---P---- 126 (343)
Q Consensus 58 ~l~n~Llr~yl~~~~~~~a~~li~k~~~p~~----~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~---~---- 126 (343)
+-+..|+|+....|+|.+|.++++.+.+... ....-.++.+||.|--|+..++|.+|.+.|..++..- -
T Consensus 123 FSligLlRvh~LLGDY~~Alk~l~~idl~~~~l~~~V~~~~is~~YyvGFaylMlrRY~DAir~f~~iL~yi~r~k~~~~ 202 (404)
T PF10255_consen 123 FSLIGLLRVHCLLGDYYQALKVLENIDLNKKGLYTKVPACHISTYYYVGFAYLMLRRYADAIRTFSQILLYIQRTKNQYH 202 (404)
T ss_pred HHHHHHHHHHHhccCHHHHHHHhhccCcccchhhccCcchheehHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhc
Confidence 5566789999999999999999998765321 1245788999999999999999999999999988621 1
Q ss_pred cc----ch-HHHHHHHHHHHHHHHHhc-CCCCChhhhhhHhHhhhhhhhHHHHHHHHhCCHHHHHHHHHhccccccccc-
Q psy1676 127 QT----AA-VGFRQTTQKLAVVVELLL-GDIPDRQIFRQAVLRRALSPYFQLTQAVRMGELQKFNEVLTTYGNQFRTDY- 199 (343)
Q Consensus 127 ~~----sa-~~~~~~i~K~li~v~LL~-G~iP~~~~~~~~~l~~~l~~Y~~L~~Av~~Gdl~~f~~~l~~~~~~f~~d~- 199 (343)
+. .. .+..+...-++.+|..+. +++|+ ++.. .++. .|.+=.....+||+..|++........|+.--
T Consensus 203 ~~~~q~d~i~K~~eqMyaLlAic~~l~p~~lde-~i~~--~lke---ky~ek~~kmq~gd~~~f~elF~~acPKFIsp~~ 276 (404)
T PF10255_consen 203 QRSYQYDQINKKNEQMYALLAICLSLCPQRLDE-SISS--QLKE---KYGEKMEKMQRGDEEAFEELFSFACPKFISPVS 276 (404)
T ss_pred cccchhhHHHhHHHHHHHHHHHHHHhCCCCCCH-HHHH--HHHH---HHHHHHHHHHccCHHHHHHHHHhhCCCccCCCC
Confidence 10 01 111222222333343333 23444 2222 1121 36666667889999999999999888887732
Q ss_pred --c-------H----------HHHHHHHHHHHHHHHHHHhhcccccChHHHHHHhCCCCHHHHHHHHH
Q psy1676 200 --T-------F----------KLILRLRHNVIKTAIRSIGASYSRITPTKIAEKLGLESPEDAEFIIA 248 (343)
Q Consensus 200 --~-------~----------~Lv~~l~~~v~r~~ir~i~~~ys~Isl~dIa~~l~l~s~~e~E~ila 248 (343)
. + ..++.++....-..||..-+.|++|+++-+|.-++++ ++++-..+.
T Consensus 277 pp~~~~~~~~~~~e~~~~Ql~~Fl~eV~~q~~l~~lRSyLKLYtti~l~KLA~fl~vd-~~~lr~~Ll 343 (404)
T PF10255_consen 277 PPDYDGPSQNKNKEPYRRQLKLFLDEVKQQQKLPTLRSYLKLYTTIPLEKLASFLDVD-EEELRSQLL 343 (404)
T ss_pred CCCcccccchhhhhHHHHHHHHHHHHHHHhhhhhHHHHHHHhhcCCCHHHHHHHcCCC-HHHHHHHHH
Confidence 1 1 1122333333344556667789999999999999995 776555443
No 20
>KOG0686|consensus
Probab=97.78 E-value=0.0017 Score=63.60 Aligned_cols=207 Identities=14% Similarity=0.139 Sum_probs=129.4
Q ss_pred HHHHHhhccHHHHHhhhhhc-CCCC-CCChHHHH--HHHHHHHHHHHHhhCHHHHHHHHHHHHh-hCCccchHHHHHHHH
Q psy1676 64 LRNYLHYNLYDQADKLVKKS-AFPE-NASNNEWA--RFHFYLGRIKAVRLEYSTAHKNLVQALR-KAPQTAAVGFRQTTQ 138 (343)
Q Consensus 64 lr~yl~~~~~~~a~~li~k~-~~p~-~~~~~~~~--~Y~YY~Gri~~~~~~y~~A~~~L~~A~~-~~~~~sa~~~~~~i~ 138 (343)
++.-+-.+++..-...+++. ..|. +.+-++.+ +-.=+.|...+..++|..|..+|..+-- .|... .+-.-.-+-
T Consensus 194 i~VSI~~~nw~hv~sy~~~A~st~~~~~~~~q~v~~kl~C~agLa~L~lkkyk~aa~~fL~~~~~~~d~~-~ivtpsdv~ 272 (466)
T KOG0686|consen 194 ILVSIYMGNWGHVLSYISKAESTPDANENLAQEVPAKLKCAAGLANLLLKKYKSAAKYFLLAEFDHCDYP-EIVTPSDVA 272 (466)
T ss_pred HHHHHhhcchhhhhhHHHHHHhCchhhhhHHHhcCcchHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcc-ceecchhhH
Confidence 55556677777777777755 3331 11112222 2234789999999999999888877665 45421 000111133
Q ss_pred HHHHHHHHhcCCCCC--hhhhhhHhHhh--hhhh-hHHHHHHHHhCCHHHHHHHHHhccccccccccH-HHHHHHHHHHH
Q psy1676 139 KLAVVVELLLGDIPD--RQIFRQAVLRR--ALSP-YFQLTQAVRMGELQKFNEVLTTYGNQFRTDYTF-KLILRLRHNVI 212 (343)
Q Consensus 139 K~li~v~LL~G~iP~--~~~~~~~~l~~--~l~~-Y~~L~~Av~~Gdl~~f~~~l~~~~~~f~~d~~~-~Lv~~l~~~v~ 212 (343)
.|-.+|.|-.=+--+ ..+..+-.++. .+.| ..++...|-++.....-+.+.+.+..+.-|--. .-|..|-..+.
T Consensus 273 iYggLcALAtfdr~~Lk~~vi~n~~Fk~flel~Pqlr~il~~fy~sky~~cl~~L~~~k~~llLD~yLaphVd~Ly~~IR 352 (466)
T KOG0686|consen 273 IYGGLCALATFDRQDLKLNVIKNESFKLFLELEPQLREILFKFYSSKYASCLELLREIKPRLLLDMYLAPHVDNLYSLIR 352 (466)
T ss_pred HHHhhHhhccCCHHHHHHHHHcchhhhhHHhcChHHHHHHHHHhhhhHHHHHHHHHHhccceeechhcchhHHHHHHHHH
Confidence 445555442111000 00111111111 1222 346777888887777778887777654444322 34455555555
Q ss_pred HHHHHHHhhcccccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEeeCCCceEEEccC
Q psy1676 213 KTAIRSIGASYSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLDREKGYMQSKES 272 (343)
Q Consensus 213 r~~ir~i~~~ys~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~Id~~~g~v~~~~~ 272 (343)
.+.+.+....|++++++.+|.+++. |+...|.=|..+|.+|.|.|+||...+++...+.
T Consensus 353 ~r~llqy~~py~s~~m~~mA~af~~-sv~~le~~l~~LI~~~~i~~rIDs~~ki~~~~~~ 411 (466)
T KOG0686|consen 353 NRALLQYLSPYSSADMSKMAEAFNT-SVAILESELLELILEGKISGRIDSHNKILYARDA 411 (466)
T ss_pred HhhHHHhcCccccchHHHHHHHhcc-cHHHHHHHHHHHHHccchheeeccccceeeeccc
Confidence 5666777889999999999999999 5999999999999999999999999999988764
No 21
>KOG2753|consensus
Probab=97.59 E-value=0.0056 Score=58.57 Aligned_cols=117 Identities=15% Similarity=0.266 Sum_probs=86.3
Q ss_pred hHHHHHHHHhCCHHHHHHHHHhccccccccccH--HHHHHHHHHHHHHHHHHHhhcccccChHHHHHHhCCCCHHHHHHH
Q psy1676 169 YFQLTQAVRMGELQKFNEVLTTYGNQFRTDYTF--KLILRLRHNVIKTAIRSIGASYSRITPTKIAEKLGLESPEDAEFI 246 (343)
Q Consensus 169 Y~~L~~Av~~Gdl~~f~~~l~~~~~~f~~d~~~--~Lv~~l~~~v~r~~ir~i~~~ys~Isl~dIa~~l~l~s~~e~E~i 246 (343)
-.+|...|-+|-+..+.++.+.|.......|.. .++.+.|...+- .+...-..||+.++++.|+++ ++|||-.
T Consensus 240 i~qLL~IF~s~~L~aYveF~~~N~~Fvqs~gl~~E~~~~KMRLLTlm----~LA~es~eisy~~l~k~LqI~-edeVE~f 314 (378)
T KOG2753|consen 240 IHQLLKIFVSGKLDAYVEFVAANSGFVQSQGLVHEQNMAKMRLLTLM----SLAEESNEISYDTLAKELQIN-EDEVELF 314 (378)
T ss_pred HHHHHHHHHhcchHHHHHHHHhChHHHHHhcccHHHHHHHHHHHHHH----HHhccCCCCCHHHHHHHhccC-HHHHHHH
Confidence 568999999999999999999998876665542 223333322221 122355899999999999996 8999999
Q ss_pred HHHhHHcCCceEEeeCCCceEEEcc-CccccccccchHHHHHHHHH
Q psy1676 247 IAKAIRDGVIEATLDREKGYMQSKE-SADIYCTVEPQLAFHQRIAF 291 (343)
Q Consensus 247 la~lI~~G~I~a~Id~~~g~v~~~~-~~~v~s~~ep~~~~~~rI~~ 291 (343)
|.++|.-|.|.|+||+.+..|+.+. ...++++.+ -..++.+++-
T Consensus 315 VIdaI~aklV~~kidq~~~~viVs~~~hR~FG~~q-W~~L~~kL~a 359 (378)
T KOG2753|consen 315 VIDAIRAKLVEGKIDQMNRTVIVSSSTHRTFGKQQ-WQQLRDKLAA 359 (378)
T ss_pred HHHHHHHHHHHhhHHhhcceEEeehhhhhhcccHH-HHHHHHHHHH
Confidence 9999999999999999987776654 556676543 3444555443
No 22
>KOG2758|consensus
Probab=97.37 E-value=0.001 Score=63.45 Aligned_cols=95 Identities=20% Similarity=0.250 Sum_probs=63.5
Q ss_pred hCCHHHHHHHHHhccccccccccH-HHHHHHHHHHHHHHHHHHhhcccccChHHHHHHhCCCCHHHHHHHHHHhHHcCCc
Q psy1676 178 MGELQKFNEVLTTYGNQFRTDYTF-KLILRLRHNVIKTAIRSIGASYSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVI 256 (343)
Q Consensus 178 ~Gdl~~f~~~l~~~~~~f~~d~~~-~Lv~~l~~~v~r~~ir~i~~~ys~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I 256 (343)
+=|..+-+..+...++.+..|-.. .++..-+.+...-.+..-+.+...|+++-+|.+|+++ ++|+|+.+.++|+...|
T Consensus 301 n~DFdgAq~kl~eCeeVl~nDfFLva~l~~F~E~ARl~ifEtfCRIHqcIti~mLA~kLnm~-~eeaErwivnlIr~~rl 379 (432)
T KOG2758|consen 301 NYDFDGAQKKLRECEEVLVNDFFLVALLDEFLENARLLIFETFCRIHQCITIDMLADKLNMD-PEEAERWIVNLIRTARL 379 (432)
T ss_pred ccchHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHHHHHHHHHHHHheeHHHHHHHhcCC-HHHHHHHHHHHHHHhhh
Confidence 334444455555555555555432 1111111111111112223456899999999999995 99999999999999999
Q ss_pred eEEeeCCCceEEEccCc
Q psy1676 257 EATLDREKGYMQSKESA 273 (343)
Q Consensus 257 ~a~Id~~~g~v~~~~~~ 273 (343)
.|+||.+-|.|+...+.
T Consensus 380 ~AkidSklg~Vvmg~~~ 396 (432)
T KOG2758|consen 380 DAKIDSKLGHVVMGHPT 396 (432)
T ss_pred hhhhccccCceeecCCC
Confidence 99999999999988653
No 23
>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A.
Probab=97.30 E-value=0.0069 Score=57.29 Aligned_cols=148 Identities=18% Similarity=0.203 Sum_probs=81.5
Q ss_pred CCcchhHHHHHHHHHHHHhh-ccHHHHHhhhhhc--CCCCCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCc
Q psy1676 51 NDFEGQAVLINCLLRNYLHY-NLYDQADKLVKKS--AFPENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQ 127 (343)
Q Consensus 51 ~~~~~~~~l~n~Llr~yl~~-~~~~~a~~li~k~--~~p~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~ 127 (343)
+++...+-+...+-++|-.. ++++.|.....+. .+............+--.|.+++..++|.+|...|+.+...+..
T Consensus 108 G~~~~aA~~~~~lA~~ye~~~~d~e~Ai~~Y~~A~~~y~~e~~~~~a~~~~~~~A~l~~~l~~y~~A~~~~e~~~~~~l~ 187 (282)
T PF14938_consen 108 GRFSQAAKCLKELAEIYEEQLGDYEKAIEYYQKAAELYEQEGSPHSAAECLLKAADLYARLGRYEEAIEIYEEVAKKCLE 187 (282)
T ss_dssp T-HHHHHHHHHHHHHHHCCTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTCCC
T ss_pred CcHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhhc
Confidence 33333344444444444444 4444444444432 11111123455566667888999999999999999999986544
Q ss_pred cc--hHHHHHHHHHHHHHHHHhcCCCCCh-hhhh-----hHhHh--hhhhhhHHHHHHHHhCCHHHHHHHHHhccccccc
Q psy1676 128 TA--AVGFRQTTQKLAVVVELLLGDIPDR-QIFR-----QAVLR--RALSPYFQLTQAVRMGELQKFNEVLTTYGNQFRT 197 (343)
Q Consensus 128 ~s--a~~~~~~i~K~li~v~LL~G~iP~~-~~~~-----~~~l~--~~l~~Y~~L~~Av~~Gdl~~f~~~l~~~~~~f~~ 197 (343)
.. ..+ ...+.--.++|.|.+|+.... ..+. .|.+. ....--..|+.|+..||...|.+.+..|...=.-
T Consensus 188 ~~l~~~~-~~~~~l~a~l~~L~~~D~v~A~~~~~~~~~~~~~F~~s~E~~~~~~l~~A~~~~D~e~f~~av~~~d~~~~l 266 (282)
T PF14938_consen 188 NNLLKYS-AKEYFLKAILCHLAMGDYVAARKALERYCSQDPSFASSREYKFLEDLLEAYEEGDVEAFTEAVAEYDSISRL 266 (282)
T ss_dssp HCTTGHH-HHHHHHHHHHHHHHTT-HHHHHHHHHHHGTTSTTSTTSHHHHHHHHHHHHHHTT-CCCHHHHCHHHTTSS--
T ss_pred ccccchh-HHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCCCcHHHHHHHHHHHHHHhCCHHHHHHHHHHHcccCcc
Confidence 31 122 333333456788999984431 1111 11111 1233345899999999999999999998775444
Q ss_pred cc
Q psy1676 198 DY 199 (343)
Q Consensus 198 d~ 199 (343)
|+
T Consensus 267 d~ 268 (282)
T PF14938_consen 267 DN 268 (282)
T ss_dssp -H
T ss_pred HH
Confidence 44
No 24
>KOG2072|consensus
Probab=97.24 E-value=0.39 Score=51.14 Aligned_cols=69 Identities=14% Similarity=0.205 Sum_probs=64.2
Q ss_pred HHHHHHHHHHHHHHHHHhhcccccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEeeCCCceEEEcc
Q psy1676 203 LILRLRHNVIKTAIRSIGASYSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLDREKGYMQSKE 271 (343)
Q Consensus 203 Lv~~l~~~v~r~~ir~i~~~ys~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~Id~~~g~v~~~~ 271 (343)
-|..|....+.++++.++++|.+||++.+.+..-+-|.-++|.+++.+...+.+..+|||..+.|+|..
T Consensus 425 YI~sLq~v~~~RllqQvSqiY~sIs~~~l~~La~F~~~~~lEk~~v~a~k~~~v~iriDH~~~~v~Fgs 493 (988)
T KOG2072|consen 425 YIPSLQDVIILRLLQQVSQIYESISFERLYKLAPFFSAFELEKLLVEAAKHNDVSIRIDHESNSVSFGS 493 (988)
T ss_pred cchhHHHHHHHHHHHHHHHHHHHHhHHHHHHHHhhcCHHHHHHHHHHHHhccceeEEeccccceeeecc
Confidence 467788899999999999999999999999888777899999999999999999999999999999985
No 25
>PF10075 PCI_Csn8: COP9 signalosome, subunit CSN8; InterPro: IPR019280 The photomorphogenic 9 (COP9) signalosome or CSN complex is composed of eight subunits: Cops1/GPS1, Cops2, Cops3, Cops4, Cops5, Cop6, Cops7 (Cops7A or Cops7B) and Cops8. In the complex, Cops8, which is the smallest subunit, probably interacts directly with Cops3, Cops4 and Cops7 (Cops7A or Cops7B). This signalosome is homologous to the lid subcomplex of the 26S proteasome and regulates the ubiquitin-proteasome pathway. It functions as a structural scaffold for subunit-subunit interactions within the complex and is a key regulator of photomorphogenic development [].; PDB: 1RZ4_A.
Probab=96.21 E-value=0.029 Score=47.67 Aligned_cols=106 Identities=22% Similarity=0.337 Sum_probs=68.4
Q ss_pred HHHHHHhcCCCCChhhhhh---HhHh---hhhhhhHHHHHHHHhCCHHHHHHHHHhccccccccccHHHHHHHHHHHHHH
Q psy1676 141 AVVVELLLGDIPDRQIFRQ---AVLR---RALSPYFQLTQAVRMGELQKFNEVLTTYGNQFRTDYTFKLILRLRHNVIKT 214 (343)
Q Consensus 141 li~v~LL~G~iP~~~~~~~---~~l~---~~l~~Y~~L~~Av~~Gdl~~f~~~l~~~~~~f~~d~~~~Lv~~l~~~v~r~ 214 (343)
+++..|+.+.+++....-. +.++ ..+..-..|.+++.+|+..+|-..++.+ .+. +..-.+|..+...+...
T Consensus 10 ~Ll~~L~~~~~~df~~~~~rip~~~~~~~~~i~~i~~l~~~L~~~~~~~~~~~~~~~--~~~-~~~~~~v~~~~~~iR~~ 86 (143)
T PF10075_consen 10 ILLKYLMQNDLSDFRLLWKRIPEELKQSDPEIKAIWSLGQALWEGDYSKFWQALRSN--PWS-PDYKPFVPGFEDTIRER 86 (143)
T ss_dssp HHHHHHHTTTSTHHHHHHHTS-HHHHTS-TTHHHHHHHHHHHHTT-HHHHHHHS-TT-------HHHHTSTTHHHHHHHH
T ss_pred HHHHHHHcCCchHHHHHHHcCCHHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHhc--cch-HHHHHHHHHHHHHHHHH
Confidence 3444566666666332211 1111 2233445789999999999999887765 121 12234566667777778
Q ss_pred HHHHHhhcccccChHHHHHHhCCCCHHHHHHHHHHh
Q psy1676 215 AIRSIGASYSRITPTKIAEKLGLESPEDAEFIIAKA 250 (343)
Q Consensus 215 ~ir~i~~~ys~Isl~dIa~~l~l~s~~e~E~ila~l 250 (343)
-+..|+.+|++||++++++.||++ .++++.++.+-
T Consensus 87 i~~~i~~aY~sIs~~~la~~Lg~~-~~el~~~~~~~ 121 (143)
T PF10075_consen 87 IAHLISKAYSSISLSDLAEMLGLS-EEELEKFIKSR 121 (143)
T ss_dssp HHHHHHHH-SEE-HHHHHHHTTS--HHHHHHHHHHH
T ss_pred HHHHHHHHHhHcCHHHHHHHhCCC-HHHHHHHHHHc
Confidence 888999999999999999999997 89999988876
No 26
>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=96.01 E-value=0.16 Score=42.74 Aligned_cols=100 Identities=22% Similarity=0.125 Sum_probs=72.4
Q ss_pred HHHHHHHHHHHHHhhcccHHHHHHHHHHHHHHhhhcCCcchhHHHHHHHHHHHHhhccHHHHHhhhhhcCCCCCCChHHH
Q psy1676 15 IAAKCYFYHSRVHELTNNLDKVRSFLNARLRIATLRNDFEGQAVLINCLLRNYLHYNLYDQADKLVKKSAFPENASNNEW 94 (343)
Q Consensus 15 ~~a~~~~y~~~~~e~~~~~~~~~~~l~~~~r~a~~~~~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~~~p~~~~~~~~ 94 (343)
.+....+..+.++=..|.++.+...|-..+... .++.......-.|.++++..++|+.|...+..+.-+ ...
T Consensus 46 ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~---~d~~l~~~a~l~LA~~~~~~~~~d~Al~~L~~~~~~-----~~~ 117 (145)
T PF09976_consen 46 YAALAALQLAKAAYEQGDYDEAKAALEKALANA---PDPELKPLARLRLARILLQQGQYDEALATLQQIPDE-----AFK 117 (145)
T ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhC---CCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHhccCc-----chH
Confidence 455667888888888899998887776544422 233222233334789999999999999999764221 233
Q ss_pred HHHHHHHHHHHHHhhCHHHHHHHHHHHH
Q psy1676 95 ARFHFYLGRIKAVRLEYSTAHKNLVQAL 122 (343)
Q Consensus 95 ~~Y~YY~Gri~~~~~~y~~A~~~L~~A~ 122 (343)
..+....|.|+...|++.+|...|+.|+
T Consensus 118 ~~~~~~~Gdi~~~~g~~~~A~~~y~~Al 145 (145)
T PF09976_consen 118 ALAAELLGDIYLAQGDYDEARAAYQKAL 145 (145)
T ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHhC
Confidence 4467789999999999999999998874
No 27
>PF13371 TPR_9: Tetratricopeptide repeat
Probab=95.75 E-value=0.032 Score=40.88 Aligned_cols=60 Identities=22% Similarity=0.281 Sum_probs=50.5
Q ss_pred HHHHHHhhccHHHHHhhhhhc--CCCCCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCcc
Q psy1676 63 LLRNYLHYNLYDQADKLVKKS--AFPENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQT 128 (343)
Q Consensus 63 Llr~yl~~~~~~~a~~li~k~--~~p~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~ 128 (343)
|..+|++.++|+.|...++.. ..| +....++..|.++...++|.+|...|+.++..+|..
T Consensus 1 l~~~~~~~~~~~~A~~~~~~~l~~~p------~~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~~~p~~ 62 (73)
T PF13371_consen 1 LKQIYLQQEDYEEALEVLERALELDP------DDPELWLQRARCLFQLGRYEEALEDLERALELSPDD 62 (73)
T ss_pred CHHHHHhCCCHHHHHHHHHHHHHhCc------ccchhhHHHHHHHHHhccHHHHHHHHHHHHHHCCCc
Confidence 357899999999999999875 233 345567789999999999999999999999988865
No 28
>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B.
Probab=95.65 E-value=0.053 Score=38.90 Aligned_cols=61 Identities=23% Similarity=0.259 Sum_probs=49.5
Q ss_pred HHHHHHhhccHHHHHhhhhhcCCCCCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCc
Q psy1676 63 LLRNYLHYNLYDQADKLVKKSAFPENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQ 127 (343)
Q Consensus 63 Llr~yl~~~~~~~a~~li~k~~~p~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~ 127 (343)
+-+.+++.|+|+.|...++...-. ..+....+|..|.++..+++|.+|...|..++...|.
T Consensus 3 ~a~~~~~~g~~~~A~~~~~~~l~~----~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~~P~ 63 (65)
T PF13432_consen 3 LARALYQQGDYDEAIAAFEQALKQ----DPDNPEAWYLLGRILYQQGRYDEALAYYERALELDPD 63 (65)
T ss_dssp HHHHHHHCTHHHHHHHHHHHHHCC----STTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT
T ss_pred HHHHHHHcCCHHHHHHHHHHHHHH----CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcC
Confidence 356789999999999999976211 1246778999999999999999999999999987664
No 29
>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=95.64 E-value=0.032 Score=34.55 Aligned_cols=32 Identities=25% Similarity=0.337 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCc
Q psy1676 96 RFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQ 127 (343)
Q Consensus 96 ~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~ 127 (343)
.++|+.|.++...++|.+|.++|..|+...|.
T Consensus 2 ~~~~~lg~~~~~~~~~~~A~~~~~~al~l~p~ 33 (34)
T PF07719_consen 2 EAWYYLGQAYYQLGNYEEAIEYFEKALELDPN 33 (34)
T ss_dssp HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHHHHCcC
Confidence 57899999999999999999999999997664
No 30
>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=95.47 E-value=0.41 Score=39.08 Aligned_cols=99 Identities=13% Similarity=-0.042 Sum_probs=67.3
Q ss_pred HHHHHHHHhhcccHHHHHHHHHHHHHHhhhcCCcchhHHHHHHHHHHHHhhccHHHHHhhhhhcCCCCCCChHHHHHHHH
Q psy1676 20 YFYHSRVHELTNNLDKVRSFLNARLRIATLRNDFEGQAVLINCLLRNYLHYNLYDQADKLVKKSAFPENASNNEWARFHF 99 (343)
Q Consensus 20 ~~y~~~~~e~~~~~~~~~~~l~~~~r~a~~~~~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~~~p~~~~~~~~~~Y~Y 99 (343)
.+-.+..+-..++..++...+-.... .+++. ......+...|+..++++.|...+....-.. ......+|
T Consensus 20 ~~~~a~~~~~~~~~~~A~~~~~~~~~-----~~p~~-~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~----p~~~~~~~ 89 (135)
T TIGR02552 20 IYALAYNLYQQGRYDEALKLFQLLAA-----YDPYN-SRYWLGLAACCQMLKEYEEAIDAYALAAALD----PDDPRPYF 89 (135)
T ss_pred HHHHHHHHHHcccHHHHHHHHHHHHH-----hCCCc-HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC----CCChHHHH
Confidence 44555555566777777655533222 12332 2344455788889999999999888652111 12355678
Q ss_pred HHHHHHHHhhCHHHHHHHHHHHHhhCCcc
Q psy1676 100 YLGRIKAVRLEYSTAHKNLVQALRKAPQT 128 (343)
Q Consensus 100 Y~Gri~~~~~~y~~A~~~L~~A~~~~~~~ 128 (343)
+.|.++...+++.+|...|..++...|..
T Consensus 90 ~la~~~~~~g~~~~A~~~~~~al~~~p~~ 118 (135)
T TIGR02552 90 HAAECLLALGEPESALKALDLAIEICGEN 118 (135)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHhcccc
Confidence 89999999999999999999999977754
No 31
>PRK15359 type III secretion system chaperone protein SscB; Provisional
Probab=95.41 E-value=0.33 Score=41.06 Aligned_cols=99 Identities=7% Similarity=-0.039 Sum_probs=73.0
Q ss_pred HHHHHHHHhhcccHHHHHHHHHHHHHHhhhcCCcchhHHHHHHHHHHHHhhccHHHHHhhhhhcCCCCCCChHHHHHHHH
Q psy1676 20 YFYHSRVHELTNNLDKVRSFLNARLRIATLRNDFEGQAVLINCLLRNYLHYNLYDQADKLVKKSAFPENASNNEWARFHF 99 (343)
Q Consensus 20 ~~y~~~~~e~~~~~~~~~~~l~~~~r~a~~~~~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~~~p~~~~~~~~~~Y~Y 99 (343)
++..+.+.-..|+.+++...+..+ +..+|+.. .....+-..+...|+++.|......+.-.. ......++
T Consensus 27 ~~~~g~~~~~~g~~~~A~~~~~~a-----l~~~P~~~-~a~~~lg~~~~~~g~~~~A~~~y~~Al~l~----p~~~~a~~ 96 (144)
T PRK15359 27 VYASGYASWQEGDYSRAVIDFSWL-----VMAQPWSW-RAHIALAGTWMMLKEYTTAINFYGHALMLD----ASHPEPVY 96 (144)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHH-----HHcCCCcH-HHHHHHHHHHHHHhhHHHHHHHHHHHHhcC----CCCcHHHH
Confidence 666788888888888776554332 23344433 334455788899999999999998763211 23456688
Q ss_pred HHHHHHHHhhCHHHHHHHHHHHHhhCCcc
Q psy1676 100 YLGRIKAVRLEYSTAHKNLVQALRKAPQT 128 (343)
Q Consensus 100 Y~Gri~~~~~~y~~A~~~L~~A~~~~~~~ 128 (343)
..|.++...|++.+|...|..|+..+|..
T Consensus 97 ~lg~~l~~~g~~~eAi~~~~~Al~~~p~~ 125 (144)
T PRK15359 97 QTGVCLKMMGEPGLAREAFQTAIKMSYAD 125 (144)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHhCCCC
Confidence 99999999999999999999999987765
No 32
>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=95.40 E-value=0.3 Score=35.04 Aligned_cols=96 Identities=19% Similarity=0.205 Sum_probs=63.4
Q ss_pred HHHHHHHHHhhcccHHHHHHHHHHHHHHhhhcCCcchhHHHHHHHHHHHHhhccHHHHHhhhhhcC--CCCCCChHHHHH
Q psy1676 19 CYFYHSRVHELTNNLDKVRSFLNARLRIATLRNDFEGQAVLINCLLRNYLHYNLYDQADKLVKKSA--FPENASNNEWAR 96 (343)
Q Consensus 19 ~~~y~~~~~e~~~~~~~~~~~l~~~~r~a~~~~~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~~--~p~~~~~~~~~~ 96 (343)
+++..+..+-..+....+...+...++. .+... .+...+..+|...++++.|...+.... .|... .
T Consensus 2 ~~~~~a~~~~~~~~~~~A~~~~~~~~~~-----~~~~~-~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~------~ 69 (100)
T cd00189 2 ALLNLGNLYYKLGDYDEALEYYEKALEL-----DPDNA-DAYYNLAAAYYKLGKYEEALEDYEKALELDPDNA------K 69 (100)
T ss_pred HHHHHHHHHHHHhcHHHHHHHHHHHHhc-----CCccH-HHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcch------h
Confidence 4556666666667777766655444332 12111 344456777888899999998887642 23211 5
Q ss_pred HHHHHHHHHHHhhCHHHHHHHHHHHHhhCC
Q psy1676 97 FHFYLGRIKAVRLEYSTAHKNLVQALRKAP 126 (343)
Q Consensus 97 Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~ 126 (343)
.++..|.++...+++.+|..++..++..+|
T Consensus 70 ~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~ 99 (100)
T cd00189 70 AYYNLGLAYYKLGKYEEALEAYEKALELDP 99 (100)
T ss_pred HHHHHHHHHHHHHhHHHHHHHHHHHHccCC
Confidence 567888888899999999999988887554
No 33
>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=95.40 E-value=0.084 Score=39.27 Aligned_cols=65 Identities=25% Similarity=0.198 Sum_probs=51.6
Q ss_pred HHHHHHHHHHHHhhccHHHHHhhhhhc-----CCCCCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHh
Q psy1676 57 AVLINCLLRNYLHYNLYDQADKLVKKS-----AFPENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALR 123 (343)
Q Consensus 57 ~~l~n~Llr~yl~~~~~~~a~~li~k~-----~~p~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~ 123 (343)
+.+.+.+-.+|...++|+.|....+++ .+++ ...+.+.-++-.|.++...++|.+|..++++|+.
T Consensus 5 a~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~--~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al~ 74 (78)
T PF13424_consen 5 ANAYNNLARVYRELGRYDEALDYYEKALDIEEQLGD--DHPDTANTLNNLGECYYRLGDYEEALEYYQKALD 74 (78)
T ss_dssp HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTT--HHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCC--CCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence 455677788899999999999988865 1222 3346788899999999999999999999999886
No 34
>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=94.86 E-value=0.64 Score=36.50 Aligned_cols=106 Identities=14% Similarity=0.102 Sum_probs=76.9
Q ss_pred HHHHHHHHHHHhhcccHHHHHHHHHHHHHHhhhcCCcchhHHHHHHHHHHHHhhccHHHHHhhhhhc--CCCCCCChHHH
Q psy1676 17 AKCYFYHSRVHELTNNLDKVRSFLNARLRIATLRNDFEGQAVLINCLLRNYLHYNLYDQADKLVKKS--AFPENASNNEW 94 (343)
Q Consensus 17 a~~~~y~~~~~e~~~~~~~~~~~l~~~~r~a~~~~~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~--~~p~~~~~~~~ 94 (343)
++++|=.+......++...+...+....+.. .+..........+-++|++.++++.|...++.. ..|.+ ...
T Consensus 2 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~---~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~---~~~ 75 (119)
T TIGR02795 2 EEAYYDAALLVLKAGDYADAIQAFQAFLKKY---PKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKYPKS---PKA 75 (119)
T ss_pred cHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC---CCccccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHCCCC---Ccc
Confidence 3567888888888899988887776554321 111111234445788999999999999999965 24432 122
Q ss_pred HHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCcc
Q psy1676 95 ARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQT 128 (343)
Q Consensus 95 ~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~ 128 (343)
...++..|.++...+++.+|..++..++...|.+
T Consensus 76 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~p~~ 109 (119)
T TIGR02795 76 PDALLKLGMSLQELGDKEKAKATLQQVIKRYPGS 109 (119)
T ss_pred cHHHHHHHHHHHHhCChHHHHHHHHHHHHHCcCC
Confidence 3457889999999999999999999999976654
No 35
>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A.
Probab=94.70 E-value=0.33 Score=36.74 Aligned_cols=58 Identities=28% Similarity=0.362 Sum_probs=44.7
Q ss_pred HHHHHHHHHHHhhccHHHHHhhhhhcCCCCCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHH
Q psy1676 58 VLINCLLRNYLHYNLYDQADKLVKKSAFPENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQA 121 (343)
Q Consensus 58 ~l~n~Llr~yl~~~~~~~a~~li~k~~~p~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A 121 (343)
++.+ +..+|++.++|+.|..++++... ....+..+|..|+.+...++|.+|..+|..|
T Consensus 27 ~~~~-la~~~~~~~~y~~A~~~~~~~~~-----~~~~~~~~~l~a~~~~~l~~y~eAi~~l~~~ 84 (84)
T PF12895_consen 27 YLYN-LAQCYFQQGKYEEAIELLQKLKL-----DPSNPDIHYLLARCLLKLGKYEEAIKALEKA 84 (84)
T ss_dssp HHHH-HHHHHHHTTHHHHHHHHHHCHTH-----HHCHHHHHHHHHHHHHHTT-HHHHHHHHHHH
T ss_pred HHHH-HHHHHHHCCCHHHHHHHHHHhCC-----CCCCHHHHHHHHHHHHHhCCHHHHHHHHhcC
Confidence 3333 78999999999999999987211 1233666777799999999999999999865
No 36
>PF13414 TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2PL2_B 3IEG_B 2FBN_A ....
Probab=94.43 E-value=0.12 Score=37.27 Aligned_cols=64 Identities=20% Similarity=0.205 Sum_probs=50.5
Q ss_pred HHHHHHHHHHHhhccHHHHHhhhhhcC-CCCCCChHHHHHHHHHHHHHHHHhh-CHHHHHHHHHHHHhhCC
Q psy1676 58 VLINCLLRNYLHYNLYDQADKLVKKSA-FPENASNNEWARFHFYLGRIKAVRL-EYSTAHKNLVQALRKAP 126 (343)
Q Consensus 58 ~l~n~Llr~yl~~~~~~~a~~li~k~~-~p~~~~~~~~~~Y~YY~Gri~~~~~-~y~~A~~~L~~A~~~~~ 126 (343)
.+...+-..++..++|+.|...++++. +. +.....+|..|.++...+ +|.+|..++..|+...|
T Consensus 4 ~~~~~~g~~~~~~~~~~~A~~~~~~ai~~~-----p~~~~~~~~~g~~~~~~~~~~~~A~~~~~~al~l~P 69 (69)
T PF13414_consen 4 EAWYNLGQIYFQQGDYEEAIEYFEKAIELD-----PNNAEAYYNLGLAYMKLGKDYEEAIEDFEKALKLDP 69 (69)
T ss_dssp HHHHHHHHHHHHTTHHHHHHHHHHHHHHHS-----TTHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHST
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-----CCCHHHHHHHHHHHHHhCccHHHHHHHHHHHHHcCc
Confidence 345566788999999999999998752 21 234557899999999999 79999999999998543
No 37
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=94.20 E-value=5.1 Score=38.71 Aligned_cols=103 Identities=17% Similarity=0.066 Sum_probs=54.6
Q ss_pred HHHHHHHHHHhhcccHHHHHHHHHHHHHHhhhcCCcchhHHHHHHHHHHHHhhccHHHHHhhhhhcC--CCCCCChHHHH
Q psy1676 18 KCYFYHSRVHELTNNLDKVRSFLNARLRIATLRNDFEGQAVLINCLLRNYLHYNLYDQADKLVKKSA--FPENASNNEWA 95 (343)
Q Consensus 18 ~~~~y~~~~~e~~~~~~~~~~~l~~~~r~a~~~~~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~~--~p~~~~~~~~~ 95 (343)
.+++..+.++...|....+...+...+.. ++. .....+.+..+|.+.++++.|...+++.. .|. .......
T Consensus 108 ~~~~~La~~~~~~g~~~~A~~~~~~~l~~-----~~~-~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~-~~~~~~~ 180 (389)
T PRK11788 108 LALQELGQDYLKAGLLDRAEELFLQLVDE-----GDF-AEGALQQLLEIYQQEKDWQKAIDVAERLEKLGGD-SLRVEIA 180 (389)
T ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHHcC-----Ccc-hHHHHHHHHHHHHHhchHHHHHHHHHHHHHhcCC-cchHHHH
Confidence 34455555555555555554444332221 111 12334445666667777777766666431 121 1112344
Q ss_pred HHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCc
Q psy1676 96 RFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQ 127 (343)
Q Consensus 96 ~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~ 127 (343)
.|++-.|.++..++++.+|...|..++...|.
T Consensus 181 ~~~~~la~~~~~~~~~~~A~~~~~~al~~~p~ 212 (389)
T PRK11788 181 HFYCELAQQALARGDLDAARALLKKALAADPQ 212 (389)
T ss_pred HHHHHHHHHHHhCCCHHHHHHHHHHHHhHCcC
Confidence 45556677777777777777777777764443
No 38
>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=93.84 E-value=0.12 Score=38.19 Aligned_cols=47 Identities=26% Similarity=0.420 Sum_probs=36.2
Q ss_pred HHHHhhcccccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEeeCC
Q psy1676 216 IRSIGASYSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLDRE 263 (343)
Q Consensus 216 ir~i~~~ys~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~Id~~ 263 (343)
|+..-....++|+++||..++++ ++.+|.++..+|..|.|+-.-...
T Consensus 5 i~~~l~~~~~~S~~eLa~~~~~s-~~~ve~mL~~l~~kG~I~~~~~~~ 51 (69)
T PF09012_consen 5 IRDYLRERGRVSLAELAREFGIS-PEAVEAMLEQLIRKGYIRKVDMSS 51 (69)
T ss_dssp HHHHHHHS-SEEHHHHHHHTT---HHHHHHHHHHHHCCTSCEEEEEE-
T ss_pred HHHHHHHcCCcCHHHHHHHHCcC-HHHHHHHHHHHHHCCcEEEecCCC
Confidence 44444566889999999999995 999999999999999998555444
No 39
>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=93.63 E-value=4 Score=36.69 Aligned_cols=118 Identities=10% Similarity=0.059 Sum_probs=73.2
Q ss_pred cchhccc---hhHHHHHHHHHHHHHHHhhcccHHHHHHHHHHHHHHhhhcCCcchhHHHHHHHHHHHHhhccHHHHHhhh
Q psy1676 4 ITSENRR---TSDLIAAKCYFYHSRVHELTNNLDKVRSFLNARLRIATLRNDFEGQAVLINCLLRNYLHYNLYDQADKLV 80 (343)
Q Consensus 4 ~~~~~~~---~~d~~~a~~~~y~~~~~e~~~~~~~~~~~l~~~~r~a~~~~~~~~~~~l~n~Llr~yl~~~~~~~a~~li 80 (343)
|++.|+- +.|...+..+|-.+..+-..++.+.+...+-..+... ..++.. ......+...|+..++++.|...+
T Consensus 17 ~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~--p~~~~~-~~a~~~la~~~~~~~~~~~A~~~~ 93 (235)
T TIGR03302 17 CSSKKKKEADPVEEWPAEELYEEAKEALDSGDYTEAIKYFEALESRY--PFSPYA-EQAQLDLAYAYYKSGDYAEAIAAA 93 (235)
T ss_pred ccCCcccccCCcccCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCchhH-HHHHHHHHHHHHhcCCHHHHHHHH
Confidence 3444444 6667777778888888877888887777766543311 111111 122344467778888888888888
Q ss_pred hhc--CCCCCCChHHHHHHHHHHHHHHHHh--------hCHHHHHHHHHHHHhhCCc
Q psy1676 81 KKS--AFPENASNNEWARFHFYLGRIKAVR--------LEYSTAHKNLVQALRKAPQ 127 (343)
Q Consensus 81 ~k~--~~p~~~~~~~~~~Y~YY~Gri~~~~--------~~y~~A~~~L~~A~~~~~~ 127 (343)
++. ..|.+. ....-+|..|.++... +++.+|...|..++..-|.
T Consensus 94 ~~~l~~~p~~~---~~~~a~~~~g~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~p~ 147 (235)
T TIGR03302 94 DRFIRLHPNHP---DADYAYYLRGLSNYNQIDRVDRDQTAAREAFEAFQELIRRYPN 147 (235)
T ss_pred HHHHHHCcCCC---chHHHHHHHHHHHHHhcccccCCHHHHHHHHHHHHHHHHHCCC
Confidence 865 355322 1122356677777654 7788888888888874443
No 40
>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A.
Probab=93.49 E-value=2.6 Score=39.71 Aligned_cols=200 Identities=16% Similarity=0.118 Sum_probs=113.1
Q ss_pred HHHHHHHHHHHHhhcccHHHHHHHHHHHHHHhhhcCCcchhHHHHHHHHHHHHhhccHHHHHhhhhhcC--CCCCCChHH
Q psy1676 16 AAKCYFYHSRVHELTNNLDKVRSFLNARLRIATLRNDFEGQAVLINCLLRNYLHYNLYDQADKLVKKSA--FPENASNNE 93 (343)
Q Consensus 16 ~a~~~~y~~~~~e~~~~~~~~~~~l~~~~r~a~~~~~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~~--~p~~~~~~~ 93 (343)
+|-.|--=+..|...+.+..+......+-....-.+++...+........+|-+. +++.|...+.++. +-..-....
T Consensus 34 Aa~~y~~Aa~~fk~~~~~~~A~~ay~kAa~~~~~~~~~~~Aa~~~~~Aa~~~k~~-~~~~Ai~~~~~A~~~y~~~G~~~~ 112 (282)
T PF14938_consen 34 AADLYEKAANCFKLAKDWEKAAEAYEKAADCYEKLGDKFEAAKAYEEAANCYKKG-DPDEAIECYEKAIEIYREAGRFSQ 112 (282)
T ss_dssp HHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHT-THHHHHHHHHHHHHHHHHCT-HHH
T ss_pred HHHHHHHHHHHHHHHhccchhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhh-CHHHHHHHHHHHHHHHHhcCcHHH
Confidence 3445666677777788887777666655443322344444444444445555444 8888887777541 222234567
Q ss_pred HHHHHHHHHHHHHHh-hCHHHHHHHHHHHHhhCCccchHHHHHHHHHHHHHHHHhcCCCCCh-hhhh--------hHhHh
Q psy1676 94 WARFHFYLGRIKAVR-LEYSTAHKNLVQALRKAPQTAAVGFRQTTQKLAVVVELLLGDIPDR-QIFR--------QAVLR 163 (343)
Q Consensus 94 ~~~Y~YY~Gri~~~~-~~y~~A~~~L~~A~~~~~~~sa~~~~~~i~K~li~v~LL~G~iP~~-~~~~--------~~~l~ 163 (343)
..+.+.-.|.+|--. +++.+|.++|.+|...............+..-+.-+.+.+|+.+.. .++. .+.++
T Consensus 113 aA~~~~~lA~~ye~~~~d~e~Ai~~Y~~A~~~y~~e~~~~~a~~~~~~~A~l~~~l~~y~~A~~~~e~~~~~~l~~~l~~ 192 (282)
T PF14938_consen 113 AAKCLKELAEIYEEQLGDYEKAIEYYQKAAELYEQEGSPHSAAECLLKAADLYARLGRYEEAIEIYEEVAKKCLENNLLK 192 (282)
T ss_dssp HHHHHHHHHHHHCCTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTCCCHCTTG
T ss_pred HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhhcccccc
Confidence 788888999999998 9999999999999983221111122223333333445667775541 2221 11112
Q ss_pred hhhhhh--HHHHHHHHhCCHHHHHHHHHhccc---cccccccHHHHHHHHHHHHHHHH
Q psy1676 164 RALSPY--FQLTQAVRMGELQKFNEVLTTYGN---QFRTDYTFKLILRLRHNVIKTAI 216 (343)
Q Consensus 164 ~~l~~Y--~~L~~Av~~Gdl~~f~~~l~~~~~---~f~~d~~~~Lv~~l~~~v~r~~i 216 (343)
.....| ..++=.+..||+..-...++++.. .|....-+.++..|...+-..-.
T Consensus 193 ~~~~~~~l~a~l~~L~~~D~v~A~~~~~~~~~~~~~F~~s~E~~~~~~l~~A~~~~D~ 250 (282)
T PF14938_consen 193 YSAKEYFLKAILCHLAMGDYVAARKALERYCSQDPSFASSREYKFLEDLLEAYEEGDV 250 (282)
T ss_dssp HHHHHHHHHHHHHHHHTT-HHHHHHHHHHHGTTSTTSTTSHHHHHHHHHHHHHHTT-C
T ss_pred hhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCCCcHHHHHHHHHHHHHHhCCH
Confidence 223322 234445568999999999999864 46555556677777666654443
No 41
>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=93.43 E-value=0.22 Score=30.87 Aligned_cols=32 Identities=22% Similarity=0.221 Sum_probs=27.4
Q ss_pred HHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCc
Q psy1676 96 RFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQ 127 (343)
Q Consensus 96 ~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~ 127 (343)
.-+|..|.++...++|.+|..+|++|+...|.
T Consensus 2 ~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~ 33 (34)
T PF00515_consen 2 EAYYNLGNAYFQLGDYEEALEYYQRALELDPD 33 (34)
T ss_dssp HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT
T ss_pred HHHHHHHHHHHHhCCchHHHHHHHHHHHHCcC
Confidence 45789999999999999999999999996653
No 42
>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=93.16 E-value=1.7 Score=38.64 Aligned_cols=63 Identities=25% Similarity=0.408 Sum_probs=43.9
Q ss_pred HHHHHHHhCCHHHHHHHHHhccccccccccH-HHHHHHHHHHHHHHHHHHhhcccc-cChHHHHHHhCC
Q psy1676 171 QLTQAVRMGELQKFNEVLTTYGNQFRTDYTF-KLILRLRHNVIKTAIRSIGASYSR-ITPTKIAEKLGL 237 (343)
Q Consensus 171 ~L~~Av~~Gdl~~f~~~l~~~~~~f~~d~~~-~Lv~~l~~~v~r~~ir~i~~~ys~-Isl~dIa~~l~l 237 (343)
++..|+..||...|=+.++.....+ .. .++......+....++.++.+|.. ||++.+++.|++
T Consensus 140 ~l~~a~~~gny~~ff~l~~~~~~~~----l~~~l~~~~~~~iR~~al~~i~~ay~~~i~l~~l~~~L~F 204 (204)
T PF03399_consen 140 ELCRALMEGNYVRFFRLYRSKSAPY----LFACLMERFFNRIRLRALQSISKAYRSSIPLSFLAELLGF 204 (204)
T ss_dssp HHHHHH--TTHHHHHHHHT-TTS-H----HHHHHHGGGHHHHHHHHHHHHHHHS-T-EEHHHHHHHTT-
T ss_pred HHHHHHHcCCHHHHHHHHhccCCCh----HHHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCC
Confidence 6889999999999999883322211 12 345556667778888999999988 999999998874
No 43
>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=93.12 E-value=0.89 Score=33.57 Aligned_cols=70 Identities=21% Similarity=0.189 Sum_probs=56.5
Q ss_pred HHHHHHHHHHHHHHhhcccHHHHHHHHHHHHHHhhhcCCcch-hHHHHHHHHHHHHhhccHHHHHhhhhhc
Q psy1676 14 LIAAKCYFYHSRVHELTNNLDKVRSFLNARLRIATLRNDFEG-QAVLINCLLRNYLHYNLYDQADKLVKKS 83 (343)
Q Consensus 14 ~~~a~~~~y~~~~~e~~~~~~~~~~~l~~~~r~a~~~~~~~~-~~~l~n~Llr~yl~~~~~~~a~~li~k~ 83 (343)
+..|.+|+.+|.++...++.+++...+-.++......++... .+...+.+-.+|...|+++.|...+.++
T Consensus 2 ~~~a~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~a 72 (78)
T PF13424_consen 2 PDTANAYNNLARVYRELGRYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYRLGDYEEALEYYQKA 72 (78)
T ss_dssp HHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence 346889999999999999999999999999987444444333 4577778899999999999999988754
No 44
>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=92.75 E-value=2.8 Score=36.93 Aligned_cols=89 Identities=12% Similarity=0.219 Sum_probs=62.4
Q ss_pred HHHHHHHHHHhhccHHHHHhhhhhc-CCCCC-CChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCc---cchHHH
Q psy1676 59 LINCLLRNYLHYNLYDQADKLVKKS-AFPEN-ASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQ---TAAVGF 133 (343)
Q Consensus 59 l~n~Llr~yl~~~~~~~a~~li~k~-~~p~~-~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~---~sa~~~ 133 (343)
+.-.++|+++..+++....+.+.++ ..++. .+..-..+..=|.|..++.+++|.+|...|..+..-... ..-..
T Consensus 75 ~~l~~irv~i~~~d~~~v~~~i~ka~~~~~~~~d~~~~nrlk~~~gL~~l~~r~f~~AA~~fl~~~~t~~~~~~~el~s- 153 (177)
T PF10602_consen 75 MCLNVIRVAIFFGDWSHVEKYIEKAESLIEKGGDWERRNRLKVYEGLANLAQRDFKEAAELFLDSLSTFTSLQYTELIS- 153 (177)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHHhchHHHHHHHHHccCcCCCCCchhhhcC-
Confidence 3335689999999999999999976 23332 234456667889999999999999999999988773221 11111
Q ss_pred HHHHHHHHHHHHHhc
Q psy1676 134 RQTTQKLAVVVELLL 148 (343)
Q Consensus 134 ~~~i~K~li~v~LL~ 148 (343)
-.-+-.|.++|.|+.
T Consensus 154 ~~d~a~Y~~l~aLat 168 (177)
T PF10602_consen 154 YNDFAIYGGLCALAT 168 (177)
T ss_pred HHHHHHHHHHHHHHh
Confidence 334566777777753
No 45
>CHL00033 ycf3 photosystem I assembly protein Ycf3
Probab=92.70 E-value=2.7 Score=36.03 Aligned_cols=105 Identities=12% Similarity=0.008 Sum_probs=67.3
Q ss_pred HHHHHHHHHHHHhhcccHHHHHHHHHHHHHHhhhcCCcchhHHHHHHHHHHHHhhccHHHHHhhhhhc-C-CCCCC-ChH
Q psy1676 16 AAKCYFYHSRVHELTNNLDKVRSFLNARLRIATLRNDFEGQAVLINCLLRNYLHYNLYDQADKLVKKS-A-FPENA-SNN 92 (343)
Q Consensus 16 ~a~~~~y~~~~~e~~~~~~~~~~~l~~~~r~a~~~~~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~-~-~p~~~-~~~ 92 (343)
.+.+|+..+..+...+..+++...+-.++.. ..++.........+-.+|...+.++.|.....++ . .|... ...
T Consensus 34 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~l---~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~~~~~~~~~~~ 110 (168)
T CHL00033 34 EAFTYYRDGMSAQSEGEYAEALQNYYEAMRL---EIDPYDRSYILYNIGLIHTSNGEHTKALEYYFQALERNPFLPQALN 110 (168)
T ss_pred HHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc---cccchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCcHHHHH
Confidence 4667788888888888887777665544332 2222223345566688899999999999988865 2 23211 223
Q ss_pred HHHHHHHHHHHHHHHhhCHHHHHHHHHHHHh
Q psy1676 93 EWARFHFYLGRIKAVRLEYSTAHKNLVQALR 123 (343)
Q Consensus 93 ~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~ 123 (343)
.....++..|+.+...+++.+|...+..|+.
T Consensus 111 ~la~i~~~~~~~~~~~g~~~~A~~~~~~a~~ 141 (168)
T CHL00033 111 NMAVICHYRGEQAIEQGDSEIAEAWFDQAAE 141 (168)
T ss_pred HHHHHHHHhhHHHHHcccHHHHHHHHHHHHH
Confidence 4555666677777788888766666655543
No 46
>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=92.56 E-value=6.2 Score=41.32 Aligned_cols=62 Identities=16% Similarity=0.145 Sum_probs=33.0
Q ss_pred HHHHHHHHHHHHhhcccHHHHHHHHHHHHHHhhhcCCcchhHHHHHHHHHHHHhhccHHHHHhhhhhc
Q psy1676 16 AAKCYFYHSRVHELTNNLDKVRSFLNARLRIATLRNDFEGQAVLINCLLRNYLHYNLYDQADKLVKKS 83 (343)
Q Consensus 16 ~a~~~~y~~~~~e~~~~~~~~~~~l~~~~r~a~~~~~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~ 83 (343)
.+..|+..+.++...++..++...+-.++.. ++.. ..+...+-.+|+..|+++.|...+.++
T Consensus 364 ~~~~~~~la~~~~~~g~~~eA~~~~~~al~~-----~p~~-~~~~~~lg~~~~~~g~~~~A~~~~~ka 425 (615)
T TIGR00990 364 VTQSYIKRASMNLELGDPDKAEEDFDKALKL-----NSED-PDIYYHRAQLHFIKGEFAQAGKDYQKS 425 (615)
T ss_pred cHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh-----CCCC-HHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence 3455666666666666666666555544332 2222 122333445556666666666665544
No 47
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=92.34 E-value=4.6 Score=39.00 Aligned_cols=101 Identities=15% Similarity=0.074 Sum_probs=73.7
Q ss_pred HHHHHHHHHhhcccHHHHHHHHHHHHHHhhhcCCcchhHHHHHHHHHHHHhhccHHHHHhhhhhcC-CCCCCChHHHHHH
Q psy1676 19 CYFYHSRVHELTNNLDKVRSFLNARLRIATLRNDFEGQAVLINCLLRNYLHYNLYDQADKLVKKSA-FPENASNNEWARF 97 (343)
Q Consensus 19 ~~~y~~~~~e~~~~~~~~~~~l~~~~r~a~~~~~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~~-~p~~~~~~~~~~Y 97 (343)
-.|+.+..+-..+..+.+...+..+++. +|.. ......+...|+..++++.|..++++.. .|. .+.......
T Consensus 37 ~~y~~g~~~~~~~~~~~A~~~~~~al~~-----~p~~-~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~~-~~~~~~~~~ 109 (389)
T PRK11788 37 RDYFKGLNFLLNEQPDKAIDLFIEMLKV-----DPET-VELHLALGNLFRRRGEVDRAIRIHQNLLSRPD-LTREQRLLA 109 (389)
T ss_pred HHHHHHHHHHhcCChHHHHHHHHHHHhc-----Cccc-HHHHHHHHHHHHHcCcHHHHHHHHHHHhcCCC-CCHHHHHHH
Confidence 3566688888888888877777665542 3333 2345556889999999999999988652 232 223345567
Q ss_pred HHHHHHHHHHhhCHHHHHHHHHHHHhhCC
Q psy1676 98 HFYLGRIKAVRLEYSTAHKNLVQALRKAP 126 (343)
Q Consensus 98 ~YY~Gri~~~~~~y~~A~~~L~~A~~~~~ 126 (343)
++.+|.++...++|.+|...|..++...|
T Consensus 110 ~~~La~~~~~~g~~~~A~~~~~~~l~~~~ 138 (389)
T PRK11788 110 LQELGQDYLKAGLLDRAEELFLQLVDEGD 138 (389)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHHHcCCc
Confidence 78889999999999999999999998544
No 48
>PRK02603 photosystem I assembly protein Ycf3; Provisional
Probab=92.21 E-value=2.8 Score=36.18 Aligned_cols=88 Identities=13% Similarity=0.074 Sum_probs=55.3
Q ss_pred HHHHHHHHHHHHHHhhcccHHHHHHHHHHHHHHhhhcCCcchhHHHHHHHHHHHHhhccHHHHHhhhhhc-C-CCCCCCh
Q psy1676 14 LIAAKCYFYHSRVHELTNNLDKVRSFLNARLRIATLRNDFEGQAVLINCLLRNYLHYNLYDQADKLVKKS-A-FPENASN 91 (343)
Q Consensus 14 ~~~a~~~~y~~~~~e~~~~~~~~~~~l~~~~r~a~~~~~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~-~-~p~~~~~ 91 (343)
.-.|..+|..+..+...+..+++...+-.++... .++.........+-.+|.+.|+++.|...+.+. . .|.
T Consensus 32 ~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al~~~---~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~---- 104 (172)
T PRK02603 32 AKEAFVYYRDGMSAQADGEYAEALENYEEALKLE---EDPNDRSYILYNMGIIYASNGEHDKALEYYHQALELNPK---- 104 (172)
T ss_pred hhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHh---hccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcc----
Confidence 3456678888888888888888776666554421 122223345556678888999999999888765 2 232
Q ss_pred HHHHHHHHHHHHHHHHhhC
Q psy1676 92 NEWARFHFYLGRIKAVRLE 110 (343)
Q Consensus 92 ~~~~~Y~YY~Gri~~~~~~ 110 (343)
....++..|.++...++
T Consensus 105 --~~~~~~~lg~~~~~~g~ 121 (172)
T PRK02603 105 --QPSALNNIAVIYHKRGE 121 (172)
T ss_pred --cHHHHHHHHHHHHHcCC
Confidence 12334445666655544
No 49
>PRK11189 lipoprotein NlpI; Provisional
Probab=92.13 E-value=1.7 Score=41.22 Aligned_cols=100 Identities=14% Similarity=0.039 Sum_probs=75.9
Q ss_pred HHHHHHHHHHHhhcccHHHHHHHHHHHHHHhhhcCCcchhHHHHHHHHHHHHhhccHHHHHhhhhhc-C-CCCCCChHHH
Q psy1676 17 AKCYFYHSRVHELTNNLDKVRSFLNARLRIATLRNDFEGQAVLINCLLRNYLHYNLYDQADKLVKKS-A-FPENASNNEW 94 (343)
Q Consensus 17 a~~~~y~~~~~e~~~~~~~~~~~l~~~~r~a~~~~~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~-~-~p~~~~~~~~ 94 (343)
|..||..+.++...|....+...+..++. .+|.. ....+.+-..|...++++.|...+++. . -|. .
T Consensus 64 a~~~~~~g~~~~~~g~~~~A~~~~~~Al~-----l~P~~-~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~P~------~ 131 (296)
T PRK11189 64 AQLHYERGVLYDSLGLRALARNDFSQALA-----LRPDM-ADAYNYLGIYLTQAGNFDAAYEAFDSVLELDPT------Y 131 (296)
T ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHHHH-----cCCCC-HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC------C
Confidence 77899999999999998888765544333 23433 345566788999999999999988876 2 232 1
Q ss_pred HHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCcc
Q psy1676 95 ARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQT 128 (343)
Q Consensus 95 ~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~ 128 (343)
...++..|.++...++|.+|...|..++...|..
T Consensus 132 ~~a~~~lg~~l~~~g~~~eA~~~~~~al~~~P~~ 165 (296)
T PRK11189 132 NYAYLNRGIALYYGGRYELAQDDLLAFYQDDPND 165 (296)
T ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCC
Confidence 2345678999999999999999999999977754
No 50
>PRK10370 formate-dependent nitrite reductase complex subunit NrfG; Provisional
Probab=91.89 E-value=3.4 Score=36.96 Aligned_cols=100 Identities=11% Similarity=0.028 Sum_probs=68.6
Q ss_pred HHHHHHHHHHHhhcccHHHHHHHHHHHHHHhhhcCCcchhHHHHHHHHHHHHhhcc--HHHHHhhhhhcC--CCCCCChH
Q psy1676 17 AKCYFYHSRVHELTNNLDKVRSFLNARLRIATLRNDFEGQAVLINCLLRNYLHYNL--YDQADKLVKKSA--FPENASNN 92 (343)
Q Consensus 17 a~~~~y~~~~~e~~~~~~~~~~~l~~~~r~a~~~~~~~~~~~l~n~Llr~yl~~~~--~~~a~~li~k~~--~p~~~~~~ 92 (343)
+..|+.+++++-..+...++...+-.+++ .+|+......++-.-+|+..|. ++.|..++++.. -|.
T Consensus 73 ~~~w~~Lg~~~~~~g~~~~A~~a~~~Al~-----l~P~~~~~~~~lA~aL~~~~g~~~~~~A~~~l~~al~~dP~----- 142 (198)
T PRK10370 73 SEQWALLGEYYLWRNDYDNALLAYRQALQ-----LRGENAELYAALATVLYYQAGQHMTPQTREMIDKALALDAN----- 142 (198)
T ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHHHH-----hCCCCHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHhCCC-----
Confidence 45688889999888888887766644333 2344444444432224567666 588888888652 222
Q ss_pred HHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCc
Q psy1676 93 EWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQ 127 (343)
Q Consensus 93 ~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~ 127 (343)
..+.++.+|..+...++|.+|..+++.++...|.
T Consensus 143 -~~~al~~LA~~~~~~g~~~~Ai~~~~~aL~l~~~ 176 (198)
T PRK10370 143 -EVTALMLLASDAFMQADYAQAIELWQKVLDLNSP 176 (198)
T ss_pred -ChhHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCC
Confidence 2356778899999999999999999999985444
No 51
>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=91.86 E-value=6.2 Score=41.65 Aligned_cols=103 Identities=17% Similarity=0.019 Sum_probs=71.1
Q ss_pred HHHHHHHHHHHHHHhhcccHHHHHHHHHHHHHHhhhcCCcchhHHHHHHHHHHHHhhccHHHHHhhhhhc--CCCCCCCh
Q psy1676 14 LIAAKCYFYHSRVHELTNNLDKVRSFLNARLRIATLRNDFEGQAVLINCLLRNYLHYNLYDQADKLVKKS--AFPENASN 91 (343)
Q Consensus 14 ~~~a~~~~y~~~~~e~~~~~~~~~~~l~~~~r~a~~~~~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~--~~p~~~~~ 91 (343)
.-.+.+++..+.++...+....+...+-.++. .+|... .....+...++..++++.|..++.+. ..|.
T Consensus 122 ~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~-----~~~~~~-~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~---- 191 (899)
T TIGR02917 122 EGAAELLALRGLAYLGLGQLELAQKSYEQALA-----IDPRSL-YAKLGLAQLALAENRFDEARALIDEVLTADPG---- 191 (899)
T ss_pred hhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHh-----cCCCCh-hhHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC----
Confidence 34566777788887777777777665544332 122222 22334577788899999999888865 2232
Q ss_pred HHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCcc
Q psy1676 92 NEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQT 128 (343)
Q Consensus 92 ~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~ 128 (343)
....+++.|.++...+++.+|...|..++...|..
T Consensus 192 --~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~p~~ 226 (899)
T TIGR02917 192 --NVDALLLKGDLLLSLGNIELALAAYRKAIALRPNN 226 (899)
T ss_pred --ChHHHHHHHHHHHhcCCHHHHHHHHHHHHhhCCCC
Confidence 23457788999999999999999999999866643
No 52
>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=91.47 E-value=8.4 Score=33.10 Aligned_cols=97 Identities=16% Similarity=0.136 Sum_probs=72.1
Q ss_pred HHHHHHHHHHHHhhcccHHHHHHHHHHHHHHhhhcCCcchhHHHHHHHHHHHHhhccHHHHHhhhhhcC--CCCCCChHH
Q psy1676 16 AAKCYFYHSRVHELTNNLDKVRSFLNARLRIATLRNDFEGQAVLINCLLRNYLHYNLYDQADKLVKKSA--FPENASNNE 93 (343)
Q Consensus 16 ~a~~~~y~~~~~e~~~~~~~~~~~l~~~~r~a~~~~~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~~--~p~~~~~~~ 93 (343)
.+.+++..+..+-..+..+.+...+...+.. +|.. ......+...|+..++++.|...+.+.. .|.
T Consensus 30 ~~~~~~~la~~~~~~~~~~~A~~~~~~~l~~-----~p~~-~~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~------ 97 (234)
T TIGR02521 30 AAKIRVQLALGYLEQGDLEVAKENLDKALEH-----DPDD-YLAYLALALYYQQLGELEKAEDSFRRALTLNPN------ 97 (234)
T ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh-----Cccc-HHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCC------
Confidence 4677888888888889888888777655442 2332 2444556889999999999999988652 232
Q ss_pred HHHHHHHHHHHHHHhhCHHHHHHHHHHHHhh
Q psy1676 94 WARFHFYLGRIKAVRLEYSTAHKNLVQALRK 124 (343)
Q Consensus 94 ~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~ 124 (343)
....++..|.++...++|.+|...+..++..
T Consensus 98 ~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~ 128 (234)
T TIGR02521 98 NGDVLNNYGTFLCQQGKYEQAMQQFEQAIED 128 (234)
T ss_pred CHHHHHHHHHHHHHcccHHHHHHHHHHHHhc
Confidence 1134667789999999999999999999984
No 53
>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=91.21 E-value=0.41 Score=29.46 Aligned_cols=31 Identities=26% Similarity=0.337 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHHhhCHHHHHHHHHHHHhhCC
Q psy1676 96 RFHFYLGRIKAVRLEYSTAHKNLVQALRKAP 126 (343)
Q Consensus 96 ~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~ 126 (343)
..++..|.++...+++.+|..+|..|++-.|
T Consensus 2 ~~~~~lg~~y~~~~~~~~A~~~~~~a~~~~~ 32 (34)
T PF13181_consen 2 EAYYNLGKIYEQLGDYEEALEYFEKALELNP 32 (34)
T ss_dssp HHHHHHHHHHHHTTSHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHHhhCC
Confidence 5688999999999999999999999998443
No 54
>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=91.17 E-value=2.9 Score=37.55 Aligned_cols=65 Identities=15% Similarity=0.071 Sum_probs=51.3
Q ss_pred HHHHHHHHhhccHHHHHhhhhhc--CCCCCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCcc
Q psy1676 61 NCLLRNYLHYNLYDQADKLVKKS--AFPENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQT 128 (343)
Q Consensus 61 n~Llr~yl~~~~~~~a~~li~k~--~~p~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~ 128 (343)
-.+...|+..++++.|...++.. ..|.+ .....-+|..|.++...++|.+|...|..+++..|..
T Consensus 37 ~~~g~~~~~~~~~~~A~~~~~~~~~~~p~~---~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~ 103 (235)
T TIGR03302 37 YEEAKEALDSGDYTEAIKYFEALESRYPFS---PYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRLHPNH 103 (235)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHhCCCc---hhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCC
Confidence 34477899999999999999865 34532 2333347889999999999999999999999976654
No 55
>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=90.76 E-value=0.24 Score=39.44 Aligned_cols=38 Identities=21% Similarity=0.352 Sum_probs=34.5
Q ss_pred cccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEeeC
Q psy1676 224 SRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLDR 262 (343)
Q Consensus 224 s~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~Id~ 262 (343)
.=|++.+|++.|+++ .++++..|-.|+.+|.|..+||-
T Consensus 64 ~Gv~v~~I~~~l~~~-~~~v~~al~~L~~eG~IYsTiDd 101 (102)
T PF08784_consen 64 EGVHVDEIAQQLGMS-ENEVRKALDFLSNEGHIYSTIDD 101 (102)
T ss_dssp TTEEHHHHHHHSTS--HHHHHHHHHHHHHTTSEEESSST
T ss_pred CcccHHHHHHHhCcC-HHHHHHHHHHHHhCCeEecccCC
Confidence 469999999999995 99999999999999999999884
No 56
>KOG4162|consensus
Probab=90.29 E-value=1.7 Score=46.26 Aligned_cols=104 Identities=18% Similarity=0.227 Sum_probs=77.4
Q ss_pred chhHHHHHHHHHHHHHHHhhcccHHHHHHHHHHHHHHhhhcCCcchhHHHHHHHHHHHHhhccHHHHHh--hhhhc-CCC
Q psy1676 10 RTSDLIAAKCYFYHSRVHELTNNLDKVRSFLNARLRIATLRNDFEGQAVLINCLLRNYLHYNLYDQADK--LVKKS-AFP 86 (343)
Q Consensus 10 ~~~d~~~a~~~~y~~~~~e~~~~~~~~~~~l~~~~r~a~~~~~~~~~~~l~n~Llr~yl~~~~~~~a~~--li~k~-~~p 86 (343)
+.+|++.+.+||--++.++..+.+.++...++.++- -||+..-.+. -+-.++++.|+...|.. +++.+ ...
T Consensus 677 ~~~~~l~~~~~~~~G~~~~~~~~~~EA~~af~~Al~-----ldP~hv~s~~-Ala~~lle~G~~~la~~~~~L~dalr~d 750 (799)
T KOG4162|consen 677 SKIDPLSASVYYLRGLLLEVKGQLEEAKEAFLVALA-----LDPDHVPSMT-ALAELLLELGSPRLAEKRSLLSDALRLD 750 (799)
T ss_pred HhcchhhHHHHHHhhHHHHHHHhhHHHHHHHHHHHh-----cCCCCcHHHH-HHHHHHHHhCCcchHHHHHHHHHHHhhC
Confidence 356788899999999999999998888876655433 3555543333 34778889999888887 77644 221
Q ss_pred CCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhh
Q psy1676 87 ENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRK 124 (343)
Q Consensus 87 ~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~ 124 (343)
. .+ -.-.||+|.+...+|+...|-++|+.|+..
T Consensus 751 p--~n---~eaW~~LG~v~k~~Gd~~~Aaecf~aa~qL 783 (799)
T KOG4162|consen 751 P--LN---HEAWYYLGEVFKKLGDSKQAAECFQAALQL 783 (799)
T ss_pred C--CC---HHHHHHHHHHHHHccchHHHHHHHHHHHhh
Confidence 1 11 123789999999999999999999999984
No 57
>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=90.23 E-value=4.3 Score=34.98 Aligned_cols=103 Identities=18% Similarity=0.135 Sum_probs=73.7
Q ss_pred HHHHHHHHHHHHhhcccHHHHHHHHHHHHHHhhhcCCcchhHHHHHHHHHHHHhhccHHHHHhhhhhcC-CCCCCChHHH
Q psy1676 16 AAKCYFYHSRVHELTNNLDKVRSFLNARLRIATLRNDFEGQAVLINCLLRNYLHYNLYDQADKLVKKSA-FPENASNNEW 94 (343)
Q Consensus 16 ~a~~~~y~~~~~e~~~~~~~~~~~l~~~~r~a~~~~~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~~-~p~~~~~~~~ 94 (343)
.+.+++..+.++...+...++...+-..+.. ++.. ......+-..|+..++++.|...+.++. .+. ....
T Consensus 64 ~~~~~~~la~~~~~~~~~~~A~~~~~~al~~-----~~~~-~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~~---~~~~ 134 (234)
T TIGR02521 64 DYLAYLALALYYQQLGELEKAEDSFRRALTL-----NPNN-GDVLNNYGTFLCQQGKYEQAMQQFEQAIEDPL---YPQP 134 (234)
T ss_pred cHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh-----CCCC-HHHHHHHHHHHHHcccHHHHHHHHHHHHhccc---cccc
Confidence 3556777888888888888887776655542 1221 2344455788899999999999998762 221 1222
Q ss_pred HHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCc
Q psy1676 95 ARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQ 127 (343)
Q Consensus 95 ~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~ 127 (343)
....+..|.++...+++.+|...|..++...|.
T Consensus 135 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~ 167 (234)
T TIGR02521 135 ARSLENAGLCALKAGDFDKAEKYLTRALQIDPQ 167 (234)
T ss_pred hHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcC
Confidence 344566899999999999999999999986554
No 58
>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=89.88 E-value=2.2 Score=40.73 Aligned_cols=90 Identities=23% Similarity=0.194 Sum_probs=49.1
Q ss_pred HHHHHHHHHHHhhccHHHHHhhhhhc-CCCCCCChH----------------HH---------------HHHHHHHHHHH
Q psy1676 58 VLINCLLRNYLHYNLYDQADKLVKKS-AFPENASNN----------------EW---------------ARFHFYLGRIK 105 (343)
Q Consensus 58 ~l~n~Llr~yl~~~~~~~a~~li~k~-~~p~~~~~~----------------~~---------------~~Y~YY~Gri~ 105 (343)
-...+.+.+|++.|.+++|.+.+++. .+.+..... +- ..=..-.+..+
T Consensus 132 E~~al~Vqi~L~~~R~dlA~k~l~~~~~~~eD~~l~qLa~awv~l~~g~e~~~~A~y~f~El~~~~~~t~~~lng~A~~~ 211 (290)
T PF04733_consen 132 ELLALAVQILLKMNRPDLAEKELKNMQQIDEDSILTQLAEAWVNLATGGEKYQDAFYIFEELSDKFGSTPKLLNGLAVCH 211 (290)
T ss_dssp HHHHHHHHHHHHTT-HHHHHHHHHHHHCCSCCHHHHHHHHHHHHHHHTTTCCCHHHHHHHHHHCCS--SHHHHHHHHHHH
T ss_pred cHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhCchhHHHHHHHHHHHHhccCCCHHHHHHHHHHH
Confidence 34456678999999999999998864 222110000 11 11122344566
Q ss_pred HHhhCHHHHHHHHHHHHhhCCccchHHHHHHHHHHHHHHHHhcCCCCC
Q psy1676 106 AVRLEYSTAHKNLVQALRKAPQTAAVGFRQTTQKLAVVVELLLGDIPD 153 (343)
Q Consensus 106 ~~~~~y~~A~~~L~~A~~~~~~~sa~~~~~~i~K~li~v~LL~G~iP~ 153 (343)
+.+++|.+|...|.+|+..-|.. . ..+--++++..++|+-++
T Consensus 212 l~~~~~~eAe~~L~~al~~~~~~--~----d~LaNliv~~~~~gk~~~ 253 (290)
T PF04733_consen 212 LQLGHYEEAEELLEEALEKDPND--P----DTLANLIVCSLHLGKPTE 253 (290)
T ss_dssp HHCT-HHHHHHHHHHHCCC-CCH--H----HHHHHHHHHHHHTT-TCH
T ss_pred HHhCCHHHHHHHHHHHHHhccCC--H----HHHHHHHHHHHHhCCChh
Confidence 66777777777777777643332 1 133446667777777543
No 59
>PRK12370 invasion protein regulator; Provisional
Probab=89.54 E-value=28 Score=36.05 Aligned_cols=180 Identities=16% Similarity=0.061 Sum_probs=95.6
Q ss_pred HHHHHHHhhccHHHHHhhhhhc--CCCCCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCccchHHHHHHHHH
Q psy1676 62 CLLRNYLHYNLYDQADKLVKKS--AFPENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQTAAVGFRQTTQK 139 (343)
Q Consensus 62 ~Llr~yl~~~~~~~a~~li~k~--~~p~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~sa~~~~~~i~K 139 (343)
.+-.++...++++.|...+++. ..|. ....+|+.|.++...+++.+|..++..|++..|...... .
T Consensus 343 ~lg~~~~~~g~~~~A~~~~~~Al~l~P~------~~~a~~~lg~~l~~~G~~~eAi~~~~~Al~l~P~~~~~~----~-- 410 (553)
T PRK12370 343 LLGLINTIHSEYIVGSLLFKQANLLSPI------SADIKYYYGWNLFMAGQLEEALQTINECLKLDPTRAAAG----I-- 410 (553)
T ss_pred HHHHHHHHccCHHHHHHHHHHHHHhCCC------CHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCChhhH----H--
Confidence 3456778899999999999875 2232 123467889999999999999999999999666531111 1
Q ss_pred HHHHHHHhcCCCCCh-hhhhhHhHhh----hhhhhHHHHHHH-HhCCHHHHHHHHHhccccccccccH-HHH----H---
Q psy1676 140 LAVVVELLLGDIPDR-QIFRQAVLRR----ALSPYFQLTQAV-RMGELQKFNEVLTTYGNQFRTDYTF-KLI----L--- 205 (343)
Q Consensus 140 ~li~v~LL~G~iP~~-~~~~~~~l~~----~l~~Y~~L~~Av-~~Gdl~~f~~~l~~~~~~f~~d~~~-~Lv----~--- 205 (343)
+...+....|+.... ..+. ..+.. .-..+..+..++ ..|+..+-...+.+.....-.+... ..+ .
T Consensus 411 ~~~~~~~~~g~~eeA~~~~~-~~l~~~~p~~~~~~~~la~~l~~~G~~~eA~~~~~~~~~~~~~~~~~~~~l~~~~~~~g 489 (553)
T PRK12370 411 TKLWITYYHTGIDDAIRLGD-ELRSQHLQDNPILLSMQVMFLSLKGKHELARKLTKEISTQEITGLIAVNLLYAEYCQNS 489 (553)
T ss_pred HHHHHHHhccCHHHHHHHHH-HHHHhccccCHHHHHHHHHHHHhCCCHHHHHHHHHHhhhccchhHHHHHHHHHHHhccH
Confidence 111224456764321 1111 11110 111234455555 5788777776665543322111110 111 0
Q ss_pred HHHHHHHHHHHHHHhhcccccChHHHHHHhCCCCHHHHHHHHHHhHHcCCc
Q psy1676 206 RLRHNVIKTAIRSIGASYSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVI 256 (343)
Q Consensus 206 ~l~~~v~r~~ir~i~~~ys~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I 256 (343)
.--...++.+++....-+. .....+....+-+..+-+....+++.+|.+
T Consensus 490 ~~a~~~l~~ll~~~~~~~~--~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~ 538 (553)
T PRK12370 490 ERALPTIREFLESEQRIDN--NPGLLPLVLVAHGEAIAEKMWNKFKNEDNI 538 (553)
T ss_pred HHHHHHHHHHHHHhhHhhc--CchHHHHHHHHHhhhHHHHHHHHhhccchH
Confidence 0111223333333332221 122233332222456777777999998877
No 60
>PF13429 TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2_B.
Probab=89.33 E-value=5.4 Score=37.05 Aligned_cols=101 Identities=21% Similarity=0.218 Sum_probs=69.1
Q ss_pred HHHHHHHHHHHHhhcccHHHHHHHHHHHHHHhhhcCCcchhHHHHHHHHHHHHhhccHHHHHhhhhhc--CCCCCCChHH
Q psy1676 16 AAKCYFYHSRVHELTNNLDKVRSFLNARLRIATLRNDFEGQAVLINCLLRNYLHYNLYDQADKLVKKS--AFPENASNNE 93 (343)
Q Consensus 16 ~a~~~~y~~~~~e~~~~~~~~~~~l~~~~r~a~~~~~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~--~~p~~~~~~~ 93 (343)
.+.+|+.++.+++..|...++...+-.+++. +|+.. .+.+.++..++..++++.+..+++.. ..|.+.
T Consensus 145 ~~~~~~~~a~~~~~~G~~~~A~~~~~~al~~-----~P~~~-~~~~~l~~~li~~~~~~~~~~~l~~~~~~~~~~~---- 214 (280)
T PF13429_consen 145 SARFWLALAEIYEQLGDPDKALRDYRKALEL-----DPDDP-DARNALAWLLIDMGDYDEAREALKRLLKAAPDDP---- 214 (280)
T ss_dssp -HHHHHHHHHHHHHCCHHHHHHHHHHHHHHH------TT-H-HHHHHHHHHHCTTCHHHHHHHHHHHHHHH-HTSC----
T ss_pred CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc-----CCCCH-HHHHHHHHHHHHCCChHHHHHHHHHHHHHCcCHH----
Confidence 3567888999999999988888666554442 34332 34555677888999999888887743 122211
Q ss_pred HHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCcc
Q psy1676 94 WARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQT 128 (343)
Q Consensus 94 ~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~ 128 (343)
.+....|..+...+++.+|..+|..++...|.+
T Consensus 215 --~~~~~la~~~~~lg~~~~Al~~~~~~~~~~p~d 247 (280)
T PF13429_consen 215 --DLWDALAAAYLQLGRYEEALEYLEKALKLNPDD 247 (280)
T ss_dssp --CHCHHHHHHHHHHT-HHHHHHHHHHHHHHSTT-
T ss_pred --HHHHHHHHHhccccccccccccccccccccccc
Confidence 134456999999999999999999999966654
No 61
>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=89.26 E-value=2.2 Score=30.31 Aligned_cols=61 Identities=23% Similarity=0.231 Sum_probs=47.8
Q ss_pred HHHHHHHhhccHHHHHhhhhhc--CCCCCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCcc
Q psy1676 62 CLLRNYLHYNLYDQADKLVKKS--AFPENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQT 128 (343)
Q Consensus 62 ~Llr~yl~~~~~~~a~~li~k~--~~p~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~ 128 (343)
.+...++..++++.|...+... ..|. .. ..++..|.++...+++.+|..+|..++...|..
T Consensus 5 ~~a~~~~~~~~~~~A~~~~~~~~~~~~~----~~--~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~ 67 (100)
T cd00189 5 NLGNLYYKLGDYDEALEYYEKALELDPD----NA--DAYYNLAAAYYKLGKYEEALEDYEKALELDPDN 67 (100)
T ss_pred HHHHHHHHHhcHHHHHHHHHHHHhcCCc----cH--HHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcc
Confidence 3467788899999999998865 2232 11 567889999999999999999999999865543
No 62
>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=89.18 E-value=5.3 Score=42.18 Aligned_cols=103 Identities=17% Similarity=0.132 Sum_probs=63.0
Q ss_pred HHHHHHHHHHHHHhhcccHHHHHHHHHHHHHHhhhcCCcchhHHHHHHHHHHHHhhccHHHHHhhhhhcCCCCCCChHHH
Q psy1676 15 IAAKCYFYHSRVHELTNNLDKVRSFLNARLRIATLRNDFEGQAVLINCLLRNYLHYNLYDQADKLVKKSAFPENASNNEW 94 (343)
Q Consensus 15 ~~a~~~~y~~~~~e~~~~~~~~~~~l~~~~r~a~~~~~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~~~p~~~~~~~~ 94 (343)
-.+.++|+.+.++...|..+++...+-.+... .+.. ......+.+.|...|+++.|...+.+.... +....
T Consensus 54 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~-----~~~~-~~~~~~~a~~~~~~g~~~~a~~~~~~~~~~---~~~~~ 124 (899)
T TIGR02917 54 NDAEARFLLGKIYLALGDYAAAEKELRKALSL-----GYPK-NQVLPLLARAYLLQGKFQQVLDELPGKTLL---DDEGA 124 (899)
T ss_pred CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc-----CCCh-hhhHHHHHHHHHHCCCHHHHHHhhcccccC---Cchhh
Confidence 35568999999999999998888776554431 1111 122234456677777777776666543211 12334
Q ss_pred HHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCC
Q psy1676 95 ARFHFYLGRIKAVRLEYSTAHKNLVQALRKAP 126 (343)
Q Consensus 95 ~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~ 126 (343)
...++..|..+...++|.+|...|..++...|
T Consensus 125 ~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~ 156 (899)
T TIGR02917 125 AELLALRGLAYLGLGQLELAQKSYEQALAIDP 156 (899)
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCC
Confidence 45566667766666777777777776666444
No 63
>KOG1840|consensus
Probab=89.06 E-value=9.6 Score=39.34 Aligned_cols=144 Identities=15% Similarity=0.090 Sum_probs=102.8
Q ss_pred cchhHHHHHHHHHHHHHHHhhcccHHHHHHHHHHHHHHhhhcC--CcchhHHHHHHHHHHHHhhccHHHHHhhhhhc-CC
Q psy1676 9 RRTSDLIAAKCYFYHSRVHELTNNLDKVRSFLNARLRIATLRN--DFEGQAVLINCLLRNYLHYNLYDQADKLVKKS-AF 85 (343)
Q Consensus 9 ~~~~d~~~a~~~~y~~~~~e~~~~~~~~~~~l~~~~r~a~~~~--~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~-~~ 85 (343)
..--|+-...+.=|.+..+...++++.+.+..-.++|..+-+. +..-.+...+.+-..|...++|.+|.++..++ ++
T Consensus 191 ~~~~~P~~~~~~~~La~~y~~~g~~e~A~~l~k~Al~~l~k~~G~~hl~va~~l~~~a~~y~~~~k~~eAv~ly~~AL~i 270 (508)
T KOG1840|consen 191 LGDEDPERLRTLRNLAEMYAVQGRLEKAEPLCKQALRILEKTSGLKHLVVASMLNILALVYRSLGKYDEAVNLYEEALTI 270 (508)
T ss_pred cccCCchHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHccCccCHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHH
Confidence 3334555666677799999999999999999888888765542 33445577788889999999999999999975 33
Q ss_pred CC---CCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHh---hCCccchHHHHHHHHHHHHHHHHhcCCCCC
Q psy1676 86 PE---NASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALR---KAPQTAAVGFRQTTQKLAVVVELLLGDIPD 153 (343)
Q Consensus 86 p~---~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~---~~~~~sa~~~~~~i~K~li~v~LL~G~iP~ 153 (343)
++ ...+..++..+-=+|..|..+++|.+|..++..|+. +-+..+ .+-+...+..+..+.-++|+.-+
T Consensus 271 ~e~~~G~~h~~va~~l~nLa~ly~~~GKf~EA~~~~e~Al~I~~~~~~~~-~~~v~~~l~~~~~~~~~~~~~Ee 343 (508)
T KOG1840|consen 271 REEVFGEDHPAVAATLNNLAVLYYKQGKFAEAEEYCERALEIYEKLLGAS-HPEVAAQLSELAAILQSMNEYEE 343 (508)
T ss_pred HHHhcCCCCHHHHHHHHHHHHHHhccCChHHHHHHHHHHHHHHHHhhccC-hHHHHHHHHHHHHHHHHhcchhH
Confidence 32 134567788888888888999999999999999998 211112 22244455555555555666444
No 64
>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A.
Probab=88.81 E-value=0.75 Score=27.81 Aligned_cols=30 Identities=17% Similarity=0.258 Sum_probs=26.9
Q ss_pred HHHHHHHHHHhhCHHHHHHHHHHHHhhCCc
Q psy1676 98 HFYLGRIKAVRLEYSTAHKNLVQALRKAPQ 127 (343)
Q Consensus 98 ~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~ 127 (343)
+|..|+++...+++.+|...|+..+...|.
T Consensus 3 ~~~~a~~~~~~g~~~~A~~~~~~~~~~~P~ 32 (33)
T PF13174_consen 3 LYRLARCYYKLGDYDEAIEYFQRLIKRYPD 32 (33)
T ss_dssp HHHHHHHHHHHCHHHHHHHHHHHHHHHSTT
T ss_pred HHHHHHHHHHccCHHHHHHHHHHHHHHCcC
Confidence 578999999999999999999999997664
No 65
>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=88.22 E-value=8 Score=40.50 Aligned_cols=104 Identities=13% Similarity=0.040 Sum_probs=77.8
Q ss_pred HHHHHHHHHHHHHHHhhcccHHHHHHHHHHHHHHhhhcCCcchhHHHHHHHHHHHHhhccHHHHHhhhhhc-C-CCCCCC
Q psy1676 13 DLIAAKCYFYHSRVHELTNNLDKVRSFLNARLRIATLRNDFEGQAVLINCLLRNYLHYNLYDQADKLVKKS-A-FPENAS 90 (343)
Q Consensus 13 d~~~a~~~~y~~~~~e~~~~~~~~~~~l~~~~r~a~~~~~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~-~-~p~~~~ 90 (343)
++-.+-+|++.+.++...|+.+++...+-.++.. +|... .....+-.+|+..++++.|...+.+. . .|.
T Consensus 327 ~~~~a~a~~~lg~~~~~~g~~~eA~~~~~kal~l-----~P~~~-~~~~~la~~~~~~g~~~eA~~~~~~al~~~p~--- 397 (615)
T TIGR00990 327 GEKEAIALNLRGTFKCLKGKHLEALADLSKSIEL-----DPRVT-QSYIKRASMNLELGDPDKAEEDFDKALKLNSE--- 397 (615)
T ss_pred ChhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc-----CCCcH-HHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC---
Confidence 4556778999999999999999888777655432 33322 22334467788999999999999875 2 232
Q ss_pred hHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCcc
Q psy1676 91 NNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQT 128 (343)
Q Consensus 91 ~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~ 128 (343)
....+|..|.++...++|.+|..+|..|+...|..
T Consensus 398 ---~~~~~~~lg~~~~~~g~~~~A~~~~~kal~l~P~~ 432 (615)
T TIGR00990 398 ---DPDIYYHRAQLHFIKGEFAQAGKDYQKSIDLDPDF 432 (615)
T ss_pred ---CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCccC
Confidence 13457889999999999999999999999966653
No 66
>PRK15174 Vi polysaccharide export protein VexE; Provisional
Probab=88.04 E-value=5.9 Score=42.08 Aligned_cols=257 Identities=12% Similarity=0.026 Sum_probs=129.0
Q ss_pred HHHHHHHHHHHhhcccHHHHHHHHHHHHHHhhhcCCcchhHHHHHHHHHHHHhhccHHHHHhhhhhcC--CCCCCChHHH
Q psy1676 17 AKCYFYHSRVHELTNNLDKVRSFLNARLRIATLRNDFEGQAVLINCLLRNYLHYNLYDQADKLVKKSA--FPENASNNEW 94 (343)
Q Consensus 17 a~~~~y~~~~~e~~~~~~~~~~~l~~~~r~a~~~~~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~~--~p~~~~~~~~ 94 (343)
+.++..++.++...++.+++...+-..++. +|+.. .+...+...|.+.++++.|...+.+.. -|. .
T Consensus 284 ~~a~~~lg~~l~~~g~~~eA~~~l~~al~l-----~P~~~-~a~~~La~~l~~~G~~~eA~~~l~~al~~~P~------~ 351 (656)
T PRK15174 284 VRIVTLYADALIRTGQNEKAIPLLQQSLAT-----HPDLP-YVRAMYARALRQVGQYTAASDEFVQLAREKGV------T 351 (656)
T ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHHHHh-----CCCCH-HHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcc------c
Confidence 445666666666666666666554433321 23322 233345677778888888887776542 221 2
Q ss_pred HHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCccchHHHHHHHHHHHHHHHHhcCCCCCh----------------hhhh
Q psy1676 95 ARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQTAAVGFRQTTQKLAVVVELLLGDIPDR----------------QIFR 158 (343)
Q Consensus 95 ~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~sa~~~~~~i~K~li~v~LL~G~iP~~----------------~~~~ 158 (343)
..+.++.|..+...+++.+|...|..+++..|......|.+++..|-=..... +.-+.. ..+.
T Consensus 352 ~~~~~~~a~al~~~G~~deA~~~l~~al~~~P~~~~~~~~ea~~~~~~~~~~~-~~~~~~~~W~~~~~~~~~~~~~~~~~ 430 (656)
T PRK15174 352 SKWNRYAAAALLQAGKTSEAESVFEHYIQARASHLPQSFEEGLLALDGQISAV-NLPPERLDWAWEVAGRQSGIERDEWE 430 (656)
T ss_pred hHHHHHHHHHHHHCCCHHHHHHHHHHHHHhChhhchhhHHHHHHHHHHHHHhc-CCccchhhHHHHHhcccccCChHHHH
Confidence 24566678888899999999999999999766543344555554433222211 211111 1111
Q ss_pred hHh----H-hh-hhhhh--------HHHHHHHHh-CCHHHHHHHHHhccccccccccHHHHHHHHHHHHHHHHHHHhhcc
Q psy1676 159 QAV----L-RR-ALSPY--------FQLTQAVRM-GELQKFNEVLTTYGNQFRTDYTFKLILRLRHNVIKTAIRSIGASY 223 (343)
Q Consensus 159 ~~~----l-~~-~l~~Y--------~~L~~Av~~-Gdl~~f~~~l~~~~~~f~~d~~~~Lv~~l~~~v~r~~ir~i~~~y 223 (343)
.+. + .. .+.|. ..+..-++- |.-..+.+.+.+.+..+.--+-++-++-+-..+-..+ ..+...|
T Consensus 431 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~kgvi~~t~H~gnwE~~~~~~~~~~-~~~~~i~ 509 (656)
T PRK15174 431 RRAKWGYLADNFLLDWLECRGEQADEPMYRLADISHVEQFFQRLQLDQRGCIIVSAHLGAMYAGPMILSLLE-MNSKWVA 509 (656)
T ss_pred HHHHhhHHHHHHHHHHHHhcccchhhHHHHHhhhhhHHHHHHHHHhcCCCEEEEecCcchhhHHHHHHHHcC-CCceeee
Confidence 110 0 00 01111 123332332 3233377777777665555555555554333222221 1344556
Q ss_pred cccChHHHHHHhCCC--C-----HHHHHHHHHHhHHcCCceEEe-eCCCceEEEccCccccccccchHHHHHHHHH
Q psy1676 224 SRITPTKIAEKLGLE--S-----PEDAEFIIAKAIRDGVIEATL-DREKGYMQSKESADIYCTVEPQLAFHQRIAF 291 (343)
Q Consensus 224 s~Isl~dIa~~l~l~--s-----~~e~E~ila~lI~~G~I~a~I-d~~~g~v~~~~~~~v~s~~ep~~~~~~rI~~ 291 (343)
..+.. +-.+.|.. + ....-.-+.+.+.+|.+-|.+ ||.-| ...-.++-|+.+-+++..-.+|+.
T Consensus 510 r~~~~--~R~~~g~~~i~~~~~~~~~~~r~i~~aLk~g~~v~il~Dq~~~--~~~~~v~FfG~~a~~~~g~~~lA~ 581 (656)
T PRK15174 510 STPGV--LKGGYGERLISVSDKSEADVVRACMQTLHSGQSLVVAIDGALN--LSAPTIDFFGQQITYSTFCSRLAW 581 (656)
T ss_pred cchHH--HHHhcCCceeccCCCCcchHHHHHHHHHHcCCeEEEEeCCCCC--CCCceeccCCCccCcCcHHHHHHH
Confidence 55542 33443321 1 123334477778888877766 44322 011223344554555555556554
No 67
>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=86.64 E-value=5.3 Score=39.87 Aligned_cols=90 Identities=20% Similarity=0.118 Sum_probs=60.0
Q ss_pred HHHHHHHHhhcccHHHHHHHHHHHHHHhhhcCCcchhHHHHHHHHHHHHhhccHHHHHhhhhhcCCCCCCChHHHHHHHH
Q psy1676 20 YFYHSRVHELTNNLDKVRSFLNARLRIATLRNDFEGQAVLINCLLRNYLHYNLYDQADKLVKKSAFPENASNNEWARFHF 99 (343)
Q Consensus 20 ~~y~~~~~e~~~~~~~~~~~l~~~~r~a~~~~~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~~~p~~~~~~~~~~Y~Y 99 (343)
.+..++++-..+.-.++...+..++. .+|.. +.+++...+.++..++|+.|..+.+++.-- + +.-.+..|
T Consensus 203 ~~~LA~v~l~~~~E~~AI~ll~~aL~-----~~p~d-~~LL~~Qa~fLl~k~~~~lAL~iAk~av~l---s-P~~f~~W~ 272 (395)
T PF09295_consen 203 AVLLARVYLLMNEEVEAIRLLNEALK-----ENPQD-SELLNLQAEFLLSKKKYELALEIAKKAVEL---S-PSEFETWY 272 (395)
T ss_pred HHHHHHHHHhcCcHHHHHHHHHHHHH-----hCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHHh---C-chhHHHHH
Confidence 44455555455544555566655552 12222 677777789999999999999998876321 1 23345567
Q ss_pred HHHHHHHHhhCHHHHHHHHH
Q psy1676 100 YLGRIKAVRLEYSTAHKNLV 119 (343)
Q Consensus 100 Y~Gri~~~~~~y~~A~~~L~ 119 (343)
+++.+|+..++|++|...+.
T Consensus 273 ~La~~Yi~~~d~e~ALlaLN 292 (395)
T PF09295_consen 273 QLAECYIQLGDFENALLALN 292 (395)
T ss_pred HHHHHHHhcCCHHHHHHHHh
Confidence 79999999999999986555
No 68
>KOG2002|consensus
Probab=86.44 E-value=4.3 Score=44.34 Aligned_cols=69 Identities=17% Similarity=0.260 Sum_probs=54.1
Q ss_pred HHHHHHHHHHHhhccHHHHHhhhhhcCCCCCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCc
Q psy1676 58 VLINCLLRNYLHYNLYDQADKLVKKSAFPENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQ 127 (343)
Q Consensus 58 ~l~n~Llr~yl~~~~~~~a~~li~k~~~p~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~ 127 (343)
++.|.|...|+..++|..|-.+-....- .+...+....=+|..||-|=.+|+|.+|+.+|++|....+.
T Consensus 271 ~~l~~LAn~fyfK~dy~~v~~la~~ai~-~t~~~~~~aes~Y~~gRs~Ha~Gd~ekA~~yY~~s~k~~~d 339 (1018)
T KOG2002|consen 271 VALNHLANHFYFKKDYERVWHLAEHAIK-NTENKSIKAESFYQLGRSYHAQGDFEKAFKYYMESLKADND 339 (1018)
T ss_pred HHHHHHHHHHhhcccHHHHHHHHHHHHH-hhhhhHHHHHHHHHHHHHHHhhccHHHHHHHHHHHHccCCC
Confidence 6677778889999999999888765411 11234566777999999999999999999999999984443
No 69
>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=86.33 E-value=9.6 Score=36.30 Aligned_cols=96 Identities=9% Similarity=-0.015 Sum_probs=54.1
Q ss_pred HHHHHHHHhhcccHHHHHHHHHHHHHHhhhcCCcchhHHHHHHHHHHHHhhccHHHHHhhhhhcC--CCCCCChHHHHHH
Q psy1676 20 YFYHSRVHELTNNLDKVRSFLNARLRIATLRNDFEGQAVLINCLLRNYLHYNLYDQADKLVKKSA--FPENASNNEWARF 97 (343)
Q Consensus 20 ~~y~~~~~e~~~~~~~~~~~l~~~~r~a~~~~~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~~--~p~~~~~~~~~~Y 97 (343)
...++.++...|.+.++...+-..+. . +|.. ......+-.+|...|.++.|...+.+.. .|. +....+..
T Consensus 117 ~~~~a~~~~~~G~~~~A~~~~~~al~----~-~p~~-~~~~~~la~i~~~~g~~~eA~~~l~~~l~~~~~--~~~~~~~~ 188 (355)
T cd05804 117 LGMLAFGLEEAGQYDRAEEAARRALE----L-NPDD-AWAVHAVAHVLEMQGRFKEGIAFMESWRDTWDC--SSMLRGHN 188 (355)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHh----h-CCCC-cHHHHHHHHHHHHcCCHHHHHHHHHhhhhccCC--CcchhHHH
Confidence 34455666666666665544433332 1 1221 2334445667777777777777776541 121 11223344
Q ss_pred HHHHHHHHHHhhCHHHHHHHHHHHHh
Q psy1676 98 HFYLGRIKAVRLEYSTAHKNLVQALR 123 (343)
Q Consensus 98 ~YY~Gri~~~~~~y~~A~~~L~~A~~ 123 (343)
++..|+++..+|++.+|...|..++.
T Consensus 189 ~~~la~~~~~~G~~~~A~~~~~~~~~ 214 (355)
T cd05804 189 WWHLALFYLERGDYEAALAIYDTHIA 214 (355)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHHhc
Confidence 55677777777777777777777764
No 70
>PRK10803 tol-pal system protein YbgF; Provisional
Probab=86.26 E-value=24 Score=33.19 Aligned_cols=105 Identities=14% Similarity=0.041 Sum_probs=66.8
Q ss_pred HHHHHHHHHHHhh-cccHHHHHHHHHHHHHHhhhcCCcchhH-HHHHHHHHHHHhhccHHHHHhhhhhc--CCCCCCChH
Q psy1676 17 AKCYFYHSRVHEL-TNNLDKVRSFLNARLRIATLRNDFEGQA-VLINCLLRNYLHYNLYDQADKLVKKS--AFPENASNN 92 (343)
Q Consensus 17 a~~~~y~~~~~e~-~~~~~~~~~~l~~~~r~a~~~~~~~~~~-~l~n~Llr~yl~~~~~~~a~~li~k~--~~p~~~~~~ 92 (343)
++.+|..+...-+ .+....+...+ +...-.+.....+ ...-.+-..|+..++|+.|...+.+. .+|.+.
T Consensus 142 e~~~Y~~A~~l~~~~~~y~~Ai~af----~~fl~~yP~s~~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP~s~--- 214 (263)
T PRK10803 142 ANTDYNAAIALVQDKSRQDDAIVAF----QNFVKKYPDSTYQPNANYWLGQLNYNKGKKDDAAYYFASVVKNYPKSP--- 214 (263)
T ss_pred HHHHHHHHHHHHHhcCCHHHHHHHH----HHHHHHCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCc---
Confidence 4667777665432 35666665444 3222222222221 22335667888999999999888876 366532
Q ss_pred HHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCcc
Q psy1676 93 EWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQT 128 (343)
Q Consensus 93 ~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~ 128 (343)
....-+|..|.++...+++.+|...|+.++...|..
T Consensus 215 ~~~dAl~klg~~~~~~g~~~~A~~~~~~vi~~yP~s 250 (263)
T PRK10803 215 KAADAMFKVGVIMQDKGDTAKAKAVYQQVIKKYPGT 250 (263)
T ss_pred chhHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCC
Confidence 223336678888888899999999999888876654
No 71
>PF12688 TPR_5: Tetratrico peptide repeat
Probab=85.87 E-value=18 Score=29.76 Aligned_cols=114 Identities=16% Similarity=0.144 Sum_probs=77.0
Q ss_pred HHHHHHHHHHHhhcccHHHHHHHHHHHHHHhhhcCCcchhHHHHHHHHHHHHhhccHHHHHhhhhhc--CCCCCCChHHH
Q psy1676 17 AKCYFYHSRVHELTNNLDKVRSFLNARLRIATLRNDFEGQAVLINCLLRNYLHYNLYDQADKLVKKS--AFPENASNNEW 94 (343)
Q Consensus 17 a~~~~y~~~~~e~~~~~~~~~~~l~~~~r~a~~~~~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~--~~p~~~~~~~~ 94 (343)
+++.|..+.++...|+-+++.+..-.++.. -+. .....-..-.+-..|-..|.++.|..++++. .+|. ...+..
T Consensus 1 ~~~~~~~A~a~d~~G~~~~Ai~~Y~~Al~~-gL~--~~~~~~a~i~lastlr~LG~~deA~~~L~~~~~~~p~-~~~~~~ 76 (120)
T PF12688_consen 1 PRALYELAWAHDSLGREEEAIPLYRRALAA-GLS--GADRRRALIQLASTLRNLGRYDEALALLEEALEEFPD-DELNAA 76 (120)
T ss_pred CchHHHHHHHHHhcCCHHHHHHHHHHHHHc-CCC--chHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCC-ccccHH
Confidence 367899999999999988888766555441 111 1111222224578889999999999999975 5664 223455
Q ss_pred HHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCccchHHHHHHHHHH
Q psy1676 95 ARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQTAAVGFRQTTQKL 140 (343)
Q Consensus 95 ~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~sa~~~~~~i~K~ 140 (343)
++++ .++.....+++.+|...+..++.+.. ..+.+++.-|
T Consensus 77 l~~f--~Al~L~~~gr~~eAl~~~l~~la~~~----~~y~ra~~~y 116 (120)
T PF12688_consen 77 LRVF--LALALYNLGRPKEALEWLLEALAETL----PRYRRAIRFY 116 (120)
T ss_pred HHHH--HHHHHHHCCCHHHHHHHHHHHHHHHH----HHHHHHHHHH
Confidence 5544 55677788999999999998887322 2445555443
No 72
>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional
Probab=85.68 E-value=3 Score=36.18 Aligned_cols=80 Identities=11% Similarity=0.034 Sum_probs=61.4
Q ss_pred HHHHHhhccHHHHHhhhhhcCCCCCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCccchHHHHHHHHHHHHH
Q psy1676 64 LRNYLHYNLYDQADKLVKKSAFPENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQTAAVGFRQTTQKLAVV 143 (343)
Q Consensus 64 lr~yl~~~~~~~a~~li~k~~~p~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~sa~~~~~~i~K~li~ 143 (343)
--.....|+++.|..++.-...-+ ....+|+|=+|.++-..++|.+|...|..|+...|... . ..-++-.
T Consensus 42 A~~ly~~G~l~~A~~~f~~L~~~D----p~~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~L~~ddp-~-----~~~~ag~ 111 (157)
T PRK15363 42 AMQLMEVKEFAGAARLFQLLTIYD----AWSFDYWFRLGECCQAQKHWGEAIYAYGRAAQIKIDAP-Q-----APWAAAE 111 (157)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHhC----cccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCc-h-----HHHHHHH
Confidence 444568999999999998653221 36688999999999999999999999999999655431 1 2235667
Q ss_pred HHHhcCCCCC
Q psy1676 144 VELLLGDIPD 153 (343)
Q Consensus 144 v~LL~G~iP~ 153 (343)
|.|.+|+++.
T Consensus 112 c~L~lG~~~~ 121 (157)
T PRK15363 112 CYLACDNVCY 121 (157)
T ss_pred HHHHcCCHHH
Confidence 8888998776
No 73
>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=84.49 E-value=1.9 Score=30.70 Aligned_cols=54 Identities=24% Similarity=0.343 Sum_probs=41.8
Q ss_pred HhhccHHHHHhhhhhc--CCCCCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCc
Q psy1676 68 LHYNLYDQADKLVKKS--AFPENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQ 127 (343)
Q Consensus 68 l~~~~~~~a~~li~k~--~~p~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~ 127 (343)
++.|+|+.|..++++. ..|. .....+..|.+++..++|.+|...|..+....|.
T Consensus 2 l~~~~~~~A~~~~~~~l~~~p~------~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~ 57 (68)
T PF14559_consen 2 LKQGDYDEAIELLEKALQRNPD------NPEARLLLAQCYLKQGQYDEAEELLERLLKQDPD 57 (68)
T ss_dssp HHTTHHHHHHHHHHHHHHHTTT------SHHHHHHHHHHHHHTT-HHHHHHHHHCCHGGGTT
T ss_pred hhccCHHHHHHHHHHHHHHCCC------CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcC
Confidence 5788999999999875 3443 2334557899999999999999999998886665
No 74
>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=84.36 E-value=1.8 Score=38.67 Aligned_cols=48 Identities=17% Similarity=0.277 Sum_probs=34.2
Q ss_pred ccccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEeeCCCceEEEcc
Q psy1676 223 YSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLDREKGYMQSKE 271 (343)
Q Consensus 223 ys~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~Id~~~g~v~~~~ 271 (343)
-..++|.|+|..+|+. ..++-..|..|..+|.|.|.||.-+.+|..++
T Consensus 111 ~Kvv~ledla~~f~l~-t~~~i~ri~~L~~~g~ltGv~DdrGkfIyIs~ 158 (188)
T PF09756_consen 111 HKVVNLEDLAAEFGLR-TQDVINRIQELEAEGRLTGVIDDRGKFIYISE 158 (188)
T ss_dssp -SEE-HHHHHHHH-S--HHHHHHHHHHHHHHSSS-EEE-TT--EEE---
T ss_pred cceeeHHHHHHHcCCC-HHHHHHHHHHHHHCCCceeeEcCCCCeEEecH
Confidence 4568899999999995 88999999999999999999999777776654
No 75
>KOG2076|consensus
Probab=84.22 E-value=70 Score=35.05 Aligned_cols=105 Identities=16% Similarity=0.133 Sum_probs=66.8
Q ss_pred hHHHHHHHHHHHHHHHhhcccHHHHHHHHHHHHHHhhhcCCcchhHHHHHHHHHHHHhhccHHHHHhhhhhcC--CCCCC
Q psy1676 12 SDLIAAKCYFYHSRVHELTNNLDKVRSFLNARLRIATLRNDFEGQAVLINCLLRNYLHYNLYDQADKLVKKSA--FPENA 89 (343)
Q Consensus 12 ~d~~~a~~~~y~~~~~e~~~~~~~~~~~l~~~~r~a~~~~~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~~--~p~~~ 89 (343)
.|+...-.||+++.+||-.|.++++-..- +-.|-+. |..- -+.-.+-...-+.+++++|.-..+++. -|+
T Consensus 168 qdp~~~~ay~tL~~IyEqrGd~eK~l~~~---llAAHL~--p~d~-e~W~~ladls~~~~~i~qA~~cy~rAI~~~p~-- 239 (895)
T KOG2076|consen 168 QDPRNPIAYYTLGEIYEQRGDIEKALNFW---LLAAHLN--PKDY-ELWKRLADLSEQLGNINQARYCYSRAIQANPS-- 239 (895)
T ss_pred hCccchhhHHHHHHHHHHcccHHHHHHHH---HHHHhcC--CCCh-HHHHHHHHHHHhcccHHHHHHHHHHHHhcCCc--
Confidence 35666777888888888888766544322 2233333 2111 344444555667888888888877652 222
Q ss_pred ChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCcc
Q psy1676 90 SNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQT 128 (343)
Q Consensus 90 ~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~ 128 (343)
...|.|=...+|--.|++..|.+.|.+.+..+|+.
T Consensus 240 ----n~~~~~ers~L~~~~G~~~~Am~~f~~l~~~~p~~ 274 (895)
T KOG2076|consen 240 ----NWELIYERSSLYQKTGDLKRAMETFLQLLQLDPPV 274 (895)
T ss_pred ----chHHHHHHHHHHHHhChHHHHHHHHHHHHhhCCch
Confidence 25555555566666688888988888888877754
No 76
>PF14853 Fis1_TPR_C: Fis1 C-terminal tetratricopeptide repeat; PDB: 1IYG_A 1PC2_A 1NZN_A 3UUX_C 1Y8M_A 2PQR_A 2PQN_A 3O48_A.
Probab=84.10 E-value=4.2 Score=28.62 Aligned_cols=33 Identities=21% Similarity=0.195 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCcc
Q psy1676 96 RFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQT 128 (343)
Q Consensus 96 ~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~ 128 (343)
.++||++.-+.-.++|.+|.++...+++.-|.+
T Consensus 2 d~lY~lAig~ykl~~Y~~A~~~~~~lL~~eP~N 34 (53)
T PF14853_consen 2 DCLYYLAIGHYKLGEYEKARRYCDALLEIEPDN 34 (53)
T ss_dssp HHHHHHHHHHHHTT-HHHHHHHHHHHHHHTTS-
T ss_pred hhHHHHHHHHHHhhhHHHHHHHHHHHHhhCCCc
Confidence 378999999999999999999999999976654
No 77
>PRK12370 invasion protein regulator; Provisional
Probab=84.08 E-value=8.9 Score=39.78 Aligned_cols=100 Identities=7% Similarity=-0.095 Sum_probs=47.9
Q ss_pred HHHHHHHHHHHHHHHhhcccHHHHHHHHHHHHHHhhhcCCcchhHHHHHHHHHHHHhhccHHHHHhhhhhc--CCCCCCC
Q psy1676 13 DLIAAKCYFYHSRVHELTNNLDKVRSFLNARLRIATLRNDFEGQAVLINCLLRNYLHYNLYDQADKLVKKS--AFPENAS 90 (343)
Q Consensus 13 d~~~a~~~~y~~~~~e~~~~~~~~~~~l~~~~r~a~~~~~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~--~~p~~~~ 90 (343)
|+=.+.+++..+.++...++.+++...+-.+++. +|.... ....+-..|+..|+++.|...+.+. .-|...
T Consensus 334 dP~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l-----~P~~~~-a~~~lg~~l~~~G~~~eAi~~~~~Al~l~P~~~- 406 (553)
T PRK12370 334 DHNNPQALGLLGLINTIHSEYIVGSLLFKQANLL-----SPISAD-IKYYYGWNLFMAGQLEEALQTINECLKLDPTRA- 406 (553)
T ss_pred CCCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHh-----CCCCHH-HHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCCh-
Confidence 3334455555666666666666555444333321 233222 2233355566666666666666654 122210
Q ss_pred hHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhh
Q psy1676 91 NNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRK 124 (343)
Q Consensus 91 ~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~ 124 (343)
...++.+.++...++|.+|...+..++..
T Consensus 407 -----~~~~~~~~~~~~~g~~eeA~~~~~~~l~~ 435 (553)
T PRK12370 407 -----AAGITKLWITYYHTGIDDAIRLGDELRSQ 435 (553)
T ss_pred -----hhHHHHHHHHHhccCHHHHHHHHHHHHHh
Confidence 11122333344455666666666666553
No 78
>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional
Probab=83.83 E-value=14 Score=36.07 Aligned_cols=89 Identities=15% Similarity=0.114 Sum_probs=61.5
Q ss_pred hcccHHHHHHHHHHHHHHhhhcCCcchhHHHHHHHHHHHHhhccHHHHHhhhhhc-CCCCCCChHHHHHHHHHHHHHHHH
Q psy1676 29 LTNNLDKVRSFLNARLRIATLRNDFEGQAVLINCLLRNYLHYNLYDQADKLVKKS-AFPENASNNEWARFHFYLGRIKAV 107 (343)
Q Consensus 29 ~~~~~~~~~~~l~~~~r~a~~~~~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~-~~p~~~~~~~~~~Y~YY~Gri~~~ 107 (343)
..+....+...+-.+++ .++... .....+...|++.++++.|...+.++ ... ......++..|.++..
T Consensus 14 ~~~~~~~Ai~~~~~Al~-----~~P~~~-~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~-----P~~~~a~~~lg~~~~~ 82 (356)
T PLN03088 14 VDDDFALAVDLYTQAID-----LDPNNA-ELYADRAQANIKLGNFTEAVADANKAIELD-----PSLAKAYLRKGTACMK 82 (356)
T ss_pred HcCCHHHHHHHHHHHHH-----hCCCCH-HHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-----cCCHHHHHHHHHHHHH
Confidence 34555666655544443 233332 23344578889999999999998876 221 1223457788999999
Q ss_pred hhCHHHHHHHHHHHHhhCCcc
Q psy1676 108 RLEYSTAHKNLVQALRKAPQT 128 (343)
Q Consensus 108 ~~~y~~A~~~L~~A~~~~~~~ 128 (343)
.++|.+|..+|..|+...|..
T Consensus 83 lg~~~eA~~~~~~al~l~P~~ 103 (356)
T PLN03088 83 LEEYQTAKAALEKGASLAPGD 103 (356)
T ss_pred hCCHHHHHHHHHHHHHhCCCC
Confidence 999999999999999976654
No 79
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=83.73 E-value=2.9 Score=35.72 Aligned_cols=38 Identities=21% Similarity=0.444 Sum_probs=34.1
Q ss_pred cccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceE---EeeC
Q psy1676 224 SRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEA---TLDR 262 (343)
Q Consensus 224 s~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a---~Id~ 262 (343)
.|+|.++||+.+|+ |+..+-.-+.+|..+|.|.+ .+|+
T Consensus 22 ~R~s~~eiA~~lgl-S~~tV~~Ri~rL~~~GvI~~~~~~v~~ 62 (153)
T PRK11179 22 ARTPYAELAKQFGV-SPGTIHVRVEKMKQAGIITGTRVDVNP 62 (153)
T ss_pred CCCCHHHHHHHHCc-CHHHHHHHHHHHHHCCCeeeEEEEECH
Confidence 89999999999999 49999999999999999974 3454
No 80
>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A.
Probab=83.63 E-value=2 Score=27.18 Aligned_cols=25 Identities=36% Similarity=0.336 Sum_probs=21.7
Q ss_pred HHHHHHHHHhhCHHHHHHHHHHHHh
Q psy1676 99 FYLGRIKAVRLEYSTAHKNLVQALR 123 (343)
Q Consensus 99 YY~Gri~~~~~~y~~A~~~L~~A~~ 123 (343)
..+|.+|...++|.+|..++++|+.
T Consensus 3 ~~Lg~~~~~~g~~~~Ai~~y~~aL~ 27 (36)
T PF13176_consen 3 NNLGRIYRQQGDYEKAIEYYEQALA 27 (36)
T ss_dssp HHHHHHHHHCT-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHH
Confidence 4689999999999999999999765
No 81
>KOG2300|consensus
Probab=83.54 E-value=42 Score=34.51 Aligned_cols=73 Identities=18% Similarity=0.072 Sum_probs=55.9
Q ss_pred chhHHHHHHHHHHHHhhccHHHHHhhhhhcCCCCCCC---hHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCC
Q psy1676 54 EGQAVLINCLLRNYLHYNLYDQADKLVKKSAFPENAS---NNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAP 126 (343)
Q Consensus 54 ~~~~~l~n~Llr~yl~~~~~~~a~~li~k~~~p~~~~---~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~ 126 (343)
+-++++.--+.-.|+..++-..-..+++.+.-|...+ .......+|..|...+.++++.+|..++...+..+.
T Consensus 401 dl~a~~nlnlAi~YL~~~~~ed~y~~ld~i~p~nt~s~ssq~l~a~~~~v~glfaf~qn~lnEaK~~l~e~Lkman 476 (629)
T KOG2300|consen 401 DLQAFCNLNLAISYLRIGDAEDLYKALDLIGPLNTNSLSSQRLEASILYVYGLFAFKQNDLNEAKRFLRETLKMAN 476 (629)
T ss_pred HHHHHHHHhHHHHHHHhccHHHHHHHHHhcCCCCCCcchHHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHhhcc
Confidence 3344444457889999998888888888765553322 236677899999999999999999999999998653
No 82
>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=83.41 E-value=4.3 Score=27.31 Aligned_cols=34 Identities=35% Similarity=0.510 Sum_probs=29.5
Q ss_pred ccccChHHHHHHhCCCCHHHHHHHHHHhHHcCCce
Q psy1676 223 YSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIE 257 (343)
Q Consensus 223 ys~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~ 257 (343)
-..+|..+||+.+|++ ..-+-.++-+|+.+|+|+
T Consensus 15 ~~~~t~~ela~~~~is-~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 15 NPRITQKELAEKLGIS-RSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp CTTS-HHHHHHHHTS--HHHHHHHHHHHHHTTSEE
T ss_pred cCCCCHHHHHHHhCCC-HHHHHHHHHHHHHCcCcC
Confidence 4669999999999995 999999999999999984
No 83
>KOG1173|consensus
Probab=82.90 E-value=64 Score=33.65 Aligned_cols=110 Identities=22% Similarity=0.170 Sum_probs=56.9
Q ss_pred cchhHHHHHHH--HHHHHHHHhhcccHHHHHHHH---H--HHHHHhhhc--CCcchhHHHHHHHHHH-------------
Q psy1676 9 RRTSDLIAAKC--YFYHSRVHELTNNLDKVRSFL---N--ARLRIATLR--NDFEGQAVLINCLLRN------------- 66 (343)
Q Consensus 9 ~~~~d~~~a~~--~~y~~~~~e~~~~~~~~~~~l---~--~~~r~a~~~--~~~~~~~~l~n~Llr~------------- 66 (343)
.+.+|.+.+|+ .||-++..|+..-.+.+-... . -.++.+|+. ++......+.+.|++.
T Consensus 241 ~~~~dll~~~ad~~y~~c~f~~c~kit~~lle~dpfh~~~~~~~ia~l~el~~~n~Lf~lsh~LV~~yP~~a~sW~aVg~ 320 (611)
T KOG1173|consen 241 AENLDLLAEKADRLYYGCRFKECLKITEELLEKDPFHLPCLPLHIACLYELGKSNKLFLLSHKLVDLYPSKALSWFAVGC 320 (611)
T ss_pred hhcHHHHHHHHHHHHHcChHHHHHHHhHHHHhhCCCCcchHHHHHHHHHHhcccchHHHHHHHHHHhCCCCCcchhhHHH
Confidence 35788998888 666677666654333222110 0 122444543 2333333444444443
Q ss_pred -HHhhccHHHHHhhhhhcCC-CCCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHh
Q psy1676 67 -YLHYNLYDQADKLVKKSAF-PENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALR 123 (343)
Q Consensus 67 -yl~~~~~~~a~~li~k~~~-p~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~ 123 (343)
|+-.+.+..|++.++|++. ......... +.|..++.+++...|..++..|-+
T Consensus 321 YYl~i~k~seARry~SKat~lD~~fgpaWl-----~fghsfa~e~EhdQAmaaY~tAar 374 (611)
T KOG1173|consen 321 YYLMIGKYSEARRYFSKATTLDPTFGPAWL-----AFGHSFAGEGEHDQAMAAYFTAAR 374 (611)
T ss_pred HHHHhcCcHHHHHHHHHHhhcCccccHHHH-----HHhHHhhhcchHHHHHHHHHHHHH
Confidence 4667999999999998743 222222111 334444444444444444444444
No 84
>CHL00033 ycf3 photosystem I assembly protein Ycf3
Probab=82.25 E-value=21 Score=30.45 Aligned_cols=75 Identities=16% Similarity=0.034 Sum_probs=57.9
Q ss_pred cCCcchhHHHHHHHHHHHHhhccHHHHHhhhhhc--CCCCCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCc
Q psy1676 50 RNDFEGQAVLINCLLRNYLHYNLYDQADKLVKKS--AFPENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQ 127 (343)
Q Consensus 50 ~~~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~--~~p~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~ 127 (343)
....+.++.....+...++..+.++.|...++++ ..|. ..+...-++-.|.++...+++.+|...+..|+...|.
T Consensus 28 ~~~~~~~a~~~~~~g~~~~~~g~~~~A~~~~~~al~l~~~---~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~~~~~ 104 (168)
T CHL00033 28 TTSGEKEAFTYYRDGMSAQSEGEYAEALQNYYEAMRLEID---PYDRSYILYNIGLIHTSNGEHTKALEYYFQALERNPF 104 (168)
T ss_pred CCchhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcccc---chhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcC
Confidence 3455566777788889999999999999999876 2332 1233445678899999999999999999999985443
No 85
>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=81.27 E-value=3.6 Score=31.30 Aligned_cols=47 Identities=30% Similarity=0.537 Sum_probs=37.2
Q ss_pred ccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEeeCCCceEEEccC
Q psy1676 225 RITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLDREKGYMQSKES 272 (343)
Q Consensus 225 ~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~Id~~~g~v~~~~~ 272 (343)
.++..+||+.++++ +..++.++.+|...|.|...=-+..||.-..+.
T Consensus 25 ~~s~~eiA~~~~i~-~~~l~kil~~L~~~Gli~s~~G~~GGy~L~~~~ 71 (83)
T PF02082_consen 25 PVSSKEIAERLGIS-PSYLRKILQKLKKAGLIESSRGRGGGYRLARPP 71 (83)
T ss_dssp -BEHHHHHHHHTS--HHHHHHHHHHHHHTTSEEEETSTTSEEEESS-C
T ss_pred CCCHHHHHHHHCcC-HHHHHHHHHHHhhCCeeEecCCCCCceeecCCH
Confidence 39999999999995 999999999999999997665555566655543
No 86
>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=80.91 E-value=4.1 Score=22.75 Aligned_cols=30 Identities=23% Similarity=0.233 Sum_probs=25.7
Q ss_pred HHHHHHHHHHHhhCHHHHHHHHHHHHhhCC
Q psy1676 97 FHFYLGRIKAVRLEYSTAHKNLVQALRKAP 126 (343)
Q Consensus 97 Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~ 126 (343)
.++-.|.++...++|.+|..+|..++...|
T Consensus 3 ~~~~~a~~~~~~~~~~~a~~~~~~~~~~~~ 32 (34)
T smart00028 3 ALYNLGNAYLKLGDYDEALEYYEKALELDP 32 (34)
T ss_pred HHHHHHHHHHHHhhHHHHHHHHHHHHccCC
Confidence 467889999999999999999999987443
No 87
>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=80.57 E-value=4 Score=29.13 Aligned_cols=34 Identities=24% Similarity=0.344 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCcc
Q psy1676 95 ARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQT 128 (343)
Q Consensus 95 ~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~ 128 (343)
...++..|.++...++|.+|..+|..|+...|..
T Consensus 3 a~~~~~~g~~~~~~~~~~~A~~~~~~ai~~~p~~ 36 (69)
T PF13414_consen 3 AEAWYNLGQIYFQQGDYEEAIEYFEKAIELDPNN 36 (69)
T ss_dssp HHHHHHHHHHHHHTTHHHHHHHHHHHHHHHSTTH
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCC
Confidence 4567889999999999999999999999977764
No 88
>PF13428 TPR_14: Tetratricopeptide repeat
Probab=80.05 E-value=3.7 Score=27.07 Aligned_cols=31 Identities=23% Similarity=0.142 Sum_probs=28.0
Q ss_pred HHHHHHHHHHhhCHHHHHHHHHHHHhhCCcc
Q psy1676 98 HFYLGRIKAVRLEYSTAHKNLVQALRKAPQT 128 (343)
Q Consensus 98 ~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~ 128 (343)
++..|+.|...|++.+|...|+.+++..|.+
T Consensus 4 ~~~la~~~~~~G~~~~A~~~~~~~l~~~P~~ 34 (44)
T PF13428_consen 4 WLALARAYRRLGQPDEAERLLRRALALDPDD 34 (44)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHHCcCC
Confidence 4578999999999999999999999988865
No 89
>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=79.80 E-value=3.5 Score=30.28 Aligned_cols=33 Identities=33% Similarity=0.362 Sum_probs=28.6
Q ss_pred ccChHHHHHHhCCCCHHHHHHHHHHhHHcCCce
Q psy1676 225 RITPTKIAEKLGLESPEDAEFIIAKAIRDGVIE 257 (343)
Q Consensus 225 ~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~ 257 (343)
.-|+.+||..+|+.|..-|-..|..|...|+|+
T Consensus 25 ~Pt~rEIa~~~g~~S~~tv~~~L~~Le~kG~I~ 57 (65)
T PF01726_consen 25 PPTVREIAEALGLKSTSTVQRHLKALERKGYIR 57 (65)
T ss_dssp ---HHHHHHHHTSSSHHHHHHHHHHHHHTTSEE
T ss_pred CCCHHHHHHHhCCCChHHHHHHHHHHHHCcCcc
Confidence 358999999999999999999999999999984
No 90
>PRK02603 photosystem I assembly protein Ycf3; Provisional
Probab=79.69 E-value=13 Score=31.90 Aligned_cols=74 Identities=18% Similarity=0.060 Sum_probs=56.4
Q ss_pred CcchhHHHHHHHHHHHHhhccHHHHHhhhhhcC--CCCCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCcc
Q psy1676 52 DFEGQAVLINCLLRNYLHYNLYDQADKLVKKSA--FPENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQT 128 (343)
Q Consensus 52 ~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~~--~p~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~ 128 (343)
...+.+.....+...|...++++.|...++++. -|. ..+...+++..|.++...++|.+|..++..|+...|..
T Consensus 30 ~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~---~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~ 105 (172)
T PRK02603 30 KKAKEAFVYYRDGMSAQADGEYAEALENYEEALKLEED---PNDRSYILYNMGIIYASNGEHDKALEYYHQALELNPKQ 105 (172)
T ss_pred cHhhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhc---cchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCccc
Confidence 344555566667888999999999999988652 122 12345678899999999999999999999999965543
No 91
>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=79.00 E-value=4.8 Score=28.30 Aligned_cols=38 Identities=24% Similarity=0.475 Sum_probs=32.4
Q ss_pred cChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEeeCCC
Q psy1676 226 ITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLDREK 264 (343)
Q Consensus 226 Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~Id~~~ 264 (343)
++.++|+..++++ ...+-.+|.+|+..|+|.-.-+..+
T Consensus 22 ~t~~~la~~l~~~-~~~vs~~v~~L~~~Glv~r~~~~~D 59 (62)
T PF12802_consen 22 LTQSELAERLGIS-KSTVSRIVKRLEKKGLVERERDPGD 59 (62)
T ss_dssp EEHHHHHHHHTS--HHHHHHHHHHHHHTTSEEEEE-SSS
T ss_pred cCHHHHHHHHCcC-HHHHHHHHHHHHHCCCEEEeCCCCC
Confidence 8999999999995 8999999999999999976665544
No 92
>PRK10803 tol-pal system protein YbgF; Provisional
Probab=78.98 E-value=20 Score=33.67 Aligned_cols=68 Identities=12% Similarity=0.170 Sum_probs=50.3
Q ss_pred HHHHHHHHHHHhhccHHHHHhhhhhc--CCCCCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCcc
Q psy1676 58 VLINCLLRNYLHYNLYDQADKLVKKS--AFPENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQT 128 (343)
Q Consensus 58 ~l~n~Llr~yl~~~~~~~a~~li~k~--~~p~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~ 128 (343)
.-.+.-+.++++.++|+.|...+++. .+|.+. ..-.-+|+.|.+|...++|.+|...|..++...|.+
T Consensus 144 ~~Y~~A~~l~~~~~~y~~Ai~af~~fl~~yP~s~---~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP~s 213 (263)
T PRK10803 144 TDYNAAIALVQDKSRQDDAIVAFQNFVKKYPDST---YQPNANYWLGQLNYNKGKKDDAAYYFASVVKNYPKS 213 (263)
T ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCc---chHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCC
Confidence 33444445556779999999888865 467532 112235899999999999999999999999976654
No 93
>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=78.96 E-value=12 Score=30.10 Aligned_cols=65 Identities=26% Similarity=0.211 Sum_probs=50.9
Q ss_pred HHHHHHHHHHHhhccHHHHHhhhhhc-C-CCCCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCcc
Q psy1676 58 VLINCLLRNYLHYNLYDQADKLVKKS-A-FPENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQT 128 (343)
Q Consensus 58 ~l~n~Llr~yl~~~~~~~a~~li~k~-~-~p~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~ 128 (343)
.....+...|+..+++..|...+.+. . .|. ....++..|..+...++|.+|...|..++...|..
T Consensus 18 ~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~p~------~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~p~~ 84 (135)
T TIGR02552 18 EQIYALAYNLYQQGRYDEALKLFQLLAAYDPY------NSRYWLGLAACCQMLKEYEEAIDAYALAAALDPDD 84 (135)
T ss_pred HHHHHHHHHHHHcccHHHHHHHHHHHHHhCCC------cHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCC
Confidence 34455678899999999999999865 2 232 23556788999999999999999999999865543
No 94
>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=78.68 E-value=13 Score=28.73 Aligned_cols=63 Identities=19% Similarity=0.295 Sum_probs=47.9
Q ss_pred HHHHHHhhccHHHHHhhhhhc--CCCCCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCcc
Q psy1676 63 LLRNYLHYNLYDQADKLVKKS--AFPENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQT 128 (343)
Q Consensus 63 Llr~yl~~~~~~~a~~li~k~--~~p~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~ 128 (343)
+...+++.++++.|...+... ..|... ....-+|..|.++...++|..|...|..++...|..
T Consensus 8 ~~~~~~~~~~~~~A~~~~~~~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~ 72 (119)
T TIGR02795 8 AALLVLKAGDYADAIQAFQAFLKKYPKST---YAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKYPKS 72 (119)
T ss_pred HHHHHHHcCCHHHHHHHHHHHHHHCCCcc---ccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHCCCC
Confidence 456778899999999998865 234321 123346789999999999999999999999866543
No 95
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=78.53 E-value=5.6 Score=33.47 Aligned_cols=38 Identities=32% Similarity=0.468 Sum_probs=33.5
Q ss_pred cccccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEe
Q psy1676 222 SYSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATL 260 (343)
Q Consensus 222 ~ys~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~I 260 (343)
.-.++|+++||+++|+ |+..+-..+-+|..+|.|+++-
T Consensus 19 ~d~r~~~~eia~~lgl-S~~~v~~Ri~~L~~~GiI~~~~ 56 (154)
T COG1522 19 EDARISNAELAERVGL-SPSTVLRRIKRLEEEGVIKGYT 56 (154)
T ss_pred HhCCCCHHHHHHHHCC-CHHHHHHHHHHHHHCCceeeEE
Confidence 3466999999999999 5999999999999999997654
No 96
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=78.30 E-value=7.2 Score=28.67 Aligned_cols=32 Identities=19% Similarity=0.330 Sum_probs=29.4
Q ss_pred ccChHHHHHHhCCCCHHHHHHHHHHhHHcCCce
Q psy1676 225 RITPTKIAEKLGLESPEDAEFIIAKAIRDGVIE 257 (343)
Q Consensus 225 ~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~ 257 (343)
.++..+||+.+|++ ...|..++.+|..+|+|.
T Consensus 22 ~~ta~eLa~~lgl~-~~~v~r~L~~L~~~G~V~ 53 (68)
T smart00550 22 TSTALQLAKNLGLP-KKEVNRVLYSLEKKGKVC 53 (68)
T ss_pred CcCHHHHHHHHCCC-HHHHHHHHHHHHHCCCEE
Confidence 39999999999996 789999999999999984
No 97
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=77.82 E-value=5.8 Score=34.34 Aligned_cols=40 Identities=23% Similarity=0.330 Sum_probs=34.8
Q ss_pred HhhcccccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEE
Q psy1676 219 IGASYSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEAT 259 (343)
Q Consensus 219 i~~~ys~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~ 259 (343)
+-+--.|+|.++||+++|+ |+..+-.-+.+|..+|.|.|+
T Consensus 22 ~Lq~d~R~s~~eiA~~lgl-S~~tv~~Ri~rL~~~GvI~~~ 61 (164)
T PRK11169 22 ELQKDGRISNVELSKRVGL-SPTPCLERVRRLERQGFIQGY 61 (164)
T ss_pred HhccCCCCCHHHHHHHHCc-CHHHHHHHHHHHHHCCCeEEE
Confidence 3345689999999999999 499999999999999999753
No 98
>PRK10049 pgaA outer membrane protein PgaA; Provisional
Probab=77.48 E-value=1.1e+02 Score=33.09 Aligned_cols=165 Identities=13% Similarity=0.055 Sum_probs=92.5
Q ss_pred HHHHHhhcccHHHHHHHHHHHHHHhhhcCCcch---hHHHHHHHHHHHHhhccHHHHHhhhhhc--CCCC---------C
Q psy1676 23 HSRVHELTNNLDKVRSFLNARLRIATLRNDFEG---QAVLINCLLRNYLHYNLYDQADKLVKKS--AFPE---------N 88 (343)
Q Consensus 23 ~~~~~e~~~~~~~~~~~l~~~~r~a~~~~~~~~---~~~l~n~Llr~yl~~~~~~~a~~li~k~--~~p~---------~ 88 (343)
++.++-..++.+++...+-..+. .++.. .......|+..+++.+.++.|...+.+. ..|. .
T Consensus 278 la~~yl~~g~~e~A~~~l~~~l~-----~~p~~~~~~~~~~~~L~~a~~~~g~~~eA~~~l~~~~~~~P~~~~~~~~~~~ 352 (765)
T PRK10049 278 VASAYLKLHQPEKAQSILTELFY-----HPETIADLSDEELADLFYSLLESENYPGALTVTAHTINNSPPFLRLYGSPTS 352 (765)
T ss_pred HHHHHHhcCCcHHHHHHHHHHhh-----cCCCCCCCChHHHHHHHHHHHhcccHHHHHHHHHHHhhcCCceEeecCCCCC
Confidence 35555556666666655443322 22221 1123334566778999999999888754 2231 2
Q ss_pred CChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCccchHHHHHHHHHHHHHHHHhcCCCCC-hhhhhhHhHh--h-
Q psy1676 89 ASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQTAAVGFRQTTQKLAVVVELLLGDIPD-RQIFRQAVLR--R- 164 (343)
Q Consensus 89 ~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~sa~~~~~~i~K~li~v~LL~G~iP~-~~~~~~~~l~--~- 164 (343)
.|+.+.....+..|.++...+++.+|...|..+....|... . +...+..+..-.|+... ...+. ..+. +
T Consensus 353 ~p~~~~~~a~~~~a~~l~~~g~~~eA~~~l~~al~~~P~n~--~----l~~~lA~l~~~~g~~~~A~~~l~-~al~l~Pd 425 (765)
T PRK10049 353 IPNDDWLQGQSLLSQVAKYSNDLPQAEMRARELAYNAPGNQ--G----LRIDYASVLQARGWPRAAENELK-KAEVLEPR 425 (765)
T ss_pred CCCchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCH--H----HHHHHHHHHHhcCCHHHHHHHHH-HHHhhCCC
Confidence 24456778888999999999999999999999999777642 1 22223333444566322 11121 1110 0
Q ss_pred hh-hhhHHHHHHHHhCCHHHHHHHHHhccccccccc
Q psy1676 165 AL-SPYFQLTQAVRMGELQKFNEVLTTYGNQFRTDY 199 (343)
Q Consensus 165 ~l-~~Y~~L~~Av~~Gdl~~f~~~l~~~~~~f~~d~ 199 (343)
.. ..|..-..+...|+...-...++.-...+-.+.
T Consensus 426 ~~~l~~~~a~~al~~~~~~~A~~~~~~ll~~~Pd~~ 461 (765)
T PRK10049 426 NINLEVEQAWTALDLQEWRQMDVLTDDVVAREPQDP 461 (765)
T ss_pred ChHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCCCCH
Confidence 01 112233356677876666666555444443333
No 99
>PRK15359 type III secretion system chaperone protein SscB; Provisional
Probab=76.58 E-value=15 Score=30.79 Aligned_cols=81 Identities=16% Similarity=-0.056 Sum_probs=56.9
Q ss_pred HHHHHHhhccHHHHHhhhhhcCCCCCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCccchHHHHHHHHHHHH
Q psy1676 63 LLRNYLHYNLYDQADKLVKKSAFPENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQTAAVGFRQTTQKLAV 142 (343)
Q Consensus 63 Llr~yl~~~~~~~a~~li~k~~~p~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~sa~~~~~~i~K~li 142 (343)
+-..++..+.++.|...+....-.. .....+++-.|.++...++|.+|..+|..|+...|... . ..-.+-
T Consensus 30 ~g~~~~~~g~~~~A~~~~~~al~~~----P~~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l~p~~~-~-----a~~~lg 99 (144)
T PRK15359 30 SGYASWQEGDYSRAVIDFSWLVMAQ----PWSWRAHIALAGTWMMLKEYTTAINFYGHALMLDASHP-E-----PVYQTG 99 (144)
T ss_pred HHHHHHHcCCHHHHHHHHHHHHHcC----CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCc-H-----HHHHHH
Confidence 4667789999999998888652111 23456778899999999999999999999999666541 1 122333
Q ss_pred HHHHhcCCCCC
Q psy1676 143 VVELLLGDIPD 153 (343)
Q Consensus 143 ~v~LL~G~iP~ 153 (343)
.+...+|+...
T Consensus 100 ~~l~~~g~~~e 110 (144)
T PRK15359 100 VCLKMMGEPGL 110 (144)
T ss_pred HHHHHcCCHHH
Confidence 34555676443
No 100
>PRK10049 pgaA outer membrane protein PgaA; Provisional
Probab=76.58 E-value=35 Score=36.91 Aligned_cols=99 Identities=12% Similarity=-0.035 Sum_probs=76.7
Q ss_pred HHHHHHHHHHhhcccHHHHHHHHHHHHHHhhhcCCcchhHHHHHHHHHHHHhhccHHHHHhhhhhc--CCCCCCChHHHH
Q psy1676 18 KCYFYHSRVHELTNNLDKVRSFLNARLRIATLRNDFEGQAVLINCLLRNYLHYNLYDQADKLVKKS--AFPENASNNEWA 95 (343)
Q Consensus 18 ~~~~y~~~~~e~~~~~~~~~~~l~~~~r~a~~~~~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~--~~p~~~~~~~~~ 95 (343)
.+++..+......+.+.++...+-..... .|.. ..+...+..++...|.++.|...++++ ..|+ ..
T Consensus 360 ~a~~~~a~~l~~~g~~~eA~~~l~~al~~-----~P~n-~~l~~~lA~l~~~~g~~~~A~~~l~~al~l~Pd------~~ 427 (765)
T PRK10049 360 QGQSLLSQVAKYSNDLPQAEMRARELAYN-----APGN-QGLRIDYASVLQARGWPRAAENELKKAEVLEPR------NI 427 (765)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHHHh-----CCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHhhCCC------Ch
Confidence 45677888888889999888776554432 3333 346666788999999999999999976 2342 23
Q ss_pred HHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCcc
Q psy1676 96 RFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQT 128 (343)
Q Consensus 96 ~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~ 128 (343)
.+.|..|..++..++|.+|...+..++..-|..
T Consensus 428 ~l~~~~a~~al~~~~~~~A~~~~~~ll~~~Pd~ 460 (765)
T PRK10049 428 NLEVEQAWTALDLQEWRQMDVLTDDVVAREPQD 460 (765)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHHHhCCCC
Confidence 477899999999999999999999999977765
No 101
>PRK10866 outer membrane biogenesis protein BamD; Provisional
Probab=76.55 E-value=63 Score=29.78 Aligned_cols=62 Identities=13% Similarity=0.098 Sum_probs=49.0
Q ss_pred HHHHHhhccHHHHHhhhhhc--CCCCCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCcc
Q psy1676 64 LRNYLHYNLYDQADKLVKKS--AFPENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQT 128 (343)
Q Consensus 64 lr~yl~~~~~~~a~~li~k~--~~p~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~ 128 (343)
...+++.++|+.|...+++. ..|.+ +....+ .|.+|..+...++|.+|...++..++.-|.+
T Consensus 39 A~~~~~~g~y~~Ai~~f~~l~~~yP~s-~~a~~a--~l~la~ayy~~~~y~~A~~~~e~fi~~~P~~ 102 (243)
T PRK10866 39 AQQKLQDGNWKQAITQLEALDNRYPFG-PYSQQV--QLDLIYAYYKNADLPLAQAAIDRFIRLNPTH 102 (243)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHhCCCC-hHHHHH--HHHHHHHHHhcCCHHHHHHHHHHHHHhCcCC
Confidence 56678899999999999865 45542 333333 6789999999999999999999999976654
No 102
>PF13429 TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2_B.
Probab=76.42 E-value=5.9 Score=36.82 Aligned_cols=69 Identities=23% Similarity=0.268 Sum_probs=45.5
Q ss_pred HHHHHHHHHHHhhccHHHHHhhhhhcCCCCCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCcc
Q psy1676 58 VLINCLLRNYLHYNLYDQADKLVKKSAFPENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQT 128 (343)
Q Consensus 58 ~l~n~Llr~yl~~~~~~~a~~li~k~~~p~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~ 128 (343)
......+.+|...++++.+..++++..- ......-..|++..|.++...|++.+|...+..|+...|.+
T Consensus 111 ~~l~~~l~~~~~~~~~~~~~~~l~~~~~--~~~~~~~~~~~~~~a~~~~~~G~~~~A~~~~~~al~~~P~~ 179 (280)
T PF13429_consen 111 RYLLSALQLYYRLGDYDEAEELLEKLEE--LPAAPDSARFWLALAEIYEQLGDPDKALRDYRKALELDPDD 179 (280)
T ss_dssp -------H-HHHTT-HHHHHHHHHHHHH---T---T-HHHHHHHHHHHHHCCHHHHHHHHHHHHHHH-TT-
T ss_pred chhhHHHHHHHHHhHHHHHHHHHHHHHh--ccCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCC
Confidence 3344567788899999999999887421 11123557788899999999999999999999999977764
No 103
>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional
Probab=76.05 E-value=57 Score=35.14 Aligned_cols=100 Identities=11% Similarity=-0.021 Sum_probs=77.5
Q ss_pred HHHHHHHHHHHhhcccHHHHHHHHHHHHHHhhhcCCcchhHHHHHHHHHHHHhhccHHHHHhhhhhcCCCCCCChHHHHH
Q psy1676 17 AKCYFYHSRVHELTNNLDKVRSFLNARLRIATLRNDFEGQAVLINCLLRNYLHYNLYDQADKLVKKSAFPENASNNEWAR 96 (343)
Q Consensus 17 a~~~~y~~~~~e~~~~~~~~~~~l~~~~r~a~~~~~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~~~p~~~~~~~~~~ 96 (343)
+..++-++++.+..+..+++...+-. ++...|+.....++. ..+..+.+.++.|.......-- ...+..+
T Consensus 86 ~~~~~~La~i~~~~g~~~ea~~~l~~-----~~~~~Pd~~~a~~~~-a~~L~~~~~~eeA~~~~~~~l~----~~p~~~~ 155 (694)
T PRK15179 86 ELFQVLVARALEAAHRSDEGLAVWRG-----IHQRFPDSSEAFILM-LRGVKRQQGIEAGRAEIELYFS----GGSSSAR 155 (694)
T ss_pred HHHHHHHHHHHHHcCCcHHHHHHHHH-----HHhhCCCcHHHHHHH-HHHHHHhccHHHHHHHHHHHhh----cCCCCHH
Confidence 77899999999999999988866643 334467766666665 6777899999999988875411 1134566
Q ss_pred HHHHHHHHHHHhhCHHHHHHHHHHHHhhCC
Q psy1676 97 FHFYLGRIKAVRLEYSTAHKNLVQALRKAP 126 (343)
Q Consensus 97 Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~ 126 (343)
.++-.|......++|.+|...|..++.+-|
T Consensus 156 ~~~~~a~~l~~~g~~~~A~~~y~~~~~~~p 185 (694)
T PRK15179 156 EILLEAKSWDEIGQSEQADACFERLSRQHP 185 (694)
T ss_pred HHHHHHHHHHHhcchHHHHHHHHHHHhcCC
Confidence 788999999999999999999999998444
No 104
>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=75.33 E-value=23 Score=25.31 Aligned_cols=42 Identities=21% Similarity=0.373 Sum_probs=33.7
Q ss_pred cccc-ChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEeeCCCceE
Q psy1676 223 YSRI-TPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLDREKGYM 267 (343)
Q Consensus 223 ys~I-sl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~Id~~~g~v 267 (343)
-.++ |..++|+.+++ |..-+...+..|..+|.|. ..+..|+.
T Consensus 21 g~~lps~~~la~~~~v-sr~tvr~al~~L~~~g~i~--~~~~~G~~ 63 (64)
T PF00392_consen 21 GDRLPSERELAERYGV-SRTTVREALRRLEAEGLIE--RRPGRGTF 63 (64)
T ss_dssp TSBE--HHHHHHHHTS--HHHHHHHHHHHHHTTSEE--EETTTEEE
T ss_pred CCEeCCHHHHHHHhcc-CCcHHHHHHHHHHHCCcEE--EECCceEE
Confidence 3799 99999999999 4899999999999999994 45555654
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=74.12 E-value=7.6 Score=26.70 Aligned_cols=38 Identities=24% Similarity=0.412 Sum_probs=31.8
Q ss_pred HhhcccccChHHHHHHhCCCCHHHHHHHHHHhHHcCCce
Q psy1676 219 IGASYSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIE 257 (343)
Q Consensus 219 i~~~ys~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~ 257 (343)
+...-..+++++|++++|++ ...+-.++..|...|++.
T Consensus 12 l~~~~~~~t~~eia~~~gl~-~stv~r~L~tL~~~g~v~ 49 (52)
T PF09339_consen 12 LAESGGPLTLSEIARALGLP-KSTVHRLLQTLVEEGYVE 49 (52)
T ss_dssp HHCTBSCEEHHHHHHHHTS--HHHHHHHHHHHHHTTSEE
T ss_pred HHcCCCCCCHHHHHHHHCcC-HHHHHHHHHHHHHCcCee
Confidence 34445668999999999996 889999999999999884
No 106
>PLN03081 pentatricopeptide (PPR) repeat-containing protein; Provisional
Probab=73.30 E-value=1.3e+02 Score=31.94 Aligned_cols=230 Identities=11% Similarity=0.096 Sum_probs=109.8
Q ss_pred HHHHHHHHHHHhhccHHHHHhhhhhcCCCCCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCccchHHHHHHH
Q psy1676 58 VLINCLLRNYLHYNLYDQADKLVKKSAFPENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQTAAVGFRQTT 137 (343)
Q Consensus 58 ~l~n~Llr~yl~~~~~~~a~~li~k~~~p~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~sa~~~~~~i 137 (343)
.+.|.|+..|.+.|+++.|..+++...-|. .++|. -+...|+..+++.+|.+.|......-....... +
T Consensus 361 ~~~~~Li~~y~k~G~~~~A~~vf~~m~~~d------~~t~n-~lI~~y~~~G~~~~A~~lf~~M~~~g~~Pd~~T----~ 429 (697)
T PLN03081 361 VANTALVDLYSKWGRMEDARNVFDRMPRKN------LISWN-ALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVT----F 429 (697)
T ss_pred eehHHHHHHHHHCCCHHHHHHHHHhCCCCC------eeeHH-HHHHHHHHcCCHHHHHHHHHHHHHhCCCCCHHH----H
Confidence 455667777788888888888877654332 12222 233345677899999999888776321111111 1
Q ss_pred HHHHHHHHHhcCCCCC-hhhhhh----HhHhhhhhhhHHHHHHH-HhCCHHHHHHHHHhccccccccccHHHHHHHHHHH
Q psy1676 138 QKLAVVVELLLGDIPD-RQIFRQ----AVLRRALSPYFQLTQAV-RMGELQKFNEVLTTYGNQFRTDYTFKLILRLRHNV 211 (343)
Q Consensus 138 ~K~li~v~LL~G~iP~-~~~~~~----~~l~~~l~~Y~~L~~Av-~~Gdl~~f~~~l~~~~~~f~~d~~~~Lv~~l~~~v 211 (343)
. -++-...-.|.+-. ..+|.. ..+.+....|..++.++ +.|++.+-.+.+++- .+..+. ..+..|...+
T Consensus 430 ~-~ll~a~~~~g~~~~a~~~f~~m~~~~g~~p~~~~y~~li~~l~r~G~~~eA~~~~~~~--~~~p~~--~~~~~Ll~a~ 504 (697)
T PLN03081 430 L-AVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYACMIELLGREGLLDEAYAMIRRA--PFKPTV--NMWAALLTAC 504 (697)
T ss_pred H-HHHHHHhcCCcHHHHHHHHHHHHHhcCCCCCccchHhHHHHHHhcCCHHHHHHHHHHC--CCCCCH--HHHHHHHHHH
Confidence 1 11111122333322 122211 11223344578888887 568887777776642 122221 1222222222
Q ss_pred HHH--------HHHHHhhcc-----cccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEeeCCCceEEEccCcccccc
Q psy1676 212 IKT--------AIRSIGASY-----SRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLDREKGYMQSKESADIYCT 278 (343)
Q Consensus 212 ~r~--------~ir~i~~~y-----s~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~Id~~~g~v~~~~~~~v~s~ 278 (343)
-++ ...++...- +-+.+..+-.+.| ..++++.+...|-..|.-+ .+.-.++......-++..
T Consensus 505 ~~~g~~~~a~~~~~~l~~~~p~~~~~y~~L~~~y~~~G--~~~~A~~v~~~m~~~g~~k---~~g~s~i~~~~~~~~f~~ 579 (697)
T PLN03081 505 RIHKNLELGRLAAEKLYGMGPEKLNNYVVLLNLYNSSG--RQAEAAKVVETLKRKGLSM---HPACTWIEVKKQDHSFFS 579 (697)
T ss_pred HHcCCcHHHHHHHHHHhCCCCCCCcchHHHHHHHHhCC--CHHHHHHHHHHHHHcCCcc---CCCeeEEEECCeEEEEcc
Confidence 111 111111111 1122333333333 4799999999999999742 112233444333333332
Q ss_pred ccchHHHHHHHHH-HHHhhHHHhhhcCCCCCC
Q psy1676 279 VEPQLAFHQRIAF-CLDLHNQSVKAMRYPPKS 309 (343)
Q Consensus 279 ~ep~~~~~~rI~~-cl~l~~~~~~am~~~~~~ 309 (343)
.+........|-. .-.|..+ ++..-|-|+.
T Consensus 580 ~d~~h~~~~~i~~~l~~l~~~-~~~~gy~~~~ 610 (697)
T PLN03081 580 GDRLHPQSREIYQKLDELMKE-ISEYGYVAEE 610 (697)
T ss_pred CCCCCccHHHHHHHHHHHHHH-HHHcCCCCCc
Confidence 2222223344533 3334444 5556787653
No 107
>PLN03077 Protein ECB2; Provisional
Probab=72.68 E-value=1.5e+02 Score=32.35 Aligned_cols=254 Identities=14% Similarity=0.097 Sum_probs=131.6
Q ss_pred HHhhcccHHHHHHHHHHHHHHhhhcCCcchhHHHHHHHHHHHHhhccHHHHHhhhhhcCCCCCCChHHHHHHHHHHHHHH
Q psy1676 26 VHELTNNLDKVRSFLNARLRIATLRNDFEGQAVLINCLLRNYLHYNLYDQADKLVKKSAFPENASNNEWARFHFYLGRIK 105 (343)
Q Consensus 26 ~~e~~~~~~~~~~~l~~~~r~a~~~~~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~~~p~~~~~~~~~~Y~YY~Gri~ 105 (343)
+.-..+.++..+...-...+.. . ..-.++.|.|+..|.+.|+++.|..+++.. -| +.+.|.- +...|
T Consensus 498 a~~~~g~l~~~~~i~~~~~~~g-~----~~~~~~~naLi~~y~k~G~~~~A~~~f~~~-~~------d~~s~n~-lI~~~ 564 (857)
T PLN03077 498 ACARIGALMCGKEIHAHVLRTG-I----GFDGFLPNALLDLYVRCGRMNYAWNQFNSH-EK------DVVSWNI-LLTGY 564 (857)
T ss_pred HHhhhchHHHhHHHHHHHHHhC-C----CccceechHHHHHHHHcCCHHHHHHHHHhc-CC------ChhhHHH-HHHHH
Confidence 3344566666665554433422 1 112366788899999999999999998865 22 2333322 22345
Q ss_pred HHhhCHHHHHHHHHHHHhh--CCccchHHHHHHHHHHHHHHHHhcCCCCC-hhhhh----hHhHhhhhhhhHHHHHHH-H
Q psy1676 106 AVRLEYSTAHKNLVQALRK--APQTAAVGFRQTTQKLAVVVELLLGDIPD-RQIFR----QAVLRRALSPYFQLTQAV-R 177 (343)
Q Consensus 106 ~~~~~y~~A~~~L~~A~~~--~~~~sa~~~~~~i~K~li~v~LL~G~iP~-~~~~~----~~~l~~~l~~Y~~L~~Av-~ 177 (343)
+..|+..+|...|.+.... .|.. ..+.- +|-..--.|.+-. ..+|. ...+.+....|..++.++ +
T Consensus 565 ~~~G~~~~A~~lf~~M~~~g~~Pd~--~T~~~-----ll~a~~~~g~v~ea~~~f~~M~~~~gi~P~~~~y~~lv~~l~r 637 (857)
T PLN03077 565 VAHGKGSMAVELFNRMVESGVNPDE--VTFIS-----LLCACSRSGMVTQGLEYFHSMEEKYSITPNLKHYACVVDLLGR 637 (857)
T ss_pred HHcCCHHHHHHHHHHHHHcCCCCCc--ccHHH-----HHHHHhhcChHHHHHHHHHHHHHHhCCCCchHHHHHHHHHHHh
Confidence 6789999999999987773 2221 11110 1111112333333 12221 112233445688888888 5
Q ss_pred hCCHHHHHHHHHhccccccccccHHHHHHHHHHHH--------HHHHHHHhhc-----ccccChHHHHHHhCCCCHHHHH
Q psy1676 178 MGELQKFNEVLTTYGNQFRTDYTFKLILRLRHNVI--------KTAIRSIGAS-----YSRITPTKIAEKLGLESPEDAE 244 (343)
Q Consensus 178 ~Gdl~~f~~~l~~~~~~f~~d~~~~Lv~~l~~~v~--------r~~ir~i~~~-----ys~Isl~dIa~~l~l~s~~e~E 244 (343)
.|++.+-.+.+++-. +..| ...+.-|...+. +...+++... -.-+.++.+-...| ..++++
T Consensus 638 ~G~~~eA~~~~~~m~--~~pd--~~~~~aLl~ac~~~~~~e~~e~~a~~l~~l~p~~~~~y~ll~n~ya~~g--~~~~a~ 711 (857)
T PLN03077 638 AGKLTEAYNFINKMP--ITPD--PAVWGALLNACRIHRHVELGELAAQHIFELDPNSVGYYILLCNLYADAG--KWDEVA 711 (857)
T ss_pred CCCHHHHHHHHHHCC--CCCC--HHHHHHHHHHHHHcCChHHHHHHHHHHHhhCCCCcchHHHHHHHHHHCC--ChHHHH
Confidence 688888777777532 2222 122222222211 1111122111 11223333333333 378999
Q ss_pred HHHHHhHHcCCceEEeeCCCceEEEccCccccccccchHHHHHHHHHHHH-hhHHHhhhcCCCCCC
Q psy1676 245 FIIAKAIRDGVIEATLDREKGYMQSKESADIYCTVEPQLAFHQRIAFCLD-LHNQSVKAMRYPPKS 309 (343)
Q Consensus 245 ~ila~lI~~G~I~a~Id~~~g~v~~~~~~~v~s~~ep~~~~~~rI~~cl~-l~~~~~~am~~~~~~ 309 (343)
.+...|...|.-+ ++.-.+|..+...-+|...+-...-.+.|-..|+ |..+ ++.+-|-|+.
T Consensus 712 ~vr~~M~~~g~~k---~~g~s~ie~~~~~~~f~~~d~~h~~~~~i~~~l~~l~~~-~~~~g~~~~~ 773 (857)
T PLN03077 712 RVRKTMRENGLTV---DPGCSWVEVKGKVHAFLTDDESHPQIKEINTVLEGFYEK-MKASGLAGSE 773 (857)
T ss_pred HHHHHHHHcCCCC---CCCccEEEECCEEEEEecCCCCCcchHHHHHHHHHHHHH-HHhCCcCCCc
Confidence 9999999999864 2222345554444444333333333455655444 4444 6667787654
No 108
>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional
Probab=72.29 E-value=33 Score=38.45 Aligned_cols=92 Identities=12% Similarity=-0.003 Sum_probs=55.8
Q ss_pred HHHHHhhcccHHHHHHHHHHHHHHhhhcCCcchhHHHHHHHHHHHHhhccHHHHHhhhhhcC--CCCCCChHHHHHHHHH
Q psy1676 23 HSRVHELTNNLDKVRSFLNARLRIATLRNDFEGQAVLINCLLRNYLHYNLYDQADKLVKKSA--FPENASNNEWARFHFY 100 (343)
Q Consensus 23 ~~~~~e~~~~~~~~~~~l~~~~r~a~~~~~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~~--~p~~~~~~~~~~Y~YY 100 (343)
++...+..|...++...+-.+++ .+|. ......+-.++.+.+.++.|...+.+.. .|. ...+++-
T Consensus 582 La~~l~~~Gr~~eAl~~~~~AL~-----l~P~--~~a~~~LA~~l~~lG~~deA~~~l~~AL~l~Pd------~~~a~~n 648 (987)
T PRK09782 582 LHAQRYIPGQPELALNDLTRSLN-----IAPS--ANAYVARATIYRQRHNVPAAVSDLRAALELEPN------NSNYQAA 648 (987)
T ss_pred HHHHHHhCCCHHHHHHHHHHHHH-----hCCC--HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC------CHHHHHH
Confidence 33344445777777655544332 2343 2233445677788888888888777642 232 2245667
Q ss_pred HHHHHHHhhCHHHHHHHHHHHHhhCCc
Q psy1676 101 LGRIKAVRLEYSTAHKNLVQALRKAPQ 127 (343)
Q Consensus 101 ~Gri~~~~~~y~~A~~~L~~A~~~~~~ 127 (343)
.|.++...+++.+|..+|..|+...|.
T Consensus 649 LG~aL~~~G~~eeAi~~l~~AL~l~P~ 675 (987)
T PRK09782 649 LGYALWDSGDIAQSREMLERAHKGLPD 675 (987)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHhCCC
Confidence 777777777777777777777775554
No 109
>PRK11447 cellulose synthase subunit BcsC; Provisional
Probab=71.80 E-value=30 Score=39.36 Aligned_cols=106 Identities=16% Similarity=0.151 Sum_probs=65.2
Q ss_pred HHHHHHHHHHHhhcccHHHHHHHHHHHHHHhhhcCCcch--------hHHHHHHHHHHHHhhccHHHHHhhhhhc--CCC
Q psy1676 17 AKCYFYHSRVHELTNNLDKVRSFLNARLRIATLRNDFEG--------QAVLINCLLRNYLHYNLYDQADKLVKKS--AFP 86 (343)
Q Consensus 17 a~~~~y~~~~~e~~~~~~~~~~~l~~~~r~a~~~~~~~~--------~~~l~n~Llr~yl~~~~~~~a~~li~k~--~~p 86 (343)
+.+++-++.++...++.+++...+-.+++..-....... ...+...+-..+++.++++.|...+.+. ..|
T Consensus 303 ~~a~~~Lg~~~~~~g~~~eA~~~l~~Al~~~p~~~~~~~~~~ll~~~~~~~~~~~g~~~~~~g~~~eA~~~~~~Al~~~P 382 (1157)
T PRK11447 303 SEALGALGQAYSQQGDRARAVAQFEKALALDPHSSNRDKWESLLKVNRYWLLIQQGDAALKANNLAQAERLYQQARQVDN 382 (1157)
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCccchhHHHHHHHhhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCC
Confidence 455677777777777777777666554432110000000 0112222345677788888888887765 223
Q ss_pred CCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCcc
Q psy1676 87 ENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQT 128 (343)
Q Consensus 87 ~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~ 128 (343)
. . ..-++.+|.++..++++.+|..+|..|+...|..
T Consensus 383 ~----~--~~a~~~Lg~~~~~~g~~~eA~~~y~~aL~~~p~~ 418 (1157)
T PRK11447 383 T----D--SYAVLGLGDVAMARKDYAAAERYYQQALRMDPGN 418 (1157)
T ss_pred C----C--HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCC
Confidence 2 1 1235568999999999999999999999865543
No 110
>PRK15331 chaperone protein SicA; Provisional
Probab=71.66 E-value=70 Score=28.04 Aligned_cols=103 Identities=16% Similarity=0.184 Sum_probs=63.3
Q ss_pred ccchhHHHHHHHHHHHHHHHhhcccHHHHHHHHHHHHHHhhhcCCcchhHHHHHHHHHHHHhhccHHHHHhhhhhc-CCC
Q psy1676 8 NRRTSDLIAAKCYFYHSRVHELTNNLDKVRSFLNARLRIATLRNDFEGQAVLINCLLRNYLHYNLYDQADKLVKKS-AFP 86 (343)
Q Consensus 8 ~~~~~d~~~a~~~~y~~~~~e~~~~~~~~~~~l~~~~r~a~~~~~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~-~~p 86 (343)
.--+||.+-+-.|-+| ..|++.++... ||-.|. .|++.--++ .-|--.|-..+.|..|..+-.-. .+.
T Consensus 33 s~~~le~iY~~Ay~~y-----~~Gk~~eA~~~----F~~L~~-~d~~n~~Y~-~GLaa~~Q~~k~y~~Ai~~Y~~A~~l~ 101 (165)
T PRK15331 33 PQDMMDGLYAHAYEFY-----NQGRLDEAETF----FRFLCI-YDFYNPDYT-MGLAAVCQLKKQFQKACDLYAVAFTLL 101 (165)
T ss_pred CHHHHHHHHHHHHHHH-----HCCCHHHHHHH----HHHHHH-hCcCcHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHcc
Confidence 3445666666555444 35677777643 333333 233333344 33466677788888888776632 111
Q ss_pred CCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCC
Q psy1676 87 ENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAP 126 (343)
Q Consensus 87 ~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~ 126 (343)
...+.+ .||.|..++..++-..|..+|..|+.+|.
T Consensus 102 ~~dp~p-----~f~agqC~l~l~~~~~A~~~f~~a~~~~~ 136 (165)
T PRK15331 102 KNDYRP-----VFFTGQCQLLMRKAAKARQCFELVNERTE 136 (165)
T ss_pred cCCCCc-----cchHHHHHHHhCCHHHHHHHHHHHHhCcc
Confidence 111111 67999999999999999999999998544
No 111
>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=71.55 E-value=9.1 Score=26.67 Aligned_cols=41 Identities=32% Similarity=0.476 Sum_probs=35.1
Q ss_pred ccccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEeeCCC
Q psy1676 223 YSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLDREK 264 (343)
Q Consensus 223 ys~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~Id~~~ 264 (343)
+..++..+||..++++ ...+-.++.+|+.+|+|.-.-++.+
T Consensus 15 ~~~~~~~~la~~~~~~-~~~~t~~i~~L~~~g~I~r~~~~~D 55 (59)
T PF01047_consen 15 NGGITQSELAEKLGIS-RSTVTRIIKRLEKKGLIERERDPDD 55 (59)
T ss_dssp HSSEEHHHHHHHHTS--HHHHHHHHHHHHHTTSEEEEEETTE
T ss_pred cCCCCHHHHHHHHCCC-hhHHHHHHHHHHHCCCEEeccCCCC
Confidence 4568999999999995 8999999999999999987777654
No 112
>PLN03081 pentatricopeptide (PPR) repeat-containing protein; Provisional
Probab=71.32 E-value=69 Score=34.07 Aligned_cols=61 Identities=11% Similarity=0.034 Sum_probs=45.6
Q ss_pred HHHHHHHHHHHHhhccHHHHHhhhhhcCCCCCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhh
Q psy1676 57 AVLINCLLRNYLHYNLYDQADKLVKKSAFPENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRK 124 (343)
Q Consensus 57 ~~l~n~Llr~yl~~~~~~~a~~li~k~~~p~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~ 124 (343)
.++.|.|+..|.+.+.++.|..+++...-|. .++|. .+...+...+++.+|...|......
T Consensus 158 ~~~~n~Li~~y~k~g~~~~A~~lf~~m~~~~------~~t~n-~li~~~~~~g~~~~A~~lf~~M~~~ 218 (697)
T PLN03081 158 QYMMNRVLLMHVKCGMLIDARRLFDEMPERN------LASWG-TIIGGLVDAGNYREAFALFREMWED 218 (697)
T ss_pred hHHHHHHHHHHhcCCCHHHHHHHHhcCCCCC------eeeHH-HHHHHHHHCcCHHHHHHHHHHHHHh
Confidence 3678888999999999999999998664332 22332 3344556779999999999998873
No 113
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=71.27 E-value=10 Score=29.03 Aligned_cols=41 Identities=12% Similarity=0.078 Sum_probs=35.2
Q ss_pred HhhcccccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEe
Q psy1676 219 IGASYSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATL 260 (343)
Q Consensus 219 i~~~ys~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~I 260 (343)
.-.-+-+.++.+|+..++.+ ++-||.++..++..|.|.-.-
T Consensus 10 ~l~~~gr~s~~~Ls~~~~~p-~~~VeaMLe~l~~kGkverv~ 50 (78)
T PRK15431 10 LLALRGRMEAAQISQTLNTP-QPMINAMLQQLESMGKAVRIQ 50 (78)
T ss_pred HHHHcCcccHHHHHHHHCcC-HHHHHHHHHHHHHCCCeEeec
Confidence 33457899999999999996 999999999999999996443
No 114
>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=70.85 E-value=31 Score=24.00 Aligned_cols=33 Identities=24% Similarity=0.453 Sum_probs=29.2
Q ss_pred cccC-hHHHHHHhCCCCHHHHHHHHHHhHHcCCce
Q psy1676 224 SRIT-PTKIAEKLGLESPEDAEFIIAKAIRDGVIE 257 (343)
Q Consensus 224 s~Is-l~dIa~~l~l~s~~e~E~ila~lI~~G~I~ 257 (343)
..++ ..+||..+++ |...+...+.+|...|.|.
T Consensus 23 ~~~~~~~~la~~~~i-s~~~v~~~l~~L~~~G~i~ 56 (66)
T cd07377 23 DRLPSERELAEELGV-SRTTVREALRELEAEGLVE 56 (66)
T ss_pred CCCCCHHHHHHHHCC-CHHHHHHHHHHHHHCCCEE
Confidence 4555 9999999999 5999999999999999985
No 115
>PLN03077 Protein ECB2; Provisional
Probab=70.42 E-value=1.3e+02 Score=32.86 Aligned_cols=60 Identities=8% Similarity=-0.049 Sum_probs=43.9
Q ss_pred HHHHHHHHHHHhhccHHHHHhhhhhcCCCCCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhh
Q psy1676 58 VLINCLLRNYLHYNLYDQADKLVKKSAFPENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRK 124 (343)
Q Consensus 58 ~l~n~Llr~yl~~~~~~~a~~li~k~~~p~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~ 124 (343)
++.|.|+..|.+.++++.|..+++...-|+. ++|.-. -..|...+++.+|...|......
T Consensus 223 ~~~n~Li~~y~k~g~~~~A~~lf~~m~~~d~------~s~n~l-i~~~~~~g~~~eAl~lf~~M~~~ 282 (857)
T PLN03077 223 DVVNALITMYVKCGDVVSARLVFDRMPRRDC------ISWNAM-ISGYFENGECLEGLELFFTMREL 282 (857)
T ss_pred chHhHHHHHHhcCCCHHHHHHHHhcCCCCCc------chhHHH-HHHHHhCCCHHHHHHHHHHHHHc
Confidence 5678899999999999999999987644332 232221 22355678999999999988773
No 116
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=70.11 E-value=9.5 Score=25.04 Aligned_cols=32 Identities=31% Similarity=0.475 Sum_probs=29.3
Q ss_pred ccChHHHHHHhCCCCHHHHHHHHHHhHHcCCce
Q psy1676 225 RITPTKIAEKLGLESPEDAEFIIAKAIRDGVIE 257 (343)
Q Consensus 225 ~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~ 257 (343)
.++..++|..++++ ...+-..+..|...|.|.
T Consensus 8 ~~s~~~la~~l~~s-~~tv~~~l~~L~~~g~l~ 39 (48)
T smart00419 8 PLTRQEIAELLGLT-RETVSRTLKRLEKEGLIS 39 (48)
T ss_pred ccCHHHHHHHHCCC-HHHHHHHHHHHHHCCCEE
Confidence 57889999999995 899999999999999995
No 117
>PRK11447 cellulose synthase subunit BcsC; Provisional
Probab=69.85 E-value=85 Score=35.74 Aligned_cols=91 Identities=12% Similarity=0.028 Sum_probs=47.4
Q ss_pred HHHHHHHHhhcccHHHHHHHHHHHHHHhhhcCCcchhHHHHHHHHHHHHhhccHHHHHhhhhhcC--CCCCCChHHHHHH
Q psy1676 20 YFYHSRVHELTNNLDKVRSFLNARLRIATLRNDFEGQAVLINCLLRNYLHYNLYDQADKLVKKSA--FPENASNNEWARF 97 (343)
Q Consensus 20 ~~y~~~~~e~~~~~~~~~~~l~~~~r~a~~~~~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~~--~p~~~~~~~~~~Y 97 (343)
+...+..+...|+.+++...+- ..|... .+...+..+|.+.++++.|...++++. -|.+ ..-
T Consensus 576 ~l~~a~~l~~~G~~~eA~~~l~---------~~p~~~-~~~~~La~~~~~~g~~~~A~~~y~~al~~~P~~------~~a 639 (1157)
T PRK11447 576 VLETANRLRDSGKEAEAEALLR---------QQPPST-RIDLTLADWAQQRGDYAAARAAYQRVLTREPGN------ADA 639 (1157)
T ss_pred HHHHHHHHHHCCCHHHHHHHHH---------hCCCCc-hHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCC------HHH
Confidence 3444555555666665554332 112111 122334566667777777776666541 2221 122
Q ss_pred HHHHHHHHHHhhCHHHHHHHHHHHHhhCC
Q psy1676 98 HFYLGRIKAVRLEYSTAHKNLVQALRKAP 126 (343)
Q Consensus 98 ~YY~Gri~~~~~~y~~A~~~L~~A~~~~~ 126 (343)
++..|+++...+++.+|...|..+....|
T Consensus 640 ~~~la~~~~~~g~~~eA~~~l~~ll~~~p 668 (1157)
T PRK11447 640 RLGLIEVDIAQGDLAAARAQLAKLPATAN 668 (1157)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHHhccCC
Confidence 44566666666777777766666665433
No 118
>PRK15174 Vi polysaccharide export protein VexE; Provisional
Probab=69.64 E-value=41 Score=35.74 Aligned_cols=102 Identities=12% Similarity=0.061 Sum_probs=59.6
Q ss_pred HHHHHHHHHHhhcccHHHHHHHHHHHHHHhhhcCCcchhHHHHHHHHHHHHhhccHHHHHhhhhhc--CCCCCCChHHHH
Q psy1676 18 KCYFYHSRVHELTNNLDKVRSFLNARLRIATLRNDFEGQAVLINCLLRNYLHYNLYDQADKLVKKS--AFPENASNNEWA 95 (343)
Q Consensus 18 ~~~~y~~~~~e~~~~~~~~~~~l~~~~r~a~~~~~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~--~~p~~~~~~~~~ 95 (343)
.+++.++..+...|+..++...-...++.+. ..+|.. ......+-..++..++++.|...++.. ..|. . .
T Consensus 247 ~~~~~Lg~~l~~~G~~~eA~~~A~~~~~~Al-~l~P~~-~~a~~~lg~~l~~~g~~~eA~~~l~~al~l~P~----~--~ 318 (656)
T PRK15174 247 ALRRSLGLAYYQSGRSREAKLQAAEHWRHAL-QFNSDN-VRIVTLYADALIRTGQNEKAIPLLQQSLATHPD----L--P 318 (656)
T ss_pred HHHHHHHHHHHHcCCchhhHHHHHHHHHHHH-hhCCCC-HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC----C--H
Confidence 4456666666666666542111222333222 223332 234444577777888888888777754 2222 1 1
Q ss_pred HHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCc
Q psy1676 96 RFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQ 127 (343)
Q Consensus 96 ~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~ 127 (343)
..++..|.++...++|.+|...|..++...|.
T Consensus 319 ~a~~~La~~l~~~G~~~eA~~~l~~al~~~P~ 350 (656)
T PRK15174 319 YVRAMYARALRQVGQYTAASDEFVQLAREKGV 350 (656)
T ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcc
Confidence 23456788888888888888888888875554
No 119
>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=68.33 E-value=8.1 Score=31.86 Aligned_cols=44 Identities=23% Similarity=0.362 Sum_probs=36.5
Q ss_pred cccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEeeCCCceEE
Q psy1676 224 SRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLDREKGYMQ 268 (343)
Q Consensus 224 s~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~Id~~~g~v~ 268 (343)
..+|..+||..++++ ..-+..++..|...|+|.+.-....||..
T Consensus 24 ~~~s~~eia~~l~is-~~~v~~~l~~L~~~Gli~~~~g~~ggy~l 67 (130)
T TIGR02944 24 QPYSAAEIAEQTGLN-APTVSKILKQLSLAGIVTSKRGVEGGYTL 67 (130)
T ss_pred CCccHHHHHHHHCcC-HHHHHHHHHHHHHCCcEEecCCCCCChhh
Confidence 579999999999995 99999999999999999775444445444
No 120
>KOG1126|consensus
Probab=67.62 E-value=35 Score=35.97 Aligned_cols=103 Identities=17% Similarity=0.159 Sum_probs=64.9
Q ss_pred HHHHHHHHHhhcccHHHHHHHHHHHHHHhhhcCCcchhHHHHHHHHHHHHhhccHHHHHhhhhhcC-C-CCCC-C-----
Q psy1676 19 CYFYHSRVHELTNNLDKVRSFLNARLRIATLRNDFEGQAVLINCLLRNYLHYNLYDQADKLVKKSA-F-PENA-S----- 90 (343)
Q Consensus 19 ~~~y~~~~~e~~~~~~~~~~~l~~~~r~a~~~~~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~~-~-p~~~-~----- 90 (343)
+||=++-+|-+.++++.+.-.+..++-+ +| .-.++...+-+.|.+.+..+.|..+++++. . |.+. +
T Consensus 491 AwYGlG~vy~Kqek~e~Ae~~fqkA~~I-----NP-~nsvi~~~~g~~~~~~k~~d~AL~~~~~A~~ld~kn~l~~~~~~ 564 (638)
T KOG1126|consen 491 AWYGLGTVYLKQEKLEFAEFHFQKAVEI-----NP-SNSVILCHIGRIQHQLKRKDKALQLYEKAIHLDPKNPLCKYHRA 564 (638)
T ss_pred HHHhhhhheeccchhhHHHHHHHhhhcC-----Cc-cchhHHhhhhHHHHHhhhhhHHHHHHHHHHhcCCCCchhHHHHH
Confidence 4777777777777777666554443332 22 224777778899999999999999998652 1 1100 0
Q ss_pred ----------------------hHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCc
Q psy1676 91 ----------------------NNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQ 127 (343)
Q Consensus 91 ----------------------~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~ 127 (343)
..+-..-+|..|+||-..++...|..+|.+|...-|.
T Consensus 565 ~il~~~~~~~eal~~LEeLk~~vP~es~v~~llgki~k~~~~~~~Al~~f~~A~~ldpk 623 (638)
T KOG1126|consen 565 SILFSLGRYVEALQELEELKELVPQESSVFALLGKIYKRLGNTDLALLHFSWALDLDPK 623 (638)
T ss_pred HHHHhhcchHHHHHHHHHHHHhCcchHHHHHHHHHHHHHHccchHHHHhhHHHhcCCCc
Confidence 0133344667777777777777777777777764443
No 121
>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=67.17 E-value=13 Score=31.00 Aligned_cols=63 Identities=19% Similarity=0.266 Sum_probs=44.6
Q ss_pred cccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEeeCCCceEEEccCccccccccchHHHHHH
Q psy1676 224 SRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLDREKGYMQSKESADIYCTVEPQLAFHQR 288 (343)
Q Consensus 224 s~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~Id~~~g~v~~~~~~~v~s~~ep~~~~~~r 288 (343)
..++.++||..++++ ...++.++.+|...|.|...=-...||.-.. +++-.+-.+.+.+++..
T Consensus 24 ~~~s~~~ia~~~~ip-~~~l~kil~~L~~~glv~s~~G~~Ggy~l~~-~~~~Itl~dv~~a~eg~ 86 (135)
T TIGR02010 24 GPVTLADISERQGIS-LSYLEQLFAKLRKAGLVKSVRGPGGGYQLGR-PAEDISVADIIDAVDES 86 (135)
T ss_pred CcCcHHHHHHHHCcC-HHHHHHHHHHHHHCCceEEEeCCCCCEeccC-CHHHCcHHHHHHHhCCC
Confidence 369999999999996 9999999999999999986444445655444 33333333444455443
No 122
>PRK11906 transcriptional regulator; Provisional
Probab=66.87 E-value=85 Score=31.99 Aligned_cols=58 Identities=10% Similarity=0.096 Sum_probs=43.8
Q ss_pred HHhhccHHHHHhhhhhcCCCCCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCcc
Q psy1676 67 YLHYNLYDQADKLVKKSAFPENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQT 128 (343)
Q Consensus 67 yl~~~~~~~a~~li~k~~~p~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~ 128 (343)
....+.++.|..+++.+..-. +..+.=+||.|.+.+..|+..+|..++..|++..|..
T Consensus 348 ~~~~~~~~~a~~~f~rA~~L~----Pn~A~~~~~~~~~~~~~G~~~~a~~~i~~alrLsP~~ 405 (458)
T PRK11906 348 TGLSGQAKVSHILFEQAKIHS----TDIASLYYYRALVHFHNEKIEEARICIDKSLQLEPRR 405 (458)
T ss_pred HHhhcchhhHHHHHHHHhhcC----CccHHHHHHHHHHHHHcCCHHHHHHHHHHHhccCchh
Confidence 344556999999998663211 1233347899999999999999999999999977753
No 123
>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=66.83 E-value=27 Score=36.21 Aligned_cols=126 Identities=17% Similarity=0.168 Sum_probs=76.9
Q ss_pred HHHHHHHHHHHhhccHHHHHhhhhhcCCCCCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCccchHHHHHHH
Q psy1676 58 VLINCLLRNYLHYNLYDQADKLVKKSAFPENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQTAAVGFRQTT 137 (343)
Q Consensus 58 ~l~n~Llr~yl~~~~~~~a~~li~k~~~p~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~sa~~~~~~i 137 (343)
.+...|...|-..|+++.|...|+++.-. .+-.+.+++..|+|+-..|++.+|..++..|=..-++.- --|-. +
T Consensus 195 w~~~~lAqhyd~~g~~~~Al~~Id~aI~h----tPt~~ely~~KarilKh~G~~~~Aa~~~~~Ar~LD~~DR-yiNsK-~ 268 (517)
T PF12569_consen 195 WTLYFLAQHYDYLGDYEKALEYIDKAIEH----TPTLVELYMTKARILKHAGDLKEAAEAMDEARELDLADR-YINSK-C 268 (517)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHHhc----CCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhCChhhH-HHHHH-H
Confidence 34556778898999999999999965211 123578899999999999999999999998887433321 11122 2
Q ss_pred HHHHHHHHHhcCCCCC----hhhhhhHh-------HhhhhhhhH-HHHHHH-HhCC----HHHHHHHHHhccc
Q psy1676 138 QKLAVVVELLLGDIPD----RQIFRQAV-------LRRALSPYF-QLTQAV-RMGE----LQKFNEVLTTYGN 193 (343)
Q Consensus 138 ~K~li~v~LL~G~iP~----~~~~~~~~-------l~~~l~~Y~-~L~~Av-~~Gd----l~~f~~~l~~~~~ 193 (343)
.||+ |-.|++-. -++|+.+. ..-.|.||. +.+.|+ |.|+ +..|..+...+..
T Consensus 269 aKy~----LRa~~~e~A~~~~~~Ftr~~~~~~~~L~~mQc~Wf~~e~a~a~~r~~~~~~ALk~~~~v~k~f~~ 337 (517)
T PF12569_consen 269 AKYL----LRAGRIEEAEKTASLFTREDVDPLSNLNDMQCMWFETECAEAYLRQGDYGLALKRFHAVLKHFDD 337 (517)
T ss_pred HHHH----HHCCCHHHHHHHHHhhcCCCCCcccCHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHH
Confidence 3343 22333322 12222111 123466775 666666 4566 5566666655544
No 124
>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=66.41 E-value=65 Score=31.86 Aligned_cols=101 Identities=15% Similarity=0.099 Sum_probs=54.6
Q ss_pred HHHHHHHHHHhhcccHHHHHHHHHHHHHHhhhcCCcchhH-HHHHHHHHHHHhhccHHHHHhhhhhc--CCCCCCChHHH
Q psy1676 18 KCYFYHSRVHELTNNLDKVRSFLNARLRIATLRNDFEGQA-VLINCLLRNYLHYNLYDQADKLVKKS--AFPENASNNEW 94 (343)
Q Consensus 18 ~~~~y~~~~~e~~~~~~~~~~~l~~~~r~a~~~~~~~~~~-~l~n~Llr~yl~~~~~~~a~~li~k~--~~p~~~~~~~~ 94 (343)
.+++.++..+...|..+.+...+-..++. .++... .+..+..-..+..++.+.+...+++. ..|+ +..
T Consensus 264 ~l~~~~a~~l~~~g~~~~A~~~l~~~l~~-----~pd~~~~~~~~l~~~~~l~~~~~~~~~~~~e~~lk~~p~----~~~ 334 (409)
T TIGR00540 264 ALKIALAEHLIDCDDHDSAQEIIFDGLKK-----LGDDRAISLPLCLPIPRLKPEDNEKLEKLIEKQAKNVDD----KPK 334 (409)
T ss_pred HHHHHHHHHHHHCCChHHHHHHHHHHHhh-----CCCcccchhHHHHHhhhcCCCChHHHHHHHHHHHHhCCC----Chh
Confidence 44555555566666655555555443331 111111 11111111222334455555555432 1222 222
Q ss_pred HHHHHHHHHHHHHhhCHHHHHHHHH--HHHhhCCc
Q psy1676 95 ARFHFYLGRIKAVRLEYSTAHKNLV--QALRKAPQ 127 (343)
Q Consensus 95 ~~Y~YY~Gri~~~~~~y~~A~~~L~--~A~~~~~~ 127 (343)
+.+...+|+++..+++|.+|.++|+ .++...|.
T Consensus 335 ~~ll~sLg~l~~~~~~~~~A~~~le~a~a~~~~p~ 369 (409)
T TIGR00540 335 CCINRALGQLLMKHGEFIEAADAFKNVAACKEQLD 369 (409)
T ss_pred HHHHHHHHHHHHHcccHHHHHHHHHHhHHhhcCCC
Confidence 5788899999999999999999999 67765453
No 125
>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=66.21 E-value=12 Score=26.54 Aligned_cols=34 Identities=26% Similarity=0.375 Sum_probs=30.7
Q ss_pred cccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceE
Q psy1676 224 SRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEA 258 (343)
Q Consensus 224 s~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a 258 (343)
..++.++||..+|++ ...+..++..|..+|.|..
T Consensus 24 ~~~s~~ela~~~g~s-~~tv~r~l~~L~~~g~i~~ 57 (67)
T cd00092 24 LPLTRQEIADYLGLT-RETVSRTLKELEEEGLISR 57 (67)
T ss_pred CCcCHHHHHHHHCCC-HHHHHHHHHHHHHCCCEEe
Confidence 468999999999995 9999999999999999953
No 126
>KOG3250|consensus
Probab=66.14 E-value=26 Score=32.16 Aligned_cols=124 Identities=11% Similarity=0.140 Sum_probs=80.2
Q ss_pred hhhhHHHHHHHHhCCHHHHHHHHHhccccccccccHHHHHHHHHHHHHHHHHHHhhcccccChHHHHHHhCCCCHHHHHH
Q psy1676 166 LSPYFQLTQAVRMGELQKFNEVLTTYGNQFRTDYTFKLILRLRHNVIKTAIRSIGASYSRITPTKIAEKLGLESPEDAEF 245 (343)
Q Consensus 166 l~~Y~~L~~Av~~Gdl~~f~~~l~~~~~~f~~d~~~~Lv~~l~~~v~r~~ir~i~~~ys~Isl~dIa~~l~l~s~~e~E~ 245 (343)
-..|..+...|-.|+...+...... |-+=.. .-+.+|++..+-++ ...-..||...+-+.+.++..-++|.
T Consensus 59 dsa~lrlL~lFa~Gt~~Dy~aea~r----lp~Ls~-~q~~kLk~ltV~sl----as~~k~lpy~~Ll~~l~~~nvrelEd 129 (258)
T KOG3250|consen 59 DSAYLRLLELFAYGTYRDYSAEALR----LPKLSL-AQLNKLKHLTVVSL----ASFEKCLPYLVLLRLLPSRNVRELED 129 (258)
T ss_pred cHHHHHHHHHHhcCchhhhhhhhhc----CCCCCH-HHHHhhhcceehhh----hhhchhhhHHHHHhhccCCchhHHHH
Confidence 4478999999999998877654321 211111 11223333222111 12235788888888888888999999
Q ss_pred HHHHhHHcCCceEEeeCCCceEEEccC--ccccc--cccchHHHHHHHHHHHHhhHH
Q psy1676 246 IIAKAIRDGVIEATLDREKGYMQSKES--ADIYC--TVEPQLAFHQRIAFCLDLHNQ 298 (343)
Q Consensus 246 ila~lI~~G~I~a~Id~~~g~v~~~~~--~~v~s--~~ep~~~~~~rI~~cl~l~~~ 298 (343)
+|..++..|.+.|+||+.+.++..... -|.-+ -.++...++.=+..|-.+--.
T Consensus 130 ~iieamya~IlrGkldqr~q~leV~faigRdlr~k~i~nm~~TL~~w~~~cenvL~~ 186 (258)
T KOG3250|consen 130 LIIEAMYADILRGKLDQRNQTLEVDFAIGRDLRSKDIDNMKYTLDEWCEGCENVLFG 186 (258)
T ss_pred HHHHHHHHHHHHhhHHhhcceEeechhhcccccHhHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999988876532 12222 225666677777777655333
No 127
>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B.
Probab=65.85 E-value=18 Score=25.28 Aligned_cols=49 Identities=20% Similarity=0.209 Sum_probs=33.8
Q ss_pred HHHHHHHHHhhCHHHHHHHHHHHHhhCCccchHHHHHHHHHHHHHHHHhcCCCCC
Q psy1676 99 FYLGRIKAVRLEYSTAHKNLVQALRKAPQTAAVGFRQTTQKLAVVVELLLGDIPD 153 (343)
Q Consensus 99 YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~sa~~~~~~i~K~li~v~LL~G~iP~ 153 (343)
|-.|+.+...++|.+|...|.+++...|.. .. +..++-.+....|+...
T Consensus 1 ~~~a~~~~~~g~~~~A~~~~~~~l~~~P~~--~~----a~~~lg~~~~~~g~~~~ 49 (65)
T PF13432_consen 1 YALARALYQQGDYDEAIAAFEQALKQDPDN--PE----AWYLLGRILYQQGRYDE 49 (65)
T ss_dssp HHHHHHHHHCTHHHHHHHHHHHHHCCSTTH--HH----HHHHHHHHHHHTT-HHH
T ss_pred ChHHHHHHHcCCHHHHHHHHHHHHHHCCCC--HH----HHHHHHHHHHHcCCHHH
Confidence 457999999999999999999999976653 11 33344444455666433
No 128
>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=65.75 E-value=14 Score=23.29 Aligned_cols=31 Identities=39% Similarity=0.524 Sum_probs=25.7
Q ss_pred ccChHHHHHHhCCCCHHHHHHHHHHhHHcCCc
Q psy1676 225 RITPTKIAEKLGLESPEDAEFIIAKAIRDGVI 256 (343)
Q Consensus 225 ~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I 256 (343)
.++-.|||..+|+. .+-|-.++.++-.+|.|
T Consensus 2 ~mtr~diA~~lG~t-~ETVSR~l~~l~~~glI 32 (32)
T PF00325_consen 2 PMTRQDIADYLGLT-RETVSRILKKLERQGLI 32 (32)
T ss_dssp E--HHHHHHHHTS--HHHHHHHHHHHHHTTSE
T ss_pred CcCHHHHHHHhCCc-HHHHHHHHHHHHHcCCC
Confidence 35678999999995 99999999999999986
No 129
>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A.
Probab=65.45 E-value=15 Score=22.92 Aligned_cols=27 Identities=22% Similarity=0.094 Sum_probs=22.8
Q ss_pred HHHHHHHHHHHhhCHHHHHHHHHHHHh
Q psy1676 97 FHFYLGRIKAVRLEYSTAHKNLVQALR 123 (343)
Q Consensus 97 Y~YY~Gri~~~~~~y~~A~~~L~~A~~ 123 (343)
-+.-+|.++..+++|.+|..++.+|+.
T Consensus 4 ~~~~la~~~~~~g~~~~A~~~~~~al~ 30 (42)
T PF13374_consen 4 ALNNLANAYRAQGRYEEALELLEEALE 30 (42)
T ss_dssp HHHHHHHHHHHCT-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhhhhcchhhHHHHHHHH
Confidence 345689999999999999999999987
No 130
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=65.26 E-value=21 Score=24.31 Aligned_cols=39 Identities=21% Similarity=0.313 Sum_probs=32.9
Q ss_pred ccccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEeeC
Q psy1676 223 YSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLDR 262 (343)
Q Consensus 223 ys~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~Id~ 262 (343)
-..+++.+|+..++++ ...+-..+..|..+|.|...-+.
T Consensus 8 ~~~~~~~~i~~~l~is-~~~v~~~l~~L~~~g~i~~~~~~ 46 (66)
T smart00418 8 EGELCVCELAEILGLS-QSTVSHHLKKLREAGLVESRREG 46 (66)
T ss_pred cCCccHHHHHHHHCCC-HHHHHHHHHHHHHCCCeeeeecC
Confidence 4568899999999995 88999999999999999755443
No 131
>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=64.64 E-value=17 Score=21.66 Aligned_cols=29 Identities=14% Similarity=0.355 Sum_probs=21.9
Q ss_pred HHHHHHHHHHHhhcccHHHHHHHHHHHHH
Q psy1676 17 AKCYFYHSRVHELTNNLDKVRSFLNARLR 45 (343)
Q Consensus 17 a~~~~y~~~~~e~~~~~~~~~~~l~~~~r 45 (343)
|++||+.+.++...++..+++..+..+++
T Consensus 1 a~~~~~lg~~~~~~~~~~~A~~~~~~al~ 29 (34)
T PF07719_consen 1 AEAWYYLGQAYYQLGNYEEAIEYFEKALE 29 (34)
T ss_dssp HHHHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence 67888889999888888888877665554
No 132
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=63.72 E-value=17 Score=28.60 Aligned_cols=33 Identities=30% Similarity=0.562 Sum_probs=31.1
Q ss_pred cccChHHHHHHhCCCCHHHHHHHHHHhHHcCCce
Q psy1676 224 SRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIE 257 (343)
Q Consensus 224 s~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~ 257 (343)
.++|.++||+.+|++ +..+-..+.+|..+|.|.
T Consensus 16 ~~~~~~~la~~l~~s-~~tv~~~l~~L~~~g~i~ 48 (108)
T smart00344 16 ARISLAELAKKVGLS-PSTVHNRVKRLEEEGVIK 48 (108)
T ss_pred CCCCHHHHHHHHCcC-HHHHHHHHHHHHHCCCee
Confidence 689999999999995 999999999999999997
No 133
>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=63.65 E-value=13 Score=30.54 Aligned_cols=44 Identities=25% Similarity=0.376 Sum_probs=35.8
Q ss_pred cccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEeeCCCceEE
Q psy1676 224 SRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLDREKGYMQ 268 (343)
Q Consensus 224 s~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~Id~~~g~v~ 268 (343)
..++.++||..++++ ...+..++..|...|+|...-....||.-
T Consensus 24 ~~~s~~eia~~~~i~-~~~v~~il~~L~~~gli~~~~g~~ggy~l 67 (132)
T TIGR00738 24 GPVSVKEIAERQGIS-RSYLEKILRTLRRAGLVESVRGPGGGYRL 67 (132)
T ss_pred CcCcHHHHHHHHCcC-HHHHHHHHHHHHHCCcEEeccCCCCCccC
Confidence 379999999999996 99999999999999999754333445443
No 134
>PRK14574 hmsH outer membrane protein; Provisional
Probab=62.07 E-value=2.5e+02 Score=30.94 Aligned_cols=90 Identities=11% Similarity=-0.001 Sum_probs=59.2
Q ss_pred hcccHHHHHHHHHHHHHHhhhcCCcchhHHHHHHHHHHHHhhccHHHHHhhhhhcCCCCCCChHHHHHHHHHHHHHHHHh
Q psy1676 29 LTNNLDKVRSFLNARLRIATLRNDFEGQAVLINCLLRNYLHYNLYDQADKLVKKSAFPENASNNEWARFHFYLGRIKAVR 108 (343)
Q Consensus 29 ~~~~~~~~~~~l~~~~r~a~~~~~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~~~p~~~~~~~~~~Y~YY~Gri~~~~ 108 (343)
..|....+...|..++ +.+|.....+. .++.++...|+..+|...+++...|...+.... --.|+++..+
T Consensus 46 r~Gd~~~Al~~L~qaL-----~~~P~~~~av~-dll~l~~~~G~~~~A~~~~eka~~p~n~~~~~l----lalA~ly~~~ 115 (822)
T PRK14574 46 RAGDTAPVLDYLQEES-----KAGPLQSGQVD-DWLQIAGWAGRDQEVIDVYERYQSSMNISSRGL----ASAARAYRNE 115 (822)
T ss_pred hCCCHHHHHHHHHHHH-----hhCccchhhHH-HHHHHHHHcCCcHHHHHHHHHhccCCCCCHHHH----HHHHHHHHHc
Confidence 4455555555554433 33555543333 778888888999999999988764432222111 1337788888
Q ss_pred hCHHHHHHHHHHHHhhCCcc
Q psy1676 109 LEYSTAHKNLVQALRKAPQT 128 (343)
Q Consensus 109 ~~y~~A~~~L~~A~~~~~~~ 128 (343)
++|.+|...|..++..-|..
T Consensus 116 gdyd~Aiely~kaL~~dP~n 135 (822)
T PRK14574 116 KRWDQALALWQSSLKKDPTN 135 (822)
T ss_pred CCHHHHHHHHHHHHhhCCCC
Confidence 99999999999999876664
No 135
>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=61.61 E-value=92 Score=25.74 Aligned_cols=64 Identities=22% Similarity=0.163 Sum_probs=44.0
Q ss_pred hHHHHHH-HHHHHHhhccHHHHHhhhhhcCCCCCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHH
Q psy1676 56 QAVLINC-LLRNYLHYNLYDQADKLVKKSAFPENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQ 120 (343)
Q Consensus 56 ~~~l~n~-Llr~yl~~~~~~~a~~li~k~~~p~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~ 120 (343)
-+.+..+ +.+.++..|+++.|...++++.-.. ....-.-.-.+.++++++.+++|.+|...|..
T Consensus 46 ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~-~d~~l~~~a~l~LA~~~~~~~~~d~Al~~L~~ 110 (145)
T PF09976_consen 46 YAALAALQLAKAAYEQGDYDEAKAALEKALANA-PDPELKPLARLRLARILLQQGQYDEALATLQQ 110 (145)
T ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhC-CCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHh
Confidence 3345554 6689999999999999998652111 11122222355689999999999999999865
No 136
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=61.24 E-value=34 Score=23.25 Aligned_cols=33 Identities=15% Similarity=0.426 Sum_probs=30.0
Q ss_pred ccc-ChHHHHHHhCCCCHHHHHHHHHHhHHcCCce
Q psy1676 224 SRI-TPTKIAEKLGLESPEDAEFIIAKAIRDGVIE 257 (343)
Q Consensus 224 s~I-sl~dIa~~l~l~s~~e~E~ila~lI~~G~I~ 257 (343)
.++ |..++|..+++ |..-+...+..|..+|.|.
T Consensus 18 ~~l~s~~~la~~~~v-s~~tv~~~l~~L~~~g~i~ 51 (60)
T smart00345 18 DKLPSERELAAQLGV-SRTTVREALSRLEAEGLVQ 51 (60)
T ss_pred CcCcCHHHHHHHHCC-CHHHHHHHHHHHHHCCCEE
Confidence 467 79999999999 5999999999999999985
No 137
>KOG1155|consensus
Probab=61.18 E-value=1e+02 Score=31.66 Aligned_cols=100 Identities=17% Similarity=0.152 Sum_probs=57.3
Q ss_pred HHHHHHHHHhhcccHHHHHHHHHHHHHHhhhcCCcchhHHHHHHHHHHHHhhccHHHHHhhhhhc---CCCCCCChHHHH
Q psy1676 19 CYFYHSRVHELTNNLDKVRSFLNARLRIATLRNDFEGQAVLINCLLRNYLHYNLYDQADKLVKKS---AFPENASNNEWA 95 (343)
Q Consensus 19 ~~~y~~~~~e~~~~~~~~~~~l~~~~r~a~~~~~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~---~~p~~~~~~~~~ 95 (343)
+|-=++.+||.+++++++. +|+.-+.+-+|.+| ...+.|.++|=+.+++..|.....+- ...+..-..+.+
T Consensus 434 lw~aLG~CY~kl~~~~eAi----KCykrai~~~dte~--~~l~~LakLye~l~d~~eAa~~yek~v~~~~~eg~~~~~t~ 507 (559)
T KOG1155|consen 434 LWVALGECYEKLNRLEEAI----KCYKRAILLGDTEG--SALVRLAKLYEELKDLNEAAQYYEKYVEVSELEGEIDDETI 507 (559)
T ss_pred HHHHHHHHHHHhccHHHHH----HHHHHHHhccccch--HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhhcccchHHH
Confidence 3444455566666666655 45554555555544 44556677787888888887776653 111111111222
Q ss_pred HHHHHHHHHHHHhhCHHHHHHHHHHHHhh
Q psy1676 96 RFHFYLGRIKAVRLEYSTAHKNLVQALRK 124 (343)
Q Consensus 96 ~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~ 124 (343)
.=.-+++..+...++|.+|..+.+.+..-
T Consensus 508 ka~~fLA~~f~k~~~~~~As~Ya~~~~~~ 536 (559)
T KOG1155|consen 508 KARLFLAEYFKKMKDFDEASYYATLVLKG 536 (559)
T ss_pred HHHHHHHHHHHhhcchHHHHHHHHHHhcC
Confidence 22334777777778888888877777664
No 138
>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=60.64 E-value=33 Score=24.52 Aligned_cols=36 Identities=22% Similarity=0.458 Sum_probs=31.0
Q ss_pred hcccccChHHHHHHhCCCCHHHHHHHHHHhHHcCCce
Q psy1676 221 ASYSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIE 257 (343)
Q Consensus 221 ~~ys~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~ 257 (343)
..-..++..+||+.|++. +..|=..+.+|-.+|+|.
T Consensus 18 ~~~~~v~~~~iA~~L~vs-~~tvt~ml~~L~~~GlV~ 53 (60)
T PF01325_consen 18 EEGGPVRTKDIAERLGVS-PPTVTEMLKRLAEKGLVE 53 (60)
T ss_dssp HCTSSBBHHHHHHHHTS--HHHHHHHHHHHHHTTSEE
T ss_pred cCCCCccHHHHHHHHCCC-hHHHHHHHHHHHHCCCEE
Confidence 345789999999999994 999999999999999883
No 139
>KOG4414|consensus
Probab=60.49 E-value=14 Score=31.67 Aligned_cols=44 Identities=27% Similarity=0.312 Sum_probs=37.3
Q ss_pred HHHHHHHHHHHHHHHHHHhhcccccChHHHHHHhCCCCHHHHHHH
Q psy1676 202 KLILRLRHNVIKTAIRSIGASYSRITPTKIAEKLGLESPEDAEFI 246 (343)
Q Consensus 202 ~Lv~~l~~~v~r~~ir~i~~~ys~Isl~dIa~~l~l~s~~e~E~i 246 (343)
.++.-+|....|+.+.-+.+.|++|...|+|.-+|++ ++++-..
T Consensus 109 ~imaAf~D~~~kR~FaLl~qAYssI~~~D~A~FlGl~-~ddAtk~ 152 (197)
T KOG4414|consen 109 DIMAAFRDATRKRAFALLLQAYSSIIADDFAAFLGLP-EDDATKG 152 (197)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC-HHHHHHH
Confidence 5677788888999999999999999999999999997 5555433
No 140
>COG3063 PilF Tfp pilus assembly protein PilF [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=60.32 E-value=1.5e+02 Score=27.69 Aligned_cols=91 Identities=21% Similarity=0.159 Sum_probs=50.9
Q ss_pred HHHHHHHHHHHhhccHHHHHhhhhhc-CCCCCCChHHHHHHHHHH-----------------------------HHHHHH
Q psy1676 58 VLINCLLRNYLHYNLYDQADKLVKKS-AFPENASNNEWARFHFYL-----------------------------GRIKAV 107 (343)
Q Consensus 58 ~l~n~Llr~yl~~~~~~~a~~li~k~-~~p~~~~~~~~~~Y~YY~-----------------------------Gri~~~ 107 (343)
..--.|--.||+.|++.+|+.-++|. ...++...++.++=+||. |-..+.
T Consensus 36 ~arlqLal~YL~~gd~~~A~~nlekAL~~DPs~~~a~~~~A~~Yq~~Ge~~~A~e~YrkAlsl~p~~GdVLNNYG~FLC~ 115 (250)
T COG3063 36 KARLQLALGYLQQGDYAQAKKNLEKALEHDPSYYLAHLVRAHYYQKLGENDLADESYRKALSLAPNNGDVLNNYGAFLCA 115 (250)
T ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcCChhhHHHHHHHHHhcCCCccchhhhhhHHHHh
Confidence 34446778899999999999999986 222222223333333332 334556
Q ss_pred hhCHHHHHHHHHHHHh-hCCccchHHHHHHHHHHHHHHHHhcCCCCC
Q psy1676 108 RLEYSTAHKNLVQALR-KAPQTAAVGFRQTTQKLAVVVELLLGDIPD 153 (343)
Q Consensus 108 ~~~y~~A~~~L~~A~~-~~~~~sa~~~~~~i~K~li~v~LL~G~iP~ 153 (343)
+++|.+|...|..|+. |.-...+. ..--+.+|.+-+|+.-.
T Consensus 116 qg~~~eA~q~F~~Al~~P~Y~~~s~-----t~eN~G~Cal~~gq~~~ 157 (250)
T COG3063 116 QGRPEEAMQQFERALADPAYGEPSD-----TLENLGLCALKAGQFDQ 157 (250)
T ss_pred CCChHHHHHHHHHHHhCCCCCCcch-----hhhhhHHHHhhcCCchh
Confidence 6677777777777766 21111011 12235566666666444
No 141
>KOG0543|consensus
Probab=60.29 E-value=35 Score=33.96 Aligned_cols=67 Identities=24% Similarity=0.201 Sum_probs=51.6
Q ss_pred HHHHHHHHHHHhhccHHHHHhhhhhcCCCCCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCcc
Q psy1676 58 VLINCLLRNYLHYNLYDQADKLVKKSAFPENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQT 128 (343)
Q Consensus 58 ~l~n~Llr~yl~~~~~~~a~~li~k~~~p~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~ 128 (343)
.+++-|.-+|++.+.|..|....+++-- ..+++-.+ +|=.|+.++..++|..|...|+.|+..-|.+
T Consensus 258 ~~~lNlA~c~lKl~~~~~Ai~~c~kvLe--~~~~N~KA--LyRrG~A~l~~~e~~~A~~df~ka~k~~P~N 324 (397)
T KOG0543|consen 258 ACHLNLAACYLKLKEYKEAIESCNKVLE--LDPNNVKA--LYRRGQALLALGEYDLARDDFQKALKLEPSN 324 (397)
T ss_pred HHhhHHHHHHHhhhhHHHHHHHHHHHHh--cCCCchhH--HHHHHHHHHhhccHHHHHHHHHHHHHhCCCc
Confidence 3444578899999999999888776621 12334444 4568999999999999999999999977765
No 142
>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=59.76 E-value=1.5e+02 Score=27.91 Aligned_cols=27 Identities=22% Similarity=0.143 Sum_probs=13.4
Q ss_pred HHHHHHHHhhCHHHHHHHHHHHHhhCC
Q psy1676 100 YLGRIKAVRLEYSTAHKNLVQALRKAP 126 (343)
Q Consensus 100 Y~Gri~~~~~~y~~A~~~L~~A~~~~~ 126 (343)
..|.++..++++.+|...+..++...|
T Consensus 119 ~~a~~~~~~G~~~~A~~~~~~al~~~p 145 (355)
T cd05804 119 MLAFGLEEAGQYDRAEEAARRALELNP 145 (355)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHhhCC
Confidence 444455555555555555555555333
No 143
>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=59.56 E-value=34 Score=23.97 Aligned_cols=41 Identities=24% Similarity=0.425 Sum_probs=34.2
Q ss_pred cChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEeeCCCceE
Q psy1676 226 ITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLDREKGYM 267 (343)
Q Consensus 226 Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~Id~~~g~v 267 (343)
++.++|+..++++ ...+-..+..|...|.|...-+...++.
T Consensus 21 ~~~~ei~~~~~i~-~~~i~~~l~~L~~~g~i~~~~~~~~~~~ 61 (78)
T cd00090 21 LTVSELAERLGLS-QSTVSRHLKKLEEAGLVESRREGRRVYY 61 (78)
T ss_pred cCHHHHHHHHCcC-HhHHHHHHHHHHHCCCeEEEEeccEEEE
Confidence 9999999999995 8899999999999999987655533333
No 144
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=59.50 E-value=79 Score=27.67 Aligned_cols=96 Identities=19% Similarity=0.250 Sum_probs=59.4
Q ss_pred HHHHHHHHHHHHHHHHHHhhccc-ccChHHHHHHh--CCCCHHHHHHHHHHhHHcCCceEEeeCCCceEEEccCcccccc
Q psy1676 202 KLILRLRHNVIKTAIRSIGASYS-RITPTKIAEKL--GLESPEDAEFIIAKAIRDGVIEATLDREKGYMQSKESADIYCT 278 (343)
Q Consensus 202 ~Lv~~l~~~v~r~~ir~i~~~ys-~Isl~dIa~~l--~l~s~~e~E~ila~lI~~G~I~a~Id~~~g~v~~~~~~~v~s~ 278 (343)
..+..=.+.++|.++. ... .-....||+++ +++ .++|+..|.-|..-|.|+ -+..++|++...... ++
T Consensus 19 ~~~~~W~~~~ir~l~~----l~~~~~d~~~iak~l~p~is-~~ev~~sL~~L~~~gli~--k~~~g~y~~t~~~l~--~~ 89 (171)
T PF14394_consen 19 EYYSSWYHPAIRELLP----LMPFAPDPEWIAKRLRPKIS-AEEVRDSLEFLEKLGLIK--KDGDGKYVQTDKSLT--TS 89 (171)
T ss_pred HHHhhhHHHHHHHHhh----cCCCCCCHHHHHHHhcCCCC-HHHHHHHHHHHHHCCCeE--ECCCCcEEEecceee--CC
Confidence 3344444555555443 221 22778999999 894 999999999999999995 333446666654332 34
Q ss_pred ccchHHHHHHHH-HHHHhhHHHhhhcCCCCC
Q psy1676 279 VEPQLAFHQRIA-FCLDLHNQSVKAMRYPPK 308 (343)
Q Consensus 279 ~ep~~~~~~rI~-~cl~l~~~~~~am~~~~~ 308 (343)
.+..+..-.+.. .|+++-.+++.. +|+.
T Consensus 90 ~~~~~~avr~~h~q~~~lA~~al~~--~p~~ 118 (171)
T PF14394_consen 90 SEIPSEAVRSYHKQMLELAQEALDR--VPPE 118 (171)
T ss_pred CCCcHHHHHHHHHHHHHHHHHHHHh--CCcc
Confidence 444455555554 688885554433 5553
No 145
>PRK11189 lipoprotein NlpI; Provisional
Probab=58.79 E-value=55 Score=30.90 Aligned_cols=70 Identities=21% Similarity=0.097 Sum_probs=45.6
Q ss_pred CcchhHHHHHHHHHHHHhhccHHHHHhhhhhc-C-CCCCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCc
Q psy1676 52 DFEGQAVLINCLLRNYLHYNLYDQADKLVKKS-A-FPENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQ 127 (343)
Q Consensus 52 ~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~-~-~p~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~ 127 (343)
+++..+-.+..+-.+|...|.++.|...+++. . .|. ....++..|.++...++|.+|...|..|+...|.
T Consensus 59 ~~~~~a~~~~~~g~~~~~~g~~~~A~~~~~~Al~l~P~------~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~P~ 130 (296)
T PRK11189 59 TDEERAQLHYERGVLYDSLGLRALARNDFSQALALRPD------MADAYNYLGIYLTQAGNFDAAYEAFDSVLELDPT 130 (296)
T ss_pred CcHhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCC------CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC
Confidence 34444444445556677778888887776654 2 222 1344567888888888888888888888875554
No 146
>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=58.79 E-value=1.3e+02 Score=26.40 Aligned_cols=82 Identities=16% Similarity=0.071 Sum_probs=61.8
Q ss_pred HHHHHhhhcCCcchhHHHHHHHHHHHHhhccHHHHHhhhhhcCCCCCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHH
Q psy1676 42 ARLRIATLRNDFEGQAVLINCLLRNYLHYNLYDQADKLVKKSAFPENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQA 121 (343)
Q Consensus 42 ~~~r~a~~~~~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~~~p~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A 121 (343)
.-++.+.....++........+...|.+.|+++.|......+. +...+..+.+..+...-++.+..++|.....++..|
T Consensus 21 ~elk~~~~n~~kesir~~~~~l~~~~~~~Gd~~~A~k~y~~~~-~~~~~~~~~id~~l~~irv~i~~~d~~~v~~~i~ka 99 (177)
T PF10602_consen 21 AELKDAKSNLGKESIRMALEDLADHYCKIGDLEEALKAYSRAR-DYCTSPGHKIDMCLNVIRVAIFFGDWSHVEKYIEKA 99 (177)
T ss_pred HHHHHHHhccchHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHh-hhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH
Confidence 3334444333444444566677899999999999999988752 223567899999999999999999999999999888
Q ss_pred Hhh
Q psy1676 122 LRK 124 (343)
Q Consensus 122 ~~~ 124 (343)
-..
T Consensus 100 ~~~ 102 (177)
T PF10602_consen 100 ESL 102 (177)
T ss_pred HHH
Confidence 873
No 147
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=58.51 E-value=18 Score=31.56 Aligned_cols=47 Identities=17% Similarity=0.388 Sum_probs=38.9
Q ss_pred cccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEeeCCCceEEEcc
Q psy1676 224 SRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLDREKGYMQSKE 271 (343)
Q Consensus 224 s~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~Id~~~g~v~~~~ 271 (343)
..+|.++||+.++++ ..-++.++.+|-..|.|...=-...||.--.+
T Consensus 24 ~~vs~~eIA~~~~ip-~~~l~kIl~~L~~aGLv~s~rG~~GGy~Lar~ 70 (164)
T PRK10857 24 GPVPLADISERQGIS-LSYLEQLFSRLRKNGLVSSVRGPGGGYLLGKD 70 (164)
T ss_pred CcCcHHHHHHHHCcC-HHHHHHHHHHHHHCCCEEeCCCCCCCeeccCC
Confidence 469999999999996 99999999999999999874455556655443
No 148
>PF10300 DUF3808: Protein of unknown function (DUF3808); InterPro: IPR019412 This entry represents a family of proteins conserved from fungi to humans. In humans this protein is expressed in primary breast carcinomas but not in normal breast tissue, and has a putative eukaryotic RNP-1 RNA binding region and a candidate anchoring transmembrane domain. The human protein is coordinately regulated with oestrogen receptor, but is not necessarily oestradiol-responsive []. Members of this family carry a tetratricopeptide repeat (IPR013105 from INTERPRO) at their C terminus.
Probab=57.65 E-value=2.2e+02 Score=28.94 Aligned_cols=120 Identities=13% Similarity=0.128 Sum_probs=71.1
Q ss_pred HHHHHHHHhhccc------HHHHHHHHHHHHHHhhhcCCcchhHHHHHHHHHHHHhhccHHHHHhhhhhcCCCCCCChHH
Q psy1676 20 YFYHSRVHELTNN------LDKVRSFLNARLRIATLRNDFEGQAVLINCLLRNYLHYNLYDQADKLVKKSAFPENASNNE 93 (343)
Q Consensus 20 ~~y~~~~~e~~~~------~~~~~~~l~~~~r~a~~~~~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~~~p~~~~~~~ 93 (343)
..||.-+-.+.+. +..+...|..... .=|.+..++... -|++...++.+.|...++++......-.+-
T Consensus 230 L~y~~~~~~~~~~~~~~~~~~~a~~lL~~~~~-----~yP~s~lfl~~~-gR~~~~~g~~~~Ai~~~~~a~~~q~~~~Ql 303 (468)
T PF10300_consen 230 LWYHLVVPSFLGIDGEDVPLEEAEELLEEMLK-----RYPNSALFLFFE-GRLERLKGNLEEAIESFERAIESQSEWKQL 303 (468)
T ss_pred HHHHHHHHHHcCCcccCCCHHHHHHHHHHHHH-----hCCCcHHHHHHH-HHHHHHhcCHHHHHHHHHHhccchhhHHhH
Confidence 5566555554443 3444444432221 234554454444 789999999999999998654221111122
Q ss_pred HHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCccchHHHHHHHHHHHHH-HHHhcCCC
Q psy1676 94 WARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQTAAVGFRQTTQKLAVV-VELLLGDI 151 (343)
Q Consensus 94 ~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~sa~~~~~~i~K~li~-v~LL~G~i 151 (343)
..--+|=.|-.++.+.+|.+|.+++........ |-.++..|+.- |.+.+|+.
T Consensus 304 ~~l~~~El~w~~~~~~~w~~A~~~f~~L~~~s~------WSka~Y~Y~~a~c~~~l~~~ 356 (468)
T PF10300_consen 304 HHLCYFELAWCHMFQHDWEEAAEYFLRLLKESK------WSKAFYAYLAAACLLMLGRE 356 (468)
T ss_pred HHHHHHHHHHHHHHHchHHHHHHHHHHHHhccc------cHHHHHHHHHHHHHHhhccc
Confidence 223356678899999999999999988777322 23344444444 44556665
No 149
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=57.56 E-value=1.4e+02 Score=26.99 Aligned_cols=77 Identities=16% Similarity=0.230 Sum_probs=53.9
Q ss_pred HhhhcC-CcchhHHHHHHHHHHHHhhccHHHHHhhhhhc-----------CCCCCCChHHHHHHHHHHHHHHHHhhCHHH
Q psy1676 46 IATLRN-DFEGQAVLINCLLRNYLHYNLYDQADKLVKKS-----------AFPENASNNEWARFHFYLGRIKAVRLEYST 113 (343)
Q Consensus 46 ~a~~~~-~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~-----------~~p~~~~~~~~~~Y~YY~Gri~~~~~~y~~ 113 (343)
++..+. ++..++.+.--+..+|=..++-..-..++.++ .+|. ..-+..+..|+.|.++--.|++.+
T Consensus 106 ~~~~~~~~~s~~A~l~LrlAWlyR~~~~~~~E~~fl~~Al~~y~~a~~~e~~~~--~~~~~~~l~YLigeL~rrlg~~~e 183 (214)
T PF09986_consen 106 CAQIKKEKPSKKAGLCLRLAWLYRDLGDEENEKRFLRKALEFYEEAYENEDFPI--EGMDEATLLYLIGELNRRLGNYDE 183 (214)
T ss_pred HHHHhCCCHHHHHHHHHHHHHHhhccCCHHHHHHHHHHHHHHHHHHHHhCcCCC--CCchHHHHHHHHHHHHHHhCCHHH
Confidence 344443 34445566666777777777766666665543 2221 234667789999999999999999
Q ss_pred HHHHHHHHHhh
Q psy1676 114 AHKNLVQALRK 124 (343)
Q Consensus 114 A~~~L~~A~~~ 124 (343)
|.++|...+..
T Consensus 184 A~~~fs~vi~~ 194 (214)
T PF09986_consen 184 AKRWFSRVIGS 194 (214)
T ss_pred HHHHHHHHHcC
Confidence 99999999983
No 150
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=57.50 E-value=15 Score=34.06 Aligned_cols=50 Identities=28% Similarity=0.399 Sum_probs=39.4
Q ss_pred HHHHHHHHHHHHhhc-ccccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceE
Q psy1676 208 RHNVIKTAIRSIGAS-YSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEA 258 (343)
Q Consensus 208 ~~~v~r~~ir~i~~~-ys~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a 258 (343)
+....|.+|...... ..++..+|||.++|+. ++.+-..+-+|+.+|+|+-
T Consensus 7 kk~~t~fqIL~ei~~~qp~v~q~eIA~~lgiT-~QaVsehiK~Lv~eG~i~~ 57 (260)
T COG1497 7 KKNLTRFQILSEIAVRQPRVKQKEIAKKLGIT-LQAVSEHIKELVKEGLIEK 57 (260)
T ss_pred cccchHHHHHHHHHHhCCCCCHHHHHHHcCCC-HHHHHHHHHHHHhccceee
Confidence 344555665443333 4899999999999995 9999999999999999964
No 151
>PRK04841 transcriptional regulator MalT; Provisional
Probab=56.91 E-value=1.7e+02 Score=31.91 Aligned_cols=106 Identities=11% Similarity=0.065 Sum_probs=67.9
Q ss_pred HHHHHHHHHHhhcccHHHHHHHHHHHHHHhhhcCCc--chhHHHHHHHHHHHHhhccHHHHHhhhhhc-CCCCCCChHHH
Q psy1676 18 KCYFYHSRVHELTNNLDKVRSFLNARLRIATLRNDF--EGQAVLINCLLRNYLHYNLYDQADKLVKKS-AFPENASNNEW 94 (343)
Q Consensus 18 ~~~~y~~~~~e~~~~~~~~~~~l~~~~r~a~~~~~~--~~~~~l~n~Llr~yl~~~~~~~a~~li~k~-~~p~~~~~~~~ 94 (343)
.++...+.++-..|.+..+...+-.++..+...+.+ .....+...+-.++...|+++.|....... ...........
T Consensus 532 ~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~ 611 (903)
T PRK04841 532 WSLLQQSEILFAQGFLQAAYETQEKAFQLIEEQHLEQLPMHEFLLRIRAQLLWEWARLDEAEQCARKGLEVLSNYQPQQQ 611 (903)
T ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccccccHHHHHHHHHHHHHHHhcCHHHHHHHHHHhHHhhhccCchHH
Confidence 345566777777788887777776666544433322 122344555667778889999988887754 11111111233
Q ss_pred HHHHHHHHHHHHHhhCHHHHHHHHHHHHh
Q psy1676 95 ARFHFYLGRIKAVRLEYSTAHKNLVQALR 123 (343)
Q Consensus 95 ~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~ 123 (343)
+..+...|+++...+++.+|...+..+..
T Consensus 612 ~~~~~~la~~~~~~G~~~~A~~~l~~a~~ 640 (903)
T PRK04841 612 LQCLAMLAKISLARGDLDNARRYLNRLEN 640 (903)
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence 44555688889999999999988888865
No 152
>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=56.70 E-value=56 Score=30.80 Aligned_cols=66 Identities=18% Similarity=0.346 Sum_probs=47.8
Q ss_pred HHHHHHHHHHhhccHHHHHhhhhhc--CCCCCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCcc
Q psy1676 59 LINCLLRNYLHYNLYDQADKLVKKS--AFPENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQT 128 (343)
Q Consensus 59 l~n~Llr~yl~~~~~~~a~~li~k~--~~p~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~ 128 (343)
..|.=+..| +.|+|..|..-+.+= .+|.+.-. -.=+|++|..+..+++|.+|-..|..+.+.-|.+
T Consensus 144 ~Y~~A~~~~-ksgdy~~A~~~F~~fi~~YP~s~~~---~nA~yWLGe~~y~qg~y~~Aa~~f~~~~k~~P~s 211 (262)
T COG1729 144 LYNAALDLY-KSGDYAEAEQAFQAFIKKYPNSTYT---PNAYYWLGESLYAQGDYEDAAYIFARVVKDYPKS 211 (262)
T ss_pred HHHHHHHHH-HcCCHHHHHHHHHHHHHcCCCCccc---chhHHHHHHHHHhcccchHHHHHHHHHHHhCCCC
Confidence 567656665 556699998877752 56653211 1126799999999999999999999999965543
No 153
>KOG2003|consensus
Probab=56.61 E-value=2.4e+02 Score=29.00 Aligned_cols=97 Identities=19% Similarity=0.123 Sum_probs=70.3
Q ss_pred HHHHHHHHHHhhcccHHHHHHHHHHHHHHhhhcCCcchhHHHHHHHHHHHHhhccHHHHHhhhhhc--CCCCCCChHHHH
Q psy1676 18 KCYFYHSRVHELTNNLDKVRSFLNARLRIATLRNDFEGQAVLINCLLRNYLHYNLYDQADKLVKKS--AFPENASNNEWA 95 (343)
Q Consensus 18 ~~~~y~~~~~e~~~~~~~~~~~l~~~~r~a~~~~~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~--~~p~~~~~~~~~ 95 (343)
...|-.+..+|.+++|+++-..++..+. .++++ +-++.++..+|=...+..+|-.++..+ .+|.. | +.
T Consensus 525 ealfniglt~e~~~~ldeald~f~klh~--il~nn----~evl~qianiye~led~aqaie~~~q~~slip~d-p--~i- 594 (840)
T KOG2003|consen 525 EALFNIGLTAEALGNLDEALDCFLKLHA--ILLNN----AEVLVQIANIYELLEDPAQAIELLMQANSLIPND-P--AI- 594 (840)
T ss_pred HHHHHhcccHHHhcCHHHHHHHHHHHHH--HHHhh----HHHHHHHHHHHHHhhCHHHHHHHHHHhcccCCCC-H--HH-
Confidence 4478888899999999988877766554 23222 345567788999999999999988743 44531 1 11
Q ss_pred HHHHHHHHHHHHhhCHHHHHHHHHHHHhhCC
Q psy1676 96 RFHFYLGRIKAVRLEYSTAHKNLVQALRKAP 126 (343)
Q Consensus 96 ~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~ 126 (343)
+--+|-+|--+++-+.|+++....++..|
T Consensus 595 --lskl~dlydqegdksqafq~~ydsyryfp 623 (840)
T KOG2003|consen 595 --LSKLADLYDQEGDKSQAFQCHYDSYRYFP 623 (840)
T ss_pred --HHHHHHHhhcccchhhhhhhhhhcccccC
Confidence 12467888899999999999999999544
No 154
>PF13281 DUF4071: Domain of unknown function (DUF4071)
Probab=56.36 E-value=2.2e+02 Score=28.37 Aligned_cols=69 Identities=23% Similarity=0.316 Sum_probs=48.3
Q ss_pred HHHHHHHHHHHhhccHHHHHhhhhhcC-CCCC-CChHHHHHHHHHHHHHH-HHhhCHHHHHHHHHHHHhhCCc
Q psy1676 58 VLINCLLRNYLHYNLYDQADKLVKKSA-FPEN-ASNNEWARFHFYLGRIK-AVRLEYSTAHKNLVQALRKAPQ 127 (343)
Q Consensus 58 ~l~n~Llr~yl~~~~~~~a~~li~k~~-~p~~-~~~~~~~~Y~YY~Gri~-~~~~~y~~A~~~L~~A~~~~~~ 127 (343)
.++|+++- |-...+|+..-+++++.. .|.. ......++|+|=.+... -..|+.++|.+.+..++.++..
T Consensus 143 iv~~lllS-yRdiqdydamI~Lve~l~~~p~~~~~~~~~i~~~yafALnRrn~~gdre~Al~il~~~l~~~~~ 214 (374)
T PF13281_consen 143 IVINLLLS-YRDIQDYDAMIKLVETLEALPTCDVANQHNIKFQYAFALNRRNKPGDREKALQILLPVLESDEN 214 (374)
T ss_pred HHHHHHHH-hhhhhhHHHHHHHHHHhhccCccchhcchHHHHHHHHHHhhcccCCCHHHHHHHHHHHHhccCC
Confidence 66776554 889999999999999763 3322 44567788888666554 2357888888888877765443
No 155
>PF09999 DUF2240: Uncharacterized protein conserved in archaea (DUF2240); InterPro: IPR018716 This family of various hypothetical archaeal proteins has no known function.
Probab=56.07 E-value=14 Score=31.60 Aligned_cols=74 Identities=27% Similarity=0.405 Sum_probs=50.3
Q ss_pred cccChHHHHHHh----CCCCHHHHHHHHHHhHHcCCceEEeeCCCceEEE-------------ccCccccccccchHHHH
Q psy1676 224 SRITPTKIAEKL----GLESPEDAEFIIAKAIRDGVIEATLDREKGYMQS-------------KESADIYCTVEPQLAFH 286 (343)
Q Consensus 224 s~Isl~dIa~~l----~l~s~~e~E~ila~lI~~G~I~a~Id~~~g~v~~-------------~~~~~v~s~~ep~~~~~ 286 (343)
.+++-+++--.| +|-|++++..++-.++..|.|.. ++|.++- +.+.+++...+||...-
T Consensus 16 ~~L~~sefv~~Ls~D~~WmspdqAk~li~~A~~eGLl~~----~~~~l~~~Fd~~~v~iP~~FkP~~~~l~e~~~fe~il 91 (144)
T PF09999_consen 16 DRLSKSEFVFALSFDRKWMSPDQAKRLIDEAIEEGLLEE----EGGYLVPNFDPSEVEIPLGFKPDEEILQERDPFERIL 91 (144)
T ss_pred cccChhheEeeEeeecCCCCHHHHHHHHHHHHHCCCeee----cCCEEEEecCccccccCCCCCCcHHHHhcccHHHHHH
Confidence 455555554333 34489999999999999999953 4555552 22233345678888888
Q ss_pred HHHHHHHHhhHHHhh
Q psy1676 287 QRIAFCLDLHNQSVK 301 (343)
Q Consensus 287 ~rI~~cl~l~~~~~~ 301 (343)
.+|..+..+..+-|-
T Consensus 92 d~ia~~~g~~~~evv 106 (144)
T PF09999_consen 92 DYIAAKTGIEKQEVV 106 (144)
T ss_pred HHHHHhcCCCHHHHH
Confidence 888888888666443
No 156
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=55.87 E-value=24 Score=23.30 Aligned_cols=34 Identities=21% Similarity=0.315 Sum_probs=30.3
Q ss_pred cccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceE
Q psy1676 224 SRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEA 258 (343)
Q Consensus 224 s~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a 258 (343)
..++..+|+..+++ +...+...+..|...|.|.-
T Consensus 13 ~~~s~~~l~~~l~~-s~~tv~~~l~~L~~~g~i~~ 46 (53)
T smart00420 13 GKVSVEELAELLGV-SEMTIRRDLNKLEEQGLLTR 46 (53)
T ss_pred CCcCHHHHHHHHCC-CHHHHHHHHHHHHHCCCEEE
Confidence 45899999999999 59999999999999999853
No 157
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=55.77 E-value=41 Score=28.78 Aligned_cols=48 Identities=17% Similarity=0.178 Sum_probs=40.4
Q ss_pred cccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEeeCCCceEEEccC
Q psy1676 224 SRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLDREKGYMQSKES 272 (343)
Q Consensus 224 s~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~Id~~~g~v~~~~~ 272 (343)
..++.++||+..+++ ..-++.+++.|...|.|...==...||.-..+.
T Consensus 23 ~~~s~~eIA~~~~is-~~~L~kIl~~L~~aGlv~S~rG~~GGy~La~~p 70 (153)
T PRK11920 23 KLSRIPEIARAYGVS-ELFLFKILQPLVEAGLVETVRGRNGGVRLGRPA 70 (153)
T ss_pred CcCcHHHHHHHHCcC-HHHHHHHHHHHHHCCCEEeecCCCCCeeecCCH
Confidence 458999999999995 999999999999999998777666676665544
No 158
>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=55.24 E-value=40 Score=24.25 Aligned_cols=38 Identities=21% Similarity=0.264 Sum_probs=32.9
Q ss_pred cccccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEe
Q psy1676 222 SYSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATL 260 (343)
Q Consensus 222 ~ys~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~I 260 (343)
.....+..+||+.++++ ...|-.+|.+|...|.|.-.-
T Consensus 19 ~~~~~t~~eIa~~l~i~-~~~v~~~L~~L~~~GlV~~~~ 56 (68)
T PF01978_consen 19 KNGPATAEEIAEELGIS-RSTVYRALKSLEEKGLVEREE 56 (68)
T ss_dssp HHCHEEHHHHHHHHTSS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred HcCCCCHHHHHHHHCcC-HHHHHHHHHHHHHCCCEEEEc
Confidence 45678899999999996 999999999999999996443
No 159
>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=54.89 E-value=34 Score=22.68 Aligned_cols=26 Identities=27% Similarity=0.350 Sum_probs=19.3
Q ss_pred cccChHHHHHHhCCCCHHHHHHHHHHh
Q psy1676 224 SRITPTKIAEKLGLESPEDAEFIIAKA 250 (343)
Q Consensus 224 s~Isl~dIa~~l~l~s~~e~E~ila~l 250 (343)
.++|+.+||+.+|++ +..|-.-+.+|
T Consensus 16 ~r~s~~~la~~lglS-~~~v~~Ri~rL 41 (42)
T PF13404_consen 16 GRRSYAELAEELGLS-ESTVRRRIRRL 41 (42)
T ss_dssp TTS-HHHHHHHHTS--HHHHHHHHHHH
T ss_pred CCccHHHHHHHHCcC-HHHHHHHHHHh
Confidence 899999999999995 77776555543
No 160
>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=54.63 E-value=45 Score=23.60 Aligned_cols=42 Identities=29% Similarity=0.408 Sum_probs=31.7
Q ss_pred hhcccccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEeeC
Q psy1676 220 GASYSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLDR 262 (343)
Q Consensus 220 ~~~ys~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~Id~ 262 (343)
......++.++|+..++++ ...+-..|-+|+..|+|.=.=|.
T Consensus 13 ~~~~~~~t~~~l~~~~~~~-~~~vs~~i~~L~~~glv~~~~~~ 54 (68)
T PF13463_consen 13 AHSDGPMTQSDLAERLGIS-KSTVSRIIKKLEEKGLVEKERDP 54 (68)
T ss_dssp T--TS-BEHHHHHHHTT---HHHHHHHHHHHHHTTSEEEEEES
T ss_pred HccCCCcCHHHHHHHHCcC-HHHHHHHHHHHHHCCCEEecCCC
Confidence 3456788999999999995 88999999999999999555444
No 161
>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional
Probab=54.56 E-value=1.7e+02 Score=32.89 Aligned_cols=95 Identities=15% Similarity=0.044 Sum_probs=64.1
Q ss_pred HHHHHH--HHHhhcccHHHHHHHHHHHHHHhhhcCCcchhHHHHHHHHHHHHhhccHHHHHhhhhhcC-CCCCCChHHHH
Q psy1676 19 CYFYHS--RVHELTNNLDKVRSFLNARLRIATLRNDFEGQAVLINCLLRNYLHYNLYDQADKLVKKSA-FPENASNNEWA 95 (343)
Q Consensus 19 ~~~y~~--~~~e~~~~~~~~~~~l~~~~r~a~~~~~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~~-~p~~~~~~~~~ 95 (343)
++|||. ..+...|...++...+ +.+ +..+|.. ..+...|.+.|++.|+++.|...+++.. ..+ .-.
T Consensus 44 ~~~~f~~a~~~~~~Gd~~~A~~~l----~~A-l~~dP~n-~~~~~~LA~~yl~~g~~~~A~~~~~kAv~ldP-----~n~ 112 (987)
T PRK09782 44 IYPRLDKALKAQKNNDEATAIREF----EYI-HQQVPDN-IPLTLYLAEAYRHFGHDDRARLLLEDQLKRHP-----GDA 112 (987)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHH----HHH-HHhCCCC-HHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCc-----ccH
Confidence 445554 4445557777666544 433 4446777 5666788999999999999999999763 211 112
Q ss_pred HHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCcc
Q psy1676 96 RFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQT 128 (343)
Q Consensus 96 ~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~ 128 (343)
.|+-.+|.+ ++|.+|...+++.+...|..
T Consensus 113 ~~~~~La~i----~~~~kA~~~ye~l~~~~P~n 141 (987)
T PRK09782 113 RLERSLAAI----PVEVKSVTTVEELLAQQKAC 141 (987)
T ss_pred HHHHHHHHh----ccChhHHHHHHHHHHhCCCC
Confidence 222223444 99999999999999977764
No 162
>PF09202 Rio2_N: Rio2, N-terminal; InterPro: IPR015285 This N-terminal domain is found in RIO2 kinases, and is structurally homologous to the winged helix (wHTH) domain. It adopts a structure consisting of four alpha helices followed by two beta strands and a fifth alpha helix. The domain confers DNA binding properties to the protein, as per other winged helix domains []. ; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0006468 protein phosphorylation; PDB: 1TQP_A 1ZAR_A 1TQI_A 1ZAO_A 1TQM_A.
Probab=53.74 E-value=40 Score=25.90 Aligned_cols=51 Identities=16% Similarity=0.145 Sum_probs=38.2
Q ss_pred HHHHHhhcccccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEeeCCCce
Q psy1676 215 AIRSIGASYSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLDREKGY 266 (343)
Q Consensus 215 ~ir~i~~~ys~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~Id~~~g~ 266 (343)
.|..-.+.|.=+|++.|++..++. ..+++..+.+++..|.|.-+..+-+||
T Consensus 14 aiE~gmk~hE~VP~~~I~~~s~l~-~~~~~~~L~~L~~~kLv~~~~~~Y~GY 64 (82)
T PF09202_consen 14 AIEMGMKNHEWVPLELIEKISGLS-EGEVEKRLKRLVKLKLVSRRNKPYDGY 64 (82)
T ss_dssp HHHTTTTT-SSEEHHHHHHHHT---HHHHHHHHHHHHHTTSEEEE-SSS-EE
T ss_pred HHHHcccCCccCCHHHHHHHhCcC-HHHHHHHHHHHHhcCCccccCCCcceE
Confidence 344445678899999999999996 999999999999999997755555565
No 163
>KOG3054|consensus
Probab=53.64 E-value=23 Score=32.96 Aligned_cols=48 Identities=15% Similarity=0.313 Sum_probs=40.7
Q ss_pred ccccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEeeCCCceEEEcc
Q psy1676 223 YSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLDREKGYMQSKE 271 (343)
Q Consensus 223 ys~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~Id~~~g~v~~~~ 271 (343)
...++|.|+|..+||- ..++-.-+..++.+|.|.|.||.-..++..+.
T Consensus 212 nKvV~ledLas~f~Lr-tqd~inriq~~l~eg~ltGVmDDRGKfIYIS~ 259 (299)
T KOG3054|consen 212 NKVVPLEDLASEFGLR-TQDSINRIQELLAEGLLTGVMDDRGKFIYISM 259 (299)
T ss_pred cCeeeHHHHHHHhCcc-HHHHHHHHHHHHHhhhheeeecCCCceEEecH
Confidence 3568999999999996 56777789999999999999998877776653
No 164
>KOG1173|consensus
Probab=53.27 E-value=69 Score=33.46 Aligned_cols=28 Identities=18% Similarity=0.135 Sum_probs=17.6
Q ss_pred HHHHHHhCCC-CHHHHHHHHHHhHHcCCc
Q psy1676 229 TKIAEKLGLE-SPEDAEFIIAKAIRDGVI 256 (343)
Q Consensus 229 ~dIa~~l~l~-s~~e~E~ila~lI~~G~I 256 (343)
+.+-+.|.+. +..-++.++..+|.+..-
T Consensus 510 d~fhKaL~l~p~n~~~~~lL~~aie~~~~ 538 (611)
T KOG1173|consen 510 DHFHKALALKPDNIFISELLKLAIEDSEC 538 (611)
T ss_pred HHHHHHHhcCCccHHHHHHHHHHHHhhhh
Confidence 3455667774 222467788888887544
No 165
>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional
Probab=51.96 E-value=1.6e+02 Score=25.56 Aligned_cols=86 Identities=9% Similarity=-0.034 Sum_probs=60.3
Q ss_pred cccHHHHHHHHHHHHHHhhhcCCcchhHHHHHHHHHHHHhhccHHHHHhhhhhc-CCCCCCChHHHHHHHHHHHHHHHHh
Q psy1676 30 TNNLDKVRSFLNARLRIATLRNDFEGQAVLINCLLRNYLHYNLYDQADKLVKKS-AFPENASNNEWARFHFYLGRIKAVR 108 (343)
Q Consensus 30 ~~~~~~~~~~l~~~~r~a~~~~~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~-~~p~~~~~~~~~~Y~YY~Gri~~~~ 108 (343)
.|+++++.. .+++.|.. |++-.-+..|+ --+|=..++|..|-..-... .+..+. -+-+++.|..++..
T Consensus 48 ~G~l~~A~~----~f~~L~~~-Dp~~~~y~~gL-G~~~Q~~g~~~~AI~aY~~A~~L~~dd-----p~~~~~ag~c~L~l 116 (157)
T PRK15363 48 VKEFAGAAR----LFQLLTIY-DAWSFDYWFRL-GECCQAQKHWGEAIYAYGRAAQIKIDA-----PQAPWAAAECYLAC 116 (157)
T ss_pred CCCHHHHHH----HHHHHHHh-CcccHHHHHHH-HHHHHHHhhHHHHHHHHHHHHhcCCCC-----chHHHHHHHHHHHc
Confidence 566777763 34544433 66665566665 44566788899988887754 222112 23366999999999
Q ss_pred hCHHHHHHHHHHHHhhCC
Q psy1676 109 LEYSTAHKNLVQALRKAP 126 (343)
Q Consensus 109 ~~y~~A~~~L~~A~~~~~ 126 (343)
++...|...|..|+..|.
T Consensus 117 G~~~~A~~aF~~Ai~~~~ 134 (157)
T PRK15363 117 DNVCYAIKALKAVVRICG 134 (157)
T ss_pred CCHHHHHHHHHHHHHHhc
Confidence 999999999999999884
No 166
>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=51.76 E-value=74 Score=21.62 Aligned_cols=38 Identities=26% Similarity=0.256 Sum_probs=29.8
Q ss_pred HHHHhhcccccChHHHHHHhCCCCHHHHHHHHHHhHHcC
Q psy1676 216 IRSIGASYSRITPTKIAEKLGLESPEDAEFIIAKAIRDG 254 (343)
Q Consensus 216 ir~i~~~ys~Isl~dIa~~l~l~s~~e~E~ila~lI~~G 254 (343)
+..+...-..+|..++|..+++ |..-+...+..+-..|
T Consensus 6 l~~L~~~~~~it~~eLa~~l~v-S~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 6 LKLLLESKEPITAKELAEELGV-SRRTIRRDIKELREWG 43 (55)
T ss_dssp HHHHHHTTTSBEHHHHHHHCTS--HHHHHHHHHHHHHTT
T ss_pred HHHHHHcCCCcCHHHHHHHhCC-CHHHHHHHHHHHHHCC
Confidence 3344344445999999999999 5899999999998888
No 167
>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=51.26 E-value=45 Score=19.88 Aligned_cols=30 Identities=13% Similarity=0.414 Sum_probs=22.0
Q ss_pred HHHHHHHHHHHhhcccHHHHHHHHHHHHHH
Q psy1676 17 AKCYFYHSRVHELTNNLDKVRSFLNARLRI 46 (343)
Q Consensus 17 a~~~~y~~~~~e~~~~~~~~~~~l~~~~r~ 46 (343)
|++||-.|.++...+..+++...+..++..
T Consensus 1 a~~~~~lg~~y~~~~~~~~A~~~~~~a~~~ 30 (34)
T PF13181_consen 1 AEAYYNLGKIYEQLGDYEEALEYFEKALEL 30 (34)
T ss_dssp -HHHHHHHHHHHHTTSHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence 567888888888888888777776665543
No 168
>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=51.24 E-value=47 Score=25.95 Aligned_cols=46 Identities=26% Similarity=0.226 Sum_probs=37.0
Q ss_pred cccccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEeeCCCceEEEc
Q psy1676 222 SYSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLDREKGYMQSK 270 (343)
Q Consensus 222 ~ys~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~Id~~~g~v~~~ 270 (343)
....||-++||..+|++ .+-|-..|..|..+|+|. .....|.+...
T Consensus 44 ~~~~is~~eLa~~~g~s-r~tVsr~L~~Le~~GlI~--r~~~~~~~~~n 89 (95)
T TIGR01610 44 KQDRVTATVIAELTGLS-RTHVSDAIKSLARRRIIF--RQGMMGIVGVN 89 (95)
T ss_pred cCCccCHHHHHHHHCcC-HHHHHHHHHHHHHCCCee--eecCCceeecC
Confidence 34678889999999995 889999999999999996 34445666554
No 169
>PF13730 HTH_36: Helix-turn-helix domain
Probab=50.76 E-value=28 Score=23.79 Aligned_cols=29 Identities=21% Similarity=0.373 Sum_probs=26.9
Q ss_pred ChHHHHHHhCCCCHHHHHHHHHHhHHcCCc
Q psy1676 227 TPTKIAEKLGLESPEDAEFIIAKAIRDGVI 256 (343)
Q Consensus 227 sl~dIa~~l~l~s~~e~E~ila~lI~~G~I 256 (343)
|.+.||..+|++ ..-|...+..|+..|.|
T Consensus 27 S~~~la~~~g~s-~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 27 SQETLAKDLGVS-RRTVQRAIKELEEKGLI 55 (55)
T ss_pred CHHHHHHHHCcC-HHHHHHHHHHHHHCcCC
Confidence 799999999995 99999999999999986
No 170
>TIGR02147 Fsuc_second hypothetical protein, TIGR02147. This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized.
Probab=50.75 E-value=2.2e+02 Score=26.87 Aligned_cols=107 Identities=17% Similarity=0.179 Sum_probs=64.8
Q ss_pred cccccccccHHHHHHHHHHHHHHHHHHHhhcccccChHHHHHHhCCC-CHHHHHHHHHHhHHcCCceEEeeCCCceEEEc
Q psy1676 192 GNQFRTDYTFKLILRLRHNVIKTAIRSIGASYSRITPTKIAEKLGLE-SPEDAEFIIAKAIRDGVIEATLDREKGYMQSK 270 (343)
Q Consensus 192 ~~~f~~d~~~~Lv~~l~~~v~r~~ir~i~~~ys~Isl~dIa~~l~l~-s~~e~E~ila~lI~~G~I~a~Id~~~g~v~~~ 270 (343)
....+...-|.....-.+.++|.++.... -.-....||++++-. |.++|...|.-|..-|+|+= +..+.|+...
T Consensus 107 ~~~~L~~~~~~y~~~W~~~virel~~~~~---~~~~~~~ia~~l~p~is~~ev~~sL~~L~~~glikk--~~~g~y~~t~ 181 (271)
T TIGR02147 107 RLRVLAADQFEYYRHWYNSVIRELLGVMP---FADDPEELAKRCFPKISAEQVKESLDLLERLGLIKK--NEDGFYKQTD 181 (271)
T ss_pred hheeccHHHHHHHHHHHHHHHHHHhhcCC---CCCCHHHHHHHhCCCCCHHHHHHHHHHHHHCCCeeE--CCCCcEEeec
Confidence 33334444566677777777777764322 222356899999932 69999999999999999962 2222366554
Q ss_pred cCccccccccchHHHHHHH-HHHHHhhHHHhhhc-CCCCC
Q psy1676 271 ESADIYCTVEPQLAFHQRI-AFCLDLHNQSVKAM-RYPPK 308 (343)
Q Consensus 271 ~~~~v~s~~ep~~~~~~rI-~~cl~l~~~~~~am-~~~~~ 308 (343)
.... ++.+..+...... ..|+++-.+ || ++|+.
T Consensus 182 ~~l~--~~~~~~~~avr~~h~q~l~lA~~---al~~~p~~ 216 (271)
T TIGR02147 182 KAVS--TGDEVIPLAVRQYQKQMIDLAKE---ALDALPPS 216 (271)
T ss_pred ceee--cCCccchHHHHHHHHHHHHHHHH---HHHhCCcc
Confidence 4222 3333334434444 569988544 55 46664
No 171
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=50.10 E-value=35 Score=24.78 Aligned_cols=34 Identities=26% Similarity=0.467 Sum_probs=29.7
Q ss_pred ccccChHHHHHHhCCCCHHHHHHHHHHhHHcCCce
Q psy1676 223 YSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIE 257 (343)
Q Consensus 223 ys~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~ 257 (343)
..-++-.|||.++|++ .-.|..++..|-.+|.|.
T Consensus 13 ~~p~~T~eiA~~~gls-~~~aR~yL~~Le~eG~V~ 46 (62)
T PF04703_consen 13 NGPLKTREIADALGLS-IYQARYYLEKLEKEGKVE 46 (62)
T ss_dssp TS-EEHHHHHHHHTS--HHHHHHHHHHHHHCTSEE
T ss_pred CCCCCHHHHHHHhCCC-HHHHHHHHHHHHHCCCEE
Confidence 5668889999999994 999999999999999995
No 172
>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=49.90 E-value=1.2e+02 Score=24.21 Aligned_cols=42 Identities=17% Similarity=0.183 Sum_probs=35.7
Q ss_pred ccccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEeeCCCc
Q psy1676 223 YSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLDREKG 265 (343)
Q Consensus 223 ys~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~Id~~~g 265 (343)
...++.++||..++++ ...+-.+|.+|..+|+|...-+..++
T Consensus 40 ~~~~t~~ela~~~~~~-~~tvs~~l~~Le~~GlI~r~~~~~D~ 81 (118)
T TIGR02337 40 QGSMEFTQLANQACIL-RPSLTGILARLERDGLVTRLKASNDQ 81 (118)
T ss_pred cCCcCHHHHHHHhCCC-chhHHHHHHHHHHCCCEEeccCCCCC
Confidence 3568899999999996 66899999999999999887776553
No 173
>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=49.84 E-value=26 Score=20.35 Aligned_cols=23 Identities=17% Similarity=0.073 Sum_probs=18.7
Q ss_pred HHHHHHHHHHHhhCHHHHHHHHH
Q psy1676 97 FHFYLGRIKAVRLEYSTAHKNLV 119 (343)
Q Consensus 97 Y~YY~Gri~~~~~~y~~A~~~L~ 119 (343)
..+.+|+.+..+|++.+|...+.
T Consensus 3 a~~~la~~~~~~G~~~eA~~~l~ 25 (26)
T PF07721_consen 3 ARLALARALLAQGDPDEAERLLR 25 (26)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHh
Confidence 45778899999999999987764
No 174
>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional
Probab=49.72 E-value=54 Score=32.01 Aligned_cols=59 Identities=12% Similarity=0.057 Sum_probs=47.8
Q ss_pred HHHHHhhccHHHHHhhhhhcC--CCCCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCcc
Q psy1676 64 LRNYLHYNLYDQADKLVKKSA--FPENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQT 128 (343)
Q Consensus 64 lr~yl~~~~~~~a~~li~k~~--~p~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~ 128 (343)
...+|..++|..|..+++++. .|. ...+++..|..+...++|.+|...+..|+...|..
T Consensus 9 a~~a~~~~~~~~Ai~~~~~Al~~~P~------~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~P~~ 69 (356)
T PLN03088 9 AKEAFVDDDFALAVDLYTQAIDLDPN------NAELYADRAQANIKLGNFTEAVADANKAIELDPSL 69 (356)
T ss_pred HHHHHHcCCHHHHHHHHHHHHHhCCC------CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCC
Confidence 566788999999999988752 232 24567899999999999999999999999976653
No 175
>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=49.68 E-value=33 Score=24.98 Aligned_cols=42 Identities=29% Similarity=0.459 Sum_probs=33.9
Q ss_pred cccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEeeCCCceEEEc
Q psy1676 224 SRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLDREKGYMQSK 270 (343)
Q Consensus 224 s~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~Id~~~g~v~~~ 270 (343)
-.++-.+||..+|+ |...+-.++..|..+|.|. + .+|.+...
T Consensus 27 ~~lt~~~iA~~~g~-sr~tv~r~l~~l~~~g~I~--~--~~~~i~I~ 68 (76)
T PF13545_consen 27 LPLTQEEIADMLGV-SRETVSRILKRLKDEGIIE--V--KRGKIIIL 68 (76)
T ss_dssp EESSHHHHHHHHTS-CHHHHHHHHHHHHHTTSEE--E--ETTEEEES
T ss_pred ecCCHHHHHHHHCC-CHHHHHHHHHHHHHCCCEE--E--cCCEEEEC
Confidence 45788999999999 4999999999999999996 2 24455544
No 176
>PRK10153 DNA-binding transcriptional activator CadC; Provisional
Probab=49.54 E-value=1.1e+02 Score=31.83 Aligned_cols=56 Identities=18% Similarity=0.102 Sum_probs=42.3
Q ss_pred HHhhccHHHHHhhhhhcCCCCCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCc
Q psy1676 67 YLHYNLYDQADKLVKKSAFPENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQ 127 (343)
Q Consensus 67 yl~~~~~~~a~~li~k~~~p~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~ 127 (343)
.+..++++.|..-++++.--. + + ...+.+.|+++...|++.+|..++..|++..|.
T Consensus 430 ~~~~g~~~~A~~~l~rAl~L~--p-s--~~a~~~lG~~~~~~G~~~eA~~~~~~A~~L~P~ 485 (517)
T PRK10153 430 ALVKGKTDEAYQAINKAIDLE--M-S--WLNYVLLGKVYELKGDNRLAADAYSTAFNLRPG 485 (517)
T ss_pred HHhcCCHHHHHHHHHHHHHcC--C-C--HHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCC
Confidence 445688999998888752211 1 1 347788999999999999999999999985554
No 177
>KOG4234|consensus
Probab=49.23 E-value=70 Score=29.38 Aligned_cols=97 Identities=20% Similarity=0.245 Sum_probs=56.0
Q ss_pred HHHHHHHHHHhhCHHHHHHHHHHHHhhCCccchHHHHHHHHHH-HHHHHHhcCCCCChhhhhhHhHhhh--hhh-hH-HH
Q psy1676 98 HFYLGRIKAVRLEYSTAHKNLVQALRKAPQTAAVGFRQTTQKL-AVVVELLLGDIPDRQIFRQAVLRRA--LSP-YF-QL 172 (343)
Q Consensus 98 ~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~sa~~~~~~i~K~-li~v~LL~G~iP~~~~~~~~~l~~~--l~~-Y~-~L 172 (343)
.---|-=.+.+++|.+|...|+.|+..||..+. . .+.|+.. --.+.|-+|+--. .+. .+.+. +.| |. .|
T Consensus 98 lK~EGN~~F~ngdyeeA~skY~~Ale~cp~~~~-e-~rsIly~Nraaa~iKl~k~e~--aI~--dcsKaiel~pty~kAl 171 (271)
T KOG4234|consen 98 LKKEGNELFKNGDYEEANSKYQEALESCPSTST-E-ERSILYSNRAAALIKLRKWES--AIE--DCSKAIELNPTYEKAL 171 (271)
T ss_pred HHHHHHHhhhcccHHHHHHHHHHHHHhCccccH-H-HHHHHHhhhHHHHHHhhhHHH--HHH--HHHhhHhcCchhHHHH
Confidence 334566778899999999999999999997642 2 3443321 1122233333111 000 00111 111 21 23
Q ss_pred HH-HHHhCCHHHHHHHHHhcccccccccc
Q psy1676 173 TQ-AVRMGELQKFNEVLTTYGNQFRTDYT 200 (343)
Q Consensus 173 ~~-Av~~Gdl~~f~~~l~~~~~~f~~d~~ 200 (343)
.+ |.---.+.+|+..++.|......|+-
T Consensus 172 ~RRAeayek~ek~eealeDyKki~E~dPs 200 (271)
T KOG4234|consen 172 ERRAEAYEKMEKYEEALEDYKKILESDPS 200 (271)
T ss_pred HHHHHHHHhhhhHHHHHHHHHHHHHhCcc
Confidence 33 44445678999999999988888764
No 178
>PRK10747 putative protoheme IX biogenesis protein; Provisional
Probab=48.99 E-value=1.6e+02 Score=29.05 Aligned_cols=33 Identities=21% Similarity=0.275 Sum_probs=29.2
Q ss_pred HHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCc
Q psy1676 95 ARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQ 127 (343)
Q Consensus 95 ~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~ 127 (343)
...++..|++++.+++|.+|.++|+.++...|.
T Consensus 328 ~~l~l~lgrl~~~~~~~~~A~~~le~al~~~P~ 360 (398)
T PRK10747 328 PLLWSTLGQLLMKHGEWQEASLAFRAALKQRPD 360 (398)
T ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCC
Confidence 456889999999999999999999999996664
No 179
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=48.72 E-value=35 Score=28.59 Aligned_cols=47 Identities=19% Similarity=0.253 Sum_probs=39.1
Q ss_pred cccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEeeCCCceEEEcc
Q psy1676 224 SRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLDREKGYMQSKE 271 (343)
Q Consensus 224 s~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~Id~~~g~v~~~~ 271 (343)
..+|.++||+.++++ ..-++.++..|-..|.|...=-...|+.....
T Consensus 24 ~~~s~~~ia~~~~is-~~~vrk~l~~L~~~Glv~s~~G~~GG~~l~~~ 70 (141)
T PRK11014 24 RMTSISEVTEVYGVS-RNHMVKIINQLSRAGYVTAVRGKNGGIRLGKP 70 (141)
T ss_pred CccCHHHHHHHHCcC-HHHHHHHHHHHHhCCEEEEecCCCCCeeecCC
Confidence 478999999999995 99999999999999999776655567666543
No 180
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=48.70 E-value=29 Score=29.70 Aligned_cols=71 Identities=21% Similarity=0.407 Sum_probs=50.0
Q ss_pred ccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEeeCCCceEEEccCccccccccchHHHHHHHH--HHHHhhH
Q psy1676 225 RITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLDREKGYMQSKESADIYCTVEPQLAFHQRIA--FCLDLHN 297 (343)
Q Consensus 225 ~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~Id~~~g~v~~~~~~~v~s~~ep~~~~~~rI~--~cl~l~~ 297 (343)
.+|.++||+..+++ +.-++.++++|-..|+|+..==+..||.--++..+ .+=-|...+++..+. .|...++
T Consensus 25 ~~s~~~IA~~~~is-~~~L~kil~~L~kaGlV~S~rG~~GGy~Lar~~~~-Isl~dVv~ave~~~~~~~c~~~~~ 97 (150)
T COG1959 25 PVSSAEIAERQGIS-PSYLEKILSKLRKAGLVKSVRGKGGGYRLARPPEE-ITLGDVVRALEGPLALVECFSITN 97 (150)
T ss_pred cccHHHHHHHhCcC-HHHHHHHHHHHHHcCCEEeecCCCCCccCCCChHH-CcHHHHHHHhcCCCCccccCCCCC
Confidence 68899999999995 99999999999999999877666677766554332 232234444444433 3555544
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=48.68 E-value=67 Score=22.59 Aligned_cols=37 Identities=30% Similarity=0.481 Sum_probs=32.4
Q ss_pred hcccccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceE
Q psy1676 221 ASYSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEA 258 (343)
Q Consensus 221 ~~ys~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a 258 (343)
......+.++|+..++++ ...+-+.+..|...|.|..
T Consensus 20 ~~~~~~t~~ela~~l~~~-~~t~s~hL~~L~~aGli~~ 56 (61)
T PF12840_consen 20 ASNGPMTVSELAEELGIS-QSTVSYHLKKLEEAGLIEV 56 (61)
T ss_dssp HHCSTBEHHHHHHHHTS--HHHHHHHHHHHHHTTSEEE
T ss_pred hcCCCCCHHHHHHHHCCC-HHHHHHHHHHHHHCCCeEE
Confidence 456789999999999996 8899999999999999964
No 182
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=48.49 E-value=51 Score=30.23 Aligned_cols=49 Identities=16% Similarity=0.317 Sum_probs=39.9
Q ss_pred HHHHHHHhhcccccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEeeC
Q psy1676 213 KTAIRSIGASYSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLDR 262 (343)
Q Consensus 213 r~~ir~i~~~ys~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~Id~ 262 (343)
|..|..+.+--..+|..++|+.||++ ...|-..+-+|..+|++....-+
T Consensus 13 r~~il~lL~~~g~~sa~elA~~Lgis-~~avR~HL~~Le~~Glv~~~~~~ 61 (218)
T COG2345 13 RERILELLKKSGPVSADELAEELGIS-PMAVRRHLDDLEAEGLVEVERQQ 61 (218)
T ss_pred HHHHHHHHhccCCccHHHHHHHhCCC-HHHHHHHHHHHHhCcceeeeecc
Confidence 34444455566789999999999995 99999999999999999888443
No 183
>KOG2076|consensus
Probab=47.00 E-value=65 Score=35.30 Aligned_cols=68 Identities=22% Similarity=0.122 Sum_probs=52.5
Q ss_pred HHHHHHHHHHHhhccHHHHHhhhhhcCCCCCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCcc
Q psy1676 58 VLINCLLRNYLHYNLYDQADKLVKKSAFPENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQT 128 (343)
Q Consensus 58 ~l~n~Llr~yl~~~~~~~a~~li~k~~~p~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~ 128 (343)
-++-.+.+.|...+.|+.|.+++..+.--+. .+..-++|-.|+.++..+.|.+|..++..++...|.+
T Consensus 415 dL~~d~a~al~~~~~~~~Al~~l~~i~~~~~---~~~~~vw~~~a~c~~~l~e~e~A~e~y~kvl~~~p~~ 482 (895)
T KOG2076|consen 415 DLYLDLADALTNIGKYKEALRLLSPITNREG---YQNAFVWYKLARCYMELGEYEEAIEFYEKVLILAPDN 482 (895)
T ss_pred HHHHHHHHHHHhcccHHHHHHHHHHHhcCcc---ccchhhhHHHHHHHHHHhhHHHHHHHHHHHHhcCCCc
Confidence 3444567888999999999999886532111 1226678889999999999999999999999976654
No 184
>COG0173 AspS Aspartyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=46.68 E-value=5 Score=41.42 Aligned_cols=101 Identities=19% Similarity=0.349 Sum_probs=70.2
Q ss_pred HHHHHHHHHHhcCC---CCC-hhhhhhHhHhhhhhhhHHHHHHHHhCCHHHHHHHHHh----cccccc-ccccHHHHHHH
Q psy1676 137 TQKLAVVVELLLGD---IPD-RQIFRQAVLRRALSPYFQLTQAVRMGELQKFNEVLTT----YGNQFR-TDYTFKLILRL 207 (343)
Q Consensus 137 i~K~li~v~LL~G~---iP~-~~~~~~~~l~~~l~~Y~~L~~Av~~Gdl~~f~~~l~~----~~~~f~-~d~~~~Lv~~l 207 (343)
..-||+|+.+--|+ +|+ ..+|+|--+-..+.-|.+++++||--|+.+=++ =+- -+..|. ++.+..+++.+
T Consensus 176 ARDfLVPSRv~~G~FYALPQSPQlfKQLLMvsGfdRYyQIarCFRDEDlRaDRQ-PEFTQiD~EmSF~~~edv~~~~E~l 254 (585)
T COG0173 176 ARDFLVPSRVHPGKFYALPQSPQLFKQLLMVAGFDRYYQIARCFRDEDLRADRQ-PEFTQIDLEMSFVDEEDVMELIEKL 254 (585)
T ss_pred ccccccccccCCCceeecCCCHHHHHHHHHHhcccceeeeeeeecccccccccC-CcceeEeEEeecCCHHHHHHHHHHH
Confidence 45589999999998 787 345565544556778999999999888754222 111 122333 34556777877
Q ss_pred HHHHHHHHH-HHHhhcccccChHHHHHHhCCC
Q psy1676 208 RHNVIKTAI-RSIGASYSRITPTKIAEKLGLE 238 (343)
Q Consensus 208 ~~~v~r~~i-r~i~~~ys~Isl~dIa~~l~l~ 238 (343)
...|++.-. -.+...+-+|++++--.+.|-|
T Consensus 255 ~~~vf~~~~~i~l~~pFprmtY~eAm~~YGSD 286 (585)
T COG0173 255 LRYVFKEVKGIELKTPFPRMTYAEAMRRYGSD 286 (585)
T ss_pred HHHHHHHhcCCccCCCcccccHHHHHHHhCCC
Confidence 777776554 4556689999999999998865
No 185
>KOG3081|consensus
Probab=45.86 E-value=1.1e+02 Score=29.07 Aligned_cols=80 Identities=20% Similarity=0.243 Sum_probs=49.9
Q ss_pred HHHHHhhCHHHHHHHHHHHHhhCCccchHHHHHHHHHHHHHHHHhcCCCCCh-h-hhhhHhHhhhhhhhHHHHHHHHhCC
Q psy1676 103 RIKAVRLEYSTAHKNLVQALRKAPQTAAVGFRQTTQKLAVVVELLLGDIPDR-Q-IFRQAVLRRALSPYFQLTQAVRMGE 180 (343)
Q Consensus 103 ri~~~~~~y~~A~~~L~~A~~~~~~~sa~~~~~~i~K~li~v~LL~G~iP~~-~-~~~~~~l~~~l~~Y~~L~~Av~~Gd 180 (343)
..++.+++|.+|...|..|+.+-+.. ...+--+|++.++.|+=|+. + .+.+- +...|=..+++-+...+
T Consensus 215 v~~l~~~~~eeAe~lL~eaL~kd~~d------petL~Nliv~a~~~Gkd~~~~~r~l~QL---k~~~p~h~~vk~~~eke 285 (299)
T KOG3081|consen 215 VCHLQLGRYEEAESLLEEALDKDAKD------PETLANLIVLALHLGKDAEVTERNLSQL---KLSHPEHPFVKHLNEKE 285 (299)
T ss_pred HHHHHhcCHHHHHHHHHHHHhccCCC------HHHHHHHHHHHHHhCCChHHHHHHHHHH---HhcCCcchHHHHHHHHH
Confidence 36678999999999999999965432 22566788899999996541 1 11110 11223334555555443
Q ss_pred HHHHHHHHHhcc
Q psy1676 181 LQKFNEVLTTYG 192 (343)
Q Consensus 181 l~~f~~~l~~~~ 192 (343)
..|++.+.++.
T Consensus 286 -aeFDrl~~qy~ 296 (299)
T KOG3081|consen 286 -AEFDRLVLQYD 296 (299)
T ss_pred -HHHHHHHHHhc
Confidence 56776666553
No 186
>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=45.41 E-value=66 Score=21.42 Aligned_cols=33 Identities=27% Similarity=0.463 Sum_probs=29.5
Q ss_pred cccChHHHHHHhCCCCHHHHHHHHHHhHHcCCce
Q psy1676 224 SRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIE 257 (343)
Q Consensus 224 s~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~ 257 (343)
...+..+|++.++++ ...+-..+..|...|.|.
T Consensus 14 ~~~~~~el~~~l~~s-~~~vs~hL~~L~~~glV~ 46 (47)
T PF01022_consen 14 GPLTVSELAEELGLS-QSTVSHHLKKLREAGLVE 46 (47)
T ss_dssp SSEEHHHHHHHHTS--HHHHHHHHHHHHHTTSEE
T ss_pred CCCchhhHHHhcccc-chHHHHHHHHHHHCcCee
Confidence 668899999999995 999999999999999884
No 187
>PRK14574 hmsH outer membrane protein; Provisional
Probab=45.38 E-value=4.6e+02 Score=28.95 Aligned_cols=69 Identities=19% Similarity=0.200 Sum_probs=59.4
Q ss_pred HHHHHHHHHhhccHHHHHhhhhhc--CCC---------CCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCcc
Q psy1676 60 INCLLRNYLHYNLYDQADKLVKKS--AFP---------ENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQT 128 (343)
Q Consensus 60 ~n~Llr~yl~~~~~~~a~~li~k~--~~p---------~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~ 128 (343)
...|+-.|+....|+.|..++.++ .-| ...++.+..++....+.+++..+++.+|.+.|+.....+|.+
T Consensus 370 ~~~L~yA~ld~e~~~~A~~~l~~~~~~~p~~~~~~~~~~~~pn~d~~~~~~l~a~~~~~~gdl~~Ae~~le~l~~~aP~n 449 (822)
T PRK14574 370 ADDLYYSLNESEQLDKAYQFAVNYSEQTPYQVGVYGLPGKEPNDDWIEGQTLLVQSLVALNDLPTAQKKLEDLSSTAPAN 449 (822)
T ss_pred HHHHHHHHHhcccHHHHHHHHHHHHhcCCcEEeccCCCCCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCC
Confidence 357899999999999999999865 223 235778999999999999999999999999999999888875
No 188
>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A.
Probab=45.04 E-value=70 Score=23.63 Aligned_cols=60 Identities=17% Similarity=0.190 Sum_probs=40.5
Q ss_pred HHHHHHHHHHHHhhcccHHHHHHHHHHHHHHhhhcCCcchhHHHHHHHHHHHHhhccHHHHHhhhhh
Q psy1676 16 AAKCYFYHSRVHELTNNLDKVRSFLNARLRIATLRNDFEGQAVLINCLLRNYLHYNLYDQADKLVKK 82 (343)
Q Consensus 16 ~a~~~~y~~~~~e~~~~~~~~~~~l~~~~r~a~~~~~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k 82 (343)
.+.++|..+.++=..++...+...+-. ...++.. .-..-++-++|++.|+|+.|...+.+
T Consensus 24 ~~~~~~~la~~~~~~~~y~~A~~~~~~------~~~~~~~-~~~~~l~a~~~~~l~~y~eAi~~l~~ 83 (84)
T PF12895_consen 24 NSAYLYNLAQCYFQQGKYEEAIELLQK------LKLDPSN-PDIHYLLARCLLKLGKYEEAIKALEK 83 (84)
T ss_dssp HHHHHHHHHHHHHHTTHHHHHHHHHHC------HTHHHCH-HHHHHHHHHHHHHTT-HHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHCCCHHHHHHHHHH------hCCCCCC-HHHHHHHHHHHHHhCCHHHHHHHHhc
Confidence 455777789999999988888766644 1112211 12222457999999999999998864
No 189
>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional
Probab=44.61 E-value=72 Score=32.44 Aligned_cols=64 Identities=19% Similarity=0.041 Sum_probs=48.7
Q ss_pred HHHHHHHHHHHhhccHHHHHhhhhhc-CC-CCCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhh
Q psy1676 58 VLINCLLRNYLHYNLYDQADKLVKKS-AF-PENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRK 124 (343)
Q Consensus 58 ~l~n~Llr~yl~~~~~~~a~~li~k~-~~-p~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~ 124 (343)
-.++.+--.|++.+.|+.|...+++. .+ |.. .+.---+|..|..|..++++.+|..+|..|+..
T Consensus 76 ~a~~NLG~AL~~lGryeEAIa~f~rALeL~Pd~---aeA~~A~yNLAcaya~LGr~dEAla~LrrALel 141 (453)
T PLN03098 76 EDAVNLGLSLFSKGRVKDALAQFETALELNPNP---DEAQAAYYNKACCHAYREEGKKAADCLRTALRD 141 (453)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCc---hHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence 34444577889999999999999875 33 321 111123689999999999999999999999984
No 190
>PRK04841 transcriptional regulator MalT; Provisional
Probab=44.59 E-value=4.5e+02 Score=28.59 Aligned_cols=107 Identities=8% Similarity=-0.014 Sum_probs=72.2
Q ss_pred HHHHHHHHHhhcccHHHHHHHHHHHHHHhhhcCCcchhHHHHHHHHHHHHhhccHHHHHhhhhhc-CC-CCC-C-ChHHH
Q psy1676 19 CYFYHSRVHELTNNLDKVRSFLNARLRIATLRNDFEGQAVLINCLLRNYLHYNLYDQADKLVKKS-AF-PEN-A-SNNEW 94 (343)
Q Consensus 19 ~~~y~~~~~e~~~~~~~~~~~l~~~~r~a~~~~~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~-~~-p~~-~-~~~~~ 94 (343)
.....+.++...|.+..++..+-.++..+...++........+.+..+++..|+++.|...+... .. ... . .....
T Consensus 493 a~~~lg~~~~~~G~~~~A~~~~~~al~~~~~~g~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~ 572 (903)
T PRK04841 493 ATSVLGEVHHCKGELARALAMMQQTEQMARQHDVYHYALWSLLQQSEILFAQGFLQAAYETQEKAFQLIEEQHLEQLPMH 572 (903)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccccccHH
Confidence 34556667777888888887777776655544445554555566788899999999999887753 11 000 0 00111
Q ss_pred HHHHHHHHHHHHHhhCHHHHHHHHHHHHhhC
Q psy1676 95 ARFHFYLGRIKAVRLEYSTAHKNLVQALRKA 125 (343)
Q Consensus 95 ~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~ 125 (343)
..-....|.++...+++.+|...+..++...
T Consensus 573 ~~~~~~la~~~~~~G~~~~A~~~~~~al~~~ 603 (903)
T PRK04841 573 EFLLRIRAQLLWEWARLDEAEQCARKGLEVL 603 (903)
T ss_pred HHHHHHHHHHHHHhcCHHHHHHHHHHhHHhh
Confidence 1124567999999999999999999998843
No 191
>PRK09954 putative kinase; Provisional
Probab=44.56 E-value=40 Score=32.72 Aligned_cols=49 Identities=20% Similarity=0.228 Sum_probs=37.9
Q ss_pred cccccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEE---eeCCCceEEEcc
Q psy1676 222 SYSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEAT---LDREKGYMQSKE 271 (343)
Q Consensus 222 ~ys~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~---Id~~~g~v~~~~ 271 (343)
-..++|.++||+.|++ |...+...+.+|..+|.|.++ +++..+.+++..
T Consensus 14 ~~~~~s~~~la~~l~~-s~~~v~~~i~~L~~~g~i~~~~~~l~~~~~v~viG~ 65 (362)
T PRK09954 14 RNPLIQQNEIADILQI-SRSRVAAHIMDLMRKGRIKGKGYILTEQEYCVVVGA 65 (362)
T ss_pred HCCCCCHHHHHHHHCC-CHHHHHHHHHHHHHCCCcCCcEEEEcCCccEEEEEE
Confidence 3468999999999999 599999999999999999543 334444445543
No 192
>KOG1840|consensus
Probab=44.51 E-value=3.8e+02 Score=27.79 Aligned_cols=131 Identities=21% Similarity=0.167 Sum_probs=91.9
Q ss_pred HHHHHHhhcccHHHHHHHHHHHHHH--hhhcCCcchhHHHHHHHHHHHHhhccHHHHHhhhhhc-CCC---CCCChHHHH
Q psy1676 22 YHSRVHELTNNLDKVRSFLNARLRI--ATLRNDFEGQAVLINCLLRNYLHYNLYDQADKLVKKS-AFP---ENASNNEWA 95 (343)
Q Consensus 22 y~~~~~e~~~~~~~~~~~l~~~~r~--a~~~~~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~-~~p---~~~~~~~~~ 95 (343)
-++..|-..++..++.+.+-.++.+ .+...+....+.+++-|-..|.+.+++..|+..++.+ .+- ...+..++.
T Consensus 246 ~~a~~y~~~~k~~eAv~ly~~AL~i~e~~~G~~h~~va~~l~nLa~ly~~~GKf~EA~~~~e~Al~I~~~~~~~~~~~v~ 325 (508)
T KOG1840|consen 246 ILALVYRSLGKYDEAVNLYEEALTIREEVFGEDHPAVAATLNNLAVLYYKQGKFAEAEEYCERALEIYEKLLGASHPEVA 325 (508)
T ss_pred HHHHHHHHhccHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHhccCChHHHHHHHHHHHHHHHHhhccChHHHH
Confidence 5666777777778888777776643 3334556666677777799999999999999888754 111 124567888
Q ss_pred HHHHHHHHHHHHhhCHHHHHHHHHHHHh---hCCccchHHHHHHHHHHHHHHHHhcCCCCC
Q psy1676 96 RFHFYLGRIKAVRLEYSTAHKNLVQALR---KAPQTAAVGFRQTTQKLAVVVELLLGDIPD 153 (343)
Q Consensus 96 ~Y~YY~Gri~~~~~~y~~A~~~L~~A~~---~~~~~sa~~~~~~i~K~li~v~LL~G~iP~ 153 (343)
..+=..|.++...++|++|...|+.++. ..|.. +..+..-+.--+-.+...+|+.-+
T Consensus 326 ~~l~~~~~~~~~~~~~Eea~~l~q~al~i~~~~~g~-~~~~~a~~~~nl~~l~~~~gk~~e 385 (508)
T KOG1840|consen 326 AQLSELAAILQSMNEYEEAKKLLQKALKIYLDAPGE-DNVNLAKIYANLAELYLKMGKYKE 385 (508)
T ss_pred HHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhhccc-cchHHHHHHHHHHHHHHHhcchhH
Confidence 8888999999999999999999999998 23332 121244444445455566788655
No 193
>KOG1129|consensus
Probab=44.48 E-value=2.5e+02 Score=27.72 Aligned_cols=57 Identities=16% Similarity=0.134 Sum_probs=43.7
Q ss_pred HHHHHHHhhccHHHHHhhhhhc--CCCCCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhh
Q psy1676 62 CLLRNYLHYNLYDQADKLVKKS--AFPENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRK 124 (343)
Q Consensus 62 ~Llr~yl~~~~~~~a~~li~k~--~~p~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~ 124 (343)
+|-|.|-+.+++..|.++++.. .|| .-++|+-=.+||+-..+++++|.+.+..++..
T Consensus 261 lLskvY~ridQP~~AL~~~~~gld~fP------~~VT~l~g~ARi~eam~~~~~a~~lYk~vlk~ 319 (478)
T KOG1129|consen 261 LLSKVYQRIDQPERALLVIGEGLDSFP------FDVTYLLGQARIHEAMEQQEDALQLYKLVLKL 319 (478)
T ss_pred HHHHHHHHhccHHHHHHHHhhhhhcCC------chhhhhhhhHHHHHHHHhHHHHHHHHHHHHhc
Confidence 3457777777777777777643 444 45778888889999999999999999999984
No 194
>KOG1127|consensus
Probab=42.66 E-value=3.4e+02 Score=30.70 Aligned_cols=129 Identities=20% Similarity=0.252 Sum_probs=75.6
Q ss_pred HHHHHHHHHHHhhccHHHHHhhhhhc-CC-CCCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCcc--chHHH
Q psy1676 58 VLINCLLRNYLHYNLYDQADKLVKKS-AF-PENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQT--AAVGF 133 (343)
Q Consensus 58 ~l~n~Llr~yl~~~~~~~a~~li~k~-~~-p~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~--sa~~~ 133 (343)
.-...+...|-+.++.++|..+.-.. +. |...-...+++ .|.+|.--+++..|..+|+-|++-.|.. ++.+-
T Consensus 527 eaaaa~adtyae~~~we~a~~I~l~~~qka~a~~~k~nW~~----rG~yyLea~n~h~aV~~fQsALR~dPkD~n~W~gL 602 (1238)
T KOG1127|consen 527 EAAAASADTYAEESTWEEAFEICLRAAQKAPAFACKENWVQ----RGPYYLEAHNLHGAVCEFQSALRTDPKDYNLWLGL 602 (1238)
T ss_pred hhHHHHHHHhhccccHHHHHHHHHHHhhhchHHHHHhhhhh----ccccccCccchhhHHHHHHHHhcCCchhHHHHHHH
Confidence 33334455666666666666553322 11 11111223333 8999999999999999999999976654 22222
Q ss_pred HHHHHHHHHHHHHhcCCCCC-hhhhhhHhHhhhhhhhHHHHHHHHhCCHHHHHHHHHhcccccccc
Q psy1676 134 RQTTQKLAVVVELLLGDIPD-RQIFRQAVLRRALSPYFQLTQAVRMGELQKFNEVLTTYGNQFRTD 198 (343)
Q Consensus 134 ~~~i~K~li~v~LL~G~iP~-~~~~~~~~l~~~l~~Y~~L~~Av~~Gdl~~f~~~l~~~~~~f~~d 198 (343)
-+++. -.|.+-. ...|..-..-.....|..+..|+..-|+.++...++..+......
T Consensus 603 GeAY~--------~sGry~~AlKvF~kAs~LrP~s~y~~fk~A~~ecd~GkYkeald~l~~ii~~~ 660 (1238)
T KOG1127|consen 603 GEAYP--------ESGRYSHALKVFTKASLLRPLSKYGRFKEAVMECDNGKYKEALDALGLIIYAF 660 (1238)
T ss_pred HHHHH--------hcCceehHHHhhhhhHhcCcHhHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHH
Confidence 22221 2344333 233432222234567888888888888888888888776544443
No 195
>PF13812 PPR_3: Pentatricopeptide repeat domain
Probab=41.79 E-value=37 Score=20.13 Aligned_cols=24 Identities=29% Similarity=0.209 Sum_probs=20.8
Q ss_pred HHHHHHHHHHhhccHHHHHhhhhh
Q psy1676 59 LINCLLRNYLHYNLYDQADKLVKK 82 (343)
Q Consensus 59 l~n~Llr~yl~~~~~~~a~~li~k 82 (343)
..|.+++.|.+.++++.|..+++.
T Consensus 3 ty~~ll~a~~~~g~~~~a~~~~~~ 26 (34)
T PF13812_consen 3 TYNALLRACAKAGDPDAALQLFDE 26 (34)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHH
Confidence 568889999999999999988874
No 196
>PHA02943 hypothetical protein; Provisional
Probab=41.30 E-value=41 Score=29.11 Aligned_cols=36 Identities=25% Similarity=0.325 Sum_probs=31.1
Q ss_pred cccccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceE
Q psy1676 222 SYSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEA 258 (343)
Q Consensus 222 ~ys~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a 258 (343)
....-+.++||+++|+ |..+|++++--+=++|.|+-
T Consensus 21 k~G~~TtseIAkaLGl-S~~qa~~~LyvLErEG~Vkr 56 (165)
T PHA02943 21 ADGCKTTSRIANKLGV-SHSMARNALYQLAKEGMVLK 56 (165)
T ss_pred hcCCccHHHHHHHHCC-CHHHHHHHHHHHHHcCceEE
Confidence 3455678999999999 59999999999999999964
No 197
>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=40.85 E-value=47 Score=21.51 Aligned_cols=31 Identities=26% Similarity=0.366 Sum_probs=24.1
Q ss_pred cChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEee
Q psy1676 226 ITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLD 261 (343)
Q Consensus 226 Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~Id 261 (343)
+++.++|+.+|++ .. -+-+++.+|.|.+...
T Consensus 2 lt~~e~a~~lgis-~~----ti~~~~~~g~i~~~~~ 32 (49)
T TIGR01764 2 LTVEEAAEYLGVS-KD----TVYRLIHEGELPAYRV 32 (49)
T ss_pred CCHHHHHHHHCCC-HH----HHHHHHHcCCCCeEEe
Confidence 5789999999995 43 5667789999987654
No 198
>PF10300 DUF3808: Protein of unknown function (DUF3808); InterPro: IPR019412 This entry represents a family of proteins conserved from fungi to humans. In humans this protein is expressed in primary breast carcinomas but not in normal breast tissue, and has a putative eukaryotic RNP-1 RNA binding region and a candidate anchoring transmembrane domain. The human protein is coordinately regulated with oestrogen receptor, but is not necessarily oestradiol-responsive []. Members of this family carry a tetratricopeptide repeat (IPR013105 from INTERPRO) at their C terminus.
Probab=40.29 E-value=2.5e+02 Score=28.66 Aligned_cols=86 Identities=12% Similarity=0.062 Sum_probs=63.0
Q ss_pred HHHHHHHHHhhcccHHHHHHHHHHHHHHhhhcCCcchhH--HHHHHHHHHHHhhccHHHHHhhhhhcCCCCCCChHHHHH
Q psy1676 19 CYFYHSRVHELTNNLDKVRSFLNARLRIATLRNDFEGQA--VLINCLLRNYLHYNLYDQADKLVKKSAFPENASNNEWAR 96 (343)
Q Consensus 19 ~~~y~~~~~e~~~~~~~~~~~l~~~~r~a~~~~~~~~~~--~l~n~Llr~yl~~~~~~~a~~li~k~~~p~~~~~~~~~~ 96 (343)
..|+-+|.+-..++++.+...+-.+.. ....+.|. ...=.+.-+++-..+|..|...+....- .++--...
T Consensus 269 fl~~~gR~~~~~g~~~~Ai~~~~~a~~----~q~~~~Ql~~l~~~El~w~~~~~~~w~~A~~~f~~L~~---~s~WSka~ 341 (468)
T PF10300_consen 269 FLFFEGRLERLKGNLEEAIESFERAIE----SQSEWKQLHHLCYFELAWCHMFQHDWEEAAEYFLRLLK---ESKWSKAF 341 (468)
T ss_pred HHHHHHHHHHHhcCHHHHHHHHHHhcc----chhhHHhHHHHHHHHHHHHHHHHchHHHHHHHHHHHHh---ccccHHHH
Confidence 478889999999999988877765553 23445555 2222467778889999999988775421 23335889
Q ss_pred HHHHHHHHHHHhhCH
Q psy1676 97 FHFYLGRIKAVRLEY 111 (343)
Q Consensus 97 Y~YY~Gri~~~~~~y 111 (343)
|.|..|-.+...++.
T Consensus 342 Y~Y~~a~c~~~l~~~ 356 (468)
T PF10300_consen 342 YAYLAAACLLMLGRE 356 (468)
T ss_pred HHHHHHHHHHhhccc
Confidence 999999999998888
No 199
>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=39.75 E-value=86 Score=21.96 Aligned_cols=35 Identities=20% Similarity=0.339 Sum_probs=31.2
Q ss_pred hcccccChHHHHHHhCCCCHHHHHHHHHHhHHcCCc
Q psy1676 221 ASYSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVI 256 (343)
Q Consensus 221 ~~ys~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I 256 (343)
.....+++.++|..+++ |+.-+..-+..|-..|.|
T Consensus 10 ~~~~~~s~~ela~~~~V-S~~TiRRDl~~L~~~g~i 44 (57)
T PF08220_consen 10 KEKGKVSVKELAEEFGV-SEMTIRRDLNKLEKQGLI 44 (57)
T ss_pred HHcCCEEHHHHHHHHCc-CHHHHHHHHHHHHHCCCE
Confidence 34578999999999999 599999999999999986
No 200
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=39.73 E-value=51 Score=27.48 Aligned_cols=42 Identities=14% Similarity=0.250 Sum_probs=36.8
Q ss_pred cccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEeeCCCce
Q psy1676 224 SRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLDREKGY 266 (343)
Q Consensus 224 s~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~Id~~~g~ 266 (343)
..++.++||..++++ ..-+=.+|.+|...|+|.=.-|..++-
T Consensus 53 ~~~t~~eLa~~l~i~-~~tvsr~l~~Le~~GlI~R~~~~~DrR 94 (144)
T PRK11512 53 ACITPVELKKVLSVD-LGALTRMLDRLVCKGWVERLPNPNDKR 94 (144)
T ss_pred CCCCHHHHHHHHCCC-HHHHHHHHHHHHHCCCEEeccCcccCC
Confidence 469999999999995 899999999999999998877766643
No 201
>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=39.16 E-value=28 Score=20.09 Aligned_cols=25 Identities=16% Similarity=0.344 Sum_probs=20.9
Q ss_pred HHHHHHHHHHhhccHHHHHhhhhhc
Q psy1676 59 LINCLLRNYLHYNLYDQADKLVKKS 83 (343)
Q Consensus 59 l~n~Llr~yl~~~~~~~a~~li~k~ 83 (343)
..|.+++.|.+.++++.|..+++..
T Consensus 2 ~y~~li~~~~~~~~~~~a~~~~~~M 26 (31)
T PF01535_consen 2 TYNSLISGYCKMGQFEEALEVFDEM 26 (31)
T ss_pred cHHHHHHHHHccchHHHHHHHHHHH
Confidence 4678899999999999999988753
No 202
>KOG0495|consensus
Probab=38.54 E-value=5.5e+02 Score=27.86 Aligned_cols=167 Identities=14% Similarity=0.193 Sum_probs=90.4
Q ss_pred HHHHHHHHhhcccHHHHHHHHHHHHHHhhhcCCcchhHHHHHHHHHHHHhhccHHHHHhhhhhcCC--CC-C-----C--
Q psy1676 20 YFYHSRVHELTNNLDKVRSFLNARLRIATLRNDFEGQAVLINCLLRNYLHYNLYDQADKLVKKSAF--PE-N-----A-- 89 (343)
Q Consensus 20 ~~y~~~~~e~~~~~~~~~~~l~~~~r~a~~~~~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~~~--p~-~-----~-- 89 (343)
|--|+..+=..|.+..+|.+|..+|..+ +.+. -|.-.-+++-+..+.++.|..++.++-. |. . +
T Consensus 587 wlM~ake~w~agdv~~ar~il~~af~~~-----pnse-eiwlaavKle~en~e~eraR~llakar~~sgTeRv~mKs~~~ 660 (913)
T KOG0495|consen 587 WLMYAKEKWKAGDVPAARVILDQAFEAN-----PNSE-EIWLAAVKLEFENDELERARDLLAKARSISGTERVWMKSANL 660 (913)
T ss_pred HHHHHHHHHhcCCcHHHHHHHHHHHHhC-----CCcH-HHHHHHHHHhhccccHHHHHHHHHHHhccCCcchhhHHHhHH
Confidence 4445555556678888888888777632 2211 1222225677788888888888776521 10 0 0
Q ss_pred -------------------ChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCccchHHHHHHHHHHHHHHHHh--c
Q psy1676 90 -------------------SNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQTAAVGFRQTTQKLAVVVELL--L 148 (343)
Q Consensus 90 -------------------~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~sa~~~~~~i~K~li~v~LL--~ 148 (343)
+..+.-.++-..|.|+=..++...|...|.+-+++||.. +.-|++++.|- .
T Consensus 661 er~ld~~eeA~rllEe~lk~fp~f~Kl~lmlGQi~e~~~~ie~aR~aY~~G~k~cP~~--------ipLWllLakleEk~ 732 (913)
T KOG0495|consen 661 ERYLDNVEEALRLLEEALKSFPDFHKLWLMLGQIEEQMENIEMAREAYLQGTKKCPNS--------IPLWLLLAKLEEKD 732 (913)
T ss_pred HHHhhhHHHHHHHHHHHHHhCCchHHHHHHHhHHHHHHHHHHHHHHHHHhccccCCCC--------chHHHHHHHHHHHh
Confidence 001222334456666666666666666666666666653 23456555552 2
Q ss_pred CCCCC-hhhhhhHhHh---hhhhhhHHHHHHHHhCCHHHHHHHHHhcccccccccc
Q psy1676 149 GDIPD-RQIFRQAVLR---RALSPYFQLTQAVRMGELQKFNEVLTTYGNQFRTDYT 200 (343)
Q Consensus 149 G~iP~-~~~~~~~~l~---~~l~~Y~~L~~Av~~Gdl~~f~~~l~~~~~~f~~d~~ 200 (343)
|.+-. ++++..-.++ ..+.+...+---+|.|+...-+..+.+--..+-..|.
T Consensus 733 ~~~~rAR~ildrarlkNPk~~~lwle~Ir~ElR~gn~~~a~~lmakALQecp~sg~ 788 (913)
T KOG0495|consen 733 GQLVRARSILDRARLKNPKNALLWLESIRMELRAGNKEQAELLMAKALQECPSSGL 788 (913)
T ss_pred cchhhHHHHHHHHHhcCCCcchhHHHHHHHHHHcCCHHHHHHHHHHHHHhCCccch
Confidence 32111 3444322222 2233333444467889988888777766555555553
No 203
>PF05331 DUF742: Protein of unknown function (DUF742); InterPro: IPR007995 This family consists of several uncharacterised Streptomyces proteins as well as one from Mycobacterium tuberculosis. The function of these proteins is unknown.
Probab=38.04 E-value=73 Score=26.12 Aligned_cols=33 Identities=18% Similarity=0.386 Sum_probs=29.6
Q ss_pred ccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceE
Q psy1676 225 RITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEA 258 (343)
Q Consensus 225 ~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a 258 (343)
.+|.++||..++++ ..-+--+++.|+..|.|..
T Consensus 55 ~~SVAEiAA~L~lP-lgVvrVLvsDL~~~G~v~v 87 (114)
T PF05331_consen 55 PLSVAEIAARLGLP-LGVVRVLVSDLADAGLVRV 87 (114)
T ss_pred CccHHHHHHhhCCC-chhhhhhHHHHHhCCCEEE
Confidence 88999999999997 7788889999999998853
No 204
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=37.18 E-value=2.9e+02 Score=24.30 Aligned_cols=48 Identities=17% Similarity=0.241 Sum_probs=38.3
Q ss_pred cccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEeeC--CCceEEEccC
Q psy1676 224 SRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLDR--EKGYMQSKES 272 (343)
Q Consensus 224 s~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~Id~--~~g~v~~~~~ 272 (343)
..++-.++|..+|+. ..+|-.++.+|-.+|.+...--. +.|+.+..+.
T Consensus 35 g~~tdeeLA~~Lgi~-~~~VRk~L~~L~e~gLv~~~r~r~~~~Gr~~y~w~ 84 (178)
T PRK06266 35 GEVTDEEIAEQTGIK-LNTVRKILYKLYDARLADYKREKDEETNWYTYTWK 84 (178)
T ss_pred CCcCHHHHHHHHCCC-HHHHHHHHHHHHHCCCeEEeeeeccCCCcEEEEEE
Confidence 468999999999995 99999999999999999754422 3566666544
No 205
>KOG1174|consensus
Probab=37.12 E-value=1.4e+02 Score=30.30 Aligned_cols=63 Identities=27% Similarity=0.321 Sum_probs=49.9
Q ss_pred HHHHHHHHHHhhccHHHHHhhhhhc--CCCCCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCcc
Q psy1676 59 LINCLLRNYLHYNLYDQADKLVKKS--AFPENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQT 128 (343)
Q Consensus 59 l~n~Llr~yl~~~~~~~a~~li~k~--~~p~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~ 128 (343)
-++.+..++..-+.+..+-.++++. .+|+ .+ .+--+|-+...++.|++|.++|+.|++.-|++
T Consensus 440 AV~~~AEL~~~Eg~~~D~i~LLe~~L~~~~D--~~-----LH~~Lgd~~~A~Ne~Q~am~~y~~ALr~dP~~ 504 (564)
T KOG1174|consen 440 AVNLIAELCQVEGPTKDIIKLLEKHLIIFPD--VN-----LHNHLGDIMRAQNEPQKAMEYYYKALRQDPKS 504 (564)
T ss_pred HHHHHHHHHHhhCccchHHHHHHHHHhhccc--cH-----HHHHHHHHHHHhhhHHHHHHHHHHHHhcCccc
Confidence 3566788889999999999999875 4553 11 23368999999999999999999999977764
No 206
>PF08898 DUF1843: Domain of unknown function (DUF1843); InterPro: IPR014994 This domain is found in functionally uncharacterised proteins. It can be found independently or at the C terminus of the protein.
Probab=36.89 E-value=90 Score=22.03 Aligned_cols=39 Identities=15% Similarity=0.279 Sum_probs=30.6
Q ss_pred HHHHHHHhCCHHHHHHHHHhccccccccccH-HHHHHHHH
Q psy1676 171 QLTQAVRMGELQKFNEVLTTYGNQFRTDYTF-KLILRLRH 209 (343)
Q Consensus 171 ~L~~Av~~Gdl~~f~~~l~~~~~~f~~d~~~-~Lv~~l~~ 209 (343)
.+-+|+.+||+.....++..-+..+...|.. ..++.|..
T Consensus 6 aiq~AiasGDLa~MK~l~~~aeq~L~~~~~i~~al~~Lk~ 45 (53)
T PF08898_consen 6 AIQQAIASGDLAQMKALAAQAEQQLAEAGDIAAALEKLKA 45 (53)
T ss_pred HHHHHHHcCcHHHHHHHHHHHHHHHccchHHHHHHHHHHH
Confidence 5778999999999999999888888777765 44555543
No 207
>KOG0495|consensus
Probab=36.89 E-value=2.5e+02 Score=30.32 Aligned_cols=107 Identities=13% Similarity=0.149 Sum_probs=64.7
Q ss_pred HHHHHHHHHHhhcccHHHHHHHHHHHHHHhhhcCCcchhHHHHHHHHHHHHhhccHHHHHhhhhhcCCCCCCChHHHHHH
Q psy1676 18 KCYFYHSRVHELTNNLDKVRSFLNARLRIATLRNDFEGQAVLINCLLRNYLHYNLYDQADKLVKKSAFPENASNNEWARF 97 (343)
Q Consensus 18 ~~~~y~~~~~e~~~~~~~~~~~l~~~~r~a~~~~~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~~~p~~~~~~~~~~Y 97 (343)
|+|--.+-++|..++++.+|..-...+|. .|. ...|.-+|.++==+.++...|..++.+..... |.+.
T Consensus 686 Kl~lmlGQi~e~~~~ie~aR~aY~~G~k~-----cP~-~ipLWllLakleEk~~~~~rAR~ildrarlkN--Pk~~---- 753 (913)
T KOG0495|consen 686 KLWLMLGQIEEQMENIEMAREAYLQGTKK-----CPN-SIPLWLLLAKLEEKDGQLVRARSILDRARLKN--PKNA---- 753 (913)
T ss_pred HHHHHHhHHHHHHHHHHHHHHHHHhcccc-----CCC-CchHHHHHHHHHHHhcchhhHHHHHHHHHhcC--CCcc----
Confidence 34445555666666666555444433332 222 23555566677777788888888888764321 1111
Q ss_pred HHHHHHHHH--HhhCHHHHHHHHHHHHhhCCccchHHHHHHH
Q psy1676 98 HFYLGRIKA--VRLEYSTAHKNLVQALRKAPQTAAVGFRQTT 137 (343)
Q Consensus 98 ~YY~Gri~~--~~~~y~~A~~~L~~A~~~~~~~sa~~~~~~i 137 (343)
.+|+..|.+ --|+-..|......|+..||.+ ..-|.++|
T Consensus 754 ~lwle~Ir~ElR~gn~~~a~~lmakALQecp~s-g~LWaEaI 794 (913)
T KOG0495|consen 754 LLWLESIRMELRAGNKEQAELLMAKALQECPSS-GLLWAEAI 794 (913)
T ss_pred hhHHHHHHHHHHcCCHHHHHHHHHHHHHhCCcc-chhHHHHH
Confidence 124444444 5689999999999999999975 45555554
No 208
>PRK10370 formate-dependent nitrite reductase complex subunit NrfG; Provisional
Probab=36.86 E-value=3e+02 Score=24.31 Aligned_cols=36 Identities=22% Similarity=0.151 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCcc
Q psy1676 93 EWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQT 128 (343)
Q Consensus 93 ~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~ 128 (343)
+....++.+|+++...++|.+|...|..|++..|..
T Consensus 71 ~~~~~w~~Lg~~~~~~g~~~~A~~a~~~Al~l~P~~ 106 (198)
T PRK10370 71 QNSEQWALLGEYYLWRNDYDNALLAYRQALQLRGEN 106 (198)
T ss_pred CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCC
Confidence 334567889999999999999999999999976654
No 209
>PF09940 DUF2172: Domain of unknown function (DUF2172); InterPro: IPR012353 The proteins in this entry are encoded by genes located in polysaccharide biosynthesis gene clusters, and are therefore believed to be involved in polysaccharide biosynthesis. The ste gene cluster (for Streptomyces eps) is involved in exopolysaccharide EPS 139A biosynthesis in Streptomyces sp. 139 []. Members of this group exhibit distant sequence similarity to aminopeptidases (IPR007484 from INTERPRO, MEROPS peptidase family M28).; PDB: 3K9T_A.
Probab=36.67 E-value=46 Score=32.98 Aligned_cols=65 Identities=15% Similarity=0.154 Sum_probs=34.6
Q ss_pred cccccccccHHHHHHHH---HHHHHHHHHHHhhcccccChHHHHHHhCCCCHHHHHHHHHHhHHcCCce
Q psy1676 192 GNQFRTDYTFKLILRLR---HNVIKTAIRSIGASYSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIE 257 (343)
Q Consensus 192 ~~~f~~d~~~~Lv~~l~---~~v~r~~ir~i~~~ys~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~ 257 (343)
+..+-+.|.|..+-.-. ....+..+--++.+=-.-||-|||++++++ .+++..++-+++..|.|+
T Consensus 319 EPqLgkrgLY~~~~~~~~~~~~~~~~~l~~L~~~DG~~slldIA~~~~~~-~~~~~~~~~~l~~~~Llk 386 (386)
T PF09940_consen 319 EPQLGKRGLYPTISGKSDAGKAQQMAMLWVLNYSDGKNSLLDIAERIGLP-FDELADAARKLLEAGLLK 386 (386)
T ss_dssp ---TTS-----------------HHHHHHHHHH-EEEEEHHHHHHHHT---HHHHHHHHHHHHHTT-EE
T ss_pred CCCCCcccCccccCCCcchhHHHHHHHHHHHHhccCCCcHHHHHHHHCcC-HHHHHHHHHHHHHcCCCC
Confidence 55777888886654322 122333333344444688999999999996 999999999999999874
No 210
>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=36.19 E-value=2.1e+02 Score=24.66 Aligned_cols=67 Identities=12% Similarity=0.183 Sum_probs=45.8
Q ss_pred cccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEe--eCCCceEEEccCccccccccchHHHHHHHHHHHH
Q psy1676 224 SRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATL--DREKGYMQSKESADIYCTVEPQLAFHQRIAFCLD 294 (343)
Q Consensus 224 s~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~I--d~~~g~v~~~~~~~v~s~~ep~~~~~~rI~~cl~ 294 (343)
+-++-.+||..+|+. ..++-.++.+|-.+|.+.-.= +.++|+....+..+ ..+....+..++..++.
T Consensus 27 ~~~tdEeLa~~Lgi~-~~~VRk~L~~L~e~~Lv~~~r~r~~~~gw~~Y~w~i~---~~~i~d~Ik~~~~~~~~ 95 (158)
T TIGR00373 27 GEFTDEEISLELGIK-LNEVRKALYALYDAGLADYKRRKDDETGWYEYTWRIN---YEKALDVLKRKLEETAK 95 (158)
T ss_pred CCCCHHHHHHHHCCC-HHHHHHHHHHHHHCCCceeeeeeecCCCcEEEEEEeC---HHHHHHHHHHHHHHHHH
Confidence 458999999999995 999999999999999994221 33457766665432 22334445555544443
No 211
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=36.10 E-value=84 Score=28.75 Aligned_cols=50 Identities=18% Similarity=0.257 Sum_probs=42.2
Q ss_pred ccccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEeeCCCceEEEccCc
Q psy1676 223 YSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLDREKGYMQSKESA 273 (343)
Q Consensus 223 ys~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~Id~~~g~v~~~~~~ 273 (343)
...||.+++|+.++++ ..-+-.+|.+|-..|+|.-..+..+..+...+..
T Consensus 19 ~~~IS~~eLA~~L~iS-~~Tvsr~Lk~LEe~GlI~R~~~~r~~~v~LTekG 68 (217)
T PRK14165 19 TVKISSSEFANHTGTS-SKTAARILKQLEDEGYITRTIVPRGQLITITEKG 68 (217)
T ss_pred CCCcCHHHHHHHHCcC-HHHHHHHHHHHHHCCCEEEEEcCCceEEEECHHH
Confidence 3579999999999995 8999999999999999998888776666666543
No 212
>COG4700 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]
Probab=35.94 E-value=1.5e+02 Score=27.05 Aligned_cols=62 Identities=16% Similarity=0.164 Sum_probs=46.9
Q ss_pred HHHHHHHhhccHHHHHhhhhhc--CCCCCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCc
Q psy1676 62 CLLRNYLHYNLYDQADKLVKKS--AFPENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQ 127 (343)
Q Consensus 62 ~Llr~yl~~~~~~~a~~li~k~--~~p~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~ 127 (343)
.+.+.-|.++.+..|...+++. ..|...+..-.+ ..||.+..++.|.+|..-|++|++..|.
T Consensus 129 glA~Aqfa~~~~A~a~~tLe~l~e~~pa~r~pd~~L----l~aR~laa~g~~a~Aesafe~a~~~ypg 192 (251)
T COG4700 129 GLAQAQFAIQEFAAAQQTLEDLMEYNPAFRSPDGHL----LFARTLAAQGKYADAESAFEVAISYYPG 192 (251)
T ss_pred HHHHHHHhhccHHHHHHHHHHHhhcCCccCCCCchH----HHHHHHHhcCCchhHHHHHHHHHHhCCC
Confidence 3477788999999999988875 224333222222 5699999999999999999999997664
No 213
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.82 E-value=44 Score=26.12 Aligned_cols=24 Identities=21% Similarity=0.241 Sum_probs=21.5
Q ss_pred cccChHHHHHHhCCCCHHHHHHHHH
Q psy1676 224 SRITPTKIAEKLGLESPEDAEFIIA 248 (343)
Q Consensus 224 s~Isl~dIa~~l~l~s~~e~E~ila 248 (343)
+++|.+.||++|++. +..+|.+++
T Consensus 22 ~~LS~~~iA~~Ln~t-~~~lekil~ 45 (97)
T COG4367 22 CPLSDEEIATALNWT-EVKLEKILQ 45 (97)
T ss_pred ccccHHHHHHHhCCC-HHHHHHHHH
Confidence 789999999999994 899999885
No 214
>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=35.03 E-value=1.7e+02 Score=20.95 Aligned_cols=35 Identities=23% Similarity=0.439 Sum_probs=29.2
Q ss_pred cccccChHHHHHHhCCCCHHHHHHHHHHhHHcCCce
Q psy1676 222 SYSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIE 257 (343)
Q Consensus 222 ~ys~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~ 257 (343)
.+.+.|+.+|.+..+++ +.++...++.||..|.+.
T Consensus 24 ~~G~ltl~~i~~~t~l~-~~~Vk~~L~~LiQh~~v~ 58 (62)
T PF08221_consen 24 SRGRLTLREIVRRTGLS-PKQVKKALVVLIQHNLVQ 58 (62)
T ss_dssp HC-SEEHHHHHHHHT---HHHHHHHHHHHHHTTSEE
T ss_pred HcCCcCHHHHHHHhCCC-HHHHHHHHHHHHHcCCee
Confidence 46799999999999995 999999999999988774
No 215
>KOG1156|consensus
Probab=34.79 E-value=4.2e+02 Score=28.35 Aligned_cols=88 Identities=17% Similarity=0.138 Sum_probs=52.0
Q ss_pred HHHHHHHHhhCHHHHHHHHHHHHhhCCccchHHHHHHHHHHHHHHHHhcCCCCC----hhhhhhHhHhhhhhhhHHHHHH
Q psy1676 100 YLGRIKAVRLEYSTAHKNLVQALRKAPQTAAVGFRQTTQKLAVVVELLLGDIPD----RQIFRQAVLRRALSPYFQLTQA 175 (343)
Q Consensus 100 Y~Gri~~~~~~y~~A~~~L~~A~~~~~~~sa~~~~~~i~K~li~v~LL~G~iP~----~~~~~~~~l~~~l~~Y~~L~~A 175 (343)
-.|.++=..++|.+|..++..|+...+.+ .++++-+-+.++-+|++-. +..+-+-.....-.+..--+.+
T Consensus 80 v~gl~~R~dK~Y~eaiKcy~nAl~~~~dN------~qilrDlslLQ~QmRd~~~~~~tr~~LLql~~~~ra~w~~~Avs~ 153 (700)
T KOG1156|consen 80 VLGLLQRSDKKYDEAIKCYRNALKIEKDN------LQILRDLSLLQIQMRDYEGYLETRNQLLQLRPSQRASWIGFAVAQ 153 (700)
T ss_pred HHHHHHhhhhhHHHHHHHHHHHHhcCCCc------HHHHHHHHHHHHHHHhhhhHHHHHHHHHHhhhhhHHHHHHHHHHH
Confidence 56899999999999999999999966654 1255555555666666433 1111111111112233334455
Q ss_pred HHhCCHHHHHHHHHhccc
Q psy1676 176 VRMGELQKFNEVLTTYGN 193 (343)
Q Consensus 176 v~~Gdl~~f~~~l~~~~~ 193 (343)
+-.|+-..=..+++.++.
T Consensus 154 ~L~g~y~~A~~il~ef~~ 171 (700)
T KOG1156|consen 154 HLLGEYKMALEILEEFEK 171 (700)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 667776665666655543
No 216
>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=34.66 E-value=1e+02 Score=21.40 Aligned_cols=42 Identities=21% Similarity=0.275 Sum_probs=28.1
Q ss_pred HHhhCHHHHHHHHHHHHhhCCccchHHHHHHHHHHHHHHHHhcCCCCC
Q psy1676 106 AVRLEYSTAHKNLVQALRKAPQTAAVGFRQTTQKLAVVVELLLGDIPD 153 (343)
Q Consensus 106 ~~~~~y~~A~~~L~~A~~~~~~~sa~~~~~~i~K~li~v~LL~G~iP~ 153 (343)
+.+++|.+|...|..++...|.+.. +...+.-+.+-.|+...
T Consensus 2 l~~~~~~~A~~~~~~~l~~~p~~~~------~~~~la~~~~~~g~~~~ 43 (68)
T PF14559_consen 2 LKQGDYDEAIELLEKALQRNPDNPE------ARLLLAQCYLKQGQYDE 43 (68)
T ss_dssp HHTTHHHHHHHHHHHHHHHTTTSHH------HHHHHHHHHHHTT-HHH
T ss_pred hhccCHHHHHHHHHHHHHHCCCCHH------HHHHHHHHHHHcCCHHH
Confidence 4679999999999999997776421 22234445566666544
No 217
>KOG0542|consensus
Probab=34.63 E-value=1.2e+02 Score=28.53 Aligned_cols=64 Identities=31% Similarity=0.365 Sum_probs=41.1
Q ss_pred ccccccccHHHHHHHHHHHHHHHHH------------HHhhc-cccc---ChHHHHHHhCC----------CCHHHHHHH
Q psy1676 193 NQFRTDYTFKLILRLRHNVIKTAIR------------SIGAS-YSRI---TPTKIAEKLGL----------ESPEDAEFI 246 (343)
Q Consensus 193 ~~f~~d~~~~Lv~~l~~~v~r~~ir------------~i~~~-ys~I---sl~dIa~~l~l----------~s~~e~E~i 246 (343)
-.|..||-+.+..-|..-+-+.+|+ ++.+. |.+. -+...-+.+|| ||...+-.|
T Consensus 155 ~Afvtdg~wDl~~~l~~qck~~~i~~P~~f~qwInirk~yk~~y~~~~~t~it~mLe~~gL~f~Gr~HsGiDDa~Nia~I 234 (280)
T KOG0542|consen 155 FAFVTDGDWDLWVFLQYQCKLKNIRIPAFFNQWINIRKIYKNFYNRPAPTNITGMLEHYGLQFEGRAHSGIDDARNIARI 234 (280)
T ss_pred eEEEeCchhhHHHHHHHHHHHhcCCCcHHHHHHhHHHHHHHHHhcCccccCHHHHHHHhCCcccCCcccCchhHHHHHHH
Confidence 3588899887777666655555444 33332 2332 35555556665 356777888
Q ss_pred HHHhHHcCCc
Q psy1676 247 IAKAIRDGVI 256 (343)
Q Consensus 247 la~lI~~G~I 256 (343)
+.+||++|.-
T Consensus 235 ~~kM~~dg~~ 244 (280)
T KOG0542|consen 235 AQKMIRDGAE 244 (280)
T ss_pred HHHHHhCCcE
Confidence 9999999954
No 218
>PF12862 Apc5: Anaphase-promoting complex subunit 5
Probab=34.61 E-value=2.1e+02 Score=21.91 Aligned_cols=63 Identities=17% Similarity=0.226 Sum_probs=39.8
Q ss_pred HHHhhccHHHHHhhhhhc-CC-CCCCChH--HHHHH-HHHHHHHHHHhhCHHHHHHHHHHHHhhCCcc
Q psy1676 66 NYLHYNLYDQADKLVKKS-AF-PENASNN--EWARF-HFYLGRIKAVRLEYSTAHKNLVQALRKAPQT 128 (343)
Q Consensus 66 ~yl~~~~~~~a~~li~k~-~~-p~~~~~~--~~~~Y-~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~ 128 (343)
..++.++|..|..-+... .+ ....... ....| ..-+|.++...|++.+|...+..|++-+.+.
T Consensus 7 ~~~~~~dy~~A~d~L~~~fD~~~~~~~~~~~~~~~~all~lA~~~~~~G~~~~A~~~l~eAi~~Are~ 74 (94)
T PF12862_consen 7 NALRSGDYSEALDALHRYFDYAKQSNNSSSNSGLAYALLNLAELHRRFGHYEEALQALEEAIRLAREN 74 (94)
T ss_pred HHHHcCCHHHHHHHHHHHHHHHhhcccchhhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH
Confidence 456788888887666543 11 1111111 11122 3457888889999999999999999965543
No 219
>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=34.57 E-value=99 Score=23.59 Aligned_cols=39 Identities=18% Similarity=0.280 Sum_probs=27.1
Q ss_pred HHHHHHHHHhhcccccChHHHHHHhCCCCHHHHHHHHHHhH
Q psy1676 211 VIKTAIRSIGASYSRITPTKIAEKLGLESPEDAEFIIAKAI 251 (343)
Q Consensus 211 v~r~~ir~i~~~ys~Isl~dIa~~l~l~s~~e~E~ila~lI 251 (343)
+++.++|-+.. =.-+|.+++|.++|++ .++++.+++.|=
T Consensus 25 L~r~LLr~LA~-G~PVt~~~LA~a~g~~-~e~v~~~L~~~p 63 (77)
T PF12324_consen 25 LLRPLLRLLAK-GQPVTVEQLAAALGWP-VEEVRAALAAMP 63 (77)
T ss_dssp HHHHHHHHHTT-TS-B-HHHHHHHHT---HHHHHHHHHH-T
T ss_pred HHHHHHHHHHc-CCCcCHHHHHHHHCCC-HHHHHHHHHhCC
Confidence 34556666655 6779999999999996 999999999873
No 220
>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=34.53 E-value=5.5e+02 Score=26.68 Aligned_cols=105 Identities=13% Similarity=0.179 Sum_probs=67.5
Q ss_pred HHHHHHHHHhhcccHHHHHHHHHHHHH-Hhh-----------hcC--Cc-------------chhH-HHHHHHHHHHHhh
Q psy1676 19 CYFYHSRVHELTNNLDKVRSFLNARLR-IAT-----------LRN--DF-------------EGQA-VLINCLLRNYLHY 70 (343)
Q Consensus 19 ~~~y~~~~~e~~~~~~~~~~~l~~~~r-~a~-----------~~~--~~-------------~~~~-~l~n~Llr~yl~~ 70 (343)
++||.|-.|...|..+++-..+-.++- |.+ +.| +- +++- ++-+...+.+++.
T Consensus 196 ~~~~lAqhyd~~g~~~~Al~~Id~aI~htPt~~ely~~KarilKh~G~~~~Aa~~~~~Ar~LD~~DRyiNsK~aKy~LRa 275 (517)
T PF12569_consen 196 TLYFLAQHYDYLGDYEKALEYIDKAIEHTPTLVELYMTKARILKHAGDLKEAAEAMDEARELDLADRYINSKCAKYLLRA 275 (517)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHC
Confidence 357888888888888777666654442 111 111 11 1111 6667788888999
Q ss_pred ccHHHHHhhhhhcCCCCCC--Ch---HHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHh
Q psy1676 71 NLYDQADKLVKKSAFPENA--SN---NEWARFHFYLGRIKAVRLEYSTAHKNLVQALR 123 (343)
Q Consensus 71 ~~~~~a~~li~k~~~p~~~--~~---~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~ 123 (343)
|..+.|..+++.-+-++.. .+ -|-+=|.-=.|.-|.-+++|..|...|.....
T Consensus 276 ~~~e~A~~~~~~Ftr~~~~~~~~L~~mQc~Wf~~e~a~a~~r~~~~~~ALk~~~~v~k 333 (517)
T PF12569_consen 276 GRIEEAEKTASLFTREDVDPLSNLNDMQCMWFETECAEAYLRQGDYGLALKRFHAVLK 333 (517)
T ss_pred CCHHHHHHHHHhhcCCCCCcccCHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence 9999998888754332211 11 25555566778888888999888888776665
No 221
>KOG2796|consensus
Probab=34.48 E-value=3.9e+02 Score=25.72 Aligned_cols=23 Identities=17% Similarity=0.290 Sum_probs=14.1
Q ss_pred HHHHHHhhCHHHHHHHHHHHHhh
Q psy1676 102 GRIKAVRLEYSTAHKNLVQALRK 124 (343)
Q Consensus 102 Gri~~~~~~y~~A~~~L~~A~~~ 124 (343)
.-++..+++|.+|+..+..+++.
T Consensus 259 a~i~lg~nn~a~a~r~~~~i~~~ 281 (366)
T KOG2796|consen 259 AFLHLGQNNFAEAHRFFTEILRM 281 (366)
T ss_pred hhheecccchHHHHHHHhhcccc
Confidence 33555666666666666666653
No 222
>KOG3364|consensus
Probab=34.21 E-value=94 Score=26.58 Aligned_cols=40 Identities=20% Similarity=0.219 Sum_probs=34.0
Q ss_pred CChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCcc
Q psy1676 89 ASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQT 128 (343)
Q Consensus 89 ~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~ 128 (343)
.+....-.|.||++.-+.-.++|+.|..+....++.-|.+
T Consensus 65 ~~~~~rRe~lyYLAvg~yRlkeY~~s~~yvd~ll~~e~~n 104 (149)
T KOG3364|consen 65 AHPERRRECLYYLAVGHYRLKEYSKSLRYVDALLETEPNN 104 (149)
T ss_pred cCcccchhhhhhhHHHHHHHhhHHHHHHHHHHHHhhCCCc
Confidence 3456778899999999999999999999999999965543
No 223
>KOG1861|consensus
Probab=33.92 E-value=5.5e+02 Score=26.51 Aligned_cols=136 Identities=21% Similarity=0.197 Sum_probs=79.2
Q ss_pred HHHHHHHHHHhhCHHHHHHHHHHHHhh-CCccchHHHHHHHHHHHHHHHHhcCCCCC-hhhhh--hHhHh--hhhhhhHH
Q psy1676 98 HFYLGRIKAVRLEYSTAHKNLVQALRK-APQTAAVGFRQTTQKLAVVVELLLGDIPD-RQIFR--QAVLR--RALSPYFQ 171 (343)
Q Consensus 98 ~YY~Gri~~~~~~y~~A~~~L~~A~~~-~~~~sa~~~~~~i~K~li~v~LL~G~iP~-~~~~~--~~~l~--~~l~~Y~~ 171 (343)
|---+||.+-.||..+--+|.++-... ++.. .++.....-|-|+--|++..-|. .+++. .+..+ .....=.+
T Consensus 351 YEtHARIALEkGD~~EfNQCQtQLk~LY~egi--pg~~~EF~AYriLY~i~tkN~~di~sll~~lt~E~ked~~V~hAL~ 428 (540)
T KOG1861|consen 351 YETHARIALEKGDLEEFNQCQTQLKALYSEGI--PGAYLEFTAYRILYYIFTKNYPDILSLLRDLTEEDKEDEAVAHALE 428 (540)
T ss_pred ehhhhHHHHhcCCHHHHHHHHHHHHHHHccCC--CCchhhHHHHHHHHHHHhcCchHHHHHHHhccHhhccCHHHHHHHH
Confidence 334578999999988877777776662 2221 12222233455555555555554 12221 11111 12233456
Q ss_pred HHHHHHhCCHHHHHHHHHhccccccccccH--HHHHHHHHHHHHHHHHHHhhccc-ccChHHHHHHhCCCCHHH
Q psy1676 172 LTQAVRMGELQKFNEVLTTYGNQFRTDYTF--KLILRLRHNVIKTAIRSIGASYS-RITPTKIAEKLGLESPED 242 (343)
Q Consensus 172 L~~Av~~Gdl~~f~~~l~~~~~~f~~d~~~--~Lv~~l~~~v~r~~ir~i~~~ys-~Isl~dIa~~l~l~s~~e 242 (343)
+-.|+..||...|-..-- .-.+. -|+..-...--+..+..|+++|. +|+++-|+.-+.+++.++
T Consensus 429 vR~A~~~GNY~kFFrLY~-------~AP~M~~yLmdlF~erER~~Al~ii~KsyrP~i~~~fi~~~laf~~~e~ 495 (540)
T KOG1861|consen 429 VRSAVTLGNYHKFFRLYL-------TAPNMSGYLMDLFLERERKKALTIICKSYRPTITVDFIASELAFDSMED 495 (540)
T ss_pred HHHHHHhccHHHHHHHHh-------hcccchhHHHHHHHHHHHHHHHHHHHHHcCCCccHHHHhhhhhhchHHH
Confidence 888999999888765532 22222 23333334445566788899997 999999999988764433
No 224
>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=32.88 E-value=1.3e+02 Score=20.03 Aligned_cols=29 Identities=28% Similarity=0.556 Sum_probs=23.9
Q ss_pred ccccChHHHHHHhCCCCHHHHHHHHHHhHH
Q psy1676 223 YSRITPTKIAEKLGLESPEDAEFIIAKAIR 252 (343)
Q Consensus 223 ys~Isl~dIa~~l~l~s~~e~E~ila~lI~ 252 (343)
+...|+++||..+|++ ...|-.+..+++.
T Consensus 18 ~~~~t~~eIa~~lg~s-~~~V~~~~~~al~ 46 (50)
T PF04545_consen 18 FEGLTLEEIAERLGIS-RSTVRRILKRALK 46 (50)
T ss_dssp TST-SHHHHHHHHTSC-HHHHHHHHHHHHH
T ss_pred cCCCCHHHHHHHHCCc-HHHHHHHHHHHHH
Confidence 6789999999999994 8888888877764
No 225
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=32.86 E-value=2.1e+02 Score=21.30 Aligned_cols=34 Identities=26% Similarity=0.397 Sum_probs=30.8
Q ss_pred cccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceE
Q psy1676 224 SRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEA 258 (343)
Q Consensus 224 s~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a 258 (343)
..+++++|++.++++ ...+-.++..|...|.|..
T Consensus 19 ~~~t~~~ia~~l~i~-~~tv~r~l~~L~~~g~l~~ 52 (91)
T smart00346 19 GGLTLAELAERLGLS-KSTAHRLLNTLQELGYVEQ 52 (91)
T ss_pred CCcCHHHHHHHhCCC-HHHHHHHHHHHHHCCCeee
Confidence 469999999999995 8999999999999999954
No 226
>PF04049 APC8: Anaphase promoting complex subunit 8 / Cdc23 ; InterPro: IPR007192 The anaphase-promoting complex is composed of eight protein subunits, including BimE (APC1), CDC27 (APC3), CDC16 (APC6), and CDC23 (APC8). This entry is for CDC23.; GO: 0030071 regulation of mitotic metaphase/anaphase transition, 0005680 anaphase-promoting complex
Probab=32.70 E-value=69 Score=27.14 Aligned_cols=45 Identities=22% Similarity=0.249 Sum_probs=35.0
Q ss_pred HHHHHHHhhccHHHHHhhhhhcCCCCCCChHHHHHHHHHHHHHHHHhhCHHH
Q psy1676 62 CLLRNYLHYNLYDQADKLVKKSAFPENASNNEWARFHFYLGRIKAVRLEYST 113 (343)
Q Consensus 62 ~Llr~yl~~~~~~~a~~li~k~~~p~~~~~~~~~~Y~YY~Gri~~~~~~y~~ 113 (343)
++.|.||-.+.|+.|.-++++.. +....|++|-.++.+.+++=.+
T Consensus 79 llAksyFD~kEy~RaA~~L~~~~-------s~~~~FL~lYs~YLa~EKr~~E 123 (142)
T PF04049_consen 79 LLAKSYFDCKEYDRAAHVLKDCK-------SPKALFLRLYSRYLAGEKRKEE 123 (142)
T ss_pred HHHHHHhchhHHHHHHHHHccCC-------CchHHHHHHHHHHHHHHHHHhh
Confidence 57899999999999999998653 4667788888888887765433
No 227
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=32.63 E-value=1.3e+02 Score=24.47 Aligned_cols=65 Identities=20% Similarity=0.186 Sum_probs=45.2
Q ss_pred cccccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEeeCCC---ceEEEccCccccccccchHHHHHHHHHHHHh
Q psy1676 222 SYSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLDREK---GYMQSKESADIYCTVEPQLAFHQRIAFCLDL 295 (343)
Q Consensus 222 ~ys~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~Id~~~---g~v~~~~~~~v~s~~ep~~~~~~rI~~cl~l 295 (343)
.-..++++++|..+.- |.-.|-.++-+|...|.|.=.=-.+. +.++|.. +|...+.+.+..+++=
T Consensus 16 ~~~~vtl~elA~~l~c-S~Rn~r~lLkkm~~~gWi~W~pg~GRG~~S~L~~l~--------~~~~~~~~~~~~~l~~ 83 (115)
T PF12793_consen 16 QPVEVTLDELAELLFC-SRRNARTLLKKMQEEGWITWQPGRGRGNRSQLTFLK--------SPEELLEQQAEELLEQ 83 (115)
T ss_pred CCcceeHHHHHHHhCC-CHHHHHHHHHHHHHCCCeeeeCCCCCCCCCeeEEee--------CHHHHHHHHHHHHHHc
Confidence 3467899999999999 59999999999999998842222222 3333332 4566666666666665
No 228
>PF12854 PPR_1: PPR repeat
Probab=32.63 E-value=70 Score=19.77 Aligned_cols=25 Identities=28% Similarity=0.331 Sum_probs=22.1
Q ss_pred HHHHHHHHHHHhhccHHHHHhhhhh
Q psy1676 58 VLINCLLRNYLHYNLYDQADKLVKK 82 (343)
Q Consensus 58 ~l~n~Llr~yl~~~~~~~a~~li~k 82 (343)
+..|.|+.-|.+.+..+.|..+++.
T Consensus 8 ~ty~~lI~~~Ck~G~~~~A~~l~~~ 32 (34)
T PF12854_consen 8 VTYNTLIDGYCKAGRVDEAFELFDE 32 (34)
T ss_pred hHHHHHHHHHHHCCCHHHHHHHHHh
Confidence 6678889999999999999999874
No 229
>PRK14720 transcript cleavage factor/unknown domain fusion protein; Provisional
Probab=32.32 E-value=5.2e+02 Score=28.92 Aligned_cols=107 Identities=12% Similarity=0.016 Sum_probs=64.5
Q ss_pred hHHHHHHHHHHHHHHHhhcccHHHHHHHHHHHHHHhhhcCCcchhH-HHHHHHHHHHHhhccHHHHHhhhhhc-CCCCCC
Q psy1676 12 SDLIAAKCYFYHSRVHELTNNLDKVRSFLNARLRIATLRNDFEGQA-VLINCLLRNYLHYNLYDQADKLVKKS-AFPENA 89 (343)
Q Consensus 12 ~d~~~a~~~~y~~~~~e~~~~~~~~~~~l~~~~r~a~~~~~~~~~~-~l~n~Llr~yl~~~~~~~a~~li~k~-~~p~~~ 89 (343)
+|+-..+++-.+...+-..+.++++...+- +.+.+.|.... ++...+ +|++.+.++.+..+ +-. .++..
T Consensus 26 ~~p~n~~a~~~Li~~~~~~~~~deai~i~~-----~~l~~~P~~i~~yy~~G~--l~~q~~~~~~~~lv-~~l~~~~~~- 96 (906)
T PRK14720 26 YSLSKFKELDDLIDAYKSENLTDEAKDICE-----EHLKEHKKSISALYISGI--LSLSRRPLNDSNLL-NLIDSFSQN- 96 (906)
T ss_pred CCcchHHHHHHHHHHHHhcCCHHHHHHHHH-----HHHHhCCcceehHHHHHH--HHHhhcchhhhhhh-hhhhhcccc-
Confidence 344455556666666666677777665553 33444565555 333333 88888888888777 322 23322
Q ss_pred ChHHHHHH--------------HHHHHHHHHHhhCHHHHHHHHHHHHhhCCc
Q psy1676 90 SNNEWARF--------------HFYLGRIKAVRLEYSTAHKNLVQALRKAPQ 127 (343)
Q Consensus 90 ~~~~~~~Y--------------~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~ 127 (343)
++-..+.| +|.+|.+|-..+++.+|...++.++..-|.
T Consensus 97 ~~~~~ve~~~~~i~~~~~~k~Al~~LA~~Ydk~g~~~ka~~~yer~L~~D~~ 148 (906)
T PRK14720 97 LKWAIVEHICDKILLYGENKLALRTLAEAYAKLNENKKLKGVWERLVKADRD 148 (906)
T ss_pred cchhHHHHHHHHHHhhhhhhHHHHHHHHHHHHcCChHHHHHHHHHHHhcCcc
Confidence 21133333 446677777778999999999888884444
No 230
>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif). This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.
Probab=32.16 E-value=48 Score=19.37 Aligned_cols=25 Identities=20% Similarity=0.179 Sum_probs=19.8
Q ss_pred HHHHHHHHHHhhccHHHHHhhhhhc
Q psy1676 59 LINCLLRNYLHYNLYDQADKLVKKS 83 (343)
Q Consensus 59 l~n~Llr~yl~~~~~~~a~~li~k~ 83 (343)
..|.++..|.+.+.++.|..+++..
T Consensus 2 ~~n~li~~~~~~~~~~~a~~~~~~M 26 (35)
T TIGR00756 2 TYNTLIDGLCKAGRVEEALELFKEM 26 (35)
T ss_pred cHHHHHHHHHHCCCHHHHHHHHHHH
Confidence 3577888888888888888888753
No 231
>COG4496 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.02 E-value=68 Score=25.19 Aligned_cols=38 Identities=26% Similarity=0.445 Sum_probs=30.0
Q ss_pred HHHHhHHcCCceEEeeCCCceEEEccCccccccccchHHHHHHHHHHHHhhHH
Q psy1676 246 IIAKAIRDGVIEATLDREKGYMQSKESADIYCTVEPQLAFHQRIAFCLDLHNQ 298 (343)
Q Consensus 246 ila~lI~~G~I~a~Id~~~g~v~~~~~~~v~s~~ep~~~~~~rI~~cl~l~~~ 298 (343)
-||+|+.+|.-...|..+.|. -.+--+|++.||+--|+
T Consensus 48 qVa~mL~eg~tY~~I~~eTGa---------------StaTIsRVkRcl~yGnd 85 (100)
T COG4496 48 QVAKMLKEGRTYRDIEDETGA---------------STATISRVKRCLNYGND 85 (100)
T ss_pred HHHHHHHcCCCcchhhhccCc---------------chhhHHHHHHHHHcCCc
Confidence 389999999999888877662 23456899999988776
No 232
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=31.71 E-value=1.1e+02 Score=26.23 Aligned_cols=41 Identities=22% Similarity=0.299 Sum_probs=33.0
Q ss_pred HHHHhhcccccChHHHHHHhCCCCHHHHHHHHHHhHHcCCce
Q psy1676 216 IRSIGASYSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIE 257 (343)
Q Consensus 216 ir~i~~~ys~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~ 257 (343)
|..+...-..+...+||..|++. +-.|-.++.+|...|+|.
T Consensus 15 Iy~l~~~~~~~~~~diA~~L~Vs-p~sVt~ml~rL~~~GlV~ 55 (154)
T COG1321 15 IYELLEEKGFARTKDIAERLKVS-PPSVTEMLKRLERLGLVE 55 (154)
T ss_pred HHHHHhccCcccHHHHHHHhCCC-cHHHHHHHHHHHHCCCeE
Confidence 33344455678899999999995 888999999999999883
No 233
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=31.70 E-value=1.3e+02 Score=25.09 Aligned_cols=36 Identities=19% Similarity=0.245 Sum_probs=31.0
Q ss_pred hcccccChHHHHHHhCCCCHHHHHHHHHHhHHcCCce
Q psy1676 221 ASYSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIE 257 (343)
Q Consensus 221 ~~ys~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~ 257 (343)
.....++.++||..++++ ...|-..|.+|...|+|.
T Consensus 18 ~~~~~~~~~ela~~l~vs-~~svs~~l~~L~~~Gli~ 53 (142)
T PRK03902 18 EEKGYARVSDIAEALSVH-PSSVTKMVQKLDKDEYLI 53 (142)
T ss_pred hcCCCcCHHHHHHHhCCC-hhHHHHHHHHHHHCCCEE
Confidence 344567889999999995 889999999999999985
No 234
>PF10557 Cullin_Nedd8: Cullin protein neddylation domain; InterPro: IPR019559 This is the neddylation site of cullin proteins, which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae (Baker's yeast), and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue []. ; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_B 1U6G_A 3O6B_J 3O2P_E 4A0K_A 2HYE_C ....
Probab=31.64 E-value=1.2e+02 Score=22.04 Aligned_cols=53 Identities=23% Similarity=0.184 Sum_probs=40.4
Q ss_pred HHHHHHHHHHHHHHHhhcccccChHHHHHH----hC---CCCHHHHHHHHHHhHHcCCce
Q psy1676 205 LRLRHNVIKTAIRSIGASYSRITPTKIAEK----LG---LESPEDAEFIIAKAIRDGVIE 257 (343)
Q Consensus 205 ~~l~~~v~r~~ir~i~~~ys~Isl~dIa~~----l~---l~s~~e~E~ila~lI~~G~I~ 257 (343)
++-|...+...|-++-+.-.+++.+++... +. ..+..++..-+-.||..|+|.
T Consensus 2 ~~~R~~~I~AaIVrimK~~k~~~~~~L~~~v~~~l~~~f~~~~~~ik~~Ie~LIekeyi~ 61 (68)
T PF10557_consen 2 EQDRKYQIDAAIVRIMKQEKKLSHDELINEVIEELKKRFPPSVSDIKKRIESLIEKEYIE 61 (68)
T ss_dssp HHHHHHHHHHHHHHHHHHSSEEEHHHHHHHHHHHTTTTS---HHHHHHHHHHHHHTTSEE
T ss_pred cchhhhhhhhheehhhhhcCceeHHHHHHHHHHHhcCCcCCCHHHHHHHHHHHHHhhhhh
Confidence 456777888888888888888888887554 32 236889999999999999984
No 235
>PF08631 SPO22: Meiosis protein SPO22/ZIP4 like; InterPro: IPR013940 SPO22 is a meiosis-specific protein with similarity to phospholipase A2, involved in completion of nuclear divisions during meiosis; induced early in meiosis []. It is also involved in sporulation [].
Probab=31.61 E-value=4.3e+02 Score=24.58 Aligned_cols=59 Identities=20% Similarity=0.161 Sum_probs=45.8
Q ss_pred HHhhccHHHHHhhhhhcCCCC-C---CChHHHHHHHHHHHHHHHHhh-CHHHHHHHHHHHHhhC
Q psy1676 67 YLHYNLYDQADKLVKKSAFPE-N---ASNNEWARFHFYLGRIKAVRL-EYSTAHKNLVQALRKA 125 (343)
Q Consensus 67 yl~~~~~~~a~~li~k~~~p~-~---~~~~~~~~Y~YY~Gri~~~~~-~y~~A~~~L~~A~~~~ 125 (343)
..+.|+++.|..++.|+.... . ......++=+|-.|.-....+ +|.+|..+|++|+.-+
T Consensus 3 A~~~~~~~~A~~~~~K~~~~~~~~~~~~~~~La~~~yn~G~~l~~~~~~~~~a~~wL~~a~~~l 66 (278)
T PF08631_consen 3 AWKQGDLDLAEHMYSKAKDLLNSLDPDMAEELARVCYNIGKSLLSKKDKYEEAVKWLQRAYDIL 66 (278)
T ss_pred chhhCCHHHHHHHHHHhhhHHhcCCcHHHHHHHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHH
Confidence 346789999999999873221 1 123466777899999999999 9999999999999953
No 236
>PF13512 TPR_18: Tetratricopeptide repeat
Probab=31.39 E-value=68 Score=27.38 Aligned_cols=62 Identities=21% Similarity=0.274 Sum_probs=38.0
Q ss_pred HHHHHHhhccHHHHHhhhhhc--CCCCCCChHHHHHHHHHHHHHHHHhhC---------------HHHHHHHHHHHHhhC
Q psy1676 63 LLRNYLHYNLYDQADKLVKKS--AFPENASNNEWARFHFYLGRIKAVRLE---------------YSTAHKNLVQALRKA 125 (343)
Q Consensus 63 Llr~yl~~~~~~~a~~li~k~--~~p~~~~~~~~~~Y~YY~Gri~~~~~~---------------y~~A~~~L~~A~~~~ 125 (343)
|.-.|++.++|..|..-...- ..|.+ ++.+.+ +|..|..+..+.+ ...|+..|...++.-
T Consensus 53 l~yayy~~~~y~~A~a~~~rFirLhP~h-p~vdYa--~Y~~gL~~~~~~~~~~~~~~~~drD~~~~~~A~~~f~~lv~~y 129 (142)
T PF13512_consen 53 LAYAYYKQGDYEEAIAAYDRFIRLHPTH-PNVDYA--YYMRGLSYYEQDEGSLQSFFRSDRDPTPARQAFRDFEQLVRRY 129 (142)
T ss_pred HHHHHHHccCHHHHHHHHHHHHHhCCCC-CCccHH--HHHHHHHHHHHhhhHHhhhcccccCcHHHHHHHHHHHHHHHHC
Confidence 578889999999888776642 23332 222332 4556777776655 666666666666654
Q ss_pred Cc
Q psy1676 126 PQ 127 (343)
Q Consensus 126 ~~ 127 (343)
|.
T Consensus 130 P~ 131 (142)
T PF13512_consen 130 PN 131 (142)
T ss_pred cC
Confidence 44
No 237
>PF07729 FCD: FCD domain; InterPro: IPR011711 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 []. 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. The winged-helix DNA-binding domain is well conserved in structure for the whole of the GntR family (IPR000524 from INTERPRO), and is similar in structure to other transcriptional regulator families. The C-terminal effector-binding and oligomerisation domains are more variable and are consequently used to define the subfamilies. Based on the sequence and structure of the C-terminal domains, the GtnR family can be divided into four major groups, as represented by FadR (IPR008920 from INTERPRO), HutC, MocR and YtrA, as well as some minor groups such as those represented by AraR and PlmA []. This entry represents the C-terminal ligand binding domain of many members of the GntR family. This domain probably binds to a range of effector molecules that regulate the transcription of genes through the action of the N-terminal DNA-binding domain. This domain is found in P45427 from SWISSPROT and P31460 from SWISSPROT that are regulators of sugar biosynthesis operons.; PDB: 3SXK_A 3SXY_A 3SXM_B 3SXZ_A 3FMS_A 2DI3_B 2HS5_A 3IHU_B 3C7J_A.
Probab=31.14 E-value=2.4e+02 Score=21.49 Aligned_cols=29 Identities=24% Similarity=0.351 Sum_probs=23.8
Q ss_pred hhhhhhhHHHHHHHHhCCHHHHHHHHHhc
Q psy1676 163 RRALSPYFQLTQAVRMGELQKFNEVLTTY 191 (343)
Q Consensus 163 ~~~l~~Y~~L~~Av~~Gdl~~f~~~l~~~ 191 (343)
...+..+..+++|+++||.....+++..|
T Consensus 94 ~~~~~~h~~i~~ai~~~d~~~a~~~~~~h 122 (125)
T PF07729_consen 94 ERSLEEHREIIDAIRAGDPEAAREALRQH 122 (125)
T ss_dssp HHHHHHHHHHHHHHHTT-HHHHHHHHHHH
T ss_pred hhhHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence 34566788999999999999999998876
No 238
>COG3071 HemY Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]
Probab=31.09 E-value=88 Score=31.19 Aligned_cols=71 Identities=18% Similarity=0.264 Sum_probs=49.9
Q ss_pred HHHHHHHHHHHhhccHHHHHhhhhhc---CC------------CCCC-Ch-----------HHHHHHHHHHHHHHHHhhC
Q psy1676 58 VLINCLLRNYLHYNLYDQADKLVKKS---AF------------PENA-SN-----------NEWARFHFYLGRIKAVRLE 110 (343)
Q Consensus 58 ~l~n~Llr~yl~~~~~~~a~~li~k~---~~------------p~~~-~~-----------~~~~~Y~YY~Gri~~~~~~ 110 (343)
-+...+.--+..+|.++.|..++..+ .+ |... +- .+.-.-++++|+.+..++.
T Consensus 264 ~l~~~~a~~li~l~~~~~A~~~i~~~Lk~~~D~~L~~~~~~l~~~d~~~l~k~~e~~l~~h~~~p~L~~tLG~L~~k~~~ 343 (400)
T COG3071 264 ELVVAYAERLIRLGDHDEAQEIIEDALKRQWDPRLCRLIPRLRPGDPEPLIKAAEKWLKQHPEDPLLLSTLGRLALKNKL 343 (400)
T ss_pred hHHHHHHHHHHHcCChHHHHHHHHHHHHhccChhHHHHHhhcCCCCchHHHHHHHHHHHhCCCChhHHHHHHHHHHHhhH
Confidence 34455566778999999999998843 11 1111 10 0111458899999999999
Q ss_pred HHHHHHHHHHHHhhCCcc
Q psy1676 111 YSTAHKNLVQALRKAPQT 128 (343)
Q Consensus 111 y~~A~~~L~~A~~~~~~~ 128 (343)
|.+|..+|.-|+..-|..
T Consensus 344 w~kA~~~leaAl~~~~s~ 361 (400)
T COG3071 344 WGKASEALEAALKLRPSA 361 (400)
T ss_pred HHHHHHHHHHHHhcCCCh
Confidence 999999999999865543
No 239
>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=30.76 E-value=68 Score=24.16 Aligned_cols=35 Identities=20% Similarity=0.245 Sum_probs=29.2
Q ss_pred hcccccChHHHHHHhCCCCHHHHHHHHHHhHHcCCc
Q psy1676 221 ASYSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVI 256 (343)
Q Consensus 221 ~~ys~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I 256 (343)
..+.-.|..+||+.+|++ +.-+...+.++...|.+
T Consensus 28 R~~eGlS~kEIAe~LGIS-~~TVk~~l~~~~~~~~~ 62 (73)
T TIGR03879 28 REEAGKTASEIAEELGRT-EQTVRNHLKGETKAGGL 62 (73)
T ss_pred HHHcCCCHHHHHHHHCcC-HHHHHHHHhcCcccchH
Confidence 344789999999999995 89999998888777765
No 240
>KOG2300|consensus
Probab=30.45 E-value=3.2e+02 Score=28.40 Aligned_cols=66 Identities=14% Similarity=0.204 Sum_probs=50.2
Q ss_pred HHHHHHHHHhhc-cHHHHHhhhhhc-CCCCCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCC
Q psy1676 60 INCLLRNYLHYN-LYDQADKLVKKS-AFPENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAP 126 (343)
Q Consensus 60 ~n~Llr~yl~~~-~~~~a~~li~k~-~~p~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~ 126 (343)
+.+|..+|++.+ .+..+++++++. +...+.+ -..+++.+.++.++.+++||..|.+.|.--...+.
T Consensus 91 ~SlLa~lh~~~~~s~~~~KalLrkaielsq~~p-~wsckllfQLaql~~idkD~~sA~elLavga~sAd 158 (629)
T KOG2300|consen 91 ASLLAHLHHQLAQSFPPAKALLRKAIELSQSVP-YWSCKLLFQLAQLHIIDKDFPSALELLAVGAESAD 158 (629)
T ss_pred HHHHHHHHHHhcCCCchHHHHHHHHHHHhcCCc-hhhHHHHHHHHHHHhhhccchhHHHHHhccccccc
Confidence 446677888888 999999999975 3322222 47788999999999999999999998665444443
No 241
>PF02064 MAS20: MAS20 protein import receptor; InterPro: IPR002056 Virtually all mitochondrial precursors are imported via the same mechanism []: precursors first bind to receptors on the mitochondrial surface, then insert into the translocation channel in the outer membrane. Many outer-membrane proteins participate in the early stages of import, four of which (MAS20, MAS22, MAS37 and MAS70) are components of the receptor. MAS20, which forms a subcomplex with MAS22, seems to interact with most or all mitochondrial precursors, suggesting that the protein binds directly to mitochondrial targeting sequences. The MAS37 and MAS70 components also form a subcomplex, the two subcomplexes possibly binding via their trans- membrane (TM) regions - the TM region of MAS70 promotes oligomerisation of attatched protein domains and shares sequence similarity with the TM region of MAS20 []. MAS20 is also known as TOM20.; GO: 0006605 protein targeting, 0006886 intracellular protein transport, 0005742 mitochondrial outer membrane translocase complex; PDB: 3AX3_A 3AWR_B 2V1S_A 3AX5_C 3AX2_C 1OM2_A 2V1T_B.
Probab=30.35 E-value=1.5e+02 Score=24.58 Aligned_cols=29 Identities=28% Similarity=0.413 Sum_probs=25.6
Q ss_pred HHHHHHHHhhCHHHHHHHHHHHHhhCCcc
Q psy1676 100 YLGRIKAVRLEYSTAHKNLVQALRKAPQT 128 (343)
Q Consensus 100 Y~Gri~~~~~~y~~A~~~L~~A~~~~~~~ 128 (343)
-+|.-.+.+|++.+|..||..|+.-||+.
T Consensus 68 ~lGE~L~~~G~~~~aa~hf~nAl~V~~qP 96 (121)
T PF02064_consen 68 QLGEQLLAQGDYEEAAEHFYNALKVCPQP 96 (121)
T ss_dssp HHHHHHHHTT-HHHHHHHHHHHHHTSSSH
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHHhCCCH
Confidence 67888899999999999999999988874
No 242
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=30.28 E-value=1.6e+02 Score=24.37 Aligned_cols=40 Identities=13% Similarity=0.194 Sum_probs=34.9
Q ss_pred ccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEeeCCCc
Q psy1676 225 RITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLDREKG 265 (343)
Q Consensus 225 ~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~Id~~~g 265 (343)
.++.++||..++++ ...+-.+|.+|..+|+|.-.-|+.++
T Consensus 46 ~~t~~eLa~~l~~~-~~tvt~~v~~Le~~GlV~r~~~~~Dr 85 (144)
T PRK03573 46 EQSQIQLAKAIGIE-QPSLVRTLDQLEEKGLISRQTCASDR 85 (144)
T ss_pred CCCHHHHHHHhCCC-hhhHHHHHHHHHHCCCEeeecCCCCc
Confidence 46789999999996 88899999999999999888777664
No 243
>KOG3252|consensus
Probab=30.21 E-value=2.3e+02 Score=25.46 Aligned_cols=89 Identities=20% Similarity=0.215 Sum_probs=64.1
Q ss_pred hhHHHHHHHHhCCHHHHHHHHHhccccccccccHHHHHHHHHHHHHHHHHHHhhcccccChHHHHHHhCCCCHHHHHHHH
Q psy1676 168 PYFQLTQAVRMGELQKFNEVLTTYGNQFRTDYTFKLILRLRHNVIKTAIRSIGASYSRITPTKIAEKLGLESPEDAEFII 247 (343)
Q Consensus 168 ~Y~~L~~Av~~Gdl~~f~~~l~~~~~~f~~d~~~~Lv~~l~~~v~r~~ir~i~~~ys~Isl~dIa~~l~l~s~~e~E~il 247 (343)
.-..|..-..+|+...|=+..+.+...|.. .-| -..+|.+-..+.++.+|-.|+=.-+|+.+|-.+..++|..+
T Consensus 100 ~ii~L~~~LEt~~Fq~FW~~~~~N~~mle~--itG----Fedsvr~yachvv~iTyQkI~k~lLaellG~~sDs~le~~~ 173 (217)
T KOG3252|consen 100 SIIDLGDYLETCRFQQFWQEADENRDMLEG--ITG----FEDSVRKYACHVVGITYQKIDKWLLAELLGGLSDSQLEVWM 173 (217)
T ss_pred HHHhHHHHHhhchHHHHhhhhccchHHhcC--CCc----HHHHHHHHHHHheechHhhchHHHHHHhhCcccHHHHHHHH
Confidence 344588888999999999888888766643 212 23455555667788999999999999999976788888887
Q ss_pred HHhHHcCCceEEeeCCCceEEE
Q psy1676 248 AKAIRDGVIEATLDREKGYMQS 269 (343)
Q Consensus 248 a~lI~~G~I~a~Id~~~g~v~~ 269 (343)
.+ .|-+..+.|.+..
T Consensus 174 ~~-------~GW~a~e~G~ifv 188 (217)
T KOG3252|consen 174 TK-------YGWIADESGQIFV 188 (217)
T ss_pred HH-------ccceecCCceEEE
Confidence 66 2444556664443
No 244
>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional
Probab=30.20 E-value=2.9e+02 Score=28.20 Aligned_cols=60 Identities=13% Similarity=-0.026 Sum_probs=42.4
Q ss_pred hHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCccchHHHHHHHHHHHHHHHHhcCCCCC
Q psy1676 91 NNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQTAAVGFRQTTQKLAVVVELLLGDIPD 153 (343)
Q Consensus 91 ~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~sa~~~~~~i~K~li~v~LL~G~iP~ 153 (343)
.......++-.|..+...++|.+|..+|..|+...|... . .+.....+-.+...+|++..
T Consensus 71 dP~~a~a~~NLG~AL~~lGryeEAIa~f~rALeL~Pd~a-e--A~~A~yNLAcaya~LGr~dE 130 (453)
T PLN03098 71 DVKTAEDAVNLGLSLFSKGRVKDALAQFETALELNPNPD-E--AQAAYYNKACCHAYREEGKK 130 (453)
T ss_pred CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCch-H--HHHHHHHHHHHHHHcCCHHH
Confidence 457778889999999999999999999999999766531 0 11122333344556777655
No 245
>KOG3677|consensus
Probab=29.87 E-value=6.1e+02 Score=25.84 Aligned_cols=217 Identities=16% Similarity=0.147 Sum_probs=107.2
Q ss_pred HHHHHHHHHHHhhccHHHH-HhhhhhcCCCCCCC--hHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCcc------
Q psy1676 58 VLINCLLRNYLHYNLYDQA-DKLVKKSAFPENAS--NNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQT------ 128 (343)
Q Consensus 58 ~l~n~Llr~yl~~~~~~~a-~~li~k~~~p~~~~--~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~------ 128 (343)
+-+-.|+|.-.-+|+ +|| ...++ ..-|+..+ ..-+++ ||.|--|+..++|.+|-+-|..++.....+
T Consensus 236 fsL~GLlR~H~lLgD-hQat~q~id-i~pk~iy~t~p~c~VT--Y~VGFayLmmrryadai~~F~niLlyIqrtks~~~~ 311 (525)
T KOG3677|consen 236 FSLLGLLRMHILLGD-HQATSQILD-IMPKEIYGTEPMCRVT--YQVGFAYLMMRRYADAIRVFLNILLYIQRTKSMFSR 311 (525)
T ss_pred HHHHHHHHHHHHhhh-hHhhhhhhh-cCchhhcCcccceeEe--eehhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Confidence 334457999999999 555 22222 11122112 124444 999999999999999999988887631110
Q ss_pred -------chHHHHHHHHHHHHHHHHhcCCCCC---hhhhhhHhHhhhhhhhHHHHHHHHhCCHHHHHHHHHhcccccccc
Q psy1676 129 -------AAVGFRQTTQKLAVVVELLLGDIPD---RQIFRQAVLRRALSPYFQLTQAVRMGELQKFNEVLTTYGNQFRTD 198 (343)
Q Consensus 129 -------sa~~~~~~i~K~li~v~LL~G~iP~---~~~~~~~~l~~~l~~Y~~L~~Av~~Gdl~~f~~~l~~~~~~f~~d 198 (343)
.... .+...-++-.|.. -.|. .++..+ +. .-|.+=---..+||+..|.+.+.--...|..-
T Consensus 312 ~~y~~d~inKq-~eqm~~llai~l~---~yPq~iDESi~s~--l~---Ek~~d~ml~mqng~~q~~ks~f~y~cpkflsp 382 (525)
T KOG3677|consen 312 TTYQYDMINKQ-NEQMHHLLAICLS---MYPQMIDESIHSQ--LA---EKYGDKMLPMQNGDPQVFKSLFSYLCPKFLSP 382 (525)
T ss_pred hhhhHhhhhhh-HHHHHHHHHHHHH---hCchhhhHHHHHH--HH---HHhcchhhhhhcCChHHHHHHHHHcCccccCC
Confidence 1111 1111112222222 2343 222221 00 01221111234599999999999887777653
Q ss_pred ------ccH------HHHHHHHHHHH-------HHHHHHHhhcccccChHHHHHHhCCCCHHHHHHHHHHh-----HHc-
Q psy1676 199 ------YTF------KLILRLRHNVI-------KTAIRSIGASYSRITPTKIAEKLGLESPEDAEFIIAKA-----IRD- 253 (343)
Q Consensus 199 ------~~~------~Lv~~l~~~v~-------r~~ir~i~~~ys~Isl~dIa~~l~l~s~~e~E~ila~l-----I~~- 253 (343)
|.+ .+..++....- ---+|.--+-|+++|..-+|.-+.+++ ++=...+..+ +-.
T Consensus 383 ~~~~~dgv~~~y~kePl~~qlq~fld~v~qq~dl~~~rsylklyTt~P~kkla~F~D~~d-~~~dk~li~Ll~~khkm~n 461 (525)
T KOG3677|consen 383 VVPNYDGVLPNYHKEPLLQQLQVFLDEVSQQADLPTIRSYLKLYTTLPVKKLASFLDLTD-QERDKFLIQLLVFKHKMKN 461 (525)
T ss_pred CCcccccccccccccHHHHHHHHHhHHHhhhccchHHHHHHHHHHhccHHHhhhccCCch-hhhhhhHHHHHHHHHHHHH
Confidence 222 23333221111 011222224568899888888777752 2211222222 222
Q ss_pred -CCceEEeeCCCceEEEccCccccccccchHHHHHHH
Q psy1676 254 -GVIEATLDREKGYMQSKESADIYCTVEPQLAFHQRI 289 (343)
Q Consensus 254 -G~I~a~Id~~~g~v~~~~~~~v~s~~ep~~~~~~rI 289 (343)
+.=.|.++ .+|--......|+|...++....+...
T Consensus 462 lv~~sg~s~-~d~~f~~~s~idfyid~dmi~iaDtkv 497 (525)
T KOG3677|consen 462 LVWTSGPSD-LDDAFFSRSEIDFYIDKDMIHIADTKV 497 (525)
T ss_pred HHHhcCCcc-ccccccCcceeeEEechhHHHHHhHHH
Confidence 22222222 334444444566777766665555443
No 246
>PF05843 Suf: Suppressor of forked protein (Suf); InterPro: IPR008847 This domain consists of several eukaryotic suppressor of forked (Suf) like proteins. The Drosophila melanogaster suppressor of forked [Su(f)] protein shares homology with the Saccharomyces cerevisiae RNA14 protein and the 77 kDa subunit of Homo sapiens cleavage stimulation factor, which are proteins involved in mRNA 3' end formation. This suggests a role for Su(f) in mRNA 3' end formation in Drosophila. The su(f) gene produces three transcripts; two of them are polyadenylated at the end of the transcription unit, and one is a truncated transcript, polyadenylated in intron 4. It is thought that su(f) plays a role in the regulation of poly(A) site utilisation and the GU-rich sequence is important for this regulation to occur [].; GO: 0006397 mRNA processing, 0005634 nucleus; PDB: 2L9B_B 2OND_B 2OOE_A 4E85_B 4EBA_C 4E6H_A 2UY1_B.
Probab=29.81 E-value=4.7e+02 Score=24.43 Aligned_cols=136 Identities=14% Similarity=0.225 Sum_probs=69.1
Q ss_pred HHHHHHHHHhhcccHHHHHHHHHHHHHHhhhcCCcchhHHHHHHHHHH-HHhhccHHHHHhhhhhc--CCCCCCChHHHH
Q psy1676 19 CYFYHSRVHELTNNLDKVRSFLNARLRIATLRNDFEGQAVLINCLLRN-YLHYNLYDQADKLVKKS--AFPENASNNEWA 95 (343)
Q Consensus 19 ~~~y~~~~~e~~~~~~~~~~~l~~~~r~a~~~~~~~~~~~l~n~Llr~-yl~~~~~~~a~~li~k~--~~p~~~~~~~~~ 95 (343)
+|==|.+.....+.++.+|..+-.+. .++.....+.-....+ |-..++...|.++++.. .||. +..-+.
T Consensus 3 v~i~~m~~~~r~~g~~~aR~vF~~a~------~~~~~~~~vy~~~A~~E~~~~~d~~~A~~Ife~glk~f~~--~~~~~~ 74 (280)
T PF05843_consen 3 VWIQYMRFMRRTEGIEAARKVFKRAR------KDKRCTYHVYVAYALMEYYCNKDPKRARKIFERGLKKFPS--DPDFWL 74 (280)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHH------CCCCS-THHHHHHHHHHHHTCS-HHHHHHHHHHHHHHHTT---HHHHH
T ss_pred HHHHHHHHHHHhCChHHHHHHHHHHH------cCCCCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHCCC--CHHHHH
Confidence 34445555556666777776554332 1222222222222333 32357777788888754 3553 223444
Q ss_pred HHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCccchHHHHHHHHHHHHHHHHhcCCCCChhhhhhHhHhhhhhhhHHHHHH
Q psy1676 96 RFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQTAAVGFRQTTQKLAVVVELLLGDIPDRQIFRQAVLRRALSPYFQLTQA 175 (343)
Q Consensus 96 ~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~sa~~~~~~i~K~li~v~LL~G~iP~~~~~~~~~l~~~l~~Y~~L~~A 175 (343)
.|.-|+ +..++...|...|+.|+...+.. ..-+..+. .|.++-
T Consensus 75 ~Y~~~l----~~~~d~~~aR~lfer~i~~l~~~--~~~~~iw~-----------------------------~~i~fE-- 117 (280)
T PF05843_consen 75 EYLDFL----IKLNDINNARALFERAISSLPKE--KQSKKIWK-----------------------------KFIEFE-- 117 (280)
T ss_dssp HHHHHH----HHTT-HHHHHHHHHHHCCTSSCH--HHCHHHHH-----------------------------HHHHHH--
T ss_pred HHHHHH----HHhCcHHHHHHHHHHHHHhcCch--hHHHHHHH-----------------------------HHHHHH--
Confidence 444443 34568888888888888865543 11011222 222222
Q ss_pred HHhCCHHHHHHHHHhccccccccc
Q psy1676 176 VRMGELQKFNEVLTTYGNQFRTDY 199 (343)
Q Consensus 176 v~~Gdl~~f~~~l~~~~~~f~~d~ 199 (343)
.+-||+....++-++....|-.+.
T Consensus 118 ~~~Gdl~~v~~v~~R~~~~~~~~~ 141 (280)
T PF05843_consen 118 SKYGDLESVRKVEKRAEELFPEDN 141 (280)
T ss_dssp HHHS-HHHHHHHHHHHHHHTTTS-
T ss_pred HHcCCHHHHHHHHHHHHHHhhhhh
Confidence 234788888877777777666644
No 247
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=29.77 E-value=2.4e+02 Score=21.17 Aligned_cols=40 Identities=23% Similarity=0.258 Sum_probs=32.4
Q ss_pred ccccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEeeCC
Q psy1676 223 YSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLDRE 263 (343)
Q Consensus 223 ys~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~Id~~ 263 (343)
-..+++++|.+.++++ ...+-..+..|...|+|.-.-...
T Consensus 12 ~~~~~f~~L~~~l~lt-~g~Ls~hL~~Le~~GyV~~~k~~~ 51 (80)
T PF13601_consen 12 NEEATFSELKEELGLT-DGNLSKHLKKLEEAGYVEVEKEFE 51 (80)
T ss_dssp HSEEEHHHHHHHTT---HHHHHHHHHHHHHTTSEEEEEE-S
T ss_pred cCCCCHHHHHHHhCcC-HHHHHHHHHHHHHCCCEEEEEecc
Confidence 3678999999999995 899999999999999997665544
No 248
>PF13041 PPR_2: PPR repeat family
Probab=29.64 E-value=74 Score=21.08 Aligned_cols=26 Identities=31% Similarity=0.423 Sum_probs=22.1
Q ss_pred HHHHHHHHHHHhhccHHHHHhhhhhc
Q psy1676 58 VLINCLLRNYLHYNLYDQADKLVKKS 83 (343)
Q Consensus 58 ~l~n~Llr~yl~~~~~~~a~~li~k~ 83 (343)
+..|.++..|.+.++++.|..+++..
T Consensus 4 ~~yn~li~~~~~~~~~~~a~~l~~~M 29 (50)
T PF13041_consen 4 VTYNTLISGYCKAGKFEEALKLFKEM 29 (50)
T ss_pred HHHHHHHHHHHHCcCHHHHHHHHHHH
Confidence 56788899999999999999998854
No 249
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=29.45 E-value=62 Score=25.38 Aligned_cols=24 Identities=33% Similarity=0.529 Sum_probs=20.9
Q ss_pred cccChHHHHHHhCCCCHHHHHHHHH
Q psy1676 224 SRITPTKIAEKLGLESPEDAEFIIA 248 (343)
Q Consensus 224 s~Isl~dIa~~l~l~s~~e~E~ila 248 (343)
+.+|.++||..|+++ ++++|.++.
T Consensus 22 ~~ls~~~ia~dL~~s-~~~le~vL~ 45 (89)
T PF10078_consen 22 SGLSLEQIAADLGTS-PEHLEQVLN 45 (89)
T ss_pred cCCCHHHHHHHhCCC-HHHHHHHHc
Confidence 678999999999994 999998874
No 250
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=29.20 E-value=1.6e+02 Score=26.15 Aligned_cols=46 Identities=15% Similarity=0.105 Sum_probs=38.4
Q ss_pred HHHhhcccccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEeeCC
Q psy1676 217 RSIGASYSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLDRE 263 (343)
Q Consensus 217 r~i~~~ys~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~Id~~ 263 (343)
+.+...+.-.+..+||+.+++ |+.-|+..+..+...|.+...+.+.
T Consensus 169 ~~~~~g~~g~s~~eIa~~l~i-S~~Tv~~~~~~~~~~~~~~~~~~~~ 214 (225)
T PRK10046 169 KLFKEPGVQHTAETVAQALTI-SRTTARRYLEYCASRHLIIAEIVHG 214 (225)
T ss_pred HHHHcCCCCcCHHHHHHHhCc-cHHHHHHHHHHHHhCCeEEEEeecC
Confidence 344444555789999999999 5999999999999999999888774
No 251
>KOG1125|consensus
Probab=28.99 E-value=86 Score=32.72 Aligned_cols=87 Identities=22% Similarity=0.211 Sum_probs=53.1
Q ss_pred HHHHHHHHHHHHHHhhhcCCcchhHHHHHHHHHHHHhhccHHHHHhhhhhc--CCCCCC---------------C-----
Q psy1676 33 LDKVRSFLNARLRIATLRNDFEGQAVLINCLLRNYLHYNLYDQADKLVKKS--AFPENA---------------S----- 90 (343)
Q Consensus 33 ~~~~~~~l~~~~r~a~~~~~~~~~~~l~n~Llr~yl~~~~~~~a~~li~k~--~~p~~~---------------~----- 90 (343)
+..|...++.+-|--...-|++-|..|- -+|-..+.|+.|-..+... .-|... +
T Consensus 410 l~~i~~~fLeaa~~~~~~~DpdvQ~~LG----VLy~ls~efdraiDcf~~AL~v~Pnd~~lWNRLGAtLAN~~~s~EAIs 485 (579)
T KOG1125|consen 410 LAHIQELFLEAARQLPTKIDPDVQSGLG----VLYNLSGEFDRAVDCFEAALQVKPNDYLLWNRLGATLANGNRSEEAIS 485 (579)
T ss_pred HHHHHHHHHHHHHhCCCCCChhHHhhhH----HHHhcchHHHHHHHHHHHHHhcCCchHHHHHHhhHHhcCCcccHHHHH
Confidence 3444444444333222223555555333 3456678899998888754 223210 0
Q ss_pred --------hHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHh
Q psy1676 91 --------NNEWARFHFYLGRIKAVRLEYSTAHKNLVQALR 123 (343)
Q Consensus 91 --------~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~ 123 (343)
....+|-+|-+|.-++-.|.|.+|..||..|+.
T Consensus 486 AY~rALqLqP~yVR~RyNlgIS~mNlG~ykEA~~hlL~AL~ 526 (579)
T KOG1125|consen 486 AYNRALQLQPGYVRVRYNLGISCMNLGAYKEAVKHLLEALS 526 (579)
T ss_pred HHHHHHhcCCCeeeeehhhhhhhhhhhhHHHHHHHHHHHHH
Confidence 025666788888888888888888888888887
No 252
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=28.90 E-value=3.2e+02 Score=24.16 Aligned_cols=33 Identities=21% Similarity=0.298 Sum_probs=26.3
Q ss_pred cccChHHHHHHhCCCCHHHHHHHHHHhHHcCCce
Q psy1676 224 SRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIE 257 (343)
Q Consensus 224 s~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~ 257 (343)
-.+++++|+.++|++ -..+=..|-+|..-|.+.
T Consensus 40 ~Pmtl~Ei~E~lg~S-ks~vS~~lkkL~~~~lV~ 72 (177)
T COG1510 40 KPLTLDEIAEALGMS-KSNVSMGLKKLQDWNLVK 72 (177)
T ss_pred CCccHHHHHHHHCCC-cchHHHHHHHHHhcchHH
Confidence 468899999999995 667777777887777774
No 253
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=28.83 E-value=2.6e+02 Score=24.91 Aligned_cols=60 Identities=8% Similarity=0.128 Sum_probs=44.2
Q ss_pred HHHHHHHHHHHHh----hcccccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEeeCCCceEEEc
Q psy1676 208 RHNVIKTAIRSIG----ASYSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLDREKGYMQSK 270 (343)
Q Consensus 208 ~~~v~r~~ir~i~----~~ys~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~Id~~~g~v~~~ 270 (343)
...++...-..|. .+-.+|+-.++|+.+|++ -.-|---+..|..+|+|. +.+..|+.+..
T Consensus 9 ~~~vy~~i~~~I~~g~l~pG~~L~e~eLae~lgVS-RtpVREAL~~L~~eGlv~--~~~~~G~~V~~ 72 (224)
T PRK11534 9 ALDGYRWLKNDIIRGNFQPDEKLRMSLLTSRYALG-VGPLREALSQLVAERLVT--VVNQKGYRVAS 72 (224)
T ss_pred hHHHHHHHHHHHHhCCCCCCCcCCHHHHHHHHCCC-hHHHHHHHHHHHHCCCEE--EeCCCceEeCC
Confidence 3344444444443 234799999999999994 778888999999999995 56677877654
No 254
>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=28.33 E-value=1.8e+02 Score=25.56 Aligned_cols=36 Identities=33% Similarity=0.360 Sum_probs=31.6
Q ss_pred ccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEe
Q psy1676 225 RITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATL 260 (343)
Q Consensus 225 ~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~I 260 (343)
..+.++||+.++++|..-+-..+..|..+|+|...=
T Consensus 25 ~~~~~ela~~~~~~s~~tv~~~l~~L~~~g~i~~~~ 60 (199)
T TIGR00498 25 PPSIREIARAVGLRSPSAAEEHLKALERKGYIERDP 60 (199)
T ss_pred CCcHHHHHHHhCCCChHHHHHHHHHHHHCCCEecCC
Confidence 377899999999976899999999999999997643
No 255
>PF07389 DUF1500: Protein of unknown function (DUF1500); InterPro: IPR009974 This family consists of several Orthopoxvirus specific proteins, which include Vaccinia virus, B6 protein, they are around 100 residues in length. The function of this family is unknown.
Probab=28.19 E-value=1.4e+02 Score=23.43 Aligned_cols=46 Identities=13% Similarity=0.142 Sum_probs=36.6
Q ss_pred HHHHHHHHHHHhhcccccChHHHHHHhCCCCHHHHHHHHHHhHHcCCc
Q psy1676 209 HNVIKTAIRSIGASYSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVI 256 (343)
Q Consensus 209 ~~v~r~~ir~i~~~ys~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I 256 (343)
...+-++|-+++.--..|++.+|-+- ++.++.+|.+|..-+.+|..
T Consensus 32 S~~IlhNIyrlftr~~vi~Fd~iVr~--mpNes~v~qWV~dtln~i~~ 77 (100)
T PF07389_consen 32 SNAILHNIYRLFTRCAVIPFDDIVRT--MPNESRVKQWVIDTLNDIMM 77 (100)
T ss_pred hHHHHHHHHHHHHhhccccHHHHHHh--CCCHHHHHHHHHHHHHhHhh
Confidence 45566777777666678899999887 56788999999999988876
No 256
>COG5010 TadD Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking and secretion]
Probab=28.14 E-value=4.2e+02 Score=24.97 Aligned_cols=66 Identities=20% Similarity=0.151 Sum_probs=43.9
Q ss_pred HHHHHHHHHHHhhccHHHHHhhhhhcCCCCCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCc
Q psy1676 58 VLINCLLRNYLHYNLYDQADKLVKKSAFPENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQ 127 (343)
Q Consensus 58 ~l~n~Llr~yl~~~~~~~a~~li~k~~~p~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~ 127 (343)
.+++.+-++-+..++|..|...+.+..-+.. + --+.+=-.|-++.-.+++..|..-|.+|+.-.+.
T Consensus 101 ~ll~~~gk~~~~~g~~~~A~~~~rkA~~l~p-~---d~~~~~~lgaaldq~Gr~~~Ar~ay~qAl~L~~~ 166 (257)
T COG5010 101 ELLAAQGKNQIRNGNFGEAVSVLRKAARLAP-T---DWEAWNLLGAALDQLGRFDEARRAYRQALELAPN 166 (257)
T ss_pred HHHHHHHHHHHHhcchHHHHHHHHHHhccCC-C---ChhhhhHHHHHHHHccChhHHHHHHHHHHHhccC
Confidence 5666678888999999999999887744321 0 0112224566777777777777777777774443
No 257
>PF10516 SHNi-TPR: SHNi-TPR; InterPro: IPR019544 The tetratrico peptide repeat region (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. This entry represents SHNi-TPR (Sim3-Hif1-NASP interrupted TPR), a sequence that is an interrupted form of TPR repeat [].
Probab=27.97 E-value=96 Score=20.14 Aligned_cols=25 Identities=24% Similarity=0.284 Sum_probs=22.2
Q ss_pred HHHHHHHHHhhCHHHHHHHHHHHHh
Q psy1676 99 FYLGRIKAVRLEYSTAHKNLVQALR 123 (343)
Q Consensus 99 YY~Gri~~~~~~y~~A~~~L~~A~~ 123 (343)
--+|-+.+-..+|..|..-|..|+.
T Consensus 5 ~~Lgeisle~e~f~qA~~D~~~aL~ 29 (38)
T PF10516_consen 5 DLLGEISLENENFEQAIEDYEKALE 29 (38)
T ss_pred HHHHHHHHHhccHHHHHHHHHHHHH
Confidence 3579999999999999999999886
No 258
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=27.73 E-value=2.6e+02 Score=26.89 Aligned_cols=60 Identities=22% Similarity=0.355 Sum_probs=47.6
Q ss_pred hhcc-cccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEeeCCCceEEEccCccccccccchHHHHHHHHHHHHh
Q psy1676 220 GASY-SRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLDREKGYMQSKESADIYCTVEPQLAFHQRIAFCLDL 295 (343)
Q Consensus 220 ~~~y-s~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~Id~~~g~v~~~~~~~v~s~~ep~~~~~~rI~~cl~l 295 (343)
+..| .-.+=++||++||+ |---|-.+++.+...|.++=+|+++. .....+.+++...+.|
T Consensus 23 ~lYY~~g~tQ~eIA~~lgi-SR~~VsRlL~~Ar~~GiV~I~I~~~~---------------~~~~~Le~~L~~~fgL 83 (318)
T PRK15418 23 WFYYHDGLTQSEIGERLGL-TRLKVSRLLEKGRQSGIIRVQINSRF---------------EGCLELENALRQHFSL 83 (318)
T ss_pred HHHHhcCCCHHHHHHHhCC-CHHHHHHHHHHHHHcCcEEEEEeCCC---------------ccHHHHHHHHHHHhCC
Confidence 3445 67889999999999 48899999999999999988887652 1235577888877777
No 259
>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=27.40 E-value=4.7e+02 Score=26.16 Aligned_cols=62 Identities=31% Similarity=0.360 Sum_probs=42.1
Q ss_pred HHHHHHHHHHHhhccHHHHHhhhhhcC--CCCCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCCcc
Q psy1676 58 VLINCLLRNYLHYNLYDQADKLVKKSA--FPENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAPQT 128 (343)
Q Consensus 58 ~l~n~Llr~yl~~~~~~~a~~li~k~~--~p~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~ 128 (343)
+|+..|++.+-..+.++.|.+++++.. .|+ -.+..+++++..++-.+|.+.+.+++...|..
T Consensus 170 yLv~~Ll~~l~~t~~~~~ai~lle~L~~~~pe---------v~~~LA~v~l~~~~E~~AI~ll~~aL~~~p~d 233 (395)
T PF09295_consen 170 YLVDTLLKYLSLTQRYDEAIELLEKLRERDPE---------VAVLLARVYLLMNEEVEAIRLLNEALKENPQD 233 (395)
T ss_pred HHHHHHHHHHhhcccHHHHHHHHHHHHhcCCc---------HHHHHHHHHHhcCcHHHHHHHHHHHHHhCCCC
Confidence 666677777777888888888887642 232 12346677777777777777777777765543
No 260
>PLN03218 maturation of RBCL 1; Provisional
Probab=27.01 E-value=9.8e+02 Score=27.29 Aligned_cols=65 Identities=11% Similarity=0.039 Sum_probs=36.9
Q ss_pred HHHHHHHHHHHhhccHHHHHhhhhhcCCCCCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHh
Q psy1676 58 VLINCLLRNYLHYNLYDQADKLVKKSAFPENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALR 123 (343)
Q Consensus 58 ~l~n~Llr~yl~~~~~~~a~~li~k~~~p~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~ 123 (343)
+..|.++..|.+.++++.|..++....-....-..+.++|.-.. ..|...+++.+|.+.|.....
T Consensus 543 vTYnsLI~a~~k~G~~deA~~lf~eM~~~~~gi~PD~vTynaLI-~ay~k~G~ldeA~elf~~M~e 607 (1060)
T PLN03218 543 VVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITVGALM-KACANAGQVDRAKEVYQMIHE 607 (1060)
T ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHHHhcCCCCCcHHHHHHHH-HHHHHCCCHHHHHHHHHHHHH
Confidence 45666777777777777777776643110000011233443322 245567788888888877776
No 261
>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=26.59 E-value=1.2e+02 Score=24.12 Aligned_cols=40 Identities=15% Similarity=0.248 Sum_probs=34.5
Q ss_pred cccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEeeCCC
Q psy1676 224 SRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLDREK 264 (343)
Q Consensus 224 s~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~Id~~~ 264 (343)
..++.++||..++++ ...+=.+|.+|...|+|.=.-|..+
T Consensus 42 ~~~t~~eL~~~l~~~-~stvs~~i~~Le~kg~I~r~~~~~D 81 (109)
T TIGR01889 42 GKLTLKEIIKEILIK-QSALVKIIKKLSKKGYLSKERSEDD 81 (109)
T ss_pred CcCcHHHHHHHHCCC-HHHHHHHHHHHHHCCCEeccCCccc
Confidence 569999999999996 8899999999999999975555544
No 262
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.
Probab=26.40 E-value=1.4e+02 Score=27.38 Aligned_cols=35 Identities=26% Similarity=0.338 Sum_probs=31.5
Q ss_pred cccccChHHHHHHhCCCCHHHHHHHHHHhHHcCCce
Q psy1676 222 SYSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIE 257 (343)
Q Consensus 222 ~ys~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~ 257 (343)
.-..+++++||+.+|++ ..-+-.++..|...|++.
T Consensus 21 ~~~~~~l~eia~~lglp-ksT~~RlL~tL~~~G~l~ 55 (248)
T TIGR02431 21 ERPRLTLTDVAEATGLT-RAAARRFLLTLVELGYVT 55 (248)
T ss_pred CCCCCCHHHHHHHHCcC-HHHHHHHHHHHHHCCCEE
Confidence 34569999999999996 889999999999999996
No 263
>COG2976 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.26 E-value=5e+02 Score=23.61 Aligned_cols=63 Identities=21% Similarity=0.037 Sum_probs=51.5
Q ss_pred HHHHH-HHHHHHhhccHHHHHhhhhhcCCCCCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhC
Q psy1676 58 VLINC-LLRNYLHYNLYDQADKLVKKSAFPENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKA 125 (343)
Q Consensus 58 ~l~n~-Llr~yl~~~~~~~a~~li~k~~~p~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~ 125 (343)
.++++ |.|+-+..+.++.|.++++.+.-+ +-..++.-..|-+++..++=.+|...+..|+..-
T Consensus 126 ~l~~lRLArvq~q~~k~D~AL~~L~t~~~~-----~w~~~~~elrGDill~kg~k~~Ar~ay~kAl~~~ 189 (207)
T COG2976 126 ALAALRLARVQLQQKKADAALKTLDTIKEE-----SWAAIVAELRGDILLAKGDKQEARAAYEKALESD 189 (207)
T ss_pred HHHHHHHHHHHHHhhhHHHHHHHHhccccc-----cHHHHHHHHhhhHHHHcCchHHHHHHHHHHHHcc
Confidence 55554 889999999999999999865433 3455566689999999999999999999999953
No 264
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=26.04 E-value=4.9e+02 Score=23.50 Aligned_cols=49 Identities=18% Similarity=0.257 Sum_probs=40.0
Q ss_pred ccccc-ChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEeeCCCceEEEccCc
Q psy1676 222 SYSRI-TPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLDREKGYMQSKESA 273 (343)
Q Consensus 222 ~ys~I-sl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~Id~~~g~v~~~~~~ 273 (343)
+-.+| +-.++|+.+|+ |-.-|---+..|-.+|+|. +-+..|+.+..-..
T Consensus 27 pG~~LPsE~eLa~~~gV-SRtpVREAL~~L~~eGlV~--~~~~~G~~V~~~~~ 76 (251)
T PRK09990 27 VGQALPSERRLCEKLGF-SRSALREGLTVLRGRGIIE--TAQGRGSFVARLNR 76 (251)
T ss_pred CCCcCcCHHHHHHHHCC-CHHHHHHHHHHHHHCCCEE--EeCCCeeEEecCCc
Confidence 45899 68899999999 4788888899999999995 56677888876433
No 265
>PF12728 HTH_17: Helix-turn-helix domain
Probab=25.72 E-value=1e+02 Score=20.55 Aligned_cols=29 Identities=31% Similarity=0.418 Sum_probs=23.1
Q ss_pred cChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEE
Q psy1676 226 ITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEAT 259 (343)
Q Consensus 226 Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~ 259 (343)
++.+++|+.||++ .. -+-+++..|.|.+.
T Consensus 2 lt~~e~a~~l~is-~~----tv~~~~~~g~i~~~ 30 (51)
T PF12728_consen 2 LTVKEAAELLGIS-RS----TVYRWIRQGKIPPF 30 (51)
T ss_pred CCHHHHHHHHCcC-HH----HHHHHHHcCCCCeE
Confidence 5789999999995 43 46678899999776
No 266
>PF13431 TPR_17: Tetratricopeptide repeat
Probab=25.57 E-value=86 Score=19.39 Aligned_cols=21 Identities=19% Similarity=0.063 Sum_probs=17.2
Q ss_pred HHHHHHHHHHHHHhhCHHHHH
Q psy1676 95 ARFHFYLGRIKAVRLEYSTAH 115 (343)
Q Consensus 95 ~~Y~YY~Gri~~~~~~y~~A~ 115 (343)
...++.+|.++...|++.+|.
T Consensus 13 ~~a~~nla~~~~~~g~~~~A~ 33 (34)
T PF13431_consen 13 AEAYNNLANLYLNQGDYEEAI 33 (34)
T ss_pred HHHHHHHHHHHHHCcCHHhhc
Confidence 345778899999999999885
No 267
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=25.56 E-value=1.6e+02 Score=18.70 Aligned_cols=29 Identities=28% Similarity=0.542 Sum_probs=21.8
Q ss_pred cChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEE
Q psy1676 226 ITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEAT 259 (343)
Q Consensus 226 Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~ 259 (343)
+++.++|+.+|++ . ..|.+++.+|.+.+.
T Consensus 1 ~s~~e~a~~lgvs-~----~tl~~~~~~g~~~~~ 29 (49)
T cd04762 1 LTTKEAAELLGVS-P----STLRRWVKEGKLKAI 29 (49)
T ss_pred CCHHHHHHHHCcC-H----HHHHHHHHcCCCCce
Confidence 4678999999995 3 356677888988654
No 268
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=25.34 E-value=1.5e+02 Score=27.74 Aligned_cols=36 Identities=11% Similarity=0.003 Sum_probs=31.3
Q ss_pred hcccccChHHHHHHhCCCCHHHHHHHHHHhHHcCCce
Q psy1676 221 ASYSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIE 257 (343)
Q Consensus 221 ~~ys~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~ 257 (343)
..-..+++++||+.+|++ ..-+=.++..|+..|++.
T Consensus 36 ~~~~~~tl~eIa~~lglp-kStv~RlL~tL~~~G~l~ 71 (271)
T PRK10163 36 KSGGSSSVSDISLNLDLP-LSTTFRLLKVLQAADFVY 71 (271)
T ss_pred hCCCCcCHHHHHHHHCcC-HHHHHHHHHHHHHCCCEE
Confidence 334569999999999996 889999999999999993
No 269
>KOG1550|consensus
Probab=25.17 E-value=3.2e+02 Score=28.42 Aligned_cols=52 Identities=21% Similarity=0.171 Sum_probs=35.4
Q ss_pred cHHHHHhhhhhcCCCCCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCC
Q psy1676 72 LYDQADKLVKKSAFPENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAP 126 (343)
Q Consensus 72 ~~~~a~~li~k~~~p~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~ 126 (343)
++..|.++..+..--....-.-.+-..|..|. ..+|+..|+++|..|-...+
T Consensus 308 d~~~A~~~~~~aA~~g~~~a~~~lg~~~~~g~---~~~d~~~A~~yy~~Aa~~G~ 359 (552)
T KOG1550|consen 308 DYEKALKLYTKAAELGNPDAQYLLGVLYETGT---KERDYRRAFEYYSLAAKAGH 359 (552)
T ss_pred cHHHHHHHHHHHHhcCCchHHHHHHHHHHcCC---ccccHHHHHHHHHHHHHcCC
Confidence 77888888886532222223455556666666 45789999999999988654
No 270
>KOG1156|consensus
Probab=25.17 E-value=3.9e+02 Score=28.58 Aligned_cols=60 Identities=15% Similarity=0.066 Sum_probs=34.0
Q ss_pred HHHHHHHHHhhccHHHHHhhhhhcCCCCCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHh
Q psy1676 60 INCLLRNYLHYNLYDQADKLVKKSAFPENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALR 123 (343)
Q Consensus 60 ~n~Llr~yl~~~~~~~a~~li~k~~~p~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~ 123 (343)
.-.+.+-|-+.++++.|...|+.+. ...+-++..+--.|||+.+.|++.+|..++..|-.
T Consensus 374 ~y~laqh~D~~g~~~~A~~yId~AI----dHTPTliEly~~KaRI~kH~G~l~eAa~~l~ea~e 433 (700)
T KOG1156|consen 374 LYFLAQHYDKLGDYEVALEYIDLAI----DHTPTLIELYLVKARIFKHAGLLDEAAAWLDEAQE 433 (700)
T ss_pred HHHHHHHHHHcccHHHHHHHHHHHh----ccCchHHHHHHHHHHHHHhcCChHHHHHHHHHHHh
Confidence 3345566666666666666665331 11224455555666666666666666666666555
No 271
>KOG4626|consensus
Probab=25.15 E-value=4.1e+02 Score=28.64 Aligned_cols=60 Identities=30% Similarity=0.267 Sum_probs=46.4
Q ss_pred HHHHHHHHhhccHHHHHhhhhhc--CCCCCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhhCC
Q psy1676 61 NCLLRNYLHYNLYDQADKLVKKS--AFPENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALRKAP 126 (343)
Q Consensus 61 n~Llr~yl~~~~~~~a~~li~k~--~~p~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~ 126 (343)
|-|-.+|-+.+.++.|..+..++ .+|+.+ .=+=-+|.+|--++++.+|..|+..|++-.|
T Consensus 358 ~NLgni~~E~~~~e~A~~ly~~al~v~p~~a------aa~nNLa~i~kqqgnl~~Ai~~YkealrI~P 419 (966)
T KOG4626|consen 358 NNLGNIYREQGKIEEATRLYLKALEVFPEFA------AAHNNLASIYKQQGNLDDAIMCYKEALRIKP 419 (966)
T ss_pred HHHHHHHHHhccchHHHHHHHHHHhhChhhh------hhhhhHHHHHHhcccHHHHHHHHHHHHhcCc
Confidence 34477899999999999999876 456532 1122467888999999999999999999444
No 272
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=24.99 E-value=1.8e+02 Score=22.22 Aligned_cols=49 Identities=20% Similarity=0.274 Sum_probs=37.8
Q ss_pred hcccccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEeeCCCceEEEc
Q psy1676 221 ASYSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLDREKGYMQSK 270 (343)
Q Consensus 221 ~~ys~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~Id~~~g~v~~~ 270 (343)
..-.-|.=..|++.++++ +.-+-..++.|-.-|+|.+.=....|++-..
T Consensus 19 ~~~~PVgSk~ia~~l~~s-~aTIRN~M~~Le~lGlve~~p~~s~GriPT~ 67 (78)
T PF03444_consen 19 ETGEPVGSKTIAEELGRS-PATIRNEMADLEELGLVESQPHPSGGRIPTD 67 (78)
T ss_pred hcCCCcCHHHHHHHHCCC-hHHHHHHHHHHHHCCCccCCCCCCCCCCcCH
Confidence 344678888999999994 8999999999999999965444455666443
No 273
>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=24.76 E-value=98 Score=24.37 Aligned_cols=35 Identities=31% Similarity=0.574 Sum_probs=26.7
Q ss_pred cccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEE
Q psy1676 224 SRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEAT 259 (343)
Q Consensus 224 s~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~ 259 (343)
..++=++||..++++ ..++-.++.+|-.+|+|...
T Consensus 26 ~~l~de~la~~~~l~-~~~vRkiL~~L~~~~lv~~~ 60 (105)
T PF02002_consen 26 GELTDEDLAKKLGLK-PKEVRKILYKLYEDGLVSYR 60 (105)
T ss_dssp --B-HHHHHHTT-S--HHHHHHHHHHHHHHSS-EEE
T ss_pred CCcCHHHHHHHhCCC-HHHHHHHHHHHHHCCCeEEE
Confidence 457789999999996 99999999999999999554
No 274
>smart00668 CTLH C-terminal to LisH motif. Alpha-helical motif of unknown function.
Probab=24.74 E-value=1.8e+02 Score=19.70 Aligned_cols=31 Identities=10% Similarity=0.126 Sum_probs=26.2
Q ss_pred HHHHHHHHhCCHHHHHHHHHhcccccccccc
Q psy1676 170 FQLTQAVRMGELQKFNEVLTTYGNQFRTDYT 200 (343)
Q Consensus 170 ~~L~~Av~~Gdl~~f~~~l~~~~~~f~~d~~ 200 (343)
..+.+++..||+...-++++.+.....+++.
T Consensus 6 ~~i~~~i~~g~~~~a~~~~~~~~~~l~~~~~ 36 (58)
T smart00668 6 KRIRELILKGDWDEALEWLSSLKPPLLERNS 36 (58)
T ss_pred HHHHHHHHcCCHHHHHHHHHHcCHHHhccCC
Confidence 4588899999999999999999887766654
No 275
>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter.
Probab=24.67 E-value=3.4e+02 Score=23.81 Aligned_cols=47 Identities=13% Similarity=0.272 Sum_probs=39.3
Q ss_pred cccccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEeeCCCceEEEcc
Q psy1676 222 SYSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLDREKGYMQSKE 271 (343)
Q Consensus 222 ~ys~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~Id~~~g~v~~~~ 271 (343)
+-.+||-.++|+.+|++ -.-|-.-+..|-.+|+|. +.+..|+++..-
T Consensus 31 pG~~L~e~~La~~lgVS-RtpVReAL~~L~~eGlv~--~~~~~G~~V~~~ 77 (212)
T TIGR03338 31 PGAKLNESDIAARLGVS-RGPVREAFRALEEAGLVR--NEKNRGVFVREI 77 (212)
T ss_pred CCCEecHHHHHHHhCCC-hHHHHHHHHHHHHCCCEE--EecCCCeEEecC
Confidence 44899999999999994 788888999999999995 566778887763
No 276
>TIGR01716 RGG_Cterm transcriptional activator, Rgg/GadR/MutR family, C-terminal domain. This model describes the whole, except for a 60 residue N-terminal helix-turn-helix DNA-binding domain (PFAM pfam01381) of the family of proteins related to the transcriptional regulator Rgg, also called RopB. Rgg is required for secretion of several proteins, including a cysteine proteinase associated with virulence. GadR is a positive regulator of a glutamate-dependent acid resistance mechanism. MutR is a transcriptional activator for mutacin biosynthesis genes in Streptococcus mutans. This family appears restricted to the low-GC Gram-positive bacteria, including at least eight members in Lactococcus lactis.
Probab=24.62 E-value=3.5e+02 Score=23.82 Aligned_cols=64 Identities=22% Similarity=0.228 Sum_probs=42.5
Q ss_pred HHHHHHHHHHHhhccHHHHHhhhhhc---CCCCCCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHh
Q psy1676 58 VLINCLLRNYLHYNLYDQADKLVKKS---AFPENASNNEWARFHFYLGRIKAVRLEYSTAHKNLVQALR 123 (343)
Q Consensus 58 ~l~n~Llr~yl~~~~~~~a~~li~k~---~~p~~~~~~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~ 123 (343)
.+.|. +-.|++.+.+..|..+++.. ..|+ ...-..+.+.||.|.+...+|+-..+.....+++.
T Consensus 130 il~N~-~~~~i~~~~~~~a~~~l~~l~~l~~~~-~~~~~ki~~~f~~~l~~y~~g~~~~~~~~i~~~i~ 196 (220)
T TIGR01716 130 LLLNI-AVLLIEKNEFSYAQYFLEKLEKILDPE-DDLYERILFNFLKGIILYKEGQKESGEEKIEQAIE 196 (220)
T ss_pred HHHHH-HHHHHHhhHHHHHHHHHHHHHHHhchh-hhHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHH
Confidence 55665 45667788999999998865 2332 12337888999999988887775554444444443
No 277
>PF06969 HemN_C: HemN C-terminal domain; InterPro: IPR010723 Proteins containing this domain are all oxygen-independent coproporphyrinogen-III oxidases (HemN). This enzyme catalyses the oxygen-independent conversion of coproporphyrinogen-III to protoporphyrinogen-IX [], one of the last steps in haem biosynthesis. The function of this domain is unclear, but comparison to other proteins containing a radical SAM domain suggest it may be a substrate binding domain.; GO: 0004109 coproporphyrinogen oxidase activity, 0006779 porphyrin-containing compound biosynthetic process, 0055114 oxidation-reduction process, 0005737 cytoplasm; PDB: 1OLT_A.
Probab=24.44 E-value=1.8e+02 Score=20.54 Aligned_cols=45 Identities=18% Similarity=0.369 Sum_probs=30.3
Q ss_pred ccccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEeeCCCceEEEcc
Q psy1676 223 YSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLDREKGYMQSKE 271 (343)
Q Consensus 223 ys~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~Id~~~g~v~~~~ 271 (343)
..-|+++++..+.|.+=.+.....+..++.+|.+. ..++.+...+
T Consensus 18 ~~Gi~~~~~~~~~g~~~~~~~~~~l~~l~~~Gll~----~~~~~l~lT~ 62 (66)
T PF06969_consen 18 NEGIDLSEFEQRFGIDFAEEFQKELEELQEDGLLE----IDGGRLRLTE 62 (66)
T ss_dssp HSEEEHHHHHHHTT--THHH-HHHHHHHHHTTSEE----E-SSEEEE-T
T ss_pred HCCcCHHHHHHHHCcCHHHHHHHHHHHHHHCCCEE----EeCCEEEECc
Confidence 46789999999999863455588999999999982 2345555443
No 278
>PRK11569 transcriptional repressor IclR; Provisional
Probab=24.36 E-value=3e+02 Score=25.66 Aligned_cols=37 Identities=16% Similarity=0.337 Sum_probs=31.9
Q ss_pred hhcccccChHHHHHHhCCCCHHHHHHHHHHhHHcCCce
Q psy1676 220 GASYSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIE 257 (343)
Q Consensus 220 ~~~ys~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~ 257 (343)
...-..+++++|++.+|++ ..-+=.++..|+..|++.
T Consensus 38 ~~~~~~~~lseia~~lglp-ksTv~RlL~tL~~~G~l~ 74 (274)
T PRK11569 38 AESNGSVALTELAQQAGLP-NSTTHRLLTTMQQQGFVR 74 (274)
T ss_pred HhCCCCcCHHHHHHHHCcC-HHHHHHHHHHHHHCCCEE
Confidence 3344568999999999996 889999999999999994
No 279
>KOG1126|consensus
Probab=24.27 E-value=96 Score=32.83 Aligned_cols=62 Identities=15% Similarity=0.112 Sum_probs=44.4
Q ss_pred HHhhccHHHHHhhhhhc-CCCC-C-----------CC-----------------hHHHHHHHHHHHHHHHHhhCHHHHHH
Q psy1676 67 YLHYNLYDQADKLVKKS-AFPE-N-----------AS-----------------NNEWARFHFYLGRIKAVRLEYSTAHK 116 (343)
Q Consensus 67 yl~~~~~~~a~~li~k~-~~p~-~-----------~~-----------------~~~~~~Y~YY~Gri~~~~~~y~~A~~ 116 (343)
|-..+++++|-..++.+ ++.+ + .. .....+=.|=+|++|+.+++|+.|..
T Consensus 431 fSLQkdh~~Aik~f~RAiQldp~faYayTLlGhE~~~~ee~d~a~~~fr~Al~~~~rhYnAwYGlG~vy~Kqek~e~Ae~ 510 (638)
T KOG1126|consen 431 FSLQKDHDTAIKCFKRAIQLDPRFAYAYTLLGHESIATEEFDKAMKSFRKALGVDPRHYNAWYGLGTVYLKQEKLEFAEF 510 (638)
T ss_pred hhhhhHHHHHHHHHHHhhccCCccchhhhhcCChhhhhHHHHhHHHHHHhhhcCCchhhHHHHhhhhheeccchhhHHHH
Confidence 44678899999988864 3221 1 00 12344446778999999999999999
Q ss_pred HHHHHHhhCCcc
Q psy1676 117 NLVQALRKAPQT 128 (343)
Q Consensus 117 ~L~~A~~~~~~~ 128 (343)
+|+.|+.--|.+
T Consensus 511 ~fqkA~~INP~n 522 (638)
T KOG1126|consen 511 HFQKAVEINPSN 522 (638)
T ss_pred HHHhhhcCCccc
Confidence 999999955654
No 280
>PRK00215 LexA repressor; Validated
Probab=24.15 E-value=3.9e+02 Score=23.50 Aligned_cols=40 Identities=28% Similarity=0.339 Sum_probs=33.0
Q ss_pred cccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEeeCC
Q psy1676 224 SRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLDRE 263 (343)
Q Consensus 224 s~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~Id~~ 263 (343)
..+++.+||+.+++.+..-+-.++.+|...|+|...-+..
T Consensus 22 ~~~s~~ela~~~~~~~~~tv~~~l~~L~~~g~i~~~~~~~ 61 (205)
T PRK00215 22 YPPSRREIADALGLRSPSAVHEHLKALERKGFIRRDPGRS 61 (205)
T ss_pred CCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEeCCCCc
Confidence 3578999999999944788999999999999997654443
No 281
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=23.80 E-value=5e+02 Score=23.87 Aligned_cols=103 Identities=18% Similarity=0.271 Sum_probs=61.9
Q ss_pred hhhHhHhhhhhhhHHHHHHHHh---CCHHHHHHHHHhccccccccccHHHHHHHHHHHHHHHHHHHhhcccccChHHHHH
Q psy1676 157 FRQAVLRRALSPYFQLTQAVRM---GELQKFNEVLTTYGNQFRTDYTFKLILRLRHNVIKTAIRSIGASYSRITPTKIAE 233 (343)
Q Consensus 157 ~~~~~l~~~l~~Y~~L~~Av~~---Gdl~~f~~~l~~~~~~f~~d~~~~Lv~~l~~~v~r~~ir~i~~~ys~Isl~dIa~ 233 (343)
|....+...|..|..--.++++ =+-..+++.+..+...-..+. |-+-+.....++....+...-...|-.++|+
T Consensus 105 f~~eRl~~aL~~y~~~r~~l~~~~~~sQ~~lD~l~~~~~k~~~~~~---LPkGi~~~Tl~~i~~~~~~~~~~~Taeela~ 181 (224)
T COG4565 105 FTFERLQQALTRYRQKRHALESHQQLSQKELDQLFNIQSKEQPPDD---LPKGLDELTLQKVREALKEPDQELTAEELAQ 181 (224)
T ss_pred eeHHHHHHHHHHHHHHHHHHhhhcccCHHHHHHHHhccccccCccc---CCCCcCHHHHHHHHHHHhCcCCccCHHHHHH
Confidence 3333444455555544444443 345666666665433222221 2122223333333333333346778899999
Q ss_pred HhCCCCHHHHHHHHHHhHHcCCceEEeeCC
Q psy1676 234 KLGLESPEDAEFIIAKAIRDGVIEATLDRE 263 (343)
Q Consensus 234 ~l~l~s~~e~E~ila~lI~~G~I~a~Id~~ 263 (343)
++|+ |---+...+.-|++.|.+++.|.+.
T Consensus 182 ~~gi-SRvTaRRYLeyl~~~~~l~a~i~yG 210 (224)
T COG4565 182 ALGI-SRVTARRYLEYLVSNGILEAEIHYG 210 (224)
T ss_pred HhCc-cHHHHHHHHHHHHhcCeeeEEeecc
Confidence 9999 4888999999999999999999876
No 282
>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=23.75 E-value=7e+02 Score=24.46 Aligned_cols=26 Identities=27% Similarity=0.317 Sum_probs=13.7
Q ss_pred HHHHHHhhCHHHHHHHHHHHHhhCCc
Q psy1676 102 GRIKAVRLEYSTAHKNLVQALRKAPQ 127 (343)
Q Consensus 102 Gri~~~~~~y~~A~~~L~~A~~~~~~ 127 (343)
+++++.+++|..|...++......|.
T Consensus 160 a~l~l~~~~~~~Al~~l~~l~~~~P~ 185 (409)
T TIGR00540 160 TRILLAQNELHAARHGVDKLLEMAPR 185 (409)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHhCCC
Confidence 55555555555555555555554443
No 283
>PF04190 DUF410: Protein of unknown function (DUF410) ; InterPro: IPR007317 This is a family of conserved eukaryotic proteins with undetermined function.; PDB: 3LKU_E 2WPV_G.
Probab=23.56 E-value=6e+02 Score=23.59 Aligned_cols=38 Identities=16% Similarity=0.341 Sum_probs=26.4
Q ss_pred HHHHHHhCCHHHHHHHHHhccccccccccH-HHHHHHHH
Q psy1676 172 LTQAVRMGELQKFNEVLTTYGNQFRTDYTF-KLILRLRH 209 (343)
Q Consensus 172 L~~Av~~Gdl~~f~~~l~~~~~~f~~d~~~-~Lv~~l~~ 209 (343)
|+.++.+++...|....++|+..+.+|..| ..++++-+
T Consensus 198 Ll~t~e~~~~~~F~~L~~~Y~~~L~rd~~~~~~L~~IG~ 236 (260)
T PF04190_consen 198 LLLTCERDNLPLFKKLCEKYKPSLKRDPSFKEYLDKIGQ 236 (260)
T ss_dssp HHHHHHHT-HHHHHHHHHHTHH---HHHHTHHHHHHHHH
T ss_pred HHHHHhcCcHHHHHHHHHHhCccccccHHHHHHHHHHHH
Confidence 677899999999999999999998888654 44554444
No 284
>KOG4056|consensus
Probab=23.44 E-value=1.4e+02 Score=25.33 Aligned_cols=46 Identities=20% Similarity=0.290 Sum_probs=35.8
Q ss_pred HHHHHHHHhhCHHHHHHHHHHHHhhCCccchHHHHHHHHHHHHHHHHhcCCCCChhhhh
Q psy1676 100 YLGRIKAVRLEYSTAHKNLVQALRKAPQTAAVGFRQTTQKLAVVVELLLGDIPDRQIFR 158 (343)
Q Consensus 100 Y~Gri~~~~~~y~~A~~~L~~A~~~~~~~sa~~~~~~i~K~li~v~LL~G~iP~~~~~~ 158 (343)
-+|.-++.+++++++..||..|+.-|++. .+ +.+++.+.+|. ++|.
T Consensus 86 ~lGE~L~~qg~~e~ga~h~~nAi~vcgqp--aq----------LL~vlq~tlp~-~if~ 131 (143)
T KOG4056|consen 86 QLGEELLAQGNEEEGAEHLANAIVVCGQP--AQ----------LLQVLQQTLPE-AIFA 131 (143)
T ss_pred HhHHHHHHccCHHHHHHHHHHHHhhcCCH--HH----------HHHHHHhhCCH-HHHH
Confidence 57889999999999999999999999875 12 12567778887 4443
No 285
>PF12645 HTH_16: Helix-turn-helix domain; InterPro: IPR024760 This domain appears to be a helix-turn-helix domain, suggesting a transcriptional regulatory protein. Some proteins with this domain are annotated as conjugative transposon proteins.
Probab=22.89 E-value=1.5e+02 Score=21.61 Aligned_cols=49 Identities=16% Similarity=0.282 Sum_probs=32.1
Q ss_pred HHHHHHHhCCHHHHHHHHHhcccccc---------ccccH-HHH-HHHHHHHHHHHHHHH
Q psy1676 171 QLTQAVRMGELQKFNEVLTTYGNQFR---------TDYTF-KLI-LRLRHNVIKTAIRSI 219 (343)
Q Consensus 171 ~L~~Av~~Gdl~~f~~~l~~~~~~f~---------~d~~~-~Lv-~~l~~~v~r~~ir~i 219 (343)
+++.+-..||..+.+++++.|+.... +.|+. +.+ +.+++.+-..+|..|
T Consensus 2 ~vI~~A~~GD~~A~~~IL~~y~~yI~kls~r~~~d~~g~~~~~vDedl~q~l~~kLi~~I 61 (65)
T PF12645_consen 2 EVIKAAKQGDPEAMEEILKHYEPYISKLSTRTLYDEYGNVYGYVDEDLKQRLEIKLIEAI 61 (65)
T ss_pred HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHhhcccccCCcCceeCHHHHHHHHHHHHHHH
Confidence 45667789999999999999987555 44443 333 455555555555444
No 286
>PRK10870 transcriptional repressor MprA; Provisional
Probab=22.83 E-value=1.5e+02 Score=25.86 Aligned_cols=41 Identities=22% Similarity=0.283 Sum_probs=35.3
Q ss_pred cccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEeeCCCc
Q psy1676 224 SRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLDREKG 265 (343)
Q Consensus 224 s~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~Id~~~g 265 (343)
..++.++||..++++ ..-+-.+|.+|...|+|.=.-+..++
T Consensus 70 ~~it~~eLa~~l~l~-~~tvsr~v~rLe~kGlV~R~~~~~Dr 110 (176)
T PRK10870 70 HSIQPSELSCALGSS-RTNATRIADELEKRGWIERRESDNDR 110 (176)
T ss_pred CCcCHHHHHHHHCCC-HHHHHHHHHHHHHCCCEEecCCCCCC
Confidence 458889999999996 88999999999999999877776654
No 287
>COG1849 Uncharacterized protein conserved in archaea [Function unknown]
Probab=22.70 E-value=1.8e+02 Score=22.82 Aligned_cols=32 Identities=22% Similarity=0.069 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHh
Q psy1676 92 NEWARFHFYLGRIKAVRLEYSTAHKNLVQALR 123 (343)
Q Consensus 92 ~~~~~Y~YY~Gri~~~~~~y~~A~~~L~~A~~ 123 (343)
-+.++=++.-|+++...|||..|+.++..|.-
T Consensus 38 ~~ma~~Y~~Dakyf~ekGD~vtAfa~~sYa~g 69 (90)
T COG1849 38 VDMAESYFEDAKYFLEKGDYVTAFAALSYAHG 69 (90)
T ss_pred HHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHH
Confidence 36777788999999999999999999887553
No 288
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=22.67 E-value=4.4e+02 Score=25.43 Aligned_cols=22 Identities=27% Similarity=0.306 Sum_probs=18.2
Q ss_pred cChHHHHHHhCCCCHHHHHHHHH
Q psy1676 226 ITPTKIAEKLGLESPEDAEFIIA 248 (343)
Q Consensus 226 Isl~dIa~~l~l~s~~e~E~ila 248 (343)
-+..+||..++++ ++++..+++
T Consensus 190 ~t~~eiA~~l~~~-~~~v~~~l~ 211 (325)
T PRK05657 190 PSAEEIAELLDKP-VDDVSRMLA 211 (325)
T ss_pred CCHHHHHHHhCcC-HHHHHHHHH
Confidence 3678999999995 888888775
No 289
>PRK03837 transcriptional regulator NanR; Provisional
Probab=22.51 E-value=4.3e+02 Score=23.65 Aligned_cols=60 Identities=10% Similarity=0.168 Sum_probs=44.2
Q ss_pred HHHHHHHHHHHhh----ccccc-ChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEeeCCCceEEEcc
Q psy1676 209 HNVIKTAIRSIGA----SYSRI-TPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLDREKGYMQSKE 271 (343)
Q Consensus 209 ~~v~r~~ir~i~~----~ys~I-sl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~Id~~~g~v~~~~ 271 (343)
..+++.....|.. +-.+| +-.++|+.+|+ |-.-|-.-+..|-.+|+|. +.+..|+.+..-
T Consensus 16 ~~v~~~l~~~I~~g~l~pG~~Lp~E~~Lae~~gV-SRt~VREAL~~L~~eGlv~--~~~~~G~~V~~~ 80 (241)
T PRK03837 16 EEVEERLEQMIRSGEFGPGDQLPSERELMAFFGV-GRPAVREALQALKRKGLVQ--ISHGERARVSRP 80 (241)
T ss_pred HHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHhCC-CHHHHHHHHHHHHHCCCEE--EecCCceeEecC
Confidence 3444444444433 33789 79999999999 4888888999999999995 467778877653
No 290
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=22.31 E-value=1.3e+02 Score=23.73 Aligned_cols=28 Identities=25% Similarity=0.347 Sum_probs=24.7
Q ss_pred HHHHHHhCCCCHHHHHHHHHHhHHcCCce
Q psy1676 229 TKIAEKLGLESPEDAEFIIAKAIRDGVIE 257 (343)
Q Consensus 229 ~dIa~~l~l~s~~e~E~ila~lI~~G~I~ 257 (343)
.-||..++++ .++|+..+-+|...|+|.
T Consensus 25 k~ia~~l~~~-~~~v~~~l~~Le~~GLle 52 (92)
T PF10007_consen 25 KSIARRLKIP-LEEVREALEKLEEMGLLE 52 (92)
T ss_pred HHHHHHHCCC-HHHHHHHHHHHHHCCCeE
Confidence 3478889996 999999999999999994
No 291
>PRK15481 transcriptional regulatory protein PtsJ; Provisional
Probab=22.25 E-value=7.6e+02 Score=24.30 Aligned_cols=45 Identities=11% Similarity=0.257 Sum_probs=36.8
Q ss_pred ccccc-ChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEEeeCCCceEEE
Q psy1676 222 SYSRI-TPTKIAEKLGLESPEDAEFIIAKAIRDGVIEATLDREKGYMQS 269 (343)
Q Consensus 222 ~ys~I-sl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~Id~~~g~v~~ 269 (343)
.-.++ |..++|+.+++ |..-|...+..|..+|.|.+ .+..|+.+.
T Consensus 25 ~g~~lps~r~la~~~~v-sr~tv~~a~~~L~~~g~i~~--~~~~G~~v~ 70 (431)
T PRK15481 25 PGDSLPPVRELASELGV-NRNTVAAAYKRLVTAGLAQS--QGRNGTVIR 70 (431)
T ss_pred CCCcCcCHHHHHHHHCC-CHHHHHHHHHHHHHCCCEEE--eCCCceEEc
Confidence 34788 68899999999 48999999999999999964 445677664
No 292
>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=22.22 E-value=5.5e+02 Score=22.65 Aligned_cols=36 Identities=22% Similarity=0.350 Sum_probs=32.3
Q ss_pred ccccChHHHHHHhCCCCHHHHHHHHHHhHHcCCceEE
Q psy1676 223 YSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIEAT 259 (343)
Q Consensus 223 ys~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~a~ 259 (343)
...++..+||..++++ ..-|-..+..|..+|+|.-.
T Consensus 13 ~~~~t~~eLA~~lgis-~~tV~~~L~~Le~~GlV~r~ 48 (203)
T TIGR02702 13 QGQATAAALAEALAIS-PQAVRRHLKDLETEGLIEYE 48 (203)
T ss_pred cCCCCHHHHHHHHCcC-HHHHHHHHHHHHHCCCeEEe
Confidence 3569999999999995 99999999999999999755
No 293
>KOG2316|consensus
Probab=21.35 E-value=74 Score=29.38 Aligned_cols=42 Identities=26% Similarity=0.458 Sum_probs=32.4
Q ss_pred hhcccccChHHHHHHhCCCC-----HHHHHHHHHHhHHcCCceEEeeC
Q psy1676 220 GASYSRITPTKIAEKLGLES-----PEDAEFIIAKAIRDGVIEATLDR 262 (343)
Q Consensus 220 ~~~ys~Isl~dIa~~l~l~s-----~~e~E~ila~lI~~G~I~a~Id~ 262 (343)
-..|.|+....||++|+|.+ ..+-|.++..||..| ++|.|-.
T Consensus 117 lS~YQr~RVEnVC~RL~L~~Ls~LW~rdQ~~LL~eMi~~g-~~AiiiK 163 (277)
T KOG2316|consen 117 LSDYQRTRVENVCSRLGLVSLSYLWQRDQEELLQEMILSG-LDAIIIK 163 (277)
T ss_pred HhHHHHHHHHHHHhhhCceeehHHHhccHHHHHHHHHHcC-CCeEEEE
Confidence 34688888899999999853 245678999999999 6676654
No 294
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=21.32 E-value=3.4e+02 Score=20.08 Aligned_cols=34 Identities=18% Similarity=0.148 Sum_probs=27.6
Q ss_pred ccccChHHHHHHhCCCCHHHHHHHHHHhHHcCCce
Q psy1676 223 YSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIE 257 (343)
Q Consensus 223 ys~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~ 257 (343)
....+.++|+...+++ ...+..++-.|+..|.|.
T Consensus 17 ~~~~~~t~i~~~~~L~-~~~~~~yL~~L~~~gLI~ 50 (77)
T PF14947_consen 17 KGGAKKTEIMYKANLN-YSTLKKYLKELEEKGLIK 50 (77)
T ss_dssp TT-B-HHHHHTTST---HHHHHHHHHHHHHTTSEE
T ss_pred cCCCCHHHHHHHhCcC-HHHHHHHHHHHHHCcCee
Confidence 5777889999999995 999999999999999994
No 295
>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=21.02 E-value=2.1e+02 Score=21.20 Aligned_cols=35 Identities=11% Similarity=0.232 Sum_probs=26.9
Q ss_pred cccccChHHHHHHhCCCCHHHHHHHHHHhHHcCCc
Q psy1676 222 SYSRITPTKIAEKLGLESPEDAEFIIAKAIRDGVI 256 (343)
Q Consensus 222 ~ys~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I 256 (343)
.-++.-+.|+++.+-=..+-++-.++..||++|.+
T Consensus 16 ~KskfYfkD~~k~~pd~k~R~vKKi~~~LV~Eg~l 50 (67)
T PF08679_consen 16 KKSKFYFKDFYKAFPDAKPREVKKIVNELVNEGKL 50 (67)
T ss_dssp HSS-EEHHHHHHH-TTS-HHHHHHHHHHHHHTTSE
T ss_pred CCCceeHHHHHHHCCCcCHHHHHHHHHHHHhhCeE
Confidence 34777899999864333589999999999999998
No 296
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=20.77 E-value=1.3e+02 Score=27.70 Aligned_cols=31 Identities=23% Similarity=0.456 Sum_probs=28.8
Q ss_pred cChHHHHHHhCCCCHHHHHHHHHHhHHcCCce
Q psy1676 226 ITPTKIAEKLGLESPEDAEFIIAKAIRDGVIE 257 (343)
Q Consensus 226 Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~ 257 (343)
+++++|++++|++ ...+=.++..|+..|++.
T Consensus 20 l~l~ela~~~glp-ksT~~RlL~tL~~~G~v~ 50 (246)
T COG1414 20 LSLAELAERLGLP-KSTVHRLLQTLVELGYVE 50 (246)
T ss_pred CCHHHHHHHhCcC-HHHHHHHHHHHHHCCCEE
Confidence 7899999999997 889999999999999983
No 297
>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=20.60 E-value=1.7e+02 Score=20.54 Aligned_cols=27 Identities=30% Similarity=0.394 Sum_probs=20.5
Q ss_pred cccChHHHHHHhCCCCHHHHHHHHHHhH
Q psy1676 224 SRITPTKIAEKLGLESPEDAEFIIAKAI 251 (343)
Q Consensus 224 s~Isl~dIa~~l~l~s~~e~E~ila~lI 251 (343)
..+++.++|..+|++ ..-+...+-++.
T Consensus 22 R~~tl~elA~~lgis-~st~~~~LRrae 48 (53)
T PF04967_consen 22 RRITLEELAEELGIS-KSTVSEHLRRAE 48 (53)
T ss_pred CcCCHHHHHHHhCCC-HHHHHHHHHHHH
Confidence 589999999999995 656655555543
No 298
>COG4235 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]
Probab=20.44 E-value=7.6e+02 Score=23.63 Aligned_cols=99 Identities=16% Similarity=0.062 Sum_probs=59.4
Q ss_pred HHHHHHHHhhcccHHHHHHHHHHHHHHhhhcCC-cchhHHHHHHHHHHHHhhc--cHHHHHhhhhhcCCCCCCChHHHHH
Q psy1676 20 YFYHSRVHELTNNLDKVRSFLNARLRIATLRND-FEGQAVLINCLLRNYLHYN--LYDQADKLVKKSAFPENASNNEWAR 96 (343)
Q Consensus 20 ~~y~~~~~e~~~~~~~~~~~l~~~~r~a~~~~~-~~~~~~l~n~Llr~yl~~~--~~~~a~~li~k~~~p~~~~~~~~~~ 96 (343)
|..++++|=..++.+.+-.-.-+++| +..+ ++-..-+... +|+..+ .-..+..++++..--+ ..-++
T Consensus 159 W~~Lg~~ym~~~~~~~A~~AY~~A~r---L~g~n~~~~~g~aea---L~~~a~~~~ta~a~~ll~~al~~D----~~~ir 228 (287)
T COG4235 159 WDLLGRAYMALGRASDALLAYRNALR---LAGDNPEILLGLAEA---LYYQAGQQMTAKARALLRQALALD----PANIR 228 (287)
T ss_pred HHHHHHHHHHhcchhHHHHHHHHHHH---hCCCCHHHHHHHHHH---HHHhcCCcccHHHHHHHHHHHhcC----CccHH
Confidence 88888888888877665533333332 2222 2222222222 233333 3455667777652211 23355
Q ss_pred HHHHHHHHHHHhhCHHHHHHHHHHHHhhCCcc
Q psy1676 97 FHFYLGRIKAVRLEYSTAHKNLVQALRKAPQT 128 (343)
Q Consensus 97 Y~YY~Gri~~~~~~y~~A~~~L~~A~~~~~~~ 128 (343)
=.||+|.-++-+++|.+|...++.-+...|..
T Consensus 229 al~lLA~~afe~g~~~~A~~~Wq~lL~~lp~~ 260 (287)
T COG4235 229 ALSLLAFAAFEQGDYAEAAAAWQMLLDLLPAD 260 (287)
T ss_pred HHHHHHHHHHHcccHHHHHHHHHHHHhcCCCC
Confidence 67899999999999999999999999865543
No 299
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=20.39 E-value=1.4e+02 Score=27.54 Aligned_cols=33 Identities=9% Similarity=0.132 Sum_probs=30.2
Q ss_pred cccChHHHHHHhCCCCHHHHHHHHHHhHHcCCce
Q psy1676 224 SRITPTKIAEKLGLESPEDAEFIIAKAIRDGVIE 257 (343)
Q Consensus 224 s~Isl~dIa~~l~l~s~~e~E~ila~lI~~G~I~ 257 (343)
..+++++||+.+|++ ..-+-.++..|...|++.
T Consensus 27 ~~l~l~eia~~lgl~-kstv~Rll~tL~~~G~l~ 59 (257)
T PRK15090 27 REIGITELSQRVMMS-KSTVYRFLQTMKTLGYVA 59 (257)
T ss_pred CCCCHHHHHHHHCcC-HHHHHHHHHHHHHCCCEE
Confidence 468999999999996 889999999999999984
No 300
>PF09114 MotA_activ: Transcription factor MotA, activation domain; InterPro: IPR015198 Transcription factor MotA is required for the activation of middle promoters in Bacteriophage T4, in addition to phage T4 co-activator AsiA, and sigma-70-containing Escherichia coli RNA polymerase. Phage T4 middle promoters have the sigma70 -10 DNA element, but not the -35 element; instead, they have a MotA box at -30 to which the transcription factor MotA binds []. MotA and AsiA interact with the C-terminal of sigma70 (region 4), which normally binds the -35 element and the beta-flap, thereby diverting sigma70 away from host promoters that require -35 element-binding to phage T4 middle promoters. Transcription factor MotA has two domains: an N-terminal domain required for binding to sigma70, and a C-terminal domain required for binding to the -30 MotA box element in the phage T4 middle promoter. This entry represents the N-terminal (activation) domain of MotA factors that binds sigma70. The N-terminal domain adopts an almost completely alpha-helical topology, with five alpha-helices and a short, two-stranded, beta-ribbon. Four alpha helices (alpha1, alpha3, alpha4 and alpha5) are amphipathic and pack their hydrophobic surfaces around the central helix alpha2 [].; PDB: 1BJA_B 1I1S_A.
Probab=20.16 E-value=1.6e+02 Score=23.20 Aligned_cols=47 Identities=28% Similarity=0.450 Sum_probs=33.1
Q ss_pred cChHHHHHHh--CCCCHHHHHHHHHHhHHcCCceEEeeCCCceEEEccCcccc
Q psy1676 226 ITPTKIAEKL--GLESPEDAEFIIAKAIRDGVIEATLDREKGYMQSKESADIY 276 (343)
Q Consensus 226 Isl~dIa~~l--~l~s~~e~E~ila~lI~~G~I~a~Id~~~g~v~~~~~~~v~ 276 (343)
|+.+.++..+ .+ +...+-.=+..||..|+|+.+ .+|+|...+..++.
T Consensus 31 it~~ev~e~l~~~~-~~~~V~SNIGvLIKkglIEKS---GDGlv~T~~g~~Ii 79 (96)
T PF09114_consen 31 ITASEVREALATEM-NKASVNSNIGVLIKKGLIEKS---GDGLVITEEGMDII 79 (96)
T ss_dssp B-HHHHHH-T-TTS--HHHHHHHHHHHHHTTSEEEE---TTEEEE-HHHHHHH
T ss_pred CCHHHHHHHHHHHh-hhhHHHHhHHHHHHcCccccc---CCceEEechHHHHH
Confidence 5778888877 34 366777779999999999875 46899887766544
Done!