Query 024742
Match_columns 263
No_of_seqs 166 out of 795
Neff 8.0
Searched_HMMs 46136
Date Fri Mar 29 07:03:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024742.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024742hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2817 Predicted E3 ubiquitin 100.0 6.7E-65 1.5E-69 452.0 15.3 262 1-262 127-394 (394)
2 KOG0396 Uncharacterized conser 100.0 1.3E-64 2.8E-69 445.2 15.3 261 1-263 126-389 (389)
3 COG5109 Uncharacterized conser 100.0 4.9E-41 1.1E-45 289.5 13.5 257 4-262 114-396 (396)
4 PF10607 CLTH: CTLH/CRA C-term 100.0 2.3E-34 5E-39 231.6 14.0 142 28-169 2-145 (145)
5 KOG2659 LisH motif-containing 100.0 1.7E-28 3.7E-33 206.6 13.6 165 1-166 37-205 (228)
6 smart00757 CRA CT11-RanBPM. pr 99.8 5.8E-19 1.3E-23 132.7 8.5 94 80-173 1-98 (99)
7 PF13445 zf-RING_UBOX: RING-ty 99.6 9.2E-16 2E-20 97.2 3.5 42 205-246 1-43 (43)
8 smart00668 CTLH C-terminal to 99.4 3.8E-13 8.2E-18 91.1 5.6 55 28-82 2-56 (58)
9 smart00504 Ubox Modified RING 99.3 5E-12 1.1E-16 87.0 4.3 53 203-261 2-54 (63)
10 PF04564 U-box: U-box domain; 99.1 1.4E-10 3.1E-15 82.3 3.7 55 201-260 3-57 (73)
11 PF04641 Rtf2: Rtf2 RING-finge 98.9 1.5E-09 3.3E-14 95.5 4.2 60 198-261 109-169 (260)
12 PF15227 zf-C3HC4_4: zinc fing 98.7 8.2E-09 1.8E-13 65.2 3.3 41 205-248 1-42 (42)
13 PLN03208 E3 ubiquitin-protein 98.7 1.4E-08 3E-13 84.3 4.2 59 201-262 17-88 (193)
14 PF11789 zf-Nse: Zinc-finger o 98.7 1.7E-08 3.6E-13 68.0 3.3 45 201-249 10-55 (57)
15 KOG3113 Uncharacterized conser 98.6 1.6E-08 3.5E-13 86.1 3.1 57 199-260 108-165 (293)
16 KOG0320 Predicted E3 ubiquitin 98.5 5.9E-08 1.3E-12 78.8 2.5 62 197-262 126-187 (187)
17 KOG0978 E3 ubiquitin ligase in 98.5 3.2E-08 6.9E-13 96.1 0.7 61 197-262 638-698 (698)
18 PF14634 zf-RING_5: zinc-RING 98.5 1.1E-07 2.3E-12 60.7 2.7 43 205-250 2-44 (44)
19 KOG0293 WD40 repeat-containing 98.4 7.8E-07 1.7E-11 80.9 8.1 162 1-169 28-216 (519)
20 PF13639 zf-RING_2: Ring finge 98.4 2.3E-07 5E-12 59.1 3.3 43 204-249 2-44 (44)
21 PF00097 zf-C3HC4: Zinc finger 98.3 1.1E-06 2.5E-11 54.9 4.1 40 205-248 1-41 (41)
22 PF13923 zf-C3HC4_2: Zinc fing 98.2 1.5E-06 3.1E-11 53.9 3.6 38 205-248 1-39 (39)
23 KOG0823 Predicted E3 ubiquitin 98.2 1.3E-06 2.9E-11 74.0 4.3 61 198-261 43-103 (230)
24 TIGR00599 rad18 DNA repair pro 98.2 1.4E-06 3E-11 80.5 3.8 66 190-261 14-79 (397)
25 PF13920 zf-C3HC4_3: Zinc fing 98.0 1.2E-05 2.5E-10 52.6 4.0 45 203-253 3-48 (50)
26 TIGR00570 cdk7 CDK-activating 97.9 8.8E-06 1.9E-10 72.5 3.8 56 204-261 5-62 (309)
27 smart00184 RING Ring finger. E 97.9 1E-05 2.2E-10 48.9 2.8 39 205-248 1-39 (39)
28 cd00162 RING RING-finger (Real 97.9 1.2E-05 2.7E-10 50.3 3.2 43 205-251 2-44 (45)
29 KOG0317 Predicted E3 ubiquitin 97.8 4.6E-05 9.9E-10 66.7 5.4 67 189-261 226-292 (293)
30 KOG3039 Uncharacterized conser 97.7 2.5E-05 5.5E-10 66.7 3.6 60 198-260 216-277 (303)
31 PHA02929 N1R/p28-like protein; 97.7 2.8E-05 6E-10 67.3 3.5 48 203-253 175-227 (238)
32 KOG2164 Predicted E3 ubiquitin 97.6 4.4E-05 9.5E-10 71.5 3.2 58 202-262 186-245 (513)
33 PHA02926 zinc finger-like prot 97.5 9.5E-05 2.1E-09 62.5 3.5 59 203-261 171-238 (242)
34 KOG2879 Predicted E3 ubiquitin 97.2 0.00028 6E-09 61.4 3.4 58 199-259 236-293 (298)
35 KOG1734 Predicted RING-contain 97.2 8.9E-05 1.9E-09 64.2 0.3 63 191-256 215-284 (328)
36 PF12678 zf-rbx1: RING-H2 zinc 97.1 0.00069 1.5E-08 47.9 3.7 31 216-249 43-73 (73)
37 KOG2177 Predicted E3 ubiquitin 97.0 0.00023 5E-09 62.4 1.1 45 199-249 10-54 (386)
38 KOG0287 Postreplication repair 97.0 0.00014 3.1E-09 64.8 -0.9 65 192-262 13-77 (442)
39 COG5243 HRD1 HRD ubiquitin lig 96.9 0.00093 2E-08 60.5 3.7 51 199-252 284-344 (491)
40 KOG1477 SPRY domain-containing 96.9 0.00074 1.6E-08 64.2 3.0 175 1-182 260-458 (469)
41 PF14447 Prok-RING_4: Prokaryo 96.8 0.001 2.2E-08 43.9 2.2 35 218-257 20-54 (55)
42 COG5574 PEX10 RING-finger-cont 96.7 0.001 2.3E-08 57.6 2.3 51 202-257 215-266 (271)
43 COG5432 RAD18 RING-finger-cont 96.4 0.0012 2.7E-08 57.8 0.9 63 191-259 14-76 (391)
44 PF12861 zf-Apc11: Anaphase-pr 96.3 0.0044 9.5E-08 44.9 3.2 51 205-256 35-85 (85)
45 COG5540 RING-finger-containing 95.8 0.007 1.5E-07 53.5 2.7 49 203-253 324-372 (374)
46 KOG4628 Predicted E3 ubiquitin 95.6 0.0068 1.5E-07 55.1 2.2 48 203-252 230-277 (348)
47 PF02891 zf-MIZ: MIZ/SP-RING z 95.3 0.027 5.8E-07 36.7 3.6 45 202-250 2-49 (50)
48 KOG0802 E3 ubiquitin ligase [P 95.2 0.012 2.7E-07 57.2 2.5 52 201-255 290-343 (543)
49 smart00744 RINGv The RING-vari 95.2 0.028 6.1E-07 36.5 3.3 44 204-249 1-49 (49)
50 KOG2979 Protein involved in DN 94.9 0.016 3.5E-07 50.2 2.1 46 202-251 176-222 (262)
51 KOG0826 Predicted E3 ubiquitin 94.8 0.017 3.8E-07 51.6 2.1 55 203-262 301-355 (357)
52 PF14835 zf-RING_6: zf-RING of 94.6 0.0071 1.5E-07 41.3 -0.6 48 203-258 8-56 (65)
53 COG5222 Uncharacterized conser 94.6 0.02 4.3E-07 50.6 1.9 43 203-250 275-318 (427)
54 PF08513 LisH: LisH; InterPro 94.0 0.024 5.3E-07 32.0 0.9 17 1-17 11-27 (27)
55 KOG0311 Predicted E3 ubiquitin 93.9 0.0074 1.6E-07 54.5 -2.1 52 197-253 38-90 (381)
56 COG5152 Uncharacterized conser 93.7 0.029 6.3E-07 46.8 1.1 45 202-252 196-240 (259)
57 KOG1645 RING-finger-containing 93.4 0.028 6.1E-07 51.7 0.6 58 204-262 6-65 (463)
58 KOG0828 Predicted E3 ubiquitin 93.3 0.046 9.9E-07 51.5 1.9 59 192-252 548-633 (636)
59 smart00667 LisH Lissencephaly 93.1 0.059 1.3E-06 31.2 1.6 20 1-20 14-33 (34)
60 KOG3800 Predicted E3 ubiquitin 92.8 0.078 1.7E-06 46.8 2.5 38 219-258 19-56 (300)
61 PF14570 zf-RING_4: RING/Ubox 92.1 0.25 5.3E-06 31.9 3.5 47 205-253 1-48 (48)
62 KOG4185 Predicted E3 ubiquitin 91.9 0.16 3.5E-06 45.3 3.5 49 201-251 2-53 (296)
63 KOG0824 Predicted E3 ubiquitin 91.8 0.086 1.9E-06 46.8 1.5 39 215-255 17-55 (324)
64 KOG1814 Predicted E3 ubiquitin 91.6 0.12 2.7E-06 47.7 2.4 41 197-237 179-219 (445)
65 smart00531 TFIIE Transcription 90.6 0.25 5.5E-06 39.6 3.1 34 222-256 104-137 (147)
66 KOG1002 Nucleotide excision re 89.7 0.19 4.1E-06 47.9 1.8 54 200-256 534-589 (791)
67 KOG1813 Predicted E3 ubiquitin 89.6 0.14 2.9E-06 45.4 0.8 45 203-253 242-286 (313)
68 COG4391 Uncharacterized protei 89.5 0.18 3.9E-06 34.0 1.1 18 238-255 44-61 (62)
69 PF10367 Vps39_2: Vacuolar sor 89.3 0.13 2.9E-06 38.4 0.4 28 205-233 81-108 (109)
70 KOG0883 Cyclophilin type, U bo 88.9 0.22 4.7E-06 45.8 1.6 68 192-260 91-159 (518)
71 KOG1940 Zn-finger protein [Gen 88.3 0.28 6E-06 43.4 1.8 46 202-250 158-204 (276)
72 KOG1941 Acetylcholine receptor 88.3 0.19 4.2E-06 46.1 0.8 47 203-250 366-413 (518)
73 KOG4159 Predicted E3 ubiquitin 88.2 0.26 5.7E-06 46.0 1.6 48 200-253 82-129 (398)
74 PF04494 TFIID_90kDa: WD40 ass 87.9 0.76 1.6E-05 36.6 4.0 53 53-109 33-85 (142)
75 PF11793 FANCL_C: FANCL C-term 87.8 0.32 6.9E-06 34.0 1.5 52 204-255 4-68 (70)
76 PF04710 Pellino: Pellino; In 87.7 0.16 3.5E-06 46.8 0.0 43 220-262 362-411 (416)
77 PF05605 zf-Di19: Drought indu 87.7 0.14 3.1E-06 33.7 -0.3 16 242-257 2-17 (54)
78 KOG0804 Cytoplasmic Zn-finger 87.3 0.3 6.5E-06 45.7 1.4 45 204-253 177-222 (493)
79 PF03966 Trm112p: Trm112p-like 87.2 0.63 1.4E-05 32.2 2.8 17 240-256 51-67 (68)
80 PF14353 CpXC: CpXC protein 87.0 0.5 1.1E-05 36.8 2.4 26 230-255 26-51 (128)
81 KOG1785 Tyrosine kinase negati 85.9 0.39 8.4E-06 44.4 1.3 53 204-260 371-423 (563)
82 cd08044 TAF5_NTD2 TAF5_NTD2 is 85.2 0.96 2.1E-05 35.6 3.2 54 54-111 23-76 (133)
83 KOG1493 Anaphase-promoting com 84.9 0.28 6E-06 34.7 -0.0 43 214-256 41-84 (84)
84 COG5175 MOT2 Transcriptional r 82.7 1 2.2E-05 40.8 2.5 55 205-261 17-72 (480)
85 KOG0827 Predicted E3 ubiquitin 82.4 0.97 2.1E-05 41.7 2.4 46 204-249 6-52 (465)
86 PF13465 zf-H2C2_2: Zinc-finge 81.6 0.79 1.7E-05 25.3 1.0 15 239-253 11-25 (26)
87 PF00096 zf-C2H2: Zinc finger, 81.5 0.71 1.5E-05 24.3 0.8 14 243-256 1-14 (23)
88 KOG0825 PHD Zn-finger protein 81.5 0.43 9.3E-06 47.6 -0.2 77 177-258 97-176 (1134)
89 KOG0297 TNF receptor-associate 80.9 0.74 1.6E-05 43.1 1.1 51 200-256 19-70 (391)
90 KOG2034 Vacuolar sorting prote 80.8 0.72 1.6E-05 46.7 1.0 21 217-237 831-851 (911)
91 KOG3161 Predicted E3 ubiquitin 80.6 0.55 1.2E-05 45.9 0.2 40 202-246 11-51 (861)
92 PF05290 Baculo_IE-1: Baculovi 80.5 1.7 3.6E-05 34.2 2.8 55 201-257 79-136 (140)
93 KOG3002 Zn finger protein [Gen 80.4 1.2 2.6E-05 40.1 2.3 48 197-253 43-91 (299)
94 KOG3039 Uncharacterized conser 79.1 1.5 3.2E-05 38.1 2.3 32 201-235 42-73 (303)
95 KOG2114 Vacuolar assembly/sort 79.1 1 2.3E-05 45.3 1.5 39 204-251 842-881 (933)
96 PF13913 zf-C2HC_2: zinc-finge 78.2 0.5 1.1E-05 26.0 -0.5 16 242-257 2-17 (25)
97 PF09723 Zn-ribbon_8: Zinc rib 77.7 0.36 7.7E-06 30.1 -1.4 26 221-250 9-34 (42)
98 KOG1039 Predicted E3 ubiquitin 77.4 1.7 3.7E-05 39.8 2.3 61 193-253 152-221 (344)
99 PF10915 DUF2709: Protein of u 76.6 3.4 7.3E-05 34.5 3.6 43 197-253 82-124 (238)
100 PF04710 Pellino: Pellino; In 76.4 0.83 1.8E-05 42.2 0.0 40 215-254 300-340 (416)
101 KOG4367 Predicted Zn-finger pr 75.8 1.2 2.7E-05 41.6 1.0 32 203-237 5-36 (699)
102 PF13894 zf-C2H2_4: C2H2-type 75.7 1.4 3E-05 22.9 0.8 14 243-256 1-14 (24)
103 PF00412 LIM: LIM domain; Int 75.7 1.3 2.8E-05 29.0 0.8 55 179-235 1-57 (58)
104 KOG0275 Conserved WD40 repeat- 75.5 11 0.00023 34.4 6.7 123 6-141 23-151 (508)
105 PF12906 RINGv: RING-variant d 75.4 2.2 4.7E-05 27.3 1.8 42 205-248 1-47 (47)
106 PF10607 CLTH: CTLH/CRA C-term 75.3 6.8 0.00015 30.7 5.1 53 2-54 12-67 (145)
107 COG5194 APC11 Component of SCF 75.1 2.9 6.2E-05 29.9 2.4 50 205-257 34-85 (88)
108 PF12660 zf-TFIIIC: Putative z 74.2 0.58 1.3E-05 35.0 -1.3 48 205-252 17-65 (99)
109 smart00782 PhnA_Zn_Ribbon PhnA 74.2 1.5 3.3E-05 28.1 0.8 37 176-212 7-46 (47)
110 PF14559 TPR_19: Tetratricopep 73.6 19 0.00042 23.6 6.4 66 37-109 1-66 (68)
111 PF04641 Rtf2: Rtf2 RING-finge 73.0 6 0.00013 34.8 4.6 60 197-262 29-93 (260)
112 PHA02862 5L protein; Provision 72.7 3.7 8E-05 32.8 2.8 47 204-255 4-55 (156)
113 KOG2462 C2H2-type Zn-finger pr 72.4 3.3 7.1E-05 36.5 2.7 77 177-254 162-255 (279)
114 PHA02825 LAP/PHD finger-like p 72.2 3.9 8.4E-05 33.2 2.9 49 204-257 10-63 (162)
115 PF10276 zf-CHCC: Zinc-finger 71.9 2 4.3E-05 26.6 0.9 12 241-252 28-39 (40)
116 cd00350 rubredoxin_like Rubred 71.7 2.8 6.1E-05 24.5 1.5 9 242-250 17-25 (33)
117 COG1579 Zn-ribbon protein, pos 71.6 2.8 6E-05 36.5 2.1 47 201-256 189-235 (239)
118 KOG2910 Uncharacterized conser 70.7 14 0.0003 30.9 5.8 63 30-94 42-117 (209)
119 PF14569 zf-UDP: Zinc-binding 70.0 8.5 0.00018 27.4 3.8 54 199-254 6-63 (80)
120 PF02591 DUF164: Putative zinc 68.7 6.4 0.00014 25.9 3.0 29 222-251 27-55 (56)
121 cd00729 rubredoxin_SM Rubredox 67.9 3.7 8.1E-05 24.3 1.5 17 202-218 2-18 (34)
122 KOG1001 Helicase-like transcri 67.7 1.5 3.2E-05 43.9 -0.5 50 203-257 455-504 (674)
123 PF13719 zinc_ribbon_5: zinc-r 67.7 3.5 7.6E-05 24.8 1.4 15 239-253 22-36 (37)
124 PF00627 UBA: UBA/TS-N domain; 67.6 8.3 0.00018 23.0 3.0 18 33-50 18-37 (37)
125 TIGR01206 lysW lysine biosynth 66.5 2.8 6.1E-05 27.7 0.8 16 242-257 2-17 (54)
126 TIGR02098 MJ0042_CXXC MJ0042 f 65.9 2.8 6E-05 25.2 0.7 14 243-256 3-16 (38)
127 PTZ00196 60S ribosomal protein 65.6 18 0.00039 27.0 5.0 44 66-109 48-93 (98)
128 PF14276 DUF4363: Domain of un 65.5 58 0.0013 24.7 8.4 50 26-75 27-76 (121)
129 PF09538 FYDLN_acid: Protein o 65.5 3.7 8E-05 31.2 1.4 14 242-255 26-39 (108)
130 KOG3842 Adaptor protein Pellin 65.3 3.7 8E-05 37.0 1.6 33 221-253 376-414 (429)
131 PF04423 Rad50_zn_hook: Rad50 65.1 3.6 7.8E-05 26.9 1.2 14 244-257 22-35 (54)
132 smart00668 CTLH C-terminal to 64.8 10 0.00022 24.5 3.3 28 69-96 4-31 (58)
133 PF06676 DUF1178: Protein of u 64.7 6.8 0.00015 31.5 2.9 29 222-252 9-42 (148)
134 PF14255 Cys_rich_CPXG: Cystei 62.2 3.1 6.7E-05 27.3 0.4 12 243-254 1-12 (52)
135 KOG2169 Zn-finger transcriptio 61.9 6.9 0.00015 39.0 3.0 55 201-258 305-361 (636)
136 cd00194 UBA Ubiquitin Associat 61.8 12 0.00026 22.1 3.0 21 31-51 15-37 (38)
137 COG1675 TFA1 Transcription ini 61.8 6 0.00013 32.8 2.1 37 218-259 113-149 (176)
138 PF13717 zinc_ribbon_4: zinc-r 61.5 4.3 9.4E-05 24.3 0.9 16 242-257 2-17 (36)
139 PF10537 WAC_Acf1_DNA_bd: ATP- 61.0 12 0.00025 28.2 3.4 38 201-251 2-39 (102)
140 COG1655 Uncharacterized protei 60.8 4.1 8.8E-05 35.1 1.0 34 177-210 20-70 (267)
141 PF01158 Ribosomal_L36e: Ribos 59.5 22 0.00047 26.5 4.5 41 69-109 51-93 (98)
142 PRK11088 rrmA 23S rRNA methylt 59.4 5 0.00011 35.3 1.4 25 203-227 3-27 (272)
143 TIGR02605 CxxC_CxxC_SSSS putat 59.2 2.6 5.6E-05 27.2 -0.4 26 221-250 9-34 (52)
144 PLN02189 cellulose synthase 59.2 7.2 0.00016 40.7 2.6 54 198-253 30-87 (1040)
145 COG2835 Uncharacterized conser 57.2 10 0.00022 25.6 2.2 19 242-260 26-44 (60)
146 COG5183 SSM4 Protein involved 56.4 8.7 0.00019 38.9 2.5 52 204-257 14-70 (1175)
147 PRK00398 rpoP DNA-directed RNA 56.4 5.6 0.00012 25.0 0.9 15 242-256 21-35 (46)
148 cd00730 rubredoxin Rubredoxin; 56.0 4.7 0.0001 26.2 0.5 11 241-251 33-43 (50)
149 PF13838 Clathrin_H_link: Clat 55.5 14 0.0003 25.5 2.7 24 68-91 8-31 (66)
150 smart00659 RPOLCX RNA polymera 55.5 7.7 0.00017 24.4 1.4 26 221-254 6-31 (44)
151 smart00165 UBA Ubiquitin assoc 55.2 18 0.00038 21.3 2.9 18 33-50 17-36 (37)
152 COG5220 TFB3 Cdk activating ki 54.8 3 6.6E-05 36.0 -0.7 37 215-253 22-64 (314)
153 PLN02436 cellulose synthase A 54.7 12 0.00025 39.3 3.2 55 197-253 31-89 (1094)
154 PF13824 zf-Mss51: Zinc-finger 53.9 7.5 0.00016 25.8 1.2 11 242-252 14-24 (55)
155 COG4049 Uncharacterized protei 53.9 4.1 8.8E-05 27.1 -0.1 17 239-255 14-30 (65)
156 PF07754 DUF1610: Domain of un 53.9 8 0.00017 21.1 1.1 11 240-250 14-24 (24)
157 PF07282 OrfB_Zn_ribbon: Putat 53.2 6.9 0.00015 26.7 1.0 15 241-255 45-59 (69)
158 KOG1812 Predicted E3 ubiquitin 52.9 6.7 0.00014 36.6 1.1 57 204-260 148-210 (384)
159 PHA02768 hypothetical protein; 52.8 14 0.00031 24.5 2.3 33 222-254 10-43 (55)
160 PF07729 FCD: FCD domain; Int 52.6 26 0.00056 25.6 4.2 27 27-53 96-122 (125)
161 PF10122 Mu-like_Com: Mu-like 52.5 7.4 0.00016 25.3 0.9 17 241-257 23-39 (51)
162 smart00734 ZnF_Rad18 Rad18-lik 52.2 5 0.00011 22.2 0.1 14 243-256 2-15 (26)
163 PF13878 zf-C2H2_3: zinc-finge 52.0 8.6 0.00019 23.7 1.2 17 241-257 12-28 (41)
164 PLN02915 cellulose synthase A 51.6 14 0.0003 38.7 3.2 57 195-253 8-68 (1044)
165 PF05265 DUF723: Protein of un 51.2 13 0.00029 25.0 2.0 16 199-214 29-44 (60)
166 KOG4172 Predicted E3 ubiquitin 51.2 5.1 0.00011 26.5 0.0 40 218-261 20-60 (62)
167 PF09986 DUF2225: Uncharacteri 50.8 6.7 0.00015 33.5 0.7 18 242-259 48-65 (214)
168 PRK04023 DNA polymerase II lar 50.0 12 0.00026 38.9 2.5 34 80-113 449-490 (1121)
169 COG5219 Uncharacterized conser 50.0 12 0.00026 38.7 2.4 55 177-254 1470-1524(1525)
170 TIGR01562 FdhE formate dehydro 49.9 9.7 0.00021 34.4 1.6 73 176-254 184-264 (305)
171 PF12895 Apc3: Anaphase-promot 49.2 63 0.0014 22.3 5.6 52 34-91 32-83 (84)
172 PLN02195 cellulose synthase A 48.6 16 0.00035 38.0 3.1 51 202-254 6-60 (977)
173 KOG3842 Adaptor protein Pellin 48.5 5.8 0.00013 35.8 -0.0 42 209-253 308-352 (429)
174 KOG1088 Uncharacterized conser 48.3 9.5 0.00021 29.3 1.1 18 240-257 96-113 (124)
175 KOG0883 Cyclophilin type, U bo 47.9 19 0.00041 33.5 3.2 53 204-262 42-94 (518)
176 PF13934 ELYS: Nuclear pore co 47.7 1E+02 0.0022 26.4 7.5 14 7-20 63-76 (226)
177 PLN02638 cellulose synthase A 46.6 20 0.00044 37.6 3.5 54 198-253 13-70 (1079)
178 KOG4275 Predicted E3 ubiquitin 46.2 4.3 9.4E-05 36.1 -1.2 41 202-252 300-341 (350)
179 PLN03086 PRLI-interacting fact 45.4 17 0.00037 35.7 2.6 51 203-253 454-515 (567)
180 COG3898 Uncharacterized membra 45.4 88 0.0019 29.6 7.0 82 5-91 98-179 (531)
181 TIGR02300 FYDLN_acid conserved 44.7 12 0.00026 29.2 1.2 26 203-228 10-37 (129)
182 PF03884 DUF329: Domain of unk 44.5 10 0.00023 25.3 0.7 14 242-255 2-15 (57)
183 COG5627 MMS21 DNA repair prote 44.2 13 0.00028 32.2 1.4 41 203-247 190-231 (275)
184 KOG4692 Predicted E3 ubiquitin 43.4 15 0.00033 33.7 1.8 44 204-253 424-467 (489)
185 PF13934 ELYS: Nuclear pore co 42.7 2.2E+02 0.0047 24.4 11.3 48 40-94 121-168 (226)
186 PRK00420 hypothetical protein; 42.2 16 0.00035 28.0 1.5 28 177-214 24-52 (112)
187 PF08274 PhnA_Zn_Ribbon: PhnA 41.8 9.6 0.00021 22.0 0.2 14 243-256 3-16 (30)
188 PHA00732 hypothetical protein 41.6 25 0.00054 25.1 2.4 32 222-253 6-38 (79)
189 smart00531 TFIIE Transcription 41.4 9.1 0.0002 30.5 0.1 21 240-260 97-117 (147)
190 KOG1333 Uncharacterized conser 41.1 98 0.0021 26.4 6.1 129 3-134 18-154 (241)
191 KOG0801 Predicted E3 ubiquitin 40.8 13 0.00028 30.3 0.8 22 241-262 137-158 (205)
192 COG5236 Uncharacterized conser 40.8 16 0.00035 33.4 1.6 46 204-253 63-108 (493)
193 PF04840 Vps16_C: Vps16, C-ter 40.6 1.5E+02 0.0032 26.9 7.8 75 1-91 187-262 (319)
194 TIGR00373 conserved hypothetic 40.6 30 0.00065 28.0 3.0 30 222-257 114-143 (158)
195 PRK10564 maltose regulon perip 40.4 31 0.00067 31.1 3.3 41 31-79 261-301 (303)
196 KOG1571 Predicted E3 ubiquitin 40.4 14 0.00031 33.8 1.2 41 204-253 307-347 (355)
197 COG1592 Rubrerythrin [Energy p 40.3 20 0.00044 29.4 2.0 25 202-226 134-158 (166)
198 KOG4265 Predicted E3 ubiquitin 40.2 24 0.00051 32.4 2.5 47 202-254 290-337 (349)
199 PHA00616 hypothetical protein 40.2 7.7 0.00017 24.5 -0.4 13 243-255 2-14 (44)
200 PRK11827 hypothetical protein; 39.8 23 0.0005 23.9 1.8 12 201-212 7-18 (60)
201 COG3364 Zn-ribbon containing p 39.5 15 0.00033 27.5 1.0 24 220-250 5-28 (112)
202 PF13432 TPR_16: Tetratricopep 39.5 65 0.0014 20.8 4.2 14 39-52 43-56 (65)
203 PRK11788 tetratricopeptide rep 38.6 1.3E+02 0.0027 27.1 7.2 17 77-93 191-207 (389)
204 PF13395 HNH_4: HNH endonuclea 38.5 15 0.00032 24.0 0.8 13 245-257 1-13 (54)
205 PF10058 DUF2296: Predicted in 38.3 18 0.00039 23.8 1.1 34 217-250 19-52 (54)
206 PF09162 Tap-RNA_bind: Tap, RN 38.0 20 0.00043 26.2 1.4 39 219-262 10-50 (88)
207 PF10571 UPF0547: Uncharacteri 37.9 17 0.00037 20.1 0.8 11 243-253 15-25 (26)
208 KOG2932 E3 ubiquitin ligase in 37.8 11 0.00024 33.9 0.0 27 220-251 106-132 (389)
209 PRK14892 putative transcriptio 37.8 36 0.00079 25.4 2.8 14 197-210 16-29 (99)
210 KOG2462 C2H2-type Zn-finger pr 37.5 44 0.00096 29.6 3.7 14 240-253 213-226 (279)
211 PF03833 PolC_DP2: DNA polymer 37.5 11 0.00024 38.5 0.0 18 81-98 470-487 (900)
212 KOG4739 Uncharacterized protei 37.4 19 0.00042 31.1 1.4 31 204-235 5-35 (233)
213 cd05804 StaR_like StaR_like; a 37.1 1.5E+02 0.0032 26.3 7.4 55 38-93 159-213 (355)
214 PF12931 Sec16_C: Sec23-bindin 36.7 87 0.0019 27.8 5.6 49 72-141 1-49 (284)
215 KOG2659 LisH motif-containing 36.6 68 0.0015 27.7 4.6 54 2-55 75-131 (228)
216 smart00355 ZnF_C2H2 zinc finge 35.7 17 0.00036 18.6 0.6 13 243-255 1-13 (26)
217 PF10827 DUF2552: Protein of u 35.7 23 0.00051 24.6 1.4 18 41-58 59-76 (79)
218 KOG1428 Inhibitor of type V ad 35.6 32 0.00069 37.7 2.9 49 205-253 3489-3544(3738)
219 PF14691 Fer4_20: Dihydroprymi 35.5 51 0.0011 25.0 3.4 28 66-93 38-65 (111)
220 KOG4642 Chaperone-dependent E3 35.3 25 0.00053 30.9 1.8 53 201-258 210-262 (284)
221 COG3357 Predicted transcriptio 35.3 7.1 0.00015 28.6 -1.3 30 216-252 57-86 (97)
222 PF04475 DUF555: Protein of un 35.1 19 0.00042 26.8 1.0 14 241-254 46-59 (102)
223 PF11251 DUF3050: Protein of u 35.1 1.8E+02 0.0038 25.3 6.9 49 33-95 101-157 (232)
224 PF01927 Mut7-C: Mut7-C RNAse 35.0 23 0.0005 28.2 1.5 35 177-211 92-133 (147)
225 PF02748 PyrI_C: Aspartate car 34.9 11 0.00024 24.6 -0.3 20 239-258 32-51 (52)
226 PF12171 zf-C2H2_jaz: Zinc-fin 34.7 24 0.00052 19.2 1.1 15 242-256 1-15 (27)
227 KOG3616 Selective LIM binding 34.4 2.7E+02 0.0059 28.8 8.8 86 19-115 1287-1374(1636)
228 KOG2042 Ubiquitin fusion degra 34.3 34 0.00074 35.5 2.9 52 201-258 869-921 (943)
229 PF14446 Prok-RING_1: Prokaryo 34.3 39 0.00084 22.3 2.2 32 204-235 7-39 (54)
230 COG4530 Uncharacterized protei 33.9 31 0.00067 26.3 1.9 32 203-234 10-43 (129)
231 COG1656 Uncharacterized conser 33.9 16 0.00035 29.8 0.4 64 146-212 69-140 (165)
232 PF13240 zinc_ribbon_2: zinc-r 33.8 23 0.00051 18.9 0.9 11 244-254 1-11 (23)
233 PF14787 zf-CCHC_5: GAG-polypr 33.4 24 0.00053 21.2 1.0 12 244-255 4-15 (36)
234 COG0268 RpsT Ribosomal protein 33.0 74 0.0016 23.2 3.7 30 31-60 32-61 (88)
235 KOG3452 60S ribosomal protein 32.9 1E+02 0.0022 22.9 4.4 41 69-109 53-95 (102)
236 PHA01735 hypothetical protein 32.8 49 0.0011 23.0 2.5 22 33-54 20-46 (76)
237 CHL00098 tsf elongation factor 32.6 53 0.0011 27.8 3.3 22 33-54 18-41 (200)
238 PF13912 zf-C2H2_6: C2H2-type 32.3 23 0.0005 19.0 0.8 13 243-255 2-14 (27)
239 PF14471 DUF4428: Domain of un 32.3 43 0.00093 21.7 2.2 30 204-235 1-30 (51)
240 PHA03096 p28-like protein; Pro 32.1 29 0.00063 31.0 1.8 37 219-255 200-236 (284)
241 PRK12332 tsf elongation factor 32.0 55 0.0012 27.6 3.3 22 33-54 21-44 (198)
242 PF03854 zf-P11: P-11 zinc fin 31.8 30 0.00064 22.3 1.3 33 218-253 14-46 (50)
243 TIGR02552 LcrH_SycD type III s 31.8 74 0.0016 23.8 3.9 87 3-96 29-115 (135)
244 PF13248 zf-ribbon_3: zinc-rib 31.8 25 0.00054 19.2 0.8 8 244-251 4-11 (26)
245 KOG0259 Tyrosine aminotransfer 31.5 32 0.00069 32.2 1.9 16 222-237 211-226 (447)
246 COG4416 Com Mu-like prophage p 31.5 42 0.0009 22.1 1.9 10 242-251 24-33 (60)
247 smart00834 CxxC_CXXC_SSSS Puta 31.2 23 0.0005 21.2 0.7 13 242-254 5-17 (41)
248 TIGR00116 tsf translation elon 31.1 54 0.0012 29.4 3.3 46 33-78 21-93 (290)
249 TIGR00373 conserved hypothetic 30.9 34 0.00074 27.7 1.9 23 240-262 107-129 (158)
250 PRK15359 type III secretion sy 30.9 2.5E+02 0.0055 21.7 8.0 14 78-91 104-117 (144)
251 PLN02400 cellulose synthase 30.8 40 0.00087 35.6 2.7 55 197-253 31-89 (1085)
252 PF14311 DUF4379: Domain of un 30.3 30 0.00066 22.5 1.2 23 222-248 33-55 (55)
253 PF14689 SPOB_a: Sensor_kinase 30.3 1.4E+02 0.0031 19.9 4.6 34 26-59 22-55 (62)
254 PF07721 TPR_4: Tetratricopept 30.2 49 0.0011 17.7 1.9 17 36-52 10-26 (26)
255 COG1885 Uncharacterized protei 30.2 25 0.00055 26.4 0.9 14 241-254 48-61 (115)
256 PF13371 TPR_9: Tetratricopept 30.1 1.6E+02 0.0034 19.3 5.0 53 37-94 5-57 (73)
257 COG5051 RPL36A Ribosomal prote 30.1 1.4E+02 0.003 21.8 4.6 39 70-109 54-92 (97)
258 PF12773 DZR: Double zinc ribb 29.8 46 0.00099 20.9 2.0 14 241-254 28-41 (50)
259 COG3024 Uncharacterized protei 29.8 28 0.0006 23.8 1.0 15 242-256 7-21 (65)
260 PRK01343 zinc-binding protein; 29.8 26 0.00057 23.4 0.8 14 241-254 8-21 (57)
261 PRK09377 tsf elongation factor 29.7 59 0.0013 29.2 3.3 46 33-78 22-94 (290)
262 PF01671 ASFV_360: African swi 29.4 92 0.002 26.5 4.2 100 10-116 3-125 (215)
263 PLN03086 PRLI-interacting fact 29.3 64 0.0014 31.8 3.7 30 222-252 458-487 (567)
264 PRK03922 hypothetical protein; 29.1 28 0.00061 26.4 1.0 14 241-254 48-61 (113)
265 KOG2660 Locus-specific chromos 29.0 21 0.00045 32.4 0.3 51 199-254 12-62 (331)
266 COG1996 RPC10 DNA-directed RNA 29.0 38 0.00082 21.9 1.4 27 221-254 10-36 (49)
267 PRK00239 rpsT 30S ribosomal pr 28.7 96 0.0021 22.6 3.7 29 31-59 32-60 (88)
268 PRK11788 tetratricopeptide rep 28.6 4.3E+02 0.0093 23.6 11.8 18 36-53 189-206 (389)
269 PF07035 Mic1: Colon cancer-as 28.1 76 0.0016 26.0 3.5 38 55-92 75-115 (167)
270 PF12756 zf-C2H2_2: C2H2 type 28.0 31 0.00066 24.6 1.0 14 242-255 50-63 (100)
271 KOG0989 Replication factor C, 27.8 3.2E+02 0.0069 25.1 7.5 58 37-94 218-283 (346)
272 PF09237 GAGA: GAGA factor; I 27.6 25 0.00054 23.0 0.4 14 242-255 24-37 (54)
273 PRK00418 DNA gyrase inhibitor; 27.5 34 0.00073 23.3 1.1 13 242-254 6-18 (62)
274 PF10552 ORF6C: ORF6C domain; 27.0 77 0.0017 24.1 3.2 22 35-56 87-108 (116)
275 PF12931 Sec16_C: Sec23-bindin 26.9 61 0.0013 28.8 3.0 24 33-56 1-24 (284)
276 TIGR01470 cysG_Nterm siroheme 26.8 1.5E+02 0.0032 24.9 5.2 53 41-93 146-204 (205)
277 PF02742 Fe_dep_repr_C: Iron d 26.8 77 0.0017 21.7 2.9 29 224-252 41-69 (71)
278 PRK11534 DNA-binding transcrip 26.8 96 0.0021 26.0 4.1 24 72-95 189-212 (224)
279 cd00189 TPR Tetratricopeptide 26.7 1.8E+02 0.0038 18.6 6.4 14 40-53 47-60 (100)
280 PRK06266 transcription initiat 26.4 46 0.001 27.5 2.0 35 216-256 115-150 (178)
281 COG0675 Transposase and inacti 26.4 34 0.00074 30.3 1.3 14 242-255 322-335 (364)
282 TIGR03831 YgiT_finger YgiT-typ 26.3 17 0.00036 22.3 -0.6 11 243-253 33-43 (46)
283 PF01399 PCI: PCI domain; Int 26.3 1.4E+02 0.0031 21.2 4.5 29 31-59 3-31 (105)
284 PF12760 Zn_Tnp_IS1595: Transp 26.3 57 0.0012 20.4 1.9 9 243-251 19-27 (46)
285 KOG1156 N-terminal acetyltrans 25.8 3.8E+02 0.0083 26.9 8.2 87 3-97 383-469 (700)
286 PHA00733 hypothetical protein 25.5 80 0.0017 24.6 3.0 34 223-256 79-113 (128)
287 PTZ00255 60S ribosomal protein 25.3 64 0.0014 23.7 2.2 20 232-251 26-45 (90)
288 PF06238 Borrelia_lipo_2: Borr 25.2 1.7E+02 0.0038 21.9 4.5 10 71-80 99-108 (111)
289 PRK14890 putative Zn-ribbon RN 24.9 90 0.002 21.0 2.7 12 239-250 45-56 (59)
290 PF15616 TerY-C: TerY-C metal 24.7 65 0.0014 25.4 2.4 42 204-257 79-120 (131)
291 KOG2930 SCF ubiquitin ligase, 24.6 57 0.0012 24.6 1.9 35 218-255 75-110 (114)
292 TIGR03338 phnR_burk phosphonat 24.2 1.2E+02 0.0025 25.2 4.1 22 72-93 185-206 (212)
293 KOG3993 Transcription factor ( 24.2 18 0.00038 34.0 -1.0 12 242-253 295-306 (500)
294 PF08209 Sgf11: Sgf11 (transcr 24.1 39 0.00085 19.9 0.8 15 241-255 3-17 (33)
295 PF12729 4HB_MCP_1: Four helix 24.1 3.3E+02 0.0072 20.8 7.4 32 67-98 122-153 (181)
296 PRK03824 hypA hydrogenase nick 23.9 31 0.00067 27.2 0.4 10 242-251 107-116 (135)
297 PRK10225 DNA-binding transcrip 23.9 1.1E+02 0.0025 26.2 4.1 25 71-95 202-226 (257)
298 KOG4185 Predicted E3 ubiquitin 23.8 17 0.00036 32.3 -1.3 33 217-251 225-265 (296)
299 COG2888 Predicted Zn-ribbon RN 23.6 1.3E+02 0.0028 20.3 3.3 11 240-250 48-58 (61)
300 PF00653 BIR: Inhibitor of Apo 23.5 73 0.0016 21.7 2.2 23 230-252 18-46 (70)
301 COG0264 Tsf Translation elonga 23.5 91 0.002 28.0 3.3 45 35-79 24-97 (296)
302 PF13453 zf-TFIIB: Transcripti 23.4 35 0.00075 20.8 0.5 11 244-254 1-11 (41)
303 PF10013 DUF2256: Uncharacteri 23.3 38 0.00082 21.1 0.6 13 242-254 8-20 (42)
304 PF03604 DNA_RNApol_7kD: DNA d 23.3 38 0.00082 19.8 0.6 23 222-252 5-27 (32)
305 smart00238 BIR Baculoviral inh 23.2 80 0.0017 21.3 2.4 23 232-254 20-48 (71)
306 TIGR00029 S20 ribosomal protei 23.1 1.4E+02 0.003 21.7 3.7 29 31-59 32-60 (87)
307 cd00022 BIR Baculoviral inhibi 23.1 81 0.0018 21.2 2.4 23 232-254 18-46 (69)
308 KOG0097 GTPase Rab14, small G 22.9 1.2E+02 0.0027 24.3 3.6 39 6-44 135-182 (215)
309 PLN03088 SGT1, suppressor of 22.5 3.5E+02 0.0076 24.7 7.2 83 3-93 14-97 (356)
310 PF14369 zf-RING_3: zinc-finge 22.5 49 0.0011 19.6 1.0 11 243-253 22-32 (35)
311 PF12793 SgrR_N: Sugar transpo 22.4 1.3E+02 0.0028 23.0 3.6 27 31-57 74-100 (115)
312 PRK10421 DNA-binding transcrip 22.3 1.3E+02 0.0029 25.7 4.2 27 28-54 191-217 (253)
313 PF03811 Zn_Tnp_IS1: InsA N-te 22.2 48 0.001 19.9 0.9 11 242-252 5-15 (36)
314 PF01877 RNA_binding: RNA bind 21.8 2.7E+02 0.0059 21.2 5.4 44 26-74 56-100 (120)
315 TIGR02812 fadR_gamma fatty aci 21.7 1.4E+02 0.0031 25.2 4.2 23 72-94 194-216 (235)
316 COG1273 Ku-homolog [Replicatio 21.6 62 0.0013 28.6 1.8 21 241-261 46-66 (278)
317 PF07191 zinc-ribbons_6: zinc- 21.5 8.8 0.00019 26.8 -2.7 38 204-252 3-40 (70)
318 smart00299 CLH Clathrin heavy 21.4 1.2E+02 0.0026 23.2 3.4 12 42-53 71-82 (140)
319 PRK04984 fatty acid metabolism 21.3 1.4E+02 0.0031 25.2 4.1 22 73-94 196-217 (239)
320 PF15391 DUF4614: Domain of un 21.3 66 0.0014 26.8 1.9 50 45-94 114-180 (181)
321 PRK14962 DNA polymerase III su 21.3 2.4E+02 0.0052 27.1 6.0 25 29-53 245-269 (472)
322 PF12862 Apc5: Anaphase-promot 21.3 3.1E+02 0.0068 19.5 5.8 28 34-61 5-32 (94)
323 COG4888 Uncharacterized Zn rib 21.1 50 0.0011 24.7 1.0 15 240-254 20-34 (104)
324 PF05191 ADK_lid: Adenylate ki 21.0 45 0.00098 19.9 0.6 12 243-254 2-13 (36)
325 PF01096 TFIIS_C: Transcriptio 20.9 38 0.00083 20.5 0.3 9 243-251 1-9 (39)
326 PF08271 TF_Zn_Ribbon: TFIIB z 20.9 63 0.0014 19.8 1.3 16 241-256 18-33 (43)
327 PF01780 Ribosomal_L37ae: Ribo 20.8 58 0.0013 23.9 1.3 14 239-252 32-45 (90)
328 COG0295 Cdd Cytidine deaminase 20.7 46 0.001 26.3 0.8 39 217-257 82-122 (134)
329 PHA00626 hypothetical protein 20.7 57 0.0012 21.7 1.1 16 240-255 21-36 (59)
330 KOG1074 Transcriptional repres 20.4 60 0.0013 33.3 1.7 41 222-262 358-401 (958)
331 PF03470 zf-XS: XS zinc finger 20.3 46 0.00099 20.9 0.6 7 245-251 1-7 (43)
332 KOG2068 MOT2 transcription fac 20.3 98 0.0021 28.2 2.9 58 193-253 240-298 (327)
333 PF14952 zf-tcix: Putative tre 20.2 46 0.001 20.9 0.6 11 241-251 10-20 (44)
334 PRK08270 anaerobic ribonucleos 20.0 67 0.0015 32.3 2.0 10 242-251 639-648 (656)
No 1
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=6.7e-65 Score=451.96 Aligned_cols=262 Identities=29% Similarity=0.520 Sum_probs=243.5
Q ss_pred CcccccHHHHHHHHHHcCCCCC--CCHHHHHHHHHHHHHHhcCChHHHHHHHHhhchhhhhCCCceeeechHHHHHHHHh
Q 024742 1 MLRMSYYETAEKLAESSNIQDL--VDIEVFQEAKKVIDALQNKEVAPALAWCSDNKSRLKKSKSKFEFQLRLQEFIELVR 78 (263)
Q Consensus 1 Llr~Gy~~ta~~f~~e~~i~~~--~d~~~~~~~~~I~~~i~~gdi~~Al~w~~~~~~~L~~~~s~LeF~L~~q~fIeLi~ 78 (263)
++|+|..|+|+.|.+|+|+... ...+.|.++++|+++|+.||+++|++|+..|+..|.+.+|.|||.||.++|+++++
T Consensus 127 ~~rqGm~dv~~~l~~Ea~~~~~~~~~~~~F~el~~Iv~~lke~Dl~~aLeWa~~~~~~L~~~~s~LE~~Lh~l~fl~l~~ 206 (394)
T KOG2817|consen 127 FYRQGMDDVGECLIKEAGLSEDESKSRTEFVELNQIVEALKERDLEPALEWAESNRQKLKEKSSSLEFKLHSLHFLSLIR 206 (394)
T ss_pred HHHcCchHHHHHHHHHhcCCCcchhhhhhHHHHHHHHHHHHhccchhHHHHHHHhhhhhccccccHHHHHHHHHHHHHHh
Confidence 4799999999999999999865 34578999999999999999999999999999999999999999999999999999
Q ss_pred cCChH--HHHHHHHHhCcchhhhhHHHHHHHHHHhhccCC-CCcchhHHhcCcccHHHHHHHHHHHHHHhhCCCCCcHHH
Q 024742 79 GENNL--RAITYARKYLAPWGATHMKELQRVMATLAFKSN-TECTTYKALFEPKQWDFLVDQFKQEFCKLYGMTLEPLLN 155 (263)
Q Consensus 79 ~~~~~--eAi~yar~~l~~~~~~~~~ei~~~~~lL~f~~~-~~~s~y~~l~~~~r~~~la~~f~~~~~~~~~~~~~s~L~ 155 (263)
.|... +||.|||+||+||+..+..|||.+|++|.|-.. .+.+||.+++++..|.++...|.++||++.|+|.+|||.
T Consensus 207 ~g~~~~~eAl~Yar~~~~~F~~~~~~eIQklm~sl~~l~~gl~~spy~~~ls~~~w~~~~~~f~r~ycallg~s~eSPL~ 286 (394)
T KOG2817|consen 207 GGKSDQREALRYARTHFAPFVADHLREIQKLMGSLLYLRNGLEKSPYSEILSPKLWKELTEEFTREYCALLGISVESPLS 286 (394)
T ss_pred cCCcCcHHHHHHHHHhcCccccchHHHHHHHHHHHHHHHcCCCCCChHHHhCHHHHHHHHHHHHHHHHHHcCCCccCcHH
Confidence 99766 999999999999999999999999999999766 577999999999999999999999999999999999999
Q ss_pred HHHHhhhhhccccccccCCCCC-CCCCCchhhhhhcCCCCCCCCcCCeeeecccccccCCCCCCeecCCCceecHHHHHH
Q 024742 156 IYLQAGLSALNTPYCYEDDCTK-EDPLSQESFRKLASPLPYSKQHHSKLVCYITKELMDTENPPQVLPNGYVYSTKALEE 234 (263)
Q Consensus 156 ~~l~~G~~al~t~~c~~~~~~~-~cp~c~~~~~~l~~~lP~~~~~~s~~~Cpi~~~~~~~~n~p~~l~cGhv~~~~~~~~ 234 (263)
+++.+|..|||++.++.++... .--|-..+.+|++++||..++|||+|+|||+||+.+++||||+|+||||||++||.+
T Consensus 287 v~v~aG~~Alp~Llk~~~v~~~~~~~W~~~deLPveIeL~~~~~fHSvF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnr 366 (394)
T KOG2817|consen 287 VLVNAGCIALPQLLKYKSVMELKHGEWNTKDELPVEIELGKEYHFHSVFICPVLKEQTSDENPPMMLICGHVISKDALNR 366 (394)
T ss_pred HHHHhhHHHHHHHHHHHHHHHHhccCccccccCccceeccccccccceeecccchhhccCCCCCeeeeccceecHHHHHH
Confidence 9999999999999999886432 123555678899999999999999999999999999999999999999999999999
Q ss_pred HHHhCCCceecCCCCcccCcccceeccc
Q 024742 235 MAKKNNGKITCPRTGLVCNYSDLVKAYI 262 (263)
Q Consensus 235 ~~~~~~~~~~CP~c~~~~~~~~~~~v~~ 262 (263)
|++++.-+|||||||.+...+++++|||
T Consensus 367 LS~ng~~sfKCPYCP~e~~~~~~kql~F 394 (394)
T KOG2817|consen 367 LSKNGSQSFKCPYCPVEQLASDTKQLYF 394 (394)
T ss_pred HhhCCCeeeeCCCCCcccCHHhcccccC
Confidence 9875545699999999999999999997
No 2
>KOG0396 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=1.3e-64 Score=445.20 Aligned_cols=261 Identities=46% Similarity=0.825 Sum_probs=251.4
Q ss_pred CcccccHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHHhcCChHHHHHHHHhhchhhhhCCCceeeechHHHHHHHHhcC
Q 024742 1 MLRMSYYETAEKLAESSNIQDLVDIEVFQEAKKVIDALQNKEVAPALAWCSDNKSRLKKSKSKFEFQLRLQEFIELVRGE 80 (263)
Q Consensus 1 Llr~Gy~~ta~~f~~e~~i~~~~d~~~~~~~~~I~~~i~~gdi~~Al~w~~~~~~~L~~~~s~LeF~L~~q~fIeLi~~~ 80 (263)
|+|+||+++|..|.|++++++++|+|.|++.+.|+++|.+|++.+||.||++|+-.|++.+|.|||.+|.|+|||||+.+
T Consensus 126 mlr~gy~~~A~~L~K~s~ledlvD~Dv~~~~~~I~~sll~~~l~~~Lswc~ehk~~LkK~~S~lEf~lRlQefIELi~~~ 205 (389)
T KOG0396|consen 126 MLRNGYFGAAVLLGKKSQLEDLVDSDVYKRAYGIRDSLLAGELEPALSWCKEHKVELKKEESSLEFQLRLQEFIELIKVD 205 (389)
T ss_pred HHHcCchhHHHHHHHhhhhhhhHhHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHhccchhhhHHHHHHHHHHHHhc
Confidence 57999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ChHHHHHHHHHhCcchhhhhHHHHHHHHHHhhccCCCCcchhHHhcCcccHHHHHHHHHHHHHHhhCCCCCcHHHHHHHh
Q 024742 81 NNLRAITYARKYLAPWGATHMKELQRVMATLAFKSNTECTTYKALFEPKQWDFLVDQFKQEFCKLYGMTLEPLLNIYLQA 160 (263)
Q Consensus 81 ~~~eAi~yar~~l~~~~~~~~~ei~~~~~lL~f~~~~~~s~y~~l~~~~r~~~la~~f~~~~~~~~~~~~~s~L~~~l~~ 160 (263)
++.+||+|+|+||+|++.++.++++.+||+|+|+...+.++|..+++++||+.+++.|.+++++++|+|.+|+|.+.+++
T Consensus 206 ~~~~Ai~~akk~f~~~~~~~~~~Lk~a~g~laF~~~t~~sky~~l~~~~rw~~l~~lF~s~a~~l~~i~~~~~L~~~l~~ 285 (389)
T KOG0396|consen 206 NYDKAIAFAKKHFAPWAKSHKSDLKLAMGLLAFPKYTSSSKYLNLLTADRWSVLADLFLSEALKLFGIPINPALTIYLQA 285 (389)
T ss_pred cHHHHHHHHHHHHhhhhhhhHHHHHHHHHhhcCccccCcccccCcccHHHHHHHHHHhhHHHHHHhCCCCCcHHHHHHHh
Confidence 99999999999999999999999999999999999888899999999999999999999999999999999999999999
Q ss_pred hhhhccccccccCCC---CCCCCCCchhhhhhcCCCCCCCCcCCeeeecccccccCCCCCCeecCCCceecHHHHHHHHH
Q 024742 161 GLSALNTPYCYEDDC---TKEDPLSQESFRKLASPLPYSKQHHSKLVCYITKELMDTENPPQVLPNGYVYSTKALEEMAK 237 (263)
Q Consensus 161 G~~al~t~~c~~~~~---~~~cp~c~~~~~~l~~~lP~~~~~~s~~~Cpi~~~~~~~~n~p~~l~cGhv~~~~~~~~~~~ 237 (263)
|+|++||+.|+.... .+.||+|++.++|++..||++|+.||+++|.+|||.||++|||+++|+||||+.++|.+|..
T Consensus 286 GLsalKTp~c~~~~~~~~~~~CpvC~~~f~~ia~~LPfah~~~S~Lvc~isge~md~~N~P~lfpnG~Vyg~~~L~s~~~ 365 (389)
T KOG0396|consen 286 GLSALKTPRCLNDESDNNPNNCPVCCEAFKPIAQALPFAHHAQSRLVCSISGELMDDDNPPHLFPNGYVYGTKALESLNE 365 (389)
T ss_pred hhhhcccccccccccCCCCCCCCCcccccchhhhcCCchhhhhhHHHhhccccccCCCCCcccccCceeehhHHHHhhcc
Confidence 999999999997643 45699999999999999999999999999999999999999999999999999999999964
Q ss_pred hCCCceecCCCCcccCcccceecccC
Q 024742 238 KNNGKITCPRTGLVCNYSDLVKAYIS 263 (263)
Q Consensus 238 ~~~~~~~CP~c~~~~~~~~~~~v~~~ 263 (263)
. +| +.||+++++|.+++..+||++
T Consensus 366 ~-~~-i~dP~~~k~f~~~~l~kvy~~ 389 (389)
T KOG0396|consen 366 D-DG-IGDPRTKKVFRYSELCKVYLS 389 (389)
T ss_pred c-CC-CcCCCCCccccHHHHHHHhcC
Confidence 3 33 899999999999999999985
No 3
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=100.00 E-value=4.9e-41 Score=289.52 Aligned_cols=257 Identities=20% Similarity=0.296 Sum_probs=218.4
Q ss_pred cccHHHHHHHHHHcCCCCCCCH-HHHHHHHHHHHHHhcCChHHHHHHHHhhchhhhhCCCceeeechHHHHH--HHHhcC
Q 024742 4 MSYYETAEKLAESSNIQDLVDI-EVFQEAKKVIDALQNKEVAPALAWCSDNKSRLKKSKSKFEFQLRLQEFI--ELVRGE 80 (263)
Q Consensus 4 ~Gy~~ta~~f~~e~~i~~~~d~-~~~~~~~~I~~~i~~gdi~~Al~w~~~~~~~L~~~~s~LeF~L~~q~fI--eLi~~~ 80 (263)
.|-..-+..++.+.|.++.+.. +.|..++.|++.|.+.+...-|+|. +....|.+.++.+++.|..-... -++..
T Consensus 114 ~~dv~~~hi~~~~~g~~e~~~~~~~f~~lK~v~~gI~~k~~~l~iE~~-Qi~gyl~kgdtesel~l~~~~~esl~l~hk- 191 (396)
T COG5109 114 CADVVERHISETKDGKDEIIKIRDGFVKLKKVISGISEKSTFLLIEFL-QIEGYLSKGDTESELELYLVSHESLLLIHK- 191 (396)
T ss_pred HHHHHHHHHHHhhcCccchhhHHHHHHHHHHHHHhhccchhHhHHHHH-HhcCccccCCchhhhHHHHHHHHHHHHHHH-
Confidence 4445557778888888877654 8899999999999999999999999 88899999888888777655544 44443
Q ss_pred ChHHHHHHHHHhCcchhhhhHHHHHHHHHHhhccCCC------C--cchhH-----HhcC---------cccHHHHHHHH
Q 024742 81 NNLRAITYARKYLAPWGATHMKELQRVMATLAFKSNT------E--CTTYK-----ALFE---------PKQWDFLVDQF 138 (263)
Q Consensus 81 ~~~eAi~yar~~l~~~~~~~~~ei~~~~~lL~f~~~~------~--~s~y~-----~l~~---------~~r~~~la~~f 138 (263)
++++|+.|+++.++.|...|..+++.+|-.+.+-+.. . ..... .+++ ...|..+...|
T Consensus 192 ~~~~a~r~c~t~~a~f~~kh~~dv~~~~~~l~nap~dcfrhrekelmqnI~~~l~ksligqPiEdIDkvnk~~k~l~~lF 271 (396)
T COG5109 192 RYDEALRLCFTKLASFVPKHIQDVKPLLRFLVNAPTDCFRHREKELMQNIQEALKKSLIGQPIEDIDKVNKSRKKLIELF 271 (396)
T ss_pred HHHHHHHHHHHHHHHHHHHhccchHHHHHHHHcCchHHhhhcchhHHHHHHHHHHHhhcCCcHHHHHHhhhhHHHHHHHH
Confidence 7999999999999999999999999999999984331 0 00111 1111 36899999999
Q ss_pred HHHHHHhhCCCCCcHHHHHHHhhhhhccccccccCCCCCC-CCCCchhhhhhcCCCCCCCCcCCeeeecccccccCCCCC
Q 024742 139 KQEFCKLYGMTLEPLLNIYLQAGLSALNTPYCYEDDCTKE-DPLSQESFRKLASPLPYSKQHHSKLVCYITKELMDTENP 217 (263)
Q Consensus 139 ~~~~~~~~~~~~~s~L~~~l~~G~~al~t~~c~~~~~~~~-cp~c~~~~~~l~~~lP~~~~~~s~~~Cpi~~~~~~~~n~ 217 (263)
.++||+..|+|.+|||..++.+|.+|++.+.++.++.... --|.+....|+++.||..+||||+|+|||++|+.+++||
T Consensus 272 ~~eycaa~gm~~~spL~~~v~tG~iaf~~l~k~~si~~~kHvdWT~~~eLP~eIklp~~~hfHs~FiCPVlKe~~t~ENp 351 (396)
T COG5109 272 KSEYCAANGMPNRSPLRELVETGTIAFLQLSKSGSILFDKHVDWTDDSELPMEIKLPKGRHFHSLFICPVLKELCTDENP 351 (396)
T ss_pred HHHHHHhcCCCccChHHHHHHhhhHHHHHHHHhhhHHHhhccCccCCCCCceEEecCCcccccceeeccccHhhhcccCC
Confidence 9999999999999999999999999999999998874311 245567788999999999999999999999999999999
Q ss_pred CeecCCCceecHHHHHHHHHhCCCceecCCCCcccCcccceeccc
Q 024742 218 PQVLPNGYVYSTKALEEMAKKNNGKITCPRTGLVCNYSDLVKAYI 262 (263)
Q Consensus 218 p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~~~~~~~v~~ 262 (263)
|||+.|||||+++|+.+++++|.-.|||||||.+..++++.||||
T Consensus 352 P~ml~CgHVIskeal~~LS~nG~~~FKCPYCP~~~~~~~~~rvrf 396 (396)
T COG5109 352 PVMLECGHVISKEALSVLSQNGVLSFKCPYCPEMSKYENILRVRF 396 (396)
T ss_pred CeeeeccceeeHHHHHHHhhcCcEEeeCCCCCcchhhhhhhcccC
Confidence 999999999999999999987777899999999999999999997
No 4
>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=100.00 E-value=2.3e-34 Score=231.62 Aligned_cols=142 Identities=39% Similarity=0.677 Sum_probs=136.8
Q ss_pred HHHHHHHHHHHhcCChHHHHHHHHhhchhhhhCCCceeeechHHHHHHHHhcCChHHHHHHHHHhCcchhhhhHHHHHHH
Q 024742 28 FQEAKKVIDALQNKEVAPALAWCSDNKSRLKKSKSKFEFQLRLQEFIELVRGENNLRAITYARKYLAPWGATHMKELQRV 107 (263)
Q Consensus 28 ~~~~~~I~~~i~~gdi~~Al~w~~~~~~~L~~~~s~LeF~L~~q~fIeLi~~~~~~eAi~yar~~l~~~~~~~~~ei~~~ 107 (263)
|+++++|+++|++||+++|++|+++|+|.|.+.++.|+|.|++|+|||||++|+..+||+|||+++.++...+.++++++
T Consensus 2 ~~~r~~I~~~I~~g~i~~Ai~w~~~~~~~l~~~~~~L~f~L~~q~fiell~~~~~~~Ai~y~r~~l~~~~~~~~~~l~~~ 81 (145)
T PF10607_consen 2 FKERKKIRQAILNGDIDPAIEWLNENFPELLKRNSSLEFELRCQQFIELLREGDIMEAIEYARKHLSPFNDEFLEELKKL 81 (145)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHcCHHHHhcCCchhHHHHHHHHHHHHHHHhHHHHHHHHHHHhhhhHHHHHHHHHHH
Confidence 78999999999999999999999999999999999999999999999999999999999999999987777789999999
Q ss_pred HHHhhccCCCC--cchhHHhcCcccHHHHHHHHHHHHHHhhCCCCCcHHHHHHHhhhhhccccc
Q 024742 108 MATLAFKSNTE--CTTYKALFEPKQWDFLVDQFKQEFCKLYGMTLEPLLNIYLQAGLSALNTPY 169 (263)
Q Consensus 108 ~~lL~f~~~~~--~s~y~~l~~~~r~~~la~~f~~~~~~~~~~~~~s~L~~~l~~G~~al~t~~ 169 (263)
|++|+|.++.+ .+||++++++++|+.+++.|++++|+.+|+|.+|||+.++++|.+++||+.
T Consensus 82 ~~lL~~~~~~~~~~s~~~~l~~~~~~~~la~~~~~~~l~~~~~~~~s~L~~~~~~g~~~l~~l~ 145 (145)
T PF10607_consen 82 MSLLAYPDPEEPLPSPYKELLSPERREELAEEFNSAILKSYGLPKESPLEVILKAGLSALKTLM 145 (145)
T ss_pred HHHHHcCCcccccchHHHHHhChHHHHHHHHHHHHHHHHHhCcCCCCHHHHHHHHHHHHhhhcC
Confidence 99999999876 689999999999999999999999999999999999999999999999974
No 5
>KOG2659 consensus LisH motif-containing protein [Cytoskeleton]
Probab=99.96 E-value=1.7e-28 Score=206.62 Aligned_cols=165 Identities=22% Similarity=0.335 Sum_probs=155.6
Q ss_pred CcccccHHHHHHHHHHcCCCC-CCCHHHHHHHHHHHHHHhcCChHHHHHHHHhhchhhhhCCCceeeechHHHHHHHHhc
Q 024742 1 MLRMSYYETAEKLAESSNIQD-LVDIEVFQEAKKVIDALQNKEVAPALAWCSDNKSRLKKSKSKFEFQLRLQEFIELVRG 79 (263)
Q Consensus 1 Llr~Gy~~ta~~f~~e~~i~~-~~d~~~~~~~~~I~~~i~~gdi~~Al~w~~~~~~~L~~~~s~LeF~L~~q~fIeLi~~ 79 (263)
|+++||.|+|+.|++|+|+.. ..|.+.+.+|.+|+.+|+.|+++.|++.+++..|.+.+.+.+|.|.|++|+||||||+
T Consensus 37 lv~eg~~EaA~~Fa~e~~i~~~~~d~~~~~eR~~Ir~~I~~G~Ie~Aie~in~l~PeiLd~n~~l~F~Lq~q~lIEliR~ 116 (228)
T KOG2659|consen 37 LVHEGYVEAAEKFAKESGIKPPSIDLDSMDERLQIRRAIEEGQIEEAIEKVNQLNPEILDTNRELFFHLQQLHLIELIRE 116 (228)
T ss_pred HHhccHHHHHHHhccccCCCCccCchhhHhHHHHHHHHHHhccHHHHHHHHHHhChHHHccchhHHHHHHHHHHHHHHHh
Confidence 578999999999999999997 7899999999999999999999999999999999999999999999999999999999
Q ss_pred CChHHHHHHHHHhCcchhhh---hHHHHHHHHHHhhccCCCCcchhHHhcCcccHHHHHHHHHHHHHHhhCCCCCcHHHH
Q 024742 80 ENNLRAITYARKYLAPWGAT---HMKELQRVMATLAFKSNTECTTYKALFEPKQWDFLVDQFKQEFCKLYGMTLEPLLNI 156 (263)
Q Consensus 80 ~~~~eAi~yar~~l~~~~~~---~~~ei~~~~~lL~f~~~~~~s~y~~l~~~~r~~~la~~f~~~~~~~~~~~~~s~L~~ 156 (263)
|...+||+|+|++++|++.. .+++++++|++|+|+++. .+|++++++.++|.++|+.+|+++++.++...++.|..
T Consensus 117 ~~~eeal~F~q~~LA~~a~e~~~~~~elE~~l~lLvf~~~~-~sp~~~l~~~s~R~kvA~~vN~aiL~~~~~~~~~~l~~ 195 (228)
T KOG2659|consen 117 GKTEEALEFAQTKLAPFAEENPKKMEELERTLALLVFELSQ-ESPSAELLSQSLRQKVASEVNSAILASQEHESEPKLPF 195 (228)
T ss_pred hhHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHcCCcc-cCcHHHHHHHHHHHHHHHHHHHHHHHHhcccccchHHH
Confidence 99999999999999999875 578999999999999754 59999999999999999999999999999999999999
Q ss_pred HHHhhhhhcc
Q 024742 157 YLQAGLSALN 166 (263)
Q Consensus 157 ~l~~G~~al~ 166 (263)
+++.+..+-+
T Consensus 196 llk~~~~~~~ 205 (228)
T KOG2659|consen 196 LLKLISWAQE 205 (228)
T ss_pred HHHHHHHHHH
Confidence 9977766543
No 6
>smart00757 CRA CT11-RanBPM. protein-protein interaction domain present in crown eukaryotes (plants, animals, fungi)
Probab=99.78 E-value=5.8e-19 Score=132.73 Aligned_cols=94 Identities=37% Similarity=0.552 Sum_probs=87.8
Q ss_pred CChHHHHHHHHHhCcchhhhh---HHHHHHHHHHhhccCCCCcchhHHhcCcccHHHHHHHHHHHHHHhh-CCCCCcHHH
Q 024742 80 ENNLRAITYARKYLAPWGATH---MKELQRVMATLAFKSNTECTTYKALFEPKQWDFLVDQFKQEFCKLY-GMTLEPLLN 155 (263)
Q Consensus 80 ~~~~eAi~yar~~l~~~~~~~---~~ei~~~~~lL~f~~~~~~s~y~~l~~~~r~~~la~~f~~~~~~~~-~~~~~s~L~ 155 (263)
+++.+||+|||+++++|..++ +++|+++||+|+|.++.+.+||++++++++|+.+++.|+++++..+ |.+.+|+|+
T Consensus 1 ~~~~eAi~yar~~l~~~~~~~~~~~~el~~~m~llaf~~~~~~sp~~~ll~~~~~~~la~~~n~~~l~~~~~~~~~s~L~ 80 (99)
T smart00757 1 GKIEEALAYARELLAPFAKEHEKFLKELEKTMALLAYPDPTEPSPYKELLSPSQREKLAEELNSAILELLHGKSSESPLE 80 (99)
T ss_pred CcHHHHHHHHHHHHhhhcccCHHHHHHHHHHHHHHhcCCCCCCccHHHHCCHHHHHHHHHHHHHHHHHHccCCCCCChHH
Confidence 357899999999999999877 8899999999999987567999999999999999999999999998 999999999
Q ss_pred HHHHhhhhhccccccccC
Q 024742 156 IYLQAGLSALNTPYCYED 173 (263)
Q Consensus 156 ~~l~~G~~al~t~~c~~~ 173 (263)
.++++|..+++|+.|+..
T Consensus 81 ~~~~~~~~~~~~l~~~~~ 98 (99)
T smart00757 81 ILLSAGLAALKTLLEKGG 98 (99)
T ss_pred HHHHHHHHHHHHHHHhcC
Confidence 999999999999999754
No 7
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=99.59 E-value=9.2e-16 Score=97.22 Aligned_cols=42 Identities=43% Similarity=0.871 Sum_probs=27.7
Q ss_pred ecccccccCCCCCCeecCCCceecHHHHHHHHHhC-CCceecC
Q 024742 205 CYITKELMDTENPPQVLPNGYVYSTKALEEMAKKN-NGKITCP 246 (263)
Q Consensus 205 Cpi~~~~~~~~n~p~~l~cGhv~~~~~~~~~~~~~-~~~~~CP 246 (263)
|||++|..+++|+||+|+||||||+++|++|++++ .+.||||
T Consensus 1 CpIc~e~~~~~n~P~~L~CGH~~c~~cl~~l~~~~~~~~~kCP 43 (43)
T PF13445_consen 1 CPICKEFSTEENPPMVLPCGHVFCKDCLQKLSKKSDRNRFKCP 43 (43)
T ss_dssp -TTT----TTSS-EEE-SSS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred CCccccccCCCCCCEEEeCccHHHHHHHHHHHhcCCCCeeeCc
Confidence 99999966889999999999999999999999865 3789998
No 8
>smart00668 CTLH C-terminal to LisH motif. Alpha-helical motif of unknown function.
Probab=99.41 E-value=3.8e-13 Score=91.05 Aligned_cols=55 Identities=38% Similarity=0.583 Sum_probs=52.5
Q ss_pred HHHHHHHHHHHhcCChHHHHHHHHhhchhhhhCCCceeeechHHHHHHHHhcCCh
Q 024742 28 FQEAKKVIDALQNKEVAPALAWCSDNKSRLKKSKSKFEFQLRLQEFIELVRGENN 82 (263)
Q Consensus 28 ~~~~~~I~~~i~~gdi~~Al~w~~~~~~~L~~~~s~LeF~L~~q~fIeLi~~~~~ 82 (263)
|..+.+|+++|+.|||++|++|++++++.+.+.+|.++|.|++|+|+|||+.|+.
T Consensus 2 ~~~~~~i~~~i~~g~~~~a~~~~~~~~~~l~~~~~~l~f~L~~q~~lell~~~~~ 56 (58)
T smart00668 2 FDERKRIRELILKGDWDEALEWLSSLKPPLLERNSKLEFELRKQKFLELVRQGKL 56 (58)
T ss_pred hHHHHHHHHHHHcCCHHHHHHHHHHcCHHHhccCCCchhHHHHHHHHHHHHcCCc
Confidence 6788999999999999999999999999999999999999999999999998864
No 9
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=99.26 E-value=5e-12 Score=86.98 Aligned_cols=53 Identities=32% Similarity=0.525 Sum_probs=48.1
Q ss_pred eeecccccccCCCCCCeecCCCceecHHHHHHHHHhCCCceecCCCCcccCcccceecc
Q 024742 203 LVCYITKELMDTENPPQVLPNGYVYSTKALEEMAKKNNGKITCPRTGLVCNYSDLVKAY 261 (263)
Q Consensus 203 ~~Cpi~~~~~~~~n~p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~~~~~~~v~ 261 (263)
|+||||++.|++ ||++||||||++++|.++.++ ..+||.|++.++.+++++..
T Consensus 2 ~~Cpi~~~~~~~---Pv~~~~G~v~~~~~i~~~~~~---~~~cP~~~~~~~~~~l~~~~ 54 (63)
T smart00504 2 FLCPISLEVMKD---PVILPSGQTYERRAIEKWLLS---HGTDPVTGQPLTHEDLIPNL 54 (63)
T ss_pred cCCcCCCCcCCC---CEECCCCCEEeHHHHHHHHHH---CCCCCCCcCCCChhhceeCH
Confidence 789999999998 999999999999999999875 35899999999999988764
No 10
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=99.05 E-value=1.4e-10 Score=82.34 Aligned_cols=55 Identities=35% Similarity=0.492 Sum_probs=43.7
Q ss_pred CeeeecccccccCCCCCCeecCCCceecHHHHHHHHHhCCCceecCCCCcccCcccceec
Q 024742 201 SKLVCYITKELMDTENPPQVLPNGYVYSTKALEEMAKKNNGKITCPRTGLVCNYSDLVKA 260 (263)
Q Consensus 201 s~~~Cpi~~~~~~~~n~p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~~~~~~~v 260 (263)
..|.||||++.|.+ ||++|+||+|++.+|++|.++ +..+||.|++..+.++++..
T Consensus 3 ~~f~CpIt~~lM~d---PVi~~~G~tyer~~I~~~l~~--~~~~~P~t~~~l~~~~l~pn 57 (73)
T PF04564_consen 3 DEFLCPITGELMRD---PVILPSGHTYERSAIERWLEQ--NGGTDPFTRQPLSESDLIPN 57 (73)
T ss_dssp GGGB-TTTSSB-SS---EEEETTSEEEEHHHHHHHHCT--TSSB-TTT-SB-SGGGSEE-
T ss_pred cccCCcCcCcHhhC---ceeCCcCCEEcHHHHHHHHHc--CCCCCCCCCCcCCcccceEC
Confidence 45899999999999 999999999999999999864 34699999999999888754
No 11
>PF04641 Rtf2: Rtf2 RING-finger
Probab=98.87 E-value=1.5e-09 Score=95.52 Aligned_cols=60 Identities=23% Similarity=0.442 Sum_probs=51.3
Q ss_pred CcCCeeeecccccccCCCCCCe-ecCCCceecHHHHHHHHHhCCCceecCCCCcccCcccceecc
Q 024742 198 QHHSKLVCYITKELMDTENPPQ-VLPNGYVYSTKALEEMAKKNNGKITCPRTGLVCNYSDLVKAY 261 (263)
Q Consensus 198 ~~~s~~~Cpi~~~~~~~~n~p~-~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~~~~~~~v~ 261 (263)
...+.|+||||+.+|++..+.+ +.|||||||++||+++. ..-.||.|++.|...|++.|.
T Consensus 109 ~~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k----~~~~Cp~c~~~f~~~DiI~Ln 169 (260)
T PF04641_consen 109 NSEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK----KSKKCPVCGKPFTEEDIIPLN 169 (260)
T ss_pred cCCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc----ccccccccCCccccCCEEEec
Confidence 3578999999999998877666 57999999999999993 124699999999999999874
No 12
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.75 E-value=8.2e-09 Score=65.23 Aligned_cols=41 Identities=32% Similarity=0.669 Sum_probs=31.8
Q ss_pred ecccccccCCCCCCeecCCCceecHHHHHHHHHhCCCc-eecCCC
Q 024742 205 CYITKELMDTENPPQVLPNGYVYSTKALEEMAKKNNGK-ITCPRT 248 (263)
Q Consensus 205 Cpi~~~~~~~~n~p~~l~cGhv~~~~~~~~~~~~~~~~-~~CP~c 248 (263)
|||..+.+++ ||.|+|||+|++.+|.++.++.++. +.||.|
T Consensus 1 CpiC~~~~~~---Pv~l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDLFKD---PVSLPCGHSFCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp ETTTTSB-SS---EEE-SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred CCccchhhCC---ccccCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence 8999999999 9999999999999999998755444 899987
No 13
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=98.70 E-value=1.4e-08 Score=84.34 Aligned_cols=59 Identities=17% Similarity=0.249 Sum_probs=50.4
Q ss_pred CeeeecccccccCCCCCCeecCCCceecHHHHHHHHHhC-------------CCceecCCCCcccCcccceeccc
Q 024742 201 SKLVCYITKELMDTENPPQVLPNGYVYSTKALEEMAKKN-------------NGKITCPRTGLVCNYSDLVKAYI 262 (263)
Q Consensus 201 s~~~Cpi~~~~~~~~n~p~~l~cGhv~~~~~~~~~~~~~-------------~~~~~CP~c~~~~~~~~~~~v~~ 262 (263)
..|.|||+.+...+ |++++|||+||+.||.+|.... .+..+||.|+..++.++++.||-
T Consensus 17 ~~~~CpICld~~~d---PVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~LvPiyg 88 (193)
T PLN03208 17 GDFDCNICLDQVRD---PVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEATLVPIYG 88 (193)
T ss_pred CccCCccCCCcCCC---cEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhcEEEeec
Confidence 45889999998876 9999999999999999986421 23579999999999999999883
No 14
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=98.68 E-value=1.7e-08 Score=68.03 Aligned_cols=45 Identities=27% Similarity=0.485 Sum_probs=32.4
Q ss_pred CeeeecccccccCCCCCCee-cCCCceecHHHHHHHHHhCCCceecCCCC
Q 024742 201 SKLVCYITKELMDTENPPQV-LPNGYVYSTKALEEMAKKNNGKITCPRTG 249 (263)
Q Consensus 201 s~~~Cpi~~~~~~~~n~p~~-l~cGhv~~~~~~~~~~~~~~~~~~CP~c~ 249 (263)
-.+.||||+..+.+ ||. ..|||+|++++|.++. ++++.++||..|
T Consensus 10 ~~~~CPiT~~~~~~---PV~s~~C~H~fek~aI~~~i-~~~~~~~CPv~G 55 (57)
T PF11789_consen 10 ISLKCPITLQPFED---PVKSKKCGHTFEKEAILQYI-QRNGSKRCPVAG 55 (57)
T ss_dssp --SB-TTTSSB-SS---EEEESSS--EEEHHHHHHHC-TTTS-EE-SCCC
T ss_pred eccCCCCcCChhhC---CcCcCCCCCeecHHHHHHHH-HhcCCCCCCCCC
Confidence 35799999999998 998 6999999999999998 456789999954
No 15
>KOG3113 consensus Uncharacterized conserved protein [Function unknown]
Probab=98.65 E-value=1.6e-08 Score=86.12 Aligned_cols=57 Identities=21% Similarity=0.349 Sum_probs=50.1
Q ss_pred cCCeeeecccccccCCCCCCe-ecCCCceecHHHHHHHHHhCCCceecCCCCcccCcccceec
Q 024742 199 HHSKLVCYITKELMDTENPPQ-VLPNGYVYSTKALEEMAKKNNGKITCPRTGLVCNYSDLVKA 260 (263)
Q Consensus 199 ~~s~~~Cpi~~~~~~~~n~p~-~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~~~~~~~v 260 (263)
.|+.|+|||+|-+|++--..+ +++||||||++|++++-. -.|+.|+..|..+|++-|
T Consensus 108 ~~a~fiCPvtgleMng~~~F~~l~~CGcV~SerAlKeika-----s~C~~C~a~y~~~dvIvl 165 (293)
T KOG3113|consen 108 QRARFICPVTGLEMNGKYRFCALRCCGCVFSERALKEIKA-----SVCHVCGAAYQEDDVIVL 165 (293)
T ss_pred ccceeecccccceecceEEEEEEeccceeccHHHHHHhhh-----ccccccCCcccccCeEee
Confidence 578999999999999877655 589999999999999842 489999999999999865
No 16
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.50 E-value=5.9e-08 Score=78.79 Aligned_cols=62 Identities=15% Similarity=0.321 Sum_probs=52.0
Q ss_pred CCcCCeeeecccccccCCCCCCeecCCCceecHHHHHHHHHhCCCceecCCCCcccCcccceeccc
Q 024742 197 KQHHSKLVCYITKELMDTENPPQVLPNGYVYSTKALEEMAKKNNGKITCPRTGLVCNYSDLVKAYI 262 (263)
Q Consensus 197 ~~~~s~~~Cpi~~~~~~~~n~p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~~~~~~~v~~ 262 (263)
+.-.+.+-|||+.+-..+.- |+-..||||||+.||+...++. .+||.|++..+..++.+||+
T Consensus 126 ~~~~~~~~CPiCl~~~sek~-~vsTkCGHvFC~~Cik~alk~~---~~CP~C~kkIt~k~~~rI~L 187 (187)
T KOG0320|consen 126 LRKEGTYKCPICLDSVSEKV-PVSTKCGHVFCSQCIKDALKNT---NKCPTCRKKITHKQFHRIYL 187 (187)
T ss_pred cccccccCCCceecchhhcc-ccccccchhHHHHHHHHHHHhC---CCCCCcccccchhhheeccC
Confidence 33445589999998887644 5779999999999999987643 69999999999999999996
No 17
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=98.48 E-value=3.2e-08 Score=96.10 Aligned_cols=61 Identities=13% Similarity=0.286 Sum_probs=53.7
Q ss_pred CCcCCeeeecccccccCCCCCCeecCCCceecHHHHHHHHHhCCCceecCCCCcccCcccceeccc
Q 024742 197 KQHHSKLVCYITKELMDTENPPQVLPNGYVYSTKALEEMAKKNNGKITCPRTGLVCNYSDLVKAYI 262 (263)
Q Consensus 197 ~~~~s~~~Cpi~~~~~~~~n~p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~~~~~~~v~~ 262 (263)
-.|.-++.||++.+-..+ .++..||||||.+|++..-. .+.-|||.|+..|..+|+.+||+
T Consensus 638 k~yK~~LkCs~Cn~R~Kd---~vI~kC~H~FC~~Cvq~r~e--tRqRKCP~Cn~aFganDv~~I~l 698 (698)
T KOG0978|consen 638 KEYKELLKCSVCNTRWKD---AVITKCGHVFCEECVQTRYE--TRQRKCPKCNAAFGANDVHRIHL 698 (698)
T ss_pred HHHHhceeCCCccCchhh---HHHHhcchHHHHHHHHHHHH--HhcCCCCCCCCCCCcccccccCC
Confidence 457889999999987777 78899999999999998764 34579999999999999999996
No 18
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.47 E-value=1.1e-07 Score=60.72 Aligned_cols=43 Identities=23% Similarity=0.497 Sum_probs=36.9
Q ss_pred ecccccccCCCCCCeecCCCceecHHHHHHHHHhCCCceecCCCCc
Q 024742 205 CYITKELMDTENPPQVLPNGYVYSTKALEEMAKKNNGKITCPRTGL 250 (263)
Q Consensus 205 Cpi~~~~~~~~n~p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~ 250 (263)
|++..+..+++.+|++++|||+|+.+++.++. +..++||.|++
T Consensus 2 C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~---~~~~~CP~C~k 44 (44)
T PF14634_consen 2 CNICFEKYSEERRPRLTSCGHIFCEKCLKKLK---GKSVKCPICRK 44 (44)
T ss_pred CcCcCccccCCCCeEEcccCCHHHHHHHHhhc---CCCCCCcCCCC
Confidence 77777777777789999999999999999986 45689999975
No 19
>KOG0293 consensus WD40 repeat-containing protein [Function unknown]
Probab=98.43 E-value=7.8e-07 Score=80.92 Aligned_cols=162 Identities=10% Similarity=0.117 Sum_probs=122.3
Q ss_pred CcccccHHHHHHHHHHcCCCC-CCCHHHHHHHHHHHHHHhcCChHHHHHHHHhhchhhhhCCCceeeechHHHHHHHHhc
Q 024742 1 MLRMSYYETAEKLAESSNIQD-LVDIEVFQEAKKVIDALQNKEVAPALAWCSDNKSRLKKSKSKFEFQLRLQEFIELVRG 79 (263)
Q Consensus 1 Llr~Gy~~ta~~f~~e~~i~~-~~d~~~~~~~~~I~~~i~~gdi~~Al~w~~~~~~~L~~~~s~LeF~L~~q~fIeLi~~ 79 (263)
|+..||-+++.+++.|+|+-. ..+...| .+++..|+++.++.-+....-+.++......|.|.+|.|+|+++.
T Consensus 28 l~slgy~~S~~~lE~es~ll~~tat~klf------~q~vlqg~w~q~v~~~~~i~~~de~~~~ea~fLv~kQ~fLEf~k~ 101 (519)
T KOG0293|consen 28 LYSLGYDHSSPLLEWESGLLIPTATTKLF------DQQVLQGQWDQQVMSLVRISFEDERNRKEAMFLVNKQIFLEFLKT 101 (519)
T ss_pred HHhcCccccchhhHHhhCcccccchHHHH------HHHHHcccHHHHHHHHhhccCcchhhhHHHHHHHHHHHHHHHHhh
Confidence 456899999999999999863 4677778 889999999999998877754456666789999999999999999
Q ss_pred CChHHHHHHHHHhCcchhhhhHHHHHHHHHHhhccCCCC-----------------cchhHHh------cCcccHHHHHH
Q 024742 80 ENNLRAITYARKYLAPWGATHMKELQRVMATLAFKSNTE-----------------CTTYKAL------FEPKQWDFLVD 136 (263)
Q Consensus 80 ~~~~eAi~yar~~l~~~~~~~~~ei~~~~~lL~f~~~~~-----------------~s~y~~l------~~~~r~~~la~ 136 (263)
|++..|+...|..+.+... +.+.+.++...|++++... ......+ +.+.|.+.|.+
T Consensus 102 ~~is~al~~l~~~~~~lr~-~~kk~~el~~sll~sn~~~~ne~~~~~~~~n~R~~ll~elskyi~p~illP~rRLehLl~ 180 (519)
T KOG0293|consen 102 GSISHALPVLRNPVLYLRK-NKKKFHELASSLLVSNDQFSNEENTTAQLNNERDKLLDELSKYIPPNILLPKRRLEHLLE 180 (519)
T ss_pred ccHhhhhHhhhcchhhhhh-hHHHHHHHHHHHhccccccccccchhhhhchhHHHHHHHHHhhCCHhhcCChHHHHHHHH
Confidence 9999999999987776654 6688899999999875420 0112222 22345566655
Q ss_pred ---HHHHHHHHhhCCCCCcHHHHHHHhhhhhccccc
Q 024742 137 ---QFKQEFCKLYGMTLEPLLNIYLQAGLSALNTPY 169 (263)
Q Consensus 137 ---~f~~~~~~~~~~~~~s~L~~~l~~G~~al~t~~ 169 (263)
..++.-|..|+--..-.|.....+|-..+|+..
T Consensus 181 qAv~~Q~d~cvyhnsldsvsll~Dh~c~~~qip~qt 216 (519)
T KOG0293|consen 181 QAVKYQRDSCVYHNSLDSVSLLSDHFCGRLQIPSQT 216 (519)
T ss_pred HHHHHHHhHhHHhcccchhhhhhhcccCcccCCchh
Confidence 566777777774444577777778888777543
No 20
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=98.42 E-value=2.3e-07 Score=59.11 Aligned_cols=43 Identities=28% Similarity=0.465 Sum_probs=37.2
Q ss_pred eecccccccCCCCCCeecCCCceecHHHHHHHHHhCCCceecCCCC
Q 024742 204 VCYITKELMDTENPPQVLPNGYVYSTKALEEMAKKNNGKITCPRTG 249 (263)
Q Consensus 204 ~Cpi~~~~~~~~n~p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~ 249 (263)
.|||..+.+.+.+.++.++|||+|..++|.+|.+++ .+||.|.
T Consensus 2 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~~---~~CP~CR 44 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKRN---NSCPVCR 44 (44)
T ss_dssp CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHHS---SB-TTTH
T ss_pred CCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHhC---CcCCccC
Confidence 499999999888889999999999999999999763 4999983
No 21
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=98.28 E-value=1.1e-06 Score=54.87 Aligned_cols=40 Identities=28% Similarity=0.626 Sum_probs=34.6
Q ss_pred ecccccccCCCCCCe-ecCCCceecHHHHHHHHHhCCCceecCCC
Q 024742 205 CYITKELMDTENPPQ-VLPNGYVYSTKALEEMAKKNNGKITCPRT 248 (263)
Q Consensus 205 Cpi~~~~~~~~n~p~-~l~cGhv~~~~~~~~~~~~~~~~~~CP~c 248 (263)
|||..+.+.+ |+ +++|||.|+..++.++.++ .+.++||.|
T Consensus 1 C~iC~~~~~~---~~~~~~C~H~fC~~C~~~~~~~-~~~~~CP~C 41 (41)
T PF00097_consen 1 CPICLEPFED---PVILLPCGHSFCRDCLRKWLEN-SGSVKCPLC 41 (41)
T ss_dssp ETTTSSBCSS---EEEETTTSEEEEHHHHHHHHHH-TSSSBTTTT
T ss_pred CCcCCccccC---CCEEecCCCcchHHHHHHHHHh-cCCccCCcC
Confidence 7888888877 66 8999999999999999875 567899987
No 22
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=98.22 E-value=1.5e-06 Score=53.92 Aligned_cols=38 Identities=26% Similarity=0.545 Sum_probs=30.7
Q ss_pred ecccccccCCCCCC-eecCCCceecHHHHHHHHHhCCCceecCCC
Q 024742 205 CYITKELMDTENPP-QVLPNGYVYSTKALEEMAKKNNGKITCPRT 248 (263)
Q Consensus 205 Cpi~~~~~~~~n~p-~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c 248 (263)
|||..+.+.+ | ++++|||+|+++++.++.++ ..+||.|
T Consensus 1 C~iC~~~~~~---~~~~~~CGH~fC~~C~~~~~~~---~~~CP~C 39 (39)
T PF13923_consen 1 CPICLDELRD---PVVVTPCGHSFCKECIEKYLEK---NPKCPVC 39 (39)
T ss_dssp ETTTTSB-SS---EEEECTTSEEEEHHHHHHHHHC---TSB-TTT
T ss_pred CCCCCCcccC---cCEECCCCCchhHHHHHHHHHC---cCCCcCC
Confidence 7888888877 7 68999999999999999764 3699987
No 23
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.22 E-value=1.3e-06 Score=73.99 Aligned_cols=61 Identities=18% Similarity=0.280 Sum_probs=56.4
Q ss_pred CcCCeeeecccccccCCCCCCeecCCCceecHHHHHHHHHhCCCceecCCCCcccCcccceecc
Q 024742 198 QHHSKLVCYITKELMDTENPPQVLPNGYVYSTKALEEMAKKNNGKITCPRTGLVCNYSDLVKAY 261 (263)
Q Consensus 198 ~~~s~~~Cpi~~~~~~~~n~p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~~~~~~~v~ 261 (263)
.--+.|-|-|+-+...+ ||+..|||.||.-||-+|..-..++..||.|+-+.+.+.++.||
T Consensus 43 ~~~~~FdCNICLd~akd---PVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~vvPlY 103 (230)
T KOG0823|consen 43 RDGGFFDCNICLDLAKD---PVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDTVVPLY 103 (230)
T ss_pred CCCCceeeeeeccccCC---CEEeecccceehHHHHHHHhhcCCCeeCCccccccccceEEeee
Confidence 55688999999999999 99999999999999999998666778899999999999999998
No 24
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.17 E-value=1.4e-06 Score=80.45 Aligned_cols=66 Identities=18% Similarity=0.347 Sum_probs=54.7
Q ss_pred cCCCCCCCCcCCeeeecccccccCCCCCCeecCCCceecHHHHHHHHHhCCCceecCCCCcccCcccceecc
Q 024742 190 ASPLPYSKQHHSKLVCYITKELMDTENPPQVLPNGYVYSTKALEEMAKKNNGKITCPRTGLVCNYSDLVKAY 261 (263)
Q Consensus 190 ~~~lP~~~~~~s~~~Cpi~~~~~~~~n~p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~~~~~~~v~ 261 (263)
.-.+|.--.+..-+.|||+.+.+.. |++++|||+||..||..+... ..+||.|+..+..+++++-+
T Consensus 14 ~t~~~~l~~Le~~l~C~IC~d~~~~---PvitpCgH~FCs~CI~~~l~~---~~~CP~Cr~~~~~~~Lr~N~ 79 (397)
T TIGR00599 14 TTPIPSLYPLDTSLRCHICKDFFDV---PVLTSCSHTFCSLCIRRCLSN---QPKCPLCRAEDQESKLRSNW 79 (397)
T ss_pred cCCcccccccccccCCCcCchhhhC---ccCCCCCCchhHHHHHHHHhC---CCCCCCCCCccccccCccch
Confidence 4466767778889999999999976 899999999999999998753 34899999999877665433
No 25
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=97.95 E-value=1.2e-05 Score=52.61 Aligned_cols=45 Identities=24% Similarity=0.316 Sum_probs=36.0
Q ss_pred eeecccccccCCCCCCeecCCCce-ecHHHHHHHHHhCCCceecCCCCcccC
Q 024742 203 LVCYITKELMDTENPPQVLPNGYV-YSTKALEEMAKKNNGKITCPRTGLVCN 253 (263)
Q Consensus 203 ~~Cpi~~~~~~~~n~p~~l~cGhv-~~~~~~~~~~~~~~~~~~CP~c~~~~~ 253 (263)
..|+|..+...+ ++++||||+ ++..++.++.+ +..+||.|.+.++
T Consensus 3 ~~C~iC~~~~~~---~~~~pCgH~~~C~~C~~~~~~---~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 3 EECPICFENPRD---VVLLPCGHLCFCEECAERLLK---RKKKCPICRQPIE 48 (50)
T ss_dssp SB-TTTSSSBSS---EEEETTCEEEEEHHHHHHHHH---TTSBBTTTTBB-S
T ss_pred CCCccCCccCCc---eEEeCCCChHHHHHHhHHhcc---cCCCCCcCChhhc
Confidence 358888887655 889999999 99999999976 3469999998764
No 26
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.91 E-value=8.8e-06 Score=72.46 Aligned_cols=56 Identities=13% Similarity=0.126 Sum_probs=40.7
Q ss_pred eeccccccc--CCCCCCeecCCCceecHHHHHHHHHhCCCceecCCCCcccCcccceecc
Q 024742 204 VCYITKELM--DTENPPQVLPNGYVYSTKALEEMAKKNNGKITCPRTGLVCNYSDLVKAY 261 (263)
Q Consensus 204 ~Cpi~~~~~--~~~n~p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~~~~~~~v~ 261 (263)
.||+++.-- +++-..++.+|||.||+.|+.++... +...||.|++.+...+++...
T Consensus 5 ~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~--~~~~CP~C~~~lrk~~fr~q~ 62 (309)
T TIGR00570 5 GCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVR--GSGSCPECDTPLRKNNFRVQL 62 (309)
T ss_pred CCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcC--CCCCCCCCCCccchhhccccc
Confidence 567766643 22222455589999999999998753 446999999999988876543
No 27
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=97.90 E-value=1e-05 Score=48.89 Aligned_cols=39 Identities=33% Similarity=0.571 Sum_probs=31.2
Q ss_pred ecccccccCCCCCCeecCCCceecHHHHHHHHHhCCCceecCCC
Q 024742 205 CYITKELMDTENPPQVLPNGYVYSTKALEEMAKKNNGKITCPRT 248 (263)
Q Consensus 205 Cpi~~~~~~~~n~p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c 248 (263)
|||..+. ...+++++|||+|+..+++.+.+ .+..+||.|
T Consensus 1 C~iC~~~---~~~~~~~~C~H~~c~~C~~~~~~--~~~~~CP~C 39 (39)
T smart00184 1 CPICLEE---LKDPVVLPCGHTFCRSCIRKWLK--SGNNTCPIC 39 (39)
T ss_pred CCcCccC---CCCcEEecCCChHHHHHHHHHHH--hCcCCCCCC
Confidence 5666666 34589999999999999999976 345689987
No 28
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=97.89 E-value=1.2e-05 Score=50.28 Aligned_cols=43 Identities=33% Similarity=0.562 Sum_probs=33.0
Q ss_pred ecccccccCCCCCCeecCCCceecHHHHHHHHHhCCCceecCCCCcc
Q 024742 205 CYITKELMDTENPPQVLPNGYVYSTKALEEMAKKNNGKITCPRTGLV 251 (263)
Q Consensus 205 Cpi~~~~~~~~n~p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~ 251 (263)
|+|..+.+ .++.++.+|||+|+..++..+.+. +..+||.|+..
T Consensus 2 C~iC~~~~--~~~~~~~~C~H~~c~~C~~~~~~~--~~~~Cp~C~~~ 44 (45)
T cd00162 2 CPICLEEF--REPVVLLPCGHVFCRSCIDKWLKS--GKNTCPLCRTP 44 (45)
T ss_pred CCcCchhh--hCceEecCCCChhcHHHHHHHHHh--CcCCCCCCCCc
Confidence 77777777 233445669999999999999864 45789999875
No 29
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=97.75 E-value=4.6e-05 Score=66.66 Aligned_cols=67 Identities=18% Similarity=0.238 Sum_probs=54.3
Q ss_pred hcCCCCCCCCcCCeeeecccccccCCCCCCeecCCCceecHHHHHHHHHhCCCceecCCCCcccCcccceecc
Q 024742 189 LASPLPYSKQHHSKLVCYITKELMDTENPPQVLPNGYVYSTKALEEMAKKNNGKITCPRTGLVCNYSDLVKAY 261 (263)
Q Consensus 189 l~~~lP~~~~~~s~~~Cpi~~~~~~~~n~p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~~~~~~~v~ 261 (263)
++..+-.....+-..-|-++.|.... |-..||||+||..||..|... +-.||.|.+.|..+++.-++
T Consensus 226 ~~~s~~~~~i~~a~~kC~LCLe~~~~---pSaTpCGHiFCWsCI~~w~~e---k~eCPlCR~~~~pskvi~Lr 292 (293)
T KOG0317|consen 226 LEDSNSLSSIPEATRKCSLCLENRSN---PSATPCGHIFCWSCILEWCSE---KAECPLCREKFQPSKVICLR 292 (293)
T ss_pred hhhccCCccCCCCCCceEEEecCCCC---CCcCcCcchHHHHHHHHHHcc---ccCCCcccccCCCcceeeec
Confidence 33445555667777889999998877 899999999999999999863 23599999999999987553
No 30
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=97.74 E-value=2.5e-05 Score=66.65 Aligned_cols=60 Identities=18% Similarity=0.410 Sum_probs=50.1
Q ss_pred CcC-CeeeecccccccCCCCC-CeecCCCceecHHHHHHHHHhCCCceecCCCCcccCcccceec
Q 024742 198 QHH-SKLVCYITKELMDTENP-PQVLPNGYVYSTKALEEMAKKNNGKITCPRTGLVCNYSDLVKA 260 (263)
Q Consensus 198 ~~~-s~~~Cpi~~~~~~~~n~-p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~~~~~~~v 260 (263)
..+ -+|+||||++.++..-| .++-|||||+..+|++++.+++ ..||.|++..+..|++.+
T Consensus 216 ~a~s~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D---~v~pv~d~plkdrdiI~L 277 (303)
T KOG3039|consen 216 IAASKRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKD---MVDPVTDKPLKDRDIIGL 277 (303)
T ss_pred hhhccceecccchhhhcCccceEEeccCCcEeeHHHHHHhcccc---ccccCCCCcCcccceEee
Confidence 445 46999999999987665 4467999999999999998643 599999999999998764
No 31
>PHA02929 N1R/p28-like protein; Provisional
Probab=97.71 E-value=2.8e-05 Score=67.27 Aligned_cols=48 Identities=19% Similarity=0.176 Sum_probs=36.8
Q ss_pred eeecccccccCCCC-----CCeecCCCceecHHHHHHHHHhCCCceecCCCCcccC
Q 024742 203 LVCYITKELMDTEN-----PPQVLPNGYVYSTKALEEMAKKNNGKITCPRTGLVCN 253 (263)
Q Consensus 203 ~~Cpi~~~~~~~~n-----~p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~ 253 (263)
..|||+.+.+.+.. -+++.+|||+|+..||.+|.+. ..+||.|...+.
T Consensus 175 ~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~---~~tCPlCR~~~~ 227 (238)
T PHA02929 175 KECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKE---KNTCPVCRTPFI 227 (238)
T ss_pred CCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhc---CCCCCCCCCEee
Confidence 56777777664322 1467899999999999999763 359999998876
No 32
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.59 E-value=4.4e-05 Score=71.55 Aligned_cols=58 Identities=19% Similarity=0.340 Sum_probs=48.9
Q ss_pred eeeecccccccCCCCCCeecCCCceecHHHHHHHHHhC--CCceecCCCCcccCcccceeccc
Q 024742 202 KLVCYITKELMDTENPPQVLPNGYVYSTKALEEMAKKN--NGKITCPRTGLVCNYSDLVKAYI 262 (263)
Q Consensus 202 ~~~Cpi~~~~~~~~n~p~~l~cGhv~~~~~~~~~~~~~--~~~~~CP~c~~~~~~~~~~~v~~ 262 (263)
-..|||+-+.-.- |++..||||||-.||.+...-+ .+..+||.|...+...|+..|++
T Consensus 186 ~~~CPICL~~~~~---p~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~kdl~pv~~ 245 (513)
T KOG2164|consen 186 DMQCPICLEPPSV---PVRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLKDLLPVFI 245 (513)
T ss_pred CCcCCcccCCCCc---ccccccCceeeHHHHHHHHhhhcccCCccCCchhhhccccceeeeee
Confidence 5689999887766 7777799999999999887533 35579999999999999999875
No 33
>PHA02926 zinc finger-like protein; Provisional
Probab=97.48 E-value=9.5e-05 Score=62.54 Aligned_cols=59 Identities=12% Similarity=0.139 Sum_probs=42.9
Q ss_pred eeecccccccCC------CCCCeecCCCceecHHHHHHHHHhC---CCceecCCCCcccCcccceecc
Q 024742 203 LVCYITKELMDT------ENPPQVLPNGYVYSTKALEEMAKKN---NGKITCPRTGLVCNYSDLVKAY 261 (263)
Q Consensus 203 ~~Cpi~~~~~~~------~n~p~~l~cGhv~~~~~~~~~~~~~---~~~~~CP~c~~~~~~~~~~~v~ 261 (263)
..|+|+.|...+ --.+++.+|||+||..||.+|.+.. +....||.|.+.|..=-..++|
T Consensus 171 ~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~~I~pSrf~ 238 (242)
T PHA02926 171 KECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFRNITMSKFY 238 (242)
T ss_pred CCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceeeeeccccce
Confidence 567777776532 1237888999999999999998632 2345799999999865555544
No 34
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.22 E-value=0.00028 Score=61.38 Aligned_cols=58 Identities=17% Similarity=0.172 Sum_probs=41.6
Q ss_pred cCCeeeecccccccCCCCCCeecCCCceecHHHHHHHHHhCCCceecCCCCcccCccccee
Q 024742 199 HHSKLVCYITKELMDTENPPQVLPNGYVYSTKALEEMAKKNNGKITCPRTGLVCNYSDLVK 259 (263)
Q Consensus 199 ~~s~~~Cpi~~~~~~~~n~p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~~~~~~~ 259 (263)
..|--.||++|+.-+ +|-++.+|||+||.-|+.+-. ..+-.|.||.||+.-..=+...
T Consensus 236 ~t~~~~C~~Cg~~Pt--iP~~~~~C~HiyCY~Ci~ts~-~~~asf~Cp~Cg~~~~~lq~sg 293 (298)
T KOG2879|consen 236 GTSDTECPVCGEPPT--IPHVIGKCGHIYCYYCIATSR-LWDASFTCPLCGENVEPLQASG 293 (298)
T ss_pred ccCCceeeccCCCCC--CCeeeccccceeehhhhhhhh-cchhhcccCccCCCCcchhhcc
Confidence 345568888887654 445578899999999997542 2345799999999877433333
No 35
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.21 E-value=8.9e-05 Score=64.20 Aligned_cols=63 Identities=21% Similarity=0.254 Sum_probs=47.0
Q ss_pred CCCCCCCCcCCeeeecccccccCCCC-------CCeecCCCceecHHHHHHHHHhCCCceecCCCCcccCccc
Q 024742 191 SPLPYSKQHHSKLVCYITKELMDTEN-------PPQVLPNGYVYSTKALEEMAKKNNGKITCPRTGLVCNYSD 256 (263)
Q Consensus 191 ~~lP~~~~~~s~~~Cpi~~~~~~~~n-------~p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~~~~ 256 (263)
..+|..|-..| +|-|+|.+++.+- .-+.|.|+||+-+.||+-|.-- +.+-+||||++..+.+.
T Consensus 215 ~glPtkhl~d~--vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWciv-GKkqtCPYCKekVdl~r 284 (328)
T KOG1734|consen 215 SGLPTKHLSDS--VCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIV-GKKQTCPYCKEKVDLKR 284 (328)
T ss_pred CCCCCCCCCcc--hhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheee-cCCCCCchHHHHhhHhh
Confidence 35666555544 6888888886543 4788999999999999988742 34569999999876553
No 36
>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....
Probab=97.07 E-value=0.00069 Score=47.91 Aligned_cols=31 Identities=26% Similarity=0.409 Sum_probs=23.7
Q ss_pred CCCeecCCCceecHHHHHHHHHhCCCceecCCCC
Q 024742 216 NPPQVLPNGYVYSTKALEEMAKKNNGKITCPRTG 249 (263)
Q Consensus 216 n~p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~ 249 (263)
-++++.+|||+|-..+|.+|.+.+ .+||.|.
T Consensus 43 ~~i~~~~C~H~FH~~Ci~~Wl~~~---~~CP~CR 73 (73)
T PF12678_consen 43 CPIVWGPCGHIFHFHCISQWLKQN---NTCPLCR 73 (73)
T ss_dssp S-EEEETTSEEEEHHHHHHHHTTS---SB-TTSS
T ss_pred cceEecccCCCEEHHHHHHHHhcC---CcCCCCC
Confidence 445567999999999999998643 3999984
No 37
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.01 E-value=0.00023 Score=62.43 Aligned_cols=45 Identities=27% Similarity=0.524 Sum_probs=40.0
Q ss_pred cCCeeeecccccccCCCCCCeecCCCceecHHHHHHHHHhCCCceecCCCC
Q 024742 199 HHSKLVCYITKELMDTENPPQVLPNGYVYSTKALEEMAKKNNGKITCPRTG 249 (263)
Q Consensus 199 ~~s~~~Cpi~~~~~~~~n~p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~ 249 (263)
....+.|||+.+.+.+ |+++||||.+|+.|+..+.. ..+.||.|.
T Consensus 10 ~~~~~~C~iC~~~~~~---p~~l~C~H~~c~~C~~~~~~---~~~~Cp~cr 54 (386)
T KOG2177|consen 10 LQEELTCPICLEYFRE---PVLLPCGHNFCRACLTRSWE---GPLSCPVCR 54 (386)
T ss_pred ccccccChhhHHHhhc---CccccccchHhHHHHHHhcC---CCcCCcccC
Confidence 4567899999999988 79999999999999999875 568999998
No 38
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=96.95 E-value=0.00014 Score=64.84 Aligned_cols=65 Identities=23% Similarity=0.360 Sum_probs=55.7
Q ss_pred CCCCCCCcCCeeeecccccccCCCCCCeecCCCceecHHHHHHHHHhCCCceecCCCCcccCcccceeccc
Q 024742 192 PLPYSKQHHSKLVCYITKELMDTENPPQVLPNGYVYSTKALEEMAKKNNGKITCPRTGLVCNYSDLVKAYI 262 (263)
Q Consensus 192 ~lP~~~~~~s~~~Cpi~~~~~~~~n~p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~~~~~~~v~~ 262 (263)
.||.-+...+.+-|-|+.|-+.- ||+.||||.||--||..... .+..||.|-.++..++++.=+|
T Consensus 13 sipslk~lD~lLRC~IC~eyf~i---p~itpCsHtfCSlCIR~~L~---~~p~CP~C~~~~~Es~Lr~n~i 77 (442)
T KOG0287|consen 13 SIPSLKTLDDLLRCGICFEYFNI---PMITPCSHTFCSLCIRKFLS---YKPQCPTCCVTVTESDLRNNRI 77 (442)
T ss_pred cCchhhhhHHHHHHhHHHHHhcC---ceeccccchHHHHHHHHHhc---cCCCCCceecccchhhhhhhhH
Confidence 46777788888999999998877 99999999999999998864 4679999999999999886544
No 39
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=96.89 E-value=0.00093 Score=60.47 Aligned_cols=51 Identities=24% Similarity=0.438 Sum_probs=39.4
Q ss_pred cCCeeeeccccccc-CCCC---------CCeecCCCceecHHHHHHHHHhCCCceecCCCCccc
Q 024742 199 HHSKLVCYITKELM-DTEN---------PPQVLPNGYVYSTKALEEMAKKNNGKITCPRTGLVC 252 (263)
Q Consensus 199 ~~s~~~Cpi~~~~~-~~~n---------~p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~ 252 (263)
..|-=+|-|++++| ..+| .|-.|||||++-..|++.|.++ +-+||+|....
T Consensus 284 ~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ER---qQTCPICr~p~ 344 (491)
T COG5243 284 TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLER---QQTCPICRRPV 344 (491)
T ss_pred cCCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHh---ccCCCcccCcc
Confidence 44555688888885 3322 2788999999999999999874 46999998863
No 40
>KOG1477 consensus SPRY domain-containing proteins [General function prediction only]
Probab=96.86 E-value=0.00074 Score=64.16 Aligned_cols=175 Identities=13% Similarity=0.037 Sum_probs=127.0
Q ss_pred CcccccHHHHHHHHHHcCCCCCCC----HHHHH--------HHHHHHHHHhcCChHHHHHHHHhhchhhhh-------CC
Q 024742 1 MLRMSYYETAEKLAESSNIQDLVD----IEVFQ--------EAKKVIDALQNKEVAPALAWCSDNKSRLKK-------SK 61 (263)
Q Consensus 1 Llr~Gy~~ta~~f~~e~~i~~~~d----~~~~~--------~~~~I~~~i~~gdi~~Al~w~~~~~~~L~~-------~~ 61 (263)
++..|+.+++..+...+.-..... ...+. .+......+-.+-+..+.+.+.+..+.... ..
T Consensus 260 ~l~~~~~~s~~~~s~~~~~~~~~~~~~e~~s~~~~~~~~~~~~~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~ 339 (469)
T KOG1477|consen 260 LLPGGYEESIAYFSTGARRFNDPFTGKEENSIDAVGSQTDKIGLDYHQRKGRGQFTRNGAYNAALIPTYRKVGQVFEVDY 339 (469)
T ss_pred ecCcchhhhhhhhcchhhccCCcccchhhhhhhccccccchhhhhhhhhcCcceeechhhhcccccccccccceeecccc
Confidence 467788899888887765322111 11111 112222222235666666666666555544 45
Q ss_pred CceeeechHHHHHHHHhcCChHHHHHHHHHhCcchhh-----hhHHHHHHHHHHhhccCCCCcchhHHhcCcccHHHHHH
Q 024742 62 SKFEFQLRLQEFIELVRGENNLRAITYARKYLAPWGA-----THMKELQRVMATLAFKSNTECTTYKALFEPKQWDFLVD 136 (263)
Q Consensus 62 s~LeF~L~~q~fIeLi~~~~~~eAi~yar~~l~~~~~-----~~~~ei~~~~~lL~f~~~~~~s~y~~l~~~~r~~~la~ 136 (263)
+...+.++++.+|++.+-+.+..++++.+.++++... ...+.++..+++|+|.++.+ ++...+.++..++-+++
T Consensus 340 ~~~~~~~~~~~~v~~~~~g~v~~e~~~~k~~l~~~~g~~~~~~~~~~~~~s~~Llays~p~~-s~~g~~~~~~~~e~v~~ 418 (469)
T KOG1477|consen 340 PQRGAKDPCGLHVNLGRAGFVFIEANAKKWELAKDYGIKKNSAAVGMLSDSSSLLAYSDPEE-SPVGYLLDPIQREPVAE 418 (469)
T ss_pred cchhhccchhhhhhHHHHHHHHHHHHHHHHhhhhhhCcCccccccccccchHHHHHhcCccc-CccccccCcccchhHHh
Confidence 7889999999999999999999999999999988765 34578999999999999875 77888889999999999
Q ss_pred HHHHHHHHhhCCCCCcHHHHHHHhhhhhccccccccCCCCCCCCCC
Q 024742 137 QFKQEFCKLYGMTLEPLLNIYLQAGLSALNTPYCYEDDCTKEDPLS 182 (263)
Q Consensus 137 ~f~~~~~~~~~~~~~s~L~~~l~~G~~al~t~~c~~~~~~~~cp~c 182 (263)
..+.+++...+.+.+++|+.++. ++..|........+|.|
T Consensus 419 ~~n~~il~t~~~~~~~~l~~~l~------~~~~~~~~~~~~~~~~~ 458 (469)
T KOG1477|consen 419 ALNSAILETDNNSKDPDLERVLS------QTPAELSLYARDNPPRN 458 (469)
T ss_pred hhcccccccCCCCccchhhhhhc------cchhhHhhhhhcCCCcc
Confidence 99999999999999999887776 66666555433344443
No 41
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=96.76 E-value=0.001 Score=43.92 Aligned_cols=35 Identities=23% Similarity=0.356 Sum_probs=28.6
Q ss_pred CeecCCCceecHHHHHHHHHhCCCceecCCCCcccCcccc
Q 024742 218 PQVLPNGYVYSTKALEEMAKKNNGKITCPRTGLVCNYSDL 257 (263)
Q Consensus 218 p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~~~~~ 257 (263)
.+++||||++++.+..-. +.--||.|+..|..++.
T Consensus 20 ~~~~pCgH~I~~~~f~~~-----rYngCPfC~~~~~~~~~ 54 (55)
T PF14447_consen 20 GTVLPCGHLICDNCFPGE-----RYNGCPFCGTPFEFDDP 54 (55)
T ss_pred cccccccceeeccccChh-----hccCCCCCCCcccCCCC
Confidence 788999999999998532 23479999999998764
No 42
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.67 E-value=0.001 Score=57.60 Aligned_cols=51 Identities=20% Similarity=0.318 Sum_probs=42.5
Q ss_pred eeeecccccccCCCCCCeecCCCceecHHHHHH-HHHhCCCceecCCCCcccCcccc
Q 024742 202 KLVCYITKELMDTENPPQVLPNGYVYSTKALEE-MAKKNNGKITCPRTGLVCNYSDL 257 (263)
Q Consensus 202 ~~~Cpi~~~~~~~~n~p~~l~cGhv~~~~~~~~-~~~~~~~~~~CP~c~~~~~~~~~ 257 (263)
-+-|+++.+.+.. |.+.|||||||.-||.. |.++. .-.||.|......+++
T Consensus 215 d~kC~lC~e~~~~---ps~t~CgHlFC~~Cl~~~~t~~k--~~~CplCRak~~pk~v 266 (271)
T COG5574 215 DYKCFLCLEEPEV---PSCTPCGHLFCLSCLLISWTKKK--YEFCPLCRAKVYPKKV 266 (271)
T ss_pred ccceeeeecccCC---cccccccchhhHHHHHHHHHhhc--cccCchhhhhccchhh
Confidence 4679999998877 99999999999999998 76542 2369999988877776
No 43
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=96.38 E-value=0.0012 Score=57.82 Aligned_cols=63 Identities=19% Similarity=0.172 Sum_probs=53.8
Q ss_pred CCCCCCCCcCCeeeecccccccCCCCCCeecCCCceecHHHHHHHHHhCCCceecCCCCcccCccccee
Q 024742 191 SPLPYSKQHHSKLVCYITKELMDTENPPQVLPNGYVYSTKALEEMAKKNNGKITCPRTGLVCNYSDLVK 259 (263)
Q Consensus 191 ~~lP~~~~~~s~~~Cpi~~~~~~~~n~p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~~~~~~~ 259 (263)
-.+|.-+...|.+.|.|+.+-+.- |+..+|||.||.-||++... .+.-||.|...+-.+-.+.
T Consensus 14 T~IPSL~~LDs~lrC~IC~~~i~i---p~~TtCgHtFCslCIR~hL~---~qp~CP~Cr~~~~esrlr~ 76 (391)
T COG5432 14 TKIPSLKGLDSMLRCRICDCRISI---PCETTCGHTFCSLCIRRHLG---TQPFCPVCREDPCESRLRG 76 (391)
T ss_pred ccCcchhcchhHHHhhhhhheeec---ceecccccchhHHHHHHHhc---CCCCCccccccHHhhhccc
Confidence 367888999999999999999998 99999999999999998863 4678999998887655443
No 44
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=96.27 E-value=0.0044 Score=44.87 Aligned_cols=51 Identities=12% Similarity=0.096 Sum_probs=37.5
Q ss_pred ecccccccCCCCCCeecCCCceecHHHHHHHHHhCCCceecCCCCcccCccc
Q 024742 205 CYITKELMDTENPPQVLPNGYVYSTKALEEMAKKNNGKITCPRTGLVCNYSD 256 (263)
Q Consensus 205 Cpi~~~~~~~~n~p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~~~~ 256 (263)
||..+..- ++-|.+.-.|||.|-.-+|.+|......+-.||.|.+++.+++
T Consensus 35 Cp~Ck~Pg-d~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~~k~ 85 (85)
T PF12861_consen 35 CPDCKFPG-DDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWKFKE 85 (85)
T ss_pred CCCccCCC-CCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeeeeCC
Confidence 44444432 2345566789999999999999875445679999999998754
No 45
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.76 E-value=0.007 Score=53.55 Aligned_cols=49 Identities=14% Similarity=0.198 Sum_probs=40.5
Q ss_pred eeecccccccCCCCCCeecCCCceecHHHHHHHHHhCCCceecCCCCcccC
Q 024742 203 LVCYITKELMDTENPPQVLPNGYVYSTKALEEMAKKNNGKITCPRTGLVCN 253 (263)
Q Consensus 203 ~~Cpi~~~~~~~~n~p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~ 253 (263)
.-|-|+.+-+.....-|++||.|+|-..|+.+|.- +.+.+||.|..+..
T Consensus 324 veCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~--~y~~~CPvCrt~iP 372 (374)
T COG5540 324 VECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLL--GYSNKCPVCRTAIP 372 (374)
T ss_pred ceEEEEhhhhcccceEEEeccCceechhHHHHHHh--hhcccCCccCCCCC
Confidence 56888888887666678899999999999999974 35679999987654
No 46
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.63 E-value=0.0068 Score=55.11 Aligned_cols=48 Identities=15% Similarity=0.270 Sum_probs=42.1
Q ss_pred eeecccccccCCCCCCeecCCCceecHHHHHHHHHhCCCceecCCCCccc
Q 024742 203 LVCYITKELMDTENPPQVLPNGYVYSTKALEEMAKKNNGKITCPRTGLVC 252 (263)
Q Consensus 203 ~~Cpi~~~~~~~~n~p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~ 252 (263)
++|-|+.|...++..-.+|||+|.|-.+||..|..+. +-.||.|++..
T Consensus 230 ~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~--r~~CPvCK~di 277 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQT--RTFCPVCKRDI 277 (348)
T ss_pred ceEEEeecccccCCeeeEecCCCchhhccchhhHhhc--CccCCCCCCcC
Confidence 7999999999988888889999999999999999753 34699999844
No 47
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=95.29 E-value=0.027 Score=36.74 Aligned_cols=45 Identities=16% Similarity=0.277 Sum_probs=26.2
Q ss_pred eeeecccccccCCCCCCee-cCCCce--ecHHHHHHHHHhCCCceecCCCCc
Q 024742 202 KLVCYITKELMDTENPPQV-LPNGYV--YSTKALEEMAKKNNGKITCPRTGL 250 (263)
Q Consensus 202 ~~~Cpi~~~~~~~~n~p~~-l~cGhv--~~~~~~~~~~~~~~~~~~CP~c~~ 250 (263)
.+.||+|+..+.- |+. ..|-|+ |..+++.+...+ .+..+||+|++
T Consensus 2 sL~CPls~~~i~~---P~Rg~~C~H~~CFDl~~fl~~~~~-~~~W~CPiC~~ 49 (50)
T PF02891_consen 2 SLRCPLSFQRIRI---PVRGKNCKHLQCFDLESFLESNQR-TPKWKCPICNK 49 (50)
T ss_dssp ESB-TTTSSB-SS---EEEETT--SS--EEHHHHHHHHHH-S---B-TTT--
T ss_pred eeeCCCCCCEEEe---CccCCcCcccceECHHHHHHHhhc-cCCeECcCCcC
Confidence 3689999999977 886 789998 666666666543 34589999986
No 48
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.19 E-value=0.012 Score=57.20 Aligned_cols=52 Identities=27% Similarity=0.468 Sum_probs=41.1
Q ss_pred CeeeecccccccCC-CC-CCeecCCCceecHHHHHHHHHhCCCceecCCCCcccCcc
Q 024742 201 SKLVCYITKELMDT-EN-PPQVLPNGYVYSTKALEEMAKKNNGKITCPRTGLVCNYS 255 (263)
Q Consensus 201 s~~~Cpi~~~~~~~-~n-~p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~~~ 255 (263)
+.-.|+|+.|.+.. +| -|-.+||||++...|+++|.++ +-.||.|...+...
T Consensus 290 ~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er---~qtCP~CR~~~~~~ 343 (543)
T KOG0802|consen 290 SDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFER---QQTCPTCRTVLYDY 343 (543)
T ss_pred cCCeeeeechhhccccccccceeecccchHHHHHHHHHHH---hCcCCcchhhhhcc
Confidence 45689999999844 33 2678999999999999999985 45999999854433
No 49
>smart00744 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class
Probab=95.16 E-value=0.028 Score=36.48 Aligned_cols=44 Identities=25% Similarity=0.412 Sum_probs=32.8
Q ss_pred eecccccccCCCCCCeecCCC-----ceecHHHHHHHHHhCCCceecCCCC
Q 024742 204 VCYITKELMDTENPPQVLPNG-----YVYSTKALEEMAKKNNGKITCPRTG 249 (263)
Q Consensus 204 ~Cpi~~~~~~~~n~p~~l~cG-----hv~~~~~~~~~~~~~~~~~~CP~c~ 249 (263)
+|.|..+ ..+++.|++.||. +.+-..+|++|.... +..+||.|+
T Consensus 1 ~CrIC~~-~~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~-~~~~C~iC~ 49 (49)
T smart00744 1 ICRICHD-EGDEGDPLVSPCRCKGSLKYVHQECLERWINES-GNKTCEICK 49 (49)
T ss_pred CccCCCC-CCCCCCeeEeccccCCchhHHHHHHHHHHHHHc-CCCcCCCCC
Confidence 4777777 3334457889986 889999999998754 345999985
No 50
>KOG2979 consensus Protein involved in DNA repair [General function prediction only]
Probab=94.87 E-value=0.016 Score=50.19 Aligned_cols=46 Identities=22% Similarity=0.300 Sum_probs=36.2
Q ss_pred eeeecccccccCCCCCCee-cCCCceecHHHHHHHHHhCCCceecCCCCcc
Q 024742 202 KLVCYITKELMDTENPPQV-LPNGYVYSTKALEEMAKKNNGKITCPRTGLV 251 (263)
Q Consensus 202 ~~~Cpi~~~~~~~~n~p~~-l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~ 251 (263)
.+.||+|+...-. |++ -.|||||-++++..+.. +....+||.-|-+
T Consensus 176 s~rdPis~~~I~n---PviSkkC~HvydrDsI~~~l~-~~~~i~CPv~gC~ 222 (262)
T KOG2979|consen 176 SNRDPISKKPIVN---PVISKKCGHVYDRDSIMQILC-DEITIRCPVLGCE 222 (262)
T ss_pred cccCchhhhhhhc---hhhhcCcCcchhhhhHHHHhc-cCceeecccccCC
Confidence 3579999777754 665 78999999999999975 3456899987665
No 51
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=94.79 E-value=0.017 Score=51.60 Aligned_cols=55 Identities=24% Similarity=0.425 Sum_probs=45.2
Q ss_pred eeecccccccCCCCCCeecCCCceecHHHHHHHHHhCCCceecCCCCcccCcccceeccc
Q 024742 203 LVCYITKELMDTENPPQVLPNGYVYSTKALEEMAKKNNGKITCPRTGLVCNYSDLVKAYI 262 (263)
Q Consensus 203 ~~Cpi~~~~~~~~n~p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~~~~~~~v~~ 262 (263)
=+|||+..- --||-++...|.|+|..|+-+... + .-+||.|+..-..++++|+|-
T Consensus 301 ~~CpvClk~--r~Nptvl~vSGyVfCY~Ci~~Yv~-~--~~~CPVT~~p~~v~~l~rl~~ 355 (357)
T KOG0826|consen 301 EVCPVCLKK--RQNPTVLEVSGYVFCYPCIFSYVV-N--YGHCPVTGYPASVDHLIRLFN 355 (357)
T ss_pred ccChhHHhc--cCCCceEEecceEEeHHHHHHHHH-h--cCCCCccCCcchHHHHHHHhc
Confidence 368887653 367788889999999999998875 2 349999999999999999884
No 52
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=94.58 E-value=0.0071 Score=41.32 Aligned_cols=48 Identities=15% Similarity=0.305 Sum_probs=24.1
Q ss_pred eeecccccccCCCCCCe-ecCCCceecHHHHHHHHHhCCCceecCCCCcccCcccce
Q 024742 203 LVCYITKELMDTENPPQ-VLPNGYVYSTKALEEMAKKNNGKITCPRTGLVCNYSDLV 258 (263)
Q Consensus 203 ~~Cpi~~~~~~~~n~p~-~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~~~~~~ 258 (263)
+-|++..+.|.+ || +..|.|+|+..++..-.. -.||.|...--.+|++
T Consensus 8 LrCs~C~~~l~~---pv~l~~CeH~fCs~Ci~~~~~-----~~CPvC~~Paw~qD~~ 56 (65)
T PF14835_consen 8 LRCSICFDILKE---PVCLGGCEHIFCSSCIRDCIG-----SECPVCHTPAWIQDIQ 56 (65)
T ss_dssp TS-SSS-S--SS----B---SSS--B-TTTGGGGTT-----TB-SSS--B-S-SS--
T ss_pred cCCcHHHHHhcC---CceeccCccHHHHHHhHHhcC-----CCCCCcCChHHHHHHH
Confidence 568888888888 87 588999999999965321 2599999998888875
No 53
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=94.56 E-value=0.02 Score=50.60 Aligned_cols=43 Identities=16% Similarity=0.351 Sum_probs=36.0
Q ss_pred eeecccccccCCCCCCeec-CCCceecHHHHHHHHHhCCCceecCCCCc
Q 024742 203 LVCYITKELMDTENPPQVL-PNGYVYSTKALEEMAKKNNGKITCPRTGL 250 (263)
Q Consensus 203 ~~Cpi~~~~~~~~n~p~~l-~cGhv~~~~~~~~~~~~~~~~~~CP~c~~ 250 (263)
+.||.++..+.. ||.. -|||.||++||....-. .-|+||.|..
T Consensus 275 LkCplc~~Llrn---p~kT~cC~~~fc~eci~~al~d--sDf~CpnC~r 318 (427)
T COG5222 275 LKCPLCHCLLRN---PMKTPCCGHTFCDECIGTALLD--SDFKCPNCSR 318 (427)
T ss_pred ccCcchhhhhhC---cccCccccchHHHHHHhhhhhh--ccccCCCccc
Confidence 899999999877 8877 59999999999965532 3489999986
No 54
>PF08513 LisH: LisH; InterPro: IPR013720 The LisH motif is found in a large number of eukaryotic proteins, from metazoa, fungi and plants that have a wide range of functions. The recently solved structure of the LisH domain in the N-terminal region of LIS1 depicted it as a novel dimerization motif, and that other structural elements are likely to play an important role in dimerisation [, , ]. The LisH (lis homology) domain mediates protein dimerisation and tetramerisation. The LisH domain is found in Sif2, a component of the Set3 complex which is responsible for repressing meiotic genes. It has been shown that the LisH domain helps mediate interaction with components of the Set3 complex []. ; PDB: 2XTE_L 2XTC_B 2XTD_A 1UUJ_B.
Probab=94.01 E-value=0.024 Score=31.95 Aligned_cols=17 Identities=29% Similarity=0.493 Sum_probs=14.3
Q ss_pred CcccccHHHHHHHHHHc
Q 024742 1 MLRMSYYETAEKLAESS 17 (263)
Q Consensus 1 Llr~Gy~~ta~~f~~e~ 17 (263)
|.++||.+||.+|.+|+
T Consensus 11 L~~~Gy~~tA~~f~~Ea 27 (27)
T PF08513_consen 11 LVENGYKETAKAFAKEA 27 (27)
T ss_dssp HHHCT-HHHHHHHHHHT
T ss_pred HHHCCcHHHHHHHHhcC
Confidence 46899999999999986
No 55
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.95 E-value=0.0074 Score=54.45 Aligned_cols=52 Identities=12% Similarity=0.148 Sum_probs=42.3
Q ss_pred CCcCCeeeecccccccCCCCCCee-cCCCceecHHHHHHHHHhCCCceecCCCCcccC
Q 024742 197 KQHHSKLVCYITKELMDTENPPQV-LPNGYVYSTKALEEMAKKNNGKITCPRTGLVCN 253 (263)
Q Consensus 197 ~~~~s~~~Cpi~~~~~~~~n~p~~-l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~ 253 (263)
..+|+-|.|||+.+.+.. .|+ -.|+|-||.+||.+-.+.++ ..||.|.+...
T Consensus 38 ~~~~~~v~c~icl~llk~---tmttkeClhrfc~~ci~~a~r~gn--~ecptcRk~l~ 90 (381)
T KOG0311|consen 38 AMFDIQVICPICLSLLKK---TMTTKECLHRFCFDCIWKALRSGN--NECPTCRKKLV 90 (381)
T ss_pred HHhhhhhccHHHHHHHHh---hcccHHHHHHHHHHHHHHHHHhcC--CCCchHHhhcc
Confidence 357889999999999877 676 45999999999998776443 48999987654
No 56
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=93.69 E-value=0.029 Score=46.78 Aligned_cols=45 Identities=20% Similarity=0.287 Sum_probs=37.3
Q ss_pred eeeecccccccCCCCCCeecCCCceecHHHHHHHHHhCCCceecCCCCccc
Q 024742 202 KLVCYITKELMDTENPPQVLPNGYVYSTKALEEMAKKNNGKITCPRTGLVC 252 (263)
Q Consensus 202 ~~~Cpi~~~~~~~~n~p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~ 252 (263)
.|+|-|+++-..+ ||+..|||-||..|.-+--+++ .+|-.|++..
T Consensus 196 PF~C~iCKkdy~s---pvvt~CGH~FC~~Cai~~y~kg---~~C~~Cgk~t 240 (259)
T COG5152 196 PFLCGICKKDYES---PVVTECGHSFCSLCAIRKYQKG---DECGVCGKAT 240 (259)
T ss_pred ceeehhchhhccc---hhhhhcchhHHHHHHHHHhccC---Ccceecchhh
Confidence 4899999999888 9999999999999876554443 4899998764
No 57
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.37 E-value=0.028 Score=51.70 Aligned_cols=58 Identities=16% Similarity=0.290 Sum_probs=43.4
Q ss_pred eeccccccc--CCCCCCeecCCCceecHHHHHHHHHhCCCceecCCCCcccCcccceeccc
Q 024742 204 VCYITKELM--DTENPPQVLPNGYVYSTKALEEMAKKNNGKITCPRTGLVCNYSDLVKAYI 262 (263)
Q Consensus 204 ~Cpi~~~~~--~~~n~p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~~~~~~~v~~ 262 (263)
+|||.-+.. ..+..-+.+.|||-|+.+||++|.- ......||-|.-+-...+++..|.
T Consensus 6 tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~-k~~~~~cp~c~~katkr~i~~e~a 65 (463)
T KOG1645|consen 6 TCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLG-KKTKMQCPLCSGKATKRQIRPEYA 65 (463)
T ss_pred cCceeeeeeeecCceEEeeecccccccHHHHHHHHh-hhhhhhCcccCChhHHHHHHHHHH
Confidence 455555544 3344556789999999999999985 334569999999988888877663
No 58
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.34 E-value=0.046 Score=51.49 Aligned_cols=59 Identities=22% Similarity=0.301 Sum_probs=42.3
Q ss_pred CCCCCCCcCCeee-------------ecccccccC---CCC---C--------CeecCCCceecHHHHHHHHHhCCCcee
Q 024742 192 PLPYSKQHHSKLV-------------CYITKELMD---TEN---P--------PQVLPNGYVYSTKALEEMAKKNNGKIT 244 (263)
Q Consensus 192 ~lP~~~~~~s~~~-------------Cpi~~~~~~---~~n---~--------p~~l~cGhv~~~~~~~~~~~~~~~~~~ 244 (263)
-+|.++.||-++- |+|+...++ .++ + =|+.||.|+|.+.||++|.. ..+..
T Consensus 548 ~lpe~YsY~r~l~~dh~~~~~~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd--~ykl~ 625 (636)
T KOG0828|consen 548 FLPEKYSYHRRLQQDHLEAFVRRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMD--TYKLI 625 (636)
T ss_pred hCccccccccccccccccchhhccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHh--hhccc
Confidence 4566677766665 999887764 222 2 23469999999999999974 34578
Q ss_pred cCCCCccc
Q 024742 245 CPRTGLVC 252 (263)
Q Consensus 245 CP~c~~~~ 252 (263)
||.|....
T Consensus 626 CPvCR~pL 633 (636)
T KOG0828|consen 626 CPVCRCPL 633 (636)
T ss_pred CCccCCCC
Confidence 99998653
No 59
>smart00667 LisH Lissencephaly type-1-like homology motif. Alpha-helical motif present in Lis1, treacle, Nopp140, some katanin p60 subunits, muskelin, tonneau, LEUNIG and numerous WD40 repeat-containing proteins. It is suggested that LisH motifs contribute to the regulation of microtubule dynamics, either by mediating dimerisation, or else by binding cytoplasmic dynein heavy chain or microtubules directly.
Probab=93.11 E-value=0.059 Score=31.24 Aligned_cols=20 Identities=45% Similarity=0.630 Sum_probs=18.1
Q ss_pred CcccccHHHHHHHHHHcCCC
Q 024742 1 MLRMSYYETAEKLAESSNIQ 20 (263)
Q Consensus 1 Llr~Gy~~ta~~f~~e~~i~ 20 (263)
|.++||.++|.+|.+|+++.
T Consensus 14 L~~~g~~~ta~~l~~e~~~~ 33 (34)
T smart00667 14 LLRNGYEETAETLQKESGLS 33 (34)
T ss_pred HHHcCHHHHHHHHHHHhCCC
Confidence 56899999999999999875
No 60
>KOG3800 consensus Predicted E3 ubiquitin ligase containing RING finger, subunit of transcription/repair factor TFIIH and CDK-activating kinase assembly factor [Posttranslational modification, protein turnover, chaperones]
Probab=92.80 E-value=0.078 Score=46.78 Aligned_cols=38 Identities=11% Similarity=0.250 Sum_probs=30.1
Q ss_pred eecCCCceecHHHHHHHHHhCCCceecCCCCcccCcccce
Q 024742 219 QVLPNGYVYSTKALEEMAKKNNGKITCPRTGLVCNYSDLV 258 (263)
Q Consensus 219 ~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~~~~~~ 258 (263)
|+-||||-+|+.|+.++... |.--||.|++....+.++
T Consensus 19 ~in~C~H~lCEsCvd~iF~~--g~~~CpeC~~iLRk~nfr 56 (300)
T KOG3800|consen 19 MINECGHRLCESCVDRIFSL--GPAQCPECMVILRKNNFR 56 (300)
T ss_pred eeccccchHHHHHHHHHHhc--CCCCCCcccchhhhcccc
Confidence 34699999999999999764 456899999877665543
No 61
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=92.10 E-value=0.25 Score=31.89 Aligned_cols=47 Identities=15% Similarity=0.241 Sum_probs=23.0
Q ss_pred ecccccccCCCCCCe-ecCCCceecHHHHHHHHHhCCCceecCCCCcccC
Q 024742 205 CYITKELMDTENPPQ-VLPNGYVYSTKALEEMAKKNNGKITCPRTGLVCN 253 (263)
Q Consensus 205 Cpi~~~~~~~~n~p~-~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~ 253 (263)
||+.-+.+++...-+ ==+||+-|++.+..++.+ +..-+||-|.+.++
T Consensus 1 cp~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~--~~~g~CPgCr~~Y~ 48 (48)
T PF14570_consen 1 CPLCDEELDETDKDFYPCECGFQICRFCYHDILE--NEGGRCPGCREPYK 48 (48)
T ss_dssp -TTTS-B--CCCTT--SSTTS----HHHHHHHTT--SS-SB-TTT--B--
T ss_pred CCCcccccccCCCccccCcCCCcHHHHHHHHHHh--ccCCCCCCCCCCCC
Confidence 678888885543222 258999999999999854 23459999998764
No 62
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.92 E-value=0.16 Score=45.34 Aligned_cols=49 Identities=24% Similarity=0.352 Sum_probs=38.8
Q ss_pred CeeeecccccccCC---CCCCeecCCCceecHHHHHHHHHhCCCceecCCCCcc
Q 024742 201 SKLVCYITKELMDT---ENPPQVLPNGYVYSTKALEEMAKKNNGKITCPRTGLV 251 (263)
Q Consensus 201 s~~~Cpi~~~~~~~---~n~p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~ 251 (263)
|.+.|=|+++..+. ++-|-.|.|||.++..++.++.. ++...||.|.+.
T Consensus 2 ~~~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~--~~~i~cpfcR~~ 53 (296)
T KOG4185|consen 2 SFPECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLG--NSRILCPFCRET 53 (296)
T ss_pred CCCceeecCccccccCcccCCcccccCceehHhHHHHHhc--CceeeccCCCCc
Confidence 34567777777643 45689999999999999999964 457899999988
No 63
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.77 E-value=0.086 Score=46.78 Aligned_cols=39 Identities=21% Similarity=0.130 Sum_probs=31.2
Q ss_pred CCCCeecCCCceecHHHHHHHHHhCCCceecCCCCcccCcc
Q 024742 215 ENPPQVLPNGYVYSTKALEEMAKKNNGKITCPRTGLVCNYS 255 (263)
Q Consensus 215 ~n~p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~~~ 255 (263)
-|-|+.|+|||++|.-||+--.+ +++..||.|...++.+
T Consensus 17 ~n~Pv~l~C~HkFCyiCiKGsy~--ndk~~CavCR~pids~ 55 (324)
T KOG0824|consen 17 GNCPVNLYCFHKFCYICIKGSYK--NDKKTCAVCRFPIDST 55 (324)
T ss_pred CCcCccccccchhhhhhhcchhh--cCCCCCceecCCCCcc
Confidence 45589999999999999986543 3456799999988754
No 64
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.62 E-value=0.12 Score=47.69 Aligned_cols=41 Identities=22% Similarity=0.216 Sum_probs=34.4
Q ss_pred CCcCCeeeecccccccCCCCCCeecCCCceecHHHHHHHHH
Q 024742 197 KQHHSKLVCYITKELMDTENPPQVLPNGYVYSTKALEEMAK 237 (263)
Q Consensus 197 ~~~~s~~~Cpi~~~~~~~~n~p~~l~cGhv~~~~~~~~~~~ 237 (263)
+-..|-|-|-|+-+.-.+...-+.+||+||+|+.|++....
T Consensus 179 ~F~~slf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~ 219 (445)
T KOG1814|consen 179 KFVNSLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFT 219 (445)
T ss_pred HHHhhcccceeeehhhcCcceeeecccchHHHHHHHHHHHH
Confidence 34567789999998888877788899999999999997654
No 65
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=90.58 E-value=0.25 Score=39.62 Aligned_cols=34 Identities=24% Similarity=0.379 Sum_probs=22.8
Q ss_pred CCCceecHHHHHHHHHhCCCceecCCCCcccCccc
Q 024742 222 PNGYVYSTKALEEMAKKNNGKITCPRTGLVCNYSD 256 (263)
Q Consensus 222 ~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~~~~ 256 (263)
.||..|+-.-...+. ...+.|.||.||.+....|
T Consensus 104 ~C~~~y~~~ea~~~~-d~~~~f~Cp~Cg~~l~~~d 137 (147)
T smart00531 104 NCQSKYTFLEANQLL-DMDGTFTCPRCGEELEEDD 137 (147)
T ss_pred CCCCEeeHHHHHHhc-CCCCcEECCCCCCEEEEcC
Confidence 478888754443332 1356699999999986655
No 66
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=89.67 E-value=0.19 Score=47.89 Aligned_cols=54 Identities=11% Similarity=0.204 Sum_probs=42.8
Q ss_pred CCeeeecccccccCCCCCCeecCCCceecHHHHHHHHHh--CCCceecCCCCcccCccc
Q 024742 200 HSKLVCYITKELMDTENPPQVLPNGYVYSTKALEEMAKK--NNGKITCPRTGLVCNYSD 256 (263)
Q Consensus 200 ~s~~~Cpi~~~~~~~~n~p~~l~cGhv~~~~~~~~~~~~--~~~~~~CP~c~~~~~~~~ 256 (263)
.+...|-++.++..+ ++...|.|+||+-|+...... .+..++||.|....+.+.
T Consensus 534 k~~~~C~lc~d~aed---~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiDl 589 (791)
T KOG1002|consen 534 KGEVECGLCHDPAED---YIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSIDL 589 (791)
T ss_pred cCceeecccCChhhh---hHhhhhhHHHHHHHHHHHHHhhhcccCCCCccccccccccc
Confidence 466789999888877 899999999999999776542 223399999998877664
No 67
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.63 E-value=0.14 Score=45.43 Aligned_cols=45 Identities=16% Similarity=0.260 Sum_probs=36.8
Q ss_pred eeecccccccCCCCCCeecCCCceecHHHHHHHHHhCCCceecCCCCcccC
Q 024742 203 LVCYITKELMDTENPPQVLPNGYVYSTKALEEMAKKNNGKITCPRTGLVCN 253 (263)
Q Consensus 203 ~~Cpi~~~~~~~~n~p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~ 253 (263)
|.|-|+++-.-. ||+..|||-||..|-.+-.+++ -+|+.|++...
T Consensus 242 f~c~icr~~f~~---pVvt~c~h~fc~~ca~~~~qk~---~~c~vC~~~t~ 286 (313)
T KOG1813|consen 242 FKCFICRKYFYR---PVVTKCGHYFCEVCALKPYQKG---EKCYVCSQQTH 286 (313)
T ss_pred cccccccccccc---chhhcCCceeehhhhccccccC---Ccceecccccc
Confidence 579999988887 9999999999999986554432 59999998654
No 68
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=89.53 E-value=0.18 Score=33.99 Aligned_cols=18 Identities=17% Similarity=0.510 Sum_probs=14.8
Q ss_pred hCCCceecCCCCcccCcc
Q 024742 238 KNNGKITCPRTGLVCNYS 255 (263)
Q Consensus 238 ~~~~~~~CP~c~~~~~~~ 255 (263)
+..+.++||||+..|++.
T Consensus 44 g~~gev~CPYC~t~y~l~ 61 (62)
T COG4391 44 GDEGEVVCPYCSTRYRLN 61 (62)
T ss_pred CCCCcEecCccccEEEec
Confidence 456789999999999764
No 69
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=89.25 E-value=0.13 Score=38.38 Aligned_cols=28 Identities=18% Similarity=0.330 Sum_probs=17.9
Q ss_pred ecccccccCCCCCCeecCCCceecHHHHH
Q 024742 205 CYITKELMDTENPPQVLPNGYVYSTKALE 233 (263)
Q Consensus 205 Cpi~~~~~~~~n~p~~l~cGhv~~~~~~~ 233 (263)
|+++++.+.. ...++.|||||+-..|++
T Consensus 81 C~vC~k~l~~-~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 81 CSVCGKPLGN-SVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred ccCcCCcCCC-ceEEEeCCCeEEeccccc
Confidence 3333333332 345679999999888765
No 70
>KOG0883 consensus Cyclophilin type, U box-containing peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=88.91 E-value=0.22 Score=45.80 Aligned_cols=68 Identities=21% Similarity=0.229 Sum_probs=52.7
Q ss_pred CCCCCCCcCCeeeecccccccCCCCCCe-ecCCCceecHHHHHHHHHhCCCceecCCCCcccCcccceec
Q 024742 192 PLPYSKQHHSKLVCYITKELMDTENPPQ-VLPNGYVYSTKALEEMAKKNNGKITCPRTGLVCNYSDLVKA 260 (263)
Q Consensus 192 ~lP~~~~~~s~~~Cpi~~~~~~~~n~p~-~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~~~~~~~v 260 (263)
.|-+.....--+.|||+-.+++.+---| +-..|.|||.++|++|.-+. ...+.-.+-+.|+..|++.+
T Consensus 91 kL~F~Kns~geyhcPvlfk~FT~~sHIvAv~TTGNvy~~eai~~LNiK~-knwkdLltdepFtR~DiIti 159 (518)
T KOG0883|consen 91 KLKFHKNSEGEYHCPVLFKVFTRFSHIVAVRTTGNVYSWEAIEELNIKT-KNWKDLLTDEPFTRADIITI 159 (518)
T ss_pred eeeeccCCCCcccCceeeeeecccceEEEEEecCceeeHHHHHHhCcch-hhHHHhhccCCcchhceeee
Confidence 3444444555688999999999875545 56899999999999996543 34788899999999998765
No 71
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=88.32 E-value=0.28 Score=43.44 Aligned_cols=46 Identities=30% Similarity=0.426 Sum_probs=37.6
Q ss_pred eeeecccccccCCCC-CCeecCCCceecHHHHHHHHHhCCCceecCCCCc
Q 024742 202 KLVCYITKELMDTEN-PPQVLPNGYVYSTKALEEMAKKNNGKITCPRTGL 250 (263)
Q Consensus 202 ~~~Cpi~~~~~~~~n-~p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~ 250 (263)
.+.||+..|-+.... .|-.++|||....++++.... ++ ..||.|.+
T Consensus 158 ~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~--~~-y~CP~C~~ 204 (276)
T KOG1940|consen 158 EFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMIC--EG-YTCPICSK 204 (276)
T ss_pred cCCCchhHHHhccccccCCccCcccchHHHHHHHHhc--cC-CCCCcccc
Confidence 345999999996654 466899999999999998864 34 89999998
No 72
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=88.28 E-value=0.19 Score=46.14 Aligned_cols=47 Identities=26% Similarity=0.514 Sum_probs=38.9
Q ss_pred eeecccccccCCCCCCe-ecCCCceecHHHHHHHHHhCCCceecCCCCc
Q 024742 203 LVCYITKELMDTENPPQ-VLPNGYVYSTKALEEMAKKNNGKITCPRTGL 250 (263)
Q Consensus 203 ~~Cpi~~~~~~~~n~p~-~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~ 250 (263)
+.|-.+||.....|--. .|||.|++-.+|+.++..++ +.-.||.|.+
T Consensus 366 L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n-~~rsCP~Crk 413 (518)
T KOG1941|consen 366 LYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENN-GTRSCPNCRK 413 (518)
T ss_pred hhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhC-CCCCCccHHH
Confidence 57999999997666444 79999999999999998755 4469999984
No 73
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.18 E-value=0.26 Score=45.97 Aligned_cols=48 Identities=19% Similarity=0.351 Sum_probs=37.2
Q ss_pred CCeeeecccccccCCCCCCeecCCCceecHHHHHHHHHhCCCceecCCCCcccC
Q 024742 200 HSKLVCYITKELMDTENPPQVLPNGYVYSTKALEEMAKKNNGKITCPRTGLVCN 253 (263)
Q Consensus 200 ~s~~~Cpi~~~~~~~~n~p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~ 253 (263)
-|-|-|-|+...+-+ |+.+||||.+|..||.+... ..-.||.|..++.
T Consensus 82 ~sef~c~vc~~~l~~---pv~tpcghs~c~~Cl~r~ld---~~~~cp~Cr~~l~ 129 (398)
T KOG4159|consen 82 RSEFECCVCSRALYP---PVVTPCGHSFCLECLDRSLD---QETECPLCRDELV 129 (398)
T ss_pred cchhhhhhhHhhcCC---CccccccccccHHHHHHHhc---cCCCCcccccccc
Confidence 566777777555544 99999999999999988543 3468999988776
No 74
>PF04494 TFIID_90kDa: WD40 associated region in TFIID subunit; InterPro: IPR007582 This region, possibly a domain is found in subunits of transcription factor TFIID. The function of this region is unknown.; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2J4B_D 2J49_A 2NXP_F.
Probab=87.93 E-value=0.76 Score=36.61 Aligned_cols=53 Identities=13% Similarity=0.395 Sum_probs=44.5
Q ss_pred hchhhhhCCCceeeechHHHHHHHHhcCChHHHHHHHHHhCcchhhhhHHHHHHHHH
Q 024742 53 NKSRLKKSKSKFEFQLRLQEFIELVRGENNLRAITYARKYLAPWGATHMKELQRVMA 109 (263)
Q Consensus 53 ~~~~L~~~~s~LeF~L~~q~fIeLi~~~~~~eAi~yar~~l~~~~~~~~~ei~~~~~ 109 (263)
.+++|. .+.|=+-..-|++||.+|...+|..|..++-.-+...+.++|+++.+
T Consensus 33 yK~EL~----~lLyPvFvh~YL~Lv~~~~~~~A~~F~~kf~~~~~~~~~~~i~~L~~ 85 (142)
T PF04494_consen 33 YKPELS----RLLYPVFVHSYLDLVSKGHPEEAKSFLEKFSPDFEDSHQEDIEKLSS 85 (142)
T ss_dssp HHHHHG----GGHHHHHHHHHHHHHHTT-HHHHHHHHHHHGGGGHGHGHHHHHHHTT
T ss_pred hHHHHH----HHHHHHHHHHHHHHHHCCChHHHHHHHHHHHHHHhHHHHHHHHHHHh
Confidence 456664 47999999999999999999999999999888888888888888764
No 75
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=87.75 E-value=0.32 Score=33.97 Aligned_cols=52 Identities=19% Similarity=0.151 Sum_probs=23.7
Q ss_pred eecccccccC-CCCCCee----cCCCceecHHHHHHHHHh--CC------CceecCCCCcccCcc
Q 024742 204 VCYITKELMD-TENPPQV----LPNGYVYSTKALEEMAKK--NN------GKITCPRTGLVCNYS 255 (263)
Q Consensus 204 ~Cpi~~~~~~-~~n~p~~----l~cGhv~~~~~~~~~~~~--~~------~~~~CP~c~~~~~~~ 255 (263)
-|+|.-+... ++.-|.+ -.||+++-..+|.+|... +. ..-+||+|.+..+.+
T Consensus 4 ~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~~~ 68 (70)
T PF11793_consen 4 ECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPISWS 68 (70)
T ss_dssp S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEEGG
T ss_pred CCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeeeEe
Confidence 3566655543 2233333 279999999999999863 11 134899999988764
No 76
>PF04710 Pellino: Pellino; InterPro: IPR006800 Pellino is involved in Toll-like signalling pathways, and associates with the kinase domain of the Pelle Ser/Thr kinase [, , ].; PDB: 3EGB_B 3EGA_A.
Probab=87.74 E-value=0.16 Score=46.75 Aligned_cols=43 Identities=19% Similarity=0.188 Sum_probs=0.0
Q ss_pred ecCCCceecHHHHHHHHHh----CC--CceecCCCCcccCc-ccceeccc
Q 024742 220 VLPNGYVYSTKALEEMAKK----NN--GKITCPRTGLVCNY-SDLVKAYI 262 (263)
Q Consensus 220 ~l~cGhv~~~~~~~~~~~~----~~--~~~~CP~c~~~~~~-~~~~~v~~ 262 (263)
.-|||||.|++..+-|++- +. =+-.||.|.....- .-..|++|
T Consensus 362 F~PCGHv~SekTa~yWs~i~lPhGt~~f~a~CPFCa~~L~g~~g~vrLiF 411 (416)
T PF04710_consen 362 FNPCGHVCSEKTAKYWSQIPLPHGTHAFHAACPFCATPLDGEQGYVRLIF 411 (416)
T ss_dssp --------------------------------------------------
T ss_pred ecccccccchhhhhhhhcCCCCCCcccccccCCcccCcccCCCCceEEEE
Confidence 3699999999999999862 11 13599999988763 34555554
No 77
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=87.69 E-value=0.14 Score=33.68 Aligned_cols=16 Identities=38% Similarity=0.536 Sum_probs=12.4
Q ss_pred ceecCCCCcccCcccc
Q 024742 242 KITCPRTGLVCNYSDL 257 (263)
Q Consensus 242 ~~~CP~c~~~~~~~~~ 257 (263)
.|+||+|++.|+..++
T Consensus 2 ~f~CP~C~~~~~~~~L 17 (54)
T PF05605_consen 2 SFTCPYCGKGFSESSL 17 (54)
T ss_pred CcCCCCCCCccCHHHH
Confidence 5899999998776554
No 78
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=87.29 E-value=0.3 Score=45.68 Aligned_cols=45 Identities=16% Similarity=0.220 Sum_probs=36.4
Q ss_pred eecccccccCCCC-CCeecCCCceecHHHHHHHHHhCCCceecCCCCcccC
Q 024742 204 VCYITKELMDTEN-PPQVLPNGYVYSTKALEEMAKKNNGKITCPRTGLVCN 253 (263)
Q Consensus 204 ~Cpi~~~~~~~~n-~p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~ 253 (263)
+|||+.|.||++= .-+...|.|.|--.|+.+|.- -.||.|.-...
T Consensus 177 TCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~~-----~scpvcR~~q~ 222 (493)
T KOG0804|consen 177 TCPVCLERMDSSTTGILTILCNHSFHCSCLMKWWD-----SSCPVCRYCQS 222 (493)
T ss_pred CcchhHhhcCccccceeeeecccccchHHHhhccc-----CcChhhhhhcC
Confidence 6999999998864 445689999999999999942 47888876555
No 79
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=87.21 E-value=0.63 Score=32.16 Aligned_cols=17 Identities=29% Similarity=0.683 Sum_probs=14.5
Q ss_pred CCceecCCCCcccCccc
Q 024742 240 NGKITCPRTGLVCNYSD 256 (263)
Q Consensus 240 ~~~~~CP~c~~~~~~~~ 256 (263)
++..+||.|+..|...|
T Consensus 51 eg~L~Cp~c~r~YPI~d 67 (68)
T PF03966_consen 51 EGELICPECGREYPIRD 67 (68)
T ss_dssp TTEEEETTTTEEEEEET
T ss_pred CCEEEcCCCCCEEeCCC
Confidence 57899999999998754
No 80
>PF14353 CpXC: CpXC protein
Probab=87.02 E-value=0.5 Score=36.79 Aligned_cols=26 Identities=19% Similarity=0.268 Sum_probs=18.1
Q ss_pred HHHHHHHHhCCCceecCCCCcccCcc
Q 024742 230 KALEEMAKKNNGKITCPRTGLVCNYS 255 (263)
Q Consensus 230 ~~~~~~~~~~~~~~~CP~c~~~~~~~ 255 (263)
+..+++..++=..++||.||..+..+
T Consensus 26 ~l~e~il~g~l~~~~CP~Cg~~~~~~ 51 (128)
T PF14353_consen 26 ELKEKILDGSLFSFTCPSCGHKFRLE 51 (128)
T ss_pred HHHHHHHcCCcCEEECCCCCCceecC
Confidence 44555554344578999999999763
No 81
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=85.86 E-value=0.39 Score=44.35 Aligned_cols=53 Identities=21% Similarity=0.265 Sum_probs=37.1
Q ss_pred eecccccccCCCCCCeecCCCceecHHHHHHHHHhCCCceecCCCCcccCcccceec
Q 024742 204 VCYITKELMDTENPPQVLPNGYVYSTKALEEMAKKNNGKITCPRTGLVCNYSDLVKA 260 (263)
Q Consensus 204 ~Cpi~~~~~~~~n~p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~~~~~~~v 260 (263)
.|.|+-|--.+ .-+=||||.+|..||..|-. +++--.||.|.-+.+=.+-+-|
T Consensus 371 LCKICaendKd---vkIEPCGHLlCt~CLa~WQ~-sd~gq~CPFCRcEIKGte~vii 423 (563)
T KOG1785|consen 371 LCKICAENDKD---VKIEPCGHLLCTSCLAAWQD-SDEGQTCPFCRCEIKGTEPVII 423 (563)
T ss_pred HHHHhhccCCC---cccccccchHHHHHHHhhcc-cCCCCCCCceeeEeccccceee
Confidence 46666553332 44679999999999999943 3334599999988776555444
No 82
>cd08044 TAF5_NTD2 TAF5_NTD2 is the second conserved N-terminal region of TATA Binding Protein (TBP) Associated Factor 5 (TAF5), involved in forming Transcription Factor IID (TFIID). The TATA Binding Protein (TBP) Associated Factor 5 (TAF5) is one of several TAFs that bind TBP and are involved in forming Transcription Factor IID (TFIID) complex. TAF5 contains three domains, two conserved sequence motifs at the N-terminal and one at the C-terminal region. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the preinitiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. In yeast and human cells, TAFs have been found as components of other complexes besides TFIID. TAF5 may play a major role in forming TFIID and its related complexes. TAFs from various
Probab=85.19 E-value=0.96 Score=35.56 Aligned_cols=54 Identities=11% Similarity=0.351 Sum_probs=44.3
Q ss_pred chhhhhCCCceeeechHHHHHHHHhcCChHHHHHHHHHhCcchhhhhHHHHHHHHHHh
Q 024742 54 KSRLKKSKSKFEFQLRLQEFIELVRGENNLRAITYARKYLAPWGATHMKELQRVMATL 111 (263)
Q Consensus 54 ~~~L~~~~s~LeF~L~~q~fIeLi~~~~~~eAi~yar~~l~~~~~~~~~ei~~~~~lL 111 (263)
+++|. .+.|=+...-|++||.+|...+|.+|.+++-.-+...|.++|+++.+..
T Consensus 23 k~EL~----~lLyPiFvh~yL~lv~~~~~~~A~~F~~~f~~~~~~~~~~~i~~L~~i~ 76 (133)
T cd08044 23 KYELS----QLLYPIFVHSYLDLVASGHLEEAKSFFERFSGDFEDSHSEDIKKLSSIT 76 (133)
T ss_pred HHHHH----HHHHHHHHHHHHHHHHCCCHHHHHHHHHHhhHhhHHHHHHHHHHHHccC
Confidence 45553 4788899999999999999999999999887777777888888885543
No 83
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=84.88 E-value=0.28 Score=34.67 Aligned_cols=43 Identities=9% Similarity=0.183 Sum_probs=34.7
Q ss_pred CCCCCeec-CCCceecHHHHHHHHHhCCCceecCCCCcccCccc
Q 024742 214 TENPPQVL-PNGYVYSTKALEEMAKKNNGKITCPRTGLVCNYSD 256 (263)
Q Consensus 214 ~~n~p~~l-~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~~~~ 256 (263)
+++-|+++ .|-|.+-.-+|.+|.....++-.||.|.++|.+.+
T Consensus 41 gDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~~~e 84 (84)
T KOG1493|consen 41 GDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQFKE 84 (84)
T ss_pred CCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeEecC
Confidence 35667765 69999999999999865566789999999997654
No 84
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=82.67 E-value=1 Score=40.84 Aligned_cols=55 Identities=18% Similarity=0.229 Sum_probs=41.9
Q ss_pred ecccccccCCCC-CCeecCCCceecHHHHHHHHHhCCCceecCCCCcccCcccceecc
Q 024742 205 CYITKELMDTEN-PPQVLPNGYVYSTKALEEMAKKNNGKITCPRTGLVCNYSDLVKAY 261 (263)
Q Consensus 205 Cpi~~~~~~~~n-~p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~~~~~~~v~ 261 (263)
||++.|.||-.. ...--|||.-+|+=|-..+-+.-+ -.||-|...++.+.++-+-
T Consensus 17 cplcie~mditdknf~pc~cgy~ic~fc~~~irq~ln--grcpacrr~y~denv~~~~ 72 (480)
T COG5175 17 CPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLN--GRCPACRRKYDDENVRYVT 72 (480)
T ss_pred CcccccccccccCCcccCCcccHHHHHHHHHHHhhcc--CCChHhhhhccccceeEEe
Confidence 888899885332 244579999999999888854323 4899999999998887554
No 85
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=82.43 E-value=0.97 Score=41.66 Aligned_cols=46 Identities=15% Similarity=0.247 Sum_probs=30.0
Q ss_pred eeccccccc-CCCCCCeecCCCceecHHHHHHHHHhCCCceecCCCC
Q 024742 204 VCYITKELM-DTENPPQVLPNGYVYSTKALEEMAKKNNGKITCPRTG 249 (263)
Q Consensus 204 ~Cpi~~~~~-~~~n~p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~ 249 (263)
+|-|+-+.. .++|-.-+-.|||||-..|+.+|.........||+|.
T Consensus 6 ~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ 52 (465)
T KOG0827|consen 6 ECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQ 52 (465)
T ss_pred eeeEeccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCcee
Confidence 455552222 1233334457999999999999987432225899998
No 86
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=81.60 E-value=0.79 Score=25.33 Aligned_cols=15 Identities=20% Similarity=0.432 Sum_probs=12.4
Q ss_pred CCCceecCCCCcccC
Q 024742 239 NNGKITCPRTGLVCN 253 (263)
Q Consensus 239 ~~~~~~CP~c~~~~~ 253 (263)
+...++||+|++.|.
T Consensus 11 ~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 11 GEKPYKCPYCGKSFS 25 (26)
T ss_dssp SSSSEEESSSSEEES
T ss_pred CCCCCCCCCCcCeeC
Confidence 456799999999885
No 87
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=81.52 E-value=0.71 Score=24.29 Aligned_cols=14 Identities=21% Similarity=0.427 Sum_probs=11.5
Q ss_pred eecCCCCcccCccc
Q 024742 243 ITCPRTGLVCNYSD 256 (263)
Q Consensus 243 ~~CP~c~~~~~~~~ 256 (263)
++||+|++.|....
T Consensus 1 y~C~~C~~~f~~~~ 14 (23)
T PF00096_consen 1 YKCPICGKSFSSKS 14 (23)
T ss_dssp EEETTTTEEESSHH
T ss_pred CCCCCCCCccCCHH
Confidence 58999999998653
No 88
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=81.50 E-value=0.43 Score=47.61 Aligned_cols=77 Identities=8% Similarity=0.103 Sum_probs=46.2
Q ss_pred CCCCCCchhhhhhc---CCCCCCCCcCCeeeecccccccCCCCCCeecCCCceecHHHHHHHHHhCCCceecCCCCcccC
Q 024742 177 KEDPLSQESFRKLA---SPLPYSKQHHSKLVCYITKELMDTENPPQVLPNGYVYSTKALEEMAKKNNGKITCPRTGLVCN 253 (263)
Q Consensus 177 ~~cp~c~~~~~~l~---~~lP~~~~~~s~~~Cpi~~~~~~~~n~p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~ 253 (263)
..|+.|+.++.+=. --+|...+.|+ -||++-.-+.+.-----.+|||.||..||..|++- --+||.|..+|.
T Consensus 97 ~Ss~~C~~E~S~~~ds~~i~P~~~~~~~--~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~---aqTCPiDR~EF~ 171 (1134)
T KOG0825|consen 97 DTSPVCEKEHSPDVDSSNICPVQTHVEN--QCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRC---AQTCPVDRGEFG 171 (1134)
T ss_pred cccchhheecCCcccccCcCchhhhhhh--hhhHHHHHHHHHhhccccccccccHHHHhhhhhhh---cccCchhhhhhh
Confidence 44777777665411 12232222222 25555444432111122689999999999999863 249999999998
Q ss_pred cccce
Q 024742 254 YSDLV 258 (263)
Q Consensus 254 ~~~~~ 258 (263)
.-.+.
T Consensus 172 ~v~V~ 176 (1134)
T KOG0825|consen 172 EVKVL 176 (1134)
T ss_pred eeeee
Confidence 65543
No 89
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=80.90 E-value=0.74 Score=43.05 Aligned_cols=51 Identities=18% Similarity=0.305 Sum_probs=40.6
Q ss_pred CCeeeecccccccCCCCCCee-cCCCceecHHHHHHHHHhCCCceecCCCCcccCccc
Q 024742 200 HSKLVCYITKELMDTENPPQV-LPNGYVYSTKALEEMAKKNNGKITCPRTGLVCNYSD 256 (263)
Q Consensus 200 ~s~~~Cpi~~~~~~~~n~p~~-l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~~~~ 256 (263)
.-.+.||+...++.+ |+- ..|||.||.-++..+... ..+||.|...-..++
T Consensus 19 ~~~l~C~~C~~vl~~---p~~~~~cgh~fC~~C~~~~~~~---~~~cp~~~~~~~~~~ 70 (391)
T KOG0297|consen 19 DENLLCPICMSVLRD---PVQTTTCGHRFCAGCLLESLSN---HQKCPVCRQELTQAE 70 (391)
T ss_pred cccccCccccccccC---CCCCCCCCCcccccccchhhcc---CcCCcccccccchhh
Confidence 344789999888888 776 699999999999998753 679999976655544
No 90
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=80.80 E-value=0.72 Score=46.66 Aligned_cols=21 Identities=24% Similarity=0.347 Sum_probs=18.2
Q ss_pred CCeecCCCceecHHHHHHHHH
Q 024742 217 PPQVLPNGYVYSTKALEEMAK 237 (263)
Q Consensus 217 ~p~~l~cGhv~~~~~~~~~~~ 237 (263)
|.|++||||-+-++||.+-..
T Consensus 831 pF~vf~CgH~FH~~Cl~~~v~ 851 (911)
T KOG2034|consen 831 PFYVFPCGHCFHRDCLIRHVL 851 (911)
T ss_pred cceeeeccchHHHHHHHHHHH
Confidence 678899999999999987653
No 91
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=80.60 E-value=0.55 Score=45.86 Aligned_cols=40 Identities=20% Similarity=0.370 Sum_probs=29.3
Q ss_pred eeeeccc-ccccCCCCCCeecCCCceecHHHHHHHHHhCCCceecC
Q 024742 202 KLVCYIT-KELMDTENPPQVLPNGYVYSTKALEEMAKKNNGKITCP 246 (263)
Q Consensus 202 ~~~Cpi~-~~~~~~~n~p~~l~cGhv~~~~~~~~~~~~~~~~~~CP 246 (263)
.+.|+|+ .+-..+.--|+-+-|||++|+.|++.+-. -.||
T Consensus 11 ~l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~lyn-----~scp 51 (861)
T KOG3161|consen 11 LLLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLYN-----ASCP 51 (861)
T ss_pred HhhchHHHHHHHHHhcCcccccccchHHHHHHHhHhh-----ccCC
Confidence 4567766 44444445689999999999999998843 3787
No 92
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=80.54 E-value=1.7 Score=34.18 Aligned_cols=55 Identities=24% Similarity=0.234 Sum_probs=43.1
Q ss_pred CeeeecccccccCCCCCCeecC---CCceecHHHHHHHHHhCCCceecCCCCcccCcccc
Q 024742 201 SKLVCYITKELMDTENPPQVLP---NGYVYSTKALEEMAKKNNGKITCPRTGLVCNYSDL 257 (263)
Q Consensus 201 s~~~Cpi~~~~~~~~n~p~~l~---cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~~~~~ 257 (263)
...-|-|.+|...|+. ++-| ||.-++--+--.|.+-..-..+||.|+..|+.+..
T Consensus 79 ~lYeCnIC~etS~ee~--FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKss~~ 136 (140)
T PF05290_consen 79 KLYECNICKETSAEER--FLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKSSSS 136 (140)
T ss_pred CceeccCcccccchhh--cCCcccccchHHHHHHHHHHHHHcccCCCCCccccccccccc
Confidence 4567888898887743 3333 89999999888888766677899999999998754
No 93
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=80.37 E-value=1.2 Score=40.05 Aligned_cols=48 Identities=17% Similarity=0.247 Sum_probs=39.8
Q ss_pred CCcCCeeeecccccccCCCCCCee-cCCCceecHHHHHHHHHhCCCceecCCCCcccC
Q 024742 197 KQHHSKLVCYITKELMDTENPPQV-LPNGYVYSTKALEEMAKKNNGKITCPRTGLVCN 253 (263)
Q Consensus 197 ~~~~s~~~Cpi~~~~~~~~n~p~~-l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~ 253 (263)
.-..+.+-|||..+.+.. |++ =++||..|-.|-.++. .+||.|...+.
T Consensus 43 ~~~~~lleCPvC~~~l~~---Pi~QC~nGHlaCssC~~~~~------~~CP~Cr~~~g 91 (299)
T KOG3002|consen 43 LLDLDLLDCPVCFNPLSP---PIFQCDNGHLACSSCRTKVS------NKCPTCRLPIG 91 (299)
T ss_pred ccchhhccCchhhccCcc---cceecCCCcEehhhhhhhhc------ccCCccccccc
Confidence 446788999999999988 887 6899999999987663 48999988776
No 94
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=79.13 E-value=1.5 Score=38.05 Aligned_cols=32 Identities=25% Similarity=0.526 Sum_probs=26.8
Q ss_pred CeeeecccccccCCCCCCeecCCCceecHHHHHHH
Q 024742 201 SKLVCYITKELMDTENPPQVLPNGYVYSTKALEEM 235 (263)
Q Consensus 201 s~~~Cpi~~~~~~~~n~p~~l~cGhv~~~~~~~~~ 235 (263)
+.=.|.+|.+.+.+ ||+.|.||+|+++||.+.
T Consensus 42 ~FdcCsLtLqPc~d---Pvit~~GylfdrEaILe~ 73 (303)
T KOG3039|consen 42 PFDCCSLTLQPCRD---PVITPDGYLFDREAILEY 73 (303)
T ss_pred CcceeeeecccccC---CccCCCCeeeeHHHHHHH
Confidence 33468888888887 999999999999999754
No 95
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=79.07 E-value=1 Score=45.34 Aligned_cols=39 Identities=26% Similarity=0.422 Sum_probs=29.6
Q ss_pred eecccccccCCCCCCee-cCCCceecHHHHHHHHHhCCCceecCCCCcc
Q 024742 204 VCYITKELMDTENPPQV-LPNGYVYSTKALEEMAKKNNGKITCPRTGLV 251 (263)
Q Consensus 204 ~Cpi~~~~~~~~n~p~~-l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~ 251 (263)
.|..++-.++- |++ +-|||.|-..|++ ++..+||.|.-+
T Consensus 842 kCs~C~~~Ldl---P~VhF~CgHsyHqhC~e------~~~~~CP~C~~e 881 (933)
T KOG2114|consen 842 KCSACEGTLDL---PFVHFLCGHSYHQHCLE------DKEDKCPKCLPE 881 (933)
T ss_pred eecccCCcccc---ceeeeecccHHHHHhhc------cCcccCCccchh
Confidence 56665555554 665 9999999999998 345799999863
No 96
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=78.23 E-value=0.5 Score=26.01 Aligned_cols=16 Identities=31% Similarity=0.503 Sum_probs=12.6
Q ss_pred ceecCCCCcccCcccc
Q 024742 242 KITCPRTGLVCNYSDL 257 (263)
Q Consensus 242 ~~~CP~c~~~~~~~~~ 257 (263)
.+.||+|++.|..+.+
T Consensus 2 l~~C~~CgR~F~~~~l 17 (25)
T PF13913_consen 2 LVPCPICGRKFNPDRL 17 (25)
T ss_pred CCcCCCCCCEECHHHH
Confidence 3689999999976654
No 97
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=77.72 E-value=0.36 Score=30.14 Aligned_cols=26 Identities=15% Similarity=0.459 Sum_probs=18.1
Q ss_pred cCCCceecHHHHHHHHHhCCCceecCCCCc
Q 024742 221 LPNGYVYSTKALEEMAKKNNGKITCPRTGL 250 (263)
Q Consensus 221 l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~ 250 (263)
..|||++... ..++. +....||.|+.
T Consensus 9 ~~Cg~~fe~~--~~~~~--~~~~~CP~Cg~ 34 (42)
T PF09723_consen 9 EECGHEFEVL--QSISE--DDPVPCPECGS 34 (42)
T ss_pred CCCCCEEEEE--EEcCC--CCCCcCCCCCC
Confidence 4689988543 34432 45689999998
No 98
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=77.42 E-value=1.7 Score=39.82 Aligned_cols=61 Identities=11% Similarity=0.183 Sum_probs=43.7
Q ss_pred CCCCCCcCCeeeecccccccCCCC-----CCeecCCCceecHHHHHHHHHhC----CCceecCCCCcccC
Q 024742 193 LPYSKQHHSKLVCYITKELMDTEN-----PPQVLPNGYVYSTKALEEMAKKN----NGKITCPRTGLVCN 253 (263)
Q Consensus 193 lP~~~~~~s~~~Cpi~~~~~~~~n-----~p~~l~cGhv~~~~~~~~~~~~~----~~~~~CP~c~~~~~ 253 (263)
.-+++.-.+...|-|++|...+-. --++.+|-|.+|.+|+.+|.... .....||.|....+
T Consensus 152 ~~~a~~~s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~ 221 (344)
T KOG1039|consen 152 RSFALQKSSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSS 221 (344)
T ss_pred hccCcCccccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccc
Confidence 333444477889999999998754 22345699999999999997322 12468999987654
No 99
>PF10915 DUF2709: Protein of unknown function (DUF2709); InterPro: IPR024484 Members of this family appear restricted to Chlamydiales. Their function is unknown.
Probab=76.61 E-value=3.4 Score=34.54 Aligned_cols=43 Identities=14% Similarity=0.255 Sum_probs=31.3
Q ss_pred CCcCCeeeecccccccCCCCCCeecCCCceecHHHHHHHHHhCCCceecCCCCcccC
Q 024742 197 KQHHSKLVCYITKELMDTENPPQVLPNGYVYSTKALEEMAKKNNGKITCPRTGLVCN 253 (263)
Q Consensus 197 ~~~~s~~~Cpi~~~~~~~~n~p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~ 253 (263)
-.+.-+++||.||.++.++ -|-=-.+||-.|.. +||.--+...
T Consensus 82 E~TkkIYICPFTGKVF~DN--------t~~nPQDAIYDWvS------kCPeN~ER~~ 124 (238)
T PF10915_consen 82 EQTKKIYICPFTGKVFGDN--------THPNPQDAIYDWVS------KCPENTERQG 124 (238)
T ss_pred cccceEEEcCCcCccccCC--------CCCChHHHHHHHHh------hCCccchhcc
Confidence 5678899999999999773 23345789999975 6776554443
No 100
>PF04710 Pellino: Pellino; InterPro: IPR006800 Pellino is involved in Toll-like signalling pathways, and associates with the kinase domain of the Pelle Ser/Thr kinase [, , ].; PDB: 3EGB_B 3EGA_A.
Probab=76.38 E-value=0.83 Score=42.25 Aligned_cols=40 Identities=25% Similarity=0.312 Sum_probs=0.0
Q ss_pred CCCCe-ecCCCceecHHHHHHHHHhCCCceecCCCCcccCc
Q 024742 215 ENPPQ-VLPNGYVYSTKALEEMAKKNNGKITCPRTGLVCNY 254 (263)
Q Consensus 215 ~n~p~-~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~~ 254 (263)
+..|. -+.||||.+.-.--.-...+...-+||.|.++-.+
T Consensus 300 ~~qP~VYl~CGHVhG~h~Wg~~~~~~~~~r~CPlCr~~g~~ 340 (416)
T PF04710_consen 300 ERQPWVYLNCGHVHGYHNWGQDSDRDPRSRTCPLCRQVGPY 340 (416)
T ss_dssp -----------------------------------------
T ss_pred ccCceeeccccceeeecccccccccccccccCCCccccCCc
Confidence 44455 59999999876543221112236799999887554
No 101
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=75.82 E-value=1.2 Score=41.57 Aligned_cols=32 Identities=16% Similarity=0.296 Sum_probs=27.9
Q ss_pred eeecccccccCCCCCCeecCCCceecHHHHHHHHH
Q 024742 203 LVCYITKELMDTENPPQVLPNGYVYSTKALEEMAK 237 (263)
Q Consensus 203 ~~Cpi~~~~~~~~n~p~~l~cGhv~~~~~~~~~~~ 237 (263)
+-|||++.-..+ |++|||||-+|+-|-..+..
T Consensus 5 lkc~vc~~f~~e---piil~c~h~lc~~ca~~~~~ 36 (699)
T KOG4367|consen 5 LKCPVCGSFYRE---PIILPCSHNLCQACARNILV 36 (699)
T ss_pred ccCceehhhccC---ceEeecccHHHHHHHHhhcc
Confidence 569999988888 99999999999999887664
No 102
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=75.73 E-value=1.4 Score=22.87 Aligned_cols=14 Identities=21% Similarity=0.451 Sum_probs=9.3
Q ss_pred eecCCCCcccCccc
Q 024742 243 ITCPRTGLVCNYSD 256 (263)
Q Consensus 243 ~~CP~c~~~~~~~~ 256 (263)
++||+|+..|...+
T Consensus 1 ~~C~~C~~~~~~~~ 14 (24)
T PF13894_consen 1 FQCPICGKSFRSKS 14 (24)
T ss_dssp EE-SSTS-EESSHH
T ss_pred CCCcCCCCcCCcHH
Confidence 57999999987644
No 103
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=75.66 E-value=1.3 Score=29.01 Aligned_cols=55 Identities=9% Similarity=0.117 Sum_probs=37.2
Q ss_pred CCCCchhhhhhcCCC-CCCCCcCCe-eeecccccccCCCCCCeecCCCceecHHHHHHH
Q 024742 179 DPLSQESFRKLASPL-PYSKQHHSK-LVCYITKELMDTENPPQVLPNGYVYSTKALEEM 235 (263)
Q Consensus 179 cp~c~~~~~~l~~~l-P~~~~~~s~-~~Cpi~~~~~~~~n~p~~l~cGhv~~~~~~~~~ 235 (263)
|+.|...+.+-+.-+ .....+|.. |.|-..+..+++.. +....|.+|++++..+.
T Consensus 1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~--~~~~~~~~~C~~c~~~~ 57 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPLNDGD--FYEKDGKPYCKDCYQKR 57 (58)
T ss_dssp BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBTTTSS--EEEETTEEEEHHHHHHH
T ss_pred CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCccCCCe--eEeECCEEECHHHHhhh
Confidence 344555444333321 233556665 99999999998765 78889999999987653
No 104
>KOG0275 consensus Conserved WD40 repeat-containing protein [General function prediction only]
Probab=75.53 E-value=11 Score=34.39 Aligned_cols=123 Identities=17% Similarity=0.137 Sum_probs=77.9
Q ss_pred cHHHHHHHHHHcCCCC-CC-CHHHHHHHHHHHHHHhcCChHHHHHHHHhhchhhhhCCCceeeechHHHHHHHHhcCChH
Q 024742 6 YYETAEKLAESSNIQD-LV-DIEVFQEAKKVIDALQNKEVAPALAWCSDNKSRLKKSKSKFEFQLRLQEFIELVRGENNL 83 (263)
Q Consensus 6 y~~ta~~f~~e~~i~~-~~-d~~~~~~~~~I~~~i~~gdi~~Al~w~~~~~~~L~~~~s~LeF~L~~q~fIeLi~~~~~~ 83 (263)
...|.+.+.+|+++.. .+ .+|.| +++|-+|.|+..+.-.+..+---++ .-.|.-|-.+|||+-....
T Consensus 23 L~rtl~tLQeEt~VSLNTVDSvd~F------v~dI~sG~WD~VL~~vqsLKLP~kk-----L~dLYEqivlEliELREL~ 91 (508)
T KOG0275|consen 23 LHRTLQTLQEETNVSLNTVDSVDGF------VNDINSGHWDTVLKTVQSLKLPDKK-----LIDLYEQIVLELIELRELG 91 (508)
T ss_pred HHHHHHHHHHhhccceeechhHHHH------HHhcccCchHHHHHHHHhccCchhH-----HHHHHHHHHHHHHHHHhhh
Confidence 3456777888887753 23 36778 9999999999999988777544333 3467888899999988888
Q ss_pred HHHHHHHHhCcc--hhhhhHHHHHHHHHHhh--ccCCCCcchhHHhcCcccHHHHHHHHHHH
Q 024742 84 RAITYARKYLAP--WGATHMKELQRVMATLA--FKSNTECTTYKALFEPKQWDFLVDQFKQE 141 (263)
Q Consensus 84 eAi~yar~~l~~--~~~~~~~ei~~~~~lL~--f~~~~~~s~y~~l~~~~r~~~la~~f~~~ 141 (263)
.|-..+|+--+- ......+..-++=.+|. |-++. +.|.+--.+.||..+|+.+..+
T Consensus 92 tAR~~lRQTdpM~~lKQ~~peRy~~lE~ll~R~YFDp~--EaY~dssKEkrRa~IAQ~ls~E 151 (508)
T KOG0275|consen 92 TARSLLRQTDPMIMLKQIQPERYIRLENLLNRSYFDPR--EAYGDSSKEKRRAVIAQALSGE 151 (508)
T ss_pred HHHHHHhccCceehhhccChHHHHHHHHHhcccccChh--hhcCcchHHHHHHHHHHHhcCc
Confidence 887777753211 11112233333334443 22222 4555544567888888877654
No 105
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=75.44 E-value=2.2 Score=27.27 Aligned_cols=42 Identities=21% Similarity=0.382 Sum_probs=25.6
Q ss_pred ecccccccCCCCCCeecCCCc-----eecHHHHHHHHHhCCCceecCCC
Q 024742 205 CYITKELMDTENPPQVLPNGY-----VYSTKALEEMAKKNNGKITCPRT 248 (263)
Q Consensus 205 Cpi~~~~~~~~n~p~~l~cGh-----v~~~~~~~~~~~~~~~~~~CP~c 248 (263)
|.|..+.-++++ |++.||+. ..-+.+|++|... .+..+|+.|
T Consensus 1 CrIC~~~~~~~~-~li~pC~C~Gs~~~vH~~CL~~W~~~-~~~~~C~~C 47 (47)
T PF12906_consen 1 CRICLEGEEEDE-PLISPCRCKGSMKYVHRSCLERWIRE-SGNRKCEIC 47 (47)
T ss_dssp ETTTTEE-SSSS--EE-SSS-SSCCGSEECCHHHHHHHH-HT-SB-TTT
T ss_pred CeEeCCcCCCCC-ceecccccCCCcchhHHHHHHHHHHh-cCCCcCCCC
Confidence 556666666555 89999875 4567899999874 345689887
No 106
>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=75.32 E-value=6.8 Score=30.70 Aligned_cols=53 Identities=9% Similarity=0.132 Sum_probs=42.1
Q ss_pred cccccHHHHHHHHHHcCC---CCCCCHHHHHHHHHHHHHHhcCChHHHHHHHHhhc
Q 024742 2 LRMSYYETAEKLAESSNI---QDLVDIEVFQEAKKVIDALQNKEVAPALAWCSDNK 54 (263)
Q Consensus 2 lr~Gy~~ta~~f~~e~~i---~~~~d~~~~~~~~~I~~~i~~gdi~~Al~w~~~~~ 54 (263)
++.|..+.|-...++-.- +...++..-....+.++.|++|++.+|++|++++-
T Consensus 12 I~~g~i~~Ai~w~~~~~~~l~~~~~~L~f~L~~q~fiell~~~~~~~Ai~y~r~~l 67 (145)
T PF10607_consen 12 ILNGDIDPAIEWLNENFPELLKRNSSLEFELRCQQFIELLREGDIMEAIEYARKHL 67 (145)
T ss_pred HHcCCHHHHHHHHHHcCHHHHhcCCchhHHHHHHHHHHHHHHHhHHHHHHHHHHHh
Confidence 467888888888877642 23456777777888899999999999999999864
No 107
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=75.07 E-value=2.9 Score=29.88 Aligned_cols=50 Identities=16% Similarity=0.147 Sum_probs=36.8
Q ss_pred ecccccccC-CCCCCeec-CCCceecHHHHHHHHHhCCCceecCCCCcccCcccc
Q 024742 205 CYITKELMD-TENPPQVL-PNGYVYSTKALEEMAKKNNGKITCPRTGLVCNYSDL 257 (263)
Q Consensus 205 Cpi~~~~~~-~~n~p~~l-~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~~~~~ 257 (263)
||-..--|+ +++-|+++ .|.|.|-.-||.+|... +-.||.+.++|-+.+-
T Consensus 34 C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~T---k~~CPld~q~w~~~~~ 85 (88)
T COG5194 34 CPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDT---KGVCPLDRQTWVLADG 85 (88)
T ss_pred CcccccCCCCCCcceEEEEecchHHHHHHHHHHHhh---CCCCCCCCceeEEecc
Confidence 444444443 34567765 69999999999999863 4599999999987664
No 108
>PF12660 zf-TFIIIC: Putative zinc-finger of transcription factor IIIC complex; InterPro: IPR024764 This zinc-finger domain is at the very C terminus of a number of different TFIIIC subunit proteins. This domain might be involved in protein-DNA and/or protein-protein interactions [].; PDB: 2J04_C.
Probab=74.22 E-value=0.58 Score=35.00 Aligned_cols=48 Identities=23% Similarity=0.333 Sum_probs=11.1
Q ss_pred ecccccccCCCCCCe-ecCCCceecHHHHHHHHHhCCCceecCCCCccc
Q 024742 205 CYITKELMDTENPPQ-VLPNGYVYSTKALEEMAKKNNGKITCPRTGLVC 252 (263)
Q Consensus 205 Cpi~~~~~~~~n~p~-~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~ 252 (263)
||++++.+.-.++-+ .=++||++.|=++.-+.-..-+...|+.|+..+
T Consensus 17 C~~C~~~i~~~~~~~~~C~~GH~w~RC~lT~l~i~~~~~r~C~~C~~~~ 65 (99)
T PF12660_consen 17 CPICGAPIPFDDLDEAQCENGHVWPRCALTFLPIQTPGVRVCPVCGRRA 65 (99)
T ss_dssp ------------SSEEE-TTS-EEEB-SSS-SBS-SS-EEE-TTT--EE
T ss_pred ccccccccccCCcCEeECCCCCEEeeeeeeeeeeccCCeeEcCCCCCEE
Confidence 444444443333322 245555554444433322222234555555444
No 109
>smart00782 PhnA_Zn_Ribbon PhnA Zinc-Ribbon. This protein family includes an uncharacterised member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterised phosphonoacetate hydrolase designated PhnA.
Probab=74.21 E-value=1.5 Score=28.09 Aligned_cols=37 Identities=14% Similarity=0.184 Sum_probs=27.3
Q ss_pred CCCCCCCchhhhhhcCCCCCC---CCcCCeeeeccccccc
Q 024742 176 TKEDPLSQESFRKLASPLPYS---KQHHSKLVCYITKELM 212 (263)
Q Consensus 176 ~~~cp~c~~~~~~l~~~lP~~---~~~~s~~~Cpi~~~~~ 212 (263)
.+.|+.|..+..=-..++|.. ..-+++++|....+|+
T Consensus 7 ~~kCELC~a~~~L~vy~Vpp~~~~~~d~~iliC~tC~~Qi 46 (47)
T smart00782 7 ESKCELCGSDSPLVVYAVPPSSDVTADNSVMLCDTCHSQI 46 (47)
T ss_pred CCcccCcCCCCCceEEecCCCCCCCccceeeechHHHHhh
Confidence 467999987543344478764 5678999999998876
No 110
>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=73.55 E-value=19 Score=23.62 Aligned_cols=66 Identities=15% Similarity=0.062 Sum_probs=39.0
Q ss_pred HHhcCChHHHHHHHHhhchhhhhCCCceeeechHHHHHHHHhcCChHHHHHHHHHhCcchhhhhHHHHHHHHH
Q 024742 37 ALQNKEVAPALAWCSDNKSRLKKSKSKFEFQLRLQEFIELVRGENNLRAITYARKYLAPWGATHMKELQRVMA 109 (263)
Q Consensus 37 ~i~~gdi~~Al~w~~~~~~~L~~~~s~LeF~L~~q~fIeLi~~~~~~eAi~yar~~l~~~~~~~~~ei~~~~~ 109 (263)
++.+|+++.|++.+++.-..- ..+.+.. ..--.=+++.|+..+|.++..+-..... ++ .++..+++
T Consensus 1 ll~~~~~~~A~~~~~~~l~~~---p~~~~~~--~~la~~~~~~g~~~~A~~~l~~~~~~~~-~~-~~~~~l~a 66 (68)
T PF14559_consen 1 LLKQGDYDEAIELLEKALQRN---PDNPEAR--LLLAQCYLKQGQYDEAEELLERLLKQDP-DN-PEYQQLLA 66 (68)
T ss_dssp HHHTTHHHHHHHHHHHHHHHT---TTSHHHH--HHHHHHHHHTT-HHHHHHHHHCCHGGGT-TH-HHHHHHHH
T ss_pred ChhccCHHHHHHHHHHHHHHC---CCCHHHH--HHHHHHHHHcCCHHHHHHHHHHHHHHCc-CH-HHHHHHHh
Confidence 367899999999987764332 1222222 2334456778999999998886443332 22 45555544
No 111
>PF04641 Rtf2: Rtf2 RING-finger
Probab=72.96 E-value=6 Score=34.78 Aligned_cols=60 Identities=17% Similarity=0.249 Sum_probs=43.5
Q ss_pred CCcCCeeeecccccccCCCCCCee-cCCCceecHHHHHHHHHhCCCceecCCCCccc----Ccccceeccc
Q 024742 197 KQHHSKLVCYITKELMDTENPPQV-LPNGYVYSTKALEEMAKKNNGKITCPRTGLVC----NYSDLVKAYI 262 (263)
Q Consensus 197 ~~~~s~~~Cpi~~~~~~~~n~p~~-l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~----~~~~~~~v~~ 262 (263)
.+.+....|++|++.+.. ||+ =.-|++|.+++|..+....... +.-++.+ .+.|+..|-|
T Consensus 29 ~~~~~w~~CaLS~~pL~~---PiV~d~~G~LynKeaile~Ll~~~~~---~~~~~~~~hI~~LKDl~~l~~ 93 (260)
T PF04641_consen 29 EREARWTHCALSQQPLED---PIVSDRLGRLYNKEAILEFLLDKKKN---KDLPKTFSHIKSLKDLVELKF 93 (260)
T ss_pred HhhCCcCcccCcCCccCC---CeeeCCCCeeEcHHHHHHHHHhcCcC---CCCccccccccCccceeeEEe
Confidence 445556789999999998 875 6899999999999887643211 3444443 6788877755
No 112
>PHA02862 5L protein; Provisional
Probab=72.69 E-value=3.7 Score=32.79 Aligned_cols=47 Identities=19% Similarity=0.276 Sum_probs=34.4
Q ss_pred eecccccccCCCCCCeecCCCc-----eecHHHHHHHHHhCCCceecCCCCcccCcc
Q 024742 204 VCYITKELMDTENPPQVLPNGY-----VYSTKALEEMAKKNNGKITCPRTGLVCNYS 255 (263)
Q Consensus 204 ~Cpi~~~~~~~~n~p~~l~cGh-----v~~~~~~~~~~~~~~~~~~CP~c~~~~~~~ 255 (263)
+|-|+.+.-+++ .-||+. ..-++||++|.. ..+...||.|+.+|...
T Consensus 4 iCWIC~~~~~e~----~~PC~C~GS~K~VHq~CL~~WIn-~S~k~~CeLCkteY~Ik 55 (156)
T PHA02862 4 ICWICNDVCDER----NNFCGCNEEYKVVHIKCMQLWIN-YSKKKECNLCKTKYNIK 55 (156)
T ss_pred EEEEecCcCCCC----cccccccCcchhHHHHHHHHHHh-cCCCcCccCCCCeEEEE
Confidence 466666665543 257665 567899999985 45678999999999754
No 113
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=72.42 E-value=3.3 Score=36.54 Aligned_cols=77 Identities=16% Similarity=0.227 Sum_probs=48.3
Q ss_pred CCCCCCchhhhhhcCCCCCCCCcCC-eeeecccccccC-------------CCCCCeecCCCceecHHHHHHHHHh---C
Q 024742 177 KEDPLSQESFRKLASPLPYSKQHHS-KLVCYITKELMD-------------TENPPQVLPNGYVYSTKALEEMAKK---N 239 (263)
Q Consensus 177 ~~cp~c~~~~~~l~~~lP~~~~~~s-~~~Cpi~~~~~~-------------~~n~p~~l~cGhv~~~~~~~~~~~~---~ 239 (263)
..|+.|.+.--.|. .|-.-.++|. ...|+|+|..++ ++.|..---||..|..++=.|--.+ +
T Consensus 162 ~~C~~C~K~YvSmp-ALkMHirTH~l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~ 240 (279)
T KOG2462|consen 162 FSCKYCGKVYVSMP-ALKMHIRTHTLPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSD 240 (279)
T ss_pred ccCCCCCceeeehH-HHhhHhhccCCCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcC
Confidence 45888877531110 1111245777 789999999886 3444444568888877664443322 3
Q ss_pred CCceecCCCCcccCc
Q 024742 240 NGKITCPRTGLVCNY 254 (263)
Q Consensus 240 ~~~~~CP~c~~~~~~ 254 (263)
..+++|+.|++.|..
T Consensus 241 ~K~~qC~~C~KsFsl 255 (279)
T KOG2462|consen 241 VKKHQCPRCGKSFAL 255 (279)
T ss_pred CccccCcchhhHHHH
Confidence 457899999999864
No 114
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=72.21 E-value=3.9 Score=33.19 Aligned_cols=49 Identities=18% Similarity=0.230 Sum_probs=34.6
Q ss_pred eecccccccCCCCCCeecCCCc-----eecHHHHHHHHHhCCCceecCCCCcccCcccc
Q 024742 204 VCYITKELMDTENPPQVLPNGY-----VYSTKALEEMAKKNNGKITCPRTGLVCNYSDL 257 (263)
Q Consensus 204 ~Cpi~~~~~~~~n~p~~l~cGh-----v~~~~~~~~~~~~~~~~~~CP~c~~~~~~~~~ 257 (263)
.|.|+.+..++ ..-||.. ..-++|+++|...+ +...||.|+.+|.....
T Consensus 10 ~CRIC~~~~~~----~~~PC~CkGs~k~VH~sCL~rWi~~s-~~~~CeiC~~~Y~i~~~ 63 (162)
T PHA02825 10 CCWICKDEYDV----VTNYCNCKNENKIVHKECLEEWINTS-KNKSCKICNGPYNIKKN 63 (162)
T ss_pred eeEecCCCCCC----ccCCcccCCCchHHHHHHHHHHHhcC-CCCcccccCCeEEEEEe
Confidence 45666555322 2358776 56789999998754 56799999999987643
No 115
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=71.95 E-value=2 Score=26.57 Aligned_cols=12 Identities=33% Similarity=0.797 Sum_probs=10.2
Q ss_pred CceecCCCCccc
Q 024742 241 GKITCPRTGLVC 252 (263)
Q Consensus 241 ~~~~CP~c~~~~ 252 (263)
+..+||||+..|
T Consensus 28 ~~~~CpYCg~~y 39 (40)
T PF10276_consen 28 GPVVCPYCGTRY 39 (40)
T ss_dssp CEEEETTTTEEE
T ss_pred CeEECCCCCCEE
Confidence 468999999876
No 116
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=71.66 E-value=2.8 Score=24.54 Aligned_cols=9 Identities=33% Similarity=0.726 Sum_probs=7.1
Q ss_pred ceecCCCCc
Q 024742 242 KITCPRTGL 250 (263)
Q Consensus 242 ~~~CP~c~~ 250 (263)
..+||.|+.
T Consensus 17 ~~~CP~Cg~ 25 (33)
T cd00350 17 PWVCPVCGA 25 (33)
T ss_pred CCcCcCCCC
Confidence 358999986
No 117
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=71.62 E-value=2.8 Score=36.47 Aligned_cols=47 Identities=15% Similarity=0.274 Sum_probs=32.1
Q ss_pred CeeeecccccccCCCCCCeecCCCceecHHHHHHHHHhCCCceecCCCCcccCccc
Q 024742 201 SKLVCYITKELMDTENPPQVLPNGYVYSTKALEEMAKKNNGKITCPRTGLVCNYSD 256 (263)
Q Consensus 201 s~~~Cpi~~~~~~~~n~p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~~~~ 256 (263)
+.=+=|+-|..+.+ |+-++...-+..+.+ ++..++||+||...-+.+
T Consensus 189 g~gvvpl~g~~C~G--------C~m~l~~~~~~~V~~-~d~iv~CP~CgRILy~~e 235 (239)
T COG1579 189 GVGVVPLEGRVCGG--------CHMKLPSQTLSKVRK-KDEIVFCPYCGRILYYDE 235 (239)
T ss_pred CceEEeecCCcccC--------CeeeecHHHHHHHhc-CCCCccCCccchHHHhhh
Confidence 34455666666665 666666777777765 677899999998654443
No 118
>KOG2910 consensus Uncharacterized conserved protein predicted to be involved in protein sorting [General function prediction only]
Probab=70.68 E-value=14 Score=30.92 Aligned_cols=63 Identities=17% Similarity=0.220 Sum_probs=47.4
Q ss_pred HHHHHHHHHhcCChHHHHHHHHhhchh-------------hhhCCCceeeechHHHHHHHHhcCChHHHHHHHHHhCc
Q 024742 30 EAKKVIDALQNKEVAPALAWCSDNKSR-------------LKKSKSKFEFQLRLQEFIELVRGENNLRAITYARKYLA 94 (263)
Q Consensus 30 ~~~~I~~~i~~gdi~~Al~w~~~~~~~-------------L~~~~s~LeF~L~~q~fIeLi~~~~~~eAi~yar~~l~ 94 (263)
++..-++.|+.|+=+.|+-.++..+-. ++..-+++||.....++++=++.|+ +||+-.++.|.
T Consensus 42 Er~~Ar~lird~rKdrAlllLKkKryQE~Ll~qt~~qL~nlEqmvsdiEft~vqk~V~~gLk~GN--~~lkkl~~~~~ 117 (209)
T KOG2910|consen 42 ERQLARDLIRDGRKDRALLLLKKKRYQEELLTQTDNQLINLEQMVSDIEFTQVQKKVMEGLKQGN--EALKKLQQEFD 117 (209)
T ss_pred HHHHHHHHHHhChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHhcC
Confidence 345567788888888888777665432 3334479999999999999999994 78888887664
No 119
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=70.00 E-value=8.5 Score=27.36 Aligned_cols=54 Identities=15% Similarity=0.227 Sum_probs=22.4
Q ss_pred cCCeeeeccccccc--CCCCCCee--cCCCceecHHHHHHHHHhCCCceecCCCCcccCc
Q 024742 199 HHSKLVCYITKELM--DTENPPQV--LPNGYVYSTKALEEMAKKNNGKITCPRTGLVCNY 254 (263)
Q Consensus 199 ~~s~~~Cpi~~~~~--~~~n~p~~--l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~~ 254 (263)
-.+.=+|-|.|+.+ +++..|++ -.||--+++.+.+-= .+ ++.-.||.|+..++.
T Consensus 6 ~~~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYE-rk-eg~q~CpqCkt~ykr 63 (80)
T PF14569_consen 6 NLNGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYE-RK-EGNQVCPQCKTRYKR 63 (80)
T ss_dssp --SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHH-HH-TS-SB-TTT--B---
T ss_pred hcCCcccccccCccccCCCCCEEEEEcccCCccchhHHHHH-hh-cCcccccccCCCccc
Confidence 34455799999988 44434443 689999999999743 23 455699999988874
No 120
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=68.71 E-value=6.4 Score=25.89 Aligned_cols=29 Identities=21% Similarity=0.411 Sum_probs=24.1
Q ss_pred CCCceecHHHHHHHHHhCCCceecCCCCcc
Q 024742 222 PNGYVYSTKALEEMAKKNNGKITCPRTGLV 251 (263)
Q Consensus 222 ~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~ 251 (263)
-|+-.++.+.+.++. +++..+.||.|+..
T Consensus 27 gC~~~l~~~~~~~i~-~~~~i~~Cp~CgRi 55 (56)
T PF02591_consen 27 GCHMELPPQELNEIR-KGDEIVFCPNCGRI 55 (56)
T ss_pred CCCEEcCHHHHHHHH-cCCCeEECcCCCcc
Confidence 588899999999995 45678999999963
No 121
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=67.90 E-value=3.7 Score=24.30 Aligned_cols=17 Identities=24% Similarity=0.466 Sum_probs=9.7
Q ss_pred eeeecccccccCCCCCC
Q 024742 202 KLVCYITKELMDTENPP 218 (263)
Q Consensus 202 ~~~Cpi~~~~~~~~n~p 218 (263)
.|+|++.|...++..+|
T Consensus 2 ~~~C~~CG~i~~g~~~p 18 (34)
T cd00729 2 VWVCPVCGYIHEGEEAP 18 (34)
T ss_pred eEECCCCCCEeECCcCC
Confidence 36676666665554443
No 122
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=67.75 E-value=1.5 Score=43.89 Aligned_cols=50 Identities=16% Similarity=0.236 Sum_probs=38.7
Q ss_pred eeecccccccCCCCCCeecCCCceecHHHHHHHHHhCCCceecCCCCcccCcccc
Q 024742 203 LVCYITKELMDTENPPQVLPNGYVYSTKALEEMAKKNNGKITCPRTGLVCNYSDL 257 (263)
Q Consensus 203 ~~Cpi~~~~~~~~n~p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~~~~~ 257 (263)
+.|++.-+ .-++++.+|||++|.+|+.......+.. +||.|......+++
T Consensus 455 ~~c~ic~~----~~~~~it~c~h~~c~~c~~~~i~~~~~~-~~~~cr~~l~~~~l 504 (674)
T KOG1001|consen 455 HWCHICCD----LDSFFITRCGHDFCVECLKKSIQQSENA-PCPLCRNVLKEKKL 504 (674)
T ss_pred cccccccc----cccceeecccchHHHHHHHhccccccCC-CCcHHHHHHHHHHH
Confidence 67888888 3348999999999999999876544443 89999887665543
No 123
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=67.69 E-value=3.5 Score=24.85 Aligned_cols=15 Identities=33% Similarity=0.773 Sum_probs=12.5
Q ss_pred CCCceecCCCCcccC
Q 024742 239 NNGKITCPRTGLVCN 253 (263)
Q Consensus 239 ~~~~~~CP~c~~~~~ 253 (263)
+++.++||.|+.+|.
T Consensus 22 ~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 22 GGRKVRCPKCGHVFR 36 (37)
T ss_pred CCcEEECCCCCcEee
Confidence 456899999999886
No 124
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=67.65 E-value=8.3 Score=22.96 Aligned_cols=18 Identities=33% Similarity=0.602 Sum_probs=14.9
Q ss_pred HHHHHHh--cCChHHHHHHH
Q 024742 33 KVIDALQ--NKEVAPALAWC 50 (263)
Q Consensus 33 ~I~~~i~--~gdi~~Al~w~ 50 (263)
..+.+|+ +||++.|++|+
T Consensus 18 ~~~~AL~~~~~nve~A~~~L 37 (37)
T PF00627_consen 18 QAREALRACNGNVERAVDWL 37 (37)
T ss_dssp HHHHHHHHTTTSHHHHHHHH
T ss_pred HHHHHHHHcCCCHHHHHHhC
Confidence 5677887 58999999996
No 125
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=66.49 E-value=2.8 Score=27.70 Aligned_cols=16 Identities=19% Similarity=0.503 Sum_probs=12.4
Q ss_pred ceecCCCCcccCcccc
Q 024742 242 KITCPRTGLVCNYSDL 257 (263)
Q Consensus 242 ~~~CP~c~~~~~~~~~ 257 (263)
.++||.|+..+...+.
T Consensus 2 ~~~CP~CG~~iev~~~ 17 (54)
T TIGR01206 2 QFECPDCGAEIELENP 17 (54)
T ss_pred ccCCCCCCCEEecCCC
Confidence 3689999998877653
No 126
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=65.95 E-value=2.8 Score=25.19 Aligned_cols=14 Identities=29% Similarity=0.515 Sum_probs=10.8
Q ss_pred eecCCCCcccCccc
Q 024742 243 ITCPRTGLVCNYSD 256 (263)
Q Consensus 243 ~~CP~c~~~~~~~~ 256 (263)
++||.|+..|..++
T Consensus 3 ~~CP~C~~~~~v~~ 16 (38)
T TIGR02098 3 IQCPNCKTSFRVVD 16 (38)
T ss_pred EECCCCCCEEEeCH
Confidence 67888888877664
No 127
>PTZ00196 60S ribosomal protein L36; Provisional
Probab=65.64 E-value=18 Score=26.96 Aligned_cols=44 Identities=27% Similarity=0.417 Sum_probs=32.6
Q ss_pred eechHHHHHHHHhcCChHHHHHHHHHhCcchhhh--hHHHHHHHHH
Q 024742 66 FQLRLQEFIELVRGENNLRAITYARKYLAPWGAT--HMKELQRVMA 109 (263)
Q Consensus 66 F~L~~q~fIeLi~~~~~~eAi~yar~~l~~~~~~--~~~ei~~~~~ 109 (263)
|.=.-.+.+|||+.+.-..|+.|+++.+..+... ..+|++.++.
T Consensus 48 faPYErr~mELLkv~kdKrAlKfaKkRlGth~RaK~Kreel~~vl~ 93 (98)
T PTZ00196 48 FSPYERRMIELLKVGKDKRALKYAKKRLGTHKRAKAKRDEIQEALR 93 (98)
T ss_pred ccHHHHHHHHHHHhcchHHHHHHHHHHhhhHHHHHHHHHHHHHHHH
Confidence 3334567899999998899999999999887642 3466665544
No 128
>PF14276 DUF4363: Domain of unknown function (DUF4363)
Probab=65.47 E-value=58 Score=24.74 Aligned_cols=50 Identities=14% Similarity=0.245 Sum_probs=43.7
Q ss_pred HHHHHHHHHHHHHhcCChHHHHHHHHhhchhhhhCCCceeeechHHHHHH
Q 024742 26 EVFQEAKKVIDALQNKEVAPALAWCSDNKSRLKKSKSKFEFQLRLQEFIE 75 (263)
Q Consensus 26 ~~~~~~~~I~~~i~~gdi~~Al~w~~~~~~~L~~~~s~LeF~L~~q~fIe 75 (263)
+.-..+..|.++|.++||+.|-.-+.+.....++....+.|.+..+++-+
T Consensus 27 ~i~~~l~~i~~~i~~~dW~~A~~~~~~l~~~W~k~~~~~~~~~~h~eid~ 76 (121)
T PF14276_consen 27 SIEEQLEQIEEAIENEDWEKAYKETEELEKEWDKNKKRWSILIEHQEIDN 76 (121)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhhchheeeeecHHHHHH
Confidence 34566888999999999999999999999999999999999998888743
No 129
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=65.45 E-value=3.7 Score=31.23 Aligned_cols=14 Identities=29% Similarity=0.560 Sum_probs=10.4
Q ss_pred ceecCCCCcccCcc
Q 024742 242 KITCPRTGLVCNYS 255 (263)
Q Consensus 242 ~~~CP~c~~~~~~~ 255 (263)
-++||+||.+|..+
T Consensus 26 PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 26 PIVCPKCGTEFPPE 39 (108)
T ss_pred CccCCCCCCccCcc
Confidence 46788888887766
No 130
>KOG3842 consensus Adaptor protein Pellino [Signal transduction mechanisms]
Probab=65.28 E-value=3.7 Score=36.95 Aligned_cols=33 Identities=21% Similarity=0.228 Sum_probs=25.5
Q ss_pred cCCCceecHHHHHHHHHh----C--CCceecCCCCcccC
Q 024742 221 LPNGYVYSTKALEEMAKK----N--NGKITCPRTGLVCN 253 (263)
Q Consensus 221 l~cGhv~~~~~~~~~~~~----~--~~~~~CP~c~~~~~ 253 (263)
-|||||-|++...-|+.- + .-.-.||.|..-..
T Consensus 376 ~PCGHv~sekt~~YWs~iplPhGT~~f~a~CPFC~~~L~ 414 (429)
T KOG3842|consen 376 NPCGHVCSEKTVKYWSQIPLPHGTHAFHAACPFCATQLA 414 (429)
T ss_pred CCcccccchhhhhHhhcCcCCCccccccccCcchhhhhc
Confidence 699999999999999852 1 12458999987654
No 131
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=65.13 E-value=3.6 Score=26.89 Aligned_cols=14 Identities=21% Similarity=0.356 Sum_probs=8.0
Q ss_pred ecCCCCcccCcccc
Q 024742 244 TCPRTGLVCNYSDL 257 (263)
Q Consensus 244 ~CP~c~~~~~~~~~ 257 (263)
+||.|+..|+.++-
T Consensus 22 ~CPlC~r~l~~e~~ 35 (54)
T PF04423_consen 22 CCPLCGRPLDEEHR 35 (54)
T ss_dssp E-TTT--EE-HHHH
T ss_pred cCCCCCCCCCHHHH
Confidence 99999999986643
No 132
>smart00668 CTLH C-terminal to LisH motif. Alpha-helical motif of unknown function.
Probab=64.78 E-value=10 Score=24.50 Aligned_cols=28 Identities=14% Similarity=0.160 Sum_probs=23.6
Q ss_pred hHHHHHHHHhcCChHHHHHHHHHhCcch
Q 024742 69 RLQEFIELVRGENNLRAITYARKYLAPW 96 (263)
Q Consensus 69 ~~q~fIeLi~~~~~~eAi~yar~~l~~~ 96 (263)
...++.+.|..|+..+|+++++++-...
T Consensus 4 ~~~~i~~~i~~g~~~~a~~~~~~~~~~l 31 (58)
T smart00668 4 ERKRIRELILKGDWDEALEWLSSLKPPL 31 (58)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHcCHHH
Confidence 3567899999999999999999876654
No 133
>PF06676 DUF1178: Protein of unknown function (DUF1178); InterPro: IPR009562 This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.
Probab=64.71 E-value=6.8 Score=31.51 Aligned_cols=29 Identities=28% Similarity=0.548 Sum_probs=21.1
Q ss_pred CCCcee-----cHHHHHHHHHhCCCceecCCCCccc
Q 024742 222 PNGYVY-----STKALEEMAKKNNGKITCPRTGLVC 252 (263)
Q Consensus 222 ~cGhv~-----~~~~~~~~~~~~~~~~~CP~c~~~~ 252 (263)
.|||+| |..++++..+ .+.+.||+||..-
T Consensus 9 ~~gH~FEgWF~ss~~fd~Q~~--~glv~CP~Cgs~~ 42 (148)
T PF06676_consen 9 ENGHEFEGWFRSSAAFDRQQA--RGLVSCPVCGSTE 42 (148)
T ss_pred CCCCccceecCCHHHHHHHHH--cCCccCCCCCCCe
Confidence 477877 5677777644 4689999999754
No 134
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=62.18 E-value=3.1 Score=27.30 Aligned_cols=12 Identities=33% Similarity=0.609 Sum_probs=9.6
Q ss_pred eecCCCCcccCc
Q 024742 243 ITCPRTGLVCNY 254 (263)
Q Consensus 243 ~~CP~c~~~~~~ 254 (263)
+.|||||+.+..
T Consensus 1 i~CPyCge~~~~ 12 (52)
T PF14255_consen 1 IQCPYCGEPIEI 12 (52)
T ss_pred CCCCCCCCeeEE
Confidence 479999998764
No 135
>KOG2169 consensus Zn-finger transcription factor [Transcription]
Probab=61.94 E-value=6.9 Score=39.01 Aligned_cols=55 Identities=18% Similarity=0.260 Sum_probs=45.6
Q ss_pred CeeeecccccccCCCCCCee-cCCCceecHHHHHHHHHh-CCCceecCCCCcccCcccce
Q 024742 201 SKLVCYITKELMDTENPPQV-LPNGYVYSTKALEEMAKK-NNGKITCPRTGLVCNYSDLV 258 (263)
Q Consensus 201 s~~~Cpi~~~~~~~~n~p~~-l~cGhv~~~~~~~~~~~~-~~~~~~CP~c~~~~~~~~~~ 258 (263)
=.|-||+++..|.- |.. ..|.|.=|-+++.-+..+ ....-.||.|.+.+.+++.+
T Consensus 305 vSL~CPl~~~Rm~~---P~r~~~CkHlQcFD~~~~lq~n~~~pTW~CPVC~~~~~~e~l~ 361 (636)
T KOG2169|consen 305 VSLNCPLSKMRMSL---PARGHTCKHLQCFDALSYLQMNEQKPTWRCPVCQKAAPFEGLI 361 (636)
T ss_pred eEecCCcccceeec---CCcccccccceecchhhhHHhccCCCeeeCccCCccccccchh
Confidence 45889999999987 774 899999999999887653 24568999999999888764
No 136
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=61.81 E-value=12 Score=22.15 Aligned_cols=21 Identities=29% Similarity=0.488 Sum_probs=16.2
Q ss_pred HHHHHHHHh--cCChHHHHHHHH
Q 024742 31 AKKVIDALQ--NKEVAPALAWCS 51 (263)
Q Consensus 31 ~~~I~~~i~--~gdi~~Al~w~~ 51 (263)
..+++.++. +||++.|++|+-
T Consensus 15 ~~~~~~AL~~~~~d~~~A~~~L~ 37 (38)
T cd00194 15 REEARKALRATNNNVERAVEWLL 37 (38)
T ss_pred HHHHHHHHHHhCCCHHHHHHHHh
Confidence 345677776 689999999973
No 137
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=61.79 E-value=6 Score=32.78 Aligned_cols=37 Identities=27% Similarity=0.276 Sum_probs=22.7
Q ss_pred CeecCCCceecHHHHHHHHHhCCCceecCCCCcccCccccee
Q 024742 218 PQVLPNGYVYSTKALEEMAKKNNGKITCPRTGLVCNYSDLVK 259 (263)
Q Consensus 218 p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~~~~~~~ 259 (263)
-++-|+||+. -++..-.. ..|+||.||......|-.+
T Consensus 113 ~y~C~~~~~r--~sfdeA~~---~~F~Cp~Cg~~L~~~d~s~ 149 (176)
T COG1675 113 YYVCPNCHVK--YSFDEAME---LGFTCPKCGEDLEEYDSSE 149 (176)
T ss_pred ceeCCCCCCc--ccHHHHHH---hCCCCCCCCchhhhccchH
Confidence 3444777765 34444332 2389999998877766543
No 138
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=61.51 E-value=4.3 Score=24.34 Aligned_cols=16 Identities=31% Similarity=0.449 Sum_probs=12.4
Q ss_pred ceecCCCCcccCcccc
Q 024742 242 KITCPRTGLVCNYSDL 257 (263)
Q Consensus 242 ~~~CP~c~~~~~~~~~ 257 (263)
.+.||.|+..|..+|-
T Consensus 2 ~i~Cp~C~~~y~i~d~ 17 (36)
T PF13717_consen 2 IITCPNCQAKYEIDDE 17 (36)
T ss_pred EEECCCCCCEEeCCHH
Confidence 4688888888887763
No 139
>PF10537 WAC_Acf1_DNA_bd: ATP-utilising chromatin assembly and remodelling N-terminal; InterPro: IPR013136 ACF (for ATP-utilising chromatin assembly and remodeling factor) is a chromatin-remodeling complex that catalyzes the ATP-dependent assembly of periodic nucleosome arrays. This reaction utilises the energy of ATP hydrolysis by ISWI, the smaller of the two subunits of ACF. Acf1, the large subunit of ACF, is essential for the full activity of the complex. The WAC (WSTF/Acf1/cbp146) domain is an ~110-residue module present at the N-termini of Acf1-related proteins in a variety of organisms. It is found in association with other domains such as the bromodomain, the PHD-type zinc finger, DDT or WAKS. The DNA-binding region of Acf1 includes the WAC domain, which is necessary for the efficient binding of ACF complex to DNA. It seems probable that the WAC domain will be involved in DNA binding in other related factors [, ]. Some proteins known to contain a WAC domain are the Drosophila melanogaster (Fruit fly) ATP-dependent chromatin assembly factor large subunit Acf1, human WSTF (Williams syndrome transcription factor), mouse cbp146, yeast imitation switch two complex protein 1 (ITC1 or YGL133w), and yeast protein YPL216w.
Probab=61.02 E-value=12 Score=28.19 Aligned_cols=38 Identities=24% Similarity=0.208 Sum_probs=27.8
Q ss_pred CeeeecccccccCCCCCCeecCCCceecHHHHHHHHHhCCCceecCCCCcc
Q 024742 201 SKLVCYITKELMDTENPPQVLPNGYVYSTKALEEMAKKNNGKITCPRTGLV 251 (263)
Q Consensus 201 s~~~Cpi~~~~~~~~n~p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~ 251 (263)
.+|.||.|||.+.+. .+.++++.-=+...+.|-.||+.
T Consensus 2 eVf~i~~T~EiF~dY-------------e~Y~~R~~~y~~~vwtC~~TGk~ 39 (102)
T PF10537_consen 2 EVFYIPFTGEIFRDY-------------EEYLKRMILYNQRVWTCEITGKS 39 (102)
T ss_pred ceEEeCCCCcccCCH-------------HHHHHHHHHHhCCeeEEecCCCC
Confidence 479999999999883 35566665444567888888873
No 140
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=60.82 E-value=4.1 Score=35.09 Aligned_cols=34 Identities=26% Similarity=0.378 Sum_probs=21.6
Q ss_pred CCCCCCchhhhh----------hcCCCCCC-------CCcCCeeeeccccc
Q 024742 177 KEDPLSQESFRK----------LASPLPYS-------KQHHSKLVCYITKE 210 (263)
Q Consensus 177 ~~cp~c~~~~~~----------l~~~lP~~-------~~~~s~~~Cpi~~~ 210 (263)
-.||+|+..+.. ++.+|... ..+-++++||++.=
T Consensus 20 ieCPvC~tkFkkeev~tgsiRiiagDld~~lkygninP~fY~VvvCP~C~y 70 (267)
T COG1655 20 IECPVCNTKFKKEEVKTGSIRIIAGDLDFFLKYGNINPYFYDVVVCPICYY 70 (267)
T ss_pred eccCcccchhhhhheeccceeEecccccceeeccccCCceeEEEEcchhhH
Confidence 569999887652 34444442 34567788887753
No 141
>PF01158 Ribosomal_L36e: Ribosomal protein L36e; InterPro: IPR000509 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 [, ]. A number of eukaryotic ribosomal proteins can be grouped on the basis of sequence similarities. The L36E ribosomal family consists of mammalian, Caenorhabditis elegans and Drosophila L36, Candida albicans L39, and yeast YL39 ribosomal proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1B_Q 4A1D_Q 4A19_Q 4A18_Q 3IZS_k 3IZR_k.
Probab=59.55 E-value=22 Score=26.53 Aligned_cols=41 Identities=27% Similarity=0.361 Sum_probs=31.4
Q ss_pred hHHHHHHHHhcCChHHHHHHHHHhCcchhh--hhHHHHHHHHH
Q 024742 69 RLQEFIELVRGENNLRAITYARKYLAPWGA--THMKELQRVMA 109 (263)
Q Consensus 69 ~~q~fIeLi~~~~~~eAi~yar~~l~~~~~--~~~~ei~~~~~ 109 (263)
.-.+-+|||+.++-..|+.|+++.+..+.. ...+|++.++.
T Consensus 51 YEkr~mELlkv~kdKrAlKf~KKRlGth~RAKrKrEel~~vl~ 93 (98)
T PF01158_consen 51 YEKRAMELLKVSKDKRALKFAKKRLGTHIRAKRKREELSNVLA 93 (98)
T ss_dssp HHHHHHHHHHHCCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHhcchhHHHHHHHHHHhhhhHHHHHHHHHHHHHHH
Confidence 446689999999999999999999987754 23566665554
No 142
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=59.44 E-value=5 Score=35.25 Aligned_cols=25 Identities=12% Similarity=0.317 Sum_probs=11.5
Q ss_pred eeecccccccCCCCCCeecCCCcee
Q 024742 203 LVCYITKELMDTENPPQVLPNGYVY 227 (263)
Q Consensus 203 ~~Cpi~~~~~~~~n~p~~l~cGhv~ 227 (263)
|.||++++.+..++..+.=++||.|
T Consensus 3 ~~CP~C~~~l~~~~~~~~C~~~h~f 27 (272)
T PRK11088 3 YQCPLCHQPLTLEENSWICPQNHQF 27 (272)
T ss_pred ccCCCCCcchhcCCCEEEcCCCCCC
Confidence 4455555555433333444445544
No 143
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=59.24 E-value=2.6 Score=27.18 Aligned_cols=26 Identities=23% Similarity=0.446 Sum_probs=17.0
Q ss_pred cCCCceecHHHHHHHHHhCCCceecCCCCc
Q 024742 221 LPNGYVYSTKALEEMAKKNNGKITCPRTGL 250 (263)
Q Consensus 221 l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~ 250 (263)
..|||+|... ..+. ......||.|+.
T Consensus 9 ~~Cg~~fe~~--~~~~--~~~~~~CP~Cg~ 34 (52)
T TIGR02605 9 TACGHRFEVL--QKMS--DDPLATCPECGG 34 (52)
T ss_pred CCCCCEeEEE--EecC--CCCCCCCCCCCC
Confidence 4689988643 2232 235578999997
No 144
>PLN02189 cellulose synthase
Probab=59.18 E-value=7.2 Score=40.68 Aligned_cols=54 Identities=17% Similarity=0.273 Sum_probs=39.6
Q ss_pred CcCCeeeecccccccC--CCCCCee--cCCCceecHHHHHHHHHhCCCceecCCCCcccC
Q 024742 198 QHHSKLVCYITKELMD--TENPPQV--LPNGYVYSTKALEEMAKKNNGKITCPRTGLVCN 253 (263)
Q Consensus 198 ~~~s~~~Cpi~~~~~~--~~n~p~~--l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~ 253 (263)
+-.+.=+|.|+|+.+. .+..|++ -.||.-+|+.|.+-- . .++.-.||.|+..++
T Consensus 30 ~~~~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cyeye-r-~eg~q~CpqCkt~Y~ 87 (1040)
T PLN02189 30 RNLDGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCYEYE-R-REGTQNCPQCKTRYK 87 (1040)
T ss_pred ccccCccccccccccCcCCCCCEEEeeccCCCccccchhhhh-h-hcCCccCcccCCchh
Confidence 3344458999999974 4444443 469999999999654 2 345669999999998
No 145
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=57.23 E-value=10 Score=25.58 Aligned_cols=19 Identities=26% Similarity=0.532 Sum_probs=10.5
Q ss_pred ceecCCCCcccCcccceec
Q 024742 242 KITCPRTGLVCNYSDLVKA 260 (263)
Q Consensus 242 ~~~CP~c~~~~~~~~~~~v 260 (263)
...||.|+..|...|=+.|
T Consensus 26 ~L~c~~~~~aYpI~dGIPv 44 (60)
T COG2835 26 ELICPRCKLAYPIRDGIPV 44 (60)
T ss_pred EEEecccCceeecccCccc
Confidence 3566666666655554433
No 146
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=56.45 E-value=8.7 Score=38.93 Aligned_cols=52 Identities=17% Similarity=0.280 Sum_probs=41.0
Q ss_pred eecccccccCCCCCCeecCCCce-----ecHHHHHHHHHhCCCceecCCCCcccCcccc
Q 024742 204 VCYITKELMDTENPPQVLPNGYV-----YSTKALEEMAKKNNGKITCPRTGLVCNYSDL 257 (263)
Q Consensus 204 ~Cpi~~~~~~~~n~p~~l~cGhv-----~~~~~~~~~~~~~~~~~~CP~c~~~~~~~~~ 257 (263)
+|.|++.+-.++| |..=||-+. +-++|+.+|... ++..||-.|+-++..+++
T Consensus 14 ~CRICr~e~~~d~-pLfhPCKC~GSIkYiH~eCL~eW~~~-s~~~kCdiChy~~~Fk~I 70 (1175)
T COG5183 14 SCRICRTEDIRDD-PLFHPCKCSGSIKYIHRECLMEWMEC-SGTKKCDICHYEYKFKDI 70 (1175)
T ss_pred hceeecCCCCCCC-cCcccccccchhHHHHHHHHHHHHhc-CCCcceeeecceeeeeee
Confidence 6999988888777 566787665 457899999864 456899999999987765
No 147
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=56.43 E-value=5.6 Score=25.05 Aligned_cols=15 Identities=20% Similarity=0.600 Sum_probs=11.8
Q ss_pred ceecCCCCcccCccc
Q 024742 242 KITCPRTGLVCNYSD 256 (263)
Q Consensus 242 ~~~CP~c~~~~~~~~ 256 (263)
.++||+||..+...+
T Consensus 21 ~~~Cp~CG~~~~~~~ 35 (46)
T PRK00398 21 GVRCPYCGYRILFKE 35 (46)
T ss_pred ceECCCCCCeEEEcc
Confidence 589999999876544
No 148
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=56.03 E-value=4.7 Score=26.19 Aligned_cols=11 Identities=27% Similarity=0.531 Sum_probs=8.5
Q ss_pred CceecCCCCcc
Q 024742 241 GKITCPRTGLV 251 (263)
Q Consensus 241 ~~~~CP~c~~~ 251 (263)
...+||.|+..
T Consensus 33 ~~w~CP~C~a~ 43 (50)
T cd00730 33 DDWVCPVCGAG 43 (50)
T ss_pred CCCCCCCCCCc
Confidence 35899999863
No 149
>PF13838 Clathrin_H_link: Clathrin-H-link; PDB: 2XZG_A 3GD1_I 1BPO_C 1C9I_B 1C9L_A.
Probab=55.54 E-value=14 Score=25.52 Aligned_cols=24 Identities=29% Similarity=0.257 Sum_probs=20.5
Q ss_pred chHHHHHHHHhcCChHHHHHHHHH
Q 024742 68 LRLQEFIELVRGENNLRAITYARK 91 (263)
Q Consensus 68 L~~q~fIeLi~~~~~~eAi~yar~ 91 (263)
|..++|-+|+..|++.+|-+.|-+
T Consensus 8 l~~~~F~~l~~~g~y~eAA~~AA~ 31 (66)
T PF13838_consen 8 LYVQQFNELFSQGQYEEAAKVAAN 31 (66)
T ss_dssp HHHHHHHHHHHTT-HHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHh
Confidence 578999999999999999888874
No 150
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=55.54 E-value=7.7 Score=24.44 Aligned_cols=26 Identities=19% Similarity=0.250 Sum_probs=16.9
Q ss_pred cCCCceecHHHHHHHHHhCCCceecCCCCcccCc
Q 024742 221 LPNGYVYSTKALEEMAKKNNGKITCPRTGLVCNY 254 (263)
Q Consensus 221 l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~~ 254 (263)
..||+.+..+ ..+.++||+||-..-+
T Consensus 6 ~~Cg~~~~~~--------~~~~irC~~CG~rIly 31 (44)
T smart00659 6 GECGRENEIK--------SKDVVRCRECGYRILY 31 (44)
T ss_pred CCCCCEeecC--------CCCceECCCCCceEEE
Confidence 3577766533 3456899999976543
No 151
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=55.24 E-value=18 Score=21.26 Aligned_cols=18 Identities=28% Similarity=0.416 Sum_probs=14.3
Q ss_pred HHHHHHh--cCChHHHHHHH
Q 024742 33 KVIDALQ--NKEVAPALAWC 50 (263)
Q Consensus 33 ~I~~~i~--~gdi~~Al~w~ 50 (263)
+++.++. +||++.|++|+
T Consensus 17 ~a~~aL~~~~~d~~~A~~~L 36 (37)
T smart00165 17 EALKALRAANGNVERAAEYL 36 (37)
T ss_pred HHHHHHHHhCCCHHHHHHHH
Confidence 5567775 68999999996
No 152
>COG5220 TFB3 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB3 [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]
Probab=54.79 E-value=3 Score=36.05 Aligned_cols=37 Identities=19% Similarity=0.372 Sum_probs=27.0
Q ss_pred CCCCe---ecC-CCceecHHHHHHHHHhCCCceecC--CCCcccC
Q 024742 215 ENPPQ---VLP-NGYVYSTKALEEMAKKNNGKITCP--RTGLVCN 253 (263)
Q Consensus 215 ~n~p~---~l~-cGhv~~~~~~~~~~~~~~~~~~CP--~c~~~~~ 253 (263)
-||-| +-| |=|-+|+.|+.++... |.-.|| -|++...
T Consensus 22 LnPdik~linPECyHrmCESCvdRIFs~--GpAqCP~~gC~kILR 64 (314)
T COG5220 22 LNPDIKILINPECYHRMCESCVDRIFSR--GPAQCPYKGCGKILR 64 (314)
T ss_pred cCCCeEEEECHHHHHHHHHHHHHHHhcC--CCCCCCCccHHHHHH
Confidence 35544 346 9999999999999864 567999 5765443
No 153
>PLN02436 cellulose synthase A
Probab=54.65 E-value=12 Score=39.34 Aligned_cols=55 Identities=18% Similarity=0.285 Sum_probs=41.4
Q ss_pred CCcCCeeeeccccccc--CCCCCCee--cCCCceecHHHHHHHHHhCCCceecCCCCcccC
Q 024742 197 KQHHSKLVCYITKELM--DTENPPQV--LPNGYVYSTKALEEMAKKNNGKITCPRTGLVCN 253 (263)
Q Consensus 197 ~~~~s~~~Cpi~~~~~--~~~n~p~~--l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~ 253 (263)
.+..+.=+|-|+|+.+ +.+..|++ -.||.-+|+.|.+-- . .++.-.||.|+..++
T Consensus 31 ~~~~~~~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cyeye-r-~eg~~~Cpqckt~Y~ 89 (1094)
T PLN02436 31 VQELSGQTCQICGDEIELTVDGEPFVACNECAFPVCRPCYEYE-R-REGNQACPQCKTRYK 89 (1094)
T ss_pred ccccCCccccccccccCcCCCCCEEEeeccCCCccccchhhhh-h-hcCCccCcccCCchh
Confidence 4455556999999997 55554553 579999999999654 2 345679999999998
No 154
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=53.94 E-value=7.5 Score=25.78 Aligned_cols=11 Identities=27% Similarity=0.821 Sum_probs=5.7
Q ss_pred ceecCCCCccc
Q 024742 242 KITCPRTGLVC 252 (263)
Q Consensus 242 ~~~CP~c~~~~ 252 (263)
.+.||.||-.+
T Consensus 14 ~~~Cp~cGipt 24 (55)
T PF13824_consen 14 NFECPDCGIPT 24 (55)
T ss_pred CCcCCCCCCcC
Confidence 35566555443
No 155
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=53.93 E-value=4.1 Score=27.06 Aligned_cols=17 Identities=29% Similarity=0.655 Sum_probs=13.1
Q ss_pred CCCceecCCCCcccCcc
Q 024742 239 NNGKITCPRTGLVCNYS 255 (263)
Q Consensus 239 ~~~~~~CP~c~~~~~~~ 255 (263)
+...++||.|+..|..+
T Consensus 14 GE~~lrCPRC~~~FR~~ 30 (65)
T COG4049 14 GEEFLRCPRCGMVFRRR 30 (65)
T ss_pred CceeeeCCchhHHHHHh
Confidence 34568999999998753
No 156
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=53.86 E-value=8 Score=21.12 Aligned_cols=11 Identities=27% Similarity=0.739 Sum_probs=8.4
Q ss_pred CCceecCCCCc
Q 024742 240 NGKITCPRTGL 250 (263)
Q Consensus 240 ~~~~~CP~c~~ 250 (263)
...|+||.||+
T Consensus 14 ~v~f~CPnCG~ 24 (24)
T PF07754_consen 14 AVPFPCPNCGF 24 (24)
T ss_pred CceEeCCCCCC
Confidence 45689999984
No 157
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=53.23 E-value=6.9 Score=26.70 Aligned_cols=15 Identities=27% Similarity=0.587 Sum_probs=9.1
Q ss_pred CceecCCCCcccCcc
Q 024742 241 GKITCPRTGLVCNYS 255 (263)
Q Consensus 241 ~~~~CP~c~~~~~~~ 255 (263)
..++||.||..++.+
T Consensus 45 r~~~C~~Cg~~~~rD 59 (69)
T PF07282_consen 45 RVFTCPNCGFEMDRD 59 (69)
T ss_pred ceEEcCCCCCEECcH
Confidence 456777777665543
No 158
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=52.88 E-value=6.7 Score=36.62 Aligned_cols=57 Identities=19% Similarity=0.216 Sum_probs=36.0
Q ss_pred eecccc-cccCCCCCCeecCCCceecHHHHHHHHHh---CCCceecCC--CCcccCcccceec
Q 024742 204 VCYITK-ELMDTENPPQVLPNGYVYSTKALEEMAKK---NNGKITCPR--TGLVCNYSDLVKA 260 (263)
Q Consensus 204 ~Cpi~~-~~~~~~n~p~~l~cGhv~~~~~~~~~~~~---~~~~~~CP~--c~~~~~~~~~~~v 260 (263)
.|+|+. +.+..+.-..+..|||-|+.+|+++-.+- ++..+.||. |+..++..++..+
T Consensus 148 ~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev~~~~~~~~~C~~~~C~~~l~~~~c~~l 210 (384)
T KOG1812|consen 148 ECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEVKLLSGTVIRCPHDGCESRLTLESCRKL 210 (384)
T ss_pred cCccCccccccHhhhHHHhcccchhhhHHhHHHhhhhhccCCCccCCCCCCCccCCHHHHhhh
Confidence 444444 33333333446889999999999977652 345678875 6666666655443
No 159
>PHA02768 hypothetical protein; Provisional
Probab=52.78 E-value=14 Score=24.49 Aligned_cols=33 Identities=6% Similarity=0.036 Sum_probs=20.5
Q ss_pred CCCceecHHHHHHHHHhCCC-ceecCCCCcccCc
Q 024742 222 PNGYVYSTKALEEMAKKNNG-KITCPRTGLVCNY 254 (263)
Q Consensus 222 ~cGhv~~~~~~~~~~~~~~~-~~~CP~c~~~~~~ 254 (263)
.||-.|++..-...-.+.+. .++|..|++.|..
T Consensus 10 ~CGK~Fs~~~~L~~H~r~H~k~~kc~~C~k~f~~ 43 (55)
T PHA02768 10 ICGEIYIKRKSMITHLRKHNTNLKLSNCKRISLR 43 (55)
T ss_pred hhCCeeccHHHHHHHHHhcCCcccCCcccceecc
Confidence 36666665544333333333 6799999998874
No 160
>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=52.55 E-value=26 Score=25.58 Aligned_cols=27 Identities=19% Similarity=0.306 Sum_probs=18.0
Q ss_pred HHHHHHHHHHHHhcCChHHHHHHHHhh
Q 024742 27 VFQEAKKVIDALQNKEVAPALAWCSDN 53 (263)
Q Consensus 27 ~~~~~~~I~~~i~~gdi~~Al~w~~~~ 53 (263)
......+|.++|++||.+.|-+++.+|
T Consensus 96 ~~~~h~~i~~ai~~~d~~~a~~~~~~h 122 (125)
T PF07729_consen 96 SLEEHREIIDAIRAGDPEAAREALRQH 122 (125)
T ss_dssp HHHHHHHHHHHHHTT-HHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence 455566677777777777777777665
No 161
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=52.48 E-value=7.4 Score=25.34 Aligned_cols=17 Identities=24% Similarity=0.421 Sum_probs=13.1
Q ss_pred CceecCCCCcccCcccc
Q 024742 241 GKITCPRTGLVCNYSDL 257 (263)
Q Consensus 241 ~~~~CP~c~~~~~~~~~ 257 (263)
-.+|||.|+........
T Consensus 23 leIKCpRC~tiN~~~a~ 39 (51)
T PF10122_consen 23 LEIKCPRCKTINHVRAT 39 (51)
T ss_pred EEEECCCCCccceEecc
Confidence 47899999998766543
No 162
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=52.17 E-value=5 Score=22.23 Aligned_cols=14 Identities=14% Similarity=0.090 Sum_probs=10.0
Q ss_pred eecCCCCcccCccc
Q 024742 243 ITCPRTGLVCNYSD 256 (263)
Q Consensus 243 ~~CP~c~~~~~~~~ 256 (263)
+.||.|.+.++..+
T Consensus 2 v~CPiC~~~v~~~~ 15 (26)
T smart00734 2 VQCPVCFREVPENL 15 (26)
T ss_pred CcCCCCcCcccHHH
Confidence 57899988875543
No 163
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=51.98 E-value=8.6 Score=23.75 Aligned_cols=17 Identities=29% Similarity=0.659 Sum_probs=13.8
Q ss_pred CceecCCCCcccCcccc
Q 024742 241 GKITCPRTGLVCNYSDL 257 (263)
Q Consensus 241 ~~~~CP~c~~~~~~~~~ 257 (263)
+..+||.|+..+...+.
T Consensus 12 ~~~~C~~CgM~Y~~~~~ 28 (41)
T PF13878_consen 12 GATTCPTCGMLYSPGSP 28 (41)
T ss_pred CCcCCCCCCCEECCCCH
Confidence 45799999999987654
No 164
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=51.60 E-value=14 Score=38.68 Aligned_cols=57 Identities=16% Similarity=0.332 Sum_probs=41.8
Q ss_pred CCCCcCCeeeeccccccc--CCCCCCee--cCCCceecHHHHHHHHHhCCCceecCCCCcccC
Q 024742 195 YSKQHHSKLVCYITKELM--DTENPPQV--LPNGYVYSTKALEEMAKKNNGKITCPRTGLVCN 253 (263)
Q Consensus 195 ~~~~~~s~~~Cpi~~~~~--~~~n~p~~--l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~ 253 (263)
..++.-+.=+|-|+|+.+ +.+..|++ -.||.-+|+.|.+- .. .++.-.||.|+..++
T Consensus 8 ~~~~~~~~~~c~iCGd~vg~~~~Ge~FVAC~eC~fpvCr~cyey-e~-~~g~~~cp~c~t~y~ 68 (1044)
T PLN02915 8 PTRQSADAKTCRVCGDEVGVKEDGQPFVACHVCGFPVCKPCYEY-ER-SEGNQCCPQCNTRYK 68 (1044)
T ss_pred ccccCCCcchhhccccccCcCCCCCEEEEeccCCCccccchhhh-hh-hcCCccCCccCCchh
Confidence 345555667899999997 44444553 68999999999953 33 345679999999998
No 165
>PF05265 DUF723: Protein of unknown function (DUF723); InterPro: IPR007929 This family contains several uncharacterised proteins from Neisseria meningitidis. These proteins may have a role in DNA binding.
Probab=51.19 E-value=13 Score=25.02 Aligned_cols=16 Identities=6% Similarity=0.085 Sum_probs=12.2
Q ss_pred cCCeeeecccccccCC
Q 024742 199 HHSKLVCYITKELMDT 214 (263)
Q Consensus 199 ~~s~~~Cpi~~~~~~~ 214 (263)
+-..+.||+.|++...
T Consensus 29 ~PvtI~CP~HG~~~~s 44 (60)
T PF05265_consen 29 TPVTIRCPKHGNFTCS 44 (60)
T ss_pred CceEEECCCCCcEEec
Confidence 3456889999988765
No 166
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=51.17 E-value=5.1 Score=26.50 Aligned_cols=40 Identities=18% Similarity=0.211 Sum_probs=27.3
Q ss_pred CeecCCCce-ecHHHHHHHHHhCCCceecCCCCcccCcccceecc
Q 024742 218 PQVLPNGYV-YSTKALEEMAKKNNGKITCPRTGLVCNYSDLVKAY 261 (263)
Q Consensus 218 p~~l~cGhv-~~~~~~~~~~~~~~~~~~CP~c~~~~~~~~~~~v~ 261 (263)
-|+..|||. ++.++=.++.+. ..-.||.|.... .|++|-|
T Consensus 20 sVlYtCGHMCmCy~Cg~rl~~~--~~g~CPiCRapi--~dvIkTY 60 (62)
T KOG4172|consen 20 SVLYTCGHMCMCYACGLRLKKA--LHGCCPICRAPI--KDVIKTY 60 (62)
T ss_pred HHHHHcchHHhHHHHHHHHHHc--cCCcCcchhhHH--HHHHHhh
Confidence 456789996 677877777654 345899998754 3555444
No 167
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=50.85 E-value=6.7 Score=33.46 Aligned_cols=18 Identities=28% Similarity=0.470 Sum_probs=13.4
Q ss_pred ceecCCCCcccCccccee
Q 024742 242 KITCPRTGLVCNYSDLVK 259 (263)
Q Consensus 242 ~~~CP~c~~~~~~~~~~~ 259 (263)
..+||.||-.+..+|..+
T Consensus 48 V~vCP~CgyA~~~~~F~~ 65 (214)
T PF09986_consen 48 VWVCPHCGYAAFEEDFEK 65 (214)
T ss_pred EEECCCCCCccccccccc
Confidence 568888888887776554
No 168
>PRK04023 DNA polymerase II large subunit; Validated
Probab=50.05 E-value=12 Score=38.91 Aligned_cols=34 Identities=21% Similarity=0.230 Sum_probs=23.3
Q ss_pred CChHHHHHHHHHhCcchhhhh--------HHHHHHHHHHhhc
Q 024742 80 ENNLRAITYARKYLAPWGATH--------MKELQRVMATLAF 113 (263)
Q Consensus 80 ~~~~eAi~yar~~l~~~~~~~--------~~ei~~~~~lL~f 113 (263)
-+..+|+.+++++=.|+...+ .+++..+...+.-
T Consensus 449 p~~~eA~~~s~~~~~PLHP~Yty~W~dis~ee~~~L~~~~~~ 490 (1121)
T PRK04023 449 PSQEEALKISEEYGVPLHPKYTYLWHDISKEELEALRNALAG 490 (1121)
T ss_pred CCHHHHHHHHHHcCCCCCCCeeeeeecCCHHHHHHHHHHHHh
Confidence 467999999999887765432 3566666655543
No 169
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=50.02 E-value=12 Score=38.75 Aligned_cols=55 Identities=15% Similarity=0.301 Sum_probs=39.2
Q ss_pred CCCCCCchhhhhhcCCCCCCCCcCCeeeecccccccCCCCCCeecCCCceecHHHHHHHHHhCCCceecCCCCcccCc
Q 024742 177 KEDPLSQESFRKLASPLPYSKQHHSKLVCYITKELMDTENPPQVLPNGYVYSTKALEEMAKKNNGKITCPRTGLVCNY 254 (263)
Q Consensus 177 ~~cp~c~~~~~~l~~~lP~~~~~~s~~~Cpi~~~~~~~~n~p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~~ 254 (263)
..|++|-..+.-.+..||... | -.|-|-+-..|+-+|++. ++.-.||.|..+++.
T Consensus 1470 eECaICYsvL~~vdr~lPskr-------C---------------~TCknKFH~~CLyKWf~S-s~~s~CPlCRseitf 1524 (1525)
T COG5219 1470 EECAICYSVLDMVDRSLPSKR-------C---------------ATCKNKFHTRCLYKWFAS-SARSNCPLCRSEITF 1524 (1525)
T ss_pred chhhHHHHHHHHHhccCCccc-------c---------------chhhhhhhHHHHHHHHHh-cCCCCCCcccccccc
Confidence 457777666655666666532 2 257788888999999974 455699999988764
No 170
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=49.94 E-value=9.7 Score=34.39 Aligned_cols=73 Identities=12% Similarity=0.021 Sum_probs=35.2
Q ss_pred CCCCCCCchhhhhhcCCCCC--CCCcCCeeeecccccccCCCCCCeecCCCceecHHHHHHHHHhC---C---CceecCC
Q 024742 176 TKEDPLSQESFRKLASPLPY--SKQHHSKLVCYITKELMDTENPPQVLPNGYVYSTKALEEMAKKN---N---GKITCPR 247 (263)
Q Consensus 176 ~~~cp~c~~~~~~l~~~lP~--~~~~~s~~~Cpi~~~~~~~~n~p~~l~cGhv~~~~~~~~~~~~~---~---~~~~CP~ 247 (263)
...||+|... |..--|=. ...-.=.+.|+.++.++.-. ...-.-||+- +.+.-++-.+ . .--.|..
T Consensus 184 ~~~CPvCGs~--P~~s~~~~~~~~~G~RyL~CslC~teW~~~-R~~C~~Cg~~---~~l~y~~~e~~~~~~~~r~e~C~~ 257 (305)
T TIGR01562 184 RTLCPACGSP--PVASMVRQGGKETGLRYLSCSLCATEWHYV-RVKCSHCEES---KHLAYLSLEHDAEKAVLKAETCDS 257 (305)
T ss_pred CCcCCCCCCh--hhhhhhcccCCCCCceEEEcCCCCCccccc-CccCCCCCCC---CceeeEeecCCCCCcceEEeeccc
Confidence 4579999552 21111110 11223357888888877652 2223445652 3333332211 1 1237888
Q ss_pred CCcccCc
Q 024742 248 TGLVCNY 254 (263)
Q Consensus 248 c~~~~~~ 254 (263)
|+.-.+.
T Consensus 258 C~~YlK~ 264 (305)
T TIGR01562 258 CQGYLKI 264 (305)
T ss_pred cccchhh
Confidence 8766554
No 171
>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A.
Probab=49.25 E-value=63 Score=22.34 Aligned_cols=52 Identities=15% Similarity=0.024 Sum_probs=28.8
Q ss_pred HHHHHhcCChHHHHHHHHhhchhhhhCCCceeeechHHHHHHHHhcCChHHHHHHHHH
Q 024742 34 VIDALQNKEVAPALAWCSDNKSRLKKSKSKFEFQLRLQEFIELVRGENNLRAITYARK 91 (263)
Q Consensus 34 I~~~i~~gdi~~Al~w~~~~~~~L~~~~s~LeF~L~~q~fIeLi~~~~~~eAi~yar~ 91 (263)
-.-..+.|+.+.|+++++. ...... . +..+...=--+++.|+..+|++...+
T Consensus 32 a~~~~~~~~y~~A~~~~~~--~~~~~~--~--~~~~~l~a~~~~~l~~y~eAi~~l~~ 83 (84)
T PF12895_consen 32 AQCYFQQGKYEEAIELLQK--LKLDPS--N--PDIHYLLARCLLKLGKYEEAIKALEK 83 (84)
T ss_dssp HHHHHHTTHHHHHHHHHHC--HTHHHC--H--HHHHHHHHHHHHHTT-HHHHHHHHHH
T ss_pred HHHHHHCCCHHHHHHHHHH--hCCCCC--C--HHHHHHHHHHHHHhCCHHHHHHHHhc
Confidence 3444568899999999877 222222 1 12222222234566888888877654
No 172
>PLN02195 cellulose synthase A
Probab=48.62 E-value=16 Score=37.96 Aligned_cols=51 Identities=22% Similarity=0.299 Sum_probs=37.4
Q ss_pred eeeeccccccc--CCCCCCee--cCCCceecHHHHHHHHHhCCCceecCCCCcccCc
Q 024742 202 KLVCYITKELM--DTENPPQV--LPNGYVYSTKALEEMAKKNNGKITCPRTGLVCNY 254 (263)
Q Consensus 202 ~~~Cpi~~~~~--~~~n~p~~--l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~~ 254 (263)
.=+|-|+|+.+ +.+..|++ -.||.-.|+.|.+- -+ .+|.-.||.|+..++.
T Consensus 6 ~~~c~~cgd~~~~~~~g~~fvaC~eC~~pvCrpCyey-er-~eg~q~CpqCkt~Yk~ 60 (977)
T PLN02195 6 APICATCGEEVGVDSNGEAFVACHECSYPLCKACLEY-EI-KEGRKVCLRCGGPYDA 60 (977)
T ss_pred CccceecccccCcCCCCCeEEEeccCCCccccchhhh-hh-hcCCccCCccCCcccc
Confidence 34789999977 33333443 68999999999953 33 3456699999999993
No 173
>KOG3842 consensus Adaptor protein Pellino [Signal transduction mechanisms]
Probab=48.50 E-value=5.8 Score=35.76 Aligned_cols=42 Identities=21% Similarity=0.302 Sum_probs=26.0
Q ss_pred ccccCCCCCCeecCCCceecHHHHHHHHHh---CCCceecCCCCcccC
Q 024742 209 KELMDTENPPQVLPNGYVYSTKALEEMAKK---NNGKITCPRTGLVCN 253 (263)
Q Consensus 209 ~~~~~~~n~p~~l~cGhv~~~~~~~~~~~~---~~~~~~CP~c~~~~~ 253 (263)
|++.++..|=|-|.||||=+.- .|-.+ +...-+||.|-.+-.
T Consensus 308 ~~~~~~~QP~vYl~CGHV~G~H---~WG~~e~~g~~~r~CPmC~~~gp 352 (429)
T KOG3842|consen 308 KRVVDEKQPWVYLNCGHVHGYH---NWGVRENTGQRERECPMCRVVGP 352 (429)
T ss_pred cccccccCCeEEEecccccccc---ccccccccCcccCcCCeeeeecc
Confidence 4555555555569999997653 33221 223569999987643
No 174
>KOG1088 consensus Uncharacterized conserved protein [Function unknown]
Probab=48.29 E-value=9.5 Score=29.29 Aligned_cols=18 Identities=44% Similarity=0.767 Sum_probs=15.4
Q ss_pred CCceecCCCCcccCcccc
Q 024742 240 NGKITCPRTGLVCNYSDL 257 (263)
Q Consensus 240 ~~~~~CP~c~~~~~~~~~ 257 (263)
+|..+||.||.+|..++=
T Consensus 96 EG~l~CpetG~vfpI~~G 113 (124)
T KOG1088|consen 96 EGELVCPETGRVFPISDG 113 (124)
T ss_pred cceEecCCCCcEeecccC
Confidence 578999999999988763
No 175
>KOG0883 consensus Cyclophilin type, U box-containing peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=47.93 E-value=19 Score=33.51 Aligned_cols=53 Identities=28% Similarity=0.337 Sum_probs=38.8
Q ss_pred eecccccccCCCCCCeecCCCceecHHHHHHHHHhCCCceecCCCCcccCcccceeccc
Q 024742 204 VCYITKELMDTENPPQVLPNGYVYSTKALEEMAKKNNGKITCPRTGLVCNYSDLVKAYI 262 (263)
Q Consensus 204 ~Cpi~~~~~~~~n~p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~~~~~~~v~~ 262 (263)
.|.+|...+.. |+..+.|.||...+|--|.++- -+=|.+|+....+|++++-|
T Consensus 42 hC~lt~~Pfe~---PvC~~dg~vFd~~~Ivp~lkk~---g~nP~tG~kl~~~dLIkL~F 94 (518)
T KOG0883|consen 42 HCSLTMLPFED---PVCTVDGTVFDLTAIVPWLKKH---GTNPITGQKLDGKDLIKLKF 94 (518)
T ss_pred hceeccccccC---cccccCCcEEeeehhhHHHHHc---CCCCCCCCccccccceeeee
Confidence 36666666555 9999999999999999998752 25577777777777766644
No 176
>PF13934 ELYS: Nuclear pore complex assembly
Probab=47.67 E-value=1e+02 Score=26.44 Aligned_cols=14 Identities=36% Similarity=0.330 Sum_probs=10.9
Q ss_pred HHHHHHHHHHcCCC
Q 024742 7 YETAEKLAESSNIQ 20 (263)
Q Consensus 7 ~~ta~~f~~e~~i~ 20 (263)
.+.+..|+...+|+
T Consensus 63 ~~~~~~Fa~~f~ip 76 (226)
T PF13934_consen 63 SELAESFARAFGIP 76 (226)
T ss_pred ccHHHHHHHHhCCC
Confidence 45788888888886
No 177
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=46.62 E-value=20 Score=37.64 Aligned_cols=54 Identities=19% Similarity=0.350 Sum_probs=39.8
Q ss_pred CcCCeeeeccccccc--CCCCCCee--cCCCceecHHHHHHHHHhCCCceecCCCCcccC
Q 024742 198 QHHSKLVCYITKELM--DTENPPQV--LPNGYVYSTKALEEMAKKNNGKITCPRTGLVCN 253 (263)
Q Consensus 198 ~~~s~~~Cpi~~~~~--~~~n~p~~--l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~ 253 (263)
+..+.=+|-|+|+.+ +.+..|++ -.||--.|+.|.+- -+ .++.-.||.|+..++
T Consensus 13 ~~~~~qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCYEY-Er-~eG~q~CPqCktrYk 70 (1079)
T PLN02638 13 KHGGGQVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCYEY-ER-KDGNQSCPQCKTKYK 70 (1079)
T ss_pred cccCCceeeecccccCcCCCCCEEEEeccCCCccccchhhh-hh-hcCCccCCccCCchh
Confidence 444555899999997 44444443 68999999999963 33 345669999999998
No 178
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=46.21 E-value=4.3 Score=36.14 Aligned_cols=41 Identities=22% Similarity=0.253 Sum_probs=29.6
Q ss_pred eeeecccccccCCCCCCeecCCCcee-cHHHHHHHHHhCCCceecCCCCccc
Q 024742 202 KLVCYITKELMDTENPPQVLPNGYVY-STKALEEMAKKNNGKITCPRTGLVC 252 (263)
Q Consensus 202 ~~~Cpi~~~~~~~~n~p~~l~cGhv~-~~~~~~~~~~~~~~~~~CP~c~~~~ 252 (263)
.-+|.|+.+.-.+ =+.|+|||.. |.+|=++| --||+|.+..
T Consensus 300 ~~LC~ICmDaP~D---CvfLeCGHmVtCt~CGkrm-------~eCPICRqyi 341 (350)
T KOG4275|consen 300 RRLCAICMDAPRD---CVFLECGHMVTCTKCGKRM-------NECPICRQYI 341 (350)
T ss_pred HHHHHHHhcCCcc---eEEeecCcEEeehhhcccc-------ccCchHHHHH
Confidence 6789888776655 7899999965 44444444 3899998754
No 179
>PLN03086 PRLI-interacting factor K; Provisional
Probab=45.45 E-value=17 Score=35.66 Aligned_cols=51 Identities=18% Similarity=0.236 Sum_probs=31.5
Q ss_pred eeecccccccCC---------CCCCeecCCCceecHHHHHHHHHh--CCCceecCCCCcccC
Q 024742 203 LVCYITKELMDT---------ENPPQVLPNGYVYSTKALEEMAKK--NNGKITCPRTGLVCN 253 (263)
Q Consensus 203 ~~Cpi~~~~~~~---------~n~p~~l~cGhv~~~~~~~~~~~~--~~~~~~CP~c~~~~~ 253 (263)
|.|+.+++.+.. ..-|+.-|||..+.+..+.+-... ....++|++|+..+.
T Consensus 454 ~~C~~Cgk~f~~s~LekH~~~~Hkpv~CpCg~~~~R~~L~~H~~thCp~Kpi~C~fC~~~v~ 515 (567)
T PLN03086 454 VHCEKCGQAFQQGEMEKHMKVFHEPLQCPCGVVLEKEQMVQHQASTCPLRLITCRFCGDMVQ 515 (567)
T ss_pred ccCCCCCCccchHHHHHHHHhcCCCccCCCCCCcchhHHHhhhhccCCCCceeCCCCCCccc
Confidence 467777766532 123454458887776666554221 245689999998885
No 180
>COG3898 Uncharacterized membrane-bound protein [Function unknown]
Probab=45.41 E-value=88 Score=29.59 Aligned_cols=82 Identities=17% Similarity=0.027 Sum_probs=59.8
Q ss_pred ccHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHHhcCChHHHHHHHHhhchhhhhCCCceeeechHHHHHHHHhcCChHH
Q 024742 5 SYYETAEKLAESSNIQDLVDIEVFQEAKKVIDALQNKEVAPALAWCSDNKSRLKKSKSKFEFQLRLQEFIELVRGENNLR 84 (263)
Q Consensus 5 Gy~~ta~~f~~e~~i~~~~d~~~~~~~~~I~~~i~~gdi~~Al~w~~~~~~~L~~~~s~LeF~L~~q~fIeLi~~~~~~e 84 (263)
|.-+.|..+.++++-....|.+.+..+-+-+-++.+||.+.|-.-++..-..- ..=+.-||.+ |||-=+.|+.+.
T Consensus 98 Gda~lARkmt~~~~~llssDqepLIhlLeAQaal~eG~~~~Ar~kfeAMl~dP----EtRllGLRgL-yleAqr~Garea 172 (531)
T COG3898 98 GDASLARKMTARASKLLSSDQEPLIHLLEAQAALLEGDYEDARKKFEAMLDDP----ETRLLGLRGL-YLEAQRLGAREA 172 (531)
T ss_pred CchHHHHHHHHHHHhhhhccchHHHHHHHHHHHHhcCchHHHHHHHHHHhcCh----HHHHHhHHHH-HHHHHhcccHHH
Confidence 44456788888887556788999999999999999999999887665542211 1113334444 788889999999
Q ss_pred HHHHHHH
Q 024742 85 AITYARK 91 (263)
Q Consensus 85 Ai~yar~ 91 (263)
|+.|+-+
T Consensus 173 Ar~yAe~ 179 (531)
T COG3898 173 ARHYAER 179 (531)
T ss_pred HHHHHHH
Confidence 9999864
No 181
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=44.66 E-value=12 Score=29.20 Aligned_cols=26 Identities=23% Similarity=0.241 Sum_probs=12.2
Q ss_pred eeecccccccCCCC-CCee-cCCCceec
Q 024742 203 LVCYITKELMDTEN-PPQV-LPNGYVYS 228 (263)
Q Consensus 203 ~~Cpi~~~~~~~~n-~p~~-l~cGhv~~ 228 (263)
.+||-+|.-+-+-| .|++ -.||.+|.
T Consensus 10 r~Cp~cg~kFYDLnk~p~vcP~cg~~~~ 37 (129)
T TIGR02300 10 RICPNTGSKFYDLNRRPAVSPYTGEQFP 37 (129)
T ss_pred ccCCCcCccccccCCCCccCCCcCCccC
Confidence 35666666654422 2333 33555543
No 182
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=44.46 E-value=10 Score=25.32 Aligned_cols=14 Identities=29% Similarity=0.700 Sum_probs=7.9
Q ss_pred ceecCCCCcccCcc
Q 024742 242 KITCPRTGLVCNYS 255 (263)
Q Consensus 242 ~~~CP~c~~~~~~~ 255 (263)
.++||.|++.....
T Consensus 2 ~v~CP~C~k~~~~~ 15 (57)
T PF03884_consen 2 TVKCPICGKPVEWS 15 (57)
T ss_dssp EEE-TTT--EEE-S
T ss_pred cccCCCCCCeeccc
Confidence 47999999988763
No 183
>COG5627 MMS21 DNA repair protein MMS21 [DNA replication, recombination, and repair]
Probab=44.19 E-value=13 Score=32.17 Aligned_cols=41 Identities=17% Similarity=0.118 Sum_probs=29.5
Q ss_pred eeecccccccCCCCCCee-cCCCceecHHHHHHHHHhCCCceecCC
Q 024742 203 LVCYITKELMDTENPPQV-LPNGYVYSTKALEEMAKKNNGKITCPR 247 (263)
Q Consensus 203 ~~Cpi~~~~~~~~n~p~~-l~cGhv~~~~~~~~~~~~~~~~~~CP~ 247 (263)
..||||-...-. |++ ..|.|+|.+++|.+... +...-.||.
T Consensus 190 nrCpitl~p~~~---pils~kcnh~~e~D~I~~~lq-~~~trvcp~ 231 (275)
T COG5627 190 NRCPITLNPDFY---PILSSKCNHKPEMDLINKKLQ-VECTRVCPR 231 (275)
T ss_pred ccCCcccCcchh---HHHHhhhcccccHHHHHHHhc-CCceeecch
Confidence 468888655433 665 68999999999998863 444567885
No 184
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=43.37 E-value=15 Score=33.67 Aligned_cols=44 Identities=9% Similarity=-0.059 Sum_probs=30.9
Q ss_pred eecccccccCCCCCCeecCCCceecHHHHHHHHHhCCCceecCCCCcccC
Q 024742 204 VCYITKELMDTENPPQVLPNGYVYSTKALEEMAKKNNGKITCPRTGLVCN 253 (263)
Q Consensus 204 ~Cpi~~~~~~~~n~p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~ 253 (263)
.|||+-.---. .|.-||||-=|..||.+..-+ ...|-+|+....
T Consensus 424 lCpICyA~pi~---Avf~PC~H~SC~~CI~qHlmN---~k~CFfCktTv~ 467 (489)
T KOG4692|consen 424 LCPICYAGPIN---AVFAPCSHRSCYGCITQHLMN---CKRCFFCKTTVI 467 (489)
T ss_pred cCcceecccch---hhccCCCCchHHHHHHHHHhc---CCeeeEecceee
Confidence 57776432111 577899999999999987653 347888887643
No 185
>PF13934 ELYS: Nuclear pore complex assembly
Probab=42.67 E-value=2.2e+02 Score=24.38 Aligned_cols=48 Identities=15% Similarity=0.151 Sum_probs=23.4
Q ss_pred cCChHHHHHHHHhhchhhhhCCCceeeechHHHHHHHHhcCChHHHHHHHHHhCc
Q 024742 40 NKEVAPALAWCSDNKSRLKKSKSKFEFQLRLQEFIELVRGENNLRAITYARKYLA 94 (263)
Q Consensus 40 ~gdi~~Al~w~~~~~~~L~~~~s~LeF~L~~q~fIeLi~~~~~~eAi~yar~~l~ 94 (263)
+|+-+-|+.+.....|.+... --..-++.++.++.+.||..|+|++-.
T Consensus 121 ~~~~~lAL~y~~~~~p~l~s~-------~~~~~~~~~La~~~v~EAf~~~R~~~~ 168 (226)
T PF13934_consen 121 RGDPKLALRYLRAVGPPLSSP-------EALTLYFVALANGLVTEAFSFQRSYPD 168 (226)
T ss_pred CCChhHHHHHHHhcCCCCCCH-------HHHHHHHHHHHcCCHHHHHHHHHhCch
Confidence 455555665555555555332 111223333555556666666665433
No 186
>PRK00420 hypothetical protein; Validated
Probab=42.23 E-value=16 Score=27.96 Aligned_cols=28 Identities=14% Similarity=0.285 Sum_probs=19.9
Q ss_pred CCCCCCchhhhhhcCCCCCCCC-cCCeeeecccccccCC
Q 024742 177 KEDPLSQESFRKLASPLPYSKQ-HHSKLVCYITKELMDT 214 (263)
Q Consensus 177 ~~cp~c~~~~~~l~~~lP~~~~-~~s~~~Cpi~~~~~~~ 214 (263)
..||+|...+ ++ .+....||.+|++...
T Consensus 24 ~~CP~Cg~pL----------f~lk~g~~~Cp~Cg~~~~v 52 (112)
T PRK00420 24 KHCPVCGLPL----------FELKDGEVVCPVHGKVYIV 52 (112)
T ss_pred CCCCCCCCcc----------eecCCCceECCCCCCeeee
Confidence 4699996543 33 5677889999987753
No 187
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=41.78 E-value=9.6 Score=21.98 Aligned_cols=14 Identities=36% Similarity=0.695 Sum_probs=4.3
Q ss_pred eecCCCCcccCccc
Q 024742 243 ITCPRTGLVCNYSD 256 (263)
Q Consensus 243 ~~CP~c~~~~~~~~ 256 (263)
-+||.|+.++.+.|
T Consensus 3 p~Cp~C~se~~y~D 16 (30)
T PF08274_consen 3 PKCPLCGSEYTYED 16 (30)
T ss_dssp ---TTT-----EE-
T ss_pred CCCCCCCCcceecc
Confidence 48999999988755
No 188
>PHA00732 hypothetical protein
Probab=41.57 E-value=25 Score=25.06 Aligned_cols=32 Identities=22% Similarity=0.323 Sum_probs=18.4
Q ss_pred CCCceecHHH-HHHHHHhCCCceecCCCCcccC
Q 024742 222 PNGYVYSTKA-LEEMAKKNNGKITCPRTGLVCN 253 (263)
Q Consensus 222 ~cGhv~~~~~-~~~~~~~~~~~~~CP~c~~~~~ 253 (263)
-||..+...+ +++-.+......+|+.|++.|.
T Consensus 6 ~Cgk~F~s~s~Lk~H~r~~H~~~~C~~CgKsF~ 38 (79)
T PHA00732 6 ICGFTTVTLFALKQHARRNHTLTKCPVCNKSYR 38 (79)
T ss_pred CCCCccCCHHHHHHHhhcccCCCccCCCCCEeC
Confidence 3666664443 3333221223358999999997
No 189
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=41.35 E-value=9.1 Score=30.55 Aligned_cols=21 Identities=14% Similarity=0.292 Sum_probs=17.6
Q ss_pred CCceecCCCCcccCcccceec
Q 024742 240 NGKITCPRTGLVCNYSDLVKA 260 (263)
Q Consensus 240 ~~~~~CP~c~~~~~~~~~~~v 260 (263)
+..+.||.|+..|+..++..+
T Consensus 97 ~~~Y~Cp~C~~~y~~~ea~~~ 117 (147)
T smart00531 97 NAYYKCPNCQSKYTFLEANQL 117 (147)
T ss_pred CcEEECcCCCCEeeHHHHHHh
Confidence 457899999999999887665
No 190
>KOG1333 consensus Uncharacterized conserved protein [Function unknown]
Probab=41.10 E-value=98 Score=26.36 Aligned_cols=129 Identities=16% Similarity=0.148 Sum_probs=72.7
Q ss_pred ccccHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHHhcCChHHHHHHH----HhhchhhhhCC----CceeeechHHHHH
Q 024742 3 RMSYYETAEKLAESSNIQDLVDIEVFQEAKKVIDALQNKEVAPALAWC----SDNKSRLKKSK----SKFEFQLRLQEFI 74 (263)
Q Consensus 3 r~Gy~~ta~~f~~e~~i~~~~d~~~~~~~~~I~~~i~~gdi~~Al~w~----~~~~~~L~~~~----s~LeF~L~~q~fI 74 (263)
-.|+..|.++|-.|...+.......=..+.+..++|..+|++.--+.- ++..++|+... ..+|-.|.+...+
T Consensus 18 frgf~~tLkalD~E~~~~Ke~~frvdrivdq~~~a~q~~Dl~aLr~~W~~l~~r~Fs~Le~~y~~~~~kle~Sl~r~yLV 97 (241)
T KOG1333|consen 18 FRGFTHTLKALDAEIKADKEKGFRVDRIVDQLQQAMQVYDLAALRDYWSYLERRLFSRLEDIYRPTIHKLETSLFRFYLV 97 (241)
T ss_pred HhhHHHHHHHHhHHHhhhhhcCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHh
Confidence 458888888888887665433322223344557788888888765533 33344444432 2456666777778
Q ss_pred HHHhcCChHHHHHHHHHhCcchhhhhHHHHHHHHHHhhccCCCCcchhHHhcCcccHHHH
Q 024742 75 ELVRGENNLRAITYARKYLAPWGATHMKELQRVMATLAFKSNTECTTYKALFEPKQWDFL 134 (263)
Q Consensus 75 eLi~~~~~~eAi~yar~~l~~~~~~~~~ei~~~~~lL~f~~~~~~s~y~~l~~~~r~~~l 134 (263)
..|..+....|=+|-++.-+... +..|=+.-+.+=-.+...+.+|++.+|+ +.|.++
T Consensus 98 ~~~q~nr~~K~~EFF~K~a~~lq--nq~eWkDWF~fPf~~~a~~tppf~~~F~-ktw~e~ 154 (241)
T KOG1333|consen 98 YTIQTNRNDKAQEFFAKQATELQ--NQAEWKDWFVLPFLPSAKDTPPFRKYFD-KTWIEI 154 (241)
T ss_pred hhhhcCChHHHHHHHHHHHHHHh--cchhhhhheecccCCCCCCCccHHHHHH-hhhhHh
Confidence 88888888887666664322211 1122222222111123345578877775 467654
No 191
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=40.79 E-value=13 Score=30.35 Aligned_cols=22 Identities=18% Similarity=0.273 Sum_probs=17.0
Q ss_pred CceecCCCCcccCcccceeccc
Q 024742 241 GKITCPRTGLVCNYSDLVKAYI 262 (263)
Q Consensus 241 ~~~~CP~c~~~~~~~~~~~v~~ 262 (263)
+-+|||+|.+....+|+.--++
T Consensus 137 ~g~KCPvC~K~V~sDd~e~Hlv 158 (205)
T KOG0801|consen 137 SGMKCPVCHKVVPSDDAEIHLV 158 (205)
T ss_pred CCccCCccccccCCCcceEEEE
Confidence 3489999999999888764443
No 192
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=40.76 E-value=16 Score=33.38 Aligned_cols=46 Identities=13% Similarity=0.100 Sum_probs=31.4
Q ss_pred eecccccccCCCCCCeecCCCceecHHHHHHHHHhCCCceecCCCCcccC
Q 024742 204 VCYITKELMDTENPPQVLPNGYVYSTKALEEMAKKNNGKITCPRTGLVCN 253 (263)
Q Consensus 204 ~Cpi~~~~~~~~n~p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~ 253 (263)
+|-|+-+-++- .-++||||-+|-.|--++-. --...-||.|..+-.
T Consensus 63 ~C~ICA~~~TY---s~~~PC~H~~CH~Ca~RlRA-LY~~K~C~~CrTE~e 108 (493)
T COG5236 63 NCQICAGSTTY---SARYPCGHQICHACAVRLRA-LYMQKGCPLCRTETE 108 (493)
T ss_pred eeEEecCCceE---EEeccCCchHHHHHHHHHHH-HHhccCCCccccccc
Confidence 45555555554 45799999999988777632 123457999987643
No 193
>PF04840 Vps16_C: Vps16, C-terminal region; InterPro: IPR006925 This protein forms part of the Class C vacuolar protein sorting (Vps) complex. Vps16 is essential for vacuolar protein sorting, which is essential for viability in plants, but not yeast []. The Class C Vps complex is required for SNARE-mediated membrane fusion at the lysosome-like yeast vacuole. It is thought to play essential roles in membrane docking and fusion at the Golgi-to-endosome and endosome-to-vacuole stages of transport []. The role of VPS16 in this complex is not known.; GO: 0006886 intracellular protein transport, 0005737 cytoplasm
Probab=40.57 E-value=1.5e+02 Score=26.94 Aligned_cols=75 Identities=21% Similarity=0.242 Sum_probs=51.2
Q ss_pred CcccccHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHHhcCChHHHHHHHHhhchhhhhCCCceeeechHHHHHHH-Hhc
Q 024742 1 MLRMSYYETAEKLAESSNIQDLVDIEVFQEAKKVIDALQNKEVAPALAWCSDNKSRLKKSKSKFEFQLRLQEFIEL-VRG 79 (263)
Q Consensus 1 Llr~Gy~~ta~~f~~e~~i~~~~d~~~~~~~~~I~~~i~~gdi~~Al~w~~~~~~~L~~~~s~LeF~L~~q~fIeL-i~~ 79 (263)
|+..|....|+.+.++.+++ |.---.-+|.-....|+|+.--.+... .+|.+=|. -|++. ++.
T Consensus 187 li~~~~~k~A~kl~k~Fkv~-----dkrfw~lki~aLa~~~~w~eL~~fa~s-------kKsPIGye----pFv~~~~~~ 250 (319)
T PF04840_consen 187 LIEMGQEKQAEKLKKEFKVP-----DKRFWWLKIKALAENKDWDELEKFAKS-------KKSPIGYE----PFVEACLKY 250 (319)
T ss_pred HHHCCCHHHHHHHHHHcCCc-----HHHHHHHHHHHHHhcCCHHHHHHHHhC-------CCCCCChH----HHHHHHHHC
Confidence 35678888999999999885 222234566667778999987777643 24555555 35543 456
Q ss_pred CChHHHHHHHHH
Q 024742 80 ENNLRAITYARK 91 (263)
Q Consensus 80 ~~~~eAi~yar~ 91 (263)
|...+|..|..+
T Consensus 251 ~~~~eA~~yI~k 262 (319)
T PF04840_consen 251 GNKKEASKYIPK 262 (319)
T ss_pred CCHHHHHHHHHh
Confidence 778888888886
No 194
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=40.56 E-value=30 Score=28.00 Aligned_cols=30 Identities=27% Similarity=0.398 Sum_probs=18.7
Q ss_pred CCCceecHHHHHHHHHhCCCceecCCCCcccCcccc
Q 024742 222 PNGYVYSTKALEEMAKKNNGKITCPRTGLVCNYSDL 257 (263)
Q Consensus 222 ~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~~~~~ 257 (263)
.||.-|+-.-... ..|+||.||.+....|-
T Consensus 114 ~c~~r~tf~eA~~------~~F~Cp~Cg~~L~~~dn 143 (158)
T TIGR00373 114 NMCVRFTFNEAME------LNFTCPRCGAMLDYLDN 143 (158)
T ss_pred CCCcEeeHHHHHH------cCCcCCCCCCEeeeccC
Confidence 3665665433222 24999999998766553
No 195
>PRK10564 maltose regulon periplasmic protein; Provisional
Probab=40.44 E-value=31 Score=31.10 Aligned_cols=41 Identities=20% Similarity=0.297 Sum_probs=29.2
Q ss_pred HHHHHHHHhcCChHHHHHHHHhhchhhhhCCCceeeechHHHHHHHHhc
Q 024742 31 AKKVIDALQNKEVAPALAWCSDNKSRLKKSKSKFEFQLRLQEFIELVRG 79 (263)
Q Consensus 31 ~~~I~~~i~~gdi~~Al~w~~~~~~~L~~~~s~LeF~L~~q~fIeLi~~ 79 (263)
.+.|.+++..||++.||..++|-.- |=+.=-++-||+.|+.
T Consensus 261 ~~aI~~AVk~gDi~KAL~LldEAe~--------LG~~~Ar~tFik~V~~ 301 (303)
T PRK10564 261 NQAIKQAVKKGDVDKALKLLDEAER--------LGSTSARSTFISSVKG 301 (303)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHH--------hCCchHHHHHHHHhhc
Confidence 4679999999999999999988732 1222235566666654
No 196
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=40.39 E-value=14 Score=33.81 Aligned_cols=41 Identities=17% Similarity=0.270 Sum_probs=25.0
Q ss_pred eecccccccCCCCCCeecCCCceecHHHHHHHHHhCCCceecCCCCcccC
Q 024742 204 VCYITKELMDTENPPQVLPNGYVYSTKALEEMAKKNNGKITCPRTGLVCN 253 (263)
Q Consensus 204 ~Cpi~~~~~~~~n~p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~ 253 (263)
.|-|+-++-.+ .+.+||||+-| |.. .+++ ..+||.|.+...
T Consensus 307 lcVVcl~e~~~---~~fvpcGh~cc--ct~-cs~~---l~~CPvCR~rI~ 347 (355)
T KOG1571|consen 307 LCVVCLDEPKS---AVFVPCGHVCC--CTL-CSKH---LPQCPVCRQRIR 347 (355)
T ss_pred ceEEecCCccc---eeeecCCcEEE--chH-HHhh---CCCCchhHHHHH
Confidence 34444444333 67799999987 332 2222 246999987654
No 197
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=40.30 E-value=20 Score=29.38 Aligned_cols=25 Identities=20% Similarity=0.162 Sum_probs=14.9
Q ss_pred eeeecccccccCCCCCCeecCCCce
Q 024742 202 KLVCYITKELMDTENPPQVLPNGYV 226 (263)
Q Consensus 202 ~~~Cpi~~~~~~~~n~p~~l~cGhv 226 (263)
+|+|||+|=.+-+++|-+---||++
T Consensus 134 ~~vC~vCGy~~~ge~P~~CPiCga~ 158 (166)
T COG1592 134 VWVCPVCGYTHEGEAPEVCPICGAP 158 (166)
T ss_pred EEEcCCCCCcccCCCCCcCCCCCCh
Confidence 7888888776665444333345544
No 198
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=40.18 E-value=24 Score=32.39 Aligned_cols=47 Identities=15% Similarity=0.160 Sum_probs=33.0
Q ss_pred eeeecccccccCCCCCCeecCCCce-ecHHHHHHHHHhCCCceecCCCCcccCc
Q 024742 202 KLVCYITKELMDTENPPQVLPNGYV-YSTKALEEMAKKNNGKITCPRTGLVCNY 254 (263)
Q Consensus 202 ~~~Cpi~~~~~~~~n~p~~l~cGhv-~~~~~~~~~~~~~~~~~~CP~c~~~~~~ 254 (263)
.--|=|+..+..+ -++|||=|. +|..|-+.|--+ .-+||+|.+.+..
T Consensus 290 gkeCVIClse~rd---t~vLPCRHLCLCs~Ca~~Lr~q---~n~CPICRqpi~~ 337 (349)
T KOG4265|consen 290 GKECVICLSESRD---TVVLPCRHLCLCSGCAKSLRYQ---TNNCPICRQPIEE 337 (349)
T ss_pred CCeeEEEecCCcc---eEEecchhhehhHhHHHHHHHh---hcCCCccccchHh
Confidence 3345555555544 889999995 788888887432 2389999987653
No 199
>PHA00616 hypothetical protein
Probab=40.17 E-value=7.7 Score=24.51 Aligned_cols=13 Identities=23% Similarity=0.399 Sum_probs=10.7
Q ss_pred eecCCCCcccCcc
Q 024742 243 ITCPRTGLVCNYS 255 (263)
Q Consensus 243 ~~CP~c~~~~~~~ 255 (263)
++||.||+.|...
T Consensus 2 YqC~~CG~~F~~~ 14 (44)
T PHA00616 2 YQCLRCGGIFRKK 14 (44)
T ss_pred CccchhhHHHhhH
Confidence 5899999998753
No 200
>PRK11827 hypothetical protein; Provisional
Probab=39.77 E-value=23 Score=23.94 Aligned_cols=12 Identities=8% Similarity=0.354 Sum_probs=6.1
Q ss_pred Ceeeeccccccc
Q 024742 201 SKLVCYITKELM 212 (263)
Q Consensus 201 s~~~Cpi~~~~~ 212 (263)
.+++||+++..+
T Consensus 7 eILaCP~ckg~L 18 (60)
T PRK11827 7 EIIACPVCNGKL 18 (60)
T ss_pred hheECCCCCCcC
Confidence 345555555443
No 201
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=39.55 E-value=15 Score=27.52 Aligned_cols=24 Identities=25% Similarity=0.490 Sum_probs=16.7
Q ss_pred ecCCCceecHHHHHHHHHhCCCceecCCCCc
Q 024742 220 VLPNGYVYSTKALEEMAKKNNGKITCPRTGL 250 (263)
Q Consensus 220 ~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~ 250 (263)
...|||||..-+-.-+ . =||.||-
T Consensus 5 CtrCG~vf~~g~~~il-~------GCp~CG~ 28 (112)
T COG3364 5 CTRCGEVFDDGSEEIL-S------GCPKCGC 28 (112)
T ss_pred ecccccccccccHHHH-c------cCccccc
Confidence 4689999988644333 2 4898874
No 202
>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B.
Probab=39.53 E-value=65 Score=20.85 Aligned_cols=14 Identities=29% Similarity=0.313 Sum_probs=7.2
Q ss_pred hcCChHHHHHHHHh
Q 024742 39 QNKEVAPALAWCSD 52 (263)
Q Consensus 39 ~~gdi~~Al~w~~~ 52 (263)
..|+++.|++++++
T Consensus 43 ~~g~~~~A~~~~~~ 56 (65)
T PF13432_consen 43 QQGRYDEALAYYER 56 (65)
T ss_dssp HTT-HHHHHHHHHH
T ss_pred HcCCHHHHHHHHHH
Confidence 45666666655543
No 203
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=38.63 E-value=1.3e+02 Score=27.15 Aligned_cols=17 Identities=18% Similarity=0.024 Sum_probs=12.1
Q ss_pred HhcCChHHHHHHHHHhC
Q 024742 77 VRGENNLRAITYARKYL 93 (263)
Q Consensus 77 i~~~~~~eAi~yar~~l 93 (263)
.+.|+..+|+++.++-+
T Consensus 191 ~~~~~~~~A~~~~~~al 207 (389)
T PRK11788 191 LARGDLDAARALLKKAL 207 (389)
T ss_pred HhCCCHHHHHHHHHHHH
Confidence 45677888888777654
No 204
>PF13395 HNH_4: HNH endonuclease
Probab=38.53 E-value=15 Score=23.97 Aligned_cols=13 Identities=31% Similarity=0.641 Sum_probs=10.7
Q ss_pred cCCCCcccCcccc
Q 024742 245 CPRTGLVCNYSDL 257 (263)
Q Consensus 245 CP~c~~~~~~~~~ 257 (263)
|||||+.....++
T Consensus 1 C~Y~g~~i~~~~l 13 (54)
T PF13395_consen 1 CPYCGKPISIENL 13 (54)
T ss_pred CCCCCCCCChhhc
Confidence 8999998887764
No 205
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=38.30 E-value=18 Score=23.82 Aligned_cols=34 Identities=18% Similarity=0.226 Sum_probs=22.0
Q ss_pred CCeecCCCceecHHHHHHHHHhCCCceecCCCCc
Q 024742 217 PPQVLPNGYVYSTKALEEMAKKNNGKITCPRTGL 250 (263)
Q Consensus 217 ~p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~ 250 (263)
..+.|-|++-.+-+.+-.-.....-+++||+|+.
T Consensus 19 ~r~aLIC~~C~~hNGla~~~~~~~i~y~C~~Cg~ 52 (54)
T PF10058_consen 19 NRYALICSKCFSHNGLAPKEEFEEIQYRCPYCGA 52 (54)
T ss_pred CceeEECcccchhhcccccccCCceEEEcCCCCC
Confidence 3566668887777776531112345799999985
No 206
>PF09162 Tap-RNA_bind: Tap, RNA-binding; InterPro: IPR015245 This domain adopts a structure consisting of an alpha+beta sandwich with an antiparallel beta-sheet, arranged in a 2(beta-alpha-beta) motif. It is mainly found in mRNA export factors, which mediate the sequence nonspecific nuclear export of cellular mRNAs as well as the sequence-specific export of retroviral mRNAs bearing the constitutive transport element []. ; GO: 0003723 RNA binding, 0006406 mRNA export from nucleus, 0005634 nucleus, 0005737 cytoplasm; PDB: 1FT8_A 1KOH_C 1KOO_C 3RW6_B 3RW7_C 1FO1_A.
Probab=37.96 E-value=20 Score=26.23 Aligned_cols=39 Identities=21% Similarity=0.359 Sum_probs=26.6
Q ss_pred eecCCCceecHHHHHHHHHhCCCceec--CCCCcccCcccceeccc
Q 024742 219 QVLPNGYVYSTKALEEMAKKNNGKITC--PRTGLVCNYSDLVKAYI 262 (263)
Q Consensus 219 ~~l~cGhv~~~~~~~~~~~~~~~~~~C--P~c~~~~~~~~~~~v~~ 262 (263)
|..|+|+-|.++-|.+..++ .| |..|..|+.+.-.-.||
T Consensus 10 VtIp~G~KYdK~wLl~~iq~-----~c~v~F~Pv~fh~~~~~a~Ff 50 (88)
T PF09162_consen 10 VTIPYGKKYDKDWLLNSIQS-----HCSVPFTPVDFHYEKNRAQFF 50 (88)
T ss_dssp EEETTGGGS-HHHHHHHHHH-----HSSS----EEEEEETTEEEEE
T ss_pred EEecCCcccCHHHHHHHHHH-----HCCCCeeeeeeeeeCCEEEEE
Confidence 57899999999999988652 56 67888888777665554
No 207
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=37.94 E-value=17 Score=20.14 Aligned_cols=11 Identities=27% Similarity=0.567 Sum_probs=7.6
Q ss_pred eecCCCCcccC
Q 024742 243 ITCPRTGLVCN 253 (263)
Q Consensus 243 ~~CP~c~~~~~ 253 (263)
..||.||-+|.
T Consensus 15 ~~Cp~CG~~F~ 25 (26)
T PF10571_consen 15 KFCPHCGYDFE 25 (26)
T ss_pred CcCCCCCCCCc
Confidence 47777777764
No 208
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=37.83 E-value=11 Score=33.94 Aligned_cols=27 Identities=15% Similarity=0.261 Sum_probs=20.3
Q ss_pred ecCCCceecHHHHHHHHHhCCCceecCCCCcc
Q 024742 220 VLPNGYVYSTKALEEMAKKNNGKITCPRTGLV 251 (263)
Q Consensus 220 ~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~ 251 (263)
|+||-||||.+|-..- ....||.|-..
T Consensus 106 mIPCkHvFCl~CAr~~-----~dK~Cp~C~d~ 132 (389)
T KOG2932|consen 106 MIPCKHVFCLECARSD-----SDKICPLCDDR 132 (389)
T ss_pred ccccchhhhhhhhhcC-----ccccCcCcccH
Confidence 6899999999997432 23489999754
No 209
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=37.79 E-value=36 Score=25.41 Aligned_cols=14 Identities=7% Similarity=0.040 Sum_probs=9.3
Q ss_pred CCcCCeeeeccccc
Q 024742 197 KQHHSKLVCYITKE 210 (263)
Q Consensus 197 ~~~~s~~~Cpi~~~ 210 (263)
......|.||.+++
T Consensus 16 ~klpt~f~CP~Cge 29 (99)
T PRK14892 16 PKLPKIFECPRCGK 29 (99)
T ss_pred cCCCcEeECCCCCC
Confidence 44456788888774
No 210
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=37.48 E-value=44 Score=29.63 Aligned_cols=14 Identities=21% Similarity=0.582 Sum_probs=10.0
Q ss_pred CCceecCCCCcccC
Q 024742 240 NGKITCPRTGLVCN 253 (263)
Q Consensus 240 ~~~~~CP~c~~~~~ 253 (263)
+.-|.||.|++.|.
T Consensus 213 EKPF~C~hC~kAFA 226 (279)
T KOG2462|consen 213 EKPFSCPHCGKAFA 226 (279)
T ss_pred CCCccCCcccchhc
Confidence 34578888888774
No 211
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=37.46 E-value=11 Score=38.46 Aligned_cols=18 Identities=17% Similarity=0.272 Sum_probs=0.0
Q ss_pred ChHHHHHHHHHhCcchhh
Q 024742 81 NNLRAITYARKYLAPWGA 98 (263)
Q Consensus 81 ~~~eAi~yar~~l~~~~~ 98 (263)
+..+|+++++++=.|+-.
T Consensus 470 ~~~eA~~~s~~~~vPLHP 487 (900)
T PF03833_consen 470 SAEEALEISEEYGVPLHP 487 (900)
T ss_dssp ------------------
T ss_pred CHHHHHHHHHHhCCCCCC
Confidence 457888888887666544
No 212
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=37.40 E-value=19 Score=31.15 Aligned_cols=31 Identities=13% Similarity=0.172 Sum_probs=20.6
Q ss_pred eecccccccCCCCCCeecCCCceecHHHHHHH
Q 024742 204 VCYITKELMDTENPPQVLPNGYVYSTKALEEM 235 (263)
Q Consensus 204 ~Cpi~~~~~~~~n~p~~l~cGhv~~~~~~~~~ 235 (263)
.|-.++---+ ..+.+++.|+||||..|...-
T Consensus 5 hCn~C~~~~~-~~~f~LTaC~HvfC~~C~k~~ 35 (233)
T KOG4739|consen 5 HCNKCFRFPS-QDPFFLTACRHVFCEPCLKAS 35 (233)
T ss_pred EeccccccCC-CCceeeeechhhhhhhhcccC
Confidence 3443333333 445678999999999998743
No 213
>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=37.12 E-value=1.5e+02 Score=26.31 Aligned_cols=55 Identities=5% Similarity=-0.052 Sum_probs=33.5
Q ss_pred HhcCChHHHHHHHHhhchhhhhCCCceeeechHHHHHHHHhcCChHHHHHHHHHhC
Q 024742 38 LQNKEVAPALAWCSDNKSRLKKSKSKFEFQLRLQEFIELVRGENNLRAITYARKYL 93 (263)
Q Consensus 38 i~~gdi~~Al~w~~~~~~~L~~~~s~LeF~L~~q~fIeLi~~~~~~eAi~yar~~l 93 (263)
...|+++.|++|+.+.-+.... ...+....+...-.-++..|+..+|+.+.++..
T Consensus 159 ~~~g~~~eA~~~l~~~l~~~~~-~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~~~ 213 (355)
T cd05804 159 EMQGRFKEGIAFMESWRDTWDC-SSMLRGHNWWHLALFYLERGDYEAALAIYDTHI 213 (355)
T ss_pred HHcCCHHHHHHHHHhhhhccCC-CcchhHHHHHHHHHHHHHCCCHHHHHHHHHHHh
Confidence 3479999999998776443221 122222222222233567799999999888754
No 214
>PF12931 Sec16_C: Sec23-binding domain of Sec16; PDB: 3MZK_C.
Probab=36.71 E-value=87 Score=27.76 Aligned_cols=49 Identities=18% Similarity=0.254 Sum_probs=26.4
Q ss_pred HHHHHHhcCChHHHHHHHHHhCcchhhhhHHHHHHHHHHhhccCCCCcchhHHhcCcccHHHHHHHHHHH
Q 024742 72 EFIELVRGENNLRAITYARKYLAPWGATHMKELQRVMATLAFKSNTECTTYKALFEPKQWDFLVDQFKQE 141 (263)
Q Consensus 72 ~fIeLi~~~~~~eAi~yar~~l~~~~~~~~~ei~~~~~lL~f~~~~~~s~y~~l~~~~r~~~la~~f~~~ 141 (263)
++-+++..|++.+|+++|-++ .. -.+++++ +...+++.|.++.+.|.+.
T Consensus 1 ~I~~~Ll~G~~~~Av~~al~~-~~----------wa~ALlL----------As~~g~e~~~~v~~~y~~~ 49 (284)
T PF12931_consen 1 KIQQLLLVGNREEAVELALDN-GL----------WAHALLL----------ASSLGPELWKKVVQEYFRR 49 (284)
T ss_dssp HHHHHHHTT-HHHHHHHHHHT-T-----------HHHHHHH----------HHTS-HHHHHHHHHHHHH-
T ss_pred CHHHHHhCCCHHHHHHHHHHC-CC----------hHHHHHH----------HHhcCHHHHHHHHHHHHHH
Confidence 345677778888888888753 11 1123332 2234666777777766655
No 215
>KOG2659 consensus LisH motif-containing protein [Cytoskeleton]
Probab=36.60 E-value=68 Score=27.71 Aligned_cols=54 Identities=11% Similarity=0.132 Sum_probs=40.2
Q ss_pred cccccHHHHHHHHHHcCCC---CCCCHHHHHHHHHHHHHHhcCChHHHHHHHHhhch
Q 024742 2 LRMSYYETAEKLAESSNIQ---DLVDIEVFQEAKKVIDALQNKEVAPALAWCSDNKS 55 (263)
Q Consensus 2 lr~Gy~~ta~~f~~e~~i~---~~~d~~~~~~~~~I~~~i~~gdi~~Al~w~~~~~~ 55 (263)
+..|..+.|-.+.....-+ ...++.......+..+.|+.|.++.|+++++.+-.
T Consensus 75 I~~G~Ie~Aie~in~l~PeiLd~n~~l~F~Lq~q~lIEliR~~~~eeal~F~q~~LA 131 (228)
T KOG2659|consen 75 IEEGQIEEAIEKVNQLNPEILDTNRELFFHLQQLHLIELIREGKTEEALEFAQTKLA 131 (228)
T ss_pred HHhccHHHHHHHHHHhChHHHccchhHHHHHHHHHHHHHHHhhhHHHHHHHHHHHcc
Confidence 4568888888877776532 23345567777789999999999999999877633
No 216
>smart00355 ZnF_C2H2 zinc finger.
Probab=35.72 E-value=17 Score=18.64 Aligned_cols=13 Identities=31% Similarity=0.621 Sum_probs=10.3
Q ss_pred eecCCCCcccCcc
Q 024742 243 ITCPRTGLVCNYS 255 (263)
Q Consensus 243 ~~CP~c~~~~~~~ 255 (263)
++|+.|++.|...
T Consensus 1 ~~C~~C~~~f~~~ 13 (26)
T smart00355 1 YRCPECGKVFKSK 13 (26)
T ss_pred CCCCCCcchhCCH
Confidence 4799999988754
No 217
>PF10827 DUF2552: Protein of unknown function (DUF2552) ; InterPro: IPR020157 This entry contains proteins with no known function.
Probab=35.68 E-value=23 Score=24.64 Aligned_cols=18 Identities=17% Similarity=0.482 Sum_probs=14.7
Q ss_pred CChHHHHHHHHhhchhhh
Q 024742 41 KEVAPALAWCSDNKSRLK 58 (263)
Q Consensus 41 gdi~~Al~w~~~~~~~L~ 58 (263)
--++.|++|+.+|.+.+-
T Consensus 59 ~tld~Ai~Wi~e~M~~iT 76 (79)
T PF10827_consen 59 PTLDLAIAWIGEHMPHIT 76 (79)
T ss_pred ccHHHHHHHHHhcccchh
Confidence 357899999999988653
No 218
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=35.65 E-value=32 Score=37.71 Aligned_cols=49 Identities=18% Similarity=0.266 Sum_probs=34.9
Q ss_pred ecccccccCCCCCCeecCCCceecHHHHHHHHHhC-------CCceecCCCCcccC
Q 024742 205 CYITKELMDTENPPQVLPNGYVYSTKALEEMAKKN-------NGKITCPRTGLVCN 253 (263)
Q Consensus 205 Cpi~~~~~~~~n~p~~l~cGhv~~~~~~~~~~~~~-------~~~~~CP~c~~~~~ 253 (263)
|=|+=.+--.--|.+-|.|||+|-..|..+...+. -+.+.||.|.....
T Consensus 3489 CmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~In 3544 (3738)
T KOG1428|consen 3489 CMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKIN 3544 (3738)
T ss_pred EEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecccccchhh
Confidence 33333333334566679999999999999888753 15679999998765
No 219
>PF14691 Fer4_20: Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster; PDB: 2VDC_G 1H7X_C 1H7W_A 1GT8_A 1GTE_B 1GTH_B.
Probab=35.51 E-value=51 Score=25.04 Aligned_cols=28 Identities=25% Similarity=0.325 Sum_probs=20.7
Q ss_pred eechHHHHHHHHhcCChHHHHHHHHHhC
Q 024742 66 FQLRLQEFIELVRGENNLRAITYARKYL 93 (263)
Q Consensus 66 F~L~~q~fIeLi~~~~~~eAi~yar~~l 93 (263)
..+....||++|+.|+..+|++..++..
T Consensus 38 ~~~dip~~i~~i~~g~~~~A~~~i~~~n 65 (111)
T PF14691_consen 38 AHIDIPEYIRLIREGNFKEAYELIREDN 65 (111)
T ss_dssp T---HHHHHHHHHCT-HHHHHHHHHHH-
T ss_pred CCCcHHHHHHHHHCCCHHHHHHHHHHhC
Confidence 3456789999999999999999998643
No 220
>KOG4642 consensus Chaperone-dependent E3 ubiquitin protein ligase (contains TPR repeats) [Posttranslational modification, protein turnover, chaperones]
Probab=35.31 E-value=25 Score=30.91 Aligned_cols=53 Identities=30% Similarity=0.392 Sum_probs=42.7
Q ss_pred CeeeecccccccCCCCCCeecCCCceecHHHHHHHHHhCCCceecCCCCcccCcccce
Q 024742 201 SKLVCYITKELMDTENPPQVLPNGYVYSTKALEEMAKKNNGKITCPRTGLVCNYSDLV 258 (263)
Q Consensus 201 s~~~Cpi~~~~~~~~n~p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~~~~~~ 258 (263)
..+-|.||-|+|++ |++.|.|-.|.+..|.+..++- |+ -.|.|....+..+.+
T Consensus 210 d~lcgkIt~el~~~---pvi~psgIty~ra~I~Ehl~rv-gh-fdpvtr~~Lte~q~i 262 (284)
T KOG4642|consen 210 DYLCGKITLELMRE---PVITPSGITYDRADIEEHLQRV-GH-FDPVTRWPLTEYQLI 262 (284)
T ss_pred chhhhhhhHHhhcC---CccCccccchhHHHHHHHHHHh-cc-CCchhcccCCHHhhc
Confidence 35678999999999 9999999999999999988753 22 468888777766544
No 221
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=35.30 E-value=7.1 Score=28.61 Aligned_cols=30 Identities=13% Similarity=0.401 Sum_probs=21.5
Q ss_pred CCCeecCCCceecHHHHHHHHHhCCCceecCCCCccc
Q 024742 216 NPPQVLPNGYVYSTKALEEMAKKNNGKITCPRTGLVC 252 (263)
Q Consensus 216 n~p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~ 252 (263)
.||..-.||.++-.+-|+.- -.||.|+.+-
T Consensus 57 ~Pa~CkkCGfef~~~~ik~p-------SRCP~CKSE~ 86 (97)
T COG3357 57 RPARCKKCGFEFRDDKIKKP-------SRCPKCKSEW 86 (97)
T ss_pred cChhhcccCccccccccCCc-------ccCCcchhhc
Confidence 45667889999977555433 2799998764
No 222
>PF04475 DUF555: Protein of unknown function (DUF555); InterPro: IPR007564 This is a family of uncharacterised, hypothetical archaeal proteins.
Probab=35.14 E-value=19 Score=26.78 Aligned_cols=14 Identities=29% Similarity=0.665 Sum_probs=11.9
Q ss_pred CceecCCCCcccCc
Q 024742 241 GKITCPRTGLVCNY 254 (263)
Q Consensus 241 ~~~~CP~c~~~~~~ 254 (263)
+...||.|+++++.
T Consensus 46 G~~~cP~Cge~~~~ 59 (102)
T PF04475_consen 46 GDTICPKCGEELDS 59 (102)
T ss_pred CcccCCCCCCccCc
Confidence 56799999999875
No 223
>PF11251 DUF3050: Protein of unknown function (DUF3050); InterPro: IPR024423 This family of proteins has no known function.
Probab=35.12 E-value=1.8e+02 Score=25.25 Aligned_cols=49 Identities=22% Similarity=0.326 Sum_probs=32.6
Q ss_pred HHHHHHhcC-ChHHHHHHHHhhchhhhhCCCceeeechHHHHH----HHHhcCC---hHHHHHHHHHhCcc
Q 024742 33 KVIDALQNK-EVAPALAWCSDNKSRLKKSKSKFEFQLRLQEFI----ELVRGEN---NLRAITYARKYLAP 95 (263)
Q Consensus 33 ~I~~~i~~g-di~~Al~w~~~~~~~L~~~~s~LeF~L~~q~fI----eLi~~~~---~~eAi~yar~~l~~ 95 (263)
+.++.+++| ++..||+-..-- .-.++|+ ++|.+|+ +..|..|+|+.+.|
T Consensus 101 ~fl~~~~~g~~v~~Al~~~~~p--------------~~~~~Fv~~Tf~~i~~~~~H~iAAaFtfGREdlIP 157 (232)
T PF11251_consen 101 RFLSLLREGTSVFEALQQADVP--------------EPAKRFVRFTFEIIAEGKPHEIAAAFTFGREDLIP 157 (232)
T ss_pred HHHHHHHcCCCHHHHHHhcCCC--------------HHHHHHHHHHHHHHhcCCHHHHHHHHHhccccchH
Confidence 447778887 888888664211 1123333 5677775 57899999999887
No 224
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=35.02 E-value=23 Score=28.17 Aligned_cols=35 Identities=11% Similarity=0.151 Sum_probs=20.8
Q ss_pred CCCCCCchhhhhhcC-----CCCCC--CCcCCeeeecccccc
Q 024742 177 KEDPLSQESFRKLAS-----PLPYS--KQHHSKLVCYITKEL 211 (263)
Q Consensus 177 ~~cp~c~~~~~~l~~-----~lP~~--~~~~s~~~Cpi~~~~ 211 (263)
+.||.|+..+.+++. .+|.. ..+...+.||-+|..
T Consensus 92 sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~ki 133 (147)
T PF01927_consen 92 SRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKI 133 (147)
T ss_pred CccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCE
Confidence 679999887655433 35553 223446677666554
No 225
>PF02748 PyrI_C: Aspartate carbamoyltransferase regulatory chain, metal binding domain; InterPro: IPR020542 Aspartate carbamoyltransferase (aspartate transcarbamylase, ATCase) 2.1.3.2 from EC is an allosteric enzyme that plays a central role in the regulation of the pyrimidine pathway in bacteria. The holoenzyme is a dodecamer composed of six catalytic chains, each with an active site, and six regulatory chains lacking catalytic activity []. The catalytic subunits exist as a dimer of catalytic trimers, (c3)2, while the regulatory subunits exist as a trimer of regulatory dimers, (r2)3, therefore the complete holoenzyme can be represented as (c3)2(r2)3. The association of the catalytic subunits c3 with the regulatory subunits r2 is responsible for the establishment of positive co-operativity between catalytic sites for the binding of aspartate and it dictates the pattern of allosteric response toward nucleotide effectors. ATCase from Escherichia coli is the most extensively studied allosteric enzyme []. The crystal structure of the T-state, the T-state with CTP bound, the R-state with N-phosphonacetyl-L-aspartate (PALA) bound, and the R-state with phosphonoacetamide plus malonate bound have been used in interpreting kinetic and mutational studies. A high-resolution structure of E. coli ATCase in the presence of PALA (a bisubstrate analog) allows a detailed description of the binding at the active site of the enzyme and allows a detailed model of the tetrahedral intermediate to be constructed. The entire regulatory chain has been traced showing that the N-terminal regions of the regulatory chains R1 and R6 are located in close proximity to each other and to the regulatory site. This portion of the molecule may be involved in the observed asymmetry between the regulatory binding sites as well as in the heterotropic response of the enzyme []. The C-terminal domain of the regulatory chains have a rubredoxin-like zinc-bound fold. ATCase from Enterobacter agglomerans (Erwinia herbicola) (Pantoea agglomerans) differs from the other investigated enterobacterial ATCases by its absence of homotropic co-operativity toward the substrate aspartate and its lack of response to ATP which is an allosteric effector (activator) of this family of enzymes. Nevertheless, the E. herbicola ATCase has the same quaternary structure, two trimers of catalytic chains with three dimers of regulatory chains, (c3)2(r2)3, as other enterobacterial ATCases and shows extensive primary structure conservation []. This entry represents the C-terminal domain.; PDB: 2YWW_B 1SKU_D 1Q95_L 8ATC_B 3AT1_D 1RAI_D 4E2F_D 1NBE_B 6AT1_B 2FZC_D ....
Probab=34.93 E-value=11 Score=24.63 Aligned_cols=20 Identities=10% Similarity=0.162 Sum_probs=13.6
Q ss_pred CCCceecCCCCcccCcccce
Q 024742 239 NNGKITCPRTGLVCNYSDLV 258 (263)
Q Consensus 239 ~~~~~~CP~c~~~~~~~~~~ 258 (263)
+...++|-||.+.++.+++.
T Consensus 32 ~~~~~rC~YCe~~~~~~eI~ 51 (52)
T PF02748_consen 32 EPIKLRCHYCERIITEDEIW 51 (52)
T ss_dssp TTCEEEETTT--EEEHHHHH
T ss_pred CCCEEEeeCCCCEecccEEe
Confidence 45678999999988877663
No 226
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=34.68 E-value=24 Score=19.21 Aligned_cols=15 Identities=7% Similarity=0.175 Sum_probs=11.2
Q ss_pred ceecCCCCcccCccc
Q 024742 242 KITCPRTGLVCNYSD 256 (263)
Q Consensus 242 ~~~CP~c~~~~~~~~ 256 (263)
++.|+.|++.|.-..
T Consensus 1 q~~C~~C~k~f~~~~ 15 (27)
T PF12171_consen 1 QFYCDACDKYFSSEN 15 (27)
T ss_dssp -CBBTTTTBBBSSHH
T ss_pred CCCcccCCCCcCCHH
Confidence 368999999987543
No 227
>KOG3616 consensus Selective LIM binding factor [Transcription]
Probab=34.42 E-value=2.7e+02 Score=28.79 Aligned_cols=86 Identities=15% Similarity=0.198 Sum_probs=54.9
Q ss_pred CCCCCCHHHHHHHHHHHHHHhcCChHHHHHHHHh-hc-hhhhhCCCceeeechHHHHHHHHhcCChHHHHHHHHHhCcch
Q 024742 19 IQDLVDIEVFQEAKKVIDALQNKEVAPALAWCSD-NK-SRLKKSKSKFEFQLRLQEFIELVRGENNLRAITYARKYLAPW 96 (263)
Q Consensus 19 i~~~~d~~~~~~~~~I~~~i~~gdi~~Al~w~~~-~~-~~L~~~~s~LeF~L~~q~fIeLi~~~~~~eAi~yar~~l~~~ 96 (263)
+..++|+|.+.. |---|.++.|+.||+-+.. |+ |.|.+ ---|.--.||+.|+...|+...-+|=.|-
T Consensus 1287 l~eli~vdviaa---idl~ien~qwdk~idtak~qnykpil~k--------yva~yaa~li~~~d~aq~lal~~q~ga~a 1355 (1636)
T KOG3616|consen 1287 LDELIDVDVIAA---IDLMIENDQWDKAIDTAKKQNYKPILDK--------YVALYAAHLIHEGDLAQALALLEQHGAPA 1355 (1636)
T ss_pred cccccchhHHHH---HHHHHhcccHHHHHHHHHhcccHHHHHH--------HHHHHHHHHHhcCcHHHHHHHHHHhCCCC
Confidence 334555555432 3334668999999988743 32 23332 23455567899999999999888888776
Q ss_pred hhhhHHHHHHHHHHhhccC
Q 024742 97 GATHMKELQRVMATLAFKS 115 (263)
Q Consensus 97 ~~~~~~ei~~~~~lL~f~~ 115 (263)
...+..-.+.+|.-++-.+
T Consensus 1356 npanfniyk~i~ed~lakp 1374 (1636)
T KOG3616|consen 1356 NPANFNIYKLIFEDMLAKP 1374 (1636)
T ss_pred CcccccHHHHHHHHHhcCC
Confidence 6655555556666555444
No 228
>KOG2042 consensus Ubiquitin fusion degradation protein-2 [Posttranslational modification, protein turnover, chaperones]
Probab=34.33 E-value=34 Score=35.53 Aligned_cols=52 Identities=17% Similarity=0.172 Sum_probs=43.1
Q ss_pred CeeeecccccccCCCCCCeecC-CCceecHHHHHHHHHhCCCceecCCCCcccCcccce
Q 024742 201 SKLVCYITKELMDTENPPQVLP-NGYVYSTKALEEMAKKNNGKITCPRTGLVCNYSDLV 258 (263)
Q Consensus 201 s~~~Cpi~~~~~~~~n~p~~l~-cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~~~~~~ 258 (263)
.-|.-|++...|.+ ||+|| .|++..|..+.+..-.+ -+.|.|....+.+++.
T Consensus 869 def~DPlm~Tlm~d---PV~LP~Srv~vDRsti~rhlLs~---~tdPFNR~pLt~d~v~ 921 (943)
T KOG2042|consen 869 DEFLDPLMSTLMSD---PVVLPSSRVTVDRSTIERHLLSD---CTDPFNREPLTEDMVS 921 (943)
T ss_pred hhhhCccccccCCC---CccCCcccccccHHHHHHHHhcC---CCCccccccCchhhcC
Confidence 34778999999999 99999 99999999999876532 4789998888877765
No 229
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=34.28 E-value=39 Score=22.33 Aligned_cols=32 Identities=16% Similarity=0.202 Sum_probs=24.6
Q ss_pred eecccccccCCCCCCee-cCCCceecHHHHHHH
Q 024742 204 VCYITKELMDTENPPQV-LPNGYVYSTKALEEM 235 (263)
Q Consensus 204 ~Cpi~~~~~~~~n~p~~-l~cGhv~~~~~~~~~ 235 (263)
.|++.|+.+.+..+-|+ -.||-+|-|++-++.
T Consensus 7 ~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~ 39 (54)
T PF14446_consen 7 KCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKA 39 (54)
T ss_pred cChhhCCcccCCCCEEECCCCCCcccHHHHhhC
Confidence 58888999876666565 569999999987654
No 230
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.92 E-value=31 Score=26.27 Aligned_cols=32 Identities=28% Similarity=0.264 Sum_probs=21.9
Q ss_pred eeecccccccCCCC-CCeecC-CCceecHHHHHH
Q 024742 203 LVCYITKELMDTEN-PPQVLP-NGYVYSTKALEE 234 (263)
Q Consensus 203 ~~Cpi~~~~~~~~n-~p~~l~-cGhv~~~~~~~~ 234 (263)
=+||=||.-+-+-| .|++.| ||..|-+..++.
T Consensus 10 ridPetg~KFYDLNrdPiVsPytG~s~P~s~fe~ 43 (129)
T COG4530 10 RIDPETGKKFYDLNRDPIVSPYTGKSYPRSYFEE 43 (129)
T ss_pred ccCccccchhhccCCCccccCcccccchHHHHHh
Confidence 36777777775544 477654 888887777765
No 231
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=33.86 E-value=16 Score=29.83 Aligned_cols=64 Identities=8% Similarity=0.047 Sum_probs=36.1
Q ss_pred hCCCCCcHHHHHHHhhh-hhccccccccCCCCCCCCCCchhhhhhcC-----CCCCC--CCcCCeeeeccccccc
Q 024742 146 YGMTLEPLLNIYLQAGL-SALNTPYCYEDDCTKEDPLSQESFRKLAS-----PLPYS--KQHHSKLVCYITKELM 212 (263)
Q Consensus 146 ~~~~~~s~L~~~l~~G~-~al~t~~c~~~~~~~~cp~c~~~~~~l~~-----~lP~~--~~~~s~~~Cpi~~~~~ 212 (263)
.-++.+++-.++...-. ..++- -.... .+.||.|+..+.++.. .+|.. -.++..+.||.+|.+.
T Consensus 69 i~i~~~s~~~Ql~e~~~~~~l~~--~~~~e-~~RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiY 140 (165)
T COG1656 69 ILIRSDSIEEQLAEFLARLGLKP--RLFPE-FSRCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIY 140 (165)
T ss_pred EEEeCCCHHHHHHHHHHHhccch--hcccc-cccCcccCCEeccCcHHHHhhccchhhhhcccceeECCCCcccc
Confidence 34566777776666411 12221 11111 3679999998765433 55643 4566677788777654
No 232
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=33.82 E-value=23 Score=18.91 Aligned_cols=11 Identities=27% Similarity=0.531 Sum_probs=7.8
Q ss_pred ecCCCCcccCc
Q 024742 244 TCPRTGLVCNY 254 (263)
Q Consensus 244 ~CP~c~~~~~~ 254 (263)
.||.||.+...
T Consensus 1 ~Cp~CG~~~~~ 11 (23)
T PF13240_consen 1 YCPNCGAEIED 11 (23)
T ss_pred CCcccCCCCCC
Confidence 48888877654
No 233
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=33.43 E-value=24 Score=21.21 Aligned_cols=12 Identities=33% Similarity=0.800 Sum_probs=8.7
Q ss_pred ecCCCCcccCcc
Q 024742 244 TCPRTGLVCNYS 255 (263)
Q Consensus 244 ~CP~c~~~~~~~ 255 (263)
.||.|++.+...
T Consensus 4 ~CprC~kg~Hwa 15 (36)
T PF14787_consen 4 LCPRCGKGFHWA 15 (36)
T ss_dssp C-TTTSSSCS-T
T ss_pred cCcccCCCcchh
Confidence 699999998864
No 234
>COG0268 RpsT Ribosomal protein S20 [Translation, ribosomal structure and biogenesis]
Probab=32.99 E-value=74 Score=23.23 Aligned_cols=30 Identities=23% Similarity=0.277 Sum_probs=25.5
Q ss_pred HHHHHHHHhcCChHHHHHHHHhhchhhhhC
Q 024742 31 AKKVIDALQNKEVAPALAWCSDNKSRLKKS 60 (263)
Q Consensus 31 ~~~I~~~i~~gdi~~Al~w~~~~~~~L~~~ 60 (263)
..++..+|..||.+.|.+.+..-.+.+++.
T Consensus 32 iKk~~~ai~~gd~~~A~~~l~~a~~~idka 61 (88)
T COG0268 32 IKKVEAAIEAGDKEAAKAALKEAQKKIDKA 61 (88)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHHHHH
Confidence 456788999999999999999999888763
No 235
>KOG3452 consensus 60S ribosomal protein L36 [Translation, ribosomal structure and biogenesis]
Probab=32.94 E-value=1e+02 Score=22.94 Aligned_cols=41 Identities=24% Similarity=0.325 Sum_probs=30.5
Q ss_pred hHHHHHHHHhcCChHHHHHHHHHhCcchhhh--hHHHHHHHHH
Q 024742 69 RLQEFIELVRGENNLRAITYARKYLAPWGAT--HMKELQRVMA 109 (263)
Q Consensus 69 ~~q~fIeLi~~~~~~eAi~yar~~l~~~~~~--~~~ei~~~~~ 109 (263)
.-.+-+||++..+-..|++++++.+..+... ..+|+..++.
T Consensus 53 yErr~meLlkvskdkrA~K~lKkRlGth~RAk~KrEELsnvl~ 95 (102)
T KOG3452|consen 53 YERRAMELLKVSKDKRALKLLKKRLGTHKRAKRKREELSNVLA 95 (102)
T ss_pred HHHHHHHHHHHcccHHHHHHHHHHhhHHHHHHHHHHHHHHHHH
Confidence 3456899999998899999999999887652 3455554443
No 236
>PHA01735 hypothetical protein
Probab=32.79 E-value=49 Score=22.98 Aligned_cols=22 Identities=14% Similarity=0.489 Sum_probs=15.6
Q ss_pred HHHHHHhcC-----ChHHHHHHHHhhc
Q 024742 33 KVIDALQNK-----EVAPALAWCSDNK 54 (263)
Q Consensus 33 ~I~~~i~~g-----di~~Al~w~~~~~ 54 (263)
+....|+.| |+..|++|++.|.
T Consensus 20 El~~RiksgeATtaDL~AA~d~Lk~Nd 46 (76)
T PHA01735 20 ELLSRIKSGEATTADLRAACDWLKSND 46 (76)
T ss_pred HHHHHHhcCcccHHHHHHHHHHHHHCC
Confidence 344555555 8889999998883
No 237
>CHL00098 tsf elongation factor Ts
Probab=32.64 E-value=53 Score=27.81 Aligned_cols=22 Identities=27% Similarity=0.227 Sum_probs=17.7
Q ss_pred HHHHHHh--cCChHHHHHHHHhhc
Q 024742 33 KVIDALQ--NKEVAPALAWCSDNK 54 (263)
Q Consensus 33 ~I~~~i~--~gdi~~Al~w~~~~~ 54 (263)
...++|. +||++.|++|++++-
T Consensus 18 dck~AL~e~~gd~~~A~~~Lr~~g 41 (200)
T CHL00098 18 DCKKALQEANGDFEKALESLRQKG 41 (200)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHhh
Confidence 3466776 699999999999874
No 238
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=32.28 E-value=23 Score=19.04 Aligned_cols=13 Identities=15% Similarity=0.314 Sum_probs=10.8
Q ss_pred eecCCCCcccCcc
Q 024742 243 ITCPRTGLVCNYS 255 (263)
Q Consensus 243 ~~CP~c~~~~~~~ 255 (263)
++|..|++.|...
T Consensus 2 ~~C~~C~~~F~~~ 14 (27)
T PF13912_consen 2 FECDECGKTFSSL 14 (27)
T ss_dssp EEETTTTEEESSH
T ss_pred CCCCccCCccCCh
Confidence 6899999999754
No 239
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=32.25 E-value=43 Score=21.70 Aligned_cols=30 Identities=13% Similarity=0.243 Sum_probs=23.5
Q ss_pred eecccccccCCCCCCeecCCCceecHHHHHHH
Q 024742 204 VCYITKELMDTENPPQVLPNGYVYSTKALEEM 235 (263)
Q Consensus 204 ~Cpi~~~~~~~~n~p~~l~cGhv~~~~~~~~~ 235 (263)
.|+|.|+...--.+ +-+..| .+|.+|++++
T Consensus 1 ~C~iCg~kigl~~~-~k~~DG-~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKR-FKIKDG-YICKDCLKKL 30 (51)
T ss_pred CCCccccccccccc-eeccCc-cchHHHHHHh
Confidence 37888877765443 668999 6999999998
No 240
>PHA03096 p28-like protein; Provisional
Probab=32.10 E-value=29 Score=31.04 Aligned_cols=37 Identities=8% Similarity=-0.091 Sum_probs=27.5
Q ss_pred eecCCCceecHHHHHHHHHhCCCceecCCCCcccCcc
Q 024742 219 QVLPNGYVYSTKALEEMAKKNNGKITCPRTGLVCNYS 255 (263)
Q Consensus 219 ~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~~~ 255 (263)
++-.|-|+++..++..|.......-.||.|++--+..
T Consensus 200 il~~c~h~fc~~ci~~wr~~~~~~e~~~~c~~~~~~~ 236 (284)
T PHA03096 200 ILSEIKHEFNIFCIKIWMTESLYKETEPENRRLNTVI 236 (284)
T ss_pred ccccCCcHHHHHHHHHHHHhhhhcccCccccchhhHH
Confidence 4457999999999999976554556788887655443
No 241
>PRK12332 tsf elongation factor Ts; Reviewed
Probab=32.04 E-value=55 Score=27.64 Aligned_cols=22 Identities=23% Similarity=0.508 Sum_probs=17.9
Q ss_pred HHHHHHh--cCChHHHHHHHHhhc
Q 024742 33 KVIDALQ--NKEVAPALAWCSDNK 54 (263)
Q Consensus 33 ~I~~~i~--~gdi~~Al~w~~~~~ 54 (263)
...++|. +||++.|++|+++.-
T Consensus 21 ~ck~AL~~~~gd~~~A~~~lr~~g 44 (198)
T PRK12332 21 DCKKALEEANGDMEKAIEWLREKG 44 (198)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHhh
Confidence 3467776 699999999999874
No 242
>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.
Probab=31.82 E-value=30 Score=22.27 Aligned_cols=33 Identities=15% Similarity=0.124 Sum_probs=21.5
Q ss_pred CeecCCCceecHHHHHHHHHhCCCceecCCCCcccC
Q 024742 218 PQVLPNGYVYSTKALEEMAKKNNGKITCPRTGLVCN 253 (263)
Q Consensus 218 p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~ 253 (263)
-.+-=..|-++.+++..|.+. .--||+|+++..
T Consensus 14 ~Li~C~dHYLCl~CLt~ml~~---s~~C~iC~~~LP 46 (50)
T PF03854_consen 14 GLIKCSDHYLCLNCLTLMLSR---SDRCPICGKPLP 46 (50)
T ss_dssp SEEE-SS-EEEHHHHHHT-SS---SSEETTTTEE--
T ss_pred CeeeecchhHHHHHHHHHhcc---ccCCCcccCcCc
Confidence 344445689999999999753 358999998754
No 243
>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=31.79 E-value=74 Score=23.80 Aligned_cols=87 Identities=14% Similarity=-0.016 Sum_probs=44.1
Q ss_pred ccccHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHHhcCChHHHHHHHHhhchhhhhCCCceeeechHHHHHHHHhcCCh
Q 024742 3 RMSYYETAEKLAESSNIQDLVDIEVFQEAKKVIDALQNKEVAPALAWCSDNKSRLKKSKSKFEFQLRLQEFIELVRGENN 82 (263)
Q Consensus 3 r~Gy~~ta~~f~~e~~i~~~~d~~~~~~~~~I~~~i~~gdi~~Al~w~~~~~~~L~~~~s~LeF~L~~q~fIeLi~~~~~ 82 (263)
..|..+.|..+.+..--....+.+....+. .-....|+.+.|++++++--. +... +..+....-. +-+.. |+.
T Consensus 29 ~~~~~~~A~~~~~~~~~~~p~~~~~~~~la--~~~~~~~~~~~A~~~~~~~~~-~~p~--~~~~~~~la~-~~~~~-g~~ 101 (135)
T TIGR02552 29 QQGRYDEALKLFQLLAAYDPYNSRYWLGLA--ACCQMLKEYEEAIDAYALAAA-LDPD--DPRPYFHAAE-CLLAL-GEP 101 (135)
T ss_pred HcccHHHHHHHHHHHHHhCCCcHHHHHHHH--HHHHHHHHHHHHHHHHHHHHh-cCCC--ChHHHHHHHH-HHHHc-CCH
Confidence 456666666655554211222333332222 222346899999998875422 2222 2333333332 22233 678
Q ss_pred HHHHHHHHHhCcch
Q 024742 83 LRAITYARKYLAPW 96 (263)
Q Consensus 83 ~eAi~yar~~l~~~ 96 (263)
.+|+++.++-+.-.
T Consensus 102 ~~A~~~~~~al~~~ 115 (135)
T TIGR02552 102 ESALKALDLAIEIC 115 (135)
T ss_pred HHHHHHHHHHHHhc
Confidence 88988888665543
No 244
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=31.78 E-value=25 Score=19.25 Aligned_cols=8 Identities=38% Similarity=0.841 Sum_probs=4.1
Q ss_pred ecCCCCcc
Q 024742 244 TCPRTGLV 251 (263)
Q Consensus 244 ~CP~c~~~ 251 (263)
.||.|+.+
T Consensus 4 ~Cp~Cg~~ 11 (26)
T PF13248_consen 4 FCPNCGAE 11 (26)
T ss_pred CCcccCCc
Confidence 45555553
No 245
>KOG0259 consensus Tyrosine aminotransferase [Amino acid transport and metabolism]
Probab=31.54 E-value=32 Score=32.18 Aligned_cols=16 Identities=44% Similarity=0.760 Sum_probs=14.9
Q ss_pred CCCceecHHHHHHHHH
Q 024742 222 PNGYVYSTKALEEMAK 237 (263)
Q Consensus 222 ~cGhv~~~~~~~~~~~ 237 (263)
|||.||+++-|++++.
T Consensus 211 PcGnVys~~HL~kiae 226 (447)
T KOG0259|consen 211 PCGNVYSEDHLKKIAE 226 (447)
T ss_pred CCcccccHHHHHHHHH
Confidence 8999999999999985
No 246
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=31.49 E-value=42 Score=22.15 Aligned_cols=10 Identities=40% Similarity=0.733 Sum_probs=8.4
Q ss_pred ceecCCCCcc
Q 024742 242 KITCPRTGLV 251 (263)
Q Consensus 242 ~~~CP~c~~~ 251 (263)
..|||.|++.
T Consensus 24 e~KCPrCK~v 33 (60)
T COG4416 24 EKKCPRCKEV 33 (60)
T ss_pred eecCCcccee
Confidence 5799999875
No 247
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=31.20 E-value=23 Score=21.18 Aligned_cols=13 Identities=15% Similarity=0.365 Sum_probs=9.0
Q ss_pred ceecCCCCcccCc
Q 024742 242 KITCPRTGLVCNY 254 (263)
Q Consensus 242 ~~~CP~c~~~~~~ 254 (263)
.++||.|+..|..
T Consensus 5 ~y~C~~Cg~~fe~ 17 (41)
T smart00834 5 EYRCEDCGHTFEV 17 (41)
T ss_pred EEEcCCCCCEEEE
Confidence 3678888877754
No 248
>TIGR00116 tsf translation elongation factor Ts. This protein is found in Bacteria, mitochondria, and chloroplasts.
Probab=31.07 E-value=54 Score=29.42 Aligned_cols=46 Identities=17% Similarity=0.217 Sum_probs=32.5
Q ss_pred HHHHHHh--cCChHHHHHHHHhhchh-------------------------hhhCCCceeeechHHHHHHHHh
Q 024742 33 KVIDALQ--NKEVAPALAWCSDNKSR-------------------------LKKSKSKFEFQLRLQEFIELVR 78 (263)
Q Consensus 33 ~I~~~i~--~gdi~~Al~w~~~~~~~-------------------------L~~~~s~LeF~L~~q~fIeLi~ 78 (263)
...++|. +||++.|++|+++.--. +.+.++.-.|--+-..|++|+.
T Consensus 21 dCKkAL~e~~gDiekAi~~LRkkG~akA~Kk~~R~a~EG~V~~~~~~~~~~ivElncETDFVArne~F~~l~~ 93 (290)
T TIGR00116 21 DCKKALTEANGDFEKAIKNLRESGIAKAAKKADRVAAEGVIVLKSDGNKAVIVEVNSETDFVAKNAGFKEFAN 93 (290)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHhchhHHHHhcccccCCcEEEEEEcCCEEEEEEEecCCccccCChHHHHHHH
Confidence 3467776 69999999999987321 2223456677777778888765
No 249
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=30.93 E-value=34 Score=27.67 Aligned_cols=23 Identities=13% Similarity=0.326 Sum_probs=18.5
Q ss_pred CCceecCCCCcccCcccceeccc
Q 024742 240 NGKITCPRTGLVCNYSDLVKAYI 262 (263)
Q Consensus 240 ~~~~~CP~c~~~~~~~~~~~v~~ 262 (263)
+..+.||.|+..|+..|+...-|
T Consensus 107 ~~~Y~Cp~c~~r~tf~eA~~~~F 129 (158)
T TIGR00373 107 NMFFICPNMCVRFTFNEAMELNF 129 (158)
T ss_pred CCeEECCCCCcEeeHHHHHHcCC
Confidence 45689999999999998876443
No 250
>PRK15359 type III secretion system chaperone protein SscB; Provisional
Probab=30.87 E-value=2.5e+02 Score=21.72 Aligned_cols=14 Identities=7% Similarity=-0.368 Sum_probs=7.5
Q ss_pred hcCChHHHHHHHHH
Q 024742 78 RGENNLRAITYARK 91 (263)
Q Consensus 78 ~~~~~~eAi~yar~ 91 (263)
+.|+..+|+.+.++
T Consensus 104 ~~g~~~eAi~~~~~ 117 (144)
T PRK15359 104 MMGEPGLAREAFQT 117 (144)
T ss_pred HcCCHHHHHHHHHH
Confidence 44555555555554
No 251
>PLN02400 cellulose synthase
Probab=30.79 E-value=40 Score=35.59 Aligned_cols=55 Identities=13% Similarity=0.227 Sum_probs=40.5
Q ss_pred CCcCCeeeeccccccc--CCCCCCee--cCCCceecHHHHHHHHHhCCCceecCCCCcccC
Q 024742 197 KQHHSKLVCYITKELM--DTENPPQV--LPNGYVYSTKALEEMAKKNNGKITCPRTGLVCN 253 (263)
Q Consensus 197 ~~~~s~~~Cpi~~~~~--~~~n~p~~--l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~ 253 (263)
.+..+.=+|-|+|+.+ +++..|++ -.||--.|+.|-+ .-+ .++.-.||.|+..++
T Consensus 31 ~~~~~gqiCqICGD~VG~t~dGe~FVAC~eCaFPVCRpCYE-YER-keGnq~CPQCkTrYk 89 (1085)
T PLN02400 31 LKNLNGQICQICGDDVGVTETGDVFVACNECAFPVCRPCYE-YER-KDGTQCCPQCKTRYR 89 (1085)
T ss_pred ccccCCceeeecccccCcCCCCCEEEEEccCCCccccchhh-eec-ccCCccCcccCCccc
Confidence 4444555899999997 44444443 6899999999995 333 345569999999998
No 252
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=30.33 E-value=30 Score=22.47 Aligned_cols=23 Identities=13% Similarity=0.239 Sum_probs=14.5
Q ss_pred CCCceecHHHHHHHHHhCCCceecCCC
Q 024742 222 PNGYVYSTKALEEMAKKNNGKITCPRT 248 (263)
Q Consensus 222 ~cGhv~~~~~~~~~~~~~~~~~~CP~c 248 (263)
.|||.|...--.+. .+.-.||+|
T Consensus 33 ~Cgh~w~~~v~~R~----~~~~~CP~C 55 (55)
T PF14311_consen 33 KCGHEWKASVNDRT----RRGKGCPYC 55 (55)
T ss_pred CCCCeeEccHhhhc----cCCCCCCCC
Confidence 57888865444443 233589998
No 253
>PF14689 SPOB_a: Sensor_kinase_SpoOB-type, alpha-helical domain; PDB: 1F51_C 2FTK_B 1IXM_B.
Probab=30.31 E-value=1.4e+02 Score=19.90 Aligned_cols=34 Identities=12% Similarity=0.178 Sum_probs=23.6
Q ss_pred HHHHHHHHHHHHHhcCChHHHHHHHHhhchhhhh
Q 024742 26 EVFQEAKKVIDALQNKEVAPALAWCSDNKSRLKK 59 (263)
Q Consensus 26 ~~~~~~~~I~~~i~~gdi~~Al~w~~~~~~~L~~ 59 (263)
|....++-|.-.+..|+.+.|.+++++....+..
T Consensus 22 D~~NhLqvI~gllqlg~~~~a~eYi~~~~~~~~~ 55 (62)
T PF14689_consen 22 DFLNHLQVIYGLLQLGKYEEAKEYIKELSKDLQQ 55 (62)
T ss_dssp HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4455566666777788888888888887766554
No 254
>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=30.22 E-value=49 Score=17.71 Aligned_cols=17 Identities=12% Similarity=-0.031 Sum_probs=12.8
Q ss_pred HHHhcCChHHHHHHHHh
Q 024742 36 DALQNKEVAPALAWCSD 52 (263)
Q Consensus 36 ~~i~~gdi~~Al~w~~~ 52 (263)
-....||++.|.+++.+
T Consensus 10 ~~~~~G~~~eA~~~l~~ 26 (26)
T PF07721_consen 10 ALLAQGDPDEAERLLRR 26 (26)
T ss_pred HHHHcCCHHHHHHHHhC
Confidence 34568999999988753
No 255
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=30.16 E-value=25 Score=26.40 Aligned_cols=14 Identities=29% Similarity=0.693 Sum_probs=11.7
Q ss_pred CceecCCCCcccCc
Q 024742 241 GKITCPRTGLVCNY 254 (263)
Q Consensus 241 ~~~~CP~c~~~~~~ 254 (263)
|...||.||..|..
T Consensus 48 G~t~CP~Cg~~~e~ 61 (115)
T COG1885 48 GSTSCPKCGEPFES 61 (115)
T ss_pred ccccCCCCCCccce
Confidence 67799999998864
No 256
>PF13371 TPR_9: Tetratricopeptide repeat
Probab=30.13 E-value=1.6e+02 Score=19.29 Aligned_cols=53 Identities=19% Similarity=0.078 Sum_probs=37.0
Q ss_pred HHhcCChHHHHHHHHhhchhhhhCCCceeeechHHHHHHHHhcCChHHHHHHHHHhCc
Q 024742 37 ALQNKEVAPALAWCSDNKSRLKKSKSKFEFQLRLQEFIELVRGENNLRAITYARKYLA 94 (263)
Q Consensus 37 ~i~~gdi~~Al~w~~~~~~~L~~~~s~LeF~L~~q~fIeLi~~~~~~eAi~yar~~l~ 94 (263)
.+.++|++.|+++++..-.. ++. ...++...=.=+.+.|+..+|++...+.+.
T Consensus 5 ~~~~~~~~~A~~~~~~~l~~----~p~-~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~ 57 (73)
T PF13371_consen 5 YLQQEDYEEALEVLERALEL----DPD-DPELWLQRARCLFQLGRYEEALEDLERALE 57 (73)
T ss_pred HHhCCCHHHHHHHHHHHHHh----Ccc-cchhhHHHHHHHHHhccHHHHHHHHHHHHH
Confidence 35689999999998765322 222 455556666667778899999988887653
No 257
>COG5051 RPL36A Ribosomal protein L36E [Translation, ribosomal structure and biogenesis]
Probab=30.09 E-value=1.4e+02 Score=21.78 Aligned_cols=39 Identities=23% Similarity=0.343 Sum_probs=29.2
Q ss_pred HHHHHHHHhcCChHHHHHHHHHhCcchhhhhHHHHHHHHH
Q 024742 70 LQEFIELVRGENNLRAITYARKYLAPWGATHMKELQRVMA 109 (263)
Q Consensus 70 ~q~fIeLi~~~~~~eAi~yar~~l~~~~~~~~~ei~~~~~ 109 (263)
-.+.|+||++.+-..|-..+++.|..+... ...++++..
T Consensus 54 Err~i~Lirns~~krArKlakKRLGs~kRA-kaKvEel~~ 92 (97)
T COG5051 54 ERRVIELIRNSQDKRARKLAKKRLGSLKRA-KAKVEELTS 92 (97)
T ss_pred HHHHHHHHHhcccHHHHHHHHHHhhhHHHH-HHHHHHHHH
Confidence 456899999998899999999999988652 234444433
No 258
>PF12773 DZR: Double zinc ribbon
Probab=29.80 E-value=46 Score=20.92 Aligned_cols=14 Identities=29% Similarity=0.418 Sum_probs=9.4
Q ss_pred CceecCCCCcccCc
Q 024742 241 GKITCPRTGLVCNY 254 (263)
Q Consensus 241 ~~~~CP~c~~~~~~ 254 (263)
....||.|+.....
T Consensus 28 ~~~~C~~Cg~~~~~ 41 (50)
T PF12773_consen 28 SKKICPNCGAENPP 41 (50)
T ss_pred CCCCCcCCcCCCcC
Confidence 34678888876543
No 259
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.80 E-value=28 Score=23.80 Aligned_cols=15 Identities=20% Similarity=0.654 Sum_probs=11.8
Q ss_pred ceecCCCCcccCccc
Q 024742 242 KITCPRTGLVCNYSD 256 (263)
Q Consensus 242 ~~~CP~c~~~~~~~~ 256 (263)
.++||.|++.....+
T Consensus 7 ~v~CP~Cgkpv~w~~ 21 (65)
T COG3024 7 TVPCPTCGKPVVWGE 21 (65)
T ss_pred cccCCCCCCcccccc
Confidence 579999999876643
No 260
>PRK01343 zinc-binding protein; Provisional
Probab=29.75 E-value=26 Score=23.40 Aligned_cols=14 Identities=21% Similarity=0.399 Sum_probs=11.1
Q ss_pred CceecCCCCcccCc
Q 024742 241 GKITCPRTGLVCNY 254 (263)
Q Consensus 241 ~~~~CP~c~~~~~~ 254 (263)
...+||.|++.+..
T Consensus 8 p~~~CP~C~k~~~~ 21 (57)
T PRK01343 8 PTRPCPECGKPSTR 21 (57)
T ss_pred CCCcCCCCCCcCcC
Confidence 35799999998763
No 261
>PRK09377 tsf elongation factor Ts; Provisional
Probab=29.74 E-value=59 Score=29.19 Aligned_cols=46 Identities=20% Similarity=0.377 Sum_probs=32.6
Q ss_pred HHHHHHh--cCChHHHHHHHHhhchh-------------------------hhhCCCceeeechHHHHHHHHh
Q 024742 33 KVIDALQ--NKEVAPALAWCSDNKSR-------------------------LKKSKSKFEFQLRLQEFIELVR 78 (263)
Q Consensus 33 ~I~~~i~--~gdi~~Al~w~~~~~~~-------------------------L~~~~s~LeF~L~~q~fIeLi~ 78 (263)
...++|. +||++.|++|+++.--. +.+.++.-.|--+-..|+.|++
T Consensus 22 dCKkAL~e~~gD~ekAi~~Lrk~G~akA~Kk~~R~a~EG~I~~~~~~~~~~~vElncETDFVArne~F~~l~~ 94 (290)
T PRK09377 22 DCKKALTEADGDIEKAIEWLRKKGLAKAAKKAGRVAAEGLVAAKVDGNKGVLVEVNSETDFVAKNEDFQALAN 94 (290)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHhchhhHHHhcCccccceEEEEEeCCCEEEEEEEecCCccccCChHHHHHHH
Confidence 3467776 69999999999986321 2223456677777788888776
No 262
>PF01671 ASFV_360: African swine fever virus multigene family 360 protein; InterPro: IPR002595 The multigene family 360 protein are found within the African swine fever virus (ASFV) genome which consist of dsDNA and has similar structural features to the poxviruses []. The biological function of this family is not known [], although Q65137 from SWISSPROT is a major structural protein [].; GO: 0042330 taxis
Probab=29.38 E-value=92 Score=26.52 Aligned_cols=100 Identities=18% Similarity=0.204 Sum_probs=60.6
Q ss_pred HHHHHHHcCCCC-CCCHHHHHHHHHHHHHHhcCChHHHHHHHHhhchhhhhCC-----CceeeechHHHHHHHHhc----
Q 024742 10 AEKLAESSNIQD-LVDIEVFQEAKKVIDALQNKEVAPALAWCSDNKSRLKKSK-----SKFEFQLRLQEFIELVRG---- 79 (263)
Q Consensus 10 a~~f~~e~~i~~-~~d~~~~~~~~~I~~~i~~gdi~~Al~w~~~~~~~L~~~~-----s~LeF~L~~q~fIeLi~~---- 79 (263)
-+.|++|.|-++ +.+.+.+.-..++....-.+++--+.+....| |-|+..+ ..+.+.|+.....+++.+
T Consensus 3 tr~LC~~LGAk~~l~~~~il~iF~~~~~~kts~nIILcheif~nN-p~l~~v~~~~l~~~I~~~l~~l~~~~~l~~~s~~ 81 (215)
T PF01671_consen 3 TRDLCRELGAKEPLNEMEILQIFFKIKRNKTSSNIILCHEIFSNN-PLLENVNNHDLRMIIYWELRRLSINEILDEISFN 81 (215)
T ss_pred HHHHHHHhCCCccccHHHHHHHHHHHHhcCCccceeeehHhhcCC-hHHhhhhHHHHHHHHHHHHccchHHHHhccchHH
Confidence 367899999885 44556665566666655567788888888877 6665432 234444444422222222
Q ss_pred -------------CChHHHHHHHHHhCcchhhhhHHHHHHHHHHhhccCC
Q 024742 80 -------------ENNLRAITYARKYLAPWGATHMKELQRVMATLAFKSN 116 (263)
Q Consensus 80 -------------~~~~eAi~yar~~l~~~~~~~~~ei~~~~~lL~f~~~ 116 (263)
-+..+||.|.-++++-+.. =+++.+|.|.+.
T Consensus 82 ~~LtkyWY~~Av~ynL~~AI~Yfyq~y~hl~~------WRL~CaL~fNnv 125 (215)
T PF01671_consen 82 EMLTKYWYAIAVQYNLKEAIQYFYQKYPHLND------WRLICALYFNNV 125 (215)
T ss_pred HHHHHHHHHHHHHhhhHHHHHHHHHhccchhh------HHHHHHHHhCCH
Confidence 2567888888877664432 256666777653
No 263
>PLN03086 PRLI-interacting factor K; Provisional
Probab=29.27 E-value=64 Score=31.79 Aligned_cols=30 Identities=23% Similarity=0.471 Sum_probs=13.3
Q ss_pred CCCceecHHHHHHHHHhCCCceecCCCCccc
Q 024742 222 PNGYVYSTKALEEMAKKNNGKITCPRTGLVC 252 (263)
Q Consensus 222 ~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~ 252 (263)
-||..|....+++-.+.-+..++|| |++.+
T Consensus 458 ~Cgk~f~~s~LekH~~~~Hkpv~Cp-Cg~~~ 487 (567)
T PLN03086 458 KCGQAFQQGEMEKHMKVFHEPLQCP-CGVVL 487 (567)
T ss_pred CCCCccchHHHHHHHHhcCCCccCC-CCCCc
Confidence 3555555444443322112345555 55443
No 264
>PRK03922 hypothetical protein; Provisional
Probab=29.12 E-value=28 Score=26.43 Aligned_cols=14 Identities=29% Similarity=0.622 Sum_probs=11.8
Q ss_pred CceecCCCCcccCc
Q 024742 241 GKITCPRTGLVCNY 254 (263)
Q Consensus 241 ~~~~CP~c~~~~~~ 254 (263)
|...||.|+++|+.
T Consensus 48 G~~~cP~cge~~~~ 61 (113)
T PRK03922 48 GLTICPKCGEPFDS 61 (113)
T ss_pred CcccCCCCCCcCCc
Confidence 56799999999875
No 265
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=29.05 E-value=21 Score=32.43 Aligned_cols=51 Identities=8% Similarity=0.219 Sum_probs=37.5
Q ss_pred cCCeeeecccccccCCCCCCeecCCCceecHHHHHHHHHhCCCceecCCCCcccCc
Q 024742 199 HHSKLVCYITKELMDTENPPQVLPNGYVYSTKALEEMAKKNNGKITCPRTGLVCNY 254 (263)
Q Consensus 199 ~~s~~~Cpi~~~~~~~~n~p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~~ 254 (263)
++.-++|++++--+.+ +--+..|=|.||+.||-+.... ...||.|+-...-
T Consensus 12 ~n~~itC~LC~GYliD--ATTI~eCLHTFCkSCivk~l~~---~~~CP~C~i~ih~ 62 (331)
T KOG2660|consen 12 LNPHITCRLCGGYLID--ATTITECLHTFCKSCIVKYLEE---SKYCPTCDIVIHK 62 (331)
T ss_pred cccceehhhccceeec--chhHHHHHHHHHHHHHHHHHHH---hccCCccceeccC
Confidence 4455778888777754 1335679999999999988764 4689999876543
No 266
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=29.00 E-value=38 Score=21.91 Aligned_cols=27 Identities=22% Similarity=0.180 Sum_probs=16.6
Q ss_pred cCCCceecHHHHHHHHHhCCCceecCCCCcccCc
Q 024742 221 LPNGYVYSTKALEEMAKKNNGKITCPRTGLVCNY 254 (263)
Q Consensus 221 l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~~ 254 (263)
..||.-+ +.+ + ...-+.||+||-..-+
T Consensus 10 ~~Cg~~~-----~~~-~-~~~~irCp~Cg~rIl~ 36 (49)
T COG1996 10 ARCGREV-----ELD-Q-ETRGIRCPYCGSRILV 36 (49)
T ss_pred hhcCCee-----ehh-h-ccCceeCCCCCcEEEE
Confidence 4677777 112 1 2345899999976543
No 267
>PRK00239 rpsT 30S ribosomal protein S20; Reviewed
Probab=28.71 E-value=96 Score=22.58 Aligned_cols=29 Identities=24% Similarity=0.207 Sum_probs=23.1
Q ss_pred HHHHHHHHhcCChHHHHHHHHhhchhhhh
Q 024742 31 AKKVIDALQNKEVAPALAWCSDNKSRLKK 59 (263)
Q Consensus 31 ~~~I~~~i~~gdi~~Al~w~~~~~~~L~~ 59 (263)
..++..+|..||.+.|.+.+....+.|++
T Consensus 32 iKk~~~ai~~~~~~~a~~~~~~a~s~iDk 60 (88)
T PRK00239 32 IKKVEAAIAAGDKEAAEEALKAAQSKIDK 60 (88)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHHHH
Confidence 44567788889999999988888887765
No 268
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=28.64 E-value=4.3e+02 Score=23.62 Aligned_cols=18 Identities=22% Similarity=0.215 Sum_probs=11.2
Q ss_pred HHHhcCChHHHHHHHHhh
Q 024742 36 DALQNKEVAPALAWCSDN 53 (263)
Q Consensus 36 ~~i~~gdi~~Al~w~~~~ 53 (263)
.....|+++.|++++++.
T Consensus 189 ~~~~~~~~~~A~~~~~~a 206 (389)
T PRK11788 189 QALARGDLDAARALLKKA 206 (389)
T ss_pred HHHhCCCHHHHHHHHHHH
Confidence 344567777777766654
No 269
>PF07035 Mic1: Colon cancer-associated protein Mic1-like; InterPro: IPR009755 This entry represents the C terminus (approximately 160 residues) of a number of proteins that resemble colon cancer-associated protein Mic1.
Probab=28.15 E-value=76 Score=26.04 Aligned_cols=38 Identities=29% Similarity=0.364 Sum_probs=24.4
Q ss_pred hhhhhCCCceeeech-H-HHHHH-HHhcCChHHHHHHHHHh
Q 024742 55 SRLKKSKSKFEFQLR-L-QEFIE-LVRGENNLRAITYARKY 92 (263)
Q Consensus 55 ~~L~~~~s~LeF~L~-~-q~fIe-Li~~~~~~eAi~yar~~ 92 (263)
|......-++...|. . ...+| |+..|++.+|+.|+|+.
T Consensus 75 ~~~~Ql~lDMLkRL~~~~~~iievLL~~g~vl~ALr~ar~~ 115 (167)
T PF07035_consen 75 PPAYQLGLDMLKRLGTAYEEIIEVLLSKGQVLEALRYARQY 115 (167)
T ss_pred hHHHHHHHHHHHHhhhhHHHHHHHHHhCCCHHHHHHHHHHc
Confidence 333333334455554 2 33455 88899999999999974
No 270
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=27.96 E-value=31 Score=24.57 Aligned_cols=14 Identities=14% Similarity=0.320 Sum_probs=10.3
Q ss_pred ceecCCCCcccCcc
Q 024742 242 KITCPRTGLVCNYS 255 (263)
Q Consensus 242 ~~~CP~c~~~~~~~ 255 (263)
.+.|++|++.|...
T Consensus 50 ~~~C~~C~~~f~s~ 63 (100)
T PF12756_consen 50 SFRCPYCNKTFRSR 63 (100)
T ss_dssp SEEBSSSS-EESSH
T ss_pred CCCCCccCCCCcCH
Confidence 58999999998643
No 271
>KOG0989 consensus Replication factor C, subunit RFC4 [Replication, recombination and repair]
Probab=27.85 E-value=3.2e+02 Score=25.05 Aligned_cols=58 Identities=12% Similarity=0.145 Sum_probs=42.7
Q ss_pred HHhcCChHHHHHHHHhhchhhhhCC-Cceee-------echHHHHHHHHhcCChHHHHHHHHHhCc
Q 024742 37 ALQNKEVAPALAWCSDNKSRLKKSK-SKFEF-------QLRLQEFIELVRGENNLRAITYARKYLA 94 (263)
Q Consensus 37 ~i~~gdi~~Al~w~~~~~~~L~~~~-s~LeF-------~L~~q~fIeLi~~~~~~eAi~yar~~l~ 94 (263)
.+-.||+..|+-.++...+..+.+. +...+ ......++++.++++..+.++|+|+-+.
T Consensus 218 ~~S~GdLR~Ait~Lqsls~~gk~It~~~~~e~~~GvVp~~~l~~lle~a~S~d~~~~v~~~Rei~~ 283 (346)
T KOG0989|consen 218 KISDGDLRRAITTLQSLSLLGKRITTSLVNEELAGVVPDEKLLDLLELALSADTPNTVKRVREIMR 283 (346)
T ss_pred HHcCCcHHHHHHHHHHhhccCcccchHHHHHHHhccCCHHHHHHHHHHHHccChHHHHHHHHHHHH
Confidence 3457999999999999988544443 21122 2236778899999999999999997544
No 272
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=27.62 E-value=25 Score=23.03 Aligned_cols=14 Identities=43% Similarity=0.615 Sum_probs=7.3
Q ss_pred ceecCCCCcccCcc
Q 024742 242 KITCPRTGLVCNYS 255 (263)
Q Consensus 242 ~~~CP~c~~~~~~~ 255 (263)
--+||.|+.++..+
T Consensus 24 PatCP~C~a~~~~s 37 (54)
T PF09237_consen 24 PATCPICGAVIRQS 37 (54)
T ss_dssp -EE-TTT--EESSH
T ss_pred CCCCCcchhhccch
Confidence 46899998887654
No 273
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=27.49 E-value=34 Score=23.30 Aligned_cols=13 Identities=23% Similarity=0.764 Sum_probs=10.5
Q ss_pred ceecCCCCcccCc
Q 024742 242 KITCPRTGLVCNY 254 (263)
Q Consensus 242 ~~~CP~c~~~~~~ 254 (263)
.++||.|++....
T Consensus 6 ~v~CP~C~k~~~w 18 (62)
T PRK00418 6 TVNCPTCGKPVEW 18 (62)
T ss_pred cccCCCCCCcccc
Confidence 4799999998654
No 274
>PF10552 ORF6C: ORF6C domain; InterPro: IPR018878 This entry represents the carboxy-terminal domain from ORF6 (Q9B012 from SWISSPROT), an antirepressor protein from Lactococcus phage bIL285 [].
Probab=27.04 E-value=77 Score=24.05 Aligned_cols=22 Identities=14% Similarity=0.265 Sum_probs=17.8
Q ss_pred HHHHhcCChHHHHHHHHhhchh
Q 024742 35 IDALQNKEVAPALAWCSDNKSR 56 (263)
Q Consensus 35 ~~~i~~gdi~~Al~w~~~~~~~ 56 (263)
..+|...|.+.|+++++.+.|.
T Consensus 87 Y~~I~~kdfd~A~~~I~~W~p~ 108 (116)
T PF10552_consen 87 YKDIPRKDFDEALEFINNWEPS 108 (116)
T ss_pred HHhhhHHHHHHHHHHHHHcCCC
Confidence 4577788999999999888775
No 275
>PF12931 Sec16_C: Sec23-binding domain of Sec16; PDB: 3MZK_C.
Probab=26.89 E-value=61 Score=28.76 Aligned_cols=24 Identities=21% Similarity=0.102 Sum_probs=19.1
Q ss_pred HHHHHHhcCChHHHHHHHHhhchh
Q 024742 33 KVIDALQNKEVAPALAWCSDNKSR 56 (263)
Q Consensus 33 ~I~~~i~~gdi~~Al~w~~~~~~~ 56 (263)
+|.+.|..||.+.|+++|-+++-.
T Consensus 1 ~I~~~Ll~G~~~~Av~~al~~~~w 24 (284)
T PF12931_consen 1 KIQQLLLVGNREEAVELALDNGLW 24 (284)
T ss_dssp HHHHHHHTT-HHHHHHHHHHTT-H
T ss_pred CHHHHHhCCCHHHHHHHHHHCCCh
Confidence 588999999999999999887554
No 276
>TIGR01470 cysG_Nterm siroheme synthase, N-terminal domain. This model represents a subfamily of CysG N-terminal region-related sequences. All sequences in the seed alignment for this model are N-terminal regions of known or predicted siroheme synthases. The C-terminal region of each is uroporphyrin-III C-methyltransferase (EC 2.1.1.107), which catalyzes the first step committed to the biosynthesis of either siroheme or cobalamin (vitamin B12) rather than protoheme (heme). The region represented by this model completes the process of oxidation and iron insertion to yield siroheme. Siroheme is a cofactor for nitrite and sulfite reductases, so siroheme synthase is CysG of cysteine biosynthesis in some organisms.
Probab=26.78 E-value=1.5e+02 Score=24.91 Aligned_cols=53 Identities=15% Similarity=0.051 Sum_probs=35.2
Q ss_pred CChHHHHHHHHhhchhhhhCCCc------eeeechHHHHHHHHhcCChHHHHHHHHHhC
Q 024742 41 KEVAPALAWCSDNKSRLKKSKSK------FEFQLRLQEFIELVRGENNLRAITYARKYL 93 (263)
Q Consensus 41 gdi~~Al~w~~~~~~~L~~~~s~------LeF~L~~q~fIeLi~~~~~~eAi~yar~~l 93 (263)
-+++.-+++..+.+..+++...+ +...+.--.|.+++++|+..+|.+++.+-+
T Consensus 146 ~~~~~~~~~~~~~R~~~k~~~~~~~~r~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~ 204 (205)
T TIGR01470 146 PSLGDLATLAATWRDAVKKRLPNGAARRRFWEKFFDGAFAERVLAGREEQAERVLATRL 204 (205)
T ss_pred hhHHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHhccHHHHHHHcCCHHHHHHHHHHhh
Confidence 36778888888888888764322 222222335678888888888888776543
No 277
>PF02742 Fe_dep_repr_C: Iron dependent repressor, metal binding and dimerisation domain; InterPro: IPR001367 The diphtheria toxin repressor protein (DTXR) is a member of this group []. In Corynebacterium diphtheriae where it has been studied in some detail this protein acts as an iron-binding repressor of dipheteria toxin gene expression and may serve as a global regulator of gene expression. The N terminus may be involved in iron binding and may associate with the Tox operator. Binding of DTXR to Tox operator requires a divalent metal ion such as cobalt, ferric, manganese and nickel whereas zinc shows weak activation [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0005506 iron ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2X4H_D 2H09_A 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A 2F5D_A 3R61_A ....
Probab=26.77 E-value=77 Score=21.66 Aligned_cols=29 Identities=24% Similarity=0.253 Sum_probs=21.0
Q ss_pred CceecHHHHHHHHHhCCCceecCCCCccc
Q 024742 224 GYVYSTKALEEMAKKNNGKITCPRTGLVC 252 (263)
Q Consensus 224 Ghv~~~~~~~~~~~~~~~~~~CP~c~~~~ 252 (263)
-|++|.+.+.++.+--+..-+||..+...
T Consensus 41 EH~is~e~~~~l~~~l~~~~~~P~~~~ip 69 (71)
T PF02742_consen 41 EHVISPETIERLCKFLGFPETCPHGNPIP 69 (71)
T ss_dssp GCCS-HHHHHHHHHHTTCTSBETTSCBST
T ss_pred HccCCHHHHHHHHHHhcCCCcCcCCCCCC
Confidence 38899999999876555566899887653
No 278
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=26.77 E-value=96 Score=26.02 Aligned_cols=24 Identities=17% Similarity=0.207 Sum_probs=15.1
Q ss_pred HHHHHHhcCChHHHHHHHHHhCcc
Q 024742 72 EFIELVRGENNLRAITYARKYLAP 95 (263)
Q Consensus 72 ~fIeLi~~~~~~eAi~yar~~l~~ 95 (263)
..++.|++||...|....+.|+..
T Consensus 189 ~Il~Ai~~~D~~~A~~~~~~Hi~~ 212 (224)
T PRK11534 189 TLTAAILARDTARASELMRQHLLT 212 (224)
T ss_pred HHHHHHHhCCHHHHHHHHHHHHHH
Confidence 355666666666666666666644
No 279
>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=26.73 E-value=1.8e+02 Score=18.56 Aligned_cols=14 Identities=14% Similarity=-0.078 Sum_probs=7.6
Q ss_pred cCChHHHHHHHHhh
Q 024742 40 NKEVAPALAWCSDN 53 (263)
Q Consensus 40 ~gdi~~Al~w~~~~ 53 (263)
.|+++.|++++++.
T Consensus 47 ~~~~~~a~~~~~~~ 60 (100)
T cd00189 47 LGKYEEALEDYEKA 60 (100)
T ss_pred HHHHHHHHHHHHHH
Confidence 35566666555443
No 280
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=26.43 E-value=46 Score=27.51 Aligned_cols=35 Identities=17% Similarity=0.151 Sum_probs=22.4
Q ss_pred CCCee-cCCCceecHHHHHHHHHhCCCceecCCCCcccCccc
Q 024742 216 NPPQV-LPNGYVYSTKALEEMAKKNNGKITCPRTGLVCNYSD 256 (263)
Q Consensus 216 n~p~~-l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~~~~ 256 (263)
|.-++ -.||.-|+-.-- + +..|+||.||.+....|
T Consensus 115 ~~~Y~Cp~C~~rytf~eA--~----~~~F~Cp~Cg~~L~~~d 150 (178)
T PRK06266 115 NMFFFCPNCHIRFTFDEA--M----EYGFRCPQCGEMLEEYD 150 (178)
T ss_pred CCEEECCCCCcEEeHHHH--h----hcCCcCCCCCCCCeecc
Confidence 34444 457877865532 2 13599999998876654
No 281
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=26.42 E-value=34 Score=30.31 Aligned_cols=14 Identities=36% Similarity=0.807 Sum_probs=7.7
Q ss_pred ceecCCCCcccCcc
Q 024742 242 KITCPRTGLVCNYS 255 (263)
Q Consensus 242 ~~~CP~c~~~~~~~ 255 (263)
.++||.||.+++.+
T Consensus 322 ~~~C~~cg~~~~rD 335 (364)
T COG0675 322 LFKCPRCGFVHDRD 335 (364)
T ss_pred eEECCCCCCeehhh
Confidence 45666666555443
No 282
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=26.35 E-value=17 Score=22.29 Aligned_cols=11 Identities=27% Similarity=0.646 Sum_probs=6.6
Q ss_pred eecCCCCcccC
Q 024742 243 ITCPRTGLVCN 253 (263)
Q Consensus 243 ~~CP~c~~~~~ 253 (263)
..||.||+.+-
T Consensus 33 ~~C~~CGE~~~ 43 (46)
T TIGR03831 33 LVCPQCGEEYL 43 (46)
T ss_pred cccccCCCEee
Confidence 36777766553
No 283
>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=26.30 E-value=1.4e+02 Score=21.16 Aligned_cols=29 Identities=10% Similarity=0.184 Sum_probs=22.4
Q ss_pred HHHHHHHHhcCChHHHHHHHHhhchhhhh
Q 024742 31 AKKVIDALQNKEVAPALAWCSDNKSRLKK 59 (263)
Q Consensus 31 ~~~I~~~i~~gdi~~Al~w~~~~~~~L~~ 59 (263)
+.++.+++..||+....++++.+...+..
T Consensus 3 ~~~l~~~~~~~~~~~~~~~l~~~~~~~~~ 31 (105)
T PF01399_consen 3 YSELLRAFRSGDLQEFEEFLEKHSESLFK 31 (105)
T ss_dssp HHHHHHHHHCT-HHHHHHHHHHTCHHHHH
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHHHHHc
Confidence 56788999999999999999999544443
No 284
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=26.27 E-value=57 Score=20.35 Aligned_cols=9 Identities=33% Similarity=0.914 Sum_probs=7.7
Q ss_pred eecCCCCcc
Q 024742 243 ITCPRTGLV 251 (263)
Q Consensus 243 ~~CP~c~~~ 251 (263)
+.||.|+..
T Consensus 19 ~~CP~Cg~~ 27 (46)
T PF12760_consen 19 FVCPHCGST 27 (46)
T ss_pred CCCCCCCCe
Confidence 789999965
No 285
>KOG1156 consensus N-terminal acetyltransferase [Chromatin structure and dynamics]
Probab=25.84 E-value=3.8e+02 Score=26.95 Aligned_cols=87 Identities=14% Similarity=0.139 Sum_probs=48.4
Q ss_pred ccccHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHHhcCChHHHHHHHHhhchhhhhCCCceeeechHHHHHHHHhcCCh
Q 024742 3 RMSYYETAEKLAESSNIQDLVDIEVFQEAKKVIDALQNKEVAPALAWCSDNKSRLKKSKSKFEFQLRLQEFIELVRGENN 82 (263)
Q Consensus 3 r~Gy~~ta~~f~~e~~i~~~~d~~~~~~~~~I~~~i~~gdi~~Al~w~~~~~~~L~~~~s~LeF~L~~q~fIeLi~~~~~ 82 (263)
+.|.++.|......+==..+.-++.|..-.+| .-.+|+++.|..|+.+.+.-...+ -.-.=++-+ -||+.+.+
T Consensus 383 ~~g~~~~A~~yId~AIdHTPTliEly~~KaRI--~kH~G~l~eAa~~l~ea~elD~aD---R~INsKcAK--YmLrAn~i 455 (700)
T KOG1156|consen 383 KLGDYEVALEYIDLAIDHTPTLIELYLVKARI--FKHAGLLDEAAAWLDEAQELDTAD---RAINSKCAK--YMLRANEI 455 (700)
T ss_pred HcccHHHHHHHHHHHhccCchHHHHHHHHHHH--HHhcCChHHHHHHHHHHHhccchh---HHHHHHHHH--HHHHcccc
Confidence 45666777666555421122334555333333 345899999999998875432221 000001222 27888888
Q ss_pred HHHHHHHHHhCcchh
Q 024742 83 LRAITYARKYLAPWG 97 (263)
Q Consensus 83 ~eAi~yar~~l~~~~ 97 (263)
.+|.+.+-+ |+.++
T Consensus 456 ~eA~~~~sk-FTr~~ 469 (700)
T KOG1156|consen 456 EEAEEVLSK-FTREG 469 (700)
T ss_pred HHHHHHHHH-hhhcc
Confidence 888877764 44444
No 286
>PHA00733 hypothetical protein
Probab=25.45 E-value=80 Score=24.55 Aligned_cols=34 Identities=15% Similarity=0.174 Sum_probs=20.1
Q ss_pred CCceecHHHHH-HHHHhCCCceecCCCCcccCccc
Q 024742 223 NGYVYSTKALE-EMAKKNNGKITCPRTGLVCNYSD 256 (263)
Q Consensus 223 cGhv~~~~~~~-~~~~~~~~~~~CP~c~~~~~~~~ 256 (263)
||..|+..+-. +-.......++|+.|++.|...+
T Consensus 79 Cgk~Fss~s~L~~H~r~h~~~~~C~~CgK~F~~~~ 113 (128)
T PHA00733 79 CLMPFSSSVSLKQHIRYTEHSKVCPVCGKEFRNTD 113 (128)
T ss_pred CCCcCCCHHHHHHHHhcCCcCccCCCCCCccCCHH
Confidence 66666554432 22111123579999999998654
No 287
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=25.29 E-value=64 Score=23.68 Aligned_cols=20 Identities=20% Similarity=0.439 Sum_probs=12.7
Q ss_pred HHHHHHhCCCceecCCCCcc
Q 024742 232 LEEMAKKNNGKITCPRTGLV 251 (263)
Q Consensus 232 ~~~~~~~~~~~~~CP~c~~~ 251 (263)
+.++....+...+||.|++.
T Consensus 26 v~kie~~q~a~y~CpfCgk~ 45 (90)
T PTZ00255 26 IKKIEISQHAKYFCPFCGKH 45 (90)
T ss_pred HHHHHHHHhCCccCCCCCCC
Confidence 33443344567899999854
No 288
>PF06238 Borrelia_lipo_2: Borrelia burgdorferi BBR25 lipoprotein; InterPro: IPR009358 This entry consists of a number of lipoproteins conserved in Borrelia species [].
Probab=25.24 E-value=1.7e+02 Score=21.90 Aligned_cols=10 Identities=20% Similarity=0.687 Sum_probs=4.8
Q ss_pred HHHHHHHhcC
Q 024742 71 QEFIELVRGE 80 (263)
Q Consensus 71 q~fIeLi~~~ 80 (263)
+.+++.++.|
T Consensus 99 keyi~~Lk~g 108 (111)
T PF06238_consen 99 KEYINILKRG 108 (111)
T ss_pred HHHHHHHhcc
Confidence 3455555544
No 289
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=24.94 E-value=90 Score=20.99 Aligned_cols=12 Identities=33% Similarity=0.919 Sum_probs=8.7
Q ss_pred CCCceecCCCCc
Q 024742 239 NNGKITCPRTGL 250 (263)
Q Consensus 239 ~~~~~~CP~c~~ 250 (263)
.....+||.||-
T Consensus 45 ~~~~Y~CP~CGF 56 (59)
T PRK14890 45 QSNPYTCPKCGF 56 (59)
T ss_pred cCCceECCCCCC
Confidence 345689999974
No 290
>PF15616 TerY-C: TerY-C metal binding domain
Probab=24.71 E-value=65 Score=25.36 Aligned_cols=42 Identities=19% Similarity=0.312 Sum_probs=27.8
Q ss_pred eecccccccCCCCCCeecCCCceecHHHHHHHHHhCCCceecCCCCcccCcccc
Q 024742 204 VCYITKELMDTENPPQVLPNGYVYSTKALEEMAKKNNGKITCPRTGLVCNYSDL 257 (263)
Q Consensus 204 ~Cpi~~~~~~~~n~p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~~~~~ 257 (263)
-||-.|.+.. .++=.||+++|-+ +.+.++||-|+++-.+...
T Consensus 79 gCP~CGn~~~----fa~C~CGkl~Ci~--------g~~~~~CPwCg~~g~~~~~ 120 (131)
T PF15616_consen 79 GCPHCGNQYA----FAVCGCGKLFCID--------GEGEVTCPWCGNEGSFGAG 120 (131)
T ss_pred CCCCCcChhc----EEEecCCCEEEeC--------CCCCEECCCCCCeeeeccc
Confidence 3555554432 2445899999753 3346899999998776554
No 291
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=24.64 E-value=57 Score=24.57 Aligned_cols=35 Identities=9% Similarity=0.134 Sum_probs=27.7
Q ss_pred Ceec-CCCceecHHHHHHHHHhCCCceecCCCCcccCcc
Q 024742 218 PQVL-PNGYVYSTKALEEMAKKNNGKITCPRTGLVCNYS 255 (263)
Q Consensus 218 p~~l-~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~~~ 255 (263)
.|.+ -|.|.|-.-||.+|.+.+ -.||.|.++-.+.
T Consensus 75 ~VaWG~CNHaFH~hCisrWlktr---~vCPLdn~eW~~q 110 (114)
T KOG2930|consen 75 TVAWGVCNHAFHFHCISRWLKTR---NVCPLDNKEWVFQ 110 (114)
T ss_pred EEEeeecchHHHHHHHHHHHhhc---CcCCCcCcceeEe
Confidence 3443 699999999999999743 5899999876554
No 292
>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter.
Probab=24.22 E-value=1.2e+02 Score=25.18 Aligned_cols=22 Identities=14% Similarity=0.202 Sum_probs=11.8
Q ss_pred HHHHHHhcCChHHHHHHHHHhC
Q 024742 72 EFIELVRGENNLRAITYARKYL 93 (263)
Q Consensus 72 ~fIeLi~~~~~~eAi~yar~~l 93 (263)
+.++.|+.||...|.+..+.|+
T Consensus 185 ~i~~ai~~~d~~~A~~~~~~Hl 206 (212)
T TIGR03338 185 AIVDAIASGDAERAGALMRAHV 206 (212)
T ss_pred HHHHHHHhCCHHHHHHHHHHHH
Confidence 3445555555555555555554
No 293
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=24.17 E-value=18 Score=34.04 Aligned_cols=12 Identities=25% Similarity=0.578 Sum_probs=10.6
Q ss_pred ceecCCCCcccC
Q 024742 242 KITCPRTGLVCN 253 (263)
Q Consensus 242 ~~~CP~c~~~~~ 253 (263)
..+||.|.++|+
T Consensus 295 EYrCPEC~KVFs 306 (500)
T KOG3993|consen 295 EYRCPECDKVFS 306 (500)
T ss_pred eecCCccccccc
Confidence 579999999996
No 294
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=24.15 E-value=39 Score=19.90 Aligned_cols=15 Identities=27% Similarity=0.457 Sum_probs=10.2
Q ss_pred CceecCCCCcccCcc
Q 024742 241 GKITCPRTGLVCNYS 255 (263)
Q Consensus 241 ~~~~CP~c~~~~~~~ 255 (263)
..+.||.|+..+..+
T Consensus 3 ~~~~C~nC~R~v~a~ 17 (33)
T PF08209_consen 3 PYVECPNCGRPVAAS 17 (33)
T ss_dssp -EEE-TTTSSEEEGG
T ss_pred CeEECCCCcCCcchh
Confidence 358999999877654
No 295
>PF12729 4HB_MCP_1: Four helix bundle sensory module for signal transduction; InterPro: IPR024478 This entry represents a four-helix bundle that operates as a ubiquitous sensory module in prokaryotic signal-transduction, which is known as four-helix bundles methyl-accepting chemotaxis protein (4HB_MCP) domain. The 4HB_MCP is always found between two predicted transmembrane helices indicating that it detects only extracellular signals. In many cases the domain is associated with a cytoplasmic HAMP domain suggesting that most proteins carrying the bundle might share the mechanism of transmembrane signalling which is well-characterised in E coli chemoreceptors [].
Probab=24.14 E-value=3.3e+02 Score=20.83 Aligned_cols=32 Identities=19% Similarity=0.065 Sum_probs=25.2
Q ss_pred echHHHHHHHHhcCChHHHHHHHHHhCcchhh
Q 024742 67 QLRLQEFIELVRGENNLRAITYARKYLAPWGA 98 (263)
Q Consensus 67 ~L~~q~fIeLi~~~~~~eAi~yar~~l~~~~~ 98 (263)
.=...+++++++.|+..+|..+......|...
T Consensus 122 ~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~ 153 (181)
T PF12729_consen 122 RKLRDQVIELAKSGDNDEARAILNGEARPAFD 153 (181)
T ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHhHHHHHH
Confidence 34467788999999999999888887776554
No 296
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=23.95 E-value=31 Score=27.18 Aligned_cols=10 Identities=30% Similarity=0.780 Sum_probs=8.0
Q ss_pred ceecCCCCcc
Q 024742 242 KITCPRTGLV 251 (263)
Q Consensus 242 ~~~CP~c~~~ 251 (263)
.+.||.||..
T Consensus 107 ~~~CP~Cgs~ 116 (135)
T PRK03824 107 FLKCPKCGSR 116 (135)
T ss_pred CcCCcCCCCC
Confidence 4689999964
No 297
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=23.90 E-value=1.1e+02 Score=26.23 Aligned_cols=25 Identities=8% Similarity=0.020 Sum_probs=17.6
Q ss_pred HHHHHHHhcCChHHHHHHHHHhCcc
Q 024742 71 QEFIELVRGENNLRAITYARKYLAP 95 (263)
Q Consensus 71 q~fIeLi~~~~~~eAi~yar~~l~~ 95 (263)
++.++.|++||...|.+..++|+..
T Consensus 202 ~~I~~Ai~~~D~~~A~~~m~~Hi~~ 226 (257)
T PRK10225 202 KQILAALIKKDARAAKLAMWQHLEN 226 (257)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHHH
Confidence 3466777777777777777777754
No 298
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=23.83 E-value=17 Score=32.34 Aligned_cols=33 Identities=21% Similarity=0.447 Sum_probs=27.2
Q ss_pred CCeecC--------CCceecHHHHHHHHHhCCCceecCCCCcc
Q 024742 217 PPQVLP--------NGYVYSTKALEEMAKKNNGKITCPRTGLV 251 (263)
Q Consensus 217 ~p~~l~--------cGhv~~~~~~~~~~~~~~~~~~CP~c~~~ 251 (263)
.|.++. |||.++..++..+..+.+ ++||.|...
T Consensus 225 ~p~vl~~~~~~~~~c~htlc~~c~~~~l~~~~--~~cp~~~~~ 265 (296)
T KOG4185|consen 225 APLVLSLSRLKEKIEGHTLCKECIDTILLQAG--IKCPFCTWS 265 (296)
T ss_pred chhHHHHHHHHHHHHHHHHHhcchHHHHHHhh--hcCCcccce
Confidence 467777 999999999999986543 899999763
No 299
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=23.65 E-value=1.3e+02 Score=20.31 Aligned_cols=11 Identities=27% Similarity=0.884 Sum_probs=7.5
Q ss_pred CCceecCCCCc
Q 024742 240 NGKITCPRTGL 250 (263)
Q Consensus 240 ~~~~~CP~c~~ 250 (263)
++..+||.||=
T Consensus 48 g~~Y~Cp~CGF 58 (61)
T COG2888 48 GNPYRCPKCGF 58 (61)
T ss_pred CCceECCCcCc
Confidence 45678888873
No 300
>PF00653 BIR: Inhibitor of Apoptosis domain; InterPro: IPR001370 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. The baculovirus inhibitor of apoptosis protein repeat (BIR) is a domain of tandem repeats separated by a variable length linker that seems to confer cell death-preventing activity [, ]. The BIR domains characterise the Inhibitor of Apoptosis (IAP) family of proteins (MEROPS proteinase inhibitor family I32, clan IV) that suppress apoptosis by interacting with and inhibiting the enzymatic activity of both initiator and effector caspases (MEROPS peptidase family C14, IPR002398 from INTERPRO). Several distinct mammalian IAPs including XIAP, c-IAP1, c-IAP2, and ML-IAP, have been identified, and they all exhibit antiapoptotic activity in cell culture. The functional unit in each IAP protein is the baculoviral IAP repeat (BIR), which contains approximately 80 amino acids folded around a zinc atom. Most mammalian IAPs have more than one BIR domain, with the different BIR domains performing distinct functions. For example, in XIAP, the third BIR domain (BIR3) potently inhibits the catalytic activity of caspase-9, whereas the linker sequences immediately preceding the second BIR domain (BIR2) selectively targets caspase-3 or -7. The first-recognised members of family MEROPS inhibitor family I32 were viral proteins that inhibited the apoptosis of infected cells: Cp-IAP from Cydia pomonella granulosis virus (CpGV) [] and Op-IAP from Orgyia pseudotsugata multicapsid polyhedrosis virus(OpMNPV) []. The discovery of homologous proteins in mammals followed soon after with the recognition that mutations in the gene for neuronal apoptosis inhibitory protein (NIAP) underlie spinal muscular atrophy []. The inhibitors in family I32 all possess one or more 80-residue domains known as BIR (baculovirus inhibitor repeat) domains and have accordingly been termed 'BIR-containing' or 'BIRC' proteins as well as IAP proteins. The mechanism of inhibition of caspases by the IAP proteins is complex, and reactive site residues cannot yet be identified with any confidence. Despite the conservation of the BIR or IAP (inhibitor of apoptosis) domains throughout the family it seems clear that other parts of the molecules also make essential contributions to inhibitory activity. Homologs of most components in the mammalian apoptotic pathway have been identified in fruit flies. The Drosophila Apaf-1, known as Dapaf-1, HAC-1 or Dark, shares significant sequence similarity with its mammalian counterpart, and is critically important for the activation of the Drosophila initiator caspase Dronc. Dronc, in turn, cleaves and activates the effector caspase DrICE. The Drosophila IAP, DIAP1, binds to and in-activates both DrICE and Dronc through its BIR1 and BIR2 domains. During apoptosis, the anti-death function of DIAP1 is countered by at least four pro-apoptotic proteins, Reaper, Hid, Grim, and sickle, through direct physical interactions. These four proteins represent the functional homologs of the mammalian protein Smac, and they all share a conserved IAP-binding motif at their N termini. The three proteins Reaper, Hid, and Grim are collectively referred to as the RHG proteins [, ]. Both XIAP and DIAP1 contain a RING domain at their C termini, and can act as an E3 ubiquitin ligase. Indeed, both XIAP and DIAP1 have been shown to promote self-ubiquitination and degradation as well as to negatively regulate the target caspases. Nonetheless, important differences exist between XIAP and DIAP1. The primary function of XIAP is thought to inhibit the catalytic activities of caspases; to what extent the ubiquitinating activity of XIAP contributes to its function remains unclear. For DIAP1, however, the ubiquitinating activity appears to be essential for its function. Recently a Drosophila p53 protein has been identified that mediates apoptosis via a novel pathway involving the activation of the Reaper gene and subsequent inhibition of the inhibitors of apoptosis (IAPs). CIAP1, a major mammalian homologue of Drosophila IAPs, is irreversibly inhibited (cleaved) during p53-dependent apoptosis and this cleavage is mediated by a serine protease. Serine protease inhibitors that block CIAP1 cleavage inhibit p53-dependent apoptosis. Furthermore, activation of the p53 protein increases the transcription of the HTRA2 gene, which encodes a serine protease that interacts with CIAP1 and potentiates apoptosis. Therefore mammalian p53 protein activates apoptosis through a novel pathway functionally similar to that in Drosophila, which involves HTRA2 and subsequent inhibition of CIAP1 by cleavage [].; GO: 0005622 intracellular; PDB: 3HL5_B 3UW5_A 3CM7_A 1G3F_A 1G73_C 3G76_G 3CM2_C 2VSL_A 2OPZ_B 3CLX_A ....
Probab=23.54 E-value=73 Score=21.65 Aligned_cols=23 Identities=22% Similarity=0.414 Sum_probs=17.4
Q ss_pred HHHHHHHHhC------CCceecCCCCccc
Q 024742 230 KALEEMAKKN------NGKITCPRTGLVC 252 (263)
Q Consensus 230 ~~~~~~~~~~------~~~~~CP~c~~~~ 252 (263)
...++|++.| ++.++|.+|+.+.
T Consensus 18 ~~~~~LA~aGFyy~~~~d~v~C~~C~~~l 46 (70)
T PF00653_consen 18 VSPEKLARAGFYYTGTGDRVRCFYCGLEL 46 (70)
T ss_dssp SHHHHHHHTTEEEESSTTEEEETTTTEEE
T ss_pred CCHHHHHHCCCEEcCCCCEEEEeccCCEE
Confidence 4456777653 4689999999987
No 301
>COG0264 Tsf Translation elongation factor Ts [Translation, ribosomal structure and biogenesis]
Probab=23.53 E-value=91 Score=28.02 Aligned_cols=45 Identities=24% Similarity=0.420 Sum_probs=33.2
Q ss_pred HHHHh--cCChHHHHHHHHhhchh---------------------------hhhCCCceeeechHHHHHHHHhc
Q 024742 35 IDALQ--NKEVAPALAWCSDNKSR---------------------------LKKSKSKFEFQLRLQEFIELVRG 79 (263)
Q Consensus 35 ~~~i~--~gdi~~Al~w~~~~~~~---------------------------L~~~~s~LeF~L~~q~fIeLi~~ 79 (263)
.++|. +||++.|++|+++.--. +.+.|+.-.|--+-..|.++.+.
T Consensus 24 KkAL~E~~Gd~EkAie~LR~kG~akA~KKa~R~AaEGli~~~~~~~~~~av~vEvN~ETDFVAkN~~F~~l~~~ 97 (296)
T COG0264 24 KKALEEANGDIEKAIEWLREKGIAKAAKKAGRIAAEGLIAAKVDGDGKKAVLVEVNCETDFVAKNAEFQELANK 97 (296)
T ss_pred HHHHHHcCCCHHHHHHHHHHhchHhhhhhcCcchhcceEEEEEcCCCcEEEEEEEeccccceeCChhHHHHHHH
Confidence 55665 79999999999987221 33345677788888888888873
No 302
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=23.37 E-value=35 Score=20.78 Aligned_cols=11 Identities=36% Similarity=0.700 Sum_probs=6.7
Q ss_pred ecCCCCcccCc
Q 024742 244 TCPRTGLVCNY 254 (263)
Q Consensus 244 ~CP~c~~~~~~ 254 (263)
+||.|+.....
T Consensus 1 ~CP~C~~~l~~ 11 (41)
T PF13453_consen 1 KCPRCGTELEP 11 (41)
T ss_pred CcCCCCcccce
Confidence 47777765443
No 303
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=23.32 E-value=38 Score=21.13 Aligned_cols=13 Identities=23% Similarity=0.524 Sum_probs=10.6
Q ss_pred ceecCCCCcccCc
Q 024742 242 KITCPRTGLVCNY 254 (263)
Q Consensus 242 ~~~CP~c~~~~~~ 254 (263)
.-.||.|+..|+.
T Consensus 8 ~K~C~~C~rpf~W 20 (42)
T PF10013_consen 8 SKICPVCGRPFTW 20 (42)
T ss_pred CCcCcccCCcchH
Confidence 4589999999974
No 304
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=23.25 E-value=38 Score=19.77 Aligned_cols=23 Identities=26% Similarity=0.417 Sum_probs=13.8
Q ss_pred CCCceecHHHHHHHHHhCCCceecCCCCccc
Q 024742 222 PNGYVYSTKALEEMAKKNNGKITCPRTGLVC 252 (263)
Q Consensus 222 ~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~ 252 (263)
.||.... + +..+.++||+||-..
T Consensus 5 ~Cg~~~~------~--~~~~~irC~~CG~RI 27 (32)
T PF03604_consen 5 ECGAEVE------L--KPGDPIRCPECGHRI 27 (32)
T ss_dssp SSSSSE-------B--STSSTSSBSSSS-SE
T ss_pred cCCCeeE------c--CCCCcEECCcCCCeE
Confidence 4666665 2 224568999999654
No 305
>smart00238 BIR Baculoviral inhibition of apoptosis protein repeat. Domain found in inhibitor of apoptosis proteins (IAPs) and other proteins. Acts as a direct inhibitor of caspase enzymes.
Probab=23.17 E-value=80 Score=21.30 Aligned_cols=23 Identities=17% Similarity=0.261 Sum_probs=16.3
Q ss_pred HHHHHHhC------CCceecCCCCcccCc
Q 024742 232 LEEMAKKN------NGKITCPRTGLVCNY 254 (263)
Q Consensus 232 ~~~~~~~~------~~~~~CP~c~~~~~~ 254 (263)
+.+|+..| ++.++|.+|+.++.-
T Consensus 20 ~~~LA~~Gfyy~~~~d~v~C~~C~~~l~~ 48 (71)
T smart00238 20 PEQLAEAGFYYTGVGDEVKCFFCGGELDN 48 (71)
T ss_pred HHHHHHcCCeECCCCCEEEeCCCCCCcCC
Confidence 55566532 457999999998753
No 306
>TIGR00029 S20 ribosomal protein S20. This family consists of bacterial (and chloroplast) examples of the bacteria ribosomal small subunit protein S20.
Probab=23.10 E-value=1.4e+02 Score=21.68 Aligned_cols=29 Identities=21% Similarity=0.234 Sum_probs=23.1
Q ss_pred HHHHHHHHhcCChHHHHHHHHhhchhhhh
Q 024742 31 AKKVIDALQNKEVAPALAWCSDNKSRLKK 59 (263)
Q Consensus 31 ~~~I~~~i~~gdi~~Al~w~~~~~~~L~~ 59 (263)
..++..+|..||.+.|.+.+....+.|++
T Consensus 32 iKk~~~ai~~~d~~~a~~~l~~a~s~iDk 60 (87)
T TIGR00029 32 IKKVYAAIAAGDKDKAQEAFKEAAKKLDR 60 (87)
T ss_pred HHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45677888889999999888888777765
No 307
>cd00022 BIR Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger.
Probab=23.05 E-value=81 Score=21.15 Aligned_cols=23 Identities=22% Similarity=0.355 Sum_probs=16.2
Q ss_pred HHHHHHhC------CCceecCCCCcccCc
Q 024742 232 LEEMAKKN------NGKITCPRTGLVCNY 254 (263)
Q Consensus 232 ~~~~~~~~------~~~~~CP~c~~~~~~ 254 (263)
+++|+..| .+.++|.+|+.++.-
T Consensus 18 ~~~La~~Gfyy~~~~d~v~C~~C~~~~~~ 46 (69)
T cd00022 18 PEKLAEAGFYYTGRGDEVKCFFCGLELKN 46 (69)
T ss_pred HHHHHHcCCeEcCCCCEEEeCCCCCCccC
Confidence 45566532 357999999998863
No 308
>KOG0097 consensus GTPase Rab14, small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport]
Probab=22.89 E-value=1.2e+02 Score=24.26 Aligned_cols=39 Identities=23% Similarity=0.402 Sum_probs=28.5
Q ss_pred cHHHHHHHHHHcCCCC-------CCCH-H-HHHHHHHHHHHHhcCChH
Q 024742 6 YYETAEKLAESSNIQD-------LVDI-E-VFQEAKKVIDALQNKEVA 44 (263)
Q Consensus 6 y~~ta~~f~~e~~i~~-------~~d~-~-~~~~~~~I~~~i~~gdi~ 44 (263)
-++.|+.|++|-|+-- ..++ | .++..++|.+.|..|.++
T Consensus 135 ~yeeak~faeengl~fle~saktg~nvedafle~akkiyqniqdgsld 182 (215)
T KOG0097|consen 135 TYEEAKEFAEENGLMFLEASAKTGQNVEDAFLETAKKIYQNIQDGSLD 182 (215)
T ss_pred cHHHHHHHHhhcCeEEEEecccccCcHHHHHHHHHHHHHHhhhcCccc
Confidence 3678999999998752 1233 3 356678899999999665
No 309
>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional
Probab=22.51 E-value=3.5e+02 Score=24.68 Aligned_cols=83 Identities=14% Similarity=0.065 Sum_probs=42.7
Q ss_pred ccccHHHHHHHHHHc-CCCCCCCHHHHHHHHHHHHHHhcCChHHHHHHHHhhchhhhhCCCceeeechHHHHHHHHhcCC
Q 024742 3 RMSYYETAEKLAESS-NIQDLVDIEVFQEAKKVIDALQNKEVAPALAWCSDNKSRLKKSKSKFEFQLRLQEFIELVRGEN 81 (263)
Q Consensus 3 r~Gy~~ta~~f~~e~-~i~~~~d~~~~~~~~~I~~~i~~gdi~~Al~w~~~~~~~L~~~~s~LeF~L~~q~fIeLi~~~~ 81 (263)
..|.++.|..+.+++ .+ ...+...+..+. .-.+..|+++.|+..+++.-. +...+ ...+.+.-+-+...|+
T Consensus 14 ~~~~~~~Ai~~~~~Al~~-~P~~~~a~~~~a--~~~~~~g~~~eAl~~~~~Al~-l~P~~----~~a~~~lg~~~~~lg~ 85 (356)
T PLN03088 14 VDDDFALAVDLYTQAIDL-DPNNAELYADRA--QANIKLGNFTEAVADANKAIE-LDPSL----AKAYLRKGTACMKLEE 85 (356)
T ss_pred HcCCHHHHHHHHHHHHHh-CCCCHHHHHHHH--HHHHHcCCHHHHHHHHHHHHH-hCcCC----HHHHHHHHHHHHHhCC
Confidence 455555555554444 22 233344443222 233456888888888765522 22211 1122333344456688
Q ss_pred hHHHHHHHHHhC
Q 024742 82 NLRAITYARKYL 93 (263)
Q Consensus 82 ~~eAi~yar~~l 93 (263)
..+|+.+.++-+
T Consensus 86 ~~eA~~~~~~al 97 (356)
T PLN03088 86 YQTAKAALEKGA 97 (356)
T ss_pred HHHHHHHHHHHH
Confidence 888888777544
No 310
>PF14369 zf-RING_3: zinc-finger
Probab=22.45 E-value=49 Score=19.61 Aligned_cols=11 Identities=27% Similarity=0.452 Sum_probs=8.6
Q ss_pred eecCCCCcccC
Q 024742 243 ITCPRTGLVCN 253 (263)
Q Consensus 243 ~~CP~c~~~~~ 253 (263)
+.||.|+..|-
T Consensus 22 ~~CP~C~~gFv 32 (35)
T PF14369_consen 22 VACPRCHGGFV 32 (35)
T ss_pred cCCcCCCCcEe
Confidence 46999998774
No 311
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=22.44 E-value=1.3e+02 Score=22.98 Aligned_cols=27 Identities=15% Similarity=0.201 Sum_probs=21.0
Q ss_pred HHHHHHHHhcCChHHHHHHHHhhchhh
Q 024742 31 AKKVIDALQNKEVAPALAWCSDNKSRL 57 (263)
Q Consensus 31 ~~~I~~~i~~gdi~~Al~w~~~~~~~L 57 (263)
...+.+.|.+|+++.|++++..+...+
T Consensus 74 ~~~~~~~l~~g~~~~a~~ll~~~~~~~ 100 (115)
T PF12793_consen 74 EQQAEELLEQGKYEQALQLLDFDQRQL 100 (115)
T ss_pred HHHHHHHHHcCCHHHHHHHHHhCHHHH
Confidence 345678888999999999998665544
No 312
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=22.30 E-value=1.3e+02 Score=25.74 Aligned_cols=27 Identities=15% Similarity=0.103 Sum_probs=14.8
Q ss_pred HHHHHHHHHHHhcCChHHHHHHHHhhc
Q 024742 28 FQEAKKVIDALQNKEVAPALAWCSDNK 54 (263)
Q Consensus 28 ~~~~~~I~~~i~~gdi~~Al~w~~~~~ 54 (263)
+.+-.+|.++|++||.+.|.+++.+|-
T Consensus 191 ~~~H~~I~~AI~~~D~~~A~~~~~~H~ 217 (253)
T PRK10421 191 TEQHQAVMDAILAGDAEGARKAMMAHL 217 (253)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence 444455555555555555555555553
No 313
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=22.18 E-value=48 Score=19.86 Aligned_cols=11 Identities=27% Similarity=0.622 Sum_probs=8.8
Q ss_pred ceecCCCCccc
Q 024742 242 KITCPRTGLVC 252 (263)
Q Consensus 242 ~~~CP~c~~~~ 252 (263)
.++||.|...-
T Consensus 5 ~v~CP~C~s~~ 15 (36)
T PF03811_consen 5 DVHCPRCQSTE 15 (36)
T ss_pred eeeCCCCCCCC
Confidence 47999998764
No 314
>PF01877 RNA_binding: RNA binding; InterPro: IPR002739 The proteins in this entry are functionally uncharacterised.; PDB: 2WNY_B 2NWU_A 2NRQ_A 2OGK_A 3D7A_B 3C9G_B 2PZZ_D.
Probab=21.75 E-value=2.7e+02 Score=21.22 Aligned_cols=44 Identities=23% Similarity=0.280 Sum_probs=34.5
Q ss_pred HHHHHHHHHHHHHhcCCh-HHHHHHHHhhchhhhhCCCceeeechHHHHH
Q 024742 26 EVFQEAKKVIDALQNKEV-APALAWCSDNKSRLKKSKSKFEFQLRLQEFI 74 (263)
Q Consensus 26 ~~~~~~~~I~~~i~~gdi-~~Al~w~~~~~~~L~~~~s~LeF~L~~q~fI 74 (263)
..-+-+.++.+.|+..++ +.|+..+.+... ++.+.|.|.+|...
T Consensus 56 ~~~~~l~~l~~~l~~~~i~d~~~~~l~~~~~-----~~~~~~rl~KQaA~ 100 (120)
T PF01877_consen 56 EALKSLKKLHELLRDQEILDTARSELEKRVD-----GNKLYFRLDKQAAY 100 (120)
T ss_dssp HHHHHHHHHHHHHHHTTHHHHHHHHHHHTBE-----TSEEEEEEEHHHHH
T ss_pred cHHHHHHHHHHHHhhhhhhhHHHHHHHhccc-----CCEEEEEEchhHhh
Confidence 456667888999999999 888876655533 67999999999865
No 315
>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR. Members of this family are FadR, a transcriptional regulator of fatty acid metabolism, including both biosynthesis and beta-oxidation. It is found exclusively in a subset of Gammaproteobacteria, with strictly one copy per genome. It has an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR from this family heterologously expressed in Escherichia coli show differences in regulatory response and fatty acid binding profiles. The family is nevertheless designated equivalog, as all member proteins have at least nominally the same function.
Probab=21.74 E-value=1.4e+02 Score=25.19 Aligned_cols=23 Identities=22% Similarity=0.241 Sum_probs=12.8
Q ss_pred HHHHHHhcCChHHHHHHHHHhCc
Q 024742 72 EFIELVRGENNLRAITYARKYLA 94 (263)
Q Consensus 72 ~fIeLi~~~~~~eAi~yar~~l~ 94 (263)
+.++.|+.||...|-+..+.|+.
T Consensus 194 ~I~~Ai~~~d~~~A~~~m~~H~~ 216 (235)
T TIGR02812 194 ELQALCKAGNHDEVPDCIRQYGI 216 (235)
T ss_pred HHHHHHHcCCHHHHHHHHHHHHH
Confidence 34555555555555555555554
No 316
>COG1273 Ku-homolog [Replication, recombination, and repair]
Probab=21.56 E-value=62 Score=28.64 Aligned_cols=21 Identities=33% Similarity=0.332 Sum_probs=18.2
Q ss_pred CceecCCCCcccCcccceecc
Q 024742 241 GKITCPRTGLVCNYSDLVKAY 261 (263)
Q Consensus 241 ~~~~CP~c~~~~~~~~~~~v~ 261 (263)
..+.|+.||++...+|..|=|
T Consensus 46 ~~~Vd~~tGk~Ve~~d~VKGY 66 (278)
T COG1273 46 YKYVDSVTGKEVERDDIVKGY 66 (278)
T ss_pred eEEeccccCCccCccceeeee
Confidence 467999999999999988765
No 317
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=21.50 E-value=8.8 Score=26.77 Aligned_cols=38 Identities=13% Similarity=0.251 Sum_probs=16.0
Q ss_pred eecccccccCCCCCCeecCCCceecHHHHHHHHHhCCCceecCCCCccc
Q 024742 204 VCYITKELMDTENPPQVLPNGYVYSTKALEEMAKKNNGKITCPRTGLVC 252 (263)
Q Consensus 204 ~Cpi~~~~~~~~n~p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~ 252 (263)
.||....+|+. ..|+.++..+-.... ..--||.|++..
T Consensus 3 ~CP~C~~~L~~-------~~~~~~C~~C~~~~~----~~a~CPdC~~~L 40 (70)
T PF07191_consen 3 TCPKCQQELEW-------QGGHYHCEACQKDYK----KEAFCPDCGQPL 40 (70)
T ss_dssp B-SSS-SBEEE-------ETTEEEETTT--EEE----EEEE-TTT-SB-
T ss_pred cCCCCCCccEE-------eCCEEECccccccce----ecccCCCcccHH
Confidence 45555554433 336666665554332 134677777654
No 318
>smart00299 CLH Clathrin heavy chain repeat homology.
Probab=21.41 E-value=1.2e+02 Score=23.18 Aligned_cols=12 Identities=8% Similarity=0.327 Sum_probs=6.9
Q ss_pred ChHHHHHHHHhh
Q 024742 42 EVAPALAWCSDN 53 (263)
Q Consensus 42 di~~Al~w~~~~ 53 (263)
|++.|+..|.++
T Consensus 71 d~~~~~~~c~~~ 82 (140)
T smart00299 71 DIEKVGKLCEKA 82 (140)
T ss_pred CHHHHHHHHHHc
Confidence 556666666554
No 319
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=21.32 E-value=1.4e+02 Score=25.21 Aligned_cols=22 Identities=18% Similarity=0.173 Sum_probs=11.0
Q ss_pred HHHHHhcCChHHHHHHHHHhCc
Q 024742 73 FIELVRGENNLRAITYARKYLA 94 (263)
Q Consensus 73 fIeLi~~~~~~eAi~yar~~l~ 94 (263)
.++.|+.||...|.+..++|+.
T Consensus 196 I~~Ai~~~D~~~a~~~~~~H~~ 217 (239)
T PRK04984 196 LSALCEEGNHDQVPECVRQYGI 217 (239)
T ss_pred HHHHHHhCCHHHHHHHHHHHHH
Confidence 4444555555555555555543
No 320
>PF15391 DUF4614: Domain of unknown function (DUF4614)
Probab=21.32 E-value=66 Score=26.76 Aligned_cols=50 Identities=18% Similarity=0.158 Sum_probs=34.2
Q ss_pred HHHHHHHhhchhhhhCCCceeeec-hHHHHHHHHhc----------------CChHHHHHHHHHhCc
Q 024742 45 PALAWCSDNKSRLKKSKSKFEFQL-RLQEFIELVRG----------------ENNLRAITYARKYLA 94 (263)
Q Consensus 45 ~Al~w~~~~~~~L~~~~s~LeF~L-~~q~fIeLi~~----------------~~~~eAi~yar~~l~ 94 (263)
.|||-+-.+.|.+...+..|-=+| ..|+|||.-+. -..+++-+|.|.|=+
T Consensus 114 dAiEALTaYSPA~lALnDMLkQQL~LTqqFve~sr~LH~Sll~SL~~~~~hY~TLEetKeyIr~hr~ 180 (181)
T PF15391_consen 114 DAIEALTAYSPAVLALNDMLKQQLSLTQQFVEASRHLHQSLLQSLDADSFHYHTLEETKEYIRRHRP 180 (181)
T ss_pred HHHHHHhccChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcceeeHHHHHHHHHHcCC
Confidence 466667777777666665565555 56889987763 136888888887744
No 321
>PRK14962 DNA polymerase III subunits gamma and tau; Provisional
Probab=21.31 E-value=2.4e+02 Score=27.10 Aligned_cols=25 Identities=20% Similarity=0.267 Sum_probs=19.3
Q ss_pred HHHHHHHHHHhcCChHHHHHHHHhh
Q 024742 29 QEAKKVIDALQNKEVAPALAWCSDN 53 (263)
Q Consensus 29 ~~~~~I~~~i~~gdi~~Al~w~~~~ 53 (263)
.....+.++|+++|.+.|+.|+.+.
T Consensus 245 ~~i~~li~si~~~d~~~Al~~l~~l 269 (472)
T PRK14962 245 EVVRDYINAIFNGDVKRVFTVLDDV 269 (472)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHH
Confidence 4456678888888888888888754
No 322
>PF12862 Apc5: Anaphase-promoting complex subunit 5
Probab=21.31 E-value=3.1e+02 Score=19.52 Aligned_cols=28 Identities=21% Similarity=0.178 Sum_probs=21.6
Q ss_pred HHHHHhcCChHHHHHHHHhhchhhhhCC
Q 024742 34 VIDALQNKEVAPALAWCSDNKSRLKKSK 61 (263)
Q Consensus 34 I~~~i~~gdi~~Al~w~~~~~~~L~~~~ 61 (263)
-.++++.||...|++-+.+....-...+
T Consensus 5 ~~~~~~~~dy~~A~d~L~~~fD~~~~~~ 32 (94)
T PF12862_consen 5 YLNALRSGDYSEALDALHRYFDYAKQSN 32 (94)
T ss_pred HHHHHHcCCHHHHHHHHHHHHHHHhhcc
Confidence 3678999999999999888876654443
No 323
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=21.09 E-value=50 Score=24.71 Aligned_cols=15 Identities=33% Similarity=0.463 Sum_probs=11.3
Q ss_pred CCceecCCCCcccCc
Q 024742 240 NGKITCPRTGLVCNY 254 (263)
Q Consensus 240 ~~~~~CP~c~~~~~~ 254 (263)
...|+||.|+.+-..
T Consensus 20 ~k~FtCp~Cghe~vs 34 (104)
T COG4888 20 PKTFTCPRCGHEKVS 34 (104)
T ss_pred CceEecCccCCeeee
Confidence 357899999987554
No 324
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=20.99 E-value=45 Score=19.94 Aligned_cols=12 Identities=25% Similarity=0.717 Sum_probs=8.6
Q ss_pred eecCCCCcccCc
Q 024742 243 ITCPRTGLVCNY 254 (263)
Q Consensus 243 ~~CP~c~~~~~~ 254 (263)
..||.||..|+.
T Consensus 2 r~C~~Cg~~Yh~ 13 (36)
T PF05191_consen 2 RICPKCGRIYHI 13 (36)
T ss_dssp EEETTTTEEEET
T ss_pred cCcCCCCCcccc
Confidence 468888877764
No 325
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=20.94 E-value=38 Score=20.50 Aligned_cols=9 Identities=44% Similarity=1.032 Sum_probs=4.2
Q ss_pred eecCCCCcc
Q 024742 243 ITCPRTGLV 251 (263)
Q Consensus 243 ~~CP~c~~~ 251 (263)
++||.|+..
T Consensus 1 ~~Cp~Cg~~ 9 (39)
T PF01096_consen 1 IKCPKCGHN 9 (39)
T ss_dssp S--SSS-SS
T ss_pred CCCcCCCCC
Confidence 479999853
No 326
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=20.88 E-value=63 Score=19.81 Aligned_cols=16 Identities=38% Similarity=0.777 Sum_probs=7.6
Q ss_pred CceecCCCCcccCccc
Q 024742 241 GKITCPRTGLVCNYSD 256 (263)
Q Consensus 241 ~~~~CP~c~~~~~~~~ 256 (263)
+.+.|+.||.+.....
T Consensus 18 g~~vC~~CG~Vl~e~~ 33 (43)
T PF08271_consen 18 GELVCPNCGLVLEENI 33 (43)
T ss_dssp TEEEETTT-BBEE-TT
T ss_pred CeEECCCCCCEeeccc
Confidence 4456666665554433
No 327
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 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 ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=20.80 E-value=58 Score=23.90 Aligned_cols=14 Identities=36% Similarity=0.653 Sum_probs=9.3
Q ss_pred CCCceecCCCCccc
Q 024742 239 NNGKITCPRTGLVC 252 (263)
Q Consensus 239 ~~~~~~CP~c~~~~ 252 (263)
.+...+||.|++.-
T Consensus 32 q~~ky~Cp~Cgk~~ 45 (90)
T PF01780_consen 32 QHAKYTCPFCGKTS 45 (90)
T ss_dssp HHS-BEESSSSSSE
T ss_pred HhCCCcCCCCCCce
Confidence 34568999998753
No 328
>COG0295 Cdd Cytidine deaminase [Nucleotide transport and metabolism]
Probab=20.69 E-value=46 Score=26.30 Aligned_cols=39 Identities=23% Similarity=0.331 Sum_probs=26.0
Q ss_pred CCeecCCCceecHHHHHHHHHhCCCceecCCCC--cccCcccc
Q 024742 217 PPQVLPNGYVYSTKALEEMAKKNNGKITCPRTG--LVCNYSDL 257 (263)
Q Consensus 217 ~p~~l~cGhv~~~~~~~~~~~~~~~~~~CP~c~--~~~~~~~~ 257 (263)
.+...|||+ ||+-|.++...+...+-++..+ +++++.|+
T Consensus 82 ~~~~sPCG~--CRQ~i~Ef~~~d~~ii~~~~~~~~~~~tl~eL 122 (134)
T COG0295 82 GKPVSPCGA--CRQVLAEFCGDDTLIILLPKDGIVKTMTLGEL 122 (134)
T ss_pred CCCcCCcHH--HHHHHHHhcCCCceEEEecCCCcEEEEEHHHh
Confidence 566789997 7888888875544555666665 55555444
No 329
>PHA00626 hypothetical protein
Probab=20.69 E-value=57 Score=21.71 Aligned_cols=16 Identities=13% Similarity=0.187 Sum_probs=12.9
Q ss_pred CCceecCCCCcccCcc
Q 024742 240 NGKITCPRTGLVCNYS 255 (263)
Q Consensus 240 ~~~~~CP~c~~~~~~~ 255 (263)
.+.++||.|+-.|+.+
T Consensus 21 snrYkCkdCGY~ft~~ 36 (59)
T PHA00626 21 SDDYVCCDCGYNDSKD 36 (59)
T ss_pred CcceEcCCCCCeechh
Confidence 3568999999988765
No 330
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=20.38 E-value=60 Score=33.30 Aligned_cols=41 Identities=10% Similarity=0.120 Sum_probs=31.7
Q ss_pred CCCceecHHHHHHHHHh---CCCceecCCCCcccCcccceeccc
Q 024742 222 PNGYVYSTKALEEMAKK---NNGKITCPRTGLVCNYSDLVKAYI 262 (263)
Q Consensus 222 ~cGhv~~~~~~~~~~~~---~~~~~~CP~c~~~~~~~~~~~v~~ 262 (263)
-|+.|++-++-.++.-+ +.+-|+|-+||..|+-.--.||.|
T Consensus 358 ~CakvfgS~SaLqiHlRSHTGERPfqCnvCG~~FSTkGNLKvH~ 401 (958)
T KOG1074|consen 358 FCAKVFGSDSALQIHLRSHTGERPFQCNVCGNRFSTKGNLKVHF 401 (958)
T ss_pred hhHhhcCchhhhhhhhhccCCCCCeeecccccccccccceeeee
Confidence 59999988877776544 356799999999999776666654
No 331
>PF03470 zf-XS: XS zinc finger domain; InterPro: IPR005381 This domain is a putative nucleic acid binding zinc finger and is found at the N terminus of proteins that also contain an adjacent XS domain IPR005380 from INTERPRO and in some proteins a C-terminal XH domain IPR005379 from INTERPRO.
Probab=20.29 E-value=46 Score=20.91 Aligned_cols=7 Identities=29% Similarity=0.368 Sum_probs=5.8
Q ss_pred cCCCCcc
Q 024742 245 CPRTGLV 251 (263)
Q Consensus 245 CP~c~~~ 251 (263)
||+|+..
T Consensus 1 CP~C~~k 7 (43)
T PF03470_consen 1 CPFCPGK 7 (43)
T ss_pred CCCCCCC
Confidence 9999865
No 332
>KOG2068 consensus MOT2 transcription factor [Transcription]
Probab=20.26 E-value=98 Score=28.20 Aligned_cols=58 Identities=19% Similarity=0.283 Sum_probs=39.8
Q ss_pred CCCCCCcCCeeeecccccccCCCCCCee-cCCCceecHHHHHHHHHhCCCceecCCCCcccC
Q 024742 193 LPYSKQHHSKLVCYITKELMDTENPPQV-LPNGYVYSTKALEEMAKKNNGKITCPRTGLVCN 253 (263)
Q Consensus 193 lP~~~~~~s~~~Cpi~~~~~~~~n~p~~-l~cGhv~~~~~~~~~~~~~~~~~~CP~c~~~~~ 253 (263)
++++-.++=.=.||++.+.++...-+++ -|||+-++.-++..++. +...||.|.+.+.
T Consensus 240 ~~~~~~~~v~~s~p~~~~~~~~~d~~~lP~~~~~~~~l~~~~t~~~---~~~~~~~~rk~~~ 298 (327)
T KOG2068|consen 240 LDFSSVTSVPPSCPICYEDLDLTDSNFLPCPCGFRLCLFCHKTISD---GDGRCPGCRKPYE 298 (327)
T ss_pred cCCccccccCCCCCCCCCcccccccccccccccccchhhhhhcccc---cCCCCCccCCccc
Confidence 3333333333579999999966544443 78999988888887754 3468999986554
No 333
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=20.20 E-value=46 Score=20.93 Aligned_cols=11 Identities=36% Similarity=0.839 Sum_probs=8.4
Q ss_pred CceecCCCCcc
Q 024742 241 GKITCPRTGLV 251 (263)
Q Consensus 241 ~~~~CP~c~~~ 251 (263)
+.-|||.||..
T Consensus 10 GirkCp~CGt~ 20 (44)
T PF14952_consen 10 GIRKCPKCGTY 20 (44)
T ss_pred ccccCCcCcCc
Confidence 45699999864
No 334
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=20.04 E-value=67 Score=32.27 Aligned_cols=10 Identities=30% Similarity=0.630 Sum_probs=8.2
Q ss_pred ceecCCCCcc
Q 024742 242 KITCPRTGLV 251 (263)
Q Consensus 242 ~~~CP~c~~~ 251 (263)
..+||.||..
T Consensus 639 ~~~CP~CG~~ 648 (656)
T PRK08270 639 HEFCPKCGEE 648 (656)
T ss_pred CCCCcCCcCc
Confidence 4799999966
Done!