Query psy4458
Match_columns 303
No_of_seqs 143 out of 669
Neff 7.8
Searched_HMMs 46136
Date Fri Aug 16 17:35:43 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4458.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4458hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1498|consensus 100.0 2.8E-70 6.1E-75 498.8 25.0 300 1-303 140-439 (439)
2 COG5071 RPN5 26S proteasome re 100.0 1.6E-61 3.5E-66 428.6 18.7 299 1-302 140-438 (439)
3 KOG1497|consensus 100.0 1.1E-51 2.5E-56 367.9 20.9 277 1-293 112-389 (399)
4 KOG0687|consensus 100.0 1.6E-36 3.4E-41 271.9 22.0 265 6-292 118-392 (393)
5 COG5187 RPN7 26S proteasome re 100.0 2.3E-30 5E-35 229.4 20.1 249 25-291 145-405 (412)
6 KOG1463|consensus 99.9 2.4E-25 5.1E-30 201.1 16.7 222 36-264 132-393 (411)
7 KOG1464|consensus 99.9 6.5E-24 1.4E-28 187.6 15.6 227 36-285 149-436 (440)
8 COG5159 RPN6 26S proteasome re 99.8 8.9E-20 1.9E-24 162.2 16.8 248 5-262 138-388 (421)
9 KOG2908|consensus 99.8 4.6E-17 9.9E-22 147.7 23.5 270 3-291 86-378 (380)
10 PF01399 PCI: PCI domain; Int 99.7 6.4E-17 1.4E-21 125.7 10.4 105 151-262 1-105 (105)
11 smart00088 PINT motif in prote 99.6 1.5E-14 3.3E-19 109.4 10.2 72 195-266 2-73 (88)
12 smart00753 PAM PCI/PINT associ 99.6 1.5E-14 3.3E-19 109.4 10.2 72 195-266 2-73 (88)
13 KOG0686|consensus 99.6 4.6E-14 1E-18 130.9 15.2 248 3-265 161-413 (466)
14 PF10602 RPN7: 26S proteasome 99.5 2.1E-13 4.6E-18 116.6 10.5 129 3-139 47-176 (177)
15 KOG2581|consensus 99.4 1.6E-11 3.4E-16 114.2 19.4 236 34-287 211-451 (493)
16 KOG2582|consensus 99.1 4.3E-09 9.3E-14 97.0 16.1 210 37-263 145-361 (422)
17 KOG2753|consensus 98.3 3.9E-05 8.4E-10 70.4 15.9 178 88-280 178-368 (378)
18 KOG1076|consensus 98.1 9.2E-06 2E-10 80.6 8.3 69 197-265 694-766 (843)
19 KOG2688|consensus 97.9 0.00021 4.5E-09 67.7 12.3 210 35-264 166-386 (394)
20 KOG2758|consensus 97.6 0.0024 5.2E-08 58.8 14.2 79 212-293 344-423 (432)
21 PF10255 Paf67: RNA polymerase 97.4 0.0042 9E-08 59.6 13.7 197 24-239 112-343 (404)
22 COG5600 Transcription-associat 97.1 0.027 5.8E-07 53.0 15.0 242 6-265 144-406 (413)
23 KOG2072|consensus 97.0 0.17 3.6E-06 52.0 21.2 67 195-261 425-492 (988)
24 PF10075 PCI_Csn8: COP9 signal 96.3 0.052 1.1E-06 44.5 10.0 83 148-241 39-121 (143)
25 PF09012 FeoC: FeoC like trans 95.6 0.032 6.9E-07 39.9 5.1 48 208-255 5-52 (69)
26 PF09756 DDRGK: DDRGK domain; 94.5 0.095 2E-06 45.2 5.9 79 211-291 107-187 (188)
27 PF09976 TPR_21: Tetratricopep 94.3 0.36 7.7E-06 39.3 8.8 83 5-100 61-143 (145)
28 PF13424 TPR_12: Tetratricopep 94.2 0.55 1.2E-05 33.6 8.7 70 32-103 5-74 (78)
29 PF14938 SNAP: Soluble NSF att 93.8 2.7 5.7E-05 38.4 14.5 170 6-176 69-261 (282)
30 PF08784 RPA_C: Replication pr 93.4 0.11 2.3E-06 40.1 3.9 37 217-253 65-101 (102)
31 PF14938 SNAP: Soluble NSF att 92.9 1.2 2.6E-05 40.7 10.6 113 6-122 49-162 (282)
32 PF12895 Apc3: Anaphase-promot 90.9 0.99 2.1E-05 32.9 6.4 82 5-100 2-83 (84)
33 PF04733 Coatomer_E: Coatomer 90.3 1.8 3.8E-05 39.9 8.8 119 4-146 114-233 (290)
34 TIGR02795 tol_pal_ybgF tol-pal 89.3 4.2 9.1E-05 30.7 9.1 94 3-105 13-106 (119)
35 PRK11788 tetratricopeptide rep 89.2 19 0.00041 33.6 15.2 90 4-103 119-208 (389)
36 PRK15431 ferrous iron transpor 88.6 0.97 2.1E-05 33.2 4.5 42 209-250 8-49 (78)
37 PF04348 LppC: LppC putative l 88.6 0.13 2.9E-06 51.5 0.0 91 4-103 36-126 (536)
38 PF14559 TPR_19: Tetratricopep 88.5 0.37 8E-06 33.4 2.3 53 4-62 3-55 (68)
39 COG3107 LppC Putative lipoprot 88.3 4 8.7E-05 40.5 9.8 88 4-101 75-162 (604)
40 PF12802 MarR_2: MarR family; 87.8 3 6.5E-05 28.3 6.6 48 209-256 11-60 (62)
41 KOG2003|consensus 87.6 2.4 5.3E-05 41.3 7.8 76 32-116 558-633 (840)
42 PF13432 TPR_16: Tetratricopep 85.7 4.8 0.0001 27.4 6.7 59 36-103 1-59 (65)
43 PF08220 HTH_DeoR: DeoR-like h 85.6 3.7 8.1E-05 28.0 5.9 47 211-261 8-54 (57)
44 PF13414 TPR_11: TPR repeat; P 84.6 6.5 0.00014 27.0 7.1 64 31-103 2-66 (69)
45 PF01047 MarR: MarR family; I 84.3 5 0.00011 27.0 6.2 48 209-256 9-56 (59)
46 KOG4414|consensus 84.1 3.1 6.6E-05 34.3 5.6 43 196-238 111-153 (197)
47 COG3063 PilF Tfp pilus assembl 83.7 32 0.0007 30.8 13.0 115 26-146 29-171 (250)
48 PF12569 NARP1: NMDA receptor- 83.7 14 0.00031 37.0 11.4 66 30-104 2-67 (517)
49 KOG3081|consensus 82.8 38 0.00083 31.0 12.8 83 3-103 119-201 (299)
50 KOG1156|consensus 82.6 50 0.0011 33.8 14.4 91 5-104 156-248 (700)
51 KOG0553|consensus 82.2 23 0.0005 32.7 11.2 152 80-249 86-250 (304)
52 smart00550 Zalpha Z-DNA-bindin 82.1 4.6 0.0001 28.6 5.4 32 218-249 23-54 (68)
53 KOG3250|consensus 81.6 2 4.2E-05 37.7 3.8 74 213-286 105-189 (258)
54 PF13412 HTH_24: Winged helix- 81.3 5.4 0.00012 25.8 5.2 33 215-247 15-47 (48)
55 TIGR01764 excise DNA binding d 80.7 4.4 9.5E-05 25.7 4.6 47 218-275 2-48 (49)
56 TIGR03879 near_KaiC_dom probab 80.4 3.3 7.2E-05 30.0 4.1 38 210-247 25-62 (73)
57 cd00090 HTH_ARSR Arsenical Res 79.8 11 0.00023 25.9 6.7 44 218-261 21-64 (78)
58 KOG1861|consensus 79.7 28 0.0006 34.2 11.2 138 75-230 348-491 (540)
59 smart00347 HTH_MARR helix_turn 79.2 22 0.00048 26.0 8.8 65 217-281 24-89 (101)
60 cd00189 TPR Tetratricopeptide 79.2 17 0.00037 24.6 8.7 85 4-103 12-96 (100)
61 PF13429 TPR_15: Tetratricopep 78.8 25 0.00055 31.5 10.5 88 4-105 89-176 (280)
62 PF02082 Rrf2: Transcriptional 78.5 5.9 0.00013 29.0 5.2 47 218-264 26-72 (83)
63 TIGR02917 PEP_TPR_lipo putativ 78.5 69 0.0015 32.8 14.9 62 34-104 161-222 (899)
64 PF03399 SAC3_GANP: SAC3/GANP/ 78.4 21 0.00045 30.4 9.5 142 74-229 55-204 (204)
65 PF12728 HTH_17: Helix-turn-he 78.1 6.3 0.00014 25.8 4.8 47 218-275 2-48 (51)
66 smart00419 HTH_CRP helix_turn_ 77.9 4.1 8.9E-05 25.9 3.8 32 217-248 8-39 (48)
67 PF09976 TPR_21: Tetratricopep 77.9 28 0.00061 28.0 9.6 87 5-100 24-110 (145)
68 KOG3054|consensus 77.6 7.5 0.00016 34.7 6.2 52 211-262 208-259 (299)
69 PF10345 Cohesin_load: Cohesin 77.4 64 0.0014 32.9 14.0 117 24-145 51-169 (608)
70 KOG1585|consensus 76.7 53 0.0011 29.9 11.3 83 8-101 74-176 (308)
71 COG3355 Predicted transcriptio 75.7 26 0.00056 28.2 8.4 70 217-286 42-120 (126)
72 smart00344 HTH_ASNC helix_turn 75.4 7.8 0.00017 29.6 5.3 39 215-253 15-56 (108)
73 cd00092 HTH_CRP helix_turn_hel 75.3 5.2 0.00011 27.4 3.9 34 216-249 24-57 (67)
74 TIGR02917 PEP_TPR_lipo putativ 75.2 80 0.0017 32.3 14.2 26 79-104 707-732 (899)
75 PRK11447 cellulose synthase su 74.7 69 0.0015 35.3 14.2 94 3-104 39-141 (1157)
76 TIGR00990 3a0801s09 mitochondr 74.4 67 0.0014 32.6 13.2 23 81-103 405-427 (615)
77 PF00325 Crp: Bacterial regula 74.4 6.8 0.00015 23.6 3.6 30 218-247 3-32 (32)
78 TIGR02552 LcrH_SycD type III s 73.8 40 0.00086 26.1 9.9 61 33-102 18-78 (135)
79 smart00418 HTH_ARSR helix_turn 73.1 10 0.00022 25.1 5.0 46 215-260 8-53 (66)
80 TIGR00990 3a0801s09 mitochondr 72.6 1.1E+02 0.0024 31.0 14.3 87 6-104 308-394 (615)
81 PF09339 HTH_IclR: IclR helix- 72.3 9.1 0.0002 25.3 4.4 38 211-248 12-49 (52)
82 PLN03218 maturation of RBCL 1; 72.0 1.6E+02 0.0035 32.4 18.0 62 34-103 581-642 (1060)
83 PF09743 DUF2042: Uncharacteri 71.6 21 0.00045 32.7 7.9 41 214-254 127-167 (272)
84 PF04703 FaeA: FaeA-like prote 71.5 12 0.00026 26.2 4.9 34 215-248 13-46 (62)
85 PRK11788 tetratricopeptide rep 71.0 89 0.0019 29.0 16.4 88 5-103 48-135 (389)
86 COG4105 ComL DNA uptake lipopr 70.7 83 0.0018 28.5 12.5 99 4-106 46-198 (254)
87 PF13174 TPR_6: Tetratricopept 69.2 12 0.00026 21.3 4.0 31 33-63 1-31 (33)
88 PF08672 APC2: Anaphase promot 69.1 15 0.00032 25.5 4.9 24 227-250 31-54 (60)
89 smart00345 HTH_GNTR helix_turn 69.0 10 0.00023 25.0 4.2 32 217-248 19-51 (60)
90 TIGR02521 type_IV_pilW type IV 68.9 65 0.0014 26.6 14.3 86 4-104 43-128 (234)
91 smart00420 HTH_DEOR helix_turn 68.5 21 0.00046 22.7 5.5 34 216-249 13-46 (53)
92 PLN03088 SGT1, suppressor of 68.1 45 0.00098 31.5 9.7 86 4-104 14-99 (356)
93 PRK11179 DNA-binding transcrip 66.9 15 0.00032 30.3 5.5 38 216-253 22-62 (153)
94 PF13545 HTH_Crp_2: Crp-like h 66.5 12 0.00026 26.4 4.3 33 216-248 27-59 (76)
95 TIGR02795 tol_pal_ybgF tol-pal 66.4 47 0.001 24.7 8.0 66 33-104 3-68 (119)
96 PF09295 ChAPs: ChAPs (Chs5p-A 66.3 21 0.00046 34.5 7.1 55 32-95 234-288 (395)
97 PRK02603 photosystem I assembl 66.1 37 0.0008 28.1 7.9 57 3-62 46-102 (172)
98 PF13404 HTH_AsnC-type: AsnC-t 65.9 17 0.00037 23.1 4.4 26 216-241 16-41 (42)
99 KOG1586|consensus 65.7 1.1E+02 0.0023 27.8 13.5 39 179-219 222-263 (288)
100 PRK11169 leucine-responsive tr 65.6 16 0.00034 30.5 5.5 45 209-253 20-67 (164)
101 PF13432 TPR_16: Tetratricopep 65.3 14 0.0003 25.0 4.3 53 4-62 9-61 (65)
102 TIGR02337 HpaR homoprotocatech 65.1 62 0.0014 25.0 8.8 43 215-257 40-82 (118)
103 cd07377 WHTH_GntR Winged helix 64.7 20 0.00044 24.1 5.1 30 219-248 27-56 (66)
104 PF13424 TPR_12: Tetratricopep 64.6 20 0.00044 25.1 5.2 58 3-61 16-75 (78)
105 PRK10803 tol-pal system protei 64.4 1.1E+02 0.0023 27.8 11.0 60 40-105 151-210 (263)
106 PRK15359 type III secretion sy 63.7 48 0.001 26.7 7.9 85 4-103 36-120 (144)
107 PF04545 Sigma70_r4: Sigma-70, 63.7 20 0.00043 23.3 4.6 30 213-242 16-45 (50)
108 KOG1941|consensus 63.5 98 0.0021 29.8 10.6 112 9-126 186-297 (518)
109 PF12755 Vac14_Fab1_bd: Vacuol 63.2 32 0.00069 26.2 6.3 50 51-102 21-70 (97)
110 TIGR02010 IscR iron-sulfur clu 62.9 17 0.00036 29.3 5.0 42 217-258 25-66 (135)
111 PF13371 TPR_9: Tetratricopept 62.7 36 0.00077 23.3 6.2 56 39-103 2-57 (73)
112 PF01325 Fe_dep_repress: Iron 62.7 31 0.00068 23.7 5.6 35 214-248 19-53 (60)
113 PRK09954 putative kinase; Prov 61.9 22 0.00047 33.5 6.3 46 215-260 15-63 (362)
114 CHL00033 ycf3 photosystem I as 61.7 88 0.0019 25.6 9.4 91 4-99 47-137 (168)
115 TIGR00373 conserved hypothetic 61.7 94 0.002 25.9 9.8 69 216-284 27-97 (158)
116 cd05804 StaR_like StaR_like; a 61.2 45 0.00097 30.7 8.2 90 3-103 125-214 (355)
117 PF13463 HTH_27: Winged helix 61.1 34 0.00075 23.3 5.8 43 213-255 14-56 (68)
118 TIGR02944 suf_reg_Xantho FeS a 60.6 14 0.0003 29.4 4.0 41 216-256 24-64 (130)
119 TIGR03302 OM_YfiO outer membra 60.1 81 0.0017 27.1 9.3 93 5-103 128-231 (235)
120 PF12895 Apc3: Anaphase-promot 59.9 18 0.0004 26.0 4.3 47 5-58 38-84 (84)
121 TIGR00738 rrf2_super rrf2 fami 59.8 16 0.00034 29.0 4.2 41 217-257 25-65 (132)
122 COG2956 Predicted N-acetylgluc 59.3 66 0.0014 30.4 8.6 93 1-103 150-242 (389)
123 COG1497 Predicted transcriptio 59.2 54 0.0012 29.5 7.7 64 216-284 24-87 (260)
124 PF14559 TPR_19: Tetratricopep 59.0 41 0.0009 22.6 5.9 54 43-105 2-55 (68)
125 PF11873 DUF3393: Domain of un 58.0 6.3 0.00014 34.4 1.7 68 114-184 109-176 (204)
126 PRK10857 DNA-binding transcrip 57.7 18 0.00039 30.4 4.4 43 216-258 24-66 (164)
127 PF01022 HTH_5: Bacterial regu 57.4 33 0.00071 22.1 4.7 33 216-248 14-46 (47)
128 PF00392 GntR: Bacterial regul 57.4 46 0.001 22.8 5.8 37 213-249 19-56 (64)
129 PRK06266 transcription initiat 57.0 71 0.0015 27.2 8.0 69 216-284 35-105 (178)
130 CHL00033 ycf3 photosystem I as 56.8 95 0.0021 25.4 8.7 88 7-104 14-101 (168)
131 PF08279 HTH_11: HTH domain; 56.7 32 0.0007 22.6 4.8 28 218-245 16-43 (55)
132 COG1522 Lrp Transcriptional re 56.1 25 0.00055 28.4 5.0 39 215-253 20-61 (154)
133 COG1959 Predicted transcriptio 55.9 34 0.00075 28.2 5.8 51 208-258 14-66 (150)
134 PF01978 TrmB: Sugar-specific 55.8 24 0.00052 24.5 4.2 39 215-253 20-58 (68)
135 PRK11014 transcriptional repre 55.2 28 0.00061 28.1 5.1 47 216-262 24-70 (141)
136 PRK10049 pgaA outer membrane p 54.3 1.6E+02 0.0035 30.9 11.7 94 3-105 321-423 (765)
137 PRK14574 hmsH outer membrane p 53.9 2.1E+02 0.0045 30.6 12.4 85 4-105 46-132 (822)
138 PRK10747 putative protoheme IX 53.2 1.8E+02 0.0038 27.8 11.0 86 5-104 97-182 (398)
139 PRK03902 manganese transport t 53.2 73 0.0016 25.7 7.2 35 215-249 20-54 (142)
140 PF04760 IF2_N: Translation in 53.1 12 0.00026 24.9 2.2 25 216-240 2-26 (54)
141 PRK03573 transcriptional regul 53.0 1.1E+02 0.0023 24.5 8.2 44 217-260 46-89 (144)
142 PF13181 TPR_8: Tetratricopept 52.4 31 0.00067 19.8 3.7 30 33-62 2-31 (34)
143 PF10300 DUF3808: Protein of u 52.3 1E+02 0.0022 30.3 9.4 88 5-103 246-333 (468)
144 PRK11447 cellulose synthase su 51.9 3.3E+02 0.007 30.2 14.0 88 4-104 541-632 (1157)
145 KOG3081|consensus 51.9 78 0.0017 29.1 7.6 56 82-143 214-270 (299)
146 PF12964 DUF3853: Protein of u 51.6 10 0.00022 28.9 1.7 40 219-262 47-86 (96)
147 PF12324 HTH_15: Helix-turn-he 51.3 18 0.00039 26.5 2.9 28 215-242 36-63 (77)
148 PF10602 RPN7: 26S proteasome 50.5 1.5E+02 0.0033 24.9 11.4 77 24-106 28-104 (177)
149 PF04492 Phage_rep_O: Bacterio 50.2 26 0.00057 26.9 3.8 36 212-247 49-84 (100)
150 PF13730 HTH_36: Helix-turn-he 50.0 23 0.0005 23.3 3.2 29 219-247 27-55 (55)
151 PRK11920 rirA iron-responsive 49.9 75 0.0016 26.2 6.9 43 216-258 23-65 (153)
152 PRK10049 pgaA outer membrane p 49.4 61 0.0013 34.0 7.7 88 3-105 370-457 (765)
153 PLN03088 SGT1, suppressor of 49.0 2E+02 0.0044 27.1 10.5 61 35-104 5-65 (356)
154 cd00189 TPR Tetratricopeptide 48.5 79 0.0017 21.0 7.5 62 34-104 2-63 (100)
155 PF07719 TPR_2: Tetratricopept 48.1 50 0.0011 18.7 4.2 30 33-62 2-31 (34)
156 PF12793 SgrR_N: Sugar transpo 47.7 49 0.0011 26.1 5.1 48 215-262 17-67 (115)
157 PF10078 DUF2316: Uncharacteri 47.5 19 0.00042 27.1 2.6 25 215-239 21-45 (89)
158 TIGR03504 FimV_Cterm FimV C-te 47.3 27 0.00058 22.6 3.0 24 36-59 3-26 (44)
159 PF13512 TPR_18: Tetratricopep 47.2 1.4E+02 0.0031 24.5 7.9 58 4-65 22-80 (142)
160 PRK11512 DNA-binding transcrip 47.0 55 0.0012 26.4 5.6 45 216-260 53-97 (144)
161 PF04967 HTH_10: HTH DNA bindi 46.9 28 0.00061 23.5 3.1 26 216-241 22-47 (53)
162 PRK09782 bacteriophage N4 rece 46.8 4.2E+02 0.0092 28.9 15.9 84 4-106 56-139 (987)
163 PF01726 LexA_DNA_bind: LexA D 46.2 55 0.0012 22.9 4.7 31 218-248 26-57 (65)
164 PRK10411 DNA-binding transcrip 45.6 47 0.001 29.6 5.4 40 210-249 11-50 (240)
165 PRK10434 srlR DNA-bindng trans 45.6 53 0.0012 29.5 5.8 40 208-247 10-49 (256)
166 PF12840 HTH_20: Helix-turn-he 45.6 51 0.0011 22.3 4.5 37 213-249 20-56 (61)
167 PLN03081 pentatricopeptide (PP 45.4 3.6E+02 0.0078 27.7 14.6 55 37-103 264-318 (697)
168 PRK04424 fatty acid biosynthes 45.3 37 0.00081 29.0 4.5 42 206-247 10-51 (185)
169 KOG1861|consensus 45.1 51 0.0011 32.5 5.7 66 33-102 349-414 (540)
170 smart00346 HTH_ICLR helix_turn 45.0 62 0.0014 23.4 5.2 34 216-249 19-52 (91)
171 KOG3677|consensus 45.0 2.3E+02 0.005 27.8 9.9 56 208-263 419-486 (525)
172 PF08281 Sigma70_r4_2: Sigma-7 44.8 30 0.00065 22.7 3.1 29 213-241 22-50 (54)
173 PF13613 HTH_Tnp_4: Helix-turn 44.8 49 0.0011 21.9 4.1 38 205-242 7-44 (53)
174 PF06971 Put_DNA-bind_N: Putat 44.5 34 0.00073 22.8 3.2 26 214-239 25-50 (50)
175 TIGR01610 phage_O_Nterm phage 44.5 55 0.0012 24.6 4.9 46 214-261 44-89 (95)
176 PRK13509 transcriptional repre 44.5 50 0.0011 29.6 5.4 40 209-248 11-50 (251)
177 PHA02943 hypothetical protein; 44.3 1.7E+02 0.0037 24.5 7.8 86 215-301 22-114 (165)
178 TIGR00540 hemY_coli hemY prote 44.0 2.7E+02 0.006 26.5 10.8 51 4-60 96-146 (409)
179 PF13428 TPR_14: Tetratricopep 43.6 54 0.0012 20.4 4.1 31 33-63 2-32 (44)
180 TIGR03826 YvyF flagellar opero 43.4 34 0.00073 28.0 3.7 38 215-256 42-81 (137)
181 smart00874 B5 tRNA synthetase 43.2 63 0.0014 22.5 4.8 61 217-289 5-67 (71)
182 smart00421 HTH_LUXR helix_turn 43.2 62 0.0014 20.6 4.5 29 214-242 15-43 (58)
183 TIGR03302 OM_YfiO outer membra 42.9 1.6E+02 0.0035 25.2 8.4 71 29-105 30-100 (235)
184 PRK10870 transcriptional repre 42.9 1.2E+02 0.0027 25.4 7.3 43 216-258 70-112 (176)
185 PRK02603 photosystem I assembl 42.8 1.9E+02 0.0041 23.7 9.1 72 27-104 30-101 (172)
186 KOG1840|consensus 42.8 1.8E+02 0.0039 29.1 9.4 97 4-102 253-352 (508)
187 cd08312 Death_MyD88 Death doma 42.7 62 0.0013 23.5 4.7 47 221-289 20-71 (79)
188 PF13414 TPR_11: TPR repeat; P 42.4 83 0.0018 21.2 5.3 28 77-104 5-32 (69)
189 PHA02591 hypothetical protein; 42.2 29 0.00062 25.5 2.7 25 216-240 58-82 (83)
190 PF12569 NARP1: NMDA receptor- 41.6 1.3E+02 0.0029 30.1 8.4 64 31-103 193-256 (517)
191 PF06163 DUF977: Bacterial pro 41.6 1E+02 0.0022 24.8 6.0 61 211-280 20-81 (127)
192 PF10743 Phage_Cox: Regulatory 41.1 36 0.00077 25.5 3.2 61 209-281 4-70 (87)
193 PRK10747 putative protoheme IX 40.6 3.3E+02 0.0071 25.9 12.2 88 4-105 130-217 (398)
194 PF13542 HTH_Tnp_ISL3: Helix-t 40.5 72 0.0016 20.6 4.4 27 215-241 25-51 (52)
195 cd06170 LuxR_C_like C-terminal 40.4 72 0.0016 20.4 4.5 28 214-241 12-39 (57)
196 COG4367 Uncharacterized protei 40.1 34 0.00075 25.7 2.9 25 215-239 21-45 (97)
197 PF04348 LppC: LppC putative l 40.1 9.5 0.0002 38.4 0.0 85 6-100 2-86 (536)
198 PF00440 TetR_N: Bacterial reg 39.9 57 0.0012 20.8 3.8 23 212-234 11-33 (47)
199 PF08679 DsrD: Dissimilatory s 39.8 56 0.0012 23.2 3.8 33 215-247 17-50 (67)
200 TIGR02521 type_IV_pilW type IV 39.5 2.1E+02 0.0046 23.4 12.8 67 29-104 28-94 (234)
201 PF14394 DUF4423: Domain of un 39.5 1.5E+02 0.0032 25.0 7.2 31 219-249 41-73 (171)
202 PRK14165 winged helix-turn-hel 39.4 84 0.0018 27.7 5.9 48 215-262 19-66 (217)
203 PF04539 Sigma70_r3: Sigma-70 39.3 34 0.00074 24.3 2.9 26 216-241 19-44 (78)
204 PRK10141 DNA-binding transcrip 38.7 2E+02 0.0042 22.7 8.6 69 217-287 30-103 (117)
205 PRK13777 transcriptional regul 38.4 2.5E+02 0.0055 24.0 10.6 45 215-259 57-101 (185)
206 PF10771 DUF2582: Protein of u 38.3 74 0.0016 22.4 4.3 44 215-260 20-63 (65)
207 PF03704 BTAD: Bacterial trans 38.3 2E+02 0.0043 22.7 9.3 62 31-101 61-122 (146)
208 PF09986 DUF2225: Uncharacteri 38.0 2.8E+02 0.006 24.3 9.6 81 26-108 112-198 (214)
209 COG3118 Thioredoxin domain-con 37.9 3.4E+02 0.0073 25.3 10.9 49 5-59 147-195 (304)
210 PRK10906 DNA-binding transcrip 37.7 84 0.0018 28.2 5.8 37 211-247 13-49 (252)
211 PF01984 dsDNA_bind: Double-st 37.7 19 0.00041 28.1 1.3 22 231-252 61-82 (107)
212 PRK11050 manganese transport r 37.1 1.9E+02 0.0041 23.7 7.4 35 216-250 50-84 (152)
213 COG1349 GlpR Transcriptional r 36.7 84 0.0018 28.2 5.6 40 209-248 11-50 (253)
214 KOG1129|consensus 36.6 1.9E+02 0.0042 27.5 7.9 84 6-105 237-320 (478)
215 KOG2002|consensus 36.4 1.5E+02 0.0033 31.9 7.9 63 35-103 273-335 (1018)
216 TIGR02702 SufR_cyano iron-sulf 35.2 1.5E+02 0.0033 25.4 6.8 36 215-250 13-48 (203)
217 PRK10046 dpiA two-component re 34.9 77 0.0017 27.3 5.0 44 210-253 170-213 (225)
218 KOG2300|consensus 34.9 4.4E+02 0.0096 26.5 10.3 74 32-107 404-477 (629)
219 PF05584 Sulfolobus_pRN: Sulfo 34.9 1.6E+02 0.0035 21.2 5.6 40 208-249 11-50 (72)
220 KOG3060|consensus 34.7 3.6E+02 0.0079 24.7 13.1 64 32-104 51-115 (289)
221 PF07064 RIC1: RIC1; InterPro 34.5 87 0.0019 28.4 5.3 58 4-61 191-249 (258)
222 PF13176 TPR_7: Tetratricopept 34.4 68 0.0015 19.1 3.3 26 35-60 2-27 (36)
223 TIGR00540 hemY_coli hemY prote 33.6 1.8E+02 0.0039 27.8 7.7 63 32-102 335-397 (409)
224 PF13601 HTH_34: Winged helix 32.7 1.9E+02 0.0042 20.9 8.3 42 215-256 12-53 (80)
225 TIGR02561 HrpB1_HrpK type III 32.4 3E+02 0.0064 23.0 8.7 67 30-105 8-74 (153)
226 PF09202 Rio2_N: Rio2, N-termi 31.9 1.2E+02 0.0026 22.3 4.8 50 212-261 19-69 (82)
227 PF13518 HTH_28: Helix-turn-he 31.4 77 0.0017 20.2 3.4 39 214-253 9-47 (52)
228 TIGR01884 cas_HTH CRISPR locus 31.4 1.5E+02 0.0033 25.4 6.2 37 216-252 156-192 (203)
229 PF00376 MerR: MerR family reg 30.9 47 0.001 20.6 2.1 18 219-236 1-18 (38)
230 PRK09334 30S ribosomal protein 30.1 2E+02 0.0043 21.5 5.7 45 215-260 39-83 (86)
231 PRK04217 hypothetical protein; 29.8 1E+02 0.0022 24.2 4.3 43 214-256 55-104 (110)
232 smart00005 DEATH DEATH domain, 29.7 1.1E+02 0.0024 22.1 4.4 54 219-289 19-78 (88)
233 PF01476 LysM: LysM domain; I 29.6 58 0.0013 20.1 2.5 19 219-237 8-26 (44)
234 PRK14720 transcript cleavage f 29.3 2.9E+02 0.0063 29.8 8.8 108 4-128 43-163 (906)
235 KOG2041|consensus 28.8 3.4E+02 0.0075 28.6 8.7 57 40-103 768-824 (1189)
236 PF00515 TPR_1: Tetratricopept 28.6 1.2E+02 0.0026 17.2 3.9 30 33-62 2-31 (34)
237 TIGR02552 LcrH_SycD type III s 28.5 2.7E+02 0.0058 21.2 12.0 86 4-104 29-114 (135)
238 PRK10681 DNA-binding transcrip 28.4 1.1E+02 0.0023 27.4 4.9 37 206-242 10-46 (252)
239 TIGR01889 Staph_reg_Sar staphy 28.3 2.7E+02 0.0058 21.2 7.9 42 216-257 42-83 (109)
240 TIGR02844 spore_III_D sporulat 27.9 1.1E+02 0.0025 22.4 4.1 23 216-238 18-40 (80)
241 COG2956 Predicted N-acetylgluc 27.9 5.2E+02 0.011 24.6 9.1 54 4-59 81-134 (389)
242 KOG1840|consensus 27.9 3.1E+02 0.0066 27.5 8.3 77 27-104 320-396 (508)
243 PF12854 PPR_1: PPR repeat 27.8 44 0.00096 19.9 1.6 16 4-19 19-34 (34)
244 PRK12798 chemotaxis protein; R 27.7 1.2E+02 0.0027 29.4 5.3 74 23-101 248-321 (421)
245 PF02042 RWP-RK: RWP-RK domain 27.6 73 0.0016 21.4 2.7 21 217-237 4-24 (52)
246 TIGR03697 NtcA_cyano global ni 27.4 80 0.0017 26.2 3.7 33 217-249 143-175 (193)
247 PRK09802 DNA-binding transcrip 27.4 1.5E+02 0.0033 26.8 5.7 38 211-248 25-62 (269)
248 PF10975 DUF2802: Protein of u 27.3 71 0.0015 22.8 2.8 24 216-239 43-66 (70)
249 PRK10370 formate-dependent nit 27.0 4E+02 0.0086 22.7 10.1 85 5-104 52-139 (198)
250 PF03297 Ribosomal_S25: S25 ri 26.9 1.6E+02 0.0035 22.9 4.9 45 215-260 57-101 (105)
251 cd05804 StaR_like StaR_like; a 26.9 2.7E+02 0.0059 25.3 7.5 66 36-103 268-335 (355)
252 TIGR02147 Fsuc_second hypothet 26.9 2E+02 0.0043 26.3 6.3 62 219-281 139-206 (271)
253 PF04157 EAP30: EAP30/Vps36 fa 26.9 1.6E+02 0.0036 25.7 5.7 37 212-248 185-221 (223)
254 PF09743 DUF2042: Uncharacteri 26.8 96 0.0021 28.3 4.3 39 215-253 190-228 (272)
255 smart00342 HTH_ARAC helix_turn 26.7 77 0.0017 21.9 3.0 24 218-241 2-25 (84)
256 COG1675 TFA1 Transcription ini 26.6 4E+02 0.0088 22.7 7.9 69 217-285 32-102 (176)
257 cd06171 Sigma70_r4 Sigma70, re 26.6 1.6E+02 0.0035 18.0 5.0 28 215-242 24-51 (55)
258 COG3413 Predicted DNA binding 26.4 67 0.0015 27.9 3.1 26 216-241 177-202 (215)
259 KOG3060|consensus 26.4 2.6E+02 0.0057 25.6 6.8 87 2-104 96-183 (289)
260 PF06711 DUF1198: Protein of u 26.2 49 0.0011 27.1 1.9 24 220-243 28-51 (148)
261 PF00165 HTH_AraC: Bacterial r 26.1 51 0.0011 20.4 1.7 24 214-237 5-28 (42)
262 PLN03077 Protein ECB2; Provisi 26.0 4.1E+02 0.009 28.1 9.5 50 5-58 602-651 (857)
263 KOG2796|consensus 25.9 1.4E+02 0.0031 27.5 5.0 73 30-105 210-282 (366)
264 KOG1126|consensus 25.7 4.3E+02 0.0093 27.2 8.8 91 7-103 334-449 (638)
265 PRK04239 hypothetical protein; 25.5 41 0.00089 26.4 1.4 21 232-252 67-87 (110)
266 PRK13918 CRP/FNR family transc 25.5 87 0.0019 26.3 3.6 42 217-262 149-190 (202)
267 COG2345 Predicted transcriptio 25.2 4.8E+02 0.01 23.0 8.4 42 213-255 21-62 (218)
268 COG2118 DNA-binding protein [G 25.1 44 0.00094 26.3 1.4 23 231-253 69-91 (116)
269 PF03485 Arg_tRNA_synt_N: Argi 25.1 1.3E+02 0.0028 21.8 4.0 40 221-260 43-83 (85)
270 PRK10803 tol-pal system protei 25.1 5.1E+02 0.011 23.3 10.8 92 87-183 155-248 (263)
271 PF13429 TPR_15: Tetratricopep 25.0 4.8E+02 0.01 23.0 10.6 86 3-101 121-209 (280)
272 PLN03081 pentatricopeptide (PP 25.0 3.1E+02 0.0067 28.2 8.2 82 5-103 475-556 (697)
273 PF13182 DUF4007: Protein of u 24.9 2E+02 0.0043 26.4 6.0 57 213-271 216-283 (286)
274 smart00531 TFIIE Transcription 24.9 3.5E+02 0.0076 22.0 7.0 71 215-285 13-88 (147)
275 PRK11753 DNA-binding transcrip 24.8 93 0.002 26.3 3.7 32 217-248 168-199 (211)
276 PRK14574 hmsH outer membrane p 24.8 7.2E+02 0.016 26.6 10.8 86 4-105 114-199 (822)
277 PF07848 PaaX: PaaX-like prote 24.6 85 0.0019 22.4 2.8 30 220-249 26-55 (70)
278 PF02002 TFIIE_alpha: TFIIE al 24.6 1.8E+02 0.0038 22.1 4.8 36 215-250 25-60 (105)
279 COG2886 Uncharacterized small 24.6 1.9E+02 0.004 21.8 4.7 26 216-241 40-65 (88)
280 TIGR02675 tape_meas_nterm tape 24.3 77 0.0017 22.8 2.6 26 220-249 47-72 (75)
281 PF13374 TPR_10: Tetratricopep 24.1 1.6E+02 0.0035 17.2 3.9 29 34-62 4-32 (42)
282 smart00028 TPR Tetratricopepti 23.9 1.2E+02 0.0025 15.5 4.0 26 78-103 4-29 (34)
283 PRK11161 fumarate/nitrate redu 23.7 98 0.0021 26.8 3.7 32 217-248 184-215 (235)
284 PLN03218 maturation of RBCL 1; 23.7 1E+03 0.022 26.3 18.1 64 33-104 615-678 (1060)
285 TIGR00498 lexA SOS regulatory 23.6 1.7E+02 0.0037 24.8 5.1 40 218-257 26-66 (199)
286 TIGR02366 DHAK_reg probable di 23.6 94 0.002 25.5 3.4 29 199-230 8-36 (176)
287 KOG2002|consensus 23.5 9.9E+02 0.021 26.1 11.9 137 33-181 453-593 (1018)
288 cd08311 Death_p75NR Death doma 23.4 1.7E+02 0.0037 21.2 4.3 45 221-287 19-67 (77)
289 PF00356 LacI: Bacterial regul 23.3 1E+02 0.0022 20.0 2.7 20 219-238 1-20 (46)
290 KOG2034|consensus 23.2 1.7E+02 0.0037 31.2 5.6 57 37-105 363-419 (911)
291 cd04762 HTH_MerR-trunc Helix-T 23.2 1E+02 0.0022 18.9 2.8 38 219-261 2-39 (49)
292 PRK04841 transcriptional regul 23.0 4.3E+02 0.0093 27.9 8.9 98 5-103 504-601 (903)
293 PF08221 HTH_9: RNA polymerase 22.8 2.6E+02 0.0057 19.2 6.6 34 215-248 25-58 (62)
294 PRK10163 DNA-binding transcrip 22.3 1.4E+02 0.0031 26.9 4.5 35 215-249 38-72 (271)
295 PF13217 DUF4025: Protein of u 21.8 42 0.00091 22.9 0.7 24 232-255 31-54 (55)
296 PF13384 HTH_23: Homeodomain-l 21.8 1E+02 0.0022 19.6 2.6 32 214-245 14-45 (50)
297 cd04761 HTH_MerR-SF Helix-Turn 21.8 1.1E+02 0.0024 19.1 2.8 38 219-261 2-39 (49)
298 PF14493 HTH_40: Helix-turn-he 21.8 1.1E+02 0.0024 22.6 3.1 32 215-246 11-42 (91)
299 TIGR00122 birA_repr_reg BirA b 21.7 1.3E+02 0.0029 20.7 3.3 31 218-248 14-44 (69)
300 PF01710 HTH_Tnp_IS630: Transp 21.6 1.7E+02 0.0036 22.9 4.3 34 208-241 62-95 (119)
301 PF10668 Phage_terminase: Phag 21.3 81 0.0018 21.9 2.0 19 217-235 22-40 (60)
302 PF10007 DUF2250: Uncharacteri 21.2 2.7E+02 0.0058 21.1 5.0 30 218-247 22-51 (92)
303 PRK09782 bacteriophage N4 rece 20.8 7.3E+02 0.016 27.2 10.1 48 46-103 590-637 (987)
304 PF11972 HTH_13: HTH DNA bindi 20.6 1.3E+02 0.0028 20.4 2.9 32 210-243 8-39 (54)
305 PRK09975 DNA-binding transcrip 20.5 1.8E+02 0.0039 24.6 4.6 36 197-232 10-46 (213)
306 PF04053 Coatomer_WDAD: Coatom 20.4 8.2E+02 0.018 24.0 10.6 80 5-101 331-415 (443)
307 PF08280 HTH_Mga: M protein tr 20.4 2.1E+02 0.0045 19.3 4.0 27 215-241 17-43 (59)
308 PRK10866 outer membrane biogen 20.3 6E+02 0.013 22.4 13.8 134 4-145 44-242 (243)
309 PF13411 MerR_1: MerR HTH fami 20.3 92 0.002 21.3 2.3 39 219-262 2-40 (69)
310 PF13118 DUF3972: Protein of u 20.2 2.6E+02 0.0056 22.5 5.0 34 223-262 2-35 (126)
311 PF10300 DUF3808: Protein of u 20.1 6.6E+02 0.014 24.7 9.0 78 4-91 279-356 (468)
312 PRK06759 RNA polymerase factor 20.1 1.4E+02 0.003 23.8 3.7 31 212-242 117-147 (154)
313 PF07106 TBPIP: Tat binding pr 20.0 5.1E+02 0.011 21.4 9.4 75 208-286 10-90 (169)
No 1
>KOG1498|consensus
Probab=100.00 E-value=2.8e-70 Score=498.80 Aligned_cols=300 Identities=56% Similarity=0.909 Sum_probs=291.3
Q ss_pred CCCccCCHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHH
Q psy4458 1 MKEDEGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRL 80 (303)
Q Consensus 1 i~e~~~~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~ 80 (303)
|+|.+|++++||++|+++||||||+|..++|+.|+|+||||||..+||.+|+++++||+.++|++++ ..++|+.||.+
T Consensus 140 ike~~Gdi~~Aa~il~el~VETygsm~~~ekV~fiLEQmrKOG~~~D~vra~i~skKI~~K~F~~~~--~~~lKlkyY~l 217 (439)
T KOG1498|consen 140 IKEEQGDIAEAADILCELQVETYGSMEKSEKVAFILEQMRLCLLRLDYVRAQIISKKINKKFFEKPD--VQELKLKYYEL 217 (439)
T ss_pred HHHHcCCHHHHHHHHHhcchhhhhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhHHhcCCcc--HHHHHHHHHHH
Confidence 5899999999999999999999999999999999999999999999999999999999999998877 99999999999
Q ss_pred HHHHHHHhhhHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHhCCCCchhhHhHHHhhhhhhcCCchHHHHHHHHh
Q psy4458 81 MIELDQHEGSYLATCKHYRAILTTPCIQSDPVQRHAVLQNVVLYLMLAPYDNEQSDLTHRVLEDKLLNEIPLYKGLLQWF 160 (303)
Q Consensus 81 ~~~~~~~~~~f~eaa~~y~e~~~t~~~~~~~~~~~~~L~~~v~~~iLs~~~~~r~~ll~~l~~~~~~~~~p~~~~L~~~f 160 (303)
|++++.|.+.|+++|++|+++++|+.++.|+..|...|..+|+|++|||++++++++++++..|+.+.++|.+..+++.|
T Consensus 218 mI~l~lh~~~Yl~v~~~Yraiy~t~~vk~d~~kw~~vL~~iv~f~~LAp~dneQsdll~~is~dKkL~e~p~~k~lLklf 297 (439)
T KOG1498|consen 218 MIRLGLHDRAYLNVCRSYRAIYDTGNVKEDPEKWIEVLRSIVSFCVLAPHDNEQSDLLARISNDKKLSELPDYKELLKLF 297 (439)
T ss_pred HHHhcccccchhhHHHHHHHHhcccccccChhhhhhhhhhheeEEeecCCCcHHHHHHHHHhcccccccCccHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCcccCchHHHHHHHHhhcccccccccchhHHhHHHHHHHHHHHHHHHHHHhhhceeeHHHHHHHhCCCHHHHHHHHHh
Q psy4458 161 TNPELIKWSGLRQLYEEELFKTSVFNQSTEEGQKCFKMLKHRVVEHNIRVMAKYYTRITLQRMCDLLGLPIEETEEFLSS 240 (303)
Q Consensus 161 ~~~~li~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~~l~~~i~ehNi~~isk~Y~~Itl~~la~ll~ls~~~vE~~l~~ 240 (303)
.+++|++|+.+...|...|....+| +....|+.||++|+.|++||||+++++||++||+.+||.++|+|++++|..||.
T Consensus 298 v~~EL~rw~s~~~~yg~~l~~~~~~-~~~~~gek~~~dL~~RIiEHNiRiiA~yYSrIt~~rl~eLLdl~~ee~E~~LS~ 376 (439)
T KOG1498|consen 298 VTMELIRWVSLVESYGDELRTNDFF-DGGEEGEKRWSDLKLRIIEHNIRIIAKYYSRITLKRLAELLDLPVEEMEKFLSD 376 (439)
T ss_pred HhcceeeehhHhhhhHHHHhhcccc-cccchhhhHHHHHHHHHHHHHHHHHHHHHhhccHHHHHHHhCCCHHHHHHHHHH
Confidence 9999999998999999999988766 667788999999999999999999999999999999999999999999999999
Q ss_pred hhhcCceEEEecCCCceEEeccCCChhHHHHHHHHHHHHHHHHHHHHHhhhhHHHHhchhhhC
Q psy4458 241 MVVSKTITAKIDRPAGIINFARNKDPGEILNEWSASLNELMKLVNNTTHLINKEQMIHQRVAA 303 (303)
Q Consensus 241 mI~~~~l~akIDq~~giV~f~~~~~~~~~l~~w~~~i~~l~~~v~~~~~lI~ke~~~~~~~~~ 303 (303)
||..|.+.||||||.|+|.|..+++.++.+++|+.++.+|+..++++||+|+||+|||+..++
T Consensus 377 lv~t~ti~aKidrpsgII~F~k~K~~~~~LneW~~nve~L~~ll~K~~HLI~KEemmhsi~~~ 439 (439)
T KOG1498|consen 377 LVVTGTIYAKIDRPSGIINFQKVKDSNEILNEWASNVEKLLGLLEKVSHLIHKEEMMHSIQKA 439 (439)
T ss_pred HHhccceEEEecCCCceEEEEecccHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 999999999999999999999999999999999999999999999999999999999998654
No 2
>COG5071 RPN5 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.6e-61 Score=428.58 Aligned_cols=299 Identities=43% Similarity=0.738 Sum_probs=284.7
Q ss_pred CCCccCCHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHH
Q psy4458 1 MKEDEGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRL 80 (303)
Q Consensus 1 i~e~~~~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~ 80 (303)
|+|.+||+++|+++|+++||||||+|...+|+.|+|+|+|||+..+||.+|.++++||+.++|++++ ..++|+.||.+
T Consensus 140 ikee~Gdi~sA~Dilcn~pVETygs~~~Sekv~fiLEQ~rL~vl~~Dy~~A~~~~kKI~KK~Fe~~d--~~slKlkyYeL 217 (439)
T COG5071 140 IKEEQGDIKSAQDILCNEPVETYGSFDLSEKVAFILEQVRLFLLRSDYYMASTYTKKINKKFFEKED--VQSLKLKYYEL 217 (439)
T ss_pred HHHHhcchhHHHHHHhcCchhhccchhHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHhcccc--HHHHHHHHHHH
Confidence 5789999999999999999999999999999999999999999999999999999999999998876 89999999999
Q ss_pred HHHHHHHhhhHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHhCCCCchhhHhHHHhhhhhhcCCchHHHHHHHHh
Q psy4458 81 MIELDQHEGSYLATCKHYRAILTTPCIQSDPVQRHAVLQNVVLYLMLAPYDNEQSDLTHRVLEDKLLNEIPLYKGLLQWF 160 (303)
Q Consensus 81 ~~~~~~~~~~f~eaa~~y~e~~~t~~~~~~~~~~~~~L~~~v~~~iLs~~~~~r~~ll~~l~~~~~~~~~p~~~~L~~~f 160 (303)
..+++.+.|.|+++|++|.++|+|-.+++|+..|..+|...++|++|+|+++++.++++++..|.++..+|....++++|
T Consensus 218 ~V~i~Lh~R~Yl~v~~y~~~vY~t~~~~~d~Akwk~VLS~~v~F~iLtpy~neq~dlvhKi~~d~kl~sl~~~~~lVk~f 297 (439)
T COG5071 218 KVRIGLHDRAYLDVCKYYRAVYDTAVVQEDPAKWKEVLSNVVCFALLTPYDNEQADLLHKINADHKLNSLPLLQQLVKCF 297 (439)
T ss_pred hheeecccHHHHHHHHHHHHHHHHHHhccCcccccchhhcceeeEEecccccHHHHHHHHhhhhhhhccchhhhhHHHHH
Confidence 99999999999999999999999999998999999999999999999999999999999999999888899999999999
Q ss_pred cCCcccCchHHHHHHHHhhcccccccccchhHHhHHHHHHHHHHHHHHHHHHhhhceeeHHHHHHHhCCCHHHHHHHHHh
Q psy4458 161 TNPELIKWSGLRQLYEEELFKTSVFNQSTEEGQKCFKMLKHRVVEHNIRVMAKYYTRITLQRMCDLLGLPIEETEEFLSS 240 (303)
Q Consensus 161 ~~~~li~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~~l~~~i~ehNi~~isk~Y~~Itl~~la~ll~ls~~~vE~~l~~ 240 (303)
..+++.+||-....|.+.|..+.. +...+.|..||.+|++|++|||+|+|+.|||+|+.++|+.++++|++++|+.+|.
T Consensus 298 ~vNelmrwp~V~~~y~~~l~~~~f-aF~~e~~~~~w~DL~krviEHN~RvI~~yYSrI~~~rl~~lld~~~s~te~~ISd 376 (439)
T COG5071 298 IVNELMRWPKVAEIYGSALRSNVF-AFNDEKGEKRWSDLRKRVIEHNIRVIANYYSRIHCSRLGVLLDMSPSETEQFISD 376 (439)
T ss_pred HHHHHHhhhHHHHHhHHHHHhhhh-hhccchhhhhHHHHHHHHHHhhHhHHHHHhhhhhHHHHHHHHcCCHHHHHHHHHH
Confidence 999999999888999998887642 2345566789999999999999999999999999999999999999999999999
Q ss_pred hhhcCceEEEecCCCceEEeccCCChhHHHHHHHHHHHHHHHHHHHHHhhhhHHHHhchhhh
Q psy4458 241 MVVSKTITAKIDRPAGIINFARNKDPGEILNEWSASLNELMKLVNNTTHLINKEQMIHQRVA 302 (303)
Q Consensus 241 mI~~~~l~akIDq~~giV~f~~~~~~~~~l~~w~~~i~~l~~~v~~~~~lI~ke~~~~~~~~ 302 (303)
||+.|-++|||+||.|||.|+++++..+.++.|+.||..++.++++++|+|.||+|+|.+.+
T Consensus 377 lVN~G~~yaKiNrpa~Ii~FEK~~n~~~~lneW~~NV~ellgklek~~HLI~KEe~m~siqa 438 (439)
T COG5071 377 LVNKGHFYAKINRPAQIISFEKSQNVQEQLNEWGSNVTELLGKLEKVRHLIIKEEMMNSIQA 438 (439)
T ss_pred HHhcCcEEEEecCccceEEeeccccHHHHHHHhcccHHHHHHHHHHHhHHHhHHHHHhhhcc
Confidence 99999999999999999999999999999999999999999999999999999999998753
No 3
>KOG1497|consensus
Probab=100.00 E-value=1.1e-51 Score=367.91 Aligned_cols=277 Identities=21% Similarity=0.351 Sum_probs=255.6
Q ss_pred CCCccCCHHHHHHHHhccccccc-cCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHH
Q psy4458 1 MKEDEGDVTEAANIIQELQVETY-GSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYR 79 (303)
Q Consensus 1 i~e~~~~~~~Aa~~L~~i~vet~-~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~ 79 (303)
|+|++++|+.||..|.+|+.+|+ ...+.+.|+..+++++|+||+.+|.+.|+.+++|++-..-+. . +.++.+.|+.
T Consensus 112 iYE~Eq~~~~aaq~L~~I~~~tg~~~~d~~~kl~l~iriarlyLe~~d~veae~~inRaSil~a~~-~--Ne~Lqie~kv 188 (399)
T KOG1497|consen 112 IYEKEQNWRDAAQVLVGIPLDTGQKAYDVEQKLLLCIRIARLYLEDDDKVEAEAYINRASILQAES-S--NEQLQIEYKV 188 (399)
T ss_pred HHHHhhhHHHHHHHHhccCcccchhhhhhHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHhhhcc-c--CHHHHHHHHH
Confidence 58999999999999999999994 678999999999999999999999999999999999876444 4 6899999999
Q ss_pred HHHHHHHHhhhHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHhCCCCchhhHhHHHhhhhhhcCCchHHHHHHHH
Q psy4458 80 LMIELDQHEGSYLATCKHYRAILTTPCIQSDPVQRHAVLQNVVLYLMLAPYDNEQSDLTHRVLEDKLLNEIPLYKGLLQW 159 (303)
Q Consensus 80 ~~~~~~~~~~~f~eaa~~y~e~~~t~~~~~~~~~~~~~L~~~v~~~iLs~~~~~r~~ll~~l~~~~~~~~~p~~~~L~~~ 159 (303)
|++|..+..|+|+|||++|++++.+.-. ++.++.++|+.++.|++|+.+||+|+++|+.+++|++++++|.|..+.++
T Consensus 189 c~ARvlD~krkFlEAAqrYyels~~ki~--~e~~~~~aL~~a~~CtlLA~~gpqrsr~Latlfkder~~~l~~y~ileKm 266 (399)
T KOG1497|consen 189 CYARVLDYKRKFLEAAQRYYELSQRKIV--DESERLEALKKALQCTLLASAGPQRSRMLATLFKDERCQKLPAYGILEKM 266 (399)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhc--chHHHHHHHHHhHhheeecCCChHHHHHHHHHhcCcccccccchHHHHHH
Confidence 9999999999999999999999988765 77889999999999999999999999999999999999999999999999
Q ss_pred hcCCcccCchHHHHHHHHhhcccccccccchhHHhHHHHHHHHHHHHHHHHHHhhhceeeHHHHHHHhCCCHHHHHHHHH
Q psy4458 160 FTNPELIKWSGLRQLYEEELFKTSVFNQSTEEGQKCFKMLKHRVVEHNIRVMAKYYTRITLQRMCDLLGLPIEETEEFLS 239 (303)
Q Consensus 160 f~~~~li~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~~l~~~i~ehNi~~isk~Y~~Itl~~la~ll~ls~~~vE~~l~ 239 (303)
|..+ +|+.+ ..+.|++.|.+|+... ..+| ...+.++++||||..+|++|.+|||+.||.+|++|++.+|++++
T Consensus 267 yl~r-iI~k~-el~ef~~~L~pHQka~--~~dg---ssil~ra~~EhNlls~Skly~nisf~~Lg~ll~i~~ekaekiaa 339 (399)
T KOG1497|consen 267 YLER-IIRKE-ELQEFEAFLQPHQKAH--TMDG---SSILDRAVIEHNLLSASKLYNNISFEELGALLKIDAEKAEKIAA 339 (399)
T ss_pred HHHH-Hhcch-hHHHHHHHhcchhhhc--ccCc---chhhhhHHHHHhHHHHHHHHHhccHHHHHHHhCCCHHHHHHHHH
Confidence 9888 55654 4688999999999742 3344 47899999999999999999999999999999999999999999
Q ss_pred hhhhcCceEEEecCCCceEEeccCCChhHHHHHHHHHHHHHHHHHHHHHhhhhH
Q psy4458 240 SMVVSKTITAKIDRPAGIINFARNKDPGEILNEWSASLNELMKLVNNTTHLINK 293 (303)
Q Consensus 240 ~mI~~~~l~akIDq~~giV~f~~~~~~~~~l~~w~~~i~~l~~~v~~~~~lI~k 293 (303)
+||.++|++|.|||.+|+|+|.+. +.+..|+++|.++|+.|+++...|.+
T Consensus 340 ~MI~qeRmng~IDQ~egiihFe~~----e~l~~wdkqi~sl~~qvNki~~~i~~ 389 (399)
T KOG1497|consen 340 QMITQERMNGSIDQIEGIIHFEDR----EELPQWDKQIQSLCNQVNKILDKISH 389 (399)
T ss_pred HHHhHHHhccchHhhcceEeecch----hhhhhhhHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999973 57899999999999999999998876
No 4
>KOG0687|consensus
Probab=100.00 E-value=1.6e-36 Score=271.87 Aligned_cols=265 Identities=17% Similarity=0.222 Sum_probs=225.8
Q ss_pred CCHHHHHHHHhccccccc-cCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHHH
Q psy4458 6 GDVTEAANIIQELQVETY-GSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIEL 84 (303)
Q Consensus 6 ~~~~~Aa~~L~~i~vet~-~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~~ 84 (303)
||.+.|.+.+.. |+ .+++.+.|+|+.+..+||+|+.+|..-....+.|++..+ +++| |||+|+||+.|+|.|
T Consensus 118 gDkena~~~~~~----t~~ktvs~g~kiDVvf~~iRlglfy~D~~lV~~~iekak~li-E~Gg--DWeRrNRlKvY~Gly 190 (393)
T KOG0687|consen 118 GDKENALEALRK----TYEKTVSLGHKIDVVFYKIRLGLFYLDHDLVTESIEKAKSLI-EEGG--DWERRNRLKVYQGLY 190 (393)
T ss_pred ccHHHHHHHHHH----HHHHHhhcccchhhHHHHHHHHHhhccHHHHHHHHHHHHHHH-HhCC--ChhhhhhHHHHHHHH
Confidence 555555555442 33 479999999999999999999999999999999999999 7899 999999999999999
Q ss_pred HHHhhhHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHhCCC-CchhhHhHHHhhhhhh----cCCchHHHHHHHH
Q psy4458 85 DQHEGSYLATCKHYRAILTTPCIQSDPVQRHAVLQNVVLYLMLAPY-DNEQSDLTHRVLEDKL----LNEIPLYKGLLQW 159 (303)
Q Consensus 85 ~~~~~~f~eaa~~y~e~~~t~~~~~~~~~~~~~L~~~v~~~iLs~~-~~~r~~ll~~l~~~~~----~~~~p~~~~L~~~ 159 (303)
.++.|||.+||..|.++..||++.+ +..+..+|.|+++++. ..+|.++.+++.+.|+ +..+|..++++.+
T Consensus 191 ~msvR~Fk~Aa~Lfld~vsTFtS~E-----l~~Y~~~v~Ytv~~g~i~leR~dlktKVi~~~Evl~vl~~l~~~~q~l~S 265 (393)
T KOG0687|consen 191 CMSVRNFKEAADLFLDSVSTFTSYE-----LMSYETFVRYTVITGLIALERVDLKTKVIKCPEVLEVLHKLPSVSQLLNS 265 (393)
T ss_pred HHHHHhHHHHHHHHHHHccccccee-----cccHHHHHHHHHHHhhheeccchHHhhhcCcHHHHHHhhcCchHHHHHHH
Confidence 9999999999999999999998732 3347888999988875 6799999999999886 4678999999999
Q ss_pred hcCCcccCc-hHHHHHHHHhhcccccccccchhHHhHHHHHHHHHHHHHHHHHHhh---hceeeHHHHHHHhCCCHHHHH
Q psy4458 160 FTNPELIKW-SGLRQLYEEELFKTSVFNQSTEEGQKCFKMLKHRVVEHNIRVMAKY---YTRITLQRMCDLLGLPIEETE 235 (303)
Q Consensus 160 f~~~~li~~-~~~~~~~~~~L~~~~~~~~~~~~~~~~~~~l~~~i~ehNi~~isk~---Y~~Itl~~la~ll~ls~~~vE 235 (303)
++.++.-+| +.+.....+.|+.+..+. + | .+--++|-.+++++|+ |++++++.||+.||||++.++
T Consensus 266 LY~C~Y~~Ff~~L~~~~~~~lk~D~~l~-----~--h---~~yyvREMR~rvY~QlLESYrsl~l~~MA~aFgVSVefiD 335 (393)
T KOG0687|consen 266 LYECDYSDFFNDLAAVEAKQLKDDRYLG-----P--H---YRYYVREMRRRVYAQLLESYRSLTLESMAKAFGVSVEFID 335 (393)
T ss_pred HHhccHHHHHHHHHHHHHHhhccchhcc-----h--H---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCchHHHHH
Confidence 988864332 343344467788877663 1 2 2234667777888875 999999999999999999999
Q ss_pred HHHHhhhhcCceEEEecCCCceEEeccCCChhHHHHHHHHHHHHHHHHHHHHHhhhh
Q psy4458 236 EFLSSMVVSKTITAKIDRPAGIINFARNKDPGEILNEWSASLNELMKLVNNTTHLIN 292 (303)
Q Consensus 236 ~~l~~mI~~~~l~akIDq~~giV~f~~~~~~~~~l~~w~~~i~~l~~~v~~~~~lI~ 292 (303)
+.++++|..|+|+|+||+++|+|+.++|+..+.....-.++.+.|++.|+|+++.|+
T Consensus 336 reL~rFI~~grL~ckIDrVnGVVEtNrpD~KN~qyq~vikqGd~LLnriQK~~rvi~ 392 (393)
T KOG0687|consen 336 RELGRFIAAGRLHCKIDRVNGVVETNRPDEKNAQYQAVIKQGDLLLNRIQKLSRVIN 392 (393)
T ss_pred hHHHHhhccCceeeeeecccceeecCCccccchHHHHHHhhhHHHHHHHHHHHHHhc
Confidence 999999999999999999999999999999888888899999999999999999886
No 5
>COG5187 RPN7 26S proteasome regulatory complex component, contains PCI domain [Posttranslational modification, protein turnover, chaperones]
Probab=99.97 E-value=2.3e-30 Score=229.39 Aligned_cols=249 Identities=15% Similarity=0.191 Sum_probs=208.9
Q ss_pred CCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHcC
Q psy4458 25 SMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIELDQHEGSYLATCKHYRAILTT 104 (303)
Q Consensus 25 ~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~~~~~~~~f~eaa~~y~e~~~t 104 (303)
.|+.+-|+|..|..+||++..+|-.-++..+.++++.+ +.+| |||+|+||+.|.+.+.+..|+|.+|+..+.++..|
T Consensus 145 a~stg~KiDv~l~kiRlg~~y~d~~vV~e~lE~~~~~i-EkGg--DWeRrNRyK~Y~Gi~~m~~RnFkeAa~Ll~d~l~t 221 (412)
T COG5187 145 AMSTGLKIDVFLCKIRLGLIYGDRKVVEESLEVADDII-EKGG--DWERRNRYKVYKGIFKMMRRNFKEAAILLSDILPT 221 (412)
T ss_pred HHhcccchhhHHHHHHHHHhhccHHHHHHHHHHHHHHH-HhCC--CHHhhhhHHHHHHHHHHHHHhhHHHHHHHHHHhcc
Confidence 48889999999999999999999999999999999998 7888 99999999999999999999999999999999999
Q ss_pred CCCCCChHHHHHHHHHHHHHHHhCCC-CchhhHhHHHhhhhhhc----CC---chHHHHHHHHhcCCccc-CchHHHHHH
Q psy4458 105 PCIQSDPVQRHAVLQNVVLYLMLAPY-DNEQSDLTHRVLEDKLL----NE---IPLYKGLLQWFTNPELI-KWSGLRQLY 175 (303)
Q Consensus 105 ~~~~~~~~~~~~~L~~~v~~~iLs~~-~~~r~~ll~~l~~~~~~----~~---~p~~~~L~~~f~~~~li-~~~~~~~~~ 175 (303)
|++.+ +..+..+|-|++.++. ..+|.++.+++.++|++ ++ +..+..|..+.+.++.- .|+.....|
T Consensus 222 F~S~E-----l~sY~~~vrYa~~~Gl~~leR~diktki~dspevl~vi~~~e~l~sl~~l~~SLy~cdY~~~F~~ll~~~ 296 (412)
T COG5187 222 FESSE-----LISYSRAVRYAIFCGLLRLERRDIKTKILDSPEVLDVIGSSEKLGSLVQLATSLYECDYGGDFMNLLYLF 296 (412)
T ss_pred ccccc-----cccHHHHHHHHHHhhhheeehhhhhhhhcCCHHHHHhccchhhhhhHHHHHHHHHHhccchhhHHHHHHH
Confidence 98732 3346778888888774 67999999999999862 22 33334555555555443 467777888
Q ss_pred HHhhcccccccccchhHHhHHHHHHHHHHHHHHHHHHhh---hceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEec
Q psy4458 176 EEELFKTSVFNQSTEEGQKCFKMLKHRVVEHNIRVMAKY---YTRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKID 252 (303)
Q Consensus 176 ~~~L~~~~~~~~~~~~~~~~~~~l~~~i~ehNi~~isk~---Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akID 252 (303)
...|+++..+. .|+.. -++|...++++|. |+.++++.||+.||+|++.++.-++++|.+|+|+|+||
T Consensus 297 ~n~L~~d~fl~-------rh~d~---fvREMRrrvYaQlLESYr~lsl~sMA~tFgVSV~yvdrDLg~FIp~~~LncvID 366 (412)
T COG5187 297 CNSLQDDVFLG-------RHVDL---FVREMRRRVYAQLLESYRLLSLESMAQTFGVSVEYVDRDLGEFIPEGRLNCVID 366 (412)
T ss_pred HhhccchHHHH-------HHHHH---HHHHHHHHHHHHHHHHHHHhhHHHHHHHhCccHHHHhhhHHhhCCCCceeeeee
Confidence 88888887642 22322 3455555777765 99999999999999999999999999999999999999
Q ss_pred CCCceEEeccCCChhHHHHHHHHHHHHHHHHHHHHHhhh
Q psy4458 253 RPAGIINFARNKDPGEILNEWSASLNELMKLVNNTTHLI 291 (303)
Q Consensus 253 q~~giV~f~~~~~~~~~l~~w~~~i~~l~~~v~~~~~lI 291 (303)
|++|+|+.++|+..+.....-.++.+.|+..++|....+
T Consensus 367 RvnGvVetnrpdekn~qy~~vVkqGd~ll~klqKy~atv 405 (412)
T COG5187 367 RVNGVVETNRPDEKNQQYSSVVKQGDDLLRKLQKYVATV 405 (412)
T ss_pred cccceEeccCcchhhhhHHHHHhcchHHHHHHHHHHHHH
Confidence 999999999999888888889999999999999876544
No 6
>KOG1463|consensus
Probab=99.93 E-value=2.4e-25 Score=201.12 Aligned_cols=222 Identities=18% Similarity=0.233 Sum_probs=180.1
Q ss_pred HHHHHHHHhhcchhHHHHHHHHhhhhccCCCC-c-----chHHHHHHH--------------------------------
Q psy4458 36 LEQMRLCLAKKDYIRTQIISKKINTKFFDDEK-D-----DVQELKLKY-------------------------------- 77 (303)
Q Consensus 36 L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~-~-----~~~e~k~~y-------------------------------- 77 (303)
-+.++||+..++|..|...++.+.+.+-.-++ + ...|-|.-|
T Consensus 132 arli~Ly~d~~~YteAlaL~~~L~rElKKlDDK~lLvev~llESK~y~~l~Nl~KakasLTsART~AnaiYcpPqlQa~l 211 (411)
T KOG1463|consen 132 ARLIRLYNDTKRYTEALALINDLLRELKKLDDKILLVEVHLLESKAYHALRNLPKAKASLTSARTTANAIYCPPQLQATL 211 (411)
T ss_pred HHHHHHHHhhHHHHHHHHHHHHHHHHHHhcccccceeeehhhhhHHHHHHhcchhHHHHHHHHHHhhcccccCHHHHHHH
Confidence 45688999999999998877666543311111 0 011222211
Q ss_pred HHHHHHHHHHhhhHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHhCCCCchhhHhHHHhhh-hhhcCCchHHHHH
Q psy4458 78 YRLMIELDQHEGSYLATCKHYRAILTTPCIQSDPVQRHAVLQNVVLYLMLAPYDNEQSDLTHRVLE-DKLLNEIPLYKGL 156 (303)
Q Consensus 78 ~~~~~~~~~~~~~f~eaa~~y~e~~~t~~~~~~~~~~~~~L~~~v~~~iLs~~~~~r~~ll~~l~~-~~~~~~~p~~~~L 156 (303)
...-|.+|.+++||..|+++|+|+|++|++..++.++..+|+||++|.|+.+...+-..+++.-.. ....+.+.+|+..
T Consensus 212 DLqSGIlha~ekDykTafSYFyEAfEgf~s~~~~v~A~~sLKYMlLcKIMln~~ddv~~lls~K~~l~y~g~~i~Amkav 291 (411)
T KOG1463|consen 212 DLQSGILHAAEKDYKTAFSYFYEAFEGFDSLDDDVKALTSLKYMLLCKIMLNLPDDVAALLSAKLALKYAGRDIDAMKAV 291 (411)
T ss_pred HHhccceeecccccchHHHHHHHHHccccccCCcHHHHHHHHHHHHHHHHhcCHHHHHHHHhhHHHHhccCcchHHHHHH
Confidence 122268889999999999999999999998766678899999999999999987766666553321 2234678899999
Q ss_pred HHHhcCCcccCchHHHHHHHHhhcccccccccchhHHhHHHHHHHHHHHHHHHHHHhhhceeeHHHHHHHhCCCHHHHHH
Q psy4458 157 LQWFTNPELIKWSGLRQLYEEELFKTSVFNQSTEEGQKCFKMLKHRVVEHNIRVMAKYYTRITLQRMCDLLGLPIEETEE 236 (303)
Q Consensus 157 ~~~f~~~~li~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~~l~~~i~ehNi~~isk~Y~~Itl~~la~ll~ls~~~vE~ 236 (303)
..+|.+|+|.+|...+..|.+.|..++++ +.|...|..+++|.|+-++..||++|.++.+|+.+|++.+.||+
T Consensus 292 AeA~~nRSLkdF~~AL~~yk~eL~~D~iv-------r~Hl~~Lyd~lLEknl~riIEPyS~Vei~hIA~~IGl~~~~VEk 364 (411)
T KOG1463|consen 292 AEAFGNRSLKDFEKALADYKKELAEDPIV-------RSHLQSLYDNLLEKNLCRIIEPYSRVEISHIAEVIGLDVPQVEK 364 (411)
T ss_pred HHHhcCCcHHHHHHHHHHhHHHHhcChHH-------HHHHHHHHHHHHHHhHHHHcCchhhhhHHHHHHHHCCCcHHHHH
Confidence 99999999999999999999999999986 46899999999999999999999999999999999999999999
Q ss_pred HHHhhhhcCceEEEecCCCce-EEeccCC
Q psy4458 237 FLSSMVVSKTITAKIDRPAGI-INFARNK 264 (303)
Q Consensus 237 ~l~~mI~~~~l~akIDq~~gi-V~f~~~~ 264 (303)
.+++||.++++.|.+||.+|. |.|+.|.
T Consensus 365 KLsqMILDKkf~G~LDQg~g~Liv~~e~~ 393 (411)
T KOG1463|consen 365 KLSQMILDKKFYGTLDQGEGCLIVFEEPP 393 (411)
T ss_pred HHHHHHHHHHhhcccccCCCeEEEeCCCC
Confidence 999999999999999999999 5666553
No 7
>KOG1464|consensus
Probab=99.91 E-value=6.5e-24 Score=187.62 Aligned_cols=227 Identities=20% Similarity=0.352 Sum_probs=180.8
Q ss_pred HHHHHHHHhhcchhHHHHHHHHhhhhccCCCCc------------------------chHHHHHHHHHHH----------
Q psy4458 36 LEQMRLCLAKKDYIRTQIISKKINTKFFDDEKD------------------------DVQELKLKYYRLM---------- 81 (303)
Q Consensus 36 L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~------------------------~~~e~k~~y~~~~---------- 81 (303)
.+...|++..++|.+.+.++++.+..|..++|+ +++.+|--|....
T Consensus 149 tKLgkl~fd~~e~~kl~KIlkqLh~SCq~edGedD~kKGtQLLEiYAlEIQmYT~qKnNKkLK~lYeqalhiKSAIPHPl 228 (440)
T KOG1464|consen 149 TKLGKLYFDRGEYTKLQKILKQLHQSCQTEDGEDDQKKGTQLLEIYALEIQMYTEQKNNKKLKALYEQALHIKSAIPHPL 228 (440)
T ss_pred chHhhhheeHHHHHHHHHHHHHHHHHhccccCchhhhccchhhhhHhhHhhhhhhhcccHHHHHHHHHHHHhhccCCchH
Confidence 567889999999999999999999999777662 3444444443222
Q ss_pred ----------------HHHHHHhhhHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHhC-----CCCchhhHhHHH
Q psy4458 82 ----------------IELDQHEGSYLATCKHYRAILTTPCIQSDPVQRHAVLQNVVLYLMLA-----PYDNEQSDLTHR 140 (303)
Q Consensus 82 ----------------~~~~~~~~~f~eaa~~y~e~~~t~~~~~~~~~~~~~L~~~v~~~iLs-----~~~~~r~~ll~~ 140 (303)
+++..+-.||++||+.|.|+ ++..+.+||+|+|++.+|. |++.+.. +
T Consensus 229 ImGvIRECGGKMHlreg~fe~AhTDFFEAFKNYDEs--------GspRRttCLKYLVLANMLmkS~iNPFDsQEA----K 296 (440)
T KOG1464|consen 229 IMGVIRECGGKMHLREGEFEKAHTDFFEAFKNYDES--------GSPRRTTCLKYLVLANMLMKSGINPFDSQEA----K 296 (440)
T ss_pred HHhHHHHcCCccccccchHHHHHhHHHHHHhccccc--------CCcchhHHHHHHHHHHHHHHcCCCCCccccc----C
Confidence 36666677777788887777 6678899999999999997 4555554 4
Q ss_pred hhhhhhcCCchHHHHHHHHhcCCcccCchHHHHHHHHhhcccc--cccccchhHHhHHHHHHHHHHHHHHHHHHhhhcee
Q psy4458 141 VLEDKLLNEIPLYKGLLQWFTNPELIKWSGLRQLYEEELFKTS--VFNQSTEEGQKCFKMLKHRVVEHNIRVMAKYYTRI 218 (303)
Q Consensus 141 l~~~~~~~~~p~~~~L~~~f~~~~li~~~~~~~~~~~~L~~~~--~~~~~~~~~~~~~~~l~~~i~ehNi~~isk~Y~~I 218 (303)
.+++ -+++-+|..|+.+|.+++++ +|++.|+.|+ ++.+++ ..+|..+|.+.++.+.+..+.+||++|
T Consensus 297 PyKN--dPEIlAMTnlv~aYQ~NdI~-------eFE~Il~~~~~~IM~DpF--IReh~EdLl~niRTQVLlkLIkPYt~i 365 (440)
T KOG1464|consen 297 PYKN--DPEILAMTNLVAAYQNNDII-------EFERILKSNRSNIMDDPF--IREHIEDLLRNIRTQVLLKLIKPYTNI 365 (440)
T ss_pred CCCC--CHHHHHHHHHHHHHhcccHH-------HHHHHHHhhhccccccHH--HHHHHHHHHHHHHHHHHHHHhcccccc
Confidence 5542 25677899999999999874 4566666554 222222 246789999999999999999999999
Q ss_pred eHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCCCceEEeccCCC----hhHHHHHHHHHHHHHHHHHH
Q psy4458 219 TLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAGIINFARNKD----PGEILNEWSASLNELMKLVN 285 (303)
Q Consensus 219 tl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~giV~f~~~~~----~~~~l~~w~~~i~~l~~~v~ 285 (303)
.+..|++.+++++.+|+.+++++|.+.+|.|+||++++++...+.++ ..++++.|.+++.++...|-
T Consensus 366 ~Ipfis~~Lnv~~~dV~~LLV~~ILD~~i~g~Ide~n~~l~~~~~~~s~~k~~~al~kW~~ql~Sl~~~i~ 436 (440)
T KOG1464|consen 366 GIPFISKELNVPEADVESLLVSCILDDTIDGRIDEVNQYLELDKSKNSGSKLYKALDKWNNQLKSLQSNIV 436 (440)
T ss_pred CchhhHhhcCCCHHHHHHHHHHHHhccccccchHHhhhHhccCccCCcchHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999877543 36789999999999987764
No 8
>COG5159 RPN6 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=99.84 E-value=8.9e-20 Score=162.21 Aligned_cols=248 Identities=17% Similarity=0.187 Sum_probs=181.5
Q ss_pred cCCHHHHHHHHhccccccccCCchH-HHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHH
Q psy4458 5 EGDVTEAANIIQELQVETYGSMEKK-EKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIE 83 (303)
Q Consensus 5 ~~~~~~Aa~~L~~i~vet~~~~~~~-~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~ 83 (303)
.|.+.+|...+..+--|- ..++++ .=++..|---+.|-+-....+++..+.-+....-..-- ..++.-.....-|.
T Consensus 138 ~~~YsdalalIn~ll~El-Kk~DDK~~Li~vhllESKvyh~irnv~KskaSLTaArt~Ans~YC--Ppqlqa~lDL~sGI 214 (421)
T COG5159 138 TGKYSDALALINPLLHEL-KKYDDKINLITVHLLESKVYHEIRNVSKSKASLTAARTLANSAYC--PPQLQAQLDLLSGI 214 (421)
T ss_pred cccHHHHHHHHHHHHHHH-HhhcCccceeehhhhhHHHHHHHHhhhhhhhHHHHHHHHhhccCC--CHHHHHHHHHhccc
Confidence 466777776666654432 222211 11233333334444444444444444333322211101 23455566667899
Q ss_pred HHHHhhhHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHhCCCCchhhHhHHHhhhhh--hcCCchHHHHHHHHhc
Q psy4458 84 LDQHEGSYLATCKHYRAILTTPCIQSDPVQRHAVLQNVVLYLMLAPYDNEQSDLTHRVLEDK--LLNEIPLYKGLLQWFT 161 (303)
Q Consensus 84 ~~~~~~~f~eaa~~y~e~~~t~~~~~~~~~~~~~L~~~v~~~iLs~~~~~r~~ll~~l~~~~--~~~~~p~~~~L~~~f~ 161 (303)
+++..+||..|+++|.|++++|+...+..++...|+|+++..|+...-.+-..+++.-+.-+ ..+.+.+|.....+|-
T Consensus 215 lhcdd~dyktA~SYF~Ea~Egft~l~~d~kAc~sLkYmlLSkIMlN~~~evk~vl~~K~t~~~y~~r~I~am~avaea~~ 294 (421)
T COG5159 215 LHCDDRDYKTASSYFIEALEGFTLLKMDVKACVSLKYMLLSKIMLNRREEVKAVLRNKNTLKHYDDRMIRAMLAVAEAFG 294 (421)
T ss_pred eeeccccchhHHHHHHHHHhccccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHccchhHhhhhhhhHHHHHHHHHHhC
Confidence 99999999999999999999999876666777889999999999876444433333222111 1245888999999999
Q ss_pred CCcccCchHHHHHHHHhhcccccccccchhHHhHHHHHHHHHHHHHHHHHHhhhceeeHHHHHHHhCCCHHHHHHHHHhh
Q psy4458 162 NPELIKWSGLRQLYEEELFKTSVFNQSTEEGQKCFKMLKHRVVEHNIRVMAKYYTRITLQRMCDLLGLPIEETEEFLSSM 241 (303)
Q Consensus 162 ~~~li~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~~l~~~i~ehNi~~isk~Y~~Itl~~la~ll~ls~~~vE~~l~~m 241 (303)
+|+|.+|.+..+.|++.|..+++. ..|+.-|...++|.|+..+..||+.+.++.||+.+|++..++|..+++|
T Consensus 295 NRsL~df~~aL~qY~~el~~D~~i-------RsHl~~LYD~LLe~Nl~kiiEPfs~VeishIa~viGldt~qvEgKLsqM 367 (421)
T COG5159 295 NRSLKDFSDALAQYSDELHQDSFI-------RSHLQYLYDVLLEKNLVKIIEPFSVVEISHIADVIGLDTNQVEGKLSQM 367 (421)
T ss_pred CCcHhhHHHHHHHhhHHhccCHHH-------HHHHHHHHHHHHHhhhhhhcCcceeeehhHHHHHhcccHHHHHHHHHHH
Confidence 999999999999999999888764 4688999999999999999999999999999999999999999999999
Q ss_pred hhcCceEEEecCCCceEEecc
Q psy4458 242 VVSKTITAKIDRPAGIINFAR 262 (303)
Q Consensus 242 I~~~~l~akIDq~~giV~f~~ 262 (303)
|.++-++|..||.+|.+....
T Consensus 368 ILDKifyG~LDqg~gcLivy~ 388 (421)
T COG5159 368 ILDKIFYGTLDQGDGCLIVYG 388 (421)
T ss_pred HHHHHHHhhhccCCceEEEeC
Confidence 999999999999999965543
No 9
>KOG2908|consensus
Probab=99.79 E-value=4.6e-17 Score=147.66 Aligned_cols=270 Identities=15% Similarity=0.234 Sum_probs=200.1
Q ss_pred CccCCHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHH-HHHHHHHHH
Q psy4458 3 EDEGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQE-LKLKYYRLM 81 (303)
Q Consensus 3 e~~~~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e-~k~~y~~~~ 81 (303)
|.-+|.++|...|.+|-=.+-..=.+..-+-+..+++|++|+.+|...++..+.......-.-++ ... ....||..-
T Consensus 86 ~~~~D~~~al~~Le~i~~~~~~~~e~~av~~~~t~~~r~~L~i~DLk~~kk~ldd~~~~ld~~~~--v~~~Vh~~fY~ls 163 (380)
T KOG2908|consen 86 EQISDKDEALEFLEKIIEKLKEYKEPDAVIYILTEIARLKLEINDLKEIKKLLDDLKSMLDSLDG--VTSNVHSSFYSLS 163 (380)
T ss_pred HHhccHHHHHHHHHHHHHHHHhhccchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHhcccC--CChhhhhhHHHHH
Confidence 34568899999999885444322233466677899999999999999999999999876633344 333 566999999
Q ss_pred HHHHHHhhhHHHHH---HHHHHHHcCCCCCCChHHHHHHHHHHHHHHHhCCC----Cc-hhhHhHHHhhhhhhcCCchHH
Q psy4458 82 IELDQHEGSYLATC---KHYRAILTTPCIQSDPVQRHAVLQNVVLYLMLAPY----DN-EQSDLTHRVLEDKLLNEIPLY 153 (303)
Q Consensus 82 ~~~~~~~~~f~eaa---~~y~e~~~t~~~~~~~~~~~~~L~~~v~~~iLs~~----~~-~r~~ll~~l~~~~~~~~~p~~ 153 (303)
..||...+||...+ ..|+.+++.... ..+++...--.+.++++|+.- |. --+.++.++.. .+..-+
T Consensus 164 sqYyk~~~d~a~yYr~~L~YL~~~d~~~l--~~se~~~lA~~L~~aALLGe~iyNfGELL~HPilesL~g----T~~eWL 237 (380)
T KOG2908|consen 164 SQYYKKIGDFASYYRHALLYLGCSDIDDL--SESEKQDLAFDLSLAALLGENIYNFGELLAHPILESLKG----TNREWL 237 (380)
T ss_pred HHHHHHHHhHHHHHHHHHHHhcccccccc--CHHHHHHHHHHHHHHHHhccccccHHHHHhhHHHHHhcC----CcHHHH
Confidence 99999999998854 456666544333 345556655678999999972 32 23333333332 233347
Q ss_pred HHHHHHhcCCcccCchHHHHHHHH--hhcccccccccchhHHhHHHHHHHHHHHHHHHHHHhh--hceeeHHHHHHHhCC
Q psy4458 154 KGLLQWFTNPELIKWSGLRQLYEE--ELFKTSVFNQSTEEGQKCFKMLKHRVVEHNIRVMAKY--YTRITLQRMCDLLGL 229 (303)
Q Consensus 154 ~~L~~~f~~~~li~~~~~~~~~~~--~L~~~~~~~~~~~~~~~~~~~l~~~i~ehNi~~isk~--Y~~Itl~~la~ll~l 229 (303)
.+++.+|..+++.+|.+....+.+ .|..+..+ -..+.-..+++| .++++| =++|||+.||++..+
T Consensus 238 ~dll~Afn~Gdl~~f~~l~~~~~~~p~L~~~e~~--------L~qKI~LmaLiE---i~F~rpa~~R~lsf~~Ia~~tki 306 (380)
T KOG2908|consen 238 KDLLIAFNSGDLKRFESLKGVWGKQPDLASNEDF--------LLQKIRLLALIE---ITFSRPANERTLSFKEIAEATKI 306 (380)
T ss_pred HHHHHHhccCCHHHHHHHHHHhccCchHHHHHHH--------HHHHHHHHHHHH---HHhcCcchhccccHHHHHHHhCC
Confidence 889999999999777655554433 33333321 122445566777 777885 889999999999999
Q ss_pred CHHHHHHHHHhhhhcCceEEEecCCCceEEeccCCC----------hhHHHHHHHHHHHHHHHHHHHHHhhh
Q psy4458 230 PIEETEEFLSSMVVSKTITAKIDRPAGIINFARNKD----------PGEILNEWSASLNELMKLVNNTTHLI 291 (303)
Q Consensus 230 s~~~vE~~l~~mI~~~~l~akIDq~~giV~f~~~~~----------~~~~l~~w~~~i~~l~~~v~~~~~lI 291 (303)
|.++||.++++.++-|-|.|.|||++|+|++.|.++ +.+.+..|.++|.++-..|+..+|.|
T Consensus 307 p~~eVE~LVMKAlslgLikG~Idqv~~~v~~swvqPRvl~~~qI~~Mk~rl~~W~~~v~~me~~ve~~~~~i 378 (380)
T KOG2908|consen 307 PNKEVELLVMKALSLGLIKGSIDQVEGVVYMSWVQPRVLDRSQIVKMKDRLDEWNKDVKSMEGLVEHRGHEI 378 (380)
T ss_pred CHHHHHHHHHHHHhccceeeeecccccEEEEecccccccCHHHHHhHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence 999999999999999999999999999999999766 35779999999999999999988876
No 10
>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=99.71 E-value=6.4e-17 Score=125.74 Aligned_cols=105 Identities=29% Similarity=0.511 Sum_probs=85.4
Q ss_pred hHHHHHHHHhcCCcccCchHHHHHHHHhhcccccccccchhHHhHHHHHHHHHHHHHHHHHHhhhceeeHHHHHHHhCCC
Q psy4458 151 PLYKGLLQWFTNPELIKWSGLRQLYEEELFKTSVFNQSTEEGQKCFKMLKHRVVEHNIRVMAKYYTRITLQRMCDLLGLP 230 (303)
Q Consensus 151 p~~~~L~~~f~~~~li~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~~l~~~i~ehNi~~isk~Y~~Itl~~la~ll~ls 230 (303)
|.|..|+++|.++++..|.+....+...+..++.+ ..+...++..+++++++.++++|++|+++.||++++++
T Consensus 1 ~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~l-------~~~~~~l~~~i~~~~l~~l~~~y~~i~~~~ia~~l~~~ 73 (105)
T PF01399_consen 1 PPYSELLRAFRSGDLQEFEEFLEKHSESLFKDPFL-------AEYVEQLKEKIRRRNLRQLSKPYSSISISEIAKALQLS 73 (105)
T ss_dssp HHHHHHHHHHHCT-HHHHHHHHHHTCHHHHHCTTH-------HHHHHHHHHHHHHHHHHHHHHC-SEEEHHHHHHHHTCC
T ss_pred CHHHHHHHHHHhCCHHHHHHHHHHHHHHHHcCccH-------HHHHHHHHHHHHHHHHHHHHHHhcccchHHHHHHhccc
Confidence 78999999999998766655555541212222222 23578899999999999999999999999999999999
Q ss_pred HHHHHHHHHhhhhcCceEEEecCCCceEEecc
Q psy4458 231 IEETEEFLSSMVVSKTITAKIDRPAGIINFAR 262 (303)
Q Consensus 231 ~~~vE~~l~~mI~~~~l~akIDq~~giV~f~~ 262 (303)
.+++|..+++||.+|.|.|+|||++|+|+|++
T Consensus 74 ~~~vE~~l~~~I~~~~i~~~ID~~~~~v~~~k 105 (105)
T PF01399_consen 74 EEEVESILIDLISNGLIKAKIDQVNGVVVFSK 105 (105)
T ss_dssp HHHHHHHHHHHHHTTSSEEEEETTTTEEEE-S
T ss_pred hHHHHHHHHHHHHCCCEEEEEECCCCEEEecC
Confidence 99999999999999999999999999999975
No 11
>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=99.58 E-value=1.5e-14 Score=109.44 Aligned_cols=72 Identities=28% Similarity=0.491 Sum_probs=67.8
Q ss_pred HHHHHHHHHHHHHHHHHHhhhceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCCCceEEeccCCCh
Q psy4458 195 CFKMLKHRVVEHNIRVMAKYYTRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAGIINFARNKDP 266 (303)
Q Consensus 195 ~~~~l~~~i~ehNi~~isk~Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~giV~f~~~~~~ 266 (303)
++..+...++.+++..++++|++|+++.||+.|++|.+++|..+++||.+|.|.|+|||.+|+|+|.+..+.
T Consensus 2 ~~~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~~~r 73 (88)
T smart00088 2 LVERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEVDPR 73 (88)
T ss_pred hHHHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCCchh
Confidence 356788899999999999999999999999999999999999999999999999999999999999987654
No 12
>smart00753 PAM PCI/PINT associated module.
Probab=99.58 E-value=1.5e-14 Score=109.44 Aligned_cols=72 Identities=28% Similarity=0.491 Sum_probs=67.8
Q ss_pred HHHHHHHHHHHHHHHHHHhhhceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCCCceEEeccCCCh
Q psy4458 195 CFKMLKHRVVEHNIRVMAKYYTRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAGIINFARNKDP 266 (303)
Q Consensus 195 ~~~~l~~~i~ehNi~~isk~Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~giV~f~~~~~~ 266 (303)
++..+...++.+++..++++|++|+++.||+.|++|.+++|..+++||.+|.|.|+|||.+|+|+|.+..+.
T Consensus 2 ~~~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~~~r 73 (88)
T smart00753 2 LVERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEVDPR 73 (88)
T ss_pred hHHHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCCchh
Confidence 356788899999999999999999999999999999999999999999999999999999999999987654
No 13
>KOG0686|consensus
Probab=99.58 E-value=4.6e-14 Score=130.92 Aligned_cols=248 Identities=14% Similarity=0.159 Sum_probs=180.7
Q ss_pred CccCCHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHH
Q psy4458 3 EDEGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMI 82 (303)
Q Consensus 3 e~~~~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~ 82 (303)
.+.|+++.|.+-...+. +-++ +.++-+++++..|++.+..++|..+-.+++++.... .......++.--+.+-+.+
T Consensus 161 ~~cG~l~~Alr~YsR~R-dYCT--s~khvInm~ln~i~VSI~~~nw~hv~sy~~~A~st~-~~~~~~~q~v~~kl~C~ag 236 (466)
T KOG0686|consen 161 LDCGQLDNALRCYSRAR-DYCT--SAKHVINMCLNLILVSIYMGNWGHVLSYISKAESTP-DANENLAQEVPAKLKCAAG 236 (466)
T ss_pred HHhccHHHHHhhhhhhh-hhhc--chHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHhCc-hhhhhHHHhcCcchHHHHH
Confidence 45788999988887732 3334 567999999999999999999999999999998764 1111001222224555678
Q ss_pred HHHHHhhhHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHhCC-CCchhhHhHHHhhhhh----hcCCchHHHHHH
Q psy4458 83 ELDQHEGSYLATCKHYRAILTTPCIQSDPVQRHAVLQNVVLYLMLAP-YDNEQSDLTHRVLEDK----LLNEIPLYKGLL 157 (303)
Q Consensus 83 ~~~~~~~~f~eaa~~y~e~~~t~~~~~~~~~~~~~L~~~v~~~iLs~-~~~~r~~ll~~l~~~~----~~~~~p~~~~L~ 157 (303)
..+...++|..|+++|+.+--+.. | ..++-+-.+..+|+.|+. ++..|.+++..+..+. .++-.|.++.++
T Consensus 237 La~L~lkkyk~aa~~fL~~~~~~~---d-~~~ivtpsdv~iYggLcALAtfdr~~Lk~~vi~n~~Fk~flel~Pqlr~il 312 (466)
T KOG0686|consen 237 LANLLLKKYKSAAKYFLLAEFDHC---D-YPEIVTPSDVAIYGGLCALATFDRQDLKLNVIKNESFKLFLELEPQLREIL 312 (466)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCcc---C-ccceecchhhHHHHhhHhhccCCHHHHHHHHHcchhhhhHHhcChHHHHHH
Confidence 888889999999999998743221 2 123444566667766654 4557888886666543 346689999999
Q ss_pred HHhcCCcccCchHHHHHHHHhhcccccccccchhHHhHHHHHHHHHHHHHHHHHHhhhceeeHHHHHHHhCCCHHHHHHH
Q psy4458 158 QWFTNPELIKWSGLRQLYEEELFKTSVFNQSTEEGQKCFKMLKHRVVEHNIRVMAKYYTRITLQRMCDLLGLPIEETEEF 237 (303)
Q Consensus 158 ~~f~~~~li~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~~l~~~i~ehNi~~isk~Y~~Itl~~la~ll~ls~~~vE~~ 237 (303)
..|+++ +|...++ +-..++++-.+ +..- ..|...|..-|+++-+..+-.||+++.+++||..||.|+.++|+.
T Consensus 313 ~~fy~s---ky~~cl~-~L~~~k~~llL-D~yL--aphVd~Ly~~IR~r~llqy~~py~s~~m~~mA~af~~sv~~le~~ 385 (466)
T KOG0686|consen 313 FKFYSS---KYASCLE-LLREIKPRLLL-DMYL--APHVDNLYSLIRNRALLQYLSPYSSADMSKMAEAFNTSVAILESE 385 (466)
T ss_pred HHHhhh---hHHHHHH-HHHHhccceee-chhc--chhHHHHHHHHHHhhHHHhcCccccchHHHHHHHhcccHHHHHHH
Confidence 999988 4543332 22334444333 2111 134677888888877777888999999999999999999999999
Q ss_pred HHhhhhcCceEEEecCCCceEEeccCCC
Q psy4458 238 LSSMVVSKTITAKIDRPAGIINFARNKD 265 (303)
Q Consensus 238 l~~mI~~~~l~akIDq~~giV~f~~~~~ 265 (303)
+.++|.+|+|.||||+.++++.....++
T Consensus 386 l~~LI~~~~i~~rIDs~~ki~~~~~~~~ 413 (466)
T KOG0686|consen 386 LLELILEGKISGRIDSHNKILYARDADS 413 (466)
T ss_pred HHHHHHccchheeeccccceeeeccccc
Confidence 9999999999999999999998876543
No 14
>PF10602 RPN7: 26S proteasome subunit RPN7; InterPro: IPR019585 This entry represents the regulatory subunit RPN7 (known as the non-ATPase regulatory subunit 6 in higher eukaryotes) of the 26S proteasome. This entry also matches the evolutionarily related subunit 1 of the COP9 signalosome complex (CSN) from Arabidopsis []. The 26S proteasome plays a major role in ATP-dependent degradation of ubiquitinated proteins. Substrate specificity is conferred by the regulatory particle (RP), which can dissociate into stable lid and base subcomplexes. The regulatory subunit RPN7 is one of the lid subunits of the 26S proteasome and has been shown in Saccharomyces cerevisiae (Baker's yeast) to be required for structural integrity []. The COP9 signalosome is a conserved protein complex composed of eight subunits, where Individual subunits of the complex have been linked to various signal transduction pathways leading to gene expression and cell cycle control []. The overall organisation and the amino acid sequences of the COP9 signalosome subunits resemble the lid subcomplex of the 19 S regulatory particle for the 26 S proteasome []. COP9 subunit 1 (CSN1 or GPS1) of the COP9 complex is an essential subunit of the complex with regard to both structural integrity and functionality. The N-terminal region of subunit 1 (CSN1-N) can inhibit c-fos expression from either a transfected template or a chromosomal transgene (fos-lacZ), and may contain the activity domain that confers most of the repression functions of CSN1. The C-terminal region of subunit 1 (CSN1-C) allows integration of the protein into the COP9 signalosome.
Probab=99.48 E-value=2.1e-13 Score=116.60 Aligned_cols=129 Identities=12% Similarity=0.093 Sum_probs=109.3
Q ss_pred CccCCHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHH
Q psy4458 3 EDEGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMI 82 (303)
Q Consensus 3 e~~~~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~ 82 (303)
.+-||+.+|.+.+..+.- ...+.+.|++++|.++|++++.+||..+..++.|+.... +.+| +|+++++++.|.|
T Consensus 47 ~~~Gd~~~A~k~y~~~~~---~~~~~~~~id~~l~~irv~i~~~d~~~v~~~i~ka~~~~-~~~~--d~~~~nrlk~~~g 120 (177)
T PF10602_consen 47 CKIGDLEEALKAYSRARD---YCTSPGHKIDMCLNVIRVAIFFGDWSHVEKYIEKAESLI-EKGG--DWERRNRLKVYEG 120 (177)
T ss_pred HHhhhHHHHHHHHHHHhh---hcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHH-hccc--hHHHHHHHHHHHH
Confidence 356999999999988542 467899999999999999999999999999999999988 6677 8999999999999
Q ss_pred HHHHHhhhHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHhCC-CCchhhHhHH
Q psy4458 83 ELDQHEGSYLATCKHYRAILTTPCIQSDPVQRHAVLQNVVLYLMLAP-YDNEQSDLTH 139 (303)
Q Consensus 83 ~~~~~~~~f~eaa~~y~e~~~t~~~~~~~~~~~~~L~~~v~~~iLs~-~~~~r~~ll~ 139 (303)
.++...|+|.+||+.|+++..|++.. +.. .+-.+..+++|++|+. .+.+|++|.+
T Consensus 121 L~~l~~r~f~~AA~~fl~~~~t~~~~-~~~-el~s~~d~a~Y~~l~aLat~~R~eLk~ 176 (177)
T PF10602_consen 121 LANLAQRDFKEAAELFLDSLSTFTSL-QYT-ELISYNDFAIYGGLCALATLDRSELKK 176 (177)
T ss_pred HHHHHhchHHHHHHHHHccCcCCCCC-chh-hhcCHHHHHHHHHHHHHHhCCHHHHcc
Confidence 99999999999999999999998741 112 2445788888888876 4678887754
No 15
>KOG2581|consensus
Probab=99.43 E-value=1.6e-11 Score=114.22 Aligned_cols=236 Identities=19% Similarity=0.223 Sum_probs=171.7
Q ss_pred HHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHcC-CCCCCChH
Q psy4458 34 LILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIELDQHEGSYLATCKHYRAILTT-PCIQSDPV 112 (303)
Q Consensus 34 ~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~~~~~~~~f~eaa~~y~e~~~t-~~~~~~~~ 112 (303)
++--+.|.||-.+-|++|...+.|..- ++... + ..--||.-|.+++...+.+|.+|.+++..+.-- |... --.
T Consensus 211 LiN~LLr~yL~n~lydqa~~lvsK~~~--pe~~s--n-ne~ARY~yY~GrIkaiqldYssA~~~~~qa~rkapq~~-alG 284 (493)
T KOG2581|consen 211 LINLLLRNYLHNKLYDQADKLVSKSVY--PEAAS--N-NEWARYLYYLGRIKAIQLDYSSALEYFLQALRKAPQHA-ALG 284 (493)
T ss_pred HHHHHHHHHhhhHHHHHHHHHhhcccC--ccccc--c-HHHHHHHHHHhhHHHhhcchhHHHHHHHHHHHhCcchh-hhh
Confidence 445578999999999999998888762 12211 1 133678888999999999999999999999732 2110 001
Q ss_pred HHHHHHHHHHHHHHhCCCCchhhHhHHHhhhhhhcCCchHHHHHHHHhcCCcccCchHHHHHHHHhhcccccccccchhH
Q psy4458 113 QRHAVLQNVVLYLMLAPYDNEQSDLTHRVLEDKLLNEIPLYKGLLQWFTNPELIKWSGLRQLYEEELFKTSVFNQSTEEG 192 (303)
Q Consensus 113 ~~~~~L~~~v~~~iLs~~~~~r~~ll~~l~~~~~~~~~p~~~~L~~~f~~~~li~~~~~~~~~~~~L~~~~~~~~~~~~~ 192 (303)
-+.++-+.+|+-.+|.+.-|+|+-.-+..++ +.+-.|-.|.++--.++|.+|.+..+.|.+.+..+..+.
T Consensus 285 f~q~v~k~~ivv~ll~geiPers~F~Qp~~~----ksL~~Yf~Lt~AVr~gdlkkF~~~leq~k~~f~~D~ty~------ 354 (493)
T KOG2581|consen 285 FRQQVNKLMIVVELLLGEIPERSVFRQPGMR----KSLRPYFKLTQAVRLGDLKKFNETLEQFKDKFQADGTYT------ 354 (493)
T ss_pred HHHHHHHHHHHHHHHcCCCcchhhhcCccHH----HHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHhhCCcch------
Confidence 2234556677777888888888744433332 124445568888888889889888888988777766542
Q ss_pred HhHHHHHHHHHHHHHHHHHHhhhceeeHHHHHHHhCCC-HHHHHHHHHhhhhcCceEEEecCCCceEEeccCC---ChhH
Q psy4458 193 QKCFKMLKHRVVEHNIRVMAKYYTRITLQRMCDLLGLP-IEETEEFLSSMVVSKTITAKIDRPAGIINFARNK---DPGE 268 (303)
Q Consensus 193 ~~~~~~l~~~i~ehNi~~isk~Y~~Itl~~la~ll~ls-~~~vE~~l~~mI~~~~l~akIDq~~giV~f~~~~---~~~~ 268 (303)
-.-.|+.+++..-||.||=.||+|++..||..|+++ ++++|-++++.|.+|-|.|+||-.+|.+.....- +..+
T Consensus 355 --LivRLR~NVIkTgIR~ISlsYSRISl~DIA~kL~l~Seed~EyiVakAIRDGvIea~Id~~~g~m~skE~~diy~t~e 432 (493)
T KOG2581|consen 355 --LIVRLRHNVIKTGIRKISLSYSRISLQDIAKKLGLNSEEDAEYIVAKAIRDGVIEAKIDHEDGFMQSKETFDIYSTRE 432 (493)
T ss_pred --HHHHHHHHHHHHhhhheeeeeeeccHHHHHHHhcCCCchhHHHHHHHHHHhccceeeeccccCceehhhhhhhhccCC
Confidence 135678889999999999999999999999999996 4559999999999999999999999987554321 1123
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q psy4458 269 ILNEWSASLNELMKLVNNT 287 (303)
Q Consensus 269 ~l~~w~~~i~~l~~~v~~~ 287 (303)
.=..++.+|.-+++.=+..
T Consensus 433 pQ~~f~~rI~fCl~LhN~~ 451 (493)
T KOG2581|consen 433 PQTAFDERIRFCLQLHNEA 451 (493)
T ss_pred chhhHhHHHHHHHHHHHHH
Confidence 3345677887776665543
No 16
>KOG2582|consensus
Probab=99.09 E-value=4.3e-09 Score=96.97 Aligned_cols=210 Identities=17% Similarity=0.192 Sum_probs=134.6
Q ss_pred HHHHHHHhhcchhHHHHHHHH-hhhhccCCCCcchHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHcCCCCCCChHHHH
Q psy4458 37 EQMRLCLAKKDYIRTQIISKK-INTKFFDDEKDDVQELKLKYYRLMIELDQHEGSYLATCKHYRAILTTPCIQSDPVQRH 115 (303)
Q Consensus 37 ~~~rL~L~~~D~~~a~~~~~k-i~~~~~~~~~~~~~e~k~~y~~~~~~~~~~~~~f~eaa~~y~e~~~t~~~~~~~~~~~ 115 (303)
....+||+.+||.-+.-+++- +-..+-.+.. .+-..-+.|.-|-|-++...++|-.|--.|..+..+|+-.... --.
T Consensus 145 ~l~~~~L~ak~y~~~~p~ld~divei~~~n~h-~~~k~fL~Y~yYgg~iciglk~fe~Al~~~e~~v~~Pa~~vs~-~hl 222 (422)
T KOG2582|consen 145 DLLQLCLEAKDYASVLPYLDDDIVEICKANPH-LDPKYFLLYLYYGGMICIGLKRFERALYLLEICVTTPAMAVSH-IHL 222 (422)
T ss_pred HHHHHHHHhhcccccCCccchhHHHHhccCCC-CCHHHHHHHHHhcceeeeccccHHHHHHHHHHHHhcchhHHHH-HHH
Confidence 355678888887765433321 1111101111 1334556777788888889999998888888888887654322 223
Q ss_pred HHH-HHHHHHHHhCCCC---ch-hhHhHHHhhhhhhcCCchHHHHHHHHhcCCcccCchHHHHHHHHhhcccccccccch
Q psy4458 116 AVL-QNVVLYLMLAPYD---NE-QSDLTHRVLEDKLLNEIPLYKGLLQWFTNPELIKWSGLRQLYEEELFKTSVFNQSTE 190 (303)
Q Consensus 116 ~~L-~~~v~~~iLs~~~---~~-r~~ll~~l~~~~~~~~~p~~~~L~~~f~~~~li~~~~~~~~~~~~L~~~~~~~~~~~ 190 (303)
+++ +++.++.|+.+-- +. -+.-.-+..+ +..|.|.+++++|.++..-..+.+..++...+..+--.
T Consensus 223 EaYkkylLvsLI~~GK~~ql~k~ts~~~~r~~K----~ms~pY~ef~~~Y~~~~~~eLr~lVk~~~~rF~kDnnt----- 293 (422)
T KOG2582|consen 223 EAYKKYLLVSLILTGKVFQLPKNTSQNAGRFFK----PMSNPYHEFLNVYLKDSSTELRTLVKKHSERFTKDNNT----- 293 (422)
T ss_pred HHHHHHHHHHhhhcCceeeccccchhhhHHhcc----cCCchHHHHHHHHhcCCcHHHHHHHHHHHHHHhhcCcH-----
Confidence 444 5667777776521 11 1111112222 34667999999998875322333444443333222210
Q ss_pred hHHhHHHHHHHHHHHHHHHHHHhhhceeeHHHHHHHhCC-CHHHHHHHHHhhhhcCceEEEecCCCceEEeccC
Q psy4458 191 EGQKCFKMLKHRVVEHNIRVMAKYYTRITLQRMCDLLGL-PIEETEEFLSSMVVSKTITAKIDRPAGIINFARN 263 (303)
Q Consensus 191 ~~~~~~~~l~~~i~ehNi~~isk~Y~~Itl~~la~ll~l-s~~~vE~~l~~mI~~~~l~akIDq~~giV~f~~~ 263 (303)
.-.+..-..+-.|||.+..|.|++++++.||++..+ +.++||+.|.+||.+|++.+.|| |.|.|...
T Consensus 294 ---~l~k~av~sl~k~nI~rltktF~sLsL~dIA~~vQLa~~qevek~Ilqmie~~~i~a~iN---G~v~f~~n 361 (422)
T KOG2582|consen 294 ---GLAKQAVSSLYKKNIQRLTKTFLSLSLSDIASRVQLASAQEVEKYILQMIEDGEIFASIN---GMVFFTDN 361 (422)
T ss_pred ---HHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcchHHHHHHHHHHhccCceEEEec---ceEEEecC
Confidence 112455566888999999999999999999998887 68899999999999999999999 99888653
No 17
>KOG2753|consensus
Probab=98.30 E-value=3.9e-05 Score=70.36 Aligned_cols=178 Identities=15% Similarity=0.129 Sum_probs=109.3
Q ss_pred hhhHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHhCCCCchhhHhHH--HhhhhhhcCCchHHHHHHHHhcCCcc
Q psy4458 88 EGSYLATCKHYRAILTTPCIQSDPVQRHAVLQNVVLYLMLAPYDNEQSDLTH--RVLEDKLLNEIPLYKGLLQWFTNPEL 165 (303)
Q Consensus 88 ~~~f~eaa~~y~e~~~t~~~~~~~~~~~~~L~~~v~~~iLs~~~~~r~~ll~--~l~~~~~~~~~p~~~~L~~~f~~~~l 165 (303)
.+.--++++.+-+.+.|++-. |.+.+...--..|+-++-+|....=..|++ .+. .++.-+ +..|++-|.++-+
T Consensus 178 ~k~~~~s~kvmt~lLgtyt~d-nas~AredA~rcV~~av~dP~~F~fD~Ll~L~pV~---qLE~d~-i~qLL~IF~s~~L 252 (378)
T KOG2753|consen 178 NKSVDESSKVMTELLGTYTED-NASEAREDAMRCVVEAVKDPKIFLFDHLLTLPPVK---QLEGDL-IHQLLKIFVSGKL 252 (378)
T ss_pred cchhhhHHHHHHHHHHHhccc-chhHHHHHHHHHHHHHHcCCceeccchhccCchHH---Hhccch-HHHHHHHHHhcch
Confidence 333446888888888888753 323333333445666666664322111111 111 122211 6779999999977
Q ss_pred cCchHHHHHHHHhhcccccccccchhHHhHHHHHHHHHHHHHHHHHHhhhceeeHHHHHHHhCCCHHHHHHHHHhhhhcC
Q psy4458 166 IKWSGLRQLYEEELFKTSVFNQSTEEGQKCFKMLKHRVVEHNIRVMAKYYTRITLQRMCDLLGLPIEETEEFLSSMVVSK 245 (303)
Q Consensus 166 i~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~~l~~~i~ehNi~~isk~Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~ 245 (303)
-.|-++...-...+..+...+ .+.-+.++---+..++..=..|+++.|++-|++.++++|..+.+.|.-|
T Consensus 253 ~aYveF~~~N~~Fvqs~gl~~----------E~~~~KMRLLTlm~LA~es~eisy~~l~k~LqI~edeVE~fVIdaI~ak 322 (378)
T KOG2753|consen 253 DAYVEFVAANSGFVQSQGLVH----------EQNMAKMRLLTLMSLAEESNEISYDTLAKELQINEDEVELFVIDAIRAK 322 (378)
T ss_pred HHHHHHHHhChHHHHHhcccH----------HHHHHHHHHHHHHHHhccCCCCCHHHHHHHhccCHHHHHHHHHHHHHHH
Confidence 556544443333333333221 1222223333344455678899999999999999999999999999999
Q ss_pred ceEEEecCCCceEEeccCC----------ChhHHHHHHH-HHHHHH
Q psy4458 246 TITAKIDRPAGIINFARNK----------DPGEILNEWS-ASLNEL 280 (303)
Q Consensus 246 ~l~akIDq~~giV~f~~~~----------~~~~~l~~w~-~~i~~l 280 (303)
-+.|||||.++.|+..+.. ...+.|..|. +++..+
T Consensus 323 lV~~kidq~~~~viVs~~~hR~FG~~qW~~L~~kL~aw~k~~~stv 368 (378)
T KOG2753|consen 323 LVEGKIDQMNRTVIVSSSTHRTFGKQQWQQLRDKLAAWGKQNLSTV 368 (378)
T ss_pred HHHhhHHhhcceEEeehhhhhhcccHHHHHHHHHHHHHHhhhhHHH
Confidence 9999999999998766541 2356678884 444433
No 18
>KOG1076|consensus
Probab=98.11 E-value=9.2e-06 Score=80.59 Aligned_cols=69 Identities=25% Similarity=0.551 Sum_probs=61.3
Q ss_pred HHHHHHHHHHHHHH----HHhhhceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCCCceEEeccCCC
Q psy4458 197 KMLKHRVVEHNIRV----MAKYYTRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAGIINFARNKD 265 (303)
Q Consensus 197 ~~l~~~i~ehNi~~----isk~Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~giV~f~~~~~ 265 (303)
..|.++|.|.-+|. ++.+|++||+..||++|.+|+..|-.+|++||.+..|.|+.|||.++|.|++..+
T Consensus 694 ~Ml~~rIqEEsLRTYLftYss~Y~SvSl~~LA~mFdLp~~~VhsIiSkmiineEl~AslDqpt~~iv~hrvE~ 766 (843)
T KOG1076|consen 694 DMLTERIQEESLRTYLFTYSSVYDSVSLAKLADMFDLPEPKVHSIISKMIINEELHASLDQPTQCIVMHRVEP 766 (843)
T ss_pred HHHHHHHHHHHHHHHHHHhhhhhhhccHHHHHHHhCCCchhHHHHHHHHHHHHHhhhccCCCcceEEEeeccc
Confidence 44556777777776 4678999999999999999999999999999999999999999999999998653
No 19
>KOG2688|consensus
Probab=97.87 E-value=0.00021 Score=67.75 Aligned_cols=210 Identities=11% Similarity=0.135 Sum_probs=135.7
Q ss_pred HHHHHHHHHhhcchhHHHHHHHHhhhhc-cCCCCcchHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHcC-CCCCCChH
Q psy4458 35 ILEQMRLCLAKKDYIRTQIISKKINTKF-FDDEKDDVQELKLKYYRLMIELDQHEGSYLATCKHYRAILTT-PCIQSDPV 112 (303)
Q Consensus 35 ~L~~~rL~L~~~D~~~a~~~~~ki~~~~-~~~~~~~~~e~k~~y~~~~~~~~~~~~~f~eaa~~y~e~~~t-~~~~~~~~ 112 (303)
.....++|+.-+.+..++..++-+.... ..... ...-.+.|.-|.+++++...||.+|...+.+++.. +... -.
T Consensus 166 ~n~lf~Iyfri~~~~L~k~l~ra~~~~~~~~~~~--~l~~~v~y~YylGr~a~~~~d~~~A~~~L~~af~~cp~~~--~~ 241 (394)
T KOG2688|consen 166 VNQLFQIYFRIEKLLLCKNLIRAFDQSGSDISDF--PLAQLVVYHYYLGRYAMFESDFLNAFLQLNEAFRLCPDLL--LK 241 (394)
T ss_pred HHHHHHHHHHHhhHHHhHHHHHHhhccccchhhc--ccccceeeeeeeeeehhhhhhHHHHHHHHHHHHHhCcHHH--Hh
Confidence 3455567777777777777777665542 11222 34455677778999999999999999999999743 3211 01
Q ss_pred HHHHHHHHHHHHHHhCCCCchhhHhHHHhhhhhhcCCchHHHHHHHHhcCCcccCchHHHHHHHHhhcccccccccchhH
Q psy4458 113 QRHAVLQNVVLYLMLAPYDNEQSDLTHRVLEDKLLNEIPLYKGLLQWFTNPELIKWSGLRQLYEEELFKTSVFNQSTEEG 192 (303)
Q Consensus 113 ~~~~~L~~~v~~~iLs~~~~~r~~ll~~l~~~~~~~~~p~~~~L~~~f~~~~li~~~~~~~~~~~~L~~~~~~~~~~~~~ 192 (303)
.....+.|++-++++..+.|... ++.+. . +..+..|+++-..+++-.+....+.-+..+....++..
T Consensus 242 n~~~iliylip~~~llg~~Pt~~-lL~~~----~---~~~~~~lv~aVr~Gnl~~f~~al~~~E~~f~~~gi~l~----- 308 (394)
T KOG2688|consen 242 NKRLILIYLIPTGLLLGRIPTKE-LLDFY----T---LDKYSPLVQAVRSGNLRLFDLALADNERFFIRSGIYLT----- 308 (394)
T ss_pred hhhhHHHHHhHHHHHhccCcchh-hHhHh----h---HHhHHHHHHHHHhccHHHHHHHHhhhHHHHHHhccHHH-----
Confidence 12235788888888887755443 22221 1 33467788888788775555444444444444333310
Q ss_pred HhHHHHHHHHHHHHHHHHHHhhh---ceeeHHHHHHHhCCC------HHHHHHHHHhhhhcCceEEEecCCCceEEeccC
Q psy4458 193 QKCFKMLKHRVVEHNIRVMAKYY---TRITLQRMCDLLGLP------IEETEEFLSSMVVSKTITAKIDRPAGIINFARN 263 (303)
Q Consensus 193 ~~~~~~l~~~i~ehNi~~isk~Y---~~Itl~~la~ll~ls------~~~vE~~l~~mI~~~~l~akIDq~~giV~f~~~ 263 (303)
...+..-+...=++.+.+.- +++.++++-.++..+ .+++|-.++.+|..|+|.|.|+.....+.|.+.
T Consensus 309 ---l~~l~lv~yrnL~kkv~~~~~~~~~lpls~~~~al~~~~~~~~~~deveciLa~lI~~G~ikgYish~~~~~V~sK~ 385 (394)
T KOG2688|consen 309 ---LEKLPLVVYRNLFKKVIQLWGKTSQLPLSRFLTALQFSGVTDVDLDEVECILANLIDLGRIKGYISHQLQTLVFSKK 385 (394)
T ss_pred ---hhhhhHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHhhcCCCCCchhhHHHHHHhhhhhccccchhchhhheEEEecC
Confidence 11122222222244455566 888899888887653 699999999999999999999999999998875
Q ss_pred C
Q psy4458 264 K 264 (303)
Q Consensus 264 ~ 264 (303)
+
T Consensus 386 ~ 386 (394)
T KOG2688|consen 386 D 386 (394)
T ss_pred C
Confidence 4
No 20
>KOG2758|consensus
Probab=97.59 E-value=0.0024 Score=58.77 Aligned_cols=79 Identities=20% Similarity=0.320 Sum_probs=61.2
Q ss_pred HhhhceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCCCceEEeccCC-ChhHHHHHHHHHHHHHHHHHHHHHhh
Q psy4458 212 AKYYTRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAGIINFARNK-DPGEILNEWSASLNELMKLVNNTTHL 290 (303)
Q Consensus 212 sk~Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~giV~f~~~~-~~~~~l~~w~~~i~~l~~~v~~~~~l 290 (303)
-+.-+.||++-||+.++++++++|.-+.++|.+-+|.||||...|-|..+.+. ++.+ .-.++..+|.-.-+++...
T Consensus 344 CRIHqcIti~mLA~kLnm~~eeaErwivnlIr~~rl~AkidSklg~Vvmg~~~~s~~q---Q~ie~tksLS~rsq~la~~ 420 (432)
T KOG2758|consen 344 CRIHQCITIDMLADKLNMDPEEAERWIVNLIRTARLDAKIDSKLGHVVMGHPTVSPHQ---QLIEKTKSLSFRSQNLAQQ 420 (432)
T ss_pred HHHHHheeHHHHHHHhcCCHHHHHHHHHHHHHHhhhhhhhccccCceeecCCCCCHHH---HHHHhccccchhHHHHHHH
Confidence 34578899999999999999999999999999999999999999999998764 3333 3345555555555555444
Q ss_pred hhH
Q psy4458 291 INK 293 (303)
Q Consensus 291 I~k 293 (303)
|.|
T Consensus 421 lek 423 (432)
T KOG2758|consen 421 LEK 423 (432)
T ss_pred HHH
Confidence 443
No 21
>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=97.38 E-value=0.0042 Score=59.60 Aligned_cols=197 Identities=17% Similarity=0.287 Sum_probs=106.7
Q ss_pred cCCchHHHHHH--HHHHHHHHHhhcchhHHHHHHHHhhhh---ccCCCCcchHHHHHHHHHHHHHHHHHhhhHHHHHHHH
Q psy4458 24 GSMEKKEKVTL--ILEQMRLCLAKKDYIRTQIISKKINTK---FFDDEKDDVQELKLKYYRLMIELDQHEGSYLATCKHY 98 (303)
Q Consensus 24 ~~~~~~~k~~~--~L~~~rL~L~~~D~~~a~~~~~ki~~~---~~~~~~~~~~e~k~~y~~~~~~~~~~~~~f~eaa~~y 98 (303)
|+-+....+=| ++-.+|+....|||..|-..+.-|... ++.. ...--+..+-+.|.-|..-|.|.+|.+.|
T Consensus 112 g~~~l~~~LGYFSligLlRvh~LLGDY~~Alk~l~~idl~~~~l~~~----V~~~~is~~YyvGFaylMlrRY~DAir~f 187 (404)
T PF10255_consen 112 GSSPLYKMLGYFSLIGLLRVHCLLGDYYQALKVLENIDLNKKGLYTK----VPACHISTYYYVGFAYLMLRRYADAIRTF 187 (404)
T ss_pred ccccHHHHhhHHHHHHHHHHHHhccCHHHHHHHhhccCcccchhhcc----CcchheehHHHHHHHHHHHHHHHHHHHHH
Confidence 33344444444 577889999999999999888777431 1111 11233445556888899999999999999
Q ss_pred HHHHcCC----------CCCCChH--HHHHHHHHHHHHHHhCCC--Cc-hhhHhHHHhhhhhh--c--CCchHHHHHHHH
Q psy4458 99 RAILTTP----------CIQSDPV--QRHAVLQNVVLYLMLAPY--DN-EQSDLTHRVLEDKL--L--NEIPLYKGLLQW 159 (303)
Q Consensus 99 ~e~~~t~----------~~~~~~~--~~~~~L~~~v~~~iLs~~--~~-~r~~ll~~l~~~~~--~--~~~p~~~~L~~~ 159 (303)
-.++... +.+.|.- ..-+.+-.+++|..|+|. +. -.+.+..+ +.+.- . ..++.+.+|-..
T Consensus 188 ~~iL~yi~r~k~~~~~~~~q~d~i~K~~eqMyaLlAic~~l~p~~lde~i~~~lkek-y~ek~~kmq~gd~~~f~elF~~ 266 (404)
T PF10255_consen 188 SQILLYIQRTKNQYHQRSYQYDQINKKNEQMYALLAICLSLCPQRLDESISSQLKEK-YGEKMEKMQRGDEEAFEELFSF 266 (404)
T ss_pred HHHHHHHHHhhhhhccccchhhHHHhHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHH-HHHHHHHHHccCHHHHHHHHHh
Confidence 8876431 1111110 011233447888888885 22 22222222 32221 1 123333322110
Q ss_pred hcCCcccCchHHHHHHHHhhccc-cc-cccc--c--hhHH-hHHHHHHHH----HHHHHHHHHHhhhceeeHHHHHHHhC
Q psy4458 160 FTNPELIKWSGLRQLYEEELFKT-SV-FNQS--T--EEGQ-KCFKMLKHR----VVEHNIRVMAKYYTRITLQRMCDLLG 228 (303)
Q Consensus 160 f~~~~li~~~~~~~~~~~~L~~~-~~-~~~~--~--~~~~-~~~~~l~~~----i~ehNi~~isk~Y~~Itl~~la~ll~ 228 (303)
-+... +.+. +. +... . .++. ...+.+... ..--+||.+-|.|++|+++.||.+++
T Consensus 267 -acPKF-------------Isp~~pp~~~~~~~~~~~e~~~~Ql~~Fl~eV~~q~~l~~lRSyLKLYtti~l~KLA~fl~ 332 (404)
T PF10255_consen 267 -ACPKF-------------ISPVSPPDYDGPSQNKNKEPYRRQLKLFLDEVKQQQKLPTLRSYLKLYTTIPLEKLASFLD 332 (404)
T ss_pred -hCCCc-------------cCCCCCCCcccccchhhhhHHHHHHHHHHHHHHHhhhhhHHHHHHHhhcCCCHHHHHHHcC
Confidence 11111 1111 10 0000 0 0121 123334443 44457888889999999999999999
Q ss_pred CCHHHHHHHHH
Q psy4458 229 LPIEETEEFLS 239 (303)
Q Consensus 229 ls~~~vE~~l~ 239 (303)
++++++-..|.
T Consensus 333 vd~~~lr~~Ll 343 (404)
T PF10255_consen 333 VDEEELRSQLL 343 (404)
T ss_pred CCHHHHHHHHH
Confidence 99997665443
No 22
>COG5600 Transcription-associated recombination protein [DNA replication, recombination, and repair]
Probab=97.07 E-value=0.027 Score=52.99 Aligned_cols=242 Identities=11% Similarity=0.129 Sum_probs=132.5
Q ss_pred CCHHHHHHHHhcc---cccccc-CCchHHHHH-HHH--HHHHHHHhhcchhHHHHHHHHhhhhccCCCCc-chHHHHHHH
Q psy4458 6 GDVTEAANIIQEL---QVETYG-SMEKKEKVT-LIL--EQMRLCLAKKDYIRTQIISKKINTKFFDDEKD-DVQELKLKY 77 (303)
Q Consensus 6 ~~~~~Aa~~L~~i---~vet~~-~~~~~~k~~-~~L--~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~-~~~e~k~~y 77 (303)
..++++++++... -++.-+ .+..+.|.- |++ -...+|+..+.+..++..++--...-. .+-+ .....-+.|
T Consensus 144 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 144 DNLSKISRLLTRMFNSILNDRSPALNPSKKVGLYYIANLLFQIYLRLGRFKLCENFLKASKEVSM-PDISEYQKSQVVVF 222 (413)
T ss_pred hhHHHHHHHHHHHHHHhcCCcCccCChhhHHHHHHHHHHHHHHHHHhccHHHHHHHHHhcccccc-cccchhhhcceeeh
Confidence 3556666666543 222211 244444444 222 234567777888777766653332110 0100 012233566
Q ss_pred HHHHHHHHHHhhhHHHHHHHHHHHHc-CCCCCCChHHHHHHHHH-HHHHHHhCCCCchhhHhHHHhhhhhhcCCchHHHH
Q psy4458 78 YRLMIELDQHEGSYLATCKHYRAILT-TPCIQSDPVQRHAVLQN-VVLYLMLAPYDNEQSDLTHRVLEDKLLNEIPLYKG 155 (303)
Q Consensus 78 ~~~~~~~~~~~~~f~eaa~~y~e~~~-t~~~~~~~~~~~~~L~~-~v~~~iLs~~~~~r~~ll~~l~~~~~~~~~p~~~~ 155 (303)
.-|.|+|+...++|-+|+-.+.+++. .+... .-. ....+.+ +..+.++....|-+. +|.+. ++ ...+.-
T Consensus 223 ~YYLG~~~l~~en~heA~~~L~~aFl~c~~l~-~~n-~~rIl~~~ipt~Llv~~~~Ptk~-~L~r~---~~---~s~~~~ 293 (413)
T COG5600 223 HYYLGIYYLLNENFHEAFLHLNEAFLQCPWLI-TRN-RKRILPYYIPTSLLVNKFPPTKD-LLERF---KR---CSVYSP 293 (413)
T ss_pred hhHHHHHHHHHHhHHHHHHHHHHHHHhChhhh-hcc-hheehhHHhhHHHHhCCCCCchH-HHHhc---cc---cchhHH
Confidence 66799999999999999999999974 33310 001 1112333 444444444555555 54432 22 445788
Q ss_pred HHHHhcCCcccCchHHHHHHHHhhcccccccccchhHHhHHHHHHHHHHHHHHHHH--Hhhh--ceeeHH--HHHHHhCC
Q psy4458 156 LLQWFTNPELIKWSGLRQLYEEELFKTSVFNQSTEEGQKCFKMLKHRVVEHNIRVM--AKYY--TRITLQ--RMCDLLGL 229 (303)
Q Consensus 156 L~~~f~~~~li~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~~l~~~i~ehNi~~i--sk~Y--~~Itl~--~la~ll~l 229 (303)
|+++.-++++-.|......-++.+.+..+.-. ......-+.-+|+.+- .-.. ++++++ .++..+..
T Consensus 294 LvkavrsGni~~~~~~l~~ner~~~~~~l~lt--------l~~~~~~V~~RNL~rk~w~~~~~qsrlp~sil~~~~qls~ 365 (413)
T COG5600 294 LVKAVRSGNIEDFDLALSRNERKFAKRGLYLT--------LLAHYPLVCFRNLFRKIWRLHGKQSRLPLSILLIVLQLSA 365 (413)
T ss_pred HHHHHHcCCHHHHHHHHHHhHHHHHHcchHHH--------HHhhccHHHHHHHHHHHHhhccccccCcHHHHHHHHHccC
Confidence 88998889876665444444444433332100 0111112333343331 1112 232233 33333332
Q ss_pred -----CHHHHHHHHHhhhhcCceEEEecCCCceEEeccCCC
Q psy4458 230 -----PIEETEEFLSSMVVSKTITAKIDRPAGIINFARNKD 265 (303)
Q Consensus 230 -----s~~~vE~~l~~mI~~~~l~akIDq~~giV~f~~~~~ 265 (303)
+.++||-.++.||..|.+.|.|-.....|.|.+..+
T Consensus 366 ~dn~~~~~~VEciL~tlI~~G~lrgYis~s~~~vV~sk~~p 406 (413)
T COG5600 366 IDNFHSFKEVECILVTLIGLGLLRGYISHSRRTVVFSKKDP 406 (413)
T ss_pred CCcccChHHHHHHHHHHHhhhhhhheecccceEEEEecCCC
Confidence 378999999999999999999999999999987643
No 23
>KOG2072|consensus
Probab=97.03 E-value=0.17 Score=52.02 Aligned_cols=67 Identities=16% Similarity=0.349 Sum_probs=60.5
Q ss_pred HHHHHHHHHHHHHHHHHHhhhceeeHHHHHHHhC-CCHHHHHHHHHhhhhcCceEEEecCCCceEEec
Q psy4458 195 CFKMLKHRVVEHNIRVMAKYYTRITLQRMCDLLG-LPIEETEEFLSSMVVSKTITAKIDRPAGIINFA 261 (303)
Q Consensus 195 ~~~~l~~~i~ehNi~~isk~Y~~Itl~~la~ll~-ls~~~vE~~l~~mI~~~~l~akIDq~~giV~f~ 261 (303)
+...|+..++-+-+..+|+.|.+|++++|.++.- ++.-++|+.+++....+-+..+||-..+.|+|.
T Consensus 425 YI~sLq~v~~~RllqQvSqiY~sIs~~~l~~La~F~~~~~lEk~~v~a~k~~~v~iriDH~~~~v~Fg 492 (988)
T KOG2072|consen 425 YIPSLQDVIILRLLQQVSQIYESISFERLYKLAPFFSAFELEKLLVEAAKHNDVSIRIDHESNSVSFG 492 (988)
T ss_pred cchhHHHHHHHHHHHHHHHHHHHHhHHHHHHHHhhcCHHHHHHHHHHHHhccceeEEeccccceeeec
Confidence 3466777778878888999999999999999876 489999999999999999999999999999998
No 24
>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=96.25 E-value=0.052 Score=44.52 Aligned_cols=83 Identities=23% Similarity=0.286 Sum_probs=52.4
Q ss_pred CCchHHHHHHHHhcCCcccCchHHHHHHHHhhcccccccccchhHHhHHHHHHHHHHHHHHHHHHhhhceeeHHHHHHHh
Q psy4458 148 NEIPLYKGLLQWFTNPELIKWSGLRQLYEEELFKTSVFNQSTEEGQKCFKMLKHRVVEHNIRVMAKYYTRITLQRMCDLL 227 (303)
Q Consensus 148 ~~~p~~~~L~~~f~~~~li~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~~l~~~i~ehNi~~isk~Y~~Itl~~la~ll 227 (303)
+.+..+-.|.+...+++ |. .|-..++.++-- + .-......|..++++.-...+++.|++|+++.+++.|
T Consensus 39 ~~i~~i~~l~~~L~~~~---~~----~~~~~~~~~~~~-~---~~~~~v~~~~~~iR~~i~~~i~~aY~sIs~~~la~~L 107 (143)
T PF10075_consen 39 PEIKAIWSLGQALWEGD---YS----KFWQALRSNPWS-P---DYKPFVPGFEDTIRERIAHLISKAYSSISLSDLAEML 107 (143)
T ss_dssp TTHHHHHHHHHHHHTT----HH----HHHHHS-TT--------HHHHTSTTHHHHHHHHHHHHHHHH-SEE-HHHHHHHT
T ss_pred HHHHHHHHHHHHHHCCC---HH----HHHHHHHhccch-H---HHHHHHHHHHHHHHHHHHHHHHHHHhHcCHHHHHHHh
Confidence 44555667788887874 33 333444443210 0 0011235577889998899999999999999999999
Q ss_pred CCCHHHHHHHHHhh
Q psy4458 228 GLPIEETEEFLSSM 241 (303)
Q Consensus 228 ~ls~~~vE~~l~~m 241 (303)
|++++++++.+.+-
T Consensus 108 g~~~~el~~~~~~~ 121 (143)
T PF10075_consen 108 GLSEEELEKFIKSR 121 (143)
T ss_dssp TS-HHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHc
Confidence 99988877777665
No 25
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=95.55 E-value=0.032 Score=39.90 Aligned_cols=48 Identities=19% Similarity=0.239 Sum_probs=36.5
Q ss_pred HHHHHhhhceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCCC
Q psy4458 208 IRVMAKYYTRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPA 255 (303)
Q Consensus 208 i~~isk~Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~ 255 (303)
|+.+.+--.++|+..||..|++|++.+|.+|..+|..|+|.-.-+...
T Consensus 5 i~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~~~~~~~ 52 (69)
T PF09012_consen 5 IRDYLRERGRVSLAELAREFGISPEAVEAMLEQLIRKGYIRKVDMSSC 52 (69)
T ss_dssp HHHHHHHS-SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCEEEEEE--
T ss_pred HHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEecCCCC
Confidence 344555678899999999999999999999999999999986555443
No 26
>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=94.50 E-value=0.095 Score=45.15 Aligned_cols=79 Identities=15% Similarity=0.248 Sum_probs=37.2
Q ss_pred HHhhhceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCCCceEEeccCCChhHHHHHHHHHHH--HHHHHHHHHH
Q psy4458 211 MAKYYTRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAGIINFARNKDPGEILNEWSASLN--ELMKLVNNTT 288 (303)
Q Consensus 211 isk~Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~giV~f~~~~~~~~~l~~w~~~i~--~l~~~v~~~~ 288 (303)
+.+-=+.+.|+.||..||++.+++..-|-.+..+|+|.|.||-....|...+.. .+.+..|..+-+ ++...+..++
T Consensus 107 yIK~~Kvv~ledla~~f~l~t~~~i~ri~~L~~~g~ltGv~DdrGkfIyIs~eE--~~~va~fi~~rGRvsi~el~~~~N 184 (188)
T PF09756_consen 107 YIKEHKVVNLEDLAAEFGLRTQDVINRIQELEAEGRLTGVIDDRGKFIYISEEE--MEAVAKFIKQRGRVSISELAQESN 184 (188)
T ss_dssp HHHH-SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-EEE-TT--EEE-------------------------------
T ss_pred HHHHcceeeHHHHHHHcCCCHHHHHHHHHHHHHCCCceeeEcCCCCeEEecHHH--HHHHHHHHHHcCCccHHHHHHHHH
Confidence 444568899999999999999999999999999999999999977777665431 233444433222 3344444444
Q ss_pred hhh
Q psy4458 289 HLI 291 (303)
Q Consensus 289 ~lI 291 (303)
.+|
T Consensus 185 ~~i 187 (188)
T PF09756_consen 185 RLI 187 (188)
T ss_dssp ---
T ss_pred hhc
Confidence 444
No 27
>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=94.31 E-value=0.36 Score=39.33 Aligned_cols=83 Identities=18% Similarity=0.223 Sum_probs=39.3
Q ss_pred cCCHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHHH
Q psy4458 5 EGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIEL 84 (303)
Q Consensus 5 ~~~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~~ 84 (303)
.|++++|...|..+--.+ -+..-+--..|..+++++..|+|..|...+..+.. + . .+-.+..+.|.+
T Consensus 61 ~g~~~~A~~~l~~~~~~~---~d~~l~~~a~l~LA~~~~~~~~~d~Al~~L~~~~~------~--~--~~~~~~~~~Gdi 127 (145)
T PF09976_consen 61 QGDYDEAKAALEKALANA---PDPELKPLARLRLARILLQQGQYDEALATLQQIPD------E--A--FKALAAELLGDI 127 (145)
T ss_pred CCCHHHHHHHHHHHHhhC---CCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHhccC------c--c--hHHHHHHHHHHH
Confidence 355556655555554321 11222233345555555566666655555543211 0 1 122244455556
Q ss_pred HHHhhhHHHHHHHHHH
Q psy4458 85 DQHEGSYLATCKHYRA 100 (303)
Q Consensus 85 ~~~~~~f~eaa~~y~e 100 (303)
+...+++-+|-..|..
T Consensus 128 ~~~~g~~~~A~~~y~~ 143 (145)
T PF09976_consen 128 YLAQGDYDEARAAYQK 143 (145)
T ss_pred HHHCCCHHHHHHHHHH
Confidence 6666666665555544
No 28
>PF13424 TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 4A1S_B 3CEQ_B 3EDT_H ....
Probab=94.17 E-value=0.55 Score=33.57 Aligned_cols=70 Identities=13% Similarity=-0.019 Sum_probs=56.4
Q ss_pred HHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHc
Q psy4458 32 VTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIELDQHEGSYLATCKHYRAILT 103 (303)
Q Consensus 32 ~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~~~~~~~~f~eaa~~y~e~~~ 103 (303)
...+..++.++...|+|.+|..+.+++-... ..-|+ +.......+..++..+...++|-+|-.+|.++++
T Consensus 5 a~~~~~la~~~~~~~~~~~A~~~~~~al~~~-~~~~~-~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al~ 74 (78)
T PF13424_consen 5 ANAYNNLARVYRELGRYDEALDYYEKALDIE-EQLGD-DHPDTANTLNNLGECYYRLGDYEEALEYYQKALD 74 (78)
T ss_dssp HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHH-HHTTT-HHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHH-HHHCC-CCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence 4567889999999999999999999998874 44442 3334467788899999999999999999998853
No 29
>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A.
Probab=93.83 E-value=2.7 Score=38.35 Aligned_cols=170 Identities=12% Similarity=0.133 Sum_probs=89.7
Q ss_pred CCHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCc-----------------
Q psy4458 6 GDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKD----------------- 68 (303)
Q Consensus 6 ~~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~----------------- 68 (303)
|+...||+.+.+ -...+......+=++++-+-+.++...|++.+|-....++...+.+..|+
T Consensus 69 ~~~~~Aa~~~~~-Aa~~~k~~~~~~Ai~~~~~A~~~y~~~G~~~~aA~~~~~lA~~ye~~~~d~e~Ai~~Y~~A~~~y~~ 147 (282)
T PF14938_consen 69 GDKFEAAKAYEE-AANCYKKGDPDEAIECYEKAIEIYREAGRFSQAAKCLKELAEIYEEQLGDYEKAIEYYQKAAELYEQ 147 (282)
T ss_dssp T-HHHHHHHHHH-HHHHHHHTTHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHCCTT--HHHHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHH-HHHHHHhhCHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHH
Confidence 444444444433 11222333444556667777777777777777777776666666332130
Q ss_pred -chHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHcCCCCC-CChHHHHHHHHHHHHHHHhCCCCchhhHhHHHhh-hhh
Q psy4458 69 -DVQELKLKYYRLMIELDQHEGSYLATCKHYRAILTTPCIQ-SDPVQRHAVLQNVVLYLMLAPYDNEQSDLTHRVL-EDK 145 (303)
Q Consensus 69 -~~~e~k~~y~~~~~~~~~~~~~f~eaa~~y~e~~~t~~~~-~~~~~~~~~L~~~v~~~iLs~~~~~r~~ll~~l~-~~~ 145 (303)
+....-...+.-.+.++...++|.+|...|.++.....-. .........+-.+++|.+..+-...=...+.+.. .+|
T Consensus 148 e~~~~~a~~~~~~~A~l~~~l~~y~~A~~~~e~~~~~~l~~~l~~~~~~~~~l~a~l~~L~~~D~v~A~~~~~~~~~~~~ 227 (282)
T PF14938_consen 148 EGSPHSAAECLLKAADLYARLGRYEEAIEIYEEVAKKCLENNLLKYSAKEYFLKAILCHLAMGDYVAARKALERYCSQDP 227 (282)
T ss_dssp TT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTCCCHCTTGHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHGTTST
T ss_pred CCChhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhhcccccchhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCC
Confidence 1222223444445788888999999999999887643211 0111223344446666666643222222333333 345
Q ss_pred hc---CCchHHHHHHHHhcCCcccCchHHHHHHH
Q psy4458 146 LL---NEIPLYKGLLQWFTNPELIKWSGLRQLYE 176 (303)
Q Consensus 146 ~~---~~~p~~~~L~~~f~~~~li~~~~~~~~~~ 176 (303)
.. ++...+..|+++|.+++.-.|...+..|.
T Consensus 228 ~F~~s~E~~~~~~l~~A~~~~D~e~f~~av~~~d 261 (282)
T PF14938_consen 228 SFASSREYKFLEDLLEAYEEGDVEAFTEAVAEYD 261 (282)
T ss_dssp TSTTSHHHHHHHHHHHHHHTT-CCCHHHHCHHHT
T ss_pred CCCCcHHHHHHHHHHHHHHhCCHHHHHHHHHHHc
Confidence 43 33445678899999998766655555553
No 30
>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=93.45 E-value=0.11 Score=40.10 Aligned_cols=37 Identities=19% Similarity=0.307 Sum_probs=34.4
Q ss_pred eeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecC
Q psy4458 217 RITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDR 253 (303)
Q Consensus 217 ~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq 253 (303)
=|+++.|++.|+++.++|...+-.|+.+|.|+..||-
T Consensus 65 Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd 101 (102)
T PF08784_consen 65 GVHVDEIAQQLGMSENEVRKALDFLSNEGHIYSTIDD 101 (102)
T ss_dssp TEEHHHHHHHSTS-HHHHHHHHHHHHHTTSEEESSST
T ss_pred cccHHHHHHHhCcCHHHHHHHHHHHHhCCeEecccCC
Confidence 4999999999999999999999999999999999994
No 31
>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A.
Probab=92.90 E-value=1.2 Score=40.67 Aligned_cols=113 Identities=15% Similarity=0.144 Sum_probs=58.2
Q ss_pred CCHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHHHH
Q psy4458 6 GDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIELD 85 (303)
Q Consensus 6 ~~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~~~ 85 (303)
|+|.+|++..... .+-+..++.....--.+..+-.++...|+..|..+.+++...+. ..| ....--+.+.-.+.++
T Consensus 49 ~~~~~A~~ay~kA-a~~~~~~~~~~~Aa~~~~~Aa~~~k~~~~~~Ai~~~~~A~~~y~-~~G--~~~~aA~~~~~lA~~y 124 (282)
T PF14938_consen 49 KDWEKAAEAYEKA-ADCYEKLGDKFEAAKAYEEAANCYKKGDPDEAIECYEKAIEIYR-EAG--RFSQAAKCLKELAEIY 124 (282)
T ss_dssp T-CHHHHHHHHHH-HHHHHHTT-HHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHH-HCT---HHHHHHHHHHHHHHH
T ss_pred hccchhHHHHHHH-HHHHHHcCCHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHHHHH-hcC--cHHHHHHHHHHHHHHH
Confidence 4555555444433 11111223333333333334444444577777777777777663 334 3444456666677777
Q ss_pred HHh-hhHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHH
Q psy4458 86 QHE-GSYLATCKHYRAILTTPCIQSDPVQRHAVLQNVV 122 (303)
Q Consensus 86 ~~~-~~f~eaa~~y~e~~~t~~~~~~~~~~~~~L~~~v 122 (303)
... +++-.|..+|..+.+.+...+.+.....++..+.
T Consensus 125 e~~~~d~e~Ai~~Y~~A~~~y~~e~~~~~a~~~~~~~A 162 (282)
T PF14938_consen 125 EEQLGDYEKAIEYYQKAAELYEQEGSPHSAAECLLKAA 162 (282)
T ss_dssp CCTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHH
T ss_pred HHHcCCHHHHHHHHHHHHHHHHHCCChhhHHHHHHHHH
Confidence 777 7888888888887766554333333444544433
No 32
>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A.
Probab=90.94 E-value=0.99 Score=32.90 Aligned_cols=82 Identities=15% Similarity=0.197 Sum_probs=58.1
Q ss_pred cCCHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHHH
Q psy4458 5 EGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIEL 84 (303)
Q Consensus 5 ~~~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~~ 84 (303)
.|++++|..+...+--.+.+ ...-.+++..++.++..|+|.+|-.++++ ... + ++ .....| ..|+.
T Consensus 2 ~~~y~~Ai~~~~k~~~~~~~----~~~~~~~~~la~~~~~~~~y~~A~~~~~~--~~~-~-~~----~~~~~~--l~a~~ 67 (84)
T PF12895_consen 2 QGNYENAIKYYEKLLELDPT----NPNSAYLYNLAQCYFQQGKYEEAIELLQK--LKL-D-PS----NPDIHY--LLARC 67 (84)
T ss_dssp TT-HHHHHHHHHHHHHHHCG----THHHHHHHHHHHHHHHTTHHHHHHHHHHC--HTH-H-HC----HHHHHH--HHHHH
T ss_pred CccHHHHHHHHHHHHHHCCC----ChhHHHHHHHHHHHHHCCCHHHHHHHHHH--hCC-C-CC----CHHHHH--HHHHH
Confidence 68999999988887643322 22666888899999999999999999988 212 1 11 223334 45898
Q ss_pred HHHhhhHHHHHHHHHH
Q psy4458 85 DQHEGSYLATCKHYRA 100 (303)
Q Consensus 85 ~~~~~~f~eaa~~y~e 100 (303)
+...++|-+|-+.|.+
T Consensus 68 ~~~l~~y~eAi~~l~~ 83 (84)
T PF12895_consen 68 LLKLGKYEEAIKALEK 83 (84)
T ss_dssp HHHTT-HHHHHHHHHH
T ss_pred HHHhCCHHHHHHHHhc
Confidence 9999999999887764
No 33
>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=90.34 E-value=1.8 Score=39.94 Aligned_cols=119 Identities=11% Similarity=0.103 Sum_probs=75.6
Q ss_pred ccCCHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHH
Q psy4458 4 DEGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIE 83 (303)
Q Consensus 4 ~~~~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~ 83 (303)
.+|++++|.++|... .-+|...-.+.++|..+.++.|+..+++....- + ...-..+....+-
T Consensus 114 ~~~~~~~AL~~l~~~-----------~~lE~~al~Vqi~L~~~R~dlA~k~l~~~~~~~--e-----D~~l~qLa~awv~ 175 (290)
T PF04733_consen 114 HEGDYEEALKLLHKG-----------GSLELLALAVQILLKMNRPDLAEKELKNMQQID--E-----DSILTQLAEAWVN 175 (290)
T ss_dssp CCCHHHHHHCCCTTT-----------TCHHHHHHHHHHHHHTT-HHHHHHHHHHHHCCS--C-----CHHHHHHHHHHHH
T ss_pred HcCCHHHHHHHHHcc-----------CcccHHHHHHHHHHHcCCHHHHHHHHHHHHhcC--C-----cHHHHHHHHHHHH
Confidence 467778887777653 336777888899999999999999998876532 2 1343455545555
Q ss_pred HHHHhhhHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHhCCC-CchhhHhHHHhhhhhh
Q psy4458 84 LDQHEGSYLATCKHYRAILTTPCIQSDPVQRHAVLQNVVLYLMLAPY-DNEQSDLTHRVLEDKL 146 (303)
Q Consensus 84 ~~~~~~~f~eaa~~y~e~~~t~~~~~~~~~~~~~L~~~v~~~iLs~~-~~~r~~ll~~l~~~~~ 146 (303)
+.....+|.+|+..|.|+.+++.. + ...+....+|.+.... +.-...+...+..+|+
T Consensus 176 l~~g~e~~~~A~y~f~El~~~~~~--t----~~~lng~A~~~l~~~~~~eAe~~L~~al~~~~~ 233 (290)
T PF04733_consen 176 LATGGEKYQDAFYIFEELSDKFGS--T----PKLLNGLAVCHLQLGHYEEAEELLEEALEKDPN 233 (290)
T ss_dssp HHHTTTCCCHHHHHHHHHHCCS----S----HHHHHHHHHHHHHCT-HHHHHHHHHHHCCC-CC
T ss_pred HHhCchhHHHHHHHHHHHHhccCC--C----HHHHHHHHHHHHHhCCHHHHHHHHHHHHHhccC
Confidence 555566899999999999887632 1 2345556667776665 3334434444444553
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=89.30 E-value=4.2 Score=30.68 Aligned_cols=94 Identities=12% Similarity=-0.032 Sum_probs=62.4
Q ss_pred CccCCHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHH
Q psy4458 3 EDEGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMI 82 (303)
Q Consensus 3 e~~~~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~ 82 (303)
...|++++|.+.+..+--...+. ....+..+..+++++..+++..|..+.+++.....+... .......++
T Consensus 13 ~~~~~~~~A~~~~~~~~~~~~~~---~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~------~~~~~~~~~ 83 (119)
T TIGR02795 13 LKAGDYADAIQAFQAFLKKYPKS---TYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKYPKSPK------APDALLKLG 83 (119)
T ss_pred HHcCCHHHHHHHHHHHHHHCCCc---cccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHCCCCCc------ccHHHHHHH
Confidence 35688889988887774322111 122455677888899999999999888888765522111 112233466
Q ss_pred HHHHHhhhHHHHHHHHHHHHcCC
Q psy4458 83 ELDQHEGSYLATCKHYRAILTTP 105 (303)
Q Consensus 83 ~~~~~~~~f~eaa~~y~e~~~t~ 105 (303)
..+...+++.+|.+.|.++...+
T Consensus 84 ~~~~~~~~~~~A~~~~~~~~~~~ 106 (119)
T TIGR02795 84 MSLQELGDKEKAKATLQQVIKRY 106 (119)
T ss_pred HHHHHhCChHHHHHHHHHHHHHC
Confidence 67778888888888888887654
No 35
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=89.20 E-value=19 Score=33.61 Aligned_cols=90 Identities=12% Similarity=0.123 Sum_probs=49.1
Q ss_pred ccCCHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHH
Q psy4458 4 DEGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIE 83 (303)
Q Consensus 4 ~~~~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~ 83 (303)
..|++++|...+....-. .......+...+.++...|+|..|.....++....... . ......++..++.
T Consensus 119 ~~g~~~~A~~~~~~~l~~------~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~-~---~~~~~~~~~~la~ 188 (389)
T PRK11788 119 KAGLLDRAEELFLQLVDE------GDFAEGALQQLLEIYQQEKDWQKAIDVAERLEKLGGDS-L---RVEIAHFYCELAQ 188 (389)
T ss_pred HCCCHHHHHHHHHHHHcC------CcchHHHHHHHHHHHHHhchHHHHHHHHHHHHHhcCCc-c---hHHHHHHHHHHHH
Confidence 356777777766665311 01123445566666677777777766666665443222 1 1122334444556
Q ss_pred HHHHhhhHHHHHHHHHHHHc
Q psy4458 84 LDQHEGSYLATCKHYRAILT 103 (303)
Q Consensus 84 ~~~~~~~f~eaa~~y~e~~~ 103 (303)
.+...+++.+|-..|.++..
T Consensus 189 ~~~~~~~~~~A~~~~~~al~ 208 (389)
T PRK11788 189 QALARGDLDAARALLKKALA 208 (389)
T ss_pred HHHhCCCHHHHHHHHHHHHh
Confidence 66666666666666666654
No 36
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=88.61 E-value=0.97 Score=33.16 Aligned_cols=42 Identities=12% Similarity=0.130 Sum_probs=36.7
Q ss_pred HHHHhhhceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEE
Q psy4458 209 RVMAKYYTRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAK 250 (303)
Q Consensus 209 ~~isk~Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~ak 250 (303)
+-+.+-+.+++...||..|+.|++-||.+|..++.-|++.-.
T Consensus 8 Rd~l~~~gr~s~~~Ls~~~~~p~~~VeaMLe~l~~kGkverv 49 (78)
T PRK15431 8 RDLLALRGRMEAAQISQTLNTPQPMINAMLQQLESMGKAVRI 49 (78)
T ss_pred HHHHHHcCcccHHHHHHHHCcCHHHHHHHHHHHHHCCCeEee
Confidence 344456899999999999999999999999999999998643
No 37
>PF04348 LppC: LppC putative lipoprotein; InterPro: IPR007443 This entry includes several bacterial outer membrane antigens, whose molecular function is unknown.; PDB: 3CKM_A.
Probab=88.58 E-value=0.13 Score=51.47 Aligned_cols=91 Identities=20% Similarity=0.253 Sum_probs=0.0
Q ss_pred ccCCHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHH
Q psy4458 4 DEGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIE 83 (303)
Q Consensus 4 ~~~~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~ 83 (303)
.+|++..|..+|..++. ..++...+.++.|-.+++.+..+++..|...++......+ ..+...+|+.+.+.
T Consensus 36 ~~g~~~~A~~ll~~l~~---~~L~~~q~~~~~Ll~A~lal~~~~~~~Al~~L~~~~~~~l------~~~~~~~~~~l~A~ 106 (536)
T PF04348_consen 36 QEGDWAQAQALLNQLDP---QQLSPSQQARYQLLRARLALAQGDPEQALSLLNAQDLWQL------PPEQQARYHQLRAQ 106 (536)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred hCCCHHHHHHHHHhccc---ccCChHHHHHHHHHHHHHHHhcCCHHHHHHHhccCCcccC------CHHHHHHHHHHHHH
Confidence 57999999999999986 4567789999999999999999999999988887554332 23566899999999
Q ss_pred HHHHhhhHHHHHHHHHHHHc
Q psy4458 84 LDQHEGSYLATCKHYRAILT 103 (303)
Q Consensus 84 ~~~~~~~f~eaa~~y~e~~~ 103 (303)
.+...++.++|++.+..+..
T Consensus 107 a~~~~~~~l~Aa~~~i~l~~ 126 (536)
T PF04348_consen 107 AYEQQGDPLAAARERIALDP 126 (536)
T ss_dssp --------------------
T ss_pred HHHhcCCHHHHHHHHHHHhh
Confidence 99999999999998877643
No 38
>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=88.55 E-value=0.37 Score=33.36 Aligned_cols=53 Identities=13% Similarity=0.174 Sum_probs=42.4
Q ss_pred ccCCHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhc
Q psy4458 4 DEGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKF 62 (303)
Q Consensus 4 ~~~~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~ 62 (303)
++|++++|.+.++.+--... .-.++.+..+++++..|++..|..+++++....
T Consensus 3 ~~~~~~~A~~~~~~~l~~~p------~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~ 55 (68)
T PF14559_consen 3 KQGDYDEAIELLEKALQRNP------DNPEARLLLAQCYLKQGQYDEAEELLERLLKQD 55 (68)
T ss_dssp HTTHHHHHHHHHHHHHHHTT------TSHHHHHHHHHHHHHTT-HHHHHHHHHCCHGGG
T ss_pred hccCHHHHHHHHHHHHHHCC------CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC
Confidence 47999999999999853321 245677889999999999999999999998755
No 39
>COG3107 LppC Putative lipoprotein [General function prediction only]
Probab=88.27 E-value=4 Score=40.51 Aligned_cols=88 Identities=17% Similarity=0.235 Sum_probs=77.0
Q ss_pred ccCCHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHH
Q psy4458 4 DEGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIE 83 (303)
Q Consensus 4 ~~~~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~ 83 (303)
++|+...|..+|..+++ .+....|.+..|--++|.+..+++..|...+.+...-.+. .-.+.|||...+.
T Consensus 75 ~e~k~~qA~~Ll~ql~~----~Ltd~Q~~~~~LL~ael~la~~q~~~Al~~L~~~~~~~ls------~~Qq~Ry~q~~a~ 144 (604)
T COG3107 75 EEGKTAQAQALLNQLPQ----ELTDAQRAEKSLLAAELALAQKQPAAALQQLAKLLPADLS------QNQQARYYQARAD 144 (604)
T ss_pred HcCChHHHHHHHHhccc----cCCHHHHHHHHHHHHHHHHhccChHHHHHHHhhcchhhcC------HHHHHHHHHHHHH
Confidence 47899999999999997 5789999999999999999999999999999998875532 2357999999999
Q ss_pred HHHHhhhHHHHHHHHHHH
Q psy4458 84 LDQHEGSYLATCKHYRAI 101 (303)
Q Consensus 84 ~~~~~~~f~eaa~~y~e~ 101 (303)
.....++-++|++-.-..
T Consensus 145 a~ea~~~~~~a~rari~~ 162 (604)
T COG3107 145 ALEARGDSIDAARARIAQ 162 (604)
T ss_pred HHhcccchHHHHHHHHHh
Confidence 999999999999876655
No 40
>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=87.84 E-value=3 Score=28.35 Aligned_cols=48 Identities=8% Similarity=0.102 Sum_probs=37.2
Q ss_pred HHHHhhhce--eeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCCCc
Q psy4458 209 RVMAKYYTR--ITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAG 256 (303)
Q Consensus 209 ~~isk~Y~~--Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~g 256 (303)
..+...+.. ++...||+.+++++.-+-..+..|+..|-+.-.-|..++
T Consensus 11 L~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~r~~~~~D~ 60 (62)
T PF12802_consen 11 LMALARHPGEELTQSELAERLGISKSTVSRIVKRLEKKGLVERERDPGDR 60 (62)
T ss_dssp HHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE-SSST
T ss_pred HHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCCCCCC
Confidence 333333444 999999999999999999999999999999877666553
No 41
>KOG2003|consensus
Probab=87.63 E-value=2.4 Score=41.28 Aligned_cols=76 Identities=9% Similarity=0.048 Sum_probs=54.8
Q ss_pred HHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHcCCCCCCCh
Q psy4458 32 VTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIELDQHEGSYLATCKHYRAILTTPCIQSDP 111 (303)
Q Consensus 32 ~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~~~~~~~~f~eaa~~y~e~~~t~~~~~~~ 111 (303)
.+.+.+++.+|=...|...|-.++.+++..+..+ ...- .-.+..|+.++|=..|++|||+++..|...-..
T Consensus 558 ~evl~qianiye~led~aqaie~~~q~~slip~d-----p~il----skl~dlydqegdksqafq~~ydsyryfp~nie~ 628 (840)
T KOG2003|consen 558 AEVLVQIANIYELLEDPAQAIELLMQANSLIPND-----PAIL----SKLADLYDQEGDKSQAFQCHYDSYRYFPCNIET 628 (840)
T ss_pred HHHHHHHHHHHHHhhCHHHHHHHHHHhcccCCCC-----HHHH----HHHHHHhhcccchhhhhhhhhhcccccCcchHH
Confidence 3455677788888889999988888888877422 2211 125778899999999999999999988763233
Q ss_pred HHHHH
Q psy4458 112 VQRHA 116 (303)
Q Consensus 112 ~~~~~ 116 (303)
.+|+.
T Consensus 629 iewl~ 633 (840)
T KOG2003|consen 629 IEWLA 633 (840)
T ss_pred HHHHH
Confidence 34544
No 42
>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B.
Probab=85.69 E-value=4.8 Score=27.39 Aligned_cols=59 Identities=14% Similarity=0.093 Sum_probs=45.6
Q ss_pred HHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHc
Q psy4458 36 LEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIELDQHEGSYLATCKHYRAILT 103 (303)
Q Consensus 36 L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~~~~~~~~f~eaa~~y~e~~~ 103 (303)
+..++.++..|||..|....+++-.... + . .......+..+...++|-+|...|.++..
T Consensus 1 ~~~a~~~~~~g~~~~A~~~~~~~l~~~P---~----~--~~a~~~lg~~~~~~g~~~~A~~~~~~a~~ 59 (65)
T PF13432_consen 1 YALARALYQQGDYDEAIAAFEQALKQDP---D----N--PEAWYLLGRILYQQGRYDEALAYYERALE 59 (65)
T ss_dssp HHHHHHHHHCTHHHHHHHHHHHHHCCST---T----H--HHHHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred ChHHHHHHHcCCHHHHHHHHHHHHHHCC---C----C--HHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence 4578899999999999999999886542 1 1 23344588888999999999999988864
No 43
>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=85.56 E-value=3.7 Score=27.97 Aligned_cols=47 Identities=13% Similarity=0.187 Sum_probs=37.8
Q ss_pred HHhhhceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCCCceEEec
Q psy4458 211 MAKYYTRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAGIINFA 261 (303)
Q Consensus 211 isk~Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~giV~f~ 261 (303)
+.+--..++++.||+.||+|+.-+-.-+..+-..|. |.++-|-+.+.
T Consensus 8 ~l~~~~~~s~~ela~~~~VS~~TiRRDl~~L~~~g~----i~r~~GG~~~~ 54 (57)
T PF08220_consen 8 LLKEKGKVSVKELAEEFGVSEMTIRRDLNKLEKQGL----IKRTHGGAVLN 54 (57)
T ss_pred HHHHcCCEEHHHHHHHHCcCHHHHHHHHHHHHHCCC----EEEEcCEEEeC
Confidence 334468999999999999999999999999999986 44555555443
No 44
>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=84.64 E-value=6.5 Score=26.97 Aligned_cols=64 Identities=11% Similarity=0.018 Sum_probs=50.3
Q ss_pred HHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHHHHHHhh-hHHHHHHHHHHHHc
Q psy4458 31 KVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIELDQHEG-SYLATCKHYRAILT 103 (303)
Q Consensus 31 k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~~~~~~~-~f~eaa~~y~e~~~ 103 (303)
..+.+...+..++..+||..|....+++-.... + +. ..+..++..+...+ +|.+|-..|..++.
T Consensus 2 ~a~~~~~~g~~~~~~~~~~~A~~~~~~ai~~~p---~--~~----~~~~~~g~~~~~~~~~~~~A~~~~~~al~ 66 (69)
T PF13414_consen 2 NAEAWYNLGQIYFQQGDYEEAIEYFEKAIELDP---N--NA----EAYYNLGLAYMKLGKDYEEAIEDFEKALK 66 (69)
T ss_dssp SHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHST---T--HH----HHHHHHHHHHHHTTTHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCC---C--CH----HHHHHHHHHHHHhCccHHHHHHHHHHHHH
Confidence 346788899999999999999999999987542 1 22 24555788888888 89999999888753
No 45
>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=84.33 E-value=5 Score=27.01 Aligned_cols=48 Identities=13% Similarity=0.103 Sum_probs=40.0
Q ss_pred HHHHhhhceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCCCc
Q psy4458 209 RVMAKYYTRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAG 256 (303)
Q Consensus 209 ~~isk~Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~g 256 (303)
..+..-+..++...||+.++++..-+=..+.+|+..|-|.-..|..|+
T Consensus 9 L~~l~~~~~~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~r~~~~~D~ 56 (59)
T PF01047_consen 9 LRILYENGGITQSELAEKLGISRSTVTRIIKRLEKKGLIERERDPDDR 56 (59)
T ss_dssp HHHHHHHSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTET
T ss_pred HHHHHHcCCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEeccCCCCC
Confidence 333445777999999999999999999999999999999888877654
No 46
>KOG4414|consensus
Probab=84.08 E-value=3.1 Score=34.33 Aligned_cols=43 Identities=14% Similarity=0.369 Sum_probs=34.9
Q ss_pred HHHHHHHHHHHHHHHHHhhhceeeHHHHHHHhCCCHHHHHHHH
Q psy4458 196 FKMLKHRVVEHNIRVMAKYYTRITLQRMCDLLGLPIEETEEFL 238 (303)
Q Consensus 196 ~~~l~~~i~ehNi~~isk~Y~~Itl~~la~ll~ls~~~vE~~l 238 (303)
...|+.+.+.+-...+++.|++|+...+|-.+|+|++++-+-+
T Consensus 111 maAf~D~~~kR~FaLl~qAYssI~~~D~A~FlGl~~ddAtk~i 153 (197)
T KOG4414|consen 111 MAAFRDATRKRAFALLLQAYSSIIADDFAAFLGLPEDDATKGI 153 (197)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHH
Confidence 4556666666666778899999999999999999999876544
No 47
>COG3063 PilF Tfp pilus assembly protein PilF [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=83.71 E-value=32 Score=30.78 Aligned_cols=115 Identities=16% Similarity=0.136 Sum_probs=80.4
Q ss_pred CchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHH------------------------
Q psy4458 26 MEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLM------------------------ 81 (303)
Q Consensus 26 ~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~------------------------ 81 (303)
-+..+-.+..++.+-=||..||+..|+..++|+-..-.+.-+ .|-..--||...
T Consensus 29 ~~~~~aa~arlqLal~YL~~gd~~~A~~nlekAL~~DPs~~~--a~~~~A~~Yq~~Ge~~~A~e~YrkAlsl~p~~GdVL 106 (250)
T COG3063 29 TDRNEAAKARLQLALGYLQQGDYAQAKKNLEKALEHDPSYYL--AHLVRAHYYQKLGENDLADESYRKALSLAPNNGDVL 106 (250)
T ss_pred ccHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcccHH--HHHHHHHHHHHcCChhhHHHHHHHHHhcCCCccchh
Confidence 456677788888888899999999999999998654322222 333322333222
Q ss_pred ---HHHHHHhhhHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHhCCC-CchhhHhHHHhhhhhh
Q psy4458 82 ---IELDQHEGSYLATCKHYRAILTTPCIQSDPVQRHAVLQNVVLYLMLAPY-DNEQSDLTHRVLEDKL 146 (303)
Q Consensus 82 ---~~~~~~~~~f~eaa~~y~e~~~t~~~~~~~~~~~~~L~~~v~~~iLs~~-~~~r~~ll~~l~~~~~ 146 (303)
+-+++..+.|-+|-..|..++..|...+ .-.++.++.+|++=+.- +..+..+...+..||.
T Consensus 107 NNYG~FLC~qg~~~eA~q~F~~Al~~P~Y~~----~s~t~eN~G~Cal~~gq~~~A~~~l~raL~~dp~ 171 (250)
T COG3063 107 NNYGAFLCAQGRPEEAMQQFERALADPAYGE----PSDTLENLGLCALKAGQFDQAEEYLKRALELDPQ 171 (250)
T ss_pred hhhhHHHHhCCChHHHHHHHHHHHhCCCCCC----cchhhhhhHHHHhhcCCchhHHHHHHHHHHhCcC
Confidence 5778888999999999999998887643 23468899999997664 4455555556666663
No 48
>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=83.67 E-value=14 Score=36.97 Aligned_cols=66 Identities=21% Similarity=0.193 Sum_probs=54.8
Q ss_pred HHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHcC
Q psy4458 30 EKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIELDQHEGSYLATCKHYRAILTT 104 (303)
Q Consensus 30 ~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~~~~~~~~f~eaa~~y~e~~~t 104 (303)
|.-|++|-++.+..+.|++.+|-..+.+....+.+. +.+....|.++..-+++.+|...|.+++..
T Consensus 2 E~SE~lLY~~~il~e~g~~~~AL~~L~~~~~~I~Dk---------~~~~E~rA~ll~kLg~~~eA~~~y~~Li~r 67 (517)
T PF12569_consen 2 EHSELLLYKNSILEEAGDYEEALEHLEKNEKQILDK---------LAVLEKRAELLLKLGRKEEAEKIYRELIDR 67 (517)
T ss_pred cHHHHHHHHHHHHHHCCCHHHHHHHHHhhhhhCCCH---------HHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence 345788999999999999999999998877766432 567777888999999999999999999864
No 49
>KOG3081|consensus
Probab=82.81 E-value=38 Score=30.99 Aligned_cols=83 Identities=11% Similarity=0.072 Sum_probs=46.3
Q ss_pred CccCCHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHH
Q psy4458 3 EDEGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMI 82 (303)
Q Consensus 3 e~~~~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~ 82 (303)
-.+|++++|.+++.. + +-+|...-.+.+.+....++.|+.-+++....- +...-.++-...+
T Consensus 119 ~~~~~~deAl~~~~~--~---------~~lE~~Al~VqI~lk~~r~d~A~~~lk~mq~id-------ed~tLtQLA~awv 180 (299)
T KOG3081|consen 119 MHDGDFDEALKALHL--G---------ENLEAAALNVQILLKMHRFDLAEKELKKMQQID-------EDATLTQLAQAWV 180 (299)
T ss_pred hcCCChHHHHHHHhc--c---------chHHHHHHHHHHHHHHHHHHHHHHHHHHHHccc-------hHHHHHHHHHHHH
Confidence 356888888888766 3 335555556666666666666666666554211 1112223444444
Q ss_pred HHHHHhhhHHHHHHHHHHHHc
Q psy4458 83 ELDQHEGSYLATCKHYRAILT 103 (303)
Q Consensus 83 ~~~~~~~~f~eaa~~y~e~~~ 103 (303)
.......++.+|+-.|.|.++
T Consensus 181 ~la~ggek~qdAfyifeE~s~ 201 (299)
T KOG3081|consen 181 KLATGGEKIQDAFYIFEELSE 201 (299)
T ss_pred HHhccchhhhhHHHHHHHHhc
Confidence 555555555555555555554
No 50
>KOG1156|consensus
Probab=82.62 E-value=50 Score=33.81 Aligned_cols=91 Identities=22% Similarity=0.241 Sum_probs=69.6
Q ss_pred cCCHHHHHHHHhccc--cccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHH
Q psy4458 5 EGDVTEAANIIQELQ--VETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMI 82 (303)
Q Consensus 5 ~~~~~~Aa~~L~~i~--vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~ 82 (303)
.|+...|.+++++.. -+|..+-..-+..+..|.+.++..+.|-+..|...+.+..+.+.+ |+.|....+
T Consensus 156 ~g~y~~A~~il~ef~~t~~~~~s~~~~e~se~~Ly~n~i~~E~g~~q~ale~L~~~e~~i~D---------kla~~e~ka 226 (700)
T KOG1156|consen 156 LGEYKMALEILEEFEKTQNTSPSKEDYEHSELLLYQNQILIEAGSLQKALEHLLDNEKQIVD---------KLAFEETKA 226 (700)
T ss_pred HHHHHHHHHHHHHHHHhhccCCCHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHhhhhHHHH---------HHHHhhhHH
Confidence 377888888887752 222234455688899999999999999988888888777766532 366777788
Q ss_pred HHHHHhhhHHHHHHHHHHHHcC
Q psy4458 83 ELDQHEGSYLATCKHYRAILTT 104 (303)
Q Consensus 83 ~~~~~~~~f~eaa~~y~e~~~t 104 (303)
.++.-.+.+.+|...|.-++.-
T Consensus 227 ~l~~kl~~lEeA~~~y~~Ll~r 248 (700)
T KOG1156|consen 227 DLLMKLGQLEEAVKVYRRLLER 248 (700)
T ss_pred HHHHHHhhHHhHHHHHHHHHhh
Confidence 8888889999999999988754
No 51
>KOG0553|consensus
Probab=82.23 E-value=23 Score=32.74 Aligned_cols=152 Identities=14% Similarity=0.118 Sum_probs=95.8
Q ss_pred HHHHHHHHhhhHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHhCCCCchhhHhHHHhhhhhhcCCchHHHHHHHH
Q psy4458 80 LMIELDQHEGSYLATCKHYRAILTTPCIQSDPVQRHAVLQNVVLYLMLAPYDNEQSDLTHRVLEDKLLNEIPLYKGLLQW 159 (303)
Q Consensus 80 ~~~~~~~~~~~f~eaa~~y~e~~~t~~~~~~~~~~~~~L~~~v~~~iLs~~~~~r~~ll~~l~~~~~~~~~p~~~~L~~~ 159 (303)
.++--+...++|.+|-..|-+++.- ++.+.+-....+..|.=|.-+..--.+-.+.+.-||.... .|..|.-+
T Consensus 86 ~eGN~~m~~~~Y~eAv~kY~~AI~l-----~P~nAVyycNRAAAy~~Lg~~~~AVkDce~Al~iDp~ysk--ay~RLG~A 158 (304)
T KOG0553|consen 86 NEGNKLMKNKDYQEAVDKYTEAIEL-----DPTNAVYYCNRAAAYSKLGEYEDAVKDCESALSIDPHYSK--AYGRLGLA 158 (304)
T ss_pred HHHHHHHHhhhHHHHHHHHHHHHhc-----CCCcchHHHHHHHHHHHhcchHHHHHHHHHHHhcChHHHH--HHHHHHHH
Confidence 5677778899999999999999753 4444444445577777777777777788888888887644 58888889
Q ss_pred hcCCcccCchHHHHHHHHhhcccccccccchhHHhHHHHHHHHHHHHHHHHHHhhhceeeHHHHHHHhCCC---------
Q psy4458 160 FTNPELIKWSGLRQLYEEELFKTSVFNQSTEEGQKCFKMLKHRVVEHNIRVMAKYYTRITLQRMCDLLGLP--------- 230 (303)
Q Consensus 160 f~~~~li~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~~l~~~i~ehNi~~isk~Y~~Itl~~la~ll~ls--------- 230 (303)
|++.. ++......|.+.|.=+|- -...++.|+. .+.+++--..+=..+.-..++.++|-.
T Consensus 159 ~~~~g--k~~~A~~aykKaLeldP~-------Ne~~K~nL~~--Ae~~l~e~~~~~~~~~~~d~~~~ig~~Pd~~s~~~~ 227 (304)
T KOG0553|consen 159 YLALG--KYEEAIEAYKKALELDPD-------NESYKSNLKI--AEQKLNEPKSSAQASGSFDMAGLIGAFPDSRSMFNG 227 (304)
T ss_pred HHccC--cHHHHHHHHHhhhccCCC-------cHHHHHHHHH--HHHHhcCCCcccccccchhhhhhccCCccchhhhcc
Confidence 87774 566666678776644441 1222233332 232222222122445556666666663
Q ss_pred ----HHHHHHHHHhhhhcCceEE
Q psy4458 231 ----IEETEEFLSSMVVSKTITA 249 (303)
Q Consensus 231 ----~~~vE~~l~~mI~~~~l~a 249 (303)
.+.+-.....|+.+|.+++
T Consensus 228 ~l~nnp~l~~~~~~m~~~~~~~~ 250 (304)
T KOG0553|consen 228 DLMNNPQLMQLASQMMKDGALNG 250 (304)
T ss_pred ccccCHHHHHHHHHHhhcccccC
Confidence 3456667788888666654
No 52
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=82.05 E-value=4.6 Score=28.59 Aligned_cols=32 Identities=25% Similarity=0.327 Sum_probs=30.2
Q ss_pred eeHHHHHHHhCCCHHHHHHHHHhhhhcCceEE
Q psy4458 218 ITLQRMCDLLGLPIEETEEFLSSMVVSKTITA 249 (303)
Q Consensus 218 Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~a 249 (303)
++...||+.+|++...|.+.|..|...|.+..
T Consensus 23 ~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~ 54 (68)
T smart00550 23 STALQLAKNLGLPKKEVNRVLYSLEKKGKVCK 54 (68)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence 99999999999999999999999999998754
No 53
>KOG3250|consensus
Probab=81.60 E-value=2 Score=37.74 Aligned_cols=74 Identities=15% Similarity=0.268 Sum_probs=57.0
Q ss_pred hhhceeeHHHHHHHhCC-CHHHHHHHHHhhhhcCceEEEecCCCceEEeccC-------CC---hhHHHHHHHHHHHHHH
Q psy4458 213 KYYTRITLQRMCDLLGL-PIEETEEFLSSMVVSKTITAKIDRPAGIINFARN-------KD---PGEILNEWSASLNELM 281 (303)
Q Consensus 213 k~Y~~Itl~~la~ll~l-s~~~vE~~l~~mI~~~~l~akIDq~~giV~f~~~-------~~---~~~~l~~w~~~i~~l~ 281 (303)
.+-+.|.-.-|-.++.+ ++-++|.+|.+.+-.+-+.|||||.++.++..+. ++ .--.|.+|.+.-..++
T Consensus 105 s~~k~lpy~~Ll~~l~~~nvrelEd~iieamya~IlrGkldqr~q~leV~faigRdlr~k~i~nm~~TL~~w~~~cenvL 184 (258)
T KOG3250|consen 105 SFEKCLPYLVLLRLLPSRNVRELEDLIIEAMYADILRGKLDQRNQTLEVDFAIGRDLRSKDIDNMKYTLDEWCEGCENVL 184 (258)
T ss_pred hhchhhhHHHHHhhccCCchhHHHHHHHHHHHHHHHHhhHHhhcceEeechhhcccccHhHHHHHHHHHHHHHHHHHHHH
Confidence 34555555667777776 5789999999999999999999999999876643 22 2346889998888888
Q ss_pred HHHHH
Q psy4458 282 KLVNN 286 (303)
Q Consensus 282 ~~v~~ 286 (303)
-.++.
T Consensus 185 ~~ie~ 189 (258)
T KOG3250|consen 185 FGIEA 189 (258)
T ss_pred HHHHh
Confidence 77765
No 54
>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=81.30 E-value=5.4 Score=25.77 Aligned_cols=33 Identities=21% Similarity=0.374 Sum_probs=28.2
Q ss_pred hceeeHHHHHHHhCCCHHHHHHHHHhhhhcCce
Q psy4458 215 YTRITLQRMCDLLGLPIEETEEFLSSMVVSKTI 247 (303)
Q Consensus 215 Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l 247 (303)
=..+|...||+.+|+|..-+-..+-+|+..|-|
T Consensus 15 ~~~~t~~ela~~~~is~~tv~~~l~~L~~~g~I 47 (48)
T PF13412_consen 15 NPRITQKELAEKLGISRSTVNRYLKKLEEKGLI 47 (48)
T ss_dssp CTTS-HHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred cCCCCHHHHHHHhCCCHHHHHHHHHHHHHCcCc
Confidence 345999999999999999999999999999976
No 55
>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=80.72 E-value=4.4 Score=25.74 Aligned_cols=47 Identities=15% Similarity=0.270 Sum_probs=33.4
Q ss_pred eeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCCCceEEeccCCChhHHHHHHHH
Q psy4458 218 ITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAGIINFARNKDPGEILNEWSA 275 (303)
Q Consensus 218 Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~giV~f~~~~~~~~~l~~w~~ 275 (303)
+|++.+|+.+|+|..- +-+++.+|.|.+... .+...|.. +.+..|-+
T Consensus 2 lt~~e~a~~lgis~~t----i~~~~~~g~i~~~~~--g~~~~~~~-----~~l~~~~~ 48 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDT----VYRLIHEGELPAYRV--GRHYRIPR-----EDVDEYLE 48 (49)
T ss_pred CCHHHHHHHHCCCHHH----HHHHHHcCCCCeEEe--CCeEEEeH-----HHHHHHHh
Confidence 4789999999999876 455678899987543 45556653 35667754
No 56
>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=80.36 E-value=3.3 Score=30.00 Aligned_cols=38 Identities=13% Similarity=0.142 Sum_probs=33.1
Q ss_pred HHHhhhceeeHHHHHHHhCCCHHHHHHHHHhhhhcCce
Q psy4458 210 VMAKYYTRITLQRMCDLLGLPIEETEEFLSSMVVSKTI 247 (303)
Q Consensus 210 ~isk~Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l 247 (303)
.+++++...|.+.||+.+|+|+.-|...+..+...|.+
T Consensus 25 ~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~~~~~~~~ 62 (73)
T TIGR03879 25 ALAREEAGKTASEIAEELGRTEQTVRNHLKGETKAGGL 62 (73)
T ss_pred HHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcCcccchH
Confidence 34467899999999999999999999999988888765
No 57
>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=79.78 E-value=11 Score=25.89 Aligned_cols=44 Identities=11% Similarity=0.233 Sum_probs=37.4
Q ss_pred eeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCCCceEEec
Q psy4458 218 ITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAGIINFA 261 (303)
Q Consensus 218 Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~giV~f~ 261 (303)
++.+.+++.+|+|...+-..+..|...|-+...-+...+...+.
T Consensus 21 ~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~~~~~~~~~~~~~ 64 (78)
T cd00090 21 LTVSELAERLGLSQSTVSRHLKKLEEAGLVESRREGRRVYYSLT 64 (78)
T ss_pred cCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEEEEeccEEEEEeC
Confidence 99999999999999999999999999999988766644444444
No 58
>KOG1861|consensus
Probab=79.70 E-value=28 Score=34.25 Aligned_cols=138 Identities=13% Similarity=0.147 Sum_probs=83.0
Q ss_pred HHHHHHHHHHHHHhhhHHHHHHHHHHHHc--CCCCCCChHHHHHHHHHHHHHHHhCCCCchhhHhHHHhhhhhhcCCchH
Q psy4458 75 LKYYRLMIELDQHEGSYLATCKHYRAILT--TPCIQSDPVQRHAVLQNVVLYLMLAPYDNEQSDLTHRVLEDKLLNEIPL 152 (303)
Q Consensus 75 ~~y~~~~~~~~~~~~~f~eaa~~y~e~~~--t~~~~~~~~~~~~~L~~~v~~~iLs~~~~~r~~ll~~l~~~~~~~~~p~ 152 (303)
+.-|...+|+.+..+|--|=-+|--.+.. .+.+. ....+..-|-|+|-|++.-.++...+|..+.. +..+-|.
T Consensus 348 veVYEtHARIALEkGD~~EfNQCQtQLk~LY~egip---g~~~EF~AYriLY~i~tkN~~di~sll~~lt~--E~ked~~ 422 (540)
T KOG1861|consen 348 VEVYETHARIALEKGDLEEFNQCQTQLKALYSEGIP---GAYLEFTAYRILYYIFTKNYPDILSLLRDLTE--EDKEDEA 422 (540)
T ss_pred eeeehhhhHHHHhcCCHHHHHHHHHHHHHHHccCCC---CchhhHHHHHHHHHHHhcCchHHHHHHHhccH--hhccCHH
Confidence 34577789999999998885444433332 33332 12466677889999998876666666665553 3334444
Q ss_pred HH---HHHHHhcCCcccCchHHHHHHHHhhcccccccccchhHHhHHHHHHHHHHHHHHHHHHhhhc-eeeHHHHHHHhC
Q psy4458 153 YK---GLLQWFTNPELIKWSGLRQLYEEELFKTSVFNQSTEEGQKCFKMLKHRVVEHNIRVMAKYYT-RITLQRMCDLLG 228 (303)
Q Consensus 153 ~~---~L~~~f~~~~li~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~~l~~~i~ehNi~~isk~Y~-~Itl~~la~ll~ 228 (303)
+. ++-.+-..++ |-.++.-|. .-|.+. |+ -++.+..+-+-.-+.++.|.|. +|+++.|++.|.
T Consensus 423 V~hAL~vR~A~~~GN---Y~kFFrLY~----~AP~M~-----~y-LmdlF~erER~~Al~ii~KsyrP~i~~~fi~~~la 489 (540)
T KOG1861|consen 423 VAHALEVRSAVTLGN---YHKFFRLYL----TAPNMS-----GY-LMDLFLERERKKALTIICKSYRPTITVDFIASELA 489 (540)
T ss_pred HHHHHHHHHHHHhcc---HHHHHHHHh----hcccch-----hH-HHHHHHHHHHHHHHHHHHHHcCCCccHHHHhhhhh
Confidence 43 3344444442 333333332 223331 11 1344555556666788999999 999999999877
Q ss_pred CC
Q psy4458 229 LP 230 (303)
Q Consensus 229 ls 230 (303)
+.
T Consensus 490 f~ 491 (540)
T KOG1861|consen 490 FD 491 (540)
T ss_pred hc
Confidence 64
No 59
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=79.23 E-value=22 Score=26.03 Aligned_cols=65 Identities=11% Similarity=0.151 Sum_probs=45.2
Q ss_pred eeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCCCceEEecc-CCChhHHHHHHHHHHHHHH
Q psy4458 217 RITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAGIINFAR-NKDPGEILNEWSASLNELM 281 (303)
Q Consensus 217 ~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~giV~f~~-~~~~~~~l~~w~~~i~~l~ 281 (303)
.++...||+.++++..-+-..+.+|...|-+...-|+.++-..+-. .......+..+...+....
T Consensus 24 ~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~~~~~~~~~r~~~~~lT~~g~~~~~~~~~~~~~~~ 89 (101)
T smart00347 24 PLSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRLPSPEDRRSVLVSLTEEGRELIEELLEARHETL 89 (101)
T ss_pred CcCHHHHHHHHCCCchhHHHHHHHHHHCCCeEecCCCCCCCeEEEEECHhHHHHHHHHHHHHHHHH
Confidence 5899999999999999999999999999999887775544432222 2222334444444444433
No 60
>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=79.20 E-value=17 Score=24.64 Aligned_cols=85 Identities=14% Similarity=0.002 Sum_probs=57.7
Q ss_pred ccCCHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHH
Q psy4458 4 DEGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIE 83 (303)
Q Consensus 4 ~~~~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~ 83 (303)
..|++.+|.+.+..+--.. +... ......+.++...+++..|..+.+++..... . +. ..+...+.
T Consensus 12 ~~~~~~~A~~~~~~~~~~~----~~~~--~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~--~---~~----~~~~~~~~ 76 (100)
T cd00189 12 KLGDYDEALEYYEKALELD----PDNA--DAYYNLAAAYYKLGKYEEALEDYEKALELDP--D---NA----KAYYNLGL 76 (100)
T ss_pred HHhcHHHHHHHHHHHHhcC----CccH--HHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC--c---ch----hHHHHHHH
Confidence 3688899998887763221 1111 5677788888888999999988887765441 1 11 33445677
Q ss_pred HHHHhhhHHHHHHHHHHHHc
Q psy4458 84 LDQHEGSYLATCKHYRAILT 103 (303)
Q Consensus 84 ~~~~~~~f~eaa~~y~e~~~ 103 (303)
.+...+++.+|...|..+..
T Consensus 77 ~~~~~~~~~~a~~~~~~~~~ 96 (100)
T cd00189 77 AYYKLGKYEEALEAYEKALE 96 (100)
T ss_pred HHHHHHhHHHHHHHHHHHHc
Confidence 77778888888887777653
No 61
>PF13429 TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2_B.
Probab=78.81 E-value=25 Score=31.49 Aligned_cols=88 Identities=17% Similarity=0.264 Sum_probs=43.6
Q ss_pred ccCCHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHH
Q psy4458 4 DEGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIE 83 (303)
Q Consensus 4 ~~~~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~ 83 (303)
..|++++|++++..- .+.+ ..-+++...+.++...++|.++...++++.... ...+ --.|+...+.
T Consensus 89 ~~~~~~~A~~~~~~~-~~~~------~~~~~l~~~l~~~~~~~~~~~~~~~l~~~~~~~-~~~~------~~~~~~~~a~ 154 (280)
T PF13429_consen 89 QDGDPEEALKLAEKA-YERD------GDPRYLLSALQLYYRLGDYDEAEELLEKLEELP-AAPD------SARFWLALAE 154 (280)
T ss_dssp ------------------------------------H-HHHTT-HHHHHHHHHHHHH-T----T-------HHHHHHHHH
T ss_pred ccccccccccccccc-cccc------cccchhhHHHHHHHHHhHHHHHHHHHHHHHhcc-CCCC------CHHHHHHHHH
Confidence 457778888776542 2221 234566677788899999999999999987432 1111 1456777899
Q ss_pred HHHHhhhHHHHHHHHHHHHcCC
Q psy4458 84 LDQHEGSYLATCKHYRAILTTP 105 (303)
Q Consensus 84 ~~~~~~~f~eaa~~y~e~~~t~ 105 (303)
++...+++.+|-..|..++...
T Consensus 155 ~~~~~G~~~~A~~~~~~al~~~ 176 (280)
T PF13429_consen 155 IYEQLGDPDKALRDYRKALELD 176 (280)
T ss_dssp HHHHCCHHHHHHHHHHHHHHH-
T ss_pred HHHHcCCHHHHHHHHHHHHHcC
Confidence 9999999999999999998643
No 62
>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=78.52 E-value=5.9 Score=29.04 Aligned_cols=47 Identities=13% Similarity=0.170 Sum_probs=37.2
Q ss_pred eeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCCCceEEeccCC
Q psy4458 218 ITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAGIINFARNK 264 (303)
Q Consensus 218 Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~giV~f~~~~ 264 (303)
+|.+.||+.+|+|+..+++.+..+...|-+.++=-+..|+.-..+++
T Consensus 26 ~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s~~G~~GGy~L~~~~~ 72 (83)
T PF02082_consen 26 VSSKEIAERLGISPSYLRKILQKLKKAGLIESSRGRGGGYRLARPPE 72 (83)
T ss_dssp BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETSTTSEEEESS-CC
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEecCCCCCceeecCCHH
Confidence 99999999999999999999999999999877655555555444443
No 63
>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=78.46 E-value=69 Score=32.80 Aligned_cols=62 Identities=16% Similarity=0.091 Sum_probs=38.6
Q ss_pred HHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHcC
Q psy4458 34 LILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIELDQHEGSYLATCKHYRAILTT 104 (303)
Q Consensus 34 ~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~~~~~~~~f~eaa~~y~e~~~t 104 (303)
.++..+++++..|++..|...++++-.... . + ...+...+.++...++|.+|...|..+...
T Consensus 161 ~~~~la~~~~~~~~~~~A~~~~~~~~~~~~--~---~----~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~ 222 (899)
T TIGR02917 161 AKLGLAQLALAENRFDEARALIDEVLTADP--G---N----VDALLLKGDLLLSLGNIELALAAYRKAIAL 222 (899)
T ss_pred hHHHHHHHHHHCCCHHHHHHHHHHHHHhCC--C---C----hHHHHHHHHHHHhcCCHHHHHHHHHHHHhh
Confidence 455566666666666666666666543321 1 1 123344677777888888888888887653
No 64
>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=78.45 E-value=21 Score=30.45 Aligned_cols=142 Identities=13% Similarity=0.199 Sum_probs=67.3
Q ss_pred HHHHHHHHHHHHHHhhhHHH---HHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHhCCCCchhhHhHHHhhhhhhcCCc
Q psy4458 74 KLKYYRLMIELDQHEGSYLA---TCKHYRAILTTPCIQSDPVQRHAVLQNVVLYLMLAPYDNEQSDLTHRVLEDKLLNEI 150 (303)
Q Consensus 74 k~~y~~~~~~~~~~~~~f~e---aa~~y~e~~~t~~~~~~~~~~~~~L~~~v~~~iLs~~~~~r~~ll~~l~~~~~~~~~ 150 (303)
-+.-+...++++...+|..+ ......+.|.................+.+++.+.....++-...+..+- ++...-
T Consensus 55 ~i~v~E~~ar~~i~~~d~~qf~~c~~~L~~lY~~~~~~~~~~~~~ef~~y~lL~~l~~~~~~~~~~~l~~l~--~~~~~~ 132 (204)
T PF03399_consen 55 AIKVYERIARFAIESGDLEQFNQCLSQLKELYDDLRDLPPSPNEAEFIAYYLLYLLCQNNIPDFHMELELLP--SEILSS 132 (204)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT---TTHHHHHHHHHHHTT-T---THHHHHHTTS---HHHHTS
T ss_pred HHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHhhccCCCCCCHHHHHHHHHHHHHHcccchHHHHHHHHCc--hhhhcC
Confidence 45666677777776655444 3333333333210000112234455566777665543333333333331 112223
Q ss_pred hHH---HHHHHHhcCCcccCchHHHHHHHHhhcccccccccchhHHhH-HHHHHHHHHHHHHHHHHhhhce-eeHHHHHH
Q psy4458 151 PLY---KGLLQWFTNPELIKWSGLRQLYEEELFKTSVFNQSTEEGQKC-FKMLKHRVVEHNIRVMAKYYTR-ITLQRMCD 225 (303)
Q Consensus 151 p~~---~~L~~~f~~~~li~~~~~~~~~~~~L~~~~~~~~~~~~~~~~-~~~l~~~i~ehNi~~isk~Y~~-Itl~~la~ 225 (303)
|.+ -.+..++..++ |..+...+.+ ...+.. ..+ ...+..+++.+=+..+.+.|.+ |+++.+++
T Consensus 133 ~~i~~al~l~~a~~~gn---y~~ff~l~~~--~~~~~l-------~~~l~~~~~~~iR~~al~~i~~ay~~~i~l~~l~~ 200 (204)
T PF03399_consen 133 PYIQFALELCRALMEGN---YVRFFRLYRS--KSAPYL-------FACLMERFFNRIRLRALQSISKAYRSSIPLSFLAE 200 (204)
T ss_dssp HHHHHHHHHHHHH--TT---HHHHHHHHT---TTS-HH-------HHHHHGGGHHHHHHHHHHHHHHHS-T-EEHHHHHH
T ss_pred HHHHHHHHHHHHHHcCC---HHHHHHHHhc--cCCChH-------HHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHH
Confidence 333 35678888775 4333332211 111111 011 1224567888888999999999 99999999
Q ss_pred HhCC
Q psy4458 226 LLGL 229 (303)
Q Consensus 226 ll~l 229 (303)
.||.
T Consensus 201 ~L~F 204 (204)
T PF03399_consen 201 LLGF 204 (204)
T ss_dssp HTT-
T ss_pred HcCC
Confidence 9874
No 65
>PF12728 HTH_17: Helix-turn-helix domain
Probab=78.10 E-value=6.3 Score=25.78 Aligned_cols=47 Identities=15% Similarity=0.301 Sum_probs=34.7
Q ss_pred eeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCCCceEEeccCCChhHHHHHHHH
Q psy4458 218 ITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAGIINFARNKDPGEILNEWSA 275 (303)
Q Consensus 218 Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~giV~f~~~~~~~~~l~~w~~ 275 (303)
+|.+.+|+.||+|..- +-+++..|.|.+. .+.+.+.|.+ +.++.|-+
T Consensus 2 lt~~e~a~~l~is~~t----v~~~~~~g~i~~~--~~g~~~~~~~-----~~l~~~~~ 48 (51)
T PF12728_consen 2 LTVKEAAELLGISRST----VYRWIRQGKIPPF--KIGRKWRIPK-----SDLDRWLE 48 (51)
T ss_pred CCHHHHHHHHCcCHHH----HHHHHHcCCCCeE--EeCCEEEEeH-----HHHHHHHH
Confidence 4789999999999877 5567789999776 3556666654 35777764
No 66
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=77.95 E-value=4.1 Score=25.90 Aligned_cols=32 Identities=28% Similarity=0.372 Sum_probs=29.7
Q ss_pred eeeHHHHHHHhCCCHHHHHHHHHhhhhcCceE
Q psy4458 217 RITLQRMCDLLGLPIEETEEFLSSMVVSKTIT 248 (303)
Q Consensus 217 ~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~ 248 (303)
.++...||+.+|+|...+-+.+..|...|-+.
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L~~~g~l~ 39 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRLEKEGLIS 39 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 47889999999999999999999999999885
No 67
>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=77.87 E-value=28 Score=27.95 Aligned_cols=87 Identities=15% Similarity=0.112 Sum_probs=63.4
Q ss_pred cCCHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHHH
Q psy4458 5 EGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIEL 84 (303)
Q Consensus 5 ~~~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~~ 84 (303)
.|++..+...+..+.-+-.+ ...-..-.|..+..++..||+..|...++++.... . +..++..-....+++
T Consensus 24 ~~~~~~~~~~~~~l~~~~~~---s~ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~----~--d~~l~~~a~l~LA~~ 94 (145)
T PF09976_consen 24 AGDPAKAEAAAEQLAKDYPS---SPYAALAALQLAKAAYEQGDYDEAKAALEKALANA----P--DPELKPLARLRLARI 94 (145)
T ss_pred CCCHHHHHHHHHHHHHHCCC---ChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhC----C--CHHHHHHHHHHHHHH
Confidence 56777777766666543222 22556667889999999999999999999987643 1 335555555568999
Q ss_pred HHHhhhHHHHHHHHHH
Q psy4458 85 DQHEGSYLATCKHYRA 100 (303)
Q Consensus 85 ~~~~~~f~eaa~~y~e 100 (303)
+...++|-+|-..+..
T Consensus 95 ~~~~~~~d~Al~~L~~ 110 (145)
T PF09976_consen 95 LLQQGQYDEALATLQQ 110 (145)
T ss_pred HHHcCCHHHHHHHHHh
Confidence 9999999998887744
No 68
>KOG3054|consensus
Probab=77.57 E-value=7.5 Score=34.71 Aligned_cols=52 Identities=13% Similarity=0.243 Sum_probs=47.1
Q ss_pred HHhhhceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCCCceEEecc
Q psy4458 211 MAKYYTRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAGIINFAR 262 (303)
Q Consensus 211 isk~Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~giV~f~~ 262 (303)
+.+--+.|-|+.||..||+-..++-.-+-.++.+|.|.|.||-....|....
T Consensus 208 YIk~nKvV~ledLas~f~Lrtqd~inriq~~l~eg~ltGVmDDRGKfIYIS~ 259 (299)
T KOG3054|consen 208 YIKKNKVVPLEDLASEFGLRTQDSINRIQELLAEGLLTGVMDDRGKFIYISM 259 (299)
T ss_pred HHHhcCeeeHHHHHHHhCccHHHHHHHHHHHHHhhhheeeecCCCceEEecH
Confidence 3455789999999999999999999999999999999999999999998764
No 69
>PF10345 Cohesin_load: Cohesin loading factor; InterPro: IPR019440 Cohesin loading factor is a conserved protein that has been characterised in fungi. It is associated with the cohesin complex and is required in G1 for cohesin binding to chromosomes, but is dispensable in G2 when cohesion has been established. It is often referred to as Ssl3 in Schizosaccharomyces pombe (Fission yeast), and Scc4 in Saccharomyces cerevisiae (Baker's yeast). It complexes with Mis4 [].
Probab=77.44 E-value=64 Score=32.87 Aligned_cols=117 Identities=9% Similarity=0.033 Sum_probs=78.0
Q ss_pred cCCchHHHHHHHHHHHHHHH-hhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Q psy4458 24 GSMEKKEKVTLILEQMRLCL-AKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIELDQHEGSYLATCKHYRAIL 102 (303)
Q Consensus 24 ~~~~~~~k~~~~L~~~rL~L-~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~~~~~~~~f~eaa~~y~e~~ 102 (303)
..+++.......|+.+++.+ +..+++.|+.++.|+-..+.. .+ ..++|.+.....++++...+-.. |-+.....+
T Consensus 51 ~~l~p~~ea~~~l~la~iL~~eT~n~~~Ae~~L~k~~~l~~~-~~--~~d~k~~~~~ll~~i~~~~~~~~-a~~~l~~~I 126 (608)
T PF10345_consen 51 FKLSPRQEARVRLRLASILLEETENLDLAETYLEKAILLCER-HR--LTDLKFRCQFLLARIYFKTNPKA-ALKNLDKAI 126 (608)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhccc-cc--hHHHHHHHHHHHHHHHHhcCHHH-HHHHHHHHH
Confidence 56899999999999999999 889999999999999888843 55 88999988888888866555555 666666655
Q ss_pred cCCCCCCChHHHHHHHHHHHHHHHhCCCCc-hhhHhHHHhhhhh
Q psy4458 103 TTPCIQSDPVQRHAVLQNVVLYLMLAPYDN-EQSDLTHRVLEDK 145 (303)
Q Consensus 103 ~t~~~~~~~~~~~~~L~~~v~~~iLs~~~~-~r~~ll~~l~~~~ 145 (303)
+.... .+...|.-++..+-+...+...+. .-.+.+..+....
T Consensus 127 ~~~~~-~~~~~w~~~frll~~~l~~~~~d~~~Al~~L~~~~~~a 169 (608)
T PF10345_consen 127 EDSET-YGHSAWYYAFRLLKIQLALQHKDYNAALENLQSIAQLA 169 (608)
T ss_pred HHHhc-cCchhHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHh
Confidence 43221 122446666666523233222222 2334455555433
No 70
>KOG1585|consensus
Probab=76.66 E-value=53 Score=29.87 Aligned_cols=83 Identities=14% Similarity=0.116 Sum_probs=56.1
Q ss_pred HHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHH---------
Q psy4458 8 VTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYY--------- 78 (303)
Q Consensus 8 ~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~--------- 78 (303)
++.|+-++++++ --.|-.+++=+-..+|.+.|-.+-|...+.|+...+ ++.+| +.-+.+|
T Consensus 74 yEqaamLake~~-------klsEvvdl~eKAs~lY~E~GspdtAAmaleKAak~l-env~P---d~AlqlYqralavve~ 142 (308)
T KOG1585|consen 74 YEQAAMLAKELS-------KLSEVVDLYEKASELYVECGSPDTAAMALEKAAKAL-ENVKP---DDALQLYQRALAVVEE 142 (308)
T ss_pred HHHHHHHHHHHH-------HhHHHHHHHHHHHHHHHHhCCcchHHHHHHHHHHHh-hcCCH---HHHHHHHHHHHHHHhc
Confidence 344555555554 234778888889999999999999999999988766 33332 2223332
Q ss_pred -----------HHHHHHHHHhhhHHHHHHHHHHH
Q psy4458 79 -----------RLMIELDQHEGSYLATCKHYRAI 101 (303)
Q Consensus 79 -----------~~~~~~~~~~~~f~eaa~~y~e~ 101 (303)
.-.++.+.--+.|.||+..++.-
T Consensus 143 ~dr~~ma~el~gk~sr~lVrl~kf~Eaa~a~lKe 176 (308)
T KOG1585|consen 143 DDRDQMAFELYGKCSRVLVRLEKFTEAATAFLKE 176 (308)
T ss_pred cchHHHHHHHHHHhhhHhhhhHHhhHHHHHHHHh
Confidence 23357778888888888777644
No 71
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=75.73 E-value=26 Score=28.23 Aligned_cols=70 Identities=16% Similarity=0.349 Sum_probs=50.8
Q ss_pred eeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEE-Eec-CCCceEEeccCCCh-------hHHHHHHHHHHHHHHHHHHH
Q psy4458 217 RITLQRMCDLLGLPIEETEEFLSSMVVSKTITA-KID-RPAGIINFARNKDP-------GEILNEWSASLNELMKLVNN 286 (303)
Q Consensus 217 ~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~a-kID-q~~giV~f~~~~~~-------~~~l~~w~~~i~~l~~~v~~ 286 (303)
-.|.+.||+.++.+..-|.+-|-+++.-|-+.- ++. ...|....-.+-++ ...+++|..++.++.....+
T Consensus 42 ~~tvdelae~lnr~rStv~rsl~~L~~~GlV~Rek~~~~~Ggy~yiY~~i~~ee~k~~i~~~l~~w~~~~~~~i~~~~~ 120 (126)
T COG3355 42 PLTVDELAEILNRSRSTVYRSLQNLLEAGLVEREKVNLKGGGYYYLYKPIDPEEIKKKILKDLDEWYDKMKQLIEEFEK 120 (126)
T ss_pred CcCHHHHHHHHCccHHHHHHHHHHHHHcCCeeeeeeccCCCceeEEEecCCHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 457789999999999999999999999998843 555 34444443333332 35688888888887776654
No 72
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=75.43 E-value=7.8 Score=29.58 Aligned_cols=39 Identities=21% Similarity=0.277 Sum_probs=34.2
Q ss_pred hceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceE---EEecC
Q psy4458 215 YTRITLQRMCDLLGLPIEETEEFLSSMVVSKTIT---AKIDR 253 (303)
Q Consensus 215 Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~---akIDq 253 (303)
..+++++.||+.+|+|+..+-+.+.+|..+|-+. +.+|+
T Consensus 15 ~~~~~~~~la~~l~~s~~tv~~~l~~L~~~g~i~~~~~~~~~ 56 (108)
T smart00344 15 DARISLAELAKKVGLSPSTVHNRVKRLEEEGVIKGYTAVINP 56 (108)
T ss_pred hCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeceEEEeCH
Confidence 4689999999999999999999999999999775 45563
No 73
>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=75.26 E-value=5.2 Score=27.44 Aligned_cols=34 Identities=26% Similarity=0.314 Sum_probs=31.0
Q ss_pred ceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEE
Q psy4458 216 TRITLQRMCDLLGLPIEETEEFLSSMVVSKTITA 249 (303)
Q Consensus 216 ~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~a 249 (303)
..++.+.||+.+|+|..-+.+.+..|...|-|..
T Consensus 24 ~~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~~ 57 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSRTLKELEEEGLISR 57 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence 3589999999999999999999999999998864
No 74
>TIGR02917 PEP_TPR_lipo putative PEP-CTERM system TPR-repeat lipoprotein. This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.
Probab=75.17 E-value=80 Score=32.34 Aligned_cols=26 Identities=27% Similarity=0.325 Sum_probs=19.8
Q ss_pred HHHHHHHHHhhhHHHHHHHHHHHHcC
Q psy4458 79 RLMIELDQHEGSYLATCKHYRAILTT 104 (303)
Q Consensus 79 ~~~~~~~~~~~~f~eaa~~y~e~~~t 104 (303)
...+..+...++|.+|-..|..++..
T Consensus 707 ~~~~~~~~~~g~~~~A~~~~~~~~~~ 732 (899)
T TIGR02917 707 ELEGDLYLRQKDYPAAIQAYRKALKR 732 (899)
T ss_pred HHHHHHHHHCCCHHHHHHHHHHHHhh
Confidence 44677777888888888888887754
No 75
>PRK11447 cellulose synthase subunit BcsC; Provisional
Probab=74.66 E-value=69 Score=35.31 Aligned_cols=94 Identities=13% Similarity=0.126 Sum_probs=67.9
Q ss_pred CccCCHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHH-----
Q psy4458 3 EDEGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKY----- 77 (303)
Q Consensus 3 e~~~~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y----- 77 (303)
+..++.+.|.+.|+.+.. ++.+. .+.+..++|+++..||...|...++|+.....+... .+.....+
T Consensus 39 ~~~~~~d~a~~~l~kl~~-----~~p~~-p~~~~~~~~~~l~~g~~~~A~~~l~~l~~~~P~~~~--~~~~~~~~~~~~~ 110 (1157)
T PRK11447 39 EATHREDLVRQSLYRLEL-----IDPNN-PDVIAARFRLLLRQGDSDGAQKLLDRLSQLAPDSNA--YRSSRTTMLLSTP 110 (1157)
T ss_pred HhhCChHHHHHHHHHHHc-----cCCCC-HHHHHHHHHHHHhCCCHHHHHHHHHHHHhhCCCChH--HHHHHHHHHhcCC
Confidence 567888899999887742 12222 667889999999999999999999999877643221 22222221
Q ss_pred ----HHHHHHHHHHhhhHHHHHHHHHHHHcC
Q psy4458 78 ----YRLMIELDQHEGSYLATCKHYRAILTT 104 (303)
Q Consensus 78 ----~~~~~~~~~~~~~f~eaa~~y~e~~~t 104 (303)
....++.+...++|-+|...|..++..
T Consensus 111 ~~~~~l~~A~ll~~~g~~~eA~~~~~~~l~~ 141 (1157)
T PRK11447 111 EGRQALQQARLLATTGRTEEALASYDKLFNG 141 (1157)
T ss_pred chhhHHHHHHHHHhCCCHHHHHHHHHHHccC
Confidence 133567788899999999999999864
No 76
>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=74.45 E-value=67 Score=32.56 Aligned_cols=23 Identities=17% Similarity=0.329 Sum_probs=12.1
Q ss_pred HHHHHHHhhhHHHHHHHHHHHHc
Q psy4458 81 MIELDQHEGSYLATCKHYRAILT 103 (303)
Q Consensus 81 ~~~~~~~~~~f~eaa~~y~e~~~ 103 (303)
.+..+...++|.+|-.+|..+..
T Consensus 405 lg~~~~~~g~~~~A~~~~~kal~ 427 (615)
T TIGR00990 405 RAQLHFIKGEFAQAGKDYQKSID 427 (615)
T ss_pred HHHHHHHcCCHHHHHHHHHHHHH
Confidence 44445555555555555555543
No 77
>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=74.42 E-value=6.8 Score=23.62 Aligned_cols=30 Identities=30% Similarity=0.392 Sum_probs=24.1
Q ss_pred eeHHHHHHHhCCCHHHHHHHHHhhhhcCce
Q psy4458 218 ITLQRMCDLLGLPIEETEEFLSSMVVSKTI 247 (303)
Q Consensus 218 Itl~~la~ll~ls~~~vE~~l~~mI~~~~l 247 (303)
+|-+.||+.+|++++-|=+.+.++-.+|-|
T Consensus 3 mtr~diA~~lG~t~ETVSR~l~~l~~~glI 32 (32)
T PF00325_consen 3 MTRQDIADYLGLTRETVSRILKKLERQGLI 32 (32)
T ss_dssp --HHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred cCHHHHHHHhCCcHHHHHHHHHHHHHcCCC
Confidence 567889999999999999999999888754
No 78
>TIGR02552 LcrH_SycD type III secretion low calcium response chaperone LcrH/SycD. ScyD/LcrH contains three central tetratricopeptide-like repeats that are predicted to fold into an all-alpha-helical array.
Probab=73.77 E-value=40 Score=26.14 Aligned_cols=61 Identities=10% Similarity=-0.029 Sum_probs=28.9
Q ss_pred HHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Q psy4458 33 TLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIELDQHEGSYLATCKHYRAIL 102 (303)
Q Consensus 33 ~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~~~~~~~~f~eaa~~y~e~~ 102 (303)
+..+..+..++..+++..|.....++-.... .. ...+..++..+...++|-+|...|..+.
T Consensus 18 ~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~p--~~-------~~~~~~la~~~~~~~~~~~A~~~~~~~~ 78 (135)
T TIGR02552 18 EQIYALAYNLYQQGRYDEALKLFQLLAAYDP--YN-------SRYWLGLAACCQMLKEYEEAIDAYALAA 78 (135)
T ss_pred HHHHHHHHHHHHcccHHHHHHHHHHHHHhCC--Cc-------HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4445555555555666666555555443221 01 1122234444445555555555555554
No 79
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=73.14 E-value=10 Score=25.11 Aligned_cols=46 Identities=9% Similarity=0.191 Sum_probs=36.9
Q ss_pred hceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCCCceEEe
Q psy4458 215 YTRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAGIINF 260 (303)
Q Consensus 215 Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~giV~f 260 (303)
-..+++..|++.+|+|...+-..+..|...|-+...-+...+...+
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~~~~~~~~~~~~~ 53 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLREAGLVESRREGKRVYYSL 53 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeeecCCEEEEEE
Confidence 4568999999999999999999999999999997654443334433
No 80
>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=72.59 E-value=1.1e+02 Score=30.98 Aligned_cols=87 Identities=11% Similarity=0.032 Sum_probs=59.4
Q ss_pred CCHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHHHH
Q psy4458 6 GDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIELD 85 (303)
Q Consensus 6 ~~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~~~ 85 (303)
|.+++|...+...- +. +... ......+...+.+++..|++..|....+++-.... + .. ..+...+..+
T Consensus 308 ~~y~~A~~~~~~al-~~-~~~~-~~~a~a~~~lg~~~~~~g~~~eA~~~~~kal~l~P---~--~~----~~~~~la~~~ 375 (615)
T TIGR00990 308 ESYEEAARAFEKAL-DL-GKLG-EKEAIALNLRGTFKCLKGKHLEALADLSKSIELDP---R--VT----QSYIKRASMN 375 (615)
T ss_pred hhHHHHHHHHHHHH-hc-CCCC-hhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCC---C--cH----HHHHHHHHHH
Confidence 56777777665432 11 1111 23445567778888999999999999999875431 1 11 2344567778
Q ss_pred HHhhhHHHHHHHHHHHHcC
Q psy4458 86 QHEGSYLATCKHYRAILTT 104 (303)
Q Consensus 86 ~~~~~f~eaa~~y~e~~~t 104 (303)
...++|-+|...|..++..
T Consensus 376 ~~~g~~~eA~~~~~~al~~ 394 (615)
T TIGR00990 376 LELGDPDKAEEDFDKALKL 394 (615)
T ss_pred HHCCCHHHHHHHHHHHHHh
Confidence 8899999999999998765
No 81
>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=72.33 E-value=9.1 Score=25.28 Aligned_cols=38 Identities=24% Similarity=0.379 Sum_probs=31.6
Q ss_pred HHhhhceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceE
Q psy4458 211 MAKYYTRITLQRMCDLLGLPIEETEEFLSSMVVSKTIT 248 (303)
Q Consensus 211 isk~Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~ 248 (303)
++..=..+++..||+.+|+|..-+-.++..|...|-+.
T Consensus 12 l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~~g~v~ 49 (52)
T PF09339_consen 12 LAESGGPLTLSEIARALGLPKSTVHRLLQTLVEEGYVE 49 (52)
T ss_dssp HHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCcCee
Confidence 34445558999999999999999999999999998764
No 82
>PLN03218 maturation of RBCL 1; Provisional
Probab=72.05 E-value=1.6e+02 Score=32.37 Aligned_cols=62 Identities=11% Similarity=0.166 Sum_probs=36.7
Q ss_pred HHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHc
Q psy4458 34 LILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIELDQHEGSYLATCKHYRAILT 103 (303)
Q Consensus 34 ~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~~~~~~~~f~eaa~~y~e~~~ 103 (303)
.+-..+..|...|++..|..+.++....-.. .. ...|..++..|...+++.+|.+.|.+...
T Consensus 581 TynaLI~ay~k~G~ldeA~elf~~M~e~gi~-p~-------~~tynsLI~ay~k~G~~deAl~lf~eM~~ 642 (1060)
T PLN03218 581 TVGALMKACANAGQVDRAKEVYQMIHEYNIK-GT-------PEVYTIAVNSCSQKGDWDFALSIYDDMKK 642 (1060)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHHHHcCCC-CC-------hHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Confidence 3444555566666666666666655543211 11 23455666667777788888877777754
No 83
>PF09743 DUF2042: Uncharacterized conserved protein (DUF2042); InterPro: IPR018611 The ubiquitin fold modifier 1 (Ufm1) is the most recently discovered ubiquitin-like modifier whose conjugation (ufmylation) system is conserved in multicellular organisms. Ufm1 is known to covalently attach with cellular protein(s) via a specific E1-activating enzyme (Uba5), an E2-conjugating enzyme (Ufc1), and a E3-ligating enzyme []. This entry represents E3 UFM1-protein ligase 1.
Probab=71.64 E-value=21 Score=32.66 Aligned_cols=41 Identities=22% Similarity=0.279 Sum_probs=36.9
Q ss_pred hhceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCC
Q psy4458 214 YYTRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRP 254 (303)
Q Consensus 214 ~Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~ 254 (303)
---.|+++.||+.+++|.+++-..+......+.|+|++|..
T Consensus 127 e~G~vsi~eLa~~~~Lp~efl~~~li~~~lg~~I~g~~d~~ 167 (272)
T PF09743_consen 127 ESGQVSISELAKQYDLPSEFLKEELISKRLGKIIKGRLDGD 167 (272)
T ss_pred HcCeEeHHHHHHhcCCcHHHHHHHHhhhhcCcceeEEEeCC
Confidence 35889999999999999999997777778889999999988
No 84
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=71.45 E-value=12 Score=26.17 Aligned_cols=34 Identities=18% Similarity=0.332 Sum_probs=30.3
Q ss_pred hceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceE
Q psy4458 215 YTRITLQRMCDLLGLPIEETEEFLSSMVVSKTIT 248 (303)
Q Consensus 215 Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~ 248 (303)
..-++-..+|+++|+|.-.+-..|..+..+|++.
T Consensus 13 ~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~ 46 (62)
T PF04703_consen 13 NGPLKTREIADALGLSIYQARYYLEKLEKEGKVE 46 (62)
T ss_dssp TS-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEE
T ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEE
Confidence 6779999999999999999999999999999885
No 85
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=71.02 E-value=89 Score=29.02 Aligned_cols=88 Identities=15% Similarity=0.081 Sum_probs=42.0
Q ss_pred cCCHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHHH
Q psy4458 5 EGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIEL 84 (303)
Q Consensus 5 ~~~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~~ 84 (303)
.|++++|...++..--... .-.+.+...+.++...|++..|..+.+++.... .. ....+...+...+..
T Consensus 48 ~~~~~~A~~~~~~al~~~p------~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~-~~----~~~~~~~~~~~La~~ 116 (389)
T PRK11788 48 NEQPDKAIDLFIEMLKVDP------ETVELHLALGNLFRRRGEVDRAIRIHQNLLSRP-DL----TREQRLLALQELGQD 116 (389)
T ss_pred cCChHHHHHHHHHHHhcCc------ccHHHHHHHHHHHHHcCcHHHHHHHHHHHhcCC-CC----CHHHHHHHHHHHHHH
Confidence 4556666666655532110 113445555666666666666665555554321 11 111222333444555
Q ss_pred HHHhhhHHHHHHHHHHHHc
Q psy4458 85 DQHEGSYLATCKHYRAILT 103 (303)
Q Consensus 85 ~~~~~~f~eaa~~y~e~~~ 103 (303)
+...++|.+|-..|.+...
T Consensus 117 ~~~~g~~~~A~~~~~~~l~ 135 (389)
T PRK11788 117 YLKAGLLDRAEELFLQLVD 135 (389)
T ss_pred HHHCCCHHHHHHHHHHHHc
Confidence 5555555555555555543
No 86
>COG4105 ComL DNA uptake lipoprotein [General function prediction only]
Probab=70.71 E-value=83 Score=28.49 Aligned_cols=99 Identities=10% Similarity=0.190 Sum_probs=68.6
Q ss_pred ccCCHHHHHHHHhcccccc-ccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCC---------------
Q psy4458 4 DEGDVTEAANIIQELQVET-YGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEK--------------- 67 (303)
Q Consensus 4 ~~~~~~~Aa~~L~~i~vet-~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~--------------- 67 (303)
..|+|++|.+-+..+.-+- ++.++.... |.++--+...+|++.|...+++-..+.....+
T Consensus 46 ~~gn~~~A~~~fe~l~~~~p~s~~~~qa~----l~l~yA~Yk~~~y~~A~~~~drFi~lyP~~~n~dY~~YlkgLs~~~~ 121 (254)
T COG4105 46 QKGNYEEAIKYFEALDSRHPFSPYSEQAQ----LDLAYAYYKNGEYDLALAYIDRFIRLYPTHPNADYAYYLKGLSYFFQ 121 (254)
T ss_pred hcCCHHHHHHHHHHHHHcCCCCcccHHHH----HHHHHHHHhcccHHHHHHHHHHHHHhCCCCCChhHHHHHHHHHHhcc
Confidence 3699999999999998655 466764433 34455567889999999888877666544332
Q ss_pred -------------------------c-----chHHHHHHHH-------H-HHHHHHHHhhhHHHHHHHHHHHHcCCC
Q psy4458 68 -------------------------D-----DVQELKLKYY-------R-LMIELDQHEGSYLATCKHYRAILTTPC 106 (303)
Q Consensus 68 -------------------------~-----~~~e~k~~y~-------~-~~~~~~~~~~~f~eaa~~y~e~~~t~~ 106 (303)
| ++.+.++.|- . .-++||...+.+..|..++.++.+++.
T Consensus 122 i~~~~rDq~~~~~A~~~f~~~i~ryPnS~Ya~dA~~~i~~~~d~LA~~Em~IaryY~kr~~~~AA~nR~~~v~e~y~ 198 (254)
T COG4105 122 IDDVTRDQSAARAAFAAFKELVQRYPNSRYAPDAKARIVKLNDALAGHEMAIARYYLKRGAYVAAINRFEEVLENYP 198 (254)
T ss_pred CCccccCHHHHHHHHHHHHHHHHHCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHhcChHHHHHHHHHHHhccc
Confidence 0 2333444332 2 236889999999999999999987754
No 87
>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A.
Probab=69.20 E-value=12 Score=21.34 Aligned_cols=31 Identities=10% Similarity=0.096 Sum_probs=26.1
Q ss_pred HHHHHHHHHHHhhcchhHHHHHHHHhhhhcc
Q psy4458 33 TLILEQMRLCLAKKDYIRTQIISKKINTKFF 63 (303)
Q Consensus 33 ~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~ 63 (303)
|-.+.+++++...||+..|..+.+++-..+.
T Consensus 1 ~a~~~~a~~~~~~g~~~~A~~~~~~~~~~~P 31 (33)
T PF13174_consen 1 DALYRLARCYYKLGDYDEAIEYFQRLIKRYP 31 (33)
T ss_dssp HHHHHHHHHHHHHCHHHHHHHHHHHHHHHST
T ss_pred CHHHHHHHHHHHccCHHHHHHHHHHHHHHCc
Confidence 3467899999999999999999998877653
No 88
>PF08672 APC2: Anaphase promoting complex (APC) subunit 2; InterPro: IPR014786 The anaphase-promoting complex (APC) or cyclosome is a multi-subunit E3 protein ubiquitin ligase that regulates important events in mitosis such as the initiation of anaphase and exit from telophase. The APC, in conjunction with other enzymes, assembles multi-ubiquitin chains on a variety of regulatory proteins, thereby targeting them for proteolysis by the 26S proteasome. Anaphase is initiated when the APC triggers the destruction of securin, thereby allowing the protease, separase, to disrupt sister-chromatid cohesion. Securin ubiquitination by the APC is inhibited by cyclin-dependent kinase 1 (Cdk1)-dependent phosphorylation []. Forkhead Box M1 (FoxM1), which is a transcription factor that is over-expressed in many cancers, is degraded in late mitosis and early G1 phase by the APC/cyclosome (APC/C) E3 ubiquitin ligase []. The APC/C targets mitotic cyclins for destruction in mitosis and G1 phase and is then inactivated at S phase. It thereby generates alternating states of high and low cyclin-Cdk activity, which is required for the alternation of mitosis and DNA replication []. The APC/C is composed of at least 13 subunits that stay tightly associated throughout the cell cycle: APC1, APC2, APC4, APC5, APC9, APC11, CDC16, CDC23, CDC26, CDC27, DOC1, MND2 and SWM1[], []. In fission yeast the 13 subunits are known as: Apc1, Apc2, Nuc2, Apc4, Apc5, Cut9, Apc8, Apc10, Apc11, Hcn1, Apc13, Apc14 and Apc15 []. This entry represents a C-terminal domain found in APC subunit 2. ; PDB: 1LDD_A.
Probab=69.12 E-value=15 Score=25.52 Aligned_cols=24 Identities=25% Similarity=0.493 Sum_probs=18.5
Q ss_pred hCCCHHHHHHHHHhhhhcCceEEE
Q psy4458 227 LGLPIEETEEFLSSMVVSKTITAK 250 (303)
Q Consensus 227 l~ls~~~vE~~l~~mI~~~~l~ak 250 (303)
.+.|.++++..+.++|.+|+|.+.
T Consensus 31 ~~~s~~eL~~fL~~lv~e~~L~~~ 54 (60)
T PF08672_consen 31 YDISLEELQEFLDRLVEEGKLECS 54 (60)
T ss_dssp TT--HHHHHHHHHHHHHTTSEE--
T ss_pred CCCCHHHHHHHHHHHHHCCcEEec
Confidence 467889999999999999999774
No 89
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=68.99 E-value=10 Score=25.02 Aligned_cols=32 Identities=16% Similarity=0.286 Sum_probs=29.5
Q ss_pred ee-eHHHHHHHhCCCHHHHHHHHHhhhhcCceE
Q psy4458 217 RI-TLQRMCDLLGLPIEETEEFLSSMVVSKTIT 248 (303)
Q Consensus 217 ~I-tl~~la~ll~ls~~~vE~~l~~mI~~~~l~ 248 (303)
.+ |...||+.+|+|..-+.+.+..|...|-+.
T Consensus 19 ~l~s~~~la~~~~vs~~tv~~~l~~L~~~g~i~ 51 (60)
T smart00345 19 KLPSERELAAQLGVSRTTVREALSRLEAEGLVQ 51 (60)
T ss_pred cCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 46 899999999999999999999999999875
No 90
>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=68.86 E-value=65 Score=26.57 Aligned_cols=86 Identities=8% Similarity=0.044 Sum_probs=53.5
Q ss_pred ccCCHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHH
Q psy4458 4 DEGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIE 83 (303)
Q Consensus 4 ~~~~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~ 83 (303)
..|++++|...+...--.. + .-.......+.++...|++..|..+.+++-.... . +. ..+...+.
T Consensus 43 ~~~~~~~A~~~~~~~l~~~----p--~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~~-~----~~----~~~~~~~~ 107 (234)
T TIGR02521 43 EQGDLEVAKENLDKALEHD----P--DDYLAYLALALYYQQLGELEKAEDSFRRALTLNP-N----NG----DVLNNYGT 107 (234)
T ss_pred HCCCHHHHHHHHHHHHHhC----c--ccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCC-C----CH----HHHHHHHH
Confidence 3577777777776542111 0 1134556677788888888888888877765431 1 11 12333566
Q ss_pred HHHHhhhHHHHHHHHHHHHcC
Q psy4458 84 LDQHEGSYLATCKHYRAILTT 104 (303)
Q Consensus 84 ~~~~~~~f~eaa~~y~e~~~t 104 (303)
.+...++|.+|-..|..+...
T Consensus 108 ~~~~~g~~~~A~~~~~~~~~~ 128 (234)
T TIGR02521 108 FLCQQGKYEQAMQQFEQAIED 128 (234)
T ss_pred HHHHcccHHHHHHHHHHHHhc
Confidence 667778888888888887654
No 91
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=68.52 E-value=21 Score=22.75 Aligned_cols=34 Identities=15% Similarity=0.299 Sum_probs=30.7
Q ss_pred ceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEE
Q psy4458 216 TRITLQRMCDLLGLPIEETEEFLSSMVVSKTITA 249 (303)
Q Consensus 216 ~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~a 249 (303)
..++...|++.+|+|+.-+...+..|...|.|..
T Consensus 13 ~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~~ 46 (53)
T smart00420 13 GKVSVEELAELLGVSEMTIRRDLNKLEEQGLLTR 46 (53)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 3489999999999999999999999999988754
No 92
>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional
Probab=68.08 E-value=45 Score=31.48 Aligned_cols=86 Identities=8% Similarity=-0.051 Sum_probs=63.5
Q ss_pred ccCCHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHH
Q psy4458 4 DEGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIE 83 (303)
Q Consensus 4 ~~~~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~ 83 (303)
.+|++.+|...+...--...+ -...++..+.+++..|++..|...+.++-.... . .. ..+..++.
T Consensus 14 ~~~~~~~Ai~~~~~Al~~~P~------~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~P--~---~~----~a~~~lg~ 78 (356)
T PLN03088 14 VDDDFALAVDLYTQAIDLDPN------NAELYADRAQANIKLGNFTEAVADANKAIELDP--S---LA----KAYLRKGT 78 (356)
T ss_pred HcCCHHHHHHHHHHHHHhCCC------CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCc--C---CH----HHHHHHHH
Confidence 368999999887665321111 245778889999999999999999998876542 1 11 23445688
Q ss_pred HHHHhhhHHHHHHHHHHHHcC
Q psy4458 84 LDQHEGSYLATCKHYRAILTT 104 (303)
Q Consensus 84 ~~~~~~~f~eaa~~y~e~~~t 104 (303)
.+...++|-+|-..|..+...
T Consensus 79 ~~~~lg~~~eA~~~~~~al~l 99 (356)
T PLN03088 79 ACMKLEEYQTAKAALEKGASL 99 (356)
T ss_pred HHHHhCCHHHHHHHHHHHHHh
Confidence 888999999999999998764
No 93
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=66.89 E-value=15 Score=30.27 Aligned_cols=38 Identities=13% Similarity=0.206 Sum_probs=34.7
Q ss_pred ceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceE---EEecC
Q psy4458 216 TRITLQRMCDLLGLPIEETEEFLSSMVVSKTIT---AKIDR 253 (303)
Q Consensus 216 ~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~---akIDq 253 (303)
-+++.+.||+.+|+|+..+-.-+-+|..+|-|. |.+|.
T Consensus 22 ~R~s~~eiA~~lglS~~tV~~Ri~rL~~~GvI~~~~~~v~~ 62 (153)
T PRK11179 22 ARTPYAELAKQFGVSPGTIHVRVEKMKQAGIITGTRVDVNP 62 (153)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeEEEEECH
Confidence 889999999999999999999999999999885 45674
No 94
>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=66.52 E-value=12 Score=26.42 Aligned_cols=33 Identities=21% Similarity=0.346 Sum_probs=30.1
Q ss_pred ceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceE
Q psy4458 216 TRITLQRMCDLLGLPIEETEEFLSSMVVSKTIT 248 (303)
Q Consensus 216 ~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~ 248 (303)
-.+|-+.||+.+|+|.+.+-+.+..|..+|-|.
T Consensus 27 ~~lt~~~iA~~~g~sr~tv~r~l~~l~~~g~I~ 59 (76)
T PF13545_consen 27 LPLTQEEIADMLGVSRETVSRILKRLKDEGIIE 59 (76)
T ss_dssp EESSHHHHHHHHTSCHHHHHHHHHHHHHTTSEE
T ss_pred ecCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 347889999999999999999999999999776
No 95
>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF. Members of this protein family are the product of one of seven genes regularly clustered in operons to encode the proteins of the tol-pal system, which is critical for maintaining the integrity of the bacterial outer membrane. The gene for this periplasmic protein has been designated orf2 and ybgF. All members of the seed alignment were from unique tol-pal gene regions from completed bacterial genomes. The architecture of this protein is a signal sequence, a low-complexity region usually rich in Asn and Gln, a well-conserved region with tandem repeats that resemble the tetratricopeptide (TPR) repeat, involved in protein-protein interaction.
Probab=66.42 E-value=47 Score=24.69 Aligned_cols=66 Identities=15% Similarity=0.157 Sum_probs=50.0
Q ss_pred HHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHcC
Q psy4458 33 TLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIELDQHEGSYLATCKHYRAILTT 104 (303)
Q Consensus 33 ~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~~~~~~~~f~eaa~~y~e~~~t 104 (303)
+.++..+...+..|++..|.....++.....+.. ...... ..++..+...++|-+|...|..+...
T Consensus 3 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~----~~~~~~--~~l~~~~~~~~~~~~A~~~~~~~~~~ 68 (119)
T TIGR02795 3 EAYYDAALLVLKAGDYADAIQAFQAFLKKYPKST----YAPNAH--YWLGEAYYAQGKYADAAKAFLAVVKK 68 (119)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCcc----ccHHHH--HHHHHHHHhhccHHHHHHHHHHHHHH
Confidence 5678889999999999999999999876542111 111122 34888999999999999999988754
No 96
>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=66.25 E-value=21 Score=34.46 Aligned_cols=55 Identities=20% Similarity=0.088 Sum_probs=35.8
Q ss_pred HHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHHHHHHhhhHHHHH
Q psy4458 32 VTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIELDQHEGSYLATC 95 (303)
Q Consensus 32 ~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~~~~~~~~f~eaa 95 (303)
.++...|++.++..+++..|..+.+++-....++-. .| ...+..|...++|.+|-
T Consensus 234 ~~LL~~Qa~fLl~k~~~~lAL~iAk~av~lsP~~f~--~W-------~~La~~Yi~~~d~e~AL 288 (395)
T PF09295_consen 234 SELLNLQAEFLLSKKKYELALEIAKKAVELSPSEFE--TW-------YQLAECYIQLGDFENAL 288 (395)
T ss_pred HHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCchhHH--HH-------HHHHHHHHhcCCHHHHH
Confidence 556667777777777777777777777665533322 23 33677777777777765
No 97
>PRK02603 photosystem I assembly protein Ycf3; Provisional
Probab=66.08 E-value=37 Score=28.09 Aligned_cols=57 Identities=7% Similarity=0.022 Sum_probs=40.5
Q ss_pred CccCCHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhc
Q psy4458 3 EDEGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKF 62 (303)
Q Consensus 3 e~~~~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~ 62 (303)
...|++++|...+...--... +..+....+...+.++...|++..|.....++-...
T Consensus 46 ~~~g~~~~A~~~~~~al~~~~---~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~ 102 (172)
T PRK02603 46 QADGEYAEALENYEEALKLEE---DPNDRSYILYNMGIIYASNGEHDKALEYYHQALELN 102 (172)
T ss_pred HHcCCHHHHHHHHHHHHHHhh---ccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC
Confidence 346899999988876531110 111345678888999999999999999888887654
No 98
>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=65.91 E-value=17 Score=23.13 Aligned_cols=26 Identities=15% Similarity=0.275 Sum_probs=20.8
Q ss_pred ceeeHHHHHHHhCCCHHHHHHHHHhh
Q psy4458 216 TRITLQRMCDLLGLPIEETEEFLSSM 241 (303)
Q Consensus 216 ~~Itl~~la~ll~ls~~~vE~~l~~m 241 (303)
.+.++..||+.+|+|+..|-.-+.+|
T Consensus 16 ~r~s~~~la~~lglS~~~v~~Ri~rL 41 (42)
T PF13404_consen 16 GRRSYAELAEELGLSESTVRRRIRRL 41 (42)
T ss_dssp TTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCccHHHHHHHHCcCHHHHHHHHHHh
Confidence 88999999999999999987766554
No 99
>KOG1586|consensus
Probab=65.69 E-value=1.1e+02 Score=27.80 Aligned_cols=39 Identities=21% Similarity=0.244 Sum_probs=24.7
Q ss_pred hcccccccccchhHHhHHHHHHHHHHHHHHHHHHh---hhceee
Q psy4458 179 LFKTSVFNQSTEEGQKCFKMLKHRVVEHNIRVMAK---YYTRIT 219 (303)
Q Consensus 179 L~~~~~~~~~~~~~~~~~~~l~~~i~ehNi~~isk---~Y~~It 219 (303)
...+|-|.++. ..+-.+.|..++-|.|+-.+.. -|.+||
T Consensus 222 ~~~dP~F~dsR--Eckflk~L~~aieE~d~e~fte~vkefDsis 263 (288)
T KOG1586|consen 222 QELDPAFTDSR--ECKFLKDLLDAIEEQDIEKFTEVVKEFDSIS 263 (288)
T ss_pred HhcCCcccccH--HHHHHHHHHHHHhhhhHHHHHHHHHhhhccc
Confidence 34577774322 1234688889999999988753 365553
No 100
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=65.63 E-value=16 Score=30.51 Aligned_cols=45 Identities=16% Similarity=0.058 Sum_probs=38.0
Q ss_pred HHHHhhhceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceE---EEecC
Q psy4458 209 RVMAKYYTRITLQRMCDLLGLPIEETEEFLSSMVVSKTIT---AKIDR 253 (303)
Q Consensus 209 ~~isk~Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~---akIDq 253 (303)
..+-+--.++|...||+.+|+|+.-+-.-+-+|..+|-|. |.+|.
T Consensus 20 L~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~GvI~~~~~~v~p 67 (164)
T PRK11169 20 LNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQGFIQGYTALLNP 67 (164)
T ss_pred HHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEEEECH
Confidence 3344567899999999999999999999999999999885 45663
No 101
>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B.
Probab=65.31 E-value=14 Score=24.97 Aligned_cols=53 Identities=11% Similarity=0.053 Sum_probs=42.2
Q ss_pred ccCCHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhc
Q psy4458 4 DEGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKF 62 (303)
Q Consensus 4 ~~~~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~ 62 (303)
..|++++|...++.+--.. + .-.+..+..++++...|++..|..+.+++-...
T Consensus 9 ~~g~~~~A~~~~~~~l~~~----P--~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~~ 61 (65)
T PF13432_consen 9 QQGDYDEAIAAFEQALKQD----P--DNPEAWYLLGRILYQQGRYDEALAYYERALELD 61 (65)
T ss_dssp HCTHHHHHHHHHHHHHCCS----T--THHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHS
T ss_pred HcCCHHHHHHHHHHHHHHC----C--CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC
Confidence 5789999999999886432 2 366788999999999999999999999886544
No 102
>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=65.06 E-value=62 Score=24.98 Aligned_cols=43 Identities=5% Similarity=-0.014 Sum_probs=38.2
Q ss_pred hceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCCCce
Q psy4458 215 YTRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAGI 257 (303)
Q Consensus 215 Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~gi 257 (303)
...++.+.||+.+|++..-+=..+..|...|-|...-|..++-
T Consensus 40 ~~~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~~~~~D~R 82 (118)
T TIGR02337 40 QGSMEFTQLANQACILRPSLTGILARLERDGLVTRLKASNDQR 82 (118)
T ss_pred cCCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEeccCCCCCC
Confidence 4578999999999999999999999999999999888766653
No 103
>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=64.65 E-value=20 Score=24.07 Aligned_cols=30 Identities=13% Similarity=0.241 Sum_probs=27.9
Q ss_pred eHHHHHHHhCCCHHHHHHHHHhhhhcCceE
Q psy4458 219 TLQRMCDLLGLPIEETEEFLSSMVVSKTIT 248 (303)
Q Consensus 219 tl~~la~ll~ls~~~vE~~l~~mI~~~~l~ 248 (303)
+...||+.+|+|...+-+.+..|...|-|.
T Consensus 27 ~~~~la~~~~is~~~v~~~l~~L~~~G~i~ 56 (66)
T cd07377 27 SERELAEELGVSRTTVREALRELEAEGLVE 56 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 499999999999999999999999999764
No 104
>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=64.57 E-value=20 Score=25.15 Aligned_cols=58 Identities=14% Similarity=0.147 Sum_probs=43.2
Q ss_pred CccCCHHHHHHHHhcc-cc-ccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhh
Q psy4458 3 EDEGDVTEAANIIQEL-QV-ETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTK 61 (303)
Q Consensus 3 e~~~~~~~Aa~~L~~i-~v-et~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~ 61 (303)
...|++++|.+.++.. ++ +++|. +....+..+..+++++...||+..|..+..++-..
T Consensus 16 ~~~~~~~~A~~~~~~al~~~~~~~~-~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al~i 75 (78)
T PF13424_consen 16 RELGRYDEALDYYEKALDIEEQLGD-DHPDTANTLNNLGECYYRLGDYEEALEYYQKALDI 75 (78)
T ss_dssp HHTT-HHHHHHHHHHHHHHHHHTTT-HHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHH
T ss_pred HHcCCHHHHHHHHHHHHHHHHHHCC-CCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence 3568999999888764 33 22333 33356888999999999999999999999988654
No 105
>PRK10803 tol-pal system protein YbgF; Provisional
Probab=64.39 E-value=1.1e+02 Score=27.80 Aligned_cols=60 Identities=12% Similarity=0.167 Sum_probs=38.2
Q ss_pred HHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHcCC
Q psy4458 40 RLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIELDQHEGSYLATCKHYRAILTTP 105 (303)
Q Consensus 40 rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~~~~~~~~f~eaa~~y~e~~~t~ 105 (303)
-+.+..++|..|....++.-..+.+.. .--...|+ .|..+...++|.+|...|..+...+
T Consensus 151 ~l~~~~~~y~~Ai~af~~fl~~yP~s~----~a~~A~y~--LG~~y~~~g~~~~A~~~f~~vv~~y 210 (263)
T PRK10803 151 ALVQDKSRQDDAIVAFQNFVKKYPDST----YQPNANYW--LGQLNYNKGKKDDAAYYFASVVKNY 210 (263)
T ss_pred HHHHhcCCHHHHHHHHHHHHHHCcCCc----chHHHHHH--HHHHHHHcCCHHHHHHHHHHHHHHC
Confidence 445556788888777777777664321 11112343 6777777888888888887777554
No 106
>PRK15359 type III secretion system chaperone protein SscB; Provisional
Probab=63.69 E-value=48 Score=26.73 Aligned_cols=85 Identities=9% Similarity=-0.094 Sum_probs=52.1
Q ss_pred ccCCHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHH
Q psy4458 4 DEGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIE 83 (303)
Q Consensus 4 ~~~~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~ 83 (303)
..|++++|+..++..---.. .-.+.+...+.++...|++..|.....++-.... +. -..+..++.
T Consensus 36 ~~g~~~~A~~~~~~al~~~P------~~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l~p--~~-------~~a~~~lg~ 100 (144)
T PRK15359 36 QEGDYSRAVIDFSWLVMAQP------WSWRAHIALAGTWMMLKEYTTAINFYGHALMLDA--SH-------PEPVYQTGV 100 (144)
T ss_pred HcCCHHHHHHHHHHHHHcCC------CcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCC--CC-------cHHHHHHHH
Confidence 35777777766655321111 1346667777777777888877777777765432 11 112233666
Q ss_pred HHHHhhhHHHHHHHHHHHHc
Q psy4458 84 LDQHEGSYLATCKHYRAILT 103 (303)
Q Consensus 84 ~~~~~~~f~eaa~~y~e~~~ 103 (303)
.+...+++-+|...|..+..
T Consensus 101 ~l~~~g~~~eAi~~~~~Al~ 120 (144)
T PRK15359 101 CLKMMGEPGLAREAFQTAIK 120 (144)
T ss_pred HHHHcCCHHHHHHHHHHHHH
Confidence 66777788888877777764
No 107
>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=63.66 E-value=20 Score=23.29 Aligned_cols=30 Identities=20% Similarity=0.531 Sum_probs=24.7
Q ss_pred hhhceeeHHHHHHHhCCCHHHHHHHHHhhh
Q psy4458 213 KYYTRITLQRMCDLLGLPIEETEEFLSSMV 242 (303)
Q Consensus 213 k~Y~~Itl~~la~ll~ls~~~vE~~l~~mI 242 (303)
.||...|++.+|+.+|+|...|-......+
T Consensus 16 ~y~~~~t~~eIa~~lg~s~~~V~~~~~~al 45 (50)
T PF04545_consen 16 RYFEGLTLEEIAERLGISRSTVRRILKRAL 45 (50)
T ss_dssp HHTST-SHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred HhcCCCCHHHHHHHHCCcHHHHHHHHHHHH
Confidence 358999999999999999998887776654
No 108
>KOG1941|consensus
Probab=63.48 E-value=98 Score=29.80 Aligned_cols=112 Identities=9% Similarity=0.057 Sum_probs=78.5
Q ss_pred HHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHHHHHHh
Q psy4458 9 TEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIELDQHE 88 (303)
Q Consensus 9 ~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~~~~~~ 88 (303)
..|+++.+.++| +.++.+++.-..++.+==+=..|....|+.+-+.+....... | |..+.-+.-.+++.+|-..
T Consensus 186 ~kA~~lv~s~~l---~d~~~kyr~~~lyhmaValR~~G~LgdA~e~C~Ea~klal~~-G--dra~~arc~~~~aDIyR~~ 259 (518)
T KOG1941|consen 186 CKAAELVNSYGL---KDWSLKYRAMSLYHMAVALRLLGRLGDAMECCEEAMKLALQH-G--DRALQARCLLCFADIYRSR 259 (518)
T ss_pred HhHHHHHHhcCc---CchhHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHh-C--ChHHHHHHHHHHHHHHHhc
Confidence 356777777776 566666666555444333335677778888888887776443 4 5777788888999999999
Q ss_pred hhHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHH
Q psy4458 89 GSYLATCKHYRAILTTPCIQSDPVQRHAVLQNVVLYLM 126 (303)
Q Consensus 89 ~~f~eaa~~y~e~~~t~~~~~~~~~~~~~L~~~v~~~i 126 (303)
+|.-.|+..|.+++.|-...+|--..+.+|..+.-|..
T Consensus 260 gd~e~af~rYe~Am~~m~~~gdrmgqv~al~g~Akc~~ 297 (518)
T KOG1941|consen 260 GDLERAFRRYEQAMGTMASLGDRMGQVEALDGAAKCLE 297 (518)
T ss_pred ccHhHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHH
Confidence 99999999999999876654443334556666655554
No 109
>PF12755 Vac14_Fab1_bd: Vacuolar 14 Fab1-binding region
Probab=63.21 E-value=32 Score=26.21 Aligned_cols=50 Identities=10% Similarity=0.054 Sum_probs=31.2
Q ss_pred HHHHHHHhhhhccCCCCcchHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Q psy4458 51 TQIISKKINTKFFDDEKDDVQELKLKYYRLMIELDQHEGSYLATCKHYRAIL 102 (303)
Q Consensus 51 a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~~~~~~~~f~eaa~~y~e~~ 102 (303)
...+++++-+-.+..-+ |.+-++||+.|.+.|....--=-+.-.+|.+++
T Consensus 21 ~~~~l~~Il~pVL~~~~--D~d~rVRy~AcEaL~ni~k~~~~~~l~~f~~IF 70 (97)
T PF12755_consen 21 ISKYLDEILPPVLKCFD--DQDSRVRYYACEALYNISKVARGEILPYFNEIF 70 (97)
T ss_pred HHHHHHHHHHHHHHHcC--CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 66777777665545444 678899999999988664332222333444443
No 110
>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=62.94 E-value=17 Score=29.26 Aligned_cols=42 Identities=12% Similarity=0.233 Sum_probs=35.8
Q ss_pred eeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCCCceE
Q psy4458 217 RITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAGII 258 (303)
Q Consensus 217 ~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~giV 258 (303)
.++.+.||+.+++|+..+++++..+...|-+...=-...|..
T Consensus 25 ~~s~~~ia~~~~ip~~~l~kil~~L~~~glv~s~~G~~Ggy~ 66 (135)
T TIGR02010 25 PVTLADISERQGISLSYLEQLFAKLRKAGLVKSVRGPGGGYQ 66 (135)
T ss_pred cCcHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEeCCCCCEe
Confidence 589999999999999999999999999998876544445543
No 111
>PF13371 TPR_9: Tetratricopeptide repeat
Probab=62.75 E-value=36 Score=23.35 Aligned_cols=56 Identities=14% Similarity=0.108 Sum_probs=43.4
Q ss_pred HHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHc
Q psy4458 39 MRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIELDQHEGSYLATCKHYRAILT 103 (303)
Q Consensus 39 ~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~~~~~~~~f~eaa~~y~e~~~ 103 (303)
..+++..+||..|..++.++-....+. ...+...|..+...++|.+|...|..++.
T Consensus 2 ~~~~~~~~~~~~A~~~~~~~l~~~p~~---------~~~~~~~a~~~~~~g~~~~A~~~l~~~l~ 57 (73)
T PF13371_consen 2 KQIYLQQEDYEEALEVLERALELDPDD---------PELWLQRARCLFQLGRYEEALEDLERALE 57 (73)
T ss_pred HHHHHhCCCHHHHHHHHHHHHHhCccc---------chhhHHHHHHHHHhccHHHHHHHHHHHHH
Confidence 357899999999999999887654221 23334488888999999999999888874
No 112
>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=62.70 E-value=31 Score=23.70 Aligned_cols=35 Identities=11% Similarity=0.172 Sum_probs=30.4
Q ss_pred hhceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceE
Q psy4458 214 YYTRITLQRMCDLLGLPIEETEEFLSSMVVSKTIT 248 (303)
Q Consensus 214 ~Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~ 248 (303)
-=..++...||+.||++++-|=..+.++-..|-+.
T Consensus 19 ~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~GlV~ 53 (60)
T PF01325_consen 19 EGGPVRTKDIAERLGVSPPTVTEMLKRLAEKGLVE 53 (60)
T ss_dssp CTSSBBHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred CCCCccHHHHHHHHCCChHHHHHHHHHHHHCCCEE
Confidence 35779999999999999999999999999998764
No 113
>PRK09954 putative kinase; Provisional
Probab=61.90 E-value=22 Score=33.46 Aligned_cols=46 Identities=9% Similarity=0.142 Sum_probs=38.9
Q ss_pred hceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEE---EecCCCceEEe
Q psy4458 215 YTRITLQRMCDLLGLPIEETEEFLSSMVVSKTITA---KIDRPAGIINF 260 (303)
Q Consensus 215 Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~a---kIDq~~giV~f 260 (303)
-.++|.+.||+.||+|...+-..+.+|..+|.+.+ .+|+..+++.+
T Consensus 15 ~~~~s~~~la~~l~~s~~~v~~~i~~L~~~g~i~~~~~~l~~~~~v~vi 63 (362)
T PRK09954 15 NPLIQQNEIADILQISRSRVAAHIMDLMRKGRIKGKGYILTEQEYCVVV 63 (362)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCcCCcEEEEcCCccEEEE
Confidence 46899999999999999999999999999998843 67777766533
No 114
>CHL00033 ycf3 photosystem I assembly protein Ycf3
Probab=61.72 E-value=88 Score=25.57 Aligned_cols=91 Identities=8% Similarity=-0.079 Sum_probs=49.2
Q ss_pred ccCCHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHH
Q psy4458 4 DEGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIE 83 (303)
Q Consensus 4 ~~~~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~ 83 (303)
..|++++|...+...--.... .......+..++.++...|++..|..+..++-........ .+-..-..+...++
T Consensus 47 ~~g~~~~A~~~~~~al~l~~~---~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~~~~~~~~--~~~~la~i~~~~~~ 121 (168)
T CHL00033 47 SEGEYAEALQNYYEAMRLEID---PYDRSYILYNIGLIHTSNGEHTKALEYYFQALERNPFLPQ--ALNNMAVICHYRGE 121 (168)
T ss_pred HcCCHHHHHHHHHHHHhcccc---chhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCcHH--HHHHHHHHHHHhhH
Confidence 357778877776655211111 1123346677788888888888888888877654322111 22222234444444
Q ss_pred HHHHhhhHHHHHHHHH
Q psy4458 84 LDQHEGSYLATCKHYR 99 (303)
Q Consensus 84 ~~~~~~~f~eaa~~y~ 99 (303)
.+...++|.+|-..|.
T Consensus 122 ~~~~~g~~~~A~~~~~ 137 (168)
T CHL00033 122 QAIEQGDSEIAEAWFD 137 (168)
T ss_pred HHHHcccHHHHHHHHH
Confidence 4445666554433333
No 115
>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=61.68 E-value=94 Score=25.86 Aligned_cols=69 Identities=17% Similarity=0.184 Sum_probs=47.8
Q ss_pred ceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEe--cCCCceEEeccCCChhHHHHHHHHHHHHHHHHH
Q psy4458 216 TRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKI--DRPAGIINFARNKDPGEILNEWSASLNELMKLV 284 (303)
Q Consensus 216 ~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akI--Dq~~giV~f~~~~~~~~~l~~w~~~i~~l~~~v 284 (303)
+-+|-+.||+.+|++..+|-+.+..+-..|-+.-+= |-.+|-.++-|.-+..+..+.-..++..+.+.+
T Consensus 27 ~~~tdEeLa~~Lgi~~~~VRk~L~~L~e~~Lv~~~r~r~~~~gw~~Y~w~i~~~~i~d~Ik~~~~~~~~~l 97 (158)
T TIGR00373 27 GEFTDEEISLELGIKLNEVRKALYALYDAGLADYKRRKDDETGWYEYTWRINYEKALDVLKRKLEETAKKL 97 (158)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCceeeeeeecCCCcEEEEEEeCHHHHHHHHHHHHHHHHHHH
Confidence 458999999999999999999999999999883321 333455666553344445555555555555444
No 116
>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=61.15 E-value=45 Score=30.67 Aligned_cols=90 Identities=9% Similarity=0.049 Sum_probs=61.8
Q ss_pred CccCCHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHH
Q psy4458 3 EDEGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMI 82 (303)
Q Consensus 3 e~~~~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~ 82 (303)
...|++++|...+...---.... .......+.++.+.|++..|..++.++-..... + .......+...+
T Consensus 125 ~~~G~~~~A~~~~~~al~~~p~~------~~~~~~la~i~~~~g~~~eA~~~l~~~l~~~~~-~----~~~~~~~~~~la 193 (355)
T cd05804 125 EEAGQYDRAEEAARRALELNPDD------AWAVHAVAHVLEMQGRFKEGIAFMESWRDTWDC-S----SMLRGHNWWHLA 193 (355)
T ss_pred HHcCCHHHHHHHHHHHHhhCCCC------cHHHHHHHHHHHHcCCHHHHHHHHHhhhhccCC-C----cchhHHHHHHHH
Confidence 45677777777665542111111 345566788888999999999998888765421 1 223345566788
Q ss_pred HHHHHhhhHHHHHHHHHHHHc
Q psy4458 83 ELDQHEGSYLATCKHYRAILT 103 (303)
Q Consensus 83 ~~~~~~~~f~eaa~~y~e~~~ 103 (303)
.++...+++-+|-..|.+...
T Consensus 194 ~~~~~~G~~~~A~~~~~~~~~ 214 (355)
T cd05804 194 LFYLERGDYEAALAIYDTHIA 214 (355)
T ss_pred HHHHHCCCHHHHHHHHHHHhc
Confidence 999999999999999998753
No 117
>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=61.11 E-value=34 Score=23.32 Aligned_cols=43 Identities=9% Similarity=0.141 Sum_probs=32.7
Q ss_pred hhhceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCCC
Q psy4458 213 KYYTRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPA 255 (303)
Q Consensus 213 k~Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~ 255 (303)
.....++...||+.++++...+-..|.+|+..|-+.=.-|..+
T Consensus 14 ~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv~~~~~~~d 56 (68)
T PF13463_consen 14 HSDGPMTQSDLAERLGISKSTVSRIIKKLEEKGLVEKERDPHD 56 (68)
T ss_dssp --TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEESSC
T ss_pred ccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEecCCCCc
Confidence 3578899999999999999999999999999999955544433
No 118
>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=60.63 E-value=14 Score=29.43 Aligned_cols=41 Identities=15% Similarity=0.261 Sum_probs=34.7
Q ss_pred ceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCCCc
Q psy4458 216 TRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAG 256 (303)
Q Consensus 216 ~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~g 256 (303)
..++...||+.+|+|+..+.+.+..+...|-+.+.-....|
T Consensus 24 ~~~s~~eia~~l~is~~~v~~~l~~L~~~Gli~~~~g~~gg 64 (130)
T TIGR02944 24 QPYSAAEIAEQTGLNAPTVSKILKQLSLAGIVTSKRGVEGG 64 (130)
T ss_pred CCccHHHHHHHHCcCHHHHHHHHHHHHHCCcEEecCCCCCC
Confidence 46899999999999999999999999999999775333333
No 119
>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=60.12 E-value=81 Score=27.14 Aligned_cols=93 Identities=14% Similarity=-0.001 Sum_probs=61.1
Q ss_pred cCCHHHHHHHHhccccccccCCch-H----------HHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHH
Q psy4458 5 EGDVTEAANIIQELQVETYGSMEK-K----------EKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQEL 73 (303)
Q Consensus 5 ~~~~~~Aa~~L~~i~vet~~~~~~-~----------~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~ 73 (303)
.|++++|.+.++.+--....+... . ......+.++++++..|++..|.....++-..+.+. .+..
T Consensus 128 ~~~~~~A~~~~~~~~~~~p~~~~~~~a~~~~~~~~~~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~p~~----~~~~ 203 (235)
T TIGR03302 128 QTAAREAFEAFQELIRRYPNSEYAPDAKKRMDYLRNRLAGKELYVARFYLKRGAYVAAINRFETVVENYPDT----PATE 203 (235)
T ss_pred HHHHHHHHHHHHHHHHHCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHCCCC----cchH
Confidence 477888888888763222121100 0 001123577889999999999999999887766322 1223
Q ss_pred HHHHHHHHHHHHHHhhhHHHHHHHHHHHHc
Q psy4458 74 KLKYYRLMIELDQHEGSYLATCKHYRAILT 103 (303)
Q Consensus 74 k~~y~~~~~~~~~~~~~f~eaa~~y~e~~~ 103 (303)
+..+ .++..+...++|-+|..++..+-.
T Consensus 204 ~a~~--~l~~~~~~lg~~~~A~~~~~~l~~ 231 (235)
T TIGR03302 204 EALA--RLVEAYLKLGLKDLAQDAAAVLGA 231 (235)
T ss_pred HHHH--HHHHHHHHcCCHHHHHHHHHHHHh
Confidence 3334 488889999999999997777643
No 120
>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A.
Probab=59.95 E-value=18 Score=25.96 Aligned_cols=47 Identities=19% Similarity=0.234 Sum_probs=33.8
Q ss_pred cCCHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHh
Q psy4458 5 EGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKI 58 (303)
Q Consensus 5 ~~~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki 58 (303)
.|++++|..+++...+ +.+. .+...-.+|.++..|+|..|...+.++
T Consensus 38 ~~~y~~A~~~~~~~~~------~~~~-~~~~~l~a~~~~~l~~y~eAi~~l~~~ 84 (84)
T PF12895_consen 38 QGKYEEAIELLQKLKL------DPSN-PDIHYLLARCLLKLGKYEEAIKALEKA 84 (84)
T ss_dssp TTHHHHHHHHHHCHTH------HHCH-HHHHHHHHHHHHHTT-HHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHhCC------CCCC-HHHHHHHHHHHHHhCCHHHHHHHHhcC
Confidence 5899999999988333 1212 344444599999999999999888764
No 121
>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=59.80 E-value=16 Score=29.01 Aligned_cols=41 Identities=10% Similarity=0.209 Sum_probs=34.6
Q ss_pred eeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCCCce
Q psy4458 217 RITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAGI 257 (303)
Q Consensus 217 ~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~gi 257 (303)
.++.+.||+.+|+|+..+.+.+..|...|-|...-....|+
T Consensus 25 ~~s~~eia~~~~i~~~~v~~il~~L~~~gli~~~~g~~ggy 65 (132)
T TIGR00738 25 PVSVKEIAERQGISRSYLEKILRTLRRAGLVESVRGPGGGY 65 (132)
T ss_pred cCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEEeccCCCCCc
Confidence 68999999999999999999999999999887643343443
No 122
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=59.35 E-value=66 Score=30.37 Aligned_cols=93 Identities=14% Similarity=0.125 Sum_probs=67.8
Q ss_pred CCCccCCHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHH
Q psy4458 1 MKEDEGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRL 80 (303)
Q Consensus 1 i~e~~~~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~ 80 (303)
|++++.+|++|.++=..+..=+...+ .-+...||-|.+.-++..+|.++|...+.|+-.--.. . +|=-..
T Consensus 150 IYQ~treW~KAId~A~~L~k~~~q~~-~~eIAqfyCELAq~~~~~~~~d~A~~~l~kAlqa~~~--c-------vRAsi~ 219 (389)
T COG2956 150 IYQATREWEKAIDVAERLVKLGGQTY-RVEIAQFYCELAQQALASSDVDRARELLKKALQADKK--C-------VRASII 219 (389)
T ss_pred HHHHhhHHHHHHHHHHHHHHcCCccc-hhHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHhhCcc--c-------eehhhh
Confidence 46778899998877554443222222 2377889999999999999999999999998642210 0 233345
Q ss_pred HHHHHHHhhhHHHHHHHHHHHHc
Q psy4458 81 MIELDQHEGSYLATCKHYRAILT 103 (303)
Q Consensus 81 ~~~~~~~~~~f~eaa~~y~e~~~ 103 (303)
+++++...++|-.|-+.|..+.+
T Consensus 220 lG~v~~~~g~y~~AV~~~e~v~e 242 (389)
T COG2956 220 LGRVELAKGDYQKAVEALERVLE 242 (389)
T ss_pred hhHHHHhccchHHHHHHHHHHHH
Confidence 88999999999999999988864
No 123
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=59.21 E-value=54 Score=29.48 Aligned_cols=64 Identities=20% Similarity=0.298 Sum_probs=47.9
Q ss_pred ceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCCCceEEeccCCChhHHHHHHHHHHHHHHHHH
Q psy4458 216 TRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAGIINFARNKDPGEILNEWSASLNELMKLV 284 (303)
Q Consensus 216 ~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~giV~f~~~~~~~~~l~~w~~~i~~l~~~v 284 (303)
-++.-+.||.-+|+|++-+-..+-+||.+|-+.- .|-.++.-.+.-.+.+-+|..++....+.+
T Consensus 24 p~v~q~eIA~~lgiT~QaVsehiK~Lv~eG~i~~-----~gR~~Y~iTkkG~e~l~~~~~dlr~f~~ev 87 (260)
T COG1497 24 PRVKQKEIAKKLGITLQAVSEHIKELVKEGLIEK-----EGRGEYEITKKGAEWLLEQLSDLRRFSEEV 87 (260)
T ss_pred CCCCHHHHHHHcCCCHHHHHHHHHHHHhccceee-----cCCeeEEEehhHHHHHHHHHHHHHHHHHHH
Confidence 4578899999999999999999999999997754 333333333334466777777777777766
No 124
>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=59.01 E-value=41 Score=22.63 Aligned_cols=54 Identities=19% Similarity=0.194 Sum_probs=40.1
Q ss_pred HhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHcCC
Q psy4458 43 LAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIELDQHEGSYLATCKHYRAILTTP 105 (303)
Q Consensus 43 L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~~~~~~~~f~eaa~~y~e~~~t~ 105 (303)
+..|||..|..+.+++-....+ +.+ +++ .++..+...++|-+|-..+..+....
T Consensus 2 l~~~~~~~A~~~~~~~l~~~p~-----~~~--~~~--~la~~~~~~g~~~~A~~~l~~~~~~~ 55 (68)
T PF14559_consen 2 LKQGDYDEAIELLEKALQRNPD-----NPE--ARL--LLAQCYLKQGQYDEAEELLERLLKQD 55 (68)
T ss_dssp HHTTHHHHHHHHHHHHHHHTTT-----SHH--HHH--HHHHHHHHTT-HHHHHHHHHCCHGGG
T ss_pred hhccCHHHHHHHHHHHHHHCCC-----CHH--HHH--HHHHHHHHcCCHHHHHHHHHHHHHHC
Confidence 5789999999999999876522 222 333 48888899999999999888886543
No 125
>PF11873 DUF3393: Domain of unknown function (DUF3393); InterPro: IPR024570 Membrane-bound lytic murein transglycosylase C (also known as murein hydrolase C), is a murein-degrading enzyme that may play a role in the recycling of muropeptides during cell elongation and/or cell division. This entry represents the N-terminal domain, whose function is currently not known.
Probab=58.05 E-value=6.3 Score=34.45 Aligned_cols=68 Identities=22% Similarity=0.319 Sum_probs=51.1
Q ss_pred HHHHHHHHHHHHHhCCCCchhhHhHHHhhhhhhcCCchHHHHHHHHhcCCcccCchHHHHHHHHhhccccc
Q psy4458 114 RHAVLQNVVLYLMLAPYDNEQSDLTHRVLEDKLLNEIPLYKGLLQWFTNPELIKWSGLRQLYEEELFKTSV 184 (303)
Q Consensus 114 ~~~~L~~~v~~~iLs~~~~~r~~ll~~l~~~~~~~~~p~~~~L~~~f~~~~li~~~~~~~~~~~~L~~~~~ 184 (303)
-...|+.+|+-++|+|.+|...|+.+. ++..++.-|.+...+....+. -|+|+--...|...|-.+.+
T Consensus 109 p~~~Lk~AIv~TLL~~~Dp~~vDl~Sd--~~i~l~g~PFLygqVlD~~g~-~I~~~wRA~ryAdYLi~n~L 176 (204)
T PF11873_consen 109 PKAHLKQAIVTTLLTPDDPSSVDLFSD--KDIPLSGEPFLYGQVLDQDGQ-PIRWEWRANRYADYLIQNKL 176 (204)
T ss_pred HHHHHHHHHHHHhcCCCCCccccCccC--CCCccCCCceehheeecCCCC-eEeeHhHHHHHHHHHHHhhh
Confidence 367899999999999999999988874 445567788877666665555 45876556778777766553
No 126
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=57.72 E-value=18 Score=30.39 Aligned_cols=43 Identities=12% Similarity=0.252 Sum_probs=37.1
Q ss_pred ceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCCCceE
Q psy4458 216 TRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAGII 258 (303)
Q Consensus 216 ~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~giV 258 (303)
..++.+.||+.+|+|+..+++++..+...|-+...=-...|+.
T Consensus 24 ~~vs~~eIA~~~~ip~~~l~kIl~~L~~aGLv~s~rG~~GGy~ 66 (164)
T PRK10857 24 GPVPLADISERQGISLSYLEQLFSRLRKNGLVSSVRGPGGGYL 66 (164)
T ss_pred CcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeCCCCCCCee
Confidence 4699999999999999999999999999999987555555554
No 127
>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=57.42 E-value=33 Score=22.06 Aligned_cols=33 Identities=15% Similarity=0.278 Sum_probs=29.1
Q ss_pred ceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceE
Q psy4458 216 TRITLQRMCDLLGLPIEETEEFLSSMVVSKTIT 248 (303)
Q Consensus 216 ~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~ 248 (303)
...++..|++.+|+|...+-..+..|...|-+.
T Consensus 14 ~~~~~~el~~~l~~s~~~vs~hL~~L~~~glV~ 46 (47)
T PF01022_consen 14 GPLTVSELAEELGLSQSTVSHHLKKLREAGLVE 46 (47)
T ss_dssp SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred CCCchhhHHHhccccchHHHHHHHHHHHCcCee
Confidence 678899999999999999999999999988663
No 128
>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=57.36 E-value=46 Score=22.76 Aligned_cols=37 Identities=14% Similarity=0.162 Sum_probs=30.6
Q ss_pred hhhcee-eHHHHHHHhCCCHHHHHHHHHhhhhcCceEE
Q psy4458 213 KYYTRI-TLQRMCDLLGLPIEETEEFLSSMVVSKTITA 249 (303)
Q Consensus 213 k~Y~~I-tl~~la~ll~ls~~~vE~~l~~mI~~~~l~a 249 (303)
++=+.+ +...||+.+|+|..-+-+.+..+..+|.+.-
T Consensus 19 ~~g~~lps~~~la~~~~vsr~tvr~al~~L~~~g~i~~ 56 (64)
T PF00392_consen 19 PPGDRLPSERELAERYGVSRTTVREALRRLEAEGLIER 56 (64)
T ss_dssp -TTSBE--HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred CCCCEeCCHHHHHHHhccCCcHHHHHHHHHHHCCcEEE
Confidence 345789 9999999999999999999999999998754
No 129
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=57.02 E-value=71 Score=27.21 Aligned_cols=69 Identities=9% Similarity=0.147 Sum_probs=47.6
Q ss_pred ceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecC--CCceEEeccCCChhHHHHHHHHHHHHHHHHH
Q psy4458 216 TRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDR--PAGIINFARNKDPGEILNEWSASLNELMKLV 284 (303)
Q Consensus 216 ~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq--~~giV~f~~~~~~~~~l~~w~~~i~~l~~~v 284 (303)
..+|-+.||..+|++..+|-+.+..+-.+|-+..+-=+ ..|-.++-|.-+..+..+.-..++..+...+
T Consensus 35 g~~tdeeLA~~Lgi~~~~VRk~L~~L~e~gLv~~~r~r~~~~Gr~~y~w~l~~~~i~d~ik~~~~~~~~kl 105 (178)
T PRK06266 35 GEVTDEEIAEQTGIKLNTVRKILYKLYDARLADYKREKDEETNWYTYTWKPELEKLPEIIKKKKMEELKKL 105 (178)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEeeeeccCCCcEEEEEEeCHHHHHHHHHHHHHHHHHHH
Confidence 45899999999999999999999999999988643322 3455666555444444444444444444443
No 130
>CHL00033 ycf3 photosystem I assembly protein Ycf3
Probab=56.82 E-value=95 Score=25.36 Aligned_cols=88 Identities=8% Similarity=-0.028 Sum_probs=63.9
Q ss_pred CHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHHHHH
Q psy4458 7 DVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIELDQ 86 (303)
Q Consensus 7 ~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~~~~ 86 (303)
++..+.+.|..+- ...+...+..+++..+.++...+++..|....+++-.... + ..+. ..-+..++..+.
T Consensus 14 ~~~~~~~~l~~~~----~~~~~~~~a~~~~~~g~~~~~~g~~~~A~~~~~~al~l~~---~--~~~~-~~~~~~lg~~~~ 83 (168)
T CHL00033 14 TFTIVADILLRIL----PTTSGEKEAFTYYRDGMSAQSEGEYAEALQNYYEAMRLEI---D--PYDR-SYILYNIGLIHT 83 (168)
T ss_pred ccccchhhhhHhc----cCCchhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhccc---c--chhh-HHHHHHHHHHHH
Confidence 3445555555442 2456677889999999999999999999999999876542 1 1111 223445788899
Q ss_pred HhhhHHHHHHHHHHHHcC
Q psy4458 87 HEGSYLATCKHYRAILTT 104 (303)
Q Consensus 87 ~~~~f~eaa~~y~e~~~t 104 (303)
..++|-+|-..|..++..
T Consensus 84 ~~g~~~eA~~~~~~Al~~ 101 (168)
T CHL00033 84 SNGEHTKALEYYFQALER 101 (168)
T ss_pred HcCCHHHHHHHHHHHHHh
Confidence 999999999999988754
No 131
>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=56.72 E-value=32 Score=22.61 Aligned_cols=28 Identities=14% Similarity=0.173 Sum_probs=25.7
Q ss_pred eeHHHHHHHhCCCHHHHHHHHHhhhhcC
Q psy4458 218 ITLQRMCDLLGLPIEETEEFLSSMVVSK 245 (303)
Q Consensus 218 Itl~~la~ll~ls~~~vE~~l~~mI~~~ 245 (303)
+|.+.||+.||+|..-+...+..+-..|
T Consensus 16 it~~eLa~~l~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 16 ITAKELAEELGVSRRTIRRDIKELREWG 43 (55)
T ss_dssp BEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred cCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 9999999999999999999999998877
No 132
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=56.14 E-value=25 Score=28.43 Aligned_cols=39 Identities=21% Similarity=0.244 Sum_probs=34.3
Q ss_pred hceeeHHHHHHHhCCCHHHHHHHHHhhhhcCce---EEEecC
Q psy4458 215 YTRITLQRMCDLLGLPIEETEEFLSSMVVSKTI---TAKIDR 253 (303)
Q Consensus 215 Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l---~akIDq 253 (303)
=.++++..||+.+|+|+..+-.-+-++..+|-| .+.+|.
T Consensus 20 d~r~~~~eia~~lglS~~~v~~Ri~~L~~~GiI~~~~~~v~~ 61 (154)
T COG1522 20 DARISNAELAERVGLSPSTVLRRIKRLEEEGVIKGYTAVLDP 61 (154)
T ss_pred hCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCceeeEEEEECH
Confidence 344999999999999999999999999999976 557775
No 133
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=55.94 E-value=34 Score=28.18 Aligned_cols=51 Identities=12% Similarity=0.138 Sum_probs=40.4
Q ss_pred HHHHHhhhc--eeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCCCceE
Q psy4458 208 IRVMAKYYT--RITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAGII 258 (303)
Q Consensus 208 i~~isk~Y~--~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~giV 258 (303)
+.-++.... -++.+.||+..|+|+..+++++..+...|-+...==...|+.
T Consensus 14 L~~LA~~~~~~~~s~~~IA~~~~is~~~L~kil~~L~kaGlV~S~rG~~GGy~ 66 (150)
T COG1959 14 LLYLALLPGGGPVSSAEIAERQGISPSYLEKILSKLRKAGLVKSVRGKGGGYR 66 (150)
T ss_pred HHHHHhCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHHcCCEEeecCCCCCcc
Confidence 334444333 689999999999999999999999999999877665555554
No 134
>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=55.82 E-value=24 Score=24.53 Aligned_cols=39 Identities=15% Similarity=0.153 Sum_probs=34.4
Q ss_pred hceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecC
Q psy4458 215 YTRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDR 253 (303)
Q Consensus 215 Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq 253 (303)
....|.+.||+.+|+|...|-..|..|...|-+.-.-.+
T Consensus 20 ~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~~~~~ 58 (68)
T PF01978_consen 20 NGPATAEEIAEELGISRSTVYRALKSLEEKGLVEREEGR 58 (68)
T ss_dssp HCHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEEEC
T ss_pred cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcCc
Confidence 678999999999999999999999999999988654433
No 135
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=55.20 E-value=28 Score=28.14 Aligned_cols=47 Identities=11% Similarity=0.159 Sum_probs=39.8
Q ss_pred ceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCCCceEEecc
Q psy4458 216 TRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAGIINFAR 262 (303)
Q Consensus 216 ~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~giV~f~~ 262 (303)
..++.+.||+.+|+|...+.+.+..+...|-+..+=-...|+....+
T Consensus 24 ~~~s~~~ia~~~~is~~~vrk~l~~L~~~Glv~s~~G~~GG~~l~~~ 70 (141)
T PRK11014 24 RMTSISEVTEVYGVSRNHMVKIINQLSRAGYVTAVRGKNGGIRLGKP 70 (141)
T ss_pred CccCHHHHHHHHCcCHHHHHHHHHHHHhCCEEEEecCCCCCeeecCC
Confidence 46899999999999999999999999999998877666667654443
No 136
>PRK10049 pgaA outer membrane protein PgaA; Provisional
Probab=54.33 E-value=1.6e+02 Score=30.87 Aligned_cols=94 Identities=9% Similarity=-0.024 Sum_probs=70.6
Q ss_pred CccCCHHHHHHHHhcccccc------c---cCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHH
Q psy4458 3 EDEGDVTEAANIIQELQVET------Y---GSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQEL 73 (303)
Q Consensus 3 e~~~~~~~Aa~~L~~i~vet------~---~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~ 73 (303)
.+.|++++|...+..+.-.. + ...+.....+..+..+.+....||+..|...+.++-.... + +.+
T Consensus 321 ~~~g~~~eA~~~l~~~~~~~P~~~~~~~~~~~~p~~~~~~a~~~~a~~l~~~g~~~eA~~~l~~al~~~P---~--n~~- 394 (765)
T PRK10049 321 LESENYPGALTVTAHTINNSPPFLRLYGSPTSIPNDDWLQGQSLLSQVAKYSNDLPQAEMRARELAYNAP---G--NQG- 394 (765)
T ss_pred HhcccHHHHHHHHHHHhhcCCceEeecCCCCCCCCchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC---C--CHH-
Confidence 46789999999988765322 1 1234446778888899999999999999999999876552 2 222
Q ss_pred HHHHHHHHHHHHHHhhhHHHHHHHHHHHHcCC
Q psy4458 74 KLKYYRLMIELDQHEGSYLATCKHYRAILTTP 105 (303)
Q Consensus 74 k~~y~~~~~~~~~~~~~f~eaa~~y~e~~~t~ 105 (303)
....++..+...+++-+|-..|..+....
T Consensus 395 ---l~~~lA~l~~~~g~~~~A~~~l~~al~l~ 423 (765)
T PRK10049 395 ---LRIDYASVLQARGWPRAAENELKKAEVLE 423 (765)
T ss_pred ---HHHHHHHHHHhcCCHHHHHHHHHHHHhhC
Confidence 33447888889999999999999997653
No 137
>PRK14574 hmsH outer membrane protein; Provisional
Probab=53.91 E-value=2.1e+02 Score=30.59 Aligned_cols=85 Identities=8% Similarity=0.013 Sum_probs=57.4
Q ss_pred ccCCHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHH--
Q psy4458 4 DEGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLM-- 81 (303)
Q Consensus 4 ~~~~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~-- 81 (303)
.+|++.+|...|+.+.---..+.+ .-. ..+.++...|++..|..+.+|+. +..+ ..|+.+.
T Consensus 46 r~Gd~~~Al~~L~qaL~~~P~~~~--av~----dll~l~~~~G~~~~A~~~~eka~----~p~n-------~~~~~llal 108 (822)
T PRK14574 46 RAGDTAPVLDYLQEESKAGPLQSG--QVD----DWLQIAGWAGRDQEVIDVYERYQ----SSMN-------ISSRGLASA 108 (822)
T ss_pred hCCCHHHHHHHHHHHHhhCccchh--hHH----HHHHHHHHcCCcHHHHHHHHHhc----cCCC-------CCHHHHHHH
Confidence 468999999999888521111110 011 66677777799999999888887 1111 2234444
Q ss_pred HHHHHHhhhHHHHHHHHHHHHcCC
Q psy4458 82 IELDQHEGSYLATCKHYRAILTTP 105 (303)
Q Consensus 82 ~~~~~~~~~f~eaa~~y~e~~~t~ 105 (303)
+..+...++|-.|...|..++...
T Consensus 109 A~ly~~~gdyd~Aiely~kaL~~d 132 (822)
T PRK14574 109 ARAYRNEKRWDQALALWQSSLKKD 132 (822)
T ss_pred HHHHHHcCCHHHHHHHHHHHHhhC
Confidence 668888899999999999998654
No 138
>PRK10747 putative protoheme IX biogenesis protein; Provisional
Probab=53.24 E-value=1.8e+02 Score=27.80 Aligned_cols=86 Identities=12% Similarity=0.055 Sum_probs=49.7
Q ss_pred cCCHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHHH
Q psy4458 5 EGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIEL 84 (303)
Q Consensus 5 ~~~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~~ 84 (303)
+|||.+|.+.+..-+-. .+...-+++--++.....||+..|..++.++..... + . .+......+++
T Consensus 97 eGd~~~A~k~l~~~~~~------~~~p~l~~llaA~aA~~~g~~~~A~~~l~~A~~~~~---~--~---~~~~~l~~a~l 162 (398)
T PRK10747 97 EGDYQQVEKLMTRNADH------AEQPVVNYLLAAEAAQQRGDEARANQHLERAAELAD---N--D---QLPVEITRVRI 162 (398)
T ss_pred CCCHHHHHHHHHHHHhc------ccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCC---c--c---hHHHHHHHHHH
Confidence 57888777777653211 111333456667777777777777777777754321 1 0 01111233666
Q ss_pred HHHhhhHHHHHHHHHHHHcC
Q psy4458 85 DQHEGSYLATCKHYRAILTT 104 (303)
Q Consensus 85 ~~~~~~f~eaa~~y~e~~~t 104 (303)
+...++|-.|-..+....+.
T Consensus 163 ~l~~g~~~~Al~~l~~~~~~ 182 (398)
T PRK10747 163 QLARNENHAARHGVDKLLEV 182 (398)
T ss_pred HHHCCCHHHHHHHHHHHHhc
Confidence 67777777777776666544
No 139
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=53.17 E-value=73 Score=25.66 Aligned_cols=35 Identities=3% Similarity=0.059 Sum_probs=30.9
Q ss_pred hceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEE
Q psy4458 215 YTRITLQRMCDLLGLPIEETEEFLSSMVVSKTITA 249 (303)
Q Consensus 215 Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~a 249 (303)
-..++++.||+.+|+|+.-|=..|..|...|-|.-
T Consensus 20 ~~~~~~~ela~~l~vs~~svs~~l~~L~~~Gli~~ 54 (142)
T PRK03902 20 KGYARVSDIAEALSVHPSSVTKMVQKLDKDEYLIY 54 (142)
T ss_pred CCCcCHHHHHHHhCCChhHHHHHHHHHHHCCCEEE
Confidence 34568899999999999999999999999998863
No 140
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=53.08 E-value=12 Score=24.94 Aligned_cols=25 Identities=24% Similarity=0.384 Sum_probs=19.7
Q ss_pred ceeeHHHHHHHhCCCHHHHHHHHHh
Q psy4458 216 TRITLQRMCDLLGLPIEETEEFLSS 240 (303)
Q Consensus 216 ~~Itl~~la~ll~ls~~~vE~~l~~ 240 (303)
..+++..||+.+|+++.++-..+..
T Consensus 2 ~~i~V~elAk~l~v~~~~ii~~l~~ 26 (54)
T PF04760_consen 2 EKIRVSELAKELGVPSKEIIKKLFK 26 (54)
T ss_dssp -EE-TTHHHHHHSSSHHHHHHHH-H
T ss_pred CceEHHHHHHHHCcCHHHHHHHHHH
Confidence 3689999999999999998888833
No 141
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=53.04 E-value=1.1e+02 Score=24.53 Aligned_cols=44 Identities=7% Similarity=0.018 Sum_probs=38.7
Q ss_pred eeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCCCceEEe
Q psy4458 217 RITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAGIINF 260 (303)
Q Consensus 217 ~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~giV~f 260 (303)
.++.+.||+.+|++..-+=..+..|...|-|.-.-|..++-+..
T Consensus 46 ~~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~r~~~~~DrR~~~ 89 (144)
T PRK03573 46 EQSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQTCASDRRAKR 89 (144)
T ss_pred CCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeeecCCCCcCeee
Confidence 46889999999999999999999999999999888877766443
No 142
>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=52.36 E-value=31 Score=19.80 Aligned_cols=30 Identities=10% Similarity=-0.098 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHhhcchhHHHHHHHHhhhhc
Q psy4458 33 TLILEQMRLCLAKKDYIRTQIISKKINTKF 62 (303)
Q Consensus 33 ~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~ 62 (303)
+.+..+.+++...||+..|..+.+++...-
T Consensus 2 ~~~~~lg~~y~~~~~~~~A~~~~~~a~~~~ 31 (34)
T PF13181_consen 2 EAYYNLGKIYEQLGDYEEALEYFEKALELN 31 (34)
T ss_dssp HHHHHHHHHHHHTTSHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHHhhC
Confidence 567889999999999999999999887543
No 143
>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=52.33 E-value=1e+02 Score=30.34 Aligned_cols=88 Identities=10% Similarity=0.081 Sum_probs=63.1
Q ss_pred cCCHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHHH
Q psy4458 5 EGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIEL 84 (303)
Q Consensus 5 ~~~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~~ 84 (303)
.++...|-++|....--- |. =.=+.+..+|+....||.+.|-...+++-... .. -.++..-.+-=++-.
T Consensus 246 ~~~~~~a~~lL~~~~~~y----P~--s~lfl~~~gR~~~~~g~~~~Ai~~~~~a~~~q---~~--~~Ql~~l~~~El~w~ 314 (468)
T PF10300_consen 246 DVPLEEAEELLEEMLKRY----PN--SALFLFFEGRLERLKGNLEEAIESFERAIESQ---SE--WKQLHHLCYFELAWC 314 (468)
T ss_pred CCCHHHHHHHHHHHHHhC----CC--cHHHHHHHHHHHHHhcCHHHHHHHHHHhccch---hh--HHhHHHHHHHHHHHH
Confidence 567777888887776322 21 12367889999999999999999998765321 11 334444444446777
Q ss_pred HHHhhhHHHHHHHHHHHHc
Q psy4458 85 DQHEGSYLATCKHYRAILT 103 (303)
Q Consensus 85 ~~~~~~f~eaa~~y~e~~~ 103 (303)
+....+|.+|+.+|..+.+
T Consensus 315 ~~~~~~w~~A~~~f~~L~~ 333 (468)
T PF10300_consen 315 HMFQHDWEEAAEYFLRLLK 333 (468)
T ss_pred HHHHchHHHHHHHHHHHHh
Confidence 8999999999999999975
No 144
>PRK11447 cellulose synthase subunit BcsC; Provisional
Probab=51.89 E-value=3.3e+02 Score=30.15 Aligned_cols=88 Identities=13% Similarity=0.171 Sum_probs=60.1
Q ss_pred ccCCHHHHHHHHhcccccccc----CCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHH
Q psy4458 4 DEGDVTEAANIIQELQVETYG----SMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYR 79 (303)
Q Consensus 4 ~~~~~~~Aa~~L~~i~vet~~----~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~ 79 (303)
..|++++|...|..++-.... .+..+-+.+..+..++.+...|++..|..++++ . ... .+ ...
T Consensus 541 ~~~~~~~Al~~l~~l~~~~~~~~~~~l~~~l~~~~~l~~a~~l~~~G~~~eA~~~l~~----~--p~~---~~----~~~ 607 (1157)
T PRK11447 541 GSDRDRAALAHLNTLPRAQWNSNIQELAQRLQSDQVLETANRLRDSGKEAEAEALLRQ----Q--PPS---TR----IDL 607 (1157)
T ss_pred hCCCHHHHHHHHHhCCchhcChhHHHHHHHHhhhHHHHHHHHHHHCCCHHHHHHHHHh----C--CCC---ch----HHH
Confidence 456777777777776533221 122233445677888999999999999988772 1 111 11 224
Q ss_pred HHHHHHHHhhhHHHHHHHHHHHHcC
Q psy4458 80 LMIELDQHEGSYLATCKHYRAILTT 104 (303)
Q Consensus 80 ~~~~~~~~~~~f~eaa~~y~e~~~t 104 (303)
..+.++...+++-+|-..|..+...
T Consensus 608 ~La~~~~~~g~~~~A~~~y~~al~~ 632 (1157)
T PRK11447 608 TLADWAQQRGDYAAARAAYQRVLTR 632 (1157)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHh
Confidence 5788899999999999999999864
No 145
>KOG3081|consensus
Probab=51.88 E-value=78 Score=29.06 Aligned_cols=56 Identities=13% Similarity=0.073 Sum_probs=31.5
Q ss_pred HHHHHHhhhHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHhCCCC-chhhHhHHHhhh
Q psy4458 82 IELDQHEGSYLATCKHYRAILTTPCIQSDPVQRHAVLQNVVLYLMLAPYD-NEQSDLTHRVLE 143 (303)
Q Consensus 82 ~~~~~~~~~f~eaa~~y~e~~~t~~~~~~~~~~~~~L~~~v~~~iLs~~~-~~r~~ll~~l~~ 143 (303)
+..+...++|-+|=....++++.... + -.+|-++++|+.+.+.+ +...+.+..+..
T Consensus 214 Av~~l~~~~~eeAe~lL~eaL~kd~~--d----petL~Nliv~a~~~Gkd~~~~~r~l~QLk~ 270 (299)
T KOG3081|consen 214 AVCHLQLGRYEEAESLLEEALDKDAK--D----PETLANLIVLALHLGKDAEVTERNLSQLKL 270 (299)
T ss_pred HHHHHHhcCHHHHHHHHHHHHhccCC--C----HHHHHHHHHHHHHhCCChHHHHHHHHHHHh
Confidence 45666677777777777666654322 2 23455666666655443 345555555554
No 146
>PF12964 DUF3853: Protein of unknown function (DUF3853); InterPro: IPR024363 This entry represents a family of uncharacterised proteins that were found by clustering human gut metagenomic sequences [].
Probab=51.62 E-value=10 Score=28.87 Aligned_cols=40 Identities=18% Similarity=0.215 Sum_probs=34.8
Q ss_pred eHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCCCceEEecc
Q psy4458 219 TLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAGIINFAR 262 (303)
Q Consensus 219 tl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~giV~f~~ 262 (303)
-+..||++||.|..- ++++-.+|.|+--|=|+.+.|.|+.
T Consensus 47 G~~GlAklfgcSv~T----a~RiK~sG~id~AI~Q~Gr~IivD~ 86 (96)
T PF12964_consen 47 GLKGLAKLFGCSVPT----ANRIKKSGKIDPAITQIGRKIIVDA 86 (96)
T ss_pred hHHHHHHHhCCCchh----HHHHHhcCCccHHHHHcCCEEEEeH
Confidence 578899999999876 5677788999999999999999985
No 147
>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=51.26 E-value=18 Score=26.48 Aligned_cols=28 Identities=29% Similarity=0.502 Sum_probs=21.0
Q ss_pred hceeeHHHHHHHhCCCHHHHHHHHHhhh
Q psy4458 215 YTRITLQRMCDLLGLPIEETEEFLSSMV 242 (303)
Q Consensus 215 Y~~Itl~~la~ll~ls~~~vE~~l~~mI 242 (303)
=.-||.+.||..+|.|.++|...+..|-
T Consensus 36 G~PVt~~~LA~a~g~~~e~v~~~L~~~p 63 (77)
T PF12324_consen 36 GQPVTVEQLAAALGWPVEEVRAALAAMP 63 (77)
T ss_dssp TS-B-HHHHHHHHT--HHHHHHHHHH-T
T ss_pred CCCcCHHHHHHHHCCCHHHHHHHHHhCC
Confidence 5668999999999999999999998874
No 148
>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=50.49 E-value=1.5e+02 Score=24.93 Aligned_cols=77 Identities=8% Similarity=-0.070 Sum_probs=62.2
Q ss_pred cCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHc
Q psy4458 24 GSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIELDQHEGSYLATCKHYRAILT 103 (303)
Q Consensus 24 ~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~~~~~~~~f~eaa~~y~e~~~ 103 (303)
.++.+.+.-+-++..+..+...||...|-....++...+. ....++......++.....+|+..+..+...+-.
T Consensus 28 ~n~~kesir~~~~~l~~~~~~~Gd~~~A~k~y~~~~~~~~------~~~~~id~~l~~irv~i~~~d~~~v~~~i~ka~~ 101 (177)
T PF10602_consen 28 SNLGKESIRMALEDLADHYCKIGDLEEALKAYSRARDYCT------SPGHKIDMCLNVIRVAIFFGDWSHVEKYIEKAES 101 (177)
T ss_pred hccchHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHhhhcC------CHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence 4677778888899999999999999999998888887763 3457788888899999999999998877666654
Q ss_pred CCC
Q psy4458 104 TPC 106 (303)
Q Consensus 104 t~~ 106 (303)
+..
T Consensus 102 ~~~ 104 (177)
T PF10602_consen 102 LIE 104 (177)
T ss_pred HHh
Confidence 443
No 149
>PF04492 Phage_rep_O: Bacteriophage replication protein O ; InterPro: IPR006497 This entry is represented by the N-terminal domain of Bacteriophage lambda, GpO. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; GO: 0006260 DNA replication
Probab=50.18 E-value=26 Score=26.94 Aligned_cols=36 Identities=19% Similarity=0.364 Sum_probs=33.7
Q ss_pred HhhhceeeHHHHHHHhCCCHHHHHHHHHhhhhcCce
Q psy4458 212 AKYYTRITLQRMCDLLGLPIEETEEFLSSMVVSKTI 247 (303)
Q Consensus 212 sk~Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l 247 (303)
.|....|+.+.++++.|+++..|.+.+..+|..|-|
T Consensus 49 nKk~d~Is~sq~~e~tg~~~~~V~~al~~Li~~~vI 84 (100)
T PF04492_consen 49 NKKMDRISNSQIAEMTGLSRDHVSKALNELIRRGVI 84 (100)
T ss_pred CCccceeeHHHHHHHHCcCHHHHHHHHHHHHHCCCE
Confidence 356789999999999999999999999999999988
No 150
>PF13730 HTH_36: Helix-turn-helix domain
Probab=49.97 E-value=23 Score=23.35 Aligned_cols=29 Identities=10% Similarity=0.180 Sum_probs=26.2
Q ss_pred eHHHHHHHhCCCHHHHHHHHHhhhhcCce
Q psy4458 219 TLQRMCDLLGLPIEETEEFLSSMVVSKTI 247 (303)
Q Consensus 219 tl~~la~ll~ls~~~vE~~l~~mI~~~~l 247 (303)
|.+.||+.+|++..-|.+.+..++..|-|
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHCcCC
Confidence 79999999999999999999999887753
No 151
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=49.90 E-value=75 Score=26.21 Aligned_cols=43 Identities=12% Similarity=0.123 Sum_probs=36.2
Q ss_pred ceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCCCceE
Q psy4458 216 TRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAGII 258 (303)
Q Consensus 216 ~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~giV 258 (303)
..++.+.||+..|+|+..+++++..+...|-+...==...|+.
T Consensus 23 ~~~s~~eIA~~~~is~~~L~kIl~~L~~aGlv~S~rG~~GGy~ 65 (153)
T PRK11920 23 KLSRIPEIARAYGVSELFLFKILQPLVEAGLVETVRGRNGGVR 65 (153)
T ss_pred CcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeecCCCCCee
Confidence 3479999999999999999999999999998877655555543
No 152
>PRK10049 pgaA outer membrane protein PgaA; Provisional
Probab=49.37 E-value=61 Score=33.99 Aligned_cols=88 Identities=9% Similarity=-0.106 Sum_probs=67.7
Q ss_pred CccCCHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHH
Q psy4458 3 EDEGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMI 82 (303)
Q Consensus 3 e~~~~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~ 82 (303)
...|++++|...|+++.-.. +.. .++.+..+.++...|++..|...++++..... + +. .+...++
T Consensus 370 ~~~g~~~eA~~~l~~al~~~----P~n--~~l~~~lA~l~~~~g~~~~A~~~l~~al~l~P--d---~~----~l~~~~a 434 (765)
T PRK10049 370 KYSNDLPQAEMRARELAYNA----PGN--QGLRIDYASVLQARGWPRAAENELKKAEVLEP--R---NI----NLEVEQA 434 (765)
T ss_pred HHcCCHHHHHHHHHHHHHhC----CCC--HHHHHHHHHHHHhcCCHHHHHHHHHHHHhhCC--C---Ch----HHHHHHH
Confidence 35689999999999875322 222 46889999999999999999999999987552 1 22 2444577
Q ss_pred HHHHHhhhHHHHHHHHHHHHcCC
Q psy4458 83 ELDQHEGSYLATCKHYRAILTTP 105 (303)
Q Consensus 83 ~~~~~~~~f~eaa~~y~e~~~t~ 105 (303)
..+...++|-+|-..+.++....
T Consensus 435 ~~al~~~~~~~A~~~~~~ll~~~ 457 (765)
T PRK10049 435 WTALDLQEWRQMDVLTDDVVARE 457 (765)
T ss_pred HHHHHhCCHHHHHHHHHHHHHhC
Confidence 78889999999999999998654
No 153
>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional
Probab=49.01 E-value=2e+02 Score=27.07 Aligned_cols=61 Identities=5% Similarity=0.034 Sum_probs=48.3
Q ss_pred HHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHcC
Q psy4458 35 ILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIELDQHEGSYLATCKHYRAILTT 104 (303)
Q Consensus 35 ~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~~~~~~~~f~eaa~~y~e~~~t 104 (303)
++.+++-.+..++|..|....+++-.... + + ..++..++..+...++|-+|...|..++..
T Consensus 5 l~~~a~~a~~~~~~~~Ai~~~~~Al~~~P--~---~----~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l 65 (356)
T PLN03088 5 LEDKAKEAFVDDDFALAVDLYTQAIDLDP--N---N----AELYADRAQANIKLGNFTEAVADANKAIEL 65 (356)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHhCC--C---C----HHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence 56788999999999999999998876442 1 2 234556788888999999999999999764
No 154
>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=48.45 E-value=79 Score=21.03 Aligned_cols=62 Identities=16% Similarity=0.056 Sum_probs=46.3
Q ss_pred HHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHcC
Q psy4458 34 LILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIELDQHEGSYLATCKHYRAILTT 104 (303)
Q Consensus 34 ~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~~~~~~~~f~eaa~~y~e~~~t 104 (303)
.+..++..+...+++..|.....++-.... . +. ......+..+...+++-+|-..|..+...
T Consensus 2 ~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~---~--~~----~~~~~~~~~~~~~~~~~~a~~~~~~~~~~ 63 (100)
T cd00189 2 ALLNLGNLYYKLGDYDEALEYYEKALELDP---D--NA----DAYYNLAAAYYKLGKYEEALEDYEKALEL 63 (100)
T ss_pred HHHHHHHHHHHHhcHHHHHHHHHHHHhcCC---c--cH----HHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 356788888999999999999888765431 1 22 33445788888889999999988888654
No 155
>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=48.12 E-value=50 Score=18.70 Aligned_cols=30 Identities=7% Similarity=-0.223 Sum_probs=24.9
Q ss_pred HHHHHHHHHHHhhcchhHHHHHHHHhhhhc
Q psy4458 33 TLILEQMRLCLAKKDYIRTQIISKKINTKF 62 (303)
Q Consensus 33 ~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~ 62 (303)
+.+..++.+++..|+|..|....+++-...
T Consensus 2 ~~~~~lg~~~~~~~~~~~A~~~~~~al~l~ 31 (34)
T PF07719_consen 2 EAWYYLGQAYYQLGNYEEAIEYFEKALELD 31 (34)
T ss_dssp HHHHHHHHHHHHTT-HHHHHHHHHHHHHHS
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHHHHC
Confidence 467788999999999999999999987654
No 156
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=47.67 E-value=49 Score=26.06 Aligned_cols=48 Identities=23% Similarity=0.275 Sum_probs=37.1
Q ss_pred hceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCCCc---eEEecc
Q psy4458 215 YTRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAG---IINFAR 262 (303)
Q Consensus 215 Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~g---iV~f~~ 262 (303)
-..+|++.||+.+..|+-.+-.+|-+|...|-|.=+-=+..| .++|..
T Consensus 17 ~~~vtl~elA~~l~cS~Rn~r~lLkkm~~~gWi~W~pg~GRG~~S~L~~l~ 67 (115)
T PF12793_consen 17 PVEVTLDELAELLFCSRRNARTLLKKMQEEGWITWQPGRGRGNRSQLTFLK 67 (115)
T ss_pred CcceeHHHHHHHhCCCHHHHHHHHHHHHHCCCeeeeCCCCCCCCCeeEEee
Confidence 457899999999999999999999999999988433322222 256654
No 157
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=47.52 E-value=19 Score=27.10 Aligned_cols=25 Identities=24% Similarity=0.412 Sum_probs=22.5
Q ss_pred hceeeHHHHHHHhCCCHHHHHHHHH
Q psy4458 215 YTRITLQRMCDLLGLPIEETEEFLS 239 (303)
Q Consensus 215 Y~~Itl~~la~ll~ls~~~vE~~l~ 239 (303)
-+.+|.+.+|.-||+|++++|+.+.
T Consensus 21 ~~~ls~~~ia~dL~~s~~~le~vL~ 45 (89)
T PF10078_consen 21 LSGLSLEQIAADLGTSPEHLEQVLN 45 (89)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 4788999999999999999999874
No 158
>TIGR03504 FimV_Cterm FimV C-terminal domain. This protein is found at the extreme C-terminus of FimV from Pseudomonas aeruginosa, and of TspA of Neisseria meningitidis. Disruption of the former blocks twitching motility from type IV pili; Semmler, et al. suggest a role in peptidoglycan layer remodelling required by type IV fimbrial systems.
Probab=47.28 E-value=27 Score=22.60 Aligned_cols=24 Identities=13% Similarity=0.162 Sum_probs=22.1
Q ss_pred HHHHHHHHhhcchhHHHHHHHHhh
Q psy4458 36 LEQMRLCLAKKDYIRTQIISKKIN 59 (303)
Q Consensus 36 L~~~rL~L~~~D~~~a~~~~~ki~ 59 (303)
|..+|-|++.||+..|..+++.+-
T Consensus 3 LdLA~ayie~Gd~e~Ar~lL~evl 26 (44)
T TIGR03504 3 LDLARAYIEMGDLEGARELLEEVI 26 (44)
T ss_pred hHHHHHHHHcCChHHHHHHHHHHH
Confidence 678999999999999999999887
No 159
>PF13512 TPR_18: Tetratricopeptide repeat
Probab=47.16 E-value=1.4e+02 Score=24.47 Aligned_cols=58 Identities=14% Similarity=0.194 Sum_probs=42.5
Q ss_pred ccCCHHHHHHHHhcccccc-ccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCC
Q psy4458 4 DEGDVTEAANIIQELQVET-YGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDD 65 (303)
Q Consensus 4 ~~~~~~~Aa~~L~~i~vet-~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~ 65 (303)
..|++++|.+.|..|.--- +|..+. .-.|.++-.++..++|+.|.....+--.+....
T Consensus 22 ~~~~Y~~A~~~le~L~~ryP~g~ya~----qAqL~l~yayy~~~~y~~A~a~~~rFirLhP~h 80 (142)
T PF13512_consen 22 QKGNYEEAIKQLEALDTRYPFGEYAE----QAQLDLAYAYYKQGDYEEAIAAYDRFIRLHPTH 80 (142)
T ss_pred HhCCHHHHHHHHHHHHhcCCCCcccH----HHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCC
Confidence 4699999999999885321 344443 334778899999999999998888776665433
No 160
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=46.97 E-value=55 Score=26.35 Aligned_cols=45 Identities=11% Similarity=0.058 Sum_probs=40.4
Q ss_pred ceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCCCceEEe
Q psy4458 216 TRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAGIINF 260 (303)
Q Consensus 216 ~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~giV~f 260 (303)
..++...||+.+|+++.-+=..+..|+..|-|.-..|..++-...
T Consensus 53 ~~~t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~R~~~~~DrR~~~ 97 (144)
T PRK11512 53 ACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNPNDKRGVL 97 (144)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCcccCCeeE
Confidence 469999999999999999999999999999999988887776443
No 161
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=46.91 E-value=28 Score=23.50 Aligned_cols=26 Identities=31% Similarity=0.497 Sum_probs=21.6
Q ss_pred ceeeHHHHHHHhCCCHHHHHHHHHhh
Q psy4458 216 TRITLQRMCDLLGLPIEETEEFLSSM 241 (303)
Q Consensus 216 ~~Itl~~la~ll~ls~~~vE~~l~~m 241 (303)
..++++.||+.||+|..-+...|-+.
T Consensus 22 R~~tl~elA~~lgis~st~~~~LRra 47 (53)
T PF04967_consen 22 RRITLEELAEELGISKSTVSEHLRRA 47 (53)
T ss_pred CcCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 48999999999999998877666544
No 162
>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional
Probab=46.85 E-value=4.2e+02 Score=28.94 Aligned_cols=84 Identities=8% Similarity=0.039 Sum_probs=61.4
Q ss_pred ccCCHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHH
Q psy4458 4 DEGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIE 83 (303)
Q Consensus 4 ~~~~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~ 83 (303)
.+|++++|...+...- + .+++. ....+..+++++..|++..|..+++++-..-. + +. .|+...+.
T Consensus 56 ~~Gd~~~A~~~l~~Al-~----~dP~n-~~~~~~LA~~yl~~g~~~~A~~~~~kAv~ldP--~---n~----~~~~~La~ 120 (987)
T PRK09782 56 KNNDEATAIREFEYIH-Q----QVPDN-IPLTLYLAEAYRHFGHDDRARLLLEDQLKRHP--G---DA----RLERSLAA 120 (987)
T ss_pred hCCCHHHHHHHHHHHH-H----hCCCC-HHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCc--c---cH----HHHHHHHH
Confidence 4699999999888763 1 12223 66669999999999999999999999986541 2 22 23332333
Q ss_pred HHHHhhhHHHHHHHHHHHHcCCC
Q psy4458 84 LDQHEGSYLATCKHYRAILTTPC 106 (303)
Q Consensus 84 ~~~~~~~f~eaa~~y~e~~~t~~ 106 (303)
+ ++|.+|...|.+++..+.
T Consensus 121 i----~~~~kA~~~ye~l~~~~P 139 (987)
T PRK09782 121 I----PVEVKSVTTVEELLAQQK 139 (987)
T ss_pred h----ccChhHHHHHHHHHHhCC
Confidence 3 999999999999987654
No 163
>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=46.23 E-value=55 Score=22.94 Aligned_cols=31 Identities=19% Similarity=0.309 Sum_probs=26.8
Q ss_pred eeHHHHHHHhCCC-HHHHHHHHHhhhhcCceE
Q psy4458 218 ITLQRMCDLLGLP-IEETEEFLSSMVVSKTIT 248 (303)
Q Consensus 218 Itl~~la~ll~ls-~~~vE~~l~~mI~~~~l~ 248 (303)
-|+.+||+.||++ +.-|...|..+...|.|.
T Consensus 26 Pt~rEIa~~~g~~S~~tv~~~L~~Le~kG~I~ 57 (65)
T PF01726_consen 26 PTVREIAEALGLKSTSTVQRHLKALERKGYIR 57 (65)
T ss_dssp --HHHHHHHHTSSSHHHHHHHHHHHHHTTSEE
T ss_pred CCHHHHHHHhCCCChHHHHHHHHHHHHCcCcc
Confidence 5999999999996 999999999999998775
No 164
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=45.63 E-value=47 Score=29.58 Aligned_cols=40 Identities=15% Similarity=0.137 Sum_probs=34.0
Q ss_pred HHHhhhceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEE
Q psy4458 210 VMAKYYTRITLQRMCDLLGLPIEETEEFLSSMVVSKTITA 249 (303)
Q Consensus 210 ~isk~Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~a 249 (303)
.+.+-...++.+.||+.||+|+.-+.+.+..|...|.+..
T Consensus 11 ~~l~~~~~~~~~eLa~~l~VS~~TiRRdL~~L~~~~~l~r 50 (240)
T PRK10411 11 DLLLNHTSLTTEALAEQLNVSKETIRRDLNELQTQGKILR 50 (240)
T ss_pred HHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence 3333468899999999999999999999999999887753
No 165
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=45.59 E-value=53 Score=29.51 Aligned_cols=40 Identities=8% Similarity=0.046 Sum_probs=34.2
Q ss_pred HHHHHhhhceeeHHHHHHHhCCCHHHHHHHHHhhhhcCce
Q psy4458 208 IRVMAKYYTRITLQRMCDLLGLPIEETEEFLSSMVVSKTI 247 (303)
Q Consensus 208 i~~isk~Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l 247 (303)
|....+-...++++.||+.||+|++-+-+-|..|-..|.+
T Consensus 10 Il~~L~~~~~v~v~eLa~~l~VS~~TIRRDL~~Le~~g~l 49 (256)
T PRK10434 10 ILEYLQKQGKTSVEELAQYFDTTGTTIRKDLVILEHAGTV 49 (256)
T ss_pred HHHHHHHcCCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCE
Confidence 3344455888999999999999999999999999999965
No 166
>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=45.56 E-value=51 Score=22.32 Aligned_cols=37 Identities=14% Similarity=0.184 Sum_probs=32.3
Q ss_pred hhhceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEE
Q psy4458 213 KYYTRITLQRMCDLLGLPIEETEEFLSSMVVSKTITA 249 (303)
Q Consensus 213 k~Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~a 249 (303)
..-...|+..||+.+|+|+.-+-..+..|...|-|..
T Consensus 20 ~~~~~~t~~ela~~l~~~~~t~s~hL~~L~~aGli~~ 56 (61)
T PF12840_consen 20 ASNGPMTVSELAEELGISQSTVSYHLKKLEEAGLIEV 56 (61)
T ss_dssp HHCSTBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred hcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEE
Confidence 3478899999999999999999999999999998764
No 167
>PLN03081 pentatricopeptide (PPR) repeat-containing protein; Provisional
Probab=45.35 E-value=3.6e+02 Score=27.73 Aligned_cols=55 Identities=7% Similarity=-0.016 Sum_probs=39.0
Q ss_pred HHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHc
Q psy4458 37 EQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIELDQHEGSYLATCKHYRAILT 103 (303)
Q Consensus 37 ~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~~~~~~~~f~eaa~~y~e~~~ 103 (303)
..+..|...|++..|..+.++... .+ ..-|..++..|...+++.+|...|.+...
T Consensus 264 ~Li~~y~k~g~~~~A~~vf~~m~~-----~~-------~vt~n~li~~y~~~g~~~eA~~lf~~M~~ 318 (697)
T PLN03081 264 ALIDMYSKCGDIEDARCVFDGMPE-----KT-------TVAWNSMLAGYALHGYSEEALCLYYEMRD 318 (697)
T ss_pred HHHHHHHHCCCHHHHHHHHHhCCC-----CC-------hhHHHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 345667777888888777765532 11 22356678888889999999999988854
No 168
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=45.31 E-value=37 Score=28.96 Aligned_cols=42 Identities=10% Similarity=0.107 Sum_probs=34.8
Q ss_pred HHHHHHHhhhceeeHHHHHHHhCCCHHHHHHHHHhhhhcCce
Q psy4458 206 HNIRVMAKYYTRITLQRMCDLLGLPIEETEEFLSSMVVSKTI 247 (303)
Q Consensus 206 hNi~~isk~Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l 247 (303)
+.|..+.+-...+++..||+.||+|+.-+-+-+..|-..|.+
T Consensus 10 ~~Il~~l~~~~~~~~~~La~~~~vS~~TiRRDl~~L~~~g~~ 51 (185)
T PRK04424 10 KALQELIEENPFITDEELAEKFGVSIQTIRLDRMELGIPELR 51 (185)
T ss_pred HHHHHHHHHCCCEEHHHHHHHHCcCHHHHHHHHHHHhcchHH
Confidence 334445555889999999999999999999999999888865
No 169
>KOG1861|consensus
Probab=45.12 E-value=51 Score=32.46 Aligned_cols=66 Identities=12% Similarity=0.137 Sum_probs=53.5
Q ss_pred HHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Q psy4458 33 TLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIELDQHEGSYLATCKHYRAIL 102 (303)
Q Consensus 33 ~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~~~~~~~~f~eaa~~y~e~~ 102 (303)
+.|=.-+|+.|+.||.......-.++..++ .++.+.. -..|-.|.+.|+.+..|+.+.-....++.
T Consensus 349 eVYEtHARIALEkGD~~EfNQCQtQLk~LY-~egipg~---~~EF~AYriLY~i~tkN~~di~sll~~lt 414 (540)
T KOG1861|consen 349 EVYETHARIALEKGDLEEFNQCQTQLKALY-SEGIPGA---YLEFTAYRILYYIFTKNYPDILSLLRDLT 414 (540)
T ss_pred eeehhhhHHHHhcCCHHHHHHHHHHHHHHH-ccCCCCc---hhhHHHHHHHHHHHhcCchHHHHHHHhcc
Confidence 345567999999999999999999999988 5544212 57888999999999999998777777663
No 170
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=44.99 E-value=62 Score=23.42 Aligned_cols=34 Identities=18% Similarity=0.306 Sum_probs=31.5
Q ss_pred ceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEE
Q psy4458 216 TRITLQRMCDLLGLPIEETEEFLSSMVVSKTITA 249 (303)
Q Consensus 216 ~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~a 249 (303)
..++++.||+.+|+|..-+-..+..|...|-+..
T Consensus 19 ~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~ 52 (91)
T smart00346 19 GGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQ 52 (91)
T ss_pred CCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeee
Confidence 3699999999999999999999999999998865
No 171
>KOG3677|consensus
Probab=44.97 E-value=2.3e+02 Score=27.78 Aligned_cols=56 Identities=25% Similarity=0.387 Sum_probs=40.5
Q ss_pred HHHHHhhhceeeHHHHHHHhCCCHHHHHHHHHhhhh-----------cCceEEEec-CCCceEEeccC
Q psy4458 208 IRVMAKYYTRITLQRMCDLLGLPIEETEEFLSSMVV-----------SKTITAKID-RPAGIINFARN 263 (303)
Q Consensus 208 i~~isk~Y~~Itl~~la~ll~ls~~~vE~~l~~mI~-----------~~~l~akID-q~~giV~f~~~ 263 (303)
++.+-++|+......+|..++++.++=++.+..++. +|.....++ +...-|-|--.
T Consensus 419 ~rsylklyTt~P~kkla~F~D~~d~~~dk~li~Ll~~khkm~nlv~~sg~s~~d~~f~~~s~idfyid 486 (525)
T KOG3677|consen 419 IRSYLKLYTTLPVKKLASFLDLTDQERDKFLIQLLVFKHKMKNLVWTSGPSDLDDAFFSRSEIDFYID 486 (525)
T ss_pred HHHHHHHHHhccHHHhhhccCCchhhhhhhHHHHHHHHHHHHHHHHhcCCccccccccCcceeeEEec
Confidence 455667899999999999999999987777776653 455555555 44445666543
No 172
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=44.82 E-value=30 Score=22.68 Aligned_cols=29 Identities=14% Similarity=0.458 Sum_probs=21.8
Q ss_pred hhhceeeHHHHHHHhCCCHHHHHHHHHhh
Q psy4458 213 KYYTRITLQRMCDLLGLPIEETEEFLSSM 241 (303)
Q Consensus 213 k~Y~~Itl~~la~ll~ls~~~vE~~l~~m 241 (303)
.++...|...+|+.+|+|+.-|...+.+.
T Consensus 22 ~~~~g~s~~eIa~~l~~s~~~v~~~l~ra 50 (54)
T PF08281_consen 22 RYFQGMSYAEIAEILGISESTVKRRLRRA 50 (54)
T ss_dssp HHTS---HHHHHHHCTS-HHHHHHHHHHH
T ss_pred HHHHCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 47899999999999999999999887654
No 173
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=44.75 E-value=49 Score=21.93 Aligned_cols=38 Identities=8% Similarity=0.198 Sum_probs=30.4
Q ss_pred HHHHHHHHhhhceeeHHHHHHHhCCCHHHHHHHHHhhh
Q psy4458 205 EHNIRVMAKYYTRITLQRMCDLLGLPIEETEEFLSSMV 242 (303)
Q Consensus 205 ehNi~~isk~Y~~Itl~~la~ll~ls~~~vE~~l~~mI 242 (303)
++-+.+..+.=.+.+.+.||..||+|..-+-+.+..++
T Consensus 7 d~lll~L~~LR~~~~~~~La~~FgIs~stvsri~~~~~ 44 (53)
T PF13613_consen 7 DQLLLTLMYLRLNLTFQDLAYRFGISQSTVSRIFHEWI 44 (53)
T ss_pred HHHHHHHHHHHcCCcHhHHhhheeecHHHHHHHHHHHH
Confidence 44455666777889999999999999998888777665
No 174
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=44.54 E-value=34 Score=22.82 Aligned_cols=26 Identities=23% Similarity=0.332 Sum_probs=19.9
Q ss_pred hhceeeHHHHHHHhCCCHHHHHHHHH
Q psy4458 214 YYTRITLQRMCDLLGLPIEETEEFLS 239 (303)
Q Consensus 214 ~Y~~Itl~~la~ll~ls~~~vE~~l~ 239 (303)
-...|+=..||+.+|+++.+|-+-++
T Consensus 25 G~~~vSS~~La~~~gi~~~qVRKDlS 50 (50)
T PF06971_consen 25 GVERVSSQELAEALGITPAQVRKDLS 50 (50)
T ss_dssp T-SEE-HHHHHHHHTS-HHHHHHHHH
T ss_pred CCeeECHHHHHHHHCCCHHHhcccCC
Confidence 36899999999999999999877654
No 175
>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=44.53 E-value=55 Score=24.61 Aligned_cols=46 Identities=20% Similarity=0.286 Sum_probs=37.8
Q ss_pred hhceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCCCceEEec
Q psy4458 214 YYTRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAGIINFA 261 (303)
Q Consensus 214 ~Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~giV~f~ 261 (303)
.-..+|-+.||+.+|++.+-|-+.|.++...|-|. .++..|.+..+
T Consensus 44 ~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~GlI~--r~~~~~~~~~n 89 (95)
T TIGR01610 44 KQDRVTATVIAELTGLSRTHVSDAIKSLARRRIIF--RQGMMGIVGVN 89 (95)
T ss_pred cCCccCHHHHHHHHCcCHHHHHHHHHHHHHCCCee--eecCCceeecC
Confidence 46788999999999999999999999999999986 23445666555
No 176
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=44.47 E-value=50 Score=29.57 Aligned_cols=40 Identities=10% Similarity=0.150 Sum_probs=34.2
Q ss_pred HHHHhhhceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceE
Q psy4458 209 RVMAKYYTRITLQRMCDLLGLPIEETEEFLSSMVVSKTIT 248 (303)
Q Consensus 209 ~~isk~Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~ 248 (303)
+.+.+-...++.+.||+.||+|+.-+.+.|..|-..|.+.
T Consensus 11 l~~l~~~~~~~~~ela~~l~vS~~TirRdL~~Le~~g~i~ 50 (251)
T PRK13509 11 LELLAQLGFVTVEKVIERLGISPATARRDINKLDESGKLK 50 (251)
T ss_pred HHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 3334457899999999999999999999999998888774
No 177
>PHA02943 hypothetical protein; Provisional
Probab=44.34 E-value=1.7e+02 Score=24.48 Aligned_cols=86 Identities=15% Similarity=0.105 Sum_probs=51.2
Q ss_pred hceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCCCceEEeccCCChhHHHHHHHHHHHHHHHHH-------HHH
Q psy4458 215 YTRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAGIINFARNKDPGEILNEWSASLNELMKLV-------NNT 287 (303)
Q Consensus 215 Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~giV~f~~~~~~~~~l~~w~~~i~~l~~~v-------~~~ 287 (303)
.-.-|.++||+.+|+|-.+++-.|--+=.+|.+.- +-+..-.+-+-.++...+.+.+.-..+-.++..- ...
T Consensus 22 ~G~~TtseIAkaLGlS~~qa~~~LyvLErEG~Vkr-V~~G~~tyw~l~~day~~~v~~~~Relwrlv~s~~~kfi~p~~l 100 (165)
T PHA02943 22 DGCKTTSRIANKLGVSHSMARNALYQLAKEGMVLK-VEIGRAAIWCLDEDAYTNLVFEIKRELWRLVCNSRLKFITPSRL 100 (165)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHHcCceEE-EeecceEEEEEChHHHHHHHHHHHHHHHHHHHhccccccChHHH
Confidence 55678999999999999999999999999998865 2233333333333222223333332222222111 123
Q ss_pred HhhhhHHHHhchhh
Q psy4458 288 THLINKEQMIHQRV 301 (303)
Q Consensus 288 ~~lI~ke~~~~~~~ 301 (303)
-++|.|+.-.|++.
T Consensus 101 ~~li~kd~~a~~~~ 114 (165)
T PHA02943 101 LRLIAKDTEAHNIF 114 (165)
T ss_pred HHHHHhCHHHHHHH
Confidence 56777777666553
No 178
>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=44.00 E-value=2.7e+02 Score=26.51 Aligned_cols=51 Identities=18% Similarity=0.197 Sum_probs=25.9
Q ss_pred ccCCHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhh
Q psy4458 4 DEGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINT 60 (303)
Q Consensus 4 ~~~~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~ 60 (303)
.+|||..|-+.+....=- +. .-.-.++-.++.....||+.+|..++.++..
T Consensus 96 ~~g~~~~A~~~l~~~~~~-----~~-~~~~~~llaA~aa~~~g~~~~A~~~l~~a~~ 146 (409)
T TIGR00540 96 AEGDYAKAEKLIAKNADH-----AA-EPVLNLIKAAEAAQQRGDEARANQHLEEAAE 146 (409)
T ss_pred hCCCHHHHHHHHHHHhhc-----CC-CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 356666666666443210 00 1233344555555666666666666655543
No 179
>PF13428 TPR_14: Tetratricopeptide repeat
Probab=43.56 E-value=54 Score=20.44 Aligned_cols=31 Identities=6% Similarity=-0.179 Sum_probs=26.6
Q ss_pred HHHHHHHHHHHhhcchhHHHHHHHHhhhhcc
Q psy4458 33 TLILEQMRLCLAKKDYIRTQIISKKINTKFF 63 (303)
Q Consensus 33 ~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~ 63 (303)
+..+..++.+...|++.+|....+++-....
T Consensus 2 ~~~~~la~~~~~~G~~~~A~~~~~~~l~~~P 32 (44)
T PF13428_consen 2 AAWLALARAYRRLGQPDEAERLLRRALALDP 32 (44)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHHHHCc
Confidence 3467789999999999999999999987663
No 180
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=43.40 E-value=34 Score=27.97 Aligned_cols=38 Identities=11% Similarity=0.106 Sum_probs=29.7
Q ss_pred hce--eeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCCCc
Q psy4458 215 YTR--ITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAG 256 (303)
Q Consensus 215 Y~~--Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~g 256 (303)
+.. .|+..+++.+|||++. |-++|-+|||.-.-+..-|
T Consensus 42 ~p~~~ati~eV~e~tgVs~~~----I~~~IreGRL~~~~~~nl~ 81 (137)
T TIGR03826 42 HENRQATVSEIVEETGVSEKL----ILKFIREGRLQLKHFPNLG 81 (137)
T ss_pred CCCCCCCHHHHHHHHCcCHHH----HHHHHHcCCeeccCCCCCc
Confidence 445 8999999999999876 6778999999765544433
No 181
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=43.20 E-value=63 Score=22.48 Aligned_cols=61 Identities=18% Similarity=0.300 Sum_probs=37.7
Q ss_pred eeeHHHHHHHhCC--CHHHHHHHHHhhhhcCceEEEecCCCceEEeccCCChhHHHHHHHHHHHHHHHHHHHHHh
Q psy4458 217 RITLQRMCDLLGL--PIEETEEFLSSMVVSKTITAKIDRPAGIINFARNKDPGEILNEWSASLNELMKLVNNTTH 289 (303)
Q Consensus 217 ~Itl~~la~ll~l--s~~~vE~~l~~mI~~~~l~akIDq~~giV~f~~~~~~~~~l~~w~~~i~~l~~~v~~~~~ 289 (303)
.++.+++.+++|+ +.+++.+.|.+|= +....+..++.+.+..|. |-..|..-++.++.+.+
T Consensus 5 ~~~~~~i~~llG~~i~~~ei~~~L~~lg----~~~~~~~~~~~~~v~~P~--------~R~Di~~~~DliEei~r 67 (71)
T smart00874 5 TLRRERINRLLGLDLSAEEIEEILKRLG----FEVEVSGDDDTLEVTVPS--------YRFDILIEADLIEEVAR 67 (71)
T ss_pred EecHHHHHHHHCCCCCHHHHHHHHHHCC----CeEEecCCCCeEEEECCC--------CccccCcccHHHHHHHH
Confidence 5678899999996 5667777777662 333333335667777664 34445555556655554
No 182
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=43.20 E-value=62 Score=20.61 Aligned_cols=29 Identities=17% Similarity=0.332 Sum_probs=24.6
Q ss_pred hhceeeHHHHHHHhCCCHHHHHHHHHhhh
Q psy4458 214 YYTRITLQRMCDLLGLPIEETEEFLSSMV 242 (303)
Q Consensus 214 ~Y~~Itl~~la~ll~ls~~~vE~~l~~mI 242 (303)
++...+...+|+.+|+|+.-+...+....
T Consensus 15 ~~~g~s~~eia~~l~is~~tv~~~~~~~~ 43 (58)
T smart00421 15 LAEGLTNKEIAERLGISEKTVKTHLSNIM 43 (58)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 35667999999999999999998887663
No 183
>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=42.95 E-value=1.6e+02 Score=25.20 Aligned_cols=71 Identities=8% Similarity=0.057 Sum_probs=54.2
Q ss_pred HHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHcCC
Q psy4458 29 KEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIELDQHEGSYLATCKHYRAILTTP 105 (303)
Q Consensus 29 ~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~~~~~~~~f~eaa~~y~e~~~t~ 105 (303)
....+..+..++.++..|+|..|.....++-.... ++ .+.....| ..+..+...++|.+|...|..++...
T Consensus 30 ~~~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~p--~~--~~~~~a~~--~la~~~~~~~~~~~A~~~~~~~l~~~ 100 (235)
T TIGR03302 30 EWPAEELYEEAKEALDSGDYTEAIKYFEALESRYP--FS--PYAEQAQL--DLAYAYYKSGDYAEAIAAADRFIRLH 100 (235)
T ss_pred cCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC--Cc--hhHHHHHH--HHHHHHHhcCCHHHHHHHHHHHHHHC
Confidence 35677889999999999999999999998866552 22 22222333 36888889999999999999997543
No 184
>PRK10870 transcriptional repressor MprA; Provisional
Probab=42.93 E-value=1.2e+02 Score=25.42 Aligned_cols=43 Identities=9% Similarity=0.012 Sum_probs=38.6
Q ss_pred ceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCCCceE
Q psy4458 216 TRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAGII 258 (303)
Q Consensus 216 ~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~giV 258 (303)
..++...||+.+|++..-+=..+.+|+..|-+.-.-|..++-+
T Consensus 70 ~~it~~eLa~~l~l~~~tvsr~v~rLe~kGlV~R~~~~~DrR~ 112 (176)
T PRK10870 70 HSIQPSELSCALGSSRTNATRIADELEKRGWIERRESDNDRRC 112 (176)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCCCCCe
Confidence 3589999999999999999999999999999988888877654
No 185
>PRK02603 photosystem I assembly protein Ycf3; Provisional
Probab=42.84 E-value=1.9e+02 Score=23.73 Aligned_cols=72 Identities=11% Similarity=-0.033 Sum_probs=55.3
Q ss_pred chHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHcC
Q psy4458 27 EKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIELDQHEGSYLATCKHYRAILTT 104 (303)
Q Consensus 27 ~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~~~~~~~~f~eaa~~y~e~~~t 104 (303)
+.......+...+.++...||+..|..+.+++-....+ . .+ ....+..++..+...++|.+|...|..++..
T Consensus 30 ~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~--~--~~--~~~~~~~la~~~~~~g~~~~A~~~~~~al~~ 101 (172)
T PRK02603 30 KKAKEAFVYYRDGMSAQADGEYAEALENYEEALKLEED--P--ND--RSYILYNMGIIYASNGEHDKALEYYHQALEL 101 (172)
T ss_pred cHhhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhc--c--ch--HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence 34466778899999999999999999999988654321 1 11 1345566888889999999999999999764
No 186
>KOG1840|consensus
Probab=42.84 E-value=1.8e+02 Score=29.14 Aligned_cols=97 Identities=13% Similarity=0.118 Sum_probs=69.0
Q ss_pred ccCCHHHHHHHHhcc---ccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHH
Q psy4458 4 DEGDVTEAANIIQEL---QVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRL 80 (303)
Q Consensus 4 ~~~~~~~Aa~~L~~i---~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~ 80 (303)
..|++++|+.++++. ..+++|.+... -...+...+-+|...|+|..|+.+..++-...-...+.+..+..-.+- .
T Consensus 253 ~~~k~~eAv~ly~~AL~i~e~~~G~~h~~-va~~l~nLa~ly~~~GKf~EA~~~~e~Al~I~~~~~~~~~~~v~~~l~-~ 330 (508)
T KOG1840|consen 253 SLGKYDEAVNLYEEALTIREEVFGEDHPA-VAATLNNLAVLYYKQGKFAEAEEYCERALEIYEKLLGASHPEVAAQLS-E 330 (508)
T ss_pred HhccHHHHHHHHHHHHHHHHHhcCCCCHH-HHHHHHHHHHHHhccCChHHHHHHHHHHHHHHHHhhccChHHHHHHHH-H
Confidence 468899999999864 56667766554 445567788899999999999999999876553322322344444443 4
Q ss_pred HHHHHHHhhhHHHHHHHHHHHH
Q psy4458 81 MIELDQHEGSYLATCKHYRAIL 102 (303)
Q Consensus 81 ~~~~~~~~~~f~eaa~~y~e~~ 102 (303)
.+..+.+.++|.+|-++|...+
T Consensus 331 ~~~~~~~~~~~Eea~~l~q~al 352 (508)
T KOG1840|consen 331 LAAILQSMNEYEEAKKLLQKAL 352 (508)
T ss_pred HHHHHHHhcchhHHHHHHHHHH
Confidence 5566788999999988888664
No 187
>cd08312 Death_MyD88 Death domain of Myeloid Differentation primary response protein MyD88. Death Domain (DD) of Myeloid Differentiation primary response protein 88 (MyD88). MyD88 is an adaptor protein involved in interleukin-1 receptor (IL-1R)- and Toll-like receptor (TLR)-induced activation of nuclear factor-kappaB (NF-kB) and mitogen activated protein kinase pathways that lead to the induction of proinflammatory cytokines. It is a key component in the signaling pathway of pathogen recognition in the innate immune system. MyD88 contains an N-terminal DD and a C-terminal Toll/IL-1 Receptor (TIR) homology domain that mediates interaction with TLRs and IL-1R. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and
Probab=42.73 E-value=62 Score=23.54 Aligned_cols=47 Identities=15% Similarity=0.462 Sum_probs=31.6
Q ss_pred HHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCCCceEEeccCCChhHHHHHHHHH-----HHHHHHHHHHHHh
Q psy4458 221 QRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAGIINFARNKDPGEILNEWSAS-----LNELMKLVNNTTH 289 (303)
Q Consensus 221 ~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~giV~f~~~~~~~~~l~~w~~~-----i~~l~~~v~~~~~ 289 (303)
..||..+|++..++..+-. .+++....|+.|..+ |..|+..+.++++
T Consensus 20 r~LA~~Lg~~~~~I~~f~~----------------------~~sPt~~lL~~W~~r~~~atv~~L~~~L~~~~R 71 (79)
T cd08312 20 TALAEEMGFEYLEIRNFET----------------------KPSPTEKVLEDWETRPDGATVGNLLELLEKLER 71 (79)
T ss_pred HHHHHHcCCCHHHHHHHcc----------------------CCChHHHHHHHHHhcCCCCcHHHHHHHHHHcCh
Confidence 4578888888777653211 135667899999766 7777777665543
No 188
>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=42.37 E-value=83 Score=21.16 Aligned_cols=28 Identities=7% Similarity=0.165 Sum_probs=24.0
Q ss_pred HHHHHHHHHHHhhhHHHHHHHHHHHHcC
Q psy4458 77 YYRLMIELDQHEGSYLATCKHYRAILTT 104 (303)
Q Consensus 77 y~~~~~~~~~~~~~f~eaa~~y~e~~~t 104 (303)
.+..+|..+...++|.+|-.+|..++..
T Consensus 5 ~~~~~g~~~~~~~~~~~A~~~~~~ai~~ 32 (69)
T PF13414_consen 5 AWYNLGQIYFQQGDYEEAIEYFEKAIEL 32 (69)
T ss_dssp HHHHHHHHHHHTTHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHHHc
Confidence 3456889999999999999999999864
No 189
>PHA02591 hypothetical protein; Provisional
Probab=42.23 E-value=29 Score=25.48 Aligned_cols=25 Identities=24% Similarity=0.615 Sum_probs=20.7
Q ss_pred ceeeHHHHHHHhCCCHHHHHHHHHh
Q psy4458 216 TRITLQRMCDLLGLPIEETEEFLSS 240 (303)
Q Consensus 216 ~~Itl~~la~ll~ls~~~vE~~l~~ 240 (303)
.-.|.+++|++||+|.+.|-+.+.+
T Consensus 58 qGlSqeqIA~~LGVsqetVrKYL~~ 82 (83)
T PHA02591 58 KGFTVEKIASLLGVSVRKVRRYLES 82 (83)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHhc
Confidence 3458899999999999998887754
No 190
>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=41.63 E-value=1.3e+02 Score=30.09 Aligned_cols=64 Identities=9% Similarity=-0.029 Sum_probs=51.3
Q ss_pred HHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHc
Q psy4458 31 KVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIELDQHEGSYLATCKHYRAILT 103 (303)
Q Consensus 31 k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~~~~~~~~f~eaa~~y~e~~~ 103 (303)
.+=.+.-++..+-..||+..|-.+++++-.... .-+.+|...|+++.|.|++.+|+..+.++-.
T Consensus 193 ~lw~~~~lAqhyd~~g~~~~Al~~Id~aI~htP---------t~~ely~~KarilKh~G~~~~Aa~~~~~Ar~ 256 (517)
T PF12569_consen 193 LLWTLYFLAQHYDYLGDYEKALEYIDKAIEHTP---------TLVELYMTKARILKHAGDLKEAAEAMDEARE 256 (517)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHHHHHhcCC---------CcHHHHHHHHHHHHHCCCHHHHHHHHHHHHh
Confidence 444556677888889999999999998865431 1267899999999999999999999888843
No 191
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=41.58 E-value=1e+02 Score=24.78 Aligned_cols=61 Identities=16% Similarity=0.331 Sum_probs=47.9
Q ss_pred HHhhhceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCCCce-EEeccCCChhHHHHHHHHHHHHH
Q psy4458 211 MAKYYTRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAGI-INFARNKDPGEILNEWSASLNEL 280 (303)
Q Consensus 211 isk~Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~gi-V~f~~~~~~~~~l~~w~~~i~~l 280 (303)
+.+-=-++|+..|...+|+|-.-+...+.+++..|.|.- .|. =.|.. ..+..+|.+.-.++
T Consensus 20 lVRe~GRiTi~ql~~~TGasR~Tvk~~lreLVa~G~l~~-----~G~~GvF~s----eqA~~dw~~~~~~~ 81 (127)
T PF06163_consen 20 LVREHGRITIKQLVAKTGASRNTVKRYLRELVARGDLYR-----HGRSGVFPS----EQARKDWDKARKKL 81 (127)
T ss_pred HHHHcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCCeEe-----CCCcccccc----HHHHHHHHHhHHhh
Confidence 445578999999999999999999999999999998853 122 23432 25788898887766
No 192
>PF10743 Phage_Cox: Regulatory phage protein cox; InterPro: IPR019679 Phage Cox proteins are expressed by Enterobacteria phages. The Cox protein is a 79-residue basic protein with a predicted strong helix-turn-helix DNA-binding motif. It inhibits integrative recombination and it activates site-specific excision of the HP1 genome from the Haemophilus influenzae chromosome, Hp1. Cox appears to function as a tetramer. Cox binding sites consist of two direct repeats of the consensus motif 5'-GGTMAWWWWA, one Cox tetramer binding to each motif. Cox binding interferes with the interaction of HP1 integrase with one of its binding sites, IBS5. This competition is central to directional control. Both Cox binding sites are needed for full inhibition of integration and for activating excision, because it plays a positive role in assembling the nucleoprotein complexes that produce excisive recombination, by inducing the formation of a critical conformation in those complexes [].
Probab=41.15 E-value=36 Score=25.50 Aligned_cols=61 Identities=15% Similarity=0.349 Sum_probs=43.1
Q ss_pred HHHHhhhceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCCCceEEeccCCChhH------HHHHHHHHHHHHH
Q psy4458 209 RVMAKYYTRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAGIINFARNKDPGE------ILNEWSASLNELM 281 (303)
Q Consensus 209 ~~isk~Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~giV~f~~~~~~~~------~l~~w~~~i~~l~ 281 (303)
.++..|=.-|+.+..|.++|-|+.. +..||..|+|-+ |++.+|.+++. .+..|++-+..+.
T Consensus 4 ~~~~~p~d~v~~~~FA~~IGKt~sA----Vr~Mi~~gKLP~--------i~~~dP~~p~~rgE~wI~~~ewn~~~~~a~ 70 (87)
T PF10743_consen 4 QVSEYPSDAVTYEKFAEYIGKTPSA----VRKMIKAGKLPV--------IEMRDPEKPNGRGEWWIYIPEWNRGVREAY 70 (87)
T ss_pred hHHhhhccccCHHHHHHHHCCCHHH----HHHHHHcCCCCe--------EeccCCCCCCCceeEEEeHHHHHHHHHHHH
Confidence 4444557789999999999999765 788999999974 56666544321 2567776665543
No 193
>PRK10747 putative protoheme IX biogenesis protein; Provisional
Probab=40.65 E-value=3.3e+02 Score=25.91 Aligned_cols=88 Identities=11% Similarity=0.156 Sum_probs=61.6
Q ss_pred ccCCHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHH
Q psy4458 4 DEGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIE 83 (303)
Q Consensus 4 ~~~~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~ 83 (303)
..|++++|...|....- .+++..+-..+..+++++..||+..|....+++.....+ . .+ .....+.
T Consensus 130 ~~g~~~~A~~~l~~A~~-----~~~~~~~~~~l~~a~l~l~~g~~~~Al~~l~~~~~~~P~--~--~~-----al~ll~~ 195 (398)
T PRK10747 130 QRGDEARANQHLERAAE-----LADNDQLPVEITRVRIQLARNENHAARHGVDKLLEVAPR--H--PE-----VLRLAEQ 195 (398)
T ss_pred HCCCHHHHHHHHHHHHh-----cCCcchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCC--C--HH-----HHHHHHH
Confidence 46889999998887742 133344445567799999999999999999998765522 1 22 2233556
Q ss_pred HHHHhhhHHHHHHHHHHHHcCC
Q psy4458 84 LDQHEGSYLATCKHYRAILTTP 105 (303)
Q Consensus 84 ~~~~~~~f~eaa~~y~e~~~t~ 105 (303)
.+...+++-+|-..+-.+-...
T Consensus 196 ~~~~~gdw~~a~~~l~~l~k~~ 217 (398)
T PRK10747 196 AYIRTGAWSSLLDILPSMAKAH 217 (398)
T ss_pred HHHHHHhHHHHHHHHHHHHHcC
Confidence 6677799988887777775443
No 194
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=40.48 E-value=72 Score=20.56 Aligned_cols=27 Identities=7% Similarity=0.177 Sum_probs=22.4
Q ss_pred hceeeHHHHHHHhCCCHHHHHHHHHhh
Q psy4458 215 YTRITLQRMCDLLGLPIEETEEFLSSM 241 (303)
Q Consensus 215 Y~~Itl~~la~ll~ls~~~vE~~l~~m 241 (303)
-...|+..+|+.+|+|..-|...+-+.
T Consensus 25 ~~~~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 25 RESRSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred hhcCCHHHHHHHHCCCHHHHHHHHHhh
Confidence 444799999999999999998877553
No 195
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=40.37 E-value=72 Score=20.42 Aligned_cols=28 Identities=18% Similarity=0.322 Sum_probs=24.1
Q ss_pred hhceeeHHHHHHHhCCCHHHHHHHHHhh
Q psy4458 214 YYTRITLQRMCDLLGLPIEETEEFLSSM 241 (303)
Q Consensus 214 ~Y~~Itl~~la~ll~ls~~~vE~~l~~m 241 (303)
++...+.+.+|+.+|+|+.-+...+..+
T Consensus 12 ~~~~~s~~eia~~l~~s~~tv~~~~~~~ 39 (57)
T cd06170 12 LAEGKTNKEIADILGISEKTVKTHLRNI 39 (57)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 3567899999999999999999887765
No 196
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=40.15 E-value=34 Score=25.65 Aligned_cols=25 Identities=12% Similarity=0.161 Sum_probs=22.8
Q ss_pred hceeeHHHHHHHhCCCHHHHHHHHH
Q psy4458 215 YTRITLQRMCDLLGLPIEETEEFLS 239 (303)
Q Consensus 215 Y~~Itl~~la~ll~ls~~~vE~~l~ 239 (303)
-+++|.+.+|..||+|+..+|+.+.
T Consensus 21 l~~LS~~~iA~~Ln~t~~~lekil~ 45 (97)
T COG4367 21 LCPLSDEEIATALNWTEVKLEKILQ 45 (97)
T ss_pred hccccHHHHHHHhCCCHHHHHHHHH
Confidence 5788999999999999999999874
No 197
>PF04348 LppC: LppC putative lipoprotein; InterPro: IPR007443 This entry includes several bacterial outer membrane antigens, whose molecular function is unknown.; PDB: 3CKM_A.
Probab=40.13 E-value=9.5 Score=38.36 Aligned_cols=85 Identities=18% Similarity=0.241 Sum_probs=0.0
Q ss_pred CCHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHHHH
Q psy4458 6 GDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIELD 85 (303)
Q Consensus 6 ~~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~~~ 85 (303)
|+..+||+.+...-= .-+..++.++.|.-++.++..||+..|..+++++.+.-+. ...+.+|..+.++..
T Consensus 2 ~~~~~aA~~yL~~A~----~a~~~~~~~~~L~Aa~a~l~~g~~~~A~~ll~~l~~~~L~------~~q~~~~~Ll~A~la 71 (536)
T PF04348_consen 2 GDPRQAAEQYLQQAQ----QASGEQRAQLLLLAARALLQEGDWAQAQALLNQLDPQQLS------PSQQARYQLLRARLA 71 (536)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred CchhHHHHHHHHHHH----hcCcHhHHHHHHHHHHHHHhCCCHHHHHHHHHhcccccCC------hHHHHHHHHHHHHHH
Confidence 444555555443331 2234789999999999999999999999999999854432 245678888999999
Q ss_pred HHhhhHHHHHHHHHH
Q psy4458 86 QHEGSYLATCKHYRA 100 (303)
Q Consensus 86 ~~~~~f~eaa~~y~e 100 (303)
...+++.+|-..+-.
T Consensus 72 l~~~~~~~Al~~L~~ 86 (536)
T PF04348_consen 72 LAQGDPEQALSLLNA 86 (536)
T ss_dssp ---------------
T ss_pred HhcCCHHHHHHHhcc
Confidence 999999998877653
No 198
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=39.92 E-value=57 Score=20.81 Aligned_cols=23 Identities=13% Similarity=0.264 Sum_probs=19.8
Q ss_pred HhhhceeeHHHHHHHhCCCHHHH
Q psy4458 212 AKYYTRITLQRMCDLLGLPIEET 234 (303)
Q Consensus 212 sk~Y~~Itl~~la~ll~ls~~~v 234 (303)
.+.|..+|+..+|+..|+|..-+
T Consensus 11 ~~G~~~~s~~~Ia~~~gvs~~~~ 33 (47)
T PF00440_consen 11 EKGYEAVSIRDIARRAGVSKGSF 33 (47)
T ss_dssp HHHTTTSSHHHHHHHHTSCHHHH
T ss_pred HhCHHhCCHHHHHHHHccchhhH
Confidence 35699999999999999997654
No 199
>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=39.85 E-value=56 Score=23.20 Aligned_cols=33 Identities=6% Similarity=0.181 Sum_probs=26.1
Q ss_pred hceeeHHHHHH-HhCCCHHHHHHHHHhhhhcCce
Q psy4458 215 YTRITLQRMCD-LLGLPIEETEEFLSSMVVSKTI 247 (303)
Q Consensus 215 Y~~Itl~~la~-ll~ls~~~vE~~l~~mI~~~~l 247 (303)
=+...|..++. ..+..+-++-+.+..||.+|++
T Consensus 17 KskfYfkD~~k~~pd~k~R~vKKi~~~LV~Eg~l 50 (67)
T PF08679_consen 17 KSKFYFKDFYKAFPDAKPREVKKIVNELVNEGKL 50 (67)
T ss_dssp SS-EEHHHHHHH-TTS-HHHHHHHHHHHHHTTSE
T ss_pred CCceeHHHHHHHCCCcCHHHHHHHHHHHHhhCeE
Confidence 45566888888 5688999999999999999987
No 200
>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=39.50 E-value=2.1e+02 Score=23.36 Aligned_cols=67 Identities=13% Similarity=0.007 Sum_probs=52.7
Q ss_pred HHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHcC
Q psy4458 29 KEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIELDQHEGSYLATCKHYRAILTT 104 (303)
Q Consensus 29 ~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~~~~~~~~f~eaa~~y~e~~~t 104 (303)
....+.+...++.++..+++..|.....++-... .+ + ...+...+..+...++|.+|-..|..+...
T Consensus 28 ~~~~~~~~~la~~~~~~~~~~~A~~~~~~~l~~~---p~--~----~~~~~~la~~~~~~~~~~~A~~~~~~al~~ 94 (234)
T TIGR02521 28 NKAAKIRVQLALGYLEQGDLEVAKENLDKALEHD---PD--D----YLAYLALALYYQQLGELEKAEDSFRRALTL 94 (234)
T ss_pred CcHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC---cc--c----HHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence 3557788899999999999999999998886432 11 1 234455788899999999999999998765
No 201
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=39.50 E-value=1.5e+02 Score=24.98 Aligned_cols=31 Identities=16% Similarity=0.128 Sum_probs=28.9
Q ss_pred eHHHHHHHh--CCCHHHHHHHHHhhhhcCceEE
Q psy4458 219 TLQRMCDLL--GLPIEETEEFLSSMVVSKTITA 249 (303)
Q Consensus 219 tl~~la~ll--~ls~~~vE~~l~~mI~~~~l~a 249 (303)
....||+.+ ++|++++++-|.-|..-|-|.=
T Consensus 41 d~~~iak~l~p~is~~ev~~sL~~L~~~gli~k 73 (171)
T PF14394_consen 41 DPEWIAKRLRPKISAEEVRDSLEFLEKLGLIKK 73 (171)
T ss_pred CHHHHHHHhcCCCCHHHHHHHHHHHHHCCCeEE
Confidence 889999999 9999999999999999998843
No 202
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=39.44 E-value=84 Score=27.72 Aligned_cols=48 Identities=15% Similarity=0.186 Sum_probs=41.7
Q ss_pred hceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCCCceEEecc
Q psy4458 215 YTRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAGIINFAR 262 (303)
Q Consensus 215 Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~giV~f~~ 262 (303)
...||.+.||+.+|+|..-+=+.|.+|...|-|.-..|..+..|....
T Consensus 19 ~~~IS~~eLA~~L~iS~~Tvsr~Lk~LEe~GlI~R~~~~r~~~v~LTe 66 (217)
T PRK14165 19 TVKISSSEFANHTGTSSKTAARILKQLEDEGYITRTIVPRGQLITITE 66 (217)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEEcCCceEEEECH
Confidence 447899999999999999999999999999999998887665566553
No 203
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=39.30 E-value=34 Score=24.30 Aligned_cols=26 Identities=27% Similarity=0.451 Sum_probs=20.5
Q ss_pred ceeeHHHHHHHhCCCHHHHHHHHHhh
Q psy4458 216 TRITLQRMCDLLGLPIEETEEFLSSM 241 (303)
Q Consensus 216 ~~Itl~~la~ll~ls~~~vE~~l~~m 241 (303)
..-|.+.||+.+|+|++++...+...
T Consensus 19 r~Pt~eEiA~~lgis~~~v~~~l~~~ 44 (78)
T PF04539_consen 19 REPTDEEIAEELGISVEEVRELLQAS 44 (78)
T ss_dssp S--BHHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCCCHHHHHHHHcccHHHHHHHHHhC
Confidence 56799999999999999999888753
No 204
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=38.74 E-value=2e+02 Score=22.75 Aligned_cols=69 Identities=10% Similarity=0.199 Sum_probs=47.4
Q ss_pred eeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCCCceEEeccCCChhHHH-----HHHHHHHHHHHHHHHHH
Q psy4458 217 RITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAGIINFARNKDPGEIL-----NEWSASLNELMKLVNNT 287 (303)
Q Consensus 217 ~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~giV~f~~~~~~~~~l-----~~w~~~i~~l~~~v~~~ 287 (303)
..+...|++.+|+|+.-+-..+..+...|-+..+-+-.. +.+.-.....+.+ ..|..+...+-..++++
T Consensus 30 ~~~v~ela~~l~lsqstvS~HL~~L~~AGLV~~~r~Gr~--~~Y~l~~~~~~~~~~~~~~~w~~~~~~l~~~l~~l 103 (117)
T PRK10141 30 ELCVCDLCTALDQSQPKISRHLALLRESGLLLDRKQGKW--VHYRLSPHIPAWAAKIIEQAWLCEQEDVQAIVRNL 103 (117)
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEEEcCE--EEEEECchHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 578899999999999999999999999999988766433 3332221111222 24666666666666554
No 205
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=38.41 E-value=2.5e+02 Score=23.98 Aligned_cols=45 Identities=4% Similarity=-0.001 Sum_probs=38.6
Q ss_pred hceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCCCceEE
Q psy4458 215 YTRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAGIIN 259 (303)
Q Consensus 215 Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~giV~ 259 (303)
...+|.+.||+.++++..-+=..+.+|...|-|.-..|..++-..
T Consensus 57 ~~~itq~eLa~~l~l~~sTvtr~l~rLE~kGlI~R~~~~~DrR~~ 101 (185)
T PRK13777 57 LKGASISEIAKFGVMHVSTAFNFSKKLEERGYLTFSKKEDDKRNT 101 (185)
T ss_pred CCCcCHHHHHHHHCCCHhhHHHHHHHHHHCCCEEecCCCCCCCee
Confidence 457999999999999999999999999999999877776666543
No 206
>PF10771 DUF2582: Protein of unknown function (DUF2582); InterPro: IPR019707 This entry represents conserved proteins found in bacteria and archaea. The function is not known. ; PDB: 2L02_B 2L01_A.
Probab=38.31 E-value=74 Score=22.44 Aligned_cols=44 Identities=11% Similarity=0.128 Sum_probs=36.6
Q ss_pred hceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCCCceEEe
Q psy4458 215 YTRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAGIINF 260 (303)
Q Consensus 215 Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~giV~f 260 (303)
-...|++.|++..|++..++-.-|.=+..+++|. +++.+|.+.+
T Consensus 20 ~~~~s~~el~k~~~l~~~~~~~AiGWLarE~KI~--~~~~~~~~~v 63 (65)
T PF10771_consen 20 NGEWSVSELKKATGLSDKEVYLAIGWLARENKIE--FEEKNGELYV 63 (65)
T ss_dssp SSSEEHHHHHHHCT-SCHHHHHHHHHHHCTTSEE--EEEETTEEEE
T ss_pred CCCcCHHHHHHHhCcCHHHHHHHHHHHhccCcee--EEeeCCEEEE
Confidence 4679999999999999999999999999999984 5567776654
No 207
>PF03704 BTAD: Bacterial transcriptional activator domain; InterPro: IPR005158 Found in the DNRI/REDD/AFSR family of regulators, this region of AFSR (P25941 from SWISSPROT) along with the C-terminal region is capable of independently directing actinorhodin production. It is important for the formation of secondary metabolites.; PDB: 2FF4_B 2FEZ_A.
Probab=38.25 E-value=2e+02 Score=22.69 Aligned_cols=62 Identities=16% Similarity=0.148 Sum_probs=38.6
Q ss_pred HHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHH
Q psy4458 31 KVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIELDQHEGSYLATCKHYRAI 101 (303)
Q Consensus 31 k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~~~~~~~~f~eaa~~y~e~ 101 (303)
-++.....+..++..|++..|.....++-..-.-++ ..+....+.+...+++.+|-+.|..+
T Consensus 61 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~l~~dP~~E---------~~~~~lm~~~~~~g~~~~A~~~Y~~~ 122 (146)
T PF03704_consen 61 YLDALERLAEALLEAGDYEEALRLLQRALALDPYDE---------EAYRLLMRALAAQGRRAEALRVYERY 122 (146)
T ss_dssp HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-H---------HHHHHHHHHHHHTT-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhccCHHHHHHHHHHHHhcCCCCH---------HHHHHHHHHHHHCcCHHHHHHHHHHH
Confidence 345567777788889999999999888876542222 23334455556666666666666555
No 208
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=38.03 E-value=2.8e+02 Score=24.26 Aligned_cols=81 Identities=16% Similarity=0.176 Sum_probs=63.0
Q ss_pred CchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccC----C-C-CcchHHHHHHHHHHHHHHHHHhhhHHHHHHHHH
Q psy4458 26 MEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFD----D-E-KDDVQELKLKYYRLMIELDQHEGSYLATCKHYR 99 (303)
Q Consensus 26 ~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~----~-~-~~~~~e~k~~y~~~~~~~~~~~~~f~eaa~~y~ 99 (303)
-....+.-++|+++.||=..+|....+..+++|-..+.. + . .....+.++.|. .|..+---++|.+|.+.|-
T Consensus 112 ~~~s~~A~l~LrlAWlyR~~~~~~~E~~fl~~Al~~y~~a~~~e~~~~~~~~~~~l~YL--igeL~rrlg~~~eA~~~fs 189 (214)
T PF09986_consen 112 EKPSKKAGLCLRLAWLYRDLGDEENEKRFLRKALEFYEEAYENEDFPIEGMDEATLLYL--IGELNRRLGNYDEAKRWFS 189 (214)
T ss_pred CCHHHHHHHHHHHHHHhhccCCHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHH--HHHHHHHhCCHHHHHHHHH
Confidence 455689999999999999999988888888888644321 1 1 111456666664 8899999999999999999
Q ss_pred HHHcCCCCC
Q psy4458 100 AILTTPCIQ 108 (303)
Q Consensus 100 e~~~t~~~~ 108 (303)
.++..+...
T Consensus 190 ~vi~~~~~s 198 (214)
T PF09986_consen 190 RVIGSKKAS 198 (214)
T ss_pred HHHcCCCCC
Confidence 999887663
No 209
>COG3118 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]
Probab=37.88 E-value=3.4e+02 Score=25.26 Aligned_cols=49 Identities=22% Similarity=0.151 Sum_probs=35.3
Q ss_pred cCCHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhh
Q psy4458 5 EGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKIN 59 (303)
Q Consensus 5 ~~~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~ 59 (303)
.|+..+|+.++...--.. .++.+..+-.++.++..||...|+.++..+-
T Consensus 147 ~e~~~~a~~~~~~al~~~------~~~~~~~~~la~~~l~~g~~e~A~~iL~~lP 195 (304)
T COG3118 147 AEDFGEAAPLLKQALQAA------PENSEAKLLLAECLLAAGDVEAAQAILAALP 195 (304)
T ss_pred ccchhhHHHHHHHHHHhC------cccchHHHHHHHHHHHcCChHHHHHHHHhCc
Confidence 567777777766653322 1336778889999999999998888877654
No 210
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=37.73 E-value=84 Score=28.20 Aligned_cols=37 Identities=8% Similarity=0.178 Sum_probs=33.1
Q ss_pred HHhhhceeeHHHHHHHhCCCHHHHHHHHHhhhhcCce
Q psy4458 211 MAKYYTRITLQRMCDLLGLPIEETEEFLSSMVVSKTI 247 (303)
Q Consensus 211 isk~Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l 247 (303)
+.+-...+++..||+.|++|++-+-+-|..+-.+|.+
T Consensus 13 ~l~~~~~~~~~ela~~l~vS~~TiRRdL~~Le~~g~l 49 (252)
T PRK10906 13 LVKQQGYVSTEELVEHFSVSPQTIRRDLNDLAEQNKI 49 (252)
T ss_pred HHHHcCCEeHHHHHHHhCCCHHHHHHHHHHHHHCCCE
Confidence 3345788999999999999999999999999999977
No 211
>PF01984 dsDNA_bind: Double-stranded DNA-binding domain; InterPro: IPR002836 This protein family is found in archaea and eukaryota. The human TFAR19 (TF-1 cell apoptosis-related protein 19) encodes a protein which shares significant homology to the corresponding proteins of species ranging from yeast to mice. TFAR19 exhibits a ubiquitous expression pattern and its expression is up-regulated in the tumour cells undergoing apoptosis. TFAR19 may play a general role in the apoptotic process []. Also included in this family is a DNA-binding protein from the archaea, Methanobacterium thermoautotrophicum.; GO: 0003677 DNA binding; PDB: 1EIJ_A 2K6B_A 2CRU_A 1YYB_A 2JXN_A 2FH0_A.
Probab=37.68 E-value=19 Score=28.10 Aligned_cols=22 Identities=27% Similarity=0.351 Sum_probs=18.2
Q ss_pred HHHHHHHHHhhhhcCceEEEec
Q psy4458 231 IEETEEFLSSMVVSKTITAKID 252 (303)
Q Consensus 231 ~~~vE~~l~~mI~~~~l~akID 252 (303)
...||..|..|...|+|.++||
T Consensus 61 A~~VE~~Liqlaq~G~l~~kI~ 82 (107)
T PF01984_consen 61 ARQVENQLIQLAQSGQLRGKID 82 (107)
T ss_dssp HHHHHHHHHHHHHCTSSSS-B-
T ss_pred HHHHHHHHHHHHHcCCCCCCcC
Confidence 3588999999999999999886
No 212
>PRK11050 manganese transport regulator MntR; Provisional
Probab=37.10 E-value=1.9e+02 Score=23.65 Aligned_cols=35 Identities=9% Similarity=0.158 Sum_probs=31.7
Q ss_pred ceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEE
Q psy4458 216 TRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAK 250 (303)
Q Consensus 216 ~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~ak 250 (303)
..++...||+.++++..-+-..+..|...|.|..+
T Consensus 50 ~~~t~~eLA~~l~is~stVsr~l~~Le~~GlI~r~ 84 (152)
T PRK11050 50 GEARQVDIAARLGVSQPTVAKMLKRLARDGLVEMR 84 (152)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 56899999999999999999999999999977654
No 213
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=36.72 E-value=84 Score=28.21 Aligned_cols=40 Identities=10% Similarity=0.178 Sum_probs=34.3
Q ss_pred HHHHhhhceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceE
Q psy4458 209 RVMAKYYTRITLQRMCDLLGLPIEETEEFLSSMVVSKTIT 248 (303)
Q Consensus 209 ~~isk~Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~ 248 (303)
..+.+--..|+++.||++||+|+.-+-+-|..+=..|.+.
T Consensus 11 l~~l~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~g~l~ 50 (253)
T COG1349 11 LELLKEKGKVSVEELAELFGVSEMTIRRDLNELEEQGLLL 50 (253)
T ss_pred HHHHHHcCcEEHHHHHHHhCCCHHHHHHhHHHHHHCCcEE
Confidence 3334447889999999999999999999999999999774
No 214
>KOG1129|consensus
Probab=36.58 E-value=1.9e+02 Score=27.50 Aligned_cols=84 Identities=12% Similarity=0.063 Sum_probs=62.0
Q ss_pred CCHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHHHH
Q psy4458 6 GDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIELD 85 (303)
Q Consensus 6 ~~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~~~ 85 (303)
|-+.+|.+.|| +++...+-.|.+|-..|.|-.-++..+|-..+...-..+. ++ +.|..-+++++
T Consensus 237 gm~r~Aekqlq-------ssL~q~~~~dTfllLskvY~ridQP~~AL~~~~~gld~fP--~~-------VT~l~g~ARi~ 300 (478)
T KOG1129|consen 237 GMPRRAEKQLQ-------SSLTQFPHPDTFLLLSKVYQRIDQPERALLVIGEGLDSFP--FD-------VTYLLGQARIH 300 (478)
T ss_pred cChhhhHHHHH-------HHhhcCCchhHHHHHHHHHHHhccHHHHHHHHhhhhhcCC--ch-------hhhhhhhHHHH
Confidence 44555666555 3445556678888888888888888888877766555442 11 56667799999
Q ss_pred HHhhhHHHHHHHHHHHHcCC
Q psy4458 86 QHEGSYLATCKHYRAILTTP 105 (303)
Q Consensus 86 ~~~~~f~eaa~~y~e~~~t~ 105 (303)
.+-+++-+|.++|..+....
T Consensus 301 eam~~~~~a~~lYk~vlk~~ 320 (478)
T KOG1129|consen 301 EAMEQQEDALQLYKLVLKLH 320 (478)
T ss_pred HHHHhHHHHHHHHHHHHhcC
Confidence 99999999999999998643
No 215
>KOG2002|consensus
Probab=36.42 E-value=1.5e+02 Score=31.92 Aligned_cols=63 Identities=16% Similarity=0.137 Sum_probs=41.6
Q ss_pred HHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHc
Q psy4458 35 ILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIELDQHEGSYLATCKHYRAILT 103 (303)
Q Consensus 35 ~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~~~~~~~~f~eaa~~y~e~~~ 103 (303)
.-..++-+.+.|||.++..+..-+-.... ..-.+-.=+-.+|+-+.+.+||-.|+++|+++..
T Consensus 273 l~~LAn~fyfK~dy~~v~~la~~ai~~t~------~~~~~aes~Y~~gRs~Ha~Gd~ekA~~yY~~s~k 335 (1018)
T KOG2002|consen 273 LNHLANHFYFKKDYERVWHLAEHAIKNTE------NKSIKAESFYQLGRSYHAQGDFEKAFKYYMESLK 335 (1018)
T ss_pred HHHHHHHHhhcccHHHHHHHHHHHHHhhh------hhHHHHHHHHHHHHHHHhhccHHHHHHHHHHHHc
Confidence 34556677777888877766554433321 1122222223489999999999999999999974
No 216
>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=35.19 E-value=1.5e+02 Score=25.39 Aligned_cols=36 Identities=11% Similarity=0.159 Sum_probs=33.1
Q ss_pred hceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEE
Q psy4458 215 YTRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAK 250 (303)
Q Consensus 215 Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~ak 250 (303)
...+|...||+.+|+++.-|=..+..|...|-|...
T Consensus 13 ~~~~t~~eLA~~lgis~~tV~~~L~~Le~~GlV~r~ 48 (203)
T TIGR02702 13 QGQATAAALAEALAISPQAVRRHLKDLETEGLIEYE 48 (203)
T ss_pred cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEe
Confidence 466999999999999999999999999999999655
No 217
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=34.92 E-value=77 Score=27.31 Aligned_cols=44 Identities=14% Similarity=0.148 Sum_probs=37.0
Q ss_pred HHHhhhceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecC
Q psy4458 210 VMAKYYTRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDR 253 (303)
Q Consensus 210 ~isk~Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq 253 (303)
.+.+-++..|.+.||+.+|+|+.-|+..+..+...|.+...++-
T Consensus 170 ~~~~g~~g~s~~eIa~~l~iS~~Tv~~~~~~~~~~~~~~~~~~~ 213 (225)
T PRK10046 170 LFKEPGVQHTAETVAQALTISRTTARRYLEYCASRHLIIAEIVH 213 (225)
T ss_pred HHHcCCCCcCHHHHHHHhCccHHHHHHHHHHHHhCCeEEEEeec
Confidence 34455556799999999999999999999999999998776653
No 218
>KOG2300|consensus
Probab=34.90 E-value=4.4e+02 Score=26.48 Aligned_cols=74 Identities=11% Similarity=-0.081 Sum_probs=56.3
Q ss_pred HHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHcCCCC
Q psy4458 32 VTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIELDQHEGSYLATCKHYRAILTTPCI 107 (303)
Q Consensus 32 ~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~~~~~~~~f~eaa~~y~e~~~t~~~ 107 (303)
.-..+-.+-.||..+|-......+..+++.....-- .+-++..++...|.+.-.+++|.||=+...|.+.-.+.
T Consensus 404 a~~nlnlAi~YL~~~~~ed~y~~ld~i~p~nt~s~s--sq~l~a~~~~v~glfaf~qn~lnEaK~~l~e~Lkmana 477 (629)
T KOG2300|consen 404 AFCNLNLAISYLRIGDAEDLYKALDLIGPLNTNSLS--SQRLEASILYVYGLFAFKQNDLNEAKRFLRETLKMANA 477 (629)
T ss_pred HHHHHhHHHHHHHhccHHHHHHHHHhcCCCCCCcch--HHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHhhcch
Confidence 334566667788889988888899999876312211 46677888888899999999999999999999865543
No 219
>PF05584 Sulfolobus_pRN: Sulfolobus plasmid regulatory protein; InterPro: IPR008848 This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus.
Probab=34.87 E-value=1.6e+02 Score=21.25 Aligned_cols=40 Identities=18% Similarity=0.247 Sum_probs=34.8
Q ss_pred HHHHHhhhceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEE
Q psy4458 208 IRVMAKYYTRITLQRMCDLLGLPIEETEEFLSSMVVSKTITA 249 (303)
Q Consensus 208 i~~isk~Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~a 249 (303)
+.++++- ..|++.|-+..|++...+-..++.|-..|.|.-
T Consensus 11 L~~ls~~--c~TLeeL~ekTgi~k~~LlV~LsrL~k~GiI~R 50 (72)
T PF05584_consen 11 LIILSKR--CCTLEELEEKTGISKNTLLVYLSRLAKRGIIER 50 (72)
T ss_pred HHHHHhc--cCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeee
Confidence 3445555 999999999999999999999999999998854
No 220
>KOG3060|consensus
Probab=34.74 E-value=3.6e+02 Score=24.69 Aligned_cols=64 Identities=17% Similarity=0.207 Sum_probs=46.8
Q ss_pred HHHHHHHHHH-HHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHcC
Q psy4458 32 VTLILEQMRL-CLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIELDQHEGSYLATCKHYRAILTT 104 (303)
Q Consensus 32 ~~~~L~~~rL-~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~~~~~~~~f~eaa~~y~e~~~t 104 (303)
.=++++|+-+ .+..+..+.|+..++..+..++.. .|-..+.+..+-+.+.|.+|-.+|..+++.
T Consensus 51 ~w~l~EqV~IAAld~~~~~lAq~C~~~L~~~fp~S---------~RV~~lkam~lEa~~~~~~A~e~y~~lL~d 115 (289)
T KOG3060|consen 51 IWTLYEQVFIAALDTGRDDLAQKCINQLRDRFPGS---------KRVGKLKAMLLEATGNYKEAIEYYESLLED 115 (289)
T ss_pred HHHHHHHHHHHHHHhcchHHHHHHHHHHHHhCCCC---------hhHHHHHHHHHHHhhchhhHHHHHHHHhcc
Confidence 3455666655 568899999999999999888432 122234566677899999999999988753
No 221
>PF07064 RIC1: RIC1; InterPro: IPR009771 This entry represents RIC1 (Ribosomal control protein1) and has been identified in yeast as a Golgi protein involved in retrograde transport to the cis-Golgi network. It forms a heterodimer with Rgp1 and functions as a guanyl-nucleotide exchange factor [] which activates YPT6 by exchanging bound GDP for free GTP. RIC1 is thereby required for efficient fusion of endosome-derived vesicles with the Golgi. The RIC1-RGP1 complex participates in the recycling of SNC1, presumably by mediating fusion of endosomal vesicles with the Golgi compartment and may also be indirectly involved in the transcription of both ribosomal protein genes and ribosomal RNA [, , ].
Probab=34.50 E-value=87 Score=28.36 Aligned_cols=58 Identities=17% Similarity=0.238 Sum_probs=45.1
Q ss_pred ccCCHHHHHHHHhccc-cccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhh
Q psy4458 4 DEGDVTEAANIIQELQ-VETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTK 61 (303)
Q Consensus 4 ~~~~~~~Aa~~L~~i~-vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~ 61 (303)
+.|+++.|+..|-=++ .|.-..+...+-.+..+++++..+..++|+.|..+++=+...
T Consensus 191 ~~~~l~tAa~yLlVl~~~e~~~~~~~~~~~~~al~LL~~a~~~~~w~Lc~eL~RFL~~l 249 (258)
T PF07064_consen 191 ENGNLKTAASYLLVLQNLEGSSVVKDEESRQCALRLLVMALESGDWDLCFELVRFLKAL 249 (258)
T ss_pred HcCcHHHHHHHHHHHHhcCCcchhhhHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHh
Confidence 3688999999887665 333233346667888999999999999999999999877654
No 222
>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A.
Probab=34.36 E-value=68 Score=19.10 Aligned_cols=26 Identities=12% Similarity=0.079 Sum_probs=20.8
Q ss_pred HHHHHHHHHhhcchhHHHHHHHHhhh
Q psy4458 35 ILEQMRLCLAKKDYIRTQIISKKINT 60 (303)
Q Consensus 35 ~L~~~rL~L~~~D~~~a~~~~~ki~~ 60 (303)
+..+++++...|||.+|..+-.++-.
T Consensus 2 l~~Lg~~~~~~g~~~~Ai~~y~~aL~ 27 (36)
T PF13176_consen 2 LNNLGRIYRQQGDYEKAIEYYEQALA 27 (36)
T ss_dssp HHHHHHHHHHCT-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence 45788999999999999998888553
No 223
>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=33.59 E-value=1.8e+02 Score=27.77 Aligned_cols=63 Identities=8% Similarity=0.033 Sum_probs=38.7
Q ss_pred HHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Q psy4458 32 VTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIELDQHEGSYLATCKHYRAIL 102 (303)
Q Consensus 32 ~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~~~~~~~~f~eaa~~y~e~~ 102 (303)
+.+.+..+|+++..|+|..|..+++++...-.. .+ ... +. ..+..+...++..+|.++|.+..
T Consensus 335 ~~ll~sLg~l~~~~~~~~~A~~~le~a~a~~~~-p~--~~~----~~-~La~ll~~~g~~~~A~~~~~~~l 397 (409)
T TIGR00540 335 CCINRALGQLLMKHGEFIEAADAFKNVAACKEQ-LD--AND----LA-MAADAFDQAGDKAEAAAMRQDSL 397 (409)
T ss_pred HHHHHHHHHHHHHcccHHHHHHHHHHhHHhhcC-CC--HHH----HH-HHHHHHHHcCCHHHHHHHHHHHH
Confidence 356667777887778888888777754432211 11 111 11 35777777777777777777653
No 224
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=32.69 E-value=1.9e+02 Score=20.90 Aligned_cols=42 Identities=12% Similarity=0.130 Sum_probs=34.6
Q ss_pred hceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCCCc
Q psy4458 215 YTRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAG 256 (303)
Q Consensus 215 Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~g 256 (303)
-..++|+.|.+.+|+|..-+-..+..+...|-+..+-.-.++
T Consensus 12 ~~~~~f~~L~~~l~lt~g~Ls~hL~~Le~~GyV~~~k~~~~~ 53 (80)
T PF13601_consen 12 NEEATFSELKEELGLTDGNLSKHLKKLEEAGYVEVEKEFEGR 53 (80)
T ss_dssp HSEEEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEE-SSS
T ss_pred cCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEEEeccCC
Confidence 578999999999999999999999999999999876555444
No 225
>TIGR02561 HrpB1_HrpK type III secretion protein HrpB1/HrpK. This gene is found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia.
Probab=32.39 E-value=3e+02 Score=22.96 Aligned_cols=67 Identities=13% Similarity=0.083 Sum_probs=52.1
Q ss_pred HHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHcCC
Q psy4458 30 EKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIELDQHEGSYLATCKHYRAILTTP 105 (303)
Q Consensus 30 ~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~~~~~~~~f~eaa~~y~e~~~t~ 105 (303)
+-+--+++.+...|...|...++.++.-++-.-.+... ...+-+.++...|+|.||.+.+.++.+..
T Consensus 8 ~iv~gLi~~~~~aL~~~d~~D~e~lLdALrvLrP~~~e---------~d~~dg~l~i~rg~w~eA~rvlr~l~~~~ 74 (153)
T TIGR02561 8 RLLGGLIEVLMYALRSADPYDAQAMLDALRVLRPNLKE---------LDMFDGWLLIARGNYDEAARILRELLSSA 74 (153)
T ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCCCccc---------cchhHHHHHHHcCCHHHHHHHHHhhhccC
Confidence 34555788999999999999999999877765533222 22357889999999999999999997654
No 226
>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=31.91 E-value=1.2e+02 Score=22.31 Aligned_cols=50 Identities=22% Similarity=0.272 Sum_probs=38.2
Q ss_pred HhhhceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCCCce-EEec
Q psy4458 212 AKYYTRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAGI-INFA 261 (303)
Q Consensus 212 sk~Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~gi-V~f~ 261 (303)
.+.|.=|.++-|.+..|++..+++..+.+++..|-+.-+.-.-+|. ++|.
T Consensus 19 mk~hE~VP~~~I~~~s~l~~~~~~~~L~~L~~~kLv~~~~~~Y~GYrLT~~ 69 (82)
T PF09202_consen 19 MKNHEWVPLELIEKISGLSEGEVEKRLKRLVKLKLVSRRNKPYDGYRLTFL 69 (82)
T ss_dssp TTT-SSEEHHHHHHHHT--HHHHHHHHHHHHHTTSEEEE-SSS-EEEE-HH
T ss_pred ccCCccCCHHHHHHHhCcCHHHHHHHHHHHHhcCCccccCCCcceEEEeec
Confidence 3679999999999999999999999999999999997766566777 5554
No 227
>PF13518 HTH_28: Helix-turn-helix domain
Probab=31.43 E-value=77 Score=20.21 Aligned_cols=39 Identities=8% Similarity=0.173 Sum_probs=29.3
Q ss_pred hhceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecC
Q psy4458 214 YYTRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDR 253 (303)
Q Consensus 214 ~Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq 253 (303)
+-...|...+|..+|+|...+..-+...=..| +.|-.++
T Consensus 9 ~~~g~s~~~~a~~~gis~~tv~~w~~~y~~~G-~~~l~~~ 47 (52)
T PF13518_consen 9 YLEGESVREIAREFGISRSTVYRWIKRYREGG-IEGLKPK 47 (52)
T ss_pred HHcCCCHHHHHHHHCCCHhHHHHHHHHHHhcC-HHHhccC
Confidence 33556999999999999999988887776666 4454443
No 228
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein. Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.
Probab=31.38 E-value=1.5e+02 Score=25.37 Aligned_cols=37 Identities=11% Similarity=0.160 Sum_probs=33.1
Q ss_pred ceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEec
Q psy4458 216 TRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKID 252 (303)
Q Consensus 216 ~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akID 252 (303)
..++...||+.+|+|+.-+-+.+..|...|-+...-+
T Consensus 156 g~~s~~eia~~l~is~stv~r~L~~Le~~GlI~r~~~ 192 (203)
T TIGR01884 156 GEKSVKNIAKKLGKSLSTISRHLRELEKKGLVEQKGR 192 (203)
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcC
Confidence 5689999999999999999999999999998876543
No 229
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 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 is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=30.87 E-value=47 Score=20.58 Aligned_cols=18 Identities=22% Similarity=0.338 Sum_probs=13.6
Q ss_pred eHHHHHHHhCCCHHHHHH
Q psy4458 219 TLQRMCDLLGLPIEETEE 236 (303)
Q Consensus 219 tl~~la~ll~ls~~~vE~ 236 (303)
|+..+|+++|+|+.-+-.
T Consensus 1 ti~e~A~~~gvs~~tlR~ 18 (38)
T PF00376_consen 1 TIGEVAKLLGVSPRTLRY 18 (38)
T ss_dssp EHHHHHHHHTS-HHHHHH
T ss_pred CHHHHHHHHCCCHHHHHH
Confidence 578999999999876543
No 230
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=30.14 E-value=2e+02 Score=21.53 Aligned_cols=45 Identities=9% Similarity=0.102 Sum_probs=38.1
Q ss_pred hceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCCCceEEe
Q psy4458 215 YTRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAGIINF 260 (303)
Q Consensus 215 Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~giV~f 260 (303)
|+-||-+.||+.++++..-+-..|.++-..|.|... .+..+...+
T Consensus 39 ~K~ITps~lserlkI~~SlAr~~Lr~L~~kG~Ik~V-~~~~~q~IY 83 (86)
T PRK09334 39 EKIVTPYTLASKYGIKISVAKKVLRELEKRGVLVLY-SKNRRTPIY 83 (86)
T ss_pred CcEEcHHHHHHHhcchHHHHHHHHHHHHHCCCEEEE-ecCCCeEEe
Confidence 999999999999999999999999999999988665 454444433
No 231
>PRK04217 hypothetical protein; Provisional
Probab=29.80 E-value=1e+02 Score=24.18 Aligned_cols=43 Identities=12% Similarity=0.101 Sum_probs=32.5
Q ss_pred hhceeeHHHHHHHhCCCHHHHH-------HHHHhhhhcCceEEEecCCCc
Q psy4458 214 YYTRITLQRMCDLLGLPIEETE-------EFLSSMVVSKTITAKIDRPAG 256 (303)
Q Consensus 214 ~Y~~Itl~~la~ll~ls~~~vE-------~~l~~mI~~~~l~akIDq~~g 256 (303)
+|..+|.+.||+.+|+|..-+. +.|.+++........+.+.+.
T Consensus 55 ~~eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre~L~~~~~~~~~~~~~~ 104 (110)
T PRK04217 55 DYEGLTQEEAGKRMGVSRGTVWRALTSARKKVAQMLVEGRELIILPQGNE 104 (110)
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhccceeEecCCcc
Confidence 4688999999999999977555 556667777777666665554
No 232
>smart00005 DEATH DEATH domain, found in proteins involved in cell death (apoptosis). Alpha-helical domain present in a variety of proteins with apoptotic functions. Some (but not all) of these domains form homotypic and heterotypic dimers.
Probab=29.74 E-value=1.1e+02 Score=22.06 Aligned_cols=54 Identities=13% Similarity=0.297 Sum_probs=36.0
Q ss_pred eHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCCCceEEeccCCChhHHHHHHHH------HHHHHHHHHHHHHh
Q psy4458 219 TLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAGIINFARNKDPGEILNEWSA------SLNELMKLVNNTTH 289 (303)
Q Consensus 219 tl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~giV~f~~~~~~~~~l~~w~~------~i~~l~~~v~~~~~ 289 (303)
.-..||..+|++..+++.+-.+--. +-..+..+.|..|.. .+..|+..+.++++
T Consensus 19 ~W~~la~~Lg~~~~~i~~i~~~~~~-----------------~~~~~~~~lL~~W~~~~g~~at~~~L~~aL~~~~~ 78 (88)
T smart00005 19 DWRELARKLGLSEADIDQIRTEAPR-----------------DLAEQSVQLLRLWEQREGKNATLGTLLEALRKMGR 78 (88)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHCCC-----------------CHHHHHHHHHHHHHHccchhhHHHHHHHHHHHcCh
Confidence 4567999999999888776655321 112345688999976 55666666665543
No 233
>PF01476 LysM: LysM domain; InterPro: IPR018392 This domain is about 40 residues long and is found in a variety of enzymes involved in bacterial cell wall degradation []. This domain may have a general peptidoglycan binding function.; GO: 0016998 cell wall macromolecule catabolic process; PDB: 2DJP_A 3ZQD_A 1Y7M_B 4A52_A 2L9Y_A 1E0G_A.
Probab=29.65 E-value=58 Score=20.08 Aligned_cols=19 Identities=26% Similarity=0.464 Sum_probs=14.1
Q ss_pred eHHHHHHHhCCCHHHHHHH
Q psy4458 219 TLQRMCDLLGLPIEETEEF 237 (303)
Q Consensus 219 tl~~la~ll~ls~~~vE~~ 237 (303)
|+..||+.+|++.+++...
T Consensus 8 tl~~IA~~~~~~~~~l~~~ 26 (44)
T PF01476_consen 8 TLWSIAKRYGISVDELMEL 26 (44)
T ss_dssp -HHHHHHHTTS-HHHHHHH
T ss_pred cHHHHHhhhhhhHhHHHHh
Confidence 6788999999999887763
No 234
>PRK14720 transcript cleavage factor/unknown domain fusion protein; Provisional
Probab=29.35 E-value=2.9e+02 Score=29.84 Aligned_cols=108 Identities=6% Similarity=0.091 Sum_probs=67.6
Q ss_pred ccCCHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHH
Q psy4458 4 DEGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIE 83 (303)
Q Consensus 4 ~~~~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~ 83 (303)
..|++++|..++. -..+.+. ..+.+++-.+-|++..+++..+-.. ++-..+ .... .|..-.-|+.+++.
T Consensus 43 ~~~~~deai~i~~-~~l~~~P-----~~i~~yy~~G~l~~q~~~~~~~~lv--~~l~~~-~~~~--~~~~ve~~~~~i~~ 111 (906)
T PRK14720 43 SENLTDEAKDICE-EHLKEHK-----KSISALYISGILSLSRRPLNDSNLL--NLIDSF-SQNL--KWAIVEHICDKILL 111 (906)
T ss_pred hcCCHHHHHHHHH-HHHHhCC-----cceehHHHHHHHHHhhcchhhhhhh--hhhhhc-cccc--chhHHHHHHHHHHh
Confidence 4688999988887 3443322 3345555555599988888877766 454444 2333 57666666767776
Q ss_pred HHHHh-------------hhHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHhC
Q psy4458 84 LDQHE-------------GSYLATCKHYRAILTTPCIQSDPVQRHAVLQNVVLYLMLA 128 (303)
Q Consensus 84 ~~~~~-------------~~f~eaa~~y~e~~~t~~~~~~~~~~~~~L~~~v~~~iLs 128 (303)
++... +++.+|...|.+++.-- +. -..+|.++.++.-..
T Consensus 112 ~~~~k~Al~~LA~~Ydk~g~~~ka~~~yer~L~~D-----~~-n~~aLNn~AY~~ae~ 163 (906)
T PRK14720 112 YGENKLALRTLAEAYAKLNENKKLKGVWERLVKAD-----RD-NPEIVKKLATSYEEE 163 (906)
T ss_pred hhhhhHHHHHHHHHHHHcCChHHHHHHHHHHHhcC-----cc-cHHHHHHHHHHHHHh
Confidence 66666 88888888888887532 11 133555555554444
No 235
>KOG2041|consensus
Probab=28.76 E-value=3.4e+02 Score=28.57 Aligned_cols=57 Identities=19% Similarity=0.104 Sum_probs=39.0
Q ss_pred HHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHc
Q psy4458 40 RLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIELDQHEGSYLATCKHYRAILT 103 (303)
Q Consensus 40 rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~~~~~~~~f~eaa~~y~e~~~ 103 (303)
.|.+..+||-++-.+++- .+++++.+.+-.=..-++.++...+++.+|+++|-..-+
T Consensus 768 elr~klgDwfrV~qL~r~-------g~~d~dD~~~e~A~r~ig~~fa~~~~We~A~~yY~~~~~ 824 (1189)
T KOG2041|consen 768 ELRKKLGDWFRVYQLIRN-------GGSDDDDEGKEDAFRNIGETFAEMMEWEEAAKYYSYCGD 824 (1189)
T ss_pred HHHHhhhhHHHHHHHHHc-------cCCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 455566777776665552 112224556666666789999999999999999987743
No 236
>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=28.59 E-value=1.2e+02 Score=17.22 Aligned_cols=30 Identities=7% Similarity=-0.124 Sum_probs=24.1
Q ss_pred HHHHHHHHHHHhhcchhHHHHHHHHhhhhc
Q psy4458 33 TLILEQMRLCLAKKDYIRTQIISKKINTKF 62 (303)
Q Consensus 33 ~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~ 62 (303)
+.+..++.+++..+++..|....+++-...
T Consensus 2 ~~~~~~g~~~~~~~~~~~A~~~~~~al~~~ 31 (34)
T PF00515_consen 2 EAYYNLGNAYFQLGDYEEALEYYQRALELD 31 (34)
T ss_dssp HHHHHHHHHHHHTT-HHHHHHHHHHHHHHS
T ss_pred HHHHHHHHHHHHhCCchHHHHHHHHHHHHC
Confidence 467788999999999999999998886543
No 237
>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=28.47 E-value=2.7e+02 Score=21.23 Aligned_cols=86 Identities=15% Similarity=0.015 Sum_probs=56.8
Q ss_pred ccCCHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHH
Q psy4458 4 DEGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIE 83 (303)
Q Consensus 4 ~~~~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~ 83 (303)
..|++.+|...++.+. +. -+ .-.+.+...+.+++..+++..|..+.+++..... . +. ..+...+.
T Consensus 29 ~~~~~~~A~~~~~~~~-~~---~p--~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~p--~---~~----~~~~~la~ 93 (135)
T TIGR02552 29 QQGRYDEALKLFQLLA-AY---DP--YNSRYWLGLAACCQMLKEYEEAIDAYALAAALDP--D---DP----RPYFHAAE 93 (135)
T ss_pred HcccHHHHHHHHHHHH-Hh---CC--CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC--C---Ch----HHHHHHHH
Confidence 4577788887776543 11 11 2356677778888888889888888887765331 1 11 22233667
Q ss_pred HHHHhhhHHHHHHHHHHHHcC
Q psy4458 84 LDQHEGSYLATCKHYRAILTT 104 (303)
Q Consensus 84 ~~~~~~~f~eaa~~y~e~~~t 104 (303)
.+...++|.+|.+.|..++..
T Consensus 94 ~~~~~g~~~~A~~~~~~al~~ 114 (135)
T TIGR02552 94 CLLALGEPESALKALDLAIEI 114 (135)
T ss_pred HHHHcCCHHHHHHHHHHHHHh
Confidence 777888888888888887654
No 238
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=28.36 E-value=1.1e+02 Score=27.43 Aligned_cols=37 Identities=16% Similarity=0.158 Sum_probs=29.6
Q ss_pred HHHHHHHhhhceeeHHHHHHHhCCCHHHHHHHHHhhh
Q psy4458 206 HNIRVMAKYYTRITLQRMCDLLGLPIEETEEFLSSMV 242 (303)
Q Consensus 206 hNi~~isk~Y~~Itl~~la~ll~ls~~~vE~~l~~mI 242 (303)
.-|.-+.+-...++...||+.||+|++=+-+-|..+=
T Consensus 10 ~~I~~~l~~~~~v~v~eLa~~~~VS~~TIRRDL~~Le 46 (252)
T PRK10681 10 GQLLQALKRSDKLHLKDAAALLGVSEMTIRRDLNAHS 46 (252)
T ss_pred HHHHHHHHHcCCCcHHHHHHHhCCCHHHHHHHHHHhh
Confidence 3344455569999999999999999998888888754
No 239
>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=28.32 E-value=2.7e+02 Score=21.17 Aligned_cols=42 Identities=5% Similarity=0.077 Sum_probs=37.1
Q ss_pred ceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCCCce
Q psy4458 216 TRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAGI 257 (303)
Q Consensus 216 ~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~gi 257 (303)
..++...||+.++++..-+=..+..|...|-|.-.-|..|+-
T Consensus 42 ~~~t~~eL~~~l~~~~stvs~~i~~Le~kg~I~r~~~~~D~R 83 (109)
T TIGR01889 42 GKLTLKEIIKEILIKQSALVKIIKKLSKKGYLSKERSEDDER 83 (109)
T ss_pred CcCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEeccCCcccCC
Confidence 459999999999999999999999999999998766666654
No 240
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID. Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.
Probab=27.94 E-value=1.1e+02 Score=22.40 Aligned_cols=23 Identities=13% Similarity=0.299 Sum_probs=20.2
Q ss_pred ceeeHHHHHHHhCCCHHHHHHHH
Q psy4458 216 TRITLQRMCDLLGLPIEETEEFL 238 (303)
Q Consensus 216 ~~Itl~~la~ll~ls~~~vE~~l 238 (303)
.++++..+|+.+|+|..-|=..+
T Consensus 18 ~~~ti~dvA~~~gvS~~TVsr~L 40 (80)
T TIGR02844 18 TKATVRETAKVFGVSKSTVHKDV 40 (80)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHh
Confidence 89999999999999998776644
No 241
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=27.90 E-value=5.2e+02 Score=24.61 Aligned_cols=54 Identities=19% Similarity=0.146 Sum_probs=45.7
Q ss_pred ccCCHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhh
Q psy4458 4 DEGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKIN 59 (303)
Q Consensus 4 ~~~~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~ 59 (303)
..|+++.|.++=|.+-- ..+++..+|+-...+.+|=|+..|=++||+.+.+..-
T Consensus 81 sRGEvDRAIRiHQ~L~~--spdlT~~qr~lAl~qL~~Dym~aGl~DRAE~~f~~L~ 134 (389)
T COG2956 81 SRGEVDRAIRIHQTLLE--SPDLTFEQRLLALQQLGRDYMAAGLLDRAEDIFNQLV 134 (389)
T ss_pred hcchHHHHHHHHHHHhc--CCCCchHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHh
Confidence 57899999998887642 2467888999999999999999999999998887665
No 242
>KOG1840|consensus
Probab=27.88 E-value=3.1e+02 Score=27.55 Aligned_cols=77 Identities=16% Similarity=0.193 Sum_probs=58.0
Q ss_pred chHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHcC
Q psy4458 27 EKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIELDQHEGSYLATCKHYRAILTT 104 (303)
Q Consensus 27 ~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~~~~~~~~f~eaa~~y~e~~~t 104 (303)
+.++--..+.+.+-++--.+++..|..+..++-..+.+..|+ +...--.++.-++..+...|+|.+|-..|.+++.-
T Consensus 320 ~~~~v~~~l~~~~~~~~~~~~~Eea~~l~q~al~i~~~~~g~-~~~~~a~~~~nl~~l~~~~gk~~ea~~~~k~ai~~ 396 (508)
T KOG1840|consen 320 SHPEVAAQLSELAAILQSMNEYEEAKKLLQKALKIYLDAPGE-DNVNLAKIYANLAELYLKMGKYKEAEELYKKAIQI 396 (508)
T ss_pred ChHHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhhccc-cchHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHH
Confidence 334444556677777778889999999999888777554442 22244578888999999999999999999988754
No 243
>PF12854 PPR_1: PPR repeat
Probab=27.78 E-value=44 Score=19.86 Aligned_cols=16 Identities=31% Similarity=0.571 Sum_probs=13.2
Q ss_pred ccCCHHHHHHHHhccc
Q psy4458 4 DEGDVTEAANIIQELQ 19 (303)
Q Consensus 4 ~~~~~~~Aa~~L~~i~ 19 (303)
+.|++++|.+++.+++
T Consensus 19 k~G~~~~A~~l~~~M~ 34 (34)
T PF12854_consen 19 KAGRVDEAFELFDEMK 34 (34)
T ss_pred HCCCHHHHHHHHHhCc
Confidence 4799999999998763
No 244
>PRK12798 chemotaxis protein; Reviewed
Probab=27.66 E-value=1.2e+02 Score=29.42 Aligned_cols=74 Identities=12% Similarity=0.078 Sum_probs=54.3
Q ss_pred ccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHH
Q psy4458 23 YGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIELDQHEGSYLATCKHYRAI 101 (303)
Q Consensus 23 ~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~~~~~~~~f~eaa~~y~e~ 101 (303)
.+.|+...+.++||.++|-.+..|....|..-+.|+.... +.++ ...-+..+| .+-......++.++......+
T Consensus 248 ls~~d~~~q~~lYL~iAR~Ali~Gk~~lA~~As~~A~~L~-~~~~--~~~~ra~LY--~aaa~v~s~~~~~al~~L~~I 321 (421)
T PRK12798 248 LSFMDPERQRELYLRIARAALIDGKTELARFASERALKLA-DPDS--ADAARARLY--RGAALVASDDAESALEELSQI 321 (421)
T ss_pred HHhcCchhHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHhc-cCCC--cchHHHHHH--HHHHccCcccHHHHHHHHhcC
Confidence 3568899999999999999999999999999999999887 4444 333444555 444445566666666544443
No 245
>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].
Probab=27.61 E-value=73 Score=21.44 Aligned_cols=21 Identities=29% Similarity=0.528 Sum_probs=11.7
Q ss_pred eeeHHHHHHHhCCCHHHHHHH
Q psy4458 217 RITLQRMCDLLGLPIEETEEF 237 (303)
Q Consensus 217 ~Itl~~la~ll~ls~~~vE~~ 237 (303)
.|+++.|+..|++|..++=+.
T Consensus 4 ~lt~~~L~~~fhlp~~eAA~~ 24 (52)
T PF02042_consen 4 SLTLEDLSQYFHLPIKEAAKE 24 (52)
T ss_pred ccCHHHHHHHhCCCHHHHHHH
Confidence 455666666666665554443
No 246
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial. Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.
Probab=27.39 E-value=80 Score=26.22 Aligned_cols=33 Identities=18% Similarity=0.295 Sum_probs=30.1
Q ss_pred eeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEE
Q psy4458 217 RITLQRMCDLLGLPIEETEEFLSSMVVSKTITA 249 (303)
Q Consensus 217 ~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~a 249 (303)
.+|-+.||+.+|++.+-+=+.+.+|-.+|.|..
T Consensus 143 ~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~ 175 (193)
T TIGR03697 143 RLSHQAIAEAIGSTRVTITRLLGDLRKKKLISI 175 (193)
T ss_pred CCCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEe
Confidence 468899999999999999999999999998854
No 247
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=27.36 E-value=1.5e+02 Score=26.78 Aligned_cols=38 Identities=8% Similarity=0.078 Sum_probs=32.8
Q ss_pred HHhhhceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceE
Q psy4458 211 MAKYYTRITLQRMCDLLGLPIEETEEFLSSMVVSKTIT 248 (303)
Q Consensus 211 isk~Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~ 248 (303)
..+-...++...||+.||+|+.=+-+-|..|=..|.+.
T Consensus 25 ~L~~~~~vtv~eLa~~l~VS~~TIRRDL~~Le~~G~l~ 62 (269)
T PRK09802 25 RLRQQGSVQVNDLSALYGVSTVTIRNDLAFLEKQGIAV 62 (269)
T ss_pred HHHHcCCEeHHHHHHHHCCCHHHHHHHHHHHHhCCCeE
Confidence 33446679999999999999999999999998888775
No 248
>PF10975 DUF2802: Protein of unknown function (DUF2802); InterPro: IPR021244 This bacterial family of proteins has no known function.
Probab=27.32 E-value=71 Score=22.82 Aligned_cols=24 Identities=25% Similarity=0.358 Sum_probs=20.3
Q ss_pred ceeeHHHHHHHhCCCHHHHHHHHH
Q psy4458 216 TRITLQRMCDLLGLPIEETEEFLS 239 (303)
Q Consensus 216 ~~Itl~~la~ll~ls~~~vE~~l~ 239 (303)
.-.+.+.|++.+|+|.+|+|-+++
T Consensus 43 ~Ga~~~el~~~CgL~~aEAeLl~~ 66 (70)
T PF10975_consen 43 QGASVEELMEECGLSRAEAELLLS 66 (70)
T ss_pred cCCCHHHHHHHcCCCHHHHHHHHH
Confidence 346889999999999999997653
No 249
>PRK10370 formate-dependent nitrite reductase complex subunit NrfG; Provisional
Probab=27.01 E-value=4e+02 Score=22.69 Aligned_cols=85 Identities=11% Similarity=-0.014 Sum_probs=50.9
Q ss_pred cCCHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHHH
Q psy4458 5 EGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIEL 84 (303)
Q Consensus 5 ~~~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~~ 84 (303)
.++.+++...|+..--... .-.+.++..+++++..|++..|....+++-....+ +.+.... .+..
T Consensus 52 ~~~~~~~i~~l~~~L~~~P------~~~~~w~~Lg~~~~~~g~~~~A~~a~~~Al~l~P~-----~~~~~~~----lA~a 116 (198)
T PRK10370 52 QQTPEAQLQALQDKIRANP------QNSEQWALLGEYYLWRNDYDNALLAYRQALQLRGE-----NAELYAA----LATV 116 (198)
T ss_pred chhHHHHHHHHHHHHHHCC------CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC-----CHHHHHH----HHHH
Confidence 4566677666655422211 22457788899999999999999998888776522 2223222 2332
Q ss_pred -HHHhhh--HHHHHHHHHHHHcC
Q psy4458 85 -DQHEGS--YLATCKHYRAILTT 104 (303)
Q Consensus 85 -~~~~~~--f~eaa~~y~e~~~t 104 (303)
+...++ +.+|-..|.++...
T Consensus 117 L~~~~g~~~~~~A~~~l~~al~~ 139 (198)
T PRK10370 117 LYYQAGQHMTPQTREMIDKALAL 139 (198)
T ss_pred HHHhcCCCCcHHHHHHHHHHHHh
Confidence 233333 46777777777643
No 250
>PF03297 Ribosomal_S25: S25 ribosomal protein; InterPro: IPR004977 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S25 ribosomal protein is a component of the 40S ribosomal subunit.; PDB: 2XZM_8 2XZN_8 3O30_Q 3U5G_Z 3IZB_V 3U5C_Z 3O2Z_Q 3IZ6_V.
Probab=26.95 E-value=1.6e+02 Score=22.88 Aligned_cols=45 Identities=11% Similarity=0.030 Sum_probs=38.3
Q ss_pred hceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCCCceEEe
Q psy4458 215 YTRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAGIINF 260 (303)
Q Consensus 215 Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~giV~f 260 (303)
|+-||-..||+.++++..-+-..|-++...|.|.-. ....+...|
T Consensus 57 ~K~ITp~~lserlkI~~SlAr~~Lr~L~~kG~Ik~V-~k~~~~~IY 101 (105)
T PF03297_consen 57 MKLITPSVLSERLKINGSLARKALRELESKGLIKPV-SKHHRQRIY 101 (105)
T ss_dssp SSCECHHHHHHHHCCSCHHHHHHHHHHHHCCSSEEE-ECCTTCEEE
T ss_pred CcEeeHHHHHHhHhhHHHHHHHHHHHHHHCCCEEEE-eccCCeEEE
Confidence 899999999999999999999999999999988765 455444444
No 251
>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=26.93 E-value=2.7e+02 Score=25.34 Aligned_cols=66 Identities=11% Similarity=0.002 Sum_probs=48.2
Q ss_pred HHHHHHHHhhcchhHHHHHHHHhhhhccC--CCCcchHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHc
Q psy4458 36 LEQMRLCLAKKDYIRTQIISKKINTKFFD--DEKDDVQELKLKYYRLMIELDQHEGSYLATCKHYRAILT 103 (303)
Q Consensus 36 L~~~rL~L~~~D~~~a~~~~~ki~~~~~~--~~~~~~~e~k~~y~~~~~~~~~~~~~f~eaa~~y~e~~~ 103 (303)
+..+|..+..+++..|...+..+...... ..+ .....+.-..+.+..+...+++-+|...+.++..
T Consensus 268 ~~~a~~~~~~~~~~~a~~~L~~l~~~~~~~~~~~--~~~~~~~~~~l~A~~~~~~g~~~~A~~~L~~al~ 335 (355)
T cd05804 268 LHAALALAGAGDKDALDKLLAALKGRASSADDNK--QPARDVGLPLAEALYAFAEGNYATALELLGPVRD 335 (355)
T ss_pred HHHHHHHhcCCCHHHHHHHHHHHHHHHhccCchh--hhHHhhhHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence 35778888888888888888887765522 023 3445667778888888888888888887777753
No 252
>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=26.92 E-value=2e+02 Score=26.28 Aligned_cols=62 Identities=8% Similarity=0.051 Sum_probs=43.2
Q ss_pred eHHHHHHHhC--CCHHHHHHHHHhhhhcCceE----EEecCCCceEEeccCCChhHHHHHHHHHHHHHH
Q psy4458 219 TLQRMCDLLG--LPIEETEEFLSSMVVSKTIT----AKIDRPAGIINFARNKDPGEILNEWSASLNELM 281 (303)
Q Consensus 219 tl~~la~ll~--ls~~~vE~~l~~mI~~~~l~----akIDq~~giV~f~~~~~~~~~l~~w~~~i~~l~ 281 (303)
....||+.++ +|+++|..-|.-|+.-|-|. |+--|.+..|+. ...-+..++.+|..+...+.
T Consensus 139 ~~~~ia~~l~p~is~~ev~~sL~~L~~~glikk~~~g~y~~t~~~l~~-~~~~~~~avr~~h~q~l~lA 206 (271)
T TIGR02147 139 DPEELAKRCFPKISAEQVKESLDLLERLGLIKKNEDGFYKQTDKAVST-GDEVIPLAVRQYQKQMIDLA 206 (271)
T ss_pred CHHHHHHHhCCCCCHHHHHHHHHHHHHCCCeeECCCCcEEeecceeec-CCccchHHHHHHHHHHHHHH
Confidence 4678999999 89999999999999999884 234444444442 22334566777766555543
No 253
>PF04157 EAP30: EAP30/Vps36 family; InterPro: IPR007286 EAP30 is a subunit of the ELL complex. The ELL is an 80kDa RNA polymerase II transcription factor. ELL interacts with three other proteins to form the complex known as ELL complex. The ELL complex is capable of increasing that catalytic rate of transcription elongation, but is unable to repress initiation of transcription by RNA polymerase II as is the case of ELL. EAP30 is thought to lead to the derepression of ELL's transcriptional inhibitory activity. ; PDB: 2ZME_A 3CUQ_A 1W7P_D 1U5T_B.
Probab=26.85 E-value=1.6e+02 Score=25.70 Aligned_cols=37 Identities=16% Similarity=0.214 Sum_probs=32.8
Q ss_pred HhhhceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceE
Q psy4458 212 AKYYTRITLQRMCDLLGLPIEETEEFLSSMVVSKTIT 248 (303)
Q Consensus 212 sk~Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~ 248 (303)
......+|...|++.+|+|+.-+...|-.|+.+|.+.
T Consensus 185 ~~~~g~vt~~~l~~~~~ws~~~a~~~L~~~~~~G~l~ 221 (223)
T PF04157_consen 185 EENGGGVTASELAEKLGWSVERAKEALEELEREGLLW 221 (223)
T ss_dssp -TTTSEEEHHHHHHHHTB-HHHHHHHHHHHHHTTSEE
T ss_pred hhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhCCCEe
Confidence 3678899999999999999999999999999999875
No 254
>PF09743 DUF2042: Uncharacterized conserved protein (DUF2042); InterPro: IPR018611 The ubiquitin fold modifier 1 (Ufm1) is the most recently discovered ubiquitin-like modifier whose conjugation (ufmylation) system is conserved in multicellular organisms. Ufm1 is known to covalently attach with cellular protein(s) via a specific E1-activating enzyme (Uba5), an E2-conjugating enzyme (Ufc1), and a E3-ligating enzyme []. This entry represents E3 UFM1-protein ligase 1.
Probab=26.77 E-value=96 Score=28.33 Aligned_cols=39 Identities=13% Similarity=0.154 Sum_probs=35.4
Q ss_pred hceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecC
Q psy4458 215 YTRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDR 253 (303)
Q Consensus 215 Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq 253 (303)
=+=++++.|.+.+|++..-+-..+.++|.+|++.|+|--
T Consensus 190 T~Pt~l~~l~~~~~~~~~l~~~il~~Li~~~~l~G~i~G 228 (272)
T PF09743_consen 190 TRPTPLSSLLKRYGFEEKLFQSILEELIKSGELPGSIVG 228 (272)
T ss_pred ccceEHHHHHHHhCCcHHHHHHHHHHHHhcCcceEEEEC
Confidence 345789999999999999999999999999999999866
No 255
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=26.68 E-value=77 Score=21.89 Aligned_cols=24 Identities=17% Similarity=0.425 Sum_probs=20.5
Q ss_pred eeHHHHHHHhCCCHHHHHHHHHhh
Q psy4458 218 ITLQRMCDLLGLPIEETEEFLSSM 241 (303)
Q Consensus 218 Itl~~la~ll~ls~~~vE~~l~~m 241 (303)
++++.||+.+|+|+..+...+.+.
T Consensus 2 ~~~~~la~~~~~s~~~l~~~f~~~ 25 (84)
T smart00342 2 LTLEDLAEALGMSPRHLQRLFKKE 25 (84)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHH
Confidence 689999999999999888877654
No 256
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=26.62 E-value=4e+02 Score=22.68 Aligned_cols=69 Identities=16% Similarity=0.280 Sum_probs=52.5
Q ss_pred eeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEE--EecCCCceEEeccCCChhHHHHHHHHHHHHHHHHHH
Q psy4458 217 RITLQRMCDLLGLPIEETEEFLSSMVVSKTITA--KIDRPAGIINFARNKDPGEILNEWSASLNELMKLVN 285 (303)
Q Consensus 217 ~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~a--kIDq~~giV~f~~~~~~~~~l~~w~~~i~~l~~~v~ 285 (303)
-+|=+.||..+|+...++-+.|..+=.+|.+.. +.|...|..+..|.-+...+...--..+..+++.+.
T Consensus 32 e~tDeela~~l~i~~~~vrriL~~L~e~~li~~~k~rd~~~~~~~y~w~~~~~~v~~~l~~~~~~~le~Lk 102 (176)
T COG1675 32 ELTDEELAELLGIKKNEVRRILYALYEDGLISYRKKRDEESGWEEYTWYINYEKVLEVLKGKKRKILEKLK 102 (176)
T ss_pred CcChHHHHHHhCccHHHHHHHHHHHHhCCceEEEeecccCCCcEEEEEEechHHHHHHHHHHHHHHHHHHH
Confidence 478899999999999999999999999998854 788888887777754444455555555555555443
No 257
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=26.56 E-value=1.6e+02 Score=18.04 Aligned_cols=28 Identities=11% Similarity=0.298 Sum_probs=23.5
Q ss_pred hceeeHHHHHHHhCCCHHHHHHHHHhhh
Q psy4458 215 YTRITLQRMCDLLGLPIEETEEFLSSMV 242 (303)
Q Consensus 215 Y~~Itl~~la~ll~ls~~~vE~~l~~mI 242 (303)
....+...+|..+|+|...+-..+....
T Consensus 24 ~~~~~~~~ia~~~~~s~~~i~~~~~~~~ 51 (55)
T cd06171 24 GEGLSYEEIAEILGISRSTVRQRLHRAL 51 (55)
T ss_pred hcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 3889999999999999998887776543
No 258
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=26.45 E-value=67 Score=27.90 Aligned_cols=26 Identities=23% Similarity=0.416 Sum_probs=22.0
Q ss_pred ceeeHHHHHHHhCCCHHHHHHHHHhh
Q psy4458 216 TRITLQRMCDLLGLPIEETEEFLSSM 241 (303)
Q Consensus 216 ~~Itl~~la~ll~ls~~~vE~~l~~m 241 (303)
.++++..||+.||+|+.-+...|.+.
T Consensus 177 R~~~l~dLA~~lGISkst~~ehLRrA 202 (215)
T COG3413 177 RRVSLKDLAKELGISKSTLSEHLRRA 202 (215)
T ss_pred ccCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 68999999999999988777666554
No 259
>KOG3060|consensus
Probab=26.44 E-value=2.6e+02 Score=25.55 Aligned_cols=87 Identities=16% Similarity=0.224 Sum_probs=50.5
Q ss_pred CCccCCHHHHHHHHhcccccccc-CCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHH
Q psy4458 2 KEDEGDVTEAANIIQELQVETYG-SMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRL 80 (303)
Q Consensus 2 ~e~~~~~~~Aa~~L~~i~vet~~-~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~ 80 (303)
+|+-|.+++|.+++..+--|..+ .+..+-|+.+... .|.-..|-.-+++--.++..+.. .| ..
T Consensus 96 lEa~~~~~~A~e~y~~lL~ddpt~~v~~KRKlAilka-------~GK~l~aIk~ln~YL~~F~~D~E--AW-------~e 159 (289)
T KOG3060|consen 96 LEATGNYKEAIEYYESLLEDDPTDTVIRKRKLAILKA-------QGKNLEAIKELNEYLDKFMNDQE--AW-------HE 159 (289)
T ss_pred HHHhhchhhHHHHHHHHhccCcchhHHHHHHHHHHHH-------cCCcHHHHHHHHHHHHHhcCcHH--HH-------HH
Confidence 46678888888887776544322 2233333333322 23333333333433344432211 33 44
Q ss_pred HHHHHHHhhhHHHHHHHHHHHHcC
Q psy4458 81 MIELDQHEGSYLATCKHYRAILTT 104 (303)
Q Consensus 81 ~~~~~~~~~~f~eaa~~y~e~~~t 104 (303)
.+.+|...++|..|+-||-|+.-+
T Consensus 160 LaeiY~~~~~f~kA~fClEE~ll~ 183 (289)
T KOG3060|consen 160 LAEIYLSEGDFEKAAFCLEELLLI 183 (289)
T ss_pred HHHHHHhHhHHHHHHHHHHHHHHc
Confidence 788899999999999999999754
No 260
>PF06711 DUF1198: Protein of unknown function (DUF1198); InterPro: IPR009587 This family consists of several bacterial proteins of around 150 residues in length which are specific to Escherichia coli, Salmonella species and Yersinia pestis. The function of this family is unknown.
Probab=26.16 E-value=49 Score=27.10 Aligned_cols=24 Identities=21% Similarity=0.288 Sum_probs=21.1
Q ss_pred HHHHHHHhCCCHHHHHHHHHhhhh
Q psy4458 220 LQRMCDLLGLPIEETEEFLSSMVV 243 (303)
Q Consensus 220 l~~la~ll~ls~~~vE~~l~~mI~ 243 (303)
.++|++.|+++|=-+|+++.+|=.
T Consensus 28 ~~~Ls~rL~I~Pv~iESMl~qMGk 51 (148)
T PF06711_consen 28 IRRLSERLNIKPVYIESMLDQMGK 51 (148)
T ss_pred HHHHHHHhCCCceeHHHHHHHHhH
Confidence 578999999999999999999843
No 261
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=26.06 E-value=51 Score=20.44 Aligned_cols=24 Identities=13% Similarity=0.264 Sum_probs=15.3
Q ss_pred hhceeeHHHHHHHhCCCHHHHHHH
Q psy4458 214 YYTRITLQRMCDLLGLPIEETEEF 237 (303)
Q Consensus 214 ~Y~~Itl~~la~ll~ls~~~vE~~ 237 (303)
+-+.++++.||..+|+|+.-.-+.
T Consensus 5 ~~~~~~l~~iA~~~g~S~~~f~r~ 28 (42)
T PF00165_consen 5 LQQKLTLEDIAEQAGFSPSYFSRL 28 (42)
T ss_dssp T-SS--HHHHHHHHTS-HHHHHHH
T ss_pred ccCCCCHHHHHHHHCCCHHHHHHH
Confidence 356789999999999987655443
No 262
>PLN03077 Protein ECB2; Provisional
Probab=26.00 E-value=4.1e+02 Score=28.07 Aligned_cols=50 Identities=12% Similarity=0.113 Sum_probs=28.2
Q ss_pred cCCHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHh
Q psy4458 5 EGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKI 58 (303)
Q Consensus 5 ~~~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki 58 (303)
.|.+++|.+++..+.-+ ++ .....+.|-..+.++-..|++..|..++++.
T Consensus 602 ~g~v~ea~~~f~~M~~~-~g---i~P~~~~y~~lv~~l~r~G~~~eA~~~~~~m 651 (857)
T PLN03077 602 SGMVTQGLEYFHSMEEK-YS---ITPNLKHYACVVDLLGRAGKLTEAYNFINKM 651 (857)
T ss_pred cChHHHHHHHHHHHHHH-hC---CCCchHHHHHHHHHHHhCCCHHHHHHHHHHC
Confidence 46667777766666411 11 1122345566666666666666666666654
No 263
>KOG2796|consensus
Probab=25.87 E-value=1.4e+02 Score=27.51 Aligned_cols=73 Identities=10% Similarity=0.062 Sum_probs=53.3
Q ss_pred HHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHcCC
Q psy4458 30 EKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIELDQHEGSYLATCKHYRAILTTP 105 (303)
Q Consensus 30 ~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~~~~~~~~f~eaa~~y~e~~~t~ 105 (303)
++-.++-..+|+.+..||-..|+++..++......-++ -+-++.-..-++.+|...+||.+|.+.|.++..+.
T Consensus 210 ~~p~L~s~Lgr~~MQ~GD~k~a~~yf~~vek~~~kL~~---~q~~~~V~~n~a~i~lg~nn~a~a~r~~~~i~~~D 282 (366)
T KOG2796|consen 210 QEPQLLSGLGRISMQIGDIKTAEKYFQDVEKVTQKLDG---LQGKIMVLMNSAFLHLGQNNFAEAHRFFTEILRMD 282 (366)
T ss_pred ccHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHhhhhc---cchhHHHHhhhhhheecccchHHHHHHHhhccccC
Confidence 45566778899999999999999999866533211111 12334444557888999999999999999998664
No 264
>KOG1126|consensus
Probab=25.66 E-value=4.3e+02 Score=27.23 Aligned_cols=91 Identities=11% Similarity=0.043 Sum_probs=61.6
Q ss_pred CHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccC-CCC-----cchHHHHHHHHH-
Q psy4458 7 DVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFD-DEK-----DDVQELKLKYYR- 79 (303)
Q Consensus 7 ~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~-~~~-----~~~~e~k~~y~~- 79 (303)
++.+|.+.++.++-.-+++. =++.++.|.|++..||..|+.+.+.++.+-.- .+| .-.|-++-.+..
T Consensus 334 ~~~~A~~~~~klp~h~~nt~------wvl~q~GrayFEl~~Y~~a~~~F~~~r~~~p~rv~~meiyST~LWHLq~~v~Ls 407 (638)
T KOG1126|consen 334 NCREALNLFEKLPSHHYNTG------WVLSQLGRAYFELIEYDQAERIFSLVRRIEPYRVKGMEIYSTTLWHLQDEVALS 407 (638)
T ss_pred HHHHHHHHHHhhHHhcCCch------HHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHhhHHHH
Confidence 57889999998876665543 35678899999999999999999888765321 122 013444433332
Q ss_pred ------------------HHHHHHHHhhhHHHHHHHHHHHHc
Q psy4458 80 ------------------LMIELDQHEGSYLATCKHYRAILT 103 (303)
Q Consensus 80 ------------------~~~~~~~~~~~f~eaa~~y~e~~~ 103 (303)
..|-.+..++|+-.|-++|..+..
T Consensus 408 ~Laq~Li~~~~~sPesWca~GNcfSLQkdh~~Aik~f~RAiQ 449 (638)
T KOG1126|consen 408 YLAQDLIDTDPNSPESWCALGNCFSLQKDHDTAIKCFKRAIQ 449 (638)
T ss_pred HHHHHHHhhCCCCcHHHHHhcchhhhhhHHHHHHHHHHHhhc
Confidence 124556677888888888887754
No 265
>PRK04239 hypothetical protein; Provisional
Probab=25.46 E-value=41 Score=26.39 Aligned_cols=21 Identities=33% Similarity=0.403 Sum_probs=18.9
Q ss_pred HHHHHHHHhhhhcCceEEEec
Q psy4458 232 EETEEFLSSMVVSKTITAKID 252 (303)
Q Consensus 232 ~~vE~~l~~mI~~~~l~akID 252 (303)
..||..|..|...|+|.++||
T Consensus 67 ~~VE~~liqlAq~G~i~~ki~ 87 (110)
T PRK04239 67 EQVEQQLIQLAQSGRIQGPID 87 (110)
T ss_pred HHHHHHHHHHHHcCCCCCCcC
Confidence 478999999999999999886
No 266
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=25.45 E-value=87 Score=26.28 Aligned_cols=42 Identities=14% Similarity=0.143 Sum_probs=33.7
Q ss_pred eeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCCCceEEecc
Q psy4458 217 RITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAGIINFAR 262 (303)
Q Consensus 217 ~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~giV~f~~ 262 (303)
.+|-+.||+.+|++++-+=+.+.+|-.+|-|. ...|.|+..+
T Consensus 149 ~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~----~~~~~i~I~d 190 (202)
T PRK13918 149 YATHDELAAAVGSVRETVTKVIGELSREGYIR----SGYGKIQLLD 190 (202)
T ss_pred cCCHHHHHHHhCccHHHHHHHHHHHHHCCCEE----cCCCEEEEEC
Confidence 46889999999999999999999999999875 2334455543
No 267
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=25.16 E-value=4.8e+02 Score=23.05 Aligned_cols=42 Identities=10% Similarity=0.197 Sum_probs=36.3
Q ss_pred hhhceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCCC
Q psy4458 213 KYYTRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPA 255 (303)
Q Consensus 213 k~Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~ 255 (303)
+.=.-+|...||+.||+|+..|-..+-.++.+|-+... .+..
T Consensus 21 ~~~g~~sa~elA~~Lgis~~avR~HL~~Le~~Glv~~~-~~~~ 62 (218)
T COG2345 21 KKSGPVSADELAEELGISPMAVRRHLDDLEAEGLVEVE-RQQG 62 (218)
T ss_pred hccCCccHHHHHHHhCCCHHHHHHHHHHHHhCcceeee-eccC
Confidence 34567899999999999999999999999999999887 4433
No 268
>COG2118 DNA-binding protein [General function prediction only]
Probab=25.13 E-value=44 Score=26.35 Aligned_cols=23 Identities=35% Similarity=0.388 Sum_probs=20.1
Q ss_pred HHHHHHHHHhhhhcCceEEEecC
Q psy4458 231 IEETEEFLSSMVVSKTITAKIDR 253 (303)
Q Consensus 231 ~~~vE~~l~~mI~~~~l~akIDq 253 (303)
.+.||..|..|...|+|..+||-
T Consensus 69 AeavE~qLi~LaqtGri~~~I~e 91 (116)
T COG2118 69 AEAVENQLIQLAQTGRITHKIDE 91 (116)
T ss_pred HHHHHHHHHHHHHcCCCCCCCCH
Confidence 45788999999999999999973
No 269
>PF03485 Arg_tRNA_synt_N: Arginyl tRNA synthetase N terminal domain; InterPro: IPR005148 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This domain is found at the N terminus of Arginyl tRNA synthetase, also called additional domain 1 (Add-1). It is about 140 residues long and it has been suggested that this domain will be involved in tRNA recognition [].; GO: 0000166 nucleotide binding, 0004814 arginine-tRNA ligase activity, 0005524 ATP binding, 0006420 arginyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1F7V_A 1F7U_A 1BS2_A 2ZUE_A 2ZUF_A 1IQ0_A 3GDZ_B.
Probab=25.12 E-value=1.3e+02 Score=21.78 Aligned_cols=40 Identities=25% Similarity=0.341 Sum_probs=32.1
Q ss_pred HHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCCC-ceEEe
Q psy4458 221 QRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPA-GIINF 260 (303)
Q Consensus 221 ~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~-giV~f 260 (303)
=.+|+.++.+|.++-..+++.+.....-.++.=.. |.|.|
T Consensus 43 ~~lak~~k~~P~~iA~~i~~~l~~~~~i~~vev~gpGFiN~ 83 (85)
T PF03485_consen 43 FRLAKKLKKNPREIAEEIAEKLEKSPIIEKVEVAGPGFINF 83 (85)
T ss_dssp HHHHHHTTS-HHHHHHHHHHCHCTTTTEEEEEEETTTEEEE
T ss_pred HHHHHHcCCCHHHHHHHHHHhcCCCCCEEEEEEcCCcEEEE
Confidence 47899999999999999999998887766777655 77776
No 270
>PRK10803 tol-pal system protein YbgF; Provisional
Probab=25.07 E-value=5.1e+02 Score=23.33 Aligned_cols=92 Identities=5% Similarity=-0.117 Sum_probs=45.5
Q ss_pred HhhhHHHHHHHHHHHHcCCCCCCChHHHHHH-HHHHHHHHHhCCCCchhhHhHHHhhhhhhcCCchH-HHHHHHHhcCCc
Q psy4458 87 HEGSYLATCKHYRAILTTPCIQSDPVQRHAV-LQNVVLYLMLAPYDNEQSDLTHRVLEDKLLNEIPL-YKGLLQWFTNPE 164 (303)
Q Consensus 87 ~~~~f~eaa~~y~e~~~t~~~~~~~~~~~~~-L~~~v~~~iLs~~~~~r~~ll~~l~~~~~~~~~p~-~~~L~~~f~~~~ 164 (303)
..++|-+|...|......+.- + ...-.+ +...-.+.-...+..-...+..-+...|..+..|+ +..+..++..
T Consensus 155 ~~~~y~~Ai~af~~fl~~yP~--s-~~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP~s~~~~dAl~klg~~~~~-- 229 (263)
T PRK10803 155 DKSRQDDAIVAFQNFVKKYPD--S-TYQPNANYWLGQLNYNKGKKDDAAYYFASVVKNYPKSPKAADAMFKVGVIMQD-- 229 (263)
T ss_pred hcCCHHHHHHHHHHHHHHCcC--C-cchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchhHHHHHHHHHHHH--
Confidence 358888888888877765421 1 100111 22223333333333333333333334455455444 3334445432
Q ss_pred ccCchHHHHHHHHhhcccc
Q psy4458 165 LIKWSGLRQLYEEELFKTS 183 (303)
Q Consensus 165 li~~~~~~~~~~~~L~~~~ 183 (303)
+-++......|+..+..+|
T Consensus 230 ~g~~~~A~~~~~~vi~~yP 248 (263)
T PRK10803 230 KGDTAKAKAVYQQVIKKYP 248 (263)
T ss_pred cCCHHHHHHHHHHHHHHCc
Confidence 2245666778888888777
No 271
>PF13429 TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2_B.
Probab=25.04 E-value=4.8e+02 Score=23.02 Aligned_cols=86 Identities=15% Similarity=0.054 Sum_probs=55.7
Q ss_pred CccCCHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHH
Q psy4458 3 EDEGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMI 82 (303)
Q Consensus 3 e~~~~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~ 82 (303)
...|++++|..++..+.- ... ...-..+++..++++...|++..|....+++-....+ +.+.... .+
T Consensus 121 ~~~~~~~~~~~~l~~~~~--~~~--~~~~~~~~~~~a~~~~~~G~~~~A~~~~~~al~~~P~-----~~~~~~~----l~ 187 (280)
T PF13429_consen 121 YRLGDYDEAEELLEKLEE--LPA--APDSARFWLALAEIYEQLGDPDKALRDYRKALELDPD-----DPDARNA----LA 187 (280)
T ss_dssp HHTT-HHHHHHHHHHHHH---T-----T-HHHHHHHHHHHHHCCHHHHHHHHHHHHHHH-TT------HHHHHH----HH
T ss_pred HHHhHHHHHHHHHHHHHh--ccC--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCC-----CHHHHHH----HH
Confidence 346899999999998661 121 2245678899999999999999999999999876632 3344333 34
Q ss_pred HHHHHhhhHHH---HHHHHHHH
Q psy4458 83 ELDQHEGSYLA---TCKHYRAI 101 (303)
Q Consensus 83 ~~~~~~~~f~e---aa~~y~e~ 101 (303)
..+...+++.+ +.+.|...
T Consensus 188 ~~li~~~~~~~~~~~l~~~~~~ 209 (280)
T PF13429_consen 188 WLLIDMGDYDEAREALKRLLKA 209 (280)
T ss_dssp HHHCTTCHHHHHHHHHHHHHHH
T ss_pred HHHHHCCChHHHHHHHHHHHHH
Confidence 44556666665 55555555
No 272
>PLN03081 pentatricopeptide (PPR) repeat-containing protein; Provisional
Probab=25.00 E-value=3.1e+02 Score=28.21 Aligned_cols=82 Identities=20% Similarity=0.259 Sum_probs=49.5
Q ss_pred cCCHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHHH
Q psy4458 5 EGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIEL 84 (303)
Q Consensus 5 ~~~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~~ 84 (303)
.|++++|.+++.+++++. -...+-..+.-|-..|++..|+...+++...-. ++ ...|.+++..
T Consensus 475 ~G~~~eA~~~~~~~~~~p--------~~~~~~~Ll~a~~~~g~~~~a~~~~~~l~~~~p--~~-------~~~y~~L~~~ 537 (697)
T PLN03081 475 EGLLDEAYAMIRRAPFKP--------TVNMWAALLTACRIHKNLELGRLAAEKLYGMGP--EK-------LNNYVVLLNL 537 (697)
T ss_pred cCCHHHHHHHHHHCCCCC--------CHHHHHHHHHHHHHcCCcHHHHHHHHHHhCCCC--CC-------CcchHHHHHH
Confidence 456666666655554321 112345555566666777777766666532221 11 2346677888
Q ss_pred HHHhhhHHHHHHHHHHHHc
Q psy4458 85 DQHEGSYLATCKHYRAILT 103 (303)
Q Consensus 85 ~~~~~~f~eaa~~y~e~~~ 103 (303)
|...+++.+|.+.+.+.-.
T Consensus 538 y~~~G~~~~A~~v~~~m~~ 556 (697)
T PLN03081 538 YNSSGRQAEAAKVVETLKR 556 (697)
T ss_pred HHhCCCHHHHHHHHHHHHH
Confidence 8888999889888887754
No 273
>PF13182 DUF4007: Protein of unknown function (DUF4007)
Probab=24.94 E-value=2e+02 Score=26.38 Aligned_cols=57 Identities=18% Similarity=0.196 Sum_probs=43.3
Q ss_pred hhhceeeHHHH-------HHHhCCCHHHHHHHHHhhhhc-CceEEEecCCCc--eEEecc-CCChhHHHH
Q psy4458 213 KYYTRITLQRM-------CDLLGLPIEETEEFLSSMVVS-KTITAKIDRPAG--IINFAR-NKDPGEILN 271 (303)
Q Consensus 213 k~Y~~Itl~~l-------a~ll~ls~~~vE~~l~~mI~~-~~l~akIDq~~g--iV~f~~-~~~~~~~l~ 271 (303)
.-.++|++++| ++.|+++++.+...|.++-.. |.|. +....| .|.+.. ..++.+.|+
T Consensus 216 ~~~~sis~~~L~~~~~sPGriF~L~~~~l~~~L~~l~~~~g~i~--~~~TaGl~qv~~~~~~~~~~~~L~ 283 (286)
T PF13182_consen 216 PGRNSISFDELLNEPGSPGRIFKLDEESLAERLEQLEEIYGFIS--WSDTAGLDQVYLKDEELDAWDVLK 283 (286)
T ss_pred CCCcEEEHHHHhcCCCCcceEeccCHHHHHHHHHHHHhhcCcEE--EEEcCCCeEEEeccccCCHHHHHH
Confidence 34889999998 579999999999999999888 6654 566666 477776 444445554
No 274
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=24.92 E-value=3.5e+02 Score=21.96 Aligned_cols=71 Identities=17% Similarity=0.200 Sum_probs=45.2
Q ss_pred hceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEE--E--ecCCCc-eEEeccCCChhHHHHHHHHHHHHHHHHHH
Q psy4458 215 YTRITLQRMCDLLGLPIEETEEFLSSMVVSKTITA--K--IDRPAG-IINFARNKDPGEILNEWSASLNELMKLVN 285 (303)
Q Consensus 215 Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~a--k--IDq~~g-iV~f~~~~~~~~~l~~w~~~i~~l~~~v~ 285 (303)
..-++=+.||+.+|++..++-+.+..+-.+|.+.+ + -|..+| ..++-|--+.....+.-..++..+...+.
T Consensus 13 ~~~~~dedLa~~l~i~~n~vRkiL~~L~ed~~~~~~~~~e~~~~~~~~~~~yw~i~y~~~~~vik~r~~~~~~~L~ 88 (147)
T smart00531 13 NGCVTEEDLAELLGIKQKQLRKILYLLYDEKLIKIDYKREKDPETKTWYRYYWYINYDTLLDVVKYKLDKMRKRLE 88 (147)
T ss_pred cCCcCHHHHHHHhCCCHHHHHHHHHHHHhhhcchhheeeeeCCCCceEEEEEEEecHHHHHHHHHHHHHHHHHHHH
Confidence 45689999999999999999999999999776522 2 344455 44444432222334444444555544443
No 275
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=24.80 E-value=93 Score=26.26 Aligned_cols=32 Identities=22% Similarity=0.244 Sum_probs=29.6
Q ss_pred eeeHHHHHHHhCCCHHHHHHHHHhhhhcCceE
Q psy4458 217 RITLQRMCDLLGLPIEETEEFLSSMVVSKTIT 248 (303)
Q Consensus 217 ~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~ 248 (303)
.+|-+.||+.+|++++-+-+.+.+|-.+|.|.
T Consensus 168 ~~t~~~lA~~lG~tr~tvsR~l~~l~~~gii~ 199 (211)
T PRK11753 168 KITRQEIGRIVGCSREMVGRVLKMLEDQGLIS 199 (211)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEE
Confidence 67889999999999999999999999999774
No 276
>PRK14574 hmsH outer membrane protein; Provisional
Probab=24.77 E-value=7.2e+02 Score=26.59 Aligned_cols=86 Identities=8% Similarity=-0.031 Sum_probs=58.1
Q ss_pred ccCCHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHH
Q psy4458 4 DEGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIE 83 (303)
Q Consensus 4 ~~~~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~ 83 (303)
..|++.+|+.++..+--.. +.. .+.++-++.++...++...|...++++.+... . +.++...+.
T Consensus 114 ~~gdyd~Aiely~kaL~~d----P~n--~~~l~gLa~~y~~~~q~~eAl~~l~~l~~~dp------~----~~~~l~lay 177 (822)
T PRK14574 114 NEKRWDQALALWQSSLKKD----PTN--PDLISGMIMTQADAGRGGVVLKQATELAERDP------T----VQNYMTLSY 177 (822)
T ss_pred HcCCHHHHHHHHHHHHhhC----CCC--HHHHHHHHHHHhhcCCHHHHHHHHHHhcccCc------c----hHHHHHHHH
Confidence 4688899999888874322 111 34445668888888888888888888775431 1 333344455
Q ss_pred HHHHhhhHHHHHHHHHHHHcCC
Q psy4458 84 LDQHEGSYLATCKHYRAILTTP 105 (303)
Q Consensus 84 ~~~~~~~f~eaa~~y~e~~~t~ 105 (303)
++....++.+|...|.+++..+
T Consensus 178 L~~~~~~~~~AL~~~ekll~~~ 199 (822)
T PRK14574 178 LNRATDRNYDALQASSEAVRLA 199 (822)
T ss_pred HHHhcchHHHHHHHHHHHHHhC
Confidence 5555777777999999998764
No 277
>PF07848 PaaX: PaaX-like protein; InterPro: IPR012906 This entry describes the N-terminal region of proteins that are similar to, and nclude, the product of the paaX gene of Escherichia coli (P76086 from SWISSPROT). PaaX is a transcriptional regulator that is always found in association with operons believed to be involved in the degradation of phenylacetic acid []. The gene product has been shown to bind to the promoter sites and repress their transcription []. ; PDB: 3KFW_X 3L09_B.
Probab=24.65 E-value=85 Score=22.37 Aligned_cols=30 Identities=20% Similarity=0.247 Sum_probs=24.1
Q ss_pred HHHHHHHhCCCHHHHHHHHHhhhhcCceEE
Q psy4458 220 LQRMCDLLGLPIEETEEFLSSMVVSKTITA 249 (303)
Q Consensus 220 l~~la~ll~ls~~~vE~~l~~mI~~~~l~a 249 (303)
+-++...||+++.-+-.-+++|..+|.|..
T Consensus 26 Li~ll~~~Gv~e~avR~alsRl~~~G~L~~ 55 (70)
T PF07848_consen 26 LIRLLAAFGVSESAVRTALSRLVRRGWLES 55 (70)
T ss_dssp HHHHHCCTT--HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHcCCChHHHHHHHHHHHHcCceee
Confidence 445667789999999999999999999966
No 278
>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=24.65 E-value=1.8e+02 Score=22.05 Aligned_cols=36 Identities=17% Similarity=0.239 Sum_probs=27.3
Q ss_pred hceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEE
Q psy4458 215 YTRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAK 250 (303)
Q Consensus 215 Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~ak 250 (303)
...++-+.||..+|+++.++-+.+..+-.+|-+..+
T Consensus 25 ~~~l~de~la~~~~l~~~~vRkiL~~L~~~~lv~~~ 60 (105)
T PF02002_consen 25 KGELTDEDLAKKLGLKPKEVRKILYKLYEDGLVSYR 60 (105)
T ss_dssp H--B-HHHHHHTT-S-HHHHHHHHHHHHHHSS-EEE
T ss_pred cCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeEEE
Confidence 356888999999999999999999999999988553
No 279
>COG2886 Uncharacterized small protein [Function unknown]
Probab=24.63 E-value=1.9e+02 Score=21.80 Aligned_cols=26 Identities=31% Similarity=0.466 Sum_probs=23.9
Q ss_pred ceeeHHHHHHHhCCCHHHHHHHHHhh
Q psy4458 216 TRITLQRMCDLLGLPIEETEEFLSSM 241 (303)
Q Consensus 216 ~~Itl~~la~ll~ls~~~vE~~l~~m 241 (303)
..|||.+.|++.|+|..+.+..+.+=
T Consensus 40 g~vSlg~Aaela~~sl~ef~~eL~~R 65 (88)
T COG2886 40 GAVSLGRAAELAGMSLNEFEEELRKR 65 (88)
T ss_pred hhhHHHHHHHHhcCCHHHHHHHHHHh
Confidence 88999999999999999999988764
No 280
>TIGR02675 tape_meas_nterm tape measure domain. Proteins containing this domain are strictly bacterial, including bacteriophage and prophage regions of bacterial genomes. Most members are 800 to 1800 amino acids long, making them among the longest predicted proteins of their respective phage genomes, where they are encoded in tail protein regions. This roughly 80-residue domain described here usually begins between residue 100 and 250. Many members are known or predicted to act as phage tail tape measure proteins, a minor tail component that regulates tail length.
Probab=24.30 E-value=77 Score=22.82 Aligned_cols=26 Identities=31% Similarity=0.470 Sum_probs=20.9
Q ss_pred HHHHHHHhCCCHHHHHHHHHhhhhcCceEE
Q psy4458 220 LQRMCDLLGLPIEETEEFLSSMVVSKTITA 249 (303)
Q Consensus 220 l~~la~ll~ls~~~vE~~l~~mI~~~~l~a 249 (303)
+..||+.+|+|..+ +-+|+.+|+|.+
T Consensus 47 ~~~lAk~~G~t~~~----l~~~~~~Gkit~ 72 (75)
T TIGR02675 47 LQALAKAMGVTRGE----LRKMLSDGKLTA 72 (75)
T ss_pred HHHHHHHhCCCHHH----HHHHHHCCCCcc
Confidence 45788999999876 578888998865
No 281
>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A.
Probab=24.15 E-value=1.6e+02 Score=17.18 Aligned_cols=29 Identities=7% Similarity=-0.091 Sum_probs=22.7
Q ss_pred HHHHHHHHHHhhcchhHHHHHHHHhhhhc
Q psy4458 34 LILEQMRLCLAKKDYIRTQIISKKINTKF 62 (303)
Q Consensus 34 ~~L~~~rL~L~~~D~~~a~~~~~ki~~~~ 62 (303)
.+-.++.++...|++..|..+..++-...
T Consensus 4 ~~~~la~~~~~~g~~~~A~~~~~~al~~~ 32 (42)
T PF13374_consen 4 ALNNLANAYRAQGRYEEALELLEEALEIR 32 (42)
T ss_dssp HHHHHHHHHHHCT-HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhhhhcchhhHHHHHHHHHH
Confidence 45567888999999999999999886654
No 282
>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=23.86 E-value=1.2e+02 Score=15.48 Aligned_cols=26 Identities=15% Similarity=0.085 Sum_probs=21.1
Q ss_pred HHHHHHHHHHhhhHHHHHHHHHHHHc
Q psy4458 78 YRLMIELDQHEGSYLATCKHYRAILT 103 (303)
Q Consensus 78 ~~~~~~~~~~~~~f~eaa~~y~e~~~ 103 (303)
+..++..+...++|.+|...|..+..
T Consensus 4 ~~~~a~~~~~~~~~~~a~~~~~~~~~ 29 (34)
T smart00028 4 LYNLGNAYLKLGDYDEALEYYEKALE 29 (34)
T ss_pred HHHHHHHHHHHhhHHHHHHHHHHHHc
Confidence 44578888889999999999988864
No 283
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=23.70 E-value=98 Score=26.76 Aligned_cols=32 Identities=22% Similarity=0.353 Sum_probs=28.9
Q ss_pred eeeHHHHHHHhCCCHHHHHHHHHhhhhcCceE
Q psy4458 217 RITLQRMCDLLGLPIEETEEFLSSMVVSKTIT 248 (303)
Q Consensus 217 ~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~ 248 (303)
.+|-+.||+.+|++.+-+=+.+.+|-.+|.|.
T Consensus 184 ~lt~~~iA~~lG~sr~tvsR~l~~l~~~g~I~ 215 (235)
T PRK11161 184 TMTRGDIGNYLGLTVETISRLLGRFQKSGMLA 215 (235)
T ss_pred cccHHHHHHHhCCcHHHHHHHHHHHHHCCCEE
Confidence 36788999999999999999999999998775
No 284
>PLN03218 maturation of RBCL 1; Provisional
Probab=23.70 E-value=1e+03 Score=26.32 Aligned_cols=64 Identities=11% Similarity=0.146 Sum_probs=47.3
Q ss_pred HHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHcC
Q psy4458 33 TLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIELDQHEGSYLATCKHYRAILTT 104 (303)
Q Consensus 33 ~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~~~~~~~~f~eaa~~y~e~~~t 104 (303)
..+-..+..|...|++..|..+.++....-.. | + ...|..++..+...+++.+|...|.+....
T Consensus 615 ~tynsLI~ay~k~G~~deAl~lf~eM~~~Gv~---P-D----~~TynsLI~a~~k~G~~eeA~~l~~eM~k~ 678 (1060)
T PLN03218 615 EVYTIAVNSCSQKGDWDFALSIYDDMKKKGVK---P-D----EVFFSALVDVAGHAGDLDKAFEILQDARKQ 678 (1060)
T ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC---C-C----HHHHHHHHHHHHhCCCHHHHHHHHHHHHHc
Confidence 45666777888899999999988887653211 1 1 334567778888899999999999988643
No 285
>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=23.64 E-value=1.7e+02 Score=24.81 Aligned_cols=40 Identities=20% Similarity=0.323 Sum_probs=34.4
Q ss_pred eeHHHHHHHhCCC-HHHHHHHHHhhhhcCceEEEecCCCce
Q psy4458 218 ITLQRMCDLLGLP-IEETEEFLSSMVVSKTITAKIDRPAGI 257 (303)
Q Consensus 218 Itl~~la~ll~ls-~~~vE~~l~~mI~~~~l~akIDq~~gi 257 (303)
.|...||+.+|++ ..-+-..|..|...|-|...=.+..|+
T Consensus 26 ~~~~ela~~~~~~s~~tv~~~l~~L~~~g~i~~~~~~~~~~ 66 (199)
T TIGR00498 26 PSIREIARAVGLRSPSAAEEHLKALERKGYIERDPGKPRAI 66 (199)
T ss_pred CcHHHHHHHhCCCChHHHHHHHHHHHHCCCEecCCCCCCeE
Confidence 7899999999998 999999999999999987765555444
No 286
>TIGR02366 DHAK_reg probable dihydroxyacetone kinase regulator. The seed alignment for this family was built from a set of closely related uncharacterized proteins associated with operons for the type of bacterial dihydroxyacetone kinase that transfers PEP-derived phosphate from a phosphoprotein, as in phosphotransferase system transport, rather than from ATP. Members have a TetR transcriptional regulator domain (pfam00440) at the N-terminus and sequence homology throughout.
Probab=23.63 E-value=94 Score=25.49 Aligned_cols=29 Identities=3% Similarity=0.201 Sum_probs=23.1
Q ss_pred HHHHHHHHHHHHHHhhhceeeHHHHHHHhCCC
Q psy4458 199 LKHRVVEHNIRVMAKYYTRITLQRMCDLLGLP 230 (303)
Q Consensus 199 l~~~i~ehNi~~isk~Y~~Itl~~la~ll~ls 230 (303)
+..++.+ +.-.++|..||++.|++.-|++
T Consensus 8 I~~a~~~---Ll~~k~~~~ITV~~I~~~Agvs 36 (176)
T TIGR02366 8 IAKAFKD---LMEVQAFSKISVSDIMSTAQIR 36 (176)
T ss_pred HHHHHHH---HHHHCCCccCCHHHHHHHhCCC
Confidence 4444454 5556889999999999999999
No 287
>KOG2002|consensus
Probab=23.46 E-value=9.9e+02 Score=26.08 Aligned_cols=137 Identities=17% Similarity=0.122 Sum_probs=80.6
Q ss_pred HHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcc---hHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHcCCCCCC
Q psy4458 33 TLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDD---VQELKLKYYRLMIELDQHEGSYLATCKHYRAILTTPCIQS 109 (303)
Q Consensus 33 ~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~---~~e~k~~y~~~~~~~~~~~~~f~eaa~~y~e~~~t~~~~~ 109 (303)
+..=-++=+.+..|++..|....+++...+.+..+.+ ...+-+.|- .++..-+-++|-.|...|.++..-..
T Consensus 453 E~LNNvaslhf~~g~~~~A~~~f~~A~~~~~~~~n~de~~~~~lt~~YN--larl~E~l~~~~~A~e~Yk~Ilkehp--- 527 (1018)
T KOG2002|consen 453 EVLNNVASLHFRLGNIEKALEHFKSALGKLLEVANKDEGKSTNLTLKYN--LARLLEELHDTEVAEEMYKSILKEHP--- 527 (1018)
T ss_pred HHHHhHHHHHHHhcChHHHHHHHHHHhhhhhhhcCccccccchhHHHHH--HHHHHHhhhhhhHHHHHHHHHHHHCc---
Confidence 3344566778888999999999999887753222210 122334554 78888899999999999999964321
Q ss_pred ChHHHHHHHHHHHHHHHhCCCCchhhHhHHHhhhhhhcCCchHHHHHHH-HhcCCcccCchHHHHHHHHhhcc
Q psy4458 110 DPVQRHAVLQNVVLYLMLAPYDNEQSDLTHRVLEDKLLNEIPLYKGLLQ-WFTNPELIKWSGLRQLYEEELFK 181 (303)
Q Consensus 110 ~~~~~~~~L~~~v~~~iLs~~~~~r~~ll~~l~~~~~~~~~p~~~~L~~-~f~~~~li~~~~~~~~~~~~L~~ 181 (303)
..+.+.-.+.-.+.....-++-+.+++.... .....|..+.|+- .|+.+. .|....+.|+..++.
T Consensus 528 ---~YId~ylRl~~ma~~k~~~~ea~~~lk~~l~--~d~~np~arsl~G~~~l~k~--~~~~a~k~f~~i~~~ 593 (1018)
T KOG2002|consen 528 ---GYIDAYLRLGCMARDKNNLYEASLLLKDALN--IDSSNPNARSLLGNLHLKKS--EWKPAKKKFETILKK 593 (1018)
T ss_pred ---hhHHHHHHhhHHHHhccCcHHHHHHHHHHHh--cccCCcHHHHHHHHHHHhhh--hhcccccHHHHHHhh
Confidence 1344433332122222333455555655553 1244666666655 776665 354444556665554
No 288
>cd08311 Death_p75NR Death domain of p75 Neurotophin Receptor. Death Domain (DD) found in p75 neurotrophin receptor (p75NTR, NGFR, TNFRSF16). p75NTR binds members of the neurotrophin (NT) family including nerve growth factor (NGF), brain-derived neurotrophic factor (BDNF), and NT3, among others. It contains an NT-binding extracellular region that bears four cysteine-rich repeats, a transmembrane domain, and an intracellular DD. p75NTR plays roles in the immune, vascular, and nervous systems, and has been shown to promote cell death or survival, and to induce neurite outgrowth or collapse depending on its ligands and co-receptors. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptor
Probab=23.38 E-value=1.7e+02 Score=21.21 Aligned_cols=45 Identities=22% Similarity=0.386 Sum_probs=31.2
Q ss_pred HHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCCCceEEeccCCChhHHHHHHHHH----HHHHHHHHHHH
Q psy4458 221 QRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAGIINFARNKDPGEILNEWSAS----LNELMKLVNNT 287 (303)
Q Consensus 221 ~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~giV~f~~~~~~~~~l~~w~~~----i~~l~~~v~~~ 287 (303)
..||..||++..+++.+-.+ +++....|..|..+ +..|++.+.++
T Consensus 19 ~~LA~~LG~~~~~I~~i~~~----------------------~~p~~~lL~~W~~r~~ATv~~L~~aL~~i 67 (77)
T cd08311 19 RSLAGELGYEDEAIDTFGRE----------------------ESPVRTLLADWSAQEGATLDALCTALRRI 67 (77)
T ss_pred HHHHHHcCCCHHHHHHHHcC----------------------hhHHHHHHHHHHHCcCchHHHHHHHHHHc
Confidence 57899999999999887533 13456789999875 44445444443
No 289
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 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. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=23.30 E-value=1e+02 Score=20.00 Aligned_cols=20 Identities=15% Similarity=0.280 Sum_probs=15.3
Q ss_pred eHHHHHHHhCCCHHHHHHHH
Q psy4458 219 TLQRMCDLLGLPIEETEEFL 238 (303)
Q Consensus 219 tl~~la~ll~ls~~~vE~~l 238 (303)
||..||+..|+|+.-|-..|
T Consensus 1 Ti~dIA~~agvS~~TVSr~l 20 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVL 20 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHH
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 68899999999987654433
No 290
>KOG2034|consensus
Probab=23.20 E-value=1.7e+02 Score=31.16 Aligned_cols=57 Identities=12% Similarity=0.159 Sum_probs=41.2
Q ss_pred HHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHcCC
Q psy4458 37 EQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIELDQHEGSYLATCKHYRAILTTP 105 (303)
Q Consensus 37 ~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~~~~~~~~f~eaa~~y~e~~~t~ 105 (303)
..-|+||..|+|..|-.+-+-- .+-...-+.-+|.++-+.++|..||.+|-+++..|
T Consensus 363 ~vWk~yLd~g~y~kAL~~ar~~------------p~~le~Vl~~qAdf~f~~k~y~~AA~~yA~t~~~F 419 (911)
T KOG2034|consen 363 DVWKTYLDKGEFDKALEIARTR------------PDALETVLLKQADFLFQDKEYLRAAEIYAETLSSF 419 (911)
T ss_pred HHHHHHHhcchHHHHHHhccCC------------HHHHHHHHHHHHHHHHhhhHHHHHHHHHHHhhhhH
Confidence 3568999999999887554311 12223344457888899999999999999996554
No 291
>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=23.16 E-value=1e+02 Score=18.93 Aligned_cols=38 Identities=24% Similarity=0.321 Sum_probs=26.3
Q ss_pred eHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCCCceEEec
Q psy4458 219 TLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAGIINFA 261 (303)
Q Consensus 219 tl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~giV~f~ 261 (303)
|+..+|+.+|+|+.-+ -.++..|.+.+.- ..+|...|.
T Consensus 2 s~~e~a~~lgvs~~tl----~~~~~~g~~~~~~-~~~~~~~~~ 39 (49)
T cd04762 2 TTKEAAELLGVSPSTL----RRWVKEGKLKAIR-TPGGHRRFP 39 (49)
T ss_pred CHHHHHHHHCcCHHHH----HHHHHcCCCCcee-CCCCceecC
Confidence 6789999999998764 4556678876642 234555554
No 292
>PRK04841 transcriptional regulator MalT; Provisional
Probab=23.01 E-value=4.3e+02 Score=27.89 Aligned_cols=98 Identities=11% Similarity=0.021 Sum_probs=56.8
Q ss_pred cCCHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHHH
Q psy4458 5 EGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIEL 84 (303)
Q Consensus 5 ~~~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~~ 84 (303)
.|++++|...+...--.....-+...........+.+++..||+..|.....++-......++++.+ ........++..
T Consensus 504 ~G~~~~A~~~~~~al~~~~~~g~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~-~~~~~~~~la~~ 582 (903)
T PRK04841 504 KGELARALAMMQQTEQMARQHDVYHYALWSLLQQSEILFAQGFLQAAYETQEKAFQLIEEQHLEQLP-MHEFLLRIRAQL 582 (903)
T ss_pred cCCHHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhcccccc-HHHHHHHHHHHH
Confidence 5777777776655432111111222334455677888999999999999988876654222210011 111123356666
Q ss_pred HHHhhhHHHHHHHHHHHHc
Q psy4458 85 DQHEGSYLATCKHYRAILT 103 (303)
Q Consensus 85 ~~~~~~f~eaa~~y~e~~~ 103 (303)
+...+++-+|...+.+...
T Consensus 583 ~~~~G~~~~A~~~~~~al~ 601 (903)
T PRK04841 583 LWEWARLDEAEQCARKGLE 601 (903)
T ss_pred HHHhcCHHHHHHHHHHhHH
Confidence 7777888887777776654
No 293
>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=22.78 E-value=2.6e+02 Score=19.16 Aligned_cols=34 Identities=18% Similarity=0.314 Sum_probs=28.4
Q ss_pred hceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceE
Q psy4458 215 YTRITLQRMCDLLGLPIEETEEFLSSMVVSKTIT 248 (303)
Q Consensus 215 Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~ 248 (303)
+-+.|+.+|.+..++|+.++-+-++-||.-|-+.
T Consensus 25 ~G~ltl~~i~~~t~l~~~~Vk~~L~~LiQh~~v~ 58 (62)
T PF08221_consen 25 RGRLTLREIVRRTGLSPKQVKKALVVLIQHNLVQ 58 (62)
T ss_dssp C-SEEHHHHHHHHT--HHHHHHHHHHHHHTTSEE
T ss_pred cCCcCHHHHHHHhCCCHHHHHHHHHHHHHcCCee
Confidence 7899999999999999999999999999887653
No 294
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=22.29 E-value=1.4e+02 Score=26.88 Aligned_cols=35 Identities=14% Similarity=0.156 Sum_probs=31.6
Q ss_pred hceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEE
Q psy4458 215 YTRITLQRMCDLLGLPIEETEEFLSSMVVSKTITA 249 (303)
Q Consensus 215 Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~a 249 (303)
-..+++++||+.+|+|..-+-.++..|+..|-+.-
T Consensus 38 ~~~~tl~eIa~~lglpkStv~RlL~tL~~~G~l~~ 72 (271)
T PRK10163 38 GGSSSVSDISLNLDLPLSTTFRLLKVLQAADFVYQ 72 (271)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence 35689999999999999999999999999998843
No 295
>PF13217 DUF4025: Protein of unknown function (DUF4025)
Probab=21.81 E-value=42 Score=22.91 Aligned_cols=24 Identities=33% Similarity=0.339 Sum_probs=20.1
Q ss_pred HHHHHHHHhhhhcCceEEEecCCC
Q psy4458 232 EETEEFLSSMVVSKTITAKIDRPA 255 (303)
Q Consensus 232 ~~vE~~l~~mI~~~~l~akIDq~~ 255 (303)
......+++...+|.|.|+||+.+
T Consensus 31 A~ThEQVSD~Y~EGTiD~~l~~~~ 54 (55)
T PF13217_consen 31 AVTHEQVSDTYAEGTIDAKLDQEN 54 (55)
T ss_pred HHHHHHHHHHHhhhhHhhhhhccc
Confidence 345667899999999999999876
No 296
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=21.79 E-value=1e+02 Score=19.62 Aligned_cols=32 Identities=6% Similarity=0.130 Sum_probs=19.5
Q ss_pred hhceeeHHHHHHHhCCCHHHHHHHHHhhhhcC
Q psy4458 214 YYTRITLQRMCDLLGLPIEETEEFLSSMVVSK 245 (303)
Q Consensus 214 ~Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~ 245 (303)
+..-.|...+|+.||+|+.-|-..+...-..|
T Consensus 14 ~~~G~s~~~ia~~lgvs~~Tv~~w~kr~~~~G 45 (50)
T PF13384_consen 14 LREGWSIREIAKRLGVSRSTVYRWIKRYREEG 45 (50)
T ss_dssp HHHT--HHHHHHHHTS-HHHHHHHHT------
T ss_pred HHCCCCHHHHHHHHCcCHHHHHHHHHHccccc
Confidence 34478999999999999999888877665544
No 297
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=21.79 E-value=1.1e+02 Score=19.12 Aligned_cols=38 Identities=11% Similarity=0.134 Sum_probs=26.0
Q ss_pred eHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCCCceEEec
Q psy4458 219 TLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAGIINFA 261 (303)
Q Consensus 219 tl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~giV~f~ 261 (303)
+++.+|+++|+|+.-+.. .+..|.+.+.-+. +|.-.|.
T Consensus 2 ~~~e~a~~~gv~~~tlr~----~~~~g~l~~~~~~-~~~~~y~ 39 (49)
T cd04761 2 TIGELAKLTGVSPSTLRY----YERIGLLSPARTE-GGYRLYS 39 (49)
T ss_pred cHHHHHHHHCcCHHHHHH----HHHCCCCCCCcCC-CCCEEeC
Confidence 678999999999987654 4677777643322 2555554
No 298
>PF14493 HTH_40: Helix-turn-helix domain
Probab=21.77 E-value=1.1e+02 Score=22.57 Aligned_cols=32 Identities=13% Similarity=0.254 Sum_probs=29.8
Q ss_pred hceeeHHHHHHHhCCCHHHHHHHHHhhhhcCc
Q psy4458 215 YTRITLQRMCDLLGLPIEETEEFLSSMVVSKT 246 (303)
Q Consensus 215 Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~ 246 (303)
=...|++.||+.-|+++.-|...|++++..|.
T Consensus 11 ~~G~si~eIA~~R~L~~sTI~~HL~~~~~~g~ 42 (91)
T PF14493_consen 11 QKGLSIEEIAKIRGLKESTIYGHLAELIESGE 42 (91)
T ss_pred HcCCCHHHHHHHcCCCHHHHHHHHHHHHHhCC
Confidence 35789999999999999999999999999997
No 299
>TIGR00122 birA_repr_reg BirA biotin operon repressor domain. This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.
Probab=21.68 E-value=1.3e+02 Score=20.72 Aligned_cols=31 Identities=6% Similarity=0.145 Sum_probs=27.4
Q ss_pred eeHHHHHHHhCCCHHHHHHHHHhhhhcCceE
Q psy4458 218 ITLQRMCDLLGLPIEETEEFLSSMVVSKTIT 248 (303)
Q Consensus 218 Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~ 248 (303)
.+.+.||+.+|+|..-+-..+..|-..|-.-
T Consensus 14 ~~~~eLa~~l~vS~~tv~~~l~~L~~~g~~i 44 (69)
T TIGR00122 14 FSGEKLGEALGMSRTAVNKHIQTLREWGVDV 44 (69)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHHCCCeE
Confidence 4689999999999999999999998887643
No 300
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=21.62 E-value=1.7e+02 Score=22.89 Aligned_cols=34 Identities=15% Similarity=0.266 Sum_probs=28.1
Q ss_pred HHHHHhhhceeeHHHHHHHhCCCHHHHHHHHHhh
Q psy4458 208 IRVMAKYYTRITLQRMCDLLGLPIEETEEFLSSM 241 (303)
Q Consensus 208 i~~isk~Y~~Itl~~la~ll~ls~~~vE~~l~~m 241 (303)
+....+-+.-+|+.+||+.||+|+.-+-..+-+|
T Consensus 62 L~~~v~~~pd~tl~Ela~~l~Vs~~ti~~~Lkrl 95 (119)
T PF01710_consen 62 LKALVEENPDATLRELAERLGVSPSTIWRALKRL 95 (119)
T ss_pred HHHHHHHCCCcCHHHHHHHcCCCHHHHHHHHHHc
Confidence 4555556999999999999999999888877665
No 301
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=21.31 E-value=81 Score=21.92 Aligned_cols=19 Identities=21% Similarity=0.450 Sum_probs=16.6
Q ss_pred eeeHHHHHHHhCCCHHHHH
Q psy4458 217 RITLQRMCDLLGLPIEETE 235 (303)
Q Consensus 217 ~Itl~~la~ll~ls~~~vE 235 (303)
.|++..||+.||+|+..|-
T Consensus 22 ~i~lkdIA~~Lgvs~~tIr 40 (60)
T PF10668_consen 22 KIKLKDIAEKLGVSESTIR 40 (60)
T ss_pred CccHHHHHHHHCCCHHHHH
Confidence 7999999999999987654
No 302
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=21.22 E-value=2.7e+02 Score=21.08 Aligned_cols=30 Identities=20% Similarity=0.248 Sum_probs=25.9
Q ss_pred eeHHHHHHHhCCCHHHHHHHHHhhhhcCce
Q psy4458 218 ITLQRMCDLLGLPIEETEEFLSSMVVSKTI 247 (303)
Q Consensus 218 Itl~~la~ll~ls~~~vE~~l~~mI~~~~l 247 (303)
=.-..||..+++|.++|+..+-++...|-|
T Consensus 22 Dy~k~ia~~l~~~~~~v~~~l~~Le~~GLl 51 (92)
T PF10007_consen 22 DYAKSIARRLKIPLEEVREALEKLEEMGLL 51 (92)
T ss_pred CcHHHHHHHHCCCHHHHHHHHHHHHHCCCe
Confidence 345668899999999999999999999865
No 303
>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional
Probab=20.77 E-value=7.3e+02 Score=27.17 Aligned_cols=48 Identities=10% Similarity=-0.110 Sum_probs=27.1
Q ss_pred cchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHc
Q psy4458 46 KDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIELDQHEGSYLATCKHYRAILT 103 (303)
Q Consensus 46 ~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~~~~~~~~f~eaa~~y~e~~~ 103 (303)
|++..|.....++-.... + ...+.-.+..+...+++-+|-..|..+..
T Consensus 590 Gr~~eAl~~~~~AL~l~P------~----~~a~~~LA~~l~~lG~~deA~~~l~~AL~ 637 (987)
T PRK09782 590 GQPELALNDLTRSLNIAP------S----ANAYVARATIYRQRHNVPAAVSDLRAALE 637 (987)
T ss_pred CCHHHHHHHHHHHHHhCC------C----HHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 677777766666654331 1 11223445566666666666666666654
No 304
>PF11972 HTH_13: HTH DNA binding domain; InterPro: IPR021068 The proteins in this entry have not been characterised. They contain a C-terminal helix-turn-helix DNA binding domain.
Probab=20.58 E-value=1.3e+02 Score=20.43 Aligned_cols=32 Identities=6% Similarity=0.296 Sum_probs=25.3
Q ss_pred HHHhhhceeeHHHHHHHhCCCHHHHHHHHHhhhh
Q psy4458 210 VMAKYYTRITLQRMCDLLGLPIEETEEFLSSMVV 243 (303)
Q Consensus 210 ~isk~Y~~Itl~~la~ll~ls~~~vE~~l~~mI~ 243 (303)
.+++|. ||...+++.+|+|+.-+.+++.++-.
T Consensus 8 l~~~P~--Vsa~mva~~L~vT~~~A~~li~eLg~ 39 (54)
T PF11972_consen 8 LLSRPL--VSAPMVAKELGVTPQAAQRLIAELGL 39 (54)
T ss_pred HHhCcc--ccHHHHHHHhCCCHHHHHHHHHHhhc
Confidence 344444 77888999999999999999877655
No 305
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=20.49 E-value=1.8e+02 Score=24.57 Aligned_cols=36 Identities=17% Similarity=0.218 Sum_probs=27.3
Q ss_pred HHHHHHHHHHHHHHHH-hhhceeeHHHHHHHhCCCHH
Q psy4458 197 KMLKHRVVEHNIRVMA-KYYTRITLQRMCDLLGLPIE 232 (303)
Q Consensus 197 ~~l~~~i~ehNi~~is-k~Y~~Itl~~la~ll~ls~~ 232 (303)
...+.+|++-=+..++ +-|..+|++.||+..|+|..
T Consensus 10 ~~~r~~Il~aa~~lf~~~G~~~~ti~~Ia~~agvsk~ 46 (213)
T PRK09975 10 LKTRQELIETAIAQFALRGVSNTTLNDIADAANVTRG 46 (213)
T ss_pred HHHHHHHHHHHHHHHHHcCcccCCHHHHHHHcCCCHH
Confidence 3445566666666665 55999999999999999955
No 306
>PF04053 Coatomer_WDAD: Coatomer WD associated region ; InterPro: IPR006692 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 WD-associated region found in coatomer subunits alpha, beta and beta' subunits. The alpha-subunit (RET1P) of the coatomer complex in Saccharomyces cerevisiae (Baker's yeast), participates in membrane transport between the endoplasmic reticulum and Golgi apparatus. The protein contains six WD-40 repeat motifs in its N-terminal region []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030117 membrane coat; PDB: 3MKQ_B.
Probab=20.43 E-value=8.2e+02 Score=23.98 Aligned_cols=80 Identities=10% Similarity=0.023 Sum_probs=52.0
Q ss_pred cCCHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhc---c--CCCCcchHHHHHHHHH
Q psy4458 5 EGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKF---F--DDEKDDVQELKLKYYR 79 (303)
Q Consensus 5 ~~~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~---~--~~~~~~~~e~k~~y~~ 79 (303)
.|+++.|.++..+++- -+.+-+.+..+|..||+.-|+....|++..- + ...| +. ..-.
T Consensus 331 lg~L~~A~~~a~~~~~-----------~~~W~~Lg~~AL~~g~~~lAe~c~~k~~d~~~L~lLy~~~g--~~----~~L~ 393 (443)
T PF04053_consen 331 LGNLDIALEIAKELDD-----------PEKWKQLGDEALRQGNIELAEECYQKAKDFSGLLLLYSSTG--DR----EKLS 393 (443)
T ss_dssp CT-HHHHHHHCCCCST-----------HHHHHHHHHHHHHTTBHHHHHHHHHHCT-HHHHHHHHHHCT---H----HHHH
T ss_pred cCCHHHHHHHHHhcCc-----------HHHHHHHHHHHHHcCCHHHHHHHHHhhcCccccHHHHHHhC--CH----HHHH
Confidence 4677777777766652 2277888999999999999999998886321 0 1122 11 1112
Q ss_pred HHHHHHHHhhhHHHHHHHHHHH
Q psy4458 80 LMIELDQHEGSYLATCKHYRAI 101 (303)
Q Consensus 80 ~~~~~~~~~~~f~eaa~~y~e~ 101 (303)
.++......+++.-|+.+++-+
T Consensus 394 kl~~~a~~~~~~n~af~~~~~l 415 (443)
T PF04053_consen 394 KLAKIAEERGDINIAFQAALLL 415 (443)
T ss_dssp HHHHHHHHTT-HHHHHHHHHHH
T ss_pred HHHHHHHHccCHHHHHHHHHHc
Confidence 3556677788888888888877
No 307
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=20.39 E-value=2.1e+02 Score=19.30 Aligned_cols=27 Identities=15% Similarity=0.250 Sum_probs=22.5
Q ss_pred hceeeHHHHHHHhCCCHHHHHHHHHhh
Q psy4458 215 YTRITLQRMCDLLGLPIEETEEFLSSM 241 (303)
Q Consensus 215 Y~~Itl~~la~ll~ls~~~vE~~l~~m 241 (303)
-..++++.||+.+|+|.--+-..+..+
T Consensus 17 ~~~~~~~ela~~l~~S~rti~~~i~~L 43 (59)
T PF08280_consen 17 NKWITLKELAKKLNISERTIKNDINEL 43 (59)
T ss_dssp HTSBBHHHHHHHCTS-HHHHHHHHHHH
T ss_pred CCCCcHHHHHHHHCCCHHHHHHHHHHH
Confidence 678999999999999998888777665
No 308
>PRK10866 outer membrane biogenesis protein BamD; Provisional
Probab=20.31 E-value=6e+02 Score=22.41 Aligned_cols=134 Identities=10% Similarity=0.096 Sum_probs=0.0
Q ss_pred ccCCHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHH-----------
Q psy4458 4 DEGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQE----------- 72 (303)
Q Consensus 4 ~~~~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e----------- 72 (303)
..|++++|.+.+..+.-.-.++ +..... .+..+..++..+||..|....++.-....+... ...
T Consensus 44 ~~g~y~~Ai~~f~~l~~~yP~s-~~a~~a--~l~la~ayy~~~~y~~A~~~~e~fi~~~P~~~~--~~~a~Y~~g~~~~~ 118 (243)
T PRK10866 44 QDGNWKQAITQLEALDNRYPFG-PYSQQV--QLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPN--IDYVLYMRGLTNMA 118 (243)
T ss_pred HCCCHHHHHHHHHHHHHhCCCC-hHHHHH--HHHHHHHHHhcCCHHHHHHHHHHHHHhCcCCCc--hHHHHHHHHHhhhh
Q ss_pred ---------------------HHHHHHHHH---------------------------------HHHHHHhhhHHHHHHHH
Q psy4458 73 ---------------------LKLKYYRLM---------------------------------IELDQHEGSYLATCKHY 98 (303)
Q Consensus 73 ---------------------~k~~y~~~~---------------------------------~~~~~~~~~f~eaa~~y 98 (303)
.+..+..+. +++|...++|..|..+|
T Consensus 119 ~~~~~~~~~~~~~~~~rD~~~~~~A~~~~~~li~~yP~S~ya~~A~~rl~~l~~~la~~e~~ia~~Y~~~~~y~AA~~r~ 198 (243)
T PRK10866 119 LDDSALQGFFGVDRSDRDPQHARAAFRDFSKLVRGYPNSQYTTDATKRLVFLKDRLAKYELSVAEYYTKRGAYVAVVNRV 198 (243)
T ss_pred cchhhhhhccCCCccccCHHHHHHHHHHHHHHHHHCcCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCchHHHHHHH
Q ss_pred HHHHcCCCCCCChHHHHHHHHHHHHHHHhCCCCchhhHhHHHhhhhh
Q psy4458 99 RAILTTPCIQSDPVQRHAVLQNVVLYLMLAPYDNEQSDLTHRVLEDK 145 (303)
Q Consensus 99 ~e~~~t~~~~~~~~~~~~~L~~~v~~~iLs~~~~~r~~ll~~l~~~~ 145 (303)
..+.+.+. +....-.+|-.++-.-.-.+...+-......+..+.
T Consensus 199 ~~v~~~Yp---~t~~~~eal~~l~~ay~~lg~~~~a~~~~~~l~~n~ 242 (243)
T PRK10866 199 EQMLRDYP---DTQATRDALPLMENAYRQLQLNAQADKVAKIIAANS 242 (243)
T ss_pred HHHHHHCC---CCchHHHHHHHHHHHHHHcCChHHHHHHHHHHhcCC
No 309
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=20.28 E-value=92 Score=21.27 Aligned_cols=39 Identities=13% Similarity=0.235 Sum_probs=27.1
Q ss_pred eHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCCCceEEecc
Q psy4458 219 TLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAGIINFAR 262 (303)
Q Consensus 219 tl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~giV~f~~ 262 (303)
|+..+|+++|+|+..+-.. ...|.+.... ..+|.-.|..
T Consensus 2 ti~eva~~~gvs~~tlr~y----~~~gll~~~~-~~~g~r~y~~ 40 (69)
T PF13411_consen 2 TIKEVAKLLGVSPSTLRYY----EREGLLPPPR-DENGYRYYSE 40 (69)
T ss_dssp EHHHHHHHTTTTHHHHHHH----HHTTSSTTBE-STTSSEEE-H
T ss_pred cHHHHHHHHCcCHHHHHHH----HHhcCccccc-ccCceeeccH
Confidence 6889999999999876655 4556565544 5666666663
No 310
>PF13118 DUF3972: Protein of unknown function (DUF3972)
Probab=20.17 E-value=2.6e+02 Score=22.51 Aligned_cols=34 Identities=21% Similarity=0.300 Sum_probs=25.0
Q ss_pred HHHHhCCCHHHHHHHHHhhhhcCceEEEecCCCceEEecc
Q psy4458 223 MCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAGIINFAR 262 (303)
Q Consensus 223 la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~giV~f~~ 262 (303)
.+++.|++.+. +-.||.+|.|.+|. .+|.+...-
T Consensus 2 F~~l~~L~~~~----v~~~i~~g~l~~K~--e~g~~~Ie~ 35 (126)
T PF13118_consen 2 FAKLTGLDREA----VLELIKRGKLKSKN--EDGKIYIEA 35 (126)
T ss_pred hHHHhCCCHHH----HHHHHhcCCccccc--cCCeEEEEc
Confidence 47788999776 45688899999988 566655543
No 311
>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=20.15 E-value=6.6e+02 Score=24.71 Aligned_cols=78 Identities=13% Similarity=0.027 Sum_probs=50.9
Q ss_pred ccCCHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHHHHH
Q psy4458 4 DEGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIE 83 (303)
Q Consensus 4 ~~~~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~~~~ 83 (303)
..|++++|...++..- ++...+..- +.=.+.+++-.++...||.+|..+..+.... . .| -|--|.-..|-
T Consensus 279 ~~g~~~~Ai~~~~~a~-~~q~~~~Ql-~~l~~~El~w~~~~~~~w~~A~~~f~~L~~~-----s--~W-Ska~Y~Y~~a~ 348 (468)
T PF10300_consen 279 LKGNLEEAIESFERAI-ESQSEWKQL-HHLCYFELAWCHMFQHDWEEAAEYFLRLLKE-----S--KW-SKAFYAYLAAA 348 (468)
T ss_pred HhcCHHHHHHHHHHhc-cchhhHHhH-HHHHHHHHHHHHHHHchHHHHHHHHHHHHhc-----c--cc-HHHHHHHHHHH
Confidence 4699999999999532 332333322 2345789999999999999999888877742 2 57 34444444444
Q ss_pred HHHHhhhH
Q psy4458 84 LDQHEGSY 91 (303)
Q Consensus 84 ~~~~~~~f 91 (303)
.+...++.
T Consensus 349 c~~~l~~~ 356 (468)
T PF10300_consen 349 CLLMLGRE 356 (468)
T ss_pred HHHhhccc
Confidence 44444444
No 312
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=20.08 E-value=1.4e+02 Score=23.76 Aligned_cols=31 Identities=3% Similarity=0.088 Sum_probs=26.6
Q ss_pred HhhhceeeHHHHHHHhCCCHHHHHHHHHhhh
Q psy4458 212 AKYYTRITLQRMCDLLGLPIEETEEFLSSMV 242 (303)
Q Consensus 212 sk~Y~~Itl~~la~ll~ls~~~vE~~l~~mI 242 (303)
..++...|.+.||+.+|+|+.-|...+.+..
T Consensus 117 l~~~~~~s~~EIA~~l~is~~tV~~~~~ra~ 147 (154)
T PRK06759 117 ERFFVGKTMGEIALETEMTYYQVRWIYRQAL 147 (154)
T ss_pred HHHhcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3568999999999999999999998887643
No 313
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=20.04 E-value=5.1e+02 Score=21.41 Aligned_cols=75 Identities=23% Similarity=0.256 Sum_probs=46.6
Q ss_pred HHHHHhhhceeeHHHHHHHh--CCCHHHHHHHHHhhhhcCceEEEecCCCceEEeccCCC----hhHHHHHHHHHHHHHH
Q psy4458 208 IRVMAKYYTRITLQRMCDLL--GLPIEETEEFLSSMVVSKTITAKIDRPAGIINFARNKD----PGEILNEWSASLNELM 281 (303)
Q Consensus 208 i~~isk~Y~~Itl~~la~ll--~ls~~~vE~~l~~mI~~~~l~akIDq~~giV~f~~~~~----~~~~l~~w~~~i~~l~ 281 (303)
+..--+||+...+ ...| +++-..|.+.|-.++.+|+|.+|. -....|.|-..+. ..+.+...+..|..+-
T Consensus 10 ~~~qNRPys~~di---~~nL~~~~~K~~v~k~Ld~L~~~g~i~~K~-~GKqkiY~~~Q~~~~~~s~eel~~ld~ei~~L~ 85 (169)
T PF07106_consen 10 MKEQNRPYSAQDI---FDNLHNKVGKTAVQKALDSLVEEGKIVEKE-YGKQKIYFANQDELEVPSPEELAELDAEIKELR 85 (169)
T ss_pred HHHcCCCCcHHHH---HHHHHhhccHHHHHHHHHHHHhCCCeeeee-ecceEEEeeCccccCCCCchhHHHHHHHHHHHH
Confidence 3334468865544 4444 689999999999999999999984 3333455544321 1234555555555554
Q ss_pred HHHHH
Q psy4458 282 KLVNN 286 (303)
Q Consensus 282 ~~v~~ 286 (303)
..+..
T Consensus 86 ~el~~ 90 (169)
T PF07106_consen 86 EELAE 90 (169)
T ss_pred HHHHH
Confidence 44443
Done!