Query 025096
Match_columns 258
No_of_seqs 142 out of 626
Neff 7.7
Searched_HMMs 46136
Date Fri Mar 29 02:39:22 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025096.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025096hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2688 Transcription-associat 100.0 1.4E-59 3.1E-64 425.8 19.8 247 1-253 140-393 (394)
2 COG5600 Transcription-associat 100.0 1.9E-56 4.2E-61 397.8 21.5 246 2-252 155-411 (413)
3 KOG2581 26S proteasome regulat 100.0 1.6E-34 3.4E-39 259.8 17.2 212 15-243 206-422 (493)
4 KOG1464 COP9 signalosome, subu 99.8 3.7E-19 8E-24 154.6 14.7 211 13-245 186-410 (440)
5 PF01399 PCI: PCI domain; Int 99.7 2.7E-16 5.9E-21 119.0 12.5 103 129-244 2-105 (105)
6 KOG2908 26S proteasome regulat 99.4 5.2E-11 1.1E-15 106.3 18.7 217 15-246 112-341 (380)
7 KOG1463 26S proteasome regulat 99.1 1.2E-09 2.5E-14 97.8 14.5 208 20-243 170-389 (411)
8 KOG2582 COP9 signalosome, subu 99.1 4.6E-09 9.9E-14 94.7 15.4 177 55-250 177-365 (422)
9 COG5159 RPN6 26S proteasome re 98.8 1E-07 2.2E-12 84.0 13.0 202 23-243 170-387 (421)
10 smart00753 PAM PCI/PINT associ 98.5 5.4E-07 1.2E-11 66.2 7.7 66 164-246 6-71 (88)
11 smart00088 PINT motif in prote 98.5 5.4E-07 1.2E-11 66.2 7.7 66 164-246 6-71 (88)
12 KOG1497 COP9 signalosome, subu 98.0 0.00017 3.6E-09 64.8 13.7 216 15-251 141-369 (399)
13 KOG2753 Uncharacterized conser 98.0 6.8E-05 1.5E-09 67.3 10.2 99 130-245 240-340 (378)
14 PF10255 Paf67: RNA polymerase 97.7 0.0027 5.8E-08 59.4 16.0 193 13-223 118-345 (404)
15 KOG0687 26S proteasome regulat 97.0 0.042 9.1E-07 49.8 15.1 167 61-244 181-362 (393)
16 COG5187 RPN7 26S proteasome re 96.8 0.052 1.1E-06 48.6 14.1 168 60-244 191-376 (412)
17 KOG2758 Translation initiation 96.7 0.01 2.2E-07 53.6 8.5 75 154-245 321-395 (432)
18 KOG1498 26S proteasome regulat 96.6 0.18 3.9E-06 46.8 16.2 210 18-244 171-398 (439)
19 PF07719 TPR_2: Tetratricopept 96.5 0.0046 9.9E-08 36.3 3.7 32 62-93 2-33 (34)
20 KOG0686 COP9 signalosome, subu 96.4 0.067 1.4E-06 49.8 12.5 160 64-242 232-408 (466)
21 PF13432 TPR_16: Tetratricopep 96.2 0.028 6.1E-07 38.0 6.7 62 24-94 3-64 (65)
22 PF13371 TPR_9: Tetratricopept 95.9 0.028 6.1E-07 38.8 5.8 63 24-95 1-63 (73)
23 PF00515 TPR_1: Tetratricopept 94.7 0.05 1.1E-06 31.9 3.3 31 63-93 3-33 (34)
24 KOG1076 Translation initiation 94.4 0.38 8.2E-06 47.7 10.3 206 23-247 489-766 (843)
25 PF12895 Apc3: Anaphase-promot 93.6 0.17 3.7E-06 36.1 5.0 54 24-87 31-84 (84)
26 PF13414 TPR_11: TPR repeat; P 93.5 0.39 8.5E-06 32.5 6.5 62 21-92 6-69 (69)
27 PF13424 TPR_12: Tetratricopep 93.2 0.29 6.2E-06 34.2 5.6 71 17-91 4-76 (78)
28 COG5071 RPN5 26S proteasome re 92.9 7.1 0.00015 35.5 16.5 210 19-245 132-399 (439)
29 TIGR02552 LcrH_SycD type III s 92.8 0.82 1.8E-05 35.1 8.2 33 62-94 86-118 (135)
30 PF13181 TPR_8: Tetratricopept 92.4 0.23 4.9E-06 28.9 3.4 31 62-92 2-32 (34)
31 PF13174 TPR_6: Tetratricopept 92.1 0.21 4.5E-06 28.6 3.0 31 64-94 3-33 (33)
32 cd00189 TPR Tetratricopeptide 91.1 2.3 4.9E-05 28.5 8.1 64 23-95 5-68 (100)
33 PF09012 FeoC: FeoC like trans 90.8 0.34 7.4E-06 33.7 3.5 38 192-234 12-49 (69)
34 PRK15359 type III secretion sy 90.7 2.1 4.5E-05 34.0 8.5 34 61-94 92-125 (144)
35 PF14938 SNAP: Soluble NSF att 90.0 1.9 4.2E-05 38.2 8.6 112 13-154 150-262 (282)
36 KOG2072 Translation initiation 89.9 1.2 2.7E-05 44.9 7.6 71 166-249 427-497 (988)
37 PF13414 TPR_11: TPR repeat; P 89.4 0.81 1.8E-05 30.9 4.5 35 62-96 4-38 (69)
38 cd00189 TPR Tetratricopeptide 88.6 1.8 4E-05 29.0 6.0 64 20-92 36-99 (100)
39 PF13428 TPR_14: Tetratricopep 87.7 0.89 1.9E-05 28.3 3.5 32 64-95 4-35 (44)
40 TIGR02795 tol_pal_ybgF tol-pal 86.2 3.4 7.4E-05 30.3 6.6 29 64-92 79-107 (119)
41 smart00028 TPR Tetratricopepti 85.9 1.2 2.6E-05 23.7 3.1 30 63-92 3-32 (34)
42 KOG2300 Uncharacterized conser 85.7 8.4 0.00018 37.2 10.1 137 11-151 397-552 (629)
43 PF04733 Coatomer_E: Coatomer 85.4 1.9 4.2E-05 38.7 5.7 96 16-117 129-252 (290)
44 PF13176 TPR_7: Tetratricopept 84.1 1.4 3.1E-05 26.2 2.9 27 65-91 3-29 (36)
45 PF14559 TPR_19: Tetratricopep 83.4 1.5 3.3E-05 29.3 3.3 57 29-94 2-58 (68)
46 PF09976 TPR_21: Tetratricopep 82.6 3.2 6.9E-05 32.7 5.3 56 23-88 90-145 (145)
47 PF08631 SPO22: Meiosis protei 81.0 32 0.0007 30.3 11.7 82 29-111 4-95 (278)
48 TIGR02795 tol_pal_ybgF tol-pal 80.9 9.7 0.00021 27.8 7.2 66 23-94 7-72 (119)
49 TIGR02552 LcrH_SycD type III s 79.7 18 0.0004 27.3 8.6 65 21-94 20-84 (135)
50 PRK02603 photosystem I assembl 79.7 22 0.00048 28.7 9.5 76 13-94 30-105 (172)
51 PF13424 TPR_12: Tetratricopep 79.5 3.6 7.8E-05 28.4 4.1 32 60-91 4-35 (78)
52 KOG3250 COP9 signalosome, subu 77.8 3.2 6.9E-05 35.7 3.9 96 127-243 59-154 (258)
53 KOG3081 Vesicle coat complex C 77.2 20 0.00042 32.1 8.7 100 13-117 132-258 (299)
54 PF09756 DDRGK: DDRGK domain; 76.8 5.8 0.00012 33.4 5.2 48 193-245 112-159 (188)
55 TIGR02521 type_IV_pilW type IV 75.8 24 0.00053 28.4 8.8 70 17-95 30-99 (234)
56 PRK10370 formate-dependent nit 75.7 17 0.00038 30.4 7.9 80 16-95 14-107 (198)
57 PF13429 TPR_15: Tetratricopep 75.2 9.9 0.00021 33.2 6.6 68 21-95 113-180 (280)
58 PRK10803 tol-pal system protei 75.1 7.2 0.00016 34.5 5.6 62 28-95 153-214 (263)
59 PF10602 RPN7: 26S proteasome 74.8 11 0.00024 31.1 6.4 68 19-89 74-141 (177)
60 PF13374 TPR_10: Tetratricopep 74.8 3.8 8.2E-05 24.3 2.8 29 64-92 5-33 (42)
61 TIGR02521 type_IV_pilW type IV 74.2 30 0.00064 27.8 8.9 63 20-91 67-129 (234)
62 PF10075 PCI_Csn8: COP9 signal 73.9 9.3 0.0002 30.2 5.5 77 130-223 44-121 (143)
63 PRK11788 tetratricopeptide rep 73.4 22 0.00047 32.3 8.6 33 61-93 180-212 (389)
64 COG1522 Lrp Transcriptional re 72.9 7.8 0.00017 30.7 4.9 41 192-237 20-60 (154)
65 PRK11788 tetratricopeptide rep 72.7 21 0.00046 32.3 8.4 69 20-93 71-139 (389)
66 PF13412 HTH_24: Winged helix- 72.7 16 0.00034 23.0 5.4 33 193-230 16-48 (48)
67 PF02064 MAS20: MAS20 protein 71.3 12 0.00026 29.2 5.4 41 67-109 69-109 (121)
68 PRK11179 DNA-binding transcrip 71.0 9.6 0.00021 30.6 5.1 36 192-232 21-56 (153)
69 PRK11169 leucine-responsive tr 70.9 13 0.00028 30.2 5.9 39 191-234 25-63 (164)
70 PRK15363 pathogenicity island 70.8 11 0.00024 30.8 5.2 19 28-46 45-63 (157)
71 KOG4234 TPR repeat-containing 70.7 19 0.0004 31.1 6.7 89 67-156 101-195 (271)
72 PF13812 PPR_3: Pentatricopept 70.2 9.5 0.00021 21.5 3.7 29 20-48 3-31 (34)
73 PF10602 RPN7: 26S proteasome 70.1 50 0.0011 27.2 9.3 57 57-115 32-88 (177)
74 PLN03088 SGT1, suppressor of 69.4 19 0.00042 33.1 7.3 65 22-95 40-104 (356)
75 PF08784 RPA_C: Replication pr 68.8 12 0.00026 27.8 4.8 38 192-234 63-100 (102)
76 TIGR03302 OM_YfiO outer membra 68.8 20 0.00044 30.1 6.9 68 22-95 37-104 (235)
77 PF08672 APC2: Anaphase promot 67.7 9.5 0.00021 25.9 3.7 37 194-230 11-52 (60)
78 PRK11189 lipoprotein NlpI; Pro 67.6 11 0.00023 33.7 5.1 39 62-100 237-275 (296)
79 PRK10866 outer membrane biogen 67.1 85 0.0018 27.2 12.8 65 25-95 39-103 (243)
80 KOG4056 Translocase of outer m 67.0 6.6 0.00014 31.3 3.1 39 57-95 72-115 (143)
81 PF14853 Fis1_TPR_C: Fis1 C-te 66.3 10 0.00022 25.0 3.5 32 63-94 3-34 (53)
82 TIGR00990 3a0801s09 mitochondr 65.8 23 0.00051 34.8 7.5 28 65-92 471-498 (615)
83 smart00344 HTH_ASNC helix_turn 64.2 24 0.00053 26.1 5.8 35 193-232 16-50 (108)
84 PF01978 TrmB: Sugar-specific 63.6 37 0.00081 22.9 6.2 36 193-233 21-56 (68)
85 PRK15331 chaperone protein Sic 63.0 14 0.0003 30.5 4.4 36 64-99 108-143 (165)
86 PRK15359 type III secretion sy 62.3 57 0.0012 25.6 7.9 64 24-96 30-93 (144)
87 COG3063 PilF Tfp pilus assembl 61.8 45 0.00097 29.2 7.5 81 4-94 16-102 (250)
88 PF13041 PPR_2: PPR repeat fam 61.6 17 0.00037 22.8 3.9 31 19-49 4-34 (50)
89 PRK10803 tol-pal system protei 61.4 37 0.00081 30.0 7.3 68 23-96 185-252 (263)
90 TIGR00990 3a0801s09 mitochondr 61.3 42 0.00092 33.0 8.4 33 62-94 400-432 (615)
91 PF09976 TPR_21: Tetratricopep 61.0 22 0.00048 27.8 5.3 64 17-86 47-110 (145)
92 PRK11906 transcriptional regul 60.6 15 0.00032 35.2 4.7 41 64-107 375-415 (458)
93 PF13432 TPR_16: Tetratricopep 60.1 15 0.00032 24.2 3.6 30 65-94 1-30 (65)
94 TIGR02917 PEP_TPR_lipo putativ 60.1 42 0.00092 33.3 8.3 63 23-94 27-89 (899)
95 PF03399 SAC3_GANP: SAC3/GANP/ 59.4 50 0.0011 27.3 7.5 138 57-205 52-203 (204)
96 PF07721 TPR_4: Tetratricopept 59.2 9.4 0.0002 20.9 2.0 23 63-85 3-25 (26)
97 PF01325 Fe_dep_repress: Iron 58.8 45 0.00097 22.4 5.7 46 175-230 8-53 (60)
98 PF09382 RQC: RQC domain; Int 58.5 71 0.0015 23.5 7.8 36 209-244 52-88 (106)
99 TIGR03302 OM_YfiO outer membra 58.5 30 0.00065 29.0 6.1 67 22-95 74-149 (235)
100 TIGR02917 PEP_TPR_lipo putativ 57.7 52 0.0011 32.6 8.4 33 62-94 194-226 (899)
101 KOG2300 Uncharacterized conser 57.5 2E+02 0.0042 28.2 12.2 123 57-184 363-515 (629)
102 TIGR00756 PPR pentatricopeptid 57.1 23 0.00049 19.6 3.6 28 21-48 3-30 (35)
103 PRK11189 lipoprotein NlpI; Pro 56.7 90 0.002 27.7 9.1 63 23-95 69-132 (296)
104 PF13512 TPR_18: Tetratricopep 56.3 42 0.00091 27.0 6.0 66 23-95 52-133 (142)
105 PF01535 PPR: PPR repeat; Int 56.3 14 0.00031 20.1 2.6 28 20-47 2-29 (31)
106 TIGR01716 RGG_Cterm transcript 56.0 41 0.00089 28.2 6.4 77 13-93 124-200 (220)
107 PRK10049 pgaA outer membrane p 56.0 65 0.0014 32.8 8.9 124 22-151 314-452 (765)
108 PRK12370 invasion protein regu 55.6 64 0.0014 31.5 8.5 63 24-95 344-406 (553)
109 PF10516 SHNi-TPR: SHNi-TPR; 53.1 21 0.00045 21.9 3.0 25 66-90 6-30 (38)
110 PF12569 NARP1: NMDA receptor- 51.9 62 0.0013 31.6 7.6 72 15-96 191-263 (517)
111 PRK02603 photosystem I assembl 51.5 18 0.00038 29.3 3.3 37 56-92 30-66 (172)
112 PRK10370 formate-dependent nit 51.4 1.1E+02 0.0023 25.6 8.2 31 63-93 146-176 (198)
113 COG1729 Uncharacterized protei 51.4 44 0.00095 29.7 5.9 69 20-95 144-212 (262)
114 KOG0543 FKBP-type peptidyl-pro 50.9 84 0.0018 29.6 7.9 68 18-95 257-325 (397)
115 CHL00033 ycf3 photosystem I as 50.8 49 0.0011 26.4 5.8 68 20-89 74-141 (168)
116 KOG2002 TPR-containing nuclear 50.8 39 0.00084 35.3 6.1 68 20-93 272-339 (1018)
117 PRK09954 putative kinase; Prov 49.6 63 0.0014 29.4 7.0 46 192-242 15-63 (362)
118 PF10300 DUF3808: Protein of u 49.5 42 0.0009 32.2 6.0 50 31-89 246-295 (468)
119 TIGR00540 hemY_coli hemY prote 49.3 31 0.00068 32.1 5.1 70 23-93 268-369 (409)
120 PF09339 HTH_IclR: IclR helix- 49.2 44 0.00095 21.4 4.3 33 193-230 17-49 (52)
121 PRK15431 ferrous iron transpor 49.1 60 0.0013 23.3 5.2 36 193-233 15-50 (78)
122 PF12802 MarR_2: MarR family; 48.9 47 0.001 21.6 4.6 38 194-236 21-58 (62)
123 KOG1156 N-terminal acetyltrans 48.6 58 0.0013 32.6 6.7 38 56-93 366-403 (700)
124 COG3071 HemY Uncharacterized e 48.5 20 0.00044 33.5 3.5 76 18-95 263-362 (400)
125 PHA02992 hypothetical protein; 47.9 1.5E+02 0.0032 30.0 9.4 111 130-241 70-261 (728)
126 PF09295 ChAPs: ChAPs (Chs5p-A 47.9 50 0.0011 31.1 6.1 64 18-94 234-297 (395)
127 PLN03088 SGT1, suppressor of 47.7 1.3E+02 0.0027 27.7 8.7 63 24-95 8-70 (356)
128 cd05804 StaR_like StaR_like; a 46.7 1.6E+02 0.0035 26.1 9.2 65 19-92 115-179 (355)
129 PRK10049 pgaA outer membrane p 46.4 84 0.0018 32.1 7.9 63 23-94 364-426 (765)
130 KOG3054 Uncharacterized conser 46.3 39 0.00085 29.7 4.6 47 193-244 213-259 (299)
131 PLN03098 LPA1 LOW PSII ACCUMUL 45.2 77 0.0017 30.4 6.9 65 18-90 75-141 (453)
132 PRK15174 Vi polysaccharide exp 44.9 1.2E+02 0.0026 30.3 8.7 33 63-95 354-386 (656)
133 PF12895 Apc3: Anaphase-promot 44.6 28 0.00061 24.3 3.1 49 31-86 2-50 (84)
134 PF13525 YfiO: Outer membrane 44.4 65 0.0014 26.8 5.8 65 25-95 12-76 (203)
135 PRK15363 pathogenicity island 44.2 1E+02 0.0023 25.1 6.7 31 63-93 71-101 (157)
136 smart00419 HTH_CRP helix_turn_ 44.1 52 0.0011 20.0 4.0 32 194-230 8-39 (48)
137 PRK10747 putative protoheme IX 44.1 55 0.0012 30.4 5.8 72 20-94 265-361 (398)
138 PF02082 Rrf2: Transcriptional 44.1 64 0.0014 22.8 5.0 44 195-244 26-69 (83)
139 PF12854 PPR_1: PPR repeat 43.8 47 0.001 19.3 3.5 26 19-44 8-33 (34)
140 PRK11447 cellulose synthase su 43.6 1.3E+02 0.0028 32.3 9.1 69 18-95 351-419 (1157)
141 PHA02608 67 prohead core prote 43.2 1.2E+02 0.0026 21.7 6.0 20 131-150 2-21 (80)
142 TIGR00985 3a0801s04tom mitocho 43.1 55 0.0012 26.5 4.8 28 67-94 96-124 (148)
143 KOG1126 DNA-binding cell divis 42.1 72 0.0016 31.8 6.3 26 65-90 493-518 (638)
144 PF07729 FCD: FCD domain; Int 41.8 1.3E+02 0.0028 21.6 7.8 26 127-152 97-122 (125)
145 smart00550 Zalpha Z-DNA-bindin 41.5 48 0.0011 22.7 3.8 33 194-231 22-54 (68)
146 PF04492 Phage_rep_O: Bacterio 41.5 65 0.0014 24.1 4.8 49 171-229 36-84 (100)
147 KOG0030 Myosin essential light 41.4 27 0.00058 28.1 2.7 39 191-229 101-140 (152)
148 PF01047 MarR: MarR family; I 41.1 49 0.0011 21.4 3.7 40 194-238 17-56 (59)
149 PRK14574 hmsH outer membrane p 40.8 98 0.0021 32.1 7.4 132 21-160 370-518 (822)
150 cd00092 HTH_CRP helix_turn_hel 40.5 65 0.0014 21.1 4.3 35 192-231 23-57 (67)
151 PLN03218 maturation of RBCL 1; 40.4 5E+02 0.011 27.9 13.8 65 18-90 579-643 (1060)
152 PF13429 TPR_15: Tetratricopep 39.6 45 0.00098 29.0 4.3 32 63-94 216-247 (280)
153 PF14559 TPR_19: Tetratricopep 39.4 56 0.0012 21.4 3.8 24 72-95 2-25 (68)
154 PLN03081 pentatricopeptide (PP 39.3 4.1E+02 0.0088 26.6 13.6 61 18-90 158-218 (697)
155 PF05158 RNA_pol_Rpc34: RNA po 38.8 10 0.00022 34.7 0.0 121 97-235 115-260 (327)
156 PF13431 TPR_17: Tetratricopep 38.6 17 0.00037 21.3 1.0 20 62-81 14-33 (34)
157 PF02847 MA3: MA3 domain; Int 38.6 1.6E+02 0.0034 21.7 8.9 93 130-229 6-112 (113)
158 PF10264 Stork_head: Winged he 38.0 1.5E+02 0.0033 21.3 6.3 37 193-229 28-67 (80)
159 KOG3060 Uncharacterized conser 37.3 2E+02 0.0044 25.7 7.7 77 17-102 51-127 (289)
160 cd05804 StaR_like StaR_like; a 37.3 1.3E+02 0.0029 26.7 7.1 66 19-89 149-214 (355)
161 PF13525 YfiO: Outer membrane 35.9 1E+02 0.0022 25.7 5.7 53 60-114 140-192 (203)
162 CHL00033 ycf3 photosystem I as 35.9 2.2E+02 0.0047 22.5 9.9 67 20-92 37-103 (168)
163 PF07219 HemY_N: HemY protein 35.7 61 0.0013 24.3 3.9 34 57-90 55-88 (108)
164 KOG1126 DNA-binding cell divis 35.4 1E+02 0.0022 30.8 6.2 23 20-42 525-547 (638)
165 PF08221 HTH_9: RNA polymerase 35.1 97 0.0021 20.9 4.4 34 193-231 26-59 (62)
166 PLN03077 Protein ECB2; Provisi 34.8 5.2E+02 0.011 26.5 14.3 65 18-94 424-488 (857)
167 smart00668 CTLH C-terminal to 34.1 1.1E+02 0.0024 19.5 4.5 31 131-161 6-36 (58)
168 PRK09782 bacteriophage N4 rece 33.9 56 0.0012 34.6 4.4 57 59-120 42-98 (987)
169 KOG2076 RNA polymerase III tra 33.2 1.5E+02 0.0032 30.9 7.0 64 23-94 419-482 (895)
170 PF13371 TPR_9: Tetratricopept 33.2 1.1E+02 0.0023 20.3 4.5 28 68-95 2-29 (73)
171 COG4700 Uncharacterized protei 33.1 2.4E+02 0.0053 24.2 7.3 65 22-93 128-192 (251)
172 TIGR02944 suf_reg_Xantho FeS a 32.8 88 0.0019 24.0 4.5 36 193-233 24-59 (130)
173 PF14394 DUF4423: Domain of un 32.7 2E+02 0.0043 23.6 6.7 57 160-230 16-72 (171)
174 COG1849 Uncharacterized protei 32.6 59 0.0013 24.0 3.1 32 59-90 39-70 (90)
175 PF08544 GHMP_kinases_C: GHMP 32.3 61 0.0013 22.4 3.2 22 133-154 1-22 (85)
176 PF13833 EF-hand_8: EF-hand do 32.1 1.1E+02 0.0024 19.2 4.2 31 193-223 3-34 (54)
177 TIGR02147 Fsuc_second hypothet 31.8 1.6E+02 0.0035 26.2 6.5 87 130-230 77-170 (271)
178 PLN03218 maturation of RBCL 1; 31.4 6.9E+02 0.015 26.9 14.9 63 19-89 473-535 (1060)
179 KOG4162 Predicted calmodulin-b 31.3 1.3E+02 0.0028 30.8 6.2 63 22-93 722-786 (799)
180 COG5240 SEC21 Vesicle coat com 30.8 3.7E+02 0.008 27.1 9.0 114 7-130 348-493 (898)
181 TIGR03504 FimV_Cterm FimV C-te 30.2 69 0.0015 20.2 2.8 24 23-46 4-27 (44)
182 KOG3060 Uncharacterized conser 30.0 1.2E+02 0.0027 27.0 5.3 66 23-94 159-224 (289)
183 smart00386 HAT HAT (Half-A-TPR 29.9 96 0.0021 16.5 4.3 19 75-93 1-19 (33)
184 KOG0547 Translocase of outer m 29.4 2E+02 0.0043 28.2 6.9 70 24-102 366-435 (606)
185 PF09295 ChAPs: ChAPs (Chs5p-A 29.3 2.3E+02 0.005 26.7 7.4 65 18-94 169-233 (395)
186 PF10607 CLTH: CTLH/CRA C-term 29.3 1.5E+02 0.0033 22.9 5.4 32 129-160 4-35 (145)
187 smart00345 HTH_GNTR helix_turn 29.2 1.5E+02 0.0032 18.6 4.5 33 193-230 18-51 (60)
188 COG3071 HemY Uncharacterized e 29.0 3.9E+02 0.0083 25.3 8.5 111 67-181 90-240 (400)
189 smart00420 HTH_DEOR helix_turn 28.5 1.3E+02 0.0027 18.4 4.0 33 194-231 14-46 (53)
190 PRK11447 cellulose synthase su 28.3 1.9E+02 0.0041 31.1 7.4 64 23-95 274-337 (1157)
191 smart00671 SEL1 Sel1-like repe 28.1 77 0.0017 17.8 2.7 17 73-89 17-33 (36)
192 PF09202 Rio2_N: Rio2, N-termi 27.7 1.5E+02 0.0033 21.3 4.7 37 192-233 22-58 (82)
193 PF01022 HTH_5: Bacterial regu 27.7 1.3E+02 0.0028 18.7 3.8 33 193-230 14-46 (47)
194 PRK14165 winged helix-turn-hel 27.4 2.5E+02 0.0054 24.2 6.7 48 192-244 19-66 (217)
195 PRK10153 DNA-binding transcrip 27.3 61 0.0013 31.6 3.3 54 30-94 432-486 (517)
196 KOG1070 rRNA processing protei 27.0 9.3E+02 0.02 27.0 15.1 69 16-93 1528-1596(1710)
197 PRK10866 outer membrane biogen 26.7 1.7E+02 0.0036 25.4 5.6 55 58-114 172-226 (243)
198 PF13463 HTH_27: Winged helix 26.4 1.1E+02 0.0024 20.1 3.6 37 193-234 17-53 (68)
199 COG2956 Predicted N-acetylgluc 26.3 5.3E+02 0.012 24.0 12.6 82 21-116 110-223 (389)
200 PF13730 HTH_36: Helix-turn-he 25.8 1.3E+02 0.0029 19.0 3.8 29 196-229 27-55 (55)
201 KOG3785 Uncharacterized conser 25.8 2E+02 0.0044 27.1 6.1 61 24-97 63-123 (557)
202 PRK15174 Vi polysaccharide exp 25.7 4.2E+02 0.0091 26.5 9.0 30 64-93 321-350 (656)
203 PF10557 Cullin_Nedd8: Cullin 25.7 2.2E+02 0.0048 19.3 6.3 38 193-230 21-61 (68)
204 KOG1840 Kinesin light chain [C 25.5 2.9E+02 0.0062 27.0 7.4 83 9-93 232-315 (508)
205 KOG4507 Uncharacterized conser 25.5 1.7E+02 0.0038 29.3 5.8 65 16-93 644-708 (886)
206 PF14658 EF-hand_9: EF-hand do 25.3 1.8E+02 0.0039 20.2 4.4 47 188-235 8-55 (66)
207 PF09639 YjcQ: YjcQ protein; 25.1 1.1E+02 0.0024 22.1 3.6 26 211-236 22-48 (88)
208 KOG4642 Chaperone-dependent E3 25.1 1.5E+02 0.0032 26.4 4.8 60 27-96 53-113 (284)
209 PF07079 DUF1347: Protein of u 24.7 2.2E+02 0.0048 27.6 6.2 87 68-154 13-104 (549)
210 TIGR00738 rrf2_super rrf2 fami 24.6 1.5E+02 0.0032 22.6 4.4 34 193-231 24-57 (132)
211 PF03979 Sigma70_r1_1: Sigma-7 24.3 2.6E+02 0.0057 19.7 6.0 33 194-228 21-53 (82)
212 KOG1328 Synaptic vesicle prote 24.3 4.5E+02 0.0097 27.2 8.4 136 60-203 384-546 (1103)
213 COG4785 NlpI Lipoprotein NlpI, 24.0 78 0.0017 27.7 2.9 29 62-90 238-266 (297)
214 TIGR02010 IscR iron-sulfur clu 23.7 1.8E+02 0.0038 22.6 4.8 46 193-244 24-69 (135)
215 KOG2002 TPR-containing nuclear 23.7 2.3E+02 0.005 29.9 6.6 40 57-96 712-751 (1018)
216 PF14561 TPR_20: Tetratricopep 23.7 2.1E+02 0.0046 20.7 4.9 46 61-106 22-68 (90)
217 PRK09782 bacteriophage N4 rece 23.7 2.6E+02 0.0057 29.7 7.3 65 22-95 613-677 (987)
218 PF12645 HTH_16: Helix-turn-he 22.5 2.6E+02 0.0056 19.1 4.8 26 132-157 2-27 (65)
219 PF12569 NARP1: NMDA receptor- 22.3 7.4E+02 0.016 24.2 11.8 113 19-163 263-375 (517)
220 PF13601 HTH_34: Winged helix 22.2 1.9E+02 0.004 20.5 4.2 40 193-237 13-52 (80)
221 PRK12370 invasion protein regu 22.1 4E+02 0.0086 25.9 7.9 64 22-94 376-439 (553)
222 KOG1173 Anaphase-promoting com 22.0 1.1E+02 0.0025 30.1 3.9 73 28-114 390-462 (611)
223 COG4235 Cytochrome c biogenesi 21.5 1E+02 0.0022 27.8 3.2 81 15-95 93-190 (287)
224 PRK03902 manganese transport t 21.5 2.9E+02 0.0062 21.5 5.6 33 193-230 21-53 (142)
225 PRK15331 chaperone protein Sic 21.4 2.2E+02 0.0049 23.4 5.0 58 26-94 45-104 (165)
226 PF04190 DUF410: Protein of un 21.4 5.2E+02 0.011 22.6 7.8 32 132-163 197-228 (260)
227 PF12862 Apc5: Anaphase-promot 21.3 1.8E+02 0.0039 21.0 4.1 31 66-96 46-76 (94)
228 TIGR00540 hemY_coli hemY prote 21.3 5.4E+02 0.012 23.8 8.3 64 23-94 123-186 (409)
229 PRK06926 flagellar motor prote 21.1 1.1E+02 0.0025 27.2 3.5 50 129-178 85-134 (271)
230 PF08069 Ribosomal_S13_N: Ribo 20.8 62 0.0013 22.0 1.3 19 211-229 28-46 (60)
231 KOG2376 Signal recognition par 20.6 2.8E+02 0.0062 27.7 6.2 69 25-93 117-207 (652)
232 KOG3233 RNA polymerase III, su 20.3 2.1E+02 0.0046 25.7 4.9 78 154-231 159-244 (297)
No 1
>KOG2688 consensus Transcription-associated recombination protein - Thp1p [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=1.4e-59 Score=425.81 Aligned_cols=247 Identities=42% Similarity=0.712 Sum_probs=237.3
Q ss_pred CcccccccCC------CchhHHHHHHHHHHHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhh
Q 025096 1 MKVFGVLAGK------GSKRVGALYLTCQLFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFN 74 (258)
Q Consensus 1 ~~~~~~~~~d------~~Kk~~~~~~~n~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~ 74 (258)
|++|+.|.+| ++|++|+++++|++|+|||+++++++|+++++++++. .+..+.++.+|.++|+||.|+++|++
T Consensus 140 ~~~f~~cl~d~~~~~~~~kk~~~~~i~n~lf~Iyfri~~~~L~k~l~ra~~~~-~~~~~~~~l~~~v~y~YylGr~a~~~ 218 (394)
T KOG2688|consen 140 SRLFSSCLSDRRADLEESKKVAMLYIVNQLFQIYFRIEKLLLCKNLIRAFDQS-GSDISDFPLAQLVVYHYYLGRYAMFE 218 (394)
T ss_pred HHHHHHHhCccccccccchhhHHHHHHHHHHHHHHHHhhHHHhHHHHHHhhcc-ccchhhcccccceeeeeeeeeehhhh
Confidence 4689999999 3899999999999999999999999999999999986 47788899999999999999999999
Q ss_pred cChHHHHHHHHHHHHhcCccChHHHHHHHHHHHHHHhhcCCCCChhhhhhccccccHHHHHHHHhCCHHHHHHHHHHcHH
Q 025096 75 ENFPAADQKLSYALINCNPQSEANIRMILKYLIPVKLSIGILPKDWLLEKYNLVEYSNIVQALRRGDLRLLRHALEEHED 154 (258)
Q Consensus 75 ~~~~~A~~~L~~A~~~c~~~~~~~~~~IL~~LIp~~Ll~G~~P~~~ll~~~~l~~y~~L~~av~~Gdl~~f~~~l~~~~~ 154 (258)
.||.+|..+|.+||.+||.....|+++|++||||++|++|++|..+++++|+++.|.++++||+.||+..|+.++++||.
T Consensus 219 ~d~~~A~~~L~~af~~cp~~~~~n~~~iliylip~~~llg~~Pt~~lL~~~~~~~~~~lv~aVr~Gnl~~f~~al~~~E~ 298 (394)
T KOG2688|consen 219 SDFLNAFLQLNEAFRLCPDLLLKNKRLILIYLIPTGLLLGRIPTKELLDFYTLDKYSPLVQAVRSGNLRLFDLALADNER 298 (394)
T ss_pred hhHHHHHHHHHHHHHhCcHHHHhhhhhHHHHHhHHHHHhccCcchhhHhHhhHHhHHHHHHHHHhccHHHHHHHHhhhHH
Confidence 99999999999999999999999999999999999999999999999999999899999999999999999999999999
Q ss_pred HHHHhcHHHHHHhhHHHHHHHHHHHHHHHhhcCCCCCCccccHHHHHHHHHhcc-CCCCHHHHHHHHHHHHHcCcceEEe
Q 025096 155 QFLRSGVYLVLEKLELQVYQRLFKKIYIIQKQKDPSKAHQMKLDVIVKALKWLE-MDMDVDEVECIVAILIHKNLVKGYF 233 (258)
Q Consensus 155 ~f~~~glylll~~l~~~v~r~L~kkv~~~~~~~~~~~~~~i~l~~i~~al~~~~-~~~~~~evE~ila~LI~~G~IkGyI 233 (258)
+|++.|+|+++++++.+|||||+||||.++ ++.+++|++.|..|++.++ .+.+.||+||++|+||++|+|||||
T Consensus 299 ~f~~~gi~l~l~~l~lv~yrnL~kkv~~~~-----~~~~~lpls~~~~al~~~~~~~~~~deveciLa~lI~~G~ikgYi 373 (394)
T KOG2688|consen 299 FFIRSGIYLTLEKLPLVVYRNLFKKVIQLW-----GKTSQLPLSRFLTALQFSGVTDVDLDEVECILANLIDLGRIKGYI 373 (394)
T ss_pred HHHHhccHHHhhhhhHHHHHHHHHHHHHHh-----CCCCCCCHHHHHHHHhhcCCCCCchhhHHHHHHhhhhhccccchh
Confidence 999999999999999999999999999998 4679999999999999987 5689999999999999999999999
Q ss_pred ecCceEEEEecCCCCCCCCC
Q 025096 234 AHKSKVVVLSKQDPFPKLNG 253 (258)
Q Consensus 234 ~~~~~~lVlsk~~pFP~~~~ 253 (258)
||+++++|+||++|||.++.
T Consensus 374 sh~~~~~V~sK~~pfp~~v~ 393 (394)
T KOG2688|consen 374 SHQLQTLVFSKKDPFPHLVL 393 (394)
T ss_pred chhhheEEEecCCCCCCCCC
Confidence 99999999999999999875
No 2
>COG5600 Transcription-associated recombination protein [DNA replication, recombination, and repair]
Probab=100.00 E-value=1.9e-56 Score=397.79 Aligned_cols=246 Identities=33% Similarity=0.627 Sum_probs=231.9
Q ss_pred cccccccCCC------chhHHHHHHHHHHHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhc
Q 025096 2 KVFGVLAGKG------SKRVGALYLTCQLFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNE 75 (258)
Q Consensus 2 ~~~~~~~~d~------~Kk~~~~~~~n~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~ 75 (258)
++|+.|.+|. +||+|+|+++|++|++||++++.++|+|++++.+..+.|+.+.++++|+|+|+||+|++|+.++
T Consensus 155 R~Fn~il~dR~p~ln~skk~g~y~iaNlL~~iY~Rl~~~~l~~n~lka~~~vs~~Di~~~~~sq~v~f~YYLG~~~l~~e 234 (413)
T COG5600 155 RMFNSILNDRSPALNPSKKVGLYYIANLLFQIYLRLGRFKLCENFLKASKEVSMPDISEYQKSQVVVFHYYLGIYYLLNE 234 (413)
T ss_pred HHHHHhcCCcCccCChhhHHHHHHHHHHHHHHHHHhccHHHHHHHHHhcccccccccchhhhcceeehhhHHHHHHHHHH
Confidence 6899999993 8999999999999999999999999999999999877888889999999999999999999999
Q ss_pred ChHHHHHHHHHHHHhcCccChHHHHHHHHHHHHHHhhc-CCCCChhhhhhcc-ccccHHHHHHHHhCCHHHHHHHHHHcH
Q 025096 76 NFPAADQKLSYALINCNPQSEANIRMILKYLIPVKLSI-GILPKDWLLEKYN-LVEYSNIVQALRRGDLRLLRHALEEHE 153 (258)
Q Consensus 76 ~~~~A~~~L~~A~~~c~~~~~~~~~~IL~~LIp~~Ll~-G~~P~~~ll~~~~-l~~y~~L~~av~~Gdl~~f~~~l~~~~ 153 (258)
++.+|+.+|++||..||.--.+|+++|+.|+||.+|+. +..|..+++++|+ .+.|.+|++|+|.||+..|+.++++|+
T Consensus 235 n~heA~~~L~~aFl~c~~l~~~n~~rIl~~~ipt~Llv~~~~Ptk~~L~r~~~~s~~~~LvkavrsGni~~~~~~l~~ne 314 (413)
T COG5600 235 NFHEAFLHLNEAFLQCPWLITRNRKRILPYYIPTSLLVNKFPPTKDLLERFKRCSVYSPLVKAVRSGNIEDFDLALSRNE 314 (413)
T ss_pred hHHHHHHHHHHHHHhChhhhhcchheehhHHhhHHHHhCCCCCchHHHHhccccchhHHHHHHHHcCCHHHHHHHHHHhH
Confidence 99999999999999999877799999999999999996 4688899999999 557999999999999999999999999
Q ss_pred HHHHHhcHHHHH-HhhHHHHHHHHHHHHHHHhhcCCCCCCccccHHHHHHHHHhccCC--CCHHHHHHHHHHHHHcCcce
Q 025096 154 DQFLRSGVYLVL-EKLELQVYQRLFKKIYIIQKQKDPSKAHQMKLDVIVKALKWLEMD--MDVDEVECIVAILIHKNLVK 230 (258)
Q Consensus 154 ~~f~~~glylll-~~l~~~v~r~L~kkv~~~~~~~~~~~~~~i~l~~i~~al~~~~~~--~~~~evE~ila~LI~~G~Ik 230 (258)
.+|.++|+|+.+ ++.+.+|||||+||+|... ++.+++|++.+..+++.++.| .+.++|||++++||.+|++|
T Consensus 315 r~~~~~~l~ltl~~~~~~V~~RNL~rk~w~~~-----~~qsrlp~sil~~~~qls~~dn~~~~~~VEciL~tlI~~G~lr 389 (413)
T COG5600 315 RKFAKRGLYLTLLAHYPLVCFRNLFRKIWRLH-----GKQSRLPLSILLIVLQLSAIDNFHSFKEVECILVTLIGLGLLR 389 (413)
T ss_pred HHHHHcchHHHHHhhccHHHHHHHHHHHHhhc-----cccccCcHHHHHHHHHccCCCcccChHHHHHHHHHHHhhhhhh
Confidence 999999999855 6899999999999999997 567899999999999998877 78999999999999999999
Q ss_pred EEeecCceEEEEecCCCCCCCC
Q 025096 231 GYFAHKSKVVVLSKQDPFPKLN 252 (258)
Q Consensus 231 GyI~~~~~~lVlsk~~pFP~~~ 252 (258)
|||+|+.+++|+||++|||...
T Consensus 390 gYis~s~~~vV~sk~~pFp~~V 411 (413)
T COG5600 390 GYISHSRRTVVFSKKDPFPVSV 411 (413)
T ss_pred heecccceEEEEecCCCCCCCC
Confidence 9999999999999999999865
No 3
>KOG2581 consensus 26S proteasome regulatory complex, subunit RPN3/PSMD3 [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.6e-34 Score=259.75 Aligned_cols=212 Identities=22% Similarity=0.342 Sum_probs=194.0
Q ss_pred HHHHHHHHHHHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCcc
Q 025096 15 VGALYLTCQLFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNPQ 94 (258)
Q Consensus 15 ~~~~~~~n~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~ 94 (258)
.|.-.+.|++++.|+..+.++++.++++.. ..|+ ...++++.+|+||+|++.+++.+|..|.++|.+|.+..|.+
T Consensus 206 e~qavLiN~LLr~yL~n~lydqa~~lvsK~---~~pe--~~snne~ARY~yY~GrIkaiqldYssA~~~~~qa~rkapq~ 280 (493)
T KOG2581|consen 206 EGQAVLINLLLRNYLHNKLYDQADKLVSKS---VYPE--AASNNEWARYLYYLGRIKAIQLDYSSALEYFLQALRKAPQH 280 (493)
T ss_pred hhHHHHHHHHHHHHhhhHHHHHHHHHhhcc---cCcc--ccccHHHHHHHHHHhhHHHhhcchhHHHHHHHHHHHhCcch
Confidence 466778999999999999999999998643 2455 45678999999999999999999999999999999999954
Q ss_pred -ChHHHHHHHHHHHHHHhhcCCCCChhhhhhcc----ccccHHHHHHHHhCCHHHHHHHHHHcHHHHHHhcHHHHHHhhH
Q 025096 95 -SEANIRMILKYLIPVKLSIGILPKDWLLEKYN----LVEYSNIVQALRRGDLRLLRHALEEHEDQFLRSGVYLVLEKLE 169 (258)
Q Consensus 95 -~~~~~~~IL~~LIp~~Ll~G~~P~~~ll~~~~----l~~y~~L~~av~~Gdl~~f~~~l~~~~~~f~~~glylll~~l~ 169 (258)
+.++++++-|..|.+++++|.+|....+.+.+ |.+|..|.+|||.||+++|++.++++.+.|..+|+|.++.|||
T Consensus 281 ~alGf~q~v~k~~ivv~ll~geiPers~F~Qp~~~ksL~~Yf~Lt~AVr~gdlkkF~~~leq~k~~f~~D~ty~LivRLR 360 (493)
T KOG2581|consen 281 AALGFRQQVNKLMIVVELLLGEIPERSVFRQPGMRKSLRPYFKLTQAVRLGDLKKFNETLEQFKDKFQADGTYTLIVRLR 360 (493)
T ss_pred hhhhHHHHHHHHHHHHHHHcCCCcchhhhcCccHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHhhCCcchHHHHHH
Confidence 45999999999999999999999999988874 6789999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhhcCCCCCCccccHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCcceEEeecCceEEEEe
Q 025096 170 LQVYQRLFKKIYIIQKQKDPSKAHQMKLDVIVKALKWLEMDMDVDEVECIVAILIHKNLVKGYFAHKSKVVVLS 243 (258)
Q Consensus 170 ~~v~r~L~kkv~~~~~~~~~~~~~~i~l~~i~~al~~~~~~~~~~evE~ila~LI~~G~IkGyI~~~~~~lVls 243 (258)
+.|+++.+|+|.+.| +||++.+|++.|.+ -+++++|.||++.|.+|.|+|.|+|++++++.+
T Consensus 361 ~NVIkTgIR~ISlsY--------SRISl~DIA~kL~l----~Seed~EyiVakAIRDGvIea~Id~~~g~m~sk 422 (493)
T KOG2581|consen 361 HNVIKTGIRKISLSY--------SRISLQDIAKKLGL----NSEEDAEYIVAKAIRDGVIEAKIDHEDGFMQSK 422 (493)
T ss_pred HHHHHHhhhheeeee--------eeccHHHHHHHhcC----CCchhHHHHHHHHHHhccceeeeccccCceehh
Confidence 999999999998887 89999999999985 267789999999999999999999999986654
No 4
>KOG1464 consensus COP9 signalosome, subunit CSN2 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=99.81 E-value=3.7e-19 Score=154.58 Aligned_cols=211 Identities=18% Similarity=0.251 Sum_probs=181.6
Q ss_pred hhHHHHHHHHHHHHHHHhcCChhhHHHHHH-Hhhc-cCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHh
Q 025096 13 KRVGALYLTCQLFKIYFKLGTVHLCRSVIR-SIET-ARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALIN 90 (258)
Q Consensus 13 Kk~~~~~~~n~l~kiyf~l~~~~~~~~l~~-~i~~-~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~ 90 (258)
|...++-+..+.+.+|-...+-...+.+.. ++.. +++|+ |. -.-.-+-++|++++.+++|++|++.|.+||++
T Consensus 186 KGtQLLEiYAlEIQmYT~qKnNKkLK~lYeqalhiKSAIPH----Pl-ImGvIRECGGKMHlreg~fe~AhTDFFEAFKN 260 (440)
T KOG1464|consen 186 KGTQLLEIYALEIQMYTEQKNNKKLKALYEQALHIKSAIPH----PL-IMGVIRECGGKMHLREGEFEKAHTDFFEAFKN 260 (440)
T ss_pred ccchhhhhHhhHhhhhhhhcccHHHHHHHHHHHHhhccCCc----hH-HHhHHHHcCCccccccchHHHHHhHHHHHHhc
Confidence 445688999999999999888888887763 2322 23664 32 24457899999999999999999999999999
Q ss_pred cCccChHHHHHHHHHHHHHHhhc-CCCCChhhhhh--cc----ccccHHHHHHHHhCCHHHHHHHHHHcH-----HHHHH
Q 025096 91 CNPQSEANIRMILKYLIPVKLSI-GILPKDWLLEK--YN----LVEYSNIVQALRRGDLRLLRHALEEHE-----DQFLR 158 (258)
Q Consensus 91 c~~~~~~~~~~IL~~LIp~~Ll~-G~~P~~~ll~~--~~----l~~y~~L~~av~~Gdl~~f~~~l~~~~-----~~f~~ 158 (258)
+.+++.+.|..+|+|||.++|++ ..+.|++..+. |. +....+++.|+.+.|+..|+.++..|+ +.|++
T Consensus 261 YDEsGspRRttCLKYLVLANMLmkS~iNPFDsQEAKPyKNdPEIlAMTnlv~aYQ~NdI~eFE~Il~~~~~~IM~DpFIR 340 (440)
T KOG1464|consen 261 YDESGSPRRTTCLKYLVLANMLMKSGINPFDSQEAKPYKNDPEILAMTNLVAAYQNNDIIEFERILKSNRSNIMDDPFIR 340 (440)
T ss_pred ccccCCcchhHHHHHHHHHHHHHHcCCCCCcccccCCCCCCHHHHHHHHHHHHHhcccHHHHHHHHHhhhccccccHHHH
Confidence 99999999999999999999996 57888888774 32 334799999999999999999999976 58999
Q ss_pred hcHHHHHHhhHHHHHHHHHHHHHHHhhcCCCCCCccccHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCcceEEeecCce
Q 025096 159 SGVYLVLEKLELQVYQRLFKKIYIIQKQKDPSKAHQMKLDVIVKALKWLEMDMDVDEVECIVAILIHKNLVKGYFAHKSK 238 (258)
Q Consensus 159 ~glylll~~l~~~v~r~L~kkv~~~~~~~~~~~~~~i~l~~i~~al~~~~~~~~~~evE~ila~LI~~G~IkGyI~~~~~ 238 (258)
..+-.++...|..|+..|+| ++++|.+..|...++ ++..|||.+++++|.+..|+|.|+..++
T Consensus 341 eh~EdLl~niRTQVLlkLIk------------PYt~i~Ipfis~~Ln-----v~~~dV~~LLV~~ILD~~i~g~Ide~n~ 403 (440)
T KOG1464|consen 341 EHIEDLLRNIRTQVLLKLIK------------PYTNIGIPFISKELN-----VPEADVESLLVSCILDDTIDGRIDEVNQ 403 (440)
T ss_pred HHHHHHHHHHHHHHHHHHhc------------cccccCchhhHhhcC-----CCHHHHHHHHHHHHhccccccchHHhhh
Confidence 99999999999999999988 457888999999987 7999999999999999999999999999
Q ss_pred EEEEecC
Q 025096 239 VVVLSKQ 245 (258)
Q Consensus 239 ~lVlsk~ 245 (258)
++.+.+.
T Consensus 404 ~l~~~~~ 410 (440)
T KOG1464|consen 404 YLELDKS 410 (440)
T ss_pred HhccCcc
Confidence 9888553
No 5
>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=99.70 E-value=2.7e-16 Score=118.99 Aligned_cols=103 Identities=31% Similarity=0.451 Sum_probs=94.8
Q ss_pred ccHHHHHHHHhCCHHHHHHHHHHc-HHHHHHhcHHHHHHhhHHHHHHHHHHHHHHHhhcCCCCCCccccHHHHHHHHHhc
Q 025096 129 EYSNIVQALRRGDLRLLRHALEEH-EDQFLRSGVYLVLEKLELQVYQRLFKKIYIIQKQKDPSKAHQMKLDVIVKALKWL 207 (258)
Q Consensus 129 ~y~~L~~av~~Gdl~~f~~~l~~~-~~~f~~~glylll~~l~~~v~r~L~kkv~~~~~~~~~~~~~~i~l~~i~~al~~~ 207 (258)
+|.++++|+.+||+..|.+.++++ +.++.+.++...++.++..+.++.+++++..+ ++|+++.++++++
T Consensus 2 ~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~~l~~~i~~~~l~~l~~~y--------~~i~~~~ia~~l~-- 71 (105)
T PF01399_consen 2 PYSELLRAFRSGDLQEFEEFLEKHSESLFKDPFLAEYVEQLKEKIRRRNLRQLSKPY--------SSISISEIAKALQ-- 71 (105)
T ss_dssp HHHHHHHHHHCT-HHHHHHHHHHTCHHHHHCTTHHHHHHHHHHHHHHHHHHHHHHC---------SEEEHHHHHHHHT--
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHHHHHHHh--------cccchHHHHHHhc--
Confidence 588999999999999999999999 88999999999999999999999999988765 8999999999998
Q ss_pred cCCCCHHHHHHHHHHHHHcCcceEEeecCceEEEEec
Q 025096 208 EMDMDVDEVECIVAILIHKNLVKGYFAHKSKVVVLSK 244 (258)
Q Consensus 208 ~~~~~~~evE~ila~LI~~G~IkGyI~~~~~~lVlsk 244 (258)
++.+|+|+++++||.+|.|+|+|||.+++|+++|
T Consensus 72 ---~~~~~vE~~l~~~I~~~~i~~~ID~~~~~v~~~k 105 (105)
T PF01399_consen 72 ---LSEEEVESILIDLISNGLIKAKIDQVNGVVVFSK 105 (105)
T ss_dssp ---CCHHHHHHHHHHHHHTTSSEEEEETTTTEEEE-S
T ss_pred ---cchHHHHHHHHHHHHCCCEEEEEECCCCEEEecC
Confidence 6889999999999999999999999999999986
No 6
>KOG2908 consensus 26S proteasome regulatory complex, subunit RPN9/PSMD13 [Posttranslational modification, protein turnover, chaperones]
Probab=99.38 E-value=5.2e-11 Score=106.30 Aligned_cols=217 Identities=14% Similarity=0.194 Sum_probs=144.4
Q ss_pred HHHHHHHHHHHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCc-
Q 025096 15 VGALYLTCQLFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNP- 93 (258)
Q Consensus 15 ~~~~~~~n~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~- 93 (258)
.++.++.....++|+..|++..|+.++...++. +.++...|.+-...|+--...+|=-.++|..++.+.-.=+ .|..
T Consensus 112 ~av~~~~t~~~r~~L~i~DLk~~kk~ldd~~~~-ld~~~~v~~~Vh~~fY~lssqYyk~~~d~a~yYr~~L~YL-~~~d~ 189 (380)
T KOG2908|consen 112 DAVIYILTEIARLKLEINDLKEIKKLLDDLKSM-LDSLDGVTSNVHSSFYSLSSQYYKKIGDFASYYRHALLYL-GCSDI 189 (380)
T ss_pred hhHHHHHHHHHHHHHhcccHHHHHHHHHHHHHH-HhcccCCChhhhhhHHHHHHHHHHHHHhHHHHHHHHHHHh-ccccc
Confidence 688999999999999999999999999887763 3333333433333343334455556678888777744333 3442
Q ss_pred -cChHHHHHHHHHHHHHHhhcCC-CCChhhhhhcc------cc--c-cHHHHHHHHhCCHHHHHHHHHHcHH-HHHHhcH
Q 025096 94 -QSEANIRMILKYLIPVKLSIGI-LPKDWLLEKYN------LV--E-YSNIVQALRRGDLRLLRHALEEHED-QFLRSGV 161 (258)
Q Consensus 94 -~~~~~~~~IL~~LIp~~Ll~G~-~P~~~ll~~~~------l~--~-y~~L~~av~~Gdl~~f~~~l~~~~~-~f~~~gl 161 (258)
+.+...++-+-+.....=++|+ +-++..+-..+ -. + -.++..|++.||+.+|++....+.. .-+...-
T Consensus 190 ~~l~~se~~~lA~~L~~aALLGe~iyNfGELL~HPilesL~gT~~eWL~dll~Afn~Gdl~~f~~l~~~~~~~p~L~~~e 269 (380)
T KOG2908|consen 190 DDLSESEKQDLAFDLSLAALLGENIYNFGELLAHPILESLKGTNREWLKDLLIAFNSGDLKRFESLKGVWGKQPDLASNE 269 (380)
T ss_pred cccCHHHHHHHHHHHHHHHHhccccccHHHHHhhHHHHHhcCCcHHHHHHHHHHhccCCHHHHHHHHHHhccCchHHHHH
Confidence 1122222233333333334443 54544333322 11 2 4789999999999999998877543 2233333
Q ss_pred HHHHHhhHHHHHHHHHHHHHHHhhcCCCCCCccccHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCcceEEeecCceEEE
Q 025096 162 YLVLEKLELQVYQRLFKKIYIIQKQKDPSKAHQMKLDVIVKALKWLEMDMDVDEVECIVAILIHKNLVKGYFAHKSKVVV 241 (258)
Q Consensus 162 ylll~~l~~~v~r~L~kkv~~~~~~~~~~~~~~i~l~~i~~al~~~~~~~~~~evE~ila~LI~~G~IkGyI~~~~~~lV 241 (258)
-.+.+|.+.+|+ +..+|... .....+|+++|+++++ ++.+|||.++++.++.|+|+|.|++..++|-
T Consensus 270 ~~L~qKI~LmaL---iEi~F~rp-----a~~R~lsf~~Ia~~tk-----ip~~eVE~LVMKAlslgLikG~Idqv~~~v~ 336 (380)
T KOG2908|consen 270 DFLLQKIRLLAL---IEITFSRP-----ANERTLSFKEIAEATK-----IPNKEVELLVMKALSLGLIKGSIDQVEGVVY 336 (380)
T ss_pred HHHHHHHHHHHH---HHHHhcCc-----chhccccHHHHHHHhC-----CCHHHHHHHHHHHHhccceeeeecccccEEE
Confidence 445566666664 55566552 3457899999999998 7999999999999999999999999999887
Q ss_pred EecCC
Q 025096 242 LSKQD 246 (258)
Q Consensus 242 lsk~~ 246 (258)
.|---
T Consensus 337 ~swvq 341 (380)
T KOG2908|consen 337 MSWVQ 341 (380)
T ss_pred Eeccc
Confidence 76543
No 7
>KOG1463 consensus 26S proteasome regulatory complex, subunit RPN6/PSMD11 [Posttranslational modification, protein turnover, chaperones]
Probab=99.15 E-value=1.2e-09 Score=97.85 Aligned_cols=208 Identities=16% Similarity=0.209 Sum_probs=147.6
Q ss_pred HHHHHHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCccCh-HH
Q 025096 20 LTCQLFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNPQSE-AN 98 (258)
Q Consensus 20 ~~n~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~~~-~~ 98 (258)
+-.+.-|.||.++|+..++.-+-.-...+. --..|...+.+----.|.+|+-+.||..|+..|.+||.-.+.-.. ..
T Consensus 170 v~llESK~y~~l~Nl~KakasLTsART~An--aiYcpPqlQa~lDLqSGIlha~ekDykTafSYFyEAfEgf~s~~~~v~ 247 (411)
T KOG1463|consen 170 VHLLESKAYHALRNLPKAKASLTSARTTAN--AIYCPPQLQATLDLQSGILHAAEKDYKTAFSYFYEAFEGFDSLDDDVK 247 (411)
T ss_pred ehhhhhHHHHHHhcchhHHHHHHHHHHhhc--ccccCHHHHHHHHHhccceeecccccchHHHHHHHHHccccccCCcHH
Confidence 334455667777776666655433332211 012467778888889999999999999999999999997765444 45
Q ss_pred HHHHHHHHHHHHhhcCCCCChh-hh-----hhcc---ccccHHHHHHHHhCCHHHHHHHHHHcHHHHHHhcHHH-HHHhh
Q 025096 99 IRMILKYLIPVKLSIGILPKDW-LL-----EKYN---LVEYSNIVQALRRGDLRLLRHALEEHEDQFLRSGVYL-VLEKL 168 (258)
Q Consensus 99 ~~~IL~~LIp~~Ll~G~~P~~~-ll-----~~~~---l~~y~~L~~av~~Gdl~~f~~~l~~~~~~f~~~glyl-ll~~l 168 (258)
-...|||++.+++.++..-.-. ++ -+|. +.....+++|+..-+++.|+.++.++...+..|.+.- -++.|
T Consensus 248 A~~sLKYMlLcKIMln~~ddv~~lls~K~~l~y~g~~i~AmkavAeA~~nRSLkdF~~AL~~yk~eL~~D~ivr~Hl~~L 327 (411)
T KOG1463|consen 248 ALTSLKYMLLCKIMLNLPDDVAALLSAKLALKYAGRDIDAMKAVAEAFGNRSLKDFEKALADYKKELAEDPIVRSHLQSL 327 (411)
T ss_pred HHHHHHHHHHHHHHhcCHHHHHHHHhhHHHHhccCcchHHHHHHHHHhcCCcHHHHHHHHHHhHHHHhcChHHHHHHHHH
Confidence 6667999999998876532211 11 1242 4457889999999999999999999876555544321 11111
Q ss_pred -HHHHHHHHHHHHHHHhhcCCCCCCccccHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCcceEEeecCceEEEEe
Q 025096 169 -ELQVYQRLFKKIYIIQKQKDPSKAHQMKLDVIVKALKWLEMDMDVDEVECIVAILIHKNLVKGYFAHKSKVVVLS 243 (258)
Q Consensus 169 -~~~v~r~L~kkv~~~~~~~~~~~~~~i~l~~i~~al~~~~~~~~~~evE~ila~LI~~G~IkGyI~~~~~~lVls 243 (258)
..+.=.|++|-| .+.+++-++-|++.+. +|...||--++.||-+....|.++|+.+|+++=
T Consensus 328 yd~lLEknl~riI---------EPyS~Vei~hIA~~IG-----l~~~~VEkKLsqMILDKkf~G~LDQg~g~Liv~ 389 (411)
T KOG1463|consen 328 YDNLLEKNLCRII---------EPYSRVEISHIAEVIG-----LDVPQVEKKLSQMILDKKFYGTLDQGEGCLIVF 389 (411)
T ss_pred HHHHHHHhHHHHc---------CchhhhhHHHHHHHHC-----CCcHHHHHHHHHHHHHHHhhcccccCCCeEEEe
Confidence 112224555533 3568888888888876 689999999999999999999999999999883
No 8
>KOG2582 consensus COP9 signalosome, subunit CSN3 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=99.08 E-value=4.6e-09 Score=94.75 Aligned_cols=177 Identities=15% Similarity=0.218 Sum_probs=132.6
Q ss_pred CCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCccChHHHHHHHHHHHHHHhh-cCCC---CChhhhh--h-c-c
Q 025096 55 FPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNPQSEANIRMILKYLIPVKLS-IGIL---PKDWLLE--K-Y-N 126 (258)
Q Consensus 55 ~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~~~~~~~~IL~~LIp~~Ll-~G~~---P~~~ll~--~-~-~ 126 (258)
.+.+..+.|+||.|.++.-..+|+.|..+|+.|+-..--+-........+..+.++|+ .|++ |+-.... + + +
T Consensus 177 ~~~k~fL~Y~yYgg~iciglk~fe~Al~~~e~~v~~Pa~~vs~~hlEaYkkylLvsLI~~GK~~ql~k~ts~~~~r~~K~ 256 (422)
T KOG2582|consen 177 LDPKYFLLYLYYGGMICIGLKRFERALYLLEICVTTPAMAVSHIHLEAYKKYLLVSLILTGKVFQLPKNTSQNAGRFFKP 256 (422)
T ss_pred CCHHHHHHHHHhcceeeeccccHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHHHHhhhcCceeeccccchhhhHHhccc
Confidence 5778899999999999999999999999999999853333345666667777778887 5875 5433211 1 1 2
Q ss_pred cc-ccHHHHHHHHhCCHHHHHHHHHHcHHHHHHhcHHHHHHh-hHHHHHHHHHH--HHHHHhhcCCCCCCccccHHHHHH
Q 025096 127 LV-EYSNIVQALRRGDLRLLRHALEEHEDQFLRSGVYLVLEK-LELQVYQRLFK--KIYIIQKQKDPSKAHQMKLDVIVK 202 (258)
Q Consensus 127 l~-~y~~L~~av~~Gdl~~f~~~l~~~~~~f~~~glylll~~-l~~~v~r~L~k--kv~~~~~~~~~~~~~~i~l~~i~~ 202 (258)
.. +|.++.++.-.+.....+..+.+|.+.|.+||.--++.. +..+--||+-| |.| ..+++++|+.
T Consensus 257 ms~pY~ef~~~Y~~~~~~eLr~lVk~~~~rF~kDnnt~l~k~av~sl~k~nI~rltktF-----------~sLsL~dIA~ 325 (422)
T KOG2582|consen 257 MSNPYHEFLNVYLKDSSTELRTLVKKHSERFTKDNNTGLAKQAVSSLYKKNIQRLTKTF-----------LSLSLSDIAS 325 (422)
T ss_pred CCchHHHHHHHHhcCCcHHHHHHHHHHHHHHhhcCcHHHHHHHHHHHHHHHHHHHHHHH-----------HHhhHHHHHH
Confidence 34 899999999999999999999999999999998754433 33332333322 222 4589999999
Q ss_pred HHHhccCCCCHHHHHHHHHHHHHcCcceEEeecCceEEEEecCCCCCC
Q 025096 203 ALKWLEMDMDVDEVECIVAILIHKNLVKGYFAHKSKVVVLSKQDPFPK 250 (258)
Q Consensus 203 al~~~~~~~~~~evE~ila~LI~~G~IkGyI~~~~~~lVlsk~~pFP~ 250 (258)
..++ .+.+|||-.+..||.+|.|-+.|+ |.+++- .||=|-
T Consensus 326 ~vQL----a~~qevek~Ilqmie~~~i~a~iN---G~v~f~-~n~e~~ 365 (422)
T KOG2582|consen 326 RVQL----ASAQEVEKYILQMIEDGEIFASIN---GMVFFT-DNPEKY 365 (422)
T ss_pred HHHh----cchHHHHHHHHHHhccCceEEEec---ceEEEe-cCcccC
Confidence 6665 378999999999999999999997 666653 354443
No 9
>COG5159 RPN6 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=98.80 E-value=1e-07 Score=84.05 Aligned_cols=202 Identities=17% Similarity=0.246 Sum_probs=139.7
Q ss_pred HHHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCccCh-HHHHH
Q 025096 23 QLFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNPQSE-ANIRM 101 (258)
Q Consensus 23 ~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~~~-~~~~~ 101 (258)
+.-|.|++++|....+.=+.+-..... --..|..-+.+----.|.++|-+.||..|+..|.+||.-.+.-.. ..-..
T Consensus 170 lESKvyh~irnv~KskaSLTaArt~An--s~YCPpqlqa~lDL~sGIlhcdd~dyktA~SYF~Ea~Egft~l~~d~kAc~ 247 (421)
T COG5159 170 LESKVYHEIRNVSKSKASLTAARTLAN--SAYCPPQLQAQLDLLSGILHCDDRDYKTASSYFIEALEGFTLLKMDVKACV 247 (421)
T ss_pred hhHHHHHHHHhhhhhhhHHHHHHHHhh--ccCCCHHHHHHHHHhccceeeccccchhHHHHHHHHHhccccccchHHHHH
Confidence 344555555555555433332222111 012455666777788999999999999999999999997664333 33456
Q ss_pred HHHHHHHHHhhcCCCCC-------hhhhhhcc---ccccHHHHHHHHhCCHHHHHHHHHHcH-----HHHHHhcHHHHHH
Q 025096 102 ILKYLIPVKLSIGILPK-------DWLLEKYN---LVEYSNIVQALRRGDLRLLRHALEEHE-----DQFLRSGVYLVLE 166 (258)
Q Consensus 102 IL~~LIp~~Ll~G~~P~-------~~ll~~~~---l~~y~~L~~av~~Gdl~~f~~~l~~~~-----~~f~~~glylll~ 166 (258)
.|+|++..++.++..-. ..-++.|+ +.....+++|+-+-++..|+.++++++ +.|+++.+--+-.
T Consensus 248 sLkYmlLSkIMlN~~~evk~vl~~K~t~~~y~~r~I~am~avaea~~NRsL~df~~aL~qY~~el~~D~~iRsHl~~LYD 327 (421)
T COG5159 248 SLKYMLLSKIMLNRREEVKAVLRNKNTLKHYDDRMIRAMLAVAEAFGNRSLKDFSDALAQYSDELHQDSFIRSHLQYLYD 327 (421)
T ss_pred HHHHHHHHHHHHhhHHHHHHHHccchhHhhhhhhhHHHHHHHHHHhCCCcHhhHHHHHHHhhHHhccCHHHHHHHHHHHH
Confidence 69999998887654322 22233343 334678899999999999999999864 5677766533222
Q ss_pred hhHHHHHHHHHHHHHHHhhcCCCCCCccccHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCcceEEeecCceEEEEe
Q 025096 167 KLELQVYQRLFKKIYIIQKQKDPSKAHQMKLDVIVKALKWLEMDMDVDEVECIVAILIHKNLVKGYFAHKSKVVVLS 243 (258)
Q Consensus 167 ~l~~~v~r~L~kkv~~~~~~~~~~~~~~i~l~~i~~al~~~~~~~~~~evE~ila~LI~~G~IkGyI~~~~~~lVls 243 (258)
.| .=.|++|-| .+.+.+-++-|+..+. .|...||--+..||-+....|.++|+++|+++-
T Consensus 328 ~L---Le~Nl~kii---------EPfs~VeishIa~viG-----ldt~qvEgKLsqMILDKifyG~LDqg~gcLivy 387 (421)
T COG5159 328 VL---LEKNLVKII---------EPFSVVEISHIADVIG-----LDTNQVEGKLSQMILDKIFYGTLDQGDGCLIVY 387 (421)
T ss_pred HH---HHhhhhhhc---------CcceeeehhHHHHHhc-----ccHHHHHHHHHHHHHHHHHHhhhccCCceEEEe
Confidence 21 224666643 2457788888888876 689999999999999999999999999999983
No 10
>smart00753 PAM PCI/PINT associated module.
Probab=98.51 E-value=5.4e-07 Score=66.17 Aligned_cols=66 Identities=21% Similarity=0.272 Sum_probs=54.0
Q ss_pred HHHhhHHHHHHHHHHHHHHHhhcCCCCCCccccHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCcceEEeecCceEEEEe
Q 025096 164 VLEKLELQVYQRLFKKIYIIQKQKDPSKAHQMKLDVIVKALKWLEMDMDVDEVECIVAILIHKNLVKGYFAHKSKVVVLS 243 (258)
Q Consensus 164 ll~~l~~~v~r~L~kkv~~~~~~~~~~~~~~i~l~~i~~al~~~~~~~~~~evE~ila~LI~~G~IkGyI~~~~~~lVls 243 (258)
+.++++..+++.+.+. .++|++++++..+. ++.+++|.++++||.+|.|+|.|+|.++++++.
T Consensus 6 l~~~~~~~~l~~l~~~------------y~~i~~~~i~~~~~-----l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~ 68 (88)
T smart00753 6 LQRKIRLTNLLQLSEP------------YSSISLSDLAKLLG-----LSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFE 68 (88)
T ss_pred HHHHHHHHHHHHHhHH------------hceeeHHHHHHHhC-----cCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEEC
Confidence 3455555555555442 37899999999987 688899999999999999999999999999998
Q ss_pred cCC
Q 025096 244 KQD 246 (258)
Q Consensus 244 k~~ 246 (258)
+..
T Consensus 69 ~~~ 71 (88)
T smart00753 69 EVD 71 (88)
T ss_pred CCc
Confidence 764
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=98.51 E-value=5.4e-07 Score=66.17 Aligned_cols=66 Identities=21% Similarity=0.272 Sum_probs=54.0
Q ss_pred HHHhhHHHHHHHHHHHHHHHhhcCCCCCCccccHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCcceEEeecCceEEEEe
Q 025096 164 VLEKLELQVYQRLFKKIYIIQKQKDPSKAHQMKLDVIVKALKWLEMDMDVDEVECIVAILIHKNLVKGYFAHKSKVVVLS 243 (258)
Q Consensus 164 ll~~l~~~v~r~L~kkv~~~~~~~~~~~~~~i~l~~i~~al~~~~~~~~~~evE~ila~LI~~G~IkGyI~~~~~~lVls 243 (258)
+.++++..+++.+.+. .++|++++++..+. ++.+++|.++++||.+|.|+|.|+|.++++++.
T Consensus 6 l~~~~~~~~l~~l~~~------------y~~i~~~~i~~~~~-----l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~ 68 (88)
T smart00088 6 LQRKIRLTNLLQLSEP------------YSSISLSDLAKLLG-----LSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFE 68 (88)
T ss_pred HHHHHHHHHHHHHhHH------------hceeeHHHHHHHhC-----cCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEEC
Confidence 3455555555555442 37899999999987 688899999999999999999999999999998
Q ss_pred cCC
Q 025096 244 KQD 246 (258)
Q Consensus 244 k~~ 246 (258)
+..
T Consensus 69 ~~~ 71 (88)
T smart00088 69 EVD 71 (88)
T ss_pred CCc
Confidence 764
No 12
>KOG1497 consensus COP9 signalosome, subunit CSN4 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=98.02 E-value=0.00017 Score=64.75 Aligned_cols=216 Identities=15% Similarity=0.235 Sum_probs=139.7
Q ss_pred HHHHHHHHHHHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCcc
Q 025096 15 VGALYLTCQLFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNPQ 94 (258)
Q Consensus 15 ~~~~~~~n~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~ 94 (258)
..-+.+...+-+.|++.++...+.-+++..+ +|--+.....-++.|.-+.+|+.=+.++|-+|...+.+-...-. -
T Consensus 141 ~~kl~l~iriarlyLe~~d~veae~~inRaS---il~a~~~Ne~Lqie~kvc~ARvlD~krkFlEAAqrYyels~~ki-~ 216 (399)
T KOG1497|consen 141 EQKLLLCIRIARLYLEDDDKVEAEAYINRAS---ILQAESSNEQLQIEYKVCYARVLDYKRKFLEAAQRYYELSQRKI-V 216 (399)
T ss_pred HHHHHHHHHHHHHHHhcCcHHHHHHHHHHHH---HhhhcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-c
Confidence 3456667788899999999999998886544 33212212223556666778887788888888777664333211 1
Q ss_pred ChHHHHHHHHHHHHHHhhcCCCCChhh--hhhc------cccccH-----HHHHHHHhCCHHHHHHHHHHcHHHHHHhcH
Q 025096 95 SEANIRMILKYLIPVKLSIGILPKDWL--LEKY------NLVEYS-----NIVQALRRGDLRLLRHALEEHEDQFLRSGV 161 (258)
Q Consensus 95 ~~~~~~~IL~~LIp~~Ll~G~~P~~~l--l~~~------~l~~y~-----~L~~av~~Gdl~~f~~~l~~~~~~f~~~gl 161 (258)
....+..-|+.-+-|-++.+-=|...- ..-| .++.|. =+-+-++..++..|...+..|+..-..+|.
T Consensus 217 ~e~~~~~aL~~a~~CtlLA~~gpqrsr~Latlfkder~~~l~~y~ileKmyl~riI~k~el~ef~~~L~pHQka~~~dgs 296 (399)
T KOG1497|consen 217 DESERLEALKKALQCTLLASAGPQRSRMLATLFKDERCQKLPAYGILEKMYLERIIRKEELQEFEAFLQPHQKAHTMDGS 296 (399)
T ss_pred chHHHHHHHHHhHhheeecCCChHHHHHHHHHhcCcccccccchHHHHHHHHHHHhcchhHHHHHHHhcchhhhcccCcc
Confidence 123456667777767666543333221 1111 122232 244678889999999999998875545553
Q ss_pred HHHHHhhHHHHHHHHHHHHHHHhhcCCCCCCccccHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCcceEEeecCceEEE
Q 025096 162 YLVLEKLELQVYQRLFKKIYIIQKQKDPSKAHQMKLDVIVKALKWLEMDMDVDEVECIVAILIHKNLVKGYFAHKSKVVV 241 (258)
Q Consensus 162 ylll~~l~~~v~r~L~kkv~~~~~~~~~~~~~~i~l~~i~~al~~~~~~~~~~evE~ila~LI~~G~IkGyI~~~~~~lV 241 (258)
-.+ .| .+.=-|++- +...+ +.|+++.+..-+. +|.+.+|.+.+.||.+|+++|+|++.++++-
T Consensus 297 sil-~r--a~~EhNlls-~Skly--------~nisf~~Lg~ll~-----i~~ekaekiaa~MI~qeRmng~IDQ~egiih 359 (399)
T KOG1497|consen 297 SIL-DR--AVIEHNLLS-ASKLY--------NNISFEELGALLK-----IDAEKAEKIAAQMITQERMNGSIDQIEGIIH 359 (399)
T ss_pred hhh-hh--HHHHHhHHH-HHHHH--------HhccHHHHHHHhC-----CCHHHHHHHHHHHHhHHHhccchHhhcceEe
Confidence 321 11 000012211 22222 4588998888776 7999999999999999999999999999999
Q ss_pred EecCCCCCCC
Q 025096 242 LSKQDPFPKL 251 (258)
Q Consensus 242 lsk~~pFP~~ 251 (258)
+-..+|.|.-
T Consensus 360 Fe~~e~l~~w 369 (399)
T KOG1497|consen 360 FEDREELPQW 369 (399)
T ss_pred ecchhhhhhh
Confidence 9888888864
No 13
>KOG2753 consensus Uncharacterized conserved protein, contains PCI domain [General function prediction only]
Probab=97.96 E-value=6.8e-05 Score=67.34 Aligned_cols=99 Identities=20% Similarity=0.334 Sum_probs=88.6
Q ss_pred cHHHHHHHHhCCHHHHHHHHHHcHHHHHHhcHH--HHHHhhHHHHHHHHHHHHHHHhhcCCCCCCccccHHHHHHHHHhc
Q 025096 130 YSNIVQALRRGDLRLLRHALEEHEDQFLRSGVY--LVLEKLELQVYQRLFKKIYIIQKQKDPSKAHQMKLDVIVKALKWL 207 (258)
Q Consensus 130 y~~L~~av~~Gdl~~f~~~l~~~~~~f~~~gly--lll~~l~~~v~r~L~kkv~~~~~~~~~~~~~~i~l~~i~~al~~~ 207 (258)
..++...+-+|-+..|.+..++|..+.-..|+. .++.|.|.+.+..|-. .+..||+..++..|+
T Consensus 240 i~qLL~IF~s~~L~aYveF~~~N~~Fvqs~gl~~E~~~~KMRLLTlm~LA~------------es~eisy~~l~k~Lq-- 305 (378)
T KOG2753|consen 240 IHQLLKIFVSGKLDAYVEFVAANSGFVQSQGLVHEQNMAKMRLLTLMSLAE------------ESNEISYDTLAKELQ-- 305 (378)
T ss_pred HHHHHHHHHhcchHHHHHHHHhChHHHHHhcccHHHHHHHHHHHHHHHHhc------------cCCCCCHHHHHHHhc--
Confidence 578899999999999999999999988889986 3788999888877744 357899999999998
Q ss_pred cCCCCHHHHHHHHHHHHHcCcceEEeecCceEEEEecC
Q 025096 208 EMDMDVDEVECIVAILIHKNLVKGYFAHKSKVVVLSKQ 245 (258)
Q Consensus 208 ~~~~~~~evE~ila~LI~~G~IkGyI~~~~~~lVlsk~ 245 (258)
+.+||||-++...|.-|+|.|.|++-+++|++|..
T Consensus 306 ---I~edeVE~fVIdaI~aklV~~kidq~~~~viVs~~ 340 (378)
T KOG2753|consen 306 ---INEDEVELFVIDAIRAKLVEGKIDQMNRTVIVSSS 340 (378)
T ss_pred ---cCHHHHHHHHHHHHHHHHHHhhHHhhcceEEeehh
Confidence 79999999999999999999999999999999764
No 14
>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=97.66 E-value=0.0027 Score=59.43 Aligned_cols=193 Identities=16% Similarity=0.254 Sum_probs=116.7
Q ss_pred hhHHHHHHHHHHHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcC
Q 025096 13 KRVGALYLTCQLFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCN 92 (258)
Q Consensus 13 Kk~~~~~~~n~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~ 92 (258)
|..| ||-...|+|++--+|++..|-.+++.|+-..---++..|.. .|+.+||.|=.||.-++|.+|-..|+..+..-.
T Consensus 118 ~~LG-YFSligLlRvh~LLGDY~~Alk~l~~idl~~~~l~~~V~~~-~is~~YyvGFaylMlrRY~DAir~f~~iL~yi~ 195 (404)
T PF10255_consen 118 KMLG-YFSLIGLLRVHCLLGDYYQALKVLENIDLNKKGLYTKVPAC-HISTYYYVGFAYLMLRRYADAIRTFSQILLYIQ 195 (404)
T ss_pred HHhh-HHHHHHHHHHHHhccCHHHHHHHhhccCcccchhhccCcch-heehHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444 45556789999999999999999998885321123444544 556669999999999999999999999887333
Q ss_pred ccC-------------hHHHHHHHHHH-HHHHhhcCCCCChhhhhhcccc-ccHHHHHHHHhCCHHHHHHHHHHcHHHHH
Q 025096 93 PQS-------------EANIRMILKYL-IPVKLSIGILPKDWLLEKYNLV-EYSNIVQALRRGDLRLLRHALEEHEDQFL 157 (258)
Q Consensus 93 ~~~-------------~~~~~~IL~~L-Ip~~Ll~G~~P~~~ll~~~~l~-~y~~L~~av~~Gdl~~f~~~l~~~~~~f~ 157 (258)
+.. .+.-.+..-.| |...+.-+++|. .+... +. .|.+=...+.+||+..|++....-...|+
T Consensus 196 r~k~~~~~~~~q~d~i~K~~eqMyaLlAic~~l~p~~lde-~i~~~--lkeky~ek~~kmq~gd~~~f~elF~~acPKFI 272 (404)
T PF10255_consen 196 RTKNQYHQRSYQYDQINKKNEQMYALLAICLSLCPQRLDE-SISSQ--LKEKYGEKMEKMQRGDEEAFEELFSFACPKFI 272 (404)
T ss_pred HhhhhhccccchhhHHHhHHHHHHHHHHHHHHhCCCCCCH-HHHHH--HHHHHHHHHHHHHccCHHHHHHHHHhhCCCcc
Confidence 222 12223333222 222222233322 11111 22 37788888999999999999986332232
Q ss_pred H--------------------hcHHHHHHhhHHHHHHHHHHHHHHHhhcCCCCCCccccHHHHHHHHHhccCCCCHHHHH
Q 025096 158 R--------------------SGVYLVLEKLELQVYQRLFKKIYIIQKQKDPSKAHQMKLDVIVKALKWLEMDMDVDEVE 217 (258)
Q Consensus 158 ~--------------------~glylll~~l~~~v~r~L~kkv~~~~~~~~~~~~~~i~l~~i~~al~~~~~~~~~~evE 217 (258)
. +-+-+.++-.+..-...-+|.....| +.|+++.++.-+. +|++++-
T Consensus 273 sp~~pp~~~~~~~~~~~e~~~~Ql~~Fl~eV~~q~~l~~lRSyLKLY--------tti~l~KLA~fl~-----vd~~~lr 339 (404)
T PF10255_consen 273 SPVSPPDYDGPSQNKNKEPYRRQLKLFLDEVKQQQKLPTLRSYLKLY--------TTIPLEKLASFLD-----VDEEELR 339 (404)
T ss_pred CCCCCCCcccccchhhhhHHHHHHHHHHHHHHHhhhhhHHHHHHHhh--------cCCCHHHHHHHcC-----CCHHHHH
Confidence 2 11222222222222222223333343 8899999877764 6777776
Q ss_pred HHHHHH
Q 025096 218 CIVAIL 223 (258)
Q Consensus 218 ~ila~L 223 (258)
..+..+
T Consensus 340 ~~Ll~~ 345 (404)
T PF10255_consen 340 SQLLCF 345 (404)
T ss_pred HHHHHH
Confidence 666544
No 15
>KOG0687 consensus 26S proteasome regulatory complex, subunit RPN7/PSMD6 [Posttranslational modification, protein turnover, chaperones]
Probab=97.01 E-value=0.042 Score=49.82 Aligned_cols=167 Identities=16% Similarity=0.204 Sum_probs=115.1
Q ss_pred hhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCccChHHHHHHHHHHHHHHhhc-CC-------CCChhhhhhc-cccccH
Q 025096 61 VTYMYYTGRLEVFNENFPAADQKLSYALINCNPQSEANIRMILKYLIPVKLSI-GI-------LPKDWLLEKY-NLVEYS 131 (258)
Q Consensus 61 v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~~~~~~~~IL~~LIp~~Ll~-G~-------~P~~~ll~~~-~l~~y~ 131 (258)
=+|.=|-|.+.|.-++|++|...|..++......-.---..+..|-|-++++. .+ +-.+++++.- ++..-.
T Consensus 181 NRlKvY~Gly~msvR~Fk~Aa~Lfld~vsTFtS~El~~Y~~~v~Ytv~~g~i~leR~dlktKVi~~~Evl~vl~~l~~~~ 260 (393)
T KOG0687|consen 181 NRLKVYQGLYCMSVRNFKEAADLFLDSVSTFTSYELMSYETFVRYTVITGLIALERVDLKTKVIKCPEVLEVLHKLPSVS 260 (393)
T ss_pred hhHHHHHHHHHHHHHhHHHHHHHHHHHcccccceecccHHHHHHHHHHHhhheeccchHHhhhcCcHHHHHHhhcCchHH
Confidence 35777899999999999999999999988655333333445566777777763 21 2233333322 133446
Q ss_pred HHHHHHHhCCHHHHHHHHHHcH------HHHHHhcHHHHHHhhHHHHHHHHHHHHHHHhhcCCCCCCccccHHHHHHHHH
Q 025096 132 NIVQALRRGDLRLLRHALEEHE------DQFLRSGVYLVLEKLELQVYQRLFKKIYIIQKQKDPSKAHQMKLDVIVKALK 205 (258)
Q Consensus 132 ~L~~av~~Gdl~~f~~~l~~~~------~~f~~~glylll~~l~~~v~r~L~kkv~~~~~~~~~~~~~~i~l~~i~~al~ 205 (258)
+++.++=.-|...|-..+...+ ++|+....-.-+--.|..+|-.++... ..+++...++++.
T Consensus 261 q~l~SLY~C~Y~~Ff~~L~~~~~~~lk~D~~l~~h~~yyvREMR~rvY~QlLESY------------rsl~l~~MA~aFg 328 (393)
T KOG0687|consen 261 QLLNSLYECDYSDFFNDLAAVEAKQLKDDRYLGPHYRYYVREMRRRVYAQLLESY------------RSLTLESMAKAFG 328 (393)
T ss_pred HHHHHHHhccHHHHHHHHHHHHHHhhccchhcchHHHHHHHHHHHHHHHHHHHHH------------HHHHHHHHHHHhC
Confidence 6677777777777777774432 223322222233446667777776642 4578999999987
Q ss_pred hccCCCCHHHHHHHHHHHHHcCcceEEeecCceEEEEec
Q 025096 206 WLEMDMDVDEVECIVAILIHKNLVKGYFAHKSKVVVLSK 244 (258)
Q Consensus 206 ~~~~~~~~~evE~ila~LI~~G~IkGyI~~~~~~lVlsk 244 (258)
++.+-++.=++..|..|.+...|+..+++|-..+
T Consensus 329 -----VSVefiDreL~rFI~~grL~ckIDrVnGVVEtNr 362 (393)
T KOG0687|consen 329 -----VSVEFIDRELGRFIAAGRLHCKIDRVNGVVETNR 362 (393)
T ss_pred -----chHHHHHhHHHHhhccCceeeeeecccceeecCC
Confidence 7899999999999999999999999999877654
No 16
>COG5187 RPN7 26S proteasome regulatory complex component, contains PCI domain [Posttranslational modification, protein turnover, chaperones]
Probab=96.84 E-value=0.052 Score=48.64 Aligned_cols=168 Identities=20% Similarity=0.260 Sum_probs=115.4
Q ss_pred hhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCccChHHHHHHHHHHHHHHhh-cC-------CCCChhhhhhcc----c
Q 025096 60 KVTYMYYTGRLEVFNENFPAADQKLSYALINCNPQSEANIRMILKYLIPVKLS-IG-------ILPKDWLLEKYN----L 127 (258)
Q Consensus 60 ~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~~~~~~~~IL~~LIp~~Ll-~G-------~~P~~~ll~~~~----l 127 (258)
+=+|.=|.|.+.|..++|.+|...|..++......-.-.-..+..|.|-++++ +. .+-+++++.-.+ +
T Consensus 191 rNRyK~Y~Gi~~m~~RnFkeAa~Ll~d~l~tF~S~El~sY~~~vrYa~~~Gl~~leR~diktki~dspevl~vi~~~e~l 270 (412)
T COG5187 191 RNRYKVYKGIFKMMRRNFKEAAILLSDILPTFESSELISYSRAVRYAIFCGLLRLERRDIKTKILDSPEVLDVIGSSEKL 270 (412)
T ss_pred hhhHHHHHHHHHHHHHhhHHHHHHHHHHhccccccccccHHHHHHHHHHhhhheeehhhhhhhhcCCHHHHHhccchhhh
Confidence 44688899999999999999999999998866544444456678888888887 32 244555555333 2
Q ss_pred cccHHHHHHHHhCCHH-HHHHHHHHc-----HHHHHHhcHHHHHHhhHHHHHHHHHHHHHHHhhcCCCCCCccccHHHHH
Q 025096 128 VEYSNIVQALRRGDLR-LLRHALEEH-----EDQFLRSGVYLVLEKLELQVYQRLFKKIYIIQKQKDPSKAHQMKLDVIV 201 (258)
Q Consensus 128 ~~y~~L~~av~~Gdl~-~f~~~l~~~-----~~~f~~~glylll~~l~~~v~r~L~kkv~~~~~~~~~~~~~~i~l~~i~ 201 (258)
.-...++.++-.-|.. -|...++.. .+.|+-+..-..+.-.|.-||-.|+.. +..+++...+
T Consensus 271 ~sl~~l~~SLy~cdY~~~F~~ll~~~~n~L~~d~fl~rh~d~fvREMRrrvYaQlLES------------Yr~lsl~sMA 338 (412)
T COG5187 271 GSLVQLATSLYECDYGGDFMNLLYLFCNSLQDDVFLGRHVDLFVREMRRRVYAQLLES------------YRLLSLESMA 338 (412)
T ss_pred hhHHHHHHHHHHhccchhhHHHHHHHHhhccchHHHHHHHHHHHHHHHHHHHHHHHHH------------HHHhhHHHHH
Confidence 2234555666566655 333333321 234555554444444555555555553 2457899999
Q ss_pred HHHHhccCCCCHHHHHHHHHHHHHcCcceEEeecCceEEEEec
Q 025096 202 KALKWLEMDMDVDEVECIVAILIHKNLVKGYFAHKSKVVVLSK 244 (258)
Q Consensus 202 ~al~~~~~~~~~~evE~ila~LI~~G~IkGyI~~~~~~lVlsk 244 (258)
.++. ++.+-++.=+++-|-+|.+...|+..+++|-..+
T Consensus 339 ~tFg-----VSV~yvdrDLg~FIp~~~LncvIDRvnGvVetnr 376 (412)
T COG5187 339 QTFG-----VSVEYVDRDLGEFIPEGRLNCVIDRVNGVVETNR 376 (412)
T ss_pred HHhC-----ccHHHHhhhHHhhCCCCceeeeeecccceEeccC
Confidence 9887 6899999999999999999999999999876644
No 17
>KOG2758 consensus Translation initiation factor 3, subunit e (eIF-3e) [Translation, ribosomal structure and biogenesis]
Probab=96.66 E-value=0.01 Score=53.60 Aligned_cols=75 Identities=24% Similarity=0.360 Sum_probs=60.0
Q ss_pred HHHHHhcHHHHHHhhHHHHHHHHHHHHHHHhhcCCCCCCccccHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCcceEEe
Q 025096 154 DQFLRSGVYLVLEKLELQVYQRLFKKIYIIQKQKDPSKAHQMKLDVIVKALKWLEMDMDVDEVECIVAILIHKNLVKGYF 233 (258)
Q Consensus 154 ~~f~~~glylll~~l~~~v~r~L~kkv~~~~~~~~~~~~~~i~l~~i~~al~~~~~~~~~~evE~ila~LI~~G~IkGyI 233 (258)
++|+-.-+-..+|..|.+++-..+| | + ..|+++.++..|. ++.+|+|++++|||..-.|.+.|
T Consensus 321 DfFLva~l~~F~E~ARl~ifEtfCR-I---H--------qcIti~mLA~kLn-----m~~eeaErwivnlIr~~rl~Aki 383 (432)
T KOG2758|consen 321 DFFLVALLDEFLENARLLIFETFCR-I---H--------QCITIDMLADKLN-----MDPEEAERWIVNLIRTARLDAKI 383 (432)
T ss_pred chhHHHHHHHHHHHHHHHHHHHHHH-H---H--------HheeHHHHHHHhc-----CCHHHHHHHHHHHHHHhhhhhhh
Confidence 3455444445668888888766655 3 2 4599999999998 78999999999999999999999
Q ss_pred ecCceEEEEecC
Q 025096 234 AHKSKVVVLSKQ 245 (258)
Q Consensus 234 ~~~~~~lVlsk~ 245 (258)
+.+-+-||...+
T Consensus 384 dSklg~Vvmg~~ 395 (432)
T KOG2758|consen 384 DSKLGHVVMGHP 395 (432)
T ss_pred ccccCceeecCC
Confidence 999999888554
No 18
>KOG1498 consensus 26S proteasome regulatory complex, subunit RPN5/PSMD12 [Posttranslational modification, protein turnover, chaperones]
Probab=96.59 E-value=0.18 Score=46.80 Aligned_cols=210 Identities=12% Similarity=0.155 Sum_probs=134.9
Q ss_pred HHHHHHHHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccc--hhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCccC
Q 025096 18 LYLTCQLFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRD--KVTYMYYTGRLEVFNENFPAADQKLSYALINCNPQS 95 (258)
Q Consensus 18 ~~~~n~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~--~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~~ 95 (258)
.-+....+|++.-.+++-++.-+-|.|+.+-+. -|..+ .+.|++-.=++++.++.|-++..++...+..-....
T Consensus 171 V~fiLEQmrKOG~~~D~vra~i~skKI~~K~F~----~~~~~~lKlkyY~lmI~l~lh~~~Yl~v~~~Yraiy~t~~vk~ 246 (439)
T KOG1498|consen 171 VAFILEQMRLCLLRLDYVRAQIISKKINKKFFE----KPDVQELKLKYYELMIRLGLHDRAYLNVCRSYRAIYDTGNVKE 246 (439)
T ss_pred HHHHHHHHHHHHHhhhHHHHHHHHHHhhHHhcC----CccHHHHHHHHHHHHHHhcccccchhhHHHHHHHHhccccccc
Confidence 344556678888888899998888888875322 13344 445555566667788999999999887776332222
Q ss_pred hHH-HHHHHHHHHHHHhhcCCCCC-hhhhhhc-------cccccHHHHHHHHhCCHHHHHHHHHHcHHHHHHhcHHH---
Q 025096 96 EAN-IRMILKYLIPVKLSIGILPK-DWLLEKY-------NLVEYSNIVQALRRGDLRLLRHALEEHEDQFLRSGVYL--- 163 (258)
Q Consensus 96 ~~~-~~~IL~~LIp~~Ll~G~~P~-~~ll~~~-------~l~~y~~L~~av~~Gdl~~f~~~l~~~~~~f~~~glyl--- 163 (258)
... ...+|.-.+...++.-.-+- .+++.+- +++.|..++..+-+|-+..|...-+.+++.+...+...
T Consensus 247 d~~kw~~vL~~iv~f~~LAp~dneQsdll~~is~dKkL~e~p~~k~lLklfv~~EL~rw~s~~~~yg~~l~~~~~~~~~~ 326 (439)
T KOG1498|consen 247 DPEKWIEVLRSIVSFCVLAPHDNEQSDLLARISNDKKLSELPDYKELLKLFVTMELIRWVSLVESYGDELRTNDFFDGGE 326 (439)
T ss_pred ChhhhhhhhhhheeEEeecCCCcHHHHHHHHHhcccccccCccHHHHHHHHHhcceeeehhHhhhhHHHHhhcccccccc
Confidence 111 22222222211122111111 1112111 13459999999999999999977777777666663221
Q ss_pred ----HHHhhHHHHHHHHHHHHHHHhhcCCCCCCccccHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCcceEEeecCceE
Q 025096 164 ----VLEKLELQVYQRLFKKIYIIQKQKDPSKAHQMKLDVIVKALKWLEMDMDVDEVECIVAILIHKNLVKGYFAHKSKV 239 (258)
Q Consensus 164 ----ll~~l~~~v~r~L~kkv~~~~~~~~~~~~~~i~l~~i~~al~~~~~~~~~~evE~ila~LI~~G~IkGyI~~~~~~ 239 (258)
-.+-|+.-++--=+|-+...| ++||+..+..-+. .+.+|+|..+.+|+..|.+.+.|+...+.
T Consensus 327 ~gek~~~dL~~RIiEHNiRiiA~yY--------SrIt~~rl~eLLd-----l~~ee~E~~LS~lv~t~ti~aKidrpsgI 393 (439)
T KOG1498|consen 327 EGEKRWSDLKLRIIEHNIRIIAKYY--------SRITLKRLAELLD-----LPVEEMEKFLSDLVVTGTIYAKIDRPSGI 393 (439)
T ss_pred hhhhHHHHHHHHHHHHHHHHHHHHH--------hhccHHHHHHHhC-----CCHHHHHHHHHHHHhccceEEEecCCCce
Confidence 112233222222334444444 8999999999886 79999999999999999999999999999
Q ss_pred EEEec
Q 025096 240 VVLSK 244 (258)
Q Consensus 240 lVlsk 244 (258)
+.+.+
T Consensus 394 I~F~k 398 (439)
T KOG1498|consen 394 INFQK 398 (439)
T ss_pred EEEEe
Confidence 98855
No 19
>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=96.49 E-value=0.0046 Score=36.26 Aligned_cols=32 Identities=22% Similarity=0.107 Sum_probs=28.7
Q ss_pred hhhhhhhHHhhhhcChHHHHHHHHHHHHhcCc
Q 025096 62 TYMYYTGRLEVFNENFPAADQKLSYALINCNP 93 (258)
Q Consensus 62 ~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~ 93 (258)
.++|+.|.+++..++|++|.+++.+|+..+|.
T Consensus 2 ~~~~~lg~~~~~~~~~~~A~~~~~~al~l~p~ 33 (34)
T PF07719_consen 2 EAWYYLGQAYYQLGNYEEAIEYFEKALELDPN 33 (34)
T ss_dssp HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHHHHCcC
Confidence 46799999999999999999999999999885
No 20
>KOG0686 consensus COP9 signalosome, subunit CSN1 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=96.44 E-value=0.067 Score=49.82 Aligned_cols=160 Identities=14% Similarity=0.162 Sum_probs=104.4
Q ss_pred hhhhhHHhhhhcChHHHHHHHHHH-HHhcCccChHHHHHHHHHHHHHHhhcCCCCChhhhh------hc----cccc-cH
Q 025096 64 MYYTGRLEVFNENFPAADQKLSYA-LINCNPQSEANIRMILKYLIPVKLSIGILPKDWLLE------KY----NLVE-YS 131 (258)
Q Consensus 64 ~YY~G~~~~~~~~~~~A~~~L~~A-~~~c~~~~~~~~~~IL~~LIp~~Ll~G~~P~~~ll~------~~----~l~~-y~ 131 (258)
.-+.|...+-.++|+.|-.+|-.| +.+|.....-...-+-.|--.+.|- -+-..++.. .| ++.+ ..
T Consensus 232 ~C~agLa~L~lkkyk~aa~~fL~~~~~~~d~~~ivtpsdv~iYggLcALA--tfdr~~Lk~~vi~n~~Fk~flel~Pqlr 309 (466)
T KOG0686|consen 232 KCAAGLANLLLKKYKSAAKYFLLAEFDHCDYPEIVTPSDVAIYGGLCALA--TFDRQDLKLNVIKNESFKLFLELEPQLR 309 (466)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCCCccCccceecchhhHHHHhhHhhc--cCCHHHHHHHHHcchhhhhHHhcChHHH
Confidence 456888888888888777665554 5677733322222232232223222 122222221 11 2333 56
Q ss_pred HHHHHHHhCCHHHHHHHHHHcH-----HHHHHhcHHHHHHhhHHHHHHHHHHHHHHHhhcCCCCCCccccHHHHHHHHHh
Q 025096 132 NIVQALRRGDLRLLRHALEEHE-----DQFLRSGVYLVLEKLELQVYQRLFKKIYIIQKQKDPSKAHQMKLDVIVKALKW 206 (258)
Q Consensus 132 ~L~~av~~Gdl~~f~~~l~~~~-----~~f~~~glylll~~l~~~v~r~L~kkv~~~~~~~~~~~~~~i~l~~i~~al~~ 206 (258)
+++.++-++-....-+.+++.+ +.++...+-.+.+++|.-+ |++-. .+...++++.++.|++
T Consensus 310 ~il~~fy~sky~~cl~~L~~~k~~llLD~yLaphVd~Ly~~IR~r~---llqy~---------~py~s~~m~~mA~af~- 376 (466)
T KOG0686|consen 310 EILFKFYSSKYASCLELLREIKPRLLLDMYLAPHVDNLYSLIRNRA---LLQYL---------SPYSSADMSKMAEAFN- 376 (466)
T ss_pred HHHHHHhhhhHHHHHHHHHHhccceeechhcchhHHHHHHHHHHhh---HHHhc---------CccccchHHHHHHHhc-
Confidence 7788888888777777777754 4677777776666666633 32211 2457899999999998
Q ss_pred ccCCCCHHHHHHHHHHHHHcCcceEEeecCceEEEE
Q 025096 207 LEMDMDVDEVECIVAILIHKNLVKGYFAHKSKVVVL 242 (258)
Q Consensus 207 ~~~~~~~~evE~ila~LI~~G~IkGyI~~~~~~lVl 242 (258)
.+..++|.=|.-||.+|.|+|.|+..++++-.
T Consensus 377 ----~sv~~le~~l~~LI~~~~i~~rIDs~~ki~~~ 408 (466)
T KOG0686|consen 377 ----TSVAILESELLELILEGKISGRIDSHNKILYA 408 (466)
T ss_pred ----ccHHHHHHHHHHHHHccchheeeccccceeee
Confidence 68999999999999999999999998887655
No 21
>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B.
Probab=96.16 E-value=0.028 Score=38.04 Aligned_cols=62 Identities=15% Similarity=0.064 Sum_probs=51.4
Q ss_pred HHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCcc
Q 025096 24 LFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNPQ 94 (258)
Q Consensus 24 l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~ 94 (258)
+-..|++.|+++.|...++.+-.. .|. ....+|..|.++...+++++|...+..+....|.+
T Consensus 3 ~a~~~~~~g~~~~A~~~~~~~l~~-~P~--------~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~~P~~ 64 (65)
T PF13432_consen 3 LARALYQQGDYDEAIAAFEQALKQ-DPD--------NPEAWYLLGRILYQQGRYDEALAYYERALELDPDN 64 (65)
T ss_dssp HHHHHHHCTHHHHHHHHHHHHHCC-STT--------HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-
T ss_pred HHHHHHHcCCHHHHHHHHHHHHHH-CCC--------CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCC
Confidence 457899999999999999887653 232 66788999999999999999999999999988754
No 22
>PF13371 TPR_9: Tetratricopeptide repeat
Probab=95.87 E-value=0.028 Score=38.80 Aligned_cols=63 Identities=16% Similarity=0.042 Sum_probs=50.8
Q ss_pred HHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCccC
Q 025096 24 LFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNPQS 95 (258)
Q Consensus 24 l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~~ 95 (258)
|..+|++.++++.+...+..+-.. .|+ ....++..|.+++..++|.+|.+.|+.++..+|.+.
T Consensus 1 l~~~~~~~~~~~~A~~~~~~~l~~-~p~--------~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~~~p~~~ 63 (73)
T PF13371_consen 1 LKQIYLQQEDYEEALEVLERALEL-DPD--------DPELWLQRARCLFQLGRYEEALEDLERALELSPDDP 63 (73)
T ss_pred CHHHHHhCCCHHHHHHHHHHHHHh-Ccc--------cchhhHHHHHHHHHhccHHHHHHHHHHHHHHCCCcH
Confidence 357899999999999888654332 132 455678899999999999999999999999999654
No 23
>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=94.65 E-value=0.05 Score=31.88 Aligned_cols=31 Identities=16% Similarity=-0.014 Sum_probs=27.3
Q ss_pred hhhhhhHHhhhhcChHHHHHHHHHHHHhcCc
Q 025096 63 YMYYTGRLEVFNENFPAADQKLSYALINCNP 93 (258)
Q Consensus 63 y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~ 93 (258)
-+|..|.+++..++|++|.+++++|+...|.
T Consensus 3 ~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~ 33 (34)
T PF00515_consen 3 AYYNLGNAYFQLGDYEEALEYYQRALELDPD 33 (34)
T ss_dssp HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT
T ss_pred HHHHHHHHHHHhCCchHHHHHHHHHHHHCcC
Confidence 4688999999999999999999999998774
No 24
>KOG1076 consensus Translation initiation factor 3, subunit c (eIF-3c) [Translation, ribosomal structure and biogenesis]
Probab=94.40 E-value=0.38 Score=47.69 Aligned_cols=206 Identities=13% Similarity=0.212 Sum_probs=128.9
Q ss_pred HHHHHHHh--cCChhhHHHHH--HHhhccCCCCCCCCCccchhhhhh---hhhHHhhhhcChHHHHHHHHHHHHhcC---
Q 025096 23 QLFKIYFK--LGTVHLCRSVI--RSIETARIFDFEEFPKRDKVTYMY---YTGRLEVFNENFPAADQKLSYALINCN--- 92 (258)
Q Consensus 23 ~l~kiyf~--l~~~~~~~~l~--~~i~~~~~p~~~~~~~~~~v~y~Y---Y~G~~~~~~~~~~~A~~~L~~A~~~c~--- 92 (258)
.||.||+. .+++..|++++ +.+.. +.+++..+-++-|+= -+|.+.|-+|-.++|+.+|+.-...-.
T Consensus 489 mLchIYh~AL~d~f~~ARDlLLMSHlQd----nI~h~D~stQIL~NRtmvQLGLCAFR~Gmi~EaH~~L~dl~st~r~kE 564 (843)
T KOG1076|consen 489 MLCHIYHHALHDNFYTARDLLLMSHLQD----NIQHADISTQILFNRTMVQLGLCAFRQGMIKEAHQCLSDLQSTGRVKE 564 (843)
T ss_pred HHHHHHHHHHHHhHHHHHHHHHHHHHHH----HhhccChhHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHhcchHHH
Confidence 45666663 45666666665 22222 112233344444432 379999999999999999987665222
Q ss_pred ------------ccCh----------------HHHHHH-HHHHHHHHhhcCCCC--------------Chhh---hhhcc
Q 025096 93 ------------PQSE----------------ANIRMI-LKYLIPVKLSIGILP--------------KDWL---LEKYN 126 (258)
Q Consensus 93 ------------~~~~----------------~~~~~I-L~~LIp~~Ll~G~~P--------------~~~l---l~~~~ 126 (258)
+.+. -|..++ -.||+ |+||+ ++| ++.. |+.++
T Consensus 565 LLgQgv~~~~~he~t~eQe~~eR~rQlPyHmHINLELlEcVyLt-caMLl-EIP~MAA~~~d~Rrr~iSk~frr~Le~se 642 (843)
T KOG1076|consen 565 LLGQGVLQRRQHEKTAEQEKIERRRQLPYHMHINLELLECVYLT-CAMLL-EIPYMAAHESDARRRMISKSFRRQLEHSE 642 (843)
T ss_pred HHhhhhhhhhhhccChhhHHHHHhhcCchhhhccHHHHHHHHHH-HHHHH-hhhHHhhhhhhhhcccccHHHHHHHHHHh
Confidence 1010 011222 24555 33433 233 2221 22221
Q ss_pred ----------cccc-HHHHHHHHhCCHHHHHHHHHHcHHHHHH----hcHH-HHHHhhHHHHHHHHHHHHHHHhhcCCCC
Q 025096 127 ----------LVEY-SNIVQALRRGDLRLLRHALEEHEDQFLR----SGVY-LVLEKLELQVYQRLFKKIYIIQKQKDPS 190 (258)
Q Consensus 127 ----------l~~y-~~L~~av~~Gdl~~f~~~l~~~~~~f~~----~gly-lll~~l~~~v~r~L~kkv~~~~~~~~~~ 190 (258)
..+| ..-.+|++.||+..-.+.|-++...|-- +.+- .+.++++.-.+|+.+=.....|
T Consensus 643 rqsf~gPPEn~RehVvaAsKAm~~Gnw~~c~~fi~nn~KvW~Lfpn~d~V~~Ml~~rIqEEsLRTYLftYss~Y------ 716 (843)
T KOG1076|consen 643 RQSFTGPPENTREHVVAASKAMQKGNWQKCFEFIVNNIKVWDLFPNADTVLDMLTERIQEESLRTYLFTYSSVY------ 716 (843)
T ss_pred hccccCCchhHHHHHHHHHHHHhcCCHHHHHHHHHhhhhHHHhcccHHHHHHHHHHHHHHHHHHHHHHHhhhhh------
Confidence 1123 3446899999999999966664443322 2232 3557888877777765554444
Q ss_pred CCccccHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCcceEEeecCceEEEEecCCC
Q 025096 191 KAHQMKLDVIVKALKWLEMDMDVDEVECIVAILIHKNLVKGYFAHKSKVVVLSKQDP 247 (258)
Q Consensus 191 ~~~~i~l~~i~~al~~~~~~~~~~evE~ila~LI~~G~IkGyI~~~~~~lVlsk~~p 247 (258)
..+|++.++..+. ++...|..|+.+||..-=|.|.+++.++++|+-+..|
T Consensus 717 --~SvSl~~LA~mFd-----Lp~~~VhsIiSkmiineEl~AslDqpt~~iv~hrvE~ 766 (843)
T KOG1076|consen 717 --DSVSLAKLADMFD-----LPEPKVHSIISKMIINEELHASLDQPTQCIVMHRVEP 766 (843)
T ss_pred --hhccHHHHHHHhC-----CCchhHHHHHHHHHHHHHhhhccCCCcceEEEeeccc
Confidence 6799999999885 7899999999999999999999999999999977554
No 25
>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A.
Probab=93.63 E-value=0.17 Score=36.14 Aligned_cols=54 Identities=17% Similarity=0.219 Sum_probs=42.8
Q ss_pred HHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHH
Q 025096 24 LFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYA 87 (258)
Q Consensus 24 l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A 87 (258)
+..+||+.++++.|-.+++..+.. ...+...|..|+.++-.++|++|.++|.+|
T Consensus 31 la~~~~~~~~y~~A~~~~~~~~~~----------~~~~~~~~l~a~~~~~l~~y~eAi~~l~~~ 84 (84)
T PF12895_consen 31 LAQCYFQQGKYEEAIELLQKLKLD----------PSNPDIHYLLARCLLKLGKYEEAIKALEKA 84 (84)
T ss_dssp HHHHHHHTTHHHHHHHHHHCHTHH----------HCHHHHHHHHHHHHHHTT-HHHHHHHHHHH
T ss_pred HHHHHHHCCCHHHHHHHHHHhCCC----------CCCHHHHHHHHHHHHHhCCHHHHHHHHhcC
Confidence 789999999999999999762211 113566677799999999999999999876
No 26
>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=93.49 E-value=0.39 Score=32.54 Aligned_cols=62 Identities=19% Similarity=0.138 Sum_probs=47.4
Q ss_pred HHHHHHHHHhcCChhhHHHHHHH-hhccCCCCCCCCCccchhhhhhhhhHHhhhhc-ChHHHHHHHHHHHHhcC
Q 025096 21 TCQLFKIYFKLGTVHLCRSVIRS-IETARIFDFEEFPKRDKVTYMYYTGRLEVFNE-NFPAADQKLSYALINCN 92 (258)
Q Consensus 21 ~n~l~kiyf~l~~~~~~~~l~~~-i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~-~~~~A~~~L~~A~~~c~ 92 (258)
...+-.+|++.++++.+...++. ++-. |+ ....+|..|.+++..+ ++.+|.++++.|+..-|
T Consensus 6 ~~~~g~~~~~~~~~~~A~~~~~~ai~~~--p~--------~~~~~~~~g~~~~~~~~~~~~A~~~~~~al~l~P 69 (69)
T PF13414_consen 6 WYNLGQIYFQQGDYEEAIEYFEKAIELD--PN--------NAEAYYNLGLAYMKLGKDYEEAIEDFEKALKLDP 69 (69)
T ss_dssp HHHHHHHHHHTTHHHHHHHHHHHHHHHS--TT--------HHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHST
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHcC--CC--------CHHHHHHHHHHHHHhCccHHHHHHHHHHHHHcCc
Confidence 45566788999999999988744 4321 22 3447789999999998 79999999999988644
No 27
>PF13424 TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 4A1S_B 3CEQ_B 3EDT_H ....
Probab=93.24 E-value=0.29 Score=34.16 Aligned_cols=71 Identities=14% Similarity=0.087 Sum_probs=53.9
Q ss_pred HHHHHHHHHHHHHhcCChhhHHHHHHH-hhcc-CCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhc
Q 025096 17 ALYLTCQLFKIYFKLGTVHLCRSVIRS-IETA-RIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINC 91 (258)
Q Consensus 17 ~~~~~n~l~kiyf~l~~~~~~~~l~~~-i~~~-~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c 91 (258)
+....+.+-.+|+++++++.|.+.++. ++-. ..++ ...+.+..++-.|.++-..+++++|.+++++|++.+
T Consensus 4 ~a~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~----~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al~i~ 76 (78)
T PF13424_consen 4 TANAYNNLARVYRELGRYDEALDYYEKALDIEEQLGD----DHPDTANTLNNLGECYYRLGDYEEALEYYQKALDIF 76 (78)
T ss_dssp HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTT----HHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCC----CCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhh
Confidence 445668889999999999999988844 3321 1221 123468888999999999999999999999999864
No 28
>COG5071 RPN5 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=92.94 E-value=7.1 Score=35.51 Aligned_cols=210 Identities=14% Similarity=0.152 Sum_probs=116.8
Q ss_pred HHHHHHHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCccChHH
Q 025096 19 YLTCQLFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNPQSEAN 98 (258)
Q Consensus 19 ~~~n~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~~~~~ 98 (258)
++.-.+-++|-..|+.+.|.+++=++.. ..+..+..++.|+|--=.=++.+.++||..|...-..-.+..-+...-.
T Consensus 132 riT~~L~~ikee~Gdi~sA~Dilcn~pV---ETygs~~~Sekv~fiLEQ~rL~vl~~Dy~~A~~~~kKI~KK~Fe~~d~~ 208 (439)
T COG5071 132 RLTQLLSQIKEEQGDIKSAQDILCNEPV---ETYGSFDLSEKVAFILEQVRLFLLRSDYYMASTYTKKINKKFFEKEDVQ 208 (439)
T ss_pred HHHHHHHHHHHHhcchhHHHHHHhcCch---hhccchhHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHhccccHH
Confidence 5667788899999999999999865442 3456677889999887778888899999999876555544433222111
Q ss_pred HHHHHHHHHHHHhhcCC--CCChh---------------------hhh--hc-c-ccccH----HHHHHHHhCCHHHHHH
Q 025096 99 IRMILKYLIPVKLSIGI--LPKDW---------------------LLE--KY-N-LVEYS----NIVQALRRGDLRLLRH 147 (258)
Q Consensus 99 ~~~IL~~LIp~~Ll~G~--~P~~~---------------------ll~--~~-~-l~~y~----~L~~av~~Gdl~~f~~ 147 (258)
-..+--|=..|++-+|+ +-... .+. -| - |.+|. +++.- .+||.+.-..
T Consensus 209 slKlkyYeL~V~i~Lh~R~Yl~v~~y~~~vY~t~~~~~d~Akwk~VLS~~v~F~iLtpy~neq~dlvhK-i~~d~kl~sl 287 (439)
T COG5071 209 SLKLKYYELKVRIGLHDRAYLDVCKYYRAVYDTAVVQEDPAKWKEVLSNVVCFALLTPYDNEQADLLHK-INADHKLNSL 287 (439)
T ss_pred HHHHHHHHHhheeecccHHHHHHHHHHHHHHHHHHhccCcccccchhhcceeeEEecccccHHHHHHHH-hhhhhhhccc
Confidence 11111122223333332 11100 111 00 0 23442 23222 3344433221
Q ss_pred HHHH----------cHHHHHHhcHHH--HH---------------HhhHHHHHHHHHHHHHHHhhcCCCCCCccccHHHH
Q 025096 148 ALEE----------HEDQFLRSGVYL--VL---------------EKLELQVYQRLFKKIYIIQKQKDPSKAHQMKLDVI 200 (258)
Q Consensus 148 ~l~~----------~~~~f~~~glyl--ll---------------~~l~~~v~r~L~kkv~~~~~~~~~~~~~~i~l~~i 200 (258)
...+ ...|-+-+.+|- +. +-|+.-|+--=+|-+... +++|+.+.+
T Consensus 288 ~~~~~lVk~f~vNelmrwp~V~~~y~~~l~~~~faF~~e~~~~~w~DL~krviEHN~RvI~~y--------YSrI~~~rl 359 (439)
T COG5071 288 PLLQQLVKCFIVNELMRWPKVAEIYGSALRSNVFAFNDEKGEKRWSDLRKRVIEHNIRVIANY--------YSRIHCSRL 359 (439)
T ss_pred hhhhhHHHHHHHHHHHhhhHHHHHhHHHHHhhhhhhccchhhhhHHHHHHHHHHhhHhHHHHH--------hhhhhHHHH
Confidence 1111 011111122221 00 111111111112222222 367888877
Q ss_pred HHHHHhccCCCCHHHHHHHHHHHHHcCcceEEeecCceEEEEecC
Q 025096 201 VKALKWLEMDMDVDEVECIVAILIHKNLVKGYFAHKSKVVVLSKQ 245 (258)
Q Consensus 201 ~~al~~~~~~~~~~evE~ila~LI~~G~IkGyI~~~~~~lVlsk~ 245 (258)
...+. .+++++|..++.|+.+|.+.+.|++..+.+-+-|.
T Consensus 360 ~~lld-----~~~s~te~~ISdlVN~G~~yaKiNrpa~Ii~FEK~ 399 (439)
T COG5071 360 GVLLD-----MSPSETEQFISDLVNKGHFYAKINRPAQIISFEKS 399 (439)
T ss_pred HHHHc-----CCHHHHHHHHHHHHhcCcEEEEecCccceEEeecc
Confidence 77765 68999999999999999999999999999888764
No 29
>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=92.80 E-value=0.82 Score=35.06 Aligned_cols=33 Identities=12% Similarity=0.061 Sum_probs=19.6
Q ss_pred hhhhhhhHHhhhhcChHHHHHHHHHHHHhcCcc
Q 025096 62 TYMYYTGRLEVFNENFPAADQKLSYALINCNPQ 94 (258)
Q Consensus 62 ~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~ 94 (258)
..+|+.|.++...+++++|...+..+++..|..
T Consensus 86 ~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~ 118 (135)
T TIGR02552 86 RPYFHAAECLLALGEPESALKALDLAIEICGEN 118 (135)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHHHhcccc
Confidence 344556666666666666666666666655543
No 30
>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=92.36 E-value=0.23 Score=28.85 Aligned_cols=31 Identities=16% Similarity=0.073 Sum_probs=28.0
Q ss_pred hhhhhhhHHhhhhcChHHHHHHHHHHHHhcC
Q 025096 62 TYMYYTGRLEVFNENFPAADQKLSYALINCN 92 (258)
Q Consensus 62 ~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~ 92 (258)
..+|-.|.++...+++++|.++|..|++..|
T Consensus 2 ~~~~~lg~~y~~~~~~~~A~~~~~~a~~~~~ 32 (34)
T PF13181_consen 2 EAYYNLGKIYEQLGDYEEALEYFEKALELNP 32 (34)
T ss_dssp HHHHHHHHHHHHTTSHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHHhhCC
Confidence 3567899999999999999999999999876
No 31
>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A.
Probab=92.14 E-value=0.21 Score=28.62 Aligned_cols=31 Identities=10% Similarity=0.039 Sum_probs=28.0
Q ss_pred hhhhhHHhhhhcChHHHHHHHHHHHHhcCcc
Q 025096 64 MYYTGRLEVFNENFPAADQKLSYALINCNPQ 94 (258)
Q Consensus 64 ~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~ 94 (258)
+|..|+++...+++++|.+.|+..+...|.+
T Consensus 3 ~~~~a~~~~~~g~~~~A~~~~~~~~~~~P~s 33 (33)
T PF13174_consen 3 LYRLARCYYKLGDYDEAIEYFQRLIKRYPDS 33 (33)
T ss_dssp HHHHHHHHHHHCHHHHHHHHHHHHHHHSTTS
T ss_pred HHHHHHHHHHccCHHHHHHHHHHHHHHCcCC
Confidence 4789999999999999999999999988853
No 32
>cd00189 TPR Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and C
Probab=91.06 E-value=2.3 Score=28.49 Aligned_cols=64 Identities=16% Similarity=0.044 Sum_probs=49.0
Q ss_pred HHHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCccC
Q 025096 23 QLFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNPQS 95 (258)
Q Consensus 23 ~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~~ 95 (258)
.+..+|+..++++.+...+...-.. .|. .. ...+..|.++...+++++|...++.+....|...
T Consensus 5 ~~a~~~~~~~~~~~A~~~~~~~~~~-~~~------~~--~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~ 68 (100)
T cd00189 5 NLGNLYYKLGDYDEALEYYEKALEL-DPD------NA--DAYYNLAAAYYKLGKYEEALEDYEKALELDPDNA 68 (100)
T ss_pred HHHHHHHHHhcHHHHHHHHHHHHhc-CCc------cH--HHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcch
Confidence 4566788899999999888654331 122 11 5678899999999999999999999999877554
No 33
>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=90.84 E-value=0.34 Score=33.69 Aligned_cols=38 Identities=16% Similarity=0.299 Sum_probs=30.9
Q ss_pred CccccHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCcceEEee
Q 025096 192 AHQMKLDVIVKALKWLEMDMDVDEVECIVAILIHKNLVKGYFA 234 (258)
Q Consensus 192 ~~~i~l~~i~~al~~~~~~~~~~evE~ila~LI~~G~IkGyI~ 234 (258)
..++++++++..+. .+.+.||.+|.-||..|+|+-.-.
T Consensus 12 ~~~~S~~eLa~~~~-----~s~~~ve~mL~~l~~kG~I~~~~~ 49 (69)
T PF09012_consen 12 RGRVSLAELAREFG-----ISPEAVEAMLEQLIRKGYIRKVDM 49 (69)
T ss_dssp S-SEEHHHHHHHTT-------HHHHHHHHHHHHCCTSCEEEEE
T ss_pred cCCcCHHHHHHHHC-----cCHHHHHHHHHHHHHCCcEEEecC
Confidence 36799999999987 799999999999999999985443
No 34
>PRK15359 type III secretion system chaperone protein SscB; Provisional
Probab=90.73 E-value=2.1 Score=34.01 Aligned_cols=34 Identities=15% Similarity=0.014 Sum_probs=20.0
Q ss_pred hhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCcc
Q 025096 61 VTYMYYTGRLEVFNENFPAADQKLSYALINCNPQ 94 (258)
Q Consensus 61 v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~ 94 (258)
...+|..|.++...|++++|.+.+..|+..+|.+
T Consensus 92 ~~a~~~lg~~l~~~g~~~eAi~~~~~Al~~~p~~ 125 (144)
T PRK15359 92 PEPVYQTGVCLKMMGEPGLAREAFQTAIKMSYAD 125 (144)
T ss_pred cHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCC
Confidence 3345556666666666666666666666665544
No 35
>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A.
Probab=90.04 E-value=1.9 Score=38.20 Aligned_cols=112 Identities=13% Similarity=0.153 Sum_probs=73.5
Q ss_pred hhHHHHHHHHHHHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcC
Q 025096 13 KRVGALYLTCQLFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCN 92 (258)
Q Consensus 13 Kk~~~~~~~n~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~ 92 (258)
+....--+...+..+|.++++++.+-.++..+-.... . +...+-..-.|+...+.+++..+|...|.+.|+..-..+|
T Consensus 150 ~~~~a~~~~~~~A~l~~~l~~y~~A~~~~e~~~~~~l-~-~~l~~~~~~~~~l~a~l~~L~~~D~v~A~~~~~~~~~~~~ 227 (282)
T PF14938_consen 150 SPHSAAECLLKAADLYARLGRYEEAIEIYEEVAKKCL-E-NNLLKYSAKEYFLKAILCHLAMGDYVAARKALERYCSQDP 227 (282)
T ss_dssp -HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTCC-C-HCTTGHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHGTTST
T ss_pred ChhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhh-c-ccccchhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCC
Confidence 3444556667788999999999999999976543211 1 0111122224556688889999999999999888777665
Q ss_pred ccC-hHHHHHHHHHHHHHHhhcCCCCChhhhhhccccccHHHHHHHHhCCHHHHHHHHHHcHH
Q 025096 93 PQS-EANIRMILKYLIPVKLSIGILPKDWLLEKYNLVEYSNIVQALRRGDLRLLRHALEEHED 154 (258)
Q Consensus 93 ~~~-~~~~~~IL~~LIp~~Ll~G~~P~~~ll~~~~l~~y~~L~~av~~Gdl~~f~~~l~~~~~ 154 (258)
.=. ++.-+ --..|++|++.||...|.+++..+..
T Consensus 228 ~F~~s~E~~----------------------------~~~~l~~A~~~~D~e~f~~av~~~d~ 262 (282)
T PF14938_consen 228 SFASSREYK----------------------------FLEDLLEAYEEGDVEAFTEAVAEYDS 262 (282)
T ss_dssp TSTTSHHHH----------------------------HHHHHHHHHHTT-CCCHHHHCHHHTT
T ss_pred CCCCcHHHH----------------------------HHHHHHHHHHhCCHHHHHHHHHHHcc
Confidence 211 11000 12578899999999999999998654
No 36
>KOG2072 consensus Translation initiation factor 3, subunit a (eIF-3a) [Translation, ribosomal structure and biogenesis]
Probab=89.91 E-value=1.2 Score=44.93 Aligned_cols=71 Identities=20% Similarity=0.243 Sum_probs=61.3
Q ss_pred HhhHHHHHHHHHHHHHHHhhcCCCCCCccccHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCcceEEeecCceEEEEecC
Q 025096 166 EKLELQVYQRLFKKIYIIQKQKDPSKAHQMKLDVIVKALKWLEMDMDVDEVECIVAILIHKNLVKGYFAHKSKVVVLSKQ 245 (258)
Q Consensus 166 ~~l~~~v~r~L~kkv~~~~~~~~~~~~~~i~l~~i~~al~~~~~~~~~~evE~ila~LI~~G~IkGyI~~~~~~lVlsk~ 245 (258)
..|+.+.++.|++.+..+| ..|+++.+..-..+ .+.-++|-+++.....|.+.-.|+|...+|.+++
T Consensus 427 ~sLq~v~~~RllqQvSqiY--------~sIs~~~l~~La~F----~~~~~lEk~~v~a~k~~~v~iriDH~~~~v~Fgs- 493 (988)
T KOG2072|consen 427 PSLQDVIILRLLQQVSQIY--------ESISFERLYKLAPF----FSAFELEKLLVEAAKHNDVSIRIDHESNSVSFGS- 493 (988)
T ss_pred hhHHHHHHHHHHHHHHHHH--------HHHhHHHHHHHHhh----cCHHHHHHHHHHHHhccceeEEeccccceeeecc-
Confidence 4588889999999999997 67899988766555 6899999999999999999999999999999986
Q ss_pred CCCC
Q 025096 246 DPFP 249 (258)
Q Consensus 246 ~pFP 249 (258)
|.|-
T Consensus 494 Dl~~ 497 (988)
T KOG2072|consen 494 DLFL 497 (988)
T ss_pred cccc
Confidence 5543
No 37
>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=89.39 E-value=0.81 Score=30.91 Aligned_cols=35 Identities=14% Similarity=0.120 Sum_probs=30.6
Q ss_pred hhhhhhhHHhhhhcChHHHHHHHHHHHHhcCccCh
Q 025096 62 TYMYYTGRLEVFNENFPAADQKLSYALINCNPQSE 96 (258)
Q Consensus 62 ~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~~~ 96 (258)
..++-.|..++..++|++|..+|+.|+..+|.+..
T Consensus 4 ~~~~~~g~~~~~~~~~~~A~~~~~~ai~~~p~~~~ 38 (69)
T PF13414_consen 4 EAWYNLGQIYFQQGDYEEAIEYFEKAIELDPNNAE 38 (69)
T ss_dssp HHHHHHHHHHHHTTHHHHHHHHHHHHHHHSTTHHH
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHH
Confidence 45678999999999999999999999999886543
No 38
>cd00189 TPR Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and C
Probab=88.59 E-value=1.8 Score=28.95 Aligned_cols=64 Identities=17% Similarity=0.020 Sum_probs=48.8
Q ss_pred HHHHHHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcC
Q 025096 20 LTCQLFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCN 92 (258)
Q Consensus 20 ~~n~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~ 92 (258)
+...+..+|...++++.+...+...-.. .|. .. ...+..|.++...+++++|...+..++..+|
T Consensus 36 ~~~~~~~~~~~~~~~~~a~~~~~~~~~~-~~~------~~--~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~ 99 (100)
T cd00189 36 AYYNLAAAYYKLGKYEEALEDYEKALEL-DPD------NA--KAYYNLGLAYYKLGKYEEALEAYEKALELDP 99 (100)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhC-CCc------ch--hHHHHHHHHHHHHHhHHHHHHHHHHHHccCC
Confidence 3455677888889999999888654432 122 11 5668899999999999999999999998776
No 39
>PF13428 TPR_14: Tetratricopeptide repeat
Probab=87.66 E-value=0.89 Score=28.33 Aligned_cols=32 Identities=16% Similarity=-0.105 Sum_probs=28.6
Q ss_pred hhhhhHHhhhhcChHHHHHHHHHHHHhcCccC
Q 025096 64 MYYTGRLEVFNENFPAADQKLSYALINCNPQS 95 (258)
Q Consensus 64 ~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~~ 95 (258)
.+-.|+.|.-.|++++|...|+.++..+|.+.
T Consensus 4 ~~~la~~~~~~G~~~~A~~~~~~~l~~~P~~~ 35 (44)
T PF13428_consen 4 WLALARAYRRLGQPDEAERLLRRALALDPDDP 35 (44)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHHCcCCH
Confidence 35679999999999999999999999998764
No 40
>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=86.20 E-value=3.4 Score=30.32 Aligned_cols=29 Identities=10% Similarity=-0.075 Sum_probs=14.1
Q ss_pred hhhhhHHhhhhcChHHHHHHHHHHHHhcC
Q 025096 64 MYYTGRLEVFNENFPAADQKLSYALINCN 92 (258)
Q Consensus 64 ~YY~G~~~~~~~~~~~A~~~L~~A~~~c~ 92 (258)
.+..|.++.-.+++.+|...+.+++...|
T Consensus 79 ~~~~~~~~~~~~~~~~A~~~~~~~~~~~p 107 (119)
T TIGR02795 79 LLKLGMSLQELGDKEKAKATLQQVIKRYP 107 (119)
T ss_pred HHHHHHHHHHhCChHHHHHHHHHHHHHCc
Confidence 34444444444555555555555554444
No 41
>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=85.90 E-value=1.2 Score=23.71 Aligned_cols=30 Identities=17% Similarity=0.032 Sum_probs=25.9
Q ss_pred hhhhhhHHhhhhcChHHHHHHHHHHHHhcC
Q 025096 63 YMYYTGRLEVFNENFPAADQKLSYALINCN 92 (258)
Q Consensus 63 y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~ 92 (258)
.++-.|.+++..+++++|..++..|+..-|
T Consensus 3 ~~~~~a~~~~~~~~~~~a~~~~~~~~~~~~ 32 (34)
T smart00028 3 ALYNLGNAYLKLGDYDEALEYYEKALELDP 32 (34)
T ss_pred HHHHHHHHHHHHhhHHHHHHHHHHHHccCC
Confidence 456789999999999999999999987654
No 42
>KOG2300 consensus Uncharacterized conserved protein [Function unknown]
Probab=85.68 E-value=8.4 Score=37.17 Aligned_cols=137 Identities=16% Similarity=0.147 Sum_probs=87.7
Q ss_pred CchhHHHHHHHHHHHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHh
Q 025096 11 GSKRVGALYLTCQLFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALIN 90 (258)
Q Consensus 11 ~~Kk~~~~~~~n~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~ 90 (258)
.+++.-..+....+.-+|++.++-+..+.++..|.... ..+...-.....++|-.|...+.++++.+|...+.+-++.
T Consensus 397 t~~~dl~a~~nlnlAi~YL~~~~~ed~y~~ld~i~p~n--t~s~ssq~l~a~~~~v~glfaf~qn~lnEaK~~l~e~Lkm 474 (629)
T KOG2300|consen 397 TESIDLQAFCNLNLAISYLRIGDAEDLYKALDLIGPLN--TNSLSSQRLEASILYVYGLFAFKQNDLNEAKRFLRETLKM 474 (629)
T ss_pred hhHHHHHHHHHHhHHHHHHHhccHHHHHHHHHhcCCCC--CCcchHHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHhh
Confidence 46666666667778889999999888888888776421 1222234446678888999999999999999999999997
Q ss_pred cCccChHHHHHHHHHHHHHHhh---cC--------CCCChhhhhhc--------cccccHHHHHHHHhCCHHHHHHHHHH
Q 025096 91 CNPQSEANIRMILKYLIPVKLS---IG--------ILPKDWLLEKY--------NLVEYSNIVQALRRGDLRLLRHALEE 151 (258)
Q Consensus 91 c~~~~~~~~~~IL~~LIp~~Ll---~G--------~~P~~~ll~~~--------~l~~y~~L~~av~~Gdl~~f~~~l~~ 151 (258)
.. .-.+-|..--+|+..+.+ .| -.|..++-++- +.+.|.+|-+|....-...-+++..+
T Consensus 475 an--aed~~rL~a~~LvLLs~v~lslgn~~es~nmvrpamqlAkKi~Di~vqLws~si~~~L~~a~g~~~~~~e~e~~~~ 552 (629)
T KOG2300|consen 475 AN--AEDLNRLTACSLVLLSHVFLSLGNTVESRNMVRPAMQLAKKIPDIPVQLWSSSILTDLYQALGEKGNEMENEAFRK 552 (629)
T ss_pred cc--hhhHHHHHHHHHHHHHHHHHHhcchHHHHhccchHHHHHhcCCCchHHHHHHHHHHHHHHHhCcchhhHHHHHHHH
Confidence 63 334445554445444432 22 24544444432 23457777777654334444444444
No 43
>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=85.43 E-value=1.9 Score=38.66 Aligned_cols=96 Identities=18% Similarity=0.168 Sum_probs=55.6
Q ss_pred HHHHHHHHHHHHHHhcCChhhHHHHHHHhhccCCCC----------CCCC---Cccchh---------------hhhhhh
Q 025096 16 GALYLTCQLFKIYFKLGTVHLCRSVIRSIETARIFD----------FEEF---PKRDKV---------------TYMYYT 67 (258)
Q Consensus 16 ~~~~~~n~l~kiyf~l~~~~~~~~l~~~i~~~~~p~----------~~~~---~~~~~v---------------~y~YY~ 67 (258)
+-+....+...+|+++|+++++++.+++++..+ .+ .+.+ .+-+.. .-..-.
T Consensus 129 ~~lE~~al~Vqi~L~~~R~dlA~k~l~~~~~~~-eD~~l~qLa~awv~l~~g~e~~~~A~y~f~El~~~~~~t~~~lng~ 207 (290)
T PF04733_consen 129 GSLELLALAVQILLKMNRPDLAEKELKNMQQID-EDSILTQLAEAWVNLATGGEKYQDAFYIFEELSDKFGSTPKLLNGL 207 (290)
T ss_dssp TCHHHHHHHHHHHHHTT-HHHHHHHHHHHHCCS-CCHHHHHHHHHHHHHHHTTTCCCHHHHHHHHHHCCS--SHHHHHHH
T ss_pred CcccHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CcHHHHHHHHHHHHHHhCchhHHHHHHHHHHHHhccCCCHHHHHHH
Confidence 445666778899999999999999999987531 11 0000 000111 111124
Q ss_pred hHHhhhhcChHHHHHHHHHHHHhcCccChHHHHHHHHHHHHHHhhcCCCC
Q 025096 68 GRLEVFNENFPAADQKLSYALINCNPQSEANIRMILKYLIPVKLSIGILP 117 (258)
Q Consensus 68 G~~~~~~~~~~~A~~~L~~A~~~c~~~~~~~~~~IL~~LIp~~Ll~G~~P 117 (258)
+..++..++|++|++.|.+|+..=|.+ ...|.-+|.+..++|+=+
T Consensus 208 A~~~l~~~~~~eAe~~L~~al~~~~~~-----~d~LaNliv~~~~~gk~~ 252 (290)
T PF04733_consen 208 AVCHLQLGHYEEAEELLEEALEKDPND-----PDTLANLIVCSLHLGKPT 252 (290)
T ss_dssp HHHHHHCT-HHHHHHHHHHHCCC-CCH-----HHHHHHHHHHHHHTT-TC
T ss_pred HHHHHHhCCHHHHHHHHHHHHHhccCC-----HHHHHHHHHHHHHhCCCh
Confidence 455677788888888888877643321 234556677777777653
No 44
>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A.
Probab=84.06 E-value=1.4 Score=26.19 Aligned_cols=27 Identities=19% Similarity=0.111 Sum_probs=22.7
Q ss_pred hhhhHHhhhhcChHHHHHHHHHHHHhc
Q 025096 65 YYTGRLEVFNENFPAADQKLSYALINC 91 (258)
Q Consensus 65 YY~G~~~~~~~~~~~A~~~L~~A~~~c 91 (258)
..+|.+|...++|++|.+.+++|+..+
T Consensus 3 ~~Lg~~~~~~g~~~~Ai~~y~~aL~l~ 29 (36)
T PF13176_consen 3 NNLGRIYRQQGDYEKAIEYYEQALALA 29 (36)
T ss_dssp HHHHHHHHHCT-HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHhc
Confidence 468999999999999999999987644
No 45
>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=83.42 E-value=1.5 Score=29.33 Aligned_cols=57 Identities=9% Similarity=-0.002 Sum_probs=43.2
Q ss_pred HhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCcc
Q 025096 29 FKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNPQ 94 (258)
Q Consensus 29 f~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~ 94 (258)
++.|+++.+..+++.+-.. .| . .....+..|.+++-.+++++|.+.|..+....|.+
T Consensus 2 l~~~~~~~A~~~~~~~l~~-~p------~--~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~~ 58 (68)
T PF14559_consen 2 LKQGDYDEAIELLEKALQR-NP------D--NPEARLLLAQCYLKQGQYDEAEELLERLLKQDPDN 58 (68)
T ss_dssp HHTTHHHHHHHHHHHHHHH-TT------T--SHHHHHHHHHHHHHTT-HHHHHHHHHCCHGGGTTH
T ss_pred hhccCHHHHHHHHHHHHHH-CC------C--CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCH
Confidence 5678888898888765432 23 2 33455689999999999999999999999987763
No 46
>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=82.57 E-value=3.2 Score=32.74 Aligned_cols=56 Identities=16% Similarity=0.192 Sum_probs=34.0
Q ss_pred HHHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHH
Q 025096 23 QLFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYAL 88 (258)
Q Consensus 23 ~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~ 88 (258)
.+-+++...++++.+...+..+.. ....-.+....|.+++-.|++++|...++.|+
T Consensus 90 ~LA~~~~~~~~~d~Al~~L~~~~~----------~~~~~~~~~~~Gdi~~~~g~~~~A~~~y~~Al 145 (145)
T PF09976_consen 90 RLARILLQQGQYDEALATLQQIPD----------EAFKALAAELLGDIYLAQGDYDEARAAYQKAL 145 (145)
T ss_pred HHHHHHHHcCCHHHHHHHHHhccC----------cchHHHHHHHHHHHHHHCCCHHHHHHHHHHhC
Confidence 355666666666666666644321 11123355667888888888888877777663
No 47
>PF08631 SPO22: Meiosis protein SPO22/ZIP4 like; InterPro: IPR013940 SPO22 is a meiosis-specific protein with similarity to phospholipase A2, involved in completion of nuclear divisions during meiosis; induced early in meiosis []. It is also involved in sporulation [].
Probab=81.01 E-value=32 Score=30.35 Aligned_cols=82 Identities=15% Similarity=0.109 Sum_probs=56.2
Q ss_pred HhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhc-ChHHHHHHHHHHHHhcCc-c--------ChHH
Q 025096 29 FKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNE-NFPAADQKLSYALINCNP-Q--------SEAN 98 (258)
Q Consensus 29 f~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~-~~~~A~~~L~~A~~~c~~-~--------~~~~ 98 (258)
-+.|+++.|..++..++... +..+.-.......=.|-.|+-...++ ++++|-.+|++|++.|.. . ...-
T Consensus 4 ~~~~~~~~A~~~~~K~~~~~-~~~~~~~~~~La~~~yn~G~~l~~~~~~~~~a~~wL~~a~~~l~~~~~~~~~~~~~~el 82 (278)
T PF08631_consen 4 WKQGDLDLAEHMYSKAKDLL-NSLDPDMAEELARVCYNIGKSLLSKKDKYEEAVKWLQRAYDILEKPGKMDKLSPDGSEL 82 (278)
T ss_pred hhhCCHHHHHHHHHHhhhHH-hcCCcHHHHHHHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhhhhccccCCcHHHH
Confidence 46789999999997776521 11111123455566677899989999 999999999999999743 1 1134
Q ss_pred HHHHHHHHHHHHh
Q 025096 99 IRMILKYLIPVKL 111 (258)
Q Consensus 99 ~~~IL~~LIp~~L 111 (258)
|-.||..|+-+-+
T Consensus 83 r~~iL~~La~~~l 95 (278)
T PF08631_consen 83 RLSILRLLANAYL 95 (278)
T ss_pred HHHHHHHHHHHHH
Confidence 6667777775443
No 48
>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=80.93 E-value=9.7 Score=27.79 Aligned_cols=66 Identities=8% Similarity=0.016 Sum_probs=49.4
Q ss_pred HHHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCcc
Q 025096 23 QLFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNPQ 94 (258)
Q Consensus 23 ~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~ 94 (258)
.+...+++.++++.+...+..+... .|. .+ ....-.|..|.+++-.+++++|...+..+....|..
T Consensus 7 ~~~~~~~~~~~~~~A~~~~~~~~~~-~~~---~~--~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~ 72 (119)
T TIGR02795 7 DAALLVLKAGDYADAIQAFQAFLKK-YPK---ST--YAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKYPKS 72 (119)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHH-CCC---cc--ccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHCCCC
Confidence 4456778899999999888766542 232 11 123346789999999999999999999999988754
No 49
>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=79.72 E-value=18 Score=27.31 Aligned_cols=65 Identities=8% Similarity=-0.055 Sum_probs=49.8
Q ss_pred HHHHHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCcc
Q 025096 21 TCQLFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNPQ 94 (258)
Q Consensus 21 ~n~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~ 94 (258)
...+...|++.++++.+...+..+-.. .|. .....+..|..+...+++.+|...+..|....|.+
T Consensus 20 ~~~~a~~~~~~~~~~~A~~~~~~~~~~-~p~--------~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~p~~ 84 (135)
T TIGR02552 20 IYALAYNLYQQGRYDEALKLFQLLAAY-DPY--------NSRYWLGLAACCQMLKEYEEAIDAYALAAALDPDD 84 (135)
T ss_pred HHHHHHHHHHcccHHHHHHHHHHHHHh-CCC--------cHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCC
Confidence 456667788999999999888765432 122 23566788999999999999999999999876654
No 50
>PRK02603 photosystem I assembly protein Ycf3; Provisional
Probab=79.66 E-value=22 Score=28.67 Aligned_cols=76 Identities=14% Similarity=-0.032 Sum_probs=53.1
Q ss_pred hhHHHHHHHHHHHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcC
Q 025096 13 KRVGALYLTCQLFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCN 92 (258)
Q Consensus 13 Kk~~~~~~~n~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~ 92 (258)
.+..-......+...|...|+++.+-..++..-.. .|. ..+....++-.|.++...++|++|...+..|+...|
T Consensus 30 ~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al~~-~~~-----~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p 103 (172)
T PRK02603 30 KKAKEAFVYYRDGMSAQADGEYAEALENYEEALKL-EED-----PNDRSYILYNMGIIYASNGEHDKALEYYHQALELNP 103 (172)
T ss_pred cHhhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH-hhc-----cchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCc
Confidence 34444445566778889999999998877543221 121 112345678889999999999999999999999766
Q ss_pred cc
Q 025096 93 PQ 94 (258)
Q Consensus 93 ~~ 94 (258)
..
T Consensus 104 ~~ 105 (172)
T PRK02603 104 KQ 105 (172)
T ss_pred cc
Confidence 43
No 51
>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=79.47 E-value=3.6 Score=28.41 Aligned_cols=32 Identities=13% Similarity=-0.147 Sum_probs=27.7
Q ss_pred hhhhhhhhhHHhhhhcChHHHHHHHHHHHHhc
Q 025096 60 KVTYMYYTGRLEVFNENFPAADQKLSYALINC 91 (258)
Q Consensus 60 ~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c 91 (258)
..+.+...|.++...++|++|.+.+++|+..+
T Consensus 4 ~a~~~~~la~~~~~~~~~~~A~~~~~~al~~~ 35 (78)
T PF13424_consen 4 TANAYNNLARVYRELGRYDEALDYYEKALDIE 35 (78)
T ss_dssp HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHH
Confidence 45667889999999999999999999999974
No 52
>KOG3250 consensus COP9 signalosome, subunit CSN7 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=77.84 E-value=3.2 Score=35.71 Aligned_cols=96 Identities=14% Similarity=0.177 Sum_probs=63.9
Q ss_pred ccccHHHHHHHHhCCHHHHHHHHHHcHHHHHHhcHHHHHHhhHHHHHHHHHHHHHHHhhcCCCCCCccccHHHHHHHHHh
Q 025096 127 LVEYSNIVQALRRGDLRLLRHALEEHEDQFLRSGVYLVLEKLELQVYQRLFKKIYIIQKQKDPSKAHQMKLDVIVKALKW 206 (258)
Q Consensus 127 l~~y~~L~~av~~Gdl~~f~~~l~~~~~~f~~~glylll~~l~~~v~r~L~kkv~~~~~~~~~~~~~~i~l~~i~~al~~ 206 (258)
.+.|..+..-+-.|++..|...-.+. -+-.+ .-+.+|+.+.+-.+.. ...-||...+...+..
T Consensus 59 dsa~lrlL~lFa~Gt~~Dy~aea~rl----p~Ls~-~q~~kLk~ltV~slas------------~~k~lpy~~Ll~~l~~ 121 (258)
T KOG3250|consen 59 DSAYLRLLELFAYGTYRDYSAEALRL----PKLSL-AQLNKLKHLTVVSLAS------------FEKCLPYLVLLRLLPS 121 (258)
T ss_pred cHHHHHHHHHHhcCchhhhhhhhhcC----CCCCH-HHHHhhhcceehhhhh------------hchhhhHHHHHhhccC
Confidence 34688888899999988776554321 11111 1123344433333322 2345788888777653
Q ss_pred ccCCCCHHHHHHHHHHHHHcCcceEEeecCceEEEEe
Q 025096 207 LEMDMDVDEVECIVAILIHKNLVKGYFAHKSKVVVLS 243 (258)
Q Consensus 207 ~~~~~~~~evE~ila~LI~~G~IkGyI~~~~~~lVls 243 (258)
-..-|+|.++.-+.+.|.++|+|++-++++-++
T Consensus 122 ----~nvrelEd~iieamya~IlrGkldqr~q~leV~ 154 (258)
T KOG3250|consen 122 ----RNVRELEDLIIEAMYADILRGKLDQRNQTLEVD 154 (258)
T ss_pred ----CchhHHHHHHHHHHHHHHHHhhHHhhcceEeec
Confidence 256799999999999999999999999998764
No 53
>KOG3081 consensus Vesicle coat complex COPI, epsilon subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=77.23 E-value=20 Score=32.11 Aligned_cols=100 Identities=15% Similarity=0.164 Sum_probs=69.5
Q ss_pred hhHHHHHHHHHHHHHHHhcCChhhHHHHHHHhhccCCC-CC--------CCCCccchhh--hhhh--------------h
Q 025096 13 KRVGALYLTCQLFKIYFKLGTVHLCRSVIRSIETARIF-DF--------EEFPKRDKVT--YMYY--------------T 67 (258)
Q Consensus 13 Kk~~~~~~~n~l~kiyf~l~~~~~~~~l~~~i~~~~~p-~~--------~~~~~~~~v~--y~YY--------------~ 67 (258)
++.+.+-.+.+--.|..|+++.+.+++-++.+..-+-. .+ ..+.....++ |++| +
T Consensus 132 ~~~~~lE~~Al~VqI~lk~~r~d~A~~~lk~mq~ided~tLtQLA~awv~la~ggek~qdAfyifeE~s~k~~~T~~lln 211 (299)
T KOG3081|consen 132 HLGENLEAAALNVQILLKMHRFDLAEKELKKMQQIDEDATLTQLAQAWVKLATGGEKIQDAFYIFEELSEKTPPTPLLLN 211 (299)
T ss_pred hccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHccchHHHHHHHHHHHHHHhccchhhhhHHHHHHHHhcccCCChHHHc
Confidence 44667777778888999999999999999987752100 01 1122233333 4444 4
Q ss_pred hH--HhhhhcChHHHHHHHHHHHHhcCccChHHHHHHHHHHHHHHhhcCCCC
Q 025096 68 GR--LEVFNENFPAADQKLSYALINCNPQSEANIRMILKYLIPVKLSIGILP 117 (258)
Q Consensus 68 G~--~~~~~~~~~~A~~~L~~A~~~c~~~~~~~~~~IL~~LIp~~Ll~G~~P 117 (258)
|+ +++..++|++|+..|..|+..-+.. -..|.-+|.+.+..|+=|
T Consensus 212 G~Av~~l~~~~~eeAe~lL~eaL~kd~~d-----petL~Nliv~a~~~Gkd~ 258 (299)
T KOG3081|consen 212 GQAVCHLQLGRYEEAESLLEEALDKDAKD-----PETLANLIVLALHLGKDA 258 (299)
T ss_pred cHHHHHHHhcCHHHHHHHHHHHHhccCCC-----HHHHHHHHHHHHHhCCCh
Confidence 44 4678899999999999999977655 345667788888889753
No 54
>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=76.80 E-value=5.8 Score=33.42 Aligned_cols=48 Identities=13% Similarity=0.253 Sum_probs=33.9
Q ss_pred ccccHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCcceEEeecCceEEEEecC
Q 025096 193 HQMKLDVIVKALKWLEMDMDVDEVECIVAILIHKNLVKGYFAHKSKVVVLSKQ 245 (258)
Q Consensus 193 ~~i~l~~i~~al~~~~~~~~~~evE~ila~LI~~G~IkGyI~~~~~~lVlsk~ 245 (258)
..+++.+++..+. ++.+++..-+..|..+|.|.|.|+...++|-+|..
T Consensus 112 Kvv~ledla~~f~-----l~t~~~i~ri~~L~~~g~ltGv~DdrGkfIyIs~e 159 (188)
T PF09756_consen 112 KVVNLEDLAAEFG-----LRTQDVINRIQELEAEGRLTGVIDDRGKFIYISEE 159 (188)
T ss_dssp SEE-HHHHHHHH------S-HHHHHHHHHHHHHHSSS-EEE-TT--EEE----
T ss_pred ceeeHHHHHHHcC-----CCHHHHHHHHHHHHHCCCceeeEcCCCCeEEecHH
Confidence 4588999999987 68899999999999999999999998888887864
No 55
>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW. Members of this family are designated PilF in ref (PubMed:8973346) and PilW in ref (PubMed:15612916). This outer membrane protein is required both for pilus stability and for pilus function such as adherence to human cells. Members of this family contain copies of the TPR (tetratricopeptide repeat) domain.
Probab=75.82 E-value=24 Score=28.36 Aligned_cols=70 Identities=13% Similarity=0.022 Sum_probs=52.7
Q ss_pred HHHHHHHHHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCccC
Q 025096 17 ALYLTCQLFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNPQS 95 (258)
Q Consensus 17 ~~~~~n~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~~ 95 (258)
.......+-..|++.++++.+...++..-.. .|. .....+..|.++...+++++|.+.+..|+...|...
T Consensus 30 ~~~~~~~la~~~~~~~~~~~A~~~~~~~l~~-~p~--------~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~ 99 (234)
T TIGR02521 30 AAKIRVQLALGYLEQGDLEVAKENLDKALEH-DPD--------DYLAYLALALYYQQLGELEKAEDSFRRALTLNPNNG 99 (234)
T ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh-Ccc--------cHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCH
Confidence 3444456778999999999999888654321 122 234567789999999999999999999999877543
No 56
>PRK10370 formate-dependent nitrite reductase complex subunit NrfG; Provisional
Probab=75.74 E-value=17 Score=30.43 Aligned_cols=80 Identities=9% Similarity=0.007 Sum_probs=55.3
Q ss_pred HHHHHHHHHHHHHHhcCChhhHHHHHHHhhccCCC-----CCCC---------CCccchhhhhhhhhHHhhhhcChHHHH
Q 025096 16 GALYLTCQLFKIYFKLGTVHLCRSVIRSIETARIF-----DFEE---------FPKRDKVTYMYYTGRLEVFNENFPAAD 81 (258)
Q Consensus 16 ~~~~~~n~l~kiyf~l~~~~~~~~l~~~i~~~~~p-----~~~~---------~~~~~~v~y~YY~G~~~~~~~~~~~A~ 81 (258)
++..+.....-.|+++|+++....--..+.....+ +.+. -..-+.....+.+|++++..+++++|.
T Consensus 14 ~~~~~~~~~~~~Y~~~g~~~~v~~~~~~~~~~~~~~~~~~~~~~~i~~l~~~L~~~P~~~~~w~~Lg~~~~~~g~~~~A~ 93 (198)
T PRK10370 14 LTILMVFLCVGSYLLSPKWQAVRAEYQRLADPLHQFASQQTPEAQLQALQDKIRANPQNSEQWALLGEYYLWRNDYDNAL 93 (198)
T ss_pred HHHHHHHHHHHHHHHcchHHHHHHHHHHHhCccccccCchhHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCHHHHH
Confidence 56677777888999999998776554333221100 0000 012234557788999999999999999
Q ss_pred HHHHHHHHhcCccC
Q 025096 82 QKLSYALINCNPQS 95 (258)
Q Consensus 82 ~~L~~A~~~c~~~~ 95 (258)
..+..|+..-|.+.
T Consensus 94 ~a~~~Al~l~P~~~ 107 (198)
T PRK10370 94 LAYRQALQLRGENA 107 (198)
T ss_pred HHHHHHHHhCCCCH
Confidence 99999999887654
No 57
>PF13429 TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2_B.
Probab=75.15 E-value=9.9 Score=33.19 Aligned_cols=68 Identities=12% Similarity=0.109 Sum_probs=47.8
Q ss_pred HHHHHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCccC
Q 025096 21 TCQLFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNPQS 95 (258)
Q Consensus 21 ~n~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~~ 95 (258)
....+.+|.+.++.+.+..+++.+... +. ..+...+++..|.++.-.|++++|.+.+..|++.-|.+.
T Consensus 113 l~~~l~~~~~~~~~~~~~~~l~~~~~~--~~-----~~~~~~~~~~~a~~~~~~G~~~~A~~~~~~al~~~P~~~ 180 (280)
T PF13429_consen 113 LLSALQLYYRLGDYDEAEELLEKLEEL--PA-----APDSARFWLALAEIYEQLGDPDKALRDYRKALELDPDDP 180 (280)
T ss_dssp -----H-HHHTT-HHHHHHHHHHHHH---T--------T-HHHHHHHHHHHHHCCHHHHHHHHHHHHHHH-TT-H
T ss_pred hhHHHHHHHHHhHHHHHHHHHHHHHhc--cC-----CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCH
Confidence 345777899999999999999887742 21 124567788899999999999999999999999888653
No 58
>PRK10803 tol-pal system protein YbgF; Provisional
Probab=75.06 E-value=7.2 Score=34.52 Aligned_cols=62 Identities=10% Similarity=-0.013 Sum_probs=45.7
Q ss_pred HHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCccC
Q 025096 28 YFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNPQS 95 (258)
Q Consensus 28 yf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~~ 95 (258)
+++.++++.+-..++.+-.. .|.-. ..-.-+|+.|..|+..++|++|...|...+...|.+.
T Consensus 153 ~~~~~~y~~Ai~af~~fl~~-yP~s~-----~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP~s~ 214 (263)
T PRK10803 153 VQDKSRQDDAIVAFQNFVKK-YPDST-----YQPNANYWLGQLNYNKGKKDDAAYYFASVVKNYPKSP 214 (263)
T ss_pred HHhcCCHHHHHHHHHHHHHH-CcCCc-----chHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCc
Confidence 34558899888777665542 34311 1233469999999999999999999999999887653
No 59
>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=74.84 E-value=11 Score=31.15 Aligned_cols=68 Identities=12% Similarity=0.124 Sum_probs=37.3
Q ss_pred HHHHHHHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHH
Q 025096 19 YLTCQLFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALI 89 (258)
Q Consensus 19 ~~~n~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~ 89 (258)
-+.-.++++.+..++...+.+.+...++. ++. .-+..-+-...=|.|..++..++|.+|-+.|-.+..
T Consensus 74 d~~l~~irv~i~~~d~~~v~~~i~ka~~~--~~~-~~d~~~~nrlk~~~gL~~l~~r~f~~AA~~fl~~~~ 141 (177)
T PF10602_consen 74 DMCLNVIRVAIFFGDWSHVEKYIEKAESL--IEK-GGDWERRNRLKVYEGLANLAQRDFKEAAELFLDSLS 141 (177)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHHHH--Hhc-cchHHHHHHHHHHHHHHHHHhchHHHHHHHHHccCc
Confidence 33445566666666666666666555432 111 011233344556666666667777766666666544
No 60
>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A.
Probab=74.78 E-value=3.8 Score=24.28 Aligned_cols=29 Identities=14% Similarity=-0.052 Sum_probs=23.8
Q ss_pred hhhhhHHhhhhcChHHHHHHHHHHHHhcC
Q 025096 64 MYYTGRLEVFNENFPAADQKLSYALINCN 92 (258)
Q Consensus 64 ~YY~G~~~~~~~~~~~A~~~L~~A~~~c~ 92 (258)
..-+|.++...++|++|...+.+|+..+-
T Consensus 5 ~~~la~~~~~~g~~~~A~~~~~~al~~~~ 33 (42)
T PF13374_consen 5 LNNLANAYRAQGRYEEALELLEEALEIRE 33 (42)
T ss_dssp HHHHHHHHHHCT-HHHHHHHHHHHHHHH-
T ss_pred HHHHHHHHHhhhhcchhhHHHHHHHHHHH
Confidence 45578999999999999999999998764
No 61
>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=74.19 E-value=30 Score=27.83 Aligned_cols=63 Identities=16% Similarity=0.100 Sum_probs=46.9
Q ss_pred HHHHHHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhc
Q 025096 20 LTCQLFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINC 91 (258)
Q Consensus 20 ~~n~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c 91 (258)
....+..+|...|+++.+...++..-.. .|. . ....+..|.+++..+++++|.+.+..++...
T Consensus 67 ~~~~la~~~~~~~~~~~A~~~~~~al~~-~~~------~--~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~ 129 (234)
T TIGR02521 67 AYLALALYYQQLGELEKAEDSFRRALTL-NPN------N--GDVLNNYGTFLCQQGKYEQAMQQFEQAIEDP 129 (234)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHHhh-CCC------C--HHHHHHHHHHHHHcccHHHHHHHHHHHHhcc
Confidence 4455778999999999999888654331 122 1 1345677999999999999999999999853
No 62
>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=73.93 E-value=9.3 Score=30.23 Aligned_cols=77 Identities=17% Similarity=0.137 Sum_probs=46.5
Q ss_pred cHHHHHHHHhCCHHHHHHHHHHcH-HHHHHhcHHHHHHhhHHHHHHHHHHHHHHHhhcCCCCCCccccHHHHHHHHHhcc
Q 025096 130 YSNIVQALRRGDLRLLRHALEEHE-DQFLRSGVYLVLEKLELQVYQRLFKKIYIIQKQKDPSKAHQMKLDVIVKALKWLE 208 (258)
Q Consensus 130 y~~L~~av~~Gdl~~f~~~l~~~~-~~f~~~glylll~~l~~~v~r~L~kkv~~~~~~~~~~~~~~i~l~~i~~al~~~~ 208 (258)
-..|.+++.+||..+|-.+++.+. ...+...+-.+.+..|.-+. ..+-.. +++|++++++..|.
T Consensus 44 i~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~iR~~i~----~~i~~a--------Y~sIs~~~la~~Lg--- 108 (143)
T PF10075_consen 44 IWSLGQALWEGDYSKFWQALRSNPWSPDYKPFVPGFEDTIRERIA----HLISKA--------YSSISLSDLAEMLG--- 108 (143)
T ss_dssp HHHHHHHHHTT-HHHHHHHS-TT----HHHHTSTTHHHHHHHHHH----HHHHHH---------SEE-HHHHHHHTT---
T ss_pred HHHHHHHHHCCCHHHHHHHHHhccchHHHHHHHHHHHHHHHHHHH----HHHHHH--------HhHcCHHHHHHHhC---
Confidence 367889999999999999888651 11222222223344444333 222223 37899999999987
Q ss_pred CCCCHHHHHHHHHHH
Q 025096 209 MDMDVDEVECIVAIL 223 (258)
Q Consensus 209 ~~~~~~evE~ila~L 223 (258)
++.+|++.++.+.
T Consensus 109 --~~~~el~~~~~~~ 121 (143)
T PF10075_consen 109 --LSEEELEKFIKSR 121 (143)
T ss_dssp --S-HHHHHHHHHHH
T ss_pred --CCHHHHHHHHHHc
Confidence 5688888888876
No 63
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=73.41 E-value=22 Score=32.26 Aligned_cols=33 Identities=15% Similarity=0.086 Sum_probs=24.0
Q ss_pred hhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCc
Q 025096 61 VTYMYYTGRLEVFNENFPAADQKLSYALINCNP 93 (258)
Q Consensus 61 v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~ 93 (258)
..+++-.|..++..+++++|...+.+++...|.
T Consensus 180 ~~~~~~la~~~~~~~~~~~A~~~~~~al~~~p~ 212 (389)
T PRK11788 180 AHFYCELAQQALARGDLDAARALLKKALAADPQ 212 (389)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHHHHHHhHCcC
Confidence 345455777777788888888888888876554
No 64
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=72.86 E-value=7.8 Score=30.65 Aligned_cols=41 Identities=15% Similarity=0.186 Sum_probs=35.7
Q ss_pred CccccHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCcceEEeecCc
Q 025096 192 AHQMKLDVIVKALKWLEMDMDVDEVECIVAILIHKNLVKGYFAHKS 237 (258)
Q Consensus 192 ~~~i~l~~i~~al~~~~~~~~~~evE~ila~LI~~G~IkGyI~~~~ 237 (258)
..++|++++++.+. +|...+-..+-+|...|.|+||-...+
T Consensus 20 d~r~~~~eia~~lg-----lS~~~v~~Ri~~L~~~GiI~~~~~~v~ 60 (154)
T COG1522 20 DARISNAELAERVG-----LSPSTVLRRIKRLEEEGVIKGYTAVLD 60 (154)
T ss_pred hCCCCHHHHHHHHC-----CCHHHHHHHHHHHHHCCceeeEEEEEC
Confidence 45799999999997 789999999999999999999755444
No 65
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=72.73 E-value=21 Score=32.31 Aligned_cols=69 Identities=10% Similarity=0.078 Sum_probs=50.3
Q ss_pred HHHHHHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCc
Q 025096 20 LTCQLFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNP 93 (258)
Q Consensus 20 ~~n~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~ 93 (258)
....+..+|++.|+++.+..+++.+... |. .+.......++..|..++..+++++|...|..+....|.
T Consensus 71 ~~~~la~~~~~~g~~~~A~~~~~~~l~~--~~---~~~~~~~~~~~~La~~~~~~g~~~~A~~~~~~~l~~~~~ 139 (389)
T PRK11788 71 LHLALGNLFRRRGEVDRAIRIHQNLLSR--PD---LTREQRLLALQELGQDYLKAGLLDRAEELFLQLVDEGDF 139 (389)
T ss_pred HHHHHHHHHHHcCcHHHHHHHHHHHhcC--CC---CCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCcc
Confidence 3455778899999999999888765542 22 122233456677899999999999999999999886443
No 66
>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=72.71 E-value=16 Score=22.97 Aligned_cols=33 Identities=15% Similarity=0.227 Sum_probs=28.2
Q ss_pred ccccHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCcce
Q 025096 193 HQMKLDVIVKALKWLEMDMDVDEVECIVAILIHKNLVK 230 (258)
Q Consensus 193 ~~i~l~~i~~al~~~~~~~~~~evE~ila~LI~~G~Ik 230 (258)
..++..+++..+. ++..-|-..+-.|..+|+|+
T Consensus 16 ~~~t~~ela~~~~-----is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 16 PRITQKELAEKLG-----ISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp TTS-HHHHHHHHT-----S-HHHHHHHHHHHHHTTSEE
T ss_pred CCCCHHHHHHHhC-----CCHHHHHHHHHHHHHCcCcC
Confidence 4699999999987 78999999999999999985
No 67
>PF02064 MAS20: MAS20 protein import receptor; InterPro: IPR002056 Virtually all mitochondrial precursors are imported via the same mechanism []: precursors first bind to receptors on the mitochondrial surface, then insert into the translocation channel in the outer membrane. Many outer-membrane proteins participate in the early stages of import, four of which (MAS20, MAS22, MAS37 and MAS70) are components of the receptor. MAS20, which forms a subcomplex with MAS22, seems to interact with most or all mitochondrial precursors, suggesting that the protein binds directly to mitochondrial targeting sequences. The MAS37 and MAS70 components also form a subcomplex, the two subcomplexes possibly binding via their trans- membrane (TM) regions - the TM region of MAS70 promotes oligomerisation of attatched protein domains and shares sequence similarity with the TM region of MAS20 []. MAS20 is also known as TOM20.; GO: 0006605 protein targeting, 0006886 intracellular protein transport, 0005742 mitochondrial outer membrane translocase complex; PDB: 3AX3_A 3AWR_B 2V1S_A 3AX5_C 3AX2_C 1OM2_A 2V1T_B.
Probab=71.28 E-value=12 Score=29.23 Aligned_cols=41 Identities=20% Similarity=0.298 Sum_probs=30.1
Q ss_pred hhHHhhhhcChHHHHHHHHHHHHhcCccChHHHHHHHHHHHHH
Q 025096 67 TGRLEVFNENFPAADQKLSYALINCNPQSEANIRMILKYLIPV 109 (258)
Q Consensus 67 ~G~~~~~~~~~~~A~~~L~~A~~~c~~~~~~~~~~IL~~LIp~ 109 (258)
.|.-.+.+|++.+|-.||..|+.-||.. ...-.|+..-+|-
T Consensus 69 lGE~L~~~G~~~~aa~hf~nAl~V~~qP--~~LL~i~q~tlP~ 109 (121)
T PF02064_consen 69 LGEQLLAQGDYEEAAEHFYNALKVCPQP--AELLQIYQKTLPP 109 (121)
T ss_dssp HHHHHHHTT-HHHHHHHHHHHHHTSSSH--HHHHHHHHHHS-H
T ss_pred HHHHHHhCCCHHHHHHHHHHHHHhCCCH--HHHHHHHHhhCCH
Confidence 6777888999999999999999999953 4445555554443
No 68
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=71.05 E-value=9.6 Score=30.59 Aligned_cols=36 Identities=8% Similarity=0.179 Sum_probs=33.3
Q ss_pred CccccHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCcceEE
Q 025096 192 AHQMKLDVIVKALKWLEMDMDVDEVECIVAILIHKNLVKGY 232 (258)
Q Consensus 192 ~~~i~l~~i~~al~~~~~~~~~~evE~ila~LI~~G~IkGy 232 (258)
+.|+|+++|++.+. +|...|-.-+.+|...|.|+||
T Consensus 21 d~R~s~~eiA~~lg-----lS~~tV~~Ri~rL~~~GvI~~~ 56 (153)
T PRK11179 21 NARTPYAELAKQFG-----VSPGTIHVRVEKMKQAGIITGT 56 (153)
T ss_pred cCCCCHHHHHHHHC-----cCHHHHHHHHHHHHHCCCeeeE
Confidence 47899999999997 7899999999999999999986
No 69
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=70.95 E-value=13 Score=30.23 Aligned_cols=39 Identities=18% Similarity=0.182 Sum_probs=35.0
Q ss_pred CCccccHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCcceEEee
Q 025096 191 KAHQMKLDVIVKALKWLEMDMDVDEVECIVAILIHKNLVKGYFA 234 (258)
Q Consensus 191 ~~~~i~l~~i~~al~~~~~~~~~~evE~ila~LI~~G~IkGyI~ 234 (258)
.+.|+|+++|++.+. +|..-+-.-+..|...|.|+||--
T Consensus 25 ~d~R~s~~eiA~~lg-----lS~~tv~~Ri~rL~~~GvI~~~~~ 63 (164)
T PRK11169 25 KDGRISNVELSKRVG-----LSPTPCLERVRRLERQGFIQGYTA 63 (164)
T ss_pred cCCCCCHHHHHHHHC-----cCHHHHHHHHHHHHHCCCeEEEEE
Confidence 467999999999997 689999999999999999998764
No 70
>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional
Probab=70.78 E-value=11 Score=30.84 Aligned_cols=19 Identities=0% Similarity=0.043 Sum_probs=13.3
Q ss_pred HHhcCChhhHHHHHHHhhc
Q 025096 28 YFKLGTVHLCRSVIRSIET 46 (258)
Q Consensus 28 yf~l~~~~~~~~l~~~i~~ 46 (258)
....|+++.++++++.+-.
T Consensus 45 ly~~G~l~~A~~~f~~L~~ 63 (157)
T PRK15363 45 LMEVKEFAGAARLFQLLTI 63 (157)
T ss_pred HHHCCCHHHHHHHHHHHHH
Confidence 3567888888888776543
No 71
>KOG4234 consensus TPR repeat-containing protein [General function prediction only]
Probab=70.71 E-value=19 Score=31.12 Aligned_cols=89 Identities=19% Similarity=0.190 Sum_probs=49.1
Q ss_pred hhHHhhhhcChHHHHHHHHHHHHhcCccChHHHHHHHH-HHHHHHhhcCCCCC--hhhhhhccccc-c-HHHH-HHHHhC
Q 025096 67 TGRLEVFNENFPAADQKLSYALINCNPQSEANIRMILK-YLIPVKLSIGILPK--DWLLEKYNLVE-Y-SNIV-QALRRG 140 (258)
Q Consensus 67 ~G~~~~~~~~~~~A~~~L~~A~~~c~~~~~~~~~~IL~-~LIp~~Ll~G~~P~--~~ll~~~~l~~-y-~~L~-~av~~G 140 (258)
-|--.|.+++|++|...+++|+..||..... -|.||- --..+.|=+++--. .+--....|.+ | ..|. +|.---
T Consensus 101 EGN~~F~ngdyeeA~skY~~Ale~cp~~~~e-~rsIly~Nraaa~iKl~k~e~aI~dcsKaiel~pty~kAl~RRAeaye 179 (271)
T KOG4234|consen 101 EGNELFKNGDYEEANSKYQEALESCPSTSTE-ERSILYSNRAAALIKLRKWESAIEDCSKAIELNPTYEKALERRAEAYE 179 (271)
T ss_pred HHHHhhhcccHHHHHHHHHHHHHhCccccHH-HHHHHHhhhHHHHHHhhhHHHHHHHHHhhHhcCchhHHHHHHHHHHHH
Confidence 4666788899999999999999999987653 233321 11112221232100 00000112333 4 2333 355556
Q ss_pred CHHHHHHHHHHcHHHH
Q 025096 141 DLRLLRHALEEHEDQF 156 (258)
Q Consensus 141 dl~~f~~~l~~~~~~f 156 (258)
+...|+++++.+...+
T Consensus 180 k~ek~eealeDyKki~ 195 (271)
T KOG4234|consen 180 KMEKYEEALEDYKKIL 195 (271)
T ss_pred hhhhHHHHHHHHHHHH
Confidence 6678888888765533
No 72
>PF13812 PPR_3: Pentatricopeptide repeat domain
Probab=70.22 E-value=9.5 Score=21.47 Aligned_cols=29 Identities=10% Similarity=0.111 Sum_probs=25.6
Q ss_pred HHHHHHHHHHhcCChhhHHHHHHHhhccC
Q 025096 20 LTCQLFKIYFKLGTVHLCRSVIRSIETAR 48 (258)
Q Consensus 20 ~~n~l~kiyf~l~~~~~~~~l~~~i~~~~ 48 (258)
..|.+++.|.+.|+.+.+..+++.++...
T Consensus 3 ty~~ll~a~~~~g~~~~a~~~~~~M~~~g 31 (34)
T PF13812_consen 3 TYNALLRACAKAGDPDAALQLFDEMKEQG 31 (34)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHHHHhC
Confidence 46889999999999999999999988653
No 73
>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=70.08 E-value=50 Score=27.22 Aligned_cols=57 Identities=16% Similarity=-0.012 Sum_probs=42.1
Q ss_pred ccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCccChHHHHHHHHHHHHHHhhcCC
Q 025096 57 KRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNPQSEANIRMILKYLIPVKLSIGI 115 (258)
Q Consensus 57 ~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~~~~~~~~IL~~LIp~~Ll~G~ 115 (258)
+.+.-.=+.-.|.+|+--||+++|.+++..+...|. +.+++..+...+|-+.+..|.
T Consensus 32 kesir~~~~~l~~~~~~~Gd~~~A~k~y~~~~~~~~--~~~~~id~~l~~irv~i~~~d 88 (177)
T PF10602_consen 32 KESIRMALEDLADHYCKIGDLEEALKAYSRARDYCT--SPGHKIDMCLNVIRVAIFFGD 88 (177)
T ss_pred hHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHhhhcC--CHHHHHHHHHHHHHHHHHhCC
Confidence 334444456789999999999999999999999887 345666666666666555553
No 74
>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional
Probab=69.41 E-value=19 Score=33.07 Aligned_cols=65 Identities=12% Similarity=-0.026 Sum_probs=47.9
Q ss_pred HHHHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCccC
Q 025096 22 CQLFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNPQS 95 (258)
Q Consensus 22 n~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~~ 95 (258)
..+...|.++|+++.|...+...-.. -|. ....++..|.+++..++|++|..+|..|+..-|.+.
T Consensus 40 ~~~a~~~~~~g~~~eAl~~~~~Al~l-~P~--------~~~a~~~lg~~~~~lg~~~eA~~~~~~al~l~P~~~ 104 (356)
T PLN03088 40 ADRAQANIKLGNFTEAVADANKAIEL-DPS--------LAKAYLRKGTACMKLEEYQTAKAALEKGASLAPGDS 104 (356)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHh-CcC--------CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCCCCH
Confidence 45567788999999998777543221 121 233567889999999999999999999999777543
No 75
>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=68.83 E-value=12 Score=27.80 Aligned_cols=38 Identities=18% Similarity=0.258 Sum_probs=32.3
Q ss_pred CccccHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCcceEEee
Q 025096 192 AHQMKLDVIVKALKWLEMDMDVDEVECIVAILIHKNLVKGYFA 234 (258)
Q Consensus 192 ~~~i~l~~i~~al~~~~~~~~~~evE~ila~LI~~G~IkGyI~ 234 (258)
..=+++++|++.+. ++.++|+..|-.|+.+|.|--.|+
T Consensus 63 ~~Gv~v~~I~~~l~-----~~~~~v~~al~~L~~eG~IYsTiD 100 (102)
T PF08784_consen 63 EEGVHVDEIAQQLG-----MSENEVRKALDFLSNEGHIYSTID 100 (102)
T ss_dssp TTTEEHHHHHHHST-----S-HHHHHHHHHHHHHTTSEEESSS
T ss_pred CCcccHHHHHHHhC-----cCHHHHHHHHHHHHhCCeEecccC
Confidence 34599999999985 789999999999999999987665
No 76
>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=68.79 E-value=20 Score=30.13 Aligned_cols=68 Identities=6% Similarity=-0.148 Sum_probs=51.1
Q ss_pred HHHHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCccC
Q 025096 22 CQLFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNPQS 95 (258)
Q Consensus 22 n~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~~ 95 (258)
-.+...|++.++++.+...+..+-.. .|. ......-+|..|..+...++|++|...+..++...|.+.
T Consensus 37 ~~~g~~~~~~~~~~~A~~~~~~~~~~-~p~-----~~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~~ 104 (235)
T TIGR03302 37 YEEAKEALDSGDYTEAIKYFEALESR-YPF-----SPYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRLHPNHP 104 (235)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHh-CCC-----chhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCC
Confidence 34556789999999999888765432 232 112223468899999999999999999999999988654
No 77
>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=67.71 E-value=9.5 Score=25.90 Aligned_cols=37 Identities=22% Similarity=0.430 Sum_probs=29.5
Q ss_pred cccHHHHHHHHHhc--c---CCCCHHHHHHHHHHHHHcCcce
Q 025096 194 QMKLDVIVKALKWL--E---MDMDVDEVECIVAILIHKNLVK 230 (258)
Q Consensus 194 ~i~l~~i~~al~~~--~---~~~~~~evE~ila~LI~~G~Ik 230 (258)
.+|++.|+..++.. + .+.+.+|++..+..++++|.+.
T Consensus 11 sl~l~RIh~mLkmf~~~~~~~~~s~~eL~~fL~~lv~e~~L~ 52 (60)
T PF08672_consen 11 SLPLDRIHSMLKMFPKDPGGYDISLEELQEFLDRLVEEGKLE 52 (60)
T ss_dssp SEEHHHHHHHHHHH-GGG--TT--HHHHHHHHHHHHHTTSEE
T ss_pred CCCHHHHHHHHHhccCCCCCCCCCHHHHHHHHHHHHHCCcEE
Confidence 38999999888865 2 3479999999999999999874
No 78
>PRK11189 lipoprotein NlpI; Provisional
Probab=67.65 E-value=11 Score=33.67 Aligned_cols=39 Identities=13% Similarity=0.052 Sum_probs=32.9
Q ss_pred hhhhhhhHHhhhhcChHHHHHHHHHHHHhcCccChHHHH
Q 025096 62 TYMYYTGRLEVFNENFPAADQKLSYALINCNPQSEANIR 100 (258)
Q Consensus 62 ~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~~~~~~~ 100 (258)
.-+||+|+++...+++++|..+|..|....|.+....+-
T Consensus 237 ea~~~Lg~~~~~~g~~~~A~~~~~~Al~~~~~~~~e~~~ 275 (296)
T PRK11189 237 ETYFYLAKYYLSLGDLDEAAALFKLALANNVYNFVEHRY 275 (296)
T ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCchHHHHHH
Confidence 457999999999999999999999999988766554443
No 79
>PRK10866 outer membrane biogenesis protein BamD; Provisional
Probab=67.06 E-value=85 Score=27.21 Aligned_cols=65 Identities=9% Similarity=0.004 Sum_probs=48.4
Q ss_pred HHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCccC
Q 025096 25 FKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNPQS 95 (258)
Q Consensus 25 ~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~~ 95 (258)
...+++.|+++.+...++.+... .|. + +-.... .|..|..+.-.++|.+|...++..++..|.+.
T Consensus 39 A~~~~~~g~y~~Ai~~f~~l~~~-yP~-s--~~a~~a--~l~la~ayy~~~~y~~A~~~~e~fi~~~P~~~ 103 (243)
T PRK10866 39 AQQKLQDGNWKQAITQLEALDNR-YPF-G--PYSQQV--QLDLIYAYYKNADLPLAQAAIDRFIRLNPTHP 103 (243)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHh-CCC-C--hHHHHH--HHHHHHHHHhcCCHHHHHHHHHHHHHhCcCCC
Confidence 44567789999999888887653 232 1 222222 57899999999999999999999999888654
No 80
>KOG4056 consensus Translocase of outer mitochondrial membrane complex, subunit TOM20 [Intracellular trafficking, secretion, and vesicular transport]
Probab=67.02 E-value=6.6 Score=31.29 Aligned_cols=39 Identities=13% Similarity=0.247 Sum_probs=30.4
Q ss_pred ccchhhhhhh-----hhHHhhhhcChHHHHHHHHHHHHhcCccC
Q 025096 57 KRDKVTYMYY-----TGRLEVFNENFPAADQKLSYALINCNPQS 95 (258)
Q Consensus 57 ~~~~v~y~YY-----~G~~~~~~~~~~~A~~~L~~A~~~c~~~~ 95 (258)
+.....=.|+ +|.-++-+++++++-.||..|+..|++..
T Consensus 72 ~d~~~~E~~Fmqqv~lGE~L~~qg~~e~ga~h~~nAi~vcgqpa 115 (143)
T KOG4056|consen 72 SDAEEVEKFFMQQVQLGEELLAQGNEEEGAEHLANAIVVCGQPA 115 (143)
T ss_pred CCHHHHHHHHHHHHHhHHHHHHccCHHHHHHHHHHHHhhcCCHH
Confidence 3334444455 67778889999999999999999999754
No 81
>PF14853 Fis1_TPR_C: Fis1 C-terminal tetratricopeptide repeat; PDB: 1IYG_A 1PC2_A 1NZN_A 3UUX_C 1Y8M_A 2PQR_A 2PQN_A 3O48_A.
Probab=66.32 E-value=10 Score=25.00 Aligned_cols=32 Identities=13% Similarity=-0.005 Sum_probs=27.6
Q ss_pred hhhhhhHHhhhhcChHHHHHHHHHHHHhcCcc
Q 025096 63 YMYYTGRLEVFNENFPAADQKLSYALINCNPQ 94 (258)
Q Consensus 63 y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~ 94 (258)
+.||++.-+.-.++|.+|......++..=|.+
T Consensus 3 ~lY~lAig~ykl~~Y~~A~~~~~~lL~~eP~N 34 (53)
T PF14853_consen 3 CLYYLAIGHYKLGEYEKARRYCDALLEIEPDN 34 (53)
T ss_dssp HHHHHHHHHHHTT-HHHHHHHHHHHHHHTTS-
T ss_pred hHHHHHHHHHHhhhHHHHHHHHHHHHhhCCCc
Confidence 68999999999999999999999999987744
No 82
>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=65.84 E-value=23 Score=34.83 Aligned_cols=28 Identities=25% Similarity=0.241 Sum_probs=15.0
Q ss_pred hhhhHHhhhhcChHHHHHHHHHHHHhcC
Q 025096 65 YYTGRLEVFNENFPAADQKLSYALINCN 92 (258)
Q Consensus 65 YY~G~~~~~~~~~~~A~~~L~~A~~~c~ 92 (258)
++.|.++...++|++|.+.+..|+...|
T Consensus 471 ~~lg~~~~~~g~~~~A~~~~~~Al~l~p 498 (615)
T TIGR00990 471 NYYGELLLDQNKFDEAIEKFDTAIELEK 498 (615)
T ss_pred HHHHHHHHHccCHHHHHHHHHHHHhcCC
Confidence 3445555555555555555555555444
No 83
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=64.21 E-value=24 Score=26.06 Aligned_cols=35 Identities=23% Similarity=0.376 Sum_probs=31.6
Q ss_pred ccccHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCcceEE
Q 025096 193 HQMKLDVIVKALKWLEMDMDVDEVECIVAILIHKNLVKGY 232 (258)
Q Consensus 193 ~~i~l~~i~~al~~~~~~~~~~evE~ila~LI~~G~IkGy 232 (258)
.++|++++++.+. ++...+-..+..|..+|+|+|+
T Consensus 16 ~~~~~~~la~~l~-----~s~~tv~~~l~~L~~~g~i~~~ 50 (108)
T smart00344 16 ARISLAELAKKVG-----LSPSTVHNRVKRLEEEGVIKGY 50 (108)
T ss_pred CCCCHHHHHHHHC-----cCHHHHHHHHHHHHHCCCeece
Confidence 4799999999987 7899999999999999999853
No 84
>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=63.64 E-value=37 Score=22.91 Aligned_cols=36 Identities=19% Similarity=0.100 Sum_probs=31.5
Q ss_pred ccccHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCcceEEe
Q 025096 193 HQMKLDVIVKALKWLEMDMDVDEVECIVAILIHKNLVKGYF 233 (258)
Q Consensus 193 ~~i~l~~i~~al~~~~~~~~~~evE~ila~LI~~G~IkGyI 233 (258)
...+.++|+..+. ++...|..+|.+|..+|+|.-.-
T Consensus 21 ~~~t~~eIa~~l~-----i~~~~v~~~L~~L~~~GlV~~~~ 56 (68)
T PF01978_consen 21 GPATAEEIAEELG-----ISRSTVYRALKSLEEKGLVEREE 56 (68)
T ss_dssp CHEEHHHHHHHHT-----SSHHHHHHHHHHHHHTTSEEEEE
T ss_pred CCCCHHHHHHHHC-----cCHHHHHHHHHHHHHCCCEEEEc
Confidence 4578899999987 79999999999999999996654
No 85
>PRK15331 chaperone protein SicA; Provisional
Probab=63.02 E-value=14 Score=30.48 Aligned_cols=36 Identities=14% Similarity=0.184 Sum_probs=27.9
Q ss_pred hhhhhHHhhhhcChHHHHHHHHHHHHhcCccChHHH
Q 025096 64 MYYTGRLEVFNENFPAADQKLSYALINCNPQSEANI 99 (258)
Q Consensus 64 ~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~~~~~~ 99 (258)
.||.|.+++.-++..+|..+|+.|..+|.....+.|
T Consensus 108 ~f~agqC~l~l~~~~~A~~~f~~a~~~~~~~~l~~~ 143 (165)
T PRK15331 108 VFFTGQCQLLMRKAAKARQCFELVNERTEDESLRAK 143 (165)
T ss_pred cchHHHHHHHhCCHHHHHHHHHHHHhCcchHHHHHH
Confidence 688899999889999999999988887654444433
No 86
>PRK15359 type III secretion system chaperone protein SscB; Provisional
Probab=62.32 E-value=57 Score=25.57 Aligned_cols=64 Identities=9% Similarity=-0.152 Sum_probs=47.8
Q ss_pred HHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCccCh
Q 025096 24 LFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNPQSE 96 (258)
Q Consensus 24 l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~~~ 96 (258)
.-..+++.|+++.+-..+...-.. -|. ...+++-.|.++...+++++|...+..|+...|.+..
T Consensus 30 ~g~~~~~~g~~~~A~~~~~~al~~-~P~--------~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l~p~~~~ 93 (144)
T PRK15359 30 SGYASWQEGDYSRAVIDFSWLVMA-QPW--------SWRAHIALAGTWMMLKEYTTAINFYGHALMLDASHPE 93 (144)
T ss_pred HHHHHHHcCCHHHHHHHHHHHHHc-CCC--------cHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCcH
Confidence 456778999999888777543221 122 3456788999999999999999999999998776543
No 87
>COG3063 PilF Tfp pilus assembly protein PilF [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=61.85 E-value=45 Score=29.23 Aligned_cols=81 Identities=17% Similarity=0.097 Sum_probs=48.5
Q ss_pred cccccCCC-----chhHHHHHHHHHHHHHHHhcCChhhHHHHH-HHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcCh
Q 025096 4 FGVLAGKG-----SKRVGALYLTCQLFKIYFKLGTVHLCRSVI-RSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENF 77 (258)
Q Consensus 4 ~~~~~~d~-----~Kk~~~~~~~n~l~kiyf~l~~~~~~~~l~-~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~ 77 (258)
+..|.+|+ .++.-.--.-..+---|+.-|++..++.-+ |+++.. |+ +..++-+.=.| |...++-
T Consensus 16 ~~~cvt~~~~~~~~~~~~aa~arlqLal~YL~~gd~~~A~~nlekAL~~D--Ps---~~~a~~~~A~~-----Yq~~Ge~ 85 (250)
T COG3063 16 LGACVTDPAPSRQTDRNEAAKARLQLALGYLQQGDYAQAKKNLEKALEHD--PS---YYLAHLVRAHY-----YQKLGEN 85 (250)
T ss_pred hhcccCCCCccccccHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--cc---cHHHHHHHHHH-----HHHcCCh
Confidence 34566663 344556666778888999999999999444 777753 32 23344333323 2344555
Q ss_pred HHHHHHHHHHHHhcCcc
Q 025096 78 PAADQKLSYALINCNPQ 94 (258)
Q Consensus 78 ~~A~~~L~~A~~~c~~~ 94 (258)
+.|.+.+.+|+..-|.+
T Consensus 86 ~~A~e~YrkAlsl~p~~ 102 (250)
T COG3063 86 DLADESYRKALSLAPNN 102 (250)
T ss_pred hhHHHHHHHHHhcCCCc
Confidence 55666666666555544
No 88
>PF13041 PPR_2: PPR repeat family
Probab=61.57 E-value=17 Score=22.84 Aligned_cols=31 Identities=16% Similarity=0.198 Sum_probs=27.4
Q ss_pred HHHHHHHHHHHhcCChhhHHHHHHHhhccCC
Q 025096 19 YLTCQLFKIYFKLGTVHLCRSVIRSIETARI 49 (258)
Q Consensus 19 ~~~n~l~kiyf~l~~~~~~~~l~~~i~~~~~ 49 (258)
...|.++..|.+.|+++.|..+++.+....+
T Consensus 4 ~~yn~li~~~~~~~~~~~a~~l~~~M~~~g~ 34 (50)
T PF13041_consen 4 VTYNTLISGYCKAGKFEEALKLFKEMKKRGI 34 (50)
T ss_pred HHHHHHHHHHHHCcCHHHHHHHHHHHHHcCC
Confidence 4568999999999999999999999987654
No 89
>PRK10803 tol-pal system protein YbgF; Provisional
Probab=61.45 E-value=37 Score=29.98 Aligned_cols=68 Identities=12% Similarity=0.054 Sum_probs=51.5
Q ss_pred HHHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCccCh
Q 025096 23 QLFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNPQSE 96 (258)
Q Consensus 23 ~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~~~ 96 (258)
.+-..|+..++++.+...++.+-.. .|. .|+ .-.-.|..|.++...+++.+|...++..+...|.+..
T Consensus 185 ~LG~~y~~~g~~~~A~~~f~~vv~~-yP~---s~~--~~dAl~klg~~~~~~g~~~~A~~~~~~vi~~yP~s~~ 252 (263)
T PRK10803 185 WLGQLNYNKGKKDDAAYYFASVVKN-YPK---SPK--AADAMFKVGVIMQDKGDTAKAKAVYQQVIKKYPGTDG 252 (263)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHH-CCC---Ccc--hhHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCCHH
Confidence 4556788999999999888766432 232 122 3334677999999999999999999999999886643
No 90
>TIGR00990 3a0801s09 mitochondrial precursor proteins import receptor (72 kDa mitochondrial outermembrane protein) (mitochondrial import receptor for the ADP/ATP carrier) (translocase of outermembrane tom70).
Probab=61.34 E-value=42 Score=33.01 Aligned_cols=33 Identities=12% Similarity=0.126 Sum_probs=22.0
Q ss_pred hhhhhhhHHhhhhcChHHHHHHHHHHHHhcCcc
Q 025096 62 TYMYYTGRLEVFNENFPAADQKLSYALINCNPQ 94 (258)
Q Consensus 62 ~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~ 94 (258)
..+|..|.+++..++|++|..++..|+..-|..
T Consensus 400 ~~~~~lg~~~~~~g~~~~A~~~~~kal~l~P~~ 432 (615)
T TIGR00990 400 DIYYHRAQLHFIKGEFAQAGKDYQKSIDLDPDF 432 (615)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHHHcCccC
Confidence 345667777777777777777777777765543
No 91
>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=60.97 E-value=22 Score=27.80 Aligned_cols=64 Identities=14% Similarity=0.069 Sum_probs=47.1
Q ss_pred HHHHHHHHHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHH
Q 025096 17 ALYLTCQLFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSY 86 (258)
Q Consensus 17 ~~~~~n~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~ 86 (258)
.....-.+.++++..|+++.+...++.+-... |+. ..... -.+.++++++-+++|++|...|..
T Consensus 47 a~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~-~d~---~l~~~--a~l~LA~~~~~~~~~d~Al~~L~~ 110 (145)
T PF09976_consen 47 AALAALQLAKAAYEQGDYDEAKAALEKALANA-PDP---ELKPL--ARLRLARILLQQGQYDEALATLQQ 110 (145)
T ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhC-CCH---HHHHH--HHHHHHHHHHHcCCHHHHHHHHHh
Confidence 34445557789999999999999997766542 321 11222 356789999999999999999965
No 92
>PRK11906 transcriptional regulator; Provisional
Probab=60.59 E-value=15 Score=35.20 Aligned_cols=41 Identities=17% Similarity=0.205 Sum_probs=33.0
Q ss_pred hhhhhHHhhhhcChHHHHHHHHHHHHhcCccChHHHHHHHHHHH
Q 025096 64 MYYTGRLEVFNENFPAADQKLSYALINCNPQSEANIRMILKYLI 107 (258)
Q Consensus 64 ~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~~~~~~~~IL~~LI 107 (258)
+||.|.+.+..|+.++|.++++.|++..|. +-+--|+|.||
T Consensus 375 ~~~~~~~~~~~G~~~~a~~~i~~alrLsP~---~~~~~~~~~~~ 415 (458)
T PRK11906 375 YYYRALVHFHNEKIEEARICIDKSLQLEPR---RRKAVVIKECV 415 (458)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHhccCch---hhHHHHHHHHH
Confidence 588999999999999999999999998773 33455666666
No 93
>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B.
Probab=60.11 E-value=15 Score=24.23 Aligned_cols=30 Identities=17% Similarity=0.088 Sum_probs=26.2
Q ss_pred hhhhHHhhhhcChHHHHHHHHHHHHhcCcc
Q 025096 65 YYTGRLEVFNENFPAADQKLSYALINCNPQ 94 (258)
Q Consensus 65 YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~ 94 (258)
|-.|+.++..++|++|...|++++..-|.+
T Consensus 1 ~~~a~~~~~~g~~~~A~~~~~~~l~~~P~~ 30 (65)
T PF13432_consen 1 YALARALYQQGDYDEAIAAFEQALKQDPDN 30 (65)
T ss_dssp HHHHHHHHHCTHHHHHHHHHHHHHCCSTTH
T ss_pred ChHHHHHHHcCCHHHHHHHHHHHHHHCCCC
Confidence 346889999999999999999999987653
No 94
>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=60.09 E-value=42 Score=33.28 Aligned_cols=63 Identities=14% Similarity=0.170 Sum_probs=49.0
Q ss_pred HHHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCcc
Q 025096 23 QLFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNPQ 94 (258)
Q Consensus 23 ~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~ 94 (258)
...+.|++.|+++.+...++..-.. .|. ...-+|+.|.+++..++|++|...|..+....|.+
T Consensus 27 ~~a~~~~~~~~~~~A~~~~~~~~~~-~p~--------~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~ 89 (899)
T TIGR02917 27 EAAKSYLQKNKYKAAIIQLKNALQK-DPN--------DAEARFLLGKIYLALGDYAAAEKELRKALSLGYPK 89 (899)
T ss_pred HHHHHHHHcCChHhHHHHHHHHHHh-CCC--------CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCh
Confidence 3467888999999999887654432 232 23467899999999999999999999999877654
No 95
>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=59.38 E-value=50 Score=27.28 Aligned_cols=138 Identities=14% Similarity=0.172 Sum_probs=75.1
Q ss_pred ccchhhhhhhhhHHhhhh---cChHHHHHHHHHHHHhcCcc-ChHHHHHHHHHHHHHHhhcCCCCChhhh-hhcc---c-
Q 025096 57 KRDKVTYMYYTGRLEVFN---ENFPAADQKLSYALINCNPQ-SEANIRMILKYLIPVKLSIGILPKDWLL-EKYN---L- 127 (258)
Q Consensus 57 ~~~~v~y~YY~G~~~~~~---~~~~~A~~~L~~A~~~c~~~-~~~~~~~IL~~LIp~~Ll~G~~P~~~ll-~~~~---l- 127 (258)
....+.-+-..+++++.. +++.+....|...+...... ...++..+.-|.+...+..+..+..... ...+ .
T Consensus 52 ~~~~i~v~E~~ar~~i~~~d~~qf~~c~~~L~~lY~~~~~~~~~~~~~ef~~y~lL~~l~~~~~~~~~~~l~~l~~~~~~ 131 (204)
T PF03399_consen 52 NDFAIKVYERIARFAIESGDLEQFNQCLSQLKELYDDLRDLPPSPNEAEFIAYYLLYLLCQNNIPDFHMELELLPSEILS 131 (204)
T ss_dssp SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT---TTHHHHHHHHHHHTT-T---THHHHHHTTS-HHHHT
T ss_pred CHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHhhccCCCCCCHHHHHHHHHHHHHHcccchHHHHHHHHCchhhhc
Confidence 344666667778887754 45566677777777664111 2356677777776655544434332221 1111 1
Q ss_pred cc---c-HHHHHHHHhCCHHHHHHHHHHcHHHHHHhcHH-HHHHhhHHHHHHHHHHHHHHHhhcCCCCCCccccHHHHHH
Q 025096 128 VE---Y-SNIVQALRRGDLRLLRHALEEHEDQFLRSGVY-LVLEKLELQVYQRLFKKIYIIQKQKDPSKAHQMKLDVIVK 202 (258)
Q Consensus 128 ~~---y-~~L~~av~~Gdl~~f~~~l~~~~~~f~~~gly-lll~~l~~~v~r~L~kkv~~~~~~~~~~~~~~i~l~~i~~ 202 (258)
.+ + .++..|+.+||...|=+.+++.....+-..+. ..+.++|...++.+.+ .+ .+.+|++.+.+
T Consensus 132 ~~~i~~al~l~~a~~~gny~~ff~l~~~~~~~~l~~~l~~~~~~~iR~~al~~i~~----ay-------~~~i~l~~l~~ 200 (204)
T PF03399_consen 132 SPYIQFALELCRALMEGNYVRFFRLYRSKSAPYLFACLMERFFNRIRLRALQSISK----AY-------RSSIPLSFLAE 200 (204)
T ss_dssp SHHHHHHHHHHHHH--TTHHHHHHHHT-TTS-HHHHHHHGGGHHHHHHHHHHHHHH----HS--------T-EEHHHHHH
T ss_pred CHHHHHHHHHHHHHHcCCHHHHHHHHhccCCChHHHHHHHHHHHHHHHHHHHHHHH----Hc-------CCCCCHHHHHH
Confidence 12 2 57889999999999999994433333333333 2556777766655544 22 11489988877
Q ss_pred HHH
Q 025096 203 ALK 205 (258)
Q Consensus 203 al~ 205 (258)
.|.
T Consensus 201 ~L~ 203 (204)
T PF03399_consen 201 LLG 203 (204)
T ss_dssp HTT
T ss_pred HcC
Confidence 653
No 96
>PF07721 TPR_4: Tetratricopeptide repeat; InterPro: IPR011717 This entry includes tetratricopeptide-like repeats not detected by the IPR001440 from INTERPRO, IPR013105 from INTERPRO and IPR011716 from INTERPRO models. The tetratricopeptide repeat (TPR) motif is a protein-protein interaction module found in multiple copies in a number of functionally different proteins that facilitates specific interactions with a partner protein(s) [].; GO: 0042802 identical protein binding
Probab=59.24 E-value=9.4 Score=20.87 Aligned_cols=23 Identities=13% Similarity=-0.009 Sum_probs=20.0
Q ss_pred hhhhhhHHhhhhcChHHHHHHHH
Q 025096 63 YMYYTGRLEVFNENFPAADQKLS 85 (258)
Q Consensus 63 y~YY~G~~~~~~~~~~~A~~~L~ 85 (258)
..+.+|+.+...|++++|...+.
T Consensus 3 a~~~la~~~~~~G~~~eA~~~l~ 25 (26)
T PF07721_consen 3 ARLALARALLAQGDPDEAERLLR 25 (26)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHh
Confidence 35778999999999999999875
No 97
>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=58.85 E-value=45 Score=22.39 Aligned_cols=46 Identities=22% Similarity=0.314 Sum_probs=35.7
Q ss_pred HHHHHHHHHhhcCCCCCCccccHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCcce
Q 025096 175 RLFKKIYIIQKQKDPSKAHQMKLDVIVKALKWLEMDMDVDEVECIVAILIHKNLVK 230 (258)
Q Consensus 175 ~L~kkv~~~~~~~~~~~~~~i~l~~i~~al~~~~~~~~~~evE~ila~LI~~G~Ik 230 (258)
+.++.||.... ....++..+|++.++ ++...|-..+..|-.+|+|.
T Consensus 8 ~YL~~Iy~l~~-----~~~~v~~~~iA~~L~-----vs~~tvt~ml~~L~~~GlV~ 53 (60)
T PF01325_consen 8 DYLKAIYELSE-----EGGPVRTKDIAERLG-----VSPPTVTEMLKRLAEKGLVE 53 (60)
T ss_dssp HHHHHHHHHHH-----CTSSBBHHHHHHHHT-----S-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHc-----CCCCccHHHHHHHHC-----CChHHHHHHHHHHHHCCCEE
Confidence 34566666652 345689999999998 78999999999999999984
No 98
>PF09382 RQC: RQC domain; InterPro: IPR018982 This entry represents the RQC domain, which is a DNA-binding domain found only in RecQ family enzymes. RecQ family helicases can unwind G4 DNA, and play important roles at G-rich domains of the genome, including the telomeres, rDNA, and immunoglobulin switch regions. This domain has a helix-turn-helix structure and acts as a high affinity G4 DNA binding domain []. Binding of RecQ to Holliday junctions involves both the RQC and the HRDC domains.; GO: 0043140 ATP-dependent 3'-5' DNA helicase activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1OYW_A 1OYY_A 3AAF_A 2AXL_A 2V1X_B 2WWY_B.
Probab=58.50 E-value=71 Score=23.45 Aligned_cols=36 Identities=19% Similarity=0.190 Sum_probs=23.6
Q ss_pred CCCCHHHHHHHHHHHHHcCcceEEee-cCceEEEEec
Q 025096 209 MDMDVDEVECIVAILIHKNLVKGYFA-HKSKVVVLSK 244 (258)
Q Consensus 209 ~~~~~~evE~ila~LI~~G~IkGyI~-~~~~~lVlsk 244 (258)
.+.+.++++.++-.||.+|+|.=..+ ....++.+++
T Consensus 52 k~~~~~~~~~li~~Li~~g~L~~~~~~~~~~~l~~~~ 88 (106)
T PF09382_consen 52 KDMSKDDWERLIRQLILEGYLSEDNGGFAYPYLKLTP 88 (106)
T ss_dssp TTS-HHHHHHHHHHHHHTTSEEEEECCCCTEEEEE-G
T ss_pred ccCCHHHHHHHHHHHHHcCCceecCCcccccEEEECH
Confidence 35799999999999999999922222 1334555543
No 99
>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=58.45 E-value=30 Score=29.03 Aligned_cols=67 Identities=10% Similarity=0.009 Sum_probs=48.7
Q ss_pred HHHHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchh-hhhhhhhHHhhhh--------cChHHHHHHHHHHHHhcC
Q 025096 22 CQLFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKV-TYMYYTGRLEVFN--------ENFPAADQKLSYALINCN 92 (258)
Q Consensus 22 n~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v-~y~YY~G~~~~~~--------~~~~~A~~~L~~A~~~c~ 92 (258)
..+..+|++.++++.+.+.++.+-.. .|. ...+ .-.|..|..+... +++++|.+.++.++..-|
T Consensus 74 ~~la~~~~~~~~~~~A~~~~~~~l~~-~p~------~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~p 146 (235)
T TIGR03302 74 LDLAYAYYKSGDYAEAIAAADRFIRL-HPN------HPDADYAYYLRGLSNYNQIDRVDRDQTAAREAFEAFQELIRRYP 146 (235)
T ss_pred HHHHHHHHhcCCHHHHHHHHHHHHHH-CcC------CCchHHHHHHHHHHHHHhcccccCCHHHHHHHHHHHHHHHHHCC
Confidence 44567899999999999998765432 232 2221 2357788888755 789999999999999877
Q ss_pred ccC
Q 025096 93 PQS 95 (258)
Q Consensus 93 ~~~ 95 (258)
.+.
T Consensus 147 ~~~ 149 (235)
T TIGR03302 147 NSE 149 (235)
T ss_pred CCh
Confidence 653
No 100
>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=57.69 E-value=52 Score=32.64 Aligned_cols=33 Identities=15% Similarity=0.003 Sum_probs=25.9
Q ss_pred hhhhhhhHHhhhhcChHHHHHHHHHHHHhcCcc
Q 025096 62 TYMYYTGRLEVFNENFPAADQKLSYALINCNPQ 94 (258)
Q Consensus 62 ~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~ 94 (258)
..+++.|.+++..+++++|...+..|+...|.+
T Consensus 194 ~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~p~~ 226 (899)
T TIGR02917 194 DALLLKGDLLLSLGNIELALAAYRKAIALRPNN 226 (899)
T ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHHHhhCCCC
Confidence 456778888888888888888888888876654
No 101
>KOG2300 consensus Uncharacterized conserved protein [Function unknown]
Probab=57.54 E-value=2e+02 Score=28.23 Aligned_cols=123 Identities=17% Similarity=0.144 Sum_probs=79.3
Q ss_pred ccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCccCh---HHHHHHHHHHHHHHhhcCCCCC-hhhhhh------cc
Q 025096 57 KRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNPQSE---ANIRMILKYLIPVKLSIGILPK-DWLLEK------YN 126 (258)
Q Consensus 57 ~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~~~---~~~~~IL~~LIp~~Ll~G~~P~-~~ll~~------~~ 126 (258)
..+-..-.|-.|.+.++-+-|+.|+.+|..|.+.-+.... -|--....|| -.|+.-+ .+.++. ..
T Consensus 363 r~~~~~ih~LlGlys~sv~~~enAe~hf~~a~k~t~~~dl~a~~nlnlAi~YL-----~~~~~ed~y~~ld~i~p~nt~s 437 (629)
T KOG2300|consen 363 RAHEAQIHMLLGLYSHSVNCYENAEFHFIEATKLTESIDLQAFCNLNLAISYL-----RIGDAEDLYKALDLIGPLNTNS 437 (629)
T ss_pred HHhHHHHHHHHhhHhhhcchHHHHHHHHHHHHHhhhHHHHHHHHHHhHHHHHH-----HhccHHHHHHHHHhcCCCCCCc
Confidence 4566777889999999999999999999999997653322 1111111222 1222110 111111 10
Q ss_pred -----cc---ccHHHHHHHHhCCHHHHHHHHHH------cHHHHHHhcHHHHHHhhHHHHH------HHHHHHHHHHh
Q 025096 127 -----LV---EYSNIVQALRRGDLRLLRHALEE------HEDQFLRSGVYLVLEKLELQVY------QRLFKKIYIIQ 184 (258)
Q Consensus 127 -----l~---~y~~L~~av~~Gdl~~f~~~l~~------~~~~f~~~glylll~~l~~~v~------r~L~kkv~~~~ 184 (258)
+. -|..=..|+.++++.+-...+.+ +++.+.-.+.++++-..-..++ ||.++....+.
T Consensus 438 ~ssq~l~a~~~~v~glfaf~qn~lnEaK~~l~e~Lkmanaed~~rL~a~~LvLLs~v~lslgn~~es~nmvrpamqlA 515 (629)
T KOG2300|consen 438 LSSQRLEASILYVYGLFAFKQNDLNEAKRFLRETLKMANAEDLNRLTACSLVLLSHVFLSLGNTVESRNMVRPAMQLA 515 (629)
T ss_pred chHHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHhhcchhhHHHHHHHHHHHHHHHHHHhcchHHHHhccchHHHHH
Confidence 11 24455678999999887766654 6788888888887777777777 88888888775
No 102
>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif). This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.
Probab=57.05 E-value=23 Score=19.57 Aligned_cols=28 Identities=14% Similarity=0.099 Sum_probs=25.0
Q ss_pred HHHHHHHHHhcCChhhHHHHHHHhhccC
Q 025096 21 TCQLFKIYFKLGTVHLCRSVIRSIETAR 48 (258)
Q Consensus 21 ~n~l~kiyf~l~~~~~~~~l~~~i~~~~ 48 (258)
.|.+++.|.+.++.+.+..+++.+....
T Consensus 3 ~n~li~~~~~~~~~~~a~~~~~~M~~~g 30 (35)
T TIGR00756 3 YNTLIDGLCKAGRVEEALELFKEMLERG 30 (35)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHHHHcC
Confidence 5789999999999999999999988754
No 103
>PRK11189 lipoprotein NlpI; Provisional
Probab=56.73 E-value=90 Score=27.65 Aligned_cols=63 Identities=21% Similarity=0.109 Sum_probs=44.9
Q ss_pred HHHHHHHhcCChhhHHHHHHH-hhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCccC
Q 025096 23 QLFKIYFKLGTVHLCRSVIRS-IETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNPQS 95 (258)
Q Consensus 23 ~l~kiyf~l~~~~~~~~l~~~-i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~~ 95 (258)
..-.+|.+.|+.+.+...++. ++. -|. ...-++..|.++...++|++|.+.+..|+..-|...
T Consensus 69 ~~g~~~~~~g~~~~A~~~~~~Al~l--~P~--------~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~P~~~ 132 (296)
T PRK11189 69 ERGVLYDSLGLRALARNDFSQALAL--RPD--------MADAYNYLGIYLTQAGNFDAAYEAFDSVLELDPTYN 132 (296)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHc--CCC--------CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCH
Confidence 334478889999988876643 332 132 134557889999999999999999999998766543
No 104
>PF13512 TPR_18: Tetratricopeptide repeat
Probab=56.35 E-value=42 Score=26.95 Aligned_cols=66 Identities=17% Similarity=0.191 Sum_probs=40.2
Q ss_pred HHHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhh-hhHHhhhhcC---------------hHHHHHHHHH
Q 025096 23 QLFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYY-TGRLEVFNEN---------------FPAADQKLSY 86 (258)
Q Consensus 23 ~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY-~G~~~~~~~~---------------~~~A~~~L~~ 86 (258)
.+...||+.+++..+..-+...-. ..|.+..+-|-|| .|..++-+.+ ..+|...|..
T Consensus 52 ~l~yayy~~~~y~~A~a~~~rFir-------LhP~hp~vdYa~Y~~gL~~~~~~~~~~~~~~~~drD~~~~~~A~~~f~~ 124 (142)
T PF13512_consen 52 DLAYAYYKQGDYEEAIAAYDRFIR-------LHPTHPNVDYAYYMRGLSYYEQDEGSLQSFFRSDRDPTPARQAFRDFEQ 124 (142)
T ss_pred HHHHHHHHccCHHHHHHHHHHHHH-------hCCCCCCccHHHHHHHHHHHHHhhhHHhhhcccccCcHHHHHHHHHHHH
Confidence 355667777777777655543321 1355556666555 6877776554 5666666666
Q ss_pred HHHhcCccC
Q 025096 87 ALINCNPQS 95 (258)
Q Consensus 87 A~~~c~~~~ 95 (258)
-++..|.+.
T Consensus 125 lv~~yP~S~ 133 (142)
T PF13512_consen 125 LVRRYPNSE 133 (142)
T ss_pred HHHHCcCCh
Confidence 666666543
No 105
>PF01535 PPR: PPR repeat; InterPro: IPR002885 This entry represents the PPR repeat. Pentatricopeptide repeat (PPR) proteins are characterised by tandem repeats of a degenerate 35 amino acid motif []. Most of PPR proteins have roles in mitochondria or plastid []. PPR repeats were discovered while screening Arabidopsis proteins for those predicted to be targeted to mitochondria or chloroplast [, ]. Some of these proteins have been shown to play a role in post-transcriptional processes within organelles and they are thought to be sequence-specific RNA-binding proteins [, , ]. Plant genomes have between one hundred to five hundred PPR genes per genome whereas non-plant genomes encode two to six PPR proteins. Although no PPR structures are yet known, the motif is predicted to fold into a helix-turn-helix structure similar to those found in the tetratricopeptide repeat (TPR) family (see PDOC50005 from PROSITEDOC) []. The plant PPR protein family has been divided in two subfamilies on the basis of their motif content and organisation [, ]. Examples of PPR repeat-containing proteins include PET309 P32522 from SWISSPROT, which may be involved in RNA stabilisation [], and crp1, which is involved in RNA processing []. The repeat is associated with a predicted plant protein O49549 from SWISSPROT that has a domain organisation similar to the human BRCA1 protein.
Probab=56.25 E-value=14 Score=20.09 Aligned_cols=28 Identities=18% Similarity=0.217 Sum_probs=24.2
Q ss_pred HHHHHHHHHHhcCChhhHHHHHHHhhcc
Q 025096 20 LTCQLFKIYFKLGTVHLCRSVIRSIETA 47 (258)
Q Consensus 20 ~~n~l~kiyf~l~~~~~~~~l~~~i~~~ 47 (258)
..|.++..|.+.++.+.+..+++.+...
T Consensus 2 ~y~~li~~~~~~~~~~~a~~~~~~M~~~ 29 (31)
T PF01535_consen 2 TYNSLISGYCKMGQFEEALEVFDEMRER 29 (31)
T ss_pred cHHHHHHHHHccchHHHHHHHHHHHhHC
Confidence 3588999999999999999999887653
No 106
>TIGR01716 RGG_Cterm transcriptional activator, Rgg/GadR/MutR family, C-terminal domain. This model describes the whole, except for a 60 residue N-terminal helix-turn-helix DNA-binding domain (PFAM pfam01381) of the family of proteins related to the transcriptional regulator Rgg, also called RopB. Rgg is required for secretion of several proteins, including a cysteine proteinase associated with virulence. GadR is a positive regulator of a glutamate-dependent acid resistance mechanism. MutR is a transcriptional activator for mutacin biosynthesis genes in Streptococcus mutans. This family appears restricted to the low-GC Gram-positive bacteria, including at least eight members in Lactococcus lactis.
Probab=56.03 E-value=41 Score=28.15 Aligned_cols=77 Identities=8% Similarity=0.068 Sum_probs=52.6
Q ss_pred hhHHHHHHHHHHHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcC
Q 025096 13 KRVGALYLTCQLFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCN 92 (258)
Q Consensus 13 Kk~~~~~~~n~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~ 92 (258)
++..+-.+.|.+ -++.+-++++.|..++..++.-..|+. ..-.++.+.||.|.+....|+-+++.+....|+..+.
T Consensus 124 ~~~i~~il~N~~-~~~i~~~~~~~a~~~l~~l~~l~~~~~---~~~~ki~~~f~~~l~~y~~g~~~~~~~~i~~~i~~l~ 199 (220)
T TIGR01716 124 RRRVIQLLLNIA-VLLIEKNEFSYAQYFLEKLEKILDPED---DLYERILFNFLKGIILYKEGQKESGEEKIEQAIEIFD 199 (220)
T ss_pred HHHHHHHHHHHH-HHHHHhhHHHHHHHHHHHHHHHhchhh---hHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHHHH
Confidence 333333444444 445666788999999999886323321 2236889999999998888887777777777777554
Q ss_pred c
Q 025096 93 P 93 (258)
Q Consensus 93 ~ 93 (258)
.
T Consensus 200 ~ 200 (220)
T TIGR01716 200 E 200 (220)
T ss_pred H
Confidence 3
No 107
>PRK10049 pgaA outer membrane protein PgaA; Provisional
Probab=55.98 E-value=65 Score=32.82 Aligned_cols=124 Identities=12% Similarity=0.046 Sum_probs=76.0
Q ss_pred HHHHHHHHhcCChhhHHHHHHHhhccCCCC-------CCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCcc
Q 025096 22 CQLFKIYFKLGTVHLCRSVIRSIETARIFD-------FEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNPQ 94 (258)
Q Consensus 22 n~l~kiyf~l~~~~~~~~l~~~i~~~~~p~-------~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~ 94 (258)
..++..|.+.++++.+...+..+... .|. ....|..+.....+..|.++...+++++|.+.|+.+....|.+
T Consensus 314 ~~L~~a~~~~g~~~eA~~~l~~~~~~-~P~~~~~~~~~~~~p~~~~~~a~~~~a~~l~~~g~~~eA~~~l~~al~~~P~n 392 (765)
T PRK10049 314 ADLFYSLLESENYPGALTVTAHTINN-SPPFLRLYGSPTSIPNDDWLQGQSLLSQVAKYSNDLPQAEMRARELAYNAPGN 392 (765)
T ss_pred HHHHHHHHhcccHHHHHHHHHHHhhc-CCceEeecCCCCCCCCchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCC
Confidence 34555678888888888887766543 232 1234555667778899999999999999999999999987765
Q ss_pred ChHHHHHHHHHHHHHHhhcCCCCChh-hhh----hcc--cc-ccHHHHHHHHhCCHHHHHHHHHH
Q 025096 95 SEANIRMILKYLIPVKLSIGILPKDW-LLE----KYN--LV-EYSNIVQALRRGDLRLLRHALEE 151 (258)
Q Consensus 95 ~~~~~~~IL~~LIp~~Ll~G~~P~~~-ll~----~~~--l~-~y~~L~~av~~Gdl~~f~~~l~~ 151 (258)
.. ++..+.-+-.-.|+...-. .++ ..+ .. .|.....+++.|++..-++.+++
T Consensus 393 ~~-----l~~~lA~l~~~~g~~~~A~~~l~~al~l~Pd~~~l~~~~a~~al~~~~~~~A~~~~~~ 452 (765)
T PRK10049 393 QG-----LRIDYASVLQARGWPRAAENELKKAEVLEPRNINLEVEQAWTALDLQEWRQMDVLTDD 452 (765)
T ss_pred HH-----HHHHHHHHHHhcCCHHHHHHHHHHHHhhCCCChHHHHHHHHHHHHhCCHHHHHHHHHH
Confidence 32 2222322222246532211 111 111 11 23444578888886666655554
No 108
>PRK12370 invasion protein regulator; Provisional
Probab=55.57 E-value=64 Score=31.46 Aligned_cols=63 Identities=13% Similarity=-0.025 Sum_probs=45.0
Q ss_pred HHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCccC
Q 025096 24 LFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNPQS 95 (258)
Q Consensus 24 l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~~ 95 (258)
+-.+|...++++.+...++..-.. .|+ .. ..+|+.|.+++..+++++|.+++..|+..-|...
T Consensus 344 lg~~~~~~g~~~~A~~~~~~Al~l-~P~------~~--~a~~~lg~~l~~~G~~~eAi~~~~~Al~l~P~~~ 406 (553)
T PRK12370 344 LGLINTIHSEYIVGSLLFKQANLL-SPI------SA--DIKYYYGWNLFMAGQLEEALQTINECLKLDPTRA 406 (553)
T ss_pred HHHHHHHccCHHHHHHHHHHHHHh-CCC------CH--HHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCCh
Confidence 345677788888888777443221 132 22 2457889999999999999999999999887643
No 109
>PF10516 SHNi-TPR: SHNi-TPR; InterPro: IPR019544 The tetratrico peptide repeat region (TPR) is a structural motif present in a wide range of proteins [, , ]. It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. The X-ray structure of a domain containing three TPRs from protein phosphatase 5 revealed that TPR adopts a helix-turn-helix arrangement, with adjacent TPR motifs packing in a parallel fashion, resulting in a spiral of repeating anti-parallel alpha-helices []. The two helices are denoted helix A and helix B. The packing angle between helix A and helix B is ~24 degrees within a single TPR and generates a right-handed superhelical shape. Helix A interacts with helix B and with helix A' of the next TPR. Two protein surfaces are generated: the inner concave surface is contributed to mainly by residue on helices A, and the other surface presents residues from both helices A and B. This entry represents SHNi-TPR (Sim3-Hif1-NASP interrupted TPR), a sequence that is an interrupted form of TPR repeat [].
Probab=53.13 E-value=21 Score=21.87 Aligned_cols=25 Identities=32% Similarity=0.320 Sum_probs=22.4
Q ss_pred hhhHHhhhhcChHHHHHHHHHHHHh
Q 025096 66 YTGRLEVFNENFPAADQKLSYALIN 90 (258)
Q Consensus 66 Y~G~~~~~~~~~~~A~~~L~~A~~~ 90 (258)
-+|-+.+-.++|.+|.+.|..|+..
T Consensus 6 ~Lgeisle~e~f~qA~~D~~~aL~i 30 (38)
T PF10516_consen 6 LLGEISLENENFEQAIEDYEKALEI 30 (38)
T ss_pred HHHHHHHHhccHHHHHHHHHHHHHH
Confidence 4788999999999999999999984
No 110
>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=51.87 E-value=62 Score=31.61 Aligned_cols=72 Identities=17% Similarity=0.053 Sum_probs=57.3
Q ss_pred HHHHHHHHHHHHHHHhcCChhhHHHHHH-HhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCc
Q 025096 15 VGALYLTCQLFKIYFKLGTVHLCRSVIR-SIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNP 93 (258)
Q Consensus 15 ~~~~~~~n~l~kiyf~l~~~~~~~~l~~-~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~ 93 (258)
...+.+...+...|-++|+++.+-..|. +|+.+ |. .+.+++..|+++=-.|++.+|.+.+..|=..=..
T Consensus 191 ~~~lw~~~~lAqhyd~~g~~~~Al~~Id~aI~ht--Pt--------~~ely~~KarilKh~G~~~~Aa~~~~~Ar~LD~~ 260 (517)
T PF12569_consen 191 STLLWTLYFLAQHYDYLGDYEKALEYIDKAIEHT--PT--------LVELYMTKARILKHAGDLKEAAEAMDEARELDLA 260 (517)
T ss_pred hHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhcC--CC--------cHHHHHHHHHHHHHCCCHHHHHHHHHHHHhCChh
Confidence 3456666777788999999999998885 66653 43 5778999999999999999999999999886555
Q ss_pred cCh
Q 025096 94 QSE 96 (258)
Q Consensus 94 ~~~ 96 (258)
+..
T Consensus 261 DRy 263 (517)
T PF12569_consen 261 DRY 263 (517)
T ss_pred hHH
Confidence 543
No 111
>PRK02603 photosystem I assembly protein Ycf3; Provisional
Probab=51.50 E-value=18 Score=29.26 Aligned_cols=37 Identities=16% Similarity=0.098 Sum_probs=32.1
Q ss_pred CccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcC
Q 025096 56 PKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCN 92 (258)
Q Consensus 56 ~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~ 92 (258)
+......++|..|..+...+++++|..++..|+...+
T Consensus 30 ~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~ 66 (172)
T PRK02603 30 KKAKEAFVYYRDGMSAQADGEYAEALENYEEALKLEE 66 (172)
T ss_pred cHhhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhh
Confidence 4556777889999999999999999999999998654
No 112
>PRK10370 formate-dependent nitrite reductase complex subunit NrfG; Provisional
Probab=51.39 E-value=1.1e+02 Score=25.57 Aligned_cols=31 Identities=10% Similarity=0.054 Sum_probs=16.7
Q ss_pred hhhhhhHHhhhhcChHHHHHHHHHHHHhcCc
Q 025096 63 YMYYTGRLEVFNENFPAADQKLSYALINCNP 93 (258)
Q Consensus 63 y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~ 93 (258)
-++.+|..++-.++|++|..+++.+++.-|+
T Consensus 146 al~~LA~~~~~~g~~~~Ai~~~~~aL~l~~~ 176 (198)
T PRK10370 146 ALMLLASDAFMQADYAQAIELWQKVLDLNSP 176 (198)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHHhhCCC
Confidence 4455555555555555555555555554444
No 113
>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=51.36 E-value=44 Score=29.67 Aligned_cols=69 Identities=10% Similarity=0.109 Sum_probs=47.9
Q ss_pred HHHHHHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCccC
Q 025096 20 LTCQLFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNPQS 95 (258)
Q Consensus 20 ~~n~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~~ 95 (258)
..+.-+..| +-|++..+..-+...=.. .|.-.. .-+=+||+|..++-+++|++|...|..+.+..|.+.
T Consensus 144 ~Y~~A~~~~-ksgdy~~A~~~F~~fi~~-YP~s~~-----~~nA~yWLGe~~y~qg~y~~Aa~~f~~~~k~~P~s~ 212 (262)
T COG1729 144 LYNAALDLY-KSGDYAEAEQAFQAFIKK-YPNSTY-----TPNAYYWLGESLYAQGDYEDAAYIFARVVKDYPKSP 212 (262)
T ss_pred HHHHHHHHH-HcCCHHHHHHHHHHHHHc-CCCCcc-----cchhHHHHHHHHHhcccchHHHHHHHHHHHhCCCCC
Confidence 334444444 456699999877654332 343211 223368999999999999999999999999888654
No 114
>KOG0543 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=50.88 E-value=84 Score=29.59 Aligned_cols=68 Identities=19% Similarity=0.189 Sum_probs=50.6
Q ss_pred HHHHHHHHHHHHhcCChhhHHHH-HHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCccC
Q 025096 18 LYLTCQLFKIYFKLGTVHLCRSV-IRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNPQS 95 (258)
Q Consensus 18 ~~~~n~l~kiyf~l~~~~~~~~l-~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~~ 95 (258)
.-..+.+.-.|.|++.+..|-.- -++++-. |+ -+.=+|-.|+.++..++|+.|...|+.|...-|.+.
T Consensus 257 ~~~~lNlA~c~lKl~~~~~Ai~~c~kvLe~~--------~~--N~KALyRrG~A~l~~~e~~~A~~df~ka~k~~P~Nk 325 (397)
T KOG0543|consen 257 LACHLNLAACYLKLKEYKEAIESCNKVLELD--------PN--NVKALYRRGQALLALGEYDLARDDFQKALKLEPSNK 325 (397)
T ss_pred HHHhhHHHHHHHhhhhHHHHHHHHHHHHhcC--------CC--chhHHHHHHHHHHhhccHHHHHHHHHHHHHhCCCcH
Confidence 44556678899999999866532 3444431 11 233468899999999999999999999999988664
No 115
>CHL00033 ycf3 photosystem I assembly protein Ycf3
Probab=50.84 E-value=49 Score=26.41 Aligned_cols=68 Identities=9% Similarity=-0.097 Sum_probs=40.0
Q ss_pred HHHHHHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHH
Q 025096 20 LTCQLFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALI 89 (258)
Q Consensus 20 ~~n~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~ 89 (258)
....+..+|.+.|+++.+...+...-.. .|... .........++..|+.+...++++.|...+.+|+.
T Consensus 74 ~~~~lg~~~~~~g~~~eA~~~~~~Al~~-~~~~~-~~~~~la~i~~~~~~~~~~~g~~~~A~~~~~~a~~ 141 (168)
T CHL00033 74 ILYNIGLIHTSNGEHTKALEYYFQALER-NPFLP-QALNNMAVICHYRGEQAIEQGDSEIAEAWFDQAAE 141 (168)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHHHh-CcCcH-HHHHHHHHHHHHhhHHHHHcccHHHHHHHHHHHHH
Confidence 4455677788888888888776443221 12211 11223334445566666688888877777776665
No 116
>KOG2002 consensus TPR-containing nuclear phosphoprotein that regulates K(+) uptake [Inorganic ion transport and metabolism]
Probab=50.80 E-value=39 Score=35.27 Aligned_cols=68 Identities=15% Similarity=0.011 Sum_probs=50.0
Q ss_pred HHHHHHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCc
Q 025096 20 LTCQLFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNP 93 (258)
Q Consensus 20 ~~n~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~ 93 (258)
+.|.|...||--+++..|..+--+....+ ...+....-+|.+||.|=.+|||++|...+.+|..--+.
T Consensus 272 ~l~~LAn~fyfK~dy~~v~~la~~ai~~t------~~~~~~aes~Y~~gRs~Ha~Gd~ekA~~yY~~s~k~~~d 339 (1018)
T KOG2002|consen 272 ALNHLANHFYFKKDYERVWHLAEHAIKNT------ENKSIKAESFYQLGRSYHAQGDFEKAFKYYMESLKADND 339 (1018)
T ss_pred HHHHHHHHHhhcccHHHHHHHHHHHHHhh------hhhHHHHHHHHHHHHHHHhhccHHHHHHHHHHHHccCCC
Confidence 45677777888888888887764433221 234455566799999999999999999999999984443
No 117
>PRK09954 putative kinase; Provisional
Probab=49.57 E-value=63 Score=29.45 Aligned_cols=46 Identities=22% Similarity=0.368 Sum_probs=37.2
Q ss_pred CccccHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCcceE--Ee-ecCceEEEE
Q 025096 192 AHQMKLDVIVKALKWLEMDMDVDEVECIVAILIHKNLVKG--YF-AHKSKVVVL 242 (258)
Q Consensus 192 ~~~i~l~~i~~al~~~~~~~~~~evE~ila~LI~~G~IkG--yI-~~~~~~lVl 242 (258)
..+++.++++..+. ++...|...+.+|..+|+|+| |+ ++...++|+
T Consensus 15 ~~~~s~~~la~~l~-----~s~~~v~~~i~~L~~~g~i~~~~~~l~~~~~v~vi 63 (362)
T PRK09954 15 NPLIQQNEIADILQ-----ISRSRVAAHIMDLMRKGRIKGKGYILTEQEYCVVV 63 (362)
T ss_pred CCCCCHHHHHHHHC-----CCHHHHHHHHHHHHHCCCcCCcEEEEcCCccEEEE
Confidence 35899999999997 789999999999999999966 43 344555555
No 118
>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=49.47 E-value=42 Score=32.23 Aligned_cols=50 Identities=16% Similarity=0.372 Sum_probs=40.9
Q ss_pred cCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHH
Q 025096 31 LGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALI 89 (258)
Q Consensus 31 l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~ 89 (258)
-.+.+.|..++.....+ ||+ -+-|.++.||++..+++.++|-+.|+.|..
T Consensus 246 ~~~~~~a~~lL~~~~~~-------yP~--s~lfl~~~gR~~~~~g~~~~Ai~~~~~a~~ 295 (468)
T PF10300_consen 246 DVPLEEAEELLEEMLKR-------YPN--SALFLFFEGRLERLKGNLEEAIESFERAIE 295 (468)
T ss_pred CCCHHHHHHHHHHHHHh-------CCC--cHHHHHHHHHHHHHhcCHHHHHHHHHHhcc
Confidence 45778888888776653 453 455899999999999999999999999995
No 119
>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=49.32 E-value=31 Score=32.12 Aligned_cols=70 Identities=13% Similarity=0.041 Sum_probs=47.5
Q ss_pred HHHHHHHhcCChhhHHHHHHHhhccCCCC--------------C----------------CCCCccchhhhhhhhhHHhh
Q 025096 23 QLFKIYFKLGTVHLCRSVIRSIETARIFD--------------F----------------EEFPKRDKVTYMYYTGRLEV 72 (258)
Q Consensus 23 ~l~kiyf~l~~~~~~~~l~~~i~~~~~p~--------------~----------------~~~~~~~~v~y~YY~G~~~~ 72 (258)
.+...+.+.|+.+.+.+++...-.. .|+ + ...|....+.+....|++++
T Consensus 268 ~~a~~l~~~g~~~~A~~~l~~~l~~-~pd~~~~~~~~l~~~~~l~~~~~~~~~~~~e~~lk~~p~~~~~~ll~sLg~l~~ 346 (409)
T TIGR00540 268 ALAEHLIDCDDHDSAQEIIFDGLKK-LGDDRAISLPLCLPIPRLKPEDNEKLEKLIEKQAKNVDDKPKCCINRALGQLLM 346 (409)
T ss_pred HHHHHHHHCCChHHHHHHHHHHHhh-CCCcccchhHHHHHhhhcCCCChHHHHHHHHHHHHhCCCChhHHHHHHHHHHHH
Confidence 3555778888888888777443321 111 0 11344444578888999999
Q ss_pred hhcChHHHHHHHH--HHHHhcCc
Q 025096 73 FNENFPAADQKLS--YALINCNP 93 (258)
Q Consensus 73 ~~~~~~~A~~~L~--~A~~~c~~ 93 (258)
..++|.+|.++|+ .|+...|.
T Consensus 347 ~~~~~~~A~~~le~a~a~~~~p~ 369 (409)
T TIGR00540 347 KHGEFIEAADAFKNVAACKEQLD 369 (409)
T ss_pred HcccHHHHHHHHHHhHHhhcCCC
Confidence 9999999999999 67776553
No 120
>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=49.18 E-value=44 Score=21.36 Aligned_cols=33 Identities=21% Similarity=0.364 Sum_probs=28.6
Q ss_pred ccccHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCcce
Q 025096 193 HQMKLDVIVKALKWLEMDMDVDEVECIVAILIHKNLVK 230 (258)
Q Consensus 193 ~~i~l~~i~~al~~~~~~~~~~evE~ila~LI~~G~Ik 230 (258)
..+++++|.+.+. ++...+.-++..|...|++.
T Consensus 17 ~~~t~~eia~~~g-----l~~stv~r~L~tL~~~g~v~ 49 (52)
T PF09339_consen 17 GPLTLSEIARALG-----LPKSTVHRLLQTLVEEGYVE 49 (52)
T ss_dssp SCEEHHHHHHHHT-----S-HHHHHHHHHHHHHTTSEE
T ss_pred CCCCHHHHHHHHC-----cCHHHHHHHHHHHHHCcCee
Confidence 4489999999997 68999999999999999985
No 121
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=49.15 E-value=60 Score=23.33 Aligned_cols=36 Identities=11% Similarity=0.056 Sum_probs=31.4
Q ss_pred ccccHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCcceEEe
Q 025096 193 HQMKLDVIVKALKWLEMDMDVDEVECIVAILIHKNLVKGYF 233 (258)
Q Consensus 193 ~~i~l~~i~~al~~~~~~~~~~evE~ila~LI~~G~IkGyI 233 (258)
.+.+.+++...++ .+.+-||.+|..++..|.|.---
T Consensus 15 gr~s~~~Ls~~~~-----~p~~~VeaMLe~l~~kGkverv~ 50 (78)
T PRK15431 15 GRMEAAQISQTLN-----TPQPMINAMLQQLESMGKAVRIQ 50 (78)
T ss_pred CcccHHHHHHHHC-----cCHHHHHHHHHHHHHCCCeEeec
Confidence 5788999999987 78999999999999999986543
No 122
>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=48.88 E-value=47 Score=21.61 Aligned_cols=38 Identities=21% Similarity=0.181 Sum_probs=31.5
Q ss_pred cccHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCcceEEeecC
Q 025096 194 QMKLDVIVKALKWLEMDMDVDEVECIVAILIHKNLVKGYFAHK 236 (258)
Q Consensus 194 ~i~l~~i~~al~~~~~~~~~~evE~ila~LI~~G~IkGyI~~~ 236 (258)
.++..+|.+.+. ++..-+-.++..|+.+|+|.=.-+..
T Consensus 21 ~~t~~~la~~l~-----~~~~~vs~~v~~L~~~Glv~r~~~~~ 58 (62)
T PF12802_consen 21 ELTQSELAERLG-----ISKSTVSRIVKRLEKKGLVERERDPG 58 (62)
T ss_dssp GEEHHHHHHHHT-----S-HHHHHHHHHHHHHTTSEEEEE-SS
T ss_pred CcCHHHHHHHHC-----cCHHHHHHHHHHHHHCCCEEEeCCCC
Confidence 489999999997 68999999999999999997665544
No 123
>KOG1156 consensus N-terminal acetyltransferase [Chromatin structure and dynamics]
Probab=48.63 E-value=58 Score=32.57 Aligned_cols=38 Identities=11% Similarity=0.111 Sum_probs=34.7
Q ss_pred CccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCc
Q 025096 56 PKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNP 93 (258)
Q Consensus 56 ~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~ 93 (258)
|....+.=.||+..-+-..++++.|.+.++.|+.|||.
T Consensus 366 ~PttllWt~y~laqh~D~~g~~~~A~~yId~AIdHTPT 403 (700)
T KOG1156|consen 366 PPTTLLWTLYFLAQHYDKLGDYEVALEYIDLAIDHTPT 403 (700)
T ss_pred CchHHHHHHHHHHHHHHHcccHHHHHHHHHHHhccCch
Confidence 56777888899999999999999999999999999995
No 124
>COG3071 HemY Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]
Probab=48.53 E-value=20 Score=33.52 Aligned_cols=76 Identities=18% Similarity=0.225 Sum_probs=50.9
Q ss_pred HHHHHHHHHHHHhcCChhhHHHHHHH-hhcc-C---------CCC-------------CCCCCccchhhhhhhhhHHhhh
Q 025096 18 LYLTCQLFKIYFKLGTVHLCRSVIRS-IETA-R---------IFD-------------FEEFPKRDKVTYMYYTGRLEVF 73 (258)
Q Consensus 18 ~~~~n~l~kiyf~l~~~~~~~~l~~~-i~~~-~---------~p~-------------~~~~~~~~~v~y~YY~G~~~~~ 73 (258)
--+.....--+.++|..+-+..+++. ++.. + ++. +...|... .-++++|++++-
T Consensus 263 p~l~~~~a~~li~l~~~~~A~~~i~~~Lk~~~D~~L~~~~~~l~~~d~~~l~k~~e~~l~~h~~~p--~L~~tLG~L~~k 340 (400)
T COG3071 263 PELVVAYAERLIRLGDHDEAQEIIEDALKRQWDPRLCRLIPRLRPGDPEPLIKAAEKWLKQHPEDP--LLLSTLGRLALK 340 (400)
T ss_pred hhHHHHHHHHHHHcCChHHHHHHHHHHHHhccChhHHHHHhhcCCCCchHHHHHHHHHHHhCCCCh--hHHHHHHHHHHH
Confidence 34455556667788888888877643 2221 0 000 11133333 467899999999
Q ss_pred hcChHHHHHHHHHHHHhcCccC
Q 025096 74 NENFPAADQKLSYALINCNPQS 95 (258)
Q Consensus 74 ~~~~~~A~~~L~~A~~~c~~~~ 95 (258)
++.|.+|.++|..|++.-|...
T Consensus 341 ~~~w~kA~~~leaAl~~~~s~~ 362 (400)
T COG3071 341 NKLWGKASEALEAALKLRPSAS 362 (400)
T ss_pred hhHHHHHHHHHHHHHhcCCChh
Confidence 9999999999999999766544
No 125
>PHA02992 hypothetical protein; Provisional
Probab=47.92 E-value=1.5e+02 Score=30.03 Aligned_cols=111 Identities=11% Similarity=0.215 Sum_probs=73.7
Q ss_pred cHHHHH-HHHhCCHHHHHHHHHHcHHHHHHhcHHHHHHhhHHHHH------HHHH-------------------------
Q 025096 130 YSNIVQ-ALRRGDLRLLRHALEEHEDQFLRSGVYLVLEKLELQVY------QRLF------------------------- 177 (258)
Q Consensus 130 y~~L~~-av~~Gdl~~f~~~l~~~~~~f~~~glylll~~l~~~v~------r~L~------------------------- 177 (258)
+.+|+. -.+.-|+..|.+.++-|..++++.+.+.++.|+-...- |-|.
T Consensus 70 f~DLi~~i~~~~nve~ya~HI~fhk~~ilq~~~~~li~kCi~yM~i~DDDiR~L~~RF~~~~vd~iL~~iN~~Si~~isy 149 (728)
T PHA02992 70 FIDLISVITKQKNVELYASHINFHKNEILQKCDKSLIAKCIPYMTISDDDIRCLRSRFYNNSVDYILSFINKESIYRMSY 149 (728)
T ss_pred HHHHHHHHHHhccHHHHHHHHHHhHHHHHHhcCHHHHHHHhhhcccccchHHHHHHHhcchhHHHHHHhcchhhhhhhhh
Confidence 677765 45789999999999999999999999888876544322 1111
Q ss_pred --------------------------------HHHHHHhhcCCC---CCCccccHHHHHHHHHhccCC------------
Q 025096 178 --------------------------------KKIYIIQKQKDP---SKAHQMKLDVIVKALKWLEMD------------ 210 (258)
Q Consensus 178 --------------------------------kkv~~~~~~~~~---~~~~~i~l~~i~~al~~~~~~------------ 210 (258)
+..+-.+ +..| |-..-++.+++.++|+..+.+
T Consensus 150 ~FSd~~~E~i~~~d~~m~~~lY~hQ~~s~~FL~~Mlyk~-GI~P~N~Gi~~~~s~~~iieiL~~~~~~~D~~~fLd~L~~ 228 (728)
T PHA02992 150 QFSESLTEKIFIQDYSMYDPLYEHQSFTSDFLTDMLYKY-GIVPNNDGILDEISIELIIEILQSIKRPRDAIRFLDMLPK 228 (728)
T ss_pred hccHHHHHHHHHhchhhhhHhhhcCcCCHHHHHHHHHHc-CCCCCCccccccCCHHHHHHHHHhcCCchHHHHHHHhcCH
Confidence 1111111 1222 223356777887877654311
Q ss_pred --CCHHHHHHHHHHHHHcCcceEEeecCceEEE
Q 025096 211 --MDVDEVECIVAILIHKNLVKGYFAHKSKVVV 241 (258)
Q Consensus 211 --~~~~evE~ila~LI~~G~IkGyI~~~~~~lV 241 (258)
++.|++-..+.+.|..|.|..|+-..+..++
T Consensus 229 ~~L~~d~~K~~ii~~I~~G~vd~y~~YA~eYL~ 261 (728)
T PHA02992 229 EQLTDDKLKNYIINKIKNGKIDQYIPYAEEFLV 261 (728)
T ss_pred HhcCchHHHHHHHHHHHcCcchHHHHHHHHHHH
Confidence 5778999999999999999888766555543
No 126
>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=47.89 E-value=50 Score=31.10 Aligned_cols=64 Identities=11% Similarity=0.000 Sum_probs=41.2
Q ss_pred HHHHHHHHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCcc
Q 025096 18 LYLTCQLFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNPQ 94 (258)
Q Consensus 18 ~~~~n~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~ 94 (258)
.-+.+...+.+.+.+++++|-.+.+..-.. .|+ .....|+++++|...++|++|...| ..||-.
T Consensus 234 ~~LL~~Qa~fLl~k~~~~lAL~iAk~av~l-sP~--------~f~~W~~La~~Yi~~~d~e~ALlaL----Ns~Pm~ 297 (395)
T PF09295_consen 234 SELLNLQAEFLLSKKKYELALEIAKKAVEL-SPS--------EFETWYQLAECYIQLGDFENALLAL----NSCPML 297 (395)
T ss_pred HHHHHHHHHHHHhcCCHHHHHHHHHHHHHh-Cch--------hHHHHHHHHHHHHhcCCHHHHHHHH----hcCcCC
Confidence 445556677777777777777776443321 132 2335577888888888888888644 456644
No 127
>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional
Probab=47.73 E-value=1.3e+02 Score=27.71 Aligned_cols=63 Identities=11% Similarity=-0.075 Sum_probs=47.8
Q ss_pred HHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCccC
Q 025096 24 LFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNPQS 95 (258)
Q Consensus 24 l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~~ 95 (258)
...-+|..++++.|-..++..-.. -|. ...+++..|.+++..+++++|...+..|+...|...
T Consensus 8 ~a~~a~~~~~~~~Ai~~~~~Al~~-~P~--------~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~P~~~ 70 (356)
T PLN03088 8 KAKEAFVDDDFALAVDLYTQAIDL-DPN--------NAELYADRAQANIKLGNFTEAVADANKAIELDPSLA 70 (356)
T ss_pred HHHHHHHcCCHHHHHHHHHHHHHh-CCC--------CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCCH
Confidence 346678889999998887543321 132 234678899999999999999999999999887543
No 128
>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=46.72 E-value=1.6e+02 Score=26.10 Aligned_cols=65 Identities=11% Similarity=-0.082 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcC
Q 025096 19 YLTCQLFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCN 92 (258)
Q Consensus 19 ~~~n~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~ 92 (258)
+....+..+|...|+++.+...++..-.. .|. . .......|.++...+++++|..++..+....+
T Consensus 115 ~~~~~~a~~~~~~G~~~~A~~~~~~al~~-~p~------~--~~~~~~la~i~~~~g~~~eA~~~l~~~l~~~~ 179 (355)
T cd05804 115 YLLGMLAFGLEEAGQYDRAEEAARRALEL-NPD------D--AWAVHAVAHVLEMQGRFKEGIAFMESWRDTWD 179 (355)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHHhh-CCC------C--cHHHHHHHHHHHHcCCHHHHHHHHHhhhhccC
Confidence 33344445555666666555555332211 121 1 22334455555555666666666666555443
No 129
>PRK10049 pgaA outer membrane protein PgaA; Provisional
Probab=46.37 E-value=84 Score=32.05 Aligned_cols=63 Identities=10% Similarity=-0.124 Sum_probs=37.0
Q ss_pred HHHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCcc
Q 025096 23 QLFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNPQ 94 (258)
Q Consensus 23 ~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~ 94 (258)
.+..++...|+++.+...+..+-.. .|. . ...++..|.++.-.+++.+|.+.|..|+..-|.+
T Consensus 364 ~~a~~l~~~g~~~eA~~~l~~al~~-~P~------n--~~l~~~lA~l~~~~g~~~~A~~~l~~al~l~Pd~ 426 (765)
T PRK10049 364 LLSQVAKYSNDLPQAEMRARELAYN-APG------N--QGLRIDYASVLQARGWPRAAENELKKAEVLEPRN 426 (765)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHh-CCC------C--HHHHHHHHHHHHhcCCHHHHHHHHHHHHhhCCCC
Confidence 4445666777777777776554332 222 1 2345566666666666666666666666655543
No 130
>KOG3054 consensus Uncharacterized conserved protein [Function unknown]
Probab=46.32 E-value=39 Score=29.68 Aligned_cols=47 Identities=13% Similarity=0.253 Sum_probs=38.5
Q ss_pred ccccHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCcceEEeecCceEEEEec
Q 025096 193 HQMKLDVIVKALKWLEMDMDVDEVECIVAILIHKNLVKGYFAHKSKVVVLSK 244 (258)
Q Consensus 193 ~~i~l~~i~~al~~~~~~~~~~evE~ila~LI~~G~IkGyI~~~~~~lVlsk 244 (258)
.-+++.+++..+.+ -..++-.-+.+++.+|+|.|.|+.-.+++-+|.
T Consensus 213 KvV~ledLas~f~L-----rtqd~inriq~~l~eg~ltGVmDDRGKfIYIS~ 259 (299)
T KOG3054|consen 213 KVVPLEDLASEFGL-----RTQDSINRIQELLAEGLLTGVMDDRGKFIYISM 259 (299)
T ss_pred CeeeHHHHHHHhCc-----cHHHHHHHHHHHHHhhhheeeecCCCceEEecH
Confidence 45899999998874 445566688999999999999999888887774
No 131
>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional
Probab=45.23 E-value=77 Score=30.40 Aligned_cols=65 Identities=18% Similarity=0.119 Sum_probs=48.4
Q ss_pred HHHHHHHHHHHHhcCChhhHHHHHHH-hhccCCCCCCCCCccchh-hhhhhhhHHhhhhcChHHHHHHHHHHHHh
Q 025096 18 LYLTCQLFKIYFKLGTVHLCRSVIRS-IETARIFDFEEFPKRDKV-TYMYYTGRLEVFNENFPAADQKLSYALIN 90 (258)
Q Consensus 18 ~~~~n~l~kiyf~l~~~~~~~~l~~~-i~~~~~p~~~~~~~~~~v-~y~YY~G~~~~~~~~~~~A~~~L~~A~~~ 90 (258)
.-..+.+--.|+++++++.+-..++. ++-. |+ .... .-+|..|-.|...+++++|.++|..|+..
T Consensus 75 a~a~~NLG~AL~~lGryeEAIa~f~rALeL~--Pd------~aeA~~A~yNLAcaya~LGr~dEAla~LrrALel 141 (453)
T PLN03098 75 AEDAVNLGLSLFSKGRVKDALAQFETALELN--PN------PDEAQAAYYNKACCHAYREEGKKAADCLRTALRD 141 (453)
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC--CC------chHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence 33445556688999999999988844 5532 33 2111 23588999999999999999999999996
No 132
>PRK15174 Vi polysaccharide export protein VexE; Provisional
Probab=44.88 E-value=1.2e+02 Score=30.35 Aligned_cols=33 Identities=6% Similarity=0.008 Sum_probs=19.8
Q ss_pred hhhhhhHHhhhhcChHHHHHHHHHHHHhcCccC
Q 025096 63 YMYYTGRLEVFNENFPAADQKLSYALINCNPQS 95 (258)
Q Consensus 63 y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~~ 95 (258)
+.++.|..+...+++++|...|..|+...|...
T Consensus 354 ~~~~~a~al~~~G~~deA~~~l~~al~~~P~~~ 386 (656)
T PRK15174 354 WNRYAAAALLQAGKTSEAESVFEHYIQARASHL 386 (656)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHHHHhChhhc
Confidence 344456666666666666666666666655543
No 133
>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A.
Probab=44.60 E-value=28 Score=24.30 Aligned_cols=49 Identities=10% Similarity=0.047 Sum_probs=33.6
Q ss_pred cCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHH
Q 025096 31 LGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSY 86 (258)
Q Consensus 31 l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~ 86 (258)
.++++.+-.++..+-.. -| .+..-.|.|..|.+++..++|++|.+.+..
T Consensus 2 ~~~y~~Ai~~~~k~~~~-~~------~~~~~~~~~~la~~~~~~~~y~~A~~~~~~ 50 (84)
T PF12895_consen 2 QGNYENAIKYYEKLLEL-DP------TNPNSAYLYNLAQCYFQQGKYEEAIELLQK 50 (84)
T ss_dssp TT-HHHHHHHHHHHHHH-HC------GTHHHHHHHHHHHHHHHTTHHHHHHHHHHC
T ss_pred CccHHHHHHHHHHHHHH-CC------CChhHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence 35666677666544332 12 111445778899999999999999999887
No 134
>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A.
Probab=44.41 E-value=65 Score=26.85 Aligned_cols=65 Identities=5% Similarity=-0.089 Sum_probs=47.9
Q ss_pred HHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCccC
Q 025096 25 FKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNPQS 95 (258)
Q Consensus 25 ~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~~ 95 (258)
-..++..|+++.+...++.+... .|. .+-++.. .+..|..+.-.++|.+|...++.-++..|.+.
T Consensus 12 a~~~~~~g~y~~Ai~~f~~l~~~-~P~---s~~a~~A--~l~la~a~y~~~~y~~A~~~~~~fi~~yP~~~ 76 (203)
T PF13525_consen 12 ALEALQQGDYEEAIKLFEKLIDR-YPN---SPYAPQA--QLMLAYAYYKQGDYEEAIAAYERFIKLYPNSP 76 (203)
T ss_dssp HHHHHHCT-HHHHHHHHHHHHHH--TT---STTHHHH--HHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-T
T ss_pred HHHHHHCCCHHHHHHHHHHHHHH-CCC---ChHHHHH--HHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCc
Confidence 35678999999999999998864 443 2334444 36889999999999999999999999988764
No 135
>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional
Probab=44.21 E-value=1e+02 Score=25.12 Aligned_cols=31 Identities=13% Similarity=-0.020 Sum_probs=16.2
Q ss_pred hhhhhhHHhhhhcChHHHHHHHHHHHHhcCc
Q 025096 63 YMYYTGRLEVFNENFPAADQKLSYALINCNP 93 (258)
Q Consensus 63 y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~ 93 (258)
|.|=+|.++=..++|++|-..+..|+..-|.
T Consensus 71 y~~gLG~~~Q~~g~~~~AI~aY~~A~~L~~d 101 (157)
T PRK15363 71 YWFRLGECCQAQKHWGEAIYAYGRAAQIKID 101 (157)
T ss_pred HHHHHHHHHHHHhhHHHHHHHHHHHHhcCCC
Confidence 3344444444555666666665555554443
No 136
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=44.14 E-value=52 Score=19.97 Aligned_cols=32 Identities=16% Similarity=0.214 Sum_probs=28.0
Q ss_pred cccHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCcce
Q 025096 194 QMKLDVIVKALKWLEMDMDVDEVECIVAILIHKNLVK 230 (258)
Q Consensus 194 ~i~l~~i~~al~~~~~~~~~~evE~ila~LI~~G~Ik 230 (258)
.++..+++..+. ++...+..++..|..+|+|.
T Consensus 8 ~~s~~~la~~l~-----~s~~tv~~~l~~L~~~g~l~ 39 (48)
T smart00419 8 PLTRQEIAELLG-----LTRETVSRTLKRLEKEGLIS 39 (48)
T ss_pred ccCHHHHHHHHC-----CCHHHHHHHHHHHHHCCCEE
Confidence 467788888887 68999999999999999996
No 137
>PRK10747 putative protoheme IX biogenesis protein; Provisional
Probab=44.11 E-value=55 Score=30.40 Aligned_cols=72 Identities=13% Similarity=0.102 Sum_probs=51.4
Q ss_pred HHHHHHHHHHhcCChhhHHHHHHHhhccCCCC---------C----------------CCCCccchhhhhhhhhHHhhhh
Q 025096 20 LTCQLFKIYFKLGTVHLCRSVIRSIETARIFD---------F----------------EEFPKRDKVTYMYYTGRLEVFN 74 (258)
Q Consensus 20 ~~n~l~kiyf~l~~~~~~~~l~~~i~~~~~p~---------~----------------~~~~~~~~v~y~YY~G~~~~~~ 74 (258)
+.....+.+...|+.+.+..++...-.. -|+ + ...| +....++..|++++..
T Consensus 265 ~~~~~A~~l~~~g~~~~A~~~L~~~l~~-~~~~~l~~l~~~l~~~~~~~al~~~e~~lk~~P--~~~~l~l~lgrl~~~~ 341 (398)
T PRK10747 265 LQVAMAEHLIECDDHDTAQQIILDGLKR-QYDERLVLLIPRLKTNNPEQLEKVLRQQIKQHG--DTPLLWSTLGQLLMKH 341 (398)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHHHhc-CCCHHHHHHHhhccCCChHHHHHHHHHHHhhCC--CCHHHHHHHHHHHHHC
Confidence 4456778888889998888887443222 111 0 0122 2345788899999999
Q ss_pred cChHHHHHHHHHHHHhcCcc
Q 025096 75 ENFPAADQKLSYALINCNPQ 94 (258)
Q Consensus 75 ~~~~~A~~~L~~A~~~c~~~ 94 (258)
++|.+|.++|+.++..-|.+
T Consensus 342 ~~~~~A~~~le~al~~~P~~ 361 (398)
T PRK10747 342 GEWQEASLAFRAALKQRPDA 361 (398)
T ss_pred CCHHHHHHHHHHHHhcCCCH
Confidence 99999999999999986644
No 138
>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=44.08 E-value=64 Score=22.79 Aligned_cols=44 Identities=14% Similarity=0.120 Sum_probs=34.5
Q ss_pred ccHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCcceEEeecCceEEEEec
Q 025096 195 MKLDVIVKALKWLEMDMDVDEVECIVAILIHKNLVKGYFAHKSKVVVLSK 244 (258)
Q Consensus 195 i~l~~i~~al~~~~~~~~~~evE~ila~LI~~G~IkGyI~~~~~~lVlsk 244 (258)
++.++|++.+. ++...++.++..|...|+|+..=-. ++-..+++
T Consensus 26 ~s~~eiA~~~~-----i~~~~l~kil~~L~~~Gli~s~~G~-~GGy~L~~ 69 (83)
T PF02082_consen 26 VSSKEIAERLG-----ISPSYLRKILQKLKKAGLIESSRGR-GGGYRLAR 69 (83)
T ss_dssp BEHHHHHHHHT-----S-HHHHHHHHHHHHHTTSEEEETST-TSEEEESS
T ss_pred CCHHHHHHHHC-----cCHHHHHHHHHHHhhCCeeEecCCC-CCceeecC
Confidence 99999999987 7999999999999999999765322 24445555
No 139
>PF12854 PPR_1: PPR repeat
Probab=43.75 E-value=47 Score=19.29 Aligned_cols=26 Identities=19% Similarity=0.181 Sum_probs=23.0
Q ss_pred HHHHHHHHHHHhcCChhhHHHHHHHh
Q 025096 19 YLTCQLFKIYFKLGTVHLCRSVIRSI 44 (258)
Q Consensus 19 ~~~n~l~kiyf~l~~~~~~~~l~~~i 44 (258)
+..|.++.-|.+.|+.+.|..+++.+
T Consensus 8 ~ty~~lI~~~Ck~G~~~~A~~l~~~M 33 (34)
T PF12854_consen 8 VTYNTLIDGYCKAGRVDEAFELFDEM 33 (34)
T ss_pred hHHHHHHHHHHHCCCHHHHHHHHHhC
Confidence 56789999999999999999999764
No 140
>PRK11447 cellulose synthase subunit BcsC; Provisional
Probab=43.56 E-value=1.3e+02 Score=32.25 Aligned_cols=69 Identities=12% Similarity=0.054 Sum_probs=52.1
Q ss_pred HHHHHHHHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCccC
Q 025096 18 LYLTCQLFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNPQS 95 (258)
Q Consensus 18 ~~~~n~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~~ 95 (258)
+......-..+++.++++.+...++..-.. -|. . ..-++.+|.++...+++++|.+++.+|+..-|...
T Consensus 351 ~~~~~~~g~~~~~~g~~~eA~~~~~~Al~~-~P~------~--~~a~~~Lg~~~~~~g~~~eA~~~y~~aL~~~p~~~ 419 (1157)
T PRK11447 351 YWLLIQQGDAALKANNLAQAERLYQQARQV-DNT------D--SYAVLGLGDVAMARKDYAAAERYYQQALRMDPGNT 419 (1157)
T ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHHHHh-CCC------C--HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCH
Confidence 445556677899999999999988654432 132 1 22356789999999999999999999999877543
No 141
>PHA02608 67 prohead core protein; Provisional
Probab=43.24 E-value=1.2e+02 Score=21.69 Aligned_cols=20 Identities=20% Similarity=0.539 Sum_probs=15.5
Q ss_pred HHHHHHHHhCCHHHHHHHHH
Q 025096 131 SNIVQALRRGDLRLLRHALE 150 (258)
Q Consensus 131 ~~L~~av~~Gdl~~f~~~l~ 150 (258)
..|+.||++||+-.-.+...
T Consensus 2 e~lIeAIKS~DLV~akK~F~ 21 (80)
T PHA02608 2 EDLIEAIKSGDLVEAKKEFA 21 (80)
T ss_pred hHHHHHHhcCcHHHHHHHHH
Confidence 47899999999976555544
No 142
>TIGR00985 3a0801s04tom mitochondrial import receptor subunit translocase of outer membrane 20 kDa subunit.
Probab=43.14 E-value=55 Score=26.49 Aligned_cols=28 Identities=14% Similarity=0.012 Sum_probs=23.8
Q ss_pred hhHHhhhhc-ChHHHHHHHHHHHHhcCcc
Q 025096 67 TGRLEVFNE-NFPAADQKLSYALINCNPQ 94 (258)
Q Consensus 67 ~G~~~~~~~-~~~~A~~~L~~A~~~c~~~ 94 (258)
.|.-.+.++ ++.+|-.||..|+..||..
T Consensus 96 ~GE~L~~~g~~~~ega~hf~nAl~Vc~qP 124 (148)
T TIGR00985 96 LGEELMAQGTNVDEGAVHFYNALKVYPQP 124 (148)
T ss_pred HHHHHHhCCCchHHHHHHHHHHHHhCCCH
Confidence 566666778 9999999999999999964
No 143
>KOG1126 consensus DNA-binding cell division cycle control protein [Cell cycle control, cell division, chromosome partitioning]
Probab=42.11 E-value=72 Score=31.82 Aligned_cols=26 Identities=19% Similarity=0.165 Sum_probs=14.0
Q ss_pred hhhhHHhhhhcChHHHHHHHHHHHHh
Q 025096 65 YYTGRLEVFNENFPAADQKLSYALIN 90 (258)
Q Consensus 65 YY~G~~~~~~~~~~~A~~~L~~A~~~ 90 (258)
|=+|.+|+-+++++.|+.+|+.|+..
T Consensus 493 YGlG~vy~Kqek~e~Ae~~fqkA~~I 518 (638)
T KOG1126|consen 493 YGLGTVYLKQEKLEFAEFHFQKAVEI 518 (638)
T ss_pred HhhhhheeccchhhHHHHHHHhhhcC
Confidence 33555555555555555555555553
No 144
>PF07729 FCD: FCD domain; InterPro: IPR011711 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector binding or oligomerisation domain at the C terminus. The winged-helix DNA-binding domain is well conserved in structure for the whole of the GntR family (IPR000524 from INTERPRO), and is similar in structure to other transcriptional regulator families. The C-terminal effector-binding and oligomerisation domains are more variable and are consequently used to define the subfamilies. Based on the sequence and structure of the C-terminal domains, the GtnR family can be divided into four major groups, as represented by FadR (IPR008920 from INTERPRO), HutC, MocR and YtrA, as well as some minor groups such as those represented by AraR and PlmA []. This entry represents the C-terminal ligand binding domain of many members of the GntR family. This domain probably binds to a range of effector molecules that regulate the transcription of genes through the action of the N-terminal DNA-binding domain. This domain is found in P45427 from SWISSPROT and P31460 from SWISSPROT that are regulators of sugar biosynthesis operons.; PDB: 3SXK_A 3SXY_A 3SXM_B 3SXZ_A 3FMS_A 2DI3_B 2HS5_A 3IHU_B 3C7J_A.
Probab=41.81 E-value=1.3e+02 Score=21.64 Aligned_cols=26 Identities=42% Similarity=0.617 Sum_probs=22.1
Q ss_pred ccccHHHHHHHHhCCHHHHHHHHHHc
Q 025096 127 LVEYSNIVQALRRGDLRLLRHALEEH 152 (258)
Q Consensus 127 l~~y~~L~~av~~Gdl~~f~~~l~~~ 152 (258)
...+..+++|+++||...-.+++..|
T Consensus 97 ~~~h~~i~~ai~~~d~~~a~~~~~~h 122 (125)
T PF07729_consen 97 LEEHREIIDAIRAGDPEAAREALRQH 122 (125)
T ss_dssp HHHHHHHHHHHHTT-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence 44689999999999999999999876
No 145
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=41.55 E-value=48 Score=22.70 Aligned_cols=33 Identities=21% Similarity=0.114 Sum_probs=29.4
Q ss_pred cccHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCcceE
Q 025096 194 QMKLDVIVKALKWLEMDMDVDEVECIVAILIHKNLVKG 231 (258)
Q Consensus 194 ~i~l~~i~~al~~~~~~~~~~evE~ila~LI~~G~IkG 231 (258)
.++..+|+..+. ++..+|.-+|..|..+|+|.-
T Consensus 22 ~~ta~eLa~~lg-----l~~~~v~r~L~~L~~~G~V~~ 54 (68)
T smart00550 22 TSTALQLAKNLG-----LPKKEVNRVLYSLEKKGKVCK 54 (68)
T ss_pred CcCHHHHHHHHC-----CCHHHHHHHHHHHHHCCCEEe
Confidence 389999999997 688899999999999999853
No 146
>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=41.53 E-value=65 Score=24.15 Aligned_cols=49 Identities=16% Similarity=0.279 Sum_probs=39.6
Q ss_pred HHHHHHHHHHHHHhhcCCCCCCccccHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCcc
Q 025096 171 QVYQRLFKKIYIIQKQKDPSKAHQMKLDVIVKALKWLEMDMDVDEVECIVAILIHKNLV 229 (258)
Q Consensus 171 ~v~r~L~kkv~~~~~~~~~~~~~~i~l~~i~~al~~~~~~~~~~evE~ila~LI~~G~I 229 (258)
-|+...+|+++-+. .+..+|+.+.+.+... ++.+.|...+-.||..|.|
T Consensus 36 ki~~ai~RkTyG~n-----Kk~d~Is~sq~~e~tg-----~~~~~V~~al~~Li~~~vI 84 (100)
T PF04492_consen 36 KILLAIIRKTYGWN-----KKMDRISNSQIAEMTG-----LSRDHVSKALNELIRRGVI 84 (100)
T ss_pred HHHHHHHHHccCCC-----CccceeeHHHHHHHHC-----cCHHHHHHHHHHHHHCCCE
Confidence 44556777777664 2457899999998876 6899999999999999999
No 147
>KOG0030 consensus Myosin essential light chain, EF-Hand protein superfamily [Cytoskeleton]
Probab=41.41 E-value=27 Score=28.12 Aligned_cols=39 Identities=15% Similarity=0.066 Sum_probs=31.9
Q ss_pred CCccccHHHHHHHHHhccCCCCHHHHHHHHHHHHHc-Ccc
Q 025096 191 KAHQMKLDVIVKALKWLEMDMDVDEVECIVAILIHK-NLV 229 (258)
Q Consensus 191 ~~~~i~l~~i~~al~~~~~~~~~~evE~ila~LI~~-G~I 229 (258)
++-.|+-+.+++.|.-.|..++++|||.+++...+. |.|
T Consensus 101 g~G~i~~aeLRhvLttlGekl~eeEVe~Llag~eD~nG~i 140 (152)
T KOG0030|consen 101 GNGTIMGAELRHVLTTLGEKLTEEEVEELLAGQEDSNGCI 140 (152)
T ss_pred CCcceeHHHHHHHHHHHHhhccHHHHHHHHccccccCCcC
Confidence 456789999999887777779999999999988776 443
No 148
>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=41.08 E-value=49 Score=21.37 Aligned_cols=40 Identities=15% Similarity=0.179 Sum_probs=33.5
Q ss_pred cccHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCcceEEeecCce
Q 025096 194 QMKLDVIVKALKWLEMDMDVDEVECIVAILIHKNLVKGYFAHKSK 238 (258)
Q Consensus 194 ~i~l~~i~~al~~~~~~~~~~evE~ila~LI~~G~IkGyI~~~~~ 238 (258)
.++..+++..+. ++..-+-.++.+|..+|+|.=.-+..++
T Consensus 17 ~~~~~~la~~~~-----~~~~~~t~~i~~L~~~g~I~r~~~~~D~ 56 (59)
T PF01047_consen 17 GITQSELAEKLG-----ISRSTVTRIIKRLEKKGLIERERDPDDR 56 (59)
T ss_dssp SEEHHHHHHHHT-----S-HHHHHHHHHHHHHTTSEEEEEETTET
T ss_pred CCCHHHHHHHHC-----CChhHHHHHHHHHHHCCCEEeccCCCCC
Confidence 488999999987 6889999999999999999877766654
No 149
>PRK14574 hmsH outer membrane protein; Provisional
Probab=40.80 E-value=98 Score=32.09 Aligned_cols=132 Identities=11% Similarity=0.021 Sum_probs=88.3
Q ss_pred HHHHHHHHHhcCChhhHHHHHHHhhccCCCC-------CCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCc
Q 025096 21 TCQLFKIYFKLGTVHLCRSVIRSIETARIFD-------FEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNP 93 (258)
Q Consensus 21 ~n~l~kiyf~l~~~~~~~~l~~~i~~~~~p~-------~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~ 93 (258)
...||.-|+..++++.+..++..+... .|. -...|+-+..++..-.+.++.+.+++.+|++.|+......|.
T Consensus 370 ~~~L~yA~ld~e~~~~A~~~l~~~~~~-~p~~~~~~~~~~~~pn~d~~~~~~l~a~~~~~~gdl~~Ae~~le~l~~~aP~ 448 (822)
T PRK14574 370 ADDLYYSLNESEQLDKAYQFAVNYSEQ-TPYQVGVYGLPGKEPNDDWIEGQTLLVQSLVALNDLPTAQKKLEDLSSTAPA 448 (822)
T ss_pred HHHHHHHHHhcccHHHHHHHHHHHHhc-CCcEEeccCCCCCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC
Confidence 467899999999999999999988863 341 123578889999999999999999999999999999999986
Q ss_pred cChHHHHHHHHHHHHHHhhcC-CCCChhh--hhh----cc--c-cccHHHHHHHHhCCHHHHHHHHHHcHHHHHHhc
Q 025096 94 QSEANIRMILKYLIPVKLSIG-ILPKDWL--LEK----YN--L-VEYSNIVQALRRGDLRLLRHALEEHEDQFLRSG 160 (258)
Q Consensus 94 ~~~~~~~~IL~~LIp~~Ll~G-~~P~~~l--l~~----~~--l-~~y~~L~~av~~Gdl~~f~~~l~~~~~~f~~~g 160 (258)
+..-. +.-..+... .-|.... ++. .+ . ..+.....+...|++.+-++.+++-...+-.+.
T Consensus 449 n~~l~-------~~~A~v~~~Rg~p~~A~~~~k~a~~l~P~~~~~~~~~~~~al~l~e~~~A~~~~~~l~~~~Pe~~ 518 (822)
T PRK14574 449 NQNLR-------IALASIYLARDLPRKAEQELKAVESLAPRSLILERAQAETAMALQEWHQMELLTDDVISRSPEDI 518 (822)
T ss_pred CHHHH-------HHHHHHHHhcCCHHHHHHHHHHHhhhCCccHHHHHHHHHHHHhhhhHHHHHHHHHHHHhhCCCch
Confidence 64311 112233322 1222221 111 01 1 124555667777888877777766444444444
No 150
>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=40.51 E-value=65 Score=21.13 Aligned_cols=35 Identities=14% Similarity=0.146 Sum_probs=30.3
Q ss_pred CccccHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCcceE
Q 025096 192 AHQMKLDVIVKALKWLEMDMDVDEVECIVAILIHKNLVKG 231 (258)
Q Consensus 192 ~~~i~l~~i~~al~~~~~~~~~~evE~ila~LI~~G~IkG 231 (258)
...++.+++++.+. ++...+.-++..|..+|+|.-
T Consensus 23 ~~~~s~~ela~~~g-----~s~~tv~r~l~~L~~~g~i~~ 57 (67)
T cd00092 23 QLPLTRQEIADYLG-----LTRETVSRTLKELEEEGLISR 57 (67)
T ss_pred cCCcCHHHHHHHHC-----CCHHHHHHHHHHHHHCCCEEe
Confidence 34689999999987 689999999999999999963
No 151
>PLN03218 maturation of RBCL 1; Provisional
Probab=40.35 E-value=5e+02 Score=27.92 Aligned_cols=65 Identities=14% Similarity=0.013 Sum_probs=43.9
Q ss_pred HHHHHHHHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHh
Q 025096 18 LYLTCQLFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALIN 90 (258)
Q Consensus 18 ~~~~n~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~ 90 (258)
....|.++..|.+.|+++.+..+++.+....+++ ..++|. -....|+..+++++|.+.|.+....
T Consensus 579 ~vTynaLI~ay~k~G~ldeA~elf~~M~e~gi~p-------~~~tyn-sLI~ay~k~G~~deAl~lf~eM~~~ 643 (1060)
T PLN03218 579 HITVGALMKACANAGQVDRAKEVYQMIHEYNIKG-------TPEVYT-IAVNSCSQKGDWDFALSIYDDMKKK 643 (1060)
T ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCC-------ChHHHH-HHHHHHHhcCCHHHHHHHHHHHHHc
Confidence 3567888899999999999999998888754321 122222 1223355678888888877776653
No 152
>PF13429 TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2_B.
Probab=39.61 E-value=45 Score=28.95 Aligned_cols=32 Identities=13% Similarity=-0.123 Sum_probs=23.4
Q ss_pred hhhhhhHHhhhhcChHHHHHHHHHHHHhcCcc
Q 025096 63 YMYYTGRLEVFNENFPAADQKLSYALINCNPQ 94 (258)
Q Consensus 63 y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~ 94 (258)
+....|..++..+++++|..+|..+...-|.+
T Consensus 216 ~~~~la~~~~~lg~~~~Al~~~~~~~~~~p~d 247 (280)
T PF13429_consen 216 LWDALAAAYLQLGRYEEALEYLEKALKLNPDD 247 (280)
T ss_dssp HCHHHHHHHHHHT-HHHHHHHHHHHHHHSTT-
T ss_pred HHHHHHHHhccccccccccccccccccccccc
Confidence 44556888888888889988888888865544
No 153
>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=39.39 E-value=56 Score=21.37 Aligned_cols=24 Identities=17% Similarity=0.111 Sum_probs=20.6
Q ss_pred hhhcChHHHHHHHHHHHHhcCccC
Q 025096 72 VFNENFPAADQKLSYALINCNPQS 95 (258)
Q Consensus 72 ~~~~~~~~A~~~L~~A~~~c~~~~ 95 (258)
+-+++|++|.+.|+.++...|.+.
T Consensus 2 l~~~~~~~A~~~~~~~l~~~p~~~ 25 (68)
T PF14559_consen 2 LKQGDYDEAIELLEKALQRNPDNP 25 (68)
T ss_dssp HHTTHHHHHHHHHHHHHHHTTTSH
T ss_pred hhccCHHHHHHHHHHHHHHCCCCH
Confidence 457899999999999999888653
No 154
>PLN03081 pentatricopeptide (PPR) repeat-containing protein; Provisional
Probab=39.27 E-value=4.1e+02 Score=26.57 Aligned_cols=61 Identities=11% Similarity=0.033 Sum_probs=42.3
Q ss_pred HHHHHHHHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHh
Q 025096 18 LYLTCQLFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALIN 90 (258)
Q Consensus 18 ~~~~n~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~ 90 (258)
.++.|.++..|.+.|+++.+..++..+.. | +.++|. ..-..++..+++++|.+.|.+....
T Consensus 158 ~~~~n~Li~~y~k~g~~~~A~~lf~~m~~---~--------~~~t~n-~li~~~~~~g~~~~A~~lf~~M~~~ 218 (697)
T PLN03081 158 QYMMNRVLLMHVKCGMLIDARRLFDEMPE---R--------NLASWG-TIIGGLVDAGNYREAFALFREMWED 218 (697)
T ss_pred hHHHHHHHHHHhcCCCHHHHHHHHhcCCC---C--------CeeeHH-HHHHHHHHCcCHHHHHHHHHHHHHh
Confidence 45667888888888888888888875542 1 233332 2333456779999999999988763
No 155
>PF05158 RNA_pol_Rpc34: RNA polymerase Rpc34 subunit; InterPro: IPR007832 The family comprises a subunit specific to RNA Pol III, the tRNA specific polymerase. The C34 subunit of Saccharomyces cerevisiae RNA Pol III is part of a subcomplex of three subunits which have no counterpart in the other two nuclear RNA polymerases. This subunit interacts with TFIIIB70 and therefore participates in Pol III recruitment [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2DK8_A 2DK5_A 2YU3_A.
Probab=38.83 E-value=10 Score=34.74 Aligned_cols=121 Identities=17% Similarity=0.216 Sum_probs=15.7
Q ss_pred HHHHHHHHHHHHHHhhcC----CCCChhhhhhccccccHHHHHHHHhCCHHHHHHHHHHcHHHHHHhcHH--HHHHhhHH
Q 025096 97 ANIRMILKYLIPVKLSIG----ILPKDWLLEKYNLVEYSNIVQALRRGDLRLLRHALEEHEDQFLRSGVY--LVLEKLEL 170 (258)
Q Consensus 97 ~~~~~IL~~LIp~~Ll~G----~~P~~~ll~~~~l~~y~~L~~av~~Gdl~~f~~~l~~~~~~f~~~gly--lll~~l~~ 170 (258)
....++||-|.-=+|+.- +.|++.++--|++.+=.+++ ...|| .+|-+ .+++.++.
T Consensus 115 ~~~~k~lk~Le~k~lIK~vksv~~~~rK~Yml~~l~Ps~eiT-----------------GG~wy-~d~e~D~efi~~l~~ 176 (327)
T PF05158_consen 115 TQLTKILKSLESKKLIKSVKSVKNPNRKVYMLYDLEPSEEIT-----------------GGPWY-TDGEFDTEFIDVLRE 176 (327)
T ss_dssp HHHHHHHHHHHHTTSEEEE--SS-SS--EEEESSS---------------------------------------------
T ss_pred HHHHHHHHHHHhCCCEEEecCcCCCCeEEEEEccCCcCcccC-----------------CCCcc-cCCcccHHHHHHHHH
Confidence 345667777766566531 34555555455554432221 23344 33433 36777888
Q ss_pred HHHHHHHHHHHHHhhc-------------CCC---CCCccccHHHHHHHHHhcc---CCCCHHHHHHHHHHHHHcCcceE
Q 025096 171 QVYQRLFKKIYIIQKQ-------------KDP---SKAHQMKLDVIVKALKWLE---MDMDVDEVECIVAILIHKNLVKG 231 (258)
Q Consensus 171 ~v~r~L~kkv~~~~~~-------------~~~---~~~~~i~l~~i~~al~~~~---~~~~~~evE~ila~LI~~G~IkG 231 (258)
.|++-+-++.+....+ ..| +..+-.+..+|...++-+| .+++.+|++.||-.||.+|.|.-
T Consensus 177 ~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~T~~eI~~fI~~sgIs~v~Ls~eDI~~LL~tLVyDgkIE~ 256 (327)
T PF05158_consen 177 QCLRFIQQKSFPSSEQISQKTSSSSADPQALPYPAGYASYPTLEEIAEFINKSGISNVELSEEDIESLLDTLVYDGKIEE 256 (327)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred HHHHHHHhCcCccccccccccccccccccccccccccCCCCCHHHHHHHHHHcCCCceecCHHHHHHHHHHHhhCceeEE
Confidence 8887777776633210 000 1122356667766665444 35899999999999999999976
Q ss_pred Eeec
Q 025096 232 YFAH 235 (258)
Q Consensus 232 yI~~ 235 (258)
..+.
T Consensus 257 v~~~ 260 (327)
T PF05158_consen 257 VRSG 260 (327)
T ss_dssp ----
T ss_pred Eecc
Confidence 6555
No 156
>PF13431 TPR_17: Tetratricopeptide repeat
Probab=38.64 E-value=17 Score=21.25 Aligned_cols=20 Identities=10% Similarity=-0.006 Sum_probs=17.3
Q ss_pred hhhhhhhHHhhhhcChHHHH
Q 025096 62 TYMYYTGRLEVFNENFPAAD 81 (258)
Q Consensus 62 ~y~YY~G~~~~~~~~~~~A~ 81 (258)
.-+|.+|.++...|++++|.
T Consensus 14 ~a~~nla~~~~~~g~~~~A~ 33 (34)
T PF13431_consen 14 EAYNNLANLYLNQGDYEEAI 33 (34)
T ss_pred HHHHHHHHHHHHCcCHHhhc
Confidence 45688999999999999986
No 157
>PF02847 MA3: MA3 domain; InterPro: IPR003891 This entry represents the MI domain (after MA-3 and eIF4G), it is a protein-protein interaction module of ~130 amino acids [, , ]. It appears in several translation factors and is found in: One copy in plant and animal eIF4G 1 and 2 (DAP-5/NAT1/p97) Two copies in the animal programmed cell death protein 4 (PDCD4) or MA-3 that is induced during programmed cell death and inhibits neoplastic transformation Four tandem-repeated copies in a group of uncharacterised plant proteins The MI domain consists of seven alpha-helices, which pack into a globular form. The packing arrangement consists of repeating pairs of antiparallel helices packed one upon the other such that a superhelical axis is generated perpendicular to the alpha-helical axes []. The MI domain has also been named MA3 domain.; PDB: 2ION_A 2IOL_B 2NSZ_A 3EIQ_C 2HM8_A 2KZT_B 2IOS_A 2RG8_B 2ZU6_E 3EIJ_A ....
Probab=38.63 E-value=1.6e+02 Score=21.68 Aligned_cols=93 Identities=15% Similarity=0.248 Sum_probs=54.4
Q ss_pred cHHHHHHHHhCCHHHHHHHHHH-----cHHHHHHhcHHHHHHhhHHHHHHHHHHHHHHHhhcCCCCCCccccHHHHHHHH
Q 025096 130 YSNIVQALRRGDLRLLRHALEE-----HEDQFLRSGVYLVLEKLELQVYQRLFKKIYIIQKQKDPSKAHQMKLDVIVKAL 204 (258)
Q Consensus 130 y~~L~~av~~Gdl~~f~~~l~~-----~~~~f~~~glylll~~l~~~v~r~L~kkv~~~~~~~~~~~~~~i~l~~i~~al 204 (258)
+.-+..++.+||....-..+.+ +...++..-+...+++ .-.+|..+-.+..... ....++-.++..++
T Consensus 6 ~~~l~ey~~~~d~~ea~~~l~el~~~~~~~~vv~~~l~~~le~--~~~~r~~~~~Ll~~L~-----~~~~~~~~~~~~gf 78 (113)
T PF02847_consen 6 FSILMEYFSSGDVDEAVECLKELKLPSQHHEVVKVILECALEE--KKSYREYYSKLLSHLC-----KRKLISKEQFQEGF 78 (113)
T ss_dssp HHHHHHHHHHT-HHHHHHHHHHTT-GGGHHHHHHHHHHHHHTS--SHHHHHHHHHHHHHHH-----HTTSS-HHHHHHHH
T ss_pred HHHHHHHhcCCCHHHHHHHHHHhCCCccHHHHHHHHHHHHhhc--cHHHHHHHHHHHHHHH-----hcCCCCHHHHHHHH
Confidence 3446678888999988888877 2334555555555554 1233333333332211 12568888888887
Q ss_pred Hhc---------cCCCCHHHHHHHHHHHHHcCcc
Q 025096 205 KWL---------EMDMDVDEVECIVAILIHKNLV 229 (258)
Q Consensus 205 ~~~---------~~~~~~~evE~ila~LI~~G~I 229 (258)
.-. ..+--.+-+..+++.+|.+|.+
T Consensus 79 ~~~l~~l~Dl~~D~P~~~~~la~~~~~~i~~~~l 112 (113)
T PF02847_consen 79 EDLLESLEDLELDIPKAPEYLAKFLARLIADGIL 112 (113)
T ss_dssp HHHHHHHHHHHHHSTTHHHHHHHHHHHHHHTTSS
T ss_pred HHHHhHhhhccccchHHHHHHHHHHHHHHHcCCc
Confidence 521 0112346788999999999876
No 158
>PF10264 Stork_head: Winged helix Storkhead-box1 domain; InterPro: IPR019391 In humans the Storkhead-box protein controls polyploidization of extravillus trophoblast and is implicated in pre-eclampsia []. This entry represents the conserved N-terminal winged-helix domain, which is likely to bind DNA.
Probab=38.04 E-value=1.5e+02 Score=21.34 Aligned_cols=37 Identities=8% Similarity=0.113 Sum_probs=28.0
Q ss_pred ccccHHHHHHHHHhc--cCC-CCHHHHHHHHHHHHHcCcc
Q 025096 193 HQMKLDVIVKALKWL--EMD-MDVDEVECIVAILIHKNLV 229 (258)
Q Consensus 193 ~~i~l~~i~~al~~~--~~~-~~~~evE~ila~LI~~G~I 229 (258)
...+.+.+.+.|.-. |.. .+.|-+..-|+.||.+|.|
T Consensus 28 ~~at~E~l~~~L~~~yp~i~~Ps~e~l~~~L~~Li~erkI 67 (80)
T PF10264_consen 28 QPATQETLREHLRKHYPGIAIPSQEVLYNTLGTLIKERKI 67 (80)
T ss_pred CcchHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHcCce
Confidence 346777787777532 332 5889999999999999998
No 159
>KOG3060 consensus Uncharacterized conserved protein [Function unknown]
Probab=37.32 E-value=2e+02 Score=25.66 Aligned_cols=77 Identities=18% Similarity=0.191 Sum_probs=57.7
Q ss_pred HHHHHHHHHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCccCh
Q 025096 17 ALYLTCQLFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNPQSE 96 (258)
Q Consensus 17 ~~~~~n~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~~~ 96 (258)
..++.-++|-.-...+..+.+...++.+.. +||+|.+|.=+ .|...=..++|++|.+.++.-+..=|.+..
T Consensus 51 ~w~l~EqV~IAAld~~~~~lAq~C~~~L~~-------~fp~S~RV~~l--kam~lEa~~~~~~A~e~y~~lL~ddpt~~v 121 (289)
T KOG3060|consen 51 IWTLYEQVFIAALDTGRDDLAQKCINQLRD-------RFPGSKRVGKL--KAMLLEATGNYKEAIEYYESLLEDDPTDTV 121 (289)
T ss_pred HHHHHHHHHHHHHHhcchHHHHHHHHHHHH-------hCCCChhHHHH--HHHHHHHhhchhhHHHHHHHHhccCcchhH
Confidence 566667777778889999999999999875 35778887432 233334669999999999988887777766
Q ss_pred HHHHHH
Q 025096 97 ANIRMI 102 (258)
Q Consensus 97 ~~~~~I 102 (258)
..+|++
T Consensus 122 ~~KRKl 127 (289)
T KOG3060|consen 122 IRKRKL 127 (289)
T ss_pred HHHHHH
Confidence 666655
No 160
>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=37.27 E-value=1.3e+02 Score=26.65 Aligned_cols=66 Identities=6% Similarity=-0.069 Sum_probs=47.9
Q ss_pred HHHHHHHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHH
Q 025096 19 YLTCQLFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALI 89 (258)
Q Consensus 19 ~~~n~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~ 89 (258)
.....+-.+|...|+++.+...+...-.. .|. +....+..++..|++++..|++++|...+..+..
T Consensus 149 ~~~~~la~i~~~~g~~~eA~~~l~~~l~~-~~~----~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~~~~ 214 (355)
T cd05804 149 WAVHAVAHVLEMQGRFKEGIAFMESWRDT-WDC----SSMLRGHNWWHLALFYLERGDYEAALAIYDTHIA 214 (355)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHhhhhc-cCC----CcchhHHHHHHHHHHHHHCCCHHHHHHHHHHHhc
Confidence 34566788999999999999888654321 121 1122334456789999999999999999999965
No 161
>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A.
Probab=35.90 E-value=1e+02 Score=25.69 Aligned_cols=53 Identities=17% Similarity=0.180 Sum_probs=38.1
Q ss_pred hhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCccChHHHHHHHHHHHHHHhhcC
Q 025096 60 KVTYMYYTGRLEVFNENFPAADQKLSYALINCNPQSEANIRMILKYLIPVKLSIG 114 (258)
Q Consensus 60 ~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~~~~~~~~IL~~LIp~~Ll~G 114 (258)
...--++.|++|+-.+.|..|-..++..+++.|.+. .....|.+++=...-+|
T Consensus 140 la~~e~~ia~~Y~~~~~y~aA~~r~~~v~~~yp~t~--~~~~al~~l~~~y~~l~ 192 (203)
T PF13525_consen 140 LAEHELYIARFYYKRGKYKAAIIRFQYVIENYPDTP--AAEEALARLAEAYYKLG 192 (203)
T ss_dssp HHHHHHHHHHHHHCTT-HHHHHHHHHHHHHHSTTSH--HHHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHHHcccHHHHHHHHHHHHHHCCCCc--hHHHHHHHHHHHHHHhC
Confidence 445567899999999999999999999999999654 34445555554433344
No 162
>CHL00033 ycf3 photosystem I assembly protein Ycf3
Probab=35.89 E-value=2.2e+02 Score=22.50 Aligned_cols=67 Identities=15% Similarity=-0.028 Sum_probs=46.0
Q ss_pred HHHHHHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcC
Q 025096 20 LTCQLFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCN 92 (258)
Q Consensus 20 ~~n~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~ 92 (258)
....+...|+..++++.+...++..-.. .|+ + .+...-++-.|.++...+++++|...+..|+..-|
T Consensus 37 ~~~~~g~~~~~~g~~~~A~~~~~~al~l-~~~----~-~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~~~~ 103 (168)
T CHL00033 37 TYYRDGMSAQSEGEYAEALQNYYEAMRL-EID----P-YDRSYILYNIGLIHTSNGEHTKALEYYFQALERNP 103 (168)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHHhc-ccc----c-hhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCc
Confidence 3344566888899999988777543211 121 1 12233457789999999999999999999998644
No 163
>PF07219 HemY_N: HemY protein N-terminus; InterPro: IPR010817 This entry represents the N terminus (approximately 150 residues) of bacterial HemY porphyrin biosynthesis proteins. These are membrane protein involved in a late step of protoheme IX synthesis [].
Probab=35.71 E-value=61 Score=24.34 Aligned_cols=34 Identities=18% Similarity=0.210 Sum_probs=28.3
Q ss_pred ccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHh
Q 025096 57 KRDKVTYMYYTGRLEVFNENFPAADQKLSYALIN 90 (258)
Q Consensus 57 ~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~ 90 (258)
+.....-....|.+.+.+|||++|++.+..|-+.
T Consensus 55 r~~ka~~al~~Gl~al~~G~~~~A~k~~~~a~~~ 88 (108)
T PF07219_consen 55 RRRKAQRALSRGLIALAEGDWQRAEKLLAKAAKL 88 (108)
T ss_pred HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc
Confidence 4445556678999999999999999999999765
No 164
>KOG1126 consensus DNA-binding cell division cycle control protein [Cell cycle control, cell division, chromosome partitioning]
Probab=35.43 E-value=1e+02 Score=30.83 Aligned_cols=23 Identities=13% Similarity=0.255 Sum_probs=16.3
Q ss_pred HHHHHHHHHHhcCChhhHHHHHH
Q 025096 20 LTCQLFKIYFKLGTVHLCRSVIR 42 (258)
Q Consensus 20 ~~n~l~kiyf~l~~~~~~~~l~~ 42 (258)
+...+-++|++++..+.+=.+++
T Consensus 525 i~~~~g~~~~~~k~~d~AL~~~~ 547 (638)
T KOG1126|consen 525 ILCHIGRIQHQLKRKDKALQLYE 547 (638)
T ss_pred HHhhhhHHHHHhhhhhHHHHHHH
Confidence 45566677888888877777764
No 165
>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa []. This region is probably a DNA-binding helix-turn-helix.; PDB: 2XV4_S 2XUB_A.
Probab=35.12 E-value=97 Score=20.85 Aligned_cols=34 Identities=26% Similarity=0.394 Sum_probs=27.7
Q ss_pred ccccHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCcceE
Q 025096 193 HQMKLDVIVKALKWLEMDMDVDEVECIVAILIHKNLVKG 231 (258)
Q Consensus 193 ~~i~l~~i~~al~~~~~~~~~~evE~ila~LI~~G~IkG 231 (258)
.+.|+.+|..... ++.++|-..++.||..|.+.-
T Consensus 26 G~ltl~~i~~~t~-----l~~~~Vk~~L~~LiQh~~v~y 59 (62)
T PF08221_consen 26 GRLTLREIVRRTG-----LSPKQVKKALVVLIQHNLVQY 59 (62)
T ss_dssp -SEEHHHHHHHHT-------HHHHHHHHHHHHHTTSEEE
T ss_pred CCcCHHHHHHHhC-----CCHHHHHHHHHHHHHcCCeee
Confidence 4789999998876 689999999999999998864
No 166
>PLN03077 Protein ECB2; Provisional
Probab=34.78 E-value=5.2e+02 Score=26.53 Aligned_cols=65 Identities=15% Similarity=0.145 Sum_probs=47.6
Q ss_pred HHHHHHHHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCcc
Q 025096 18 LYLTCQLFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNPQ 94 (258)
Q Consensus 18 ~~~~n~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~ 94 (258)
..+.|.++..|.+.|+++.+..+++.+... +.++|.- ...-++..+++++|.+.|.+......++
T Consensus 424 ~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~-----------d~vs~~~-mi~~~~~~g~~~eA~~lf~~m~~~~~pd 488 (857)
T PLN03077 424 VVVANALIEMYSKCKCIDKALEVFHNIPEK-----------DVISWTS-IIAGLRLNNRCFEALIFFRQMLLTLKPN 488 (857)
T ss_pred hHHHHHHHHHHHHcCCHHHHHHHHHhCCCC-----------CeeeHHH-HHHHHHHCCCHHHHHHHHHHHHhCCCCC
Confidence 457789999999999999999999876542 2333322 2233567899999999999988765544
No 167
>smart00668 CTLH C-terminal to LisH motif. Alpha-helical motif of unknown function.
Probab=34.09 E-value=1.1e+02 Score=19.49 Aligned_cols=31 Identities=16% Similarity=0.169 Sum_probs=26.2
Q ss_pred HHHHHHHHhCCHHHHHHHHHHcHHHHHHhcH
Q 025096 131 SNIVQALRRGDLRLLRHALEEHEDQFLRSGV 161 (258)
Q Consensus 131 ~~L~~av~~Gdl~~f~~~l~~~~~~f~~~gl 161 (258)
..+.+++..||+..-.++++.+.....+.+-
T Consensus 6 ~~i~~~i~~g~~~~a~~~~~~~~~~l~~~~~ 36 (58)
T smart00668 6 KRIRELILKGDWDEALEWLSSLKPPLLERNS 36 (58)
T ss_pred HHHHHHHHcCCHHHHHHHHHHcCHHHhccCC
Confidence 5678999999999999999998887766653
No 168
>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional
Probab=33.86 E-value=56 Score=34.60 Aligned_cols=57 Identities=11% Similarity=-0.056 Sum_probs=40.3
Q ss_pred chhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCccChHHHHHHHHHHHHHHhhcCCCCChh
Q 025096 59 DKVTYMYYTGRLEVFNENFPAADQKLSYALINCNPQSEANIRMILKYLIPVKLSIGILPKDW 120 (258)
Q Consensus 59 ~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~~~~~~~~IL~~LIp~~Ll~G~~P~~~ 120 (258)
-++.|+|-.|+.+..+++|.+|...|..|+..-|.+..- ...|.-.-+-.|+.+.-.
T Consensus 42 ~~~~~~f~~a~~~~~~Gd~~~A~~~l~~Al~~dP~n~~~-----~~~LA~~yl~~g~~~~A~ 98 (987)
T PRK09782 42 FVIYPRLDKALKAQKNNDEATAIREFEYIHQQVPDNIPL-----TLYLAEAYRHFGHDDRAR 98 (987)
T ss_pred HHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCCHHH-----HHHHHHHHHHCCCHHHHH
Confidence 377788889999999999999999999999987766321 122332333357666533
No 169
>KOG2076 consensus RNA polymerase III transcription factor TFIIIC [Transcription]
Probab=33.19 E-value=1.5e+02 Score=30.89 Aligned_cols=64 Identities=13% Similarity=0.050 Sum_probs=49.5
Q ss_pred HHHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCcc
Q 025096 23 QLFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNPQ 94 (258)
Q Consensus 23 ~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~ 94 (258)
.+...|...++++.|-+++..+-+. | ..+..-+.|-.|++++..+.+++|.+.+..++..-|.+
T Consensus 419 d~a~al~~~~~~~~Al~~l~~i~~~--~------~~~~~~vw~~~a~c~~~l~e~e~A~e~y~kvl~~~p~~ 482 (895)
T KOG2076|consen 419 DLADALTNIGKYKEALRLLSPITNR--E------GYQNAFVWYKLARCYMELGEYEEAIEFYEKVLILAPDN 482 (895)
T ss_pred HHHHHHHhcccHHHHHHHHHHHhcC--c------cccchhhhHHHHHHHHHHhhHHHHHHHHHHHHhcCCCc
Confidence 4566777888888888888766543 2 22334466779999999999999999999999987754
No 170
>PF13371 TPR_9: Tetratricopeptide repeat
Probab=33.16 E-value=1.1e+02 Score=20.29 Aligned_cols=28 Identities=18% Similarity=0.107 Sum_probs=23.8
Q ss_pred hHHhhhhcChHHHHHHHHHHHHhcCccC
Q 025096 68 GRLEVFNENFPAADQKLSYALINCNPQS 95 (258)
Q Consensus 68 G~~~~~~~~~~~A~~~L~~A~~~c~~~~ 95 (258)
..+|+.+++|++|.+.++.++..-|.+.
T Consensus 2 ~~~~~~~~~~~~A~~~~~~~l~~~p~~~ 29 (73)
T PF13371_consen 2 KQIYLQQEDYEEALEVLERALELDPDDP 29 (73)
T ss_pred HHHHHhCCCHHHHHHHHHHHHHhCcccc
Confidence 4678899999999999999999766543
No 171
>COG4700 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]
Probab=33.09 E-value=2.4e+02 Score=24.21 Aligned_cols=65 Identities=11% Similarity=0.113 Sum_probs=48.2
Q ss_pred HHHHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCc
Q 025096 22 CQLFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNP 93 (258)
Q Consensus 22 n~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~ 93 (258)
..+.+--|.++...+|.+.+..+-.. .|... .|-.+ --.||.+--.|.+.+|+..|++|...+|.
T Consensus 128 LglA~Aqfa~~~~A~a~~tLe~l~e~-~pa~r-~pd~~-----Ll~aR~laa~g~~a~Aesafe~a~~~ypg 192 (251)
T COG4700 128 LGLAQAQFAIQEFAAAQQTLEDLMEY-NPAFR-SPDGH-----LLFARTLAAQGKYADAESAFEVAISYYPG 192 (251)
T ss_pred HHHHHHHHhhccHHHHHHHHHHHhhc-CCccC-CCCch-----HHHHHHHHhcCCchhHHHHHHHHHHhCCC
Confidence 34556678899999999998776653 24332 23222 23589999999999999999999998774
No 172
>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=32.83 E-value=88 Score=24.01 Aligned_cols=36 Identities=14% Similarity=0.099 Sum_probs=32.1
Q ss_pred ccccHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCcceEEe
Q 025096 193 HQMKLDVIVKALKWLEMDMDVDEVECIVAILIHKNLVKGYF 233 (258)
Q Consensus 193 ~~i~l~~i~~al~~~~~~~~~~evE~ila~LI~~G~IkGyI 233 (258)
..++.++|+..+. ++..-+..++..|...|+|.++-
T Consensus 24 ~~~s~~eia~~l~-----is~~~v~~~l~~L~~~Gli~~~~ 59 (130)
T TIGR02944 24 QPYSAAEIAEQTG-----LNAPTVSKILKQLSLAGIVTSKR 59 (130)
T ss_pred CCccHHHHHHHHC-----cCHHHHHHHHHHHHHCCcEEecC
Confidence 5689999999987 78999999999999999998753
No 173
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=32.69 E-value=2e+02 Score=23.64 Aligned_cols=57 Identities=16% Similarity=0.156 Sum_probs=42.1
Q ss_pred cHHHHHHhhHHHHHHHHHHHHHHHhhcCCCCCCccccHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCcce
Q 025096 160 GVYLVLEKLELQVYQRLFKKIYIIQKQKDPSKAHQMKLDVIVKALKWLEMDMDVDEVECIVAILIHKNLVK 230 (258)
Q Consensus 160 glylll~~l~~~v~r~L~kkv~~~~~~~~~~~~~~i~l~~i~~al~~~~~~~~~~evE~ila~LI~~G~Ik 230 (258)
.-+...+.|...++|.|+.- ....-....|+..+. +.++.+||+..|.-|..-|+|+
T Consensus 16 ~~~~~~~~W~~~~ir~l~~l-----------~~~~~d~~~iak~l~---p~is~~ev~~sL~~L~~~gli~ 72 (171)
T PF14394_consen 16 DEFEYYSSWYHPAIRELLPL-----------MPFAPDPEWIAKRLR---PKISAEEVRDSLEFLEKLGLIK 72 (171)
T ss_pred HHHHHHhhhHHHHHHHHhhc-----------CCCCCCHHHHHHHhc---CCCCHHHHHHHHHHHHHCCCeE
Confidence 34556677888888888762 122225677877773 2389999999999999999995
No 174
>COG1849 Uncharacterized protein conserved in archaea [Function unknown]
Probab=32.57 E-value=59 Score=23.99 Aligned_cols=32 Identities=19% Similarity=0.112 Sum_probs=27.5
Q ss_pred chhhhhhhhhHHhhhhcChHHHHHHHHHHHHh
Q 025096 59 DKVTYMYYTGRLEVFNENFPAADQKLSYALIN 90 (258)
Q Consensus 59 ~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~ 90 (258)
++..-++.-|+++.-.||+..|+.+++.|.-.
T Consensus 39 ~ma~~Y~~Dakyf~ekGD~vtAfa~~sYa~g~ 70 (90)
T COG1849 39 DMAESYFEDAKYFLEKGDYVTAFAALSYAHGW 70 (90)
T ss_pred HHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHH
Confidence 45566788999999999999999999999873
No 175
>PF08544 GHMP_kinases_C: GHMP kinases C terminal ; InterPro: IPR013750 This domain is found in homoserine kinases (2.7.1.39 from EC), galactokinases (2.7.1.6 from EC) and mevalonate kinases (2.7.1.36 from EC). These kinases make up the GHMP kinase superfamily of ATP-dependent enzymes []. These enzymes are involved in the biosynthesis of isoprenes and amino acids as well as in carbohydrate metabolism. The C-terminal domain of homoserine kinase has a central alpha-beta plait fold and an insertion of four helices, which, together with the N-terminal fold, create a novel nucleotide binding fold [].; PDB: 2R3V_C 4EMD_A 4DXL_A 4ED4_A 2GS8_A 1K47_E 3GON_A 3K17_B 1PIE_A 2AJ4_A ....
Probab=32.32 E-value=61 Score=22.44 Aligned_cols=22 Identities=36% Similarity=0.729 Sum_probs=19.4
Q ss_pred HHHHHHhCCHHHHHHHHHHcHH
Q 025096 133 IVQALRRGDLRLLRHALEEHED 154 (258)
Q Consensus 133 L~~av~~Gdl~~f~~~l~~~~~ 154 (258)
+++|+.+||+..|.+.+..+..
T Consensus 1 m~~al~~~d~~~~~~~~~~~~~ 22 (85)
T PF08544_consen 1 MIKALAEGDLELLGELMNENQE 22 (85)
T ss_dssp HHHHHHTTCHHHHHHHHHHHHH
T ss_pred CHHHHHCcCHHHHHHHHHHhhh
Confidence 5789999999999999997655
No 176
>PF13833 EF-hand_8: EF-hand domain pair; PDB: 3KF9_A 1TTX_A 1WLZ_A 1ALV_A 1NX3_A 1ALW_A 1NX2_A 1NX1_A 1NX0_A 1DF0_A ....
Probab=32.10 E-value=1.1e+02 Score=19.20 Aligned_cols=31 Identities=16% Similarity=0.275 Sum_probs=24.5
Q ss_pred ccccHHHHHHHHHhccCC-CCHHHHHHHHHHH
Q 025096 193 HQMKLDVIVKALKWLEMD-MDVDEVECIVAIL 223 (258)
Q Consensus 193 ~~i~l~~i~~al~~~~~~-~~~~evE~ila~L 223 (258)
-.|+.+++..++...|.. ++.+|++.++..+
T Consensus 3 G~i~~~~~~~~l~~~g~~~~s~~e~~~l~~~~ 34 (54)
T PF13833_consen 3 GKITREEFRRALSKLGIKDLSEEEVDRLFREF 34 (54)
T ss_dssp SEEEHHHHHHHHHHTTSSSSCHHHHHHHHHHH
T ss_pred CEECHHHHHHHHHHhCCCCCCHHHHHHHHHhc
Confidence 468889999999766777 8999988877643
No 177
>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=31.82 E-value=1.6e+02 Score=26.18 Aligned_cols=87 Identities=10% Similarity=0.086 Sum_probs=55.9
Q ss_pred cHHHHHHHHhCCHHH----HHHHHH---HcHHHHHHhcHHHHHHhhHHHHHHHHHHHHHHHhhcCCCCCCccccHHHHHH
Q 025096 130 YSNIVQALRRGDLRL----LRHALE---EHEDQFLRSGVYLVLEKLELQVYQRLFKKIYIIQKQKDPSKAHQMKLDVIVK 202 (258)
Q Consensus 130 y~~L~~av~~Gdl~~----f~~~l~---~~~~~f~~~glylll~~l~~~v~r~L~kkv~~~~~~~~~~~~~~i~l~~i~~ 202 (258)
|..|+..-+..+-.. |++.++ .+...-+...-+...+.|..-++|.|+.-. .-.-+...|+.
T Consensus 77 F~~lV~f~~ak~~~~k~~~~~~~~~~~~~~~~~~L~~~~~~y~~~W~~~virel~~~~-----------~~~~~~~~ia~ 145 (271)
T TIGR02147 77 FEAMVNFGQAKTDTEKQQFFEEMQALKPRPRLRVLAADQFEYYRHWYNSVIRELLGVM-----------PFADDPEELAK 145 (271)
T ss_pred HHHHHHHhccCCHHHHHHHHHHHHHHhhhchheeccHHHHHHHHHHHHHHHHHHhhcC-----------CCCCCHHHHHH
Confidence 356666666665433 333332 222233444556677889999999997721 11223456777
Q ss_pred HHHhccCCCCHHHHHHHHHHHHHcCcce
Q 025096 203 ALKWLEMDMDVDEVECIVAILIHKNLVK 230 (258)
Q Consensus 203 al~~~~~~~~~~evE~ila~LI~~G~Ik 230 (258)
.+. +.++.+||...|.-|..-|+|+
T Consensus 146 ~l~---p~is~~ev~~sL~~L~~~glik 170 (271)
T TIGR02147 146 RCF---PKISAEQVKESLDLLERLGLIK 170 (271)
T ss_pred HhC---CCCCHHHHHHHHHHHHHCCCee
Confidence 664 5589999999999999999995
No 178
>PLN03218 maturation of RBCL 1; Provisional
Probab=31.45 E-value=6.9e+02 Score=26.89 Aligned_cols=63 Identities=14% Similarity=-0.049 Sum_probs=35.0
Q ss_pred HHHHHHHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHH
Q 025096 19 YLTCQLFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALI 89 (258)
Q Consensus 19 ~~~n~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~ 89 (258)
++.|.++..|.+.|+.+.+..+++.+....+. -+.++|.-. -..|+-.+++++|.+.|.+...
T Consensus 473 ~tynsLI~~y~k~G~vd~A~~vf~eM~~~Gv~-------PdvvTynaL-I~gy~k~G~~eeAl~lf~~M~~ 535 (1060)
T PLN03218 473 KLYTTLISTCAKSGKVDAMFEVFHEMVNAGVE-------ANVHTFGAL-IDGCARAGQVAKAFGAYGIMRS 535 (1060)
T ss_pred HHHHHHHHHHHhCcCHHHHHHHHHHHHHcCCC-------CCHHHHHHH-HHHHHHCcCHHHHHHHHHHHHH
Confidence 44566666666666666666666665543211 123333222 2335566777777777766544
No 179
>KOG4162 consensus Predicted calmodulin-binding protein [Signal transduction mechanisms]
Probab=31.34 E-value=1.3e+02 Score=30.78 Aligned_cols=63 Identities=17% Similarity=0.193 Sum_probs=46.2
Q ss_pred HHHHHHHHhcCChhhHHH--HHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCc
Q 025096 22 CQLFKIYFKLGTVHLCRS--VIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNP 93 (258)
Q Consensus 22 n~l~kiyf~l~~~~~~~~--l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~ 93 (258)
-.+-+++.+.|+..++.. +++..=. +. |..+ .-.||+|.+...+|+.++|-++|+.|+..-+.
T Consensus 722 ~Ala~~lle~G~~~la~~~~~L~dalr--~d-----p~n~--eaW~~LG~v~k~~Gd~~~Aaecf~aa~qLe~S 786 (799)
T KOG4162|consen 722 TALAELLLELGSPRLAEKRSLLSDALR--LD-----PLNH--EAWYYLGEVFKKLGDSKQAAECFQAALQLEES 786 (799)
T ss_pred HHHHHHHHHhCCcchHHHHHHHHHHHh--hC-----CCCH--HHHHHHHHHHHHccchHHHHHHHHHHHhhccC
Confidence 346778888898888887 6653221 11 1122 35699999999999999999999999996443
No 180
>COG5240 SEC21 Vesicle coat complex COPI, gamma subunit [Intracellular trafficking and secretion]
Probab=30.79 E-value=3.7e+02 Score=27.06 Aligned_cols=114 Identities=20% Similarity=0.261 Sum_probs=71.0
Q ss_pred ccCCCchhHHHHHHHHHHHHHHHhcCChhhHHHHHHHhhcc--CCC------------CCC-CCCccchhhhhhhhhHHh
Q 025096 7 LAGKGSKRVGALYLTCQLFKIYFKLGTVHLCRSVIRSIETA--RIF------------DFE-EFPKRDKVTYMYYTGRLE 71 (258)
Q Consensus 7 ~~~d~~Kk~~~~~~~n~l~kiyf~l~~~~~~~~l~~~i~~~--~~p------------~~~-~~~~~~~v~y~YY~G~~~ 71 (258)
..+|.+|-...|.+..+ +|.|+-+-...+++.|-+- ++. +++ .|| +.+..|.=++|-..
T Consensus 348 LIsd~Nr~IstyAITtL-----LKTGt~e~idrLv~~I~sfvhD~SD~FKiI~ida~rsLsl~Fp-~k~~s~l~FL~~~L 421 (898)
T COG5240 348 LISDENRTISTYAITTL-----LKTGTEETIDRLVNLIPSFVHDMSDGFKIIAIDALRSLSLLFP-SKKLSYLDFLGSSL 421 (898)
T ss_pred HhhcccccchHHHHHHH-----HHcCchhhHHHHHHHHHHHHHhhccCceEEeHHHHHHHHhhCc-HHHHHHHHHHHHHH
Confidence 34677888888887754 5889888888777766541 111 011 255 45566888899999
Q ss_pred hhhcChH---HHHHHHHHHHHhcCccChHHHHHHHHHH-----------HHHHhh--cC-CCCChhhhhhcccccc
Q 025096 72 VFNENFP---AADQKLSYALINCNPQSEANIRMILKYL-----------IPVKLS--IG-ILPKDWLLEKYNLVEY 130 (258)
Q Consensus 72 ~~~~~~~---~A~~~L~~A~~~c~~~~~~~~~~IL~~L-----------Ip~~Ll--~G-~~P~~~ll~~~~l~~y 130 (258)
+.+|.|+ .+-+.+..++.+-|++ |+++|--| |.++++ +| +-|+.+-..+|-...|
T Consensus 422 ~~eGg~eFK~~~Vdaisd~~~~~p~s----kEraLe~LC~fIEDcey~~I~vrIL~iLG~EgP~a~~P~~yvrhIy 493 (898)
T COG5240 422 LQEGGLEFKKYMVDAISDAMENDPDS----KERALEVLCTFIEDCEYHQITVRILGILGREGPRAKTPGKYVRHIY 493 (898)
T ss_pred HhcccchHHHHHHHHHHHHHhhCchH----HHHHHHHHHHHHhhcchhHHHHHHHHHhcccCCCCCCcchHHHHHH
Confidence 9888664 4556677777776643 34444322 456666 46 5777665555533344
No 181
>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=30.15 E-value=69 Score=20.19 Aligned_cols=24 Identities=17% Similarity=0.454 Sum_probs=20.6
Q ss_pred HHHHHHHhcCChhhHHHHHHHhhc
Q 025096 23 QLFKIYFKLGTVHLCRSVIRSIET 46 (258)
Q Consensus 23 ~l~kiyf~l~~~~~~~~l~~~i~~ 46 (258)
-+.+.|.++|+.+.++.++..+-.
T Consensus 4 dLA~ayie~Gd~e~Ar~lL~evl~ 27 (44)
T TIGR03504 4 DLARAYIEMGDLEGARELLEEVIE 27 (44)
T ss_pred HHHHHHHHcCChHHHHHHHHHHHH
Confidence 467899999999999999976654
No 182
>KOG3060 consensus Uncharacterized conserved protein [Function unknown]
Probab=30.03 E-value=1.2e+02 Score=26.99 Aligned_cols=66 Identities=17% Similarity=0.119 Sum_probs=41.1
Q ss_pred HHHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCcc
Q 025096 23 QLFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNPQ 94 (258)
Q Consensus 23 ~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~ 94 (258)
.+.-+|+..+.+..+-=.+..+=-. .|. +..--.....-+|+.|- ..+++.|.+++..|++.|+..
T Consensus 159 eLaeiY~~~~~f~kA~fClEE~ll~-~P~-n~l~f~rlae~~Yt~gg----~eN~~~arkyy~~alkl~~~~ 224 (289)
T KOG3060|consen 159 ELAEIYLSEGDFEKAAFCLEELLLI-QPF-NPLYFQRLAEVLYTQGG----AENLELARKYYERALKLNPKN 224 (289)
T ss_pred HHHHHHHhHhHHHHHHHHHHHHHHc-CCC-cHHHHHHHHHHHHHHhh----HHHHHHHHHHHHHHHHhChHh
Confidence 4567889999988888777554321 132 11101112223344444 568899999999999999843
No 183
>smart00386 HAT HAT (Half-A-TPR) repeats. Present in several RNA-binding proteins. Structurally and sequentially thought to be similar to TPRs.
Probab=29.85 E-value=96 Score=16.53 Aligned_cols=19 Identities=16% Similarity=0.062 Sum_probs=16.4
Q ss_pred cChHHHHHHHHHHHHhcCc
Q 025096 75 ENFPAADQKLSYALINCNP 93 (258)
Q Consensus 75 ~~~~~A~~~L~~A~~~c~~ 93 (258)
++++.|...++.|...||.
T Consensus 1 ~~~~~~r~i~e~~l~~~~~ 19 (33)
T smart00386 1 GDIERARKIYERALEKFPK 19 (33)
T ss_pred CcHHHHHHHHHHHHHHCCC
Confidence 4678999999999999983
No 184
>KOG0547 consensus Translocase of outer mitochondrial membrane complex, subunit TOM70/TOM72 [Intracellular trafficking, secretion, and vesicular transport]
Probab=29.38 E-value=2e+02 Score=28.17 Aligned_cols=70 Identities=11% Similarity=0.058 Sum_probs=46.7
Q ss_pred HHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCccChHHHHHH
Q 025096 24 LFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNPQSEANIRMI 102 (258)
Q Consensus 24 l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~~~~~~~~I 102 (258)
+--+|...++.....+.+..-+.- -|+ ... -+|-.|.++++-++|++|-..|+.|...-|.+...+.++.
T Consensus 366 ~a~~y~d~~~~~~~~~~F~~A~~l-dp~------n~d--vYyHRgQm~flL~q~e~A~aDF~Kai~L~pe~~~~~iQl~ 435 (606)
T KOG0547|consen 366 RAAAYADENQSEKMWKDFNKAEDL-DPE------NPD--VYYHRGQMRFLLQQYEEAIADFQKAISLDPENAYAYIQLC 435 (606)
T ss_pred HHHHHhhhhccHHHHHHHHHHHhc-CCC------CCc--hhHhHHHHHHHHHHHHHHHHHHHHHhhcChhhhHHHHHHH
Confidence 344566666666555555332221 021 111 2477999999999999999999999999998876655544
No 185
>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=29.34 E-value=2.3e+02 Score=26.66 Aligned_cols=65 Identities=14% Similarity=0.048 Sum_probs=48.1
Q ss_pred HHHHHHHHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCcc
Q 025096 18 LYLTCQLFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNPQ 94 (258)
Q Consensus 18 ~~~~n~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~ 94 (258)
=+++-.++++.-..++++.|.++++.+.+.. |+ -.+..+++++..++-.+|-..+++|+...|.+
T Consensus 169 NyLv~~Ll~~l~~t~~~~~ai~lle~L~~~~-pe-----------v~~~LA~v~l~~~~E~~AI~ll~~aL~~~p~d 233 (395)
T PF09295_consen 169 NYLVDTLLKYLSLTQRYDEAIELLEKLRERD-PE-----------VAVLLARVYLLMNEEVEAIRLLNEALKENPQD 233 (395)
T ss_pred hHHHHHHHHHHhhcccHHHHHHHHHHHHhcC-Cc-----------HHHHHHHHHHhcCcHHHHHHHHHHHHHhCCCC
Confidence 3566667888888889999999998887642 32 12457777777777788888888888776655
No 186
>PF10607 CLTH: CTLH/CRA C-terminal to LisH motif domain; InterPro: IPR019589 This entry represents the CRA (or CT11-RanBPM) domain, which is a protein-protein interaction domain present in crown eukaryotes (plants, animals, fungi) and which is found in Ran-binding proteins such as Ran-binding protein 9 (RanBP9 or RanBPM) and RanBP10. RanBPM is a scaffolding protein important in regulating cellular function in both the immune system and the nervous system, and may act as an adapter protein to couple membrane receptors to intracellular signaling pathways. This domain is at the C terminus of the proteins and is the binding domain for the CRA motif, which is comprised of approximately 100 amino acids at the C-terminal of RanBPM. It was found to be important for the interaction of RanBPM with fragile X mental retardation protein (FMRP), but its functional significance has yet to be determined [].
Probab=29.30 E-value=1.5e+02 Score=22.88 Aligned_cols=32 Identities=28% Similarity=0.325 Sum_probs=26.7
Q ss_pred ccHHHHHHHHhCCHHHHHHHHHHcHHHHHHhc
Q 025096 129 EYSNIVQALRRGDLRLLRHALEEHEDQFLRSG 160 (258)
Q Consensus 129 ~y~~L~~av~~Gdl~~f~~~l~~~~~~f~~~g 160 (258)
....+.+++++||+..--++++++...+.+.+
T Consensus 4 ~r~~I~~~I~~g~i~~Ai~w~~~~~~~l~~~~ 35 (145)
T PF10607_consen 4 ERKKIRQAILNGDIDPAIEWLNENFPELLKRN 35 (145)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHcCHHHHhcC
Confidence 34678899999999999999999887777765
No 187
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=29.23 E-value=1.5e+02 Score=18.61 Aligned_cols=33 Identities=15% Similarity=0.169 Sum_probs=28.8
Q ss_pred ccc-cHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCcce
Q 025096 193 HQM-KLDVIVKALKWLEMDMDVDEVECIVAILIHKNLVK 230 (258)
Q Consensus 193 ~~i-~l~~i~~al~~~~~~~~~~evE~ila~LI~~G~Ik 230 (258)
.++ +..++++.+. ++..-+...+..|..+|+|.
T Consensus 18 ~~l~s~~~la~~~~-----vs~~tv~~~l~~L~~~g~i~ 51 (60)
T smart00345 18 DKLPSERELAAQLG-----VSRTTVREALSRLEAEGLVQ 51 (60)
T ss_pred CcCcCHHHHHHHHC-----CCHHHHHHHHHHHHHCCCEE
Confidence 467 7899999987 68999999999999999985
No 188
>COG3071 HemY Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]
Probab=29.00 E-value=3.9e+02 Score=25.27 Aligned_cols=111 Identities=21% Similarity=0.227 Sum_probs=69.2
Q ss_pred hhHHhhhhcChHHHHHHHHHHHHhcCccCh-----------------HH-----------HHHHHHHHHHHHhhc--CCC
Q 025096 67 TGRLEVFNENFPAADQKLSYALINCNPQSE-----------------AN-----------IRMILKYLIPVKLSI--GIL 116 (258)
Q Consensus 67 ~G~~~~~~~~~~~A~~~L~~A~~~c~~~~~-----------------~~-----------~~~IL~~LIp~~Ll~--G~~ 116 (258)
-|.+.+.+|+|.+|+..+..+=.+-+.... .| .....+.|.-+++++ |++
T Consensus 90 egl~~l~eG~~~qAEkl~~rnae~~e~p~l~~l~aA~AA~qrgd~~~an~yL~eaae~~~~~~l~v~ltrarlll~~~d~ 169 (400)
T COG3071 90 EGLLKLFEGDFQQAEKLLRRNAEHGEQPVLAYLLAAEAAQQRGDEDRANRYLAEAAELAGDDTLAVELTRARLLLNRRDY 169 (400)
T ss_pred HHHHHHhcCcHHHHHHHHHHhhhcCcchHHHHHHHHHHHHhcccHHHHHHHHHHHhccCCCchHHHHHHHHHHHHhCCCc
Confidence 577778889999999998887765542210 01 223445566666664 567
Q ss_pred CChhh-----hhhcccc-cc--HHHHHHHHhCCHHHHHHHHHHcHHHHHHhcHHH--HHHhhHHHHHHHHHHHHH
Q 025096 117 PKDWL-----LEKYNLV-EY--SNIVQALRRGDLRLLRHALEEHEDQFLRSGVYL--VLEKLELQVYQRLFKKIY 181 (258)
Q Consensus 117 P~~~l-----l~~~~l~-~y--~~L~~av~~Gdl~~f~~~l~~~~~~f~~~glyl--ll~~l~~~v~r~L~kkv~ 181 (258)
|.... ++.-+.. +- ...-..++.|+.......+.+ +.+.|++. -..+++.-.++++++..-
T Consensus 170 ~aA~~~v~~ll~~~pr~~~vlrLa~r~y~~~g~~~~ll~~l~~----L~ka~~l~~~e~~~le~~a~~glL~q~~ 240 (400)
T COG3071 170 PAARENVDQLLEMTPRHPEVLRLALRAYIRLGAWQALLAILPK----LRKAGLLSDEEAARLEQQAWEGLLQQAR 240 (400)
T ss_pred hhHHHHHHHHHHhCcCChHHHHHHHHHHHHhccHHHHHHHHHH----HHHccCCChHHHHHHHHHHHHHHHHHHh
Confidence 75321 2211111 11 223347888999888888876 66777763 567888888888877543
No 189
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=28.50 E-value=1.3e+02 Score=18.36 Aligned_cols=33 Identities=9% Similarity=0.144 Sum_probs=28.7
Q ss_pred cccHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCcceE
Q 025096 194 QMKLDVIVKALKWLEMDMDVDEVECIVAILIHKNLVKG 231 (258)
Q Consensus 194 ~i~l~~i~~al~~~~~~~~~~evE~ila~LI~~G~IkG 231 (258)
.++..+++..+. ++...+...+..|...|+|.-
T Consensus 14 ~~s~~~l~~~l~-----~s~~tv~~~l~~L~~~g~i~~ 46 (53)
T smart00420 14 KVSVEELAELLG-----VSEMTIRRDLNKLEEQGLLTR 46 (53)
T ss_pred CcCHHHHHHHHC-----CCHHHHHHHHHHHHHCCCEEE
Confidence 478899999986 689999999999999999853
No 190
>PRK11447 cellulose synthase subunit BcsC; Provisional
Probab=28.33 E-value=1.9e+02 Score=31.09 Aligned_cols=64 Identities=11% Similarity=-0.137 Sum_probs=48.8
Q ss_pred HHHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCccC
Q 025096 23 QLFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNPQS 95 (258)
Q Consensus 23 ~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~~ 95 (258)
..-..++..++++.+...++..-.. .|. ...-++.+|.+++..+++++|...|..|+...|...
T Consensus 274 ~~G~~~~~~g~~~~A~~~l~~aL~~-~P~--------~~~a~~~Lg~~~~~~g~~~eA~~~l~~Al~~~p~~~ 337 (1157)
T PRK11447 274 AQGLAAVDSGQGGKAIPELQQAVRA-NPK--------DSEALGALGQAYSQQGDRARAVAQFEKALALDPHSS 337 (1157)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHh-CCC--------CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcc
Confidence 3356788899999999888654332 232 133467899999999999999999999999887653
No 191
>smart00671 SEL1 Sel1-like repeats. These represent a subfamily of TPR (tetratricopeptide repeat) sequences.
Probab=28.06 E-value=77 Score=17.75 Aligned_cols=17 Identities=12% Similarity=0.001 Sum_probs=13.9
Q ss_pred hhcChHHHHHHHHHHHH
Q 025096 73 FNENFPAADQKLSYALI 89 (258)
Q Consensus 73 ~~~~~~~A~~~L~~A~~ 89 (258)
...|.++|..+++.|-.
T Consensus 17 ~~~d~~~A~~~~~~Aa~ 33 (36)
T smart00671 17 VKKDLEKALEYYKKAAE 33 (36)
T ss_pred CCcCHHHHHHHHHHHHH
Confidence 45699999999998865
No 192
>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=27.71 E-value=1.5e+02 Score=21.25 Aligned_cols=37 Identities=24% Similarity=0.196 Sum_probs=29.4
Q ss_pred CccccHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCcceEEe
Q 025096 192 AHQMKLDVIVKALKWLEMDMDVDEVECIVAILIHKNLVKGYF 233 (258)
Q Consensus 192 ~~~i~l~~i~~al~~~~~~~~~~evE~ila~LI~~G~IkGyI 233 (258)
..-+|.+.|....+ ++..+++..+..|+..|+|.-..
T Consensus 22 hE~VP~~~I~~~s~-----l~~~~~~~~L~~L~~~kLv~~~~ 58 (82)
T PF09202_consen 22 HEWVPLELIEKISG-----LSEGEVEKRLKRLVKLKLVSRRN 58 (82)
T ss_dssp -SSEEHHHHHHHHT-------HHHHHHHHHHHHHTTSEEEE-
T ss_pred CccCCHHHHHHHhC-----cCHHHHHHHHHHHHhcCCccccC
Confidence 34599999998876 67999999999999999997643
No 193
>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=27.66 E-value=1.3e+02 Score=18.70 Aligned_cols=33 Identities=15% Similarity=0.213 Sum_probs=28.3
Q ss_pred ccccHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCcce
Q 025096 193 HQMKLDVIVKALKWLEMDMDVDEVECIVAILIHKNLVK 230 (258)
Q Consensus 193 ~~i~l~~i~~al~~~~~~~~~~evE~ila~LI~~G~Ik 230 (258)
...+..++.+.+. ++...+-..+..|...|+|+
T Consensus 14 ~~~~~~el~~~l~-----~s~~~vs~hL~~L~~~glV~ 46 (47)
T PF01022_consen 14 GPLTVSELAEELG-----LSQSTVSHHLKKLREAGLVE 46 (47)
T ss_dssp SSEEHHHHHHHHT-----S-HHHHHHHHHHHHHTTSEE
T ss_pred CCCchhhHHHhcc-----ccchHHHHHHHHHHHCcCee
Confidence 3478899999997 78999999999999999985
No 194
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=27.43 E-value=2.5e+02 Score=24.15 Aligned_cols=48 Identities=4% Similarity=0.122 Sum_probs=40.1
Q ss_pred CccccHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCcceEEeecCceEEEEec
Q 025096 192 AHQMKLDVIVKALKWLEMDMDVDEVECIVAILIHKNLVKGYFAHKSKVVVLSK 244 (258)
Q Consensus 192 ~~~i~l~~i~~al~~~~~~~~~~evE~ila~LI~~G~IkGyI~~~~~~lVlsk 244 (258)
...++.+++++.+. +|..-+-.++..|-.+|+|.-..+...+.+.++.
T Consensus 19 ~~~IS~~eLA~~L~-----iS~~Tvsr~Lk~LEe~GlI~R~~~~r~~~v~LTe 66 (217)
T PRK14165 19 TVKISSSEFANHTG-----TSSKTAARILKQLEDEGYITRTIVPRGQLITITE 66 (217)
T ss_pred CCCcCHHHHHHHHC-----cCHHHHHHHHHHHHHCCCEEEEEcCCceEEEECH
Confidence 45799999999987 6899999999999999999888877666666643
No 195
>PRK10153 DNA-binding transcriptional activator CadC; Provisional
Probab=27.32 E-value=61 Score=31.60 Aligned_cols=54 Identities=15% Similarity=0.062 Sum_probs=39.3
Q ss_pred hcCChhhHHHHHHH-hhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCcc
Q 025096 30 KLGTVHLCRSVIRS-IETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNPQ 94 (258)
Q Consensus 30 ~l~~~~~~~~l~~~-i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~ 94 (258)
..|+++.+..-++. ++ ++ | + ...+.+.|+++...|++++|.+++++|+..-|..
T Consensus 432 ~~g~~~~A~~~l~rAl~------L~--p-s--~~a~~~lG~~~~~~G~~~eA~~~~~~A~~L~P~~ 486 (517)
T PRK10153 432 VKGKTDEAYQAINKAID------LE--M-S--WLNYVLLGKVYELKGDNRLAADAYSTAFNLRPGE 486 (517)
T ss_pred hcCCHHHHHHHHHHHHH------cC--C-C--HHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCC
Confidence 34677777765532 22 11 2 2 3467889999999999999999999999987754
No 196
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=27.01 E-value=9.3e+02 Score=27.02 Aligned_cols=69 Identities=17% Similarity=0.172 Sum_probs=48.1
Q ss_pred HHHHHHHHHHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCc
Q 025096 16 GALYLTCQLFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNP 93 (258)
Q Consensus 16 ~~~~~~n~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~ 93 (258)
..|-+.-.|++||-+..+++.+..+++.+=.+ + .+ ..+-++.| |-..+-+.+-++|++-|.+|+.--|.
T Consensus 1528 d~~~V~~~L~~iy~k~ek~~~A~ell~~m~KK-F---~q-~~~vW~~y----~~fLl~~ne~~aa~~lL~rAL~~lPk 1596 (1710)
T KOG1070|consen 1528 DAYTVHLKLLGIYEKSEKNDEADELLRLMLKK-F---GQ-TRKVWIMY----ADFLLRQNEAEAARELLKRALKSLPK 1596 (1710)
T ss_pred chHHHHHHHHHHHHHhhcchhHHHHHHHHHHH-h---cc-hhhHHHHH----HHHHhcccHHHHHHHHHHHHHhhcch
Confidence 35667778899999999999999888776543 1 10 12333433 55556777778999999999996664
No 197
>PRK10866 outer membrane biogenesis protein BamD; Provisional
Probab=26.70 E-value=1.7e+02 Score=25.36 Aligned_cols=55 Identities=9% Similarity=0.025 Sum_probs=40.4
Q ss_pred cchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCccChHHHHHHHHHHHHHHhhcC
Q 025096 58 RDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNPQSEANIRMILKYLIPVKLSIG 114 (258)
Q Consensus 58 ~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~~~~~~~~IL~~LIp~~Ll~G 114 (258)
......-++.|++|+-.++|..|-..++..+.++|.+. .....|-+++-.-.-+|
T Consensus 172 ~~la~~e~~ia~~Y~~~~~y~AA~~r~~~v~~~Yp~t~--~~~eal~~l~~ay~~lg 226 (243)
T PRK10866 172 DRLAKYELSVAEYYTKRGAYVAVVNRVEQMLRDYPDTQ--ATRDALPLMENAYRQLQ 226 (243)
T ss_pred HHHHHHHHHHHHHHHHcCchHHHHHHHHHHHHHCCCCc--hHHHHHHHHHHHHHHcC
Confidence 33455667899999999999999999999999999654 34555555554433334
No 198
>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=26.42 E-value=1.1e+02 Score=20.13 Aligned_cols=37 Identities=22% Similarity=0.178 Sum_probs=28.7
Q ss_pred ccccHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCcceEEee
Q 025096 193 HQMKLDVIVKALKWLEMDMDVDEVECIVAILIHKNLVKGYFA 234 (258)
Q Consensus 193 ~~i~l~~i~~al~~~~~~~~~~evE~ila~LI~~G~IkGyI~ 234 (258)
..++..++...+. ++...+-.++-+|+..|+|.=.-+
T Consensus 17 ~~~t~~~l~~~~~-----~~~~~vs~~i~~L~~~glv~~~~~ 53 (68)
T PF13463_consen 17 GPMTQSDLAERLG-----ISKSTVSRIIKKLEEKGLVEKERD 53 (68)
T ss_dssp S-BEHHHHHHHTT-------HHHHHHHHHHHHHTTSEEEEEE
T ss_pred CCcCHHHHHHHHC-----cCHHHHHHHHHHHHHCCCEEecCC
Confidence 5678899999886 688999999999999999944433
No 199
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=26.35 E-value=5.3e+02 Score=23.99 Aligned_cols=82 Identities=12% Similarity=0.132 Sum_probs=54.1
Q ss_pred HHHHHHHHHhcCChhhHHHHHHHhhccCCCCCC--------------------------------CCCccchhhhhhhhh
Q 025096 21 TCQLFKIYFKLGTVHLCRSVIRSIETARIFDFE--------------------------------EFPKRDKVTYMYYTG 68 (258)
Q Consensus 21 ~n~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~--------------------------------~~~~~~~v~y~YY~G 68 (258)
.-.|-+-|..-|-+|.+++++..+-.. |++. +-..-+...|+.=++
T Consensus 110 l~qL~~Dym~aGl~DRAE~~f~~L~de--~efa~~AlqqLl~IYQ~treW~KAId~A~~L~k~~~q~~~~eIAqfyCELA 187 (389)
T COG2956 110 LQQLGRDYMAAGLLDRAEDIFNQLVDE--GEFAEGALQQLLNIYQATREWEKAIDVAERLVKLGGQTYRVEIAQFYCELA 187 (389)
T ss_pred HHHHHHHHHHhhhhhHHHHHHHHHhcc--hhhhHHHHHHHHHHHHHhhHHHHHHHHHHHHHHcCCccchhHHHHHHHHHH
Confidence 446778888888888888888765431 1110 011334444544467
Q ss_pred HHhhhhcChHHHHHHHHHHHHhcCccChHHHHHHHHHHHHHHhhcCCC
Q 025096 69 RLEVFNENFPAADQKLSYALINCNPQSEANIRMILKYLIPVKLSIGIL 116 (258)
Q Consensus 69 ~~~~~~~~~~~A~~~L~~A~~~c~~~~~~~~~~IL~~LIp~~Ll~G~~ 116 (258)
.-++..+++++|.+.+..|+.--|... =++|++|++
T Consensus 188 q~~~~~~~~d~A~~~l~kAlqa~~~cv------------RAsi~lG~v 223 (389)
T COG2956 188 QQALASSDVDRARELLKKALQADKKCV------------RASIILGRV 223 (389)
T ss_pred HHHhhhhhHHHHHHHHHHHHhhCccce------------ehhhhhhHH
Confidence 777888999999999999999554432 256777766
No 200
>PF13730 HTH_36: Helix-turn-helix domain
Probab=25.84 E-value=1.3e+02 Score=19.03 Aligned_cols=29 Identities=21% Similarity=0.279 Sum_probs=25.6
Q ss_pred cHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCcc
Q 025096 196 KLDVIVKALKWLEMDMDVDEVECIVAILIHKNLV 229 (258)
Q Consensus 196 ~l~~i~~al~~~~~~~~~~evE~ila~LI~~G~I 229 (258)
|.+.+++.+. ++...|...+..|...|+|
T Consensus 27 S~~~la~~~g-----~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 27 SQETLAKDLG-----VSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred CHHHHHHHHC-----cCHHHHHHHHHHHHHCcCC
Confidence 7888888886 6889999999999999986
No 201
>KOG3785 consensus Uncharacterized conserved protein [Function unknown]
Probab=25.80 E-value=2e+02 Score=27.06 Aligned_cols=61 Identities=10% Similarity=0.032 Sum_probs=40.9
Q ss_pred HHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCccChH
Q 025096 24 LFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNPQSEA 97 (258)
Q Consensus 24 l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~~~~ 97 (258)
+...||++|+++.+-+..+.+..++-|+ ++. --+++-.+++-+.|.+|... -.+||.+...
T Consensus 63 ia~C~fhLgdY~~Al~~Y~~~~~~~~~~------~el---~vnLAcc~FyLg~Y~eA~~~----~~ka~k~pL~ 123 (557)
T KOG3785|consen 63 IAHCYFHLGDYEEALNVYTFLMNKDDAP------AEL---GVNLACCKFYLGQYIEAKSI----AEKAPKTPLC 123 (557)
T ss_pred HHHHHHhhccHHHHHHHHHHHhccCCCC------ccc---chhHHHHHHHHHHHHHHHHH----HhhCCCChHH
Confidence 3467999999999999998887653222 221 12456667777788888763 4457766443
No 202
>PRK15174 Vi polysaccharide export protein VexE; Provisional
Probab=25.73 E-value=4.2e+02 Score=26.51 Aligned_cols=30 Identities=10% Similarity=-0.085 Sum_probs=18.9
Q ss_pred hhhhhHHhhhhcChHHHHHHHHHHHHhcCc
Q 025096 64 MYYTGRLEVFNENFPAADQKLSYALINCNP 93 (258)
Q Consensus 64 ~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~ 93 (258)
.+..|.++...+++++|...+..+....|.
T Consensus 321 ~~~La~~l~~~G~~~eA~~~l~~al~~~P~ 350 (656)
T PRK15174 321 RAMYARALRQVGQYTAASDEFVQLAREKGV 350 (656)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHHHHhCcc
Confidence 345566666666666666666666665443
No 203
>PF10557 Cullin_Nedd8: Cullin protein neddylation domain; InterPro: IPR019559 This is the neddylation site of cullin proteins, which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae (Baker's yeast), and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue []. ; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_B 1U6G_A 3O6B_J 3O2P_E 4A0K_A 2HYE_C ....
Probab=25.67 E-value=2.2e+02 Score=19.32 Aligned_cols=38 Identities=16% Similarity=0.310 Sum_probs=24.7
Q ss_pred ccccHHHHHHHHHh-c--cCCCCHHHHHHHHHHHHHcCcce
Q 025096 193 HQMKLDVIVKALKW-L--EMDMDVDEVECIVAILIHKNLVK 230 (258)
Q Consensus 193 ~~i~l~~i~~al~~-~--~~~~~~~evE~ila~LI~~G~Ik 230 (258)
.+++.+++.....- . ....+..++..-+-.||.+|||+
T Consensus 21 k~~~~~~L~~~v~~~l~~~f~~~~~~ik~~Ie~LIekeyi~ 61 (68)
T PF10557_consen 21 KKLSHDELINEVIEELKKRFPPSVSDIKKRIESLIEKEYIE 61 (68)
T ss_dssp SEEEHHHHHHHHHHHTTTTS---HHHHHHHHHHHHHTTSEE
T ss_pred CceeHHHHHHHHHHHhcCCcCCCHHHHHHHHHHHHHhhhhh
Confidence 45777766544321 1 22368899999999999999985
No 204
>KOG1840 consensus Kinesin light chain [Cytoskeleton]
Probab=25.52 E-value=2.9e+02 Score=27.05 Aligned_cols=83 Identities=14% Similarity=0.058 Sum_probs=59.5
Q ss_pred CCCchhHHHHHHHHHHHHHHHhcCChhhHHHHHHH-hhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHH
Q 025096 9 GKGSKRVGALYLTCQLFKIYFKLGTVHLCRSVIRS-IETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYA 87 (258)
Q Consensus 9 ~d~~Kk~~~~~~~n~l~kiyf~l~~~~~~~~l~~~-i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A 87 (258)
+.+.+...+--..+.+-..|..+++++.+.++++. +.... -.+. -..-++++.+-=+|..|.-+++|.+|..++..|
T Consensus 232 ~~G~~hl~va~~l~~~a~~y~~~~k~~eAv~ly~~AL~i~e-~~~G-~~h~~va~~l~nLa~ly~~~GKf~EA~~~~e~A 309 (508)
T KOG1840|consen 232 TSGLKHLVVASMLNILALVYRSLGKYDEAVNLYEEALTIRE-EVFG-EDHPAVAATLNNLAVLYYKQGKFAEAEEYCERA 309 (508)
T ss_pred ccCccCHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHH-HhcC-CCCHHHHHHHHHHHHHHhccCChHHHHHHHHHH
Confidence 33455666677777888999999999999999853 32210 0010 023446777777899999999999999999999
Q ss_pred HHhcCc
Q 025096 88 LINCNP 93 (258)
Q Consensus 88 ~~~c~~ 93 (258)
....-.
T Consensus 310 l~I~~~ 315 (508)
T KOG1840|consen 310 LEIYEK 315 (508)
T ss_pred HHHHHH
Confidence 985543
No 205
>KOG4507 consensus Uncharacterized conserved protein, contains TPR repeats [Function unknown]
Probab=25.47 E-value=1.7e+02 Score=29.31 Aligned_cols=65 Identities=14% Similarity=0.076 Sum_probs=42.2
Q ss_pred HHHHHHHHHHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCc
Q 025096 16 GALYLTCQLFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNP 93 (258)
Q Consensus 16 ~~~~~~n~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~ 93 (258)
.++-++|.+++.=+.++-......-+.-. + ++-+ ++|-.|+.|+.-.+..+|.++|..|++.-|.
T Consensus 644 ~~v~la~~~~~~~~~~da~~~l~q~l~~~-~-----------sepl-~~~~~g~~~l~l~~i~~a~~~~~~a~~~~~~ 708 (886)
T KOG4507|consen 644 PLVNLANLLIHYGLHLDATKLLLQALAIN-S-----------SEPL-TFLSLGNAYLALKNISGALEAFRQALKLTTK 708 (886)
T ss_pred cHHHHHHHHHHhhhhccHHHHHHHHHhhc-c-----------cCch-HHHhcchhHHHHhhhHHHHHHHHHHHhcCCC
Confidence 45566666666554444333333222211 1 2222 6688999999999999999999999996554
No 206
>PF14658 EF-hand_9: EF-hand domain
Probab=25.35 E-value=1.8e+02 Score=20.16 Aligned_cols=47 Identities=13% Similarity=0.172 Sum_probs=33.4
Q ss_pred CCCCCccccHHHHHHHHHhccC-CCCHHHHHHHHHHHHHcCcceEEeec
Q 025096 188 DPSKAHQMKLDVIVKALKWLEM-DMDVDEVECIVAILIHKNLVKGYFAH 235 (258)
Q Consensus 188 ~~~~~~~i~l~~i~~al~~~~~-~~~~~evE~ila~LI~~G~IkGyI~~ 235 (258)
++.+.-+++.+.|..-|+..+. ..++.+++.+.+.+==+|. .|.|+.
T Consensus 8 D~~~tG~V~v~~l~~~Lra~~~~~p~e~~Lq~l~~elDP~g~-~~~v~~ 55 (66)
T PF14658_consen 8 DTQKTGRVPVSDLITYLRAVTGRSPEESELQDLINELDPEGR-DGSVNF 55 (66)
T ss_pred CCcCCceEeHHHHHHHHHHHcCCCCcHHHHHHHHHHhCCCCC-CceEeH
Confidence 3456678999999988887776 5778888888775544554 555554
No 207
>PF09639 YjcQ: YjcQ protein; InterPro: IPR018597 YjcQ is a protein of approx. 100 residues containing four alpha helices and three beta strands. It is found in bacteria and also in the Lactococcus phage Tuc2009. In bacteria it appears to be under the regulation of SigD RNA polymerase which is responsible for the expression of many genes encoding cell-surface proteins related to flagellar assembly, motility, chemotaxis and autolysis in the late exponential growth phase. The exact function of YjcQ is unknown []. However, it is thought to be the major head protein in viruses [] and is found in prophage in bacteria. ; PDB: 2HGC_A.
Probab=25.09 E-value=1.1e+02 Score=22.11 Aligned_cols=26 Identities=15% Similarity=0.172 Sum_probs=19.0
Q ss_pred CCHHHHHHHHHHHHHcCcceE-EeecC
Q 025096 211 MDVDEVECIVAILIHKNLVKG-YFAHK 236 (258)
Q Consensus 211 ~~~~evE~ila~LI~~G~IkG-yI~~~ 236 (258)
...+....++..|.++|+|+| .+.+.
T Consensus 22 ~~~~~~~~il~~L~d~GyI~G~~~~~~ 48 (88)
T PF09639_consen 22 ITDSYWSDILRMLQDEGYIKGVSVVRY 48 (88)
T ss_dssp S-HHHHHHHHHHHHHHTSEE--EESSS
T ss_pred hhHHHHHHHHHHHHHCCCccceEEEec
Confidence 455788899999999999999 44343
No 208
>KOG4642 consensus Chaperone-dependent E3 ubiquitin protein ligase (contains TPR repeats) [Posttranslational modification, protein turnover, chaperones]
Probab=25.06 E-value=1.5e+02 Score=26.37 Aligned_cols=60 Identities=17% Similarity=0.103 Sum_probs=45.2
Q ss_pred HHHhcCChhhHH-HHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCccCh
Q 025096 27 IYFKLGTVHLCR-SVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNPQSE 96 (258)
Q Consensus 27 iyf~l~~~~~~~-~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~~~ 96 (258)
.|+++++.++|. +..++++- .|+ .|.=.|+.|...+.-..|.+|-.+|++|+++...+..
T Consensus 53 chlk~~~~~~v~~dcrralql--~~N--------~vk~h~flg~~~l~s~~~~eaI~~Lqra~sl~r~~~~ 113 (284)
T KOG4642|consen 53 CHLKLKHWEPVEEDCRRALQL--DPN--------LVKAHYFLGQWLLQSKGYDEAIKVLQRAYSLLREQPF 113 (284)
T ss_pred HHHHhhhhhhhhhhHHHHHhc--ChH--------HHHHHHHHHHHHHhhccccHHHHHHHHHHHHHhcCCC
Confidence 577888888876 45555542 122 4666799999999999999999999999886655443
No 209
>PF07079 DUF1347: Protein of unknown function (DUF1347); InterPro: IPR010764 This family consists of several hypothetical bacterial proteins of around 610 residues in length. Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.
Probab=24.67 E-value=2.2e+02 Score=27.61 Aligned_cols=87 Identities=15% Similarity=0.049 Sum_probs=53.0
Q ss_pred hHHhhhhcChHHHHHHHHHHHHhcCccChHHHHHHHHHHHHHHhhcCCCCChhh----hh-hccccccHHHHHHHHhCCH
Q 025096 68 GRLEVFNENFPAADQKLSYALINCNPQSEANIRMILKYLIPVKLSIGILPKDWL----LE-KYNLVEYSNIVQALRRGDL 142 (258)
Q Consensus 68 G~~~~~~~~~~~A~~~L~~A~~~c~~~~~~~~~~IL~~LIp~~Ll~G~~P~~~l----l~-~~~l~~y~~L~~av~~Gdl 142 (258)
|=+-=-++++++|++-|..-++....+..-.++.++-=.|.-.-.+..++-.+. ++ ..+-.+|.+|..|+-.---
T Consensus 13 gf~Lqkq~~~~esEkifskI~~e~~~~~f~lkeEvl~grilnAffl~nld~Me~~l~~l~~~~~~s~~l~LF~~L~~Y~~ 92 (549)
T PF07079_consen 13 GFILQKQKKFQESEKIFSKIYDEKESSPFLLKEEVLGGRILNAFFLNNLDLMEKQLMELRQQFGKSAYLPLFKALVAYKQ 92 (549)
T ss_pred hHHHHHHhhhhHHHHHHHHHHHHhhcchHHHHHHHHhhHHHHHHHHhhHHHHHHHHHHHHHhcCCchHHHHHHHHHHHHh
Confidence 333335689999999999999976655566676665444444444444433221 11 2244478888776666556
Q ss_pred HHHHHHHHHcHH
Q 025096 143 RLLRHALEEHED 154 (258)
Q Consensus 143 ~~f~~~l~~~~~ 154 (258)
+.|+++++....
T Consensus 93 k~~~kal~~ls~ 104 (549)
T PF07079_consen 93 KEYRKALQALSV 104 (549)
T ss_pred hhHHHHHHHHHH
Confidence 667777766433
No 210
>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=24.56 E-value=1.5e+02 Score=22.62 Aligned_cols=34 Identities=18% Similarity=0.195 Sum_probs=30.6
Q ss_pred ccccHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCcceE
Q 025096 193 HQMKLDVIVKALKWLEMDMDVDEVECIVAILIHKNLVKG 231 (258)
Q Consensus 193 ~~i~l~~i~~al~~~~~~~~~~evE~ila~LI~~G~IkG 231 (258)
..++.++|++.+. ++...++.++..|...|+|..
T Consensus 24 ~~~s~~eia~~~~-----i~~~~v~~il~~L~~~gli~~ 57 (132)
T TIGR00738 24 GPVSVKEIAERQG-----ISRSYLEKILRTLRRAGLVES 57 (132)
T ss_pred CcCcHHHHHHHHC-----cCHHHHHHHHHHHHHCCcEEe
Confidence 4689999999987 789999999999999999965
No 211
>PF03979 Sigma70_r1_1: Sigma-70 factor, region 1.1; InterPro: IPR007127 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 [, ]. This entry represents Region 1.1 which modulates DNA binding by region 2 and 4 when sigma is unbound by the core RNA polymerase [, ]. Region 1.1 is also involved in promoter binding.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2K6X_A.
Probab=24.31 E-value=2.6e+02 Score=19.73 Aligned_cols=33 Identities=27% Similarity=0.389 Sum_probs=22.3
Q ss_pred cccHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCc
Q 025096 194 QMKLDVIVKALKWLEMDMDVDEVECIVAILIHKNL 228 (258)
Q Consensus 194 ~i~l~~i~~al~~~~~~~~~~evE~ila~LI~~G~ 228 (258)
.|++++|..+|. ...++.+.++.++..|-..|.
T Consensus 21 ~lT~~eI~~~L~--~~~~~~e~id~i~~~L~~~gI 53 (82)
T PF03979_consen 21 YLTYDEINDALP--EDDLDPEQIDEIYDTLEDEGI 53 (82)
T ss_dssp S-BHHHHHHH-S---S---HHHHHHHHHHHHTT--
T ss_pred cCCHHHHHHHcC--ccCCCHHHHHHHHHHHHHCCC
Confidence 499999999986 334789999999999988774
No 212
>KOG1328 consensus Synaptic vesicle protein BAIAP3, involved in vesicle priming/regulation [Intracellular trafficking, secretion, and vesicular transport; Signal transduction mechanisms]
Probab=24.25 E-value=4.5e+02 Score=27.20 Aligned_cols=136 Identities=13% Similarity=0.134 Sum_probs=74.9
Q ss_pred hhhhhhhhhHHhhhhcChHH-------HHHHHHHHHHhcCccChHHHHH--------------HHHHHHHHHhhcCCCCC
Q 025096 60 KVTYMYYTGRLEVFNENFPA-------ADQKLSYALINCNPQSEANIRM--------------ILKYLIPVKLSIGILPK 118 (258)
Q Consensus 60 ~v~y~YY~G~~~~~~~~~~~-------A~~~L~~A~~~c~~~~~~~~~~--------------IL~~LIp~~Ll~G~~P~ 118 (258)
.+-|.|..|.+.=++.+|+. -++.|..||.-..+-+....++ =|..|+-|-=.+|.+|.
T Consensus 384 ~ld~s~L~~lL~di~~~W~~~~qL~~e~E~~LaDs~s~F~e~~l~~~r~hRd~Fpa~n~~s~~rle~LlkClg~L~~~~~ 463 (1103)
T KOG1328|consen 384 DLDFSLLYKLLQDIIDKWQPLTQLDKEEEDMLADSFSSFDEYCLRMMREHRDKFPASNRNSGERLESLLKCLGALRESPF 463 (1103)
T ss_pred CCCHHHHHHHHHHHHHhhcCcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCchHHHHHHHHHHHHHHhcCcc
Confidence 45577777777766666653 3566776666333211111111 12222222112344544
Q ss_pred hhhhhhccccccHHHHHHHHhCCHHHHHHHHHHcHH------HHHHhcHHHHHHhhHHHHHHHHHHHHHHHhhcCCCCCC
Q 025096 119 DWLLEKYNLVEYSNIVQALRRGDLRLLRHALEEHED------QFLRSGVYLVLEKLELQVYQRLFKKIYIIQKQKDPSKA 192 (258)
Q Consensus 119 ~~ll~~~~l~~y~~L~~av~~Gdl~~f~~~l~~~~~------~f~~~glylll~~l~~~v~r~L~kkv~~~~~~~~~~~~ 192 (258)
..-.-.|+-.-=.++..|++.|+..-++..++.-++ ...-..++.- ...+..+|-.|++.+..+ .+
T Consensus 464 ~~~~cPf~~~~~~~~~~al~kg~~~w~dr~~~~~q~~~~p~l~~~~~~i~~d-~q~~~~~Yaalf~~v~~i-------dy 535 (1103)
T KOG1328|consen 464 YQKYCPFKRPFHAHLESALVKGAEDWIDRSIESVQDPDPPKLLLQLLNIVND-QQSRFLHYAALFREVARI-------DY 535 (1103)
T ss_pred hHhhCCCCccchHHHHHHHHhhhHHHHHHHHhccCCCCCchhHHHHHHHHHH-HHHHHHHHHHHHHHhhcc-------ce
Confidence 332222222223689999999999999999987543 1111111111 457788888888887655 35
Q ss_pred ccccHHHHHHH
Q 025096 193 HQMKLDVIVKA 203 (258)
Q Consensus 193 ~~i~l~~i~~a 203 (258)
.+|.+..+...
T Consensus 536 f~lt~~q~drl 546 (1103)
T KOG1328|consen 536 FQLTLNQFDRL 546 (1103)
T ss_pred eeeeHHHHHHH
Confidence 67777776544
No 213
>COG4785 NlpI Lipoprotein NlpI, contains TPR repeats [General function prediction only]
Probab=24.04 E-value=78 Score=27.75 Aligned_cols=29 Identities=17% Similarity=0.279 Sum_probs=25.7
Q ss_pred hhhhhhhHHhhhhcChHHHHHHHHHHHHh
Q 025096 62 TYMYYTGRLEVFNENFPAADQKLSYALIN 90 (258)
Q Consensus 62 ~y~YY~G~~~~~~~~~~~A~~~L~~A~~~ 90 (258)
.-+||+|+.++..|+..+|...|.-|+.+
T Consensus 238 EtyFYL~K~~l~~G~~~~A~~LfKLaian 266 (297)
T COG4785 238 ETYFYLGKYYLSLGDLDEATALFKLAVAN 266 (297)
T ss_pred HHHHHHHHHHhccccHHHHHHHHHHHHHH
Confidence 34689999999999999999999988885
No 214
>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=23.74 E-value=1.8e+02 Score=22.62 Aligned_cols=46 Identities=20% Similarity=0.159 Sum_probs=35.2
Q ss_pred ccccHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCcceEEeecCceEEEEec
Q 025096 193 HQMKLDVIVKALKWLEMDMDVDEVECIVAILIHKNLVKGYFAHKSKVVVLSK 244 (258)
Q Consensus 193 ~~i~l~~i~~al~~~~~~~~~~evE~ila~LI~~G~IkGyI~~~~~~lVlsk 244 (258)
..++.++|+..++ ++...++.++..|-..|+|...=-...+ ..+++
T Consensus 24 ~~~s~~~ia~~~~-----ip~~~l~kil~~L~~~glv~s~~G~~Gg-y~l~~ 69 (135)
T TIGR02010 24 GPVTLADISERQG-----ISLSYLEQLFAKLRKAGLVKSVRGPGGG-YQLGR 69 (135)
T ss_pred CcCcHHHHHHHHC-----cCHHHHHHHHHHHHHCCceEEEeCCCCC-EeccC
Confidence 3589999999987 7999999999999999999753222223 34544
No 215
>KOG2002 consensus TPR-containing nuclear phosphoprotein that regulates K(+) uptake [Inorganic ion transport and metabolism]
Probab=23.71 E-value=2.3e+02 Score=29.88 Aligned_cols=40 Identities=15% Similarity=0.113 Sum_probs=32.2
Q ss_pred ccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCccCh
Q 025096 57 KRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNPQSE 96 (258)
Q Consensus 57 ~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~~~ 96 (258)
....+.-.-|+||.+.-.+.|++|-+.+..|.+.-|.+..
T Consensus 712 ~~~~~~vl~~Lara~y~~~~~~eak~~ll~a~~~~p~~~~ 751 (1018)
T KOG2002|consen 712 KKNRSEVLHYLARAWYEAGKLQEAKEALLKARHLAPSNTS 751 (1018)
T ss_pred ccCCHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhCCccch
Confidence 4556666778899988888899999999999988886654
No 216
>PF14561 TPR_20: Tetratricopeptide repeat; PDB: 3QOU_A 2R5S_A 3QDN_B.
Probab=23.70 E-value=2.1e+02 Score=20.66 Aligned_cols=46 Identities=11% Similarity=0.070 Sum_probs=32.5
Q ss_pred hhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCcc-ChHHHHHHHHHH
Q 025096 61 VTYMYYTGRLEVFNENFPAADQKLSYALINCNPQ-SEANIRMILKYL 106 (258)
Q Consensus 61 v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~-~~~~~~~IL~~L 106 (258)
+.-+|-.+..++..+++++|.+.|...++.-+.. ...-|+..+..+
T Consensus 22 ~~ar~~lA~~~~~~g~~e~Al~~Ll~~v~~dr~~~~~~ar~~ll~~f 68 (90)
T PF14561_consen 22 LDARYALADALLAAGDYEEALDQLLELVRRDRDYEDDAARKRLLDIF 68 (90)
T ss_dssp HHHHHHHHHHHHHTT-HHHHHHHHHHHHCC-TTCCCCHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCccccccHHHHHHHHHH
Confidence 4567889999999999999999999999975433 224444444333
No 217
>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional
Probab=23.68 E-value=2.6e+02 Score=29.69 Aligned_cols=65 Identities=14% Similarity=0.001 Sum_probs=43.9
Q ss_pred HHHHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCccC
Q 025096 22 CQLFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNPQS 95 (258)
Q Consensus 22 n~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~~ 95 (258)
..+-.++.++|+++.+...+...-.. -|+ ....++-.|..+...+++++|.+.+..|+..-|.+.
T Consensus 613 ~~LA~~l~~lG~~deA~~~l~~AL~l-~Pd--------~~~a~~nLG~aL~~~G~~eeAi~~l~~AL~l~P~~~ 677 (987)
T PRK09782 613 VARATIYRQRHNVPAAVSDLRAALEL-EPN--------NSNYQAALGYALWDSGDIAQSREMLERAHKGLPDDP 677 (987)
T ss_pred HHHHHHHHHCCCHHHHHHHHHHHHHh-CCC--------CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCH
Confidence 45567888899999888877543321 132 224566777777777788888888888877666543
No 218
>PF12645 HTH_16: Helix-turn-helix domain; InterPro: IPR024760 This domain appears to be a helix-turn-helix domain, suggesting a transcriptional regulatory protein. Some proteins with this domain are annotated as conjugative transposon proteins.
Probab=22.51 E-value=2.6e+02 Score=19.07 Aligned_cols=26 Identities=19% Similarity=0.367 Sum_probs=22.6
Q ss_pred HHHHHHHhCCHHHHHHHHHHcHHHHH
Q 025096 132 NIVQALRRGDLRLLRHALEEHEDQFL 157 (258)
Q Consensus 132 ~L~~av~~Gdl~~f~~~l~~~~~~f~ 157 (258)
+++.+-+.||..+.+++++.++....
T Consensus 2 ~vI~~A~~GD~~A~~~IL~~y~~yI~ 27 (65)
T PF12645_consen 2 EVIKAAKQGDPEAMEEILKHYEPYIS 27 (65)
T ss_pred HHHHHHHcCCHHHHHHHHHHHHHHHH
Confidence 57888899999999999999888555
No 219
>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=22.33 E-value=7.4e+02 Score=24.22 Aligned_cols=113 Identities=12% Similarity=0.158 Sum_probs=67.4
Q ss_pred HHHHHHHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCccChHH
Q 025096 19 YLTCQLFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNPQSEAN 98 (258)
Q Consensus 19 ~~~n~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~~~~~ 98 (258)
|+-+...|.+++.|+.+.+..+++-....+....+....-|-+=|.-=.|+-|...++|..|...+....++..
T Consensus 263 yiNsK~aKy~LRa~~~e~A~~~~~~Ftr~~~~~~~~L~~mQc~Wf~~e~a~a~~r~~~~~~ALk~~~~v~k~f~------ 336 (517)
T PF12569_consen 263 YINSKCAKYLLRAGRIEEAEKTASLFTREDVDPLSNLNDMQCMWFETECAEAYLRQGDYGLALKRFHAVLKHFD------ 336 (517)
T ss_pred HHHHHHHHHHHHCCCHHHHHHHHHhhcCCCCCcccCHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHH------
Confidence 56777788888888888888887765443211111111112232333367777777888777776655555321
Q ss_pred HHHHHHHHHHHHhhcCCCCChhhhhhccccccHHHHHHHHhCCHHHHHHHHHHcHHHHHHhcHHH
Q 025096 99 IRMILKYLIPVKLSIGILPKDWLLEKYNLVEYSNIVQALRRGDLRLLRHALEEHEDQFLRSGVYL 163 (258)
Q Consensus 99 ~~~IL~~LIp~~Ll~G~~P~~~ll~~~~l~~y~~L~~av~~Gdl~~f~~~l~~~~~~f~~~glyl 163 (258)
.+.-+.|.--.-++|.|.+..|-+.|. +++.+..+..|.
T Consensus 337 -------------------------~~~~DQfDFH~Yc~RK~t~r~Y~~~L~-~ed~l~~~~~y~ 375 (517)
T PF12569_consen 337 -------------------------DFEEDQFDFHSYCLRKMTLRAYVDMLR-WEDKLRSHPFYR 375 (517)
T ss_pred -------------------------HHhcccccHHHHHHhhccHHHHHHHHH-HHHHhhcCHHHH
Confidence 111122333344999999999999985 566566655554
No 220
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=22.16 E-value=1.9e+02 Score=20.48 Aligned_cols=40 Identities=8% Similarity=0.027 Sum_probs=31.8
Q ss_pred ccccHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCcceEEeecCc
Q 025096 193 HQMKLDVIVKALKWLEMDMDVDEVECIVAILIHKNLVKGYFAHKS 237 (258)
Q Consensus 193 ~~i~l~~i~~al~~~~~~~~~~evE~ila~LI~~G~IkGyI~~~~ 237 (258)
..++|+++.+.+. ++...+-..+..|...|+|+-.-....
T Consensus 13 ~~~~f~~L~~~l~-----lt~g~Ls~hL~~Le~~GyV~~~k~~~~ 52 (80)
T PF13601_consen 13 EEATFSELKEELG-----LTDGNLSKHLKKLEEAGYVEVEKEFEG 52 (80)
T ss_dssp SEEEHHHHHHHTT-------HHHHHHHHHHHHHTTSEEEEEE-SS
T ss_pred CCCCHHHHHHHhC-----cCHHHHHHHHHHHHHCCCEEEEEeccC
Confidence 4689999999987 789999999999999999977555443
No 221
>PRK12370 invasion protein regulator; Provisional
Probab=22.07 E-value=4e+02 Score=25.92 Aligned_cols=64 Identities=8% Similarity=-0.154 Sum_probs=43.4
Q ss_pred HHHHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCcc
Q 025096 22 CQLFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNPQ 94 (258)
Q Consensus 22 n~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~ 94 (258)
..+..+|+..|+++.+...+...-.. -|. . ....+..+..++..+++++|...+..+....+++
T Consensus 376 ~~lg~~l~~~G~~~eAi~~~~~Al~l-~P~------~--~~~~~~~~~~~~~~g~~eeA~~~~~~~l~~~~p~ 439 (553)
T PRK12370 376 YYYGWNLFMAGQLEEALQTINECLKL-DPT------R--AAAGITKLWITYYHTGIDDAIRLGDELRSQHLQD 439 (553)
T ss_pred HHHHHHHHHCCCHHHHHHHHHHHHhc-CCC------C--hhhHHHHHHHHHhccCHHHHHHHHHHHHHhcccc
Confidence 44567889999999999888554331 132 1 1123445556667889999999999998765443
No 222
>KOG1173 consensus Anaphase-promoting complex (APC), Cdc16 subunit [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=22.00 E-value=1.1e+02 Score=30.11 Aligned_cols=73 Identities=15% Similarity=0.199 Sum_probs=0.0
Q ss_pred HHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCccChHHHHHHHHHHH
Q 025096 28 YFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNPQSEANIRMILKYLI 107 (258)
Q Consensus 28 yf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~~~~~~~~IL~~LI 107 (258)
|.++|++.+++.++..--.- .|+ ..--+-+.|.++.-.+.|.+|..+|+.|+..-+.....-. .|.
T Consensus 390 y~~t~n~kLAe~Ff~~A~ai-~P~--------Dplv~~Elgvvay~~~~y~~A~~~f~~~l~~ik~~~~e~~-----~w~ 455 (611)
T KOG1173|consen 390 YMRTNNLKLAEKFFKQALAI-APS--------DPLVLHELGVVAYTYEEYPEALKYFQKALEVIKSVLNEKI-----FWE 455 (611)
T ss_pred HHHhccHHHHHHHHHHHHhc-CCC--------cchhhhhhhheeehHhhhHHHHHHHHHHHHHhhhcccccc-----chh
Q ss_pred HHHhhcC
Q 025096 108 PVKLSIG 114 (258)
Q Consensus 108 p~~Ll~G 114 (258)
|....+|
T Consensus 456 p~~~NLG 462 (611)
T KOG1173|consen 456 PTLNNLG 462 (611)
T ss_pred HHHHhHH
No 223
>COG4235 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]
Probab=21.52 E-value=1e+02 Score=27.78 Aligned_cols=81 Identities=14% Similarity=-0.004 Sum_probs=50.2
Q ss_pred HHHHHHHHHHHHHHHhcCChhhHHHHHH---Hhhcc--CCCCCCC------------CCccchhhhhhhhhHHhhhhcCh
Q 025096 15 VGALYLTCQLFKIYFKLGTVHLCRSVIR---SIETA--RIFDFEE------------FPKRDKVTYMYYTGRLEVFNENF 77 (258)
Q Consensus 15 ~~~~~~~n~l~kiyf~l~~~~~~~~l~~---~i~~~--~~p~~~~------------~~~~~~v~y~YY~G~~~~~~~~~ 77 (258)
.++..++..+.--|+..+.+.....--. .+... ..|.-+. -..-+.+.=...+|++|+..+++
T Consensus 93 ~~~v~~~~v~~~~y~~~g~y~~vg~~~q~~~r~~~~~a~~~~~~~~~~l~a~Le~~L~~nP~d~egW~~Lg~~ym~~~~~ 172 (287)
T COG4235 93 ARVVALVAVLALSYLLLGLYQAVGAPEQPADRLADPLAQPPAEQEMEALIARLETHLQQNPGDAEGWDLLGRAYMALGRA 172 (287)
T ss_pred HHHHHHHHHHHHHHHHhhhhhhcCCccccchhhhcccccCCCcccHHHHHHHHHHHHHhCCCCchhHHHHHHHHHHhcch
Confidence 3466666777777777776654432111 11110 1111000 11223445568899999999999
Q ss_pred HHHHHHHHHHHHhcCccC
Q 025096 78 PAADQKLSYALINCNPQS 95 (258)
Q Consensus 78 ~~A~~~L~~A~~~c~~~~ 95 (258)
..|...+..|.+..|++.
T Consensus 173 ~~A~~AY~~A~rL~g~n~ 190 (287)
T COG4235 173 SDALLAYRNALRLAGDNP 190 (287)
T ss_pred hHHHHHHHHHHHhCCCCH
Confidence 999999999999988653
No 224
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=21.48 E-value=2.9e+02 Score=21.50 Aligned_cols=33 Identities=18% Similarity=0.174 Sum_probs=28.2
Q ss_pred ccccHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCcce
Q 025096 193 HQMKLDVIVKALKWLEMDMDVDEVECIVAILIHKNLVK 230 (258)
Q Consensus 193 ~~i~l~~i~~al~~~~~~~~~~evE~ila~LI~~G~Ik 230 (258)
..++.++++..+. ++...|--.+..|..+|+|.
T Consensus 21 ~~~~~~ela~~l~-----vs~~svs~~l~~L~~~Gli~ 53 (142)
T PRK03902 21 GYARVSDIAEALS-----VHPSSVTKMVQKLDKDEYLI 53 (142)
T ss_pred CCcCHHHHHHHhC-----CChhHHHHHHHHHHHCCCEE
Confidence 3457899999987 68888999999999999986
No 225
>PRK15331 chaperone protein SicA; Provisional
Probab=21.44 E-value=2.2e+02 Score=23.40 Aligned_cols=58 Identities=16% Similarity=0.166 Sum_probs=41.5
Q ss_pred HHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhh--hhcChHHHHHHHHHHHHhcCcc
Q 025096 26 KIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEV--FNENFPAADQKLSYALINCNPQ 94 (258)
Q Consensus 26 kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~--~~~~~~~A~~~L~~A~~~c~~~ 94 (258)
.-.+..|+++.+.++++-+-.- + -..+.|+.|.=.+ ..++|++|...+..|+..-+.+
T Consensus 45 y~~y~~Gk~~eA~~~F~~L~~~---d--------~~n~~Y~~GLaa~~Q~~k~y~~Ai~~Y~~A~~l~~~d 104 (165)
T PRK15331 45 YEFYNQGRLDEAETFFRFLCIY---D--------FYNPDYTMGLAAVCQLKKQFQKACDLYAVAFTLLKND 104 (165)
T ss_pred HHHHHCCCHHHHHHHHHHHHHh---C--------cCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccCC
Confidence 4567889999999999877531 1 1225567776665 5589999999999998865543
No 226
>PF04190 DUF410: Protein of unknown function (DUF410) ; InterPro: IPR007317 This is a family of conserved eukaryotic proteins with undetermined function.; PDB: 3LKU_E 2WPV_G.
Probab=21.36 E-value=5.2e+02 Score=22.56 Aligned_cols=32 Identities=16% Similarity=0.262 Sum_probs=23.2
Q ss_pred HHHHHHHhCCHHHHHHHHHHcHHHHHHhcHHH
Q 025096 132 NIVQALRRGDLRLLRHALEEHEDQFLRSGVYL 163 (258)
Q Consensus 132 ~L~~av~~Gdl~~f~~~l~~~~~~f~~~glyl 163 (258)
-|+.++.+++...|....++++..+.++..+.
T Consensus 197 lLl~t~e~~~~~~F~~L~~~Y~~~L~rd~~~~ 228 (260)
T PF04190_consen 197 LLLLTCERDNLPLFKKLCEKYKPSLKRDPSFK 228 (260)
T ss_dssp HHHHHHHHT-HHHHHHHHHHTHH---HHHHTH
T ss_pred HHHHHHhcCcHHHHHHHHHHhCccccccHHHH
Confidence 46789999999999999999988776665543
No 227
>PF12862 Apc5: Anaphase-promoting complex subunit 5
Probab=21.33 E-value=1.8e+02 Score=20.95 Aligned_cols=31 Identities=16% Similarity=0.060 Sum_probs=26.0
Q ss_pred hhhHHhhhhcChHHHHHHHHHHHHhcCccCh
Q 025096 66 YTGRLEVFNENFPAADQKLSYALINCNPQSE 96 (258)
Q Consensus 66 Y~G~~~~~~~~~~~A~~~L~~A~~~c~~~~~ 96 (258)
-.|.++...|++++|...+.+|++...+...
T Consensus 46 ~lA~~~~~~G~~~~A~~~l~eAi~~Are~~D 76 (94)
T PF12862_consen 46 NLAELHRRFGHYEEALQALEEAIRLARENGD 76 (94)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHHHHHHHCC
Confidence 3677778889999999999999998876554
No 228
>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=21.25 E-value=5.4e+02 Score=23.77 Aligned_cols=64 Identities=8% Similarity=-0.009 Sum_probs=33.9
Q ss_pred HHHHHHHhcCChhhHHHHHHHhhccCCCCCCCCCccchhhhhhhhhHHhhhhcChHHHHHHHHHHHHhcCcc
Q 025096 23 QLFKIYFKLGTVHLCRSVIRSIETARIFDFEEFPKRDKVTYMYYTGRLEVFNENFPAADQKLSYALINCNPQ 94 (258)
Q Consensus 23 ~l~kiyf~l~~~~~~~~l~~~i~~~~~p~~~~~~~~~~v~y~YY~G~~~~~~~~~~~A~~~L~~A~~~c~~~ 94 (258)
...+++.+.|+++.+...++..... .|. .. +...--.+++++.++++++|.+.++......|.+
T Consensus 123 laA~aa~~~g~~~~A~~~l~~a~~~-~p~------~~-l~~~~~~a~l~l~~~~~~~Al~~l~~l~~~~P~~ 186 (409)
T TIGR00540 123 KAAEAAQQRGDEARANQHLEEAAEL-AGN------DN-ILVEIARTRILLAQNELHAARHGVDKLLEMAPRH 186 (409)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHh-CCc------Cc-hHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCC
Confidence 3445666666666666666543221 121 11 1111112666666677777777766666665544
No 229
>PRK06926 flagellar motor protein MotP; Reviewed
Probab=21.13 E-value=1.1e+02 Score=27.18 Aligned_cols=50 Identities=24% Similarity=0.461 Sum_probs=39.2
Q ss_pred ccHHHHHHHHhCCHHHHHHHHHHcHHHHHHhcHHHHHHhhHHHHHHHHHH
Q 025096 129 EYSNIVQALRRGDLRLLRHALEEHEDQFLRSGVYLVLEKLELQVYQRLFK 178 (258)
Q Consensus 129 ~y~~L~~av~~Gdl~~f~~~l~~~~~~f~~~glylll~~l~~~v~r~L~k 178 (258)
...++.+-.|+..+-.+++.+++.++.|+++|+-+++.-...-.+|.++.
T Consensus 85 ~l~~la~~aRk~GlLaLE~~~~~~~d~Fl~~gl~lvvDG~~~~~i~~iLe 134 (271)
T PRK06926 85 TFVSLSEKARREGLLSLEAELEEVKDPFIKKGLLLAIDGWEPETIRDIMM 134 (271)
T ss_pred HHHHHHHHHHhcCHHHHHhhhcCCCChHHHHHHHHHHCCCCHHHHHHHHH
Confidence 45678888899999999999999889999999998885544444454444
No 230
>PF08069 Ribosomal_S13_N: Ribosomal S13/S15 N-terminal domain; InterPro: IPR012606 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 [, ]. This domain is found at the N terminus of ribosomal S13 and S15 proteins. This domain is also identified as NUC021 [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3U5C_N 3O30_G 3IZB_O 3O2Z_G 3U5G_N 2XZN_O 2XZM_O 3IZ6_O.
Probab=20.77 E-value=62 Score=22.02 Aligned_cols=19 Identities=32% Similarity=0.424 Sum_probs=16.1
Q ss_pred CCHHHHHHHHHHHHHcCcc
Q 025096 211 MDVDEVECIVAILIHKNLV 229 (258)
Q Consensus 211 ~~~~evE~ila~LI~~G~I 229 (258)
.+.||||.++.+|-.+|+-
T Consensus 28 ~~~~eVe~~I~klakkG~t 46 (60)
T PF08069_consen 28 YSPEEVEELIVKLAKKGLT 46 (60)
T ss_dssp S-HHHHHHHHHHHCCTTHC
T ss_pred CCHHHHHHHHHHHHHcCCC
Confidence 6899999999999998874
No 231
>KOG2376 consensus Signal recognition particle, subunit Srp72 [Intracellular trafficking, secretion, and vesicular transport]
Probab=20.63 E-value=2.8e+02 Score=27.66 Aligned_cols=69 Identities=17% Similarity=0.261 Sum_probs=43.9
Q ss_pred HHHHHhcCChhhHHHHHHHhhccCCCCC--------------------CCCC--ccchhhhhhhhhHHhhhhcChHHHHH
Q 025096 25 FKIYFKLGTVHLCRSVIRSIETARIFDF--------------------EEFP--KRDKVTYMYYTGRLEVFNENFPAADQ 82 (258)
Q Consensus 25 ~kiyf~l~~~~~~~~l~~~i~~~~~p~~--------------------~~~~--~~~~v~y~YY~G~~~~~~~~~~~A~~ 82 (258)
..+.-++++++.|-.+...+-+++.++. ...| ..+...-.|-.+-+++-.++|.+|.+
T Consensus 117 AQvlYrl~~ydealdiY~~L~kn~~dd~d~~~r~nl~a~~a~l~~~~~q~v~~v~e~syel~yN~Ac~~i~~gky~qA~e 196 (652)
T KOG2376|consen 117 AQVLYRLERYDEALDIYQHLAKNNSDDQDEERRANLLAVAAALQVQLLQSVPEVPEDSYELLYNTACILIENGKYNQAIE 196 (652)
T ss_pred HHHHHHHhhHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHhhhHHHHHhccCCCcchHHHHHHHHHHHHhcccHHHHHH
Confidence 3455577777777777666633222211 0111 12233445667777888899999999
Q ss_pred HHHHHHHhcCc
Q 025096 83 KLSYALINCNP 93 (258)
Q Consensus 83 ~L~~A~~~c~~ 93 (258)
.|+.|.+.|.+
T Consensus 197 lL~kA~~~~~e 207 (652)
T KOG2376|consen 197 LLEKALRICRE 207 (652)
T ss_pred HHHHHHHHHHH
Confidence 99999998874
No 232
>KOG3233 consensus RNA polymerase III, subunit C34 [Transcription]
Probab=20.29 E-value=2.1e+02 Score=25.69 Aligned_cols=78 Identities=15% Similarity=0.264 Sum_probs=53.4
Q ss_pred HHHHHhcHH-HHHHhhHHHHHHHHHHHHHHHhhc-CCCC--C-CccccHHHHHHHHH---hccCCCCHHHHHHHHHHHHH
Q 025096 154 DQFLRSGVY-LVLEKLELQVYQRLFKKIYIIQKQ-KDPS--K-AHQMKLDVIVKALK---WLEMDMDVDEVECIVAILIH 225 (258)
Q Consensus 154 ~~f~~~gly-lll~~l~~~v~r~L~kkv~~~~~~-~~~~--~-~~~i~l~~i~~al~---~~~~~~~~~evE~ila~LI~ 225 (258)
.||-.+.+- ..++.|..+|+|-|=++.+..-.+ .+|. + .+-.+..+|..-+. .+..+++++++|.++=-+|+
T Consensus 159 ~WytDqdlDvEfIe~L~~~c~~fl~~~~~~~~~~~~gp~~~~~~~~~t~~ei~~~i~~l~I~nV~Lsl~dleti~~vlvy 238 (297)
T KOG3233|consen 159 TWYTDQDLDVEFIEVLKQICVRFLESKRFPAEKNVEGPMFVRNESYPTVQEIKEFIRNLNILNVELSLEDLETILDVLVY 238 (297)
T ss_pred cccccccccHHHHHHHHHHHHHHHHhcccchhhccccchhhhhccCCCHHHHHHHHHHcCcccccccHHHHHHHhHHhee
Confidence 455555554 488999999998887776655311 1221 1 34466666655543 44566899999999999999
Q ss_pred cCcceE
Q 025096 226 KNLVKG 231 (258)
Q Consensus 226 ~G~IkG 231 (258)
+|.+-=
T Consensus 239 DGkvE~ 244 (297)
T KOG3233|consen 239 DGKVEK 244 (297)
T ss_pred cceeee
Confidence 999955
Done!